diff --git a/dev/_images/1086e3e87714a5cb1429d09c5d7a78b45f3365d68f5b1ca5a8876f368c74697b.png b/dev/_images/1086e3e87714a5cb1429d09c5d7a78b45f3365d68f5b1ca5a8876f368c74697b.png
new file mode 100644
index 0000000..fee1100
Binary files /dev/null and b/dev/_images/1086e3e87714a5cb1429d09c5d7a78b45f3365d68f5b1ca5a8876f368c74697b.png differ
diff --git a/dev/_images/1195b127fad3625a72ada5c2193f1c5bdee94c13668995b4504cb38db0ee318f.png b/dev/_images/1195b127fad3625a72ada5c2193f1c5bdee94c13668995b4504cb38db0ee318f.png
new file mode 100644
index 0000000..7b0f74b
Binary files /dev/null and b/dev/_images/1195b127fad3625a72ada5c2193f1c5bdee94c13668995b4504cb38db0ee318f.png differ
diff --git a/dev/_images/3a7c8a8ae94793051bd4c57639ebe6e2ead7eea62d1c946714786f8fc8c4df21.png b/dev/_images/3a7c8a8ae94793051bd4c57639ebe6e2ead7eea62d1c946714786f8fc8c4df21.png
deleted file mode 100644
index 21b7d8a..0000000
Binary files a/dev/_images/3a7c8a8ae94793051bd4c57639ebe6e2ead7eea62d1c946714786f8fc8c4df21.png and /dev/null differ
diff --git a/dev/_images/6b874f41bc4b9a1e3fa9f7328a16551ca824c8fcc40c1bb8eaf979843cd479ed.png b/dev/_images/6b874f41bc4b9a1e3fa9f7328a16551ca824c8fcc40c1bb8eaf979843cd479ed.png
new file mode 100644
index 0000000..e4c0404
Binary files /dev/null and b/dev/_images/6b874f41bc4b9a1e3fa9f7328a16551ca824c8fcc40c1bb8eaf979843cd479ed.png differ
diff --git a/dev/_images/8c1b08809b96cd936e3cb345f39c97903ed5cca26086345e91a676b947c8d1fe.png b/dev/_images/8c1b08809b96cd936e3cb345f39c97903ed5cca26086345e91a676b947c8d1fe.png
deleted file mode 100644
index 07e7a24..0000000
Binary files a/dev/_images/8c1b08809b96cd936e3cb345f39c97903ed5cca26086345e91a676b947c8d1fe.png and /dev/null differ
diff --git a/dev/_images/96404594bcd3b160493e2cb8f7fa0307315a740dcec9bd6c9063c2f1a029c123.png b/dev/_images/96404594bcd3b160493e2cb8f7fa0307315a740dcec9bd6c9063c2f1a029c123.png
deleted file mode 100644
index 7bdd3f8..0000000
Binary files a/dev/_images/96404594bcd3b160493e2cb8f7fa0307315a740dcec9bd6c9063c2f1a029c123.png and /dev/null differ
diff --git a/dev/_images/9c3951e794c484f757cbe28207a466781ac7f577d41bd1126fece8e0bb9b801e.png b/dev/_images/9c3951e794c484f757cbe28207a466781ac7f577d41bd1126fece8e0bb9b801e.png
new file mode 100644
index 0000000..8028ec0
Binary files /dev/null and b/dev/_images/9c3951e794c484f757cbe28207a466781ac7f577d41bd1126fece8e0bb9b801e.png differ
diff --git a/dev/_images/c000731b43c7d6ee84ed48c3dddb82ca0894b06a4fc582ee651bfb625bda1538.png b/dev/_images/c000731b43c7d6ee84ed48c3dddb82ca0894b06a4fc582ee651bfb625bda1538.png
new file mode 100644
index 0000000..468c27a
Binary files /dev/null and b/dev/_images/c000731b43c7d6ee84ed48c3dddb82ca0894b06a4fc582ee651bfb625bda1538.png differ
diff --git a/dev/_images/d8c765fe5b406648c97cdd10aa2bcb4663ca4aef76711e93a09f838c560f4213.png b/dev/_images/d8c765fe5b406648c97cdd10aa2bcb4663ca4aef76711e93a09f838c560f4213.png
deleted file mode 100644
index 2fde8aa..0000000
Binary files a/dev/_images/d8c765fe5b406648c97cdd10aa2bcb4663ca4aef76711e93a09f838c560f4213.png and /dev/null differ
diff --git a/dev/_images/f0faf8d6e1ddd0e8c85d1dadaa35e4b5b6686b3bda9a5df982c1e1dfaf5ffece.png b/dev/_images/f0faf8d6e1ddd0e8c85d1dadaa35e4b5b6686b3bda9a5df982c1e1dfaf5ffece.png
deleted file mode 100644
index 247be7b..0000000
Binary files a/dev/_images/f0faf8d6e1ddd0e8c85d1dadaa35e4b5b6686b3bda9a5df982c1e1dfaf5ffece.png and /dev/null differ
diff --git a/dev/notebooks/model_solver.html b/dev/notebooks/model_solver.html
index 6d76a6a..b5ce4cf 100644
--- a/dev/notebooks/model_solver.html
+++ b/dev/notebooks/model_solver.html
@@ -692,7 +692,7 @@ <h3>Random parameters<a class="headerlink" href="#random-parameters" title="Perm
 </div>
 </details>
 <div class="cell_output docutils container">
-<img alt="../_images/96404594bcd3b160493e2cb8f7fa0307315a740dcec9bd6c9063c2f1a029c123.png" src="../_images/96404594bcd3b160493e2cb8f7fa0307315a740dcec9bd6c9063c2f1a029c123.png" />
+<img alt="../_images/1195b127fad3625a72ada5c2193f1c5bdee94c13668995b4504cb38db0ee318f.png" src="../_images/1195b127fad3625a72ada5c2193f1c5bdee94c13668995b4504cb38db0ee318f.png" />
 </div>
 </div>
 <!-- ```{tip}
@@ -845,7 +845,7 @@ <h3>Fixed parameters<a class="headerlink" href="#id3" title="Permalink to this h
 </div>
 </details>
 <div class="cell_output docutils container">
-<img alt="../_images/8c1b08809b96cd936e3cb345f39c97903ed5cca26086345e91a676b947c8d1fe.png" src="../_images/8c1b08809b96cd936e3cb345f39c97903ed5cca26086345e91a676b947c8d1fe.png" />
+<img alt="../_images/6b874f41bc4b9a1e3fa9f7328a16551ca824c8fcc40c1bb8eaf979843cd479ed.png" src="../_images/6b874f41bc4b9a1e3fa9f7328a16551ca824c8fcc40c1bb8eaf979843cd479ed.png" />
 </div>
 </div>
 </section>
@@ -954,7 +954,7 @@ <h3>Random parameters<a class="headerlink" href="#id4" title="Permalink to this
 </div>
 </details>
 <div class="cell_output docutils container">
-<img alt="../_images/f0faf8d6e1ddd0e8c85d1dadaa35e4b5b6686b3bda9a5df982c1e1dfaf5ffece.png" src="../_images/f0faf8d6e1ddd0e8c85d1dadaa35e4b5b6686b3bda9a5df982c1e1dfaf5ffece.png" />
+<img alt="../_images/9c3951e794c484f757cbe28207a466781ac7f577d41bd1126fece8e0bb9b801e.png" src="../_images/9c3951e794c484f757cbe28207a466781ac7f577d41bd1126fece8e0bb9b801e.png" />
 </div>
 </div>
 </section>
@@ -1003,7 +1003,7 @@ <h2>Summary<a class="headerlink" href="#summary" title="Permalink to this headin
 </div>
 </details>
 <div class="cell_output docutils container">
-<img alt="../_images/d8c765fe5b406648c97cdd10aa2bcb4663ca4aef76711e93a09f838c560f4213.png" src="../_images/d8c765fe5b406648c97cdd10aa2bcb4663ca4aef76711e93a09f838c560f4213.png" />
+<img alt="../_images/1086e3e87714a5cb1429d09c5d7a78b45f3365d68f5b1ca5a8876f368c74697b.png" src="../_images/1086e3e87714a5cb1429d09c5d7a78b45f3365d68f5b1ca5a8876f368c74697b.png" />
 </div>
 </div>
 <!-- ## Repeatable Simulation
diff --git a/dev/notebooks/paramfit/params_via_optimization.html b/dev/notebooks/paramfit/params_via_optimization.html
index 152d3e6..35630fe 100644
--- a/dev/notebooks/paramfit/params_via_optimization.html
+++ b/dev/notebooks/paramfit/params_via_optimization.html
@@ -547,7 +547,7 @@ <h2>Gradient calculations<a class="headerlink" href="#gradient-calculations" tit
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>29.6 ms ± 206 μs per loop (mean ± std. dev. of 7 runs, 10 loops each)
+<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>30.4 ms ± 197 μs per loop (mean ± std. dev. of 7 runs, 10 loops each)
 </pre></div>
 </div>
 </div>
@@ -559,7 +559,7 @@ <h2>Gradient calculations<a class="headerlink" href="#gradient-calculations" tit
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>260 ms ± 1.38 ms per loop (mean ± std. dev. of 7 runs, 1 loop each)
+<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>264 ms ± 838 μs per loop (mean ± std. dev. of 7 runs, 1 loop each)
 </pre></div>
 </div>
 </div>
diff --git a/dev/notebooks/unroll/unrollSimple.html b/dev/notebooks/unroll/unrollSimple.html
index 3541741..69e1bdd 100644
--- a/dev/notebooks/unroll/unrollSimple.html
+++ b/dev/notebooks/unroll/unrollSimple.html
@@ -535,7 +535,7 @@ <h2>SIR with births and deaths<a class="headerlink" href="#sir-with-births-and-d
 </div>
 </div>
 <div class="cell_output docutils container">
-<img alt="../../_images/3a7c8a8ae94793051bd4c57639ebe6e2ead7eea62d1c946714786f8fc8c4df21.png" src="../../_images/3a7c8a8ae94793051bd4c57639ebe6e2ead7eea62d1c946714786f8fc8c4df21.png" />
+<img alt="../../_images/c000731b43c7d6ee84ed48c3dddb82ca0894b06a4fc582ee651bfb625bda1538.png" src="../../_images/c000731b43c7d6ee84ed48c3dddb82ca0894b06a4fc582ee651bfb625bda1538.png" />
 </div>
 </div>
 </section>
diff --git a/dev/searchindex.js b/dev/searchindex.js
index 5b93705..8c7a080 100644
--- a/dev/searchindex.js
+++ b/dev/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"docnames": ["md/bib", "md/building_doc", "md/common_models", "md/faq", "md/installation", "md/intro", "md/parameter_fitting", "md/solving", "notebooks/common_models/FitzHugh", "notebooks/common_models/Legrand_Ebola_SEIHFR", "notebooks/common_models/Lotka_Volterra", "notebooks/common_models/SEIR", "notebooks/common_models/SEIR_Birth_Death_Periodic_Waning_Intro", "notebooks/common_models/SEIR_Multiple", "notebooks/common_models/SIR", "notebooks/common_models/SIR_Birth_Death", "notebooks/common_models/SIS", "notebooks/common_models/SIS_Periodic", "notebooks/epijson", "notebooks/extract_info", "notebooks/insights", "notebooks/model_params", "notebooks/model_solver", "notebooks/model_spec", "notebooks/paramfit/bvpSimple", "notebooks/paramfit/params_via_abc", "notebooks/paramfit/params_via_optimization", "notebooks/time_dependent_params", "notebooks/unroll/unrollSimple", "rst/autodoc-abc", "rst/autodoc-loss", "rst/autodoc-model", "rst/autodoc-utilR"], "filenames": ["md/bib.md", "md/building_doc.md", "md/common_models.md", "md/faq.md", "md/installation.md", "md/intro.md", "md/parameter_fitting.md", "md/solving.md", "notebooks/common_models/FitzHugh.ipynb", "notebooks/common_models/Legrand_Ebola_SEIHFR.ipynb", "notebooks/common_models/Lotka_Volterra.ipynb", "notebooks/common_models/SEIR.ipynb", "notebooks/common_models/SEIR_Birth_Death_Periodic_Waning_Intro.ipynb", "notebooks/common_models/SEIR_Multiple.ipynb", "notebooks/common_models/SIR.ipynb", "notebooks/common_models/SIR_Birth_Death.ipynb", "notebooks/common_models/SIS.ipynb", "notebooks/common_models/SIS_Periodic.ipynb", "notebooks/epijson.ipynb", "notebooks/extract_info.ipynb", "notebooks/insights.ipynb", "notebooks/model_params.ipynb", "notebooks/model_solver.ipynb", "notebooks/model_spec.ipynb", "notebooks/paramfit/bvpSimple.ipynb", "notebooks/paramfit/params_via_abc.ipynb", "notebooks/paramfit/params_via_optimization.ipynb", "notebooks/time_dependent_params.ipynb", "notebooks/unroll/unrollSimple.ipynb", "rst/autodoc-abc.rst", "rst/autodoc-loss.rst", "rst/autodoc-model.rst", "rst/autodoc-utilR.rst"], "titles": ["Bibliography", "Building the documentation locally", "Pre-defined examples - common epi models", "Frequently asked questions", "Installation", "Welcome to the documentation for PyGOM", "Parameter fitting", "Producing forecasts", "FitzHugh", "Legrand Ebola SEIHFR", "Lotka Volterra", "SEIR", "SEIR, birth, death, periodic, waning and introductions", "SEIR, multiple", "SIR", "SIR, birth and death", "SIS", "SIS, periodic", "Reading and using EpiJSON data", "Extracting model information", "ODE Insights", "Parameterisation", "Finding ODE solutions", "Defining an ODE system", "Solving Boundary Value Problems", "Parameter Estimation: Approximate Bayesian Computation", "Parameter Estimation: Maximum likelihood", "Time dependent parameters", "Deducing transitions from equations", "approximate_bayesian_computation", "loss", "model", "utilR"], "terms": {"1": [0, 5, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32], "fred": 0, "brauer": [0, 13], "mathemat": [0, 27, 30], "epidemiologi": [0, 2, 5], "volum": 0, "1945": 0, "springer": 0, "berlin": 0, "heidelberg": 0, "2008": [0, 30, 32], "isbn": 0, "978": 0, "3": [0, 8, 9, 10, 11, 14, 15, 18, 19, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31], "540": 0, "78910": 0, "9": [0, 9, 10, 17, 25, 30, 31], "url": 0, "http": [0, 4, 32], "link": 0, "com": [0, 4], "10": [0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 24, 25, 26, 27, 30, 31], "1007": 0, "78911": 0, "6": [0, 8, 9, 10, 13, 18, 22, 25, 26, 30, 31], "doi": 0, "2": [0, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 22, 24, 25, 26, 27, 30, 31, 32], "yang": 0, "cao": 0, "daniel": 0, "t": [0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31], "gillespi": 0, "linda": 0, "r": [0, 1, 4, 8, 11, 12, 14, 15, 18, 21, 22, 23, 25, 27, 28, 30, 31, 32], "petzold": 0, "effici": 0, "step": [0, 19, 22, 25, 26, 30, 31], "size": [0, 11, 15, 22, 23, 26, 29, 31, 32], "select": [0, 22, 30, 31], "tau": [0, 22, 27, 31], "leap": [0, 22, 31], "simul": [0, 5, 7, 10, 15, 20, 21, 22, 23, 25, 31], "method": [0, 3, 6, 8, 20, 22, 24, 25, 26, 30, 31], "journal": [0, 30], "chemic": 0, "physic": 0, "2006": 0, "1063": 0, "2159468": 0, "thoma": 0, "j": [0, 13, 15, 22, 23, 30, 31], "finni": 0, "andi": 0, "south": 0, "ana": 0, "bento": 0, "elli": 0, "sherrard": 0, "smith": 0, "thibaut": 0, "jombart": 0, "epijson": 0, "unifi": 0, "data": [0, 6, 22, 25, 26, 30], "format": [0, 18, 31], "epidem": [0, 6, 11, 12, 14, 16, 22, 23, 25, 26, 27], "2016": 0, "1016": 0, "2015": 0, "12": [0, 8, 18, 30, 32], "002": 0, "4": [0, 8, 11, 12, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 29, 30, 31], "richard": [0, 30], "fitzhugh": [0, 31], "impuls": 0, "physiolog": 0, "state": [0, 8, 9, 10, 12, 13, 15, 16, 18, 19, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32], "theoret": 0, "model": [0, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 16, 17, 18, 20, 21, 22, 24, 27, 29, 30, 32], "nerv": 0, "membran": [0, 8], "biophys": 0, "1961": 0, "s0006": 0, "3495": 0, "61": 0, "86902": 0, "5": [0, 9, 10, 15, 16, 17, 18, 22, 24, 25, 26, 27, 30, 31], "exact": [0, 26, 30, 31], "stochast": [0, 5, 7, 10, 15, 25, 27, 31], "coupl": [0, 13, 25, 31], "reaction": [0, 8, 22, 31], "The": [0, 1, 3, 4, 5, 8, 9, 10, 13, 14, 15, 18, 21, 22, 23, 25, 26, 28, 30, 31, 32], "chemistri": 0, "81": [0, 9, 31], "25": [0, 9, 10, 21, 22, 25, 26, 27, 30, 31], "2340": 0, "2361": 0, "1977": [0, 30], "mark": 0, "girolami": 0, "ben": 0, "calderhead": 0, "riemann": 0, "manifold": 0, "langevin": 0, "hamiltonian": 0, "mont": [0, 25, 26], "carlo": [0, 25, 26], "royal": 0, "statist": [0, 3], "societi": 0, "seri": [0, 22, 25, 26, 30], "b": [0, 8, 23, 26, 28, 30, 31, 32], "methodologi": 0, "2011": 0, "1111": 0, "1467": 0, "9868": 0, "2010": 0, "00765": 0, "x": [0, 10, 24, 26, 30, 31, 32], "7": [0, 9, 25, 26, 30, 31], "legrand": [0, 31], "f": [0, 4, 9, 10, 11, 12, 14, 15, 16, 17, 19, 22, 23, 24, 25, 26, 27, 28, 30, 31], "grai": 0, "p": [0, 12, 13, 17, 23, 27, 28, 30, 31, 32], "y": [0, 10, 15, 23, 24, 26, 29, 30, 31], "boell": 0, "A": [0, 3, 5, 9, 10, 11, 21, 22, 25, 28, 30, 31], "valleron": 0, "flahault": 0, "understand": [0, 7], "dynam": [0, 9, 22], "ebola": [0, 31], "infect": [0, 12, 14, 15, 16, 17, 22, 23, 26, 27, 28, 31], "135": 0, "610": 0, "621": 0, "2007": 0, "1017": 0, "s0950268806007217": 0, "8": [0, 5, 13, 17, 22, 25, 27, 30, 31], "alun": 0, "l": [0, 26, 28, 30, 31], "lloyd": [0, 13], "robert": 0, "m": [0, 10, 26, 29, 30, 31, 32], "mai": [0, 1, 3, 4, 6, 7, 12, 13, 15, 16, 19, 21, 22, 23, 25, 26, 27, 28, 30, 31], "spatial": [0, 31], "heterogen": [0, 23, 31], "biologi": 0, "1996": 0, "1006": 0, "jtbi": 0, "0042": 0, "alfr": 0, "lotka": [0, 31], "analyt": [0, 20, 24], "note": [0, 17, 24, 26, 30, 31, 32], "certain": [0, 15], "rhythmic": 0, "relat": [0, 6, 24, 31], "organ": [0, 5], "system": [0, 7, 8, 10, 12, 15, 16, 19, 21, 22, 24, 25, 26, 27, 28, 31], "proceed": 0, "nation": 0, "academi": 0, "scienc": [0, 30], "1920": 0, "1073": 0, "pna": 0, "410": 0, "o": [0, 30], "ramsai": 0, "g": [0, 24, 25, 29, 30], "hooker": 0, "d": [0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 22, 23, 24, 27, 28, 30, 31], "campbel": 0, "paramet": [0, 5, 7, 9, 11, 14, 15, 19, 20, 23, 28, 30, 31, 32], "estim": [0, 5, 6, 24, 30], "differenti": [0, 5, 30, 31], "equat": [0, 3, 5, 8, 12, 14, 15, 17, 19, 21, 22, 24, 26, 27, 30, 31, 32], "gener": [0, 1, 3, 5, 7, 19, 22, 25, 26, 29, 31, 32], "smooth": [0, 30], "approach": [0, 6, 23, 25, 26], "00610": 0, "11": [0, 8, 24, 25, 30], "h": [0, 9, 31], "robertson": [0, 8, 31], "solut": [0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 24, 26, 27, 28, 29, 30, 31], "set": [0, 2, 9, 11, 12, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31], "rate": [0, 9, 12, 15, 17, 21, 22, 23, 25, 27, 28, 29, 31, 32], "academ": 0, "press": [0, 30, 32], "page": [0, 5, 31], "178": 0, "182": 0, "1966": 0, "www": [0, 32], "scirp": 0, "org": [0, 32], "28": [0, 22, 25, 31], "28vtj3fa45qm1ean45vvffcz55": 0, "29": [0, 18, 26], "refer": [0, 21, 23, 30, 31, 32], "referencespap": 0, "aspx": 0, "referenceid": 0, "2485718": 0, "balth": 0, "van": [0, 8, 31], "der": [0, 8, 30, 31], "pol": [0, 8, 31], "On": 0, "relax": 0, "oscil": [0, 8, 17, 27], "london": 0, "edinburgh": 0, "dublin": 0, "philosoph": 0, "magazin": 0, "992": 0, "1926": 0, "1080": 0, "14786442608564127": 0, "which": [1, 2, 3, 4, 5, 6, 8, 10, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32], "you": [1, 4, 5, 19, 30, 31], "ar": [1, 2, 3, 4, 5, 8, 9, 11, 13, 15, 18, 19, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31], "current": [1, 3, 5, 19, 22, 25, 26, 28, 31, 32], "read": [1, 9], "built": [1, 3, 5, 25, 26, 31], "first": [1, 3, 6, 10, 18, 19, 21, 22, 24, 25, 26, 28, 29, 30, 31], "instal": [1, 3], "addit": [1, 9, 12, 19, 23, 24, 25, 26, 30, 31], "packag": [1, 3, 26, 29, 32], "requir": [1, 3, 4, 5, 9, 18, 19, 20, 21, 22, 24, 25, 26, 27, 30, 31], "specif": [1, 22, 23, 30], "pip": [1, 4], "doc": 1, "txt": [1, 4, 25, 26], "Then": 1, "from": [1, 2, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31], "command": [1, 4], "line": [1, 4, 19, 22], "jupyt": [1, 32], "book": [1, 23], "html": [1, 32], "file": [1, 3, 4, 18, 25, 30, 31, 32], "save": [1, 2, 19, 25], "copi": [1, 31], "your": [1, 4, 5], "repositori": [1, 4], "under": [1, 3, 4, 18, 19, 23, 24, 25, 26, 30], "pygom": [1, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32], "_build": 1, "can": [1, 4, 5, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31], "view": [1, 18, 22, 23, 28, 31], "open": 1, "index": [1, 29], "browser": 1, "choic": [1, 21, 25], "we": [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31], "have": [2, 9, 12, 16, 19, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31], "modul": [2, 19, 22, 23, 31], "common_model": [2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 31], "most": [2, 26, 27], "draw": [2, 22, 25], "commonli": [2, 8, 9, 10, 20, 23, 24, 25, 27], "us": [2, 4, 6, 7, 8, 9, 11, 13, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32], "includ": [2, 4, 5, 8, 12, 22, 23, 25, 26, 27, 28, 29, 31], "primarili": 2, "time": [2, 5, 7, 8, 10, 11, 12, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 28, 29, 30, 31], "user": [2, 3, 4, 5, 7, 22, 23, 24, 29, 30, 31], "also": [2, 4, 6, 8, 9, 10, 11, 15, 17, 19, 23, 24, 26, 27, 30, 31], "serv": [2, 12, 24, 30], "few": [2, 5, 25], "outsid": [2, 12, 30], "task": [2, 6], "test": [2, 8, 31, 32], "numer": [2, 5, 7, 8, 19, 21, 22, 24, 26, 29, 30, 31], "solver": [2, 10, 11, 12, 14, 15, 16, 17, 21, 22, 24, 26, 30], "These": [3, 22, 26], "faq": 3, "": [3, 5, 6, 9, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31], "particularli": [3, 26], "date": [3, 6], "so": [3, 9, 17, 20, 23, 24, 25, 27, 28, 30, 31], "might": [3, 4, 20, 23, 25, 27, 30], "thi": [3, 4, 6, 7, 10, 12, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32], "becaus": [3, 25, 26, 27, 28, 30, 31], "optim": [3, 24, 25, 26, 30], "although": [3, 25, 26, 30], "main": [3, 5, 23], "function": [3, 5, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32], "lambdifi": 3, "cython": [3, 31], "avail": [3, 5, 23, 25, 26, 30, 31], "mani": [3, 19, 23], "more": [3, 4, 5, 6, 9, 10, 11, 12, 20, 22, 23, 25, 26, 28, 29, 30, 31], "done": [3, 21, 24, 28], "setup": [3, 4], "ha": [3, 4, 19, 22, 23, 26, 28, 30, 31], "been": [3, 22, 23, 28, 30, 31], "simplifi": [3, 22], "much": [3, 22, 27, 30], "possibl": [3, 21, 22, 23, 25, 30], "If": [3, 4, 23, 25, 26, 28, 30, 31, 32], "look": 3, "close": [3, 15, 22, 30], "enough": [3, 26], "realiz": [3, 30, 31], "onli": [3, 5, 19, 21, 23, 26, 28, 30, 31], "f2py": [3, 31], "prepar": [3, 18], "all": [3, 5, 9, 18, 23, 25, 26, 27, 28, 30, 31], "check": [3, 4, 19, 26, 30, 31], "e": [3, 9, 11, 12, 19, 24, 29, 30, 31], "exist": [3, 9, 31], "gcc": 3, "wa": [3, 21, 28, 30, 31], "python": [3, 4, 5, 19, 26, 31], "share": [3, 22, 23], "etc": [3, 30], "veri": [3, 22, 31], "awar": [3, 4, 5], "benefit": 3, "especi": 3, "consid": [3, 10, 15, 23, 24, 25, 27, 28, 30], "gpu": 3, "fair": 3, "number": [3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 22, 25, 26, 27, 28, 29, 30, 31, 32], "oper": [3, 5, 18, 30, 31], "depend": [3, 4, 22, 23, 26, 28, 30, 31], "scipi": [3, 22, 24, 26, 30, 31], "obvious": 3, "solv": [3, 5, 6, 8, 10, 12, 14, 22, 26, 27, 30, 31], "od": [3, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 24, 25, 26, 27, 28, 29, 30, 31], "standard": [3, 9, 11, 14, 21, 22, 23, 25, 28, 30, 31], "linear": [3, 15, 19, 30, 31], "algebra": [3, 5, 31], "unfortun": 3, "routin": [3, 26, 30], "mostli": 3, "base": [3, 30], "numpi": [3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 24, 25, 26, 27, 30, 31, 32], "It": [3, 24, 26, 30, 31], "alwai": [3, 21, 28, 30, 31], "due": [3, 15, 17, 23, 24, 26, 27, 31], "design": [3, 15], "where": [3, 5, 13, 17, 19, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31], "initi": [3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 26, 27, 28, 29, 30, 31], "class": [3, 5, 15, 18, 20, 22, 23, 25, 26, 28, 30, 31], "fast": [3, 30], "find": [3, 5, 7, 19, 20, 21, 23, 24, 26, 30, 31], "deriv": [3, 9, 13, 15, 19, 27, 30, 31], "inform": [3, 5, 18, 21, 23, 25, 26, 28, 30, 31], "dure": [3, 22, 26], "runtim": [3, 26], "after": [3, 16, 24, 25, 26, 28, 29, 31], "calcul": [3, 5, 18, 19, 20, 21, 22, 25, 28, 30, 31, 32], "thing": [3, 22], "should": [3, 4, 5, 9, 22, 24, 25, 26, 28, 29, 30, 31], "significantli": 3, "faster": [3, 24, 30, 31], "follow": [3, 8, 14, 15, 17, 21, 23, 25, 27, 28, 30, 31], "answer": 3, "intend": [3, 30], "differ": [3, 15, 19, 22, 23, 26, 28, 30, 31], "detect": 3, "either": [3, 7, 19, 30, 31], "exp": [3, 9, 30, 32], "log": [3, 29, 30, 31, 32], "forc": [3, 12], "ensur": [3, 4, 21, 24, 25, 28], "highest": 3, "precis": [3, 24, 25, 27, 30], "To": [3, 5, 21, 22, 25, 30, 31], "turn": [3, 28], "off": [3, 19, 22], "featur": [3, 14, 18, 20, 21, 23, 25], "futur": [3, 29, 30], "implement": [3, 5, 22, 23], "end": [3, 5, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 27, 28, 31], "fulli": [3, 4, 19], "being": [3, 13, 23, 26, 31], "defin": [3, 10, 12, 14, 17, 19, 21, 22, 24, 25, 27, 28, 30, 31], "evalu": [3, 10, 11, 12, 14, 15, 16, 17, 22, 26, 27, 30, 31], "full": [3, 9, 15, 22, 28, 30], "befor": [3, 20, 21, 22, 24, 25, 26], "extract": [3, 28], "them": [3, 4, 10, 19, 21, 23, 31], "out": [3, 22, 23, 25, 26, 28, 31], "reason": 3, "stop": 3, "u": [3, 10, 19, 20, 25, 26, 28, 30], "symbol": [3, 9, 19, 21, 31], "mean": [3, 5, 9, 19, 21, 22, 23, 24, 25, 26, 30, 31, 32], "one": [3, 19, 22, 23, 25, 26, 27, 28, 30, 31], "call": [3, 23, 25, 28, 30, 31], "return": [3, 15, 19, 30, 31, 32], "would": [3, 23, 26, 28], "appropri": [3, 8, 31, 32], "element": [3, 30, 31], "matrix": [3, 19, 23, 25, 28, 30, 31], "amount": [3, 25, 26, 30], "small": [3, 22], "best": [3, 26, 27], "necessari": [3, 19, 21, 26, 28], "work": [3, 4, 22, 26, 28, 30], "both": [3, 5, 7, 21, 22, 24, 26, 28, 30, 31], "within": [3, 4, 5, 23, 25], "later": [3, 23, 24, 25, 26], "variabl": [3, 19, 21, 23, 24, 25, 27, 30, 31], "ad": [3, 27, 28, 30], "delet": [3, 22], "perform": [3, 5, 7, 10, 19, 25, 26, 28, 30, 31], "consider": 3, "instruct": [4, 5], "found": [4, 5, 22, 26, 29, 30, 31], "github": [4, 5], "project": 4, "readm": 4, "here": [4, 5, 9, 15, 19, 22, 23, 24, 25, 26, 28, 30, 31], "code": [4, 5, 19, 25, 26, 27], "download": [4, 5], "ukhsa": 4, "collabor": 4, "git": 4, "clone": 4, "pleas": [4, 5], "redund": 4, "i": [4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32], "activ": [4, 6], "develop": [4, 5, 19, 26], "latest": 4, "review": 4, "version": [4, 9, 26, 30, 31, 32], "master": 4, "branch": 4, "recommend": [4, 30], "relev": [4, 23, 24, 26], "via": [4, 6, 15, 21, 22, 23, 24, 26, 30, 31, 32], "bash": 4, "name": [4, 9, 21, 23, 25, 26, 29, 31], "an": [4, 7, 8, 9, 11, 12, 15, 16, 17, 18, 22, 24, 26, 27, 28, 29, 30, 31, 32], "easi": [4, 5], "wai": [4, 5, 21, 22, 23, 25, 26, 31], "creat": [4, 31, 32], "new": [4, 21, 22, 23, 25, 26, 29, 30, 31, 32], "conda": 4, "environ": 4, "env": 4, "yml": 4, "process": [4, 5, 7, 9, 12, 13, 18, 22, 23, 25, 26, 28, 31], "altern": [4, 28], "add": [4, 5, 15, 22, 23, 27], "own": [4, 5], "final": [4, 11, 22, 25, 28, 30, 31], "prerequisit": 4, "window": 4, "machin": [4, 30], "need": [4, 21, 23, 25, 26, 27, 30, 31], "graphviz": [4, 31], "microsoft": 4, "visual": [4, 26], "c": [4, 8, 9, 23, 30, 31], "14": [4, 18, 27, 30], "0": [4, 5, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32], "greater": [4, 26, 30], "get": [4, 26, 28, 30], "build": [4, 5, 19, 23, 26, 31], "tool": [4, 5, 28], "abl": [4, 15, 22, 30], "py": 4, "anticip": 4, "make": [4, 8, 9, 19, 21, 22, 23, 26, 30], "frequent": [4, 8, 19, 23], "chang": [4, 5, 11, 21, 22, 23, 24, 25, 29, 30, 31], "conveni": [4, 30], "mode": [4, 30], "instead": [4, 5, 9, 21, 22, 23, 24, 25, 27, 28, 31], "releas": 4, "run": [4, 5, 10, 11, 12, 14, 15, 16, 17, 21, 22, 25, 26, 27, 28, 29], "complet": [4, 29, 30], "successfulli": [4, 24, 26, 30], "take": [4, 7, 20, 22, 23, 25, 26, 27, 30, 31, 32], "some": [4, 9, 19, 21, 22, 23, 25, 26, 27, 28, 30, 32], "minut": 4, "provid": [5, 12, 15, 18, 19, 20, 22, 25, 26, 27, 30, 31], "simpl": [5, 22, 28, 31], "interfac": [5, 30, 31], "construct": [5, 30], "ordinari": 5, "focu": [5, 24], "compartment": [5, 21, 23], "back": [5, 12, 24], "comprehens": [5, 22], "box": 5, "easili": [5, 7], "common": [5, 22, 23, 25, 31], "determinist": [5, 7, 8, 10, 11, 12, 14, 15, 16, 27, 31], "evolut": [5, 7, 8, 11, 14, 15, 17, 27], "sourc": [5, 12, 29, 30, 31, 32], "freeli": 5, "host": 5, "permit": [5, 10], "extens": [5, 11, 17, 31], "With": [5, 22, 26], "automat": [5, 23, 24, 30], "still": [5, 22, 24, 25, 26, 28], "access": [5, 19, 25], "freed": 5, "object": [5, 11, 12, 14, 15, 16, 17, 18, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32], "how": [5, 6, 7, 10, 16, 17, 18, 23, 24, 25, 26, 28, 30, 31], "underli": [5, 25, 26, 28, 30], "larg": [5, 22], "unchang": 5, "sinc": [5, 10, 21, 22, 23, 26, 30], "previou": [5, 21, 22, 25, 26], "bar": 5, "minor": 5, "bug": 5, "fix": [5, 7, 23, 24, 30], "signific": 5, "move": [5, 20, 31], "awai": 5, "deterministicod": [5, 29, 30, 31], "emploi": [5, 22, 26], "simulateod": [5, 20, 21, 22, 23, 24, 25, 27, 28, 31], "our": [5, 7, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31], "well": [5, 6, 22, 23, 26, 30, 31], "fit": [5, 18, 20, 23, 26, 30], "random": [5, 10, 11, 14, 15, 25, 30, 31, 32], "special": [5, 23, 30], "now": [5, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31], "recognis": 5, "type": [5, 19, 21, 22, 23, 30, 31, 32], "hand": [5, 23], "act": [5, 25], "accordingli": 5, "outlin": [5, 6, 19, 23, 26], "detail": [5, 12, 30], "produc": [5, 6, 25, 31], "forecast": [5, 6], "section": [5, 6, 22, 25, 26, 30], "jupyterbook": 5, "local": [5, 25, 26, 30], "content": [5, 30], "notebook": [5, 22, 30, 32], "start": [5, 21, 23, 24, 25, 26, 30, 31], "point": [5, 15, 18, 22, 23, 24, 25, 26, 29, 30, 31], "triall": 5, "analys": 5, "ani": [5, 13, 16, 18, 23, 25, 30, 31], "exampl": [5, 7, 9, 15, 17, 19, 21, 22, 24, 25, 27, 28, 30, 31], "icon": 5, "desir": [5, 22, 30, 31], "locat": [5, 26], "top": [5, 9, 22, 30, 31], "right": [5, 9, 10, 12, 17, 19, 23, 26, 27, 28, 30, 32], "see": [5, 10, 11, 15, 16, 22, 23, 24, 25, 26, 28, 30, 31, 32], "guidanc": 5, "rais": [5, 30, 31], "issu": [5, 28, 30], "incorpor": [5, 17], "pull": [5, 24], "request": 5, "acknowledg": 5, "As": [6, 15, 19, 22, 25, 26, 27, 31], "anoth": [6, 19, 23, 24, 28], "kei": [6, 22, 23, 25, 30, 31], "infecti": [6, 7, 9, 11, 19, 23], "diseas": [6, 7, 15, 23, 24, 25, 31], "infer": [6, 25, 26, 29, 30], "case": [6, 9, 10, 12, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31], "In": [6, 7, 12, 17, 19, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32], "chapter": [6, 7, 25], "assist": [6, 19], "endeavour": 6, "present": [6, 22, 31], "up": [6, 11, 12, 14, 15, 16, 17, 19, 22, 24, 25, 26, 27, 28, 30], "approxim": [6, 12, 22, 30, 31], "bayesian": 6, "comput": [6, 22, 23, 30, 31], "abc": [6, 25, 26, 29], "classic": [6, 17], "maximum": [6, 10, 11, 12, 14, 15, 16, 17, 22, 29, 30, 31], "likelihood": [6, 30], "mle": [6, 26, 30], "demonstr": [6, 11, 15, 18, 21, 23, 24, 25, 28], "abil": 6, "less": [6, 22, 26, 30], "epidemiolog": [6, 9, 18], "boundari": [6, 26, 30], "valu": [6, 7, 15, 18, 21, 22, 25, 26, 27, 29, 30, 31], "problem": [6, 26, 28, 30, 31], "exercis": 7, "central": [7, 23], "studi": [7, 15, 19, 20, 23], "inde": [7, 23, 25, 30], "like": [7, 11, 14, 15, 22, 24, 26, 27, 29, 30, 31, 32], "allow": [7, 12, 18, 19, 22, 23, 24, 31], "obtain": [7, 19, 25, 26, 29, 30], "furthermor": [7, 23, 25], "specifi": [7, 19, 22, 23, 24, 25, 26, 27, 29, 30, 31], "drawn": [7, 21, 22], "randomli": [7, 21, 22], "probabl": [7, 21, 23, 25, 26, 32], "distribut": [7, 21, 22, 25, 26, 29, 30, 32], "sir": [7, 11, 19, 20, 21, 22, 27, 31], "introduc": [7, 22, 28], "prescrib": 7, "parameteris": [7, 32], "output": [7, 11, 13, 18, 22, 25, 26, 30, 31], "without": [8, 13, 26, 30, 31], "extern": [8, 12, 31], "stimulu": 8, "softwar": 8, "itself": [8, 23, 31], "describ": [8, 9, 23, 25, 30, 31], "excit": 8, "neuron": 8, "spike": 8, "pass": [8, 22, 25, 26, 28, 30, 31], "other": [8, 12, 23, 25, 26, 27, 28, 30], "integr": [8, 9, 13, 19, 22, 24, 26, 30, 31], "vanderpol": [8, 31], "begin": [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 22, 23, 24, 25, 27, 28, 31], "align": [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 27, 28], "frac": [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 26, 27, 28, 30, 31, 32], "mathrm": [8, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 27, 28], "v": [8, 19, 24, 30, 31], "br": [8, 31], "import": [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31], "np": [8, 10, 11, 12, 14, 15, 16, 17, 22, 24, 25, 26, 27, 30, 31], "matplotlib": [8, 10, 11, 12, 14, 15, 16, 17, 22, 24, 25, 26, 27, 30, 31], "pyplot": [8, 10, 11, 12, 14, 15, 16, 17, 22, 24, 25, 26, 27, 30, 31], "plt": [8, 10, 11, 12, 14, 15, 16, 17, 22, 24, 25, 26, 27, 30, 31], "linspac": [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 24, 27, 30, 31], "20": [8, 12, 15, 18, 24, 25, 31], "101": [8, 31], "x0": [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 24, 25, 26, 27, 29, 30, 31], "initial_valu": [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 24, 26, 27, 31], "solve_determ": [8, 10, 11, 12, 14, 16, 17, 22, 24, 27, 31], "plot": [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 24, 25, 26, 27, 29, 30, 31], "reveal": [8, 12], "sharp": 8, "transit": [8, 12, 19, 22, 24, 27, 31], "legrand_ebola_seihfr": [9, 31], "literatur": 9, "captur": [9, 18, 28], "outbreak": 9, "propos": [9, 25], "et": 9, "al": 9, "There": [9, 23, 25, 31], "two": [9, 19, 21, 22, 23, 24, 26, 28, 29, 30, 31], "extra": [9, 19, 27, 30, 31], "compart": [9, 15, 22, 23, 25, 28, 31], "seir": [9, 31], "hospiti": 9, "funer": [9, 31], "total": [9, 10, 15, 21, 22, 23, 25, 26, 27, 28, 29, 31], "ten": 9, "invers": [9, 30], "beta_": [9, 13, 31], "transmiss": [9, 23, 28], "commun": 9, "hospit": [9, 31], "gamma_": [9, 31], "onset": 9, "death": [9, 13, 18, 23, 25, 31], "hospitil": 9, "burial": 9, "alpha": [9, 10, 11, 12, 15, 17, 22, 25, 26, 28, 30, 31, 32], "durat": 9, "incub": [9, 11], "period": [9, 10, 11, 25, 27, 31], "theta": [9, 23, 24, 26, 30, 31], "proport": [9, 23, 28], "delta": [9, 10, 12, 17, 27, 28, 31], "ftaliti": 9, "ratio": 9, "denot": 9, "invert": 9, "sens": [9, 23, 25, 31], "natur": [9, 23, 28, 32], "replac": [9, 24, 26, 30, 31], "gamma": [9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 21, 22, 23, 25, 26, 27, 28, 30, 31, 32], "omega": 9, "omega_": 9, "directli": [9, 18, 32], "give": [9, 22, 23, 30], "intuit": [9, 23], "five": 9, "fatal": 9, "delta_": [9, 31], "ih": [9, 31], "dh": [9, 31], "adjust": 9, "theta_": [9, 23, 31], "readi": [9, 20, 23], "dt": [9, 10, 11, 12, 14, 15, 16, 17, 19, 22, 23, 27, 31], "n": [9, 11, 12, 13, 14, 15, 16, 17, 19, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32], "si": [9, 11, 12, 14, 15, 23, 27, 28, 31], "sh": [9, 31], "sf": [9, 31], "de": [9, 31], "di": [9, 19, 31], "df": [9, 18, 31, 32], "dr": [9, 19, 31], "otherwis": [9, 30, 31], "slightli": [9, 21], "modifi": [9, 30], "sigmoid": 9, "logist": 9, "left": [9, 12, 17, 19, 23, 27, 28, 30, 32], "kappa": [9, 28, 31], "brief": 9, "given": [9, 10, 18, 21, 23, 24, 25, 26, 28, 30, 31, 32], "200000": [9, 31], "100": [9, 12, 13, 15, 21, 22, 24, 30, 31], "beta_i": [9, 31], "588": [9, 31], "beta_h": [9, 31], "794": [9, 31], "beta_f": [9, 31], "653": [9, 31], "omega_i": [9, 31], "omega_d": [9, 31], "omega_h": [9, 31], "omega_f": [9, 31], "alphainv": [9, 31], "80": [9, 31], "300": [9, 18, 22, 31], "interventiontim": [9, 31], "suscept": [9, 11, 12, 14, 15, 16, 22, 23, 31], "equal": [9, 23, 25, 30, 31], "whole": 9, "popul": [9, 10, 12, 15, 21, 22, 23, 25, 26, 27, 28, 29, 31], "doe": [9, 23, 28, 30, 31], "lotka_volterra": [10, 31], "basic": [10, 19, 31], "predat": 10, "prei": 10, "express": [10, 19, 31], "term": [10, 19, 24, 28, 30, 31, 32], "area": 10, "densiti": [10, 32], "respect": [10, 19, 21, 22, 23, 26, 30, 31], "though": [10, 23, 25, 28], "absolut": 10, "decis": 10, "rather": [10, 19, 22, 23, 25, 28, 31], "than": [10, 12, 19, 22, 23, 25, 26, 30, 31], "beta": [10, 11, 12, 14, 15, 16, 17, 19, 21, 22, 23, 25, 26, 27, 28, 31, 32], "math": [10, 11, 12, 14, 15, 16, 17, 22, 30, 32], "per": [10, 12, 15, 22, 23, 26, 31], "squar": [10, 30, 31], "wish": [10, 21, 22, 23, 24, 25, 26, 31], "200": [10, 22, 30], "anim": 10, "tmax": [10, 11, 12, 14, 15, 16, 17, 22, 27], "over": [10, 11, 12, 14, 15, 16, 17, 21, 22, 26, 30, 31], "timestep": [10, 11, 12, 14, 15, 16, 17, 22, 27], "n_timestep": [10, 11, 12, 14, 15, 16, 17, 22, 27], "ceil": [10, 11, 12, 14, 15, 16, 17, 22], "iter": [10, 11, 12, 14, 15, 16, 17, 22, 25, 27, 30, 31], "show": [10, 11, 12, 14, 15, 16, 17, 19, 21, 22, 24, 26, 27, 30, 31], "behaviour": [10, 30], "phase": [10, 28], "shift": 10, "between": [10, 22, 23, 26, 27, 28, 30, 31], "ax": [10, 12, 17, 22], "subplot": [10, 11, 12, 14, 15, 16, 17, 22, 24, 25, 26, 27], "figsiz": [10, 11, 12, 14, 15, 16, 17, 22, 25, 26, 27], "set_xlabel": [10, 11, 12, 14, 15, 16, 17, 22, 24, 25, 26, 27], "set_ylabel": [10, 11, 12, 14, 15, 16, 17, 22, 26], "label": [10, 26], "legend": [10, 26], "loc": [10, 26], "upper": [10, 19, 30], "evolv": [10, 16, 27], "seed": [10, 15, 22, 25, 31, 32], "n_sim": [10, 15, 22], "simt": [10, 15, 22], "solve_stochast": [10, 15, 22, 25, 31], "full_output": [10, 13, 15, 22, 30, 31], "true": [10, 13, 15, 19, 22, 24, 25, 26, 29, 30, 31, 32], "dstack": [10, 15, 22], "appear": [10, 28], "unstabl": 10, "undergo": [10, 11, 15], "increasingli": 10, "extrem": 10, "peak": 10, "trough": 10, "confirm": 10, "examin": 10, "diagram": 10, "wherebi": [10, 23], "trajectori": [10, 14, 15, 17, 22, 24, 27], "space": [10, 26, 30], "spiral": 10, "outward": 10, "expos": 11, "recov": [11, 12, 14, 15, 23, 24, 25, 28], "realist": [11, 31], "individu": [11, 12, 15, 16, 22, 23, 25, 28, 31], "do": [11, 16, 20, 21, 22, 23, 25, 27, 28, 30, 31], "becom": [11, 22, 23, 26, 28], "instantli": 11, "upon": [11, 16], "exposur": 11, "timescal": [11, 27], "govern": [11, 22, 23], "flu": [11, 14], "dai": 11, "n_pop": [11, 12, 14, 15, 16, 17, 22, 25, 26, 27], "1e4": [11, 14, 15, 16, 17, 21, 22, 25, 26, 27], "r0": [11, 14, 15, 27, 31], "rang": [11, 12, 14, 15, 16, 17, 22, 27, 30, 31], "increment": [11, 12, 14, 15, 16, 17, 22, 27], "365": [11, 12, 14, 15, 27, 31], "condit": [11, 12, 13, 14, 15, 16, 17, 19, 22, 26, 27, 29, 30, 31], "i0": [11, 14, 15, 16, 17, 22, 25, 26, 27, 31], "same": [11, 15, 21, 22, 25, 26, 27, 30, 31, 32], "compar": [11, 22, 26, 31], "solution2": 11, "profil": [11, 26, 30], "overal": 11, "axarr": [11, 14, 15, 16, 22, 24, 25, 26, 27], "layout": [11, 14, 15, 16, 22, 24, 25, 26, 27], "constrain": [11, 14, 15, 16, 22, 24, 25, 26, 27], "colour": [11, 14, 16, 22], "c1": [11, 14, 15, 16, 22, 26, 27], "c3": [11, 27], "c0": [11, 14, 15, 16, 22, 26, 27], "c2": [11, 14, 15, 22, 27], "statelist": [11, 14, 15, 16, 22, 23, 24, 27, 28, 31], "color": [11, 14, 15, 16, 22, 26, 27], "linestyl": 11, "dash": 11, "els": [11, 28, 30, 31], "rotat": [11, 14, 15, 16, 17, 22, 26], "seir_birth_death_periodic_waning_intro": 12, "rel": [12, 28, 30], "pre": [12, 31], "templat": 12, "complex": [12, 20, 23], "season": [12, 17, 27], "drive": 12, "immun": [12, 16, 23, 27], "w": [12, 27, 30, 31], "ii": 12, "analog": [12, 30], "epsilon": [12, 13, 31], "mu": [12, 15, 23, 28, 31, 32], "beta_0": [12, 17, 27], "co": [12, 17, 27, 30, 31], "pi": [12, 17, 27, 30, 31], "1e5": [12, 15, 31], "01": [12, 13, 15, 17, 18, 24, 26, 30, 31], "n_su": 12, "frac_su": 12, "30": [12, 25, 31], "year": [12, 15, 27], "last": [12, 25, 30, 31], "beta0": [12, 17, 27, 31], "preval": 12, "eventu": [12, 15, 28], "reach": [12, 15, 16, 22], "annual": 12, "30000": 12, "seir_multipl": [13, 31], "togeth": [13, 25, 30], "birth": [13, 23, 31], "s_": [13, 31], "dn_": [13, 31], "ds_": [13, 31], "lambda_": [13, 31], "e_": [13, 31], "i_": [13, 31], "r_": 13, "dr_": [13, 31], "sum_": [13, 30, 31], "neq": [13, 31], "patch": [13, 31, 32], "factor": [13, 28, 30, 31], "paramev": [13, 25, 26, 31], "beta_00": [13, 31], "0010107": [13, 31], "beta_01": [13, 31], "beta_10": [13, 31], "beta_11": [13, 31], "02": [13, 18, 24, 30, 31], "45": [13, 18, 31], "73": [13, 25, 31], "n_0": [13, 31], "n_1": [13, 31], "36139": [13, 31], "3224081278": [13, 31], "422": [13, 31], "560577637822": [13, 31], "263": [13, 31], "883351688369": [13, 31], "963174": [13, 31], "233662546": [13, 31], "param": [13, 21, 22, 23, 25, 26, 27, 28, 30, 31, 32], "40": [13, 25, 30, 31], "x01": [13, 31], "arrai": [13, 19, 29, 30, 31, 32], "float": [13, 29, 30, 31], "those": [13, 23, 28, 31], "stabil": [13, 19, 31], "while": [13, 30, 31], "notat": [13, 31, 32], "taken": [13, 26, 30], "heavili": 14, "throughout": [14, 23], "document": [14, 19], "result": [14, 15, 19, 22, 23, 24, 25, 27, 28, 30, 31], "familiar": [14, 21, 22], "sir_birth_death": [15, 31], "remov": [15, 23, 26, 31], "each": [15, 22, 23, 25, 26, 28, 29, 30, 31], "uniform": [15, 25, 32], "person": [15, 23], "replenish": 15, "thu": [15, 25, 27, 28], "conserv": [15, 28, 29], "For": [15, 19, 23, 24, 26, 28, 30, 31], "remain": [15, 21, 23, 25, 28, 29], "constant": [15, 21, 23, 31], "wherea": [15, 28], "fluctuat": 15, "around": [15, 28, 30], "measl": 15, "threshold": [15, 22, 25, 29], "order": [15, 22, 23, 24, 27, 30, 31], "support": [15, 23, 30], "endem": 15, "circul": 15, "pathogen": 15, "15": [15, 18, 24, 25, 31], "equilibrium": [15, 16, 31], "stationari": [15, 31], "def": [15, 30], "sir_bd_endemic_eq": 15, "s0": [15, 27], "floor": 15, "try": [15, 22, 24, 26, 31], "larger": [15, 25, 26, 30], "updat": [15, 23, 31], "recalcul": 15, "ic": 15, "solution_2": 15, "simt_2": 15, "y_2": 15, "even": [15, 19, 25, 30], "1e6": 15, "solution_3": 15, "simt_3": 15, "y_3": 15, "000": [15, 26], "critic": [15, 22], "zero": [15, 22, 30, 31], "lead": [15, 26], "extinct": [15, 22], "cours": [15, 25, 26], "signifi": 15, "stabl": [15, 31], "growth": 15, "turnov": 15, "when": [15, 18, 19, 21, 22, 23, 24, 25, 26, 28, 30, 31, 32], "subset": [15, 28], "typic": [15, 23, 25], "500": 15, "persist": 15, "titl": [15, 22, 32], "idx": [15, 22], "enumer": [15, 22], "set_titl": [15, 22, 24, 25, 27], "perhap": [16, 23, 26, 28], "simplest": 16, "recoveri": [16, 22, 23, 27], "50": [16, 22, 25, 30, 31], "suffici": [16, 22, 23], "long": [16, 30], "sis_period": [17, 31], "could": [17, 23, 24, 26, 28, 30], "mimic": 17, "variat": [17, 22], "yearli": 17, "contact": [17, 23, 31], "pattern": 17, "climat": 17, "driver": 17, "baselin": [17, 27], "magnitud": [17, 27, 30], "elimin": [17, 22, 28], "heathcot": 17, "5t": [17, 31], "framework": 18, "tri": [18, 30, 31], "json": 18, "its": [18, 23, 30], "variou": [18, 20, 23, 31], "previous": [18, 19, 21, 22, 23], "discuss": [18, 23], "guid": 18, "input": [18, 23, 25, 26, 30, 31, 32], "string": [18, 29, 30, 31], "alreadi": [18, 23, 31, 32], "dict": [18, 21, 22, 30, 31], "cumul": [18, 30], "form": [18, 19, 21, 26, 27, 31], "default": [18, 30, 31, 32], "shown": 18, "below": [18, 23, 24, 25, 26, 30, 32], "panda": 18, "datafram": 18, "loss": [18, 25, 32], "read_epijson": 18, "epijson_to_data_fram": 18, "pkgutil": 18, "get_data": 18, "eg1": 18, "print": [18, 19, 22, 24, 25, 26, 30, 31], "1854": 18, "04": [18, 25, 30, 31], "17": [18, 25, 26], "56": 18, "51": [18, 25], "00": [18, 26, 30], "18": [18, 25], "26": 18, "09": 18, "58": 18, "21": [18, 25], "24": 18, "46": [18, 25], "16": [18, 24, 30], "03": [18, 21, 30], "aim": 18, "load": [18, 21, 22, 25, 26], "usual": [18, 25, 28, 30], "epijsonloss": 18, "poisson": [18, 25, 27, 30, 32], "hood": 18, "epijson_loss": 18, "sir_norm": [18, 31], "obj": [18, 22, 24, 30], "005": 18, "cost": [18, 22, 24, 26, 30, 31], "865594602563727": 18, "_df": 18, "inherit": 18, "baseloss": [18, 30], "abov": [18, 22, 23, 24, 27, 28, 31], "rest": [18, 28], "breviti": 18, "frame": 18, "store": [18, 19, 30], "insid": 18, "retriev": 18, "inspect": [18, 19, 22, 25, 26, 28], "suppli": [18, 22], "treat": [18, 22, 24, 27], "t0": [18, 24, 26, 29, 30, 31], "indic": [18, 23, 25, 29, 30], "column": [18, 25, 29, 30, 31], "correspond": [18, 25, 26, 30, 31], "belong": [18, 31], "again": [19, 22, 23, 25, 26], "predefin": 19, "avoid": [19, 29, 31], "scratch": [19, 22], "initialis": [19, 22, 23], "seen": [19, 22], "get_ode_eqn": [19, 23, 31], "verifi": [19, 23, 26, 28], "expect": [19, 25, 28, 30, 31], "displaystyl": [19, 23, 28], "displai": 19, "latex": [19, 30, 31, 32], "port": 19, "print_od": [19, 31], "\u03b2": 19, "\u03b3": 19, "cc": 19, "definit": [19, 22, 30, 32], "get_transition_matrix": [19, 28, 31], "diagon": [19, 30, 31], "triangl": 19, "graphic": 19, "get_transition_graph": [19, 28, 31], "briefli": 19, "quickli": 19, "firstli": [19, 23], "linear_od": [19, 31], "fals": [19, 25, 29, 30, 31, 32], "analysi": [19, 22, 30, 31], "speed": [19, 24, 30], "know": [19, 23, 24, 25, 26], "jacobian": [19, 26, 30, 31], "hessian": [19, 26, 30, 31], "three": [19, 30, 31], "2d": [19, 31], "3d": [19, 31], "gradient": [19, 30, 31], "context": 19, "sure": 19, "get_jacobian_eqn": [19, 31], "get_hessian_eqn": [19, 31], "get_grad_eqn": [19, 31], "reproduct": [19, 31], "r_0": [19, 26], "next": [19, 25], "assum": [19, 23, 24, 25, 26, 28, 30, 31], "must": [19, 21, 22, 23, 24, 25, 27, 28, 30], "repres": [19, 22, 23, 27, 30, 31, 32], "epi_analysi": 19, "disease_progression_matric": [19, 31], "r0_from_matrix": [19, 31], "encapsul": [20, 21, 23], "advantag": [20, 23, 31], "sever": 20, "sort": 20, "ourselv": 20, "pen": 20, "paper": 20, "until": [21, 22, 30], "dealt": 21, "howev": [21, 22, 23, 25, 26, 28, 30], "fed": 21, "accept": [21, 23, 25, 26, 29, 30, 31], "thei": [21, 25, 26, 31], "simpli": [21, 30, 31], "list": [21, 23, 25, 27, 29, 30, 31], "tupl": [21, 29, 30, 31], "fixed_param_set": [21, 22], "imagin": [21, 24], "prior": [21, 25, 29], "uncertainti": [21, 26], "reflect": [21, 23, 25, 28], "varieti": 21, "suitabl": [21, 30, 31], "posit": [21, 23, 24, 26, 30, 31], "ll": [21, 23], "keep": [21, 23, 28], "mixtur": 21, "syntax": [21, 26], "cumbersom": 21, "item": [21, 30, 31], "handl": [21, 23, 27, 30], "second": [21, 24, 28, 31], "utilr": [21, 22], "rgamma": [21, 22, 32], "random_param_set": [21, 22], "contain": [21, 22, 25, 29, 30, 31], "shape": [21, 22, 26, 30, 31, 32], "400": [21, 25], "333": 21, "33": [21, 25, 26], "deviat": [21, 22, 30], "025": [21, 25], "good": [21, 26, 30], "idea": [21, 26], "leftov": 21, "workflow": 22, "transitiontyp": [22, 23, 24, 27, 28, 31], "paramlist": [22, 23, 24, 27, 28], "transitionlist": 22, "origin": [22, 23, 24, 27, 28, 31], "destin": [22, 23, 28, 31], "transition_typ": [22, 23, 24, 27, 28, 31], "beta_mn": 22, "35": [22, 25, 26, 31], "actual": [22, 25, 30, 31], "gamma_mn": 22, "gamma_var": 22, "10th": 22, "gamma_shap": 22, "gamma_r": 22, "beta_var": 22, "beta_shap": 22, "beta_r": 22, "involv": [22, 31], "reproduc": [22, 24, 26], "determin": [22, 30, 31], "short": [22, 23], "reduc": [22, 23, 24, 25, 28], "error": [22, 23, 30, 31], "too": [22, 27], "odeint": [22, 31], "wrap": 22, "member": [22, 23], "d_f": 22, "suffix": 22, "impli": [22, 23, 27, 28], "deterministic_fix": 22, "ode_d_f": 22, "timepoint": [22, 24, 25, 27], "solution_d_f": 22, "yield": [22, 24], "increas": [22, 25, 30], "exponenti": [22, 26, 32], "deplet": [22, 23], "declin": 22, "1000": [22, 30, 31], "repetit": 22, "ode_d_r": 22, "n_param_draw": 22, "ymean": 22, "solution_d_r": 22, "messag": [22, 24, 25, 26, 30], "connect": 22, "mpi": 22, "backend": [22, 31], "capabl": [22, 26, 28], "parallel": [22, 31], "ipython": 22, "visualis": 22, "secondli": 22, "confid": [22, 30], "interv": [22, 25, 30], "95": [22, 25], "median": [22, 25], "y_d_r": 22, "unpack": 22, "i_rand": 22, "sampl": [22, 25, 29, 30], "ci": [22, 26], "y_d_r_lolo": 22, "percentil": 22, "axi": [22, 30], "y_d_r_lo": 22, "y_d_r_hi": 22, "75": [22, 25], "y_d_r_hihi": 22, "97": [22, 30], "y_d_r_md": 22, "fill_between": 22, "facecolor": 22, "dark": 22, "shade": 22, "light": 22, "continuum": [22, 23], "break": 22, "down": [22, 30], "regim": 22, "continu": [22, 30], "flow": [22, 23, 28], "event": [22, 23, 31], "occur": [22, 23, 30], "assumpt": [22, 23, 26, 30], "wait": 22, "memoryless": 22, "quicker": 22, "algorithm": [22, 25, 26, 28, 29, 30, 31], "interact": [22, 23], "ode_s_f": 22, "solution_s_f": 22, "y_s_f": 22, "final_size_s_f": 22, "figur": [22, 25, 29, 31], "xlabel": 22, "ylabel": 22, "count": [22, 28], "hist": 22, "bin": 22, "chain": [22, 26], "fail": [22, 26, 30, 31], "i_success_s_f": 22, "2000": 22, "y_fail_s_f": 22, "min": [22, 30, 32], "proce": [22, 25, 26], "exhibit": 22, "i_fail_s_f": 22, "y_success_s_f": 22, "y_s_f_lolo": 22, "y_s_f_lo": 22, "y_s_f_hi": 22, "y_s_f_hihi": 22, "y_s_f_md": 22, "explor": 22, "scenario": [22, 24, 31], "ode_s_r": 22, "solution_s_r": 22, "y_s_r": 22, "final_size_s_r": 22, "spread": 22, "ow": 22, "separ": [22, 28], "success": [22, 24, 26, 30, 31], "clear": [22, 31], "cut": 22, "judg": 22, "ey": 22, "i_fail_s_r": 22, "y_success_s_r": 22, "y_s_r_lolo": 22, "y_s_r_lo": 22, "y_s_r_hi": 22, "y_s_r_hihi": 22, "y_s_r_md": 22, "four": [22, 23, 31], "configur": [22, 28], "side": [22, 23], "illustr": 22, "qualit": 22, "ymax": 22, "1250": 22, "fig": 22, "axarr2": 22, "set_ylim": 22, "bottom": [22, 31], "onc": [23, 26, 29], "instanc": [23, 26], "applic": [23, 27, 30], "think": [23, 28], "about": [23, 25, 26, 30], "mathbf": 23, "boldsymbol": 23, "y_": [23, 30, 31], "ldot": [23, 31], "vector": [23, 30, 31], "categori": [23, 28], "interpret": [23, 28, 30, 31], "group": 23, "y_i": 23, "rightarrow": 23, "y_j": 23, "f_": [23, 31], "symmetr": 23, "cannot": [23, 27, 30], "half": [23, 25], "flexibl": 23, "choos": [23, 25, 30, 31], "perspect": 23, "combin": [23, 25], "convert": [23, 30, 31], "attempt": [23, 25, 26, 28, 29, 31], "revers": [23, 28], "engin": [23, 28], "reli": 23, "tutori": [23, 30], "moment": 23, "ambigu": 23, "latter": [23, 31], "distinct": [23, 28], "made": [23, 25, 29, 30], "who": 23, "longer": 23, "acquir": 23, "induc": 23, "effect": [23, 26, 27], "wane": [23, 27], "versu": 23, "distinguish": [23, 28], "real": [23, 31], "world": 23, "therefor": 23, "reserv": 23, "sole": 23, "surviv": 23, "averag": 23, "transmit": 23, "receiv": 23, "unit": [23, 31], "carri": [23, 31], "cp": 23, "what": [23, 25, 28, 31], "incid": [23, 28], "oppos": 23, "mass": [23, 32], "action": [23, 31], "mix": [23, 28], "entir": 23, "No": 23, "migrat": 23, "entri": [23, 30], "departur": [23, 25], "uscept": [23, 28], "nfect": 23, "ecov": 23, "valid": [23, 28, 30], "subject": 23, "One": [23, 28, 31], "languag": 23, "benefici": 23, "enabl": 23, "forget": 23, "recipi": 23, "had": [23, 31], "rememb": [23, 31], "opposit": 23, "sign": 23, "feed": 23, "argument": [23, 24, 25, 30, 31], "let": [23, 24, 25, 26, 27, 28], "ve": 23, "just": [23, 25, 30], "option": [23, 25, 30, 31], "summaris": 23, "tabl": 23, "pertain": 23, "dy_i": 23, "arguabl": 23, "convent": 23, "adopt": 23, "better": 23, "incorrectli": 23, "place": [23, 27, 30], "through": [23, 30, 31], "odelist": [23, 27, 28], "translist": 23, "model_od": 23, "model_tra": 23, "equival": [23, 25, 30], "sai": [23, 30, 31], "complic": 23, "cancel": 23, "balanc": [23, 28], "achiev": [23, 31], "param_list": 23, "enter": [23, 27, 28], "birthdeathlist": 23, "birth_death_list": 23, "correctli": [23, 25], "ivp": 24, "bvp": 24, "littl": 24, "bit": 24, "essenti": [24, 26], "shoot": 24, "observ": [24, 25, 26, 29, 30, 32], "projectil": 24, "motion": 24, "domain": 24, "anywai": 24, "launch": 24, "ball": 24, "straight": 24, "air": 24, "height": 24, "ignor": [24, 30], "resist": 24, "graviti": 24, "acceler": 24, "veloc": 24, "suppos": 24, "land": 24, "10m": 24, "trivial": 24, "quick": 24, "15m": 24, "target": [24, 30, 31], "hope": 24, "artefact": 24, "soon": 24, "ode1": 24, "ode2": 24, "explicitli": [24, 27, 28], "20m": 24, "subsequ": [24, 25], "satisfi": [24, 30], "guess": [24, 25, 26, 30], "admittedli": 24, "ineffici": 24, "twice": [24, 30], "target_st": [24, 30], "minim": [24, 26, 30], "squareloss": [24, 29, 30], "initialst": 24, "state_nam": [24, 26, 29, 30], "And": 24, "costiv": 24, "thetahat": 24, "fun": [24, 26, 30], "termin": [24, 26, 30], "statu": [24, 26], "987646893079144e": 24, "500e": 24, "nit": [24, 26], "jac": [24, 26, 31], "122e": 24, "hess_inv": 24, "556e": 24, "nfev": [24, 26, 30], "njev": [24, 26], "tolist": 24, "known": 24, "pretend": 24, "omit": [24, 25], "declar": [24, 27], "1241808584714344e": 24, "000e": 24, "068e": 24, "469e": 24, "posterior": [25, 26, 29], "candid": [25, 26], "synthet": 25, "quad": [25, 30], "n_": 25, "text": 25, "pop": [25, 31], "loadtxt": [25, 26], "seir_epi_data": [25, 26], "sol_i_r": [25, 26], "daili": 25, "rcparam": 25, "scatter": 25, "regard": [25, 28], "report": [25, 29, 30], "unlik": 25, "unless": [25, 30], "high": 25, "nevertheless": 25, "purpos": 25, "realiti": 25, "undermin": 25, "go": [25, 28], "unknown": [25, 26], "unrealist": 25, "sake": 25, "simplic": [25, 31], "interest": [25, 30], "create_loss": [25, 29], "predict": [25, 30, 32], "overspecifi": 25, "overrod": 25, "ode_seir": [25, 26], "seir_n": [25, 26, 31], "approximate_bayesian_comput": 25, "unif": 25, "logscal": [25, 29], "poissonloss": [25, 26, 30], "everyth": 25, "objseir": [25, 26], "abcseir": 25, "sequenti": 25, "smc": [25, 29], "smaller": [25, 30], "perturb": 25, "weight": [25, 29, 30], "multivari": [25, 30], "normal": [25, 30, 31, 32], "covari": [25, 30], "get_posterior_sampl": 25, "q": [25, 29, 30, 32], "quantil": [25, 29], "whilst": [25, 27, 28], "toler": [25, 29, 30], "difficult": [25, 28], "th": 25, "distanc": 25, "reduct": 25, "higher": 25, "250": 25, "tol": [25, 29, 30], "inf": 25, "progress": [25, 26, 29, 31], "74": 25, "364073": 25, "42362": 25, "62": 25, "72191": 25, "64935": 25, "21204": 25, "77097": 25, "53": 25, "7452": 25, "74757": 25, "3250": 25, "22571": 25, "want": [25, 29, 31], "continue_posterior_sampl": [25, 29], "along": [25, 30], "next_tol": 25, "attribut": [25, 30], "2232": 25, "01873": 25, "13": [25, 30], "1833": 25, "77615": 25, "76": 25, "plot_posterior_histogram": [25, 29], "plot_pointwise_predict": [25, 29], "abcsir": 25, "re": [25, 26, 30, 31], "credibl": [25, 26], "consist": [25, 28], "3f": 25, "975": 25, "350": 25, "318": 25, "388": 25, "566": 25, "437": 25, "712": 25, "254": 25, "231": 25, "281": 25, "concern": 25, "compon": 25, "wise": [25, 30], "objseir2": 25, "epi": 25, "abcseir2": 25, "57967": 25, "89694": 25, "23": 25, "14573": 25, "65549": 25, "63": 25, "4955": 25, "22257": 25, "07": 25, "1747": 25, "46397": 25, "1008": 25, "39222": 25, "795": 25, "51825": 25, "750": 25, "03026": 25, "85": 25, "362": 25, "326": 25, "413": 25, "516": 25, "345": 25, "785": 25, "260": [25, 26], "240": 25, "284": 25, "agreement": [25, 26], "Of": 25, "mechan": 25, "similar": [25, 26, 27, 31], "doen": 25, "e0": 25, "ode_sir": 25, "objsir": 25, "97090": 25, "54633": 25, "57": 25, "26871": 25, "99949": 25, "27": 25, "06": 25, "7946": 25, "79001": 25, "05": [25, 30], "2164": 25, "64690": 25, "86": 25, "1108": 25, "75380": 25, "83": 25, "936": 25, "24091": 25, "32": 25, "900": 25, "98276": 25, "31": 25, "69": 25, "restrict": [25, 30, 31], "inappropri": 25, "poorer": 25, "certainti": 25, "objseir3": 25, "abcseir3": 25, "72": 25, "89": 25, "58067": 25, "08238": 25, "15858": 25, "17892": 25, "94": 25, "5420": 25, "38644": 25, "54": 25, "2185": 25, "32098": 25, "41": 25, "1182": 25, "18264": 25, "42": 25, "878": 25, "11360": 25, "777": 25, "43372": 25, "64": 25, "307": 25, "623": 25, "366": 25, "141": 25, "408": 25, "278": 25, "230": 25, "368": 25, "701": 25, "106": 25, "wider": 25, "markov": 26, "techniqu": [26, 30], "level": [26, 30], "landscap": 26, "outdat": 26, "practic": [26, 28], "older": 26, "public": 26, "minimis": 26, "remind": 26, "i_0": 26, "ones": 26, "target_param": [26, 30], "decai": 26, "substanti": 26, "neighbourhood": 26, "similarli": [26, 28], "bad": 26, "navig": 26, "sensit": [26, 31], "adjoint": [26, 31], "3473286": 26, "37537513": 26, "648419": 26, "19492932": 26, "3962185": 26, "9873881": 26, "3439949": 26, "96665263": 26, "651037": 26, "89808302": 26, "3920356": 26, "14337017": 26, "timeit": 26, "206": 26, "\u03bc": 26, "loop": [26, 31], "std": 26, "dev": 26, "38": 26, "ran": 26, "properti": [26, 31], "quit": 26, "evid": 26, "discret": 26, "forward": [26, 30, 31], "affect": 26, "obviou": 26, "interpol": [26, 30, 31], "consecut": 26, "length": [26, 30, 31], "fewer": 26, "accur": 26, "univari": [26, 30], "spline": [26, 30], "limit": [26, 30], "ideal": [26, 29], "prefer": [26, 30, 31], "adapt": [26, 30], "hermit": 26, "chebyshev": 26, "procedur": 26, "sensibl": 26, "boxbound": 26, "slsqp": 26, "bfg": 26, "tnc": 26, "trust": 26, "ncg": 26, "bound": [26, 30], "1651": 26, "1282171916191": 26, "537e": 26, "384e": 26, "559e": 26, "683e": 26, "730e": 26, "709e": 26, "par": 26, "ode_est": 26, "lower": [26, 30], "incomplet": 26, "measur": 26, "fall": 26, "part": 26, "carefulli": 26, "confidence_interv": 26, "asymptot": [26, 30], "bootstrap": [26, 30], "geometr": [26, 30], "Such": 27, "situat": 27, "vari": [27, 31], "intervent": 27, "wit": 27, "multipl": [27, 28, 31], "dummi": 27, "plai": 27, "role": 27, "append": [27, 31], "tau_0": 27, "t_0": 27, "put": 27, "derived_param": [27, 31], "tau0": 27, "int": [27, 30, 31, 32], "accord": [27, 31], "sim": 27, "vagu": 27, "lose": 27, "lost": 28, "constitu": 28, "explain": 28, "caution": 28, "potenti": 28, "tricki": 28, "split": 28, "necessarili": [28, 30], "track": 28, "encount": 28, "live": 28, "difficulti": 28, "care": 28, "get_unrolled_obj": [28, 31], "implic": 28, "substitut": 28, "everywher": 28, "empti": 28, "match": 28, "nlive": 28, "limitless": 28, "reservoir": 28, "come": [28, 31], "graph": [28, 31], "map": 28, "atent": 28, "leav": 28, "fraction": 28, "nfectiv": 28, "symptomat": 28, "onward": 28, "emov": 28, "eta": [28, 31], "die": 28, "outflow": 28, "compos": 28, "partit": 28, "dead": 28, "notic": [28, 30], "born": 28, "incorrect": 28, "loss_object": 29, "constraint": 29, "none": [29, 30, 31, 32], "integ": [29, 30, 32], "sequenc": [29, 30], "decreas": [29, 30], "mnn": 29, "nearest": 29, "neighbour": 29, "bool": [29, 30, 31], "rerun": 29, "get_posterior_sample_origin": 29, "get_toler": 29, "plot_stat": 29, "new_tim": 29, "max_ncol": 29, "temporarili": 29, "overwrit": 29, "revert": 29, "pure": 29, "squash": 29, "plot_param": 29, "plot_scatt": 29, "pair": [29, 30, 31], "whether": [29, 30, 31], "scale": [29, 30, 31], "sigma_nearest_neighbour": 29, "xx": 29, "distnam": 29, "distpar": 29, "chosen": [29, 30], "loss_typ": 29, "state_weight": [29, 30], "sigma": [29, 30, 31, 32], "were": [29, 31], "str": [29, 30, 31], "came": 29, "normalloss": [29, 30], "get_funct": 29, "diff2loss": 30, "yhat": 30, "apply_weight": 30, "jupit": 30, "ipnyb": [30, 32], "boolean": [30, 31], "multipli": [30, 31], "residu": 30, "raw": 30, "scnd_deriv_yhat": 30, "hat": 30, "diff_loss": 30, "first_deriv_yhat": 30, "neg": [30, 31, 32], "distirbut": 30, "bolker": [30, 32], "ecolog": [30, 32], "pp": [30, 32], "131": [30, 32], "133": [30, 32], "princeton": [30, 32], "univers": [30, 32], "kept": 30, "miss": 30, "mathcal": [30, 32], "gammaloss": 30, "negbinom": 30, "k": [30, 31, 32], "binomi": [30, 32], "overdispers": [30, 32], "varianc": [30, 31, 32], "124": [30, 32], "126": [30, 32], "negbinomloss": 30, "nabla": 30, "mathcalfrac": 30, "sqrt": [30, 31], "2pi": 30, "2sigma": 30, "scalar": 30, "_": [30, 31], "Not": 30, "realli": 30, "univariatesplin": 30, "bbox": 30, "ext": 30, "check_finit": 30, "spl": 30, "degre": 30, "knot": 30, "array_lik": 30, "independ": 30, "strictli": 30, "cubic": 30, "sum": 30, "ab": 30, "001": 30, "len": [30, 31], "interpolatedunivariatesplin": 30, "control": 30, "tradeoff": 30, "datapoint": 30, "extrapol": 30, "valueerror": 30, "const": 30, "finit": 30, "disabl": 30, "gain": 30, "crash": 30, "non": [30, 31], "sensic": 30, "infin": 30, "nan": 30, "bivariatesplin": 30, "bivari": 30, "smoothbivariatesplin": 30, "lsqbivariatesplin": 30, "least": 30, "rectspherebivariatesplin": 30, "rectangular": 30, "mesh": 30, "sphere": 30, "smoothspherebivariatesplin": 30, "spheric": 30, "coordin": 30, "lsqspherebivariatesplin": 30, "rectbivariatesplin": 30, "bisplrep": 30, "represent": 30, "surfac": 30, "bisplev": 30, "splrep": 30, "curv": 30, "splev": 30, "sproot": 30, "root": 30, "splint": 30, "spald": 30, "deal": 30, "workaround": 30, "isnan": 30, "matter": 30, "dierckx": 30, "experiment": 30, "comp": 30, "appl": 30, "1975": 30, "165": 30, "184": 30, "grid": 30, "siam": 30, "anal": 30, "19": 30, "1982": 30, "1286": 30, "1304": 30, "improv": 30, "tw54": 30, "dept": 30, "leuven": 30, "1981": 30, "monograph": 30, "oxford": 30, "1993": 30, "rng": 30, "default_rng": 30, "standard_norm": 30, "ro": 30, "lw": 30, "manual": [30, 32], "set_smoothing_factor": 30, "antideriv": 30, "k2": 30, "splantid": 30, "70": 30, "sin": 30, "accumul": 30, "1565429877197317": 30, "1565429877201865": 30, "ispl": 30, "2572053588768486": 30, "ellipt": 30, "int_0": 30, "dx": [30, 31], "ellipk": 30, "2572053268208538": 30, "splder": 30, "maxima": 30, "nb": 30, "50000001": 30, "49999998": 30, "agre": 30, "ndarrai": [30, 31], "get_coeff": 30, "coeffici": 30, "get_knot": 30, "interior": 30, "intern": [30, 31], "get_residu": 30, "caveat": 30, "fitpack": 30, "ppoli": 30, "happen": 30, "coincid": 30, "96": 30, "98": 30, "99": 30, "365470e": 30, "790580e": 30, "204320e": 30, "607270e": 30, "440892e": 30, "616930e": 30, "243000e": 30, "877670e": 30, "520430e": 30, "170770e": 30, "dtype": 30, "float64": 30, "tck": 30, "from_splin": 30, "lb": 30, "ub": 30, "2n": 30, "cost_grad_interpol": 30, "spline_list": 30, "doubl": [30, 31], "cost_interpol": 30, "vec": 30, "aggreg": 30, "paramt": 30, "flatten": 30, "cost_sampl": 30, "fxapprox": 30, "xapprox": 30, "simpson": 30, "rule": 30, "appli": 30, "integrand": 30, "dimens": [30, 31], "residual_sampl": 30, "jtj": 30, "geometri": 30, "fisher": 30, "cov": 30, "nabla_": [30, 31], "moolgavkar1987": 30, "l_path": 30, "u_path": 30, "path": 30, "get_init": 30, "grad_sampl": 30, "output_residu": 30, "jac_sampl": 30, "row": [30, 31], "splinelist": 30, "leastsq": 30, "func": [30, 31], "arg": [30, 31], "dfun": 30, "col_deriv": 30, "ftol": 30, "49012e": 30, "08": 30, "xtol": 30, "gtol": 30, "maxfev": 30, "epsfcn": 30, "diag": 30, "callabl": [30, 31], "possibli": 30, "across": 30, "ier": 30, "transpos": [30, 31], "orthogon": 30, "unsuccess": 30, "cov_x": 30, "fjac": 30, "ipvt": 30, "singular": 30, "curvatur": 30, "flat": 30, "curve_fit": 30, "infodict": 30, "dictionari": [30, 31], "fvec": 30, "permut": 30, "qr": 30, "triangular": 30, "nonincreas": 30, "ident": [30, 31], "qtf": 30, "mesg": 30, "caus": 30, "failur": 30, "flag": 30, "least_squar": 30, "newer": 30, "nonlinear": 30, "lm": 30, "particular": 30, "wrapper": [30, 31], "minpack": 30, "lmdif": 30, "lmder": 30, "ydata": 30, "xdata": 30, "regardless": 30, "99999999": 30, "minimize_scalar": 30, "bracket": 30, "brent": 30, "golden": 30, "tripl": 30, "xa": 30, "xb": 30, "xc": 30, "downhil": 30, "search": 30, "mandatori": 30, "custom": 30, "maxit": 30, "disp": 30, "converg": 30, "show_opt": 30, "optimizeresult": 30, "exit": 30, "descript": 30, "unbound": 30, "minimum": [30, 31], "parabol": 30, "bisect": 30, "x1": 30, "xopt": 30, "x2": 30, "guarante": 30, "global_optim": 30, "librari": [30, 32], "frontend": 30, "kwarg": 30, "except": 30, "shall": 30, "arbitrari": 30, "expand": 30, "teukolski": 30, "vetterl": 30, "flanneri": 30, "recip": 30, "cambridg": 30, "forsyth": 30, "malcolm": 30, "moler": 30, "prentic": 30, "hall": 30, "259": 30, "courier": 30, "corpor": 30, "2013": 30, "9149495908": 30, "28077640403": 30, "28365179850e": 30, "0000002026": 30, "partial": [30, 31], "keyword": 30, "residual_interpol": 30, "simp": 30, "composit": 30, "odd": 30, "quadratur": 30, "quadpack": 30, "fixed_quad": 30, "gaussian": 30, "dblquad": 30, "tplquad": 30, "romb": 30, "cumulative_trapezoid": 30, "cumulative_simpson": 30, "polynomi": 30, "cartwright": 30, "kenneth": 30, "excel": 30, "irregularli": 30, "educ": 30, "arang": 30, "power": 30, "1640": 30, "lambda": [30, 31], "compilecanari": 31, "hold": 31, "compil": 31, "subclass": 31, "watch": 31, "trip": 31, "reset": [31, 32], "direct": 31, "assign": 31, "canari": 31, "rtype": 31, "dfe": 31, "disease_st": 31, "free": 31, "baseodemodel": 31, "diseasest": 31, "birth_death": 31, "state_param": 31, "lagrangian": 31, "mayb": 31, "backward": 31, "adjoint_t": 31, "adjoint_interpol": 31, "adjoint_interpolate_t": 31, "objinput": 31, "adjoint_interpolate_jacobian": 31, "dimension": 31, "adjoint_jacobian": 31, "singl": 31, "adjoint_interpolate_jacobian_t": 31, "adjoint_jacobian_t": 31, "diff_jacobian": 31, "diff_jacobian_t": 31, "eval_diff_jacobian": 31, "mpmath": 31, "eval_forwardforward": 31, "ff": 31, "fact": 31, "3rd": 31, "tensor": 31, "aka": 31, "eval_grad": 31, "grad": 31, "eval_grad_jacobian": 31, "grad_jacobian": 31, "get_grad_jacobian_eqn": 31, "eval_hessian": 31, "sympi": 31, "matrici": 31, "eval_jacobian": 31, "eval_od": 31, "eval_sens_jacobian_st": 31, "sen": 31, "sens_jacobian_st": 31, "eval_sensit": 31, "by_stat": 31, "arrang": 31, "block": 31, "structur": 31, "eval_sensitivityiv": 31, "iv": 31, "x_": 31, "sensitivityiv": 31, "forwardforward": 31, "forwardforward_t": 31, "get_diff_jacobian_eqn": 31, "num": 31, "matric": 31, "deliber": 31, "confus": 31, "param_sub": 31, "file_nam": 31, "digraph": 31, "grad_t": 31, "grad_jacobi": 31, "initial_st": 31, "initial_tim": 31, "integrate2": 31, "vode": 31, "ivod": 31, "stiff": 31, "eigenvalu": 31, "is_stiff": 31, "classifi": 31, "jacobian_t": 31, "jacobian_eigenvalu": 31, "ode_t": 31, "ode_and_forwardforward": 31, "ode_and_forwardforward_t": 31, "odeandforwardforward": 31, "ode_and_forwardforward_jacobian": 31, "ode_and_forwardforward_jacobian_t": 31, "ode_and_sensit": 31, "sensitivity_": 31, "led": 31, "concaten": 31, "ode_and_sensitivityiv": 31, "ode_and_sensitivityiv_t": 31, "ode_and_sensitivityiv_jacobian": 31, "spars": 31, "bystat": 31, "ode_and_sensitivityiv_jacobian_t": 31, "ode_and_sensitivity_t": 31, "ode_and_sensitivity_jacobian": 31, "ode_and_sensitivity_jacobian_t": 31, "odeutil": 31, "latex_output": 31, "onto": 31, "screen": 31, "consol": 31, "word": 31, "ye": 31, "formula": 31, "sens_jacobian_state_t": 31, "2p": 31, "3p": 31, "sensiv": 31, "sensitivityiv_t": 31, "sensitivity_t": 31, "fitzhugh1961": 31, "dv": 31, "influenza_sliarn": 31, "influenza": 31, "brauer2008": 31, "323": 31, "dl": 31, "da": 31, "dn": 31, "legrand2007": 31, "autonom": 31, "convers": 31, "lorenz": 31, "attractor": 31, "rho": 31, "lorenz1963": 31, "dy": 31, "z": 31, "dz": 31, "xy": 31, "volterra": 31, "lotka1920": 31, "cxy": 31, "10000": 31, "lotka_volterra_4st": 31, "grass": 31, "rabbit": 31, "fox": 31, "k_": 31, "db": 31, "150": 31, "odevari": 31, "id": 31, "identifi": 31, "human": 31, "readabl": 31, "ordereddict": 31, "insert": 31, "shallow": 31, "fromkei": 31, "move_to_end": 31, "keyerror": 31, "popitem": 31, "lifo": 31, "fifo": 31, "setdefault": 31, "lack": 31, "diseasestateindex": 31, "getdiseaseprogressionmatric": 31, "getr0givenmatrix": 31, "getr0": 31, "matrixbas": 31, "secondari": 31, "fv": 31, "robertson1966": 31, "dy_": 31, "cdot": 31, "logspac": 31, "1800": 31, "84": 31, "1001": 31, "0658": 31, "0007": 31, "0002": 31, "seir_birth_death": 31, "aron1984": 31, "apart": 31, "seir_birth_death_period": 31, "beta1": 31, "sir_period": 31, "180": 31, "lloyd1996": 31, "de_": 31, "di_": 31, "init": 31, "everyon": 31, "730": 31, "126372": 31, "7781984": 31, "10001": 31, "065": 31, "123": 31, "hethcote1973": 31, "suggest": 31, "outcom": 31, "birth_death_r": 31, "cle": 31, "t1": 31, "output_tim": 31, "euler": 31, "maruyama": 31, "transition_func": 31, "eval_birth_death_r": 31, "setparamet": 31, "eval_transition_matrix": 31, "eval_transition_mean": 31, "eval_transition_var": 31, "eval_transition_vector": 31, "get_bd_from_od": 31, "unrol": 31, "get_birth_death_r": 31, "get_transition_vector": 31, "get_transitions_from_od": 31, "hybrid": 31, "sim_x": 31, "sim_t": 31, "simulate_jump": 31, "unequ": 31, "record": 31, "jump": 31, "switch": 31, "processor": 31, "simulate_param": 31, "y_all": 31, "total_transit": 31, "transition_matrix": 31, "transition_mean": 31, "a_": 31, "v_": 31, "mu_": 31, "transition_var": 31, "transition_vector": 31, "1d": 31, "enum": 31, "throw": 31, "_equat": 31, "is_between_st": 31, "feasibl": 31, "check_array_typ": 31, "accept_boolean": 31, "check_dimens": 31, "compilecod": 31, "compileexpr": 31, "inputsymb": 31, "inputexpr": 31, "compiletyp": 31, "expr": 31, "compileexprandformat": 31, "outtyp": 31, "transform": 31, "against": 31, "closur": 31, "diff": 31, "integratefuncjac": 31, "includeorigin": 31, "nstep": 31, "pick": 31, "correct": 31, "j_": 31, "availbl": 31, "ev": 31, "maxev": 31, "minev": 31, "suc": 31, "is_list_lik": 31, "behav": 31, "anyth": 31, "plot_det": 31, "ystatelist": 31, "plot_stoc": 31, "stochastic_model": 31, "stocast": 31, "shapeadjust": 31, "numstat": 31, "numparam": 31, "numtarget": 31, "vice": 31, "versa": 31, "kronparam": 31, "otim": 31, "kron": 31, "kronstat": 31, "mattovecff": 31, "mattovecsen": 31, "vectomatff": 31, "vectomatsen": 31, "str_or_list": 31, "vanderpol1926": 31, "prime": 31, "dbeta": 32, "shape1": 32, "shape2": 32, "stat": 32, "ethz": 32, "ch": 32, "dbinom": 32, "prob": 32, "dchisq": 32, "chisquar": 32, "dexp": 32, "dgamma": 32, "gammadist": 32, "dmvnorm": 32, "rdocument": 32, "mvtnorm": 32, "topic": 32, "mvnorm": 32, "dnbinom": 32, "devel": 32, "negbinomi": 32, "dnorm": 32, "sd": 32, "dpoi": 32, "dunif": 32, "max": 32, "gamma_mu_shap": 32, "pdf": 32, "distrbut": 32, "pmf": 32, "ln": 32, "nb2pmf": 32, "often": 32, "lpha": 32, "mathcalp": 32, "xright": 32, "kright": 32, "pbinom": 32, "pchisq": 32, "pexp": 32, "pgamma": 32, "pnbinom": 32, "lower_tail": 32, "pnorm": 32, "ppoi": 32, "punif": 32, "qbeta": 32, "qbinom": 32, "qchisq": 32, "qexp": 32, "qgamma": 32, "qnbinom": 32, "qnorm": 32, "qpoi": 32, "qunif": 32, "rbeta": 32, "rbinom": 32, "randomst": 32, "rchisq": 32, "rexp": 32, "rmvnorm": 32, "rnorm": 32, "rpoi": 32, "runif": 32, "test_se": 32, "global": 32}, "objects": {"pygom": [[29, 0, 0, "-", "approximate_bayesian_computation"], [30, 0, 0, "-", "loss"], [31, 0, 0, "-", "model"], [32, 0, 0, "-", "utilR"]], "pygom.approximate_bayesian_computation": [[29, 1, 1, "", "ABC"], [29, 1, 1, "", "Parameter"], [29, 3, 1, "", "create_loss"], [29, 3, 1, "", "get_function"]], "pygom.approximate_bayesian_computation.ABC": [[29, 2, 1, "", "continue_posterior_sample"], [29, 2, 1, "", "get_posterior_sample"], [29, 2, 1, "", "get_posterior_sample_original"], [29, 2, 1, "", "get_tolerance"], [29, 2, 1, "", "plot_pointwise_predictions"], [29, 2, 1, "", "plot_posterior_histograms"], [29, 2, 1, "", "plot_scatter"], [29, 2, 1, "", "sigma_nearest_neighbours"]], "pygom.loss": [[30, 1, 1, "", "Gamma"], [30, 1, 1, "", "GammaLoss"], [30, 1, 1, "", "NegBinom"], [30, 1, 1, "", "NegBinomLoss"], [30, 1, 1, "", "Normal"], [30, 1, 1, "", "NormalLoss"], [30, 1, 1, "", "Poisson"], [30, 1, 1, "", "PoissonLoss"], [30, 1, 1, "", "Square"], [30, 1, 1, "", "SquareLoss"], [30, 1, 1, "", "UnivariateSpline"], [30, 3, 1, "", "asymptotic"], [30, 3, 1, "", "bootstrap"], [30, 3, 1, "", "cost_grad_interpolant"], [30, 3, 1, "", "cost_interpolant"], [30, 3, 1, "", "cost_sample"], [30, 3, 1, "", "geometric"], [30, 3, 1, "", "get_init"], [30, 3, 1, "", "grad_sample"], [30, 3, 1, "", "interpolate"], [30, 3, 1, "", "jac_sample"], [30, 3, 1, "", "leastsq"], [30, 3, 1, "", "minimize_scalar"], [30, 1, 1, "", "partial"], [30, 3, 1, "", "profile"], [30, 3, 1, "", "residual_interpolant"], [30, 3, 1, "", "residual_sample"], [30, 3, 1, "", "simps"]], "pygom.loss.Gamma": [[30, 2, 1, "", "diff2Loss"], [30, 2, 1, "", "diff_loss"], [30, 2, 1, "", "loss"]], "pygom.loss.NegBinom": [[30, 2, 1, "", "diff2Loss"], [30, 2, 1, "", "diff_loss"], [30, 2, 1, "", "loss"]], "pygom.loss.Normal": [[30, 2, 1, "", "diff2Loss"], [30, 2, 1, "", "diff_loss"], [30, 2, 1, "", "loss"]], "pygom.loss.Poisson": [[30, 2, 1, "", "diff2Loss"], [30, 2, 1, "", "diff_loss"], [30, 2, 1, "", "loss"]], "pygom.loss.Square": [[30, 2, 1, "", "diff2Loss"], [30, 2, 1, "", "diff_loss"], [30, 2, 1, "", "loss"]], "pygom.loss.UnivariateSpline": [[30, 2, 1, "", "antiderivative"], [30, 2, 1, "", "derivative"], [30, 2, 1, "", "derivatives"], [30, 2, 1, "", "get_coeffs"], [30, 2, 1, "", "get_knots"], [30, 2, 1, "", "get_residual"], [30, 2, 1, "", "integral"], [30, 2, 1, "", "roots"], [30, 2, 1, "", "set_smoothing_factor"]], "pygom.loss.partial": [[30, 4, 1, "", "args"], [30, 4, 1, "", "func"], [30, 4, 1, "", "keywords"]], "pygom.model": [[31, 1, 1, "", "CompileCanary"], [31, 3, 1, "", "DFE"], [31, 1, 1, "", "DeterministicOde"], [31, 3, 1, "", "FitzHugh"], [31, 3, 1, "", "Influenza_SLIARN"], [31, 3, 1, "", "Legrand_Ebola_SEIHFR"], [31, 3, 1, "", "Lorenz"], [31, 3, 1, "", "Lotka_Volterra"], [31, 3, 1, "", "Lotka_Volterra_4State"], [31, 1, 1, "", "ODEVariable"], [31, 1, 1, "", "OrderedDict"], [31, 3, 1, "", "R0"], [31, 3, 1, "", "R0_from_matrix"], [31, 3, 1, "", "Robertson"], [31, 3, 1, "", "SEIR"], [31, 3, 1, "", "SEIR_Birth_Death"], [31, 3, 1, "", "SEIR_Birth_Death_Periodic"], [31, 3, 1, "", "SEIR_Multiple"], [31, 3, 1, "", "SEIR_N"], [31, 3, 1, "", "SIR"], [31, 3, 1, "", "SIR_Birth_Death"], [31, 3, 1, "", "SIR_norm"], [31, 3, 1, "", "SIS"], [31, 3, 1, "", "SIS_Periodic"], [31, 1, 1, "", "SimulateOde"], [31, 1, 1, "", "Transition"], [31, 1, 1, "", "TransitionType"], [31, 3, 1, "", "check_array_type"], [31, 3, 1, "", "check_dimension"], [31, 1, 1, "", "compileCode"], [31, 3, 1, "", "disease_progression_matrices"], [31, 3, 1, "", "integrate"], [31, 3, 1, "", "integrateFuncJac"], [31, 3, 1, "", "is_list_like"], [31, 3, 1, "", "plot_det"], [31, 3, 1, "", "plot_stoc"], [31, 1, 1, "", "shapeAdjust"], [31, 3, 1, "", "str_or_list"], [31, 3, 1, "", "vanDerPol"]], "pygom.model.CompileCanary": [[31, 2, 1, "", "reset"], [31, 2, 1, "", "trip"]], "pygom.model.DeterministicOde": [[31, 2, 1, "", "adjoint"], [31, 2, 1, "", "adjoint_T"], [31, 2, 1, "", "adjoint_interpolate"], [31, 2, 1, "", "adjoint_interpolate_T"], [31, 2, 1, "", "adjoint_interpolate_jacobian"], [31, 2, 1, "", "adjoint_interpolate_jacobian_T"], [31, 2, 1, "", "adjoint_jacobian"], [31, 2, 1, "", "adjoint_jacobian_T"], [31, 2, 1, "", "diff_jacobian"], [31, 2, 1, "", "diff_jacobian_T"], [31, 2, 1, "", "eval_diff_jacobian"], [31, 2, 1, "", "eval_forwardforward"], [31, 2, 1, "", "eval_grad"], [31, 2, 1, "", "eval_grad_jacobian"], [31, 2, 1, "", "eval_hessian"], [31, 2, 1, "", "eval_jacobian"], [31, 2, 1, "", "eval_ode"], [31, 2, 1, "", "eval_sens_jacobian_state"], [31, 2, 1, "", "eval_sensitivity"], [31, 2, 1, "", "eval_sensitivityIV"], [31, 2, 1, "", "forwardforward"], [31, 2, 1, "", "forwardforward_T"], [31, 2, 1, "", "get_diff_jacobian_eqn"], [31, 2, 1, "", "get_grad_eqn"], [31, 2, 1, "", "get_grad_jacobian_eqn"], [31, 2, 1, "", "get_hessian_eqn"], [31, 2, 1, "", "get_jacobian_eqn"], [31, 2, 1, "", "get_ode_eqn"], [31, 2, 1, "", "get_transition_graph"], [31, 2, 1, "", "grad"], [31, 2, 1, "", "grad_T"], [31, 2, 1, "", "grad_jacobian"], [31, 2, 1, "", "grad_jacobianT"], [31, 2, 1, "", "hessian"], [31, 5, 1, "", "initial_state"], [31, 5, 1, "", "initial_time"], [31, 5, 1, "", "initial_values"], [31, 2, 1, "", "integrate"], [31, 2, 1, "", "integrate2"], [31, 2, 1, "", "is_stiff"], [31, 2, 1, "", "jacobian"], [31, 2, 1, "", "jacobian_T"], [31, 2, 1, "", "jacobian_eigenvalue"], [31, 2, 1, "", "linear_ode"], [31, 2, 1, "", "ode"], [31, 2, 1, "", "ode_T"], [31, 2, 1, "", "ode_and_forwardforward"], [31, 2, 1, "", "ode_and_forwardforward_T"], [31, 2, 1, "", "ode_and_forwardforward_jacobian"], [31, 2, 1, "", "ode_and_forwardforward_jacobian_T"], [31, 2, 1, "", "ode_and_sensitivity"], [31, 2, 1, "", "ode_and_sensitivityIV"], [31, 2, 1, "", "ode_and_sensitivityIV_T"], [31, 2, 1, "", "ode_and_sensitivityIV_jacobian"], [31, 2, 1, "", "ode_and_sensitivityIV_jacobian_T"], [31, 2, 1, "", "ode_and_sensitivity_T"], [31, 2, 1, "", "ode_and_sensitivity_jacobian"], [31, 2, 1, "", "ode_and_sensitivity_jacobian_T"], [31, 2, 1, "", "plot"], [31, 2, 1, "", "print_ode"], [31, 2, 1, "", "sens_jacobian_state"], [31, 2, 1, "", "sens_jacobian_state_T"], [31, 2, 1, "", "sensitivity"], [31, 2, 1, "", "sensitivityIV"], [31, 2, 1, "", "sensitivityIV_T"], [31, 2, 1, "", "sensitivity_T"]], "pygom.model.OrderedDict": [[31, 2, 1, "", "clear"], [31, 2, 1, "", "copy"], [31, 2, 1, "", "fromkeys"], [31, 2, 1, "", "items"], [31, 2, 1, "", "keys"], [31, 2, 1, "", "move_to_end"], [31, 2, 1, "", "pop"], [31, 2, 1, "", "popitem"], [31, 2, 1, "", "setdefault"], [31, 2, 1, "", "update"], [31, 2, 1, "", "values"]], "pygom.model.SimulateOde": [[31, 2, 1, "", "birth_death_rate"], [31, 2, 1, "", "cle"], [31, 2, 1, "", "eval_birth_death_rate"], [31, 2, 1, "", "eval_transition_matrix"], [31, 2, 1, "", "eval_transition_mean"], [31, 2, 1, "", "eval_transition_var"], [31, 2, 1, "", "eval_transition_vector"], [31, 2, 1, "", "exact"], [31, 2, 1, "", "get_bd_from_ode"], [31, 2, 1, "", "get_birth_death_rate"], [31, 2, 1, "", "get_transition_matrix"], [31, 2, 1, "", "get_transition_vector"], [31, 2, 1, "", "get_transitions_from_ode"], [31, 2, 1, "", "get_unrolled_obj"], [31, 2, 1, "", "hybrid"], [31, 2, 1, "", "plot"], [31, 2, 1, "", "simulate_jump"], [31, 2, 1, "", "simulate_param"], [31, 2, 1, "", "solve_determ"], [31, 2, 1, "", "solve_stochast"], [31, 2, 1, "", "total_transition"], [31, 2, 1, "", "transition_matrix"], [31, 2, 1, "", "transition_mean"], [31, 2, 1, "", "transition_var"], [31, 2, 1, "", "transition_vector"]], "pygom.model.Transition": [[31, 5, 1, "", "destination"], [31, 5, 1, "", "equation"], [31, 2, 1, "", "is_between_state"], [31, 5, 1, "", "origin"], [31, 5, 1, "", "transition_type"]], "pygom.model.compileCode": [[31, 2, 1, "", "compileExpr"], [31, 2, 1, "", "compileExprAndFormat"]], "pygom.model.shapeAdjust": [[31, 2, 1, "", "kronParam"], [31, 2, 1, "", "kronState"], [31, 2, 1, "", "matToVecFF"], [31, 2, 1, "", "matToVecSens"], [31, 2, 1, "", "vecToMatFF"], [31, 2, 1, "", "vecToMatSens"]], "pygom.utilR": [[32, 3, 1, "", "dbeta"], [32, 3, 1, "", "dbinom"], [32, 3, 1, "", "dchisq"], [32, 3, 1, "", "dexp"], [32, 3, 1, "", "dgamma"], [32, 3, 1, "", "dmvnorm"], [32, 3, 1, "", "dnbinom"], [32, 3, 1, "", "dnorm"], [32, 3, 1, "", "dpois"], [32, 3, 1, "", "dunif"], [32, 3, 1, "", "gamma_mu_shape"], [32, 3, 1, "", "nb2pmf"], [32, 3, 1, "", "pbinom"], [32, 3, 1, "", "pchisq"], [32, 3, 1, "", "pexp"], [32, 3, 1, "", "pgamma"], [32, 3, 1, "", "pnbinom"], [32, 3, 1, "", "pnorm"], [32, 3, 1, "", "ppois"], [32, 3, 1, "", "punif"], [32, 3, 1, "", "qbeta"], [32, 3, 1, "", "qbinom"], [32, 3, 1, "", "qchisq"], [32, 3, 1, "", "qexp"], [32, 3, 1, "", "qgamma"], [32, 3, 1, "", "qnbinom"], [32, 3, 1, "", "qnorm"], [32, 3, 1, "", "qpois"], [32, 3, 1, "", "qunif"], [32, 3, 1, "", "rbeta"], [32, 3, 1, "", "rbinom"], [32, 3, 1, "", "rchisq"], [32, 3, 1, "", "rexp"], [32, 3, 1, "", "rgamma"], [32, 3, 1, "", "rmvnorm"], [32, 3, 1, "", "rnorm"], [32, 3, 1, "", "rpois"], [32, 3, 1, "", "runif"], [32, 3, 1, "", "test_seed"]]}, "objtypes": {"0": "py:module", "1": "py:class", "2": "py:method", "3": "py:function", "4": "py:attribute", "5": "py:property"}, "objnames": {"0": ["py", "module", "Python module"], "1": ["py", "class", "Python class"], "2": ["py", "method", "Python method"], "3": ["py", "function", "Python function"], "4": ["py", "attribute", "Python attribute"], "5": ["py", "property", "Python property"]}, "titleterms": {"bibliographi": 0, "build": 1, "document": [1, 5], "local": 1, "pre": 2, "defin": [2, 23], "exampl": [2, 23, 26], "common": 2, "epi": 2, "model": [2, 19, 23, 25, 26, 28, 31], "frequent": 3, "ask": 3, "question": 3, "why": 3, "doe": [3, 5], "code": 3, "run": 3, "slowli": 3, "compil": 3, "numer": 3, "comput": [3, 25], "form": 3, "sympi": 3, "against": 3, "theano": 3, "us": [3, 5, 18], "mpmath": 3, "librari": 3, "throughout": 3, "i": [3, 5, 26], "gradient": [3, 26], "squareloss": 3, "slow": 3, "some": 3, "my": 3, "fortran": 3, "object": 3, "can": 3, "you": 3, "convert": 3, "non": 3, "autonum": 3, "system": [3, 23], "an": [3, 23, 25], "autonom": 3, "me": 3, "automat": 3, "get": 3, "sensit": 3, "from": [3, 4, 28], "did": 3, "speed": 3, "up": 3, "when": 3, "restrict": 3, "set": 3, "paramet": [3, 6, 21, 22, 24, 25, 26, 27, 29], "do": [3, 5], "have": 3, "option": 3, "obtain": 3, "via": 3, "complex": 3, "differenc": 3, "instal": 4, "sourc": 4, "pypi": 4, "test": 4, "packag": [4, 5], "welcom": 5, "pygom": [5, 23], "what": 5, "thi": 5, "new": 5, "releas": 5, "contribut": 5, "fit": [6, 25], "produc": 7, "forecast": 7, "fitzhugh": 8, "legrand": 9, "ebola": 9, "seihfr": 9, "lotka": 10, "volterra": 10, "seir": [11, 12, 13, 25, 26], "birth": [12, 15, 28], "death": [12, 15, 28], "period": [12, 17], "wane": 12, "introduct": 12, "multipl": 13, "sir": [14, 15, 23, 25, 28], "si": [16, 17], "read": 18, "epijson": 18, "data": 18, "extract": 19, "inform": 19, "verif": 19, "algebra": 19, "insight": [19, 20], "epidemiologi": 19, "specif": 19, "od": [20, 22, 23], "parameteris": 21, "fix": [21, 22], "random": [21, 22], "find": 22, "solut": 22, "determinist": 22, "evolut": 22, "stochast": 22, "summari": 22, "equat": [23, 28], "v": 23, "transit": [23, 28], "modifi": 23, "solv": 24, "boundari": 24, "valu": 24, "problem": 24, "unknown": 24, "initi": [24, 25], "condit": [24, 25], "estim": [25, 26], "approxim": 25, "bayesian": 25, "infect": 25, "remov": 25, "known": [25, 26], "onli": 25, "maximum": 26, "likelihood": 26, "r": 26, "calcul": 26, "optimis": 26, "result": 26, "confid": 26, "interv": 26, "time": 27, "depend": 27, "deduc": 28, "sliar": 28, "epidem": 28, "approximate_bayesian_comput": 29, "same": 29, "get_posterior_sampl": 29, "see": 29, "also": 29, "class": 29, "baseloss": 29, "loss": 30, "utilr": 32}, "envversion": {"sphinx.domains.c": 2, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 8, "sphinx.domains.index": 1, "sphinx.domains.javascript": 2, "sphinx.domains.math": 2, "sphinx.domains.python": 3, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.intersphinx": 1, "sphinx.ext.viewcode": 1, "sphinxcontrib.bibtex": 9, "sphinx": 57}, "alltitles": {"Bibliography": [[0, "bibliography"]], "Building the documentation locally": [[1, "building-the-documentation-locally"]], "Pre-defined examples - common epi models": [[2, "pre-defined-examples-common-epi-models"]], "Frequently asked questions": [[3, "frequently-asked-questions"]], "Why does code run slowly?": [[3, "why-does-code-run-slowly"]], "Why not compile the numeric computation form sympy against Theano?": [[3, "why-not-compile-the-numeric-computation-form-sympy-against-theano"]], "Why not use mpmath library throughout?": [[3, "why-not-use-mpmath-library-throughout"]], "Why is computing the gradient using SquareLoss slow?": [[3, "why-is-computing-the-gradient-using-squareloss-slow"]], "Why is some of my code not a fortran object?": [[3, "why-is-some-of-my-code-not-a-fortran-object"]], "Can you not convert a non-autonumous system to an autonomous system for me automatically?": [[3, "can-you-not-convert-a-non-autonumous-system-to-an-autonomous-system-for-me-automatically"]], "Getting the sensitivities from SquareLoss did not get a speed up when I used a restricted set of parameters": [[3, "getting-the-sensitivities-from-squareloss-did-not-get-a-speed-up-when-i-used-a-restricted-set-of-parameters"]], "Why do not have the option to obtain gradient via complex differencing?": [[3, "why-do-not-have-the-option-to-obtain-gradient-via-complex-differencing"]], "Installation": [[4, "installation"]], "From source": [[4, "from-source"]], "From PyPI": [[4, "from-pypi"]], "Testing the package": [[4, "testing-the-package"]], "Welcome to the documentation for PyGOM": [[5, "welcome-to-the-documentation-for-pygom"]], "What does this package do?": [[5, "what-does-this-package-do"]], "What is new in this release?": [[5, "what-is-new-in-this-release"]], "Using this documentation": [[5, "using-this-documentation"]], "Contributing to PyGOM": [[5, "contributing-to-pygom"]], "Parameter fitting": [[6, "parameter-fitting"]], "Producing forecasts": [[7, "producing-forecasts"]], "FitzHugh": [[8, "fitzhugh"]], "Legrand Ebola SEIHFR": [[9, "legrand-ebola-seihfr"]], "Lotka Volterra": [[10, "lotka-volterra"]], "SEIR": [[11, "seir"]], "SEIR, birth, death, periodic, waning and introductions": [[12, "seir-birth-death-periodic-waning-and-introductions"]], "SEIR, multiple": [[13, "seir-multiple"]], "SIR": [[14, "sir"]], "SIR, birth and death": [[15, "sir-birth-and-death"]], "SIS": [[16, "sis"]], "SIS, periodic": [[17, "sis-periodic"]], "Reading and using EpiJSON data": [[18, "reading-and-using-epijson-data"]], "Extracting model information": [[19, "extracting-model-information"]], "Verification": [[19, "verification"]], "Algebraic insights": [[19, "algebraic-insights"]], "Epidemiology specific insights": [[19, "epidemiology-specific-insights"]], "ODE Insights": [[20, "ode-insights"]], "Parameterisation": [[21, "parameterisation"]], "Fixed parameters": [[21, "fixed-parameters"], [22, "fixed-parameters"], [22, "id3"]], "Random parameters": [[21, "random-parameters"], [22, "random-parameters"], [22, "id4"]], "Finding ODE solutions": [[22, "finding-ode-solutions"]], "Deterministic evolution": [[22, "deterministic-evolution"]], "Stochastic evolution": [[22, "stochastic-evolution"]], "Summary": [[22, "summary"]], "Defining an ODE system": [[23, "defining-an-ode-system"]], "Equations vs Transitions": [[23, "equations-vs-transitions"]], "Example: SIR model": [[23, "example-sir-model"]], "Defining the model with PyGOM": [[23, "defining-the-model-with-pygom"]], "Modifying models": [[23, "modifying-models"]], "Solving Boundary Value Problems": [[24, "solving-boundary-value-problems"]], "Problem": [[24, "problem"]], "Unknown initial conditions": [[24, "unknown-initial-conditions"]], "Unknown parameters": [[24, "unknown-parameters"]], "Parameter Estimation: Approximate Bayesian Computation": [[25, "parameter-estimation-approximate-bayesian-computation"]], "Fitting an SEIR model (with Infected and Removed known)": [[25, "fitting-an-seir-model-with-infected-and-removed-known"]], "Fitting an SEIR model (with only Infected known)": [[25, "fitting-an-seir-model-with-only-infected-known"]], "Fitting an SIR model (with only Infected known)": [[25, "fitting-an-sir-model-with-only-infected-known"]], "Initial conditions": [[25, "initial-conditions"]], "Parameter Estimation: Maximum likelihood": [[26, "parameter-estimation-maximum-likelihood"]], "Example: SEIR model (with I and R known)": [[26, "example-seir-model-with-i-and-r-known"]], "Gradient calculations": [[26, "gradient-calculations"]], "Optimised result": [[26, "optimised-result"]], "Confidence intervals of estimated parameters": [[26, "confidence-intervals-of-estimated-parameters"]], "Time dependent parameters": [[27, "time-dependent-parameters"]], "Deducing transitions from equations": [[28, "deducing-transitions-from-equations"]], "SIR with births and deaths": [[28, "sir-with-births-and-deaths"]], "SLIAR epidemic model": [[28, "sliar-epidemic-model"]], "approximate_bayesian_computation": [[29, "module-pygom.approximate_bayesian_computation"]], "Parameters (same as get_posterior_sample)": [[29, "parameters-same-as-get-posterior-sample"]], "Parameters (see also class BaseLoss)": [[29, "parameters-see-also-class-baseloss"]], "loss": [[30, "module-pygom.loss"]], "model": [[31, "module-pygom.model"]], "utilR": [[32, "module-pygom.utilR"]]}, "indexentries": {"abc (class in pygom.approximate_bayesian_computation)": [[29, "pygom.approximate_bayesian_computation.ABC"]], "parameter (class in pygom.approximate_bayesian_computation)": [[29, "pygom.approximate_bayesian_computation.Parameter"]], "continue_posterior_sample() (pygom.approximate_bayesian_computation.abc method)": [[29, "pygom.approximate_bayesian_computation.ABC.continue_posterior_sample"]], "create_loss() (in module pygom.approximate_bayesian_computation)": [[29, "pygom.approximate_bayesian_computation.create_loss"]], "get_function() (in module pygom.approximate_bayesian_computation)": [[29, "pygom.approximate_bayesian_computation.get_function"]], "get_posterior_sample() (pygom.approximate_bayesian_computation.abc method)": [[29, "pygom.approximate_bayesian_computation.ABC.get_posterior_sample"]], "get_posterior_sample_original() (pygom.approximate_bayesian_computation.abc method)": [[29, "pygom.approximate_bayesian_computation.ABC.get_posterior_sample_original"]], "get_tolerance() (pygom.approximate_bayesian_computation.abc method)": [[29, "pygom.approximate_bayesian_computation.ABC.get_tolerance"]], "module": [[29, "module-pygom.approximate_bayesian_computation"], [30, "module-pygom.loss"], [31, "module-pygom.model"], [32, "module-pygom.utilR"]], "plot_pointwise_predictions() (pygom.approximate_bayesian_computation.abc method)": [[29, "pygom.approximate_bayesian_computation.ABC.plot_pointwise_predictions"]], "plot_posterior_histograms() (pygom.approximate_bayesian_computation.abc method)": [[29, "pygom.approximate_bayesian_computation.ABC.plot_posterior_histograms"]], "plot_scatter() (pygom.approximate_bayesian_computation.abc method)": [[29, "pygom.approximate_bayesian_computation.ABC.plot_scatter"]], "pygom.approximate_bayesian_computation": [[29, "module-pygom.approximate_bayesian_computation"]], "sigma_nearest_neighbours() (pygom.approximate_bayesian_computation.abc method)": [[29, "pygom.approximate_bayesian_computation.ABC.sigma_nearest_neighbours"]], "gamma (class in pygom.loss)": [[30, "pygom.loss.Gamma"]], "gammaloss (class in pygom.loss)": [[30, "pygom.loss.GammaLoss"]], "negbinom (class in pygom.loss)": [[30, "pygom.loss.NegBinom"]], "negbinomloss (class in pygom.loss)": [[30, "pygom.loss.NegBinomLoss"]], "normal (class in pygom.loss)": [[30, "pygom.loss.Normal"]], "normalloss (class in pygom.loss)": [[30, "pygom.loss.NormalLoss"]], "poisson (class in pygom.loss)": [[30, "pygom.loss.Poisson"]], "poissonloss (class in pygom.loss)": [[30, "pygom.loss.PoissonLoss"]], "square (class in pygom.loss)": [[30, "pygom.loss.Square"]], "squareloss (class in pygom.loss)": [[30, "pygom.loss.SquareLoss"]], "univariatespline (class in pygom.loss)": [[30, "pygom.loss.UnivariateSpline"]], "antiderivative() (pygom.loss.univariatespline method)": [[30, "pygom.loss.UnivariateSpline.antiderivative"]], "args (pygom.loss.partial attribute)": [[30, "pygom.loss.partial.args"]], "asymptotic() (in module pygom.loss)": [[30, "pygom.loss.asymptotic"]], "bootstrap() (in module pygom.loss)": [[30, "pygom.loss.bootstrap"]], "cost_grad_interpolant() (in module pygom.loss)": [[30, "pygom.loss.cost_grad_interpolant"]], "cost_interpolant() (in module pygom.loss)": [[30, "pygom.loss.cost_interpolant"]], "cost_sample() (in module pygom.loss)": [[30, "pygom.loss.cost_sample"]], "derivative() (pygom.loss.univariatespline method)": [[30, "pygom.loss.UnivariateSpline.derivative"]], "derivatives() (pygom.loss.univariatespline method)": [[30, "pygom.loss.UnivariateSpline.derivatives"]], "diff2loss() (pygom.loss.gamma method)": [[30, "pygom.loss.Gamma.diff2Loss"]], "diff2loss() (pygom.loss.negbinom method)": [[30, "pygom.loss.NegBinom.diff2Loss"]], "diff2loss() (pygom.loss.normal method)": [[30, "pygom.loss.Normal.diff2Loss"]], "diff2loss() (pygom.loss.poisson method)": [[30, "pygom.loss.Poisson.diff2Loss"]], "diff2loss() (pygom.loss.square method)": [[30, "pygom.loss.Square.diff2Loss"]], "diff_loss() (pygom.loss.gamma method)": [[30, "pygom.loss.Gamma.diff_loss"]], "diff_loss() (pygom.loss.negbinom method)": [[30, "pygom.loss.NegBinom.diff_loss"]], "diff_loss() (pygom.loss.normal method)": [[30, "pygom.loss.Normal.diff_loss"]], "diff_loss() (pygom.loss.poisson method)": [[30, "pygom.loss.Poisson.diff_loss"]], "diff_loss() (pygom.loss.square method)": [[30, "pygom.loss.Square.diff_loss"]], "func (pygom.loss.partial attribute)": [[30, "pygom.loss.partial.func"]], "geometric() (in module pygom.loss)": [[30, "pygom.loss.geometric"]], "get_coeffs() (pygom.loss.univariatespline method)": [[30, "pygom.loss.UnivariateSpline.get_coeffs"]], "get_init() (in module pygom.loss)": [[30, "pygom.loss.get_init"]], "get_knots() (pygom.loss.univariatespline method)": [[30, "pygom.loss.UnivariateSpline.get_knots"]], "get_residual() (pygom.loss.univariatespline method)": [[30, "pygom.loss.UnivariateSpline.get_residual"]], "grad_sample() (in module pygom.loss)": [[30, "pygom.loss.grad_sample"]], "integral() (pygom.loss.univariatespline method)": [[30, "pygom.loss.UnivariateSpline.integral"]], "interpolate() (in module pygom.loss)": [[30, "pygom.loss.interpolate"]], "jac_sample() (in module pygom.loss)": [[30, "pygom.loss.jac_sample"]], "keywords (pygom.loss.partial attribute)": [[30, "pygom.loss.partial.keywords"]], "leastsq() (in module pygom.loss)": [[30, "pygom.loss.leastsq"]], "loss() (pygom.loss.gamma method)": [[30, "pygom.loss.Gamma.loss"]], "loss() (pygom.loss.negbinom method)": [[30, "pygom.loss.NegBinom.loss"]], "loss() (pygom.loss.normal method)": [[30, "pygom.loss.Normal.loss"]], "loss() (pygom.loss.poisson method)": [[30, "pygom.loss.Poisson.loss"]], "loss() (pygom.loss.square method)": [[30, "pygom.loss.Square.loss"]], "minimize_scalar() (in module pygom.loss)": [[30, "pygom.loss.minimize_scalar"]], "partial (class in pygom.loss)": [[30, "pygom.loss.partial"]], "profile() (in module pygom.loss)": [[30, "pygom.loss.profile"]], "pygom.loss": [[30, "module-pygom.loss"]], "residual_interpolant() (in module pygom.loss)": [[30, "pygom.loss.residual_interpolant"]], "residual_sample() (in module pygom.loss)": [[30, "pygom.loss.residual_sample"]], "roots() (pygom.loss.univariatespline method)": [[30, "pygom.loss.UnivariateSpline.roots"]], "set_smoothing_factor() (pygom.loss.univariatespline method)": [[30, "pygom.loss.UnivariateSpline.set_smoothing_factor"]], "simps() (in module pygom.loss)": [[30, "pygom.loss.simps"]], "compilecanary (class in pygom.model)": [[31, "pygom.model.CompileCanary"]], "dfe() (in module pygom.model)": [[31, "pygom.model.DFE"]], "deterministicode (class in pygom.model)": [[31, "pygom.model.DeterministicOde"]], "fitzhugh() (in module pygom.model)": [[31, "pygom.model.FitzHugh"]], "influenza_sliarn() (in module pygom.model)": [[31, "pygom.model.Influenza_SLIARN"]], "legrand_ebola_seihfr() (in module pygom.model)": [[31, "pygom.model.Legrand_Ebola_SEIHFR"]], "lorenz() (in module pygom.model)": [[31, "pygom.model.Lorenz"]], "lotka_volterra() (in module pygom.model)": [[31, "pygom.model.Lotka_Volterra"]], "lotka_volterra_4state() (in module pygom.model)": [[31, "pygom.model.Lotka_Volterra_4State"]], "odevariable (class in pygom.model)": [[31, "pygom.model.ODEVariable"]], "ordereddict (class in pygom.model)": [[31, "pygom.model.OrderedDict"]], "r0() (in module pygom.model)": [[31, "pygom.model.R0"]], "r0_from_matrix() (in module pygom.model)": [[31, "pygom.model.R0_from_matrix"]], "robertson() (in module pygom.model)": [[31, "pygom.model.Robertson"]], "seir() (in module pygom.model)": [[31, "pygom.model.SEIR"]], "seir_birth_death() (in module pygom.model)": [[31, "pygom.model.SEIR_Birth_Death"]], "seir_birth_death_periodic() (in module pygom.model)": [[31, "pygom.model.SEIR_Birth_Death_Periodic"]], "seir_multiple() (in module pygom.model)": [[31, "pygom.model.SEIR_Multiple"]], "seir_n() (in module pygom.model)": [[31, "pygom.model.SEIR_N"]], "sir() (in module pygom.model)": [[31, "pygom.model.SIR"]], "sir_birth_death() (in module pygom.model)": [[31, "pygom.model.SIR_Birth_Death"]], "sir_norm() (in module pygom.model)": [[31, "pygom.model.SIR_norm"]], "sis() (in module pygom.model)": [[31, "pygom.model.SIS"]], "sis_periodic() (in module pygom.model)": [[31, "pygom.model.SIS_Periodic"]], "simulateode (class in pygom.model)": [[31, "pygom.model.SimulateOde"]], "transition (class in pygom.model)": [[31, "pygom.model.Transition"]], "transitiontype (class in pygom.model)": [[31, "pygom.model.TransitionType"]], "adjoint() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.adjoint"]], "adjoint_t() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.adjoint_T"]], "adjoint_interpolate() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.adjoint_interpolate"]], "adjoint_interpolate_t() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.adjoint_interpolate_T"]], "adjoint_interpolate_jacobian() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.adjoint_interpolate_jacobian"]], "adjoint_interpolate_jacobian_t() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.adjoint_interpolate_jacobian_T"]], "adjoint_jacobian() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.adjoint_jacobian"]], "adjoint_jacobian_t() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.adjoint_jacobian_T"]], "birth_death_rate() (pygom.model.simulateode method)": [[31, "pygom.model.SimulateOde.birth_death_rate"]], "check_array_type() (in module pygom.model)": [[31, "pygom.model.check_array_type"]], "check_dimension() (in module pygom.model)": [[31, "pygom.model.check_dimension"]], "cle() (pygom.model.simulateode method)": [[31, "pygom.model.SimulateOde.cle"]], "clear() (pygom.model.ordereddict method)": [[31, "pygom.model.OrderedDict.clear"]], "compilecode (class in pygom.model)": [[31, "pygom.model.compileCode"]], "compileexpr() (pygom.model.compilecode method)": [[31, "pygom.model.compileCode.compileExpr"]], "compileexprandformat() (pygom.model.compilecode method)": [[31, "pygom.model.compileCode.compileExprAndFormat"]], "copy() (pygom.model.ordereddict method)": [[31, "pygom.model.OrderedDict.copy"]], "destination (pygom.model.transition property)": [[31, "pygom.model.Transition.destination"]], "diff_jacobian() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.diff_jacobian"]], "diff_jacobian_t() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.diff_jacobian_T"]], "disease_progression_matrices() (in module pygom.model)": [[31, "pygom.model.disease_progression_matrices"]], "equation (pygom.model.transition property)": [[31, "pygom.model.Transition.equation"]], "eval_birth_death_rate() (pygom.model.simulateode method)": [[31, "pygom.model.SimulateOde.eval_birth_death_rate"]], "eval_diff_jacobian() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.eval_diff_jacobian"]], "eval_forwardforward() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.eval_forwardforward"]], "eval_grad() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.eval_grad"]], "eval_grad_jacobian() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.eval_grad_jacobian"]], "eval_hessian() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.eval_hessian"]], "eval_jacobian() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.eval_jacobian"]], "eval_ode() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.eval_ode"]], "eval_sens_jacobian_state() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.eval_sens_jacobian_state"]], "eval_sensitivity() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.eval_sensitivity"]], "eval_sensitivityiv() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.eval_sensitivityIV"]], "eval_transition_matrix() (pygom.model.simulateode method)": [[31, "pygom.model.SimulateOde.eval_transition_matrix"]], "eval_transition_mean() (pygom.model.simulateode method)": [[31, "pygom.model.SimulateOde.eval_transition_mean"]], "eval_transition_var() (pygom.model.simulateode method)": [[31, "pygom.model.SimulateOde.eval_transition_var"]], "eval_transition_vector() (pygom.model.simulateode method)": [[31, "pygom.model.SimulateOde.eval_transition_vector"]], "exact() (pygom.model.simulateode method)": [[31, "pygom.model.SimulateOde.exact"]], "forwardforward() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.forwardforward"]], "forwardforward_t() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.forwardforward_T"]], "fromkeys() (pygom.model.ordereddict method)": [[31, "pygom.model.OrderedDict.fromkeys"]], "get_bd_from_ode() (pygom.model.simulateode method)": [[31, "pygom.model.SimulateOde.get_bd_from_ode"]], "get_birth_death_rate() (pygom.model.simulateode method)": [[31, "pygom.model.SimulateOde.get_birth_death_rate"]], "get_diff_jacobian_eqn() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.get_diff_jacobian_eqn"]], "get_grad_eqn() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.get_grad_eqn"]], "get_grad_jacobian_eqn() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.get_grad_jacobian_eqn"]], "get_hessian_eqn() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.get_hessian_eqn"]], "get_jacobian_eqn() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.get_jacobian_eqn"]], "get_ode_eqn() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.get_ode_eqn"]], "get_transition_graph() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.get_transition_graph"]], "get_transition_matrix() (pygom.model.simulateode method)": [[31, "pygom.model.SimulateOde.get_transition_matrix"]], "get_transition_vector() (pygom.model.simulateode method)": [[31, "pygom.model.SimulateOde.get_transition_vector"]], "get_transitions_from_ode() (pygom.model.simulateode method)": [[31, "pygom.model.SimulateOde.get_transitions_from_ode"]], "get_unrolled_obj() (pygom.model.simulateode method)": [[31, "pygom.model.SimulateOde.get_unrolled_obj"]], "grad() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.grad"]], "grad_t() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.grad_T"]], "grad_jacobian() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.grad_jacobian"]], "grad_jacobiant() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.grad_jacobianT"]], "hessian() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.hessian"]], "hybrid() (pygom.model.simulateode method)": [[31, "pygom.model.SimulateOde.hybrid"]], "initial_state (pygom.model.deterministicode property)": [[31, "pygom.model.DeterministicOde.initial_state"]], "initial_time (pygom.model.deterministicode property)": [[31, "pygom.model.DeterministicOde.initial_time"]], "initial_values (pygom.model.deterministicode property)": [[31, "pygom.model.DeterministicOde.initial_values"]], "integrate() (in module pygom.model)": [[31, "pygom.model.integrate"]], "integrate() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.integrate"]], "integrate2() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.integrate2"]], "integratefuncjac() (in module pygom.model)": [[31, "pygom.model.integrateFuncJac"]], "is_between_state() (pygom.model.transition method)": [[31, "pygom.model.Transition.is_between_state"]], "is_list_like() (in module pygom.model)": [[31, "pygom.model.is_list_like"]], "is_stiff() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.is_stiff"]], "items() (pygom.model.ordereddict method)": [[31, "pygom.model.OrderedDict.items"]], "jacobian() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.jacobian"]], "jacobian_t() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.jacobian_T"]], "jacobian_eigenvalue() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.jacobian_eigenvalue"]], "keys() (pygom.model.ordereddict method)": [[31, "pygom.model.OrderedDict.keys"]], "kronparam() (pygom.model.shapeadjust method)": [[31, "pygom.model.shapeAdjust.kronParam"]], "kronstate() (pygom.model.shapeadjust method)": [[31, "pygom.model.shapeAdjust.kronState"]], "linear_ode() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.linear_ode"]], "mattovecff() (pygom.model.shapeadjust method)": [[31, "pygom.model.shapeAdjust.matToVecFF"]], "mattovecsens() (pygom.model.shapeadjust method)": [[31, "pygom.model.shapeAdjust.matToVecSens"]], "move_to_end() (pygom.model.ordereddict method)": [[31, "pygom.model.OrderedDict.move_to_end"]], "ode() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.ode"]], "ode_t() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.ode_T"]], "ode_and_forwardforward() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.ode_and_forwardforward"]], "ode_and_forwardforward_t() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.ode_and_forwardforward_T"]], "ode_and_forwardforward_jacobian() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.ode_and_forwardforward_jacobian"]], "ode_and_forwardforward_jacobian_t() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.ode_and_forwardforward_jacobian_T"]], "ode_and_sensitivity() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.ode_and_sensitivity"]], "ode_and_sensitivityiv() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.ode_and_sensitivityIV"]], "ode_and_sensitivityiv_t() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.ode_and_sensitivityIV_T"]], "ode_and_sensitivityiv_jacobian() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.ode_and_sensitivityIV_jacobian"]], "ode_and_sensitivityiv_jacobian_t() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.ode_and_sensitivityIV_jacobian_T"]], "ode_and_sensitivity_t() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.ode_and_sensitivity_T"]], "ode_and_sensitivity_jacobian() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.ode_and_sensitivity_jacobian"]], "ode_and_sensitivity_jacobian_t() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.ode_and_sensitivity_jacobian_T"]], "origin (pygom.model.transition property)": [[31, "pygom.model.Transition.origin"]], "plot() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.plot"]], "plot() (pygom.model.simulateode method)": [[31, "pygom.model.SimulateOde.plot"]], "plot_det() (in module pygom.model)": [[31, "pygom.model.plot_det"]], "plot_stoc() (in module pygom.model)": [[31, "pygom.model.plot_stoc"]], "pop() (pygom.model.ordereddict method)": [[31, "pygom.model.OrderedDict.pop"]], "popitem() (pygom.model.ordereddict method)": [[31, "pygom.model.OrderedDict.popitem"]], "print_ode() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.print_ode"]], "pygom.model": [[31, "module-pygom.model"]], "reset() (pygom.model.compilecanary method)": [[31, "pygom.model.CompileCanary.reset"]], "sens_jacobian_state() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.sens_jacobian_state"]], "sens_jacobian_state_t() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.sens_jacobian_state_T"]], "sensitivity() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.sensitivity"]], "sensitivityiv() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.sensitivityIV"]], "sensitivityiv_t() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.sensitivityIV_T"]], "sensitivity_t() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.sensitivity_T"]], "setdefault() (pygom.model.ordereddict method)": [[31, "pygom.model.OrderedDict.setdefault"]], "shapeadjust (class in pygom.model)": [[31, "pygom.model.shapeAdjust"]], "simulate_jump() (pygom.model.simulateode method)": [[31, "pygom.model.SimulateOde.simulate_jump"]], "simulate_param() (pygom.model.simulateode method)": [[31, "pygom.model.SimulateOde.simulate_param"]], "solve_determ() (pygom.model.simulateode method)": [[31, "pygom.model.SimulateOde.solve_determ"]], "solve_stochast() (pygom.model.simulateode method)": [[31, "pygom.model.SimulateOde.solve_stochast"]], "str_or_list() (in module pygom.model)": [[31, "pygom.model.str_or_list"]], "total_transition() (pygom.model.simulateode method)": [[31, "pygom.model.SimulateOde.total_transition"]], "transition_matrix() (pygom.model.simulateode method)": [[31, "pygom.model.SimulateOde.transition_matrix"]], "transition_mean() (pygom.model.simulateode method)": [[31, "pygom.model.SimulateOde.transition_mean"]], "transition_type (pygom.model.transition property)": [[31, "pygom.model.Transition.transition_type"]], "transition_var() (pygom.model.simulateode method)": [[31, "pygom.model.SimulateOde.transition_var"]], "transition_vector() (pygom.model.simulateode method)": [[31, "pygom.model.SimulateOde.transition_vector"]], "trip() (pygom.model.compilecanary method)": [[31, "pygom.model.CompileCanary.trip"]], "update() (pygom.model.ordereddict method)": [[31, "pygom.model.OrderedDict.update"]], "values() (pygom.model.ordereddict method)": [[31, "pygom.model.OrderedDict.values"]], "vanderpol() (in module pygom.model)": [[31, "pygom.model.vanDerPol"]], "vectomatff() (pygom.model.shapeadjust method)": [[31, "pygom.model.shapeAdjust.vecToMatFF"]], "vectomatsens() (pygom.model.shapeadjust method)": [[31, "pygom.model.shapeAdjust.vecToMatSens"]], "dbeta() (in module pygom.utilr)": [[32, "pygom.utilR.dbeta"]], "dbinom() (in module pygom.utilr)": [[32, "pygom.utilR.dbinom"]], "dchisq() (in module pygom.utilr)": [[32, "pygom.utilR.dchisq"]], "dexp() (in module pygom.utilr)": [[32, "pygom.utilR.dexp"]], "dgamma() (in module pygom.utilr)": [[32, "pygom.utilR.dgamma"]], "dmvnorm() (in module pygom.utilr)": [[32, "pygom.utilR.dmvnorm"]], "dnbinom() (in module pygom.utilr)": [[32, "pygom.utilR.dnbinom"]], "dnorm() (in module pygom.utilr)": [[32, "pygom.utilR.dnorm"]], "dpois() (in module pygom.utilr)": [[32, "pygom.utilR.dpois"]], "dunif() (in module pygom.utilr)": [[32, "pygom.utilR.dunif"]], "gamma_mu_shape() (in module pygom.utilr)": [[32, "pygom.utilR.gamma_mu_shape"]], "nb2pmf() (in module pygom.utilr)": [[32, "pygom.utilR.nb2pmf"]], "pbinom() (in module pygom.utilr)": [[32, "pygom.utilR.pbinom"]], "pchisq() (in module pygom.utilr)": [[32, "pygom.utilR.pchisq"]], "pexp() (in module pygom.utilr)": [[32, "pygom.utilR.pexp"]], "pgamma() (in module pygom.utilr)": [[32, "pygom.utilR.pgamma"]], "pnbinom() (in module pygom.utilr)": [[32, "pygom.utilR.pnbinom"]], "pnorm() (in module pygom.utilr)": [[32, "pygom.utilR.pnorm"]], "ppois() (in module pygom.utilr)": [[32, "pygom.utilR.ppois"]], "punif() (in module pygom.utilr)": [[32, "pygom.utilR.punif"]], "pygom.utilr": [[32, "module-pygom.utilR"]], "qbeta() (in module pygom.utilr)": [[32, "pygom.utilR.qbeta"]], "qbinom() (in module pygom.utilr)": [[32, "pygom.utilR.qbinom"]], "qchisq() (in module pygom.utilr)": [[32, "pygom.utilR.qchisq"]], "qexp() (in module pygom.utilr)": [[32, "pygom.utilR.qexp"]], "qgamma() (in module pygom.utilr)": [[32, "pygom.utilR.qgamma"]], "qnbinom() (in module pygom.utilr)": [[32, "pygom.utilR.qnbinom"]], "qnorm() (in module pygom.utilr)": [[32, "pygom.utilR.qnorm"]], "qpois() (in module pygom.utilr)": [[32, "pygom.utilR.qpois"]], "qunif() (in module pygom.utilr)": [[32, "pygom.utilR.qunif"]], "rbeta() (in module pygom.utilr)": [[32, "pygom.utilR.rbeta"]], "rbinom() (in module pygom.utilr)": [[32, "pygom.utilR.rbinom"]], "rchisq() (in module pygom.utilr)": [[32, "pygom.utilR.rchisq"]], "rexp() (in module pygom.utilr)": [[32, "pygom.utilR.rexp"]], "rgamma() (in module pygom.utilr)": [[32, "pygom.utilR.rgamma"]], "rmvnorm() (in module pygom.utilr)": [[32, "pygom.utilR.rmvnorm"]], "rnorm() (in module pygom.utilr)": [[32, "pygom.utilR.rnorm"]], "rpois() (in module pygom.utilr)": [[32, "pygom.utilR.rpois"]], "runif() (in module pygom.utilr)": [[32, "pygom.utilR.runif"]], "test_seed() (in module pygom.utilr)": [[32, "pygom.utilR.test_seed"]]}})
\ No newline at end of file
+Search.setIndex({"docnames": ["md/bib", "md/building_doc", "md/common_models", "md/faq", "md/installation", "md/intro", "md/parameter_fitting", "md/solving", "notebooks/common_models/FitzHugh", "notebooks/common_models/Legrand_Ebola_SEIHFR", "notebooks/common_models/Lotka_Volterra", "notebooks/common_models/SEIR", "notebooks/common_models/SEIR_Birth_Death_Periodic_Waning_Intro", "notebooks/common_models/SEIR_Multiple", "notebooks/common_models/SIR", "notebooks/common_models/SIR_Birth_Death", "notebooks/common_models/SIS", "notebooks/common_models/SIS_Periodic", "notebooks/epijson", "notebooks/extract_info", "notebooks/insights", "notebooks/model_params", "notebooks/model_solver", "notebooks/model_spec", "notebooks/paramfit/bvpSimple", "notebooks/paramfit/params_via_abc", "notebooks/paramfit/params_via_optimization", "notebooks/time_dependent_params", "notebooks/unroll/unrollSimple", "rst/autodoc-abc", "rst/autodoc-loss", "rst/autodoc-model", "rst/autodoc-utilR"], "filenames": ["md/bib.md", "md/building_doc.md", "md/common_models.md", "md/faq.md", "md/installation.md", "md/intro.md", "md/parameter_fitting.md", "md/solving.md", "notebooks/common_models/FitzHugh.ipynb", "notebooks/common_models/Legrand_Ebola_SEIHFR.ipynb", "notebooks/common_models/Lotka_Volterra.ipynb", "notebooks/common_models/SEIR.ipynb", "notebooks/common_models/SEIR_Birth_Death_Periodic_Waning_Intro.ipynb", "notebooks/common_models/SEIR_Multiple.ipynb", "notebooks/common_models/SIR.ipynb", "notebooks/common_models/SIR_Birth_Death.ipynb", "notebooks/common_models/SIS.ipynb", "notebooks/common_models/SIS_Periodic.ipynb", "notebooks/epijson.ipynb", "notebooks/extract_info.ipynb", "notebooks/insights.ipynb", "notebooks/model_params.ipynb", "notebooks/model_solver.ipynb", "notebooks/model_spec.ipynb", "notebooks/paramfit/bvpSimple.ipynb", "notebooks/paramfit/params_via_abc.ipynb", "notebooks/paramfit/params_via_optimization.ipynb", "notebooks/time_dependent_params.ipynb", "notebooks/unroll/unrollSimple.ipynb", "rst/autodoc-abc.rst", "rst/autodoc-loss.rst", "rst/autodoc-model.rst", "rst/autodoc-utilR.rst"], "titles": ["Bibliography", "Building the documentation locally", "Pre-defined examples - common epi models", "Frequently asked questions", "Installation", "Welcome to the documentation for PyGOM", "Parameter fitting", "Producing forecasts", "FitzHugh", "Legrand Ebola SEIHFR", "Lotka Volterra", "SEIR", "SEIR, birth, death, periodic, waning and introductions", "SEIR, multiple", "SIR", "SIR, birth and death", "SIS", "SIS, periodic", "Reading and using EpiJSON data", "Extracting model information", "ODE Insights", "Parameterisation", "Finding ODE solutions", "Defining an ODE system", "Solving Boundary Value Problems", "Parameter Estimation: Approximate Bayesian Computation", "Parameter Estimation: Maximum likelihood", "Time dependent parameters", "Deducing transitions from equations", "approximate_bayesian_computation", "loss", "model", "utilR"], "terms": {"1": [0, 5, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32], "fred": 0, "brauer": [0, 13], "mathemat": [0, 27, 30], "epidemiologi": [0, 2, 5], "volum": 0, "1945": 0, "springer": 0, "berlin": 0, "heidelberg": 0, "2008": [0, 30, 32], "isbn": 0, "978": 0, "3": [0, 8, 9, 10, 11, 14, 15, 18, 19, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31], "540": 0, "78910": 0, "9": [0, 9, 10, 17, 25, 30, 31], "url": 0, "http": [0, 4, 32], "link": 0, "com": [0, 4], "10": [0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 22, 24, 25, 26, 27, 30, 31], "1007": 0, "78911": 0, "6": [0, 8, 9, 10, 13, 18, 22, 25, 30, 31], "doi": 0, "2": [0, 8, 9, 10, 11, 12, 13, 15, 16, 17, 18, 19, 22, 24, 25, 26, 27, 30, 31, 32], "yang": 0, "cao": 0, "daniel": 0, "t": [0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31], "gillespi": 0, "linda": 0, "r": [0, 1, 4, 8, 11, 12, 14, 15, 18, 21, 22, 23, 25, 27, 28, 30, 31, 32], "petzold": 0, "effici": 0, "step": [0, 19, 22, 25, 26, 30, 31], "size": [0, 11, 15, 22, 23, 26, 29, 31, 32], "select": [0, 22, 30, 31], "tau": [0, 22, 27, 31], "leap": [0, 22, 31], "simul": [0, 5, 7, 10, 15, 20, 21, 22, 23, 25, 31], "method": [0, 3, 6, 8, 20, 22, 24, 25, 26, 30, 31], "journal": [0, 30], "chemic": 0, "physic": 0, "2006": 0, "1063": 0, "2159468": 0, "thoma": 0, "j": [0, 13, 15, 22, 23, 30, 31], "finni": 0, "andi": 0, "south": 0, "ana": 0, "bento": 0, "elli": 0, "sherrard": 0, "smith": 0, "thibaut": 0, "jombart": 0, "epijson": 0, "unifi": 0, "data": [0, 6, 22, 25, 26, 30], "format": [0, 18, 31], "epidem": [0, 6, 11, 12, 14, 16, 22, 23, 25, 26, 27], "2016": 0, "1016": 0, "2015": 0, "12": [0, 8, 18, 30, 32], "002": 0, "4": [0, 8, 11, 12, 14, 15, 16, 17, 18, 22, 23, 24, 25, 26, 27, 29, 30, 31], "richard": [0, 30], "fitzhugh": [0, 31], "impuls": 0, "physiolog": 0, "state": [0, 8, 9, 10, 12, 13, 15, 16, 18, 19, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32], "theoret": 0, "model": [0, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 16, 17, 18, 20, 21, 22, 24, 27, 29, 30, 32], "nerv": 0, "membran": [0, 8], "biophys": 0, "1961": 0, "s0006": 0, "3495": 0, "61": 0, "86902": 0, "5": [0, 9, 10, 15, 16, 17, 18, 22, 24, 25, 26, 27, 30, 31], "exact": [0, 26, 30, 31], "stochast": [0, 5, 7, 10, 15, 25, 27, 31], "coupl": [0, 13, 25, 31], "reaction": [0, 8, 22, 31], "The": [0, 1, 3, 4, 5, 8, 9, 10, 13, 14, 15, 18, 21, 22, 23, 25, 26, 28, 30, 31, 32], "chemistri": 0, "81": [0, 9, 31], "25": [0, 9, 10, 21, 22, 25, 26, 27, 30, 31], "2340": 0, "2361": 0, "1977": [0, 30], "mark": 0, "girolami": 0, "ben": 0, "calderhead": 0, "riemann": 0, "manifold": 0, "langevin": 0, "hamiltonian": 0, "mont": [0, 25, 26], "carlo": [0, 25, 26], "royal": 0, "statist": [0, 3], "societi": 0, "seri": [0, 22, 25, 26, 30], "b": [0, 8, 23, 26, 28, 30, 31, 32], "methodologi": 0, "2011": 0, "1111": 0, "1467": 0, "9868": 0, "2010": 0, "00765": 0, "x": [0, 10, 24, 26, 30, 31, 32], "7": [0, 9, 25, 26, 30, 31], "legrand": [0, 31], "f": [0, 4, 9, 10, 11, 12, 14, 15, 16, 17, 19, 22, 23, 24, 25, 26, 27, 28, 30, 31], "grai": 0, "p": [0, 12, 13, 17, 23, 27, 28, 30, 31, 32], "y": [0, 10, 15, 23, 24, 26, 29, 30, 31], "boell": 0, "A": [0, 3, 5, 9, 10, 11, 21, 22, 25, 28, 30, 31], "valleron": 0, "flahault": 0, "understand": [0, 7], "dynam": [0, 9, 22], "ebola": [0, 31], "infect": [0, 12, 14, 15, 16, 17, 22, 23, 26, 27, 28, 31], "135": 0, "610": 0, "621": 0, "2007": 0, "1017": 0, "s0950268806007217": 0, "8": [0, 5, 13, 17, 22, 25, 27, 30, 31], "alun": 0, "l": [0, 26, 28, 30, 31], "lloyd": [0, 13], "robert": 0, "m": [0, 10, 26, 29, 30, 31, 32], "mai": [0, 1, 3, 4, 6, 7, 12, 13, 15, 16, 19, 21, 22, 23, 25, 26, 27, 28, 30, 31], "spatial": [0, 31], "heterogen": [0, 23, 31], "biologi": 0, "1996": 0, "1006": 0, "jtbi": 0, "0042": 0, "alfr": 0, "lotka": [0, 31], "analyt": [0, 20, 24], "note": [0, 17, 24, 26, 30, 31, 32], "certain": [0, 15], "rhythmic": 0, "relat": [0, 6, 24, 31], "organ": [0, 5], "system": [0, 7, 8, 10, 12, 15, 16, 19, 21, 22, 24, 25, 26, 27, 28, 31], "proceed": 0, "nation": 0, "academi": 0, "scienc": [0, 30], "1920": 0, "1073": 0, "pna": 0, "410": 0, "o": [0, 30], "ramsai": 0, "g": [0, 24, 25, 29, 30], "hooker": 0, "d": [0, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 22, 23, 24, 27, 28, 30, 31], "campbel": 0, "paramet": [0, 5, 7, 9, 11, 14, 15, 19, 20, 23, 28, 30, 31, 32], "estim": [0, 5, 6, 24, 30], "differenti": [0, 5, 30, 31], "equat": [0, 3, 5, 8, 12, 14, 15, 17, 19, 21, 22, 24, 26, 27, 30, 31, 32], "gener": [0, 1, 3, 5, 7, 19, 22, 25, 26, 29, 31, 32], "smooth": [0, 30], "approach": [0, 6, 23, 25, 26], "00610": 0, "11": [0, 8, 24, 25, 30], "h": [0, 9, 31], "robertson": [0, 8, 31], "solut": [0, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 21, 24, 26, 27, 28, 29, 30, 31], "set": [0, 2, 9, 11, 12, 14, 15, 16, 17, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31], "rate": [0, 9, 12, 15, 17, 21, 22, 23, 25, 27, 28, 29, 31, 32], "academ": 0, "press": [0, 30, 32], "page": [0, 5, 31], "178": 0, "182": 0, "1966": 0, "www": [0, 32], "scirp": 0, "org": [0, 32], "28": [0, 22, 25, 31], "28vtj3fa45qm1ean45vvffcz55": 0, "29": [0, 18, 26], "refer": [0, 21, 23, 30, 31, 32], "referencespap": 0, "aspx": 0, "referenceid": 0, "2485718": 0, "balth": 0, "van": [0, 8, 31], "der": [0, 8, 30, 31], "pol": [0, 8, 31], "On": 0, "relax": 0, "oscil": [0, 8, 17, 27], "london": 0, "edinburgh": 0, "dublin": 0, "philosoph": 0, "magazin": 0, "992": 0, "1926": 0, "1080": 0, "14786442608564127": 0, "which": [1, 2, 3, 4, 5, 6, 8, 10, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32], "you": [1, 4, 5, 19, 30, 31], "ar": [1, 2, 3, 4, 5, 8, 9, 11, 13, 15, 18, 19, 21, 22, 23, 24, 25, 26, 28, 29, 30, 31], "current": [1, 3, 5, 19, 22, 25, 26, 28, 31, 32], "read": [1, 9], "built": [1, 3, 5, 25, 26, 31], "first": [1, 3, 6, 10, 18, 19, 21, 22, 24, 25, 26, 28, 29, 30, 31], "instal": [1, 3], "addit": [1, 9, 12, 19, 23, 24, 25, 26, 30, 31], "packag": [1, 3, 26, 29, 32], "requir": [1, 3, 4, 5, 9, 18, 19, 20, 21, 22, 24, 25, 26, 27, 30, 31], "specif": [1, 22, 23, 30], "pip": [1, 4], "doc": 1, "txt": [1, 4, 25, 26], "Then": 1, "from": [1, 2, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31], "command": [1, 4], "line": [1, 4, 19, 22], "jupyt": [1, 32], "book": [1, 23], "html": [1, 32], "file": [1, 3, 4, 18, 25, 30, 31, 32], "save": [1, 2, 19, 25], "copi": [1, 31], "your": [1, 4, 5], "repositori": [1, 4], "under": [1, 3, 4, 18, 19, 23, 24, 25, 26, 30], "pygom": [1, 4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 24, 25, 26, 27, 28, 29, 30, 31, 32], "_build": 1, "can": [1, 4, 5, 10, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31], "view": [1, 18, 22, 23, 28, 31], "open": 1, "index": [1, 29], "browser": 1, "choic": [1, 21, 25], "we": [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31], "have": [2, 9, 12, 16, 19, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31], "modul": [2, 19, 22, 23, 31], "common_model": [2, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 25, 26, 31], "most": [2, 26, 27], "draw": [2, 22, 25], "commonli": [2, 8, 9, 10, 20, 23, 24, 25, 27], "us": [2, 4, 6, 7, 8, 9, 11, 13, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32], "includ": [2, 4, 5, 8, 12, 22, 23, 25, 26, 27, 28, 29, 31], "primarili": 2, "time": [2, 5, 7, 8, 10, 11, 12, 14, 15, 16, 17, 18, 19, 22, 23, 24, 25, 26, 28, 29, 30, 31], "user": [2, 3, 4, 5, 7, 22, 23, 24, 29, 30, 31], "also": [2, 4, 6, 8, 9, 10, 11, 15, 17, 19, 23, 24, 26, 27, 30, 31], "serv": [2, 12, 24, 30], "few": [2, 5, 25], "outsid": [2, 12, 30], "task": [2, 6], "test": [2, 8, 31, 32], "numer": [2, 5, 7, 8, 19, 21, 22, 24, 26, 29, 30, 31], "solver": [2, 10, 11, 12, 14, 15, 16, 17, 21, 22, 24, 26, 30], "These": [3, 22, 26], "faq": 3, "": [3, 5, 6, 9, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31], "particularli": [3, 26], "date": [3, 6], "so": [3, 9, 17, 20, 23, 24, 25, 27, 28, 30, 31], "might": [3, 4, 20, 23, 25, 27, 30], "thi": [3, 4, 6, 7, 10, 12, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32], "becaus": [3, 25, 26, 27, 28, 30, 31], "optim": [3, 24, 25, 26, 30], "although": [3, 25, 26, 30], "main": [3, 5, 23], "function": [3, 5, 8, 9, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32], "lambdifi": 3, "cython": [3, 31], "avail": [3, 5, 23, 25, 26, 30, 31], "mani": [3, 19, 23], "more": [3, 4, 5, 6, 9, 10, 11, 12, 20, 22, 23, 25, 26, 28, 29, 30, 31], "done": [3, 21, 24, 28], "setup": [3, 4], "ha": [3, 4, 19, 22, 23, 26, 28, 30, 31], "been": [3, 22, 23, 28, 30, 31], "simplifi": [3, 22], "much": [3, 22, 27, 30], "possibl": [3, 21, 22, 23, 25, 30], "If": [3, 4, 23, 25, 26, 28, 30, 31, 32], "look": 3, "close": [3, 15, 22, 30], "enough": [3, 26], "realiz": [3, 30, 31], "onli": [3, 5, 19, 21, 23, 26, 28, 30, 31], "f2py": [3, 31], "prepar": [3, 18], "all": [3, 5, 9, 18, 23, 25, 26, 27, 28, 30, 31], "check": [3, 4, 19, 26, 30, 31], "e": [3, 9, 11, 12, 19, 24, 29, 30, 31], "exist": [3, 9, 31], "gcc": 3, "wa": [3, 21, 28, 30, 31], "python": [3, 4, 5, 19, 26, 31], "share": [3, 22, 23], "etc": [3, 30], "veri": [3, 22, 31], "awar": [3, 4, 5], "benefit": 3, "especi": 3, "consid": [3, 10, 15, 23, 24, 25, 27, 28, 30], "gpu": 3, "fair": 3, "number": [3, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 22, 25, 26, 27, 28, 29, 30, 31, 32], "oper": [3, 5, 18, 30, 31], "depend": [3, 4, 22, 23, 26, 28, 30, 31], "scipi": [3, 22, 24, 26, 30, 31], "obvious": 3, "solv": [3, 5, 6, 8, 10, 12, 14, 22, 26, 27, 30, 31], "od": [3, 5, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 24, 25, 26, 27, 28, 29, 30, 31], "standard": [3, 9, 11, 14, 21, 22, 23, 25, 28, 30, 31], "linear": [3, 15, 19, 30, 31], "algebra": [3, 5, 31], "unfortun": 3, "routin": [3, 26, 30], "mostli": 3, "base": [3, 30], "numpi": [3, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 24, 25, 26, 27, 30, 31, 32], "It": [3, 24, 26, 30, 31], "alwai": [3, 21, 28, 30, 31], "due": [3, 15, 17, 23, 24, 26, 27, 31], "design": [3, 15], "where": [3, 5, 13, 17, 19, 21, 22, 23, 24, 26, 27, 28, 29, 30, 31], "initi": [3, 11, 12, 13, 14, 15, 16, 17, 18, 19, 22, 26, 27, 28, 29, 30, 31], "class": [3, 5, 15, 18, 20, 22, 23, 25, 26, 28, 30, 31], "fast": [3, 30], "find": [3, 5, 7, 19, 20, 21, 23, 24, 26, 30, 31], "deriv": [3, 9, 13, 15, 19, 27, 30, 31], "inform": [3, 5, 18, 21, 23, 25, 26, 28, 30, 31], "dure": [3, 22, 26], "runtim": [3, 26], "after": [3, 16, 24, 25, 26, 28, 29, 31], "calcul": [3, 5, 18, 19, 20, 21, 22, 25, 28, 30, 31, 32], "thing": [3, 22], "should": [3, 4, 5, 9, 22, 24, 25, 26, 28, 29, 30, 31], "significantli": 3, "faster": [3, 24, 30, 31], "follow": [3, 8, 14, 15, 17, 21, 23, 25, 27, 28, 30, 31], "answer": 3, "intend": [3, 30], "differ": [3, 15, 19, 22, 23, 26, 28, 30, 31], "detect": 3, "either": [3, 7, 19, 30, 31], "exp": [3, 9, 30, 32], "log": [3, 29, 30, 31, 32], "forc": [3, 12], "ensur": [3, 4, 21, 24, 25, 28], "highest": 3, "precis": [3, 24, 25, 27, 30], "To": [3, 5, 21, 22, 25, 30, 31], "turn": [3, 28], "off": [3, 19, 22], "featur": [3, 14, 18, 20, 21, 23, 25], "futur": [3, 29, 30], "implement": [3, 5, 22, 23], "end": [3, 5, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 27, 28, 31], "fulli": [3, 4, 19], "being": [3, 13, 23, 26, 31], "defin": [3, 10, 12, 14, 17, 19, 21, 22, 24, 25, 27, 28, 30, 31], "evalu": [3, 10, 11, 12, 14, 15, 16, 17, 22, 26, 27, 30, 31], "full": [3, 9, 15, 22, 28, 30], "befor": [3, 20, 21, 22, 24, 25, 26], "extract": [3, 28], "them": [3, 4, 10, 19, 21, 23, 31], "out": [3, 22, 23, 25, 26, 28, 31], "reason": 3, "stop": 3, "u": [3, 10, 19, 20, 25, 26, 28, 30], "symbol": [3, 9, 19, 21, 31], "mean": [3, 5, 9, 19, 21, 22, 23, 24, 25, 26, 30, 31, 32], "one": [3, 19, 22, 23, 25, 26, 27, 28, 30, 31], "call": [3, 23, 25, 28, 30, 31], "return": [3, 15, 19, 30, 31, 32], "would": [3, 23, 26, 28], "appropri": [3, 8, 31, 32], "element": [3, 30, 31], "matrix": [3, 19, 23, 25, 28, 30, 31], "amount": [3, 25, 26, 30], "small": [3, 22], "best": [3, 26, 27], "necessari": [3, 19, 21, 26, 28], "work": [3, 4, 22, 26, 28, 30], "both": [3, 5, 7, 21, 22, 24, 26, 28, 30, 31], "within": [3, 4, 5, 23, 25], "later": [3, 23, 24, 25, 26], "variabl": [3, 19, 21, 23, 24, 25, 27, 30, 31], "ad": [3, 27, 28, 30], "delet": [3, 22], "perform": [3, 5, 7, 10, 19, 25, 26, 28, 30, 31], "consider": 3, "instruct": [4, 5], "found": [4, 5, 22, 26, 29, 30, 31], "github": [4, 5], "project": 4, "readm": 4, "here": [4, 5, 9, 15, 19, 22, 23, 24, 25, 26, 28, 30, 31], "code": [4, 5, 19, 25, 26, 27], "download": [4, 5], "ukhsa": 4, "collabor": 4, "git": 4, "clone": 4, "pleas": [4, 5], "redund": 4, "i": [4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32], "activ": [4, 6], "develop": [4, 5, 19, 26], "latest": 4, "review": 4, "version": [4, 9, 26, 30, 31, 32], "master": 4, "branch": 4, "recommend": [4, 30], "relev": [4, 23, 24, 26], "via": [4, 6, 15, 21, 22, 23, 24, 26, 30, 31, 32], "bash": 4, "name": [4, 9, 21, 23, 25, 26, 29, 31], "an": [4, 7, 8, 9, 11, 12, 15, 16, 17, 18, 22, 24, 26, 27, 28, 29, 30, 31, 32], "easi": [4, 5], "wai": [4, 5, 21, 22, 23, 25, 26, 31], "creat": [4, 31, 32], "new": [4, 21, 22, 23, 25, 26, 29, 30, 31, 32], "conda": 4, "environ": 4, "env": 4, "yml": 4, "process": [4, 5, 7, 9, 12, 13, 18, 22, 23, 25, 26, 28, 31], "altern": [4, 28], "add": [4, 5, 15, 22, 23, 27], "own": [4, 5], "final": [4, 11, 22, 25, 28, 30, 31], "prerequisit": 4, "window": 4, "machin": [4, 30], "need": [4, 21, 23, 25, 26, 27, 30, 31], "graphviz": [4, 31], "microsoft": 4, "visual": [4, 26], "c": [4, 8, 9, 23, 30, 31], "14": [4, 18, 27, 30], "0": [4, 5, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32], "greater": [4, 26, 30], "get": [4, 26, 28, 30], "build": [4, 5, 19, 23, 26, 31], "tool": [4, 5, 28], "abl": [4, 15, 22, 30], "py": 4, "anticip": 4, "make": [4, 8, 9, 19, 21, 22, 23, 26, 30], "frequent": [4, 8, 19, 23], "chang": [4, 5, 11, 21, 22, 23, 24, 25, 29, 30, 31], "conveni": [4, 30], "mode": [4, 30], "instead": [4, 5, 9, 21, 22, 23, 24, 25, 27, 28, 31], "releas": 4, "run": [4, 5, 10, 11, 12, 14, 15, 16, 17, 21, 22, 25, 26, 27, 28, 29], "complet": [4, 29, 30], "successfulli": [4, 24, 26, 30], "take": [4, 7, 20, 22, 23, 25, 26, 27, 30, 31, 32], "some": [4, 9, 19, 21, 22, 23, 25, 26, 27, 28, 30, 32], "minut": 4, "provid": [5, 12, 15, 18, 19, 20, 22, 25, 26, 27, 30, 31], "simpl": [5, 22, 28, 31], "interfac": [5, 30, 31], "construct": [5, 30], "ordinari": 5, "focu": [5, 24], "compartment": [5, 21, 23], "back": [5, 12, 24], "comprehens": [5, 22], "box": 5, "easili": [5, 7], "common": [5, 22, 23, 25, 31], "determinist": [5, 7, 8, 10, 11, 12, 14, 15, 16, 27, 31], "evolut": [5, 7, 8, 11, 14, 15, 17, 27], "sourc": [5, 12, 29, 30, 31, 32], "freeli": 5, "host": 5, "permit": [5, 10], "extens": [5, 11, 17, 31], "With": [5, 22, 26], "automat": [5, 23, 24, 30], "still": [5, 22, 24, 25, 26, 28], "access": [5, 19, 25], "freed": 5, "object": [5, 11, 12, 14, 15, 16, 17, 18, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32], "how": [5, 6, 7, 10, 16, 17, 18, 23, 24, 25, 26, 28, 30, 31], "underli": [5, 25, 26, 28, 30], "larg": [5, 22], "unchang": 5, "sinc": [5, 10, 21, 22, 23, 26, 30], "previou": [5, 21, 22, 25, 26], "bar": 5, "minor": 5, "bug": 5, "fix": [5, 7, 23, 24, 30], "signific": 5, "move": [5, 20, 31], "awai": 5, "deterministicod": [5, 29, 30, 31], "emploi": [5, 22, 26], "simulateod": [5, 20, 21, 22, 23, 24, 25, 27, 28, 31], "our": [5, 7, 9, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31], "well": [5, 6, 22, 23, 26, 30, 31], "fit": [5, 18, 20, 23, 26, 30], "random": [5, 10, 11, 14, 15, 25, 30, 31, 32], "special": [5, 23, 30], "now": [5, 9, 20, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31], "recognis": 5, "type": [5, 19, 21, 22, 23, 30, 31, 32], "hand": [5, 23], "act": [5, 25], "accordingli": 5, "outlin": [5, 6, 19, 23, 26], "detail": [5, 12, 30], "produc": [5, 6, 25, 31], "forecast": [5, 6], "section": [5, 6, 22, 25, 26, 30], "jupyterbook": 5, "local": [5, 25, 26, 30], "content": [5, 30], "notebook": [5, 22, 30, 32], "start": [5, 21, 23, 24, 25, 26, 30, 31], "point": [5, 15, 18, 22, 23, 24, 25, 26, 29, 30, 31], "triall": 5, "analys": 5, "ani": [5, 13, 16, 18, 23, 25, 30, 31], "exampl": [5, 7, 9, 15, 17, 19, 21, 22, 24, 25, 27, 28, 30, 31], "icon": 5, "desir": [5, 22, 30, 31], "locat": [5, 26], "top": [5, 9, 22, 30, 31], "right": [5, 9, 10, 12, 17, 19, 23, 26, 27, 28, 30, 32], "see": [5, 10, 11, 15, 16, 22, 23, 24, 25, 26, 28, 30, 31, 32], "guidanc": 5, "rais": [5, 30, 31], "issu": [5, 28, 30], "incorpor": [5, 17], "pull": [5, 24], "request": 5, "acknowledg": 5, "As": [6, 15, 19, 22, 25, 26, 27, 31], "anoth": [6, 19, 23, 24, 28], "kei": [6, 22, 23, 25, 30, 31], "infecti": [6, 7, 9, 11, 19, 23], "diseas": [6, 7, 15, 23, 24, 25, 31], "infer": [6, 25, 26, 29, 30], "case": [6, 9, 10, 12, 19, 21, 22, 23, 24, 25, 28, 29, 30, 31], "In": [6, 7, 12, 17, 19, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31, 32], "chapter": [6, 7, 25], "assist": [6, 19], "endeavour": 6, "present": [6, 22, 31], "up": [6, 11, 12, 14, 15, 16, 17, 19, 22, 24, 25, 26, 27, 28, 30], "approxim": [6, 12, 22, 30, 31], "bayesian": 6, "comput": [6, 22, 23, 30, 31], "abc": [6, 25, 26, 29], "classic": [6, 17], "maximum": [6, 10, 11, 12, 14, 15, 16, 17, 22, 29, 30, 31], "likelihood": [6, 30], "mle": [6, 26, 30], "demonstr": [6, 11, 15, 18, 21, 23, 24, 25, 28], "abil": 6, "less": [6, 22, 26, 30], "epidemiolog": [6, 9, 18], "boundari": [6, 26, 30], "valu": [6, 7, 15, 18, 21, 22, 25, 26, 27, 29, 30, 31], "problem": [6, 26, 28, 30, 31], "exercis": 7, "central": [7, 23], "studi": [7, 15, 19, 20, 23], "inde": [7, 23, 25, 30], "like": [7, 11, 14, 15, 22, 24, 26, 27, 29, 30, 31, 32], "allow": [7, 12, 18, 19, 22, 23, 24, 31], "obtain": [7, 19, 25, 26, 29, 30], "furthermor": [7, 23, 25], "specifi": [7, 19, 22, 23, 24, 25, 26, 27, 29, 30, 31], "drawn": [7, 21, 22], "randomli": [7, 21, 22], "probabl": [7, 21, 23, 25, 26, 32], "distribut": [7, 21, 22, 25, 26, 29, 30, 32], "sir": [7, 11, 19, 20, 21, 22, 27, 31], "introduc": [7, 22, 28], "prescrib": 7, "parameteris": [7, 32], "output": [7, 11, 13, 18, 22, 25, 26, 30, 31], "without": [8, 13, 26, 30, 31], "extern": [8, 12, 31], "stimulu": 8, "softwar": 8, "itself": [8, 23, 31], "describ": [8, 9, 23, 25, 30, 31], "excit": 8, "neuron": 8, "spike": 8, "pass": [8, 22, 25, 26, 28, 30, 31], "other": [8, 12, 23, 25, 26, 27, 28, 30], "integr": [8, 9, 13, 19, 22, 24, 26, 30, 31], "vanderpol": [8, 31], "begin": [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 22, 23, 24, 25, 27, 28, 31], "align": [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 27, 28], "frac": [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 23, 24, 26, 27, 28, 30, 31, 32], "mathrm": [8, 10, 11, 12, 13, 14, 15, 16, 17, 23, 24, 27, 28], "v": [8, 19, 24, 30, 31], "br": [8, 31], "import": [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 21, 22, 23, 24, 25, 26, 27, 28, 30, 31], "np": [8, 10, 11, 12, 14, 15, 16, 17, 22, 24, 25, 26, 27, 30, 31], "matplotlib": [8, 10, 11, 12, 14, 15, 16, 17, 22, 24, 25, 26, 27, 30, 31], "pyplot": [8, 10, 11, 12, 14, 15, 16, 17, 22, 24, 25, 26, 27, 30, 31], "plt": [8, 10, 11, 12, 14, 15, 16, 17, 22, 24, 25, 26, 27, 30, 31], "linspac": [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 24, 27, 30, 31], "20": [8, 12, 15, 18, 24, 25, 31], "101": [8, 31], "x0": [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 24, 25, 26, 27, 29, 30, 31], "initial_valu": [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 24, 26, 27, 31], "solve_determ": [8, 10, 11, 12, 14, 16, 17, 22, 24, 27, 31], "plot": [8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 22, 24, 25, 26, 27, 29, 30, 31], "reveal": [8, 12], "sharp": 8, "transit": [8, 12, 19, 22, 24, 27, 31], "legrand_ebola_seihfr": [9, 31], "literatur": 9, "captur": [9, 18, 28], "outbreak": 9, "propos": [9, 25], "et": 9, "al": 9, "There": [9, 23, 25, 31], "two": [9, 19, 21, 22, 23, 24, 26, 28, 29, 30, 31], "extra": [9, 19, 27, 30, 31], "compart": [9, 15, 22, 23, 25, 28, 31], "seir": [9, 31], "hospiti": 9, "funer": [9, 31], "total": [9, 10, 15, 21, 22, 23, 25, 26, 27, 28, 29, 31], "ten": 9, "invers": [9, 30], "beta_": [9, 13, 31], "transmiss": [9, 23, 28], "commun": 9, "hospit": [9, 31], "gamma_": [9, 31], "onset": 9, "death": [9, 13, 18, 23, 25, 31], "hospitil": 9, "burial": 9, "alpha": [9, 10, 11, 12, 15, 17, 22, 25, 26, 28, 30, 31, 32], "durat": 9, "incub": [9, 11], "period": [9, 10, 11, 25, 27, 31], "theta": [9, 23, 24, 26, 30, 31], "proport": [9, 23, 28], "delta": [9, 10, 12, 17, 27, 28, 31], "ftaliti": 9, "ratio": 9, "denot": 9, "invert": 9, "sens": [9, 23, 25, 31], "natur": [9, 23, 28, 32], "replac": [9, 24, 26, 30, 31], "gamma": [9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 21, 22, 23, 25, 26, 27, 28, 30, 31, 32], "omega": 9, "omega_": 9, "directli": [9, 18, 32], "give": [9, 22, 23, 30], "intuit": [9, 23], "five": 9, "fatal": 9, "delta_": [9, 31], "ih": [9, 31], "dh": [9, 31], "adjust": 9, "theta_": [9, 23, 31], "readi": [9, 20, 23], "dt": [9, 10, 11, 12, 14, 15, 16, 17, 19, 22, 23, 27, 31], "n": [9, 11, 12, 13, 14, 15, 16, 17, 19, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32], "si": [9, 11, 12, 14, 15, 23, 27, 28, 31], "sh": [9, 31], "sf": [9, 31], "de": [9, 31], "di": [9, 19, 31], "df": [9, 18, 31, 32], "dr": [9, 19, 31], "otherwis": [9, 30, 31], "slightli": [9, 21], "modifi": [9, 30], "sigmoid": 9, "logist": 9, "left": [9, 12, 17, 19, 23, 27, 28, 30, 32], "kappa": [9, 28, 31], "brief": 9, "given": [9, 10, 18, 21, 23, 24, 25, 26, 28, 30, 31, 32], "200000": [9, 31], "100": [9, 12, 13, 15, 21, 22, 24, 30, 31], "beta_i": [9, 31], "588": [9, 31], "beta_h": [9, 31], "794": [9, 31], "beta_f": [9, 31], "653": [9, 31], "omega_i": [9, 31], "omega_d": [9, 31], "omega_h": [9, 31], "omega_f": [9, 31], "alphainv": [9, 31], "80": [9, 31], "300": [9, 18, 22, 31], "interventiontim": [9, 31], "suscept": [9, 11, 12, 14, 15, 16, 22, 23, 31], "equal": [9, 23, 25, 30, 31], "whole": 9, "popul": [9, 10, 12, 15, 21, 22, 23, 25, 26, 27, 28, 29, 31], "doe": [9, 23, 28, 30, 31], "lotka_volterra": [10, 31], "basic": [10, 19, 31], "predat": 10, "prei": 10, "express": [10, 19, 31], "term": [10, 19, 24, 28, 30, 31, 32], "area": 10, "densiti": [10, 32], "respect": [10, 19, 21, 22, 23, 26, 30, 31], "though": [10, 23, 25, 28], "absolut": 10, "decis": 10, "rather": [10, 19, 22, 23, 25, 28, 31], "than": [10, 12, 19, 22, 23, 25, 26, 30, 31], "beta": [10, 11, 12, 14, 15, 16, 17, 19, 21, 22, 23, 25, 26, 27, 28, 31, 32], "math": [10, 11, 12, 14, 15, 16, 17, 22, 30, 32], "per": [10, 12, 15, 22, 23, 26, 31], "squar": [10, 30, 31], "wish": [10, 21, 22, 23, 24, 25, 26, 31], "200": [10, 22, 30], "anim": 10, "tmax": [10, 11, 12, 14, 15, 16, 17, 22, 27], "over": [10, 11, 12, 14, 15, 16, 17, 21, 22, 26, 30, 31], "timestep": [10, 11, 12, 14, 15, 16, 17, 22, 27], "n_timestep": [10, 11, 12, 14, 15, 16, 17, 22, 27], "ceil": [10, 11, 12, 14, 15, 16, 17, 22], "iter": [10, 11, 12, 14, 15, 16, 17, 22, 25, 27, 30, 31], "show": [10, 11, 12, 14, 15, 16, 17, 19, 21, 22, 24, 26, 27, 30, 31], "behaviour": [10, 30], "phase": [10, 28], "shift": 10, "between": [10, 22, 23, 26, 27, 28, 30, 31], "ax": [10, 12, 17, 22], "subplot": [10, 11, 12, 14, 15, 16, 17, 22, 24, 25, 26, 27], "figsiz": [10, 11, 12, 14, 15, 16, 17, 22, 25, 26, 27], "set_xlabel": [10, 11, 12, 14, 15, 16, 17, 22, 24, 25, 26, 27], "set_ylabel": [10, 11, 12, 14, 15, 16, 17, 22, 26], "label": [10, 26], "legend": [10, 26], "loc": [10, 26], "upper": [10, 19, 30], "evolv": [10, 16, 27], "seed": [10, 15, 22, 25, 31, 32], "n_sim": [10, 15, 22], "simt": [10, 15, 22], "solve_stochast": [10, 15, 22, 25, 31], "full_output": [10, 13, 15, 22, 30, 31], "true": [10, 13, 15, 19, 22, 24, 25, 26, 29, 30, 31, 32], "dstack": [10, 15, 22], "appear": [10, 28], "unstabl": 10, "undergo": [10, 11, 15], "increasingli": 10, "extrem": 10, "peak": 10, "trough": 10, "confirm": 10, "examin": 10, "diagram": 10, "wherebi": [10, 23], "trajectori": [10, 14, 15, 17, 22, 24, 27], "space": [10, 26, 30], "spiral": 10, "outward": 10, "expos": 11, "recov": [11, 12, 14, 15, 23, 24, 25, 28], "realist": [11, 31], "individu": [11, 12, 15, 16, 22, 23, 25, 28, 31], "do": [11, 16, 20, 21, 22, 23, 25, 27, 28, 30, 31], "becom": [11, 22, 23, 26, 28], "instantli": 11, "upon": [11, 16], "exposur": 11, "timescal": [11, 27], "govern": [11, 22, 23], "flu": [11, 14], "dai": 11, "n_pop": [11, 12, 14, 15, 16, 17, 22, 25, 26, 27], "1e4": [11, 14, 15, 16, 17, 21, 22, 25, 26, 27], "r0": [11, 14, 15, 27, 31], "rang": [11, 12, 14, 15, 16, 17, 22, 27, 30, 31], "increment": [11, 12, 14, 15, 16, 17, 22, 27], "365": [11, 12, 14, 15, 27, 31], "condit": [11, 12, 13, 14, 15, 16, 17, 19, 22, 26, 27, 29, 30, 31], "i0": [11, 14, 15, 16, 17, 22, 25, 26, 27, 31], "same": [11, 15, 21, 22, 25, 26, 27, 30, 31, 32], "compar": [11, 22, 26, 31], "solution2": 11, "profil": [11, 26, 30], "overal": 11, "axarr": [11, 14, 15, 16, 22, 24, 25, 26, 27], "layout": [11, 14, 15, 16, 22, 24, 25, 26, 27], "constrain": [11, 14, 15, 16, 22, 24, 25, 26, 27], "colour": [11, 14, 16, 22], "c1": [11, 14, 15, 16, 22, 26, 27], "c3": [11, 27], "c0": [11, 14, 15, 16, 22, 26, 27], "c2": [11, 14, 15, 22, 27], "statelist": [11, 14, 15, 16, 22, 23, 24, 27, 28, 31], "color": [11, 14, 15, 16, 22, 26, 27], "linestyl": 11, "dash": 11, "els": [11, 28, 30, 31], "rotat": [11, 14, 15, 16, 17, 22, 26], "seir_birth_death_periodic_waning_intro": 12, "rel": [12, 28, 30], "pre": [12, 31], "templat": 12, "complex": [12, 20, 23], "season": [12, 17, 27], "drive": 12, "immun": [12, 16, 23, 27], "w": [12, 27, 30, 31], "ii": 12, "analog": [12, 30], "epsilon": [12, 13, 31], "mu": [12, 15, 23, 28, 31, 32], "beta_0": [12, 17, 27], "co": [12, 17, 27, 30, 31], "pi": [12, 17, 27, 30, 31], "1e5": [12, 15, 31], "01": [12, 13, 15, 17, 18, 24, 26, 30, 31], "n_su": 12, "frac_su": 12, "30": [12, 25, 26, 31], "year": [12, 15, 27], "last": [12, 25, 30, 31], "beta0": [12, 17, 27, 31], "preval": 12, "eventu": [12, 15, 28], "reach": [12, 15, 16, 22], "annual": 12, "30000": 12, "seir_multipl": [13, 31], "togeth": [13, 25, 30], "birth": [13, 23, 31], "s_": [13, 31], "dn_": [13, 31], "ds_": [13, 31], "lambda_": [13, 31], "e_": [13, 31], "i_": [13, 31], "r_": 13, "dr_": [13, 31], "sum_": [13, 30, 31], "neq": [13, 31], "patch": [13, 31, 32], "factor": [13, 28, 30, 31], "paramev": [13, 25, 26, 31], "beta_00": [13, 31], "0010107": [13, 31], "beta_01": [13, 31], "beta_10": [13, 31], "beta_11": [13, 31], "02": [13, 18, 24, 30, 31], "45": [13, 18, 31], "73": [13, 25, 31], "n_0": [13, 31], "n_1": [13, 31], "36139": [13, 31], "3224081278": [13, 31], "422": [13, 31], "560577637822": [13, 31], "263": [13, 31], "883351688369": [13, 31], "963174": [13, 31], "233662546": [13, 31], "param": [13, 21, 22, 23, 25, 26, 27, 28, 30, 31, 32], "40": [13, 25, 30, 31], "x01": [13, 31], "arrai": [13, 19, 29, 30, 31, 32], "float": [13, 29, 30, 31], "those": [13, 23, 28, 31], "stabil": [13, 19, 31], "while": [13, 30, 31], "notat": [13, 31, 32], "taken": [13, 26, 30], "heavili": 14, "throughout": [14, 23], "document": [14, 19], "result": [14, 15, 19, 22, 23, 24, 25, 27, 28, 30, 31], "familiar": [14, 21, 22], "sir_birth_death": [15, 31], "remov": [15, 23, 26, 31], "each": [15, 22, 23, 25, 26, 28, 29, 30, 31], "uniform": [15, 25, 32], "person": [15, 23], "replenish": 15, "thu": [15, 25, 27, 28], "conserv": [15, 28, 29], "For": [15, 19, 23, 24, 26, 28, 30, 31], "remain": [15, 21, 23, 25, 28, 29], "constant": [15, 21, 23, 31], "wherea": [15, 28], "fluctuat": 15, "around": [15, 28, 30], "measl": 15, "threshold": [15, 22, 25, 29], "order": [15, 22, 23, 24, 27, 30, 31], "support": [15, 23, 30], "endem": 15, "circul": 15, "pathogen": 15, "15": [15, 18, 24, 25, 31], "equilibrium": [15, 16, 31], "stationari": [15, 31], "def": [15, 30], "sir_bd_endemic_eq": 15, "s0": [15, 27], "floor": 15, "try": [15, 22, 24, 26, 31], "larger": [15, 25, 26, 30], "updat": [15, 23, 31], "recalcul": 15, "ic": 15, "solution_2": 15, "simt_2": 15, "y_2": 15, "even": [15, 19, 25, 30], "1e6": 15, "solution_3": 15, "simt_3": 15, "y_3": 15, "000": [15, 26], "critic": [15, 22], "zero": [15, 22, 30, 31], "lead": [15, 26], "extinct": [15, 22], "cours": [15, 25, 26], "signifi": 15, "stabl": [15, 31], "growth": 15, "turnov": 15, "when": [15, 18, 19, 21, 22, 23, 24, 25, 26, 28, 30, 31, 32], "subset": [15, 28], "typic": [15, 23, 25], "500": 15, "persist": 15, "titl": [15, 22, 32], "idx": [15, 22], "enumer": [15, 22], "set_titl": [15, 22, 24, 25, 27], "perhap": [16, 23, 26, 28], "simplest": 16, "recoveri": [16, 22, 23, 27], "50": [16, 22, 25, 30, 31], "suffici": [16, 22, 23], "long": [16, 30], "sis_period": [17, 31], "could": [17, 23, 24, 26, 28, 30], "mimic": 17, "variat": [17, 22], "yearli": 17, "contact": [17, 23, 31], "pattern": 17, "climat": 17, "driver": 17, "baselin": [17, 27], "magnitud": [17, 27, 30], "elimin": [17, 22, 28], "heathcot": 17, "5t": [17, 31], "framework": 18, "tri": [18, 30, 31], "json": 18, "its": [18, 23, 30], "variou": [18, 20, 23, 31], "previous": [18, 19, 21, 22, 23], "discuss": [18, 23], "guid": 18, "input": [18, 23, 25, 26, 30, 31, 32], "string": [18, 29, 30, 31], "alreadi": [18, 23, 31, 32], "dict": [18, 21, 22, 30, 31], "cumul": [18, 30], "form": [18, 19, 21, 26, 27, 31], "default": [18, 30, 31, 32], "shown": 18, "below": [18, 23, 24, 25, 26, 30, 32], "panda": 18, "datafram": 18, "loss": [18, 25, 32], "read_epijson": 18, "epijson_to_data_fram": 18, "pkgutil": 18, "get_data": 18, "eg1": 18, "print": [18, 19, 22, 24, 25, 26, 30, 31], "1854": 18, "04": [18, 25, 30, 31], "17": [18, 25, 26], "56": 18, "51": [18, 25], "00": [18, 26, 30], "18": [18, 25], "26": 18, "09": 18, "58": 18, "21": [18, 25], "24": 18, "46": [18, 25], "16": [18, 24, 30], "03": [18, 21, 30], "aim": 18, "load": [18, 21, 22, 25, 26], "usual": [18, 25, 28, 30], "epijsonloss": 18, "poisson": [18, 25, 27, 30, 32], "hood": 18, "epijson_loss": 18, "sir_norm": [18, 31], "obj": [18, 22, 24, 30], "005": 18, "cost": [18, 22, 24, 26, 30, 31], "865594602563727": 18, "_df": 18, "inherit": 18, "baseloss": [18, 30], "abov": [18, 22, 23, 24, 27, 28, 31], "rest": [18, 28], "breviti": 18, "frame": 18, "store": [18, 19, 30], "insid": 18, "retriev": 18, "inspect": [18, 19, 22, 25, 26, 28], "suppli": [18, 22], "treat": [18, 22, 24, 27], "t0": [18, 24, 26, 29, 30, 31], "indic": [18, 23, 25, 29, 30], "column": [18, 25, 29, 30, 31], "correspond": [18, 25, 26, 30, 31], "belong": [18, 31], "again": [19, 22, 23, 25, 26], "predefin": 19, "avoid": [19, 29, 31], "scratch": [19, 22], "initialis": [19, 22, 23], "seen": [19, 22], "get_ode_eqn": [19, 23, 31], "verifi": [19, 23, 26, 28], "expect": [19, 25, 28, 30, 31], "displaystyl": [19, 23, 28], "displai": 19, "latex": [19, 30, 31, 32], "port": 19, "print_od": [19, 31], "\u03b2": 19, "\u03b3": 19, "cc": 19, "definit": [19, 22, 30, 32], "get_transition_matrix": [19, 28, 31], "diagon": [19, 30, 31], "triangl": 19, "graphic": 19, "get_transition_graph": [19, 28, 31], "briefli": 19, "quickli": 19, "firstli": [19, 23], "linear_od": [19, 31], "fals": [19, 25, 29, 30, 31, 32], "analysi": [19, 22, 30, 31], "speed": [19, 24, 30], "know": [19, 23, 24, 25, 26], "jacobian": [19, 26, 30, 31], "hessian": [19, 26, 30, 31], "three": [19, 30, 31], "2d": [19, 31], "3d": [19, 31], "gradient": [19, 30, 31], "context": 19, "sure": 19, "get_jacobian_eqn": [19, 31], "get_hessian_eqn": [19, 31], "get_grad_eqn": [19, 31], "reproduct": [19, 31], "r_0": [19, 26], "next": [19, 25], "assum": [19, 23, 24, 25, 26, 28, 30, 31], "must": [19, 21, 22, 23, 24, 25, 27, 28, 30], "repres": [19, 22, 23, 27, 30, 31, 32], "epi_analysi": 19, "disease_progression_matric": [19, 31], "r0_from_matrix": [19, 31], "encapsul": [20, 21, 23], "advantag": [20, 23, 31], "sever": 20, "sort": 20, "ourselv": 20, "pen": 20, "paper": 20, "until": [21, 22, 30], "dealt": 21, "howev": [21, 22, 23, 25, 26, 28, 30], "fed": 21, "accept": [21, 23, 25, 26, 29, 30, 31], "thei": [21, 25, 26, 31], "simpli": [21, 30, 31], "list": [21, 23, 25, 27, 29, 30, 31], "tupl": [21, 29, 30, 31], "fixed_param_set": [21, 22], "imagin": [21, 24], "prior": [21, 25, 29], "uncertainti": [21, 26], "reflect": [21, 23, 25, 28], "varieti": 21, "suitabl": [21, 30, 31], "posit": [21, 23, 24, 26, 30, 31], "ll": [21, 23], "keep": [21, 23, 28], "mixtur": 21, "syntax": [21, 26], "cumbersom": 21, "item": [21, 30, 31], "handl": [21, 23, 27, 30], "second": [21, 24, 28, 31], "utilr": [21, 22], "rgamma": [21, 22, 32], "random_param_set": [21, 22], "contain": [21, 22, 25, 29, 30, 31], "shape": [21, 22, 26, 30, 31, 32], "400": [21, 25], "333": 21, "33": [21, 25, 26], "deviat": [21, 22, 30], "025": [21, 25], "good": [21, 26, 30], "idea": [21, 26], "leftov": 21, "workflow": 22, "transitiontyp": [22, 23, 24, 27, 28, 31], "paramlist": [22, 23, 24, 27, 28], "transitionlist": 22, "origin": [22, 23, 24, 27, 28, 31], "destin": [22, 23, 28, 31], "transition_typ": [22, 23, 24, 27, 28, 31], "beta_mn": 22, "35": [22, 25, 26, 31], "actual": [22, 25, 30, 31], "gamma_mn": 22, "gamma_var": 22, "10th": 22, "gamma_shap": 22, "gamma_r": 22, "beta_var": 22, "beta_shap": 22, "beta_r": 22, "involv": [22, 31], "reproduc": [22, 24, 26], "determin": [22, 30, 31], "short": [22, 23], "reduc": [22, 23, 24, 25, 28], "error": [22, 23, 30, 31], "too": [22, 27], "odeint": [22, 31], "wrap": 22, "member": [22, 23], "d_f": 22, "suffix": 22, "impli": [22, 23, 27, 28], "deterministic_fix": 22, "ode_d_f": 22, "timepoint": [22, 24, 25, 27], "solution_d_f": 22, "yield": [22, 24], "increas": [22, 25, 30], "exponenti": [22, 26, 32], "deplet": [22, 23], "declin": 22, "1000": [22, 30, 31], "repetit": 22, "ode_d_r": 22, "n_param_draw": 22, "ymean": 22, "solution_d_r": 22, "messag": [22, 24, 25, 26, 30], "connect": 22, "mpi": 22, "backend": [22, 31], "capabl": [22, 26, 28], "parallel": [22, 31], "ipython": 22, "visualis": 22, "secondli": 22, "confid": [22, 30], "interv": [22, 25, 30], "95": [22, 25], "median": [22, 25], "y_d_r": 22, "unpack": 22, "i_rand": 22, "sampl": [22, 25, 29, 30], "ci": [22, 26], "y_d_r_lolo": 22, "percentil": 22, "axi": [22, 30], "y_d_r_lo": 22, "y_d_r_hi": 22, "75": [22, 25], "y_d_r_hihi": 22, "97": [22, 30], "y_d_r_md": 22, "fill_between": 22, "facecolor": 22, "dark": 22, "shade": 22, "light": 22, "continuum": [22, 23], "break": 22, "down": [22, 30], "regim": 22, "continu": [22, 30], "flow": [22, 23, 28], "event": [22, 23, 31], "occur": [22, 23, 30], "assumpt": [22, 23, 26, 30], "wait": 22, "memoryless": 22, "quicker": 22, "algorithm": [22, 25, 26, 28, 29, 30, 31], "interact": [22, 23], "ode_s_f": 22, "solution_s_f": 22, "y_s_f": 22, "final_size_s_f": 22, "figur": [22, 25, 29, 31], "xlabel": 22, "ylabel": 22, "count": [22, 28], "hist": 22, "bin": 22, "chain": [22, 26], "fail": [22, 26, 30, 31], "i_success_s_f": 22, "2000": 22, "y_fail_s_f": 22, "min": [22, 30, 32], "proce": [22, 25, 26], "exhibit": 22, "i_fail_s_f": 22, "y_success_s_f": 22, "y_s_f_lolo": 22, "y_s_f_lo": 22, "y_s_f_hi": 22, "y_s_f_hihi": 22, "y_s_f_md": 22, "explor": 22, "scenario": [22, 24, 31], "ode_s_r": 22, "solution_s_r": 22, "y_s_r": 22, "final_size_s_r": 22, "spread": 22, "ow": 22, "separ": [22, 28], "success": [22, 24, 26, 30, 31], "clear": [22, 31], "cut": 22, "judg": 22, "ey": 22, "i_fail_s_r": 22, "y_success_s_r": 22, "y_s_r_lolo": 22, "y_s_r_lo": 22, "y_s_r_hi": 22, "y_s_r_hihi": 22, "y_s_r_md": 22, "four": [22, 23, 31], "configur": [22, 28], "side": [22, 23], "illustr": 22, "qualit": 22, "ymax": 22, "1250": 22, "fig": 22, "axarr2": 22, "set_ylim": 22, "bottom": [22, 31], "onc": [23, 26, 29], "instanc": [23, 26], "applic": [23, 27, 30], "think": [23, 28], "about": [23, 25, 26, 30], "mathbf": 23, "boldsymbol": 23, "y_": [23, 30, 31], "ldot": [23, 31], "vector": [23, 30, 31], "categori": [23, 28], "interpret": [23, 28, 30, 31], "group": 23, "y_i": 23, "rightarrow": 23, "y_j": 23, "f_": [23, 31], "symmetr": 23, "cannot": [23, 27, 30], "half": [23, 25], "flexibl": 23, "choos": [23, 25, 30, 31], "perspect": 23, "combin": [23, 25], "convert": [23, 30, 31], "attempt": [23, 25, 26, 28, 29, 31], "revers": [23, 28], "engin": [23, 28], "reli": 23, "tutori": [23, 30], "moment": 23, "ambigu": 23, "latter": [23, 31], "distinct": [23, 28], "made": [23, 25, 29, 30], "who": 23, "longer": 23, "acquir": 23, "induc": 23, "effect": [23, 26, 27], "wane": [23, 27], "versu": 23, "distinguish": [23, 28], "real": [23, 31], "world": 23, "therefor": 23, "reserv": 23, "sole": 23, "surviv": 23, "averag": 23, "transmit": 23, "receiv": 23, "unit": [23, 31], "carri": [23, 31], "cp": 23, "what": [23, 25, 28, 31], "incid": [23, 28], "oppos": 23, "mass": [23, 32], "action": [23, 31], "mix": [23, 28], "entir": 23, "No": 23, "migrat": 23, "entri": [23, 30], "departur": [23, 25], "uscept": [23, 28], "nfect": 23, "ecov": 23, "valid": [23, 28, 30], "subject": 23, "One": [23, 28, 31], "languag": 23, "benefici": 23, "enabl": 23, "forget": 23, "recipi": 23, "had": [23, 31], "rememb": [23, 31], "opposit": 23, "sign": 23, "feed": 23, "argument": [23, 24, 25, 30, 31], "let": [23, 24, 25, 26, 27, 28], "ve": 23, "just": [23, 25, 30], "option": [23, 25, 30, 31], "summaris": 23, "tabl": 23, "pertain": 23, "dy_i": 23, "arguabl": 23, "convent": 23, "adopt": 23, "better": 23, "incorrectli": 23, "place": [23, 27, 30], "through": [23, 30, 31], "odelist": [23, 27, 28], "translist": 23, "model_od": 23, "model_tra": 23, "equival": [23, 25, 30], "sai": [23, 30, 31], "complic": 23, "cancel": 23, "balanc": [23, 28], "achiev": [23, 31], "param_list": 23, "enter": [23, 27, 28], "birthdeathlist": 23, "birth_death_list": 23, "correctli": [23, 25], "ivp": 24, "bvp": 24, "littl": 24, "bit": 24, "essenti": [24, 26], "shoot": 24, "observ": [24, 25, 26, 29, 30, 32], "projectil": 24, "motion": 24, "domain": 24, "anywai": 24, "launch": 24, "ball": 24, "straight": 24, "air": 24, "height": 24, "ignor": [24, 30], "resist": 24, "graviti": 24, "acceler": 24, "veloc": 24, "suppos": 24, "land": 24, "10m": 24, "trivial": 24, "quick": 24, "15m": 24, "target": [24, 30, 31], "hope": 24, "artefact": 24, "soon": 24, "ode1": 24, "ode2": 24, "explicitli": [24, 27, 28], "20m": 24, "subsequ": [24, 25], "satisfi": [24, 30], "guess": [24, 25, 26, 30], "admittedli": 24, "ineffici": 24, "twice": [24, 30], "target_st": [24, 30], "minim": [24, 26, 30], "squareloss": [24, 29, 30], "initialst": 24, "state_nam": [24, 26, 29, 30], "And": 24, "costiv": 24, "thetahat": 24, "fun": [24, 26, 30], "termin": [24, 26, 30], "statu": [24, 26], "987646893079144e": 24, "500e": 24, "nit": [24, 26], "jac": [24, 26, 31], "122e": 24, "hess_inv": 24, "556e": 24, "nfev": [24, 26, 30], "njev": [24, 26], "tolist": 24, "known": 24, "pretend": 24, "omit": [24, 25], "declar": [24, 27], "1241808584714344e": 24, "000e": 24, "068e": 24, "469e": 24, "posterior": [25, 26, 29], "candid": [25, 26], "synthet": 25, "quad": [25, 30], "n_": 25, "text": 25, "pop": [25, 31], "loadtxt": [25, 26], "seir_epi_data": [25, 26], "sol_i_r": [25, 26], "daili": 25, "rcparam": 25, "scatter": 25, "regard": [25, 28], "report": [25, 29, 30], "unlik": 25, "unless": [25, 30], "high": 25, "nevertheless": 25, "purpos": 25, "realiti": 25, "undermin": 25, "go": [25, 28], "unknown": [25, 26], "unrealist": 25, "sake": 25, "simplic": [25, 31], "interest": [25, 30], "create_loss": [25, 29], "predict": [25, 30, 32], "overspecifi": 25, "overrod": 25, "ode_seir": [25, 26], "seir_n": [25, 26, 31], "approximate_bayesian_comput": 25, "unif": 25, "logscal": [25, 29], "poissonloss": [25, 26, 30], "everyth": 25, "objseir": [25, 26], "abcseir": 25, "sequenti": 25, "smc": [25, 29], "smaller": [25, 30], "perturb": 25, "weight": [25, 29, 30], "multivari": [25, 30], "normal": [25, 30, 31, 32], "covari": [25, 30], "get_posterior_sampl": 25, "q": [25, 29, 30, 32], "quantil": [25, 29], "whilst": [25, 27, 28], "toler": [25, 29, 30], "difficult": [25, 28], "th": 25, "distanc": 25, "reduct": 25, "higher": 25, "250": 25, "tol": [25, 29, 30], "inf": 25, "progress": [25, 26, 29, 31], "74": 25, "364073": 25, "42362": 25, "62": 25, "72191": 25, "64935": 25, "21204": 25, "77097": 25, "53": 25, "7452": 25, "74757": 25, "3250": 25, "22571": 25, "want": [25, 29, 31], "continue_posterior_sampl": [25, 29], "along": [25, 30], "next_tol": 25, "attribut": [25, 30], "2232": 25, "01873": 25, "13": [25, 30], "1833": 25, "77615": 25, "76": 25, "plot_posterior_histogram": [25, 29], "plot_pointwise_predict": [25, 29], "abcsir": 25, "re": [25, 26, 30, 31], "credibl": [25, 26], "consist": [25, 28], "3f": 25, "975": 25, "350": 25, "318": 25, "388": 25, "566": 25, "437": 25, "712": 25, "254": 25, "231": 25, "281": 25, "concern": 25, "compon": 25, "wise": [25, 30], "objseir2": 25, "epi": 25, "abcseir2": 25, "57967": 25, "89694": 25, "23": 25, "14573": 25, "65549": 25, "63": 25, "4955": 25, "22257": 25, "07": 25, "1747": 25, "46397": 25, "1008": 25, "39222": 25, "795": 25, "51825": 25, "750": 25, "03026": 25, "85": 25, "362": 25, "326": 25, "413": 25, "516": 25, "345": 25, "785": 25, "260": 25, "240": 25, "284": 25, "agreement": [25, 26], "Of": 25, "mechan": 25, "similar": [25, 26, 27, 31], "doen": 25, "e0": 25, "ode_sir": 25, "objsir": 25, "97090": 25, "54633": 25, "57": 25, "26871": 25, "99949": 25, "27": 25, "06": 25, "7946": 25, "79001": 25, "05": [25, 30], "2164": 25, "64690": 25, "86": 25, "1108": 25, "75380": 25, "83": 25, "936": 25, "24091": 25, "32": 25, "900": 25, "98276": 25, "31": 25, "69": 25, "restrict": [25, 30, 31], "inappropri": 25, "poorer": 25, "certainti": 25, "objseir3": 25, "abcseir3": 25, "72": 25, "89": 25, "58067": 25, "08238": 25, "15858": 25, "17892": 25, "94": 25, "5420": 25, "38644": 25, "54": 25, "2185": 25, "32098": 25, "41": 25, "1182": 25, "18264": 25, "42": 25, "878": 25, "11360": 25, "777": 25, "43372": 25, "64": 25, "307": 25, "623": 25, "366": 25, "141": 25, "408": 25, "278": 25, "230": 25, "368": 25, "701": 25, "106": 25, "wider": 25, "markov": 26, "techniqu": [26, 30], "level": [26, 30], "landscap": 26, "outdat": 26, "practic": [26, 28], "older": 26, "public": 26, "minimis": 26, "remind": 26, "i_0": 26, "ones": 26, "target_param": [26, 30], "decai": 26, "substanti": 26, "neighbourhood": 26, "similarli": [26, 28], "bad": 26, "navig": 26, "sensit": [26, 31], "adjoint": [26, 31], "3473286": 26, "37537513": 26, "648419": 26, "19492932": 26, "3962185": 26, "9873881": 26, "3439949": 26, "96665263": 26, "651037": 26, "89808302": 26, "3920356": 26, "14337017": 26, "timeit": 26, "197": 26, "\u03bc": 26, "loop": [26, 31], "std": 26, "dev": 26, "264": 26, "838": 26, "ran": 26, "properti": [26, 31], "quit": 26, "evid": 26, "discret": 26, "forward": [26, 30, 31], "affect": 26, "obviou": 26, "interpol": [26, 30, 31], "consecut": 26, "length": [26, 30, 31], "fewer": 26, "accur": 26, "univari": [26, 30], "spline": [26, 30], "limit": [26, 30], "ideal": [26, 29], "prefer": [26, 30, 31], "adapt": [26, 30], "hermit": 26, "chebyshev": 26, "procedur": 26, "sensibl": 26, "boxbound": 26, "slsqp": 26, "bfg": 26, "tnc": 26, "trust": 26, "ncg": 26, "bound": [26, 30], "1651": 26, "1282171916191": 26, "537e": 26, "384e": 26, "559e": 26, "683e": 26, "730e": 26, "709e": 26, "par": 26, "ode_est": 26, "lower": [26, 30], "incomplet": 26, "measur": 26, "fall": 26, "part": 26, "carefulli": 26, "confidence_interv": 26, "asymptot": [26, 30], "bootstrap": [26, 30], "geometr": [26, 30], "Such": 27, "situat": 27, "vari": [27, 31], "intervent": 27, "wit": 27, "multipl": [27, 28, 31], "dummi": 27, "plai": 27, "role": 27, "append": [27, 31], "tau_0": 27, "t_0": 27, "put": 27, "derived_param": [27, 31], "tau0": 27, "int": [27, 30, 31, 32], "accord": [27, 31], "sim": 27, "vagu": 27, "lose": 27, "lost": 28, "constitu": 28, "explain": 28, "caution": 28, "potenti": 28, "tricki": 28, "split": 28, "necessarili": [28, 30], "track": 28, "encount": 28, "live": 28, "difficulti": 28, "care": 28, "get_unrolled_obj": [28, 31], "implic": 28, "substitut": 28, "everywher": 28, "empti": 28, "match": 28, "nlive": 28, "limitless": 28, "reservoir": 28, "come": [28, 31], "graph": [28, 31], "map": 28, "atent": 28, "leav": 28, "fraction": 28, "nfectiv": 28, "symptomat": 28, "onward": 28, "emov": 28, "eta": [28, 31], "die": 28, "outflow": 28, "compos": 28, "partit": 28, "dead": 28, "notic": [28, 30], "born": 28, "incorrect": 28, "loss_object": 29, "constraint": 29, "none": [29, 30, 31, 32], "integ": [29, 30, 32], "sequenc": [29, 30], "decreas": [29, 30], "mnn": 29, "nearest": 29, "neighbour": 29, "bool": [29, 30, 31], "rerun": 29, "get_posterior_sample_origin": 29, "get_toler": 29, "plot_stat": 29, "new_tim": 29, "max_ncol": 29, "temporarili": 29, "overwrit": 29, "revert": 29, "pure": 29, "squash": 29, "plot_param": 29, "plot_scatt": 29, "pair": [29, 30, 31], "whether": [29, 30, 31], "scale": [29, 30, 31], "sigma_nearest_neighbour": 29, "xx": 29, "distnam": 29, "distpar": 29, "chosen": [29, 30], "loss_typ": 29, "state_weight": [29, 30], "sigma": [29, 30, 31, 32], "were": [29, 31], "str": [29, 30, 31], "came": 29, "normalloss": [29, 30], "get_funct": 29, "diff2loss": 30, "yhat": 30, "apply_weight": 30, "jupit": 30, "ipnyb": [30, 32], "boolean": [30, 31], "multipli": [30, 31], "residu": 30, "raw": 30, "scnd_deriv_yhat": 30, "hat": 30, "diff_loss": 30, "first_deriv_yhat": 30, "neg": [30, 31, 32], "distirbut": 30, "bolker": [30, 32], "ecolog": [30, 32], "pp": [30, 32], "131": [30, 32], "133": [30, 32], "princeton": [30, 32], "univers": [30, 32], "kept": 30, "miss": 30, "mathcal": [30, 32], "gammaloss": 30, "negbinom": 30, "k": [30, 31, 32], "binomi": [30, 32], "overdispers": [30, 32], "varianc": [30, 31, 32], "124": [30, 32], "126": [30, 32], "negbinomloss": 30, "nabla": 30, "mathcalfrac": 30, "sqrt": [30, 31], "2pi": 30, "2sigma": 30, "scalar": 30, "_": [30, 31], "Not": 30, "realli": 30, "univariatesplin": 30, "bbox": 30, "ext": 30, "check_finit": 30, "spl": 30, "degre": 30, "knot": 30, "array_lik": 30, "independ": 30, "strictli": 30, "cubic": 30, "sum": 30, "ab": 30, "001": 30, "len": [30, 31], "interpolatedunivariatesplin": 30, "control": 30, "tradeoff": 30, "datapoint": 30, "extrapol": 30, "valueerror": 30, "const": 30, "finit": 30, "disabl": 30, "gain": 30, "crash": 30, "non": [30, 31], "sensic": 30, "infin": 30, "nan": 30, "bivariatesplin": 30, "bivari": 30, "smoothbivariatesplin": 30, "lsqbivariatesplin": 30, "least": 30, "rectspherebivariatesplin": 30, "rectangular": 30, "mesh": 30, "sphere": 30, "smoothspherebivariatesplin": 30, "spheric": 30, "coordin": 30, "lsqspherebivariatesplin": 30, "rectbivariatesplin": 30, "bisplrep": 30, "represent": 30, "surfac": 30, "bisplev": 30, "splrep": 30, "curv": 30, "splev": 30, "sproot": 30, "root": 30, "splint": 30, "spald": 30, "deal": 30, "workaround": 30, "isnan": 30, "matter": 30, "dierckx": 30, "experiment": 30, "comp": 30, "appl": 30, "1975": 30, "165": 30, "184": 30, "grid": 30, "siam": 30, "anal": 30, "19": 30, "1982": 30, "1286": 30, "1304": 30, "improv": 30, "tw54": 30, "dept": 30, "leuven": 30, "1981": 30, "monograph": 30, "oxford": 30, "1993": 30, "rng": 30, "default_rng": 30, "standard_norm": 30, "ro": 30, "lw": 30, "manual": [30, 32], "set_smoothing_factor": 30, "antideriv": 30, "k2": 30, "splantid": 30, "70": 30, "sin": 30, "accumul": 30, "1565429877197317": 30, "1565429877201865": 30, "ispl": 30, "2572053588768486": 30, "ellipt": 30, "int_0": 30, "dx": [30, 31], "ellipk": 30, "2572053268208538": 30, "splder": 30, "maxima": 30, "nb": 30, "50000001": 30, "49999998": 30, "agre": 30, "ndarrai": [30, 31], "get_coeff": 30, "coeffici": 30, "get_knot": 30, "interior": 30, "intern": [30, 31], "get_residu": 30, "caveat": 30, "fitpack": 30, "ppoli": 30, "happen": 30, "coincid": 30, "96": 30, "98": 30, "99": 30, "365470e": 30, "790580e": 30, "204320e": 30, "607270e": 30, "440892e": 30, "616930e": 30, "243000e": 30, "877670e": 30, "520430e": 30, "170770e": 30, "dtype": 30, "float64": 30, "tck": 30, "from_splin": 30, "lb": 30, "ub": 30, "2n": 30, "cost_grad_interpol": 30, "spline_list": 30, "doubl": [30, 31], "cost_interpol": 30, "vec": 30, "aggreg": 30, "paramt": 30, "flatten": 30, "cost_sampl": 30, "fxapprox": 30, "xapprox": 30, "simpson": 30, "rule": 30, "appli": 30, "integrand": 30, "dimens": [30, 31], "residual_sampl": 30, "jtj": 30, "geometri": 30, "fisher": 30, "cov": 30, "nabla_": [30, 31], "moolgavkar1987": 30, "l_path": 30, "u_path": 30, "path": 30, "get_init": 30, "grad_sampl": 30, "output_residu": 30, "jac_sampl": 30, "row": [30, 31], "splinelist": 30, "leastsq": 30, "func": [30, 31], "arg": [30, 31], "dfun": 30, "col_deriv": 30, "ftol": 30, "49012e": 30, "08": 30, "xtol": 30, "gtol": 30, "maxfev": 30, "epsfcn": 30, "diag": 30, "callabl": [30, 31], "possibli": 30, "across": 30, "ier": 30, "transpos": [30, 31], "orthogon": 30, "unsuccess": 30, "cov_x": 30, "fjac": 30, "ipvt": 30, "singular": 30, "curvatur": 30, "flat": 30, "curve_fit": 30, "infodict": 30, "dictionari": [30, 31], "fvec": 30, "permut": 30, "qr": 30, "triangular": 30, "nonincreas": 30, "ident": [30, 31], "qtf": 30, "mesg": 30, "caus": 30, "failur": 30, "flag": 30, "least_squar": 30, "newer": 30, "nonlinear": 30, "lm": 30, "particular": 30, "wrapper": [30, 31], "minpack": 30, "lmdif": 30, "lmder": 30, "ydata": 30, "xdata": 30, "regardless": 30, "99999999": 30, "minimize_scalar": 30, "bracket": 30, "brent": 30, "golden": 30, "tripl": 30, "xa": 30, "xb": 30, "xc": 30, "downhil": 30, "search": 30, "mandatori": 30, "custom": 30, "maxit": 30, "disp": 30, "converg": 30, "show_opt": 30, "optimizeresult": 30, "exit": 30, "descript": 30, "unbound": 30, "minimum": [30, 31], "parabol": 30, "bisect": 30, "x1": 30, "xopt": 30, "x2": 30, "guarante": 30, "global_optim": 30, "librari": [30, 32], "frontend": 30, "kwarg": 30, "except": 30, "shall": 30, "arbitrari": 30, "expand": 30, "teukolski": 30, "vetterl": 30, "flanneri": 30, "recip": 30, "cambridg": 30, "forsyth": 30, "malcolm": 30, "moler": 30, "prentic": 30, "hall": 30, "259": 30, "courier": 30, "corpor": 30, "2013": 30, "9149495908": 30, "28077640403": 30, "28365179850e": 30, "0000002026": 30, "partial": [30, 31], "keyword": 30, "residual_interpol": 30, "simp": 30, "composit": 30, "odd": 30, "quadratur": 30, "quadpack": 30, "fixed_quad": 30, "gaussian": 30, "dblquad": 30, "tplquad": 30, "romb": 30, "cumulative_trapezoid": 30, "cumulative_simpson": 30, "polynomi": 30, "cartwright": 30, "kenneth": 30, "excel": 30, "irregularli": 30, "educ": 30, "arang": 30, "power": 30, "1640": 30, "lambda": [30, 31], "compilecanari": 31, "hold": 31, "compil": 31, "subclass": 31, "watch": 31, "trip": 31, "reset": [31, 32], "direct": 31, "assign": 31, "canari": 31, "rtype": 31, "dfe": 31, "disease_st": 31, "free": 31, "baseodemodel": 31, "diseasest": 31, "birth_death": 31, "state_param": 31, "lagrangian": 31, "mayb": 31, "backward": 31, "adjoint_t": 31, "adjoint_interpol": 31, "adjoint_interpolate_t": 31, "objinput": 31, "adjoint_interpolate_jacobian": 31, "dimension": 31, "adjoint_jacobian": 31, "singl": 31, "adjoint_interpolate_jacobian_t": 31, "adjoint_jacobian_t": 31, "diff_jacobian": 31, "diff_jacobian_t": 31, "eval_diff_jacobian": 31, "mpmath": 31, "eval_forwardforward": 31, "ff": 31, "fact": 31, "3rd": 31, "tensor": 31, "aka": 31, "eval_grad": 31, "grad": 31, "eval_grad_jacobian": 31, "grad_jacobian": 31, "get_grad_jacobian_eqn": 31, "eval_hessian": 31, "sympi": 31, "matrici": 31, "eval_jacobian": 31, "eval_od": 31, "eval_sens_jacobian_st": 31, "sen": 31, "sens_jacobian_st": 31, "eval_sensit": 31, "by_stat": 31, "arrang": 31, "block": 31, "structur": 31, "eval_sensitivityiv": 31, "iv": 31, "x_": 31, "sensitivityiv": 31, "forwardforward": 31, "forwardforward_t": 31, "get_diff_jacobian_eqn": 31, "num": 31, "matric": 31, "deliber": 31, "confus": 31, "param_sub": 31, "file_nam": 31, "digraph": 31, "grad_t": 31, "grad_jacobi": 31, "initial_st": 31, "initial_tim": 31, "integrate2": 31, "vode": 31, "ivod": 31, "stiff": 31, "eigenvalu": 31, "is_stiff": 31, "classifi": 31, "jacobian_t": 31, "jacobian_eigenvalu": 31, "ode_t": 31, "ode_and_forwardforward": 31, "ode_and_forwardforward_t": 31, "odeandforwardforward": 31, "ode_and_forwardforward_jacobian": 31, "ode_and_forwardforward_jacobian_t": 31, "ode_and_sensit": 31, "sensitivity_": 31, "led": 31, "concaten": 31, "ode_and_sensitivityiv": 31, "ode_and_sensitivityiv_t": 31, "ode_and_sensitivityiv_jacobian": 31, "spars": 31, "bystat": 31, "ode_and_sensitivityiv_jacobian_t": 31, "ode_and_sensitivity_t": 31, "ode_and_sensitivity_jacobian": 31, "ode_and_sensitivity_jacobian_t": 31, "odeutil": 31, "latex_output": 31, "onto": 31, "screen": 31, "consol": 31, "word": 31, "ye": 31, "formula": 31, "sens_jacobian_state_t": 31, "2p": 31, "3p": 31, "sensiv": 31, "sensitivityiv_t": 31, "sensitivity_t": 31, "fitzhugh1961": 31, "dv": 31, "influenza_sliarn": 31, "influenza": 31, "brauer2008": 31, "323": 31, "dl": 31, "da": 31, "dn": 31, "legrand2007": 31, "autonom": 31, "convers": 31, "lorenz": 31, "attractor": 31, "rho": 31, "lorenz1963": 31, "dy": 31, "z": 31, "dz": 31, "xy": 31, "volterra": 31, "lotka1920": 31, "cxy": 31, "10000": 31, "lotka_volterra_4st": 31, "grass": 31, "rabbit": 31, "fox": 31, "k_": 31, "db": 31, "150": 31, "odevari": 31, "id": 31, "identifi": 31, "human": 31, "readabl": 31, "ordereddict": 31, "insert": 31, "shallow": 31, "fromkei": 31, "move_to_end": 31, "keyerror": 31, "popitem": 31, "lifo": 31, "fifo": 31, "setdefault": 31, "lack": 31, "diseasestateindex": 31, "getdiseaseprogressionmatric": 31, "getr0givenmatrix": 31, "getr0": 31, "matrixbas": 31, "secondari": 31, "fv": 31, "robertson1966": 31, "dy_": 31, "cdot": 31, "logspac": 31, "1800": 31, "84": 31, "1001": 31, "0658": 31, "0007": 31, "0002": 31, "seir_birth_death": 31, "aron1984": 31, "apart": 31, "seir_birth_death_period": 31, "beta1": 31, "sir_period": 31, "180": 31, "lloyd1996": 31, "de_": 31, "di_": 31, "init": 31, "everyon": 31, "730": 31, "126372": 31, "7781984": 31, "10001": 31, "065": 31, "123": 31, "hethcote1973": 31, "suggest": 31, "outcom": 31, "birth_death_r": 31, "cle": 31, "t1": 31, "output_tim": 31, "euler": 31, "maruyama": 31, "transition_func": 31, "eval_birth_death_r": 31, "setparamet": 31, "eval_transition_matrix": 31, "eval_transition_mean": 31, "eval_transition_var": 31, "eval_transition_vector": 31, "get_bd_from_od": 31, "unrol": 31, "get_birth_death_r": 31, "get_transition_vector": 31, "get_transitions_from_od": 31, "hybrid": 31, "sim_x": 31, "sim_t": 31, "simulate_jump": 31, "unequ": 31, "record": 31, "jump": 31, "switch": 31, "processor": 31, "simulate_param": 31, "y_all": 31, "total_transit": 31, "transition_matrix": 31, "transition_mean": 31, "a_": 31, "v_": 31, "mu_": 31, "transition_var": 31, "transition_vector": 31, "1d": 31, "enum": 31, "throw": 31, "_equat": 31, "is_between_st": 31, "feasibl": 31, "check_array_typ": 31, "accept_boolean": 31, "check_dimens": 31, "compilecod": 31, "compileexpr": 31, "inputsymb": 31, "inputexpr": 31, "compiletyp": 31, "expr": 31, "compileexprandformat": 31, "outtyp": 31, "transform": 31, "against": 31, "closur": 31, "diff": 31, "integratefuncjac": 31, "includeorigin": 31, "nstep": 31, "pick": 31, "correct": 31, "j_": 31, "availbl": 31, "ev": 31, "maxev": 31, "minev": 31, "suc": 31, "is_list_lik": 31, "behav": 31, "anyth": 31, "plot_det": 31, "ystatelist": 31, "plot_stoc": 31, "stochastic_model": 31, "stocast": 31, "shapeadjust": 31, "numstat": 31, "numparam": 31, "numtarget": 31, "vice": 31, "versa": 31, "kronparam": 31, "otim": 31, "kron": 31, "kronstat": 31, "mattovecff": 31, "mattovecsen": 31, "vectomatff": 31, "vectomatsen": 31, "str_or_list": 31, "vanderpol1926": 31, "prime": 31, "dbeta": 32, "shape1": 32, "shape2": 32, "stat": 32, "ethz": 32, "ch": 32, "dbinom": 32, "prob": 32, "dchisq": 32, "chisquar": 32, "dexp": 32, "dgamma": 32, "gammadist": 32, "dmvnorm": 32, "rdocument": 32, "mvtnorm": 32, "topic": 32, "mvnorm": 32, "dnbinom": 32, "devel": 32, "negbinomi": 32, "dnorm": 32, "sd": 32, "dpoi": 32, "dunif": 32, "max": 32, "gamma_mu_shap": 32, "pdf": 32, "distrbut": 32, "pmf": 32, "ln": 32, "nb2pmf": 32, "often": 32, "lpha": 32, "mathcalp": 32, "xright": 32, "kright": 32, "pbinom": 32, "pchisq": 32, "pexp": 32, "pgamma": 32, "pnbinom": 32, "lower_tail": 32, "pnorm": 32, "ppoi": 32, "punif": 32, "qbeta": 32, "qbinom": 32, "qchisq": 32, "qexp": 32, "qgamma": 32, "qnbinom": 32, "qnorm": 32, "qpoi": 32, "qunif": 32, "rbeta": 32, "rbinom": 32, "randomst": 32, "rchisq": 32, "rexp": 32, "rmvnorm": 32, "rnorm": 32, "rpoi": 32, "runif": 32, "test_se": 32, "global": 32}, "objects": {"pygom": [[29, 0, 0, "-", "approximate_bayesian_computation"], [30, 0, 0, "-", "loss"], [31, 0, 0, "-", "model"], [32, 0, 0, "-", "utilR"]], "pygom.approximate_bayesian_computation": [[29, 1, 1, "", "ABC"], [29, 1, 1, "", "Parameter"], [29, 3, 1, "", "create_loss"], [29, 3, 1, "", "get_function"]], "pygom.approximate_bayesian_computation.ABC": [[29, 2, 1, "", "continue_posterior_sample"], [29, 2, 1, "", "get_posterior_sample"], [29, 2, 1, "", "get_posterior_sample_original"], [29, 2, 1, "", "get_tolerance"], [29, 2, 1, "", "plot_pointwise_predictions"], [29, 2, 1, "", "plot_posterior_histograms"], [29, 2, 1, "", "plot_scatter"], [29, 2, 1, "", "sigma_nearest_neighbours"]], "pygom.loss": [[30, 1, 1, "", "Gamma"], [30, 1, 1, "", "GammaLoss"], [30, 1, 1, "", "NegBinom"], [30, 1, 1, "", "NegBinomLoss"], [30, 1, 1, "", "Normal"], [30, 1, 1, "", "NormalLoss"], [30, 1, 1, "", "Poisson"], [30, 1, 1, "", "PoissonLoss"], [30, 1, 1, "", "Square"], [30, 1, 1, "", "SquareLoss"], [30, 1, 1, "", "UnivariateSpline"], [30, 3, 1, "", "asymptotic"], [30, 3, 1, "", "bootstrap"], [30, 3, 1, "", "cost_grad_interpolant"], [30, 3, 1, "", "cost_interpolant"], [30, 3, 1, "", "cost_sample"], [30, 3, 1, "", "geometric"], [30, 3, 1, "", "get_init"], [30, 3, 1, "", "grad_sample"], [30, 3, 1, "", "interpolate"], [30, 3, 1, "", "jac_sample"], [30, 3, 1, "", "leastsq"], [30, 3, 1, "", "minimize_scalar"], [30, 1, 1, "", "partial"], [30, 3, 1, "", "profile"], [30, 3, 1, "", "residual_interpolant"], [30, 3, 1, "", "residual_sample"], [30, 3, 1, "", "simps"]], "pygom.loss.Gamma": [[30, 2, 1, "", "diff2Loss"], [30, 2, 1, "", "diff_loss"], [30, 2, 1, "", "loss"]], "pygom.loss.NegBinom": [[30, 2, 1, "", "diff2Loss"], [30, 2, 1, "", "diff_loss"], [30, 2, 1, "", "loss"]], "pygom.loss.Normal": [[30, 2, 1, "", "diff2Loss"], [30, 2, 1, "", "diff_loss"], [30, 2, 1, "", "loss"]], "pygom.loss.Poisson": [[30, 2, 1, "", "diff2Loss"], [30, 2, 1, "", "diff_loss"], [30, 2, 1, "", "loss"]], "pygom.loss.Square": [[30, 2, 1, "", "diff2Loss"], [30, 2, 1, "", "diff_loss"], [30, 2, 1, "", "loss"]], "pygom.loss.UnivariateSpline": [[30, 2, 1, "", "antiderivative"], [30, 2, 1, "", "derivative"], [30, 2, 1, "", "derivatives"], [30, 2, 1, "", "get_coeffs"], [30, 2, 1, "", "get_knots"], [30, 2, 1, "", "get_residual"], [30, 2, 1, "", "integral"], [30, 2, 1, "", "roots"], [30, 2, 1, "", "set_smoothing_factor"]], "pygom.loss.partial": [[30, 4, 1, "", "args"], [30, 4, 1, "", "func"], [30, 4, 1, "", "keywords"]], "pygom.model": [[31, 1, 1, "", "CompileCanary"], [31, 3, 1, "", "DFE"], [31, 1, 1, "", "DeterministicOde"], [31, 3, 1, "", "FitzHugh"], [31, 3, 1, "", "Influenza_SLIARN"], [31, 3, 1, "", "Legrand_Ebola_SEIHFR"], [31, 3, 1, "", "Lorenz"], [31, 3, 1, "", "Lotka_Volterra"], [31, 3, 1, "", "Lotka_Volterra_4State"], [31, 1, 1, "", "ODEVariable"], [31, 1, 1, "", "OrderedDict"], [31, 3, 1, "", "R0"], [31, 3, 1, "", "R0_from_matrix"], [31, 3, 1, "", "Robertson"], [31, 3, 1, "", "SEIR"], [31, 3, 1, "", "SEIR_Birth_Death"], [31, 3, 1, "", "SEIR_Birth_Death_Periodic"], [31, 3, 1, "", "SEIR_Multiple"], [31, 3, 1, "", "SEIR_N"], [31, 3, 1, "", "SIR"], [31, 3, 1, "", "SIR_Birth_Death"], [31, 3, 1, "", "SIR_norm"], [31, 3, 1, "", "SIS"], [31, 3, 1, "", "SIS_Periodic"], [31, 1, 1, "", "SimulateOde"], [31, 1, 1, "", "Transition"], [31, 1, 1, "", "TransitionType"], [31, 3, 1, "", "check_array_type"], [31, 3, 1, "", "check_dimension"], [31, 1, 1, "", "compileCode"], [31, 3, 1, "", "disease_progression_matrices"], [31, 3, 1, "", "integrate"], [31, 3, 1, "", "integrateFuncJac"], [31, 3, 1, "", "is_list_like"], [31, 3, 1, "", "plot_det"], [31, 3, 1, "", "plot_stoc"], [31, 1, 1, "", "shapeAdjust"], [31, 3, 1, "", "str_or_list"], [31, 3, 1, "", "vanDerPol"]], "pygom.model.CompileCanary": [[31, 2, 1, "", "reset"], [31, 2, 1, "", "trip"]], "pygom.model.DeterministicOde": [[31, 2, 1, "", "adjoint"], [31, 2, 1, "", "adjoint_T"], [31, 2, 1, "", "adjoint_interpolate"], [31, 2, 1, "", "adjoint_interpolate_T"], [31, 2, 1, "", "adjoint_interpolate_jacobian"], [31, 2, 1, "", "adjoint_interpolate_jacobian_T"], [31, 2, 1, "", "adjoint_jacobian"], [31, 2, 1, "", "adjoint_jacobian_T"], [31, 2, 1, "", "diff_jacobian"], [31, 2, 1, "", "diff_jacobian_T"], [31, 2, 1, "", "eval_diff_jacobian"], [31, 2, 1, "", "eval_forwardforward"], [31, 2, 1, "", "eval_grad"], [31, 2, 1, "", "eval_grad_jacobian"], [31, 2, 1, "", "eval_hessian"], [31, 2, 1, "", "eval_jacobian"], [31, 2, 1, "", "eval_ode"], [31, 2, 1, "", "eval_sens_jacobian_state"], [31, 2, 1, "", "eval_sensitivity"], [31, 2, 1, "", "eval_sensitivityIV"], [31, 2, 1, "", "forwardforward"], [31, 2, 1, "", "forwardforward_T"], [31, 2, 1, "", "get_diff_jacobian_eqn"], [31, 2, 1, "", "get_grad_eqn"], [31, 2, 1, "", "get_grad_jacobian_eqn"], [31, 2, 1, "", "get_hessian_eqn"], [31, 2, 1, "", "get_jacobian_eqn"], [31, 2, 1, "", "get_ode_eqn"], [31, 2, 1, "", "get_transition_graph"], [31, 2, 1, "", "grad"], [31, 2, 1, "", "grad_T"], [31, 2, 1, "", "grad_jacobian"], [31, 2, 1, "", "grad_jacobianT"], [31, 2, 1, "", "hessian"], [31, 5, 1, "", "initial_state"], [31, 5, 1, "", "initial_time"], [31, 5, 1, "", "initial_values"], [31, 2, 1, "", "integrate"], [31, 2, 1, "", "integrate2"], [31, 2, 1, "", "is_stiff"], [31, 2, 1, "", "jacobian"], [31, 2, 1, "", "jacobian_T"], [31, 2, 1, "", "jacobian_eigenvalue"], [31, 2, 1, "", "linear_ode"], [31, 2, 1, "", "ode"], [31, 2, 1, "", "ode_T"], [31, 2, 1, "", "ode_and_forwardforward"], [31, 2, 1, "", "ode_and_forwardforward_T"], [31, 2, 1, "", "ode_and_forwardforward_jacobian"], [31, 2, 1, "", "ode_and_forwardforward_jacobian_T"], [31, 2, 1, "", "ode_and_sensitivity"], [31, 2, 1, "", "ode_and_sensitivityIV"], [31, 2, 1, "", "ode_and_sensitivityIV_T"], [31, 2, 1, "", "ode_and_sensitivityIV_jacobian"], [31, 2, 1, "", "ode_and_sensitivityIV_jacobian_T"], [31, 2, 1, "", "ode_and_sensitivity_T"], [31, 2, 1, "", "ode_and_sensitivity_jacobian"], [31, 2, 1, "", "ode_and_sensitivity_jacobian_T"], [31, 2, 1, "", "plot"], [31, 2, 1, "", "print_ode"], [31, 2, 1, "", "sens_jacobian_state"], [31, 2, 1, "", "sens_jacobian_state_T"], [31, 2, 1, "", "sensitivity"], [31, 2, 1, "", "sensitivityIV"], [31, 2, 1, "", "sensitivityIV_T"], [31, 2, 1, "", "sensitivity_T"]], "pygom.model.OrderedDict": [[31, 2, 1, "", "clear"], [31, 2, 1, "", "copy"], [31, 2, 1, "", "fromkeys"], [31, 2, 1, "", "items"], [31, 2, 1, "", "keys"], [31, 2, 1, "", "move_to_end"], [31, 2, 1, "", "pop"], [31, 2, 1, "", "popitem"], [31, 2, 1, "", "setdefault"], [31, 2, 1, "", "update"], [31, 2, 1, "", "values"]], "pygom.model.SimulateOde": [[31, 2, 1, "", "birth_death_rate"], [31, 2, 1, "", "cle"], [31, 2, 1, "", "eval_birth_death_rate"], [31, 2, 1, "", "eval_transition_matrix"], [31, 2, 1, "", "eval_transition_mean"], [31, 2, 1, "", "eval_transition_var"], [31, 2, 1, "", "eval_transition_vector"], [31, 2, 1, "", "exact"], [31, 2, 1, "", "get_bd_from_ode"], [31, 2, 1, "", "get_birth_death_rate"], [31, 2, 1, "", "get_transition_matrix"], [31, 2, 1, "", "get_transition_vector"], [31, 2, 1, "", "get_transitions_from_ode"], [31, 2, 1, "", "get_unrolled_obj"], [31, 2, 1, "", "hybrid"], [31, 2, 1, "", "plot"], [31, 2, 1, "", "simulate_jump"], [31, 2, 1, "", "simulate_param"], [31, 2, 1, "", "solve_determ"], [31, 2, 1, "", "solve_stochast"], [31, 2, 1, "", "total_transition"], [31, 2, 1, "", "transition_matrix"], [31, 2, 1, "", "transition_mean"], [31, 2, 1, "", "transition_var"], [31, 2, 1, "", "transition_vector"]], "pygom.model.Transition": [[31, 5, 1, "", "destination"], [31, 5, 1, "", "equation"], [31, 2, 1, "", "is_between_state"], [31, 5, 1, "", "origin"], [31, 5, 1, "", "transition_type"]], "pygom.model.compileCode": [[31, 2, 1, "", "compileExpr"], [31, 2, 1, "", "compileExprAndFormat"]], "pygom.model.shapeAdjust": [[31, 2, 1, "", "kronParam"], [31, 2, 1, "", "kronState"], [31, 2, 1, "", "matToVecFF"], [31, 2, 1, "", "matToVecSens"], [31, 2, 1, "", "vecToMatFF"], [31, 2, 1, "", "vecToMatSens"]], "pygom.utilR": [[32, 3, 1, "", "dbeta"], [32, 3, 1, "", "dbinom"], [32, 3, 1, "", "dchisq"], [32, 3, 1, "", "dexp"], [32, 3, 1, "", "dgamma"], [32, 3, 1, "", "dmvnorm"], [32, 3, 1, "", "dnbinom"], [32, 3, 1, "", "dnorm"], [32, 3, 1, "", "dpois"], [32, 3, 1, "", "dunif"], [32, 3, 1, "", "gamma_mu_shape"], [32, 3, 1, "", "nb2pmf"], [32, 3, 1, "", "pbinom"], [32, 3, 1, "", "pchisq"], [32, 3, 1, "", "pexp"], [32, 3, 1, "", "pgamma"], [32, 3, 1, "", "pnbinom"], [32, 3, 1, "", "pnorm"], [32, 3, 1, "", "ppois"], [32, 3, 1, "", "punif"], [32, 3, 1, "", "qbeta"], [32, 3, 1, "", "qbinom"], [32, 3, 1, "", "qchisq"], [32, 3, 1, "", "qexp"], [32, 3, 1, "", "qgamma"], [32, 3, 1, "", "qnbinom"], [32, 3, 1, "", "qnorm"], [32, 3, 1, "", "qpois"], [32, 3, 1, "", "qunif"], [32, 3, 1, "", "rbeta"], [32, 3, 1, "", "rbinom"], [32, 3, 1, "", "rchisq"], [32, 3, 1, "", "rexp"], [32, 3, 1, "", "rgamma"], [32, 3, 1, "", "rmvnorm"], [32, 3, 1, "", "rnorm"], [32, 3, 1, "", "rpois"], [32, 3, 1, "", "runif"], [32, 3, 1, "", "test_seed"]]}, "objtypes": {"0": "py:module", "1": "py:class", "2": "py:method", "3": "py:function", "4": "py:attribute", "5": "py:property"}, "objnames": {"0": ["py", "module", "Python module"], "1": ["py", "class", "Python class"], "2": ["py", "method", "Python method"], "3": ["py", "function", "Python function"], "4": ["py", "attribute", "Python attribute"], "5": ["py", "property", "Python property"]}, "titleterms": {"bibliographi": 0, "build": 1, "document": [1, 5], "local": 1, "pre": 2, "defin": [2, 23], "exampl": [2, 23, 26], "common": 2, "epi": 2, "model": [2, 19, 23, 25, 26, 28, 31], "frequent": 3, "ask": 3, "question": 3, "why": 3, "doe": [3, 5], "code": 3, "run": 3, "slowli": 3, "compil": 3, "numer": 3, "comput": [3, 25], "form": 3, "sympi": 3, "against": 3, "theano": 3, "us": [3, 5, 18], "mpmath": 3, "librari": 3, "throughout": 3, "i": [3, 5, 26], "gradient": [3, 26], "squareloss": 3, "slow": 3, "some": 3, "my": 3, "fortran": 3, "object": 3, "can": 3, "you": 3, "convert": 3, "non": 3, "autonum": 3, "system": [3, 23], "an": [3, 23, 25], "autonom": 3, "me": 3, "automat": 3, "get": 3, "sensit": 3, "from": [3, 4, 28], "did": 3, "speed": 3, "up": 3, "when": 3, "restrict": 3, "set": 3, "paramet": [3, 6, 21, 22, 24, 25, 26, 27, 29], "do": [3, 5], "have": 3, "option": 3, "obtain": 3, "via": 3, "complex": 3, "differenc": 3, "instal": 4, "sourc": 4, "pypi": 4, "test": 4, "packag": [4, 5], "welcom": 5, "pygom": [5, 23], "what": 5, "thi": 5, "new": 5, "releas": 5, "contribut": 5, "fit": [6, 25], "produc": 7, "forecast": 7, "fitzhugh": 8, "legrand": 9, "ebola": 9, "seihfr": 9, "lotka": 10, "volterra": 10, "seir": [11, 12, 13, 25, 26], "birth": [12, 15, 28], "death": [12, 15, 28], "period": [12, 17], "wane": 12, "introduct": 12, "multipl": 13, "sir": [14, 15, 23, 25, 28], "si": [16, 17], "read": 18, "epijson": 18, "data": 18, "extract": 19, "inform": 19, "verif": 19, "algebra": 19, "insight": [19, 20], "epidemiologi": 19, "specif": 19, "od": [20, 22, 23], "parameteris": 21, "fix": [21, 22], "random": [21, 22], "find": 22, "solut": 22, "determinist": 22, "evolut": 22, "stochast": 22, "summari": 22, "equat": [23, 28], "v": 23, "transit": [23, 28], "modifi": 23, "solv": 24, "boundari": 24, "valu": 24, "problem": 24, "unknown": 24, "initi": [24, 25], "condit": [24, 25], "estim": [25, 26], "approxim": 25, "bayesian": 25, "infect": 25, "remov": 25, "known": [25, 26], "onli": 25, "maximum": 26, "likelihood": 26, "r": 26, "calcul": 26, "optimis": 26, "result": 26, "confid": 26, "interv": 26, "time": 27, "depend": 27, "deduc": 28, "sliar": 28, "epidem": 28, "approximate_bayesian_comput": 29, "same": 29, "get_posterior_sampl": 29, "see": 29, "also": 29, "class": 29, "baseloss": 29, "loss": 30, "utilr": 32}, "envversion": {"sphinx.domains.c": 2, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 8, "sphinx.domains.index": 1, "sphinx.domains.javascript": 2, "sphinx.domains.math": 2, "sphinx.domains.python": 3, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.intersphinx": 1, "sphinx.ext.viewcode": 1, "sphinxcontrib.bibtex": 9, "sphinx": 57}, "alltitles": {"Bibliography": [[0, "bibliography"]], "Building the documentation locally": [[1, "building-the-documentation-locally"]], "Pre-defined examples - common epi models": [[2, "pre-defined-examples-common-epi-models"]], "Frequently asked questions": [[3, "frequently-asked-questions"]], "Why does code run slowly?": [[3, "why-does-code-run-slowly"]], "Why not compile the numeric computation form sympy against Theano?": [[3, "why-not-compile-the-numeric-computation-form-sympy-against-theano"]], "Why not use mpmath library throughout?": [[3, "why-not-use-mpmath-library-throughout"]], "Why is computing the gradient using SquareLoss slow?": [[3, "why-is-computing-the-gradient-using-squareloss-slow"]], "Why is some of my code not a fortran object?": [[3, "why-is-some-of-my-code-not-a-fortran-object"]], "Can you not convert a non-autonumous system to an autonomous system for me automatically?": [[3, "can-you-not-convert-a-non-autonumous-system-to-an-autonomous-system-for-me-automatically"]], "Getting the sensitivities from SquareLoss did not get a speed up when I used a restricted set of parameters": [[3, "getting-the-sensitivities-from-squareloss-did-not-get-a-speed-up-when-i-used-a-restricted-set-of-parameters"]], "Why do not have the option to obtain gradient via complex differencing?": [[3, "why-do-not-have-the-option-to-obtain-gradient-via-complex-differencing"]], "Installation": [[4, "installation"]], "From source": [[4, "from-source"]], "From PyPI": [[4, "from-pypi"]], "Testing the package": [[4, "testing-the-package"]], "Welcome to the documentation for PyGOM": [[5, "welcome-to-the-documentation-for-pygom"]], "What does this package do?": [[5, "what-does-this-package-do"]], "What is new in this release?": [[5, "what-is-new-in-this-release"]], "Using this documentation": [[5, "using-this-documentation"]], "Contributing to PyGOM": [[5, "contributing-to-pygom"]], "Parameter fitting": [[6, "parameter-fitting"]], "Producing forecasts": [[7, "producing-forecasts"]], "FitzHugh": [[8, "fitzhugh"]], "Legrand Ebola SEIHFR": [[9, "legrand-ebola-seihfr"]], "Lotka Volterra": [[10, "lotka-volterra"]], "SEIR": [[11, "seir"]], "SEIR, birth, death, periodic, waning and introductions": [[12, "seir-birth-death-periodic-waning-and-introductions"]], "SEIR, multiple": [[13, "seir-multiple"]], "SIR": [[14, "sir"]], "SIR, birth and death": [[15, "sir-birth-and-death"]], "SIS": [[16, "sis"]], "SIS, periodic": [[17, "sis-periodic"]], "Reading and using EpiJSON data": [[18, "reading-and-using-epijson-data"]], "Extracting model information": [[19, "extracting-model-information"]], "Verification": [[19, "verification"]], "Algebraic insights": [[19, "algebraic-insights"]], "Epidemiology specific insights": [[19, "epidemiology-specific-insights"]], "ODE Insights": [[20, "ode-insights"]], "Parameterisation": [[21, "parameterisation"]], "Fixed parameters": [[21, "fixed-parameters"], [22, "fixed-parameters"], [22, "id3"]], "Random parameters": [[21, "random-parameters"], [22, "random-parameters"], [22, "id4"]], "Finding ODE solutions": [[22, "finding-ode-solutions"]], "Deterministic evolution": [[22, "deterministic-evolution"]], "Stochastic evolution": [[22, "stochastic-evolution"]], "Summary": [[22, "summary"]], "Defining an ODE system": [[23, "defining-an-ode-system"]], "Equations vs Transitions": [[23, "equations-vs-transitions"]], "Example: SIR model": [[23, "example-sir-model"]], "Defining the model with PyGOM": [[23, "defining-the-model-with-pygom"]], "Modifying models": [[23, "modifying-models"]], "Solving Boundary Value Problems": [[24, "solving-boundary-value-problems"]], "Problem": [[24, "problem"]], "Unknown initial conditions": [[24, "unknown-initial-conditions"]], "Unknown parameters": [[24, "unknown-parameters"]], "Parameter Estimation: Approximate Bayesian Computation": [[25, "parameter-estimation-approximate-bayesian-computation"]], "Fitting an SEIR model (with Infected and Removed known)": [[25, "fitting-an-seir-model-with-infected-and-removed-known"]], "Fitting an SEIR model (with only Infected known)": [[25, "fitting-an-seir-model-with-only-infected-known"]], "Fitting an SIR model (with only Infected known)": [[25, "fitting-an-sir-model-with-only-infected-known"]], "Initial conditions": [[25, "initial-conditions"]], "Parameter Estimation: Maximum likelihood": [[26, "parameter-estimation-maximum-likelihood"]], "Example: SEIR model (with I and R known)": [[26, "example-seir-model-with-i-and-r-known"]], "Gradient calculations": [[26, "gradient-calculations"]], "Optimised result": [[26, "optimised-result"]], "Confidence intervals of estimated parameters": [[26, "confidence-intervals-of-estimated-parameters"]], "Time dependent parameters": [[27, "time-dependent-parameters"]], "Deducing transitions from equations": [[28, "deducing-transitions-from-equations"]], "SIR with births and deaths": [[28, "sir-with-births-and-deaths"]], "SLIAR epidemic model": [[28, "sliar-epidemic-model"]], "approximate_bayesian_computation": [[29, "module-pygom.approximate_bayesian_computation"]], "Parameters (same as get_posterior_sample)": [[29, "parameters-same-as-get-posterior-sample"]], "Parameters (see also class BaseLoss)": [[29, "parameters-see-also-class-baseloss"]], "loss": [[30, "module-pygom.loss"]], "model": [[31, "module-pygom.model"]], "utilR": [[32, "module-pygom.utilR"]]}, "indexentries": {"abc (class in pygom.approximate_bayesian_computation)": [[29, "pygom.approximate_bayesian_computation.ABC"]], "parameter (class in pygom.approximate_bayesian_computation)": [[29, "pygom.approximate_bayesian_computation.Parameter"]], "continue_posterior_sample() (pygom.approximate_bayesian_computation.abc method)": [[29, "pygom.approximate_bayesian_computation.ABC.continue_posterior_sample"]], "create_loss() (in module pygom.approximate_bayesian_computation)": [[29, "pygom.approximate_bayesian_computation.create_loss"]], "get_function() (in module pygom.approximate_bayesian_computation)": [[29, "pygom.approximate_bayesian_computation.get_function"]], "get_posterior_sample() (pygom.approximate_bayesian_computation.abc method)": [[29, "pygom.approximate_bayesian_computation.ABC.get_posterior_sample"]], "get_posterior_sample_original() (pygom.approximate_bayesian_computation.abc method)": [[29, "pygom.approximate_bayesian_computation.ABC.get_posterior_sample_original"]], "get_tolerance() (pygom.approximate_bayesian_computation.abc method)": [[29, "pygom.approximate_bayesian_computation.ABC.get_tolerance"]], "module": [[29, "module-pygom.approximate_bayesian_computation"], [30, "module-pygom.loss"], [31, "module-pygom.model"], [32, "module-pygom.utilR"]], "plot_pointwise_predictions() (pygom.approximate_bayesian_computation.abc method)": [[29, "pygom.approximate_bayesian_computation.ABC.plot_pointwise_predictions"]], "plot_posterior_histograms() (pygom.approximate_bayesian_computation.abc method)": [[29, "pygom.approximate_bayesian_computation.ABC.plot_posterior_histograms"]], "plot_scatter() (pygom.approximate_bayesian_computation.abc method)": [[29, "pygom.approximate_bayesian_computation.ABC.plot_scatter"]], "pygom.approximate_bayesian_computation": [[29, "module-pygom.approximate_bayesian_computation"]], "sigma_nearest_neighbours() (pygom.approximate_bayesian_computation.abc method)": [[29, "pygom.approximate_bayesian_computation.ABC.sigma_nearest_neighbours"]], "gamma (class in pygom.loss)": [[30, "pygom.loss.Gamma"]], "gammaloss (class in pygom.loss)": [[30, "pygom.loss.GammaLoss"]], "negbinom (class in pygom.loss)": [[30, "pygom.loss.NegBinom"]], "negbinomloss (class in pygom.loss)": [[30, "pygom.loss.NegBinomLoss"]], "normal (class in pygom.loss)": [[30, "pygom.loss.Normal"]], "normalloss (class in pygom.loss)": [[30, "pygom.loss.NormalLoss"]], "poisson (class in pygom.loss)": [[30, "pygom.loss.Poisson"]], "poissonloss (class in pygom.loss)": [[30, "pygom.loss.PoissonLoss"]], "square (class in pygom.loss)": [[30, "pygom.loss.Square"]], "squareloss (class in pygom.loss)": [[30, "pygom.loss.SquareLoss"]], "univariatespline (class in pygom.loss)": [[30, "pygom.loss.UnivariateSpline"]], "antiderivative() (pygom.loss.univariatespline method)": [[30, "pygom.loss.UnivariateSpline.antiderivative"]], "args (pygom.loss.partial attribute)": [[30, "pygom.loss.partial.args"]], "asymptotic() (in module pygom.loss)": [[30, "pygom.loss.asymptotic"]], "bootstrap() (in module pygom.loss)": [[30, "pygom.loss.bootstrap"]], "cost_grad_interpolant() (in module pygom.loss)": [[30, "pygom.loss.cost_grad_interpolant"]], "cost_interpolant() (in module pygom.loss)": [[30, "pygom.loss.cost_interpolant"]], "cost_sample() (in module pygom.loss)": [[30, "pygom.loss.cost_sample"]], "derivative() (pygom.loss.univariatespline method)": [[30, "pygom.loss.UnivariateSpline.derivative"]], "derivatives() (pygom.loss.univariatespline method)": [[30, "pygom.loss.UnivariateSpline.derivatives"]], "diff2loss() (pygom.loss.gamma method)": [[30, "pygom.loss.Gamma.diff2Loss"]], "diff2loss() (pygom.loss.negbinom method)": [[30, "pygom.loss.NegBinom.diff2Loss"]], "diff2loss() (pygom.loss.normal method)": [[30, "pygom.loss.Normal.diff2Loss"]], "diff2loss() (pygom.loss.poisson method)": [[30, "pygom.loss.Poisson.diff2Loss"]], "diff2loss() (pygom.loss.square method)": [[30, "pygom.loss.Square.diff2Loss"]], "diff_loss() (pygom.loss.gamma method)": [[30, "pygom.loss.Gamma.diff_loss"]], "diff_loss() (pygom.loss.negbinom method)": [[30, "pygom.loss.NegBinom.diff_loss"]], "diff_loss() (pygom.loss.normal method)": [[30, "pygom.loss.Normal.diff_loss"]], "diff_loss() (pygom.loss.poisson method)": [[30, "pygom.loss.Poisson.diff_loss"]], "diff_loss() (pygom.loss.square method)": [[30, "pygom.loss.Square.diff_loss"]], "func (pygom.loss.partial attribute)": [[30, "pygom.loss.partial.func"]], "geometric() (in module pygom.loss)": [[30, "pygom.loss.geometric"]], "get_coeffs() (pygom.loss.univariatespline method)": [[30, "pygom.loss.UnivariateSpline.get_coeffs"]], "get_init() (in module pygom.loss)": [[30, "pygom.loss.get_init"]], "get_knots() (pygom.loss.univariatespline method)": [[30, "pygom.loss.UnivariateSpline.get_knots"]], "get_residual() (pygom.loss.univariatespline method)": [[30, "pygom.loss.UnivariateSpline.get_residual"]], "grad_sample() (in module pygom.loss)": [[30, "pygom.loss.grad_sample"]], "integral() (pygom.loss.univariatespline method)": [[30, "pygom.loss.UnivariateSpline.integral"]], "interpolate() (in module pygom.loss)": [[30, "pygom.loss.interpolate"]], "jac_sample() (in module pygom.loss)": [[30, "pygom.loss.jac_sample"]], "keywords (pygom.loss.partial attribute)": [[30, "pygom.loss.partial.keywords"]], "leastsq() (in module pygom.loss)": [[30, "pygom.loss.leastsq"]], "loss() (pygom.loss.gamma method)": [[30, "pygom.loss.Gamma.loss"]], "loss() (pygom.loss.negbinom method)": [[30, "pygom.loss.NegBinom.loss"]], "loss() (pygom.loss.normal method)": [[30, "pygom.loss.Normal.loss"]], "loss() (pygom.loss.poisson method)": [[30, "pygom.loss.Poisson.loss"]], "loss() (pygom.loss.square method)": [[30, "pygom.loss.Square.loss"]], "minimize_scalar() (in module pygom.loss)": [[30, "pygom.loss.minimize_scalar"]], "partial (class in pygom.loss)": [[30, "pygom.loss.partial"]], "profile() (in module pygom.loss)": [[30, "pygom.loss.profile"]], "pygom.loss": [[30, "module-pygom.loss"]], "residual_interpolant() (in module pygom.loss)": [[30, "pygom.loss.residual_interpolant"]], "residual_sample() (in module pygom.loss)": [[30, "pygom.loss.residual_sample"]], "roots() (pygom.loss.univariatespline method)": [[30, "pygom.loss.UnivariateSpline.roots"]], "set_smoothing_factor() (pygom.loss.univariatespline method)": [[30, "pygom.loss.UnivariateSpline.set_smoothing_factor"]], "simps() (in module pygom.loss)": [[30, "pygom.loss.simps"]], "compilecanary (class in pygom.model)": [[31, "pygom.model.CompileCanary"]], "dfe() (in module pygom.model)": [[31, "pygom.model.DFE"]], "deterministicode (class in pygom.model)": [[31, "pygom.model.DeterministicOde"]], "fitzhugh() (in module pygom.model)": [[31, "pygom.model.FitzHugh"]], "influenza_sliarn() (in module pygom.model)": [[31, "pygom.model.Influenza_SLIARN"]], "legrand_ebola_seihfr() (in module pygom.model)": [[31, "pygom.model.Legrand_Ebola_SEIHFR"]], "lorenz() (in module pygom.model)": [[31, "pygom.model.Lorenz"]], "lotka_volterra() (in module pygom.model)": [[31, "pygom.model.Lotka_Volterra"]], "lotka_volterra_4state() (in module pygom.model)": [[31, "pygom.model.Lotka_Volterra_4State"]], "odevariable (class in pygom.model)": [[31, "pygom.model.ODEVariable"]], "ordereddict (class in pygom.model)": [[31, "pygom.model.OrderedDict"]], "r0() (in module pygom.model)": [[31, "pygom.model.R0"]], "r0_from_matrix() (in module pygom.model)": [[31, "pygom.model.R0_from_matrix"]], "robertson() (in module pygom.model)": [[31, "pygom.model.Robertson"]], "seir() (in module pygom.model)": [[31, "pygom.model.SEIR"]], "seir_birth_death() (in module pygom.model)": [[31, "pygom.model.SEIR_Birth_Death"]], "seir_birth_death_periodic() (in module pygom.model)": [[31, "pygom.model.SEIR_Birth_Death_Periodic"]], "seir_multiple() (in module pygom.model)": [[31, "pygom.model.SEIR_Multiple"]], "seir_n() (in module pygom.model)": [[31, "pygom.model.SEIR_N"]], "sir() (in module pygom.model)": [[31, "pygom.model.SIR"]], "sir_birth_death() (in module pygom.model)": [[31, "pygom.model.SIR_Birth_Death"]], "sir_norm() (in module pygom.model)": [[31, "pygom.model.SIR_norm"]], "sis() (in module pygom.model)": [[31, "pygom.model.SIS"]], "sis_periodic() (in module pygom.model)": [[31, "pygom.model.SIS_Periodic"]], "simulateode (class in pygom.model)": [[31, "pygom.model.SimulateOde"]], "transition (class in pygom.model)": [[31, "pygom.model.Transition"]], "transitiontype (class in pygom.model)": [[31, "pygom.model.TransitionType"]], "adjoint() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.adjoint"]], "adjoint_t() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.adjoint_T"]], "adjoint_interpolate() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.adjoint_interpolate"]], "adjoint_interpolate_t() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.adjoint_interpolate_T"]], "adjoint_interpolate_jacobian() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.adjoint_interpolate_jacobian"]], "adjoint_interpolate_jacobian_t() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.adjoint_interpolate_jacobian_T"]], "adjoint_jacobian() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.adjoint_jacobian"]], "adjoint_jacobian_t() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.adjoint_jacobian_T"]], "birth_death_rate() (pygom.model.simulateode method)": [[31, "pygom.model.SimulateOde.birth_death_rate"]], "check_array_type() (in module pygom.model)": [[31, "pygom.model.check_array_type"]], "check_dimension() (in module pygom.model)": [[31, "pygom.model.check_dimension"]], "cle() (pygom.model.simulateode method)": [[31, "pygom.model.SimulateOde.cle"]], "clear() (pygom.model.ordereddict method)": [[31, "pygom.model.OrderedDict.clear"]], "compilecode (class in pygom.model)": [[31, "pygom.model.compileCode"]], "compileexpr() (pygom.model.compilecode method)": [[31, "pygom.model.compileCode.compileExpr"]], "compileexprandformat() (pygom.model.compilecode method)": [[31, "pygom.model.compileCode.compileExprAndFormat"]], "copy() (pygom.model.ordereddict method)": [[31, "pygom.model.OrderedDict.copy"]], "destination (pygom.model.transition property)": [[31, "pygom.model.Transition.destination"]], "diff_jacobian() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.diff_jacobian"]], "diff_jacobian_t() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.diff_jacobian_T"]], "disease_progression_matrices() (in module pygom.model)": [[31, "pygom.model.disease_progression_matrices"]], "equation (pygom.model.transition property)": [[31, "pygom.model.Transition.equation"]], "eval_birth_death_rate() (pygom.model.simulateode method)": [[31, "pygom.model.SimulateOde.eval_birth_death_rate"]], "eval_diff_jacobian() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.eval_diff_jacobian"]], "eval_forwardforward() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.eval_forwardforward"]], "eval_grad() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.eval_grad"]], "eval_grad_jacobian() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.eval_grad_jacobian"]], "eval_hessian() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.eval_hessian"]], "eval_jacobian() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.eval_jacobian"]], "eval_ode() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.eval_ode"]], "eval_sens_jacobian_state() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.eval_sens_jacobian_state"]], "eval_sensitivity() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.eval_sensitivity"]], "eval_sensitivityiv() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.eval_sensitivityIV"]], "eval_transition_matrix() (pygom.model.simulateode method)": [[31, "pygom.model.SimulateOde.eval_transition_matrix"]], "eval_transition_mean() (pygom.model.simulateode method)": [[31, "pygom.model.SimulateOde.eval_transition_mean"]], "eval_transition_var() (pygom.model.simulateode method)": [[31, "pygom.model.SimulateOde.eval_transition_var"]], "eval_transition_vector() (pygom.model.simulateode method)": [[31, "pygom.model.SimulateOde.eval_transition_vector"]], "exact() (pygom.model.simulateode method)": [[31, "pygom.model.SimulateOde.exact"]], "forwardforward() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.forwardforward"]], "forwardforward_t() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.forwardforward_T"]], "fromkeys() (pygom.model.ordereddict method)": [[31, "pygom.model.OrderedDict.fromkeys"]], "get_bd_from_ode() (pygom.model.simulateode method)": [[31, "pygom.model.SimulateOde.get_bd_from_ode"]], "get_birth_death_rate() (pygom.model.simulateode method)": [[31, "pygom.model.SimulateOde.get_birth_death_rate"]], "get_diff_jacobian_eqn() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.get_diff_jacobian_eqn"]], "get_grad_eqn() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.get_grad_eqn"]], "get_grad_jacobian_eqn() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.get_grad_jacobian_eqn"]], "get_hessian_eqn() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.get_hessian_eqn"]], "get_jacobian_eqn() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.get_jacobian_eqn"]], "get_ode_eqn() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.get_ode_eqn"]], "get_transition_graph() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.get_transition_graph"]], "get_transition_matrix() (pygom.model.simulateode method)": [[31, "pygom.model.SimulateOde.get_transition_matrix"]], "get_transition_vector() (pygom.model.simulateode method)": [[31, "pygom.model.SimulateOde.get_transition_vector"]], "get_transitions_from_ode() (pygom.model.simulateode method)": [[31, "pygom.model.SimulateOde.get_transitions_from_ode"]], "get_unrolled_obj() (pygom.model.simulateode method)": [[31, "pygom.model.SimulateOde.get_unrolled_obj"]], "grad() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.grad"]], "grad_t() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.grad_T"]], "grad_jacobian() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.grad_jacobian"]], "grad_jacobiant() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.grad_jacobianT"]], "hessian() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.hessian"]], "hybrid() (pygom.model.simulateode method)": [[31, "pygom.model.SimulateOde.hybrid"]], "initial_state (pygom.model.deterministicode property)": [[31, "pygom.model.DeterministicOde.initial_state"]], "initial_time (pygom.model.deterministicode property)": [[31, "pygom.model.DeterministicOde.initial_time"]], "initial_values (pygom.model.deterministicode property)": [[31, "pygom.model.DeterministicOde.initial_values"]], "integrate() (in module pygom.model)": [[31, "pygom.model.integrate"]], "integrate() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.integrate"]], "integrate2() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.integrate2"]], "integratefuncjac() (in module pygom.model)": [[31, "pygom.model.integrateFuncJac"]], "is_between_state() (pygom.model.transition method)": [[31, "pygom.model.Transition.is_between_state"]], "is_list_like() (in module pygom.model)": [[31, "pygom.model.is_list_like"]], "is_stiff() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.is_stiff"]], "items() (pygom.model.ordereddict method)": [[31, "pygom.model.OrderedDict.items"]], "jacobian() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.jacobian"]], "jacobian_t() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.jacobian_T"]], "jacobian_eigenvalue() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.jacobian_eigenvalue"]], "keys() (pygom.model.ordereddict method)": [[31, "pygom.model.OrderedDict.keys"]], "kronparam() (pygom.model.shapeadjust method)": [[31, "pygom.model.shapeAdjust.kronParam"]], "kronstate() (pygom.model.shapeadjust method)": [[31, "pygom.model.shapeAdjust.kronState"]], "linear_ode() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.linear_ode"]], "mattovecff() (pygom.model.shapeadjust method)": [[31, "pygom.model.shapeAdjust.matToVecFF"]], "mattovecsens() (pygom.model.shapeadjust method)": [[31, "pygom.model.shapeAdjust.matToVecSens"]], "move_to_end() (pygom.model.ordereddict method)": [[31, "pygom.model.OrderedDict.move_to_end"]], "ode() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.ode"]], "ode_t() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.ode_T"]], "ode_and_forwardforward() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.ode_and_forwardforward"]], "ode_and_forwardforward_t() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.ode_and_forwardforward_T"]], "ode_and_forwardforward_jacobian() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.ode_and_forwardforward_jacobian"]], "ode_and_forwardforward_jacobian_t() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.ode_and_forwardforward_jacobian_T"]], "ode_and_sensitivity() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.ode_and_sensitivity"]], "ode_and_sensitivityiv() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.ode_and_sensitivityIV"]], "ode_and_sensitivityiv_t() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.ode_and_sensitivityIV_T"]], "ode_and_sensitivityiv_jacobian() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.ode_and_sensitivityIV_jacobian"]], "ode_and_sensitivityiv_jacobian_t() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.ode_and_sensitivityIV_jacobian_T"]], "ode_and_sensitivity_t() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.ode_and_sensitivity_T"]], "ode_and_sensitivity_jacobian() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.ode_and_sensitivity_jacobian"]], "ode_and_sensitivity_jacobian_t() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.ode_and_sensitivity_jacobian_T"]], "origin (pygom.model.transition property)": [[31, "pygom.model.Transition.origin"]], "plot() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.plot"]], "plot() (pygom.model.simulateode method)": [[31, "pygom.model.SimulateOde.plot"]], "plot_det() (in module pygom.model)": [[31, "pygom.model.plot_det"]], "plot_stoc() (in module pygom.model)": [[31, "pygom.model.plot_stoc"]], "pop() (pygom.model.ordereddict method)": [[31, "pygom.model.OrderedDict.pop"]], "popitem() (pygom.model.ordereddict method)": [[31, "pygom.model.OrderedDict.popitem"]], "print_ode() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.print_ode"]], "pygom.model": [[31, "module-pygom.model"]], "reset() (pygom.model.compilecanary method)": [[31, "pygom.model.CompileCanary.reset"]], "sens_jacobian_state() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.sens_jacobian_state"]], "sens_jacobian_state_t() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.sens_jacobian_state_T"]], "sensitivity() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.sensitivity"]], "sensitivityiv() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.sensitivityIV"]], "sensitivityiv_t() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.sensitivityIV_T"]], "sensitivity_t() (pygom.model.deterministicode method)": [[31, "pygom.model.DeterministicOde.sensitivity_T"]], "setdefault() (pygom.model.ordereddict method)": [[31, "pygom.model.OrderedDict.setdefault"]], "shapeadjust (class in pygom.model)": [[31, "pygom.model.shapeAdjust"]], "simulate_jump() (pygom.model.simulateode method)": [[31, "pygom.model.SimulateOde.simulate_jump"]], "simulate_param() (pygom.model.simulateode method)": [[31, "pygom.model.SimulateOde.simulate_param"]], "solve_determ() (pygom.model.simulateode method)": [[31, "pygom.model.SimulateOde.solve_determ"]], "solve_stochast() (pygom.model.simulateode method)": [[31, "pygom.model.SimulateOde.solve_stochast"]], "str_or_list() (in module pygom.model)": [[31, "pygom.model.str_or_list"]], "total_transition() (pygom.model.simulateode method)": [[31, "pygom.model.SimulateOde.total_transition"]], "transition_matrix() (pygom.model.simulateode method)": [[31, "pygom.model.SimulateOde.transition_matrix"]], "transition_mean() (pygom.model.simulateode method)": [[31, "pygom.model.SimulateOde.transition_mean"]], "transition_type (pygom.model.transition property)": [[31, "pygom.model.Transition.transition_type"]], "transition_var() (pygom.model.simulateode method)": [[31, "pygom.model.SimulateOde.transition_var"]], "transition_vector() (pygom.model.simulateode method)": [[31, "pygom.model.SimulateOde.transition_vector"]], "trip() (pygom.model.compilecanary method)": [[31, "pygom.model.CompileCanary.trip"]], "update() (pygom.model.ordereddict method)": [[31, "pygom.model.OrderedDict.update"]], "values() (pygom.model.ordereddict method)": [[31, "pygom.model.OrderedDict.values"]], "vanderpol() (in module pygom.model)": [[31, "pygom.model.vanDerPol"]], "vectomatff() (pygom.model.shapeadjust method)": [[31, "pygom.model.shapeAdjust.vecToMatFF"]], "vectomatsens() (pygom.model.shapeadjust method)": [[31, "pygom.model.shapeAdjust.vecToMatSens"]], "dbeta() (in module pygom.utilr)": [[32, "pygom.utilR.dbeta"]], "dbinom() (in module pygom.utilr)": [[32, "pygom.utilR.dbinom"]], "dchisq() (in module pygom.utilr)": [[32, "pygom.utilR.dchisq"]], "dexp() (in module pygom.utilr)": [[32, "pygom.utilR.dexp"]], "dgamma() (in module pygom.utilr)": [[32, "pygom.utilR.dgamma"]], "dmvnorm() (in module pygom.utilr)": [[32, "pygom.utilR.dmvnorm"]], "dnbinom() (in module pygom.utilr)": [[32, "pygom.utilR.dnbinom"]], "dnorm() (in module pygom.utilr)": [[32, "pygom.utilR.dnorm"]], "dpois() (in module pygom.utilr)": [[32, "pygom.utilR.dpois"]], "dunif() (in module pygom.utilr)": [[32, "pygom.utilR.dunif"]], "gamma_mu_shape() (in module pygom.utilr)": [[32, "pygom.utilR.gamma_mu_shape"]], "nb2pmf() (in module pygom.utilr)": [[32, "pygom.utilR.nb2pmf"]], "pbinom() (in module pygom.utilr)": [[32, "pygom.utilR.pbinom"]], "pchisq() (in module pygom.utilr)": [[32, "pygom.utilR.pchisq"]], "pexp() (in module pygom.utilr)": [[32, "pygom.utilR.pexp"]], "pgamma() (in module pygom.utilr)": [[32, "pygom.utilR.pgamma"]], "pnbinom() (in module pygom.utilr)": [[32, "pygom.utilR.pnbinom"]], "pnorm() (in module pygom.utilr)": [[32, "pygom.utilR.pnorm"]], "ppois() (in module pygom.utilr)": [[32, "pygom.utilR.ppois"]], "punif() (in module pygom.utilr)": [[32, "pygom.utilR.punif"]], "pygom.utilr": [[32, "module-pygom.utilR"]], "qbeta() (in module pygom.utilr)": [[32, "pygom.utilR.qbeta"]], "qbinom() (in module pygom.utilr)": [[32, "pygom.utilR.qbinom"]], "qchisq() (in module pygom.utilr)": [[32, "pygom.utilR.qchisq"]], "qexp() (in module pygom.utilr)": [[32, "pygom.utilR.qexp"]], "qgamma() (in module pygom.utilr)": [[32, "pygom.utilR.qgamma"]], "qnbinom() (in module pygom.utilr)": [[32, "pygom.utilR.qnbinom"]], "qnorm() (in module pygom.utilr)": [[32, "pygom.utilR.qnorm"]], "qpois() (in module pygom.utilr)": [[32, "pygom.utilR.qpois"]], "qunif() (in module pygom.utilr)": [[32, "pygom.utilR.qunif"]], "rbeta() (in module pygom.utilr)": [[32, "pygom.utilR.rbeta"]], "rbinom() (in module pygom.utilr)": [[32, "pygom.utilR.rbinom"]], "rchisq() (in module pygom.utilr)": [[32, "pygom.utilR.rchisq"]], "rexp() (in module pygom.utilr)": [[32, "pygom.utilR.rexp"]], "rgamma() (in module pygom.utilr)": [[32, "pygom.utilR.rgamma"]], "rmvnorm() (in module pygom.utilr)": [[32, "pygom.utilR.rmvnorm"]], "rnorm() (in module pygom.utilr)": [[32, "pygom.utilR.rnorm"]], "rpois() (in module pygom.utilr)": [[32, "pygom.utilR.rpois"]], "runif() (in module pygom.utilr)": [[32, "pygom.utilR.runif"]], "test_seed() (in module pygom.utilr)": [[32, "pygom.utilR.test_seed"]]}})
\ No newline at end of file