Release 0.2.2.

nathangeffen · Aug 17, 2019 · 300ec9d · 300ec9d
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diff --git a/Makefile b/Makefile
@@ -236,18 +236,18 @@ OBJEXT = o
 PACKAGE = faststi
 PACKAGE_BUGREPORT = [email protected]
 PACKAGE_NAME = faststi
-PACKAGE_STRING = faststi 0.2.1
+PACKAGE_STRING = faststi 0.2.2
 PACKAGE_TARNAME = faststi
 PACKAGE_URL = 
-PACKAGE_VERSION = 0.2.1
+PACKAGE_VERSION = 0.2.2
 PATH_SEPARATOR = :
 PKG_CONFIG = /usr/bin/pkg-config
 PKG_CONFIG_LIBDIR = 
 PKG_CONFIG_PATH = 
 SET_MAKE = 
 SHELL = /bin/bash
 STRIP = 
-VERSION = 0.2.1
+VERSION = 0.2.2
 abs_builddir = /home/nathan/workspace/C/faststi
 abs_srcdir = /home/nathan/workspace/C/faststi
 abs_top_builddir = /home/nathan/workspace/C/faststi
@@ -312,6 +312,7 @@ EXTRA_DIST = simulations/examples/eg1.ini		\
 		data/dataset_mortality_simple.csv	\
 		data/dataset_rel.csv			\
 		data/dataset_single.csv			\
+		scripts/processResultsFile.py		\
 		scripts/processResultsFile.R		\
 		scripts/README
 

diff --git a/configure.ac b/configure.ac
@@ -1,4 +1,4 @@
-AC_INIT([faststi], [0.2.1], [[email protected]])
+AC_INIT([faststi], [0.2.2], [[email protected]])
 AM_INIT_AUTOMAKE([-Wall -Werror foreign subdir-objects])
 AC_PROG_CC
 # CFLAGS+=" -std=c11 -Wall -Werror -pedantic"

diff --git a/docs/_build/doctrees/credits.doctree b/docs/_build/doctrees/credits.doctree
diff --git a/docs/_build/doctrees/environment.pickle b/docs/_build/doctrees/environment.pickle
diff --git a/docs/_build/doctrees/events.doctree b/docs/_build/doctrees/events.doctree
diff --git a/docs/_build/doctrees/example.doctree b/docs/_build/doctrees/example.doctree
diff --git a/docs/_build/doctrees/extending.doctree b/docs/_build/doctrees/extending.doctree
diff --git a/docs/_build/doctrees/getstart.doctree b/docs/_build/doctrees/getstart.doctree
diff --git a/docs/_build/doctrees/guide.doctree b/docs/_build/doctrees/guide.doctree
diff --git a/docs/_build/doctrees/improve.doctree b/docs/_build/doctrees/improve.doctree
diff --git a/docs/_build/doctrees/index.doctree b/docs/_build/doctrees/index.doctree
diff --git a/docs/_build/doctrees/inputformats.doctree b/docs/_build/doctrees/inputformats.doctree
diff --git a/docs/_build/doctrees/installation.doctree b/docs/_build/doctrees/installation.doctree
diff --git a/docs/_build/doctrees/intro.doctree b/docs/_build/doctrees/intro.doctree
diff --git a/docs/_build/doctrees/license.doctree b/docs/_build/doctrees/license.doctree
diff --git a/docs/_build/doctrees/outputformats.doctree b/docs/_build/doctrees/outputformats.doctree
diff --git a/docs/_build/doctrees/parameters.doctree b/docs/_build/doctrees/parameters.doctree
diff --git a/docs/_build/doctrees/refs.doctree b/docs/_build/doctrees/refs.doctree
diff --git a/docs/_build/html/.buildinfo b/docs/_build/html/.buildinfo
@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 8e18b96cacb840126c7c47821b7d27aa
+config: c4f29da0b244d8f4b0022960ba4ead53
 tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/docs/_build/html/_sources/events.rst.txt b/docs/_build/html/_sources/events.rst.txt
@@ -596,89 +596,9 @@ initial_infect_stage parameter are consistent with each other.
 Dataset: dataset_infect_stage
 
 This is quite a complicated dataset and is best understood by looking at the
-commented example in the data directory called dataset_infect_stage.csv. For
-convenience here it is:
-
-.. code-block:: none
-   :linenos:
-
-        # Dataset used by _stage event (defined in fsti-events.c as fsti_event_stage)
-        #
-        # The first three columns are used for matching and correspond to agent fields
-        # or properties.
-        #
-        # The next six columns are instructions on how and when to change the stage.
-        #
-        # Columns:
-        #
-        #  1. infected - the infection stage of the agent (0 is uninfected)
-        #  2. treated - the treatment regimen of the agent. This particular file
-        #               allows for 3 treatment regimens.
-        #  3. resistant - 0 if the agent is drug-susceptible to this treatment regimen
-        #                 1 if the agent is drug-resistant to this treatment regimen
-        #  4. prob_stage_change - probability that the infection stage changes for
-        #                         this time step (1 day)
-        #  5. stage_incr - if a uniformly generated random number < prob_stage_change
-        #                  then change the infect property by this increment
-        #  6. prob_treatment_change - probability treatment changes
-        #  7. treatment_incr - if a uniformly rand number < prob_treatment_change
-        #                      then change the treatment property by this increment
-        #  8. prob_resistant - probability resistance status changes
-        #  9. resistant_incr - if a uniformly random number < prob_resistant_change
-        #                      change the resistant value by this amount
-        #
-        # Note the |6 after resistant_incr means that there are six columns at the end
-        # of each line that are not agent properties.
-        #
-        # Infection stages:;;;;;;;;
-        #  0 = uninfected;;;;;;;;
-        #  1 = virally suppressed (usually on treatment);;;;;;;;
-        #  2 = primary infection (highly infectious);;;;;;;;
-        #  3 = chronic infection;;;;;;;;
-        #  4 = Final stage;;;;;;;;
-        #
-        # HEADER ROW FOLLOWS
-        infected;treated;resistant;prob_stage_change;stage_incr;prob_treatment_change;treatment_incr;prob_resistant;resistant_incr|6
-        0;0;0;0;0;0;0;0;0
-        0;0;1;0;0;0;0;0;0
-        0;1;0;0;0;0;0;0;0
-        0;1;1;0;0;0;0;0;0
-        0;2;0;0;0;0;0;0;0
-        0;2;1;0;0;0;0;0;0
-        0;3;0;0;0;0;0;0;0
-        0;3;1;0;0;0;0;0;0
-        1;0;0;0.1;1;0.0001;1;0;0
-        1;0;1;0.1;1;0.0001;1;0;0
-        1;1;0;0.00001;1;0.00001;1;0.00001;1
-        1;1;1;0.1;1;0.0001;1;0;0
-        1;2;0;0.00001;1;0.00001;1;0.00001;1
-        1;2;1;0.1;1;0.0001;1;0;0
-        1;3;0;0.00001;1;0;0;0.0001;1
-        1;3;1;0.1;1;0;0;0;0
-        2;0;0;0.1;1;0.001;1;0;0
-        2;0;1;0.1;1;0.001;1;0;0
-        2;1;0;0.1;-1;0;0;0.0001;1
-        2;1;1;0.1;1;0.001;1;0;0
-        2;2;0;0.1;-1;0;0;0.0001;1
-        2;2;1;0.1;1;0.001;1;0;0
-        2;3;0;0.1;-1;0;0;0.0001;1
-        2;3;1;0.1;1;0;0;0;0
-        3;0;0;0.004;1;0.0001;1;0;0
-        3;0;1;0.001;1;0.0001;1;0;0
-        3;1;0;0.1;-1;0;0;0.0001;1
-        3;1;1;0.002;1;0.005;1;0;0
-        3;2;0;0.1;-1;0;0;0.0001;1
-        3;2;1;0.002;1;0.001;1;0;0
-        3;3;0;0.1;-1;0;0;0.0001;1
-        3;3;1;0.002;1;0;0;0;0
-        4;0;0;0;0;0.005;1;0;0
-        4;0;1;0;0;0.005;1;0;0
-        4;1;0;0.1;-1;0;0;0.0001;1
-        4;1;1;0;0;0.01;1;0;0
-        4;2;0;0.1;-1;0;0;0.0001;1
-        4;2;1;0;0;0.01;1;0;0
-        4;3;0;0.1;-1;0;0;0.0001;1
-        4;3;1;0;0;0;0;0;0
+commented example in the data directory called dataset_infect_stage.csv. It's
+also included for convenience in the parameter description of
+:ref:`dataset_infect_stage_ref`.
 
 *********
 _coinfect

diff --git a/docs/_build/html/_sources/installation.rst.txt b/docs/_build/html/_sources/installation.rst.txt
@@ -20,14 +20,12 @@ On Ubuntu, Debian, Mint etc. this should do the trick: ::
   sudo apt install build-essential libgsl-dev libglib2.0-dev
 
 
-2. Download the |PROJECT| `archived distribution
-<https://www.simhub.online/media/dist/faststi/latest.tar.gz>`_ and decompress
+2. Download |PROJECT| from |DOWNLOAD| and decompress
 it.
 
-E.g. ::
+E.g.
 
-  wget https://www.simhub.online/media/dist/faststi/latest.tar.gz
-  tar xzvf latest.tar.gz
+   |CODE_TO_DOWNLOAD|
 
 This should create a directory called |DIRNAME| which contains the |PROJECT| files.
 

diff --git a/docs/_build/html/_sources/parameters.rst.txt b/docs/_build/html/_sources/parameters.rst.txt
@@ -493,6 +493,159 @@ Examples: ::
 
   dataset_gen_infect = dataset_gen_infect.csv
 
+
+.. _dataset_infect_stage_ref:
+
+********************
+dataset_infect_stage
+********************
+
+Specifies the location of a dataset used to determine if an infected agent
+should change the infection stage it is in.
+
+Default: _no_op # i.e. there is no dataset file specified.
+
+Examples: ::
+
+  dataset_gen_infect = dataset_gen_infect.csv
+
+This is quite a complicated dataset and is best understood by looking at the
+commented example in the data directory called dataset_infect_stage.csv. For
+convenience here it is:
+
+.. code-block:: none
+   :linenos:
+
+        # Dataset used by _stage event (defined in fsti-events.c as fsti_event_stage)
+        #
+        # The first three columns are used for matching and correspond to agent fields
+        # or properties.
+        #
+        # The next six columns are instructions on how and when to change the stage.
+        #
+        # Columns:
+        #
+        #  1. infected - the infection stage of the agent (0 is uninfected)
+        #  2. treated - the treatment regimen of the agent. This particular file
+        #               allows for 3 treatment regimens.
+        #  3. resistant - 0 if the agent is drug-susceptible to this treatment regimen
+        #                 1 if the agent is drug-resistant to this treatment regimen
+        #  4. prob_stage_change - probability that the infection stage changes for
+        #                         this time step (1 day)
+        #  5. stage_incr - if a uniformly generated random number < prob_stage_change
+        #                  then change the infect property by this increment
+        #  6. prob_treatment_change - probability treatment changes
+        #  7. treatment_incr - if a uniformly rand number < prob_treatment_change
+        #                      then change the treatment property by this increment
+        #  8. prob_resistant - probability resistance status changes
+        #  9. resistant_incr - if a uniformly random number < prob_resistant_change
+        #                      change the resistant value by this amount
+        #
+        # Note the |6 after resistant_incr means that there are six columns at the end
+        # of each line that are not agent properties.
+        #
+        # Infection stages:;;;;;;;;
+        #  0 = uninfected;;;;;;;;
+        #  1 = virally suppressed (usually on treatment);;;;;;;;
+        #  2 = primary infection (highly infectious);;;;;;;;
+        #  3 = chronic infection;;;;;;;;
+        #  4 = Final stage;;;;;;;;
+        #
+        # HEADER ROW FOLLOWS
+        infected;treated;resistant;prob_stage_change;stage_incr;prob_treatment_change;treatment_incr;prob_resistant;resistant_incr|6
+        0;0;0;0;0;0;0;0;0
+        0;0;1;0;0;0;0;0;0
+        0;1;0;0;0;0;0;0;0
+        0;1;1;0;0;0;0;0;0
+        0;2;0;0;0;0;0;0;0
+        0;2;1;0;0;0;0;0;0
+        0;3;0;0;0;0;0;0;0
+        0;3;1;0;0;0;0;0;0
+        1;0;0;0.1;1;0.0001;1;0;0
+        1;0;1;0.1;1;0.0001;1;0;0
+        1;1;0;0.00001;1;0.00001;1;0.00001;1
+        1;1;1;0.1;1;0.0001;1;0;0
+        1;2;0;0.00001;1;0.00001;1;0.00001;1
+        1;2;1;0.1;1;0.0001;1;0;0
+        1;3;0;0.00001;1;0;0;0.0001;1
+        1;3;1;0.1;1;0;0;0;0
+        2;0;0;0.1;1;0.001;1;0;0
+        2;0;1;0.1;1;0.001;1;0;0
+        2;1;0;0.1;-1;0;0;0.0001;1
+        2;1;1;0.1;1;0.001;1;0;0
+        2;2;0;0.1;-1;0;0;0.0001;1
+        2;2;1;0.1;1;0.001;1;0;0
+        2;3;0;0.1;-1;0;0;0.0001;1
+        2;3;1;0.1;1;0;0;0;0
+        3;0;0;0.004;1;0.0001;1;0;0
+        3;0;1;0.001;1;0.0001;1;0;0
+        3;1;0;0.1;-1;0;0;0.0001;1
+        3;1;1;0.002;1;0.005;1;0;0
+        3;2;0;0.1;-1;0;0;0.0001;1
+        3;2;1;0.002;1;0.001;1;0;0
+        3;3;0;0.1;-1;0;0;0.0001;1
+        3;3;1;0.002;1;0;0;0;0
+        4;0;0;0;0;0.005;1;0;0
+        4;0;1;0;0;0.005;1;0;0
+        4;1;0;0.1;-1;0;0;0.0001;1
+        4;1;1;0;0;0.01;1;0;0
+        4;2;0;0.1;-1;0;0;0.0001;1
+        4;2;1;0;0;0.01;1;0;0
+        4;3;0;0.1;-1;0;0;0.0001;1
+        4;3;1;0;0;0;0;0;0
+
+*****************
+dataset_mortality
+*****************
+
+Specifies the location of a dataset used to determine if an agent should die on
+the current time step.
+
+See the data/dataset_mortality.csv file for an example of this dataset.
+
+Default: _no_op # i.e. there is no dataset file specified.
+
+Examples: ::
+
+    dataset_mortality = dataset_mortality.csv
+
+
+******************
+dataset_rel_period
+******************
+
+Specifies the location of a dataset used to determine the length of time an
+agent relationship should be.
+
+This dataset requires two dependent variable columns: scale and shape, which are
+used to draw a random number from a Weibull distribution for each agent in the
+relationship. The values returned are the number of time steps (iterations). The
+duration of the relationship is the mean of the two random numbers drawn.
+
+Default: _no_op # i.e. there is no dataset file specified.
+
+Examples: ::
+
+    dataset_rel_period = dataset_rel_period.csv
+
+
+*********************
+dataset_single_period
+*********************
+
+Specifies the location of a dataset used to determine the length of time an
+agent should remain single.
+
+This dataset requires two dependent variable columns: scale and shape, which are
+used to draw a random number from a Weibull distribution for the agent. The
+value drawn is the number of time steps the agent should remain single.
+
+Default: _no_op # i.e. there is no dataset file specified.
+
+Examples: ::
+
+    dataset_single_period = dataset_single_period.csv
+
 .. _during_events_ref:
 
 *************
@@ -532,25 +685,49 @@ Examples: ::
 
     report_frequency = 365 # Report every 365 time steps.
 
+********************
+initial_infect_stage
+********************
 
-TO DO
+When an agent is infected, this parameter determines the initial infection
+stage.
 
+Default: 2. In the default simulation provided by FastSTI, the agent infected
+property of 1 implies it is on treatment. No one is on treatment when infected,
+so 2 represents the primary infection stage, and this is therefore the default
+value that initial_infect_stage is set to.
 
-dataset_infect_stage; CSV file of values to determine when agent advances to next stage of infection; _no_op
+Events used in: _infect
 
-dataset_mortality; CSV file of values to determine agent deaths; _no_op
+Example: ::
 
-dataset_rel_period; CSV file of values to determine period agent is in relationship; _no_op
+  initial_infect_stage = 2
 
+*******
+match_k
+*******
+
+The value of k when using nearest-neighbour type agent matching algorithms. The
+agent matching algorithm supplied with GroundUp (implemented by the
+:ref:`rkpm_ref` event) chooses the best match for the current agent being
+considered for matching in the mating pool from the k unmatched agents adjacent
+to it.
 
-dataset_single_period; CSV file of values to determine period agent is single; _no_op
+If k is set to 1, this is random matching matching. If k is set larger than the
+possible number of agents in the mating pool, then this is a kind of brute force
+matching.
 
+Default: 100 This is usually a good compromise value. The algorithm will execute
+quickly and the agent selected will on average be a better match than 99% of the
+remaining agents in the mating pool.
 
-event_test_freq; Run test cases in test events every nth iteration; 100
+Events used in: _rpkm
 
-initial_infect_stage; When infected this is the integer to set infected to; 2
+Example: ::
+
+  match_k = 300
 
-match_k; Value for k when using matching algorithms; 100
+TO DO
 
 max_stage; Maximum infection stage (e.g. 6 for HIV 1=virally suppressed, 2=primary 3-6=WHO 1-4); 6
 

diff --git a/docs/_build/html/_static/documentation_options.js b/docs/_build/html/_static/documentation_options.js
@@ -1,6 +1,6 @@
 var DOCUMENTATION_OPTIONS = {
     URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: '0.2.1',
+    VERSION: '0.2.2',
     LANGUAGE: 'None',
     COLLAPSE_INDEX: false,
     FILE_SUFFIX: '.html',

diff --git a/docs/_build/html/credits.html b/docs/_build/html/credits.html
@@ -8,7 +8,7 @@
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0">
 
-  <title>Credits &mdash; FastSTI 0.2.1 documentation</title>
+  <title>Credits &mdash; FastSTI 0.2.2 documentation</title>
 
 
 
@@ -88,7 +88,7 @@
 <li class="toctree-l1"><a class="reference internal" href="intro.html">Introduction</a></li>
 <li class="toctree-l1"><a class="reference internal" href="installation.html">Installation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="getstart.html">Getting started</a></li>
-<li class="toctree-l1"><a class="reference internal" href="guide.html">Tutorial: Creating a simulation</a></li>
+<li class="toctree-l1"><a class="reference internal" href="guide.html">Tutorial: Creating simulations</a></li>
 <li class="toctree-l1"><a class="reference internal" href="example.html">Interesting example</a></li>
 <li class="toctree-l1"><a class="reference internal" href="inputformats.html">Input file formats</a></li>
 <li class="toctree-l1"><a class="reference internal" href="outputformats.html">Output file formats</a></li>