Merge pull request #343 from AdityaSavara/develop

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AdityaSavara · Oct 26, 2024 · f56515b · f56515b
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diff --git a/Examples/Example00/0-Example00Explanation.docx b/Examples/Example00/0-Example00Explanation.docx
diff --git a/Examples/Example00/CITATIONS/CITATIONS.cff b/Examples/Example00/CITATIONS/CITATIONS.cff
@@ -0,0 +1,11 @@
+---
+cff-version: 1.2.0
+message:2024-10-26T16:55:03
+title: zeus
+identifiers: 
+ - type: unique_id
+   value: https://github.com/minaskar/zeus
+authors: 
+ - name: Minas Karamanis
+ - name: Florian Beutler
+version: 2.0.0
diff --git a/Examples/Example00/CITATIONS/CiteSoftwareCheckpointsLog.txt b/Examples/Example00/CITATIONS/CiteSoftwareCheckpointsLog.txt
@@ -20,3 +20,26 @@
     cite:
         - >-
             Savara, A. and Walker, E.A. (2020), PEUQSE Intro 1: Bayesian Parameter Estimation Considering Uncertainty or Error from both Experiments and Theory. ChemCatChem. Accepted. doi:10.1002/cctc.202000953
+---
+-
+    timestamp: >-
+        2024-10-26T16:55:03
+    unique_id: >-
+        https://github.com/minaskar/zeus
+    software_name: >-
+        zeus
+    version:
+        - >-
+            2.0.0
+    author:
+        - >-
+            Minas Karamanis
+        - >-
+            Florian Beutler
+    cite:
+        - >-
+            Minas Karamanis and Florian Beutler. zeus: A Python Implementation of the Ensemble Slice Sampling method. 2020. 
+        - >-
+            https://arxiv.org/abs/2002.06212
+        - >-
+            @article{ess,  title={Ensemble Slice Sampling}, author={Minas Karamanis and Florian Beutler}, year={2020}, eprint={2002.06212}, archivePrefix={arXiv}, primaryClass={stat.ML} }
diff --git a/Examples/Example00/CITATIONS/CiteSoftwareConsolidatedLog.txt b/Examples/Example00/CITATIONS/CiteSoftwareConsolidatedLog.txt
@@ -0,0 +1,45 @@
+#Warning: CiteSoftwareConsolidatedLog.txt may not include all softwares used. It is the end-user�s responsibility to verify that the no software citations are missing relative to those recorded in the complete logfile, CiteSoftwareCheckpointsLog.txt . This verification is important to do when using two or more codes together for the first time.
+---
+-
+    timestamp: >-
+        2022-11-17T14:25:17
+    unique_id: >-
+        https://doi.org/10.1002/cctc.202000953
+    software_name: >-
+        PEUQSE Bayesian Parameter Estimation
+    version:
+        - >-
+            1.0.0
+    author:
+        - >-
+            Aditya Savara
+        - >-
+            Eric A. Walker
+    doi:
+        - >-
+            https://doi.org/10.1002/cctc.202000953
+    cite:
+        - >-
+            Savara, A. and Walker, E.A. (2020), PEUQSE Intro 1: Bayesian Parameter Estimation Considering Uncertainty or Error from both Experiments and Theory. ChemCatChem. Accepted. doi:10.1002/cctc.202000953
+-
+    timestamp: >-
+        2024-10-26T16:55:03
+    unique_id: >-
+        https://github.com/minaskar/zeus
+    software_name: >-
+        zeus
+    version:
+        - >-
+            2.0.0
+    author:
+        - >-
+            Minas Karamanis
+        - >-
+            Florian Beutler
+    cite:
+        - >-
+            Minas Karamanis and Florian Beutler. zeus: A Python Implementation of the Ensemble Slice Sampling method. 2020. 
+        - >-
+            https://arxiv.org/abs/2002.06212
+        - >-
+            @article{ess,  title={Ensemble Slice Sampling}, author={Minas Karamanis and Florian Beutler}, year={2020}, eprint={2002.06212}, archivePrefix={arXiv}, primaryClass={stat.ML} }
diff --git a/Examples/Example00/CITATIONS/CiteSoftwareUniqueIDs.txt b/Examples/Example00/CITATIONS/CiteSoftwareUniqueIDs.txt
@@ -1 +1,2 @@
 https://doi.org/10.1002/cctc.202000953
+https://github.com/minaskar/zeus
diff --git a/Examples/Example00/CITATIONS/IndividualCff/https___github.com_minaskar_zeus.cff b/Examples/Example00/CITATIONS/IndividualCff/https___github.com_minaskar_zeus.cff
@@ -0,0 +1,10 @@
+cff-version: 1.2.0
+message:2024-10-26T16:55:03
+title: zeus
+identifiers: 
+ - type: unique_id
+   value: https://github.com/minaskar/zeus
+authors: 
+ - name: Minas Karamanis
+ - name: Florian Beutler
+version: 2.0.0
diff --git a/Examples/Example00/calculated_resultObj1.p b/Examples/Example00/calculated_resultObj1.p
diff --git a/Examples/Example00/expected_resultObj1.p b/Examples/Example00/expected_resultObj1.p
diff --git a/Examples/Example00/graphs/AutoCorrelationPlot_Combined_Parameters.png b/Examples/Example00/graphs/AutoCorrelationPlot_Combined_Parameters.png
diff --git a/Examples/Example00/graphs/AutoCorrelationPlot_a.png b/Examples/Example00/graphs/AutoCorrelationPlot_a.png
diff --git a/Examples/Example00/graphs/AutoCorrelationPlot_b.png b/Examples/Example00/graphs/AutoCorrelationPlot_b.png
diff --git a/Examples/Example00/graphs/GewekeDiagnostic_Combined_Parameters.png b/Examples/Example00/graphs/GewekeDiagnostic_Combined_Parameters.png
diff --git a/Examples/Example00/graphs/GewekeDiagnostic_a.png b/Examples/Example00/graphs/GewekeDiagnostic_a.png
diff --git a/Examples/Example00/graphs/GewekeDiagnostic_b.png b/Examples/Example00/graphs/GewekeDiagnostic_b.png
diff --git a/Examples/Example00/graphs/Heat_Scatter_a_b.png b/Examples/Example00/graphs/Heat_Scatter_a_b.png
diff --git a/Examples/Example00/graphs/Heat_Scatter_b_a.png b/Examples/Example00/graphs/Heat_Scatter_b_a.png
diff --git a/Examples/Example00/graphs/Histogram_sampling_0_a.png b/Examples/Example00/graphs/Histogram_sampling_0_a.png
diff --git a/Examples/Example00/graphs/Histogram_sampling_1_b.png b/Examples/Example00/graphs/Histogram_sampling_1_b.png
diff --git a/Examples/Example00/graphs/PosteriorContourPlots__0_1.png b/Examples/Example00/graphs/PosteriorContourPlots__0_1.png
diff --git a/Examples/Example00/graphs/PosteriorContourPlots__combined.png b/Examples/Example00/graphs/PosteriorContourPlots__combined.png
diff --git a/Examples/Example00/graphs/Posterior_Simulated.png b/Examples/Example00/graphs/Posterior_Simulated.png
diff --git a/Examples/Example00/graphs/Posterior_Simulated_combined.png b/Examples/Example00/graphs/Posterior_Simulated_combined.png
diff --git a/Examples/Example00/graphs/Scatter_a_b.png b/Examples/Example00/graphs/Scatter_a_b.png
diff --git a/Examples/Example00/graphs/Scatter_b_a.png b/Examples/Example00/graphs/Scatter_b_a.png
diff --git a/Examples/Example00/graphs/scatter_matrix_posterior.png b/Examples/Example00/graphs/scatter_matrix_posterior.png
diff --git a/...les/Example00/logs_and_csvs/ExportedResponsesData__last_called__ResponsesConsolidated.csv b/...les/Example00/logs_and_csvs/ExportedResponsesData__last_called__ResponsesConsolidated.csv
@@ -0,0 +1,4 @@
+ResponseAbscissa,Response0
+6.000000000000000000e+02,6.788783719642001670e+05
+1.100000000000000000e+03,1.205881348876372911e+06
+1.400000000000000000e+03,1.762083135023676325e+06
diff --git a/Examples/Example00/logs_and_csvs/ExportedResponsesData__muap__ResponsesConsolidated.csv b/Examples/Example00/logs_and_csvs/ExportedResponsesData__muap__ResponsesConsolidated.csv
@@ -0,0 +1,4 @@
+ResponseAbscissa,Response0
+6.000000000000000000e+02,2.773841475740034948e+05
+1.100000000000000000e+03,8.874248144291497301e+05
+1.400000000000000000e+03,1.493449214542237343e+06
diff --git a/Examples/Example00/logs_and_csvs/mcmc_burn_in_logP_and_parameter_samples.csv b/Examples/Example00/logs_and_csvs/mcmc_burn_in_logP_and_parameter_samples.csv
diff --git a/Examples/Example00/logs_and_csvs/mcmc_logP_and_parameter_samples.csv b/Examples/Example00/logs_and_csvs/mcmc_logP_and_parameter_samples.csv
diff --git a/Examples/Example00/logs_and_csvs/mcmc_log_file.txt b/Examples/Example00/logs_and_csvs/mcmc_log_file.txt
@@ -1,12 +1,12 @@
 self.initial_point_parameters:[200. 500.]
-MAP_logP:[-42.63740123]
-self.map_parameter_set:[165.27138721 499.15891705]
-self.map_index:1978
-self.mu_AP_parameter_set:[167.49588332 503.60518447]
-self.stdap_parameter_set:[ 51.98513273 176.02359081]
-self.info_gain:0.044163013263335826
-evidence:3.154245445068923e-24
+MAP_logP:[-40.56390523]
+self.map_parameter_set:[   236.46711094 172816.9013801 ]
+self.map_index:11808
+self.mu_AP_parameter_set:[   239.95933314 147754.86578451]
+self.stdap_parameter_set:[1.70209025e+02 2.94668210e+05]
+self.info_gain:8.644232734220434e-05
+evidence:3.2453675898950584e-26
 posterior_cov_matrix:
-[[ 2702.77091673    41.81195912]
- [   41.81195912 30987.93776494]]
+[[2.89732576e+04 4.49569896e+07]
+ [4.49569896e+07 8.68357843e+10]]
 Convergence Status: The difference between the MAP parameter set and mu_AP parameter set is less than 10% of the prior standard deviations for each parameter. There is no general method for knowing when the correct solution has been obtained, but this small difference is one sign of a converged solution.
diff --git a/Examples/Example00/logs_and_csvs/multistart_MAP_logP_and_parameters_values.csv b/Examples/Example00/logs_and_csvs/multistart_MAP_logP_and_parameters_values.csv
@@ -1,9 +1,9 @@
 -4.263738740051095988e+01,1.651709157178113401e+02,5.000228008216587341e+02
--4.263738746218145792e+01,1.651526515942228173e+02,4.999897227603483998e+02
+-4.263738746218145792e+01,1.651526515942227888e+02,4.999897227603483429e+02
 -4.263738730919835263e+01,1.651707311974578261e+02,5.000615222463072769e+02
--4.263738765355596883e+01,1.651230422188899354e+02,5.002939061421724887e+02
--4.263738738928292094e+01,1.651285856038028044e+02,5.000471980402375607e+02
--4.263738735893460330e+01,1.651243925352550264e+02,5.001859937340127544e+02
--4.263738736710693900e+01,1.651249122942219856e+02,5.000753896910200069e+02
--4.263738736036667376e+01,1.651783534942703113e+02,5.002110564608926779e+02
--4.263738732180944879e+01,1.651750549040160649e+02,5.000686998595569435e+02
+-4.263738763857771374e+01,1.651224203356981377e+02,5.002885633578309239e+02
+-4.263738740081498690e+01,1.651282560486523892e+02,5.000431993182538122e+02
+-4.263738734873029301e+01,1.651250722095641379e+02,5.001825377490075084e+02
+-4.263738738759376901e+01,1.651240500230159114e+02,5.000673485825173543e+02
+-4.263738732344320681e+01,1.651776842079039795e+02,5.001916162297255255e+02
+-4.263738731052364273e+01,1.651776206429131548e+02,5.000891582579897090e+02
diff --git a/Examples/Example00/pickles/mcmc_burn_in_logP_and_parameter_samples.pkl b/Examples/Example00/pickles/mcmc_burn_in_logP_and_parameter_samples.pkl
diff --git a/Examples/Example00/pickles/mcmc_initial_point_parameters.pkl b/Examples/Example00/pickles/mcmc_initial_point_parameters.pkl
diff --git a/Examples/Example00/pickles/mcmc_last_point_sampled.pkl b/Examples/Example00/pickles/mcmc_last_point_sampled.pkl
diff --git a/Examples/Example00/pickles/mcmc_logP_and_parameter_samples.pkl b/Examples/Example00/pickles/mcmc_logP_and_parameter_samples.pkl
diff --git a/Examples/Example00/pickles/mcmc_map_logP.pkl b/Examples/Example00/pickles/mcmc_map_logP.pkl
diff --git a/Examples/Example00/pickles/mcmc_map_parameter_set.pkl b/Examples/Example00/pickles/mcmc_map_parameter_set.pkl
diff --git a/Examples/Example00/pickles/mcmc_post_burn_in_statistics.pkl b/Examples/Example00/pickles/mcmc_post_burn_in_statistics.pkl
diff --git a/Examples/Example00/pickles/multistart_MAP_logP_and_parameters_values.pkl b/Examples/Example00/pickles/multistart_MAP_logP_and_parameters_values.pkl
diff --git a/Examples/Example00/runfile_Example_00c7_BPE_uninformed_ESS_threshold_filter_example.py b/Examples/Example00/runfile_Example_00c7_BPE_uninformed_ESS_threshold_filter_example.py
@@ -23,8 +23,8 @@
     #UserInput.model['InputParameterInitialGuess'] = [150,400] #Can optionally change the initial guess to be different from prior means.
 
 UserInput.model['simulateByInputParametersOnlyFunction'] = simulation_model_00.simulation_function_wrapper #This must simulate with *only* the parameters listed above, and no other arguments.
-UserInput.parameter_estimation_settings['mcmc_burn_in'] = 100
-UserInput.parameter_estimation_settings['mcmc_length'] = 1500 #The uninformed prior int his example has a "bad" MCMC walker so requires lots of sampling to converge.
+UserInput.parameter_estimation_settings['mcmc_burn_in'] = 1500
+UserInput.parameter_estimation_settings['mcmc_length'] = 15000 #The uninformed prior int his example has a "bad" MCMC walker so requires lots of sampling to converge.
 UserInput.parameter_estimation_settings['mcmc_checkPointFrequency'] = 10 #This example is long enough that it's good to get updates.
 #After making the UserInput, now we make a 'parameter_estimation' object from it.
 PE_object = PEUQSE.parameter_estimation(UserInput)

diff --git a/Examples/Example07/CITATIONS/CiteSoftwareConsolidatedLog.txt b/Examples/Example07/CITATIONS/CiteSoftwareConsolidatedLog.txt
@@ -0,0 +1,23 @@
+#Warning: CiteSoftwareConsolidatedLog.txt may not include all softwares used. It is the end-user�s responsibility to verify that the no software citations are missing relative to those recorded in the complete logfile, CiteSoftwareCheckpointsLog.txt . This verification is important to do when using two or more codes together for the first time.
+---
+-
+    timestamp: >-
+        2022-11-17T14:25:56
+    unique_id: >-
+        https://doi.org/10.1002/cctc.202000953
+    software_name: >-
+        PEUQSE Bayesian Parameter Estimation
+    version:
+        - >-
+            1.0.0
+    author:
+        - >-
+            Aditya Savara
+        - >-
+            Eric A. Walker
+    doi:
+        - >-
+            https://doi.org/10.1002/cctc.202000953
+    cite:
+        - >-
+            Savara, A. and Walker, E.A. (2020), PEUQSE Intro 1: Bayesian Parameter Estimation Considering Uncertainty or Error from both Experiments and Theory. ChemCatChem. Accepted. doi:10.1002/cctc.202000953
diff --git a/Examples/Example07/calculated_resultObj1.p b/Examples/Example07/calculated_resultObj1.p
diff --git a/Examples/Example07/expected_resultObj1.p b/Examples/Example07/expected_resultObj1.p
diff --git a/Examples/Example07/graphs/AutoCorrelationPlot_Combined_Parameters.png b/Examples/Example07/graphs/AutoCorrelationPlot_Combined_Parameters.png
diff --git a/Examples/Example07/graphs/AutoCorrelationPlot_theta_1.png b/Examples/Example07/graphs/AutoCorrelationPlot_theta_1.png
diff --git a/Examples/Example07/graphs/AutoCorrelationPlot_theta_2.png b/Examples/Example07/graphs/AutoCorrelationPlot_theta_2.png
diff --git a/Examples/Example07/graphs/GewekeDiagnostic_Combined_Parameters.png b/Examples/Example07/graphs/GewekeDiagnostic_Combined_Parameters.png
diff --git a/Examples/Example07/graphs/GewekeDiagnostic_theta_1.png b/Examples/Example07/graphs/GewekeDiagnostic_theta_1.png
diff --git a/Examples/Example07/graphs/GewekeDiagnostic_theta_2.png b/Examples/Example07/graphs/GewekeDiagnostic_theta_2.png
diff --git a/Examples/Example07/graphs/Heat_Scatter_theta_1_theta_2.png b/Examples/Example07/graphs/Heat_Scatter_theta_1_theta_2.png
diff --git a/Examples/Example07/graphs/Heat_Scatter_theta_2_theta_1.png b/Examples/Example07/graphs/Heat_Scatter_theta_2_theta_1.png
diff --git a/Examples/Example07/graphs/Histogram_sampling_0_theta_1.png b/Examples/Example07/graphs/Histogram_sampling_0_theta_1.png
diff --git a/Examples/Example07/graphs/Histogram_sampling_1_theta_2.png b/Examples/Example07/graphs/Histogram_sampling_1_theta_2.png
diff --git a/Examples/Example07/graphs/PosteriorContourPlots__0_1.png b/Examples/Example07/graphs/PosteriorContourPlots__0_1.png
diff --git a/Examples/Example07/graphs/PosteriorContourPlots__combined.png b/Examples/Example07/graphs/PosteriorContourPlots__combined.png
diff --git a/Examples/Example07/graphs/Posterior_Simulated_0.png b/Examples/Example07/graphs/Posterior_Simulated_0.png
diff --git a/Examples/Example07/graphs/Posterior_Simulated_1.png b/Examples/Example07/graphs/Posterior_Simulated_1.png
diff --git a/Examples/Example07/graphs/Posterior_Simulated_combined.png b/Examples/Example07/graphs/Posterior_Simulated_combined.png
diff --git a/Examples/Example07/graphs/scatter_matrix_posterior.png b/Examples/Example07/graphs/scatter_matrix_posterior.png
diff --git a/Examples/Example07/pickles/mcmc_burn_in_logP_and_parameter_samples.pkl b/Examples/Example07/pickles/mcmc_burn_in_logP_and_parameter_samples.pkl
diff --git a/Examples/Example07/pickles/mcmc_initial_point_parameters.pkl b/Examples/Example07/pickles/mcmc_initial_point_parameters.pkl
diff --git a/Examples/Example07/pickles/mcmc_last_point_sampled.pkl b/Examples/Example07/pickles/mcmc_last_point_sampled.pkl
diff --git a/Examples/Example07/pickles/mcmc_logP_and_parameter_samples.pkl b/Examples/Example07/pickles/mcmc_logP_and_parameter_samples.pkl
diff --git a/Examples/Example07/pickles/mcmc_map_logP.pkl b/Examples/Example07/pickles/mcmc_map_logP.pkl
diff --git a/Examples/Example07/pickles/mcmc_map_parameter_set.pkl b/Examples/Example07/pickles/mcmc_map_parameter_set.pkl
diff --git a/Examples/Example07/pickles/mcmc_post_burn_in_statistics.pkl b/Examples/Example07/pickles/mcmc_post_burn_in_statistics.pkl
diff --git a/Examples/Example13doeFunctionExample/CITATIONS/CiteSoftwareConsolidatedLog.txt b/Examples/Example13doeFunctionExample/CITATIONS/CiteSoftwareConsolidatedLog.txt
@@ -0,0 +1,46 @@
+#Warning: CiteSoftwareConsolidatedLog.txt may not include all softwares used. It is the end-user�s responsibility to verify that the no software citations are missing relative to those recorded in the complete logfile, CiteSoftwareCheckpointsLog.txt . This verification is important to do when using two or more codes together for the first time.
+---
+-
+    timestamp: >-
+        2022-11-17T14:26:45
+    unique_id: >-
+        https://doi.org/10.1002/cctc.202000953
+    software_name: >-
+        PEUQSE Bayesian Parameter Estimation
+    version:
+        - >-
+            1.0.0
+    author:
+        - >-
+            Aditya Savara
+        - >-
+            Eric A. Walker
+    doi:
+        - >-
+            https://doi.org/10.1002/cctc.202000953
+    cite:
+        - >-
+            Savara, A. and Walker, E.A. (2020), PEUQSE Intro 1: Bayesian Parameter Estimation Considering Uncertainty or Error from both Experiments and Theory. ChemCatChem. Accepted. doi:10.1002/cctc.202000953
+-
+    timestamp: >-
+        2022-11-17T14:26:45
+    unique_id: >-
+        https://doi.org/10.1002/cctc.202000976
+    software_name: >-
+        PEUQSE Bayesian Design of Experiments
+    version:
+        - >-
+            1.0.2
+    author:
+        - >-
+            Eric A. Walker
+        - >-
+            Kishore Ravisankar
+        - >-
+            Aditya Savara
+    doi:
+        - >-
+            https://doi.org/10.1002/cctc.202000976
+    cite:
+        - >-
+            Eric Alan Walker, Kishore Ravisankar, Aditya Savara. PEUQSE Intro 2: Harnessing Uncertainties from Data Sets, Bayesian Design of Experiments in Chemical Kinetics. ChemCatChem. Accepted. doi:10.1002/cctc.202000976
diff --git a/Examples/Example13doeFunctionExample/calculated_resultObj1.p b/Examples/Example13doeFunctionExample/calculated_resultObj1.p
diff --git a/Examples/Example13doeFunctionExample/calculated_resultObj2.p b/Examples/Example13doeFunctionExample/calculated_resultObj2.p
diff --git a/Examples/Example13doeFunctionExample/calculated_resultObj3.p b/Examples/Example13doeFunctionExample/calculated_resultObj3.p
diff --git a/Examples/Example13doeFunctionExample/calculated_resultObj4.p b/Examples/Example13doeFunctionExample/calculated_resultObj4.p
diff --git a/Examples/Example13doeFunctionExample/expected_resultObj3.p b/Examples/Example13doeFunctionExample/expected_resultObj3.p
diff --git a/Examples/Example13doeFunctionExample/expected_resultObj4.p b/Examples/Example13doeFunctionExample/expected_resultObj4.p
diff --git a/...s/Example13doeFunctionExample/graphs/Info_gain_Meshgrid_modulation_1_manual.png b/...s/Example13doeFunctionExample/graphs/Info_gain_Meshgrid_modulation_1_manual.png
diff --git a/...ple13doeFunctionExample/graphs/Info_gain_TrisurfacePlot_modulation_1_manual.png b/...ple13doeFunctionExample/graphs/Info_gain_TrisurfacePlot_modulation_1_manual.png
diff --git a/...nctionExample/logs_and_csvs/ExportedResponsesData__last_called__ResponsesConsolidated.csv b/...nctionExample/logs_and_csvs/ExportedResponsesData__last_called__ResponsesConsolidated.csv
@@ -1,4 +1,4 @@
 ResponseAbscissa,Response0
-3.731499999999999773e+02,-1.259100327572904687e+00
-3.981499999999999773e+02,-1.302522908825510806e+00
-4.231499999999999773e+02,-1.219373337033631044e+00
+3.731499999999999773e+02,-1.915483275647804406e+00
+3.981499999999999773e+02,-1.977225512324277235e+00
+4.231499999999999773e+02,-1.858775381117029779e+00
diff --git a/...e13doeFunctionExample/logs_and_csvs/ExportedResponsesData__map__ResponsesConsolidated.csv b/...e13doeFunctionExample/logs_and_csvs/ExportedResponsesData__map__ResponsesConsolidated.csv
@@ -1,4 +1,4 @@
 ResponseAbscissa,Response0
-3.731499999999999773e+02,-9.485350461578517800e-01
-3.981499999999999773e+02,-9.819816564434895589e-01
-4.231499999999999773e+02,-9.180496078959553552e-01
+3.731499999999999773e+02,-1.915483275647804406e+00
+3.981499999999999773e+02,-1.977225512324277235e+00
+4.231499999999999773e+02,-1.858775381117029779e+00
diff --git a/...13doeFunctionExample/logs_and_csvs/ExportedResponsesData__muap__ResponsesConsolidated.csv b/...13doeFunctionExample/logs_and_csvs/ExportedResponsesData__muap__ResponsesConsolidated.csv
@@ -1,4 +1,4 @@
 ResponseAbscissa,Response0
-3.731499999999999773e+02,-1.259100327572904687e+00
-3.981499999999999773e+02,-1.302522908825510806e+00
-4.231499999999999773e+02,-1.219373337033631044e+00
+3.731499999999999773e+02,-1.915483275647804406e+00
+3.981499999999999773e+02,-1.977225512324277235e+00
+4.231499999999999773e+02,-1.858775381117029779e+00
diff --git a/...eFunctionExample/logs_and_csvs/ExportedResponsesData__observed__ResponsesConsolidated.csv b/...eFunctionExample/logs_and_csvs/ExportedResponsesData__observed__ResponsesConsolidated.csv
@@ -1,4 +1,4 @@
 ResponseAbscissa,Response0
-3.731499999999999773e+02,-5.707256172139105743e-01
-3.981499999999999773e+02,-6.172571180883399400e-01
-4.231499999999999773e+02,-5.294719068553805918e-01
+3.731499999999999773e+02,-1.577303054557956052e+00
+3.981499999999999773e+02,-1.686306387970618825e+00
+4.231499999999999773e+02,-1.477671344387389896e+00
diff --git a/...les/Example13doeFunctionExample/logs_and_csvs/mcmc_burn_in_logP_and_parameter_samples.csv b/...les/Example13doeFunctionExample/logs_and_csvs/mcmc_burn_in_logP_and_parameter_samples.csv
@@ -1 +1 @@
--8.686043871940245253e+01,1.709999999999999298e-01,-5.000000000000013115e-05
+-4.935237394914908649e+00,1.709999999999999298e-01,-5.000000000000013115e-05
diff --git a/Examples/Example13doeFunctionExample/logs_and_csvs/mcmc_logP_and_parameter_samples.csv b/Examples/Example13doeFunctionExample/logs_and_csvs/mcmc_logP_and_parameter_samples.csv
@@ -1,3 +1,3 @@
--8.686043871940245253e+01,1.709999999999999298e-01,-5.000000000000013115e-05
--6.438891032982789753e+00,1.027142785743617448e-01,3.729274392085922139e-05
--6.438891032982789753e+00,1.027142785743617448e-01,3.729274392085922139e-05
+-4.935237394914908649e+00,1.709999999999999298e-01,-5.000000000000013115e-05
+-4.935237394914908649e+00,1.709999999999999298e-01,-5.000000000000013115e-05
+-4.935237394914908649e+00,1.709999999999999298e-01,-5.000000000000013115e-05
diff --git a/Examples/Example13doeFunctionExample/logs_and_csvs/mcmc_log_file.txt b/Examples/Example13doeFunctionExample/logs_and_csvs/mcmc_log_file.txt
@@ -1,12 +1,12 @@
 self.initial_point_parameters:[ 1.71e-01 -5.00e-05]
-MAP_logP:[-6.43889103]
-self.map_parameter_set:[1.02714279e-01 3.72927439e-05]
-self.map_index:1
-self.mu_AP_parameter_set:[1.25476186e-01 8.19516261e-06]
-self.stdap_parameter_set:[3.21901978e-02 4.11501941e-05]
+MAP_logP:[-4.93523739]
+self.map_parameter_set:[ 1.71e-01 -5.00e-05]
+self.map_index:0
+self.mu_AP_parameter_set:[ 1.71e-01 -5.00e-05]
+self.stdap_parameter_set:[0. 0.]
 self.info_gain:0.0
-evidence:0.004748659499016179
+evidence:0.02427151448860008
 posterior_cov_matrix:
-[[ 1.55431325e-03 -1.98694933e-06]
- [-1.98694933e-06  2.54000771e-09]]
-Convergence Status: Warning - The difference between the MAP parameter set and mu_AP parameter set is greater than 10% of the prior standard deviations in at least one parameter. This means that either your posterior distribution is asymmetric or that it is not yet converged. This may mean that you need to increase your mcmc_length, increase or decrease your mcmc_relative_step_length, or change what is used for the model response.  There is no general method for knowing the right  value for mcmc_relative_step_length since it depends on the sharpness and smoothness of the response. See for example https://www.sciencedirect.com/science/article/pii/S0039602816300632
+[[0. 0.]
+ [0. 0.]]
+Convergence Status: The difference between the MAP parameter set and mu_AP parameter set is less than 10% of the prior standard deviations for each parameter. There is no general method for knowing when the correct solution has been obtained, but this small difference is one sign of a converged solution.
diff --git a/Examples/Example13doeFunctionExample/pickles/mcmc_burn_in_logP_and_parameter_samples.pkl b/Examples/Example13doeFunctionExample/pickles/mcmc_burn_in_logP_and_parameter_samples.pkl
diff --git a/Examples/Example13doeFunctionExample/pickles/mcmc_initial_point_parameters.pkl b/Examples/Example13doeFunctionExample/pickles/mcmc_initial_point_parameters.pkl
diff --git a/Examples/Example13doeFunctionExample/pickles/mcmc_last_point_sampled.pkl b/Examples/Example13doeFunctionExample/pickles/mcmc_last_point_sampled.pkl
diff --git a/Examples/Example13doeFunctionExample/pickles/mcmc_logP_and_parameter_samples.pkl b/Examples/Example13doeFunctionExample/pickles/mcmc_logP_and_parameter_samples.pkl
diff --git a/Examples/Example13doeFunctionExample/pickles/mcmc_map_logP.pkl b/Examples/Example13doeFunctionExample/pickles/mcmc_map_logP.pkl
diff --git a/Examples/Example13doeFunctionExample/pickles/mcmc_map_parameter_set.pkl b/Examples/Example13doeFunctionExample/pickles/mcmc_map_parameter_set.pkl
diff --git a/Examples/Example13doeFunctionExample/pickles/mcmc_post_burn_in_statistics.pkl b/Examples/Example13doeFunctionExample/pickles/mcmc_post_burn_in_statistics.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod1_cond1.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod1_cond1.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod1_cond2.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod1_cond2.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod1_cond3.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod1_cond3.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod1_cond4.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod1_cond4.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod1_cond5.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod1_cond5.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod1_cond6.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod1_cond6.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod1_cond7.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod1_cond7.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod1_cond8.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod1_cond8.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod1_cond9.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod1_cond9.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod2_cond1.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod2_cond1.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod2_cond2.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod2_cond2.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod2_cond3.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod2_cond3.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod2_cond4.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod2_cond4.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod2_cond5.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod2_cond5.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod2_cond6.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod2_cond6.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod2_cond7.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod2_cond7.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod2_cond8.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod2_cond8.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod2_cond9.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod2_cond9.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod3_cond1.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod3_cond1.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod3_cond2.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod3_cond2.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod3_cond3.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod3_cond3.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod3_cond4.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod3_cond4.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod3_cond5.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod3_cond5.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod3_cond6.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod3_cond6.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod3_cond7.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod3_cond7.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod3_cond8.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod3_cond8.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod3_cond9.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod3_cond9.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod4_cond1.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod4_cond1.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod4_cond2.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod4_cond2.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod4_cond3.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod4_cond3.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod4_cond4.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod4_cond4.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod4_cond5.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod4_cond5.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod4_cond6.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod4_cond6.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod4_cond7.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod4_cond7.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod4_cond8.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod4_cond8.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod4_cond9.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod4_cond9.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod5_cond1.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod5_cond1.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod5_cond2.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod5_cond2.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod5_cond3.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod5_cond3.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod5_cond4.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod5_cond4.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod5_cond5.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod5_cond5.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod5_cond6.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod5_cond6.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod5_cond7.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod5_cond7.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod5_cond8.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod5_cond8.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod5_cond9.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod5_cond9.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod6_cond1.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod6_cond1.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod6_cond2.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod6_cond2.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod6_cond3.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod6_cond3.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod6_cond4.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod6_cond4.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod6_cond5.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod6_cond5.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod6_cond6.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod6_cond6.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod6_cond7.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod6_cond7.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod6_cond8.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod6_cond8.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod6_cond9.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod6_cond9.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod7_cond1.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod7_cond1.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod7_cond2.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod7_cond2.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod7_cond3.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod7_cond3.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod7_cond4.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod7_cond4.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod7_cond5.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod7_cond5.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod7_cond6.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod7_cond6.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod7_cond7.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod7_cond7.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod7_cond8.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod7_cond8.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod7_cond9.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod7_cond9.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod8_cond1.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod8_cond1.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod8_cond2.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod8_cond2.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod8_cond3.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod8_cond3.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod8_cond4.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod8_cond4.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod8_cond5.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod8_cond5.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod8_cond6.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod8_cond6.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod8_cond7.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod8_cond7.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod8_cond8.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod8_cond8.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod8_cond9.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod8_cond9.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod9_cond1.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod9_cond1.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod9_cond2.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod9_cond2.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod9_cond3.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod9_cond3.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod9_cond4.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod9_cond4.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod9_cond5.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod9_cond5.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod9_cond6.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod9_cond6.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod9_cond7.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod9_cond7.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod9_cond8.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod9_cond8.pkl
diff --git a/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod9_cond9.pkl b/...eFunctionExample/pickles/mpi_cached_files/conditionsPermutationAndInfoGain_mod9_cond9.pkl
diff --git a/...doeFunctionExample/pickles/mpi_cached_files/mcmc_burn_in_logP_and_parameter_samples_1.pkl b/...doeFunctionExample/pickles/mpi_cached_files/mcmc_burn_in_logP_and_parameter_samples_1.pkl
diff --git a/...doeFunctionExample/pickles/mpi_cached_files/mcmc_burn_in_logP_and_parameter_samples_2.pkl b/...doeFunctionExample/pickles/mpi_cached_files/mcmc_burn_in_logP_and_parameter_samples_2.pkl
diff --git a/...doeFunctionExample/pickles/mpi_cached_files/mcmc_burn_in_logP_and_parameter_samples_3.pkl b/...doeFunctionExample/pickles/mpi_cached_files/mcmc_burn_in_logP_and_parameter_samples_3.pkl
diff --git a/...doeFunctionExample/pickles/mpi_cached_files/mcmc_burn_in_logP_and_parameter_samples_4.pkl b/...doeFunctionExample/pickles/mpi_cached_files/mcmc_burn_in_logP_and_parameter_samples_4.pkl
diff --git a/...doeFunctionExample/pickles/mpi_cached_files/mcmc_burn_in_logP_and_parameter_samples_5.pkl b/...doeFunctionExample/pickles/mpi_cached_files/mcmc_burn_in_logP_and_parameter_samples_5.pkl
diff --git a/...doeFunctionExample/pickles/mpi_cached_files/mcmc_burn_in_logP_and_parameter_samples_6.pkl b/...doeFunctionExample/pickles/mpi_cached_files/mcmc_burn_in_logP_and_parameter_samples_6.pkl
diff --git a/...doeFunctionExample/pickles/mpi_cached_files/mcmc_burn_in_logP_and_parameter_samples_7.pkl b/...doeFunctionExample/pickles/mpi_cached_files/mcmc_burn_in_logP_and_parameter_samples_7.pkl
diff --git a/...doeFunctionExample/pickles/mpi_cached_files/mcmc_burn_in_logP_and_parameter_samples_8.pkl b/...doeFunctionExample/pickles/mpi_cached_files/mcmc_burn_in_logP_and_parameter_samples_8.pkl
diff --git a/...doeFunctionExample/pickles/mpi_cached_files/mcmc_burn_in_logP_and_parameter_samples_9.pkl b/...doeFunctionExample/pickles/mpi_cached_files/mcmc_burn_in_logP_and_parameter_samples_9.pkl
diff --git a/.../Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_initial_point_parameters_1.pkl b/.../Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_initial_point_parameters_1.pkl
diff --git a/.../Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_initial_point_parameters_2.pkl b/.../Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_initial_point_parameters_2.pkl
diff --git a/.../Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_initial_point_parameters_3.pkl b/.../Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_initial_point_parameters_3.pkl
diff --git a/.../Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_initial_point_parameters_4.pkl b/.../Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_initial_point_parameters_4.pkl
diff --git a/.../Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_initial_point_parameters_5.pkl b/.../Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_initial_point_parameters_5.pkl
diff --git a/.../Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_initial_point_parameters_6.pkl b/.../Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_initial_point_parameters_6.pkl
diff --git a/.../Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_initial_point_parameters_7.pkl b/.../Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_initial_point_parameters_7.pkl
diff --git a/.../Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_initial_point_parameters_8.pkl b/.../Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_initial_point_parameters_8.pkl
diff --git a/.../Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_initial_point_parameters_9.pkl b/.../Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_initial_point_parameters_9.pkl
diff --git a/Examples/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_last_point_sampled_1.pkl b/Examples/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_last_point_sampled_1.pkl
diff --git a/Examples/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_last_point_sampled_2.pkl b/Examples/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_last_point_sampled_2.pkl
diff --git a/Examples/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_last_point_sampled_3.pkl b/Examples/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_last_point_sampled_3.pkl
diff --git a/Examples/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_last_point_sampled_4.pkl b/Examples/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_last_point_sampled_4.pkl
diff --git a/Examples/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_last_point_sampled_5.pkl b/Examples/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_last_point_sampled_5.pkl
diff --git a/Examples/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_last_point_sampled_6.pkl b/Examples/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_last_point_sampled_6.pkl
diff --git a/Examples/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_last_point_sampled_7.pkl b/Examples/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_last_point_sampled_7.pkl
diff --git a/Examples/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_last_point_sampled_8.pkl b/Examples/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_last_point_sampled_8.pkl
diff --git a/Examples/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_last_point_sampled_9.pkl b/Examples/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_last_point_sampled_9.pkl
diff --git a/...xample13doeFunctionExample/pickles/mpi_cached_files/mcmc_logP_and_parameter_samples_1.pkl b/...xample13doeFunctionExample/pickles/mpi_cached_files/mcmc_logP_and_parameter_samples_1.pkl
diff --git a/...xample13doeFunctionExample/pickles/mpi_cached_files/mcmc_logP_and_parameter_samples_2.pkl b/...xample13doeFunctionExample/pickles/mpi_cached_files/mcmc_logP_and_parameter_samples_2.pkl
diff --git a/...xample13doeFunctionExample/pickles/mpi_cached_files/mcmc_logP_and_parameter_samples_3.pkl b/...xample13doeFunctionExample/pickles/mpi_cached_files/mcmc_logP_and_parameter_samples_3.pkl
diff --git a/...xample13doeFunctionExample/pickles/mpi_cached_files/mcmc_logP_and_parameter_samples_4.pkl b/...xample13doeFunctionExample/pickles/mpi_cached_files/mcmc_logP_and_parameter_samples_4.pkl
diff --git a/...xample13doeFunctionExample/pickles/mpi_cached_files/mcmc_logP_and_parameter_samples_5.pkl b/...xample13doeFunctionExample/pickles/mpi_cached_files/mcmc_logP_and_parameter_samples_5.pkl
diff --git a/...xample13doeFunctionExample/pickles/mpi_cached_files/mcmc_logP_and_parameter_samples_6.pkl b/...xample13doeFunctionExample/pickles/mpi_cached_files/mcmc_logP_and_parameter_samples_6.pkl
diff --git a/...xample13doeFunctionExample/pickles/mpi_cached_files/mcmc_logP_and_parameter_samples_7.pkl b/...xample13doeFunctionExample/pickles/mpi_cached_files/mcmc_logP_and_parameter_samples_7.pkl
diff --git a/...xample13doeFunctionExample/pickles/mpi_cached_files/mcmc_logP_and_parameter_samples_8.pkl b/...xample13doeFunctionExample/pickles/mpi_cached_files/mcmc_logP_and_parameter_samples_8.pkl
diff --git a/...xample13doeFunctionExample/pickles/mpi_cached_files/mcmc_logP_and_parameter_samples_9.pkl b/...xample13doeFunctionExample/pickles/mpi_cached_files/mcmc_logP_and_parameter_samples_9.pkl
diff --git a/Examples/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_map_logP_1.pkl b/Examples/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_map_logP_1.pkl
diff --git a/Examples/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_map_logP_2.pkl b/Examples/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_map_logP_2.pkl
diff --git a/Examples/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_map_logP_3.pkl b/Examples/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_map_logP_3.pkl
diff --git a/Examples/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_map_logP_4.pkl b/Examples/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_map_logP_4.pkl
diff --git a/Examples/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_map_logP_5.pkl b/Examples/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_map_logP_5.pkl
diff --git a/Examples/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_map_logP_6.pkl b/Examples/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_map_logP_6.pkl
diff --git a/Examples/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_map_logP_7.pkl b/Examples/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_map_logP_7.pkl
diff --git a/Examples/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_map_logP_8.pkl b/Examples/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_map_logP_8.pkl
diff --git a/Examples/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_map_logP_9.pkl b/Examples/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_map_logP_9.pkl
diff --git a/Examples/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_map_parameter_set_1.pkl b/Examples/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_map_parameter_set_1.pkl
diff --git a/Examples/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_map_parameter_set_2.pkl b/Examples/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_map_parameter_set_2.pkl
diff --git a/Examples/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_map_parameter_set_3.pkl b/Examples/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_map_parameter_set_3.pkl
diff --git a/Examples/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_map_parameter_set_4.pkl b/Examples/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_map_parameter_set_4.pkl
diff --git a/Examples/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_map_parameter_set_5.pkl b/Examples/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_map_parameter_set_5.pkl
diff --git a/Examples/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_map_parameter_set_6.pkl b/Examples/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_map_parameter_set_6.pkl
diff --git a/Examples/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_map_parameter_set_7.pkl b/Examples/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_map_parameter_set_7.pkl
diff --git a/Examples/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_map_parameter_set_8.pkl b/Examples/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_map_parameter_set_8.pkl
diff --git a/Examples/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_map_parameter_set_9.pkl b/Examples/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_map_parameter_set_9.pkl
diff --git a/...s/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_post_burn_in_statistics_1.pkl b/...s/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_post_burn_in_statistics_1.pkl
diff --git a/...s/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_post_burn_in_statistics_2.pkl b/...s/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_post_burn_in_statistics_2.pkl
diff --git a/...s/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_post_burn_in_statistics_3.pkl b/...s/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_post_burn_in_statistics_3.pkl
diff --git a/...s/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_post_burn_in_statistics_4.pkl b/...s/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_post_burn_in_statistics_4.pkl
diff --git a/...s/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_post_burn_in_statistics_5.pkl b/...s/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_post_burn_in_statistics_5.pkl
diff --git a/...s/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_post_burn_in_statistics_6.pkl b/...s/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_post_burn_in_statistics_6.pkl
diff --git a/...s/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_post_burn_in_statistics_7.pkl b/...s/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_post_burn_in_statistics_7.pkl
diff --git a/...s/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_post_burn_in_statistics_8.pkl b/...s/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_post_burn_in_statistics_8.pkl
diff --git a/...s/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_post_burn_in_statistics_9.pkl b/...s/Example13doeFunctionExample/pickles/mpi_cached_files/mcmc_post_burn_in_statistics_9.pkl
diff --git a/...Example13doeFunctionExample/pickles/mpi_cached_files/parModulationInfoGainMatrix_mod1.pkl b/...Example13doeFunctionExample/pickles/mpi_cached_files/parModulationInfoGainMatrix_mod1.pkl
diff --git a/...Example13doeFunctionExample/pickles/mpi_cached_files/parModulationInfoGainMatrix_mod2.pkl b/...Example13doeFunctionExample/pickles/mpi_cached_files/parModulationInfoGainMatrix_mod2.pkl
diff --git a/...Example13doeFunctionExample/pickles/mpi_cached_files/parModulationInfoGainMatrix_mod3.pkl b/...Example13doeFunctionExample/pickles/mpi_cached_files/parModulationInfoGainMatrix_mod3.pkl
diff --git a/...Example13doeFunctionExample/pickles/mpi_cached_files/parModulationInfoGainMatrix_mod4.pkl b/...Example13doeFunctionExample/pickles/mpi_cached_files/parModulationInfoGainMatrix_mod4.pkl
diff --git a/...Example13doeFunctionExample/pickles/mpi_cached_files/parModulationInfoGainMatrix_mod5.pkl b/...Example13doeFunctionExample/pickles/mpi_cached_files/parModulationInfoGainMatrix_mod5.pkl
diff --git a/...Example13doeFunctionExample/pickles/mpi_cached_files/parModulationInfoGainMatrix_mod6.pkl b/...Example13doeFunctionExample/pickles/mpi_cached_files/parModulationInfoGainMatrix_mod6.pkl
diff --git a/...Example13doeFunctionExample/pickles/mpi_cached_files/parModulationInfoGainMatrix_mod7.pkl b/...Example13doeFunctionExample/pickles/mpi_cached_files/parModulationInfoGainMatrix_mod7.pkl
diff --git a/...Example13doeFunctionExample/pickles/mpi_cached_files/parModulationInfoGainMatrix_mod8.pkl b/...Example13doeFunctionExample/pickles/mpi_cached_files/parModulationInfoGainMatrix_mod8.pkl
diff --git a/...Example13doeFunctionExample/pickles/mpi_cached_files/parModulationInfoGainMatrix_mod9.pkl b/...Example13doeFunctionExample/pickles/mpi_cached_files/parModulationInfoGainMatrix_mod9.pkl
diff --git a/...Example13doeFunctionExample/runfile_for_unit_test_parallel_doe_conditions_exploration.pkl b/...Example13doeFunctionExample/runfile_for_unit_test_parallel_doe_conditions_exploration.pkl
diff --git a/Examples/Example13doeFunctionExample/runfile_for_unit_test_parallel_doe_control.pkl b/Examples/Example13doeFunctionExample/runfile_for_unit_test_parallel_doe_control.pkl
diff --git a/...s/Example13doeFunctionExample/runfile_for_unit_test_parallel_doe_parameter_modulation.pkl b/...s/Example13doeFunctionExample/runfile_for_unit_test_parallel_doe_parameter_modulation.pkl
diff --git a/Examples/Example24/CITATIONS/CiteSoftwareConsolidatedLog.txt b/Examples/Example24/CITATIONS/CiteSoftwareConsolidatedLog.txt
@@ -0,0 +1,23 @@
+#Warning: CiteSoftwareConsolidatedLog.txt may not include all softwares used. It is the end-user�s responsibility to verify that the no software citations are missing relative to those recorded in the complete logfile, CiteSoftwareCheckpointsLog.txt . This verification is important to do when using two or more codes together for the first time.
+---
+-
+    timestamp: >-
+        2022-11-17T14:30:08
+    unique_id: >-
+        https://doi.org/10.1002/cctc.202000953
+    software_name: >-
+        PEUQSE Bayesian Parameter Estimation
+    version:
+        - >-
+            1.0.0
+    author:
+        - >-
+            Aditya Savara
+        - >-
+            Eric A. Walker
+    doi:
+        - >-
+            https://doi.org/10.1002/cctc.202000953
+    cite:
+        - >-
+            Savara, A. and Walker, E.A. (2020), PEUQSE Intro 1: Bayesian Parameter Estimation Considering Uncertainty or Error from both Experiments and Theory. ChemCatChem. Accepted. doi:10.1002/cctc.202000953
diff --git a/Examples/Example24/calculated_resultObj1.p b/Examples/Example24/calculated_resultObj1.p
diff --git a/Examples/Example24/expected_resultObj1.p b/Examples/Example24/expected_resultObj1.p
diff --git a/Examples/Example24/graphs/AutoCorrelationPlot_Combined_Parameters.png b/Examples/Example24/graphs/AutoCorrelationPlot_Combined_Parameters.png
diff --git a/Examples/Example24/graphs/AutoCorrelationPlot_Ea.png b/Examples/Example24/graphs/AutoCorrelationPlot_Ea.png
diff --git a/Examples/Example24/graphs/AutoCorrelationPlot_logA.png b/Examples/Example24/graphs/AutoCorrelationPlot_logA.png
diff --git a/Examples/Example24/graphs/GewekeDiagnostic_Combined_Parameters.png b/Examples/Example24/graphs/GewekeDiagnostic_Combined_Parameters.png
diff --git a/Examples/Example24/graphs/GewekeDiagnostic_Ea.png b/Examples/Example24/graphs/GewekeDiagnostic_Ea.png
diff --git a/Examples/Example24/graphs/GewekeDiagnostic_logA.png b/Examples/Example24/graphs/GewekeDiagnostic_logA.png
diff --git a/Examples/Example24/graphs/Heat_Scatter_Ea_logA.png b/Examples/Example24/graphs/Heat_Scatter_Ea_logA.png
diff --git a/Examples/Example24/graphs/Heat_Scatter_logA_Ea.png b/Examples/Example24/graphs/Heat_Scatter_logA_Ea.png
diff --git a/Examples/Example24/graphs/Histogram_sampling_0_logA.png b/Examples/Example24/graphs/Histogram_sampling_0_logA.png
diff --git a/Examples/Example24/graphs/Histogram_sampling_1_Ea.png b/Examples/Example24/graphs/Histogram_sampling_1_Ea.png
diff --git a/Examples/Example24/graphs/PosteriorContourPlotDisproportionation__0_1.png b/Examples/Example24/graphs/PosteriorContourPlotDisproportionation__0_1.png
diff --git a/Examples/Example24/graphs/PosteriorContourPlotDisproportionation__combined.png b/Examples/Example24/graphs/PosteriorContourPlotDisproportionation__combined.png
diff --git a/Examples/Example24/graphs/PosteriorContourPlots__0_1.png b/Examples/Example24/graphs/PosteriorContourPlots__0_1.png
diff --git a/Examples/Example24/graphs/PosteriorContourPlots__combined.png b/Examples/Example24/graphs/PosteriorContourPlots__combined.png
diff --git a/Examples/Example24/graphs/Posterior_Simulated.png b/Examples/Example24/graphs/Posterior_Simulated.png
diff --git a/Examples/Example24/graphs/Posterior_Simulated_combined.png b/Examples/Example24/graphs/Posterior_Simulated_combined.png
diff --git a/Examples/Example24/graphs/scatter_matrix_posterior.png b/Examples/Example24/graphs/scatter_matrix_posterior.png
diff --git a/Examples/Example24/logs_and_csvs/mcmc_log_file.txt b/Examples/Example24/logs_and_csvs/mcmc_log_file.txt
@@ -5,7 +5,7 @@ self.map_index:1115
 self.mu_AP_parameter_set:[1.15915966e+01 1.31522493e+05]
 self.stdap_parameter_set:[8.26751149e-01 9.25040879e+03]
 self.info_gain:2.16427885413888
-evidence:3.3235588713850923e-15
+evidence:3.323558871385092e-15
 posterior_cov_matrix:
 [[6.83597706e-01 6.15878775e+03]
  [6.15878775e+03 8.55801085e+07]]

diff --git a/Examples/Example24/pickles/mcmc_burn_in_logP_and_parameter_samples.pkl b/Examples/Example24/pickles/mcmc_burn_in_logP_and_parameter_samples.pkl
diff --git a/Examples/Example24/pickles/mcmc_initial_point_parameters.pkl b/Examples/Example24/pickles/mcmc_initial_point_parameters.pkl
diff --git a/Examples/Example24/pickles/mcmc_last_point_sampled.pkl b/Examples/Example24/pickles/mcmc_last_point_sampled.pkl
diff --git a/Examples/Example24/pickles/mcmc_logP_and_parameter_samples.pkl b/Examples/Example24/pickles/mcmc_logP_and_parameter_samples.pkl
diff --git a/Examples/Example24/pickles/mcmc_map_logP.pkl b/Examples/Example24/pickles/mcmc_map_logP.pkl
diff --git a/Examples/Example24/pickles/mcmc_map_parameter_set.pkl b/Examples/Example24/pickles/mcmc_map_parameter_set.pkl
diff --git a/Examples/Example24/pickles/mcmc_post_burn_in_statistics.pkl b/Examples/Example24/pickles/mcmc_post_burn_in_statistics.pkl
diff --git a/Examples/Example26/CITATIONS/CITATIONS.cff b/Examples/Example26/CITATIONS/CITATIONS.cff
@@ -0,0 +1,12 @@
+---
+cff-version: 1.2.0
+message:2024-10-26T18:14:53
+title: PEUQSE Bayesian Parameter Estimation
+identifiers: 
+ - type: unique_id
+   value: https://doi.org/10.1002/cctc.202000953
+authors: 
+ - name: Aditya Savara
+ - name: Eric A. Walker
+version: 1.0.0
+doi: https://doi.org/10.1002/cctc.202000953
diff --git a/Examples/Example26/CITATIONS/CiteSoftwareCheckpointsLog.txt b/Examples/Example26/CITATIONS/CiteSoftwareCheckpointsLog.txt
@@ -0,0 +1,22 @@
+---
+-
+    timestamp: >-
+        2024-10-26T18:14:53
+    unique_id: >-
+        https://doi.org/10.1002/cctc.202000953
+    software_name: >-
+        PEUQSE Bayesian Parameter Estimation
+    version:
+        - >-
+            1.0.0
+    author:
+        - >-
+            Aditya Savara
+        - >-
+            Eric A. Walker
+    doi:
+        - >-
+            https://doi.org/10.1002/cctc.202000953
+    cite:
+        - >-
+            Savara, A. and Walker, E.A. (2020), PEUQSE Intro 1: Bayesian Parameter Estimation Considering Uncertainty or Error from both Experiments and Theory. ChemCatChem. Accepted. doi:10.1002/cctc.202000953
diff --git a/Examples/Example26/CITATIONS/CiteSoftwareUniqueIDs.txt b/Examples/Example26/CITATIONS/CiteSoftwareUniqueIDs.txt
@@ -0,0 +1 @@
+https://doi.org/10.1002/cctc.202000953
diff --git a/Examples/Example26/CITATIONS/IndividualCff/https___doi.org_10.1002_cctc.202000953.cff b/Examples/Example26/CITATIONS/IndividualCff/https___doi.org_10.1002_cctc.202000953.cff
@@ -0,0 +1,11 @@
+cff-version: 1.2.0
+message:2024-10-26T18:14:53
+title: PEUQSE Bayesian Parameter Estimation
+identifiers: 
+ - type: unique_id
+   value: https://doi.org/10.1002/cctc.202000953
+authors: 
+ - name: Aditya Savara
+ - name: Eric A. Walker
+version: 1.0.0
+doi: https://doi.org/10.1002/cctc.202000953
Original file line number	Diff line number	Diff line change
		@@ -1 +1,2 @@
		https://doi.org/10.1002/cctc.202000953
		https://github.com/minaskar/zeus
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		-8.686043871940245253e+01,1.709999999999999298e-01,-5.000000000000013115e-05
		-4.935237394914908649e+00,1.709999999999999298e-01,-5.000000000000013115e-05