Merge pull request #47 from YeChen-IDM/snakemake_integration

Snakemake plotting and reporting scripts integration; Update to the latest Eradication on M-O; update to version v1.1.0
InstituteforDiseaseModeling · Dec 5, 2022 · d363687 · d363687
2 parents 08a0362 + c6580bd
commit d363687
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diff --git a/README.md b/README.md
@@ -14,7 +14,7 @@
   - [Option 2_Run all Sites with Snakemake (Recommended)](#option-2_run-all-sites-with-snakemake-recommended)
     - [How to Change Default Setting](#how-to-change-default-setting)
     - [Snakemake Tips](#snakemake-tips)
-- [Generate Plots and Final Reports](#generate-plots-and-final-reports)
+- [Check Plots and Final Report](#check-plots-and-final-report)
 
 <!-- END doctoc generated TOC please keep comment here to allow auto update -->
 
@@ -112,23 +112,35 @@ snakemake -j
   snakemake -j
   ```
 
-  - If you want to re-run the analyzers steps with previous experiments you ran, you can delete the analyzer id files and run:
+  - If you want to re-run the analyzers steps with previous experiments you ran, you can delete the analyzer id files and all following the analyzers steps and run:
   ```bash
-  snakemake clean_ana clean_download -j
+  snakemake clean_ana -j
   snakemake -j
   ```
 
-  - Simular to previous scenario, if you want to run only the download and plotting steps:
+  - Simular to previous scenario, if you want to only re-run starting from the download steps:
   ```bash
   snakemake clean_download -j
   snakemake -j
+  ```
+
+  - Simular to previous scenario, if you want to only re-run starting from the plotting steps:
+  ```bash
+  snakemake clean_plot -j
+  snakemake -j
+  ```
+  - Simular to previous scenario, if you want to only re-run starting from the reporting steps:
+  ```bash
+  snakemake clean_report -j
+  snakemake -j
   ```
 
-  - If you want to re-run simulations for certain sites, delete COMPS ID files for those sites that you want to -re-run 
-    (/simulations/COMPS_ID/{site_name}_COMPS_ID_exp_submit, _analyzers and _download files) and run "snakemake -j" again.
+    - If you want to re-run simulations for certain sites, delete COMPS ID files for those sites that you want to -re-run 
+      (/simulations/COMPS_ID/{site_name}_COMPS_ID_exp_submit, _analyzers and _download files) and run
+      "snakemake clean_plot -j" and then "snakemake -j" again.
 
-  - If you want to re-run the analyzers and plotting steps for certain sites, delete the {site_name}_COMPS_ID_analyzers 
-    and _download files only and re-run "snakemake -j".
+    - If you want to re-run the analyzers and plotting steps for certain sites, delete the {site_name}_COMPS_ID_analyzers 
+      and _download files only and run "snakemake clean_plot -j" and then "snakemake -j".
 
 - Other snakemake tips:
   - Snakemake log can be found in '\malaria-model_validation\simulations\.snakemake\log'.
@@ -137,10 +149,6 @@ snakemake -j
   - If you have incompleted file from previous snakemake instance, you can run "snakemake --cleanup-metadata 
     <filenames>" to clean up the metadata. Or you can delete the '.snakemake' folder to clean up the metadata manually.
 
-
-# Generate Plots and Final Reports
-Run Plotting and reportting scripts with site(s) that you ran:
-```bash
-Rscript create_plots\run_generate_validation_comparisons_site.R
-python3 report\create_pdf_report_3.py
-```
+# Check Plots and Final Report
+You can check the plots in \malaria-model_validation\report\_plots folder and final report:
+\malaria-model_validation\report\Malaria_model_validation_output_{date}}({time}).pdf.
diff --git a/create_plots/run_generate_validation_comparisons_site.py b/create_plots/run_generate_validation_comparisons_site.py
@@ -6,7 +6,7 @@
 # reference dataset.
 
 from simulations.manifest import simulation_output_filepath, benchmark_simulation_filepath, \
-     base_reference_filepath, plot_output_filepath
+     base_reference_filepath, plot_output_filepath, comps_id_folder
 from simulations.helpers import load_coordinator_df
 from create_plots.helpers_coordinate_each_relationship import generate_age_incidence_outputs, \
     generate_age_prevalence_outputs, generate_parasite_density_outputs, generate_infectiousness_outputs, \
@@ -67,6 +67,9 @@ def run():
     generate_age_infection_duration_outputs(coord_csv, simulation_output_filepath, base_reference_filepath,
                                             plot_output_filepath, pos_thresh_dens, duration_bins,
                                             benchmark_simulation_filepath=benchmark_simulation_filepath)
+    # generate dummy file for snakemake plot rule.
+    with open(comps_id_folder + 'plot_completed', 'w') as file:
+        file.write('Plotting is completed.')
 
 
 if __name__ == '__main__':

diff --git a/report/Malaria_model_validation_output_06-06-2022_12-08-52.pdf b/report/Malaria_model_validation_output_06-06-2022_12-08-52.pdf
diff --git a/...ion_output_22-07-2022_11-02-06_v0.1.0.pdf → ...alaria_model_validation_output_v0.1.0.pdf b/...ion_output_22-07-2022_11-02-06_v0.1.0.pdf → ...alaria_model_validation_output_v0.1.0.pdf
diff --git a/...ion_output_22-07-2022_11-40-46_v1.0.0.pdf → ...alaria_model_validation_output_v1.0.0.pdf b/...ion_output_22-07-2022_11-40-46_v1.0.0.pdf → ...alaria_model_validation_output_v1.0.0.pdf
diff --git a/report/Malaria_model_validation_output_v1.1.0.pdf b/report/Malaria_model_validation_output_v1.1.0.pdf
diff --git a/report/_plots_Python/comparison_metric_table_incidence_age.csv b/report/_plots_Python/comparison_metric_table_incidence_age.csv
@@ -1,8 +1,8 @@
 Site,mean_rel_diff,mean_abs_diff,corr_slope,corr_r_squared,mean_rel_slope_diff,mean_abs_slpe_diff
-chonyi_1999,2.359037548734484,0.9527363074851136,1.0864286693488938,0.4909669217402624,8.439261308486314,0.14796578722119713
-dielmo_1990,1.4081812654541295,1.2458223958828658,1.4662896933383196,0.9136326384809177,2.7887861639664027,0.33110512980784795
-dongubougou_1999,0.20347658923882478,0.20058805816706715,1.084140813158362,0.8655226920015983,0.5908511281184664,0.055915663172901274
-ebolakounou_1997,3.5298250987213704,1.3500864647430642,1.5910150844822293,0.36079816878572557,5.540963413406026,0.09385532642413291
+chonyi_1999,2.359037548734484,0.9527363074851135,1.0864286693488938,0.4909669217402626,8.439261308486312,0.14796578722119708
+dielmo_1990,1.4081812654541295,1.2458223958828656,1.4662896933383196,0.9136326384809177,2.788786163966403,0.3311051298078479
+dongubougou_1999,0.20347658923882472,0.20058805816706715,1.0841408131583619,0.8655226920015985,0.5908511281184664,0.05591566317290126
+ebolakounou_1997,3.5298250987213704,1.3500864647430642,1.591015084482229,0.36079816878572557,5.540963413406026,0.09385532642413291
 koundou_1997,2.4201137951985316,2.1409045381563216,2.4059180140110406,0.583784813025154,4.061363882148547,0.2988974553053057
 ndiop_1993,0.46935752353216675,0.5183624018079345,1.3707184658549694,0.8617239579850393,1.4238643917237108,0.06385891135139789
 ngerenya_1999,2.1701872774703364,0.6138116970950674,-0.060277891520447935,0.015456288322816111,1.8822112986842252,0.15579650258632832

diff --git a/report/_plots_Python/comparison_metric_table_prevalence_age.csv b/report/_plots_Python/comparison_metric_table_prevalence_age.csv
@@ -1,12 +1,12 @@
 Site,mean_rel_diff,mean_abs_diff,corr_slope,corr_r_squared,mean_rel_slope_diff,mean_abs_slpe_diff
-chonyi_1999_month7,0.6825254910261515,0.3393820994465812,0.1566309755712942,0.4301695105868464,12.214132279434569,0.042317923534964316
-dielmo_1990_monthmultiple,0.5711687112890077,0.3965314003825952,0.6219099246260963,0.9274859257167195,0.8630959749052143,0.020346956805853512
+chonyi_1999_month7,0.6825254910261515,0.3393820994465812,0.15663097557129418,0.4301695105868461,12.214132279434569,0.042317923534964316
+dielmo_1990_monthmultiple,0.5711687112890077,0.3965314003825952,0.6219099246260962,0.9274859257167193,0.8630959749052138,0.02034695680585351
 dongubougou_1999_monthmultiple,0.2921917392007317,0.17073999016392666,0.13038640523567407,0.09423861595745166,0.6506923472111071,0.02470917658914631
 ebolakounou_1997_monthmultiple,0.6858638609195971,0.3886452217302862,-0.10398602600941884,0.09180777382837431,0.8668243442164759,0.010454242841899759
 koundou_1997_monthmultiple,0.5614177043381496,0.3462386846857258,0.43728547052724426,0.7472381451807503,1.3249240850644364,0.005923631221470194
 matsari_1970_month10,0.39820928816459034,0.18674109376023418,0.7863094941336288,0.9256435924626562,1.3770296193627964,0.012248340369871116
 matsari_1970_month2,0.6299855911450253,0.3950905744647875,0.7864003185032957,0.9932297717710127,,0.0024505860481569366
-matsari_1970_month7,0.4404135744799402,0.23401638055083646,0.676475606141136,0.8707864429680627,0.9187147875941257,0.008318495110730701
+matsari_1970_month7,0.4404135744799402,0.23401638055083646,0.676475606141136,0.8707864429680627,0.9187147875941255,0.0083184951107307
 ndiop_1993_monthmultiple,0.4657205735231557,0.14894292742359438,0.5214373120598216,0.795715073267172,0.6319126797626777,0.008540974359763517
 ngerenya_1999_month7,0.8510846198405031,0.2561096994580539,-0.002692043148475209,0.00011484196242583909,0.9246367805158168,0.03231061623631442
 rafin_marke_1970_month10,0.33576501065627096,0.14162445663845127,0.889262048689702,0.7164946161179646,0.5855068867610722,0.01670433705872292

diff --git a/report/_plots_Python/corr_ref_sim_points_incidence_age.png b/report/_plots_Python/corr_ref_sim_points_incidence_age.png
diff --git a/report/_plots_Python/corr_ref_sim_points_prevalence_age.png b/report/_plots_Python/corr_ref_sim_points_prevalence_age.png
diff --git a/report/_plots_Python/loglikelihood_prevalence_age.csv b/report/_plots_Python/loglikelihood_prevalence_age.csv
@@ -1,5 +1,5 @@
 site_month,loglikelihood_new_sim,loglikelihood_benchmark_sim
-dielmo_1990_monthmultiple,-3466.6023937629193,-3466.6023937629193
+dielmo_1990_monthmultiple,-3466.6023937629197,-3466.6023937629197
 dongubougou_1999_monthmultiple,-84.26103051901676,-84.26103051901676
 ebolakounou_1997_monthmultiple,-1363.029630690697,-1363.029630690697
 koundou_1997_monthmultiple,-1245.5403763380814,-1245.5403763380814

diff --git a/report/_plots_Python/scatter_benchmark_asex_dens.png b/report/_plots_Python/scatter_benchmark_asex_dens.png
diff --git a/report/_plots_Python/scatter_benchmark_gamet_dens.png b/report/_plots_Python/scatter_benchmark_gamet_dens.png
diff --git a/report/_plots_Python/scatter_benchmark_incidence_age.png b/report/_plots_Python/scatter_benchmark_incidence_age.png
diff --git a/report/_plots_Python/scatter_benchmark_infectiousness.png b/report/_plots_Python/scatter_benchmark_infectiousness.png
diff --git a/report/_plots_Python/scatter_benchmark_prevalence_age.png b/report/_plots_Python/scatter_benchmark_prevalence_age.png
diff --git a/report/_plots_Python/scatter_regression_incidence_age_correlation.png b/report/_plots_Python/scatter_regression_incidence_age_correlation.png
diff --git a/report/_plots_Python/scatter_regression_incidence_age_slope_correlation.png b/report/_plots_Python/scatter_regression_incidence_age_slope_correlation.png
diff --git a/report/_plots_Python/scatter_regression_prevalence_age_correlation.png b/report/_plots_Python/scatter_regression_prevalence_age_correlation.png
diff --git a/report/_plots_Python/scatter_regression_prevalence_age_slope_correlation.png b/report/_plots_Python/scatter_regression_prevalence_age_slope_correlation.png
diff --git a/report/_plots_Python/site_compare_asex_dens_age_dapelogo_2007.png b/report/_plots_Python/site_compare_asex_dens_age_dapelogo_2007.png
diff --git a/report/_plots_Python/site_compare_asex_dens_age_laye_2007.png b/report/_plots_Python/site_compare_asex_dens_age_laye_2007.png
diff --git a/report/_plots_Python/site_compare_asex_dens_age_matsari_1970.png b/report/_plots_Python/site_compare_asex_dens_age_matsari_1970.png
diff --git a/report/_plots_Python/site_compare_asex_dens_age_rafin_marke_1970.png b/report/_plots_Python/site_compare_asex_dens_age_rafin_marke_1970.png
diff --git a/report/_plots_Python/site_compare_asex_dens_age_sugungum_1970.png b/report/_plots_Python/site_compare_asex_dens_age_sugungum_1970.png
diff --git a/report/_plots_Python/site_compare_barplot_asex_dens_age.png b/report/_plots_Python/site_compare_barplot_asex_dens_age.png
diff --git a/report/_plots_Python/site_compare_barplot_gamet_dens_age.png b/report/_plots_Python/site_compare_barplot_gamet_dens_age.png
diff --git a/report/_plots_Python/site_compare_gamet_dens_age_dapelogo_2007.png b/report/_plots_Python/site_compare_gamet_dens_age_dapelogo_2007.png
diff --git a/report/_plots_Python/site_compare_gamet_dens_age_laye_2007.png b/report/_plots_Python/site_compare_gamet_dens_age_laye_2007.png
diff --git a/report/_plots_Python/site_compare_gamet_dens_age_matsari_1970.png b/report/_plots_Python/site_compare_gamet_dens_age_matsari_1970.png
diff --git a/report/_plots_Python/site_compare_gamet_dens_age_rafin_marke_1970.png b/report/_plots_Python/site_compare_gamet_dens_age_rafin_marke_1970.png
diff --git a/report/_plots_Python/site_compare_gamet_dens_age_sugungum_1970.png b/report/_plots_Python/site_compare_gamet_dens_age_sugungum_1970.png
diff --git a/report/_plots_Python/site_compare_incidence_age.png b/report/_plots_Python/site_compare_incidence_age.png
diff --git a/report/_plots_Python/site_compare_infect_duration_age_navrongo_2000.png b/report/_plots_Python/site_compare_infect_duration_age_navrongo_2000.png
diff --git a/report/_plots_Python/site_compare_infect_duration_measures_navrongo_2000.png b/report/_plots_Python/site_compare_infect_duration_measures_navrongo_2000.png
diff --git a/report/_plots_Python/site_compare_infect_duration_navrongo_2000.png b/report/_plots_Python/site_compare_infect_duration_navrongo_2000.png
diff --git a/report/_plots_Python/site_compare_infectiousness_dapelogo_2007.png b/report/_plots_Python/site_compare_infectiousness_dapelogo_2007.png
diff --git a/report/_plots_Python/site_compare_infectiousness_laye_2007.png b/report/_plots_Python/site_compare_infectiousness_laye_2007.png
diff --git a/report/_plots_Python/site_compare_prevalence_age.png b/report/_plots_Python/site_compare_prevalence_age.png
diff --git a/...comparison_metric_table_incidence_age.csv → ...comparison_metric_table_incidence_age.csv b/...comparison_metric_table_incidence_age.csv → ...comparison_metric_table_incidence_age.csv
diff --git a/...omparison_metric_table_prevalence_age.csv → ...omparison_metric_table_prevalence_age.csv b/...omparison_metric_table_prevalence_age.csv → ...omparison_metric_table_prevalence_age.csv
diff --git a/...2_v0.1.0/loglikelihood_prevalence_age.csv → ...s_v0.1.0/loglikelihood_prevalence_age.csv b/...2_v0.1.0/loglikelihood_prevalence_age.csv → ...s_v0.1.0/loglikelihood_prevalence_age.csv
diff --git a/..._07_22_v0.1.0/loglikelihoods_par_dens.csv → ..._plots_v0.1.0/loglikelihoods_par_dens.csv b/..._07_22_v0.1.0/loglikelihoods_par_dens.csv → ..._plots_v0.1.0/loglikelihoods_par_dens.csv
diff --git a/...22_v0.1.0/scatter_benchmark_asex_dens.png → ...ts_v0.1.0/scatter_benchmark_asex_dens.png b/...22_v0.1.0/scatter_benchmark_asex_dens.png → ...ts_v0.1.0/scatter_benchmark_asex_dens.png
diff --git a/...2_v0.1.0/scatter_benchmark_gamet_dens.png → ...s_v0.1.0/scatter_benchmark_gamet_dens.png b/...2_v0.1.0/scatter_benchmark_gamet_dens.png → ...s_v0.1.0/scatter_benchmark_gamet_dens.png
diff --git a/...0.1.0/scatter_benchmark_incidence_age.png → ...0.1.0/scatter_benchmark_incidence_age.png b/...0.1.0/scatter_benchmark_incidence_age.png → ...0.1.0/scatter_benchmark_incidence_age.png
diff --git a/....1.0/scatter_benchmark_infectiousness.png → ....1.0/scatter_benchmark_infectiousness.png b/....1.0/scatter_benchmark_infectiousness.png → ....1.0/scatter_benchmark_infectiousness.png
diff --git a/....1.0/scatter_benchmark_prevalence_age.png → ....1.0/scatter_benchmark_prevalence_age.png b/....1.0/scatter_benchmark_prevalence_age.png → ....1.0/scatter_benchmark_prevalence_age.png
diff --git a/....1.0/scatter_regression_incidence_age.png → ....1.0/scatter_regression_incidence_age.png b/....1.0/scatter_regression_incidence_age.png → ....1.0/scatter_regression_incidence_age.png
diff --git a/...1.0/scatter_regression_prevalence_age.png → ...1.0/scatter_regression_prevalence_age.png b/...1.0/scatter_regression_prevalence_age.png → ...1.0/scatter_regression_prevalence_age.png
diff --git a/...e_compare_asex_dens_age_dapelogo_2007.png → ...e_compare_asex_dens_age_dapelogo_2007.png b/...e_compare_asex_dens_age_dapelogo_2007.png → ...e_compare_asex_dens_age_dapelogo_2007.png
diff --git a/.../site_compare_asex_dens_age_laye_2007.png → .../site_compare_asex_dens_age_laye_2007.png b/.../site_compare_asex_dens_age_laye_2007.png → .../site_compare_asex_dens_age_laye_2007.png
diff --git a/...te_compare_asex_dens_age_matsari_1970.png → ...te_compare_asex_dens_age_matsari_1970.png b/...te_compare_asex_dens_age_matsari_1970.png → ...te_compare_asex_dens_age_matsari_1970.png
diff --git a/...ompare_asex_dens_age_rafin_marke_1970.png → ...ompare_asex_dens_age_rafin_marke_1970.png b/...ompare_asex_dens_age_rafin_marke_1970.png → ...ompare_asex_dens_age_rafin_marke_1970.png
diff --git a/...e_compare_asex_dens_age_sugungum_1970.png → ...e_compare_asex_dens_age_sugungum_1970.png b/...e_compare_asex_dens_age_sugungum_1970.png → ...e_compare_asex_dens_age_sugungum_1970.png
diff --git a/...0/site_compare_barplot_asex_dens_age_.png → ...0/site_compare_barplot_asex_dens_age_.png b/...0/site_compare_barplot_asex_dens_age_.png → ...0/site_compare_barplot_asex_dens_age_.png
diff --git a/.../site_compare_barplot_gamet_dens_age_.png → .../site_compare_barplot_gamet_dens_age_.png b/.../site_compare_barplot_gamet_dens_age_.png → .../site_compare_barplot_gamet_dens_age_.png
diff --git a/..._compare_gamet_dens_age_dapelogo_2007.png → ..._compare_gamet_dens_age_dapelogo_2007.png b/..._compare_gamet_dens_age_dapelogo_2007.png → ..._compare_gamet_dens_age_dapelogo_2007.png
diff --git a/...site_compare_gamet_dens_age_laye_2007.png → ...site_compare_gamet_dens_age_laye_2007.png b/...site_compare_gamet_dens_age_laye_2007.png → ...site_compare_gamet_dens_age_laye_2007.png
diff --git a/...e_compare_gamet_dens_age_matsari_1970.png → ...e_compare_gamet_dens_age_matsari_1970.png b/...e_compare_gamet_dens_age_matsari_1970.png → ...e_compare_gamet_dens_age_matsari_1970.png
diff --git a/...mpare_gamet_dens_age_rafin_marke_1970.png → ...mpare_gamet_dens_age_rafin_marke_1970.png b/...mpare_gamet_dens_age_rafin_marke_1970.png → ...mpare_gamet_dens_age_rafin_marke_1970.png
diff --git a/..._compare_gamet_dens_age_sugungum_1970.png → ..._compare_gamet_dens_age_sugungum_1970.png b/..._compare_gamet_dens_age_sugungum_1970.png → ..._compare_gamet_dens_age_sugungum_1970.png
diff --git a/..._22_v0.1.0/site_compare_incidence_age.png → ...ots_v0.1.0/site_compare_incidence_age.png b/..._22_v0.1.0/site_compare_incidence_age.png → ...ots_v0.1.0/site_compare_incidence_age.png
diff --git a/...are_infect_duration_age_navrongo_2000.png → ...are_infect_duration_age_navrongo_2000.png b/...are_infect_duration_age_navrongo_2000.png → ...are_infect_duration_age_navrongo_2000.png
diff --git a/...nfect_duration_measures_navrongo_2000.png → ...nfect_duration_measures_navrongo_2000.png b/...nfect_duration_measures_navrongo_2000.png → ...nfect_duration_measures_navrongo_2000.png
diff --git a/...compare_infect_duration_navrongo_2000.png → ...compare_infect_duration_navrongo_2000.png b/...compare_infect_duration_navrongo_2000.png → ...compare_infect_duration_navrongo_2000.png
diff --git a/..._compare_infectiousness_dapelogo_2007.png → ..._compare_infectiousness_dapelogo_2007.png b/..._compare_infectiousness_dapelogo_2007.png → ..._compare_infectiousness_dapelogo_2007.png
diff --git a/...site_compare_infectiousness_laye_2007.png → ...site_compare_infectiousness_laye_2007.png b/...site_compare_infectiousness_laye_2007.png → ...site_compare_infectiousness_laye_2007.png
diff --git a/...22_v0.1.0/site_compare_prevalence_age.png → ...ts_v0.1.0/site_compare_prevalence_age.png b/...22_v0.1.0/site_compare_prevalence_age.png → ...ts_v0.1.0/site_compare_prevalence_age.png
diff --git a/...22_v0.1.0/summary_table_sim_benchmark.csv → ...ts_v0.1.0/summary_table_sim_benchmark.csv b/...22_v0.1.0/summary_table_sim_benchmark.csv → ...ts_v0.1.0/summary_table_sim_benchmark.csv
diff --git a/...comparison_metric_table_incidence_age.csv → ...comparison_metric_table_incidence_age.csv b/...comparison_metric_table_incidence_age.csv → ...comparison_metric_table_incidence_age.csv
diff --git a/...omparison_metric_table_prevalence_age.csv → ...omparison_metric_table_prevalence_age.csv b/...omparison_metric_table_prevalence_age.csv → ...omparison_metric_table_prevalence_age.csv
diff --git a/...2_v1.0.0/loglikelihood_prevalence_age.csv → ...s_v1.0.0/loglikelihood_prevalence_age.csv b/...2_v1.0.0/loglikelihood_prevalence_age.csv → ...s_v1.0.0/loglikelihood_prevalence_age.csv
diff --git a/..._07_22_v1.0.0/loglikelihoods_par_dens.csv → ..._plots_v1.0.0/loglikelihoods_par_dens.csv b/..._07_22_v1.0.0/loglikelihoods_par_dens.csv → ..._plots_v1.0.0/loglikelihoods_par_dens.csv
diff --git a/...22_v1.0.0/scatter_benchmark_asex_dens.png → ...ts_v1.0.0/scatter_benchmark_asex_dens.png b/...22_v1.0.0/scatter_benchmark_asex_dens.png → ...ts_v1.0.0/scatter_benchmark_asex_dens.png
diff --git a/...2_v1.0.0/scatter_benchmark_gamet_dens.png → ...s_v1.0.0/scatter_benchmark_gamet_dens.png b/...2_v1.0.0/scatter_benchmark_gamet_dens.png → ...s_v1.0.0/scatter_benchmark_gamet_dens.png
diff --git a/...1.0.0/scatter_benchmark_incidence_age.png → ...1.0.0/scatter_benchmark_incidence_age.png b/...1.0.0/scatter_benchmark_incidence_age.png → ...1.0.0/scatter_benchmark_incidence_age.png
diff --git a/....0.0/scatter_benchmark_infectiousness.png → ....0.0/scatter_benchmark_infectiousness.png b/....0.0/scatter_benchmark_infectiousness.png → ....0.0/scatter_benchmark_infectiousness.png
diff --git a/....0.0/scatter_benchmark_prevalence_age.png → ....0.0/scatter_benchmark_prevalence_age.png b/....0.0/scatter_benchmark_prevalence_age.png → ....0.0/scatter_benchmark_prevalence_age.png
diff --git a/....0.0/scatter_regression_incidence_age.png → ....0.0/scatter_regression_incidence_age.png b/....0.0/scatter_regression_incidence_age.png → ....0.0/scatter_regression_incidence_age.png
diff --git a/...0.0/scatter_regression_prevalence_age.png → ...0.0/scatter_regression_prevalence_age.png b/...0.0/scatter_regression_prevalence_age.png → ...0.0/scatter_regression_prevalence_age.png
diff --git a/...e_compare_asex_dens_age_dapelogo_2007.png → ...e_compare_asex_dens_age_dapelogo_2007.png b/...e_compare_asex_dens_age_dapelogo_2007.png → ...e_compare_asex_dens_age_dapelogo_2007.png
diff --git a/.../site_compare_asex_dens_age_laye_2007.png → .../site_compare_asex_dens_age_laye_2007.png b/.../site_compare_asex_dens_age_laye_2007.png → .../site_compare_asex_dens_age_laye_2007.png
diff --git a/...te_compare_asex_dens_age_matsari_1970.png → ...te_compare_asex_dens_age_matsari_1970.png b/...te_compare_asex_dens_age_matsari_1970.png → ...te_compare_asex_dens_age_matsari_1970.png
diff --git a/...ompare_asex_dens_age_rafin_marke_1970.png → ...ompare_asex_dens_age_rafin_marke_1970.png b/...ompare_asex_dens_age_rafin_marke_1970.png → ...ompare_asex_dens_age_rafin_marke_1970.png
diff --git a/...e_compare_asex_dens_age_sugungum_1970.png → ...e_compare_asex_dens_age_sugungum_1970.png b/...e_compare_asex_dens_age_sugungum_1970.png → ...e_compare_asex_dens_age_sugungum_1970.png
diff --git a/...0/site_compare_barplot_asex_dens_age_.png → ...0/site_compare_barplot_asex_dens_age_.png b/...0/site_compare_barplot_asex_dens_age_.png → ...0/site_compare_barplot_asex_dens_age_.png
diff --git a/.../site_compare_barplot_gamet_dens_age_.png → .../site_compare_barplot_gamet_dens_age_.png b/.../site_compare_barplot_gamet_dens_age_.png → .../site_compare_barplot_gamet_dens_age_.png
diff --git a/..._compare_gamet_dens_age_dapelogo_2007.png → ..._compare_gamet_dens_age_dapelogo_2007.png b/..._compare_gamet_dens_age_dapelogo_2007.png → ..._compare_gamet_dens_age_dapelogo_2007.png
diff --git a/...site_compare_gamet_dens_age_laye_2007.png → ...site_compare_gamet_dens_age_laye_2007.png b/...site_compare_gamet_dens_age_laye_2007.png → ...site_compare_gamet_dens_age_laye_2007.png
diff --git a/...e_compare_gamet_dens_age_matsari_1970.png → ...e_compare_gamet_dens_age_matsari_1970.png b/...e_compare_gamet_dens_age_matsari_1970.png → ...e_compare_gamet_dens_age_matsari_1970.png
diff --git a/...mpare_gamet_dens_age_rafin_marke_1970.png → ...mpare_gamet_dens_age_rafin_marke_1970.png b/...mpare_gamet_dens_age_rafin_marke_1970.png → ...mpare_gamet_dens_age_rafin_marke_1970.png
diff --git a/..._compare_gamet_dens_age_sugungum_1970.png → ..._compare_gamet_dens_age_sugungum_1970.png b/..._compare_gamet_dens_age_sugungum_1970.png → ..._compare_gamet_dens_age_sugungum_1970.png
diff --git a/..._22_v1.0.0/site_compare_incidence_age.png → ...ots_v1.0.0/site_compare_incidence_age.png b/..._22_v1.0.0/site_compare_incidence_age.png → ...ots_v1.0.0/site_compare_incidence_age.png
diff --git a/...are_infect_duration_age_navrongo_2000.png → ...are_infect_duration_age_navrongo_2000.png b/...are_infect_duration_age_navrongo_2000.png → ...are_infect_duration_age_navrongo_2000.png
diff --git a/...nfect_duration_measures_navrongo_2000.png → ...nfect_duration_measures_navrongo_2000.png b/...nfect_duration_measures_navrongo_2000.png → ...nfect_duration_measures_navrongo_2000.png
diff --git a/...compare_infect_duration_navrongo_2000.png → ...compare_infect_duration_navrongo_2000.png b/...compare_infect_duration_navrongo_2000.png → ...compare_infect_duration_navrongo_2000.png
diff --git a/..._compare_infectiousness_dapelogo_2007.png → ..._compare_infectiousness_dapelogo_2007.png b/..._compare_infectiousness_dapelogo_2007.png → ..._compare_infectiousness_dapelogo_2007.png
diff --git a/...site_compare_infectiousness_laye_2007.png → ...site_compare_infectiousness_laye_2007.png b/...site_compare_infectiousness_laye_2007.png → ...site_compare_infectiousness_laye_2007.png
diff --git a/...22_v1.0.0/site_compare_prevalence_age.png → ...ts_v1.0.0/site_compare_prevalence_age.png b/...22_v1.0.0/site_compare_prevalence_age.png → ...ts_v1.0.0/site_compare_prevalence_age.png
diff --git a/...22_v1.0.0/summary_table_sim_benchmark.csv → ...ts_v1.0.0/summary_table_sim_benchmark.csv b/...22_v1.0.0/summary_table_sim_benchmark.csv → ...ts_v1.0.0/summary_table_sim_benchmark.csv
diff --git a/report/_plots_v1.1.0/comparison_metric_table_incidence_age.csv b/report/_plots_v1.1.0/comparison_metric_table_incidence_age.csv
@@ -0,0 +1,10 @@
+Site,mean_rel_diff,mean_abs_diff,corr_slope,corr_r_squared,mean_rel_slope_diff,mean_abs_slpe_diff
+chonyi_1999,2.359037548734484,0.9527363074851135,1.0864286693488938,0.4909669217402626,8.439261308486312,0.14796578722119708
+dielmo_1990,1.4081812654541295,1.2458223958828656,1.4662896933383196,0.9136326384809177,2.788786163966403,0.3311051298078479
+dongubougou_1999,0.20347658923882472,0.20058805816706715,1.0841408131583619,0.8655226920015985,0.5908511281184664,0.05591566317290126
+ebolakounou_1997,3.5298250987213704,1.3500864647430642,1.591015084482229,0.36079816878572557,5.540963413406026,0.09385532642413291
+koundou_1997,2.4201137951985316,2.1409045381563216,2.4059180140110406,0.583784813025154,4.061363882148547,0.2988974553053057
+ndiop_1993,0.46935752353216675,0.5183624018079345,1.3707184658549694,0.8617239579850393,1.4238643917237108,0.06385891135139789
+ngerenya_1999,2.1701872774703364,0.6138116970950674,-0.060277891520447935,0.015456288322816111,1.8822112986842252,0.15579650258632832
+sotuba_1999,0.3696682793427051,0.5674355266406905,0.07836804114542992,0.018623563537865394,1.0594253967100906,0.040875299422955785
+all_sites,1.6610911744982817,0.9404107512855068,,,,
diff --git a/report/_plots_v1.1.0/comparison_metric_table_prevalence_age.csv b/report/_plots_v1.1.0/comparison_metric_table_prevalence_age.csv
@@ -0,0 +1,19 @@
+Site,mean_rel_diff,mean_abs_diff,corr_slope,corr_r_squared,mean_rel_slope_diff,mean_abs_slpe_diff
+chonyi_1999_month7,0.6825254910261515,0.3393820994465812,0.15663097557129418,0.4301695105868461,12.214132279434569,0.042317923534964316
+dielmo_1990_monthmultiple,0.5711687112890077,0.3965314003825952,0.6219099246260962,0.9274859257167193,0.8630959749052138,0.02034695680585351
+dongubougou_1999_monthmultiple,0.2921917392007317,0.17073999016392666,0.13038640523567407,0.09423861595745166,0.6506923472111071,0.02470917658914631
+ebolakounou_1997_monthmultiple,0.6858638609195971,0.3886452217302862,-0.10398602600941884,0.09180777382837431,0.8668243442164759,0.010454242841899759
+koundou_1997_monthmultiple,0.5614177043381496,0.3462386846857258,0.43728547052724426,0.7472381451807503,1.3249240850644364,0.005923631221470194
+matsari_1970_month10,0.39820928816459034,0.18674109376023418,0.7863094941336288,0.9256435924626562,1.3770296193627964,0.012248340369871116
+matsari_1970_month2,0.6299855911450253,0.3950905744647875,0.7864003185032957,0.9932297717710127,,0.0024505860481569366
+matsari_1970_month7,0.4404135744799402,0.23401638055083646,0.676475606141136,0.8707864429680627,0.9187147875941255,0.0083184951107307
+ndiop_1993_monthmultiple,0.4657205735231557,0.14894292742359438,0.5214373120598216,0.795715073267172,0.6319126797626777,0.008540974359763517
+ngerenya_1999_month7,0.8510846198405031,0.2561096994580539,-0.002692043148475209,0.00011484196242583909,0.9246367805158168,0.03231061623631442
+rafin_marke_1970_month10,0.33576501065627096,0.14162445663845127,0.889262048689702,0.7164946161179646,0.5855068867610722,0.01670433705872292
+rafin_marke_1970_month2,0.6895323478189561,0.39644790640199684,0.3791186726125504,0.9147342032022373,0.49487086565326166,0.007303359628916402
+rafin_marke_1970_month7,0.36662216745724924,0.1732038206493545,0.5313418689033182,0.8040591037631534,60.7957816844913,0.010211641021033455
+sotuba_1999_monthmultiple,2.484336072291313,0.18349964579147138,0.1513331198191235,0.01728434589322891,3.9181738234540444,0.008653389560842968
+sugungum_1970_month10,0.46487882168073275,0.21334317162823746,0.892301300941384,0.9153345760653759,1.881581244676297,0.008059387929131905
+sugungum_1970_month2,0.6236851050207368,0.3273411507035959,0.5575133570794679,0.8693862147591017,1.8861647797218364,0.009580442352786923
+sugungum_1970_month7,0.2850904482414568,0.12479898222550063,0.7565180071793607,0.7648414997099265,1.7616882910570792,0.012480177680226892
+all_sites,0.7060172162703156,0.26559137003721556,,,,
diff --git a/report/_plots_v1.1.0/corr_ref_sim_points_incidence_age.png b/report/_plots_v1.1.0/corr_ref_sim_points_incidence_age.png
diff --git a/report/_plots_v1.1.0/corr_ref_sim_points_prevalence_age.png b/report/_plots_v1.1.0/corr_ref_sim_points_prevalence_age.png
diff --git a/report/_plots_v1.1.0/loglikelihood_prevalence_age.csv b/report/_plots_v1.1.0/loglikelihood_prevalence_age.csv
@@ -0,0 +1,16 @@
+site_month,loglikelihood_new_sim,loglikelihood_benchmark_sim
+dielmo_1990_monthmultiple,-3466.6023937629197,-3466.6023937629197
+dongubougou_1999_monthmultiple,-84.26103051901676,-84.26103051901676
+ebolakounou_1997_monthmultiple,-1363.029630690697,-1363.029630690697
+koundou_1997_monthmultiple,-1245.5403763380814,-1245.5403763380814
+matsari_1970_month10,-50.662599543326195,-50.662599543326195
+matsari_1970_month2,-263.25804760282097,-263.25804760282097
+matsari_1970_month7,-67.33292846410185,-67.33292846410185
+ndiop_1993_monthmultiple,,
+rafin_marke_1970_month10,-29.387106539215623,-29.387106539215623
+rafin_marke_1970_month2,-145.89519905060365,-145.89519905060365
+rafin_marke_1970_month7,-63.78842174861791,-63.78842174861791
+sotuba_1999_monthmultiple,-272.37015246943747,-272.37015246943747
+sugungum_1970_month10,-152.7494668500975,-152.7494668500975
+sugungum_1970_month2,-335.01903047385656,-335.01903047385656
+sugungum_1970_month7,-31.504463570505617,-31.504463570505617
diff --git a/report/_plots_v1.1.0/loglikelihoods_par_dens.csv b/report/_plots_v1.1.0/loglikelihoods_par_dens.csv
@@ -0,0 +1,16 @@
+site_month,loglike_asex,benchmark_loglike_asex,loglike_gamet,benchmark_loglike_gamet
+matsari_1970_month2,-388.5658647314641,-388.5658647314641,-1126.5067540609252,-1126.5067540609252
+matsari_1970_month7,-622.6123330019673,-622.6123330019673,-647.0310739624263,-647.0310739624263
+matsari_1970_month10,-925.2131658352293,-925.2131658352293,-1214.3526893895782,-1214.3526893895782
+rafin_marke_1970_month2,-151.38873119340678,-151.38873119340678,-239.0289626836029,-239.0289626836029
+rafin_marke_1970_month7,-646.3403432364206,-646.3403432364206,-661.756709133003,-661.756709133003
+rafin_marke_1970_month10,-554.7327641446915,-554.7327641446915,-876.7543574963095,-876.7543574963095
+sugungum_1970_month2,-547.6560613702462,-547.6560613702462,-1327.1606844138018,-1327.1606844138018
+sugungum_1970_month7,-1105.657401526858,-1105.657401526858,-982.89151714405,-982.89151714405
+sugungum_1970_month10,-1513.5441864504005,-1513.5441864504005,-2254.2505145215273,-2254.2505145215273
+laye_2007_month7,-63.207838404281006,-63.207838404281006,-74.69789236018474,-74.69789236018474
+laye_2007_month9,-85.93548761815548,-85.93548761815548,-inf,-inf
+laye_2007_month1,-37.23525174199905,-37.23525174199905,-25.42118634676641,-25.42118634676641
+dapelogo_2007_month7,-70.52422100003385,-70.52422100003385,-inf,-inf
+dapelogo_2007_month9,-55.79528949321428,-55.79528949321428,-43.3042021524024,-43.3042021524024
+dapelogo_2007_month1,-51.00728916075721,-51.00728916075721,-inf,-inf
diff --git a/report/_plots_v1.1.0/scatter_benchmark_asex_dens.png b/report/_plots_v1.1.0/scatter_benchmark_asex_dens.png
diff --git a/report/_plots_v1.1.0/scatter_benchmark_gamet_dens.png b/report/_plots_v1.1.0/scatter_benchmark_gamet_dens.png
diff --git a/report/_plots_v1.1.0/scatter_benchmark_incidence_age.png b/report/_plots_v1.1.0/scatter_benchmark_incidence_age.png
diff --git a/report/_plots_v1.1.0/scatter_benchmark_infectiousness.png b/report/_plots_v1.1.0/scatter_benchmark_infectiousness.png
diff --git a/report/_plots_v1.1.0/scatter_benchmark_prevalence_age.png b/report/_plots_v1.1.0/scatter_benchmark_prevalence_age.png
diff --git a/report/_plots_v1.1.0/scatter_regression_incidence_age_correlation.png b/report/_plots_v1.1.0/scatter_regression_incidence_age_correlation.png
diff --git a/report/_plots_v1.1.0/scatter_regression_incidence_age_slope_correlation.png b/report/_plots_v1.1.0/scatter_regression_incidence_age_slope_correlation.png
diff --git a/report/_plots_v1.1.0/scatter_regression_prevalence_age_correlation.png b/report/_plots_v1.1.0/scatter_regression_prevalence_age_correlation.png
diff --git a/report/_plots_v1.1.0/scatter_regression_prevalence_age_slope_correlation.png b/report/_plots_v1.1.0/scatter_regression_prevalence_age_slope_correlation.png
diff --git a/report/_plots_v1.1.0/site_compare_asex_dens_age_dapelogo_2007.png b/report/_plots_v1.1.0/site_compare_asex_dens_age_dapelogo_2007.png
diff --git a/report/_plots_v1.1.0/site_compare_asex_dens_age_laye_2007.png b/report/_plots_v1.1.0/site_compare_asex_dens_age_laye_2007.png
diff --git a/report/_plots_v1.1.0/site_compare_asex_dens_age_matsari_1970.png b/report/_plots_v1.1.0/site_compare_asex_dens_age_matsari_1970.png
diff --git a/report/_plots_v1.1.0/site_compare_asex_dens_age_rafin_marke_1970.png b/report/_plots_v1.1.0/site_compare_asex_dens_age_rafin_marke_1970.png
diff --git a/report/_plots_v1.1.0/site_compare_asex_dens_age_sugungum_1970.png b/report/_plots_v1.1.0/site_compare_asex_dens_age_sugungum_1970.png
diff --git a/report/_plots_v1.1.0/site_compare_barplot_asex_dens_age.png b/report/_plots_v1.1.0/site_compare_barplot_asex_dens_age.png
diff --git a/report/_plots_v1.1.0/site_compare_barplot_gamet_dens_age.png b/report/_plots_v1.1.0/site_compare_barplot_gamet_dens_age.png
diff --git a/report/_plots_v1.1.0/site_compare_gamet_dens_age_dapelogo_2007.png b/report/_plots_v1.1.0/site_compare_gamet_dens_age_dapelogo_2007.png
diff --git a/report/_plots_v1.1.0/site_compare_gamet_dens_age_laye_2007.png b/report/_plots_v1.1.0/site_compare_gamet_dens_age_laye_2007.png
diff --git a/report/_plots_v1.1.0/site_compare_gamet_dens_age_matsari_1970.png b/report/_plots_v1.1.0/site_compare_gamet_dens_age_matsari_1970.png
diff --git a/report/_plots_v1.1.0/site_compare_gamet_dens_age_rafin_marke_1970.png b/report/_plots_v1.1.0/site_compare_gamet_dens_age_rafin_marke_1970.png
diff --git a/report/_plots_v1.1.0/site_compare_gamet_dens_age_sugungum_1970.png b/report/_plots_v1.1.0/site_compare_gamet_dens_age_sugungum_1970.png
diff --git a/report/_plots_v1.1.0/site_compare_incidence_age.png b/report/_plots_v1.1.0/site_compare_incidence_age.png
diff --git a/report/_plots_v1.1.0/site_compare_infect_duration_age_navrongo_2000.png b/report/_plots_v1.1.0/site_compare_infect_duration_age_navrongo_2000.png
diff --git a/report/_plots_v1.1.0/site_compare_infect_duration_measures_navrongo_2000.png b/report/_plots_v1.1.0/site_compare_infect_duration_measures_navrongo_2000.png
diff --git a/report/_plots_v1.1.0/site_compare_infect_duration_navrongo_2000.png b/report/_plots_v1.1.0/site_compare_infect_duration_navrongo_2000.png
diff --git a/report/_plots_v1.1.0/site_compare_infectiousness_dapelogo_2007.png b/report/_plots_v1.1.0/site_compare_infectiousness_dapelogo_2007.png
diff --git a/report/_plots_v1.1.0/site_compare_infectiousness_laye_2007.png b/report/_plots_v1.1.0/site_compare_infectiousness_laye_2007.png
diff --git a/report/_plots_v1.1.0/site_compare_prevalence_age.png b/report/_plots_v1.1.0/site_compare_prevalence_age.png
diff --git a/report/_plots_v1.1.0/summary_table_sim_benchmark.csv b/report/_plots_v1.1.0/summary_table_sim_benchmark.csv
@@ -0,0 +1,6 @@
+validation_relationship,abs_diff_new,abs_diff_bench,num_sites_better,num_sites_similar,num_sites_worse
+age_incidence,0.9404107512855068,0.9404107512855068,0,8,0
+age_prevalence,0.2655913700372155,0.2655913700372155,0,17,0
+asexual_par_dens,0.188549310757321,0.188549310757321,0,15,0
+gamet_par_dens,0.2416610186586396,0.2416610186586396,0,15,0
+infectiousness,0.14141331785076117,0.14141331785076117,0,6,0