-
Notifications
You must be signed in to change notification settings - Fork 3
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #59 from YeChen-IDM/fix_51_57
- Loading branch information
Showing
66 changed files
with
1,702 additions
and
84 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file not shown.
12 changes: 6 additions & 6 deletions
12
report/_plots_Python/comparison_metric_table_incidence_age.csv
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -1,10 +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 | ||
chonyi_1999,2.359037548734484,0.9527363074851135,1.0864286693488938,0.4909669217402626,8.43926130848631,0.14796578722119694 | ||
dielmo_1990,1.4081812654541295,1.2458223958828658,1.4662896933383196,0.9136326384809175,2.7887861639664027,0.33110512980784806 | ||
dongubougou_1999,0.20347658923882464,0.20058805816706704,1.0841408131583619,0.8655226920015985,0.5908511281184662,0.055915663172901246 | ||
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 | ||
koundou_1997,2.4201137951985316,2.1409045381563216,2.4059180140110406,0.5837848130251536,4.061363882148547,0.29889745530530576 | ||
ndiop_1993,0.46935752353216664,0.5183624018079344,1.3707184658549694,0.8617239579850393,1.4238643917237106,0.06385891135139789 | ||
ngerenya_1999,2.1701872774703364,0.6138116970950674,-0.060277891520447935,0.015456288322816111,1.8822112986842252,0.15579650258632835 | ||
sotuba_1999,0.3696682793427051,0.5674355266406905,0.07836804114542992,0.018623563537865394,1.0594253967100906,0.040875299422955785 | ||
all_sites,1.6610911744982817,0.9404107512855068,,,, |
6 changes: 3 additions & 3 deletions
6
report/_plots_Python/comparison_metric_table_prevalence_age.csv
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Binary file modified
BIN
+3 Bytes
(100%)
report/_plots_Python/scatter_regression_incidence_age_correlation.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified
BIN
-4.66 KB
(90%)
report/_plots_Python/site_compare_infect_duration_age_navrongo_2000.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified
BIN
+107 Bytes
(100%)
report/_plots_Python/site_compare_infect_duration_measures_navrongo_2000.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file modified
BIN
+13 Bytes
(100%)
report/_plots_Python/site_compare_infect_duration_navrongo_2000.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
10 changes: 10 additions & 0 deletions
10
report/_plots_v1.2.0/comparison_metric_table_incidence_age.csv
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -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_1999,2.359037548734484,0.9527363074851135,1.0864286693488938,0.4909669217402626,8.43926130848631,0.14796578722119694 | ||
dielmo_1990,1.4081812654541295,1.2458223958828658,1.4662896933383196,0.9136326384809175,2.7887861639664027,0.33110512980784806 | ||
dongubougou_1999,0.20347658923882464,0.20058805816706704,1.0841408131583619,0.8655226920015985,0.5908511281184662,0.055915663172901246 | ||
ebolakounou_1997,3.5298250987213704,1.3500864647430642,1.591015084482229,0.36079816878572557,5.540963413406026,0.09385532642413291 | ||
koundou_1997,2.4201137951985316,2.1409045381563216,2.4059180140110406,0.5837848130251536,4.061363882148547,0.29889745530530576 | ||
ndiop_1993,0.46935752353216664,0.5183624018079344,1.3707184658549694,0.8617239579850393,1.4238643917237106,0.06385891135139789 | ||
ngerenya_1999,2.1701872774703364,0.6138116970950674,-0.060277891520447935,0.015456288322816111,1.8822112986842252,0.15579650258632835 | ||
sotuba_1999,0.3696682793427051,0.5674355266406905,0.07836804114542992,0.018623563537865394,1.0594253967100906,0.040875299422955785 | ||
all_sites,1.6610911744982817,0.9404107512855068,,,, |
19 changes: 19 additions & 0 deletions
19
report/_plots_v1.2.0/comparison_metric_table_prevalence_age.csv
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -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,0.5711687112890077,0.3965314003825952,0.6219099246260963,0.9274859257167195,0.8630959749052143,0.020346956805853512 | ||
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 | ||
ndiop_1993_monthmultiple,0.4657205735231557,0.14894292742359438,0.5214373120598216,0.795715073267172,0.6319126797626777,0.008540974359763517 | ||
ngerenya_1999_month7,0.8510846198405031,0.2561096994580539,-0.002692043148475208,0.00011484196242583901,0.9246367805158167,0.03231061623631442 | ||
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,,,, |
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,16 @@ | ||
site_month,loglikelihood_new_sim,loglikelihood_benchmark_sim | ||
dielmo_1990_monthmultiple,-3466.6023937629193,-3466.6023937629193 | ||
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 |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -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 |
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added
BIN
+66.5 KB
report/_plots_v1.2.0/scatter_regression_incidence_age_correlation.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added
BIN
+46.2 KB
report/_plots_v1.2.0/scatter_regression_incidence_age_slope_correlation.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added
BIN
+135 KB
report/_plots_v1.2.0/scatter_regression_prevalence_age_correlation.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file added
BIN
+78.4 KB
report/_plots_v1.2.0/scatter_regression_prevalence_age_slope_correlation.png
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Oops, something went wrong.
Oops, something went wrong.
Oops, something went wrong.
Oops, something went wrong.
Oops, something went wrong.
Oops, something went wrong.
Oops, something went wrong.
Binary file added
BIN
+40.9 KB
report/_plots_v1.2.0/site_compare_infect_duration_age_navrongo_2000.png
Oops, something went wrong.
Binary file added
BIN
+23.1 KB
report/_plots_v1.2.0/site_compare_infect_duration_measures_navrongo_2000.png
Oops, something went wrong.
Oops, something went wrong.
Oops, something went wrong.
Oops, something went wrong.
Oops, something went wrong.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -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 |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
|
@@ -4,6 +4,6 @@ fpdf2~=2.6 | |
seaborn~=0.12 | ||
scikit-learn~=1.1 | ||
scipy~=1.9 | ||
snakemake~=7.18 | ||
snakemake~=7.19 | ||
plotnine~=0.10 | ||
datar~=0.9 |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Binary file not shown.
Oops, something went wrong.