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add functions and update snt defaults #83

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add functions and update snt defaults #83

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7e0e97f
adding check that experiment succeeded before writing out experiment …
stitova-idm Sep 15, 2023
a034ac6
removing "wait_on_done" parameter as it's default and will be removed…
stitova-idm Sep 18, 2023
31bfd9a
changing to cores = 1, because of the race condition
stitova-idm Sep 18, 2023
f2a80e4
updating requirements so jenkins works (gets the older urlib3)
stitova-idm Sep 18, 2023
f359da4
i think it's the slashes
stitova-idm Sep 18, 2023
df930b8
debug and path cleanup
stitova-idm Sep 18, 2023
8464c39
adding dowloand folder
stitova-idm Sep 18, 2023
b4c36e3
stalling from staging because emodpy-snt needs not-yet-released emodp…
stitova-idm Sep 18, 2023
e2c3f42
to pick up unreleased malaria
stitova-idm Sep 18, 2023
54b4e0a
credentials update
stitova-idm Sep 18, 2023
abe0833
update filepaths and sif_id for Monique's setup
MAmbrose-IDM Sep 6, 2023
74b56e8
add missing platform name to PlatformAnalysis function
MAmbrose-IDM Sep 19, 2023
6661fa2
update paths and add dtk_sif.id
MAmbrose-IDM Sep 19, 2023
624b43b
update run platform nodes and experiment IDs
MAmbrose-IDM Sep 20, 2023
d92e050
separate example calibration outputs into separate folders for season…
MAmbrose-IDM Sep 20, 2023
f588d21
specify default land and air temperatures
MAmbrose-IDM Oct 27, 2023
7ad773b
add function for reading in intervention files
MAmbrose-IDM Oct 27, 2023
5604abe
add analyzer for optuna calibration attempt
MAmbrose-IDM Jan 4, 2024
f4f502b
add RDT prevalence as a metric for calibrating transmission intensity
MAmbrose-IDM Jan 4, 2024
ac99dff
debug and fix problem with inconsistently-ordered calibration outputs…
MAmbrose-IDM Jan 4, 2024
9009604
update calibration ranges, filepaths, mismatched LGA names, and code …
MAmbrose-IDM Jan 4, 2024
d3924bf
add additional type of vaccine with specified daily efficacy values a…
MAmbrose-IDM Feb 15, 2024
b8f6152
update SMC parameters
MAmbrose-IDM Feb 20, 2024
e840b81
add additional DHS variables for estimating effective CM and add plot…
MAmbrose-IDM Apr 10, 2024
07443ab
add row reordering to make sure output dataframe is consistent with e…
MAmbrose-IDM Apr 10, 2024
fde38a4
process output and create plots for state-level timeseries plotted in…
MAmbrose-IDM Apr 10, 2024
77ff76c
fix bug in IRS decay time specification
MAmbrose-IDM Apr 10, 2024
38f80af
add analyzer looking at monthly intervention events and remove 'Succe…
MAmbrose-IDM Apr 10, 2024
2c522c5
add plots of data and simulation inputs
MAmbrose-IDM Sep 15, 2024
db1c281
add option for the effect of imperfect ACT adherence
MAmbrose-IDM Sep 15, 2024
4139b65
update file paths and coded names
MAmbrose-IDM Sep 15, 2024
92d35ab
plot simulation output results for burden and intervention coverage
MAmbrose-IDM Sep 15, 2024
8755812
check IPTp inputs include needed years
MAmbrose-IDM Oct 29, 2024
fa68abf
add and update plots of intervention coverages
MAmbrose-IDM Oct 29, 2024
e7de4a4
change how vaccine coverage is calculated from DHS (different denomin…
MAmbrose-IDM Oct 29, 2024
a21fb40
create plots of intervention coverage through time based on input files
MAmbrose-IDM Oct 29, 2024
17ea87f
add function to plot burden and burden averted by state in grid layout
MAmbrose-IDM Oct 30, 2024
8c9d0c2
change DHS codes associated with receiving ACT
MAmbrose-IDM Oct 30, 2024
553746b
add functions to process data and create new plots of simulation inpu…
MAmbrose-IDM Nov 3, 2024
67db3f6
accomodate additional naming differences for input data files
MAmbrose-IDM Nov 18, 2024
e4b9d40
add functions to extract MICS EPI data
MAmbrose-IDM Nov 18, 2024
867a8a3
add calculation of severe disease and add option for IPTp coverage ch…
MAmbrose-IDM Dec 3, 2024
c0c17a0
create separate script with functions for plotting counterfactual tim…
MAmbrose-IDM Dec 3, 2024
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4 changes: 3 additions & 1 deletion .idea/emodpy-snt.iml
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2 changes: 1 addition & 1 deletion .idea/misc.xml
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2 changes: 2 additions & 0 deletions .idea/modules.xml
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3 changes: 2 additions & 1 deletion .idea/vcs.xml
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6 changes: 3 additions & 3 deletions Jenkinsfile
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Expand Up @@ -59,8 +59,8 @@ podTemplate(
def wheelFile = sh(returnStdout: true, script: "find ./dist -name '*.whl'").toString().trim()
//def wheelFile = sh(returnStdout: true, script: "python3 ./.github/scripts/get_wheel_filename.py --package-file package_setup.py").toString().trim()
echo "This is the package file: ${wheelFile}"
sh "pip3 install $wheelFile --index-url=https://packages.idmod.org/api/pypi/pypi-production/simple"
//sh "pip3 install $wheelFile --index-url=https://packages.idmod.org/api/pypi/pypi-production/simple"
sh "pip3 install $wheelFile --index-url=https://stitova@idmod.org:tWIoY8i6DuYX!tWp@packages.idmod.org/api/pypi/pypi-staging/simple --pre"
//sh "pip3 install dataclasses"
sh 'pip3 install keyrings.alt'
sh "pip3 freeze"
Expand Down Expand Up @@ -108,7 +108,7 @@ podTemplate(
echo "Running examples"
dir('examples') {
sh 'pip3 install snakemake'
sh 'snakemake --cores=10 --config python_version=python3'
sh 'snakemake --cores=1 --config python_version=python3'
}
}

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28 changes: 14 additions & 14 deletions data/example_files/simulation_inputs/larval_habitats/larval_habitat_multipliers_v1.csv
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Expand Up @@ -4,16 +4,16 @@ AA,1,1.5848931924611125
AA,2,1.5848931924611125
AA,3,1.5848931924611125
AA,4,1.5848931924611125
BB,0,0.3981071705534972
BB,1,0.3981071705534972
BB,2,0.3981071705534972
BB,3,0.3981071705534972
BB,4,0.3981071705534972
CC,0,0.3981071705534972
CC,1,0.3981071705534972
CC,2,0.3981071705534972
CC,3,0.3981071705534972
CC,4,0.3981071705534972
BB,0,0.3981071705534971
BB,1,0.3981071705534971
BB,2,0.3981071705534971
BB,3,0.3981071705534971
BB,4,0.3981071705534971
CC,0,0.3981071705534971
CC,1,0.3981071705534971
CC,2,0.3981071705534971
CC,3,0.3981071705534971
CC,4,0.3981071705534971
DD,0,1.5848931924611125
DD,1,1.5848931924611125
DD,2,1.5848931924611125
Expand All @@ -24,13 +24,13 @@ EE,1,0.1
EE,2,0.1
EE,3,0.1
EE,4,0.1
FF,0,25.118864315095795
FF,0,6.30957344480193
FF,1,25.118864315095795
FF,2,25.118864315095795
FF,3,25.118864315095795
FF,2,6.30957344480193
FF,3,6.30957344480193
FF,4,25.118864315095795
GG,0,6.30957344480193
GG,1,6.30957344480193
GG,2,6.30957344480193
GG,3,25.118864315095795
GG,3,6.30957344480193
GG,4,6.30957344480193
7 changes: 7 additions & 0 deletions ...example_files/simulation_output/baseline_calibration/LL_allxLH_each_admin_run/AA_run0.csv
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Habitat_Multiplier,score
0.0251188643150957,-186.53927596010544
0.1,-173.99270893245284
0.3981071705534971,-43.328227823219095
1.5848931924611125,-36.99050230882267
6.30957344480193,-63.36162503360811
25.118864315095795,-107.3877951284203
7 changes: 7 additions & 0 deletions ...example_files/simulation_output/baseline_calibration/LL_allxLH_each_admin_run/AA_run1.csv
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Habitat_Multiplier,score
0.0251188643150957,-187.96837742501248
0.1,-169.88709236992327
0.3981071705534971,-49.83678889213934
1.5848931924611125,-34.59288010625551
6.30957344480193,-68.88023543974077
25.118864315095795,-109.24930340285187
7 changes: 7 additions & 0 deletions ...example_files/simulation_output/baseline_calibration/LL_allxLH_each_admin_run/AA_run2.csv
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Habitat_Multiplier,score
0.0251188643150957,-184.72220058141465
0.1,-177.14934300759796
0.3981071705534971,-52.487039231733434
1.5848931924611125,-33.83493750639718
6.30957344480193,-66.37750093306386
25.118864315095795,-109.31340763089884
7 changes: 7 additions & 0 deletions ...example_files/simulation_output/baseline_calibration/LL_allxLH_each_admin_run/AA_run3.csv
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Habitat_Multiplier,score
0.0251188643150957,-183.47705926267008
0.1,-174.5735622262191
0.3981071705534971,-46.80607847423926
1.5848931924611125,-33.31510489048787
6.30957344480193,-63.13828873477496
25.118864315095795,-106.39338101279372
7 changes: 7 additions & 0 deletions ...example_files/simulation_output/baseline_calibration/LL_allxLH_each_admin_run/AA_run4.csv
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Habitat_Multiplier,score
0.0251188643150957,-184.45584172722283
0.1,-175.89478428984603
0.3981071705534971,-44.62845603284677
1.5848931924611125,-32.934052221396996
6.30957344480193,-67.5044917321784
25.118864315095795,-107.62870247898059
7 changes: 7 additions & 0 deletions ...example_files/simulation_output/baseline_calibration/LL_allxLH_each_admin_run/BB_run0.csv
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Habitat_Multiplier,score
0.0251188643150957,-27.033116866266937
0.1,-27.356654998702652
0.3981071705534971,-8.485222803619763
1.5848931924611125,-36.874366108000686
6.30957344480193,-70.89105429326037
25.118864315095795,-116.53092179312557
7 changes: 7 additions & 0 deletions ...example_files/simulation_output/baseline_calibration/LL_allxLH_each_admin_run/BB_run1.csv
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Habitat_Multiplier,score
0.0251188643150957,-26.97143185031564
0.1,-22.27926965982806
0.3981071705534971,-9.316039939631992
1.5848931924611125,-34.43602847985585
6.30957344480193,-70.97168387938336
25.118864315095795,-117.13331939317959
7 changes: 7 additions & 0 deletions ...example_files/simulation_output/baseline_calibration/LL_allxLH_each_admin_run/BB_run2.csv
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Habitat_Multiplier,score
0.0251188643150957,-26.80327572636361
0.1,-24.683700927392238
0.3981071705534971,-9.092472534654917
1.5848931924611125,-34.760006129154135
6.30957344480193,-69.47273092803562
25.118864315095795,-114.81930669831922
7 changes: 7 additions & 0 deletions ...example_files/simulation_output/baseline_calibration/LL_allxLH_each_admin_run/BB_run3.csv
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Habitat_Multiplier,score
0.0251188643150957,-26.811226179147525
0.1,-23.857127563115682
0.3981071705534971,-9.051516152425393
1.5848931924611125,-33.65637336876125
6.30957344480193,-68.92247219646424
25.118864315095795,-116.60216094848033
7 changes: 7 additions & 0 deletions ...example_files/simulation_output/baseline_calibration/LL_allxLH_each_admin_run/BB_run4.csv
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Habitat_Multiplier,score
0.0251188643150957,-27.17112028549036
0.1,-22.824627237911955
0.3981071705534971,-8.662181215167038
1.5848931924611125,-30.40498344885691
6.30957344480193,-68.58206853965248
25.118864315095795,-118.99564023167181
7 changes: 7 additions & 0 deletions ...example_files/simulation_output/baseline_calibration/LL_allxLH_each_admin_run/CC_run0.csv
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Habitat_Multiplier,score
0.0251188643150957,-173.55736663503012
0.1,-176.40241934866935
0.3981071705534971,-68.77171027877739
1.5848931924611125,-101.14599112571022
6.30957344480193,-123.1568561675831
25.118864315095795,-166.1208407207837
7 changes: 7 additions & 0 deletions ...example_files/simulation_output/baseline_calibration/LL_allxLH_each_admin_run/CC_run1.csv
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Habitat_Multiplier,score
0.0251188643150957,-179.41269285253657
0.1,-170.638777924878
0.3981071705534971,-71.65817539777709
1.5848931924611125,-101.40499060383036
6.30957344480193,-127.22801602148229
25.118864315095795,-167.59705648855106
7 changes: 7 additions & 0 deletions ...example_files/simulation_output/baseline_calibration/LL_allxLH_each_admin_run/CC_run2.csv
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Habitat_Multiplier,score
0.0251188643150957,-178.11526268026773
0.1,-179.4486602904799
0.3981071705534971,-81.93241394747929
1.5848931924611125,-100.30025278982157
6.30957344480193,-121.18038215910656
25.118864315095795,-158.80202843669053
7 changes: 7 additions & 0 deletions ...example_files/simulation_output/baseline_calibration/LL_allxLH_each_admin_run/CC_run3.csv
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Habitat_Multiplier,score
0.0251188643150957,-181.84368195171282
0.1,-177.04291191645098
0.3981071705534971,-65.31578731455102
1.5848931924611125,-106.3231530635635
6.30957344480193,-119.41683306074492
25.118864315095795,-164.76795794522286
7 changes: 7 additions & 0 deletions ...example_files/simulation_output/baseline_calibration/LL_allxLH_each_admin_run/CC_run4.csv
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Habitat_Multiplier,score
0.0251188643150957,-173.4211960238954
0.1,-174.25585497637712
0.3981071705534971,-71.7669950804875
1.5848931924611125,-102.35741991027953
6.30957344480193,-120.02040205670255
25.118864315095795,-164.0832913651684
7 changes: 7 additions & 0 deletions ...example_files/simulation_output/baseline_calibration/LL_allxLH_each_admin_run/DD_run0.csv
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Habitat_Multiplier,score
0.0251188643150957,-159.82702309561319
0.1,-153.35259280040827
0.3981071705534971,-38.39998383076363
1.5848931924611125,-30.500651619162
6.30957344480193,-41.761525098297625
25.118864315095795,-65.48557119778889
7 changes: 7 additions & 0 deletions ...example_files/simulation_output/baseline_calibration/LL_allxLH_each_admin_run/DD_run1.csv
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Habitat_Multiplier,score
0.0251188643150957,-159.3648492153534
0.1,-145.3103088819371
0.3981071705534971,-46.02593146845811
1.5848931924611125,-30.521665855256288
6.30957344480193,-41.84082765868743
25.118864315095795,-73.8452958663022
7 changes: 7 additions & 0 deletions ...example_files/simulation_output/baseline_calibration/LL_allxLH_each_admin_run/DD_run2.csv
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Habitat_Multiplier,score
0.0251188643150957,-158.824883567293
0.1,-140.49395099979847
0.3981071705534971,-48.19606890857813
1.5848931924611125,-31.0333996146328
6.30957344480193,-40.852238605119965
25.118864315095795,-74.09121043983532
7 changes: 7 additions & 0 deletions ...example_files/simulation_output/baseline_calibration/LL_allxLH_each_admin_run/DD_run3.csv
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Habitat_Multiplier,score
0.0251188643150957,-161.3797659552356
0.1,-142.98849957960556
0.3981071705534971,-43.6127655689952
1.5848931924611125,-32.63237622024735
6.30957344480193,-40.95657805794622
25.118864315095795,-70.84064244293268
7 changes: 7 additions & 0 deletions ...example_files/simulation_output/baseline_calibration/LL_allxLH_each_admin_run/DD_run4.csv
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Habitat_Multiplier,score
0.0251188643150957,-160.3892279968004
0.1,-152.45620330340898
0.3981071705534971,-42.30347028002507
1.5848931924611125,-31.06034277200979
6.30957344480193,-38.77199487420694
25.118864315095795,-72.35240770470205
7 changes: 7 additions & 0 deletions ...example_files/simulation_output/baseline_calibration/LL_allxLH_each_admin_run/EE_run0.csv
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Habitat_Multiplier,score
0.0251188643150957,-37.854650365159614
0.1,-17.13012477925531
0.3981071705534971,-31.267075636078516
1.5848931924611125,-92.85118040666566
6.30957344480193,-111.40001559250322
25.118864315095795,-139.4825035598942
7 changes: 7 additions & 0 deletions ...example_files/simulation_output/baseline_calibration/LL_allxLH_each_admin_run/EE_run1.csv
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0.0251188643150957,-37.47865655154237
0.1,-19.556382086146186
0.3981071705534971,-32.27834172900975
1.5848931924611125,-87.55260192051992
6.30957344480193,-114.8709116380478
25.118864315095795,-139.12566874570803
7 changes: 7 additions & 0 deletions ...example_files/simulation_output/baseline_calibration/LL_allxLH_each_admin_run/EE_run2.csv
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Habitat_Multiplier,score
0.0251188643150957,-37.740776471961
0.1,-26.957675795469186
0.3981071705534971,-32.90366613324568
1.5848931924611125,-86.76201218468486
6.30957344480193,-110.48589128043955
25.118864315095795,-143.77322788173774
7 changes: 7 additions & 0 deletions ...example_files/simulation_output/baseline_calibration/LL_allxLH_each_admin_run/EE_run3.csv
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0.0251188643150957,-37.393443932532136
0.1,-17.703431520160848
0.3981071705534971,-31.200901281641563
1.5848931924611125,-91.0988168915494
6.30957344480193,-109.80978507180089
25.118864315095795,-143.7966168980779
7 changes: 7 additions & 0 deletions ...example_files/simulation_output/baseline_calibration/LL_allxLH_each_admin_run/EE_run4.csv
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Habitat_Multiplier,score
0.0251188643150957,-37.61549312922489
0.1,-22.662258710705828
0.3981071705534971,-31.908370708685197
1.5848931924611125,-86.13536325978566
6.30957344480193,-113.84904864103032
25.118864315095795,-140.3943139794585
7 changes: 7 additions & 0 deletions ...example_files/simulation_output/baseline_calibration/LL_allxLH_each_admin_run/FF_run0.csv
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Habitat_Multiplier,score
0.0251188643150957,-282.21911977322543
0.1,-276.2133589090281
0.3981071705534971,-102.97853433258479
1.5848931924611125,-45.58003104489717
6.30957344480193,-18.959367482504604
25.118864315095795,-19.511596758250334
7 changes: 7 additions & 0 deletions ...example_files/simulation_output/baseline_calibration/LL_allxLH_each_admin_run/FF_run1.csv
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Habitat_Multiplier,score
0.0251188643150957,-283.73793380850384
0.1,-281.50580974889
0.3981071705534971,-99.80048409489791
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