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Migrate CSV files from LFS to regular Git (#1819)
* Update root dir .gitattributes to not put any CSV into LFS * Remove doc/.gitattributes * Add GHA workflow to check no CSVs tracked by LFS
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‎.gitattributes‎

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*.csv filter=lfs diff=lfs merge=lfs -text
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*.dbf filter=lfs diff=lfs merge=lfs -text
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*.docx filter=lfs diff=lfs merge=lfs -text
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*.jpg filter=lfs diff=lfs merge=lfs -text
@@ -8,5 +7,8 @@
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*.shx filter=lfs diff=lfs merge=lfs -text
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*.xlsx filter=lfs diff=lfs merge=lfs -text
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*.pickle filter=lfs diff=lfs merge=lfs -text
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*.csv -filter -diff -merge text
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resources/** filter=lfs diff=lfs merge=lfs -text
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resources/**/*.md !filter !diff !merge !text
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resources/**/*.md -filter -diff -merge text
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resources/**/*.csv -filter -diff -merge text
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‎.github/workflows/lfs-csv-check.yml‎

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name: No CSV files tracked by Git LFS
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on:
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push:
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schedule:
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- cron: 0 0 * * *
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jobs:
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no-csv-in-lfs:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout
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uses: actions/checkout@v6
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with:
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fetch-depth: 0
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- name: Install Git LFS
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run: |
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sudo apt-get update
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sudo apt-get install -y git-lfs
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git lfs install --local
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- name: Fail if any .csv files are tracked by Git LFS
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shell: bash
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run: |
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set -eo pipefail
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lfs_paths=$(git lfs ls-files --name-only | grep -E "\.csv$" || true)
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if [[ -z "${lfs_paths}" ]]; then
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echo "No CSV files are tracked by Git LFS."
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exit 0
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fi
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echo "ERROR: CSV files tracked by Git LFS:"
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printf '%s\n' "${lfs_paths}"
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exit 1

‎docs/.gitattributes‎

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This file was deleted.

‎docs/data_sources.csv‎

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‎resources/ResourceFile_Alri/GBD_Malawi_estimates.csv‎

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version https://git-lfs.github.com/spec/v1
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oid sha256:055fede60df7e2db3000aa39090153dd79e82c7e56e8fc5000582dd103e53475
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size 980
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Year,Death_per100k_children,Death_per100k_lower,Death_per100k_upper,Incidence_per100_children,Incidence_per100_lower,Incidence_per100_upper,DALYs,DALYs_lower,DALYs_upper
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2010,258.35,194.1,330.88,13.18731,10.76878,15.93407,567888.17,427703.4,727013.82
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2011,257.73,193.89,332.68,12.68264,10.3766,15.28863,570660.95,429499.34,735641.6
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2012,246.35,185.74,318.6,12.11023,9.89684,14.62139,549033.08,413888.11,708912.86
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2013,232.42,172.61,306.36,11.51721,9.42606,13.89671,520890.3,387277.64,688318.87
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2014,220.58,164.09,291.38,10.95107,8.84937,13.31381,475401.63,353235.51,629467.42
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2015,210.56,156.42,278.84,10.45947,8.44016,12.80907,496502.96,369176.93,655152.96
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2016,195.02,141.1,258.3,10.00938,8.06142,12.39414,441063.74,319309.61,583925.32
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2017,176.39,127.85,236.58,9.68916,7.72748,12.18477,399055.36,289916.58,535253.57
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2018,169.27,120.13,232.52,9.52978,7.56549,12.00051,383027.08,271830.35,526008.43
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2019,158.72,111.41,220.28,9.44652,7.44754,11.9048,360718.95,253591.27,500057.08

‎resources/ResourceFile_Alri/McAllister_2019.csv‎

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version https://git-lfs.github.com/spec/v1
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oid sha256:eb68ea76fc2aa1c045b035c5d0e6b8a54fc139c8dc5ec67b5e061522ac3a651b
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size 177
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Year,Incidence_per100_children,Incidence_per100_lower,Incidence_per100_upper,Death_per1000_livebirths
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2000,39.6,23.5,66.9,28.2
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2005,,,,15.6
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2010,,,,11.7
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2015,22.1,13.2,37.5,8.6

‎resources/ResourceFile_Alri/parameter_values.csv‎

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version https://git-lfs.github.com/spec/v1
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oid sha256:e2b417a870b56a1301f13c0fa9e0624a395e4e5e598b506052db7b741d42ea16
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size 13358
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parameter_name,value,param_label,prior_min,prior_max,prior_note,resource,notes
2+
base_inc_rate_ALRI_by_RSV,"[0.165623001012122,0.0368943809605977,0.011883807410198]",local,"[0,0,0]","[1,1,1]",vague prior,,
3+
base_inc_rate_ALRI_by_Rhinovirus,"[0.0243368081563306,0.0564272209432261,0.0181754025659935]",local,"[0,0,0]","[1,1,1]",vague prior,,
4+
base_inc_rate_ALRI_by_HMPV,"[0.0316242920447732,0.01106932885584,0.00356546901880363]",local,"[0,0,0]","[1,1,1]",vague prior,,
5+
base_inc_rate_ALRI_by_Parainfluenza,"[0.0400689053941642,0.0125990679490263,0.00405820325903094]",local,"[0,0,0]","[1,1,1]",vague prior,,
6+
base_inc_rate_ALRI_by_Strep_pneumoniae_PCV13,"[0.00839805492638728,0.0086009815601405,0.00277040583791159]",local,"[0,0,0]","[1,1,1]",vague prior,,
7+
base_inc_rate_ALRI_by_Strep_pneumoniae_non_PCV13,"[0.00971808948465436,0.0056295094957977,0.00181328443302487]",local,"[0,0,0]","[1,1,1]",vague prior,,
8+
base_inc_rate_ALRI_by_Hib,"[0.00456369209787862,0.00223809928508262,0.000720899502209533]",local,"[0,0,0]","[1,1,1]",vague prior,,
9+
base_inc_rate_ALRI_by_H.influenzae_non_type_b,"[0.0178046628079453,0.00771804577106646,0.00248600917371134]",local,"[0,0,0]","[1,1,1]",vague prior,,
10+
base_inc_rate_ALRI_by_Staph_aureus,"[0.0230583713892271,0.00164959730828988,0.000531340984878809]",local,"[0,0,0]","[1,1,1]",vague prior,,
11+
base_inc_rate_ALRI_by_Enterobacteriaceae,"[0.00577447898013911,0.00776959582619209,0.002502613624339]",local,"[0,0,0]","[1,1,1]",vague prior,,
12+
base_inc_rate_ALRI_by_other_Strepto_Enterococci,"[0.00739221008020393,0.000441075977443103,0.000142072094251877]",local,"[0,0,0]","[1,1,1]",vague prior,,
13+
base_inc_rate_ALRI_by_Influenza,"[0.0156895896609387,0.00577122651203705,0.00185893197294524]",local,"[0,0,0]","[1,1,1]",vague prior,,
14+
base_inc_rate_ALRI_by_P.jirovecii,"[0.00532021183938121,0.00406616141018573,0.00130972462037058]",local,"[0,0,0]","[1,1,1]",vague prior,,
15+
base_inc_rate_ALRI_by_other_viral_pathogens,"[0.0289052989892286,0.0340001707821008,0.0109515723253317]",local,"[0,0,0]","[1,1,1]",vague prior,,
16+
base_inc_rate_ALRI_by_other_bacterial_pathogens,"[0.0340967151177136,0.0275272316777052,0.00886661630515269]",local,"[0,0,0]","[1,1,1]",vague prior,,
17+
base_inc_rate_ALRI_by_other_pathogens_NoS,"[0.012096954443426,0.0244908799021158,0.00788859692140824]",local,"[0,0,0]","[1,1,1]",vague prior,,
18+
proportion_pneumonia_in_RSV_ALRI,"[0.469523118748083,0.493147834326293]",local,"[0,0]","[1,1]",vague prior,,
19+
proportion_pneumonia_in_Rhinovirus_ALRI,"[0.233411098940226,0.300943850285401]",local,"[0,0]","[1,1]",vague prior,,
20+
proportion_pneumonia_in_HMPV_ALRI,"[0.514096212711081,0.607661832402657]",local,"[0,0]","[1,1]",vague prior,,
21+
proportion_pneumonia_in_Parainfluenza_ALRI,"[0.381306534835401,0.586394378700289]",local,"[0,0]","[1,1]",vague prior,,
22+
proportion_pneumonia_in_Strep_pneumoniae_PCV13_ALRI,"[0.419837201436785,1]",local,"[0,0]","[1,1]",vague prior,,
23+
proportion_pneumonia_in_Strep_pneumoniae_non_PCV13_ALRI,"[0.584526531211357,0.47010416567094]",local,"[0,0]","[1,1]",vague prior,,
24+
proportion_pneumonia_in_Hib_ALRI,"[0.643816417750475,0.591228432603006]",local,"[0,0]","[1,1]",vague prior,,
25+
proportion_pneumonia_in_H.influenzae_non_type_b_ALRI,"[0.484067635967411,0.685783925920651]",local,"[0,0]","[1,1]",vague prior,,
26+
proportion_pneumonia_in_Staph_aureus_ALRI,"[0.314311461687961,0.668460076932899]",local,"[0,0]","[1,1]",vague prior,,
27+
proportion_pneumonia_in_Enterobacteriaceae_ALRI,"[0.542743088827561,0.397386416381317]",local,"[0,0]","[1,1]",vague prior,,
28+
proportion_pneumonia_in_other_Strepto_Enterococci_ALRI,"[0.794939501527616,1]",local,"[0,0]","[1,1]",vague prior,,
29+
proportion_pneumonia_in_Influenza_ALRI,"[0.274661773216931,0.477667070122735]",local,"[0,0]","[1,1]",vague prior,,
30+
proportion_pneumonia_in_P.jirovecii_ALRI,"[0.773174448993322,0.650848699225084]",local,"[0,0]","[1,1]",vague prior,,
31+
proportion_pneumonia_in_other_viral_pathogens_ALRI,"[0.264286065267648,0.301616616612727]",local,"[0,0]","[1,1]",vague prior,,
32+
proportion_pneumonia_in_other_bacterial_pathogens_ALRI,"[0.321708555070697,0.424616377668989]",local,"[0,0]","[1,1]",vague prior,,
33+
proportion_pneumonia_in_other_pathogens_NoS_ALRI,"[0.323847892119005,0.256639724815326]",local,"[0,0]","[1,1]",vague prior,,
34+
rr_ALRI_HIV/AIDS,6.51,universal,0.01,100,vague prior,Jackson et al. 2013,
35+
rr_ALRI_incomplete_measles_immunisation,1.8,universal,0.01,100,vague prior,Jackson et al. 2013,
36+
rr_ALRI_low_birth_weight,3.6,universal,0.01,100,vague prior,Jackson et al. 2013,
37+
rr_ALRI_non_exclusive_breastfeeding,2.7,universal,0.01,100,vague prior,Jackson et al. 2013,
38+
rr_ALRI_indoor_air_pollution,1.57,universal,0.01,100,vague prior,Jackson et al. 2013,
39+
rr_Strep_pneum_VT_ALRI_with_PCV13_age<2y,0.18,universal,0.01,1,vague prior,Mackenzie et al. 2016 Lancet,
40+
rr_Strep_pneum_VT_ALRI_with_PCV13_age2to5y,0.32,universal,0.01,1,vague prior,Mackenzie et al. 2016 Lancet,
41+
rr_all_strains_Strep_pneum_ALRI_with_PCV13,0.45,undetermined,0.01,1,calibration,Mackenzie et al. 2016 Lancet,for calibration
42+
effectiveness_Hib_vaccine_on_Hib_strains,0.86,universal,0,1,vague prior,Obonyo and Lau 2006,
43+
rr_Hib_ALRI_with_Hib_vaccine,0.14,universal,0.01,1,vague prior,,
44+
prob_viral_pneumonia_bacterial_coinfection,0.3,universal,0,1,vague prior,,
45+
proportion_bacterial_coinfection_pathogen,"[0.107,0.072,0.038,0.141,0.134,0.117,0.052,0.338]",local,"[0,0,0,0,0,0,0,0]","[1,1,1,1,1,1,1,1]",vague prior,,
46+
overall_progression_to_severe_ALRI,0.12,undetermined,0,1,calibration,Walker et al. 2013,for calibration
47+
prob_pulmonary_complications_in_pneumonia,0.215,universal,0,1,vague prior,Resti et al. 2010,
48+
prob_pleural_effusion_in_pulmonary_complicated_pneumonia,0.938,universal,0,1,vague prior,Resti et al. 2010,
49+
prob_empyema_in_pulmonary_complicated_pneumonia,0.315,universal,0,1,vague prior,Resti et al. 2010,
50+
prob_lung_abscess_in_pulmonary_complicated_pneumonia,0.049,universal,0,1,vague prior,"Resti et al. 2010, assumed from necrotising pneumonia",
51+
prob_pneumothorax_in_pulmonary_complicated_pneumonia,0.049,universal,0,1,vague prior,"Resti et al. 2010, assumed from atelectasia",
52+
prob_hypoxaemia_in_pneumonia,0.479,universal,0,1,vague prior,Fancourt et al 2017,
53+
prob_hypoxaemia_in_other_alri,0.273,universal,0,1,vague prior,Fancourt et al 2017,
54+
prob_bacteraemia_in_pneumonia,0.039,universal,0,1,vague prior,Sebavonge et al. 2016,
55+
prob_progression_to_sepsis_with_bacteraemia,0.3,universal,0,1,vague prior,Fritz et al. 2019,
56+
prob_cough_in_pneumonia,1,universal,0,1,vague prior,Rees et al 2020,0.77
57+
prob_difficult_breathing_in_pneumonia,1,universal,0,1,vague prior,Rees et al 2020,0.7
58+
prob_fever_in_pneumonia,0.82,universal,0,1,vague prior,Rees et al 2020,
59+
prob_chest_indrawing_in_pneumonia,0.74,universal,0,1,vague prior,Rees et al 2020,
60+
prob_tachypnoea_in_pneumonia,0.834,universal,0,1,vague prior,Fancourt et al 2017,
61+
prob_danger_signs_in_pneumonia,0.28,universal,0,1,vague prior,Rees et al 2020,
62+
prob_cyanosis_in_pneumonia,0.06,universal,0,1,vague prior,Rees et al 2020,
63+
prob_cough_in_other_alri,1,universal,0,1,vague prior,,assumed
64+
prob_difficult_breathing_in_other_alri,1,universal,0,1,vague prior,,assumed
65+
prob_fever_in_other_alri,0.76,universal,0,1,vague prior,,calculated using OR=1.41 temp>38C from Fancourt and the prob_fever_in_pneumonia
66+
prob_chest_indrawing_in_other_alri,0.33,universal,0,1,vague prior,,assumed (based on Eric' Bangladesh trial - outpatient pneumonia)
67+
prob_tachypnoea_in_other_alri,0.758,universal,0,1,vague prior,Fancourt et al 2017,
68+
prob_danger_signs_in_other_alri,0.3,universal,0,1,vague prior,Rees et al 2020 (or or 0.03 assumed (based on Eric' Bangladesh trial - outpatient pneumonia)),1-specificity
69+
prob_cyanosis_in_other_alri,0.04,universal,0,1,vague prior,Rees et al 2020,1-specificity
70+
prob_danger_signs_in_sepsis,1,universal,0,1,vague prior,,assumed
71+
prob_danger_signs_in_SpO2<90%,0.313,universal,0,1,vague prior,McCollum et al. 2016,HC only
72+
prob_danger_signs_in_SpO2_90-92%,0.133,universal,0,1,vague prior,McCollum et al. 2016,HC only
73+
prob_chest_indrawing_in_SpO2<90%,0.701,universal,0,1,vague prior,McCollum et al. 2016,HC & CHW combined
74+
prob_chest_indrawing_in_SpO2_90-92%,0.445,universal,0,1,vague prior,McCollum et al. 2016,HC & CHW combined
75+
proportion_hypoxaemia_with_SpO2<90%,0.3576,local,0,1,vague prior,McCollum et al. 2016,prevalence of SpO2 <90% over total prevalence of hypoxaemia
76+
prob_cyanosis_in_SpO2<90%,0.078,universal,0,1,vague prior,Bassat et al 2016,cyanosis in Hypoxaemic children < 90% in Mozambique study. Non-hypoxaemic children had 1.5%
77+
max_alri_duration_in_days_without_treatment,14,universal,7,28,vague prior,,
78+
days_between_treatment_and_cure,28,universal,14,42,vague prior,,7 inpatient days + 3 weeks oral antibiotics course
79+
tf_3day_amoxicillin_for_fast_breathing_with_SpO2>=90%,0.101,universal,0,1,vague prior,Ginsburg et al. 2019,treatment failure or relapse by day 14
80+
tf_5day_amoxicillin_for_chest_indrawing_with_SpO2>=90%,0.108,universal,0,1,vague prior,Ginsburg et al. 2020,treatment failure or relapse by day 14
81+
tf_3day_amoxicillin_for_chest_indrawing_with_SpO2>=90%,0.125,universal,0,1,vague prior,Ginsburg et al. 2020,treatment failure or relapse by day 15
82+
tf_7day_amoxicillin_for_fast_breathing_pneumonia_in_young_infants,0.054,universal,0,1,vague prior,,"EMPIC study 2021, 6.3% TF by standard 1st dose antibiotic and referral"
83+
tf_oral_amoxicillin_only_for_severe_pneumonia_with_SpO2>=90%,0.6,universal,0,1,vague prior,,
84+
tf_oral_amoxicillin_only_for_non_severe_pneumonia_with_SpO2<90%,0.2826,universal,0,1,vague prior,,calculated using 0.17 and pOR=0.52
85+
tf_oral_amoxicillin_only_for_severe_pneumonia_with_SpO2<90%,0.8,universal,0,1,vague prior,,
86+
sensitivity_of_classification_of_fast_breathing_pneumonia_facility_level0,0.7,universal,0,1,vague prior,HHFA 2018,Boyce et al 2019
87+
sensitivity_of_classification_of_danger_signs_pneumonia_facility_level0,0.7,universal,0,1,vague prior,HHFA 2018,Boyce et al 2019
88+
sensitivity_of_classification_of_non_severe_pneumonia_facility_level1,0.7,universal,0,1,vague prior,HHFA 2018,Bjornstad et al 2014
89+
sensitivity_of_classification_of_severe_pneumonia_facility_level1,0.7,universal,0,1,vague prior,HHFA 2018,Bjornstad et al 2014
90+
sensitivity_of_classification_of_non_severe_pneumonia_facility_level2,0.7,universal,0,1,vague prior,HHFA 2018,Uwemedimo et al. 2018
91+
sensitivity_of_classification_of_severe_pneumonia_facility_level2,0.7,universal,0,1,vague prior,HHFA 2018,
92+
prob_iCCM_severe_pneumonia_treated_as_fast_breathing_pneumonia,0.7,universal,0,1,vague prior,,dummy
93+
prob_IMCI_severe_pneumonia_treated_as_non_severe_pneumonia,0.7,universal,0,1,vague prior,,dummy
94+
scaler_on_risk_of_death,0.75,undetermined,0.1,2,calibration,,For Calibration
95+
base_odds_death_ALRI_age<2mo,0.041965,local,0.01,0.2,vague prior,Lazzerini et al 2016,
96+
or_death_ALRI_age<2mo_very_severe_pneumonia,3.994783,universal,1,10,vague prior,Lazzerini et al 2016,
97+
or_death_ALRI_age<2mo_P.jirovecii,5.460986,universal,1,10,vague prior,Lazzerini et al 2016,
98+
or_death_ALRI_age<2mo_by_month_increase_in_age,0.6033254,universal,0.1,1,vague prior,Lazzerini et al 2016,
99+
base_odds_death_ALRI_age2_59mo,0.0244725,local,0.01,0.2,vague prior,Lazzerini et al 2016,calculated
100+
or_death_ALRI_age2_59mo_very_severe_pneumonia,8.382832,universal,1,20,vague prior,Lazzerini et al 2016,
101+
or_death_ALRI_age2_59mo_P.jirovecii,13.74696,universal,1,20,vague prior,Lazzerini et al 2016,
102+
or_death_ALRI_age2_59mo_SAM,7.216448,universal,1,20,vague prior,Lazzerini et al 2016,
103+
or_death_ALRI_age2_59mo_by_month_increase_in_age,0.9661072,universal,0.5,1,vague prior,Lazzerini et al 2016,
104+
or_death_ALRI_age2_59mo_female,1.327285,universal,0.5,2,vague prior,Lazzerini et al 2016,
105+
or_death_ALRI_SpO2<90%,5.04,universal,1,10,vague prior,Hooli et al. 2016,
106+
or_death_ALRI_SpO2_90_92%,1.54,universal,1,5,vague prior,Hooli et al. 2016,
107+
or_death_ALRI_sepsis,151.9,universal,50,300,vague prior,,
108+
or_death_ALRI_pneumothorax,77.4,universal,20,150,vague prior,,
109+
tf_1st_line_antibiotic_for_severe_pneumonia,0.11,universal,0,1,vague prior,Lassi et al 2013,0.171 overall value in source
110+
rr_tf_1st_line_antibiotics_if_cyanosis,1.55,universal,1,5,vague prior,Muro et al 2020,
111+
rr_tf_1st_line_antibiotics_if_SpO2<90%,1.28,universal,1,5,vague prior,Muro et al 2020,
112+
rr_tf_1st_line_antibiotics_if_abnormal_CXR,1.71,universal,1,5,vague prior,Muro et al 2020,
113+
rr_tf_1st_line_antibiotics_if_HIV/AIDS,1.8,universal,1,5,vague prior,Muro et al 2020,
114+
rr_tf_1st_line_antibiotics_if_MAM,1.48,universal,1,5,vague prior,Muro et al 2020,
115+
rr_tf_1st_line_antibiotics_if_SAM,2.02,universal,1,5,vague prior,Muro et al 2020,
116+
or_mortality_improved_oxygen_systems,0.52,universal,0.1,1,vague prior,Lam et al 2021,
117+
pulse_oximeter_and_oxygen_is_available,Default,scenario,NA,NA,vague prior,,
118+
or_care_seeking_perceived_severe_illness,2.4,local,1,5,vague prior,Lungu et al 2020,"perceived severe illness, OR used for seeking care for chest-indrawing"
119+
tf_2nd_line_antibiotic_for_severe_pneumonia,0.235,universal,0,1,vague prior,,
120+
prob_for_followup_if_treatment_failure,0.3,local,0,1,vague prior,,
121+
child_age_threshold,5,local,2,18,vague prior,,
122+
main_polling_frequency,2,undetermined,1,12,design decision,,
123+
inpatient_bed_days,7,local,3,14,vague prior,,
124+
treatment_window_days,1,local,0,3,vague prior,,
125+
follow_up_appointment_days,5,local,3,7,vague prior,,

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