Parameter values (.csv)

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	parameter_name	value	source	notes	Unnamed: 4	Unnamed: 5
0	base_inc_rate_ALRI_by_RSV	[0.165623001012122,0.0368943809605977,0.011883807410198]
1	base_inc_rate_ALRI_by_Rhinovirus	[0.0243368081563306,0.0564272209432261,0.0181754025659935]
2	base_inc_rate_ALRI_by_HMPV	[0.0316242920447732,0.01106932885584,0.00356546901880363]
3	base_inc_rate_ALRI_by_Parainfluenza	[0.0400689053941642,0.0125990679490263,0.00405820325903094]
4	base_inc_rate_ALRI_by_Strep_pneumoniae_PCV13	[0.00839805492638728,0.0086009815601405,0.00277040583791159]
5	base_inc_rate_ALRI_by_Strep_pneumoniae_non_PCV13	[0.00971808948465436,0.0056295094957977,0.00181328443302487]
6	base_inc_rate_ALRI_by_Hib	[0.00456369209787862,0.00223809928508262,0.000720899502209533]
7	base_inc_rate_ALRI_by_H.influenzae_non_type_b	[0.0178046628079453,0.00771804577106646,0.00248600917371134]
8	base_inc_rate_ALRI_by_Staph_aureus	[0.0230583713892271,0.00164959730828988,0.000531340984878809]
9	base_inc_rate_ALRI_by_Enterobacteriaceae	[0.00577447898013911,0.00776959582619209,0.002502613624339]
10	base_inc_rate_ALRI_by_other_Strepto_Enterococci	[0.00739221008020393,0.000441075977443103,0.000142072094251877]
11	base_inc_rate_ALRI_by_Influenza	[0.0156895896609387,0.00577122651203705,0.00185893197294524]
12	base_inc_rate_ALRI_by_P.jirovecii	[0.00532021183938121,0.00406616141018573,0.00130972462037058]
13	base_inc_rate_ALRI_by_other_viral_pathogens	[0.0289052989892286,0.0340001707821008,0.0109515723253317]
14	base_inc_rate_ALRI_by_other_bacterial_pathogens	[0.0340967151177136,0.0275272316777052,0.00886661630515269]
15	base_inc_rate_ALRI_by_other_pathogens_NoS	[0.012096954443426,0.0244908799021158,0.00788859692140824]
16	proportion_pneumonia_in_RSV_ALRI	[0.469523118748083,0.493147834326293]
17	proportion_pneumonia_in_Rhinovirus_ALRI	[0.233411098940226,0.300943850285401]
18	proportion_pneumonia_in_HMPV_ALRI	[0.514096212711081,0.607661832402657]
19	proportion_pneumonia_in_Parainfluenza_ALRI	[0.381306534835401,0.586394378700289]
20	proportion_pneumonia_in_Strep_pneumoniae_PCV13_ALRI	[0.419837201436785,1]
21	proportion_pneumonia_in_Strep_pneumoniae_non_PCV13_ALRI	[0.584526531211357,0.47010416567094]
22	proportion_pneumonia_in_Hib_ALRI	[0.643816417750475,0.591228432603006]
23	proportion_pneumonia_in_H.influenzae_non_type_b_ALRI	[0.484067635967411,0.685783925920651]
24	proportion_pneumonia_in_Staph_aureus_ALRI	[0.314311461687961,0.668460076932899]
25	proportion_pneumonia_in_Enterobacteriaceae_ALRI	[0.542743088827561,0.397386416381317]
26	proportion_pneumonia_in_other_Strepto_Enterococci_ALRI	[0.794939501527616,1]
27	proportion_pneumonia_in_Influenza_ALRI	[0.274661773216931,0.477667070122735]
28	proportion_pneumonia_in_P.jirovecii_ALRI	[0.773174448993322,0.650848699225084]
29	proportion_pneumonia_in_other_viral_pathogens_ALRI	[0.264286065267648,0.301616616612727]
30	proportion_pneumonia_in_other_bacterial_pathogens_ALRI	[0.321708555070697,0.424616377668989]
31	proportion_pneumonia_in_other_pathogens_NoS_ALRI	[0.323847892119005,0.256639724815326]
32
33	rr_ALRI_HIV/AIDS	6.51	Jackson et al. 2013
34	rr_ALRI_incomplete_measles_immunisation	1.8	Jackson et al. 2013
35	rr_ALRI_low_birth_weight	3.6	Jackson et al. 2013
36	rr_ALRI_non_exclusive_breastfeeding	2.7	Jackson et al. 2013
37	rr_ALRI_indoor_air_pollution	1.57	Jackson et al. 2013
38
39	rr_Strep_pneum_VT_ALRI_with_PCV13_age<2y	0.18	Mackenzie et al. 2016 Lancet
40	rr_Strep_pneum_VT_ALRI_with_PCV13_age2to5y	0.32	Mackenzie et al. 2016 Lancet
41	rr_all_strains_Strep_pneum_ALRI_with_PCV13	0.45	Mackenzie et al. 2016 Lancet	for calibration
42	effectiveness_Hib_vaccine_on_Hib_strains	0.86	Obonyo and Lau 2006
43	rr_Hib_ALRI_with_Hib_vaccine	0.14
44	prob_viral_pneumonia_bacterial_coinfection	0.3
45	proportion_bacterial_coinfection_pathogen	[0.107,0.072,0.038,0.141,0.134,0.117,0.052,0.338]
46	overall_progression_to_severe_ALRI	0.12	Walker et al. 2013	for calibration
47	prob_pulmonary_complications_in_pneumonia	0.215	Resti et al. 2010
48	prob_pleural_effusion_in_pulmonary_complicated_pneumonia	0.938	Resti et al. 2010
49	prob_empyema_in_pulmonary_complicated_pneumonia	0.315	Resti et al. 2010
50	prob_lung_abscess_in_pulmonary_complicated_pneumonia	0.049	Resti et al. 2010, assumed from necrotising pneumonia
51	prob_pneumothorax_in_pulmonary_complicated_pneumonia	0.049	Resti et al. 2010, assumed from atelectasia
52	prob_hypoxaemia_in_pneumonia	0.479	Fancourt et al 2017
53	prob_hypoxaemia_in_other_alri	0.273	Fancourt et al 2017
54	prob_bacteraemia_in_pneumonia	0.039	Sebavonge et al. 2016
55	prob_progression_to_sepsis_with_bacteraemia	0.3	Fritz et al. 2019
56	prob_cough_in_pneumonia	1	Rees et al 2020	0.77
57	prob_difficult_breathing_in_pneumonia	1	Rees et al 2020	0.7
58	prob_fever_in_pneumonia	0.82	Rees et al 2020
59	prob_chest_indrawing_in_pneumonia	0.74	Rees et al 2020
60	prob_tachypnoea_in_pneumonia	0.834	Fancourt et al 2017
61	prob_danger_signs_in_pneumonia	0.28	Rees et al 2020
62	prob_cyanosis_in_pneumonia	0.06	Rees et al 2020
63	prob_cough_in_other_alri	1	assumed
64	prob_difficult_breathing_in_other_alri	1	assumed
65	prob_fever_in_other_alri	0.76		calculated using OR=1.41 temp>38C from Fancourt and the prob_fever_in_pneumonia
66	prob_chest_indrawing_in_other_alri	0.33		assumed (based on Eric’ Bangladesh trial - outpatient pneumonia)
67	prob_tachypnoea_in_other_alri	0.758	Fancourt et al 2017
68	prob_danger_signs_in_other_alri	0.3	Rees et al 2020	1-specificity	or 0.03 assumed (based on Eric’ Bangladesh trial - outpatient pneumonia)
69	prob_cyanosis_in_other_alri	0.04	Rees et al 2020	1-specificity
70	prob_danger_signs_in_sepsis	1	assumed
71	prob_danger_signs_in_SpO2<90%	0.313	McCollum et al. 2016	HC only
72	prob_danger_signs_in_SpO2_90-92%	0.133	McCollum et al. 2016	HC only
73	prob_chest_indrawing_in_SpO2<90%	0.701	McCollum et al. 2016	HC & CHW combined
74	prob_chest_indrawing_in_SpO2_90-92%	0.445	McCollum et al. 2016	HC & CHW combined
75	proportion_hypoxaemia_with_SpO2<90%	0.3576	McCollum et al. 2016	prevalence of SpO2 <90% over total prevalence of hypoxaemia
76	prob_cyanosis_in_SpO2<90%	0.078	Bassat et al 2016	cyanosis in Hypoxaemic children < 90% in Mozambique study. Non-hypoxaemic children had 1.5%
77
78	max_alri_duration_in_days_without_treatment	14
79	days_between_treatment_and_cure	28		7 inpatient days + 3 weeks oral antibiotics course
80
81	tf_3day_amoxicillin_for_fast_breathing_with_SpO2>=90%	0.101	Ginsburg et al. 2019	treatment failure or relapse by day 14
82	tf_5day_amoxicillin_for_chest_indrawing_with_SpO2>=90%	0.108	Ginsburg et al. 2020	treatment failure or relapse by day 14	5-day course of oral amoxicillin treatment failure of non-hypoxaemic (>=90%) chest-indrawing pneumonia — 4.3% — check with ref. EMPIC Study Group (Malawi smaller sample size)
83	tf_3day_amoxicillin_for_chest_indrawing_with_SpO2>=90%	0.125	Ginsburg et al. 2020	treatment failure or relapse by day 15
84	tf_7day_amoxicillin_for_fast_breathing_pneumonia_in_young_infants	0.054		EMPIC study 2021, 6.3% TF by standard 1st dose antibiotic and referral
85	tf_oral_amoxicillin_only_for_severe_pneumonia_with_SpO2>=90%	0.6
86	tf_oral_amoxicillin_only_for_non_severe_pneumonia_with_SpO2<90%	0.2826		calculated using 0.17 and pOR=0.52
87	tf_oral_amoxicillin_only_for_severe_pneumonia_with_SpO2<90%	0.8
88
89	sensitivity_of_classification_of_fast_breathing_pneumonia_facility_level0	0.7	HHFA 2018		0.746	Boyce et al 2019
90	sensitivity_of_classification_of_danger_signs_pneumonia_facility_level0	0.7	HHFA 2018		0.708	Boyce et al 2019
91	sensitivity_of_classification_of_non_severe_pneumonia_facility_level1	0.7	HHFA 2018		0.3	Bjornstad et al 2014
92	sensitivity_of_classification_of_severe_pneumonia_facility_level1	0.7	HHFA 2018		0.0592	Bjornstad et al 2014
93	sensitivity_of_classification_of_non_severe_pneumonia_facility_level2	0.7	HHFA 2018		0.23	Uwemedimo et al. 2018
94	sensitivity_of_classification_of_severe_pneumonia_facility_level2	0.7	HHFA 2018
95	prob_iCCM_severe_pneumonia_treated_as_fast_breathing_pneumonia	0.7	dummy
96	prob_IMCI_severe_pneumonia_treated_as_non_severe_pneumonia	0.7	dummy
97
98	scaler_on_risk_of_death	0.75	For Calibration
99	base_odds_death_ALRI_age<2mo	0.041965	Lazzerini et al 2016
100	or_death_ALRI_age<2mo_very_severe_pneumonia	3.994783	Lazzerini et al 2016
101	or_death_ALRI_age<2mo_P.jirovecii	5.460986	Lazzerini et al 2016
102	or_death_ALRI_age<2mo_by_month_increase_in_age	0.6033254	Lazzerini et al 2016
103
104	base_odds_death_ALRI_age2_59mo	0.0244725	Lazzerini et al 2016	calculated
105	or_death_ALRI_age2_59mo_very_severe_pneumonia	8.382832	Lazzerini et al 2016
106	or_death_ALRI_age2_59mo_P.jirovecii	13.74696	Lazzerini et al 2016
107	or_death_ALRI_age2_59mo_SAM	7.216448	Lazzerini et al 2016
108	or_death_ALRI_age2_59mo_by_month_increase_in_age	0.9661072	Lazzerini et al 2016
109	or_death_ALRI_age2_59mo_female	1.327285	Lazzerini et al 2016
110	or_death_ALRI_SpO2<90%	5.04	Hooli et al. 2016
111	or_death_ALRI_SpO2_90_92%	1.54	Hooli et al. 2016
112	or_death_ALRI_sepsis	151.9
113	or_death_ALRI_pneumothorax	77.4
114
115	tf_1st_line_antibiotic_for_severe_pneumonia	0.11	Lassi et al 2013	0.171 overall value in source
116	rr_tf_1st_line_antibiotics_if_cyanosis	1.55	Muro et al 2020
117	rr_tf_1st_line_antibiotics_if_SpO2<90%	1.28	Muro et al 2020
118	rr_tf_1st_line_antibiotics_if_abnormal_CXR	1.71	Muro et al 2020
119	rr_tf_1st_line_antibiotics_if_HIV/AIDS	1.8	Muro et al 2020
120	rr_tf_1st_line_antibiotics_if_MAM	1.48	Muro et al 2020
121	rr_tf_1st_line_antibiotics_if_SAM	2.02	Muro et al 2020
122	or_mortality_improved_oxygen_systems	0.52	Lam et al 2021
123
124	pulse_oximeter_and_oxygen_is_available	Default
125
126	or_care_seeking_perceived_severe_illness	2.4	Lungu et al 2020	perceived severe illness, OR used for seeking care for chest-indrawing
127
128	tf_2nd_line_antibiotic_for_severe_pneumonia	0.235
129
130	prob_for_followup_if_treatment_failure	0.3