Alri (.xlsx)

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Calculations

	parameter_name	1-11	12-23	24-59	Unnamed: 4	Unnamed: 5	Unnamed: 6	Unnamed: 7	Unnamed: 8	Unnamed: 9	Unnamed: 10	Unnamed: 11
0	base_incidence_ALRI_by_agecat	0.607	0.3429	0.1204
1	proportion of CXR+	0.50475	0.5452	0.4421
2	Target values for 12 monthly incidence rate - PNEUMONIA ONLY				1-11	12-23	24-59
3	base_incidence_pneumonia_all_pathogen				0.30638325	0.18694908	0.05322884
4					Pneumonia incidence by pathogen
5	pneumonia_attributable_fraction_RSV	0.397	0.164	0.165	0.12163415025	0.03065964912	0.008782758600000001
6	pneumonia_attributable_fraction_rhinovirus	0.029	0.152	0.159	0.008885114250000001	0.028416260159999998	0.00846338556
7	pneumonia_attributable_fraction_hmpv	0.083	0.063	0.059	0.02542980975	0.011777792039999999	0.00314050156
8	pneumonia_attributable_fraction_parainfluenza	0.078	0.067	0.068	0.0238978935	0.01252558836	0.0036195611200000003
9	pneumonia_attributable_fraction_streptococcus	0.047	0.106	0.092	0.01440001275	0.019816602479999997	0.00489705328
10	pneumonia_attributable_fraction_hib	0.059	0.067	0.044	0.01807661175	0.01252558836	0.0023420689599999997
11	pneumonia_attributable_fraction_TB	0.067	0.039	0.059	0.02052767775	0.00729101412	0.00314050156
12	pneumonia_attributable_fraction_staph	0.037	0.009	0.012	0.01133618025	0.0016825417199999998	0.00063874608
13	pneumonia_attributable_fraction_influenza	0.016	0.029	0.032	0.004902132	0.00542152332	0.0017033228800000001
14	pneumonia_attributable_fraction_jirovecii	0.03	0.004	0.002	0.0091914975	0.0007477963199999999	0.00010645768000000001
15	pneumonia_attributable_fraction_adenovirus	0	0	0	0	0	0
16	pneumonia_attributable_fraction_coronavirus	0	0	0	0	0	0
17	pneumonia_attributable_fraction_bocavirus	0	0	0	0	0	0
18	pneumonia_attributable_fraction_other_pathogens	0.098	0.274	0.282	0.0300255585	0.05122404792	0.015010532879999998
19	pneumonia_attributable_fraction_other_cause	0.05899999999999994	0.025999999999999912	0.0259999999999998	0.01807661174999998	0.004860676079999984	0.0013839498399999895
20	proportion of CXR- (bronchiolitis)	0.49524999999999997	0.4548	N/A	Bronchiolitis incidence by pathogen
21	fraction due to malaria, diarrhoea, anaemia etc…	0.15	0.15	0.15	0.2555242375	0.132558282
22	bronchiolitis_attributable_fraction_RSV	0.6	0.6		0.15331454249999998	0.0795349692
23	bronchiolitis_attributable_fraction_rhinovirus	0.05	0.05		0.012776211874999999	0.0066279141
24	bronchiolitis_attributable_fraction_hmpv	0.05	0.05		0.012776211874999999	0.0066279141
25	bronchiolitis_attributable_fraction_parainfluenza	0.05	0.05		0.012776211874999999	0.0066279141
26	bronchiolitis_attributable_fraction_streptococcus	0	0		0	0
27	bronchiolitis_attributable_fraction_hib	0	0		0	0
28	bronchiolitis_attributable_fraction_TB	0	0		0	0
29	bronchiolitis_attributable_fraction_staph	0	0		0	0
30	bronchiolitis_attributable_fraction_influenza	0.05	0.05		0.012776211874999999	0.0066279141
31	bronchiolitis_attributable_fraction_jirovecii	0	0		0	0
32	bronchiolitis_attributable_fraction_adenovirus	0.05	0.05		0.012776211874999999	0.0066279141
33	bronchiolitis_attributable_fraction_coronavirus	0.05	0.05		0.012776211874999999	0.0066279141
34	bronchiolitis_attributable_fraction_bocavirus	0.05	0.05		0.012776211874999999	0.0066279141
35	bronchiolitis_attributable_fraction_other_pathogens	0.05	0.05		0.012776211874999999	0.0066279141
36					0.2555242375	0.13255828199999994	Check if match or lower than incidence bronchiolitis
37	Total incidence ALRI by pathogen				Total incidence ALRI by pathogen
38	base_inc_rate_ALRI_by_RSV				0.27494869275	0.11019461831999999	0.008782758600000001
39	base_inc_rate_ALRI_by_Rhinovirus				0.021661326124999998	0.03504417426	0.00846338556
40	base_inc_rate_ALRI_by_HMPV				0.038206021625	0.01840570614	0.00314050156
41	base_inc_rate_ALRI_by_Parainfluenza				0.036674105375	0.01915350246	0.0036195611200000003
42	base_inc_rate_ALRI_by_Strep_pneumoniae_PCV13				0.01440001275	0.019816602479999997	0.00489705328
43	base_inc_rate_ALRI_by_Strep_pneumoniae_non_PCV13
44	base_inc_rate_ALRI_by_Hib
45	base_inc_rate_ALRI_by_H.influenzae_non_type_b				0.01807661175	0.01252558836	0.0023420689599999997
46	base_inc_rate_ALRI_by_TB				0.02052767775	0.00729101412	0.00314050156
47	base_inc_rate_ALRI_by_Staph_aureus				0.01133618025	0.0016825417199999998	0.00063874608
48	base_inc_rate_ALRI_by_Enterobacteriaceae
49	base_inc_rate_ALRI_by_other_Strepto_Enterococci
50	base_inc_rate_ALRI_by_Influenza				0.017678343875	0.01204943742	0.0017033228800000001
51	base_inc_rate_ALRI_by_P.jirovecii				0.0091914975	0.0007477963199999999	0.00010645768000000001
52	base_inc_rate_ALRI_by_Bocavirus				0.012776211874999999	0.0066279141	0
53	base_inc_rate_ALRI_by_Adenovirus				0.012776211874999999	0.0066279141	0
54	base_inc_rate_ALRI_by_other_viral_pathogens
55	base_inc_rate_ALRI_by_other_bacterial_pathogens				0.042801770375	0.05785196202	0.015010532879999998
56
57
58	ALRI_attributable_fraction_RSV				[0.27494869275,0.11019461832,0.0087827586]
59	ALRI_attributable_fraction_rhinovirus				[0.021661326125,0.03504417426,0.00846338556]
60	ALRI_attributable_fraction_hmpv				[0.038206021625,0.01840570614,0.00314050156]
61	ALRI_attributable_fraction_parainfluenza				[0.036674105375,0.01915350246,0.00361956112]
62	ALRI_attributable_fraction_streptococcus				[0.01440001275,0.01981660248,0.00489705328]
63	ALRI_attributable_fraction_hib				[0.01807661175,0.01252558836,0.00234206896]
64	ALRI_attributable_fraction_TB				[0.02052767775,0.00729101412,0.00314050156]
65	ALRI_attributable_fraction_staph				[0.01133618025,0.00168254172,0.00063874608]
66	ALRI_attributable_fraction_influenza				[0.017678343875,0.01204943742,0.00170332288]
67	ALRI_attributable_fraction_jirovecii				[0.0091914975,0.00074779632,0.00010645768]
68	ALRI_attributable_fraction_adenovirus				[0.012776211875,0.0066279141,0]
69	ALRI_attributable_fraction_coronavirus				[,,]
70	ALRI_attributable_fraction_bocavirus				[0.012776211875,0.0066279141,0]
71	ALRI_attributable_fraction_other_pathogens				[0.042801770375,0.05785196202,0.01501053288]
72
73	Total incidence ALRI by pathogen				Total incidence ALRI by pathogen
74	base_inc_rate_ALRI_by_RSV				0.27494869275	0.11019461832	0.008782758600000001		0.27494869275	0.11019461832	0.008782758600000001	0.2749, 0.1102, 0.0088
75	base_inc_rate_ALRI_by_Rhinovirus				0.021661326124999998	0.03504417426	0.00846338556		0.021661326124999998	0.03504417426	0.00846338556	0.0217, 0.035, 0.0085
76	base_inc_rate_ALRI_by_HMPV				0.038206021625	0.01840570614	0.00314050156		0.038206021625	0.01840570614	0.00314050156	0.0382, 0.0184, 0.0031
77	base_inc_rate_ALRI_by_Parainfluenza				0.036674105375	0.01915350246	0.0036195611200000003		0.036674105375	0.01915350246	0.0036195611200000003	0.0367, 0.0192, 0.0036
78	base_inc_rate_ALRI_by_Strep_pneumoniae_PCV13				0.007200006375	0.009908301239999999	0.00244852664		0.007200006375	0.009908301239999999	0.00244852664	0.0072, 0.0099, 0.0024
79	base_inc_rate_ALRI_by_Strep_pneumoniae_non_PCV13				0.007200006375	0.009908301239999999	0.00244852664		0.007200006375	0.009908301239999999	0.00244852664	0.0072, 0.0099, 0.0024
80	base_inc_rate_ALRI_by_Hib				0.009038305875	0.00626279418	0.0011710344799999999		0.009038305875	0.00626279418	0.0011710344799999999	0.009, 0.0063, 0.0012
81	base_inc_rate_ALRI_by_H.influenzae_non_type_b				0.009038305875	0.00626279418	0.0011710344799999999		0.009038305875	0.00626279418	0.0011710344799999999	0.009, 0.0063, 0.0012
82	base_inc_rate_ALRI_by_TB				0.02052767775	0.00729101412	0.00314050156		0.02052767775	0.00729101412	0.00314050156	0.0205, 0.0073, 0.0031
83	base_inc_rate_ALRI_by_Staph_aureus				0.01133618025	0.0016825417199999998	0.00063874608		0.01133618025	0.0016825417199999998	0.00063874608	0.0113, 0.0017, 0.0006
84	base_inc_rate_ALRI_by_Enterobacteriaceae				0.010263838875	0.00364550706	0.00157025078		0.010263838875	0.00364550706	0.00157025078	0.0103, 0.0036, 0.0016
85	base_inc_rate_ALRI_by_other_Strepto_Enterococci				0.010263838875	0.00364550706	0.00157025078		0.010263838875	0.00364550706	0.00157025078	0.0103, 0.0036, 0.0016
86	base_inc_rate_ALRI_by_Influenza				0.017678343875	0.01204943742	0.0017033228800000001		0.017678343875	0.01204943742	0.0017033228800000001	0.0177, 0.012, 0.0017
87	base_inc_rate_ALRI_by_P.jirovecii				0.0091914975	0.0007477963199999999	0.00010645768000000001		0.0091914975	0.0007477963199999999	0.00010645768000000001	0.0092, 0.0007, 0.0001
88	base_inc_rate_ALRI_by_Bocavirus				0.012776211874999999	0.0066279141	0		0.012776211874999999	0.0066279141	0	0.0128, 0.0066, 0
89	base_inc_rate_ALRI_by_Adenovirus				0.012776211874999999	0.0066279141	0		0.012776211874999999	0.0066279141	0	0.0128, 0.0066, 0
90	base_inc_rate_ALRI_by_other_viral_pathogens				0.0001	0.0001	0.0001		0.0001	0.0001	0.0001	0.0001, 0.0001, 0.0001
91	base_inc_rate_ALRI_by_other_bacterial_pathogens				0.042801770375	0.05785196202	0.015010532879999998		0.042801770375	0.05785196202	0.015010532879999998	0.0428, 0.0579, 0.015
92
93
94	base_inc_rate_ALRI_by_RSV				[0.27494869275,0.11019461832,0.0087827586]
95	base_inc_rate_ALRI_by_Rhinovirus				[0.021661326125,0.03504417426,0.00846338556]
96	base_inc_rate_ALRI_by_HMPV				[0.038206021625,0.01840570614,0.00314050156]
97	base_inc_rate_ALRI_by_Parainfluenza				[0.036674105375,0.01915350246,0.00361956112]
98	base_inc_rate_ALRI_by_Strep_pneumoniae_PCV13				[0.007200006375,0.00990830124,0.00244852664]
99	base_inc_rate_ALRI_by_Strep_pneumoniae_non_PCV13				[0.007200006375,0.00990830124,0.00244852664]
100	base_inc_rate_ALRI_by_Hib				[0.009038305875,0.00626279418,0.00117103448]
101	base_inc_rate_ALRI_by_H.influenzae_non_type_b				[0.009038305875,0.00626279418,0.00117103448]
102	base_inc_rate_ALRI_by_Staph_aureus				[0.01133618025,0.00168254172,0.00063874608]
103	base_inc_rate_ALRI_by_Enterobacteriaceae				[0.010263838875,0.00364550706,0.00157025078]
104	base_inc_rate_ALRI_by_other_Strepto_Enterococci				[0.010263838875,0.00364550706,0.00157025078]
105	base_inc_rate_ALRI_by_Influenza				[0.017678343875,0.01204943742,0.00170332288]
106	base_inc_rate_ALRI_by_P.jirovecii				[0.0091914975,0.00074779632,0.00010645768]
107	base_inc_rate_ALRI_by_Bocavirus				[0.012776211875,0.0066279141,0]
108	base_inc_rate_ALRI_by_Adenovirus				[0.012776211875,0.0066279141,0]
109	base_inc_rate_ALRI_by_other_viral_pathogens				[0.0001,0.0001,0.0001]
110	base_inc_rate_ALRI_by_other_bacterial_pathogens				[0.042801770375,0.05785196202,0.01501053288]

Parameter_values

	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

GBD_Malawi_estimates

	Year	Death_per100k_children	Death_per100k_lower	Death_per100k_upper	Incidence_per100_children	Incidence_per100_lower	Incidence_per100_upper	DALYs	DALYs_lower	DALYs_upper
0	2010	258.35	194.1	330.88	13.1873	10.7688	15.9341	567888	427703	727014
1	2011	257.73	193.89	332.68	12.6826	10.3766	15.2886	570661	429499	735642
2	2012	246.35	185.74	318.6	12.1102	9.89684	14.6214	549033	413888	708913
3	2013	232.42	172.61	306.36	11.5172	9.42606	13.8967	520890	387278	688319
4	2014	220.58	164.09	291.38	10.9511	8.84937	13.3138	475402	353236	629467
5	2015	210.56	156.42	278.84	10.4595	8.44016	12.8091	496503	369177	655153
6	2016	195.02	141.1	258.3	10.0094	8.06142	12.3941	441064	319310	583925
7	2017	176.39	127.85	236.58	9.68916	7.72748	12.1848	399055	289917	535254
8	2018	169.27	120.13	232.52	9.52978	7.56549	12.0005	383027	271830	526008
9	2019	158.72	111.41	220.28	9.44652	7.44754	11.9048	360719	253591	500057

McAllister_2019

	Year	Incidence_per100_children	Incidence_per100_lower	Incidence_per100_upper	Death_per1000_livebirths
0	2000	39.6	23.5	66.9	28.2
1	2005				15.6
2	2010				11.7
3	2015	22.1	13.2	37.5	8.6

Lazzerini CFR

	Year	CFR	CFR_lower	CFR_upper	Unnamed: 4	Unnamed: 5
0	2001	15.2	13.3	17.3
1	2002	11.3	10.2	12.6
2	2003	9.1	8.2	10
3	2004	9.2	8.3	10.2
4	2005	9.7	9	10.5
5	2006	7.4	6.8	8
6	2007	6.8	6.4	7.4
7	2008	7.3	6.8	7.9
8	2009	6.1	5.7	6.5
9	2010	5.3	4.9	5.6
10	2011	4.1	3.8	4.4
11	2012	4.5	4.2	4.9
12						note: In-hospital CFR

Pathogen_specific

	Year	Inc_RSV_ALRI_per100	Inc_RSV_ALRI_per100_lower	Inc_RSV_ALRI_per100_upper	Inc_Influenza_ALRI_per100	Inc_Influenza_ALRI_per100_lower	Inc_Influenza_ALRI_per100_upper	Inc_HMPV_ALRI_per100	Inc_HMPV_ALRI_per100_lower	Inc_HMPV_ALRI_per100_upper	Inc_Parainfluenza_ALRI_per100	Inc_Parainfluenza_ALRI_per100_lower	Inc_Parainfluenza_ALRI_per100_upper
0
1	2015	5.89	3.72	9.26
2	2018				1.46	0.92	2.33	2.13	1.55	2.93	3.77	2.78	5.1
3
4								RSV ref (Malawi-specific) : Global, regional, and national disease burden estimates of acute lower respiratory infections due to respiratory syncytial virus in young children in 2015: a systematic review and modelling study
5								Influenza ref (LMIC) : Global burden of respiratory infections associated with seasonal influenza in children under 5 years in 2018: a systematic review and modelling study
6								HMPV ref (LMIC) : Global burden of acute lower respiratory infection associated with human metapneumovirus in children under 5 years in 2018: a systematic review and modelling study
7								Parainfluenza ref (LMIC): Global burden of acute lower respiratory infection associated with human parainfluenza virus in children younger than 5 years for 2018: a systematic review and meta-analysis