Childhood Pneumonia (.xlsx)

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Cover Sheet

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1		Name:	Childhood Pneumonia
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3		Link to Python Code on GitHub:
4		Link to Issue Discussion on GitHub:
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6		Type of Module:	Disease
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8		Author:	Ines
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10		Major Amendments Revision History:
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12		Other Aspects of the Model Addressed:
13		Diseases:
14		Interventions:
15		Lifestyle Elements:
16		P-variables:
17		H-variables:
18		E-variables:
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20		Proccessed
21		Completed by author:
22		Coded in main framework:
23		Reviwed by Team:

Structure

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43	Description of Events and Parameters
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48	Parameter	Description	Notes	Value	Ref
49	base_incidence_pneumonia_by pathogen[age_category]	a list of incidence of diarrhoea caused by individual pathogens in each age group [0-11, 12-59]; pneumonia caused by RSV, rhinovirus, hMPV, parainfluenza, streptococcus, hib, TB, stapylococcus, influenza, and P. jirovecii in a susceptible population of children under 5, with base group of no handwashing with soap, indoor air pollution, and no exclusive or continued breastfeeding, HIV negative, no SAM, no pneumococcal vaccination, no hib vaccination, no influenza vaccination	base_incidence_pneumonia_by_RSV[at age 0-11, 12-59]
50			base_incidence_pneumonia_by_rhinovirus[at age 0-11, 12-59]
51			base_incidence_pneumonia_by_hMPV[at age 0-11, 12-59]
52			base_incidence_pneumonia_by_parainfluenza[at age 0-11, 12-59]
53			base_incidence_pneumonia_by_streptococcus[at age 0-11, 12-59]
54			base_incidence_pneumonia_by_hib[at age 0-11, 12-59]
55			base_incidence_pneumonia_by_TB[at age 0-11, 12-59]
56			base_incidence_pneumonia_by_staph[at age 0-11, 12-59]
57			base_incidence_pneumonia_by_influenza[at age 0-11, 12-59]
58			base_incidence_pneumonia_by_jirovecii[at age 0-11, 12-59]
59	rr_ri_pneumonia_Hhhandwashing	relative rate of acquiring pneumonia for children with household handwashing with soap	independent risk factors assumed to have the same values for all pathogens for now
60	rr_ri_pneumonia_excl_breastfeeding	relative rate of acquiring pneumonia for children that are exclusively breastfeed
61	rr_ri_pneumonia_HIV	relative rate of pneumonia for HIV+ status
62	rr_ri_pneumonia_malnutrition	relative rate of pneumonia for severe acute malnutrition
63	rr_ri_pneumonia_conti_breast	relative rate of pneumonia for not continued breastfeeding
64	rr_ri_diarrhoea_pneumococcal_vaccination	relative rate of pneumonia for children that are vaccinated for pneumococcal	only for strep. pneumoniae-cause pneumonia
65	rr_ri_pneumonia_hib_vaccination	relative rate of acquiring pneumonia for children that are vaccinated for Hib	only for hib-cause pneumonia
66	rr_ri_pneumonia_influenza_vaccination	relative rate of acquiring pneumonia for children that are vaccinated for influenza	only for influenza-cause pneumonia
67	r_progress_to_severe_pneumonia	rate of progression to severe penumonia in baseline group: age 2-11 months, no HIV, no SAM, bacterial-cause
68	rr_progress_severe_pneum_age	relative rate of progression to severe penumonia for ages 12-23, 24-59 months
69	rr_progress_severe_pneum_HIV	relative rate of progression to severe penumonia for HIV positive
70	rr_progress_severe_pneum_SAM	relative rate of progression to severe penumonia for severe acute malnutrition
71	rr_progress_severe_pneum_viral	relative rate of progression to severe penumonia for viral-cause pneumonia
72	r_progress_to_very_sev_pneumonia	rate of progression to severe penumonia in baseline group: age 2-11 months, no HIV, no SAM, bacterial-cause
73	rr_progress_very_sev_pneum_age	relative rate of progression to severe penumonia for ages 12-23, 24-59 months
74	rr_progress_very_sev_pneum_HIV	relative rate of progression to severe penumonia for HIV positive
75	rr_progress_very_sev_pneum_SAM	relative rate of progression to severe penumonia for severe acute malnutrition
76	rr_progress_very_sev_pneum_viral	relative rate of progression to severe penumonia for viral-cause pneumonia
77	r_death_pneumonia
78		relative rate of death from dysentery for ages 12-13, 24-59 months
79		relative rate of death from dysentery for HIV+ status
80		relative rate of death from dysentery for severe acute malnutrition
81		relative rate of death from dysentery for no treatment with antibiotics
82	r_death_watery_diarrhoea	death rate from acute watery diarrhoea, baseline group: 0-11 months, HIV negative, no SAM, ORS given
83	rr_death_watery_diarrhoea_age_category	relative rate of death from acute watery diarrhoea for ages 12-13, 24-59 months
84	rr_death_watery_diarrhoea_HIV	relative rate of death from acute watery diarrhoea for HIV+ status
85	rr_death_watery_diarrhoea_malnutrition	relative rate of death from acute watery diarrhoea for severe acute malnutrition
86	r_death_persistent_diarrhoea	death rate from persistent diarrhoea, baseline group: 0-11 months, HIV negative, no SAM
87	rr_death_persistent_diarrhoea_age_category	relative rate of death from persistent diarrhoea for ages 12-13, 24-59 months
88	rr_death_persistent_diarrhoea_HIV	relative rate of death from persistent diarrhoea for HIV+ status
89	rr_death_persistent_diarrhoea_malnutrition	relative rate of death from persistent diarrhoea for severe acute malnutrition

Parameter_values

	parameter_name	value	value2	value3	Unnamed: 4	Unnamed: 5	Unnamed: 6	Unnamed: 7
0	base_incidence_pneumonia_by_agecat	0.607	0.3429	0.1204
1	pn_attributable_fraction_RSV	0.397	0.164	0.165
2	pn_attributable_fraction_rhinovirus	0.029	0.152	0.159
3	pn_attributable_fraction_hmpv	0.083	0.063	0.059
4	pn_attributable_fraction_parainfluenza	0.078	0.067	0.068
5	pn_attributable_fraction_streptococcus	0.047	0.106	0.092
6	pn_attributable_fraction_hib	0.059	0.067	0.044
7	pn_attributable_fraction_TB	0.067	0.039	0.059
8	pn_attributable_fraction_staph	0.037	0.009	0.012
9	pn_attributable_fraction_influenza	0.016	0.029	0.032
10	pn_attributable_fraction_jirovecii	0.03	0.004	0.002
11	pn_attributable_fraction_other_pathogens	0.098	0.274	0.282
12	pn_attributable_fraction_other_cause	0.05899999999999994	0.025999999999999912	0.0259999999999998		Target values for 12 monthly incidence rate
13	base_inc_rate_pneumonia_by_RSV	[0.240979,0.0562356,0.019866]				0.240979	0.0562356	0.019865999999999998
14	base_inc_rate_pneumonia_by_rhinovirus	[0.017603,0.0521208,0.0191436]				0.017603	0.052120799999999995	0.0191436
15	base_inc_rate_pneumonia_by_hMPV	[0.050381,0.0216027,0.0071036]				0.050381	0.0216027	0.007103599999999999
16	base_inc_rate_pneumonia_by_parainfluenza	[0.047346,0.0229743,0.0081872]				0.047346	0.0229743	0.0081872
17	base_inc_rate_pneumonia_by_streptococcus	[0.028529,0.027915478,0.004884]				0.028529	0.027915478	0.004884
18	base_inc_rate_pneumonia_by_hib	[0.035813,0.170477152,0.019758]				0.035813	0.170477152	0.019758
19	base_inc_rate_pneumonia_by_TB	[0.040669,0.132603114,0.00555]				0.040669000000000004	0.132603114	0.00555
20	base_inc_rate_pneumonia_by_staphylococcus	[0.014689,0.066146727,0.000888]				0.014689	0.066146727	0.000888
21	base_inc_rate_pneumonia_by_influenza	[0.000464,0.035974076,0.001332]				0.00046400000000000006	0.035974076	0.001332
22	base_inc_rate_pneumonia_by_jirovecii	[0.00249,0.022716889,0.001998]				0.00249	0.022716889	0.001998
23	base_inc_rate_pneumonia_by_other_pathogens	[0.059486,0.0939546,0.0339528]				0.059486000000000004	0.0939546	0.0339528
24	rr_ri_pneumonia_HHhandwashing	0.7
25	rr_ri_pneumonia_indoor_air_pollution	0.8
26	rr_ri_pneumonia_excl_breastfeeding	0.5
27	rr_ri_pneumonia_cont_breast	0.9
28	rr_ri_pneumonia_HIV	1.3
29	rr_ri_pneumonia_SAM	1.4
30	rr_ri_pneumonia_pneumococcal_vaccine	0.5
31	rr_ri_pneumonia_hib_vaccine	0.5
32	rr_ri_pneumonia_influenza_vaccine	0.5
33	r_progress_to_severe_pneumonia	[0.2117, 0.17335, 0.11287]
34	rr_progress_severe_pneum_age12to23mo	0.7
35	rr_progress_severe_pneum_age24to59mo	0.2
36	rr_progress_severe_pneum_HIV	1.3
37	rr_progress_severe_pneum_SAM	1.4
38	rr_progress_severe_pneum_viral	0.7
39	r_death_pneumonia	0.4
40	rr_death_pneumonia_agelt2mo	1.4
41	rr_death_pneumonia_age12to23mo	0.8
42	rr_death_pneumonia_age24to59mo	0.3
43	rr_death_pneumonia_HIV	1.4
44	rr_death_pneumonia_SAM	1.4

Pneumonia

	Age	Sex	Smoking	…	Probability of Affliction	Unnamed: 5	Unnamed: 6	symptoms	pneumonia	severe pneumonia	very severe pneumonia
0	15	Male	Yes		0.2			fever
1	16	Male	Yes		0.001			cough and/or difficult breathing
2	17	Male	Yes		0.1			fast breathing
3	18	Male	Yes		0			chest indrawing
4	15	Male	No		0			stridor
5	16	Male	No		0			lethargic/unconscious
6	17	Male	No		0			not able to drink/ breastfeed
7	18	Male	No		0			convulsions
8								vomiting everything

Severe pneumonia

	Age	Sex	Smoking	…	Probability of Affliction
0	15	Male	Yes		0.2
1	16	Male	Yes		0.001
2	17	Male	Yes		0.1
3	18	Male	Yes		0
4	15	Male	No		0
5	16	Male	No		0
6	17	Male	No		0
7	18	Male	No		0

Very severe pneumonia

	Parameters	Description	Value	Reference and Notes
0	base_incidence_pneumonia_by_agecat	incidence of pneumonia in each age group: [0-11, 12-23, 24-59 months]	0.666, 0.367, 0.127	Yearly incidence rate in cases per child, calculated from the McCollum ED et al, 2017 data.
1	rr_ri_pneumonia_HHhandwashing		0.7
2	rr_ri_pneumonia_indoor_air_pollution		0.8
3	rr_ri_pneumonia_excl_breastfeeding		0.5
4	rr_ri_pneumonia_cont_breast		0.9
5	rr_ri_pneumonia_HIV		1.1
6	rr_ri_pneumonia_malnutrition		1.4
7	rr_ri_pneumonia_pneumococcal_vaccine		0.5
8	rr_ri_pneumonia_hib_vaccine		0.5
9	rr_ri_pneumonia_influenza_vaccine		0.5
10	r_progress_to_severe_penum	baseline rate of progression of non-severe to severe or very severe pneumonia for ages [0-11, 12-23, 24-59 months]	0.67, 0.62, 0.47
11	r_progress_to_very_sev_penum	baseline rate of progression of severe to very severe pneumonia for ages [0-11, 12-23, 24-59 months]	0.27, 0.26, 0.195
12	pn_attributable_fraction_RSV	attributable fraction of RSV in age groups: [0-11, 12-23, 24-59 months]	0.397, 0.164, 0.165
13	pn_attributable_fraction_rhinovirus	attributable fraction of rhinovirus in age groups: [0-11, 12-23, 24-59 months]	0.029, 0.152, 0.159
14	pn_attributable_fraction_hmpv	attributable fraction of hMPV in age groups: [0-11, 12-23, 24-59 months]	0.083, 0.063, 0.059
15	pn_attributable_fraction_parainfluenza	attributable fraction of parainfluenza in age groups: [0-11, 12-23, 24-59 months]	0.078, 0.067, 0.068
16	pn_attributable_fraction_streptococcus	attributable fraction of streptococcus in age groups: [0-11, 12-23, 24-59 months]	0.047, 0.106, 0.092
17	pn_attributable_fraction_hib	attributable fraction of Hib in age groups: [0-11, 12-23, 24-59 months]	0.059, 0.067, 0.044
18	pn_attributable_fraction_TB	attributable fraction of TB in age groups: [0-11, 12-23, 24-59 months]	0.067, 0.039, 0.059	need to call from TB module those infected.
19	pn_attributable_fraction_staph	attributable fraction of staphylococcus in age groups: [0-11, 12-23, 24-59 months]	0.037, 0.009, 0.012
20	pn_attributable_fraction_influenza	attributable fraction of influenza in age groups: [0-11, 12-23, 24-59 months]	0.016, 0.029, 0.032
21	pn_attributable_fraction_jirovecii	attributable fraction of P. jirovecii in age groups: [0-11, 12-23, 24-59 months]	0.03, 0.004, 0.002
22	pn_attributable_fraction_other_pathogens	attributable fraction of other pathogens in age groups: [0-11, 12-23, 24-59 months]	0.098, 0.274, 0.282
23	pn_attributable_fraction_other_cause	attributable fraction of other causes in age groups: [0-11, 12-23, 24-59 months]	0.059, 0.026, 0.026
24	rr_prog_very_sev_pneum_RSV	relative progression to very severe pneumonia for RSV	0.7159
25	rr_prog_very_sev_pneum_rhinovirus	relative progression to very severe pneumonia for rhinovirus	0.9506
26	rr_prog_very_sev_pneum_hmpv	relative progression to very severe pneumonia for Hmpv	0.9512
27	rr_prog_very_sev_pneum_parainfluenza	relative progression to very severe pneumonia for parainfluenza	0.5556
28	rr_prog_very_sev_pneum_streptococcus	relative progression to very severe pneumonia for streptococcus	2.1087
29	rr_prog_very_sev_pneum_hib	relative progression to very severe pneumonia for hib	1.6122
30	rr_prog_very_sev_pneum_TB	relative progression to very severe pneumonia for TB	1.1667
31	rr_prog_very_sev_pneum_staph	relative progression to very severe pneumonia for staph	5.2727
32	rr_prog_very_sev_pneum_influenza	relative progression to very severe pneumonia for influenza	1.4
33	rr_prog_very_sev_pneum_jirovecii	relative progression to very severe pneumonia for P. jirovecii	1.9167
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46	rr_progress_severe_pneum_HIV	1.3
47	rr_progress_severe_pneum_SAM	1.4
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52	rr_progress_very_sev_pneum_HIV	1.3
53	rr_progress_very_sev_pneum_SAM	1.4
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55	r_death_pneumonia	0.4
56	rr_death_pneumonia_HIV	0.45

_Parameter1

	Age	Sex	Smoking	…	Assignment	Probability of Assignement
0	15	Male	Yes			0.2
1	16	Male	Yes			0.001
2	17	Male	Yes			0.1
3	18	Male	Yes			0
4	15	Male	No			0
5	16	Male	No			0
6	17	Male	No			0
7	18	Male	No			0

References