Calculations (.csv)

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	parameter_name	1-11	12-23	24-59	Unnamed: 4	Unnamed: 5	Unnamed: 6	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	0	0	0
16	pneumonia_attributable_fraction_coronavirus	0.0	0.0	0.0	0	0	0
17	pneumonia_attributable_fraction_bocavirus	0.0	0.0	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		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		0	0
27	bronchiolitis_attributable_fraction_hib	0.0	0.0		0	0
28	bronchiolitis_attributable_fraction_TB	0.0	0.0		0	0
29	bronchiolitis_attributable_fraction_staph	0.0	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		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	0.0128, 0.0066, 0
89	base_inc_rate_ALRI_by_Adenovirus				0.012776211874999999	0.0066279141	0	0.012776211874999999	0.0066279141	0.0	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]