Alri (.xlsx)
Download original .xlsx file from GitHub
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 |