Alri (.xlsx) ============ :download:`Download original .xlsx file from GitHub ` .. contents:: 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 ==== ====== ======================== =============================== =============================== ============================== ===================================== ===================================== =============================================================================================================================================================================================================================== ================================ ================================ ================================== ========================================= =========================================