Parameter values (.csv) ======================= :download:`Download original .csv file from GitHub ` ==== ================================================================================= =============================================================== ===================================================== =========================================================================================== ================================================================================================================================================================================== ===================== .. 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 ==== ================================================================================= =============================================================== ===================================================== =========================================================================================== ================================================================================================================================================================================== =====================