Childhood Pneumonia (.xlsx) =========================== :download:`Download original .xlsx file from GitHub ` .. contents:: Cover Sheet ----------- ==== ============ ===================================== =================== .. Unnamed: 0 Unnamed: 1 Unnamed: 2 ==== ============ ===================================== =================== 0 1 Name: Childhood Pneumonia 2 3 Link to Python Code on GitHub: 4 Link to Issue Discussion on GitHub: 5 6 Type of Module: Disease 7 8 Author: Ines 9 10 Major Amendments Revision History: 11 12 Other Aspects of the Model Addressed: 13 Diseases: 14 Interventions: 15 Lifestyle Elements: 16 P-variables: 17 H-variables: 18 E-variables: 19 20 Proccessed 21 Completed by author: 22 Coded in main framework: 23 Reviwed by Team: ==== ============ ===================================== =================== Structure --------- ==== ====================================================== ============================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== ================================================================================== ============ ============ .. Unnamed: 0 Unnamed: 1 Unnamed: 2 Unnamed: 3 Unnamed: 4 ==== ====================================================== ============================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== ================================================================================== ============ ============ 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 Description of Events and Parameters 44 45 46 47 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 34 35 36 37 38 39 40 41 42 43 44 45 46 rr\_progress\_severe\_pneum\_HIV 1.3 47 rr\_progress\_severe\_pneum\_SAM 1.4 48 49 50 51 52 rr\_progress\_very\_sev\_pneum\_HIV 1.3 53 rr\_progress\_very\_sev\_pneum\_SAM 1.4 54 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 ----------