Calculations (.csv) =================== :download:`Download original .csv file from GitHub ` ==== ============================================================ =================== ==================== ================== ============================================ ===================== ==================================================== ============ ==================== ===================== ====================== ====================== .. 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 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] ==== ============================================================ =================== ==================== ================== ============================================ ===================== ==================================================== ============ ==================== ===================== ====================== ======================