Childhood Pneumonia (.xlsx)
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Cover Sheet
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Name: |
Childhood Pneumonia |
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Link to Python Code on GitHub: |
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Link to Issue Discussion on GitHub: |
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Type of Module: |
Disease |
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Author: |
Ines |
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Major Amendments Revision History: |
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Other Aspects of the Model Addressed: |
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Diseases: |
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Interventions: |
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Lifestyle Elements: |
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P-variables: |
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H-variables: |
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E-variables: |
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Proccessed |
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Completed by author: |
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Coded in main framework: |
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Reviwed by Team: |
Structure
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Description of Events and Parameters |
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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] |
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base_incidence_pneumonia_by_rhinovirus[at age 0-11, 12-59] |
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base_incidence_pneumonia_by_hMPV[at age 0-11, 12-59] |
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base_incidence_pneumonia_by_parainfluenza[at age 0-11, 12-59] |
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base_incidence_pneumonia_by_streptococcus[at age 0-11, 12-59] |
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base_incidence_pneumonia_by_hib[at age 0-11, 12-59] |
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base_incidence_pneumonia_by_TB[at age 0-11, 12-59] |
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base_incidence_pneumonia_by_staph[at age 0-11, 12-59] |
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57 |
base_incidence_pneumonia_by_influenza[at age 0-11, 12-59] |
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58 |
base_incidence_pneumonia_by_jirovecii[at age 0-11, 12-59] |
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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 |
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60 |
rr_ri_pneumonia_excl_breastfeeding |
relative rate of acquiring pneumonia for children that are exclusively breastfeed |
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61 |
rr_ri_pneumonia_HIV |
relative rate of pneumonia for HIV+ status |
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62 |
rr_ri_pneumonia_malnutrition |
relative rate of pneumonia for severe acute malnutrition |
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63 |
rr_ri_pneumonia_conti_breast |
relative rate of pneumonia for not continued breastfeeding |
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64 |
rr_ri_diarrhoea_pneumococcal_vaccination |
relative rate of pneumonia for children that are vaccinated for pneumococcal |
only for strep. pneumoniae-cause pneumonia |
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65 |
rr_ri_pneumonia_hib_vaccination |
relative rate of acquiring pneumonia for children that are vaccinated for Hib |
only for hib-cause pneumonia |
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66 |
rr_ri_pneumonia_influenza_vaccination |
relative rate of acquiring pneumonia for children that are vaccinated for influenza |
only for influenza-cause pneumonia |
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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 |
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rr_progress_severe_pneum_age |
relative rate of progression to severe penumonia for ages 12-23, 24-59 months |
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rr_progress_severe_pneum_HIV |
relative rate of progression to severe penumonia for HIV positive |
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rr_progress_severe_pneum_SAM |
relative rate of progression to severe penumonia for severe acute malnutrition |
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rr_progress_severe_pneum_viral |
relative rate of progression to severe penumonia for viral-cause pneumonia |
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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 |
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rr_progress_very_sev_pneum_age |
relative rate of progression to severe penumonia for ages 12-23, 24-59 months |
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rr_progress_very_sev_pneum_HIV |
relative rate of progression to severe penumonia for HIV positive |
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rr_progress_very_sev_pneum_SAM |
relative rate of progression to severe penumonia for severe acute malnutrition |
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rr_progress_very_sev_pneum_viral |
relative rate of progression to severe penumonia for viral-cause pneumonia |
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r_death_pneumonia |
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relative rate of death from dysentery for ages 12-13, 24-59 months |
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relative rate of death from dysentery for HIV+ status |
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relative rate of death from dysentery for severe acute malnutrition |
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81 |
relative rate of death from dysentery for no treatment with antibiotics |
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r_death_watery_diarrhoea |
death rate from acute watery diarrhoea, baseline group: 0-11 months, HIV negative, no SAM, ORS given |
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rr_death_watery_diarrhoea_age_category |
relative rate of death from acute watery diarrhoea for ages 12-13, 24-59 months |
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rr_death_watery_diarrhoea_HIV |
relative rate of death from acute watery diarrhoea for HIV+ status |
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rr_death_watery_diarrhoea_malnutrition |
relative rate of death from acute watery diarrhoea for severe acute malnutrition |
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r_death_persistent_diarrhoea |
death rate from persistent diarrhoea, baseline group: 0-11 months, HIV negative, no SAM |
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rr_death_persistent_diarrhoea_age_category |
relative rate of death from persistent diarrhoea for ages 12-13, 24-59 months |
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rr_death_persistent_diarrhoea_HIV |
relative rate of death from persistent diarrhoea for HIV+ status |
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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 |
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0 |
base_incidence_pneumonia_by_agecat |
0.607 |
0.3429 |
0.1204 |
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1 |
pn_attributable_fraction_RSV |
0.397 |
0.164 |
0.165 |
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2 |
pn_attributable_fraction_rhinovirus |
0.029 |
0.152 |
0.159 |
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3 |
pn_attributable_fraction_hmpv |
0.083 |
0.063 |
0.059 |
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4 |
pn_attributable_fraction_parainfluenza |
0.078 |
0.067 |
0.068 |
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5 |
pn_attributable_fraction_streptococcus |
0.047 |
0.106 |
0.092 |
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6 |
pn_attributable_fraction_hib |
0.059 |
0.067 |
0.044 |
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7 |
pn_attributable_fraction_TB |
0.067 |
0.039 |
0.059 |
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8 |
pn_attributable_fraction_staph |
0.037 |
0.009 |
0.012 |
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9 |
pn_attributable_fraction_influenza |
0.016 |
0.029 |
0.032 |
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10 |
pn_attributable_fraction_jirovecii |
0.03 |
0.004 |
0.002 |
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11 |
pn_attributable_fraction_other_pathogens |
0.098 |
0.274 |
0.282 |
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12 |
pn_attributable_fraction_other_cause |
0.05899999999999994 |
0.025999999999999912 |
0.0259999999999998 |
Target values for 12 monthly incidence rate |
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13 |
base_inc_rate_pneumonia_by_RSV |
[0.240979,0.0562356,0.019866] |
0.240979 |
0.0562356 |
0.019865999999999998 |
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14 |
base_inc_rate_pneumonia_by_rhinovirus |
[0.017603,0.0521208,0.0191436] |
0.017603 |
0.052120799999999995 |
0.0191436 |
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15 |
base_inc_rate_pneumonia_by_hMPV |
[0.050381,0.0216027,0.0071036] |
0.050381 |
0.0216027 |
0.007103599999999999 |
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16 |
base_inc_rate_pneumonia_by_parainfluenza |
[0.047346,0.0229743,0.0081872] |
0.047346 |
0.0229743 |
0.0081872 |
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17 |
base_inc_rate_pneumonia_by_streptococcus |
[0.028529,0.027915478,0.004884] |
0.028529 |
0.027915478 |
0.004884 |
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18 |
base_inc_rate_pneumonia_by_hib |
[0.035813,0.170477152,0.019758] |
0.035813 |
0.170477152 |
0.019758 |
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base_inc_rate_pneumonia_by_TB |
[0.040669,0.132603114,0.00555] |
0.040669000000000004 |
0.132603114 |
0.00555 |
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20 |
base_inc_rate_pneumonia_by_staphylococcus |
[0.014689,0.066146727,0.000888] |
0.014689 |
0.066146727 |
0.000888 |
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21 |
base_inc_rate_pneumonia_by_influenza |
[0.000464,0.035974076,0.001332] |
0.00046400000000000006 |
0.035974076 |
0.001332 |
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22 |
base_inc_rate_pneumonia_by_jirovecii |
[0.00249,0.022716889,0.001998] |
0.00249 |
0.022716889 |
0.001998 |
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23 |
base_inc_rate_pneumonia_by_other_pathogens |
[0.059486,0.0939546,0.0339528] |
0.059486000000000004 |
0.0939546 |
0.0339528 |
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24 |
rr_ri_pneumonia_HHhandwashing |
0.7 |
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25 |
rr_ri_pneumonia_indoor_air_pollution |
0.8 |
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26 |
rr_ri_pneumonia_excl_breastfeeding |
0.5 |
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27 |
rr_ri_pneumonia_cont_breast |
0.9 |
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28 |
rr_ri_pneumonia_HIV |
1.3 |
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rr_ri_pneumonia_SAM |
1.4 |
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30 |
rr_ri_pneumonia_pneumococcal_vaccine |
0.5 |
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31 |
rr_ri_pneumonia_hib_vaccine |
0.5 |
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32 |
rr_ri_pneumonia_influenza_vaccine |
0.5 |
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33 |
r_progress_to_severe_pneumonia |
[0.2117, 0.17335, 0.11287] |
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34 |
rr_progress_severe_pneum_age12to23mo |
0.7 |
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35 |
rr_progress_severe_pneum_age24to59mo |
0.2 |
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36 |
rr_progress_severe_pneum_HIV |
1.3 |
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37 |
rr_progress_severe_pneum_SAM |
1.4 |
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38 |
rr_progress_severe_pneum_viral |
0.7 |
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39 |
r_death_pneumonia |
0.4 |
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rr_death_pneumonia_agelt2mo |
1.4 |
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41 |
rr_death_pneumonia_age12to23mo |
0.8 |
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rr_death_pneumonia_age24to59mo |
0.3 |
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43 |
rr_death_pneumonia_HIV |
1.4 |
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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 |
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0 |
15 |
Male |
Yes |
0.2 |
fever |
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1 |
16 |
Male |
Yes |
0.001 |
cough and/or difficult breathing |
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2 |
17 |
Male |
Yes |
0.1 |
fast breathing |
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3 |
18 |
Male |
Yes |
0 |
chest indrawing |
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4 |
15 |
Male |
No |
0 |
stridor |
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5 |
16 |
Male |
No |
0 |
lethargic/unconscious |
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6 |
17 |
Male |
No |
0 |
not able to drink/ breastfeed |
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7 |
18 |
Male |
No |
0 |
convulsions |
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8 |
vomiting everything |
Severe pneumonia
Age |
Sex |
Smoking |
… |
Probability of Affliction |
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0 |
15 |
Male |
Yes |
0.2 |
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1 |
16 |
Male |
Yes |
0.001 |
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2 |
17 |
Male |
Yes |
0.1 |
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3 |
18 |
Male |
Yes |
0 |
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4 |
15 |
Male |
No |
0 |
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5 |
16 |
Male |
No |
0 |
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6 |
17 |
Male |
No |
0 |
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7 |
18 |
Male |
No |
0 |
Very severe pneumonia
Parameters |
Description |
Value |
Reference and Notes |
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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 |
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2 |
rr_ri_pneumonia_indoor_air_pollution |
0.8 |
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3 |
rr_ri_pneumonia_excl_breastfeeding |
0.5 |
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4 |
rr_ri_pneumonia_cont_breast |
0.9 |
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5 |
rr_ri_pneumonia_HIV |
1.1 |
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6 |
rr_ri_pneumonia_malnutrition |
1.4 |
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7 |
rr_ri_pneumonia_pneumococcal_vaccine |
0.5 |
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8 |
rr_ri_pneumonia_hib_vaccine |
0.5 |
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9 |
rr_ri_pneumonia_influenza_vaccine |
0.5 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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24 |
rr_prog_very_sev_pneum_RSV |
relative progression to very severe pneumonia for RSV |
0.7159 |
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25 |
rr_prog_very_sev_pneum_rhinovirus |
relative progression to very severe pneumonia for rhinovirus |
0.9506 |
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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 |
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30 |
rr_prog_very_sev_pneum_TB |
relative progression to very severe pneumonia for TB |
1.1667 |
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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 |
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34 |
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35 |
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36 |
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37 |
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38 |
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39 |
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40 |
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41 |
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42 |
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43 |
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44 |
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45 |
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46 |
rr_progress_severe_pneum_HIV |
1.3 |
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47 |
rr_progress_severe_pneum_SAM |
1.4 |
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48 |
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49 |
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50 |
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51 |
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52 |
rr_progress_very_sev_pneum_HIV |
1.3 |
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53 |
rr_progress_very_sev_pneum_SAM |
1.4 |
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54 |
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55 |
r_death_pneumonia |
0.4 |
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56 |
rr_death_pneumonia_HIV |
0.45 |
_Parameter1
Age |
Sex |
Smoking |
… |
Assignment |
Probability of Assignement |
|
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0 |
15 |
Male |
Yes |
0.2 |
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1 |
16 |
Male |
Yes |
0.001 |
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2 |
17 |
Male |
Yes |
0.1 |
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3 |
18 |
Male |
Yes |
0 |
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4 |
15 |
Male |
No |
0 |
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5 |
16 |
Male |
No |
0 |
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6 |
17 |
Male |
No |
0 |
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7 |
18 |
Male |
No |
0 |