## ----include = FALSE---------------------------------------------------------- knitr::opts_chunk$set( collapse = TRUE, comment = "#>" ) ## ----results='asis', echo=FALSE----------------------------------------------- cat(' ') ## ----eval=F------------------------------------------------------------------- # install.packages("vacalibration") # install # library(vacalibration) # load ## ----eval=F------------------------------------------------------------------- # data(comsamoz_public_openVAout) # load data in R environment # # class(comsamoz_public_openVAout) # list # names(comsamoz_public_openVAout) # different components # # comsamoz_public_openVAout$age_group # age group # comsamoz_public_openVAout$va_algo # algorithm # head(comsamoz_public_openVAout$data) # head of the specific COD data # # for these 6 individuals, the causes of deaths are "Other and unspecified neonatal CoD", # # "Birth asphyxia", "Neonatal sepsis", "Birth asphyxia", "Birth asphyxia", "Neonatal sepsis" ## ----eval=F------------------------------------------------------------------- # data(comsamoz_public_broad) # load data in R environment # head(comsamoz_public_broad$data) # head of the stored broad COD data # # for these 6 individuals, the causes of deaths are "other", "ipre", "sepsis_meningitis_inf", # # "ipre", "ipre", "sepsis_meningitis_inf" ## ----eval=F, results = 'hide', message = FALSE, warning = FALSE, fig.show = "hide"---- # calib_out_specific = vacalibration(va_data = setNames(list(comsamoz_public_openVAout$data), # list(comsamoz_public_openVAout$va_algo)), # age_group = comsamoz_public_openVAout$age_group, # country = "Mozambique") ## ----eval=F------------------------------------------------------------------- # round(calib_out_specific$p_uncalib, 3) # uncalibrated (rounded upto 3 significant digits) # round(calib_out_specific$pcalib_postsumm["insilicova",,], 3) # calibrated (rounded upto 3 significant digits) ## ----eval=F, results = 'hide', message = FALSE, warning = FALSE, fig.show = "hide"---- # calib_out_broad = vacalibration(va_data = setNames(list(comsamoz_public_broad$data), # list(comsamoz_public_broad$va_algo)), # age_group = comsamoz_public_broad$age_group, # country = "Mozambique") ## ----eval=F, results = 'hide', message = FALSE, warning = FALSE, fig.show = "hide"---- # calib_out_deathcount = vacalibration(va_data = setNames(list(colSums(comsamoz_public_broad$data)), # list(comsamoz_public_broad$va_algo)), # age_group = comsamoz_public_broad$age_group, # country = "Mozambique") ## ----eval=F------------------------------------------------------------------- # #################################### uncalibrated #################################### # round(calib_out_specific$p_uncalib, 3) # specific cause # round(calib_out_broad$p_uncalib, 3) # broad cause # round(calib_out_deathcount$p_uncalib, 3) # broad-cause-specific death count # # # #################################### calibrated #################################### # round(calib_out_specific$pcalib_postsumm["insilicova",,], 3) # specific cause # round(calib_out_broad$pcalib_postsumm["insilicova",,], 3) # broad cause # round(calib_out_deathcount$pcalib_postsumm["insilicova",,], 3) # broad-cause-specific death count ## ----eval=F, results = 'hide', message = FALSE, warning = FALSE, fig.show = "hide"---- # # default # calib_out_specific = vacalibration(va_data = setNames(list(comsamoz_public_openVAout$data), # list(comsamoz_public_openVAout$va_algo)), # age_group = comsamoz_public_openVAout$age_group, # country = "Mozambique") # # # misclassification estimates provided by user # calib_out_specific_mmat = vacalibration(va_data = setNames(list(comsamoz_public_openVAout$data), # list(comsamoz_public_openVAout$va_algo)), # Mmat.asDirich = setNames(list(Mmat_champs[[comsamoz_public_openVAout$age_group]][[comsamoz_public_openVAout$va_algo]]$asDirich[["Mozambique"]]), # list(comsamoz_public_openVAout$va_algo)), # age_group = comsamoz_public_openVAout$age_group, # country = "Mozambique") ## ----eval=F------------------------------------------------------------------- # #################################### uncalibrated #################################### # round(calib_out_specific$p_uncalib, 3) # default # round(calib_out_specific_mmat$p_uncalib, 3) # user provided misclassification estimate # # # #################################### calibrated #################################### # round(calib_out_specific$pcalib_postsumm["insilicova",,], 3) # default # round(calib_out_specific_mmat$pcalib_postsumm["insilicova",,], 3) # user provided misclassification estimate ## ----eval=F------------------------------------------------------------------- # va_data_example = list("eava" = c("congenital_malformation" = 40, "pneumonia" = 175, # "sepsis_meningitis_inf" = 265, "ipre" = 220, # "other" = 30, "prematurity" = 170), # "insilicova" = c("congenital_malformation" = 5, "pneumonia" = 145, # "sepsis_meningitis_inf" = 370, "ipre" = 330, # "other" = 60, "prematurity" = 290)) ## ----eval=F, results = 'hide', message = FALSE, warning = FALSE, fig.show = "hide"---- # calib_out_ensemble = vacalibration(va_data = va_data_example, # age_group = "neonate", country = "Mozambique") ## ----eval=F------------------------------------------------------------------- # round(calib_out_ensemble$p_uncalib, 3) # uncalibrated # round(calib_out_ensemble$pcalib_postsumm["eava",,], 3) # EAVA-specific calibration # round(calib_out_ensemble$pcalib_postsumm["insilicova",,], 3) # InSilicoVA-specific calibration # round(calib_out_ensemble$pcalib_postsumm["ensemble",,], 3) # Ensemble calibration