## ----include = FALSE----------------------------------------------------------
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

## ----results='asis', echo=FALSE-----------------------------------------------
cat('
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## ----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