data-raw/test-pjnz.R

In mrc-ide/eppasm: Age-structured EPP Model for HIV Epidemic Estimates

library(devtools)
devtools::load_all()
system.file("extdata")

#' This script adds some PNJZ files to the package for software testing and illustration purposes.
#' Files are taken from UNAIDS estimates files produced by national HIV estimates teams for UNAIDS.
#' However, files may not include the most current data and have been modified to test or demonstrate
#' specific software features and thus **should NOT be taken as estimates for given countries.**
#'
#' To access data and estimates for these and other countries, please visit http://aidsinfo.unaids.org/
#' or http://www.unaids.org/en/dataanalysis/datatools/spectrum-epp to request the most recent Spectrum
#' estimates files.


#' ## Botswana 2017 file
file.copy("~/Documents/Data/Spectrum files/2017 final/2017 Final Spectrum files/SSA/Botswana_29_05_2017 updated BF.PJNZ",
          "~/Documents/Code/R/eppasm/inst/extdata/testpjnz/Botswana2017.PJNZ")

fp <- "~/Documents/Code/R/eppasm/inst/extdata/testpjnz/Botswana2017.PJNZ"
utils::unzip(fp, list=TRUE)

## Remove files to reduce size
zip(fp, grep("bm2$", utils::unzip(fp, list=TRUE)$Name, value=TRUE), flags="-d")
zip(fp, grep("SPU$", utils::unzip(fp, list=TRUE)$Name, value=TRUE), flags="-d")
zip(fp, grep("UAC$", utils::unzip(fp, list=TRUE)$Name, value=TRUE), flags="-d")


#' ## Dominican Republic 2017 file

file <- "~/Documents/Code/R/eppasm/inst/extdata/testpjnz/DominicanRepublic2017.PJNZ"

file.copy("~/Documents/Data/Spectrum files/2017 final/CAR/Dominican Republic_2017_final.PJNZ", file)

utils::unzip(fp, list=TRUE)

## Remove files to reduce size
zip(file, grep("bm2$", utils::unzip(file, list=TRUE)$Name, value=TRUE), flags="-d")
zip(file, grep("SPU$", utils::unzip(file, list=TRUE)$Name, value=TRUE), flags="-d")
zip(file, grep("UAC$", utils::unzip(file, list=TRUE)$Name, value=TRUE), flags="-d")


#' ## Dominican Republic 2017 file

file <- "~/Documents/Code/R/eppasm/inst/extdata/testpjnz/Netherlands2017.PJNZ"

file.copy("~/Documents/Data/Spectrum files/2017 final/WCENA/Netherlands_2017_final.PJNZ", file)

utils::unzip(fp, list=TRUE)

## Remove files to reduce size
zip(file, grep("bm2$", utils::unzip(file, list=TRUE)$Name, value=TRUE), flags="-d")
zip(file, grep("SPU$", utils::unzip(file, list=TRUE)$Name, value=TRUE), flags="-d")
zip(file, grep("UAC$", utils::unzip(file, list=TRUE)$Name, value=TRUE), flags="-d")



## Botswana 2018 file
file.copy("~/Documents/Data/Spectrum files/2018 final/SSA/Botswana_ 2018 updated ART.PJNZ",
          "~/Documents/Code/R/eppasm/inst/extdata/testpjnz/Botswana2018.PJNZ")

fp <- "~/Documents/Code/R/eppasm/inst/extdata/testpjnz/Botswana2018.PJNZ"
utils::unzip(fp, list=TRUE)

## Remove files to reduce size
zip(fp, grep("bm2$", utils::unzip(fp, list=TRUE)$Name, value=TRUE), flags="-d")
zip(fp, grep("SPU$", utils::unzip(fp, list=TRUE)$Name, value=TRUE), flags="-d")
zip(fp, grep("UAC$", utils::unzip(fp, list=TRUE)$Name, value=TRUE), flags="-d")
zip(fp, grep("DPUAD_AUA$", utils::unzip(fp, list=TRUE)$Name, value=TRUE), flags="-d")


## Mozambique Maputo Cidade 2018 file
file.copy("~/Documents/Data/Spectrum files/2018 final/SSA/11_MZ_Maputo Cidade_v5_63_updated census_22_01_2018.PJNZ",
          here::here("inst/extdata/testpjnz/Mozambique_Maputo_Cidade2018.PJNZ"))

fp <- here::here("inst/extdata/testpjnz/Mozambique_Maputo_Cidade2018.PJNZ")
utils::unzip(fp, list=TRUE)

## Remove files to reduce size
zip(fp, grep("bm2$", utils::unzip(fp, list=TRUE)$Name, value=TRUE), flags="-d")
zip(fp, grep("SPU$", utils::unzip(fp, list=TRUE)$Name, value=TRUE), flags="-d")
zip(fp, grep("UAC$", utils::unzip(fp, list=TRUE)$Name, value=TRUE), flags="-d")
zip(fp, grep("DPUAD_AUA$", utils::unzip(fp, list=TRUE)$Name, value=TRUE), flags="-d")
zip(fp, grep("ep5.bak$", utils::unzip(fp, list=TRUE)$Name, value=TRUE), flags="-d")