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Replace utils read with readr read function #442

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Oct 7, 2024
Merged

Replace utils read with readr read function #442

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13 changes: 8 additions & 5 deletions R/inputs-spectrum.R
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Original file line number Diff line number Diff line change
Expand Up @@ -185,7 +185,7 @@ read_dp_art_dec31 <- function(dp) {

## In Spectrum 2023, "<NeedARTDec31 MV>" was updated to include children in the totals
## -> now need to sum over 5-year age groups for age 15+ to get the adult ART need

male_15plus_needart <- dpsub("<NeedARTDec31 MV>", 4:17*3 + 3, timedat.idx)
male_15plus_needart <- vapply(lapply(male_15plus_needart, as.numeric), sum, numeric(1))

Expand All @@ -195,14 +195,14 @@ read_dp_art_dec31 <- function(dp) {
art15plus_need <- rbind(male_15plus_needart, female_15plus_needart)
dimnames(art15plus_need) <- list(sex = c("male", "female"), year = proj.years)


if (any(art15plus_num[art15plus_isperc == 1] < 0 |
art15plus_num[art15plus_isperc == 1] > 100)) {
stop("Invalid percentage on ART entered for adult ART")
}

## # Adult on ART adjustment factor
##
##
## * Implemented from around Spectrum 6.2 (a few versions before)
## * Allows user to specify scalar to reduce number on ART in each year ("<AdultARTAdjFactor>")
## * Enabled / disabled by checkbox flag ("<AdultARTAdjFactorFlag>")
Expand Down Expand Up @@ -281,7 +281,7 @@ read_dp_art_dec31 <- function(dp) {
names(child_art) <- proj.years

## # Child on ART adjustment factor
##
##
## * Implemented same as adult adjustment factor above

if (exists_dptag("<ChildARTAdjFactorFlag>") &&
Expand Down Expand Up @@ -686,5 +686,8 @@ extract_eppasm_pregprev <- function(mod, fp, years = NULL) {

read_dp <- function(pjnz) {
dpfile <- grep(".DP$", utils::unzip(pjnz, list = TRUE)$Name, value = TRUE)
utils::read.csv(unz(pjnz, dpfile), as.is = TRUE)
as.data.frame(
readr::read_csv(unz(pjnz, dpfile),
name_repair = "minimal",
col_types = readr::cols(.default = "c")))
}
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