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# Main function for generating docs
.rd_generator <- function(study_name, dir, overwrite) {
# Add any studies whose documentation is to be overwritten
if (!missing(overwrite)) {
study_name <- c(study_name, overwrite)
study_name <- gsub(".Rd", "", study_name) # remove file ext if need be
}
# Loop through datasets and create template documentation
# Will only be > 1 if overwrite is specified
for (i in seq_along(study_name)) {
# Open new file connection
con <- try(file(file.path(paste0(dir, "/man/"), paste0(study_name[i], ".Rd")), "w"))
# Write the single preamble
write.table(.preamble_table(study_name[i]), con, row.names = FALSE, col.names = FALSE, quote = FALSE)
# Write the meta-data table header
write.table(.tabular(study_name[i]), con, row.names = FALSE, col.names = FALSE, quote = FALSE)
# Load dataset
data <- get(load(paste0(dir, "/data/", as.character(study_name[[i]]), ".rda")))
# Write main metadata
write.table(.meta_dat_table(data), con, row.names = FALSE, col.names = FALSE, quote = FALSE, na = "")
# Write the postamble
write.table(.postamble_table(study_name[i]), con, row.names = FALSE, col.names = FALSE, quote = FALSE)
# Close the file connection
close(con)
}
}
# Generate preamble
.preamble_table <- function(study.name) {
name <- paste0("\\name{", study.name, "}")
docType <- "\\docType{data}"
alias <- paste0("\\alias{", study.name, "}")
title <- "\\title{ADD_TITLE}"
descrp <- "\\description{ADD_DESCRIPTION}"
use <- paste0("\\usage{\n", study.name, "\n}")
format <- paste0("\\format{")
out <- rbind(name, docType, alias, title, descrp, use, format)
return(data.frame(out, stringsAsFactors = FALSE, row.names = 1:nrow(out)))
}
# Generate table start
.tabular <- function(study.name) {
info <- paste0("The data frame contains the following columns:")
tabular <- "\\tabular{lll}{"
out <- rbind(info, tabular)
}
# Generate metadata table
.meta_dat_table <- function(data) {
variables <- paste0("\\bold{", colnames(data), "}")
type <- paste0("\\tab", " ", "\\code{", as.vector(sapply(data, class)), "}")
descrp <- rep(paste0("\\tab", " ADD_DESCRIPTION ", "\\cr"), length = length(variables))
closer <- c("}", NA, NA)
meta_dat_table <- cbind(variables, type, descrp, deparse.level = 0)
meta_dat_table <- rbind(meta_dat_table, closer)
return(data.frame(meta_dat_table, stringsAsFactors = FALSE, row.names = 1:nrow(meta_dat_table)))
}
# Generate postamble
.postamble_table <- function(study.name) {
closer <- "}"
details <- "\\details{ADD_DETAILS}"
source <- "\\source{ADD_REFERENCE}"
author <- "\\author{ADD_CONTRIBUTOR_NAME, \\email{ADD_EMAIL}}"
eg1 <- "\\examples{"
eg2 <- "### copy data into 'dat' and examine data"
eg3 <- paste0("dat <- ", study.name)
eg4 <- "dat\n"
eg5 <- "\\dontrun{\n"
eg6 <- "ADD_DETAILED_EXAMPLE\n"
keyword <- "\\keyword{datasets}"
concept <- "\\concept{ADD_CONCEPT}"
out <- rbind(closer, details, source, author, eg1, eg2, eg3, eg4, eg5, eg6, closer, closer, keyword, concept)
return(data.frame(out, stringsAsFactors = FALSE, row.names = 1:nrow(out)))
}
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