Nothing
###
#' Calculate the correlations
#'
#' @description Calculate both Spearman and Pearson correlations for the
#' provided ENAset
#'
#' @param enaset ENAset to view methods of
#' @param tool c("rENA","webENA")
#' @param tool.version as.character(packageVersion(tool))
#' @param comparison character string representing the comparison used, c(NULL, "parametric", "non-parametric"). Default NULL
#' @param comparison.groups Groups that were used for the comparison
#' @param sig.dig Integer for the number of digits to round to
#' @param output_dir Where to save the output file
#' @param type c("file","stream") File will save to a file in output_dir, Stream returns the contents directly
#' @param theory Logical indicating whether to include theory in the writeup
#' @param methods Logical indicating whether to include methods in the writeup
#' @param params additional parameters for rmarkdown::render
#' @param output_file character
#' @param output_format character
#'
#' @export
#'
#' @return String representing the methods used to generate the model
ena.writeup <- function(
enaset,
tool = "rENA", tool.version = as.character(packageVersion(tool)),
comparison = NULL, comparison.groups = NULL, sig.dig = 2,
output_dir = getwd(), type = c("file","stream"), theory = T, methods = T,
params = NULL, output_file = NULL, output_format = NULL
) {
if(is.null(enaset$`_function.params`$weight.by))
enaset$`_function.params`$weight.by <- enaset$`_function.params`$args$weight.by
type = match.arg(type, choices = c("file","stream"), several.ok = FALSE)
if(type == "file") {
output_format = "word_document"
}
file = rmarkdown::render(system.file("rmd","methods.rmd", package="rENA"), output_dir = output_dir,
knit_root_dir = output_dir, intermediates_dir = output_dir, quiet = TRUE,
params = params, output_file = output_file
,output_format = output_format
# ,output_format = ifelse(type == "file", rENA::methods_report, rENA::methods_report_stream)
)
if(type == "file")
file
else if (type == "stream" && endsWith(file, ".plain"))
readChar(file, file.info(file)$size)
}
#' @title methods_report
#' @description Methods report for rmarkdwon
#' @param toc [TBD]
#' @param toc_depth [TBD]
#' @param fig_width [TBD]
#' @param fig_height [TBD]
#' @param keep_md [TBD]
#' @param md_extensions [TBD]
#' @param pandoc_args [TBD]
#'
#' @export
methods_report <- function(toc = FALSE,
toc_depth = 3,
fig_width = 5,
fig_height = 4,
keep_md = FALSE,
md_extensions = NULL,
pandoc_args = NULL) {
# knitr options and hooks
knitr <- rmarkdown::knitr_options(
opts_chunk = list(dev = 'png',
dpi = 96,
fig.width = fig_width,
fig.height = fig_height)
)
# build pandoc args
args <- c("--standalone")
# table of contents
args <- c(args, rmarkdown::pandoc_toc_args(toc, toc_depth))
# pandoc args
args <- c(args, pandoc_args)
preserved_chunks <- character()
# pre_processor <- function(metadata, input_file, runtime, knit_meta,
# files_dir, output_dir) {
# preserved_chunks <<- extract_preserve_chunks(input_file, knitr::extract_raw_output)
# NULL
# }
# post_processor <- function(metadata, input_file, output_file, clean, verbose) {
# output_str <- readLines(output_file, encoding = 'UTF-8')
# output_res <- knitr::restore_raw_output(output_str, preserved_chunks)
# if (!identical(output_str, output_res))
# writeLines(enc2utf8(output_res), output_file, useBytes = TRUE)
# output_file
# }
# return output format
rmarkdown::output_format(
knitr = knitr,
pandoc = rmarkdown::pandoc_options(to = "docx",
from = rmarkdown::from_rmarkdown(extensions = md_extensions),
args = args),
keep_md = keep_md
# ,pre_processor = pre_processor,
# post_processor = post_processor
)
}
#' @title methods_report_stream
#' @description Methods report for rmarkdwon
#' @param toc [TBD]
#' @param toc_depth [TBD]
#' @param fig_width [TBD]
#' @param fig_height [TBD]
#' @param keep_md [TBD]
#' @param md_extensions [TBD]
#' @param pandoc_args [TBD]
#'
#' @export
methods_report_stream <- function(toc = FALSE,
toc_depth = 3,
fig_width = 5,
fig_height = 4,
keep_md = FALSE,
md_extensions = NULL,
pandoc_args = NULL) {
# knitr options and hooks
knitr <- rmarkdown::knitr_options(
opts_chunk = list(dev = 'png',
dpi = 96,
fig.width = fig_width,
fig.height = fig_height)
)
# build pandoc args
args <- c("--standalone")
# table of contents
args <- c(args, rmarkdown::pandoc_toc_args(toc, toc_depth))
# pandoc args
args <- c(args, pandoc_args)
preserved_chunks <- character()
# return output format
rmarkdown::output_format(
knitr = knitr,
pandoc = rmarkdown::pandoc_options(to = "plain",
from = rmarkdown::from_rmarkdown(extensions = md_extensions),
args = args),
keep_md = keep_md
)
}
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