Create function to run all chunks in a Rmd file

R/runAllChunks.R

+#' @title Run all chunks in a Rmd file
+#'
+#' @name runAllChunks
+#'
+#' @description This function was developed to run all chunks in a knitr
+#' Rmd (R markdown) file at once. Mainly for exploring and debugging
+#' purposes.
+#'
+#' @param Rmd the name of the Rmd file.
+#'
+#' @param envir the environment in which the chunks will be
+#' evaluated. By default it is the GlobalEnv.
+#'
+#' @references This function was based on this
+#'     \href{http://stackoverflow.com/questions/24753969/knitr-run-all-chunks-in-an-rmarkdown-document}{SO
+#'     thread}.
+#'
+#' @return Objects created in the chunks from the Rmd file.
+#'
+#' @import knitr
+#'
+#' @author Fernando Mayer, \email{fernando.mayer@@ufpr.br}
+#'
+#' @export
+runAllChunks <- function(Rmd, envir = globalenv()){
+    if (!requireNamespace("knitr", quietly = TRUE)){
+        stop("`knitr` needed for this function to work. Please install it.",
+             call. = FALSE)
+    }
+    tempR <- tempfile(tmpdir = ".", fileext = ".R")
+    on.exit(unlink(tempR))
+    purl(Rmd, output = tempR)
+    sys.source(tempR, envir = envir)
+}

man/runAllChunks.Rd

+% Generated by roxygen2 (4.1.1): do not edit by hand
+% Please edit documentation in R/runAllChunks.R
+\name{runAllChunks}
+\alias{runAllChunks}
+\title{Run all chunks in a Rmd file}
+\usage{
+runAllChunks(Rmd, envir = globalenv())
+}
+\arguments{
+\item{Rmd}{the name of the Rmd file.}
+
+\item{envir}{the environment in which the chunks will be
+evaluated. By default it is the GlobalEnv.}
+}
+\value{
+Objects created in the chunks from the Rmd file.
+}
+\description{
+This function was developed to run all chunks in a knitr
+Rmd (R markdown) file at once. Mainly for exploring and debugging
+purposes.
+}
+\author{
+Fernando Mayer, \email{fernando.mayer@ufpr.br}
+}
+\references{
+This function was based on this
+    \href{http://stackoverflow.com/questions/24753969/knitr-run-all-chunks-in-an-rmarkdown-document}{SO
+    thread}.
+}
+