From cd8079dc88612dfb9ff70654498910be4122e4ce Mon Sep 17 00:00:00 2001
From: Fernando Mayer <fernandomayer@gmail.com>
Date: Fri, 28 Aug 2015 17:05:32 -0300
Subject: [PATCH] Create function to run all chunks in a Rmd file
---
R/runAllChunks.R | 34 ++++++++++++++++++++++++++++++++++
man/runAllChunks.Rd | 31 +++++++++++++++++++++++++++++++
2 files changed, 65 insertions(+)
create mode 100644 R/runAllChunks.R
create mode 100644 man/runAllChunks.Rd
diff --git a/R/runAllChunks.R b/R/runAllChunks.R
new file mode 100644
index 0000000..cc7ff57
--- /dev/null
+++ b/R/runAllChunks.R
@@ -0,0 +1,34 @@
+#' @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)
+}
diff --git a/man/runAllChunks.Rd b/man/runAllChunks.Rd
new file mode 100644
index 0000000..3602646
--- /dev/null
+++ b/man/runAllChunks.Rd
@@ -0,0 +1,31 @@
+% 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}.
+}
+
--
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