From 6e60b9ef07e4bc4ad6330de39e6cecd69eb22c6d Mon Sep 17 00:00:00 2001
From: Holger Brandl <brandl@mpi-cbg.de>
Date: Thu, 18 Sep 2014 12:54:34 +0200
Subject: [PATCH] started spinr wrapper
---
R/utils/spinr.R | 42 ++++++++++++++++++++++++++++++++++++++++++
R/utils/spinr.sh | 26 ++++++++++++++++++++++++++
2 files changed, 68 insertions(+)
create mode 100644 R/utils/spinr.R
create mode 100644 R/utils/spinr.sh
diff --git a/R/utils/spinr.R b/R/utils/spinr.R
new file mode 100644
index 0000000..d61a394
--- /dev/null
+++ b/R/utils/spinr.R
@@ -0,0 +1,42 @@
+## a thin wrapper around spin to make it more useful with more custom output
+require(knitr)
+require(stringr)
+
+options(width=150)
+
+#https://groups.google.com/forum/#!topic/knitr/ojcnq5Nm298
+
+## better table css: http://www.stat.ubc.ca/~jenny/STAT545A/topic10_tablesCSS.html
+
+#setwd("/local/home/brandl/mnt/mack/project-raphael/reports/spin_report")
+#setwd("/home/brandl/mnt/mack/project-raphael/reports/spin_report")
+
+#rScript='/home/brandl/mnt/mack/project-raphael/Rcode/misc/DivisionPerpendicularity.R'
+#rScript='/home/brandl/mnt/mack/project-raphael/Rcode/misc/Test.R'
+
+#spinr <- function(rScript){
+ print(Sys.getenv("TISSMORH_SCRIPTS"))
+ spin(rScript, knit=F)
+
+ mdScript <- str_replace(rScript, "[.]R$", ".Rmd")
+
+ system(paste("mv", mdScript, "tmp.Rmd"))
+ system(paste("cat tmp.Rmd | grep -Ev '^#+$' | grep -Fv '#!/usr/bin/env Rscript' >", basename(mdScript)))
+
+ cssHeader='
+ <style type="text/css">
+ body {
+ max-width: 90%;
+ }
+ </style>
+ '
+ ls()
+
+ opts_chunk$set(cache = TRUE, fig.width=10, width=120)
+ knit2html(basename(mdScript))
+
+ #file.remove(mdScript)
+#}
+
+# spinr("/home/brandl/mnt/mack/project-raphael/Rcode/misc/DivisionPerpendicularity.R")
+# spinr("/home/brandl/mnt/mack/project-raphael/Rcode/misc/Test.R")
diff --git a/R/utils/spinr.sh b/R/utils/spinr.sh
new file mode 100644
index 0000000..34d78dc
--- /dev/null
+++ b/R/utils/spinr.sh
@@ -0,0 +1,26 @@
+
+
+spinr(){
+ if [ $# -ne 1 ]; then
+ echo -e "Usage: spinr <script.R>\nJust knit R documents as they are, no markdown is required (but supported to some extent)"
+ return
+ fi
+
+ rscript=$1
+
+ if [ ! -f $rscript ]; then
+ >&2 echo "$rscript does not exist"; exit;
+ fi
+
+ ## rscript=/Users/brandl/Dropbox/Public/datautils/R/rknit/rknit_example.R
+
+# echo 'devtools::source_url("https://dl.dropboxusercontent.com/u/113630701/datautils/R/utils/spinr.R"); spinr("'$rscript'")' | R --vanilla -q
+ echo 'rScript="'$rscript'"; devtools::source_url("https://dl.dropboxusercontent.com/u/113630701/datautils/R/utils/spinr.R")' | R --vanilla -q
+}
+
+
+#' cd /home/brandl/mnt/mack/project-raphael/reports/spin_report
+#' source <(curl https://dl.dropboxusercontent.com/u/113630701/datautils/R/utils/spinr.sh)
+#' spinr /home/brandl/mnt/mack/project-raphael/Rcode/misc/DivisionPerpendicularity.R
+#' spinr /home/brandl/mnt/mack/project-raphael/Rcode/misc/Test.R
+
--
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