rstudio-knitr-report

An example of a PDF report generated with RStudio, R and knitr where data from a fictitious non-interventional study was analyzed.

See final statistical PDF report: ALEA01.pdf

Overview

The goal of this set of .Rnw programs is to generate a PDF report in RStudio with R and knitr that can be used as a template for generating statistical analysis reports including tables (e.g., R packages stats, Hmisc, reporttools, texreg, survival, user-defined R functions), listings (package xtable) and figures (packages ggplot2, survminer).

All code for generating this report is included in the appendix of the report and in the majority of cases R syntax highlighting has been used within the report.

All analysis data sets (SAS xpt files) are fictitious and were generated with SAS v. 9.4 (SAS Institue Inc., Cary, NC, USA) using e.g. following functions: rand("BINOMIAL", p, n), rand("NORMAL", mu, sigma), exp(rand("NORMAL", mu, sigma)) and -log(ranuni(x)).

There is one master program (ALEA01.Rnw) and following child programs:

• 00_TITLE_PAGE.Rnw
• 00_ABBREVIATIONS.Rnw
• impsas_xpt.R (for importing SAS xpt files)
• 00_chunks.R
• 00_r_functions.R
• 01_DEMOG.Rnw
• 01_DEMOG_FIG.Rnw
• 01_LINEAR_MODEL.Rnw
• 02_KAPLAN.Rnw
• 03_LAB_HGB.Rnw
• 03_LAB_WBC.Rnw
• 04_RESPONSE.Rnw
• 99_HISTORY.Rnw

Endpoints/Statistical Methods

• Demographics, summary statistics, geometric mean +/- 95% CIs (body weight)
• Demographics: Wilcoxon test, Fisher’s exact test, Pearson’s chi2 test
• Demographics: histograms, qqplot, box plots, density plot, polar chart, (stacked/side-by-side) bar chart, pie chart
• Demographics: scatterplot matrix
• Linear regression analysis, scatterplot, diagnostic plots
• ANOVA: Sum of Squares Type I, II, III
• Overall survival, Kaplan-Meier curves, KM quartiles +/- 95% CIs, log-rank test
• Laboratory values, summary statistics, 95% CIs, boxplot, jitter plot (mean +/- SD) , shift tables (plot)
• Shift tables: McNemar’s test/Bowker’s symmetry test
• Tumor response: no. and percentage, 95% Wilson-score CIs

Platform

Windows 7, RStudio IDE, R, knitr, Tex Live 2017

Usage

1. Create the directory C:\Temp\Alea01 and copy all files (.R, .Rnw, .xpt, .pdf, .jpg) into this directory. In the case that a different R working directory will be used, the correct path has to be specified in the program impsas_xpt.R with the statement: setwd("path")

2. Create an empty sub-directory C:\Temp\Alea01\Figure

3. Open ALEA01.Rnw and click on Compile PDF in RStudio

Compile PDF -> ALEA01.tex -> ALEA01.pdf will be automatically generated and opened

Requirements

RStudio IDE

https://www.rstudio.com/products/rstudio/download/

RStudio Gobal Options: knitr and pdfLaTeX - Default Settings

knitr

https://yihui.name/knitr/

install.packages("knitr", dependencies = TRUE)

LaTeX Environment

Install a LaTeX environment on Windows, e.g,:

• MiKTeX https://miktex.org/ or

• TeX Live https://www.tug.org/texlive/

1. Download Texlive-yyyyddmm.iso (~3.5 GB): http://mirror.ctan.org/systems/texlive/Images/
2. Download program for mounting ISO e.g. http://wincdemu.sysprogs.org/ and install
3. Mount ISO by double click on iso file -> ok
4. Execute install-tl-windows.bat
5. Start → Control Panel → System → Advanced system settings → Advanced → Enviroment Variables → System variables → Path

Set Path environment variables (examples only), e.g.

C:\Program Files\R\R-3.4.2\bin\x64;
C:\Rtools\bin;
C:\Rtools\mingw_32\bin;
C:\texlive\2017\bin\win32;
%SystemRoot%\system32;
%SystemRoot%;%SystemRoot%\System32\Wbem;
%SYSTEMROOT%\System32\WindowsPowerShell\v1.0\;

Search the internet for complete instructions (especially when an other operating system will be used).

R packages

Following R packages must be installed:

library(knitr)
library(foreign)
library(tidyverse)
library(xtable)
library(gridExtra)
library(survminer)
library(ggthemes)
library(reporttools)
library(texreg)
library(car)
library(Hmisc)

Test Environment

The programs were tested on: windows 7 64-bit, SAS 9.4, R 3.4.2, RStudio 1.1.383, TeX Live 2017

Error Handling - some Tips

In case of errors test each chunk - step by step - for correct functionality. Use comment/uncomment to deactivate/activate code (use for remarks: percentage % within LaTeX, hash # within R code).

Please note, that different versions of R packages may cause problems, e.g. because some settings were deprecated.

1. First, run impsas_xpt.R and check if all required R packages are installed (e.g. knitr, gridExtra, tidyverse, Hmisc, etc.). Use e.g. install.packages("Hmisc") to install R package Hmisc.
2. Check correct functionality of the LaTex environment, e.g. compile ALEA01.tex in a LaTeX editor
3. Execute each chunk separately to test the R code for correct functionality
4. Assure that chunk labels are unique (<<ChunkLabel, options>>=)
5. Assure that label(s) within R function latex(label = "mylabel") - for referencing of tables - are unique (avoid error: There were multiply-defined labels)
6. If you change the file name ALEA01.Rnw change also line 198 in newfile.Rnw (VerbatimInput)
7. Search the internet

Conclusion

This set of .Rnw programs generates a PDF report including tables, listings and figures and can be used as a template, e.g. for analysis of non-interventional studies. The PDF report has a a title page, a table of content with hyper-references, a header with a logo, page numbering in the footer, an embeded PDF document, figure and table references, landscape PDF pages, a list of abbreviations, a history page, R syntax highlighting within the document and all code that generates the report is included in the appendix - all in compliance with reproducible research "best practices".

Using R in a Regulatory Environment

NOTE: For Regulatory Compliance and Validation Issues see, e.g.,

• http://blog.revolutionanalytics.com/2017/06/r-fda.html
• http://www.r-project.org/doc/R-FDA.pdf
• https://www.ispe.org/publications/guidance-documents/gamp-5