-
Notifications
You must be signed in to change notification settings - Fork 2
/
Copy pathREADME.Rmd
154 lines (107 loc) · 6.24 KB
/
README.Rmd
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
---
output: github_document
---
<!-- README.Rmd markdown file generates README.md -->
# 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](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/
``` r
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:
``` r
library(knitr)
library(foreign)
library(tidyverse)
library(Hmisc)
library(xtable)
library(gridExtra)
library(survminer)
library(ggthemes)
library(reporttools)
library(texreg)
library(car)
```
## 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. 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