Analyses run through the Advanced Workflow tool within Analyze use R for computation. tranSMART allows you to:
Note
For more information on The r Project for Statistical Computing, visit the following site: www.r-project.org.
To download advanced workflow analyses as raw R data:
Click the tranSMART Analyze tool to display the Analyze window.
Select the study you want to use and drag it into a subset definition box in Subset 1.
Click the Advanced Workflow tab and select the analysis you want to run.
Define the variables accordingly.
Click Run.
Your analysis appears below the variable selection boxes.
Click Download raw R data at the bottom of the page.
A dialog box similar to the following appears:
Decide whether you want to open the file or save it to your hard drive, then click OK.
To review the R version information for an analysis:
Click the tranSMART Analyze tool to display the Analyze window.
Select the study you want to use and drag it into a subset definition box in Subset 1.
Click the Advanced Workflow tab and select the analysis you want to run.
Define the variables accordingly.
Click Run.
Your analysis appears below the variable selection boxes.
Click R Version Information at the bottom of the page.
The following R version data displays:
Information about the R installation:
A table of the packages that are included in the installation. Although not all packages may be used, all are listed. The version number is especially useful - if you want to re-create an analysis, the version number indicates the specific version used to create the original analysis.
This sample shows a portion of the table:
You can view the full table in grid format when you select the Download raw R data option. Just click sessionInfo.txt to open the file:
To export R code and data so it is executable in R:
Click the tranSMART Analyze tool to display the Analyze window.
Select the study you want to use and drag it into a subset definition box in Subset 1.
Click the Advanced Workflow tab and select the analysis you want to run.
Define the variables accordingly.
Click Run.
Your analysis appears below the variable selection boxes.
Click Download raw R Data at the bottom of the page.
A dialog box similar to the following appears:
Open the file and copy the R commands from the file jobcommands.txt.
Be sure you delete the analysis image from the Advanced Workflow page.
Paste the R commands from the downloaded file into R.
Run R. R creates the appropriate analysis image.
When opening R, change the working directory to your downloaded raw R data folder
# In R environment, set your working directory:
setwd("C:\\users\\username\\Desktop\\workingDirectory").
Install the following packages:
install.packages("plyr")
install.packages("ggplot2")
install.packages("Cairo")
install.packages("rmeta")
install.packages("visreg")