R reports are ordinarily associated with individual data grids. Choose the dataset of interest and further filter the grid as needed. Only the portion of the dataset visible within this data grid become part of the analyzed dataset.
To use the sample dataset we describe in this tutorial, please Tutorial: Set Up a New Study if you have not already done so. Alternately, you may simply add the PhysicalExam.xls demo dataset to an existing study for completing the tutorial. You may also work with your own dataset, in which case steps and screencaps will differ.
R reports do not necessarily need to be associated with individual data grids. You can also create an R report that is independent of any grid:
R reports associated with a grid automatically load the grid data into the object "labkey.data". R reports created independently of grids do not have access to labkey.data objects. R reports that pull data from additional tables (other than the associated grid) must use the Rlabkey API to access the other table(s). For details on using Rlabkey, see Rlabkey Package. By default, R reports not associated with a grid are listed under the Uncategorized heading in the list on the Manage Views page.
The R report builder opens on the Source tab which looks like this. Enter the R script for execution or editing into the Script Source box. Notice the options available below the source entry panel, describe below.
When you select the Report tab, you'll see the resulting graphics and console output for your R report. If the pipeline option is not selected, the script will be run in batch mode on the server.
Select the data tab to see the data on which your R report is based. This can be a helpful resource as you write or refine your script.
When your script is complete and report is satisfactory, return to the Source tab, scroll down, and click Save to save both the script and the report you generated.
A saved report will look similar to the results in the design view tab, minus the help text. Reports are saved on the LabKey Server, not on your local file system. They can be accessed through the Reports drop-down menu on the grid view of you dataset, or directly from the Data Views web part.
The script used to create a saved report becomes available to source() in future scripts. Saved scripts are listed under the “Shared Scripts” section of the LabKey R report builder.
This Syntax Reference list provides a quick summary of the substitution parameters for LabKey R. See Input/Output Substitutions Reference for further details.
On the Source Tab you can expand additional option sections. Not all options are available to all users, based on permission roles granted.
Options
Note that reports are always generated from live data by re-running their associated scripts. This makes it particularly important to run computationally intensive scripts as pipeline jobs when their associated reports are regenerated often.
Knitr Options
Regardless of where you have accessed the R report builder, you can create a first R report which is data independent. This sample was adapted from the R help files.
options(echo=TRUE);
# Execute 100 Bernoulli trials;
coin_flip_results = sample(c(0,1), 100, replace = TRUE);
coin_flip_results;
mean(coin_flip_results);
By default, most R commands do not generate output to the console as part of your script. To enable output to console, use the following line at the start of your scripts:
options(echo=TRUE);
Note that when the results of functions are assigned, they are also not printed to the console. To see the output of a function, assign the output to a variable, then just call the variable. For further details, please see the FAQs for LabKey R Reports.
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