Create a (reproducible) report using Rmarkdown
The best way to store your work in Radiant is to use the Report > Rmd feature and save a state file with all your results and settings. The report feature in Radiant should be used in conjunction with the icons shown on the bottom left of your screen on most pages.
The editor shown on the left in Report > Rmd shows past
commands in R-code chunks. These chunks can
include R-code you typed or R-code generated by Radiant and added to the
report after clicking an
icon. All code chunks
start with ```{r} and are closed by ```
By default Radiant will add the R-code generated for the analysis you just completed to the bottom of the report. After clicking a icon Radiant will, by default, switch to the Report > Rmd tab. Click inside the editor window on the left and scroll down to see the generated commands.
If you want more control over where the R-code generated by Radiant
is put into your report, choose Manual paste instead or
Auto paste from the appropriate drop-down in the Report
> Rmd tab. When Manual paste is selected, the code
is put into the clipboard when you click
and you can paste it
where you want in the editor window.
If you started Radiant from Rstudio, you can also choose to have
commands sent to an Rmarkdown (R-code) document open in Rstudio by
selecting To Rmd (To R) instead of
Auto paste or Manual paste. If you choose
To Rmd the editor in Report > Rmd will be
hidden (i.e., “Preview only”) and clicking on
Knit report (Rmd) will source the text and code directly
from Rstudio.
By default, the app will switch to the Report > Rmd tab
after you click the
icon. However, if you don’t want to switch tabs after clicking a
icon, choose
Don't switch tab from the appropriate drop-down in the
Report > Rmd tab. Don't switch tab is the
default option when you choose To Rmd.
You can add text or additional commands to create an Rmarkdown document. An Rmarkdown file (extension .Rmd) is a plain text file that can be opened in Notepad (Windows), TextEdit (Mac), Rstudio, Sublime Text, or any other text editor. Please do not use Word to edit Rmarkdown files.
Using Rmarkdown is extremely powerful because you can replicate your
entire analysis quickly without having to generate all the required
R-code again. By clicking the Knit report (Rmd) button on
the top-left of your screen, the output from the analysis will be
(re)created and shown on the right of the Report > Rmd page.
To evaluate only a part of the report use the cursor to select a section
and press CTRL-enter (CMD-enter on mac) to
create the (partial) output.
You can add text, bullets, headers, etc. around the code chunks to describe and explain the results using markdown. For an interactive markdown tutorial visit commonmark.org.
If you started Radiant from Rstudio you can save the report in
various formats (i.e., Notebook, HTML, Word, Powerpoint, or PDF). For
more on generating powerpoint presentation see
https://bookdown.org/yihui/rmarkdown/powerpoint-presentation.html.
To save the Rmarkdown file open in the editor select Rmd
(or Rmd + Data (zip)) and press Save report.
Previously saved Rmarkdown files can be loaded into Radiant by using the
Load report button. For more
You can also click the Read files button to browse for
files and generate code to read it into Radiant. For example, read rda,
rds, xls, yaml, and feather and add them to the Datasets
dropdown. You can also read images, R-code, and text (e.g., Rmd or md)
to include in your report. If the file type you want to load is not
currently supported, the path to the file will be returned. If Radiant
was started from an Rstudio project, the file paths used will be
relative to the project root. Paths to files synced to local Dropbox or
Google Drive folder will use the find_dropbox and
find_gdrive functions to enhances reproducibility.
The best way to save your analyses and settings is to save the
state of the application to a file by clicking on the
icon in the navbar and then
clicking on Save radiant state file. The state file
(extension rda) will contain (1) the data loaded in Radiant, (2)
settings for the analyses you were working on, (3) and any reports or
code from the Report > Rmd and Report > R. Save
the state file to your hard-disk and, when you are ready to continue,
simply load it by icon in the
navbar and then clicking on Load radiant state file
If you are using Radiant for a class I suggest you use the Report
> Rmd feature to complete assignments and cases. When you are
done, generate an (HTML) Notebook (or Word or PDF) report by clicking
the Save report button. Submit both the report and your
state file.
The editor used in Report > Rmd and Report >
R has several options that can be set in .Rprofile.
You can use usethis::edit_r_profile() to alter the settings
in .Rprofile
options(radiant.ace_vim.keys = FALSE)
options(radiant.ace_theme = "cobalt")
options(radiant.ace_tabSize = 2)
options(radiant.ace_useSoftTabs = TRUE)
options(radiant.ace_showInvisibles = TRUE)
options(radiant.ace_autoComplete = "live")
options(radiant.powerpoint_style = "~/Dropbox/rmd-styles/style.potx")
options(radiant.word_style = "~/Dropbox/rmd-styles/style.docx")
options(radiant.theme = bslib::bs_theme(version = 4, bootswatch = "darkly"))Notes:
vim.keys enables a set of special keyboard short-cuts.
If you have never used VIM you probably don’t want thisshinyAce::getAceThemes()showInvisibles shows tabs and spaces in the editoroptions as shown above to tell Radiant where
to find the style files you want to use.
theme option can be used to change the appearance
of the Radiant interface. For an overview of available themes see:
https://rstudio.github.io/bslib/articles/theming/index.html#bootswatchFor an overview of related R-functions used by Radiant to generate reproducible reports see Report