Some libraries, such as DEseq2, are quite chatty when loaded, and this adds a lot of visual clutter to our rendered pages, without adding much information for the user. This PR seeks to cut that down by adding message=FALSE to code blocks with library() calls. In our current template, there is one of these blocks per page.
Issue addressed
closes #367
Gotchas the reviewer should know about
I think this is overall pretty straightforward; the changes in .Rmd files are small, and I don't think I missed any. The rendered files change more, of course, but these seem to all be the expected changes.
I also did change the template file, so future pages should get this change by default.
Remaining concerns and questions
Occasionally, there might be messages in this block that are useful to users, so it might be nice if they showed up when users run the notebook on their own. This could be done by selectively adding message=FALSE in preprocessing before rendering (as we do with the bibliography) to chunks with some kind of special tag, but I think that is well out of scope for now.
Purpose
Some libraries, such as DEseq2, are quite chatty when loaded, and this adds a lot of visual clutter to our rendered pages, without adding much information for the user. This PR seeks to cut that down by adding
message=FALSEto code blocks withlibrary()calls. In our current template, there is one of these blocks per page.Issue addressed
closes #367
Gotchas the reviewer should know about
I think this is overall pretty straightforward; the changes in .Rmd files are small, and I don't think I missed any. The rendered files change more, of course, but these seem to all be the expected changes.
I also did change the template file, so future pages should get this change by default.
Remaining concerns and questions
Occasionally, there might be messages in this block that are useful to users, so it might be nice if they showed up when users run the notebook on their own. This could be done by selectively adding
message=FALSEin preprocessing before rendering (as we do with the bibliography) to chunks with some kind of special tag, but I think that is well out of scope for now.