There are some R Markdown features that are not readily supported in Jupyter notebooks, such as options in the YAML header for setting the theme and configuring a table of contents, as well as advanced code appearance settings for including or excluding source code, printing out warnings and errors, etc. The conversion maximally tries to preserve all settings and configuration of the R markdown files, but some things can get lost. If your R Markdown files contain some of the configuration mentioned above, please review the resulting Jupyter notebook files after the conversion has happened.