With a simple combination of mutate_if and fct_explicit_na, you can replace all NAs in all factors with “Missing”: dplyr reference: http://dplyr.tidyverse.org/reference forcats reference: http://dplyr.tidyverse.org/reference
To create a .bib file that only includes the citations you used in the manuscript: bibexport -o extracted_file.bib manuscript.aux There are a few issues with this though. The command bibexport comes with the installation of TexLive, but my Windows computer (bless) does not cooperate (“bibexport is not recognised as an internal or external command…") . So I can only use it on my Mac (luv ya).
ggplot includes built in and seamless functionality that summarises your data before plotting it. As shown in the example below, ggplot_build() can be used to access the summarised dataset. fill y count prop x PANEL group ... #D7301F 0.2147239 35 1 1 1 4 ... #FC8D59 0.6871166 77 1 1 1 3 ... #FDCC8A 0.9570552 44 1 1 1 2 ... #FEF0D9 1.0000000 7 1 1 1 1 ... #D7301F 0.