Modifying R package data

Question

The bio.infer package contains a data frame /usr/lib/R/library/bio.infer/data/itis.ttable.rda that needs to be modified.

After loading the bio.infer package and attaching the data frame with the data() function, I wrote the data frame to a text file with write.table().

Using emacs I added another row to the data frame then applied read.table() to create a data frame, but it's in my pwd, not the R library data subdirectory for the bio.infer package.

What is the R function to copy/save/write either the text file or the local copy of itis.ttable to /usr/lib/R/library/bio.infer/data/itis.ttable.rda? I've looked in the R docs and my library of R books without seeing how to add this row to the library's data frame.

Answer 1

Use load and save with rda files.

#Path to the data file
fname <- system.file("data", "itis.ttable.rda", package = "bio.infer")
stopifnot(file.exists(fname))

#Load data into new environment
e <- new.env()
load(fname, envir = e)

#Manipulate it
e$itis.ttable <- rev(e$itis.ttable) #or whatever

#Write back to file
save(itis.ttable, file = fname, envir = e)

Though as David Robinson mentioned, you probably shouldn't be overwriting the copy in the package. It is likely more sensible to make your own copy.