Have you checked the RMarkdown window in RStudio? When I tried rendering index.Rmd, I got
Error in rawToChar(out) :
embedded nul in string: 'https://oskicat.berkeley.edu/search{~}S1?/.b15152566/.b15152566/1{\\\0C1{\\\0C1{\\\0CB/frameset{~}b15152566'
Calls: <Anonymous> ... <Anonymous> -> move_files_html -> vapply -> FUN -> rawToChar
In addition: Warning messages:
1: In FUN(X[[i]], ...) :
out-of-range values treated as 0 in coercion to raw
2: In FUN(X[[i]], ...) :
out-of-range values treated as 0 in coercion to raw
3: In FUN(X[[i]], ...) :
out-of-range values treated as 0 in coercion to raw
Execution halted
and, of course, no output. The repo is public (you might want to change that). And I'll delete it from my laptop if there are no further questions