Process completed with exit code 31.

file=R/estimate_infections.R,line=336,col=39,[missing_argument_linter] Missing argument in function call.

file=R/estimate_infections.R,line=453,col=9,[if_not_else_linter] In a simple if/else statement, prefer `if (A) x else y` to the less-readable `if (!A) y else x`.

file=R/extract.R,line=105,col=56,[fixed_regex_linter] This regular expression is static, i.e., its matches can be expressed as a fixed substring expression, which is faster to compute. Here, you can use "," with fixed = TRUE.

file=R/opts.R,line=795,col=5,[unnecessary_nested_if_linter] Don't use nested `if` statements, where a single `if` with the combined conditional expression will do. For example, instead of `if (x) { if (y) { ... }}`, use `if (x && y) { ... }`.

file=R/opts.R,line=795,col=10,[missing_package_linter] Package 'cmdstanr' is not installed.

file=R/opts.R,line=796,col=7,[condition_message_linter] Don't use paste0 to build stop strings. Instead use the fact that these functions build condition message strings from their input (using "" as a separator). For translatable strings, prefer using gettextf().

file=R/stan.R,line=38,col=39,[paste_linter] toString(.) is more expressive than paste(., collapse = ", "). Note also glue::glue_collapse() and and::and() for constructing human-readable / translation-friendly lists