Clean up a few more issues

[dajmcdon]

• Closes Improve epi_slide error messaging on bad ref_time_values #65
• Closes Improve documentation for epi_slide's f parameter when it's a function with named arguments #66
• Closes Add final newline to epi_archive print statement #68

[dajmcdon]

Note: there's some weird formatting. I'm going to clean that up after (to avoid continued maintenance on 2 remotes).

[brookslogan]

• Confirming that the improved error messaging works to resolve Improve epi_slide error messaging on bad ref_time_values #65. But beyond Improve epi_slide error messaging on bad ref_time_values #65 we should probably be more stringent on ref_time_values and require them to all be in unique(x$time_value) rather than silently filtering to such values + disallow passing in 0 ref_time_values. That should also give users an easier time debugging as they don't have to track down what starts and stops are.
  • ---> This can be filed in a new Issue & addressed later.
• Re. Improve documentation for epi_slide's f parameter when it's a function with named arguments #66:
  • The main @param f documentation is still wrong and doesn't reference the clarifying @details in this section: "If a function, f must take x, a data frame with the same column names as the original object; followed by any number of named arguments; and ending with ...". I think the proper thing may be that f should take x, g/k/key/think-of-a-better-name, and named args (dots don't seem necessary; I think originally they were just there to absorb the unlisted g).
  • In @details, the following text too specific to the particular example that follows: "if a tibble with an unnamed grouping variable is passed in as the method argument to f". This explanatory text may be unnecessary anyway once the main @param f documentation is fixed. The dots in the example may be unnecessary. The example code could also use a library(dplyr), and these interspersed details&code could be turned into @examples comments&code so users can more easily run them and so package checks ensure that these examples run. (Separately, as part of Implement testing across the package #42, maybe these examples should be turned into tests as well?)
• Re. Add final newline to epi_archive print statement #68: archive_cases_dv_subset needs to be regenerated or reworked to form an epi_archive from more basic parts on demand; it currently appears to load with the old class definition, missing the extra "\n", plus some bad srcrefs that may make user debugging of tweaked examples harder:

archive_cases_dv_subset$print
<srcref: file "C:/Users/chloe/Desktop/Summer2022/epiprocess/R/archive.R" chars 162:19 to 187:11>
<environment: 0x55c5b02d6358>
Warning message:
In getSrcLines(srcfile, x[7L], x[8L]) :
  restarting interrupted promise evaluation
> body(archive_cases_dv_subset$print)
{
    cat("An `epi_archive` object, with metadata:\n")
    cat(sprintf("* %-9s = %s\n", "geo_type", self$geo_type))
    cat(sprintf("* %-9s = %s\n", "time_type", self$time_type))
    if (!is.null(self$additional_metadata)) {
        sapply(self$additional_metadata, function(m) {
            cat(sprintf("* %-9s = %s\n", names(m), m))
        })
    }
    cat("----------\n")
    cat(sprintf("* %-14s = %s\n", "min time value", min(self$DT$time_value)))
    cat(sprintf("* %-14s = %s\n", "max time value", max(self$DT$time_value)))
    cat(sprintf("* %-14s = %s\n", "min version", min(self$DT$version)))
    cat(sprintf("* %-14s = %s\n", "max version", max(self$DT$version)))
    cat("----------\n")
    cat(sprintf("Data archive (stored in DT field): %i x %i\n", 
        nrow(self$DT), ncol(self$DT)))
    cat("----------\n")
    cat(sprintf("Public methods: %s", paste(names(epi_archive$public_methods), 
        collapse = ", ")))
}

The quick fix is to just regenerate the object + file an Issue to later figure out how to generate the example epi_archive on demand or otherwise ensure that it is current with the implementation of epi_archive. The less-quick fix is to try to immediately address this issue.

[brookslogan]

Re. #68 and regenerating / syncing the example archive object: the simple way is just to re-run to regenerate the archive object. The more complex way is to store its DT and reconstruct the archive on demand; I've implemented this as part of 8f36d44, but based on an older version/name of the archive object, and involving the compactify parameter under development in #101, so it will need a little tweaking.