plot.fit_model() help is incorrect and other issues

[John-R-Wallace-NOAA]

The help for plot.fit_model() gives the description for the 'what' argument as:

String specifying what elements of results to plot; options include 'extrapolation_grid', 'spatial_mesh', and 'results'

However looking in the code shows that only:

c("spatial_info", "inla_mesh")

will run FishStatsUtils:::plot.make_spatial_info

Something close to:

plot.fit_model <- 
function (x, what = c("results", "all", "extrapolation_grid", "inla_mesh")[1], ...) 
{
    if (!is.character(what)) 
        stop("Check `what` in `plot.fit_model`")
    if (any(what %in% c("extrapolation_grid", "all"))) {
        cat("\n### Running `plot.make_extrapolation_info`\n")
        plot(x$extrapolation_list)
        return(invisible(NULL))
    }
    if (any(what %in% c("spatial_info", "inla_mesh", "all"))) {
        cat("\n### Running `plot.make_spatial_info`\n")
        plot(x$spatial_list)
        return(invisible(NULL))
    }
    if (any(what %in% c("results", "all"))) {
        cat("\n### Running `plot_results`\n")
        ans = plot_results(x, ...)
        return(invisible(ans))
    }
    stop("input `what` not matching available options")
}

shows available options for 'what' (except "spatial_info") when using args() or str(), keeps the "results" only default, and adds an "all" option (which could be made the default).

Also, both FishStatsUtils:::plot.make_spatial_info() and FishStatsUtils:::plot.make_extrapolation_info() do not have internal calls to png() and so the figures are not automatically saved external to R like the rest of the figures in VAST.