option to name directory for output would be nice - I tried running this on server R and got interesting results - the default location will only work for windows machines with directories that match IMO using the current wd would be better.
example should load the parameter files, or at least the report.sso from "simple" SS3 example (I think that is the intended example file)
requires functions from satf (suggest adding remotes::install_github("nmfs-ost/satf") to readme
maybe add require("satf") somewhere? there are several references to satf functions from within the other satf functions that aren't receded by satf:: or satf::: that cause errors otherwise.

bugs in satf::table_indices

flextable::add_header_row(top = TRUE, values = c(
        "", rep(ind_fleets, each = 2))
      )

lacks the colwidths argument which causes an error - I am not sure how to fix this - one I tried

 flextable::add_header_row(top = TRUE
          ,values = c("", rep(intersect(ind_fleets,fleet_names), each = 2))
          ,colwidths = c(1,rep(2,length=length(ind_fleets)))
      )

but this does not put the header in the correct place

bugs in satf::plot_spawning_biomass

the first line

model <- match.arg(model, several.ok = FALSE)

causes an error because the call to the function redefines model from the vector of possible values to 'SS3'. I think this needs an argument

choices= c('SS3','BAM', 'ASAP', 'AMAK', 'WHAM', "standard")

or some way to make this the default? I am not sure what you are going for here, but it throws an error for me.

I think you need to add else endyr=end_year in several places. For example line 68 - basically anywhere that if (is.null(end_year)){ is tested.

@DHennen1 thanks for testing the tool Dan! I have addressed your first bullet by designating the output directory to the user's working directory with the option of changing it using the parameter file_dir. I have also added the direction to install the satf package in the readme (third bullet).

In regards to the remaining bullets,

"example should load the parameter files, or at least the report.sso from "simple" SS3 example (I think that is the intended example file)" The example is a generic input of a SS3 report file with no linked example. The current blank template or example does not actually use or convert the data. I am in the works of changing this chunk in the base template. https://github.com/nmfs-ost/asar/blob/d9b69a1912f36a127e8d52dd69ef93f9f475f662/R/create_template.R#L466-L487 I plan to upload a full working example with what should be produced in the next week that will be reflected in the example in the README.

"Bugs in SATF [functions]" satf is still in the beginning stages of development and I have recently had to make changes with how it worked specifically for SS3 output files. Thank you for pointing out these bugs. I opened a new issue in the satf repo describing these bugs.

nmfs-ost / asar

Bugs found in testing asar (running list) #42

bugs in satf::table_indices

bugs in satf::plot_spawning_biomass