Did you encounter any issues or errors?

[Schiano-NOAA]

Indicate your answer to this question after completing the activity.

[BenWilliams-NOAA]

Both remotes and pak still throw github PAT errors for me - so may want to add in the install.packages("asar", repos = c("https://nmfs-ost.r-universe.dev", "https://cloud.r-project.org")) method to the the pdf?

[BenWilliams-NOAA]

The create_template() function effectively dies if the author name is not in the database, it compiles the skeleton if left blank but does not work using "Ben Williams" or "Benjamin C. Williams" - my general recommendation is to get rid of the authorship function that is trying to lookup from a .csv - the names on this list are frequently changing (there are now a number of names in there that no longer work for NOAA :( and whom is going to do long-term maintenance of such a list is unclear). Similarly, as I recall mentioning in another issue - the address may be incorrect e.g., the AFSC address for a SAFE is the Council address. I also recommend removing the autofill functionality and simply having people provide the appropriate address.

[BenWilliams-NOAA]

The exp_all_figs_tables() returned the following:

plot_abundance_at_age failed to run. Tip: check that your arguments are correct.
<error/rlang_error>
Error in dplyr::filter():
ℹ In argument: time%%1 != 0.5.
Caused by error in time %% 1:
! non-numeric argument to binary operator

Backtrace:
▆

1. └─stockplotr::exp_all_figs_tables(...)
2. ├─base::tryCatch(...)
3. │ └─base (local) tryCatchList(expr, classes, parentenv, handlers)
4. │ └─base (local) tryCatchOne(expr, names, parentenv, handlers[[1L]])
5. │ └─base (local) doTryCatch(return(expr), name, parentenv, handler)
6. └─stockplotr::plot_abundance_at_age(...)

7. ├─dplyr::ungroup(...)
   

8. ├─dplyr::summarise(...)
   

9. ├─dplyr::group_by(dplyr::filter(b, time%%1 != 0.5), age, year)
   

10. ├─dplyr::filter(b, time%%1 != 0.5)
    

11. └─dplyr:::filter.data.frame(b, time%%1 != 0.5)
    

12.   └─dplyr:::filter_rows(.data, dots, by)
    

13.     └─dplyr:::filter_eval(...)
    

14.       ├─base::withCallingHandlers(...)
    

15.       └─mask$eval_all_filter(dots, env_filter)
    

16.         └─dplyr (local) eval()
    

[MOshima-PIFSC]

I had this same issue. I found that if I used the output object I created in r
dat <- asar::convert_output() the time column is converted to a character which is what caused the error for me.
When I saved the output and then read the csv back into R, I didn't get this error, likely because time wasn't forced into a character type since it reads it in as a dataframe, not a tibble.

[MOshima-PIFSC]

I cannot get the create_figures_doc() function to work.
input:
create_figures_doc(subdir = file.path(getwd(), "report"))
output message:
Recruitment time series figure not created. Spawning biomass time series figure not created. Biomass time series figure not created. Landings time series figure not created. Recruitment deviations figure not created. Stock-Recruitment figure not created. Indices of abundance figure not created. Abundance at age figure not created. Biomass at age figure not created.

And 09_figures.qmd is blank.

I got create_tables_doc() to work though.

[Schiano-NOAA]

Interesting that you were able to get create_tables_doc working and not create_figures_doc using the same argument. You should have to also indicate where the rda is located using the argument rda_dir.

Have you tried running?:

create_figures_doc(subdir = file.path(getwd(), "report"), rda_dir = getwd()) # change path to where the rda_files folder is located

[MOshima-PIFSC]

Yea I tried that. I get fewer errors (Stock-recruitment figure, indices of abundance, and biomass at age) but still the 09_figures.qmd is empty. Also, in create_tables_doc I didn't have to specify the rda_dir and it worked.

[Schiano-NOAA]

The sr, indices, and biomass plots don't get output in this example so that is fine, but I am a little stumped as to why this wouldn't work. Does your rda_files folder contain objects with the figures names?

I also am not entirely sure how create_tables_doc would have identified the rda_files folder. Could you push your current progress to github and I can take a look?

[MOshima-PIFSC]

When I went to push my changes I realized that at one point there were changes to the 09_figures file and then it was overwriting them. So I discarded the new changes and now its good. I'm not sure at which point it was correct and which point it overwrote everything but looks like the issue is resolved for now.
Also, when I was looking through the documentation for create_template() it said that for rda_dir argument, if you use exp_all_figs_tables() to make the figures and rda files, you don't need to specify the path.

[Schiano-NOAA]

Glad you were able to get it working. I will note this issue down and set some checks in the functions to check if they are already formatted and set options to append if indicated by the user.

"Also, when I was looking through the documentation for create_template() it said that for rda_dir argument, if you use exp_all_figs_tables() to make the figures and rda files, you don't need to specify the path."

Yes that's right. This is only the case when you run exp_all_figs_tables before you run create_template. The default for create_figures_doc and create_tables_doc is not inherited from create_template. If this isn't working as intended though, it would help if you opened an issue on asar so we can put it in our todos :)

I made this activity based on the thought process that the report writing process will start before you have a base model.

[MOshima-PIFSC]

Next error: when running create_template to update the preamble with results, I am getting
Error in stri_replace_first_regex(string, pattern, fix_replacement(replacement), : Error in {min,max} interval. (U_REGEX_BAD_INTERVAL, context=title: 'Stock Assessment for Opakapaka (\textit{Pristipomoides filamentosus}) on U.S. West Coast in 2024')

[Schiano-NOAA]

Could you provide your code?

[MOshima-PIFSC]

create_template(rerender_skeleton = TRUE, file_dir = file.path(getwd(), "report"), model_results = "opaka_convert_output.csv", resdir = getwd())

[MOshima-PIFSC]

also this is the repo where I'm working https://github.com/MOshima-PIFSC/workflow_workthrough

[Schiano-NOAA]

So I looked into it and this is due to the latin name formatting in the title - I will have to think about how to approach this. I am not sure why this wasn't a problem before. For now, I would recommend removing the latin name formatting from the title then retry.

(\textit{Pristipomoides filamentosus}) --> (Pristipomoides filamentosus)

[MOshima-PIFSC]

thanks that worked!

[MOshima-PIFSC]

Even though I used put opaka as the species for my template, the image that is in report/support_files is yelloweye rockfish, not Opaka.

[lisaailloud-NOAA]

The description of the stockplotr function plot_biomass says
unit_label units for recruitment
should say units for biomass

[Schiano-NOAA]

Opened an issue into stockplotr. Thanks Lisa!

[lisaailloud-NOAA]

I can't get plot_indices to work with the Yelloweye rockfish example.

plot_indices(dat=dat1, end_year = 2024)
Error in dplyr::mutate():
ℹ In argument: estimate_lower = dplyr::case_when(...).
Caused by error in dplyr::case_when():
! Failed to evaluate the right-hand side of formula 1.
Caused by error:
! object 'estimate' not found
Run rlang::last_trace() to see where the error occurred.
rlang::last_trace()
<error/dplyr:::mutate_error>
Error in dplyr::mutate():
ℹ In argument: estimate_lower = dplyr::case_when(...).
Caused by error in dplyr::case_when():
! Failed to evaluate the right-hand side of formula 1.
Caused by error:
! object 'estimate' not found

---

Backtrace:
▆

1. ├─stockplotr::plot_indices(dat = dat1, end_year = 2024)
2. │ ├─dplyr::filter(...)
3. │ ├─dplyr::mutate(...)
4. │ └─dplyr:::mutate.data.frame(...)
5. │ └─dplyr:::mutate_cols(.data, dplyr_quosures(...), by)
6. │ ├─base::withCallingHandlers(...)
7. │ └─dplyr:::mutate_col(dots[[i]], data, mask, new_columns)
8. │ └─mask$eval_all_mutate(quo)
9. │ └─dplyr (local) eval()
10. └─dplyr::case_when(...)
11. └─dplyr:::case_formula_evaluate(...)

12. ├─base::withCallingHandlers(...)
    

13. └─rlang::eval_tidy(pair$rhs, env = default_env)
    

[kellijohnson-NOAA]

Users should not have to specify arguments that have default arguments. There is a default for every argument of convert_output() but the function doesn't work. And, the error message was not super helpful for someone that is new.

output <- convert_output(output_file = "report.sso")
Error in if (model %in% c("ss3", "SS3")) { : argument is of length zero

[BenWilliams-NOAA]

If one tries to use a docx format I'm getting an error that File template.docx not found in resource path and I do not see the template in the inst folder.