Organizing Functions and Major Changes #112
Description
*Preliminary list for review
General
- @Schiano-NOAA Review unnecessary arguments @ end
- @sbreitbart-NOAA Organize arguments in function based on priority Restructure argument order for all functions #81
- Set defaults or required in place of NULL where applicable
- @sbreitbart-NOAA Substitute cli in interface for messages and such throughout package (Check)
- @Schiano-NOAA Update README
- @sbreitbart-NOAA Add examples to README -- Sam did this when updating the README
- @sbreitbart-NOAA Add more helpful error messages to assist users in debugging/understanding what's going on
- @Schiano-NOAA Look at Ben’s code -- follow up in coworking
- Change end_year default to current year Change end_year default #122
- Choose a plot and a table that will contain all of the documentation that every other plot will inherit. For example, all tables inherit args from table_landings and all figures inherit args from plot_recruitment (for end)
- Plot: @sbreitbart-NOAA suggests plot_biomass or plot_spawning_biomass because they have the most arguments (notably, ref_line and ref_point, which aren't covered in plot_recruitment, which is the plot from which the rest inherit their args)
- Table: @sbreitbart-NOAA isn't sure, but is leaning towards table_bnc. Rationale: There are only 3 tables, all with the same args except for those associated with units. Indices has no units args; landings has one general arg (unit_label); bnc has three specific args (biomass_unit_label, catch_unit_label, sb_unit_label). It's probably easier for the user to see a simple unit_label when they're making one plot at a time, but if they're using save_all_plots() (which I'm guessing will be used frequently compared to the individual plots), then they'll need arguments with names that differentiate the unit types. In that case, I think we should consider giving each plot's unit-related argument a name that reflects the specific plot so that it can be easily inherited or copied into save_all_plots(). That would mean table_bnc would be the optimal plot here.
exp_all_figs_tables
- consider changing function name
- prioritize arguments
- remove any lists and set a default in argument
- set defaults for ALL arguments
export_rda
- rename
finalargument to x or object - adjust so table or figure goes to respective table or figure folder (according to new formatting)
- Set defaults/required
write_captions
- set defaults/required
For now, let's leave be all of the plotting and table functions. Since we might completely change their structure, I don't want to end up doing duplicate work. I think as we make adjustments to the functions after we agree upon the one, then we just keep in mind these concepts as we modify the code.
all figures/tables
- Add more info to summarize and join fxns to reduce unnecessary messages/warnings in console
- Think about making separate functions to calculate ref_line, ref_pt, etc.
key quantities
quantities are calc'd in write_captions*
- @Schiano-NOAA spr.min, max still aren't coming out right
- @Schiano-NOAA Natural Mortality at age plot
- Downloaded asar@cleanup-pkg to test out how new converter affects dataset
- Still having issues creating an m dataset; as written in the issue, this persists (for bsb): BAM should use a.series, probably, but bsb has only age 0 for that module
- @sbreitbart-NOAA Ensure other key quantities accurate and updated
- Take care of these three related issues:
- [ ] Catch composition plot #69
- [ ] natural mortality (m) at age plot #67
- [ ] Biomass plot: make sure reference point is not plotted as a part of the graph but just the line #95