Short trend install

[BBeltz1]

Installed short term trend in the following plot functions:

• plot_SAV.R
• plot_aggregate_biomass.R*
• plot_bottom_temp.R*
• plot_bottom_temp_comp.R
• plot_bottom_temp_glorys.R
• plot_ches_bay_wq.R
• plot_cold_pool.R
• plot_comdat.R
• plot_exp_n.R
• plot_forage_anomaly.R
• plot_forage_index.R
• plot_function_template.R
• plot_gom_salmon.R
• plot_heatwave.R
• plot_hudson_river_flow.R
• plot_long_term_sst.R
• plot_mab_inshore_survey.R
• plot_mass_inshore_survey.R*
• plot_recdat.R
• plot_seabird_ne.R
• plot_seasonal_oisst_anom.R
• plot_spawn_timing.R*
• plot_species_dist.R*
• plot_storminess.R
• plot_survey_shannon.R*
• plot_trans_dates.R
• plot_zoo_abundance_anom.R*
• plot_zoo_diversity.R*
• plot_zoo_strat_abun.R*

*Datasets have missing years for some variables, which prevent short term trend analysis. These datasets will be corrected when updated for 2025. Plot functions have an added safeguard and will work as normal so long as variable n is not specified.

[andybeet]

All looks good other than plot_mab_inshore_survey. Seems like all fits are commented out. Is there a reason for that?

[BBeltz1]

I did not comment out geom_gls, it was already commented out. So when I added geom_lm, I commented it out for consistency. I wanted to find out why geom_gls was turned off before turning either on.

[andybeet]

ok. sounds good.

Adding an additional argument, like we have done, is going to affect catalog i think. The make_rmd uses the number of arguments and/or the attributes (see here). We may need to take a look at this. Could also result in editing the attributes in each of the plot functions

[andybeet]

Also, this is just a subset of the plot functions. Is that because these are the only ones that are a line graph?

[BBeltz1]

Yes it's a subset, I wanted to prioritize this installation to the plot functions that are actively using geom_gls.