Revamped tables#168

Merged

Schiano-NOAA merged 63 commits intomainfrom

revamped-tables

Jan 23, 2026

Commits on Jan 5, 2026

change method of way lines are applied to rec devs
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Apply viridis palette to figures (#135)

sbreitbart-NOAA
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Revamped sr, aa plots, recruitment ts, and more (#130)

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fix spelling errors
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change x_n_breaks function to instead work with scales::pretty_breaks to better fit axes for all functions
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adjust caption and alt text depending on what the graph is showing if predicted recruitment is present
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open geom options for plots; adjust text size in theme; move error cloud under line plot
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replace axis_breaks to use pretty breaks in scales package and set ref line as subscript in annotation in ggplot2::annotate for reference line label
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fix issue with biomass plot where if group or facet is used (or not used) then any extra occurrances in the data are included resulting in an incorrect plot
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adjust to all instead of all_of for check. Setting now so plot does not fail when the group doesn't exist
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fix error with biomass plot and grouping/faceting variables
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update prepare_data to summarize data even when group is selected in the case there is only one group and the data gets repeated
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update plot_biomass to summarize ret, sel, and dead biomass from ss3 models when it's present
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update save_all_plots and work on tests
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update documentation; remove non-revamped plots and tables for release to package; fix tests and comment out unused tests
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updates to plot_landings and adjustment to utils
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update documentation
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update stockplotr tests
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minor changes so fxn works with bam and incorporate && in if statements
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fix error in using wrong df in process_data fxn
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Add process_data to plots (#153)
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Hotfix revamped plots round 2 (#154)
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create new utils file and uncomment landings tbl
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add foundation of making latex table
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Update create_table() to fix bugs producing latex-based table from data frame

sbreitbart-NOAA
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Update name of latex table-producing function (create_latex_table), arguments, code, and documentation

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Update export_rda() to be able to intake a latex table as an arg; update table_landings() to create a latex-based table and add it to the rda; update documentation

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Uncomment code in table_landings() that creates a table (though it's not working as expected)

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Remove extra line breaks from latex tables

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Start setting up table_landings() for filter_data()/process_data() workflow

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Continue developing landings table, and basic workflow needed for all tables

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Finish first draft of landings table; update documentation

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Update documentation

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Develop plot_landings() further to work for bam and ss3 data

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Fix save_all_plots except for fishing.mortality plot

sbreitbart-NOAA
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Uncomment code that exports all figures in save_all_plots(); comment out code causing issues related to missing alt text for fishing mortality plot

sbreitbart-NOAA
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Update save_all_plots() test

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Fix example error; update documentation

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Add row in the alt text/captions csv for new figure: relative fishing mortality

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add 'gt' to DESCRIPTION's Imports; remove flextable

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Add theme for gt tables

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Update table_landings() so that fleets are ordered properly, with a mix of numerically and alphabetically

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Round landings and uncertainty cols in table_landings()

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Select first label if provided >1, in table_landings()

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Commits on Jan 6, 2026

make adjustments to table_landings
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Commits on Jan 8, 2026

Commits on Jan 12, 2026

continue modifying function to allow customaizaiton -- honestly forgot to commit all day
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Commits on Jan 13, 2026

changes to issues with NAs in error
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