Package: stockplotr 0.12.1.9000

Samantha Schiano

stockplotr: Tables and Figures for Stock Assessments

Creates exploratory and finished tables and figures for stock assessment documents from U.S. stock assessment model outputs. This packages addresses parts of the stock assessment workflow that interprets outputs of stock assessment models as well as allows the analyst to create report ready tables and figures, reducing the need to create their own and format then when adding into a report. This package is intended to be used in conjuction with 'asar', a partially automated template for writing various stock assessment reports. Throughout development, we will be creating a set of standardized figures and tables for a stock assessment report, developing functions to produce a variety of diagonostic plots, and other helpful materials. The advantage of using this package over others is that it applies to a range of stock assessment model outputs and standardizes them.

Authors:Samantha Schiano [aut, cre], Sophie Breitbart [aut, ctb], Steve Saul [aut], Kelli Johnson [ctb], Megumi Oshima [ctb]

stockplotr_0.12.1.9000.tar.gz
stockplotr_0.12.1.9000.zip(r-4.7)stockplotr_0.12.1.9000.zip(r-4.6)stockplotr_0.12.1.9000.zip(r-4.5)
stockplotr_0.12.1.9000.tgz(r-4.6-any)stockplotr_0.12.1.9000.tgz(r-4.5-any)
stockplotr_0.12.1.9000.tar.gz(r-4.7-any)stockplotr_0.12.1.9000.tar.gz(r-4.6-any)
stockplotr_0.12.1.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
stockplotr/json (API)

# Install 'stockplotr' in R:
install.packages('stockplotr', repos = c('https://noaa-fisheries-integrated-toolbox.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/nmfs-ost/stockplotr/issues

Datasets:

On CRAN:

Conda:

6.74 score 19 stars 13 scripts 30 exports 118 dependencies

Last updated from:511223e507. Checks:7 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64WARNING644
source / vignettesOK276
linux-release-x86_64WARNING466
macos-release-arm64WARNING664
macos-oldrel-arm64WARNING525
windows-develWARNING722
windows-releaseWARNING788
windows-oldrelWARNING725
wasm-releaseOK175

Exports:add_themeconvert_outputcreate_latex_tablecreate_rdaexport_rdaextract_caps_alttextfilter_datahtml_all_figs_tablesplot_aaplot_abundance_at_ageplot_biomassplot_biomass_at_ageplot_catch_compplot_fishing_mortalityplot_indexplot_landingsplot_natural_mortalityplot_obsvpredplot_recruitmentplot_recruitment_deviationsplot_spawning_biomassplot_stock_recruitmentplot_timeseriesprocess_dataprocess_tablereference_linesave_all_plotstable_indextable_landingstheme_noaa

Dependencies:askpassbase64encbigDbitbit64bitopsbslibcachemclicliprcodetoolscommonmarkcpp11crayoncurldata.tablediagramdigestdplyrevaluatefarverfastmapflextablefontawesomefontBitstreamVerafontLiberationfontquiverforcatsfsfuturefuture.applygdtoolsgenericsggplot2globalsgluegridExtragtgtablehighrhmshtmltoolshtmlwidgetshttrisobandjquerylibjsonlitejuicyjuicekableExtraKernSmoothknitrlabelinglatticelavalifecyclelistenvlitedownmagrittrmarkdownMatrixmemoisemimenaniarnormnumDerivofficeropensslparallellypillarpkgconfigplyrprettyunitsprodlimprogressprogressrpurrrR6raggrappdirsRColorBrewerRcppreactablereactRreadrrlangrmarkdownrstudioapiS7sassscalesshapeSQUAREMstringistringrsurvivalsvglitesyssystemfontstextshapingtibbletidyrtidyselecttinytextzdbUpSetRutf8uuidV8vctrsviridisviridisLitevisdatvroomwithrxfunxml2yamlzip

Frequently Asked Questions (FAQs)
Captions and alternative text (alt text) | How are captions and alt text constructed? | How can I alter the captions and/or alt text? | If I recreate a figure or table, will its caption and/or alt text be updated/overwritten? | How can I change or update captions and alt text? | Individual figures/tables (e.g., plot_biomass()) | All available figures and tables (e.g., save_all_plots())
Rendered fromfaqs.Rmdusingknitr::rmarkdown

Last update: 2026-06-30
Started: 2026-05-08

Standardizing Assessment Model Output
Background | Set up and format | Naming Conventions | Final Formatting | Helpful Functions to Manipulate Data
Rendered fromconvert_output_details.Rmdusingknitr::rmarkdown

Last update: 2026-05-18
Started: 2025-12-31

How captions and alternative text are generated
Templates | Calculating and exporting captions and alternative text | Connecting the tables & figures with the captions & alternative text | Expected outcomes | Single plot functions | Multi-plot functions
Rendered fromhow-caps-alttext-are-made.Rmdusingknitr::rmarkdown

Last update: 2026-03-31
Started: 2025-03-18

Readme and manuals

Help Manual

Help pageTopics
Add NOAA formatting to figure or tableadd_theme
Create loop to test for differences in column valuescheck_label_differences
Convert Outputconvert_output
Create the rda package for a plot or tablecreate_latex_table
Create the rda package for a plot or tablecreate_rda
SS3 Example dataexample_data
Export updated key quantities templateexport_kqs
Export a figure or table to rdaexport_rda
Extract captions and alternative textsextract_caps_alttext
Substitute key quantities' values into templatefill_in_kqs
Filter data for input into aesthetics for ggplot2filter_data
Make an html file with all figures and tableshtml_all_figs_tables
Insert key quantities into the captions and alternative text fileinsert_kqs
Rename columns and merge estimate and uncertainty columns for table presentationmerge_error
Create "at-age" plotplot_aa
Plot Abundance at Ageplot_abundance_at_age
Plot Total Biomassplot_biomass
Plot Total Biomass at Age (BAA)plot_biomass_at_age
Plot catch compositionplot_catch_comp
Create plot with errorplot_error
Plot fishing mortality timeseriesplot_fishing_mortality
Plot Index of Abundanceplot_index
Plot observed landingsplot_landings
Plot natural mortality (M) at ageplot_natural_mortality
Plot observed vs. predicted dataplot_obsvpred
Plot Recruitmentplot_recruitment
Plot recruitment deviationsplot_recruitment_deviations
Plot spawning biomass (SB)plot_spawning_biomass
Plot Stock Recruit Relationshipplot_stock_recruitment
Plot time series trendsplot_timeseries
Processing for figuresprocess_data
Processing for tablesprocess_table
Preformatted reference linereference_line
Export all figures and tablessave_all_plots
Index of abundance tabletable_index
Landed catch by fleet and year tabletable_landings
Add NOAA theming to ggplot2 object. The palette is from the 'viridis' package, which contains palettes distinguishable by those with color vision deficiency.theme_noaa