Package: jjmR 1.2020.1

Ricardo Oliveros-Ramos

jjmR: Graphics and diagnostics tools for SPRFMO's Joint Jack Mackerel model

Graphics and diagnostics tools for SPRFMO's Joint Jack Mackerel model.

Authors:Ricardo Oliveros-Ramos [cre, aut], Wencheng Lau-Medrano [aut], Giancarlo Moron [aut], Josymar Torrejon-Magallanes [aut], Niels Hintzen [aut], Enrique Ramos-Vasquez [ctb], Jim Ianelli [aut]

jjmR_1.2020.1.tar.gz
jjmR_1.2020.1.zip(r-4.7)jjmR_1.2020.1.zip(r-4.6)jjmR_1.2020.1.zip(r-4.5)
jjmR_1.2020.1.tgz(r-4.6-any)jjmR_1.2020.1.tgz(r-4.5-any)
jjmR_1.2020.1.tar.gz(r-4.7-any)jjmR_1.2020.1.tar.gz(r-4.6-any)
jjmR_1.2020.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
jjmR/json (API)

# Install 'jjmR' in R:
install.packages('jjmR', repos = c('https://sprfmo.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/sprfmo/jjmr/issues

On CRAN:

Conda:

5.13 score 3 stars 1 packages 99 scripts 86 exports 88 dependencies

Last updated from:80ca41cd88. Checks:9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK248
source / vignettesOK232
linux-release-x86_64OK239
macos-release-arm64OK145
macos-oldrel-arm64OK185
windows-develOK141
windows-releaseOK153
windows-oldrelOK149
wasm-releaseOK133

Exports:.getJjmConfig%>%annotate_cohortscalc_mohn_rhochangeNameModelcombineModelscomp_fig_heightcompareModelsdiagnosticsextr_agefits_fshextr_agefits_srvextr_catchextr_catch_cvextr_cvextr_effnextr_fished_unfishedextr_francisextr_indicesextr_kobeextr_lenfits_fshextr_meanage_fshextr_meanage_srvextr_meanlen_fshextr_q_breaksextr_q_trajectoryextr_retroextr_sel_breaksextr_sel_fshextr_sel_srvextr_srextr_survey_skillextr_wtat_fshextr_wtat_srvfacet_fig_heightfixed_bmsyget_age_fitsget_catchabilitiesget_fishing_mortalityget_index_fitsget_len_fitsget_msy_mtget_recruitsget_selectivitiesget_totalsgethgettergray_ramphas_compjjm_labeljjm_pfa_palettekobemelt_matrixplot_catch_fleetplot_comp_fitsplot_comp_ridgeplot_effnplot_fished_unfishedplot_fishery_weightplot_fit_diagnosticsplot_francisplot_historic_retroplot_indices_v2plot_kobeplot_meanstatplot_metadata_overviewplot_q_trajectoryplot_retroplot_sel_ridgeplot_selectivitiesplot_srplot_summary_sheetplot_survey_skillplot_wtatplot_wtat_cohortread_historic_retroreadExFilesreadJJMreadJJMConfigreportretrorunitrunJJMstrong_cohortstheme_jjmtidy_JJMwriteJJM

Dependencies:backportsbase64encbootbroombslibcachemclicodetoolscolorspacecowplotcpp11deldirDerivdigestdoBydplyrevaluatefarverfastmapfontawesomeforcatsforeachforecastfracdifffsgenericsggplot2ggridgesgluegridExtragtablehighrhtmltoolsicesAdviceinterpisobanditeratorsjpegjquerylibjsonliteknitrlabelinglatticelatticeExtralifecyclelmtestmagrittrMASSMatrixmemoisemicrobenchmarkmimemodelrnlmennetpatchworkPBSmodellingpillarpkgconfigpngpurrrR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenrlangrmarkdownS7sassscalesstringistringrtibbletidyrtidyselecttimeDatetinytexurcautf8vctrsviridisLitewithrxfunXMLyamlzoo

Readme and manuals

Help Manual

Help pageTopics
Create a jjm.config object.getJjmConfig
Annex diagnostic plotting helpersannex_diagnostics annotate_cohorts calc_mohn_rho comp_fig_height extr_agefits_fsh extr_agefits_srv extr_catch extr_catch_cv extr_cv extr_effn extr_fished_unfished extr_francis extr_indices extr_kobe extr_lenfits_fsh extr_meanage_fsh extr_meanage_srv extr_meanlen_fsh extr_q_breaks extr_q_trajectory extr_retro extr_sel_breaks extr_sel_fsh extr_sel_srv extr_sr extr_survey_skill extr_wtat_fsh extr_wtat_srv facet_fig_height has_comp jjm_label jjm_pfa_palette plot_catch_fleet plot_comp_fits plot_comp_ridge plot_effn plot_fished_unfished plot_fit_diagnostics plot_francis plot_historic_retro plot_indices_v2 plot_kobe plot_meanstat plot_metadata_overview plot_q_trajectory plot_retro plot_sel_ridge plot_sr plot_summary_sheet plot_survey_skill plot_wtat plot_wtat_cohort read_historic_retro strong_cohorts
Change the internal name of a modelchangeNameModel
Coerce a vector to character or numericcoerce
Combine outputscombineModels
Compare combined JJM outputscompareModels
Generate Assessment plots from single modeldiagnostics
Calculate or input a fixed Bmsy value for the jjm model Updates the msy_mt table in the jjm output with new B/Bmsy ratios.fixed_bmsy
Get fits to indicesget_age_fits
Get estimated catchability coefficientsget_catchabilities
Get fishing mortality at ageget_fishing_mortality
Get fits to indicesget_index_fits
Get fits to length compositionsget_len_fits
Get and tidy msy_my tableget_msy_mt
Get estimated recruitsget_recruits
Get and tidy selectivity-at-age ogives over time by model and fleetget_selectivities
Get total metrics (biomass, spawning biomass, and recruitment)get_totals
Add hypothesis number to a model namegeth
Get elements of a list by string matching on namegetter
Compute a gray color rampgray_ramp
Kobe plotkobe
Melt an age‐or‐length matrix into a long tibblemelt_matrix
Plot weight at age in the fisheryplot_fishery_weight
Plot selectivities by age, year, fleet, and modelplot_selectivities
Plot method for jjm.diag objectsplot.jjm.diag
Plot diagnosticsplot.jjm.diagnostics
Plot method for jjm.output objectsplot.jjm.output
Print a jjm.config objectprint.jjm.config
Print method for jjm.diag objectsprint.jjm.diag
Print method for jjm.output objectsprint.jjm.output
Print a summary of jjm.configprint.summary.jjm.config
Print method for summary.jjm.diag objectsprint.summary.jjm.diag
Print method for summary.jjm.output objectsprint.summary.jjm.output
Read external filesreadExFiles
Read a model or list of modelsreadJJM
Read dat and ctl files from disk to create a jjm.config object.readJJMConfig
Create a report from JJM outputsreport
Run a retrospective analysis diagnostic for a JJM modelretro
Fit, run, read and plot a JJM modelrunit
Run a JJM modelrunJJM
Run JJM models (default method)runJJM.default
Run JJM models for jjm.configrunJJM.jjm.config
Run JJM models for jjm.outputrunJJM.jjm.output
Summarize a jjm.config objectsummary.jjm.config
Summary method for jjm.diag objectssummary.jjm.diag
Summarize all diagnostics from a jjm runsummary.jjm.diagnostics
Summary method for jjm.output objectssummary.jjm.output
ggplot2 theme for jjmRtheme_jjm
Tidy results of JJM modeltidy_JJM
Write dat and ctl files from a JJM model stored in RwriteJJM