Package: JABBA3 3.0.0.9000

JABBA3: Bayesian State-Space Surplus Production Models in 'RTMB'

The next generation of 'JABBA' (Just Another Bayesian Biomass Assessment), now with hyperdrive. Fits Bayesian state-space surplus production models in 'RTMB' in well under a second, so you can spend less time waiting for chains to converge and more time arguing about priors. Full posteriors are available through 'tmbstan' (NUTS) for those who still like their MCMC. Inputs and outputs follow 'FLR' conventions for use with 'ggplotFL', 'FLRef' and 'mse', and helpers convert classic 'JABBA' inputs so old scripts survive the jump to hyperspace.

Authors:Henning Winker [aut, cre]

JABBA3_3.0.0.9000.tar.gz
JABBA3_3.0.0.9000.zip(r-4.7-any)JABBA3_3.0.0.9000.zip(r-4.6-any)JABBA3_3.0.0.9000.zip(r-4.5-any)
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JABBA3_3.0.0.9000.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
JABBA3/json (API)

# Install 'JABBA3' in R:
install.packages('JABBA3', repos = c('https://henning-winker.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/henning-winker/jabba3/issues

Datasets:
  • iccat - Iccat example stocks
  • jara_examples - Example data for the data-exploration (JARA) models

On CRAN:

Conda:

2.00 score 1 stars 6 scripts 111 exports 24 dependencies

Last updated from:dbc9d7057b. Checks:6 ERROR, 2 OK, 1 WARNING. Indexed: yes.

TargetResultTimeFilesSyslog
linux-develERROR244
source / vignettesOK244
linux-releaseWARNING182
macos-releaseERROR230
macos-oldrelERROR185
windows-develERROR157
windows-releaseERROR168
windows-oldrelERROR151
wasm-releaseOK111

Exports:flr2jbdatjabba3jabba3_infojabbaplot3jb3_alignjb3_bpriorjb3_catchfilljb3_contractionjb3_convergencejb3_datajb3_data_jabbajb3_diagsjb3_drawsjb3_ensemblejb3_fill_tablejb3_flparjb3_flqsjb3_FLStockRjb3_fmsy2rjb3_fwdjb3_fwdtablejb3_hcrjb3_hindcastjb3_jointindexjb3_kobematrixjb3_kobematrix_gfcmjb3_kobematrix_icesjb3_kobematrix_iotcjb3_lesliejb3_modeljb3_noisejb3_nuts_diagsjb3_nuts_essjb3_osajb3_partablejb3_priorsjb3_projectjb3_projtablejb3_qtablejb3_r2fmsyjb3_retrojb3_rho_gtjb3_rho_tablejb3_runsjb3_sel5jb3_selexjb3_splitindexjb3_tier1jb3_tier2jb3_trendjb3_tstablejb3_weightsjb3_workflowjb3colsjbcatch2flqjbdat2flrjbidx2FLIndicesjbinput2jabba3jbplot_advicejbplot_alljbplot_auxfitsjbplot_biplotjbplot_bpriorjbplot_catchjbplot_catcherrorjbplot_catchfilljbplot_contractionjbplot_criskjbplot_datajbplot_ebsb_statusjbplot_energyjbplot_ensemblejbplot_fitsjbplot_hcrjbplot_hcxvaljbplot_indexcorjbplot_indicesjbplot_jointindexjbplot_kobejbplot_kobematrixjbplot_mcmcacfjbplot_mcmcdensjbplot_noisejbplot_nutsjbplot_nutsdiagsjbplot_pairsjbplot_ppcjbplot_priorpostjbplot_priorpost_trjjbplot_procdevjbplot_productionjbplot_projectionjbplot_qjbplot_rankjbplot_residualsjbplot_retrojbplot_rhatjbplot_runsjbplot_selexjbplot_spdiagsjbplot_spdynjbplot_spphasejbplot_stdresidualsjbplot_stepsjbplot_summaryjbplot_tracejbplot_trendjbplot_trjscale_x_yearspictinp2jabba3theme_jabba3

Dependencies:clicpp11farverggplot2gluegtableisobandlabelinglatticelifecycleMASSMatrixR6RColorBrewerRcppRcppEigenrlangRTMBS7scalesTMBvctrsviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
Convert FLR inputs back to classic JABBA data framesflr2jbdat
Iccat example stocks (from JABBA)iccat
Fit a JABBA3 modeljabba3
Engines and status of this JABBA3 installationjabba3_info
JABBA3 summary plot with selectable panelsjabbaplot3 plot.jabba3
Example data for the data-exploration (JARA) modelsjara_examples
Alignment of the input seriesjb3_align
Status priors (JABBA b.prior)jb3_bprior
Reconstruct catch series through missing yearsjb3_catchfill
Prior-posterior contraction and shiftjb3_contraction
Convergence checksjb3_convergence
Assessment data for JABBA3jb3_data
Convert classic JABBA inputsjb3_data_jabba
Residual diagnostics: JABBA set + SPiCT setjb3_diags
Pseudo-posterior draws at the modejb3_draws
Weighted ensemble of fitsjb3_ensemble
Original series with missing values filledjb3_fill_table
FLR outputsjb3_flpar jb3_flqs
Convert a JABBA3 fit to an FLStockRjb3_FLStockR
Convert between Fmsy and the surplus production r for a given shapejb3_fmsy2r jb3_r2fmsy
Forward projections with a forecast control (fwdctrl)jb3_fwd
Fishing opportunities tablejb3_fwdtable
Hockey-stick harvest control rulejb3_hcr
Hindcast cross-validationjb3_hindcast
Joint index from a trend fitjb3_jointindex
Kobe II strategy matrixjb3_kobematrix
Kobe II strategy matrix, GFCM formatjb3_kobematrix_gfcm jb3_kobematrix_ices
Kobe II strategy matrix, IOTC formatjb3_kobematrix_iotc
Intrinsic rate of increase and generation time from a Leslie matrixjb3_leslie
Model structure for JABBA3jb3_model
Observation and process noise of indicesjb3_noise
NUTS convergence summaryjb3_nuts_diags
Effective sample size of the derived statesjb3_nuts_ess
One-step-ahead residualsjb3_osa
Parameter and reference point tablejb3_partable
Priors for JABBA3jb3_priors
Projectionsjb3_project
Projection tablesjb3_projtable
Catchability relative to the reference indexjb3_qtable
Retrospective analysisjb3_retro
Life-history guidance for the AR(1) persistence of process errorjb3_rho_gt jb3_rho_table
Runs test with three-sigma control limitsjb3_runs
JABBA 5-parameter selectivityjb3_sel5
Selex inputs from length-based selectivity: EB/SB curves for the spawning-biomass statejb3_selex
Split an index at a change in vessel, gear or methodjb3_splitindex
State-space trend models for abundance indices (JARA)jb3_trend
Time series table of estimated quantitiesjb3_tstable
Ensemble weights from model diagnosticsjb3_weights
BioProcDyn workflows: Tier 1, Tier 2 and Selexjb3_tier1 jb3_tier2 jb3_workflow
Colours for runs, scenarios or peels (r4ss rule, as JAGG and ss3diags)jb3cols
Convert classic JABBA data frames to FLR objectsjbcatch2flq jbdat2flr jbidx2FLIndices
Convert a JABBA input object to JABBA3jbinput2jabba3
Advice plotjbplot_advice
Save the standard plot setjbplot_all
Fits to the auxiliary datajbplot_auxfits
Stock status biplotjbplot_biplot
Status priors: prior against posteriorjbplot_bprior
Catch: observed and estimatedjbplot_catch
Catch error: observed and estimated catchjbplot_catcherror
Plot prior-posterior contraction against shiftjbplot_contraction
Catch risk curvesjbplot_crisk
Data overviewjbplot_data
Selex: spawning and exploitable biomass statusjbplot_ebsb_status
Ensemble of fitsjbplot_ensemble
Fits to the abundance indicesjbplot_fits
Harvest control rule plotjbplot_hcr
Hindcast cross-validation plot with MASEjbplot_hcxval
Pairwise correlation of abundance indicesjbplot_indexcor
Abundance indices with observation errorjbplot_indices
Kobe plotjbplot_kobe
Plot a Kobe II strategy matrixjbplot_kobematrix
Plot observation and process noise of indicesjbplot_noise
NUTS diagnostic plotsjbplot_energy jbplot_mcmcacf jbplot_mcmcdens jbplot_nuts jbplot_nutsdiags jbplot_pairs jbplot_rank jbplot_rhat jbplot_trace
Posterior predictive checkjbplot_ppc
Prior and posterior distributionsjbplot_priorpost
Prior predictive against posteriorjbplot_priorpost_trj
Process error deviations and process SDjbplot_procdev
Projection plotjbplot_projection
Distribution of catchability relative to the reference indexjbplot_q
Index residuals by yearjbplot_residuals
Retrospective plot with Mohn's rhojbplot_retro
Runs testjbplot_runs
Selectivity and EB/SB curvesjbplot_selex
SPiCT-style residual diagnosticsjbplot_spdiags
Surplus production phase and dynamics plotsjbplot_production jbplot_spdyn jbplot_spphase
Standardised residualsjbplot_stdresiduals
Workflow comparisonjbplot_steps
Summary of one or several fitsjbplot_summary
Trend plotsjbplot_catchfill jbplot_jointindex jbplot_trend
Trajectories with credible intervalsjbplot_trj
Integer year axisscale_x_year
Convert a SPiCT input list to JABBA3spictinp2jabba3
JABBA3 ggplot themetheme_jabba3