Introduction | Assessments | Age-structured assessment and FLBRP | SPiCT | JABBA | Time series | Kobe phase plot | Production functions | Fits to the data | Residuals | Process residuals | Retrospective analysis | Hindcast cross-validation | Priors and posteriors
This package is hidden from search results because it is not hosted in the universe of the upstream owner
lauriekell. To fix this you can add URL: https://flr.r-universe.dev/mpb to the package DESCRIPTION file. See also theR-universe documentation.Package: mpb 3.5.4
Laurence Kell
mpb: Management Procedures
mpb is an R package for running and simulation testing biomass based stock assessment models.
Authors:
mpb_3.5.4.tar.gz
mpb_3.5.4.zip(r-4.7-any)mpb_3.5.4.zip(r-4.6-any)mpb_3.5.4.zip(r-4.5-any)
mpb_3.5.4.tgz(r-4.6-any)
mpb_3.5.4.tar.gz(r-4.7-any)mpb_3.5.4.tar.gz(r-4.6-any)
mpb_3.5.4.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
mpb/json (API)
| # Install 'mpb' in R: |
| install.packages('mpb', repos = c('https://flr.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/lauriekell/mpb/issues
Last updated from:e40abde185. Checks:7 ERROR, 1 FAIL, 1 OK. Indexed: no.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | ERROR | 172 | ||
| source / vignettes | ERROR | 290 | ||
| linux-release | ERROR | 199 | ||
| macos-release | ERROR | 160 | ||
| macos-oldrel | FAIL | 86 | ||
| windows-devel | ERROR | 164 | ||
| windows-release | ERROR | 165 | ||
| windows-oldrel | ERROR | 165 | ||
| wasm-release | OK | 114 |
Exports:aspicaspicsbiodynbiodyn2cmpbmsybootchkIterscmpACFcmpAssesscmpFitcmpHindcastcmpHindcastDFcmpKobecmpMASEcmpPriorscmpProcesscmpProductioncmpQQcmpRetrocmpRunscmpStatuscmpTScontrolcontrol<-controlFndiagsdiagsFnfapexAgefeasiblefitflbrp2cmpfmsyfnProfilefwdharvesthcrhcrParamhrateis.aspicis.biodynjabba2biodynjabba2cmpjkKkobemfclGrwmixnormmohnsRhomseBiodynmsymvnnllnmcFnpplotplotCcfplotEqlplotHcrplotIndexplotIndexResidualplotJackplotMSEfnplotPEplotProductionplotSpictACFplotSpictFitplotSpictHindcastplotSpictKobeplotSpictPriorsplotSpictProcessplotSpictProductionplotSpictQQplotSpictRetroplotSpictRunsplotSpictStatusplotSpictTSprdResidproductionprofileFnrandFnrandJackFnreadAspicrebuildTimerecoverBDrefptsrefptSDresamplerunsTestsetControl<-setMPsetParams<-simspict2biodynspict2cmpspict2FLQuantsspictInpspictParspictPrdspictPriorsspictTStactimeSerieswriteAspicxval
Dependencies:clicowplotcpp11data.tablefarverFLBRPFLCoreggplot2ggplotFLggrepelgluegridExtragtableisobanditeratorslabelinglatticelifecyclemagrittrMASSMatrixpatchworkplyrR6RColorBrewerRcppreshaperlangS7scalesstringistringrvctrsviridisLitewithr
Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.
Comparing assessment methods with common ggplot2/ggplotFL plots
Last update: 2026-10-15
Started: 2026-10-15
Fitting SPiCT with priors derived from an FLBRP
Introduction | Stock | Equilibrium reference points | Priors from the FLBRP | SPiCT input | Fit | Convergence | Prior and posterior | Residuals | Retrospective analysis | SPiCT compared with the FLBRP | Comparison figures | Trajectories | Production functions | Process error | Coercing to biodyn | Recovery from 0.3BMSY at zero catch | Notes | Session information | References
Last update: 2026-10-15
Started: 2026-10-15
ggplot2 and ggplotFL plots for SPiCT fits
Introduction | Fit | Time series | As FLQuants | Kobe phase plot | Production function | Model fit | Residuals | One-step-ahead residuals | Process residuals | Retrospective analysis | Hindcast cross-validation | Priors and posteriors | References
Last update: 2026-10-15
Started: 2026-10-15
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Returns length age data from Multifan-CL as a list with four data frames | alkMFCL |
| as("biodyn", "FLStock") | as |
| aspic constructor | aspic aspic,ANY,ANY-method aspic,ANY-method aspic,character-method aspic,data.frame-method aspic,missing-method aspic-method |
| ASPIC Biomass Dynamic Model Class | aspic,biodyn,FLQuant-method aspic,biodyn,FLQuants,FLQuant-method aspic,biodyn,FLQuants-method aspic,character,missing,FLQuant-method aspic,character,missing-method aspic,data.frame,missing,FLQuant-method aspic,data.frame,missing-method aspic,FLQuant-method aspic,FLStock,missing-method aspic,missing,missing,FLQuant-method aspic,missing,missing-method aspic-class catch,aspic-method catch<- |
| aspics | aspics aspics,ANY-method aspics,aspic-method aspics,character-method aspics,list-method aspics,missing-method aspics-method aspics-methods |
| aspics a class that contains a list of ASPIC biomass dynamic stock assessment model classes | aspics-class |
| biodyn constructor | biodyn |
| biodyn class | biodyn,character,FLPar-method biodyn,character,missing-method biodyn,factor,FLPar-method biodyn,factor,missing-method biodyn,FLQuant,FLPar-method biodyn,FLQuant,missing-method biodyn,FLStock,FLPar-method biodyn,FLStock,missing-method biodyn,missing,FLPar-method biodyn,missing,missing-method biodyn-class |
| Create biodyn Object from FLPar Parameters | biodyn,FLPar,missing-method |
| Convert a biodyn to a cmpAssess | biodyn2cmp |
| biodyns creates a list of biodyn objects | biodyns,biodyn-method |
| fit | boot fit,aspic,missing-method |
| boot, Bootstraps biodyn. | boot,aspic-method boot,aspics-method boot,biodyn-method boot-method |
| Autocorrelation of residuals for one or more assessments | cmpACF |
| Common assessment summary for comparing methods | cmpAssess |
| Observed and fitted values of one or more assessments | cmpFit |
| Hindcast cross-validation of one or more assessments | cmpHindcast |
| Hindcast predictions from retrospective peels | cmpHindcastDF |
| Kobe phase plot for one or more assessments | cmpKobe |
| Mean absolute scaled error | cmpMASE |
| Prior and posterior densities for one or more assessments | cmpPriors |
| Process residuals with runs tests for one or more assessments | cmpProcess |
| Production functions of one or more assessments | cmpProduction |
| Normal QQ plot of residuals for one or more assessments | cmpQQ |
| Retrospective analysis of one or more assessments | cmpRetro |
| Observation residuals with runs tests for one or more assessments | cmpRuns |
| Stock status of one or more assessments | cmpStatus |
| Time series of one or more assessments | cmpTS |
| control | control,biodyn-method |
| control<- | control<-,biodyn,FLPar-method |
| controlFn | controlFn |
| params | diags setParams<-,aspic,data.frame-method setParams<-,biodyn,data.frame-method setParams<-,biodyn,FLPar-method setParams<-,biodyn,FLQuant-method setParams<-,biodyn,FLQuants-method |
| fit | diagsFn fit,aspics,missing-method fit,biodyn,FLQuantJK-method fit,biodyn,FLQuantJKs-method fit,FLPar,FLQuant-method |
| mng | aspic,missing biodyn,missing fapexAge timeSeries timeSeries,aspic,missing-method timeSeries,biodyn,missing-method timeSeries,FLStock,FLBRP-method timeSeries,FLStocks,FLBRP-method timeSeries,FLStocks,FLBRPs-method timeSeries-method |
| feasible | feasible feasible,biodyn,missing-method feasible,data.frame,FLQuant-method feasible,FLPar,FLQuant-method |
| fit | fit fit,aspic-method fit,aspics-method fit,biodyn,FLQuant-method fit,biodyn,FLQuants-method |
| -mcmc 100000 -mcsave 100' | fitPella |
| Convert an age-structured assessment (FLStock and FLBRP) to a cmpAssess | flbrp2cmp |
| Class FLQuantJKs | FLQuantJKs FLQuantJKs,ANY-method FLQuantJKs,FLQuantJKs-method FLQuantJKs,list-method FLQuantJKs,missing-method FLQuantJKs-class FLQuantJKs-methods |
| fnProfile | fnProfile |
| fwd | fwd,biodyn,FLQuants,missing fwd,biodyn,FLQuants-method fwd,biodyn,missing,missing fwd,biodyn,missing,missing-method fwd,biodyn,missing-method fwd,FLPar,missing,missing fwd,FLPar,missing-method fwd-method |
| harvest | harvest harvest,aspic-method harvest,biodyn,missing-method harvest,biodyn-method |
| hcr | hcr,biodyn,FLPar-method hcr,biodyn-method hcr,FLStock,FLBRP-method |
| hcrParam | hcrParam |
| hrate | hrate hrate,aspic-method hrate,biodyn-method |
| is.aspic | is.aspic |
| is.biodyn | is.biodyn |
| Coerce a JABBA fit to a biodyn | jabba2biodyn |
| Convert a JABBA fit to a cmpAssess | jabba2cmp |
| jk | chkIters jk jk,aspic-method jk,biodyn,FLQuant-method jk,biodyn,FLQuants-method |
| Carrying capacity | K |
| kobe | kobe kobe,biodyn,missing-method kobe,biodyns,ANY-method kobe,biodyns,missing-method |
| Returns von Bertalannfy growth parameters from Multifan-CL | mfclGrw |
| mixnorm | mixnorm |
| Mohn's rho | mohnsRho |
| mseBiodyn | mse mseBiodyn |
| mvn | mvn |
| nll | nll,biodyn,FLQuant,missing-method nll,biodyn,FLQuants,missing-method nll,FLQuant,FLQuant,FLPar-method nll,FLQuant,FLQuants,FLPar-method |
| nmc | nmcFn |
| om | om |
| plot | plot,aspics,missing plot,biodyn,missing-method plot,biodyns,missing-method plotCcf,biodyns,missing-method plotCcf,FLQuants-method plotEql,biodyn,FLQuant plotIndex,biodyn |
| plotEql | plotEql,biodyn,missing-method |
| plotHcr | plotHcr,biodyn-method plotHcr-method |
| plotIndex | plotIndex,aspic,missing-method plotIndex,biodyn,missing-method plotIndex,FLQuants,missing-method plotIndex,FLQuants-method |
| plotIndexResidual | plotIndexResidual,aspic,missing-method plotIndexResidual,biodyn,missing-method plotIndexResidual,FLQuants,missing-method plotIndexResidual,FLQuants-method |
| plotJack | plotJack |
| plotMSE | harvest'=catch(om)/stock(om)%/%(brp@refpts['msy','yield']/brp@refpts['msy','biomass']), plotMSE,biodyn,FLStock,FLBRP-method plotMSEfn |
| plot aspics,missing plotIndex aspic plotIndex aspics | plotProduction plotProduction,biodyn,FLBRP-method plotProduction,biodyn,FLQuant-method plotProduction,biodyn,missing-method plotProduction,biodyns,missing-method |
| Plots of a SPiCT fit | plotSpict plotSpictACF plotSpictFit plotSpictHindcast plotSpictKobe plotSpictPriors plotSpictProcess plotSpictProduction plotSpictQQ plotSpictRetro plotSpictRuns plotSpictStatus plotSpictTS |
| production | production,biodyn,FLQuant production,biodyn-method production,FLStock,missing productionFn |
| profile | profileFn |
| rand | numeric,biodyn,biodyn-method numeric,FLPar,FLPar-method numeric,FLQuant,FLQuant-method rand, rand,numeric,biodyn,biodyn-method rand,numeric,biodyn-method rand,numeric,FLPar,FLPar-method rand,numeric,FLQuant,FLQuant-method rand-method randFn |
| randJack | randJack,numeric,biodyn,biodyn-method randJack,numeric,biodyn-method randJack,numeric,FLPar,FLPar-method randJack,numeric,FLQuant,FLQuant-method randJack-method randJackFn |
| readAspic | readAspic readAspic,character-method |
| Calculate Rebuild Trajectories | rebuildTime |
| msy reference points | bmsy bmsy,aspic-method bmsy,biodyn-method bmsy,FLPar-method bmsy-method fmsy fmsy,aspic-method fmsy,biodyn-method fmsy,FLPar-method fmsy-method msy msy,aspic,missing-method msy,aspic-method msy,biodyn-method msy,FLPar-method msy-method refpts,aspic,missing-method refpts,biodyn,missing-method refpts,character,FLPar-method refpts,factor,FLPar-method refpts,FLPar,missing-method refptSD refptSD,biodyn,missing-method refptSD,character,FLPar-method refptSD,factor,FLPar-method |
| resample | resample,FLPar-method resample,FLQuant-method |
| Runs test on residuals | runsTest |
| setControl<- | setControl<-,aspic,FLPar-method setControl<-,biodyn,FLPar-method setControl<-,biodyn,FLQuant-method setControl<-,biodyn,FLQuants-method |
| setParams<- | biodyn,biodyn,data.frame-method biodyn,biodyn,FLQuant-method biodyn,biodyn,FLQuants-method biodyn,FLPar-method setParams<- setParams<-, |
| sim | sim,FLStock,ANY-method sim,missing,missing-method sim-method |
| SPiCT helpers: priors from an FLBRP, input from an FLStock, coercion to biodyn, process-error diagnostics and recovery at zero catch | plotPE prdResid recoverBD spict-helpers spict2biodyn spictInp spictPar spictPrd spictPriors |
| Convert a SPiCT fit to a cmpAssess | spict2cmp |
| Coerce a SPiCT fit to FLQuants | spict2FLQuants |
| Time series of a SPiCT fit as a data.frame | spictTS |
| tac , | tac tac,biodyn-method tac-method |
| ts | timeSeries,FLStock,FLPar-method ts,biodyn,FLPar-method ts,FLStock,FLBRP-method ts,FLStock,FLPar-method ts,FLStocks,FLBRP-method ts,FLStocks,FLBRPs-method |
| writeAspic | writeAspic writeAspic,aspic-method |
| xval | xval,biodyn,ANY-method xval,biodyn-method xval-method |
| xval | xval,biodyn,missing-method |