Package: multiStockassessment 0.4.0

multiStockassessment: Fitting Multiple State-Space Assessment Models

Fitting multiple SAM models.

Authors:Christoffer Moesgaard Albertsen [aut, cre]

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multiStockassessment.pdf |multiStockassessment.html✨
multiStockassessment/json (API)
NEWS

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

Bug tracker:https://github.com/calbertsen/multi_sam/issues

Uses libs:
  • c++– GNU Standard C++ Library v3

On CRAN:

Conda:

fisheriesfisheries-stock-assessmentstock-assessmentstockassessmentcpp

2.88 score 5 stars 5 scripts 8 exports 7 dependencies

Last updated 3 months agofrom:ede24b3312 (on shared_obs). Checks:1 OK, 8 WARNING. Indexed: yes.

TargetResultLatest binary
Doc / VignettesOKFeb 17 2025
R-4.5-win-x86_64WARNINGFeb 17 2025
R-4.5-linux-x86_64WARNINGFeb 17 2025
R-4.4-win-x86_64WARNINGFeb 17 2025
R-4.4-mac-x86_64WARNINGFeb 17 2025
R-4.4-mac-aarch64WARNINGFeb 17 2025
R-4.3-win-x86_64WARNINGFeb 17 2025
R-4.3-mac-x86_64WARNINGFeb 17 2025
R-4.3-mac-aarch64WARNINGFeb 17 2025

Exports:dataperiodplotgen2PCAholdoutmohn_CImohn_sim_CImultisam.fitread.gensuggestCorStructure

Dependencies:ellipselatticeMatrixRcppRcppEigenstockassessmentTMB

Readme and manuals

Help Manual

Help pageTopics
Add transparency to a coloraddTrans
Collect msam objectsc.msam
Catch plotcatchplot.msam
Catch Tablecatchtable.msam
Extract parameter estimates of msam objectcoef.msam
Correlation and partial correlation plot between survival processescorplot.msam
Deterministic reference pointsdeterministicReferencepoints.msam
F-at-age Tablefaytable.msam
Fbar plot for msam objectfbarplot.msam
Fbar Tablefbartable.msam
Fit plotfitplot.msam
F selectivity plotfselectivityplot.msam
Prepare allele matrix for PCA analysisgen2PCA
Calculate gradient of a functiongrad
Calculate hessian of a functionhessian
Holdout forecast for validationholdout holdout.msam
Calculate jacobian of a functionjacobian
Jitter runsjit.msam
Life expectancy plotlifeexpectancyplot.msam
SSB Tablelifeexpectancytable.msam
Forecast of a multiStockassessmentmodelforecast.msam
Model tablemodeltable.msam
Model tablemodeltable.msamset
Fit multiple SAM models with correlationsmultisam.fit
N Tablentable.msam
Parameter plotparplot.msam
Parameter plotparplot.msamset
Parameter tablepartable.msam
Function to actually do the plottingplotit.msam plotit.msamforecast
Print result from multisam.fitprint.msam
Print msam coef objectprint.msamcoef
Read genepop data filesread.gen
Recruitment plotrecplot.msam
Recruitment Tablerectable.msam
Simulate from a msam objectsimulate.msam
Stock-recruitment plotsrplot.msam
SSB plotssbplot.msam
SSB Tablessbtable.msam
Suggest correlation structuresuggestCorStructure
Summary of msam objectsummary.msam
Table helpertableit tableit.msam
TSB plottsbplot.msam
TSB Tabletsbtable.msam
Life Years lost to fishing plotyearslostplot.msam
Yield per recruit calculationypr.msam