Package: FLfse 1.0.2

Simon Fischer

FLfse: Fisheries Sampling Evaluation In FLR

Fisheries Sampling Evaluation in FLR. A package to interface betwen the SAM stock assessments and FLR, and aid the inclusion of SAM into Management Strategy Evaluation (MSE), including the set up of operating models mimicking SAM.

Authors:Simon H. Fischer [aut, cre], Sven Kupschus [aut]

FLfse_1.0.2.tar.gz
FLfse_1.0.2.zip(r-4.5)FLfse_1.0.2.zip(r-4.4)FLfse_1.0.2.zip(r-4.3)
FLfse_1.0.2.tgz(r-4.4-any)FLfse_1.0.2.tgz(r-4.3-any)
FLfse_1.0.2.tar.gz(r-4.5-noble)FLfse_1.0.2.tar.gz(r-4.4-noble)
FLfse_1.0.2.tgz(r-4.4-emscripten)FLfse_1.0.2.tgz(r-4.3-emscripten)
FLfse.pdf |FLfse.html✨
FLfse/json (API)
NEWS

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

Peer review:

Bug tracker:https://github.com/flr/flfse/issues

Datasets:

On CRAN:

2.71 score 2 stars 51 scripts 5 exports 32 dependencies

Last updated 3 years agofrom:7ddf642e0f. Checks:OK: 1 ERROR: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 27 2024
R-4.5-winERROROct 27 2024
R-4.5-linuxERROROct 27 2024
R-4.4-winERROROct 27 2024
R-4.4-macERROROct 27 2024
R-4.3-winERROROct 27 2024
R-4.3-macERROROct 27 2024

Exports:FLR_SAMFLR_SPiCTgetparsSAM_uncertaintySAM2FLStock

Dependencies:clicodetoolscolorspacefansifarverFLCoreforeachggplot2gluegtableisobanditeratorslabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigR6RColorBrewerrlangscalestibbleutf8vctrsviridisLitewithr

Readme and manuals

Help Manual

Help pageTopics
North Sea codcod4_conf_sam cod4_idx cod4_idx_2019 cod4_stk cod4_stk_2019
Run SAM with FLR objects.FLR_SAM FLR_SAM,FLStock,FLIndex-method FLR_SAM,FLStock,FLIndices-method
Run SPiCT with FLR objects.FLR_SPiCT FLR_SPiCT,FLStock,FLIndex-method FLR_SPiCT,FLStock,FLIndices-method
Get parameter estimates from SAM model fit.getpars getpars,sam-method getpars,sam_list-method
North Sea haddockhad4_conf_sam had4_idx had4_stk
North Sea herringher4_conf_sam her4_idx her4_stk
Northeast Atlantic mackerel 2019mac.27.nea_conf_2019 mac.27.nea_idx_2019 mac.27.nea_stk_2019
Irish Sea plaiceple7a_conf_sam ple7a_idx ple7a_idx_2019 ple7a_stk ple7a_stk_2019
Create replicates/iterations of SAM model fit based on variance-covariance matrixSAM_uncertainty SAM_uncertainty,sam-method
Coerce SAM output into 'FLStock' objectSAM2FLStock SAM2FLStock,sam,FLStock-method SAM2FLStock,sam,missing-method SAM2FLStock,sam_list,FLStock-method SAM2FLStock,sam_list,missing-method
North Sea whitingwhg4_conf_sam whg4_idx whg4_stk