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://ices-tools-prod.r-universe.dev', 'https://cloud.r-project.org'))

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

Datasets:

cod4_conf_sam - North Sea cod
cod4_idx - North Sea cod
cod4_idx_2019 - North Sea cod
cod4_stk - North Sea cod
cod4_stk_2019 - North Sea cod
had4_conf_sam - North Sea haddock
had4_idx - North Sea haddock
had4_stk - North Sea haddock
her4_conf_sam - North Sea herring
her4_idx - North Sea herring
her4_stk - North Sea herring
mac.27.nea_conf_2019 - Northeast Atlantic mackerel 2019
mac.27.nea_idx_2019 - Northeast Atlantic mackerel 2019
mac.27.nea_stk_2019 - Northeast Atlantic mackerel 2019
ple7a_conf_sam - Irish Sea plaice
ple7a_idx - Irish Sea plaice
ple7a_idx_2019 - Irish Sea plaice
ple7a_stk - Irish Sea plaice
ple7a_stk_2019 - Irish Sea plaice
whg4_conf_sam - North Sea whiting
whg4_idx - North Sea whiting
whg4_stk - North Sea whiting

On CRAN:

5 exports 1 stars 0.09 score 32 dependencies 51 scripts

Last updated 3 years agofrom:7ddf642e0f. Checks:OK: 1 WARNING: 4 ERROR: 2. Indexed: no.

Target	Result	Date
Doc / Vignettes	OK	Aug 28 2024
R-4.5-win	WARNING	Aug 28 2024
R-4.5-linux	WARNING	Aug 28 2024
R-4.4-win	WARNING	Aug 28 2024
R-4.4-mac	ERROR	Aug 28 2024
R-4.3-win	WARNING	Aug 28 2024
R-4.3-mac	ERROR	Aug 28 2024

Exports:FLR_SAM FLR_SPiCT getpars SAM_uncertainty SAM2FLStock

Dependencies:cli codetools colorspace fansi farver FLCore foreach ggplot2 glue gtable isoband iterators labeling lattice lifecycle magrittr MASS Matrix mgcv munsell nlme pillar pkgconfig R6 RColorBrewer rlang scales tibble utf8 vctrs viridisLite withr

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
North Sea cod	cod4_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 haddock	had4_conf_sam had4_idx had4_stk
North Sea herring	her4_conf_sam her4_idx her4_stk
Northeast Atlantic mackerel 2019	mac.27.nea_conf_2019 mac.27.nea_idx_2019 mac.27.nea_stk_2019
Irish Sea plaice	ple7a_conf_sam ple7a_idx ple7a_idx_2019 ple7a_stk ple7a_stk_2019
Create replicates/iterations of SAM model fit based on variance-covariance matrix	SAM_uncertainty SAM_uncertainty,sam-method
Coerce SAM output into 'FLStock' object	SAM2FLStock SAM2FLStock,sam,FLStock-method SAM2FLStock,sam,missing-method SAM2FLStock,sam_list,FLStock-method SAM2FLStock,sam_list,missing-method
North Sea whiting	whg4_conf_sam whg4_idx whg4_stk