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:
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
- 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
Last updated 3 years agofrom:7ddf642e0f. Checks:OK: 1 WARNING: 4 ERROR: 2. Indexed: no.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Dec 26 2024 |
| R-4.5-win | WARNING | Dec 26 2024 |
| R-4.5-linux | WARNING | Dec 26 2024 |
| R-4.4-win | WARNING | Dec 26 2024 |
| R-4.4-mac | ERROR | Dec 26 2024 |
| R-4.3-win | WARNING | Dec 26 2024 |
| R-4.3-mac | ERROR | Dec 26 2024 |
Exports:FLR_SAMFLR_SPiCTgetparsSAM_uncertaintySAM2FLStock
Dependencies:clicodetoolscolorspacefansifarverFLCoreforeachggplot2gluegtableisobanditeratorslabelinglatticelifecyclemagrittrMASSMatrixmgcvmunsellnlmepillarpkgconfigR6RColorBrewerrlangscalestibbleutf8vctrsviridisLitewithr
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 |
