Package: FLjjm 0.3.10

Iago Mosqueira

FLjjm: Running the JJM Stock Assessment Model Inside the MSE FLR System

Runs the JJM stock assessment model for Chilean Jack Mackerel inside the MSE system of FLR's mse package.

Authors:Iago Mosqueira [aut, cre], Karolina Molla Gazi [aut]

FLjjm_0.3.10.tar.gz
FLjjm_0.3.10.zip(r-4.7)FLjjm_0.3.10.zip(r-4.6)FLjjm_0.3.10.zip(r-4.5)
FLjjm_0.3.10.tgz(r-4.6-any)FLjjm_0.3.10.tgz(r-4.5-any)
FLjjm_0.3.10.tar.gz(r-4.7-any)FLjjm_0.3.10.tar.gz(r-4.6-any)
FLjjm_0.3.10.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
FLjjm/json (API)

# Install 'FLjjm' in R:

install.packages('FLjjm', repos = c('https://sprfmo.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/sprfmo/fljjm/issues

On CRAN:

3.78 score 8 scripts 35 exports 103 dependencies

Last updated from:732a89da20. Checks:2 ERROR, 2 OK, 5 WARNING. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	ERROR	367
source / vignettes	OK	263
linux-release-x86_64	WARNING	349
macos-release-arm64	WARNING	177
macos-oldrel-arm64	WARNING	190
windows-devel	ERROR	228
windows-release	WARNING	232
windows-oldrel	WARNING	215
wasm-release	OK	172

Exports:buildFLBjjm buildFLBsjjm buildFLFsjjm buildFLIsjjm buildFLRPsjjm buildFLSjjm buildFLSsjjm buildjjmctl buildjjmdata calljjms cjm.iem cjm.oem cjmage2len exejjms fwdmov fwdmov.om get_os getjjms jjms jjms.sa jmets loadJJMS perfect.oem readFLBjjm readFLFsjjm readFLIsjjm readFLoemjjm readFLomjjm readFLRPsjjm readFLSjjm readFLSsjjm readMod readRep runjjms slick_performance

Dependencies:backports base64enc boot broom bslib cachem cli codetools colorspace cowplot cpp11 data.table deldir Deriv digest doBy doFuture dplyr evaluate farver fastmap FLasher FLBRP FLCore FLFishery fontawesome forcats foreach forecast fracdiff fs future future.apply generics ggplot2 ggplotFL ggrepel ggridges globals glue gridExtra gtable highr htmltools icesAdvice interp isoband iterators jjmR jpeg jquerylib jsonlite knitr labeling lattice latticeExtra lifecycle listenv lmtest magrittr MASS Matrix memoise mime modelr mse nlme nnet parallelly patchwork PBSmodelling pillar pkgconfig png progressr purrr R6 rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen rlang rmarkdown S7 sass scales stringi stringr tibble tidyr tidyselect timeDate tinytex urca utf8 vctrs viridisLite withr xfun XML yaml zoo

Description of the FLjjm package

Rendered fromFLjjm.Rmdusingknitr::rmarkdown

Last update: 2026-05-31
Started: 2024-01-19

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Combine Fisheries Model Results	.combinejjmsout
Convert Age Composition to Length Composition	AgeToLengthComp
Build Functions for FLjjm Package	build
Build an FLBiol from a jjm.output object	buildFLBjjm
Build FLFisheries from JJMS Model Output	buildFLFsjjm
Construct FLIndices from a jjm.output object	buildFLIsjjm
Build reference points (FLPar) from jjm.output	buildFLRPsjjm
Build FLStock from jjm.output	buildFLSjjm
Build FLStock with areas from jjm.output	buildFLSojjm
Build multiple FLStock objects from jjm.output	buildFLSsjjm
Updating dat and ctl file lists from FLstock(s) and FLIndices	buildjjmctl
Calculate Total Catch across FLStocks	catch,FLStocks-method
Observation Error Model wrapper for CJM within MSE workflows	cjm.oem
Convert Age Composition to Length Composition for Landings	cjmage2len
Converts FLQuants with Fleets as Areas into a fwdControl Object	cjmfwc
Execute JJMS Model	exejjms
Calculate Average Fishing Mortality across FLStocks	fbar,FLStocks-method
FLjjm: An R Package for Interacting with JJMS Stock Assessment Model in FLR	FLjjm
Forward Movement Simulation	fwdmov
Forward Movement Operation Model	fwdmov.om
Run JJMS Model for Fisheries Stock Assessment	jjms
JJMS Stock Assessment	jjms.sa
Load FLStocks from JJMS Model	loadFLSjjms
Load JJMS Model Components	loadJJMS
Get Name of JJMS Model	namejjms
Get Number of Stocks in JJMS Model	nStocksjjms
Clean Up JJMS Model Run Directory	packjjmsrun
Create an FLBiol from a JJMS model run directory	readFLBjjm
Create FLFisheries objects from a JJMS model run directory	readFLFsjjm
Create an FLIndices object from a JJMS model run directory	readFLIsjjm
Read FLIndices with OEM iterations and MC outputs	readFLoemjjm
Create an FLombf object from a JJMS model run directory	readFLomjjm
Create an FLPar contaning reference points from a JJMS model run directory	readFLRPsjjm
Create an FLStock from a JJMS model run directory	readFLSjjm
Create an FLStocks from a two-stock JJMS model run directory	readFLSsjjm
Run JJMS Model	runjjms
Compute performance metrics for MPs and OM in slick format	slick_performance
Calculate Total Spawning Stock Biomass across FLStocks	ssb,FLStocks-method
Construct Components of Fisheries Model	yourFunctionName