Package: ss3om 0.5.3.9004

Iago Mosqueira

ss3om: Tools for Conditioning Fisheries Operating Models Using Stock Synthesis 3

Tools for loading Stock Synthesis (SS3) models into FLR. Used in conditioning of Operating Models based on SS3 by considering structural uncertainty in input parameters and assumptions. A grid of SS3 runs can be created and results loaded on objects of various FLR classes.

Authors:Iago Mosqueira [aut, cre]

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ss3om.pdf |ss3om.html✨
ss3om/json (API)
NEWS

# Install 'ss3om' in R:

install.packages('ss3om', repos = c('https://flr.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/flr/ss3om/issues

On CRAN:

fisheries ss3 flr

3.94 score 44 scripts 49 exports 99 dependencies

Last updated 1 months agofrom:83a4b0e475. Checks:1 OK, 7 WARNING. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Mar 01 2025
R-4.5-win	WARNING	Mar 01 2025
R-4.5-mac	WARNING	Mar 01 2025
R-4.5-linux	WARNING	Mar 01 2025
R-4.4-win	WARNING	Mar 01 2025
R-4.4-mac	WARNING	Mar 01 2025
R-4.3-win	WARNING	Mar 01 2025
R-4.3-mac	WARNING	Mar 01 2025

Exports:buildFLBFss3 buildFLBFss330 buildFLIBss3 buildFLIBss330 buildFLRPss3 buildFLRPss330 buildFLSRss3 buildFLSss3 buildFLSss330 buildKobess3 buildKobess330 buildLCss330 buildRESss3 buildRESss330 convergencelevel extractDevs extractFbar extractRec extractSSB extractZatage loadFLQs loadFLS loadOM loadOMS loadOUT loadRES loadRESIDs loadRPs nameGrid packss3run prepareRetro readCDss3 readFLIBss3 readFLoemss3 readFLomss3 readFLRPss3 readFLSRss3 readFLSss3 readKobess3 readOMSss3 readOutputss3 readRESIDss3 readRESss3 readSRIss3 results results<-runss3grid runtime ssmvln

Dependencies:askpass base64enc bslib cachem cli coda codetools colorspace corpcor cowplot cpp11 curl data.table digest doFuture dplyr evaluate fansi farver fastmap FLasher FLBRP FLCore FLFishery fontawesome forcats foreach fs furrr future future.apply generics ggplot2 ggplotFL ggrepel gh gitcreds globals glue gridExtra gtable highr htmltools httr2 ini isoband iterators jquerylib jsonlite kableExtra knitr labeling lattice lifecycle listenv magrittr MASS Matrix memoise mgcv mime mse munsell mvtnorm nlme openssl parallelly patchwork pillar pkgconfig progressr purrr r4ss R6 rappdirs RColorBrewer Rcpp rlang rmarkdown rstudioapi sass scales stringi stringr svglite sys systemfonts tibble tidyr tidyselect tinytex utf8 vctrs viridis viridisLite withr xfun xml2 yaml

Loading your SS3 results into FLR with ss3om

Iago Mosqueira (EC JRC) [email protected]

Rendered fromss3om.Rmdusingknitr::rmarkdownon Mar 01 2025.

Last update: 2024-09-24
Started: 2024-09-24

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Creates an FLQuants from length-distributions by fleet	buildLCss330
Extracts derived quantities from SS output	extractDevs extractFbar extractRec extractSSB extractZatage
nameGrid	nameGrid
A function to read the CPUE series from an SS3 run into an 'FLIndex' object	readFLIBss3
A function to read the stock-recruit relationships from an SS3 run into an 'FLSR' object	readFLSRss3
A function to read SS3 results as an FLStock object	readFLSss3
Functions to convert SS3 output into FLQuant(s)	ss3catch ss3catch30 ss3index ss3index.q ss3index.res ss3index.var ss3m ss3m30 ss3mat ss3mat30 ss3n ss3n30 ss3sel.pattern ss3slot ss3wt