Package: jjmR 1.2020.1

Ricardo Oliveros-Ramos

jjmR: Graphics and diagnostics tools for SPRFMO's Joint Jack Mackerel model

Graphics and diagnostics tools for SPRFMO's Joint Jack Mackerel model.

Authors:Ricardo Oliveros-Ramos [cre, aut], Wencheng Lau-Medrano [aut], Giancarlo Moron [aut], Josymar Torrejon-Magallanes [aut], Niels Hintzen [aut], Enrique Ramos-Vasquez [ctb], Jim Ianelli [aut]

jjmR_1.2020.1.tar.gz
jjmR_1.2020.1.zip(r-4.5)jjmR_1.2020.1.zip(r-4.4)jjmR_1.2020.1.zip(r-4.3)
jjmR_1.2020.1.tgz(r-4.4-any)jjmR_1.2020.1.tgz(r-4.3-any)
jjmR_1.2020.1.tar.gz(r-4.5-noble)jjmR_1.2020.1.tar.gz(r-4.4-noble)
jjmR_1.2020.1.tgz(r-4.4-emscripten)jjmR_1.2020.1.tgz(r-4.3-emscripten)
jjmR.pdf |jjmR.html✨
jjmR/json (API)

# Install 'jjmR' in R:

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

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

On CRAN:

3.94 score 2 stars 1 packages 12 scripts 29 exports 84 dependencies

Last updated 2 months agofrom:3a927fb8c8. Checks:OK: 1 WARNING: 6. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 03 2024
R-4.5-win	WARNING	Nov 03 2024
R-4.5-linux	WARNING	Nov 03 2024
R-4.4-win	WARNING	Nov 03 2024
R-4.4-mac	WARNING	Nov 03 2024
R-4.3-win	WARNING	Nov 03 2024
R-4.3-mac	WARNING	Nov 03 2024

Exports:%>%changeNameModel combineModels compareModels diagnostics fixed_bmsy get_age_fits get_catchabilities get_fishing_mortality get_index_fits get_len_fits get_msy_mt get_recruits get_selectivities get_totals geth getter kobe plot_selectivities readExFiles readJJM readJJMConfig report retro runit runJJM theme_jjm tidy_JJM writeJJM

Dependencies:backports base64enc boot broom bslib cachem cli codetools colorspace cowplot cpp11 deldir Deriv digest doBy doSNOW dplyr evaluate fansi farver fastmap fontawesome forcats foreach fs generics ggplot2 ggridges glue gridExtra gtable highr htmltools icesAdvice interp isoband iterators jpeg jquerylib jsonlite knitr labeling lattice latticeExtra lifecycle magrittr MASS Matrix memoise mgcv microbenchmark mime modelr munsell nlme pander PBSmodelling pillar pkgconfig png purrr R6 rappdirs RColorBrewer Rcpp RcppEigen rlang rmarkdown sass scales snow stringi stringr tibble tidyr tidyselect tinytex utf8 vctrs viridisLite withr xfun XML yaml

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Change the internal name of a model	changeNameModel
Combine outputs	combineModels
Compare combined JJM outputs	compareModels
Generate Assessment plots from single model	diagnostics
Calculate or input a fixed Bmsy value for the jjm model Updates the msy_mt table in the jjm output with new B/Bmsy ratios.	fixed_bmsy
Get fits to indices	get_age_fits
Get estimated catchability coefficients	get_catchabilities
Get fishing mortality at age	get_fishing_mortality
Get fits to indices	get_index_fits
Get fits to length compositions	get_len_fits
Get and tidy msy_my table	get_msy_mt
Get estimated recruits	get_recruits
Get and tidy selectivity-at-age ogives over time by model and fleet	get_selectivities
Get total metrics (biomass, spawning biomass, and recruitment)	get_totals
Add hypothesis number to a model name	geth
Get elements of a list by string matching on name	getter
Kobe plot	kobe
Plot selectivities by age, year, fleet, and model	plot_selectivities
Read external files	readExFiles
Read a model or list of models	readJJM
Read dat and ctl files from disk to create a jjm.config object.	readJJMConfig
Create a report from JJM outputs	report
Run a retrospective analysis diagnostic for a JJM model	retro
Fit, run, read and plot a JJM model	runit
Run a JJM model	runJJM
ggplot2 theme for jjmR	theme_jjm
Tidy results of JJM model	tidy_JJM
Write dat and ctl files from a JJM model stored in R	writeJJM