Package: LBSPR 0.1.9

LBSPR: Length-Based Spawning Potential Ratio

Simulate expected equilibrium length composition, yield-per-recruit, and the spawning potential ratio (SPR) using the length-based SPR (LBSPR) model. Fit the LBSPR model to length data to estimate selectivity, relative apical fishing mortality, and the spawning potential ratio for data-limited fisheries. See Hordyk et al (2016) <doi:10.1139/cjfas-2015-0422> for more information about the LBSPR assessment method.

Authors:Adrian Hordyk [aut, cre]

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LBSPR.pdf |LBSPR.html✨
LBSPR/json (API)

# Install 'LBSPR' in R:

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

Bug tracker:https://github.com/adrianhordyk/lbspr/issues

Uses libs:

c++– GNU Standard C++ Library v3

On CRAN:

4.90 score 7 stars 113 scripts 248 downloads 19 exports 61 dependencies

Last updated 1 years agofrom:45db8de5f0. Checks:ERROR: 1 WARNING: 8. Indexed: yes.

Target	Result	Date
Doc / Vignettes	FAIL	Nov 04 2024
R-4.5-win-x86_64	WARNING	Nov 04 2024
R-4.5-linux-x86_64	WARNING	Nov 04 2024
R-4.4-win-x86_64	WARNING	Nov 04 2024
R-4.4-mac-x86_64	WARNING	Nov 04 2024
R-4.4-mac-aarch64	WARNING	Nov 04 2024
R-4.3-win-x86_64	WARNING	Nov 04 2024
R-4.3-mac-x86_64	WARNING	Nov 04 2024
R-4.3-mac-aarch64	WARNING	Nov 04 2024

Exports:calcCurves DataDir FilterSmooth getFMfun LBSPR_NLLabsel LBSPR_NLLgtg LBSPRfit LBSPRfit_LBSPRopt LBSPRsim LBSPRsim_plotCurves plotEsts plotMat plotSim plotSize plotSPRCirc plotTarg Shiny

Dependencies:base64enc bslib cachem cli colorspace commonmark cpp11 crayon digest dplyr fansi farver fastmap fontawesome fs generics ggplot2 glue gridExtra gtable htmltools httpuv isoband jquerylib jsonlite labeling later lattice lifecycle magrittr MASS Matrix memoise mgcv mime munsell nlme pillar pkgconfig plotrix promises purrr R6 rappdirs RColorBrewer Rcpp rlang sass scales shiny sourcetools stringi stringr tibble tidyr tidyselect utf8 vctrs viridisLite withr xtable

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

Help page	Topics
Calculate Relative Yield, YPR, SPR, SSB, and Recruitment curves for F/M	calcCurves
Report the location of the Data Files	DataDir
Kalman filter and Rauch-Tung-Striebel smoother	FilterSmooth
Calculate F/M given SPR and other parameters	getFMfun
Create a new LB_lengths object	initialize,LB_lengths-method
Create a new LB_obj object	initialize,LB_obj-method
Create a new LB_pars object	initialize,LB_pars-method
An S4 class containing length data	LB_lengths-class
An S4 class containing all parameters for the LBSPR model	LB_obj-class
An S4 class containing life history and other parameters	LB_pars-class
LBSPR Optimization function for age-based selectivity model	LBSPR_NLLabsel
LBSPR Optimization function for GTG model	LBSPR_NLLgtg
Fit LBSPR model to length data	LBSPRfit
Internal function to fit LBSPR model to length data	LBSPRfit_
Optimisation Routine for fitting LBSPR	LBSPRopt
LBSPR Simulation Model	LBSPRsim
Internal LBSPR Simulation Model	LBSPRsim_
Plot the Relative Yield, YPR, SPR, SSB, and Recruitment curves	plotCurves
Plot LBSPR model estimates	plotEsts
Plot the maturity-at-length and selectivity-at-length curves	plotMat
General plotting function for simulated data	plotSim
Plot the size data and model fits	plotSize
Circle of estimated SPR and target and limit points	plotSPRCirc
Plot sampled length structure against target simulated size composition	plotTarg
Run a Shiny Application	Shiny

Package: LBSPR 0.1.9

LBSPR: Length-Based Spawning Potential Ratio

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