Package: wham 1.0.9

Tim Miller

wham: Woods Hole Assessment Model (WHAM)

The Woods Hole Assessment Model (WHAM) is a state-space age-structured stock assessment model that can include environmental effects on population processes. WHAM can be configured to estimate a range of assessment models: a traditional statistical catch-at-age (SCAA) model with recruitments as fixed effects, SCAA with recruitments as random effects, or a "full state-space" model with abundance at all ages treated as random effects. WHAM is a generalization of the R and TMB code from Miller et al. (2016), Miller and Hyun (2018), and Miller et al. (2018). WHAM also has many similarities of input data sources with ASAP (Legault and Restrepo 1999) and provides functions to generate a WHAM input file from an ASAP3 dat file. Many of the plotting functions for input data, results, and diagnostics are modified from ASAP code written by Chris Legault and Liz Brooks.

Authors:Tim Miller [aut, cre], Brian Stock [aut], Liz Brooks [ctb], Chris Legault [ctb], Jim Thorson [ctb]

wham_1.0.9.tar.gz

wham_1.0.9.tar.gz(r-4.4-noble)
wham_1.0.9.tgz(r-4.4-emscripten)wham_1.0.9.tgz(r-4.3-emscripten)
wham.pdf |wham.html✨
wham/json (API)

# Install 'wham' in R:

install.packages('wham', repos = c('https://noaa-fisheries-integrated-toolbox.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/timjmiller/wham/issues

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

On CRAN:

fisheries-stock-assessment state-space

6.50 score 32 stars 354 scripts 17 exports 94 dependencies

Last updated 4 months agofrom:89b3fd5c62. Checks:ERROR: 1. Indexed: no.

Target	Result	Date
Doc / Vignettes	FAIL	Nov 04 2024

Exports:%>%check_convergence check_estimability compare_wham_models fit_peel fit_wham make_osa_residuals mohns_rho plot_wham_output prepare_wham_input project_wham read_asap3_dat read_asap3_fit read_wham_fit retro retro_res set_age_sel0

Dependencies:abind backports base64enc bitops bslib cachem caTools checkmate cli cluster colorspace cpp11 data.table Deriv digest dotCall64 dplyr ellipse evaluate fansi farver fastmap fields fontawesome foreign Formula fs generics ggplot2 glue gplots gridExtra gtable gtools highr Hmisc htmlTable htmltools htmlwidgets isoband jquerylib jsonlite kableExtra KernSmooth knitr labeling lattice lifecycle magrittr maps MASS Matrix memoise mgcv mime mnormt munsell nlme nnet pander pillar pkgconfig plotrix purrr R6 rappdirs RColorBrewer Rcpp RcppEigen rlang rmarkdown rpart rstudioapi sass scales sessioninfo spam stringi stringr svglite systemfonts tibble tidyr tidyselect tinytex TMB utf8 vctrs viridis viridisLite withr xfun xml2 yaml

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
Pipe function	%>%
Check convergence of WHAM model	check_convergence
Check for identifiability of fixed effects Originally provided by https://github.com/kaskr/TMB_contrib_R/TMBhelper Internal function called by 'fit_tmb'.	check_estimability
Compare multiple WHAM (or ASAP) models	compare_wham_models
Extract fixed effects Originally provided by https://github.com/kaskr/TMB_contrib_R/TMBhelper Internal function called by 'check_estimability'.	extract_fixed
Fit model peeling off _i_ years of data	fit_peel
Fit TMB model using nlminb	fit_tmb
Fit WHAM model	fit_wham
Calculate one-step-ahead residuals	make_osa_residuals
Calculate Mohn's rho for a WHAM model with peels	mohns_rho
Plot WHAM output	plot_wham_output
Prepare input data and parameters to project an already fit WHAM model	prepare_projection
Prepare input data and parameters for WHAM model	prepare_wham_input
Project a fit WHAM model	project_wham
Read an ASAP3 .dat file into R	read_asap3_dat
Read ASAP3 fit	read_asap3_fit
Read WHAM fit	read_wham_fit
Run retrospective analysis	retro
Extract retrospective results for plotting	retro_res
Make one or more selectivity blocks with age-specific parameters	set_age_sel0
Create HTML file to view output plots in browser	wham_html

Package: wham 1.0.9

wham: Woods Hole Assessment Model (WHAM)

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