Package: BayesGrowth 1.0.0.9000

Jonathan Smart

BayesGrowth: Estimate Fish Growth Using MCMC Analysis

Estimate fish length-at-age models using MCMC analysis with 'rstan' models. This package allows a multimodel approach to growth fitting to be applied to length-at-age data and is supported by further analyses to determine model selection and result presentation. The core methods of this package are presented in Smart and Grammer (2021) "Modernising fish and shark growth curves with Bayesian length-at-age models". PLOS ONE 16(2): e0246734 <doi:10.1371/journal.pone.0246734>.

Authors:Jonathan Smart [aut, cre, ctb, cph]

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BayesGrowth/json (API)
NEWS

# Install 'BayesGrowth' in R:

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

Bug tracker:https://github.com/jonathansmart/bayesgrowth/issues

Uses libs:

c++– GNU Standard C++ Library v3

Datasets:

Looic_example_results - Example MCMC model comparison outputs outputs
MCMC_example_results - Example MCMC model outputs
example_data - Example length-at-age data

On CRAN:

7 exports 11 stars 1.70 score 90 dependencies 8 scripts 192 downloads

Last updated 10 months agofrom:b874ef7bb3. Checks:OK: 1 NOTE: 8. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Aug 27 2024
R-4.5-win-x86_64	NOTE	Aug 27 2024
R-4.5-linux-x86_64	NOTE	Aug 27 2024
R-4.4-win-x86_64	NOTE	Aug 27 2024
R-4.4-mac-x86_64	NOTE	Aug 27 2024
R-4.4-mac-aarch64	NOTE	Aug 27 2024
R-4.3-win-x86_64	NOTE	Aug 27 2024
R-4.3-mac-x86_64	NOTE	Aug 27 2024
R-4.3-mac-aarch64	NOTE	Aug 27 2024

Exports:Calc_Gompertz_LAA Calc_Logistic_LAA Calc_VBGF_LAA Calculate_MCMC_growth_curve Compare_Growth_Models Estimate_MCMC_Growth Get_MCMC_parameters

Dependencies:abind AquaticLifeHistory arrayhelpers backports bayesplot BH bit bit64 broom callr checkmate cli clipr coda colorspace cpp11 crayon data.table desc distributional dplyr fansi farver generics ggdist ggplot2 ggridges glue gridExtra gtable hms inline insight isoband jsonlite labeling lattice lifecycle loo magrittr MASS Matrix matrixStats mgcv minpack.lm MuMIn munsell nlme numDeriv pillar pkgbuild pkgconfig plyr posterior prettyunits processx progress ps purrr quadprog QuickJSR R6 RColorBrewer Rcpp RcppEigen RcppParallel readr reshape2 rlang rlist rstan rstantools scales StanHeaders stringi stringr svUnit tensorA tibble tidybayes tidyr tidyselect tzdb utf8 vctrs viridisLite vroom withr XML yaml

Estimate growth using MCMC

Rendered fromMCMC-example.Rmdusingknitr::rmarkdownon Aug 27 2024.

Last update: 2023-11-17
Started: 2020-11-10

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
BayesGrowth	BayesGrowth
Calc_Gompertz_LAA	Calc_Gompertz_LAA
Calc_Logistic_LAA	Calc_Logistic_LAA
Calc_VBGF_LAA	Calc_VBGF_LAA
Calculate_MCMC_growth_curve	Calculate_MCMC_growth_curve
Compare_Growth_Models	Compare_Growth_Models
Estimate_MCMC_Growth	Estimate_MCMC_Growth
Example length-at-age data	example_data
Get_MCMC_parameters	Get_MCMC_parameters
Example MCMC model comparison outputs outputs	Looic_example_results
Example MCMC model outputs	MCMC_example_results