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Fit and forecast from Larkin and Ricker stock-recruitment models

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larkin

Forecast from Larkin and Ricker stock-recruitment models

R-CMD-check Project Status: WIP – Initial development is in progress, but there has not yet been a stable, usable release suitable for the public.

Installation

  1. Install the R package cmdstanr (see https://mc-stan.org/cmdstanr/index.html).
install.packages("cmdstanr", repos = c("https://mc-stan.org/r-packages/", getOption("repos")))
  1. Install CmdStan (see https://mc-stan.org/cmdstanr/articles/cmdstanr.html).
cmdstanr::check_cmdstan_toolchain()
cmdstanr::install_cmdstan(cores = parallel::detectCores())
  1. Install larkin.
remotes::install_github("pbs-assess/larkin")

Changes implemented on 21 July 2023

  • forecast no longer includes random error. A single, deterministic forecast is generated for each posterior draw.
  • timevary input parameter was removed as this is determined by value of prior on omega
  • the MLE of larkin model was included as an alternative to Bayesian estimation, in forecast() using cmdstanr's optimize() function

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