larkin

Forecast from Larkin and Ricker stock-recruitment models

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")))

2. Install CmdStan (see https://mc-stan.org/cmdstanr/articles/cmdstanr.html).

cmdstanr::check_cmdstan_toolchain()
cmdstanr::install_cmdstan(cores = parallel::detectCores())

3. 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