README.md

In ChristineStawitz-NOAA/stspsize: State-Space Autoregressive Length-at-Age Model

sarla

State space autoregressive length-at-age model

installing in R

You can install the sarla package from Github. You will need to install the CmdStanR package first using these instructions. The main branch right now works with a full matrix of data while we are adding support for missing data on the missingdata branch.

remotes::install_github("WGGRAFY/sarla")
require(sarla)

testing with simulated data

You can test with simulated data using the following code. Full code is in inst

#simulate data
dat <- sarla_sim(
  Nages = 7, Nyears = 22, sigma_o = 0.2, beta = 0.7,
  gamma_y_sd = 0.2, delta_c_sd = 0, eta_c_sd = 0.2, sigma_p_X0 = 0
)

#create the dat model input object
stan_dat <- plot_and_fill_data(dat)

#Fit the model
fit <- fit_sarla(stan_dat,
  chains = 1,
  iter = 100
)

The fit_sarla function accepts any arguments that can be passed to sample. Documentation for sample here.

ChristineStawitz-NOAA/stspsize documentation built on July 16, 2025, 8:15 p.m.