marssTMB

{marssTMB} is in active development and not all code has been tested. Also the following are not allowed currently: R or Q with 0s on the diagonal, R or Q with “equalvarcov”, B estimation. Time-varying parameters has been coded but not tested.

To use

Install MARSS 3.11.6 (development version)

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

Install marssTMB

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

Fit a MARSS model

See the Quick Start Guide to get started. Call MARSS() with method="TMB"

library(MARSS)
y <- t(harborSealWA); dat <- dat[2:4, ]
MARSS(y, method="TMB")

Note R and Q can only be diagonal, unconstrained or fixed. equalvarcov is not available nor are zeros allowed on the diagonal as is available with the Kalman filter + EM and BFGS algorithm in MARSS(). But TMB is very fast. Also be aware that {marssTMB} is still in early development and you should check your answers against method="kem" and method="BFGS".

Developer notes

Install {TMBtools} package which is being used to help with set-up.

Rebuilding

  • Add or edit models in src as hpp files. See TMBtools documentation on how to make a cpp file into a hpp file.
  • Run TMBtools::export_models() whenever changes are made to any hpp files
  • Rebuild the package
  • Add helper files (includes) to inst/include/marssTMB and then put a #include marssTMB/newfile.hpp in your hpp file.
  • Build package and documentation with pkgdown::build_site()

NOAA Disclaimer

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