Minimal error checking is done in this function. Normal calling function is MARSS_tmb() which in turn calls this function. Note when MARSS is updated, the normal calling function will be MARSS::MARSS(). Restrictions

MARSStmb(MLEobj)

Arguments

MLEobj

A properly formatted MARSS model as output by MARSS_tmb()

Value

A MARSS::marssMLE object

Details

  • No time-varying parameters

  • Currently only DFA models are coded up

  • x0 and V0 fixed (stochastic prior)

  • Q is fixed (not estimated)

This function returns MARSS::marssMLE object. For the iter.record element of the object, the following are returned as a list:

  • obj.function is the raw output from the TMB::MakeADFun() call.

  • opt.output is the raw output from the optimization call (optim or nlminb)

Author

Eli Holmes. This function is inspired by dfaTMB.R written by Tim Cline while a graduate student in the Fish 507 Time Series Analysis course.

Examples

library(MARSS)
data(lakeWAplankton, package = "MARSS")
phytoplankton <- c("Cryptomonas", "Diatoms", "Greens", "Unicells", "Other.algae")
dat <- as.data.frame(lakeWAplanktonTrans) |>
  subset(Year >= 1980 & Year <= 1989) |>
  subset(select=phytoplankton) |>
  t() |>
  MARSS::zscore()

# set-up the model
mod <- MARSS_tmb(dat, model=list(m=3, tinitx=1), form="dfa", fit=FALSE)
# fit
fit <- MARSStmb(mod)