Residuals Chapter

[eeholmes]

Add this chapter. Address this issue in there

apply(MARSS:::MARSSresiduals.tT(fit2)$mar.resid,1,var,na.rm=TRUE) not that close to 1

dat <- t(harborSealWA)
dat <- dat[2:4, ] # remove the year row
# fit a model with 1 hidden state and 3 observation time series
kemfit <- MARSS(dat, model = list(
  Z = matrix(1, 3, 1),
  R = "diagonal and equal"
))

[eeholmes]

Discuss what the getDFAfits() function does and why that is the same as what residuals(..., type="tT") returns for model residuals. How is that different than what fitted() returns?