Plot states from a DFA using ggplot

Requires MARSS 3.10.4+

Required packages

library(MARSS)
library(broom)
library(ggplot2)

Load data and zscore

data(lakeWAplankton)
# we want lakeWAplanktonTrans, which has been log-transformed
# and the 0s replaced with NAs
plankdat = lakeWAplanktonTrans
years = plankdat[,"Year"]>=1980 & plankdat[,"Year"]<1990
phytos = c("Cryptomonas", "Diatoms", "Greens",
                  "Unicells", "Other.algae")
dat.spp.1980 = plankdat[years,phytos]
# transpose data so time goes across columns
dat.spp.1980 = t(dat.spp.1980)
dat.z = zscore(dat.spp.1980)

Fit a DFA with 3 trends. Setting maxit to 50, so it runs fast.

model.list = list(m=3, R="diagonal and unequal")
kemz.3 = MARSS(dat.spp.1980, model=model.list,
    z.score=TRUE, form="dfa", control=list(maxit=50))

Make a plot of trends with CIs

theme_set(theme_bw())
d <- tidy(kemz.3, type="states")
 ggplot(data = d) + 
   geom_line(aes(t, estimate)) +
   geom_ribbon(aes(x=t, ymin=conf.low, ymax=conf.high), linetype=2, alpha=0.1) +
   facet_grid(~term) +
   xlab("Time Step") + ylab("Val")