inst/userguide/figures/CS7--Cs12_load-plankton-data.R

In nwfsc-timeseries/MARSS: Multivariate Autoregressive State-Space Modeling

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### code chunk number 15: Cs12_load-plankton-data
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# only use the plankton, daphnia, & non-daphnia
plank.spp <- c("Large Phyto", "Small Phyto", "Daphnia", "Non-daphnia")
plank.dat <- ivesDataByWeek[, plank.spp]
# The data are not logged
plank.dat <- log(plank.dat)
# Transpose to get time going across the columns
plank.dat <- t(plank.dat)
# make a demeaned version
d.plank.dat <- (plank.dat - apply(plank.dat, 1, mean, na.rm = TRUE))