9 Hidden Markov Modelling (HMM)
9.1 Prep the data
create a single clean data frame containing data for every file
Run a 2state HMMM, have to run the following for the HMM:
prepData()
define variables: stateNames <- dry, wet stepPar <- (inital mean for states based on prop_wet) anglePar <- (no angle parameter for our analysis)
fitHMM() plotSates() - visualize the model
test with different binning intervals (2hr, 5hr?)
test covariates
- wetness level (0-20) as a covariate.
- maybe seasonality or a day/night indicator?
REFERENCES: https://cran.r-project.org/web/packages/momentuHMM/vignettes/momentuHMM.pdf