fitDrate: 'fitDrate' Fit state-space model to weighted drift dive...

In embiuw/drifteR: Drift dive detection, weighting and estimation

Description

fitDrate Fit state-space model to weighted drift dive record

Usage

fitDrate(data, weight = "default", prefilter = 0)

Arguments

data	Data frame with dive data output from the pDrift function.
weight	Select weightingbvariables to be used. Default is to use weight created by pDrift. See example for how to specify other weighting
prefilter	Should any prefiltering be done (based on selected weight) prior to running the model.

Details

Takes a dive set of dive data from SRDLs (Sea Mammal Research Unit), with added variables from rbs and pDrift and fits a state-space model to change over time (using TMB).

Value

A list with several objects from fit:

data	Original input data
w	Weighting used for probability of drift dive
tSeq	Regular time series (e.g. whole days) where predictions are obtained
obj	TMB object
opt	TMB optimization
par	Fitted parameters
rep	TMB report
allsd	Standard deviation of fitted values
plsd	Fitted values

Author(s)

Martin Biuw

See Also

rbs Reverse Broken Stick algorithm

check.pDrift to interactively check drift dive weightings

pDrift to calculate drift rate and probability weightings for drift dive detection

fitPlot To plot output from fitDrift

Other Drift dive functions: check.pDrift(), fitPlot(), pDrift(), rbs()

Examples

rbs(data=dive, num=100, n.bs=4)
dive <- rbs(data=dive, num=NA, n.bs=4)
dive <- pDrift(dive)
fit <- fitDrate(dive, prefilter=0.01)
fit2 <- fitDrate(dive, weight='rRes*span*dWt', prefilter=0.01)

embiuw/drifteR documentation built on March 1, 2021, 6:40 a.m.