assign_tseg: Add segment numbers to observations

In bayesmove: Non-Parametric Bayesian Analyses of Animal Movement

Description

After breakpoints have been extracted for each animal ID, this function assigns the associated segment number to observations for each animal ID. These segments of observations will be used in the second stage of the model framework to perform mixed-membership clustering by Latent Dirichlet Allocation.

Usage

assign_tseg(dat, brkpts)

Arguments

dat	A list where each element stores the data for a unique animal ID. Each element is a data frame that contains all data associated for a given animal ID and must include a column labeled time1 that numbers each of the observations in consecutive order. This variable is automatically generated by the filter_time function during data preparation.
brkpts	A data frame of breakpoints for each animal ID (as generated by get_breakpts).

Value

A data frame that updates the original data object by including the segment number associated with each observation in relation to the extracted breakpoints.

Examples

#load data
data(tracks.list)

#subset only first track
tracks.list<- tracks.list[1]

#only retain id and discretized step length (SL) and turning angle (TA) columns
tracks.list2<- purrr::map(tracks.list,
                   subset,
                  select = c(id, SL, TA))


set.seed(1)

# Define model params
alpha<- 1
ngibbs<- 1000
nbins<- c(5,8)

#future::plan(future::multisession)  #run all MCMC chains in parallel
dat.res<- segment_behavior(data = tracks.list2, ngibbs = ngibbs, nbins = nbins,
                           alpha = alpha)


# Determine MAP iteration for selecting breakpoints and store breakpoints
MAP.est<- get_MAP(dat = dat.res$LML, nburn = ngibbs/2)
brkpts<- get_breakpts(dat = dat.res$brkpts, MAP.est = MAP.est)


# Assign track segments to all observations by ID
tracks.seg<- assign_tseg(dat = tracks.list, brkpts = brkpts)

bayesmove documentation built on Oct. 22, 2021, 9:08 a.m.