assign_behavior {bayesmove}R Documentation

Assign behavior estimates to observations


Assign behavior estimates to observations


assign_behavior(dat.orig, dat.seg.list, theta.estim.long, behav.names)



A data frame that contains all of the original data for all animal IDs. Must be same as was used to originally segment the tracks. Must have columns obs and time1 generated by filter_time.


A list of data associated with each animal ID where names of list elements are the ID names and tracks have already been segmented. Must have columns obs and time1 generated by filter_time.


A data frame in long format where each observation (time1) of each track segment (tseg) of each animal ID (id) has separate rows for behavior proportion estimates per state. Columns for behavior and proportion estimates should be labeled behavior and prop, respectively. Date (in POSIXct format) should also be included as a column labeled date.


character. A vector of names to label each state (in order).


A data frame of all animal IDs where columns (with names from behav.names) include proportions of each behavioral state per observation, as well as a column that stores the dominant behavior within a given track segment for which the observation belongs (behav). This is merged with the original data frame dat.orig, so any observations that were excluded (not at primary time interval) will show NA for behavior estimates.


#load original and segmented data

#convert segmented dataset into list
tracks.list<- df_to_list(dat = tracks.seg, ind = "id")

#select only id, tseg, SL, and TA columns
tracks.seg2<- tracks.seg[,c("id","tseg","SL","TA")]

#summarize data by track segment
obs<- summarize_tsegs(dat = tracks.seg2, nbins = c(5,8))

#cluster data with LDA
res<- cluster_segments(dat = obs, gamma1 = 0.1, alpha = 0.1, ngibbs = 1000,
                       nburn = 500, nmaxclust = 7, ndata.types = 2)

#Extract proportions of behaviors per track segment
theta.estim<- extract_prop(res = res, ngibbs = 1000, nburn = 500, nmaxclust = 7)

#Create augmented matrix by replicating rows (tsegs) according to obs per tseg
theta.estim.long<- expand_behavior(dat = tracks.seg, theta.estim = theta.estim, obs = obs,
                               nbehav = 3, behav.names = c("Encamped","ARS","Transit"),
                               behav.order = c(1,2,3))

#Run function
dat.out<- assign_behavior(dat.orig = tracks, dat.seg.list = tracks.list,
                          theta.estim.long = theta.estim.long,
                          behav.names = c("Encamped","ARS","Transit"))

[Package bayesmove version 0.2.0 Index]