trackdem (version 0.6)

mergeTracks: Merge track records

Description

mergeTracks attempts to merge to two track objects as obtained by trackParticles.

Usage

mergeTracks(records1, records2, L = NULL, weight = NULL, logsizes = FALSE)

Value

A list of class 'TrDm' and 'records'. Use 'summary' and 'plot'.

Arguments

records1

Object of class 'tracked', obtained using trackParticles.

records2

Object of class 'tracked', obtained using trackParticles that should be linked to records1.

L

Numeric. Maximum cost for linking a particle to another particle. When the cost is larger, particles will be not be linked (resulting in the begin or end of a segment). If NULL, the same L as used to create records2 is used.

weight

Vector containing 3 weights to calculate costs. Depending on the study system user may want to value certain elements over others. Weights are ordered as follows; first number gives the weight for differences in x and y coordinates; second number gives the weight for particle size differences. Note that the difference between the predicted location and the observed location is not taken into account in this function. If NULL, the same weights as used to create records2 is used.

logsizes

Logical. Default is FALSE. Set to TRUE to take the natural logarithm of body sizes, when calculating the cost of linking two particles.

Author

Marjolein Bruijning, Caspar A. Hallmann & Marco D. Visser

Examples

if (FALSE) {
## Create image sequence
dir.create("images")
traj <- simulTrajec(path="images",
                    nframes=60,nIndividuals=20,domain="square",
                    h=0.01,rho=0.9,sizes=runif(20,0.004,0.006))
## Analyse first part
dir <- "images"
allFullImages1 <- loadImages (dirPictures=dir,nImages=1:30)
stillBack1 <- createBackground(allFullImages1)
allImages1 <- subtractBackground(bg=stillBack1)
partIden1 <- identifyParticles(sbg=allImages1,
                              pixelRange=c(1,500),
                              threshold=-0.1)
records1 <- trackParticles(partIden1,L=20,R=2)
## Analyse second part
allFullImages2 <- loadImages (dirPictures=dir,nImages=31:60)
stillBack2 <- createBackground(allFullImages2)
allImages2 <- subtractBackground(bg=stillBack2)
partIden2 <- identifyParticles(sbg=allImages2,
                              pixelRange=c(1,500),
                              threshold=-0.1)
records2 <- trackParticles(partIden2,L=20,R=2)
## Merge tracks
records <- mergeTracks(records1,records2)
plot(records,colorimages=allFullImages1,type="trajectories",incThres=10)
}