Skip to contents

Determine active or inactive states according to the speed of a particles along its trajectory.

Source: R/activity1.R
activity1.Rd

Given a data frames containing tracking information for a given tracklet including speed, this function return a vector containing numeric values indicating whether the particle is "active" (1) or "inactive" (0).

Usage

activity1(df, speedCol = NULL, minSpeed = NULL)

Arguments

df

A data frame containing x and y coordinates in columns named "x.pos", "y.pos" for a given tracklet, as well as a column containing the speed of the particle, whatever the unit, over the tracklet.

speedCol

A character string corresponding to the name of the column containing the speed of the particles over the tracklet, whatever the unit.

minSpeed

A numeric value expressed in the same unit than speed, corresponding to the threshold above which the particle is considered as active.

Value

This function returns a vector containing numeric values indicating whether the particle is "active" (1) or "inactive" (0).

Author

Quentin PETITJEAN

Examples


set.seed(2023)
# generate a dummy tracklet
## start to specify some parameters to generate the tracklet
TrackL <-
  100 # the length of the tracklet or a sequence to randomly sample tracklet's length

TrackDatTemp <-
  trajr::TrajGenerate(sample(TrackL, 1), random = TRUE, fps = 1)
TrackDat <- data.frame(
  x.pos = TrackDatTemp[["x"]] - min(TrackDatTemp[["x"]]),
  y.pos = TrackDatTemp[["y"]] - min(TrackDatTemp[["y"]]),
  frame = TrackDatTemp[["time"]]
)

# compute the speed of the particle along its trajectory
TrackDat[["speed"]] <-
  MoveR::speed(TrackDat)

# we can then define the speed treshold above which the particle is considered actives using quantiles
# here we use the 0.025 quantile to find the minimum speed treshold
hist(log10(TrackDat[["speed"]][-is.na(TrackDat[["speed"]])]))
tresh <-
  quantile(log10(TrackDat[["speed"]][-is.na(TrackDat[["speed"]])]), 0.025)
abline(v = tresh)


TrackDat[["activity1"]] <-
  MoveR::activity1(TrackDat, speedCol = "speed", minSpeed = 10 ^ tresh)

# draw the particle' trajectory and spot the inactive moments using red dots
MoveR::drawTracklets(MoveR::trackletsClass(list(TrackDat)),
                 add2It = list(points(
                   TrackDat[["x.pos"]][which(TrackDat[["activity1"]] == 0)],
                   TrackDat[["y.pos"]][which(TrackDat[["activity1"]] ==  0)],
                   col = "red",
                   pch = 19,
                   cex = 1.5
                 )))