Nothing
R/calculate_apa_metrics.R
In Rtrack: Spatial Navigation Strategy Analysis
Defines functions
calculate_apa_metrics
#' @importFrom terra unwrap vect convHull expanse crds centroids relate
#' @importFrom KernSmooth bkde2D
#' @importFrom stats quantile
#' @importFrom utils globalVariables
utils::globalVariables(c("velocity.quantile", "immobility.quantile", "angle.from.aversive.zone.quantile"))
calculate_apa_metrics = function(path, arena){
# Deserialise arena zones, but retain wrapped version to return.
wrapped.arena.zones = arena$zones
arena$zones = lapply(arena$zones, terra::unwrap)
# Check for presence of optional zones (terra cannot handle missing data).
aversive.zone.present = !is.null(arena$zones$aversive.zone)
old.aversive.zone.present = !is.null(arena$zones$old.aversive.zone)
# APA has two frames of reference. Calculate local (subject) frame coordinates.
rotated.angle = arena$correction$e$arena.rotation * (path$t) # Rotated angle changes over time.
rotated.points = spin(path$x, path$y, deg2rad(rotated.angle))
path$local.x = rotated.points$x
path$local.y = rotated.points$y
# Movement metrics are calculated in either the local frame (of the subject) or the global frame (of the room).
# Area covered by the swim path as a fraction of the total arena
local.path.values = cbind(x = path$local.x, y = path$local.y)
local.pathpoints = terra::vect(local.path.values, type = "points", crs = "local") # With closed path.
global.path.values = cbind(x = path$x, y = path$y)
global.pathpoints = terra::vect(global.path.values, type = "points", crs = "local") # With closed path.
pathpoly = terra::vect(local.path.values, type = "polygons", crs = "local")
coverage = terra::expanse(terra::convHull(pathpoly), transform = FALSE) / terra::expanse(arena$zones$arena, transform = FALSE) # Arena circle is actually a 360-point polygon approximation of a circle (area < pi r^2).
path.centroid = terra::crds(terra::centroids(pathpoly))
d.centroid = ((path$x - path.centroid[1]) ^ 2 + (path$y - path.centroid[2]) ^ 2) ^ .5
d.origin = ((path$x) ^ 2 + (path$y) ^ 2) ^ .5
in.zones = lapply(arena$zones, function(zone) as.logical(rowSums(terra::relate(local.pathpoints, zone, relation = "intersects"))) )
if(aversive.zone.present) in.zones$aversive.zone = as.logical(rowSums(terra::relate(global.pathpoints, arena$zones$aversive.zone, relation = "intersects"))) # In GLOBAL frame.
if(old.aversive.zone.present) in.zones$old.aversive.zone = as.logical(rowSums(terra::relate(global.pathpoints, arena$zones$old.aversive.zone, relation = "intersects"))) # In GLOBAL frame.
# Path length
path.segment.lengths = sqrt(diff(local.path.values[, "x"]) ^ 2 + diff(local.path.values[, "y"]) ^ 2)
path.length = sum(path.segment.lengths)
# 'Turning' behaviour measured by angular displacement at each timepoint
dx = diff(global.path.values[, "x"])
dy = diff(global.path.values[, "y"])
angle.from.xaxis = atan2(dy, dx)
turning = diff(angle.from.xaxis)
# Angle from aversive zone.
x = global.path.values[, "x"]
y = global.path.values[, "y"]
angle.from.xaxis = ((atan2(y, x) * sign(arena$correction$e$arena.rotation) + pi) / (2 * pi) * 360 + 180) %% 360
angle.from.aversive.zone = NA
if(aversive.zone.present){
aversive.zone.width = arena$aversive.zone$end.angle - arena$aversive.zone$start.angle
angle.from.aversive.zone = 0
if(sign(arena$correction$e$arena.rotation) == -1){
angle.from.aversive.zone = (((angle.from.xaxis + 90 + 360) - (arena$aversive.zone$start.angle)) %% 360) - aversive.zone.width
angle.from.aversive.zone[angle.from.aversive.zone < 0] = 0 # Inside aversive zone = zero distance.
}else{
angle.from.aversive.zone = (((arena$aversive.zone$end.angle + 360) - (angle.from.xaxis + 90)) %% 360) - aversive.zone.width
angle.from.aversive.zone[angle.from.aversive.zone < 0] = 0 # Inside aversive zone = zero distance.
}
}
angle.from.old.aversive.zone = NA
if(old.aversive.zone.present){
old.aversive.zone.width = arena$old.aversive.zone$end.angle - arena$old.aversive.zone$start.angle
angle.from.old.aversive.zone = 0
if(sign(arena$correction$e$arena.rotation) == -1){
angle.from.old.aversive.zone = (((angle.from.xaxis + 90 + 360) - (arena$old.aversive.zone$start.angle)) %% 360) - old.aversive.zone.width
angle.from.old.aversive.zone[angle.from.old.aversive.zone < 0] = 0 # Inside aversive zone = zero distance.
}else{
angle.from.old.aversive.zone = (((arena$old.aversive.zone$end.angle + 360) - (angle.from.xaxis + 90)) %% 360) - old.aversive.zone.width
angle.from.old.aversive.zone[angle.from.old.aversive.zone < 0] = 0 # Inside aversive zone = zero distance.
}
}
# Speed in zones (total time using normalised units)
total.time = diff(range(path$t, na.rm = T))
intervals = diff(path$t)
negligible = intervals == 0 # This can happen due to rounding precision.
velocity = path.segment.lengths[!negligible] / intervals[!negligible]
velocity[is.infinite(velocity) | is.nan(velocity)] = NA
velocity.in.zone = lapply(in.zones, function(in.zone){
median(velocity[which(in.zone[!negligible])], na.rm = TRUE)
})
if(!aversive.zone.present) velocity.in.zone$aversive.zone = NA
if(!old.aversive.zone.present) velocity.in.zone$old.aversive.zone = NA
# Immobility in each zone.
immobile = c(velocity < 0.001, FALSE) # Additional dummy interval as padding.
immobility = sum(intervals[which(immobile)], na.rm = TRUE)
immobility.in.zone = lapply(in.zones, function(in.zone){
sum(intervals[which(immobile & in.zone[!negligible])], na.rm = TRUE)
})
if(!aversive.zone.present) immobility.in.zone$aversive.zone = NA
if(!old.aversive.zone.present) immobility.in.zone$old.aversive.zone = NA
# Latency to enter zone
latency.to.zone = lapply(in.zones, function(in.zone){
path$t[which(in.zone)[1]] - path$t[1]
})
if(!aversive.zone.present) latency.to.zone$aversive.zone = NA
if(!old.aversive.zone.present) latency.to.zone$old.aversive.zone = NA
# Roaming entropy
gridsize = 50
freq = KernSmooth::bkde2D(local.path.values, range.x = list(c(-1, 1), c(-1, 1)), bandwidth = c(1 / gridsize, 1 / gridsize), gridsize = c(gridsize, gridsize))$fhat
sequence = seq(-1, 1, length.out = gridsize)
grid = terra::vect(cbind(x = rep(sequence, times = gridsize), y = rep(sequence, each = gridsize)), type = "points")
sum = sum(freq, na.rm = T)
p = (freq / sum)[freq > 0]
roaming.entropy = -sum(p * log(p)) / log(length(p))
# Here the time spent in each defined zone is calculated
time.in.zone = lapply(in.zones, function(in.zone) sum(in.zone, na.rm = T) / length(path$t) )
if(!aversive.zone.present) time.in.zone$aversive.zone = NA
if(!old.aversive.zone.present) time.in.zone$old.aversive.zone = NA
zone.crossings = lapply(in.zones, function(in.zone){
ceiling(length(which(in.zone[-length(in.zone)] != in.zone[-1])) / 2) # Half the transitions between 'in'/'out' are 'crossings'
})
if(!aversive.zone.present) zone.crossings$aversive.zone = NA
if(!old.aversive.zone.present) zone.crossings$old.aversive.zone = NA
velocity.quantile = unname(stats::quantile(velocity, na.rm = TRUE))
immobility.quantile = unname(stats::quantile(immobility, na.rm = TRUE))
angle.from.aversive.zone.quantile = rep(NA, 5)
if(!is.null(arena$zones$aversive.zone)) angle.from.aversive.zone.quantile = unname(stats::quantile(angle.from.aversive.zone, na.rm = TRUE))
angle.from.old.aversive.zone.quantile = rep(NA, 5)
if(!is.null(arena$zones$old.aversive.zone)) angle.from.old.aversive.zone.quantile = unname(stats::quantile(angle.from.old.aversive.zone, na.rm = TRUE))
metrics = list(
id = path$id,
arena = arena,
area = sapply(arena$zones, terra::expanse, transform = FALSE),
path = path, # This path has local coordinates embedded (use for plotting).
path.length = path.length,
velocity = velocity,
immobile = immobile,
immobile.x = path$x[immobile],
immobile.y = path$y[immobile],
immobility = immobility,
total.time = total.time,
angle.from.aversive.zone = angle.from.aversive.zone,
angle.from.old.aversive.zone = angle.from.old.aversive.zone,
goal.crossings = zone.crossings$aversive.zone,
coverage = coverage,
roaming.entropy = roaming.entropy,
velocity.in.zone = velocity.in.zone,
immobility.in.zone = immobility.in.zone,
latency.to.zone = latency.to.zone,
time.in.zone = time.in.zone,
zone.crossings = zone.crossings,
features = c(
path.length = path.length,
lower.velocity = velocity.quantile[2],
median.velocity = velocity.quantile[3],
upper.velocity = velocity.quantile[4],
lower.immobility = immobility.quantile[2],
median.immobility = immobility.quantile[3],
upper.immobility = immobility.quantile[4],
coverage = coverage,
turning = sum(turning, na.rm = T) / total.time,
absolute.turning = sum(abs(turning), na.rm = T) / total.time,
lower.angle.from.aversive.zone = angle.from.aversive.zone.quantile[2],
median.angle.from.aversive.zone = angle.from.aversive.zone.quantile[3],
upper.angle.from.aversive.zone = angle.from.aversive.zone.quantile[4],
lower.angle.from.old.aversive.zone = angle.from.old.aversive.zone.quantile[2],
median.angle.from.old.aversive.zone = angle.from.old.aversive.zone.quantile[3],
upper.angle.from.old.aversive.zone = angle.from.old.aversive.zone.quantile[4],
roaming.entropy = roaming.entropy,
velocity.in.centre.zone = velocity.in.zone$centre,
velocity.in.wall.zone = velocity.in.zone$wall,
velocity.in.aversive.zone = ifelse(!is.null(velocity.in.zone$aversive.zone), velocity.in.zone$aversive.zone, NA),
velocity.in.old.aversive.zone = ifelse(!is.null(velocity.in.zone$old.aversive.zone), velocity.in.zone$old.aversive.zone, NA),
immobility.in.centre.zone = immobility.in.zone$centre,
immobility.in.wall.zone = immobility.in.zone$wall,
immobility.in.aversive.zone = ifelse(!is.null(immobility.in.zone$aversive.zone), immobility.in.zone$aversive.zone, NA),
immobility.in.old.aversive.zone = ifelse(!is.null(immobility.in.zone$old.aversive.zone), immobility.in.zone$old.aversive.zone, NA),
latency.to.centre.zone = latency.to.zone$centre,
latency.to.wall.zone = latency.to.zone$wall,
latency.to.aversive.zone = ifelse(!is.null(latency.to.zone$aversive.zone), latency.to.zone$aversive.zone, NA),
latency.to.old.aversive.zone = ifelse(!is.null(latency.to.zone$old.aversive.zone), latency.to.zone$old.aversive.zone, NA),
time.in.centre.zone = time.in.zone$centre,
time.in.wall.zone = time.in.zone$wall,
time.in.aversive.zone = ifelse(!is.null(time.in.zone$aversive.zone), time.in.zone$aversive.zone, NA),
time.in.old.aversive.zone = ifelse(!is.null(time.in.zone$old.aversive.zone), time.in.zone$old.aversive.zone, NA),
centre.zone.crossings = zone.crossings$centre,
wall.zone.crossings = zone.crossings$wall,
aversive.zone.crossings = ifelse(!is.null(zone.crossings$aversive.zone), zone.crossings$aversive.zone, NA),
old.aversive.zone.crossings = ifelse(!is.null(zone.crossings$old.aversive.zone), zone.crossings$old.aversive.zone, NA)
),
summary = c(
path.length = path.length * arena$correction$r,
total.time = total.time * arena$correction$t,
velocity = velocity.quantile[3] * arena$correction$r * arena$correction$t,
immobility = immobility.quantile[3] * arena$correction$r * arena$correction$t,
angle.from.aversive.zone = angle.from.aversive.zone.quantile[3],
angle.from.old.aversive.zone = angle.from.old.aversive.zone.quantile[3],
roaming.entropy = roaming.entropy,
latency.to.aversive.zone = ifelse(!is.null(latency.to.zone$aversive.zone), latency.to.zone$aversive.zone, NA) * arena$correction$t,
latency.to.old.aversive.zone = ifelse(!is.null(latency.to.zone$old.aversive.zone), latency.to.zone$old.aversive.zone, NA) * arena$correction$t,
time.in.centre.zone = time.in.zone$centre * total.time,
time.in.wall.zone = time.in.zone$wall * total.time * arena$correction$t,
time.in.aversive.zone = ifelse(!is.null(time.in.zone$aversive.zone), time.in.zone$aversive.zone, NA) * total.time * arena$correction$t,
time.in.old.aversive.zone = ifelse(!is.null(time.in.zone$old.aversive.zone), time.in.zone$old.aversive.zone, NA) * total.time * arena$correction$t,
aversive.zone.crossings = ifelse(!is.null(zone.crossings$aversive.zone), zone.crossings$aversive.zone, NA),
old.aversive.zone.crossings = ifelse(!is.null(zone.crossings$old.aversive.zone), zone.crossings$old.aversive.zone, NA)
)
)
# Replace serialised arena zones and add additionals.
metrics$arena$zones = wrapped.arena.zones
class(metrics) = "rtrack_metrics"
return(metrics)
}
Try the Rtrack package in your browser
Any scripts or data that you put into this service are public.
Rtrack documentation built on Aug. 10, 2023, 9:10 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions calculate_apa_metrics
#' @importFrom terra unwrap vect convHull expanse crds centroids relate
#' @importFrom KernSmooth bkde2D
#' @importFrom stats quantile
#' @importFrom utils globalVariables
utils::globalVariables(c("velocity.quantile", "immobility.quantile", "angle.from.aversive.zone.quantile"))
calculate_apa_metrics = function(path, arena){
# Deserialise arena zones, but retain wrapped version to return.
wrapped.arena.zones = arena$zones
arena$zones = lapply(arena$zones, terra::unwrap)
# Check for presence of optional zones (terra cannot handle missing data).
aversive.zone.present = !is.null(arena$zones$aversive.zone)
old.aversive.zone.present = !is.null(arena$zones$old.aversive.zone)
# APA has two frames of reference. Calculate local (subject) frame coordinates.
rotated.angle = arena$correction$e$arena.rotation * (path$t) # Rotated angle changes over time.
rotated.points = spin(path$x, path$y, deg2rad(rotated.angle))
path$local.x = rotated.points$x
path$local.y = rotated.points$y
# Movement metrics are calculated in either the local frame (of the subject) or the global frame (of the room).
# Area covered by the swim path as a fraction of the total arena
local.path.values = cbind(x = path$local.x, y = path$local.y)
local.pathpoints = terra::vect(local.path.values, type = "points", crs = "local") # With closed path.
global.path.values = cbind(x = path$x, y = path$y)
global.pathpoints = terra::vect(global.path.values, type = "points", crs = "local") # With closed path.
pathpoly = terra::vect(local.path.values, type = "polygons", crs = "local")
coverage = terra::expanse(terra::convHull(pathpoly), transform = FALSE) / terra::expanse(arena$zones$arena, transform = FALSE) # Arena circle is actually a 360-point polygon approximation of a circle (area < pi r^2).
path.centroid = terra::crds(terra::centroids(pathpoly))
d.centroid = ((path$x - path.centroid[1]) ^ 2 + (path$y - path.centroid[2]) ^ 2) ^ .5
d.origin = ((path$x) ^ 2 + (path$y) ^ 2) ^ .5
in.zones = lapply(arena$zones, function(zone) as.logical(rowSums(terra::relate(local.pathpoints, zone, relation = "intersects"))) )
if(aversive.zone.present) in.zones$aversive.zone = as.logical(rowSums(terra::relate(global.pathpoints, arena$zones$aversive.zone, relation = "intersects"))) # In GLOBAL frame.
if(old.aversive.zone.present) in.zones$old.aversive.zone = as.logical(rowSums(terra::relate(global.pathpoints, arena$zones$old.aversive.zone, relation = "intersects"))) # In GLOBAL frame.
# Path length
path.segment.lengths = sqrt(diff(local.path.values[, "x"]) ^ 2 + diff(local.path.values[, "y"]) ^ 2)
path.length = sum(path.segment.lengths)
# 'Turning' behaviour measured by angular displacement at each timepoint
dx = diff(global.path.values[, "x"])
dy = diff(global.path.values[, "y"])
angle.from.xaxis = atan2(dy, dx)
turning = diff(angle.from.xaxis)
# Angle from aversive zone.
x = global.path.values[, "x"]
y = global.path.values[, "y"]
angle.from.xaxis = ((atan2(y, x) * sign(arena$correction$e$arena.rotation) + pi) / (2 * pi) * 360 + 180) %% 360
angle.from.aversive.zone = NA
if(aversive.zone.present){
aversive.zone.width = arena$aversive.zone$end.angle - arena$aversive.zone$start.angle
angle.from.aversive.zone = 0
if(sign(arena$correction$e$arena.rotation) == -1){
angle.from.aversive.zone = (((angle.from.xaxis + 90 + 360) - (arena$aversive.zone$start.angle)) %% 360) - aversive.zone.width
angle.from.aversive.zone[angle.from.aversive.zone < 0] = 0 # Inside aversive zone = zero distance.
}else{
angle.from.aversive.zone = (((arena$aversive.zone$end.angle + 360) - (angle.from.xaxis + 90)) %% 360) - aversive.zone.width
angle.from.aversive.zone[angle.from.aversive.zone < 0] = 0 # Inside aversive zone = zero distance.
}
}
angle.from.old.aversive.zone = NA
if(old.aversive.zone.present){
old.aversive.zone.width = arena$old.aversive.zone$end.angle - arena$old.aversive.zone$start.angle
angle.from.old.aversive.zone = 0
if(sign(arena$correction$e$arena.rotation) == -1){
angle.from.old.aversive.zone = (((angle.from.xaxis + 90 + 360) - (arena$old.aversive.zone$start.angle)) %% 360) - old.aversive.zone.width
angle.from.old.aversive.zone[angle.from.old.aversive.zone < 0] = 0 # Inside aversive zone = zero distance.
}else{
angle.from.old.aversive.zone = (((arena$old.aversive.zone$end.angle + 360) - (angle.from.xaxis + 90)) %% 360) - old.aversive.zone.width
angle.from.old.aversive.zone[angle.from.old.aversive.zone < 0] = 0 # Inside aversive zone = zero distance.
}
}
# Speed in zones (total time using normalised units)
total.time = diff(range(path$t, na.rm = T))
intervals = diff(path$t)
negligible = intervals == 0 # This can happen due to rounding precision.
velocity = path.segment.lengths[!negligible] / intervals[!negligible]
velocity[is.infinite(velocity) | is.nan(velocity)] = NA
velocity.in.zone = lapply(in.zones, function(in.zone){
median(velocity[which(in.zone[!negligible])], na.rm = TRUE)
})
if(!aversive.zone.present) velocity.in.zone$aversive.zone = NA
if(!old.aversive.zone.present) velocity.in.zone$old.aversive.zone = NA
# Immobility in each zone.
immobile = c(velocity < 0.001, FALSE) # Additional dummy interval as padding.
immobility = sum(intervals[which(immobile)], na.rm = TRUE)
immobility.in.zone = lapply(in.zones, function(in.zone){
sum(intervals[which(immobile & in.zone[!negligible])], na.rm = TRUE)
})
if(!aversive.zone.present) immobility.in.zone$aversive.zone = NA
if(!old.aversive.zone.present) immobility.in.zone$old.aversive.zone = NA
# Latency to enter zone
latency.to.zone = lapply(in.zones, function(in.zone){
path$t[which(in.zone)[1]] - path$t[1]
})
if(!aversive.zone.present) latency.to.zone$aversive.zone = NA
if(!old.aversive.zone.present) latency.to.zone$old.aversive.zone = NA
# Roaming entropy
gridsize = 50
freq = KernSmooth::bkde2D(local.path.values, range.x = list(c(-1, 1), c(-1, 1)), bandwidth = c(1 / gridsize, 1 / gridsize), gridsize = c(gridsize, gridsize))$fhat
sequence = seq(-1, 1, length.out = gridsize)
grid = terra::vect(cbind(x = rep(sequence, times = gridsize), y = rep(sequence, each = gridsize)), type = "points")
sum = sum(freq, na.rm = T)
p = (freq / sum)[freq > 0]
roaming.entropy = -sum(p * log(p)) / log(length(p))
# Here the time spent in each defined zone is calculated
time.in.zone = lapply(in.zones, function(in.zone) sum(in.zone, na.rm = T) / length(path$t) )
if(!aversive.zone.present) time.in.zone$aversive.zone = NA
if(!old.aversive.zone.present) time.in.zone$old.aversive.zone = NA
zone.crossings = lapply(in.zones, function(in.zone){
ceiling(length(which(in.zone[-length(in.zone)] != in.zone[-1])) / 2) # Half the transitions between 'in'/'out' are 'crossings'
})
if(!aversive.zone.present) zone.crossings$aversive.zone = NA
if(!old.aversive.zone.present) zone.crossings$old.aversive.zone = NA
velocity.quantile = unname(stats::quantile(velocity, na.rm = TRUE))
immobility.quantile = unname(stats::quantile(immobility, na.rm = TRUE))
angle.from.aversive.zone.quantile = rep(NA, 5)
if(!is.null(arena$zones$aversive.zone)) angle.from.aversive.zone.quantile = unname(stats::quantile(angle.from.aversive.zone, na.rm = TRUE))
angle.from.old.aversive.zone.quantile = rep(NA, 5)
if(!is.null(arena$zones$old.aversive.zone)) angle.from.old.aversive.zone.quantile = unname(stats::quantile(angle.from.old.aversive.zone, na.rm = TRUE))
metrics = list(
id = path$id,
arena = arena,
area = sapply(arena$zones, terra::expanse, transform = FALSE),
path = path, # This path has local coordinates embedded (use for plotting).
path.length = path.length,
velocity = velocity,
immobile = immobile,
immobile.x = path$x[immobile],
immobile.y = path$y[immobile],
immobility = immobility,
total.time = total.time,
angle.from.aversive.zone = angle.from.aversive.zone,
angle.from.old.aversive.zone = angle.from.old.aversive.zone,
goal.crossings = zone.crossings$aversive.zone,
coverage = coverage,
roaming.entropy = roaming.entropy,
velocity.in.zone = velocity.in.zone,
immobility.in.zone = immobility.in.zone,
latency.to.zone = latency.to.zone,
time.in.zone = time.in.zone,
zone.crossings = zone.crossings,
features = c(
path.length = path.length,
lower.velocity = velocity.quantile[2],
median.velocity = velocity.quantile[3],
upper.velocity = velocity.quantile[4],
lower.immobility = immobility.quantile[2],
median.immobility = immobility.quantile[3],
upper.immobility = immobility.quantile[4],
coverage = coverage,
turning = sum(turning, na.rm = T) / total.time,
absolute.turning = sum(abs(turning), na.rm = T) / total.time,
lower.angle.from.aversive.zone = angle.from.aversive.zone.quantile[2],
median.angle.from.aversive.zone = angle.from.aversive.zone.quantile[3],
upper.angle.from.aversive.zone = angle.from.aversive.zone.quantile[4],
lower.angle.from.old.aversive.zone = angle.from.old.aversive.zone.quantile[2],
median.angle.from.old.aversive.zone = angle.from.old.aversive.zone.quantile[3],
upper.angle.from.old.aversive.zone = angle.from.old.aversive.zone.quantile[4],
roaming.entropy = roaming.entropy,
velocity.in.centre.zone = velocity.in.zone$centre,
velocity.in.wall.zone = velocity.in.zone$wall,
velocity.in.aversive.zone = ifelse(!is.null(velocity.in.zone$aversive.zone), velocity.in.zone$aversive.zone, NA),
velocity.in.old.aversive.zone = ifelse(!is.null(velocity.in.zone$old.aversive.zone), velocity.in.zone$old.aversive.zone, NA),
immobility.in.centre.zone = immobility.in.zone$centre,
immobility.in.wall.zone = immobility.in.zone$wall,
immobility.in.aversive.zone = ifelse(!is.null(immobility.in.zone$aversive.zone), immobility.in.zone$aversive.zone, NA),
immobility.in.old.aversive.zone = ifelse(!is.null(immobility.in.zone$old.aversive.zone), immobility.in.zone$old.aversive.zone, NA),
latency.to.centre.zone = latency.to.zone$centre,
latency.to.wall.zone = latency.to.zone$wall,
latency.to.aversive.zone = ifelse(!is.null(latency.to.zone$aversive.zone), latency.to.zone$aversive.zone, NA),
latency.to.old.aversive.zone = ifelse(!is.null(latency.to.zone$old.aversive.zone), latency.to.zone$old.aversive.zone, NA),
time.in.centre.zone = time.in.zone$centre,
time.in.wall.zone = time.in.zone$wall,
time.in.aversive.zone = ifelse(!is.null(time.in.zone$aversive.zone), time.in.zone$aversive.zone, NA),
time.in.old.aversive.zone = ifelse(!is.null(time.in.zone$old.aversive.zone), time.in.zone$old.aversive.zone, NA),
centre.zone.crossings = zone.crossings$centre,
wall.zone.crossings = zone.crossings$wall,
aversive.zone.crossings = ifelse(!is.null(zone.crossings$aversive.zone), zone.crossings$aversive.zone, NA),
old.aversive.zone.crossings = ifelse(!is.null(zone.crossings$old.aversive.zone), zone.crossings$old.aversive.zone, NA)
),
summary = c(
path.length = path.length * arena$correction$r,
total.time = total.time * arena$correction$t,
velocity = velocity.quantile[3] * arena$correction$r * arena$correction$t,
immobility = immobility.quantile[3] * arena$correction$r * arena$correction$t,
angle.from.aversive.zone = angle.from.aversive.zone.quantile[3],
angle.from.old.aversive.zone = angle.from.old.aversive.zone.quantile[3],
roaming.entropy = roaming.entropy,
latency.to.aversive.zone = ifelse(!is.null(latency.to.zone$aversive.zone), latency.to.zone$aversive.zone, NA) * arena$correction$t,
latency.to.old.aversive.zone = ifelse(!is.null(latency.to.zone$old.aversive.zone), latency.to.zone$old.aversive.zone, NA) * arena$correction$t,
time.in.centre.zone = time.in.zone$centre * total.time,
time.in.wall.zone = time.in.zone$wall * total.time * arena$correction$t,
time.in.aversive.zone = ifelse(!is.null(time.in.zone$aversive.zone), time.in.zone$aversive.zone, NA) * total.time * arena$correction$t,
time.in.old.aversive.zone = ifelse(!is.null(time.in.zone$old.aversive.zone), time.in.zone$old.aversive.zone, NA) * total.time * arena$correction$t,
aversive.zone.crossings = ifelse(!is.null(zone.crossings$aversive.zone), zone.crossings$aversive.zone, NA),
old.aversive.zone.crossings = ifelse(!is.null(zone.crossings$old.aversive.zone), zone.crossings$old.aversive.zone, NA)
)
)
# Replace serialised arena zones and add additionals.
metrics$arena$zones = wrapped.arena.zones
class(metrics) = "rtrack_metrics"
return(metrics)
}
Try the Rtrack package in your browser
Any scripts or data that you put into this service are public.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.