`ColonyTrack_metrics_description.Rmd`

The `colonytrack_metrics`

object contains features/metrics
calculated from the tracking data. The data are segmented by day
(technically by ‘window’; see the following section) and processed in
parallel to extract a range of metrics describing the activity of the
subjects and their interactions with each other. Details of the
resulting `colonytrack_metrics`

object are given below.

The metrics are calculated for blocks of time, referred to as
‘windows’. In the current version of the software, these windows default
to a 12-hour period during the dark phase (ZT12–ZT24). Support for
calculation of light phase metrics (and limited support for customised
window intervals) will be added to an upcoming version. An additional
parameter `trim`

allows for hours to be trimmed off the start
and end of the metrics calculation period. This makes it possible to
remove the first and last hours of data—in the situation that the light
cycle is not strictly maintained for example. This feature could also
enable the user to focus on a particular period of interest—although it
is recommended to perform such trimming during later analysis of the
metrics results. The `trim`

parameter will only accept
integer values (rounded hours) and care should be taken in interpreting
the results if this feature is used. The windows are described in the
`windows`

section of the `info`

component and
consist of an ID (by default the date in YYYY-MM-DD format) and a start
and end time as UNIX timestamps.

The cage layout is described in the `cage.layout`

section
of the `info`

component as a list of `igraph`

objects (see the data
object description for additional background). This list, with one
cage layout per day, allows for the flexibility to include modifications
of the cage layout during an experiment. The `igraph`

objects
are passed through from the `colonytrack_data`

object and
contain the same information.

The `calculate_metrics`

function generates a list of 109
variables, many of which are derivatives (e.g. mean, median, variance)
of the same information (see the detailed description below for a list
of all metrics that are calculated). All of these values describe the
underlying data in subtly different ways and are thus useful for certain
applications such as machine learning. Reflecting this intended purpose,
these variables are referred to in the metrics object as ‘features’. A
list of the feature names can also be obtained computationally by
querying a `colonytrack_metrics`

object and inspecting the
`metrics$info$feature.names`

component.

For general use, however, the large collection of partially redundant
variables is not helpful, so a select subset is returned in the
`individual`

component of the metrics object. The names of
the individual metrics can be recalled from the
`metrics$info$var.names`

component of a
`colonytrack_metrics`

object. These individual metrics are
accessible for plotting by the `plot_metric`

function. For a
detailed description of each of the `individual`

metrics,
please refer to the separate metrics details
vignette).

The `cage.use`

component holds a list for each day of
tracking which is further subdivided into each cage; where the
proportion of time spent in each cage by each subject is recorded. Thus
the values for the first subject over all cages in one day should sum to
1. This enables the time spent in a cage of interest (e.g. a cage with
water access) to be easily calculated and can provide the basis for a
customised analysis of your cage set-up.

The ethogram is calculated hourly and is used as the basis for the
built-in `plot_ethogram`

function. The ethogram uses 3
summary metrics to encapsulate the ‘activity’, ‘exploration’ and
‘sociality’ dimensions of the subjects behaviour. Although this does not
make use of the full multi-parametric power of ColonyTrack, it provides
a rapid and intuitive overview (for users with full colour vision) of
the behavioural patterns for very many subjects over long periods of
time. The `ethogram`

component makes the numeric data
underlying the ethogram plot accessible to users—for example to enable
custom plots to be generated. Split into a list by day, the three
dimensions (‘activity’, ‘exploration’ and ‘sociality’) are available as
a numeric matrix with 12 columns (one for each hour of the day) and a
row for each subject. Users can, for example, build a custom one-colour
heatmap for each dimension separately using an appropriate palette to
provide colourblind-friendly output.

The group-housing nature of the ColonyRack enables interactions
between subjects to be recorded. Different to the individual metrics,
these social interactions are reported as a subject x subject matrix.
The group metrics that are calculated are `interaction.time`

(the amount of time that each pair of subjects spend in the same cage),
`social.distance`

(the average number of cages separating
each pair of subjects; technically, the mean shortest path in the cage
network between the two subjects over the course of the day^{1}) and
`following`

(the number of times one subject [rows] follows
another [columns]; see the section on ‘following’ below). With the
exception of `following`

, these interaction matrices are
symmetrical (in graph theory parlance, they are undirected networks).
The `following`

network, on the other hand, is directed—the
subject doing the following (the ‘aggressor’) is in the rows with the
subject being followed (the ‘victim’) in the columns^{2}.

A follow event is defined as two subjects passing through the same
tunnel in the same direction in rapid (less than 1 second delay)
succession. The second subject passing through the tunnel is understood
to be pursuing the first (this interpretation has been initially
confirmed using video observation of the cage system). The directed
nature of this interaction means that a hierarchy can be calculated by
summing the ‘wins’ (the number of times a subject was the pursuer) for
each pair of subjects. A subject with more ‘wins’ over another is taken
to be dominant in the social hierarchy. The results are presented using
this terminology for practical convenience—the actual dominance
relationships identified by this method are interpretations from the
automated data. The `dominance`

score for each subject is
pre-calculated for convenience from the follow network for each day. It
is provided as a raw sum of ‘wins’ and ‘losses’ and can be converted to
ranks by the user if desired^{3}.

Below is an overview of the hierarchy of the
`colonytrack_metrics`

object together with the names and
classes of each component. Where the class is not part of the R base
package, the package providing it is given in square brackets after the
class name.

```
metrics : colonytrack_metrics [ColonyTrack]
info : list
windows : colonytrack_windows [ColonyTrack]
id : character
start : numeric
end : numeric
subjects : character
subject.info : data.frame
SubjectID : character
Tag : character
(optional additional user-defined columns)
feature.names : character
var.names : character
cage.layout : list
(window) : igraph [igraph]
processed : POSIXct
version : character
features : list
(subject) : data.frame
path.length : numeric
max.time.in.cage : numeric
mean.time.in.cage : numeric
min.time.in.cage : numeric
sd.time.in.cage : numeric
upper.time.in.cage : numeric
median.time.in.cage : numeric
lower.time.in.cage : numeric
time.high.activity : numeric
time.sustained.activity : numeric
time.active : numeric
time.inactive : numeric
total.activity.burst.time : numeric
max.activity.burst.length : numeric
max.activity.burst.time : numeric
max.cage.use : numeric
mean.cage.use : numeric
min.cage.use : numeric
sd.cage.use : numeric
upper.cage.use : numeric
median.cage.use : numeric
lower.cage.use : numeric
cage.time.entropy : numeric
max.adj.cage.use : numeric
mean.adj.cage.use : numeric
min.adj.cage.use : numeric
sd.adj.cage.use : numeric
upper.adj.cage.use : numeric
median.adj.cage.use : numeric
lower.adj.cage.use : numeric
adjusted.cage.time.entropy : numeric
max.cage.transitions : numeric
mean.cage.transitions : numeric
min.cage.transitions : numeric
sd.cage.transitions : numeric
upper.cage.transitions : numeric
median.cage.transitions : numeric
lower.cage.transitions : numeric
cage.location.entropy : numeric
max.adj.cage.transitions : numeric
mean.adj.cage.transitions : numeric
min.adj.cage.transitions : numeric
sd.adj.cage.transitions : numeric
upper.adj.cage.transitions : numeric
median.adj.cage.transitions : numeric
lower.adj.cage.transitions : numeric
adjusted.cage.location.entropy : numeric
max.revisit.time : numeric
mean.revisit.time : numeric
min.revisit.time : numeric
sd.revisit.time : numeric
upper.revisit.time : numeric
median.revisit.time : numeric
lower.revisit.time : numeric
max.revisit.length : numeric
mean.revisit.length : numeric
min.revisit.length : numeric
sd.revisit.length : numeric
upper.revisit.length : numeric
median.revisit.length : numeric
lower.revisit.length : numeric
peak.inactive.timepoint : numeric
peak.active.timepoint : numeric
number.activity.blocks : numeric
max.cage.sharing : numeric
mean.cage.sharing : numeric
upper.cage.sharing : numeric
median.cage.sharing : numeric
lower.cage.sharing : numeric
time.alone : numeric
max.social.interaction.time : numeric
mean.social.interaction.time : numeric
min.social.interaction.time : numeric
sd.social.interaction.time : numeric
upper.social.interaction.time : numeric
median.social.interaction.time: numeric
lower.social.interaction.time : numeric
social.exposure : numeric
max.distance.from.all : numeric
mean.distance.from.all : numeric
min.distance.from.all : numeric
sd.distance.from.all : numeric
upper.distance.from.all : numeric
median.distance.from.all : numeric
lower.distance.from.all : numeric
max.distance.from.each : numeric
min.distance.from.each : numeric
sd.distance.from.each : numeric
upper.distance.from.each : numeric
median.distance.from.each : numeric
lower.distance.from.each : numeric
max.sharing.change : numeric
mean.sharing.change : numeric
min.sharing.change : numeric
sd.sharing.change : numeric
upper.sharing.change : numeric
median.sharing.change : numeric
lower.sharing.change : numeric
max.influence : numeric
mean.influence : numeric
min.influence : numeric
sd.influence : numeric
upper.influence : numeric
median.influence : numeric
lower.influence : numeric
number.follow.events : numeric
sd.follow.events : numeric
mean.follow.wins : numeric
sd.follow.wins : numeric
follow.sds : numeric
individual : list
(subject) : data.frame
distance.moved : numeric
time.per.cage : numeric
high.activity : numeric
sustained.activity : numeric
cage.variability : numeric
cage.time.entropy : numeric
adjusted.cage.time.entropy : numeric
cage.location.entropy : numeric
revisit.time : numeric
revisit.length : numeric
peak.inactive : numeric
peak.active : numeric
activity.blocks : numeric
cage.sharing : numeric
time.alone : numeric
social.interaction : numeric
social.distance : numeric
social.gradient : numeric
social.influence : numeric
follow.events : numeric
follow.dominance : numeric
cage.use : list
(window) : data.frame
(cage) : numeric
ethogram : list
(window) : list
activity : numeric
exploration : numeric
sociality : numeric
clustering : list
interaction.time : list
(window) : numeric matrix
social.distance : list
(window) : numeric matrix
following : list
(window) : numeric matrix
dominance : list
(window) : numeric
follow.events : list
(window) : list
(subject) : list
(subject) : data.frame
Timestamp : numeric
Transition : character
development : list
elapsed.time : numeric
threads : list
start.time : numeric
end.time : numeric
elapsed.time : numeric
```

The calculation of this component changed in version 1.0.4 to use weighted means—See the description of the social.distance metric for more information.↩︎

Note that this has changed in v1.0.2 and was transposed in earlier ColonyTrack versions.↩︎

Other scores, such as the commonly-used David’s score, can be calculated from the

`following`

tables in the`clustering`

component. Future versions of ColonyTrack may offer multiple variants of the dominance score.↩︎