Summarize representative trajectories

Summarize the properties of representative trajectories returned by retra_edr() or define_retra()

Usage

# S3 method for class 'RETRA'
summary(object, ...)

Arguments

object

An object of class RETRA.

...

(not used)

Value

Data frame with nine columns and one row for each representative trajectory in object. The columns in the returned data frame contain the following information:

ID

Identifier of the representative trajectories.

Size

Number of states forming each representative trajectory.

Length

Sum of the dissimilarities in d between every pair of consecutive states forming the representative trajectories.

Avg_link

Mean value of the dissimilarities between consecutive states of the representative trajectories that do not belong to the same ecological trajectory or site (i.e., artificial links).

Sum_link

Sum of the dissimilarities between consecutive states of the representative trajectories that do not belong to the same ecological trajectory or site (i.e., artificial links).

Avg_density

Mean value of the number of segments represented by each segment of the representative trajectory (excluding artificial links).

Max_density

Maximum number of segments represented by at least one of the segments of the representative trajectory (excluding artificial links).

Avg_depth

Mean value of the k-d tree depths, that is, the number of partitions of the ordination space until finding a region with minSegs segments or less.

Max_depth

Maximum depth in the k-d tree, that is, the number of partitions of the ordination space until finding a region with minSegs segments or less.

See also

retra_edr() for identifying representative trajectories in EDRs applying RETRA-EDR.

define_retra() for generating an object of class RETRA from trajectory features.

Examples

# Apply RETRA-EDR to identify representative trajectories
d = EDR_data$EDR1$state_dissim
trajectories = EDR_data$EDR1$abundance$traj
states = EDR_data$EDR1$abundance$state
RT <- retra_edr(d = d, trajectories = trajectories, states = states, minSegs = 5)

# Summarize the properties of the representative trajectories in a data frame
summary(RT)
#>    ID Size    Length   Avg_link  Sum_link Avg_density Max_density Avg_depth
#> T1 T1    3 0.2669408         NA        NA    6.500000           7  4.500000
#> T2 T2   15 0.9270207 0.05244879 0.3146927    7.125000           9  5.125000
#> T3 T3   13 0.6756596 0.04291652 0.2145826    7.428571           9  5.285714
#>    Max_depth
#> T1         5
#> T2         7
#> T3         7