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Representative trajectories in Ecological Dynamic Regimes (RETRA-EDR)

Source: R/retra_edr.R
retra_edr.Rd

retra_edr() applies the algorithm RETRA-EDR (Sánchez-Pinillos et al., 2023) to identify representative trajectories summarizing the main dynamical patterns of an Ecological Dynamic Regime (EDR).

Usage

retra_edr(
  d,
  trajectories,
  states,
  minSegs,
  dSegs = NULL,
  coordSegs = NULL,
  traj_Segs = NULL,
  state1_Segs = NULL,
  state2_Segs = NULL,
  Dim = NULL,
  eps = 0
)

Arguments

d

Either a symmetric matrix or an object of class dist containing the dissimilarities between each pair of states of all trajectories in the EDR.

trajectories

Vector indicating the trajectory or site to which each state in d belongs.

states

Vector of integers indicating the order of the states in d for each trajectory.

minSegs

Integer indicating the minimum number of segments in a region of the EDR represented by a segment of the representative trajectory.

dSegs

Either a symmetric matrix or an object of class dist containing the dissimilarities between every pair of trajectory segments (see Details).

coordSegs

Matrix containing the coordinates of trajectory segments (rows) in each axis (columns) of an ordination space (see Details).

traj_Segs

Vector indicating the trajectory to which each segment in dSeg and/or coordSegs belongs. Only required if dSegs or coordSegs are not NULL.

state1_Segs

Vector indicating the initial state of each segment in dSegs and/or coordSegs according to the values given in states. Only required if dSegs or coordSegs are not NULL.

state2_Segs

Vector indicating the final state of each segment in dSegs and/or coordSegs according to the values given in states. Only required if dSegs or coordSegs are not NULL.

Dim

Optional integer indicating the number of axes considered to partition the segment space and generate a k-d tree. By default (Dim = NULL), all axes are considered.

eps

Numeric value indicating the minimum length in the axes of the segment space to be partitioned when the k-d tree is generated. If eps = 0 (default), partitions are made regardless of the size.

Value

The function retra_edr() returns an object of class RETRA, which is a list of length equal to the number of representative trajectories identified. For each trajectory, the following information is returned:

minSegs

Value of the minSegs parameter.

Segments

Vector of strings including the sequence of segments forming the representative trajectory. Each segment is identified by a string of the form traj[st1-st2], where traj is the identifier of the original trajectory to which the segment belongs and st1 and st2 are identifiers of the initial and final states defining the segment.

Size

Numeric value indicating the number of states forming the representative trajectory.

Length

Numeric value indicating the length of the representative trajectory, calculated as the sum of the dissimilarities in d between every pair of consecutive states.

Link_distance

Data frame of two columns indicating artificial links between representative segments (Link) and the dissimilarity between the connected states (Distance). When two representative segments are linked by a common state or by two consecutive states of the same trajectory, the link distance is zero or equal to the length of a real segment, respectively. In both cases, the link is not considered in the returned data frame.

Seg_density

Data frame of two columns and one row for each representative segment. Density contains the number of segments in the EDR that is represented by each segment of the representative trajectory. kdTree_depth contains the depth of the k-d tree for each leaf represented by the corresponding segment. That is, the number of partitions of the ordination space until finding a region with minSegs segments or less.

Details

The algorithm RETRA-EDR is based on a partition-and-group approach by which it identifies regions densely crossed by ecological trajectories in an EDR, selects a representative segment in each dense region, and joins the representative segments by a set of artificial Links to generate a network of representative trajectories. For that, RETRA-EDR splits the trajectories of the EDR into segments and uses an ordination space generated from a matrix containing the dissimilarities between trajectory segments. Dense regions are identified by applying a k-d tree to the ordination space.

By default, RETRA-EDR calculates segment dissimilarities following the approach by De Cáceres et al. (2019) and applies metric multidimensional scaling (mMDS, Borg and Groenen, 2005) to generate the ordination space. It is possible to use other dissimilarity metrics and/or ordination methods and reduce the computational time by indicating the dissimilarity matrix and the coordinates of the segments in the ordination space through the arguments dSegs and coordSegs, respectively.

  • If !is.null(dSegs) and is.null(coordSegs), RETRA-EDR is computed by applying mMDS to dSegs.

  • If !is.null(dSegs) and !is.null(coordSegs), RETRA-EDR is directly computed from the coordinates provided in coordSegs and representative segments are identified using dSegs. coordSegs should be calculated by the user from dSegs.

  • If is.null(dSegs) and !is.null(coordSegs) (not recommended), RETRA-EDR is directly computed from the coordinates provided in coordSegs. As dSegs is not provided, retra_edr() assumes that the ordination space is metric and identifies representative segments using the Euclidean distance.

References

Borg, I., & Groenen, P. J. F. (2005). Modern Multidimensional Scaling (2nd ed.). Springer.

De Cáceres, M, Coll L, Legendre P, Allen RB, Wiser SK, Fortin MJ, Condit R & Hubbell S. (2019). Trajectory analysis in community ecology. Ecological Monographs.

Sánchez-Pinillos, M., Kéfi, S., De Cáceres, M., Dakos, V. 2023. Ecological Dynamic Regimes: Identification, characterization, and comparison. Ecological Monographs. doi:10.1002/ecm.1589

See also

summary() for summarizing the characteristics of the representative trajectories.

plot() for plotting representative trajectories in an ordination space representing the state space of the EDR.

define_retra() for defining representative trajectories from a subset of segments or trajectory features.

Author

Martina Sánchez-Pinillos

Examples

# Example 1 -----------------------------------------------------------------
# Identify representative trajectories from state dissimilarities

# Calculate state dissimilarities (Bray-Curtis) from species abundances
abundance <- data.frame(EDR_data$EDR1$abundance)
d <- vegan::vegdist(abundance[, -c(1:3)], method = "bray")

# Identify the trajectory (or site) and states in d
trajectories <- abundance$traj
states <- as.integer(abundance$state)

# Compute RETRA-EDR
RT1 <- retra_edr(d = d, trajectories = trajectories, states = states,
                 minSegs = 5)

# Example 2 -----------------------------------------------------------------
# Identify representative trajectories from segment dissimilarities

# Calculate segment dissimilarities using the Hausdorff distance
dSegs <- ecotraj::segmentDistances(ecotraj::defineTrajectories(d = d, sites = trajectories,
                                                               surveys = states),
                                   distance.type = "Hausdorff")
dSegs <- dSegs$Dseg

# Identify the trajectory (or site) and states in dSegs:
# Split the labels of dSegs (traj[st1-st2]) into traj, st1, and st2
seg_components <- strsplit(gsub("\\]", "", gsub("\\[", "-", labels(dSegs))), "-")
traj_Segs <- sapply(seg_components, "[", 1)
state1_Segs <- as.integer(sapply(seg_components, "[", 2))
state2_Segs <- as.integer(sapply(seg_components, "[", 3))

# Compute RETRA-EDR
RT2 <- retra_edr(d = d, trajectories = trajectories, states = states, minSegs = 5,
                dSegs = dSegs, traj_Segs = traj_Segs,
                state1_Segs = state1_Segs, state2_Segs = state2_Segs)