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Metrics of Ecological Dynamic Regimes

Source: R/EDR_metrics.R
EDR_metrics.Rd

Set of metrics to analyze the distribution and variability of trajectories in Ecological Dynamic Regimes (EDR), including dynamic dispersion (dDis), dynamic beta diversity (dBD), and dynamic evenness (dEve).

Usage

dDis(
  d,
  d.type,
  trajectories,
  states = NULL,
  reference,
  w.type = "none",
  w.values,
  ...
)

dBD(d, d.type, trajectories, states = NULL, ...)

dEve(d, d.type, trajectories, states = NULL, w.type = "none", w.values, ...)

Arguments

d

Symmetric matrix or object of class dist containing the dissimilarities between each pair of states of all trajectories in the EDR or the dissimilarities between each pair of trajectories. To compute dDis, d needs to include the dissimilarities between all states/trajectories and the states/trajectory of reference.

d.type

One of "dStates" (if d contains state dissimilarities) or "dTraj" (if d contains trajectory dissimilarities).

trajectories

Vector indicating the trajectory or site corresponding to each entry in d.

states

Only if d.type = "dStates". Vector of integers indicating the order of the states in d for each trajectory.

reference

Vector of the same class as trajectories and length equal to one, indicating the reference trajectory to compute dDis.

w.type

Method used to weight individual trajectories:

  • "none": All trajectories are considered equally relevant (default).

  • "length": Trajectories are weighted by their length, calculated as the sum of the dissimilarities between every pair of consecutive states. d must contain dissimilarities between trajectory states and d.type = "dStates".

  • "size": Trajectories are weighted by their size, calculated as the number of states forming the trajectory. d must contain dissimilarities between trajectory states and d.type = "dStates".

  • "precomputed": Trajectories weighted according to different criteria.

w.values

Only if w.type = "precomputed". Numeric vector of length equal to the number of trajectories containing the weight of each trajectory.

...

Only if d.type = "dStates". Further arguments to calculate trajectory dissimilarities. See ecotraj::trajectoryDistances().

Value

  • dDis() returns the value of dynamic dispersion for a given trajectory taken as a reference.

  • dBD() returns the value of dynamic beta diversity.

  • dEve() returns the value of dynamic evenness.

Details

Dynamic dispersion (dDis())

dDis is calculated as the average dissimilarity between each trajectory in an EDR and a target trajectory taken as reference (Sánchez-Pinillos et al., 2023).

\( dDis = \frac{\sum_{i=1}^{m}d_{i\alpha}}{m} \)

where \(d_{i\alpha}\) is the dissimilarity between trajectory \(i\) and the trajectory of reference \(\alpha\), and \(m\) is the number of trajectories.

Alternatively, it is possible to calculate a weighted mean of the dissimilarities by assigning a weight to each trajectory.

\( dDis = \frac{\sum_{i=1}^{m}w_{i}d_{i\alpha}}{\sum_{i=1}^{m}w_{i}} \)

where \(w_{i}\) is the weight assigned to trajectory \(i\).

Dynamic beta diversity (dBD())

dBD quantifies the overall variation of the trajectories in an EDR and is equivalent to the average distance to the centroid of the EDR (De Cáceres et al., 2019).

\( dBD = \frac{\sum_{i=1}^{m-1}\sum_{j=i+1}^{m}d_{ij}^{2}}{m(m-1)} \)

Dynamic evenness (dEve())

dEve quantifies the regularity with which an EDR is filled by the individual trajectories (Sánchez-Pinillos et al., 2023).

\( dEve = \frac{\sum_{l=1}^{m-1}\min(\frac{d_{ij}}{\sum_{l=1}^{m-1}d_{ij}}, \frac{1}{m-1}) - \frac{1}{m-1}}{1-\frac{1}{1-1}} \)

where \(d_{ij}\) is the dissimilarity between trajectories \(i\) and \(j\) linked in a minimum spanning tree by the link \(l\).

Optionally, it is possible to weight the trajectories of the EDR. In that case, dEve becomes analogous to the functional evenness index proposed by Villéger et al. (2008).

\( dEve_{w} = \frac{\sum_{l=1}^{m-1}\min(\frac{EW_{ij}}{\sum_{l=1}^{m-1}EW_{ij}}, \frac{1}{m-1}) - \frac{1}{m-1}}{1-\frac{1}{1-1}} \)

where \(EW_{ij}\) is the weighted evenness:

\( EW_{ij} = \frac{d_{ij}}{w_i + w_j} \)

References

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

Villéger, S., Mason, N.W.H., Mouillot, D. (2008) New multidimensional functional diversity indices for a multifaced framework in functional ecology. Ecology.

Author

Martina Sánchez-Pinillos

Examples

# Data to compute dDis, dBD, and dEve
dStates <- EDR_data$EDR1$state_dissim
dTraj <- EDR_data$EDR1$traj_dissim
trajectories <- paste0("T", EDR_data$EDR1$abundance$traj)
states <- EDR_data$EDR1$abundance$state

# Dynamic dispersion taking the first trajectory as reference
dDis(d = dTraj, d.type = "dTraj", trajectories = unique(trajectories),
         reference = "T1")
#> dDis (ref. T1) 
#>       0.267622 

# Dynamic dispersion weighting trajectories by their length
dDis(d = dStates, d.type = "dStates", trajectories = trajectories, states = states,
         reference = "T1", w.type = "length")
#> dDis (ref. T1) 
#>      0.3548963 

# Dynamic beta diversity using trajectory dissimilarities
dBD(d = dTraj, d.type = "dTraj", trajectories = unique(trajectories))
#>        dBD 
#> 0.03969095 

# Dynamic evenness
dEve(d = dStates, d.type = "dStates", trajectories = trajectories, states = states)
#>      dEve 
#> 0.7100773 

# Dynamic evenness considering that the 10 first trajectories are three times
# more relevant than the rest
w.values <- c(rep(3, 10), rep(1, length(unique(trajectories))-10))
dEve(d = dTraj, d.type = "dTraj", trajectories = unique(trajectories),
         w.type = "precomputed", w.values = w.values)
#>      dEve 
#> 0.7392367