Ecological quality assessment

Functions to assess the variability of ecological reference envelopes and to assess the ecological quality of target stations/observations with respect to reference envelopes (Sturbois et al., under review).

Usage

trajectoryEnvelopeVariability(
  d,
  sites,
  surveys = NULL,
  envelope = NULL,
  nboot.ci = NULL,
  alpha.ci = 0.05,
  ...
)

stateEnvelopeVariability(d, envelope = NULL, nboot.ci = NULL, alpha.ci = 0.05)

compareToTrajectoryEnvelope(
  d,
  sites,
  envelope,
  surveys = NULL,
  m = 1.5,
  comparison_target = "trajectories",
  distances_to_envelope = FALSE,
  distance_percentiles = FALSE,
  ...
)

compareToStateEnvelope(
  d,
  envelope,
  m = 1.5,
  nboot.ci = NULL,
  alpha.ci = 0.05,
  distances_to_envelope = FALSE,
  distance_percentiles = FALSE,
  ...
)

Arguments

d: A symmetric matrix or an object of class dist containing the distance values between pairs of ecosystem states (see details).
sites: A vector indicating the site corresponding to each ecosystem state.
surveys: A vector indicating the survey corresponding to each ecosystem state (only necessary when surveys are not in order).
envelope: A vector indicating the set of sites that conform the reference envelope (other sites will be compared to the envelope)
nboot.ci: Number of bootstrap samples for confidence intervals. If nboot.ci = NULL then confidence intervals are not estimated.
alpha.ci: Error in confidence intervals.
...: Additional parameters for function trajectoryDistances
m: Fuzziness exponent for quality value assessment
comparison_target: String indicating the component to be compared to the reference envelope. Either 'trajectories' (to compare complete trajectories) or 'states' (to compare individual trajectory states).
distances_to_envelope: Flag to indicate that distances to envelope should be included in the result
distance_percentiles: Flag to include the percentage of distances to the envelope (among sites corresponding to the reference) that are smaller than that of the site.

Value

Functions stateEnvelopeVariability and trajectoryEnvelopeVariability are used to assess the
Functions compareToStateEnvelope and compareToTrajectoryEnvelope return data frame with columns identifying the envelope and the Q statistic for the ecological quality with respect to the envelope. If nboot.ci != NULL extra columns are added to indicate the boundaries of a confidence interval for Q, built using bootstrap samples of the reference envelope.

Details

Functions stateEnvelopeVariability and trajectoryEnvelopeVariability are used to assess the variability of reference envelopes. Functions compareToStateEnvelope and compareToTrajectoryEnvelope are used to evaluate the ecological quality of stations/observations with respect to a predefined reference envelope.

References

Sturbois, A., De Cáceres, M., Bifolchi, A., Bioret, F., Boyé, A., Gauthier, O., Grall, J., Grémare, A., Labrune, C., Robert, A., Schaal, G., Desroy, N. (2023). Ecological Quality Assessment: a general multivariate framework to report the quality of ecosystems and their dynamics with respect to reference conditions. Ecosphere.

Author

Miquel De Cáceres, CREAF

Anthony Sturbois, Vivarmor nature, Réserve Naturelle nationale de la Baie de Saint-Brieuc

Examples

data(glomel)
 
# Extract compositional data matrix
glomel_comp <- as.matrix(glomel[,!(names(glomel) %in% c("ID", "Ref", "Complementary"))])
rownames(glomel_comp) <- glomel$ID
 
# Calculate Bray-Curtis distance matrix 
glomel_bc <- vegan::vegdist(glomel_comp, method = "bray")
 
# Define reference envelope (5 stations) by observation ID
glomel_env <- glomel$ID[glomel$Ref]
 
# Assess quality with respect to reference envelope
compareToStateEnvelope(glomel_bc, glomel_env)
#>    Observation Envelope          Q
#> 1           1A     TRUE 1.00000000
#> 2           1B     TRUE 0.81060634
#> 3           1C     TRUE 0.56214189
#> 4           5A     TRUE 1.00000000
#> 5           13     TRUE 0.88208650
#> 6            2    FALSE 0.57224382
#> 7           3A    FALSE 0.39919080
#> 8           3B    FALSE 1.00000000
#> 9           3C    FALSE 0.42318855
#> 10          5B    FALSE 0.28846018
#> 11          6A    FALSE 0.04261028
#> 12          6C    FALSE 0.34551240
#> 13          6D    FALSE 0.02853182
#> 14          7A    FALSE 0.04810891
#> 15          8A    FALSE 0.15160202
#> 16          8B    FALSE 0.11181164
#> 17          8C    FALSE 0.02057370
#> 18           9    FALSE 0.09946578
#> 19          10    FALSE 0.81557507
#> 20          11    FALSE 0.56752876
#> 21          12    FALSE 1.00000000
#> 22         14A    FALSE 0.66577245
#> 23         14B    FALSE 0.09988729