referenceEnvelopes | R Documentation |
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).
trajectoryEnvelopeVariability(
d,
sites,
surveys = NULL,
nboot.ci = NULL,
alpha.ci = 0.05,
...
)
stateEnvelopeVariability(d, nboot.ci = NULL, alpha.ci = 0.05)
compareToTrajectoryEnvelope(
d,
sites,
envelope,
surveys = NULL,
m = 1.5,
nboot.ci = NULL,
alpha.ci = 0.05,
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,
...
)
d |
A symmetric |
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). |
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 |
envelope |
A vector indicating the set of sites that conform the reference envelope (other sites will be compared to the envelope) |
m |
Fuzziness exponent for quality value assessment |
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. |
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.
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.
Miquel De Cáceres, CREAF
Anthony Sturbois, Vivarmor nature, Réserve Naturelle nationale de la Baie de Saint-Brieuc
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.
trajectorymetrics
, glomel
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)
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