SimilarityMult: Estimation various $N$-community similarity indices. The richness-based indices
include the classic $N$-community Jaccard and Sorensen indices; the abundance-based indices include the Horn, Morisita-Horn, regional species-overlap, and the $N$-community Bray-Curtis indices.
Three types of data are supported: Type (1) abundance data (datatype="abundance"), Type (2)
incidence-frequency data (datatype="incidence_freq"), and Type (2B) incidence-raw data
(datatype="incidence_raw"); see SpadeR-package details for data input formats.
SimilarityMult(X, datatype = c("abundance", "incidence_freq", "incidence_raw"), units, q = 2, nboot = 200, goal = "relative")datatype = "incidence_raw", users must specify the number of sampling units taken from each community. This argument is not needed for "abundance" and "incidence_freq" data. q = 0, this function computes the estimated pairwise richness-based Jaccard and
Sorensen similarity indices.
If q = 1 and goal=relative, this function computes the estimated pairwise equal-weighted and size-weighted Horn indices based on Shannon entropy;
If q = 1 and goal=absolute, this function computes the estimated pairwise Shannon-entropy-based measure for comparing absolute abundances. If q = 2 and goal=relative,
this function computes the estimated pairwise Morisita-Horn and regional species-overlap indices based on species relative abundances.
If q = 2 and goal=absolute,
this function computes the estimated pairwise Morisita-Horn and regional species-overlap indices based on species absolute abundances.goal=relative) or comparing species absolute abundances (goal=absolute). $datatype for showing the specified data types (abundance or incidence).
$info for summarizing data information.
$Empirical_richness for showing the observed values of the richness-based similarity indices
include the classic $N$-community Jaccard and Sorensen indices.
$Empirical_relative for showing the observed values of the equal-weighted similarity indices
for comparing species relative abundances including Horn, Morisita-Horn and regional overlap measures.
$Empirical_WtRelative for showing the observed value of the Horn similarity index for comparing
size-weighted species relative abundances based on Shannon entropy under equal-effort sampling.
$Empirical_absolute for showing the observed values of the similarity indices for comparing
absolute abundances. These measures include the Shannon-entropy-based measure, Morisita-Horn and the regional species-overlap measures based on species absolute abundance, as well as the $N$-community Bray-Curtis index.
All measures are valid only under equal-effort sampling.
The corresponding four objects for showing the estimated similarity indices are:
$estimated_richness, $estimated_relative, $estimated_WtRelative and $estimated_absolute.
$pairwise and $similarity.matrix for showing respectively the pairwise dis-similarity
estimates (with related statistics) and the similarity matrix for various measures depending on the
diversity order q and the goal aspecified in the function arguments.
$goal for showing the goal specified in the argument goal (absolute or relative) used to compute pairwise similarity.
$q for showing which diversity order q specified to compute pairwise similarity.
## Not run:
# data(SimilarityMultData)
# # Type (1) abundance data
# SimilarityMult(SimilarityMultData$Abu,"abundance",q=2,nboot=200,"relative")
# # Type (2) incidence-frequency data
# SimilarityMult(SimilarityMultData$Inci,"incidence_freq",q=2,nboot=200,"relative")
# # Type (2B) incidence-raw data
# SimilarityMult(SimilarityMultData$Inci_raw,"incidence_raw",
# units=c(19,17,15),q=2,nboot=200,"relative")
# ## End(Not run)
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