ses.comdistnt2 | R Documentation |
Standardized effect size of MNTD (mean nearest taxon distance) separating taxa in two communities, a measure of phylogenetic beta diversity
ses.comdistnt2( samp, dis, method = "quasiswap", fixedmar = "both", shuffle = "both", strata = NULL, mtype = "count", burnin = 0, thin = 1, abundance.weighted = FALSE, exclude.conspecifics = FALSE, runs = 999, cores = 1 )
samp |
Community data matrix with samples as rows |
dis |
Distance matrix (generally a phylogenetic distance matrix) |
method |
Character for method used for the swap algorithm ("swap", "tswap", "quasiswap", "backtrack"). If NULL no swap algorithm is applied (uses permatfull from vegan). If mtype="count" the "quasiswap", "swap", "swsh" and "abuswap" methods are available (see details). |
fixedmar |
Character, stating which of the row/column sums should be preserved ("none", "rows", "columns", "both"). |
shuffle |
Character, indicating whether individuals ("ind"), samples ("samp") or both ("both") should be shuffled, see details. |
strata |
Numeric vector or factor with length same as nrow(m) for grouping rows within strata for restricted permutations. Unique values or levels are used. |
mtype |
Matrix data type, either "count" for count data, or "prab" for presence-absence type incidence data. |
burnin |
Number of null communities discarded before proper analysis in sequential ("swap", "tswap") methods. |
thin |
Number of discarded permuted matrices between two evaluations in sequential ("swap", "tswap") methods. |
abundance.weighted |
Should mean nearest taxon distances for each species be weighted by species abundance? (default = FALSE) |
exclude.conspecifics |
Should conspecific taxa in different communities be exclude from MNTD calculations? (default = FALSE) |
runs |
Number of randomizations |
cores |
Number of cores to use for parallel computing |
See permat (vegan) for detailed options
A list of results:
ntaxa - Number of taxa in community
comdistnt.obs - Observed mntd between communities
comdistnt.rand.mean - Mean mntd between null communities
comdistnt.rand.sd - Standard deviation of mntd between null communities
comdistnt.obs.rank - Rank of observed mntd vs. null mntd
comdistnt.obs.z - Standardized effect size of mntd vs. null mntd (= (comdistnt.obs - comdistnt.rand.mean) / comdistnt.rand.sd, equivalent to -betaNTI)
comdistnt.obs.p - P-value (quantile) of observed mntd vs. null communities (= comdistnt.obs.rank / runs + 1)
runs - Number of randomizations
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