Calculates a set of standard beta diversity metrics
Arguments
- x
(
data.frame) BioTIME data table in the format of the output of theresamplingfunctions. Theresampcolumn is optional.- measure
(
character) chosen currency defined by a single column name.
Value
Returns a data.frame with results for Jaccard dissimilarity
(JaccardDiss), Morisita-Horn dissimilarity (MorisitaHornDiss),
and Bray-Curtis dissimilarity (BrayCurtsDiss) for each year and
assemblageID.
Details
The function getBetaMetrics computes three beta diversity metrics
for a given community data frame, where measure is a character input
specifying the abundance or biomass field used for the calculations.
getBetaMetrics calls the vegdist function which
calculates for each row the following metrics: Jaccard dissimilarity
(method = "jaccard"), Morisita-Horn dissimilarity (method =
"horn") and Bray-Curtis dissimilarity (method = "bray"). Here, the
dissimilarity metrics are calculated against the baseline year of each
assemblage time series i.e. the first year of each time series. Note that the
input data frame needs to be in the format of the output of the
gridding and/or resampling functions, which
includes keeping the default BioTIME data column names. If such columns are
not found an error is issued and the computations are halted. There is an
exception for the resamp column: the function runs even without it.
Examples
gridding(BTsubset_meta, BTsubset_data) |>
resampling(measure = "BIOMASS", verbose = FALSE, resamps = 2) |>
getBetaMetrics(measure = "BIOMASS") |>
head()
#> OK: all SL studies have 1 grid cell
#> resamp assemblageID YEAR JaccardDiss MorisitaHornDiss BrayCurtisDiss
#> 1 1 211_504467 1984 0.5928486 0.38435410 0.4998241
#> 2 1 211_504467 1985 NA NA NA
#> 3 1 211_516855 1982 0.7413888 0.10720618 0.3723366
#> 4 1 211_516855 1983 0.7263079 0.09252659 0.9407762
#> 5 1 211_516855 1984 0.7004768 0.02577689 0.7943522
#> 6 1 211_516855 1985 0.6608817 0.15917918 0.9261414