Compute functional dendogram from the ecological parameters.

Functional dendrograms measure functional diversity (Petchey & Gaston, 2007). The dendograms cluster species with similar traits in the same or closely linked clusters, a precursor to under the species interactions at the species-species level. In fwtraits, these interactions can be examined by providing the species’ ecological parameters or traits.

library(fwtraits)

Data collation

The data was obtained from the www.freshwaterecology.info database using the fw_fetchdata function.

data("speciesdata")

set.seed(1135)
speciesdata$abund <- rnorm(n = nrow(speciesdata), 4.3, 1.2)

#species with geographical coordinates

geospdata <- speciesdata |> 
  sf::st_as_sf(coords = c('decimalLongitude', 'decimalLatitude'), 
               crs = sf::st_crs(4326))

Data retrieval from the database

fishtraits <- fw_fetchdata(data = speciesdata, 
                         ecoparams = c('rheophily habitat', 'spawning habitat',
                                       'feeding diet adult'), 
                         taxonomic_column = 'scientificName',
                         organismgroup = 'fi')

Data visualistion and compute the functional dendogram.

fdendoclust <- fw_fdendro(fwdata = fishtraits, plot = TRUE)

head(fdendoclust, 3)
#>                   rheophily_habitat spawning_habitat feeding_diet_adult cluster
#> Abramis brama          rheophilic B      euryoparous         omnivorous       1
#> Alburnus alburnus         eurytopic      euryoparous         omnivorous       1
#> Anguilla anguilla         eurytopic      limnoparous         omnivorous       2

table(fdendoclust$cluster)
#> 
#> 1 2 3 4 
#> 6 6 8 1

References

Petchey, O. L., & Gaston, K. J. (2007). Dendrograms and measuring functional diversity. Oikos, 116(8), 1422-1426.