evenness {BAT} | R Documentation |
Regularity of abundances and distances (if PD/FD) between species in a community.
evenness(
comm,
tree,
distance,
method = "expected",
func = "camargo",
abund = TRUE
)
comm |
A sites x species matrix, with either abundance or incidence data. If missing, the evenness using the full tree or distance matrix is calculated. |
tree |
A phylo or hclust object (used only for PD or FD) or alternatively a species x traits matrix or data.frame to build a functional tree. |
distance |
A dist or matrix object representing the phylogenetic or functional distance between species. If both tree and distance are missing, taxonomic evenness is calculated. |
method |
Calculate evenness using "expected" values (default) or values based on "contribution" of species to the tree. |
func |
Calculate evenness using "Camargo" (default) or "Bulla" index. |
abund |
A boolean (T/F) indicating whether evenness should be calculated using abundance data. |
Evenness is calculated based on the index of Camargo (1993) or Bulla (1994) using the values of both species abundances and edge lengths in the tree (if PD/FD).
If no tree or distance is provided the result is the original index.
If any site has < 2 species its value will be NA.
A vector of values per site (or a single value if no comm is given).
Bulla, L. (1994) An index of evenness and its associated diversity measure. Oikos, 70: 167-171.
Camargo, J.A. (1993) Must dominance increase with the number of subordinate species in competitive interactions? Journal of Theoretical Biology, 161: 537-542.
comm <- matrix(c(1,2,0,0,0,1,1,0,0,0,0,2,2,0,0,1,1,1,1,100), nrow = 4, byrow = TRUE)
distance <- dist(c(1:5), method = "euclidean")
tree <- hclust(distance, method = "average")
evenness(comm)
evenness(tree = tree, func = "bulla")
evenness(comm, tree)
evenness(comm, tree, method = "contribution")
evenness(comm, tree, abund = FALSE)