View source: R/fcts_used_for_ind_comp.R
vertices | R Documentation |
This function identifies species that are vertices of the minimal convex
hull enclosing a community in a multidimensional functional space. This
function is using the convhulln
function.
vertices(sp_faxes_coord, order_2D = FALSE, check_input = FALSE)
sp_faxes_coord |
a matrix of species coordinates in a chosen functional
space. Species coordinates have been retrieved thanks to
|
order_2D |
a logical value defining whether vertices names are
reordered so that they define a convex polygon in 2D which is convenient
for plotting. Default is |
check_input |
a logical value defining whether inputs are checked
before computation: species names must be put as row.names, there must be
no NA and species number must be superior to (axes number + 1). Default:
|
A vector containing names of species being vertices vert_nm
.
Camille Magneville and Sebastien Villeger
# Load Species*Traits dataframe:
data("fruits_traits", package = "mFD")
# Load Assemblages*Species dataframe:
data("baskets_fruits_weights", package = "mFD")
# Load Traits categories dataframe:
data("fruits_traits_cat", package = "mFD")
# Compute functional distance
sp_dist_fruits <- mFD::funct.dist(sp_tr = fruits_traits,
tr_cat = fruits_traits_cat,
metric = "gower",
scale_euclid = "scale_center",
ordinal_var = "classic",
weight_type = "equal",
stop_if_NA = TRUE)
# Compute functional spaces quality to retrieve species coordinates matrix:
fspaces_quality_fruits <- mFD::quality.fspaces(
sp_dist = sp_dist_fruits,
maxdim_pcoa = 10,
deviation_weighting = "absolute",
fdist_scaling = FALSE,
fdendro = "average")
# Retrieve species coordinates matrix:
sp_faxes_coord_fruits <- fspaces_quality_fruits$details_fspaces$sp_pc_coord
# Compute vertices and order them clockwise:
vert_nm <- vertices(sp_faxes_coord_fruits[ , c("PC1", "PC2")],
order_2D = TRUE, check_input = TRUE)
vert_nm
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