| beta.multidim.plot {mFD} | R Documentation |
Illustrate Functional beta-Diversity indices for pairs of assemblages in a multidimensional space
Description
Illustrate overlap between convex hulls shaping species assemblages in a
multidimensional functional space.Before plotting beta functional
diversity indices should have been computed using the
beta.fd.multidim function.
Usage
beta.multidim.plot(
output_beta_fd_multidim,
plot_asb_nm,
beta_family,
plot_sp_nm = NULL,
faxes = NULL,
name_file = NULL,
faxes_nm = NULL,
range_faxes = c(NA, NA),
color_bg = "grey95",
shape_sp = c(pool = 3, asb1 = 22, asb2 = 21),
size_sp = c(pool = 0.7, asb1 = 1.2, asb2 = 1),
color_sp = c(pool = "grey50", asb1 = "blue", asb2 = "red"),
fill_sp = c(pool = NA, asb1 = "white", asb2 = "white"),
fill_vert = c(pool = NA, asb1 = "blue", asb2 = "red"),
color_ch = c(pool = NA, asb1 = "blue", asb2 = "red"),
fill_ch = c(pool = "white", asb1 = "blue", asb2 = "red"),
alpha_ch = c(pool = 1, asb1 = 0.3, asb2 = 0.3),
nm_size = 3,
nm_color = "black",
nm_fontface = "plain",
check_input = TRUE
)
Arguments
output_beta_fd_multidim |
the list returned by
|
plot_asb_nm |
a vector with names of the 2 assemblages for which functional beta-diversity will be illustrated. |
beta_family |
a character string for the type of beta-diversity index
for which values will be printed, |
plot_sp_nm |
a vector containing species names that are to be plotted.
Default: |
faxes |
a vector with names of axes to plot (as columns names in
|
name_file |
a character string with name of file to save the figure
(without extension). Default: |
faxes_nm |
a vector with axes labels for figure. Default: as
|
range_faxes |
a vector with minimum and maximum values of axes. Note
that to have a fair representation of position of species in all plots,
they should have the same range. Default: |
color_bg |
a R color name or an hexadecimal code used to fill
plot background. Default: |
shape_sp |
a vector with 3 numeric values referring to the shape of
symbol used for species from the 'pool' absent from the 2 assemblages, and
for species present in the 2 assemblages ('asb1', and 'asb2'),
respectively. Default: |
size_sp |
a numeric value referring to the size of symbols for
species. Default: |
color_sp |
a vector with 3 names or hexadecimal codes referring to the
colour of symbol for species. Default is:
|
fill_sp |
a vector with 3 names or hexadecimal codes referring to the
color to fill symbol (if |
fill_vert |
a vector with 3 names or hexadecimal codes
referring to the colour to fill symbol (if |
color_ch |
a vector with 3 names or hexadecimal codes referring to the
border of the convex hulls of the pool of species and by the 2 assemblages.
Default is: |
fill_ch |
a vector with 3 names or hexadecimal codes referring to the
filling of the convex hull of the pool of species and of the 2 assemblages.
Default is |
alpha_ch |
a vector with 3 numeric value for transparency of
the filling of the convex hulls (0 = high transparency, 1 = no
transparency). Default is:
|
nm_size |
a numeric value for size of species label. Default is |
nm_color |
a R color name or an hexadecimal code referring to the color
of species label. Default is |
nm_fontface |
a character string for font of species labels (e.g.
"italic", "bold"). Default is |
check_input |
a logical value indicating whether key features the
inputs are checked (e.g. class and/or mode of objects, names of rows
and/or columns, missing values). If an error is detected, a detailed
message is returned. Default: |
Value
If name_file is NULL, it returns a patchwork
figure with overlap between convex hulls projected in 2-dimensional spaces
for the given pair of assemblages. Values of functional beta-diversity
indices are shown on top-right corner of the figure. If name_file is
not NULL, the plot is saved locally.
Author(s)
Sebastien Villeger and Camille Magneville
Examples
# 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
# Get the occurrence dataframe:
asb_sp_fruits_summ <- mFD::asb.sp.summary(asb_sp_w = baskets_fruits_weights)
asb_sp_fruits_occ <- asb_sp_fruits_summ$"asb_sp_occ"
# Compute beta diversity indices:
beta_fd_fruits <- mFD::beta.fd.multidim(
sp_faxes_coord = sp_faxes_coord_fruits[, c("PC1", "PC2", "PC3", "PC4")],
asb_sp_occ = asb_sp_fruits_occ,
check_input = TRUE,
beta_family = c("Jaccard"),
details_returned = TRUE)
# Compute beta fd plots:
beta.multidim.plot(
output_beta_fd_multidim = beta_fd_fruits,
plot_asb_nm = c("basket_1", "basket_6"),
beta_family = c("Jaccard"),
plot_sp_nm = c("apple", "cherry", "lemon"),
faxes = paste0("PC", 1:4),
name_file = NULL,
faxes_nm = NULL,
range_faxes = c(NA, NA),
color_bg = "grey95",
shape_sp = c(pool = 3, asb1 = 22, asb2 = 21),
size_sp = c(pool = 0.8, asb1 = 1, asb2 = 1),
color_sp = c(pool = "grey50", asb1 = "blue",
asb2 = "red"),
fill_sp = c(pool = NA, asb1 = "white", asb2 = "white"),
fill_vert = c(pool = NA, asb1 = "blue", asb2 = "red"),
color_ch = c(pool = NA, asb1 = "blue", asb2 = "red"),
fill_ch = c(pool = "white", asb1 = "blue",
asb2 = "red"),
alpha_ch = c(pool = 1, asb1 = 0.3, asb2 = 0.3),
nm_size = 3,
nm_color = "black",
nm_fontface = "plain",
check_input = TRUE)