gg_envfit: Vegan envfit plot

In jfq3/ggordiplots: Make 'ggplot2' Versions of Vegan's Ordiplots

Vegan envfit plot

Description

Fits environmental parameters to an ordination plot of sites and plots them as arrows or centroid labels.

Usage

gg_envfit(
  ord,
  env,
  groups = NA,
  scaling = 1,
  choices = c(1, 2),
  perm = 999,
  alpha = 0.05,
  angle = 20,
  len = 0.5,
  unit = "cm",
  arrow.col = "red",
  pt.size = 3,
  show_factors = FALSE,
  plot = TRUE
)

Arguments

ord	An ordination object.
env	A data frame of environmental parameters.
groups	A vector of groups.
scaling	Scaling value for plot.
choices	Axes to plot.
perm	Number of permutations.
alpha	Maximum alpha value to be included in plot.
angle	Angle of arrow tips.
len	Arrow tip length.
unit	Unit for length ("cm", "in")
arrow.col	Arrow color.
pt.size	Symbol size.
show_factors	A logical for including factors on the plot; defaults to FALSE.
plot	A logical for plotting; defaults to TRUE.

Details

Vegan's envfit function fits environmental variables to an ordination. If the variable is numeric, an arrow is fitted to the ordination plot indicating the direction in which that variable increases. If the variable is a factor (or character vector), vegan's envfit plotting function treats levels of the factor as groups and adds labels for the factor's level to the ordination plot at each group's centroid center. This behavior is now enabled in gg_envfit() if show_factors is set to TRUE.

Value

Silently returns the plot and data frames used for the plotting if the fit of any variable is significant at alpha. Otherwise returns a message that no variable is significant.

Note

In order for the arrow tips to be labeled with the names of the variables, they must be supplied as a matrix or data frame. If a single variable is supplied as a vector, the arrow tip will be labeled with "1". A way-around is to convert the vector to a data frame with the column named for the variable.

Examples

data("varespec")
data("varechem")
vare.dist <- vegdist(varespec)
vare.mds <- monoMDS(vare.dist)
gg_envfit(ord=vare.mds, env=varechem)

data("dune")
data("dune.env")
dune.dist <- vegdist(dune)
dune.mds <- monoMDS(dune.dist)
# A1 supplied as a vector
gg_envfit(dune.mds, env=dune.env$A1, groups=dune.env$Management)
# A1 supplied as a data frame
A1 <- as.data.frame(dune.env$A1)
colnames(A1) <- "A1"
gg_envfit(dune.mds, env=A1, groups=dune.env$Management)

jfq3/ggordiplots documentation built on Oct. 27, 2024, 11:01 p.m.