subplot_sp: Plot a species subniche under each sub-environmental space K
In subniche: Within Outlying Mean Indexes: Refining the OMI Analysis

View source: R/subplot_sp.R

subplot_sp

R Documentation

Plot a species subniche under each sub-environmental space K

Description

The function to represent the species subniche under each subenvironment K with their respective marginality from G_K.

Usage

subplot_sp(
  subnic,
  sp,
  main = NULL,
  col.axis = "azure3",
  lty.axis = 2,
  lwd.axis = 2,
  xlab = NULL,
  ylab = NULL,
  border.E = "black",
  col.E = "#92c5de",
  lty.E = 1,
  lwd.E = 1,
  border.K = "black",
  lwd.K = 1,
  col.K = "#2c7fb8",
  lty.K = 1,
  col.Gk.pos = "red",
  col.Gk.pt = "black",
  cex.Gk.pos = 1,
  pch.Gk.pos = 21,
  border.SP = "#bc5090",
  col.SB = "#ffff99",
  lty.SP = 1,
  lwd.SP = 2,
  border.NR = "#fdb462",
  col.NR = NA,
  lty.NR = 1,
  lwd.NR = 2,
  border.SR = "#a1d99b",
  col.SR = "#a1d99b",
  lty.SR = 1,
  lwd.SR = 1,
  pch.SR.pos = 19,
  cex.SR.pos = 1,
  col.SR.pt = "black",
  col.SR.pos = "black",
  cex.SR.lab = 0.7,
  col.SR.lab = "black",
  fac.SR.lab = 1.2,
  font.sp = 2,
  col.arrow = "black",
  angle.arrow = 20,
  lwd.arrow = 2,
  length.arrow = 0.1,
  leg = T,
  posi.leg = "topleft",
  bty.leg = "n",
  ...
)

Arguments

`subnic`	an object of class `subniche`.
`sp`	a character string of the species name.
`main`	a main title for the plot, see title for more details.
`col.axis`	axis color, see par for more details.
`lty.axis`	axis line type, see par for more details.
`lwd.axis`	axis width, see par for more details.
`xlab`	label for x-axis, see title for more details.
`ylab`	label for y-axis, see title for more details.
`border.E`	color border of E polygon, see polygon for more details.
`col.E`	inside color of E polygon, see polygon for more details.
`lty.E`	line type for the E border, see polygon for more details.
`lwd.E`	line width for the E border, see polygon for more details.
`border.K`	color border of K polygon, see polygon for more details.
`lwd.K`	line width for the K border, see polygon for more details.
`col.K`	inside color of K polygon, see polygon for more details.
`lty.K`	line type for the K border, see polygon for more details.
`col.Gk.pos`	color of the point representing G_k, see points for more details.
`col.Gk.pt`	point color contour if pch=21:25.
`cex.Gk.pos`	size of the point representing G_k, see points for more details.
`pch.Gk.pos`	type of the point representing G_k, see points for more details.
`border.SP`	color border of species subniche polygon, see polygon for more details.
`col.SB`	color of the SB area.
`lty.SP`	line type for the SP border, see polygon for more details.
`lwd.SP`	line width for the SP border, see polygon for more details.
`border.NR`	color border of NR polygon, see polygon for more details.
`col.NR`	inside color of NR polygon, see polygon for more details.
`lty.NR`	line type for the NR border, see polygon for more details.
`lwd.NR`	line width for the NR border, see polygon for more details.
`border.SR`	color border of SR polygon, see polygon for more details.
`col.SR`	inside color of SR polygon, see polygon for more details.
`lty.SR`	line type for the SR border, see polygon for more details.
`lwd.SR`	line width for the SR border, see polygon for more details.
`pch.SR.pos`	type of points representing the SR position, see points for more details.
`cex.SR.pos`	size of points representing the SR position, see points for more details.
`col.SR.pt`	point color contour if pch=21:25.
`col.SR.pos`	color of points representing the SR position, see points for more details.
`cex.SR.lab`	size of the species label representing the SR position, see text for more details.
`col.SR.lab`	color of the species label representing the SR position, see text for more details.
`fac.SR.lab`	factor for moving the SR labels from its original coordinates for clarity, by defaults they are multiply 1.2
`font.sp`	An integer which specifies which font to use for species label. 1 corresponds to plain text (the default), 2 to bold face, 3 to italic and 4 to bold italic, see par for more details.
`col.arrow`	arrow color, see arrows for more details.
`angle.arrow`	arrow angle head, see arrows for more details.
`lwd.arrow`	arrow width, see arrows for more details.
`length.arrow`	arrow head length, see arrows for more details.
`leg`	a logical option for legend to be plotted or not, default leg=T.
`posi.leg`	legend location in the graph, see legend for more details.
`bty.leg`	the type of box to be drawn around the legends. The allowed values are "o" (the default) and "n". See legend for more details
`...`	further arguments passed to or from other methods.

Examples

library(subniche)
data(doubs)
dudi1 <- dudi.pca(doubs$env, scale = TRUE, scan = FALSE, nf = 3)
nic1 <- niche(dudi1, doubs$fish, scann = FALSE)
# number of sites
N <- dim(nic1$ls)[1]
#Create a factor which defines the subsets
fact <- factor(c(rep(1,N/2),rep(2,N/2)))
# nic1 will be use as reference and fact will be use to define the subniches environment
subnic1 <- subniche(nic1, fact)
eig <- round(subnic1$eig/sum(subnic1$eig)*100,2)[1:2]
#Two graphs are drawn one after the other
subplot_sp(subnic1,"Neba")

subniche documentation built on July 15, 2022, 5:05 p.m.