plot_dym_sp: Species subniches dynamic
In subniche: Within Outlying Mean Indexes: Refining the OMI Analysis

View source: R/plot_dym_sp.R

plot_dym_sp

R Documentation

Species subniches dynamic

Description

The function represents the species' subniches SR within its realized niche NR.

Usage

plot_dym_sp(
  subnic,
  sp,
  xlab = NULL,
  ylab = NULL,
  main = NA,
  col.axis = "azure3",
  lty.axis = 2,
  lwd.axis = 2,
  border.E = "black",
  col.E = "#92c5de",
  lty.E = 1,
  lwd.E = 1,
  col.NR = "#fdb462",
  border.NR = "black",
  lty.NR = 1,
  lwd.NR = 1,
  col.NR.lab = "black",
  cex.NR.lab = 0.7,
  pch.NR.pos = 21,
  col.NR.pos = "black",
  col.NR.pt = "black",
  cex.NR.pos = 1,
  border.SR = "black",
  col.SR = "#a1d99b",
  lty.SR = 1,
  lwd.SR = 1,
  col.SR.lab = "black",
  cex.SR.lab = 0.7,
  fac.SR.lab = 1.2,
  pch.SR.pos = 21,
  col.SR.pos = "#ffa600",
  col.SR.pt = "black",
  cex.SR.pos = 1,
  col.arrow = "black",
  angle.arrow = 20,
  lwd.arrow = 2,
  length.arrow = 0.1,
  font.sp = 2,
  leg = T,
  posi.leg = "topleft",
  bty.leg = "n",
  ...
)

Arguments

`subnic`	an object of class `subniche`.
`sp`	a character string of the species name.
`xlab`	label for x-axis, see title for more details.
`ylab`	label for y-axis, see title for more details.
`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.
`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.
`col.NR`	inside color of NR polygon, see polygon for more details.
`border.NR`	color border 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.
`col.NR.lab`	color of the species label representing the NR position, see textplot for more details.
`cex.NR.lab`	size of the species label representing the NR position, see textplot for more details.
`pch.NR.pos`	the type of points representing the NR position, see points for more details.
`col.NR.pos`	the color of points representing the NR position, see points for more details.
`col.NR.pt`	point color contour if pch=21:25.
`cex.NR.pos`	size of points representing the SR position, see points 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.
`col.SR.lab`	color of the species label representing the SR position, see text for more details.
`cex.SR.lab`	size 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
`pch.SR.pos`	type of points representing the SR position, see points for more details.
`col.SR.pos`	color of points representing the SR position, see points for more details.
`col.SR.pt`	point color contour if pch=21:25.
`cex.SR.pos`	size of points representing the SR position, see points 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.
`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.
`leg`	a logical option for legend to be plotted or not, default leg=T.
`posi.leg`	setting legend positions with the following keywords "bottomright", "bottom", "bottomleft", "left", "topleft", "top", "topright", "right" and "center", see legend for more details.
`bty.leg`	the type of box to be drawn around the legend. The allowed values are "o" (the default) and "n", see legend for more details.
`...`	further arguments passed to or from other methods.

Details

The convex hulls measured are :

E is the environmental space.
NR the realized subniche.
SR the species realized subniche.

The arrows represent the species' subniche marginality from the origin G. See doi: 10.7717/peerj.3364 for more details on the subniche concept.

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)
plot_dym_sp(subnic1, "Neba")

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