plot_dym_sp: Species subniches dynamic

In polak51/WitOMI: Within Outlying Mean Indexes: Refining the OMI Analysis

Description

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

Usage

plot_dym_sp(
  subnic,
  sp,
  main = NA,
  col.axis = "azure3",
  lty.axis = 2,
  lwd.axis = 2,
  border.E = "#92c5de",
  col.E = "#92c5de",
  lty.E = 1,
  lwd.E = 1,
  border.NR = "#fdb462",
  col.NR = "#fdb462",
  border.SR = "#a1d99b",
  col.SR = "#a1d99b",
  col.SRc = "black",
  lty.SR = 1,
  lwd.SR = 1,
  pch.SR = 19,
  cex.SR = 1,
  lty.NR = 1,
  lwd.NR = 2,
  col.arrow = "black",
  col.sp = "black",
  cex.sp = 1,
  show.lines = F,
  angle.arrow = 20,
  lwd.arrow = 2,
  length.arrow = 0.1,
  font.sp = 1,
  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.
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.NR	color border of NR polygon, see polygon for more details.
col.NR	inside color of NR polygon, 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.
col.SRc	color of points representing the SR position, see points 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	type of points representing the SR position, see points for more details.
cex.SR	size of points representing the SR position, see points 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.arrow	arrow color, see arrows for more details.
col.sp	color of the species label representing the NR position, see textplot for more details.
cex.sp	size of the species label representing the NR position, see textplot for more details.
show.lines	if true, then lines are plotted between x,y and the word, for those words not covering their x,y coordinates, see textplot 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.
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 :

1. E is the environmental space.

2. NR the realized subniche.

3. SR the species realized subniche.

The arrows represent the species' subniche marginality from the origin G. See Karasiewicz,et al. (2017) 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")
plot_dym_sp(subnic1,"Cyca", lwd.NR = 5, col.sp="red",lty.NR=3, border.E="green",col.E=NA, col.NR=NA)

polak51/WitOMI documentation built on April 4, 2020, 6:14 p.m.