plot_NR: Community niche distribution

In subniche: Within Outlying Mean Indexes: Refining the OMI Analysis

Community niche distribution

Description

The function represents the species' niche NR position within the environmental space E.

Usage

plot_NR(
  subnic,
  sig = NULL,
  sig_thres = 0.05,
  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,
  pch.NR.pos = 21,
  cex.NR.pos = 1,
  col.NR.pos = "#a1d99b",
  col.NR.pt = "black",
  col.NR.lab = "black",
  cex.NR.lab = NA,
  fac.NR.lab = 1.2,
  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.
sig	a factor defining the significance species, default NULL.
sig_thres	value for minimum significance, default 0.05
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.
pch.NR.pos	type of points representing the NR position, see points for more details.
cex.NR.pos	size of points representing the NR position, see points for more details.
col.NR.pos	color of points representing the NR position, see points for more details.
col.NR.pt	point color contour if pch=21:25.
col.NR.lab	color of the species labels, see see text for more details.
cex.NR.lab	size of the species labels defautls NA for no labels, see see text for more details.
fac.NR.lab	factor for moving the NR labels from its original coordinates for clarity, by defaults they are multiply 1.2
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 is E is the environmental space. The arrows represent the species' NR 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$ls)[1]
#Create a factor which defines the subsets
fact <- factor(c(rep(1,N/2),rep(2,N/2)))
# nic1 will be use as reference and fact will be use to define the subniches environment
subnic1 <- subniche(nic1, fact)
sigi <- rtest(nic1,10)
M <- length(sigi$pvalue)
plot_NR(subnic1, sig=sigi$pvalue[-M], sig_thres= 0.1)

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