subniche (version 1.5)

plot_dym: Communities subniches dynamic

Description

The function represents the species' subniches SR position within the environmental space E.

Usage

plot_dym(
  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.SR.pos = 21,
  cex.SR.pos = 1,
  col.SR.pos = "#ffa600",
  col.SR.pt = "black",
  col.SR.lab = "black",
  cex.SR.lab = NA,
  fac.SR.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.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.pos

color of points representing the SR position, see points for more details.

col.SR.pt

point color contour if pch=21:25.

col.SR.lab

color of the species labels, see see text for more details.

cex.SR.lab

size of the species labels defautls NA for no labels, see 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

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' subniche marginality from the origin G. See tools:::Rd_expr_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$ls)[1]
#Create a factor which defines the subsets
fact <- factor(c(rep(1,N/2),rep(2,N/2)))
# nic1 will be use as reference and fact will be use to define the subniches environment
subnic1 <- subniche(nic1, fact)
sigg <- rtestrefor(subnic1,10)
sig = c(sigg$`1`$witomigtest$subni.pvalue[-28],sigg$`2`$witomigtest$subni.pvalue[-28])
plot_dym(subnic1, sig=sig, sig_thres= 0.1)