The function represents the species' subniches SR within its realized niche NR.
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",
...
)an object of class subniche.
a character string of the species name.
label for x-axis, see title for more details.
label for y-axis, see title for more details.
a main title for the plot, see title for more details.
axis color, see par for more details.
axis line type, see par for more details.
axis width, see par for more details.
color border of E polygon, see polygon for more details.
inside color of E polygon, see polygon for more details.
line type for the E border, see polygon for more details.
line width for the E border, see polygon for more details.
inside color of NR polygon, see polygon for more details.
color border of NR polygon, see polygon for more details.
line type for the NR border, see polygon for more details.
line width for the NR border, see polygon for more details.
color of the species label representing the NR position, see textplot for more details.
size of the species label representing the NR position, see textplot for more details.
the type of points representing the NR position, see points for more details.
the color of points representing the NR position, see points for more details.
point color contour if pch=21:25.
size of points representing the SR position, see points for more details.
color border of SR polygon, see polygon for more details.
inside color of SR polygon, see polygon for more details.
line type for the SR border, see polygon for more details.
line width for the SR border, see polygon for more details.
color of the species label representing the SR position, see text for more details.
size of the species label representing the SR position, see text for more details.
factor for moving the SR labels from its original coordinates for clarity, by defaults they are multiply 1.2
type of points representing the SR position, see points for more details.
color of points representing the SR position, see points for more details.
point color contour if pch=21:25.
size of points representing the SR position, see points for more details.
arrow color, see arrows for more details.
arrow angle head, see arrows for more details.
arrow width, see arrows for more details.
arrow head length, see arrows for more details.
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.
a logical option for legend to be plotted or not, default leg=T.
setting legend positions with the following keywords "bottomright", "bottom", "bottomleft", "left", "topleft", "top", "topright", "right" and "center", see legend for more details.
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.
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 tools:::Rd_expr_doi("10.7717/peerj.3364") for more details on the subniche concept.
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")
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