Description Usage Arguments Examples
The function to represent the species subniche under each subenvironment K with their respective marginality from G_K.
1 2 3 4 5 6 7 8 9 | subplot_sp(subnic, sp, main=NULL, col.axis="azure3", lty.axis=2, lwd.axis=2,
xlab=NULL, ylab=NULL, col.sublab="black", font.sublab=2, cex.sublab=0.7, show.lines=F,
border.E="#92c5de", col.E="#92c5de", lty.E=1, lwd.E=1, border.K ="#2c7fb8",lwd.K=1,
col.K ="#2c7fb8", lty.K=1, col.arrow="black",angle.arrow=20, lwd.arrow=2,
length.arrow=0.1, col.G_k= "red", cex.G_k=1, border.SP="#fec44f", col.SB="#d95f0e",
lty.SP=1, lwd.SP=1, border.NR ="#fdb462", col.NR =NA,cex.sp=1, col.sp="black",
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, pch.G_k=19, col.su="#b35806", cex.su=0.5, pch.su=1,
posi.leg="topleft", bty.leg="n", ... )
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subnic |
an object of class |
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. |
xlab |
label for x-axis, see title for more details. |
ylab |
label for y-axis, see title for more details. |
col.sublab |
color of the species labels, see textplot for more details. |
font.sublab |
font of the species labels, see textplot for more details. |
cex.sublab |
size of the species labels, 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. |
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.K |
color border of K polygon, see polygon for more details. |
lwd.K |
line width for the K border, see polygon for more details. |
col.K |
inside color of K polygon, see polygon for more details. |
lty.K |
line type for the K border, see polygon 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. |
col.G_k |
color of the point representing G_k, see points for more details. |
cex.G_k |
size of the point representing G_k, see points for more details. |
border.SP |
color border of species subniche polygon, see polygon for more details. |
col.SB |
color of the SB area. |
lty.SP |
line type for the SP border, see polygon for more details. |
lwd.SP |
line width for the SP 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. |
cex.sp |
size of the species label representing the NR position, see textplot for more details. |
col.sp |
color of the species label representing the NR position, see textplot 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. |
pch.G_k |
type of the point representing G_k, see points for more details. |
col.su |
color of the points representing the sampling units (SU), see points for more details. |
cex.su |
size of the points representing the sampling units (SU), see points for more details. |
pch.su |
type of the points representing the sampling units (SU), see points for more details. |
posi.leg |
legend location in the graph, see legend for more details. |
bty.leg |
the type of box to be drawn around the legends. The allowed values are "o" (the default) and "n". See legend for more details |
... |
further arguments passed to or from other methods. |
1 2 3 4 5 6 7 8 9 10 11 12 13 | 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$ls)[1]
#Create a factor which defines the subsets
fact <- factor(c(rep(1,N/2),rep(2,N/2)))
# nic1 will be use as reference and fact will be use to define the subniches environment
subnic1 <- subniche(nic1, fact)
eig <- round(subnic1$eig/sum(subnic1$eig)*100,2)[1:2]
#Two graphs are drawn one after the other
subplot_sp(subnic1,"Neba",main="Species subniche in K")
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