Show GAM results
0.2 m2 results
cooc.02.gam.sqrt.te<-gam(cooc.02.z~te(phy.dist.sqrt,gen.spec.02), dat=data.cooc.02)
summary(cooc.02.gam.sqrt.te)
##
## Family: gaussian
## Link function: identity
##
## Formula:
## cooc.02.z ~ te(phy.dist.sqrt, gen.spec.02)
##
## Parametric coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) -0.1695 0.1007 -1.682 0.0931 .
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Approximate significance of smooth terms:
## edf Ref.df F p-value
## te(phy.dist.sqrt,gen.spec.02) 7.595 9.646 2.668 0.00397 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## R-sq.(adj) = 0.0411 Deviance explained = 5.41%
## GCV = 5.7821 Scale est. = 5.6935 n = 561
#only those species pairs <30my
cooc.02.gam.30<-gam(cooc.z.02.30~te(phy.dist.30.sqrt,gen.spec.02.30), dat=data.cooc.02.30)
summary(cooc.02.gam.30)
##
## Family: gaussian
## Link function: identity
##
## Formula:
## cooc.z.02.30 ~ te(phy.dist.30.sqrt, gen.spec.02.30)
##
## Parametric coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) -0.6138 0.1711 -3.587 0.00051 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Approximate significance of smooth terms:
## edf Ref.df F p-value
## te(phy.dist.30.sqrt,gen.spec.02.30) 16.05 18.13 2.079 0.011 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## R-sq.(adj) = 0.191 Deviance explained = 29.8%
## GCV = 4.1527 Scale est. = 3.5725 n = 122
1.0 m2 results
# final GAM models
cooc.gam.sqrt.te<-gam(cooc.z~te(phy.dist.sqrt,gen.spec), dat=data.cooc)
summary(cooc.gam.sqrt.te)
##
## Family: gaussian
## Link function: identity
##
## Formula:
## cooc.z ~ te(phy.dist.sqrt, gen.spec)
##
## Parametric coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) -0.1580 0.1139 -1.387 0.166
##
## Approximate significance of smooth terms:
## edf Ref.df F p-value
## te(phy.dist.sqrt,gen.spec) 13.83 16.01 3.84 7.41e-07 ***
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## R-sq.(adj) = 0.0876 Deviance explained = 11%
## GCV = 7.4778 Scale est. = 7.2801 n = 561
#only those species pairs <30my
cooc.gam.30<-gam(cooc.z.30~te(phy.dist.30.sqrt,gen.spec.30), dat=data.cooc.30)
summary(cooc.gam.30)
##
## Family: gaussian
## Link function: identity
##
## Formula:
## cooc.z.30 ~ te(phy.dist.30.sqrt, gen.spec.30)
##
## Parametric coefficients:
## Estimate Std. Error t value Pr(>|t|)
## (Intercept) -0.6962 0.2142 -3.251 0.00154 **
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## Approximate significance of smooth terms:
## edf Ref.df F p-value
## te(phy.dist.30.sqrt,gen.spec.30) 14.83 16.9 1.795 0.0379 *
## ---
## Signif. codes: 0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
##
## R-sq.(adj) = 0.157 Deviance explained = 26%
## GCV = 6.43 Scale est. = 5.5959 n = 122
Plot GAMS
# Top graphs are for 0.2m2 plots, whereas bottom are for 1.0m2 plots
textClick.bold<-function(express,col="black",font=2,cex=NULL){
par(mar = rep(0, 4),xpd=NA)
text(locator(1),express,col=col,cex=cex)
}
#Plot four plots side-by-side
#dev.new(width=4.9, height=6)
#layout(matrix(1:4,ncol=2), width = c(1,1),height = c(1,1))
par(mfrow=c(2,2))
par(mar=c(3.5,3,2.75,0.75), mgp=c(1.5,0.3,0), las=0)
my.vis.gam(cooc.02.gam.sqrt.te, axes=FALSE, type="response", plot.type = "contour", color="gray", main="", mgp=c(1.75,0.5,0),xlab="Phylogenetic distance (sqrt)",cex.main=0.1, lwd=2,cex.lab=1.15, cex=2, ylab="Mean niche width", font.lab=1)
axis(1, tck=0.025, cex.lab=1.25, cex.axis=1)
axis(2, tck=0.025, cex.lab=1.25, cex.axis=1)
box(bty="o", lwd=2)
my.vis.gam(cooc.02.gam.30, axes=FALSE, type="response", plot.type = "contour", color="gray", main="", mgp=c(1.75,0.5,0),xlab="Phylogenetic distance (sqrt)",cex.main=0.1, lwd=2,cex.lab=1.15, cex=2, ylab="Mean niche width", font.lab=1)
axis(1, tck=0.025, cex.lab=1.25, cex.axis=1)
axis(2, tck=0.025, cex.lab=1.25, cex.axis=1)
box(bty="o", lwd=2)
my.vis.gam(cooc.gam.sqrt.te, axes=FALSE, type="response", plot.type = "contour", color="gray", main="", mgp=c(1.75,0.5,0),xlab="Phylogenetic distance (sqrt)",cex.main=0.1, lwd=2,cex.lab=1.15, cex=2, ylab="Mean niche width", font.lab=1)
axis(1, tck=0.025, cex.lab=1.25, cex.axis=1)
axis(2, tck=0.025, cex.lab=1.25, cex.axis=1)
box(bty="o", lwd=2)
my.vis.gam(cooc.gam.30, axes=FALSE, type="response", plot.type = "contour", color="gray", main="", mgp=c(1.75,0.5,0),xlab="Phylogenetic distance (sqrt)",cex.main=0.1, lwd=2,cex.lab=1.15, cex=2, ylab="Mean niche width", font.lab=1)
axis(1, tck=0.025, cex.lab=1.5, cex.axis=1)
axis(2, tck=0.025, cex.lab=1.5, cex.axis=1)
box(bty="o", lwd=2)
#textClick.bold("(a)", cex=1.25)
#textClick.bold("(b)", cex=1.25)
#textClick.bold("(c)", cex=1.25)
#textClick.bold("(d)", cex=1.25)