In allanecology/BetaDivMultifun: Testing effects of multitrophic beta-diversity and land-use intensity (LUI) on ecosystem multifunctionality

#############################
#  PLOTTING I - SPLINES
#
vars_in_model <- c(funs,typeofbeta,which_beta_detail)
# to plot each spline in a separate plot
# plot(gdm_actual, plot.layout = c(3, 2), plot.color = "grey",main="GDM",sub= paste(vars_in_model, collapse=', '))

# produce a "normal" plot ---------
groesse <- 0.5 # size of text in plot
pdf('../test.pdf',paper='a4r')
par(xpd = T, mar = par()$mar + c(0,0,0,6))
plot(exSplines[[1]][,1], exSplines[[2]][,1], type="l",
     lwd=2, xlab="jtest", ylab="Partial Ecological Distance",ylim=c(0,0.65),main="GDM",sub= paste(vars_in_model, collapse=', '),
     cex=groesse, cex.axis= groesse, cex.lab= groesse, cex.sub=groesse*1.5)
for(i in 1:ncol(exSplines[[1]])){
  lines(exSplines[[1]][,i], exSplines[[2]][,i], col=colr[i],lwd=2,lty=ltyp[i])
}
legend(1.05,0.675,legend_names, lty=ltyp,lwd=c(1.5,1.5),col=colr[1:ncol(exSplines[[1]])],cex = 0.5) 
par(mar=c(5, 4, 4, 2) + 0.1)
dev.off()

#############################
#  ESTIMATING P - VALUES
#
# takes too long on my computer yet. but I can change, so it doesn't do aic and only looks at the full model - much faster! todo
varimp_output <- gdm.varImp(meltset, geo=F, parallel=T, nPerm =1) #, fullModelOnly=T)

#############################
#  SAVE PRODUCED DATA
#
# save current gdm_actual so I can get back to it
namegdm <- paste(funs, typeofbeta, paste(which_beta_detail, collapse="_"), sep="_")
assign(namegdm, gdm_actual)
namegdm <- paste(namegdm, "VARIMP_OUTPUT", sep="_")
assign(namegdm, varimp_output)
rm(namegdm)

#############################
#  Plotting P - VALUES
#
legend_names <- gsub("_abund_","_ab_", legend_names)
pvals <- mod1_pvals[[3]][,1]
legend_names[which(as.vector(pvals)== 0)] <- paste(legend_names[which(as.vector(pvals)== 0)],'*')

groesse <- 0.5 # size of text in plot
pdf('../test.pdf',paper='a4r')
par(xpd = T, mar = par()$mar + c(0,0,0,6))
plot(exSplines[[1]][,1], exSplines[[2]][,1], type="l",
     lwd=2, xlab="predictors", ylab="Partial Ecological Distance",ylim=c(0,0.65),main="GDM",
     sub= "subtitle",
     cex=groesse, cex.axis= groesse, cex.lab= groesse, cex.sub=groesse*1.5)
for(i in 1:ncol(exSplines[[1]])){
  lines(exSplines[[1]][,i], exSplines[[2]][,i], col=colr[i],lwd=2,lty=ltyp[i])
}
legend(1.05,0.675,legend_names, lty=ltyp,lwd=c(1.5,1.5),col=colr[1:ncol(exSplines[[1]])],cex = 0.5) 
par(mar=c(5, 4, 4, 2) + 0.1)
dev.off()

allanecology/BetaDivMultifun documentation built on Nov. 9, 2023, 8:47 p.m.