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Plotting the Autoecology and Synecology of Pinus Cembra


Introduction

  • Autoecology: the branch of ecology which deals with individual species and their reactions to environmental factors. sources
  • Synecology : The branch of ecology which deals with the distribution, abundance, demography, and interactions between coexisting populations.

In this exercise we are going to plot the presence / absence of Pinus Cembra, the presence of its co-occurring species (Larix Decidua and Picea Abies) and the rest of the european tree species according to bioclimatic factors.

Dataset details

Code Bioclimatic factor
pr105 Maximum Temperature warmest month
pr106 Minimum Temperature coldest month
pr112 Annual Precipitation
pr118 Summer Precipitation
pr134 Compensated summer ombrothermic index
pr198 Accumulated Annual Evapotranspiration


Code Tree species
S116 Larix decidua
S118 Picea abies
S123 Pinus cembra


There are no explanations in the script. Try to understand it and play with its functions.

Hands-on

load("~/ost4sem/exercise/
 basic_adv_r/inputs/advanceRdata")
 
FFD =advanceRdata
 
# i = 123
 
mod <- paste("S",i,sep="")
presence = subset(FFD,FFD[[mod]]==1)
absence = subset(FFD,FFD[[mod]]!=1)
 
presence.larix = subset(FFD,FFD$S116==1)
presence.picea = subset(FFD,FFD$S118==1)
 
png("~/ost4sem/exercise/basic_adv_r/outputs/synecology_cembro.png",
 width = 800, height = 800)
# png("/home/stefano/ubun/cembro
# /figures/synecology_cembro1.png", 
# width = 8, height = 8, units = cm )
 
nf <- layout(matrix(c(1,2,3,4),2,2,byrow=TRUE), 
c(1,1), c(1,1), TRUE) 
layout.show(nf)
par(mar=c(5,5,1,1))
 
## plot Annual Precipitation vs Minimum Temperature
plot(absence$pr112,absence$pr106, 
 type = "p", col = "gray40", lwd=0.2, pch=19,
 xlab="Annual precipitation (mm/yr)", 
 ylab="Mean Min Temp. coldest month", cex.lab = 2)
 
points(presence.picea$pr112,presence.picea$pr106,
 type = "p", col = "red", lwd=0.5,pch=20, cex=1)
 
points(presence.larix$pr112,presence.larix$pr106,
 type = "p", col = "blue", lwd=0.5,pch=20, cex=1)
 
points(presence$pr112,presence$pr106, 
 type = "p", col = "green3", lwd=1,pch=20, cex=2)
 
 
## plot Summer Precipitation vs Minimum Temperature
plot(absence$pr118,absence$pr106, 
 type = "p", col = "grey40", lwd=0.2, pch=19, 
 xlab="Summer precipitation (mm/yr)", 
 ylab="", 
 cex.lab = 2)
 
points(presence.picea$pr118,presence.picea$pr106,
 type = "p", col = "red", lwd=0.5,pch=20, cex=1)
 
points(presence.larix$pr118,presence.larix$pr106,
 type = "p", col = "blue", lwd=0.5,pch=20, cex=1)
 
points(presence$pr118,presence$pr106,
 type = "p", col = "green3", lwd=1, pch=20, cex=2)
 
## Compensated summer ombrothermic index vs Sum of T non frozen months 
plot(absence$pr134,absence$pr198, 
 type = "p", col = "grey40", lwd=0.2, pch=19, 
 xlab="Summer Ombrothermic index", 
 ylab="Accumulated ETP (mm/yr)", 
 cex.lab = 2)
 
points(presence.picea$pr134,presence.picea$pr198,
 type = "p", col = "red", lwd=0.5,pch=20, cex=1)
 
points(presence.larix$pr134,presence.larix$pr198,
 type = "p", col = "blue", lwd=0.5,pch=20, cex=1)
 points(presence$pr134,presence$pr198,
 type = "p", col = "green3", lwd=1, pch=20, cex=2)
 
legend (13,900, c("Pinus c.","Picea a.","Larix d.","other spp."),
 bty = "n", col=c("green","red","blue","grey40"), 
 pch=c(19,20,20,20),cex=2)
 
 
## Max temp warmest month vs ETP
plot(absence$pr105,absence$pr198, type = "p", col = "grey40", lwd=0.2, pch=19, xlab="Mean Max. Temp. warmest month", ylab="", cex.lab = 2)
 
points(presence.picea$pr105,presence.picea$pr198,type = "p", col = "red", lwd=0.5,pch=20, cex=1)
 
points(presence.larix$pr105,presence.larix$pr198,type = "p", col = "blue", lwd=0.5,pch=20, cex=1)
 
points(presence$pr105,presence$pr198,type = "p", col = "green3", lwd=1, pch=20, cex=2)
 
dev.off()
wiki/pcem_syneco_r.txt · Last modified: 2017/12/05 22:53 (external edit)