Worked example 2 illustrates the use
of Diversity.R functions to perform
multivariate analyses that are consistent with diversity measurements, the
CA-richness and NSCA-Simpson strategies from Pélissier
et al. (2003). It is based on analyses of PSE data set,
from a 10-ha rainforest plot at Piste de St-Elie station (PSE) in French
Guiana (Sabatier et al. 1997).
1 -
PSE data set
Once the library diversity
has been installed and loaded:
#List
of 3
# $ Tfac: Factor w/ 113 levels "Alexa wache..",..: 1 1 2 2 3 3 3 4 5 6 ...
# $ Sfac: Factor w/ 9 levels "Alt","DVD","DhS",..: 7 5 2 1 2 1 2 3 1 3 ...
# $ Qfac: Factor w/ 80 levels "q1","q10","q11",..: 10 13 46 64 45 20 48 52
31 15 ...
PSE$Tfac is a factor of 113 species names
assigned to 381 trees ;
PSE$Sfac is a factor of 9 soil classes
assigned to 381 trees ;
PSE$Qfac is a factor of 80 quadrat codes
assigned to 381 trees.
2 - CA-richness and NSCA-Simpson
strategies with respect to the soil classes
Use the following commands
to perform a CA-richness strategy with respect to the soil classes:
rich.sol<-ca.richness(PSE$Tfac~PSE$Sfac)
#Select the number of axes:
2
summary(rich.sol)
#class: div between dudi
#metric: Richness
#call: ca.richness.formula(formula = PSE$Tfac ~ PSE$Sfac)
#total diversity: 112
#explained diversity: 2.33
#ratio of explained diversity: 0.0208
#Pr(>ratio): 0.551 based on 999 replicates
3 - CA-richness and NSCA-Simpson strategies with respect to the partition into quadrats
Use the following commands to perform a CA-richness strategy with respect to quadrats:plot(simp.quad)
Projection of the soil classes at the weigthed mean position of their occurrences (as in Fig.4b in Pélissier et al. 2003) can be obtained from:
> s.class(simp.quad$ls,PSE$Sfac,cell=0,cstar=0,cpoint=0,xlim=c(-0.4,0.2),ylim=c(-0.2,0.2))
These results conform to Table 3 and Figure 4 in Pélissier
et al. (2003).
Sabatier, D., Grimaldi, M., Prévost, M.-F. , Guillaume, J., Godron, M., Dosso, M. and Curmi, P. 1997. The influence of soil cover organization on the floristic and structural heterogeneity of a Guianan rain forest. Plant Ecology, 131:81-108
Pélissier,
R., Couteron, P., Dray, S. and Sabatier, D. 2003. Consistency between
ordination techniques and diversity measurements: two strategies for species
occurrence data. Ecology, 84:242-251.