I am continuing the analysis of the ant assemblage data in the Fort Worth Nature Center with an RDA (redundancy analysis) on species occurrence (or presence/absence data). I conducted a DCCA (detrended canonical correspondence analysis) for this data. All the DCCA’s had short segments (less than 4) and thus, indicated that RDA was the appropriate followup to the PCA. All these tests were done using CANOCO.
The PCA for the environmental variables (a mix of soil and vegetation characteristics) indicated that the variables chosen were pretty good at discriminating the sites. The hypothesis is that the ant species use these same characteristics or some combination of them in their choice of habitat. Thus, the ants should also be indicative of the different habitats and therefore, possibly useful as indicator species.
The PCA on the ant species had rather low values which I originally considered abysmal. However, low values are not unexpected for occurrence data. At any rate, it is the RDA in which both the environmental variables and species occurrences are considered which is the crucial point. The PCA on species occurrence did not include the environmental data.
I conducted RDA on the species occurrences for each month (June, July, and August) and for the summer pooled. The RDA also included forward selection of variables and a Monte Carlo test for significance. Although it is interesting to see a comparison of the significant factors by month, for species occurrence it is really the pooled data (summer) that is of importance. The by month data is related to seasonality or activity of the species and not just occurrence. (This is one of the difficulties of ant data — colonies can hang out in the ground or their nest for days, weeks, or months and since they are social, counting individual ants is not the same as counting individuals of other kinds of organisms.).
So, the results of the RDA:
There were 10 environmental variables used in the RDA: 5 for soil and 5 for vegetation. Soil variables included: drainage, soil penetration, latitude, slope, and depth to the restrictive layer. Vegetation variables included: ecological site, percent bare ground, percent litter cover, percent plant cover, and percent total cover. Of these variables, drainage and percent litter cover were consistently significant in the full RDA and when these sets of variables were used as covariates. Drainage and percent litter cover accounted for 24% of the variation in the species occurrence data for the summer. This percentage varied somewhat from month to month.
The speciesenvironment correlations for each RDA varied from about 70% – 99% with most in the 80s – 90s range. This indicates a strong relationship between the axes of the ordination and the species.
Still more of the RDA to think through and more followup is needed to look at the contributions of the variables to each axis. I also need to figure out how to cleanup the biplots and triplots.
Here are the RDA summaries and current biplots
Summer, full RDA:
**** Summary of RDA for Summer Species Presence****

Axes 
1 
2 
3 
4 
Total variance 
Eigenvalues 
0.158

0.119

0.099

0.082

1.000

Speciesenvironment correlations 
0.937

0.969

0.979

.9020


Cumulative percentage variance of species data 
15.8

27.7

37.6

45.8


Cumulative percentage variance of speciesenvironment relation 
23.6

41.4

56.2

68.5


Sum of all eigenvalues 




1.000

Sum of all canonical eigenvalues 




0.669

Summer, Soil:
**** Summary of Summer RDA with Partials ****

Axes 
1

2

3

4

Total variance

Eigenvalues 
0.103

0.089

0.042

0.033

1.000

Speciesenvironment correlations 
0.949

0.978

0.747

0.904


Cumulative percentage variance of species data 
15.0

28.0

34.0

38.9


Cumulative percentage variance of speciesenvironment relation 
35.3

65.6

79.9

91.2


Sum of all eigenvalues 




0.686

Sum of all canonical eigenvalues 




0.292

Summer, Vegetation
**** Summary of August RDA with Partials ****

Axes 
1

2

3

4

Total variance

Eigenvalues 
0.123

0.070

0.055

0.037

1.000

Speciesenvironment correlations 
0.937

0.923

0.927

0.898


Cumulative percentage variance of species data 
18.1

28.4

36.5

42.0


Cumulative percentage variance of speciesenvironment relation 
43.2

67.7

86.9

100.0


Sum of all eigenvalues 




0.678

Sum of all canonical eigenvalues 




0.285
