distdisplayed {BiodiversityR} | R Documentation |
This function compares the distance among sites as displayed in an ordination diagram (generated by ordiplot
) with the actual distances among sites as available from a distance matrix (as generated by vegdist
).
distdisplayed(x, ordiplot, distx = "bray", plotit = T, addit = F, method = "spearman", permutations = 100, abline = F, gam = T, ...)
x |
Community data frame (with sites as rows, species as columns and species abundance as cell values) or distance matrix. |
ordiplot |
Ordination diagram generated by ordiplot or distance matrix. |
distx |
Ecological distance used to calculated the distance matrix (theoretically the same distance as displayed in the ordination diagram); passed to vegdist and partial match to "manhattan", "euclidean", "canberra", "bray", "kulczynski", "jaccard", "gower", "morisita", "horn", "mountford", "raup" , "binomial" or "chao". This argument is ignored in case that "x" is already a distance matrix. |
plotit |
Should a plot comparing the distance in ordination diagram (or the distance matrix) with the distance from the distance matrix be generated (or not). |
addit |
Should the GAM regression result be added to an existing plot (or not). |
method |
Method for calculating the correlation between the ordination distance and the complete distance; from function mantel passed to function cor : "pearson", "spearman" or "kendall". |
permutations |
Number of permutations to assess the significance of the Mantel test; passed to mantel . |
abline |
Should a reference line (y=x) be added to the graph (or not). |
gam |
Evaluate the correspondence between the original distance and the distance from the ordination diagram with GAMas estimated by gam . |
... |
Other arguments passed to mantel . |
This function compares the Euclidean distances (between sites) displayed in an ordination diagram with the distances of a distance matrix. Alternatively, the distances of one distance matrix are compared against the distances of another distance matrix.
These distances are compared by a Mantel test (mantel
) and (optionally) a GAM regression (gam
). Optionally, a graph is provided compairing the distances and adding GAM results.
.
The function returns the results of a Mantel test and (optionally) the results of a GAM analysis.
Roeland Kindt (World Agroforestry Centre)
Kindt, R. & Coe, R. (2005) Tree diversity analysis: A manual and software for common statistical methods for ecological and biodiversity studies.
http://www.worldagroforestry.org/treesandmarkets/tree_diversity_analysis.asp
library(vegan) library(mgcv) data(dune) distmatrix <- vegdist(dune,method="kulc") ordination.model1 <- cmdscale(distmatrix,k=2) ordiplot1 <- ordiplot(ordination.model1) distdisplayed(dune,ordiplot=ordiplot1,distx="kulc",plotit=TRUE, method="spearman",permutations=100,gam=TRUE)