dist.eval {BiodiversityR} | R Documentation |
Distance Matrix Evaluation
Description
Function dist.eval
provides one test of a distance matrix, and then continues with distconnected
(vegan). Function prepare.bioenv
converts selected variables to numeric variables and then excludes all categorical variables in preparation of applying bioenv
(vegan).
Usage
dist.eval(x, dist)
prepare.bioenv(env, as.numeric = c())
Arguments
x |
Community data frame with sites as rows, species as columns and species abundance as cell values. |
env |
Environmental data frame with sites as rows and variables as columns. |
dist |
Method for calculating ecological distance with function |
as.numeric |
Vector with names of variables in the environmental data set to be converted to numeric variables. |
Details
Function dist.eval
provides two tests of a distance matrix:
(i) The first test checks whether any pair of sites that share some species have a larger distance than any other pair of sites that do not share any species. In case that cases are found, then a warning message is given.
(ii) The second test is the one implemented by the distconnected
function (vegan). The distconnected test is only calculated for distances that calculate a value of 1 if sites share no species (i.e. not manhattan or euclidean), using the threshold of 1 as an indication that the sites do not share any species. Interpretation of analysis of distance matrices that provided these warnings should be cautious.
Function prepare.bioenv
provides some simple methods of dealing with categorical variables prior to applying bioenv
.
Value
The function tests whether distance matrices have some desirable properties and provide warnings if this is not the case.
Author(s)
Roeland Kindt (World Agroforestry Centre)
References
Kindt, R. & Coe, R. (2005) Tree diversity analysis: A manual and software for common statistical methods for ecological and biodiversity studies.
https://www.worldagroforestry.org/output/tree-diversity-analysis
Examples
library(vegan)
data(dune)
dist.eval(dune,"euclidean")
dist.eval(dune,"bray")
## Not run:
data(dune.env)
dune.env2 <- dune.env[,c('A1', 'Moisture', 'Manure')]
dune.env2$Moisture <- as.numeric(dune.env2$Moisture)
dune.env2$Manure <- as.numeric(dune.env2$Manure)
sol <- bioenv(dune ~ A1 + Moisture + Manure, dune.env2)
sol
summary(sol)
dune.env3 <- prepare.bioenv(dune.env, as.numeric=c('Moisture', 'Manure'))
bioenv(dune, dune.env3)
## End(Not run)