|
This series of functions serve to compute dissimilarity matrices for phylogenetic beta diversity
● Data Source:
CranContrib
● Keywords: internal
● Alias: recluster.phybetadiv
●
0 images
|
|
This function plots the RGB dots belonging to a matrix obtained by recluster.col on a user defined set of coordinates (usually longitude and latitude) for original sites.
● Data Source:
CranContrib
● Keywords: plot
● Alias: recluster.plot.sites.col
●
0 images
|
|
This function rotates the points of a configuration to a new configuration where a line identified by its intercept and its angular coefficient is rotated to become horizontal. The function can also flip or centre a configuration
● Data Source:
CranContrib
● Keywords: configurations
● Alias: recluster.rotate
●
0 images
|
|
This function identifies a line in a configuration based on different criteria and produces its slope and intercept values. I can be used together with recluster.rotate used to rotate a configuration on the basis of a custom line.
● Data Source:
CranContrib
● Keywords: configurations
● Alias: recluster.line
●
0 images
|
|
This function projects a two dimensional matrix into a RGB space with red, green, yellow and blue at its four corners. RGB combination for each case corresponding to its position in this space is provided together with new coordinates.
● Data Source:
CranContrib
● Keywords: plot
● Alias: recluster.col
●
0 images
|
|
This function creates a histogram where the number of cells with zero value are explicitely showed in the first bar. Moreover, it provides the percentage of cells having equal values in the matrix.
● Data Source:
CranContrib
● Keywords: dissimilarity
● Alias: recluster.hist
●
0 images
|
|
This function computes dissimilarity matrices based on the two most popular partitions of faunistic and phylogenitic beta-diversity. In particular Jaccard = beta3 + richness (Carvalho et al. 2012), Jaccard = Jturnover + Jnestedness (Baselga, 2012) and Sorensen = Simpson + nestedness (Baselga 2010) for faunistic indexes and Unifrac = Unifrac_turn + Unifrac_PD and PhyloSor = PhyloSor_turn + Phylosor_PD (Leprieur et al. 2012). Any other binary index can be included in brackets by using the syntax of designdist function of the vegan package.
● Data Source:
CranContrib
● Keywords: array
● Alias: recluster.dist
●
0 images
|
|
This function compute the fraction of the distances contained in a dissimilarity matrix which is explained by a clustering solution of the elements. The value is obtained by computing the sum of all the dissimilarity values among elements belonging to different clusters and diving this sum for the sum of all the cells of the original dissimilarity matrix.
● Data Source:
CranContrib
● Keywords: cluster
● Alias: recluster.expl
●
0 images
|
|
This function produces plots for recluster trees and assign single or pairs of support values belonging to single or multiscale analyses.
● Data Source:
CranContrib
● Keywords: hplot
● Alias: recluster.plot
●
0 images
|
|
This function plots a matrix obtained by recluster.col in the RGB space.
● Data Source:
CranContrib
● Keywords: plot
● Alias: recluster.plot.col
●
0 images
|
providing 
.