.layouterize |
Set layout for plots |
.layouterizeRatio |
Set layout for plots |
.orderGrArg |
Reordering vector or matrix of settings. |
barplot.phylo4d |
Barplot of Traits Values along a Phylogeny |
descentsNames |
Names of descents |
directDescents |
ID of direct descents |
distEq |
Pairwise Distance from Regularly Distributed Points |
dotplot |
Dotplot |
dotplot.phylo4d |
Dotplot of Traits Values along a Phylogeny |
evenColors |
Palette of evenly distributed colors |
focusStop |
Focus on sub parts of a plot |
focusTips |
Focus on sub parts of a plot |
focusTraits |
Focus on sub parts of a plot |
focusTree |
Focus on sub parts of a plot |
graphClust |
Phylogenetically constrained clustering |
gridplot |
Gridplot |
gridplot.phylo4d |
Gridplot of Traits Values along a Phylogeny |
kStarTest |
Computes permutation test for Blomberg's K Star |
kTest |
Computes permutation test for Blomberg's K |
lambdaTest |
Test Pagel's Lambda Optimize Pagel's Lambda and do a likelihood ratio test. |
lipaMoran |
Local Indicator of Phylogenetic Association |
mantelStat |
Mantel statistic |
matchTipsAndTraits |
Match matrix row/col names with phylo4d tips/traits |
moranTest |
Computes permutation test for Moran's I |
multiplot.phylo4d |
Plots of Traits Values along a Phylogeny |
navic |
Phylogeny and pollution sensitivity of diatoms |
pagelLogLik |
Computes log-likelihood for data and a given value of Pagel's Lambda |
phyloCorrelogram |
Phylogenetic correlogram |
phyloSignal |
Computes phylogenetic signal with different methods |
phylosignal |
phylosignal |
phyloSignalBS |
Computes phylogenetic signal for bootstrapped replicates of a phylogeny. |
phyloSignalINT |
Computes phylogenetic signal at each internal node of a phylogeny |
phyloSim |
Simulate the behaviour of phylogenetic signal statistics with a given phylogeny |
phyloSimSignal |
Phylogenetic signal estimation as a fraction of a Brownian Motion process. |
phyloWeights |
Phylogenetic weights matrix |
plot.graphclust |
Plot phylogenetically constrained clustering |
plot.phylocorrelogram |
Plot a phylogenetic correlogram |
plot.phylosim |
Plot 'phylosim' object |
plot.phylosimsignal |
Plot signal estimation as a fraction of a Brownian Motion process. |
print.graphclust |
#' Print results of phylogenetically constrained clustering |
print.phylosimsignal |
Print signal estimation as a fraction of a Brownian Motion process. |
read.p4d |
Read a phylo4d object from files |
rTraitContWeight |
Traits Values Simulation |
subsetPhyloSimSignal |
phyloSimSignal subsetting |
white2red |
Color Palette |