Exploring the Phylogenetic Signal in Continuous Traits
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Documentation for package ‘phylosignal’ version 1.3
Help Pages
| phylosignal-package | phylosignal |
| .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 |