geiger-defunct: deprecated functions in GEIGER

In geiger: Analysis of Evolutionary Diversification

deprecated functions in GEIGER

Description

This function has been deprecated in geiger and auteur or may be available from another package. Below shows the original function and the suggested function to use in its place.

Details

• area.between.curves: use geiger:::.area.between.curves

• BDsim: use sim.bd

• birthdeath.tree: use sim.bdtree

• calibrate.proposalwidth: use calibrate.rjmcmc

• deltaTree: use rescale.phylo

• disp.calc: use disparity

• dtt.full: use dtt

• exponentialchangeTree: use rescale.phylo

• get.simulation.matrix: use geiger:::.get.simulation.matrix

• getAncStates: use fastAnc

• ic.sigma: use ratematrix

• intercalate.samples: use geiger:::.intercalate.rjmcmc

• kappaTree: use rescale.phylo

• lambdaTree: use rescale.phylo

• linearchangeTree: use rescale.phylo

• name.check: use geiger:::.treedata

• node.leaves: use tips

• node.sons: use geiger:::.get.desc.of.node

• ouTree: use rescale.phylo

• phy.anova: use aov.phylo

• phy.manova: use aov.phylo

• pool.rjmcmcsamples: use load

• prune.extinct.taxa: use drop.extinct

• prune.random.taxa: use drop.random

• rate.estimate: use bd.ms or bd.km

• rescaleTree: use rescale.phylo

• runMedusa: use medusa

• shifts.plot: use plot

• speciationalTree: use rescale.phylo

• tip.disparity: use disparity

• tracer: use of plot.mcmc and other functions in coda recommended

• transform.phylo: use rescale.phylo

• tworateTree: use rescale.phylo

• vmat: use geiger:::.vmat

geiger documentation built on April 4, 2023, 1:07 a.m.