motmot.2.0 v1.1.2
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Models of Trait Macroevolution on Trees
Functions for fitting models of trait evolution
on phylogenies for continuous traits. The majority of functions
described in Thomas and Freckleton (2011) <doi:10.1111/j.2041-210X.2011.00132.x> and include functions that allow for tests of variation in the rates of trait evolution.
Functions in motmot.2.0
| Name | Description | |
| allCladeMembers | allCladeMembers (internal function) | |
| ancState | Extimate ancestral state (internal function) | |
| ML.RatePhylo | Maximum likelihood rate estimation for traits and phylogenies | |
| RatePhylo.CI | Confidence intervals for rate parameters | |
| make.anc | Create design matrix (internal function) | |
| make.likRatePhylo | Internal function | |
| nodeTimes | Get times for nodes and tips | |
| optim.likRatePhylo | Maximum likelihood rate estimation for traits and phylogenies | |
| anolis.data | Anolis phenotype data | |
| name.check | Name check (internal function) | |
| node.descendents | Identify nodes and tips descended from a node (internal function). | |
| plotPhylo.motmot | Tree plotting for rates Plots trees with colours based on rates of trait evolution. Also provides simple coloured plotting for trait values using the "ace" function in the ape library. | |
| removeNonBin | remove species occuring before time in the past (internal function) | |
| traitMedusaSummary | Identify shifts in the rate of trait diversification | |
| anolis.tree | Anolis phylogeny | |
| as.rateData | Conversion among data and phylogeny objects | |
| as.rateMatrix | Conversion among data and phylogeny objects | |
| cladeIdentity | Identify branches (including tips) descended from a node (internal function). | |
| contemporaryPhy | prune tree and data to lineages present in a time bin in the past | |
| transformPhylo.ML | Maximum likelihood for models of trait evoluion | |
| transformPhylo | Phylogenetic tree transformations | |
| likRatePhylo | Log-likelihood rate estimation for traits and phylogenies | |
| likTraitPhylo | Log-likelihood rate estimation for traits and phylogenies | |
| phyloCovar | Calculation of Brownian (co)variance using independent contrasts. | |
| phyloMean | Calculation of phylogenetically corrected mean. | |
| sortTraitData | Sort data and remove missing entries for tree and trait data | |
| timeSliceSummary | Identify shifts in the rate of trait diversification through time | |
| transformPhylo.MCMC | Bayesian MCMC for models of trait evolution | |
| RatePhylo.allCI | Confidence intervals for rate parameters | |
| addFossilToPhy | add a fossil to an interior branch of a time-scaled phylogeny | |
| dropTipPartial | Drop tips from a phylogenetic tree while preserving deleted nodes | |
| fairProportions | Calculate fair proportions phylogenetic diversity metric | |
| sampleHiddenSp | Sample hidden speciation events along branches of a tree (internal function) | |
| sliceTree | Slice tree (internal function) | |
| transformPhylo.ll | Log-likelhood for models of trait evolution. | |
| transformPhylo.sim | Phylogenetic tree transformations | |
| phyloVar | Calculation of Brownian variance. | |
| pic.motmot | Phylogenetically independent contrasts (internal) | |
| timeTravelPhy | timeTravelPhy (internal function) | |
| traitData.plot | plot a univariate continuous trait data on a phylogeny | |
| transformRateMatrix | Conversion among data and phylogeny objects | |
| No Results! | ||
Vignettes of motmot.2.0
| Name | ||
| motmot.2.0.vignette.Rmd | ||
| myref_small.bib | ||
| No Results! | ||
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Details
| Type | Package |
| Date | 2018-01-10 |
| License | GPL (>= 2) |
| Repository | CRAN |
| URL | https://puttickbiology.wordpress.com/motmot/ |
| RoxygenNote | 6.0.1 |
| LazyData | true |
| VignetteBuilder | knitr |
| NeedsCompilation | no |
| Packaged | 2018-01-10 18:30:29 UTC; mp1728 |
| Date/Publication | 2018-01-10 18:51:44 UTC |
| depends | ape (>= 3.0-7) , caper , coda , MASS , mvtnorm , R (>= 2.10.0) |
| suggests | knitr , rmarkdown |
| Contributors | Rob Freckleton, Emmanuel Paradis, David Orme, Gavin Thomas, Travis Ingram, Mark Puttick |
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