R Graphical Manual

Last data update: 2014.03.03

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Results 1 - 10 of 71 found.
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metricTester : Test Metric and Null Model Statistical Performance

Package: metricTester
Title: Test Metric and Null Model Statistical Performance
Description: Explore the behavior and performance of phylogenetic metrics and
null models.
Version: 1.2.2
Date: 2016-6-24
Author: Eliot Miller, Chris Trisos & Damien Farine
Maintainer: Eliot Miller <eliot.isaac@gmail.com>
URL: https://github.com/eliotmiller/metricTester
BugReports: https://github.com/eliotmiller/metricTester/issues
Depends: R (>= 3.1.1), ape
Imports: methods, geiger, spacodiR, dplyr, picante, foreach,
doParallel, colorRamps, MASS
Suggests: testthat
License: GPL-3
LazyData: true
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-06-25 02:39:11 UTC; eliotmiller
Repository: CRAN
Date/Publication: 2016-06-25 19:07:45

● Data Source: CranContrib
● 0 images, 76 functions, 0 datasets
● Reverse Depends: 0

laser : Likelihood Analysis of Speciation/Extinction Rates from Phylogenies

Package: laser
Version: 2.4-1
Date: 2013-09-03
Title: Likelihood Analysis of Speciation/Extinction Rates from
Phylogenies
Author: Dan Rabosky, Klaus Schliep
Maintainer: Dan Rabosky <drabosky@umich.edu>
Depends: R (>= 2.6), ape, geiger (>= 1.99-3)
Suggests:
Description: laser implements maximum likelihood methods based on the
birth-death process to test whether diversification rates have
changed over time and whether rates vary among lineages.
License: GPL (>= 2)
Packaged: 2013-09-04 10:43:28 UTC; danrabosky
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-09-04 14:58:43

● Data Source: CranContrib
● 0 images, 23 functions, 4 datasets
● Reverse Depends: 1

geiger : Analysis of Evolutionary Diversification

Package: geiger
Type: Package
Title: Analysis of Evolutionary Diversification
Version: 2.0.6
Date: 2015-09-07
Author: Luke Harmon <lukeh@uidaho.edu>, Jason Weir, Chad Brock, Rich
Glor, Wendell Challenger, Gene Hunt, Rich FitzJohn, Matt Pennell, Graham Slater, Joseph Brown, Josef Uyeda, and Jon Eastman <jonathan.eastman@gmail.com>
Maintainer: Matt Pennell <mwpennell@gmail.com>
Depends: ape (>= 3.0-6), R (>= 2.15.0)
Imports: MASS, mvtnorm, subplex, deSolve (>= 1.7), digest, Rcpp (>=
0.9.0), coda, ncbit, colorspace, methods
LinkingTo: Rcpp
Description: Methods for fitting macroevolutionary models to phylogenetic trees.
License: GPL (>= 2)
URL: http://www.webpages.uidaho.edu/~lukeh/software.html
ByteCompile: yes
NeedsCompilation: yes
Packaged: 2015-09-07 18:19:34 UTC; mwpennell
Repository: CRAN
Date/Publication: 2015-09-07 21:26:42

● Data Source: CranContrib
● Cran Task View: Phylogenetics
● 0 images, 39 functions, 1 datasets
● Reverse Depends: 8

geomorph : Geometric Morphometric Analyses of 2D/3D Landmark Data

Package: geomorph
Date: 2016-03-22
Type: Package
Title: Geometric Morphometric Analyses of 2D/3D Landmark Data
Version: 3.0.1
Author: Dean Adams, Michael Collyer, Emma Sherratt
Maintainer: Dean Adams <dcadams@iastate.edu>
Depends: rgl, ape, R (>= 3.1.0)
Imports: graphics, grDevices, stats, utils, jpeg, geiger, Matrix
Description: Read, manipulate, and digitize landmark data, generate shape
variables via Procrustes analysis for points, curves and surfaces, perform
shape analyses, and provide graphical depictions of shapes and patterns of
shape variation.
License: GPL (>= 2)
Packaged: 2016-03-25 15:34:16 UTC; Dean
Repository: CRAN
Date/Publication: 2016-03-25 20:00:54
RoxygenNote: 5.0.1
NeedsCompilation: no

● Data Source: CranContrib
● Cran Task View: Phylogenetics
● 0 images, 91 functions, 11 datasets
● Reverse Depends: 0

mvMORPH : Multivariate Comparative Tools for Fitting Evolutionary Models to Morphometric Data

Package: mvMORPH
Type: Package
Title: Multivariate Comparative Tools for Fitting Evolutionary Models
to Morphometric Data
Version: 1.0.7
Date: 2016-05-25
Author: Julien Clavel, with contributions from Aaron King, and Emmanuel Paradis
Maintainer: Julien Clavel <julien.clavel@hotmail.fr>
Description: Fits multivariate (Brownian Motion, Early Burst, ACDC, Ornstein-Uhlenbeck and Shifts) models of continuous traits evolution on trees and time series.
Depends: R (>= 2.9.1), phytools, ape, corpcor, subplex
Imports: stats, spam
Suggests: knitr, car
License: GPL (>= 2.0)
URL: https://github.com/JClavel/mvMORPH
VignetteBuilder: knitr
NeedsCompilation: yes
Repository: CRAN
Packaged: 2016-06-17 23:25:59 UTC; julienclavel
Date/Publication: 2016-06-18 10:06:57

● Data Source: CranContrib
● Cran Task View: Phylogenetics
● 0 images, 15 functions, 0 datasets
● Reverse Depends: 0

mvSLOUCH : Multivariate Stochastic Linear Ornstein-Uhlenbeck Models for Phylogenetic Comparative Hypotheses

Package: mvSLOUCH
Type: Package
Title: Multivariate Stochastic Linear Ornstein-Uhlenbeck Models for
Phylogenetic Comparative Hypotheses
Version: 1.3.2
Date: 2015-07-16
Author: Krzysztof Bartoszek <bartoszekkj@gmail.com>
Maintainer: Krzysztof Bartoszek <bartoszekkj@gmail.com>
Description: Fits multivariate Ornstein-Uhlenbeck types of models to continues trait data from species related by a common evolutionary history.
Depends: R (>= 2.9.1), ouch, ape, numDeriv, mvtnorm, corpcor
License: GPL (>= 2) | file LICENCE
LazyLoad: yes
Collate: regimes.R treeDists.R grid.R matrixexps.R
matrixparametrizations.R modelparamstransform.R precalcs.R
sdemoments.R sdemomentsphyl.R loglik.R ci.R phylgls.R
modelparamssummary.R modelparams.R estimBM.R estimGLSGC.R
estimMAXLIK.R simulVasicekproc.R simulVasicekprocphyl.R
PhyloSDEestim.R MVslouchSimulStudy.R wrappers.R fitch.mvsl.R
ouch2slouch.mvsl.R make.states.mvsl.R evolmodelest.R getESS.R
Imports: methods
Packaged: 2016-06-06 16:58:03 UTC; bart
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2016-06-06 20:25:26

● Data Source: CranContrib
● 0 images, 15 functions, 0 datasets
● Reverse Depends: 0

DDD : Diversity-Dependent Diversification

Package: DDD
Type: Package
Title: Diversity-Dependent Diversification
Version: 3.2
Date: 2016-2-5
Depends: R (>= 3.0.2), deSolve, ape, ade4
Imports: phytools, subplex, Matrix, expoRkit, SparseM
Author: Rampal S. Etienne & Bart Haegeman
Maintainer: Rampal S. Etienne <r.s.etienne@rug.nl>
License: GPL-3
Description:
Implements maximum likelihood methods based on the diversity-dependent birth-death process to test whether speciation or extinction are diversity-dependent.
See Etienne et al. 2012, Proc. Roy. Soc. B 279: 1300-1309, <DOI:10.1098/rspb.2011.1439>.
Also implements maximum likelihood methods to detect various types of key innovations in the light of diversity-dependence.
See Etienne & Haegeman 2012, Am. Nat. 180: E75-E89, <DOI:10.1086/667574>.
Finally, DDD contains a function to simulate the diversity-dependent process.
NeedsCompilation: no
Packaged: 2016-02-09 08:59:36 UTC; rampa
Repository: CRAN
Date/Publication: 2016-02-09 10:24:37

● Data Source: CranContrib
● Cran Task View: Phylogenetics
● 4 images, 16 functions, 0 datasets
● Reverse Depends: 0

MCMCglmm : MCMC Generalised Linear Mixed Models

Package: MCMCglmm
Version: 2.22.1
Date: 2015-09-21
Title: MCMC Generalised Linear Mixed Models
Depends: Matrix, coda, ape
Imports: corpcor, tensorA, cubature, methods
Suggests: rgl, combinat, mvtnorm, orthopolynom
Author: Jarrod Hadfield
Maintainer: Jarrod Hadfield <j.hadfield@ed.ac.uk>
Description: MCMC Generalised Linear Mixed Models.
License: GPL (>= 2)
NeedsCompilation: yes
Packaged: 2016-01-30 12:16:26 UTC; ripley
Repository: CRAN
Date/Publication: 2016-01-30 13:41:43

● Data Source: CranContrib
● Cran Task View: Bayesian, Phylogenetics, Psychometrics, Survival
● 9 images, 41 functions, 6 datasets
● Reverse Depends: 3

HAP.ROR : Recursive Organizer (ROR)

Package: HAP.ROR
Type: Package
Title: Recursive Organizer (ROR)
Version: 1.0
Date: 2013-03-23
Author: Lue Ping Zhao and Xin Huang
Maintainer: Xin Huang <xhuang.fhcrc@gmail.com>
Depends: R (>= 2.15.2), hash, ape
Description: Functions to perform ROR for sequence-based association
analysis
License: GPL-2
Packaged: 2013-03-24 18:31:29 UTC; xinhuang
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2013-03-25 06:57:39

● Data Source: CranContrib
● 2 images, 8 functions, 5 datasets
● Reverse Depends: 0

HyPhy : Macroevolutionary phylogentic analysis of species trees and gene trees

Package: HyPhy
Type: Package
Title: Macroevolutionary phylogentic analysis of species trees and gene
trees
Version: 1.0
Date: 2012-07-25
Authors@R: person("Nathaniel", "Hallinan", role = c("aut", "cre"),
email = "nmhallinan@gmail.com")
Author: Nathaniel Malachi Hallinan
Maintainer: Nathaniel Malachi Hallinan <nmhallinan@gmail.com>
Depends: ape, R.utils
Description: A Bay Area high level phylogenetic analysis package mostly
using the birth-death process. Analysis of species tree
branching times and simulation of species trees under a number
of different time variable birth-death processes. Analysis of
gene tree species tree reconciliations and simulations of gene
trees in species trees.
License: GPL-2
Packaged: 2012-07-29 23:15:47 UTC; Nat
Repository: CRAN
Date/Publication: 2012-07-30 04:09:01

● Data Source: CranContrib
● Cran Task View: Phylogenetics
● 80 images, 5 functions, 0 datasets
● Reverse Depends: 0