Parallel computing with phangornUpdated 2 days ago

Klaus Schliep

Rendered from Parallel.Rmd in phangorn 3.0.0.1.
Ancestral Sequence ReconstructionUpdated 7 days ago

Klaus Schliep

Rendered from Ancestral.Rmd in phangorn 3.0.0.1.
Estimating phylogenetic trees with phangornUpdated 7 days ago

Klaus Schliep, Iris Bardel-Kahr

Rendered from Trees.Rmd in phangorn 3.0.0.1.
Intertwining phylogenetic trees and networks: R Example ScriptUpdated 7 days ago

Klaus Schliep, Alastair Potts, David Morrison and Guido Grimm

Rendered from IntertwiningTreesAndNetworks.Rmd in phangorn 3.0.0.1.
Markov models and transition rate matricesUpdated 7 days ago

Klaus Schliep, Iris Bardel-Kahr

Rendered from AdvancedFeatures.Rmd in phangorn 3.0.0.1.
Maximum likelihood by handUpdated 7 days ago

Klaus Schliep, Iris Bardel-Kahr

Rendered from MLbyHand.Rmd in phangorn 3.0.0.1.
Phylogenetic trees from morphological dataUpdated 7 days ago

Iris Bardel-Kahr, Klaus Schliep

Rendered from Morphological.Rmd in phangorn 3.0.0.1.
Splits and NetworxUpdated 7 days ago

Klaus Schliep

Rendered from Networx.Rmd in phangorn 3.0.0.1.
vegan FAQUpdated 15 days ago

Jari Oksanen

Rendered from FAQ-vegan.Rmd in vegan 2.8-0.
Plotting probabilitiesUpdated 21 days ago

Thijs Janzen

Rendered from plotting_states.Rmd in secsse 3.7.0.
Using secsse with complete phylogenies (with extinction)Updated 21 days ago

Pedro Santos Neves

Rendered from complete_tree.Rmd in secsse 3.7.0.
AnnotationBustR TutorialUpdated 21 days ago

Samuel R. Borstein

Rendered from AnnotationBustR-vignette.Rmd in AnnotationBustR 1.3.0.
Starting secsseUpdated 1 months ago

Thijs Janzen

Rendered from starting_secsse.Rmd in secsse 3.7.0.
Calculation UpdateUpdated 1 months ago

Priscilla Lau, Bjørn Kopperud, Sebastian Höhna, Jeremy M. Beaulieu, and Brian C. O'Meara

Rendered from calculationUpdate.Rmd in OUwie 3.02.
Diversity analysis in veganUpdated 2 months ago

Jari Oksanen

Rendered from diversity-vegan.Rnw in vegan 2.8-0.
Evolutionary biology in R (evobiR) tutorialUpdated 3 months ago

Michelle Jonika, Jeffery Demuth, Richard H. Adams, and Heath Blackmon

Rendered from evolutionary.biology.in.R.Rmd in evobiR 2.2.
Getting started with QuartetUpdated 3 months ago

Martin R. Smith

Rendered from Using-Quartet.Rmd in Quartet 1.4.0.
About the quartet distanceUpdated 3 months ago

Martin R. Smith

Rendered from Quartet-Distance.Rmd in Quartet 1.4.0.
Exporting sampled ancestor treesUpdated 3 months ago

Joelle Barido-Sottani

Rendered from SAtree.Rmd in FossilSim 2.4.4.
corHMM 2.1: Generalized hidden Markov modelsUpdated 3 months ago

James D. Boyko and Jeremy M. Beaulieu

Rendered from corHMMv2.1-vignette.Rmd in corHMM 2.10.4.
Introduction to ordination in veganUpdated 3 months ago

Jari Oksanen

Rendered from intro-vegan.Rnw in vegan 2.8-0.
Comparing sets of trees from different analysesUpdated 4 months ago

Martin R. Smith

Rendered from compare-treesets.Rmd in TreeDist 2.14.0.9001.
Contextualizing tree distancesUpdated 4 months ago

Martin R. Smith

Rendered from using-distances.Rmd in TreeDist 2.14.0.9001.
Analysing landscapes of phylogenetic treesUpdated 4 months ago

Martin R. Smith

Rendered from landscapes.Rmd in TreeDist 2.14.0.9001.
Calculate tree similarity with 'TreeDist'Updated 4 months ago

Martin R. Smith

Rendered from Using-TreeDist.Rmd in TreeDist 2.14.0.9001.
Tree space analysisUpdated 4 months ago

Martin R. Smith

Rendered from treespace.Rmd in TreeDist 2.14.0.9001.
The 'aphid' package for analysis with profile hidden Markov modelsUpdated 4 months ago

Shaun Wilkinson

Rendered from aphid-vignette.Rmd in aphid 1.3.6.
Connecting data to Open Tree treesUpdated 5 months ago

David Winter

Rendered from data_mashups.Rmd in rotl 3.1.1.
How to use rotl?Updated 5 months ago

François Michonneau

Rendered from rotl.Rmd in rotl 3.1.1.
Using the Open Tree synthesis in a comparative analysisUpdated 5 months ago

David Winter

Rendered from meta-analysis.Rmd in rotl 3.1.1.
MCMCglmm Course NotesUpdated 5 months ago

Jarrod Hadfield

Rendered from CourseNotes.Rmd in MCMCglmm 2.37.
Introduction to using the 'ratematrix' packageUpdated 6 months ago

Daniel S. Caetano

Rendered from Intro_on_the_package.Rmd in ratematrix 1.2.5.
Set custom starting point with 'ratematrix'Updated 6 months ago

Daniel S. Caetano

Rendered from Set_custom_starting_point.Rmd in ratematrix 1.2.5.
Using prior distributions with 'ratematrix'Updated 6 months ago

Daniel S. Caetano

Rendered from Making_prior_on_ratematrix.Rmd in ratematrix 1.2.5.
Adding geological timescales to phylogeniesUpdated 6 months ago

William Gearty

Rendered from phylogenies.Rmd in deeptime 2.3.1.9000.
Transforming coordinate systemsUpdated 7 months ago

William Gearty

Rendered from coord.Rmd in deeptime 2.3.1.9000.
Molecular Clock Dating of Influenza H3N2Updated 9 months ago

Erik Volz

Rendered from h3n2.Rmd in treedater 1.0.2.
Plotting geological/stratigraphical patternsUpdated 9 months ago

William Gearty

Rendered from geo.Rmd in deeptime 2.3.1.9000.
Analyzing FBD ParametersUpdated 9 months ago

Tiago Simoes

Rendered from fbd-params.Rmd in EvoPhylo 0.3.5.
Analyzing Trees With OffsetsUpdated 9 months ago

Tiago Simoes

Rendered from offset_handling.Rmd in EvoPhylo 0.3.5.
Character PartitioningUpdated 9 months ago

Tiago Simoes

Rendered from char-part.Rmd in EvoPhylo 0.3.5.
Evolutionary Rates & Selection Mode (BEAST2)Updated 9 months ago

Tiago Simoes

Rendered from rates-selection_BEAST2.Rmd in EvoPhylo 0.3.5.
Evolutionary Rates & Selection Mode (Mr.Bayes)Updated 9 months ago

Tiago Simoes

Rendered from rates-selection_MrBayes.Rmd in EvoPhylo 0.3.5.
Theoretical backgroundUpdated 9 months ago

Tiago Simoes

Rendered from data_treatment.Rmd in EvoPhylo 0.3.5.
Partition of VariationUpdated 10 months ago

Jari Oksanen

Rendered from partitioning.Rnw in vegan 2.8-0.
Phylogenetic tree manipulationUpdated 11 months ago

Silvia Castiglione, Carmela Serio, Pasquale Raia

Rendered from Tree-Manipulation.Rmd in RRphylo 3.0.2.
Plotting temporal dataUpdated 1 years ago

William Gearty

Rendered from time.Rmd in deeptime 2.3.1.9000.
Loading phylogenetic data into RUpdated 1 years ago

Martin R. Smith [email protected]

Rendered from load-data.Rmd in TreeTools 2.4.0.9000.
Creating alternative phylogenies from a starting treeUpdated 1 years ago

Silvia Castiglione, Carmela Serio, Giorgia Girardi, Pasquale Raia

Rendered from Alternative-trees.Rmd in RRphylo 3.0.2.
Testing RRphylo methods overfitUpdated 1 years ago

Silvia Castiglione, Carmela Serio, Giorgia Girardi, Pasquale Raia

Rendered from overfit.Rmd in RRphylo 3.0.2.
Plotting toolsUpdated 1 years ago

Silvia Castiglione, Carmela Serio, Pasquale Raia

Rendered from Plotting-tools.Rmd in RRphylo 3.0.2.
RRphyloUpdated 1 years ago

Silvia Castiglione, Carmela Serio, Pasquale Raia

Rendered from RRphylo.Rmd in RRphylo 3.0.2.
Searching for morphological convergenceUpdated 1 years ago

Silvia Castiglione, Carmela Serio, Pasquale Raia

Rendered from search.conv.Rmd in RRphylo 3.0.2.
Searching for temporal trends in phenotypes or ratesUpdated 1 years ago

Silvia Castiglione, Carmela Serio, Pasquale Raia

Rendered from search.trend.Rmd in RRphylo 3.0.2.
Searching for rate shiftsUpdated 1 years ago

Silvia Castiglione, Carmela Serio, Pasquale Raia

Rendered from search.shift.Rmd in RRphylo 3.0.2.
File system navigation in RUpdated 1 years ago

Martin R. Smith [email protected]

Rendered from filesystem-navigation.Rmd in TreeTools 2.4.0.9000.
Total-evidence dating of carnivores integrating molecular and morphometric dataUpdated 1 years ago

Sandra Álvarez-Carretero and Mario dos Reis

Rendered from Reproduce_Carnivora_analysis.Rmd in mcmc3r 0.6.0.
Running GeoHiSSEUpdated 2 years ago

Daniel Caetano and Jeremy M. Beaulieu

Rendered from GeoHiSSE-vignette.Rmd in hisse 2.1.13.
Type I errors, Model rejection, & HiSSE vs. FiSSEUpdated 2 years ago

Jeremy M. Beaulieu & Brian C. O'Meara

Rendered from hisse-fisse-type1-vignette.Rmd in hisse 2.1.13.
dietr TutorialUpdated 2 years ago

Samuel R. Borstein

Rendered from dietr-vignette.Rmd in dietr 1.1.6-1.
New additions as of OUwie 2.1Updated 2 years ago

Jeremy M. Beaulieu and Brian C. O'Meara

Rendered from OUwie_2.1_adds.Rmd in OUwie 3.02.
Adding geological timescales to plotsUpdated 2 years ago

William Gearty

Rendered from coord_geo.Rmd in deeptime 2.3.1.9000.
Extending the Robinson-Foulds metricUpdated 2 years ago

Martin R. Smith

Rendered from Robinson-Foulds.Rmd in TreeDist 2.14.0.9001.
Using RRPPUpdated 2 years ago

Michael Collyer

Rendered from Using.RRPP.Rmd in RRPP 2.1.2.999.
Basics of paleoTSUpdated 2 years ago

Gene Hunt

Rendered from paleoTS_basics.Rmd in paleoTS 0.6.2.
ANOVA versus MANOVA in RRPPUpdated 2 years ago

Michael L. Collyer

Rendered from ANOVA.vs.MANOVA.Rmd in RRPP 2.1.2.999.
MonoPhy TutorialUpdated 2 years ago

Orlando Schwery

Rendered from MonoPhyVignette.Rmd in MonoPhy 1.3.2.
Case study: the true finchesUpdated 2 years ago

Luna L. Sanchez Reyes

Rendered from fringiliidae.Rmd in datelife 0.6.9.
Getting startedUpdated 2 years ago

Luna L. Sanchez Reyes

Rendered from Getting_started_with_datelife.Rmd in datelife 0.6.9.
Making a DateLife queryUpdated 2 years ago

Luna L. Sanchez Reyes

Rendered from make_datelife_query.Rmd in datelife 0.6.9.
Generalized Robinson-Foulds distancesUpdated 2 years ago

Martin R. Smith

Rendered from Generalized-RF.Rmd in TreeDist 2.14.0.9001.
Treebase TutorialUpdated 2 years ago

Carl Boettiger

Rendered from vignette.Rmd in treebase 0.1.5.
The phylo4 classes and methodsUpdated 2 years ago

Ben Bolker, Peter Cowan, François Michonneau

Rendered from phylobase.Rmd in phylobase 0.8.12.
Phylogenetic Methods for Multiple Gene DataUpdated 2 years ago

Thibaut Jombart

Rendered from apex.Rmd in apex 1.0.7.
Combining and arranging plotsUpdated 2 years ago

William Gearty

Rendered from ggarrange2.Rmd in deeptime 2.3.1.9000.
Plotting trait dataUpdated 2 years ago

William Gearty

Rendered from traits.Rmd in deeptime 2.3.1.9000.
Detecting rogue taxa in Bayesian posterior tree setsUpdated 3 years ago

Martin R. Smith, Durham University

Rendered from Bayesian.Rmd in Rogue 2.2.0.
Paleobuddy overviewUpdated 3 years ago

Bruno do Rosario Petrucci

Rendered from overview.Rmd in paleobuddy 1.1.0.
adephylo: exploratory analyses for the phylogenetic comparative methodUpdated 3 years ago

Aurélie Siberchicot

Rendered from adephylo.Rnw in adephylo 1.1-17.
Incorporating Fossils in HiSSE, MuHiSSE, and MiSSEUpdated 3 years ago

Jeremy M. Beaulieu

Rendered from adding_fossils.Rmd in hisse 2.1.13.
The Problem with Clade-specific Sampling FractionsUpdated 3 years ago

Jeremy M. Beaulieu

Rendered from Clade-specific-sampling.Rmd in hisse 2.1.13.
Simulating with secsseUpdated 3 years ago

Thijs Janzen

Rendered from sim_with_secsse.Rmd in secsse 3.7.0.
entropartUpdated 3 years ago

Eric Marcon

Rendered from entropart.Rmd in entropart 1.6-16.
Loading phylogenetic trees into RUpdated 3 years ago

Martin R. Smith [email protected]

Rendered from load-trees.Rmd in TreeTools 2.4.0.9000.
phylotaR TutorialUpdated 3 years ago

Shixiang Wang

Rendered from phylotaR.Rmd in phylotaR 1.3.0.
pmc tutorialUpdated 3 years ago

Carl Boettiger

Rendered from pmc_tutorial.Rmd in pmc 1.0.6.
Exploration of landscapes of phylogenetic treesUpdated 3 years ago

Thibaut Jombart, Michelle Kendall

Rendered from introduction.Rmd in treespace 1.1.4.4.
Introduction to dendextendUpdated 3 years ago

Tal Galili

Rendered from dendextend.Rmd in dendextend 1.19.1.
How to use mvMORPH?Updated 3 years ago

Julien Clavel

Rendered from How_to_use_mvMORPH.Rmd in mvMORPH 1.2.2.
Trees with different leavesUpdated 3 years ago

Martin R. Smith

Rendered from different-leaves.Rmd in TreeDist 2.14.0.9001.
hOUwie User GuideUpdated 3 years ago

.

Rendered from hOUwieStarterGuide.Rmd in OUwie 3.02.
Estimating initial branch lengthsUpdated 3 years ago

Luna L. Sanchez Reyes

Rendered from making_bold_trees.Rmd in datelife 0.6.9.
Introduction to the phylocomr packageUpdated 4 years ago

Scott Chamberlain and Jeroen Ooms

Rendered from phylocomr.Rmd in phylocomr 0.3.4.
An introduction to the phyloregion packageUpdated 4 years ago

Barnabas H. Daru, Piyal Karunarathne & Klaus Schliep

Rendered from phyloregion-intro.Rmd in phyloregion 1.0.9.
Benchmarking phyloregionUpdated 4 years ago

Barnabas H. Daru, Piyal Karunarathne & Klaus Schliep

Rendered from Benchmark.Rmd in phyloregion 1.0.9.
Fast Evolutionary DistinctivenessUpdated 4 years ago

Barnabas H. Daru

Rendered from ed.Rmd in phyloregion 1.0.9.
Comparing splits using information theoryUpdated 4 years ago

Martin R. Smith

Rendered from information.Rmd in TreeDist 2.14.0.9001.
Hierarchical cluster analysis on famous data sets - enhanced with the dendextend packageUpdated 4 years ago

Tal Galili

Rendered from Cluster_Analysis.Rmd in dendextend 1.19.1.
Frequently asked questionsUpdated 4 years ago

Tal Galili

Rendered from FAQ.Rmd in dendextend 1.19.1.
beastier demoUpdated 4 years ago

Richèl J.C. Bilderbeek

Rendered from demo.Rmd in beastier 2.5.3.
beautier demoUpdated 4 years ago

Richèl J.C. Bilderbeek

Rendered from demo.Rmd in beautier 2.6.16.
ExamplesUpdated 4 years ago

Richèl J.C. Bilderbeek

Rendered from examples.Rmd in beautier 2.6.16.
Inference ModelsUpdated 4 years ago

Richèl J.C. Bilderbeek

Rendered from inference_models.Rmd in beautier 2.6.16.
Simulation and InferenceUpdated 5 years ago

George G. Vega Yon

Rendered from example.Rmd in aphylo 0.3-6.
Running MiSSEUpdated 5 years ago

Jeremy M. Beaulieu

Rendered from MiSSE-vignette.Rmd in hisse 2.1.13.
Additional Functions for Manipulating Data in treedata.tableUpdated 5 years ago

Josef Uyeda, Cristian Roman-Palacios, April Wright

Rendered from D_AdditionalFunctions_treedata.table.Rmd in treedata.table 0.1.1.
Breve Introducción al Paquete treedata.tableUpdated 5 years ago

Cristian Roman-Palacios, April Wright, Josef Uyeda

Rendered from AB_treedata.table_intro_spanish.Rmd in treedata.table 0.1.1.
Getting Started With The treedata.table PackageUpdated 5 years ago

Josef Uyeda, Cristian Roman-Palacios, April Wright

Rendered from AA_treedata.table_intro_english.Rmd in treedata.table 0.1.1.
Partially Matching of Trait Data and Tree(s) in treedata.tableUpdated 5 years ago

Josef Uyeda, Cristian Roman-Palacios, April Wright

Rendered from C_PartialMatching.Rmd in treedata.table 0.1.1.
Working With multiPhylo Objects in treedata.tableUpdated 5 years ago

Josef Uyeda, Cristian Roman-Palacios, April Wright

Rendered from B_multiphylo_treedata.table.Rmd in treedata.table 0.1.1.
Using FishPhyloMaker to build phylogenies for finned-ray fishesUpdated 5 years ago

Gabriel Nakamura

Rendered from FishPhyloMaker_vignette.Rmd in FishPhyloMaker 0.2.0.
How to know which species must be added to phylogeny?Updated 5 years ago

Gabriel Nakamura

Rendered from whichFishAdd_vignette.Rmd in FishPhyloMaker 0.2.0.
How to map species insertions in phylogenetic tree?Updated 5 years ago

Gabriel Nakamura

Rendered from mappingInsertions_vignette.Rmd in FishPhyloMaker 0.2.0.
CALANGO ParametersUpdated 5 years ago

Felipe Campelo

Rendered from CALANGO_Parameters.Rmd in CALANGO 1.0.20.
Cophylogenetic simulationUpdated 5 years ago

Wade Dismukes

Rendered from cophylogenetic_sim.Rmd in treeducken 1.1.0.9999.
A newer, faster HiSSE functionUpdated 5 years ago

Jeremy M. Beaulieu

Rendered from hisse-new-vignette.Rmd in hisse 2.1.13.
Running a Multistate HiSSE modelUpdated 5 years ago

Jeremy M. Beaulieu

Rendered from MuHiSSE-vignette.Rmd in hisse 2.1.13.
tracerer versus Tracer demoUpdated 5 years ago

Richèl J.C. Bilderbeek

Rendered from demo.Rmd in tracerer 2.2.4.
The FossilSim packageUpdated 5 years ago

Joelle Barido-Sottani, Rachel C. M. Warnock

Rendered from intro.Rmd in FossilSim 2.4.4.
Building supermatrix matrices using the phylotools packageUpdated 5 years ago

Jinlong Zhang

Rendered from phylotools-vignette.Rmd in phylotools 0.2.5.
treespace worked example: Transmission treesUpdated 5 years ago

Michelle Kendall

Rendered from TransmissionTreesVignette.Rmd in treespace 1.1.4.4.
Running the old HiSSE functionUpdated 5 years ago

Jeremy M. Beaulieu

Rendered from hisse-vignette.Rmd in hisse 2.1.13.
phyclust-guideUpdated 5 years ago

Wei-Chen Chen

Rendered from phyclust-guide.Rnw in phyclust 0.1-34.
treespace worked example: Dengue treesUpdated 6 years ago

Michelle Kendall, Thibaut Jombart

Rendered from DengueVignette.Rmd in treespace 1.1.4.4.
Comparing trees by tip label categoriesUpdated 6 years ago

Michelle Kendall

Rendered from tipCategories.Rmd in treespace 1.1.4.4.
Using TBRDistUpdated 6 years ago

Martin R. Smith

Rendered from TBRDist.Rmd in TBRDist 2.0.0.
Quick IntroductionUpdated 6 years ago

Tal Galili

Rendered from Quick_Introduction.Rmd in dendextend 1.19.1.
Analyzing Trait Evolution with Approximate Bayesian Computation in TreEvoUpdated 6 years ago

David W. Bapst

Rendered from treevo_ABC_vignette.Rmd in TreEvo 0.22.1.
phrapl_vignetteUpdated 6 years ago

Nathan Jackson

Rendered from phrapl_vignette.Rmd in phrapl 0.6.5.
A Brief Introduction to RNeXMLUpdated 6 years ago

Carl Boettiger, Scott Chamberlain, Rutger Vos, Hilmar Lapp

Rendered from intro.Rmd in RNeXML 2.4.11.
Extending NeXML: an example based on simmapUpdated 6 years ago

Carl Boettiger, Scott Chamberlain, Rutger Vos, Hilmar Lapp

Rendered from simmap.Rmd in RNeXML 2.4.11.
SPARQL with RNeXMLUpdated 6 years ago

Carl Boettiger, Scott Chamberlain, Rutger Vos, Hilmar Lapp

Rendered from sparql.Rmd in RNeXML 2.4.11.
Handling Metadata in RNeXMLUpdated 6 years ago

Carl Boettiger, Scott Chamberlain, Rutger Vos, Hilmar Lapp

Rendered from metadata.Rmd in RNeXML 2.4.11.
The nexml S4 ObjectUpdated 6 years ago

Carl Boettiger, Scott Chamberlain, Rutger Vos, Hilmar Lapp

Rendered from S4.Rmd in RNeXML 2.4.11.
sensiPhy: R-package for sensitivity analysis in phylogenetic comparative methods.Updated 6 years ago

Gustavo Paterno, Caterina Penone, Gijsbert Werner

Rendered from sensiPhy_vignette.Rmd in sensiPhy 0.8.5.
Simulating trees from the fossilized birth-death processUpdated 7 years ago

Walker Pett

Rendered from simfbd.Rmd in FossilSim 2.4.4.
Data and analysis in picanteUpdated 7 years ago

Steven W. Kembel

Rendered from picante-intro.Rnw in picante 1.8.3.
Package overviewUpdated 7 years ago

Francois Keck

Rendered from Basics.Rmd in phylosignal 1.3.2.
Plotting functionsUpdated 7 years ago

Francois Keck

Rendered from Demo_plots.Rmd in phylosignal 1.3.2.
Simulating fossilsUpdated 8 years ago

Rachel C. M. Warnock

Rendered from fossils.Rmd in FossilSim 2.4.4.
Simulating taxonomyUpdated 8 years ago

Joelle Barido-Sottani, Rachel C. M. Warnock

Rendered from taxonomy.Rmd in FossilSim 2.4.4.
Converting from and to paleotree formatUpdated 8 years ago

Joelle Barido-Sottani

Rendered from paleotree.Rmd in FossilSim 2.4.4.
phylogram: an R package for phylogenetic analysis with dendrogramsUpdated 8 years ago

Shaun P. Wilkinson ^1,2^ and Simon K. Davy ^1^

Rendered from phylogram-vignette.Rmd in phylogram 2.1.0.9000.
Advanced Use of PhylocanvasUpdated 9 years ago

zach charlop-powers

Rendered from Advanced_Usage.Rmd in phylocanvas 0.1.3.
Basic Use of PhylocanvasUpdated 9 years ago

Zach Chrlop-Powers

Rendered from Basic_Use.Rmd in phylocanvas 0.1.3.
Design decisions and implementationUpdated 9 years ago

Jari Oksanen

Rendered from decision-vegan.Rnw in vegan 2.8-0.
mvMORPH: an R package for fitting multivariate evolutionary modelsUpdated 10 years ago

Julien Clavel

Rendered from tutorial_mvMORPH.Rmd in mvMORPH 1.2.2.