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King et al. - 2016 - Placoderm R functions
King et al. - 2016 - Placoderm R functions
 
 
*BEAST to ASTRAL pipeline.R
*BEAST to ASTRAL pipeline.R
 
 
.DS_Store
.DS_Store
 
 
.RData
.RData
 
 
.Rhistory
.Rhistory
 
 
.gitattributes
.gitattributes
 
 
ASR Under Mode Variable Model.R
ASR Under Mode Variable Model.R
 
 
Add Root to Set of Trees.R
Add Root to Set of Trees.R
 
 
Adding Aged Tips.R
Adding Aged Tips.R
 
 
Addressing Extinction in Mode-Shifting Models.R
Addressing Extinction in Mode-Shifting Models.R
 
 
Alignment_Alterations.R
Alignment_Alterations.R
 
 
Ancestral SVL Reconstruction.R
Ancestral SVL Reconstruction.R
 
 
BBCA_and_BEAST.pl
BBCA_and_BEAST.pl
 
 
BEAST2 Starting Tree
BEAST2 Starting Tree
 
 
Backwards Trait Simulator.R
Backwards Trait Simulator.R
 
 
Binding Ultrametric Trees Together.R
Binding Ultrametric Trees Together.R
 
 
Biogeography_RASE.R
Biogeography_RASE.R
 
 
Biostrings.R
Biostrings.R
 
 
Build_a_GIF.R
Build_a_GIF.R
 
 
Building Trees of Desired Size.R
Building Trees of Desired Size.R
 
 
Calculate_AICs.R
Calculate_AICs.R
 
 
Change_AHE_Taxa_Labels.R
Change_AHE_Taxa_Labels.R
 
 
Check_Monophyly_Genera.R
Check_Monophyly_Genera.R
 
 
Chira et al. - Methods.R
Chira et al. - Methods.R
 
 
Clavel fit_env Model.R
Clavel fit_env Model.R
 
 
CoPhylo Plots - Tree Comparison.R
CoPhylo Plots - Tree Comparison.R
 
 
Coalescent_Simulation_Exercise.R
Coalescent_Simulation_Exercise.R
 
 
ColorBranches_gCF.R
ColorBranches_gCF.R
 
 
Combine Ultrametrics.R
Combine Ultrametrics.R
 
 
Compare Node Ages Across Trees - PaleoTree.R
Compare Node Ages Across Trees - PaleoTree.R
 
 
Composite Bar Graph in GGPlot.R
Composite Bar Graph in GGPlot.R
 
 
Condensing_Alignments.R
Condensing_Alignments.R
 
 
CreateGeoObject_fromSP.R
CreateGeoObject_fromSP.R
 
 
Data Processing Steps - Cichlids - 1-s2.0-S1055790317305213-mmc3.txt
Data Processing Steps - Cichlids - 1-s2.0-S1055790317305213-mmc3.txt
 
 
Declines vs. Species.R
Declines vs. Species.R
 
 
Distance_Matrices_from_LatLon.R
Distance_Matrices_from_LatLon.R
 
 
Diversity Dependence Tutorial.R
Diversity Dependence Tutorial.R
 
 
Drop Tips from Batch of Trees.R
Drop Tips from Batch of Trees.R
 
 
Drop.tip - Non-monophyletic group.R
Drop.tip - Non-monophyletic group.R
 
 
Duration of Speciation - Etienne et al. 2014.R
Duration of Speciation - Etienne et al. 2014.R
 
 
Extract Trees by a Focal Node Age.R
Extract Trees by a Focal Node Age.R
 
 
Extract_Data_from_AHE_labels.R
Extract_Data_from_AHE_labels.R
 
 
Fancy Geoscaled Plot with CI.R
Fancy Geoscaled Plot with CI.R
 
 
For_Carlos.R
For_Carlos.R
 
 
Functional_Diversity.R
Functional_Diversity.R
 
 
Functional_Diversity2.R
Functional_Diversity2.R
 
 
Functions_ContTraitSim.R
Functions_ContTraitSim.R
 
 
GAMM Models and Derivatives.R
GAMM Models and Derivatives.R
 
 
Gamma Statistic - Pybus & Harvey.R
Gamma Statistic - Pybus & Harvey.R
 
 
GarbageScript.R
GarbageScript.R
 
 
Geiger - Discrete Trait Fitting.R
Geiger - Discrete Trait Fitting.R
 
 
Geiger DTT Continuous Data.R
Geiger DTT Continuous Data.R
 
 
Gene_Tree_Tools.R
Gene_Tree_Tools.R
 
 
Geological Time Scale.R
Geological Time Scale.R
 
 
Get.Descendant.Edges.R
Get.Descendant.Edges.R
 
 
GitHub - Test Shift Timing and Alpha LOOP.R
GitHub - Test Shift Timing and Alpha LOOP.R
 
 
GitHub - geiger + OUwie LOOP.R
GitHub - geiger + OUwie LOOP.R
 
 
Halliday & Goswami - 2016 - Eutherian Morphology
Halliday & Goswami - 2016 - Eutherian Morphology
 
 
Halliday & Goswami - 2016 - Eutherian Morphology.R
Halliday & Goswami - 2016 - Eutherian Morphology.R
 
 
Histogram and Density Distribution PLOT.R
Histogram and Density Distribution PLOT.R
 
 
Histogram, Binned in ggplot.R
Histogram, Binned in ggplot.R
 
 
IQtree_Shell.R
IQtree_Shell.R
 
 
Impute_Fossil_Taxa.R
Impute_Fossil_Taxa.R
 
 
Instructions for RAxML Internode Certainty.txt
Instructions for RAxML Internode Certainty.txt
 
 
Intro_Plotly.R
Intro_Plotly.R
 
 
Keep Node Labels to Plot and Manipulate Trees.R
Keep Node Labels to Plot and Manipulate Trees.R
 
 
L1OU - Lasso OU Method - Khabbazian 2016.R
L1OU - Lasso OU Method - Khabbazian 2016.R
 
 
L1OU_for_Damien.R
L1OU_for_Damien.R
 
 
LTT and Pure Birth Null Simulations.R
LTT and Pure Birth Null Simulations.R
 
 
Levolution Tutorial.R
Levolution Tutorial.R
 
 
Likelihood and AIC comparison (LASER vs. TreePar).R
Likelihood and AIC comparison (LASER vs. TreePar).R
 
 
MCMC Diagnosis with Coda.R
MCMC Diagnosis with Coda.R
 
 
MCMCTreeR Tutorial.R
MCMCTreeR Tutorial.R
 
 
MCMCtree Shortcuts
MCMCtree Shortcuts
 
 
MDS_Clustering_Source.R
MDS_Clustering_Source.R
 
 
Make Ultrametric - BEAST Starting Tree.R
Make Ultrametric - BEAST Starting Tree.R
 
 
Manceau et al Tutorial.R
Manceau et al Tutorial.R
 
 
Map_Plotting_Processing.R
Map_Plotting_Processing.R
 
 
Measurement_Error.R
Measurement_Error.R
 
 
Messy_Alignment_Cleanup.R
Messy_Alignment_Cleanup.R
 
 
Model Rate Estimates for Lauren.R
Model Rate Estimates for Lauren.R
 
 
ModelExtraction_PRSB.R
ModelExtraction_PRSB.R
 
 
ModelFitting_PRSB.R
ModelFitting_PRSB.R
 
 
Morphological_Alignment.R
Morphological_Alignment.R
 
 
Multi-OU Simulation Visualization.R
Multi-OU Simulation Visualization.R
 
 
Muscle - Combining and Aligning.R
Muscle - Combining and Aligning.R
 
 
New.Models.adapted.from.Slater.2013.R
New.Models.adapted.from.Slater.2013.R
 
 
OLD_Check_Range_Overlaps.R
OLD_Check_Range_Overlaps.R
 
 
OUwie+Simmap Basics.R
OUwie+Simmap Basics.R
 
 
Oz_Reptile_Amphibian_Phylogenomics_List.R
Oz_Reptile_Amphibian_Phylogenomics_List.R
 
 
PBD Protracted Speciation.R
PBD Protracted Speciation.R
 
 
PGLS - Continuous vs. Discrete Traits.R
PGLS - Continuous vs. Discrete Traits.R
 
 
PGLS Gamma vs. Whatever.R
PGLS Gamma vs. Whatever.R
 
 
PGLS for S.R
PGLS for S.R
 
 
Parameter_Identifiability_PLOTS.R
Parameter_Identifiability_PLOTS.R
 
 
Parsimony Informative Sites R.R
Parsimony Informative Sites R.R
 
 
PhySortR - Segregating Gene Trees.R
PhySortR - Segregating Gene Trees.R
 
 
Phylip to Fasta.R
Phylip to Fasta.R
 
 
PhyloMetrics Tree Trait .R
PhyloMetrics Tree Trait .R
 
 
PhylogeneticEM - Lasso OU Method.R
PhylogeneticEM - Lasso OU Method.R
 
 

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