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Live-streaming lectures today on phylogenetic comparative methods
I'm currently participating (for the third time) in a workshop entitled Evolutionary Quantitative Genetics, co-organized by Joe Felsenstein and Steve Arnold. In the past, this workshop has been hosted...
View ArticleBug fix in Rphylip function Rthreshml
In the processing of updating one of my tutorials for the Evolutionary Quantitative Genetics workshop at NIMBioS in Knoxville Tennessee I discovered a bug in Rthreshml that prevents the output file...
View ArticleNew version of threshBayes with option to supress MCMC status
I just posted a new version of the phytools function threshBayes with the option to suppress the a status update of the MCMC from printing to screen. This option can be toggled off using...
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Bug fix in read.simmap
pre .operator, pre .paren { color: rgb(104, 118, 135) } pre .literal { color: #990073 } pre .number { color: #099; } pre .comment { color: #998; font-style: italic } pre .keyword { color: #900;...
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Remove a set of tips matching a regular expression
pre .operator, pre .paren { color: rgb(104, 118, 135) } pre .literal { color: #990073 } pre .number { color: #099; } pre .comment { color: #998; font-style: italic } pre .keyword { color: #900;...
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Plotting multiple binary characters at nodes on the tree using pie charts
pre .operator, pre .paren { color: rgb(104, 118, 135) } pre .literal { color: #990073 } pre .number { color: #099; } pre .comment { color: #998; font-style: italic } pre .keyword { color: #900;...
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Modern Phylogenetic Comparative Methods book now available
László Garamszegi's new edited volume, Modern Phylogenetic Comparative Methods (and their application in evolutionary biology) is now out from Springer and it looks great! Check out the book's website...
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drop.tip method for object of class "contMap"; and code to specify internal...
pre .operator, pre .paren { color: rgb(104, 118, 135) } pre .literal { color: #990073 } pre .number { color: #099; } pre .comment { color: #998; font-style: italic } pre .keyword { color: #900;...
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Applying extract.clade.simmap to a set of trees in a list
pre .operator, pre .paren { color: rgb(104, 118, 135) } pre .literal { color: #990073 } pre .number { color: #099; } pre .comment { color: #998; font-style: italic } pre .keyword { color: #900;...
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drop.tip methods for contMap & densityMap now in phytools
pre .operator, pre .paren { color: rgb(104, 118, 135) } pre .literal { color: #990073 } pre .number { color: #099; } pre .comment { color: #998; font-style: italic } pre .keyword { color: #900;...
View ArticleComparing models fit using GLS with different (nested) parameterizations of...
pre .operator, pre .paren { color: rgb(104, 118, 135) } pre .literal { color: #990073 } pre .number { color: #099; } pre .comment { color: #998; font-style: italic } pre .keyword { color: #900;...
View ArticleNew version of phytools submitted to CRAN
pre .operator, pre .paren { color: rgb(104, 118, 135) } pre .literal { color: #990073 } pre .number { color: #099; } pre .comment { color: #998; font-style: italic } pre .keyword { color: #900;...
View ArticleFaster version of read.newick
pre .operator, pre .paren { color: rgb(104, 118, 135) } pre .literal { color: #990073 } pre .number { color: #099; } pre .comment { color: #998; font-style: italic } pre .keyword { color: #900;...
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Counting edges from a Newick string
pre .operator, pre .paren { color: rgb(104, 118, 135) } pre .literal { color: #990073 } pre .number { color: #099; } pre .comment { color: #998; font-style: italic } pre .keyword { color: #900;...
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New function to ladderize tree with mapped discrete character
pre .operator, pre .paren { color: rgb(104, 118, 135) } pre .literal { color: #990073 } pre .number { color: #099; } pre .comment { color: #998; font-style: italic } pre .keyword { color: #900;...
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On the loss of phylogenetic diversity when extinction risks evolves under the...
pre .operator, pre .paren { color: rgb(104, 118, 135) } pre .literal { color: #990073 } pre .number { color: #099; } pre .comment { color: #998; font-style: italic } pre .keyword { color: #900;...
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Update to sim.history including sensible error handling
pre .operator, pre .paren { color: rgb(104, 118, 135) } pre .literal { color: #990073 } pre .number { color: #099; } pre .comment { color: #998; font-style: italic } pre .keyword { color: #900;...
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Small update to fancyTree method "phenogram95" to permit control of shading
pre .operator, pre .paren { color: rgb(104, 118, 135) } pre .literal { color: #990073 } pre .number { color: #099; } pre .comment { color: #998; font-style: italic } pre .keyword { color: #900;...
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Redundant phytools functions to replicate phylogenies in a list
pre .operator, pre .paren { color: rgb(104, 118, 135) } pre .literal { color: #990073 } pre .number { color: #099; } pre .comment { color: #998; font-style: italic } pre .keyword { color: #900;...
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Colors terminal edges in plotTree.wBars by a discrete trait
pre .operator, pre .paren { color: rgb(104, 118, 135) } pre .literal { color: #990073 } pre .number { color: #099; } pre .comment { color: #998; font-style: italic } pre .keyword { color: #900;...
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