Releases: pdpolly/Phylogenetics-for-Mathematica
v.6.9
Changes in 6.9: Updated KappaMultivariate to trap a variable “v” that was set globally instead of locally. No functional change, but the leaky variable could potentially cause conflicts if “v” was set elsewhere in the user’s code.
Installation: The file is in Mathematica's ".m" format, which can be imported into Mathematica 6.0 and later (functions do not work in earlier versions of Mathematica). Install using the "Install" item on the "File" menu. Once installed, you must load the package like any other with the line <<PollyPhylogenetics, using either this suggested name or another.
Cite as: Polly, P.D. 2023. Phylogenetics for Mathematica. Version 6.9. https://github.com/pdpolly/Phylogenetics-for-Mathematica
v.6.8
Changes in Version 6.8: Updated PagelLambda and PhylogeneticRegressionWithLambda to use PseudoInverse (i.e., Moore/Penrose inverse) to avoid errors with singular matrices when lambda is large.
Installation: The file is in Mathematica's ".m" format, which can be imported into Mathematica 6.0 and later (functions do not work in earlier versions of Mathematica). Install using the "Install" item on the "File" menu. Once installed, you must load the package like any other with the line <<PollyPhylogenetics, using either this suggested name or another.
Cite as: Polly, P.D. 2023. Phylogenetics for Mathematica. Version 6.8. https://github.com/pdpolly/Phylogenetics-for-Mathematica DOI:
User guide at https://github.com/pdpolly/Phylogenetics-for-Mathematica/blob/main/Guide%20to%20PollyPhylogenetics%206.8.pdf
v.6.7
Changes in Version 6.7: PhylogeneticRegressionWithLambda (new function): Allows users to scale the internal branches of a phylogenetic tree with a Pagel’s lambda value to conform to a non-Brownian motion model of evolution. UltrametricizeTree (new function): Turns a non-ultrametric tree into ultrametric by lengthening all tip branches to be coeval with the longest tip. DrawNewickTree (improved function): added new autoscaling capability and user-set aspect ratio option to the graphical output of DrawNewickTree.
Installation: The file is in Mathematica's ".m" format, which can be imported into Mathematica 6.0 and later (functions do not work in earlier versions of Mathematica). Install using the "Install" item on the "File" menu. Once installed, you must load the package like any other with the line <<PollyPhylogenetics, using either this suggested name or another.
Cite as: Polly, P.D. 2023. Phylogenetics for Mathematica. Version 6.7. https://github.com/pdpolly/Phylogenetics-for-Mathematica
User guide at https://github.com/pdpolly/Phylogenetics-for-Mathematica/releases/download/v.6.7/Guide.to.PollyPhylogenetics.6.7.pdf
v.6.6
Changes in Version 6.6. Updated PagelsLambda[] function and added LambdaMultiplication[]
Installation. The file is in Mathematica's ".m" format, which can be imported into Mathematica 6.0 and later (functions do not work in earlier versions of Mathematica). Install using the "Install" item on the "File" menu. Once installed, you must load the package like any other with the line <<PollyPhylogenetics, using either this suggested name or another.
Cite as: Polly, P.D. 2022. Phylogenetics for Mathematica. Version 6.6. https://github.com/pdpolly/Phylogenetics-for-Mathematica
User's Guide: https://github.com/pdpolly/Phylogenetics-for-Mathematica/releases/download/v.6.6/Guide.to.PollyPhylogenetics.6.6.pdf
v.6.5
Changes in Version 6.x. Many new functions. PhylogeneticRegression performs a PGLS linear regression, MapTraitsOntoTree produces a colored graphic showing estimated trait values on a phylogenetic tree, PruneTree extracts a tree for a selected subset of taxa in a larger tree, Kappa estimates Blomberg's K for a univariate trait, KappaMultivariate estimates Adams' K for a highly multivariate geometric morphometric data set, and SharedPhylogeneticHistory and MeanTreeDistance report statistics useful in the study of phylogenetic community assembly. New and more efficient functions are also available for estimating rates and ancestral node values for traits. Changed all "Modules" to "Blocks" for improved efficiency.
Installation. The file is in Mathematica's ".m" format, which can be imported into Mathematica 6.0 and later (functions do not work in earlier versions of Mathematica). Install using the "Install" item on the "File" menu. Once installed, you must load the package like any other with the line <<PollyPhylogenetics, using either this suggested name or another.
Cite as: Polly, P.D. 2019. Phylogenetics for Mathematica. Version 6.5. Department of Earth and Atmospheric Sciences, Indiana University: Bloomington, Indiana. https://github.com/pdpolly/Phylogenetics-for-Mathematica