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Commits on Aug 19, 2019

• commit coevolution YAML params before creating branch for separate R coevolution analysis using python nestedCoalescent

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Commits on Aug 15, 2019

• New YAML for coevolution simulation

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Commits on Aug 13, 2019

• Issue #145 modified some functions to use mclapply

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Commits on Feb 22, 2019

• fixes #144

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Commits on Feb 15, 2019

• removed pkg/src directory

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• MAJOR CHANGE: tore out C-igraph, tore out colgem; need to add twt as replacement simulator

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• kernel in R now passes unit tests, need to reimplement labeled kernel

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Commits on Feb 13, 2019

• fixes #142

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Commits on Feb 6, 2019

• closes #140

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Commits on Jun 2, 2018

• more work on porting kernel

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Commits on Jun 1, 2018

• working on .get.branchlengths

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• Merge branch 'master' of https://github.com/PoonLab/Kaphi

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• drop C and igraph - port kernel into R

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Commits on Apr 26, 2018

• test file for profiling kernel distances for phyloK3_2.py in PoonLab/Coevolution (to generate trees using the BiSSE model)

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Commits on Mar 15, 2018

• log scale plot with mean kernel distance on the y axis and q01/q10 on the x axis(log scale)

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Commits on Mar 13, 2018

• R code to plot mean kernel distance on the y axis and q01/q10 on the x axis

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• Added R script to plot correlation between q01 and q10 in BiSSE model by visualizing kernel score(size of points)

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Commits on Mar 6, 2018

• R script to plot profiles of the BiSSE parameters using different distance metrics

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Commits on Mar 2, 2018

• Error message catching for Trip distance metric Issue #137

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Commits on Feb 16, 2018

• Merge branch 'master' of https://github.com/PoonLab/Kaphi

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• Changed BiSSE parameters and updated YAML file for labelled kernel.

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Commits on Feb 15, 2018

• Update diversitree-wrappers.R

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Commits on Feb 12, 2018

• Modified config$model variable in plotting back to explicit 'BiSSE' name

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Commits on Feb 9, 2018

• Update example-bd.R

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• Update example-bisse.R

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Commits on Feb 8, 2018

• Update DistanceMetrics.md

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• Update smcConfig.R to include Node.dist as a valid distance metric

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Commits on Jan 30, 2018

• resolved merge conflict; I discarded my docstrings because they are deprecated by moving .r.mast function into MAST()

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• write a bit of documentation in treedists, turned off LTT test

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Commits on Jan 24, 2018

• Added comments for MAST, added a reference for MAST.Rd

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Commits on Jan 22, 2018

• Implemented @ArtPoon suggestions in Issue #128; further improved MAST speed.

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Commits on Jan 19, 2018

• Issue #128 Improved MAST computation speed; refactored using postorder traversal

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Commits on Jan 15, 2018

• After revert commit ce74bdc, re-implemented error fixes in commit 1bee3c3; now test suite errors resolved (still have nLTT test failure)

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• Merge branch 'master' of https://github.com/PoonLab/Kaphi

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• Reverting to the state of the project at 4bb02d7

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