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View Code? Open in Web Editor NEWR package for phylogenetic tree search under custom optimality criteria
Home Page: https://ms609.github.io/TreeSearch/
License: GNU General Public License v3.0
R package for phylogenetic tree search under custom optimality criteria
Home Page: https://ms609.github.io/TreeSearch/
License: GNU General Public License v3.0
Check that all nodes are bifurcating before running NNI/TBR/SPR, which will crash R.
Support stats like:
phangorn:CI()
MorphyBootstrap()
, though Jackknife()
is usually more appropriate.Ability to
And update inst/CITATION
Either
Hi Martin,
My name is Eunok Lee from the Westmead Institute for Medical Research. I am trying to load the tree using ape and phytool packages and I ran into the issues below:
When I tried to load my phylogenetic tree using read.tree(mytree.newick), I found that some tip labels were removed. When I opened the same newick file in text, I could see the tip label that I am interested in. I reinstalled the ape package and re-loaded in R, but the same problem occurred.... Could you help me how to fix this issue?
Due to the problem above, I tried using phytools::read.newick(). This does import the tree with all the tip labels; however, the tip label is only showing up to 22 characters. What should do to make the tip label to display the tip labels in a full character length?
Thank you and I look forward to your advice!
With kind regards,
Eunok
Turbinicarpus ss_26 paupout.txt
I have tested the package with some data (attached).
Here the code that causes the crash. This snippet is taken from vignettes/inapplicable.rmd example code, which runs flawlessly.
turbini.data <- ReadAsPhyDat("Turbinicarpus ss_26 paupout.nex")
RNGversion("3.5.0")
set.seed(0)
nj.tree <- NJTree(turbini.data)
outgroup <- c("beguinii")
rooted.tree <- EnforceOutgroup(nj.tree, outgroup)
better.tree <- TreeSearch(tree=rooted.tree, dataset=turbini.data,
EdgeSwapper=RootedNNISwap, verbosity=3)
Thank you very much for the help.
Reproduce by:
EasyTrees()
Possibly implemented in phangorn; add to app.R
Should be straightforward, and will reduce duplication
Check whether using order(method='radix')
improves search speed (https://csgillespie.github.io/efficientR/efficient-performance.html)
in phylo.R:
name[order(tips)] <- tipLabel[tips]
edge2[isTip] <- order(tips)
Review and implement appropriate methods reviewed in Grant & Kluge (2003)
Test case is disabled.
the old mpl_visualise functions might be given new life using our Inapp visualizer.
See branch: pp-vignettes
Save converting from edge to and from morphy's parentof/left/right notation by performing tree reordering using this notation.
Tree: hy_iw_k4_16.868_ERROR.txt
Dataset: X24932.txt
Warning message:
In if (homoplasies < 0) stop("Minimum steps have been miscalculated.\n Please report this bug at\n https://github.com/ms609/TreeSearch/issues/new") :
hopefully we don't need it any more
Hi,
I update the package to version 0.4.0 . But it doesn't work. Below is the error
library(TreeSearch)
Warning message:
package ‘TreeSearch’ was built under R version 3.5.3
SampleOne(1:10,len=10)
Error in SampleOne(1:10, len = 10) : could not find function "SampleOne"
A substantial proportion of time is being spent sampling, and in the overhead of decomposing a tree into variables. If we could list all trees that were 1 SPR step away from the current tree and score those, we'd save a lot of time in rearrangements.
In Rd documentation for the functions themselves, as well as in vignette
Function to complement [MinimumLength()
] is advertised in NEWS.md but doesn't yet exist.
Should cite TreeSearch as standalone package, with MorphyLib & algorithm paper to be cited when used (cf. profile parsimony / successive approx / etc context)
Decide this, then add to DESCRIPTION
Can we implement a third? A fourth?
Concordance.R
should be completed or omitted before release of v1.0.0
See Minh et al. (2020)
Was other colour customization planned too?
See "decisiveness" branch.
Adapting the functions developed for Inapp.
Recall that hcl.colors() is available for nice visualizations.
Once in play, make following updates:
StepInformation()
– provide alternative to Carter1()
ConcordantInformation()
: update docsFunction doesn't work with
dataset <- inapplicable.datasets[['Longrich2010']]
Requires scores to be calculated on polytomies.
See Kearney 2002, Syst Biol, for a potential use wrt rogue taxa.
@article{Nixon1996,
title = {On consensus, collapsibility, and clade concordance},
author = {Nixon, Kevin C. and Carpenter, James M.},
year = {1996},
journal = {Cladistics},
volume = {12},
number = {4},
pages = {305--321},
doi = {10.1111/j.1096-0031.1996.tb00017.x}
}
@article{Kearney2002,
title = {Fragmentary taxa, missing data, and ambiguity: mistaken assumptions and conclusions},
author = {Kearney, Maureen},
year = {2002},
journal = {Systematic Biology},
volume = {51},
number = {2},
pages = {369--381},
doi = {10.1080/10635150252899824}
}
Use TreeTools function; see TreeTools#53.
Introduce:
Need to support it.
It, and related functions, should at least display a message when DNA data is fed to it.
IW now active; integrate into vignette
Do this by first matching all identical splits, then only calculating the information content of non-identical split pairings.
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