And update inst/CITATION

hopefully we don't need it any more

Use TreeTools function; see TreeTools#53.

Either

• Remove rgl from imports, and from the app
  or
• Add 3d plotting functionality to the app

See branch: pp-vignettes

Introduce:

• Installing R
• Installing packages

Was other colour customization planned too?

Should cite TreeSearch as standalone package, with MorphyLib & algorithm paper to be cited when used (cf. profile parsimony / successive approx / etc context)

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:

1. 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?

2. 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

Review and implement appropriate methods reviewed in Grant & Kluge (2003)

See "decisiveness" branch.

Save converting from edge to and from morphy's parentof/left/right notation by performing tree reordering using this notation.

It, and related functions, should at least display a message when DNA data is fed to it.

IW now active; integrate into vignette

Can we implement a third? A fourth?

Possibly venues: JOSS; R journal

Possibly implemented in phangorn; add to app.R

Adapting the functions developed for Inapp.
Recall that hcl.colors() is available for nice visualizations.

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.

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}
}

the old mpl_visualise functions might be given new life using our Inapp visualizer.

Need to support it.

Decide this, then add to DESCRIPTION

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.

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)

Once in play, make following updates:

• StepInformation() – provide alternative to Carter1()
• ConcordantInformation(): update docs

Function doesn't work with
dataset <- inapplicable.datasets[['Longrich2010']]

Check that all nodes are bifurcating before running NNI/TBR/SPR, which will crash R.

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.

Concordance.R should be completed or omitted before release of v1.0.0

See Minh et al. (2020)

• app.R
• inst/References.bib

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") :

Do this by first matching all identical splits, then only calculating the information content of non-identical split pairings.

Reproduce by:

• Run EasyTrees()
• Map character
• Set a root
• Tips aligned regardless of "Align tips" value

#' @template InitializeDataParam
#' @template ClearUpDataParam
#' @template TreeScorerParam

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"

Test case is disabled.

• IPC
• Promising approaches
• Alternative approach (incompatible with progress bars?)

https://cran.r-project.org/web/packages/Rdpack/vignettes/Inserting_bibtex_references.pdf

Should be straightforward, and will reduce duplication

• Support stats like:

  • Bremer/branch supports
  • CI/RI: See phangorn:CI()
  • bootstrapping: See MorphyBootstrap(), though Jackknife() is usually more appropriate.

• Ability to

  • 'force' a tip into a clade
  • & run a Templeton test for alternative hypotheses
  • [MS note for v1.0:] Can profile parsimony offer a better test?