Questions tagged [phylogeny]

Phylogeny is the study of relationships between items (organisms, concepts, etc); typically represented by phylogenetic trees. Such trees may simply reflect evolutionary relationships; or their branches may be scaled according to some measure of evolutionary distance, such as accumulated mutations or time.

Phylogeny is the study of relationships between items (organisms, concepts, etc). The primary use of phylogeny is in systematics, the inference of evolutionary history from morphological and/or molecular data; this typically requires computational methods. Relationships are often depicted as trees, whose branches may scale according to an aspect of evolutionary distance, such as number of mutations, or time. When temporal and/or geographic data are available, phylodynamic or phylogeographic analyses can be performed.

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how can I expand tree in ggtree?

Is there any way how to stretch the phylogenetic tree in ggtree along the y axis. I mean to do the same thing as does expansion in Figtree. Without this each terminal branch is too close to another if there are many tips.
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Fail to attach "treescape" package in R

I did as the the follows below: 1.install package "devtools". 2.library(devtools) install_github("thibautjombart/treescape") Or using install.packages("treescape") 3.library("treescape") However, this package cannot be attached and R gave me such…
Charles Yan
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R: help directing to an object, not an atomic vector

I have a large set of phylogenetic trees (phylo objects) which I am attempting to compare. The name of each comparison is stored in the list Newickand the number of the two files are stored in the matrix cc[1:2,i]. However, when I try to run…
Jautis
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Reading a newick format phylogeny in r using caper

I desire to perform comparative analysis using independent contrasts which I believe can be done in ape. I have a phylogeny of the cat family in newick format, and when I try to read in the file I get the error…
KB2
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Error in "birthdeath" function (phylogenetic tree analysis)

I want to determine birth and death rate of a given phylogenetic tree using birthdeath of the ape package, and I get the following error: birthdeath(phy) Error in solve.default(out$hessian) : Lapack routine dgesv: system is exactly singular:…
Robert
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Loop over individual trees in 'multiphylo' object in R

I am trying to run functions over multiple phylogenetic trees (files of class multiphylo). Most of these functions come with specific R packages, but are only applicable to single trees (class phylo). Essentially, multiphylo object consists of many…
Anurag Mishra
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How to keep track of a data frame and save it in each round of a loop?

I simply need to save df each time it goes through the loop and save it as a csv or something similar! #Q are matrices and trees are phyllo objects library(ape) library(phytools) for(l in 1:length(Q.all)){ for(k in 1:length(trees)){ tree<-…
Jack
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problems with multiDiv in paleotree package

I am trying to use the package paleotree to build LTT plots, but I get the following error when I try to input my trees. a=read.tree(file.choose()) # to choose newick/nexus file multiDiv(a) Error in multiDiv(a) : Data of Unknown Type Does…
Anurag Mishra
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Phylogenetic generalized linear models with no. of successes/failures as response in r

I have a plant dataset containing information about how often each plant species (n=550) succeeds or fails to do something, i.e. the number of successes and the number of failures. The dataset also contains data on each plant species'…
Greforb
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How to write a loop to remove the NULLs from output and shrink it to a desirable length?

The following code simulate a number of phylogenetic trees(here 100). But due to chance event of extinction some trees are NULL. I need to verify those NULL trees, drop them from the output object and select x out of N trees from the remaining…
Jack
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How to write a loop to calculate a score for the number of simulations repeatedly?

I need a pretty simple loop that takes each phylogenetic tree from the multiphylo object and calculate the Ic for each tree and put it in a dataframe. sorry if it is so simple, I'm new to R and I couldn't figure it out! library(apTreeshape) …
Jack
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'ape' phylogenetic gls - warning message, data not in same order as tree

Hello – I am conducting a phylogenetic analysis of lizard data. I have imported a phylogenetic tree into the “ape” package in R. For two species I am missing data, so I have used the drop.tip function to match the tree data to the species trait data…
GTC
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Loop or Vectorize this function for Phylogenetic Tree Clade Dropping

I have a process which I would like to repeat a known number of times, but with a catch. The first iteration should be with the original dataset, then the next should be with the result of the first, the next with the result of the second,…
branch.lizard
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How to pass a fixed igraph layout to plot.networx in phangorn?

Despite the relative popularity of neighborNets, I couldn't find any solutions to the following problem. In R, I'm trying to plot a neighborNet (created using package phangorn, object class networx). The package uses igraph for plotting static 2D…
user3554004
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floating.pie error while using nodelables from ape package

I get an error while using the ARD model of the ace function in R. The error is Error in floating.pie.asp(XX[i], YY[i], pie[i, ], radius = xrad[i], col = piecol) : floating.pie: x values must be…
user6385
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