Re: [R-sig-phylo] ape package in R

Hi, Actually, Ranjita can use the number of gene copies if it is reasonable to assume that these numbers evolve among samples, maybe a stepwise model with transitions: n -> n + 1 n -> n - 1 In that case, a simple approach is to calculate the Euclidean distances among samples and do an NJ or

Re: [R-sig-phylo] ape package in R

If you want to use ape for making a phylogenetic tree, I think you need the actual sequences of the genes, and not only the copy numbers El sáb., 19 sept. 2020 a las 21:40, Ranjita Thapa () escribió: > Hi, > > I want to construct a phylogenetic tree with ape package. I have a csv > file with

[R-sig-phylo] ape package in R

Hi, I want to construct a phylogenetic tree with ape package. I have a csv file with gene ids and copy number for each gene across different samples. I want to construct phylogenetic tree. I am wondering how could I convert the csv file to input file for ape. Could you please suggest me how

Re: [R-sig-phylo] ape-package: unknown states in ace analyses?

Paradis Envoy� : vendredi, 22 juin 2018 15:45:05 � : Th�o L�ger; r-sig-phylo@r-project.org Objet : Re: [R-sig-phylo] ape-package: unknown states in ace analyses? Two more comments: 1/ The first insertion in the code of ace() below is not needed if the user replaces "?" (or any coding fo

Re: [R-sig-phylo] ape-package: unknown states in ace analyses?

This is so cool. Thanks Liam! J > On Jun 21, 2018, at 8:22 PM, Liam J. Revell wrote: > > Dear Theo. > > This can be done with the function rerootingMethod as described here > http://blog.phytools.org/2013/04/estimating-ancestral-states-when.html, > although it is *very* important to note

Re: [R-sig-phylo] ape-package: unknown states in ace analyses?

Two more comments: 1/ The first insertion in the code of ace() below is not needed if the user replaces "?" (or any coding for unknown/uncertain state) with NA -- which seems reasonable to do. 2/ This approach of taking uncertainty into account in likelihood ancestral state reconstruction

Re: [R-sig-phylo] ape-package: unknown states in ace analyses?

Hi Théo, It is possible to modify the code of ace() to take uncertain character states into account. If you edit the code with fix(ace), after these four lines: if (method != "ML") stop("only ML estimation is possible for discrete characters.") if (any(phy$edge.length <= 0))

[R-sig-phylo] ape-package: unknown states in ace analyses?

Hello, I am working on the phylogeny of a subfamily of moths and I use ace from the ape-package to reconstruct the ancestral state of a bunch of morphological characters. I encountered a problem with the few unknown states I have on my matrix (coded "?", either because material for

[R-sig-phylo] ape package: improvement suggestion in color handling for mosaic in phydataplot?

Dear all, I am trying to use the phydataplot function in the ape package with the style mosaic. I am having difficulty getting the colors of the rectangles to be the color I desire in an automatic way. I have come to the conclusion that I can’t do and it would have to be an enhancement to the

Re: [R-sig-phylo] ape package gives 'Error in FI[i]:LA[i] : NA/NaN argument'

Emmanuel Paradis writes: > > Hi Matt, > > This is because this accession number does not point to the sequence. > For this particular one, you could use: > > seq1 <- read.GenBank("U00096.3") > > Best, > > Emmanuel > > Le 27/02/2014 01:35, Matt Curcio a écrit : > >

Re: [R-sig-phylo] Ape package.

You need put the path of the directory with this simbol / and not this \, so the correct path is F:*/*tetrapods_tree.txt. Cheers! On Sun, Apr 20, 2014 at 5:17 PM, Alexey Fomin lesh...@rambler.ru wrote: Hi! Whether someone work with ape package? I have long tree (see attached, it is in

Re: [R-sig-phylo] Ape package.

The tree file is not proper formatted, it is missing a ; in the end. Regards, Klaus On Sun, Apr 20, 2014 at 10:17 PM, Alexey Fomin lesh...@rambler.ru wrote: Hi! Whether someone work with ape package? I have long tree (see attached, it is in newick format, it is ultra metric, it is from

[R-sig-phylo] ape package.

Whether anybody help? I can non start the ape package. when I do library(ape) it give: Error in library(ape) : there is no package called 'ape' (I use R-3.0.3-win) ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org

Re: [R-sig-phylo] ape package gives 'Error in FI[i]:LA[i] : NA/NaN argument'

Hi Matt, This is because this accession number does not point to the sequence. For this particular one, you could use: seq1 - read.GenBank(U00096.3) Best, Emmanuel Le 27/02/2014 01:35, Matt Curcio a écrit : Greetings all,, I received this error while using R version 2.15.1 and ape 3.0.11.

[R-sig-phylo] ape package gives 'Error in FI[i]:LA[i] : NA/NaN argument'

Greetings all,, I received this error while using R version 2.15.1 and ape 3.0.11. Error in FI[i]:LA[i] : NA/NaN argument I have tried several approaches: ref = NC_000913.3 seq1 = read.GenBank(ref) Error in FI[i]:LA[i] : NA/NaN argument ref = read.csv(file=test2.csv, head=T) ref = str(ref) #

Re: [R-sig-phylo] ape-package/ possibility to get the transformed residuals (phylogentic corrected residuals)?

Actually, the function residuals.gls calculates 3 different types of residuals: response or raw residuals, pearson or standardized residuals, and normalized residuals. For diagnostic purposes, you probably want the normalized residuals. The default is the response residuals (although the