Displaying 20 results from an estimated 700 matches similar to: "Package for phylogenetic tree analyses"
2005 Jan 03
1
building phylogenetic trees
Hello,
My name is Sivan and I am a master degree student in statistics,my problem is as follows:
I have a dataset containing gene sequences and I would like to create a phylogenetic tree from it.
The problem that I can't seem to find a function to do this kind of operation. I read the ape package manual and I haven't found a command that takes raw data and turns it into a tree.
does anyone
2011 Apr 14
1
Overlaying images at nodes of phylogenetic tree
Can you recommend an R library that will help me create a diagram of a
phylogenetic tree on which specific images are placed at appropriate nodes of
the tree?
For example, I have specific image files associated with each member of the
phylogenetic tree, and I would like to automate the display of the image next to
the correct node of the tree. I can provide an image file with an example.
2013 Jun 03
1
Mixed effects model with a phylogenetic tree/ distance matrix as a random effect
Hi,
I'm trying to build a mixed-effects model in which I'd like to include
either a distance matrix or a phylogenetic tree as a random effect.
The troubles I've had are that:
1. Function lmer() in package lme4 only accepts a data frame column as a
random factor and not a distance matrix.
2. Function MCMCglmm() in package MCMCglmm only accepts a rooted and
ultrametric phylogenetic
2010 Nov 11
1
metafor: including phylogenetic non-independence among species?
Hello, Is it possible to include information about phylogenetic relatedness
among species (when species are replicates for each study within a
meta-analysis) in a meta-anlaysis in the metafor package?
Alternatively, I wonder if the method f Lajeunesse 2009 American Naturalist
has been adopted in R in any fashion?
Thanks, Scott Chamberlain
[[alternative HTML version deleted]]
2006 May 01
4
table of means/medians across bins used for a histogram
Hi
I am trying to get a table of means of parameter 1
across BINS of parameter 2.
I am working in proteomics and a sample of my data is
as follows
cluster-age clock-rate(evolutionary rate) scopclass
0.002 10 A
0.045 0.1 B
0.13 15 A
0.15 34 D
....
....
....
2011 May 05
1
functions pandit and treebase in the package apTreeshape
Hello.
I'm trying to use the functions pandit and treebase. They are in the package apTreeshape. Once I've loaded the package, R responses:
- no function pandit/treebase.
Somebody knows why or what is the reason?
Thanks,
Arnau.
------------------------------------------------------------
Arnau Mir Torres
Edifici A. Turmeda
Campus UIB
Ctra. Valldemossa, km. 7,5
07122 Palma de Mca.
2007 Feb 28
3
Packages in R for least median squares regression and computing outliers (thompson tau technique etc.)
Hi
I am looking for suitable packages in R that do
regression analyses using least median squares method
(or better). Additionally, I am also looking for
packages that implement algorithms/methods for
detecting outliers that can be discarded before doing
the regression analyses.
Although some websites refer to "lms" method under
package "lps" in R, I am unable to find such a
2019 Apr 05
0
new R packages for phylogenetic compartive methods
Dear all,
I wanted to let you know about four phylogenetic comparative methods (PCM) packages that have become available on (3 on CRAN and 1 on GitHub) recently that hopefully will be interesting to somebody. Three of them go significantly beyond the Brownian motion (BM) and Ornstein-Uhlenbeck (OU) processes.
1) There is a new version of mvSLOUCH available. The most important change is that
the
2019 Apr 05
0
new R packages for phylogenetic compartive methods
Dear all,
I wanted to let you know about four phylogenetic comparative methods (PCM) packages that have become available on (3 on CRAN and 1 on GitHub) recently that hopefully will be interesting to somebody. Three of them go significantly beyond the Brownian motion (BM) and Ornstein-Uhlenbeck (OU) processes.
1) There is a new version of mvSLOUCH available. The most important change is that
the
2012 Jun 18
0
Obtaining r-squared values from phylogenetic autoregression in ape
Hello,
I am trying to carry out a phylogenetic autoregression to test whether my
data show a phylogenetic signal, but I keep calculating bizzare R-squared
values.
My script is:
> library(ape)
> x <-
2006 Oct 26
2
Query about using table
Hi
I have data of the following form
ID age member_FLAG
1 25 Y
2 36.75 N
3 75.5 N
.........
.........
I want to get a histogram of this data showing
distribution of member_flag in each age-bin i.e. how
many values in each age bin have a member_flag of 'Y'
and how many have 'N'.
I was able to do the same using barplot2.
However I also need similar
2013 Jun 04
0
Mixed effects model with a phylogenetic tree/ distance, matrix as a random effect
Take a look at lmekin() in the coxme package. The motivating data set for my development
of coxme was the Minnesota Family Breast Cancer project: 24050 subjects in 462 families.
The random effect is an intercept per subject with sigma^2 K as its variance where K is
the kinship matrix (1 for self-self, .5 for parent-child or sib-sib, .25 for uncle-neice,
etc). lmekin is a linear models front
2004 Aug 01
0
phylogenetic trees calculation
Dear all,
I would like to ask you the following:
I have data about different manuscripts, together with data about the
presence/absence of copying errors, in the days when manuscript were
really manuscripts. I would ideally like to use the data to draw a
phylogenetic tree, so that I can infer which ms was copied from which.
The error presence/absence is coded in binary format. The plan is to use
2009 Jun 15
0
How to build phylogenetic tree by R program from distance any distance matrix
Hello R users,
Can any one please help me to find a way to build phylogenetic tree by R
program from any distance matrix.
Suppose I have a data like :
MATRIX
[1] '1' 0.0
[2] '2' 0.071 0.0
[3] '3' 0.036 0.286 0.0
[4] '4' 0.429 0.75 0.714 0.0
[5] '5' 0.679 0.179 0.214 0.536 0.0
[6] '6' 0.893 0.929 0.964 0.464 0.357 0.0
[7]
2009 Sep 17
1
How to colour the tip labels in a phylogenetic tree
Hi,
Using Ape, I have constructed an object of class "phylo", using the
method 'nj' (lets call the object 'tree_ja').
I also have a given subset of 'tree_ja' in a vector (lets call the
vector 'subspecies').
What I want to do, is construct a nj tree - plot(tree_ja) - but have the
species in vector 'subspecies' shown as red at the tips of the
2012 Jan 27
2
Placing a Shaded Box on a Plot
Hello,
I would like to place shaded boxes on different areas of a
phylogenetic tree plot. Since I can not determine how to find axes on
the phylogenetic tree plot I am not able to place the box over certain
areas. Below is example code for the shaded box that I have tried to
use, and the first four values specify the position.
rect(110, 400, 135, 450, col="grey",
2007 Mar 01
2
Query about data manipulation
Hi
Thanks much for the prompt response to my earlier
enquiry on packages for regression analyses.
Along the same topic(?), I have another question about
which I could use some input.
I am retreiving data from a MySQL database using
RODBC.
The table has many BLOB columns and each BLOB column
has data in the format
"id1 \t id2 \t measure \n id3 \t id4 \t measure...."
(i.e. multiple rows
2010 Mar 09
1
Computation of AIC for gls models
Dear Colleagues,
We are using the phylog.gls.fit() function from the R package "PHYLOGR" (Diaz-Uriarte R, Garland T: PHYLOGR: Functions for phylogenetically based statistical analyses. 2007. Available at [http://cran.r-project.org/web/packages/PHYLOGR/index.html]) to correct for lack of independence between data points. (In our particular case, the lack of independence is due to
2006 Jul 11
1
Query about getting averages across a certain parameter in a table
Hi
I have a table that goes
data
cluster_ac clockrate age class
7337 0.9 0.001 alpha_proteins
7888 0.1 0.78 beta proteins
etc
The class column can have 7-8 different unique values
While the clockrate and age columns are floats varying
from 0 to 1.
I wish to get the average clockrate across each of the
classes for this data.
I would appreciate your help
2007 Jan 25
1
unique/subset problem
Hi
I am new to R programming and am using subset to
extract part of a data as follows
names(dataset) =
c("genome1","genome2","dist","score");
prunedrelatives <- subset(dataset, score < -5);
However when I use unique to find the number of unique
genomes now present in prunedrelatives I get results
identical to calling unique(dataset$genome1) although