p
> *Envoyé :* dimanche 26 août 2018 05:36
> *À :* bome...@utk.edu
> *Cc :* mailman, r-sig-phylo; Agus Camacho
> *Objet :* Re: [R-sig-phylo] understanding variance-covariance matrix
>
> I'll second Brian's self-citation. O'Meara et al. 2006 is I think one of
> the best introdu
Dear list users,
I am trying to make an easy R demonstration to teach the
variance-covariance matrix to students. However, After consulting the
internet and books, I found myself facing three difficulties to understand
the math and code behind this important matrix. As this list is answered by
new Mammal Diversity Database
> <https://mammaldiversity.org/>
> Taxonomy Advisor, IUCN/SSC Small Mammal Specialist Group
>
> e: nathan.up...@yale.edu | Skype: nate_upham | Twitter: @n8_upham
>
>
>
>
>
>
> On Feb 13, 2018, at 9:11 PM, Agus Camacho <agus.cama...@gm
ent for details)]
>
> BEGIN TREES;
> TREE tree_4104 =
> TREE tree_9438 =
> ...
> TREE tree_1868 =
> TREE tree_0011 =
> END;
>
>
> Looks like your download did not work and the error message from
> read.nexus could improve.
>
> Cheers,
> Klaus
Dear list,
I am puzzled with this error when importing a bird tree subset from
https://birdtree.org/subsets/ .
The subset is supposed to be in nexus format. However,
trees<-read.nexus("output.nex")
Error in if (tp[3] != "") obj$node.label <- tp[3] :
missing value where TRUE/FALSE needed
Dear list,
Im confronting this error in a script i have long used before without
problems. I've been searching through the internet and despite several
reports of similar errors, could not find an appropriate solution.
Some times, i get this additional error:
Error in .getMeVersion() : file
Dear list users,
Im trying to use arrows or triangles to plot wether a trait increased or
decreased its value during an ancestral state reconstruction.
I think id need to condition pch and cex values to the magnitude and
direction of differences between the trait to be plotted at the
Just answered with Robert Hijmans in GEOstat course:
r=raster(c) does not necessarily use the extent of c, so the correct way
to have a raster with the extent of a group of coordinates should be r=
raster(extent(c))
Cheers
Agus
2014-06-11 21:56 GMT+02:00 Agus Camacho agus.cama...@gmail.com
It seems the function was masked from some other package:
This works:
require(geiger)
geo - get(data(geospiza))
lphy - geiger::rescale(geo$phy, lambda, 0.9) # transform tree in one
fell swoop
Thanks again,
2014-05-16 15:49 GMT-03:00 Agus Camacho agus.cama...@gmail.com:
Thank you both
/2014 2:20 PM, Agus Camacho wrote:
Dear list users,
Im trying to show what happens when we apply lambda transformations to a
tree.
For that, I was following swenson's book explanations:
library(geiger)
lambda.phylo=transform(tree,1)
however, I got the following errors:
lambda.phylo
Dear coleagues,
Anybody knows how to read only one tree from a tree list? I went throught
the help and available tutorials but could find nothing.
Thanks in advance.
Agus
--
Agustín Camacho Guerrero.
Doutor em Zoologia.
Laboratório de Herpetologia, Departamento de Zoologia, Instituto de
Dear all,
I've performed a phylogenetic ancova using pGLS with one continous
variable, one continous factor and a categorical one.
Lambda tells me the phylogenetic signal is relatively low for the
relationship:
lambda
0.3282688
However, when I calculate the phylogenetic signal for each of
, it may be
more appropriately fixed by transforming an independent variable than a
dependent one. If the dependent itself is normal, then nonnormal!
ity might be introduced in the residuals because of the distribution of a
particular independent variable.
Best
Luke
2013/11/29 Agus Camacho agus.cama
Dear colleagues,
Im having difficulties to decide whether I choose a phylogenetic GLS model
with a higher fit (lower AIC and BIC), or a model in which normality of the
residuals, after accounting for phylogenetic signal, is compromised. The
number of species is reasonably high (87), but i dont
Dear R-sig-phylo users,
Im trygin to use the cool phenogram (Revell's phytools) to plot two graphs
together.
The code to do that comes below.
1. Id like to adjust the margins of the figure and the position of the
names so I can avoid the names getting cropped by the margins of the figure
2. id
are available from me or from the individual authors)
From: r-sig-phylo-boun...@r-project.org [r-sig-phylo-boun...@r-project.org]
on behalf of Brian O'Meara [bome...@utk.edu]
Sent: Tuesday, September 18, 2012 1:25 PM
To: Agus Camacho
Cc: r-sig-phylo@r
Hope not being abusing of this list.
Possibly, I missed something. I tried both with matrix and dataframe and
reached to the same problem:
phy.manova(tree, c(table$option,table$difoption), table$morph,
data.names=NULL, nsim=1000, test=Wilks)Warning: no tip labels, order
assumed to be the
Dear all, I tried to test something similar to Jason, but relating the
change in rates to the acquisition of a trait, instead to a specific date.
For that, I used a phylogeny with ten taxa, without outgroup.
I used exactly the same script gently proposed by Liam but got the
following error
Dear list,
Anybody knows if it would be possible to do a phylogenetic quantile
regression procedure in R or other software?
Im trying to model a relationship in which other factors beyond the ones
which entered in the analysis are potentially misleading the analysis
results. Quantile regression
Dear all,
Im trying to handle an error when executing phyl.pairedttest from
Phylotools in R. apparently, is due to an error wih the tree.
However, given that i used the tree tips to order the table(see below)
and that the few species I used are all in the tree and in the table,
i just cant
Dear all,
Sorry to take your time. At the moment, Im trying to fgure out how to
analyze a dataset, and though that given your experience in the are could
give me som light on this.
My dataset consist of an escape response variable (coded as a three level
categorial variable) and two, two-level
Many thanks Marcio and Emmanuel!
That solved my problems to plot the tree.
2012/8/22 Emmanuel Paradis emmanuel.para...@ird.fr
Agus,
Whether the background appears transparent or not depends on the device
where you plot the tree. On Linux, the default device (X11) is transparent:
par(bg)
Dear list,
Im trying to plot a coloured tree with transparent background, to do that,
im using the following script:
require(ape)
require(geiger)
tree - read.tree(text=
Calyptommatus leiolepis:0.0168, Calyptommatus nicterus:0.0099):0.0242
,Calyptommatus sinebrachiatus:0.038):0.0724
Many thanks, Emmanuel,
Setting the number of nodes to 9 solved the problem.
Cheers
Agus
2012/5/25 Agus Camacho agus.cama...@gmail.com
Thanks emmanuel,
Got this:
tree$node.label [1] 1 2 3 4 5 6 7 8 9 10 tree$Nnode[1] 9
Wonder how is that possible. So im sending how i generated
emmanuel.para...@ird.fr
Hi Agus,
It seems the problem comes when pic() tries to create names to the
contrasts. Probably your tree has badly formatted node labels. What do the
following commands return?
tree$node.label
tree$Nnode
Cheers,
Emmanuel
Agus Camacho wrote on 25/05/2012 01:58
Hi all,
When calculating independent contrasts of a variable, I get the following
message:
ContrastWeight - pic(Weight,tree)Error en names(contr) - lbls :
el atributo 'names' [10] debe tener la misma longitud que el vector [9]
The attribute names [10] must have the same length than the
Dear all,
fitcontinuous is giving me a warning generally related to non
correspondence between tree tips and data. However name.check and the tree
tips seems ok.
Anybody has a hint on this?
Thanks in advance.
Agus
name.check(tree, tp)[1] OK BMfit - fitContinuous(tree, tp$temperature,
= tp$temperature, model=BM,
data.names = rownames(tp)
that should work without a warning. If your tip data are in the same order
as the tip labels, the model output won't change. If they're not.
Graham
On May 23, 2012, at 1:16 PM, Agus Camacho wrote:
Dear all,
fitcontinuous
Dear all,
I just had the following result fitting a Pgls with both, brownian and O-U
correlation structures.
I was wandering what could have made the value and Sd go to zero. Altitude
values were considered continuous but were strongly grouped in two levels.
Might that have to do with the result?
Dear all,
I am trying to compare environmental vs phylogenetic effects over one trait
that has evolved in a single branch. For that, I have 10 closely species
that have been collected over 7 localities. The number of localities in
which each species has been collected varies from 1 to 3. So some
:13 PM, Agus Camacho wrote:
Dear all,
I had the same problem as T. Gamble and tried the advice from L. Revell
and Rich over my own tree (attached), all of the hints produced a df with
Nas. Also, I cant see any difference between rownames on my matrix and tree
tip labels...
Could anyone
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