My apologies, I just noticed that the cumulative plot was already on the
page, I had misinterpreted what that plot meant.
Russell
On Sat, Oct 28, 2023 at 10:56 PM Russell Engelman
wrote:
> Dear Liam,
>
> This is great, almost exactly what I needed. I will have to get our tree
>
hould be pretty useable for ggplot, too. I
> think the function has a plot argument that you can just set to False.
>
> On Sat, Oct 28, 2023, 6:37 PM Russell Engelman
>
> wrote:
>
>
> It looks like what Liam wrote (specifically, the final figure in the post)
>
ords() which returns a
>> matrix with 2 columns giving the number of lineages for each node time of
>> the tree. I guess you'll need to do a bit of programming to combine the
>> different outputs from different trees.
>>
>> Best,
>>
>> Emmanuel
>>
>> ---
Dear R-Sig-Phylo,
I was wondering if there was any way to color-code a lineage-through-time
plot, to highlight the proportion of taxa at specific intervals that belong
to a particular clade. I.e., an LTT plot of tetrapod diversity through
time, and I want to highlight the number of lineages at
# correct, I think..
>
> I tested it on a toy example of a tree with 5 species and it works fine..
>
> I hope there are no other mistakes! See other comments below.
>
> Cheers,
>
> Simone.
> On 3/7/21 8:40 am, Russell Engelman wrote:
>
> Dear All,
>
> Okay, so I tried
rection WRONG!!
> C <- (lambda*mat)+(1-lambda)*diag(diag(mat)) ## correct, I think..
>
> I tested it on a toy example of a tree with 5 species and it works fine..
>
> I hope there are no other mistakes! See other comments below.
>
> Cheers,
>
> Simone.
> On 3/7/21 8:40 am, Ru
Dear All,
Okay, so I tried the code that Dr. Blomberg provided, and it doesn't seem
to work. I rewrote the code slightly in order for it to try and predict the
body mass of the taxa used to calculate the line, rather than some new
taxon, because I need to do that in order to calculate prediction
Dear All,
Okay, I've read all of the papers that people have linked, and I have an
understanding of the theory. However, where I am struggling now is trying
to figure out how to actually perform a PGLS that incorporates signal when
predicting new data in R. I tested a bunch of gls functions in
Dear All,
What you see is the large uncertainty in “ancestral” states, which is part
> of the intercept here. The linear relationship that you overlaid on top of
> your data is the relationship predicted at the root of the tree (as if such
> a thing existed!). There is a lot of uncertainty about
VRHpiQgbwg43i6eS6kArrabLdFL4bntzUSRmlRP2CW4lbZqeEcColw>
> | ASU profile <https://isearch.asu.edu/profile/3682356>
> e: nathan.up...@asu.edu | Skype: nate_upham | Twitter: @n8_upham
> <https://twitter.com/n8_upham>
>
> =
>
>
>
> On Jun 28, 2021, at 10:47 AM, Russell Engel
Dear R-Sig-Phylo Mailing List,
I ran into a rather unusual problem. I was doing an analysis using the
mammal trees from Upham et al. (2019) downloaded off of the VertLife site.
The model statistics for my data initially suggested that the OLS model was
better supported than a PGLS model based on
ound to more formally publishing
> tests of it. Also, I'm fairly sure Jonathan Chang et al. wrote a relevant R
> package here which also automates most of this, and used it for a big fish
> phylogeny. That'd be worth a look if you're trying to do this across
> hundreds or thousands of species.
&
Dear R-Sig-Phylo Group,
I had a question regarding the calculation of regression statistics using
PGLS. When I obtain the degrees of freedom from a PGLS object using ape in
R, I notice that it returns the same number of degrees of freedom as under
OLS, and the AIC of a bivariate function is
%7C637582763674848184%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000sdata=kgDYJXKFXRFIM8mv1x8fViY6QDiEjTQ8qP5mQ0SUq3k%3Dreserved=0
> The only paper it's described in
> >>> remains
> https://nam10.safelinks.protection.outlook.com/?url=
%7C637582763674848184%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000sdata=kgDYJXKFXRFIM8mv1x8fViY6QDiEjTQ8qP5mQ0SUq3k%3Dreserved=0
> The only paper it's described in
> >>> remains
> https://nam10.safelinks.protection.outlook.com/?url=
Dear R-sig-phylo,
I have been working with a mammalian phylogeny I recently downloaded from
VertLife (http://vertlife.org/phylosubsets/). Unfortunately, the phylogeny
is missing a large number of species, so I am trying to manually add these
taxa to the phylogeny. I have a series of 100 trees
la Ssma Concepción [Adj. Res.]
>
> Web & phytools:
> http://faculty.umb.edu/liam.revell/, http://www.phytools.org,
> http://blog.phytools.org
>
> Academic Director UMass Boston Chile Abroad:
> https://www.umb.edu/academics/caps/international/biology_chile
>
> U.S. COVID-19
Dear R-sig-phylo,
I am a researcher who has been trying to plot a continuous trait map onto a
phylogeny using the phytools and ape packages in R. I have been trying to
denote specific clades using the arc.cladelabels function in phytools, but
I have also been trying to color-code the text, curve,
18 matches
Mail list logo
