Re: [R-sig-phylo] How to sort trait data according to tree
Emmanuel,
Yes, that was exactly what I was confused about (even str(cbm) wasnʻt very
illuminating). Thank you so much for your explanation. CorBrownian is only
storing the formula and the tree, and the data are gathered by gls. I agree
this is a very good way to keep everything in its proper order.
Thanks again for your kind replies,
Marguerite
On Sun, May 16, 2021 at 8:58 PM Emmanuel Paradis
wrote:
> - Le 17 Mai 21, à 13:41, Marguerite Butler a
> écrit :
>
> Thank you very much for the reply Emmanuel!
>
> OK, yes I just tried and Iʻm surprised that this works:
>
> > dat <- data.frame(Species = c("Homo", "Pongo", "Macaca", "Ateles",
> "Galago"), X = X, Y = Y)
> > cbm <- corBrownian(1, tree, form = ~Species)
> > gls(Y ~ X, dat, correlation = cbm)
>
> How does corBrownian know about Species, when it is only defined as an
> element of dat, and not known in the global environment?
>
> corBrownian() doesn't know where all these variables are located. Indeed,
> if you print 'cbm':
>
> R> cbm
> Uninitialized correlation structure of class corBrownian
>
> It's gls() that looks for them. When you think about it, using "data =
> ..." is really a good way to be sure that all variables are ordered
> correctly whether they are involved as predictors (in 'model = '), in the
> correlation structure, or in the variance function ('weights = ').
>
> Best,
>
> Emmanuem
>
> Anyway, thank you!
> Marguerite
>
>
> On Sun, May 16, 2021 at 7:03 PM Emmanuel Paradis
> wrote:
>
>> Hi Marguerite,
>>
>> The issue is about nlme::gls. The help page ?gls says:
>>
>> data: an optional data frame containing the variables named in
>> ‘model’, ‘correlation’, ‘weights’, and ‘subset’. By default
>> the variables are taken from the environment from which ‘gls’
>> is called.
>>
>> So you make it work by removing "dat$" in the call to corBrownian():
>>
>> cbm <- corBrownian(1, tree, form = ~Species)
>>
>> Best,
>>
>> Emmanuel
>>
>> - Le 17 Mai 21, à 6:22, Marguerite Butler mbutler...@gmail.com a
>> écrit :
>>
>> > Aloha all,
>> >
>> > Does anyone know the answer to this question - how does ape pass the
>> > species name information into gls? Seems to be a global environment
>> issue
>> > when using apeʻs corBrownian and nlmeʻs gls? and a very specific form
>> is
>> > required, but why?
>> >
>> > Modified from ape help page for CorClasses:
>> >
>> > ---
>> >
>> > library(nlme)
>> > library(ape)
>> >
>> > tree <- read.tree(text =
>> >
>> "Homo:0.21,Pongo:0.21):0.28,Macaca:0.49):0.13,Ateles:0.62):0.38,Galago:1.00);")
>> > X <- c(4.09434, 3.61092, 2.37024, 2.02815, -1.46968)
>> > Y <- c(4.74493, 3.33220, 3.36730, 2.89037, 2.30259)
>> > dat <- data.frame(Species = c("Homo", "Pongo", "Macaca", "Ateles",
>> > "Galago"), X = X, Y = Y)
>> >
>> > gls(Y ~ X, dat, correlation=corBrownian(1, tree.primates, form =
>> ~Species))
>> > ---
>> >
>> > The above works just fine. However, if we try to calculate corBrownian
>> > separately, gls cannot understand the corBrownian object:
>> > ---
>> >> cbm <- corBrownian(1, tree, form = ~dat$Species)# calculate
>> correlation
>> >> separately
>> >> gls(Y ~ X, dat, correlation = cbm) ## does not work, invalid
>> type
>> >> (list) for dat
>> > Error in model.frame.default(formula = ~dat + Species + Y + X, data =
>> list( :
>> > invalid type (list) for variable 'dat'
>> > ---
>> >
>> > If we put the species information into a vector in the global
>> > environment it works. Why canʻt we use dat$Species?
>> > ---
>> > spp <- dat$Species # save species as vector in global environment
>> > cbm <- corBrownian(1, tree, form = ~spp)# calculate correlation
>> separately
>> > gls(Y ~ X, dat, correlation = cbm) ## works!
>> >
>> > Thanks,
>> >
>> > Marguerite
>> >
>> >
>> >
>> > On Fri, May 14, 2021 at 10:21 PM Marguerite Butler <
>> mbutler...@gmail.com>
>> > wrote:
>> >
>> >> Aloha Oliver,
>> >>
>> >> From the cor.Brownian help page, the explanation for the form argument
>> is
>> >> this:
>> >>
>> >> a one sided formula of the form ~ t, or ~ t | g, specifying the taxa
>> >> covariate t and, optionally, a grouping factor g. A covariate for this
>> >> correlation structure must be character valued, with entries matching
>> the
>> >> tip labels in the phylogenetic tree. When a grouping factor is present
>> in
>> >> form, the correlation structure is assumed to apply only to
>> observations
>> >> within the same grouping level; observations with different grouping
>> levels
>> >> are assumed to be uncorrelated. Defaults to ~ 1, which corresponds to
>> using
>> >> the order of the observations in the data as a covariate, and no
>> groups.
>> >>
>> >> This means that "t" should contain the species names or tip labels,
>> >> spelled exactly as they are in your phylogeny. So for example if your
>> data
>> >> SteninaeData
>> >> has a column for species names called "species" then you would specify:
>> >>
>> >> cor.BM <- corBrownian(phy=SteninaeTre
Re: [R-sig-phylo] How to sort trait data according to tree
- Le 17 Mai 21, à 13:41, Marguerite Butler a écrit :
> Thank you very much for the reply Emmanuel!
> OK, yes I just tried and Iʻm surprised that this works:
>> dat <- data.frame(Species = c("Homo", "Pongo", "Macaca", "Ateles",
>> "Galago"), X
> > = X, Y = Y)
> > cbm <- corBrownian(1, tree, form = ~Species)
> > gls(Y ~ X, dat, correlation = cbm)
> How does corBrownian know about Species, when it is only defined as an element
> of dat, and not known in the global environment?
corBrownian() doesn't know where all these variables are located. Indeed, if
you print 'cbm':
R> cbm
Uninitialized correlation structure of class corBrownian
It's gls() that looks for them. When you think about it, using "data = ..." is
really a good way to be sure that all variables are ordered correctly whether
they are involved as predictors (in 'model = '), in the correlation structure,
or in the variance function ('weights = ').
Best,
Emmanuem
> Anyway, thank you!
> Marguerite
> On Sun, May 16, 2021 at 7:03 PM Emmanuel Paradis < [
> mailto:emmanuel.para...@ird.fr | emmanuel.para...@ird.fr ] > wrote:
>> Hi Marguerite,
>> The issue is about nlme::gls. The help page ?gls says:
>> data: an optional data frame containing the variables named in
>> ‘model’, ‘correlation’, ‘weights’, and ‘subset’. By default
>> the variables are taken from the environment from which ‘gls’
>> is called.
>> So you make it work by removing "dat$" in the call to corBrownian():
>> cbm <- corBrownian(1, tree, form = ~Species)
>> Best,
>> Emmanuel
>> - Le 17 Mai 21, à 6:22, Marguerite Butler [ mailto:mbutler...@gmail.com |
>> mbutler...@gmail.com ] a écrit :
>> > Aloha all,
>> > Does anyone know the answer to this question - how does ape pass the
>> > species name information into gls? Seems to be a global environment issue
>> > when using apeʻs corBrownian and nlmeʻs gls? and a very specific form is
>> > required, but why?
>> > Modified from ape help page for CorClasses:
>> > ---
>> > library(nlme)
>> > library(ape)
>> > tree <- read.tree(text =
>> > "Homo:0.21,Pongo:0.21):0.28,Macaca:0.49):0.13,Ateles:0.62):0.38,Galago:1.00);")
>> > X <- c(4.09434, 3.61092, 2.37024, 2.02815, -1.46968)
>> > Y <- c(4.74493, 3.33220, 3.36730, 2.89037, 2.30259)
>> > dat <- data.frame(Species = c("Homo", "Pongo", "Macaca", "Ateles",
>> > "Galago"), X = X, Y = Y)
>> > gls(Y ~ X, dat, correlation=corBrownian(1, tree.primates, form = ~Species))
>> > ---
>> > The above works just fine. However, if we try to calculate corBrownian
>> > separately, gls cannot understand the corBrownian object:
>> > ---
>> >> cbm <- corBrownian(1, tree, form = ~dat$Species) # calculate correlation
>> >> separately
>> >> gls(Y ~ X, dat, correlation = cbm) ## does not work, invalid type
>> >> (list) for dat
>> > Error in model.frame.default(formula = ~dat + Species + Y + X, data =
>> > list( :
>> > invalid type (list) for variable 'dat'
>> > ---
>> > If we put the species information into a vector in the global
>> > environment it works. Why canʻt we use dat$Species?
>> > ---
>> > spp <- dat$Species # save species as vector in global environment
>> > cbm <- corBrownian(1, tree, form = ~spp) # calculate correlation separately
>> > gls(Y ~ X, dat, correlation = cbm) ## works!
>> > Thanks,
>> > Marguerite
>>> On Fri, May 14, 2021 at 10:21 PM Marguerite Butler < [
>> > mailto:mbutler...@gmail.com | mbutler...@gmail.com ] >
>> > wrote:
>> >> Aloha Oliver,
>> >> From the cor.Brownian help page, the explanation for the form argument is
>> >> this:
>> >> a one sided formula of the form ~ t, or ~ t | g, specifying the taxa
>> >> covariate t and, optionally, a grouping factor g. A covariate for this
>> >> correlation structure must be character valued, with entries matching the
>> >> tip labels in the phylogenetic tree. When a grouping factor is present in
>> >> form, the correlation structure is assumed to apply only to observations
>> >> within the same grouping level; observations with different grouping
>> >> levels
>> >> are assumed to be uncorrelated. Defaults to ~ 1, which corresponds to
>> >> using
>> >> the order of the observations in the data as a covariate, and no groups.
>> >> This means that "t" should contain the species names or tip labels,
>> >> spelled exactly as they are in your phylogeny. So for example if your data
>> >> SteninaeData
>> >> has a column for species names called "species" then you would specify:
>> >> cor.BM <- corBrownian(phy=SteninaeTree, form = ~dat$species)
>> >> and then proceed with your regression model as above.
>> >> You can also follow the example on the corClasses page:
[ http://127.0.0.1:27386/library/ape/html/corClasses.html |
>> >> http://127.0.0.1:27386/library/ape/html/corClasses.html ]
>> >> Slightly modified here:
>> >> ---
>> >> library(nlme)
>> >> library(ape)
>> >> tree <-
>> >> read.tree(text="Homo:0.21,Pongo:0.21):0.28,Macaca:0.49):0.13,Ateles:0.62):0.38,Galago:1.00);"
>> >> X <
Re: [R-sig-phylo] How to sort trait data according to tree
Thank you very much for the reply Emmanuel!
OK, yes I just tried and Iʻm surprised that this works:
> dat <- data.frame(Species = c("Homo", "Pongo", "Macaca", "Ateles",
"Galago"), X = X, Y = Y)
> cbm <- corBrownian(1, tree, form = ~Species)
> gls(Y ~ X, dat, correlation = cbm)
How does corBrownian know about Species, when it is only defined as an
element of dat, and not known in the global environment?
Anyway, thank you!
Marguerite
On Sun, May 16, 2021 at 7:03 PM Emmanuel Paradis
wrote:
> Hi Marguerite,
>
> The issue is about nlme::gls. The help page ?gls says:
>
> data: an optional data frame containing the variables named in
> ‘model’, ‘correlation’, ‘weights’, and ‘subset’. By default
> the variables are taken from the environment from which ‘gls’
> is called.
>
> So you make it work by removing "dat$" in the call to corBrownian():
>
> cbm <- corBrownian(1, tree, form = ~Species)
>
> Best,
>
> Emmanuel
>
> - Le 17 Mai 21, à 6:22, Marguerite Butler mbutler...@gmail.com a
> écrit :
>
> > Aloha all,
> >
> > Does anyone know the answer to this question - how does ape pass the
> > species name information into gls? Seems to be a global environment issue
> > when using apeʻs corBrownian and nlmeʻs gls? and a very specific form is
> > required, but why?
> >
> > Modified from ape help page for CorClasses:
> >
> > ---
> >
> > library(nlme)
> > library(ape)
> >
> > tree <- read.tree(text =
> >
> "Homo:0.21,Pongo:0.21):0.28,Macaca:0.49):0.13,Ateles:0.62):0.38,Galago:1.00);")
> > X <- c(4.09434, 3.61092, 2.37024, 2.02815, -1.46968)
> > Y <- c(4.74493, 3.33220, 3.36730, 2.89037, 2.30259)
> > dat <- data.frame(Species = c("Homo", "Pongo", "Macaca", "Ateles",
> > "Galago"), X = X, Y = Y)
> >
> > gls(Y ~ X, dat, correlation=corBrownian(1, tree.primates, form =
> ~Species))
> > ---
> >
> > The above works just fine. However, if we try to calculate corBrownian
> > separately, gls cannot understand the corBrownian object:
> > ---
> >> cbm <- corBrownian(1, tree, form = ~dat$Species)# calculate
> correlation
> >> separately
> >> gls(Y ~ X, dat, correlation = cbm) ## does not work, invalid
> type
> >> (list) for dat
> > Error in model.frame.default(formula = ~dat + Species + Y + X, data =
> list( :
> > invalid type (list) for variable 'dat'
> > ---
> >
> > If we put the species information into a vector in the global
> > environment it works. Why canʻt we use dat$Species?
> > ---
> > spp <- dat$Species # save species as vector in global environment
> > cbm <- corBrownian(1, tree, form = ~spp)# calculate correlation
> separately
> > gls(Y ~ X, dat, correlation = cbm) ## works!
> >
> > Thanks,
> >
> > Marguerite
> >
> >
> >
> > On Fri, May 14, 2021 at 10:21 PM Marguerite Butler >
> > wrote:
> >
> >> Aloha Oliver,
> >>
> >> From the cor.Brownian help page, the explanation for the form argument
> is
> >> this:
> >>
> >> a one sided formula of the form ~ t, or ~ t | g, specifying the taxa
> >> covariate t and, optionally, a grouping factor g. A covariate for this
> >> correlation structure must be character valued, with entries matching
> the
> >> tip labels in the phylogenetic tree. When a grouping factor is present
> in
> >> form, the correlation structure is assumed to apply only to observations
> >> within the same grouping level; observations with different grouping
> levels
> >> are assumed to be uncorrelated. Defaults to ~ 1, which corresponds to
> using
> >> the order of the observations in the data as a covariate, and no groups.
> >>
> >> This means that "t" should contain the species names or tip labels,
> >> spelled exactly as they are in your phylogeny. So for example if your
> data
> >> SteninaeData
> >> has a column for species names called "species" then you would specify:
> >>
> >> cor.BM <- corBrownian(phy=SteninaeTree, form = ~dat$species)
> >>
> >> and then proceed with your regression model as above.
> >>
> >>
> >> You can also follow the example on the corClasses page:
> >> http://127.0.0.1:27386/library/ape/html/corClasses.html
> >>
> >> Slightly modified here:
> >>
> >> ---
> >>
> >> library(nlme)
> >>
> >> library(ape)
> >>
> >> tree <-
> >>
> read.tree(text="Homo:0.21,Pongo:0.21):0.28,Macaca:0.49):0.13,Ateles:0.62):0.38,Galago:1.00);"
> >>
> >> X <- c(4.09434, 3.61092, 2.37024, 2.02815, -1.46968) # a vector
> >>
> >> Y <- c(4.74493, 3.33220, 3.36730, 2.89037, 2.30259) # a vector
> >>
> >> Species <- c("Homo", "Pongo", "Macaca", "Ateles", "Galago") # a vector
> >>
> >> dat <- data.frame(Species = Species, X = X, Y = Y)# make a dataframe
> >> with Species, X, Y, can also read in .csv
> >> cbm <- corBrownian(1, tree, form = ~dat$Species)
> >>
> >> m1 <- gls(Y ~ X, dat, correlation=cbm)
> >>
> >> m1
> >>
> >> ---
> >>
> >> hth,
> >>
> >> Marguerite
> >>
> >> On Fri, May 14, 2021 at 9:46 PM Oliver Betz <
> oliver.b...@uni-tuebingen.de>
> >> wrote:
> >>
> >>> Dear all:
> >>>
> >>> I am currently facing the
Re: [R-sig-phylo] How to sort trait data according to tree
Hi Marguerite,
The issue is about nlme::gls. The help page ?gls says:
data: an optional data frame containing the variables named in
‘model’, ‘correlation’, ‘weights’, and ‘subset’. By default
the variables are taken from the environment from which ‘gls’
is called.
So you make it work by removing "dat$" in the call to corBrownian():
cbm <- corBrownian(1, tree, form = ~Species)
Best,
Emmanuel
- Le 17 Mai 21, à 6:22, Marguerite Butler mbutler...@gmail.com a écrit :
> Aloha all,
>
> Does anyone know the answer to this question - how does ape pass the
> species name information into gls? Seems to be a global environment issue
> when using apeʻs corBrownian and nlmeʻs gls? and a very specific form is
> required, but why?
>
> Modified from ape help page for CorClasses:
>
> ---
>
> library(nlme)
> library(ape)
>
> tree <- read.tree(text =
> "Homo:0.21,Pongo:0.21):0.28,Macaca:0.49):0.13,Ateles:0.62):0.38,Galago:1.00);")
> X <- c(4.09434, 3.61092, 2.37024, 2.02815, -1.46968)
> Y <- c(4.74493, 3.33220, 3.36730, 2.89037, 2.30259)
> dat <- data.frame(Species = c("Homo", "Pongo", "Macaca", "Ateles",
> "Galago"), X = X, Y = Y)
>
> gls(Y ~ X, dat, correlation=corBrownian(1, tree.primates, form = ~Species))
> ---
>
> The above works just fine. However, if we try to calculate corBrownian
> separately, gls cannot understand the corBrownian object:
> ---
>> cbm <- corBrownian(1, tree, form = ~dat$Species)# calculate correlation
>> separately
>> gls(Y ~ X, dat, correlation = cbm) ## does not work, invalid type
>> (list) for dat
> Error in model.frame.default(formula = ~dat + Species + Y + X, data = list( :
> invalid type (list) for variable 'dat'
> ---
>
> If we put the species information into a vector in the global
> environment it works. Why canʻt we use dat$Species?
> ---
> spp <- dat$Species # save species as vector in global environment
> cbm <- corBrownian(1, tree, form = ~spp)# calculate correlation separately
> gls(Y ~ X, dat, correlation = cbm) ## works!
>
> Thanks,
>
> Marguerite
>
>
>
> On Fri, May 14, 2021 at 10:21 PM Marguerite Butler
> wrote:
>
>> Aloha Oliver,
>>
>> From the cor.Brownian help page, the explanation for the form argument is
>> this:
>>
>> a one sided formula of the form ~ t, or ~ t | g, specifying the taxa
>> covariate t and, optionally, a grouping factor g. A covariate for this
>> correlation structure must be character valued, with entries matching the
>> tip labels in the phylogenetic tree. When a grouping factor is present in
>> form, the correlation structure is assumed to apply only to observations
>> within the same grouping level; observations with different grouping levels
>> are assumed to be uncorrelated. Defaults to ~ 1, which corresponds to using
>> the order of the observations in the data as a covariate, and no groups.
>>
>> This means that "t" should contain the species names or tip labels,
>> spelled exactly as they are in your phylogeny. So for example if your data
>> SteninaeData
>> has a column for species names called "species" then you would specify:
>>
>> cor.BM <- corBrownian(phy=SteninaeTree, form = ~dat$species)
>>
>> and then proceed with your regression model as above.
>>
>>
>> You can also follow the example on the corClasses page:
>> http://127.0.0.1:27386/library/ape/html/corClasses.html
>>
>> Slightly modified here:
>>
>> ---
>>
>> library(nlme)
>>
>> library(ape)
>>
>> tree <-
>> read.tree(text="Homo:0.21,Pongo:0.21):0.28,Macaca:0.49):0.13,Ateles:0.62):0.38,Galago:1.00);"
>>
>> X <- c(4.09434, 3.61092, 2.37024, 2.02815, -1.46968) # a vector
>>
>> Y <- c(4.74493, 3.33220, 3.36730, 2.89037, 2.30259) # a vector
>>
>> Species <- c("Homo", "Pongo", "Macaca", "Ateles", "Galago") # a vector
>>
>> dat <- data.frame(Species = Species, X = X, Y = Y)# make a dataframe
>> with Species, X, Y, can also read in .csv
>> cbm <- corBrownian(1, tree, form = ~dat$Species)
>>
>> m1 <- gls(Y ~ X, dat, correlation=cbm)
>>
>> m1
>>
>> ---
>>
>> hth,
>>
>> Marguerite
>>
>> On Fri, May 14, 2021 at 9:46 PM Oliver Betz
>> wrote:
>>
>>> Dear all:
>>>
>>> I am currently facing the following problem:
>>>
>>> Unsing ape, nlme por phylolm for PGLS I was wondering how to sort my
>>> trait data (the ones in my csv file) according to the tree, so that
>>> both are in the same order. I learned how to check whether the data &
>>> the tree coincide in both number of species and names, but I do not
>>> nderstand how to perform the mentioned sorting task.
>>>
>>> Once I am running the PGLS commands such as
>>> cor.BM <- corBrownian(phy=SteninaeTree)
>>> pgls <- gls(LOG_rel_Attachment_force_smooth ~
>>> LOG_rel_Anzahl_Hafthaare_4.Vordertarsus, correlation = cor.BM, data =
>>> SteninaeData, method = "ML")"
>>>
>>> I regularly receive the follwing warning note:
>>> "In Initialize.corPhyl(X[[i]], ...) :
>>> No covariate specified, species will be taken as ordered in the data
>>> frame. To
Re: [R-sig-phylo] How to sort trait data according to tree
Aloha all,
Does anyone know the answer to this question - how does ape pass the
species name information into gls? Seems to be a global environment issue
when using apeʻs corBrownian and nlmeʻs gls? and a very specific form is
required, but why?
Modified from ape help page for CorClasses:
---
library(nlme)
library(ape)
tree <- read.tree(text =
"Homo:0.21,Pongo:0.21):0.28,Macaca:0.49):0.13,Ateles:0.62):0.38,Galago:1.00);")
X <- c(4.09434, 3.61092, 2.37024, 2.02815, -1.46968)
Y <- c(4.74493, 3.33220, 3.36730, 2.89037, 2.30259)
dat <- data.frame(Species = c("Homo", "Pongo", "Macaca", "Ateles",
"Galago"), X = X, Y = Y)
gls(Y ~ X, dat, correlation=corBrownian(1, tree.primates, form = ~Species))
---
The above works just fine. However, if we try to calculate corBrownian
separately, gls cannot understand the corBrownian object:
---
> cbm <- corBrownian(1, tree, form = ~dat$Species)# calculate correlation
> separately
> gls(Y ~ X, dat, correlation = cbm) ## does not work, invalid type
> (list) for dat
Error in model.frame.default(formula = ~dat + Species + Y + X, data = list( :
invalid type (list) for variable 'dat'
---
If we put the species information into a vector in the global
environment it works. Why canʻt we use dat$Species?
---
spp <- dat$Species # save species as vector in global environment
cbm <- corBrownian(1, tree, form = ~spp)# calculate correlation separately
gls(Y ~ X, dat, correlation = cbm) ## works!
Thanks,
Marguerite
On Fri, May 14, 2021 at 10:21 PM Marguerite Butler
wrote:
> Aloha Oliver,
>
> From the cor.Brownian help page, the explanation for the form argument is
> this:
>
> a one sided formula of the form ~ t, or ~ t | g, specifying the taxa
> covariate t and, optionally, a grouping factor g. A covariate for this
> correlation structure must be character valued, with entries matching the
> tip labels in the phylogenetic tree. When a grouping factor is present in
> form, the correlation structure is assumed to apply only to observations
> within the same grouping level; observations with different grouping levels
> are assumed to be uncorrelated. Defaults to ~ 1, which corresponds to using
> the order of the observations in the data as a covariate, and no groups.
>
> This means that "t" should contain the species names or tip labels,
> spelled exactly as they are in your phylogeny. So for example if your data
> SteninaeData
> has a column for species names called "species" then you would specify:
>
> cor.BM <- corBrownian(phy=SteninaeTree, form = ~dat$species)
>
> and then proceed with your regression model as above.
>
>
> You can also follow the example on the corClasses page:
> http://127.0.0.1:27386/library/ape/html/corClasses.html
>
> Slightly modified here:
>
> ---
>
> library(nlme)
>
> library(ape)
>
> tree <-
> read.tree(text="Homo:0.21,Pongo:0.21):0.28,Macaca:0.49):0.13,Ateles:0.62):0.38,Galago:1.00);"
>
> X <- c(4.09434, 3.61092, 2.37024, 2.02815, -1.46968) # a vector
>
> Y <- c(4.74493, 3.33220, 3.36730, 2.89037, 2.30259) # a vector
>
> Species <- c("Homo", "Pongo", "Macaca", "Ateles", "Galago") # a vector
>
> dat <- data.frame(Species = Species, X = X, Y = Y)# make a dataframe
> with Species, X, Y, can also read in .csv
> cbm <- corBrownian(1, tree, form = ~dat$Species)
>
> m1 <- gls(Y ~ X, dat, correlation=cbm)
>
> m1
>
> ---
>
> hth,
>
> Marguerite
>
> On Fri, May 14, 2021 at 9:46 PM Oliver Betz
> wrote:
>
>> Dear all:
>>
>> I am currently facing the following problem:
>>
>> Unsing ape, nlme por phylolm for PGLS I was wondering how to sort my
>> trait data (the ones in my csv file) according to the tree, so that
>> both are in the same order. I learned how to check whether the data &
>> the tree coincide in both number of species and names, but I do not
>> nderstand how to perform the mentioned sorting task.
>>
>> Once I am running the PGLS commands such as
>> cor.BM <- corBrownian(phy=SteninaeTree)
>> pgls <- gls(LOG_rel_Attachment_force_smooth ~
>> LOG_rel_Anzahl_Hafthaare_4.Vordertarsus, correlation = cor.BM, data =
>> SteninaeData, method = "ML")"
>>
>> I regularly receive the follwing warning note:
>> "In Initialize.corPhyl(X[[i]], ...) :
>> No covariate specified, species will be taken as ordered in the data
>> frame. To avoid this message, specify a covariate containing the
>> species names with the 'form' argument."
>>
>> Since this is just a warning message, I usually was going on with the
>> "summary(pgls)" command, where I was getting my results.
>>
>>
>> Anyhow, I was wondering whether it is OK to just ignore this warning
>> or whether it means that I will have to sort the sequence of the
>> sepcies trait data in my data file (csv) exactly according to the
>> sequence of the species as they occur at the tips of my tree file.
>> Since the spelling of the species names is exactly the same in both
>> the tree file and the data file, I thought that such sorting is
>> automatically done by the algori
Re: [R-sig-phylo] How to sort trait data according to tree
Aloha Oliver,
>From the cor.Brownian help page, the explanation for the form argument is
this:
a one sided formula of the form ~ t, or ~ t | g, specifying the taxa
covariate t and, optionally, a grouping factor g. A covariate for this
correlation structure must be character valued, with entries matching the
tip labels in the phylogenetic tree. When a grouping factor is present in
form, the correlation structure is assumed to apply only to observations
within the same grouping level; observations with different grouping levels
are assumed to be uncorrelated. Defaults to ~ 1, which corresponds to using
the order of the observations in the data as a covariate, and no groups.
This means that "t" should contain the species names or tip labels, spelled
exactly as they are in your phylogeny. So for example if your data
SteninaeData
has a column for species names called "species" then you would specify:
cor.BM <- corBrownian(phy=SteninaeTree, form = ~dat$species)
and then proceed with your regression model as above.
You can also follow the example on the corClasses page:
http://127.0.0.1:27386/library/ape/html/corClasses.html
Slightly modified here:
---
library(nlme)
library(ape)
tree <-
read.tree(text="Homo:0.21,Pongo:0.21):0.28,Macaca:0.49):0.13,Ateles:0.62):0.38,Galago:1.00);"
X <- c(4.09434, 3.61092, 2.37024, 2.02815, -1.46968) # a vector
Y <- c(4.74493, 3.33220, 3.36730, 2.89037, 2.30259) # a vector
Species <- c("Homo", "Pongo", "Macaca", "Ateles", "Galago") # a vector
dat <- data.frame(Species = Species, X = X, Y = Y)# make a dataframe
with Species, X, Y, can also read in .csv
cbm <- corBrownian(1, tree, form = ~dat$Species)
m1 <- gls(Y ~ X, dat, correlation=cbm)
m1
---
hth,
Marguerite
On Fri, May 14, 2021 at 9:46 PM Oliver Betz
wrote:
> Dear all:
>
> I am currently facing the following problem:
>
> Unsing ape, nlme por phylolm for PGLS I was wondering how to sort my
> trait data (the ones in my csv file) according to the tree, so that
> both are in the same order. I learned how to check whether the data &
> the tree coincide in both number of species and names, but I do not
> nderstand how to perform the mentioned sorting task.
>
> Once I am running the PGLS commands such as
> cor.BM <- corBrownian(phy=SteninaeTree)
> pgls <- gls(LOG_rel_Attachment_force_smooth ~
> LOG_rel_Anzahl_Hafthaare_4.Vordertarsus, correlation = cor.BM, data =
> SteninaeData, method = "ML")"
>
> I regularly receive the follwing warning note:
> "In Initialize.corPhyl(X[[i]], ...) :
> No covariate specified, species will be taken as ordered in the data
> frame. To avoid this message, specify a covariate containing the
> species names with the 'form' argument."
>
> Since this is just a warning message, I usually was going on with the
> "summary(pgls)" command, where I was getting my results.
>
>
> Anyhow, I was wondering whether it is OK to just ignore this warning
> or whether it means that I will have to sort the sequence of the
> sepcies trait data in my data file (csv) exactly according to the
> sequence of the species as they occur at the tips of my tree file.
> Since the spelling of the species names is exactly the same in both
> the tree file and the data file, I thought that such sorting is
> automatically done by the algorithm?
>
> I will be glad if you have any hint how ro resove this.
>
> My best wishes,
>
> Oliver Betz
> (University of Tübingen, Gernmany)
>
> ___
> R-sig-phylo mailing list - R-sig-phylo@r-project.org
> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
> Searchable archive at
> http://www.mail-archive.com/r-sig-phylo@r-project.org/
>
--
Marguerite A. Butler
Professor
Department of Biology
2538 McCarthy Mall, Edmondson Hall 216
Honolulu, HI 96822
Office: 808-956-4713
Dept: 808-956-8617
Lab: 808-956-5867
FAX: 808-956-4745
http://butlerlab.org
http://manoa.hawaii.edu/biology/people/marguerite-butler
http://www2.hawaii.edu/~mbutler
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[R-sig-phylo] How to sort trait data according to tree
Dear all: I am currently facing the following problem: Unsing ape, nlme por phylolm for PGLS I was wondering how to sort my trait data (the ones in my csv file) according to the tree, so that both are in the same order. I learned how to check whether the data & the tree coincide in both number of species and names, but I do not nderstand how to perform the mentioned sorting task. Once I am running the PGLS commands such as cor.BM <- corBrownian(phy=SteninaeTree) pgls <- gls(LOG_rel_Attachment_force_smooth ~ LOG_rel_Anzahl_Hafthaare_4.Vordertarsus, correlation = cor.BM, data = SteninaeData, method = "ML")" I regularly receive the follwing warning note: "In Initialize.corPhyl(X[[i]], ...) : No covariate specified, species will be taken as ordered in the data frame. To avoid this message, specify a covariate containing the species names with the 'form' argument." Since this is just a warning message, I usually was going on with the "summary(pgls)" command, where I was getting my results. Anyhow, I was wondering whether it is OK to just ignore this warning or whether it means that I will have to sort the sequence of the sepcies trait data in my data file (csv) exactly according to the sequence of the species as they occur at the tips of my tree file. Since the spelling of the species names is exactly the same in both the tree file and the data file, I thought that such sorting is automatically done by the algorithm? I will be glad if you have any hint how ro resove this. My best wishes, Oliver Betz (University of Tübingen, Gernmany) ___ R-sig-phylo mailing list - R-sig-phylo@r-project.org https://stat.ethz.ch/mailman/listinfo/r-sig-phylo Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/
