[ESS] A discrepancy between elpa version and ubuntu/mint version
Hi all, I think I've found a discrepancy in file /home/user/.emacs.d/elpa/ess-20221108.1714/ess-r-mode.el at lines 264-270 I can find the variable ess-r-mode-map while in /usr/share/emacs/site-lisp/elpa-src/ess-18.10.2//ess-r-mode.el there's not such a variable. I realize this because on two identical systems (Mint 20.03, emacs 26.3) there were two different versions installed PS My previous problems with lintr were due to ~/.cache/R/lintr not writable for some obscure reasons. Thanks Rodney for your advice. __ ESS-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/ess-help
Re: [R] A question related to extracting peptides from indels for mouse
Probably not here. Better here: https://bioconductor.org/help/ -- Bert On Thu, Nov 17, 2022 at 6:43 AM Li, Aiguo (NIH/NCI) [E] via R-help < r-help@r-project.org> wrote: > Dear all, > > I need to extract peptides from a long list of indels of mouse for > neoantigen analysis. Does anyone know a tool that will do it? > > Thanks, > > Anna > > [[alternative HTML version deleted]] > > __ > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide > http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
[R] A question related to extracting peptides from indels for mouse
Dear all, I need to extract peptides from a long list of indels of mouse for neoantigen analysis. Does anyone know a tool that will do it? Thanks, Anna [[alternative HTML version deleted]] __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Rare behaviour for nlme::reStruct example and question about ?lmeObject
Thank you Martin,
Regarding my question about `terms`, I meant the `terms` component of
the `lme` output. For example, for
fm1 <- lme(distance ~ age, data = Orthodont)
I can see through str(fm1), the next:
$ terms :Classes 'terms', 'formula' language distance ~ age
.. ..- attr(*, "variables")= language list(distance, age)
.. ..- attr(*, "factors")= int [1:2, 1] 0 1
.. .. ..- attr(*, "dimnames")=List of 2
.. .. .. ..$ : chr [1:2] "distance" "age"
.. .. .. ..$ : chr "age"
.. ..- attr(*, "term.labels")= chr "age"
.. ..- attr(*, "order")= int 1
.. ..- attr(*, "intercept")= int 1
.. ..- attr(*, "response")= int 1
.. ..- attr(*, ".Environment")=
.. ..- attr(*, "predvars")= language list(distance, age)
.. ..- attr(*, "dataClasses")= Named chr [1:2] "numeric" "numeric"
.. .. ..- attr(*, "names")= chr [1:2] "distance" "age"
However, there is no paragraph for this component among those in
?lmeObject (in the Value section) as there is for fixDF, apVar, call,
etc.. If not needed, I assume the explanation would be that `terms` does
not need to be included in a legitimate ´"lme"´ object'.
Kind regards,
Iago
On 17/11/2022 09:16, Martin Maechler wrote:
Andrew Simmons
on Tue, 15 Nov 2022 18:01:55 -0500 writes:
> This seems to be a bug. I tried creating this function in the global
> environment:
> str.pdMat <- function (object, ...)
> {
> if (nlme::isInitialized(object)) {
> NextMethod()
> }
> else {
> cat(" Uninitialized positive definite matrix structure of class ",
> class(object)[1], ".\n", sep = "")
> }
> }
Thank you, Iago, for the question and Andrew for your proposal.
Yes, I agree that something like the above -- which is derived from the
print.pdMat method -- should be added to nlme and will do this
myself.
> and the code you sent works:
>
> > library(nlme)
> > rs1 <- reStruct(list(Dog = ~day, Side = ~1), data = Pixel)
> > rs1
> Uninitialized random effects structure
> > str(rs1)
> List of 2
> $ Side: Uninitialized positive definite matrix structure of class
pdLogChol.
> $ Dog : Uninitialized positive definite matrix structure of class
pdLogChol.
> - attr(*, "settings")= int [1:5] 0 1 0 4 4
> - attr(*, "class")= chr "reStruct"
In addition, Iago, asked
> > > In addition to that I would like to ask if shouldn't be `terms`
> > > documented in `?lmeObject`.
I probably have misunderstood the question completely (?)
I've now searched through ?lmeObject
which was written under the assumption that the reader has
already read (parts of) the ?lme help page.
Now "terms" only appears in ?lmeObject in this paragraph
fixDF: a list with components ‘X’ and ‘terms’ specifying the
denominator degrees of freedom for, respectively, t-tests for
the individual fixed effects and F-tests for the
fixed-effects terms in the models.
and I don't think that there needs to be more explanation.
(??)
Martin
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Rare behaviour for nlme::reStruct example and question about ?lmeObject
> Martin Maechler
> on Thu, 17 Nov 2022 09:16:04 +0100 writes:
> Andrew Simmons
> on Tue, 15 Nov 2022 18:01:55 -0500 writes:
>> This seems to be a bug. I tried creating this function in the global
>> environment:
>> str.pdMat <- function (object, ...)
>> {
>> if (nlme::isInitialized(object)) {
>> NextMethod()
>> }
>> else {
>> cat(" Uninitialized positive definite matrix structure of class ",
>> class(object)[1], ".\n", sep = "")
>> }
>> }
> Thank you, Iago, for the question and Andrew for your proposal.
> Yes, I agree that something like the above -- which is derived from the
> print.pdMat method -- should be added to nlme and will do this
> myself.
My current working proposal gives this:
> (rs <- reStruct(list(Dog = ~day, Side = ~1), data = Pixel))
Uninitialized random effects structure
> str(rs)
List of 2
$ Side:Uninitialized 'pdLogChol', 'pdSymm', 'pdMat': ~1
$ Dog :Uninitialized 'pdLogChol', 'pdSymm', 'pdMat': ~day
- attr(*, "settings")= int [1:5] 0 1 0 4 4
- attr(*, "class")= chr "reStruct"
>
Martin
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
Re: [R] Rare behaviour for nlme::reStruct example and question about ?lmeObject
> Andrew Simmons
> on Tue, 15 Nov 2022 18:01:55 -0500 writes:
> This seems to be a bug. I tried creating this function in the global
> environment:
> str.pdMat <- function (object, ...)
> {
> if (nlme::isInitialized(object)) {
> NextMethod()
> }
> else {
> cat(" Uninitialized positive definite matrix structure of class ",
> class(object)[1], ".\n", sep = "")
> }
> }
Thank you, Iago, for the question and Andrew for your proposal.
Yes, I agree that something like the above -- which is derived from the
print.pdMat method -- should be added to nlme and will do this
myself.
> and the code you sent works:
>
> > library(nlme)
> > rs1 <- reStruct(list(Dog = ~day, Side = ~1), data = Pixel)
> > rs1
> Uninitialized random effects structure
> > str(rs1)
> List of 2
> $ Side: Uninitialized positive definite matrix structure of class
pdLogChol.
> $ Dog : Uninitialized positive definite matrix structure of class
pdLogChol.
> - attr(*, "settings")= int [1:5] 0 1 0 4 4
> - attr(*, "class")= chr "reStruct"
In addition, Iago, asked
> > > In addition to that I would like to ask if shouldn't be `terms`
> > > documented in `?lmeObject`.
I probably have misunderstood the question completely (?)
I've now searched through ?lmeObject
which was written under the assumption that the reader has
already read (parts of) the ?lme help page.
Now "terms" only appears in ?lmeObject in this paragraph
fixDF: a list with components ‘X’ and ‘terms’ specifying the
denominator degrees of freedom for, respectively, t-tests for
the individual fixed effects and F-tests for the
fixed-effects terms in the models.
and I don't think that there needs to be more explanation.
(??)
Martin
__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.
