Re: [R] Problem launching Rcmdr

[Peter Dalgaard]

Any chance that a virus checker is interfering?

-pd

> On 10 Mar 2020, at 23:43 , Fox, John  wrote:
> 
> Dear Brian,
> 
> (Please keep r-help in the loop so that if someone else has this problem 
> they'll have something to refer to.)
> 
> Your session at start-up seems completely clean, so I'm at a loss to 
> understand what the problem is. I, and I assume very many other people, are 
> using the Rcmdr with essentially the same Windows setup. What's particularly 
> hard for me to understand is that you're able to start the Rcmdr in a second 
> R session. Does the first R session have to remain open for this to work?
> 
> A next step is to reinstall packages, starting with the Rcmdr package, if you 
> haven't already tried that, and eventually to reinstall R, including deleting 
> the R package library. BTW, I usually prefer to install R in c:\R\ rather 
> than under Program Files so that the system library is used for packages that 
> I subsequently install, although it should work perfectly fine to install 
> packages into a personal library.
> 
> Best,
> John
> 
>> -Original Message-
>> From: Brian Grossman 
>> Sent: Tuesday, March 10, 2020 5:07 PM
>> To: Fox, John 
>> Subject: Re: [R] Problem launching Rcmdr
>> 
>> John,
>> 
>> Thanks for the reply. Here is the output from running sessionInfo() right 
>> after
>> opening R.
>> 
>>> sessionInfo()
>> R version 3.6.2 (2019-12-12)
>> Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 x64
>> (build 18362)
>> 
>> Matrix products: default
>> 
>> locale:
>> [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United
>> States.1252 [3] LC_MONETARY=English_United States.1252 [4]
>> LC_NUMERIC=C [5] LC_TIME=English_United States.1252
>> 
>> attached base packages:
>> [1] stats graphics  grDevices utils datasets  methods   base
>> 
>> loaded via a namespace (and not attached):
>> [1] compiler_3.6.2
>> 
>> 
>> Brian
>> 
>> On Tue, Mar 10, 2020 at 8:46 AM Fox, John >  > wrote:
>> 
>> 
>>  Dear Brian,
>> 
>>  Normally I'd expect that a workspace saved from a previous session
>> and loaded at the start of the current session would cause this kind of
>> anomalous behaviour, but that doesn't explain why the Rcmdr starts up
>> properly in a second (concurrent?) session, nor why it doesn't start up
>> properly when R is run with the --vanilla switch.
>> 
>>  Can you report the result of sessionInfo() at the start of a session?
>> 
>>  If all else fails, you could try uninstalling and reinstalling R and
>> packages.
>> 
>>  Best,
>>   John
>> 
>>-
>>John Fox, Professor Emeritus
>>McMaster University
>>Hamilton, Ontario, Canada
>>Web: http::/socserv.mcmaster.ca/jfox
>> 
>> 
>>  > On Mar 9, 2020, at 3:25 PM, Brian Grossman
>> mailto:gross...@umich.edu> > wrote:
>>  >
>>  > I'm having a problem with launching Rcmdr. When I try to launch it
>> the
>>  > first time through R using the command library(Rcmdr) it will go
>> through
>>  > the process of launching and get to the point where it says
>>  >
>>  > "Registered S3 methods overwritten by 'lme4':
>>  >  method  from
>>  >  cooks.distance.influence.merMod car
>>  >  influence.merModcar
>>  >  dfbeta.influence.merMod car
>>  >  dfbetas.influence.merModcar
>>  > lattice theme set by effectsTheme()
>>  > See ?effectsTheme for details."
>>  >
>>  > and then it just hangs there and never launches Rcmdr. If you
>> launch
>>  > another instance of R and run the same command it will complete
>> and launch
>>  > Rcmdr successfully. I have tried launching R with R.exe --vanilla with
>> the
>>  > same results.
>>  >
>>  > The system information is Windows 10 version 1903, i5 8500
>> processor, 8GB
>>  > RAM, 256Gb  SSD. R version 3.6.2 Platform: x86_64-w64-
>> mingw32/x64 (64-bit)
>>  >
>>  > Hopefully I haven't left out any important information. Thank you
>> for any
>>  > suggestions.
>>  >
>>  >   [[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-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.

-- 
Peter Dalgaard, Profess

Re: [R] Problem launching Rcmdr

[Pfaff, Bernhard Dr.]

Good catch, Peter; Cylance might be the culprit - at least I encountered 
problems by compiling C++ sources and/or building packages with interfaced 
routines and here a memory checker kicked in.
Maybe something akin is happening by launching Rcmdr (tcl/tk)?

-Ursprüngliche Nachricht-
Von: R-help  Im Auftrag von Peter Dalgaard
Gesendet: Mittwoch, 11. März 2020 10:29
An: Fox, John 
Cc: r-help@r-project.org
Betreff: [EXT] Re: [R] Problem launching Rcmdr

Any chance that a virus checker is interfering?

-pd

> On 10 Mar 2020, at 23:43 , Fox, John  wrote:
> 
> Dear Brian,
> 
> (Please keep r-help in the loop so that if someone else has this 
> problem they'll have something to refer to.)
> 
> Your session at start-up seems completely clean, so I'm at a loss to 
> understand what the problem is. I, and I assume very many other people, are 
> using the Rcmdr with essentially the same Windows setup. What's particularly 
> hard for me to understand is that you're able to start the Rcmdr in a second 
> R session. Does the first R session have to remain open for this to work?
> 
> A next step is to reinstall packages, starting with the Rcmdr package, if you 
> haven't already tried that, and eventually to reinstall R, including deleting 
> the R package library. BTW, I usually prefer to install R in c:\R\ rather 
> than under Program Files so that the system library is used for packages that 
> I subsequently install, although it should work perfectly fine to install 
> packages into a personal library.
> 
> Best,
> John
> 
>> -Original Message-
>> From: Brian Grossman 
>> Sent: Tuesday, March 10, 2020 5:07 PM
>> To: Fox, John 
>> Subject: Re: [R] Problem launching Rcmdr
>> 
>> John,
>> 
>> Thanks for the reply. Here is the output from running sessionInfo() 
>> right after opening R.
>> 
>>> sessionInfo()
>> R version 3.6.2 (2019-12-12)
>> Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10 
>> x64 (build 18362)
>> 
>> Matrix products: default
>> 
>> locale:
>> [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United
>> States.1252 [3] LC_MONETARY=English_United States.1252 [4] 
>> LC_NUMERIC=C [5] LC_TIME=English_United States.1252
>> 
>> attached base packages:
>> [1] stats graphics  grDevices utils datasets  methods   base
>> 
>> loaded via a namespace (and not attached):
>> [1] compiler_3.6.2
>> 
>> 
>> Brian
>> 
>> On Tue, Mar 10, 2020 at 8:46 AM Fox, John >  > wrote:
>> 
>> 
>>  Dear Brian,
>> 
>>  Normally I'd expect that a workspace saved from a previous session 
>> and loaded at the start of the current session would cause this kind 
>> of anomalous behaviour, but that doesn't explain why the Rcmdr starts 
>> up properly in a second (concurrent?) session, nor why it doesn't 
>> start up properly when R is run with the --vanilla switch.
>> 
>>  Can you report the result of sessionInfo() at the start of a session?
>> 
>>  If all else fails, you could try uninstalling and reinstalling R and 
>> packages.
>> 
>>  Best,
>>   John
>> 
>>-
>>John Fox, Professor Emeritus
>>McMaster University
>>Hamilton, Ontario, Canada
>>Web: http::/socserv.mcmaster.ca/jfox 
>> > .ca_jfox&d=DwIFAg&c=MWFkEADu9ctt4KEmLIuwsQ&r=OhbxYoJKYsmfC2WjzTKFj7Fw
>> 1qyrbJIFo5BfgVqACaM&m=385Kfv02lZxykzhYHnbjRxxzMBywESQnuptbnhDtfTc&s=a
>> eoHPeyoWEbF1Lq409kfGNS_AauUuCunIr_B_-mNx68&e= >
>> 
>>  > On Mar 9, 2020, at 3:25 PM, Brian Grossman >  > wrote:
>>  >
>>  > I'm having a problem with launching Rcmdr. When I try to launch it 
>> the
>>  > first time through R using the command library(Rcmdr) it will go 
>> through
>>  > the process of launching and get to the point where it says
>>  >
>>  > "Registered S3 methods overwritten by 'lme4':
>>  >  method  from
>>  >  cooks.distance.influence.merMod car
>>  >  influence.merModcar
>>  >  dfbeta.influence.merMod car
>>  >  dfbetas.influence.merModcar
>>  > lattice theme set by effectsTheme()
>>  > See ?effectsTheme for details."
>>  >
>>  > and then it just hangs there and never launches Rcmdr. If you 
>> launch
>>  > another instance of R and run the same command it will complete 
>> and launch
>>  > Rcmdr successfully. I have tried launching R with R.exe --vanilla 
>> with the
>>  > same results.
>>  >
>>  > The system information is Windows 10 version 1903, i5 8500 
>> processor, 8GB
>>  > RAM, 256Gb  SSD. R version 3.6.2 Platform: x86_64-w64-
>> mingw32/x64 (64-bit)
>>  >
>>  > Hopefully I haven't left out any important information. Thank you 
>> for any
>>  > suggestions.
>>  >
>>  >   [[alternative HTML version deleted]]
>>  >
>>  > 

[R] Installing Packages

[Jeff Reichman]

R-Help

 

Recently I've started receiving the following message when updating packages
- "Do you want to install from sources the packages which need compilation."
I generally click "Yes," but what is this asking me. That is it appears to
be re-compiling certain packages? Why?

 

RStudio version: 1.2.5033

R version: 3.6.3

 

 

Sincerely

 

Jeff Reichman

 


[[alternative HTML version deleted]]

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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Installing Packages

[Wang Jiefei]

Hi,

This means that the package you were trying to install does not have a
compiled version stored on the server. Sometimes you would not see the
question because the server has compiled the package for you, but sometimes
it doesn't.

Cheers,
Jiefei



On Wed, Mar 11, 2020 at 10:46 AM Jeff Reichman 
wrote:

> R-Help
>
>
>
> Recently I've started receiving the following message when updating
> packages
> - "Do you want to install from sources the packages which need
> compilation."
> I generally click "Yes," but what is this asking me. That is it appears to
> be re-compiling certain packages? Why?
>
>
>
> RStudio version: 1.2.5033
>
> R version: 3.6.3
>
>
>
>
>
> Sincerely
>
>
>
> Jeff Reichman
>
>
>
>
> [[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]]

__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Installing Packages

[Jeff Newmiller]

Because pre-compiled (binary) versions of packages are getting built slower 
than the introduction of new versions of the packages are getting approved.

On March 11, 2020 7:46:22 AM PDT, Jeff Reichman  wrote:
>R-Help
>
> 
>
>Recently I've started receiving the following message when updating
>packages
>- "Do you want to install from sources the packages which need
>compilation."
>I generally click "Yes," but what is this asking me. That is it appears
>to
>be re-compiling certain packages? Why?
>
> 
>
>RStudio version: 1.2.5033
>
>R version: 3.6.3
>
> 
>
> 
>
>Sincerely
>
> 
>
>Jeff Reichman
>
> 
>
>
>   [[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.

-- 
Sent from my phone. Please excuse my brevity.

__
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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Installing Packages

[Duncan Murdoch]

On 11/03/2020 7:46 a.m., Jeff Reichman wrote:

R-Help

  


Recently I've started receiving the following message when updating packages
- "Do you want to install from sources the packages which need compilation."
I generally click "Yes," but what is this asking me. That is it appears to
be re-compiling certain packages? Why?



As the others answered:  that's because compiled versions aren't 
available on the server yet.


What they didn't say is why you might want to say "no".  You would say 
that if you expect the compile on your own system to fail, perhaps 
because you don't have compilers or special libraries installed.  R can 
install packages whose source is all in R, but needs external tools to 
install packages that incorporate other languages like C, C++ and 
Fortran.  Even if you have those compilers, some packages will need to 
link to libraries outside of R.


If you say "no", then R will look for an older compiled version of the 
package and install that.  This might cause trouble if some other 
package depends on the latest version of its dependencies:  you won't be 
able to install the latest version of that package either.


I'd recommend trying with "yes", then trying again with "no" if there 
were any install failures.


Duncan Murdoch

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Re: [R] Problem launching Rcmdr

[Fox, John]

Dear Bernhard, Peter, and Brian,

Thanks, Peter, for the suggestion. If you're right then the problem is with 
tcltk more generally and not directly with the Rcmdr package.

Brian: That's easily checked and might clarify what's going on: Load the tcltk 
package via library(tcltk), and then try the following example from 
?TkWidgetcmds:

 snip --

tt <- tktoplevel()
tkpack(txt.w <- tktext(tt))
tkinsert(txt.w, "0.0", "plot(1:10)")
eval.txt <- function()
   eval(parse(text = tclvalue(tkget(txt.w, "0.0", "end"
tkpack(but.w <- tkbutton(tt, text = "Submit", command = eval.txt))

## Try pressing the button, edit the text and when finished:

tkdestroy(tt)

 snip --

Best,
 John


> -Original Message-
> From: Pfaff, Bernhard Dr. 
> Sent: Wednesday, March 11, 2020 9:18 AM
> To: Peter Dalgaard ; Fox, John 
> Cc: r-help@r-project.org
> Subject: AW: Re: [R] Problem launching Rcmdr
> 
> Good catch, Peter; Cylance might be the culprit - at least I encountered
> problems by compiling C++ sources and/or building packages with interfaced
> routines and here a memory checker kicked in.
> Maybe something akin is happening by launching Rcmdr (tcl/tk)?
> 
> -Ursprüngliche Nachricht-
> Von: R-help  Im Auftrag von Peter Dalgaard
> Gesendet: Mittwoch, 11. März 2020 10:29
> An: Fox, John 
> Cc: r-help@r-project.org
> Betreff: [EXT] Re: [R] Problem launching Rcmdr
> 
> Any chance that a virus checker is interfering?
> 
> -pd
> 
> > On 10 Mar 2020, at 23:43 , Fox, John  wrote:
> >
> > Dear Brian,
> >
> > (Please keep r-help in the loop so that if someone else has this
> > problem they'll have something to refer to.)
> >
> > Your session at start-up seems completely clean, so I'm at a loss to
> understand what the problem is. I, and I assume very many other people,
> are using the Rcmdr with essentially the same Windows setup. What's
> particularly hard for me to understand is that you're able to start the Rcmdr 
> in
> a second R session. Does the first R session have to remain open for this to
> work?
> >
> > A next step is to reinstall packages, starting with the Rcmdr package, if 
> > you
> haven't already tried that, and eventually to reinstall R, including deleting 
> the
> R package library. BTW, I usually prefer to install R in c:\R\ rather than 
> under
> Program Files so that the system library is used for packages that I
> subsequently install, although it should work perfectly fine to install 
> packages
> into a personal library.
> >
> > Best,
> > John
> >
> >> -Original Message-
> >> From: Brian Grossman 
> >> Sent: Tuesday, March 10, 2020 5:07 PM
> >> To: Fox, John 
> >> Subject: Re: [R] Problem launching Rcmdr
> >>
> >> John,
> >>
> >> Thanks for the reply. Here is the output from running sessionInfo()
> >> right after opening R.
> >>
> >>> sessionInfo()
> >> R version 3.6.2 (2019-12-12)
> >> Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10
> >> x64 (build 18362)
> >>
> >> Matrix products: default
> >>
> >> locale:
> >> [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United
> >> States.1252 [3] LC_MONETARY=English_United States.1252 [4]
> >> LC_NUMERIC=C [5] LC_TIME=English_United States.1252
> >>
> >> attached base packages:
> >> [1] stats graphics  grDevices utils datasets  methods   base
> >>
> >> loaded via a namespace (and not attached):
> >> [1] compiler_3.6.2
> >>
> >>
> >> Brian
> >>
> >> On Tue, Mar 10, 2020 at 8:46 AM Fox, John  >>  > wrote:
> >>
> >>
> >>Dear Brian,
> >>
> >>Normally I'd expect that a workspace saved from a previous session
> >> and loaded at the start of the current session would cause this kind
> >> of anomalous behaviour, but that doesn't explain why the Rcmdr starts
> >> up properly in a second (concurrent?) session, nor why it doesn't
> >> start up properly when R is run with the --vanilla switch.
> >>
> >>Can you report the result of sessionInfo() at the start of a session?
> >>
> >>If all else fails, you could try uninstalling and reinstalling R and
> >> packages.
> >>
> >>Best,
> >> John
> >>
> >>  -
> >>  John Fox, Professor Emeritus
> >>  McMaster University
> >>  Hamilton, Ontario, Canada
> >>  Web: http::/socserv.mcmaster.ca/jfox
> >>  3A__socserv.mcmaster
> >>
> .ca_jfox&d=DwIFAg&c=MWFkEADu9ctt4KEmLIuwsQ&r=OhbxYoJKYsmfC2Wj
> zTKFj7Fw
> >>
> 1qyrbJIFo5BfgVqACaM&m=385Kfv02lZxykzhYHnbjRxxzMBywESQnuptbnhDtf
> Tc&s=a
> >> eoHPeyoWEbF1Lq409kfGNS_AauUuCunIr_B_-mNx68&e= >
> >>
> >>> On Mar 9, 2020, at 3:25 PM, Brian Grossman
>  >>  > wrote:
> >>>
> >>> I'm having a problem with launching Rcmdr. When I try to launch it
> >> the
> >>> first time through R using the command library(Rcmdr) it will go
> >> through
> >>> the process of launching and get to the point where it says
> >> 

Re: [R] power for repeated measures ANCOVA

[Abby Spurdle]

I don't know the answer to your question.
But I was wondering if "repeated measures ANCOVA" could fall under other
headings?

If you search for  R>, substituting , maybe
you'll get lucky.

On Wed, Mar 11, 2020 at 6:42 AM Debbie Hahs-Vaughn <
debbie.hahs-vau...@ucf.edu> wrote:

> Is anyone aware of an R package for computing power analysis with repeated
> measures ANCOVA? I realize this message was posted many years ago so am
> wondering if something is now available.
>
> 
>
> [[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]]

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Re: [R] how do I add text lables on QQ plot

[Abby Spurdle]

> and I would like to get the plot like the one in attach.
> Please advise,

This is a bad idea.
Plots should be *easy* to interpret.

Try to keep plots relatively simple, avoiding unnecessary details.
For nontrivial plots, use a caption to describe the main features of the plot.
(That's where your text should go).

I note that you've asked a number of questions about QQ plots.
I'd recommend that you use QQ plots in a standard way, without
frequently trying to modify/customize them.

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and provide commented, minimal, self-contained, reproducible code.

Re: [R] how do I add text lables on QQ plot

[Ana Marija]

Thanks for getting back to me but I would need this text labels added in
this particular instance

On Wed, 11 Mar 2020 at 19:37, Abby Spurdle  wrote:

> > and I would like to get the plot like the one in attach.
> > Please advise,
>
> This is a bad idea.
> Plots should be *easy* to interpret.
>
> Try to keep plots relatively simple, avoiding unnecessary details.
> For nontrivial plots, use a caption to describe the main features of the
> plot.
> (That's where your text should go).
>
> I note that you've asked a number of questions about QQ plots.
> I'd recommend that you use QQ plots in a standard way, without
> frequently trying to modify/customize them.
>

[[alternative HTML version deleted]]

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PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] how do I add text lables on QQ plot

[Abby Spurdle]

Ok, then.

What graphics system is the qq function using?
Assuming that it's using the base graphics system, look at the
graphics::text function.

text (1:10, 1:10, LETTERS [1:10])

If it's a different graphics system, then I don't know, but hopefully
someone else will help.

On Thu, Mar 12, 2020 at 1:48 PM Ana Marija  wrote:
>
> Thanks for getting back to me but I would need this text labels added in this 
> particular instance
>
> On Wed, 11 Mar 2020 at 19:37, Abby Spurdle  wrote:
>>
>> > and I would like to get the plot like the one in attach.
>> > Please advise,
>>
>> This is a bad idea.
>> Plots should be *easy* to interpret.
>>
>> Try to keep plots relatively simple, avoiding unnecessary details.
>> For nontrivial plots, use a caption to describe the main features of the 
>> plot.
>> (That's where your text should go).
>>
>> I note that you've asked a number of questions about QQ plots.
>> I'd recommend that you use QQ plots in a standard way, without
>> frequently trying to modify/customize them.

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and provide commented, minimal, self-contained, reproducible code.

Re: [R] how do I add text lables on QQ plot

[Abby Spurdle]

One more thing, I can't find a CRAN package named "ggman".

On Thu, Mar 12, 2020 at 1:59 PM Abby Spurdle  wrote:
>
> Ok, then.
>
> What graphics system is the qq function using?
> Assuming that it's using the base graphics system, look at the
> graphics::text function.
>
> text (1:10, 1:10, LETTERS [1:10])
>
> If it's a different graphics system, then I don't know, but hopefully
> someone else will help.
>
> On Thu, Mar 12, 2020 at 1:48 PM Ana Marija  
> wrote:
> >
> > Thanks for getting back to me but I would need this text labels added in 
> > this particular instance
> >
> > On Wed, 11 Mar 2020 at 19:37, Abby Spurdle  wrote:
> >>
> >> > and I would like to get the plot like the one in attach.
> >> > Please advise,
> >>
> >> This is a bad idea.
> >> Plots should be *easy* to interpret.
> >>
> >> Try to keep plots relatively simple, avoiding unnecessary details.
> >> For nontrivial plots, use a caption to describe the main features of the 
> >> plot.
> >> (That's where your text should go).
> >>
> >> I note that you've asked a number of questions about QQ plots.
> >> I'd recommend that you use QQ plots in a standard way, without
> >> frequently trying to modify/customize them.

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Re: [R] how do I add text lables on QQ plot

[John Kane]

No idua how it works but the name suggests it in out of the Hadley universe
and not basic graphics.

On Wed, 11 Mar 2020 at 21:14, Abby Spurdle  wrote:

> One more thing, I can't find a CRAN package named "ggman".
>
> On Thu, Mar 12, 2020 at 1:59 PM Abby Spurdle  wrote:
> >
> > Ok, then.
> >
> > What graphics system is the qq function using?
> > Assuming that it's using the base graphics system, look at the
> > graphics::text function.
> >
> > text (1:10, 1:10, LETTERS [1:10])
> >
> > If it's a different graphics system, then I don't know, but hopefully
> > someone else will help.
> >
> > On Thu, Mar 12, 2020 at 1:48 PM Ana Marija 
> wrote:
> > >
> > > Thanks for getting back to me but I would need this text labels added
> in this particular instance
> > >
> > > On Wed, 11 Mar 2020 at 19:37, Abby Spurdle 
> wrote:
> > >>
> > >> > and I would like to get the plot like the one in attach.
> > >> > Please advise,
> > >>
> > >> This is a bad idea.
> > >> Plots should be *easy* to interpret.
> > >>
> > >> Try to keep plots relatively simple, avoiding unnecessary details.
> > >> For nontrivial plots, use a caption to describe the main features of
> the plot.
> > >> (That's where your text should go).
> > >>
> > >> I note that you've asked a number of questions about QQ plots.
> > >> I'd recommend that you use QQ plots in a standard way, without
> > >> frequently trying to modify/customize them.
>
> __
> 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.
>


-- 
John Kane
Kingston ON Canada

[[alternative HTML version deleted]]

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Re: [R] power for repeated measures ANCOVA

[Bert Gunter]

You should probably post this on a statistics site like
stats.stackexchange.com. I suspect the answer is something like "are you
serious?!," because I presume any such analysis would have to specify a
complex VCOV matrix with many parameters that would have to be pulled more
or less out of thin air. In other words, a fantasy. But don't take my word
for it -- knowledgeable people at a stats site would be far more reliable.

Bert Gunter

"The trouble with having an open mind is that people keep coming along and
sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )


On Wed, Mar 11, 2020 at 1:09 PM Abby Spurdle  wrote:

> I don't know the answer to your question.
> But I was wondering if "repeated measures ANCOVA" could fall under other
> headings?
>
> If you search for  R>, substituting , maybe
> you'll get lucky.
>
> On Wed, Mar 11, 2020 at 6:42 AM Debbie Hahs-Vaughn <
> debbie.hahs-vau...@ucf.edu> wrote:
>
> > Is anyone aware of an R package for computing power analysis with
> repeated
> > measures ANCOVA? I realize this message was posted many years ago so am
> > wondering if something is now available.
> >
> > 
> >
> > [[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.
>

[[alternative HTML version deleted]]

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Re: [R] Problem launching Rcmdr

[Fox, John]

Dear Brian,

I'm afraid that I have no idea about what's going on, particularly why your 
second attempt to start the Rcmdr works, whether after a first attempt, or now 
after using tcltk. 

Did you follow up on Peter's suggestion that your antivirus software may be the 
source of the problem?

Best,
 John

> On Mar 11, 2020, at 4:42 PM, Brian Grossman  wrote:
> 
> I did some testing and was able to run the tcltk commands without any 
> problems. It brought up the graph normally when I hit the submit button and 
> when I changed the values and hit submit it would change the graph 
> accordingly.The interesting thing is that after the tkdestroy(tt) command I 
> tried running library(Rcmdr) and it launched successfully. I'm not sure what 
> that means, but hopefully someone else will.
> 
> Thank you,
> 
> Brian
> 
> On Wed, Mar 11, 2020 at 1:02 PM Fox, John  wrote:
> Dear Bernhard, Peter, and Brian,
> 
> Thanks, Peter, for the suggestion. If you're right then the problem is with 
> tcltk more generally and not directly with the Rcmdr package.
> 
> Brian: That's easily checked and might clarify what's going on: Load the 
> tcltk package via library(tcltk), and then try the following example from 
> ?TkWidgetcmds:
> 
>  snip --
> 
> tt <- tktoplevel()
> tkpack(txt.w <- tktext(tt))
> tkinsert(txt.w, "0.0", "plot(1:10)")
> eval.txt <- function()
>eval(parse(text = tclvalue(tkget(txt.w, "0.0", "end"
> tkpack(but.w <- tkbutton(tt, text = "Submit", command = eval.txt))
> 
> ## Try pressing the button, edit the text and when finished:
> 
> tkdestroy(tt)
> 
>  snip --
> 
> Best,
>  John
> 
> 
> > -Original Message-
> > From: Pfaff, Bernhard Dr. 
> > Sent: Wednesday, March 11, 2020 9:18 AM
> > To: Peter Dalgaard ; Fox, John 
> > Cc: r-help@r-project.org
> > Subject: AW: Re: [R] Problem launching Rcmdr
> > 
> > Good catch, Peter; Cylance might be the culprit - at least I encountered
> > problems by compiling C++ sources and/or building packages with interfaced
> > routines and here a memory checker kicked in.
> > Maybe something akin is happening by launching Rcmdr (tcl/tk)?
> > 
> > -Ursprüngliche Nachricht-
> > Von: R-help  Im Auftrag von Peter Dalgaard
> > Gesendet: Mittwoch, 11. März 2020 10:29
> > An: Fox, John 
> > Cc: r-help@r-project.org
> > Betreff: [EXT] Re: [R] Problem launching Rcmdr
> > 
> > Any chance that a virus checker is interfering?
> > 
> > -pd
> > 
> > > On 10 Mar 2020, at 23:43 , Fox, John  wrote:
> > >
> > > Dear Brian,
> > >
> > > (Please keep r-help in the loop so that if someone else has this
> > > problem they'll have something to refer to.)
> > >
> > > Your session at start-up seems completely clean, so I'm at a loss to
> > understand what the problem is. I, and I assume very many other people,
> > are using the Rcmdr with essentially the same Windows setup. What's
> > particularly hard for me to understand is that you're able to start the 
> > Rcmdr in
> > a second R session. Does the first R session have to remain open for this to
> > work?
> > >
> > > A next step is to reinstall packages, starting with the Rcmdr package, if 
> > > you
> > haven't already tried that, and eventually to reinstall R, including 
> > deleting the
> > R package library. BTW, I usually prefer to install R in c:\R\ rather than 
> > under
> > Program Files so that the system library is used for packages that I
> > subsequently install, although it should work perfectly fine to install 
> > packages
> > into a personal library.
> > >
> > > Best,
> > > John
> > >
> > >> -Original Message-
> > >> From: Brian Grossman 
> > >> Sent: Tuesday, March 10, 2020 5:07 PM
> > >> To: Fox, John 
> > >> Subject: Re: [R] Problem launching Rcmdr
> > >>
> > >> John,
> > >>
> > >> Thanks for the reply. Here is the output from running sessionInfo()
> > >> right after opening R.
> > >>
> > >>> sessionInfo()
> > >> R version 3.6.2 (2019-12-12)
> > >> Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10
> > >> x64 (build 18362)
> > >>
> > >> Matrix products: default
> > >>
> > >> locale:
> > >> [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United
> > >> States.1252 [3] LC_MONETARY=English_United States.1252 [4]
> > >> LC_NUMERIC=C [5] LC_TIME=English_United States.1252
> > >>
> > >> attached base packages:
> > >> [1] stats graphics  grDevices utils datasets  methods   base
> > >>
> > >> loaded via a namespace (and not attached):
> > >> [1] compiler_3.6.2
> > >>
> > >>
> > >> Brian
> > >>
> > >> On Tue, Mar 10, 2020 at 8:46 AM Fox, John  > >>  > wrote:
> > >>
> > >>
> > >>Dear Brian,
> > >>
> > >>Normally I'd expect that a workspace saved from a previous session
> > >> and loaded at the start of the current session would cause this kind
> > >> of anomalous behaviour, but that doesn't explain why the Rcmdr starts
> > >> up properly in a second (concurrent?) session, nor why it doesn't
> > >

Re: [R] how do I add text lables on QQ plot

[Ana Marija]

I don’t need to use qqman package... if someone has any other solution
would be the most appreciated


On Wed, 11 Mar 2020 at 20:28, John Kane  wrote:

> No idua how it works but the name suggests it in out of the Hadley
> universe and not basic graphics.
>
> On Wed, 11 Mar 2020 at 21:14, Abby Spurdle  wrote:
>
>> One more thing, I can't find a CRAN package named "ggman".
>>
>> On Thu, Mar 12, 2020 at 1:59 PM Abby Spurdle  wrote:
>> >
>> > Ok, then.
>> >
>> > What graphics system is the qq function using?
>> > Assuming that it's using the base graphics system, look at the
>> > graphics::text function.
>> >
>> > text (1:10, 1:10, LETTERS [1:10])
>> >
>> > If it's a different graphics system, then I don't know, but hopefully
>> > someone else will help.
>> >
>> > On Thu, Mar 12, 2020 at 1:48 PM Ana Marija 
>> wrote:
>> > >
>> > > Thanks for getting back to me but I would need this text labels added
>> in this particular instance
>> > >
>> > > On Wed, 11 Mar 2020 at 19:37, Abby Spurdle 
>> wrote:
>> > >>
>> > >> > and I would like to get the plot like the one in attach.
>> > >> > Please advise,
>> > >>
>> > >> This is a bad idea.
>> > >> Plots should be *easy* to interpret.
>> > >>
>> > >> Try to keep plots relatively simple, avoiding unnecessary details.
>> > >> For nontrivial plots, use a caption to describe the main features of
>> the plot.
>> > >> (That's where your text should go).
>> > >>
>> > >> I note that you've asked a number of questions about QQ plots.
>> > >> I'd recommend that you use QQ plots in a standard way, without
>> > >> frequently trying to modify/customize them.
>>
>> __
>
>
>> 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.
>>
>
>
> --
> John Kane
> Kingston ON Canada
>

[[alternative HTML version deleted]]

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Re: [R] how do I add text lables on QQ plot

[David Winsemius]

On 3/10/20 9:51 PM, Ana Marija wrote:

Hello,

I am making QQ plot via:

library(ggman)
qq(fdr2_sorted$FDR.q.val2, main = "RG_All", pch = 17,
col=fdr1_sorted$group, cex = 1, las = 1)



I think you may be confusing the audience. There is no qq function in 
the ggman package. There is however a qq function in the qqman package.



Running the example in help page for qqman::qq and looking at the code 
suggests this is a base plot function, so the text function will allow 
you to put any particular string within the plot area:


library(qqman)

qq(gwasResults$P)
text( 2, 6, "arbitrary")  # puts text "arbitrary" at postion (x=2, y=6)



data frames used look like this:


head(fdr1_sorted)


You should use `dput` to post reproducible data examples.

HTH;

David.


NAME GS follow
link to MSigDB  GS DETAILS SIZE ES   NES NOM p-val
1: GO_DNA_PACKAGING_COMPLEX
GO_DNA_PACKAGING_COMPLEX Details ...   77  0.6757226  2.466745
0
2:   GO_PROTEIN_DNA_COMPLEX
GO_PROTEIN_DNA_COMPLEX Details ...  132  0.5958179  2.346520 0
3: GO_RESPONSE_TO_TYPE_I_INTERFERON
GO_RESPONSE_TO_TYPE_I_INTERFERON Details ...   52 -0.7521569 -2.533148
 0
4:  GO_RESPONSE_TO_INTERFERON_GAMMA
GO_RESPONSE_TO_INTERFERON_GAMMA Details ...  101 -0.6370415 -2.420473
0
5: GO_CELLULAR_RESPONSE_TO_INTERFERON_GAMMA
GO_CELLULAR_RESPONSE_TO_INTERFERON_GAMMA Details ...   85 -0.6571892
-2.402153 0
6: GO_GRANULOCYTE_MIGRATION
GO_GRANULOCYTE_MIGRATION Details ...   43 -0.7332099 -2.398983
0
FDR q-val FWER p-val RANK AT MAX   LEADING EDGE V12
group FDR.q.val2
1: 0  0 tags=43%, list=10%, signal=47%  NA
 2  1e-10
2: 0  01516 tags=39%, list=13%, signal=45%  NA
 2  1e-10
3: 0  01427 tags=54%, list=12%, signal=61%  NA
 4  1e-10
4: 0  01819 tags=45%, list=16%, signal=52%  NA
 4  1e-10
5: 0  01216 tags=38%, list=11%, signal=42%  NA
 4  1e-10
6: 0  0 491  tags=28%, list=4%, signal=29%  NA
 4  1e-10


head(fdr2_sorted)

NAME GS follow
link to MSigDB  GS DETAILS SIZE ES   NES NOM p-val
1: GO_DNA_PACKAGING_COMPLEX
GO_DNA_PACKAGING_COMPLEX Details ...   77  0.6757226  2.466745
0
2:   GO_PROTEIN_DNA_COMPLEX
GO_PROTEIN_DNA_COMPLEX Details ...  132  0.5958179  2.346520 0
3: GO_RESPONSE_TO_TYPE_I_INTERFERON
GO_RESPONSE_TO_TYPE_I_INTERFERON Details ...   52 -0.7521569 -2.533148
 0
4:  GO_RESPONSE_TO_INTERFERON_GAMMA
GO_RESPONSE_TO_INTERFERON_GAMMA Details ...  101 -0.6370415 -2.420473
0
5: GO_CELLULAR_RESPONSE_TO_INTERFERON_GAMMA
GO_CELLULAR_RESPONSE_TO_INTERFERON_GAMMA Details ...   85 -0.6571892
-2.402153 0
6: GO_GRANULOCYTE_MIGRATION
GO_GRANULOCYTE_MIGRATION Details ...   43 -0.7332099 -2.398983
0
FDR q-val FWER p-val RANK AT MAX   LEADING EDGE V12
FDR.q.val2
1: 0  0 tags=43%, list=10%, signal=47%  NA
  1e-10
2: 0  01516 tags=39%, list=13%, signal=45%  NA
  1e-10
3: 0  01427 tags=54%, list=12%, signal=61%  NA
  1e-10
4: 0  01819 tags=45%, list=16%, signal=52%  NA
  1e-10
5: 0  01216 tags=38%, list=11%, signal=42%  NA
  1e-10
6: 0  0 491  tags=28%, list=4%, signal=29%  NA
  1e-10

and I would like to get the plot like the one in attach.

Please advise,
Ana

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Re: [R] Problem launching Rcmdr

[Brian Grossman]

I did some testing and was able to run the tcltk commands without any
problems. It brought up the graph normally when I hit the submit button and
when I changed the values and hit submit it would change the graph
accordingly.The interesting thing is that after the tkdestroy(tt) command I
tried running library(Rcmdr) and it launched successfully. I'm not sure
what that means, but hopefully someone else will.

Thank you,

Brian

On Wed, Mar 11, 2020 at 1:02 PM Fox, John  wrote:

> Dear Bernhard, Peter, and Brian,
>
> Thanks, Peter, for the suggestion. If you're right then the problem is
> with tcltk more generally and not directly with the Rcmdr package.
>
> Brian: That's easily checked and might clarify what's going on: Load the
> tcltk package via library(tcltk), and then try the following example from
> ?TkWidgetcmds:
>
>  snip --
>
> tt <- tktoplevel()
> tkpack(txt.w <- tktext(tt))
> tkinsert(txt.w, "0.0", "plot(1:10)")
> eval.txt <- function()
>eval(parse(text = tclvalue(tkget(txt.w, "0.0", "end"
> tkpack(but.w <- tkbutton(tt, text = "Submit", command = eval.txt))
>
> ## Try pressing the button, edit the text and when finished:
>
> tkdestroy(tt)
>
>  snip --
>
> Best,
>  John
>
>
> > -Original Message-
> > From: Pfaff, Bernhard Dr. 
> > Sent: Wednesday, March 11, 2020 9:18 AM
> > To: Peter Dalgaard ; Fox, John 
> > Cc: r-help@r-project.org
> > Subject: AW: Re: [R] Problem launching Rcmdr
> >
> > Good catch, Peter; Cylance might be the culprit - at least I encountered
> > problems by compiling C++ sources and/or building packages with
> interfaced
> > routines and here a memory checker kicked in.
> > Maybe something akin is happening by launching Rcmdr (tcl/tk)?
> >
> > -Ursprüngliche Nachricht-
> > Von: R-help  Im Auftrag von Peter Dalgaard
> > Gesendet: Mittwoch, 11. März 2020 10:29
> > An: Fox, John 
> > Cc: r-help@r-project.org
> > Betreff: [EXT] Re: [R] Problem launching Rcmdr
> >
> > Any chance that a virus checker is interfering?
> >
> > -pd
> >
> > > On 10 Mar 2020, at 23:43 , Fox, John  wrote:
> > >
> > > Dear Brian,
> > >
> > > (Please keep r-help in the loop so that if someone else has this
> > > problem they'll have something to refer to.)
> > >
> > > Your session at start-up seems completely clean, so I'm at a loss to
> > understand what the problem is. I, and I assume very many other people,
> > are using the Rcmdr with essentially the same Windows setup. What's
> > particularly hard for me to understand is that you're able to start the
> Rcmdr in
> > a second R session. Does the first R session have to remain open for
> this to
> > work?
> > >
> > > A next step is to reinstall packages, starting with the Rcmdr package,
> if you
> > haven't already tried that, and eventually to reinstall R, including
> deleting the
> > R package library. BTW, I usually prefer to install R in c:\R\ rather
> than under
> > Program Files so that the system library is used for packages that I
> > subsequently install, although it should work perfectly fine to install
> packages
> > into a personal library.
> > >
> > > Best,
> > > John
> > >
> > >> -Original Message-
> > >> From: Brian Grossman 
> > >> Sent: Tuesday, March 10, 2020 5:07 PM
> > >> To: Fox, John 
> > >> Subject: Re: [R] Problem launching Rcmdr
> > >>
> > >> John,
> > >>
> > >> Thanks for the reply. Here is the output from running sessionInfo()
> > >> right after opening R.
> > >>
> > >>> sessionInfo()
> > >> R version 3.6.2 (2019-12-12)
> > >> Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 10
> > >> x64 (build 18362)
> > >>
> > >> Matrix products: default
> > >>
> > >> locale:
> > >> [1] LC_COLLATE=English_United States.1252 [2] LC_CTYPE=English_United
> > >> States.1252 [3] LC_MONETARY=English_United States.1252 [4]
> > >> LC_NUMERIC=C [5] LC_TIME=English_United States.1252
> > >>
> > >> attached base packages:
> > >> [1] stats graphics  grDevices utils datasets  methods   base
> > >>
> > >> loaded via a namespace (and not attached):
> > >> [1] compiler_3.6.2
> > >>
> > >>
> > >> Brian
> > >>
> > >> On Tue, Mar 10, 2020 at 8:46 AM Fox, John  > >>  > wrote:
> > >>
> > >>
> > >>Dear Brian,
> > >>
> > >>Normally I'd expect that a workspace saved from a previous session
> > >> and loaded at the start of the current session would cause this kind
> > >> of anomalous behaviour, but that doesn't explain why the Rcmdr starts
> > >> up properly in a second (concurrent?) session, nor why it doesn't
> > >> start up properly when R is run with the --vanilla switch.
> > >>
> > >>Can you report the result of sessionInfo() at the start of a
> session?
> > >>
> > >>If all else fails, you could try uninstalling and reinstalling R
> and
> > >> packages.
> > >>
> > >>Best,
> > >> John
> > >>
> > >>  -
> > >>  John Fox, Professor Emeritus
> > >>  McMaster University
> > >>