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Installing lme4 package in Windows Vista

Angela Radulescu
Hi all,

I have a problem with package installing in Windows, on my PC machine. The end goal is to be able to use the lme() function. Here's what I did so far:

> install.packages("lme4")
Warning in install.packages("lme4") :
  argument 'lib' is missing: using 'C:\Users\Angela\Documents/R/win-library/2.9'
--- Please select a CRAN mirror for use in this session ---
trying URL 'http://cran.cnr.Berkeley.edu/bin/windows/contrib/2.9/lme4_0.999375-31.zip'
Content type 'application/zip' length 1140865 bytes (1.1 Mb)
opened URL
downloaded 1.1 Mb

package 'lme4' successfully unpacked and MD5 sums checked

The downloaded packages are in
        C:\Users\Angela\AppData\Local\Temp\Rtmp1t8vjT\downloaded_packages
updating HTML package descriptions
Warning message:
In file.create(f.tg) :
  cannot create file 'C:\PROGRA~1\R\R-29~1.1/doc/html/packages.html', reason 'Permission denied'


I had to change permissions on some of the "library" folder before this. Still, after installation, R cannot find the "lme" function of interest.

> lme
Error: object 'lme' not found


Does anyone know why this is happening, and what the solution to the problem is?

Many thanks,
Angela
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Re: Installing lme4 package in Windows Vista

Rolf Turner

The function lme() is in the package nmle, ***not*** in lme4.

The somewhat analagous (but very different) function in lme4
is lmer().

        cheers,

                Rolf Turner

>
> Hi all,
>
> I have a problem with package installing in Windows, on my PC  
> machine. The
> end goal is to be able to use the lme() function. Here's what I did  
> so far:
>
>> install.packages("lme4")
> Warning in install.packages("lme4") :
>   argument 'lib' is missing: using
> 'C:\Users\Angela\Documents/R/win-library/2.9'
> --- Please select a CRAN mirror for use in this session ---
> trying URL
> 'http://cran.cnr.Berkeley.edu/bin/windows/contrib/2.9/ 
> lme4_0.999375-31.zip'
> Content type 'application/zip' length 1140865 bytes (1.1 Mb)
> opened URL
> downloaded 1.1 Mb
>
> package 'lme4' successfully unpacked and MD5 sums checked
>
> The downloaded packages are in
>         C:\Users\Angela\AppData\Local\Temp\Rtmp1t8vjT
> \downloaded_packages
> updating HTML package descriptions
> Warning message:
> In file.create(f.tg) :
>   cannot create file 'C:\PROGRA~1\R\R-29~1.1/doc/html/
> packages.html', reason
> 'Permission denied'
>
> I had to change permissions on some of the "library" folder before  
> this.
> Still, after installation, R cannot find the "lme" function of  
> interest.
>
>> lme
> Error: object 'lme' not found
>
> Does anyone know why this is happening, and what the solution to  
> the problem
> is?
>
> Many thanks,
> Angela
> --
> View this message in context: http://www.nabble.com/Installing-lme4- 
> package-in-Windows-Vista-tp24709932p24709932.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> [hidden email] mailing list
> 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.


######################################################################
Attention:\ This e-mail message is privileged and confid...{{dropped:9}}

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Re: Installing lme4 package in Windows Vista

Wincent
In reply to this post by Angela Radulescu
After installation of lme4, you need to load it before use it.
>library(lme4)
>?lmer

2009/7/29 Angela Radulescu <[hidden email]>:

>
> Hi all,
>
> I have a problem with package installing in Windows, on my PC machine. The
> end goal is to be able to use the lme() function. Here's what I did so far:
>
>> install.packages("lme4")
> Warning in install.packages("lme4") :
>  argument 'lib' is missing: using
> 'C:\Users\Angela\Documents/R/win-library/2.9'
> --- Please select a CRAN mirror for use in this session ---
> trying URL
> 'http://cran.cnr.Berkeley.edu/bin/windows/contrib/2.9/lme4_0.999375-31.zip'
> Content type 'application/zip' length 1140865 bytes (1.1 Mb)
> opened URL
> downloaded 1.1 Mb
>
> package 'lme4' successfully unpacked and MD5 sums checked
>
> The downloaded packages are in
>        C:\Users\Angela\AppData\Local\Temp\Rtmp1t8vjT\downloaded_packages
> updating HTML package descriptions
> Warning message:
> In file.create(f.tg) :
>  cannot create file 'C:\PROGRA~1\R\R-29~1.1/doc/html/packages.html', reason
> 'Permission denied'
>
> I had to change permissions on some of the "library" folder before this.
> Still, after installation, R cannot find the "lme" function of interest.
>
>> lme
> Error: object 'lme' not found
>
> Does anyone know why this is happening, and what the solution to the problem
> is?
>
> Many thanks,
> Angela
> --
> View this message in context: http://www.nabble.com/Installing-lme4-package-in-Windows-Vista-tp24709932p24709932.html
> Sent from the R help mailing list archive at Nabble.com.
>
> ______________________________________________
> [hidden email] mailing list
> 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.
>



--
HUANG Ronggui, Wincent
PhD Candidate
Dept of Public and Social Administration
City University of Hong Kong
Home page: http://asrr.r-forge.r-project.org/rghuang.html

______________________________________________
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Re: Installing lme4 package in Windows Vista

ONKELINX, Thierry
In reply to this post by Angela Radulescu
Dear Angela,

lme() is a part of the nlme package. The lme4 package has the function
lmer() which is the equivalent of lme() from nlme. Both function differ
in their capabilities. Briefly: lmer() can (easly) do crossed random
effects and GLMM, lme() can handle variance and correlation structures.

HTH,

Thierry

PS Don't for get that you need to load a package before using it! Just
installing it is not sufficient.

library(lme4)
?lmer

library(nlme)
?lme


------------------------------------------------------------------------
----
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature
and Forest
Cel biometrie, methodologie en kwaliteitszorg / Section biometrics,
methodology and quality assurance
Gaverstraat 4
9500 Geraardsbergen
Belgium
tel. + 32 54/436 185
[hidden email]
www.inbo.be

To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to
say what the experiment died of.
~ Sir Ronald Aylmer Fisher

The plural of anecdote is not data.
~ Roger Brinner

The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of
data.
~ John Tukey

-----Oorspronkelijk bericht-----
Van: [hidden email] [mailto:[hidden email]]
Namens Angela Radulescu
Verzonden: woensdag 29 juli 2009 1:48
Aan: [hidden email]
Onderwerp: [R] Installing lme4 package in Windows Vista


Hi all,

I have a problem with package installing in Windows, on my PC machine.
The end goal is to be able to use the lme() function. Here's what I did
so far:

> install.packages("lme4")
Warning in install.packages("lme4") :
  argument 'lib' is missing: using
'C:\Users\Angela\Documents/R/win-library/2.9'
--- Please select a CRAN mirror for use in this session --- trying URL
'http://cran.cnr.Berkeley.edu/bin/windows/contrib/2.9/lme4_0.999375-31.z
ip'
Content type 'application/zip' length 1140865 bytes (1.1 Mb) opened URL
downloaded 1.1 Mb

package 'lme4' successfully unpacked and MD5 sums checked

The downloaded packages are in

C:\Users\Angela\AppData\Local\Temp\Rtmp1t8vjT\downloaded_packages
updating HTML package descriptions
Warning message:
In file.create(f.tg) :
  cannot create file 'C:\PROGRA~1\R\R-29~1.1/doc/html/packages.html',
reason 'Permission denied'

I had to change permissions on some of the "library" folder before this.
Still, after installation, R cannot find the "lme" function of interest.


> lme
Error: object 'lme' not found

Does anyone know why this is happening, and what the solution to the
problem is?

Many thanks,
Angela
--
View this message in context:
http://www.nabble.com/Installing-lme4-package-in-Windows-Vista-tp2470993
2p24709932.html
Sent from the R help mailing list archive at Nabble.com.

______________________________________________
[hidden email] mailing list
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.

Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver weer
en binden het INBO onder geen enkel beding, zolang dit bericht niet bevestigd is
door een geldig ondertekend document. The views expressed in  this message
and any annex are purely those of the writer and may not be regarded as stating
an official position of INBO, as long as the message is not confirmed by a duly
signed document.

______________________________________________
[hidden email] mailing list
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.
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Re: Installing lme4 package in Windows Vista

Angela Radulescu
Thanks everyone!

It works now :)

Cheers,
a.


ONKELINX, Thierry wrote
Dear Angela,

lme() is a part of the nlme package. The lme4 package has the function
lmer() which is the equivalent of lme() from nlme. Both function differ
in their capabilities. Briefly: lmer() can (easly) do crossed random
effects and GLMM, lme() can handle variance and correlation structures.

HTH,

Thierry

PS Don't for get that you need to load a package before using it! Just
installing it is not sufficient.

library(lme4)
?lmer

library(nlme)
?lme


------------------------------------------------------------------------
----
ir. Thierry Onkelinx
Instituut voor natuur- en bosonderzoek / Research Institute for Nature
and Forest
Cel biometrie, methodologie en kwaliteitszorg / Section biometrics,
methodology and quality assurance
Gaverstraat 4
9500 Geraardsbergen
Belgium
tel. + 32 54/436 185
Thierry.Onkelinx@inbo.be
www.inbo.be

To call in the statistician after the experiment is done may be no more
than asking him to perform a post-mortem examination: he may be able to
say what the experiment died of.
~ Sir Ronald Aylmer Fisher

The plural of anecdote is not data.
~ Roger Brinner

The combination of some data and an aching desire for an answer does not
ensure that a reasonable answer can be extracted from a given body of
data.
~ John Tukey

-----Oorspronkelijk bericht-----
Van: r-help-bounces@r-project.org [mailto:r-help-bounces@r-project.org]
Namens Angela Radulescu
Verzonden: woensdag 29 juli 2009 1:48
Aan: r-help@r-project.org
Onderwerp: [R] Installing lme4 package in Windows Vista


Hi all,

I have a problem with package installing in Windows, on my PC machine.
The end goal is to be able to use the lme() function. Here's what I did
so far:

> install.packages("lme4")
Warning in install.packages("lme4") :
  argument 'lib' is missing: using
'C:\Users\Angela\Documents/R/win-library/2.9'
--- Please select a CRAN mirror for use in this session --- trying URL
'http://cran.cnr.Berkeley.edu/bin/windows/contrib/2.9/lme4_0.999375-31.z
ip'
Content type 'application/zip' length 1140865 bytes (1.1 Mb) opened URL
downloaded 1.1 Mb

package 'lme4' successfully unpacked and MD5 sums checked

The downloaded packages are in

C:\Users\Angela\AppData\Local\Temp\Rtmp1t8vjT\downloaded_packages
updating HTML package descriptions
Warning message:
In file.create(f.tg) :
  cannot create file 'C:\PROGRA~1\R\R-29~1.1/doc/html/packages.html',
reason 'Permission denied'

I had to change permissions on some of the "library" folder before this.
Still, after installation, R cannot find the "lme" function of interest.


> lme
Error: object 'lme' not found

Does anyone know why this is happening, and what the solution to the
problem is?

Many thanks,
Angela
--
View this message in context:
http://www.nabble.com/Installing-lme4-package-in-Windows-Vista-tp2470993
2p24709932.html
Sent from the R help mailing list archive at Nabble.com.

______________________________________________
R-help@r-project.org mailing list
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.

Dit bericht en eventuele bijlagen geven enkel de visie van de schrijver weer
en binden het INBO onder geen enkel beding, zolang dit bericht niet bevestigd is
door een geldig ondertekend document. The views expressed in  this message
and any annex are purely those of the writer and may not be regarded as stating
an official position of INBO, as long as the message is not confirmed by a duly
signed document.

______________________________________________
R-help@r-project.org mailing list
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.
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