Re: [R] Network issue

[James Powell]

Hi Stephen,
Thanks again for getting back to me, Ivan Krylov responded also and suggested 
windows binaries and I must confess I was only familiar with installing from 
files via the package sources (apart from the conventional install.packages 
method), so the solution was as simple as installing via the binaries. Thanks 
again, best wishes, James

From: stephen sefick 
Sent: Wednesday 21 February 2024 12:25
To: James Powell 
Cc: r-help@r-project.org
Subject: Re: [R] Network issue

CAUTION: This email originated from outside of the organisation. Do not click 
links or open attachments unless you recognise the sender and know the content 
is safe.

My suggestion is probably overkill. Sorry about that. I don't know much about 
windows.

Have you tried posit package manager? Maybe that is not blocked? I think 
windows binaries are installable from there?

A workaround, that I don't think I would suggest, might be RSelinium to 
automate the download process since it seems you have web access?

Best of luck!
Kindest regards,

Stephen Sefick

On Wed, Feb 21, 2024, 01:09 James Powell 
mailto:james.pow...@hse.ie>> wrote:
Hi Stephen,
I didn’t see this suggested previously, but yes I have made repeated attempts 
to gain access to CRAN via R but to no avail. Mirroring CRAN is a really good 
idea, but I’m not sure how to get R to recognise the local file locations when 
the installation files seek access to CRAN via urls. Thanks again for your 
help. Regards, James

From: stephen sefick mailto:ssef...@gmail.com>>
Sent: Wednesday 21 February 2024 00:04
To: James Powell mailto:james.pow...@hse.ie>>
Cc: r-help@r-project.org<mailto:r-help@r-project.org>
Subject: Re: [R] Network issue

CAUTION: This email originated from outside of the organisation. Do not click 
links or open attachments unless you recognise the sender and know the content 
is safe.

As stated in an earlier email, this might be better directed to your IT? You 
might think about mirroring CRAN locally, but this would be non-trivial.

Stephen Sefick

On Tue, Feb 20, 2024, 17:26 James Powell 
mailto:james.pow...@hse.ie>> wrote:
Hi Stephen,
Thanks very much for getting back to me. My problem is described below. Any 
help would be greatly appreciated. Thanks, James

Hi,
Sorry for bothering you because I know that your time is voluntary, but I would 
really appreciate some help. I work in a hospital in part of Ireland’s national 
health service, a service which was struck by a massive cyber attack a couple 
of years ago. Since then their security has been very tight, and I can’t access 
the internet through my R or R Studio. To install packages I need to download 
the files through a browser (Chrome by default) and install them from the 
files, which is very tedious when you consider the amount of dependencies, but 
I’m happy to do it.

This was working fine until yesterday when I had error messages trying to 
install some packages. See enclosed “S2” for example. It looks like it is 
trying to download a file as part of the installation, but of course can’t. If 
you could help with this I would be very grateful. Other examples are jqr, 
protolite, curl.

I came across a different error message when trying to install openssl, 
although the issue may be the same. For this package it says

Warning in file(name, "wb") :
  cannot open file 'openssl/tests/keys/message.rsa.crypt': Permission denied
Error in file(name, "wb") : cannot open the connection

I have tried going into the archive of these packages and installing older 
versions, but no luck with those either.
I hope you can help. Best wishes, James


From: stephen sefick mailto:ssef...@gmail.com>>
Sent: Tuesday 20 February 2024 19:43
To: James Powell mailto:james.pow...@hse.ie>>
Cc: r-help@r-project.org<mailto:r-help@r-project.org>
Subject: Re: [R] Network issue

CAUTION: This email originated from outside of the organisation. Do not click 
links or open attachments unless you recognise the sender and know the content 
is safe.

Maybe I missed the rest of the post? You are more likely to get help with your 
problems if you create a minimal reproducible example.
Kindest regards,

Stephen Sefick

On Tue, Feb 20, 2024, 12:24 James Powell 
mailto:james.pow...@hse.ie>> wrote:



Need information and advice on COVID-19? Go to 
www.hse.ie/coronavirus<https://scanner.topsec.com/?d=2120=show=https%3A%2F%2Fwww.hse.ie%2Fcoronavirus=ceec0a7bd0b1f730294db0447d2a0c1ad2741351>


"Tá an fhaisnéis sa ríomhphost seo (ceangaltáin san áireamh) faoi rún. Baineann 
sé leis an té ar seoladh chuige amháin agus tá sé ar intinn go bhfaighfidh 
siadsan amháin é agus gurb iadsan amháin a dhéanfaidh breithniú air. Más rud é 
nach tusa an duine ar leis é, tá cosc iomlán ar aon fhaisnéis atá ann, a úsáid, 
a chraobhscaoileadh, a scaipeadh, a nochtadh, a fhoilsiú, ná a chóipeáil . 
Seains gurb iad tuairimí pearsanta an úd

Re: [R] Network issue

[James Powell]

Hi Stephen,
Thanks very much for getting back to me. My problem is described below. Any 
help would be greatly appreciated. Thanks, James

Hi,
Sorry for bothering you because I know that your time is voluntary, but I would 
really appreciate some help. I work in a hospital in part of Ireland’s national 
health service, a service which was struck by a massive cyber attack a couple 
of years ago. Since then their security has been very tight, and I can’t access 
the internet through my R or R Studio. To install packages I need to download 
the files through a browser (Chrome by default) and install them from the 
files, which is very tedious when you consider the amount of dependencies, but 
I’m happy to do it.

This was working fine until yesterday when I had error messages trying to 
install some packages. See enclosed “S2” for example. It looks like it is 
trying to download a file as part of the installation, but of course can’t. If 
you could help with this I would be very grateful. Other examples are jqr, 
protolite, curl.

I came across a different error message when trying to install openssl, 
although the issue may be the same. For this package it says

Warning in file(name, "wb") :
  cannot open file 'openssl/tests/keys/message.rsa.crypt': Permission denied
Error in file(name, "wb") : cannot open the connection

I have tried going into the archive of these packages and installing older 
versions, but no luck with those either.
I hope you can help. Best wishes, James


From: stephen sefick 
Sent: Tuesday 20 February 2024 19:43
To: James Powell 
Cc: r-help@r-project.org
Subject: Re: [R] Network issue

CAUTION: This email originated from outside of the organisation. Do not click 
links or open attachments unless you recognise the sender and know the content 
is safe.

Maybe I missed the rest of the post? You are more likely to get help with your 
problems if you create a minimal reproducible example.
Kindest regards,

Stephen Sefick

On Tue, Feb 20, 2024, 12:24 James Powell 
mailto:james.pow...@hse.ie>> wrote:



Need information and advice on COVID-19? Go to 
www.hse.ie/coronavirus<https://www.hse.ie/coronavirus>


"Tá an fhaisnéis sa ríomhphost seo (ceangaltáin san áireamh) faoi rún. Baineann 
sé leis an té ar seoladh chuige amháin agus tá sé ar intinn go bhfaighfidh 
siadsan amháin é agus gurb iadsan amháin a dhéanfaidh breithniú air. Más rud é 
nach tusa an duine ar leis é, tá cosc iomlán ar aon fhaisnéis atá ann, a úsáid, 
a chraobhscaoileadh, a scaipeadh, a nochtadh, a fhoilsiú, ná a chóipeáil . 
Seains gurb iad tuairimí pearsanta an údar atá san ríomhphost agus nach 
tuairimí FSS iad.

Má fuair tú an ríomhphost seo trí dhearmad, bheadh muid buíoch dá gcuirfeá in 
iúil don Deasc Seirbhísí ECT ar an nguthán ag +353 818 
300300 nó ar an ríomhphost chuig 
service.d...@hse.ie<mailto:service.d...@hse.ie> agus ansin glan an ríomhphost 
seo ded' chóras."



"Information in this email (including attachments) is confidential. It is 
intended for receipt and consideration only by the intended recipient. If you 
are not an addressee or intended recipient, any use, dissemination, 
distribution, disclosure, publication or copying of information contained in 
this email is strictly prohibited. Opinions expressed in this email may be 
personal to the author and are not necessarily the opinions of the HSE.

If this email has been received by you in error we would be grateful if you 
could immediately notify the ICT Service Desk by telephone at +353 818 
300300 or by email to 
service.d...@hse.ie<mailto:service.d...@hse.ie> and thereafter delete this 
e-mail from your system"





R version 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> utils:::menuInstallPkgs()
--- Please select a CRAN mirror for use in this session ---
Warning: failed to download mirrors file (cannot open URL 
'https://cran.r-project.org/CRAN_mirrors.csv'); using local file 
'C:/PROGRA~1/R/R-43~1.1/doc/CRAN_mirrors.csv'
Error in contrib.url(repos, type) : 
  trying to use CRAN without setting a mirror
In addition: Warning message:
In download.file(url, destfile = f, quiet = TRUE) :
  URL 'https://cran.r-project.org/CRAN_mirrors.csv': status was 'SSL connect 
error'
> util

Re: [R] Network issue

[James Powell]

Hi Ivan,
Thanks very much for your response, I'll definitely give that a go. Best 
wishes, James

-Original Message-
From: Ivan Krylov 
Sent: Wednesday 21 February 2024 10:38
To: James Powell 
Cc: r-help@r-project.org
Subject: Re: [R] Network issue

CAUTION: This email originated from outside of the organisation. Do not click 
links or open attachments unless you recognise the sender and know the content 
is safe.


В Wed, 21 Feb 2024 06:09:51 +
James Powell  пишет:

> This was working fine until yesterday when I had error messages trying
> to install some packages. See enclosed “S2” for example. It looks like
> it is trying to download a file as part of the installation, but of
> course can’t.

Since you're on Windows and running R-4.3, it should be easier to download and 
install the binary package, 
https://scanner.topsec.com/?d=2120=show=https%3A%2F%2Fcran.r-project.org%2Fbin%2Fwindows%2Fcontrib%2F4.3%2Fs2_1.1.6.zip=40c0076a9193368805cc3e637e09c680a3e72586.

Installing this package from source involves downloading a few binaries anyway. 
You could try unpacking the source package, downloading OpenSSL 1.1.1k binaries 
from 
https://scanner.topsec.com/?d=2120=show=https%3A%2F%2Fgithub.com%2Frwinlib%2Fopenssl%2Ftree%2Fv1.1.1k=10f7c80b5f4e5dcf0d0f3bd203a067fec29f43a4
into a new subdirectory called windows/ in the package root, just like the 
https://scanner.topsec.com/?d=2120=show=https%3A%2F%2Fgithub.com%2Fr-spatial%2Fs2%2Fblob%2Fmain%2Ftools%2Fwinlibs.R=fd500ed04f0fa1a24bbd7e7e50df6aa7f4bb654c
 script tries to do during the installation, then installing the resulting 
directory as if it was a source package.

--
Best regards,
Ivan


Need information and advice on COVID-19? Go to 
www.hse.ie/coronavirus<https://www.hse.ie/coronavirus>


"Tá an fhaisnéis sa ríomhphost seo (ceangaltáin san áireamh) faoi rún. Baineann 
sé leis an té ar seoladh chuige amháin agus tá sé ar intinn go bhfaighfidh 
siadsan amháin é agus gurb iadsan amháin a dhéanfaidh breithniú air. Más rud é 
nach tusa an duine ar leis é, tá cosc iomlán ar aon fhaisnéis atá ann, a úsáid, 
a chraobhscaoileadh, a scaipeadh, a nochtadh, a fhoilsiú, ná a chóipeáil . 
Seains gurb iad tuairimí pearsanta an údar atá san ríomhphost agus nach 
tuairimí FSS iad.

Má fuair tú an ríomhphost seo trí dhearmad, bheadh muid buíoch dá gcuirfeá in 
iúil don Deasc Seirbhísí ECT ar an nguthán ag +353 818 
300300 nó ar an ríomhphost chuig 
service.d...@hse.ie<mailto:service.d...@hse.ie> agus ansin glan an ríomhphost 
seo ded' chóras."



"Information in this email (including attachments) is confidential. It is 
intended for receipt and consideration only by the intended recipient. If you 
are not an addressee or intended recipient, any use, dissemination, 
distribution, disclosure, publication or copying of information contained in 
this email is strictly prohibited. Opinions expressed in this email may be 
personal to the author and are not necessarily the opinions of the HSE.

If this email has been received by you in error we would be grateful if you 
could immediately notify the ICT Service Desk by telephone at +353 818 
300300 or by email to 
service.d...@hse.ie<mailto:service.d...@hse.ie> and thereafter delete this 
e-mail from your system"




__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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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] Network issue

[James Powell]

Hi Stephen,
I didn’t see this suggested previously, but yes I have made repeated attempts 
to gain access to CRAN via R but to no avail. Mirroring CRAN is a really good 
idea, but I’m not sure how to get R to recognise the local file locations when 
the installation files seek access to CRAN via urls. Thanks again for your 
help. Regards, James

From: stephen sefick 
Sent: Wednesday 21 February 2024 00:04
To: James Powell 
Cc: r-help@r-project.org
Subject: Re: [R] Network issue

CAUTION: This email originated from outside of the organisation. Do not click 
links or open attachments unless you recognise the sender and know the content 
is safe.

As stated in an earlier email, this might be better directed to your IT? You 
might think about mirroring CRAN locally, but this would be non-trivial.

Stephen Sefick

On Tue, Feb 20, 2024, 17:26 James Powell 
mailto:james.pow...@hse.ie>> wrote:
Hi Stephen,
Thanks very much for getting back to me. My problem is described below. Any 
help would be greatly appreciated. Thanks, James

Hi,
Sorry for bothering you because I know that your time is voluntary, but I would 
really appreciate some help. I work in a hospital in part of Ireland’s national 
health service, a service which was struck by a massive cyber attack a couple 
of years ago. Since then their security has been very tight, and I can’t access 
the internet through my R or R Studio. To install packages I need to download 
the files through a browser (Chrome by default) and install them from the 
files, which is very tedious when you consider the amount of dependencies, but 
I’m happy to do it.

This was working fine until yesterday when I had error messages trying to 
install some packages. See enclosed “S2” for example. It looks like it is 
trying to download a file as part of the installation, but of course can’t. If 
you could help with this I would be very grateful. Other examples are jqr, 
protolite, curl.

I came across a different error message when trying to install openssl, 
although the issue may be the same. For this package it says

Warning in file(name, "wb") :
  cannot open file 'openssl/tests/keys/message.rsa.crypt': Permission denied
Error in file(name, "wb") : cannot open the connection

I have tried going into the archive of these packages and installing older 
versions, but no luck with those either.
I hope you can help. Best wishes, James


From: stephen sefick mailto:ssef...@gmail.com>>
Sent: Tuesday 20 February 2024 19:43
To: James Powell mailto:james.pow...@hse.ie>>
Cc: r-help@r-project.org<mailto:r-help@r-project.org>
Subject: Re: [R] Network issue

CAUTION: This email originated from outside of the organisation. Do not click 
links or open attachments unless you recognise the sender and know the content 
is safe.

Maybe I missed the rest of the post? You are more likely to get help with your 
problems if you create a minimal reproducible example.
Kindest regards,

Stephen Sefick

On Tue, Feb 20, 2024, 12:24 James Powell 
mailto:james.pow...@hse.ie>> wrote:



Need information and advice on COVID-19? Go to 
www.hse.ie/coronavirus<https://scanner.topsec.com/?d=2120=show=https%3A%2F%2Fwww.hse.ie%2Fcoronavirus=ceec0a7bd0b1f730294db0447d2a0c1ad2741351>


"Tá an fhaisnéis sa ríomhphost seo (ceangaltáin san áireamh) faoi rún. Baineann 
sé leis an té ar seoladh chuige amháin agus tá sé ar intinn go bhfaighfidh 
siadsan amháin é agus gurb iadsan amháin a dhéanfaidh breithniú air. Más rud é 
nach tusa an duine ar leis é, tá cosc iomlán ar aon fhaisnéis atá ann, a úsáid, 
a chraobhscaoileadh, a scaipeadh, a nochtadh, a fhoilsiú, ná a chóipeáil . 
Seains gurb iad tuairimí pearsanta an údar atá san ríomhphost agus nach 
tuairimí FSS iad.

Má fuair tú an ríomhphost seo trí dhearmad, bheadh muid buíoch dá gcuirfeá in 
iúil don Deasc Seirbhísí ECT ar an nguthán ag +353 818 
300300 nó ar an ríomhphost chuig 
service.d...@hse.ie<mailto:service.d...@hse.ie> agus ansin glan an ríomhphost 
seo ded' chóras."



"Information in this email (including attachments) is confidential. It is 
intended for receipt and consideration only by the intended recipient. If you 
are not an addressee or intended recipient, any use, dissemination, 
distribution, disclosure, publication or copying of information contained in 
this email is strictly prohibited. Opinions expressed in this email may be 
personal to the author and are not necessarily the opinions of the HSE.

If this email has been received by you in error we would be grateful if you 
could immediately notify the ICT Service Desk by telephone at +353 818 
300300 or by email to 
service.d...@hse.ie<mailto:service.d...@hse.ie> and thereafter delete this 
e-mail from your system"







Need information and advice on COVID-19? Go to 
www.hse.ie/coronavirus<https://www.hse.ie/coronavirus>

__

[R] Network issue

[James Powell]

R version 4.3.1 (2023-06-16 ucrt) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> utils:::menuInstallPkgs()
--- Please select a CRAN mirror for use in this session ---
Warning: failed to download mirrors file (cannot open URL 
'https://cran.r-project.org/CRAN_mirrors.csv'); using local file 
'C:/PROGRA~1/R/R-43~1.1/doc/CRAN_mirrors.csv'
Error in contrib.url(repos, type) : 
  trying to use CRAN without setting a mirror
In addition: Warning message:
In download.file(url, destfile = f, quiet = TRUE) :
  URL 'https://cran.r-project.org/CRAN_mirrors.csv': status was 'SSL connect 
error'
> utils:::menuInstallLocal()
Warning in file(name, "wb") :
  cannot open file 'openssl/tests/keys/message.rsa.crypt': Permission denied
Error in file(name, "wb") : cannot open the connection
Warning message:
In install.packages(files[tarballs], .libPaths()[1L], repos = NULL,  :
  installation of package ‘C:/Users/jpowell/DOWNLO~1/openssl_2.1.1 (1).tar.gz’ 
had non-zero exit status
> utils:::menuInstallLocal()
* installing *source* package 's2' ...
** package 's2' successfully unpacked and MD5 sums checked
** using staged installation
** libs
using C compiler: 'gcc.exe (GCC) 12.2.0'
using C++ compiler: 'G__~1.EXE (GCC) 12.2.0'
using C++11
g++  -std=gnu++11 -I"C:/PROGRA~1/R/R-43~1.1/include" -DNDEBUG 
-DS2_USE_EXACTFLOAT -D_USE_MATH_DEFINES -DNDEBUG -DIS_LITTLE_ENDIAN 
-DOMIT_STRPTIME -I../windows/openssl-1.1.1k/include -I../src 
-I'C:/Users/jpowell/AppData/Local/R/win-library/4.3/Rcpp/include' 
-I'C:/Users/jpowell/AppData/Local/R/win-library/4.3/wk/include'   
-I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall  
-mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++  -std=gnu++11 -I"C:/PROGRA~1/R/R-43~1.1/include" -DNDEBUG 
-DS2_USE_EXACTFLOAT -D_USE_MATH_DEFINES -DNDEBUG -DIS_LITTLE_ENDIAN 
-DOMIT_STRPTIME -I../windows/openssl-1.1.1k/include -I../src 
-I'C:/Users/jpowell/AppData/Local/R/win-library/4.3/Rcpp/include' 
-I'C:/Users/jpowell/AppData/Local/R/win-library/4.3/wk/include'   
-I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall  
-mfpmath=sse -msse2 -mstackrealign  -c cpp-compat.cpp -o cpp-compat.o
g++  -std=gnu++11 -I"C:/PROGRA~1/R/R-43~1.1/include" -DNDEBUG 
-DS2_USE_EXACTFLOAT -D_USE_MATH_DEFINES -DNDEBUG -DIS_LITTLE_ENDIAN 
-DOMIT_STRPTIME -I../windows/openssl-1.1.1k/include -I../src 
-I'C:/Users/jpowell/AppData/Local/R/win-library/4.3/Rcpp/include' 
-I'C:/Users/jpowell/AppData/Local/R/win-library/4.3/wk/include'   
-I"C:/rtools43/x86_64-w64-mingw32.static.posix/include" -O2 -Wall  
-mfpmath=sse -msse2 -mstackrealign  -c init.cpp -o init.o
g+
In file included from ../src/s2/s2cap.h:26,
 from ../src/s2/s2convex_hull_query.h:25,
 from s2geography/accessors-geog.h:4,
 from s2geography.h:4,
 from geography.h:7,
 from geography-operator.h:7,
 from s2-accessors.cpp:2:
../src/s2/encoded_uint_vector.h: In function 'void 
s2coding::EncodeUintWithLength(T, int, Encoder*)':
../src/s2/base/logging.h:169:47: warning: comparison of integer expressions of 
different signedness: 'size_t' {aka 'long long unsigned int'} and 'int' 
[-Wsign-compare]
  169 | #define S2_DCHECK_GE(val1, val2) S2_DCHECK_OP(>=, val1, val2)
  |   ^
../src/s2/base/logging.h:151:22: note: in definition of macro 'S2_DCHECK'
  151 | while (false && (condition)) S2NullStream()
  |  ^
../src/s2/base/logging.h:169:34: note: in expansion of macro 'S2_DCHECK_OP'
  169 | #define S2_DCHECK_GE(val1, val2) S2_DCHECK_OP(>=, val1, val2)
  |  ^~~~
../src/s2/encoded_uint_vector.h:134:3: note: in expansion of macro 
'S2_DCHECK_GE'
  134 |   S2_DCHECK_GE(encoder->avail(), length);
  |   ^~~~
../src/s2/encoded_uint_vector.h: In instantiation of 'T 
s2coding::EncodedUintVector::operator[](int) const [with T = long long 
unsigned int]':
../src/s2/encoded_string_vector.h:146:47:   required from here
../src/s2/encoded_uint_vector.h:246:25: warning: comparison of integer 
expressions of different signedness: 'int' and 'const uint32' {aka 'const 
unsigned int'} [-Wsign-compare]
  246 |   S2_DCHECK(i >= 0 && i < size_);
  |   ~~^~~

Re: [ESS] emacs theme for polymode with noweb files

[James W. MacDonald via ESS-help]

I personally like Dracula mode, although Nord seems pretty nice as well.

-Original Message-
From: ESS-help  On Behalf Of LaurentEss via 
ESS-help
Sent: Sunday, December 3, 2023 5:48 PM
To: ess-help@r-project.org
Subject: [ESS] emacs theme for polymode with noweb files

Dear ESS-list,

   I tried many dark color themes to do literate programming with polymode 
(.rnw file) but there are always some drawbacks : the color of the beginning 
and the end of the chunks (<<>>= and @) are unreadable, the color of the 
text when I want to see the available buffers (C-x C-b) is unreadable, etc...

May you please tell me the name of a color theme which works fine with polymode 
for noweb files ?

I tried to find an answer on the web without success.

Thank you

Best regards

Laurent

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Re: [R] Different TFIDF settings in test set prevent testing model

[James C Schopf]

Thank you Bert and Ivan,

I was building the SVM model in hopes of applying it to future cases and hoped 
that the model would be able to deal with new words it hadn't encountered 
during training.   But I tried Bert's suggestion by converting all of the data 
to tokens, creating a DTM, transforming the whole thing with TFI DF, and then 
separating it 75%/25%.  But when I began to train the SVM on the training data, 
R said it needed 26GB for a vector and crashed. I tried again, it crashed 
again.I don't know why this would happen.  I'd just trained 4 SVM models 
using my previous method without any memory trouble on my 8GB CPU.I 
unsuccessfully tried to remove the new words from the new test data. Should I 
try that?  Is there a way to stop my system from crashing with the new method?

Thank you for any ideas.

Here is the code I used when I separated the data after converting to tokens 
and applying TFI DF:

url <- "D:/test/M2.csv"
data <- read_csv(url)
text_corpus <- Corpus(VectorSource(data$Text))
tokenize_document <- function(doc) {
doc_tokens <- unlist(tokenize_words(doc))
doc_bigrams <- unlist(tokenize_ngrams(doc, n = 2))
doc_trigrams <- unlist(tokenize_ngrams(doc, n = 3))
all_tokens <- c(doc_tokens, doc_bigrams, doc_trigrams)
return(all_tokens)
}
all_tokens <- lapply(text_corpus, tokenize_document)
text_dtm <- DocumentTermMatrix(Corpus(VectorSource(all_tokens)))
text_tfidf <- weightTfIdf(text_dtm)
processed_data <- data.frame(M2 = data$M2, text_tfidf = as.matrix(text_tfidf))
indexes <- createDataPartition(processed_data$M2, p = 0.75, list = FALSE)
trainData <- processed_data[indexes,]
testData <- processed_data[-indexes,]
ctrl <- trainControl(method = "repeatedcv", number = 5, repeats = 2, classProbs 
= TRUE)
model_svmRadial <- train(M2 ~ ., data = trainData, method = "svmRadial", 
trControl = ctrl)






____
From: Ivan Krylov 
Sent: Saturday, August 12, 2023 12:49 AM
To: James C Schopf 
Cc: r-help@r-project.org 
Subject: Re: [R] Different TFIDF settings in test set prevent testing model

� Fri, 11 Aug 2023 10:20:27 +
James C Schopf  �:

> > train_text_dtm <-
> > DocumentTermMatrix(Corpus(VectorSource(all_train_tokens)))

> > test_text_dtm <-
> > DocumentTermMatrix(Corpus(VectorSource(all_test_tokens)))

I understand the need to prepare the test dataset separately
(e.g. in order to be able to work with text that don't exist at the
time when model is trained), but since the model has no representation
for tokens it (well, the tokeniser) hasn't seen during the training
process, you have to ensure that test_text_dtm references exactly the
same tokens as train_text_dtm, in the same order of the columns.

Also, it probably makes sense to reuse the term frequency learned on
the training document set; otherwise you may be importance-weighting
different tokens than ones your SVM has learned as important if your
test set has a significantly different distribution from that of the
training set.

Bert is probably right: with the API given by the tm package, it's
seems easiest to tokenise and weight document-term matrices first, then
split them into the train and test subsets. It may be worth asking the
maintainer about applying previously "learned" transformations to new
corpora.

--
Best regards,
Ivan

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[R] Different TFIDF settings in test set prevent testing model

[James C Schopf]

Hello, I'd be very grateful for your help.

I randomly separated a .csv file with 1287 documents 75%/25% into 2 csv files, 
one for training an algorithm and the other for testing the algorithm.  I 
applied similar preprocessing, including TFIDF transformation, to both sets, 
but R won't let me make predictions on the test set due to a different TFIDF 
matrix.
I get the error message:

Error: variable 'text_tfidf' was fitted with type "nmatrix.67503" but type 
"nmatrix.27118" was supplied

I'd greatly appreciate a suggestion to overcome this problem.
Thanks!


Here's my R codes:

> library(tidyverse)
> library(tidytext)
> library(caret)
> library(kernlab)
> library(tokenizers)
> library(tm)
> library(e1071)

***LOAD TRAINING SET/959 rows with text in column1 and yes/no in column2 
(labelled M2)
> url <- "D:/test/M2_75.csv"
> d <- read_csv(url)
***CREATE TEXT CORPUS FROM TEXT COLUMN
> train_text_corpus <- Corpus(VectorSource(d$Text))
***DEFINE TOKENS FOR EACH DOCUMENT IN CORPUS AND COMBINE THEM
> tokenize_document <- function(doc) {
+ doc_tokens <- unlist(tokenize_words(doc))
+ doc_bigrams <- unlist(tokenize_ngrams(doc, n = 2))
+ doc_trigrams <- unlist(tokenize_ngrams(doc, n = 3))
+ all_tokens <- c(doc_tokens, doc_bigrams, doc_trigrams)
+ return(all_tokens)
+ }
***APPLY TOKENS TO DOCUMENTS
> all_train_tokens <- lapply(train_text_corpus, tokenize_document)
***CREATE A DTM FROM THE TOKENS
> train_text_dtm <- DocumentTermMatrix(Corpus(VectorSource(all_train_tokens)))
***TRANSFORM THE DTM INTO A TF-IDF MATRIX
> train_text_tfidf <- weightTfIdf(train_text_dtm)
***CREATE A NEW DATA FRAME WITH M2 COLUMN FROM ORIGINAL DATA
> trainData <- data.frame(M2 = d$M2)
***ADD NEW TFIDF transformed TEXT COLUMN NEXT TO DATA FRAME
> trainData$text_tfidf <- I(as.matrix(train_text_tfidf))
***DEFINE THE ML MODEL
> ctrl <- trainControl(method = "repeatedcv", number = 5, repeats = 2, 
> classProbs = TRUE)
***TRAIN SVM
> model_svmRadial <- train(M2 ~ ., data = trainData, method = "svmRadial", 
> trControl = ctrl)
***SAVE SVM
> saveRDS(model_svmRadial, file = "D:/SML/model_M23_svmRadial_UP.RDS")

R code on my test set, which didn't work at last step:

***LOAD TEST SET/ 309 rows with text in column1 and yes/no in column2 (labelled 
M2)
> url <- "D:/test/M2_25.csv"
> d <- read_csv(url)
***CREATE TEXT CORPUS FROM TEXT COLUMN
> test_text_corpus <- Corpus(VectorSource(d$Text))
***DEFINE TOKENS FOR EACH DOCUMENT IN CORPUS AND COMBINE THEM
> tokenize_document <- function(doc) {
 doc_tokens <- unlist(tokenize_words(doc))
 doc_bigrams <- unlist(tokenize_ngrams(doc, n = 2))
 doc_trigrams <- unlist(tokenize_ngrams(doc, n = 3))
 all_tokens <- c(doc_tokens, doc_bigrams, doc_trigrams)
 return(all_tokens)
 }
***APPLY TOKEN TO DOCUMENTS
> all_test_tokens <- lapply(test_text_corpus, tokenize_document)
***CREATE A DTM FROM THE TOKENS
> test_text_dtm <- DocumentTermMatrix(Corpus(VectorSource(all_test_tokens)))
***TRANSFORM THE DTM INTO A TF-IDF MATRIX
> test_text_tfidf <- weightTfIdf(test_text_dtm)
***CREATE A NEW DATA WITH M2 COLUMN FROM ORIGINAL TEST DATA
> testData <- data.frame(M2 = d$M2)
***ADD NEW TFIDF transformed TEXT COLUMN NEXT TO TEST DATA
> testData$text_tfidf <- I(as.matrix(test_text_tfidf))
***LOAD OLD MODEL
model_svmRadial <- readRDS("D:/SML/model_M2_75_svmRadial.RDS")
 ***MAKE PREDICTIONS
predictions <- predict(model_svmRadial, newdata = testData)

This last line produces the error message:

Error: variable 'text_tfidf' was fitted with type "nmatrix.67503" but type 
"nmatrix.27118" was supplied

Please help.  Thanks!








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[R] Help sourcing datasets (.csv)

[james carrigan]

Dear Sir or Madam
I’m trying to compile a collection of datasets that require use of the 
following hypothesis tests.
Are there datasets within the R library that I can get access to?
Kind regards
James Carrigan 

Hypothesis Testing
t.test(X,Y) 
— performs a two sample t-test between X and Y 
t.test(X,Y,paired=TRUE) 
— performs a paired t-test between X and Y
prop.test(x = c(a, b), n = c(n1, n2)) 
— performs a 2-sample test for equality of proportions with continuity 
correction

Sent from my iPad Sent from my iPhone
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[R] useR 2023 regional events

[Black, James via R-help]

With the support of the R Foundation Conference Committee, we are happy to
announce the promotion of regional R events to connect our R community and
bridge us till useR! 2024.

On July 21st we hold an event in Basel, with all ticket sales for the
Basel event being directly donated to the R Foundation. Similar events are
being planned in Shanghai and San Francisco this summer.

Basel event link (call for abstracts is currently open):
https://user-regional-2023.gitlab.io/basel/

We also wanted to help promote events beyond those organised in
collaboration with the R Foundation and R User Group (RUGs), so are hosting
this dashboard of R events this summer which will also include the Shanghai
and San Francisco events when they are launched:
https://user-regional-2023.gitlab.io/user-regional-2023.io/

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[R] Install Rmpi on Linux on a HPC

[James Li]

Hi,

Recently, I have had a hard time installing and running the package on an
HPC.

The HPC sysadmin installed Rmpi package without any error.

However, when he tried a simple R script with only one line:
 library(Rmpi)
the job caused "Segmentation Fault" error.

Currently, we have no clue to solve this problem. I am writing this
email to ask for help.

System info
uname -a
Linux ito-1 3.10.0-514.26.2.el7.x86_64 #1 SMP Fri Jun 30 05:26:04 UTC 2017
x86_64 x86_64 x86_64 GNU/Linux

Thank you

Best regards

-- 
---
Li

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[R] pseudoreplication

[James Henson]

Greetings R Community
The ASReml-R package will analyze data from experiments with
pseudoreplications.

Dealing with Pseudo-Replication in Linear Mixed Models
https://www.vsni.co.uk/case-studies/dealing-with-pseudo-replication-in-linear-mixed-models

Will the ‘lme4’ package return an equivalent analysis of data from
experiments with pseudoreplications?
Thank you for your assistance.

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[R] Replacing certain rows with values from a different column

[James Milks via R-help]

I have two columns in a larger data set that list countries in one column and, 
in some cases, individual provinces within a country or oversea territories in 
another. I have country population in a second data set that I’m planning to 
use to calculate per capita rates in the first data set. My issue: I need to 
match my two data sets. Here are some examples:

First data set:

Province <- c("Australian Capital Territory", "New South Wales", "Northern 
Territory", "Queensland", "South Australia", "Tasmania", "Victoria", "Western 
Australia", "", "", "", "Faroe Islands", "Greenland")

Country <- c("Australia", "Australia", "Australia", "Australia", "Australia", 
"Australia", "Australia", "Australia", "Austria", "Azerbaijan", "Denmark", 
"Denmark", "Denmark")

firstdf <- data.frame(Province, Country)

Second data set:

Country <- c("Australia", "Austria", "Azerbaijan", "Denmark", "Faroe Islands", 
"Greenland")

seconddf <- data.frame(Country)

In this example, I need to aggregate sum Australia while keeping Faroe Islands 
and Greenland separate from Denmark. What I’d like to do is create a column 
that looks like this:

firstdf$nation <- c("Australia", "Australia", "Australia", "Australia", 
"Australia", "Australia", "Australia", "Australia", "Austria", "Azerbaijan", 
"Denmark", “Faroe Islands", “Greenland”)

Is there a way to do this or am I stuck doing this by hand?

Thanks for any help on this vexing issue.

Jim Milks
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[R] calculating area of ellipse

[james meyer]

In doing meta-analysis of diagnostic accuracy I produce ellipses of confidence
and prediction intervals in two dimensions.  How can I calculate the area of
the ellipse in ggplot2 or base R?

thank you
James Meyer

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Re: [R] COVID-19 datasets...

[James Spottiswoode]

Sure. COVID-19 Data Repository by the Center for Systems Science and 
Engineering (CSSE) at Johns Hopkins University is available here:

https://github.com/CSSEGISandData/COVID-19

All in csv fiormat.


> On May 4, 2020, at 11:31 AM, Bernard McGarvey  
> wrote:
> 
> Just curious does anyone know of a website that has data available in a 
> format that R can download and analyze?
>  
> Thanks
> 
> 
> Bernard McGarvey
> 
> 
> Director, Fort Myers Beach Lions Foundation, Inc.
> 
> 
> Retired (Lilly Engineering Fellow).
> 
> __
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> and provide commented, minimal, self-contained, reproducible code.
> 

James Spottiswoode
Applied Mathematics & Statistics
(310) 270 6220
jamesspottiswoode Skype
ja...@jsasoc.com




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[R] How to parallelize a process called by a socket connection

[James Spottiswoode]

Hi R Experts,

I’m using R version 3.4.3 running under Linux on an AWS EC2 instance.  I have 
an R code listening on a port for a socket connection which passes incoming 
data to a function the results of which are then passed back to the calling 
machine.  Here’s the function that listens for a socket connection:

# define server function
server <- function() {  
  while(TRUE){
con <- socketConnection(host="localhost", port = server_port, 
blocking=TRUE,
server=TRUE, open="r+", timeout = 1)
data <- readLines(con, 1L, skipNul = T, ok = T)
response <- check(data)
if (!is.null(response)) writeLines(response, con)
  }
}

The server function expects to receive a character string which is then passed 
to the function check().  check() is a large, complex routine which does text 
analysis and many other things and returns a JSON string to be passed back to 
the calling machine.  

This all works perfectly except that while check() spends ~50ms doing its stuff 
no more requests can be received and processed. Therefore if a new request 
comes in sooner than ~50ms after the last one, it is not processed. I would 
therefore like to parallelize this so that the box can be running more than one 
check() process simulatanously.  I’m familar with several of the paralyzing R 
packages but I cannot see how to integrate them with the socket connection side 
of things.  

Currently I have a kludge which is a round-robin approach to solving the 
problem.  I have 4 versions of the whole R code listening on 4 different ports, 
say P1, P2, P3, P4, and the calling machine issues calls in sequence to ports 
P1,P2,P3,P4,P1… etc. This mitigates, but doesn’t solve, the problem.

Any advice would be greatly appreciated!  Thanks.

James 

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Re: [R] File names for mac newby

[James Spottiswoode]

OSX is based on BSD UNIX so paths use the forward slash as separator, e.g.

temps <- 
read.table("c:/Users/DFP/Documents/ah/house/HouseTemps.txt",header=T,row.names=1)

Best James

> On Jan 21, 2020, at 9:20 AM, David  wrote:
> 
> I moved to a mac a few months ago after years in windows, and I'm still 
> learning basics.  I'm wanting to create a data frame based on a text file 
> called HouseTemps.txt.  That's a file within one called house which is within 
> one called ah.  That may further be in one called  Documents.  I tried 
> various lines like:
> 
> temps <- 
> read.table("c:\\Users\\DFP\\Documents\\ah\\house\\HouseTemps.txt",header=T,row.names=1)
> 
> based on my windows DOS experience, but nothing I try works.  So my question 
> is, what do complete file names look like in a mac?
> 
> I tried Apple support, but they couldn't help me with R.
> 
> __
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> and provide commented, minimal, self-contained, reproducible code.
> 



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[R] R package for meta-analysis from z scores

[james poweraid]

Hello,

I have a set of Z scores from an N=2 studies and I need to run a
meta-analysis across the two Z scores for many N variables. I do not have
effect sizes and SEs. I realize there are many different meta analysis
packages in R, but I only have Z scores and it seems to me this is
limiting. I am using the metap package because this very conveniently
accepts directly p values which I can get from my Z scores. I have applied
what is called in metap package the sumlog Fisher’s method Chi square (2
df).

I have three questions:

   1. Is this the same as a fixed effect meta-analysis without weights?
   2. Is there any way to do a random effects meta-analysis starting only
   with Z scores?
   3. Is there a way to get the I2 heterogeneity across studies from this
   or from other packages? It looks like I need the estimates for this. Is
   there another package that can easily get this using as input Z scores or P
   values?

Data

library(metap)

zscores = cbind(c(4, 2, 0.1),c(5, 2.5, 0.1))

pvalues = apply(zscores, 1:2, function(x)  2*(pnorm( abs(x) ,
lower.tail=F)))

meta = apply(pvalues, MARGIN=1, FUN=sumlog)



Thank you much

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Re: [R] Global curve fitting/shared parameters with nls() alternatives

[James Wagstaff]

Dear Bert
Thanks for getting back to me. Yes that is exactly the sort of problem I am
trying to solve. I am aware of the option of hard coding the experimental
groups as you suggested, but was hoping for an easy out of the box approach
as I have many groups!
Thanks
James

On Tue, 5 Nov 2019 at 20:28, Bert Gunter  wrote:

> A simplified example of what you wish to do might help to clarify here.
>
> Here's my guess. Feel free to dismiss if I'm off base.
>
> Suppose your model is:
> y = exp(a*x) + b
>
> and you wish the b to be constant but the a to vary across expts. Then can
> you not combine the data from both into single x, y vectors, add a variable
> expt that takes the value 1 for expt1 and 2 for expt 2 and fit the single
> model:
>
> y = (expt ==1)*(exp(a1*x) + b)   +  (expt == 2)* (exp(a2*x) + b)
>
> This would obtain separate estimates of a1 and a2 but a single estimate of
> b .
>
> There are probably better ways to do this, but I've done hardly any
> nonlinear model fitting (so warning!) and can only offer this brute force
> approach; so wait for someone to suggest something better before trying it.
>
> Cheers,
> Bert
>
>
> On Tue, Nov 5, 2019 at 9:12 AM James Wagstaff 
> wrote:
>
>> Hello
>> I am trying to determine least-squares estimates of the parameters of a
>> nonlinear model, where I expect some parameters to remain constant across
>> experiments, and for others to vary. I believe this is typically referred
>> to as global curve fitting, or the presence of shared/nested parameters.
>> The "[]" syntax in the stats::nls() function is an extremely convenient
>> solution (
>>
>> https://r.789695.n4.nabble.com/How-to-do-global-curve-fitting-in-R-td4712052.html
>> ),
>> but in my case I seem to need the Levenberg-Marquardt/Marquardt solvers
>> such as nlsr::nlxb() and minpack.lm::nlsLM. I can not find any
>> examples/documentation explaining a similar syntax for these tools. Is
>> anyone aware of a nls-like tool with this functionality, or an alternative
>> approach?
>> Best wishes
>> James Wagstaff
>>
>> [[alternative HTML version deleted]]
>>
>> __
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>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>

-- 
James Wagstaff

+447910113349

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[R] Global curve fitting/shared parameters with nls() alternatives

[James Wagstaff]

Hello
I am trying to determine least-squares estimates of the parameters of a
nonlinear model, where I expect some parameters to remain constant across
experiments, and for others to vary. I believe this is typically referred
to as global curve fitting, or the presence of shared/nested parameters.
The "[]" syntax in the stats::nls() function is an extremely convenient
solution (
https://r.789695.n4.nabble.com/How-to-do-global-curve-fitting-in-R-td4712052.html),
but in my case I seem to need the Levenberg-Marquardt/Marquardt solvers
such as nlsr::nlxb() and minpack.lm::nlsLM. I can not find any
examples/documentation explaining a similar syntax for these tools. Is
anyone aware of a nls-like tool with this functionality, or an alternative
approach?
Best wishes
James Wagstaff

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Re: [R] Parameters optimization in r

[James Spottiswoode]

Hi,

I’ve often come across this problem and have found genetic algorithms (GA) to 
be extremely useful. I wrote my first GA code in the 80’s and have extensive 
experience with the method. The package rgenoud is a very full featured  GA 
implementation.  Just code up your parameters as arguments to the function 
giving your method, random forests or whatever, then define a target variable 
for performance or fitness such as AUC or R^2, whatever is appropriate, and let 
the GA climb to the top of the fitness landscape.  If you have a large problem 
you may want to speed things up by using parallel processes across cores or 
machines.  Rgenoud handles that well.

Good luck!

James


> On Oct 11, 2019, at 4:21 PM, javed khan  wrote:
> 
> Hi
> 
> I will appreciate if someone provide the link to some tutorials/videos
> where parameters running are performed in R. For instance, if we have to
> perform predictions/classification using random forest or other algorithm,
> how different optimization algorithms tune the parameters of random forest
> such as numbers of trees etc.
> 
> Best regards
> 
>   [[alternative HTML version deleted]]
> 
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> and provide commented, minimal, self-contained, reproducible code.
> 

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[R] Large mixed & crossed-effect model looking at educational spending on crime rates with error messages

[Ades, James]

I posted my question at Stack Overflow, where it didn’t get much of a response, 
and I was pointed in this direction by Ben Bolker. I’m happy to send the whole 
dataset to anyone who wants but thought that it would be presumptuous to 
include an enormous dput() here.

I’m looking at the effects of education spending per school district on crime 
rate (FBI crime data/UCR) within the cities and towns those school districts 
serve over a fifteen year period. The DV now has 203,410 observations of 
city/town crime data over those fifteen years. (I use that figure with some 
reticence, because there are so many moving parts and things to account for, 
but having employed over 100 datasets and hours passing through the code again, 
I think that figure is correct.)

Cities are technically crossed with school district, in that one city might 
attend multiple school districts. This means that one city could have multiple 
values for expenditure per student. School districts, however, also overlap 
with counties. As if things weren’t complicated enough, cities are mostly 
nested within county (though there are cities that exist in two counties, but 
it’s not often, and it’s usually by a small amount). Given that each city/town 
has a distinct PLACE_ID, my understanding is that this could be represented as 
(1|PLACE_ID) + (1|STATE/COUNTY_ID) or (1|STATE/COUNTY_ID/PLACE_ID).

I’m pretty familiar with mixed-effect models, and I’ve looked through clear and 
informative posts such as this one: 
https://stats.stackexchange.com/questions/228800/crossed-vs-nested-random-effects-how-do-they-differ-and-how-are-they-specified.
 I believe things would remain sane to include school district 
(full_district_id) as another crossed effect, as below:
glmer.total <- glmer(CRIME_TOTAL ~ 1 + (year|PLACE_ID) + (1|STATE/COUNTY_ID) + 
(year|full_district_id), family = "poisson", control = glmerControl(optimizer = 
"nloptwrap", calc.derivs = FALSE), REML = FALSE, total.years, na.action = 
"na.omit")

Variables (not included in this model, to keep things null and simple) are 
centered and logged: pop per city, pop.dens per city, year, unemployment rate 
per county, proportion children living in poverty per school district, per 
capita income per county, difference in those who voted democrat in 
presidential elections per county, log enforcement per city/town, centered 
expenditure per student/ 1000 (per school district). PLACE_ID corresponds to 
cities and towns, COUNTY_ID to counties, full_district_id to school districts, 
and state.

First, if I try to run the full model, using UCSD’s supercomputer, I get the 
error that the job was killed, presumably because it got to a point where it 
consumed too much ram (I think 125mb).

I then tried to create a small subsection of data with arrange(STATE, 
COUNTY_ID, PLACE_ID) and then slicing by the first ten states (up through 
Delaware), so that I have 26,599 values. If I run this null model with the 
above code, I get the following error:

```
Error in getOptfun(optimizer) :
  optimizer function must use (at least) formal parameters ‘fn’, ‘par’, 
‘lower’, ‘control’
```

Then I tried with the optimx, with these configurations: control = 
glmerControl(optimizer = "optimx”,
optCtrl = list(method = "nlminb”,
maxit=1,
iter.max=1,
eval.max=1,
lower = c(0,0,0),
upper = c(Inf,10,1)))

and I received the following warning…since this is a null model, there aren’t 
any variables to really rescale.\

```
Warning messages:
1: In nlminb(start = par, objective = ufn, gradient = ugr, lower = lower,  :
  unrecognized control elements named ‘lower’, ‘upper’ ignored
2: In nlminb(start = par, objective = ufn, gradient = ugr, lower = lower,  :
  unrecognized control elements named ‘lower’, ‘upper’ ignored
3: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model failed to converge with max|grad| = 0.00102386 (tol = 0.001, component 
1)
4: In checkConv(attr(opt, "derivs"), opt$par, ctrl = control$checkConv,  :
  Model is nearly unidentifiable: very large eigenvalue
 - Rescale variables?
```

I then tried more values (to 92,486, through Missouri). First, I tried the 
optimizer nloptr, and then I tried the optimix. I still received the same above 
errors.

I’ve checked and rechecked everything, so I wanted to solicit advice, either 
for where I might be going wrong, or for what I could do to resolve these error 
messages.

I’ve provided a brief snippet of the data below (randomly pulling a number of 
cities within counties of Arkansas, Arizona, and Alabama, as a dput.

Thanks!




231, 206, 935, 1070, 974, 1108, 1244, 1095, 1131, 1151, 1420,
1316, 1321, 1414, 1484), full_district_id = c("0100240", "0100240",
"0100240", "0100240", "0100240", "0100240", "0100240", "0100240",
"0100240", "0100240", "0100240", "0100240", "0100240", "0100240",
"0100240", "0100240", "0100240", "0100240", "0100240", "0100240",
"0100240", "0100240", "0100240", "0100240", "0100240", "0100240",
"0100240", 

Re: [R] Problem parallelizing across cores

[James Spottiswoode]

> On Aug 28, 2019, at 4:44 PM, James Spottiswoode  wrote:
> 
> Hi Bert,
> 
> Thanks for your advice.  Actually i’ve already done this and have checked out 
> doParallel and future packages.  The trouble with doParallel is that it forks 
> R processes which spend a lot of time loading data and packages whereas my 
> function runs in 100ms so the parallelization doesn’t help.  The future 
> package keeps it’s children running but I haven’t figured out how to get it 
> to work in my application.
> 
> Best — James
> 
> 
>> On Aug 28, 2019, at 3:39 PM, Bert Gunter > <mailto:bgunter.4...@gmail.com>> wrote:
>> 
>> 
>> I would suggest that that you search on "parallel computing" at the 
>> Rseek.org <http://rseek.org/> site. This brought up what seemed to be many 
>> relevant hits including, of course, the High Performance and parallel 
>> Computing Cran task view.
>> 
>> Cheers,
>> Bert
>> 
>> 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, Aug 28, 2019 at 3:18 PM James Spottiswoode 
>> mailto:james.spottiswo...@gmail.com>> wrote:
>> Hi All,
>> 
>> I have a piece of well optimized R code for doing text analysis running
>> under Linux on an AWS instance.  The code first loads a number of packages
>> and some needed data and the actual analysis is done by a function called,
>> say, f(string).  I would like to parallelize calling this function across
>> the 8 cores of the instance to increase throughput.  I have looked at the
>> packages doParallel and future but am not clear how to do this.  Any method
>> that brings up an R instance when the function is called will not work for
>> me as the time to load the packages and data is comparable to the execution
>> time of the function leading to no speed up.  Therefore I need to keep a
>> number of instances of the R code running continuously so that the data
>> loading only occurs once when the R processes are first started and
>> thereafter the function f(string) is ready to run in each instance.  I hope
>> I have put this clearly.
>> 
>> I’d much appreciate any suggestions.  Thanks in advance,
>> 
>> James Spottiswoode
>> 
>> 
>> --
>> 
>> [[alternative HTML version deleted]]
>> 
>> __
>> R-help@r-project.org <mailto:R-help@r-project.org> mailing list -- To 
>> UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help 
>> <https://stat.ethz.ch/mailman/listinfo/r-help>
>> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html 
>> <http://www.r-project.org/posting-guide.html>
>> and provide commented, minimal, self-contained, reproducible code.
> 
> James Spottiswoode
> Applied Mathematics & Statistics
> (310) 270 6220
> jamesspottiswoode Skype
> ja...@jsasoc.com <mailto:ja...@jsasoc.com>

James Spottiswoode
Applied Mathematics & Statistics
(310) 270 6220
jamesspottiswoode Skype
ja...@jsasoc.com


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[R] Problem parallelizing across cores

[James Spottiswoode]

Hi All,

I have a piece of well optimized R code for doing text analysis running
under Linux on an AWS instance.  The code first loads a number of packages
and some needed data and the actual analysis is done by a function called,
say, f(string).  I would like to parallelize calling this function across
the 8 cores of the instance to increase throughput.  I have looked at the
packages doParallel and future but am not clear how to do this.  Any method
that brings up an R instance when the function is called will not work for
me as the time to load the packages and data is comparable to the execution
time of the function leading to no speed up.  Therefore I need to keep a
number of instances of the R code running continuously so that the data
loading only occurs once when the R processes are first started and
thereafter the function f(string) is ready to run in each instance.  I hope
I have put this clearly.

I’d much appreciate any suggestions.  Thanks in advance,

James Spottiswoode


--

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[R] Application Sizing

[James Bowery]

Given an "R" application's source code, how does one measure the number of
bytes taken by just the compiled application, not including the CRAN
libraries?

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[R] Fwd: Custom legend in ggplot - stat_summary shape and geom_bar fill

[James Dare]

Hi Everyone,

I am spending far to much time on this problem.  Every post I read gets me
closer to a solution,  but I am still not quite there.

I am trying to create a bar plot similar to the one below:

<http://r.789695.n4.nabble.com/file/t124289/Desired_Output.png>

My code is as follows:

q92 <- function(x) {quantile(x,probs=0.92,na.rm = TRUE)}

ggplot(River_Df, aes(x= reorder(Name, ECOLI, FUN = q92, order=TRUE),
y=ECOLI))+
  geom_bar(stat="summary",fun.y="median",aes(colour = "Median"),
fill="#2eb82e")+
  stat_summary(fun.y=q92, geom ="point",size=3, shape=18,aes(colour ="95th
Percentile"),show_guide = FALSE)+
  theme(axis.text.x = element_text(angle = 90, hjust = 1))+
  xlab(paste("Monitored River Sites
",format(min(River_Df$Time),"%Y"),"-",format(max(River_Df$Time),"%Y"),sep=""))+
  ylab("E. coli (cfu/100mL)")

As you can see, I end up with two legend items, '95th Percentile' and
'Median'.  However, I would like the '95th Percentile' item to be a darkred
diamond with no background.

Any ideas how to do this?  The dataset is attached below:

Datafile.csv <http://r.789695.n4.nabble.com/file/t124289/Datafile.csv>

Thanks in advance for your help.

James

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[R] [R-pkgs] New package: collateral 0.4.2 on CRAN

[James Goldie]

Hi everyone,

Collateral is now available on CRAN. If you've used purrr's side effect
capturing functions before, you'll love collateral: it provides you with
map variants that automatically wrap your mapped function in safely() or
quietly() and provide nicely printed output, allowing you to quickly see
which elements of a list returned results, and which returned errors,
warnings or messages. The package also provides helpers to let you
summarise your results and filter or aggregate the captured side effects.

If you haven't used a list-column workflow before, I've included a vignette
with collateral to get you started:
https://rensa.co/collateral/articles/collateral.html

If you'd like to contribute to collateral, you can find it on GitHub:
https://github.com/rensa/collateral

Thanks very much!

<https://rensa.co/collateral/articles/collateral.html>
-- 
=
James Goldie: PhD Student, Climate Change Research Centre
Email: j.gol...@unsw.edu.au, m...@rensa.co
Tel: +61 421 747 208
Skype: james-goldie
Web: https://rensa.co

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Re: [R] Best Optimization Routines

[JamesRyan(Ryan James)/E North America Business Division]

Thanks Paul.  Appreciate the help.  I'll give this a shot.  

Ryan James
D: 713.395.1794
M: 214.843.7301

-Original Message-
From: Paul Smith [mailto:phh...@gmail.com] 
Sent: Thursday, February 15, 2018 7:12 AM
To: Ryan James/E North America Business Division/SKI
Cc: r-help@r-project.org
Subject: Re: [R] Best Optimization Routines

On Tue, Feb 13, 2018 at 7:55 PM, JamesRyan(Ryan James)/E North America 
Business Division <rja...@sk.com> wrote:
> I have a set of data, the production of oil from a well.  And an equation to 
> predict that forecast.
>
> The equation requires 5 input variables which are real numbers with upper and 
> lower bounds, 1 input variable which must be an integer and 1 input variable 
> which can be 1 of 2 string variables.
>
> What is the best optimization routine (I am using nlminb) to use in R to 
> determine the best set of inputs and how to I handle the integer and string 
> inputs when optimizing?
>
> I have attached a plot of what I am trying to accomplish as well as my sample 
> code.

If I understand correctly your problem, your equation is linear, and you have 
continuous and integer variables (the string input can be coded as a binary 
integer variable). Thus, you can use a package to deal with mixed integer 
programming:

http://blog.revolutionanalytics.com/2016/12/mixed-integer-programming-in-r-with-the-ompr-package.html

Hope this helps you,

Paul
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[R] Best Optimization Routines

[JamesRyan(Ryan James)/E North America Business Division]

I have a set of data, the production of oil from a well.  And an equation to 
predict that forecast.  

The equation requires 5 input variables which are real numbers with upper and 
lower bounds, 1 input variable which must be an integer and 1 input variable 
which can be 1 of 2 string variables.  

What is the best optimization routine (I am using nlminb) to use in R to 
determine the best set of inputs and how to I handle the integer and string 
inputs when optimizing?  

I have attached a plot of what I am trying to accomplish as well as my sample 
code.  

Thanks,

Ryan




Rplot.pdf
Description: Rplot.pdf
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Re: [R] Error in loadNamespace

[James Henson]

Thanks David!, that fixed the problem.
Best regards,
James

On Thu, Dec 7, 2017 at 1:19 PM, David Winsemius <dwinsem...@comcast.net>
wrote:

>
> > On Dec 7, 2017, at 10:47 AM, James Henson <jfhens...@gmail.com> wrote:
> >
> > Hello R Community,
> >
> > I inadvertently updated packages via R Studio when a package was open.
> Now
> > when R Studio is opened the message below appears in the console panel.
> >
> > Error in loadNamespace(name) : there is no package called ‘yaml’
> >
> > Error in loadNamespace(name) : there is no package called ‘yaml’
> >
> > When running R code, so far the only function that has not worked is
> > datatable () in the ‘DT’ package.  Removing the ‘DT’ package and
> > reinstalling it had no effect.  A possible fix is to update R from an
> older
> > version, which was not running when I made the mistake.  Is this a good
> > idea?
>
> There is a package on CRAN named "yaml". Have your tried installing it?
> >
> > Thanks for your help.
> >
> > James F. Henson
> >
> >   [[alternative HTML version deleted]]
>
> Rhelp is a plain text mailing list.
>
> >
> > __
> > 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.
>
> David Winsemius
> Alameda, CA, USA
>
> 'Any technology distinguishable from magic is insufficiently advanced.'
>  -Gehm's Corollary to Clarke's Third Law
>
>
>
>
>
>

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[R] Error in loadNamespace

[James Henson]

Hello R Community,

I inadvertently updated packages via R Studio when a package was open.  Now
when R Studio is opened the message below appears in the console panel.

Error in loadNamespace(name) : there is no package called ‘yaml’

Error in loadNamespace(name) : there is no package called ‘yaml’

When running R code, so far the only function that has not worked is
datatable () in the ‘DT’ package.  Removing the ‘DT’ package and
reinstalling it had no effect.  A possible fix is to update R from an older
version, which was not running when I made the mistake.  Is this a good
idea?

Thanks for your help.

James F. Henson

[[alternative HTML version deleted]]

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[R] tidyquant error downloading symbols for Index

[Sparks, John James]

Hi R Helpers,

I recently tried to take advantage of the ability to download all the
tickers in the S 500 using the functionality of tidyquant, but it threw
an error.

For summary, the set of commands that I ran was

library(tidyquant)
tq_index_options()
tq_index("SP500")
sessionInfo()


R feedback including error message and sessionInfo are provided below.

Guidance would be appreciated.

--John J. Sparks, Ph.D.


> library(tidyquant)
Loading required package: lubridate

Attaching package: ‘lubridate’

The following object is masked from ‘package:base’:

date

Loading required package: PerformanceAnalytics
Loading required package: xts
Loading required package: zoo

Attaching package: ‘zoo’

The following objects are masked from ‘package:base’:

as.Date, as.Date.numeric


Package PerformanceAnalytics (1.4.3541) loaded.
Copyright (c) 2004-2014 Peter Carl and Brian G. Peterson, GPL-2 | GPL-3
http://r-forge.r-project.org/projects/returnanalytics/


Attaching package: ‘PerformanceAnalytics’

The following object is masked from ‘package:graphics’:

legend

Loading required package: quantmod
Loading required package: TTR
Version 0.4-0 included new data defaults. See ?getSymbols.
Learn from a quantmod author:
https://www.datacamp.com/courses/importing-and-managing-financial-data-in-r
Loading required package: tidyverse
Loading tidyverse: ggplot2
Loading tidyverse: tibble
Loading tidyverse: tidyr
Loading tidyverse: readr
Loading tidyverse: purrr
Loading tidyverse: dplyr
Conflicts with tidy packages
-
as.difftime(): lubridate, base
date():lubridate, base
filter():  dplyr, stats
first():   dplyr, xts
intersect():   lubridate, base
lag(): dplyr, stats
last():dplyr, xts
setdiff(): lubridate, base
union():   lubridate, base

Attaching package: ‘tidyquant’

The following object is masked from ‘package:dplyr’:

as_tibble

The following object is masked from ‘package:tibble’:

as_tibble

There were 14 warnings (use warnings() to see them)
> tq_index_options()
[1] "RUSSELL1000" "RUSSELL2000" "RUSSELL3000" "DOW" "DOWGLOBAL"
[6] "SP400"   "SP500"   "SP600"   "SP1000"
> tq_index("SP500")
Getting holdings for SP500
# A tibble: 0 x 0
Warning message:
In tq_index("SP500") : Error at SP500 during download.
Error: .onLoad failed in loadNamespace() for 'rJava', details:
  call: fun(libname, pkgname)
  error: No CurrentVersion entry in Software/JavaSoft registry! Try
re-installing Java and make sure R and Java have matching architectures.

> sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base

other attached packages:
 [1] tidyquant_0.5.3   dplyr_0.7.2
 [3] purrr_0.2.3   readr_1.1.1
 [5] tidyr_0.6.3   tibble_1.3.3
 [7] ggplot2_2.2.1 tidyverse_1.1.1
 [9] quantmod_0.4-10   TTR_0.23-2
[11] PerformanceAnalytics_1.4.3541 xts_0.10-0
[13] zoo_1.8-0 lubridate_1.6.0

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.12 cellranger_1.1.0 plyr_1.8.4   bindr_0.1
 [5] forcats_0.2.0tools_3.3.2  jsonlite_1.5 nlme_3.1-131
 [9] gtable_0.2.0 lattice_0.20-35  pkgconfig_2.0.1  rlang_0.1.1
[13] psych_1.7.5  curl_2.8.1   parallel_3.3.2   haven_1.1.0
[17] bindrcpp_0.2 xml2_1.1.1   httr_1.2.1   stringr_1.2.0
[21] hms_0.3  grid_3.3.2   glue_1.1.1   R6_2.2.2
[25] Quandl_2.8.0 readxl_1.0.0 foreign_0.8-69   modelr_0.1.1
[29] reshape2_1.4.2   magrittr_1.5 scales_0.4.1 rvest_0.3.2
[33] assertthat_0.2.0 mnormt_1.5-5 colorspace_1.3-2 stringi_1.1.5
[37] lazyeval_0.2.0   munsell_0.4.3broom_0.4.2

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[R] Looping Through QuantMod Objects

[Sparks, John James]

Dear R Helpers,

I have run into a problem trying to perform a number of actions on a set
of quantmod data objects through a loop and I am hoping that this is an
easy problem for someone else as opposed to very  difficult for me.

The example task is to get the first three objects of the quarterly
balance sheet for a number of companies from the getFinancials object and
put them together into a single file.  I can do this one by one, but if I
try to build a loop and use the get function then the results are not
anticipated and leave me baffled.

If I do it one at a time all is good.


require(quantmod)

getFinancials("AAPL")
getFinancials("IBM")
getFinancials("MSFT")


items=c("Cash & Equivalents","Short Term Investments","Cash and Short Term
Investments")

HoldQuart<-AAPL.f$BS$Q
CashHold<-subset(HoldQuart,rownames(HoldQuart) %in% items)
CashT<-t(CashHold)
Cashdf<-data.frame(CashT)
Cashdf$tic<-"AAPL"
AAPL.c<-Cashdf

HoldQuart<-IBM.f$BS$Q
CashHold<-subset(HoldQuart,rownames(HoldQuart) %in% items)
CashT<-t(CashHold)
Cashdf<-data.frame(CashT)
Cashdf$tic<-"IBM"
IBM.c<-Cashdf


HoldQuart<-MSFT.f$BS$Q
CashHold<-subset(HoldQuart,rownames(HoldQuart) %in% items)
CashT<-t(CashHold)
Cashdf<-data.frame(CashT)
Cashdf$tic<-"MSFT"
MSFT.c<-Cashdf


BigCash<-rbind(AAPL.c, IBM.c, MSFT.c)
#setwd<-("C:/Users/HP USER/Documents")
#write.csv(BigCash,file="CashList.csv")


When I try to process through this using a loop, however, things go south
pretty quickly.

tickerlist<-ls(pattern="^[A-Z]+\\.f")

for( i in 1:1)
{
test<-get(paste0(tickerlist[i],"$BS$Q"))
}

Error in get(paste0(tickerlist[i], "$BS$Q")) :
  object 'AAPL.f$BS$Q' not found

So I tried to break it up into smaller steps, but the resulting matrix
seems to have lost its structure (see below).

If someone could help me out, I sure would appreciate.

Thanks.
--John Sparks


tickerlist<-ls(pattern="^[A-Z]+\\.f")
for( i in 1:1)
{
HoldFin<-get(tickerlist[i])
BSQ<-as.matrix(paste0(HoldFin,"$BS$Q"))
}
BSQ

[1,] "list(Q = c(52896, NA, 52896, 32305, 20591, 3718, 2776, NA, NA, NA,
NA, 38799, 14097, NA, NA, -165, 14684, 11029, NA, NA, 11029, NA, NA, NA,
11029, NA, 11029, 11029, NA, NA, NA, NA, 5261.69, 2.1, NA, 0.57, NA, NA,
NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 2.1, 78351, NA, 78351, 48175,
30176, 3946, 2871, NA, NA, NA, NA, 54992, 23359, NA, NA, 122, 24180,
17891, NA, NA, 17891, NA, NA, NA, 17891, NA, 17891, 17891, NA, NA, NA, NA,
5327.99, 3.36, NA, 0.57, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
3.36, \n46852, NA, 46852, 29039, 17813, 3482, 2570, NA, NA, NA, NA, 35091,
11761, NA, NA, -159, 12188, 9014, NA, NA, 9014, NA, NA, NA, 9014, NA,
9014, 9014, NA, NA, NA, NA, 5393.33, 1.67, NA, 0.57, NA, NA, NA, NA, NA,
NA, NA, NA, NA, NA, NA, NA, 1.67, 42358, NA, 42358, 26252, 16106, 3441,
2560, NA, NA, NA, NA, 32253, 10105, NA, NA, -263, 10469, 7796, NA, NA,
7796, NA, NA, NA, 7796, NA, 7796, 7796, NA, NA, NA, NA, 5472.78, 1.42, NA,
0.57, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 1.42, 50557, NA,
50557, \n30636, 19921, 3423, 2511, NA, NA, NA, NA, 36570, 13987, NA, NA,
-510, 14142, 10516, NA, NA, 10516, NA, NA, NA, 10516, NA, 10516, 10516,
NA, NA, NA, NA, 5540.89, 1.9, NA, 0.52, NA, NA, NA, NA, NA, NA, NA, NA,
NA, NA, NA, NA, 1.9), A = c(215639, NA, 215639, 131376, 84263, 14194,
10045, NA, NA, NA, NA, 155615, 60024, NA, NA, -1195, 61372, 45687, NA, NA,
45687, NA, NA, NA, 45687, NA, 45687, 45687, NA, NA, NA, NA, 5500.28, 8.31,
NA, 2.18, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 8.31, 233715,
NA, \n233715, 140089, 93626, 14329, 8067, NA, NA, NA, NA, 162485, 71230,
NA, NA, -903, 72515, 53394, NA, NA, 53394, NA, NA, NA, 53394, NA, 53394,
53394, NA, NA, NA, NA, 5793.07, 9.22, NA, 1.98, NA, NA, NA, NA, NA, NA,
NA, NA, NA, NA, NA, NA, 9.22, 182795, NA, 182795, 112258, 70537, 11993,
6041, NA, NA, NA, NA, 130292, 52503, NA, NA, -311, 53483, 39510, NA, NA,
39510, NA, NA, NA, 39510, NA, 39510, 39510, NA, NA, NA, 0, 6122.66, 6.45,
NA, 1.81, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 6.45, 170910,
\nNA, 170910, 106606, 64304, 10830, 4475, NA, NA, NA, NA, 121911, 48999,
NA, NA, -24, 50155, 37037, NA, NA, 37037, NA, NA, NA, 37037, NA, 37037,
37037, NA, NA, NA, 0, 6521.5, 5.68, NA, 1.63, NA, NA, NA, NA, NA, NA, NA,
NA, NA, NA, NA, NA, 5.68))$BS$Q"
[2,] "list(Q = c(NA, 59501, 67101, 11579, NA, 20612, 2910, NA, 11367,
101990, 65124, -37961, 5473, 2617, 189740, 7549, 334532, 28573, 21665,
9992, 3999, 9113, 73342, 84531, NA, 84531, 98522, 28226, NA, 14351,
200450, NA, NA, 33579, NA, 100925, NA, -902, 134082, 334532, NA, 5205.81,
NA, 51093, 60452, 14057, NA, 27977, 2712, NA, 12191, 103332, 62759,
-36249, 5423, 2848, 185638, 7390, 331141, 38510, 21895, 10493, 3499, 9733,
84130, 73557, NA, 73557, 87549, 26948, NA, 14116, 198751, NA, NA, 32144,
NA, 11, \nNA, -1567, 132390, 331141, NA, 5255.42, NA, 58554, 67155,
15754, NA, 29299, 2132, NA, 8283, 106869, 61245, -34235, 5414, 3206,
170430, 8757, 321686, 37294, 20951, 8105, 3500, 9156, 79006, 75427, NA,
75427, 87032, 26019, NA, 12985, 

[R] Bayes Factor

[James Henson]

Hello R Community;

Just posted a question about Bayes Factor.  But, just answered my own question.
What is needed is to convert a 'dplyr' data frame into a standard data frame.
competition2 <- data.frame(competition), where 'competition' is a
'dplyr' data frame with the following class structure.
[1] "tbl_df"  "tbl"  "data.frame".

Best regards,
James

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[R] Bayes Factor

[James Henson]

Hello R Community,
Subject: Bayes Factor
A Bayesian ANOVA of the form:
competitionBayesOut <- anovaBF(biomass ~ clipping, data = competition)
Returns the following Error message:
Error in (function (classes, fdef, mtable)  :
  unable to find an inherited method for function ‘compare’ for
signature ‘"BFlinearModel", "missing", "tbl_df"’

My guess the problem is in the ‘class’, which is:
[1] “tbl_df”  “tbl”  “data.frame”
The data was imported via the ‘readr’ package through R Studio, and
then saved as a RData file.
My code is below, and the data is attached as a text file.

Thanks for your assistance.
Best regards,
James

# Plots for Interpreting One-Way ANOVA

library(digest)

library(DT)

datatable(competition)

# Characterize the data.

class(competition)

str(competition)

competition$clipping <- as.factor(competition$clipping)

competition$biomass <- as.numeric(competition$biomass)

str(competition)

#

tapply(competition$biomass, competition$clipping, mean)

tapply(competition$biomass, competition$clipping, sd)





# Bayesian Procedure for ANOVA



# Calculate Bayes Factors

library(BayesFactor)

competitionBayesOut <- anovaBF(biomass ~ clipping, data = competition)

# Run mcmc iterations

mcmcOut2 <- posterior(competitionBayesOut, iterations = 1)

# boxplot of the posteriors for the groups

boxplot(as.matrix(mcmcOut2[,2:6]))

# Show the HDIs

summary(mcmcOut2)

# Calculate the Bayes Factor

competitionBayesOut



# Pairwise "post hoc" tests

library(rjags)

library(BEST)



# competitionare 'r5' vs. 'control'

plot(BESTmcmc(competition[competition$clpping=="r5",2],
competition[competition$clipping=="control",2]))

#

plot(BESTmcmc(competition[competition$clpping=="r10",2],
competition[competition$clipping=="control",2]))

# competitionare 'n10' vs. 'control'

plot(BESTmcmc(competition[competition$clipping=="n10",2],
competition[competition$clipping=="control",2]))

# competitionare 'n50' vs. 'control'

plot(BESTmcmc(competition[competition$clipping=="n50",2],
competition[competition$clipping=="control",2]))
clippingbiomass
n25 551
n25 457
n25 450
n25 731
n25 499
n25 632
n50 595
n50 580
n50 508
n50 583
n50 633
n50 517
r5  639
r5  615
r5  511
r5  573
r5  648
r5  677
control 417
control 449
control 517
control 438
control 415
control 555
r10 563
r10 631
r10 522
r10 613
r10 656
r10 679
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Re: [ESS] knitr tutorial for ESS

[James W. MacDonald]

Vincent Goulet has an installer that sets everything up for you, that you
can get here.  https://vigou3.github.io/emacs-modified-windows/

It does all the syntax highlighting, plus has polymode support which is
nice for Rmd files.

I can't help with any key combinations to build output. I just set up the
yaml section to define the output, and use the rmarkdown package (the
render function) to do everything.


On Jun 8, 2017 9:35 PM, "Vince Forgetta"  wrote:

Hi,

I would like to use ESS to work with Rmarkdown. Specifically, I would like
to:

1. Enable syntax highlighting of Rmd files.
2. convert Rmd document to HTML or PDF.

Is there a tutorial anywhere on how to do this in Windows?

I am already quite comfortable with ESS, but I cannot find documentation on
the ESS website that describes how to use it with knitr.

Thanks,

Vince

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Re: [R] Setting .Rprofile for RStudio on a Windows 7 x64bit

[Sparks, John James]

Bruce,

Do you think that you could post the final solution to the problem?  That
way it would be stored with this thread and the next person who has the
same problem would be able to locate the FINAL solution.

--JJS


On Mon, April 17, 2017 12:47 pm, BR_email wrote:
> TO _ALL_:
> THANK YOU. THANK YOU. THANK YOU.
> After hours, and hours, and hours, and ... , and hours: Success.
> To all who helped, thanks.
> My quest was minor, but major for me, as I learn from the path of one,
> whether big or small begets another.
>
> I never look down at anyone, except to help him/her up.
>
> With gratitude,
> Bruce
>
> Bruce Ratner, Ph.D.
> The Significant Statistician™
> (516) 791-3544
> Statistical Predictive Analtyics -- www.DMSTAT1.com
> Machine-Learning Data Mining and Modeling -- www.GenIQ.net
>
>
> Peter Dalgaard wrote:
>>> On 17 Apr 2017, at 19:01 , BR_email  wrote:
>>>
>>> Berend: Something looks good, but RStudio still Rprofile still doees
>>> not affect the launch.
>>>
 source(echo=TRUE, "C:/Users/BruceRatner/Documents/.Rprofile.site")
 options(prompt="R> ")
 set.seed(12345)
 rm(list=ls())
>>> R>
>>>
>>>
>>> Bruce Ratner, Ph.D.
>>> The Significant Statistician™
>>> (516) 791-3544
>>> Statistical Predictive Analtyics -- www.DMSTAT1.com
>>> Machine-Learning Data Mining and Modeling -- www.GenIQ.net
>>>
>>> Berend Hasselman wrote:
 source(echo=TRUE, ""C:/Users/BruceRatner/Documents/.Rprofile.site")
>> According to the gospel of St.Henrik, that filename is wrong, and
>> possibly the directory too.
>>
>> So try his suggestions. What is the output (show us!) of
>>
>> normalizePath("./.Rprofile")
>> normalizePath("~/.Rprofile")
>>
>> Assuming that the former is
>>
>> "C:/Users/BruceRatner/Documents/.Rprofile"
>>
>> you could try renaming the .Rprofile.site file to that. If need be, use
>> file.rename, as in
>>
>> file.rename(from="C:/Users/BruceRatner/Documents/.Rprofile.site",
>> to="C:/Users/BruceRatner/Documents/.Rprofile")
>>
>> (and restart, obviously).
>>
>> [I wouldn't set the seed in a .Rprofile file, nor would I use rm()
>> there, but that is a different kettle of fish.]
>>
>
> __
> 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.

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[R] Windows server 2012

[Yates, James W T]

Hello

I'm investigating installing R in a virtual machine environment. Does anyone 
have experience running R on windows server 2012?

Regards

James


AstraZeneca UK Limited is a company incorporated in Engl...{{dropped:16}}

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Re: [R] Marg.fct function

[James Henson]

Greetings Peter and Jeff,

Thanks for this information.  Will try these type of analyses in SAS.
Sure they are doable in R, but developing a procedure is difficult.
Alan Agresti gives a cookbook SAS method in An Introduction to
Categorical Analysis.

Thanks,
James

On Sun, Feb 5, 2017 at 3:47 PM, Jeff Newmiller <jdnew...@dcn.davis.ca.us> wrote:
> It is not part of "R". You can dig through all of the packages that the 
> author mentions,  or send an email to the author.
> --
> Sent from my phone. Please excuse my brevity.
>
> On February 5, 2017 11:44:40 AM PST, James Henson <jfhens...@gmail.com> wrote:
>>Greetings R Community,
>>
>>An attempt to reproduce the results from code in the source below
>>fails.  R cannot find the function ‘Marg.fct’. An Internet search for
>>the ‘Marg.fct’ function was not fruitful.  I appreciate your help.
>>Best regards, James F. Henson.
>>
>>R (and S-PLUS) Manual to Accompany Agresti’s Categorical Data Analysis
>>(2002) 2nd edition Laura A. Thompson, 2009©
>>
>>http://www.stat.ufl.edu/~aa/cda/Thompson_manual.pdf  page 181
>>
>>The code is:
>>
>># Code from Manual to Accompany Agresti’s Categorical Data Analysis
>>(2002) 2nd edition Laura A. Thompson, 2009
>>
>>y <- c(144, 33, 84, 126, 2, 4, 14, 29, 0, 2, 6, 25, 0, 0, 1, 5)
>>
>>ZF <- Z <- matrix(1,16,1)
>>
>>#
>>
>>M1 <- Marg.fct(1,rep(4,2)) # used to get m1+, etc
>>
>>Error: could not find function "Marg.fct"
>>
>>
>>
>>M2 <- Marg.fct(2,rep(4,2)) # used to get m+1, etc
>>
>>#
>>
>>C.matrix <- matrix(c(
>>
>>  1, 0, 0, 0, -1, 0, 0, 0, # y1+ = y+1
>>
>>  0, 1, 0, 0, 0, -1, 0, 0, # y2+ = y+2
>>
>>  0, 0, 1, 0, 0, 0, -1, 0), # y3+ = y+3
>>
>>  3,8,byrow=T)
>>
>>h.fct <- function(m) { # constraint function
>>
>> marg <- rbind(M1%*%m, M2%*%m) # y1+, y2+, y3+, y4+, y+1, y+2, y+3, y+4
>>
>>  C.matrix%*%marg # y1+ = y+1, y2+ = y+2, etc
>>
>>}
>>
>>#
>>
>>a <- mph.fit(y=y,Z=Z,ZF=ZF,h.fct=h.fct)
>>
>>mph.summary(a)
>>
>>__
>>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.

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[R] Marg.fct function

[James Henson]

Greetings R Community,

An attempt to reproduce the results from code in the source below
fails.  R cannot find the function ‘Marg.fct’. An Internet search for
the ‘Marg.fct’ function was not fruitful.  I appreciate your help.
Best regards, James F. Henson.

R (and S-PLUS) Manual to Accompany Agresti’s Categorical Data Analysis
(2002) 2nd edition Laura A. Thompson, 2009©

http://www.stat.ufl.edu/~aa/cda/Thompson_manual.pdf  page 181

The code is:

# Code from Manual to Accompany Agresti’s Categorical Data Analysis
(2002) 2nd edition Laura A. Thompson, 2009

y <- c(144, 33, 84, 126, 2, 4, 14, 29, 0, 2, 6, 25, 0, 0, 1, 5)

ZF <- Z <- matrix(1,16,1)

#

M1 <- Marg.fct(1,rep(4,2)) # used to get m1+, etc

Error: could not find function "Marg.fct"



M2 <- Marg.fct(2,rep(4,2)) # used to get m+1, etc

#

C.matrix <- matrix(c(

  1, 0, 0, 0, -1, 0, 0, 0, # y1+ = y+1

  0, 1, 0, 0, 0, -1, 0, 0, # y2+ = y+2

  0, 0, 1, 0, 0, 0, -1, 0), # y3+ = y+3

  3,8,byrow=T)

h.fct <- function(m) { # constraint function

  marg <- rbind(M1%*%m, M2%*%m) # y1+, y2+, y3+, y4+, y+1, y+2, y+3, y+4

  C.matrix%*%marg # y1+ = y+1, y2+ = y+2, etc

}

#

a <- mph.fit(y=y,Z=Z,ZF=ZF,h.fct=h.fct)

mph.summary(a)

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[R] cforest Single Tree Output for Categorical Variable

[Sparks, John James]

Hello R Helpers,

I am building a random forest using the cforest method in the party
package.  I then want to have a look at the characteristics of a few of
the trees.  I get the output for one of the trees by executing

pt <- party:::prettytree(cforest@ensemble[[3]],
names(cforest@data@get("input")))
pt

The first splitting variable is a categorical variable (here named cat,
which contains value 0 through 9 and is a factor), but the output does not
specify which values went into which part of the tree:

1) cat == {}; criterion = 1, statistic = 32.792

Can anyone help me to get the detail on this splitting variable to appear
in the output?

I regret that I cannot send a reproducible example because the data is
proprietary.  I will try to work up an example with a public data set that
has the same problem.

Any help would be much appreciated.

Best wishes,
--John J. Sparks, Ph.D.

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Re: [R] confidence intervals for orthogonal contrasts

[James Henson]

Richard,

Thanks, Have not previously used the HH package, but looks as if it
contains many useful tools.  Will check out your book also.

Best regards,
James

On Thu, Dec 1, 2016 at 10:18 PM, Richard M. Heiberger <r...@temple.edu> wrote:
> James,
>
> Please look at the maiz example, the last example in ?MMC
> help("MMC", package="HH")
> where I show how to construct and calculate a set of orthogonal contrasts
> for a factor in an analysis of variance setting.  mmc and mmcplot use glht
> in the multcomp package for the underlying calculations.
>
> If yo don't have HH, you can get it with
> install.packages("HH")
>
> See the references in ?MMC to my book and paper.  The second edition
> of the book is now available.
>
> Rich
>
> On Thu, Dec 1, 2016 at 4:17 PM, James Henson <jfhens...@gmail.com> wrote:
>> Hi R users,
>> Is there a way to calculate a confidence interval for each contrast in
>> a set of orthogonal contrasts?  The ‘multcomp’ package will calculate
>> a CIs at the 95% family-wise confidence level.  But, these confidence
>> intervals are extremely wide.
>> Thanks for your help.
>> Best regards,
>> James
>>
>> __
>> 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.

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[R] confidence intervals for orthogonal contrasts

[James Henson]

Hi R users,
Is there a way to calculate a confidence interval for each contrast in
a set of orthogonal contrasts?  The ‘multcomp’ package will calculate
a CIs at the 95% family-wise confidence level.  But, these confidence
intervals are extremely wide.
Thanks for your help.
Best regards,
James

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Re: [R] Is this foreach behaviour correct?

[James Hirschorn]

I'm still not clear about whether this is a bug in foreach. Should c.Date be 
invoked by foreach with .combine='c'?

On 11/06/2016 07:02 PM, William Dunlap wrote:
Note that in the OP's example c.Date is never invoked.  c.Date is called if 
.combine
calls c rather than if .combine is c:

> library(zoo)
> trace(c.Date, quote(print(sys.call(
Tracing function "c.Date" in package "base"
[1] "c.Date"
> foreach(i=1:10003, .combine=c) %do% { as.Date(i) }
[1] 1 10001 10002 10003
> foreach(i=1:10003, .combine=function(...)c(...)) %do% { as.Date(i) }
Tracing c.Date(...) on entry
eval(expr, envir, enclos)
Tracing c.Date(...) on entry
eval(expr, envir, enclos)
Tracing c.Date(...) on entry
eval(expr, envir, enclos)
[1] "1997-05-19" "1997-05-20" "1997-05-21" "1997-05-22"


Bill Dunlap
TIBCO Software
wdunlap tibco.com<http://tibco.com>

On Sun, Nov 6, 2016 at 2:20 PM, Duncan Murdoch 
<murdoch.dun...@gmail.com<mailto:murdoch.dun...@gmail.com>> wrote:
On 06/11/2016 5:02 PM, Jim Lemon wrote:
hi James,
I think you have to have a starting date ("origin") for as.Date to
convert numbers to dates.

That's true with the function in the base package, but the zoo package also has 
an as.Date() function, which defaults the origin to "1970-01-01".  If James is 
using zoo his code would be okay.  If he's not, he would have got an error, so 
I think he must have been.

Duncan Murdoch



Jim

On Sun, Nov 6, 2016 at 12:10 PM, James Hirschorn
<james.hirsch...@hotmail.com<mailto:james.hirsch...@hotmail.com>> wrote:
This seemed odd so I wanted to check:

 > x <- foreach(i=1:10100, .combine='c') %do% { as.Date(i) }

yields a numeric vector for x:

 > class(x)
[1] "numeric"

Should it not be a vector of Date?

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Re: [R] Is this foreach behaviour correct?

[James Hirschorn]

Yes, I should have put

 > library(foreach)

 > library(zoo)

at the top.

On 11/06/2016 05:20 PM, Duncan Murdoch wrote:
> On 06/11/2016 5:02 PM, Jim Lemon wrote:
>> hi James,
>> I think you have to have a starting date ("origin") for as.Date to
>> convert numbers to dates.
>
> That's true with the function in the base package, but the zoo package 
> also has an as.Date() function, which defaults the origin to 
> "1970-01-01".  If James is using zoo his code would be okay. If he's 
> not, he would have got an error, so I think he must have been.
>
> Duncan Murdoch
>
>>
>> Jim
>>
>> On Sun, Nov 6, 2016 at 12:10 PM, James Hirschorn
>> <james.hirsch...@hotmail.com> wrote:
>>> This seemed odd so I wanted to check:
>>>
>>>  > x <- foreach(i=1:10100, .combine='c') %do% { as.Date(i) }
>>>
>>> yields a numeric vector for x:
>>>
>>>  > class(x)
>>> [1] "numeric"
>>>
>>> Should it not be a vector of Date?
>>>
>>> __
>>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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>>> 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
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>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>>
>
> .
>

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Re: [R] isssues with predict.coxph, offset, type = "expected", and newdata

[David James]

Thanks Terry,

Re: the second case (predicting from a null model with a newdata=
argument), I agree that it looks a bit over the top for such a
straight forward computation, so maybe it is more a wish than anything
else.  In this one instance, this computation is embedded in a wider
multi-state simulation in Epi::simLexis() where transition hazards are
modeled  as functions of covariates via Cox proportional hazards, and
a subset of transitions happen not to depend on any covariate, thus
the null model(s).   There are ways to circumvent this special case
within Epi::simLexis(), so even in this one example I wouldn't
consider it high priority at all.  But maybe it would be nice to have.


On Sat, Oct 1, 2016 at 10:44 PM, Therneau, Terry M., Ph.D.
 wrote:
> I'm off on vacation and checking email only intermittently.
> Wrt the offset issue, I expect that you are correct.  This is not a case that 
> I had ever envisioned, and so was not on my "list" when writing the code and 
> certainly has no test case.  That does not mean that it shouldn't work, just 
> that I am not shocked to see it.   I will look into this.
>
> For the second case of a NULL model I am less sympathetic.  This is, in 
> theory, just reading off values from a Nelson hazard estimate at specific 
> time points; using a coxph call to do so is a case of swatting a fly with a 
> hammer.   A bit more background might make me more excited about extending 
> the code to this case.
>
> Terry Therneau

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[R] isssues with predict.coxph, offset, type = "expected", and newdata?

[David James]

Hi,

It seems there might be two issues with predict.coxph(), and I'd
appreciate confirmation before submitting a bug report to the package
author.

(1)  predict() seems to produce incorrect predictions when using type
= "expected" from a Cox model with an offset and specifying a new data
for prediction (see Example 1 below).

(2)  predict() produces an error for a call with a null model and a
newdata= argument (see Example 2 below).

Please note that I didn't check these cases with additional
complications, like strata(), cluster(), etc.

SessionInfo() at the bottom of this email (notice I'm using survival
2.39-5, the current version in CRAN).

Thanks,

David

--

Example 1

> library("survival")
> data(lung)
>
> # simulate a three-fold genetic effect (worsening)
> set.seed(123)
> lung$gene.eff <- sample(log(c(1, 3)), size=nrow(lung), replace=TRUE, 
> prob=c(0.5, 0.5))
>
> # fix the gene effect, do not estimate it
> m1 <- coxph(Surv(time, status) ~ age + sex + offset(gene.eff), data = lung)
>
> # two hypothetical individuals differing only on gene.eff
> nd <- expand.grid(time=180, status=1, age=65, sex=1, gene.eff=log(c(1,3)))
>
> p1.lp <- predict(m1, newdata = nd, type = "lp")
> p1.rsk <- predict(m1, newdata = nd, type = "risk")
> p1.exp <- predict(m1, newdata = nd, type = "expected")
>
> # output from type "lp" (linear predictor) and "risk" are ok,
> # but not from type "expected"
> all.equal(3, exp(p1.lp[2]-p1.lp[1]), check.names = FALSE)
[1] TRUE
> all.equal(3, p1.rsk[2]/p1.rsk[1], check.names = FALSE)
[1] TRUE
> all.equal(3, p1.exp[2]/p1.exp[1], check.names = FALSE)
[1] "Mean relative difference: 0.667"
>
> # notice that predict() produces the same expected number of
> # events for both hypothetical individuals
> print(p1.exp)
[1] 0.1882663 0.1882663


Example 2

> # null model
> m0 <- coxph(Surv(time, status) ~ 1, data = lung)
>
> # time points at which we want predictions
> nd <- data.frame(time=seq(from=0, to=360, by=30), status=rep(1, 13))
>
> # predictions are produced for types "lp" and "risk", but not "expected"
> p0.lp <- predict(m0, type="lp", newdata = nd)
> p0.rsk <- predict(m0, type="risk", newdata = nd)
> p0.exp <- predict(m0, type="expected", newdata = nd)
Error in newx %*% object$coef :
  requires numeric/complex matrix/vector arguments
>

Session Info:

> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: i386-w64-mingw32/i386 (32-bit)
Running under: Windows 7 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United
States.1252LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C   LC_TIME=English_United
States.1252

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base

other attached packages:
[1] survival_2.39-5

loaded via a namespace (and not attached):
[1] Matrix_1.2-6tools_3.3.1 splines_3.3.1   grid_3.3.1
lattice_0.20-33

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Re: [R] yuen function of the WRS2 package

[James Henson]

Thanks,
The 'droplevels' statement works.
Best regards,
James Henson

On Tue, Aug 30, 2016 at 5:34 PM, William Dunlap <wdun...@tibco.com> wrote:
> yuen does not work when there unused levels in the factors given to it.
>
>>  yuen(GoalsGame ~ League, tr=0.2, data = SpainGer)
> Call:
> yuen(formula = GoalsGame ~ League, data = SpainGer, tr = 0.2)
>
> Test statistic: NaN (df = NA), p-value = NA
>
> Trimmed mean difference:  NaN
> 95 percent confidence interval:
> NaN NaN
>
>>  yuen(GoalsGame ~ League, tr=0.2, data = droplevels(SpainGer))
> Call:
> yuen(formula = GoalsGame ~ League, data = droplevels(SpainGer),
> tr = 0.2)
>
> Test statistic: 0.8394 (df = 16.17), p-value = 0.4135
>
> Trimmed mean difference:  -0.11494
> 95 percent confidence interval:
> -0.405 0.1751
>
> Complain to WSR2's maintainer.
>> maintainer("WRS2")
> [1] "Patrick Mair <m...@fas.harvard.edu>"
>
>
>
> Bill Dunlap
> TIBCO Software
> wdunlap tibco.com
>
> On Tue, Aug 30, 2016 at 2:07 PM, James Henson <jfhens...@gmail.com> wrote:
>>
>> Greetings R community,
>> Here is a small but perplexing problem with the ‘yuen’ function in the
>> ‘WRS2’ package.
>> I begin with the ‘eurosoccer’ data frame from the ‘WRS2’ package.
>> Then make a subset that contains only two Leagues Spain and Germany
>> (subset data frame is ‘SpainGer’).   The ‘yuen’ function cannot read
>> the data in subset data frame ‘SpainGer’.  My code is below.
>> Thanks you for your help.
>> James F. Henson
>>
>>
>> # Examples from 'Robust Statistical Methods on R Using the WRS2 Package’
>> # Robust t-test, and ANOVA (pages5-13)
>> library(WRS2)
>> data("eurosoccer")
>> class(eurosoccer)
>> print(eurosoccer)
>> library("digest")
>> library("DT")
>> datatable(eurosoccer)
>> str(eurosoccer)
>> # make a subset with only Spain and Germany
>> SpainGer <- subset (eurosoccer, subset = League =="Spain" | League ==
>> "Germany")
>> print(SpainGer)
>> class(SpainGer)
>> str(SpainGer)
>> # The 'yuen' function can not read the data in the subset data.frame
>> "SpainGer"
>> yuen(GoalsGame ~ League, tr=0.2, data = SpainGer)
>> # the 'yuen' function works on the orginioal data.frame
>> yuen(GoalsGame ~ League, tr=0.2, data = eurosoccer)
>> # the 'aov' function reads the data in the subset data.frame "SpainGer"
>> Goals.fit <- aov(GoalsGame ~ League, data = SpainGer)
>> summary(Goals.fit)
>>
>> __
>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help
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>> http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>
>

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[R] yuen function of the WRS2 package

[James Henson]

Greetings R community,
Here is a small but perplexing problem with the ‘yuen’ function in the
‘WRS2’ package.
I begin with the ‘eurosoccer’ data frame from the ‘WRS2’ package.
Then make a subset that contains only two Leagues Spain and Germany
(subset data frame is ‘SpainGer’).   The ‘yuen’ function cannot read
the data in subset data frame ‘SpainGer’.  My code is below.
Thanks you for your help.
James F. Henson


# Examples from 'Robust Statistical Methods on R Using the WRS2 Package’
# Robust t-test, and ANOVA (pages5-13)
library(WRS2)
data("eurosoccer")
class(eurosoccer)
print(eurosoccer)
library("digest")
library("DT")
datatable(eurosoccer)
str(eurosoccer)
# make a subset with only Spain and Germany
SpainGer <- subset (eurosoccer, subset = League =="Spain" | League == "Germany")
print(SpainGer)
class(SpainGer)
str(SpainGer)
# The 'yuen' function can not read the data in the subset data.frame "SpainGer"
yuen(GoalsGame ~ League, tr=0.2, data = SpainGer)
# the 'yuen' function works on the orginioal data.frame
yuen(GoalsGame ~ League, tr=0.2, data = eurosoccer)
# the 'aov' function reads the data in the subset data.frame "SpainGer"
Goals.fit <- aov(GoalsGame ~ League, data = SpainGer)
summary(Goals.fit)

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[R] [R-pkgs] new package clubSandwich: Cluster-Robust (Sandwich) Variance Estimators with Small-Sample Corrections

[James Pustejovsky]

Dear R users:

I'm happy to announce the first CRAN release of the clubSandwich package:

https://cran.r-project.org/web/packages/clubSandwich

clubSandwich provides several variants of the cluster-robust variance
estimator for ordinary and weighted least squares linear regression models,
including the bias-reduced linearization estimator of Bell and McCaffrey
(2002). The package includes functions for estimating the
variance-covariance matrix and for testing single- and multiple-contrast
hypotheses based on Wald test statistics. The hypothesis tests incorporate
small-sample corrections that lead to more accurate rejection rates when
the number of clusters is small or the design is unbalanced/leveraged.
Tests of single regression coefficients use Satterthwaite or saddle-point
corrections. Tests of multiple-contrast hypotheses use an approximation to
Hotelling's T-squared distribution. Methods are provided for a variety of
fitted models, including lm(), plm() (from package 'plm'), gls() and lme()
(from 'nlme'), robu() (from 'robumeta'), and rma.uni() and rma.mv() (from
'metafor').

The package includes two vignettes that demonstrate its use for estimation
of panel data models and meta-regression models.

Bug reports, suggestions, and feature requests are welcome
at https://github.com/jepusto/clubSandwich

Cheers,
James


___
James Pustejovsky
Assistant Professor, Quantitative Methods Program
Educational Psychology Department
The University of Texas at Austin
http://jepusto.github.io/

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[R] Anybody know the cause of this?

[James Plante]

Just upgraded to R 3.3.1; when I updated the packages on CRAN, I got a BUNCH of 
warning messages like the ones below:

2016-07-01 14:44:19.840 R[369:3724] IMKClient Stall detected, *please Report* 
your user scenario attaching a spindump (or sysdiagnose) that captures the 
problem - (imkxpc_windowLevelWithReply:) block performed very slowly (2.40 
secs).
starting httpd help server ... done
> spindump()
Error: could not find function "spindump"
In addition: Warning message:
In library() :
  library ‘/Users/jimplante/Library/R/3.3/library’ contains no packages
2016-07-01 14:47:32.774 R[369:3724] IMKClient Stall detected, *please Report* 
your user scenario attaching a spindump (or sysdiagnose) that captures the 
problem - (imkxpc_attributesForCharacterIndex:reply:) block performed very 
slowly (1.42 secs).
> 

This is not interfering with any of my work, but I’m curious to know what it’s 
warning me about. 
Two more questions: 1) What’s a spindump; and 2) What’s a sysdiagnose? 
And finally, how would I get either one of those, and to whom would I send them?

Thanks,

Jim
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[R] Rpart plot produces no text

[Thompson, James]

I am using R Studio and am able to fit a tree with RPlot, however, the tree in 
the viewer has no text (see image attached).

Jim Thompson
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Re: [R] Whether statistical background is must to learn R language

[James Henson]

Greetings Prasad,

Here are some tutorials on statistics using R.Statistics and Actuarial
Science – Carl James Schwarz

http://people.stat.sfu.ca/~cschwarz/CourseNotes/



Statistics and Actuarial Science – Carl James Schwarz - Programs

http://people.stat.sfu.ca/~cschwarz/Stat-650/Notes/MyPrograms/



Design Analysis and Interpretation of Experiments

http://www.unh.edu/halelab/BIOL933/

Great YouTube channel of R tutorials by Mike Marin,

https://www.youtube.com/user/marinstatlectures

Best regards,
James


On Tue, May 31, 2016 at 8:04 AM, PIKAL Petr <petr.pi...@precheza.cz> wrote:
> Hi
>
> Well, it seems to me like cooking.
>
> You does not have to be educated cook to be able prepare some food in your 
> kitchen, but knowledge of some recipes can lead to tasty results
>
> Regards
> Petr
>
>> -Original Message-
>> From: R-help [mailto:r-help-boun...@r-project.org] On Behalf Of Prasad
>> Kale
>> Sent: Tuesday, May 31, 2016 9:23 AM
>> To: R-help@r-project.org
>> Subject: [R] Whether statistical background is must to learn R language
>>
>> Hi,
>>
>> I am very new to R and just started learning R. But i am not from statistical
>> background so can i learn R or to learn R statistical background is must.
>>
>> Please guide.
>>
>> Thanks in Advance
>> Prasad
>>
>>   [[alternative HTML version deleted]]
>>
>> __
>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
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>> and provide commented, minimal, self-contained, reproducible code.
>
> 
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Re: [R] mixed models

[James Henson]

Greetings David,
I am new to R and neglected to check vigorously for missing values.
Apologize for posting without checking and finding the one NA.

I appreciate your help.
Thanks.
James F. Henson

On Fri, May 27, 2016 at 1:49 PM, David Winsemius <dwinsem...@comcast.net> wrote:
>
>> On May 27, 2016, at 10:07 AM, James Henson <jfhens...@gmail.com> wrote:
>>
>> Greetings Jeff,
>> You are correct that the unequal number of levels is not the problem.
>> I revised the data frame so that the number of levels was equal and
>> the same error message occurred.  The code is below, and the
>> Eboni2.txt file is attached. This problem baffles me.  I appreciate
>> any help.
>> Best regards,
>> James
>> Eboni2 <- read.csv("Eboni2.csv", header = TRUE)
>>
>> library("nlme")
>>
>> str(Eboni2)
>>
>> head(Eboni2)
>>
>> model1 <- lme(preDawn ~ Irrigation, random=~season_order|treeNo, data=Eboni2)
>
> I downloaded the attached file to your first posting that was called a "csv" 
> file but it was tab-separated (as could be clearly seen with the str output, 
> so would only load properly with read.delim rather than read.csv. Running 
> then with the lme call, it produced this message
>
>> model1 <- lme(preDawn ~ Irrigation, random=~season_order|treeNo, data=Eboni2)
> Error in na.fail.default(list(season_order = c(5L, 5L, 5L, 5L, 5L, 5L,  :
>   missing values in object
>
> And looking at the str result made it clear that there were many NA's in the 
> file.
>
>> head(Eboni2)
>   number Location   Season season_order Month  treeID treeNo preDawn midday
> 1  1  UCC November5   Nov UCCLO 1 60 1.41.3
> 2  2  UCC November5   Nov UCCLO 2 72 1.21.3
> 3  3  UCC November5   Nov UCCLO 3 78 1.11.2
> 4  4  UCC November5   Nov UCCLO 4 79 1.12.1
> 5  5  UCC November5   Nov UCCLO 5 80 1.41.3
> 6  6  UCC November5   Nov UCCLO 6 81 0.61.8
>   Irrigation PnetGsE  WUE d15N   d13C Nper  Cper include2
> 1  N9 0.2907004 3.766207 2.389672   NA NA   NANA   no
> 2  N   11 0.3262582 3.120574 3.524993   NA NA   NANA   no
> 3  N8 0.2870957 1.693821 4.723050 3.00 -27.44 2.12 52.12  yes
> 4  N   10 0.2475180 1.839343 5.436724 3.61 -29.50 1.42 51.97  yes
> 5  N   13 0.3009228 3.082278 4.217660   NA NA   NANA   no
> 6  N   17 0.3487337 2.534550 6.707304 2.79 -30.50 1.49 49.94  yes
>
> And even more importantly, there was one NA in your outcome variable:
>> sum( is.na(Eboni2$Irrigation))
> [1] 0
>> sum( is.na(Eboni2$preDawn))
> [1] 1
>
> So after restricting to complete.cases, I then formed the hypothesis that you 
> reversed the order of the variables in the formula for the random parameter:
>
>> table(Eboni2$season_order)
>
>  1  2  3  4  5
> 83 83 83 83 83
>> length( Eboni2$treeNo)
> [1] 415
>
> So it seemed unreasonable to have a "grouping" on variable with only one item 
> per group.
>
>> model1 <- lme(preDawn ~ Irrigation, random=~treeNo|season_order, 
>> data=Eboni2[ complete.cases( Eboni2[ , 
>> c('preDawn','Irrigation','season_order','treeNo')]), ] )
>> model1
> Linear mixed-effects model fit by REML
>   Data: Eboni2[complete.cases(Eboni2[, c("preDawn", "Irrigation", 
> "season_order",  "treeNo")]), ]
>   Log-restricted-likelihood: -183.4708
>   Fixed: preDawn ~ Irrigation
> (Intercept) IrrigationY
>  1.04520145 -0.06037706
>
> Random effects:
>  Formula: ~treeNo | season_order
>  Structure: General positive-definite, Log-Cholesky parametrization
> StdDev  Corr
> (Intercept) 0.140239324 (Intr)
> treeNo  0.003766019 -0.725
> Residual0.365678898
>
> Number of Observations: 414
> Number of Groups: 5
>
> (Warning, I'm not a frequent user of this package or any of the mixed effects 
> packages.)
>
>
>
> Just to correct some misinformation that appeared earlier: You can attach 
> "csv" or "tsv" files as long as you name them with an .txt extension so the 
> mail clients and servers consider them to be MIME-text.
>
> --
> David.
>
>
>> On Wed, May 25, 2016 at 6:23 PM, Jeff Newmiller
>> <jdnew...@dcn.davis.ca.us> wrote:
>>> Please keep the mailing list in the loop by using reply-all.
>>>
>>> I don't think there is a requirement that the number of levels is 

Re: [R] mixed models

[James Henson]

Greetings Jeff,
You are correct that the unequal number of levels is not the problem.
I revised the data frame so that the number of levels was equal and
the same error message occurred.  The code is below, and the
Eboni2.txt file is attached. This problem baffles me.  I appreciate
any help.
Best regards,
James
 Eboni2 <- read.csv("Eboni2.csv", header = TRUE)

library("nlme")

str(Eboni2)

head(Eboni2)

model1 <- lme(preDawn ~ Irrigation, random=~season_order|treeNo, data=Eboni2)

On Wed, May 25, 2016 at 6:23 PM, Jeff Newmiller
<jdnew...@dcn.davis.ca.us> wrote:
> Please keep the mailing list in the loop by using reply-all.
>
> I don't think there is a requirement that the number of levels is equal, but
> there may be problems if you don't have the minimum number of records
> corresponding to each combination of levels specified in your model.
>
> You can change the csv extension to txt and attach for the mailing list. Or,
> better yet, you can use the dput function to embed the data directly in your
> sample code.
>
> Also, please learn to post plain text email to avoid corruption of R code by
> the HTML formatting.
> --
> Sent from my phone. Please excuse my brevity.
>
> On May 25, 2016 2:26:54 PM PDT, James Henson <jfhens...@gmail.com> wrote:
>>
>> Good afternoon Jeff,
>> The sample sizes for levels of the factor "Irrigation" are not equal. If
>> 'nlme' requires equal sample sizes this may be the problem. The same data
>> frame runs in 'lme4' without a problem.
>>
>> Best regards,
>> James
>>
>>
>> On Wed, May 25, 2016 at 3:41 PM, James Henson <jfhens...@gmail.com> wrote:
>>>
>>> Good afternoon Jeff,
>>>
>>> When working with this data frame, I just open the .csv file in R Studio.
>>> But, we should not send .csv file to R_help.  What should I send?
>>>
>>> Best regards,
>>> James
>>>
>>> On Wed, May 25, 2016 at 2:52 PM, Jeff Newmiller
>>> <jdnew...@dcn.davis.ca.us> wrote:
>>>>
>>>> You forgot to show the commands to us that you used to read the data in
>>>> with (your example is not "reproducible"). This step can make all the
>>>> difference in the world as to whether your analysis commands will work or
>>>> not.
>>>> --
>>>> Sent from my phone. Please excuse my brevity.
>>>>
>>>> On May 25, 2016 11:59:06 AM PDT, James Henson <jfhens...@gmail.com>
>>>> wrote:
>>>>>
>>>>> Greetings R community,
>>>>>
>>>>> My aim is to analyze a mixed-effects model with temporal
>>>>> pseudo-replication
>>>>> (repeated measures on the same experimental unit) using ‘nlme’.
>>>>> However,
>>>>> my code returns the error message “Error in na.fail.default’, even
>>>>> though
>>>>> the data frame does not contain missing values. My code is below, and
>>>>> the
>>>>> data file is attached as ‘Eboni2.txt.
>>>>>
>>>>> library("nlme")
>>>>>
>>>>> str(Eboni2)
>>>>>
>>>>> head(Eboni2)
>>>>>
>>>>> model1 <- lme(preDawn ~ Irrigation, random=~season_order|treeNo,
>>>>> data=Eboni2)
>>>>>
>>>>> I am genuinely confused.  Hope someone can help.
>>>>>
>>>>> Best regards,
>>>>>
>>>>> James F. Henson
>>>>>
>>>>> 
>>>>>
>>>>> 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.
>>>
>>>
>>
>

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[R] mixed models

[James Henson]

Greetings R community,

My aim is to analyze a mixed-effects model with temporal pseudo-replication
(repeated measures on the same experimental unit) using ‘nlme’.  However,
my code returns the error message “Error in na.fail.default’, even though
the data frame does not contain missing values. My code is below, and the
data file is attached as ‘Eboni2.txt.

library("nlme")

str(Eboni2)

head(Eboni2)

model1 <- lme(preDawn ~ Irrigation, random=~season_order|treeNo,
data=Eboni2)

I am genuinely confused.  Hope someone can help.

Best regards,

James F. Henson
number  LocationSeason  season_orderMonth   treeID  treeNo  preDawn 
midday  Irrigation  PnetGs  E   WUE d15Nd13CNper
Cperinclude2
1   UCC November5   Nov UCCLO 1 60  1.4 1.3 
N   9   0.290700373 3.766207481 2.38967185  
no
2   UCC November5   Nov UCCLO 2 72  1.2 1.3 
N   11  0.326258186 3.120573618 3.524992949 
no
3   UCC November5   Nov UCCLO 3 78  1.1 1.2 
N   8   0.287095701 1.693820753 4.723049937 3   -27.44  
2.1252.12   yes
4   UCC November5   Nov UCCLO 4 79  1.1 2.1 
N   10  0.247517983 1.83934285  5.436724317 3.61-29.5   
1.4251.97   yes
5   UCC November5   Nov UCCLO 5 80  1.4 1.3 
N   13  0.300922817 3.082277827 4.217660032 
no
6   UCC November5   Nov UCCLO 6 81  0.6 1.8 
N   17  0.348733689 2.534550345 6.70730413  2.79-30.5   
1.4949.94   yes
7   UCC November5   Nov UCCLO 7 82  0.9 1.2 
N   12  0.272690759 1.809851748 6.630377328 2.43-29.4   
1.5553.12   yes
8   UCC November5   Nov UCCLO 8 83  1.4 1.1 
N   11  0.269862804 1.919849835 5.729614785 2.85-28.37  
1.7853.52   yes
9   UCC November5   Nov UCCLO 9 84  0.8 1   
N   16  0.32333 2.394825767 6.68107059  2.43-30.1   
1.5452.88   yes
10  UCC November5   Nov UCCLO 1062  0.9 
1.2 N   17  0.29488545  1.429058721 11.89594224 1.51
-31.96  1.6152.94   yes
11  UCC November5   Nov UCCLO 1163  1.3 
2   N   14  0.241601092 3.29815495  4.244797535 
no
12  UCC November5   Nov UCCLO 1264  1.2 
1.3 N   11  0.261040739 1.610353496 6.83079835  2.62
-28.94  1.4651.9yes
13  UCC November5   Nov UCCLO 1365  1.2 
1.3 N   13  0.238863129 2.221057396 5.853068012 1.13
-28.81  2.0851.43   yes
14  UCC November5   Nov UCCLO 1466  1.1 
1.5 N   9   0.309603194 2.859756011 3.14712163  
no
15  UCC November5   Nov UCCLO 1567  1.1 
1.3 N   18  0.383441504 2.949059627 6.103640576 1.51
-30.14  1.6552.04   yes
16  UCC November5   Nov UCCLO 1668  1.3 
2.7 N   13  0.269711187 1.430856375 9.085468137 1.99
-29.09  1.8751.21   yes
17  UCC November5   Nov UCCLO 1769  0.8 
1.4 N   13  0.245685997 3.808576972 3.41334837  
no
18  UCC November5   Nov UCCLO 1870  1.6 
1.8 N   11  0.271419599 2.305398713 4.771408926 2.94
-29.22  1.9351.46   yes
19  UCC November5   Nov UCCLO 1971  1   
1.5 N   18  0.338103566 2.303586185 7.813903435 2.93
-30.27  1.9251.51   yes
20  UCC November5   Nov UCCLO 2073  1.1 
1.2 N   11  0.27096196  3.230604699 3.404935307 
no
21  UCC November5   Nov UCCLO 2174  1.2 
1.5 N   10  0.294348983 3.319661403 3.012355414 
no
22  UCC November5   Nov UCCLO 2275  1.5 
1.9 N   12  0.230438536 2.935053987 4.088510825 1.74
-29.49  1.6450.28   yes
23  UCC November5   Nov UCCLO 2376  1.1 
1.4 N   14  0.264963659 3.689609021   

[R] Reduce does not work with data.table?

[James Hirschorn]

Reduce is failing when applied to a list of elements of class 
data.table. Perhaps this is a bug?


Example:

library(data.table)

dt1 <- data.table(x = 1:3, y = 4:6)
dt2 <- data.table(x = 4:6, y = 1:3)
dt3 <- data.table(x = 0:-2, y = 0:-2)

# This works fine
dt1 + dt2 + dt2
#x y
# 1: 5 5
# 2: 6 6
# 3: 7 7

# But:
dt_list <- list(dt1, dt2, dt3)
Reduce("+", dt_list)
# Error in f(init, x[[i]]) : non-numeric argument to binary operator
# In addition: Warning message:
# In Reduce("+", dt_list) :
#   Incompatible methods ("Ops.data.frame", "Ops.data.table") for "+"

If I use data.frame instead of data.table, Reduce works properly.

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Re: [R] a replace for subset

[James C. Whanger]

Would facet_wrap or facet_grid give you what you want?

On Sat, Apr 16, 2016 at 8:45 AM, ch.elahe via R-help <r-help@r-project.org>
wrote:

> Hi,
> I have a data set (mydata), which a part of this is like the following:
>
>
> 'data.frame':   36190 obs. of 16 variables:
> $ RE: int  38 41 11 67 30 18 38 41 41 30 ...
> $ LU : int  4200 3330 530 4500 3000 1790 4700 3400
> 3640 4000 ...
> $ COUNTRY: Factor w/ 4 levels "DE","FR","JP", "FR"…
> $Light  : Factor w/2 levels   "ON","OFF","ON", ….
> $OR : Factor w/2 levels   "S","T","S",….
> $PAT  : Factor w/3 levels   "low", "high", "middle",….
>
>
> Now I want to plot RE vs LU with ggplot2 for all the possible cases, I
> know how to do subsetting for the data but I want to know is there any
> shorter way to do that? For example I want to have a plot for RE vs LU for
> (COUNTRY= FR, Light=off, OR=S, PAT=low) and one for (COUNTRY= FR, Light=on,
> OR=S, PAT=high) and …., as you see doing subset is time consuming, is there
> any other way?
> Thank you for any help.
> Elahe
>
> __
> 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.




-- 
*James C. Whanger*

[[alternative HTML version deleted]]

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Re: [R] ggplot2

[James Henson]

Thanks, the stat="identity" worked.

On Tue, Apr 12, 2016 at 3:34 PM, Huzefa Khalil <huzefa.kha...@umich.edu>
wrote:

> Hi James,
>
> If you want to specify the y-values, you need to use stat="identity" as
> below:
>
> ggplot(probability, aes(x=Fertilizer, y=prob)) +
> geom_bar(stat="identity", aes(fill=Treatment))
>
>
> best,
> huzefa
>
> On Tue, Apr 12, 2016 at 1:02 PM, James Henson <jfhens...@gmail.com> wrote:
> > Dear R Community,
> >
> > Below is a problem with a simple ggplot2 graph. The code returns the
> error
> > message below.
> >
> > Error: stat_count() must not be used with a y aesthetic.
> >
> > My code is below and the data is attached as a ‘text’ file.
> >
> >
> >
> > # Graph of the probabilities
> >
> > library(digest)
> >
> > library(DT)
> >
> > datatable(probability)
> >
> > str(probability)
> >
> > probability$Fertilizer <- as.factor(probability$Fertilizer)
> >
> > str(probability)
> >
> > library(ggplot2)
> >
> > plot1 <- ggplot(probability, aes(x=Fertilizer, y=prob)) +
> > geom_bar(aes(fill=Treatment))
> >
> > plot1
> >
> >
> >
> > Thanks.
> >
> > Best regards,
> >
> > James F. Henson
> >
> > __
> > 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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[R] ggplot2

[James Henson]

Dear R Community,

Below is a problem with a simple ggplot2 graph. The code returns the error
message below.

Error: stat_count() must not be used with a y aesthetic.

My code is below and the data is attached as a ‘text’ file.



# Graph of the probabilities

library(digest)

library(DT)

datatable(probability)

str(probability)

probability$Fertilizer <- as.factor(probability$Fertilizer)

str(probability)

library(ggplot2)

plot1 <- ggplot(probability, aes(x=Fertilizer, y=prob)) +
geom_bar(aes(fill=Treatment))

plot1



Thanks.

Best regards,

James F. Henson
Trt probLL  UL  Fertilizer  Treatment
S0  0.  0.0154  0.4998  0   S
S2  0.  0.0154  0.4998  2   S
S4  0.  0.0154  0.4998  4   S
S6  0.  0.0154  0.4998  6   S
P0  0.  0.056   0.579   0   P
P2  0.7778  0.4208  0.9439  2   P
P3  0.333   0.  0.6665  4   P
P4  0.6667  0.3334  0.  6   P
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[R] Is this a bug in quantmod::OpCl?

[James Hirschorn]

OpCl works on xts objects but not on quantmod.OHLC objects. Is this a bug?

Example error:

x.Date <- as.Date("2003-02-01") + c(1, 3, 7, 9, 14) - 1
set.seed(1)
x <- zoo(matrix(runif(20, 0, 1), nrow=5, ncol=4), x.Date)
q <- as.quantmod.OHLC(x,c("Open","High","Low","Close"))

# error
OpCl(q)
#> Error in `colnames<-`(`*tmp*`, value = "OpCl.q") : 
#>  attempt to set 'colnames' on an object with less than two dimensions

# OK
OpCl(as.xts(q))

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Re: [R] installing packages

[James Henson]

To All,
Thanks for your help.

I uninstalled R, the 3.2 library and R Studio.  Reinstalled R and R Studio.
Now the temp files move the newly installed packages into the
R-.23.2.4revised library.

> .libPaths()
[1] "C:/Users/james_henson/Desktop/Documents/R/win-library/3.2"
[2] "C:/Program Files/R/R-3.2.4revised/library"





On Mon, Mar 21, 2016 at 9:57 PM, Jeff Newmiller <jdnew...@dcn.davis.ca.us>
wrote:

> I hope not. That directory is not for working in. suggestion to restart R
> sounds most likely to fix the issue.
> --
> Sent from my phone. Please excuse my brevity.
>
> On March 21, 2016 2:10:01 PM PDT, KMNanus <kmna...@gmail.com> wrote:
>>
>> Have you set your working directory to the “3.2” folder?
>> Ken
>> kmna...@gmail.com
>> 914-450-0816 (tel)
>> 347-730-4813 (fax)
>>
>>
>>
>>  On Mar 21, 2016, at 5:07 PM, James Henson <jfhens...@gmail.com> wrote:
>>>
>>>  Dear R community,
>>>
>>>  When I install or update a package, R prints the waring below.  I go to the
>>>  ‘downloaded_packages’ folder in the Temp file and manually move the new or
>>>  updated package to the folder ‘3.2’.   How can I instruct R to download new
>>>  and updates packages into the ‘3.2’ folder?
>>>
>>>  Warning in install.packages :
>>>
>>>   unable to move temporary installation
>>>  
>>> ‘C:\Users\james_henson\Desktop\Documents\R\win-library\3.2\file1c5c6f1731c8\nlme’
>>>  to ‘C:\Users\james_henson\Desktop\Documents\R\win-library\3.2\nlme
>>>
>>>
>>>
>>>  The downloaded binary packages are in
>>>
>>>
>>>  C:\Users\james_henson\AppData\Local\Temp\RtmpIZmUa3\downloaded_packages
>>>
>>>
>>>
>>>  Thank for your help.
>>>
>>>  James F. Henson
>>>
>>>   [[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.
>>
>>

[[alternative HTML version deleted]]

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[R] installing packages

[James Henson]

Dear R community,

When I install or update a package, R prints the waring below.  I go to the
‘downloaded_packages’ folder in the Temp file and manually move the new or
updated package to the folder ‘3.2’.   How can I instruct R to download new
and updates packages into the ‘3.2’ folder?

Warning in install.packages :

  unable to move temporary installation
‘C:\Users\james_henson\Desktop\Documents\R\win-library\3.2\file1c5c6f1731c8\nlme’
to ‘C:\Users\james_henson\Desktop\Documents\R\win-library\3.2\nlme



The downloaded binary packages are in


C:\Users\james_henson\AppData\Local\Temp\RtmpIZmUa3\downloaded_packages



Thank for your help.

James F. Henson

[[alternative HTML version deleted]]

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[R] Removing a dollar sign from a character vector

[James Plante]

What I’ve got:
# sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.3 (El Capitan)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] stats graphics  grDevices utils datasets  methods   base 

other attached packages:
[1] XML_3.98-1.3 dplyr_0.4.3 

loaded via a namespace (and not attached):
[1] magrittr_1.5  R6_2.1.2  assertthat_0.1rsconnect_0.4.1.4
[5] parallel_3.2.3DBI_0.3.1 tools_3.2.3   Rcpp_0.12.3 

> str(y) #toy vector, subset of larger vector in a dataframe of ~4,600 rows.
 chr [1:5] "$1,000.00 " "$1,000.00 " "$1,000.00 " "$2,600.00 " "$2,600.00 “

y is a subset of a column in a dataframe that’s too big to post. I tried the 
commands listed here on the dataframe and it didn’t work. So I’m using a small 
subset to find out where my error is. It’s being a PITA, and I’m trying to 
solve it. What I want is a vector of numbers: 1000, 1000, 1000, 2600, 2,600. 

What I’ve tried:
> y
[1] "$1,000.00 " "$1,000.00 " "$1,000.00 " "$2,600.00 " "$2,600.00 "
> gsub("$", "", y)
[1] "$1,000.00 " "$1,000.00 " "$1,000.00 " "$2,600.00 " "$2,600.00 “ # no 
change. Why?
> gsub(".00", "", y)  # note: that’s dot zero zero, replace with “"
[1] "$10 " "$10 " "$10 " "$2, " "$2, “  #WTF?

I’ve also tried sapply and apply, but haven’t yet tried a loop. (These were 
done in desperation; gsub ought to work the way the help says.) I’ve tried lots 
more than is listed here, over and over, with no results. I’d be grateful for 
any guidance you can provide. 

Thanks in advance,

Jim Plante

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[R] package broom

[James Henson]

Dear R community

My version is R version 3.2.3.
The package "broom" appears to install, but it will not load.
The error message is below.


> library(broom)
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck
= vI[[j]]) :
  there is no package called ‘mnormt’
Error: package or namespace load failed for ‘broom’


Thanks,
James F. Henson

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[R] how to plot two variables in a figure using ggplot2

[Gullen, James (MDE)]

Greetings!

You don't specify what type of "figure" you're looking for...here are two 
possibilities to get you started:

As a note, it would have made things slightly easier if you had used dput() to 
provide the data to us. It took a little massaging in notepad before getting it 
into R.

#Read data from clipboard after removing blank line and column numbers in 
notepad...
mydata <- read.table(file="clipboard", sep=" ", header =TRUE)
str(mydata)

#Restructure the data to long for ggplot2...there are other ways to do this, 
also.
mydata2 <- data.frame(group=rep(c("OA","KA"),  each=9), xvar=rep(mydata$XX, 
times=2), yvar=c(mydata$OA, mydata$KA))

 #Look at format of the data
mydata2

#Now to the plotting...
require(ggplot2)

#You might want a barplot...
plot1 <- ggplot(data=mydata2, aes(x=xvar, y=yvar,group=group, fill=group)) +
  geom_bar(stat="identity", position="dodge") + ggtitle("Barchart of OA and KA")

plot1

#..or you might want a lineplot...
plot2 <-ggplot(data=mydata2, aes(x=xvar, y=yvar, group=group, colour=group)) +
  geom_line() + ggtitle("Linechart of OA and KA")

plot2

The line chart is very easy to do in ggplot2 even if you don't restructure the 
data to long format, if that is what you were looking for.

Hope this helps and best regards!

Jim Gullen, Ph.D
Higher Education Data Reporting Consultant
Office of Professional Preparation Services
Michigan Department of Education

Customer Service is a priority at the Michigan Department of Education - 
helping Michigan schools, families, and communities improve the achievement and 
well-being of ALL our children.

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Re: [R] value of variable in ls()

[James Toll]

> On Oct 18, 2015, at 10:51 AM, Christian Hoffmann <christ...@echoffmann.ch> 
> wrote:
> 
> How can I do e.g. print("unknown"(ls())) and get the variable values in my 
> current environment?

>From your example, it sounds like what you want is simply this:

sapply(ls(), get)


James

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[R] rvest and the not css selector

[James Toll]

Hi,

I'm trying to use rvest to scrape a page and I am having difficulty excluding 
child element superscripts via a CSS selector.  For example, here I've read the 
html and selected nodes.


p <- read_html(targetUrl)
p %>% html_nodes("td.xyz")


The result looks something like this:

{xml_nodeset (20)}
 [1] Foo9:
 [2] Bar3:
[...]


I would like to extract the words "Foo" and "Bar" without the superscripts by 
passing along to html_text().  I thought something like this would work, but it 
returns just the superscripts. 

p %>% 
html_nodes("td.xyz") %>%
html_nodes(":not(sup)") %>% 
html_text()


Perhaps I’m using the not selector improperly.  Any suggestions on how to get 
this to work properly?  Thanks.


James

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[R] contrasts among simple effects

[James Henson]

Greetings R Community

My goal is to make orthogonal contrasts among simple effects in analysis of
repeated measures data.  The SAS publication, on page 1224, shows how to
make this type of contrasts in SAS.  But, my search of books about repeated
measures analysis using R, and on-line has not yielded a methodology.
Hopefully, someone can direct me to a book or publication that will show me
a methodology.

Statistical Analysis of Repeated Measures Data Using SAS Procedures

http://cslras.pbworks.com/f/littell_j_anim_sci_76_4_analysis_of_repeated_measures_using_sas.pdf



Attached is a csv data file (file name = heartRate.csv).  My code for the
repeated measures analysis is below.


library("nlme")

# with AR1 variance/covariance structure, with ordered statement

heartRate$time <- factor(heartRate$time)

model2a <- lme(HR ~ drug*ordered(time), random =~1|person, correlation
=corAR1(, form=~1|person), data = heartRate)

summary(model2a)

anova(model2a)


Making a new variable ‘simple’ that merges the variables drug and time will
enable me to make orthogonal contrasts among the simple effects.  But, when
using the variable ‘simple’ as the independent variable, the data will no
longer be fitted to the AR1 variance/co-variance structure.

Thanks.

Best regards,

James F.Henson
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[R] contrasts among simple effects - 2

[James Henson]

Greetings R Community

Apologize for previously sending a csv file.

My goal is to make orthogonal contrasts among simple effects in analysis of
repeated measures data.  The SAS publication, on page 1224, shows how to
make this type of contrasts in SAS.  But, my search of books about repeated
measures analysis using R, and on-line has not yielded a methodology.
Hopefully, someone can direct me to a book or publication that will show me
a methodology.

Statistical Analysis of Repeated Measures Data Using SAS Procedures

http://cslras.pbworks.com/f/littell_j_anim_sci_76_4_analysis_of_repeated_measures_using_sas.pdf



Attached is a txt data file (file name = heart_rate.txt).  My code for the
repeated measures analysis is below.

library("nlme")

# with AR1 variance/covariance structure, with ordered statement

heartRate$time <- factor(heartRate$time)

model2a <- lme(HR ~ drug*ordered(time), random =~1|person, correlation
=corAR1(, form=~1|person), data = heartRate)

summary(model2a)

anova(model2a)


Making a new variable ‘simple’ that merges the variables drug and time will
enable me to make orthogonal contrasts among the simple effects.  But, when
using the variable ‘simple’ as the independent variable, the data will no
longer be fitted to the AR1 variance/covariance structure.

Thanks.

Best regards,

James F.Henson
drugperson  timeHR
a   1   1   72
a   4   1   78
a   7   1   71
a   10  1   72
a   13  1   66
a   16  1   74
a   19  1   62
a   22  1   69
b   2   1   85
b   5   1   82
b   8   1   71
b   11  1   83
b   14  1   86
b   17  1   85
b   20  1   79
b   23  1   83
c   3   1   69
c   6   1   66
c   9   1   84
c   12  1   80
c   15  1   72
c   18  1   65
c   21  1   75
c   24  1   71
a   1   2   86
a   4   2   83
a   7   2   82
a   10  2   83
a   13  2   79
a   16  2   83
a   19  2   73
a   22  2   75
b   2   2   86
b   5   2   86
b   8   2   78
b   11  2   88
b   14  2   85
b   17  2   82
b   20  2   83
b   23  2   84
c   3   2   73
c   6   2   62
c   9   2   90
c   12  2   81
c   15  2   72
c   18  2   62
c   21  2   69
c   24  2   70
a   1   3   81
a   4   3   88
a   7   3   81
a   10  3   83
a   13  3   77
a   16  3   84
a   19  3   78
a   22  3   76
b   2   3   83
b   5   3   80
b   8   3   70
b   11  3   79
b   14  3   76
b   17  3   83
b   20  3   80
b   23  3   78
c   3   3   72
c   6   3   67
c   9   3   88
c   12  3   77
c   15  3   69
c   18  3   65
c   21  3   69
c   24  3   65
a   1   4   77
a   4   4   81
a   7   4   75
a   10  4   69
a   13  4   66
a   16  4   77
a   19  4   70
a   22  4   70
b   2   4   80
b   5   4   84
b   8   4   75
b   11  4   81
b   14  4   76
b   17  4   80
b   20  4   81
b   23  4   81
c   3   4   74
c   6   4   73
c   9   4   87
c   12  4   72
c   15  4   70
c   18  4   61
c   21  4   68
c   24  4   63
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Re: [R] Two conditions selection

[James Hedges]

cycle %% filter(col == blue, cycle == 1)
On Tue, Aug 4, 2015 at 18:59 Rodrigo Díaz rodlupa...@hotmail.com wrote:

 Hi. I have a matrix like this:

 cycle=c(rep(1,3),rep(2,3),rep(3,3),rep(4,3))col=c(rep(blue,2),rep(green,2),rep(blue,2),rep(green,2),rep(blue,2),rep(green,2))values=c(1:12)data.frame(cycle,col,values)
 #  cycle   col values#1  1  blue  1#2  1  blue  2#3  1
 green  3#4  2 green  4#5  2  blue  5#6  2  blue
   6#7  3 green  7#8  3 green  8#9  3  blue  9#10
  4  blue 10#11 4 green 11#12 4 green 12
 I want to select or extract values matching 2 conditions. For example:
 values from col blue and cycle 1. If I use : values[col==blue] I get
 all blue values. I tried using values[c(col==blue,cycle==1)] but is not
 working. Please help. I have a very big data matrix and I do not wanna go
 to excel and start cutting the data. Thanks.


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Re: [R] Two conditions selection

[James Hedges]

Sorry. In dplyr:
data %% filter(col == blue, cycle ==1) %% select(values)

On Tue, Aug 4, 2015 at 19:54 James Hedges jhedg...@gmail.com wrote:

 cycle %% filter(col == blue, cycle == 1)
 On Tue, Aug 4, 2015 at 18:59 Rodrigo Díaz rodlupa...@hotmail.com wrote:

 Hi. I have a matrix like this:

 cycle=c(rep(1,3),rep(2,3),rep(3,3),rep(4,3))col=c(rep(blue,2),rep(green,2),rep(blue,2),rep(green,2),rep(blue,2),rep(green,2))values=c(1:12)data.frame(cycle,col,values)
 #  cycle   col values#1  1  blue  1#2  1  blue  2#3
 1 green  3#4  2 green  4#5  2  blue  5#6  2  blue
 6#7  3 green  7#8  3 green  8#9  3  blue  9#10
4  blue 10#11 4 green 11#12 4 green 12
 I want to select or extract values matching 2 conditions. For example:
 values from col blue and cycle 1. If I use : values[col==blue] I get
 all blue values. I tried using values[c(col==blue,cycle==1)] but is not
 working. Please help. I have a very big data matrix and I do not wanna go
 to excel and start cutting the data. Thanks.


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[R] Combining estimates from multiple regressions

[James Shaw]

I am interested in using quantile regression to fit the following model at
different quantiles of a response variable:

(1)  y = b0 + b1*g1 + b2*g2 + B*Z

where b0 is an intercept, g1 and g2 are dummy variables for 2 of 3
independent groups, and Z is a matrix of covariates to be adjusted for in
the estimation (e.g., age, gender).  The problem is that estimates for g2
and g1 are not estimable at all quantiles.  To overcome this, one option is
to fit a separate model for each group (i.e., group 0, which is reflected
by intercept above, group 1, and group 2):

(2)  y = b11 + B1*Z (model for group 0)
(3)  y = b12 + B2*Z (model for group 1)
(4)  y = b13 + B3*Z (model for group 2)

This would correspond to fitting a single model in which group membership
was interacted with all covariates, albeit some of the interaction terms
would not be estimable for the reason noted above.  However, I ultimately
would like to base inferences on a single set of estimates.

Can anyone suggest an approach to combine estimates from models (2)-(4),
perhaps through weighted averaging, to generate estimates for the model
presented in (1) above?  An approach is not immediately clear to me since
the group effects are subsumed in the intercepts in (2)-(4), whereas (1)
includes separate estimates of group effects instead of a single weighted
average.

Regards,

Jim

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Re: [R] Combining estimates from multiple regressions

[James Shaw]

Thanks for the suggestions, Gunter.



On Wed, Jun 24, 2015 at 10:33 AM, Bert Gunter bgunter.4...@gmail.com wrote:
 Not an answer to your question, but you should not be using dummy
 variables in R. Use factors instead. Please read a R tutorial or text
 -- there are many -- to learn how to fit models in R. You might also
 wish to consult a local statistician or post on a statistics list like
 stats.stackexchange.com for statistics questions, which are off topic
 here.

 Further, when you post here, please read and follow the posting guide
 (below) and post in plain text, not HTML.

 Cheers,
 Bert
 Bert Gunter

 Data is not information. Information is not knowledge. And knowledge
 is certainly not wisdom.
-- Clifford Stoll


 On Wed, Jun 24, 2015 at 3:27 AM, James Shaw sha...@gmail.com wrote:
 I am interested in using quantile regression to fit the following model at
 different quantiles of a response variable:

 (1)  y = b0 + b1*g1 + b2*g2 + B*Z

 where b0 is an intercept, g1 and g2 are dummy variables for 2 of 3
 independent groups, and Z is a matrix of covariates to be adjusted for in
 the estimation (e.g., age, gender).  The problem is that estimates for g2
 and g1 are not estimable at all quantiles.  To overcome this, one option is
 to fit a separate model for each group (i.e., group 0, which is reflected
 by intercept above, group 1, and group 2):

 (2)  y = b11 + B1*Z (model for group 0)
 (3)  y = b12 + B2*Z (model for group 1)
 (4)  y = b13 + B3*Z (model for group 2)

 This would correspond to fitting a single model in which group membership
 was interacted with all covariates, albeit some of the interaction terms
 would not be estimable for the reason noted above.  However, I ultimately
 would like to base inferences on a single set of estimates.

 Can anyone suggest an approach to combine estimates from models (2)-(4),
 perhaps through weighted averaging, to generate estimates for the model
 presented in (1) above?  An approach is not immediately clear to me since
 the group effects are subsumed in the intercepts in (2)-(4), whereas (1)
 includes separate estimates of group effects instead of a single weighted
 average.

 Regards,

 Jim

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Re: [R] [FORGED] Re: Dunnett Test in 'multicomp' package

[James Henson]

Thanks. A useful tip for a long-time SAS user.
James F. Henson

On Fri, Jun 5, 2015 at 3:47 AM, Gerrit Eichner 
gerrit.eich...@math.uni-giessen.de wrote:

 Hello, everyone,

 aside from Rolf's hint (and Richard's warning!) you could also consider
 relevel():

 viagraData$dose - relevel( viagraData$dose, ref = placebo)

  Hth  --  Gerrit


 On Fri, 5 Jun 2015, Rolf Turner wrote:

  On 05/06/15 11:08, Jim Lemon wrote:

 Hi James,
 You can change the order of levels like this:

 levels(viagraData$dose)-c(placebo,low dose,high dose)


 SNIP

 As Richard Heiberger has pointed out, this is wrong.

 What *does* work is:

 viagraData$dose)-factor(viagraData$dose,
levels=c(placebo,low dose,high dose)

 This is a trap into which many a Young Player (including my very good
 self) has fallen.

 cheers,

 Rolf Turner



 --
 Technical Editor ANZJS
 Department of Statistics
 University of Auckland
 Phone: +64-9-373-7599 ext. 88276

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[R] Dunnett Test in 'multicomp' package

[James F. Henson]

Greetings

Below is my code.

library(multcomp)
viaModel1 - aov(libido ~ dose, data=viagraData)
dunnettModel - glht(viaModel1 , linfct = mcp(dose = Dunnett), base = 
placebo)

The code base=placebo is ignored.  All treatments are compared to the first 
treatment in the order, which is high dose.  It is possible to rearrange the 
order so that placebo' is first, but this is inconvenient.

Thanks,
James F. Henson

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[R] MCMCglmm Intersex covariance set to 0

[Rapkin, James]

Dear all

I'm trying to examine the effect that the additive genetic covariance (B) 
between the sexes has on the predicted response to selection on life-history 
traits in the sexes. 

Using the method of Argrawal and Stinchcombe (2009) this is done by calculating 
the response to selection following the method of Lande (1980):

(Delta_Z_Male = 1/2 ( GmB(beta m
 Delta_Z_Female)B   Gf) beta f) 

when B was estimated from my breeding design versus when it was set to zero to 
reflect the case where genetic covariance between the sexes does not constrain 
the evolution of shared life-history traits. 

My experiment was a half-sib quantitative breeding design which looked at 
nutrient intake, specifically protein and carbohydrate, using artificial diets 
of known nutritional content, in males and females. 

My life history traits are lifespan and reproductive effort. 

I have used an MCMCglmm model to calculate the response to selection when B was 
predicted from my breeding design using the following as an example:

prior1.1 - list(G = list(G1 = list(V = diag(4), n = 1.002)), R = list(V = 
diag(4), n = 1.002))

model1.1 - MCMCglmm(cbind(Total_P_Eaten_Male_Daily, Total_C_Eaten_Male_Daily, 
Total_P_Eaten_Female_Daily, Total_C_Eaten_Female_Daily) ~ trait -1, random = 
~us(trait):animal, 
 rcov = ~us(trait):units, family = c(gaussian, 
gaussian, gaussian, gaussian), 
 pedigree = Ped, data = Data, nitt=15000, thin = 50, 
burnin=100,
 prior = prior1.1, verbose = T)

modelBM1 - MCMCglmm(Z_MLS ~ Z_MP + Z_MC-1, data = Male.Data, nitt=15000, 
thin=50, burnin=100)
modelBF1 - MCMCglmm(Z_FLS ~ Z_FP + Z_FC-1, data = Female.Data, nitt=15000, 
thin=50, burnin=100)

# Calculate delta_z
MP_LS_delta_z-numeric(298)
for(i in 1:298){
  MP_MP - model1.1$VCV[i, 1]
  MP_MC - model1.1$VCV[i, 2]
  MP_FP - model1.1$VCV[i, 3]
  MP_FC - model1.1$VCV[i, 4]
  MP_LS - modelBM1$Sol[i, 1]
  MC_LS - modelBM1$Sol[i, 2]
  FP_LS - modelBF1$Sol[i, 1]
  FC_LS - modelBF1$Sol[i, 2]
  
MP_LS_delta_z[i]- ((MP_MP*MP_LS)+(MP_MC*MC_LS)+(MP_FP*FP_LS)+(MP_FC*FC_LS))
}
#Summary of deltaz including confidence
summary(MP_LS_delta_z)

This has allowed me to calculate the confidence interval of my predicted 
responses and I would like to be able to do this for when my between sex 
genetic covariance is set to 0, but I am having trouble doing this. 

Is there a way to set my B to 0? I know how to set all my off diagonal 
components to 0 but this isn't exactly what I want to do.

Here is an example of my G matrix:

G1  G2  G3  G4
G1  G1,1G1,2G1,3G1,4
G2  G1,2G2,2G2,3G2,4
G3  G1,3G2,3G3,3G3,4
G4  G1,4G2,4G3,4G4,4

I have read the help (?MCMCglmm) and searched through the R help pages but if 
the answer is there I'm not able to find/understand it. 

Any help would be greatly appreciated. 

Thank you. 

James Rapkin

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[R] Fwd: PLEASE HELP ON R-LANGUAGE

[Daniel James]

Subject: PLEASE HELP ON R-LANGUAGE


I am writing my project on The effect of Bootstrapping on Time Series
Data. My problem is how I will write r programme to run a non stationary
time series data. I am familia to r language already.
Please help me.

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[R] print vectors with consecutive numbers

[James Wei]

Hi all,

I have a matrix with consecutive and non-consecutive numbers
in columns. For example, the first 2 columns have consecutive numbers. I want R
to print only columns with consecutive numbers. Here is the matrix and how I
did using conditional statement: 

##

mat=matrix(data=c(9,2,3,4,5,6,10,13,15,17,19,22,
25,27,29,31,34,37,39,41),ncol=5)

mat

difference = diff(mat)==1

difference

y1=difference[1,]

y2=difference[2,]

y3=difference[3,]

y=(y1|y2|y3)

y

 

if (y==TRUE) mat else 0

## 

However, R still print all 5 columns, not the first 2
columns I wanted. I got the Warning message:

In if (y == TRUE) mat else 0 :

  the condition has
length  1 and only the first element will be used 

How can I change the code to get only the first 2 columns
with consecutive numbers printed? I am new to R.  

Thanks in advance for your help. James  

  
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Re: [R] print vectors with consecutive numbers

[James Wei]

Hi Jorge,
 
Thanks so much, it is working perfectly. There are so many for me to learn.
 
Cheers.
 
James
 
From: jorgeivanve...@gmail.com
Date: Fri, 22 Aug 2014 22:28:40 +1000
Subject: Re: [R] print vectors with consecutive numbers
To: zwei0...@hotmail.com
CC: r-help@r-project.org

Hi James,


Try
mat[, apply(mat, 2, function(x) any(diff(x) == 1))]



HTH,

Jorge.-


On Fri, Aug 22, 2014 at 10:18 PM, James Wei zwei0...@hotmail.com wrote:






Hi all,



I have a matrix with consecutive and non-consecutive numbers

in columns. For example, the first 2 columns have consecutive numbers. I want R

to print only columns with consecutive numbers. Here is the matrix and how I

did using conditional statement:



##



mat=matrix(data=c(9,2,3,4,5,6,10,13,15,17,19,22,

25,27,29,31,34,37,39,41),ncol=5)



mat



difference = diff(mat)==1



difference



y1=difference[1,]



y2=difference[2,]



y3=difference[3,]



y=(y1|y2|y3)



y







if (y==TRUE) mat else 0



##



However, R still print all 5 columns, not the first 2

columns I wanted. I got the Warning message:



In if (y == TRUE) mat else 0 :



  the condition has

length  1 and only the first element will be used



How can I change the code to get only the first 2 columns

with consecutive numbers printed? I am new to R.



Thanks in advance for your help. James





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Re: [R] Installing manual package problem

[James Holland]

Thank you all, I didn't know about the install_github function.

Sorry, forgot to switch to plain text

On Sat, Aug 9, 2014 at 10:11 AM, Ista Zahn istaz...@gmail.com wrote:
 If you just want to install the package from github, the easy way is to
 first install the devtools package and use the install_github function.

 Best,
 Ista

 On Aug 8, 2014 4:21 PM, James Holland holland.ag...@gmail.com wrote:

 Running R 3.03 on Windows 7

 I am trying to install a package from a github repository.

 https://github.com/google/glassbox

 I downloaded the repository as a zip file, extracted it to get the
 glassbox
 folder and re-zipped it with 7-zip.

 I then ran

 #-Start code---#

 install.packages(C:/Users/jholland/Downloads/glassbox.zip, repos=NULL,
 type=source)

 #-#

 The output message said

 Installing package into ‘C:/Users/jholland/Documents/R/win-library/3.0’
 (as ‘lib’ is unspecified)

  library(glassbox)
 Error in library(glassbox) : ‘glassbox’ is not a valid installed package

 I'm not sure what I'm doing wrong.  When I look in the R library folder
 (...R/win-library/3.0) I see the glassbox folder there.

 I'm new to using packages not from the CRAN list so I'm trying to learn
 fast.  I tried some searching and this seems to be what I'm suppossed to
 do, but perhaps I need to use dev mode ?

 Thank you for the help.

 ~James

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[R] Installing manual package problem

[James Holland]

Running R 3.03 on Windows 7

I am trying to install a package from a github repository.

https://github.com/google/glassbox

I downloaded the repository as a zip file, extracted it to get the glassbox
folder and re-zipped it with 7-zip.

I then ran

#-Start code---#

install.packages(C:/Users/jholland/Downloads/glassbox.zip, repos=NULL,
type=source)

#-#

The output message said

Installing package into ‘C:/Users/jholland/Documents/R/win-library/3.0’
(as ‘lib’ is unspecified)

 library(glassbox)
Error in library(glassbox) : ‘glassbox’ is not a valid installed package

I'm not sure what I'm doing wrong.  When I look in the R library folder
(...R/win-library/3.0) I see the glassbox folder there.

I'm new to using packages not from the CRAN list so I'm trying to learn
fast.  I tried some searching and this seems to be what I'm suppossed to
do, but perhaps I need to use dev mode ?

Thank you for the help.

~James

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Re: [R] Installing manual package problem

[James Holland]

I re-zipped it because when I downloaded from GitHub, it had the actual
glassbox folder within the glassbox-master folder, so I zipped that
glassbox folder because my understanding was the install.package

On Aug 8, 2014, at 1:29 PM, James Holland wrote:

 Running R 3.03 on Windows 7

 I am trying to install a package from a github repository.

 https://github.com/google/glassbox

 I downloaded the repository as a zip file, extracted it to get the
glassbox
 folder and re-zipped it with 7-zip.

Why?


 I then ran

 #-Start code---#

 install.packages(C:/Users/jholland/Downloads/glassbox.zip, repos=NULL,
 type=source)


I'm a Mac user but when I look at the directory created by expanding that
zip file, it appears ready to just move/drag to the library without further
installation. It is, however, not named 'glassbox' but rather
'glassbox-master' so perhaps you forgot to rename it?


 The output message said

 Installing package into ‘C:/Users/jholland/Documents/R/win-library/3.0’
 (as ‘lib’ is unspecified)

 library(glassbox)
 Error in library(glassbox) : ‘glassbox’ is not a valid installed package

 I'm not sure what I'm doing wrong.  When I look in the R library folder
 (...R/win-library/3.0) I see the glassbox folder there.



 I'm new to using packages not from the CRAN list so I'm trying to learn
 fast.  I tried some searching and this seems to be what I'm suppossed to
 do, but perhaps I need to use dev mode ?

 Thank you for the help.

 ~James

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This is a plain text mailing list.

--


David Winsemius
Alameda, CA, USA

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Re: [R] Installing manual package problem

[James Holland]

I re-zipped it because when I downloaded from GitHub, it had the actual
glassbox folder within the glassbox-master folder, so I zipped that
glassbox folder because my understanding was the install.package function
only works on zipped files.

And it does seem like it installed within my R library (I see the glassbox
folder in there) but the library function doesn't attach the package.

~James


On Fri, Aug 8, 2014 at 6:50 PM, David Winsemius dwinsem...@comcast.net
wrote:


 On Aug 8, 2014, at 1:29 PM, James Holland wrote:

  Running R 3.03 on Windows 7
 
  I am trying to install a package from a github repository.
 
  https://github.com/google/glassbox
 
  I downloaded the repository as a zip file, extracted it to get the
 glassbox
  folder and re-zipped it with 7-zip.

 Why?

 
  I then ran
 
  #-Start code---#
 
  install.packages(C:/Users/jholland/Downloads/glassbox.zip, repos=NULL,
  type=source)
 

 I'm a Mac user but when I look at the directory created by expanding that
 zip file, it appears ready to just move/drag to the library without further
 installation. It is, however, not named 'glassbox' but rather
 'glassbox-master' so perhaps you forgot to rename it?

 
  The output message said
 
  Installing package into ‘C:/Users/jholland/Documents/R/win-library/3.0’
  (as ‘lib’ is unspecified)
 
  library(glassbox)
  Error in library(glassbox) : ‘glassbox’ is not a valid installed package
 
  I'm not sure what I'm doing wrong.  When I look in the R library folder
  (...R/win-library/3.0) I see the glassbox folder there.


 
  I'm new to using packages not from the CRAN list so I'm trying to learn
  fast.  I tried some searching and this seems to be what I'm suppossed to
  do, but perhaps I need to use dev mode ?
 
  Thank you for the help.
 
  ~James
 
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 This is a plain text mailing list.

 --


 David Winsemius
 Alameda, CA, USA



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Re: [R] Importing random subsets of a data file

[James White]

Here's a stack overflow question addressing the same issue. 
http://stackoverflow.com/a/22261345
Hopefully it will help.
Thanks
 Date: Wed, 23 Jul 2014 12:33:11 -0300
 From: khurram.na...@gmail.com
 To: r-help@r-project.org
 Subject: [R] Importing random subsets of a data file
 
 Hi R folks,
 
 Here is my problem.
 
 *1.* I have a large data file (say, in .csv or .txt format) containing 1
 million rows and 500 variables (columns).
 
 *2.* My statistical algorithm does not require the entire dataset but just
 a small random sample from the original 1 million rows.
 
 *3. *This algorithm needs to be applied 1 times, each time generating a
 different random sample from the 'big' file as described in (2) above.
 
 Is there a way to 'import' only a (random) subset of rows from the .csv
 file without importing the entire dataset? A quick search on various R
 forums suggest that read.table() does not have this functionality.
 Obviously, I want to avoid importing the whole file because of memory
 issues. Looking forward to your help.
 
 Thanks,
 Khurram
 
  Khurram Nadeem
  Postdoctoral Research Fellow
  Department of Mathematics  Statistics
  Acadia University, NS, Canada.
 
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[R] plotGooglemaps - Problem with the legend.

[James Holland]

I cannot get the legend to display the cut points I want correctly.
Instead of doing the colors at 1, 2, 3, 4, 5 - its doing the color breaks
at odd points on the legends.  The labels seem to get coded correctly
however.

#   Code Below

#.

#  Messing around with Student Engagement Survey data
library(RgoogleMaps)
library(PBSmapping)
library(maptools)
library(reshape)
library(RColorBrewer)
library(plotGoogleMaps)
library(rgdal)

rm(list=ls())

mydata - data.frame(NAME=c(James Elem,Chloe MS,Logan HS, Kristen
Elem, Heather HS, Nora MS, Elizabeth JH),
   i1.a.=c(0,1,2, 2.4, 3.5, 4.3, 5),
   lat = c(32.968, 32.874, 32.884, 32.91538, 32.91810, 32.87884, 32.94468),
   lon = c(-96.692, -96.725, -96.708, -96.72321, -96.71760, -96.73990,
-96.72850)
   )



# --- #


# --- #
# -- Ploting School Locations --- #

coordinates(mydata) - ~lon + lat
proj4string(mydata) - CRS(+proj=longlat +datum=WGS84)

#SchoolRaceP - SpatialPointsDataFrame, data

# Playing around with various options

m - plotGoogleMaps(mydata, zcol=i1.a.,
at=0:4,
colPalette = c(#FF,#FF9900,#00,#0066FF,#00CC00),
layerName=Some Schools,
filename=MyMap.html)

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[R] Ridge regression for beta and gamma models

[john james]

Dear All,

Please, is there any package in R that has implemented ridge regression for 
beta and gamma models?

If not, kindly help me to adjust my model below for the beta regression so as 
to accommodate ridge
penalty. Thanks.



lbeta - function(par,y,X){
n -length(y)
k - ncol(X)
beta - par[1:k]
phi - par[k+1]
if(phi  0)return(NA)
mu - X%*%beta
val - vector()
mu - X%*%beta
mul - exp(mu)/(1+exp(mu))
p - phi*mul; q - phi*(1-mul)
for(i in 1:n) val[i] - dbeta(y[i],p[i,],q[i,],log=TRUE)
return(-sum(val))
}

James
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[R] Pull Stock Symbol Out of String

[Sparks, John James]

Dear R Helpers,

My regex skills are beginner to intermediate and banging around the web
has not resulted in a solution to the problem below so I hope that one of
you who has mad skills can help me out.

I want to extract the stock ticker--AMT-- out of the string

American Tower Corporation (REIT) (AMT)

The presence of the other parenthetical text (REIT) makes this difficult. 
Please note that the string may or may not have a interfering set of
characters such as the (REIT) so the solution needs to be generalizable to
the last set of characters that are contained in parentheses in the larger
string.  So an example of a string without the interfering (REIT) would be

Aetna Inc. (AET)


Your assistance would be very much appreciated.

--John Sparks

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[R] rehh package for iHS and Rsb on NGS data

[James Abugri]

Hello expert community.
Is there anybody whose used rehh package for iHS and rsb. I have gone through 
the tutorial a dozen times, I need expert help to enable me apply it to my 
p.falciparum snp data from the illumina platform.

Thanks
James Abugri
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[R] looping in R

[Abugri James]

I ran the following loop on my SNP data and got an error message as
indicated
for (i in genenames){
+   current - fst1[which(fst1$Gene == i),]
+   num - nrow(current)
+   fst - max(current$fst)
+   position - mean(current$pos)
+   nposition - mean(current$newpos)
+   numhigh - nrow(current[which(current$fst  threshold),])
+   colors - mean(current$colors)
+   output - matrix(NA,nrow=1,ncol=8)
+   numthresh - paste(# SNPs  Fst = , threshold, sep=)
+   colnames(output) - c(gene, gene_old, pos, newpos, # Snps,
numthresh, Max.Fst, colors)
+   output[1,1] - i
+   output[1,2] - as.character(current[1, gene_old])
+   output[1,3] - position
+   output[1,4] - nposition
+   output[1,5] - num
+   output[1,6] - numhigh
+   output[1,7] - fst
+   output[1,8] - colors
+   maxfstgene - rbind(maxfstgene, output)
+ }
Error in output[1, 2] - as.character(current[1, gene_old]) :
  replacement has length zero
In addition: Warning message:
In mean.default(current$pos) :
  argument is not numeric or logical: returning NA
--

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[R] Emacs/R/SSH But View( ) Doesn't Work

[Allison Sr James L]

I successfully run Emacs on a Windows laptop then use Emacs' Tramp to connect 
to a Linux server using SSH. Emacs in this fashion supports editing .R files 
resident on the remote machine and running of R in an inferior Emacs shell. The 
R process runs on the server. Also, I successfully use Putty and Xming to allow 
display of R plots executed in R on the remote machine to be displayed on the 
Windows laptop.

One last thing that would complete this configuration is if I could use the R 
View( ) command to look at data frames resident within the R process. The 
following is the error:

 View(cars)
Error in .External2(C_dataviewer, x, title) : invalid device
In addition: Warning message:
In View(cars) : unable to open display


Has anyone been able to either get View( ) to work under this configuration or 
devised another solution? I have used Sweave with xtable and then displayed the 
pdf file in the Putty/Xming window on the laptop but this is slow.

Thanks,
Dr. Jim Allison

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[R] Font Path question

[James W. MacDonald]

I am having weird problems where more recent installs of R cannot find 
the Font path. I don't have sudo access, so install R in my personal 
directory on an Ubuntu box, from source.


$ ls -lah R-3.0.1/bin/ | grep -w R
-rwxr-xr-x  1 jmacdon staff 8.5K Aug 30 14:04 R
$ ls -lah R-3.0.2/bin/ | grep -w R
-rwxr-xr-x  1 jmacdon staff 8.5K Sep 26 09:24 R
$ ls -lah R-2.15.1/bin/ | grep -w R
-rwxr-xr-x  1 jmacdon staff 8.5K Dec 19 12:58 R
$ ls -lah R-devel/bin/ | grep -w R
-rwxr-xr-x  1 jmacdon staff 8.5K Feb 11 09:47 R

Neither R-2.15.1 nor R-devel can find the Font Path, but R-3.0.1 and 
R-3.0.2 can:


 plot(1:10) ## no problems here
 sessionInfo()
R version 3.0.2 (2013-09-25)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8   LC_NAME=C
 [9] LC_ADDRESS=C   LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats graphics  grDevices utils datasets  methods base


 plot(1:10)   #urgh
Error in axis(side = side, at = at, labels = labels, ...) :
  could not find any X11 fonts
Check that the Font Path is correct.
 sessionInfo()
R Under development (unstable) (2014-02-10 r64961)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8   LC_NUMERIC=C
 [3] LC_TIME=en_US.UTF-8LC_COLLATE=en_US.UTF-8
 [5] LC_MONETARY=en_US.UTF-8LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8   LC_NAME=C
 [9] LC_ADDRESS=C   LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats graphics  grDevices utils datasets  methods base

Any suggestions as to how I might track this down?

Best,

Jim

--
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

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[R] Best practices for loading large datasets into R

[James Mahon]

Hello,

I'm working with a 22 GB datasets with ~100 million observations and ~40
variables. It's store in SQLite and I use the RSQLite package to load it
into memory. Loading the full population, even for only a few variables,
can be very slow and I was wondering if there are best practices for how to
manage large datasets when doing analysis in R. Is there an alternative
file format / relational datbase in which I should be storing the data?

Best,

James
-- 
James F. Mahon III, Ph.D. Candidate
Harvard University
Tel: (857) 209-8438
Fax: (270) 813-3498
Web: http://www.people.fas.harvard.edu/~jmahon/

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Re: [R] [BioC] Why daisy() in cluster library failed to exclude NA when computing dissimilarity

[James W. MacDonald]

Hi Gundala,

This question isn't about a Bioconductor package, so should be asked on 
R-help instead.


Best,

Jim

On Sunday, December 08, 2013 2:11:12 AM, Gundala Viswanath wrote:

Hi,


According to daisy function from cluster documentation, it can compute
dissimilarity when NA (missing) value(s) is present.

http://stat.ethz.ch/R-manual/R-devel/library/cluster/html/daisy.html

But why when I tried this code

library(cluster)
x - c(1.115,NA,NA,0.971,NA)
y - c(NA,1.006,NA,NA,0.645)
df - as.data.frame(rbind(x,y))
daisy(df,metric=gower)

It gave this message:

Dissimilarities :
x
y NA

Metric :  mixed ;  Types = I, I, I, I, I
Number of objects : 2
Warning messages:
1: In min(x) : no non-missing arguments to min; returning Inf
2: In max(x) : no non-missing arguments to max; returning -Inf

I welcome other alternative than gower.

I expect the dissimilarity output gives a non-NA value e.g. 0. What's
the right way to do it?

G.V.

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Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099

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[R] Finding absolute viewport location in grid / lattice

[James Price]

I'm trying to do some post-plot manipulation of some lattice graphics, in which 
I need to get the absolute viewport locations on the plotting device. So for 
example:

library(lattice)
print(xyplot(Petal.Length ~ Sepal.Length | Species, iris, layout = c(2, 2)))
trellis.focus('panel', 1, 1)

This shows the item I want to identify. I need to know, for example, that the 
lower left corner of the highlighted panel is at (0.1, 0.1) of the plotting 
device. Hopefully there's some grid shenanigans I can use to do so.

To put the question into context (in case there's an alternative way): I'm 
constructing PDF reports that are an amalgam of PDF figures, constructed 
through LaTeX programmatically constructed in R, and I'd like to be able to add 
tooltips to some of the data points on the graphs. To do so, I'm overlaying a 
tikz (empty) image that uses the pdfcomment package to add the tooltips. Hence 
I need to be able to calculate where some of the points are on the screen so I 
can calculate where to put the tooltip 'hit-zones'. This would be fairly 
trivial using javascript / actionscript and mouseover hooks, but I'm 
constrained by PDF. 

Thanks,
Jim Price.
Strength in Numbers.

  
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[R] [R-pkgs] scholar 0.1.0 on CRAN

[James Keirstead]

Dear R users,

A new package 'scholar' (version 0.1.0) is now available on CRAN: 
http://cran.r-project.org/web/packages/scholar/index.html.


The scholar package provides functions to extract citation data from 
Google Scholar.  In addition to retrieving basic information about a 
single scholar, the package also allows you to compare multiple scholars 
and predict future h-index values based on the method of Acuna et al.  
For example, we can compare the careers of Richard Feynman and Stephen 
Hawking as follows:


   ids - c('B7vSqZsJ', 'qj74uXkJ')
   df - compare_scholar_careers(ids)
   ggplot(df, aes(x=career_year, y=cites)) + geom_line(aes(linetype=name))

For more information and examples of how to use the package, please see 
https://github.com/jkeirstead/scholar.


Your comments and suggestions would be appreciated.

Best wishes,
James

--
Dr James Keirstead
Lecturer
Dept of Civil and Environmental Engineering
Imperial College
South Kensington, London
SW7 2AZ

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[R] Windows The system cannot find the path specified error when submitting R in batch mode

[James Hackett]

This is an R and operating system related question. I am not able to submit an 
R program to be executed in batch mode by Windows. I have confirmed the 
location of the R.exe file. I am following the directions I found in Quick-R, 
but neither of the following work from a DOS prompt ...

D:\chip\Projects\Crescendo Bioscience\Studies\024-CL-01 - BRASS 
FM\biostat\programs\R\024-CL-01 - BRASS FM - ManuscriptC:\Program 
Files\R\R-2.15.2\bin\R.exe CMD BATCH boxplotByMBDAAndCRP.R
The system cannot find the path specified.

D:\chip\Projects\Crescendo Bioscience\Studies\024-CL-01 - BRASS 
FM\biostat\programs\R\024-CL-01 - BRASS FM - ManuscriptC:\Program 
Files\R\R-2.15.2\bin\R.exe CMD BATCH D:\chip\Projects\Crescendo 
Bioscience\Studies\024-CL-01 - BRASS FM\biostat\programs\R\024-CL-01 - BRASS FM 
- Manuscript\boxplotByMBDAAndCRP.R
The system cannot find the path specified.



Thank you for any help you can provide,
Chip

James Chip Hackett, Ph.D. | Statistical Consultant | Hackett  Associates, 
Inc. | c...@hackettassociates.net | 408.416.3747 (Office) | 805.509.0741 
(Mobile)

The material in this transmission may contain confidential information intended 
only for the  addressee. If you are not the addressee, any disclosure or use of 
this information by you is strictly prohibited. If you have received this 
transmission in error, please delete it, destroy all copies, and notify the 
sender immediately by reply or by calling 1-408-416-3747.



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Re: [R] Grap Element from Web Page

[Sparks, John James]

Thanks, the second approach worked fine on Windows.

--JJS

On Thu, August 15, 2013 8:38 am, Jeffrey Dick wrote:
 Sorry, I can't generate an error when running those commands in R on Linux
 64-bit. But if I move to Windows (R version 3.0.1, XML_3.98-1.1), I get a
 different error ...

 require(XML)
 Loading required package: XML
 doc - htmlTreeParse(
 http://www.sec.gov/cgi-bin/browse-edgar?CIK=MSFTFind=Searchowner=excludeaction=getcompany
 )
 node - getNodeSet(doc[[1]], //link[@rel='alternate'] )
 Input is not proper UTF-8, indicate encoding !
 Bytes: 0xC2 0x0A 0x20 0x20
 Error: 1: Input is not proper UTF-8, indicate encoding !
 Bytes: 0xC2 0x0A 0x20 0x20
 node - getNodeSet(doc, //link[@rel='alternate'] )
 Error in UseMethod(xpathApply) :
   no applicable method for 'xpathApply' applied to an object of class
 XMLDocumentContent

 ... note that I've tried both doc[[1]] and doc in the function call. Also,
 only the XML library is required. I'm not sure what's going on with the
 character encoding error, might be my system settings. Reading the help
 page (?htmlTreeParse) provides a clue to use the htmlParse function
 instead, equivalent to setting the useInternalNodes parameter to TRUE ...
 These can then be searched using XPath expressions via 'xpathApply' and
 'getNodeSet'. That seems to be relevant to this case.

 doc - htmlParse(
 http://www.sec.gov/cgi-bin/browse-edgar?CIK=MSFTFind=Searchowner=excludeaction=getcompany
 )
 node - xpathSApply(doc, //link[@rel='alternate'], xmlAttrs)
 node

 [,1]

 rel
 alternate

 type
 application/atom+xml

 title
 ATOM

 href
 /cgi-bin/browse-edgar?action=getcompanyCIK=789019type=dateb=owner=excludecount=40output=atom
 strsplit(strsplit(node[[4]], CIK=)[[1]][2], type)[[1]][1]
 [1] 789019

 Perhaps that approach is less prone to error.


 On Thu, Aug 15, 2013 at 12:48 PM, Sparks, John James
 jspa...@uic.eduwrote:

 Thanks so much for looking into this for me.

 Unfortunately, I get an error when I execute your code.  Is there a
 library that you loaded that I haven't?

 require(scrapeR)
 require(XML)
 require(RCurl)
 doc-htmlTreeParse(
 http://www.sec.gov/cgi-bin/browse-edgar?CIK=MSFTFind=Searchowner=excludeaction=getcompany
 )
 node - getNodeSet(doc[[1]], //link[@rel='alternate'] )
 Error in UseMethod(xpathApply) :
   no applicable method for 'xpathApply' applied to an object of class
 character


 Guidance would be much appreciated.

 --JJS



 On Wed, August 14, 2013 4:19 am, Jeffrey Dick wrote:
  Hi,
 
  There are many occurrences of the CIK number in the page source. This
  pulls
  out the first node containing it:
 
  node - getNodeSet(doc[[1]], //link[@rel='alternate'] )
 
  From there you can extract the number. Here's one way to do it.
 
  strsplit(strsplit(unlist(node)[[5]], CIK=)[[1]][2], type)[[1]][1]
 
  Jeff
 
 
  On Wed, Aug 14, 2013 at 1:34 PM, Sparks, John James jspa...@uic.edu
  wrote:
 
  Dear R Helpers,
 
  I would like to pull the CIK number from the web page
 
 
 
 http://www.sec.gov/cgi-bin/browse-edgar?CIK=MSFTFind=Searchowner=excludeaction=getcompany
 
  If you put this web page into your browser you will see the CIK
 number
  in
  red on the left side of the page near the top.
 
  When I try the basic
  require(scrapeR)
  require(XML)
  require(RCurl)
  doc
  -htmlTreeParse(
 
 http://www.sec.gov/cgi-bin/browse-edgar?CIK=MSFTFind=Searchowner=excludeaction=getcompany
  )
  str(doc)
 
  I get a large number of items in the data frame that I don't know how
 to
  interpret.  Both
  tables - readHTMLTable(doc)
 
  and
 
  list-xmlToList(doc)
 
  result in errors.
 
  Any (positive) guidance would be much appreciated.
 
  --John J. Sparks, Ph.D.
 
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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.
 
 





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

Re: [R] Grap Element from Web Page

[Sparks, John James]

Thanks so much for looking into this for me.

Unfortunately, I get an error when I execute your code.  Is there a
library that you loaded that I haven't?

require(scrapeR)
require(XML)
require(RCurl)
doc-htmlTreeParse(http://www.sec.gov/cgi-bin/browse-edgar?CIK=MSFTFind=Searchowner=excludeaction=getcompany;)
node - getNodeSet(doc[[1]], //link[@rel='alternate'] )
Error in UseMethod(xpathApply) :
  no applicable method for 'xpathApply' applied to an object of class
character


Guidance would be much appreciated.

--JJS



On Wed, August 14, 2013 4:19 am, Jeffrey Dick wrote:
 Hi,

 There are many occurrences of the CIK number in the page source. This
 pulls
 out the first node containing it:

 node - getNodeSet(doc[[1]], //link[@rel='alternate'] )

 From there you can extract the number. Here's one way to do it.

 strsplit(strsplit(unlist(node)[[5]], CIK=)[[1]][2], type)[[1]][1]

 Jeff


 On Wed, Aug 14, 2013 at 1:34 PM, Sparks, John James jspa...@uic.edu
 wrote:

 Dear R Helpers,

 I would like to pull the CIK number from the web page


 http://www.sec.gov/cgi-bin/browse-edgar?CIK=MSFTFind=Searchowner=excludeaction=getcompany

 If you put this web page into your browser you will see the CIK number
 in
 red on the left side of the page near the top.

 When I try the basic
 require(scrapeR)
 require(XML)
 require(RCurl)
 doc
 -htmlTreeParse(
 http://www.sec.gov/cgi-bin/browse-edgar?CIK=MSFTFind=Searchowner=excludeaction=getcompany
 )
 str(doc)

 I get a large number of items in the data frame that I don't know how to
 interpret.  Both
 tables - readHTMLTable(doc)

 and

 list-xmlToList(doc)

 result in errors.

 Any (positive) guidance would be much appreciated.

 --John J. Sparks, Ph.D.

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

[R] Grap Element from Web Page

[Sparks, John James]

Dear R Helpers,

I would like to pull the CIK number from the web page

http://www.sec.gov/cgi-bin/browse-edgar?CIK=MSFTFind=Searchowner=excludeaction=getcompany

If you put this web page into your browser you will see the CIK number in
red on the left side of the page near the top.

When I try the basic
require(scrapeR)
require(XML)
require(RCurl)
doc
-htmlTreeParse(http://www.sec.gov/cgi-bin/browse-edgar?CIK=MSFTFind=Searchowner=excludeaction=getcompany;)
str(doc)

I get a large number of items in the data frame that I don't know how to
interpret.  Both
tables - readHTMLTable(doc)

and

list-xmlToList(doc)

result in errors.

Any (positive) guidance would be much appreciated.

--John J. Sparks, Ph.D.

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