[R] Clustering Functions used by Reverse-Dependencies

[Leo Mada via R-help]

Dear R Users,

Are there any tools to extract the function names called by 
reverse-dependencies?

I would like to group these functions using clustering methods based on the 
co-occurrence in the reverse-dependencies.

Utility: It may be possible to split complex packages into modules with fewer 
reverse-dependencies.

Package pkgdepR may offer some of the functionality; but I did not have time to 
fully explore it:
https://cran.r-project.org/web/packages/pkgdepR/index.html

If such tools are not yet available, I have opened an issue on GitHub and would 
like to collect any ideas:
https://github.com/discoleo/PackageBrowser/issues/1

There are some model packages that could be used to test the clustering:
1) Rcpp, xml: the core-functionality will always be needed; splitting into 
modules may not be possible/useful;

2) pracma: most reverse-dependencies are likely using only a small subset of 
the functions in pracma;
(there was some discussion on R-package-devel about reverse dependencies a few 
weeks ago)

3) survival: I have no idea in which category it falls - but it has a lot of 
reverse-dependencies;

Note:
I missed some important functionality from the pkgsearch package. I have 
started therefore work on a new package (PackageBrowser) - although it is not 
yet published on CRAN:
https://github.com/discoleo/PackageBrowser

It does not yet process recursively the reverse-dependencies; although this 
does not seem a big challenge. The real challenge is to parse the code and 
extract function names. I did some work in the past, but never had time for a 
full implementation.

Many thanks,

Leonard


[[alternative HTML version deleted]]

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Re: [R] Rtools and things dependent on it

[David Winsemius]

Sent from my iPhone

> On Feb 23, 2024, at 18:19, Sorkin, John  wrote:
> 
> David,
> 
> I greatly appreciate the explanation you gave regarding R tools providing 
> tools available in Linux distros, but not found in Windows. (I am using a 
> windows system). Does this mean that Linux users don't need to use R tools 
> when they want to compile R code. 

Yes. That’s been true for me anyway. On a Mac I need to make sure I have the 
proper C and Fortran compilers and the proper environment variables , which are 
always provided by Saint  Simon Urbanek at the att.research site. 

— 
David. 
> 
> Additionally, thank you for the information about what I should read. I will 
> look at the material again, and hopefully things the material you suggest I 
> read will be more understandable.
> 
> John
> 
> P.S. This email should be in txt format, not html. I sent if from my desktop 
> windows machine which provides more options than does my iPhone.
> 
> 
> 
> John David Sorkin M.D., Ph.D.
> Professor of Medicine, University of Maryland School of Medicine;
> Associate Director for Biostatistics and Informatics, Baltimore VA Medical 
> Center Geriatrics Research, Education, and Clinical Center;
> PI Biostatistics and Informatics Core, University of Maryland School of 
> Medicine Claude D. Pepper Older Americans Independence Center;
> Senior Statistician University of Maryland Center for Vascular Research;
> 
> Division of Gerontology and Paliative Care,
> 10 North Greene Street
> GRECC (BT/18/GR)
> Baltimore, MD 21201-1524
> Cell phone 443-418-5382
> 
> 
> 
> 
> 
> From: David Winsemius 
> Sent: Friday, February 23, 2024 8:14 PM
> To: Sorkin, John
> Cc: avi.e.gr...@gmail.com; r-help@r-project.org
> Subject: Re: [R] Rtools and things dependent on it
> 
> 
> On 2/23/24 16:28, Sorkin, John wrote:
> David,
> My apologies regarding the format of my email. I am replying using my iPhone, 
> and I can’t find a way to switch from what I suspect is html to txt format.
> The link you sent told me that R tools allows compilation of code.
> 
> 
> It's specifically designed to provide the code tools missing in Windows that 
> would other wise have been provided by a typical Linux distro. More 
> expansively, it allows compilation of code written in C and/or Fortran using 
> the version that was used to build the matching R version and allows it to be 
> called by the routines written in R that bind a package together.
> 
> This is good to know, but beyond this important fact, the rest of the 
> material was close to unintelligible.
> 
> The phrase "the rest of the material" is not specific enough to offer more 
> explanation. You should quote material that is beyond your understanding. You 
> should only be reading the sections named: "Installing Rtools43" and 
> "Building packages from source using Rtools43". I doubt that material further 
> on would be relevant.
> 
> --
> 
> David
> 
> I doubt this is the fault of the author, it is probably because I lack some 
> basic knowledge. Can you suggest some more basic material I can read. Please 
> note. I am not computer naive, I am simply missing basic knowledge of the 
> material discussed in the web page.
> Thank you,
> John
> John David Sorkin M.D., Ph.D.
> Professor of Medicine
> Chief, Biostatistics and Informatics
> University of Maryland School of Medicine Division of Gerontology and 
> Geriatric Medicine
> Baltimore VA Medical Center
> 10 North Greene Street
> GRECC (BT/18/GR)
> Baltimore, MD 21201-1524
> (Phone) 410-605-7119
> (Fax) 410-605-7913 (Please call phone number above prior to 
> faxing)
> 
> On Feb 23, 2024, at 7:01 PM, David Winsemius 
>  wrote:
> 
> 
> On 2/23/24 14:34, avi.e.gr...@gmail.com wrote:
> This may be a dumb question and the answer may make me feel dumber.
> 
> I have had trouble for years with R packages wanting Rtools on my machine
> and not being able to use it. Many packages are fine as binaries are
> available. I have loaded Rtools and probably need to change my PATH or
> something.
> 
> 
> I suppose making sure that whatever directory holds your Rtools code is
> on your path would be a good idea. I wondered if there's an environment
> variable that could be set, but reading the page on using Rtools did not
> mention one until I got down to the section on building R from source
> which is surely NOT what you want to do.. You should read the
> information on installation and building packages from source.
> https://cran.r-project.org/bin/windows/base/howto-R-devel.html
>  which
> includes this sentence:
> 
> "It is recommended to use the defaults and install into|c:/rtools43|.
> When done that way, Rtools43 may be used in the same R session which
> installed it or which was started before Rtools43 was installed."
> 
> 
> But I recently suggested to someone that they might want to use 

Re: [R] Rtools and things dependent on it

[Sorkin, John]

David,

I greatly appreciate the explanation you gave regarding R tools providing tools 
available in Linux distros, but not found in Windows. (I am using a windows 
system). Does this mean that Linux users don't need to use R tools when they 
want to compile R code?

Additionally, thank you for the information about what I should read. I will 
look at the material again, and hopefully things the material you suggest I 
read will be more understandable.

John

P.S. This email should be in txt format, not html. I sent if from my desktop 
windows machine which provides more options than does my iPhone.



John David Sorkin M.D., Ph.D.
Professor of Medicine, University of Maryland School of Medicine;
Associate Director for Biostatistics and Informatics, Baltimore VA Medical 
Center Geriatrics Research, Education, and Clinical Center;
PI Biostatistics and Informatics Core, University of Maryland School of 
Medicine Claude D. Pepper Older Americans Independence Center;
Senior Statistician University of Maryland Center for Vascular Research;

Division of Gerontology and Paliative Care,
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
Cell phone 443-418-5382





From: David Winsemius 
Sent: Friday, February 23, 2024 8:14 PM
To: Sorkin, John
Cc: avi.e.gr...@gmail.com; r-help@r-project.org
Subject: Re: [R] Rtools and things dependent on it


On 2/23/24 16:28, Sorkin, John wrote:
David,
My apologies regarding the format of my email. I am replying using my iPhone, 
and I can’t find a way to switch from what I suspect is html to txt format.
The link you sent told me that R tools allows compilation of code.


It's specifically designed to provide the code tools missing in Windows that 
would other wise have been provided by a typical Linux distro. More 
expansively, it allows compilation of code written in C and/or Fortran using 
the version that was used to build the matching R version and allows it to be 
called by the routines written in R that bind a package together.

This is good to know, but beyond this important fact, the rest of the material 
was close to unintelligible.

The phrase "the rest of the material" is not specific enough to offer more 
explanation. You should quote material that is beyond your understanding. You 
should only be reading the sections named: "Installing Rtools43" and "Building 
packages from source using Rtools43". I doubt that material further on would be 
relevant.

--

David

I doubt this is the fault of the author, it is probably because I lack some 
basic knowledge. Can you suggest some more basic material I can read. Please 
note. I am not computer naive, I am simply missing basic knowledge of the 
material discussed in the web page.
Thank you,
John
John David Sorkin M.D., Ph.D.
Professor of Medicine
Chief, Biostatistics and Informatics
University of Maryland School of Medicine Division of Gerontology and Geriatric 
Medicine
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
(Phone) 410-605-7119
(Fax) 410-605-7913 (Please call phone number above prior to 
faxing)

On Feb 23, 2024, at 7:01 PM, David Winsemius 
 wrote:


On 2/23/24 14:34, avi.e.gr...@gmail.com wrote:
This may be a dumb question and the answer may make me feel dumber.

I have had trouble for years with R packages wanting Rtools on my machine
and not being able to use it. Many packages are fine as binaries are
available. I have loaded Rtools and probably need to change my PATH or
something.


I suppose making sure that whatever directory holds your Rtools code is
on your path would be a good idea. I wondered if there's an environment
variable that could be set, but reading the page on using Rtools did not
mention one until I got down to the section on building R from source
which is surely NOT what you want to do.. You should read the
information on installation and building packages from source.
https://cran.r-project.org/bin/windows/base/howto-R-devel.html
 which
includes this sentence:

"It is recommended to use the defaults and install into|c:/rtools43|.
When done that way, Rtools43 may be used in the same R session which
installed it or which was started before Rtools43 was installed."


But I recently suggested to someone that they might want to use the tabyl()
function in the janitor package that I find helpful. I get a warning when I
install it about Rtools but it works fine. When they install it, it fails. I
assumed they would get it from CRAN the same way I did as we are both using
Windows and from within RSTUDIO.

In the past, I have run into other packages I could not use and just moved
on but it seems like time to see if this global problem has a work-around.

And, in particular, I have the latest versions of both R and RSTUDIO which
can be a problem when other things are not as 

Re: [R] Rtools and things dependent on it

[David Winsemius]

On 2/23/24 16:28, Sorkin, John wrote:
> David,
> My apologies regarding the format of my email. I am replying using my 
> iPhone, and I can’t find a way to switch from what I suspect is html 
> to txt format.
> The link you sent told me that R tools allows compilation of code.


It's specifically designed to provide the code tools missing in Windows 
that would other wise have been provided by a typical Linux distro. More 
expansively, it allows compilation of code written in C and/or Fortran 
using the version that was used to build the matching R version and 
allows it to be called by the routines written in R that bind a package 
together.

> This is good to know, but beyond this important fact, the rest of the 
> material was close to unintelligible.

The phrase "the rest of the material" is not specific enough to offer 
more explanation. You should quote material that is beyond your 
understanding. You should only be reading the sections named:"Installing 
Rtools43" and "Building packages from source using Rtools43". I doubt 
that material further on would be relevant.

-- 

David

> I doubt this is the fault of the author, it is probably because I lack 
> some basic knowledge. Can you suggest some more basic material I can 
> read. Please note. I am not computer naive, I am simply missing basic 
> knowledge of the material discussed in the web page.
> Thank you,
> John
>> John David Sorkin M.D., Ph.D.
>> Professor of Medicine
>> Chief, Biostatistics and Informatics
>> University of Maryland School of Medicine Division of Gerontology and 
>> Geriatric Medicine
>> Baltimore VA Medical Center
>> 10 North Greene Street 
>> GRECC  (BT/18/GR)
>> Baltimore, MD 21201-1524 
>> (Phone) 410-605-711 9
>> (Fax)410-605-7913  (Please call phone number above 
>> prior to faxing)
>
>> On Feb 23, 2024, at 7:01 PM, David Winsemius  
>> wrote:
>>
>> 
>> On 2/23/24 14:34, avi.e.gr...@gmail.com wrote:
>>> This may be a dumb question and the answer may make me feel dumber.
>>>
>>> I have had trouble for years with R packages wanting Rtools on my 
>>> machine
>>> and not being able to use it. Many packages are fine as binaries are
>>> available. I have loaded Rtools and probably need to change my PATH or
>>> something.
>>
>>
>> I suppose making sure that whatever directory holds your Rtools code is
>> on your path would be a good idea. I wondered if there's an environment
>> variable that could be set, but reading the page on using Rtools did not
>> mention one until I got down to the section on building R from source
>> which is surely NOT what you want to do.. You should read the
>> information on installation and building packages from source.
>> https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fcran.r-project.org%2Fbin%2Fwindows%2Fbase%2Fhowto-R-devel.html=05%7C02%7CJSorkin%40som.umaryland.edu%7C7000449b5bd74e1d6cbb08dc34cbcba8%7C717009a620de461a88940312a395cac9%7C0%7C0%7C638443297110517980%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C=%2B1tC1ROo11Bj1dPg7Ho9lDcVfL31Y3mCYUYqwDcyKs4%3D=0
>>  
>> which
>> includes this sentence:
>>
>> "It is recommended to use the defaults and install into|c:/rtools43|.
>> When done that way, Rtools43 may be used in the same R session which
>> installed it or which was started before Rtools43 was installed."
>>
>>>
>>> But I recently suggested to someone that they might want to use the 
>>> tabyl()
>>> function in the janitor package that I find helpful. I get a warning 
>>> when I
>>> install it about Rtools but it works fine. When they install it, it 
>>> fails. I
>>> assumed they would get it from CRAN the same way I did as we are 
>>> both using
>>> Windows and from within RSTUDIO.
>>>
>>> In the past, I have run into other packages I could not use and just 
>>> moved
>>> on but it seems like time to see if this global problem has a 
>>> work-around.
>>>
>>> And, in particular, I have the latest versions of both R and RSTUDIO 
>>> which
>>> can be a problem when other things are not as up-to-date.
>>>
>>> Or, maybe some people with R packages could be convinced to make 
>>> binaries
>>> available in the first place?
>>
>> Binaries are automatically produced by CRAN but perhaps you are trying
>> to install from some other source? It would help if you could be
>> specific about several missing pieces of information: Operating system,
>> R version, Rtools version, current location of Rtools, names of packages
>> and where they were obtained.
>>
>>
>> Regards and good luck;
>>
>> David (a.k.a IRTFM)
>>
>>> Avi
>>>
>>>    [[alternative HTML version deleted]]
>> Rhelp is a plain text mailing list. You should configure your email
>> client to send only plain-text and NOT html.
>>    [[alternative HTML version deleted]]
>>
>> __
>> R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> 

Re: [R] Rtools and things dependent on it

[Jeff Newmiller via R-help]

RTools is a set of command-line programs needed for compiling R and its 
packages on Windows. You don't need it if your OS is not Windows.

In theory, users on Windows should not need to worry about compiling packages 
to binary (zip) form, because CRAN compiles the source code for every package 
that supports Windows and just updating in a few days should bring in the 
current binaries. In practice, that task seems to always be lagging for certain 
packages, so you may end up using old versions of packages if you only rely on 
binary packages. Tidyverse packages seem to be among the worst in this 
respect.. there are many many dependencies and getting just one old one can 
make it all but impossible to get a current set of top-level Tidyverse 
packages. I think this is the strongest argument for teaching beginners to use 
Bsse R at first... the most plaintive cries come from beginners tasked with 
preparing their Windows computers to use tidyverse for their "class" at times 
when the binary files are very out of date.

Once installed and an RtoolsXX directory is present, it is still necessary to 
add the Rtools\mingw64\bin directory to your PATH environment variable so R can 
find it. Unfortunately there is no one way to do this because some people use 
multiple versions of R/Rtools and you can't just add all of them to your PATH. 
One of my preferred ways is to put the following in a newly-created .Rprofile 
text file in the Documents directory

Sys.setenv( PATH=paste( "C:\\Rtools43\\mingw64", Sys.getenv( "PATH" ), sep=";" 
) )

after restarting R it should be ready to install source packages when needed.

The problem is that beginners rarely remember doing this and after updating to 
R/Rtools 4.4.0 they will not understand why all their existing packages 
disappear (they must be reinstalled for each x.y version of R) nor why the 
source install doesn't work anymore (the 43 in their .Rprofile file which they 
have long ago forgotten must be updated to 44).

On February 23, 2024 3:39:28 PM PST, "Sorkin, John"  
wrote:
>Avi ,
>Your question is not dumb. Let me ask a more fundamental question. What is R 
>tools, what does it do, and how is it used. From time to time, I receive a 
>message when I down load a package saying I need R tools. When I receive the 
>message, I don’t know what I should do, other than down load R tools.
>John
>John David Sorkin M.D., Ph.D.
>Professor of Medicine
>Chief, Biostatistics and Informatics
>University of Maryland School of Medicine Division of Gerontology and 
>Geriatric Medicine
>Baltimore VA Medical Center
>10 North Greene Street
>GRECC (BT/18/GR)
>Baltimore, MD 21201-1524
>(Phone) 410-605-7119
>(Fax) 410-605-7913 (Please call phone number above prior to 
>faxing)
>
>On Feb 23, 2024, at 5:34 PM, avi.e.gr...@gmail.com wrote:
>
>This may be a dumb question and the answer may make me feel dumber.
>
>I have had trouble for years with R packages wanting Rtools on my machine
>and not being able to use it. Many packages are fine as binaries are
>available. I have loaded Rtools and probably need to change my PATH or
>something.
>
>But I recently suggested to someone that they might want to use the tabyl()
>function in the janitor package that I find helpful. I get a warning when I
>install it about Rtools but it works fine. When they install it, it fails. I
>assumed they would get it from CRAN the same way I did as we are both using
>Windows and from within RSTUDIO.
>
>In the past, I have run into other packages I could not use and just moved
>on but it seems like time to see if this global problem has a work-around.
>
>And, in particular, I have the latest versions of both R and RSTUDIO which
>can be a problem when other things are not as up-to-date.
>
>Or, maybe some people with R packages could be convinced to make binaries
>available in the first place?
>
>Avi
>
>
>   [[alternative HTML version deleted]]
>
>__
>R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>https://nam11.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fr-help=05%7C02%7CJSorkin%40som.umaryland.edu%7C8d5f2c8346f24559a7f908dc34bf9979%7C717009a620de461a88940312a395cac9%7C0%7C0%7C638443244987424663%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C6%7C%7C%7C=BO9wgkrjNmI4j2deiBDxHw%2F9tVjynfQYEHhBZ8BGq%2Fk%3D=0
>PLEASE do read the posting guide 
>https://nam11.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.r-project.org%2Fposting-guide.html=05%7C02%7CJSorkin%40som.umaryland.edu%7C8d5f2c8346f24559a7f908dc34bf9979%7C717009a620de461a88940312a395cac9%7C0%7C0%7C638443244987432863%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C6%7C%7C%7C=kVnTbE6ZEpmJ88Zmu%2FUbUH%2F%2FnjoSHSmDjuIxxxw3uz8%3D=0
>and provide commented, minimal, self-contained, reproducible code.
>
>   [[alternative HTML version deleted]]
>

Re: [R] Rtools and things dependent on it

[David Winsemius]

On 2/23/24 15:39, Sorkin, John wrote:

Avi ,
Your question is not dumb. Let me ask a more fundamental question. What is R 
tools, what does it do, and how is it used. From time to time, I receive a 
message when I down load a package saying I need R tools. When I receive the 
message, I don’t know what I should do, other than down load R tools.


https://cran.r-project.org/bin/windows/base/howto-R-devel.html


And do configure your client to send only plain-text.


--

David.


John
John David Sorkin M.D., Ph.D.
Professor of Medicine
Chief, Biostatistics and Informatics
University of Maryland School of Medicine Division of Gerontology and Geriatric 
Medicine
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
(Phone) 410-605-7119
(Fax) 410-605-7913 (Please call phone number above prior to 
faxing)

On Feb 23, 2024, at 5:34 PM, avi.e.gr...@gmail.com wrote:

This may be a dumb question and the answer may make me feel dumber.


__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Rtools and things dependent on it

[David Winsemius]

On 2/23/24 14:34, avi.e.gr...@gmail.com wrote:
> This may be a dumb question and the answer may make me feel dumber.
>   
> I have had trouble for years with R packages wanting Rtools on my machine
> and not being able to use it. Many packages are fine as binaries are
> available. I have loaded Rtools and probably need to change my PATH or
> something.


I suppose making sure that whatever directory holds your Rtools code is 
on your path would be a good idea. I wondered if there's an environment 
variable that could be set, but reading the page on using Rtools did not 
mention one until I got down to the section on building R from source 
which is surely NOT what you want to do.. You should read the 
information on installation and building packages from source. 
https://cran.r-project.org/bin/windows/base/howto-R-devel.html which 
includes this sentence:

"It is recommended to use the defaults and install into|c:/rtools43|. 
When done that way, Rtools43 may be used in the same R session which 
installed it or which was started before Rtools43 was installed."

>   
> But I recently suggested to someone that they might want to use the tabyl()
> function in the janitor package that I find helpful. I get a warning when I
> install it about Rtools but it works fine. When they install it, it fails. I
> assumed they would get it from CRAN the same way I did as we are both using
> Windows and from within RSTUDIO.
>   
> In the past, I have run into other packages I could not use and just moved
> on but it seems like time to see if this global problem has a work-around.
>   
> And, in particular, I have the latest versions of both R and RSTUDIO which
> can be a problem when other things are not as up-to-date.
>   
> Or, maybe some people with R packages could be convinced to make binaries
> available in the first place?

Binaries are automatically produced by CRAN but perhaps you are trying 
to install from some other source? It would help if you could be 
specific about several missing pieces of information: Operating system, 
R version, Rtools version, current location of Rtools, names of packages 
and where they were obtained.


Regards and good luck;

David (a.k.a IRTFM)

> Avi
>
>   [[alternative HTML version deleted]]
Rhelp is a plain text mailing list. You should configure your email 
client to send only plain-text and NOT html.
[[alternative HTML version deleted]]

__
R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
https://stat.ethz.ch/mailman/listinfo/r-help
PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
and provide commented, minimal, self-contained, reproducible code.

Re: [R] Rtools and things dependent on it

[Sorkin, John]

Avi ,
Your question is not dumb. Let me ask a more fundamental question. What is R 
tools, what does it do, and how is it used. From time to time, I receive a 
message when I down load a package saying I need R tools. When I receive the 
message, I don’t know what I should do, other than down load R tools.
John
John David Sorkin M.D., Ph.D.
Professor of Medicine
Chief, Biostatistics and Informatics
University of Maryland School of Medicine Division of Gerontology and Geriatric 
Medicine
Baltimore VA Medical Center
10 North Greene Street
GRECC (BT/18/GR)
Baltimore, MD 21201-1524
(Phone) 410-605-7119
(Fax) 410-605-7913 (Please call phone number above prior to 
faxing)

On Feb 23, 2024, at 5:34 PM, avi.e.gr...@gmail.com wrote:

This may be a dumb question and the answer may make me feel dumber.

I have had trouble for years with R packages wanting Rtools on my machine
and not being able to use it. Many packages are fine as binaries are
available. I have loaded Rtools and probably need to change my PATH or
something.

But I recently suggested to someone that they might want to use the tabyl()
function in the janitor package that I find helpful. I get a warning when I
install it about Rtools but it works fine. When they install it, it fails. I
assumed they would get it from CRAN the same way I did as we are both using
Windows and from within RSTUDIO.

In the past, I have run into other packages I could not use and just moved
on but it seems like time to see if this global problem has a work-around.

And, in particular, I have the latest versions of both R and RSTUDIO which
can be a problem when other things are not as up-to-date.

Or, maybe some people with R packages could be convinced to make binaries
available in the first place?

Avi


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

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[R] Rtools and things dependent on it

[avi.e.gross]

This may be a dumb question and the answer may make me feel dumber.
 
I have had trouble for years with R packages wanting Rtools on my machine
and not being able to use it. Many packages are fine as binaries are
available. I have loaded Rtools and probably need to change my PATH or
something.
 
But I recently suggested to someone that they might want to use the tabyl()
function in the janitor package that I find helpful. I get a warning when I
install it about Rtools but it works fine. When they install it, it fails. I
assumed they would get it from CRAN the same way I did as we are both using
Windows and from within RSTUDIO.
 
In the past, I have run into other packages I could not use and just moved
on but it seems like time to see if this global problem has a work-around.
 
And, in particular, I have the latest versions of both R and RSTUDIO which
can be a problem when other things are not as up-to-date.
 
Or, maybe some people with R packages could be convinced to make binaries
available in the first place?
 
Avi
 

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Re: [R] help - Package: stats - function ar.ols

[Ebert,Timothy Aaron]

The data came through fine, the program was a miss. Can you paste the program 
into a ".txt" document like a notepad file and send that? You could also paste 
it into your email IF your email is configured to send text and NOT html.

TIm

-Original Message-
From: R-help  On Behalf Of Pedro Gavronski.
Sent: Friday, February 23, 2024 5:00 AM
To: Rui Barradas 
Cc: r-help@r-project.org; r-help-requ...@r-project.org
Subject: Re: [R] help - Package: stats - function ar.ols

[External Email]

Hello,

Thanks for the reply Rui and for pointing out that I forgot to attach my code. 
Please find attached in this email my code and data.

Thanks in advance.

Best regards, Pedro Gerhardt Gavronski.

On Fri, Feb 23, 2024 at 5:50 AM Rui Barradas  wrote:
>
> Às 16:34 de 22/02/2024, Pedro Gavronski. escreveu:
> > Hello,
> >
> > My name is Pedro and it is nice to meet you all. I am having trouble
> > understanding a message that I receive when use function ar.ols from
> > package stats, it says that "Warning message:
> > In ar.ols(x = dtb[2:6966, ], demean = FALSE, intercept = TRUE,
> > prewhite = TRUE) :
> >model order:  2 singularities in the computation of the
> > projection matrix results are only valid up to model order 1, which
> > I do not know what it means, if someone could clarify it, I would
> > really appreciate it.
> >
> > Attached to this email you will find my code and data I used to run
> > this formula.
> >
> > Thanks in advance.
> >
> > Best regards,  Pedro.
> >
> >
> > __
> > R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> > https://st/
> > at.ethz.ch%2Fmailman%2Flistinfo%2Fr-help=05%7C02%7Ctebert%40ufl
> > .edu%7C0afd65836d774adc099408dc349f53c7%7C0d4da0f84a314d76ace60a6233
> > 1e1b84%7C0%7C0%7C638443106144255449%7CUnknown%7CTWFpbGZsb3d8eyJWIjoi
> > MC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C
> > %7C=12OGc13jk3Lejmcvx5WH8Bko8JSpRxbtW3mzL3OIjyk%3D=0
> > PLEASE do read the posting guide
> > http://www/
> > .r-project.org%2Fposting-guide.html=05%7C02%7Ctebert%40ufl.edu%
> > 7C0afd65836d774adc099408dc349f53c7%7C0d4da0f84a314d76ace60a62331e1b8
> > 4%7C0%7C0%7C638443106144262387%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wL
> > jAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C
> > data=fAVz0iQ0zS5pmrxrzNeazRrrv%2FyjFdWvwMfgjhibdEA%3D=0
> > and provide commented, minimal, self-contained, reproducible code.
> Hello,
>
> Thanks for the data but the code is missing from the attachment.
> Can you please post your code? In an attachment or directly in the
> e-mail body.
>
> Rui Barradas
>
>
> --
> Este e-mail foi analisado pelo software antivírus AVG para verificar a 
> presença de vírus.
> http://www.a/
> vg.com%2F=05%7C02%7Ctebert%40ufl.edu%7C0afd65836d774adc099408dc34
> 9f53c7%7C0d4da0f84a314d76ace60a62331e1b84%7C0%7C0%7C638443106144266047
> %7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6I
> k1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C=rdqEhXdZ5%2FThzbhuKgspNaBPyhf
> aC%2BWh7MFq4iq%2BxVE%3D=0
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Re: [R] [External] Extracting Plot Arguments

[Richard M. Heiberger]

Does the grid.echo function in the gridGraphics package do what you want?

Description
Convert a scene that was drawn using the graphics package to an identical scene 
drawn with the
grid package.

> On Feb 21, 2024, at 22:49, Reed A. Cartwright  wrote:
>
> Hi All,
>
> I'm building an autograding framework for my biostatistics class this
> semester, and I am exploring different ways to automatically grade
> figures.
>
> In other classes, I teach ggplot2 and I extract information directly
> from the ggplot2 object. However, in this class we are using base R
> and I need to extract information from base-r graphics.
>
> I've tried several different approaches, but I'm not sure which one is
> the easiest and most effective. Has anyone ever tried this? Are there
> any packages to help with this?
>
> (1) Storing `recordedplots` objects and trying to extract information
> from them. This data structure felt very low level, and I wasn't sure
> how easy it was to map the results to user-level function calls.
>
> (2) Use the `svglite` device to produce svg files, which can be
> parsed. This also worked, but required a lot of code to parse the
> resulting images and identify things like labels, and coordinate
> locations. I got tired of having to figure how to extract information
> from an SVG.
>
> (3) Use a wrapper on specific graphics functions that records the
> function arguments. This turns out to be a bit too high level, as I
> have to manually massage inputs. E.g. handle both xy plots and formula
> + data plots. (We teach both styles.)
>
> Are there any other ideas that I can try? My students are using an
> RMarkdown worksheet and answering questions by putting code in
> specific chunks. I've already hooked into knitr so I can record the
> chunk lines as they are being run and  get the results and
> side-effects.
>
> Thanks,
> Reed
>
> --
> Reed A. Cartwright, PhD
> Associate Professor of Genomics, Evolution, and Bioinformatics
> School of Life Sciences and The Biodesign Institute
> Arizona State University
> ==
> Address: The Biodesign Institute, PO Box 876401, Tempe, AZ 85287-6401 USA
> Packages: The Biodesign Institute, 1001 S. McAllister Ave, Tempe, AZ
> 85287-6401 USA
> Office: Biodesign B-220C, 1-480-965-9949
> Website: http://cartwrig.ht/
>
> __
> 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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Re: [ESS] FW: [GNU ELPA] ESS version 24.1.1

[Sparapani, Rodney via ESS-help]

Hi Michael:

Yes, a manual intervention appears to be necessary.  So copy
that file over and hopefully then it will work. FWIW. I installed
ESS with �make� and then �make install� for emacs 29.1.

--
Rodney Sparapani, Associate Professor of Biostatistics, He/Him/His
Vice President, Wisconsin Chapter of the American Statistical Association
Institute for Health and Equity, Division of Biostatistics
Medical College of Wisconsin, Milwaukee Campus

If this is outside of working hours, then please respond when convenient.

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Re: [R] help - Package: stats - function ar.ols

[Rui Barradas]

Às 16:34 de 22/02/2024, Pedro Gavronski. escreveu:

Hello,

My name is Pedro and it is nice to meet you all. I am having trouble
understanding a message that I receive when use function ar.ols from
package stats, it says that "Warning message:
In ar.ols(x = dtb[2:6966, ], demean = FALSE, intercept = TRUE,
prewhite = TRUE) :
   model order:  2 singularities in the computation of the projection
matrix results are only valid up to model order 1, which I do not know
what it means, if someone could clarify it, I would really appreciate
it.

Attached to this email you will find my code and data I used to run
this formula.

Thanks in advance.

Best regards,  Pedro.


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

Hello,

Thanks for the data but the code is missing from the attachment.
Can you please post your code? In an attachment or directly in the 
e-mail body.


Rui Barradas


--
Este e-mail foi analisado pelo software antivírus AVG para verificar a presença 
de vírus.
www.avg.com

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