Re: [R] Unable to install gsynth without life package

[Tariq Khasiri]

The R community is full of kind people! Much obliged for being so polite!

On Mon, 30 May 2022 at 21:24, Jeff Newmiller 
wrote:

> Either:
>
> 1) Convince the Gsynth package maintainer to resolve the problem for you,
> or
>
> 2) start hacking on the source code of either lfe or Gsynth until they
> both install and work together.
>
> It is not as though the members of this list have a magic wand that can
> fix the problems of many thousands of _contributed_ packages.
>
> On May 30, 2022 9:08:04 PM PDT, Tariq Khasiri 
> wrote:
> >Hello R Community,
> >
> >I'm trying to install Gsynth packaged from the instruction given on this
> >website ( https://yiqingxu.org/packages/gsynth/index.html ). Out of all
> the
> >dependency packages lfe is removed from CRAN I believe. Therefore, I'm
> >unable to install gsynth. I've looked for the solution on google but
> >nothing helped so far.
> >
> >Any suggestion I how I can install lfe and eventually install gsynth
> >successfully? All the dependency packages are given on the link above
> >where the developer built the package.
> >
> >
> >ERROR: dependency ‘lfe’ is not available for package ‘gsynth’
> >* removing
> >‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/gsynth’
> >Warning in install.packages :
> >  installation of package ‘gsynth’ had a non-zero exit status
> >
> >   [[alternative HTML version deleted]]
> >
> >__
> >R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
> >https://stat.ethz.ch/mailman/listinfo/r-help
> >PLEASE do read the posting guide
> http://www.R-project.org/posting-guide.html
> >and provide commented, minimal, self-contained, reproducible code.
>
> --
> Sent from my phone. Please excuse my brevity.
>

[[alternative HTML version deleted]]

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Re: [R] Unable to install gsynth without life package

[Jeff Newmiller]

Either:

1) Convince the Gsynth package maintainer to resolve the problem for you, or

2) start hacking on the source code of either lfe or Gsynth until they both 
install and work together.

It is not as though the members of this list have a magic wand that can fix the 
problems of many thousands of _contributed_ packages.

On May 30, 2022 9:08:04 PM PDT, Tariq Khasiri  wrote:
>Hello R Community,
>
>I'm trying to install Gsynth packaged from the instruction given on this
>website ( https://yiqingxu.org/packages/gsynth/index.html ). Out of all the
>dependency packages lfe is removed from CRAN I believe. Therefore, I'm
>unable to install gsynth. I've looked for the solution on google but
>nothing helped so far.
>
>Any suggestion I how I can install lfe and eventually install gsynth
>successfully? All the dependency packages are given on the link above
>where the developer built the package.
>
>
>ERROR: dependency ‘lfe’ is not available for package ‘gsynth’
>* removing
>‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library/gsynth’
>Warning in install.packages :
>  installation of package ‘gsynth’ had a non-zero exit status
>
>   [[alternative HTML version deleted]]
>
>__
>R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see
>https://stat.ethz.ch/mailman/listinfo/r-help
>PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
>and provide commented, minimal, self-contained, reproducible code.

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

__
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Re: [R] if zlib version >= 1.2.5... no

[David Winsemius]

Pasting a prior posted thread on the R-Mac list:

Ah, well, I see now that libR.dylib was not built or linked in
tools.so simply because I had not configured with --enable-R-shlib
... 'make' succeeds but only when I build R as a shared library.

The dlopen error isn't seen in the nightly builds, which also use
--enable-R-shlib. It would be good to know if others are able to
reproduce the error when configuring in the _default_ way, i.e.,
without --enable-R-shlib.

Mikael

> On 2022-02-10 4:30 pm, Mikael Jagan wrote:
>> On 2022-02-10 1:42 pm, Mikael Jagan wrote:
>> It seems my first message to mailing list, which had all of the attachments,
>> was caught in the spam filter. In case it helps, I've dumped the config.site,
>> config.log, and build.out on GitHub:
>> 
>> https://github.com/jaganmn/attachments/tree/6a7257014792f5e8cf7bb0bcd3bb27c7fabf7577/r-sig-mac/2022-02-10
>>  
>> 
>>> On 2022-02-10 1:11 pm, Prof Brian Ripley wrote:
 On 10/02/2022 17:28, Mikael Jagan wrote:
 Oops - forgot to mention: I am trying to build R-devel, currently at 
 r81706.
 
 Mikael
 
> On 2022-02-10 12:13 pm, Mikael Jagan wrote:
> Hello,
> 
> I am running Big Sur on an M1 Mac and trying to build R from sources.
> Some system details:
> 
> R> sessionInfo()
>  > Platform: aarch64-apple-darwin20 (64-bit)
>  > Running under: macOS Big Sur 11.6.3
> 
> $ clang --version
>  > Apple clang version 13.0.0 (clang-1300.0.29.30)
>  > Target: arm64-apple-darwin20.6.0
> 
> $ /opt/R/arm64/gfortran/bin/gfortran --version
>  > GNU Fortran (GCC) 11.0.0 20201219 (experimental)
> 
> It has been a few months since I last built R on this machine.
> At the time, I was building with LLVM clang rather than Apple clang
> to obtain OpenMP support. I was recently nudged about the OpenMP
> runtime library made available here:
> 
> https://mac.r-project.org/openmp/
> 
> which would allow me to build "normally" with Apple clang.
> I am trying now to make the switch.
> 
> I have installed all of the binaries hosted here
> 
> https://mac.r-project.org/bin/darwin20/arm64/
> 
> rather than those hosted here
> 
> https://mac.r-project.org/libs-arm64/
> 
> which I had previously installed. (Though: the first URL is missing
> binaries for gfortran, pandoc, tcl, tk, and tkTable. I obtained
> these from the second URL. _Both_ URLs are missing a zlib binary,
> so I reluctantly obtained zlib from Homebrew.)
>>> 
>>> zlib is part of the OS.  For pkg-config you need the zlib stub available 
>>> from https://mac.r-project.org/libs-4/.  That *is* in the R-admin manual.  
>>> Also, that tcl, tk, and tkTable can be installed as part of an R binary 
>>> installation.
>> 
>> Thanks - I wasn't sure whether that zlib stub was suitable for my system.
>> 
>>> 
>>> For pandoc I use the official Intel builds under emulation without any 
>>> problems (including checking all of CRAN).  But you don't need pandoc to 
>>> build R.
>>> 
>>> I understand that the transition to https://mac.r-project.org/bin is work 
>>> in progress, but its newer versions of libs are preferred.
>>> 
> 
> Anyway, I'm running into trouble now... I have attached my
> config.site, config.log, and build.out (from 'make >&') ...
> config.log seems completely normal, but in build.out I see
> many linker warnings of the form
> 
>  > ld: warning: could not create compact unwind for _dchdc_: registers 72 
> and 73 not saved contiguously in frame
>  > ld: warning: could not create compact unwind for _dpoco_: registers 72 
> and 73 not saved contiguously in frame
>  > ld: warning: object file (/opt/R/arm64/lib/libreadline.a(history.o)) 
> was built for newer macOS version (20.0) than being linked (11.0)
>  > ld: warning: object file 
> (/opt/R/arm64/lib/liblzma.a(liblzma_la-alone_decoder.o)) was built for 
> newer macOS version (20.0) than being linked (11.0)
>>> 
>>> Hmm, that's about a binary liblzma.  I'd download again (maybe try both 
>>> sites), and if it is still wrong, build from the sources.
>> If you search build.out, you'll find that this warning is issued
>> for _every_ binary obtained from
>> 
>> https://mac.r-project.org/bin/darwin20/arm64/
>> 
>> I'll try the old site again.
> Reverting to the old binaries resolves all of the version mismatch warnings,
> so perhaps there is just a glitch in the way the new binaries were built.
>> 
> And the build eventually fails for a seemingly unrelated
> reason:
> 
>  > clang -arch arm64 -dynamiclib -Wl,-headerpad_max_install_names 
> -undefined dynamic_lookup -single_module -multiply_defined suppress 
> -falign-functions=64 -g -O2 -Wall -pedantic 
> -Wno-implicit-function-declaration -flto=thin -fPIC -Wl,-mllvm,-threads=4 
> -L/opt/homebrew/opt/zlib/lib -L/opt/R/arm64/lib -L/usr/local/lib -lomp -o 

[R] [R-pkgs] shadowr: Selenium plugin to manage multiple levels of shadow elements on web page

[ricardo.landolt]

Dear R users,


I am happy to announce that my new package shadowr is now available on
CRAN.

The package enables to use the shadow selenium 
plugin to manage multi 
level shadow DOM elements on web page.

Shadow DOM is a web standard that offers component style and markup 
encapsulation.

It is a critically important piece of the Web Components story as it ensures 
that a component will work in

any environment even if other CSS or JavaScript is at play on the page.

The problem is that Custom HTML tags can�t be directly identified with selenium 
tools.

If you just need to click a cookie accept button and if there is only a one 
level shadow dom structure,

you could just copy the js path and let the selenium driver execute this js 
code.

For details and examples please check out the github page.

But when you have a multi level shadow dom structure and have to do different 
things with the elements like get the text or click them,

sooner or later things get complicated.

You would have to handle a lot of long strings and depending on the action and 
amount of elements also modify/extend the strings.

Shadowr enable R users a more comfortable and reliable way to work with shadow 
dom elements.


https://cran.r-project.org/web/packages/shadowr/index.html, README file on CRAN 
page

https://cran.r-project.org/package=shadowr or blog article 
https://www.shadowr.org/.


Best regards,
Ricardo Landolt



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[R] Request for some help about uncertainty analysis using bootstrap approach

[Bhaskar Mitra]

Hello Everyone,

I have a query about uncertainty analysis and would really appreciate some
help  in this regard.

I intend to gapfill the NAs in the “X” column of the dataframe (Df1). I
have grouped the data using the column “Group” ,
determined the mean and generated the “Z” column.

While I am using the mean and standard error approach to generate the
uncertainty analysis, can we use the bootstrap approach to
generate the uncertainty for the “Z” column? Any help in this regard will
be really appreciated.

Regards,
Bhaskar
---

Df1 <-

Group XYZ
1   2  3 2
1  NA3 3
13 3 3
1   4  34
22 21
2  NA23
2   NA   23
24 24
3 222
3 NA 2 2
3  2   2 2

---
Codes:

Df1 <- Df1 %>% group_by(Group) %>% summarise(Y= mean(X), na.rm=T)

Df1  <- Df1%>% mutate(Z= coalesce(X,Y))

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Re: [R] Circular Graph Recommendation Request

[Stephen H. Dawson, DSL via R-help]

Hi Christopher,


Thanks for the reply. Your comments are helpful.

I agree with you about relative position in relation to geography.

The thing with this particular circular graph is it speaks to the 
executive ranks a bit more than a bar or line graph.



Kindest Regards,
*Stephen Dawson, DSL*
/Executive Strategy Consultant/
Business & Technology
+1 (865) 804-3454
http://www.shdawson.com


On 5/29/22 22:10, Christopher W. Ryan via R-help wrote:

If the units of analysis are real spatial regions (e.g. states), how
about a cartogram?

https://gisgeography.com/cartogram-maps/

An R package (I have no experience with it)

https://cran.r-project.org/web/packages/cartogram/index.html

The advantage of a cartogram is that it is a single graphic, rather than
2 like the original post referenced. No need to move eye back and forth
to decode the colors. And it maintains---as much as possible given the
distortion, which is the whole point of a cartogram--- the relative
spatial positions of the areal units (in this case, states.)  The round
figure in the original post has the northern midwestern region in the
7:00 to 8:00-ish position, what might be considered notionally the
"southwest."  A little counterintuitive.

--Chris Ryan

Bert Gunter wrote:

Very nice plot. Thanks for sharing.
Can't help directly, but as the plot is sort of a map with polygonal
areas encoding the value of a variable, you might try posting on
r-sig-geo instead where there might be more relevant expertise in such
  things -- or perhaps suggestions for alternative visualizations that
work similarly.

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 Sat, May 28, 2022 at 8:39 AM Stephen H. Dawson, DSL via R-help
 wrote:

https://www.visualcapitalist.com/us-goods-exports-by-state/
Visualizing U.S. Exports by State

Good Morning,


https://www.visualcapitalist.com/wp-content/uploads/2022/05/us-exports-by-state-infographic.jpg

Saw an impressive graph today. Sharing with the list.

The size proportionality of the state segments in a circle graph is catchy.

QUESTION
Is there a package one could use with R to accomplish this particular
circular-style graph?


Kindest Regards,
--
*Stephen Dawson, DSL*
/Executive Strategy Consultant/
Business & Technology
+1 (865) 804-3454
http://www.shdawson.com

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Re: [R] How to represent tree-structured values

[Jan van der Laan]

For visualising hierarchical data a treemap can also work well. For 
example, using the treemap package:


n <- 1000

library(data.table)
library(treemap)

dta <- data.table(
  level1 = sample(LETTERS[1:5], n, replace = TRUE),
  level2 = sample(letters[1:5], n, replace = TRUE),
  level3 = sample(1:9, n, replace = TRUE),
  event = sample(0:1, n, replace = TRUE)
  )

tab <- dta[, .(n = .N, rate = sum(event)/.N),
  by = .(level1, level2, level3)]

treemap(tab, index = names(tab)[1:3], vSize = "n", vColor = "rate",
  type = "value", fontsize.labels = 20*c(1, 0.7, 0))


--

Jan




On 30-05-2022 11:40, Jim Lemon wrote:

Hi Richard,
Thinking about this, you might also find intersectDiagram, also in
plotrix, to be useful.

Jim

On Mon, May 30, 2022 at 4:37 PM Jim Lemon  wrote:

Hi Richard,
Some years ago I had a try at illustrating Multiple Causes of Death
(MCoD) data. I settled on what is sometimes called a "sizetree". You
can see some examples in the sizetree function help page in "plotrix".
Unfortunately I can't use the original data as it was confidential.

Jim

On Mon, May 30, 2022 at 2:55 PM Richard O'Keefe  wrote:

There is a kind of data I run into fairly often
which I have never known how to represent in R,
and nothing I've tried really satisfies me.

Consider for example
  ...
  - injuries
...
- injuries to limbs
  ...
  - injuries to extremities
...
- injuries to hands
  - injuries to dominant hand
  - injuries to non-dominant hand
...
  ...
...

This isn't ordinal data, because there is no
"left to right" order on the values.  But there
IS a "part/whole" order, which an analysis should
respect, so it's not pure nominal data either.

As one particular example, if I want to
tabulate data like this, an occurrence of one
value should be counted as an occurrence of
*every* superordinate value.

Examples of such data include "why is this patient
being treated", "what drug is this patient being
treated with", "what geographic region is this
school from", "what biological group does this
insect belong to".

So what is the recommended way to represent
and the recommended way to analyse such data in R?

 [[alternative HTML version deleted]]

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Re: [R] How to represent tree-structured values

[Jim Lemon]

Hi Richard,
Thinking about this, you might also find intersectDiagram, also in
plotrix, to be useful.

Jim

On Mon, May 30, 2022 at 4:37 PM Jim Lemon  wrote:
>
> Hi Richard,
> Some years ago I had a try at illustrating Multiple Causes of Death
> (MCoD) data. I settled on what is sometimes called a "sizetree". You
> can see some examples in the sizetree function help page in "plotrix".
> Unfortunately I can't use the original data as it was confidential.
>
> Jim
>
> On Mon, May 30, 2022 at 2:55 PM Richard O'Keefe  wrote:
> >
> > There is a kind of data I run into fairly often
> > which I have never known how to represent in R,
> > and nothing I've tried really satisfies me.
> >
> > Consider for example
> >  ...
> >  - injuries
> >...
> >- injuries to limbs
> >  ...
> >  - injuries to extremities
> >...
> >- injuries to hands
> >  - injuries to dominant hand
> >  - injuries to non-dominant hand
> >...
> >  ...
> >...
> >
> > This isn't ordinal data, because there is no
> > "left to right" order on the values.  But there
> > IS a "part/whole" order, which an analysis should
> > respect, so it's not pure nominal data either.
> >
> > As one particular example, if I want to
> > tabulate data like this, an occurrence of one
> > value should be counted as an occurrence of
> > *every* superordinate value.
> >
> > Examples of such data include "why is this patient
> > being treated", "what drug is this patient being
> > treated with", "what geographic region is this
> > school from", "what biological group does this
> > insect belong to".
> >
> > So what is the recommended way to represent
> > and the recommended way to analyse such data in R?
> >
> > [[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.

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Re: [R] How to represent tree-structured values

[Jim Lemon]

Hi Richard,
Some years ago I had a try at illustrating Multiple Causes of Death
(MCoD) data. I settled on what is sometimes called a "sizetree". You
can see some examples in the sizetree function help page in "plotrix".
Unfortunately I can't use the original data as it was confidential.

Jim

On Mon, May 30, 2022 at 2:55 PM Richard O'Keefe  wrote:
>
> There is a kind of data I run into fairly often
> which I have never known how to represent in R,
> and nothing I've tried really satisfies me.
>
> Consider for example
>  ...
>  - injuries
>...
>- injuries to limbs
>  ...
>  - injuries to extremities
>...
>- injuries to hands
>  - injuries to dominant hand
>  - injuries to non-dominant hand
>...
>  ...
>...
>
> This isn't ordinal data, because there is no
> "left to right" order on the values.  But there
> IS a "part/whole" order, which an analysis should
> respect, so it's not pure nominal data either.
>
> As one particular example, if I want to
> tabulate data like this, an occurrence of one
> value should be counted as an occurrence of
> *every* superordinate value.
>
> Examples of such data include "why is this patient
> being treated", "what drug is this patient being
> treated with", "what geographic region is this
> school from", "what biological group does this
> insect belong to".
>
> So what is the recommended way to represent
> and the recommended way to analyse such data in R?
>
> [[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.

__
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