Re: [R] [EXT] Re: Inappropriate color name

[Rainer Krug via R-help]

Could we please stop this thread here? Please take any further discussions 
off-list, or we would need an R-chat list for these kind of discussions (I 
would subscribe, though).

Cheers,

Rainer


> On 20 Nov 2020, at 11:28, Charles Novaes de Santana 
>  wrote:
> 
> The fact that for the first time we have so many messages in this group is
> proof that the question asked by Lainey is appropriate and necessary.
> 
> No language is static, they evolve thanks to discussions like this.
> Remember that github  stopped using the term "master" to describe the main
> branch of a repository for example.
> 
> I wonder what would happen if there was a color named "redneck" instead of
> "indianred".
> 
> Charles
> 
> On Fri, 20 Nov 2020 at 10:37, Marc Roos  wrote:
> 
>> 
>>> name since it conveys the wrong indication of its purpose.  But the
>>> word 'racist' in itself is not offensive.  The act of being racist is
>>> offensive and wrong.  Purging the word 'racist' won't help rid the
>>> world of racism.
>> 
>> Indeed, if you would go down this road, where does it stop? You would be
>> eligible getting discussions why the female species is described with a
>> longer word than the male. Why is there even a 'man' part in 'woman'. I
>> can bet there are man and woman finding this offensive ;)
>> What do you think about these symbols for male and female? Should be
>> changed also, this male is now pointing up to heaven =  good, and female
>> pointing down to hell =  bad? ;)
>> 
>> 
>> 
>> __
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>> and provide commented, minimal, self-contained, reproducible code.
>> 
> 
> 
> -- 
> Um axé! :)
> 
> --
> Charles Novaes de Santana, PhD
> https://github.com/cndesantana
> 
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> 
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--
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, 
UCT), Dipl. Phys. (Germany)

Orcid ID: -0002-7490-0066

Department of Evolutionary Biology and Environmental Studies
University of Zürich
Office Y34-J-74
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Re: [R] Indian Red

[Rainer Krug via R-help]

Let’s switch to the German name - “Indisch Rot” instead...

> On 20 Nov 2020, at 12:08, Neotropical bat risk assessments and acoustic tools 
>  wrote:
> 
> FWIW,
> 
> There is also Naples Yellow and other colors related to "place names" on 
> artist palettes.  "Indian Red" is not related to North American Native 
> peoples.
> "/India Red/: Originally a natural, more purple iron oxide imported from 
> /India/. First synthesized in the 18th century as a “Mars” color, 
> contemporary ...
> 
> Let it rest people.
> 
> Bruce Miller
> 
> 
> -- 
> Bruce W. Miller, PhD.
> Neotropical bat risk and acoustic assessments
> Conservation Fellow - Wildlife Conservation Society
> Research Associate, American Museum of Natural History
> 
> If we lose the bats, we may lose much of the tropical vegetation and the 
> lungs of the planet
> 
> Using acoustic sampling to identify and map species distributions
> and pioneering acoustic tools for ecology and conservation of bats for >25 
> years.
> 
> Key projects include providing free interactive identification keys and call 
> fact sheets for the vocal signatures of New World Bats
> 
> 
>   [[alternative HTML version deleted]]
> 
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--
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, 
UCT), Dipl. Phys. (Germany)

Orcid ID: -0002-7490-0066

Department of Evolutionary Biology and Environmental Studies
University of Zürich
Office Y34-J-74
Winterthurerstrasse 190
8075 Zürich
Switzerland

Office: +41 (0)44 635 47 64
Cell:   +41 (0)78 630 66 57
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Re: [R] build a literature database

[Rainer Krug via R-help]

I agree with Duncan.

I co-ordinated a large literature review with initially more than 5000 papers 
and about 30 reviewers, and all the bibliometrics information was in bibtex 
format, as it is easy to interchange between programs.

Cheers,

Rainer

> On 4 Nov 2020, at 10:28, Duncan Murdoch  wrote:
> 
> On 04/11/2020 4:22 a.m., John wrote:
>> Hi,
>>I 'd like to create a table for literature review. Is there any good
>> data structure (database) I may use? Now I just use a simple dataframe as
>> follows, but in the second item I swap the order of year and author, and it
>> records 2013 as author and "XH" as year.  Is there any better structure ?
>> If not, how may I fix the current condition?Thanks!
>> df <- data.frame(author = NA, year = NA, title = NA, country = NA, sample =
>> NA, data = NA, result = NA, note = NA, stringsAsFactors=FALSE)
>> df[1, ]<-c(
>>author = "Moore",
>>year = 2020,
>>title = "Statistics and data analysis",
>>country = "Colombia",
>>sample = NA,
>>data = "firm level",
>>result = NA,
>>note = NA)
>> df[nrow(df)+1,]<- c(year = 2013,
>> author = "XH",
>> title = NA,
>> country = NA,
>> sample = NA,
>> data = NA,
>> result = NA,
>> note = NA)
> 
> If you changed the last statement to
> 
> df <- rbind(df, data.frame(year = 2013,
>  author = "XH",
>  title = NA,
>  country = NA,
>  sample = NA,
>  data = NA,
>  result = NA,
>  note = NA))
> 
> it would correctly sort out the reordered columns.
> 
> As to a better data structure:  bibliographic data is hard, because different 
> forms of publication should have different fields.  I'd suggest storing the 
> data in some existing format rather than rolling your own.  For example, the 
> utils::bibentry function is quite a bit like BibTeX.
> 
> Duncan Murdoch
> 
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> 
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--
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, 
UCT), Dipl. Phys. (Germany)

Orcid ID: -0002-7490-0066

Department of Evolutionary Biology and Environmental Studies
University of Zürich
Office Y34-J-74
Winterthurerstrasse 190
8075 Zürich
Switzerland

Office: +41 (0)44 635 47 64
Cell:   +41 (0)78 630 66 57
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Re: [R] Strange behaviour of R?

[Rainer Krug via R-help]

Hi

> On 17 Jan 2020, at 08:33, Sigbert Klinke  wrote:
> 
> Hi,
> 
> I wrote a function like
> 
> test <- function(FUN, args) {
>  print(FUN)
>  FUN(args)
> }
> 
> When I call it lieke this
> 
> test(mean, 1:10)
> test(NULL, 1:10)
> 
> then the second call still uses mean, although I set FUN to NULL. Is that ok?

Not for me - macOS, R 3.6.2


> 
> Actually, I used something like
> 
> test(mean, list(x=1:10, na.rm=TRUE))

Fails as expected,

Rainer

> 
> which actually crashed R, but I can not reproduce it. Of course, when I 
> replaced FUN(args) with do.call(FUN, args) then everything works fine.
> 
> Sigbert
> 
> -- 
> https://hu.berlin/sk
> https://hu.berlin/mmstat3
> 
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--
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, 
UCT), Dipl. Phys. (Germany)

Orcid ID: -0002-7490-0066

Department of Evolutionary Biology and Environmental Studies
University of Zürich
Office Y34-J-74
Winterthurerstrasse 190
8075 Zürich
Switzerland

Office: +41 (0)44 635 47 64
Cell:   +41 (0)78 630 66 57
email:  rainer.k...@uzh.ch
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Re: [R] Philip Morris International - Windows10 migration assessment

[Rainer Krug]

Let’s not alienate the business users!

I agree that this is not the right / best forum to ask these type of questions, 
but where is? I would suggest to at least point them to the right resources. 
and not say that there questions are inappropriate here.

Actually, if I as a private user would ask that question, I guess I would get 
an answer here.

So please - not alienate the business users.

Cheers and good luck with Windows,

Rainer




> On 2 Aug 2018, at 16:54, Bert Gunter  wrote:
> 
> R is free and open source. Your queries are inappropriate for this list,
> which is about help for programming in R.  Please go here and follow the
> relevant links to answer your questions:
> 
> https://www.r-project.org/
> 
> 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 Thu, Aug 2, 2018 at 1:45 AM, Flament, Kevin 
> wrote:
> 
>> Dear R Project team,
>> 
>> I am representing the System Toxicology department of Philip Morris
>> International in the scope of a Windows 10 migration project.
>> This project is currently at the end of the assessment phase. We would
>> require an answer to this email by the end of this week.
>> 
>> I would like to ask you some questions related to the following software
>> we are using at PMI :
>> 
>> R for Windows 3.0.2
>> R for Windows 3.1.2
>> 
>> Are all of those software compatible with Windows 10 Enterprise (version
>> 10.0.16299 build 16299)?
>> Are all of those software compatible with Windows 10 LTSC (version
>> 14393.2399)?
>> Are those software compatible with a 32 and/or 64 bit version of Windows
>> 10?
>> Are those application dependent on MS Office?
>> Have those applications any pre-requisites? Such as Java, .Net, Oracle.
>> 
>> If the software are not compatible, do you have a new version of this
>> software compatible with the mentioned version of Windows 10?
>> What would be the cost of such migration (instrument replacement if
>> necessary, licence cost, ...)?
>> 
>> If the software are not compatible and a new version is not yet available,
>> could you give me an estimation for the future release availability?
>> 
>> Best Regards,
>> 
>> Kevin Flament
>> 
>> Data & Systems Specialist
>> PMI Science and Innovation
>> Quai Jeanrenaud 3
>> 2000 Neuchâtel
>> 
>>[[alternative HTML version deleted]]
>> 
>> 
>> __
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>> posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>> 
>> 
> 
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> 
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--
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, 
UCT), Dipl. Phys. (Germany)

University of Zürich

Cell:   +41 (0)78 630 66 57
email:  rai...@krugs.de
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Re: [R] Unexpected YAML

[Rainer Krug via R-help]

.RData does not save any info abut previously loaded packages - so this would 
not cause the problem.

Rainer



> On 30 Jul 2018, at 21:27, Rui Barradas  wrote:
> 
> Hello,
> 
> Maybe R is loading a previously saved session.
> Check whether you have a file named .RData in your working directory.
> (This is not a file extension, it's the full filename.)
> 
> Hope this helps,
> 
> Rui Barradas
> 
> Às 20:14 de 30-07-2018, jlu...@ria.buffalo.edu escreveu:
>> R Users:
>> Whenever I fire up R, I now get the following message (red) at the end of
>> the prologue.
>> R version 3.5.1 (2018-07-02) -- "Feather Spray"
>> Copyright (C) 2018 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.
>> 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.
>> Error in loadNamespace(name) : there is no package called ‘yaml’
>> How do I get rid of it?
>> Joe
>>  [[alternative HTML version deleted]]
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>> 
> 
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--
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, 
UCT), Dipl. Phys. (Germany)

University of Zürich

Cell:   +41 (0)78 630 66 57
email:  rai...@krugs.de
Skype:  RMkrug

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[R] Trusted Timestamps - has anybody used OriginStamp? I am lost with their R-client

[Rainer Krug]

Hi

I am looking into obtaining trusted timestamps in R for data files. I am 
considering using OriginStamp and their API which you can find at 
https://doc.originstamp.org/#!/default/getHashInformation . They have an R 
client code which is available here http://originstamp.org/dev but I have no 
clue on how I can use it - maybe because I have never used R6 classes and the 
whole topic of trusted timestamps is quite new to me.

Has anybody used this API or other code to obtain a Trusted Timestamp?

Any examples on how I can use it?

Thanks,

Rainer




--
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, 
UCT), Dipl. Phys. (Germany)

University of Zürich

Cell:   +41 (0)78 630 66 57
email:  rai...@krugs.de
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Re: [R] Include pre-existing PDF files as vignettes in an R package?

[Rainer Krug]

> On 19 Feb 2018, at 12:25, Duncan Murdoch  > wrote:
> 
> On 19/02/2018 5:47 AM, Michael Hannon wrote:
>> Thanks, Duncan.  The files in question are Emacs Org-mode files, and I
>> think these are more or less isomorphic to Rmd files, but I haven't
>> used Org-mode in a long time, so I think the mapping (Org-mode ==>
>> Rmd) would be painful.

That should be easy - you can export org-mode files directly to LaTex. I 
haven’t used org-mode for some time, but I think it is Ctrl - C - E and than 
follow the prompts (obviously in emacs).

Rainer


> 
> If they aren't LaTeX then they won't be able to masquerade as Sweave files, 
> so things are more complicated.
> 
> I think there are two possibilities.  The better but harder one is to write 
> your own "vignette engine".  Section 1.4.2 of the manual describes the 
> process, and ?tools::vignetteEngine describes what is needed in your engine.
> 
> The other possibility is to manually edit an inst/doc/index.html file to 
> include links to your documents.  They won't be treated as vignettes, but at 
> least users will be able to find them.  The other disadvantage of this 
> approach is that you'll need to edit it for all vignettes, not just the 
> strange ones.
> 
> Duncan Murdoch
> 
> 
>> -- Mike
>> On Mon, Feb 19, 2018 at 1:20 AM, Duncan Murdoch
>> > wrote:
>>> On 18/02/2018 9:06 PM, Michael Hannon wrote:
 
 Greetings.  The group that I work with has just started using the approach
 outlined in Karl Broman's handy primer:
 
  http://kbroman.org/pkg_primer/pages/vignettes.html 
 
 
 to create vignettes for a couple of R packages.
 
 This works fine as long as we have a current Rmd version of the vignette.
 But
 we have some old PDF documents that we'd like to include as vignettes as
 well.
 I'd like to know if there's a way to include such PDF files as vignettes.
 
 We *do* have the source files for the PDF files in question, but it would
 be
 tedious to convert those source files to Rmd format.
 
 My first thought was simply to add the PDF files to the .../vignettes
 subdirectory and run the devtools::build_vignettes() function (mentioned
 in
 the Broman tutorial), but that doesn't work.  I.e., the PDF files don't
 appear
 in the list of vignettes for the package.
 
 And after running devtools::build_vignettes I see that there's a lot of
 additional stuff in:
 
  ...lib/R/site-library//...
 
 so I don't see any obvious way to "fool" R into using the PDF files that
 haven't gone through the whole knitr/rmarkdown process.  (Not to mention
 that
 such an approach would be fragile at best.)
>>> 
>>> 
>>> You don't say what format the source is, but if it is LaTeX, you just need
>>> to add some comments at the beginning, rename ending in .Rnw, and R will
>>> recognize plain LaTeX files as Sweave vignettes.
>>> 
>>> See the Writing R Extensions manual, section 1.4.
>>> 
>>> Duncan Murdoch
>>> 
 
 Suggestions welcome.  Thanks.
 
 -- Mike
 
 __
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>>> 
> 
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UCT), Dipl. Phys. (Germany)

University of Zürich

Cell:   +41 (0)78 630 66 57
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Re: [R] Preventing repeated package installation, or pre installing packages

[Rainer Krug]

> On 29 Nov 2017, at 15:28, Larry Martell  wrote:
> 
> I have a R script that I call from python using rpy2. It uses dplyr, doBy,
> and ggplot2. The script has install.packages commands for these 3 packages.
> Even thought the packages are already installed it still downloads,
> builds, and installs them, which is very time consuming. Is there a way to
> have it only do the install if the package is not already installed?

You could use something like


if (!require(dplyr)) {
install.packages(“dplyr”)
library(dplyr)
}

where require() returns FALSE if it fails to load the package.


> 
> Also, I run in a docker container, so after the container is instantiated
> the packages are not there the first time the script runs. Is there a way
> to pre load the packages, in which case I would not need the
> install.packages commands for these packages and my above question would
> become moot.

Yes - add them to you Docker file, but this is a docker question, not R. Check 
out the Rocker Dockerfiles to see how you can do this.

Rainer

> 
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--
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, 
UCT), Dipl. Phys. (Germany)

University of Zürich

Cell:   +41 (0)78 630 66 57
email:  rai...@krugs.de
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Re: [R] [R-pkgs] Release of ess 0.0.1

[Rainer Krug]

> On 9 Nov 2017, at 15:57, Sam Steingold  wrote:
> 
>> * Jorge Cimentada  [2017-11-09 00:02:53 +0100]:
>> 
>> I'm happy to announce the release of ess 0.0.1 a package designed to
>> download data from the European Social Survey
> 
> Given the existence of ESS (Emacs Speaks Statistics -
> https://ess.r-project.org/) the package name "ess" seems unfortunate.

Agreed. I would suggest to rename the package to avoid conflicts (ESS includes 
some R code, And I wouldn’t wonder if they would like to include it in a 
package?).


> 
> -- 
> Sam Steingold (http://sds.podval.org/) on darwin Ns 10.3.1504
> http://steingoldpsychology.com http://www.childpsy.net http://iris.org.il
> http://mideasttruth.com http://thereligionofpeace.com https://jihadwatch.org
> MS Windows: error: the operation completed successfully.
> 
> __
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--
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, 
UCT), Dipl. Phys. (Germany)

University of Zürich

Cell:   +41 (0)78 630 66 57
email:  rai...@krugs.de
Skype:  RMkrug

PGP: 0x0F52F982




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Re: [R] Interesting behavior of lm() with small, problematic data sets

[Rainer Krug]

Same version on Mac, same results.


> On 6 Sep 2017, at 15:22, JRG  wrote:
> 
> Indeed (version-specific).
> 
> With R 3.4.1 on linux, I get coefficients and residuals that are
> numerically exact, F-statistic = NaN, p-value = NA, R-squared = NaN, etc.
> 
> All of which is what ought to happen, given that the response variable
> (y) is not actually variable.
> 
> 
> ---JRG
> John R. Gleason
> 
> 
> On 09/06/2017 09:10 AM, S Ellison wrote:
>>> I think what you're seeing is
>>> https://en.wikipedia.org/wiki/Loss_of_significance.
>> 
>> Almost. 
>> All the results in the OP's summary are reflections of finite precision in 
>> the analytically exact solution, leading to residuals smaller than the 
>> double precision limit. The summary is correctly warning that it's all 
>> potentially nonsense, and indeed the only things you can trust are the 
>> coefficient values (to within .Machine$double.eps or thereabouts)
>> 
>> Interestingly, though, my current version of R (3.4.0) gives numerically 
>> exact coefficients (c(1,0) and identically zero standard errors.
>> 
>> So this particular example is apparently version-specific.
>> 
>> S Ellison
>> 
>> 
>> ***
>> This email and any attachments are confidential. Any use...{{dropped:8}}
>> 
>> __
>> 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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> and provide commented, minimal, self-contained, reproducible code.

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Re: [R] Conduct Network Analysis

[Rainer Krug]

I don’t know anything about network analysis, but I really guess that more 
information is needed to give an answer.

Cheers,

Rainer

> On 14 Jul 2017, at 05:08, SEB140004 Student  wrote:
> 
> Greeting.
> 
> Dear Mr/Mrs/Miss,
> 
> I want to create a network by using R but I only have a table that contain
> OTU ID and the abundance value of two samples ONLY.
> 
> Isn't possible? If can, which package can be used?
> Greatly appreciated to any suggestions and helps.
> 
> Thank you.
> 
> Best regards,
> Kang Chin Yi
> 
>   [[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] Conduct Network Analysis

[Rainer Krug]

I don’t know anything about network analysis, but I really guess that more 
information is needed to give an answer.

Cheers,

Rainer

> On 14 Jul 2017, at 05:08, SEB140004 Student  wrote:
> 
> Greeting.
> 
> Dear Mr/Mrs/Miss,
> 
> I want to create a network by using R but I only have a table that contain
> OTU ID and the abundance value of two samples ONLY.
> 
> Isn't possible? If can, which package can be used?
> Greatly appreciated to any suggestions and helps.
> 
> Thank you.
> 
> Best regards,
> Kang Chin Yi
> 
>   [[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.



--
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, 
UCT), Dipl. Phys. (Germany)

University of Zürich

Cell:   +41 (0)78 630 66 57

Fax (D):+49 - (0)3 21 21 25 22 44

email:  rai...@krugs.de

Skype:  RMkrug



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[R] Plantuml package for R

[Rainer Krug]

Hi

I hope I can use this R mailing list for this but it seems appropriate.

I started writing a small package which enables me to create plantuml graphs 
from within R. It is working and available on GitHub at

https://github.com/rkrug/plantuml

It is at the moment very rudimentary and can either display the generated graph 
in an R graphic device or save them in a file, but it works nicely (and it 
takes care of the installation and download of plantuml.jar!).

I am looking for feedback and ideas in which direction this can move. Ideas are 
for example conversion of R types (lists, data.frames, …) into graphs.


Please try it out and file suggestions, comments, bug reports on the GitHub 
issues tracker at https://github.com/rkrug/plantuml/issues

or if you have more general questions or suggestions, please discuss them here.

Thanks,

Rainer

--
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, 
UCT), Dipl. Phys. (Germany)

University of Zürich

Cell:   +41 (0)78 630 66 57

Fax (D):+49 - (0)3 21 21 25 22 44

email:  rai...@krugs.de

Skype:  RMkrug



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Re: [R] error while creating a simple graph

[Rainer Krug]

> On 20 Jun 2017, at 07:18, Yogesh Gupta  wrote:
> 
> Dear All,
> 
> I am learning R so it's a very simple problem but I do not understand while
> I am not able to generate a graph from two vectors.
> 
> when I type this code, it generates a very nice graph.
> 
> pdf("mygraph.pdf")
>> attach(mtcars)
>> plot(wt,mpg)
>> abline(lm(mpg~wt))
>> title("Regreesion of mpg")
>> detach(mtcars)
>> dev.off()
> 
> But I am trying to create a graph from this code, it generates a pdf with
> nothing.
> 
> 
>> dev.new()
>> pdf("test.pdf")
>> x <- c(1,3,6,9,12)
>> y <- c(1.5,2,7,8,15)
>> plot(x,y)
> 

As in your first example, you have to with of the device by using dev.off(). 
Only then is the pdf completed.

Rainer
> 
> Thanks
> Yogesh
> 
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> 
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> and provide commented, minimal, self-contained, reproducible code.

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