Re: [R] R does not run under latest RStudio

[John Dougherty via R-help]

On Thu, 6 Apr 2023 17:28:32 +0800
"Steven T. Yen"  wrote:

> I updated to latest RStudio (RStudio-2023.03.0-386.exe) but
> R would not run. Error message:
> 
> Error Starting R
> The R session failed to start.
> 
> RSTUDIO VERSION
> RStudio 2023.03.0+386 "Cherry Blossom " (3c53477a, 2023-03-09) for
> Windows [No error available]
> 
> I also tried RStudio 2022.12.0+353 --- same problem.
> 
> I then tried another older version of RStudio (not sure version
> as I changed file name by accident) and R ran.
> 
> Any clues? Please help. Thanks.
> 
> __
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> minimal, self-contained, reproducible code.
> 

Just to be thorough, what version of R are you running.  RStudio is its
own project, and they have shifted their emphasis somewhat regarding R
somewhat.  The web site now states that the organization - now
called Posit - is not de-emphasizing R so much as extending to empbrase
Python.  The current version of RStudio requires R 3.3.0 or later.

JWDougherty

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Re: [R] startup loading issue

[John Dougherty via R-help]

On Tue, 25 Oct 2022 08:33:10 -0500
ken eagle  wrote:

> I thought I was loading a ~300M binary (bigwig) file into another
> application . . .

Is the other application R dependent, written in R, or call R
capacities? If it doesn't, the issue might be with the "other
application rather than R.

JWDougherty

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Re: [R] Creating NA equivalent

[John Dougherty via R-help]

On Tue, 21 Dec 2021 05:41:31 +0100
Marc Girondot via R-help  wrote:

> Dear members,
> 
> I work about dosage and some values are bellow the detection limit. I 
> would like create new "numbers" like LDL (to represent lower than 
> detection limit) and UDL (upper the detection limit) that behave like 
> NA, with the possibility to test them using for example is.LDL() or 
> is.UDL().
> 
> Note that NA is not the same than LDL or UDL: NA represent missing
> data. Here the data is available as LDL or UDL.
> 
> NA is built in R language very deep... any option to create new
> version of NA-equivalent ?
> 
> Thanks
> 
> Marc

You are concerned with a distinct quality in the data with respect to a
specific method. You might want to code a qualitative variable that
defines the detectability state of the specific reading.  Then filter on
the state of interest, and as a means of establishing the quality of the
method or the data, summarize the detection properties in your sample
for the anaytical method employed. I had an engineer tell me flatly
that the measures claimed in a paper were "impossible."  The method
used was already common, but his system was not sensitive enough.  

As far as the statistical properties go, there are measures that could
be made and measures that could not be made.  If a different method
became available, you would probably still desire to either reanalyze
the older data employing the new method, or append new measures where
they were previously unavailable. Either way you encounter
data range or compatibility issues that have to be addressed
methodologically.

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Re: [R] ggplot2: multiple box plots, different tibbles/dataframes

[John Dougherty via R-help]

On Wed, 10 Nov 2021 11:44:07 -0800 (PST)
Rich Shepard  wrote:

> I have the code to create ggplot2 boxplots using two attributes (e.g.,
> chemical concentration and month) from the same tibble. Is there an
> example from which I can learn how to make boxplots from different
> tibbles/dataframes (e.g., chemical concentrations and monitoring
> location)?
> 
> TIA,
> 
> Rich
> 
You should probably glance at the R Graphics Cookbook.  That was my
gateway to ggplot.  I believe ggplot is a part of the tidyverse so
there should good information.

JWDougherty

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Re: [R] No "doc" directory in my installation of R.

[John Dougherty via R-help]

On Sat, 7 Aug 2021 20:26:13 -0700 (PDT)
Jeff Newmiller  wrote:

Documentation on most Linux systems, regardless of release, is commonly
located under the /usr/share directory.  For R that is
/usr/share/doc/R.  There is also a "man" entry for R.  The rstudio help
list might be able to help more than this list.  

> R documentation on my Ubuntu 20.20 is in /usr/share/R/doc.
> 
> I see no doc directories in the locations you mention using
> 
>locate /doc/
> 
> Maybe you should be asking on R-sig-debian, perhaps with less noise
> about RStudio?
> 
> On Sun, 8 Aug 2021, Rolf Turner wrote:
> 
> >
> > Should/shouldn't there be one?
> >
> > My R seems to be installed in /usr/lib/R.  If do an "ls" of this
> > directory, I get:
> >  
> >> bin/  COPYING@ etc/  lib/  library/  modules/
> >> site-library/  SVN-REVISION  
> >
> > Definitely no "doc".
> >
> > The (only) reason that I am concerned about this, is that I have
> > decided to experiment a bit with Rstudio, and it apparently wants a
> > "doc" directory.  When I try to start Rstudio I get a pop-up window
> > with the error message
> >  
> >> R doc dir (/usr/local/lib64/R/doc) not found.  
> >
> > Note that /usr/local/lib64/R is a symbolic link to /usr/lib/R.
> > The latter is where my installation put R; the former seems to be
> > where Rstudio wants it to.  So I created the symbolic link.
> >
> > The discrepancy between locations is another puzzle/worry.
> >
> > My installation comes from a pre-built binary ("sudo apt install
> > r-base").  I apparently have the latest version.  I remark that I am
> > running Ubuntu 20.04 with a Mate 1.20.4 desktop.
> >
> > How can I get a "doc" directory into my R directory and make Rstudio
> > happy?
> >
> > cheers,
> >
> > Rolf Turner
> >
> > P.S. I have also tried to ask about this on the  Rstudio community
> > forum, but it seems to me to more of an R question than an Rstudio
> > one.
> >
> > R. T.
> >
> > --
> > Honorary Research Fellow
> > Department of Statistics
> > University of Auckland
> > Phone: +64-9-373-7599 ext. 88276
> >
> > __
> > 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. 
> 
> ---
> Jeff NewmillerThe .   .  Go
> Live... DCN:Basics: ##.#.
> ##.#.  Live Go... Live:   OO#.. Dead: OO#..  Playing
> Research Engineer (Solar/BatteriesO.O#.   #.O#.  with
> /Software/Embedded Controllers)   .OO#.   .OO#.
> rocks...1k
> 
> __
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> minimal, self-contained, reproducible code.
>

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Re: [R] Variable labels

[John Dougherty via R-help]

On Fri, 14 May 2021 17:20:20 +0800
Steven Yen  wrote:

> Thanks to all, for bearing with me.
> 
> Now I realize expss may not be what I need. I have now written a 
> self-runnable, replicable set of codes (listed below). Perhaps that 
> gives an idea of what I need. Question is, whethet this is the right
> way to do this (to have a clickable object to learn about variable 
> definitions) or whether there are better ways. Thanks!
> 
> Steven
> 
>From your example, after loading "try1.RData" you see a
"definitions" entry in the Environment pane.  Clicking on the name
"definitions" as opposed to the icon to expand the entry opens the
"definitions" data frame in its own tab in a pane on the upper left
where files such as scripts are displayed.  Clicking that tab opens the
list of "definitions" which is a list of three entries, where the
variable ids from the "mydata" file are row names.  

That will be the case in any session accessed using RStudio and opening
your saved .RData file.

If you are concerned about non-RStudio users being able to access that
data.frame in the Windows version R, if they load the .RData file that
will load the "definitions" data frame, which can be listed simply
typing "definitions" at the command prompt.

There is no "right way" do this.  Your approach works, though it will
get awkward if the data frame contains very many definitions.  If you
look at SPSS (or PSPP) for instance the Data Name and Label are both
elements of the definition of the variable, and the Label element of
the SPSS variable definition is essentially what your example seems to
use as a definition.  Otherwise you seem to be treading around the edges
of metadata which is also a set of data definitions.

R is more flexible about these things, which makes it somewhat more of
a chore at times.  

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Re: [R] vars package - irf() does not work

[John Dougherty]

On Wed, 22 Feb 2017 09:57:00 +
"T.Riedle"  wrote:

> Dear all,
> 
> I have not received any response on this email. Is there anybody who
> can help me?
> 
> I want to run an impulse response analysis using the vars() package.
> The code looks as follwows.
> 
> 
> # list of class varest
> varest.USA<-VAR(VAR_analsis_DataUSA, lag.max = 24, ic = "SC", type =
> "both")
> 
> varest.USA
> 
> summary(varest.USA)
> 
> 
> 
> #Run irf analysis
> irf.USAg<-irf(varest.USA, response = "g", n.ahead = 48, boot = TRUE,
> ci=0.95)
> 
> plot(irf.USAg)
> 
> 
> The problem is that R returns an error that the arguments in irf are
> unused. That is, unused arguments (response="g", n.ahead = 48, boot =
> TRUE, ci=0.95) The strangeness is that it sometimes works but most of
> the time it does not. I installed vars() last month and irf() worked
> well but now it does only occasionally. I have just edited the data
> but kept the code unchanged.
> 
> 
> In addition, I have the same problem when I am trying to replicate
> the example on irf() in the vars vignette althoug it also worked well
> when I installed vars and run the example.
> 
> 
> Does anybody have an idea what is wrong?
> 
Two guesses are 1) you are not consistently entering the commands and
thus get variable outcomes, and 2) possibly there are "depends" that
irf() needs that need to updated.  You could also contact the package
creators.  I would also observe that this looks remarkably like you
might be asking for help on your homework.  

I would create a script of the commands you use as they work, each
entered in sequence as you used it. You use it essentially as a lab
notebook that documents procedures.  RStudio works well for this, since
you can copy each line that works from the Console to a script file in
the editor.  You can do the same with a text editor, while using R from
a console, but it is somewhat more clumsy.  


-- 

John

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Re: [R] Gaussian Filter

[John Dougherty]

On Tue, 7 Feb 2017 19:51:21 +0200
catalin roibu  wrote:

The simplest way to get answers to such questions is run an internet
search on your terms: "R Gaussian filter."  Google reports 6,600,000
hits.  The hits you are interested in are near the top.  It wastes
less time that way.  

BTW, is the data mean average temperature date, or
just "like" mean average temperature data.  

-- 

John

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Re: [R] Cronbach's Alpha

[John Dougherty]

On Tue, 17 Jan 2017 12:45:10 -0400
Jim Silverton  wrote:

> Dear all,
> 
> I have 12 companies and I am developing a scale for innovation. I
> want to check the reliability of my scale. I delivered it to
> different (engineers, managers etc) people in each company and an
> unequal number of values. For example:
> Company 12 engineers  2 managers
> Company 24 engineers 10 managers
> etc.
> 
> My question is can I use 'ordinary Cronbach's alpha or do I need a
> modified weighted cronbach's alpha. If so, does such a thing exist in
> R?
> 

More a statistical question than an R question.  You might want to
search sites that deal with specifically statistical aspects.

-- 

John

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Re: [R] Export R output in Excel

[John Dougherty]

On Wed, 28 Dec 2016 13:45:25 -0800
Bryan Mac  wrote:

> Hi,
> 
> How do I export results from R to Excel in a format-friendly way? For
> example, when I copy and paste my results into excel, the formatting
> is messed up.
> 
> Thanks.
>  
> Bryan Mac
> bryanmac...@gmail.com
>
Your purpose is not clear.  If you are planning to do MORE statistical
work with excel using R output, don't do it.  Learn the R equivalents.
There's nothing that you can do in Excel that can't be done in R.  And,
while Microsoft has made great strides in the reliability of it's
numbers and calculating routines, it is still a spreadsheet.

If you want to add tabular data to a word file from R, out
put it to a csv or tab delimited format and then copy into Word or
LibreOffice Writer. From there you can select the text of the table and
transform it into a table using the table menu. If you want formatted
statistical output, you can sink() the output to an asscii or utf
text file, paste it into Word and then convert the font of the pasted
segment to a fixed pitch font.  R output tends to follow the old-time
typewriter approach to formatting (spaces and tabs), meaning that kerned
fonts behave in horrible ways, fonts are rubbery, etc.


-- 

John

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Re: [R] transpose rows and columns for large data

[John Dougherty]

On Tue, 29 Nov 2016 17:22:47 + (UTC)
Elham - via R-help  wrote:

> Is there another way (I prefer a way with Excel)?

Search on "friends don't let friends use excel for statistics."
Spreadsheets are an inherently perilous way to do statistics and Excel
specifically is notoriously poor. In fact the reason I originally began
using dedicated statistical packages (STATA first and now R) is that
spreadsheets (Excel in my case) can throw subtle errors that can create
problems. immediately, or even worse - later.  I had Excel return a
negative variance. Since variance is a squared value, unless you are
dealing with some very exotic numbers including imaginary values, a
negative variance is an absurd result.  Further investigation revealed
that other stat routines provided with Excel at the time were also
throwing errors that could look reasonable and thus be missed.  It was
also simply using erroneously constructed methods and providing
outright wrong results to things like Chi-square calculations.  

-- 

John

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Re: [R] Error in a regression

[John Dougherty]

On Mon, 24 Oct 2016 10:54:00 -0500
Andrea Marcela Huerfano Barbosa  wrote:

> Hi guys,
> When I try to do a linear regression into the console appears this
> warning message:
> 
> >* attempting model selection on an essentially perfect fit is
> >nonsense*
> 
> Some one could tell me what does it mean and maybe a way to solve it.
> 
> Thanks in advance,
> 
> Andrea Marcela
> 
Andrea, there is far too little information in your post for us to help
you.  The standard lm() routine doesn't produce that message in any
model. You need to provide a sample the data and explain what routine
you are using to select the model.

-- 

John

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Re: [R] (no subject)

[John Dougherty]

On 6 Oct 2016 07:55:28 -
"abhishek pandey"  wrote:

> kindly solve my problem sir.
> 
> 
The answer obviously is 42.

JWDougherty

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Re: [R] add outlier in data set

[John Dougherty]

On Mon, 19 Sep 2016 12:25:08 +
"Muhammad  Kashif"  wrote:

> Dear Ellison
> 
> yes its working but if i want to replaced the any value in the the
> output . e.g i want to replace 0.65 with 10. then what i do
> 
Save the data as a CSV file.  Edit the file with a basic ascii text
editor (these days unicode perhaps).  Read the new data back into R.
There also ways to do this within R:

https://therostrumblog.wordpress.com/2014/01/29/basic-data-frame-manipulations-in-r/
 

see "Altering a value".

There is a great deal of "help" in R using either the "?" or
apropos().  It is worth using these.  Also some useful free books are
available from the R Project site.  

-- 

John

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Re: [R] Retrieving data from survey in R Studio

[John Dougherty]

On Thu, 18 Aug 2016 09:19:05 +
Barathan Roy Pinas  wrote:

> Hello,
> 
> 
> I have been given a .csv file and it is not loading. This is what I
> did.
> 
> 
> survey=read.csv("http://www.maths.usyd.edu.au/u/UG/IM/STAT2012/r/survey.csv;)
> attach(survey)
> pulse.sf=pulse[smoke==1 & sex==2]
> pulse.sf
> 
...

A couple of points.  First, your question addresses RStudio which has
its own list.  Next, the issue appears to be homework, and that is
not something many will help you with.  However, since the actual issue
is generic to R, let that slide. You want to be sure the address is
correctly typed. Is the "r" supposed to be lower case? Then, do you
have the appropriate permissions to enter that page? Since that is a
university server, you may need to be logged in through your student
account to access the page with the data.  Even if you are, will it
let RStudio access it?  It would probably be simplest to simply download
the data to your system, then read in the local copy.

-- 

John

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Re: [R] R Package installation

[John Dougherty]

On Fri, 12 Aug 2016 06:53:03 -0400
"Dayalan, Nithya"  wrote:

You don't say what OS you are using, though the packages you were
trying to obtain are apparently for Windows.  You also don't say
whether you are using something like R-Studio, or whether you are on a
company network behind a firewall.

If you have a sysop, you probably should be going through him or her.
There's a very good chance that your system is lacking in permissions.
Your network's settings are problem, or Windows or a recent update may
be causing your trouble. You should also simply try opening the specific
mirror URL sans the package info to see if you can see the page.  

-- 

John

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Re: [R] Please help: cannot import files from Windows into R

[John Dougherty]

Christa,

As others are noting, the file is not a text file.

Open the file in Notebook or Notepad.  If the editor complains, then
open it in Word.  Save it as a "plain text" file.  You will have to
choose the file type in the "Save As" dialog.  You may run into other
issues such as the field separator.  It is best to limit the file to a
header line containing any field names separated by commas or tabs,
followed by columnar data, again with values separated by the same
sepator used to separate the field names.  Any metadata can be
maintained in a separate text file.  

All of this presumes that your file came from Word or a compatible word
processor.  If it came from some other program and the "txt" type was
simply by you added when you saved the file, we'll need to know what
program the data was created in.

-- 

John

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Re: [R] New installation

[John Dougherty]

On Thu, 9 Jun 2016 13:44:52 -0700
jax200  wrote:

> Hi
> 
> I'm starting off with both R and Linux Mint.  During a recent R
> course, I had multiple difficulties with installing updates needed
> for the course.
> 
> As such, I'd like to hit the restart button with fresh installs of
> Linux and R.  I would appreciate your help with which Linux platform
> works best with R, and how to go about getting all the updates
> installed for both programs.
> 
> Many thanks,  Jack
> 
Any Linux distribution is likely to work well with R.  The chief hick-up
is keeping you R release up to date.  Typical linux releases including
Ubuntu, Opensuse and Fedora R versions available through their system
updates all tend to lag behind the R release version available on CRAN.
Asking for help will inevitably result in responders asking about the R
version you used, and, if it is significantly older than the current
version, you will be asked to update R and retry your problem
procedure.  That means that you will probably want to handle updating R
manually to remain current rather than rely on the Linux release
updating system.

JDougherty

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Re: [R] strange error

[John Dougherty]

On Wed, 25 May 2016 18:56:47 +0200
alicekalk...@freenet.de wrote:

Alice,

Have you tried running the code in R in a terminal?  If the error
persists, then this may be the right place to ask for help.  If it is
specific to R Studio, then you need to ask them.
-- 

John

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Re: [R] What is the easiest way to turn a dataframe into a barplot?

[John Dougherty]

On Thu, 12 May 2016 13:19:54 -0400
"yoursurrogate...@gmail.com"  wrote:

> Hello, I can't post my code since it's on a work computer.
> 
> But basically, I have a dataframe that has two columns, one is a
> string and the other is an integer.  I want to turn this into a
> vertival barplot where on the x-axis I have the string in the first
> columb and then the plot will display the integer count.
> 
> I have found many examples online and most of those matched either
> odd edge cases or putting the data into a format that strips out some
> of the data and I can't use it later.
> 
> This should be a breeze, what am I missing?

Without showing a data sample, no one can really do more than guess
what you are asking.  Among other things, no one "turns" a
dataframe "into" a barplot, ever.  It would defeat the purpose of
collecting the data to begin with.  It is also unclear what data the
process could strip out, or why you can't use the data again, unless
you are attempting to overwrite the dataframe with the bar plot.  

A barplot is a visual summary of data. So, best to bite the bullet and
supply an example. That way we can understand what you are attempting to
summarize.  As long as it has a similar structure and data types, you
can make it up. You would also benefit a great deal from reading up on
R and communicating in a manner that the community can follow. Sadly, no
specialized community exists without its own specialized jargon and
R-help is an intersection of at least two such communities.

JWDougherty

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