[BlindRUG] R Questions

Sun Mar 7 08:06:57 UTC 2021

Hello Jonathan,

Thanks for your mails.

I think the most important step is to configure R so that you can work
with it as a blind person. Once R is properly configured for the
blind, then theoretically you can work with R like sighted people.

Many years ago I attended an R course for blind people. At that time I
was taught two things:

Work with the R terminal

Configure the file Rprofile

>From today's point of view, neither seems to be necessary anymore.
However, I'm not that familiar with Mark Down yet. I'll have to take a
look at the current procedure. I'm sure I'll have more questions about
it.

Kind regards

Niels

2021-03-07 8:04 GMT+01:00, Godfrey, Jonathan via BlindRUG <blindrug at nfbnet.org>:
> Hello Niels,
>
> I used to put the selection of my preferred CRAN mirror in the R profile.
>
> Back when I was helping make sure a set of windows machines in a computer
> lab next to my office played nicely for the students, I would do some things
> that are less necessary now that almost everyone (else) uses RStudio. That
> was before RStudio existed so there was no cloud server at position 1 on the
> list that came up for students. I hard coded which CRAN mirror our lab
> machines looked at.
>
> Before tab completion, typing the full command to choose the CRAN mirror was
> irritating enough to want it automatically set for me all the time. That
> then featured in the profile for the folder I used just for maintaining my R
> installation.
>
> Other things I did over the years lowered in importance.
> I did switch the pager to notepad, I did have to force help in HTML (now
> standard) and toyed with cosmetic things at various times
>
> Henrik's warnings seem interesting, but I can't think of situations when I
> shorten arguments. I do need to watch that I name arguments when showing
> sample code to my students though.
>
> Jonathan
>
>
> -----Original Message-----
> From: BlindRUG <blindrug-bounces at nfbnet.org> On Behalf Of Niels Luithardt
> via BlindRUG
> Sent: Sunday, 7 March 2021 7:03 PM
> To: Blind R Users Group <blindrug at nfbnet.org>
> Cc: Niels Luithardt <niels.luithardt at googlemail.com>
> Subject: Re: [BlindRUG] R Questions
>
> Hello Henrik,
>
> Thank you very much for your answer. I would be very interested to know what
> you have adjusted in the Rprofile file.
>
> In my file it's just a few settings. For example, I replaced the
> non-accessible pager with notepad. I would be very happy about further
> recommendations!
>
> Kind regards
>
> Niels
>
>
>
>
> 2021-03-07 3:04 GMT+01:00, Henrik Bengtsson via BlindRUG
> <blindrug at nfbnet.org>:
>> Regarding:
>>
>>> 1. On windows, the default global R profile is part of the installation.
>>> Each time I update R, the profile is in the wrong place and needs
>>> moving.
>>> I did do that occasionally but that was years ago now.
>>
>> So, you must have ended up editing the "site-wide" Rprofile one, that
>> comes with the R Windows installation, e.g.
>> C:/PROGRA~1/R/R-40~1.4/etc/Rprofile.site.  A good rule of thumb is to
>> never edit or add anything to the folder where R itself is installed.
>> I never had to do that during the two decades I've use R.
>>
>> A better option is to use a folder-specific or a user-specific
>> .Rprofile file.  Those ones will survive R upgrades since they live
>> under you home folder.  When R starts, it looks for a .Rprofile file
>> in the following order: If .Rprofile exists in the current folder
>> where R is started, then that is sourced during the R startup process.
>> If that doesn't exist, then it looks for .Rprofile in your home
>> folder.   The latter is by far most commonly used one by people. BTW,
>> the format of this file must be a valid R script with a trailing
>> newline.  If you forget the newline at the end, R will silently ignore
>> the file (which is such an annoying misfeature).
>>
>> One MS Windows, it is a bit confusing what R considers to be your home
>> folder.  It is not C:\Users\alice\ as one would expect.  Instead, it
>> is C:\Users\alice\Documents\.  That is vhere you want to put your
>> .Rprofile file in order for R to source it every time you start R
>> regardless from where you start R and regardless which version of R
>> you start.  The easiest way to find the exact location is to do the
>> following from within R:
>>
>>> normalizePath("~/.Rprofile")
>> [1] "C:\\Users\\alice\\Documents\\.Rprofile"
>>
>> That is the file you want to create.  I have such a file on my machine
>> and I had it there for many years.  I use it for different things,
>> e.g. tweaking the prompt, tweaking R option warnPartialMatchArgs=TRUE
>> to remind me to not use partial argument names, and so on.
>>
>> Hope this helps,
>>
>> Henrik
>>
>> On Sat, Mar 6, 2021 at 3:03 PM Godfrey, Jonathan via BlindRUG
>> <blindrug at nfbnet.org> wrote:
>>>
>>> Hello Niels,
>>>
>>> I seldom adjust the R profile nowadays. I have several reasons.
>>>
>>> 1. On windows, the default global R profile is part of the installation.
>>> Each time I update R, the profile is in the wrong place and needs
>>> moving.
>>> I did do that occasionally but that was years ago now.
>>> 2. I might edit the copy of the r profile in a specific work folder,
>>> but again, the usefulness to me has reduced. The reason relates to
>>> your next question.
>>>
>>> You will not edit an R script from the R terminal. It is just a plain
>>> text file though so you could edit it using any text editor of your
>>> choosing.
>>> If you do this, you need to pull the script into the R session using
>>> `source()`, with the filename in the brackets as a quoted string. I
>>> do this very rarely nowadays.
>>>
>>> The use of R markdown has made the above all quite inefficient. I do
>>> practically all work inside an R markdown file because that speeds up
>>> the time to production of the final product I want to share. I only
>>> use the R prompt (terminal or GUI version) for little jobs or to get
>>> at help functionality.
>>>
>>> My data analysis workflow (today) is to
>>>
>>> 1. make a text file with the *.Rmd extension. I use WriteR and
>>> sometimes just plain old notepad. I might start from a blank file, a
>>> template, or sometimes using an old Rmd file that has a lot of what I
>>> want in it.
>>> 2. If using WriteR, I process to html using the f5 key.
>>> 3. if not using WriteR, I use rmarkdown::render() to process the file
>>> from the R terminal.
>>> 4. to see my results, I open (and keep it open)  the html file step 2
>>> or 3 created, and refresh it as I update my Rmd file and re-process
>>> it. In most browsers that uses f5.
>>>
>>>
>>> I still use R script files for package development of course. There
>>> are some rare occasions when an analysis job involves very long
>>> processing times and those tend to be done using an R script too, but
>>> that's mostly old habits.
>>>
>>>
>>> HTH
>>> Jonathan
>>>
>>> -----Original Message-----
>>> From: BlindRUG <blindrug-bounces at nfbnet.org> On Behalf Of Niels
>>> Luithardt via BlindRUG
>>> Sent: Sunday, 7 March 2021 6:13 AM
>>> To: blindrug at nfbnet.org
>>> Cc: Niels Luithardt <niels.luithardt at googlemail.com>
>>> Subject: [BlindRUG] R Questions
>>>
>>> Hello,
>>>
>>> I have a few questions about the program R and hope you can help me.
>>>
>>> 1) Is it useful to customize the Rprofile file?
>>>
>>> 2) How can I open/run a script in RTerm?
>>>
>>> Kind regards
>>>
>>> Niels
>>>
>>> _______________________________________________
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>>> The list archive can be viewed at:
>>> http://www.nfbnet.org/pipermail/blindrug_nfbnet.org
>>> More information and useful links about using R as a blind person can
>>> be obtained at:
>>> http://R-Resources.massey.ac.nz
>>>
>>> Look for help using R commands by reading the accessible e-book
>>> "Let's Use R Now" compiled by Jonathan Godfrey at:
>>> http://R-Resources.massey.ac.nz/lurn/front.html
>>>
>>> _______________________________________________
>>> BlindRUG mailing list
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>>> BlindRUG:
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>>> n%40gmail.com
>>> The list archive can be viewed at:
>>> http://www.nfbnet.org/pipermail/blindrug_nfbnet.org
>>> More information and useful links about using R as a blind person can
>>> be obtained at:
>>> http://R-Resources.massey.ac.nz
>>>
>>> Look for help using R commands by reading the accessible e-book
>>> "Let's Use R Now" compiled by Jonathan Godfrey at:
>>> http://R-Resources.massey.ac.nz/lurn/front.html
>>
>> _______________________________________________
>> BlindRUG mailing list
>> BlindRUG at nfbnet.org
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>> To unsubscribe, change your list options or get your account info for
>> BlindRUG:
>> http://nfbnet.org/mailman/options/blindrug_nfbnet.org/niels.luithardt%
>> 40googlemail.com
>> The list archive can be viewed at:
>> http://www.nfbnet.org/pipermail/blindrug_nfbnet.org
>> More information and useful links about using R as a blind person can
>> be obtained at:
>> http://R-Resources.massey.ac.nz
>>
>> Look for help using R commands by reading the accessible e-book "Let's
>> Use R Now" compiled by Jonathan Godfrey at:
>> http://R-Resources.massey.ac.nz/lurn/front.html
>>
>
> _______________________________________________
> BlindRUG mailing list
> BlindRUG at nfbnet.org
> http://nfbnet.org/mailman/listinfo/blindrug_nfbnet.org
> To unsubscribe, change your list options or get your account info for
> BlindRUG:
> http://nfbnet.org/mailman/options/blindrug_nfbnet.org/a.j.godfrey%40massey.ac.nz
> The list archive can be viewed at:
> http://www.nfbnet.org/pipermail/blindrug_nfbnet.org
> More information and useful links about using R as a blind person can be
> obtained at:
> http://R-Resources.massey.ac.nz
>
> Look for help using R commands by reading the accessible e-book "Let's Use R
> Now" compiled by Jonathan Godfrey at:
> http://R-Resources.massey.ac.nz/lurn/front.html
>
> _______________________________________________
> BlindRUG mailing list
> BlindRUG at nfbnet.org
> http://nfbnet.org/mailman/listinfo/blindrug_nfbnet.org
> To unsubscribe, change your list options or get your account info for
> BlindRUG:
> http://nfbnet.org/mailman/options/blindrug_nfbnet.org/niels.luithardt%40googlemail.com
> The list archive can be viewed at:
> http://www.nfbnet.org/pipermail/blindrug_nfbnet.org
> More information and useful links about using R as a blind person can be
> obtained at:
> http://R-Resources.massey.ac.nz
>
> Look for help using R commands by reading the accessible e-book "Let's Use R
> Now" compiled by Jonathan Godfrey at:
> http://R-Resources.massey.ac.nz/lurn/front.html
>