Re: [NTG-context] Filter module for R
On Mon, 15 Jun 2020, Fabrice L wrote:
Dear Aditya,
Le 15 juin 2020 à 01:45, Aditya Mahajan a écrit :
This is an adapted version of the code that I use for my course where I use the
vim module to do the typesetting:
\usemodule[filter]
\usemodule[vim]
\definecolor [darkblue] [r=0.1, g=0.11, b=0.84]
\definecolor [darkgreen] [g=0.7]
\definecolor [lightblue] [h=87cefa]
\definecolor [lightgreen] [g=0.95,b=0.8,r=0.8]
\defineframedtext
[leftbartext]
[
width=local,
frame=off,
framecolor=darkblue,
leftframe=on,
rulethickness=1ex,
offset=0.25ex,
loffset=3ex,
background=color,
backgroundcolor=lightblue,
]
\definevimtyping
[RCODE]
[
syntax=r,
directory=output,
strip=yes,
escape=yes,
before={\blank[quarterline]\startleftbartext},
after={\stopleftbartext},
]
\define[1]\ShowOutput
{\typeRCODEfile{\externalfilterinputfile}
\startleftbartext[framecolor=darkgreen, backgroundcolor=lightgreen]
\setupalign[flushleft, verytolerant]
% range={1,-1} not currently supported
% See below for details
\typefile[range={1,-1}]{#1}
\stopleftbartext}
\defineexternalfilter
[R]
[ filtercommand={R CMD BATCH -q --no-timing --save --restore
\externalfilterinputfile\space \externalfilteroutputfile},
output=\externalfilterbasefile.out,
directory=output,
readcommand=\ShowOutput,
read=no,
cache=yes,
purge=yes, % THE COMMA WAS MISSING
]
\starttext
Some text...
\startR[read=yes]
pdf("RPlots/MyHistogram.pdf",5,5)
X <- rnorm(200,mean=10,sd=2)
hist(X, col = "red3" , xlab="Score QI" , main="", ylab="fréquence")
\stopR
\externalfigure[RPlots/MyHistogram.pdf][width=.5\textwidth]
\stoptext
Thanks so much for your answer. I had (of course) to install nvim in order the
code to work, but this works !
Sorry, that was a leftover. I was testing in a docker container where I did not
have vim installed. This will also work with regular vim.
Thanks also for your additional work regarding the locale setting.. this is
really deep magic for me.
I think the facility to run R code directly from context can open ConTeXt to
new users. The alliance between R and LaTeX is a winning combination to a lot
of my colleagues. Do you think this would be appropriate to do a simple page on
the wiki explaining how R code can be done in ConTeXt, with eventual
formatting, with some simple examples, or this is too much noise ?
Definitely. I think there is already a short page. But it will be good to add
more detailed instructions.
Aditya___
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Re: [NTG-context] Filter module for R
Dear Aditya,
> Le 15 juin 2020 à 01:45, Aditya Mahajan a écrit :
>
> This is an adapted version of the code that I use for my course where I use
> the vim module to do the typesetting:
>
> \usemodule[filter]
> \usemodule[vim]
>
> \definecolor [darkblue] [r=0.1, g=0.11, b=0.84]
> \definecolor [darkgreen] [g=0.7]
> \definecolor [lightblue] [h=87cefa]
> \definecolor [lightgreen] [g=0.95,b=0.8,r=0.8]
>
> \defineframedtext
> [leftbartext]
> [
>width=local,
>frame=off,
>framecolor=darkblue,
>leftframe=on,
>rulethickness=1ex,
>offset=0.25ex,
>loffset=3ex,
>background=color,
>backgroundcolor=lightblue,
> ]
>
> \definevimtyping
> [RCODE]
> [
>syntax=r,
>directory=output,
>strip=yes,
>escape=yes,
>before={\blank[quarterline]\startleftbartext},
>after={\stopleftbartext},
> ]
>
> \define[1]\ShowOutput
>{\typeRCODEfile{\externalfilterinputfile}
> \startleftbartext[framecolor=darkgreen, backgroundcolor=lightgreen]
> \setupalign[flushleft, verytolerant]
> % range={1,-1} not currently supported
> % See below for details
> \typefile[range={1,-1}]{#1}
> \stopleftbartext}
>
>
> \defineexternalfilter
> [R]
> [ filtercommand={R CMD BATCH -q --no-timing --save --restore
> \externalfilterinputfile\space \externalfilteroutputfile},
> output=\externalfilterbasefile.out,
> directory=output,
> readcommand=\ShowOutput,
> read=no,
> cache=yes,
> purge=yes, % THE COMMA WAS MISSING
> ]
>
> \starttext
>
> Some text...
>
> \startR[read=yes]
> pdf("RPlots/MyHistogram.pdf",5,5)
> X <- rnorm(200,mean=10,sd=2)
> hist(X, col = "red3" , xlab="Score QI" , main="", ylab="fréquence")
> \stopR
>
> \externalfigure[RPlots/MyHistogram.pdf][width=.5\textwidth]
>
> \stoptext
>
>
Thanks so much for your answer. I had (of course) to install nvim in order the
code to work, but this works ! Thanks also for your additional work regarding
the locale setting.. this is really deep magic for me.
I think the facility to run R code directly from context can open ConTeXt to
new users. The alliance between R and LaTeX is a winning combination to a lot
of my colleagues. Do you think this would be appropriate to do a simple page on
the wiki explaining how R code can be done in ConTeXt, with eventual
formatting, with some simple examples, or this is too much noise ?
Thanks. Fabrice.
___
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Wiki!
maillist : ntg-context@ntg.nl / http://www.ntg.nl/mailman/listinfo/ntg-context
webpage : http://www.pragma-ade.nl / http://context.aanhet.net
archive : https://bitbucket.org/phg/context-mirror/commits/
wiki : http://contextgarden.net
___
Re: [NTG-context] Filter module for R
On Mon, 15 Jun 2020, Aditya Mahajan wrote:
On Mon, 15 Jun 2020, Aditya Mahajan wrote:
On Sun, 14 Jun 2020, Fabrice L wrote:
Hi,
Following a question about the broken R module (R the statistical
software), Aditya suggested me the filter module (thanks to him). I’m
about to distribute a set of course notes to colleagues, and I need to
deal with details now. I have one problem and two questions.
1) the filter collect R code between \startR / \stopR and submit this code
to R. As it can be seen in the following minimal example, when a label
contains an accented character (« Fréquence » in my example), the pdf
graphic does not contains the « é ». Strangely, the snippet of code (which
is saved locally as « test2-temp-R-0.tmp » (for test2.tex)) when submitted
with the same command as the filtercommand, works correctly; that means
the same file works when submitted to R outside of ConTeXt. I have no idea
how to solve this.
Are you running the exact same command as the `filtercommand`. If so, I
don't know why running the `filtercommand` through context vs directly
typing it on the terminal should behave differently. The filter module
effectively just runs os.execute("filtercommand"). I don't use R so I am
unable to debug further.
I can reproduce this output side the filter module. If I directly run
os.execute(...) from a lua session, the output is correct but running it
through context gives the wrong output. I am guessing this is something to do
with locale. I notice that the output of os.execute("locale") from context is
different from that from my shell. But I don't know why locale should affect
UTF characters in R.
It is indeed related to locale. Here is a minimal example that works. I use a
beforebuffer to set the locale so that you don't have to do it in each snippet
and then filter out the first line in the typeset code listing and filter out
the first two lines in the output.
\usemodule[filter]
\usemodule[vim]
\definecolor [darkblue] [r=0.1, g=0.11, b=0.84]
\definecolor [darkgreen] [g=0.7]
\definecolor [lightblue] [h=87cefa]
\definecolor [lightgreen] [g=0.95,b=0.8,r=0.8]
\defineframedtext
[leftbartext]
[
width=local,
frame=off,
framecolor=darkblue,
leftframe=on,
rulethickness=1ex,
offset=0.25ex,
loffset=3ex,
background=color,
backgroundcolor=lightblue,
]
\definevimtyping
[RCODE]
[
vimcommand=nvim,
syntax=r,
directory=output,
strip=yes,
escape=yes,
before={\blank[quarterline]\startleftbartext},
after={\stopleftbartext},
]
\define[1]\ShowOutput
{\typeRCODEfile[start=2]{\externalfilterinputfile}
\startleftbartext[framecolor=darkgreen, backgroundcolor=lightgreen]
\setupalign[flushleft, verytolerant]
\typefile[range={3,-1}]{#1}
\stopleftbartext}
\startbuffer[locale]
Sys.setlocale(category="LC_ALL", locale="en_US.UTF-8")
\stopbuffer
\defineexternalfilter
[R]
[ filtercommand={R CMD BATCH -q --no-timing --save --restore
\externalfilterinputfile\space \externalfilteroutputfile},
output=\externalfilterbasefile.out,
directory=output,
readcommand=\ShowOutput,
read=no,
bufferbefore=locale,
cache=yes,
purge=yes,
]
\starttext
Some text...
\startR[read=yes]
pdf("RPlots/MyHistogram.pdf",5,5)
X <- rnorm(200,mean=10,sd=2)
hist(X, col = "red3" , xlab="Score QI" , main="", ylab="fréquence")
\stopR
\externalfigure[RPlots/MyHistogram.pdf][width=.5\textwidth]
\stoptext
Aditya___
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Wiki!
maillist : ntg-context@ntg.nl / http://www.ntg.nl/mailman/listinfo/ntg-context
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archive : https://bitbucket.org/phg/context-mirror/commits/
wiki : http://contextgarden.net
___
Re: [NTG-context] Filter module for R
On Mon, 15 Jun 2020, Aditya Mahajan wrote:
On Sun, 14 Jun 2020, Fabrice L wrote:
Hi,
Following a question about the broken R module (R the statistical
software), Aditya suggested me the filter module (thanks to him). I’m about
to distribute a set of course notes to colleagues, and I need to deal with
details now. I have one problem and two questions.
1) the filter collect R code between \startR / \stopR and submit this code
to R. As it can be seen in the following minimal example, when a label
contains an accented character (« Fréquence » in my example), the pdf
graphic does not contains the « é ». Strangely, the snippet of code (which
is saved locally as « test2-temp-R-0.tmp » (for test2.tex)) when submitted
with the same command as the filtercommand, works correctly; that means the
same file works when submitted to R outside of ConTeXt. I have no idea how
to solve this.
Are you running the exact same command as the `filtercommand`. If so, I don't
know why running the `filtercommand` through context vs directly typing it on
the terminal should behave differently. The filter module effectively just
runs os.execute("filtercommand"). I don't use R so I am unable to debug
further.
I can reproduce this output side the filter module. If I directly run os.execute(...)
from a lua session, the output is correct but running it through context gives the wrong
output. I am guessing this is something to do with locale. I notice that the output of
os.execute("locale") from context is different from that from my shell. But I
don't know why locale should affect UTF characters in R. Perhaps someone with more
knowledge of R can comment on that.
\starttext
\startluacode
lfs.mkdir("output/")
\stopluacode
\startbuffer[code]
pdf("output/MyHistogram.pdf",5,5)
X <- rnorm(200,mean=10,sd=2)
hist(X, col = "red3" , xlab="Score QI" , main="", ylab="fréquence")
\stopbuffer
\savebuffer[prefix=no, list=code, file={output/code.r}]
\startluacode
print("", "RUNNING R CMD")
os.execute("R CMD BATCH --no-timing --save --restore output/code.r
output/out")
\stopluacode
\externalfigure[RPlots/MyHistogram.pdf][width=.5\textwidth]
\stoptext
Aditya___
If your question is of interest to others as well, please add an entry to the
Wiki!
maillist : ntg-context@ntg.nl / http://www.ntg.nl/mailman/listinfo/ntg-context
webpage : http://www.pragma-ade.nl / http://context.aanhet.net
archive : https://bitbucket.org/phg/context-mirror/commits/
wiki : http://contextgarden.net
___
Re: [NTG-context] Filter module for R
On Sun, 14 Jun 2020, Fabrice L wrote:
Hi,
Following a question about the broken R module (R the statistical software),
Aditya suggested me the filter module (thanks to him). I’m about to distribute
a set of course notes to colleagues, and I need to deal with details now. I
have one problem and two questions.
1) the filter collect R code between \startR / \stopR and submit this code to
R. As it can be seen in the following minimal example, when a label contains an
accented character (« Fréquence » in my example), the pdf graphic does not
contains the « é ». Strangely, the snippet of code (which is saved locally as «
test2-temp-R-0.tmp » (for test2.tex)) when submitted with the same command as
the filtercommand, works correctly; that means the same file works when
submitted to R outside of ConTeXt. I have no idea how to solve this.
Are you running the exact same command as the `filtercommand`. If so, I don't know why
running the `filtercommand` through context vs directly typing it on the terminal should
behave differently. The filter module effectively just runs
os.execute("filtercommand"). I don't use R so I am unable to debug further.
2) In a teaching context, we may want sometimes to show the code. The filter
module actually permits to show the output of the code submitted to R (which
can include or not the input commands); would it be possible to typeset the
submitted code ?
This is an adapted version of the code that I use for my course where I use the
vim module to do the typesetting:
\usemodule[filter]
\usemodule[vim]
\definecolor [darkblue] [r=0.1, g=0.11, b=0.84]
\definecolor [darkgreen] [g=0.7]
\definecolor [lightblue] [h=87cefa]
\definecolor [lightgreen] [g=0.95,b=0.8,r=0.8]
\defineframedtext
[leftbartext]
[
width=local,
frame=off,
framecolor=darkblue,
leftframe=on,
rulethickness=1ex,
offset=0.25ex,
loffset=3ex,
background=color,
backgroundcolor=lightblue,
]
\definevimtyping
[RCODE]
[
syntax=r,
directory=output,
strip=yes,
escape=yes,
before={\blank[quarterline]\startleftbartext},
after={\stopleftbartext},
]
\define[1]\ShowOutput
{\typeRCODEfile{\externalfilterinputfile}
\startleftbartext[framecolor=darkgreen, backgroundcolor=lightgreen]
\setupalign[flushleft, verytolerant]
% range={1,-1} not currently supported
% See below for details
\typefile[range={1,-1}]{#1}
\stopleftbartext}
\defineexternalfilter
[R]
[ filtercommand={R CMD BATCH -q --no-timing --save --restore
\externalfilterinputfile\space \externalfilteroutputfile},
output=\externalfilterbasefile.out,
directory=output,
readcommand=\ShowOutput,
read=no,
cache=yes,
purge=yes, % THE COMMA WAS MISSING
]
\starttext
Some text...
\startR[read=yes]
pdf("RPlots/MyHistogram.pdf",5,5)
X <- rnorm(200,mean=10,sd=2)
hist(X, col = "red3" , xlab="Score QI" , main="", ylab="fréquence")
\stopR
\externalfigure[RPlots/MyHistogram.pdf][width=.5\textwidth]
\stoptext
3) Finally, using "R CMD BATCH… » as the filtercommand add an extra line at the
end of the output file which can be typeset to visualize results. Would it be
possible by a magic trick to deleter the last line of the file ?
It is possible to filter lines using `\typefile[range={start,
stop}]{filename}`. You can use `range={1,3}` to only include lines 1 upto 3 or
`range={1, +2}` to include line 1 followed by 2 lines. What you want is
something like `range={1,-1}`, i.e., include from the first to last-1 line, but
this is not currently supported. You could ask Hans to do so, as it is
relatively simple to add. Of course, you will then need to document this on the
wiki.
Aditya___
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Wiki!
maillist : ntg-context@ntg.nl / http://www.ntg.nl/mailman/listinfo/ntg-context
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archive : https://bitbucket.org/phg/context-mirror/commits/
wiki : http://contextgarden.net
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[NTG-context] Filter module for R
Hi,Following a question about the broken R module (R the statistical software), Aditya suggested me the filter module (thanks to him). I’m about to distribute a set of course notes to colleagues, and I need to deal with details now. I have one problem and two questions.1) the filter collect R code between \startR / \stopR and submit this code to R. As it can be seen in the following minimal example, when a label contains an accented character (« Fréquence » in my example), the pdf graphic does not contains the « é ». Strangely, the snippet of code (which is saved locally as « test2-temp-R-0.tmp » (for test2.tex)) when submitted with the same command as the filtercommand, works correctly; that means the same file works when submitted to R outside of ConTeXt. I have no idea how to solve this. 2) In a teaching context, we may want sometimes to show the code. The filter module actually permits to show the output of the code submitted to R (which can include or not the input commands); would it be possible to typeset the submitted code ?3) Finally, using "R CMD BATCH… » as the filtercommand add an extra line at the end of the output file which can be typeset to visualize results. Would it be possible by a magic trick to deleter the last line of the file ?Here is a minimal code:% —\usemodule[filter]\defineexternalfilter [R] [ filtercommand={R CMD BATCH -q --no-timing --save --restore \externalfilterinputfile\space \externalfilteroutputfile}, output=\externalfilterbasefile.out, directory=output, readcommand=\typefile, read=no, cache=yes, purge=yes ]\starttextSome text...\startR[read=yes] pdf("RPlots/MyHistogram.pdf",5,5) X <- rnorm(200,mean=10,sd=2) hist(X, col = "red3" , xlab="Score QI" , main="", ylab="fréquence")\stopR\externalfigure[MyHistogram.pdf][width=.5\textwidth] \stoptext% —Sorry for the three questions… and thanks for any help.Fabrice.
MyHistogram.pdf
Description: Adobe PDF document
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Wiki!
maillist : ntg-context@ntg.nl / http://www.ntg.nl/mailman/listinfo/ntg-context
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archive : https://bitbucket.org/phg/context-mirror/commits/
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