Can anyone connect context to R or python?

Can anyone connect context to R or python?

[Kelley, Claire]

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Hi All,
I am very interested in creating pdf documents using Context with calculations done in R or Python and then added into the document.

If you were using traditional latex this could be accomplished through R markdown or Sweave- is there any way to connect these to Context?

Best,
Claire

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Re: Can anyone connect context to R or python?

[Henning Hraban Ramm]

Am 2018-10-05 um 16:55 schrieb Kelley, Claire <ckelley@air.org>:

> Hi All, 
> I am very interested in creating pdf documents using Context with calculations done in R or Python and then added into the document. 
> 
> If you were using traditional latex this could be accomplished through R markdown or Sweave- is there any way to connect these to Context? 

Hi Claire,

you should use Aditya’s filter module to call external programs:
https://github.com/adityam/filter

There’s a module for R in the distribution (see https://source.contextgarden.net/tex/context/modules/mkii/m-r.mkii), but it’s only for MkII and AFAIK superseded by the filter module.

Greetlings, Hraban
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Re: Can anyone connect context to R or python?

[Pablo Rodriguez]

On 10/5/18 4:55 PM, Kelley, Claire wrote:
> Hi All, 
> I am very interested in creating pdf documents using Context with
> calculations done in R or Python and then added into the document. 

Hi Claire,

ConTeXt MkIV comes with Lua inside.

Would Lua fit your purposes?

> If you were using traditional latex this could be accomplished through R
> markdown or Sweave- is there any way to connect these to Context? 

I’m afraid that my background is in humanities. If you need R, I wonder
whether this can be easily done with ConTeXt.

Just in case it helps,

Pablo
-- 
http://www.ousia.tk
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Re: Can anyone connect context to R or python?

[Kelley, Claire]

Thank you for all the answers so far !



Ive gathered from that I need to use filter to call R externally.

 What I am still most interested in is how I could get a single value from R to be part of the Context code. (Like you would do with \Sexpr{} in sweave. The use case for this is that I have some complicated tikz code that makes a fancy matrix - I want to fill it in with numbers that r reads from a csv file and processes. 
 

On 10/5/18, 1:48 PM, "ntg-context on behalf of Pablo Rodriguez" <ntg-context-bounces@ntg.nl on behalf of oinos@gmx.es> wrote:

>Lua
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Re: Can anyone connect context to R or python?

[Hans Hagen]

On 10/5/2018 8:00 PM, Kelley, Claire wrote:
> Thank you for all the answers so far !
> 
> 
> 
> Ive gathered from that I need to use filter to call R externally.
> 
>   What I am still most interested in is how I could get a single value from R to be part of the Context code. (Like you would do with \Sexpr{} in sweave. The use case for this is that I have some complicated tikz code that makes a fancy matrix - I want to fill it in with numbers that r reads from a csv file and processes.
Can you give an example? Do you only need R for reading the csv?

Hans ntg-context@ntg.nl


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Re: Can anyone connect context to R or python?

[Alan Braslau]

On Fri, 5 Oct 2018 20:07:27 +0200
Hans Hagen <j.hagen@xs4all.nl> wrote:

> > I want to fill it in with numbers that r reads from a csv file and processes.  
> Can you give an example? Do you only need R for reading the csv?

The processing is done by R.

Of course, it *could* be done in Lua, but this all depends on what processing is needed, for R contains many libraries of routines (but so *can* lua).


For the list, this discussion between Hans and myself follows a presentation that I made at the last ConTeXt Meeting regarding handling large data files in lua (+MetaPost). We are presently working on an article for the Context Journal to document this.

Alan

P.S. Lua is rather magical...
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Re: Can anyone connect context to R or python?

[Kelley, Claire]

Again thank you everyone for their incredibly helpful advice and responsiveness! 

The work flow I am envisioning is: 

1) Use R to read in a csv file, filter according to some rules and then use propensity score matching (based on r packages) to create a model. 
2) The final data output is a table with standardize coefficients and mean values. 
3) This final data output is then used to create a table using Context/ Tikz to create the very specific format that I need for the final report. 
 
I can do this using Sweave, but I need to be able to  use context for some additional features (in particular the tagging/back end structure). 

Best, 
Claire 




On 10/5/18, 2:07 PM, "Hans Hagen" <j.hagen@xs4all.nl> wrote:

>On 10/5/2018 8:00 PM, Kelley, Claire wrote:
>> Thank you for all the answers so far !
>> 
>> 
>> 
>> Ive gathered from that I need to use filter to call R externally.
>> 
>>   What I am still most interested in is how I could get a single value from R to be part of the Context code. (Like you would do with \Sexpr{} in sweave. The use case for this is that I have some complicated tikz code that makes a fancy matrix - I want to fill it in with numbers that r reads from a csv file and processes.
>Can you give an example? Do you only need R for reading the csv?
>
>Hans ntg-context@ntg.nl
>
>
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>               Ridderstraat 27 | 8061 GH Hasselt | The Netherlands
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>
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Re: Can anyone connect context to R or python?

[Aditya Mahajan]

On Sat, 6 Oct 2018, Kelley, Claire wrote:

> Again thank you everyone for their incredibly helpful advice and responsiveness!
>
> The work flow I am envisioning is:
>
> 1) Use R to read in a csv file, filter according to some rules and then use propensity score matching (based on r packages) to create a model.
> 2) The final data output is a table with standardize coefficients and mean values.
> 3) This final data output is then used to create a table using Context/ Tikz to create the very specific format that I need for the final report.

Is the final post-processed data a table that can be saved to a CSV file? 
If so, the simplest solution will be to write R code (inside a \startR ... 
\stopR environment) that does the post-processing and saves the data as a 
CSV file.

Both ConTeXt and TikZ can easily read CSV table and format as desired.

---

I also want to take this opportunity to express my views on intefacing 
with external programs. The file based interaction provided by the filter 
module is okay for small projects but it is not ideal. Slightly better is 
to use pipes (popen to a REPL) or use FFI 
(e.g https://adityam.github.io/context-blog/post/interfacing-with-julia), 
but neither of these is easy to implement and needs to be done on a 
per-language basis. Henri Menke had a Tugboat article on this as well.

In my opinion, a better long-term option is to write a jupyter client in 
lua that can be called by context. Then we can easily interface with all 
languages that provide a jupyter kernel 
(https://github.com/jupyter/jupyter/wiki/Jupyter-kernels).

The interface of a jupter-client is available here
https://jupyter-client.readthedocs.io/en/stable/index.html. It seems 
relatively straight forward (send a JSON message and receive a JSON 
message). Translating the JSON messages to ConTeXt should also be easy. 
Is there anyone who wants to play around trying to implement this?

Aditya
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Re: Can anyone connect context to R or python?

[Kelley, Claire]

I also just got an incredibly helpful answer over on stack overflow : https://tex.stackexchange.com/questions/453868/how-can-i-use-context-and-r-together
Which shows how to use Lua and filter together 
Claire 



On 10/6/18, 1:06 PM, "ntg-context on behalf of Aditya Mahajan" <ntg-context-bounces@ntg.nl on behalf of adityam@umich.edu> wrote:

>On Sat, 6 Oct 2018, Kelley, Claire wrote:
>
>> Again thank you everyone for their incredibly helpful advice and responsiveness!
>>
>> The work flow I am envisioning is:
>>
>> 1) Use R to read in a csv file, filter according to some rules and then use propensity score matching (based on r packages) to create a model.
>> 2) The final data output is a table with standardize coefficients and mean values.
>> 3) This final data output is then used to create a table using Context/ Tikz to create the very specific format that I need for the final report.
>
>Is the final post-processed data a table that can be saved to a CSV file? 
>If so, the simplest solution will be to write R code (inside a \startR ... 
>\stopR environment) that does the post-processing and saves the data as a 
>CSV file.
>
>Both ConTeXt and TikZ can easily read CSV table and format as desired.
>
>---
>
>I also want to take this opportunity to express my views on intefacing 
>with external programs. The file based interaction provided by the filter 
>module is okay for small projects but it is not ideal. Slightly better is 
>to use pipes (popen to a REPL) or use FFI 
>(e.g https://adityam.github.io/context-blog/post/interfacing-with-julia), 
>but neither of these is easy to implement and needs to be done on a 
>per-language basis. Henri Menke had a Tugboat article on this as well.
>
>In my opinion, a better long-term option is to write a jupyter client in 
>lua that can be called by context. Then we can easily interface with all 
>languages that provide a jupyter kernel 
>(https://github.com/jupyter/jupyter/wiki/Jupyter-kernels).
>
>The interface of a jupter-client is available here
>https://jupyter-client.readthedocs.io/en/stable/index.html. It seems 
>relatively straight forward (send a JSON message and receive a JSON 
>message). Translating the JSON messages to ConTeXt should also be easy. 
>Is there anyone who wants to play around trying to implement this?
>
>Aditya
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>If your question is of interest to others as well, please add an entry to the Wiki!
>
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Re: Can anyone connect context to R or python?

[Wolfgang Schuster]

Aditya Mahajan schrieb am 06.10.18 um 19:06:
> The interface of a jupter-client is available here
> https://jupyter-client.readthedocs.io/en/stable/index.html. It seems 
> relatively straight forward (send a JSON message and receive a JSON 
> message). Translating the JSON messages to ConTeXt should also be 
> easy. Is there anyone who wants to play around trying to implement this?

ConTeXt can read JSON files, see util-jsn.lua

Wolfgang
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Re: Can anyone connect context to R or python?

[Alan Braslau]

On Sat, 6 Oct 2018 13:06:18 -0400 (EDT)
Aditya Mahajan <adityam@umich.edu> wrote:

> In my opinion, a better long-term option is to write a jupyter client in 
> lua that can be called by context. Then we can easily interface with all 
> languages that provide a jupyter kernel 
> (https://github.com/jupyter/jupyter/wiki/Jupyter-kernels).
> 
> The interface of a jupter-client is available here
> https://jupyter-client.readthedocs.io/en/stable/index.html. It seems 
> relatively straight forward (send a JSON message and receive a JSON 
> message). Translating the JSON messages to ConTeXt should also be easy. 
> Is there anyone who wants to play around trying to implement this?

jupyter runs python code. Have you ever tried doing any real heavy data analysis using jupyter? My experience is that it chokes on large data sets... So why write lua code to call a jupyter kernel running python? Would it not make more sense developing code directly in lua in this case?

The one thing that python (and jupyter) brings, or R for that matter, are libraries of calculation routines. These can be quite sophisticated, some efficient, and some not so efficient. My approach has always been to write my own routines or to adapt algorithms, at least then I know what the calculation is actually doing. Of course, this means that I spend time redoing what might have been done elsewhere, but the variety of routines that I actually use is rather small.

Our experimentation with lua and with MetaPost is that one can achieve HUGE differences in efficiencies through efficient programming, factors of 2-3 or even orders of magnitude. (Hans can usually succeed in speeding-up my lua code.) Sometimes surprising things can make huge differences (never surprising once one understands what is happening). One can hope that python and R (and other) developers are efficient-minded programmers, but this is not always the case.

Alan
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Re: Can anyone connect context to R or python?

[Aditya Mahajan]

On Sat, 6 Oct 2018, Alan Braslau wrote:

> On Sat, 6 Oct 2018 13:06:18 -0400 (EDT)
> Aditya Mahajan <adityam@umich.edu> wrote:
>
>> In my opinion, a better long-term option is to write a jupyter client in
>> lua that can be called by context. Then we can easily interface with all
>> languages that provide a jupyter kernel
>> (https://github.com/jupyter/jupyter/wiki/Jupyter-kernels).
>>
>> The interface of a jupter-client is available here
>> https://jupyter-client.readthedocs.io/en/stable/index.html. It seems
>> relatively straight forward (send a JSON message and receive a JSON
>> message). Translating the JSON messages to ConTeXt should also be easy.
>> Is there anyone who wants to play around trying to implement this?
>
> jupyter runs python code.
>
> Have you ever tried doing any real heavy data analysis using jupyter? My 
> experience is that it chokes on large data sets... So why write lua code 
> to call a jupyter kernel running python?

That's why I want to write a jupyter client in lua (so that there is no 
python code involved).

> Would it not make more sense developing code directly in lua in this 
> case?

Yes, but let me try to explain. When creating homework assignments for a
course I teach, I often have documents as follows:

     \starttext
     Consider an LTI system with the transfer function
     \placefigure[eq:sys] \startformula
       H(s) = \frac{1}{s^2 + 2s + 2}
     \stopformula
     The step response of the system is shown in Figure \in[fig:plot]. Note
     that the step response settles to a final value of $0.5$
     \startplacefigure
       [title={Step response of the LTI system described in \eqref[eq:sys]}]
       \externalfigure[step-response.pdf]
     \stopplacefigure
     \stoptext

What I want to do is to be able to change the transfer function (given in the
formula) and regenerate the plot. Something like the following:

     \defineLTIsystem[example][num={1}, den={1,2,2}]

     \starttext
     Consider an LTI system with the transfer function
     \placefigure[eq:sys] \startformula
       H(s) = \TF[example]
     \stopformula
     The step response of the system is shown in Figure \in[fig:plot]. Note
     that the step response settles to a final value of
     $\calculate{lim(s*TF[example], s, 0)}$.
     \startplacefigure
       [title={Step response of the LTI system described in \eqref[eq:sys]}]
       \STEP[example]
     \stopplacefigure
     \stoptext

Now, it is possible to write the code to generate the step response in
Lua/Metapost. But it quickly gets tiring and one essentially ends up creating
a domain specific computational library in Lua.

An alternative approach, is to use an existing library written in some other
programming language (say Matlab or R or Julia or whatever). It is possible to
do so using the `filter` module (plus some lua code). In this case, the user
simply calls "context filename" and ConTeXt macros take care of calling an
external program (say matlab) to generate the plot and do the algebraic
calculations.

Another approach which is taken by programs like Sweave and Knitr is to first
run the program through R (or someother programming language). These are
typically written for LaTeX. So code that is between \begin{Rcode} ..
\end{Rcode} and \Rexp{...} (or something similar, haven't used R in a decade)
is treated as R code and everything else is treated as comments. The evaluated
file can then be run through `latex` or `context` or any typesetting program.
The drawback of this approach is that not all programming languages have such
a program.

Now, what I want to do (at some stage) is to extend the functionality of the
filter module to call jupyter kernels. So, instead of passing messages between
context and the external program through text files, the messages can be
passed as JSON objects (using sockets, I believe). The advantage is that you
avoid multiple restarts of the external program (which is what the filter
module currently does).

> The one thing that python (and jupyter) brings, or R for that matter, 
> are libraries of calculation routines. These can be quite sophisticated, 
> some efficient, and some not so efficient. My approach has always been 
> to write my own routines or to adapt algorithms, at least then I know 
> what the calculation is actually doing. Of course, this means that I 
> spend time redoing what might have been done elsewhere, but the variety 
> of routines that I actually use is rather small.

If you have the time (and the expertise) then this is a good strategy. For me,
this is not always the case.

Aditya
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Re: Can anyone connect context to R or python?

[Hans Hagen]

On 10/6/2018 10:19 PM, Aditya Mahajan wrote:

> Now, what I want to do (at some stage) is to extend the functionality of 
> the
> filter module to call jupyter kernels. So, instead of passing messages 
> between
> context and the external program through text files, the messages can be
> passed as JSON objects (using sockets, I believe). The advantage is that 
> you
> avoid multiple restarts of the external program (which is what the filter
> module currently does).
but that assumes that the listener is not restarting the a program (i.e. 
that e.g. r is listening and sending, right?

Hans

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Re: Can anyone connect context to R or python?

[Stanislav Sokolenko]

On 2018-10-06 02:06 PM, Aditya Mahajan wrote:

>
> I also want to take this opportunity to express my views on intefacing 
> with external programs. The file based interaction provided by the 
> filter module is okay for small projects but it is not ideal. Slightly 
> better is to use pipes (popen to a REPL) or use FFI (e.g 
> https://adityam.github.io/context-blog/post/interfacing-with-julia), 
> but neither of these is easy to implement and needs to be done on a 
> per-language basis. Henri Menke had a Tugboat article on this as well.
>
> In my opinion, a better long-term option is to write a jupyter client 
> in lua that can be called by context. Then we can easily interface 
> with all languages that provide a jupyter kernel 
> (https://github.com/jupyter/jupyter/wiki/Jupyter-kernels).
>
> The interface of a jupter-client is available here
> https://jupyter-client.readthedocs.io/en/stable/index.html. It seems 
> relatively straight forward (send a JSON message and receive a JSON 
> message). Translating the JSON messages to ConTeXt should also be 
> easy. Is there anyone who wants to play around trying to implement this?
>

I have recently come across the SciLua project 
(http://scilua.org/index.html) which has a built-in LuaJIT client for 
Rserve (http://scilua.org/rclient.html) and may be relevant to the 
discussion. Although it certainly isn't as general as something like 
jupyter, leaning on SciLua may be an easier means of getting access to 
scientific computation with R and basic numerical methods. I am 
personally planning to look into switching from filter to SciLua if it 
means that I can get more efficient data transfer between R and ConTeXt. 
But I'm a ConTeXt and Lua neophyte so I doubt my personal efforts will 
be translatable into something more general like a module.

Stan

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Re: Can anyone connect context to R or python?

[Alan Braslau]

On Mon, 8 Oct 2018 15:58:25 -0300
Stanislav Sokolenko <stanislav@sokolenko.net> wrote:

> I have recently come across the SciLua project 
> (http://scilua.org/index.html) which has a built-in LuaJIT client for 
> Rserve (http://scilua.org/rclient.html) and may be relevant to the 
> discussion. Although it certainly isn't as general as something like 
> jupyter, leaning on SciLua may be an easier means of getting access to 
> scientific computation with R and basic numerical methods. I am 
> personally planning to look into switching from filter to SciLua if it 
> means that I can get more efficient data transfer between R and ConTeXt. 
> But I'm a ConTeXt and Lua neophyte so I doubt my personal efforts will 
> be translatable into something more general like a module.
> 
> Stan

With some work, the scilua routines (which depend on OpenBLAS) could probably be made to work as a module under luatex with no need for an external client.

Alan
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webpage  : http://www.pragma-ade.nl / http://context.aanhet.net
archive  : https://bitbucket.org/phg/context-mirror/commits/
wiki     : http://contextgarden.net
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