R - OpenCPU

xholonWorkbook.xml

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<!--Xholon Workbook http://www.primordion.com/Xholon/gwt/ MIT License, Copyright (C) Ken Webb, Sun Dec 30 2018 07:50:41 GMT-0500 (Eastern Standard Time)-->
<XholonWorkbook>

<Notes><![CDATA[
Xholon
------
Title: R - OpenCPU
Description: 
Url: http://www.primordion.com/Xholon/gwt/
InternalName: 934af431ea402100efa07206751e8dbb
Keywords: 

My Notes
--------
December 28, 2018

Use XholonOpenCpuR.html, for example:
http://127.0.0.1:8888/XholonOpenCpuR.html?app=HelloWorld&gui=clsc

http://127.0.0.1:8888/XholonOpenCpuR.html?app=R%20-%20OpenCPU&src=lstr&gui=clsc

Chrome Dev Apps
---------------
ocpu.seturl("http://localhost:5656/ocpu/library/stats/R"); // this works
result:
------
Setting path to CORS server http://localhost:5656/ocpu/library/stats/R
undefined
opencpu-0.5.js:402 Path updated. Available objects/functions:
acf
acf2AR
add1
...

test (I did this after the above ocpu.seturl(...) )
----
var mydata = [1,2,3,4,5,6,7,8,9,10,11,12,13,14,15];
//call R function: stats::sd(x=data)
var req = ocpu.rpc("sd",{
  x : mydata
}, function(output){
  alert("Standard Deviation equals: " + output);
});
//optional
req.fail(function(){
  alert("R returned an error: " + req.responseText);
});
result (alert):
------
Standard Deviation equals: 4.4721

TODO
----
(1) OK run just R rather than RStudio (the following works, from a Ubuntu terminal):
R
 library(opencpu)
 ocpu_start_app("rwebapps/appdemo")
then:
http://127.0.0.1:8888/XholonOpenCpuR.html?app=R%20-%20OpenCPU&src=lstr&gui=clsc
http://localhost:5656/ocpu/apps/rwebapps/appdemo/www/plot.html
http://localhost:5656/ocpu/apps/rwebapps/appdemo/www/hello.html
http://localhost:5656/ocpu/tmp/x065cad66e63d78/graphics/last/svg?width=11.69&height=8.27

(2) write an opencpu app
(3) OK add jquery and opencpu JS libraries to Xholon public/lib
(4) write R/RStudio functions


References
----------
(1) https://www.opencpu.org
    OpenCPU is a system for embedded scientific computing and reproducible research.
    The OpenCPU server provides a reliable and interoperable HTTP API for data analysis based on R.
    You can either use the public servers or host your own.

    Seamless R and JavaScript Integration
    The OpenCPU JavaScript client library provides the most seamless integration of R and JavaScript available today.
    Enjoy simple RPC and data I/O through standard Ajax techniques.
    Check for yourself by trying the jsfiddle examples.

(2) https://www.opencpu.org/download.html
    #Local Single-User Server (do this in R)
    # Install OpenCPU
    install.packages("opencpu")
    # Run Apps directly from Github
    library(opencpu)
    ocpu_start_app("rwebapps/nabel")
    ocpu_start_app("rwebapps/markdownapp")
    ocpu_start_app("rwebapps/stockapp")
    ocpu_start_app("rwebapps/appdemo")

(3) https://www.opencpu.org/jslib.html

(4) https://github.com/rwebapps/appdemo

(5) http://adv-r.had.co.nz/
    Advanced R by Hadley Wickham

(6) http://r-pkgs.had.co.nz/
    R packages by Hadley Wickham

(7) http://r4ds.had.co.nz/
    R for Data Science: Import, Tidy, Transform, Visualize, and Model Data, by Hadley Wickham and Garrett Grolemund

(8) http://had.co.nz/ggplot2/

(9) https://github.com/hadley/

(10) https://support.rstudio.com/hc/en-us/articles/115010915687
    Using RStudio Connections
   ) https://db.rstudio.com/
   ) https://db.rstudio.com/rstudio/connections/
   ) https://db.rstudio.com/best-practices/drivers/
    Setting up ODBC Drivers
    includes info on "Linux Debian / Ubuntu"
     sudo apt-get update
     sudo apt-get install unixodbc unixodbc-dev --install-suggests
     sudo apt-get install odbc-postgresql
     and then read rest of instructions
      edit 2 text files that are in /etc

]]></Notes> 

<_-.XholonClass>
  <PhysicalSystem/>
  <OpenCpuTest01/>
  <OpenCpuTest02/>
  
</_-.XholonClass>

<xholonClassDetails>
  
</xholonClassDetails>

<PhysicalSystem>
  <OpenCpuTest01/>
  <OpenCpuTest02/>
</PhysicalSystem>

<OpenCpuTest01behavior implName="org.primordion.xholon.base.Behavior_gwtjs"><![CDATA[
var me, beh = {
postConfigure: function() {
  me = this.cnode.parent();
  $wnd.ocpu.seturl("http://localhost:5656/ocpu/library/stats/R");
},
act: function() {
  var mydata = [1,2,3,4,5,6,7,8,9,10,11,12,13,14,15];
  //call R function: stats::sd(x=data)
  var req = $wnd.ocpu.rpc("sd",{
    x : mydata
  }, function(output){
    me.println("Standard Deviation equals: " + output); // result: Standard Deviation equals: 4.4721
  });
  //optional
  req.fail(function(){
    me.println("R returned an error: " + req.responseText);
  });
}
// result in RStudio R console:
//[2018-12-28 10:07:34] OPTIONS /ocpu/library/stats/R/sd
//[2018-12-28 10:07:34] POST /ocpu/library/stats/R/sd
//[2018-12-28 10:07:34] GET /ocpu/tmp/x0c010c1652adb6/R/.val/json
}
//# sourceURL=OpenCpuTest01behavior.js
]]></OpenCpuTest01behavior>

<OpenCpuTest02behavior implName="org.primordion.xholon.base.Behavior_gwtjs"><![CDATA[
var me, beh = {
postConfigure: function() {
  me = this.cnode.parent();
  //$wnd.ocpu.seturl("http://localhost:5656/ocpu/library/stats/R");
},
act: function() {
  var req = $wnd.ocpu.call("rnorm", {n: 100}, function(session){
    me.println(session.getKey());
    me.println(session.getLoc());
    //retrieve session console (stdout) async
    session.getConsole(function(outtxt) {
      $wnd.console.log(session);
      me.println(outtxt);
    });
    //retrieve the returned object async; the following code does nothing ?
    session.getObject(function(data) {
      $wnd.console.log(data);
      //data is the object returned by the R function
      //alert("Array of length " + data.length + ".\nFirst few values:" + data.slice(0,3));
      me.println("Array of length " + data.length + ".\nFirst few values:" + data.slice(0,3));
    });
  }).fail(function(){
    me.println("OpenCpuTest02behavior R returned an error: " + req.responseText);
  });
}
}
//# sourceURL=OpenCpuTest02behavior.js
]]></OpenCpuTest02behavior>

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<svg width="100" height="50" xmlns="http://www.w3.org/2000/svg">
  <g>
    <title>OpenCpuTest01</title>
    <rect id="PhysicalSystem/OpenCpuTest01" fill="#98FB98" height="50" width="50" x="25" y="0"/>
    <g>
      <title>OpenCpuTest01behavior</title>
      <rect id="PhysicalSystem/OpenCpuTest01/OpenCpuTest01behavior" fill="#6AB06A" height="50" width="10" x="80" y="0"/>
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