From morkus at protonmail.com  Sat Oct 28 13:12:54 2017
From: morkus at protonmail.com (Morkus)
Date: Sat, 28 Oct 2017 07:12:54 -0400
Subject: [Rd] Cannot Compute Box's M (Three Days Trying...)
In-Reply-To: <abfb1feb-1da9-8c88-ceb5-98cef28ef406@gmail.com>
References: <yNSrSEBSEthk1cJc2W6y3M50LXPWIRpFNyUtLE8yIZMb4guTLWuQi9XjWd4MHnt5vxOZAK1bO32QWqqM26bRU_XpiYnip5jDiyjKWUKIH7w=@protonmail.com>
 <3e5b4dc9-1b9a-4c63-a929-82a127856dbe@gmail.com>
 <P6V3IIqCfJ4SUFtNl9ML3Wmo2cvnL50vlzlUJdvRaAj106MjIojw5ITRt5ZQdkeOa9rnyS6HTxRgg7SUwmPY4CqGPbQFWqYEKCTr_yDVZdM=@protonmail.com>
 <abfb1feb-1da9-8c88-ceb5-98cef28ef406@gmail.com>
Message-ID: <rl0BFmHLQl4yweaOtoWaJJEScu0VetftcUuusTtgU1qjAdU-8pgrnohMfnzvJQZTY2jPjjraq6xgDDAlxfHHZunKbfGydZILJQ8xk4g0IWc=@protonmail.com>

Thanks Duncan. Awesome ideas!

I think we're getting closer!

I tried what you suggested and got a possibly better error...
.
.
.
rConnection.assign("boxMVariable", myDf);

String resultBV = "str(boxMVariable)";   // your suggestion.

RESULTING ERROR:

Error in format.default(nam.ob, width = max(ncn), justify = "left") :  invalid 'width' argument

(No idea what this means).

For testing, I'm using the same standard IRIS dataset as the Box's M documentation shows in biotools:

Examples

data(iris)

boxM(iris[, -5], iris[, 5])

-------

Now, in the debugger, the built values of myDf are these:

myDf = {org.rosuda.REngine.REXPGenericVector at 562} "org.rosuda.REngine.REXPGenericVector at 17d99928+[5]?


? payload = {org.rosuda.REngine.RList at 566} size = 5
? 0 = {org.rosuda.REngine.REXPDouble at 570} "org.rosuda.REngine.REXPDouble at 6fffcba5[150]"
? 1 = {org.rosuda.REngine.REXPDouble at 571} "org.rosuda.REngine.REXPDouble at 34340fab[150]?
? 2 = {org.rosuda.REngine.REXPDouble at 572} "org.rosuda.REngine.REXPDouble at 2aafb23c[150]"
? 3 = {org.rosuda.REngine.REXPDouble at 573} "org.rosuda.REngine.REXPDouble at 2b80d80f[150]?
? 4 = {org.rosuda.REngine.REXPString at 574} "org.rosuda.REngine.REXPString at 3ab39c39[150]?

Does this help?

Please let me know what else I can try.

Thanks,

Sent from [ProtonMail](https://protonmail.com), Swiss-based encrypted email.

> -------- Original Message --------
> Subject: Re: [Rd] Cannot Compute Box's M (Three Days Trying...)
> Local Time: October 28, 2017 6:48 AM
> UTC Time: October 28, 2017 10:48 AM
> From: murdoch.duncan at gmail.com
> To: Morkus <morkus at protonmail.com>
> r-devel at r-project.org <r-devel at r-project.org>
>
> On 28/10/2017 6:26 AM, Morkus wrote:
>
>> I'm not sure what you mean. Could you please be more specific?
>>
>> You were trying to eval an expression that you constructed in Java. I
>> was suggesting that before you eval it, you print it.
>> If I print the string, I get: boxM(boxMVariable[, -5], boxMVariable[, 5])
>>
>> Right, that's what I was suggesting you do. Now you've fixed the syntax
>> error, that looks okay.
>>
>> If I'm reading these messages in the right order, your latest error is
>>
>> Error in [.data.frame(boxMVariable, , -5) : undefined columns selected
>>
>> The expression there is a funny way of printing boxMVariable[,-5]. So
>> now you need to figure out why it thinks you've selected undefined
>> columns. This is a little perplexing, because you're asking for all
>> columns except column 5, and that works whether or not you have a column
>
> -
>
> So I'd guess there's something weird about boxMVariable. You should ask
> R to print it, and to print str(boxMVariable), to make sure it's a
> regular dataframe containing 4 numeric columns and one factor or
> character column.
>
> Duncan Murdoch
>
>> From this code:
>> .
>> .
>> .
>> /// assign the data to a variable.
>> /rConnection.assign("boxMVariable", myDf);
>> /// create a string command with that variable name.
>> /String boxVariable = "boxM(boxMVariable[, -5], boxMVariable[, 5])";
>> System./out/.println(boxVariable);  // print the string? Not sure
>> what is meant.
>> Sorry if I didn't understand your suggestion.
>> Look forward to hearing back from you.
>> Thanks,
>> Sent from ProtonMail https://protonmail.com, Swiss-based encrypted email.
>>
>>> -------- Original Message --------
>>> Subject: Re: [Rd] Cannot Compute Box's M (Three Days Trying...)
>>> Local Time: October 27, 2017 6:09 PM
>>> UTC Time: October 27, 2017 10:09 PM
>>> From: murdoch.duncan at gmail.com
>>> To: Morkus morkus at protonmail.com, r-devel at r-project.org
>>> r-devel at r-project.org
>>> Just print the string you are asking to R to evaluate. It doesn't make
>>> any sense as an R expression. Fix that, and things will work.
>>> Duncan Murdoch
>>> On 27/10/2017 3:41 PM, Morkus via R-devel wrote:
>>>
>>> It can't be this hard, right? I really need a shove in the right
>>> direction here. Been spinning wheels for three days. Cannot get
>>> past the errors.
>>> I'm doing something wrong, obviously, since I can easily compute
>>> the Box's M right there in RStudio
>>> But I don't see what is wrong below with the coding equivalent.
>>> The entire code snippet is below. The code fails below on the call
>>> to the boxM statistic call.
>>> PLEASE HELP!!!
>>> Thanks in advance,
>>> ------------------------------------------------------------------------
>>>
>>> rConnection.eval("library('biotools')");
>>> String inputIris = "5.1,3.5,1.4,0.2,setosa\n" +
>>> "4.9,3,1.4,0.2,setosa\n" +
>>> "4.7,3.2,1.3,0.2,setosa\n" +
>>> "4.6,3.1,1.5,0.2,setosa\n" +
>>> "5,3.6,1.4,0.2,setosa\n" +
>>> "5.4,3.9,1.7,0.4,setosa\n" +
>>> "4.6,3.4,1.4,0.3,setosa\n" +
>>> "5,3.4,1.5,0.2,setosa\n" +
>>> "4.4,2.9,1.4,0.2,setosa\n" +
>>> "4.9,3.1,1.5,0.1,setosa\n" +
>>> "5.4,3.7,1.5,0.2,setosa\n" +
>>> "4.8,3.4,1.6,0.2,setosa\n" +
>>> "4.8,3,1.4,0.1,setosa\n" +
>>> "4.3,3,1.1,0.1,setosa\n" +
>>> "5.8,4,1.2,0.2,setosa\n" +
>>> "5.7,4.4,1.5,0.4,setosa\n" +
>>> "5.4,3.9,1.3,0.4,setosa\n" +
>>> "5.1,3.5,1.4,0.3,setosa\n" +
>>> "5.7,3.8,1.7,0.3,setosa\n" +
>>> "5.1,3.8,1.5,0.3,setosa\n" +
>>> "5.4,3.4,1.7,0.2,setosa\n" +
>>> "5.1,3.7,1.5,0.4,setosa\n" +
>>> "4.6,3.6,1,0.2,setosa\n" +
>>> "5.1,3.3,1.7,0.5,setosa\n" +
>>> "4.8,3.4,1.9,0.2,setosa\n" +
>>> "5,3,1.6,0.2,setosa\n" +
>>> "5,3.4,1.6,0.4,setosa\n" +
>>> "5.2,3.5,1.5,0.2,setosa\n" +
>>> "5.2,3.4,1.4,0.2,setosa\n" +
>>> "4.7,3.2,1.6,0.2,setosa\n" +
>>> "4.8,3.1,1.6,0.2,setosa\n" +
>>> "5.4,3.4,1.5,0.4,setosa\n" +
>>> "5.2,4.1,1.5,0.1,setosa\n" +
>>> "5.5,4.2,1.4,0.2,setosa\n" +
>>> "4.9,3.1,1.5,0.2,setosa\n" +
>>> "5,3.2,1.2,0.2,setosa\n" +
>>> "5.5,3.5,1.3,0.2,setosa\n" +
>>> "4.9,3.6,1.4,0.1,setosa\n" +
>>> "4.4,3,1.3,0.2,setosa\n" +
>>> "5.1,3.4,1.5,0.2,setosa\n" +
>>> "5,3.5,1.3,0.3,setosa\n" +
>>> "4.5,2.3,1.3,0.3,setosa\n" +
>>> "4.4,3.2,1.3,0.2,setosa\n" +
>>> "5,3.5,1.6,0.6,setosa\n" +
>>> "5.1,3.8,1.9,0.4,setosa\n" +
>>> "4.8,3,1.4,0.3,setosa\n" +
>>> "5.1,3.8,1.6,0.2,setosa\n" +
>>> "4.6,3.2,1.4,0.2,setosa\n" +
>>> "5.3,3.7,1.5,0.2,setosa\n" +
>>> "5,3.3,1.4,0.2,setosa\n" +
>>> "7,3.2,4.7,1.4,versicolor\n" +
>>> "6.4,3.2,4.5,1.5,versicolor\n" +
>>> "6.9,3.1,4.9,1.5,versicolor\n" +
>>> "5.5,2.3,4,1.3,versicolor\n" +
>>> "6.5,2.8,4.6,1.5,versicolor\n" +
>>> "5.7,2.8,4.5,1.3,versicolor\n" +
>>> "6.3,3.3,4.7,1.6,versicolor\n" +
>>> "4.9,2.4,3.3,1,versicolor\n" +
>>> "6.6,2.9,4.6,1.3,versicolor\n" +
>>> "5.2,2.7,3.9,1.4,versicolor\n" +
>>> "5,2,3.5,1,versicolor\n" +
>>> "5.9,3,4.2,1.5,versicolor\n" +
>>> "6,2.2,4,1,versicolor\n" +
>>> "6.1,2.9,4.7,1.4,versicolor\n" +
>>> "5.6,2.9,3.6,1.3,versicolor\n" +
>>> "6.7,3.1,4.4,1.4,versicolor\n" +
>>> "5.6,3,4.5,1.5,versicolor\n" +
>>> "5.8,2.7,4.1,1,versicolor\n" +
>>> "6.2,2.2,4.5,1.5,versicolor\n" +
>>> "5.6,2.5,3.9,1.1,versicolor\n" +
>>> "5.9,3.2,4.8,1.8,versicolor\n" +
>>> "6.1,2.8,4,1.3,versicolor\n" +
>>> "6.3,2.5,4.9,1.5,versicolor\n" +
>>> "6.1,2.8,4.7,1.2,versicolor\n" +
>>> "6.4,2.9,4.3,1.3,versicolor\n" +
>>> "6.6,3,4.4,1.4,versicolor\n" +
>>> "6.8,2.8,4.8,1.4,versicolor\n" +
>>> "6.7,3,5,1.7,versicolor\n" +
>>> "6,2.9,4.5,1.5,versicolor\n" +
>>> "5.7,2.6,3.5,1,versicolor\n" +
>>> "5.5,2.4,3.8,1.1,versicolor\n" +
>>> "5.5,2.4,3.7,1,versicolor\n" +
>>> "5.8,2.7,3.9,1.2,versicolor\n" +
>>> "6,2.7,5.1,1.6,versicolor\n" +
>>> "5.4,3,4.5,1.5,versicolor\n" +
>>> "6,3.4,4.5,1.6,versicolor\n" +
>>> "6.7,3.1,4.7,1.5,versicolor\n" +
>>> "6.3,2.3,4.4,1.3,versicolor\n" +
>>> "5.6,3,4.1,1.3,versicolor\n" +
>>> "5.5,2.5,4,1.3,versicolor\n" +
>>> "5.5,2.6,4.4,1.2,versicolor\n" +
>>> "6.1,3,4.6,1.4,versicolor\n" +
>>> "5.8,2.6,4,1.2,versicolor\n" +
>>> "5,2.3,3.3,1,versicolor\n" +
>>> "5.6,2.7,4.2,1.3,versicolor\n" +
>>> "5.7,3,4.2,1.2,versicolor\n" +
>>> "5.7,2.9,4.2,1.3,versicolor\n" +
>>> "6.2,2.9,4.3,1.3,versicolor\n" +
>>> "5.1,2.5,3,1.1,versicolor\n" +
>>> "5.7,2.8,4.1,1.3,versicolor\n" +
>>> "6.3,3.3,6,2.5,virginica\n" +
>>> "5.8,2.7,5.1,1.9,virginica\n" +
>>> "7.1,3,5.9,2.1,virginica\n" +
>>> "6.3,2.9,5.6,1.8,virginica\n" +
>>> "6.5,3,5.8,2.2,virginica\n" +
>>> "7.6,3,6.6,2.1,virginica\n" +
>>> "4.9,2.5,4.5,1.7,virginica\n" +
>>> "7.3,2.9,6.3,1.8,virginica\n" +
>>> "6.7,2.5,5.8,1.8,virginica\n" +
>>> "7.2,3.6,6.1,2.5,virginica\n" +
>>> "6.5,3.2,5.1,2,virginica\n" +
>>> "6.4,2.7,5.3,1.9,virginica\n" +
>>> "6.8,3,5.5,2.1,virginica\n" +
>>> "5.7,2.5,5,2,virginica\n" +
>>> "5.8,2.8,5.1,2.4,virginica\n" +
>>> "6.4,3.2,5.3,2.3,virginica\n" +
>>> "6.5,3,5.5,1.8,virginica\n" +
>>> "7.7,3.8,6.7,2.2,virginica\n" +
>>> "7.7,2.6,6.9,2.3,virginica\n" +
>>> "6,2.2,5,1.5,virginica\n" +
>>> "6.9,3.2,5.7,2.3,virginica\n" +
>>> "5.6,2.8,4.9,2,virginica\n" +
>>> "7.7,2.8,6.7,2,virginica\n" +
>>> "6.3,2.7,4.9,1.8,virginica\n" +
>>> "6.7,3.3,5.7,2.1,virginica\n" +
>>> "7.2,3.2,6,1.8,virginica\n" +
>>> "6.2,2.8,4.8,1.8,virginica\n" +
>>> "6.1,3,4.9,1.8,virginica\n" +
>>> "6.4,2.8,5.6,2.1,virginica\n" +
>>> "7.2,3,5.8,1.6,virginica\n" +
>>> "7.4,2.8,6.1,1.9,virginica\n" +
>>> "7.9,3.8,6.4,2,virginica\n" +
>>> "6.4,2.8,5.6,2.2,virginica\n" +
>>> "6.3,2.8,5.1,1.5,virginica\n" +
>>> "6.1,2.6,5.6,1.4,virginica\n" +
>>> "7.7,3,6.1,2.3,virginica\n" +
>>> "6.3,3.4,5.6,2.4,virginica\n" +
>>> "6.4,3.1,5.5,1.8,virginica\n" +
>>> "6,3,4.8,1.8,virginica\n" +
>>> "6.9,3.1,5.4,2.1,virginica\n" +
>>> "6.7,3.1,5.6,2.4,virginica\n" +
>>> "6.9,3.1,5.1,2.3,virginica\n" +
>>> "5.8,2.7,5.1,1.9,virginica\n" +
>>> "6.8,3.2,5.9,2.3,virginica\n" +
>>> "6.7,3.3,5.7,2.5,virginica\n" +
>>> "6.7,3,5.2,2.3,virginica\n" +
>>> "6.3,2.5,5,1.9,virginica\n" +
>>> "6.5,3,5.2,2,virginica\n" +
>>> "6.2,3.4,5.4,2.3,virginica\n" +
>>> "5.9,3,5.1,1.8,virginica\n";
>>> List tableRead = rConnection.eval(
>>> "read.csv(textConnection("" + inputIris + ""), header =
>>> FALSE)").asList(); // works!
>>> double[] d1 = ((REXPVector) ((RList) tableRead).get(0)).asDoubles();
>>> double[] d2 = ((REXPVector) ((RList) tableRead).get(1)).asDoubles();
>>> double[] d3 = ((REXPVector) ((RList) tableRead).get(2)).asDoubles();
>>> double[] d4 = ((REXPVector) ((RList) tableRead).get(3)).asDoubles();
>>> String[] d5 = ((REXPVector) ((RList) tableRead).get(4)).asStrings();
>>> // create data frame with data.REXP myDf =
>>> REXP.createDataFrame(new RList(
>>> new REXP[]
>>> {
>>> new REXPDouble(d1),
>>> new REXPDouble(d2),
>>> new REXPDouble(d3),
>>> new REXPDouble(d4),
>>> new REXPString(d5)
>>> }));
>>> // assign the data to a variable as was
>>> suggested.rConnection.assign("boxMVariable", myDf);
>>> // create a string command with that variable name.String
>>> boxVariable = "boxM(boxMVariable [,-5], boxMVariable[,5]";
>>> // try to execute the command...
>>> // FAILS with org.rosuda.REngine.Rserve.RserveException: eval
>>> failed, request status: R parser: input incomplete>>>> FAILS !
>>>>>>> REXP theBoxMResult = rConnection.eval(boxVariable); <<<<
>>> FAILS <<<<<
>>> sent from ProtonMail <https://protonmail.com>, Swiss-based
>>> encrypted email.
>>> [[alternative HTML version deleted]]
>>> ------------------------------------------------------------------------
>>>
>>> R-devel at r-project.org <mailto:R-devel at r-project.org> mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-devel
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[Rd] Cannot Compute Box's M (Three Days Trying...)
Morkus