[Rd] Cannot Compute Box's M (Three Days Trying...)
Duncan Murdoch
murdoch.duncan at gmail.com
Sat Oct 28 13:31:41 CEST 2017
On 28/10/2017 7:12 AM, Morkus wrote:
> 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).
That looks like an error occurring in the str() function. I've never
seen such a think in a regular R session, so I would guess that either
your boxMVariable object is set up in a weird way that is confusing
str(), or your R session in Java is messed up.
This is likely to be pretty hard to debug. As a general strategy, I'd
try to find out exactly what is in boxMVariable first. Since str()
doesn't work, try printing things like
head(boxMVariable)
class(boxMVariable)
names(boxMVariable)
ncol(boxMVariable)
nrow(boxMVariable)
typeof(boxMVariable)
for (i in 1:5)
print(typeof(boxMVariable[[i]]))
etc.
Make sure the values match what you see in a regular R session:
> boxMVariable <- iris
>
> head(boxMVariable)
Sepal.Length Sepal.Width Petal.Length Petal.Width Species
1 5.1 3.5 1.4 0.2 setosa
2 4.9 3.0 1.4 0.2 setosa
3 4.7 3.2 1.3 0.2 setosa
4 4.6 3.1 1.5 0.2 setosa
5 5.0 3.6 1.4 0.2 setosa
6 5.4 3.9 1.7 0.4 setosa
> class(boxMVariable)
[1] "data.frame"
> names(boxMVariable)
[1] "Sepal.Length" "Sepal.Width" "Petal.Length" "Petal.Width"
"Species"
> ncol(boxMVariable)
[1] 5
> nrow(boxMVariable)
[1] 150
> typeof(boxMVariable)
[1] "list"
> for (i in 1:5)
+ print(typeof(boxMVariable[[i]]))
[1] "double"
[1] "double"
[1] "double"
[1] "double"
[1] "integer"
>
> 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*@17d99928+[5]”
>
> ▼ payload = {org.rosuda.REngine.*RList*@566} size = 5
> ► 0 = {org.rosuda.REngine.REXPDouble at 570}
> "org.rosuda.REngine.*REXPDouble*@6fffcba5[150]"
> ► 1 = {org.rosuda.REngine.REXPDouble at 571}
> "org.rosuda.REngine.*REXPDouble*@34340fab[150]”
> ► 2 = {org.rosuda.REngine.REXPDouble at 572}
> "org.rosuda.REngine.*REXPDouble*@2aafb23c[150]"
> ► 3 = {org.rosuda.REngine.REXPDouble at 573}
> "org.rosuda.REngine.*REXPDouble*@2b80d80f[150]”
> ► 4 = {org.rosuda.REngine.REXPString at 574}
> "org.rosuda.REngine.*REXPString*@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
>>
>> 5.
>>
>>
>>
>> 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 <mailto:murdoch.duncan at gmail.com>
>> To: Morkus morkus at protonmail.com
>> <mailto:morkus at protonmail.com>, r-devel at r-project.org
>> <mailto:r-devel at r-project.org>
>> r-devel at r-project.org <mailto: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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