[Rd] Cannot Compute Box's M (Three Days Trying...)
Duncan Murdoch
murdoch.duncan at gmail.com
Sun Oct 29 12:45:09 CET 2017
On 29/10/2017 7:26 AM, Morkus wrote:
> Thanks Duncan. I can't tell you how helpful all your terrific replies
> have been.
>
> I think the biggest surprise is that nobody appears to be using Java and
> R together like I"m trying to do. I suppose it should be a surprise
> since there are no books on the subject and almost no technical
> documentation other than a few sites here and there.
>
> -----
>
> I originally had the "int" as the return type for the factors, but that
> didn't make any difference.
>
> So, let me ask you. *What I can get working is* calling an R Script from
> Java. Literally opening the ".R" file and reading it line by line and
> evaluating it. That works. Is there any reason why that's not a viable
> way to go?
I can't answer this very specifically, because it depends so much on
your circumstances. But why bother with the file system at all?
Presumably if you can read a string, you can construct the same string
within your Java program (perhaps as a literal string, perhaps by
building it from local variables).
>
> The one thing I don't know how to do is pass a parameter to an RScript
> from Java. *Is it possible to pass a parameter to an RScript from Java?*
> If I can pass a parameter to an RScript, then it's not static and I
> could use it as a "function" to call for different values.
>
> Look forward to your reply.
I can't really answer that question, since I have no experience at all
in calling R from Java. But if you want to pass a parameter named "x"
with value 123 from Java to R, why not just construct and evaluate the
statement "x <- 123"?
Duncan Murdoch
>
>
>
> 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 4:51 PM
>> UTC Time: October 28, 2017 8:51 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>
>>
>> On 28/10/2017 8:59 AM, Morkus wrote:
>>
>> Hey Duncan,
>> Hard to debug? That's an understatement. Eyes bleeding....
>> In any case, I tried all your suggestions. To get "integer" for the
>> final column, I had to change the code to get integers instead of
>> strings.
>>
>> The last column in iris is actually a factor. That's stored as an
>> S3-classed integer vector with an attribute listing the levels. Using
>> strings instead can cause problems in a few R functions (they want
>> factors, and don't do automatic conversions), but the errors you're
>> seeing seem more fundamental.
>> 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();
>> /int/*[] d5 = ((REXPVector) ((RList)
>> tableRead).get(*4*)).asIntegers();*
>> /// 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 */REXPInteger(d5)/
>> }));
>> Here are the results from the eval debug code.
>> head(boxMVariable) — Gives the high level 5 objects.
>> typeof(boxMVariable): “list”
>> class(boxMVariable) : “data.frame”
>> names(boxMVariable) — String object returned (couldn't evaluate it)
>>
>> That sounds like it could be serious. Dataframe names shouldn't be
>> particularly complicated, so there shouldn't be a problem evaluating
>> them. (But maybe this is just hard in Java for some reason. As I've
>> mentioned, I'm not familiar with the R Java interface.) If there
>> really
>> is a problem with the way the names have been constructed, that would
>> explain the error in str(), and would lead to lots of other weird
>> problems.
>>
>> Another way to look at R objects from within R is to use
>> .Internal(inspect( x )). For example,
>>
>> .Internal(inspect(names(iris)))
>> @7f898ff9e2e8 16 STRSXP g0c4 [NAM(2)] (len=5, tl=0)
>> @7f8992c41878 09 CHARSXP g0c2 [gp=0x61,ATT] [ASCII] [cached]
>> "Sepal.Length"
>> @7f8992c41840 09 CHARSXP g0c2 [gp=0x61] [ASCII] [cached] "Sepal.Width"
>> @7f8992c41808 09 CHARSXP g0c2 [gp=0x61,ATT] [ASCII] [cached]
>> "Petal.Length"
>> @7f898ba99f78 09 CHARSXP g0c2 [gp=0x61,ATT] [ASCII] [cached]
>> "Petal.Width"
>> @7f898b9a3468 09 CHARSXP g0c1 [gp=0x61,ATT] [ASCII] [cached] "Species"
>>
>> You can also look at R objects while in a debugger like gdb using the
>> R_PV() function; see Writing R Extensions for details if this is
>> something available to you.
>>
>> ncol(boxMVariable) - 5
>> nrow(boxMVariable) - 150
>> typeof(boxMVariable)
>> for (i in 1:5) print(typeof(boxMVariable[[i]]))
>> /I get:/
>> 1 —> double
>> 2 —> double
>> 3 —> double
>> 4 —> double
>> 5 -> integer
>> Is this problem "debug-proof"?
>> Does anyone out there actually use Java and R?
>>
>> I don't know anyone who does that. It seems like a bad idea just
>> because it's always easiest to do what everyone else does.
>>
>> I think it's more common to call Java from R than the reverse.
>>
>> Duncan Murdoch
>> Sigh...
>> 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 7:31 AM
>> UTC Time: October 28, 2017 11:31 AM
>> 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>
>> 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
>> <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> 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]]
>> ------------------------------------------------------------------------
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>> | | |
>>
>>
>
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