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? 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. 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.dun...@gmail.com > To: Morkus <mor...@protonmail.com> > r-devel@r-project.org <r-devel@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.dun...@gmail.com >>> To: Morkus mor...@protonmail.com >>> r-devel@r-project.org r-devel@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@562} >>> "org.rosuda.REngine./REXPGenericVector/@17d99928+[5]” >>> ▼ payload = {org.rosuda.REngine./RList/@566} size = 5 >>> ► 0 = {org.rosuda.REngine.REXPDouble@570} >>> "org.rosuda.REngine./REXPDouble/@6fffcba5[150]" >>> ► 1 = {org.rosuda.REngine.REXPDouble@571} >>> "org.rosuda.REngine./REXPDouble/@34340fab[150]” >>> ► 2 = {org.rosuda.REngine.REXPDouble@572} >>> "org.rosuda.REngine./REXPDouble/@2aafb23c[150]" >>> ► 3 = {org.rosuda.REngine.REXPDouble@573} >>> "org.rosuda.REngine./REXPDouble/@2b80d80f[150]” >>> ► 4 = {org.rosuda.REngine.REXPString@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.dun...@gmail.com <mailto:murdoch.dun...@gmail.com> >>> To: Morkus mor...@protonmail.com <mailto:mor...@protonmail.com> >>> r-devel@r-project.org <mailto:r-devel@r-project.org> >>> r-devel@r-project.org <mailto:r-devel@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.dun...@gmail.com >>> <mailto:murdoch.dun...@gmail.com> To: Morkus >>> mor...@protonmail.com <mailto:mor...@protonmail.com>, >>> r-devel@r-project.org <mailto:r-devel@r-project.org> >>> r-devel@r-project.org <mailto:r-devel@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@r-project.org <mailto:R-devel@r-project.org> mailing >>> list https://stat.ethz.ch/mailman/listinfo/r-devel | | [[alternative HTML version deleted]] ______________________________________________ R-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-devel
