Bill, Using R-2.6.0 alpha, the binary version of the package (for 2.6.0) of polycor seems to work fine. See below.
Don't think the version of the R GUI makes a difference here. Regards, Rob R version 2.6.0 alpha (2007-09-06 r42791) Copyright (C) 2007 The R Foundation for Statistical Computing ISBN 3-900051-07-0 ... trying URL 'http://cran.cnr.Berkeley.edu/bin/macosx/universal/contrib/ 2.6/polycor_0.7-3.tgz' Content type 'application/x-gzip' length 16643 bytes (16 Kb) opened URL ================================================== downloaded 16 Kb The downloaded packages are in /tmp/Rtmp87kMzX/downloaded_packages > library(polycor) Loading required package: mvtnorm > data <- rmvnorm(1000, c(0, 0), matrix(c(1, .5, .5, 1), 2, 2)) > x <- data[,1] > y <- data[,2] > cor(x, y) # sample correlation [1] 0.5285446 > x <- cut(x, c(-Inf, .75, Inf)) > y <- cut(y, c(-Inf, -1, .5, 1.5, Inf)) > polychor(x, y) # 2-step estimate [1] 0.5365251 > polychor(x, y, ML=TRUE, std.err=TRUE) Polychoric Correlation, ML est. = 0.5364 (0.03775) Test of bivariate normality: Chisquare = 0.545, df = 2, p = 0.7615 Row Threshold Threshold Std.Err. 0.7292 0.04368 Column Thresholds Threshold Std.Err. 1 -0.9947 0.04767 2 0.5100 0.04145 3 1.5450 0.06265 > On Sep 15, 2007, at 10:49 AM, William Revelle wrote: > John, > I have been testing out R2.6.0 alpha to see if my psych package > works. I am running the R Gui for the Mac. > > There seems to be a problem with the polychor function in your > polycor package. I think this might be a general problem with R > 2.6.0 alpha but I am not sure. I am copying the R mac list to see > if this is a general problem with the alpha gui. > > Bill > > > From a clean start > > [Workspace restored from /Volumes/WR/bill/.RData] > >> version > _ > platform i386-apple-darwin8.10.1 > arch i386 > os darwin8.10.1 > system i386, darwin8.10.1 > status alpha > major 2 > minor 6.0 > year 2007 > month 09 > day 14 > svn rev 42851 > language R > version.string R version 2.6.0 alpha (2007-09-14 r42851) > > >> library(polycor) > Loading required package: mvtnorm >> ?polychor #to get the help file with the following demo >> set.seed(12345) >> data <- rmvnorm(1000, c(0, 0), matrix(c(1, .5, .5, 1), 2, 2)) >> x <- data[,1] >> y <- data[,2] >> cor(x, y) # sample correlation > [1] 0.5285446 >> x <- cut(x, c(-Inf, .75, Inf)) >> y <- cut(y, c(-Inf, -1, .5, 1.5, Inf)) >> polychor(x, y) # 2-step estimate > > *** caught bus error *** > address 0x0, cause 'non-existent physical address' > > Traceback: > 1: .Fortran("mvtdst", N = as.integer(n), NU = as.integer(df), LOWER > = as.double(lower), UPPER = as.double(upper), INFIN = > as.integer(infin), CORREL = as.double(corrF), DELTA = > as.double(delta), MAXPTS = as.integer(maxpts), ABSEPS = > as.double(abseps), RELEPS = as.double(releps), error = > as.double(error), value = as.double(value), inform = > as.integer(inform), PACKAGE = "mvtnorm") > 2: mvt(lower = lower, upper = upper, df = 0, corr = corr, delta = > mean, maxpts = maxpts, abseps = abseps, releps = releps) > 3: pmvnorm(lower = c(row.cuts[i], col.cuts[j]), upper = c(row.cuts[i > + 1], col.cuts[j + 1]), corr = R) > 4: binBvn(rho, row.cuts, col.cuts) > 5: f(arg, ...) > 6: function (arg) f(arg, ...)(-0.23606797749979) > 7: optimise(f, interval = c(-1, 1)) > 8: polychor(x, y) > > > > Bill > > -- > William Revelle http://personality-project.org/revelle.html > Professor http://personality-project.org/personality.html > Department of Psychology http:// > www.wcas.northwestern.edu/psych/ > Northwestern University http://www.northwestern.edu/ > Use R for statistics: http://personality- > project.org/r > > _______________________________________________ > R-SIG-Mac mailing list > [email protected] > https://stat.ethz.ch/mailman/listinfo/r-sig-mac _______________________________________________ R-SIG-Mac mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-mac
