[R-SIG-Mac] bug in polychor with R 2.6.0

[Rob J Goedman]

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
>
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