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

[John Fox]

Dear Bill,

This works fine for me under Windows XP with R 2.6.0 alpha, so I suspect a
problem with the Mac build:

> example(polychor)

plychr> set.seed(12345)

plychr> data <- rmvnorm(1000, c(0, 0), matrix(c(1, .5, .5, 1), 2, 2))

plychr> x <- data[,1]

plychr> y <- data[,2]

plychr> cor(x, y)  # sample correlation
[1] 0.5285446

plychr> x <- cut(x, c(-Inf, .75, Inf))

plychr> y <- cut(y, c(-Inf, -1, .5, 1.5, Inf))

plychr> polychor(x, y)  # 2-step estimate
[1] 0.5365251

plychr> polychor(x, y, ML=TRUE, std.err=TRUE)  # ML estimate

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


Regards,
 John

--------------------------------
John Fox, Professor
Department of Sociology
McMaster University
Hamilton, Ontario
Canada L8S 4M4
905-525-9140x23604
http://socserv.mcmaster.ca/jfox 
-------------------------------- 

> -----Original Message-----
> From: William Revelle [mailto:revelle at northwestern.edu] 
> Sent: Saturday, September 15, 2007 1:50 PM
> To: John Fox
> Cc: R-Sig-Mac
> Subject: bug in polychor with R 2.6.0
> 
> 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
>