# Silent failure with NA results in fligner.test() Classic List Threaded 4 messages Open this post in threaded view
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## Silent failure with NA results in fligner.test()

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## Re: Silent failure with NA results in fligner.test()

 >>>>> Karolis K writes: Any preferences? Best -k > Hello, > In certain cases fligner.test() returns NaN statistic and NA p-value. > The issue happens when, after centering with the median, all absolute values become constant, which ten leads to identical ranks. > Below are a few examples: > # 2 groups, 2 values each > # issue is caused by residual values after centering (-0.5, 0.5, -0.5, 0.5) > # then, after taking the absolute value, all the ranks become identical. >> fligner.test(c(2,3,4,5), gl(2,2)) >         Fligner-Killeen test of homogeneity of variances > data:  c(2, 3, 4, 5) and gl(2, 2) > Fligner-Killeen:med chi-squared = NaN, df = 1, p-value = NA > # similar situation with more observations and 3 groups >> fligner.test(c(2,3,2,3,4,4,5,5,8,9,9,8), gl(3,4)) >         Fligner-Killeen test of homogeneity of variances > data:  c(2, 3, 2, 3, 4, 4, 5, 5, 8, 9, 9, 8) and gl(3, 4) > Fligner-Killeen:med chi-squared = NaN, df = 2, p-value = NA > Two simple patches are proposed below. One returns an error, and another returns a p-value of 1. > Not sure which one is more appropriate, so submitting both. > Warm regards, > Karolis Koncevičius > --- > Index: fligner.test.R > =================================================================== > --- fligner.test.R (revision 79650) > +++ fligner.test.R (working copy) > @@ -59,8 +59,13 @@ >          stop("data are essentially constant")   >      a <- qnorm((1 + rank(abs(x)) / (n + 1)) / 2) > -    STATISTIC <- sum(tapply(a, g, "sum")^2 / tapply(a, g, "length")) > -    STATISTIC <- (STATISTIC - n * mean(a)^2) / var(a) > +    if (var(a) > 0) { > +        STATISTIC <- sum(tapply(a, g, "sum")^2 / tapply(a, g, "length")) > +        STATISTIC <- (STATISTIC - n * mean(a)^2) / var(a) > +    } > +    else { > +        STATISTIC <- 0 > +    } >      PARAMETER <- k - 1 >      PVAL <- pchisq(STATISTIC, PARAMETER, lower.tail = FALSE) >      names(STATISTIC) <- "Fligner-Killeen:med chi-squared” > --- > Index: fligner.test.R > =================================================================== > --- fligner.test.R (revision 79650) > +++ fligner.test.R (working copy) > @@ -57,6 +57,8 @@ >      x <- x - tapply(x,g,median)[g] >      if (all(x == 0)) >          stop("data are essentially constant") > +    if (var(abs(x)) == 0) > +        stop("absolute residuals from the median are essentially constant")   >      a <- qnorm((1 + rank(abs(x)) / (n + 1)) / 2) >      STATISTIC <- sum(tapply(a, g, "sum")^2 / tapply(a, g, "length")) > ______________________________________________ > [hidden email] mailing list > https://stat.ethz.ch/mailman/listinfo/r-devel______________________________________________ [hidden email] mailing list https://stat.ethz.ch/mailman/listinfo/r-devel