Elinor Lichtenberg wrote: > Hi. I am currently trying to run some Spearman correlations, and have > encountered two issues. > > 1) When using cor.test() with a variable that includes ties, I get the > "Cannot compute exact p-values with ties" error. I have read that this > function now uses an asymptotic formula that allows for ties, so do not > understand why I am getting this error. (I am running version 2.4.0.) > > Because asymptotic formulas are not exact!
> I read the following data in from a CSV file: > species,ecoldom,ecolrank,abundance,persistence,behavdom,behavrank,aggrlevel > Fv,0.108333333,6,2.5,0,0.351351351,5,0.12195122 > Mq,0.114583333,5,2,0,0.167539267,5,0.287878788 > N,0.125,3,0.5,0,0.285714286,5,0.333333333 > S,0.116792929,4,11,0.125,0.684027778,2,0.723214286 > Th,0.164737654,1,22.5,0.875,0.717948718,2,1.614285714 > Ts,0.131944444,2,3,0,0.712328767,2,1.068965517 > > I then use: > cor.test(ecoldom, persistence, method="spearman") > > > 2) I have tried using spearman.test() as an alternative to cor.test() and > get different p-values (although the rho values are the same). Here is an > example: > > >> spearman(ecoldom, abundance) >> > rho > 0.4857143 > >> spearman.test(ecoldom, abundance) >> > Rsquare F df1 df2 pvalue n > 0.2359184 1.2350427 1.0000000 4.0000000 0.3287230 6.0000000 > >> cor.test(ecoldom, abundance, method="spearman") >> > > Spearman's rank correlation rho > > data: ecoldom and abundance > S = 18, p-value = 0.3556 > alternative hypothesis: true rho is not equal to 0 > sample estimates: > rho > 0.4857143 > > Is this difference due to the two functions using different algorithms? > > What spearman.test? It is not standard, and you're not telling us which package it came from. Offhand I would guess that cor.test is using the exact formula and spearman.test an asymptotic one. You can force cor.test to use the asymptotic formula by setting exact=FALSE (oops, there's a documentation buglet there). ______________________________________________ R-help@stat.math.ethz.ch mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
