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POKruskal-Wallis test with details on pairwise comparisons
 

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    <p>The standard stats::kruskal.test module allows to calculate the kruskal-wallis test on a dataset:</p> <pre><code>&gt;&gt;&gt; data(diamonds) &gt;&gt;&gt; kruskal.test(price~carat, data=diamonds) Kruskal-Wallis rank sum test data: price by carat by color Kruskal-Wallis chi-squared = 50570.15, df = 272, p-value &lt; 2.2e-16 </code></pre> <p>This is correct, it is giving me a probability that all the groups in the data have the same mean.</p> <p>However, I would like to have the details for each pair comparison, like if diamonds of colors D and E have the same mean price, as some other softwares do (SPSS) when you ask for a Kruskal test.</p> <p>I have found <a href="http://bm2.genes.nig.ac.jp/RGM2/R_current/library/pgirmess/man/kruskalmc.html" rel="noreferrer">kruskalmc</a> from the package pgirmess which allows me to do what I want to do:</p> <pre><code>&gt; kruskalmc(diamonds$price, diamonds$color) Multiple comparison test after Kruskal-Wallis p.value: 0.05 Comparisons obs.dif critical.dif difference D-E 571.7459 747.4962 FALSE D-F 2237.4309 751.5684 TRUE D-G 2643.1778 726.9854 TRUE D-H 4539.4392 774.4809 TRUE D-I 6002.6286 862.0150 TRUE D-J 8077.2871 1061.7451 TRUE E-F 2809.1767 680.4144 TRUE E-G 3214.9237 653.1587 TRUE E-H 5111.1851 705.6410 TRUE E-I 6574.3744 800.7362 TRUE E-J 8649.0330 1012.6260 TRUE F-G 405.7470 657.8152 FALSE F-H 2302.0083 709.9533 TRUE F-I 3765.1977 804.5390 TRUE F-J 5839.8562 1015.6357 TRUE G-H 1896.2614 683.8760 TRUE G-I 3359.4507 781.6237 TRUE G-J 5434.1093 997.5813 TRUE H-I 1463.1894 825.9834 TRUE H-J 3537.8479 1032.7058 TRUE I-J 2074.6585 1099.8776 TRUE </code></pre> <p>However, this package only allows for one categoric variable (e.g. I can't study the prices clustered by color and by carat, as I can do with kruskal.test), and I don't know anything about the pgirmess package, whether it is maintained or not, or if it is tested.</p> <p>Can you recommend me a package to execute the Kruskal-Wallis test which returns details for every comparison? How would you handle the problem?</p>
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    1. COThere is `kruskal` function in `agricolae` package. You could check if fits your needs.
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    2. COObviously you mean kruskal.test (without the second .test). I guess you are using the diamonds dataset from ggplot2 package. Well, I can't figure out why, but when I try loading it I get an error `internal error -3 in R_decompress1 In addition: Warning message: restarting interrupted promise evaluation`. (I know, this looks like a question I should post, but has anyone faced the same problem?)
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    3. CO@ Marek: thank you very much. I saw agricolae but it seems to have the same problem as pgirmess :-( @gd047: I have no idea what your error may be, really. Maybe you should try to reinstall ggplot2. Do you have the same error with other datasets or packages?
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