[R] How to get significance codes after Kruskal Wallis test
David L Carlson
dcarlson at tamu.edu
Mon Sep 28 16:28:31 CEST 2015
The kruskalmc() function in package pgirmess performs a multiple comparisons analysis using the kruskal-wallis test. It indicates which pairs are significantly different, but it does not summarize the results in a compact letter display.
> library(pgirmess)
> kruskalmc(Heliocide~Treatment, dta)
Multiple comparison test after Kruskal-Wallis
p.value: 0.05
Comparisons
obs.dif critical.dif difference
1_2d-1_7d 6.045455 19.11021 FALSE
1_2d-3_2d 3.833333 18.69015 FALSE
1_2d-9_2d 21.500000 19.60240 TRUE
1_2d-C 17.045455 19.11021 FALSE
1_7d-3_2d 2.212121 19.11021 FALSE
1_7d-9_2d 15.454545 20.00331 FALSE
1_7d-C 23.090909 19.52123 TRUE
3_2d-9_2d 17.666667 19.60240 FALSE
3_2d-C 20.878788 19.11021 TRUE
9_2d-C 38.545455 20.00331 TRUE
-------------------------------------
David L Carlson
Department of Anthropology
Texas A&M University
College Station, TX 77840-4352
-----Original Message-----
From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of David Winsemius
Sent: Saturday, September 26, 2015 11:07 AM
To: Michael Eisenring
Cc: 'r-help'
Subject: Re: [R] How to get significance codes after Kruskal Wallis test
On Sep 26, 2015, at 6:48 AM, Michael Eisenring wrote:
> Thank you very much Kristina,
>
> Unfortunately that's not what I am looking for.
>
> I am just very surprised if there would be no possibility to get the significance codes for Kruskal Wallis (I would have suggested that this is a pretty common test.)
Well, it is modestly common test but its really a global test, and not a pairwise one.
> I found another option called kruskal() which does pairwise comparison, but without significance codes.
>
> Maybe another R-list member knows more.
>
I'm not sure I "know more", and it's very possible I "know less". In particular I don't really know what the term "significance code" actually means. (I'm hoping it's not a request for "significance stars", a feature which is roundly deprecated by more knowledgeable R users.)
However, looking at the agricolae::kruskal function's help page and submitting the data in the non-formulaic manner it expects, I get this output very similar in form the the HSD.test output that it appeared you considered satisfied satisfactory:
(an.dta3<-kruskal(dta$Heliocide, dta$Treatment))
#--------------------
$statistics
Chisq p.chisq
30.25246 4.348055e-06
$parameters
Df ntr t.value
4 5 2.007584
$means
dta$Heliocide std r Min Max
1_2d 1992.7707 1747.1879 12 334.53973 4929.372
1_7d 2368.8057 1187.9285 11 767.22881 4624.945
3_2d 2640.1286 2659.5800 12 615.91181 8559.142
9_2d 5338.6711 1579.4428 10 3328.89713 8014.897
C 397.9086 443.6019 11 75.73956 1588.431
$rankMeans
dta$Treatment dta$Heliocide r
1 1_2d 26.000000 12
2 1_7d 32.045455 11
3 3_2d 29.833333 12
4 9_2d 47.500000 10
5 C 8.954545 11
$comparison
NULL
$groups
trt means M
1 9_2d 47.500000 a
2 1_7d 32.045455 b
3 3_2d 29.833333 b
4 1_2d 26.000000 b
5 C 8.954545 c
>From context I am guessing that the "significance codes" you ask for are the items in the M column of the "groups" element of the list output.
--
David.
>
>
> Thank you,
>
> Mike
>
>
>
> Von: Kristina Wolf [mailto:kmwolf at ucdavis.edu]
> Gesendet: Freitag, 25. September 2015 23:26
> An: Michael Eisenring <michael.eisenring at gmx.ch>
> Cc: r-help <r-help at r-project.org>
> Betreff: Re: [R] How to get significance codes after Kruskal Wallis test
>
>
>
> Perhaps look into the function friedman.test.with.post.hoc()
>
> There is more information here: http://www.r-statistics.com/wp-content/uploads/2010/02/Friedman-Test-with-Post-Hoc.r.txt
>
>
>
> Note, this does not handle NA's though, and technically it is for blocked designs, but maybe it will lead you somewhere useful or could be adapted?
>
>
> ~ Kristina
>
> Kristina Wolf
> Ph.D. Candidate, Graduate Group in Ecology
> M.S. Soil Science
>
>
>
> On Fri, Sep 25, 2015 at 10:01 PM, Michael Eisenring <michael.eisenring at gmx.ch <mailto:michael.eisenring at gmx.ch> > wrote:
>
> Is there a way to get significance codes after a pairwise comparisons to a
> Kruskall wallis test? With significance codes I mean letter codes (a, b,c)
> that are assigned to treatments to indicate where differences are
> significant.
>
> With a traditional anova such a test can be performed using HSD.test from
> the agricolae library but for non parametric counterparts of anova I have
> not been able to find anything.
>
> Can anyone help me?
>
> Thanks mike
>
>
>
> I added two example codes.
>
> First code represents an ANOVA and a HSD.test() giving me significant codes
>
> #FIRST CODE USING ANOVA
>
> library(agricolae)
> an.dta<-aov(Gossypol~Treatment,data=dta)
> summary(an.dta)
>
> HSD.test(an.dta,"Treatment")
> # The level by alpha default is 0.05.
> outT<-HSD.test(an.dta,"Treatment", group=T)
> outT
>
> #I receive significant codes.
>
>
> #SECOND CODE USING KRUSKAL WALLIs
>
> library(agricolae)
> an.dta2<-kruskal.test(Heliocide~Treatment,dta)
> summary(an.dta2)
>
> HSD.test(an.dta2,"Treatment")
>
> #ERROR MESSAGE no significance codes, why??
>
>
>
> #DATA FOR CODES
>
>
> structure(list(Treatment = structure(c(1L, 3L, 4L, 2L, 1L, 3L,
> 4L, 2L, 5L, 1L, 3L, 2L, 5L, 1L, 3L, 4L, 2L, 5L, 1L, 3L, 4L, 2L,
> 5L, 1L, 3L, 4L, 2L, 5L, 1L, 3L, 4L, 2L, 5L, 1L, 3L, 4L, 2L, 5L,
> 1L, 3L, 4L, 2L, 5L, 1L, 3L, 4L, 2L, 5L, 1L, 3L, 4L, 2L, 5L, 1L,
> 3L, 5L), .Label = c("1_2d", "1_7d", "3_2d", "9_2d", "C"), class = "factor"),
>
> Code = structure(c(1L, 2L, 3L, 4L, 18L, 19L, 20L, 21L, 22L,
> 23L, 24L, 25L, 26L, 27L, 28L, 29L, 30L, 31L, 32L, 33L, 34L,
> 35L, 36L, 37L, 38L, 39L, 40L, 41L, 42L, 43L, 44L, 45L, 46L,
> 47L, 48L, 49L, 50L, 51L, 52L, 53L, 54L, 55L, 56L, 5L, 6L,
> 7L, 8L, 9L, 10L, 11L, 12L, 13L, 14L, 15L, 16L, 17L), .Label =
> c("1_2d_1c",
> "1_2d_3c", "1_2d_9c", "1_7d_1c", "10_2d_1c", "10_2d_3c",
> "10_2d_9c", "10_7d_1c", "10_C", "11_2d_1c", "11_2d_3c", "11_2d_9c",
> "11_7d_1c", "11_C", "12_2d_1c", "12_2d_3c", "12_C", "2_2d_1c",
> "2_2d_3c", "2_2d_9c", "2_7d_1c", "2_C", "3_2d_1c", "3_2d_3c",
> "3_7d_1c", "3_C", "4_2d_1c", "4_2d_3c", "4_2d_9c", "4_7d_1c",
> "4_C", "5_2d_1c", "5_2d_3c", "5_2d_9c", "5_7d_1c", "5_C",
> "6_2d_1c", "6_2d_3c", "6_2d_9c", "6_7d_1c", "6_C", "7_2d_1c",
> "7_2d_3c", "7_2d_9c", "7_7d_1c", "7_C", "8_2d_1c", "8_2d_3c",
> "8_2d_9c", "8_7d_1c", "8_C", "9_2d_1c", "9_2d_3c", "9_2d_9c",
> "9_7d_1c", "9_C"), class = "factor"), Glands = c(165, 289.3333333,
> 319.3333333, 472, 334.6666667, 259, 373.3333333, 525.6666667,
> 275.3333333, 230.6666667, 346.3333333, 377.6666667, 255.3333333,
> 217.6666667, 266, 300.3333333, 354.3333333, 225.3333333,
> 294, 359, 359, 222.6666667, 103, 246.6666667, 324.6666667,
> 277, 460, 163.6666667, 226.3333333, 228, 357.6666667, 505,
> 142.6666667, 324, 278.6666667, 317.3333333, 335.6666667,
> 193.6666667, 188, 255, 252, 393.3333333, 248.3333333, 353,
> 320.6666667, 228.3333333, 497, 165.6666667, 209.3333333,
> 162.3333333, 280, 337, 169.6666667, 231.6666667, 257.6666667,
> 218.6666667), Tannin = c(0.334252451, 1.376077586, 0.896849593,
> 0.888621795, 0.464285714, 0.830236486, 0.870881783, 0.768489583,
> 0.647727273, 0.81372549, 0.51380814, 0.859923246, 0.495265152,
> 0.699932796, 1.09375, 0.785037879, 0.892650463, 0.518963675,
> 1.05859375, 0.447916667, 1.269097222, 1.147522523, 0.391276042,
> 0.883400538, 1.523989899, 0.907930108, 0.749155405, 0.450126263,
> 0.562239583, 0.911151961, 0.611111111, 1.610677083, 0.446428571,
> 0.601151316, 1.073635057, 1.359923246, 1.00154321, 0.90933642,
> 0.012054398, 1.102083333, 1.017361111, 1.052372685, 0.958607456,
> 1.224702381, 0.982291667, 1.045138889, 1.611607143, 0.662574405,
> 1.385416667, 0.464518229, 0.994444444, 1.239583333, 0.877514368,
> 0.74453125, 0.804315476, 1.024066092), H.polone = c(6754.067177,
> 22380.26652, 23622.79158, 23733.77678, 13099.20833, 23564.74907,
> 2725.016387, 18751.03986, 4283.098494, 23008.35336, 10205.56354,
> 19787.63361, 4302.050374, 7400.640798, 22442.86044, 34315.09631,
> 16498.66728, 14170.13252, 9509.1073, 6265.29637, 20671.56905,
> 14517.15648, 2643.950729, 4974.607571, 14782.87029, 13918.82361,
> 12526.27863, 1236.908141, 4854.469195, 4076.396504, 9603.950212,
> 13762.57476, 2298.727719, 3514.186757, 5705.140289, 14178.21668,
> 14277.39878, 2656.552509, 8184.633961, 9931.163373, 21474.90732,
> 18522.74376, 9884.406532, 17242.54114, 8431.506608, 14601.11606,
> 15748.4912, 2849.90903, 16747.27644, 9396.645481, 21996.95822,
> 5767.358748, 5767.358748, 14207.1734, 10353.21833, 2859.51171
> ), Gossypol = c(1036.331811, 4171.427741, 6039.995102, 5909.068158,
> 4140.242559, 4854.985845, 6982.035521, 6132.876396, 948.2418407,
> 3618.448997, 3130.376482, 5113.942098, 1180.171957, 1500.863038,
> 4576.787021, 5629.979049, 3378.151945, 3589.187889, 2508.417927,
> 1989.576826, 5972.926124, 2867.610671, 450.7205451, 1120.955,
> 3470.09352, 3575.043632, 2952.931863, 349.0864019, 1013.807628,
> 910.8879471, 3743.331903, 3350.203452, 592.3403778, 1517.045807,
> 1504.491931, 3736.144027, 2818.419785, 723.885643, 1782.864308,
> 1414.161257, 3723.629772, 3747.076592, 2005.919344, 4198.569251,
> 2228.522959, 3322.115942, 4274.324792, 720.9785449, 2874.651764,
> 2287.228752, 5654.858696, 1247.806111, 1247.806111, 2547.326207,
> 2608.716056, 1079.846532), Heliocide = c(711.1776124, 8559.141828,
> 8014.897387, 3972.305107, 3227.467943, 5778.242027, 3628.427557,
> 3177.426984, 325.1764586, 3774.732152, 3111.880146, 4624.945228,
> 160.8912744, 336.4018128, 5207.091788, 6360.856306, 1740.091298,
> 1588.430761, 3509.141442, 685.6917982, 4664.118976, 1477.26149,
> 75.73956465, 402.1570283, 3703.317553, 4235.211434, 1730.465296,
> 91.53557346, 334.5397274, 698.1713846, 3328.897126, 1742.69355,
> 231.9097243, 513.7933372, 774.6461158, 4687.003829, 1692.296924,
> 179.1968506, 1022.628651, 1199.898583, 6132.303567, 1971.798098,
> 413.3375988, 4072.908467, 615.911814, 4906.642605, 3160.349616,
> 117.642134, 4929.371855, 616.8755006, 7428.352411, 767.2288107,
> 767.2288107, 1078.928494, 730.6740868, 425.9053258), Damage..cm. =
> c(0.4955,
> 1.516, 4.409, 3.2665, 0.491, 2.3035, 3.51, 1.8115, 0, 0.4435,
> 1.573, 1.8595, 0, 0.142, 2.171, 4.023, 4.9835, 0, 0.6925,
> 1.989, 5.683, 3.547, 0, 0.756, 2.129, 9.437, 3.211, 0, 0.578,
> 2.966, 4.7245, 1.8185, 0, 1.0475, 1.62, 5.568, 9.7455, 0,
> 0.8295, 2.411, 7.272, 4.516, 0, 0.4035, 2.974, 8.043, 4.809,
> 0, 0.6965, 1.313, 5.681, 3.474, 0, 0.5895, 2.559, 0)), .Names =
> c("Treatment",
> "Code", "Glands", "Tannin", "H.polone", "Gossypol", "Heliocide",
> "Damage..cm."), class = "data.frame", row.names = c(NA, -56L))
>
>
> [[alternative HTML version deleted]]
>
David Winsemius
Alameda, CA, USA
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