[R] How to get significance codes after Kruskal Wallis test

Sat Sep 26 08:25:41 CEST 2015

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
,

B.S. Animal Science

KristinaMWolf.com
Restoration Ecology Lab

Department of Plant Sciences

University of California, Davis

(530) 750-9771

"We have to remember that what we observe is not nature herself, but nature
exposed to our method of questioning." ~ Werner Heisenberg

On Fri, Sep 25, 2015 at 10:01 PM, Michael Eisenring <
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))
>
>
>
>
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>
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