[R] Repeated Measures ANOVA and the Bonferroni post hoc test different results of significantly

Wed Jun 24 03:28:52 CEST 2015

Hi All and thanks for Help

I am doing an Repeated Measures ANOVA and the Bonferroni post hoc test for
my data using R project. The ANOVA gives a significantly difference between
the data but not the  Bonferroni post hoc test.

    > anova(aov2)
                numDF denDF   F-value p-value
    (Intercept)     1  1366 110.51125  <.0001
    time            5  1366   9.84684  <.0001

while

    > pairwise.t.test(x=table.metric2$value, g=table.metric2$time,
p.adj="bonf")

            Pairwise comparisons using t tests with pooled SD

    data:  table.metric2$value and table.metric2$time

        Su1 Su2 Su3 Su4 Su5
    Su2 1   -   -   -   -
    Su3 1   1   -   -   -
    Su4 1   1   1   -   -
    Su5 1   1   1   1   -
    Su6 1   1   1   1   1

    P value adjustment method: bonferroni

These are my data with the code used

    plot <- c(rep(1:275))

    Su1 <- c(13.5584,0.0000,2.0710,0.4826,1.2761,1.6690,3.5188,
13.7578,0.0000,0.0000,0.0004,0.0000,0.0000,0.0000,4.4634,3.0151,2.1719,5.2861,4.9651,0.7908,0.0000,0.0000,0.0000,0.0000,

0.0000,5.2749,5.4706,4.4416,3.2166,0.0000,0.1929,0.0000,0.0000,0.0000,0.0000,0.0000,4.6765,1.7761,4.3579,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,

0.0000,6.1794,2.4194,1.4319,0.0000,0.0327,0.0000,0.4633,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0018,0.0000,0.0000,

0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,

0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.5425,0.5274,2.0883,0.6024,0.0000,0.0018,0.0000,0.0000,0.0015,0.0012,0.0000,0.0000,0.0000,

0.4560,2.1256,0.0295,0.0328,0.0000,1.6447,0.0428,0.0067,0.0058,0.0000,0.0000,0.0000,0.0001,0.3317,0.2898,3.5134,0.1539,0.0199,0.0000,0.0494,0.1159,2.0976,0.0644,0.9730,

0.0010,0.5074,0.0003,0.0000,0.1188,1.8818,0.0000,0.1213,0.3585,7.3932,0.5492,0.0045,0.9879,0.0010,0.7625,0.1695,0.1211,0.3164,2.6750,3.8926,0.0000,3.4626,0.0000,5.8339,

6.7315,0.0244,4.8770,2.6237,2.3700,0.5338,0.0215,3.2196,1.9811,3.3825,3.3929,1.5426,0.9165,
10.6561,3.2154,4.1531,5.3381,3.9432,4.8675,0.0047,0.0026,0.2058,1.8509,0.3697,
    0.3131,0.0707,4.7908,6.4087,
10.3670,5.7662,4.0460,3.2571,9.1767,0.0116,0.0908,0.0053,0.1480,0.9063,5.4331,5.7945,
14.4097,6.9635,7.0637,0.1064,9.9095, 11.8432, 10.0234,0.0000,
    0.0491,5.0472,5.3094,5.1657, 14.3944,7.6244,0.0034,1.4953,
14.7658,6.1775,7.1567,0.0296,0.0911,3.5552,4.9543,3.1200,1.9774,0.0000,4.1663,0.0000,2.3672,0.0638,1.8952,4.1948,
    6.4229,
10.7573,0.0008,1.3818,6.0011,3.6791,9.7816,1.5203,0.8616,1.5483,5.4174,2.7070,2.1627,0.0000,1.7360,3.7292,2.4638,7.4498,4.2343,6.8263,3.2410,0.0001,0.0001,9.7424,
    4.2861,2.9912,0.4316,
11.6082,2.0138,0.0002,1.8783,0.9934,0.2983,1.4013,0.1429)

    Su2 <- c(10.4361,0.0000,2.3346,0.5769,1.3392,1.5908,3.5759,
13.3183,0.0005,0.0000,0.0019,0.0000,0.0000,0.0000,4.4862,3.0418,2.3991,5.4263,4.9456,0.6907,0.0000,0.0007,0.0000,0.0000,

0.0000,5.1065,5.1748,4.2888,3.3633,0.0000,0.1791,0.0000,0.0000,0.0000,0.0000,0.0000,5.3485,1.9216,4.2880,0.0000,0.0001,0.0001,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,

0.0000,6.3664,2.2888,1.4636,0.0000,0.0282,0.0000,0.5838,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0013,0.0000,0.0000,

0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0002,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,

0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.6240,0.6401,1.9324,0.6263,0.0000,0.0020,0.0000,0.0001,0.0039,0.0018,0.0000,0.0000,0.0000,

0.4321,1.9815,0.0528,0.0350,0.0000,1.6519,0.0328,0.0153,0.0171,0.0000,0.0000,0.0000,0.0000,0.3966,0.2957,3.4653,0.1473,0.0038,0.0000,0.0774,0.1180,2.2780,0.0611,0.9490,

0.0024,0.8337,0.0000,0.0000,0.1531,1.9778,0.0000,0.1171,0.3485,7.2378,0.7476,0.0028,1.2072,0.0015,0.7425,0.1352,0.1908,0.3092,2.3735,3.9768,0.0000,3.8786,0.0000,6.5420,

6.8490,0.0256,5.8268,2.7856,2.4640,0.6399,0.0215,5.3411,1.7939,3.3401,3.2942,1.4990,0.9264,
10.6864,3.3749,4.7978,5.2929,3.8639,5.3890,0.0027,0.0486,0.2105,1.8514,0.3526,
    0.3146,0.0950,4.8061,6.2244,
10.1131,5.8538,3.8861,4.4240,9.5952,0.0255,0.0533,0.0085,0.1742,1.0188,7.7153,5.4663,14.6060,6.8725,6.7284,0.0841,
10.2016, 11.3384,9.8938,0.0000,
    0.0749,5.0774,7.2876,5.2040, 14.7609,7.7862,0.0005,1.4099,
14.8639,6.8801,7.2587,0.0125,0.0513,3.1338,7.1539,3.1733,1.9729,0.0000,4.5081,0.0000,2.1572,0.0452,1.8866,8.0198,
    9.7868,
10.8746,0.0000,1.5011,6.0825,3.6705,9.9171,1.7091,0.8267,1.4186,6.4235,2.9303,1.9019,0.0000,1.5869,4.4028,2.4186,7.7739,4.6728,8.7722,3.9859,0.0001,0.0001,
10.1583,
    5.4758,2.8977,0.9716,
11.5342,2.6111,0.0000,1.7497,1.0041,0.3273,1.1953,0.2289)

    Su3 <-
c(12.5808,0.0000,2.7244,0.1119,1.2633,0.9702,2.4513,2.4419,0.0014,0.0000,0.0000,0.0000,0.0019,0.0105,3.5392,2.4033,2.1847,5.5912,4.8628,0.9449,0.0000,0.0000,0.0000,0.0000,

0.0000,4.2928,5.0754,3.4644,2.8663,0.0066,0.0043,0.0000,0.0000,0.0000,0.0000,0.0000,3.5292,1.4846,4.6333,0.0000,0.0003,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,

0.0000,7.0110,2.7508,2.0824,0.0001,0.0001,0.0000,0.0770,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0023,0.0000,0.0000,

0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,

0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.4546,0.1491,2.2391,0.4464,0.0000,0.0007,0.0000,0.0000,0.0000,0.0238,0.0000,0.0000,0.0000,

0.5663,1.5734,0.0247,0.0259,0.0000,0.6823,0.0101,0.0000,0.1171,0.0000,0.0000,0.0000,0.0000,0.1110,0.0960,2.2888,0.1338,0.0000,0.0000,0.0294,0.1273,2.3082,0.0081,0.6343,

0.0021,0.1690,0.0000,0.0000,0.3456,1.7644,0.0000,0.0175,0.1027,9.8583,0.5133,0.0002,0.8704,0.0000,0.0850,0.1183,0.0949,0.0369,2.8741,1.0065,0.0000,4.6330,0.0000,7.7170,

7.7201,0.0038,3.7342,2.6457,1.6262,0.2836,0.0008,2.2052,2.6186,3.1951,5.4121,0.5787,1.4276,
12.5830,5.0891,3.7475,4.8317,0.3612,5.0634,0.0001,0.0002,0.2396,2.8372,0.5667,

0.0024,0.0396,4.4980,6.6203,11.8869,7.5642,4.4144,1.1202,7.8870,0.0214,0.0323,0.0000,0.1492,1.0881,3.4938,6.4025,
13.7996,5.3475,7.2365,0.4289, 10.5106, 12.1750,7.8348,0.0000,
    0.0104,0.0126,4.7145,3.5840,11.1274,7.1017,0.4464,1.3384,
14.9060,4.1969,7.7008,0.0214,0.0022,2.6731,1.7724,3.0937,1.3026,1.1184,1.0817,0.0000,1.6675,0.0879,1.6432,4.3482,
    3.5927,3.3646,0.0000,1.2088,2.6632,2.6712,
10.0635,6.1788,0.9486,0.8011,2.5326,5.1218,0.1574,0.0000,1.7523,5.2613,2.8762,6.7293,7.9969,3.7011,1.9242,0.0002,0.0000,6.8359,

3.4735,4.8440,1.0125,4.3772,1.9227,0.0034,1.0078,2.7654,0.0246,0.4001,0.2570)

    Su4 <-
c(NA,0.0001,NA,0.3616,0.2848,1.5804,3.2575,6.9722,0.0000,0.0053,0.0001,0.0000,0.0002,0.0000,4.9185,3.6967,1.9675,7.7624,4.0516,0.7658,0.0001,0.0018,0.0000,0.0000,

0.0000,5.4964,5.2645,5.0756,1.9665,0.0011,0.3481,0.0001,0.0000,0.0000,0.0000,0.0000,4.6501,1.6375,1.1133,0.0016,0.0063,0.0007,0.0000,0.0001,0.0008,0.0000,0.0000,0.0000,

0.0000,5.9308,2.0694,0.3611,0.0035,0.0126,0.0000,0.4887,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0001,0.0000,0.0000,

0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0002,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,

0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.6246,0.4996,1.2273,0.5902,0.0000,0.0016,0.0000,0.0000,0.0004,0.0010,0.0000,0.0000,0.0000,

0.4431,1.6631,0.0234,0.0230,0.0000,1.4833,0.0134,0.0321,0.0283,0.0000,0.0000,0.0000,0.0000,0.2446,0.1740,3.4582,0.0757,0.0092,0.0000,0.0202,0.1099,2.1932,0.0565,0.9499,

0.0176,0.2146,0.0001,0.0000,0.1009,1.8096,0.0000,0.0413,0.2970,7.6015,0.4349,0.0121,0.8901,0.0024,0.4629,0.0843,0.0934,0.2790,2.5034,3.0369,0.0000,4.1673,0.0000,6.2014,

5.6363,0.0211,5.2860,2.7722,1.7316,0.3452,0.0099,2.6113,1.8183,3.2228,3.1208,1.4761,0.9326,9.7211,4.4282,4.0727,5.1978,3.3293,5.8666,0.0013,0.0413,0.0958,1.3760,0.2844,
    0.1587,0.0197,3.4947,6.2988,
10.5278,5.6255,3.7482,4.0839,9.5720,0.0113,0.0060,0.0005,0.2592,1.1092,6.5303,5.7979,
15.0240,6.6722,7.0578,0.0507,9.6608, 12.2310,7.6133,0.0002,
    0.0147,4.6729,4.1950,5.4444, 13.3876,8.7654,0.0001,1.3864,
15.5325,5.2633,9.7407,0.0160,0.0069,3.3050,7.6701,2.8048,1.1736,0.0000,4.8370,0.0000,1.4801,0.0014,1.3862,7.8413,
    3.9453,11.0588,0.0000,1.7270,6.0988,4.2754,
10.7927,1.1768,0.6381,0.1779,6.2290,2.9297,0.4520,0.0012,0.9822,6.6041,2.8147,6.9679,3.5493,9.5997,4.5469,0.0007,0.0004,6.7922,
    5.2609,2.4192,0.0459,
10.4127,3.9877,0.0000,1.1876,0.8595,0.5107,0.8049,0.1749)

    Su5 <- c(10.4824,0.0000,2.0018,0.2817,1.0086,1.1640,2.6718,
11.2732,0.0000,0.0000,0.0003,0.0000,0.0000,0.0000,5.1846,3.1089,1.6050,5.3045,5.1410,0.7458,0.0000,0.0000,0.0000,0.0000,

0.0000,5.8211,5.6094,4.2910,2.6412,0.0000,0.0404,0.0000,0.0000,0.0000,0.0000,0.0000,4.8222,1.7778,1.6938,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,

0.0000,5.3706,2.1161,0.5845,0.0000,0.0154,0.0000,0.6280,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0001,0.0000,0.0000,

0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,

0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.5967,0.6631,1.2776,0.8574,0.0000,0.0010,0.0000,0.0000,0.0016,0.0010,0.0000,0.0000,0.0000,

0.4013,1.7534,0.0341,0.0360,0.0000,1.8029,0.0163,0.0280,0.0541,0.0000,0.0000,0.0000,0.0000,0.2873,0.2288,3.3035,0.0943,0.0277,0.0000,0.0273,0.1230,1.1606,0.0553,0.9261,

0.0006,0.2793,0.0001,0.0000,0.0702,1.7861,0.0000,0.0441,0.6919,7.2771,0.4737,0.0001,0.9996,0.0028,0.7776,0.0760,0.2064,0.3322,2.1804,3.8545,0.0000,3.8377,0.0000,6.0567,

6.7315,0.0168,6.6603,2.2872,2.7505,0.6174,0.0235,2.5142,1.3832,3.0431,2.3944,1.4855,0.5978,9.6032,3.2907,3.7126,5.1397,3.7415,5.0454,0.0003,0.0361,0.0761,1.4128,0.3045,

0.4881,0.0392,3.8213,5.8874,9.9054,4.9779,3.2351,4.7589,9.2551,0.0108,0.0184,0.0086,0.1905,1.0657,8.1882,5.5578,
14.6536,7.3801,7.8668,0.0315,9.0087, 10.1677,9.6868,0.0001,
    0.0797,5.6032,5.4432,5.9958, 15.4570,8.1095,0.0000,1.1854,
14.0602,5.9429,8.4364,0.0056,0.0163,4.0671,5.5083,3.2078,1.8711,0.0000,6.0628,0.0000,1.8110,0.0941,1.8252,8.3102,

9.3829,5.5418,0.0000,1.4030,8.6327,4.3226,9.3724,1.6725,1.0198,1.4480,6.7463,1.7035,1.3542,0.0000,1.4079,4.2148,2.6589,7.3225,4.6582,9.1156,4.0312,0.0000,0.0000,9.2176,

5.5112,2.1917,0.5516,9.7061,2.7556,0.0000,1.0919,1.0696,0.5361,1.0160,0.1019)

    Su6 <-
c(9.3294,0.0001,1.7365,0.2030,0.5796,0.3794,2.4745,0.0104,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,2.2045,2.8210,1.0607,4.9375,0.0892,1.1530,0.0000,0.0000,0.0000,0.0000,

0.0000,5.5562,5.9813,4.6396,3.0815,0.0000,0.1245,0.0000,0.0000,0.0000,0.0000,0.0000,4.4952,1.3822,5.3511,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,

0.0000,2.4023,0.3491,2.0235,0.0000,0.0469,0.0000,0.3316,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,

0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,

0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.0000,0.5361,0.5083,2.4144,1.6541,0.0000,0.0009,0.0000,0.0000,0.0007,0.0084,0.0000,0.0000,0.0000,

0.7155,2.4862,2.8153,2.0548,0.0000,1.0062,0.1725,0.0028,0.0404,0.0000,0.0000,0.0000,0.0000,2.0952,1.8754,2.3209,0.1329,0.0025,0.0000,0.0134,0.1656,1.9201,0.0624,0.9148,

0.2393,1.8717,0.0000,0.0000,0.2733,1.3219,0.0000,0.0502,0.4294,6.5172,0.4368,0.0001,2.5930,0.0024,1.1465,0.0857,0.1336,0.1791,2.2427,1.7424,0.0000,4.5865,0.0000,7.4015,

5.1587,0.0953,1.9529,1.7191,2.6812,1.0850,0.0133,3.5750,1.3194,2.2280,2.7217,2.5155,0.6812,
10.1853,0.3850,4.3999,3.9028,1.5311,5.2335,0.0006,0.0359,0.2206,1.5833,0.1611,
    0.2389,0.2579,4.7568,5.7652,
11.4255,3.1828,1.8413,3.6434,6.6662,0.0148,0.0166,0.0284,0.4646,1.2736,5.3859,6.2033,
14.0715,5.1563,7.2547,0.0163,9.8463,9.7350,7.7685,0.0015,
    0.0694,2.4957,5.9204,3.0981, 13.9429,6.0630,0.0000,0.4167,
16.6025,8.0124,6.8630,0.0314,0.0453,5.1017,7.6560,2.2824,1.6168,0.0000,1.5369,0.0000,1.4277,0.1390,1.3599,5.5345,
    7.0305,4.4969,0.0000,1.4448,3.2237,3.5196,
11.8150,1.1668,0.5838,1.5561,2.9927,1.8511,1.4603,0.0000,1.2046,1.1346,2.0005,7.2672,6.1411,3.1801,1.8131,0.0005,0.0000,4.1790,
    3.8307,1.0645,NA,NA,0.0119,0.0001,1.1278,0.1273,0.0837,0.0863,0.6916)

    table.metric <- data.frame(plot,Su1, Su2, Su3, Su4, Su5, Su6)
    plot <- table.metric$plot
    table.metric$plot <- NULL
    table.metric2 <- stack(table.metric)
    plot.metrics = factor(rep(plot,6))
    table.metric2[3] = plot.metrics
    names(table.metric2) <- c("value", "time", "plot")
    aov2 <- lme(fixed= value~time, random=~1|plot, na.action=na.omit,
data=table.metric2)
    summary(aov2)
    anova(aov2)
    pairwise.t.test(x=table.metric2$value, g=table.metric2$time,
p.adj="bonf")

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