Use the method M4 in Bernal Vasquez (2016). Bonferroni Holm test to judge residuals standardized by the re scaled MAD (BH MADR).
References
Bernal Vasquez, Angela Maria, et al. “Outlier Detection Methods for Generalized Lattices: A Case Study on the Transition from ANOVA to REML.” Theoretical and Applied Genetics, vol. 129, no. 4, Apr. 2016.
Examples
library(inti)
rmout <- potato %>% outliers_remove(
data = .
, trait ="stemdw"
, model = "0 + treat*geno + (1|bloque)"
, drop_na = FALSE
)
rmout
#> $data
#> treat geno bloque stemdw
#> 1 sequia G01 II 14.87
#> 2 sequia G02 IV 8.63
#> 3 irrigado G01 III NA
#> 4 sequia G02 I 6.58
#> 5 irrigado G03 II 12.63
#> 6 irrigado G04 V 17.46
#> 7 irrigado G01 I 15.32
#> 8 irrigado G05 IV 14.55
#> 9 sequia G06 II 21.19
#> 10 sequia G05 I NA
#> 11 irrigado G01 II 18.13
#> 12 sequia G07 II 3.70
#> 13 irrigado G08 II 12.48
#> 14 irrigado G06 III 29.49
#> 15 irrigado G09 III 16.96
#> 16 irrigado G10 II 8.20
#> 17 sequia G11 I 7.90
#> 18 sequia G12 III 9.19
#> 19 irrigado G07 I 2.48
#> 20 irrigado G04 II 20.75
#> 21 irrigado G13 II 18.97
#> 22 irrigado G14 III 14.57
#> 23 irrigado G04 IV 18.84
#> 24 sequia G04 V 8.79
#> 25 sequia G08 V 8.17
#> 26 sequia G04 III 12.53
#> 27 sequia G01 IV 16.26
#> 28 irrigado G10 I 11.19
#> 29 irrigado G08 V 11.18
#> 30 irrigado G02 V 12.14
#> 31 irrigado G07 III 4.78
#> 32 irrigado G08 I 12.52
#> 33 irrigado G14 V 23.96
#> 34 irrigado G03 I 11.18
#> 35 sequia G13 III 7.79
#> 36 sequia G01 V 11.97
#> 37 sequia G03 I 9.03
#> 38 irrigado G15 III 11.17
#> 39 irrigado G03 IV 12.20
#> 40 irrigado G09 IV 18.17
#> 41 irrigado G11 II 4.90
#> 42 sequia G03 V 8.73
#> 43 sequia G11 III 5.56
#> 44 irrigado G06 V 23.77
#> 45 sequia G05 V NA
#> 46 sequia G08 IV 8.44
#> 47 irrigado G11 IV 7.53
#> 48 sequia G11 II 3.11
#> 49 irrigado G10 III 14.77
#> 50 sequia G06 IV 17.45
#> 51 sequia G09 I 13.36
#> 52 irrigado G11 I 7.27
#> 53 sequia G11 IV 5.72
#> 54 irrigado G15 IV 11.76
#> 55 irrigado G13 IV 19.83
#> 56 sequia G14 V 12.94
#> 57 irrigado G02 IV 14.01
#> 58 irrigado G09 II 19.20
#> 59 irrigado G02 III 12.12
#> 60 sequia G08 III 10.10
#> 61 irrigado G06 II 24.35
#> 62 sequia G13 IV 11.52
#> 63 sequia G14 III 13.37
#> 64 sequia G04 II 15.02
#> 65 irrigado G11 III 10.32
#> 66 irrigado G07 II 1.71
#> 67 irrigado G08 IV 14.28
#> 68 sequia G05 IV NA
#> 69 irrigado G04 I 12.80
#> 70 irrigado G11 V 7.99
#> 71 irrigado G12 I 19.60
#> 72 sequia G14 IV 13.97
#> 73 sequia G07 III 3.09
#> 74 irrigado G03 III 8.56
#> 75 sequia G01 I 10.44
#> 76 sequia G04 I 13.73
#> 77 sequia G03 II 8.33
#> 78 irrigado G15 II 11.78
#> 79 sequia G12 IV 12.30
#> 80 sequia G12 I 13.91
#> 81 sequia G08 I 5.14
#> 82 sequia G05 II NA
#> 83 sequia G02 II 8.46
#> 84 sequia G10 I 9.84
#> 85 sequia G15 I 11.43
#> 86 irrigado G07 V 1.71
#> 87 sequia G10 V 6.36
#> 88 sequia G13 II 12.34
#> 89 sequia G07 V 2.71
#> 90 sequia G03 III 7.16
#> 91 sequia G15 IV 11.19
#> 92 sequia G13 I 12.23
#> 93 sequia G03 IV 8.37
#> 94 irrigado G10 V 11.74
#> 95 sequia G13 V 11.82
#> 96 sequia G09 II 17.02
#> 97 irrigado G14 IV 17.89
#> 98 irrigado G01 V 13.80
#> 99 sequia G01 III 15.37
#> 100 irrigado G06 IV 33.52
#> 101 sequia G04 IV 12.56
#> 102 irrigado G15 V 12.13
#> 103 irrigado G13 III 17.36
#> 104 irrigado G02 II 12.58
#> 105 sequia G08 II 10.31
#> 106 irrigado G04 III 19.29
#> 107 sequia G02 V 8.39
#> 108 sequia G06 V 13.12
#> 109 irrigado G15 I 12.14
#> 110 irrigado G13 V 18.16
#> 111 irrigado G05 V 12.03
#> 112 sequia G09 III 16.71
#> 113 sequia G09 V 10.97
#> 114 sequia G10 II 7.44
#> 115 irrigado G07 IV 4.06
#> 116 irrigado G05 I 13.07
#> 117 irrigado G02 I 8.54
#> 118 sequia G05 III NA
#> 119 irrigado G12 II 17.81
#> 120 sequia G15 III 10.95
#> 121 irrigado G13 I 16.27
#> 122 sequia G14 II 17.86
#> 123 sequia G12 II 16.82
#> 124 sequia G15 II 11.82
#> 125 irrigado G09 V 14.22
#> 126 sequia G06 I 16.22
#> 127 sequia G09 IV 14.02
#> 128 sequia G15 V 10.32
#> 129 irrigado G14 I 19.93
#> 130 sequia G06 III 17.45
#> 131 irrigado G01 IV 16.97
#> 132 irrigado G12 III 19.78
#> 133 sequia G12 V 14.22
#> 134 irrigado G12 V 17.61
#> 135 sequia G11 V 3.95
#> 136 irrigado G12 IV 19.87
#> 137 irrigado G09 I 16.05
#> 138 sequia G02 III 9.76
#> 139 sequia G07 I 2.97
#> 140 irrigado G08 III 11.61
#> 141 irrigado G06 I 26.46
#> 142 irrigado G10 IV NA
#> 143 irrigado G03 V 10.76
#> 144 sequia G07 IV 0.97
#> 145 irrigado G05 III 15.19
#> 146 sequia G14 I 10.62
#> 147 sequia G10 III 11.27
#> 148 irrigado G14 II 17.86
#> 149 irrigado G05 II 16.57
#> 150 sequia G10 IV 6.58
#>
#> $outliers
#> treat geno bloque stemdw resi res_MAD rawp.BHStud index
#> 3 irrigado G01 III 24.19 6.520276 4.031041 5.553035e-05 3
#> 10 sequia G05 I 11.14 -13.467719 -8.326170 0.000000e+00 10
#> 45 sequia G05 V 11.52 -13.006525 -8.041046 8.881784e-16 45
#> 68 sequia G05 IV 80.65 54.860861 33.916722 0.000000e+00 68
#> 82 sequia G05 II 11.65 -13.422893 -8.298457 0.000000e+00 82
#> 118 sequia G05 III 10.02 -14.963724 -9.251048 0.000000e+00 118
#> 142 irrigado G10 IV 5.03 -5.949139 -3.677946 2.351195e-04 142
#> adjp bholm out_flag
#> 3 5.553035e-05 8.051901e-03 OUTLIER
#> 10 0.000000e+00 0.000000e+00 OUTLIER
#> 45 8.881784e-16 1.296740e-13 OUTLIER
#> 68 0.000000e+00 0.000000e+00 OUTLIER
#> 82 0.000000e+00 0.000000e+00 OUTLIER
#> 118 0.000000e+00 0.000000e+00 OUTLIER
#> 142 2.351195e-04 3.385720e-02 OUTLIER
#>