Use the method M4 in Bernal Vasquez (2016). Bonferroni Holm test to judge residuals standardized by the re scaled MAD (BH MADR).
Arguments
- data
Experimental design data frame with the factors and traits.
- trait
Name of the trait.
- model
The fixed or random effects in the model.
- drop_na
drop NA values from the data.frame
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 <- outliers_remove(
data = potato
, trait ="stemdw"
, model = "0 + treat*geno + (1|bloque) + geno"
, 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
#>