Use the method M4 in Bernal Vasquez (2016). Bonferroni Holm test to judge residuals standardized by the re scaled MAD (BH MADR).
Usage
remove_outliers(
data,
formula,
drop_na = FALSE,
plot_diag = FALSE,
title = "Diagnostic Plot"
)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 %>%
remove_outliers(data = .
, formula = stemdw ~ 0 + (1|bloque) + treat*geno
, plot_diag = TRUE
, drop_na = FALSE
, title = "Plot Diagnostic"
)
#> fixed-effect model matrix is rank deficient so dropping 1 column / coefficient
#> fixed-effect model matrix is rank deficient so dropping 1 column / coefficient
rmout
#> $data
#> $data$raw
#> index bloque treat geno stemdw
#> 1 1 II sequia G01 14.87
#> 2 2 IV sequia G02 8.63
#> 3 3 III irrigado G01 24.19
#> 4 4 I sequia G02 6.58
#> 5 5 II irrigado G03 12.63
#> 6 6 V irrigado G04 17.46
#> 7 7 I irrigado G01 15.32
#> 8 8 IV irrigado G05 14.55
#> 9 9 II sequia G06 21.19
#> 10 10 I sequia G05 11.14
#> 11 11 II irrigado G01 18.13
#> 12 12 II sequia G07 3.70
#> 13 13 II irrigado G08 12.48
#> 14 14 III irrigado G06 29.49
#> 15 15 III irrigado G09 16.96
#> 16 16 II irrigado G10 8.20
#> 17 17 I sequia G11 7.90
#> 18 18 III sequia G12 9.19
#> 19 19 I irrigado G07 2.48
#> 20 20 II irrigado G04 20.75
#> 21 21 II irrigado G13 18.97
#> 22 22 III irrigado G14 14.57
#> 23 23 IV irrigado G04 18.84
#> 24 24 V sequia G04 8.79
#> 25 25 V sequia G08 8.17
#> 26 26 III sequia G04 12.53
#> 27 27 IV sequia G01 16.26
#> 28 28 I irrigado G10 11.19
#> 29 29 V irrigado G08 11.18
#> 30 30 V irrigado G02 12.14
#> 31 31 III irrigado G07 4.78
#> 32 32 I irrigado G08 12.52
#> 33 33 V irrigado G14 23.96
#> 34 34 I irrigado G03 11.18
#> 35 35 III sequia G13 7.79
#> 36 36 V sequia G01 11.97
#> 37 37 I sequia G03 9.03
#> 38 38 III irrigado G15 11.17
#> 39 39 IV irrigado G03 12.20
#> 40 40 IV irrigado G09 18.17
#> 41 41 II irrigado G11 4.90
#> 42 42 V sequia G03 8.73
#> 43 43 III sequia G11 5.56
#> 44 44 V irrigado G06 23.77
#> 45 45 V sequia G05 11.52
#> 46 46 IV sequia G08 8.44
#> 47 47 IV irrigado G11 7.53
#> 48 48 II sequia G11 3.11
#> 49 49 III irrigado G10 14.77
#> 50 50 IV sequia G06 17.45
#> 51 51 I sequia G09 13.36
#> 52 52 I irrigado G11 7.27
#> 53 53 IV sequia G11 5.72
#> 54 54 IV irrigado G15 11.76
#> 55 55 IV irrigado G13 19.83
#> 56 56 V sequia G14 12.94
#> 57 57 IV irrigado G02 14.01
#> 58 58 II irrigado G09 19.20
#> 59 59 III irrigado G02 12.12
#> 60 60 III sequia G08 10.10
#> 61 61 II irrigado G06 24.35
#> 62 62 IV sequia G13 11.52
#> 63 63 III sequia G14 13.37
#> 64 64 II sequia G04 15.02
#> 65 65 III irrigado G11 10.32
#> 66 66 II irrigado G07 1.71
#> 67 67 IV irrigado G08 14.28
#> 68 68 IV sequia G05 80.65
#> 69 69 I irrigado G04 12.80
#> 70 70 V irrigado G11 7.99
#> 71 71 I irrigado G12 19.60
#> 72 72 IV sequia G14 13.97
#> 73 73 III sequia G07 3.09
#> 74 74 III irrigado G03 8.56
#> 75 75 I sequia G01 10.44
#> 76 76 I sequia G04 13.73
#> 77 77 II sequia G03 8.33
#> 78 78 II irrigado G15 11.78
#> 79 79 IV sequia G12 12.30
#> 80 80 I sequia G12 13.91
#> 81 81 I sequia G08 5.14
#> 82 82 II sequia G05 11.65
#> 83 83 II sequia G02 8.46
#> 84 84 I sequia G10 9.84
#> 85 85 I sequia G15 11.43
#> 86 86 V irrigado G07 1.71
#> 87 87 V sequia G10 6.36
#> 88 88 II sequia G13 12.34
#> 89 89 V sequia G07 2.71
#> 90 90 III sequia G03 7.16
#> 91 91 IV sequia G15 11.19
#> 92 92 I sequia G13 12.23
#> 93 93 IV sequia G03 8.37
#> 94 94 V irrigado G10 11.74
#> 95 95 V sequia G13 11.82
#> 96 96 II sequia G09 17.02
#> 97 97 IV irrigado G14 17.89
#> 98 98 V irrigado G01 13.80
#> 99 99 III sequia G01 15.37
#> 100 100 IV irrigado G06 33.52
#> 101 101 IV sequia G04 12.56
#> 102 102 V irrigado G15 12.13
#> 103 103 III irrigado G13 17.36
#> 104 104 II irrigado G02 12.58
#> 105 105 II sequia G08 10.31
#> 106 106 III irrigado G04 19.29
#> 107 107 V sequia G02 8.39
#> 108 108 V sequia G06 13.12
#> 109 109 I irrigado G15 12.14
#> 110 110 V irrigado G13 18.16
#> 111 111 V irrigado G05 12.03
#> 112 112 III sequia G09 16.71
#> 113 113 V sequia G09 10.97
#> 114 114 II sequia G10 7.44
#> 115 115 IV irrigado G07 4.06
#> 116 116 I irrigado G05 13.07
#> 117 117 I irrigado G02 8.54
#> 118 118 III sequia G05 10.02
#> 119 119 II irrigado G12 17.81
#> 120 120 III sequia G15 10.95
#> 121 121 I irrigado G13 16.27
#> 122 122 II sequia G14 17.86
#> 123 123 II sequia G12 16.82
#> 124 124 II sequia G15 11.82
#> 125 125 V irrigado G09 14.22
#> 126 126 I sequia G06 16.22
#> 127 127 IV sequia G09 14.02
#> 128 128 V sequia G15 10.32
#> 129 129 I irrigado G14 19.93
#> 130 130 III sequia G06 17.45
#> 131 131 IV irrigado G01 16.97
#> 132 132 III irrigado G12 19.78
#> 133 133 V sequia G12 14.22
#> 134 134 V irrigado G12 17.61
#> 135 135 V sequia G11 3.95
#> 136 136 IV irrigado G12 19.87
#> 137 137 I irrigado G09 16.05
#> 138 138 III sequia G02 9.76
#> 139 139 I sequia G07 2.97
#> 140 140 III irrigado G08 11.61
#> 141 141 I irrigado G06 26.46
#> 142 142 IV irrigado G10 5.03
#> 143 143 V irrigado G03 10.76
#> 144 144 IV sequia G07 0.97
#> 145 145 III irrigado G05 15.19
#> 146 146 I sequia G14 10.62
#> 147 147 III sequia G10 11.27
#> 148 148 II irrigado G14 17.86
#> 149 149 II irrigado G05 16.57
#> 150 150 IV sequia G10 6.58
#>
#> $data$clean
#> index bloque treat geno stemdw
#> 1 1 II sequia G01 14.87
#> 2 2 IV sequia G02 8.63
#> 3 3 III irrigado G01 NA
#> 4 4 I sequia G02 6.58
#> 5 5 II irrigado G03 12.63
#> 6 6 V irrigado G04 17.46
#> 7 7 I irrigado G01 15.32
#> 8 8 IV irrigado G05 14.55
#> 9 9 II sequia G06 21.19
#> 10 10 I sequia G05 NA
#> 11 11 II irrigado G01 18.13
#> 12 12 II sequia G07 3.70
#> 13 13 II irrigado G08 12.48
#> 14 14 III irrigado G06 29.49
#> 15 15 III irrigado G09 16.96
#> 16 16 II irrigado G10 8.20
#> 17 17 I sequia G11 7.90
#> 18 18 III sequia G12 9.19
#> 19 19 I irrigado G07 2.48
#> 20 20 II irrigado G04 20.75
#> 21 21 II irrigado G13 18.97
#> 22 22 III irrigado G14 14.57
#> 23 23 IV irrigado G04 18.84
#> 24 24 V sequia G04 8.79
#> 25 25 V sequia G08 8.17
#> 26 26 III sequia G04 12.53
#> 27 27 IV sequia G01 16.26
#> 28 28 I irrigado G10 11.19
#> 29 29 V irrigado G08 11.18
#> 30 30 V irrigado G02 12.14
#> 31 31 III irrigado G07 4.78
#> 32 32 I irrigado G08 12.52
#> 33 33 V irrigado G14 23.96
#> 34 34 I irrigado G03 11.18
#> 35 35 III sequia G13 7.79
#> 36 36 V sequia G01 11.97
#> 37 37 I sequia G03 9.03
#> 38 38 III irrigado G15 11.17
#> 39 39 IV irrigado G03 12.20
#> 40 40 IV irrigado G09 18.17
#> 41 41 II irrigado G11 4.90
#> 42 42 V sequia G03 8.73
#> 43 43 III sequia G11 5.56
#> 44 44 V irrigado G06 23.77
#> 45 45 V sequia G05 NA
#> 46 46 IV sequia G08 8.44
#> 47 47 IV irrigado G11 7.53
#> 48 48 II sequia G11 3.11
#> 49 49 III irrigado G10 14.77
#> 50 50 IV sequia G06 17.45
#> 51 51 I sequia G09 13.36
#> 52 52 I irrigado G11 7.27
#> 53 53 IV sequia G11 5.72
#> 54 54 IV irrigado G15 11.76
#> 55 55 IV irrigado G13 19.83
#> 56 56 V sequia G14 12.94
#> 57 57 IV irrigado G02 14.01
#> 58 58 II irrigado G09 19.20
#> 59 59 III irrigado G02 12.12
#> 60 60 III sequia G08 10.10
#> 61 61 II irrigado G06 24.35
#> 62 62 IV sequia G13 11.52
#> 63 63 III sequia G14 13.37
#> 64 64 II sequia G04 15.02
#> 65 65 III irrigado G11 10.32
#> 66 66 II irrigado G07 1.71
#> 67 67 IV irrigado G08 14.28
#> 68 68 IV sequia G05 NA
#> 69 69 I irrigado G04 12.80
#> 70 70 V irrigado G11 7.99
#> 71 71 I irrigado G12 19.60
#> 72 72 IV sequia G14 13.97
#> 73 73 III sequia G07 3.09
#> 74 74 III irrigado G03 8.56
#> 75 75 I sequia G01 10.44
#> 76 76 I sequia G04 13.73
#> 77 77 II sequia G03 8.33
#> 78 78 II irrigado G15 11.78
#> 79 79 IV sequia G12 12.30
#> 80 80 I sequia G12 13.91
#> 81 81 I sequia G08 5.14
#> 82 82 II sequia G05 NA
#> 83 83 II sequia G02 8.46
#> 84 84 I sequia G10 9.84
#> 85 85 I sequia G15 11.43
#> 86 86 V irrigado G07 1.71
#> 87 87 V sequia G10 6.36
#> 88 88 II sequia G13 12.34
#> 89 89 V sequia G07 2.71
#> 90 90 III sequia G03 7.16
#> 91 91 IV sequia G15 11.19
#> 92 92 I sequia G13 12.23
#> 93 93 IV sequia G03 8.37
#> 94 94 V irrigado G10 11.74
#> 95 95 V sequia G13 11.82
#> 96 96 II sequia G09 17.02
#> 97 97 IV irrigado G14 17.89
#> 98 98 V irrigado G01 13.80
#> 99 99 III sequia G01 15.37
#> 100 100 IV irrigado G06 33.52
#> 101 101 IV sequia G04 12.56
#> 102 102 V irrigado G15 12.13
#> 103 103 III irrigado G13 17.36
#> 104 104 II irrigado G02 12.58
#> 105 105 II sequia G08 10.31
#> 106 106 III irrigado G04 19.29
#> 107 107 V sequia G02 8.39
#> 108 108 V sequia G06 13.12
#> 109 109 I irrigado G15 12.14
#> 110 110 V irrigado G13 18.16
#> 111 111 V irrigado G05 12.03
#> 112 112 III sequia G09 16.71
#> 113 113 V sequia G09 10.97
#> 114 114 II sequia G10 7.44
#> 115 115 IV irrigado G07 4.06
#> 116 116 I irrigado G05 13.07
#> 117 117 I irrigado G02 8.54
#> 118 118 III sequia G05 NA
#> 119 119 II irrigado G12 17.81
#> 120 120 III sequia G15 10.95
#> 121 121 I irrigado G13 16.27
#> 122 122 II sequia G14 17.86
#> 123 123 II sequia G12 16.82
#> 124 124 II sequia G15 11.82
#> 125 125 V irrigado G09 14.22
#> 126 126 I sequia G06 16.22
#> 127 127 IV sequia G09 14.02
#> 128 128 V sequia G15 10.32
#> 129 129 I irrigado G14 19.93
#> 130 130 III sequia G06 17.45
#> 131 131 IV irrigado G01 16.97
#> 132 132 III irrigado G12 19.78
#> 133 133 V sequia G12 14.22
#> 134 134 V irrigado G12 17.61
#> 135 135 V sequia G11 3.95
#> 136 136 IV irrigado G12 19.87
#> 137 137 I irrigado G09 16.05
#> 138 138 III sequia G02 9.76
#> 139 139 I sequia G07 2.97
#> 140 140 III irrigado G08 11.61
#> 141 141 I irrigado G06 26.46
#> 142 142 IV irrigado G10 NA
#> 143 143 V irrigado G03 10.76
#> 144 144 IV sequia G07 0.97
#> 145 145 III irrigado G05 15.19
#> 146 146 I sequia G14 10.62
#> 147 147 III sequia G10 11.27
#> 148 148 II irrigado G14 17.86
#> 149 149 II irrigado G05 16.57
#> 150 150 IV sequia G10 6.58
#>
#>
#> $outliers
#> index bloque treat geno stemdw resi res_MAD rawp.BHStud
#> 3 3 III irrigado G01 24.19 6.520276 4.031041 5.553035e-05
#> 10 10 I sequia G05 11.14 -13.467719 -8.326170 0.000000e+00
#> 45 45 V sequia G05 11.52 -13.006525 -8.041046 8.881784e-16
#> 68 68 IV sequia G05 80.65 54.860861 33.916722 0.000000e+00
#> 82 82 II sequia G05 11.65 -13.422893 -8.298457 0.000000e+00
#> 118 118 III sequia G05 10.02 -14.963724 -9.251048 0.000000e+00
#> 142 142 IV irrigado G10 5.03 -5.949139 -3.677946 2.351195e-04
#> 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
#>
#> $diagplot
#>
#> $model
#> $model$raw
#> Linear mixed model fit by REML ['lmerMod']
#> Formula: stemdw ~ 0 + (1 | bloque) + treat * geno
#> Data: rawdt
#> REML criterion at convergence: 822.7055
#> Random effects:
#> Groups Name Std.Dev.
#> bloque (Intercept) 0.8331
#> Residual 6.0516
#> Number of obs: 150, groups: bloque, 5
#> Fixed Effects:
#> treatirrigado treatsequia genoG02
#> 17.682 13.782 -5.804
#> genoG03 genoG04 genoG05
#> -6.616 0.146 -3.400
#> genoG06 genoG07 genoG08
#> 9.836 -14.734 -5.268
#> genoG09 genoG10 genoG11
#> -0.762 -7.496 -10.080
#> genoG12 genoG13 genoG14
#> 1.252 0.436 1.160
#> genoG15 treatsequia:genoG02 treatsequia:genoG03
#> -5.886 0.386 1.158
#> treatsequia:genoG04 treatsequia:genoG05 treatsequia:genoG06
#> -1.402 14.614 -6.532
#> treatsequia:genoG07 treatsequia:genoG08 treatsequia:genoG09
#> 3.640 -0.082 1.396
#> treatsequia:genoG10 treatsequia:genoG11 treatsequia:genoG12
#> 2.012 1.546 -1.746
#> treatsequia:genoG13 treatsequia:genoG14 treatsequia:genoG15
#> -3.078 -1.190 3.246
#>
#> $model$clean
#> Linear mixed model fit by REML ['lmerMod']
#> Formula: stemdw ~ 0 + (1 | bloque) + treat * geno
#> Data: cleandt
#> REML criterion at convergence: 537.8671
#> Random effects:
#> Groups Name Std.Dev.
#> bloque (Intercept) 0.6007
#> Residual 2.0454
#> Number of obs: 143, groups: bloque, 5
#> Fixed Effects:
#> treatirrigado treatsequia genoG02
#> 16.09325 13.78200 -4.21525
#> genoG03 genoG04 genoG05
#> -5.02725 1.73475 -1.81125
#> genoG06 genoG07 genoG08
#> 11.42475 -13.14525 -3.67925
#> genoG09 genoG10 genoG11
#> 0.82675 -4.51258 -8.49125
#> genoG12 genoG13 genoG14
#> 2.84075 2.02475 2.74875
#> genoG15 treatsequia:genoG02 treatsequia:genoG03
#> -4.29725 -1.20275 -0.43075
#> treatsequia:genoG04 treatsequia:genoG06 treatsequia:genoG07
#> -2.99075 -8.12075 2.05125
#> treatsequia:genoG08 treatsequia:genoG09 treatsequia:genoG10
#> -1.67075 -0.19275 -0.97142
#> treatsequia:genoG11 treatsequia:genoG12 treatsequia:genoG13
#> -0.04275 -3.33475 -4.66675
#> treatsequia:genoG14 treatsequia:genoG15
#> -2.77875 1.65725
#> fit warnings:
#> fixed-effect model matrix is rank deficient so dropping 1 column / coefficient
#>
#>