mem.plotran: Plot random effects histograms for a fitted mixed-effects...

Description Usage Arguments Author(s) See Also Examples

View source: R/memtools.R

Description

This plot creates histogram plots for the columns extracted from random effects from a model fit. This is useful for model diagnostics, such as observing deviations from normality in the random effects.

Usage

1
mem.plotran(fit, breaks = 100)

Arguments

fit

A fitted mixed-effects model generated either through the lme4 or the nlme package.

breaks

Number of breaks in the histograms (passed to the 'hist'-function)

Author(s)

Teemu Daniel Laajala <teelaa@utu.fi>

See Also

mem.getcomp, mem.plotresid

Examples

1
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9
data(vcaplong)

exdat <- vcaplong[vcaplong[,"Group"] %in% c("Vehicle", "ARN"),]

library(lme4)
f1 <- lmer(log2PSA ~ 1 + DrugWeek + DrugWeek:ARN + (1 + DrugWeek|ID), data = exdat)

ranef(f1) # Histograms are plotted for these columns
mem.plotran(f1)

Example output

Loading required package: Matrix
$ID
      (Intercept)    DrugWeek
ID003  1.02994526 -0.24945102
ID009  0.09322637 -0.02924680
ID010 -0.39914405  0.08240203
ID016  0.43698593  0.03367724
ID031 -1.00714050  0.03092497
ID032 -0.47100869  0.02826516
ID037  0.42179935  0.17701942
ID040  0.66041311  0.03790908
ID045  0.13393772  0.04567836
ID054  1.58133264  0.03686119
ID056  0.93192560  0.08947408
ID075 -0.55850323  0.15256946
ID078 -0.57013198 -0.10206459
ID084 -0.60103865 -0.03846438
ID101  0.21780943  0.01149466
ID103 -0.36902838 -0.04919024
ID104 -0.42458519 -0.13116677
ID113 -0.53245319 -0.08580474
ID116  0.74422907 -0.46904159
ID125  0.24882778 -0.07803225
ID141 -0.61018503  0.05710768
ID144 -0.31226034  0.10897810
ID152  0.32515455  0.04884603
ID157 -0.50032013  0.14382223
ID158 -0.80996791 -0.05418933
ID160  0.57334350 -0.04578621
ID162 -0.08643625  0.01917847
ID174  0.48548965  0.05996185
ID182 -0.53662533  0.07864144
ID198 -0.09559112  0.08962648

with conditional variances for "ID" 
$ID
$ID$`(Intercept)`
$breaks
  [1] -1.02 -1.00 -0.98 -0.96 -0.94 -0.92 -0.90 -0.88 -0.86 -0.84 -0.82 -0.80
 [13] -0.78 -0.76 -0.74 -0.72 -0.70 -0.68 -0.66 -0.64 -0.62 -0.60 -0.58 -0.56
 [25] -0.54 -0.52 -0.50 -0.48 -0.46 -0.44 -0.42 -0.40 -0.38 -0.36 -0.34 -0.32
 [37] -0.30 -0.28 -0.26 -0.24 -0.22 -0.20 -0.18 -0.16 -0.14 -0.12 -0.10 -0.08
 [49] -0.06 -0.04 -0.02  0.00  0.02  0.04  0.06  0.08  0.10  0.12  0.14  0.16
 [61]  0.18  0.20  0.22  0.24  0.26  0.28  0.30  0.32  0.34  0.36  0.38  0.40
 [73]  0.42  0.44  0.46  0.48  0.50  0.52  0.54  0.56  0.58  0.60  0.62  0.64
 [85]  0.66  0.68  0.70  0.72  0.74  0.76  0.78  0.80  0.82  0.84  0.86  0.88
 [97]  0.90  0.92  0.94  0.96  0.98  1.00  1.02  1.04  1.06  1.08  1.10  1.12
[109]  1.14  1.16  1.18  1.20  1.22  1.24  1.26  1.28  1.30  1.32  1.34  1.36
[121]  1.38  1.40  1.42  1.44  1.46  1.48  1.50  1.52  1.54  1.56  1.58  1.60

$counts
  [1] 1 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 2 0 1 1 2 1 0 1 0 1 0 1 1 0 0 1 0
 [38] 0 0 0 0 0 0 0 0 0 2 0 0 0 0 0 0 0 0 1 0 1 0 0 0 1 0 1 0 0 0 1 0 0 0 0 2 0
 [75] 0 1 0 0 0 1 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 0 0 0 0 0
[112] 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1

$density
  [1] 1.666667 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
  [9] 0.000000 0.000000 1.666667 0.000000 0.000000 0.000000 0.000000 0.000000
 [17] 0.000000 0.000000 0.000000 0.000000 3.333333 0.000000 1.666667 1.666667
 [25] 3.333333 1.666667 0.000000 1.666667 0.000000 1.666667 0.000000 1.666667
 [33] 1.666667 0.000000 0.000000 1.666667 0.000000 0.000000 0.000000 0.000000
 [41] 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 3.333333 0.000000
 [49] 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.666667
 [57] 0.000000 1.666667 0.000000 0.000000 0.000000 1.666667 0.000000 1.666667
 [65] 0.000000 0.000000 0.000000 1.666667 0.000000 0.000000 0.000000 0.000000
 [73] 3.333333 0.000000 0.000000 1.666667 0.000000 0.000000 0.000000 1.666667
 [81] 0.000000 0.000000 0.000000 0.000000 1.666667 0.000000 0.000000 0.000000
 [89] 1.666667 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
 [97] 0.000000 1.666667 0.000000 0.000000 0.000000 0.000000 1.666667 0.000000
[105] 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
[113] 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
[121] 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000
[129] 0.000000 0.000000 1.666667

$mids
  [1] -1.01 -0.99 -0.97 -0.95 -0.93 -0.91 -0.89 -0.87 -0.85 -0.83 -0.81 -0.79
 [13] -0.77 -0.75 -0.73 -0.71 -0.69 -0.67 -0.65 -0.63 -0.61 -0.59 -0.57 -0.55
 [25] -0.53 -0.51 -0.49 -0.47 -0.45 -0.43 -0.41 -0.39 -0.37 -0.35 -0.33 -0.31
 [37] -0.29 -0.27 -0.25 -0.23 -0.21 -0.19 -0.17 -0.15 -0.13 -0.11 -0.09 -0.07
 [49] -0.05 -0.03 -0.01  0.01  0.03  0.05  0.07  0.09  0.11  0.13  0.15  0.17
 [61]  0.19  0.21  0.23  0.25  0.27  0.29  0.31  0.33  0.35  0.37  0.39  0.41
 [73]  0.43  0.45  0.47  0.49  0.51  0.53  0.55  0.57  0.59  0.61  0.63  0.65
 [85]  0.67  0.69  0.71  0.73  0.75  0.77  0.79  0.81  0.83  0.85  0.87  0.89
 [97]  0.91  0.93  0.95  0.97  0.99  1.01  1.03  1.05  1.07  1.09  1.11  1.13
[109]  1.15  1.17  1.19  1.21  1.23  1.25  1.27  1.29  1.31  1.33  1.35  1.37
[121]  1.39  1.41  1.43  1.45  1.47  1.49  1.51  1.53  1.55  1.57  1.59

$xname
[1] "y"

$equidist
[1] TRUE

attr(,"class")
[1] "histogram"

$ID$DrugWeek
$breaks
  [1] -0.470 -0.465 -0.460 -0.455 -0.450 -0.445 -0.440 -0.435 -0.430 -0.425
 [11] -0.420 -0.415 -0.410 -0.405 -0.400 -0.395 -0.390 -0.385 -0.380 -0.375
 [21] -0.370 -0.365 -0.360 -0.355 -0.350 -0.345 -0.340 -0.335 -0.330 -0.325
 [31] -0.320 -0.315 -0.310 -0.305 -0.300 -0.295 -0.290 -0.285 -0.280 -0.275
 [41] -0.270 -0.265 -0.260 -0.255 -0.250 -0.245 -0.240 -0.235 -0.230 -0.225
 [51] -0.220 -0.215 -0.210 -0.205 -0.200 -0.195 -0.190 -0.185 -0.180 -0.175
 [61] -0.170 -0.165 -0.160 -0.155 -0.150 -0.145 -0.140 -0.135 -0.130 -0.125
 [71] -0.120 -0.115 -0.110 -0.105 -0.100 -0.095 -0.090 -0.085 -0.080 -0.075
 [81] -0.070 -0.065 -0.060 -0.055 -0.050 -0.045 -0.040 -0.035 -0.030 -0.025
 [91] -0.020 -0.015 -0.010 -0.005  0.000  0.005  0.010  0.015  0.020  0.025
[101]  0.030  0.035  0.040  0.045  0.050  0.055  0.060  0.065  0.070  0.075
[111]  0.080  0.085  0.090  0.095  0.100  0.105  0.110  0.115  0.120  0.125
[121]  0.130  0.135  0.140  0.145  0.150  0.155  0.160  0.165  0.170  0.175
[131]  0.180

$counts
  [1] 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
 [38] 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 1
 [75] 0 0 1 0 1 0 0 0 0 1 2 0 1 0 1 0 0 0 0 0 0 0 1 1 0 1 2 2 0 2 0 2 0 0 0 1 1
[112] 2 0 0 0 1 0 0 0 0 0 0 1 0 1 0 0 0 0 1

$density
  [1]  6.666667  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000
  [8]  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000
 [15]  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000
 [22]  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000
 [29]  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000
 [36]  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000
 [43]  0.000000  0.000000  6.666667  0.000000  0.000000  0.000000  0.000000
 [50]  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000
 [57]  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000  0.000000
 [64]  0.000000  0.000000  0.000000  0.000000  6.666667  0.000000  0.000000
 [71]  0.000000  0.000000  0.000000  6.666667  0.000000  0.000000  6.666667
 [78]  0.000000  6.666667  0.000000  0.000000  0.000000  0.000000  6.666667
 [85] 13.333333  0.000000  6.666667  0.000000  6.666667  0.000000  0.000000
 [92]  0.000000  0.000000  0.000000  0.000000  0.000000  6.666667  6.666667
 [99]  0.000000  6.666667 13.333333 13.333333  0.000000 13.333333  0.000000
[106] 13.333333  0.000000  0.000000  0.000000  6.666667  6.666667 13.333333
[113]  0.000000  0.000000  0.000000  6.666667  0.000000  0.000000  0.000000
[120]  0.000000  0.000000  0.000000  6.666667  0.000000  6.666667  0.000000
[127]  0.000000  0.000000  0.000000  6.666667

$mids
  [1] -0.4675 -0.4625 -0.4575 -0.4525 -0.4475 -0.4425 -0.4375 -0.4325 -0.4275
 [10] -0.4225 -0.4175 -0.4125 -0.4075 -0.4025 -0.3975 -0.3925 -0.3875 -0.3825
 [19] -0.3775 -0.3725 -0.3675 -0.3625 -0.3575 -0.3525 -0.3475 -0.3425 -0.3375
 [28] -0.3325 -0.3275 -0.3225 -0.3175 -0.3125 -0.3075 -0.3025 -0.2975 -0.2925
 [37] -0.2875 -0.2825 -0.2775 -0.2725 -0.2675 -0.2625 -0.2575 -0.2525 -0.2475
 [46] -0.2425 -0.2375 -0.2325 -0.2275 -0.2225 -0.2175 -0.2125 -0.2075 -0.2025
 [55] -0.1975 -0.1925 -0.1875 -0.1825 -0.1775 -0.1725 -0.1675 -0.1625 -0.1575
 [64] -0.1525 -0.1475 -0.1425 -0.1375 -0.1325 -0.1275 -0.1225 -0.1175 -0.1125
 [73] -0.1075 -0.1025 -0.0975 -0.0925 -0.0875 -0.0825 -0.0775 -0.0725 -0.0675
 [82] -0.0625 -0.0575 -0.0525 -0.0475 -0.0425 -0.0375 -0.0325 -0.0275 -0.0225
 [91] -0.0175 -0.0125 -0.0075 -0.0025  0.0025  0.0075  0.0125  0.0175  0.0225
[100]  0.0275  0.0325  0.0375  0.0425  0.0475  0.0525  0.0575  0.0625  0.0675
[109]  0.0725  0.0775  0.0825  0.0875  0.0925  0.0975  0.1025  0.1075  0.1125
[118]  0.1175  0.1225  0.1275  0.1325  0.1375  0.1425  0.1475  0.1525  0.1575
[127]  0.1625  0.1675  0.1725  0.1775

$xname
[1] "y"

$equidist
[1] TRUE

attr(,"class")
[1] "histogram"

hamlet documentation built on May 1, 2019, 8:40 p.m.