Extracting Random Effects

Intro

This creates a table of random effects, including the uncertainty in the estimate where applicable.

Examples

library(dplyr)

library(lme4)
library(glmmTMB)
library(nlme)
library(brms)
library(rstanarm)
library(mgcv)


lmer_model <-
  lmer(Reaction ~ Days + (1 + Days | Subject), data = sleepstudy)

lme_model  <-
  lme(Reaction ~ Days, random = ~ 1 + Days | Subject, data = sleepstudy)

tmb_model  <-
  glmmTMB(Reaction ~ Days + (1 + Days | Subject), data = sleepstudy)

# brms_model <-
#   brm(Reaction ~ Days + (1 + Days | Subject), 
#       data = sleepstudy,
#       cores = 4,
#       refresh = -1,
#       verbose = FALSE
#   )

# rstanarm_model <-
#   stan_glmer(Reaction ~ Days + (1 + Days | Subject), 
#       data = sleepstudy,
#       cores = 4,
#       refresh = -1,
#       verbose = FALSE
#   )

# this is akin to (1 | Subject) + (0 + Days | Subject) in lme4
mgcv_model <-
  gam(
    Reaction ~  Days +
      s(Subject, bs = 're') +
      s(Days, Subject, bs = 're'),
    data   = lme4::sleepstudy,
    method = 'REML'
  )

library(mixedup)

extract_random_effects(lmer_model)
 [38;5;246m# A tibble: 36 × 7 [39m
   group_var effect    group   value    se lower_2.5 upper_97.5
    [3m [38;5;246m<chr> [39m [23m      [3m [38;5;246m<chr> [39m [23m      [3m [38;5;246m<fct> [39m [23m    [3m [38;5;246m<dbl> [39m [23m  [3m [38;5;246m<dbl> [39m [23m      [3m [38;5;246m<dbl> [39m [23m       [3m [38;5;246m<dbl> [39m [23m
 [38;5;250m 1 [39m Subject   Intercept 308     2.26   12.1   - [31m21 [39m [31m. [39m [31m4 [39m         25.9
 [38;5;250m 2 [39m Subject   Intercept 309   - [31m40 [39m [31m. [39m [31m4 [39m    12.1   - [31m64 [39m [31m. [39m [31m1 [39m        - [31m16 [39m [31m. [39m [31m7 [39m
 [38;5;250m 3 [39m Subject   Intercept 310   - [31m39 [39m [31m. [39m [31m0 [39m    12.1   - [31m62 [39m [31m. [39m [31m6 [39m        - [31m15 [39m [31m. [39m [31m3 [39m
 [38;5;250m 4 [39m Subject   Intercept 330    23.7    12.1     0.032       47.3
 [38;5;250m 5 [39m Subject   Intercept 331    22.3    12.1    - [31m1 [39m [31m. [39m [31m40 [39m        45.9
 [38;5;250m 6 [39m Subject   Intercept 332     9.04   12.1   - [31m14 [39m [31m. [39m [31m6 [39m         32.7
 [38;5;250m 7 [39m Subject   Intercept 333    16.8    12.1    - [31m6 [39m [31m. [39m [31m82 [39m        40.5
 [38;5;250m 8 [39m Subject   Intercept 334    - [31m7 [39m [31m. [39m [31m23 [39m   12.1   - [31m30 [39m [31m. [39m [31m9 [39m         16.4
 [38;5;250m 9 [39m Subject   Intercept 335    - [31m0 [39m [31m. [39m [31m334 [39m  12.1   - [31m24 [39m [31m. [39m [31m0 [39m         23.3
 [38;5;250m10 [39m Subject   Intercept 337    34.9    12.1    11.2         58.5
 [38;5;246m# … with 26 more rows [39m


extract_random_effects(lme_model)
 [38;5;246m# A tibble: 36 × 4 [39m
   group_var effect group   value
    [3m [38;5;246m<chr> [39m [23m      [3m [38;5;246m<chr> [39m [23m   [3m [38;5;246m<chr> [39m [23m    [3m [38;5;246m<dbl> [39m [23m
 [38;5;250m 1 [39m Subject   Days   308     9.20 
 [38;5;250m 2 [39m Subject   Days   309    - [31m8 [39m [31m. [39m [31m62 [39m 
 [38;5;250m 3 [39m Subject   Days   310    - [31m5 [39m [31m. [39m [31m45 [39m 
 [38;5;250m 4 [39m Subject   Days   330    - [31m4 [39m [31m. [39m [31m81 [39m 
 [38;5;250m 5 [39m Subject   Days   331    - [31m3 [39m [31m. [39m [31m0 [39m [31m7 [39m 
 [38;5;250m 6 [39m Subject   Days   332    - [31m0 [39m [31m. [39m [31m272 [39m
 [38;5;250m 7 [39m Subject   Days   333    - [31m0 [39m [31m. [39m [31m224 [39m
 [38;5;250m 8 [39m Subject   Days   334     1.08 
 [38;5;250m 9 [39m Subject   Days   335   - [31m10 [39m [31m. [39m [31m8 [39m  
 [38;5;250m10 [39m Subject   Days   337     8.63 
 [38;5;246m# … with 26 more rows [39m


extract_random_effects(tmb_model)
 [38;5;246m# A tibble: 36 × 7 [39m
   group_var effect    group  value    se lower_2.5 upper_97.5
    [3m [38;5;246m<chr> [39m [23m      [3m [38;5;246m<chr> [39m [23m      [3m [38;5;246m<fct> [39m [23m   [3m [38;5;246m<dbl> [39m [23m  [3m [38;5;246m<dbl> [39m [23m      [3m [38;5;246m<dbl> [39m [23m       [3m [38;5;246m<dbl> [39m [23m
 [38;5;250m 1 [39m Subject   Intercept 308     2.82  13.7    - [31m23 [39m [31m. [39m [31m9 [39m        29.6
 [38;5;250m 2 [39m Subject   Intercept 309   - [31m40 [39m [31m. [39m [31m0 [39m   13.8    - [31m67 [39m [31m. [39m [31m2 [39m       - [31m12 [39m [31m. [39m [31m9 [39m
 [38;5;250m 3 [39m Subject   Intercept 310   - [31m38 [39m [31m. [39m [31m4 [39m   13.7    - [31m65 [39m [31m. [39m [31m4 [39m       - [31m11 [39m [31m. [39m [31m5 [39m
 [38;5;250m 4 [39m Subject   Intercept 330    22.8   13.9     - [31m4 [39m [31m. [39m [31m51 [39m       50.2
 [38;5;250m 5 [39m Subject   Intercept 331    21.6   13.6     - [31m5 [39m [31m. [39m [31m11 [39m       48.2
 [38;5;250m 6 [39m Subject   Intercept 332     8.82  12.9    - [31m16 [39m [31m. [39m [31m5 [39m        34.1
 [38;5;250m 7 [39m Subject   Intercept 333    16.4   13.1     - [31m9 [39m [31m. [39m [31m23 [39m       42.1
 [38;5;250m 8 [39m Subject   Intercept 334    - [31m7 [39m [31m. [39m [31m00 [39m  12.9    - [31m32 [39m [31m. [39m [31m3 [39m        18.3
 [38;5;250m 9 [39m Subject   Intercept 335    - [31m1 [39m [31m. [39m [31m0 [39m [31m4 [39m  14.0    - [31m28 [39m [31m. [39m [31m5 [39m        26.4
 [38;5;250m10 [39m Subject   Intercept 337    34.7   13.6      7.94       61.4
 [38;5;246m# … with 26 more rows [39m

extract_random_effects(brms_model)
 [38;5;246m# A tibble: 36 × 7 [39m
   group_var effect    group   value    se lower_2.5 upper_97.5
    [3m [38;5;246m<chr> [39m [23m      [3m [38;5;246m<chr> [39m [23m      [3m [38;5;246m<chr> [39m [23m    [3m [38;5;246m<dbl> [39m [23m  [3m [38;5;246m<dbl> [39m [23m      [3m [38;5;246m<dbl> [39m [23m       [3m [38;5;246m<dbl> [39m [23m
 [38;5;250m 1 [39m Subject   Intercept 308     2.82   12.9    - [31m23 [39m [31m. [39m [31m5 [39m        28.6
 [38;5;250m 2 [39m Subject   Intercept 309   - [31m39 [39m [31m. [39m [31m0 [39m    13.2    - [31m64 [39m [31m. [39m [31m4 [39m       - [31m16 [39m [31m. [39m [31m7 [39m
 [38;5;250m 3 [39m Subject   Intercept 310   - [31m38 [39m [31m. [39m [31m6 [39m    13.5    - [31m68 [39m [31m. [39m [31m2 [39m       - [31m12 [39m [31m. [39m [31m1 [39m
 [38;5;250m 4 [39m Subject   Intercept 330    23.4    14.6     - [31m2 [39m [31m. [39m [31m46 [39m       55.4
 [38;5;250m 5 [39m Subject   Intercept 331    23.6    16.3     - [31m7 [39m [31m. [39m [31m90 [39m       54.6
 [38;5;250m 6 [39m Subject   Intercept 332    10.1    14.0    - [31m17 [39m [31m. [39m [31m8 [39m        34.8
 [38;5;250m 7 [39m Subject   Intercept 333    18.2    15.4    - [31m10 [39m [31m. [39m [31m4 [39m        48.1
 [38;5;250m 8 [39m Subject   Intercept 334    - [31m5 [39m [31m. [39m [31m50 [39m   13.6    - [31m34 [39m [31m. [39m [31m4 [39m        18.5
 [38;5;250m 9 [39m Subject   Intercept 335    - [31m0 [39m [31m. [39m [31m964 [39m  16.5    - [31m34 [39m [31m. [39m [31m7 [39m        27.9
 [38;5;250m10 [39m Subject   Intercept 337    37.0    16.1     11.1        71.7
 [38;5;246m# … with 26 more rows [39m


extract_random_effects(rstanarm_model)
 [38;5;246m# A tibble: 36 × 7 [39m
   group_var effect    group  value    se lower_2.5 upper_97.5
    [3m [38;5;246m<chr> [39m [23m      [3m [38;5;246m<chr> [39m [23m      [3m [38;5;246m<fct> [39m [23m   [3m [38;5;246m<dbl> [39m [23m  [3m [38;5;246m<dbl> [39m [23m      [3m [38;5;246m<dbl> [39m [23m       [3m [38;5;246m<dbl> [39m [23m
 [38;5;250m 1 [39m Subject   Intercept 308     3.93  12.3    - [31m20 [39m [31m. [39m [31m3 [39m        28.1
 [38;5;250m 2 [39m Subject   Intercept 309   - [31m38 [39m [31m. [39m [31m4 [39m   12.3    - [31m62 [39m [31m. [39m [31m6 [39m       - [31m14 [39m [31m. [39m [31m2 [39m
 [38;5;250m 3 [39m Subject   Intercept 310   - [31m37 [39m [31m. [39m [31m3 [39m   12.3    - [31m61 [39m [31m. [39m [31m5 [39m       - [31m13 [39m [31m. [39m [31m1 [39m
 [38;5;250m 4 [39m Subject   Intercept 330    22.1   12.3     - [31m2 [39m [31m. [39m [31m10 [39m       46.3
 [38;5;250m 5 [39m Subject   Intercept 331    18.1   12.3     - [31m6 [39m [31m. [39m [31m11 [39m       42.3
 [38;5;250m 6 [39m Subject   Intercept 332     7.91  12.3    - [31m16 [39m [31m. [39m [31m3 [39m        32.1
 [38;5;250m 7 [39m Subject   Intercept 333    12.5   12.3    - [31m11 [39m [31m. [39m [31m7 [39m        36.7
 [38;5;250m 8 [39m Subject   Intercept 334    - [31m8 [39m [31m. [39m [31m20 [39m  12.3    - [31m32 [39m [31m. [39m [31m4 [39m        16.0
 [38;5;250m 9 [39m Subject   Intercept 335    - [31m4 [39m [31m. [39m [31m0 [39m [31m3 [39m  12.3    - [31m28 [39m [31m. [39m [31m2 [39m        20.2
 [38;5;250m10 [39m Subject   Intercept 337    31.5   12.3      7.27       55.7
 [38;5;246m# … with 26 more rows [39m


extract_random_effects(mgcv_model)
 [38;5;246m# A tibble: 36 × 7 [39m
   group_var effect    group   value    se lower_2.5 upper_97.5
    [3m [38;5;246m<chr> [39m [23m      [3m [38;5;246m<chr> [39m [23m      [3m [38;5;246m<chr> [39m [23m    [3m [38;5;246m<dbl> [39m [23m  [3m [38;5;246m<dbl> [39m [23m      [3m [38;5;246m<dbl> [39m [23m       [3m [38;5;246m<dbl> [39m [23m
 [38;5;250m 1 [39m Subject   Intercept 308     1.51   13.3    - [31m24 [39m [31m. [39m [31m5 [39m        27.5
 [38;5;250m 2 [39m Subject   Intercept 309   - [31m40 [39m [31m. [39m [31m4 [39m    13.3    - [31m66 [39m [31m. [39m [31m4 [39m       - [31m14 [39m [31m. [39m [31m3 [39m
 [38;5;250m 3 [39m Subject   Intercept 310   - [31m39 [39m [31m. [39m [31m2 [39m    13.3    - [31m65 [39m [31m. [39m [31m2 [39m       - [31m13 [39m [31m. [39m [31m2 [39m
 [38;5;250m 4 [39m Subject   Intercept 330    24.5    13.3     - [31m1 [39m [31m. [39m [31m51 [39m       50.5
 [38;5;250m 5 [39m Subject   Intercept 331    22.9    13.3     - [31m3 [39m [31m. [39m [31m11 [39m       48.9
 [38;5;250m 6 [39m Subject   Intercept 332     9.22   13.3    - [31m16 [39m [31m. [39m [31m8 [39m        35.2
 [38;5;250m 7 [39m Subject   Intercept 333    17.2    13.3     - [31m8 [39m [31m. [39m [31m87 [39m       43.2
 [38;5;250m 8 [39m Subject   Intercept 334    - [31m7 [39m [31m. [39m [31m45 [39m   13.3    - [31m33 [39m [31m. [39m [31m5 [39m        18.6
 [38;5;250m 9 [39m Subject   Intercept 335     0.579  13.3    - [31m25 [39m [31m. [39m [31m4 [39m        26.6
 [38;5;250m10 [39m Subject   Intercept 337    34.8    13.3      8.74       60.8
 [38;5;246m# … with 26 more rows [39m

Options

lmer_model <-
  lmer(y ~ service + (1 | d) + (1 | s), data = InstEval[1:5000,])

extract_random_effects(
  lmer_model,
  ci_level = .9,
  digits   = 2
) %>% 
  head()
 [38;5;246m# A tibble: 6 × 7 [39m
  group_var effect    group value    se lower_5 upper_95
   [3m [38;5;246m<chr> [39m [23m      [3m [38;5;246m<chr> [39m [23m      [3m [38;5;246m<fct> [39m [23m  [3m [38;5;246m<dbl> [39m [23m  [3m [38;5;246m<dbl> [39m [23m    [3m [38;5;246m<dbl> [39m [23m     [3m [38;5;246m<dbl> [39m [23m
 [38;5;250m1 [39m d         Intercept 1     - [31m0 [39m [31m. [39m [31m0 [39m [31m2 [39m  0.39   - [31m0 [39m [31m. [39m [31m66 [39m     0.62
 [38;5;250m2 [39m d         Intercept 6      0.09  0.34   - [31m0 [39m [31m. [39m [31m46 [39m     0.65
 [38;5;250m3 [39m d         Intercept 7      0.3   0.41   - [31m0 [39m [31m. [39m [31m38 [39m     0.98
 [38;5;250m4 [39m d         Intercept 8     - [31m0 [39m [31m. [39m [31m18 [39m  0.39   - [31m0 [39m [31m. [39m [31m82 [39m     0.46
 [38;5;250m5 [39m d         Intercept 12     0.21  0.31   - [31m0 [39m [31m. [39m [31m3 [39m      0.73
 [38;5;250m6 [39m d         Intercept 13     0.58  0.31    0.07     1.1

tmb_zip <- glmmTMB(
  count ~ spp + mined + (1 | site),
  zi =  ~ spp + mined + (1 | site),
  family = truncated_poisson,
  data   = Salamanders
)

extract_random_effects(
  tmb_zip,
  component = 'zi'
) %>% 
  head()
 [38;5;246m# A tibble: 6 × 7 [39m
  group_var effect    group  value    se lower_2.5 upper_97.5
   [3m [38;5;246m<chr> [39m [23m      [3m [38;5;246m<chr> [39m [23m      [3m [38;5;246m<fct> [39m [23m   [3m [38;5;246m<dbl> [39m [23m  [3m [38;5;246m<dbl> [39m [23m      [3m [38;5;246m<dbl> [39m [23m       [3m [38;5;246m<dbl> [39m [23m
 [38;5;250m1 [39m site      Intercept R-1   - [31m0 [39m [31m. [39m [31m0 [39m [31m2 [39m  0.126    - [31m0 [39m [31m. [39m [31m267 [39m      0.227
 [38;5;250m2 [39m site      Intercept R-2    0.037 0.125    - [31m0 [39m [31m. [39m [31m209 [39m      0.283
 [38;5;250m3 [39m site      Intercept R-3    0.051 0.135    - [31m0 [39m [31m. [39m [31m214 [39m      0.316
 [38;5;250m4 [39m site      Intercept R-4    0.434 0.123     0.193      0.675
 [38;5;250m5 [39m site      Intercept R-5    0.069 0.125    - [31m0 [39m [31m. [39m [31m177 [39m      0.314
 [38;5;250m6 [39m site      Intercept R-6    0.096 0.12     - [31m0 [39m [31m. [39m [31m139 [39m      0.331

Michael Clark

2022-10-10

Intro

Examples

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