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Mixed Design Simulation

Source: vignettes/sim_mixed.Rmd
sim_mixed.Rmd

This paper provides a tutorial and examples for more complex designs.

Building multilevel designs

You can build up a mixed effects model by adding random factors in a stepwise fashion using add_random(). The example below simulates 3 schools with 2, 3 and 4 classes nested in each school.

data <- add_random(school = 3) %>%
  add_random(class = c(2, 3, 4), .nested_in = "school")
school class
school1 class1
school1 class2
school2 class3
school2 class4
school2 class5
school3 class6
school3 class7
school3 class8
school3 class9

A cross-classified design with 2 subjects and 3 items.

data <- add_random(subj = 2, item = 3)
subj item
subj1 item1
subj1 item2
subj1 item3
subj2 item1
subj2 item2
subj2 item3

You can also name the items directly if you don’t like the default names. Crossed factors can be named with a vector of names, while nested factors need to be a list with one vector of names for each nesting level.

data <- add_random(school = c("Hyndland Primary", "Hyndland Secondary")) %>%
  add_random(class = list(paste0("P", 1:2),
                          paste0("S", 1:2)),
             .nested_in = "school")
school class
Hyndland Primary P1
Hyndland Primary P2
Hyndland Secondary S1
Hyndland Secondary S2

Adding fixed factors

Add within factors with add_within().

data <- add_random(subj = 2) %>%
  add_within("subj", time = c("pre", "post"),
             condition = c("control", "test"))
subj time condition
subj1 pre control
subj1 pre test
subj1 post control
subj1 post test
subj2 pre control
subj2 pre test
subj2 post control
subj2 post test

Add between factors with add_between(). If you have more than one factor, they will be crossed. If you set .shuffle = TRUE, the factors will be added randomly (not in “order”), and separately added factors may end up confounded. This simulates true random allocation.

data <- add_random(subj = 4, item = 2) %>%
  add_between("subj", cond = c("control", "test"), gen = c("X", "Z")) %>%
  add_between("item", version = c("A", "B")) %>%
  add_between(c("subj", "item"), shuffled = 1:4, .shuffle = TRUE) %>%
  add_between(c("subj", "item"), not_shuffled = 1:4, .shuffle = FALSE)
subj item cond gen version shuffled not_shuffled
subj1 item1 control X A 2 1
subj1 item2 control X B 3 2
subj2 item1 control Z A 2 3
subj2 item2 control Z B 1 4
subj3 item1 test X A 3 1
subj3 item2 test X B 4 2
subj4 item1 test Z A 4 3
subj4 item2 test Z B 1 4

Unequal cells

If the levels of a factor don’t have equal probability, set the probability with .prob. If the sum of the values equals the number of groups, you will always get those exact numbers (e.g., always 8 control and 2 test; set shuffle = TRUE to get them in a random order). Otherwise, the values are sampled and the exact proportions will change for each simulation.

data <- add_random(subj = 10) %>%
  add_between("subj", cond = c("control", "test"), .prob = c(8, 2)) %>%
  add_between("subj", age = c("young", "old"), .prob = c(.8, .2))
subj cond age
subj01 control old
subj02 control young
subj03 control old
subj04 control young
subj05 control young
subj06 control young
subj07 control young
subj08 control old
subj09 test young
subj10 test young

If you have more than one between-subject factor, setting them together allows you to set joint proportions for each cell.

data <- add_random(subj = 10) %>%
  add_between("subj", 
              cond = c("control", "test"),
              age = c("young", "old"), 
              .prob = c(2, 3, 4, 1))
subj cond age
subj01 control young
subj02 control young
subj03 control old
subj04 control old
subj05 control old
subj06 test young
subj07 test young
subj08 test young
subj09 test young
subj10 test old

Counterbalanced designs

You can use the filter() function from dplyr to create counterbalanced designs. For example, if your items are grouped into A and B counterbalanced groups, add a between-subjects and a between-items factor with the same levels and filter only rows where the subject value matches the item value. In the example below, odd-numbered subjects only respond to odd-numbered items.

data <- add_random(subj = 4, item = 4) %>%
  add_between("subj", subj_cb = c("odd", "even")) %>%
  add_between("item", item_cb = c("odd", "even")) %>%
  dplyr::filter(subj_cb == item_cb)
subj item subj_cb item_cb
subj1 item1 odd odd
subj1 item3 odd odd
subj2 item2 even even
subj2 item4 even even
subj3 item1 odd odd
subj3 item3 odd odd
subj4 item2 even even
subj4 item4 even even

Recoding

To set up data for analysis, you often need to recode categorical variables. Use the helper function add_contrast() for this. The code below creates anova-coded and treatment-coded versions of “cond” and the two variables needed to treatment-code the 3-level variable “type”. See the contrasts vignette for more details.

You can add_recode() for setting a manual contrast that isn’t available in add_contrast(), such as weighted contrasts.

data <- add_random(subj = 2, item = 3) %>%
  add_between("subj", cond = c("A", "B")) %>%
  add_between("item", type = c("X", "Y", "Z")) %>%
  # add contrasts
  add_contrast("cond", "anova", add_cols = TRUE) %>%
  add_contrast("cond", "treatment", add_cols = TRUE) %>%
  # you can change the default column names
  add_contrast("type", "treatment", add_cols = TRUE, colnames = c("Y", "Z")) %>%
  add_recode("type", "type.w", X = -1.3, Y = 0, Z = 0.92)
subj item cond type cond.B-A cond.B-A.tr Y Z type.w
subj1 item1 A X -0.5 0 0 0 -1.30
subj1 item2 A Y -0.5 0 1 0 0.00
subj1 item3 A Z -0.5 0 0 1 0.92
subj2 item1 B X 0.5 1 0 0 -1.30
subj2 item2 B Y 0.5 1 1 0 0.00
subj2 item3 B Z 0.5 1 0 1 0.92

Adding random effects

To simulate multilevel data, you need to add random intercepts and slopes for each random factor (or combination of random factors). These are randomly sampled each time you simulate a new sample, so you can only characterise them by their standard deviation. You can use the function add_ranef() to add random effects with specified SDs. If you add more than one random effect for the same group (e.g., a random intercept and a random slope), you can specify their correlation with .cors (you can specify correlations in the same way as for rnorm_multi()).

The code below sets up a simple cross-classified design where 2 subjects are crossed with 2 items. It adds a between-subject, within-item factor of “version”. Then it adds random effects by subject, item, and their interaction, as well as an error term (sigma).

data <- add_random(subj = 4, item = 2) %>%
  add_between("subj", version = 1:2) %>%
  # add by-subject random intercept
  add_ranef("subj", u0s = 1.3) %>%
  # add by-item random intercept and slope
  add_ranef("item", u0i = 1.5, u1i = 1.5, .cors = 0.3) %>%
  # add by-subject:item random intercept
  add_ranef(c("subj", "item"), u0si = 1.7) %>%
  # add error term (by observation)
  add_ranef(sigma = 2.2)
subj item version u0s u0i u1i u0si sigma
subj1 item1 1 1.175 -2.549 0.952 -1.531 1.503
subj1 item2 1 1.175 -0.811 -1.595 -0.256 1.518
subj2 item1 2 -2.014 -2.549 0.952 -1.407 1.174
subj2 item2 2 -2.014 -0.811 -1.595 3.376 -0.409
subj3 item1 1 1.329 -2.549 0.952 0.075 0.842
subj3 item2 1 1.329 -0.811 -1.595 -0.687 0.828
subj4 item1 2 0.195 -2.549 0.952 -0.804 2.538
subj4 item2 2 0.195 -0.811 -1.595 -0.705 3.465

Simulating data

Now you can define your data-generating parameters and put everything together to simulate a dataset. In this example,subject are crossed with items, and there is a single treatment-coded between-subject, within-item fixed factor of condition with levels “control” and “test”. The intercept and effect of condition are both set to 0. The SDs of the random intercepts and slopes are all set to 1 (you will need pilot data to estimate realistic values for your design), the correlation between the random intercept and slope by items is set to 0. The SD of the error term is set to 2.

# define parameters
subj_n = 10  # number of subjects
item_n = 10  # number of items
b0 = 0       # intercept
b1 = 0       # fixed effect of condition
u0s_sd = 1   # random intercept SD for subjects
u0i_sd = 1   # random intercept SD for items
u1i_sd = 1   # random b1 slope SD for items
r01i = 0     # correlation between random effects 0 and 1 for items
sigma_sd = 2 # error SD
  
# set up data structure
data <- add_random(subj = subj_n, item = item_n) %>%
  # add and recode categorical variables
  add_between("subj", cond = c("control", "test")) %>%
  add_recode("cond", "cond.t", control = 0, test = 1) %>%
  # add random effects 
  add_ranef("subj", u0s = u0s_sd) %>%
  add_ranef("item", u0i = u0i_sd, u1i = u1i_sd, .cors = r01i) %>%
  add_ranef(sigma = sigma_sd) %>%
  # calculate DV
  mutate(dv = b0 + u0s + u0i + (b1 + u1i) * cond.t + sigma)
subj item cond cond.t u0s u0i u1i sigma dv
subj01 item01 control 0 0.589 2.135 0.684 -2.351 0.373
subj01 item02 control 0 0.589 -0.214 -0.252 -0.284 0.090
subj01 item03 control 0 0.589 0.947 -0.151 1.802 3.337
subj01 item04 control 0 0.589 0.652 -0.875 0.716 1.957
subj01 item05 control 0 0.589 -0.729 -1.977 -1.837 -1.977
subj01 item06 control 0 0.589 -1.050 0.238 -2.644 -3.105

Analysing your multilevel data

You can analyse these data with lme4::lmer().

m <- lmer(dv ~ cond.t + (1 | subj) + (1 + cond.t | item), data = data)

summary(m)
#> Linear mixed model fit by REML. t-tests use Satterthwaite's method [
#> lmerModLmerTest]
#> Formula: dv ~ cond.t + (1 | subj) + (1 + cond.t | item)
#>    Data: data
#> 
#> REML criterion at convergence: 421
#> 
#> Scaled residuals: 
#>      Min       1Q   Median       3Q      Max 
#> -1.94554 -0.66137  0.03661  0.66655  2.39501 
#> 
#> Random effects:
#>  Groups   Name        Variance Std.Dev. Corr 
#>  subj     (Intercept) 0.3239   0.5691        
#>  item     (Intercept) 0.7649   0.8746        
#>           cond.t      1.1253   1.0608   -0.66
#>  Residual             3.2817   1.8115        
#> Number of obs: 100, groups:  subj, 10; item, 10
#> 
#> Fixed effects:
#>             Estimate Std. Error       df t value Pr(>|t|)
#> (Intercept) -0.05392    0.45486  9.66296  -0.119    0.908
#> cond.t      -0.58770    0.61102  9.08258  -0.962    0.361
#> 
#> Correlation of Fixed Effects:
#>        (Intr)
#> cond.t -0.690

Power simulation

Include this code in a function so you can easily change the Ns, fixed effects, and random effects to any values. Then run a mixed effects model on the data and return the model.

sim <- function(subj_n = 10, item_n = 10,
                b0 = 0, b1 = 0,         # fixed effects 
                u0s_sd = 1, u0i_sd = 1, # random intercepts
                u1i_sd = 1, r01i = 0,   # random slope and cor
                sigma_sd = 2,           # error term
                ... # helps the function work with pmap() below
                ) {

  # set up data structure
  data <- add_random(subj = subj_n, item = item_n) %>%
    # add and recode categorical variables
    add_between("subj", cond = c("control", "test")) %>%
    add_recode("cond", "cond.t", control = 0, test = 1) %>%
    # add random effects 
    add_ranef("subj", u0s = u0s_sd) %>%
    add_ranef("item", u0i = u0i_sd, u1i = u1i_sd, .cors = r01i) %>%
    add_ranef(sigma = sigma_sd) %>%
    # calculate DV
    mutate(dv = b0 + u0s + u0i + (b1 + u1i) * cond.t + sigma)

  # run mixed effect model and return relevant values
  m <- lmer(dv ~ cond.t + (1 | subj) + (1 + cond.t | item), data = data)

  broom.mixed::tidy(m)
}

Check the function. Here, we’re simulating a fixed effect of condition (b1) of 0.5 for 50 subjects and 40 items, with a correlation between the random intercept and slope for items of 0.2, and the default values for all other parameters that we set above.

sim(subj_n = 50, item_n = 40, b1 = 0.5, r01i = 0.2)
#> # A tibble: 7 × 8
#>   effect   group    term              estimate std.error statistic    df p.value
#>   <chr>    <chr>    <chr>                <dbl>     <dbl>     <dbl> <dbl>   <dbl>
#> 1 fixed    NA       (Intercept)        -0.0715     0.286    -0.250  71.4   0.803
#> 2 fixed    NA       cond.t              0.499      0.395     1.27   68.1   0.210
#> 3 ran_pars subj     sd__(Intercept)     1.19      NA        NA      NA    NA    
#> 4 ran_pars item     sd__(Intercept)     0.913     NA        NA      NA    NA    
#> 5 ran_pars item     cor__(Intercept)…   0.256     NA        NA      NA    NA    
#> 6 ran_pars item     sd__cond.t          1.16      NA        NA      NA    NA    
#> 7 ran_pars Residual sd__Observation     2.08      NA        NA      NA    NA

Run the simulation repeatedly. I’m only running it 50 times per parameter combination here so my demo doesn’t take forever to run, but once you are done testing a range of parameters, you probably want to run the final simulation 100-1000 times. You might get a few warnings like “Model failed to converge” or “singular boundary”. You don’t need to worry too much if you only get a few of these. If most of your models have warnings, the simulation parameters are likely to be off.

x <- crossing(
  rep = 1:50, # number of replicates
  subj_n = c(50, 100), # range of subject N
  item_n = 25, # fixed item N
  b1 = c(0.25, 0.5, 0.75), # range of effects
  r01i = 0.2 # fixed correlation
) %>%
  mutate(analysis = pmap(., sim)) %>%
  unnest(analysis)

Filter and/or group the resulting table and calculate the proportion of p.values above your alpha threshold to get power for the fixed effects.

# calculate power for alpha = 0.05
filter(x, effect == "fixed", term == "cond.t") %>%
  group_by(b1, subj_n) %>% 
  summarise(power = mean(p.value < .05), 
            .groups = "drop") %>%
  ggplot(aes(b1, subj_n, fill = power)) +
  geom_tile() +
  geom_text(aes(label = sprintf("%.2f", power)), color = "white", size = 10) +
  scale_fill_viridis_c(limits = c(0, 1))