# Simulation

There are multiple ways to simulate MMRM datasets using `brms` and `brms.mmrm`.

# 1 Simple

`brm_simulate_simple()` simulates a dataset from the prior predictive distribution of a simple special case of an MMRM.1

    library(brms.mmrm)
    set.seed(0)
    sim <- brm_simulate_simple(
      n_group = 3,
      n_patient = 100,
      n_time = 4
    )

The `data` element has a classed `tibble` you can directly supply to `brm_formula()` and `brm_model()`.

    sim$data
    #> # A tibble: 1,200 × 4
    #>    response group   time   patient
    #>       <dbl> <chr>   <chr>  <chr>
    #>  1    1.11  group_1 time_1 patient_001
    #>  2    2.15  group_1 time_2 patient_001
    #>  3    2.54  group_1 time_3 patient_001
    #>  4   -1.73  group_1 time_4 patient_001
    #>  5    1.11  group_1 time_1 patient_002
    #>  6    2.64  group_1 time_2 patient_002
    #>  7    1.69  group_1 time_3 patient_002
    #>  8    0.783 group_1 time_4 patient_002
    #>  9    0.118 group_1 time_1 patient_003
    #> 10    2.48  group_1 time_2 patient_003
    #> # ℹ 1,190 more rows

The `parameters` element has the corresponding parameter values simulated from the joint prior. Arguments to `brm_simulate_simple()` control hyperparameters.

    str(sim$parameters)
    #> List of 5
    #>  $ beta      : num [1:6] 1.263 -0.326 1.33 1.272 0.415 ...
    #>  $ tau       : num [1:4] -0.092857 -0.029472 -0.000577 0.240465
    #>  $ sigma     : num [1:4] 0.911 0.971 0.999 1.272
    #>  $ lambda    : num [1:4, 1:4] 1 0.415 -0.818 -0.282 0.415 ...
    #>  $ covariance: num [1:4, 1:4] 0.831 0.368 -0.745 -0.326 0.368 ...

And the `model_matrix` element has the regression model matrix of fixed effect parameters.

    head(sim$model_matrix)
    #>   groupgroup_1 groupgroup_2 groupgroup_3 timetime_2 timetime_3 timetime_4
    #> 1            1            0            0          0          0          0
    #> 2            1            0            0          1          0          0
    #> 3            1            0            0          0          1          0
    #> 4            1            0            0          0          0          1
    #> 5            1            0            0          0          0          0
    #> 6            1            0            0          1          0          0

# 2 Change from baseline

`brm_data_change()` can convert the outcome variable from raw response to change from baseline. This applies to real datasets passed through [brm_data()] as well as simulated ones from e.g. [brm_simulate_simple()]. The dataset above uses raw response with a baseline time point of `"time_1"`

    sim$data
    #> # A tibble: 1,200 × 4
    #>    response group   time   patient
    #>       <dbl> <chr>   <chr>  <chr>
    #>  1    1.11  group_1 time_1 patient_001
    #>  2    2.15  group_1 time_2 patient_001
    #>  3    2.54  group_1 time_3 patient_001
    #>  4   -1.73  group_1 time_4 patient_001
    #>  5    1.11  group_1 time_1 patient_002
    #>  6    2.64  group_1 time_2 patient_002
    #>  7    1.69  group_1 time_3 patient_002
    #>  8    0.783 group_1 time_4 patient_002
    #>  9    0.118 group_1 time_1 patient_003
    #> 10    2.48  group_1 time_2 patient_003
    #> # ℹ 1,190 more rows

`brm_data_change()` subtracts baseline, replaces the raw response column with a new change from baseline column, adds a new column for the original baseline raw response, and adjusts the internal attributes of the classed object accordingly.

    brm_data_change(
      data = sim$data,
      name_change = "new_change",
      name_baseline = "new_baseline"
    )
    #> # A tibble: 900 × 5
    #>    new_change new_baseline group   time   patient
    #>         <dbl>        <dbl> <chr>   <chr>  <chr>
    #>  1      1.04         1.11  group_1 time_2 patient_001
    #>  2      1.43         1.11  group_1 time_3 patient_001
    #>  3     -2.84         1.11  group_1 time_4 patient_001
    #>  4      1.53         1.11  group_1 time_2 patient_002
    #>  5      0.576        1.11  group_1 time_3 patient_002
    #>  6     -0.328        1.11  group_1 time_4 patient_002
    #>  7      2.37         0.118 group_1 time_2 patient_003
    #>  8      3.07         0.118 group_1 time_3 patient_003
    #>  9     -1.14         0.118 group_1 time_4 patient_003
    #> 10      1.57         1.29  group_1 time_2 patient_004
    #> # ℹ 890 more rows

# 3 Advanced

For a more nuanced simulation, build up the dataset layer by layer. Begin with `brm_simulate_outline()` to create an initial structure and a random missingness pattern. In `brm_simulate_outline()`, missing responses can come from either transitory intercurrent events or from dropouts. The `missing` column indicates which outcome values will be missing (`NA_real_`) in a later step. The `response` column is entirely missing for now and will be simulated later.

    data <- brm_simulate_outline(
      n_group = 2,
      n_patient = 100,
      n_time = 4,
      rate_dropout = 0.3
    )

    data
    #> # A tibble: 800 × 5
    #>    response missing group   time   patient
    #>       <dbl> <lgl>   <chr>   <chr>  <chr>
    #>  1       NA FALSE   group_1 time_1 patient_001
    #>  2       NA TRUE    group_1 time_2 patient_001
    #>  3       NA TRUE    group_1 time_3 patient_001
    #>  4       NA TRUE    group_1 time_4 patient_001
    #>  5       NA FALSE   group_1 time_1 patient_002
    #>  6       NA FALSE   group_1 time_2 patient_002
    #>  7       NA TRUE    group_1 time_3 patient_002
    #>  8       NA TRUE    group_1 time_4 patient_002
    #>  9       NA FALSE   group_1 time_1 patient_003
    #> 10       NA FALSE   group_1 time_2 patient_003
    #> # ℹ 790 more rows

Optionally add random continuous covariates `brm_simulate_continuous()` and random categorical covariates using `brm_simulate_categorical()`. In each case, the covariates are non-time-varying, which means each patient gets only one unique value.

    data <- data |>
      brm_simulate_continuous(names = c("biomarker1", "biomarker2")) |>
      brm_simulate_categorical(
        names = c("status1", "status2"),
        levels = c("present", "absent")
      )

    data
    #> # A tibble: 800 × 9
    #>    response missing group   time   patient biomarker1 biomarker2 status1 status2
    #>       <dbl> <lgl>   <chr>   <chr>  <chr>        <dbl>      <dbl> <chr>   <chr>
    #>  1       NA FALSE   group_1 time_1 patien…      0.328     -0.655 present absent
    #>  2       NA TRUE    group_1 time_2 patien…      0.328     -0.655 present absent
    #>  3       NA TRUE    group_1 time_3 patien…      0.328     -0.655 present absent
    #>  4       NA TRUE    group_1 time_4 patien…      0.328     -0.655 present absent
    #>  5       NA FALSE   group_1 time_1 patien…      1.04      -0.779 absent  absent
    #>  6       NA FALSE   group_1 time_2 patien…      1.04      -0.779 absent  absent
    #>  7       NA TRUE    group_1 time_3 patien…      1.04      -0.779 absent  absent
    #>  8       NA TRUE    group_1 time_4 patien…      1.04      -0.779 absent  absent
    #>  9       NA FALSE   group_1 time_1 patien…      0.717     -0.954 present absent
    #> 10       NA FALSE   group_1 time_2 patien…      0.717     -0.954 present absent
    #> # ℹ 790 more rows

As described in the next section, `brms.mmrm` has a convenient function `brm_simulate_prior()` to simulate the outcome variable `response` using the data skeleton above and the prior predictive distribution. However, if you prefer a full custom approach, you may need granular details about the parameterization, which requires the model matrix. Fortunately, `brms` supports a `make_standata()` function to provide this, given a dataset and a formula. You may need to temporarily set the response variable to something non-missing, and you may wish to specify a custom prior.

    library(brms)
    formula <- brm_formula(data = data)
    #> Warning: Rows containing NAs were excluded from the model.
    #> Error: All observations in the data were removed presumably because of NA values.
    formula
    #> response ~ group + group:time + time + unstr(time = time, gr = patient)
    #> sigma ~ 0 + time

    stan_data <- make_standata(
      formula = formula,
      data = mutate(data, response = 0)
    )
    model_matrix <- stan_data$X
    head(model_matrix)
    #>   Intercept groupgroup_2 timetime_2 timetime_3 timetime_4
    #> 1         1            0          0          0          0
    #> 2         1            0          1          0          0
    #> 3         1            0          0          1          0
    #> 4         1            0          0          0          1
    #> 5         1            0          0          0          0
    #> 6         1            0          1          0          0
    #>   groupgroup_2:timetime_2 groupgroup_2:timetime_3 groupgroup_2:timetime_4
    #> 1                       0                       0                       0
    #> 2                       0                       0                       0
    #> 3                       0                       0                       0
    #> 4                       0                       0                       0
    #> 5                       0                       0                       0
    #> 6                       0                       0                       0

# 4 Prior

Function `brm_simulate_prior()` simulates from the prior predictive distribution. It requires a dataset and a formula, and it accepts a custom prior constructed with `brms::set_prior()`.

    formula <- brm_formula(data = data)
    #> Error: All observations in the data were removed presumably because of NA values.

    library(brms)
    prior <- set_prior("student_t(3, 0, 1.3)", class = "Intercept") +
      set_prior("student_t(3, 0, 1.2)", class = "b") +
      set_prior("student_t(3, 0, 1.1)", class = "b", dpar = "sigma") +
      set_prior("lkj(1)", class = "cortime")

    prior
    #>                 prior     class coef group resp  dpar nlpar   lb   ub source
    #>  student_t(3, 0, 1.3) Intercept                             <NA> <NA>   user
    #>  student_t(3, 0, 1.2)         b                             <NA> <NA>   user
    #>  student_t(3, 0, 1.1)         b                 sigma       <NA> <NA>   user
    #>                lkj(1)   cortime                             <NA> <NA>   user

    sim <- brm_simulate_prior(
      data = data,
      formula = formula,
      prior = prior,
      refresh = 0
    )

The output object `sim` has multiple draws from the prior predictive distribution. `sim$outcome` has outcome draws, and `sim$parameters` has parameter draws. `sim$model_matrix` has the model matrix, and `sim$model` has the full `brms` model fit object. You can pass `sim$model` to functions from `brms` and `bayesplot` such as `pp_check()`.

    names(sim)
    #> [1] "data"         "model"        "model_matrix" "outcome"      "parameters"

In addition, `sim$data` has a copy of the original dataset, but with the outcome variable taken from the final draw from the prior predictive distribution. In addition, the missingness pattern is automatically applied so that `sim$data$response` is `NA_real_` whenever `sim$data$missing` equals `TRUE`.

    sim$data
    #> # A tibble: 800 × 9
    #>    response missing group   time   patient biomarker1 biomarker2 status1 status2
    #>       <dbl> <lgl>   <chr>   <chr>  <chr>        <dbl>      <dbl> <chr>   <chr>
    #>  1  -0.0490 FALSE   group_1 time_1 patien…      0.328     -0.655 present absent
    #>  2  NA      TRUE    group_1 time_2 patien…      0.328     -0.655 present absent
    #>  3  NA      TRUE    group_1 time_3 patien…      0.328     -0.655 present absent
    #>  4  NA      TRUE    group_1 time_4 patien…      0.328     -0.655 present absent
    #>  5   7.19   FALSE   group_1 time_1 patien…      1.04      -0.779 absent  absent
    #>  6   3.18   FALSE   group_1 time_2 patien…      1.04      -0.779 absent  absent
    #>  7  NA      TRUE    group_1 time_3 patien…      1.04      -0.779 absent  absent
    #>  8  NA      TRUE    group_1 time_4 patien…      1.04      -0.779 absent  absent
    #>  9  15.6    FALSE   group_1 time_1 patien…      0.717     -0.954 present absent
    #> 10   0.203  FALSE   group_1 time_2 patien…      0.717     -0.954 present absent
    #> # ℹ 790 more rows

# 5 Posterior

`brms` supports posterior predictive simulations and checks through functions `posteiror_predict()`, `posterior_epred()`, and `pp_check()`. These can be used with a `brms` model fit object either from `brm_model()` or from `brm_simulate_prior()`.

    data <- sim$data
    formula <- brm_formula(data = data)
    model <- brm_model(data = data, formula = formula, refresh = 0)
    outcome_draws <- posterior_predict(object = model)

The returned `outcome_draws` object is a numeric array of posterior predictive draws, with one row per draw and one column per non-missing observation (row) in the original data.

    str(outcome_draws)
    #>  num [1:4000, 1:659] 11.742 0.536 0.686 -8.36 -6.803 ...

    dim(data)
    #> [1] 800   9

    sum(!is.na(data$response))
    #> [1] 659

1. The function help file explains the details about the model parameterization.↩︎