MMRMG01

Plots for Mixed-Effect Model Repeated Measures Analysis

Given an MMRM fitted with s_mmrm, g_mmrm_lsmeans displays for each visit the adjusted means within group and/or difference in adjusted means between groups. g_mmrm_diagnostic displays marginal residual plots for evaluating model fit.

Least Squares Means:
Estimates Within Groups

Considering the treatment variable in the model

Code
plot <- g_mmrm_lsmeans(
  mmrm_results,
  select = "estimates",
  xlab = "Visit"
)
plot

Considering the treatment variable in the model, with lines

Code
plot <- g_mmrm_lsmeans(
  mmrm_results,
  select = "estimates",
  xlab = "Visit",
  show_lines = TRUE
)
plot

Considering the treatment variable in the model, with statistics table

Code
plot <- g_mmrm_lsmeans(
  mmrm_results,
  select = "estimates",
  xlab = "Visit",
  table_stats = c("n", "estimate", "se", "ci"),
  table_font_size = 4,
  table_rel_height = 0.6
)
plot

Least Squares Means:
Contrasts Between Groups

Users can choose to display both estimates and contrasts together by running g_mmrm_lsmeans(mmrm_results).

Code
plot <- g_mmrm_lsmeans(
  mmrm_results,
  select = "contrasts",
  titles = c(contrasts = "Contrasts of FKSI-FWB means"),
  xlab = "Visit"
)
Coordinate system already present.
ℹ Adding new coordinate system, which will replace the existing one.
Code
plot

Model Diagnostics: Marginal
Fitted Values vs. Residuals

Code
plot <- g_mmrm_diagnostic(mmrm_results)
plot

Model Diagnostics: Normality
of Marginal Residuals

Code
plot <- g_mmrm_diagnostic(mmrm_results, type = "q-q-residual")
plot

Data Setup and
Model Fitting

Code
library(dplyr)
library(tern.mmrm)
library(nestcolor)

adsl <- random.cdisc.data::cadsl
adqs <- random.cdisc.data::cadqs

adqs_f <- adqs %>%
  dplyr::filter(PARAMCD == "FKSI-FWB" & !AVISIT %in% c("BASELINE")) %>%
  droplevels() %>%
  dplyr::mutate(ARM = factor(ARM, levels = c("B: Placebo", "A: Drug X", "C: Combination"))) %>%
  dplyr::mutate(AVISITN = rank(AVISITN) %>% as.factor() %>% as.numeric() %>% as.factor())

mmrm_results <- fit_mmrm(
  vars = list(
    response = "AVAL",
    covariates = c("STRATA2"),
    id = "USUBJID",
    arm = "ARM",
    visit = "AVISIT"
  ),
  data = adqs_f
)

teal App

Code
library(teal.modules.clinical)

## Data reproducible code
data <- teal_data()
data <- within(data, {
  library(dplyr)

  ADSL <- random.cdisc.data::cadsl
  ADQS <- random.cdisc.data::cadqs %>%
    filter(ABLFL != "Y" & ABLFL2 != "Y") %>%
    filter(AVISIT %in% c("WEEK 1 DAY 8", "WEEK 2 DAY 15", "WEEK 3 DAY 22")) %>%
    mutate(
      AVISIT = as.factor(AVISIT),
      AVISITN = rank(AVISITN) %>%
        as.factor() %>%
        as.numeric() %>%
        as.factor() # making consecutive numeric factor
    )
})
join_keys(data) <- default_cdisc_join_keys[c("ADSL", "ADQS")]

arm_ref_comp <- list(
  ARMCD = list(
    ref = "ARM A",
    comp = c("ARM B", "ARM C")
  )
)

## Reusable Configuration For Modules
ADQS <- data[["ADQS"]]

## Setup App
app <- init(
  data = data,
  modules = modules(
    tm_a_mmrm(
      label = "MMRM",
      dataname = "ADQS",
      aval_var = choices_selected(c("AVAL", "CHG"), "AVAL"),
      id_var = choices_selected(c("USUBJID", "SUBJID"), "USUBJID"),
      arm_var = choices_selected(c("ARM", "ARMCD"), "ARMCD"),
      visit_var = choices_selected(c("AVISIT", "AVISITN"), "AVISIT"),
      arm_ref_comp = arm_ref_comp,
      paramcd = choices_selected(
        choices = value_choices(ADQS, "PARAMCD", "PARAM"),
        selected = "FKSI-FWB"
      ),
      cov_var = choices_selected(c("BASE", "AGE", "SEX", "BASE:AVISIT"), NULL),
      conf_level = choices_selected(c(0.95, 0.9, 0.8), 0.95)
    )
  )
)

shinyApp(app$ui, app$server)

Reproducibility

Timestamp

[1] "2026-06-17 18:51:16 UTC"

Session Info

─ Session info ───────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.5.2 (2025-10-31)
 os       Ubuntu 24.04.4 LTS
 system   x86_64, linux-gnu
 ui       X11
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       Etc/UTC
 date     2026-06-17
 pandoc   3.9 @ /usr/bin/ (via rmarkdown)
 quarto   1.9.38 @ /usr/local/bin/quarto

─ Packages ───────────────────────────────────────────────────────────────────
 package               * version   date (UTC) lib source
 backports               1.5.1     2026-04-03 [1] CRAN (R 4.5.2)
 brio                    1.1.5     2024-04-24 [1] CRAN (R 4.5.2)
 broom                   1.0.13    2026-05-14 [1] CRAN (R 4.5.2)
 bsicons                 0.1.2     2023-11-04 [1] CRAN (R 4.5.2)
 bslib                   0.11.0    2026-05-16 [1] CRAN (R 4.5.2)
 cachem                  1.1.0     2024-05-16 [1] CRAN (R 4.5.2)
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 mmrm                    0.3.17    2026-01-08 [1] CRAN (R 4.5.2)
 mvtnorm                 1.4-1     2026-06-06 [1] RSPM
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 pkgcache                2.2.5     2026-04-09 [1] CRAN (R 4.5.2)
 pkgconfig               2.0.3     2019-09-22 [1] CRAN (R 4.5.2)
 processx                3.9.0     2026-04-22 [1] CRAN (R 4.5.2)
 promises                1.5.0     2025-11-01 [1] CRAN (R 4.5.2)
 ps                      1.9.3     2026-04-20 [1] CRAN (R 4.5.2)
 purrr                   1.2.2     2026-04-10 [1] CRAN (R 4.5.2)
 R6                      2.6.1     2025-02-15 [1] CRAN (R 4.5.2)
 ragg                    1.5.2     2026-03-23 [1] CRAN (R 4.5.2)
 random.cdisc.data       0.3.16    2024-10-10 [1] CRAN (R 4.5.2)
 rbibutils               2.4.1     2026-01-21 [1] CRAN (R 4.5.2)
 RColorBrewer            1.1-3     2022-04-03 [1] CRAN (R 4.5.2)
 Rcpp                    1.1.1-1.1 2026-04-24 [1] CRAN (R 4.5.2)
 Rdpack                  2.6.6     2026-02-08 [1] CRAN (R 4.5.2)
 rlang                   1.2.0     2026-04-06 [1] CRAN (R 4.5.2)
 rmarkdown               2.31      2026-03-26 [1] CRAN (R 4.5.2)
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 shinyvalidate           0.1.3     2023-10-04 [1] CRAN (R 4.5.2)
 shinyWidgets            0.9.1     2026-03-09 [1] CRAN (R 4.5.2)
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 survival                3.8-6     2026-01-16 [2] CRAN (R 4.5.2)
 systemfonts             1.3.2     2026-03-05 [1] CRAN (R 4.5.2)
 teal                  * 1.1.0     2025-11-17 [1] CRAN (R 4.5.2)
 teal.code             * 0.7.1     2026-01-20 [1] CRAN (R 4.5.2)
 teal.data             * 0.8.0     2025-08-19 [1] CRAN (R 4.5.2)
 teal.logger             0.4.1     2025-12-02 [1] CRAN (R 4.5.2)
 teal.modules.clinical * 0.12.0    2025-12-04 [1] CRAN (R 4.5.2)
 teal.reporter           0.6.1     2026-02-20 [1] CRAN (R 4.5.2)
 teal.slice            * 0.8.0     2026-06-04 [1] CRAN (R 4.5.2)
 teal.transform        * 0.7.1     2025-12-03 [1] CRAN (R 4.5.2)
 teal.widgets            0.6.0     2026-02-24 [1] CRAN (R 4.5.2)
 tern                  * 0.9.10    2025-12-18 [1] CRAN (R 4.5.2)
 tern.mmrm             * 0.3.3     2025-07-04 [1] CRAN (R 4.5.2)
 testthat                3.3.2     2026-01-11 [1] CRAN (R 4.5.2)
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 xtable                  1.8-8     2026-02-22 [1] CRAN (R 4.5.2)
 yaml                    2.3.12    2025-12-10 [1] CRAN (R 4.5.2)

 [1] /usr/local/lib/R/site-library
 [2] /usr/local/lib/R/library
 [3] /github/home/R/x86_64-pc-linux-gnu-library/4.5
 * ── Packages attached to the search path.

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