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. 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
    )
})
datanames <- c("ADSL", "ADQS")
datanames(data) <- datanames
Warning: `datanames<-()` was deprecated in teal.data 0.7.0.
ℹ invalid to use `datanames()<-` or `names()<-` on an object of class
  `teal_data`. See ?names.teal_data
Code
join_keys(data) <- default_cdisc_join_keys[datanames]

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] "2025-07-05 17:58:35 UTC"

Session Info

─ Session info ───────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.5.0 (2025-04-11)
 os       Ubuntu 24.04.2 LTS
 system   x86_64, linux-gnu
 ui       X11
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       Etc/UTC
 date     2025-07-05
 pandoc   3.7.0.2 @ /usr/bin/ (via rmarkdown)
 quarto   1.7.32 @ /usr/local/bin/quarto

─ Packages ───────────────────────────────────────────────────────────────────
 package               * version  date (UTC) lib source
 backports               1.5.0    2024-05-23 [1] RSPM
 brio                    1.1.5    2024-04-24 [1] RSPM
 broom                   1.0.8    2025-03-28 [1] RSPM
 bslib                   0.9.0    2025-01-30 [1] RSPM
 cachem                  1.1.0    2024-05-16 [1] RSPM
 callr                   3.7.6    2024-03-25 [1] RSPM
 checkmate               2.3.2    2024-07-29 [1] RSPM
 chromote                0.5.1    2025-04-24 [1] RSPM
 cli                     3.6.5    2025-04-23 [1] RSPM
 coda                    0.19-4.1 2024-01-31 [1] CRAN (R 4.5.0)
 codetools               0.2-20   2024-03-31 [2] CRAN (R 4.5.0)
 cowplot                 1.1.3    2024-01-22 [1] RSPM
 curl                    6.4.0    2025-06-22 [1] RSPM
 dichromat               2.0-0.1  2022-05-02 [1] CRAN (R 4.5.0)
 digest                  0.6.37   2024-08-19 [1] RSPM
 dplyr                 * 1.1.4    2023-11-17 [1] RSPM
 emmeans                 1.11.1   2025-05-04 [1] RSPM
 estimability            1.5.1    2024-05-12 [1] RSPM
 evaluate                1.0.4    2025-06-18 [1] RSPM
 farver                  2.1.2    2024-05-13 [1] RSPM
 fastmap                 1.2.0    2024-05-15 [1] RSPM
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 ggplot2                 3.5.2    2025-04-09 [1] RSPM
 glue                    1.8.0    2024-09-30 [1] RSPM
 gtable                  0.3.6    2024-10-25 [1] RSPM
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 htmlwidgets             1.6.4    2023-12-06 [1] RSPM
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 jsonlite                2.0.0    2025-03-27 [1] RSPM
 knitr                   1.50     2025-03-16 [1] RSPM
 labeling                0.4.3    2023-08-29 [1] RSPM
 later                   1.4.2    2025-04-08 [1] RSPM
 lattice                 0.22-7   2025-04-02 [2] CRAN (R 4.5.0)
 lifecycle               1.0.4    2023-11-07 [1] RSPM
 logger                  0.4.0    2024-10-22 [1] RSPM
 magrittr              * 2.0.3    2022-03-30 [1] RSPM
 MASS                    7.3-65   2025-02-28 [2] CRAN (R 4.5.0)
 Matrix                  1.7-3    2025-03-11 [1] CRAN (R 4.5.0)
 memoise                 2.0.1    2021-11-26 [1] RSPM
 mime                    0.13     2025-03-17 [1] RSPM
 mmrm                    0.3.15   2025-06-10 [1] RSPM
 multcomp                1.4-28   2025-01-29 [1] RSPM
 mvtnorm                 1.3-3    2025-01-10 [1] RSPM
 nestcolor             * 0.1.3    2025-01-21 [1] RSPM
 nlme                    3.1-168  2025-03-31 [2] CRAN (R 4.5.0)
 parallelly              1.45.0   2025-06-02 [1] RSPM
 pillar                  1.11.0   2025-07-04 [1] RSPM
 pkgcache                2.2.4    2025-05-26 [1] RSPM
 pkgconfig               2.0.3    2019-09-22 [1] RSPM
 processx                3.8.6    2025-02-21 [1] RSPM
 promises                1.3.3    2025-05-29 [1] RSPM
 ps                      1.9.1    2025-04-12 [1] RSPM
 purrr                   1.0.4    2025-02-05 [1] RSPM
 R6                      2.6.1    2025-02-15 [1] RSPM
 random.cdisc.data       0.3.16   2024-10-10 [1] RSPM
 rbibutils               2.3      2024-10-04 [1] RSPM
 RColorBrewer            1.1-3    2022-04-03 [1] RSPM
 Rcpp                    1.1.0    2025-07-02 [1] RSPM
 Rdpack                  2.6.4    2025-04-09 [1] RSPM
 rlang                   1.1.6    2025-04-11 [1] RSPM
 rmarkdown               2.29     2024-11-04 [1] RSPM
 rtables               * 0.6.13   2025-06-19 [1] RSPM
 sandwich                3.1-1    2024-09-15 [1] RSPM
 sass                    0.4.10   2025-04-11 [1] RSPM
 scales                  1.4.0    2025-04-24 [1] RSPM
 sessioninfo             1.2.3    2025-02-05 [1] any (@1.2.3)
 shiny                 * 1.11.1   2025-07-03 [1] RSPM
 shinycssloaders         1.1.0    2024-07-30 [1] RSPM
 shinyjs                 2.1.0    2021-12-23 [1] RSPM
 shinyvalidate           0.1.3    2023-10-04 [1] RSPM
 shinyWidgets            0.9.0    2025-02-21 [1] RSPM
 stringi                 1.8.7    2025-03-27 [1] RSPM
 stringr                 1.5.1    2023-11-14 [1] RSPM
 survival                3.8-3    2024-12-17 [2] CRAN (R 4.5.0)
 teal                  * 0.16.0   2025-02-23 [1] RSPM
 teal.code             * 0.6.1    2025-02-14 [1] RSPM
 teal.data             * 0.7.0    2025-01-28 [1] RSPM
 teal.logger             0.3.2    2025-02-14 [1] RSPM
 teal.modules.clinical * 0.10.0   2025-02-28 [1] RSPM
 teal.reporter           0.4.0    2025-01-24 [1] RSPM
 teal.slice            * 0.6.0    2025-02-03 [1] RSPM
 teal.transform        * 0.6.0    2025-02-12 [1] RSPM
 teal.widgets            0.4.3    2025-01-31 [1] RSPM
 tern                  * 0.9.9    2025-06-20 [1] RSPM
 tern.gee                0.1.5    2024-08-23 [1] RSPM
 tern.mmrm             * 0.3.3    2025-07-04 [1] RSPM
 testthat                3.2.3    2025-01-13 [1] RSPM
 TH.data                 1.1-3    2025-01-17 [1] RSPM
 tibble                  3.3.0    2025-06-08 [1] RSPM
 tidyr                   1.3.1    2024-01-24 [1] RSPM
 tidyselect              1.2.1    2024-03-11 [1] RSPM
 TMB                     1.9.17   2025-03-10 [1] RSPM
 vctrs                   0.6.5    2023-12-01 [1] RSPM
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 webshot2                0.1.2    2025-04-23 [1] RSPM
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 withr                   3.0.2    2024-10-28 [1] RSPM
 xfun                    0.52     2025-04-02 [1] RSPM
 xtable                  1.8-4    2019-04-21 [1] RSPM
 yaml                    2.3.10   2024-07-26 [1] RSPM
 zoo                     1.8-14   2025-04-10 [1] RSPM

 [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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