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 0.6.1.
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] "2024-12-21 17:34:31 UTC"

Session Info

─ Session info ───────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.4.1 (2024-06-14)
 os       Ubuntu 22.04.5 LTS
 system   x86_64, linux-gnu
 ui       X11
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       Etc/UTC
 date     2024-12-21
 pandoc   3.4 @ /usr/bin/ (via rmarkdown)

─ 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                   1.0.7       2024-09-26 [1] RSPM
 bslib                   0.8.0       2024-07-29 [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                0.3.1       2024-08-30 [1] RSPM
 cli                     3.6.3       2024-06-21 [1] RSPM
 coda                    0.19-4.1    2024-01-31 [1] CRAN (R 4.4.1)
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 colorspace              2.1-1       2024-07-26 [1] RSPM
 cowplot                 1.1.3       2024-01-22 [1] RSPM
 curl                    6.0.1       2024-11-14 [1] RSPM
 digest                  0.6.37      2024-08-19 [1] RSPM
 dplyr                 * 1.1.4       2023-11-17 [1] RSPM
 emmeans                 1.10.6      2024-12-12 [1] RSPM
 estimability            1.5.1       2024-05-12 [1] RSPM
 evaluate                1.0.1       2024-10-10 [1] RSPM
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 fontawesome             0.5.3       2024-11-16 [1] RSPM
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 gtable                  0.3.6       2024-10-25 [1] RSPM
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 httpuv                  1.6.15      2024-03-26 [1] RSPM
 jquerylib               0.1.4       2021-04-26 [1] RSPM
 jsonlite                1.8.9       2024-09-20 [1] RSPM
 knitr                   1.49        2024-11-08 [1] RSPM
 labeling                0.4.3       2023-08-29 [1] RSPM
 later                   1.4.1       2024-11-27 [1] RSPM
 lattice                 0.22-6      2024-03-20 [2] CRAN (R 4.4.1)
 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                    7.3-61      2024-06-13 [2] CRAN (R 4.4.1)
 Matrix                  1.7-1       2024-10-18 [1] RSPM
 memoise                 2.0.1       2021-11-26 [1] RSPM
 mime                    0.12        2021-09-28 [1] RSPM
 mmrm                    0.3.14.9001 2024-12-21 [1] https://p~
 multcomp                1.4-26      2024-07-18 [1] CRAN (R 4.4.1)
 munsell                 0.5.1       2024-04-01 [1] RSPM
 mvtnorm                 1.3-2       2024-11-04 [1] RSPM
 nestcolor             * 0.1.2.9017  2024-12-21 [1] https://p~
 nlme                    3.1-166     2024-08-14 [2] CRAN (R 4.4.1)
 parallelly              1.41.0      2024-12-18 [1] RSPM
 pillar                  1.10.0      2024-12-17 [1] RSPM
 pkgcache                2.2.3       2024-09-12 [1] RSPM
 pkgconfig               2.0.3       2019-09-22 [1] RSPM
 processx                3.8.4       2024-03-16 [1] RSPM
 promises                1.3.2       2024-11-28 [1] RSPM
 ps                      1.8.1       2024-10-28 [1] RSPM
 purrr                   1.0.2       2023-08-10 [1] RSPM
 R6                      2.5.1       2021-08-19 [1] RSPM
 random.cdisc.data       0.3.16.9001 2024-12-21 [1] https://p~
 rbibutils               2.3         2024-10-04 [1] RSPM
 Rcpp                    1.0.13-1    2024-11-02 [1] RSPM
 Rdpack                  2.6.2       2024-11-15 [1] RSPM
 rlang                   1.1.4       2024-06-04 [1] RSPM
 rmarkdown               2.29        2024-11-04 [1] RSPM
 rtables               * 0.6.10.9014 2024-12-21 [1] https://p~
 sandwich                3.1-1       2024-09-15 [1] CRAN (R 4.4.1)
 sass                    0.4.9       2024-03-15 [1] RSPM
 scales                  1.3.0       2023-11-28 [1] RSPM
 sessioninfo             1.2.2       2021-12-06 [1] any (@1.2.2)
 shiny                 * 1.10.0      2024-12-14 [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            0.8.7       2024-09-23 [1] RSPM
 stringi                 1.8.4       2024-05-06 [1] RSPM
 stringr                 1.5.1       2023-11-14 [1] RSPM
 survival                3.8-3       2024-12-17 [1] RSPM
 teal                  * 0.15.2.9097 2024-12-21 [1] https://p~
 teal.code             * 0.5.0.9021  2024-12-21 [1] https://p~
 teal.data             * 0.6.0.9023  2024-12-21 [1] https://p~
 teal.logger             0.3.0.9003  2024-12-21 [1] https://p~
 teal.modules.clinical * 0.9.1.9043  2024-12-21 [1] https://p~
 teal.reporter           0.3.1.9021  2024-12-21 [1] https://p~
 teal.slice            * 0.5.1.9019  2024-12-21 [1] https://p~
 teal.transform        * 0.5.0.9018  2024-12-21 [1] https://p~
 teal.widgets            0.4.2.9025  2024-12-21 [1] https://p~
 tern                  * 0.9.6.9017  2024-12-21 [1] https://p~
 tern.gee                0.1.5.9004  2024-12-21 [1] https://p~
 tern.mmrm             * 0.3.2.9002  2024-12-21 [1] https://p~
 testthat                3.2.2       2024-12-10 [1] RSPM
 TH.data                 1.1-2       2023-04-17 [1] CRAN (R 4.4.1)
 tibble                  3.2.1       2023-03-20 [1] RSPM
 tidyr                   1.3.1       2024-01-24 [1] RSPM
 tidyselect              1.2.1       2024-03-11 [1] RSPM
 TMB                     1.9.15      2024-09-09 [1] RSPM
 vctrs                   0.6.5       2023-12-01 [1] RSPM
 webshot                 0.5.5       2023-06-26 [1] CRAN (R 4.4.1)
 webshot2                0.1.1       2023-08-11 [1] RSPM
 websocket               1.4.2       2024-07-22 [1] RSPM
 withr                   3.0.2       2024-10-28 [1] RSPM
 xfun                    0.49        2024-10-31 [1] RSPM
 xtable                  1.8-4       2019-04-21 [1] RSPM
 yaml                    2.3.10      2024-07-26 [1] RSPM
 zoo                     1.8-12      2023-04-13 [1] CRAN (R 4.4.1)

 [1] /usr/local/lib/R/site-library
 [2] /usr/local/lib/R/library

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