MNG01

Mean Plot

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Code

plot <- g_lineplot(
  df = adlb_f,
  alt_counts_df = adsl_f,
  subtitle = "Laboratory Test:"
)
plot

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Code

plot <- g_lineplot(
  df = advs_f,
  alt_counts_df = adsl_f,
  variables = control_lineplot_vars(y = "CHG"),
  title = "Plot of Mean and 95% Confidence Intervals of Change from Baseline by Visit",
  subtitle = "Assessment:"
)
plot

Experimental use!

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Code

plot <- g_lineplot(
  df = adlb_f,
  alt_counts_df = adsl_f,
  interval = "mean_sdi",
  whiskers = c("mean_sdi_lwr", "mean_sdi_upr"),
  title = "Plot of Mean (+/-SD)",
  subtitle = "Laboratory Test:"
)
plot

Experimental use!

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Code

plot <- g_lineplot(
  df = adlb_f,
  alt_counts_df = adsl_f,
  control = control_analyze_vars(conf_level = 0.80),
  title = "Plot of Mean and 80% Confidence Limits by Visit",
  subtitle = "Laboratory Test:"
)
plot

Experimental use!

WebR is a tool allowing you to run R code in the web browser. Modify the code below and click run to see the results. Alternatively, copy the code and click here to open WebR in a new tab.

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Code

plot <- g_lineplot(
  df = adlb_f,
  alt_counts_df = adsl_f,
  table = "n",
  subtitle = "Laboratory Test:"
)
plot

Experimental use!

WebR is a tool allowing you to run R code in the web browser. Modify the code below and click run to see the results. Alternatively, copy the code and click here to open WebR in a new tab.

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Code

plot <- g_lineplot(
  df = adlb_f,
  alt_counts_df = adsl_f,
  table = c("n", "mean", "mean_ci"),
  subtitle = "Laboratory Test:"
)
plot

Experimental use!

WebR is a tool allowing you to run R code in the web browser. Modify the code below and click run to see the results. Alternatively, copy the code and click here to open WebR in a new tab.

This option is not supported.

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Try this using WebR

Code

plot <- g_lineplot(
  df = adlb_f,
  alt_counts_df = adsl_f,
  whiskers = "mean_ci_upr",
  subtitle = "Laboratory Test:"
)
plot

Experimental use!

WebR is a tool allowing you to run R code in the web browser. Modify the code below and click run to see the results. Alternatively, copy the code and click here to open WebR in a new tab.

Code

library(dplyr)
library(tern)
library(nestcolor)

adsl <- random.cdisc.data::cadsl
adlb <- random.cdisc.data::cadlb
advs <- random.cdisc.data::cadvs

adsl_f <- adsl %>%
  filter(SAFFL == "Y") %>%
  df_explicit_na()

adlb_f <- adlb %>%
  mutate(AVISIT = forcats::fct_reorder(AVISIT, AVISITN, min)) %>%
  dplyr::filter(
    SAFFL == "Y",
    ANL01FL == "Y",
    ONTRTFL == "Y",
    PARAMCD == "ALT",
    AVISIT != "SCREENING"
  ) %>%
  droplevels() %>%
  df_explicit_na()

advs_f <- advs %>%
  mutate(AVISIT = forcats::fct_reorder(AVISIT, AVISITN, min)) %>%
  dplyr::filter(
    SAFFL == "Y",
    ONTRTFL == "Y",
    PARAMCD == "DIABP",
    AVISIT != "SCREENING"
  ) %>%
  droplevels() %>%
  df_explicit_na()

Code

library(teal.modules.clinical)

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

  ADSL <- random.cdisc.data::cadsl
  ADLB <- random.cdisc.data::cadlb %>%
    mutate(AVISIT = fct_reorder(AVISIT, AVISITN, min))
})
datanames <- c("ADSL", "ADLB")
datanames(data) <- datanames
join_keys(data) <- default_cdisc_join_keys[datanames]

## Reusable Configuration For Modules
ADSL <- data[["ADSL"]]
ADLB <- data[["ADLB"]]

## Setup App
app <- init(
  data = data,
  modules = modules(
    tm_g_lineplot(
      label = "LINE PLOT",
      dataname = "ADLB",
      strata = choices_selected(
        variable_choices(ADSL, c("ARM", "ARMCD", "ACTARMCD")),
        "ARM"
      ),
      y = choices_selected(
        variable_choices(ADLB, c("AVAL", "BASE", "CHG", "PCHG")),
        "AVAL"
      ),
      param = choices_selected(
        value_choices(ADLB, "PARAMCD", "PARAM"),
        "ALT"
      )
    )
  )
)

shinyApp(app$ui, app$server)

Warning: Error in : unused argument (strata = "ARM") 
 when evaluating qenv code:
variables <- control_lineplot_vars(x = "AVISIT", y = "AVAL", strata = "ARM", paramcd = "PARAMCD", y_unit = "AVALU")

Experimental use!

shinylive allow you to modify to run shiny application entirely in the web browser. Modify the code below and click re-run the app to see the results. The performance is slighly worse and some of the features (e.g. downloading) might not work at all.

#| standalone: true
#| viewerHeight: 800
#| editorHeight: 200
#| components: [viewer, editor]
#| layout: vertical

# -- WEBR HELPERS --
options(webr_pkg_repos = c("r-universe" = "https://insightsengineering.r-universe.dev", getOption("webr_pkg_repos")))

# -- APP CODE --
library(teal.modules.clinical)

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

  ADSL <- random.cdisc.data::cadsl
  ADLB <- random.cdisc.data::cadlb %>%
    mutate(AVISIT = fct_reorder(AVISIT, AVISITN, min))
})
datanames <- c("ADSL", "ADLB")
datanames(data) <- datanames
join_keys(data) <- default_cdisc_join_keys[datanames]

## Reusable Configuration For Modules
ADSL <- data[["ADSL"]]
ADLB <- data[["ADLB"]]

## Setup App
app <- init(
  data = data,
  modules = modules(
    tm_g_lineplot(
      label = "LINE PLOT",
      dataname = "ADLB",
      strata = choices_selected(
        variable_choices(ADSL, c("ARM", "ARMCD", "ACTARMCD")),
        "ARM"
      ),
      y = choices_selected(
        variable_choices(ADLB, c("AVAL", "BASE", "CHG", "PCHG")),
        "AVAL"
      ),
      param = choices_selected(
        value_choices(ADLB, "PARAMCD", "PARAM"),
        "ALT"
      )
    )
  )
)

shinyApp(app$ui, app$server)

Reproducibility

Timestamp

[1] "2024-11-02 17:55:29 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     2024-11-02
 pandoc   3.4 @ /usr/bin/ (via rmarkdown)

─ Packages ───────────────────────────────────────────────────────────────────
 package               * version  date (UTC) lib source
 backports               1.5.0    2024-05-23 [1] CRAN (R 4.4.1)
 brio                    1.1.5    2024-04-24 [1] CRAN (R 4.4.1)
 broom                   1.0.7    2024-09-26 [1] CRAN (R 4.4.1)
 bslib                   0.8.0    2024-07-29 [1] CRAN (R 4.4.1)
 cachem                  1.1.0    2024-05-16 [1] CRAN (R 4.4.1)
 callr                   3.7.6    2024-03-25 [1] CRAN (R 4.4.1)
 checkmate               2.3.2    2024-07-29 [1] CRAN (R 4.4.1)
 chromote                0.3.1    2024-08-30 [1] CRAN (R 4.4.1)
 cli                     3.6.3    2024-06-21 [1] CRAN (R 4.4.1)
 coda                    0.19-4.1 2024-01-31 [1] CRAN (R 4.4.1)
 codetools               0.2-20   2024-03-31 [2] CRAN (R 4.4.1)
 colorspace              2.1-1    2024-07-26 [1] CRAN (R 4.4.1)
 cowplot                 1.1.3    2024-01-22 [1] CRAN (R 4.4.1)
 crayon                  1.5.3    2024-06-20 [1] CRAN (R 4.4.1)
 digest                  0.6.37   2024-08-19 [1] CRAN (R 4.4.1)
 dplyr                 * 1.1.4    2023-11-17 [1] CRAN (R 4.4.1)
 emmeans                 1.10.5   2024-10-14 [1] CRAN (R 4.4.1)
 estimability            1.5.1    2024-05-12 [1] CRAN (R 4.4.1)
 evaluate                1.0.1    2024-10-10 [1] CRAN (R 4.4.1)
 fansi                   1.0.6    2023-12-08 [1] CRAN (R 4.4.1)
 farver                  2.1.2    2024-05-13 [1] CRAN (R 4.4.1)
 fastmap                 1.2.0    2024-05-15 [1] CRAN (R 4.4.1)
 fontawesome             0.5.2    2023-08-19 [1] CRAN (R 4.4.1)
 forcats               * 1.0.0    2023-01-29 [1] CRAN (R 4.4.1)
 formatR                 1.14     2023-01-17 [1] CRAN (R 4.4.1)
 formatters            * 0.5.9    2024-09-12 [1] CRAN (R 4.4.1)
 geepack                 1.3.12   2024-09-23 [1] CRAN (R 4.4.1)
 generics                0.1.3    2022-07-05 [1] CRAN (R 4.4.1)
 ggplot2                 3.5.1    2024-04-23 [1] CRAN (R 4.4.1)
 glue                    1.8.0    2024-09-30 [1] CRAN (R 4.4.1)
 gtable                  0.3.6    2024-10-25 [1] CRAN (R 4.4.1)
 htmltools               0.5.8.1  2024-04-04 [1] CRAN (R 4.4.1)
 htmlwidgets             1.6.4    2023-12-06 [1] CRAN (R 4.4.1)
 httpuv                  1.6.15   2024-03-26 [1] CRAN (R 4.4.1)
 jquerylib               0.1.4    2021-04-26 [1] CRAN (R 4.4.1)
 jsonlite                1.8.9    2024-09-20 [1] CRAN (R 4.4.1)
 knitr                   1.48     2024-07-07 [1] CRAN (R 4.4.1)
 labeling                0.4.3    2023-08-29 [1] CRAN (R 4.4.1)
 later                   1.3.2    2023-12-06 [1] CRAN (R 4.4.1)
 lattice                 0.22-6   2024-03-20 [2] CRAN (R 4.4.1)
 lifecycle               1.0.4    2023-11-07 [1] CRAN (R 4.4.1)
 logger                  0.4.0    2024-10-22 [1] CRAN (R 4.4.1)
 magrittr              * 2.0.3    2022-03-30 [1] CRAN (R 4.4.1)
 MASS                    7.3-61   2024-06-13 [2] CRAN (R 4.4.1)
 Matrix                  1.7-0    2024-04-26 [1] CRAN (R 4.4.1)
 memoise                 2.0.1    2021-11-26 [1] CRAN (R 4.4.1)
 mime                    0.12     2021-09-28 [1] CRAN (R 4.4.1)
 multcomp                1.4-26   2024-07-18 [1] CRAN (R 4.4.1)
 munsell                 0.5.1    2024-04-01 [1] CRAN (R 4.4.1)
 mvtnorm                 1.3-1    2024-09-03 [1] CRAN (R 4.4.1)
 nestcolor             * 0.1.2    2023-06-09 [1] CRAN (R 4.4.1)
 nlme                    3.1-166  2024-08-14 [2] CRAN (R 4.4.1)
 pillar                  1.9.0    2023-03-22 [1] CRAN (R 4.4.1)
 pkgconfig               2.0.3    2019-09-22 [1] CRAN (R 4.4.1)
 processx                3.8.4    2024-03-16 [1] CRAN (R 4.4.1)
 promises                1.3.0    2024-04-05 [1] CRAN (R 4.4.1)
 ps                      1.8.1    2024-10-28 [1] CRAN (R 4.4.1)
 purrr                   1.0.2    2023-08-10 [1] CRAN (R 4.4.1)
 R6                      2.5.1    2021-08-19 [1] CRAN (R 4.4.1)
 random.cdisc.data       0.3.16   2024-11-02 [1] https://insightsengineering.r-universe.dev (R 4.4.1)
 rbibutils               2.3      2024-10-04 [1] CRAN (R 4.4.1)
 Rcpp                    1.0.13   2024-07-17 [1] CRAN (R 4.4.1)
 Rdpack                  2.6.1    2024-08-06 [1] CRAN (R 4.4.1)
 rlang                   1.1.4    2024-06-04 [1] CRAN (R 4.4.1)
 rmarkdown               2.28     2024-08-17 [1] CRAN (R 4.4.1)
 rtables               * 0.6.10   2024-09-20 [1] CRAN (R 4.4.1)
 sandwich                3.1-1    2024-09-15 [1] CRAN (R 4.4.1)
 sass                    0.4.9    2024-03-15 [1] CRAN (R 4.4.1)
 scales                  1.3.0    2023-11-28 [1] CRAN (R 4.4.1)
 sessioninfo             1.2.2    2021-12-06 [1] CRAN (R 4.4.1)
 shiny                 * 1.9.1    2024-08-01 [1] CRAN (R 4.4.1)
 shinycssloaders         1.1.0    2024-07-30 [1] CRAN (R 4.4.1)
 shinyjs                 2.1.0    2021-12-23 [1] CRAN (R 4.4.1)
 shinyvalidate           0.1.3    2023-10-04 [1] CRAN (R 4.4.1)
 shinyWidgets            0.8.7    2024-09-23 [1] CRAN (R 4.4.1)
 stringi                 1.8.4    2024-05-06 [1] CRAN (R 4.4.1)
 stringr                 1.5.1    2023-11-14 [1] CRAN (R 4.4.1)
 survival                3.7-0    2024-06-05 [2] CRAN (R 4.4.1)
 teal                  * 0.15.2   2024-03-07 [1] CRAN (R 4.4.1)
 teal.code             * 0.5.0    2024-01-11 [1] CRAN (R 4.4.1)
 teal.data             * 0.6.0    2024-04-30 [1] CRAN (R 4.4.1)
 teal.logger             0.3.0    2024-11-02 [1] https://insightsengineering.r-universe.dev (R 4.4.1)
 teal.modules.clinical * 0.9.1    2024-04-27 [1] CRAN (R 4.4.1)
 teal.reporter           0.3.1    2024-03-15 [1] CRAN (R 4.4.1)
 teal.slice            * 0.5.1    2024-04-30 [1] CRAN (R 4.4.1)
 teal.transform        * 0.5.0    2024-02-17 [1] CRAN (R 4.4.1)
 teal.widgets            0.4.2    2023-12-14 [1] CRAN (R 4.4.1)
 tern                  * 0.9.6    2024-09-24 [1] CRAN (R 4.4.1)
 tern.gee                0.1.5    2024-08-23 [1] CRAN (R 4.4.1)
 testthat                3.2.1.1  2024-04-14 [1] CRAN (R 4.4.1)
 TH.data                 1.1-2    2023-04-17 [1] CRAN (R 4.4.1)
 tibble                  3.2.1    2023-03-20 [1] CRAN (R 4.4.1)
 tidyr                   1.3.1    2024-01-24 [1] CRAN (R 4.4.1)
 tidyselect              1.2.1    2024-03-11 [1] CRAN (R 4.4.1)
 utf8                    1.2.4    2023-10-22 [1] CRAN (R 4.4.1)
 vctrs                   0.6.5    2023-12-01 [1] CRAN (R 4.4.1)
 webshot                 0.5.5    2023-06-26 [1] CRAN (R 4.4.1)
 webshot2                0.1.1    2023-08-11 [1] CRAN (R 4.4.1)
 websocket               1.4.2    2024-07-22 [1] CRAN (R 4.4.1)
 withr                   3.0.2    2024-10-28 [1] CRAN (R 4.4.1)
 xfun                    0.49     2024-10-31 [1] CRAN (R 4.4.1)
 xtable                  1.8-4    2019-04-21 [1] CRAN (R 4.4.1)
 yaml                    2.3.10   2024-07-26 [1] CRAN (R 4.4.1)
 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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teal App

Reproducibility

Timestamp

Session Info

.lock file

`teal` App

`.lock` file