CIG01

Confidence Interval Plot

Preview
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The function stat_mean_ci from the tern package can be used with default values to draw the 95% confidence interval around the mean.

Code

plot <- ggplot(
  data = adlb,
  mapping = aes(
    x = ARMCD, y = AVAL, color = SEX,
    lty = SEX, shape = SEX
  )
) +
  stat_summary(
    fun.data = tern::stat_mean_ci,
    geom = "errorbar",
    width = 0.1,
    position = position_dodge(width = 0.5)
  ) +
  stat_summary(
    fun = mean,
    geom = "point",
    position = position_dodge(width = 0.5)
  ) +
  labs(
    title = "Confidence Interval Plot by Treatment Group",
    caption = "Mean and 95% CIs for mean are displayed.",
    x = "Treatment Group",
    y = paste0(adlb$PARAMCD[1], " (", adlb$AVALU[1], ")")
  )
plot

Experimental use!

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Preview
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Code

plot <- ggplot(
  data = adlb,
  mapping = aes(
    x = ARMCD, y = AVAL, color = STRATA2,
    lty = STRATA2, shape = STRATA2
  )
) +
  stat_summary(
    fun.data = tern::stat_mean_ci,
    geom = "errorbar",
    width = 0.1,
    position = position_dodge(width = 0.5)
  ) +
  stat_summary(
    fun = mean,
    geom = "point",
    position = position_dodge(width = 0.5)
  ) +
  labs(
    title = "Confidence Interval Plot by Treatment Group",
    caption = "Mean and 95% CIs for mean are displayed.",
    x = "Treatment Group",
    y = paste0(adlb$PARAMCD[1], " (", adlb$AVALU[1], ")")
  )
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.

Preview
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The function stat_median_ci from the tern package works similarly to stat_mean_ci.

Code

plot <- ggplot(
  data = adlb,
  mapping = aes(
    x = ARMCD, y = AVAL, color = STRATA1,
    lty = STRATA1, shape = STRATA1
  )
) +
  stat_summary(
    fun.data = stat_median_ci,
    geom = "errorbar",
    width = 0.1,
    position = position_dodge(width = 0.5)
  ) +
  stat_summary(
    fun = median,
    geom = "point",
    position = position_dodge(width = 0.5)
  ) +
  labs(
    title = "Confidence Interval Plot by Treatment Group",
    caption = "Median and 95% CIs for median are displayed.",
    x = "Treatment Group",
    y = paste0(adlb$PARAMCD[1], " (", adlb$AVALU[1], ")")
  )
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.

Preview
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To modify the confidence level for the estimation of the confidence interval, the call to stat_mean_ci (or stat_median_ci) can be slightly modified.

Code

plot <- ggplot(
  data = adlb,
  mapping = aes(
    x = ARMCD, y = AVAL, color = SEX,
    lty = SEX, shape = SEX
  )
) +
  stat_summary(
    fun.data = function(x) tern::stat_mean_ci(x, conf_level = 0.9),
    geom = "errorbar",
    width = 0.1,
    position = position_dodge(width = 0.5)
  ) +
  stat_summary(
    fun = mean,
    geom = "point",
    position = position_dodge(width = 0.5)
  ) +
  labs(
    title = "Confidence Interval Plot by Treatment Group",
    caption = "Mean and 90% CIs for mean are displayed.",
    x = "Treatment Group",
    y = paste0(adlb$PARAMCD[1], " (", adlb$AVALU[1], ")")
  )
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.

Preview
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The corresponding table is simply obtained using the rtables framework:

Code

lyt <- basic_table() %>%
  split_cols_by(var = "ARMCD") %>%
  analyze_vars(vars = "AVAL", .stats = c("mean_sd", "median"))
table <- build_table(lyt = lyt, df = adlb)
table

              ARM A        ARM B        ARM C   
————————————————————————————————————————————————
Mean (SD)   17.7 (9.9)   18.7 (9.8)   19.5 (9.1)
Median         17.5         18.2         19.0

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(tern)
library(ggplot2)
library(dplyr)
library(nestcolor)

adlb <- random.cdisc.data::cadlb %>%
  filter(PARAMCD == "ALT", AVISIT == "BASELINE")

Code

library(teal.modules.clinical)

## Data reproducible code
data <- teal_data()
data <- within(data, {
  ADSL <- random.cdisc.data::cadsl
  ADLB <- random.cdisc.data::cadlb
})
datanames <- c("ADSL", "ADLB")
datanames(data) <- datanames
join_keys(data) <- default_cdisc_join_keys[datanames]

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

## Setup App
app <- init(
  data = data,
  modules = modules(
    tm_g_ci(
      label = "Confidence Interval Plot",
      x_var = data_extract_spec(
        dataname = "ADSL",
        select = select_spec(
          choices = c("ARMCD", "BMRKR2"),
          selected = c("ARMCD"),
          multiple = FALSE,
          fixed = FALSE
        )
      ),
      y_var = data_extract_spec(
        dataname = "ADLB",
        filter = list(
          filter_spec(
            vars = "PARAMCD",
            choices = levels(ADLB$PARAMCD),
            selected = levels(ADLB$PARAMCD)[1],
            multiple = FALSE,
            label = "Select lab:"
          ),
          filter_spec(
            vars = "AVISIT",
            choices = levels(ADLB$AVISIT),
            selected = levels(ADLB$AVISIT)[1],
            multiple = FALSE,
            label = "Select visit:"
          )
        ),
        select = select_spec(
          label = "Analyzed Value",
          choices = c("AVAL", "CHG"),
          selected = "AVAL",
          multiple = FALSE,
          fixed = FALSE
        )
      ),
      color = data_extract_spec(
        dataname = "ADSL",
        select = select_spec(
          label = "Color by variable",
          choices = c("SEX", "STRATA1", "STRATA2"),
          selected = c("STRATA1"),
          multiple = FALSE,
          fixed = FALSE
        )
      )
    )
  ),
  header = "Example of Confidence Interval Plot",
  footer = tags$p(
    class = "text-muted", "Source: `teal.modules.clinical::tm_g_ci`"
  )
)

shinyApp(app$ui, app$server)

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://pharmaverse.r-universe.dev", getOption("webr_pkg_repos")))

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

## Data reproducible code
data <- teal_data()
data <- within(data, {
  ADSL <- random.cdisc.data::cadsl
  ADLB <- random.cdisc.data::cadlb
})
datanames <- c("ADSL", "ADLB")
datanames(data) <- datanames
join_keys(data) <- default_cdisc_join_keys[datanames]

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

## Setup App
app <- init(
  data = data,
  modules = modules(
    tm_g_ci(
      label = "Confidence Interval Plot",
      x_var = data_extract_spec(
        dataname = "ADSL",
        select = select_spec(
          choices = c("ARMCD", "BMRKR2"),
          selected = c("ARMCD"),
          multiple = FALSE,
          fixed = FALSE
        )
      ),
      y_var = data_extract_spec(
        dataname = "ADLB",
        filter = list(
          filter_spec(
            vars = "PARAMCD",
            choices = levels(ADLB$PARAMCD),
            selected = levels(ADLB$PARAMCD)[1],
            multiple = FALSE,
            label = "Select lab:"
          ),
          filter_spec(
            vars = "AVISIT",
            choices = levels(ADLB$AVISIT),
            selected = levels(ADLB$AVISIT)[1],
            multiple = FALSE,
            label = "Select visit:"
          )
        ),
        select = select_spec(
          label = "Analyzed Value",
          choices = c("AVAL", "CHG"),
          selected = "AVAL",
          multiple = FALSE,
          fixed = FALSE
        )
      ),
      color = data_extract_spec(
        dataname = "ADSL",
        select = select_spec(
          label = "Color by variable",
          choices = c("SEX", "STRATA1", "STRATA2"),
          selected = c("STRATA1"),
          multiple = FALSE,
          fixed = FALSE
        )
      )
    )
  ),
  header = "Example of Confidence Interval Plot",
  footer = tags$p(
    class = "text-muted", "Source: `teal.modules.clinical::tm_g_ci`"
  )
)

shinyApp(app$ui, app$server)

Reproducibility

Timestamp

[1] "2024-11-02 17:37:33 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
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 brio                    1.1.5       2024-04-24 [1] CRAN (R 4.4.1)
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 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)
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 formatR                 1.14        2023-01-17 [1] CRAN (R 4.4.1)
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 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)
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 nestcolor             * 0.1.2.9017  2024-11-02 [1] git2r (https://github.com/insightsengineering/nestcolor.git@3d2ce62)
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 random.cdisc.data       0.3.16.9001 2024-11-02 [1] git2r (https://github.com/insightsengineering/random.cdisc.data.git@a65bfbe)
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 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               * 0.6.10.9002 2024-11-02 [1] git2r (https://github.com/insightsengineering/rtables.git@d2cc7a0)
 sandwich                3.1-1       2024-09-15 [1] CRAN (R 4.4.1)
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 sessioninfo             1.2.2       2021-12-06 [1] CRAN (R 4.4.1)
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 shinycssloaders         1.1.0       2024-07-30 [1] CRAN (R 4.4.1)
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 teal.code             * 0.5.0.9012  2024-11-02 [1] git2r (https://github.com/insightsengineering/teal.code.git@86aa265)
 teal.data             * 0.6.0.9015  2024-11-02 [1] git2r (https://github.com/insightsengineering/teal.data.git@eca9695)
 teal.logger             0.3.0.9000  2024-11-02 [1] git2r (https://github.com/insightsengineering/teal.logger.git@cd9cc7e)
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 tern                  * 0.9.6.9013  2024-11-02 [1] git2r (https://github.com/insightsengineering/tern.git@435fd51)
 tern.gee                0.1.5.9004  2024-11-02 [1] git2r (https://github.com/insightsengineering/tern.gee.git@458172d)
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 [1] /usr/local/lib/R/site-library
 [2] /usr/local/lib/R/library

──────────────────────────────────────────────────────────────────────────────

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Reproducibility

Timestamp

Session Info

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