diff --git a/404.html b/404.html index a4bb271..b6ebe71 100644 --- a/404.html +++ b/404.html @@ -50,6 +50,7 @@
  • + Static Forest Plot Controlling Layout
    More articles... diff --git a/LICENSE.html b/LICENSE.html index 3f0b83a..95361bb 100644 --- a/LICENSE.html +++ b/LICENSE.html @@ -27,6 +27,7 @@
  • + Static Forest Plot Controlling Layout
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  • + Static Forest Plot Controlling Layout
    More articles... diff --git a/articles/forest-plot-static.html b/articles/forest-plot-static.html new file mode 100644 index 0000000..3d7a1b5 --- /dev/null +++ b/articles/forest-plot-static.html @@ -0,0 +1,187 @@ + + + + + + + + +Static Forest Plot • forestly + + + + + + + + + + + + + + + + + + Skip to contents + + +
    + + + + +
    +
    +

    Static Forest Plot

    + + + Source: vignettes/forest-plot-static.Rmd +
    forest-plot-static.Rmd
    +
    + + + + +
    +forestly_adsl$TRTA <- factor(
+  forestly_adsl$TRT01A,
+  levels = c("Xanomeline Low Dose", "Placebo"),
+  labels = c("Low Dose", "Placebo")
+)
+
+forestly_adae$TRTA <- factor(
+  forestly_adae$TRTA,
+  levels = c("Xanomeline Low Dose", "Placebo"),
+  labels = c("Low Dose", "Placebo")
+)
+
+meta <- meta_forestly(
+  dataset_adsl = forestly_adsl,
+  dataset_adae = forestly_adae,
+  population_term = "apat",
+  observation_term = "wk12",
+  parameter_term = "any;rel;ser"
+) |>
+  prepare_ae_forestly() |>
+  format_ae_forestly()
    +
    +meta_any <- meta$tbl[1:20, ] |> dplyr::filter(parameter == "any")
    +
    +p1 <- meta_any |>
+  dplyr::select(name, prop_1, prop_2) |>
+  plot_dot(
+    y_var = "name",
+    label = c("Treatment", "Placebo")
+  )
+p1
    +

    +
    +p2 <- meta_any |>
+  dplyr::select(name, diff_1, lower_1, upper_1) |>
+  plot_errorbar(
+    y_var = "name",
+    label = c("Treatment", "Placebo"),
+    legend_nrow = NULL,
+    theme = theme_panel(show_ticks = FALSE, show_text = FALSE)
+  )
+p2
    +

    +
    +meta_any$stat_1 <- paste0(meta_any$n_1, "(", meta_any$prop_1, ")")
+meta_any$stat_2 <- paste0(meta_any$n_2, "(", meta_any$prop_2, ")")
+
+p3 <- meta_any |>
+  dplyr::select(name, stat_1, stat_2) |>
+  table_panel(
+    y_var = "name",
+    theme = theme_panel(show_ticks = FALSE, show_text = FALSE),
+    x_label = c("Treatment \n n(%)", "Placebo \n n(%)")
+  )
+p3
    +

    +
    +do.call(patchwork::wrap_plots, list(p1, p2, p3)) +
+  # Define outer margin for assembled plot
+  patchwork::plot_annotation(
+    theme = theme(plot.margin = margin(1, 1, 1, 1, unit = "lines"))
+  ) +
+  patchwork::plot_layout(guides = "collect") & # Shared legend
+  theme(legend.position = "bottom")
    +

    +
    +
    + + + + +
    + + + + + + + diff --git a/articles/forest-plot-static_files/figure-html/unnamed-chunk-5-1.png b/articles/forest-plot-static_files/figure-html/unnamed-chunk-5-1.png new file mode 100644 index 0000000..9821e16 Binary files /dev/null and b/articles/forest-plot-static_files/figure-html/unnamed-chunk-5-1.png differ diff --git a/articles/forest-plot-static_files/figure-html/unnamed-chunk-6-1.png b/articles/forest-plot-static_files/figure-html/unnamed-chunk-6-1.png new file mode 100644 index 0000000..62a8bff Binary files /dev/null and b/articles/forest-plot-static_files/figure-html/unnamed-chunk-6-1.png differ diff --git a/articles/forest-plot-static_files/figure-html/unnamed-chunk-7-1.png b/articles/forest-plot-static_files/figure-html/unnamed-chunk-7-1.png new file mode 100644 index 0000000..2cc84b7 Binary files /dev/null and b/articles/forest-plot-static_files/figure-html/unnamed-chunk-7-1.png differ diff --git a/articles/forest-plot-static_files/figure-html/unnamed-chunk-8-1.png b/articles/forest-plot-static_files/figure-html/unnamed-chunk-8-1.png new file mode 100644 index 0000000..c44805d Binary files /dev/null and b/articles/forest-plot-static_files/figure-html/unnamed-chunk-8-1.png differ diff --git a/articles/forestly-cran.html b/articles/forestly-cran.html index 600a39a..3a5487b 100644 --- a/articles/forestly-cran.html +++ b/articles/forestly-cran.html @@ -52,6 +52,7 @@
  • + Static Forest Plot Controlling Layout
    More articles... diff --git a/articles/forestly.html b/articles/forestly.html index c769142..5fedbe1 100644 --- a/articles/forestly.html +++ b/articles/forestly.html @@ -52,6 +52,7 @@
  • + Static Forest Plot Controlling Layout
    More articles... @@ -165,9 +166,9 @@

    Overview

    - -
    - + +
    +
    @@ -463,9 +464,9 @@

    Workflow
    - -
    - + +
    +
    @@ -508,9 +509,9 @@

    Workflow
    - -
    - + +
    +
    @@ -644,9 +645,9 @@

    Define metadata
    - -
    - + +
    +
    @@ -693,9 +694,9 @@

    Define metadata
    - -
    - + +
    +
    diff --git a/articles/index.html b/articles/index.html index ea93936..777f109 100644 --- a/articles/index.html +++ b/articles/index.html @@ -27,6 +27,7 @@
  • + Static Forest Plot Controlling Layout
    More articles... @@ -67,7 +68,9 @@

    Get started

    Examples

    -
    Controlling Layout
    +
    Static Forest Plot
    +
    +
    Controlling Layout
    diff --git a/articles/layout.html b/articles/layout.html index 8de5f67..62fcfc4 100644 --- a/articles/layout.html +++ b/articles/layout.html @@ -52,6 +52,7 @@
  • + Static Forest Plot Controlling Layout
    More articles... @@ -179,9 +180,9 @@

    Overview

    - -
    - + +
    +
    @@ -230,9 +231,9 @@

    Change color - -
    - + +
    + @@ -278,9 +279,9 @@

    Display different columns
    - -
    - + +
    +
    @@ -322,9 +323,9 @@

    Display different columns
    - -
    - + +
    +
    @@ -372,9 +373,9 @@

    Control column width - -
    - + +
    + @@ -437,9 +438,9 @@

    Change variable listed in dr
    - -
    - + +
    +
    diff --git a/authors.html b/authors.html index e9e1c90..5e341ef 100644 --- a/authors.html +++ b/authors.html @@ -27,6 +27,7 @@
  • + Static Forest Plot Controlling Layout
    More articles... @@ -77,6 +78,10 @@

    Authors

    Hiroaki Fukuda. Contributor.

    • +
  • +

    Yulia Sidi. Contributor. +

    +

  • Xuan Deng. Contributor.

    diff --git a/favicon-16x16.png b/favicon-16x16.png index 1797310..0c25dcd 100644 Binary files a/favicon-16x16.png and b/favicon-16x16.png differ diff --git a/favicon-32x32.png b/favicon-32x32.png index 3e79997..28f465b 100644 Binary files a/favicon-32x32.png and b/favicon-32x32.png differ diff --git a/index.html b/index.html index e24b54d..495874e 100644 --- a/index.html +++ b/index.html @@ -52,6 +52,7 @@
  • + Static Forest Plot Controlling Layout
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  • + Static Forest Plot Controlling Layout
    More articles... diff --git a/pkgdown.yml b/pkgdown.yml index c1685b1..ddd771e 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -3,10 +3,11 @@ pkgdown: 2.0.9 pkgdown_sha: ~ articles: design-pattern: design-pattern.html + forest-plot-static: forest-plot-static.html forestly-cran: forestly-cran.html forestly: forestly.html layout: layout.html -last_built: 2024-05-12T17:56Z +last_built: 2024-05-15T03:17Z urls: reference: https://merck.github.io/forestly/reference article: https://merck.github.io/forestly/articles diff --git a/reference/Rplot001.png b/reference/Rplot001.png index 17a3580..31b85fd 100644 Binary files a/reference/Rplot001.png and b/reference/Rplot001.png differ diff --git a/reference/Rplot002.png b/reference/Rplot002.png new file mode 100644 index 0000000..9c64e35 Binary files /dev/null and b/reference/Rplot002.png differ diff --git a/reference/ae_forestly.html b/reference/ae_forestly.html index 33f2b69..b5bff1c 100644 --- a/reference/ae_forestly.html +++ b/reference/ae_forestly.html @@ -27,6 +27,7 @@
  • + Static Forest Plot Controlling Layout
    More articles... diff --git a/reference/background_panel-1.png b/reference/background_panel-1.png new file mode 100644 index 0000000..1bfe43c Binary files /dev/null and b/reference/background_panel-1.png differ diff --git a/reference/background_panel.html b/reference/background_panel.html new file mode 100644 index 0000000..5c97ea5 --- /dev/null +++ b/reference/background_panel.html @@ -0,0 +1,135 @@ + +Add background for creating plot with customized color — background_panel • forestly + Skip to contents + + +
    +
    +
    +

    Add background for creating plot with customized color

    + Source: R/plot.R +
    background_panel.Rd
    +
    + +
    +

    Creates colored background for panels of rainfall or forest plot.

    +
    + +
    +

    Usage

    + 
    background_panel(
+  g,
+  background_color = c("#69B8F7", "#FFFFFF"),
+  background_alpha = 0.3
+)
    +
    + +
    +

    Arguments

    +
    g
    +

    A ggplot object for adding colored background.

    + + +
    background_color
    +

    A vector of colors that defines the color for the +plot background. Default is c("#69B8F7", "#FFFFFF"), +which are pastel blue and white. The colors will be recycled.

    + + +
    background_alpha
    +

    Opacity of a geom. Default is 0.3.

    + +
    +
    +

    Value

    + + +

    Plot as a colored background to add panels for rainfall or forest plot.

    +
    + +
    +

    Examples

    + 
    library(ggplot2)
+
+df <- data.frame(
+  study = c("S1", "S2", "S3", "S4", "S5", "S6", "S7"),
+  item = as.factor(1:7),
+  effect = c(-.4, -.25, -.1, .1, .15, .2, .3),
+  lower = c(-.43, -.29, -.17, -.02, .04, .17, .27),
+  upper = c(-.37, -.21, -.03, .22, .24, .23, .33)
+)
+
+ggplot(data = df) |>
+  background_panel(background_color = c("grey", "white"), background_alpha = 0.4) +
+  geom_point(aes(y = item, x = effect)) +
+  geom_errorbar(aes(y = item, x = effect, xmin = lower, xmax = upper), width = 0.4) +
+  scale_y_discrete(name = "", breaks = 1:nrow(df), labels = df$study)
+
+
    +
    +
    + + +
    +

    Developed by Yilong Zhang, Benjamin Wang, Yujie Zhao. Site built with pkgdown 2.0.9.
    Copyright © 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates. All rights reserved.

    +
    + +
    +

    +
    + +
    + + + + + + + diff --git a/reference/forestly_adae.html b/reference/forestly_adae.html index 8524b20..ca6fbd4 100644 --- a/reference/forestly_adae.html +++ b/reference/forestly_adae.html @@ -29,6 +29,7 @@
  • + Static Forest Plot Controlling Layout
    More articles... diff --git a/reference/forestly_adae_3grp.html b/reference/forestly_adae_3grp.html index e1a8443..da2009f 100644 --- a/reference/forestly_adae_3grp.html +++ b/reference/forestly_adae_3grp.html @@ -29,6 +29,7 @@
  • + Static Forest Plot Controlling Layout
    More articles... diff --git a/reference/forestly_adsl.html b/reference/forestly_adsl.html index 052265d..8ce4263 100644 --- a/reference/forestly_adsl.html +++ b/reference/forestly_adsl.html @@ -29,6 +29,7 @@
  • + Static Forest Plot Controlling Layout
    More articles... diff --git a/reference/forestly_adsl_3grp.html b/reference/forestly_adsl_3grp.html index 017bebb..b2d9db5 100644 --- a/reference/forestly_adsl_3grp.html +++ b/reference/forestly_adsl_3grp.html @@ -29,6 +29,7 @@
  • + Static Forest Plot Controlling Layout
    More articles... diff --git a/reference/format_ae_forestly.html b/reference/format_ae_forestly.html index d753ccd..d54b206 100644 --- a/reference/format_ae_forestly.html +++ b/reference/format_ae_forestly.html @@ -27,6 +27,7 @@
  • + Static Forest Plot Controlling Layout
    More articles... diff --git a/reference/index.html b/reference/index.html index 807363a..b02c192 100644 --- a/reference/index.html +++ b/reference/index.html @@ -27,6 +27,7 @@
  • + Static Forest Plot Controlling Layout
    More articles... @@ -86,6 +87,42 @@

    Adverse event analysis
    Display interactive forest plot

    +

    Static plot

    + + + + +
    + + + + +
    + + background_panel() +
    +
    Add background for creating plot with customized color
    +
    + + plot_dot() +
    +
    Dot plot
    +
    + + plot_errorbar() +
    +
    Plot to display risk difference
    +
    + + table_panel() +
    +
    Create table panel ggplot2 object for rainfall or forest plot
    +
    + + theme_panel() +
    +
    Theme function for plot with multiple panels
    +

    Example data

    diff --git a/reference/meta_forestly.html b/reference/meta_forestly.html index 6370fb8..983fc33 100644 --- a/reference/meta_forestly.html +++ b/reference/meta_forestly.html @@ -27,6 +27,7 @@
  • + Static Forest Plot Controlling Layout
    More articles... diff --git a/reference/plot_dot-1.png b/reference/plot_dot-1.png new file mode 100644 index 0000000..f98fff6 Binary files /dev/null and b/reference/plot_dot-1.png differ diff --git a/reference/plot_dot.html b/reference/plot_dot.html new file mode 100644 index 0000000..f76561d --- /dev/null +++ b/reference/plot_dot.html @@ -0,0 +1,205 @@ + +Dot plot — plot_dot • forestly + Skip to contents + + +
    +
    +
    +

    Dot plot

    + Source: R/plot.R +
    plot_dot.Rd
    +
    + +
    +

    Create a dot plot by item. For instance, this could be used to create AEs +incidence plot by Preferred Term and treatment group, as part of a +rainfall plot.

    +
    + +
    +

    Usage

    + 
    plot_dot(
+  tbl,
+  y_var,
+  label,
+  x_breaks = NULL,
+  color = NULL,
+  shape = NULL,
+  title = "AE (%)",
+  background_color = c("#69B8F7", "#FFFFFF"),
+  background_alpha = 0.3,
+  theme = theme_panel(show_text = TRUE, show_ticks = TRUE),
+  legend_nrow = 1
+)
    +
    + +
    +

    Arguments

    +
    tbl
    +

    A data frame selected from input data set to display on this plot. +y and x variables are required.

    + + +
    y_var
    +

    A character string that specifies a variable to be displayed +on the y-axis.

    + + +
    label
    +

    A character vector of labels for each treatment group. +The control group label should be specified as the last element +of the vector.

    + + +
    x_breaks
    +

    A numeric vector for x-axis breaks. Default is NULL, +which uses a default ggplot2 x-axis breaks presentation.

    + + +
    color
    +

    Color for each treatment group.

    + + +
    shape
    +

    Shape for each treatment group. Default is circle and square. +Input values could be either a character or numeric value, For details, +see https://ggplot2.tidyverse.org/articles/ggplot2-specs.html.

    + + +
    title
    +

    Panel title. Default is "AE (%)".

    + + +
    background_color
    +

    Plot background color. Default is +c("#69B8F7", "#FFFFFF"), which are pastel blue and white. +The value of this argument is used as input for the background_color +argument in background_panel().

    + + +
    background_alpha
    +

    Opacity of the background. Default is 0.3. +The value of this argument is the input for background_alpha argument in +background_panel().

    + + +
    theme
    +

    Panel theme, including the y-axis text, ticks, and plot margin. +Default is theme_panel(show_text = TRUE, show_ticks = TRUE). +For more details, refer to theme_panel.

    + + +
    legend_nrow
    +

    Integer, the number of rows for a legend display. +Must be smaller than or equal to the number of the treatment groups. +To omit the legend, set this to NULL. Default is 1.

    + +
    +
    +

    Value

    + + +

    AEs incidence plot by item and treatment group.

    +
    + +
    +

    Examples

    + 
    forestly_adsl$TRTA <- factor(
+  forestly_adsl$TRT01A,
+  levels = c("Xanomeline Low Dose", "Placebo"),
+  labels = c("Low Dose", "Placebo")
+)
+forestly_adae$TRTA <- factor(
+  forestly_adae$TRTA,
+  levels = c("Xanomeline Low Dose", "Placebo"),
+  labels = c("Low Dose", "Placebo")
+)
+
+meta <- meta_forestly(
+  dataset_adsl = forestly_adsl,
+  dataset_adae = forestly_adae,
+  population_term = "apat",
+  observation_term = "wk12",
+  parameter_term = "any;rel;ser"
+) |>
+  prepare_ae_forestly() |>
+  format_ae_forestly()
+
+meta_any <- meta$tbl[1:20, ] |> dplyr::filter(parameter == "any")
+meta_any |>
+  dplyr::select(name, prop_1, prop_2) |>
+  plot_dot("name", label = c("Treatment", "Placebo"))
+
+
    +
    +
    + + +
    +

    Developed by Yilong Zhang, Benjamin Wang, Yujie Zhao. Site built with pkgdown 2.0.9.
    Copyright © 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates. All rights reserved.

    +
    + +
    +

    +
    + +
    + + + + + + + diff --git a/reference/plot_errorbar-1.png b/reference/plot_errorbar-1.png new file mode 100644 index 0000000..0c8513b Binary files /dev/null and b/reference/plot_errorbar-1.png differ diff --git a/reference/plot_errorbar.html b/reference/plot_errorbar.html new file mode 100644 index 0000000..e243c5f --- /dev/null +++ b/reference/plot_errorbar.html @@ -0,0 +1,246 @@ + +Plot to display risk difference — plot_errorbar • forestly + Skip to contents + + +
    +
    +
    +

    Plot to display risk difference

    + Source: R/plot.R +
    plot_errorbar.Rd
    +
    + +
    +

    Create a plot to display risk difference for each item.

    +
    + +
    +

    Usage

    + 
    plot_errorbar(
+  tbl,
+  y_var,
+  errbar_width = 0.4,
+  color = NULL,
+  shape = NULL,
+  label,
+  x_breaks = NULL,
+  grp_abbrev = "paired",
+  favor_direction = "negative",
+  vline = NULL,
+  line_type = 1,
+  title = "Risk Diff. + 95% CI \n (Percentage Points)",
+  background_color = c("#69B8F7", "#FFFFFF"),
+  background_alpha = 0.3,
+  theme = theme_panel(show_text = TRUE, show_ticks = TRUE),
+  legend_nrow = 1
+)
    +
    + +
    +

    Arguments

    +
    tbl
    +

    A data frame selected from input data set to display on this plot. +y and x variables are required.

    + + +
    y_var
    +

    A character string that specifies a variable to be displayed +on the y-axis.

    + + +
    errbar_width
    +

    A numeric value to define the error bar width. +Default is 0.4. Value of this argument will be a half length of the +error bar, for example, errorbar_width = 0.2 means half of the error bar +width is 0.2 unit length. If y = 4, the error bar will range from +y = 3.8 to y = 4.2.

    + + +
    color
    +

    Color for each treatment group.

    + + +
    shape
    +

    Shape for each treatment group. Default is circle and square. +Input values could be either a character or numeric value, For details, +see https://ggplot2.tidyverse.org/articles/ggplot2-specs.html.

    + + +
    label
    +

    A character vector of labels for each treatment group. +The control group label should be specified as the last element +of the vector.

    + + +
    x_breaks
    +

    A numeric vector for x-axis breaks. Default is NULL, +which uses a default ggplot2 x-axis breaks presentation.

    + + +
    grp_abbrev
    +

    A character vector for displaying the treatment groups +on a favor bar. +If grp_abbrev = "paired", treatment label on the error bar will be +the same as in the label argument. +If grp_abbrev = "none", the error bar will not be shown. +Also, for customized terms, users can provide an alternative vector +of treatment labels. +Default is "paired".

    + + +
    favor_direction
    +

    The position of a favor label under the condition +"comparison is treatment – control". For AEs, favor_direction should be +"negative"; for efficacy, favor_direction should be "positive".

    + + +
    vline
    +

    Vertical reference line position. Default is NULL. +Users can define one or multiple numeric values in a vector as a +reference line position.

    + + +
    line_type
    +

    Reference line type. Default is solid line. +Users can define one or multiple line types in a vector +(can be numeric such as 1, 2, 3 or character such as "solid", "dashed"). +The values will be recycled and the order will be consistent with the +argument vline.

    + + +
    title
    +

    Plot title. Default is "Risk Diff. + 95% CI \\n (Percentage Points)".

    + + +
    background_color
    +

    Plot background color. Default is +c("#69B8F7", "#FFFFFF"), which are pastel blue and white. +The value of this argument is used as input for the background_color +argument in background_panel().

    + + +
    background_alpha
    +

    Opacity of the background. Default is 0.3. +The value of this argument is the input for background_alpha argument in +background_panel().

    + + +
    theme
    +

    Panel theme, including the y-axis text, ticks, and plot margin. +Default is theme_panel(show_text = TRUE, show_ticks = TRUE). +For more details, refer to theme_panel.

    + + +
    legend_nrow
    +

    Integer, the number of rows for a legend display. +Must be smaller than or equal to the number of the treatment groups. +To omit the legend, set this to NULL. Default is 1.

    + +
    +
    +

    Value

    + + +

    A risk difference plot for each item.

    +
    + +
    +

    Examples

    + 
    forestly_adsl$TRTA <- factor(
+  forestly_adsl$TRT01A,
+  levels = c("Xanomeline Low Dose", "Placebo"),
+  labels = c("Low Dose", "Placebo")
+)
+forestly_adae$TRTA <- factor(
+  forestly_adae$TRTA,
+  levels = c("Xanomeline Low Dose", "Placebo"),
+  labels = c("Low Dose", "Placebo")
+)
+
+meta <- meta_forestly(
+  dataset_adsl = forestly_adsl,
+  dataset_adae = forestly_adae,
+  population_term = "apat",
+  observation_term = "wk12",
+  parameter_term = "any;rel;ser"
+) |>
+  prepare_ae_forestly() |>
+  format_ae_forestly()
+
+meta_any <- meta$tbl[1:20, ] |> dplyr::filter(parameter == "any")
+meta_any |>
+  dplyr::select(name, diff_1, lower_1, upper_1) |>
+  plot_errorbar(
+    y_var = "name",
+    label = c("Treatment", "Placebo")
+  )
+
+
    +
    +
    + + +
    +

    Developed by Yilong Zhang, Benjamin Wang, Yujie Zhao. Site built with pkgdown 2.0.9.
    Copyright © 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates. All rights reserved.

    +
    + +
    +

    +
    + +
    + + + + + + + diff --git a/reference/prepare_ae_forestly.html b/reference/prepare_ae_forestly.html index 6edbd53..d239225 100644 --- a/reference/prepare_ae_forestly.html +++ b/reference/prepare_ae_forestly.html @@ -27,6 +27,7 @@
  • + Static Forest Plot Controlling Layout
    More articles... diff --git a/reference/table_panel-1.png b/reference/table_panel-1.png new file mode 100644 index 0000000..dcb69c2 Binary files /dev/null and b/reference/table_panel-1.png differ diff --git a/reference/table_panel.html b/reference/table_panel.html new file mode 100644 index 0000000..4a0ad84 --- /dev/null +++ b/reference/table_panel.html @@ -0,0 +1,186 @@ + +Create table panel ggplot2 object for rainfall or forest plot — table_panel • forestly + Skip to contents + + +
    +
    +
    +

    Create table panel ggplot2 object for rainfall or forest plot

    + Source: R/plot.R +
    table_panel.Rd
    +
    + +
    +

    Creates a table panel ggplot2 object for rainfall or forest plot.

    +
    + +
    +

    Usage

    + 
    table_panel(
+  tbl,
+  y_var,
+  x_label = NULL,
+  text_color = NULL,
+  text_size = 8,
+  text_format_by = "column",
+  background_color = c("#69B8F7", "#FFFFFF"),
+  theme = theme_panel(show_ticks = TRUE, show_text = TRUE),
+  background_alpha = 0.3
+)
    +
    + +
    +

    Arguments

    +
    tbl
    +

    A data frame to be displayed in this table.

    + + +
    y_var
    +

    A string of a variable name from tbl for the y axis variable.

    + + +
    x_label
    +

    Labels displayed on the top of table for each column of table. +Default is NULL, variable name will display as label.

    + + +
    text_color
    +

    Defines colors to display each treatment group.

    + + +
    text_size
    +

    Numeric font size for data on each column. +Default is 8 for each column.

    + + +
    text_format_by
    +

    An option for formatting a data by columns or rows. +Default is "column" and text color will be varied by column. +If text_format_by = "row", then text color will be varied by row. +If text_format_by = "group", then text color will be varied by treatment group.

    + + +
    background_color
    +

    Color for the plot background. +Default is c("#69B8F7", "#FFFFFF") which are pastel blue and white. +The value of this argument will be the input value for the +background_color argument in background_panel().

    + + +
    theme
    +

    Controls display of y axis text, ticks and plot margin. +By default, theme_panel(show_text = TRUE, show_ticks = TRUE) is used. +Users are suggested to use theme_panel().

    + + +
    background_alpha
    +

    Opacity of the background. Default is 0.3. +The value of this argument will be the input value for the +background_alpha argument in background_panel().

    + +
    +
    +

    Value

    + + +

    A ggplot2 object for table panel.

    +
    + +
    +

    Examples

    + 
    forestly_adsl$TRTA <- factor(
+  forestly_adsl$TRT01A,
+  levels = c("Xanomeline Low Dose", "Placebo"),
+  labels = c("Low Dose", "Placebo")
+)
+forestly_adae$TRTA <- factor(
+  forestly_adae$TRTA,
+  levels = c("Xanomeline Low Dose", "Placebo"),
+  labels = c("Low Dose", "Placebo")
+)
+
+meta <- meta_forestly(
+  dataset_adsl = forestly_adsl,
+  dataset_adae = forestly_adae,
+  population_term = "apat",
+  observation_term = "wk12",
+  parameter_term = "any;rel;ser"
+) |>
+  prepare_ae_forestly() |>
+  format_ae_forestly()
+
+meta_any <- meta$tbl[1:20, ] |> dplyr::filter(parameter == "any")
+
+meta_any |>
+  dplyr::select(name, diff_1, lower_1, upper_1) |>
+  table_panel(y_var = "name")
+
+
    +
    +
    + + +
    +

    Developed by Yilong Zhang, Benjamin Wang, Yujie Zhao. Site built with pkgdown 2.0.9.
    Copyright © 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates. All rights reserved.

    +
    + +
    +

    +
    + +
    + + + + + + + diff --git a/reference/theme_panel-1.png b/reference/theme_panel-1.png new file mode 100644 index 0000000..6984ce6 Binary files /dev/null and b/reference/theme_panel-1.png differ diff --git a/reference/theme_panel-2.png b/reference/theme_panel-2.png new file mode 100644 index 0000000..b79d091 Binary files /dev/null and b/reference/theme_panel-2.png differ diff --git a/reference/theme_panel.html b/reference/theme_panel.html new file mode 100644 index 0000000..4776b9b --- /dev/null +++ b/reference/theme_panel.html @@ -0,0 +1,120 @@ + +Theme function for plot with multiple panels — theme_panel • forestly + Skip to contents + + +
    +
    +
    +

    Theme function for plot with multiple panels

    + Source: R/plot.R +
    theme_panel.Rd
    +
    + +
    +

    Specifies theme for a plot with multiple panels.

    +
    + +
    +

    Usage

    + 
    theme_panel(show_text = TRUE, show_ticks = TRUE)
    +
    + +
    +

    Arguments

    +
    show_text
    +

    A logical value that controls text display on the y axis. +Default is TRUE.

    + + +
    show_ticks
    +

    A logical value that controls ticks display on the y axis. +Default is TRUE.

    + +
    +
    +

    Value

    + + +

    Theme for a specific panel.

    +
    + +
    +

    Examples

    + 
    library(ggplot2)
+
+p <- ggplot(mpg, aes(displ, hwy, colour = class)) +
+  geom_point()
+
+p
+
+p + theme_panel()
+
+
    +
    +
    + + +
    +

    Developed by Yilong Zhang, Benjamin Wang, Yujie Zhao. Site built with pkgdown 2.0.9.
    Copyright © 2023 Merck & Co., Inc., Rahway, NJ, USA and its affiliates. All rights reserved.

    +
    + +
    +

    +
    + +
    + + + + + + + diff --git a/search.json b/search.json index e50f46f..fb4d5b7 100644 --- a/search.json +++ b/search.json @@ -1 +1 @@ -[{"path":"https://merck.github.io/forestly/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"GNU General Public License","title":"GNU General Public License","text":"Version 3, 29 June 2007Copyright © 2007 Free Software Foundation, Inc.  Everyone permitted copy distribute verbatim copies license document, changing allowed.","code":""},{"path":"https://merck.github.io/forestly/LICENSE.html","id":"preamble","dir":"","previous_headings":"","what":"Preamble","title":"GNU General Public License","text":"GNU General Public License free, copyleft license software kinds works. licenses software practical works designed take away freedom share change works. contrast, GNU General Public License intended guarantee freedom share change versions program–make sure remains free software users. , Free Software Foundation, use GNU General Public License software; applies also work released way authors. can apply programs, . speak free software, referring freedom, price. General Public Licenses designed make sure freedom distribute copies free software (charge wish), receive source code can get want , can change software use pieces new free programs, know can things. protect rights, need prevent others denying rights asking surrender rights. Therefore, certain responsibilities distribute copies software, modify : responsibilities respect freedom others. example, distribute copies program, whether gratis fee, must pass recipients freedoms received. must make sure , , receive can get source code. must show terms know rights. Developers use GNU GPL protect rights two steps: (1) assert copyright software, (2) offer License giving legal permission copy, distribute /modify . developers’ authors’ protection, GPL clearly explains warranty free software. users’ authors’ sake, GPL requires modified versions marked changed, problems attributed erroneously authors previous versions. devices designed deny users access install run modified versions software inside , although manufacturer can . fundamentally incompatible aim protecting users’ freedom change software. systematic pattern abuse occurs area products individuals use, precisely unacceptable. Therefore, designed version GPL prohibit practice products. problems arise substantially domains, stand ready extend provision domains future versions GPL, needed protect freedom users. Finally, every program threatened constantly software patents. States allow patents restrict development use software general-purpose computers, , wish avoid special danger patents applied free program make effectively proprietary. prevent , GPL assures patents used render program non-free. precise terms conditions copying, distribution modification follow.","code":""},{"path":[]},{"path":"https://merck.github.io/forestly/LICENSE.html","id":"id_0-definitions","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"0. Definitions","title":"GNU General Public License","text":"“License” refers version 3 GNU General Public License. “Copyright” also means copyright-like laws apply kinds works, semiconductor masks. “Program” refers copyrightable work licensed License. licensee addressed “”. “Licensees” “recipients” may individuals organizations. “modify” work means copy adapt part work fashion requiring copyright permission, making exact copy. resulting work called “modified version” earlier work work “based ” earlier work. “covered work” means either unmodified Program work based Program. “propagate” work means anything , without permission, make directly secondarily liable infringement applicable copyright law, except executing computer modifying private copy. Propagation includes copying, distribution (without modification), making available public, countries activities well. “convey” work means kind propagation enables parties make receive copies. 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Source Code","title":"GNU General Public License","text":"“source code” work means preferred form work making modifications . “Object code” means non-source form work. “Standard Interface” means interface either official standard defined recognized standards body, , case interfaces specified particular programming language, one widely used among developers working language. “System Libraries” executable work include anything, work whole, () included normal form packaging Major Component, part Major Component, (b) serves enable use work Major Component, implement Standard Interface implementation available public source code form. “Major Component”, context, means major essential component (kernel, window system, ) specific operating system () executable work runs, compiler used produce work, object code interpreter used run . “Corresponding Source” work object code form means source code needed generate, install, (executable work) run object code modify work, including scripts control activities. 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Conveying Verbatim Copies","title":"GNU General Public License","text":"may convey verbatim copies Program’s source code receive , medium, provided conspicuously appropriately publish copy appropriate copyright notice; keep intact notices stating License non-permissive terms added accord section 7 apply code; keep intact notices absence warranty; give recipients copy License along Program. may charge price price copy convey, may offer support warranty protection fee.","code":""},{"path":"https://merck.github.io/forestly/LICENSE.html","id":"id_5-conveying-modified-source-versions","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"5. 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Conveying Non-Source Forms","title":"GNU General Public License","text":"may convey covered work object code form terms sections 4 5, provided also convey machine-readable Corresponding Source terms License, one ways: ) Convey object code , embodied , physical product (including physical distribution medium), accompanied Corresponding Source fixed durable physical medium customarily used software interchange. b) Convey object code , embodied , physical product (including physical distribution medium), accompanied written offer, valid least three years valid long offer spare parts customer support product model, give anyone possesses object code either (1) copy Corresponding Source software product covered License, durable physical medium customarily used software interchange, price reasonable cost physically performing conveying source, (2) access copy Corresponding Source network server charge. c) Convey individual copies object code copy written offer provide Corresponding Source. alternative allowed occasionally noncommercially, received object code offer, accord subsection 6b. d) Convey object code offering access designated place (gratis charge), offer equivalent access Corresponding Source way place charge. need require recipients copy Corresponding Source along object code. place copy object code network server, Corresponding Source may different server (operated third party) supports equivalent copying facilities, provided maintain clear directions next object code saying find Corresponding Source. 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Also add information contact electronic paper mail. program terminal interaction, make output short notice like starts interactive mode: hypothetical commands show w show c show appropriate parts General Public License. course, program’s commands might different; GUI interface, use “box”. also get employer (work programmer) school, , sign “copyright disclaimer” program, necessary. information , apply follow GNU GPL, see . GNU General Public License permit incorporating program proprietary programs. program subroutine library, may consider useful permit linking proprietary applications library. want , use GNU Lesser General Public License instead License. first, please read .","code":" Copyright (C) This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see . Copyright (C) This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free software, and you are welcome to redistribute it under certain conditions; type 'show c' for details."},{"path":"https://merck.github.io/forestly/articles/design-pattern.html","id":"overview","dir":"Articles","previous_headings":"","what":"Overview","title":"Design Plan of R Package forestly","text":"forestly package developed generate interactive forest plot safety analysis clinical trials. generate interactive forest plot, develop three main functions listed . details three main functions introduced next three sections separately. tidy_ae_table: function used obtain adverse event (AE) information ready visualization. download_ae_reports: function used generate download button, users can download AE summary tables clicking button. forestly: function used generate interactive forest plot. minimal example summarized major steps using forestly package ","code":"mydata <- tidy_ae_table(...) # Step 1: create tidy AE data download_ae_reports(mydata) # Step 2: generate download button forestly(mydata) # Step 3: generate interactive forest plot # (the order of Step 2 and Step 3 can be reversed)"},{"path":"https://merck.github.io/forestly/articles/design-pattern.html","id":"main-function-1-tidy_ae_table","dir":"Articles","previous_headings":"","what":"Main function 1: tidy_ae_table()","title":"Design Plan of R Package forestly","text":"main function tidy_ae_table() used obtain AE information ready visualization. Specifically speaking, merges standardized adsl adae tables together, outputs AE summary table. AE summary table summarizes number/ratio subjects experiencing certain AE treatment arm control arm. utility functions developed inside tidy_ae_table() list follows. tidy_population(): function used prepare observation datasets use function tidy_ae_table(). function filter adsl dataset, define proper treatment order dataset. tidy_observation(): function used prepare observation datasets use function tidy_ae_table(). function filter adae dataset, define proper treatment order dataset. `prop_test_mn(): function tests equal proportion using Miettinen Nurminen method. forestly package, generates confidence interval (CI) risk difference treatment arm control arm. define_ae_selectList(): function specify AE labels displayed select list interactive forestly plot. two arguments, (1) ae_criterion (2) ae_label. first argument ae_criterion (vector ) string, defines criterion select class AE display interactive forest plot. example, ae_criterion = 'AESER == \"Y\"', select serious AE. second argument ae_label (vector ) string, defines labels displayed select list interactive forest plot. two arguments string vectors, must 1:1 map. function used arguments ae_interested = function tidy_ae_table() (see examples ). throws errors length ae_criterion doesn’t match ae_label. tidy_multi_ae_label(): function design rbind data together according interested AE labels defined ae_interested =. example, use Example 1 , tidy_multi_ae_label() generate AE summary table rbind(summary table AE, summary serious AE). tidy_ae_listing(): function generates data frame serves listed details reactable.","code":"# Example 1: if you would like to display the serious AE tidy_ae_table(..., ae_interested = define_ae_selectList(ae_criterion = 'AESER == \"Y\"', ae_label = \"serious AE\"), ...). # Example 2: if you would like to display both serious AE and drug-related AE tidy_ae_table(..., ae_interested = define_ae_selectList(ae_criterion = c('AESER != \"N\"', 'AEREL != \"None\"'), ae_label = c(\"serious AE\", \"drug-related AE\") ...)."},{"path":"https://merck.github.io/forestly/articles/design-pattern.html","id":"main-function-2-tlf_download","dir":"Articles","previous_headings":"","what":"Main function 2: tlf_download()","title":"Design Plan of R Package forestly","text":"function generates download button users download AE tables. Example: https://merck.github.io/r2rtf/articles/example-ae-summary.html tlf_ae_specific: function create specific AE table. tlf_ae_listing: function create AE listing. output tlf_xxx functions r2rtf objects created rtf_encode tlf_download: function download multiple TLFs Rmarkdown. Rewrite ae_download_report allow use tlf_xxx functions input.","code":"tlf_ae_summary() # generate the AE summary table tlf_ae_specific() # generate the specific AE table # tlf[[4]] <- tlf_ae_listing() # As needed ???? tlf_download() # download the above tables"},{"path":"https://merck.github.io/forestly/articles/design-pattern.html","id":"main-function-3-forestly","dir":"Articles","previous_headings":"","what":"Main function 3: forestly()","title":"Design Plan of R Package forestly","text":"function generates interactive forest plot returned objected tidy_ae_table(). interactive forstly plot, consists two blocks. first block select list. items listed select list specified ae_label = function tidy_ae_table(..., ae_interested = , ...). clicking different AE labels, different reactable generated. example, click “serious AE”, reactable display serious AE summary table. main tool develop block crosstalk::filter_select(). second block reactable. reactable summarizes AE information selected AE label. main tool develop block reactable::reactable(). utility functions used develop forestly() listed follows. forestly_design_details(): function returns design details reactable forest plot, including design details cell two proportions; design details cell CI; design details footer two proportions; design details footer CI. design details returned another utility function sparkline_point_js(), introduce details later. generate design details, users need specify elements design, including color: color two proportion/CI plot (see arguments fig_prop_color = fig_diff_color =); label: labels displayed two proportion/CI plot (see arguments fig_prop_label = fig_diff_label =); column width: column width two proportion/CI plot (see arguments fig_prop_colwidth = fig_diff_colwidth =); range: x-axis range plot two proportion/CI plot (see arguments fig_prop_range = fig_diff_range =). sparkline_point_js(): function generates Javascript rendered. used design details reactables, including cell footer. dependence files path forestly/inst/js/sparkline.js. mk_reactable(): function used create data table tabular data sorting pagination default. Essentially, wrapper function reactable() robust BAAMR usage. dependence R package reactable.","code":""},{"path":"https://merck.github.io/forestly/articles/design-pattern.html","id":"other-utility-filesfunctions","dir":"Articles","previous_headings":"","what":"Other utility files/functions","title":"Design Plan of R Package forestly","text":"important_functions.R: used declare R-package dependency functions used develop functions.","code":""},{"path":"https://merck.github.io/forestly/articles/forestly.html","id":"overview","dir":"Articles","previous_headings":"","what":"Overview","title":"Interactive Forest Plot","text":"forestly package creates interactive forest plots clinical trial analysis & reporting. Specific adverse events analysis Subgroup analysis assume ADaM datasets ready analysis leverage metalite data structure define inputs outputs.","code":"forestly_adsl$TRTA <- factor(forestly_adsl$TRT01A, levels = c(\"Xanomeline Low Dose\", \"Placebo\"), labels = c(\"Low Dose\", \"Placebo\")) forestly_adae$TRTA <- factor(forestly_adae$TRTA, levels = c(\"Xanomeline Low Dose\", \"Placebo\"), labels = c(\"Low Dose\", \"Placebo\")) meta_forestly( dataset_adsl = forestly_adsl, dataset_adae = forestly_adae, parameter_term = \"any;rel;ser\" ) |> prepare_ae_forestly() |> format_ae_forestly() |> ae_forestly()"},{"path":"https://merck.github.io/forestly/articles/forestly.html","id":"interactive-features","dir":"Articles","previous_headings":"","what":"Interactive features","title":"Interactive Forest Plot","text":"interactive features example include: Select different AE criteria. Filter incidence AE one group. Revealed information hovering mouse point. Search bars find subjects selected adverse events (AE). Sort value click column header. Drill-listing clicking \\(\\blacktriangleright\\).","code":""},{"path":"https://merck.github.io/forestly/articles/forestly.html","id":"workflow","dir":"Articles","previous_headings":"","what":"Workflow","title":"Interactive Forest Plot","text":"general workflow : meta_forestly() constructs input metadata treatment analysis ADaM datasets. prepare_ae_forestly() prepares datasets interactive forest plot. format_ae_forestly() formats output layout. ae_forestly() generates interactive forest plot. meta_forestly() wrapper function metalite package. function users simplify process define input parameters required generate interactive forest plot. meta_forestly function require dataset_adsl, dataset_adae, observation_term population_term arguments. dataset_adsl, dataset_adae input ADaM dataset population observation. example, use “apat” population_term “wk12” observation_term. subset creteria terms, using SAFFL == \"Y\" default meta_forestly(). user wants customize definitions terms define new terms, tutorials can found link. paramter level metadata, parameter_term selected predefined terms listed . default, choose three parameter terms rel, ser use “;” concatenate allow three types AE displayed one interactive forest plot. following example, define ITT subset criteria ITTFL == \"Y\"population TEAE subset criteria TRTEMFL == \"Y\" observation. parameter, choose ser nonser pre-defined parameter list. metadata defined, can create interactive forest plot . section, calculate statistics prepare plotting dataset using prepare_ae_forestly(). Argument parameter required since can select parameter one defined metadata. use format_ae_forestly() format output ae_forestly() create interactive forest plot. Default value used arguments two functions. first example, select , ser nonser. example select , rel ser.","code":"meta_forestly( dataset_adsl = forestly_adsl, dataset_adae = forestly_adae, parameter_term = \"any;rel;ser\" ) #> ADaM metadata: #> .$data_population Population data with 170 subjects #> .$data_observation Observation data with 736 records #> .$plan Analysis plan with 1 plans #> #> #> Analysis population type: #> name id group var subset label #> 1 'apat' 'USUBJID' 'TRTA' SAFFL == 'Y' '' #> #> #> Analysis observation type: #> name id group var subset label #> 1 'safety' 'USUBJID' 'TRTA' SAFFL == 'Y' '' #> #> #> Analysis parameter type: #> name label subset #> 1 'any' 'any adverse events' #> 2 'rel' 'drug-related adverse events' toupper(AREL) == 'RELATED' #> 3 'ser' 'serious adverse events' AESER == 'Y' #> #> #> Analysis function: #> name label #> 1 'ae_forestly' 'Interactive forest plot' meta <- meta_forestly( dataset_adsl = forestly_adsl, dataset_adae = forestly_adae, population_term = \"ITT\", population_subset = ITTFL == \"Y\", observation_term = \"TEAE\", observation_subset = TRTEMFL == \"Y\", parameter_term = \"any;ser;nonser;rel\" ) meta #> ADaM metadata: #> .$data_population Population data with 170 subjects #> .$data_observation Observation data with 736 records #> .$plan Analysis plan with 1 plans #> #> #> Analysis population type: #> name id group var subset label #> 1 'ITT' 'USUBJID' 'TRTA' ITTFL == 'Y' '' #> #> #> Analysis observation type: #> name id group var subset label #> 1 'TEAE' 'USUBJID' 'TRTA' TRTEMFL == 'Y' '' #> #> #> Analysis parameter type: #> name label subset #> 1 'any' 'any adverse events' #> 2 'ser' 'serious adverse events' AESER == 'Y' #> 3 'nonser' 'non-serious adverse events' AESER != 'Y' | is.na(AESER) #> 4 'rel' 'drug-related adverse events' toupper(AREL) == 'RELATED' #> #> #> Analysis function: #> name label #> 1 'ae_forestly' 'Interactive forest plot' meta |> prepare_ae_forestly(parameter = \"any;ser;nonser\") |> format_ae_forestly() |> ae_forestly() meta |> prepare_ae_forestly(parameter = \"any;rel;ser\") |> format_ae_forestly() |> ae_forestly()"},{"path":"https://merck.github.io/forestly/articles/forestly.html","id":"define-metadata","dir":"Articles","previous_headings":"","what":"Define metadata","title":"Interactive Forest Plot","text":"order provide flexibility different analysis, forestly package also allows way construct metadata. show simplified example metalite package. details can found metalite package website. start construct metadata using metalite. output metadata contains two observation wk12 period1 illustration purpose. Also, parameter, subset criteria AEREL %% c(\"POSSIBLE\", \"PROBABLE\") instead toupper(AREL) == \"RELATED\" order fit observation dataset. metadata defined, can create interactive forest plot wk12 . Using similar approach, create interactive forest plot period1.","code":"library(metalite) meta <- meta_adam( population = forestly_adsl, observation = forestly_adae ) |> define_plan(plan = plan( analysis = \"ae_forestly\", population = \"apat\", observation = c(\"wk12\", \"period1\"), parameter = \"any;rel;ser\" )) |> define_population( name = \"apat\", group = \"TRTA\", subset = quote(SAFFL == \"Y\") ) |> define_observation( name = \"wk12\", group = \"TRTA\", subset = quote(SAFFL == \"Y\"), label = \"Weeks 0 to 12\" ) |> define_observation( name = \"period1\", group = \"TRTA\", var = \"AEDECOD\", subset = quote(TRTEMFL == \"Y\" & SAFFL == \"Y\"), label = \"Period 1\" ) |> define_parameter( name = \"rel\", subset = quote(AEREL %in% c(\"POSSIBLE\", \"PROBABLE\")) ) |> define_analysis( name = \"ae_forestly\", label = \"Interactive forest plot\" ) |> meta_build() meta #> ADaM metadata: #> .$data_population Population data with 170 subjects #> .$data_observation Observation data with 736 records #> .$plan Analysis plan with 2 plans #> #> #> Analysis population type: #> name id group var subset label #> 1 'apat' 'USUBJID' 'TRTA' SAFFL == 'Y' 'All Participants as Treated' #> #> #> Analysis observation type: #> name id group var subset #> 1 'wk12' 'USUBJID' 'TRTA' SAFFL == 'Y' #> 2 'period1' 'USUBJID' 'TRTA' 'AEDECOD' TRTEMFL == 'Y' & SAFFL == 'Y' #> label #> 1 'Weeks 0 to 12' #> 2 'Period 1' #> #> #> Analysis parameter type: #> name label subset #> 1 'rel' 'drug-related adverse events' AEREL %in% c('POSSIBLE', 'PROBABLE') #> 2 'any' 'any adverse events' #> 3 'ser' 'serious adverse events' AESER == 'Y' #> #> #> Analysis function: #> name label #> 1 'ae_forestly' 'Interactive forest plot' meta |> prepare_ae_forestly( population = \"apat\", observation = \"wk12\", parameter = \"any;rel;ser\" ) |> format_ae_forestly() |> ae_forestly() meta |> prepare_ae_forestly( population = \"apat\", observation = \"period1\", parameter = \"any;rel;ser\" ) |> format_ae_forestly() |> ae_forestly()"},{"path":"https://merck.github.io/forestly/articles/layout.html","id":"overview","dir":"Articles","previous_headings":"","what":"Overview","title":"Controlling Layout","text":"forestly package controls forest plot layouts simple effective approach. illustrate idea, use ADSL (forestly_adsl_3grp) ADAE (forestly_adae_3grp) datasets forestly package contain three treatment groups. first step create required metadata using meta_forestly(). use prepare_ae_forestly() prepare input datasets interactive forest plot. outdata contains parameters required generate interactive forest plot. interactive forest plot default style can generated.","code":"metadata <- meta_forestly( dataset_adsl = forestly_adsl_3grp, dataset_adae = forestly_adae_3grp, parameter_term = \"any;rel;ser\" ) outdata <- metadata |> prepare_ae_forestly() outdata #> List of 17 #> $ meta :List of 7 #> $ population : chr \"apat\" #> $ observation : chr \"safety\" #> $ parameter : chr \"any;rel;ser\" #> $ n :'data.frame': 361 obs. of 4 variables: #> $ order : num [1:361] 1030 1031 1032 1033 1034 ... #> $ group : chr [1:4] \"Placebo\" \"Low Dose\" \"High Dose\" \"Total\" #> $ reference_group: num 1 #> $ parameter_order: Factor w/ 3 levels \"any\",\"rel\",\"ser\": 1 1 1 1 1 1 1 1 1 1 ... #> $ prop :'data.frame': 361 obs. of 4 variables: #> $ diff :'data.frame': 361 obs. of 2 variables: #> $ n_pop :'data.frame': 1 obs. of 4 variables: #> $ name : chr [1:361] \"Atrial fibrillation\" \"Atrial flutter\" \"Atrial hypertrophy\" \"Atrioventricular block first degree\" ... #> $ ci_lower :'data.frame': 361 obs. of 2 variables: #> $ ci_upper :'data.frame': 361 obs. of 2 variables: #> $ p :'data.frame': 361 obs. of 2 variables: #> $ ae_listing :'data.frame': 1898 obs. of 14 variables: outdata |> format_ae_forestly() |> ae_forestly()"},{"path":"https://merck.github.io/forestly/articles/layout.html","id":"change-color","dir":"Articles","previous_headings":"","what":"Change color","title":"Controlling Layout","text":"default, forestly using teal treatment group plum control group. user wants change color, color argument format_ae_forestly() function can used. example interactive forest plot using black grey.","code":"outdata |> format_ae_forestly(color = c(\"black\", \"grey60\", \"grey40\")) |> ae_forestly()"},{"path":"https://merck.github.io/forestly/articles/layout.html","id":"display-different-columns","dir":"Articles","previous_headings":"","what":"Display different columns","title":"Controlling Layout","text":"using display argument format_ae_forestly(), can display total column. can also display risk difference columns similar approach.","code":"outdata |> format_ae_forestly(display = c(\"n\", \"prop\", \"fig_prop\", \"fig_diff\", \"total\")) |> ae_forestly() outdata |> format_ae_forestly(display = c(\"n\", \"prop\", \"fig_prop\", \"fig_diff\", \"diff\")) |> ae_forestly()"},{"path":"https://merck.github.io/forestly/articles/layout.html","id":"control-column-width","dir":"Articles","previous_headings":"","what":"Control column width","title":"Controlling Layout","text":"can control column width customize layout.","code":"outdata |> format_ae_forestly( width_fig = 230, footer_space = 110 ) |> ae_forestly(width = 1000)"},{"path":"https://merck.github.io/forestly/articles/layout.html","id":"horizontal-scrolling","dir":"Articles","previous_headings":"","what":"Horizontal scrolling","title":"Controlling Layout","text":"Set ae_forestly(..., width = NULL) make element scrollable horizontally. particularly useful embedding plot pages responsive design, using frameworks Bootstrap.","code":""},{"path":"https://merck.github.io/forestly/articles/layout.html","id":"change-variable-listed-in-drill-down-table","dir":"Articles","previous_headings":"","what":"Change variable listed in drill-down table","title":"Controlling Layout","text":"Users can explore AE listing clicking \\(\\blacktriangleright\\) row specify column names ae_listing_display.","code":"listing_var <- c( \"SEX\", \"RACE\", \"AGE\", \"SITEID\", \"AESEV\", \"STUDYID\", \"AESER\", \"AEREL\", \"ASTDT\", \"AENDT\" ) metadata |> prepare_ae_forestly( ae_listing_display = listing_var ) |> format_ae_forestly() |> ae_forestly()"},{"path":"https://merck.github.io/forestly/articles/layout.html","id":"hide-filters","dir":"Articles","previous_headings":"","what":"Hide filters","title":"Controlling Layout","text":"can use simple CSS rules hide incidence rate filter element. example, R Markdown document, use:","code":"```{css, echo=FALSE} #filter_subject { display: none; } ```"},{"path":"https://merck.github.io/forestly/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Yilong Zhang. Author. Benjamin Wang. Author, maintainer. Yujie Zhao. Author. Nan Xiao. Contributor. Hiroaki Fukuda. Contributor. Xuan Deng. Contributor. Merck & Co., Inc., Rahway, NJ, USA affiliates. Copyright holder.","code":""},{"path":"https://merck.github.io/forestly/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Zhang Y, Wang B, Zhao Y (2024). forestly: Interactive Forest Plot. R package version 0.1.1, https://github.com/Merck/forestly, https://merck.github.io/forestly/.","code":"@Manual{, title = {forestly: Interactive Forest Plot}, author = {Yilong Zhang and Benjamin Wang and Yujie Zhao}, year = {2024}, note = {R package version 0.1.1, https://github.com/Merck/forestly}, url = {https://merck.github.io/forestly/}, }"},{"path":[]},{"path":"https://merck.github.io/forestly/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Interactive Forest Plot","text":"easiest way get forestly install CRAN: Alternatively, use new feature get bug fix, can install development version forestly GitHub:","code":"install.packages(\"forestly\") # install.packages(\"remotes\") remotes::install_github(\"Merck/forestly\")"},{"path":"https://merck.github.io/forestly/index.html","id":"overview","dir":"","previous_headings":"","what":"Overview","title":"Interactive Forest Plot","text":"forestly package creates interactive forest plots clinical trial analysis & reporting. Specific adverse events analysis Subgroup analysis assume ADaM datasets ready analysis leverage metalite data structure define inputs outputs.","code":""},{"path":"https://merck.github.io/forestly/index.html","id":"workflow","dir":"","previous_headings":"","what":"Workflow","title":"Interactive Forest Plot","text":"general workflow : meta_forestly() constructs input metadata treatment analysis ADaM datasets. prepare_ae_forestly() prepares datasets interactive forest plot. format_ae_forestly() formats output layout. ae_forestly() generates interactive forest plot. quick example","code":"library(\"forestly\") meta_forestly( forestly_adsl, forestly_adae ) |> prepare_ae_forestly(parameter = \"any;rel;ser\") |> format_ae_forestly() |> ae_forestly()"},{"path":"https://merck.github.io/forestly/index.html","id":"interactive-features","dir":"","previous_headings":"","what":"Interactive features","title":"Interactive Forest Plot","text":"interactive features safety analysis include: Select different AE criteria. Filter incidence AE one groups. Reveal information hovering mouse data point. Search bars find subjects selected adverse events (AEs). Sort value clicking column header. Drill-listing clicking ▸.","code":""},{"path":"https://merck.github.io/forestly/index.html","id":"references","dir":"","previous_headings":"","what":"References","title":"Interactive Forest Plot","text":"Paper: 2023 PHUSE US Connect Talk: 2021 R/Pharma Conference","code":""},{"path":"https://merck.github.io/forestly/reference/ae_forestly.html","id":null,"dir":"Reference","previous_headings":"","what":"Display interactive forest plot — ae_forestly","title":"Display interactive forest plot — ae_forestly","text":"Display interactive forest plot","code":""},{"path":"https://merck.github.io/forestly/reference/ae_forestly.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Display interactive forest plot — ae_forestly","text":"","code":"ae_forestly(outdata, filter = c(\"prop\", \"n\"), width = 1400)"},{"path":"https://merck.github.io/forestly/reference/ae_forestly.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Display interactive forest plot — ae_forestly","text":"outdata outdata object created format_ae_forestly(). filter character value filter variable. width numeric value width table pixels.","code":""},{"path":"https://merck.github.io/forestly/reference/ae_forestly.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Display interactive forest plot — ae_forestly","text":"AE forest plot saved shiny.tag.list object.","code":""},{"path":"https://merck.github.io/forestly/reference/ae_forestly.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Display interactive forest plot — ae_forestly","text":"","code":"adsl <- forestly_adsl[1:100, ] adae <- forestly_adae[1:100, ] if (interactive()) { meta_forestly( dataset_adsl = adsl, dataset_adae = adae, ) |> prepare_ae_forestly() |> format_ae_forestly() |> ae_forestly() }"},{"path":"https://merck.github.io/forestly/reference/forestly_adae.html","id":null,"dir":"Reference","previous_headings":"","what":"An adverse event dataset — forestly_adae","title":"An adverse event dataset — forestly_adae","text":"dataset containing adverse event information clinical trial following CDISC ADaM standard.","code":""},{"path":"https://merck.github.io/forestly/reference/forestly_adae.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"An adverse event dataset — forestly_adae","text":"","code":"forestly_adae"},{"path":"https://merck.github.io/forestly/reference/forestly_adae.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"An adverse event dataset — forestly_adae","text":"data frame 736 rows 56 variables.","code":""},{"path":"https://merck.github.io/forestly/reference/forestly_adae.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"An adverse event dataset — forestly_adae","text":"https://github.com/phuse-org/phuse-scripts/tree/master/data/adam/cdisc","code":""},{"path":"https://merck.github.io/forestly/reference/forestly_adae.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"An adverse event dataset — forestly_adae","text":"Definition variable can found https://github.com/phuse-org/phuse-scripts/tree/master/data/adam/cdisc.","code":""},{"path":"https://merck.github.io/forestly/reference/forestly_adae_3grp.html","id":null,"dir":"Reference","previous_headings":"","what":"An adverse event dataset — forestly_adae_3grp","title":"An adverse event dataset — forestly_adae_3grp","text":"dataset containing adverse event information clinical trial following CDISC ADaM standard.","code":""},{"path":"https://merck.github.io/forestly/reference/forestly_adae_3grp.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"An adverse event dataset — forestly_adae_3grp","text":"","code":"forestly_adae_3grp"},{"path":"https://merck.github.io/forestly/reference/forestly_adae_3grp.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"An adverse event dataset — forestly_adae_3grp","text":"data frame 1191 rows 56 variables.","code":""},{"path":"https://merck.github.io/forestly/reference/forestly_adae_3grp.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"An adverse event dataset — forestly_adae_3grp","text":"https://github.com/phuse-org/phuse-scripts/tree/master/data/adam/cdisc","code":""},{"path":"https://merck.github.io/forestly/reference/forestly_adae_3grp.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"An adverse event dataset — forestly_adae_3grp","text":"Definition variable can found https://github.com/phuse-org/phuse-scripts/tree/master/data/adam/cdisc.","code":""},{"path":"https://merck.github.io/forestly/reference/forestly_adsl.html","id":null,"dir":"Reference","previous_headings":"","what":"A subject level demographic dataset — forestly_adsl","title":"A subject level demographic dataset — forestly_adsl","text":"dataset containing demographic information clinical trial following CDISC ADaM standard.","code":""},{"path":"https://merck.github.io/forestly/reference/forestly_adsl.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A subject level demographic dataset — forestly_adsl","text":"","code":"forestly_adsl"},{"path":"https://merck.github.io/forestly/reference/forestly_adsl.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"A subject level demographic dataset — forestly_adsl","text":"data frame 170 rows 49 variables.","code":""},{"path":"https://merck.github.io/forestly/reference/forestly_adsl.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"A subject level demographic dataset — forestly_adsl","text":"https://github.com/phuse-org/phuse-scripts/tree/master/data/adam/cdisc","code":""},{"path":"https://merck.github.io/forestly/reference/forestly_adsl.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"A subject level demographic dataset — forestly_adsl","text":"Definition variable can found https://github.com/phuse-org/phuse-scripts/tree/master/data/adam/cdisc.","code":""},{"path":"https://merck.github.io/forestly/reference/forestly_adsl_3grp.html","id":null,"dir":"Reference","previous_headings":"","what":"A subject level demographic dataset — forestly_adsl_3grp","title":"A subject level demographic dataset — forestly_adsl_3grp","text":"dataset containing demographic information clinical trial following CDISC ADaM standard.","code":""},{"path":"https://merck.github.io/forestly/reference/forestly_adsl_3grp.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A subject level demographic dataset — forestly_adsl_3grp","text":"","code":"forestly_adsl_3grp"},{"path":"https://merck.github.io/forestly/reference/forestly_adsl_3grp.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"A subject level demographic dataset — forestly_adsl_3grp","text":"data frame 254 rows 49 variables.","code":""},{"path":"https://merck.github.io/forestly/reference/forestly_adsl_3grp.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"A subject level demographic dataset — forestly_adsl_3grp","text":"https://github.com/phuse-org/phuse-scripts/tree/master/data/adam/cdisc","code":""},{"path":"https://merck.github.io/forestly/reference/forestly_adsl_3grp.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"A subject level demographic dataset — forestly_adsl_3grp","text":"Definition variable can found https://github.com/phuse-org/phuse-scripts/tree/master/data/adam/cdisc.","code":""},{"path":"https://merck.github.io/forestly/reference/format_ae_forestly.html","id":null,"dir":"Reference","previous_headings":"","what":"Format outdata for interactive forest plot — format_ae_forestly","title":"Format outdata for interactive forest plot — format_ae_forestly","text":"Format outdata interactive forest plot","code":""},{"path":"https://merck.github.io/forestly/reference/format_ae_forestly.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format outdata for interactive forest plot — format_ae_forestly","text":"","code":"format_ae_forestly( outdata, display = c(\"n\", \"prop\", \"fig_prop\", \"fig_diff\"), digits = 1, width_term = 200, width_fig = 320, width_n = 40, width_prop = 60, width_diff = 80, footer_space = 90, color = NULL, diff_label = \"Treatment <- Favor -> Placebo\", show_ae_parameter = FALSE )"},{"path":"https://merck.github.io/forestly/reference/format_ae_forestly.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format outdata for interactive forest plot — format_ae_forestly","text":"outdata outdata object created prepare_ae_forestly(). display character vector measurement displayed. n: Number subjects AE. prop: Proportion subjects AE. total: Total columns. diff: Risk difference. digits value digits displayed proportion risk difference. width_term Width px AE term column. width_fig Width px proportion risk difference figure. width_n Width px \"N\" columns. width_prop Width px \"(%)\" columns. width_diff Width px risk difference columns. footer_space Space px footer display legend. color vector colors analysis groups. Default value supports 4 groups. diff_label x-axis label risk difference. show_ae_parameter boolean value display AE parameter column.","code":""},{"path":"https://merck.github.io/forestly/reference/format_ae_forestly.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Format outdata for interactive forest plot — format_ae_forestly","text":"outdata object.","code":""},{"path":"https://merck.github.io/forestly/reference/format_ae_forestly.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Format outdata for interactive forest plot — format_ae_forestly","text":"","code":"adsl <- forestly_adsl[1:100,] adae <- forestly_adae[1:100,] meta_forestly( dataset_adsl = adsl, dataset_adae = adae ) |> prepare_ae_forestly()|> format_ae_forestly() #> Warning: In observation level data, force group variable 'TRTA' be a factor #> Warning: In observation level data, force group variable 'TRTA' be a factor #> List of 23 #> $ meta :List of 7 #> $ population : chr \"apat\" #> $ observation : chr \"safety\" #> $ parameter : chr \"any;rel\" #> $ n :'data.frame':\t60 obs. of 3 variables: #> $ order : num [1:60] 1008 1009 2019 2021 2022 ... #> $ group : chr [1:3] \"Placebo\" \"Xanomeline Low Dose\" \"Total\" #> $ reference_group : num 2 #> $ parameter_order : Factor w/ 2 levels \"any\",\"rel\": 1 1 1 1 1 1 1 1 1 1 ... #> $ prop :'data.frame':\t60 obs. of 3 variables: #> $ diff :'data.frame':\t60 obs. of 1 variable: #> $ n_pop :'data.frame':\t1 obs. of 3 variables: #> $ name : chr [1:60] \"Atrioventricular block second degree\" \"Bundle branch block left\" \"Eye allergy\" \"Eye pruritus\" ... #> $ ci_lower :'data.frame':\t60 obs. of 1 variable: #> $ ci_upper :'data.frame':\t60 obs. of 1 variable: #> $ p :'data.frame':\t60 obs. of 1 variable: #> $ ae_listing :'data.frame':\t151 obs. of 14 variables: #> $ tbl :'data.frame':\t60 obs. of 13 variables: #> $ reactable_columns :List of 13 #> $ reactable_columns_group:List of 3 #> $ display : chr [1:4] \"n\" \"prop\" \"fig_prop\" \"fig_diff\" #> $ fig_prop_color : chr [1:2] \"#00857C\" \"#66203A\" #> $ fig_diff_color : chr \"#00857C\""},{"path":"https://merck.github.io/forestly/reference/meta_forestly.html","id":null,"dir":"Reference","previous_headings":"","what":"Create metadata for interactive forest plot — meta_forestly","title":"Create metadata for interactive forest plot — meta_forestly","text":"Create metadata interactive forest plot","code":""},{"path":"https://merck.github.io/forestly/reference/meta_forestly.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create metadata for interactive forest plot — meta_forestly","text":"","code":"meta_forestly( dataset_adsl, dataset_adae, population_term = \"apat\", observation_term = \"safety\", parameter_term = \"any;rel\", population_subset = SAFFL == \"Y\", observation_subset = SAFFL == \"Y\", treatment_group = \"TRTA\" )"},{"path":"https://merck.github.io/forestly/reference/meta_forestly.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create metadata for interactive forest plot — meta_forestly","text":"dataset_adsl ADSL source dataset. dataset_adae ADAE source dataset. population_term character value population term name. observation_term character value observation term name. parameter_term character value parameter term name. population_subset unquoted condition selecting populations ADSL dataset. observation_subset unquoted condition selecting observations ADAE dataset. treatment_group character value treatment group name.","code":""},{"path":"https://merck.github.io/forestly/reference/meta_forestly.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create metadata for interactive forest plot — meta_forestly","text":"metalite object.","code":""},{"path":"https://merck.github.io/forestly/reference/meta_forestly.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create metadata for interactive forest plot — meta_forestly","text":"","code":"meta_forestly( forestly_adsl, forestly_adae, population_term = \"apat\", observation_term = \"safety\", parameter_term = \"any;rel\" ) #> ADaM metadata: #> .$data_population \tPopulation data with 170 subjects #> .$data_observation \tObservation data with 736 records #> .$plan \tAnalysis plan with 1 plans #> #> #> Analysis population type: #> name id group var subset label #> 1 'apat' 'USUBJID' 'TRTA' SAFFL == 'Y' '' #> #> #> Analysis observation type: #> name id group var subset label #> 1 'safety' 'USUBJID' 'TRTA' SAFFL == 'Y' '' #> #> #> Analysis parameter type: #> name label subset #> 1 'any' 'any adverse events' #> 2 'rel' 'drug-related adverse events' toupper(AREL) == 'RELATED' #> #> #> Analysis function: #> name label #> 1 'ae_forestly' 'Interactive forest plot' #>"},{"path":"https://merck.github.io/forestly/reference/prepare_ae_forestly.html","id":null,"dir":"Reference","previous_headings":"","what":"Prepare datasets for interactive forest plot — prepare_ae_forestly","title":"Prepare datasets for interactive forest plot — prepare_ae_forestly","text":"Prepare datasets interactive forest plot","code":""},{"path":"https://merck.github.io/forestly/reference/prepare_ae_forestly.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Prepare datasets for interactive forest plot — prepare_ae_forestly","text":"","code":"prepare_ae_forestly( meta, population = NULL, observation = NULL, parameter = NULL, reference_group = NULL, ae_listing_display = c(\"USUBJID\", \"SITEID\", \"SEX\", \"RACE\", \"AGE\", \"ASTDY\", \"AESER\", \"AEREL\", \"AEACN\", \"AEOUT\", \"ADURN\", \"ADURU\"), ae_listing_unique = FALSE )"},{"path":"https://merck.github.io/forestly/reference/prepare_ae_forestly.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Prepare datasets for interactive forest plot — prepare_ae_forestly","text":"meta metadata object created metalite. population character value population term name. term name used key link information. observation character value observation term name. term name used key link information. parameter character value parameter term name. term name used key link information. reference_group integer indicate reference group. Default 2 2 groups, otherwise, default 1. ae_listing_display vector name variables used display AE listing table. ae_listing_unique logical value display unique records AE listing table.","code":""},{"path":"https://merck.github.io/forestly/reference/prepare_ae_forestly.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Prepare datasets for interactive forest plot — prepare_ae_forestly","text":"outdata object.","code":""},{"path":"https://merck.github.io/forestly/reference/prepare_ae_forestly.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Prepare datasets for interactive forest plot — prepare_ae_forestly","text":"","code":"adsl <- forestly_adsl[1:100,] adae <- forestly_adae[1:100,] meta_forestly( dataset_adsl = adsl, dataset_adae = adae ) |> prepare_ae_forestly() #> Warning: In observation level data, force group variable 'TRTA' be a factor #> Warning: In observation level data, force group variable 'TRTA' be a factor #> List of 17 #> $ meta :List of 7 #> $ population : chr \"apat\" #> $ observation : chr \"safety\" #> $ parameter : chr \"any;rel\" #> $ n :'data.frame':\t60 obs. of 3 variables: #> $ order : num [1:60] 1008 1009 2019 2021 2022 ... #> $ group : chr [1:3] \"Placebo\" \"Xanomeline Low Dose\" \"Total\" #> $ reference_group: num 2 #> $ parameter_order: Factor w/ 2 levels \"any\",\"rel\": 1 1 1 1 1 1 1 1 1 1 ... #> $ prop :'data.frame':\t60 obs. of 3 variables: #> $ diff :'data.frame':\t60 obs. of 1 variable: #> $ n_pop :'data.frame':\t1 obs. of 3 variables: #> $ name : chr [1:60] \"Atrioventricular block second degree\" \"Bundle branch block left\" \"Eye allergy\" \"Eye pruritus\" ... #> $ ci_lower :'data.frame':\t60 obs. of 1 variable: #> $ ci_upper :'data.frame':\t60 obs. of 1 variable: #> $ p :'data.frame':\t60 obs. of 1 variable: #> $ ae_listing :'data.frame':\t151 obs. of 14 variables:"},{"path":"https://merck.github.io/forestly/news/index.html","id":"forestly-011","dir":"Changelog","previous_headings":"","what":"forestly 0.1.1","title":"forestly 0.1.1","text":"Fix bug record selected AE category (#9). Fix bug multiple plots displayed one page (#12). Update dataset forestly_adae since variable factor unexpected.","code":""},{"path":"https://merck.github.io/forestly/news/index.html","id":"forestly-010","dir":"Changelog","previous_headings":"","what":"forestly 0.1.0","title":"forestly 0.1.0","text":"CRAN release: 2023-07-19 Initial version. Added NEWS.md file track changes package.","code":""}] +[{"path":"https://merck.github.io/forestly/LICENSE.html","id":null,"dir":"","previous_headings":"","what":"GNU General Public License","title":"GNU General Public License","text":"Version 3, 29 June 2007Copyright © 2007 Free Software Foundation, Inc.  Everyone permitted copy distribute verbatim copies license document, changing allowed.","code":""},{"path":"https://merck.github.io/forestly/LICENSE.html","id":"preamble","dir":"","previous_headings":"","what":"Preamble","title":"GNU General Public License","text":"GNU General Public License free, copyleft license software kinds works. licenses software practical works designed take away freedom share change works. contrast, GNU General Public License intended guarantee freedom share change versions program–make sure remains free software users. , Free Software Foundation, use GNU General Public License software; applies also work released way authors. can apply programs, . speak free software, referring freedom, price. 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Nothing License shall construed excluding limiting implied license defenses infringement may otherwise available applicable patent law.","code":""},{"path":"https://merck.github.io/forestly/LICENSE.html","id":"id_12-no-surrender-of-others-freedom","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"12. No Surrender of Others’ Freedom","title":"GNU General Public License","text":"conditions imposed (whether court order, agreement otherwise) contradict conditions License, excuse conditions License. convey covered work satisfy simultaneously obligations License pertinent obligations, consequence may convey . example, agree terms obligate collect royalty conveying convey Program, way satisfy terms License refrain entirely conveying Program.","code":""},{"path":"https://merck.github.io/forestly/LICENSE.html","id":"id_13-use-with-the-gnu-affero-general-public-license","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"13. Use with the GNU Affero General Public License","title":"GNU General Public License","text":"Notwithstanding provision License, permission link combine covered work work licensed version 3 GNU Affero General Public License single combined work, convey resulting work. terms License continue apply part covered work, special requirements GNU Affero General Public License, section 13, concerning interaction network apply combination .","code":""},{"path":"https://merck.github.io/forestly/LICENSE.html","id":"id_14-revised-versions-of-this-license","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"14. Revised Versions of this License","title":"GNU General Public License","text":"Free Software Foundation may publish revised /new versions GNU General Public License time time. new versions similar spirit present version, may differ detail address new problems concerns. version given distinguishing version number. Program specifies certain numbered version GNU General Public License “later version” applies , option following terms conditions either numbered version later version published Free Software Foundation. Program specify version number GNU General Public License, may choose version ever published Free Software Foundation. Program specifies proxy can decide future versions GNU General Public License can used, proxy’s public statement acceptance version permanently authorizes choose version Program. Later license versions may give additional different permissions. However, additional obligations imposed author copyright holder result choosing follow later version.","code":""},{"path":"https://merck.github.io/forestly/LICENSE.html","id":"id_15-disclaimer-of-warranty","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"15. Disclaimer of Warranty","title":"GNU General Public License","text":"WARRANTY PROGRAM, EXTENT PERMITTED APPLICABLE LAW. EXCEPT OTHERWISE STATED WRITING COPYRIGHT HOLDERS /PARTIES PROVIDE PROGRAM “” WITHOUT WARRANTY KIND, EITHER EXPRESSED IMPLIED, INCLUDING, LIMITED , IMPLIED WARRANTIES MERCHANTABILITY FITNESS PARTICULAR PURPOSE. ENTIRE RISK QUALITY PERFORMANCE PROGRAM . PROGRAM PROVE DEFECTIVE, ASSUME COST NECESSARY SERVICING, REPAIR CORRECTION.","code":""},{"path":"https://merck.github.io/forestly/LICENSE.html","id":"id_16-limitation-of-liability","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"16. Limitation of Liability","title":"GNU General Public License","text":"EVENT UNLESS REQUIRED APPLICABLE LAW AGREED WRITING COPYRIGHT HOLDER, PARTY MODIFIES /CONVEYS PROGRAM PERMITTED , LIABLE DAMAGES, INCLUDING GENERAL, SPECIAL, INCIDENTAL CONSEQUENTIAL DAMAGES ARISING USE INABILITY USE PROGRAM (INCLUDING LIMITED LOSS DATA DATA RENDERED INACCURATE LOSSES SUSTAINED THIRD PARTIES FAILURE PROGRAM OPERATE PROGRAMS), EVEN HOLDER PARTY ADVISED POSSIBILITY DAMAGES.","code":""},{"path":"https://merck.github.io/forestly/LICENSE.html","id":"id_17-interpretation-of-sections-15-and-16","dir":"","previous_headings":"TERMS AND CONDITIONS","what":"17. Interpretation of Sections 15 and 16","title":"GNU General Public License","text":"disclaimer warranty limitation liability provided given local legal effect according terms, reviewing courts shall apply local law closely approximates absolute waiver civil liability connection Program, unless warranty assumption liability accompanies copy Program return fee. END TERMS CONDITIONS","code":""},{"path":"https://merck.github.io/forestly/LICENSE.html","id":"how-to-apply-these-terms-to-your-new-programs","dir":"","previous_headings":"","what":"How to Apply These Terms to Your New Programs","title":"GNU General Public License","text":"develop new program, want greatest possible use public, best way achieve make free software everyone can redistribute change terms. , attach following notices program. safest attach start source file effectively state exclusion warranty; file least “copyright” line pointer full notice found. Also add information contact electronic paper mail. program terminal interaction, make output short notice like starts interactive mode: hypothetical commands show w show c show appropriate parts General Public License. course, program’s commands might different; GUI interface, use “box”. also get employer (work programmer) school, , sign “copyright disclaimer” program, necessary. information , apply follow GNU GPL, see . GNU General Public License permit incorporating program proprietary programs. program subroutine library, may consider useful permit linking proprietary applications library. want , use GNU Lesser General Public License instead License. first, please read .","code":" Copyright (C) This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see . Copyright (C) This program comes with ABSOLUTELY NO WARRANTY; for details type 'show w'. This is free software, and you are welcome to redistribute it under certain conditions; type 'show c' for details."},{"path":"https://merck.github.io/forestly/articles/design-pattern.html","id":"overview","dir":"Articles","previous_headings":"","what":"Overview","title":"Design Plan of R Package forestly","text":"forestly package developed generate interactive forest plot safety analysis clinical trials. generate interactive forest plot, develop three main functions listed . details three main functions introduced next three sections separately. tidy_ae_table: function used obtain adverse event (AE) information ready visualization. download_ae_reports: function used generate download button, users can download AE summary tables clicking button. forestly: function used generate interactive forest plot. minimal example summarized major steps using forestly package ","code":"mydata <- tidy_ae_table(...) # Step 1: create tidy AE data download_ae_reports(mydata) # Step 2: generate download button forestly(mydata) # Step 3: generate interactive forest plot # (the order of Step 2 and Step 3 can be reversed)"},{"path":"https://merck.github.io/forestly/articles/design-pattern.html","id":"main-function-1-tidy_ae_table","dir":"Articles","previous_headings":"","what":"Main function 1: tidy_ae_table()","title":"Design Plan of R Package forestly","text":"main function tidy_ae_table() used obtain AE information ready visualization. Specifically speaking, merges standardized adsl adae tables together, outputs AE summary table. AE summary table summarizes number/ratio subjects experiencing certain AE treatment arm control arm. utility functions developed inside tidy_ae_table() list follows. tidy_population(): function used prepare observation datasets use function tidy_ae_table(). function filter adsl dataset, define proper treatment order dataset. tidy_observation(): function used prepare observation datasets use function tidy_ae_table(). function filter adae dataset, define proper treatment order dataset. `prop_test_mn(): function tests equal proportion using Miettinen Nurminen method. forestly package, generates confidence interval (CI) risk difference treatment arm control arm. define_ae_selectList(): function specify AE labels displayed select list interactive forestly plot. two arguments, (1) ae_criterion (2) ae_label. first argument ae_criterion (vector ) string, defines criterion select class AE display interactive forest plot. example, ae_criterion = 'AESER == \"Y\"', select serious AE. second argument ae_label (vector ) string, defines labels displayed select list interactive forest plot. two arguments string vectors, must 1:1 map. function used arguments ae_interested = function tidy_ae_table() (see examples ). throws errors length ae_criterion doesn’t match ae_label. tidy_multi_ae_label(): function design rbind data together according interested AE labels defined ae_interested =. example, use Example 1 , tidy_multi_ae_label() generate AE summary table rbind(summary table AE, summary serious AE). tidy_ae_listing(): function generates data frame serves listed details reactable.","code":"# Example 1: if you would like to display the serious AE tidy_ae_table(..., ae_interested = define_ae_selectList(ae_criterion = 'AESER == \"Y\"', ae_label = \"serious AE\"), ...). # Example 2: if you would like to display both serious AE and drug-related AE tidy_ae_table(..., ae_interested = define_ae_selectList(ae_criterion = c('AESER != \"N\"', 'AEREL != \"None\"'), ae_label = c(\"serious AE\", \"drug-related AE\") ...)."},{"path":"https://merck.github.io/forestly/articles/design-pattern.html","id":"main-function-2-tlf_download","dir":"Articles","previous_headings":"","what":"Main function 2: tlf_download()","title":"Design Plan of R Package forestly","text":"function generates download button users download AE tables. Example: https://merck.github.io/r2rtf/articles/example-ae-summary.html tlf_ae_specific: function create specific AE table. tlf_ae_listing: function create AE listing. output tlf_xxx functions r2rtf objects created rtf_encode tlf_download: function download multiple TLFs Rmarkdown. Rewrite ae_download_report allow use tlf_xxx functions input.","code":"tlf_ae_summary() # generate the AE summary table tlf_ae_specific() # generate the specific AE table # tlf[[4]] <- tlf_ae_listing() # As needed ???? tlf_download() # download the above tables"},{"path":"https://merck.github.io/forestly/articles/design-pattern.html","id":"main-function-3-forestly","dir":"Articles","previous_headings":"","what":"Main function 3: forestly()","title":"Design Plan of R Package forestly","text":"function generates interactive forest plot returned objected tidy_ae_table(). interactive forstly plot, consists two blocks. first block select list. items listed select list specified ae_label = function tidy_ae_table(..., ae_interested = , ...). clicking different AE labels, different reactable generated. example, click “serious AE”, reactable display serious AE summary table. main tool develop block crosstalk::filter_select(). second block reactable. reactable summarizes AE information selected AE label. main tool develop block reactable::reactable(). utility functions used develop forestly() listed follows. forestly_design_details(): function returns design details reactable forest plot, including design details cell two proportions; design details cell CI; design details footer two proportions; design details footer CI. design details returned another utility function sparkline_point_js(), introduce details later. generate design details, users need specify elements design, including color: color two proportion/CI plot (see arguments fig_prop_color = fig_diff_color =); label: labels displayed two proportion/CI plot (see arguments fig_prop_label = fig_diff_label =); column width: column width two proportion/CI plot (see arguments fig_prop_colwidth = fig_diff_colwidth =); range: x-axis range plot two proportion/CI plot (see arguments fig_prop_range = fig_diff_range =). sparkline_point_js(): function generates Javascript rendered. used design details reactables, including cell footer. dependence files path forestly/inst/js/sparkline.js. mk_reactable(): function used create data table tabular data sorting pagination default. Essentially, wrapper function reactable() robust BAAMR usage. dependence R package reactable.","code":""},{"path":"https://merck.github.io/forestly/articles/design-pattern.html","id":"other-utility-filesfunctions","dir":"Articles","previous_headings":"","what":"Other utility files/functions","title":"Design Plan of R Package forestly","text":"important_functions.R: used declare R-package dependency functions used develop functions.","code":""},{"path":"https://merck.github.io/forestly/articles/forestly.html","id":"overview","dir":"Articles","previous_headings":"","what":"Overview","title":"Interactive Forest Plot","text":"forestly package creates interactive forest plots clinical trial analysis & reporting. Specific adverse events analysis Subgroup analysis assume ADaM datasets ready analysis leverage metalite data structure define inputs outputs.","code":"forestly_adsl$TRTA <- factor(forestly_adsl$TRT01A, levels = c(\"Xanomeline Low Dose\", \"Placebo\"), labels = c(\"Low Dose\", \"Placebo\")) forestly_adae$TRTA <- factor(forestly_adae$TRTA, levels = c(\"Xanomeline Low Dose\", \"Placebo\"), labels = c(\"Low Dose\", \"Placebo\")) meta_forestly( dataset_adsl = forestly_adsl, dataset_adae = forestly_adae, parameter_term = \"any;rel;ser\" ) |> prepare_ae_forestly() |> format_ae_forestly() |> ae_forestly()"},{"path":"https://merck.github.io/forestly/articles/forestly.html","id":"interactive-features","dir":"Articles","previous_headings":"","what":"Interactive features","title":"Interactive Forest Plot","text":"interactive features example include: Select different AE criteria. Filter incidence AE one group. Revealed information hovering mouse point. Search bars find subjects selected adverse events (AE). Sort value click column header. Drill-listing clicking \\(\\blacktriangleright\\).","code":""},{"path":"https://merck.github.io/forestly/articles/forestly.html","id":"workflow","dir":"Articles","previous_headings":"","what":"Workflow","title":"Interactive Forest Plot","text":"general workflow : meta_forestly() constructs input metadata treatment analysis ADaM datasets. prepare_ae_forestly() prepares datasets interactive forest plot. format_ae_forestly() formats output layout. ae_forestly() generates interactive forest plot. meta_forestly() wrapper function metalite package. function users simplify process define input parameters required generate interactive forest plot. meta_forestly function require dataset_adsl, dataset_adae, observation_term population_term arguments. dataset_adsl, dataset_adae input ADaM dataset population observation. example, use “apat” population_term “wk12” observation_term. subset creteria terms, using SAFFL == \"Y\" default meta_forestly(). user wants customize definitions terms define new terms, tutorials can found link. paramter level metadata, parameter_term selected predefined terms listed . default, choose three parameter terms rel, ser use “;” concatenate allow three types AE displayed one interactive forest plot. following example, define ITT subset criteria ITTFL == \"Y\"population TEAE subset criteria TRTEMFL == \"Y\" observation. parameter, choose ser nonser pre-defined parameter list. metadata defined, can create interactive forest plot . section, calculate statistics prepare plotting dataset using prepare_ae_forestly(). Argument parameter required since can select parameter one defined metadata. use format_ae_forestly() format output ae_forestly() create interactive forest plot. Default value used arguments two functions. first example, select , ser nonser. example select , rel ser.","code":"meta_forestly( dataset_adsl = forestly_adsl, dataset_adae = forestly_adae, parameter_term = \"any;rel;ser\" ) #> ADaM metadata: #> .$data_population Population data with 170 subjects #> .$data_observation Observation data with 736 records #> .$plan Analysis plan with 1 plans #> #> #> Analysis population type: #> name id group var subset label #> 1 'apat' 'USUBJID' 'TRTA' SAFFL == 'Y' '' #> #> #> Analysis observation type: #> name id group var subset label #> 1 'safety' 'USUBJID' 'TRTA' SAFFL == 'Y' '' #> #> #> Analysis parameter type: #> name label subset #> 1 'any' 'any adverse events' #> 2 'rel' 'drug-related adverse events' toupper(AREL) == 'RELATED' #> 3 'ser' 'serious adverse events' AESER == 'Y' #> #> #> Analysis function: #> name label #> 1 'ae_forestly' 'Interactive forest plot' meta <- meta_forestly( dataset_adsl = forestly_adsl, dataset_adae = forestly_adae, population_term = \"ITT\", population_subset = ITTFL == \"Y\", observation_term = \"TEAE\", observation_subset = TRTEMFL == \"Y\", parameter_term = \"any;ser;nonser;rel\" ) meta #> ADaM metadata: #> .$data_population Population data with 170 subjects #> .$data_observation Observation data with 736 records #> .$plan Analysis plan with 1 plans #> #> #> Analysis population type: #> name id group var subset label #> 1 'ITT' 'USUBJID' 'TRTA' ITTFL == 'Y' '' #> #> #> Analysis observation type: #> name id group var subset label #> 1 'TEAE' 'USUBJID' 'TRTA' TRTEMFL == 'Y' '' #> #> #> Analysis parameter type: #> name label subset #> 1 'any' 'any adverse events' #> 2 'ser' 'serious adverse events' AESER == 'Y' #> 3 'nonser' 'non-serious adverse events' AESER != 'Y' | is.na(AESER) #> 4 'rel' 'drug-related adverse events' toupper(AREL) == 'RELATED' #> #> #> Analysis function: #> name label #> 1 'ae_forestly' 'Interactive forest plot' meta |> prepare_ae_forestly(parameter = \"any;ser;nonser\") |> format_ae_forestly() |> ae_forestly() meta |> prepare_ae_forestly(parameter = \"any;rel;ser\") |> format_ae_forestly() |> ae_forestly()"},{"path":"https://merck.github.io/forestly/articles/forestly.html","id":"define-metadata","dir":"Articles","previous_headings":"","what":"Define metadata","title":"Interactive Forest Plot","text":"order provide flexibility different analysis, forestly package also allows way construct metadata. show simplified example metalite package. details can found metalite package website. start construct metadata using metalite. output metadata contains two observation wk12 period1 illustration purpose. Also, parameter, subset criteria AEREL %% c(\"POSSIBLE\", \"PROBABLE\") instead toupper(AREL) == \"RELATED\" order fit observation dataset. metadata defined, can create interactive forest plot wk12 . Using similar approach, create interactive forest plot period1.","code":"library(metalite) meta <- meta_adam( population = forestly_adsl, observation = forestly_adae ) |> define_plan(plan = plan( analysis = \"ae_forestly\", population = \"apat\", observation = c(\"wk12\", \"period1\"), parameter = \"any;rel;ser\" )) |> define_population( name = \"apat\", group = \"TRTA\", subset = quote(SAFFL == \"Y\") ) |> define_observation( name = \"wk12\", group = \"TRTA\", subset = quote(SAFFL == \"Y\"), label = \"Weeks 0 to 12\" ) |> define_observation( name = \"period1\", group = \"TRTA\", var = \"AEDECOD\", subset = quote(TRTEMFL == \"Y\" & SAFFL == \"Y\"), label = \"Period 1\" ) |> define_parameter( name = \"rel\", subset = quote(AEREL %in% c(\"POSSIBLE\", \"PROBABLE\")) ) |> define_analysis( name = \"ae_forestly\", label = \"Interactive forest plot\" ) |> meta_build() meta #> ADaM metadata: #> .$data_population Population data with 170 subjects #> .$data_observation Observation data with 736 records #> .$plan Analysis plan with 2 plans #> #> #> Analysis population type: #> name id group var subset label #> 1 'apat' 'USUBJID' 'TRTA' SAFFL == 'Y' 'All Participants as Treated' #> #> #> Analysis observation type: #> name id group var subset #> 1 'wk12' 'USUBJID' 'TRTA' SAFFL == 'Y' #> 2 'period1' 'USUBJID' 'TRTA' 'AEDECOD' TRTEMFL == 'Y' & SAFFL == 'Y' #> label #> 1 'Weeks 0 to 12' #> 2 'Period 1' #> #> #> Analysis parameter type: #> name label subset #> 1 'rel' 'drug-related adverse events' AEREL %in% c('POSSIBLE', 'PROBABLE') #> 2 'any' 'any adverse events' #> 3 'ser' 'serious adverse events' AESER == 'Y' #> #> #> Analysis function: #> name label #> 1 'ae_forestly' 'Interactive forest plot' meta |> prepare_ae_forestly( population = \"apat\", observation = \"wk12\", parameter = \"any;rel;ser\" ) |> format_ae_forestly() |> ae_forestly() meta |> prepare_ae_forestly( population = \"apat\", observation = \"period1\", parameter = \"any;rel;ser\" ) |> format_ae_forestly() |> ae_forestly()"},{"path":"https://merck.github.io/forestly/articles/layout.html","id":"overview","dir":"Articles","previous_headings":"","what":"Overview","title":"Controlling Layout","text":"forestly package controls forest plot layouts simple effective approach. illustrate idea, use ADSL (forestly_adsl_3grp) ADAE (forestly_adae_3grp) datasets forestly package contain three treatment groups. first step create required metadata using meta_forestly(). use prepare_ae_forestly() prepare input datasets interactive forest plot. outdata contains parameters required generate interactive forest plot. interactive forest plot default style can generated.","code":"metadata <- meta_forestly( dataset_adsl = forestly_adsl_3grp, dataset_adae = forestly_adae_3grp, parameter_term = \"any;rel;ser\" ) outdata <- metadata |> prepare_ae_forestly() outdata #> List of 17 #> $ meta :List of 7 #> $ population : chr \"apat\" #> $ observation : chr \"safety\" #> $ parameter : chr \"any;rel;ser\" #> $ n :'data.frame': 361 obs. of 4 variables: #> $ order : num [1:361] 1030 1031 1032 1033 1034 ... #> $ group : chr [1:4] \"Placebo\" \"Low Dose\" \"High Dose\" \"Total\" #> $ reference_group: num 1 #> $ parameter_order: Factor w/ 3 levels \"any\",\"rel\",\"ser\": 1 1 1 1 1 1 1 1 1 1 ... #> $ prop :'data.frame': 361 obs. of 4 variables: #> $ diff :'data.frame': 361 obs. of 2 variables: #> $ n_pop :'data.frame': 1 obs. of 4 variables: #> $ name : chr [1:361] \"Atrial fibrillation\" \"Atrial flutter\" \"Atrial hypertrophy\" \"Atrioventricular block first degree\" ... #> $ ci_lower :'data.frame': 361 obs. of 2 variables: #> $ ci_upper :'data.frame': 361 obs. of 2 variables: #> $ p :'data.frame': 361 obs. of 2 variables: #> $ ae_listing :'data.frame': 1898 obs. of 14 variables: outdata |> format_ae_forestly() |> ae_forestly()"},{"path":"https://merck.github.io/forestly/articles/layout.html","id":"change-color","dir":"Articles","previous_headings":"","what":"Change color","title":"Controlling Layout","text":"default, forestly using teal treatment group plum control group. user wants change color, color argument format_ae_forestly() function can used. example interactive forest plot using black grey.","code":"outdata |> format_ae_forestly(color = c(\"black\", \"grey60\", \"grey40\")) |> ae_forestly()"},{"path":"https://merck.github.io/forestly/articles/layout.html","id":"display-different-columns","dir":"Articles","previous_headings":"","what":"Display different columns","title":"Controlling Layout","text":"using display argument format_ae_forestly(), can display total column. can also display risk difference columns similar approach.","code":"outdata |> format_ae_forestly(display = c(\"n\", \"prop\", \"fig_prop\", \"fig_diff\", \"total\")) |> ae_forestly() outdata |> format_ae_forestly(display = c(\"n\", \"prop\", \"fig_prop\", \"fig_diff\", \"diff\")) |> ae_forestly()"},{"path":"https://merck.github.io/forestly/articles/layout.html","id":"control-column-width","dir":"Articles","previous_headings":"","what":"Control column width","title":"Controlling Layout","text":"can control column width customize layout.","code":"outdata |> format_ae_forestly( width_fig = 230, footer_space = 110 ) |> ae_forestly(width = 1000)"},{"path":"https://merck.github.io/forestly/articles/layout.html","id":"horizontal-scrolling","dir":"Articles","previous_headings":"","what":"Horizontal scrolling","title":"Controlling Layout","text":"Set ae_forestly(..., width = NULL) make element scrollable horizontally. particularly useful embedding plot pages responsive design, using frameworks Bootstrap.","code":""},{"path":"https://merck.github.io/forestly/articles/layout.html","id":"change-variable-listed-in-drill-down-table","dir":"Articles","previous_headings":"","what":"Change variable listed in drill-down table","title":"Controlling Layout","text":"Users can explore AE listing clicking \\(\\blacktriangleright\\) row specify column names ae_listing_display.","code":"listing_var <- c( \"SEX\", \"RACE\", \"AGE\", \"SITEID\", \"AESEV\", \"STUDYID\", \"AESER\", \"AEREL\", \"ASTDT\", \"AENDT\" ) metadata |> prepare_ae_forestly( ae_listing_display = listing_var ) |> format_ae_forestly() |> ae_forestly()"},{"path":"https://merck.github.io/forestly/articles/layout.html","id":"hide-filters","dir":"Articles","previous_headings":"","what":"Hide filters","title":"Controlling Layout","text":"can use simple CSS rules hide incidence rate filter element. example, R Markdown document, use:","code":"```{css, echo=FALSE} #filter_subject { display: none; } ```"},{"path":"https://merck.github.io/forestly/authors.html","id":null,"dir":"","previous_headings":"","what":"Authors","title":"Authors and Citation","text":"Yilong Zhang. Author. Benjamin Wang. Author, maintainer. Yujie Zhao. Author. Nan Xiao. Contributor. Hiroaki Fukuda. Contributor. Yulia Sidi. Contributor. Xuan Deng. Contributor. Merck & Co., Inc., Rahway, NJ, USA affiliates. Copyright holder.","code":""},{"path":"https://merck.github.io/forestly/authors.html","id":"citation","dir":"","previous_headings":"","what":"Citation","title":"Authors and Citation","text":"Zhang Y, Wang B, Zhao Y (2024). forestly: Interactive Forest Plot. R package version 0.1.1, https://github.com/Merck/forestly, https://merck.github.io/forestly/.","code":"@Manual{, title = {forestly: Interactive Forest Plot}, author = {Yilong Zhang and Benjamin Wang and Yujie Zhao}, year = {2024}, note = {R package version 0.1.1, https://github.com/Merck/forestly}, url = {https://merck.github.io/forestly/}, }"},{"path":[]},{"path":"https://merck.github.io/forestly/index.html","id":"installation","dir":"","previous_headings":"","what":"Installation","title":"Interactive Forest Plot","text":"easiest way get forestly install CRAN: Alternatively, use new feature get bug fix, can install development version forestly GitHub:","code":"install.packages(\"forestly\") # install.packages(\"remotes\") remotes::install_github(\"Merck/forestly\")"},{"path":"https://merck.github.io/forestly/index.html","id":"overview","dir":"","previous_headings":"","what":"Overview","title":"Interactive Forest Plot","text":"forestly package creates interactive forest plots clinical trial analysis & reporting. Specific adverse events analysis Subgroup analysis assume ADaM datasets ready analysis leverage metalite data structure define inputs outputs.","code":""},{"path":"https://merck.github.io/forestly/index.html","id":"workflow","dir":"","previous_headings":"","what":"Workflow","title":"Interactive Forest Plot","text":"general workflow : meta_forestly() constructs input metadata treatment analysis ADaM datasets. prepare_ae_forestly() prepares datasets interactive forest plot. format_ae_forestly() formats output layout. ae_forestly() generates interactive forest plot. quick example","code":"library(\"forestly\") meta_forestly( forestly_adsl, forestly_adae ) |> prepare_ae_forestly(parameter = \"any;rel;ser\") |> format_ae_forestly() |> ae_forestly()"},{"path":"https://merck.github.io/forestly/index.html","id":"interactive-features","dir":"","previous_headings":"","what":"Interactive features","title":"Interactive Forest Plot","text":"interactive features safety analysis include: Select different AE criteria. Filter incidence AE one groups. Reveal information hovering mouse data point. Search bars find subjects selected adverse events (AEs). Sort value clicking column header. Drill-listing clicking ▸.","code":""},{"path":"https://merck.github.io/forestly/index.html","id":"references","dir":"","previous_headings":"","what":"References","title":"Interactive Forest Plot","text":"Paper: 2023 PHUSE US Connect Talk: 2021 R/Pharma Conference","code":""},{"path":"https://merck.github.io/forestly/reference/ae_forestly.html","id":null,"dir":"Reference","previous_headings":"","what":"Display interactive forest plot — ae_forestly","title":"Display interactive forest plot — ae_forestly","text":"Display interactive forest plot","code":""},{"path":"https://merck.github.io/forestly/reference/ae_forestly.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Display interactive forest plot — ae_forestly","text":"","code":"ae_forestly(outdata, filter = c(\"prop\", \"n\"), width = 1400)"},{"path":"https://merck.github.io/forestly/reference/ae_forestly.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Display interactive forest plot — ae_forestly","text":"outdata outdata object created format_ae_forestly(). filter character value filter variable. width numeric value width table pixels.","code":""},{"path":"https://merck.github.io/forestly/reference/ae_forestly.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Display interactive forest plot — ae_forestly","text":"AE forest plot saved shiny.tag.list object.","code":""},{"path":"https://merck.github.io/forestly/reference/ae_forestly.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Display interactive forest plot — ae_forestly","text":"","code":"adsl <- forestly_adsl[1:100, ] adae <- forestly_adae[1:100, ] if (interactive()) { meta_forestly( dataset_adsl = adsl, dataset_adae = adae, ) |> prepare_ae_forestly() |> format_ae_forestly() |> ae_forestly() }"},{"path":"https://merck.github.io/forestly/reference/background_panel.html","id":null,"dir":"Reference","previous_headings":"","what":"Add background for creating plot with customized color — background_panel","title":"Add background for creating plot with customized color — background_panel","text":"Creates colored background panels rainfall forest plot.","code":""},{"path":"https://merck.github.io/forestly/reference/background_panel.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Add background for creating plot with customized color — background_panel","text":"","code":"background_panel( g, background_color = c(\"#69B8F7\", \"#FFFFFF\"), background_alpha = 0.3 )"},{"path":"https://merck.github.io/forestly/reference/background_panel.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Add background for creating plot with customized color — background_panel","text":"g ggplot object adding colored background. background_color vector colors defines color plot background. Default c(\"#69B8F7\", \"#FFFFFF\"), pastel blue white. colors recycled. background_alpha Opacity geom. Default 0.3.","code":""},{"path":"https://merck.github.io/forestly/reference/background_panel.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Add background for creating plot with customized color — background_panel","text":"Plot colored background add panels rainfall forest plot.","code":""},{"path":"https://merck.github.io/forestly/reference/background_panel.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Add background for creating plot with customized color — background_panel","text":"","code":"library(ggplot2) df <- data.frame( study = c(\"S1\", \"S2\", \"S3\", \"S4\", \"S5\", \"S6\", \"S7\"), item = as.factor(1:7), effect = c(-.4, -.25, -.1, .1, .15, .2, .3), lower = c(-.43, -.29, -.17, -.02, .04, .17, .27), upper = c(-.37, -.21, -.03, .22, .24, .23, .33) ) ggplot(data = df) |> background_panel(background_color = c(\"grey\", \"white\"), background_alpha = 0.4) + geom_point(aes(y = item, x = effect)) + geom_errorbar(aes(y = item, x = effect, xmin = lower, xmax = upper), width = 0.4) + scale_y_discrete(name = \"\", breaks = 1:nrow(df), labels = df$study)"},{"path":"https://merck.github.io/forestly/reference/forestly_adae.html","id":null,"dir":"Reference","previous_headings":"","what":"An adverse event dataset — forestly_adae","title":"An adverse event dataset — forestly_adae","text":"dataset containing adverse event information clinical trial following CDISC ADaM standard.","code":""},{"path":"https://merck.github.io/forestly/reference/forestly_adae.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"An adverse event dataset — forestly_adae","text":"","code":"forestly_adae"},{"path":"https://merck.github.io/forestly/reference/forestly_adae.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"An adverse event dataset — forestly_adae","text":"data frame 736 rows 56 variables.","code":""},{"path":"https://merck.github.io/forestly/reference/forestly_adae.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"An adverse event dataset — forestly_adae","text":"https://github.com/phuse-org/phuse-scripts/tree/master/data/adam/cdisc","code":""},{"path":"https://merck.github.io/forestly/reference/forestly_adae.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"An adverse event dataset — forestly_adae","text":"Definition variable can found https://github.com/phuse-org/phuse-scripts/tree/master/data/adam/cdisc.","code":""},{"path":"https://merck.github.io/forestly/reference/forestly_adae_3grp.html","id":null,"dir":"Reference","previous_headings":"","what":"An adverse event dataset — forestly_adae_3grp","title":"An adverse event dataset — forestly_adae_3grp","text":"dataset containing adverse event information clinical trial following CDISC ADaM standard.","code":""},{"path":"https://merck.github.io/forestly/reference/forestly_adae_3grp.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"An adverse event dataset — forestly_adae_3grp","text":"","code":"forestly_adae_3grp"},{"path":"https://merck.github.io/forestly/reference/forestly_adae_3grp.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"An adverse event dataset — forestly_adae_3grp","text":"data frame 1191 rows 56 variables.","code":""},{"path":"https://merck.github.io/forestly/reference/forestly_adae_3grp.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"An adverse event dataset — forestly_adae_3grp","text":"https://github.com/phuse-org/phuse-scripts/tree/master/data/adam/cdisc","code":""},{"path":"https://merck.github.io/forestly/reference/forestly_adae_3grp.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"An adverse event dataset — forestly_adae_3grp","text":"Definition variable can found https://github.com/phuse-org/phuse-scripts/tree/master/data/adam/cdisc.","code":""},{"path":"https://merck.github.io/forestly/reference/forestly_adsl.html","id":null,"dir":"Reference","previous_headings":"","what":"A subject level demographic dataset — forestly_adsl","title":"A subject level demographic dataset — forestly_adsl","text":"dataset containing demographic information clinical trial following CDISC ADaM standard.","code":""},{"path":"https://merck.github.io/forestly/reference/forestly_adsl.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A subject level demographic dataset — forestly_adsl","text":"","code":"forestly_adsl"},{"path":"https://merck.github.io/forestly/reference/forestly_adsl.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"A subject level demographic dataset — forestly_adsl","text":"data frame 170 rows 49 variables.","code":""},{"path":"https://merck.github.io/forestly/reference/forestly_adsl.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"A subject level demographic dataset — forestly_adsl","text":"https://github.com/phuse-org/phuse-scripts/tree/master/data/adam/cdisc","code":""},{"path":"https://merck.github.io/forestly/reference/forestly_adsl.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"A subject level demographic dataset — forestly_adsl","text":"Definition variable can found https://github.com/phuse-org/phuse-scripts/tree/master/data/adam/cdisc.","code":""},{"path":"https://merck.github.io/forestly/reference/forestly_adsl_3grp.html","id":null,"dir":"Reference","previous_headings":"","what":"A subject level demographic dataset — forestly_adsl_3grp","title":"A subject level demographic dataset — forestly_adsl_3grp","text":"dataset containing demographic information clinical trial following CDISC ADaM standard.","code":""},{"path":"https://merck.github.io/forestly/reference/forestly_adsl_3grp.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"A subject level demographic dataset — forestly_adsl_3grp","text":"","code":"forestly_adsl_3grp"},{"path":"https://merck.github.io/forestly/reference/forestly_adsl_3grp.html","id":"format","dir":"Reference","previous_headings":"","what":"Format","title":"A subject level demographic dataset — forestly_adsl_3grp","text":"data frame 254 rows 49 variables.","code":""},{"path":"https://merck.github.io/forestly/reference/forestly_adsl_3grp.html","id":"source","dir":"Reference","previous_headings":"","what":"Source","title":"A subject level demographic dataset — forestly_adsl_3grp","text":"https://github.com/phuse-org/phuse-scripts/tree/master/data/adam/cdisc","code":""},{"path":"https://merck.github.io/forestly/reference/forestly_adsl_3grp.html","id":"details","dir":"Reference","previous_headings":"","what":"Details","title":"A subject level demographic dataset — forestly_adsl_3grp","text":"Definition variable can found https://github.com/phuse-org/phuse-scripts/tree/master/data/adam/cdisc.","code":""},{"path":"https://merck.github.io/forestly/reference/format_ae_forestly.html","id":null,"dir":"Reference","previous_headings":"","what":"Format outdata for interactive forest plot — format_ae_forestly","title":"Format outdata for interactive forest plot — format_ae_forestly","text":"Format outdata interactive forest plot","code":""},{"path":"https://merck.github.io/forestly/reference/format_ae_forestly.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Format outdata for interactive forest plot — format_ae_forestly","text":"","code":"format_ae_forestly( outdata, display = c(\"n\", \"prop\", \"fig_prop\", \"fig_diff\"), digits = 1, width_term = 200, width_fig = 320, width_n = 40, width_prop = 60, width_diff = 80, footer_space = 90, color = NULL, diff_label = \"Treatment <- Favor -> Placebo\", show_ae_parameter = FALSE )"},{"path":"https://merck.github.io/forestly/reference/format_ae_forestly.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Format outdata for interactive forest plot — format_ae_forestly","text":"outdata outdata object created prepare_ae_forestly(). display character vector measurement displayed. n: Number subjects AE. prop: Proportion subjects AE. total: Total columns. diff: Risk difference. digits value digits displayed proportion risk difference. width_term Width px AE term column. width_fig Width px proportion risk difference figure. width_n Width px \"N\" columns. width_prop Width px \"(%)\" columns. width_diff Width px risk difference columns. footer_space Space px footer display legend. color vector colors analysis groups. Default value supports 4 groups. diff_label x-axis label risk difference. show_ae_parameter boolean value display AE parameter column.","code":""},{"path":"https://merck.github.io/forestly/reference/format_ae_forestly.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Format outdata for interactive forest plot — format_ae_forestly","text":"outdata object.","code":""},{"path":"https://merck.github.io/forestly/reference/format_ae_forestly.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Format outdata for interactive forest plot — format_ae_forestly","text":"","code":"adsl <- forestly_adsl[1:100,] adae <- forestly_adae[1:100,] meta_forestly( dataset_adsl = adsl, dataset_adae = adae ) |> prepare_ae_forestly()|> format_ae_forestly() #> Warning: In observation level data, force group variable 'TRTA' be a factor #> Warning: In observation level data, force group variable 'TRTA' be a factor #> List of 23 #> $ meta :List of 7 #> $ population : chr \"apat\" #> $ observation : chr \"safety\" #> $ parameter : chr \"any;rel\" #> $ n :'data.frame':\t60 obs. of 3 variables: #> $ order : num [1:60] 1008 1009 2019 2021 2022 ... #> $ group : chr [1:3] \"Placebo\" \"Xanomeline Low Dose\" \"Total\" #> $ reference_group : num 2 #> $ parameter_order : Factor w/ 2 levels \"any\",\"rel\": 1 1 1 1 1 1 1 1 1 1 ... #> $ prop :'data.frame':\t60 obs. of 3 variables: #> $ diff :'data.frame':\t60 obs. of 1 variable: #> $ n_pop :'data.frame':\t1 obs. of 3 variables: #> $ name : chr [1:60] \"Atrioventricular block second degree\" \"Bundle branch block left\" \"Eye allergy\" \"Eye pruritus\" ... #> $ ci_lower :'data.frame':\t60 obs. of 1 variable: #> $ ci_upper :'data.frame':\t60 obs. of 1 variable: #> $ p :'data.frame':\t60 obs. of 1 variable: #> $ ae_listing :'data.frame':\t151 obs. of 14 variables: #> $ tbl :'data.frame':\t60 obs. of 13 variables: #> $ reactable_columns :List of 13 #> $ reactable_columns_group:List of 3 #> $ display : chr [1:4] \"n\" \"prop\" \"fig_prop\" \"fig_diff\" #> $ fig_prop_color : chr [1:2] \"#00857C\" \"#66203A\" #> $ fig_diff_color : chr \"#00857C\""},{"path":"https://merck.github.io/forestly/reference/meta_forestly.html","id":null,"dir":"Reference","previous_headings":"","what":"Create metadata for interactive forest plot — meta_forestly","title":"Create metadata for interactive forest plot — meta_forestly","text":"Create metadata interactive forest plot","code":""},{"path":"https://merck.github.io/forestly/reference/meta_forestly.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create metadata for interactive forest plot — meta_forestly","text":"","code":"meta_forestly( dataset_adsl, dataset_adae, population_term = \"apat\", observation_term = \"safety\", parameter_term = \"any;rel\", population_subset = SAFFL == \"Y\", observation_subset = SAFFL == \"Y\", treatment_group = \"TRTA\" )"},{"path":"https://merck.github.io/forestly/reference/meta_forestly.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create metadata for interactive forest plot — meta_forestly","text":"dataset_adsl ADSL source dataset. dataset_adae ADAE source dataset. population_term character value population term name. observation_term character value observation term name. parameter_term character value parameter term name. population_subset unquoted condition selecting populations ADSL dataset. observation_subset unquoted condition selecting observations ADAE dataset. treatment_group character value treatment group name.","code":""},{"path":"https://merck.github.io/forestly/reference/meta_forestly.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create metadata for interactive forest plot — meta_forestly","text":"metalite object.","code":""},{"path":"https://merck.github.io/forestly/reference/meta_forestly.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create metadata for interactive forest plot — meta_forestly","text":"","code":"meta_forestly( forestly_adsl, forestly_adae, population_term = \"apat\", observation_term = \"safety\", parameter_term = \"any;rel\" ) #> ADaM metadata: #> .$data_population \tPopulation data with 170 subjects #> .$data_observation \tObservation data with 736 records #> .$plan \tAnalysis plan with 1 plans #> #> #> Analysis population type: #> name id group var subset label #> 1 'apat' 'USUBJID' 'TRTA' SAFFL == 'Y' '' #> #> #> Analysis observation type: #> name id group var subset label #> 1 'safety' 'USUBJID' 'TRTA' SAFFL == 'Y' '' #> #> #> Analysis parameter type: #> name label subset #> 1 'any' 'any adverse events' #> 2 'rel' 'drug-related adverse events' toupper(AREL) == 'RELATED' #> #> #> Analysis function: #> name label #> 1 'ae_forestly' 'Interactive forest plot' #>"},{"path":"https://merck.github.io/forestly/reference/plot_dot.html","id":null,"dir":"Reference","previous_headings":"","what":"Dot plot — plot_dot","title":"Dot plot — plot_dot","text":"Create dot plot item. instance, used create AEs incidence plot Preferred Term treatment group, part rainfall plot.","code":""},{"path":"https://merck.github.io/forestly/reference/plot_dot.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Dot plot — plot_dot","text":"","code":"plot_dot( tbl, y_var, label, x_breaks = NULL, color = NULL, shape = NULL, title = \"AE (%)\", background_color = c(\"#69B8F7\", \"#FFFFFF\"), background_alpha = 0.3, theme = theme_panel(show_text = TRUE, show_ticks = TRUE), legend_nrow = 1 )"},{"path":"https://merck.github.io/forestly/reference/plot_dot.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Dot plot — plot_dot","text":"tbl data frame selected input data set display plot. y x variables required. y_var character string specifies variable displayed y-axis. label character vector labels treatment group. control group label specified last element vector. x_breaks numeric vector x-axis breaks. Default NULL, uses default ggplot2 x-axis breaks presentation. color Color treatment group. shape Shape treatment group. Default circle square. Input values either character numeric value, details, see https://ggplot2.tidyverse.org/articles/ggplot2-specs.html. title Panel title. Default \"AE (%)\". background_color Plot background color. Default c(\"#69B8F7\", \"#FFFFFF\"), pastel blue white. value argument used input background_color argument background_panel(). background_alpha Opacity background. Default 0.3. value argument input background_alpha argument background_panel(). theme Panel theme, including y-axis text, ticks, plot margin. Default theme_panel(show_text = TRUE, show_ticks = TRUE). details, refer theme_panel. legend_nrow Integer, number rows legend display. Must smaller equal number treatment groups. omit legend, set NULL. Default 1.","code":""},{"path":"https://merck.github.io/forestly/reference/plot_dot.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Dot plot — plot_dot","text":"AEs incidence plot item treatment group.","code":""},{"path":"https://merck.github.io/forestly/reference/plot_dot.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Dot plot — plot_dot","text":"","code":"forestly_adsl$TRTA <- factor( forestly_adsl$TRT01A, levels = c(\"Xanomeline Low Dose\", \"Placebo\"), labels = c(\"Low Dose\", \"Placebo\") ) forestly_adae$TRTA <- factor( forestly_adae$TRTA, levels = c(\"Xanomeline Low Dose\", \"Placebo\"), labels = c(\"Low Dose\", \"Placebo\") ) meta <- meta_forestly( dataset_adsl = forestly_adsl, dataset_adae = forestly_adae, population_term = \"apat\", observation_term = \"wk12\", parameter_term = \"any;rel;ser\" ) |> prepare_ae_forestly() |> format_ae_forestly() meta_any <- meta$tbl[1:20, ] |> dplyr::filter(parameter == \"any\") meta_any |> dplyr::select(name, prop_1, prop_2) |> plot_dot(\"name\", label = c(\"Treatment\", \"Placebo\"))"},{"path":"https://merck.github.io/forestly/reference/plot_errorbar.html","id":null,"dir":"Reference","previous_headings":"","what":"Plot to display risk difference — plot_errorbar","title":"Plot to display risk difference — plot_errorbar","text":"Create plot display risk difference item.","code":""},{"path":"https://merck.github.io/forestly/reference/plot_errorbar.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Plot to display risk difference — plot_errorbar","text":"","code":"plot_errorbar( tbl, y_var, errbar_width = 0.4, color = NULL, shape = NULL, label, x_breaks = NULL, grp_abbrev = \"paired\", favor_direction = \"negative\", vline = NULL, line_type = 1, title = \"Risk Diff. + 95% CI \\n (Percentage Points)\", background_color = c(\"#69B8F7\", \"#FFFFFF\"), background_alpha = 0.3, theme = theme_panel(show_text = TRUE, show_ticks = TRUE), legend_nrow = 1 )"},{"path":"https://merck.github.io/forestly/reference/plot_errorbar.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Plot to display risk difference — plot_errorbar","text":"tbl data frame selected input data set display plot. y x variables required. y_var character string specifies variable displayed y-axis. errbar_width numeric value define error bar width. Default 0.4. Value argument half length error bar, example, errorbar_width = 0.2 means half error bar width 0.2 unit length. y = 4, error bar range y = 3.8 y = 4.2. color Color treatment group. shape Shape treatment group. Default circle square. Input values either character numeric value, details, see https://ggplot2.tidyverse.org/articles/ggplot2-specs.html. label character vector labels treatment group. control group label specified last element vector. x_breaks numeric vector x-axis breaks. Default NULL, uses default ggplot2 x-axis breaks presentation. grp_abbrev character vector displaying treatment groups favor bar. grp_abbrev = \"paired\", treatment label error bar label argument. grp_abbrev = \"none\", error bar shown. Also, customized terms, users can provide alternative vector treatment labels. Default \"paired\". favor_direction position favor label condition \"comparison treatment – control\". AEs, favor_direction \"negative\"; efficacy, favor_direction \"positive\". vline Vertical reference line position. Default NULL. Users can define one multiple numeric values vector reference line position. line_type Reference line type. Default solid line. Users can define one multiple line types vector (can numeric 1, 2, 3 character \"solid\", \"dashed\"). values recycled order consistent argument vline. title Plot title. Default \"Risk Diff. + 95% CI \\\\n (Percentage Points)\". background_color Plot background color. Default c(\"#69B8F7\", \"#FFFFFF\"), pastel blue white. value argument used input background_color argument background_panel(). background_alpha Opacity background. Default 0.3. value argument input background_alpha argument background_panel(). theme Panel theme, including y-axis text, ticks, plot margin. Default theme_panel(show_text = TRUE, show_ticks = TRUE). details, refer theme_panel. legend_nrow Integer, number rows legend display. Must smaller equal number treatment groups. omit legend, set NULL. Default 1.","code":""},{"path":"https://merck.github.io/forestly/reference/plot_errorbar.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Plot to display risk difference — plot_errorbar","text":"risk difference plot item.","code":""},{"path":"https://merck.github.io/forestly/reference/plot_errorbar.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Plot to display risk difference — plot_errorbar","text":"","code":"forestly_adsl$TRTA <- factor( forestly_adsl$TRT01A, levels = c(\"Xanomeline Low Dose\", \"Placebo\"), labels = c(\"Low Dose\", \"Placebo\") ) forestly_adae$TRTA <- factor( forestly_adae$TRTA, levels = c(\"Xanomeline Low Dose\", \"Placebo\"), labels = c(\"Low Dose\", \"Placebo\") ) meta <- meta_forestly( dataset_adsl = forestly_adsl, dataset_adae = forestly_adae, population_term = \"apat\", observation_term = \"wk12\", parameter_term = \"any;rel;ser\" ) |> prepare_ae_forestly() |> format_ae_forestly() meta_any <- meta$tbl[1:20, ] |> dplyr::filter(parameter == \"any\") meta_any |> dplyr::select(name, diff_1, lower_1, upper_1) |> plot_errorbar( y_var = \"name\", label = c(\"Treatment\", \"Placebo\") )"},{"path":"https://merck.github.io/forestly/reference/prepare_ae_forestly.html","id":null,"dir":"Reference","previous_headings":"","what":"Prepare datasets for interactive forest plot — prepare_ae_forestly","title":"Prepare datasets for interactive forest plot — prepare_ae_forestly","text":"Prepare datasets interactive forest plot","code":""},{"path":"https://merck.github.io/forestly/reference/prepare_ae_forestly.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Prepare datasets for interactive forest plot — prepare_ae_forestly","text":"","code":"prepare_ae_forestly( meta, population = NULL, observation = NULL, parameter = NULL, reference_group = NULL, ae_listing_display = c(\"USUBJID\", \"SITEID\", \"SEX\", \"RACE\", \"AGE\", \"ASTDY\", \"AESER\", \"AEREL\", \"AEACN\", \"AEOUT\", \"ADURN\", \"ADURU\"), ae_listing_unique = FALSE )"},{"path":"https://merck.github.io/forestly/reference/prepare_ae_forestly.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Prepare datasets for interactive forest plot — prepare_ae_forestly","text":"meta metadata object created metalite. population character value population term name. term name used key link information. observation character value observation term name. term name used key link information. parameter character value parameter term name. term name used key link information. reference_group integer indicate reference group. Default 2 2 groups, otherwise, default 1. ae_listing_display vector name variables used display AE listing table. ae_listing_unique logical value display unique records AE listing table.","code":""},{"path":"https://merck.github.io/forestly/reference/prepare_ae_forestly.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Prepare datasets for interactive forest plot — prepare_ae_forestly","text":"outdata object.","code":""},{"path":"https://merck.github.io/forestly/reference/prepare_ae_forestly.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Prepare datasets for interactive forest plot — prepare_ae_forestly","text":"","code":"adsl <- forestly_adsl[1:100,] adae <- forestly_adae[1:100,] meta_forestly( dataset_adsl = adsl, dataset_adae = adae ) |> prepare_ae_forestly() #> Warning: In observation level data, force group variable 'TRTA' be a factor #> Warning: In observation level data, force group variable 'TRTA' be a factor #> List of 17 #> $ meta :List of 7 #> $ population : chr \"apat\" #> $ observation : chr \"safety\" #> $ parameter : chr \"any;rel\" #> $ n :'data.frame':\t60 obs. of 3 variables: #> $ order : num [1:60] 1008 1009 2019 2021 2022 ... #> $ group : chr [1:3] \"Placebo\" \"Xanomeline Low Dose\" \"Total\" #> $ reference_group: num 2 #> $ parameter_order: Factor w/ 2 levels \"any\",\"rel\": 1 1 1 1 1 1 1 1 1 1 ... #> $ prop :'data.frame':\t60 obs. of 3 variables: #> $ diff :'data.frame':\t60 obs. of 1 variable: #> $ n_pop :'data.frame':\t1 obs. of 3 variables: #> $ name : chr [1:60] \"Atrioventricular block second degree\" \"Bundle branch block left\" \"Eye allergy\" \"Eye pruritus\" ... #> $ ci_lower :'data.frame':\t60 obs. of 1 variable: #> $ ci_upper :'data.frame':\t60 obs. of 1 variable: #> $ p :'data.frame':\t60 obs. of 1 variable: #> $ ae_listing :'data.frame':\t151 obs. of 14 variables:"},{"path":"https://merck.github.io/forestly/reference/table_panel.html","id":null,"dir":"Reference","previous_headings":"","what":"Create table panel ggplot2 object for rainfall or forest plot — table_panel","title":"Create table panel ggplot2 object for rainfall or forest plot — table_panel","text":"Creates table panel ggplot2 object rainfall forest plot.","code":""},{"path":"https://merck.github.io/forestly/reference/table_panel.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Create table panel ggplot2 object for rainfall or forest plot — table_panel","text":"","code":"table_panel( tbl, y_var, x_label = NULL, text_color = NULL, text_size = 8, text_format_by = \"column\", background_color = c(\"#69B8F7\", \"#FFFFFF\"), theme = theme_panel(show_ticks = TRUE, show_text = TRUE), background_alpha = 0.3 )"},{"path":"https://merck.github.io/forestly/reference/table_panel.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Create table panel ggplot2 object for rainfall or forest plot — table_panel","text":"tbl data frame displayed table. y_var string variable name tbl y axis variable. x_label Labels displayed top table column table. Default NULL, variable name display label. text_color Defines colors display treatment group. text_size Numeric font size data column. Default 8 column. text_format_by option formatting data columns rows. Default \"column\" text color varied column. text_format_by = \"row\", text color varied row. text_format_by = \"group\", text color varied treatment group. background_color Color plot background. Default c(\"#69B8F7\", \"#FFFFFF\") pastel blue white. value argument input value background_color argument background_panel(). theme Controls display y axis text, ticks plot margin. default, theme_panel(show_text = TRUE, show_ticks = TRUE) used. Users suggested use theme_panel(). background_alpha Opacity background. Default 0.3. value argument input value background_alpha argument background_panel().","code":""},{"path":"https://merck.github.io/forestly/reference/table_panel.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Create table panel ggplot2 object for rainfall or forest plot — table_panel","text":"ggplot2 object table panel.","code":""},{"path":"https://merck.github.io/forestly/reference/table_panel.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Create table panel ggplot2 object for rainfall or forest plot — table_panel","text":"","code":"forestly_adsl$TRTA <- factor( forestly_adsl$TRT01A, levels = c(\"Xanomeline Low Dose\", \"Placebo\"), labels = c(\"Low Dose\", \"Placebo\") ) forestly_adae$TRTA <- factor( forestly_adae$TRTA, levels = c(\"Xanomeline Low Dose\", \"Placebo\"), labels = c(\"Low Dose\", \"Placebo\") ) meta <- meta_forestly( dataset_adsl = forestly_adsl, dataset_adae = forestly_adae, population_term = \"apat\", observation_term = \"wk12\", parameter_term = \"any;rel;ser\" ) |> prepare_ae_forestly() |> format_ae_forestly() meta_any <- meta$tbl[1:20, ] |> dplyr::filter(parameter == \"any\") meta_any |> dplyr::select(name, diff_1, lower_1, upper_1) |> table_panel(y_var = \"name\")"},{"path":"https://merck.github.io/forestly/reference/theme_panel.html","id":null,"dir":"Reference","previous_headings":"","what":"Theme function for plot with multiple panels — theme_panel","title":"Theme function for plot with multiple panels — theme_panel","text":"Specifies theme plot multiple panels.","code":""},{"path":"https://merck.github.io/forestly/reference/theme_panel.html","id":"ref-usage","dir":"Reference","previous_headings":"","what":"Usage","title":"Theme function for plot with multiple panels — theme_panel","text":"","code":"theme_panel(show_text = TRUE, show_ticks = TRUE)"},{"path":"https://merck.github.io/forestly/reference/theme_panel.html","id":"arguments","dir":"Reference","previous_headings":"","what":"Arguments","title":"Theme function for plot with multiple panels — theme_panel","text":"show_text logical value controls text display y axis. Default TRUE. show_ticks logical value controls ticks display y axis. Default TRUE.","code":""},{"path":"https://merck.github.io/forestly/reference/theme_panel.html","id":"value","dir":"Reference","previous_headings":"","what":"Value","title":"Theme function for plot with multiple panels — theme_panel","text":"Theme specific panel.","code":""},{"path":"https://merck.github.io/forestly/reference/theme_panel.html","id":"ref-examples","dir":"Reference","previous_headings":"","what":"Examples","title":"Theme function for plot with multiple panels — theme_panel","text":"","code":"library(ggplot2) p <- ggplot(mpg, aes(displ, hwy, colour = class)) + geom_point() p p + theme_panel()"},{"path":"https://merck.github.io/forestly/news/index.html","id":"forestly-011","dir":"Changelog","previous_headings":"","what":"forestly 0.1.1","title":"forestly 0.1.1","text":"Fix bug record selected AE category (#9). Fix bug multiple plots displayed one page (#12). Update dataset forestly_adae since variable factor unexpected.","code":""},{"path":"https://merck.github.io/forestly/news/index.html","id":"forestly-010","dir":"Changelog","previous_headings":"","what":"forestly 0.1.0","title":"forestly 0.1.0","text":"CRAN release: 2023-07-19 Initial version. Added NEWS.md file track changes package.","code":""}] diff --git a/sitemap.xml b/sitemap.xml index 417766d..9cd1c0f 100644 --- a/sitemap.xml +++ b/sitemap.xml @@ -9,6 +9,9 @@ https://merck.github.io/forestly/articles/design-pattern.html + + https://merck.github.io/forestly/articles/forest-plot-static.html + https://merck.github.io/forestly/articles/forestly-cran.html @@ -33,6 +36,9 @@ https://merck.github.io/forestly/reference/ae_forestly.html + + https://merck.github.io/forestly/reference/background_panel.html + https://merck.github.io/forestly/reference/forestly_adae.html @@ -54,7 +60,19 @@ https://merck.github.io/forestly/reference/meta_forestly.html + + https://merck.github.io/forestly/reference/plot_dot.html + + + https://merck.github.io/forestly/reference/plot_errorbar.html + https://merck.github.io/forestly/reference/prepare_ae_forestly.html + + https://merck.github.io/forestly/reference/table_panel.html + + + https://merck.github.io/forestly/reference/theme_panel.html +