few enhancements

insightsengineering · Jan 24, 2024 · dfc4e77 · dfc4e77
1 parent 063ae3e
commit dfc4e77
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Showing 20 changed files with 152 additions and 175 deletions.
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -66,4 +66,4 @@ Encoding: UTF-8
 Language: en-US
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.0
diff --git a/R/teal_goshawk.R b/R/teal_goshawk.R
@@ -5,16 +5,11 @@
 #' The data used for teal.goshawk have some constraints.
 #' It must contain the columns `AVISITCD`, `BASE`, `BASE2`, `AVALU`, `LBSTRESC`, `LOQFL`, `CHG2`, and `PCHG2`.
 #'
-#' @docType package
-#'
-#' @name teal_goshawk
-#'
 #' @import goshawk
 #' @import shiny
 #' @import teal
 #' @import teal.transform
 #' @importFrom ggplot2 ggplot
 #' @importFrom rlang .data sym
 #' @importFrom teal.transform choices_selected
-#' @keywords internal
-NULL
+"_PACKAGE"
diff --git a/R/tm_g_gh_boxplot.R b/R/tm_g_gh_boxplot.R
@@ -46,7 +46,6 @@
 #' @export
 #'
 #' @examples
-#'
 #' # Example using ADaM structure analysis dataset.
 #' data <- teal_data()
 #' data <- within(data, {
@@ -60,8 +59,8 @@
 #'     "C: Combination" = "Combination"
 #'   )
 #'   set.seed(1)
-#'   ADSL <- goshawk::rADSL
-#'   ADLB <- goshawk::rADLB
+#'   ADSL <- rADSL
+#'   ADLB <- rADLB
 #'   var_labels <- lapply(ADLB, function(x) attributes(x)$label)
 #'   ADLB <- ADLB %>%
 #'     dplyr::mutate(
@@ -117,10 +116,10 @@
 #'
 #' join_keys(data) <- default_cdisc_join_keys[datanames]
 #'
-#' app <- teal::init(
+#' app <- init(
 #'   data = data,
-#'   modules = teal::modules(
-#'     teal.goshawk::tm_g_gh_boxplot(
+#'   modules = modules(
+#'     tm_g_gh_boxplot(
 #'       label = "Box Plot",
 #'       dataname = "ADLB",
 #'       param_var = "PARAMCD",

diff --git a/R/tm_g_gh_correlationplot.R b/R/tm_g_gh_correlationplot.R
@@ -50,7 +50,6 @@
 #' @author Balazs Toth (tothb2)  [email protected]
 #'
 #' @examples
-#'
 #' # Example using ADaM structure analysis dataset.
 #' data <- teal_data()
 #' data <- within(data, {
@@ -65,8 +64,8 @@
 #'   shape_manual <- c("N" = 1, "Y" = 2, "NA" = 0)
 #'
 #'   set.seed(1)
-#'   ADSL <- goshawk::rADSL
-#'   ADLB <- goshawk::rADLB
+#'   ADSL <- rADSL
+#'   ADLB <- rADLB
 #'   var_labels <- lapply(ADLB, function(x) attributes(x)$label)
 #'   ADLB <- ADLB %>%
 #'     dplyr::mutate(AVISITCD = dplyr::case_when(
@@ -139,10 +138,10 @@
 #'
 #' join_keys(data) <- default_cdisc_join_keys[datanames]
 #'
-#' app <- teal::init(
+#' app <- init(
 #'   data = data,
-#'   modules = teal::modules(
-#'     teal.goshawk::tm_g_gh_correlationplot(
+#'   modules = modules(
+#'     tm_g_gh_correlationplot(
 #'       label = "Correlation Plot",
 #'       dataname = "ADLB",
 #'       param_var = "PARAMCD",

diff --git a/R/tm_g_gh_density_distribution_plot.R b/R/tm_g_gh_density_distribution_plot.R
@@ -33,7 +33,6 @@
 #' @export
 #'
 #' @examples
-#'
 #' # Example using ADaM structure analysis dataset.
 #' data <- teal_data()
 #' data <- within(data, {
@@ -44,8 +43,8 @@
 #'     "B: Placebo" = "Placebo",
 #'     "C: Combination" = "Combination"
 #'   )
-#'   ADSL <- goshawk::rADSL
-#'   ADLB <- goshawk::rADLB
+#'   ADSL <- rADSL
+#'   ADLB <- rADLB
 #'   var_labels <- lapply(ADLB, function(x) attributes(x)$label)
 #'   ADLB <- ADLB %>%
 #'     dplyr::mutate(
@@ -81,10 +80,10 @@
 #' datanames(data) <- datanames
 #' join_keys(data) <- default_cdisc_join_keys[datanames]
 #'
-#' app <- teal::init(
+#' app <- init(
 #'   data = data,
-#'   modules = teal::modules(
-#'     teal.goshawk::tm_g_gh_density_distribution_plot(
+#'   modules = modules(
+#'     tm_g_gh_density_distribution_plot(
 #'       label = "Density Distribution Plot",
 #'       dataname = "ADLB",
 #'       param_var = "PARAMCD",

diff --git a/R/tm_g_gh_lineplot.R b/R/tm_g_gh_lineplot.R
@@ -51,7 +51,6 @@
 #' @export
 #'
 #' @examples
-#'
 #' # Example using ADaM structure analysis dataset.
 #' data <- teal_data()
 #' data <- within(data, {
@@ -66,8 +65,8 @@
 #'     "C: Combination" = "Combination"
 #'   )
 #'
-#'   ADSL <- goshawk::rADSL
-#'   ADLB <- goshawk::rADLB
+#'   ADSL <- rADSL
+#'   ADLB <- rADLB
 #'   var_labels <- lapply(ADLB, function(x) attributes(x)$label)
 #'   ADLB <- ADLB %>%
 #'     dplyr::mutate(
@@ -102,10 +101,10 @@
 #' datanames(data) <- datanames
 #' join_keys(data) <- default_cdisc_join_keys[datanames]
 #'
-#' app <- teal::init(
+#' app <- init(
 #'   data = data,
-#'   modules = teal::modules(
-#'     teal.goshawk::tm_g_gh_lineplot(
+#'   modules = modules(
+#'     tm_g_gh_lineplot(
 #'       label = "Line Plot",
 #'       dataname = "ADLB",
 #'       param_var = "PARAMCD",

diff --git a/R/tm_g_gh_scatterplot.R b/R/tm_g_gh_scatterplot.R
@@ -38,7 +38,6 @@
 #' @author Balazs Toth (tothb2)  [email protected]
 #'
 #' @examples
-#'
 #' # Example using ADaM structure analysis dataset.
 #' data <- teal_data()
 #' data <- within(data, {
@@ -49,8 +48,8 @@
 #'     "C: Combination" = "Combination"
 #'   )
 #'
-#'   ADSL <- goshawk::rADSL
-#'   ADLB <- goshawk::rADLB
+#'   ADSL <- rADSL
+#'   ADLB <- rADLB
 #'   var_labels <- lapply(ADLB, function(x) attributes(x)$label)
 #'   ADLB <- ADLB %>%
 #'     dplyr::mutate(
@@ -86,10 +85,10 @@
 #' join_keys(data) <- default_cdisc_join_keys[datanames]
 #'
 #'
-#' app <- teal::init(
+#' app <- init(
 #'   data = data,
-#'   modules = teal::modules(
-#'     teal.goshawk::tm_g_gh_scatterplot(
+#'   modules = modules(
+#'     tm_g_gh_scatterplot(
 #'       label = "Scatter Plot",
 #'       dataname = "ADLB",
 #'       param_var = "PARAMCD",

diff --git a/R/tm_g_gh_spaghettiplot.R b/R/tm_g_gh_spaghettiplot.R
@@ -55,7 +55,6 @@
 #' @export
 #'
 #' @examples
-#'
 #' # Example using ADaM structure analysis dataset.
 #' data <- teal_data()
 #' data <- within(data, {
@@ -68,8 +67,8 @@
 #'     "C: Combination" = "Combination"
 #'   )
 #'   set.seed(1)
-#'   ADSL <- goshawk::rADSL
-#'   ADLB <- goshawk::rADLB
+#'   ADSL <- rADSL
+#'   ADLB <- rADLB
 #'   var_labels <- lapply(ADLB, function(x) attributes(x)$label)
 #'   ADLB <- ADLB %>%
 #'     dplyr::mutate(
@@ -121,10 +120,10 @@
 #' datanames(data) <- datanames
 #' join_keys(data) <- default_cdisc_join_keys[datanames]
 #'
-#' app <- teal::init(
+#' app <- init(
 #'   data = data,
-#'   modules = teal::modules(
-#'     teal.goshawk::tm_g_gh_spaghettiplot(
+#'   modules = modules(
+#'     tm_g_gh_spaghettiplot(
 #'       label = "Spaghetti Plot",
 #'       dataname = "ADLB",
 #'       param_var = "PARAMCD",

diff --git a/R/toggleable_slider.R b/R/toggleable_slider.R
@@ -28,47 +28,34 @@
 #' @examples
 #' value <- c(20.3, 81.5) # dichotomous slider
 #' # value <- c(50.1) # normal slider
-#' app <- shinyApp(
-#'   ui = div(
-#'     teal.goshawk:::toggle_slider_ui(
-#'       "toggle_slider", "Select value",
-#'       min = 0.2, max = 100.1, value = value,
-#'       slider_initially = FALSE, step_slider = 0.1, step_numeric = 0.001
-#'     ),
-#'     verbatimTextOutput("value")
-#'   ),
-#'   server = function(input, output, session) {
-#'     is_dichotomous_slider <- (length(value) == 2)
-#'     range_value <- toggle_slider_server("toggle_slider",
-#'       is_dichotomous_slider = is_dichotomous_slider
-#'     )
-#'     messages <- reactiveVal() # to keep history
-#'     observeEvent(range_value$state(), {
-#'       list_with_names_str <- function(x) paste(names(x), x, sep = ": ", collapse = ", ")
-#'       messages(c(messages(), list_with_names_str(range_value$state())))
-#'     })
-#'     output$value <- renderText({
-#'       paste(messages(), collapse = "\n")
-#'     })
 #'
-#'     # for stress-testing example, update slider settings
-#'     # bug with invalidateLater not working inside `observeEvent`
-#'     # observe({
-#'     #   invalidateLater(1000, session)
-#'     #   a <- sample(0:100, 1) # for range
-#'     #   b <- sample(0:100, 1)
-#'     #   isolate(do.call(
-#'     #     range_value$update_state,
-#'     #     list(
-#'     #       value = sort(sample(0:100, if (is_dichotomous_slider) 2 else 1)),
-#'     #       min = min(a, b), max = max(a, b),
-#'     #       step = sample(1:20, 1) / 10
-#'     #     )[sample(1:4, sample(4, 1))] # select up to four fields from the list
-#'     #   ))
-#'     # })
-#'   }
+#' ui <- div(
+#'   teal.goshawk:::toggle_slider_ui(
+#'     "toggle_slider", "Select value",
+#'     min = 0.2, max = 100.1, value = value,
+#'     slider_initially = FALSE, step_slider = 0.1, step_numeric = 0.001
+#'   ),
+#'   verbatimTextOutput("value")
 #' )
-#' shinyApp(app$ui, app$server) %>% invisible()
+#'
+#' server <- function(input, output, session) {
+#'   is_dichotomous_slider <- (length(value) == 2)
+#'   range_value <- toggle_slider_server("toggle_slider",
+#'     is_dichotomous_slider = is_dichotomous_slider
+#'   )
+#'   messages <- reactiveVal() # to keep history
+#'   observeEvent(range_value$state(), {
+#'     list_with_names_str <- function(x) paste(names(x), x, sep = ": ", collapse = ", ")
+#'     messages(c(messages(), list_with_names_str(range_value$state())))
+#'   })
+#'   output$value <- renderText({
+#'     paste(messages(), collapse = "\n")
+#'   })
+#' }
+#'
+#' if (interactive()) {
+#'   shinyApp(ui, server)
+#' }
 toggle_slider_ui <- function(id,
                              label,
                              min,

diff --git a/R/utils-maptrt.r b/R/utils-maptrt.r
@@ -13,8 +13,7 @@
 #' @export
 #'
 #' @examples
-#'
-#' ADSL <- goshawk::rADSL
+#' ADSL <- rADSL
 #'
 #' # get treatment mapping code
 #' maptrt(df_armvar = ADSL$ARMCD, code = "M")

diff --git a/man/maptrt.Rd b/man/maptrt.Rd
diff --git a/man/teal.goshawk-package.Rd b/man/teal.goshawk-package.Rd
diff --git a/man/teal_goshawk.Rd b/man/teal_goshawk.Rd