few enhancements (#254)

- fixed package level Rd file - removed unnecessary empty first line in examples as this is actually being rendered - removed `pkg::` from docs for packages in Depends - fixed example of `toggle_slider_ui` --------- Co-authored-by: 27856297+dependabot-preview[bot]@users.noreply.github.com <27856297+dependabot-preview[bot]@users.noreply.github.com> Co-authored-by: unknown <[email protected]> Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
insightsengineering · Mar 18, 2024 · fe05e76 · fe05e76
1 parent dacc6a7
commit fe05e76
Show file tree

Hide file tree

Showing 18 changed files with 272 additions and 270 deletions.
diff --git a/R/teal_goshawk.R b/R/teal_goshawk.R
@@ -5,14 +5,13 @@
 #' The data used for teal.goshawk have some constraints.
 #' It must contain the columns `AVISITCD`, `BASE`, `BASE2`, `AVALU`, `LBSTRESC`, `LOQFL`, `CHG2`, and `PCHG2`.
 #'
-#' @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
 "_PACKAGE"
diff --git a/R/tm_g_gh_boxplot.R b/R/tm_g_gh_boxplot.R
@@ -46,12 +46,15 @@
 #' @export
 #'
 #' @examples
-#'
 #' # Example using ADaM structure analysis dataset.
 #' data <- teal_data()
 #' data <- within(data, {
 #'   library(dplyr)
 #'   library(nestcolor)
+#'   library(stringr)
+#'
+#'   # use non-exported function from goshawk
+#'   h_identify_loq_values <- getFromNamespace("h_identify_loq_values", "goshawk")
 #'
 #'   # original ARM value = dose value
 #'   arm_mapping <- list(
@@ -60,25 +63,25 @@
 #'     "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(
-#'       AVISITCD = dplyr::case_when(
+#'     mutate(
+#'       AVISITCD = case_when(
 #'         AVISIT == "SCREENING" ~ "SCR",
 #'         AVISIT == "BASELINE" ~ "BL",
-#'         grepl("WEEK", AVISIT) ~ paste("W", stringr::str_extract(AVISIT, "(?<=(WEEK ))[0-9]+")),
+#'         grepl("WEEK", AVISIT) ~ paste("W", str_extract(AVISIT, "(?<=(WEEK ))[0-9]+")),
 #'         TRUE ~ as.character(NA)
 #'       ),
-#'       AVISITCDN = dplyr::case_when(
+#'       AVISITCDN = case_when(
 #'         AVISITCD == "SCR" ~ -2,
 #'         AVISITCD == "BL" ~ 0,
 #'         grepl("W", AVISITCD) ~ as.numeric(gsub("[^0-9]*", "", AVISITCD)),
 #'         TRUE ~ as.numeric(NA)
 #'       ),
 #'       AVISITCD = factor(AVISITCD) %>% reorder(AVISITCDN),
-#'       TRTORD = dplyr::case_when(
+#'       TRTORD = case_when(
 #'         ARMCD == "ARM C" ~ 1,
 #'         ARMCD == "ARM B" ~ 2,
 #'         ARMCD == "ARM A" ~ 3
@@ -90,13 +93,13 @@
 #'       ANRLO = 50,
 #'       ANRHI = 75
 #'     ) %>%
-#'     dplyr::rowwise() %>%
-#'     dplyr::group_by(PARAMCD) %>%
-#'     dplyr::mutate(LBSTRESC = ifelse(
+#'     rowwise() %>%
+#'     group_by(PARAMCD) %>%
+#'     mutate(LBSTRESC = ifelse(
 #'       USUBJID %in% sample(USUBJID, 1, replace = TRUE),
 #'       paste("<", round(runif(1, min = 25, max = 30))), LBSTRESC
 #'     )) %>%
-#'     dplyr::mutate(LBSTRESC = ifelse(
+#'     mutate(LBSTRESC = ifelse(
 #'       USUBJID %in% sample(USUBJID, 1, replace = TRUE),
 #'       paste(">", round(runif(1, min = 70, max = 75))), LBSTRESC
 #'     )) %>%
@@ -108,19 +111,19 @@
 #'   attr(ADLB[["ANRHI"]], "label") <- "Analysis Normal Range Upper Limit"
 #'
 #'   # add LLOQ and ULOQ variables
-#'   ALB_LOQS <- goshawk:::h_identify_loq_values(ADLB, "LOQFL")
-#'   ADLB <- dplyr::left_join(ADLB, ALB_LOQS, by = "PARAM")
+#'   ALB_LOQS <- h_identify_loq_values(ADLB, "LOQFL")
+#'   ADLB <- left_join(ADLB, ALB_LOQS, by = "PARAM")
 #' })
 #'
 #' datanames <- c("ADSL", "ADLB")
 #' 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_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
@@ -50,10 +50,15 @@
 #' @author Balazs Toth (tothb2)  [email protected]
 #'
 #' @examples
-#'
 #' # Example using ADaM structure analysis dataset.
 #' data <- teal_data()
 #' data <- within(data, {
+#'   library(dplyr)
+#'   library(stringr)
+#'
+#'   # use non-exported function from goshawk
+#'   h_identify_loq_values <- getFromNamespace("h_identify_loq_values", "goshawk")
+#'
 #'   # original ARM value = dose value
 #'   arm_mapping <- list(
 #'     "A: Drug X" = "150mg QD",
@@ -65,11 +70,11 @@
 #'   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(
+#'     mutate(AVISITCD = case_when(
 #'       AVISIT == "SCREENING" ~ "SCR",
 #'       AVISIT == "BASELINE" ~ "BL",
 #'       grepl("WEEK", AVISIT) ~
@@ -79,48 +84,48 @@
 #'             substr(
 #'               AVISIT,
 #'               start = 6,
-#'               stop = stringr::str_locate(AVISIT, "DAY") - 1
+#'               stop = str_locate(AVISIT, "DAY") - 1
 #'             )
 #'           )
 #'         ),
 #'       TRUE ~ NA_character_
 #'     )) %>%
-#'     dplyr::mutate(AVISITCDN = dplyr::case_when(
+#'     mutate(AVISITCDN = case_when(
 #'       AVISITCD == "SCR" ~ -2,
 #'       AVISITCD == "BL" ~ 0,
 #'       grepl("W", AVISITCD) ~ as.numeric(gsub("[^0-9]*", "", AVISITCD)),
 #'       TRUE ~ NA_real_
 #'     )) %>%
 #'     # use ARMCD values to order treatment in visualization legend
-#'     dplyr::mutate(TRTORD = ifelse(grepl("C", ARMCD), 1,
+#'     mutate(TRTORD = ifelse(grepl("C", ARMCD), 1,
 #'       ifelse(grepl("B", ARMCD), 2,
 #'         ifelse(grepl("A", ARMCD), 3, NA)
 #'       )
 #'     )) %>%
-#'     dplyr::mutate(ARM = as.character(arm_mapping[match(ARM, names(arm_mapping))])) %>%
-#'     dplyr::mutate(ARM = factor(ARM) %>%
+#'     mutate(ARM = as.character(arm_mapping[match(ARM, names(arm_mapping))])) %>%
+#'     mutate(ARM = factor(ARM) %>%
 #'       reorder(TRTORD)) %>%
-#'     dplyr::mutate(
-#'       ANRHI = dplyr::case_when(
+#'     mutate(
+#'       ANRHI = case_when(
 #'         PARAMCD == "ALT" ~ 60,
 #'         PARAMCD == "CRP" ~ 70,
 #'         PARAMCD == "IGA" ~ 80,
 #'         TRUE ~ NA_real_
 #'       ),
-#'       ANRLO = dplyr::case_when(
+#'       ANRLO = case_when(
 #'         PARAMCD == "ALT" ~ 20,
 #'         PARAMCD == "CRP" ~ 30,
 #'         PARAMCD == "IGA" ~ 40,
 #'         TRUE ~ NA_real_
 #'       )
 #'     ) %>%
-#'     dplyr::rowwise() %>%
-#'     dplyr::group_by(PARAMCD) %>%
-#'     dplyr::mutate(LBSTRESC = ifelse(
+#'     rowwise() %>%
+#'     group_by(PARAMCD) %>%
+#'     mutate(LBSTRESC = ifelse(
 #'       USUBJID %in% sample(USUBJID, 1, replace = TRUE),
 #'       paste("<", round(runif(1, min = 25, max = 30))), LBSTRESC
 #'     )) %>%
-#'     dplyr::mutate(LBSTRESC = ifelse(
+#'     mutate(LBSTRESC = ifelse(
 #'       USUBJID %in% sample(USUBJID, 1, replace = TRUE),
 #'       paste(">", round(runif(1, min = 70, max = 75))), LBSTRESC
 #'     )) %>%
@@ -130,19 +135,19 @@
 #'   attr(ADLB[["ANRLO"]], "label") <- "Analysis Normal Range Lower Limit"
 #'
 #'   # add LLOQ and ULOQ variables
-#'   ADLB_LOQS <- goshawk:::h_identify_loq_values(ADLB, "LOQFL")
-#'   ADLB <- dplyr::left_join(ADLB, ADLB_LOQS, by = "PARAM")
+#'   ADLB_LOQS <- h_identify_loq_values(ADLB, "LOQFL")
+#'   ADLB <- left_join(ADLB, ADLB_LOQS, by = "PARAM")
 #' })
 #'
 #' datanames <- c("ADSL", "ADLB")
 #' 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_correlationplot(
+#'   modules = modules(
+#'     tm_g_gh_correlationplot(
 #'       label = "Correlation Plot",
 #'       dataname = "ADLB",
 #'       param_var = "PARAMCD",
@@ -170,7 +175,7 @@
 #'       hline_arb_color = c("red", "blue"),
 #'       hline_vars = c("ANRHI", "ANRLO", "ULOQN", "LLOQN"),
 #'       hline_vars_colors = c("green", "blue", "purple", "cyan"),
-#'       hline_vars_label = c("ANRHI Label", "ANRLO Label", "ULOQN Label", "LLOQN Label"),
+#'       hline_vars_labels = c("ANRHI Label", "ANRLO Label", "ULOQN Label", "LLOQN Label"),
 #'       vline_vars = c("ANRHI", "ANRLO", "ULOQN", "LLOQN"),
 #'       vline_vars_colors = c("yellow", "orange", "brown", "gold"),
 #'       vline_vars_labels = c("ANRHI Label", "ANRLO Label", "ULOQN Label", "LLOQN Label"),

diff --git a/R/tm_g_gh_density_distribution_plot.R b/R/tm_g_gh_density_distribution_plot.R
@@ -33,36 +33,37 @@
 #' @export
 #'
 #' @examples
-#'
 #' # Example using ADaM structure analysis dataset.
 #' data <- teal_data()
 #' data <- within(data, {
 #'   library(dplyr)
+#'   library(stringr)
+#'
 #'   # original ARM value = dose value
 #'   arm_mapping <- list(
 #'     "A: Drug X" = "150mg QD",
 #'     "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(
-#'       AVISITCD = dplyr::case_when(
+#'     mutate(
+#'       AVISITCD = case_when(
 #'         AVISIT == "SCREENING" ~ "SCR",
 #'         AVISIT == "BASELINE" ~ "BL",
-#'         grepl("WEEK", AVISIT) ~ paste("W", stringr::str_extract(AVISIT, "(?<=(WEEK ))[0-9]+")),
+#'         grepl("WEEK", AVISIT) ~ paste("W", str_extract(AVISIT, "(?<=(WEEK ))[0-9]+")),
 #'         TRUE ~ as.character(NA)
 #'       ),
-#'       AVISITCDN = dplyr::case_when(
+#'       AVISITCDN = case_when(
 #'         AVISITCD == "SCR" ~ -2,
 #'         AVISITCD == "BL" ~ 0,
 #'         grepl("W", AVISITCD) ~ as.numeric(gsub("[^0-9]*", "", AVISITCD)),
 #'         TRUE ~ as.numeric(NA)
 #'       ),
 #'       AVISITCD = factor(AVISITCD) %>% reorder(AVISITCDN),
-#'       TRTORD = dplyr::case_when(
+#'       TRTORD = case_when(
 #'         ARMCD == "ARM C" ~ 1,
 #'         ARMCD == "ARM B" ~ 2,
 #'         ARMCD == "ARM A" ~ 3
@@ -81,10 +82,10 @@
 #' 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, {
@@ -66,25 +65,25 @@
 #'     "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(
-#'       AVISITCD = dplyr::case_when(
+#'     mutate(
+#'       AVISITCD = case_when(
 #'         AVISIT == "SCREENING" ~ "SCR",
 #'         AVISIT == "BASELINE" ~ "BL",
-#'         grepl("WEEK", AVISIT) ~ paste("W", stringr::str_extract(AVISIT, "(?<=(WEEK ))[0-9]+")),
+#'         grepl("WEEK", AVISIT) ~ paste("W", str_extract(AVISIT, "(?<=(WEEK ))[0-9]+")),
 #'         TRUE ~ as.character(NA)
 #'       ),
-#'       AVISITCDN = dplyr::case_when(
+#'       AVISITCDN = case_when(
 #'         AVISITCD == "SCR" ~ -2,
 #'         AVISITCD == "BL" ~ 0,
 #'         grepl("W", AVISITCD) ~ as.numeric(gsub("[^0-9]*", "", AVISITCD)),
 #'         TRUE ~ as.numeric(NA)
 #'       ),
 #'       AVISITCD = factor(AVISITCD) %>% reorder(AVISITCDN),
-#'       TRTORD = dplyr::case_when(
+#'       TRTORD = case_when(
 #'         ARMCD == "ARM C" ~ 1,
 #'         ARMCD == "ARM B" ~ 2,
 #'         ARMCD == "ARM A" ~ 3
@@ -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",