decouple scda

.Rbuildignore

@@ -1,44 +1,7 @@
-^renv$
-^renv\.lock$
-CODE_OF_CONDUCT.md
-SECURITY.md
-^_dev$
+data-raw/data.R
+.gitlab-ci.yml
+.lintr
+.pre-commit-config.yaml
+.github
 ^.*\.Rproj$
-^[^/]+\.html$
-^[^/]+\.png$
-^[^/]+\.R$
-^[^/]+\.Rmd$
-^\_pkgdown\.yaml$
-^\_pkgdown\.yml
-^\.CI-FORCE-RELEASE-VERSION$
-^\.drone\.yml$
-^\.github$
-^\.lintr$
-^\.Rprofile$
 ^\.Rproj\.user$
-^\.travis\.yml$
-^build_docker_image$
-^cache$
-^data-raw$
-^data/script\.R$
-^design$
-^dev$
-^doc$
-^docs$
-^Jenkinsfile$
-^logs$
-^Makefile$
-^man-roxygen$
-^Meta$
-^outputdir$
-^scratch$
-^stubs$
-^temp$
-^templates$
-^test_full_example$
-^TODO\.md$
-^staged_dependencies\.yaml$
-^\.gitlab-ci\.yml$
-^LICENSE\.md$
-coverage.*
-^\.pre-commit-config\.yaml

DESCRIPTION

@@ -43,15 +43,10 @@ Suggests:
     knitr,
     nestcolor (>= 0.1.0),
     rmarkdown,
-    scda (>= 0.1.5),
-    scda.2022 (>= 0.1.3),
     testthat (>= 2.0),
     tidyr
 VignetteBuilder:
     knitr
-Remotes:
-    insightsengineering/scda.2022@*release,
-    insightsengineering/scda@*release
 Config/Needs/website: insightsengineering/nesttemplate
 Encoding: UTF-8
 Language: en-US

R/data.R

@@ -0,0 +1,25 @@
+#' Random lab analysis
+#'
+#' @description Random lab analysis
+#' @docType data
+#'
+#' @usage goshawk::rADLB
+#'
+#' @keywords datasets internal
+#'
+#' @source internal
+#' @name rADLB
+"rADLB"
+
+#' Random patient listing
+#'
+#' @description Random patient listing
+#' @docType data
+#'
+#' @keywords datasets internal
+#'
+#' @usage goshawk::rADSL
+#'
+#' @source internal
+#' @name rADSL
+"rADSL"

R/g_boxplot.R

@@ -51,13 +51,11 @@
 #'
 #' @examples
 #'
-#'
 #' # Example using ADaM structure analysis dataset.
 #'
-#' library(scda)
 #' library(nestcolor)
 #'
-#' ADLB <- synthetic_cdisc_data("latest")$adlb
+#' ADLB <- goshawk::rADLB
 #' var_labels <- lapply(ADLB, function(x) attributes(x)$label)
 #' ADLB <- ADLB %>%
 #'   mutate(AVISITCD = case_when(

R/g_correlationplot.R

@@ -61,7 +61,6 @@
 #' @examples
 #' # Example using ADaM structure analysis dataset.
 #'
-#' library(scda)
 #' library(stringr)
 #' library(tidyr)
 #'
@@ -75,7 +74,7 @@
 #' # assign LOQ flag symbols: circles for "N" and triangles for "Y", squares for "NA"
 #' shape_manual <- c("N" = 1, "Y" = 2, "NA" = 0)
 #'
-#' ADLB <- synthetic_cdisc_data("latest")$adlb
+#' ADLB <- goshawk::rADLB
 #' var_labels <- lapply(ADLB, function(x) attributes(x)$label)
 #' ADLB <- ADLB %>%
 #'   mutate(AVISITCD = case_when(

R/g_density_distribution_plot.R

@@ -38,7 +38,6 @@
 #'
 #' # Example using ADaM structure analysis dataset.
 #'
-#' library(scda)
 #' library(stringr)
 #'
 #' # original ARM value = dose value
@@ -47,7 +46,7 @@
 #' )
 #' color_manual <- c("150mg QD" = "#000000", "Placebo" = "#3498DB", "Combination" = "#E74C3C")
 #'
-#' ADLB <- synthetic_cdisc_data("latest")$adlb
+#' ADLB <- goshawk::rADLB
 #' var_labels <- lapply(ADLB, function(x) attributes(x)$label)
 #' ADLB <- ADLB %>%
 #'   mutate(AVISITCD = case_when(

R/g_lineplot.R

@@ -53,7 +53,6 @@
 #'
 #' # Example using ADaM structure analysis dataset.
 #'
-#' library(scda)
 #' library(stringr)
 #' library(dplyr)
 #' library(nestcolor)
@@ -65,9 +64,8 @@
 #' color_manual <- c("150mg QD" = "thistle", "Placebo" = "orange", "Combination" = "steelblue")
 #' type_manual <- c("150mg QD" = "solid", "Placebo" = "dashed", "Combination" = "dotted")
 #'
-#' ADSL <- synthetic_cdisc_data("latest")$adsl %>%
-#'   filter(!(ARM == "B: Placebo" & AGE < 40))
-#' ADLB <- synthetic_cdisc_data("latest")$adlb
+#' ADSL <- goshawk::rADSL %>% filter(!(ARM == "B: Placebo" & AGE < 40))
+#' ADLB <- goshawk::rADLB
 #' ADLB <- right_join(ADLB, ADSL[, c("STUDYID", "USUBJID")])
 #' var_labels <- lapply(ADLB, function(x) attributes(x)$label)
 #'

R/g_scatterplot.R

@@ -45,7 +45,6 @@
 #' @examples
 #' # Example using ADaM structure analysis dataset.
 #'
-#' library(scda)
 #' library(stringr)
 #'
 #' # original ARM value = dose value
@@ -56,7 +55,7 @@
 #' # assign LOQ flag symbols: circles for "N" and triangles for "Y", squares for "NA"
 #' shape_manual <- c("N" = 1, "Y" = 2, "NA" = 0)
 #'
-#' ADLB <- synthetic_cdisc_data("latest")$adlb
+#' ADLB <- goshawk::rADLB
 #' var_labels <- lapply(ADLB, function(x) attributes(x)$label)
 #' ADLB <- ADLB %>%
 #'   mutate(AVISITCD = case_when(

R/g_spaghettiplot.R

@@ -47,7 +47,6 @@
 #'
 #' # Example using ADaM structure analysis dataset.
 #'
-#' library(scda)
 #' library(stringr)
 #'
 #' # original ARM value = dose value
@@ -56,7 +55,7 @@
 #' )
 #' color_manual <- c("150mg QD" = "#000000", "Placebo" = "#3498DB", "Combination" = "#E74C3C")
 #'
-#' ADLB <- synthetic_cdisc_data("latest")$adlb
+#' ADLB <- goshawk::rADLB
 #' var_labels <- lapply(ADLB, function(x) attributes(x)$label)
 #' ADLB <- ADLB %>%
 #'   mutate(AVISITCD = case_when(

R/t_summarytable.R

@@ -25,15 +25,14 @@
 #' @examples
 #' # Example using ADaM structure analysis dataset.
 #'
-#' library(scda)
 #' library(stringr)
 #'
 #' # original ARM value = dose value
 #' arm_mapping <- list(
 #'   "A: Drug X" = "150mg QD", "B: Placebo" = "Placebo", "C: Combination" = "Combination"
 #' )
 #'
-#' ADLB <- synthetic_cdisc_data("latest")$adlb
+#' ADLB <- goshawk::rADLB
 #' ADLB <- ADLB %>%
 #'   mutate(AVISITCD = case_when(
 #'     AVISIT == "SCREENING" ~ "SCR",

R/utils.R

@@ -12,11 +12,8 @@
 #' @keywords internal
 #'
 #' @examples
-#' library(scda)
 #'
-#' ADLB <- synthetic_cdisc_data("latest")$adlb
-#'
-#' goshawk:::h_identify_loq_values(loqs_data = ADLB)
+#' goshawk:::h_identify_loq_values(loqs_data = goshawk::rADLB)
 h_identify_loq_values <- function(loqs_data) {
   ifelse(
     !grep("PARAM", names(loqs_data)),
@@ -79,9 +76,7 @@ h_identify_loq_values <- function(loqs_data) {
 #' @keywords internal
 #'
 #' @examples
-#' library(scda)
-#' ADLB <- synthetic_cdisc_data("latest")$adlb
-#' caption_label <- goshawk:::h_caption_loqs_label(loqs_data = ADLB)
+#' caption_label <- goshawk:::h_caption_loqs_label(loqs_data = goshawk::rADLB)
 h_caption_loqs_label <- function(loqs_data) {
   loq_values <- h_identify_loq_values(loqs_data)
 

data-raw/data.R

@@ -0,0 +1,6 @@
+library(scda)
+rADLB <- synthetic_cdisc_data("latest")$adlb
+usethis::use_data(rADLB)
+
+rADSL <- synthetic_cdisc_data("latest")$adsl
+usethis::use_data(rADSL)