222 decouple scda

.Rbuildignore

@@ -42,3 +42,12 @@ SECURITY.md
 ^LICENSE\.md$
 coverage.*
 ^\.pre-commit-config\.yaml
+_pkgdown.yml
+staged_dependencies.yaml
+data-raw/data.R
+.gitlab-ci.yml
+.lintr
+.pre-commit-config.yaml
+.github
+^.*\.Rproj$
+^\.Rproj\.user$

.github/workflows/check.yaml

@@ -34,6 +34,7 @@ jobs:
     with:
       additional-env-vars: |
         _R_CHECK_CRAN_INCOMING_REMOTE_=false
+        _R_CHECK_EXAMPLE_TIMING_THRESHOLD_=10
       additional-r-cmd-check-params: --as-cran
       enforce-note-blocklist: true
       note-blocklist: |

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

NEWS.md

@@ -1,16 +1,15 @@
 # goshawk 0.1.14.9010
 
-# Examples now use `scda.2022` data instead of `scda.2021`.
-
 ### Miscellaneous
 
 * Deprecated `g_scatterplot`. Use `g_correlationplot` instead.
+* Removed `scda` package dependency from examples.
 
 # goshawk 0.1.14
 
 ### Fixes
 
 * Fixed `h_caption_loqs_label` to handle multiple parameters when data frame is returned from `h_identify_loq_values`.
 
 ### Enhancements
 
@@ -51,7 +50,7 @@
 
 ### Miscellaneous
 
 * Added R version requirement `R >= 3.6`.
 * Removed dependency on the `test.nest` package.
 * Removed dependency on the `utils.nest` package and replaced its functions with equivalents from the `checkmate` package.
 
@@ -96,14 +95,14 @@
    - Rug plot option added.
 * `g_lineplot`:
     - Argument changes: `font_size` --> `plot_font_size`
     - Line and symbol type can now be configured. especially useful if line splitting is used.
     - Added minimum records threshold.
     - Table font size can now be controlled.
     - Decreased width of error bars.
     - Horizontal and columned legend orientation.
 
 ### General
 * Added additional validation and description for the `loq_legend` argument.
 * Set legend label as variable label attribute of `trt_group` across all modules.
 
 # goshawk 0.1.5

R/data.R

@@ -0,0 +1,25 @@
+#' Random lab analysis
+#'
+#' @description Random lab analysis
+#' @docType data
+#'
+#' @usage rADLB
+#'
+#' @keywords datasets internal
+#'
+#' @source internal
+#' @name rADLB
+"rADLB"
+
+#' Random patient listing
+#'
+#' @description Random patient listing
+#' @docType data
+#'
+#' @keywords datasets internal
+#'
+#' @usage 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(
@@ -263,7 +261,7 @@ g_boxplot <- function(data,
 
   # Add facetting.
   if (!is.null(facet_var)) {
-    if (facet_var != "None" & facet_var %in% names(data)) {
+    if (facet_var != "None" & facet_var %in% names(data)) { # nolint
       if (!is_finite(facet_ncol)) facet_ncol <- 0
       if (facet_ncol >= 1) {
         plot1 <- plot1 +

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")$adlb # nolint
+usethis::use_data(rADLB)
+
+rADSL <- synthetic_cdisc_data("latest")$adsl # nolint
+usethis::use_data(rADSL)