Update docs to use the new teal_data instead of TealData (#245)

fixes #243 part of insightsengineering/nestdevs-tasks#41 insightsengineering/teal.data#184 - [x] add the news section for change. - [x] update the examples in the documentation to pass teal_data. - [x] update join_keys calls once the pull request is completed at insightsengineering/teal.data#184. - [x] Revise and update the vignettes accordingly. - [ ] make version bump once insightsengineering/teal.data#184. is merged. --------- Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: 27856297+dependabot-preview[bot]@users.noreply.github.com <27856297+dependabot-preview[bot]@users.noreply.github.com> Co-authored-by: vedhav <vedhaviyash4@gmail.com>
insightsengineering · Nov 20, 2023 · bd74b80 · bd74b80
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -29,7 +29,7 @@ Depends:
     goshawk (>= 0.1.15),
     R (>= 3.6),
     shiny,
-    teal (>= 0.14.0)
+    teal (>= 0.14.0.9019)
 Imports:
     checkmate,
     colourpicker,
@@ -47,15 +47,15 @@ Imports:
     teal.code (>= 0.4.0),
     teal.logger (>= 0.1.1),
     teal.reporter (>= 0.2.0),
-    teal.transform (>= 0.4.0),
+    teal.transform (>= 0.4.0.9007),
     teal.widgets (>= 0.4.0),
     tidyr
 Suggests:
     knitr,
     nestcolor (>= 0.1.0),
     rmarkdown,
     stringr,
-    teal.data (>= 0.3.0),
+    teal.data (>= 0.3.0.9010),
     tern (>= 0.7.10),
     testthat (>= 2.0),
     utils

diff --git a/NEWS.md b/NEWS.md
@@ -1,5 +1,9 @@
 # teal.goshawk 0.1.15.9002
 
+### Enhancements
+
+* Updated the documentation and vignettes to demonstrate method to pass `teal_data` object to `teal::init()`.
+
 # teal.goshawk 0.1.15
 
 ### Enhancements

diff --git a/R/tm_g_gh_boxplot.R b/R/tm_g_gh_boxplot.R
@@ -48,121 +48,77 @@
 #' @examples
 #'
 #' # Example using ADaM structure analysis dataset.
+#' data <- teal_data()
+#' data <- within(data, {
+#'   library(dplyr)
+#'   library(nestcolor)
 #'
-#' library(dplyr)
-#' library(nestcolor)
+#'   # original ARM value = dose value
+#'   arm_mapping <- list(
+#'     "A: Drug X" = "150mg QD",
+#'     "B: Placebo" = "Placebo",
+#'     "C: Combination" = "Combination"
+#'   )
+#'   set.seed(1)
+#'   ADSL <- goshawk::rADSL
+#'   ADLB <- goshawk::rADLB
+#'   var_labels <- lapply(ADLB, function(x) attributes(x)$label)
+#'   ADLB <- ADLB %>%
+#'     dplyr::mutate(
+#'       AVISITCD = dplyr::case_when(
+#'         AVISIT == "SCREENING" ~ "SCR",
+#'         AVISIT == "BASELINE" ~ "BL",
+#'         grepl("WEEK", AVISIT) ~ paste("W", stringr::str_extract(AVISIT, "(?<=(WEEK ))[0-9]+")),
+#'         TRUE ~ as.character(NA)
+#'       ),
+#'       AVISITCDN = dplyr::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(
+#'         ARMCD == "ARM C" ~ 1,
+#'         ARMCD == "ARM B" ~ 2,
+#'         ARMCD == "ARM A" ~ 3
+#'       ),
+#'       ARM = as.character(arm_mapping[match(ARM, names(arm_mapping))]),
+#'       ARM = factor(ARM) %>% reorder(TRTORD),
+#'       ACTARM = as.character(arm_mapping[match(ACTARM, names(arm_mapping))]),
+#'       ACTARM = factor(ACTARM) %>% reorder(TRTORD),
+#'       ANRLO = 50,
+#'       ANRHI = 75
+#'     ) %>%
+#'     dplyr::rowwise() %>%
+#'     dplyr::group_by(PARAMCD) %>%
+#'     dplyr::mutate(LBSTRESC = ifelse(
+#'       USUBJID %in% sample(USUBJID, 1, replace = TRUE),
+#'       paste("<", round(runif(1, min = 25, max = 30))), LBSTRESC
+#'     )) %>%
+#'     dplyr::mutate(LBSTRESC = ifelse(
+#'       USUBJID %in% sample(USUBJID, 1, replace = TRUE),
+#'       paste(">", round(runif(1, min = 70, max = 75))), LBSTRESC
+#'     )) %>%
+#'     ungroup()
 #'
-#' # original ARM value = dose value
-#' arm_mapping <- list(
-#'   "A: Drug X" = "150mg QD",
-#'   "B: Placebo" = "Placebo",
-#'   "C: Combination" = "Combination"
-#' )
+#'   attr(ADLB[["ARM"]], "label") <- var_labels[["ARM"]]
+#'   attr(ADLB[["ACTARM"]], "label") <- var_labels[["ACTARM"]]
+#'   attr(ADLB[["ANRLO"]], "label") <- "Analysis Normal Range Lower Limit"
+#'   attr(ADLB[["ANRHI"]], "label") <- "Analysis Normal Range Upper Limit"
 #'
-#' set.seed(1)
-#' ADSL <- goshawk::rADSL
-#' ADLB <- goshawk::rADLB
-#' var_labels <- lapply(ADLB, function(x) attributes(x)$label)
-#' ADLB <- ADLB %>%
-#'   dplyr::mutate(
-#'     AVISITCD = dplyr::case_when(
-#'       AVISIT == "SCREENING" ~ "SCR",
-#'       AVISIT == "BASELINE" ~ "BL",
-#'       grepl("WEEK", AVISIT) ~ paste("W", stringr::str_extract(AVISIT, "(?<=(WEEK ))[0-9]+")),
-#'       TRUE ~ as.character(NA)
-#'     ),
-#'     AVISITCDN = dplyr::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(
-#'       ARMCD == "ARM C" ~ 1,
-#'       ARMCD == "ARM B" ~ 2,
-#'       ARMCD == "ARM A" ~ 3
-#'     ),
-#'     ARM = as.character(arm_mapping[match(ARM, names(arm_mapping))]),
-#'     ARM = factor(ARM) %>% reorder(TRTORD),
-#'     ACTARM = as.character(arm_mapping[match(ACTARM, names(arm_mapping))]),
-#'     ACTARM = factor(ACTARM) %>% reorder(TRTORD),
-#'     ANRLO = 50,
-#'     ANRHI = 75
-#'   ) %>%
-#'   dplyr::rowwise() %>%
-#'   dplyr::group_by(PARAMCD) %>%
-#'   dplyr::mutate(LBSTRESC = ifelse(
-#'     USUBJID %in% sample(USUBJID, 1, replace = TRUE),
-#'     paste("<", round(runif(1, min = 25, max = 30))), LBSTRESC
-#'   )) %>%
-#'   dplyr::mutate(LBSTRESC = ifelse(
-#'     USUBJID %in% sample(USUBJID, 1, replace = TRUE),
-#'     paste(">", round(runif(1, min = 70, max = 75))), LBSTRESC
-#'   )) %>%
-#'   ungroup()
+#'   # add LLOQ and ULOQ variables
+#'   ALB_LOQS <- goshawk:::h_identify_loq_values(ADLB)
+#'   ADLB <- dplyr::left_join(ADLB, ALB_LOQS, by = "PARAM")
+#' })
 #'
-#' attr(ADLB[["ARM"]], "label") <- var_labels[["ARM"]]
-#' attr(ADLB[["ACTARM"]], "label") <- var_labels[["ACTARM"]]
-#' attr(ADLB[["ANRLO"]], "label") <- "Analysis Normal Range Lower Limit"
-#' attr(ADLB[["ANRHI"]], "label") <- "Analysis Normal Range Upper Limit"
+#' datanames <- c("ADSL", "ADLB")
+#' datanames(data) <- datanames
 #'
-#' # add LLOQ and ULOQ variables
-#' ALB_LOQS <- goshawk:::h_identify_loq_values(ADLB)
-#' ADLB <- dplyr::left_join(ADLB, ALB_LOQS, by = "PARAM")
+#' join_keys(data) <- default_cdisc_join_keys[datanames]
 #'
 #' app <- teal::init(
-#'   data = teal.data::cdisc_data(
-#'     adsl <- teal.data::cdisc_dataset("ADSL", ADSL, code = "ADSL <- goshawk::rADSL"),
-#'     teal.data::cdisc_dataset(
-#'       "ADLB",
-#'       ADLB,
-#'       code = "
-#'         set.seed(1)
-#'         ADLB <- goshawk::rADLB
-#'         var_labels <- lapply(ADLB, function(x) attributes(x)$label)
-#'         ADLB <- ADLB %>%
-#'           dplyr::mutate(AVISITCD = dplyr::case_when(
-#'             AVISIT == 'SCREENING' ~ 'SCR',
-#'             AVISIT == 'BASELINE' ~ 'BL',
-#'             grepl('WEEK', AVISIT) ~ paste('W', stringr::str_extract(AVISIT, '(?<=(WEEK ))[0-9]+')),
-#'             TRUE ~ as.character(NA)),
-#'             AVISITCDN = dplyr::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(
-#'               ARMCD == 'ARM C' ~ 1,
-#'               ARMCD == 'ARM B' ~ 2,
-#'               ARMCD == 'ARM A' ~ 3),
-#'             ARM = as.character(arm_mapping[match(ARM, names(arm_mapping))]),
-#'             ARM = factor(ARM) %>% reorder(TRTORD),
-#'             ACTARM = as.character(arm_mapping[match(ACTARM, names(arm_mapping))]),
-#'             ACTARM = factor(ACTARM) %>% reorder(TRTORD),
-#'             ANRLO = 50,
-#'             ANRHI = 75) %>%
-#'           dplyr::rowwise() %>%
-#'           dplyr::group_by(PARAMCD) %>%
-#'           dplyr::mutate(LBSTRESC = ifelse(
-#'             USUBJID %in% sample(USUBJID, 1, replace = TRUE),
-#'             paste('<', round(runif(1, min = 25, max = 30))), LBSTRESC)) %>%
-#'           dplyr::mutate(LBSTRESC = ifelse(
-#'             USUBJID %in% sample(USUBJID, 1, replace = TRUE),
-#'             paste( '>', round(runif(1, min = 70, max = 75))), LBSTRESC)) %>%
-#'           ungroup()
-#'         attr(ADLB[['ARM']], 'label') <- var_labels[['ARM']]
-#'         attr(ADLB[['ACTARM']], 'label') <- var_labels[['ACTARM']]
-#'         attr(ADLB[['ANRLO']], 'label') <- 'Analysis Normal Range Lower Limit'
-#'         attr(ADLB[['ANRHI']], 'label') <- 'Analysis Normal Range Upper Limit'
-#'         # add LLOQ and ULOQ variables
-#'         ALB_LOQS <- goshawk:::h_identify_loq_values(ADLB)
-#'         ADLB <- left_join(ADLB, ALB_LOQS, by = 'PARAM')",
-#'       vars = list(ADSL = adsl, arm_mapping = arm_mapping)
-#'     ),
-#'     check = FALSE # to shorten the example check = FALSE, in real scenarios use check = TRUE
-#'   ),
+#'   data = data,
 #'   modules = teal::modules(
 #'     teal.goshawk::tm_g_gh_boxplot(
 #'       label = "Box Plot",