Update docs to use the new teal_data instead of TealData (#853)

fixes #842 part of insightsengineering/nestdevs-tasks#41 insightsengineering/teal.data#184 - [x] add thenews 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: 27856297+dependabot-preview[bot]@users.noreply.github.com <27856297+dependabot-preview[bot]@users.noreply.github.com> Co-authored-by: vedhav <[email protected]>
insightsengineering · Nov 20, 2023 · bcb9ae1 · bcb9ae1
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -26,7 +26,7 @@ BugReports:
     https://github.com/insightsengineering/teal.modules.clinical/issues
 Depends:
     R (>= 4.0),
-    teal (>= 0.14.0),
+    teal (>= 0.14.0.9019),
     tern (>= 0.8.2)
 Imports:
     assertthat,
@@ -54,10 +54,10 @@ Imports:
     stats,
     styler,
     teal.code (>= 0.4.0),
-    teal.data (>= 0.3.0.9009),
+    teal.data (>= 0.3.0.9010),
     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),
     tern.gee (>= 0.1.0),
     tern.mmrm (>= 0.2.1),
@@ -69,6 +69,7 @@ Suggests:
     knitr,
     lubridate,
     nestcolor (>= 0.1.0),
+    teal.data (>= 0.3.0.9010),
     testthat (>= 3.0)
 VignetteBuilder:
     knitr

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,8 @@
+# teal.modules.clinical 0.8.16.9011
+
+### Enhancements
+* Updated the documentation and vignettes to demonstrate method to pass `teal_data` object to `teal::init()`.
+
 # teal.modules.clinical 0.8.16.9010
 
 ### Enhancements
@@ -13,7 +18,7 @@
 * Updated `tm_t_pp_basic_info`, `tm_t_pp_medical_history`, `tm_g_pp_therapy`, `tm_g_pp_adverse_events`, and `tm_t_pp_laboratory` to print patient ID above table.
 * Updated `tm_t_pp_basic_info`, `tm_g_pp_therapy`, `tm_g_pp_adverse_events`, and `tm_t_pp_laboratory` to use `rlistings` to print data neatly in reports.
 * Updated `tm_g_lineplot` to allow user to remove interval from plot.
-
+* Updated the documentation and vignettes to demonstrate method to pass `teal_data` object to `teal::init()`.
 
 ### Bug fixes
 * Fixed bug in `tm_t_coxreg` preventing table from being displayed when no covariates are selected.

diff --git a/R/tm_a_gee.R b/R/tm_a_gee.R
@@ -128,24 +128,27 @@ template_a_gee <- function(output_table,
 #' @export
 #'
 #' @examples
-#' adsl <- tmc_ex_adsl
-#' adqs <- tmc_ex_adqs %>%
-#'   dplyr::filter(ABLFL != "Y" & ABLFL2 != "Y") %>%
-#'   dplyr::mutate(
-#'     AVISIT = as.factor(AVISIT),
-#'     AVISITN = rank(AVISITN) %>%
-#'       as.factor() %>%
-#'       as.numeric() %>%
-#'       as.factor(),
-#'     AVALBIN = AVAL < 50 # Just as an example to get a binary endpoint.
-#'   ) %>%
-#'   droplevels()
+#' data <- teal_data()
+#' data <- within(data, {
+#'   ADSL <- tmc_ex_adsl
+#'   ADQS <- tmc_ex_adqs %>%
+#'     dplyr::filter(ABLFL != "Y" & ABLFL2 != "Y") %>%
+#'     dplyr::mutate(
+#'       AVISIT = as.factor(AVISIT),
+#'       AVISITN = rank(AVISITN) %>%
+#'         as.factor() %>%
+#'         as.numeric() %>%
+#'         as.factor(),
+#'       AVALBIN = AVAL < 50 #' Just as an example to get a binary endpoint.
+#'     ) %>%
+#'     droplevels()
+#' })
+#' datanames <- c("ADSL", "ADQS")
+#' datanames(data) <- datanames
+#' join_keys(data) <- default_cdisc_join_keys[datanames]
 #'
 #' app <- init(
-#'   data = cdisc_data(
-#'     cdisc_dataset("ADSL", adsl),
-#'     cdisc_dataset("ADQS", adqs)
-#'   ),
+#'   data = data,
 #'   modules = modules(
 #'     tm_a_gee(
 #'       label = "GEE",
@@ -155,7 +158,7 @@ template_a_gee <- function(output_table,
 #'       arm_var = choices_selected(c("ARM", "ARMCD"), "ARM"),
 #'       visit_var = choices_selected(c("AVISIT", "AVISITN"), "AVISIT"),
 #'       paramcd = choices_selected(
-#'         choices = value_choices(adqs, "PARAMCD", "PARAM"),
+#'         choices = value_choices(data[["ADQS"]], "PARAMCD", "PARAM"),
 #'         selected = "FKSI-FWB"
 #'       ),
 #'       cov_var = choices_selected(c("BASE", "AGE", "SEX", "BASE:AVISIT"), NULL)
@@ -444,14 +447,14 @@ srv_gee <- function(id,
       datasets = data,
       selector_list = selector_list,
       merge_function = "dplyr::inner_join",
-      join_keys = teal.data::get_join_keys(data)
+      join_keys = teal.data::join_keys(data)
     )
 
     adsl_inputs <- teal.transform::merge_expression_module(
       datasets = data,
       data_extract = list(arm_var = arm_var),
       anl_name = "ANL_ADSL",
-      join_keys = teal.data::get_join_keys(data)
+      join_keys = teal.data::join_keys(data)
     )
 
     anl_q <- shiny::reactive({

diff --git a/R/tm_a_mmrm.R b/R/tm_a_mmrm.R
@@ -452,30 +452,33 @@ template_mmrm_plots <- function(fit_name,
 #' numerical precision.
 #'
 #' @examples
-#' adsl <- tmc_ex_adsl
-#' adqs <- tmc_ex_adqs %>%
-#'   dplyr::filter(ABLFL != "Y" & ABLFL2 != "Y") %>%
-#'   dplyr::filter(AVISIT %in% c("WEEK 1 DAY 8", "WEEK 2 DAY 15", "WEEK 3 DAY 22")) %>%
-#'   dplyr::mutate(
-#'     AVISIT = as.factor(AVISIT),
-#'     AVISITN = rank(AVISITN) %>%
-#'       as.factor() %>%
-#'       as.numeric() %>%
-#'       as.factor() # making consecutive numeric factor
-#'   )
-#'
 #' arm_ref_comp <- list(
 #'   ARMCD = list(
 #'     ref = "ARM B",
 #'     comp = c("ARM A", "ARM C")
 #'   )
 #' )
 #'
+#' data <- teal_data()
+#' data <- within(data, {
+#'   ADSL <- tmc_ex_adsl
+#'   ADQS <- tmc_ex_adqs %>%
+#'     dplyr::filter(ABLFL != "Y" & ABLFL2 != "Y") %>%
+#'     dplyr::filter(AVISIT %in% c("WEEK 1 DAY 8", "WEEK 2 DAY 15", "WEEK 3 DAY 22")) %>%
+#'     dplyr::mutate(
+#'       AVISIT = as.factor(AVISIT),
+#'       AVISITN = rank(AVISITN) %>%
+#'         as.factor() %>%
+#'         as.numeric() %>%
+#'         as.factor() #' making consecutive numeric factor
+#'     )
+#' })
+#'
+#' datanames <- c("ADSL", "ADQS")
+#' datanames(data) <- datanames
+#' join_keys(data) <- default_cdisc_join_keys[datanames]
 #' app <- init(
-#'   data = cdisc_data(
-#'     cdisc_dataset("ADSL", adsl),
-#'     cdisc_dataset("ADQS", adqs)
-#'   ),
+#'   data = data,
 #'   modules = modules(
 #'     tm_a_mmrm(
 #'       label = "MMRM",
@@ -486,7 +489,7 @@ template_mmrm_plots <- function(fit_name,
 #'       visit_var = choices_selected(c("AVISIT", "AVISITN"), "AVISIT"),
 #'       arm_ref_comp = arm_ref_comp,
 #'       paramcd = choices_selected(
-#'         choices = value_choices(adqs, "PARAMCD", "PARAM"),
+#'         choices = value_choices(data[["ADQS"]], "PARAMCD", "PARAM"),
 #'         selected = "FKSI-FWB"
 #'       ),
 #'       cov_var = choices_selected(c("BASE", "AGE", "SEX", "BASE:AVISIT"), NULL)
@@ -917,14 +920,14 @@ srv_mmrm <- function(id,
     anl_inputs <- teal.transform::merge_expression_srv(
       datasets = data,
       selector_list = selector_list_without_cov,
-      join_keys = teal.data::get_join_keys(data),
+      join_keys = teal.data::join_keys(data),
       merge_function = "dplyr::inner_join"
     )
 
     adsl_merge_inputs <- teal.transform::merge_expression_module(
       datasets = data,
       data_extract = list(arm_var = arm_var),
-      join_keys = teal.data::get_join_keys(data),
+      join_keys = teal.data::join_keys(data),
       anl_name = "ANL_ADSL"
     )
 

diff --git a/R/tm_g_barchart_simple.R b/R/tm_g_barchart_simple.R
@@ -16,14 +16,21 @@
 #' @examples
 #' library(nestcolor)
 #'
-#' adsl <- tmc_ex_adsl %>% dplyr::mutate(ITTFL = factor("Y") %>%
-#'   formatters::with_label("Intent-To-Treat Population Flag"))
-#' adae <- tmc_ex_adae %>% dplyr::filter(!((AETOXGR == 1) & (AESEV == "MILD") & (ARM == "A: Drug X")))
+#' ADSL <- tmc_ex_adsl %>%
+#'   dplyr::mutate(ITTFL = factor("Y") %>%
+#'     formatters::with_label("Intent-To-Treat Population Flag"))
+#' ADAE <- tmc_ex_adae %>%
+#'   dplyr::filter(!((AETOXGR == 1) & (AESEV == "MILD") & (ARM == "A: Drug X")))
 #'
 #' app <- init(
 #'   data = cdisc_data(
-#'     cdisc_dataset("ADSL", adsl),
-#'     cdisc_dataset("ADAE", adae)
+#'     ADSL = ADSL,
+#'     ADAE = ADAE,
+#'     code = "ADSL <- tmc_ex_adsl %>%
+#'               dplyr::mutate(ITTFL = factor(\"Y\") %>%
+#'               formatters::with_label(\"Intent-To-Treat Population Flag\"))
+#'             ADAE <- tmc_ex_adae %>%
+#'               dplyr::filter(!((AETOXGR == 1) & (AESEV == \"MILD\") & (ARM == \"A: Drug X\")))"
 #'   ),
 #'   modules = modules(
 #'     tm_g_barchart_simple(
@@ -32,7 +39,7 @@
 #'         dataname = "ADSL",
 #'         select = select_spec(
 #'           choices = variable_choices(
-#'             adsl,
+#'             ADSL,
 #'             c(
 #'               "ARM", "ACTARM", "SEX",
 #'               "RACE", "ITTFL", "SAFFL", "STRATA2"
@@ -47,7 +54,7 @@
 #'           dataname = "ADSL",
 #'           select = select_spec(
 #'             choices = variable_choices(
-#'               adsl,
+#'               ADSL,
 #'               c(
 #'                 "ARM", "ACTARM", "SEX",
 #'                 "RACE", "ITTFL", "SAFFL", "STRATA2"
@@ -60,7 +67,7 @@
 #'         data_extract_spec(
 #'           dataname = "ADAE",
 #'           select = select_spec(
-#'             choices = variable_choices(adae, c("AETOXGR", "AESEV", "AESER")),
+#'             choices = variable_choices(ADAE, c("AETOXGR", "AESEV", "AESER")),
 #'             selected = NULL,
 #'             multiple = FALSE
 #'           )
@@ -70,7 +77,7 @@
 #'         data_extract_spec(
 #'           dataname = "ADAE",
 #'           select = select_spec(
-#'             choices = variable_choices(adae, c("AETOXGR", "AESEV", "AESER")),
+#'             choices = variable_choices(ADAE, c("AETOXGR", "AESEV", "AESER")),
 #'             selected = "AETOXGR",
 #'             multiple = FALSE
 #'           )
@@ -79,7 +86,7 @@
 #'           dataname = "ADSL",
 #'           select = select_spec(
 #'             choices = variable_choices(
-#'               adsl,
+#'               ADSL,
 #'               c(
 #'                 "ARM", "ACTARM", "SEX",
 #'                 "RACE", "ITTFL", "SAFFL", "STRATA2"
@@ -94,7 +101,7 @@
 #'         data_extract_spec(
 #'           dataname = "ADAE",
 #'           select = select_spec(
-#'             choices = variable_choices(adae, c("AETOXGR", "AESEV", "AESER")),
+#'             choices = variable_choices(ADAE, c("AETOXGR", "AESEV", "AESER")),
 #'             selected = "AESEV",
 #'             multiple = FALSE
 #'           )
@@ -103,7 +110,7 @@
 #'           dataname = "ADSL",
 #'           select = select_spec(
 #'             choices = variable_choices(
-#'               adsl,
+#'               ADSL,
 #'               c(
 #'                 "ARM", "ACTARM", "SEX",
 #'                 "RACE", "ITTFL", "SAFFL", "STRATA2"
@@ -374,7 +381,7 @@ srv_g_barchart_simple <- function(id,
 
     anl_inputs <- teal.transform::merge_expression_srv(
       datasets = data,
-      join_keys = teal.data::get_join_keys(data),
+      join_keys = teal.data::join_keys(data),
       selector_list = selector_list
     )
 

diff --git a/R/tm_g_ci.R b/R/tm_g_ci.R
@@ -192,13 +192,17 @@ template_g_ci <- function(dataname, # nolint
 #' @examples
 #' library(nestcolor)
 #'
-#' adsl <- tmc_ex_adsl
-#' adlb <- tmc_ex_adlb
+#' ADSL <- tmc_ex_adsl
+#' ADLB <- tmc_ex_adlb
 #'
 #' app <- init(
 #'   data = cdisc_data(
-#'     cdisc_dataset("ADSL", adsl),
-#'     cdisc_dataset("ADLB", adlb)
+#'     ADSL = ADSL,
+#'     ADLB = ADLB,
+#'     code = "
+#'       ADSL <- tmc_ex_adsl
+#'       ADLB <- tmc_ex_adlb
+#'     "
 #'   ),
 #'   modules = modules(
 #'     tm_g_ci(
@@ -217,15 +221,15 @@ template_g_ci <- function(dataname, # nolint
 #'         filter = list(
 #'           filter_spec(
 #'             vars = "PARAMCD",
-#'             choices = levels(adlb$PARAMCD),
-#'             selected = levels(adlb$PARAMCD)[1],
+#'             choices = levels(ADLB$PARAMCD),
+#'             selected = levels(ADLB$PARAMCD)[1],
 #'             multiple = FALSE,
 #'             label = "Select lab:"
 #'           ),
 #'           filter_spec(
 #'             vars = "AVISIT",
-#'             choices = levels(adlb$AVISIT),
-#'             selected = levels(adlb$AVISIT)[1],
+#'             choices = levels(ADLB$AVISIT),
+#'             selected = levels(ADLB$AVISIT)[1],
 #'             multiple = FALSE,
 #'             label = "Select visit:"
 #'           )
@@ -399,7 +403,7 @@ srv_g_ci <- function(id, # nolint
 
     anl_inputs <- teal.transform::merge_expression_srv(
       datasets = data,
-      join_keys = teal.data::get_join_keys(data),
+      join_keys = teal.data::join_keys(data),
       selector_list = selector_list
     )