adding code for reproducibility and updated news

insightsengineering · Nov 8, 2023 · 2bfb054 · 2bfb054
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diff --git a/NEWS.md b/NEWS.md
@@ -13,7 +13,7 @@
 * 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
+#' data@join_keys <- cdisc_join_keys(!!!datanames)
 #'
 #' app <- init(
-#'   data = cdisc_data(
-#'     ADSL = adsl,
-#'     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 = get_join_keys(data)
+      join_keys = teal.data::get_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 = get_join_keys(data)
+      join_keys = teal.data::get_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
+#' data@join_keys <- cdisc_join_keys(!!!datanames)
 #' app <- init(
-#'   data = cdisc_data(
-#'     ADSL = adsl,
-#'     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 = get_join_keys(data),
+      join_keys = teal.data::get_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 = get_join_keys(data),
+      join_keys = teal.data::get_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 +16,17 @@
 #' @examples
 #' library(nestcolor)
 #'
-#' adsl <- tmc_ex_adsl %>% dplyr::mutate(ITTFL = factor("Y") %>%
+#' 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")))
+#' ADAE <- tmc_ex_adae %>% dplyr::filter(!((AETOXGR == 1) & (AESEV == "MILD") & (ARM == "A: Drug X")))
 #'
 #' app <- init(
 #'   data = cdisc_data(
-#'     ADSL = adsl,
-#'     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 +35,7 @@
 #'         dataname = "ADSL",
 #'         select = select_spec(
 #'           choices = variable_choices(
-#'             adsl,
+#'             ADSL,
 #'             c(
 #'               "ARM", "ACTARM", "SEX",
 #'               "RACE", "ITTFL", "SAFFL", "STRATA2"
@@ -47,7 +50,7 @@
 #'           dataname = "ADSL",
 #'           select = select_spec(
 #'             choices = variable_choices(
-#'               adsl,
+#'               ADSL,
 #'               c(
 #'                 "ARM", "ACTARM", "SEX",
 #'                 "RACE", "ITTFL", "SAFFL", "STRATA2"
@@ -60,7 +63,7 @@
 #'         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 +73,7 @@
 #'         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 +82,7 @@
 #'           dataname = "ADSL",
 #'           select = select_spec(
 #'             choices = variable_choices(
-#'               adsl,
+#'               ADSL,
 #'               c(
 #'                 "ARM", "ACTARM", "SEX",
 #'                 "RACE", "ITTFL", "SAFFL", "STRATA2"
@@ -94,7 +97,7 @@
 #'         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 +106,7 @@
 #'           dataname = "ADSL",
 #'           select = select_spec(
 #'             choices = variable_choices(
-#'               adsl,
+#'               ADSL,
 #'               c(
 #'                 "ARM", "ACTARM", "SEX",
 #'                 "RACE", "ITTFL", "SAFFL", "STRATA2"
@@ -374,7 +377,7 @@ srv_g_barchart_simple <- function(id,
 
     anl_inputs <- teal.transform::merge_expression_srv(
       datasets = data,
-      join_keys = get_join_keys(data),
+      join_keys = teal.data::get_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(
-#'     ADSL = adsl,
-#'     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 = get_join_keys(data),
+      join_keys = teal.data::get_join_keys(data),
       selector_list = selector_list
     )
 

diff --git a/R/tm_g_forest_rsp.R b/R/tm_g_forest_rsp.R
@@ -217,8 +217,8 @@ template_forest_rsp <- function(dataname = "ANL",
 #' @examples
 #' library(nestcolor)
 #'
-#' adsl <- tmc_ex_adsl
-#' adrs <- tmc_ex_adrs %>%
+#' ADSL <- tmc_ex_adsl
+#' ADRS <- tmc_ex_adrs %>%
 #'   dplyr::mutate(AVALC = tern::d_onco_rsp_label(AVALC) %>%
 #'     formatters::with_label("Character Result/Finding")) %>%
 #'   dplyr::filter(PARAMCD != "OVRINV" | AVISIT == "FOLLOW UP")
@@ -236,28 +236,35 @@ template_forest_rsp <- function(dataname = "ANL",
 #'
 #' app <- init(
 #'   data = cdisc_data(
-#'     ADSL = adsl,
-#'     ADRS = adrs
+#'     ADSL = ADSL,
+#'     ADRS = ADRS,
+#'     code = "
+#'       ADSL <- tmc_ex_adsl
+#'       ADRS <- tmc_ex_adrs %>%
+#'         dplyr::mutate(AVALC = tern::d_onco_rsp_label(AVALC) %>%
+#'           formatters::with_label(\"Character Result/Finding\")) %>%
+#'         dplyr::filter(PARAMCD != \"OVRINV\" | AVISIT == \"FOLLOW UP\")
+#'     "
 #'   ),
 #'   modules = modules(
 #'     tm_g_forest_rsp(
 #'       label = "Forest Response",
 #'       dataname = "ADRS",
 #'       arm_var = choices_selected(
-#'         variable_choices(adsl, c("ARM", "ARMCD")),
+#'         variable_choices(ADSL, c("ARM", "ARMCD")),
 #'         "ARMCD"
 #'       ),
 #'       arm_ref_comp = arm_ref_comp,
 #'       paramcd = choices_selected(
-#'         value_choices(adrs, "PARAMCD", "PARAM"),
+#'         value_choices(ADRS, "PARAMCD", "PARAM"),
 #'         "INVET"
 #'       ),
 #'       subgroup_var = choices_selected(
-#'         variable_choices(adsl, names(adsl)),
+#'         variable_choices(ADSL, names(ADSL)),
 #'         c("BMRKR2", "SEX")
 #'       ),
 #'       strata_var = choices_selected(
-#'         variable_choices(adsl, c("STRATA1", "STRATA2")),
+#'         variable_choices(ADSL, c("STRATA1", "STRATA2")),
 #'         "STRATA2"
 #'       ),
 #'       plot_height = c(600L, 200L, 2000L),
@@ -514,13 +521,13 @@ srv_g_forest_rsp <- function(id,
       datasets = data,
       selector_list = selector_list,
       merge_function = "dplyr::inner_join",
-      join_keys = get_join_keys(data)
+      join_keys = teal.data::get_join_keys(data)
     )
 
     adsl_inputs <- teal.transform::merge_expression_module(
       datasets = data,
       data_extract = list(arm_var = arm_var, subgroup_var = subgroup_var, strata_var = strata_var),
-      join_keys = get_join_keys(data),
+      join_keys = teal.data::get_join_keys(data),
       anl_name = "ANL_ADSL"
     )