options for strict tests; few enhancements

insightsengineering · Jan 24, 2024 · a6b690f · a6b690f
1 parent 6e1a17d
commit a6b690f
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diff --git a/.lintr b/.lintr
@@ -4,3 +4,35 @@ linters: linters_with_defaults(
   object_usage_linter = NULL,
   indentation_linter = NULL
   )
+exclusions: list(
+    "vignettes/teal-modules-general.Rmd" = list(
+      object_name_linter = Inf
+    ),
+    "vignettes/using-association-plot.Rmd" = list(
+      object_name_linter = Inf
+    ),
+    "vignettes/using-bivariate-plot.Rmd" = list(
+      object_name_linter = Inf
+    ),
+    "vignettes/using-cross-table.Rmd" = list(
+      object_name_linter = Inf
+    ),
+    "vignettes/using-data-table.Rmd" = list(
+      object_name_linter = Inf
+    ),
+    "vignettes/using-outliers-module.Rmd" = list(
+      object_name_linter = Inf
+    ),
+    "vignettes/using-regression-plots.Rmd" = list(
+      object_name_linter = Inf
+    ),
+    "vignettes/using-response-plot.Rmd" = list(
+      object_name_linter = Inf
+    ),
+    "vignettes/using-scatterplot-matrix.Rmd" = list(
+      object_name_linter = Inf
+    ),
+    "vignettes/using-scatterplot.Rmd" = list(
+      object_name_linter = Inf
+    )
+  )
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -65,26 +65,27 @@ Suggests:
     rtables (>= 0.5.1),
     sparkline,
     teal.data (>= 0.3.0.9018),
-    testthat (>= 3.0.4)
+    testthat (>= 3.0.4),
+    withr (>= 2.0.0)
 VignetteBuilder:
     knitr
 Config/Needs/verdepcheck: haleyjeppson/ggmosaic, tidyverse/ggplot2,
-    rstudio/shiny, shinyTree/shinyTree, insightsengineering/teal,
+    rstudio/shiny, shinyTree/shinyTree, insightsengineering/teal, insightsengineering/teal.transform,
     mllg/checkmate, tidyverse/dplyr, rstudio/DT, tidyverse/forcats,
     daroczig/logger, tidyverse/magrittr, r-lib/scales, daattali/shinyjs,
     rstudio/shinyvalidate, dreamRs/shinyWidgets, tidyverse/stringr,
     insightsengineering/teal.code, insightsengineering/teal.logger,
-    insightsengineering/teal.reporter, insightsengineering/teal.transform,
+    insightsengineering/teal.reporter,
     insightsengineering/teal.widgets, insightsengineering/tern,
     tidyverse/tibble, tidyverse/tidyr, r-lib/tidyselect, tidymodels/broom,
     daattali/colourpicker, daattali/ggExtra, aphalo/ggpmisc, aphalo/ggpp,
     baddstats/goftest, gridExtra, ramnathv/htmlwidgets, jeroen/jsonlite,
     yihui/knitr, deepayan/lattice, MASS, insightsengineering/nestcolor,
     r-lib/rlang, insightsengineering/rtables, sparkline,
-    insightsengineering/teal.data, r-lib/testthat
+    insightsengineering/teal.data, r-lib/testthat, r-lib/withr
 Config/Needs/website: insightsengineering/nesttemplate
 Encoding: UTF-8
 Language: en-US
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.0
diff --git a/R/teal.modules.general.R b/R/teal.modules.general.R
@@ -12,10 +12,8 @@
 #' @importFrom magrittr %>%
 #'
 #'
-#' @docType package
-#' @name teal.modules.general
 #' @keywords internal
-NULL
+"_PACKAGE"
 
 # nolint start
 # Note ggmosaic (version <= 0.3.3) needs to be in DEPENDS as the following does not work if it is imported

diff --git a/R/tm_a_pca.R b/R/tm_a_pca.R
@@ -21,26 +21,26 @@
 #' @export
 #'
 #' @examples
-#'
 #' # ADSL example
 #'
 #' data <- teal_data()
 #' data <- within(data, {
 #'   library(nestcolor)
-#'   ADSL <- teal.modules.general::rADSL
+#'   ADSL <- rADSL
 #' })
 #' datanames <- c("ADSL")
 #' datanames(data) <- datanames
 #' join_keys(data) <- default_cdisc_join_keys[datanames]
-#' app <- teal::init(
+#'
+#' app <- init(
 #'   data = data,
-#'   modules = teal::modules(
-#'     teal.modules.general::tm_a_pca(
+#'   modules = modules(
+#'     tm_a_pca(
 #'       "PCA",
-#'       dat = teal.transform::data_extract_spec(
+#'       dat = data_extract_spec(
 #'         dataname = "ADSL",
-#'         select = teal.transform::select_spec(
-#'           choices = teal.transform::variable_choices(
+#'         select = select_spec(
+#'           choices = variable_choices(
 #'             data = data[["ADSL"]], c("BMRKR1", "AGE", "EOSDY")
 #'           ),
 #'           selected = c("BMRKR1", "AGE"),

diff --git a/R/tm_a_regression.R b/R/tm_a_regression.R
@@ -37,32 +37,32 @@
 #' data <- teal_data()
 #' data <- within(data, {
 #'   library(nestcolor)
-#'   ADSL <- teal.modules.general::rADSL
+#'   ADSL <- rADSL
 #' })
 #' datanames <- c("ADSL")
 #' datanames(data) <- datanames
 #' join_keys(data) <- default_cdisc_join_keys[datanames]
 #'
-#' app <- teal::init(
+#' app <- init(
 #'   data = data,
-#'   modules = teal::modules(
-#'     teal.modules.general::tm_a_regression(
+#'   modules = modules(
+#'     tm_a_regression(
 #'       label = "Regression",
-#'       response = teal.transform::data_extract_spec(
+#'       response = data_extract_spec(
 #'         dataname = "ADSL",
-#'         select = teal.transform::select_spec(
+#'         select = select_spec(
 #'           label = "Select variable:",
 #'           choices = "BMRKR1",
 #'           selected = "BMRKR1",
 #'           multiple = FALSE,
 #'           fixed = TRUE
 #'         )
 #'       ),
-#'       regressor = teal.transform::data_extract_spec(
+#'       regressor = data_extract_spec(
 #'         dataname = "ADSL",
-#'         select = teal.transform::select_spec(
+#'         select = select_spec(
 #'           label = "Select variables:",
-#'           choices = teal.transform::variable_choices(data[["ADSL"]], c("AGE", "SEX", "RACE")),
+#'           choices = variable_choices(data[["ADSL"]], c("AGE", "SEX", "RACE")),
 #'           selected = "AGE",
 #'           multiple = TRUE,
 #'           fixed = FALSE

diff --git a/R/tm_data_table.R b/R/tm_data_table.R
@@ -27,20 +27,19 @@
 #'   Note though that sorting of numeric columns with `NA`/`Inf` will be lexicographic not numerical.
 #' @export
 #' @examples
-#'
 #' data <- teal_data()
 #' data <- within(data, {
 #'   library(nestcolor)
-#'   ADSL <- teal.modules.general::rADSL
+#'   ADSL <- rADSL
 #' })
 #' datanames <- c("ADSL")
 #' datanames(data) <- datanames
 #' join_keys(data) <- default_cdisc_join_keys[datanames]
 #'
-#' app <- teal::init(
+#' app <- init(
 #'   data = data,
-#'   modules = teal::modules(
-#'     teal.modules.general::tm_data_table(
+#'   modules = modules(
+#'     tm_data_table(
 #'       variables_selected = list(ADSL = c("STUDYID", "USUBJID", "SUBJID", "SITEID", "AGE", "SEX")),
 #'       dt_args = list(caption = "ADSL Table Caption")
 #'     )

diff --git a/R/tm_file_viewer.R b/R/tm_file_viewer.R
@@ -19,10 +19,10 @@
 #' })
 #' datanames(data) <- c("data")
 #'
-#' app <- teal::init(
+#' app <- init(
 #'   data = data,
-#'   modules = teal::modules(
-#'     teal.modules.general::tm_file_viewer(
+#'   modules = modules(
+#'     tm_file_viewer(
 #'       input_path = list(
 #'         folder = system.file("sample_files", package = "teal.modules.general"),
 #'         png = system.file("sample_files/sample_file.png", package = "teal.modules.general"),

diff --git a/R/tm_front_page.R b/R/tm_front_page.R
@@ -16,11 +16,10 @@
 #' @return A `teal` module to be used in `teal` applications
 #' @export
 #' @examples
-#'
 #' data <- teal_data()
 #' data <- within(data, {
 #'   library(nestcolor)
-#'   ADSL <- teal.modules.general::rADSL
+#'   ADSL <- rADSL
 #'   attr(ADSL, "metadata") <- list("Author" = "NEST team", "data_source" = "synthetic data")
 #' })
 #' datanames <- c("ADSL")
@@ -37,10 +36,10 @@
 #'   "Table 3" = table_3
 #' )
 #'
-#' app <- teal::init(
+#' app <- init(
 #'   data = data,
-#'   modules = teal::modules(
-#'     teal.modules.general::tm_front_page(
+#'   modules = modules(
+#'     tm_front_page(
 #'       header_text = c(
 #'         "Important information" = "It can go here.",
 #'         "Other information" = "Can go here."

diff --git a/R/tm_g_association.R b/R/tm_g_association.R
@@ -28,33 +28,33 @@
 #' data <- teal_data()
 #' data <- within(data, {
 #'   library(nestcolor)
-#'   ADSL <- teal.modules.general::rADSL
+#'   ADSL <- rADSL
 #' })
 #' datanames <- c("ADSL")
 #' datanames(data) <- datanames
 #' join_keys(data) <- default_cdisc_join_keys[datanames]
 #'
-#' app <- teal::init(
+#' app <- init(
 #'   data = data,
-#'   modules = teal::modules(
-#'     teal.modules.general::tm_g_association(
-#'       ref = teal.transform::data_extract_spec(
+#'   modules = modules(
+#'     tm_g_association(
+#'       ref = data_extract_spec(
 #'         dataname = "ADSL",
-#'         select = teal.transform::select_spec(
+#'         select = select_spec(
 #'           label = "Select variable:",
-#'           choices = teal.transform::variable_choices(
+#'           choices = variable_choices(
 #'             data[["ADSL"]],
 #'             c("SEX", "RACE", "COUNTRY", "ARM", "STRATA1", "STRATA2", "ITTFL", "BMRKR2")
 #'           ),
 #'           selected = "RACE",
 #'           fixed = FALSE
 #'         )
 #'       ),
-#'       vars = teal.transform::data_extract_spec(
+#'       vars = data_extract_spec(
 #'         dataname = "ADSL",
-#'         select = teal.transform::select_spec(
+#'         select = select_spec(
 #'           label = "Select variables:",
-#'           choices = teal.transform::variable_choices(
+#'           choices = variable_choices(
 #'             data[["ADSL"]],
 #'             c("SEX", "RACE", "COUNTRY", "ARM", "STRATA1", "STRATA2", "ITTFL", "BMRKR2")
 #'           ),

diff --git a/R/tm_g_bivariate.R b/R/tm_g_bivariate.R
@@ -48,49 +48,49 @@
 #' data <- teal_data()
 #' data <- within(data, {
 #'   library(nestcolor)
-#'   ADSL <- teal.modules.general::rADSL
+#'   ADSL <- rADSL
 #' })
 #' datanames <- c("ADSL")
 #' datanames(data) <- datanames
 #' join_keys(data) <- default_cdisc_join_keys[datanames]
 #'
-#' app <- teal::init(
+#' app <- init(
 #'   data = data,
-#'   modules = teal::modules(
-#'     teal.modules.general::tm_g_bivariate(
-#'       x = teal.transform::data_extract_spec(
+#'   modules = modules(
+#'     tm_g_bivariate(
+#'       x = data_extract_spec(
 #'         dataname = "ADSL",
-#'         select = teal.transform::select_spec(
+#'         select = select_spec(
 #'           label = "Select variable:",
-#'           choices = teal.transform::variable_choices(data[["ADSL"]]),
+#'           choices = variable_choices(data[["ADSL"]]),
 #'           selected = "AGE",
 #'           fixed = FALSE
 #'         )
 #'       ),
-#'       y = teal.transform::data_extract_spec(
+#'       y = data_extract_spec(
 #'         dataname = "ADSL",
-#'         select = teal.transform::select_spec(
+#'         select = select_spec(
 #'           label = "Select variable:",
-#'           choices = teal.transform::variable_choices(data[["ADSL"]]),
+#'           choices = variable_choices(data[["ADSL"]]),
 #'           selected = "SEX",
 #'           multiple = FALSE,
 #'           fixed = FALSE
 #'         )
 #'       ),
-#'       row_facet = teal.transform::data_extract_spec(
+#'       row_facet = data_extract_spec(
 #'         dataname = "ADSL",
-#'         select = teal.transform::select_spec(
+#'         select = select_spec(
 #'           label = "Select variable:",
-#'           choices = teal.transform::variable_choices(data[["ADSL"]]),
+#'           choices = variable_choices(data[["ADSL"]]),
 #'           selected = "ARM",
 #'           fixed = FALSE
 #'         )
 #'       ),
-#'       col_facet = teal.transform::data_extract_spec(
+#'       col_facet = data_extract_spec(
 #'         dataname = "ADSL",
-#'         select = teal.transform::select_spec(
+#'         select = select_spec(
 #'           label = "Select variable:",
-#'           choices = teal.transform::variable_choices(data[["ADSL"]]),
+#'           choices = variable_choices(data[["ADSL"]]),
 #'           selected = "COUNTRY",
 #'           fixed = FALSE
 #'         )
@@ -652,7 +652,6 @@ srv_g_bivariate <- function(id,
 #' @noRd
 #'
 #' @examples
-#'
 #' bivariate_plot_call("ANL", "BAGE", "RACE", "numeric", "factor")
 #' bivariate_plot_call("ANL", "BAGE", character(0), "numeric", "NULL")
 bivariate_plot_call <- function(data_name,
@@ -922,7 +921,6 @@ bivariate_ggplot_call <- function(x_class = c("NULL", "numeric", "integer", "fac
 #' @noRd
 #'
 #' @examples
-#'
 #' facet_ggplot_call(LETTERS[1:3])
 #' facet_ggplot_call(NULL, LETTERS[23:26])
 #' facet_ggplot_call(LETTERS[1:3], LETTERS[23:26])