Merge pull request #2 from Boehringer-Ingelheim/rc/v0.0.5

Release candidate v0.0.5

DESCRIPTION

@@ -1,7 +1,7 @@
-Package: dv.biomarker.general
+Package: dv.explorer.parameter
 Type: Package
-Title: Biomarker Visualization Modules
-Version: 0.0.4-900
+Title: Parameter exploration modules
+Version: 0.0.5
 Authors@R: c(
         person("Boehringer-Ingelheim Pharma GmbH & Co.KG", role = c("cph", "fnd")),
         person(given = "Luis", family = "Moris Fernandez", role = c("aut", "cre"), email = "[email protected]"),

NEWS.md

@@ -1,3 +1,9 @@
+# dv.explorer.parameter 0.0.5
+
+* First Github release
+* Renamed to dv.explorer.parameter
+
+
 # dv.biomarker.general 0.0.4
 
 * Correlation heatmap:

R/archived/mock_volcano.Rback

@@ -34,7 +34,7 @@ mock_app_volcano <- function(in_fluid = TRUE, defaults = list()) {
 
 mock_app_volcano_mm <- function() {
   module_list <- list(
-    "Volcano" = dv.biomarker.general::mod_volcano(
+    "Volcano" = dv.explorer.parameter::mod_volcano(
       module_id = "vp",
       bm_disp = dv.manager::mm_dispatch("filtered_dataset", "bm"),
       group_disp = dv.manager::mm_dispatch("filtered_dataset", "sl"),

R/imod_bar_plot_d3.R

@@ -330,7 +330,7 @@ bar_D3 <- function(data, # nolintr
 
   r2d3::r2d3(
     data = data,
-    script = system.file("www/dist/d3_barplot.js", package = "dv.biomarker.general", mustWork = TRUE),
+    script = system.file("www/dist/d3_barplot.js", package = "dv.explorer.parameter", mustWork = TRUE),
     options = list(
       parent = parent_id,
       x_axis = x_axis, y_axis = y_axis, z_axis = z_axis,

R/imod_heatmap_plot_d3.R

@@ -344,7 +344,7 @@ heatmap_plot_d3 <- function(data,
 
   r2d3::r2d3(
     data = data,
-    script = system.file("www/dist/d3_heatmap.js", package = "dv.biomarker.general", mustWork = TRUE),
+    script = system.file("www/dist/d3_heatmap.js", package = "dv.explorer.parameter", mustWork = TRUE),
     options = list(
       parent = parent_id,
       x_axis = x_axis, y_axis = y_axis, z_axis = z_axis,

R/mock_boxplot.R

@@ -67,7 +67,7 @@ mock_app_boxplot_mm <- function(update_query_string = TRUE) {
         bm_dataset_disp = dv.manager::mm_dispatch("filtered_dataset", "bm"),
         group_dataset_disp = dv.manager::mm_dispatch("filtered_dataset", "adsl"),
         visit_var = "VISIT",
-        value_var = c("VALUE1", "VALUE2"),
+        value_vars = c("VALUE1", "VALUE2"),
         subjid_var = "SUBJID",
         cat_var = "PARCAT"
       )

R/mock_corr_hm.R

@@ -52,7 +52,7 @@ mock_app_correlation_hm_mm <- function() {
   }
 
   module_list <- list(
-    "correlation heatmap" = dv.biomarker.general::mod_corr_hm(
+    "correlation heatmap" = dv.explorer.parameter::mod_corr_hm(
       module_id = "corr_hm",
       bm_dataset_disp = dv.manager::mm_dispatch("filtered_dataset", "bm"),
       visit_var = "VISIT",
@@ -78,7 +78,7 @@ mock_app_correlation_hm_mm_safetyData <- function() { # nolint
   }
 
   module_list <- list(
-    "correlation heatmap" = dv.biomarker.general::mod_corr_hm(
+    "correlation heatmap" = dv.explorer.parameter::mod_corr_hm(
       module_id = "corr_hm",
       bm_dataset_disp = dv.manager::mm_dispatch("filtered_dataset", "bm"),
       visit_var = "VISIT",

R/mock_forest.R

@@ -66,7 +66,7 @@ mock_app_forest_mm <- function() {
   numeric_factor_functions <- list("Odds Ratio" = odds_ratio)
 
   module_list <- list(
-    "forest" = dv.biomarker.general::mod_forest(
+    "forest" = dv.explorer.parameter::mod_forest(
       module_id = "forest",
       bm_dataset_disp = dv.manager::mm_dispatch("filtered_dataset", "bm"),
       group_dataset_disp = dv.manager::mm_dispatch("filtered_dataset", "sl"),

R/mock_lineplot.R

@@ -132,7 +132,7 @@ mock_app_lineplot_mm <- function() {
     stop("Install dv.manager")
   }
   module_list <- list(
-    "lineplot" = dv.biomarker.general::mod_lineplot(
+    "lineplot" = dv.explorer.parameter::mod_lineplot(
       module_id = "lineplot",
       bm_dataset_disp = dv.manager::mm_dispatch("filtered_dataset", "bm"),
       group_dataset_disp = dv.manager::mm_dispatch("filtered_dataset", "sl"),
@@ -160,7 +160,7 @@ mock_app_lineplot_mm_safetyData <- function() { # nolint
   }
 
   module_list <- list(
-    "lineplot" = dv.biomarker.general::mod_lineplot(
+    "lineplot" = dv.explorer.parameter::mod_lineplot(
       module_id = "lineplot",
       bm_dataset_disp = dv.manager::mm_dispatch("filtered_dataset", "bm"),
       group_dataset_disp = dv.manager::mm_dispatch("filtered_dataset", "sl"),

R/mock_safetyData.R

@@ -9,14 +9,14 @@ safety_data <- function() {
   avisitn_mask <- is.finite(adlb[["AVISITN"]]) & adlb[["AVISITN"]] < 99
   adlb <- adlb[avisitn_mask, ]
 
-  adsl_labels <- dv.biomarker.general::get_lbls_robust(adsl)
-  adlb_labels <- dv.biomarker.general::get_lbls_robust(adlb)
+  adsl_labels <- dv.explorer.parameter::get_lbls_robust(adsl)
+  adlb_labels <- dv.explorer.parameter::get_lbls_robust(adlb)
 
   adsl <- adsl |>
     dplyr::mutate(
       dplyr::across(dplyr::where(is.character), factor)
     ) |>
-    dv.biomarker.general::set_lbls(adsl_labels)
+    dv.explorer.parameter::set_lbls(adsl_labels)
 
   visits_ <- unique(adlb[c("AVISITN", "VISIT")])
   visits <- visits_[order(visits_[["AVISITN"]]), ][["VISIT"]]
@@ -26,7 +26,7 @@ safety_data <- function() {
     dplyr::mutate(
       dplyr::across(dplyr::where(is.character), factor)
     ) |>
-    dv.biomarker.general::set_lbls(adlb_labels)
+    dv.explorer.parameter::set_lbls(adlb_labels)
 
   list(sl = adsl, bm = adlb)
 }

R/mock_scatter.R

@@ -63,7 +63,7 @@ mock_app_scatterplot_mm <- function(in_fluid = TRUE, defaults = list(), update_q
         bm_dataset_disp = dv.manager::mm_dispatch("filtered_dataset", "bm"),
         group_dataset_disp = dv.manager::mm_dispatch("filtered_dataset", "adsl"),
         visit_var = "VISIT",
-        value_var = c("VALUE1", "VALUE2"),
+        value_vars = c("VALUE1", "VALUE2"),
         subjid_var = "SUBJID",
         cat_var = "PARCAT"
       )

R/mock_scatter_matrix.R

@@ -63,7 +63,7 @@ mock_app_scatterplotmatrix_mm <- function(in_fluid = TRUE, defaults = list(), up
         bm_dataset_disp = dv.manager::mm_dispatch("filtered_dataset", "bm"),
         group_dataset_disp = dv.manager::mm_dispatch("filtered_dataset", "adsl"),
         visit_var = "VISIT",
-        value_var = c("VALUE1", "VALUE2"),
+        value_vars = c("VALUE1", "VALUE2"),
         subjid_var = "SUBJID",
         cat_var = "PARCAT"
       )

R/mock_wfphm.R

@@ -24,7 +24,7 @@ mock_wfphm_mm_app <- function() {
           }),
           cat_var = "PARCAT",
           visit_var = "VISIT",
-          value_var = c("VALUE1", "VALUE2"),
+          value_vars = c("VALUE1", "VALUE2"),
           module_id = "mod_WF"
         )
       ),

R/mod_boxplot.R

@@ -718,6 +718,8 @@ boxplot_server <- function(id,
 #'
 #' @param receiver_id Name of the tab containing the receiver module
 #'
+#' @param ... Same set of parameters as [mod_boxplot]
+#'
 #' @keywords main
 #'
 #'

R/mod_corr_hm.R

@@ -693,9 +693,9 @@ corr_hm_server <- function(id,
 
       corr_fun <- NULL
       if (method == CH_ID$CORR_METHOD_PEARSON) {
-        corr_fun <- dv.biomarker.general::pearson_correlation
+        corr_fun <- dv.explorer.parameter::pearson_correlation
       } else {
-        if (method == CH_ID$CORR_METHOD_SPEARMAN) corr_fun <- dv.biomarker.general::spearman_correlation
+        if (method == CH_ID$CORR_METHOD_SPEARMAN) corr_fun <- dv.explorer.parameter::spearman_correlation
       }
       shiny::req(corr_fun)
       corr_fun <- corr_fun

R/mod_forest.R

@@ -505,9 +505,9 @@ gen_result_table_fun <- strict(gen_result_table_fun_)
 #' The values returned by the functions are be captured on the output table and are also displayed
 #' as part of the forest plot.
 #'
-#' `numeric_numeric_functions` take two numeric parameters (e.g. `dv.biomarker.general::pearson_correlation`)
+#' `numeric_numeric_functions` take two numeric parameters (e.g. `dv.explorer.parameter::pearson_correlation`)
 #' and `numeric_factor_functions` should accept a numeric first parameter and a categorical (factor) second parameter
-#' (e.g. `dv.biomarker.general::odds_ratio`).
+#' (e.g. `dv.explorer.parameter::odds_ratio`).
 #'
 #' @param subjid_var `[character(1)]`
 #'

R/mod_lineplot.R

@@ -1401,9 +1401,6 @@ lineplot_server <- function(id, # nolint cyclomatic
 #' Name of the module receiving the selected subject ID in the single subject listing. The name must be present in
 #' the module list or NULL.
 #'
-#' @param ...
-#'
-#' Parameters passed to [lineplot_server]
 #'
 #' @name mod_lineplot
 #'

R/mod_roc.R

@@ -4,7 +4,7 @@
 poc <- pack_of_constants
 
 # nocov start
-# dv.biomarker.general
+# dv.explorer.parameter
 
 # IDs
 
@@ -1198,7 +1198,7 @@ test_one_cat_per_par <- function(ds, cat_col, par_col) {
 #'
 #' @description
 #'
-#' This functions prepares the basic input for the rest of dv.biomarker.general functions.
+#' This functions prepares the basic input for the rest of dv.explorer.parameter functions.
 #'
 #'
 #' It subsets and joins the datasets based on the predictor/response category/parameter/visit and group selections.
@@ -4214,9 +4214,9 @@ parse_ci <- function(str) {
 
 roc_dependencies <- function() {
   htmltools::htmlDependency(
-    name = "dv.biomarker.general",
+    name = "dv.explorer.parameter",
     version = "1.0",
-    package = "dv.biomarker.general",
+    package = "dv.explorer.parameter",
     src = "assets",
     stylesheet = "css/roc.css",
     all_files = FALSE
@@ -4619,7 +4619,7 @@ mock_roc_mm_app <- function(adbm = test_roc_data()[["adbm"]],
         )
       ),
       module_list = list(
-        "ROC" = dv.biomarker.general::mod_roc(
+        "ROC" = dv.explorer.parameter::mod_roc(
           module_id = "mod_roc",
           pred_dataset_name = "adbm",
           resp_dataset_disp = dv.manager::mm_dispatch("filtered_dataset", "adbin"),
@@ -4641,12 +4641,12 @@ mock_roc_mm_app <- function(adbm = test_roc_data()[["adbm"]],
 mock_roc_app <- function() {
   ui <- function(request) {
     shiny::fluidPage(
-      dv.biomarker.general::roc_UI("roc")
+      dv.explorer.parameter::roc_UI("roc")
     )
   }
 
   server <- function(input, output, session) {
-    dv.biomarker.general::roc_server(
+    dv.explorer.parameter::roc_server(
       id = "roc",
       pred_dataset = shiny::reactive(test_roc_data()[["adbm"]]),
       resp_dataset = shiny::reactive(test_roc_data()[["adbin"]]),
@@ -4684,7 +4684,7 @@ mock_roc_app_file_upload <- function() {
         multiple = FALSE,
         accept = c(".rda")
       ),
-      dv.biomarker.general::roc_UI("roc")
+      dv.explorer.parameter::roc_UI("roc")
     )
   }
 
@@ -4719,7 +4719,7 @@ mock_roc_app_file_upload <- function() {
       proceed(shiny::isolate(proceed() + 1))
     })
 
-    dv.biomarker.general::roc_server(
+    dv.explorer.parameter::roc_server(
       id = "roc",
       dataset_name = shiny::reactive(proceed()),
       pred_dataset = adbm,

R/mod_wfphm.R

@@ -2263,8 +2263,6 @@ tr_mapper_def <- function() {
 #' Dataset dispatcher. This parameter is incompatible with its `bm_dataset_name`/`group_dataset_name` counterpart.
 #' Only for advanced use.
 #'
-#' @param dataset_disp DEPRECATED
-#'
 #' @export
 mod_wfphm <- function(
     module_id, bm_dataset_name, group_dataset_name,

R/utils-selectors.R

@@ -404,7 +404,7 @@ add_warning_mark_dependency <- function() {
   htmltools::htmlDependency(
     "warning_mark_lib",
     "0.1",
-    src = system.file("warning_mark_lib", package = "dv.biomarker.general", mustWork = TRUE),
+    src = system.file("warning_mark_lib", package = "dv.explorer.parameter", mustWork = TRUE),
     script = "warning_mark.js",
     stylesheet = "warning_mark.css"
   )
@@ -414,7 +414,7 @@ add_top_menu_dependency <- function() {
   htmltools::htmlDependency(
     "top_menu",
     "0.1",
-    src = system.file("assets/css", package = "dv.biomarker.general", mustWork = TRUE),
+    src = system.file("assets/css", package = "dv.explorer.parameter", mustWork = TRUE),
     stylesheet = "top_menu.css"
   )
 }

R/html_dependencies.R → R/utils_html_dependencies.R

@@ -4,7 +4,7 @@ ebas_sel_css_dep <- function() {
   htmltools::htmlDependency(
     name = "ebas_sel",
     version = "1.0",
-    src = system.file("www/css", package = "dv.biomarker.general", mustWork = TRUE),
+    src = system.file("www/css", package = "dv.explorer.parameter", mustWork = TRUE),
     stylesheet = "ebas_sel.css"
   )
 }
@@ -14,7 +14,7 @@ dvd3h_dep <- function() {
   htmltools::htmlDependency(
     name = "dvd3h",
     version = "1.0",
-    src = system.file("www/dist", package = "dv.biomarker.general", mustWork = TRUE),
+    src = system.file("www/dist", package = "dv.explorer.parameter", mustWork = TRUE),
     script = "dv_d3_helpers.js"
   )
 }
@@ -25,8 +25,20 @@ screenshot_deps <- function() {
     htmltools::htmlDependency(
       name = "wfphm-msg-handlers",
       version = "1.0",
-      src = system.file("www/msg-handlers", package = "dv.biomarker.general", mustWork = TRUE),
+      src = system.file("www/msg-handlers", package = "dv.explorer.parameter", mustWork = TRUE),
       script = "msg-handlers.js"
     )
   )
 }
+
+#' @keywords intermal
+roc_dependencies <- function() {
+  htmltools::htmlDependency(
+    name = "dv.explorer.parameter",
+    version = "1.0",
+    package = "dv.explorer.parameter",
+    src = "assets",
+    stylesheet = "css/bp.css",
+    all_files = FALSE
+  )
+}

README.md

@@ -1,9 +1,9 @@
-# dv.biomarker.general
+# dv.explorer.parameter
 
 # Installation
 
 ``` r
 if (!require("remotes")) install.packages("remotes")
-remotes::install_github("Boehringer-Ingelheim/dv.biomarker.general")
+remotes::install_github("Boehringer-Ingelheim/dv.explorer.parameter")
 ```
 

inst/validation/utils-validation.R

@@ -93,7 +93,7 @@ local({
   list(
     specs = specs,
     spec_id_list = spec_id_list,
-    add_spec = function(desc, spec, spec_id) {      
+    add_spec = function(desc, spec, spec_id) {
       if (missing(spec_id)) {
         if (!is.character(spec) || length(spec) == 0) stop("spec must be a non-empty character vector")
         s_spec <- substitute(spec)