diff --git a/DESCRIPTION b/DESCRIPTION index b9cbdef..9733733 100644 --- a/DESCRIPTION +++ b/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 = "luis.moris.fernandez@gmail.com"), diff --git a/NEWS.md b/NEWS.md index 53548da..b1df3c5 100644 --- a/NEWS.md +++ b/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: diff --git a/R/archived/mock_volcano.Rback b/R/archived/mock_volcano.Rback index 6fe8b07..6a610a2 100644 --- a/R/archived/mock_volcano.Rback +++ b/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"), diff --git a/R/html_deps.R b/R/html_deps.R deleted file mode 100644 index 931de11..0000000 --- a/R/html_deps.R +++ /dev/null @@ -1,10 +0,0 @@ -roc_dependencies <- function() { - htmltools::htmlDependency( - name = "dv.biomarker.general", - version = "1.0", - package = "dv.biomarker.general", - src = "assets", - stylesheet = "css/bp.css", - all_files = FALSE - ) -} diff --git a/R/imod_bar_plot_d3.R b/R/imod_bar_plot_d3.R index 586ef3a..0c7ad03 100644 --- a/R/imod_bar_plot_d3.R +++ b/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, diff --git a/R/imod_heatmap_plot_d3.R b/R/imod_heatmap_plot_d3.R index bad27e8..cb97b32 100644 --- a/R/imod_heatmap_plot_d3.R +++ b/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, diff --git a/R/mock_boxplot.R b/R/mock_boxplot.R index d0fb2c8..08b5d5c 100644 --- a/R/mock_boxplot.R +++ b/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" ) diff --git a/R/mock_corr_hm.R b/R/mock_corr_hm.R index 2d9972a..20b0b04 100644 --- a/R/mock_corr_hm.R +++ b/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", diff --git a/R/mock_forest.R b/R/mock_forest.R index 1ff8c48..d0a0ab2 100644 --- a/R/mock_forest.R +++ b/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"), diff --git a/R/mock_lineplot.R b/R/mock_lineplot.R index 202d593..f3b21ce 100644 --- a/R/mock_lineplot.R +++ b/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"), diff --git a/R/mock_safetyData.R b/R/mock_safetyData.R index c009826..293afee 100644 --- a/R/mock_safetyData.R +++ b/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) } diff --git a/R/mock_scatter.R b/R/mock_scatter.R index 53730e0..b7426da 100644 --- a/R/mock_scatter.R +++ b/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" ) diff --git a/R/mock_scatter_matrix.R b/R/mock_scatter_matrix.R index 278c783..0b7ee29 100644 --- a/R/mock_scatter_matrix.R +++ b/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" ) diff --git a/R/mock_wfphm.R b/R/mock_wfphm.R index e8fb34d..0ed1897 100644 --- a/R/mock_wfphm.R +++ b/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" ) ), diff --git a/R/mod_boxplot.R b/R/mod_boxplot.R index b44b0e4..7acc3f0 100644 --- a/R/mod_boxplot.R +++ b/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 #' #' diff --git a/R/mod_corr_hm.R b/R/mod_corr_hm.R index 346c254..cdf3391 100644 --- a/R/mod_corr_hm.R +++ b/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 diff --git a/R/mod_forest.R b/R/mod_forest.R index 63c257b..f335d0e 100644 --- a/R/mod_forest.R +++ b/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)]` #' diff --git a/R/mod_lineplot.R b/R/mod_lineplot.R index abbadbe..ba6cfc9 100644 --- a/R/mod_lineplot.R +++ b/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 #' diff --git a/R/mod_roc.R b/R/mod_roc.R index e13ef1e..d0a53ef 100644 --- a/R/mod_roc.R +++ b/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, diff --git a/R/mod_wfphm.R b/R/mod_wfphm.R index b5a5570..f848ec8 100644 --- a/R/mod_wfphm.R +++ b/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, diff --git a/R/utils-selectors.R b/R/utils-selectors.R index 328a7ae..a6b4291 100644 --- a/R/utils-selectors.R +++ b/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" ) } diff --git a/R/html_dependencies.R b/R/utils_html_dependencies.R similarity index 50% rename from R/html_dependencies.R rename to R/utils_html_dependencies.R index 4f3df39..e2ef047 100644 --- a/R/html_dependencies.R +++ b/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 + ) +} diff --git a/README.md b/README.md index dfac930..eea8139 100644 --- a/README.md +++ b/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") ``` diff --git a/inst/validation/results/val_param.rds b/inst/validation/results/val_param.rds deleted file mode 100644 index 8fa38e1..0000000 Binary files a/inst/validation/results/val_param.rds and /dev/null differ diff --git a/inst/validation/results/val_report.html b/inst/validation/results/val_report.html deleted file mode 100644 index a45caaa..0000000 --- a/inst/validation/results/val_report.html +++ /dev/null @@ -1,3729 +0,0 @@ - - - - - - - - - - - - - -Quality Control - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
- - - - - - -
-


-Index

- -
- - -
# Import vdoc functions ----
-vdoc <- local({
-  #                      ##########
-  # package_name is used # INSIDE # the sourced file below
-  #                      ##########  
-  package_name <- params[["package"]]
-  utils_file_path <- system.file("validation", "utils-validation.R", package = package_name, mustWork = TRUE)
-  source(utils_file_path, local = TRUE)[["value"]]
-})
-
-# Set required packages ----
-suppressPackageStartupMessages(stopifnot(requireNamespace("DT")))
-suppressPackageStartupMessages(stopifnot(requireNamespace("devtools")))
-
-# Parse tests ----
-
-tests <- as.data.frame(params[["tests"]])
-tests[["validation_data"]] <- vdoc[["get_spec"]](tests[["test"]], vdoc[["specs"]])
-tests[["spec_id"]] <- sapply(tests[["validation_data"]], function(x) x[["spec_id"]])
-tests[["spec"]] <- sapply(tests[["validation_data"]], function(x) x[["spec"]])
-tests[["spec_id_paste"]] <- vapply(tests[["spec_id"]], function(x) paste(x, collapse = "\n"), FUN.VALUE = character(1))
-tests[["spec_paste"]] <- vapply(tests[["spec"]], function(x) paste(x, collapse = "\n"), FUN.VALUE = character(1))
-tests[["desc"]] <- paste0("(#", seq_len(nrow(tests)), "): ", tests[["test"]])
-tests[["with_spec"]] <- vapply(tests[["spec_id"]], Negate(is.null), FUN.VALUE = logical(1))
-
-spec_tests <- tests[tests[["with_spec"]], ]
-no_spec_tests <- tests[!tests[["with_spec"]], ]
-
-declared_spec <- vdoc[["spec_id_list"]]
-tested_spec <- unique(unlist(tests[["spec_id"]]))
-uncovered_spec <- declared_spec[!declared_spec %in% tested_spec]
-undeclared_spec <- tested_spec[!tested_spec %in% declared_spec]
-
-spec_tests[["are_declared"]] <- sapply(spec_tests[["spec_id"]], function(x) all(x %in% declared_spec))
-
-# Count tests in the different categories ----
-mask_failed <- !!spec_tests[["failed"]] | spec_tests[["error"]]
-mask_skipped <- !!spec_tests[["skipped"]]
-mask_declared <- spec_tests[["are_declared"]]
-n_pass_dec <- sum(!mask_failed & !mask_skipped & mask_declared)
-n_fail_dec <- sum(mask_failed & mask_declared)
-n_skip_dec <- sum(mask_skipped & mask_declared)
-n_uncov <- length(uncovered_spec)
-n_undec <- sum(!mask_declared)
-
-render_spec_table <- function(t) {
-  t <- t[trac_matrix_col]
-  colnames(t) <- names(trac_matrix_col)
-  t <- t[order(t[["Spec ID"]]), ]
-  DT::datatable(t, options = list(dom = "ltp"), filter = list(position = "top"))
-}
-
-data_frame_by_row <- function(colnames, data) {
-  n <- length(data)
-  n_cols <- length(colnames)
-  stopifnot(n %% n_cols == 0)
-  columns <- vector("list", length = n_cols)
-  for (i in 1:n_cols) columns[[i]] <- unlist(data[seq(i, n, n_cols)])
-  do.call(data.frame, setNames(columns, colnames))
-}
-
-# Select columns to be included in the tables ----
-trac_matrix_col <- c("Spec ID" = "spec_id_paste", "Spec" = "spec_paste", "Test Desc" = "desc", "File" = "file")
-
-# Check that validation passes and set title ----
-VALIDATION_PASSED <- n_fail_dec == 0 && n_uncov == 0 && n_undec == 0 && n_uncov == 0 # nolint
-
-result_symbol <- if (VALIDATION_PASSED) "\U02705" else "\U274C"
-title <- paste(result_symbol, params[["package"]], params[["version"]])
-
-

❌ dv.biomarker.general 0.0.3-140

-

Date: 2024-Jul-29 11:22:07

-

The following document generates a report for R packages, to satisfy -the criteria of a “Released” status under the Non-GxP -project. The QC report contains the following information:

- -
-

Please be advised that the QC report generated for this module does -not imply validation according to any other GxP criteria. The QC report -only satisfies our internally developed quality checks for non-GxP -criteria. For clinical reporting purposes, it is essential to note that -any outputs generated using this module must be checked and verified -within a validated system that adheres to the appropriate GxP -guidelines.

-
-
-
-
-

Traceability matrix

-

In this traceability matrix only those tests that point to an -specification are included.

-

Test cases can contain several expectations a test is considered:

- -

A test can be both failed and -skipped.

-
-

Summary

-
data_frame_by_row(
-  colnames = c("Spec Exists", "Test", "Count", "color"),
-  data = list(
-    "Yes", "Pass", n_pass_dec, "white",
-    "Yes", "Failed", n_fail_dec, if (n_fail_dec > 0) "red" else "green",
-    "Yes", "Skipped", n_skip_dec, if (n_skip_dec > 0) "red" else "green",
-    "Yes", "No Test", n_uncov, if (n_uncov > 0) "red" else "green",
-    "No", "NA", n_undec, if (n_undec > 0) "red" else "green"
-  )
-) |>
-  DT::datatable(
-    rownames = FALSE,
-    options = list(columnDefs = list(list(visible = FALSE, targets = c(3))), dom = "tp"),
-    filter = list(position = "top")
-  ) |>
-  DT::formatStyle(
-    c("Count"),
-    valueColumns = "color",
-    backgroundColor = DT::JS("value")
-  )
-
- -
-
-

Passed tests

-
render_spec_table(spec_tests[!mask_failed & !mask_skipped & mask_declared, ])
-
- -
-
-

Failed tests

-
render_spec_table(spec_tests[mask_failed & mask_declared, ])
-
- -
-
-

Skipped tests

-
render_spec_table(spec_tests[mask_skipped & mask_declared, ])
-
- -
-
-

Uncovered specifications

-
- -
-
-

Undeclared specifications

-

This should always be empty, as non existant specs are controlled -during test execution.

-
- -
-
-
-

Session Info and System Configuration

-
devtools::session_info()
-
## ─ Session info ───────────────────────────────────────────────────────────────
-##  setting  value
-##  version  R version 4.3.2 (2023-10-31)
-##  os       Ubuntu 22.04.3 LTS
-##  system   x86_64, linux-gnu
-##  ui       X11
-##  language (EN)
-##  collate  en_US.UTF-8
-##  ctype    en_US.UTF-8
-##  tz       Etc/UTC
-##  date     2024-07-29
-##  pandoc   3.1.11.1 @ /usr/bin/ (via rmarkdown)
-## 
-## ─ Packages ───────────────────────────────────────────────────────────────────
-##  ! package              * version   date (UTC) lib source
-##    assertthat             0.2.1     2019-03-21 [2] RSPM (R 4.3.0)
-##    backports              1.4.1     2021-12-13 [2] RSPM
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-##    later                  1.3.2     2023-12-06 [2] RSPM
-##    lazyeval               0.2.2     2019-03-15 [2] RSPM
-##    lifecycle              1.0.4     2023-11-07 [2] RSPM
-##    lintr                  3.1.1     2023-11-07 [2] RSPM
-##    magrittr               2.0.3     2022-03-30 [2] RSPM
-##    markdown               1.12      2023-12-06 [1] RSPM (R 4.3.0)
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-##    pkgconfig              2.0.3     2019-09-22 [2] RSPM
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-##    selectr                0.4-2     2019-11-20 [2] RSPM
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-##    shinyWidgets           0.8.1     2024-01-10 [2] RSPM
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-##    testthat             * 3.2.1     2023-12-02 [2] RSPM
-##    tibble                 3.2.1     2023-03-20 [2] RSPM
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-## 
-##  [1] /tmp/workspace/ndvcdmod/lib
-##  [2] /usr/local/lib/R/site-library
-##  [3] /usr/local/lib/R/library
-## 
-##  P ── Loaded and on-disk path mismatch.
-## 
-## ──────────────────────────────────────────────────────────────────────────────
-
-
-

List of specifications

-
j <- vapply(
-  vdoc[["spec_id_list"]],
-  function(x) {
-    eval(
-      str2expression(
-        paste0("vdoc[[\"specs\"]]$", x)
-      )
-    )
-  },
-  FUN.VALUE = character(1)
-) |>
-  gsub("\n", "</br>", x = _, fixed = TRUE)
-
-data.frame(spec_id = names(j), spec = j) |>
-  DT::datatable(
-    rownames = FALSE,
-    options = list(
-      dom = "ltp"
-    ),
-    filter = list(position = "top"),
-    escape = FALSE
-  )
-
- -
- - - - -
- - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/inst/validation/utils-validation.R b/inst/validation/utils-validation.R index 5f04eee..06eeb3d 100644 --- a/inst/validation/utils-validation.R +++ b/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) diff --git a/man/mod_boxplot.Rd b/man/mod_boxplot.Rd index 3ae2175..2feeb36 100644 --- a/man/mod_boxplot.Rd +++ b/man/mod_boxplot.Rd @@ -103,6 +103,8 @@ Dataset dispatcher. This parameter is incompatible with its *_dataset_name count A function that will be applied to the server returned value. Only for advanced use. See the example in mod_box_plot_papo} + +\item{...}{Same set of parameters as \link{mod_boxplot}} } \description{ \code{mod_boxplot} is a Shiny module prepared to display data with boxplot charts with different levels of grouping. diff --git a/man/mod_forest.Rd b/man/mod_forest.Rd index 731bcef..24d1092 100644 --- a/man/mod_forest.Rd +++ b/man/mod_forest.Rd @@ -108,9 +108,9 @@ The module will offer the functions as part of its interface and will run each f The values returned by the functions are be captured on the output table and are also displayed as part of the forest plot. -\code{numeric_numeric_functions} take two numeric parameters (e.g. \code{dv.biomarker.general::pearson_correlation}) +\code{numeric_numeric_functions} take two numeric parameters (e.g. \code{dv.explorer.parameter::pearson_correlation}) and \code{numeric_factor_functions} should accept a numeric first parameter and a categorical (factor) second parameter -(e.g. \code{dv.biomarker.general::odds_ratio}).} +(e.g. \code{dv.explorer.parameter::odds_ratio}).} \item{subjid_var}{\verb{[character(1)]} diff --git a/man/mod_lineplot.Rd b/man/mod_lineplot.Rd index 4de8aee..2beea0a 100644 --- a/man/mod_lineplot.Rd +++ b/man/mod_lineplot.Rd @@ -141,8 +141,6 @@ the module list or NULL.} \item{bm_dataset_disp, group_dataset_disp}{\verb{[mm_dispatcher(1)]} module manager dispatchers that used as \code{bm_dataset} and \code{group_dataset} to \code{lineplot_server}} - -\item{...}{Parameters passed to \link{lineplot_server}} } \description{ Display line plots of raw or summary data over time. Summaries include measures of central tendency diff --git a/man/roc_subset_data.Rd b/man/roc_subset_data.Rd index 084b48d..34eb090 100644 --- a/man/roc_subset_data.Rd +++ b/man/roc_subset_data.Rd @@ -84,7 +84,7 @@ Additionally: } } \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. } diff --git a/man/wfphm.Rd b/man/wfphm.Rd index e8ae45f..94d63b1 100644 --- a/man/wfphm.Rd +++ b/man/wfphm.Rd @@ -102,8 +102,6 @@ show x ticks in the parameter heatmap} \item{bm_dataset_disp, group_dataset_disp}{Dataset dispatcher. This parameter is incompatible with its \code{bm_dataset_name}/\code{group_dataset_name} counterpart. Only for advanced use.} - -\item{dataset_disp}{DEPRECATED} } \value{ \subsection{UI}{ diff --git a/tests/testthat.R b/tests/testthat.R index d1c6abe..91712ac 100644 --- a/tests/testthat.R +++ b/tests/testthat.R @@ -1,4 +1,4 @@ -pkg_name <- "dv.biomarker.general" +pkg_name <- "dv.explorer.parameter" library(testthat) library(pkg_name, character.only = TRUE) diff --git a/tests/testthat/_snaps/wfphm.md b/tests/testthat/_snaps/wfphm.md index 1c9e3d5..9d3e0b9 100644 --- a/tests/testthat/_snaps/wfphm.md +++ b/tests/testthat/_snaps/wfphm.md @@ -4989,7 +4989,7 @@ (x - mean(x, na.rm = TRUE))/stats::sd(x, na.rm = TRUE) } - + $tr_mapper$`Scale by result/Gini's Mean Difference of each parameter` function (x) @@ -4997,7 +4997,7 @@ x/Hmisc::GiniMd(x, na.rm = TRUE) } - + $tr_mapper$`Scale by parameter with truncation` function (x, trunc_min = -3, trunc_max = 3) @@ -5008,7 +5008,7 @@ z } - + $tr_mapper$`Normalize (result-min)/max` function (x) @@ -5017,7 +5017,7 @@ na.rm = TRUE)) } - + $tr_mapper$`Percentize (rank of result/maximal rank)` function (x) @@ -5030,7 +5030,7 @@ } } - + $margin diff --git a/tests/testthat/apps/heatmap/regular/app.R b/tests/testthat/apps/heatmap/regular/app.R index f401acf..4b7ee85 100644 --- a/tests/testthat/apps/heatmap/regular/app.R +++ b/tests/testthat/apps/heatmap/regular/app.R @@ -117,7 +117,7 @@ server <- function(input, output, session) { # Non reactive input should usually be first checked with shiny::req as there are no internal controls in the # module for "strange" values in them - returned_values <<- dv.biomarker.general:::heatmap_d3_server( + returned_values <<- dv.explorer.parameter:::heatmap_d3_server( "mod", data = solver(r_ipt[["data"]], as_reactive = TRUE), x_axis = solver(r_ipt[["x_axis"]], as_reactive = TRUE), @@ -136,7 +136,7 @@ server <- function(input, output, session) { # UIs must be static shiny::tagList( - dv.biomarker.general:::heatmap_d3_UI("mod"), + dv.explorer.parameter:::heatmap_d3_UI("mod"), shiny::verbatimTextOutput("out") ) }) diff --git a/tests/testthat/test-boxplot_app.R b/tests/testthat/test-boxplot_app.R index 00e9166..43c43d9 100644 --- a/tests/testthat/test-boxplot_app.R +++ b/tests/testthat/test-boxplot_app.R @@ -37,7 +37,7 @@ ID <- poc( # nolint ) ) -root_app <- start_app_driver(dv.biomarker.general::mock_app_boxplot()) +root_app <- start_app_driver(dv.explorer.parameter::mock_app_boxplot()) on.exit(if ("stop" %in% names(root_app)) root_app$stop()) fail_if_app_not_started <- function() { @@ -318,7 +318,7 @@ test_that("default values are set", { app <- start_app_driver( rlang::quo( - dv.biomarker.general::mock_app_boxplot( + dv.explorer.parameter::mock_app_boxplot( srv_defaults = !!srv_defaults ) ) diff --git a/tests/testthat/test-corr_hm.R b/tests/testthat/test-corr_hm.R index 601dc4d..5ca7aa5 100644 --- a/tests/testthat/test-corr_hm.R +++ b/tests/testthat/test-corr_hm.R @@ -69,7 +69,7 @@ test_that("apply_correlation_function generates data for a heatmap", { a <- df[[CNT$VAL]][1:3] b <- df[[CNT$VAL]][4:6] - pearson <- dv.biomarker.general::pearson_correlation + pearson <- dv.explorer.parameter::pearson_correlation label <- "label" res <- apply_correlation_function(df, pearson, label) par_1_2_index <- res[["x"]] == "par_1" & res[["y"]] == "par_2" @@ -77,7 +77,7 @@ test_that("apply_correlation_function generates data for a heatmap", { expected_v <- pearson(a, b)[["result"]] expect_equal(res[par_1_2_index, ][["z"]], expected_v) - spearman <- dv.biomarker.general::spearman_correlation + spearman <- dv.explorer.parameter::spearman_correlation res <- apply_correlation_function(df, spearman, label) par_1_2_index <- res[["x"]] == "par_1" & res[["y"]] == "par_2" @@ -97,7 +97,7 @@ test_that("ch_listings_table returns unique combinations of heatmap data and sum }) |> type("data_subset") - pearson <- dv.biomarker.general::pearson_correlation |> type("fun") + pearson <- dv.explorer.parameter::pearson_correlation |> type("fun") label <- "label" |> type("S") corr_df <- apply_correlation_function(ds, pearson, label) diff --git a/tests/testthat/test-corr_hm_app.R b/tests/testthat/test-corr_hm_app.R index 5e1a54c..da72c20 100644 --- a/tests/testthat/test-corr_hm_app.R +++ b/tests/testthat/test-corr_hm_app.R @@ -25,7 +25,7 @@ ID <- poc( # nolint ) ) -root_app <- start_app_driver(dv.biomarker.general::mock_app_corr_hm()) +root_app <- start_app_driver(dv.explorer.parameter::mock_app_corr_hm()) on.exit(if ("stop" %in% names(root_app)) root_app$stop()) fail_if_app_not_started <- function() { @@ -157,7 +157,7 @@ test_that("default values are set", { app <- start_app_driver( rlang::quo( - dv.biomarker.general::mock_app_corr_hm( + dv.explorer.parameter::mock_app_corr_hm( ui_defaults = !!ui_defaults, srv_defaults = !!srv_defaults ) diff --git a/tests/testthat/test-forest_plot.R b/tests/testthat/test-forest_plot.R index b65a502..de62ccb 100644 --- a/tests/testthat/test-forest_plot.R +++ b/tests/testthat/test-forest_plot.R @@ -1,7 +1,7 @@ test_that( "Generates proper SVG", { - type <- dv.biomarker.general:::type + type <- dv.explorer.parameter:::type output_size <- c(w = 100, h = 200) |> type("size") df <- data.frame( result = c(1, 2, 3), @@ -11,7 +11,7 @@ test_that( table_row_order <- seq_len(nrow(df)) |> type("sequence_permutation") axis_config <- c(x_min = -1, x_max = 1, ref_line_x = 0, tick_count = 5) |> type("axis_config") - svg <- dv.biomarker.general:::gen_svg(output_size, df, table_row_order, axis_config) + svg <- dv.explorer.parameter:::gen_svg(output_size, df, table_row_order, axis_config) expect_snapshot(svg) } ) diff --git a/tests/testthat/test-forestplot_app.R b/tests/testthat/test-forestplot_app.R index 118a7d6..dd01d0a 100644 --- a/tests/testthat/test-forestplot_app.R +++ b/tests/testthat/test-forestplot_app.R @@ -23,7 +23,7 @@ ID <- poc( # nolint ) ) -root_app <- start_app_driver(dv.biomarker.general::mock_app_forest()) +root_app <- start_app_driver(dv.explorer.parameter::mock_app_forest()) on.exit(if ("stop" %in% names(root_app)) root_app$stop()) @@ -191,7 +191,7 @@ test_that("default values are set. Odds", { app <- start_app_driver( rlang::quo( - dv.biomarker.general::mock_app_forest( + dv.explorer.parameter::mock_app_forest( ui_defaults = !!ui_defaults, srv_defaults = !!srv_defaults ) @@ -227,7 +227,7 @@ test_that("default values are set. Continuous", { app <- start_app_driver( rlang::quo( - dv.biomarker.general::mock_app_forest( + dv.explorer.parameter::mock_app_forest( ui_defaults = !!ui_defaults, srv_defaults = !!srv_defaults ) diff --git a/tests/testthat/test-lineplot_app.R b/tests/testthat/test-lineplot_app.R index 6454025..0d84155 100644 --- a/tests/testthat/test-lineplot_app.R +++ b/tests/testthat/test-lineplot_app.R @@ -29,7 +29,7 @@ ID <- poc( # nolint ) ) -root_app <- start_app_driver(dv.biomarker.general::mock_app_lineplot()) +root_app <- start_app_driver(dv.explorer.parameter::mock_app_lineplot()) on.exit(if ("stop" %in% names(root_app)) root_app$stop()) @@ -252,7 +252,7 @@ test_that("default values are set", { app <- start_app_driver( rlang::quo( - dv.biomarker.general::mock_app_lineplot( + dv.explorer.parameter::mock_app_lineplot( srv_defaults = !!srv_defaults ) ) @@ -277,9 +277,9 @@ test_that("module tolerates the absence of visit-dependent data", { testthat::skip_if_not(run_shiny_tests) skip_if_suspect_check() - data <- dv.biomarker.general:::test_data() + data <- dv.explorer.parameter:::test_data() data[["bm"]] <- data[["bm"]][0, ] # zero rows, equivalent to dv.filtering everything out - app <- start_app_driver(rlang::quo(dv.biomarker.general::mock_app_lineplot(data = data))) + app <- start_app_driver(rlang::quo(dv.explorer.parameter::mock_app_lineplot(data = data))) testthat::expect_true(!is.null(app)) # `app` is NULL if it crashes on load }) # nolint end diff --git a/tests/testthat/test-roc-running-app.R b/tests/testthat/test-roc-running-app.R index f916d66..0ecd86f 100644 --- a/tests/testthat/test-roc-running-app.R +++ b/tests/testthat/test-roc-running-app.R @@ -59,7 +59,7 @@ inputs2 <- rlang::list2( !!ID$PRED$PAR := c("A1", "A2"), !!ID$RESP$PAR := c("BinA1") ) -app <- start_app_driver(dv.biomarker.general:::roc_test_app()) +app <- start_app_driver(dv.explorer.parameter:::roc_test_app()) fail_if_app_not_started <- function() { if (is.null(app)) rlang::abort("App could not be started") } diff --git a/tests/testthat/test-scatterplot_app.R b/tests/testthat/test-scatterplot_app.R index 2b958c9..ba31e1f 100644 --- a/tests/testthat/test-scatterplot_app.R +++ b/tests/testthat/test-scatterplot_app.R @@ -33,7 +33,7 @@ ID <- poc( # nolint ) ) -root_app <- start_app_driver(dv.biomarker.general::mock_app_scatterplot()) +root_app <- start_app_driver(dv.explorer.parameter::mock_app_scatterplot()) on.exit(if ("stop" %in% names(root_app)) root_app$stop()) fail_if_app_not_started <- function() { @@ -216,7 +216,7 @@ test_that("default values are set", { app <- start_app_driver( rlang::quo( - dv.biomarker.general::mock_app_scatterplot( + dv.explorer.parameter::mock_app_scatterplot( srv_defaults = !!srv_defaults ) ) diff --git a/tests/testthat/test-scatterplotmatrix_app.R b/tests/testthat/test-scatterplotmatrix_app.R index 83ebd57..528ab04 100644 --- a/tests/testthat/test-scatterplotmatrix_app.R +++ b/tests/testthat/test-scatterplotmatrix_app.R @@ -18,7 +18,7 @@ ID <- poc( # nolint ) ) -root_app <- start_app_driver(dv.biomarker.general::mock_app_scatterplotmatrix()) +root_app <- start_app_driver(dv.explorer.parameter::mock_app_scatterplotmatrix()) on.exit(if ("stop" %in% names(root_app)) root_app$stop()) fail_if_app_not_started <- function() { @@ -145,7 +145,7 @@ test_that("default values are set", { app <- start_app_driver( rlang::quo( - dv.biomarker.general::mock_app_scatterplotmatrix( + dv.explorer.parameter::mock_app_scatterplotmatrix( srv_defaults = !!srv_defaults ) ) diff --git a/vignettes/boxplot.Rmd b/vignettes/boxplot.Rmd index 1cc3831..bd70a8c 100644 --- a/vignettes/boxplot.Rmd +++ b/vignettes/boxplot.Rmd @@ -43,7 +43,7 @@ It supports bookmarking. # Arguments for the module -`dv.biomarker.general::mod_boxplot()` +`dv.explorer.parameter::mod_boxplot()` module uses several arguments with the following being mandatory and the rest optional. As part of app creation, the app creator should specify the values for these arguments as applicable. @@ -67,7 +67,7 @@ creator should specify the values for these arguments as applicable. It expects a dataset with an structure similar to https://www.cdisc.org/kb/examples/adam-subject-level-analysis-adsl-dataset-80283806 , one record per subject It expects to contain, at least, `subjid_var` -Refer to `dv.biomarker.general::mod_boxplot()` for the complete list of arguments and their description. +Refer to `dv.explorer.parameter::mod_boxplot()` for the complete list of arguments and their description. # Input menus @@ -118,7 +118,7 @@ A table containing a set of statistical tests comparing the means of different g # Creating a boxplot application ```{r, eval=FALSE} -adbm_dataset <- dv.biomarker.general::adbm_example %>% +adbm_dataset <- dv.explorer.parameter::adbm_example %>% dplyr::mutate( USUBJID = factor(USUBJID), PARCAT1 = factor(PARCAT1), @@ -126,13 +126,13 @@ adbm_dataset <- dv.biomarker.general::adbm_example %>% AVISIT = factor(AVISIT) ) -adsl_dataset <- dv.biomarker.general::adsl_example %>% +adsl_dataset <- dv.explorer.parameter::adsl_example %>% dplyr::mutate(USUBJID = factor(USUBJID)) dv.manager::run_app( data = list(dummy = list(adbm = adbm_dataset, adsl = adsl_dataset)), module_list = list( - Boxplot = dv.biomarker.general::mod_boxplot( + Boxplot = dv.explorer.parameter::mod_boxplot( "boxplot", bm_dataset_name = "adbm", group_dataset_name = "adsl", diff --git a/vignettes/correlation_heatmap.Rmd b/vignettes/correlation_heatmap.Rmd index 086337b..ffa9347 100644 --- a/vignettes/correlation_heatmap.Rmd +++ b/vignettes/correlation_heatmap.Rmd @@ -108,7 +108,7 @@ Decimal values on this table are rounded (mathematical, round-to-even) to four d ```{r, eval=FALSE} adbm_dataset <- dplyr::mutate( - dv.biomarker.general::adbm_example, + dv.explorer.parameter::adbm_example, USUBJID = factor(USUBJID), PARCAT1 = factor(PARCAT1), PARAM = factor(PARAM), @@ -116,14 +116,14 @@ adbm_dataset <- dplyr::mutate( ) adsl_dataset <- dplyr::mutate( - dv.biomarker.general::adsl_example, + dv.explorer.parameter::adsl_example, USUBJID = factor(USUBJID) ) dv.manager::run_app( data = list("DS" = list(adbm = adbm_dataset, adsl = adsl_dataset)), module_list = list( - "Correlation Heatmap" = dv.biomarker.general::mod_corr_hm( + "Correlation Heatmap" = dv.explorer.parameter::mod_corr_hm( "forestplot", bm_dataset_name = "adbm", subjid_var = "USUBJID", diff --git a/vignettes/forest.Rmd b/vignettes/forest.Rmd index 6da4ca1..2d1c3f7 100644 --- a/vignettes/forest.Rmd +++ b/vignettes/forest.Rmd @@ -104,7 +104,7 @@ the data. Controls embedded in the table headings allow arbitrary reorderings of ```{r, eval=FALSE} adbm_dataset <- dplyr::mutate( - dv.biomarker.general::adbm_example, + dv.explorer.parameter::adbm_example, USUBJID = factor(USUBJID), PARCAT1 = factor(PARCAT1), PARAM = factor(PARAM), @@ -112,22 +112,22 @@ adbm_dataset <- dplyr::mutate( ) adsl_dataset <- dplyr::mutate( - dv.biomarker.general::adsl_example, + dv.explorer.parameter::adsl_example, USUBJID = factor(USUBJID) ) fp_numeric_numeric_functions <- list( - "Pearson Correlation" = dv.biomarker.general::pearson_correlation, - "Spearman Correlation" = dv.biomarker.general::spearman_correlation + "Pearson Correlation" = dv.explorer.parameter::pearson_correlation, + "Spearman Correlation" = dv.explorer.parameter::spearman_correlation ) fp_numeric_factor_functions <- list( - "Odds Ratio" = dv.biomarker.general::odds_ratio + "Odds Ratio" = dv.explorer.parameter::odds_ratio ) dv.manager::run_app( data = list("DS" = list(adbm = adbm_dataset, adsl = adsl_dataset)), module_list = list( - "Forest Plot" = dv.biomarker.general::mod_forest( + "Forest Plot" = dv.explorer.parameter::mod_forest( "forestplot", bm_dataset_name = "adbm", group_dataset_name = "adsl", diff --git a/vignettes/lineplot.Rmd b/vignettes/lineplot.Rmd index aedd9c2..57a937f 100644 --- a/vignettes/lineplot.Rmd +++ b/vignettes/lineplot.Rmd @@ -116,7 +116,7 @@ A table that provides the count of samples per group and time point for the whol ```{r, eval=FALSE} module_list <- list( - "lineplot" = dv.biomarker.general::mod_lineplot( + "lineplot" = dv.explorer.parameter::mod_lineplot( module_id = "lineplot", bm_dataset_name = "bm", group_dataset_name = "sl", diff --git a/vignettes/scatterplot.Rmd b/vignettes/scatterplot.Rmd index 2e1b9fb..605d1df 100644 --- a/vignettes/scatterplot.Rmd +++ b/vignettes/scatterplot.Rmd @@ -39,7 +39,7 @@ It supports bookmarking. # Arguments for the module -`dv.biomarker.general::mod_scatterplot()` +`dv.explorer.parameter::mod_scatterplot()` module uses several arguments with the following being mandatory and the rest optional. As part of app creation, the app creator should specify the values for these arguments as applicable. @@ -63,7 +63,7 @@ creator should specify the values for these arguments as applicable. It expects a dataset with an structure similar to https://www.cdisc.org/kb/examples/adam-subject-level-analysis-adsl-dataset-80283806 , one record per subject It expects to contain, at least, `subjid_var` -Refer to `dv.biomarker.general::mod_scatterplot()` for the complete list of arguments and their description. +Refer to `dv.explorer.parameter::mod_scatterplot()` for the complete list of arguments and their description. # Input menus @@ -99,7 +99,7 @@ A table containing a set of statistics regarding the regression and correlation. # Creating a boxplot application ```{r, eval=FALSE} -adbm_dataset <- dv.biomarker.general::adbm_example %>% +adbm_dataset <- dv.explorer.parameter::adbm_example %>% dplyr::mutate( USUBJID = factor(USUBJID), PARCAT1 = factor(PARCAT1), @@ -107,13 +107,13 @@ adbm_dataset <- dv.biomarker.general::adbm_example %>% AVISIT = factor(AVISIT) ) -adsl_dataset <- dv.biomarker.general::adsl_example %>% +adsl_dataset <- dv.explorer.parameter::adsl_example %>% dplyr::mutate(USUBJID = factor(USUBJID)) dv.manager::run_app( data = list(dummy = list(adbm = adbm_dataset, adsl = adsl_dataset)), module_list = list( - Scatterplot = dv.biomarker.general::mod_scatterplot( + Scatterplot = dv.explorer.parameter::mod_scatterplot( "scatterplot", bm_dataset_name = "adbm", group_dataset_name = "adsl", diff --git a/vignettes/scatterplotmatrix.Rmd b/vignettes/scatterplotmatrix.Rmd index 4e8f6a9..fa131e3 100644 --- a/vignettes/scatterplotmatrix.Rmd +++ b/vignettes/scatterplotmatrix.Rmd @@ -37,7 +37,7 @@ It supports bookmarking. # Arguments for the module -`dv.biomarker.general::mod_scatterplotmatrix()` +`dv.explorer.parameter::mod_scatterplotmatrix()` module uses several arguments with the following being mandatory and the rest optional. As part of app creation, the app creator should specify the values for these arguments as applicable. @@ -61,7 +61,7 @@ creator should specify the values for these arguments as applicable. It expects a dataset with an structure similar to https://www.cdisc.org/kb/examples/adam-subject-level-analysis-adsl-dataset-80283806 , one record per subject It expects to contain, at least, `subjid_var` -Refer to `dv.biomarker.general::mod_scatterplotmatrix()` for the complete list of arguments and their description. +Refer to `dv.explorer.parameter::mod_scatterplotmatrix()` for the complete list of arguments and their description. # Input menus @@ -82,7 +82,7 @@ This visualizations consists of a matrix of scatterplots with correlation statis # Creating a scatterplotmatrix application ```{r, eval=FALSE} -adbm_dataset <- dv.biomarker.general::adbm_example %>% +adbm_dataset <- dv.explorer.parameter::adbm_example %>% dplyr::mutate( USUBJID = factor(USUBJID), PARCAT1 = factor(PARCAT1), @@ -90,13 +90,13 @@ adbm_dataset <- dv.biomarker.general::adbm_example %>% AVISIT = factor(AVISIT) ) -adsl_dataset <- dv.biomarker.general::adsl_example %>% +adsl_dataset <- dv.explorer.parameter::adsl_example %>% dplyr::mutate(USUBJID = factor(USUBJID)) dv.manager::run_app( data = list(dummy = list(adbm = adbm_dataset, adsl = adsl_dataset)), module_list = list( - "Scatterplot Matrix" = dv.biomarker.general::mod_scatterplotmatrix( + "Scatterplot Matrix" = dv.explorer.parameter::mod_scatterplotmatrix( "scatterplotmatrix", bm_dataset_name = "adbm", group_dataset_name = "adsl", diff --git a/vignettes/wfphm.Rmd b/vignettes/wfphm.Rmd index d7a7b0f..a59ae88 100644 --- a/vignettes/wfphm.Rmd +++ b/vignettes/wfphm.Rmd @@ -407,11 +407,10 @@ As per the selections made in the screenshot: The last plot is the parameter heatmap that plots a heatmap where the rows represent different parameters. -The menus in this plot follow similar rules to those presented in the -[Plotting Parameter](../articles/dv-wfphm.html#plotting-parameters) -section in the Waterfall plot with the difference that the *Category* -and *Parameter* menus now accept selecting multiple values. The -*Transformation* menu will be covered in a separate section below. +The menus in this plot follow similar rules to those presented in the +Plotting Parameter section in the Waterfall plot with the difference +that the *Category* and *Parameter* menus now accept selecting multiple values. +The *Transformation* menu will be covered in a separate section below. ![](images/hmpar_app.png){width="100%"}