teal.modules.general 0.7.0

Enhancements

• Modules now return a teal_report object that contains the data, code and reporter. All the reporter buttons were removed from the modules’ UI.
• Support case when both variables are categorical in association and bivariate plots.
• Improve tm_missing_data visualization (#495).
• tm_g_scatterplotmatrix() has been rewritten to use ggplot2 and patchwork instead of lattice. Panel text scales automatically with the number of variables so labels remain readable at any matrix size. NA handling retains the familiar Omit NAs checkbox (default, use = "pairwise.complete.obs"); unchecking it reveals a dropdown with all five stats::cor() use options. get_scatterplotmatrix_stats() has been removed (#986).
• Multiple decorators can be applied to the same output object (#978).
• Replaced deprecated ggplot2::aes_string() with aes() using tidy evaluation idioms, and renamed sec_axis(trans=) to sec_axis(transform=) (#629).

Bug fixes

• Improved user-facing robustness by reporting table creation errors to users (#982).
• Show only distinct rows in tm_data_table no longer shows an extra count column n (#983).
• Fixed overlapping UI elements in the output panel of tm_g_distribution (#896).

Miscellaneous

• Extensive test coverage increases across modules:
  • tm_front_page (#961)
  • tm_missing_data (#960)
  • tm_variable_browser (#963)
  • tm_g_distribution (#962)
  • tm_rmarkdown (#967)
  • tm_a_pca (#966)
  • tm_outliers (#965)
  • tm_data_table (#970)
  • broader coverage improvements (#959)
  • additional targeted tests (tm_a_regression, tm_file_viewer, etc.; #969, #968, #964)
  • Linting rule expansion for object names (#977)
  • Dependency/workflow maintenance:
    • added/fixed copilot setup workflow (#957, #958)
• Timeout and integration test stability adjustments (#946, #950, #945).
• Re-enabled tm_g_association tests after upstream ggmosaic issue resolution (PR #991).

teal.modules.general 0.5.1

• Removed ggmosaic package dependency to avoid being archived on CRAN (#932).

teal.modules.general 0.5.0

Breaking changes

• Removed the table object decoration in tm_missing_data and tm_outliers (#899).
• Removed the summary_table and test_table object decoration in tm_g_distribution (#897).

Bug fixes

• Fixed “Add to Report” functionality in tm_outliers, tm_missing_data and tm_g_distribution modules (#899 and #897).
• Fixes a bug in tm_outliers that fails when data has no join keys (#650).

Enhancements

• Improved the layout and appearance of the app using bslib components.
• Fixed deprecation warning for tern::stack_grobs in tm_g_association (#903).
• Allow search feature in tm_file_viewer (#152).
• Added remove_zero_columns to tm_t_crosstable to add an option to remove empty columns (#890)

teal.modules.general 0.4.1

Bug fixes

• Fixes output is not updated when filter is added for the modules: tm_a_pca, tm_a_regression, tm_g_scatterplot, tm_g_association, tm_g_bivariate, tm_g_distribution, tm_g_response, tm_t_crosstable (#870)

teal.modules.general 0.4.0

Enhancements

• Introduced transformators and decorators argument to modules (#863).
• Modules’ Show R Code widgets include library calls to boost reproducibility (#786).
• Removed Show Warnings modals from modules.

Miscellaneous

• Soft deprecated datasets_selected argument of modules in favor of datanames.
• Soft deprecated show_metadata argument of tm_front_page() in favor of datanames.
• Added teal.logger functionality for logging changes in shiny inputs in all modules.
• All example data is now sourced from teal.data.
• Update tm_g_distribution to not start with validation error (#823).

Bug fixes

• Fixed a bug in tm_missing_data in “Group by Subject” that was not using reactive data call (#772).
• Fixed out-of-bound labels for tm_g_regression (#66).
• Fixed a bug in tm_g_association where the app would crash when a selected categorical variable was a factor instead of a character (#645).

teal.modules.general 0.3.0

Enhancements

• Updated the package docs and vignettes with the new way of specifying data for teal::init(). The data argument will accept a teal_data object.

Bug fixes

• Outlier labels no longer appear out of bounds in tm_a_regression.
• Fixed a bug in tm_outliers when changing the selected variable would cause a popup.

Miscellaneous

• Removed teal.slice dependencies.
• Specified minimal version of package dependencies.

teal.modules.general 0.2.16

Breaking changes

• Replaced chunks with simpler qenv class.
• Replaced datasets argument containing FilteredData with the new arguments data (tdata object) and filter_panel_api (FilterPanelAPI).

Enhancements

• Added parent_dataname argument to tm_variable_browser and tm_missing_data to allow specification of parent dataset for these modules.
• Improved UI labels and plot panel title in tm_g_association.
• Added inputs tm_variable_browser module for text size and plot theme.
• Forced ggplot theme to be always selected in all modules.
• Updated encodings input checks to use shinyvalidate::InputValidator instead of shiny::validate for better UI experience.

Bug fixes

• Fixed a bug in tm_g_scatterplot when selected x and y facets were the same.
• Fixed a bug in tm_g_distribution to plot the theoretical distribution with newer ggplot2 version.
• Fixed a bug in tm_g_bivariate when adding lines checkbox was available if one of x or y was deselected.
• Fixed a bug in tm_variable_browser when changing filters would reset the selected variable to the first on the list.

Miscellaneous

• Removed scda package dependency from examples.
• Replaced deprecated ggplot2 functions ..count.., ..density.. and ..prop...
• Version bump on forcats dependency.
• Replaced scda data generation functions with random.cdisc.data

teal.modules.general 0.2.15

Enhancements

• Added the teal.reporter functionality to all modules.
• Implemented nestcolor in the examples, refactored tm_a_pca and tm_missing_data to allow using nestcolor.
• Added log transformation options to tm_g_scatterplot.
• Added server_rendering flag to tm_data_table to control whether the table is rendered server or client side.

Bug fixes

• Fixed the overflow of very wide tm_a_pca tables.
• Fixed the join type functionality in tm_t_crosstable.
• Fixed a bug in tm_missing_data when selecting only variables with missings.
• Fixed a bug in tm_missing_data when using any_na.

Miscellaneous

• Moved packages only used in one module from Imports to Suggests in the DESCRIPTION file.
• Moved magrittr package from Depends to Imports in the DESCRIPTION file.

teal.modules.general 0.2.14

Enhancements

• New teal module tm_front_page to simplify creating a front page for teal apps.
• Added a slider widget to control the font size of the label in tm_g_scatterplot.
• Output integers without decimal places when selecting points in tm_g_scatterplot.
• Improved the names of the code chunks shown in Debug Info.
• Improved a validation message when the number of regressors is too big in tm_a_regression.R.

Bug fixes

• Fixed a wrong validation in tm_a_pca.
• Fixed a crash when deselecting the categorical factor in tm_outliers.

Miscellaneous

• Added a template to the pkgdown site.
• Updated package authors.

teal.modules.general 0.2.13

Enhancements

• Rewrote modules to use moduleServer and updated call to plot_with_settings_srv after changes in teal.devel.
• Fixed tracking of the selection order in data_extract_ui. All selectors can return ordered selection if one specifies ordered = TRUE in select_spec.
• Switched order of tm_missing_data combination plot to show data in descending order.
• Changed By variable levels output in tm_missing_data to allow numerical sorting.

Miscellaneous

• Removed unneeded n row in tm_t_crosstable.
• Replaced calls to teal::root_modules with teal::modules following deprecation of teal::root_modules.
• Adjusted package imports to take into account changes to the teal framework.
• Added the “Getting started with teal.modules.general” vignette.
• Updated README file.
• Moved the ggmosaic package from Depends to Imports in the DESCRIPTION file.

teal.modules.general 0.2.12

Enhancements

• Added support for logging with the logger package and added info level logs upon initialization of a module.
• Added support for custom arguments for ggplot2::labs and ggplot2::theme in plot based modules.
• Added support for custom arguments for rtables::basic_table in tm_t_crosstable.
• Updated tm_outliers, tm_g_scatterplotmatrix, tm_g_association, and tm_t_crosstable modules to adopt the new teal.transform::data_merge_srv and teal.transform::data_extract_multiple_srv modules.
• Distinguished bars representing NA in plot depicting counts of tm_variable_browser with a different color fill.
• Modified the summary statistics table for numeric columns in tm_variable_browser to reflect the plot after outliers are removed.
• Added an option to remove missing values in a tm_variable_browser histogram for factor like variables.
• Added ability to sort by Variable and Type in tm_variable_browser by separating the variable type icons into their own column.
• Updated the Grouped by Subject tab of the tm_missing_data module to present data the same way the Summary tab does.
• Added support for NA level in grouping variable in By variable levels table in tm_missing_data module.
• Added informative labels for each level of grouping variable in By variable levels table in tm_missing_data module.
• Added a checkbox to tm_g_scatterplot to toggle the option to free up the x and y axis scales whenever faceting arguments are provided.
• Used browser-side processing in tm_data_table so that Buttons extension could download full table. Added example for advanced usage of DT in the module.

Bug fixes

• Fixed an error in tm_variable_browser when the selected column is logical(1).
• Fixed bugs in the modules’ vignette examples.

Miscellaneous

• Added R version requirement R >= 3.6.
• Removed input_id argument from teal.transform::data_merge_module calls in all modules.
• Refactored the defunct teal.devel::data_extract_input into its replacement teal.transform::data_extract_ui.
• Updated teal.transform::data_merge_srv to use dplyr::inner_join instead of dplyr::left_join in tm_outliers module.
• Removed the overlay statistics table in tm_g_distribution module.
• Removed dependency on test.nest package.
• Removed dependency on utils.nest package and replaced its functions with equivalents from the checkmate package.

teal.modules.general 0.2.11

New features

• A new module, tm_file_viewer, was added for the visualization of static files.
• A new module, tm_g_distribution, was added for distribution analysis.

Bug fixes

• Fixed the bar plot order for factor variables in tm_variable_browser.

Enhancements

tm_variable_browser

• Added sparkline support for Date/POSIXct/POSIXlt variable types.
• Fixed histograms to contain at least two bars.

tm_outliers

• Added filter_spec support.
• Simplified returned R code.
• Support select_spec for categorical variables.

tm_g_scatterplotmatrix

• Added ordered select input support.
• Decoupled the dataset list from the variables list parameters.

tm_g_association

• Added ordered select input support.

tm_t_crosstable

• Added ordered select input support.

tm_g_scatterplot

• Modified the trend line feature of the scatterplot to display the raw equation that will equal the actual y value when the actual x values are plugged in.

Miscellaneous

• Updated LICENCE and README with new package references.
• Added error_on_lint: TRUE to .lintr.
• Updated quantile type = 2 argument in tm_variable_browser to be in line with STREAM.

teal.modules.general 0.2.10

Enhancements

• Refactored the internal code of all the modules to optimize their performance.
• Refactored tm_g_scatterplot to compute trend line statistics using ggpmisc::stat_poly_eq to simplify code and to have labels for each group on the plot.
• Refactored tm_g_scatterplot to enable filtering via the Encoding Panel using the new filter_spec functionality.
• Added support for logical variables in tm_variable_browser.
• Updated tm_outliers to handle non-CDISC datasets.
• Updated UI of tm_variable_browser for factor and character variables with more than 30 levels.
• Updated sparklines to remove NA values for numeric variables.
• Added checkbox to display number of observations on plot to tm_g_scatterplot.
• Added validation statements to tm_g_scatterplot handling users choosing more than one facet variable.
• Improved performance of tm_variable_browser by a more efficient sparkline generation.
• Added the html code type for all datasets labels inside tm_missing_data.
• Improved the styling of tool tips in tm_a_regression, tm_missing_data and tm_variable_browser.

teal.modules.general 0.2.9

Enhancements

• Added download, enlarge and resize graph options to tm_variable_browser module.
• Added download and expand options to the table in tm_t_crosstable.
• Enabled selection of custom datasets for tm_variable_browser with datasets_selected argument.
• Allowed all dataset variables to be used as grouping variables in by variable levels tab of tm_missing_data, not just those selected to be displayed as rows in the table.
• Enabled the brushing of points in NA categories when facetting in tm_g_scatterplot.

Bug fixes

• Added persistence for the number of entries displayed in data tables.
• Removed ‘treat variable as factor’ checkbox in tm_variable_browser if no graph shown.
• Fixed DT length reset in tm_variable_browser on “Show parent dataset variables” checkbox tick.

teal.modules.general 0.2.8

New Module

tm_outliers

• Added new module tm_outliers to analyze outliers in datasets.

Enhancements

tm_g_scatterplot

• Added max_deg optional argument to scatterplot to allow users to choose the maximum smoothing degree for the trend line.
• Added column and row facetting functionality to the scatterplot.
• Added possibility to specify type of join in tm_t_crosstable. Incorporate missings resulting from non inner join.

Bug Fixes

• Fixed edge case errors in tm_missing_data caused by input dataset not having categorical variables or being a data.frame instead of tibble.
• Fixed tm_a_pca biplot plot when coloring with a factor/character/numeric with < 6 values variable.
• Fixed typo in outlier definition in tm_variable_browser.

Miscellaneous

• Sparklines no longer shown for numeric variables with more than 100000 rows.
• Colors legend for each plot.
• Replaced "Show variables other than in ADSL" checkbox to more general "Show parent dataset variables".
• Capitalize default module labels.
• Some of the outputs of tm_missing_data are conditional to the data being a CDISC data.
• Added pre_output and post_output arguments to tm_data_table, tm_missing_data, tm_variable_browser.
• Fixed issue in tm_data_table when selecting “show distinct rows” if variable names had non-alphanumeric characters.

teal.modules.general 0.2.7

Enhancements

tm_variable_browser

• Introduced sparklines for quick, inline variable summaries.
• Added option to remove outliers.
• Histograms and statistics tables are now displayed for variables of type Date, POSIXct and POSIXlt.
• Character variable summary statistics tables are now displayed in decreasing order of occurrences instead of alphabetical.
• Display number of non-missing rows n in statistics table for numeric variables.
• Added ability to treat numeric variables as categorical.
• tm_variable_browser shows from 30 up to 50 levels divided in 2 columns for character/factor variables with more than 30 unique levels.

tm_a_regression

• Added support for outlier labels to tm_a_regression and provided an additional optional argument, default_outlier_label which can be used to specify the default column used to label outliers.

tm_g_scatterplot

• Implemented trend line.
• Added marginal density plots.
• Added option to display rug plot to both axes.
• Added shape and point color arguments. The latter users colourpicker::colourInput.
• Added size_by variable to scatterplot and allowed for point size to be mapped to a numeric variable.

tm_missing_data

• Added bar chart to missing data combination plot.
• Removed keys from missing data combinations plot in when they have not been selected.

tm_g_bivariate

• Bivariate plots with two continuous variables now allow adding lines.
• Show labels on x axis when selecting a categorical variable and fixed issues when deselecting variables and datasets in the encodings panel (including the addition of meaningful warnings).

tm_a_pca

• Updated to include Plot settings and Plot specific settings.

Miscellaneous

• Integrated is_single_dataset argument for data_extract_input function calls to simplify encodings panel UI.
• Moved code argument to cdisc_dataset (from cdisc_data) in examples and vignettes.
• Require ggmosaic version >= 0.3.0.

teal.modules.general 0.2.6

• Adds additional plot settings such as themes for tm_g_association, tm_g_response, and tm_g_scatterplot, as well as point size and opacity settings for tm_g_association and tm_g_scatterplot.
• Replace pickerInput with optionalSelectInput for tm_data_table.
• Adds new facet parameter to tm_g_bivariate to specify whether the facet encodings elements should be visible to the user by default.
• Replace plot_with_height module with new plot_with_settings module.
• Missing data module now uses chunks to get reproducible R code.
• New theme for missing data module and new label positioning.
• tm_data_table: allow developers to pass arguments to DT::dataTable and use pickerInput to select variables.
• tm_g_response a new argument count_labels. Counts might be assessed for the frequency plot too.
• Moved missing data module summary plot footer elements to tool tip in encodings panels.
• Replaced base plots in tm_a_regression with ggplot2.
• Added optional slider to adjust width in plot_with_settings.
• Handle Inf in data gracefully.
• tm_variable_browser now outputs the summary table for factors with all missing values.

teal.modules.general 0.2.5

• Adds ggplot call inside chunks in modules.
• Pass on dataname to get_rcode_srv.
• Uses utils function to standardize plot label generation.
• Improved handling of variable labels.
• Removed “Add as filter variable” button from variable browser module.
• Scatterplot matrix module now automatically converts characters to factors with a message.

teal.modules.general 0.2.4

• New PCA module.
• Documentation fix for cross table module.
• Display variable labels in drop-down menu of data table (#393).
• Optional subsetting and ordering datasets for tm_data_table.
• Use teal.code::chunks_push_data_merge to include merge code into reproducibility code.
• More consistent coloring behavior between bivariate plots.
• Updates to missing data module.
• Updated graph axis labels for the following modules: bivariate plot, missing data, response plot, regression module, scatterplot, scatterplot matrix.
• Simplify scatterplot matrix to display plot within one dataset only.

teal.modules.general 0.2.3

• Fixed naming in tm_variable_browser.
• Correlation added to Scatter Plot Matrix.
• Opacity slider added to tm_bivariate.
• Fixes due to bug in teal.devel#313.
• Performance enhancements to missing data module.
• Fix bug with reactivity in scatterplot matrix module.

teal.modules.general 0.2.2

• New module to summarize missing data.
• Refactor of variable browser module.
• Correct display of density / frequency option in bivariate plot.

teal.modules.general 0.2.1

• Fix magrittr loading in reproducible code.

teal.modules.general 0.2.0

• Refactor functions with data extract and data merge.
• Create sample_app.R demonstrating teal.modules.general modules.
• Rename tm_table on tm_cross_table.
• Include show R code in all modules.
• Merge tm_cross_table and tm_t_percentage_table into one module.

teal.modules.general 0.1.0

• Initial release.