NEWS.md

teal.modules.general 0.6.0.9023

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).
• Multiple decorators can be applied to the same output object (#978).
• Introduced tm_gtsummary(), a new module for generating tables using the gtsummary package (#973).

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.