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Changelog

Source: NEWS.md

teal.modules.general 0.3.0.9053

  • Removed Show Warnings modals from modules.

Enhancements

  • Added teal.logger functionality for logging changes in shiny inputs in all modules.

Bug fixes

  • Fixed a bug in tm_missing_data in “Group by Subject” that was not using reactive data call.

teal.modules.general 0.3.0

CRAN release: 2024-03-05

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.