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ggpedigree (development version)

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ggpedigree 1.1.0.3

API notes

• Documented ggPedigree() / ggPedigreeInteractive() / ggRelatednessMatrix() as canonical entry points while retaining backward-compatible aliases.

New data

• Added a preliminary Wars of the Roses pedigree dataset.
• Improved dataset documentation.
• Tweaked the GoT dataset example for improved clarity.
• Split the squirrel dataset into smaller pedigrees for testing.

New features

• Added a greyscale option to color_theme.
• Added automatic point scaling based on pedigree size.
• Added optional segment size scaling based on pedigree size.
• Hid the Sex key by default in ggpedigree.
• Added two vignettes describing ggpedigree configuration options.
• Cross-referenced vignettes in function documentation.

Validation and messages

• Performed required-column checks earlier in ggpedigree(), including sex.
• Improved errors for invalid or non-standard sex coding.
• Improved the warning message used in tryCatch().
• Made code_male handling more resilient when using config values.

Bug fixes

• Standardized naming by replacing midparent with mid_parent.
• Fixed inconsistent handling of character vs numeric IDs.

Internal changes

• Changed default colors and sizes for better visibility.
• Saved raw Excel inputs as CSV for non-proprietary storage.
• Refactored kinship2 internals for maintainability.
• Refactored node-adding internals.
• Remove reshape2 dependency
• Deprecating plotPedigree function in favor of kinship2_plotPedigree

Testing

• Expanded tests for ID and sex-code inputs, including type, missingness, and configuration scenarios.

ggpedigree 1.0.0.1

cran resubmission

• Fixed a minor documentation issue with a URL whose certificate had expired.

ggpedigree 1.0.0

cran submission

• Integrated kinship2 functions to remove the dependency
• Made kinship2 package optional, required for plotPedigree (a kinship2 wrapper)
• Importing relevant tests from kinship2 package
• Updated documentation to reflect changes
• Refactored code to improve maintainability
• Added more unit tests for the new functions
• Add max_message_n to pedigree function to allow users to get more messages about pedigree complexity

ggpedigree 0.9.1

• Minor documentation revisions to complement JOSS paper update
• Added test coverage for buildSpouseSegments

ggpedigree 0.9.0

cran release

• smarter segment coloring
• added setting to hide legend for sex
• avoided sapply() in ggPedigreeInteractive
• added subfunction for adding twins
• add non-dot versions of internal functions for evaluating complexity
• added alpha settings
• added compatibility with pedigree objects from kinship2
• exposed code_female, code_na to config
• added tests for kinship2 compatibility
• Updated JOSS paper
• Refactored step 2+3 of the ggpedigree function to .transformPed()
• Renamed p variable as plotObject in ggpedigree subfunctions
• Smarter implementation of aliases
• Updated hex to actually use ggpedigree
• Exposed ‘relations’ and ‘hints’ inputs to ggpedigree
• Added more intuitive defaults
• refactor calcCoordinates with alignPedigreeWithHints and alignPedigreeWithRelations
• Vectorized part of calcCoordinates
• removed redundant plotPedigree verbose section
• add log2 option for relatedness
• Improve plotly conversion

ggpedigree 0.8.0

joss paper submitted

• Makes ggrepel a suggested package instead of a required one.
• Make connections included in the plot by default.
• Expose linejoin in ggRelatednessMatrix
• Expose outline_additive and outline_alpha to ggpedigree
• Refactored the ggpedigree function to improve readability and maintainability.
• Transferring ASOIAF data from BGmisc to ggpedigree

ggpedigree 0.7.1

• Fixed focal_fill ID indexing to row order instead of ID order.
• Fixed bug in using fam_x and fam_y in with generation_height
• Add option to add phantom parents to the pedigree plot.
• Alerts when duplicate or bad configs appear
• Make palleter suggested instead of required

ggpedigree 0.7.0

• Changed the default behavior of ggPedigree to use x_fam and y_fam for positioning families, rather than x_mid_parent and y_mid_parent. This change improves visualization of pedigrees with many families.
• Changed the get midpoint of curvature to better approximate geom_curv behavior.
• reduced redundancy in code base by not calculating the parent midpoints when not needed.
• Added default_config support for ggRelatednessMatrix functions.

ggpedigree 0.6.1

• Transferred plotPedigree() function from BGmisc to ggpedigree.

ggpedigree 0.6.0

• Implemented fill by matID, patID using various scales, such as hue, viridis, and others.
• Added support for emojis in the ggpedigree function.
• Solved the bug that created excessive branches
• Made the twin sibling segments smarter
• Adding more debug support

ggpedigree 0.5.1

• Fix tooltip appearing in ggPedigreeInteractive when tooltip_include is FALSE.

ggpedigree 0.5.0

• Added segment_linetype and custom affected labels to the ggpedigree function.
• Added usage of color_palette to the ggpedigree function.
• Added curvature option to the ggpedigree function.
• Add support for custom affected labels for affected individuals in the ggpedigree function.
• Add support for removing diagonal, upper triangle, and lower triangle in the ggRelatednessMatrix function.
• Add support for labeling tiles
• Added new tests for the ggRelatednessMatrix function.
• Added new phenotype plotting function ggPhenotypebyDegree to visualize phenotypes by degree of relatedness.
• Added new vignette to explain ggPhenotypebyDegree.
• Added a new function getDefaultPlotConfig to set default configuration options for the package.
• Harmonized the configuration options across the package to use getDefaultPlotConfig and buildPlotConfig
• Added unit tests for getDefaultPlotConfig and ggPhenotypebyDegree
• Added workaround for plotly non-support for geom_curve with computeCurvedMidpoint
• Adding fully twin plotting features
• Added ability to fill colors as a function of the degree of relatedness to a focal person
• Add getDefaultPlotConfig functionality to ggPhenotypebyDegree
• Fully documented getDefaultPlotConfig so that each config option is clear and understandable.

ggpedigree 0.4.1

Status: Submitted to CRAN

• Fixed a bug in the ggpedigree function that caused an error when using a custom ID name and requesting the plot as a ggplot object.

ggpedigree 0.4.0

• Allows support for character-based IDs
• Added linejoin, lineend, segment_self_linetype, option to the ggpedigree functions.
• Added unit tests for calculateConnections and ggpedigree functions.
• Refactored ggpedigree function into ggpedigree.core and .addScales and .addLabels functions to improve readability and maintainability.
• Renamed symKey to makeSymmetricKey, extended it to support character-based IDs, and added unit tests.
• Added a new function ggPedigreeInteractive to create interactive pedigree plots using plotly. Added a vignette to show its usage.
• Added redsquirrels dataset to the package for testing and examples.
• Added a new function ggRelatednessMatrix and subfunction ggRelatednessMatrix.core to create heatmaps of relatedness matrices.
• Added new vignette to explain ggRelatednessMatrix
• Added graphic tests for ggpedigree, ggPedigreeInteractive, and ggRelatednessMatrix functions.
• Updated the README and vignettes to reflect the new features and improvements.
• Updated description to meet CRAN policies.

ggpedigree 0.3.0

• Expose more labeling options in the ggpedigree function to allow for more customization, including nudging labels, and changing the variable used.
• Added option to add an outline to the pedigree plot.
• Made the config options more consistent and user-friendly.
• Enhance the narrative of the plotting vignette to explain the new features and provide clearer examples.
• Added missing examples to the ggpedigree function documentation.

ggpedigree 0.2.0

• Extended functionality to include new plotting features, like handling repeated instances of the same individual in a pedigree.
• Improved documentation and examples for better user guidance.
• Added unit tests for describeHelpers

ggpedigree 0.1.0

• Implemented pedigree plotting functions for ggplot2.
• Added vignette to explain the use of the package in basic plotting.
• Created a DESCRIPTION file to define the package and its dependencies.
• Added a LICENSE file to specify the terms under which the package applies.
• Created a CODE_OF_CONDUCT.md file to outline the expected behavior of contributors and maintainers.
• Added a NEWS.md file to track changes to the package.
• Created a CONTRIBUTING.md file to guide contributors on how to contribute to the package.
• Added a README.Rmd file to provide an overview of the package and its functions.
• Added a cran-comments.md file to document the submission process to CRAN.
• Initial version launched

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