BGmisc NEWS

BGmisc 1.6.0.1

CRAN submission

• Add OpenMx pedigree model builders and docs
• Added vignette for OpenMx pedigree model builders
• Add option for MZ twins in the additive genetic matrix
• Add option to select sex for MZ twin generation.
• Add option to tweak pedigree with one id provided
• Add helper functions for checkParents etc
• fixed incorrect direction so that parents are pointing to children in the graphs
• Optimize simulatePedigree and helpers for speed and memory usage
• Major gains (>x10) in speed for deeper pedigrees
• Added more tests for simulatePedigree
• Fix error when not enough single people available

BGmisc 1.5.2

• More flexible ID generation for simulatePedigree
• Created ped2gen function to extract generation information from pedigree data.frames
• Added tests for ped2gen
• Fixed handling of character ID variables leading to a warning in ped2fam
• Added famIDs to phantom parents
• Tweaked how sex coding is handled to allow for unknown sex

BGmisc 1.5.1

CRAN submission

• partially refactored summarizePedigree to be more modular
• added compression control to ped2com
• Minor copy editing

BGmisc 1.5.0

CRAN submission

• Removed ASOIAF dataset from BGmisc, now in ggpedigree
• Enhancing potter family tree
• updated tests to handle the transition of ASOIAF data to ggpedigree
• smarter aliases
• smarter CIs
• tweaking variable inputs

BGmisc 1.4.4

• Updated ASOIAF pedigree to include Tarths, Brackens
• Added sliceFamilies function with working tests
• Better messaging for sliceFamilies
• Now has some error handling for sliceFamilies
• Added option to restore variable names in selected places

BGmisc 1.4.3.2

• Slightly expanded vignettes to include more examples of the new features in BGmisc and ggpedigree.
• Updated ASOIAF pedigree to reduce missing parents.
• Added tests to check if data are acyclic
• reduce file size for royal92

BGmisc 1.4.3.1

• Updated ASOIAF pedigree to reduce missing parents.

BGmisc 1.4.3

• transferred plotPedigree to ggpedigree

BGmisc 1.4.2

• Added twinIDs for potter and asoiaf pedigrees
• Added twinID to simulatePedigree function, and extended to include MZ, DZ, and SS twins.
• Added a few more tests for simulatePedigree
• Added function to easily add new person to a pedigree
• Updated ASOIAF pedigree to reduce missing parents
• Added a few more tests for simulatePedigree helpers
• Allow simulatePedigree to accept variable names and coding for sex

BGmisc 1.4.1

• replaced print with message in all functions
• Exposed several internal functions to the user
• refactored addPhantomParents to be more efficient
• add mtdna and mitochondria as aliases for mitochondrial
• reorganized unit tests
• introduces the new calculateCIs function for computing confidence intervals for correlation coefficients
• added comprehensive tests and corresponding documentation updates for calculateCI

BGmisc 1.4.0

• revived checkParents function to check for handling phantom parents and missing parents
• added tests for checkParents function
• added GoT analysis
• reduced complexity of com2links, summarizePedigree, and checkIDs with the use of subfunctions
• allow verbose argument to be passed to standardizeColnames
• list SimPed and related_coef as aliases for functions
• harmonizing function names like calcFamilySize from famSizeCal
• implemented adjBeta function to evaluation alternative build method
• reorganize file names to be more consistent
• harmonized famID

BGmisc 1.3.5.1

• Setting the default for the sparse argument in ped2com() to TRUE

BGmisc 1.3.5

• Add calculateCIs and readDelimitedData functions
• Added ASOIAF pedigree
• Added com2links() function to convert components to kinship links, with accompanying tests
• Added extractWikiFamilyTree() function to parse family trees from wiki templates, with accompanying tests
• Created vignette demonstrating adjacency matrix methods and applications
• Improved plotPedigree() function by silencing unnecessary invisible list outputs
• Added checkPedigreeNetwork() function for validating pedigree network structure, with accompanying tests

BGmisc 1.3.4.1

• Hot fix to resolve issue with list of adjacency matrix not loading saved version
• Reoptimized generation calculation

BGmisc 1.3.4

• Added alternative (and faster) methods to create the adjacency matrix
• Add tests for comparison of adjacency matrix build methods
• Added Royal Family pedigree

BGmisc 1.3.3

• Added ability to save and reload pedigree objects that are used by ped2Com
• Optimized generation calculation
• Added more tests for summarizePedigree
• enhanced documentation

BGmisc 1.3.2.1

• Added ability to pass additional arguments to the ped2FOO functions

BGmisc 1.3.2

• Added some more tests of identifyModel.R
• Modified tests to be MKL friendly

BGmisc 1.3.1

• Confirmed that all orcids are correct
• Added gedcom importer

BGmisc 1.3.0.1

• Created subfunctions to reduce function complexity

BGmisc 1.3.0

• Harmonized function names
• Fixed incorrectly spelled last name in Potter pedigree
• Added function to summarize variables by family, matrilinael, and patrilineal lines
• Added within row duplicate ID checks
• Added data validation vignettes
• Harmonized function names and arguments

BGmisc 1.2.1

• Added alternative transpose options for the matrix
• Added generalization of Falconer’s formula

BGmisc 1.2.0

• Added numerous code checks, increased code coverage to 85%
• Replaced sapply usage
• Added additional data validation checks
• Accompanying paper published in the Journal of Open Source Software

BGmisc 1.1.0

• Added ability to simulate twins
• Can now trace paternal and maternal lines
• There’s now a Harry Potter pedigree

BGmisc 1.0.1

• Hot fix to resolve plotPedigree wrapper function breaking for pedigrees that contained multiple families

BGmisc 1.0

• Added major update to include simulations, plotting, and examples.

BGmisc 0.1

• Added a NEWS.md file to track changes to the package.
• Initial version launched