NEWS

---

BGmisc 1.9.0

• Added addParentalChain() and addParentalFlag() for tracing parental lineages. These functions support general parental-chain construction and convenient maternal and paternal lineage workflows. addParentalFlag() adds a binary indicator for whether each individual belongs to a specified parental chain, which can be useful for filtering, grouping, and lineage-specific summaries.
• Fixed silent mis-scoring in ped2com(), ped2add(), and related component wrappers when momID or dadID referenced a parent ID that was not present as its own row in ped, such as an unrecorded founder or a parent excluded from a pedigree subset. Previously, isChild_method = "partialparent" treated these parents as known because their IDs were non-missing, while adjacency builders treated the corresponding parent-child link as absent. This could understate diagonal values and remove covariance between siblings who shared the missing rowless parent.
• ped2com() now warns when rowless parents are detected. The new repair_rowless_parents argument provides two repair strategies:
  • "rows" adds one placeholder founder row for each unique missing parent ID to a working copy of ped, then restricts the returned matrix back to the original individuals through keep_ids, unless keep_ids is already supplied.
  • "schur" applies a Schur-complement update to the block-triangular RAM system. For each missing parent, its known children define a rank-1 update, v %*% t(v), where v is that parent's traced genetic contribution to every individual. This update is added to the relatedness matrix at the tcrossprod step. The "schur" method currently supports only component = "additive".

BGmisc 1.8.0

• Optimized the GEDCOM reader and com2links() for speed and memory usage, especially for large pedigrees.
• Fixed a GEDCOM reader bug that caused document records to be added to the final person in the pedigree.
• Added unit tests for the GEDCOM reader and data parser.
• Improved GEDCOM parsing, including more robust event parsing, better support for different GEDCOM versions, and improved usability.
• Optimized sliceFamilies() to be more general and to no longer require mitochondrial DNA information.
• Added .require_openmx() to make OpenMx-dependent functionality easier to use without making OpenMx a package dependency.
• Improved string ID handling in ped2id().
• Fixed handling of different-sized matrices in com2links().
• Added alignPhenToMatrix() to align phenotypic data to the order of a relatedness matrix.
• Added simulatePedigrees() to simulate multiple families at once and return them as a single combined data frame.
• Refactored OpenMx wrapper functions.
• Added ped2focal() and component-specific wrappers, including ped2addFocal(), ped2mitFocal(), ped2mtFocal(), ped2cnFocal(), and ped2genFocal(), to compute relatedness between all pedigree members and a focal individual. These functions append the focal relatedness values to the pedigree data frame, with individuals excluded by keep_ids coded as NA and genuine zero values retained.
• Added getGenDist(), ped2genDistFocal(), and ped2genDist() for computing generational distance between individuals. Supported methods include generation-rank differences, shortest parent-child paths through shared ancestors, and most-recent-common-ancestor based distances. tput fs includeongle pairs, a focal column appended to the pedigree, and a full n×n pairwise matrixix.
• Optimized countPatternRows() in the GEDCOM reader by using fixed string matching and a pre-extracted column vector, reducing redundant work across repeated pattern checks.

BGmisc 1.7.0.0

• Fixed a bug in parList.
• Moved ped2com() wrappers to their own .R file.
• Fixed a missing checkpoint for ram_checkpoint.
• Added a chunk_size argument to ped2com() to reduce memory usage during matrix transposition.
• Added an individual-ID filtering method for selecting whose relatedness values are returned.
• Renamed ytemp parameter to obs_ids in buildOneFamilyGroup() and buildFamilyGroups() for clarity
• Expanded v6 vignettes with a data requirements reference and a real-data workflow using the hazard dataset.
• Added support for confidence intervals in pedigree OpenMx wrappers.

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 additional 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