Changes in version 1.8.0 - Optimized gedcom reader, com2links for speed and memory usage, with a focus on large pedigrees - Fixed bug in gedcom reader that resulted in document records being added to the final person in the pedigree - Added more unit tests for gedcom reader and data parser - Optimized sliceFamilies to be more abstract, and no longer require mtdna - Created .require_openmx() to make it easier to use OpenMx functions without making OpenMx a dependency - Smarter string ID handling for ped2id - Fixed how different-sized matrices are handled by com2links() - Added alignPhenToMatrix function to align phenotypic data to the order of the relatedness matrix - Added simulatePedigrees() function to easily simulate multiple families at once and return them as a single combined data frame - Refactor openmx wrapper functions - Added ped2focal() core function and component-specific wrappers (ped2addFocal(), ped2mitFocal()/ped2mtFocal(), ped2cnFocal(), ped2genFocal) to compute relatedness between all pedigree members and a single focal individual, appending the result as a new column on the pedigree data frame. ped2focal() is a general function that can be used with any relatedness method, while the component-specific wrappers provide convenient shortcuts for common use cases. Note that Individuals excluded via keep_ids are coded as NA; all others receive their computed value with genuine zeros made explicit. - Added getGenDist(), ped2genDistFocal(), and ped2genDist() for computing generational distance between individuals. Supports five methods: rank (absolute generation-number difference via ped2gen), path (minimum parent-child steps through any shared ancestor), mrca_min (total steps via the most recent common ancestor), mrca_max (total steps via the most distant common ancestor), and mrca_all (aggregation across all common ancestors — strategy to be defined). Output forms cover single pairs, a focal column appended to the pedigree, and a full n×n pairwise matrix. - Optimized countPatternRows() in the GEDCOM reader to use fixed = TRUE string matching and a pre-extracted column vector, reducing redundant work across 31 pattern passes BGmisc 1.7.0.0 - Fixed bug in parList - Moved wrappers of ped2com to own .R file - Fixed missing checkpoint for ram_checkpoint - Try a chunk_size argument for ped2com to reduce memory usage during transpose - Try filter method for whose relatedness to return by individual ID - Renamed ytemp parameter to obs_ids in buildOneFamilyGroup() and buildFamilyGroups() for clarity - Expanded v6 vignettes with data requirements reference and real-data workflow using the hazard dataset - Allow confidence intervals for pedigree mx 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