NEWS.md

In OchoaLab/simfam: Simulate and Model Family Pedigrees with Structured Founders

simfam 0.0.0.9000 (2021-07-30)

• First commit of redesigned family structure simulation code, meant for public (eventually).
• Original (scripts in a private repository, not a proper package) was not tested systematically, assumed a rigid setup with every individual paired in the next generation and exactly two children per family, and sex retroactively assigned as needed.
• New code draws sex first and respects those values while pairing (resulting in more realistic constraints), allows unpaired individuals (fixes cases in old setup where pairing everybody was impossible and restarts were required, which in extreme cases led to infinite loops), variable number of children per family (constrained to target population size, which may vary per generation).
• Also, new code for calculating kinship and admixture matrices, and drawing genotypes, work for arbitrary FAM tables (i.e. arbitrary pedigrees). Again, old code was very rigid in assuming non-overlapping generations and fixed family sizes, and accepted a more limited data structure for the same reason.
• This early version is thoroughly tested, but not documented at all. No functions are exported.

simfam 0.0.1.9000 (2021-07-31)

• Documented (Roxygen2) and exported main functions: sim_pedigree, kinship_fam, admix_fam, draw_geno_fam, draw_sex, prune_fam.
• Function sim_pedigree: made n first and only mandatory argument (used to be second), now G is second (used to be first) and defaults to G = length(n).
• Fixed import namespaces, other minor changes to pass R checks.

simfam 0.0.2.9000 (2021-08-03)

• Function sim_pedigree now assigns IDs without g prefix (format is just \d+-\d+ with two integers denoting generation and index, separated by a dash).

simfam 0.0.3.9000 (2021-08-03)

• Function sim_pedigree now returns parents of founders as NA (used to be 0).
• All functions that accept a FAM table as input now treat NA parents correctly as missing (i.e., those individuals with missing parents are treated as founders), and by default the empty strings ('') and zero (0) are also treated as missing (used to be only 0 was treated as missing).

simfam 0.0.4.9000 (2021-08-04)

• Added vignette with beautiful examples!

simfam 0.0.5.9000 (2021-08-04)

• Added README
• Added documentation for package entry (simfam-package).
• Fixed wording in DESCRIPTION and vignette.

simfam 0.0.6.9000 (2021-08-04)

• Function sim_pedigree removed verbose option (it was a holdout from original code, which could get stuck in some situations; the new code doesn't get stuck).

simfam 0.0.7.9000 (2021-08-05)

• Function sim_pedigree now returns ids (ids of IDs separated by generation) among its list elements, after fam but before kinship_local.

simfam 0.0.8.9000 (2021-08-05)

• Added function draw_geno_last_gen for drawing genotypes for last generation only, of a pedigree with non-overlapping generations, saving lots of memory when the number of generations is large (behavior resembles original function, though internally it's a wrapper around the more general draw_geno_fam).

simfam 0.0.9.9000 (2021-08-06)

• Rewrote core of function draw_geno_fam in C++ (using Rcpp). New version is much faster and uses about half as much memory as the previous pure-R version!

simfam 0.0.10.9000 (2021-08-06)

• Added function kinship_last_gen for calculating kinship for last generation only, of a pedigree with non-overlapping generations, saving lots of memory when the number of generations is large (behavior resembles original function, though internally it's a wrapper around the more general kinship_fam).
• Other functions now inherit parameters, the main function being draw_geno_fam (for the other *_fam functions, which are respectively sources for *_last_gen functions).
• Removed obsolete comments.

simfam 0.0.11.9000 (2021-08-06)

• Added function admix_last_gen. same deal as previous *_last_gen functions (less coding in practice, memory savings).
• Fixed some minor typos in other functions, added drop = FALSE in some necessary cases.

simfam 0.0.12.9000 (2021-08-06)

• Dropped redundant draw_ prefix from genotype functions:
• draw_geno_fam -> geno_fam
• draw_geno_last_gen -> geno_last_gen

simfam 1.0.0 (2021-08-09)

• First version publicly available on GitHub!
• Changes prepping for first CRAN submission
• Corrected spelling errors
• Clarified bnpsd dependence (older versions don't propagate names, which the vignette relies upon).

simfam 1.0.1 (2021-08-12)

• More changes prepping for CRAN submission (based on feedback from another new package).
• Added bioRxiv paper reference to description.
• Reset par() in vignette examples.

simfam 1.0.2 (2021-08-31)

• First CRAN submission!
• README
• Uncommented CRAN installation instructions
• Corrected GitHub installation instructions to use build_vignettes = TRUE instead of build_opts = c() (which did not build vignettes anymore).
• Function draw_couples_nearest removed unnecessary checks (redundant with unit tests)
• Added file cran-comments.md.
• DESCRIPTION corrected title for proper title case

simfam 1.0.3 (2021-09-27)

• 2nd CRAN submission!
• Tests: adjusted sample sizes in an internal unit test to make a particular sim_pedigree error rate ~100x less likely than before (error due to not being able to pair everybody; previously, this unlikely error expected 0.4% of the time actually occurred on CRAN, now it is expected 0.002% of the time).

simfam 1.1.0.9000 (2022-04-26)

First set of updates for simulating with recombination!

• Updated reference DOI to newest preprint
• Added functions recomb_fam and recomb_init_founders for simulating recombination breaks for a pedigree!
• These breaks are on genetic distance only so far.
• Other nice features (drawing genotypes, calculating kinship, or local ancestry) are not yet present but they are planned.

simfam 1.1.1.9000 (2022-06-06)

• Added simplified human genome recombination maps (data) and the functions used to create them.
• Added function recomb_map_fix_ends_chr to shift and extrapolate genetic map to chromosome ends.
• Added function recomb_map_simplify_chr to simplify genetic maps by removing rows that can be interpolated to within a desired error.
• Added and documented data recomb_map_hg38 and recomb_map_hg37, which was created from existing maps processed by the above two functions.

simfam 1.1.2.9000 (2022-06-15)

• Functions recomb_fam and recomb_init_founders slight change in input and output formats: each chromosome list now has column posg indicating end of recombination block in genetic position (the column used to be called end; changed to match notation in recombination map, where pos is position in base pairs and posg is in genetic distance).
• Function recomb_init_founders argument lengs may now be a recombination map for simplicity, from which the desired chromosome lengths are extracted, rather than having to extract them in a separate step.
• Added function recomb_map_inds to map recombination breaks from genetic positions to base pair coordinates.

simfam 1.1.3.9000 (2022-06-24)

• Added function recomb_last_gen, a wrapper around recomb_fam that processes data in discrete generations and returns the recombination breaks/blocks of the final generation only, to reduce memory usage. Same analogy of previous *_last_gen functions and their corresponding *_fam versions.
• Added function recomb_haplo_inds to construct the haplotypes of descendant individuals given the haplotypes of the ancestors.
• Added function recomb_geno_inds to construct a standard genotype matrix from the haplotypes of individuals (a complex nested list structure).

simfam 1.1.4.9000 (2022-06-27)

• Added function fam_ancestors to construct simple ancestor pedigrees for a single person with a desired number of generations, and automatic names.

simfam 1.1.5.9000 (2022-06-28)

• Added function recomb_admix_inds to produce true population ancestry dosage matrices that parallel genotype matrices, useful for regression models that incorporate local ancestry.

simfam 1.1.6 (2023-01-06)

• CRAN submission
• Documentation edits
• Updated hyperlink to raw genetic maps.
• Fixed typos
• Escaped more code to simplify spellcheck in the future.
• Updated cran-comments.md

simfam 1.1.6.9000 (2023-06-22)

• Added a logo for the package, displayed at the top of the README.md page
• Minor documentation correction for data recomb_map_hg.

simfam 1.1.7.9000 (2024-01-25)

• Added function bim_add_posg to calculate genetic positions from base pair positions and a genetic map.
• In DESCRIPTION, updated citation to published paper.

simfam 1.1.8.9000 (2024-07-09)

• Added function pop_recomb to simulate genotypes with linkage disequilibrium (LD) given a population of haplotypes, using a Li-Stephens-like model of haplotype copying

simfam 1.1.9.9000 (2024-07-17)

• Function pop_recomb added support for option haps to be a BEDMatrix object, and added option loci_on_cols to accept a transposed haps input.

simfam 1.1.10.9000 (2024-10-22)

• Function pop_recomb added option indexes_loci to simulate only a portion of the genome available.
• Added functions tidy_recomb_map_inds and recomb_founder_blocks_inherited to create and manipulate tidy versions of our recombination data structure, which are more useful in some cases, currently focused on identifying founder blocks that are inherited by focal individuals.
• Added dplyr and tidyselect as new package dependencies, which is used for both of these new functions that manipulate tidy tables.

simfam 1.1.11.9000 (2024-10-29)

• Added function geno_last_gen_admix_recomb that efficiently simulates admixed families with LD in the ancestors
• Added package dependencies rlang, Matrix, and methods, which are used by the new function
• Function recomb_haplo_inds now accepts Matrix-package objects (including sparse matrices) as input haplotype matrix
• Function recomb_admix_inds now accepts inputs with a single ancestry (which may happen when used through geno_last_gen_admix_recomb). Before it required at least two ancestries.

simfam 1.1.12.9000 (2024-11-15)

• Sped up the following functions by restricting locus subsets to be contiguous
• Functions pop_recomb and geno_last_gen_admix_recomb added option indexes_chr_ends to provided precalculated chromosome end indexes, which can result in improved runtime when looped.
• Added function indexes_chr to precalculate chromosome end indexes, to provide to the above functions if desired.
• Function pop_recomb option indexes_loci now must be a range (start and end indexes) rather than take on arbitrary values.

simfam 1.1.13.9000 (2024-11-19)

• Functions pop_recomb and geno_last_gen_admix_recomb further optimized based on code profiling, and smarter coding

simfam 1.1.14.9000 (2025-01-03)

• Functions kinship_fam and sim_pedigree added option sparse to handle sparse kinship matrices, which reduce memory usage when applicable but are currently slower algorithms otherwise.

simfam 1.1.15.9000 (2025-01-07)

• Function kinship_fam runtime optimized for sparse case: internal C++ code has new structure for extracting rows considerably faster (at the expense of somewhat more memory).

simfam 1.1.16.9000 (2025-12-08)

• Function sim_pedigree optimized for sparse case: internal C++ code now identifies all close relatives in a single scan of the sparse structure, which is much faster than the repeated queries performed before.

OchoaLab/simfam documentation built on Jan. 11, 2025, 12:23 a.m.