sim_pedigree, kinship_fam,
admix_fam, draw_geno_fam,
draw_sex, prune_fam.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).sim_pedigree now assigns IDs without
g prefix (format is just \d+-\d+ with two
integers denoting generation and index, separated by a dash).sim_pedigree now returns parents of founders
as NA (used to be 0).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-package).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).sim_pedigree now returns ids (ids
of IDs separated by generation) among its list elements, after
fam but before kinship_local.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).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!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).draw_geno_fam (for the other *_fam functions,
which are respectively sources for *_last_gen
functions).admix_last_gen. same deal as previous
*_last_gen functions (less coding in practice, memory
savings).drop = FALSE in some necessary cases.draw_ prefix from genotype functions:
draw_geno_fam -> geno_famdraw_geno_last_gen ->
geno_last_genpar() in vignette examples.build_vignettes = TRUE instead of
build_opts = c() (which did not build vignettes
anymore).draw_couples_nearest removed unnecessary
checks (redundant with unit tests)cran-comments.md.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).First set of updates for simulating with recombination!
recomb_fam and
recomb_init_founders for simulating recombination breaks
for a pedigree!
recomb_map_fix_ends_chr to shift and
extrapolate genetic map to chromosome ends.recomb_map_simplify_chr to simplify
genetic maps by removing rows that can be interpolated to within a
desired error.recomb_map_hg38 and
recomb_map_hg37, which was created from existing maps
processed by the above two 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).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.recomb_map_inds to map recombination
breaks from genetic positions to base pair coordinates.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.recomb_haplo_inds to construct the
haplotypes of descendant individuals given the haplotypes of the
ancestors.recomb_geno_inds to construct a standard
genotype matrix from the haplotypes of individuals (a complex nested
list structure).fam_ancestors to construct simple
ancestor pedigrees for a single person with a desired number of
generations, and automatic names.recomb_admix_inds to produce true
population ancestry dosage matrices that parallel genotype matrices,
useful for regression models that incorporate local ancestry.cran-comments.md