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.

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).

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).

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).

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

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).

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!

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.

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.

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

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).

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

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

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).