- Public release!

- Minor non-code changes for first CRAN submission.

- README.md now contains instructions for installing from CRAN as well as from GitHub.

Added option

`noFixed`

to function`rbnpsd`

to redraw loci that were drawn fixed for a single allele. These loci are not polymorphic so they would normally not be considered in analyses.Added function

`fixed_loci`

to test for fixed loci within rbnpsd.

- Added function
`coanc_to_kinship`

to easily obtain kinship matrices from coancestry matrices.

- Second CRAN submission.

- Converted the vignette from PDF to HTML

`qis`

now returns a numeric admixture proportions matrix (used to be logical).`q1d`

and`q1dc`

now handle`sigma = 0`

special case.`q1d`

and`q1dc`

now provide more informative out-of-bounds messages when`sigma`

is missing (and`s`

is provided)`sigma`

root finding in`q1d`

and`q1dc`

(when`s`

is provided) is now more robust, explicitly tested at boundaries (min`s > 0`

achieved at`sigma = 0`

and max`s = 1`

achieved at`sigma = Inf`

).- Removed arguments
`interval`

and`tol`

from both`q1d`

and`q1dc`

(users would never need to set them now that procedure is more robust).

- Removed arguments
- Updated coding style, renamed some internal functions and variables.

- Renamed most functions for clarity:
`coanc`

->`coanc_admix`

`q1d`

->`admix_prop_1d_linear`

`q1dc`

->`admix_prop_1d_circular`

`qis`

->`admix_prop_indep_subpops`

`rpanc`

->`draw_p_anc`

`rpint`

->`draw_p_subpops`

`rpiaf`

->`make_p_ind_admix`

`rgeno`

->`draw_genotypes_admix`

`rbnpsd`

->`draw_all_admix`

`fst`

->`fst_admix`

(no deprecated version available in this case, to eliminate conflict with`popkin::fst`

)- Functions with old names remain for now as deprecated functions (to be removed in the future).

- Renamed several recurrent argument names for clarity:
`Q`

->`admix_proportions`

`F`

->`coanc_subpops`

(if general matrix is accepted),`inbr_subpops`

(vector or scalar versions required)`s`

->`bias_coeff`

`w`

->`weights`

`Theta`

->`coancestry`

`m`

->`m_loci`

`n`

->`n_ind`

`k`

->`k_subpops`

`pAnc`

->`p_anc`

`B`

->`p_subpops`

`P`

->`p_ind`

- Deprecated functions still accept old argument names.

- Fixed a
`sigma = 0`

bug in`admix_prop_1d_circular`

. - Changed default values for
`draw_all_admix`

(compared to deprecated`rbnpsd`

, which retains old defaults):`require_polymorphic_loci`

(old`noFixed`

) is now`TRUE`

by default.`want_p_ind`

and`want_p_subpops`

(old`wantP`

and`wantB`

) are now`FALSE`

by default.- Names (following above conventions) and order of items in return list changed.

`draw_p_subpops`

now admits scalar inputs`p_anc`

and`inbr_subpops`

, while number of loci and number of subpopulations can be provided as additional options.- Added more input checks to functions, informative error messages.
- Updated documentation, particularly on whether intermediate subpopulation coancestries are accepted generally (
`coanc_subpops`

) or if the diagonal matrix case is required (specified as vector or scalar`inbr_subpops`

).

- Third CRAN submission.
- Added ORCIDs to authors.
- Corrected doc typos.
- Adjusted layout of subpopulations and individuals (default limits) for circular 1D geography (
`admix_prop_1d_circular`

) to prevent overlapping individuals on the edges, and to better agree visually with the linear version (`admix_prop_1d_linear`

).