# Tests for Segregation Distortion in Polyploids

## Documentation for package ‘segtest’ version 2.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

beta_bounds | Bounds on the distortion at simplex loci caused by double reduction.
chisq_g | Chi Square test when genotypes are known
chisq_g4 | Chi Square test when genotypes are known
chisq_gl | Chi-Sq for GL
chisq_gl4 | Chi-Sq for GL
drbounds | Upper bounds on double reduction rates.
em_li | EM algorithm from Li (2011)
gamfreq | Gamete frequencies under a generalized model
gcount_to_gvec | Converts genotype counts to genotype vectors.
gf_freq | Genotype frequencies of an F1 population under a generalized model.
gvec_to_gcount | Inverse function of 'gcount_to_gvec()'.
is_valid_2 | Tests if the two parameter model is valid
iter.array | Iterator over array
like_gknown_2 | Likelihood under three parameter model when genotypes are known
like_gknown_3 | Likelihood under three parameter model when genotypes are known
like_glpknown_2 | Likelihood under three parameter model when using offspring genotypes likelihoods but parent genotypes are known.
like_glpknown_3 | Likelihood under three parameter model when using offspring genotypes likelihoods but parent genotypes are known.
llike_li | Objective function for 'em_li()'
lrt_men_g4 | Likelihood ratio test for segregation distortion with known genotypes
lrt_men_gl4 | Likelihood ratio test using genotype likelihoods.
multidog_to_g | Converts multidog output to a format usable for seg_multi() and multi_lrt()
multi_lrt | Parallelized likelihood ratio test for segregation distortion.
nextElem.arrayiter | Next element in an array
n_pp_mix | Number of mixture components
offspring_geno | Simulates genotypes given genotype frequencies.
offspring_gf_2 | Calculates offspring genotype frequencies under the two-parameter model.
offspring_gf_3 | Calculates offspring genotype frequencies under the three-parameter model.
otest_g | Jointly tests for segregation distortion and number of incompatible genotypes
polymapr_test | Run segregation distortion tests as implemented in the polymapR package.
po_gl | Generate genotype likelihoods from offspring genotypes.
pvec_tet_2 | Tetraploid gamete frequencies of gametes when one parent's genotype is known
pvec_tet_3 | Tetraploid gamete frequencies of gametes when one parent's genotype is known
seg | Disomic and polysomic segregation patterns
seg_lrt | Test for segregation distortion in a polyploid F1 population.
seg_multi | Parallelized likelihood ratio test for segregation distortion for arbitrary (even) ploidies.
simf1g | Simulate genotype counts from F1 individuals
simf1gl | Simulate genotype likelihoods of F1 individuals.
simgl | Simulate genotype (log) likelihoods from genotype counts
three_to_two | Convert from three parameters to two parameters
ufit | Genotype data from Cappai et al. (2020)
ufit2 | Genotype data from Cappai et al. (2020)
ufit3 | Genotype data from Cappai et al. (2020)