|
double | a_n (size_t n) |
| Compute a_n , the sum of reciprocals. More...
|
|
double | alpha_star (double n) |
| Compute alpha* according to Achaz 2008 and Kofler et al. 2011. More...
|
|
double | b_n (size_t n) |
| Compute b_n , the sum of squared reciprocals. More...
|
|
double | beta_star (double n) |
| Compute beta* according to Achaz 2008 and Kofler et al. 2011. More...
|
|
double | f_star (double a_n, double n) |
| Compute f* according to Achaz 2008 and Kofler et al. 2011. More...
|
|
double | heterozygosity (BaseCounts const &sample, bool with_bessel=false) |
| Compute classic heterozygosity. More...
|
|
double | n_base (size_t coverage, size_t poolsize) |
| Compute the n_base term used for Tajima's D in Kofler et al. 2011, using a faster closed form expression. More...
|
|
double | n_base_matrix (size_t coverage, size_t poolsize) |
| Compute the n_base term used for Tajima's D in Kofler et al. 2011, following their approach. More...
|
|
template<class ForwardIterator > |
PoolDiversityResults | pool_diversity_measures (PoolDiversitySettings const &settings, ForwardIterator begin, ForwardIterator end) |
| Compute Theta Pi, Theta Watterson, and Tajia's D in their pool-sequencing corrected versions according to Kofler et al. More...
|
|
template<class ForwardIterator > |
double | tajima_d_pool (PoolDiversitySettings const &settings, ForwardIterator begin, ForwardIterator end) |
| Compute the pool-sequencing corrected version of Tajima's D according to Kofler et al. More...
|
|
template<class ForwardIterator > |
double | tajima_d_pool (PoolDiversitySettings const &settings, ForwardIterator begin, ForwardIterator end, double theta_pi, double theta_watterson) |
| Compute the pool-sequencing corrected version of Tajima's D according to Kofler et al. More...
|
|
double | tajima_d_pool_denominator (PoolDiversitySettings const &settings, size_t snp_count, double theta) |
| Compute the denominator for the pool-sequencing correction of Tajima's D according to Kofler et al. More...
|
|
template<class ForwardIterator > |
double | theta_pi (ForwardIterator begin, ForwardIterator end, bool with_bessel=true) |
| Compute classic theta pi, that is, the sum of heterozygosities. More...
|
|
double | theta_pi_pool (PoolDiversitySettings const &settings, BaseCounts const &sample) |
| Compute theta pi with pool-sequencing correction according to Kofler et al, for a single BaseCounts, that is, its heterozygosity() including Bessel's correction for the total nucleotide count at each position, divided by the correction denominator. More...
|
|
template<class ForwardIterator > |
double | theta_pi_pool (PoolDiversitySettings const &settings, ForwardIterator begin, ForwardIterator end) |
| Compute theta pi with pool-sequencing correction according to Kofler et al, that is, the sum of heterozygosities divided by the correction denominator. More...
|
|
double | theta_pi_pool_denominator (PoolDiversitySettings const &settings, size_t nucleotide_count) |
| Compute the denominator for the pool-sequencing correction of theta pi according to Kofler et al. More...
|
|
template<class ForwardIterator > |
double | theta_pi_within_pool (ForwardIterator begin, ForwardIterator end, size_t poolsize) |
| Compute classic theta pi (within a population), that is, the sum of heterozygosities including Bessel's correction for total nucleotide sum at each position, and Bessel's correction for the pool size. More...
|
|
template<class ForwardIterator > |
double | theta_watterson_pool (PoolDiversitySettings const &settings, ForwardIterator begin, ForwardIterator end) |
| Compute theta watterson with pool-sequencing correction according to Kofler et al. More...
|
|
double | theta_watterson_pool_denominator (PoolDiversitySettings const &settings, size_t nucleotide_count) |
| Compute the denominator for the pool-sequencing correction of theta watterson according to Kofler et al. More...
|
|