Package index • wgsLR

All functions

add_errors_Ha_w(): Add Hd-errors to table for one error probability, $w$

add_errors_Ha_wTwR(): Add Hd-errors to table for sample-dependent error probabilities, $w_t$ and $w_r$

add_errors_Hp_w(): Add Hp-errors to table for one error probability, $w$

add_errors_Hp_wTwR(): Add Hp-errors to table for sample-dependent error probabilities, $w_t$ and $w_r$

add_errors_to_genotypes(): Add errors to genotypes

allele_probs_to_geno_probs(): Allele probabilities to genotype probabilities assuming Hardy-Weinberg equilibrium

rbeta05() pbeta05() qbeta05() dbeta05(): Beta distribution on (0, 0.5)

calc_LRs_w(): Calculate LR for a profile for one error probability, $w$

calc_LRs_wTwR(): Calculate LR for a profile for sample-specific error probabilities

calc_WoE_wTwR_integrate_wT_mc(): Calculate WoE for a profile for sample-specific error probabilities integrated over the donor prior distribution using Monte Carlo integration

calc_WoE_wTwR_integrate_wT_num(): Calculate WoE for sample-specific error probabilities integrated over the donor prior distribution using numerical integration

calc_WoE_wTwR_profilemax_wT_num(): Calculate WoE for sample-specific error probabilities using profile likelihood using numerical optimisation

d_LR_w: Formulas for LR grouped by $X^D$ and $X^S$ for one error probability, $w$

d_LR_wTwR: Formulas for LR grouped by $X^D$ and $X^S$ for sample-dependent error probabilities, $w_t$ and $w_r$

d_formulas_Ha_w: Enumeration of possibilities under Hd for one error probability, $w$

d_formulas_Ha_wTwR: Enumeration of possibilities under Hd for sample-dependent error probabilities, $w_t$ and $w_r$

d_formulas_Hp_w: Enumeration of possibilities under Hp for one error probability, $w$

d_formulas_Hp_wTwR: Enumeration of possibilities under Hp for sample-dependent error probabilities, $w_t$ and $w_r$

d_formulas_single: Enumeration of possibilities for single observation

d_prob_Ha_w: Formulas under Hd grouped by $X^D$ and $X^S$ for one error probability, $w$

d_prob_Ha_wTwR: Formulas under Hd grouped by $X^D$ and $X^S$ for sample-dependent error probabilities, $w_t$ and $w_r$

d_prob_Hp_w: Formulas under Hp grouped by $X^D$ and $X^S$ for one error probability, $w$

d_prob_Hp_wTwR: Formulas under Hp grouped by $X^D$ and $X^S$ for sample-dependent error probabilities, $w_t$ and $w_r$

d_probtable_Ha_w: Probabilties for efficient sampling under Hd for one error probability, $w$

d_probtable_Ha_wTwR: Probabilties for efficient sampling under Hd for one error probability, $w$

d_probtable_Hp_w: Probabilties for efficient sampling under Hp for one error probability, $w$

d_probtable_Hp_wTwR: Probabilties for efficient sampling under Hp for sample-dependent error probabilities, $w_t$ and $w_r$

estimate_w(): Estimate error probability, w

estimate_w_bayesian(): Estimate error probability, w, using a Bayesian approach

estimate_w_se(): Estimate standard error of error probability, w

get_beta_mu_sigma(): Parameterisation conversion for beta distribution

get_beta_parameters(): Parameterisation conversion for beta distribution

get_ns(): Get counts from table

graph_Ha_w: Graph for enumeration of possibilities under Hd for one error probability, $w$

graph_Ha_wTwR: Graph for enumeration of possibilities under Hd for sample-dependent error probabilities, $w_t$ and $w_r$

graph_Hp_w: Graph for enumeration of possibilities under Hp for one error probability, $w$

graph_Hp_wTwR: Graph for enumeration of possibilities under Hp for sample-dependent error probabilities, $w_t$ and $w_r$

graph_single: Graph for enumeration of possibilities for single observation

posterior_samples(): Extract posterior samples

reuse_genotype_probs(): Re-use genotype probabilities

sample_data_Ha_w(): Sample cases under Hd for one error probability, $w$

sample_data_Ha_wTwR(): Sample cases under Hd for sample-dependent error probabilities, $w_t$ and $w_r$

sample_data_Hp_w(): Sample cases under Hp for one error probability, $w$

sample_data_Hp_wTwR(): Sample cases under Hp for sample-dependent error probabilities, $w_t$ and $w_r$

sample_profiles_without_error(): Sample genotype without error

to012(): Convert to 0/1/2 notation