dbernbinom |
Special case of betabinomial where the beta is bernoulli mu. |
dbetabinom |
The Beta-Binomial Distribution |
dbetabinom_alpha_beta_double |
Density function of betabinomial with the shape parameterizations |
dbetabinom_double |
The density function of the beta-binomial distribution. |
dc_dtau |
Derivative of c = (1 - tau) / tau with respect to tau. |
df_deps |
Derivative of f with respect to eps. |
dlbeta_dc |
Derivative of the log-beta density with respect to c where c = (1 - tau)/tau where tau is the overdispersion parameter. |
dlbeta_deps |
Derivative of the log-beta-binomial density with respect to the sequencing error rate. |
dlbeta_dh |
Derivative of log-betabinomial density with respect to bias parameter. |
dlbeta_dtau |
Derivative of the log-beta-binomial density with respect to the overdispersion parameter. |
dlbeta_dxi |
Derivative of the log-betabinomial density with respect to the mean of the underlying beta. |
doutdist |
The outlier distribution we use. Right now it is just a beta binomial with mean 1/2 and od 1/3 (so underlying beta is just a uniform from 0 to 1). |
dpen_deps |
Derivative of -log(epsilon(1 - epsilon)) - (logit(epsilon) - mu_{epsilon})^2 / (2sigma_{epsilon}^2) with respect to epsilon. |
dpen_dh |
Derivative of -log(h) - (log(h) - mu_h)^2 / (2sigma_h^2) with respect to h. |
dr_pen |
Penalty used in 'update_dr'. |
dxi_df |
Derivative of xi with respect to f. |
dxi_dh |
Derivative of xi-function with respect to bias parameter. |
get_bivalent_probs |
Returns segregation probabilities, pairing representation and number of ref alleles given the ploidy. |
get_bivalent_probs_dr |
Double reduction version of 'get_bivalent_probs'. |
get_conv_inner_weights |
Get the inner weights used for the em update in 'update_pp_f1' when there are more than two bivalent components for one of the parents. |
get_dimname |
Returns a vector character strings that are all of the possible combinations of the reference allele and the non-reference allele. |
get_hyper_weights |
Return mixture weights needed to obtain a hypergeometric distribution. |
get_inner_weights |
Compute inner weights for updating the mixing proportions when using ash model. |
get_probk_vec |
Obtain the genotype distribution given the distribution of discrete uniforms. |
get_q_array |
Return the probabilities of an offspring's genotype given its parental genotypes for all possible combinations of parental and offspring genotypes. This is for species with polysomal inheritance and bivalent, non-preferential pairing. |
get_uni_rep |
Get the representation of a discrete unimodal probability distribution. |
get_wik_mat |
E-step in 'flexdog'. |
get_wik_mat_out |
E-step in 'flexdog' where we now allow an outlier distribution. |
grad_for_eps |
Gradient for 'obj_for_eps'. |
grad_for_mu_sigma2 |
Gradient for 'obj_for_mu_sigma2' with respect for 'mu' and 'sigma2'. |
grad_for_mu_sigma2_wrapper |
Gradient for 'obj_for_mu_sigma2_wrapper' with respect for 'muSigma2' and a wrapper for 'grad_for_mu_sigma2' |
grad_for_weighted_lbb |
Gradient for 'obj_for_weighted_lbb'. |
grad_for_weighted_lnorm |
Gradient for 'obj_for_weighted_lnorm'. |
obj_for_alpha |
Objective function when updating alpha |
obj_for_eps |
Objective function for updating sequencing error rate, bias, and overdispersion parameters. |
obj_for_mu_sigma2 |
Objective function when updating mu and sigma2. |
obj_for_mu_sigma2_wrapper |
Wrapper for 'obj_for_mu_sigma2' so that I can use it in 'optim'. |
obj_for_rho |
Objective function when updating a single inbreeding coefficient. |
obj_for_weighted_lbb |
Objective function for updating the beta-binomial genotype distribution when 'model = "bb"' in 'flex_update_pivec'. |
obj_for_weighted_lnorm |
Objective funtion for updating discrete normal genotype distribution when 'model = "normal"' in 'flex_update_pivec'. |
oracle_cor |
Calculates the correlation between the true genotype and an oracle estimator. |
oracle_cor_from_joint |
Calculate the correlation of the oracle estimator with the true genotype from the joint distribution matrix. |
oracle_joint |
The joint probability of the genotype and the genotype estimate of an oracle estimator. |
oracle_mis |
Calculate oracle misclassification error rate. |
oracle_mis_from_joint |
Get the oracle misclassification error rate directly from the joint distribution of the genotype and the oracle estimator. |
oracle_mis_vec |
Returns the oracle misclassification rates for each genotype. |
oracle_mis_vec_from_joint |
Get the oracle misclassification error rates (conditional on true genotype) directly from the joint distribution of the genotype and the oracle estimator. |
oracle_plot |
Construct an oracle plot from the output of 'oracle_joint'. |
pbetabinom |
The Beta-Binomial Distribution |
pbetabinom_double |
The distribution function of the betabinomial. This is generally only adviseable if q is relatively small. |
pen_bias |
Penalty on bias parameter. |
pen_seq_error |
Penalty on sequencing error rate. |
pivec_from_segmats |
Function to get the segregation probabilities from the distributions of each component and the weights of each component. |
plot.flexdog |
Draw a genotype plot from the output of 'flexdog'. |
plot.mupdog |
Draw a genotype plot from the output of 'mupdog'. |
plot_geno |
Make a genotype plot. |
post_prob |
Variational posterior probability of having 'dosage' A alleles when the ploidy is 'ploidy', the allele frequency is 'alpha', the individual-specific overdispersion parameter is 'rho', the variational mean is 'mu', and the variational variance is 'sigma2'. |
pp_brent_obj |
Objective function when doing Brent's method in 'update_pp_f1' when one parent only has two mixing components. |
uitdewilligen |
Subset of individuals and SNPs from Uitdewilligen et al (2013). |
uni_em |
EM algorithm to fit weighted ash objective. |
uni_em_const |
EM algorithm to fit weighted ash objective with a uniform mixing component. |
uni_obj |
Objective function optimized by 'uni_em'. |
uni_obj_const |
Objective function optimized by 'uni_em_const'. |
update_dr |
Same as 'update_pp_f1' but I exclusively use the EM (instead of also Brent's method), and I allow for priors on the mixing proportions. |
update_pp_f1 |
Function to update the parameters in the preferential pairing F1 model. |
update_pp_s1 |
Same as 'update_pp_f1' but only allow s1. |
update_R |
Update the underlying correlation matrix. |
updog |
'updog' Flexible Genotyping for Polyploids |