| bb_post | Posterior inference in beta-binomial model. |
| bbpost_double | Posterior inference under the beta-binomial model with... |
| bbpost_tot | Posterior inference for each individual. |
| bb_simple_post | Simple posterior inference for beta-binomial when ncounts and... |
| bin_post | Calculates posterior probabilities of a genotype given just... |
| colSums_cpp | Stupid implementation of colSums because I guess not... |
| dbetabinom | Beta-binomial density function. |
| dbetabinom_cpp | An Rcpp version of the 'dbetabinom'. |
| dbetabinom_mu_rho | beta-binomial density function in terms of mean and... |
| dbetabinom_mu_rho_cpp | An Rcpp version of 'dbetabinom_mu_rho'. |
| dbetabinom_mu_rho_cpp_double | double version of betabinomial density. |
| dbeta_dd | Derivative of betabinomial density w.r.t. original bias... |
| dbeta_deps | Derivative of beta density w.r.t. sequencing error rate. |
| dbeta_dh | Derivative of overdispersion parameter of beta density. |
| dbeta_dl | Derivative of beta density w.r.t. unconstrained... |
| dbeta_dprop | Derivative of mean of beta density. |
| dbeta_dr | Derivative of beta(x|n, xi, r), where r = log(h) from... |
| dbeta_dr_ell | Same as 'dbeta_dh', but with same inputs as 'dbeta_ds' and... |
| dbeta_ds | Derivative of betabinomial density w.r.t. bias parameter. |
| dbeta_dtau | Derivative of beta(x|n, xi, tau). |
| dbeta_dtau_withxi | Derivative of overdispersion parameter with mean already... |
| dd_ds | Just a wrapper for 'std::exp'. |
| deps_dell | Derivative of exp(ell) / (1 + exp(ell)) |
| df_deps | Returns derivative of p(1 - eps) + (1 - p) * eps |
| dh_dr | Just a wrapper for 'std::exp'. |
| dh_dtau | Derivative of h(tau) = (1 - tau) / tau. |
| dhyper_cpp | Vectorized version of 'dhyper' for C++ implementation. |
| dupdog | Returns log-likelihood of 'updog' object. |
| dxi_dd | Derivative w.r.t. d of xi(d, f) = f / (d * (1 - f) + f) |
| dxi_df | Returns derivative to f / (d * (1 - f) + f) |
| est_seq_error | Estimate sequencing error from counts. |
| est_seq_post | Use posterior probabilities to update the estimated... |
| expit | The expit function. |
| fn_cov_mle | Wrapper for 'obj_offspring_reparam'. |
| get_cov_mle | Calculate the negative inverse hessian of the parameters from... |
| get_dimname | Returns a vector character strings that are all of the... |
| get_out_prop | E step in EM algorithm for a single individual. |
| get_parent_outprop | E-step for the parents. |
| get_prob_geno | Rcpp function to get genotype probabilities assuming either... |
| get_pvec | Gets all possible binomial probabilities for a given ploidy,... |
| get_q_array | Derive the probabilities of an offspring's genotype given its... |
| get_q_array_cpp | Rcpp implementation of 'get_q_array'. |
| get_transition_mat | Get the transition probabilities from going from one ploidy... |
| good_bb_obj | Objective function for non-outlier model |
| grad_offspring | Gradient of 'obj_offspring_reparam'. |
| grad_offspring_mat | Gradient of 'obj_offspring_reparam' for each individual. |
| grad_offspring_mat_original | Gradient of 'obj_offspring' for each individual. This is in... |
| grad_offspring_original | Gradient of 'obj_offspring' using the original... |
| grad_offspring_weights | Gradient of 'obj_offspring_weights_reparam' |
| grad_offspring_weights_original | Gradient of 'obj_offspring_weights' using original... |
| grad_parent | Gradient of 'obj_parent' (when 'outlier = FALSE') with... |
| grad_parent_reparam | The gradient of 'obj_parent_reparam' with respect to 's',... |
| grad_wrapp_all | wrapper for 'grad_offspring_weights' |
| is.updog | Tests if its argument is an updog. |
| logsumexp | Log-sum-exponential trick that I use all the time. |
| obj_offspring | Objective function for the offspring. |
| obj_offspring_reparam | Just a reparameterization of 'obj_offspring'. |
| obj_offspring_vec | Vector of objective functions for offspring. |
| obj_offspring_weights | Same thing as 'obj_offspring', but each sample's log-density... |
| obj_offspring_weights_reparam | Reparameterization of 'obj_offspring_weights'. |
| obj_parent | Parent contribution to objective function. |
| obj_parent_reparam | A reparameterization of 'obj_parent' |
| obj_wrapp_all | wrapper for 'obj_offspring_weights_reparam' |
| out_grad_parent | Gradient function for 'dbetabinom_mu_rho_cpp_double'. |
| out_grad_wrapp | Wrapper for 'outlier_grad'. |
| outlier_bb_obj | Objective function for outlier model. |
| outlier_grad | The gradient of 'outlier_obj'. |
| outlier_obj | Objective function of outlier part in EM step |
| out_obj_wrapp | Wrapper for 'outlier_obj'. |
| pbias | Returns the probability of seeing the reference allele after... |
| pbias_double | A double version of 'pbias'. |
| plot_beta_dist | Plot the beta distribution. |
| plot_beta_dist_gg | Plot the beta distribution using ggplot2. |
| plot_geno | Make a genotype plot. |
| plot_geno_base | The base R graphics version of 'plot_geno'. |
| plot_problines | Plots the genotype lines for a given sequencing error rate,... |
| plot.updog | Draw a genotype plot from the output of 'updog'. |
| rbetabinom_mu_rho | Draw from beta-binomial distribution parameterized by mean... |
| rupdog | Samples counts using the parameter values in an 'updog'... |
| screen_oracle | Returns the distribution of proportion of individuals... |
| snpdat | GBS data from Shirasawa et al (2017) |
| summary.updog | Summary method for class "'updog'". |
| up_bb_fix | EM iteration for overdispersed binomial mixture model. |
| up_bb_obj | Objective function for overdispersed binomial mixture model |
| update_good | Update the OK points |
| updog | Using Parental Data for Offspring Genotyping. |
| updog_iterate | Iterate between indiividual level estimates and joint... |
| updog_maximize | Estimate parental genotypes using offspring genotypes. |
| updog_mcmc | The updog Gibbs sampler to jointly estimate the parental and... |
| updog_old | Using Parental Data for Offspring Genotyping. |
| updog_update_all | This is the main optimization function for updog. |
| updog_vanilla | Using Parental Data for Offspring Genotyping. |
| up_fix | Fixed-point iteration for updog EM. |
| up_max_bb | EM algorithm for over-dispersed mixture model. |
| up_obj | The objective function |
