ash Adaptive Shrinkage ash_pois Performs adaptive shrinkage on Poisson data ashci Credible Interval Computation for the ash object ashr ashr calc_logLR Compute loglikelihood ratio for data from ash fit calc_loglik Compute loglikelihood for data from ash fit calc_mixmean Generic function of calculating the overall mean of the mixture calc_mixsd Generic function of calculating the overall standard deviation of the mixture calc_null_loglik Compute loglikelihood for data under null that all beta are 0 calc_null_vloglik Compute vector of loglikelihood for data under null that all beta are 0 calc_vlogLR Compute vector of loglikelihood ratio for data from ash fit calc_vloglik Compute vector of loglikelihood for data from ash fit cdf.ash cdf method for ash object cdf_conv cdf_conv cdf_post cdf_post comp_cdf Generic function of computing the cdf for each component comp_cdf_conv comp_cdf_conv comp_cdf_conv.normalmix comp_cdf_conv.normalmix comp_cdf_conv.unimix cdf of convolution of each component of a unif mixture comp_cdf_post comp_cdf_post comp_dens Generic function of calculating the component densities of the mixture comp_dens_conv comp_dens_conv comp_dens_conv.normalmix comp_dens_conv.normalmix comp_dens_conv.unimix density of convolution of each component of a unif mixture comp_mean Generic function of calculating the first moment of components of the mixture comp_mean.normalmix comp_mean.normalmix comp_mean.tnormalmix comp_mean.tnormalmix comp_mean2 Generic function of calculating the second moment of components of the mixture comp_postmean comp_postmean comp_postmean2 comp_postmean2 comp_postprob comp_postprob comp_postsd comp_postsd comp_sd Generic function to extract the standard deviations of components of the mixture comp_sd.normalmix comp_sd.normalmix comp_sd.tnormalmix comp_sd.normalmix compute_lfsr Function to compute the local false sign rate cxxMixSquarem Brief description of function. dens Find density at y, a generic function dens_conv dens_conv dlogf The log-F distribution estimate_mixprop Estimate mixture proportions of a mixture g given noisy (error-prone) data from that mixture. gen_etruncFUN gen_etruncFUN get_density Density method for ash object get_lfsr Return lfsr from an ash object get_post_sample Sample from posterior igmix Constructor for igmix class lik_binom Likelihood object for Binomial error distribution lik_logF Likelihood object for logF error distribution lik_normal Likelihood object for normal error distribution lik_normalmix Likelihood object for normal mixture error distribution lik_pois Likelihood object for Poisson error distribution lik_t Likelihood object for t error distribution log_comp_dens_conv log_comp_dens_conv log_comp_dens_conv.normalmix log_comp_dens_conv.normalmix log_comp_dens_conv.unimix log density of convolution of each component of a unif mixture loglik_conv loglik_conv loglik_conv.default loglik_conv.default mixEM Estimate mixture proportions of a mixture model by EM algorithm mixIP Estimate mixture proportions of a mixture model by Interior Point method mixSQP Estimate mixture proportions of a mixture model using mix-SQP algorithm. mixVBEM Estimate posterior distribution on mixture proportions of a mixture model by a Variational Bayes EM algorithm mixcdf mixcdf mixcdf.default mixcdf.default mixmean2 Generic function of calculating the overall second moment of the mixture mixprop Generic function of extracting the mixture proportions my_e2truncbeta second moment of truncated Beta distribution my_e2truncgamma second moment of truncated gamma distribution my_e2truncnorm Expected Squared Value of Truncated Normal my_e2trunct my_e2trunct my_etruncbeta mean of truncated Beta distribution my_etruncgamma mean of truncated gamma distribution my_etrunclogf my_etrunclogf my_etruncnorm Expected Value of Truncated Normal my_etrunct my_etrunct my_vtruncnorm Variance of Truncated Normal ncomp ncomp ncomp.default ncomp.default normalmix Constructor for normalmix class pcdf_post pcdf_post plogf The log-F distribution plot.ash Plot method for ash object plot_diagnostic Diagnostic plots for ash object pm_on_zero Generic function to extract which components of mixture are point mass on 0 post_sample post_sample post_sample.normalmix post_sample.normalmix post_sample.unimix post_sample.unimix posterior_dist Compute Posterior postmean postmean postmean2 postmean2 postsd postsd print.ash Print method for ash object prune prune qval.from.lfdr Function to compute q values from local false discovery rates set_data Takes raw data and sets up data object for use by ash summary.ash Summary method for ash object tnormalmix Constructor for tnormalmix class unimix Constructor for unimix class vcdf_post vcdf_post w_mixEM Estimate mixture proportions of a mixture model by EM algorithm (weighted version)