Methods for Adaptive Shrinkage, using Empirical Bayes


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Documentation for package ‘ashr’ version 2.2-47

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A C D E G I L M N P Q S U V W

-- A --

ash Adaptive Shrinkage
ash.workhorse Adaptive Shrinkage
ashci Credible Interval Computation for the ash object
ashr ashr
ash_pois Performs adaptive shrinkage on Poisson data

-- C --

calc_loglik Compute loglikelihood for data from ash fit
calc_logLR Compute loglikelihood ratio 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_vloglik Compute vector of loglikelihood for data from ash fit
calc_vlogLR Compute vector of loglikelihood ratio for data from ash fit
cdf.ash cdf method for ash object
cdf_conv cdf_conv
cdf_post cdf_post
compute_lfsr Function to compute the local false sign rate
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_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
cxxMixSquarem Brief description of function.

-- D --

dens Find density at y, a generic function
dens_conv dens_conv
dlogf The log-F distribution

-- E --

estimate_mixprop Estimate mixture proportions of a mixture g given noisy (error-prone) data from that mixture.

-- G --

gen_etruncFUN gen_etruncFUN
get_density Density method for ash object
get_fitted_g Return lfsr from an ash object
get_lfdr Return lfsr from an ash object
get_lfsr Return lfsr from an ash object
get_loglik Return lfsr from an ash object
get_logLR Return lfsr from an ash object
get_np Return lfsr from an ash object
get_pi0 Return lfsr from an ash object
get_pm Return lfsr from an ash object
get_post_sample Sample from posterior
get_pp Return lfsr from an ash object
get_psd Return lfsr from an ash object
get_qvalue Return lfsr from an ash object
get_svalue Return lfsr from an ash object

-- I --

igmix Constructor for igmix class

-- L --

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
loglik_conv loglik_conv
loglik_conv.default loglik_conv.default
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

-- M --

mixcdf mixcdf
mixcdf.default mixcdf.default
mixEM Estimate mixture proportions of a mixture model by EM algorithm
mixIP Estimate mixture proportions of a mixture model by Interior Point method
mixmean2 Generic function of calculating the overall second moment of the mixture
mixprop Generic function of extracting the mixture proportions
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
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

-- N --

ncomp ncomp
ncomp.default ncomp.default
normalmix Constructor for normalmix class

-- P --

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
posterior_dist Compute Posterior
postmean postmean
postmean2 postmean2
postsd postsd
post_sample post_sample
post_sample.normalmix post_sample.normalmix
post_sample.unimix post_sample.unimix
print.ash Print method for ash object
prune prune

-- Q --

qval.from.lfdr Function to compute q values from local false discovery rates

-- S --

set_data Takes raw data and sets up data object for use by ash
summary.ash Summary method for ash object

-- U --

unimix Constructor for unimix class

-- V --

vcdf_post vcdf_post

-- W --

w_mixEM Estimate mixture proportions of a mixture model by EM algorithm (weighted version)