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NAMESPACE
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NAMESPACE
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# Generated by roxygen2: do not edit by hand
S3method(Eloglik,susiF)
S3method(HMM_regression,susiF)
S3method(L_mixsq,mixture_normal)
S3method(L_mixsq,mixture_normal_per_scale)
S3method(TI_regression,susiF)
S3method(cal_KL_l,susiF)
S3method(cal_clfsr,mixture_normal)
S3method(cal_clfsr,mixture_normal_per_scale)
S3method(cal_partial_resid,EBmvFR)
S3method(cal_partial_resid,susiF)
S3method(check_cs,susiF)
S3method(discard_cs,susiF)
S3method(estimate_residual_variance,EBmvFR)
S3method(estimate_residual_variance,susiF)
S3method(get_ER2,EBmvFR)
S3method(get_ER2,susiF)
S3method(get_G_prior,EBmvFR)
S3method(get_G_prior,susiF)
S3method(get_alpha,susiF)
S3method(get_fitted_effect,susiF)
S3method(get_lBF,susiF)
S3method(get_objective,susiF)
S3method(get_pi,susiF)
S3method(get_pi0,pi_mixture_normal)
S3method(get_pi0,pi_mixture_normal_per_scale)
S3method(get_pi_G_prior,mixture_normal)
S3method(get_pi_G_prior,mixture_normal_per_scale)
S3method(get_post_F,susiF)
S3method(get_post_F2,susiF)
S3method(get_sd_G_prior,mixture_normal)
S3method(get_sd_G_prior,mixture_normal_per_scale)
S3method(greedy_backfit,susiF)
S3method(init_prior,default)
S3method(log_BF,mixture_normal)
S3method(log_BF,mixture_normal_per_scale)
S3method(loglik_SFR,susiF)
S3method(loglik_SFR_post,susiF)
S3method(m_step,lik_mixture_normal)
S3method(m_step,lik_mixture_normal_per_scale)
S3method(merge_effect,susiF)
S3method(name_cs,susiF)
S3method(out_prep,EBmvFR)
S3method(out_prep,susiF)
S3method(plot,susiF)
S3method(post_mat_mean,mixture_normal)
S3method(post_mat_mean,mixture_normal_per_scale)
S3method(post_mat_sd,mixture_normal)
S3method(post_mat_sd,mixture_normal_per_scale)
S3method(test_stop_cond,EBmvFR)
S3method(test_stop_cond,susiF)
S3method(update_ELBO,susiF)
S3method(update_KL,susiF)
S3method(update_alpha,susiF)
S3method(update_alpha_hist,susiF)
S3method(update_cal_credible_band,susiF)
S3method(update_cal_cs,susiF)
S3method(update_cal_fit_func,EBmvFR)
S3method(update_cal_fit_func,susiF)
S3method(update_cal_indf,EBmvFR)
S3method(update_cal_pip,susiF)
S3method(update_lBF,susiF)
S3method(update_lfsr,susiF)
S3method(update_lfsr_effect,susiF)
S3method(update_pi,susiF)
S3method(update_prior,mixture_normal)
S3method(update_prior,mixture_normal_per_scale)
S3method(update_residual_variance,EBmvFR)
S3method(update_residual_variance,susiF)
S3method(update_susiF_obj,susiF)
S3method(which_dummy_cs,susiF)
export(EBmvFR)
export(EBmvFR.workhorse)
export(Eloglik)
export(Eloglik.susiF)
export(HMM_regression)
export(HMM_regression.susiF)
export(L_mixsq)
export(L_mixsq.mixture_normal)
export(L_mixsq.mixture_normal_per_scale)
export(TI_regression)
export(TI_regression.susiF)
export(affected_reg)
export(cal_KL_l)
export(cal_KL_l.susiF)
export(cal_clfsr)
export(cal_clfsr.mixture_normal)
export(cal_clfsr.mixture_normal_per_scale)
export(cal_cor_cs)
export(cal_lfsr)
export(cal_lik)
export(cal_partial_resid)
export(cal_partial_resid.EBmvFR)
export(cal_partial_resid.susiF)
export(cal_purity)
export(cal_zeta)
export(check_cs)
export(check_cs.susiF)
export(colScale)
export(discard_cs)
export(discard_cs.susiF)
export(estimate_residual_variance)
export(estimate_residual_variance.EBmvFR)
export(estimate_residual_variance.susiF)
export(gen_wavelet_indx)
export(get_ER2)
export(get_ER2.EBmvFR)
export(get_ER2.susiF)
export(get_G_prior)
export(get_G_prior.susiF)
export(get_fitted_effect)
export(get_fitted_effect.susiF)
export(get_objective)
export(get_objective.susiF)
export(get_pi0)
export(get_pi0.pi_mixture_normal)
export(get_pi0.pi_mixture_normal_per_scale)
export(get_pi_G_prior)
export(get_pi_G_prior.mixture_normal)
export(get_pi_G_prior.mixture_normal_per_scale)
export(get_sd_G_prior)
export(get_sd_G_prior.mixture_normal)
export(get_sd_G_prior.mixture_normal_per_scale)
export(greedy_backfit)
export(greedy_backfit.susiF)
export(init_EBmvFR_obj)
export(init_prior)
export(init_susiF_obj)
export(log_BF)
export(log_BF.mixture_normal)
export(log_BF.mixture_normal_per_scale)
export(loglik_SFR)
export(loglik_SFR.susiF)
export(loglik_SFR_post)
export(loglik_SFR_post.susiF)
export(m_step)
export(m_step.lik_mixture_normal)
export(m_step.lik_mixture_normal_per_scale)
export(merge_effect)
export(merge_effect.susiF)
export(out_prep)
export(out_prep.EBmvFR)
export(out_prep.susiF)
export(plot_susiF)
export(plot_susiF_effect)
export(plot_susiF_pip)
export(post_mat_mean)
export(post_mat_mean.mixture_normal)
export(post_mat_mean.mixture_normal_per_scale)
export(post_mat_sd)
export(post_mat_sd.mixture_normal)
export(post_mat_sd.mixture_normal_per_scale)
export(remap_data)
export(simu_IBSS_ash_vanilla)
export(simu_IBSS_per_level)
export(susiF)
export(susiF.workhorse)
export(test_stop_cond)
export(test_stop_cond.EBmvFR)
export(test_stop_cond.susiF)
export(update_ELBO)
export(update_ELBO.susiF)
export(update_KL)
export(update_KL.susiF)
export(update_alpha)
export(update_alpha.susiF)
export(update_alpha_hist)
export(update_alpha_hist.susiF)
export(update_ash_pi)
export(update_cal_cs)
export(update_cal_cs.susiF)
export(update_cal_fit_func)
export(update_cal_fit_func.EBmvFR)
export(update_cal_fit_func.susiF)
export(update_cal_pip)
export(update_cal_pip.susiF)
export(update_lBF)
export(update_lBF.susiF)
export(update_lfsr)
export(update_lfsr.susiF)
export(update_lfsr_effect)
export(update_lfsr_effect.susiF)
export(update_prior)
export(update_prior.mixture_normal)
export(update_prior.mixture_normal_per_scale)
export(update_residual_variance)
export(update_residual_variance.EBmvFR)
export(update_residual_variance.susiF)
export(which_dummy_cs)
export(which_dummy_cs.susiF)
export(which_lowcount)
importFrom(Rfast,colVars)
importFrom(Rfast,colsums)
importFrom(Rfast,cova)
importFrom(ashr,ash)
importFrom(ashr,calc_loglik)
importFrom(ashr,cdf_post)
importFrom(ashr,comp_postprob)
importFrom(ashr,compute_lfsr)
importFrom(ashr,get_fitted_g)
importFrom(ashr,mixcdf)
importFrom(ashr,mixprop)
importFrom(ashr,normalmix)
importFrom(ashr,pm_on_zero)
importFrom(ashr,set_data)
importFrom(cowplot,theme_cowplot)
importFrom(ggplot2,aes)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,facet_grid)
importFrom(ggplot2,facet_wrap)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_ribbon)
importFrom(ggplot2,geom_segment)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,labs)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,theme)
importFrom(ggplot2,xlab)
importFrom(ggplot2,ylab)
importFrom(graphics,legend)
importFrom(graphics,lines)
importFrom(graphics,plot)
importFrom(matrixStats,colSds)
importFrom(mixsqp,mixsqp)
importFrom(stats,"tsp<-")
importFrom(stats,complete.cases)
importFrom(stats,cor)
importFrom(stats,dnorm)
importFrom(stats,lm)
importFrom(stats,median)
importFrom(stats,pt)
importFrom(stats,qnorm)
importFrom(stats,qqnorm)
importFrom(stats,rchisq)
importFrom(stats,rnorm)
importFrom(stats,runif)
importFrom(stats,tsp)
importFrom(stats,var)
importFrom(utils,head)
importFrom(utils,tail)
importFrom(wavethresh,DJ.EX)
importFrom(wavethresh,IsPowerOfTwo)
importFrom(wavethresh,accessC)
importFrom(wavethresh,accessD)
importFrom(wavethresh,av.basis)
importFrom(wavethresh,convert)
importFrom(wavethresh,filter.select)
importFrom(wavethresh,first.last)
importFrom(wavethresh,getarrvec)
importFrom(wavethresh,nlevelsWT)
importFrom(wavethresh,putC)
importFrom(wavethresh,putD)
importFrom(wavethresh,wd)
importFrom(wavethresh,wd.int)
importFrom(wavethresh,wr)
importFrom(wavethresh,wst)