| draw_beta | Draw from a mixture of normals. |
| dt_wrap | Wrapper for dt with a non-zero mena and non-1 standard... |
| factor_mle | Regularized maximum likelihood factor analysis with... |
| fit_succotash_unif_coord | Coordinate ascent algorithm for normal likelihood and... |
| fn_ab | Function to optimize wrt alpha and beta |
| fn_l | Function to minimize wrt the loadings. |
| fun_scale | Objective function in intermediate step of EM algorithm when... |
| fun_unif_scale | Criterion function for the scale parameter as an intermediate... |
| f_val | Regularized normal log-likelihood. |
| get_pdiffs | Calculate the difference in cdfs. |
| gr_ab | Gradient of function to optimize wrt alpha and beta. |
| gr_l | Gradient of function to minimize wrt loadings. |
| lfdr_to_q | Transform local false discovery rates to q-values. |
| llike_unif_simp | Me being as careful as possible when calculating the... |
| minus_trigamma | Trigamma minus a constant. |
| mod_fa | Moderated factor analysis. Optimize over loadings, factors,... |
| normal_coord | Coordinate ascent for normal mixtures with normal likelihood. |
| normal_llike_grad | Gradient of the log-likelihood wrt Z. |
| normal_llike_simp | Me being super careful in calculating the normal mixtures... |
| normal_only_z | Wrapper for 'succotash_llike', but useful when calling optim. |
| only_Z | Wrapper for 'succotash_llike_unif' but useful for optim where... |
| only_Z_grad | Wrapper for 'unif_grad_simp', but useful for optim where only... |
| pca_naive | Basic PCA. |
| pca_shrinkvar | Use PCA to estimate confounders, then shrink variances using... |
| pt_wrap | Wrapper for pt with a non-zero mena and non-1 standard... |
| succotash | Surrogate and Confounder Correction Occuring Together with... |
| succotash_em | An EM algorithm for maximizing the SUCCOTASH log-likelihood. |
| succotash_fixed | A fixed-point iteration of the EM algorithm. |
| succotash_given_alpha | Maximize the SUCCOTASH log-likelihood and return posterior... |
| succotash_llike | The SUCCOTASH log-likelihood. |
| succotash_llike_unif | Calculates the loglikelihood of the SUCCOTASH model under... |
| succotashr | 'succotashr': An 'R' package for running Surrogate and... |
| succotash_summaries | Provides posterior summaries in the SUCCOTASH model. |
| succotash_unif_fixed | A fixed point iteration in the mixture of uniforms EM. |
| tfun | Function to optimize over Z in EM step. |
| tgrad | Gradient of function to optimize over Z in EM step. |
| trim | Truncates small numbers to 0. |
| t_succotash_llike_unif | Calculates the loglikelihood of the SUCCOTASH model under... |
| t_succotash_unif_fixed | A fixed point iteration in the mixture of uniforms EM and a... |
| t_unif_em | EM algorithm for uniform mixtures and t-likelihood |
| t_uniform_succ_given_alpha | Second step of SUCCOTASH with uniform mixture and a... |
| tupdate_pi | EM step to update pi |
| unif_grad_llike | My first attempt at calculating the gradient of the... |
| unif_grad_simp | This is me being very careful about calculating the gradient... |
| uniform_succ_em | EM algorithm for second step of SUCCOTASH |
| uniform_succ_given_alpha | Second step of SUCCOTASH with uniform mixture. |
| unif_update_pi | E step in EM algorithm. |
| unif_update_z | Runs a few newton steps to update Z given scale_val. |
| update_A | Update low rank mean in regularized maximum likelihood factor... |
| update_ab | Updates the hyperparameters for the gamma prior. |
| update_f | Update the factors given the loadings and the data matrix. |
| update_l | Update the loadings given the factors, the data matrix, and... |
| update_sigma | Update variances in regularized maximum likelihood factor... |
