Man pages for DongyueXie/stm
Empirical Bayes Poisson Matrix Factorization
| adjLF | Make Init L and F on similar scale |
| adjust_var_shape | adjust var shape for vga. For computation purpose. |
| BMSM | Bayesian Multiscale Model for Smoothing Poisson sequence |
| bmsm_control_default | Default control list of BMSM |
| calc_ebpmf_log_obj | Calc elbo |
| check_flash_signs | Check loadings and factors signs, to make sure they match... |
| cluster.mix | Xing's smoothed topic model |
| ebbp_beta_mixture | Empirical Bayes for estimating Binomial probability |
| ebnm_dwt | Empirical Bayes wavelet smoothing DWT wrapper for flashier |
| ebnm_dwt_haar | Empirical Bayes wavelet smoothing haar wavelet for flashier |
| ebnm_dwt_symlet | Empirical Bayes wavelet smoothing symlet wavelet for flashier |
| ebnm_ndwt | This function is an EBNM function that fits ndwt method |
| ebpmf_identity | Smoothed Poisson Topic Model |
| ebpmf_identity_init | initialize the ebpmf identity model |
| ebpmf_identity_smooth_control_default | Default parameters of smooth split |
| ebpmf_log | Fit empirical Bayes Poisson matrix factorization with log... |
| ebpmf_log_flash_control_default | default flash parameters |
| ebpmf_log_flash_init | the init fit of flash in ebpmf log function |
| ebpmf_log_flash_update | this function fits flash during ebpmf log iterations |
| ebpmf_log_init | this function initializes the ebpmf with log link |
| ebpmf_log_update_sigma2 | update sigma2 |
| flash_extra_control | This function returns init.fn.flash and no_backfit_kset |
| get_var_b | get posterior variance of b_ij = sum_j l_ik * f_jk |
| hello | Hello, World! |
| init.fn.fix | init flash add greedy |
| log_for_ebmf | Log transformation of scRNA-seq count matrix for EBMF |
| mKL | calculate mean KL divergence of 2 nonnegative matrices |
| NMF_HALS | HALS algorithm for NMF |
| plot_stm | Summary of ebmpmf output |
| poisson_to_multinom | standard loadings and factors from Poisson matrix... |
| sim_data_log | simulate Poisson matrix |
| sim_data_log_simple | simulate simple Poisson matrix |
| sim_data_real | simulate Poisson matrix based on real data output |
| spmf | Poisson MF but with smoothed factors using smash.pois |
| spmf_update_rank1 | update spmf model, rank 1 |
| stm_update_rank1 | rank 1 update of the model |
| sum_lfactorial_sparseMat | calculate sum of log factorial of all elements of a sparse... |
| test_ebnm_fn_sign | test ebnm.fn 's sign |
| vga_pois_solver_mat_newton | a matrix version of the vga solver using Newton's method |
| vga_pois_solver_mat_newton_fixed_iter | vga solver for fixed iteration, not necessary to convergence |
| vga_pois_solver_mat_newton_low_memory | a matrix version of the vga solver using Newton's method, low... |
| V_M | Calc V given M |
