Man pages for Rmomal/VEMtree
Network inference from Species counTs with missing actORs
| alphaMax | Heuristic for an upper value of tempering parameter alpha |
| auc | wraper of auc from ROCR |
| boot_FitSparsePCA | Finds initial cliques using a sparse PCA on bootstraps... |
| complement_spca | Select the k first components and their complement as initial... |
| computeOmega | Updates the precision terms |
| computeWg | Updates the variational edges weights inside the VEM. |
| det.fractional | Get numerator and denominators |
| exactMeila | Calculates the Meila matrix using exact computation |
| FitSparsePCA | Fit sparse PCA on a grid of alpha |
| generate_missing_data | Simulate data and parameters including missing actors. |
| ggimage | ggplot heatmap |
| init_blockmodels | Find initial cliques using blockmodels on the initial... |
| init_mclust | Find initial cliques using mclust on the estimated... |
| initOmega | Initialize Sigma and Omega using an initial clique of... |
| initVEM | Initialize all parameters for the variational inference |
| inverse.gmp | Computes exact inverses using gmp package |
| Kirshner | Computes edges probability from weights W (Kirshner (07)... |
| List.nestorFit | Run function nestorFit on a list of initial cliques using... |
| logSumTree | Exact computation of matrix tree log determinant |
| LowerBound | Computes the lower bound. |
| Mstep | Computes the maximization step of the algorithm |
| nestorFit | Core function of nestorFit |
| nestor-package | nestor: Network inference from Species counTs with missing... |
| norm_PLN | Runs PLN function from the PLNmodels package and normalized... |
| plotConv | Plot function for nestorFit convergence |
| plotPerf | Comparaitve plot of estimated edge probabilities and original... |
| ppvtpr | Computes precision and recall statistics separating observed... |
| VEstep | Computes the variational expectation step of the algorithm |
