Man pages for BayesfMRI
Spatial Bayesian Methods for Task Functional MRI Studies
| activations | Identify field activations |
| activations.classical | Identification of areas of activation in a General Linear... |
| activations.posterior | Identify activations using joint posterior probabilities |
| AICc | Corrected AIC |
| aic_Param | aic |
| ar_order_Param | ar_order |
| ar_smooth_Param | ar_smooth |
| BayesfMRI-package | BayesfMRI: Spatial Bayesian Methods for Task Functional MRI... |
| BayesGLM | BayesGLM for CIFTI |
| BayesGLM2 | Group-level Bayesian GLM |
| BayesGLM_argChecks | Bayes GLM arg checks |
| BayesGLM_format_cifti | Format fit_bayesglm results into '"xifti"' objects |
| BayesGLM_format_design | Format design |
| BayesGLM_format_nuisance | Format nuisance |
| BayesGLM_format_scrub | Format scrub |
| BayesGLM_is_valid_one_design | Is a valid design? |
| BayesGLM_is_valid_one_nuisance | Is a valid nuisance? |
| BayesGLM_is_valid_one_scrub | Is a valid scrub? |
| BayesGLM_session_names | Get 'session_names' for GLM |
| Bayes_Param | Bayes |
| beta.posterior.thetasamp | Beta posterior theta sampling |
| BOLD_Param_BayesGLM | BOLD |
| brainstructures_Param_BayesGLM | brainstructures |
| buffer_Param | buffer |
| cbind2 | 'cbind' if first argument might be 'NULL' |
| check_INLA | Check INLA and PARDISO |
| cholQsample | Sample from the multivariate normal distribution with... |
| Connectome_Workbench_Description | Connectome Workbench |
| contrasts_Param | contrasts |
| create_listRcpp | Function to prepare objects for use in Rcpp functions |
| design_Param_BayesGLM | design |
| dgCMatrix_cols_to_zero | Set column values to zero for sparse matrix |
| do_QC | Mask out invalid data |
| dot-findTheta | Perform the EM algorithm of the Bayesian GLM fitting |
| dot-getSqrtInvCpp | Get the prewhitening matrix for a single data location |
| dot-initialKP | Find the initial values of kappa2 and phi |
| dot-logDetQt | Find the log of the determinant of Q_tilde |
| ELL | Expected log-likelihood function |
| EM_Param | EM |
| emTol_Param | emTol |
| extract_estimates | Extract Estimates of Activation |
| faces_Param | faces |
| field_names_Param | field_names |
| fit_bayesglm | fit_bayesglm |
| F.logwt | F logwt |
| galerkin_db | Create FEM matrices |
| get_nV | Get number of locations for various masks |
| get_posterior_densities | Extracts posterior density estimates for hyperparameters |
| get_posterior_densities2 | Extracts posterior density estimates for hyperparameters for... |
| GLM_classical | Classical GLM |
| GLM_compare | Classical GLM for multiple models |
| GLMEM_fixptseparate | Fixed point function for the joint BayesGLM EM update... |
| GLMEM_objfn | Objective function for the BayesGLM EM algorithm |
| GLM_est_resid_var_pw | Standardize data variance, and prewhiten if applicable |
| hpf_Param_BayesGLM | hpf |
| init_fixpt | The fix point function for the initialization of kappa2 and... |
| init_objfn | Objective function for the initialization of kappa2 and phi |
| INLA_deps | Import INLA dependencies |
| INLA_Description | INLA |
| INLA_Latent_Fields_Limit_Description | INLA Latent Fields |
| intersect_mask | Intersection mask for BayesGLM or activations result |
| is_matrix_or_df | Is a matrix or data.frame? |
| kappa_init_fn | Function to optimize over kappa2 |
| log_kappa_tau | Make 'log_kappa' and 'log_tau' |
| make_A_mat | Make A matrix |
| make_A_mat_rs | Make A matrix with resampling framework |
| make_data_list | Make data list for 'estimate_model' |
| make_mesh | Make Mesh |
| make_Q | Make the full SPDE precision based on theta, the spde, and... |
| make_replicates | Make replicates |
| make_sqrtInv_all | Make 'sqrtInv_all' |
| mask_Param_vertices | mask: vertices |
| max_threads_Param | max_threads |
| mean_var_Tol_Param | mean and variance tolerance |
| mesh_Param_either | mesh: either |
| mesh_Param_inla | mesh: INLA only |
| nbhd_order_Param | nbhd_order |
| neg_kappa_fn | The negative of the objective function for kappa |
| neg_kappa_fn2 | The negative of the objective function for kappa without... |
| neg_kappa_fn3 | Streamlined negative objective function for kappa2 using... |
| neg_kappa_fn4 | Streamlined negative objective function for kappa2 using... |
| n_threads_Param | n_threads |
| nuisance_Param_BayesGLM | nuisance |
| plot.act_BGLM | S3 method: use 'view_xifti' to plot a '"act_BGLM"' object |
| plot.BGLM | S3 method: use 'view_xifti' to plot a '"BGLM"' object |
| plot.BGLM2 | S3 method: use 'view_xifti' to plot a '"BGLM2"' object |
| plot.prev_BGLM | S3 method: use 'view_xifti' to plot a '"prev_BGLM"' object |
| prep_kappa2_optim | Find values for coefficients used in objective function for... |
| prevalence | Activations prevalence. |
| pw_estimate | Estimate residual autocorrelation for prewhitening |
| pw_smooth | Smooth AR coefficients and white noise variance |
| Q_prime | Q prime |
| qsample | Sample from a multivariate normal with mean and precision |
| resamp_res_Param_BayesGLM | resamp_res |
| retro_mask_act | Retroactively mask activations |
| retro_mask_fit_bglm | Retroactively mask locations from fit_bglm result. |
| retro_mask_mesh | Retroactively mask locations from mesh. |
| return_INLA_Param | return_INLA |
| s2m | Sequential 2-means variable selection |
| s2m_B | Sequential 2-means on array B |
| scale_BOLD | Scale the BOLD timeseries |
| scale_BOLD_Param | scale_BOLD |
| scale_design_mat | Scale the design matrix |
| scrub_Param_BayesGLM | scrub |
| seed_Param | seed |
| session_names_Param | session_names |
| sparse_and_PW | Organize data for Bayesian GLM |
| SPDE_from_vertex | SPDE from mesh model |
| SPDE_from_voxel | SPDE from voxel model |
| spde_Q_phi | Calculate the SPDE covariance |
| summary.act_BGLM | Summarize a '"act_BGLM"' object |
| summary.act_fit_bglm | Summarize a '"act_fit_bglm"' object |
| summary.BGLM | Summarize a '"BGLM"' object |
| summary.BGLM2 | Summarize a '"BGLM2"' object |
| summary.fit_bglm | Summarize a '"fit_bglm"' object |
| summary.fit_bglm2 | Summarize a '"fit_bglm2"' object |
| summary.prev_BGLM | Summarize a '"prev_BGLM"' object |
| summary.prev_fit_bglm | Summarize a '"prev_fit_bglm"' object |
| surfaces_Param_BayesGLM | surfaces |
| trim_INLA_model_obj | Trim INLA object |
| trim_INLA_Param | trim_INLA |
| TR_Param_BayesGLM | TR |
| TrQbb | Trace of Q beta' beta |
| TrQEww | Trace approximation function |
| TrSigB | Hutchinson estimator of the trace |
| unmask_Mdat2In | Unmask data |
| validate_spatial | Validate 'spatial' |
| verbose_Param | verbose |
| vertex_areas | Surface area of each vertex |
| vertices_Param | vertices |
| vol2spde | Construct a triangular mesh from a 3D volumetric mask |
