R: Estimate Brain Networks and Connectivity with ICA and Empirical Priors

# Estimate Brain Networks and Connectivity with ICA and Empirical Priors

## Documentation for package ‘templateICAr’ version 0.10.0

- DESCRIPTION file
- Package NEWS
- Package README

## Help Pages

activations | Activations of (spatial) template ICA
bdiag_m2 | Bdiag m2
Chol_samp_fun | Cholesky-based FC sampling
dim_reduce | PCA-based Dimension Reduction and Prewhitening
EM_templateICA | EM Algorithms for Template ICA Models
EM_templateICA.independent | EM Algorithms for Template ICA Models
EM_templateICA.spatial | EM Algorithms for Template ICA Models
estimate.ESS | Estimation of effective sample size
estimate_nu | Universally estimate IW dof parameter nu based on method of moments, so that no empirical variance is under-estimated
estimate_nu_matrix | Estimate IW dof parameter nu based on method of moments
estimate_template | Estimate template
estimate_template.cifti | Estimate template
estimate_template.gifti | Estimate template
estimate_template.nifti | Estimate template
estimate_template_FC | Estimate FC template
estimate_template_from_DR | Estimate template from DR
export_template | Export template
getInvCovAR | Compute inverse covariance matrix for AR process (up to a constant scaling factor)
groupICA.cifti | Perform group ICA based on CIFTI data
IW_var | Compute theoretical Inverse-Wishart variance of covariance matrix elements
IW_var_cor | Compute theoretical Inverse-Wishart variance of correlation matrix elements
lik | Compute likelihood in SPDE model for ESS estimation
make_mesh | Make INLA mesh from '"surf"' object
make_mesh_2D | Make 2D INLA mesh
norm_BOLD | Normalize BOLD data
orthonorm | Orthonormalizes a square, invertible matrix
plot.template.cifti | Plot template
plot.template.gifti | Plot template
plot.template.matrix | Plot template
plot.template.nifti | Plot template
plot.tICA.cifti | Plot template
plot.tICA.matrix | Plot template
plot.tICA.nifti | Plot template
plot.tICA_act.cifti | Plot activations
print.summary.template.cifti | Summarize a '"template.cifti"' object
print.summary.template.gifti | Summarize a '"template.gifti"' object
print.summary.template.matrix | Summarize a '"template.matrix"' object
print.summary.template.nifti | Summarize a '"template.nifti"' object
print.summary.tICA.cifti | Summarize a '"tICA.cifti"' object
print.summary.tICA.matrix | Summarize a '"tICA.matrix"' object
print.summary.tICA.nifti | Summarize a '"tICA.nifti"' object
print.summary.tICA_act.cifti | Summarize a '"tICA_act.cifti"' object
print.summary.tICA_act.matrix | Summarize a '"tICA_act.matrix"' object
print.summary.tICA_act.nifti | Summarize a '"tICA_act.nifti"' object
print.template.cifti | Summarize a '"template.cifti"' object
print.template.gifti | Summarize a '"template.gifti"' object
print.template.matrix | Summarize a '"template.matrix"' object
print.template.nifti | Summarize a '"template.nifti"' object
print.tICA.cifti | Summarize a '"tICA.cifti"' object
print.tICA.matrix | Summarize a '"tICA.matrix"' object
print.tICA.nifti | Summarize a '"tICA.nifti"' object
print.tICA_act.cifti | Summarize a '"tICA_act.cifti"' object
print.tICA_act.matrix | Summarize a '"tICA_act.matrix"' object
print.tICA_act.nifti | Summarize a '"tICA_act.nifti"' object
pw_estimate | Estimate residual autocorrelation for prewhitening
resample_template | Resample CIFTI template
sqrt_XtX | Compute matrix square root of X'X
summary.template.cifti | Summarize a '"template.cifti"' object
summary.template.gifti | Summarize a '"template.gifti"' object
summary.template.matrix | Summarize a '"template.matrix"' object
summary.template.nifti | Summarize a '"template.nifti"' object
summary.tICA.cifti | Summarize a '"tICA.cifti"' object
summary.tICA.matrix | Summarize a '"tICA.matrix"' object
summary.tICA.nifti | Summarize a '"tICA.nifti"' object
summary.tICA_act.cifti | Summarize a '"tICA_act.cifti"' object
summary.tICA_act.matrix | Summarize a '"tICA_act.matrix"' object
summary.tICA_act.nifti | Summarize a '"tICA_act.nifti"' object
templateICA | Template ICA
UpdateTheta_templateICA | Parameter Estimates in EM Algorithm for Template ICA Model
UpdateTheta_templateICA.independent | Parameter Estimates in EM Algorithm for Template ICA Model
UpdateTheta_templateICA.spatial | Parameter Estimates in EM Algorithm for Template ICA Model
UT2mat | Transform upper-triangular elements to matrix form
var_sq_err | Compute the error between empirical and theoretical variance of covariance matrix elements
var_sq_err_constrained | Compute the overall error between empirical and theoretical variance of CORRELATION matrix elements