This package is considered a duplicate. The official version of this package is found at:https://mandymejia.r-universe.dev/templateICAr

Package: templateICAr 0.9.1

Amanda Mejia

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

Implements the template ICA (independent components analysis) model proposed in Mejia et al. (2020) <doi:10.1080/01621459.2019.1679638> and the spatial template ICA model proposed in proposed in Mejia et al. (2022) <doi:10.1080/10618600.2022.2104289>. Both models estimate subject-level brain as deviations from known population-level networks, which are estimated using standard ICA algorithms. Both models employ an expectation-maximization algorithm for estimation of the latent brain networks and unknown model parameters. Includes direct support for 'CIFTI', 'GIFTI', and 'NIFTI' neuroimaging file formats.

Authors:Amanda Mejia [aut, cre], Damon Pham [aut], Daniel Spencer [ctb], Mary Beth Nebel [ctb]

templateICAr_0.9.1.tar.gz
templateICAr_0.9.1.tar.gz(r-4.5-noble)templateICAr_0.9.1.tar.gz(r-4.4-noble)
templateICAr_0.9.1.tgz(r-4.4-emscripten)templateICAr_0.9.1.tgz(r-4.3-emscripten)
templateICAr.pdf |templateICAr.html✨
templateICAr/json (API)
NEWS

# Install 'templateICAr' in R:

install.packages('templateICAr', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/mandymejia/templateicar/issues

3.92 score 24 scripts 23k downloads 15 exports 61 dependencies

Last updated 4 days agofrom:663f14aa5b. Checks:OK: 2. Indexed: no.

Target	Result	Date
Doc / Vignettes	OK	Nov 25 2024
R-4.5-linux	OK	Nov 25 2024

Exports:activations dim_reduce estimate_template estimate_template_FC estimate_template_from_DR export_template getInvCovAR groupICA.cifti make_mesh make_mesh_2D norm_BOLD orthonorm resample_template sqrt_XtX templateICA

Dependencies:abind cellWise class cli codetools colorspace DEoptimR e1071 expm fansi farver fMRIscrub fMRItools foreach gamlss gamlss.data gamlss.dist ggplot2 glue gridExtra gtable ica isoband iterators labeling lattice lifecycle magrittr MASS Matrix matrixStats mgcv munsell mvtnorm nlme pcaPP pesel pillar pkgconfig plyr proxy R6 RColorBrewer Rcpp RcppArmadillo reshape2 rlang robustbase rrcov scales shape SQUAREM stringi stringr survival svd tibble utf8 vctrs viridisLite withr

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

Package: templateICAr 0.9.1

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

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