Imports: rstan (>= 2.18.1), loo (>= 2.0), grid, parallel, ggplot2,

various computational models with a single line of coding

Collate: 'HDIofMCMC.R' 'preprocess_funcs.R' 'stanmodels.R' 'settings.R'

'ts_par6.R' 'ts_par7.R' 'ug_bayes.R' 'ug_delta.R' 'wcs_sql.R'

Title: Hierarchical Item Response Theory Models
Authors@R: person("Xiang", "Zhou", email = "xiang_zhou@fas.harvard.edu",
Description: Implementation of a class of hierarchical item response
theory (IRT) models where both the mean and the variance of latent preferences
(ability parameters) can depend on observed covariates. The current
implementation includes both the two-parameter latent trait model and the
graded response model for ordinal data. Both are fitted via the
Expectation-Maximization (EM) algorithm. Asymptotic standard errors are derived

graded response model. Both are fitted via the Expectation-Maximization (EM)
algorithm. Asymptotic standard errors are derived from the observed information

(ability parameters) may depend on observed covariates. The current
implementation includes both the two-parameter latent trait model for binary data and the
graded response model for ordinal data. Both are fitted via the Expectation-Maximization (EM)

Suggests: ggplot2 (>= 2.2.1), knitr, rmarkdown

Title: Hierarchical Joint Analysis of Marginal Summary Statistics
Description: Provides functions to implement a hierarchical approach which is designed to perform joint analysis of summary statistics using the framework of Mendelian Randomization or transcriptome analysis. Reference: Lai Jiang, Shujing Xu, Nicholas Mancuso, Paul J. Newcombe, David V. Conti (2020). "A Hierarchical Approach Using Marginal Summary Statistics for Multiple Intermediates in a Mendelian Randomization or Transcriptome Analysis." <bioRxiv><doi:10.1101/2020.02.03.924241>.
Imports: ggplot2, ggpubr, dplyr, reshape2

Title: Hierarchical Non-Negative Matrix Factorization
Description: Hierarchical non-negative matrix factorization
for tumor segmentation based on multi-parametric MRI data.
Imports: NMF, oro.nifti, tcltk, nnls, R.matlab, spatialfil,