Package: DGP4LCF 1.0.0

Jiachen Cai

DGP4LCF: Dependent Gaussian Processes for Longitudinal Correlated Factors

Functionalities for analyzing high-dimensional and longitudinal biomarker data to facilitate precision medicine, using a joint model of Bayesian sparse factor analysis and dependent Gaussian processes. This paper illustrates the method in detail: J Cai, RJB Goudie, C Starr, BDM Tom (2023) <doi:10.48550/arXiv.2307.02781>.

Authors:Jiachen Cai [aut, cre]

DGP4LCF_1.0.0.tar.gz
DGP4LCF_1.0.0.tar.gz(r-4.5-noble)DGP4LCF_1.0.0.tar.gz(r-4.4-noble)
DGP4LCF.pdf |DGP4LCF.html✨
DGP4LCF/json (API)

# Install 'DGP4LCF' in R:

install.packages('DGP4LCF', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Uses libs:

openblas– Optimized BLAS
c++– GNU Standard C++ Library v3

Datasets:

sim_fcs_init - Initials values.
sim_fcs_results_irregular_6_8 - Results when people have irregularly observed time points (some 6 while others 8).
sim_fcs_results_regular_8 - Results when people are observed at common 8 time points.
sim_fcs_truth - Truth of simulated data.

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.30 score 3 scripts 461 downloads 13 exports 77 dependencies

Last updated 5 months agofrom:ae46984161. Checks:OK: 2. Indexed: no.

Target	Result	Date
Doc / Vignettes	OK	Oct 26 2024
R-4.5-linux-x86_64	OK	Oct 26 2024

Exports:factor_loading_heatmap factor_score_trajectory gibbs_after_mcem_algorithm gibbs_after_mcem_combine_chains gibbs_after_mcem_diff_initials gibbs_after_mcem_load_chains mcem_algorithm mcem_cov_plot mcem_parameter_setup numerics_summary_do_not_need_alignment numerics_summary_need_alignment subject_specific_objects table_generator

Dependencies:ash bitops cli cluster coda codetools colorspace combinat corrplot deldir deSolve doParallel dotCall64 factor.switching fansi farver fda fda.usc fds fields FNN foreach ggplot2 glue GPFDA gtable HDInterval hdrcde interp isoband iterators kernlab KernSmooth ks kSamples labeling lattice lifecycle locfit lpSolve magrittr maps MASS Matrix MatrixModels mclust mcmc MCMCpack mgcv multicool munsell mvtnorm nlme pcaPP pheatmap pillar pkgconfig pracma quantreg R6 rainbow RColorBrewer Rcpp RcppArmadillo RcppEigen RCurl rlang scales spam SparseM SuppDists survival tibble utf8 vctrs viridisLite withr

An Example of Irregular Data Analysis

Rendered frombsfadgp_irregular_data_example.Rmdusingknitr::rmarkdownon Oct 26 2024.

Last update: 2024-05-29
Started: 2024-05-29

An Example of Regular Data Analysis

Rendered frombsfadgp_regular_data_example.Rmdusingknitr::rmarkdownon Oct 26 2024.

Last update: 2024-05-29
Started: 2024-05-29

Citation

Readme and manuals

Help Manual

Help page	Topics
Displaying significant factor loadings in the heatmap.	factor_loading_heatmap
Plotting figures for factor score trajectory.	factor_score_trajectory
Generating posterior samples for parameters (other than DGP parameters) in the model and predicted gene expression for one chain.	gibbs_after_mcem_algorithm
Combining from all chains the posterior samples for parameters in the model and predicted gene expressions.	gibbs_after_mcem_combine_chains
Generating different initials for multiple chains.	gibbs_after_mcem_diff_initials
Loading the saved posterior samples for parameters in the model and predicted gene expressions.	gibbs_after_mcem_load_chains
Monte Carlo Expectation Maximization (MCEM) algorithm to return the Maximum Likelihood Estimate (MLE) of DGP Parameters.	mcem_algorithm
Visualizing cross-correlations among factors.	mcem_cov_plot
Parameters' setup and initial value assignment for the Monte Carlo Expectation Maximization (MCEM) algorithm.	mcem_parameter_setup
Numerical summary for important continuous variables that do not need alignment.	numerics_summary_do_not_need_alignment
Numerical summary for factor loadings and factor scores, which need alignment.	numerics_summary_need_alignment
Initials values.	sim_fcs_init
Results when people have irregularly observed time points (some 6 while others 8).	sim_fcs_results_irregular_6_8
Results when people are observed at common 8 time points.	sim_fcs_results_regular_8
Truth of simulated data.	sim_fcs_truth
Constructing subject-specific objects required for Gibbs sampler (for subjects with incomplete observations only).	subject_specific_objects
Generating a table listing all possible combinations of the binary variables for one gene.	table_generator