R: A Tool for 'Covariate'-Sensitive Longitudinal Analysis on 'omics' Data

# A Tool for 'Covariate'-Sensitive Longitudinal Analysis on 'omics' Data

## Documentation for package ‘LongDat’ version 1.1.4

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

cliff_cal | Effect size (Cliff's delta) calculation in longdat_disc() pipeline
ConModelTest_cont | Covariate model test in longdat_cont() pipeline
ConModelTest_disc | Covariate model test in longdat_disc() pipeline
correlation_posthoc | Post-hoc test based on correlation test for longdat_cont().
cuneiform_plot | Create cuneiform plots of result table from longdat_disc() or longdat_cont()
data_preprocess | Data preprocessing
factor_p_cal | Calculate the p values for every factor (used for selecting factors later)
final_result_summarize_cont | Generate result table as output in longdat_cont()
final_result_summarize_disc | Generate result table as output in longdat_disc()
fix_name_fun | Replace the symbols in variable and covariate names in raw input
longdat_cont | Longitudinal analysis with time as continuous variable
LongDat_cont_feature_table | data/LongDat_cont_feature_table.RData documentation
LongDat_cont_master_table | data/LongDat_cont_master_table.RData documentation
LongDat_cont_metadata_table | data/LongDat_cont_metadata_table.RData documentation
longdat_disc | Longitudinal analysis with time as discrete variable
LongDat_disc_feature_table | data/LongDat_disc_feature_table.RData documentation
LongDat_disc_master_table | data/LongDat_disc_master_table.RData documentation
LongDat_disc_metadata_table | data/LongDat_disc_metadata_table.RData documentation
make_master_table | Create input master table from metadata and feature tables for longdat_disc() and longdat_cont()
NuModelTest_cont | Null Model Test and post-hoc Test in longdat_cont() pipeline
NuModelTest_disc | Null Model Test and post-hoc Test in longdat_disc() pipeline
random_neg_ctrl_cont | Randomized negative control for count data in longdat_cont()
random_neg_ctrl_disc | Randomized negative control for count data in longdat_disc()
rm_sparse_cont | Remove the dependent variables that are below the threshold of sparsity when the data type is count data in longdat_cont()
rm_sparse_disc | Remove the dependent variables that are below the threshold of sparsity when the data type is count data in longdat_disc()
theta_plot | Plot theta values of negative binomial models versus non-zero count for count data
unlist_table | Unlist confound (covariate) and inverse confound (covariate) tables, turn them into tables
wilcox_posthoc | Wilcoxon post-hoc test