Fitting and testing probabilistic knowledge structures,
  especially the basic local independence model (BLIM, Doignon & Flamagne,
  1999) and the simple learning model (SLM), using the minimum discrepancy
  maximum likelihood (MDML) method (Heller & Wickelmaier, 2013
  <doi:10.1016/j.endm.2013.05.145>).

A tool for inferring kinase activity changes from 
    phosphoproteomics data. 'pKSEA' uses kinase-substrate 
    prediction scores to weight observed changes in 
    phosphopeptide abundance to calculate a phosphopeptide-level 
    contribution score, then sums up these contribution scores by 
    kinase to obtain a phosphoproteome-level kinase activity 
    change score (KAC score). 'pKSEA' then assesses the 
    significance of changes in predicted substrate abundances for 
    each kinase using permutation testing. This results in a 
    permutation score (pKSEA significance score) reflecting the 
    likelihood of a similarly high or low KAC from random chance, 
    which can then be interpreted in an analogous manner to an 
    empirically calculated p-value. 'pKSEA' contains default 
    databases of kinase-substrate predictions from 'NetworKIN' 
    (NetworKINPred_db) <http://networkin.info> 
    Horn, et. al (2014) <doi:10.1038/nmeth.2968>
    and of known kinase-substrate links from 'PhosphoSitePlus' 
    (KSEAdb) <https://www.phosphosite.org/>
    Hornbeck PV, et. al (2015) <doi:10.1093/nar/gku1267>.

Applying the global sensitivity analysis workflow to investigate 
    the parameter uncertainty and sensitivity in physiologically based 
    kinetic (PK) models, especially the physiologically based 
    pharmacokinetic/toxicokinetic model with multivariate outputs. 
    The package also provides some functions to check the convergence 
    and sensitivity of model parameters. The workflow was first mentioned 
    in Hsieh et al., (2018) <doi:10.3389/fphar.2018.00588>, then further 
    refined (Hsieh et al., 2020 <doi:10.1016/j.softx.2020.100609>).

Tools to process legacy format summary redistricting data files
    produced by the United States Census Bureau pursuant to P.L. 94-171. These
    files are generally available earlier but are difficult to work with as-is.