Data analysis package for estimating potential biological effects from chemical concentrations in environmental samples. Included are a set of functions to analyze, visualize, and organize measured concentration data as it relates to user-selected chemical-biological interaction benchmark data such as water quality criteria. The intent of these analyses is to develop a better understanding of the potential biological relevance of environmental chemistry data. Results can be used to prioritize which chemicals at which sites may be of greatest concern. These methods are meant to be used as a screening technique to predict potential for biological influence from chemicals that ultimately need to be validated with direct biological assays. A description of the analysis can be found in Blackwell (2017) <doi:10.1021/acs.est.7b01613>.

Enables users to build 'ToxPi' prioritization models and provides 
  functionality within the grid framework for plotting ToxPi graphs.
  'toxpiR' allows for more customization than the 'ToxPi GUI' 
  (<https://toxpi.org>) and integration into existing workflows for greater 
  ease-of-use, reproducibility, and transparency.
  toxpiR package behaves nearly identically to the GUI; the package 
  documentation includes notes about all differences.
  The vignettes download example files from 
  <https://github.com/ToxPi/ToxPi-example-files>.

A 'shiny' app that generates plots and summary tables from repeat-dose
        toxicology study results to facilitate holistic evaluation of the drug safety of 
        active pharmaceutical ingredients (API) prior to initiation of clinical trials.

Estimation of transition probabilities for the illness-death model. Both the Aalen-Johansen estimator for a Markov model and a novel non-Markovian estimator by de Una-Alvarez and Meira-Machado (2015) <doi:10.1111/biom.12288>, see also Balboa and de Una-Alvarez (2018) <doi:10.18637/jss.v083.i10>, are included.

Contains logic for single sample gene set testing of cancer transcriptomic data with adjustment for normal tissue-specificity.
  Frost, H. Robert (2023) "Tissue-adjusted pathway analysis of cancer (TPAC)" <doi:10.1101/2022.03.17.484779>.