Pharmacometric Power calculations for mixed study designs
This package contains functions performing power calculations for mixed (sparse/dense sampled) pharmacokinetic study designs. The input data for these functions is tailored for NONMEM .phi files.

Large-Scale Analysis of Pharmacogenomic Data
Petr Smirnov, Zhaleh Safikhani, Benjamin Haibe-Kains
Contains a set of functions to perform large-scale analysis of pharmacogenomic data.
Biobase, piano, magicaxis, RColorBrewer, parallel, caTools,
methods, downloader, stats, utils, graphics, grDevices

Analysis of Large-Scale Pharmacogenomic Data

Biobase, piano, magicaxis, RColorBrewer, parallel, caTools,
methods, downloader, stats, utils, graphics, grDevices, lsa

Simulating and Conducting Phase 123 Trials
Contains three simulation functions for implementing the entire Phase 123 trial and the separate Eff-Tox and Phase 3 portions of the trial, which may be beneficial for use on clusters. The functions AssignEffTox() and RandomizeEffTox() assign doses to patient cohorts during phase 12 and Reoptimize() determines the optimal dose to continue with during Phase 3. The functions ReturnMeansAgent() and ReturnMeanControl() gives the true mean survival for the agent doses and control and ReturnOCS() gives the operating characteristics of the design.

Simulates SPSO and Efftox Phase 12 Trials with Correlated
Outcomes
Simulating and conducting four phase 12 clinical trials with correlated binary bivariate outcomes described. Uses the 'Efftox' (efficacy and toxicity tradeoff, <https://biostatistics.mdanderson.org/SoftwareDownload/SingleSoftware/Index/2>) and SPSO (Semi-Parametric Stochastic Ordering) models with Utility and Desirability based objective functions for dose finding.

Functions to perform Bayesian inference on absorption time
data for Phase-type distributions.  Plans to expand this to
include frequentist inference and simulation tools.

c(
person("Iker", "Rivas-González", , "ikerrivas96@gmail.com", role = c("aut", "cre"),
comment = c(ORCID = "0000-0002-0515-0628")),
person("Colin", "Guetemme", , "colin.guetemme@live.fr", role = "aut"),
person("Asger", "Hobolth", , "asger@math.au.dk", role = "aut"),
person("Lars Nørvang", "Andersen", , "larsa@math.au.dk", role = "aut")
)
General implementation of core function from phase-type
theory. 'PhaseTypeR' can be used to model continuous and discrete
phase-type distributions, both univariate and multivariate. The
package includes functions for outputting the mean and (co)variance of
phase-type distributions; their density, probability and quantile
functions; functions for random draws; functions for
reward-transformation; and functions for plotting the distributions as
networks. For more information on these functions please refer to
Bladt and Nielsen (2017, ISBN: 978-1-4939-8377-3) and Campillo Navarro
(2019)
<https://orbit.dtu.dk/en/publications/order-statistics-and-multivariate-discrete-phase-type-distributio>.
Iker Rivas-González [aut, cre]
(<https://orcid.org/0000-0002-0515-0628>),
Colin Guetemme [aut],
Asger Hobolth [aut],
Lars Nørvang Andersen [aut]