R packages for Pharma and Medicine #rstats

There is a dedicated CRAN task view on the various options within the R ecosystem for Clinical Trails

CRAN Task View: Clinical Trial Design, Monitoring, and Analysis http://cran.r-project.org/web/views/ClinicalTrials.html This task view gathers information on specific R packages for design, monitoring and analysis of data from clinical trials. It focuses on including packages for clinical trial design and monitoring in general plus data analysis packages for a specific type of design. Also, it gives a brief introduction to important packages for analyzing clinical trial data . It has the following sub headings.


  1. Design and Monitoring
  2. Design and Analysis
  3. Analysis for Specific Designs
  4. Analysis in General
  5. Meta-Analysis


 and an additional one on PharmaKinetic Data

CRAN Task View: Analysis of Pharmacokinetic Data http://cran.r-project.org/web/views/Pharmacokinetics.html The primary goal of pharmacokinetic (PK) data analysis is to determine the relationship between the dosing regimen and the body’s exposure to the drug as measured by the nonlinear concentration time curve or related summaries (e.g. the area under the curve). Base R contains nls which can be used to calculate nonlinear least-squares estimates of the parameters from a PK model. It returns an object of the class "nls" having methods coef(),formula()resid()print()summary()AIC()fitted() and vcov(). Four packages are available in CRAN that directly aid in PK data analysis, including; the packages PKPKfitnlmeODE which incorporates nlme and deSolve, and the package PKtools. While PK provides basic pharmacokinetics functions which implement non-compartmental analysis methods, the latter three packages focus on modeling methods.

A relatively new [package] is Greport

http://biostat.mc.vanderbilt.edu/wiki/Main/Greport The greport package contains many functions useful for monitoring and reporting the results of clinical trials and other experiments in which treatments are compared. LaTeX is used to typeset the resulting reports, recommended to be in the context of knitr. The Hmisc and lattice packages are used by greport for high-level graphics.

(NOTE- I wish there was some way to group packages and functions along business domains like finance, telecom, pharma, retail , entertainment) the current system of CRAN views is purely a clustering of packages of similar techniques but not business domains)

Author: Ajay Ohri


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