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StatCharrms (Statistical analysis of Chemistry, Histopathology, and Reproduction endpoints using Repeated measures and Multi-generation Studies) is a graphic user front end for ease of use in analyzing data generated from the Medaka Extended One Generation Reproduction Test (MEOGRT) and Larval Amphibian Gonad Development Assay (LAGDA).  The analyses StatCharrms is capable of performing are; Rao-Scott adjusted Cochran- Armitage test for trend By Slices (RSCABS), a Standard Cochran- Armitage test for trend By Slices (SCABS), mixed effects Cox proportional model, Jonckheere-Terpstra step down trend test, Kruskal–Wallis, Dunn test, one way ANOVA, weighted ANOVA, mixed effects ANOVA, repeated measures ANOVA, and Dunnett test.

The Installation Guide (PDF) (pp 11, 376KB) gives step by step instructions on how to install StatCharrms and gives answers to some of the more frequently asked questions about the installation process.  The User’s Manual (PDF) (pp 44, 1447KB) steps though how to use every module in StatCharrms as well as explaining what statistical tests are used.

The file (StatCharrmsV-80.zip) (252KB) contains an R database file containing all the functions needed to run StatCharrms.  StatCharrms also includes a module that creates example data sets with their corresponding analyses.  These examples are used in the User Manual.  The command, “Install.StatCharrms()” is used to install all of the packages used in StatCharrms and the command, “Run.StatCharrms()” is used to start the program.  See the Installation Guide for further details.

StatCharrms was created under R version 3.0.1 and will require that version or later to run. The latest version of R can be found here (http://cran.r-project.org/) on the CRAN webpage. During the installation process R will install Gtk2 from the gnome foundation as well as the packages; RGtk2, R2HTML, gWidgetsRGtk2, multcomp, nlme, lattice, ggplot2, cairoDevice, car, clinfun, zoo, coxme, agricolae, and each of the packages those packages depends on; from a CRAN mirror.


Background references separated by category:

General Use, Graphic, and I/O Packages

http://www.gtk.org/ maintained by the GNOME foundation

RGtk2 Package
Michael Lawrence, Duncan Temple Lang (2010). RGtk2: A Graphical User Interface Toolkit for R. Journal of Statistical Software, 37(8), 1-52. URL http://www.jstatsoft.org/v37/i08/.

gWidgetsRGtk2 Package
Michael Lawrence and John Verzani (2013). gWidgetsRGtk2: Toolkit implementation of gWidgets for RGtk2. R package version 0.0-82. http://CRAN.R-project.org/package=gWidgetsRGtk2

R2HTML Package
Lecoutre, Eric (2003). The R2HTML Package. R News, Vol 3. N. 3, Vienna, Austria.

lattice Package
Sarkar, Deepayan (2008) Lattice: Multivariate Data Visualization with R. Springer, New York. ISBN 978-0-387-75968-5

ggplot2 Package
H. Wickham. ggplot2: elegant graphics for data analysis. Springer New York, 2009.

cairoDevice Package
Michael Lawrence (2014). cairoDevice: Cairo-based cross-platform antialiased graphics device driver.. R package version 2.20. http://CRAN.R-project.org/package=cairoDevice

multcomp Package
Torsten Hothorn, Frank Bretz and Peter Westfall (2008). Simultaneous Inference in General Parametric Models. Biometrical Journal 50(3), 346--363.


John W. Green et al.
Statistical analysis of histopathology endpoints
Environmental Toxicology
Volume 33, Issue 5 ,pages 1108-16, Epub 2014 Mar 21

J. N. K. Rao and A. J. Scott
A simple method for analyzing overdispersion in clustered Poisson data
Statistics in Medicine
Volume 18, Issue 11, pages 1373-1385, 15 June 1999

J. N. K. Rao and A. J. Scott
A Simple Method for the Analysis of Clustered Binary Data
Vol. 48, No. 2 (Jun., 1992), pp. 577-585


Pinheiro J, Bates D, DebRoy S, Sarkar D and R Core Team (2014). nlme: Linear and Nonlinear Mixed Effects Models_. R package version 3.1-115,URL: http://CRAN.R-project.org/package=nlme.

Analysis of Other Endpoints

Zoo Package
Achim Zeileis and Gabor Grothendieck (2005). zoo: S3 Infrastructure for Regular and Irregular Time Series. Journal of Statistical Software, 14(6), 1-27. URL http://www.jstatsoft.org/v14/i06/

car Package
John Fox and Sanford Weisberg (2011). An {R} Companion to Applied Regression, Second Edition. Thousand Oaks CA: Sage. URL: http://socserv.socsci.mcmaster.ca/jfox/Books/Companion

clinfun Package
Venkatraman E. Seshan (2013). clinfun: Clinical Trial Design and Data Analysis Functions. R package version 1.0.5. http://CRAN.R-project.org/package=clinfun

Agricolae Package
Felipe de Mendiburu (2014). agricolae: Statistical Procedures for Agricultural Research. R package version 1.1-8. http://CRAN.R-project.org/package=agricolae

Time to Event Analysis

Coxme Package
Terry Therneau (2012). coxme: Mixed Effects Cox Models.. R package version 2.2-3. http://CRAN.R-project.org/package=coxme

For further information, please contact Kevin Flynn Flynn.kevin@epa.gov, 218-529-5120.

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