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S-PLUS/R FunctionsLocal Extensions to the S LanguageAll files below contain source code only, bundled and compressed to a "tar.gz" format. The first section contains packages; and the last section contains useful functions that can be loaded into an S-PLUS or R session for general use. Some packages contain C code (e.g., armitage, haplo.stats, kinship, multic, rpart, and survival) and require a compiler. While some users may not have the expertise or required software to do the compilation, particularly on Windows systems, we are not able to provide binary versions. However, many of the packages have been ported to R, and binary versions are made available on sites like the Contributed R Archives Network (CRAN). You can find package distributions below, along with a brief description, and where indicated, a readme, user manual, and note regarding where it is publicly available. This software is free. You can redistribute and/or modify it under the terms of the GNU General Public License, as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This program is distributed with helpful intent, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. Please give credit where credit is due. If you use functions from Mayo Clinic, please acknowledge the original contributor of the material. PackagesarmitageArmitage trend chi-square statistics to evaluate the association of a trait with SNP genotype predictors given a dose vector of length 3. Distributed for R and S-PLUS with install steps given in the README. Dan Schaid, Shannon McDonnell, and Jason Sinnwell. [05/2010] bilinear.fitA suite of S-PLUS routines for preforming bilinear regression fits to 16O/18O isotope labeling of experiments. Jeanette Eckel Passow, Douglas Mahoney. [11/2010] Haplo StatsA suite of R routines for the analysis of indirectly measured haplotypes. The statistical methods assume that all subjects are unrelated and that haplotypes are ambiguous (due to unknown linkage phase of the genetic markers). The genetic markers are assumed to be codominant (i.e., one-to-one correspondence between their genotypes and their phenotypes). Dan Schaid and Jason Sinnwell. [12/2011] Distributions for R can also be found on CRAN. hweTest the fit of genotype frequencies to Hardy-Weinberg Equilibrium proportions for autosomes and the X chromosome. Different statistical tests are provided, as well as an option to evaluate statistical significance by either exact methods or simulations. README and package sources are provided for S-PLUS and R. [02/2011] kinshipThis is a suite of interrelated routines, of which the primary ones are coxme (general mixed-effects Cox models), kinship (routines to create and manipulate n by n matrices that describe the genetic relationships between n persons), and pedigree (create and plot pedigrees). Terry Therneau & Beth Atkinson. [04/2005] Ported to R, can be found on CRAN. kinship2(Contains functions from former package called pedigree.shrink.) Routines to handle family data with a pedigree object. The initial purpose was to create correlation structures that describe family relationships such as kinship and identity-by-descent, which can be used to model family data in mixed effects models, such as in the coxme function. Also includes a tool for pedigree drawing which is focused on producing compact layouts without intervention. Recent additions include utilities to trim the pedigree object with various criteria. Terry Therneau, Beth Atkinson, Dan Schaid, Jason Sinnwell, Shannon McDonnell, and Martha Matsumoto.[12/2011] mend.errCheck Pedigrees for Mendelian Errors and, when errors are found, systematically jackknifes every typed pedigree member to determine if eliminating this member will remove all Mendelian Errors from the pedigree. Dan Schaid and Daniel Folie. [02/2011] MulticS-PLUS/R routines for quantitative linkage analysis using variance components approach, based on the multic routines found in the package ACT. This release allows for univariate, multivariate and longitudinal endpoints and includes model diagnostic tools and easy-to-read result summaries. Mariza de Andrade, Patrick Votruba, and Beth Atkinson. [02/2007] Distributions for R can also be found on CRAN. rocThese functions create a variety of plots associated with sensitivity and specificity, along with pairwise comparisons of the area under the curve. Beth Atkinson and Doug Mahoney. [06/2004] rpartRecursive partitioning, an alternative to tree, allows users to create their own splitting rules using code written in Splus. Terry Therneau & Beth Atkinson. [04/2002] Ported to R by Brian Ripley. Versions for R are available on CRAN. SpatialNorm6Spatial normalization of Affymetrix SNP 6.0 cel file, which adjusts for spatial bias based on wavelet decomposition. High Seng Chai. [07/2010] survivalThese functions for survival analysis have been posted to Statlib at irregular intervals as survival (5/90), survival2 (6/91), survival3 (4/93), survival4 (10/94), and survival5 (2/99). The functions are also incorporated directly into S-Plus. The S-Plus versions are normally more up-to-date than the statlib code. Terry Therneau (therneau@mayo.edu). [11/2004] Distributions for R can also be found on R-Forge. It is currently part of the standard distribution of R.
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