Splus Functions

Local Extensions To The Splus Language

These files contain source code only. This means that those packages that contain C code (rpart, survival, kinship) require a compiler. Although we realize that some will not have the expertise or perhaps the software to do the compilation, particularly on Windows systems, we do not have the time or the necessary equipment to provide binary versions. All the libraries and "useful functions" are stored using the tar.gz format. Versions for R and Windows are noted when available. Otherwise, assume the code was written for Splus on a Unix system.

Copyright 2005 Mayo Foundations for Medical Education and Research. This software is free software; you can redistribute it 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 in the hope that it will be useful, 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.

Credit where credit is due. If you use functions from Mayo Clinic, please acknowledge the original contributor of the material.

Libraries

Haplo Stats: S-PLUS/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. [6/APR/2005]

Download: haplo.stats_1.2.0_S.tar.gz or haplo.stats_1.2.0_R.tar.gz.
See also the Readme file.

kinship: This 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. [8/APR/2005]

Download: kinship_1.2_S.tar.gz.
See the pdf report for details.

Multic: S-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. [12/FEB/2007]

Download: multic_0.3.0_S.tar.gz or multic_0.3.0_R.tar.gz.

roc: These 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 [3/JUN/2004]

Download: roc3_S.tar.gz.

rpart: Recursive partitioning, an alternative to tree, allows users to create their own splitting rules using code written in Splus. Terry Therneau & Beth Atkinson [24/APR/2002]

Download: rpart3_S.tar.gz.
See Brian Ripley's homepage for ports of rpart to the Window's and R environments.

survival: These 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). [23/NOV/2004]

Download: surv6.tar.gz.

Useful Functions