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Seraphim: Illumina GA basecalling - Seraphim is an R package for model-based quality assessment and base-calling of second-generation sequencing data produced by Illumina's GA technology.
This project has not yet categorized itself in the Trove Software Map	Register Date: 2009-12-09 23:14

Shrinkage Estimation - `shrink' is an R package for James-Stein-type shrinkage estimation of the parameters of a linear regression model. This is a work in progress jointly with S. Ejaz Ahmed (seahmed at uwindsor dot ca).
Development Status : 1 - Planning License : OSI Approved : GNU General Public License (GPL) Natural Language : English Operating System : Microsoft : Windows : Windows Vista Operating System : POSIX : Linux Programming Language : R Programming Language : S/S Plus Topic : Regression Models	Register Date: 2010-09-04 03:45

Similarity Surfaces - Suitability maps (also referred to bioclimatic envelopes, obtained e.g through climate matching) are a useful tool. This package implements methods to assess the similarity of any given point to the refeence points in regards to it's variable values.
This project has not yet categorized itself in the Trove Software Map	Register Date: 2010-10-14 18:50

Simple Prediction Intervals - Calculation of prediction intervals to include k of m future observations for normal and non-normal data. Also precedence intervals should be computed to include the future median.
Development Status : 2 - Pre-Alpha Environment : Console (Text Based) Intended Audience : End Users/Desktop License : Public Domain Natural Language : English Programming Language : R Topic : Other/Nonlisted Topic	Register Date: 2010-09-20 07:18

Simplified Bayesian Sensitivity Analysis - SBSA package implements simplified Bayesian sensitivity analysis of models with partially observed confounders.
This project has not yet categorized itself in the Trove Software Map	Register Date: 2011-12-08 21:08

Simulation of clustered multi-state data - R functions implementing the simulation procedure proposed at http://www.slideshare.net/federicorotolo/a-copulabased-simulation-method-for-clustered-multistate-survival-data to generate survival data with a clustered and multi-state structure.

Simulation of stochastic kinetic models - This package was developed for the book chapter in "In silico Systems Biology: A systems-based approach to understanding biological processes" published by Humana Press. This book is part of the Methods in Molecular Biology series.
This project has not yet categorized itself in the Trove Software Map	Register Date: 2012-10-02 08:40

Single Equation Instrumental Variable - This project demonstrates set identification in instrumental variable models for discrete outcomes.
This project has not yet categorized itself in the Trove Software Map	Register Date: 2009-11-03 11:00

Small Area Estimation with R - SAE is a package that implements some small area estimators. It also includes vignettes with examples on how to use these methods.
This project has not yet categorized itself in the Trove Software Map	Register Date: 2008-04-18 12:27

Software Development @ ISU - This is a project intended to provide support to software development in the Department of Statistics, Iowa State University.
This project has not yet categorized itself in the Trove Software Map	Register Date: 2010-01-13 05:44

Soil water - "Soil water" provides soil water retention functions and soil hydraulic conductivity functions and pedotransfer functions to estimate their parameter from easily available soil properties.
Development Status : 5 - Production/Stable Environment : Console (Text Based) Intended Audience : Developers Intended Audience : End Users/Desktop License : OSI Approved : GNU General Public License (GPL) Natural Language : English Operating System : MacOS Operating System : Microsoft Operating System : POSIX : Linux Programming Language : R Topic : Environmetrics	Register Date: 2010-08-17 21:13

SoilR - The objective of this project is the development of an R package for modeling soil organic matter decomposition. The package contains a collection of different functions commonly used to represent soil organic matter dynamics.
This project has not yet categorized itself in the Trove Software Map	Register Date: 2012-01-17 15:38

Space-Time Point Patterns - A package for simulation, display, and analysis of space-time point patterns. It builds on the work of splancs to add the temporal dimension to point patterns.
Development Status : 4 - Beta Intended Audience : End Users/Desktop License : OSI Approved : GNU General Public License (GPL) Topic : Spatial Data & Statistics : Point Pattern Analysis	Register Date: 2008-10-20 15:08

Sparse LDA - This package implements elasticnet-like sparseness in linear and mixture discriminant analysis as described in "Sparse Discriminant Analysis" by Line Clemmensen, Trevor Hastie and Bjarne Ersb
Development Status : 4 - Beta Intended Audience : End Users/Desktop License : OSI Approved : GNU General Public License (GPL) Natural Language : English Programming Language : R Topic : Machine Learning : Regularized and Shrinkage Methods Topic : Multivariate Statistics : Supervised Classification and Discriminant Analysis	Register Date: 2009-01-22 16:44

Sparse Multivariate Diffusions - Inference for discretely observed high dimensional diffusions given by SDEs with a sparse drift based on penalized loss function estimation and subsampling methods.
Development Status : 3 - Alpha Intended Audience : Developers License : OSI Approved : GNU General Public License (GPL) Natural Language : English Programming Language : R Topic : Machine Learning : Model Selection and Validation Topic : Machine Learning : Regularized and Shrinkage Methods Topic : Numerical Analysis : Prob\. Methods, Simulation and Stochastic Differential Equations	Register Date: 2010-07-05 09:50

SparseGrid - SparseGrid is an R translation of the Matlab code on http://www.sparse-grids.de Sparse grids can be used to numerically approximate integrals of high dimension, with fewer nodes than grids constructed by a product rule.
Development Status : 4 - Beta Intended Audience : Developers License : OSI Approved : GNU General Public License (GPL) Natural Language : English Programming Language : R Topic : Econometrics Topic : Numerical Analysis	Register Date: 2011-11-27 17:21

SparseM - SparseM provides some basic R functionality for linear algebra with sparse matrices.
This project has not yet categorized itself in the Trove Software Map	Register Date: 2007-08-27 22:03

Sparsity by Quadratic Penalties - This package fits classical sparse regression models with efficient active set algorithms by solving quadratic problems. Also provides a few methods for model selection purpose (cross-validation, stability selection).
Natural Language : English Operating System : OS Independent Programming Language : C/C\+\+ Programming Language : R Topic : Machine Learning : Regularized and Shrinkage Methods Topic : Multivariate Statistics : Linear Models Topic : Regression Models	Register Date: 2013-03-21 09:55

Spatial Exploratory Data Analysis - GeoXp is a package already available on CRAN. We are trying to modify the structure of this package by using the S4 classes used in sp package. We are also interested by modifying the interface of GeoXp, using some Rtkplot or similar tools...
Development Status : 5 - Production/Stable Intended Audience : End Users/Desktop License : OSI Approved : GNU General Public License (GPL) Natural Language : English Natural Language : French Operating System : OS Independent Programming Language : R Topic : Spatial Data & Statistics	Register Date: 2010-03-03 14:57

Spatial dependence - A collection of functions to create spatial weights objects, for summarizing these objects, and for permitting their use in spatial data analysis; a collection of tests for spatial autocorrelation and functions for fitting spatial regression models.
Development Status : 5 - Production/Stable Environment : Other Environment Intended Audience : Developers Intended Audience : End Users/Desktop License : OSI Approved : GNU General Public License (GPL) Operating System : OS Independent Programming Language : C/C\+\+ Programming Language : R Topic : Spatial Data & Statistics : Disease Mapping and Areal Data Analysis	Register Date: 2008-04-22 09:08