Description: R codes for the (adaptive) Sum of Powered Score ('SPU' and 'aSPU') tests, inverse variance weighted Sum of Powered score ('SPUw' and 'aSPUw') tests and gene-based and some pathway based association tests (Pathway based Sum of Powered Score tests ('SPUpath'), adaptive 'SPUpath' ('aSPUpath') test, 'GEEaSPU' test for multiple traits - single 'SNP' (single-nucleotide-polymorphism) association in generalized estimation equations, 'MTaSPUs' test for multiple traits - single 'SNP' association with Genome Wide Association Studies ('GWAS') summary statistics, Gene-based Association Test that uses an extended Simes procedure ('GATES'), Hybrid Set-based Test ('HYST') and extended version of 'GATES' test for pathway-based association testing ('GATES-Simes'). ). The tests can be used with genetic and other data sets with covariates. The response variable is binary or quantitative. Summary; (1) Single trait-'SNP' set association with individual-level data ('aSPU', 'aSPUw'), (2) Single trait-'SNP' set association with summary statistics ('aSPUs'), (3) Single trait-pathway association with individual-level data ('aSPUpath'), (4) Single trait-pathway association with summary statistics ('aSPUsPath'), (5) Multiple traits-single 'SNP' association with individual-level data ('GEEaSPU'), (6) Multiple traits-single SNP association with summary statistics ('MTaSPUs').
Depends: R(>= 3.1.0), gee, MASS, mvtnorm, matrixStats

Description: Contains some tools for testing, analyzing time series data and
fitting popular time series models such as ARIMA, Moving Average and Holt
Winters, etc. Most functions also provide nice and clear outputs like SAS
does, such as identify, estimate and forecast, which are the same statements

Title: Adaptation of Virtual Twins Method from Jared Foster
Authors@R: person("Francois", "Vieille", email = "vieille.francois@gmail.com",
Description: Research of subgroups in random clinical trials with binary outcome and two treatments groups. This is an adaptation of the Jared Foster method.
Imports: rpart, party, methods, randomForest, stats
Collate: 'aVirtualTwins.R' 'data.R' 'object.R' 'difft.R' 'setClass.R'