R packages Maintained by Jing Hua Zhao
The R commands for installation (e.g., CGR and R/gap) are as follows,
> install.packages("CGR",contriburl="http://www.mrc-epid.cam.ac.uk/~jinghua.zhao/software")
# MRC site
> install.packages("CGR","R",contriburl="http://www.mrc-epid.cam.ac.uk/~jinghua.zhao/software")
# under Unix/Linux, where
"R" is a user directory
> install.packages("gap",
repos="http://cran.r-project.org") # repos is an option specifying CRAN or one of the mirror sites
Here are some frequently-asked questions (FAQs) and pedigree diagrams by pedtodot in R/gap as viewed by dotty and neato of graphviz for the GAW14 data. There is also a pedigree (pre, dot, pdf) created for the data provided by Richard Mott as prompted by a pedigree (pre, dot, pdf) from Jinliang Wang.
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Version: |
1.0-5 |
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Date: |
2006-5-22 |
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Title: |
Classic Genetics in R |
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Author: |
Jing hua Zhao in collaboration with other colleagues |
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Maintainer: |
Jing hua Zhao
<jinghua.zhao@mrc-epid.cam.ac.uk> |
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BundleDescription: |
This is an experimental package bundle based on the R packages pathmix and pointer. |
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License: |
Programs included in this package by Jing hua Zhao will be under GPL. Specific requirement may be possible for programs written by other authors. |
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URL: |
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Name: |
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Version: |
1.0-17 |
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Date: |
2009-1-2 |
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Author: |
Jing hua Zhao in collaboration with other colleagues, and with help from Kurt Hornik and Brian Ripley of the R core development team |
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Maintainer: |
Jing hua Zhao
<jinghua.zhao@mrc-epid.cam.ac.uk> |
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Description: |
It is designed as an integrated package for genetic data analysis of both population and family data. Currently, it contains functions for sample size calculations of both population-based and family-based designs, classic twin models, probability of familial disease aggregation, kinship calculation, some statistics in linkage analysis, and association analysis involving one or more genetic markers including haplotype analysis with or without environmental covariates. |
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License: |
Programs included in this package by Jing hua Zhao will be under GPL. Specific requirement may be possible for programs written by other authors. |
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URL: |
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Name: |
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Version: |
1.1.0-22 |
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Date: |
2008-12-30 |
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Title: |
mixed-effects Cox models, sparse matrices, and modeling data from large pedigrees |
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Author: |
Beth Atkinson (atkinson@mayo.edu)
for pedigree functions. |
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Maintainer: |
Jing hua Zhao
<jinghua.zhao@mrc-epid.cam.ac.uk> |
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Depends: |
survival, nlme, lattice |
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Description: |
coxme: general mixed-effects Cox models; kinship: routines to create and manipulate n by n matrices that describe the genetic relationships between n persons; pedigree: create and plot pedigrees; bdsmatrix: a class of objects for sparse block-diagonal matrices (which is how kinship matrices are stored); gchol: generalized cholesky decompositions. |
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License: |
GPL (>=2) |
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URL: |
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Name: |
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Version: |
0.3-5 |
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Date: |
2008-8-26 |
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Title: |
Linear mixed models |
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Author: |
Original by Joseph L. Schafer <jls@stat.psu.edu>. |
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Maintainer: |
Jing hua Zhao
<jinghua.zhao@mrc-epid.cam.ac.uk> |
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Description: |
Some improved procedures for linear mixed models |
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License: |
The software may be distributed free of charge and used by anyone if credit is given. It has been tested fairly well, but it comes with no guarantees and the authors assume no liability for its use or misuse. |
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URL: |
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Name: |
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Version: |
0.2-6 |
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Date: |
2008-5-14 |
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Title: |
Multiple imputation for multivariate panel or clustered data |
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Author: |
Original by Joseph L. Schafer <jls@stat.psu.edu>. |
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Maintainer: |
Jing hua Zhao
<jinghua.zhao@mrc-epid.cam.ac.uk> |
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Description: |
Multiple imputation for multivariate panel or clustered data |
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License: |
The software may be distributed free of charge and used by anyone if credit is given. It has been tested fairly well, but it comes with no guarantees and the authors assume no liability for its use or misuse. |
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URL: |
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Name: |
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Version: |
1.1-2 |
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Date: |
2007-11-22 |
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Title: |
TDT tests for extended haplotypes |
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Author: |
David Clayton |
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Maintainer: |
Jing hua Zhao
<
jinghua.zhao@mrc-epid.cam.ac.uk> |
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Depends |
R (>=1.5.0) |
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Description: |
Clayton, D. and Jones, H.B. (1999), Transmission/disequilibrium tests for extended marker haplotypes, Am. J. Hum. Genet., 65:1161-1169. |
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License: |
Artistic |
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URL: |
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Date last changed 2/1/2009