qgtools (version 2.0)

ad.reml.jack: AD model with REML analysis and jackknife resampling test

Description

AD model can be analyzed by REML approach for variance components, fixed effects, random effects and tested by a jackknife approach

Usage

ad.reml.jack(Y, Ped, JacNum = NULL, JacRep = NULL)

Arguments

Y

A trait matrix including one or more than one traits.

Ped

A pedigree matrix including Environment, Female, Male, Generation, with or without block is required. So the matrix should include either 4 columns or 5 columns.

JacNum

Number of groups to be jackknifed. The default is 10.

JacRep

Number of jackknife process to be repeated. The default is 1

Value

Return a list of results: variance components, propotional variance components, fixed effects, and random effects.

Details

A pedigree matrix used for analysis is required in the order of Environment (column 1), Female(column 2), Male(column 3), Generation (column 4). Column 5 for block can be default. Even though there is only one environment, this column is needed.

References

Rao, C.R. 1971. Estimation of variance and covariance components-MINQUE theory. J Multiva Ana 1:19

Wu, J., McCarty Jr., J.C., Jenkins, J.N. 2010. Cotton chromosome substitution lines crossed with cultivars: Genetic model evaluation and seed trait analyses. Theoretical and Applied Genetics 120:1473-1483.

Wu, J., J. N. Jenkins, J. C. McCarty, K. Glover, and W. Berzonsky. 2010. Presentation titled by "Unbalanced Genetic Data Analysis: model evaluation and application" was offered at ASA, CSSA, & SSSA 2010 International Annual Meetings, Long Beach, CA.

Wu, J., J. N. Jenkins, and J.C., McCarty. 2011. A generalized approach and computer tool for quantitative genetics study. Proceedings Applied Statistics in Agriculture, April 25-27, 2010, Manhattan, KS. p.85-106.

Wu, J. 2012. GenMod: An R package for various agricultural data analyses. ASA, CSSA, and SSSA 2012 International Annual Meetings, Cincinnati, OH, p 127

Wu J., Bondalapati K., Glover K., Berzonsky W., Jenkins J.N., McCarty J.C. 2013. Genetic analysis without replications: model evaluation and application in spring wheat. Euphytica. 190:447-458

Zhu J. 1989. Estimation of Genetic Variance Components in the General Mixed Model. Ph.D. Dissertation, NC State University, Raleigh, U.S.A

Examples

# NOT RUN {
 library(qgtools)
 data(cotf2)
 dat=cotf2[which(cotf2$Env==1),]
 Ped=dat[,c(1:5)]
 Y=dat[,-c(1:5)]
 
 res=ad.reml.jack(Y,Ped)
 res$Var
 res$FixedEffect
 res$RandomEffect

 ##End

# }