ad.reml.jack: AD model with REML analysis and jackknife resampling test
In qgtools: Generalized Quantitative Genetics Data Analyses

Description Usage Arguments Details Value Author(s) References Examples

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

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

`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

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.

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

Jixiang Wu <qgtools@gmail.com>

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

 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

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