adrc.mq: AD model with row and column effects

In qgtools: Generalized Quantitative Genetics Data Analyses

Description

An AD model with row and column effects included is used for controlling field variation. The data set can be irregular or missing but the field layout should be rectangular. It can analyze any genetic mating designs and data including F1, F2, or F3 with parents..

Usage

adrc.mq(Y, Ped, Row = NULL, Col = NULL)

Arguments

Y	A data matrix for one or more traits
Ped	A pedigree matrix including Environment, Female, Male, Generation is required.
Row	A vector for field rows. It can be default.
Col	A vector for field colums.It can be default.

Details

If only row or column vector is included, this is equivallent to an AD model with block effects.

Value

Return a list of results: estimated variance components, estimated fixed effects, and predicted random effects

Author(s)

Jixiang Wu <[e-mail]>

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

  library(qgtools)
  data(adrcdat)
  dat=adrcdat[which(adrcdat$Env==1),]
  Ped=dat[,c(1,4,5,6)]
  Y=dat[,c(8:10)]
  Row=dat$Row
  Col=dat$Column
      
  res=adrc.mq(Y,Ped,Row=Row,Col=Col) ##run AD model without jackknifing under row and column effects
  res$Var
  res$FixedEffect
  res$RandomEffect

qgtools documentation built on Dec. 19, 2019, 1:09 a.m.