WheatPDA {pda}R Documentation

Wheat virus in plant sap

Description

An agronomist (Katsiotis 1993) studied the effect of ploidy (number of copies of DNA chromosomes – humans have 2) on the yield in several species of alfalfa. The ploidy ranged from 2 to 8, with one to five species per ploidy. Within each species several matings (known as crosses) were arranged. Each mating produced about five accessions. Roughly 15 offspring from each accession were planted and later harvested to measure yield. This completely nested design has a mix of fixed effects (ploidy, species) and random effects (crosses, accessions, offspring).

Usage

data(WheatPDA)
data(BactRoom)

Format

Wheat data frame with 192 observations on 8 variables.
[,1] id factor bird identifier
[,2] bact factor wheat or control
[,3] temp factor room temperature
[,4] inoc factor when innoculated
[,5] bill numeric bill length
[,6] leg numeric leg length
[,7] code factor plot code
[,8] trt trt bact*trt combination

BactRoom data frame with 2685 observations on 8 variables.
[,1] ploidy ordered ploidy number
[,2] species factor species name
[,3] cross factor cross identifier
[,4] accession factor accession number
[,5] plant factor plant number
[,6] tr1 numeric trial 3 yield
[,7] tr2 numeric trial 3 yield
[,8] tr3 numeric trial 3 yield

Source

A Katsiotis, UW-Madison Agronomy Department (http://agronomy.wisc.edu)

References

Katsiotis A (1993) `The determination and use of pollen grain size in four ploidy levels and the cytogenetics of tetraploid-octoploid hybrids in search of 2n gametes of Avena', PhD Dissertation, Department of Agronomy, University of Wisconsin-Madison.

Examples

data( WheatPDA )

# H:22.3 Wheat BLUEs and BLUPs
class( WheatPDA$ploidy ) = factor( WheatPDA$ploidy, ordered = FALSE )
WheatPDA$sp = interaction( WheatPDA$ploidy, WheatPDA$species)
WheatPDA$cr = interaction( WheatPDA$sp, WheatPDA$cross)
WheatPDA$ac = interaction( WheatPDA$cr, WheatPDA$accession)

## Not run: 
## this does not work properly: singular X'X matrix
library( lme4 )
Wheat.lme = lmer( tr1 ~ ploidy + sp + (1|cr) + (1|ac),
  data = WheatPDA, na.action = na.omit )
Wheat.lme = lmer( tr1 ~ ploidy + sp + (1|cross),
  data = WheatPDA, na.action = na.omit )
## End(Not run)

[Package pda version 1.2-1 Index]