hanover.whitepine: Mating crosses of white pine trees

In kwstat/agridat: Agricultural Datasets

Mating crosses of white pine trees

Description

Mating crosses of white pine trees

Usage

data("hanover.whitepine")

Format

A data frame with 112 observations on the following 4 variables.

rep

replicate

female

female parent

male

male parent

length

epicotyl length, cm

Details

Four male (pollen parent) White Pine trees were mated to seven female trees and 2654 progeny were grown in four replications, one plot per mating in each replication. Parent trees were sourced from Idaho, USA. The data are plot means of epicotyl length.

Becker (1984) used these data to demonstrate the calculation of heritability.

Source

Hanover, James W and Barnes, Burton V. (1962). Heritability of height growth in year-old western white pine. Proc Forest Genet Workshop. 22, 71–76.

Walter A. Becker (1984). Manual of Quantitative Genetics, 4th ed. Page 83.

References

None

Examples

## Not run: 
  
  library(agridat)
  data(hanover.whitepine)
  dat <- hanover.whitepine

  libs(lattice)
  # Relatively high male-female interaction in growth comared
  # to additive gene action. Response is more consistent within
  # male progeny than female progeny.
  # with(dat, interaction.plot(female, male, length))
  # with(dat, interaction.plot(male, female, length))
  bwplot(length ~ male|female, data=dat,
         main="hanover.whitepine - length for male:female crosses",
         xlab="Male parent", ylab="Epicotyl length")
  
  # Progeny sums match Becker p 83
  sum(dat$length) # 380.58
  aggregate(length ~  female + male, data=dat, FUN=sum)
  
  # Sum of squares matches Becker p 85
  m1 <- aov(length ~ rep + male + female + male:female, data=dat)
  anova(m1)
  
  # Variance components match Becker p. 85
  libs(lme4)
  libs(lucid)
  m2 <- lmer(length ~ (1|rep) + (1|male) + (1|female) + (1|male:female), data=dat)
  #as.data.frame(lme4::VarCorr(m2))
  vc(m2)
  ##         grp        var1 var2    vcov  sdcor
  ## male:female (Intercept) <NA> 0.1369  0.3699
  ##      female (Intercept) <NA> 0.02094 0.1447
  ##        male (Intercept) <NA> 0.1204  0.3469
  ##         rep (Intercept) <NA> 0.01453 0.1205
  ##    Residual        <NA> <NA> 0.2004  0.4477
  
  # Becker used this value for variability between individuals, within plot
  s2w <- 1.109
  
  # Calculating heritability for individual trees
  s2m <- .120
  s2f <- .0209
  s2mf <- .137
  vp <- s2m + s2f + s2mf + s2w  # variability of phenotypes = 1.3869
  4*s2m / vp # heritability male 0.346
  4*s2f / vp # heritability female 0.06
  2*(s2m+s2f)/vp # heritability male+female .203
  # As shown in the boxplot, heritability is stronger through the
  # males than through the females.

## End(Not run)

kwstat/agridat documentation built on Nov. 2, 2024, 6:19 a.m.