Weight of cork samples on four sides of trees
The cork data gives the weights of cork borings of the trunk for 28 trees on the north (N), east (E), south (S) and west (W) directions.
Data frame with 28 observations on the following 5 variables.
tree
tree number
dir
direction N,E,S,W
y
weight of cork deposit (centigrams), north direction
C.R. Rao (1948). Tests of significance in multivariate analysis. Biometrika, 35, 58-79. https://doi.org/10.2307/2332629
K.V. Mardia, J.T. Kent and J.M. Bibby (1979) Multivariate Analysis, Academic Press.
Russell D Wolfinger, (1996). Heterogeneous Variance: Covariance Structures for Repeated Measures. Journal of Agricultural, Biological, and Environmental Statistics, 1, 205-230.
## Not run: library(agridat) data(box.cork) dat <- box.cork libs(reshape2, lattice) dat2 <- acast(dat, tree ~ dir, value.var='y') splom(dat2, pscales=3, prepanel.limits = function(x) c(25,100), main="box.cork", xlab="Cork yield on side of tree", panel=function(x,y,...){ panel.splom(x,y,...) panel.abline(0,1,col="gray80") }) ## Radial star plot, each tree is one line libs(plotrix) libs(reshape2) dat2 <- acast(dat, tree ~ dir, value.var='y') radial.plot(dat2, start=pi/2, rp.type='p', clockwise=TRUE, radial.lim=c(0,100), main="box.cork", lwd=2, labels=c('North','East','South','West'), line.col=rep(c("royalblue","red","#009900","dark orange", "#999999","#a6761d","deep pink"), length=nrow(dat2))) # asreml 4 libs(asreml) # Unstructured covariance dat$dir <- factor(dat$dir) dat$tree <- factor(dat$tree) dat <- dat[order(dat$tree, dat$dir), ] # Unstructured covariance matrix m1 <- asreml(y~dir, data=dat, residual = ~ tree:us(dir)) libs(lucid) vc(m1) # Note: 'rcor' is a personal function to extract the correlations # into a matrix format # round(kw::rcor(m1)$dir, 2) # E N S W # E 219.93 223.75 229.06 171.37 # N 223.75 290.41 288.44 226.27 # S 229.06 288.44 350.00 259.54 # W 171.37 226.27 259.54 226.00 # Note: Wolfinger used a common diagonal variance # Factor Analytic with different specific variances # fixme: does not work with asreml4 # m2 <- update(m1, residual = ~tree:facv(dir,1)) # round(kw::rcor(m2)$dir, 2) # E N S W # E 219.94 209.46 232.85 182.27 # N 209.46 290.41 291.82 228.43 # S 232.85 291.82 349.99 253.94 # W 182.27 228.43 253.94 225.99 ## End(Not run)
Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.