R setup
library("knitr")
knitr::opts_chunk$set(fig.align="center", fig.width=6, fig.height=6)
options(width=90)Example 1
First, a plot of the experimental design of the oats data from Yates (1935).
library(agridat)
library(desplot)
data(yates.oats)
# Older versions of agridat used x/y here instead of col/row
if(is.element("x",names(yates.oats)))
yates.oats <- transform(yates.oats, col=x, row=y)
desplot(yates.oats, block ~ col+row,
col=nitro, text=gen, cex=1, out1=block,
out2=gen, out2.gpar=list(col = "gray50", lwd = 1, lty = 1))
Example 2
This next example is from Ryder (1981).
Fit an ordinary RCB model with fixed effects for block and
genotype. Plot a heatmap of the residuals.
library(agridat)
library(desplot)
data(ryder.groundnut)
gnut <- ryder.groundnut
m1 <- lm(dry ~ block + gen, gnut) # Standard RCB model
gnut$res <- resid(m1)
desplot(gnut, res ~ col + row, text=gen, cex=1,
main="ryder.groundnut residuals from RCB model")
Note the largest positive/negative residuals are adjacent to each other,
perhaps caused by the original data values being swapped. Checking with
experiment investigators (managers, data collectors, etc.) is
recommended.
References
Ryder, K. 1981. “Field Plans: Why the Biometrician Finds Them
Useful.” Experimental Agriculture 17: 243–56. https://doi.org/10.1017/S0014479700011601.
Yates, Frank. 1935. “Complex Experiments.” Journal of
the Royal Statistical Society Suppl 2: 181–247. https://doi.org/10.2307/2983638.