Plotting field maps with the desplot package"

Abstract

This short note shows how to plot a field map from an agricultural experiment and why that may be useful.

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 @yates1935complex.

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(block ~ col+row, yates.oats,
        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 @ryder1981field. 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(res ~ col + row, gnut, 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.

Session info

sessionInfo()

References



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desplot documentation built on April 3, 2018, 5:03 p.m.