Description Usage Format Source References Examples
The scientist examined the effects of rate of
application of a certain herbicide (pyridate) on a range of closely
related crop
s. The experiment was conducted over two
year
s, with three block
s each year
.
The two year
s were conducted in roughly the same location,
but there was separate randomization in each year
. Three
herbicide rates (pyrrat
= 0, 1, 2) were randomly assigned
to separate rows within each crop
plot. Recorded values
consist of yield
per row for each crop*pyrrat
combination within each block
for each year
.
Since crop
2 was not used in the second year
, it
is dropped from further consideration.
1 |
Brassica data frame with 144 observations on 10 variables.
[,1] | crop | factor | crop identifier (1-7) |
[,2] | pyrrat | ordered | pyridate level (0-2) |
[,3] | block | factor | block (1-3) |
[,4] | inj7dat | numeric | injury after 7 days |
[,5] | in14dat | numeric | injury after 14 days |
[,6] | yldkga | numeric | yield in kilograms |
[,7] | pconyld | numeric | percent control yield |
[,8] | pcnblk | numeric | percent control in block yield |
[,9] | year | ordered | year - 1990 |
[,10] | trt | factor | treatment code |
Alan Miller, U WI Horticulture (http://www.hort.wisc.edu)
Miller A (1993) 'Pyridate tolerance in Brassicaceae crops', PhD Dissertation, Department of Horticulture, University of Wisconsin-Madison.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 | # full data set--code not ready yet!
# model fits for bill and leg
data( Brassica )
# drop Crop 2
Brassica <- data.frame(Brassica[ Brassica$crop != 2, ])
Brassica$crop <- factor( as.character( Brassica$crop ))
# Analysis based on lmer()
library(lme4)
Brassica1 <- data.frame( Brassica[ Brassica$year == 1, ] )
Brassica.lme <- lmer( yldkga ~ crop * pyrrat + (1|crop:block),
data = Brassica1 )
anova( Brassica.lme )
VarCorr( Brassica.lme )
# Analysis based on aov() using Error() specification
Brassica.aov <- aov ( yldkga ~ crop * pyrrat +
Error( block/crop ), Brassica1 )
summary( Brassica.aov )
# Analysis of full data set: both years
Brassica.full <- aov ( yldkga ~ crop * pyrrat * year +
Error( year:block + crop:year:block ), Brassica )
Brassica.red <- aov ( yldkga ~ crop * year + pyrrat + crop:pyrrat +
Error( year:block + crop:year:block ), Brassica)
# Analysis based on lmer()
Brassica1 <- data.frame( Brassica[ Brassica$year == 1, ] )
Brassica.lme <- lmer( yldkga ~ crop * pyrrat + (1|block:crop),
data = Brassica1 )
Brassica$yrblk = interaction(Brassica[,c("year","block")])
Brassica$cropyrblk = interaction(Brassica[,c("crop","year","block")])
Brassica.fulle = lmer(yldkga ~ crop * pyrrat * year +
(1|yrblk:cropyrblk), data = Brassica )
anova(Brassica.fulle)
Brassica.rede = lmer(yldkga ~ crop * year + pyrrat + crop:pyrrat +
(1|yrblk:cropyrblk), data = Brassica )
anova(Brassica.rede)
anova(Brassica.rede,Brassica.fulle)
lsd.plot(Brassica.rede,factor=c("pyrrat","crop"),
xlab = "pyr rate by crop",
ylab = "mean crop yield" )
## Not run:
# The following code is specialized to get plots for the book.
# It is not recommended as standard practice, but presented to
# show one torturous way to get LSMEANS for a nested design.
Brassica.red <- aov (yldkga ~ crop * year + pyrrat + crop:pyrrat +
Error(year:block + crop:year:block), Brassica, qr = TRUE)
Brassica.proj <- proj ( Brassica.red )
Brassica.ref <- data.frame(Reference=c(Brassica.proj[[1]]))
for (i in names(Brassica.proj)[-1])
Brassica.ref[[i]] <- apply( Brassica.proj[[i]], 1, sum )
# whole plot
Brassica.wp <- nested( Brassica.proj, Brassica, c("block","year","crop"), "yldkga",
c(1,3), Brassica.ref )
Brassica.wpaov <- aov( yldkga ~ year*block + crop + crop:year, Brassica.wp,
weight = Brassica.wp$weight)
# split plot
Brassica.sp <- nested( Brassica.proj, Brassica, c("block","year","crop","pyrrat"),
"yldkga", c(1,4), Brassica.ref )
Brassica.spaov <- aov( yldkga ~ year*block*crop + pyrrat +
crop:pyrrat, Brassica.sp )
margin.plot( Brassica.wpaov, factors = c("crop","year"),
xlab = "(a) crop by year", ylab = "yield in 10000 kg" )
#Figure H:24.1 Brassicaica split split plot anova
lsd.plot( Brassica.spaov, factors = c("pyrrat","crop"),
xpos = .6, ypos = 3.25,
xlab = "(b) pyr rate by crop",
ylab = "deviation from mean crop yield" )
## End(Not run)
|
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