demo/SPET.R

In ScottKnott: The ScottKnott Clustering Algorithm

##
## Example: Split-plot Experiment in time (SPET)
##

## The parameters can be: formula, aov, lm or lmer.

## Note: The factors are in uppercase and its levels in lowercase!

library(ScottKnott)
data(SPET)

## From: formula
## Main factor: year
sk1 <- with(SPET,
            SK(y ~ blk + tra*year + Error(blk/tra),
               dfm,
               which='year'))
summary(sk1)

## Nested: crotjuncea/year
sk2 <- with(SPET,
            SK(y ~ blk + tra*year + Error(blk/tra),
               dfm,
               which='tra:year',
               fl1=2))
summary(sk2)

## Nested: year_1/tra
## It is necessary to inform how to combinate the errors
sk3 <- with(SPET,
            SK(y ~ blk + tra*year + Error(blk/tra),
               dfm,
               which='year:tra',
               error='Within/blk:tra',
               fl1=1))
summary(sk3)

## From: lm
lm1 <- with(SPET,
            lm(y ~ blk*tra + tra*year,
               data=dfm))

## Nested: tra1/year
sk4 <- SK(lm1,
          which='tra:year',
          fl1=1)

summary(sk4)

## Nested: year1/tra
## It is necessary to inform how to combinate the errors
sk5 <- SK(lm1,
          which='year:tra',
          error='Within/blk:tra',
          fl1=1)
summary(sk5,
        complete=FALSE)

## Nested: year2/tra
## It is necessary to inform how to combinate the errors
sk6 <- SK(lm1,
          which='year:tra',
          error='Within/blk:tra',
          fl1=2)
summary(sk6,
        complete=FALSE)

## From: aov
av1 <- with(SPET,
            aov(y ~ blk + tra*year + Error(blk/tra),
                data=dfm))
summary(av1)

## Main factor: year
sk7 <- SK(av1,
              which='year')
summary(sk7)

## Main factor: tra
## It is necessary to inform the appropriate error for the test
sk8 <- SK(av1,
          which='tra',
          error='blk:tra')
summary(sk8,
        complete=FALSE)

## Nested: crotjuncea/year
sk9 <- SK(av1,
          which='tra:year',
          fl1=2)
summary(sk9)

## Nested: guandu/year
sk10 <- SK(av1,
           which='tra:year',
           fl1=4)
summary(sk10)

## Nested: year_1/tra - it is necessary to inform how to combinate the errors
sk11 <- SK(av1,
           which='year:tra',
           error='Within/blk:tra',
           fl1=1)
summary(sk11,
        complete=FALSE)

op <- par(mar=c(6, 3, 3, 2))
plot(sk10,
     id.las=2,
     xlab='',
     di='sd',
     d.col='red',
     d.lty=3)

## Nested: year_2/tra - it is necessary to inform how to combinate the errors
sk12 <- SK(av1,
           which='year:tra',
           error='Within/blk:tra',
           fl1=2)
summary(sk12)
op <- par(mar=c(7, 3, 3, 2))
plot(sk12,
     id.las=2,
     xlab='',
     di='sd',
     d.col='red',
     d.lty=3)
par(op)