burgueno.unreplicated {agridat} | R Documentation

## Field experiment with unreplicated genotypes plus one repeated check.

### Description

Field experiment with unreplicated genotypes plus one repeated check.

### Usage

    data("burgueno.unreplicated")

### Format

A data frame with 434 observations on the following 4 variables.

`gen`

  genotype, 281 levels

`col`

  column

`row`

  row

`yield`

  yield, tons/ha

### Details

A field experiment with 280 new genotypes. A check genotype is planted in every 4th column.

The plot size is not given.

### Source

J Burgueno, A Cadena, J Crossa, M Banziger, A Gilmour, B Cullis. 2000. User's guide for spatial analysis of field variety trials using ASREML. CIMMYT.

Electronic version of the data obtained from CropStat software.

Used with permission of Juan Burgueno.

### Examples

    data(burgueno.unreplicated)
    dat <- burgueno.unreplicated

    # Define a 'check' variable for colors
    dat$check <- ifelse(dat$gen=="G000", 2, 1)
    # Every fourth column is the 'check' genotype
    if(require(desplot)){
      desplot(yield ~ col*row, data=dat,
              col=check, num=gen, #text=gen, cex=.3, # aspect unknown
              main="burgueno.unreplicated")
    }

    # ----------------------------------------------------------------------------

    ## Not run:
      # asreml3
      require(asreml)
      require(lucid)

      # AR1 x AR1 with random genotypes
      dat <- transform(dat, xf=factor(col), yf=factor(row))
      dat <- dat[order(dat$xf,dat$yf),]
      m2 <- asreml(yield ~ 1, data=dat, random = ~ gen,
                   rcov = ~ ar1(xf):ar1(yf))
      vc(m2)
      # Note the strong saw-tooth pattern in the variogram.  Seems to
      # be column effects.
      plot(variogram(m2), xlim=c(0,15), ylim=c(0,9), zlim=c(0,0.5),
           main="burgueno.unreplicated - AR1xAR1")
      # library(lattice) # Show how odd columns are high
      # bwplot(resid(m2) ~ col, data=dat, horizontal=FALSE)

      # Define an even/odd column factor as fixed effect
      # dat$oddcol <- factor(dat$col
      # The modulus operator throws a bug, so do it the hard way.
      dat$oddcol <- factor(dat$col - floor(dat$col / 2) *2 )

      m3 <- update(m2, yield ~ 1 + oddcol)
      m3$loglik # Matches Burgueno table 3, line 3
      plot(variogram(m3), xlim=c(0,15), ylim=c(0,9), zlim=c(0,0.5),
           main="burgueno.unreplicated - AR1xAR1 + Even/Odd")
      # Much better-looking variogram

    ## End(Not run)

    # ----------------------------------------------------------------------------

    ## Not run:
      ## require(asreml4)
      ## require(lucid)

      ## # AR1 x AR1 with random genotypes
      ## dat <- transform(dat, xf=factor(col), yf=factor(row))
      ## dat <- dat[order(dat$xf,dat$yf),]
      ## m2 <- asreml(yield ~ 1, data=dat, random = ~ gen,
      ##              resid = ~ ar1(xf):ar1(yf))
      ## vc(m2)
      ## ##       effect component std.error z.ratio bound
      ## ##          gen    0.9122   0.127       7.2     P 0
      ## ##     xf:yf(R)    0.4993   0.05601     8.9     P 0
      ## ## xf:yf!xf!cor   -0.2431   0.09156    -2.7     U 0
      ## ## xf:yf!yf!cor    0.1255   0.07057     1.8     U 0.1

      ## # Note the strong saw-tooth pattern in the variogram.  Seems to
      ## # be column effects.
      ## plot(varioGram(m2), xlim=c(0,15), ylim=c(0,9), zlim=c(0,0.5),
      ##      main="burgueno.unreplicated - AR1xAR1")
      ## # library(lattice) # Show how odd columns are high
      ## # bwplot(resid(m2) ~ col, data=dat, horizontal=FALSE)

      ## # Define an even/odd column factor as fixed effect
      ## # dat$oddcol <- factor(dat$col
      ## # The modulus operator throws a bug, so do it the hard way.
      ## dat$oddcol <- factor(dat$col - floor(dat$col / 2) *2 )

      ## m3 <- update(m2, yield ~ 1 + oddcol)
      ## m3$loglik # Matches Burgueno table 3, line 3

      ## plot(varioGram(m3), xlim=c(0,15), ylim=c(0,9), zlim=c(0,0.5),
      ##      main="burgueno.unreplicated - AR1xAR1 + Even/Odd")
      ## # Much better-looking variogram

    ## End(Not run)

[Package agridat version 1.16 Index]