gathmann.bt {agridat} | R Documentation

## Impact of Bt corn on non-target species

### Description

Impact of Bt corn on non-target species

### Format

A data frame with 16 observations on the following 3 variables.

`gen`

  genotype/maize, `Bt` `ISO`

`thysan`

  thysan abundance

`aranei`

  aranei abundance

### Details

The experiment involved comparing a Bt maize and a near-isogenic control variety.

Species abundances were measured for Thysanoptera (thrips) and Araneida (spiders) in 8 different plots.

Each response is probably a mean across repeated measurements.

### Source

L. A. Hothorn, 2005. Evaluation of Bt-Maize Field Trials by a Proof of Safety. http://www.seedtest.org/upload/cms/user/presentation7Hothorn.pdf

Used with permission of Achim Gathmann.

### Examples

    data(gathmann.bt)
    dat <- gathmann.bt

    # EDA suggests Bt vs ISO is significant for thysan, not for aranei
    require(lattice)
    if(require(reshape2)){
    d2 <- melt(dat, id.var='gen')
    bwplot(value ~ gen|variable, d2,
           main="gathmann.bt", ylab="Insect abundance",
           panel=function(x,y,...){
             panel.xyplot(jitter(as.numeric(x)),y,...)
             panel.bwplot(x,y,...)
           },
           scales=list(relation="free"))
    }

    ## Not run:

      # ----- Parametric CI.  Thysan significant, aranei not significant.
      require(equivalence)

      th0 <- with(dat, tost(thysan[1:8], thysan[9:16], alpha=.05, paired=FALSE))
      lapply(th0[c("estimate","tost.interval")], round, 2)
      # 14.28-8.72=5.56, (2.51, 8.59) # match Gathmann p. 11

      ar0 <- with(dat, tost(aranei[1:8], aranei[9:16], alpha=.05, epsilon=.4))
      lapply(ar0[c("estimate","tost.interval")], round, 2)
      # .57-.47=.10, (-0.19, 0.40) # match Gathmann p. 11

      # ----- Non-parametric exact CI.  Same result.
      require(coin)

      th1 <- wilcox_test(thysan ~ gen, data=dat, conf.int=TRUE, conf.level=0.90)
      lapply(confint(th1), round, 2)
      # 6.36, (2.8, 9.2) # Match Gathmann p. 11

      ar1 <- wilcox_test(aranei ~ gen, data=dat, conf.int=TRUE, conf.level=0.90)
      lapply(confint(ar1), round, 2)
      # .05 (-.2, .4)

      # ----- Log-transformed exact CI. Same result.
      th2 <- wilcox_test(log(thysan) ~ gen, data=dat, alternative=c("two.sided"),
                         conf.int=TRUE, conf.level=0.9)
      lapply(confint(th2), function(x) round(exp(x),2))
      # 1.66, (1.38, 2.31) # Match Gathmann p 11

      # ----- Log-transform doesn't work on aranei, but asinh(x/2) does
      ar2 <- wilcox_test(asinh(aranei/2) ~ gen, data=dat,
                         alternative=c("two.sided"),
                         conf.int=TRUE, conf.level=0.9)
      lapply(confint(ar2), function(x) round(sinh(x)*2,1))

    ## End(Not run)

[Package agridat version 1.16 Index]