agridat (version 1.27)

gathmann.bt: 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, either 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.

Based on the decimal values in the response (.0 .2 .4 .6 .8) it appears that each response value is probably the mean of 5 repeated measurements.

The assumption of Normality is questionable, which is why Hothorn used exact tests.

Used with permission of Achim Gathmann.

References

Gathmann et al (2006). Impact of Bt maize pollen (Mon810) on lepidopteran larvae living on accompanying weeds. Molecular Ecology, 15, 2677-2685. https://doi.org/10.1111/j.1365-294X.2006.02962.x

Examples

if (FALSE) {

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


# EDA suggests Bt vs ISO is significant for thysan, not for aranei
libs(lattice)
libs(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"))


if(0){

  # ----- Parametric CI.  Thysan significant, aranei not significant.
  libs(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.
  libs(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 Non-param for Bt thysan

  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))

}

}