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.

Used with permission of Achim Gathmann.

Source

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

Examples

## Not run: 

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

  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 1.18 Index]