toxtestD (version 2.0)

toxtestD-package: Experimental design for binary toxicity tests

Description

Calculates sample size and dose allocation for binary toxicity tests, using the Fish Embryo Toxicity Test as example. An optimal test design is obtained by running (i) spoD (calculate the number of individuals to test under control conditions), (ii) setD (estimate the minimal sample size per treatment given the users precision requirements) and (iii) doseD (construct an individual dose scheme).

Details

Package:

toxtestD

Type:

Package

Version:

2.0

Date:

2014-10-27

License:

GPL-2

References

Optimal test design for binary response data: the example of the Fish Embryo Toxicity Test. Submitted.

See Also

None

Examples

# == spoD ==
# determine spontaneous rate

  #1a: planning
  spoD(n=600,SL.p=3.5,SLmin=NA,SLmax=NA,bio.sd.p=2.008)
  spoD(n=600,SL.p=NA,SLmin=3,SLmax=4)
  spoD(n=600,SL.p=3.5,SLmin=NA,SLmax=NA,bio.sd.p=2.008,print.result="spoDa.txt")
  spoD(n=600,SL.p=3.5,SLmin=NA,SLmax=NA,bio.sd.p=2.008,print.result=FALSE)

  #1b: analysis
  SLdataset <- data.frame(n=rep(60,times=4),bearer=c(1,5,8,3))
  spoD(analysis=TRUE,SLdataset=SLdataset)
  spoD(analysis=TRUE,SLdataset=SLdataset,print.result="spoDb.txt")
  spoD(analysis=TRUE,SLdataset=SLdataset,print.result=FALSE)


# == setD ==
# determine sample size

  setD(nmax=350,SL.p=5.5,immunity.p=0,risk.type=2,target.EC=10,
       alpha.p=5,beta.p=20,plot="single")
  setD(nmax=350,SL.p=3,target.EC=5,plot="FALSE")
  setD(nmax=350,SL.p=3,target.EC=5,plot="FALSE",print.result="setD.txt")
  setD(nmax=350,SL.p=3,target.EC=5,plot="FALSE",print.result=FALSE)


# == doseD ==
# dose allocation

  DP <- data.frame(   name=c("neg.control",rep("substance",times=6)),
                      organisms=c(42,41,42,42,38,42,39),
                      death= c(1,3,40,20,12,40,13),
                      concentration=c(0.0,2.0,3.5,4.0,6.0,8.0,6.0),
                      unit=rep("mg/ml",times=7)  ) 
  doseD(DP=DP,immunity.p=4.7,SL.p=9,target.EC.p=c(15,30,40),
        nconc=9,text=TRUE,risk.type=1)
  doseD(DP=DP,immunity.p=4.7,SL.p=9,target.EC.p=c(15,30,40),
        nconc=9,text=TRUE,risk.type=2)
  doseD(DP=DP,immunity.p=4.7,SL.p=9,target.EC.p=c(15,30,40),
        nconc=9,text=TRUE,risk.type=3)
  doseD(DP=DP,immunity.p=4.7,SL.p=9,target.EC.p=c(15,30,40),
        nconc=9,text=TRUE,risk.type=3,print.result="doseD4.txt")
  doseD(DP=DP,immunity.p=4.7,SL.p=9,target.EC.p=c(15,30,40),
        nconc=9,text=TRUE,risk.type=3,print.result=FALSE)