Description Details Author(s) References See Also Examples
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).
Package: | toxtestD |
Type: | Package |
Version: | 2.0 |
Date: | 2014-10-27 |
License: | GPL-2 |
Nadia Keddig & Werner Wosniok
Maintainer: Nadia Keddig <publication@gmx.net>
Optimal test design for binary response data: the example of the Fish Embryo Toxicity Test. Submitted.
None
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 | # == 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)
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