[R] Fwd: Re: Finney's fiducial confidence intervals of LD50

From: carlos riveira <carlos.riveira_at_yahoo.com>
Date: Tue 22 Aug 2006 - 01:46:24 EST


thanks a lot Renaud.
  but i was interested in Finney's fiducial confidence intervals of LD50 so to obtain comparable results with SPSS.    

  But your reply leads me to the next question: does anybody know what is the best method (asymptotic, bootstrap etc.) for calculating confidence intervals of LD50?    

  i could "get rid" of Finney's fiducial confidence intervals but only if there was a better method..    

  any idea?       

Renaud Lancelot <renaud.lancelot@gmail.com> wrote:   Date: Mon, 21 Aug 2006 16:35:49 +0200
From: "Renaud Lancelot" <renaud.lancelot@gmail.com> To: "carlos riveira" <carlos.riveira@yahoo.com> Subject: Re: [R] Finney's fiducial confidence intervals of LD50 CC: r-help@stat.math.ethz.ch

Sorry there was a typo in my previous reply:

> D50 <- 10^c(logD50 + c(0, -1.96, 1.96) * attr(logD50, "SE"))
> names(D50) <- c("D50", "lower", "upper")
> D50
D50 lower upper
140.8353 103.3171 191.9777

Best,

Renaud

2006/8/21, Renaud Lancelot :
> I don't know what Finney's fiducial confidence interval is but if your
> problem is to handle the output of dose.p (from MASS), you can do as
> follows:
>
> > library(MASS)
> > Response <- c(0, 7, 26, 27, 0, 5, 13, 29, 0, 4, 11, 25)
> > Tot <- rep(30.5, 12)
> > Dose <- rep(c(10, 40, 160, 640), 3)
> > fm <- glm(Response/Tot ~ log10(Dose), family = quasibinomial(link = probit))
> > logD50 <- dose.p(fm, cf = 1:2, p = 0.5)
> > D50 <- 10^c(logD50 + c(1, -1.96, 1.96) * attr(logD50, "SE"))
> > names(D50) <- c("D50", "lower", "upper")
> > D50
> D50 lower upper
> 164.9506 103.3171 191.9777
>
> Best,
>
> Renaud
>
> 2006/8/21, carlos riveira :
> > I am working with Probit regression (I cannot switch to logit) can anybody help me in finding out how to obtain with R Finney's fiducial confidence intervals for the levels of the predictor (Dose) needed to produce a proportion of 50% of responses(LD50, ED50 etc.)?
> > If the Pearson chi-square goodness-of-fit test is significant (by default), a heterogeneity factor should be used to calculate the limits.
> >
> > Response<-c(0,7,26,27,0,5,13,29,0,4,11,25)
> > Tot<-rep(30.5,12)
> > Dose<-rep(c(10,40,160,640),3)
> > probit<-glm(formula = Response/Tot~ log10(Dose), family=quasibinomial
> > (link=probit))
> > D50<- round(10^(dose.p(probit,cf=1:2,p=0.5)))
> >
> > #This is what SPSS calculates. I would like to reproduce these results with R:
> > #SPSS RESULTS:
> > #PRNT50= 140,83525
> > #CI = 98,37857;205,34483
> > #Regr.coeff= 1,91676 (S.E.=0,16765)
> > #Intercept=-4,11856 (S.E.=0,36355)
> > Thanks a lot for your help.
> >
> > Carlos
> >
> > __________________________________________________
> >
> >
> >
> > [[alternative HTML version deleted]]
> >
> > ______________________________________________
> > R-help@stat.math.ethz.ch mailing list
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> > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
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> >
>
>
> --
> Renaud LANCELOT
> Département Elevage et Médecine Vétérinaire (EMVT) du CIRAD
> Directeur adjoint chargé des affaires scientifiques
>
> CIRAD, Animal Production and Veterinary Medicine Department
> Deputy director for scientific affairs
>
> Campus international de Baillarguet
> TA 30 / B (Bât. B, Bur. 214)
> 34398 Montpellier Cedex 5 - France
> Tél +33 (0)4 67 59 37 17
> Secr. +33 (0)4 67 59 39 04
> Fax +33 (0)4 67 59 37 95
>

-- 
Renaud LANCELOT
Département Elevage et Médecine Vétérinaire (EMVT) du CIRAD
Directeur adjoint chargé des affaires scientifiques

CIRAD, Animal Production and Veterinary Medicine Department
Deputy director for scientific affairs

Campus international de Baillarguet
TA 30 / B (Bât. B, Bur. 214)
34398 Montpellier Cedex 5 - France
Tél +33 (0)4 67 59 37 17
Secr. +33 (0)4 67 59 39 04
Fax +33 (0)4 67 59 37 95


 		
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