R help - Aug 2006 - Fwd: Re: Finney's fiducial confidence intervals of LD50

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
> > https://stat.ethz.ch/mailman/listinfo/r-help
> > PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> > and provide commented, minimal, self-contained, reproducible code.
> >
>
>
> --
> 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


 		
---------------------------------

	[[alternative HTML version deleted]]

Finney's method for finding the confidence interval for a ratio of
parameters is quite simple and is probably described in his book
'Probit analysis'. It is also known as Fieller's method so an
RSiteSearch on 'Fieller' might show something useful.


On Mon, Aug 21, 2006 at 08:46:24AM -0700, carlos riveira
wrote:
> 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 at gmail.com> wrote:
>   Date: Mon, 21 Aug 2006 16:35:49 +0200
> From: "Renaud Lancelot" <renaud.lancelot at gmail.com>
> To: "carlos riveira" <carlos.riveira at yahoo.com>
> Subject: Re: [R] Finney's fiducial confidence intervals of LD50
> CC: r-help at 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 at stat.math.ethz.ch mailing list
> > > https://stat.ethz.ch/mailman/listinfo/r-help
> > > PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> > > and provide commented, minimal, self-contained, reproducible
code.
> > >
> >
> >
> > --
> > Renaud LANCELOT
> > D?partement Elevage et M?decine V?t?rinaire (EMVT) du CIRAD
> > Directeur adjoint charg? des affaires scientifiques
> >
> > CIRAD, Animal Production and Veterinary Medicine Department
> > Deputy director for scientific affairs
> >
> > Campus international de Baillarguet
> > TA 30 / B (B?t. B, Bur. 214)
> > 34398 Montpellier Cedex 5 - France
> > T?l +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
> D?partement Elevage et M?decine V?t?rinaire (EMVT) du CIRAD
> Directeur adjoint charg? des affaires scientifiques
> 
> CIRAD, Animal Production and Veterinary Medicine Department
> Deputy director for scientific affairs
> 
> Campus international de Baillarguet
> TA 30 / B (B?t. B, Bur. 214)
> 34398 Montpellier Cedex 5 - France
> T?l +33 (0)4 67 59 37 17
> Secr. +33 (0)4 67 59 39 04
> Fax +33 (0)4 67 59 37 95
> 
> 
>  		
> ---------------------------------
> 
> 	[[alternative HTML version deleted]]
> 
> ______________________________________________
> R-help at stat.math.ethz.ch mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

-- 
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