diff options
| -rw-r--r-- | DESCRIPTION | 4 | ||||
| -rw-r--r-- | R/drfit.R | 43 | ||||
| -rw-r--r-- | man/drfit.Rd | 4 |
3 files changed, 26 insertions, 25 deletions
diff --git a/DESCRIPTION b/DESCRIPTION index eb6d9b2..e59d6c6 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: drfit -Version: 0.04-33 -Date: 2005-07-27 +Version: 0.04-34 +Date: 2005-08-02 Title: Dose-response data evaluation Author: Johannes Ranke <jranke@uni-bremen.de> Maintainer: Johannes Ranke <jranke@uni-bremen.de> @@ -126,11 +126,11 @@ drfit <- function(data, startlogEC50 = NA, chooseone=TRUE, } } - if (weibull && + if (probit && length(subset(allWrong,allWrong == i))==0) { - m <- try(nls(response ~ pweibull(-log10(dose)+location,shape), - data=tmp, - start=list(location=startlogEC50[[i]],shape=s0))) + m <- try(nls(response ~ pnorm(-log10(dose),-logEC50,scale), + data=tmp, + start=list(logEC50=startlogEC50[[i]],scale=1))) if (chooseone==FALSE || fit==FALSE) { if (!inherits(m, "try-error")) { fit <- TRUE @@ -142,13 +142,8 @@ drfit <- function(data, startlogEC50 = NA, chooseone=TRUE, runit[[ri]] <- unit rlld[[ri]] <- log10(lowestdose) rlhd[[ri]] <- log10(highestdose) - mtype[[ri]] <- "weibull" - a[[ri]] <- coef(m)[["location"]] - b[[ri]] <- coef(m)[["shape"]] - sqrdev <- function(logdose) { - (0.5 - pweibull( - logdose + a[[ri]], b[[ri]]))^2 - } - logEC50[[ri]] <- nlm(sqrdev,startlogEC50[[i]])$estimate + mtype[[ri]] <- "probit" + logEC50[[ri]] <- coef(m)[["logEC50"]] c[[ri]] <- NA if (logEC50[[ri]] > rlhd[[ri]]) { logEC50[[ri]] <- NA @@ -156,7 +151,9 @@ drfit <- function(data, startlogEC50 = NA, chooseone=TRUE, a[[ri]] <- NA b[[ri]] <- NA } else { - stderrlogEC50[[ri]] <- NA + stderrlogEC50[[ri]] <- s$parameters["logEC50","Std. Error"] + a[[ri]] <- coef(m)[["logEC50"]] + b[[ri]] <- coef(m)[["scale"]] } } } @@ -194,11 +191,11 @@ drfit <- function(data, startlogEC50 = NA, chooseone=TRUE, } } - if (probit && + if (weibull && length(subset(allWrong,allWrong == i))==0) { - m <- try(nls(response ~ pnorm(-log10(dose),-logEC50,scale), - data=tmp, - start=list(logEC50=startlogEC50[[i]],scale=1))) + m <- try(nls(response ~ pweibull(-log10(dose)+location,shape), + data=tmp, + start=list(location=startlogEC50[[i]],shape=s0))) if (chooseone==FALSE || fit==FALSE) { if (!inherits(m, "try-error")) { fit <- TRUE @@ -210,8 +207,13 @@ drfit <- function(data, startlogEC50 = NA, chooseone=TRUE, runit[[ri]] <- unit rlld[[ri]] <- log10(lowestdose) rlhd[[ri]] <- log10(highestdose) - mtype[[ri]] <- "probit" - logEC50[[ri]] <- coef(m)[["logEC50"]] + mtype[[ri]] <- "weibull" + a[[ri]] <- coef(m)[["location"]] + b[[ri]] <- coef(m)[["shape"]] + sqrdev <- function(logdose) { + (0.5 - pweibull( - logdose + a[[ri]], b[[ri]]))^2 + } + logEC50[[ri]] <- nlm(sqrdev,startlogEC50[[i]])$estimate c[[ri]] <- NA if (logEC50[[ri]] > rlhd[[ri]]) { logEC50[[ri]] <- NA @@ -219,14 +221,13 @@ drfit <- function(data, startlogEC50 = NA, chooseone=TRUE, a[[ri]] <- NA b[[ri]] <- NA } else { - stderrlogEC50[[ri]] <- s$parameters["logEC50","Std. Error"] - a[[ri]] <- coef(m)[["logEC50"]] - b[[ri]] <- coef(m)[["scale"]] + stderrlogEC50[[ri]] <- NA } } } } + } else { inactive <- TRUE } diff --git a/man/drfit.Rd b/man/drfit.Rd index 35d6d94..75f48ed 100644 --- a/man/drfit.Rd +++ b/man/drfit.Rd @@ -51,8 +51,8 @@ An optional vector containing the names of the substances for which all functions produce a wrong fit.} \item{chooseone}{ - If TRUE (default), the models are tried in the order linlogit, weibull, - logit, probit, and the first model that produces a valid fit is used. + If TRUE (default), the models are tried in the order linlogit, probit, + logit, weibull, and the first model that produces a valid fit is used. If FALSE, all models that are set to TRUE and that can be fitted will be reported.} \item{s0}{ |