Now the weibull model has an automatic choice of starting values, fixing a bug that prevented

fitting the weibull function in most cases in the last version. Also, the log EC50 is reported
as estimated with nlm from the fitted weibull model. Because of the important changes, mainly 
in naming the different models which leads to incompatibility with the old drfit syntax,
I am increasing the minor version number to 0.04 with this release.



git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@30 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc

1 files changed, 4 insertions, 5 deletions

diff --git a/R/drfit.R b/R/drfit.R
index 603cf94..527b756 100644
--- a/R/drfit.R
+++ b/R/drfit.R
@@ -39,7 +39,7 @@ linlogitf <- function(x,k,f,mu,b)
 drfit <- function(data, startlogEC50 = NA, chooseone=TRUE,
         probit = TRUE, logit = FALSE, weibull = FALSE,
         linlogit = FALSE, linlogitWrong = NA, allWrong = NA,
-        b0 = 2, f0 = 0)
+        s0 = 0.5, b0 = 2, f0 = 0)
 {
     if(!is.null(data$ok)) data <- subset(data,ok!="no fit") # Don't use data where ok 
                                                             # was set to "no fit"
@@ -130,7 +130,7 @@ drfit <- function(data, startlogEC50 = NA, chooseone=TRUE,
                     length(subset(allWrong,allWrong == i))==0) {
                     m <- try(nls(response ~ pweibull(-log10(dose)+location,shape),
                             data=tmp,
-                            start=list(location=-0.16,shape=0.4659)))
+                            start=list(location=startlogEC50[[i]],shape=s0)))
                     if (chooseone==FALSE || fit==FALSE) {
                         if (!inherits(m, "try-error")) {
                             fit <- TRUE
@@ -179,7 +179,8 @@ drfit <- function(data, startlogEC50 = NA, chooseone=TRUE,
                             rlld[[ri]] <- log10(lowestdose)
                             rlhd[[ri]] <- log10(highestdose)
                             mtype[[ri]] <- "logit"
-                            logEC50[[ri]] <- coef(m)[["logEC50"]]
+                            logEC50[[ri]] <- a[[ri]] <- coef(m)[["logEC50"]]
+                            b[[ri]] <- coef(m)[["scale"]]
                             c[[ri]] <- NA
                             if (logEC50[[ri]] > rlhd[[ri]]) {
                                 logEC50[[ri]] <- NA
@@ -188,8 +189,6 @@ drfit <- function(data, startlogEC50 = NA, chooseone=TRUE,
                                 b[[ri]] <- NA
                             } else {
                                 stderrlogEC50[[ri]] <- s$parameters["logEC50","Std. Error"]
-                                a[[ri]] <- coef(m)[["logEC50"]]
-                                b[[ri]] <- coef(m)[["scale"]]
                             }
                         }
                     }