From c5f30593d42ecd9a21f799a4943709b1b73a1162 Mon Sep 17 00:00:00 2001
From: ranke <ranke@d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc>
Date: Tue, 2 Aug 2005 12:15:15 +0000
Subject: drplot: Added the pointsize argument for postscript and png graphs
 drfit: Changed the order of fits in the case of chooseone=TRUE

git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@34 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
---
 R/drfit.R | 43 ++++++++++++++++++++++---------------------
 1 file changed, 22 insertions(+), 21 deletions(-)

(limited to 'R')

diff --git a/R/drfit.R b/R/drfit.R
index d8ad40b..f2480d2 100644
--- a/R/drfit.R
+++ b/R/drfit.R
@@ -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
             }
-- 
cgit v1.2.1