From d89badab8c65995b6381418989ffed965fa9d626 Mon Sep 17 00:00:00 2001
From: ranke <ranke@d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc>
Date: Fri, 25 Nov 2005 16:45:01 +0000
Subject: Fixed the check for dose == 0 in drplot() and improved the model
 naming in the result table given by drfit()

git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@47 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
---
 R/drfit.R | 16 +++++++++++-----
 1 file changed, 11 insertions(+), 5 deletions(-)

(limited to 'R')

diff --git a/R/drfit.R b/R/drfit.R
index 9c99b1a..d8631e6 100644
--- a/R/drfit.R
+++ b/R/drfit.R
@@ -117,15 +117,16 @@ drfit <- function(data, startlogEC50 = NA, chooseone=TRUE,
                         runit[[ri]] <- unit
                         rlld[[ri]] <- log10(lowestdose)
                         rlhd[[ri]] <- log10(highestdose)
-                        mtype[[ri]] <- "linlogit"
                         logEC50[[ri]] <- coef(m)[["logEC50"]]
                         if (logEC50[[ri]] > rlhd[[ri]]) {
+                            mtype[[ri]] <- "no fit"
                             logEC50[[ri]] <- NA
                             stderrlogEC50[[ri]] <- NA
                             a[[ri]] <- NA
                             b[[ri]] <- NA
                             c[[ri]] <- NA
                         } else {
+                            mtype[[ri]] <- "linlogit"
                             stderrlogEC50[[ri]] <- s$parameters["logEC50","Std. Error"]
                             a[[ri]] <- coef(m)[["logEC50"]]
                             b[[ri]] <- coef(m)[["b"]]
@@ -150,15 +151,16 @@ drfit <- function(data, startlogEC50 = NA, chooseone=TRUE,
                             runit[[ri]] <- unit
                             rlld[[ri]] <- log10(lowestdose)
                             rlhd[[ri]] <- log10(highestdose)
-                            mtype[[ri]] <- "probit"
                             logEC50[[ri]] <- coef(m)[["logEC50"]]
                             c[[ri]] <- NA
                             if (logEC50[[ri]] > rlhd[[ri]]) {
+                                mtype[[ri]] <- "no fit"
                                 logEC50[[ri]] <- NA
                                 stderrlogEC50[[ri]] <- NA
                                 a[[ri]] <- NA
                                 b[[ri]] <- NA
                             } else {
+                                mtype[[ri]] <- "probit"
                                 stderrlogEC50[[ri]] <- s$parameters["logEC50","Std. Error"]
                                 a[[ri]] <- coef(m)[["logEC50"]]
                                 b[[ri]] <- coef(m)[["scale"]]
@@ -183,16 +185,17 @@ drfit <- function(data, startlogEC50 = NA, chooseone=TRUE,
                             runit[[ri]] <- unit
                             rlld[[ri]] <- log10(lowestdose)
                             rlhd[[ri]] <- log10(highestdose)
-                            mtype[[ri]] <- "logit"
                             logEC50[[ri]] <- a[[ri]] <- coef(m)[["logEC50"]]
                             b[[ri]] <- coef(m)[["scale"]]
                             c[[ri]] <- NA
                             if (logEC50[[ri]] > rlhd[[ri]]) {
+                                mtype[[ri]] <- "no fit"
                                 logEC50[[ri]] <- NA
                                 stderrlogEC50[[ri]] <- NA
                                 a[[ri]] <- NA
                                 b[[ri]] <- NA
                             } else {
+                                mtype[[ri]] <- "logit"
                                 stderrlogEC50[[ri]] <- s$parameters["logEC50","Std. Error"]
                             }
                         }
@@ -215,7 +218,6 @@ drfit <- function(data, startlogEC50 = NA, chooseone=TRUE,
                             runit[[ri]] <- unit
                             rlld[[ri]] <- log10(lowestdose)
                             rlhd[[ri]] <- log10(highestdose)
-                            mtype[[ri]] <- "weibull"
                             a[[ri]] <- coef(m)[["location"]]
                             b[[ri]] <- coef(m)[["shape"]]
                             sqrdev <- function(logdose) {
@@ -224,11 +226,13 @@ drfit <- function(data, startlogEC50 = NA, chooseone=TRUE,
                             logEC50[[ri]] <- nlm(sqrdev,startlogEC50[[i]])$estimate
                             c[[ri]] <- NA
                             if (logEC50[[ri]] > rlhd[[ri]]) {
+                                mtype[[ri]] <- "no fit"
                                 logEC50[[ri]] <- NA
                                 stderrlogEC50[[ri]] <- NA
                                 a[[ri]] <- NA
                                 b[[ri]] <- NA
                             } else {
+                                mtype[[ri]] <- "weibull"
                                 stderrlogEC50[[ri]] <- NA
                             }
                         }
@@ -280,6 +284,7 @@ drplot <- function(drresults, data, dtype = "std", alpha = 0.95,
         pointsize = 12,
         colors = 1:8, devoff=T, lpos="topright")
 {
+    # Check if all data have the same unit
     unitlevels <- levels(as.factor(drresults$unit))
     if (length(unitlevels) == 1) {
         unit <- unitlevels
@@ -289,7 +294,7 @@ drplot <- function(drresults, data, dtype = "std", alpha = 0.95,
 
     # Get the plot limits on the x-axis (log of the dose)
     if(is.data.frame(data)) {
-        if (min(data$dose == 0)) {
+        if (min(data$dose) == 0) {
             cat("At least one of the dose levels is 0 - this is not a valid dose.")
         } else {
             lld <- log10(min(data$dose))
@@ -336,6 +341,7 @@ drplot <- function(drresults, data, dtype = "std", alpha = 0.95,
     # Plot the data either as raw data or as error bars
     if(is.data.frame(data)) {
         splitted <- split(data,data$substance)
+        # n is the index for the dose-response curves
         n <- 0
         if (bw) colors <- rep("black",length(dsubstances))
         # Loop over the substances in the data
-- 
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