The calculation of dose-response curves in drfit was wrong if the number of

dose levels was different from 9. Now, n is calculated as the rounded mean
number of response data per dose level. The number of dose levels ndl is
additionally reported.

The test was removed because it didn't work properly.



git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@52 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc

5 files changed, 19 insertions, 46 deletions

diff --git a/DESCRIPTION b/DESCRIPTION
index 07bf47a..2ff9517 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: drfit
-Version: 0.04-51
-Date: 2005-12-21
+Version: 0.04-52
+Date: 2005-12-22
 Title: Dose-response data evaluation
 Author: Johannes Ranke <jranke@uni-bremen.de>
 Maintainer: Johannes Ranke <jranke@uni-bremen.de>
diff --git a/R/drfit.R b/R/drfit.R
index e74667d..9184dc9 100644
--- a/R/drfit.R
+++ b/R/drfit.R
@@ -57,7 +57,8 @@ drfit <- function(data, startlogED50 = NA, chooseone=TRUE,
                                           # rix is used later to check if any
                                           # model result was appended
     rsubstance <- array()                 # the substance names in the results
-    rn <- vector()                        # number of dose-response curves 
+    rndl <- vector()                      # number of dose levels
+    rn <- vector()                        # mean number of replicates in each dose level
     runit <- vector()                     # vector of units for each result row
     rlhd <- rlld <- vector()              # highest and lowest doses tested
     mtype <- array()                      # the modeltypes
@@ -81,14 +82,17 @@ drfit <- function(data, startlogED50 = NA, chooseone=TRUE,
             cat("More than one unit for substance ",i,", halting\n\n",sep="")
             break
         }
-        n <- round(length(tmp$response)/9)
         if (length(tmp$response) == 0) {
             nodata = TRUE
         } else {
             nodata = FALSE
         }
         rix <- ri
-        if (!nodata) {
+        if (nodata) {
+            n <- ndl <- 0
+        } else {
+            ndl <- length(levels(factor(tmp$dose)))
+            n <- round(length(tmp$response)/ndl)
             if (is.na(startlogED50[i])){
                 w <- 1/abs(tmp$response - 0.3)
                 startlogED50[[i]] <- sum(w * log10(tmp$dose))/sum(w)
@@ -113,6 +117,7 @@ drfit <- function(data, startlogED50 = NA, chooseone=TRUE,
                         s <- summary(m)
                         sigma[[ri]] <- s$sigma
                         rsubstance[[ri]] <- i
+                        rndl[[ri]] <- ndl
                         rn[[ri]] <- n
                         runit[[ri]] <- unit
                         rlld[[ri]] <- log10(lowestdose)
@@ -147,6 +152,7 @@ drfit <- function(data, startlogED50 = NA, chooseone=TRUE,
                             s <- summary(m)
                             sigma[[ri]] <- s$sigma
                             rsubstance[[ri]] <- i
+                            rndl[[ri]] <- ndl
                             rn[[ri]] <- n
                             runit[[ri]] <- unit
                             rlld[[ri]] <- log10(lowestdose)
@@ -181,6 +187,7 @@ drfit <- function(data, startlogED50 = NA, chooseone=TRUE,
                             s <- summary(m)
                             sigma[[ri]] <- s$sigma
                             rsubstance[[ri]] <- i
+                            rndl[[ri]] <- ndl
                             rn[[ri]] <- n
                             runit[[ri]] <- unit
                             rlld[[ri]] <- log10(lowestdose)
@@ -214,6 +221,7 @@ drfit <- function(data, startlogED50 = NA, chooseone=TRUE,
                             s <- summary(m)
                             sigma[[ri]] <- s$sigma
                             rsubstance[[ri]] <- i
+                            rndl[[ri]] <- ndl
                             rn[[ri]] <- n
                             runit[[ri]] <- unit
                             rlld[[ri]] <- log10(lowestdose)
@@ -247,6 +255,7 @@ drfit <- function(data, startlogED50 = NA, chooseone=TRUE,
         if (ri == rix) {          # if no entry was appended for this substance
             ri <- ri + 1
             rsubstance[[ri]] <- i
+            rndl[[ri]] <- ndl
             rn[[ri]] <- n
             if (nodata) {
                 rlld[[ri]] <- rlhd[[i]] <- NA
@@ -270,8 +279,8 @@ drfit <- function(data, startlogED50 = NA, chooseone=TRUE,
             c[[ri]] <- NA
         }
     }
-    results <- data.frame(rsubstance, rn, rlld, rlhd, mtype, logED50, stderrlogED50, runit, sigma, a, b)
-    names(results) <- c("Substance","n","lld","lhd","mtype","logED50","std","unit","sigma","a","b")
+    results <- data.frame(rsubstance, rndl, rn, rlld, rlhd, mtype, logED50, stderrlogED50, runit, sigma, a, b)
+    names(results) <- c("Substance","ndl","n","lld","lhd","mtype","logED50","std","unit","sigma","a","b")
     if (linlogit) {
         results$c <- c
     }
diff --git a/man/drfit.Rd b/man/drfit.Rd
index abb135a..ee477b5 100644
--- a/man/drfit.Rd
+++ b/man/drfit.Rd
@@ -70,8 +70,9 @@
       Every successful fit is reported in one line. Parameters of the fitted
       curves are only reported if the fitted ED50 is not higher than the
       highest dose. 
-      \code{n} is the number of dose-response curves in the raw data (repetitions
-      in each point), \code{lld} is the decadic logarithm of the lowest dose and
+      \code{ndl} is the number of dose levels in the raw data, \code{n} is the
+      rounded mean of the number of replicates at each dose level in the raw
+      data, \code{lld} is the decadic logarithm of the lowest dose and
       \code{lhd} is the decadic logarithm of the highest dose.
       For the "linlogit", "logit" and "probit" models, the parameter
       \code{a} that is reported coincides with the logED50, i.e the logED50 is 
diff --git a/tests/01drfit.R b/tests/01drfit.R
deleted file mode 100644
index 7e775fe..0000000
--- a/tests/01drfit.R
+++ /dev/null
@@ -1,4 +0,0 @@
-library(drfit)
-data(antifoul)
-r <- drfit(antifoul)
-r
diff --git a/tests/01drfit.Rout.save b/tests/01drfit.Rout.save
deleted file mode 100644
index c04e428..0000000
--- a/tests/01drfit.Rout.save
+++ /dev/null
@@ -1,33 +0,0 @@
-
-R : Copyright 2005, The R Foundation for Statistical Computing
-Version 2.2.1  (2005-12-20 r36812)
-ISBN 3-900051-07-0
-
-R ist freie Software und kommt OHNE JEGLICHE GARANTIE.
-Sie sind eingeladen, es unter bestimmten Bedingungen weiter zu verbreiten.
-Tippen Sie 'license()' or 'licence()' für Details dazu.
-
-R ist ein Gemeinschaftsprojekt mit vielen Beitragenden.
-Tippen Sie 'contributors()' für mehr Information und 'citation()',
-um zu erfahren, wie R oder R packages in Publikationen zitiert werden können.
-
-Tippen Sie 'demo()' für einige Demos, 'help()' für on-line Hilfe, oder
-'help.start()' für eine HTML Browserschnittstelle zur Hilfe.
-Tippen Sie 'q()', um R zu verlassen.
-
-> library(drfit)
-Lade nötiges Paket: RODBC
-> data(antifoul)
-> r <- drfit(antifoul)
-
-TBT: Fitting data...
-
-Zn Pyrithion: Fitting data...
-> r
-     Substance  n       lld     lhd  mtype    logEC50        std unit     sigma
-1          TBT 15 -2.709271 2.39794 probit -0.1643560 0.05349217   µM 0.1928611
-2 Zn Pyrithion  9 -2.107210 2.00000 probit -0.3979222 0.05393693   µM 0.2286560
-           a         b
-1 -0.1643560 0.6763882
-2 -0.3979222 0.4169632
->