- Added a little documentation of the sample data in inst/doc.

- Added the possibility to show standard deviation or confidence
  interval for the mean of the control values, if present in 
  the dose-response data. Also, control data (with dose=0)
  are not listed in the results data frame of drfit any more.



git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@54 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc

6 files changed, 92 insertions, 13 deletions

diff --git a/DESCRIPTION b/DESCRIPTION
index 2ff9517..1f7becb 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: drfit
-Version: 0.04-52
-Date: 2005-12-22
+Version: 0.04-54
+Date: 2006-01-02
 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 9184dc9..ac3ad3e 100644
--- a/R/drfit.R
+++ b/R/drfit.R
@@ -287,7 +287,8 @@ drfit <- function(data, startlogED50 = NA, chooseone=TRUE,
     return(results)
 }
 
-drplot <- function(drresults, data, dtype = "std", alpha = 0.95,
+drplot <- function(drresults, data, 
+        dtype = "std", alpha = 0.95, ctype = "none",
         path = "./", fileprefix = "drplot", overlay = FALSE,
         postscript = FALSE, png = FALSE, bw = TRUE,
         pointsize = 12,
@@ -301,16 +302,30 @@ drplot <- function(drresults, data, dtype = "std", alpha = 0.95,
         unit <- "different units"
     }
 
-    # Get the plot limits on the x-axis (log of the dose)
+    # Get the plot limits on the x-axis (log of the dose) and y axis
     if(is.data.frame(data)) {
-        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))
+        nonzerodata <- subset(data,dose!=0)
+        nonzerodata$substance <- factor(nonzerodata$substance) # Get rid of pseudo substance names of controls
+        zerodata <- subset(data,dose==0)
+        nc <- length(zerodata$dose)     # Number of control points
+        sdc <- sd(zerodata$response)    # Standard deviation of control responses
+        controlconf <- sdc * qt((1 + alpha)/2, nc - 1) / sqrt(nc)
+        if (nc > 0) {
+            cat("There are ",nc,"data points with dose 0 (control values)\n")
+            cat("with a standard deviation of",sdc,"\n")
+            cat("and a confidence interval of",controlconf,"\n")
+            if (nc < 3) {
+                cat("\nThere are less than 3 control points, therefore their scatter\n")
+                cat("will not be displayed\n")
+                ctype = "none"
+            }
         }
-        lhd <- log10(max(data$dose))
-        hr <- max(data$response)
-        dsubstances <- levels(data$substance)    
+        lld <- log10(min(nonzerodata$dose))
+        lhd <- log10(max(nonzerodata$dose))
+        hr <- max(nonzerodata$response)
+        if (ctype == "std") hr <- max(hr,1 + sdc)
+        if (ctype == "conf") hr <- max(hr,1 + controlconf)
+        dsubstances <- levels(nonzerodata$substance)    
     } else {
         lld <- min(drresults[["logED50"]],na.rm=TRUE) - 2
         lhd <- max(drresults[["logED50"]],na.rm=TRUE) + 2
@@ -349,7 +364,7 @@ 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$substance)
+        splitted <- split(nonzerodata,nonzerodata$substance)
         # n is the index for the dose-response curves
         n <- 0
         if (bw) colors <- rep("black",length(dsubstances))
@@ -389,6 +404,17 @@ drplot <- function(drresults, data, dtype = "std", alpha = 0.95,
                                                     # factor has all levels, not 
                                                     # only the ones tested with
                                                     # this substance
+
+                # Plot the control lines, if requested
+                if (ctype == "std") {
+                    abline(h = 1 - sdc, lty = 2)
+                    abline(h = 1 + sdc, lty = 2)
+                }
+                if (ctype == "conf") {
+                    abline(h = 1 - controlconf, lty = 2) 
+                    abline(h = 1 + controlconf, lty = 2)
+                }
+
                 # Plot the data, if requested
                 if (dtype != "none") {
                     if (dtype == "raw") {
diff --git a/inst/doc/README.txt b/inst/doc/README.txt
new file mode 100644
index 0000000..10945d9
--- /dev/null
+++ b/inst/doc/README.txt
@@ -0,0 +1,14 @@
+This sample data is provided to show how dose-response data can be collected
+with a spreadsheet program like OpenOfficeCalc (sampledata.ods) or 
+MS Excel (sampledata.xls) and exported to CSV (comma separated values) format.
+OpenOfficeCalc 2.0 (German version, decimal separator is ',') produces
+sampledata.csv which can be read in by
+
+	>sampledata <- read.csv('sampledata.csv',skip=2,dec=',')
+
+and MS Excel 97 produces sampledata.csv2 which can be read in by
+
+	>sampledata <- read.csv2('sampledata2.csv',skip=2)
+
+if the working directory of R was set to the directory where these
+files reside.
diff --git a/inst/doc/sampledata.xls b/inst/doc/sampledata.xls
index 0951ae0..513123b 100644
--- a/inst/doc/sampledata.xls
+++ b/inst/doc/sampledata.xls
diff --git a/inst/doc/sampledata2.csv b/inst/doc/sampledata2.csv
new file mode 100644
index 0000000..f778dab
--- /dev/null
+++ b/inst/doc/sampledata2.csv
@@ -0,0 +1,33 @@
+Concentration-response data for the Lemna growth test with Substances X and Y;;;;;

+;;;;;

+nr.;substance;dose;unit;fronds;response

+1;Control;0;mg/L;174;1,134782609

+2;Control;0;mg/L;143;0,932608696

+3;Control;0;mg/L;143;0,932608696

+4;Substance X;10;mg/L;147;0,958695652

+5;Substance X;10;mg/L;148;0,965217391

+6;Substance X;10;mg/L;148;0,965217391

+7;Substance X;100;mg/L;63;0,410869565

+8;Substance X;100;mg/L;65;0,423913043

+9;Substance X;100;mg/L;55;0,358695652

+10;Substance X;300;mg/L;20;0,130434783

+11;Substance X;300;mg/L;22;0,143478261

+12;Substance X;300;mg/L;25;0,163043478

+13;Substance X;1000;mg/L;13;0,084782609

+14;Substance X;1000;mg/L;16;0,104347826

+15;Substance X;1000;mg/L;16;0,104347826

+16;Control;0;mg/L;153;0,997826087

+17;Control;0;mg/L;144;0,939130435

+18;Control;0;mg/L;163;1,063043478

+19;Substance Y;10;mg/L;20;0,130434783

+20;Substance Y;10;mg/L;19;0,123913043

+21;Substance Y;10;mg/L;21;0,136956522

+22;Substance Y;100;mg/L;13;0,084782609

+23;Substance Y;100;mg/L;12;0,07826087

+24;Substance Y;100;mg/L;13;0,084782609

+25;Substance Y;300;mg/L;12;0,07826087

+26;Substance Y;300;mg/L;12;0,07826087

+27;Substance Y;300;mg/L;14;0,091304348

+28;Substance Y;1000;mg/L;12;0,07826087

+29;Substance Y;1000;mg/L;12;0,07826087

+30;Substance Y;1000;mg/L;12;0,07826087

diff --git a/man/drplot.Rd b/man/drplot.Rd
index 25b598c..99f77ab 100644
--- a/man/drplot.Rd
+++ b/man/drplot.Rd
@@ -6,7 +6,7 @@
   either combined or separately, for one or more substances.
 }
 \usage{
-  drplot(drresults, data, dtype, alpha, path, fileprefix, overlay,
+  drplot(drresults, data, dtype, alpha, ctype, path, fileprefix, overlay,
     postscript, png, bw, pointsize, colors, devoff, lpos)
 }
 \arguments{
@@ -31,6 +31,12 @@
     The confidence level, defaulting to 0.95, only used if dtype "conf" has been
     chosen.
     }
+  \item{ctype}{
+    This argument decides if horizontal lines are drawn to show the scatter of 
+    the control values (dose = 0, mean response = 1). Defaults to "none",
+    further allowed values are "std" and "conf" for displaying the standard deviation
+    of the controls or the confidence interval for the mean of the controls.
+    }
   \item{path}{
     The path where graphic files should be put if any are produced. Defaults
     to "./" i.e. the current working directory of R.