From f6ca9cbb4b1ca8056cd9668760e8d55d638154aa Mon Sep 17 00:00:00 2001
From: ranke <ranke@d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc>
Date: Fri, 21 Apr 2006 21:28:41 +0000
Subject: Working version of the checkexperiment function, including
 documentation, but R CMD check tells me that "use of NULL environment is
 deprecated"

git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@66 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc
---
 R/checkexperiment.R | 82 ++++++++++++++++++++++++++++++++---------------------
 1 file changed, 50 insertions(+), 32 deletions(-)

(limited to 'R/checkexperiment.R')

diff --git a/R/checkexperiment.R b/R/checkexperiment.R
index 68169c7..c29b1e5 100644
--- a/R/checkexperiment.R
+++ b/R/checkexperiment.R
@@ -1,4 +1,4 @@
-checkexperiment <- function(id,db="cytotox")
+checkexperiment <- function(id,db="ecotox")
 {
     databases <- data.frame(
         responsetype=c("viability","activity","response"),
@@ -34,15 +34,25 @@ checkexperiment <- function(id,db="cytotox")
         controls <- subset(controldata,type=="control")
 
         numberOfBlinds <- length(blinds$response)
-        stdOfBlinds <- sd(blinds$response)
+        meanOfBlinds <- signif(mean(blinds$response),2)
+        stdOfBlinds <- signif(sd(blinds$response),2)
     } else {
         controls <- subset(expdata,conc == 0)
+        expdata <- subset(expdata, conc != 0)
 
         numberOfBlinds <- NA
+        meanOfBlinds <- NA
         stdOfBlinds <- NA
         
     }
-
+    numberOfControls <- length(controls$response)
+    if (numberOfControls > 0) {
+        meanOfControls <- signif(mean(controls$response),2)
+        stdOfControls <- signif(sd(controls$response),2)
+        percentstdOfcontrols <-signif(stdOfControls *100/meanOfControls,2)
+    } else {
+        meanOfControls <- stdOfControls <- percentstdOfcontrols <- NA
+    }
 
     if (length(expdata$experimentator) < 1) {
         stop("There is no response data for ",exptype," ",
@@ -50,43 +60,51 @@ checkexperiment <- function(id,db="cytotox")
     } 
     expdata$experimentator <- factor(expdata$experimentator)
     expdata$type <- factor(expdata[[testtype]])
+    expdata$performed <- factor(as.character(expdata$performed))
     expdata$substance <- factor(expdata$substance)
     expdata$unit <- factor(expdata$unit)
-    expdata$performed <- factor(expdata$performed)
     expdata$ok <- factor(expdata$ok)
     
-    numberOfControls <- length(controls$response)
-    
-    meanOfBlinds <- mean(blinds$response)
-    meanOfControls <- mean(controls$response)
-    stdOfControls <- sd(controls$response)
-    percentstdOfcontrols <-stdOfControls *100/meanOfControls
-    
-    cat("Plate ",plate," from database ",db,"\n",
-        "\tExperimentator: ",levels(platedata$experimentator),"\n",
-        "\tType(s): ",levels(platedata$type),"\n",
-        "\tPerformed on : ",levels(platedata$performed),"\n",
-        "\tSubstance(s): ",levels(platedata$substance),"\n",
-        "\tConcentration unit: ",levels(platedata$unit),"\n",
-        "\tOK: ",levels(platedata$ok),"\n",
-        "\t\tNumber \tMean \t\tStandard Deviation \t% Standard Deviation \n",
+    cat("\n",exptype," ",id," from database ",db,"\n",
+        "\tExperimentator(s): ",levels(expdata$experimentator),"\n",
+        "\tType(s): ",levels(expdata$type),"\n",
+        "\tPerformed on: ",levels(expdata$performed),"\n",
+        "\tSubstance(s): ",levels(expdata$substance),"\n",
+        "\tConcentration unit(s): ",levels(expdata$unit),"\n",
+        "\tOK: ",levels(expdata$ok),"\n",
+        "\t\tNumber \tMean \tStd. Dev. \t% Std. Dev.\n",
         "\tblind\t",numberOfBlinds,"\t",meanOfBlinds,"\t",stdOfBlinds,"\n",
-        "\tcontrol\t",numberOfControls,"\t",meanOfControls,"\t",stdOfControls,"\t\t",percentstdOfcontrols,"\n")
+        "\tcontrol\t",numberOfControls,"\t",meanOfControls,"\t",
+            stdOfControls,"\t\t",percentstdOfcontrols,"\n")
     
-    par(ask=TRUE)
-
-    boxplot(blinds$response,controls$response,
-        names=c("blinds","controls"),
-        ylab="Response",main=paste("Plate ",plate))
+    get(getOption("device"))(width=10,height=5)
+    par(mfcol=c(1,2))
+    if (db == "ecotox") {
+        boxplot(controls$response,
+            names="controls",
+            ylab="Response",
+            ylim=c(0,max(controls$response)),
+            boxwex=0.4,
+            main=paste("Plate ",id))
+    } else {
+        boxplot(blinds$response,controls$response,
+            names=c("blinds","controls"),
+            ylab="Response",
+            boxwex=0.4,
+            main=paste("Plate ",id))
+    }
     
-    drdata <- platedata[c(2,4,6)]
+    drdata <- expdata[c(2,4,6)]
     drdata$substance <- factor(drdata$substance)
     substances <- levels(drdata$substance)
        
-    plot(log10(drdata$conc),drdata$viability,
-        xlim=c(-2.5, 4.5), 
+    lld <- log10(min(subset(drdata,conc!=0)$conc))
+    lhd <- log10(max(drdata$conc))
+
+    plot(1,type="n",
+        xlim=c(lld - 0.5, lhd + 2), 
         ylim= c(-0.1, 2), 
-        xlab=paste("decadic logarithm of the concentration in ",levels(platedata$unit)),
+        xlab=paste("decadic logarithm of the concentration in ",levels(expdata$unit)),
         ylab=responsetype)
     
     drdatalist <- split(drdata,drdata$substance)
@@ -95,7 +113,7 @@ checkexperiment <- function(id,db="cytotox")
         points(log10(drdatalist[[i]]$conc),drdatalist[[i]][[responsetype]],col=i);
     }
 
-    legend("topleft",substances, pch=1, col=1:length(substances), inset=0.05)
-    title(main=paste("Plate ",plate," - ",
-        levels(platedata$experimentator)," - ",levels(platedata$type)))
+    legend("topright",substances, pch=1, col=1:length(substances), inset=0.05)
+    title(main=paste(levels(expdata$experimentator),
+        " - ",levels(expdata$type)))
 }
-- 
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