- Releasable version for CRAN

- Changed usage of cat() to message() because the latter does not interfere
  with Sweave. Left cat() in checkexperiment.R and checksubstance.R



git-svn-id: http://kriemhild.uft.uni-bremen.de/svn/drfit@92 d1b72e20-2ee0-0310-a1c4-ad5adbbefcdc

3 files changed, 21 insertions, 13 deletions

diff --git a/R/checkexperiment.R b/R/checkexperiment.R
index 941856b..58fecad 100644
--- a/R/checkexperiment.R
+++ b/R/checkexperiment.R
@@ -11,9 +11,16 @@ checkexperiment <- function(id, db = "ecotox", endpoint = "%")
     library(RODBC) 
     channel <- odbcConnect(db,uid="cytotox",pwd="cytotox",case="tolower")
 
+
     responsename = as.character(databases[db,1])
     testtype = as.character(databases[db,2])
     exptype = as.character(databases[db,3])
+
+    exptable <- paste(exptype, "s", sep="")
+    commentquery <- paste("SELECT comment FROM ", exptable ,
+        " WHERE ", exptype, " = ", id)
+    commentdata <- sqlQuery(channel,commentquery)
+    comment <- as.character(commentdata[[1]])
         
     expquery <- paste("SELECT experimentator,substance, ",
         testtype, ",conc,unit,", responsename, ",performed,ok",
@@ -83,7 +90,8 @@ checkexperiment <- function(id, db = "ecotox", endpoint = "%")
         "\tPerformed on:\t\t",levels(expdata$performed),"\n",
         "\tSubstance(s):\t\t",levels(expdata$substance),"\n",
         "\tConcentration unit(s):\t",levels(expdata$unit),"\n",
-        "\tOK:\t\t\t",levels(expdata$ok),"\n",
+        "\tComment:\t\t",comment,"\n",
+        "\tOK Levels:\t\t\t",levels(expdata$ok),"\n",
         "\t\tNumber \tMean \tStd. Dev. \t% Std. Dev.\n",
         "\tblind\t",numberOfBlinds,"\t",meanOfBlinds,"\t",stdOfBlinds,"\n",
         "\tcontrol\t",numberOfControls,"\t",meanOfControls,"\t",
diff --git a/R/drfit.R b/R/drfit.R
index 3bd9021..462bc43 100644
--- a/R/drfit.R
+++ b/R/drfit.R
@@ -32,13 +32,13 @@ drfit <- function(data, startlogED50 = NA, chooseone=TRUE,
         fit <- FALSE
         if (length(tmp) != 0) {
             unit <- levels(as.factor(as.vector(tmp$unit)))
-            cat("\n",i,": Fitting data...\n",sep="")
+            message("\n",i,": Fitting data...\n")
         } else {
             unit <- ""
-            cat("\n",i,": No data\n",sep="")
+            message("\n",i,": No data\n")
         }
         if (length(unit) > 1) {
-            cat("More than one unit for substance ",i,", halting\n\n",sep="")
+            message("More than one unit for substance ",i,", halting\n\n")
             break
         }
         if (length(tmp$response) == 0) {
@@ -211,8 +211,8 @@ drfit <- function(data, startlogED50 = NA, chooseone=TRUE,
                                 }
                                 logED50[[ri]] <- nlm(sqrdev,startlogED50[[i]])$estimate
                                 if (sqrdev(logED50[[ri]]) > 0.1) {
-                                    cat("\nCan't find ED50 for fitted weibull model of ",i,
-                                        "data\nwith startlogED50", startlogED50[[i]],"\n")
+                                    message("\nCan't find ED50 for fitted weibull model of ",i,
+                                        " data\nwith startlogED50 ", startlogED50[[i]],"\n")
                                     ri <- ri - 1
                                     length(a) <- length(b) <- ri
                                     length(logED50) <- ri
diff --git a/R/drplot.R b/R/drplot.R
index 08a92d1..507119c 100644
--- a/R/drplot.R
+++ b/R/drplot.R
@@ -65,19 +65,19 @@ drplot <- function(drresults, data,
             filename = paste(path,fileprefix,".eps",sep="")
             postscript(file=filename,
                     paper="special",width=7,height=7,horizontal=FALSE, pointsize=pointsize)
-            cat("Created File: ",filename,"\n")
+            message("Created File: ",filename,"\n")
         } 
         if (pdf) {
             filename = paste(path,fileprefix,".pdf",sep="")
             pdf(file=filename,
                     paper="special",width=7,height=7,horizontal=FALSE, pointsize=pointsize)
-            cat("Created File: ",filename,"\n")
+            message("Created File: ",filename,"\n")
         } 
         if (png) {
             filename = paste(path,fileprefix,".png",sep="")
             png(filename=filename,
                 width=500, height=500, pointsize=pointsize)
-            cat("Created File: ",filename,"\n")
+            message("Created File: ",filename,"\n")
         }
             
         plot(0,type="n",
@@ -114,19 +114,19 @@ drplot <- function(drresults, data,
                         filename = paste(path,fileprefix,sub(" ","_",i),".eps",sep="")
                         postscript(file=filename,
                                 paper="special",width=7,height=7,horizontal=FALSE,pointsize=pointsize)
-                        cat("Created File: ",filename,"\n")
+                        message("Created File: ",filename,"\n")
                     } 
                     if (pdf) {
                         filename = paste(path,fileprefix,sub(" ","_",i),".pdf",sep="")
                         pdf(file=filename,
                                 paper="special",width=7,height=7,horizontal=FALSE,pointsize=pointsize)
-                        cat("Created File: ",filename,"\n")
+                        message("Created File: ",filename,"\n")
                     } 
                     if (png) {
                         filename = paste(path,fileprefix,sub(" ","_",i),".png",sep="")
                         png(filename=filename,
                             width=500, height=500, pointsize=pointsize)
-                        cat("Created File: ",filename,"\n")
+                        message("Created File: ",filename,"\n")
                     }
                         
                     plot(0,type="n",
@@ -222,7 +222,7 @@ drplot <- function(drresults, data,
                 }
                 if (!overlay && (postscript || png || pdf)) dev.off()
             } else {
-                cat("No data for ",i,"\n")
+                message("No data for ",i,"\n")
             }
         }
     }