From 1066c87b174f2b3df19e54adee1ee435021441c9 Mon Sep 17 00:00:00 2001 From: ranke Date: Fri, 23 Nov 2007 16:19:08 +0000 Subject: - 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 --- R/checkexperiment.R | 10 +++++++++- R/drfit.R | 10 +++++----- R/drplot.R | 14 +++++++------- 3 files changed, 21 insertions(+), 13 deletions(-) (limited to 'R') 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") } } } -- cgit v1.2.1