Suppress error messages in dr(c)fit, maintenance

- Checking examples fails if error messages in dr(c)fit stemming from
failed fits are printed
- Delete trailing whitespace
- Update packaging

10 files changed, 115 insertions, 98 deletions

diff --git a/.Rbuildignore b/.Rbuildignore
index 7e262d7..91c0bbb 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -6,3 +6,4 @@ blg$
 aux$
 log$
 test.R
+^docs/*
diff --git a/.gitignore b/.gitignore
index 9484aca..18c7c89 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1 +1,3 @@
 test.R
+drfit*.tar.gz
+drfit.Rcheck
diff --git a/DESCRIPTION b/DESCRIPTION
index 61c9551..173e9c6 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,10 +1,10 @@
 Package: drfit
-Version: 0.6.5
-Date: 2015-12-15
+Version: 0.7.1
+Date: 2017-03-24
 Title: Dose-Response Data Evaluation
 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre"), 
                     email = "jranke@uni-bremen.de"))
-Imports: graphics, grDevices, MASS, drc
+Imports: graphics, grDevices, MASS, drc, reshape2, qcc
 Suggests: RODBC
 Description: A somewhat outdated package of basic and easy-to-use functions for
   fitting dose-response curves to continuous dose-response data, calculating some
diff --git a/NAMESPACE b/NAMESPACE
index 91a4d4a..120d052 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -8,3 +8,5 @@ import(
 )
 
 importFrom("drc", drm, ED, LN.2, LL.2, BC.4, W1.2)
+importFrom("reshape2", melt, acast)
+importFrom("qcc", qcc)
diff --git a/R/checkexperiment.R b/R/checkexperiment.R
index b264243..b69b81f 100644
--- a/R/checkexperiment.R
+++ b/R/checkexperiment.R
@@ -9,7 +9,7 @@ checkexperiment <- function(id, db = "ecotox", endpoint = "%")
 
     if (!(db %in% rownames(databases))) stop("Database is not supported")
 
-    if (require("RODBC")) {
+    if (requireNamespace("RODBC")) {
       channel <- RODBC::odbcConnect(db, uid="cytotox", pwd="cytotox", case="tolower")
     } else {
       stop("For this function, the RODBC package has to be installed and configured.")
@@ -25,21 +25,21 @@ checkexperiment <- function(id, db = "ecotox", endpoint = "%")
         " WHERE ", exptype, " = ", id)
     commentdata <- RODBC::sqlQuery(channel,commentquery)
     comment <- as.character(commentdata[[1]])
-        
+
     expquery <- paste("SELECT experimentator,substance, ",
         testtype, ",conc,unit,", responsename, ",performed,ok",
-        " FROM ",db," WHERE ",exptype,"=", id, 
+        " FROM ",db," WHERE ",exptype,"=", id,
             sep = "")
 
     if (db == "ecotox") {
-        expquery <- paste(expquery, " AND type LIKE '", 
+        expquery <- paste(expquery, " AND type LIKE '",
                 endpoint, "'", sep = "")
     }
 
     expdata <- RODBC::sqlQuery(channel,expquery)
 
     if (db %in% c("cytotox","enzymes")) {
-        controlquery <- paste("SELECT type,response FROM controls 
+        controlquery <- paste("SELECT type,response FROM controls
             WHERE plate=",id)
         controldata <- RODBC::sqlQuery(channel,controlquery)
     }
@@ -63,7 +63,7 @@ checkexperiment <- function(id, db = "ecotox", endpoint = "%")
         numberOfBlinds <- NA
         meanOfBlinds <- NA
         stdOfBlinds <- NA
-        
+
     }
     numberOfControls <- length(controls$response)
     if (numberOfControls > 0) {
@@ -78,7 +78,7 @@ checkexperiment <- function(id, db = "ecotox", endpoint = "%")
     if (length(expdata$experimentator) < 1) {
         stop("There is no response data for ",exptype," ",
             id," in database ",db,"\n")
-    } 
+    }
     exptypestring <- paste(toupper(substring(exptype,1,1)),
         substring(exptype,2),sep="")
     expdata$experimentator <- factor(expdata$experimentator)
@@ -87,7 +87,7 @@ checkexperiment <- function(id, db = "ecotox", endpoint = "%")
     expdata$substance <- factor(expdata$substance)
     expdata$unit <- factor(expdata$unit)
     expdata$ok <- factor(expdata$ok)
-    
+
     cat("\n",exptypestring,id,"from database",db,":\n\n",
         "\tExperimentator(s):\t",levels(expdata$experimentator),"\n",
         "\tType(s):\t\t",levels(expdata$type),"\n",
@@ -100,7 +100,7 @@ checkexperiment <- function(id, db = "ecotox", endpoint = "%")
         "\tblind\t",numberOfBlinds,"\t",meanOfBlinds,"\t",stdOfBlinds,"\n",
         "\tcontrol\t",numberOfControls,"\t",meanOfControls,"\t",
             stdOfControls,"\t\t",percentstdOfcontrols,"\n")
-    
+
 
     if (db == "ecotox") {
         boxplot(controls$response,
@@ -116,22 +116,22 @@ checkexperiment <- function(id, db = "ecotox", endpoint = "%")
             boxwex=0.4,
             main=paste("Plate ",id))
     }
-    
+
     drdata <- expdata[c(2,4,6)]
     drdata$substance <- factor(drdata$substance)
     substances <- levels(drdata$substance)
-       
+
     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), 
+        xlim=c(lld - 0.5, lhd + 2),
+        ylim= c(-0.1, 2),
         xlab=paste("decadic logarithm of the concentration in ",levels(expdata$unit)),
         ylab=responsename)
-    
+
     drdatalist <- split(drdata,drdata$substance)
-    
+
     for (i in 1:length(drdatalist)) {
         points(log10(drdatalist[[i]]$conc),drdatalist[[i]][[responsename]],col=i);
     }
diff --git a/R/checksubstance.R b/R/checksubstance.R
index 790182f..06cc635 100644
--- a/R/checksubstance.R
+++ b/R/checksubstance.R
@@ -1,7 +1,7 @@
 checksubstance <- function(substance, db = "cytotox", experimentator = "%",
-        celltype = "%", enzymetype = "%", organism = "%", 
+        celltype = "%", enzymetype = "%", organism = "%",
         endpoint = "%",
-        whereClause = "1", ok= "%") 
+        whereClause = "1", ok= "%")
 {
     databases <- data.frame(
         responsename=c("viability","activity","response"),
@@ -11,7 +11,7 @@ checksubstance <- function(substance, db = "cytotox", experimentator = "%",
 
     if (!(db %in% rownames(databases))) stop("Database is not supported")
 
-    if (require("RODBC")) {
+    if (requireNamespace("RODBC")) {
       channel <- RODBC::odbcConnect(db, uid="cytotox", pwd="cytotox", case="tolower")
     } else {
       stop("For this function, the RODBC package has to be installed and configured.")
@@ -23,13 +23,13 @@ checksubstance <- function(substance, db = "cytotox", experimentator = "%",
 
     if (db == "cytotox") {
         type <- celltype
-    } 
+    }
     if (db == "enzymes") {
         type <- enzymetype
-    } 
+    }
     if (db == "ecotox") {
         type <- organism
-    } 
+    }
 
     query <- paste("SELECT experimentator,substance,",
         testtype, ",", exptype, ",conc,unit,",responsename,",ok",
@@ -41,7 +41,7 @@ checksubstance <- function(substance, db = "cytotox", experimentator = "%",
                 sep = "")
 
     if (db == "ecotox") {
-        query <- paste(query, " AND type LIKE '", 
+        query <- paste(query, " AND type LIKE '",
                 endpoint, "'", sep = "")
     }
 
@@ -51,39 +51,39 @@ checksubstance <- function(substance, db = "cytotox", experimentator = "%",
     if (length(data$experimentator) < 1) {
         stop(paste("\nNo response data for",substance,"in database",
                 db,"found with these parameters\n"))
-    } 
-    
-    data$experimentator <- factor(data$experimentator)    
+    }
+
+    data$experimentator <- factor(data$experimentator)
     data$substance <- factor(data$substance)
-    substances <- levels(data$substance)    
-    data$type <- factor(data[[testtype]])                
-    data[[exptype]] <- factor(data[[exptype]])                        
+    substances <- levels(data$substance)
+    data$type <- factor(data[[testtype]])
+    data[[exptype]] <- factor(data[[exptype]])
     experiments <- levels(data[[exptype]])
     concentrations <- split(data$conc,data$conc)
     concentrations <- as.numeric(names(concentrations))
-    data$unit <- factor(data$unit)                        
+    data$unit <- factor(data$unit)
     data$ok <- factor(data$ok)
 
     if (length(experiments)>6) {
-        palette(rainbow(length(experiments)))      
+        palette(rainbow(length(experiments)))
     }
- 
+
     plot(log10(data$conc),data[[responsename]],
-        xlim=c(-2.5, 4.5),                                                                  
-        ylim= c(-0.1, 2),                                                                 
-        xlab=paste("decadic logarithm of the concentration in ",levels(data$unit)),    
-        ylab=responsename)  
-        
+        xlim=c(-2.5, 4.5),
+        ylim= c(-0.1, 2),
+        xlab=paste("decadic logarithm of the concentration in ",levels(data$unit)),
+        ylab=responsename)
+
     explist <- split(data,data[[exptype]])
-   
-    for (i in 1:length(explist)) {    
-        points(log10(explist[[i]]$conc),explist[[i]][[responsename]],col=i);          
-    }       
-    
+
+    for (i in 1:length(explist)) {
+        points(log10(explist[[i]]$conc),explist[[i]][[responsename]],col=i);
+    }
+
     legend("topleft", experiments, pch=1, col=1:length(experiments), inset=0.05)
     title(main=paste(substance," - ",levels(data$experimentator)," - ",levels(data$type)))
 
-    exptypename <-  paste(toupper(substring(exptype,1,1)), 
+    exptypename <-  paste(toupper(substring(exptype,1,1)),
         substring(exptype,2), sep = "")
     experimentators <- paste(levels(data$experimentator), collapse = " ")
     types <- paste(levels(data$type), collapse = " ")
diff --git a/R/drcfit.R b/R/drcfit.R
index 8c52f6d..0d27c1c 100644
--- a/R/drcfit.R
+++ b/R/drcfit.R
@@ -14,7 +14,7 @@ drcfit <- function(data, chooseone=TRUE,
                                     # model result was appended
     rsubstance <- array()           # the substance names in the results
     rndl <- vector()                # number of dose levels
-    rn <- vector()                  # mean number of replicates 
+    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
@@ -69,7 +69,8 @@ drcfit <- function(data, chooseone=TRUE,
                     active <- FALSE
                     if (linlogit)
                     {
-                        m <- try(drm(response ~ dose, data = tmp, fct = BC.4(fixed = c(NA, 1, NA, NA))))
+                        m <- try(drm(response ~ dose, data = tmp, fct = BC.4(fixed = c(NA, 1, NA, NA))),
+                                 silent = TRUE)
                         if (chooseone==FALSE || fit==FALSE) {
                             if (!inherits(m, "try-error")) {
                                 fit <- TRUE
@@ -90,10 +91,11 @@ drcfit <- function(data, chooseone=TRUE,
                                 a[[ri]] <- coef(m)[[2]]
                                 b[[ri]] <- coef(m)[[1]]
                                 c[[ri]] <- coef(m)[[3]]
-                                ED50 <- try(ED(m, 50, interval = "delta", 
+                                ED50 <- try(ED(m, 50, interval = "delta",
                                                lower = lowestdose / 10,
                                                upper = highestdose * 10,
-                                               display = FALSE))
+                                               display = FALSE),
+                                               silent = TRUE)
                                 if (!inherits(ED50, "try-error")) {
                                     logED50[[ri]] <- log10(ED50["1:50", "Estimate"])
                                     logED50low[[ri]] <- log10(ED50["1:50", "Lower"])
@@ -101,14 +103,14 @@ drcfit <- function(data, chooseone=TRUE,
                                     if (logED50[[ri]] > rlhd[[ri]]) {
                                         mtype[[ri]] <- "no fit"
                                     }
-                                } 
+                                }
                             }
                         }
                     }
                     if (probit)
                     {
-                        m <- try(drm(response ~ dose, data = tmp, 
-                                     fct = LN.2()))
+                        m <- try(drm(response ~ dose, data = tmp,
+                                     fct = LN.2()), silent = TRUE)
                         if (chooseone==FALSE || fit==FALSE) {
                             if (!inherits(m, "try-error")) {
                                 fit <- TRUE
@@ -142,7 +144,8 @@ drcfit <- function(data, chooseone=TRUE,
                     }
                     if (logit)
                     {
-                        m <- try(drm(response ~ dose, data = tmp, fct = LL.2()))
+                        m <- try(drm(response ~ dose, data = tmp, fct = LL.2()),
+                                 silent = TRUE)
                         if (chooseone==FALSE || fit==FALSE) {
                             if (!inherits(m, "try-error")) {
                                 fit <- TRUE
@@ -179,7 +182,8 @@ drcfit <- function(data, chooseone=TRUE,
                     }
                     if (weibull)
                     {
-                        m <- try(drm(response ~ dose, data = tmp, fct = W1.2()))
+                        m <- try(drm(response ~ dose, data = tmp, fct = W1.2()),
+                                 silent = TRUE)
                         if (chooseone==FALSE || fit==FALSE) {
                             if (!inherits(m, "try-error")) {
                                 fit <- TRUE
@@ -252,7 +256,7 @@ drcfit <- function(data, chooseone=TRUE,
         }
     }
 
-    results <- data.frame(rsubstance, rndl, rn, rlld, rlhd, mtype, 
+    results <- data.frame(rsubstance, rndl, rn, rlld, rlhd, mtype,
         logED50, logED50low, logED50high, runit, sigma, a, b)
     lower_level_percent = paste(100 * (1 - level)/2, "%", sep = "")
     upper_level_percent = paste(100 * (1 + level)/2, "%", sep = "")
@@ -275,12 +279,13 @@ drcfit <- function(data, chooseone=TRUE,
             mtype <- as.character(results[row.i, "mtype"])
             if (mtype %in% c("probit", "logit", "weibull", "linlogit")) {
                 for (EDi in EDx) {
-                    EDx.drc = try(ED(m, EDi, interval = "delta", display = FALSE, level = level))
+                    EDx.drc = try(ED(m, EDi, interval = "delta", display = FALSE, level = level),
+                                  silent = TRUE)
                     if (!inherits(EDx.drc, "try-error")) {
                         results[row.i, paste0("EDx", EDi)] <- EDx.drc[paste0("1:", EDi), "Estimate"]
-                        results[row.i, paste0("EDx", EDi, " ", lower_level_percent)] <- EDx.drc[paste0("1:", EDi), 
+                        results[row.i, paste0("EDx", EDi, " ", lower_level_percent)] <- EDx.drc[paste0("1:", EDi),
                                                                                                 "Lower"]
-                        results[row.i, paste0("EDx", EDi, " ", upper_level_percent)] <- EDx.drc[paste0("1:", EDi), 
+                        results[row.i, paste0("EDx", EDi, " ", upper_level_percent)] <- EDx.drc[paste0("1:", EDi),
                                                                                                 "Upper"]
                     }
                 }
diff --git a/R/drdata.R b/R/drdata.R
index eda1249..dc741a6 100644
--- a/R/drdata.R
+++ b/R/drdata.R
@@ -3,7 +3,7 @@ drdata <- function(substances, experimentator = "%", db = "cytotox",
     organism = "Vibrio fischeri", endpoint = "Luminescence", whereClause = "1",
     ok = "'ok','no fit'")
 {
-  if (require("RODBC")) {
+  if (requireNamespace("RODBC")) {
     channel <- RODBC::odbcConnect(db,uid="cytotox",pwd="cytotox",case="tolower")
     slist <- paste(substances,collapse="','")
     if (db == "cytotox") {
@@ -21,7 +21,7 @@ drdata <- function(substances, experimentator = "%", db = "cytotox",
             type <- organism
         }
     }
-        
+
     query <- paste("SELECT conc,",responsetype,",unit,experimentator,substance,",testtype,
         ",ok FROM ", db, " WHERE substance IN ('",
         slist,"') AND experimentator LIKE '",
diff --git a/R/drfit.R b/R/drfit.R
index 7fa53bf..65ab8e4 100644
--- a/R/drfit.R
+++ b/R/drfit.R
@@ -18,7 +18,7 @@ drfit <- function(data, startlogED50 = NA, chooseone=TRUE,
                                     # model result was appended
     rsubstance <- array()           # the substance names in the results
     rndl <- vector()                # number of dose levels
-    rn <- vector()                  # mean number of replicates 
+    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
@@ -75,12 +75,13 @@ drfit <- function(data, startlogED50 = NA, chooseone=TRUE,
                     active <- TRUE
                 } else {
                     active <- FALSE
-                    if (linlogit && 
+                    if (linlogit &&
                         length(subset(linlogitWrong,linlogitWrong == i))==0 &&
                         length(subset(allWrong,allWrong == i))==0) {
                         m <- try(nls(response ~ linlogitf(dose,1,f,logED50,b),
-                                data=tmp, algorithm="port",
-                                start=list(f=f0,logED50=startlogED50[[i]],b=b0)))
+                                     data=tmp, algorithm="port",
+                                     start=list(f=f0,logED50=startlogED50[[i]],b=b0)),
+                                 silent = TRUE)
                         if (!inherits(m, "try-error")) {
                             fit <- TRUE
                             ri <- ri + 1
@@ -104,7 +105,8 @@ drfit <- function(data, startlogED50 = NA, chooseone=TRUE,
                                 c[[ri]] <- NA
                             } else {
                                 mtype[[ri]] <- "linlogit"
-                                logED50conf <- try(confint(m,"logED50",level=level))
+                                logED50conf <- try(confint(m,"logED50",level=level),
+                                                   silent = TRUE)
                                 if (!inherits(logED50conf, "try-error")) {
                                     logED50low[[ri]] <- logED50conf[[1]]
                                     logED50high[[ri]] <- logED50conf[[2]]
@@ -122,8 +124,9 @@ drfit <- function(data, startlogED50 = NA, chooseone=TRUE,
                     if (probit &&
                         length(subset(allWrong,allWrong == i))==0) {
                         m <- try(nls(response ~ pnorm(-log10(dose),-logED50,scale),
-                                    data=tmp, algorithm="port",
-                                    start=list(logED50=startlogED50[[i]],scale=ps0)))
+                                     data=tmp, algorithm="port",
+                                     start=list(logED50=startlogED50[[i]],scale=ps0)),
+                                 silent = TRUE)
                         if (chooseone==FALSE || fit==FALSE) {
                             if (!inherits(m, "try-error")) {
                                 fit <- TRUE
@@ -148,7 +151,8 @@ drfit <- function(data, startlogED50 = NA, chooseone=TRUE,
                                     b[[ri]] <- NA
                                 } else {
                                     mtype[[ri]] <- "probit"
-                                    logED50conf <- try(confint(m,"logED50",level=level))
+                                    logED50conf <- try(confint(m,"logED50",level=level),
+                                                       silent = TRUE)
                                     if (!inherits(logED50conf, "try-error")) {
                                         logED50low[[ri]] <- logED50conf[[1]]
                                         logED50high[[ri]] <- logED50conf[[2]]
@@ -166,8 +170,9 @@ drfit <- function(data, startlogED50 = NA, chooseone=TRUE,
                     if (logit &&
                         length(subset(allWrong,allWrong == i))==0) {
                         m <- try(nls(response ~ plogis(-log10(dose),-logED50,scale),
-                                data=tmp, algorithm="port",
-                                start=list(logED50=startlogED50[[i]],scale=ls0)))
+                                     data=tmp, algorithm="port",
+                                     start=list(logED50=startlogED50[[i]],scale=ls0)),
+                                 silent = TRUE)
                         if (chooseone==FALSE || fit==FALSE) {
                             if (!inherits(m, "try-error")) {
                                 fit <- TRUE
@@ -193,7 +198,8 @@ drfit <- function(data, startlogED50 = NA, chooseone=TRUE,
                                     b[[ri]] <- NA
                                 } else {
                                     mtype[[ri]] <- "logit"
-                                    logED50conf <- try(confint(m,"logED50",level=level))
+                                    logED50conf <- try(confint(m,"logED50",level=level),
+                                                       silent = TRUE)
                                     if (!inherits(logED50conf, "try-error")) {
                                         logED50low[[ri]] <- logED50conf[[1]]
                                         logED50high[[ri]] <- logED50conf[[2]]
@@ -209,8 +215,9 @@ drfit <- function(data, startlogED50 = NA, chooseone=TRUE,
                     if (weibull &&
                         length(subset(allWrong,allWrong == i))==0) {
                         m <- try(nls(response ~ pweibull(-log10(dose)+location,shape),
-                                data=tmp, algorithm="port",
-                                start=list(location=startlogED50[[i]],shape=ws0)))
+                                     data=tmp, algorithm="port",
+                                     start=list(location=startlogED50[[i]],shape=ws0)),
+                                 silent = TRUE)
                         if (chooseone==FALSE || fit==FALSE) {
                             if (!inherits(m, "try-error")) {
                                 ri <- ri + 1
@@ -218,7 +225,7 @@ drfit <- function(data, startlogED50 = NA, chooseone=TRUE,
                                 a[[ri]] <- coef(m)[["location"]]
                                 b[[ri]] <- coef(m)[["shape"]]
                                 sqrdev <- function(logdose) {
-                                    (0.5 - pweibull( - logdose + a[[ri]], b[[ri]]))^2 
+                                    (0.5 - pweibull( - logdose + a[[ri]], b[[ri]]))^2
                                 }
                                 logED50[[ri]] <- nlm(sqrdev,startlogED50[[i]])$estimate
                                 if (sqrdev(logED50[[ri]]) > 0.1) {
@@ -291,7 +298,7 @@ drfit <- function(data, startlogED50 = NA, chooseone=TRUE,
             c[[ri]] <- NA
         }
     }
-    results <- data.frame(rsubstance, rndl, rn, rlld, rlhd, mtype, 
+    results <- data.frame(rsubstance, rndl, rn, rlld, rlhd, mtype,
         logED50, logED50low, logED50high, runit, sigma, a, b)
     lower_level_percent = paste(100 * (1 - level)/2, "%", sep = "")
     upper_level_percent = paste(100 * (1 + level)/2, "%", sep = "")
@@ -311,18 +318,18 @@ drfit <- function(data, startlogED50 = NA, chooseone=TRUE,
             if (mtype[[row.i]] %in% c("probit", "logit", "weibull", "linlogit")) {
                 for (ED in EDx) {
                     of <- function(x) {
-                        abs(predict(models[[row.i]], data.frame(dose = 10^x)) - 
+                        abs(predict(models[[row.i]], data.frame(dose = 10^x)) -
                             (1 - (ED/100)))
-                    } 
-                    # Search over interval starting an order of magnitude below 
+                    }
+                    # Search over interval starting an order of magnitude below
                     # the lowest dose up to one order of magnitude above the
                     # highest dose
-                    o = optimize(of, 
+                    o = optimize(of,
                                  results[row.i, c("lld", "lhd")] + c(-1, 1))
                     # Only keep results within the tolerance
                     if ((o$objective) < EDx.tolerance) {
                         logdose.ED = o$minimum
-                        results[row.i, paste0("EDx", ED)] <- 10^logdose.ED 
+                        results[row.i, paste0("EDx", ED)] <- 10^logdose.ED
                     }
                 }
             }
diff --git a/R/drplot.R b/R/drplot.R
index 11c4d42..1e6b2cd 100644
--- a/R/drplot.R
+++ b/R/drplot.R
@@ -1,12 +1,12 @@
 if(getRversion() >= '2.15.1') utils::globalVariables(c("dose", "Substance", "mtype"))
-drplot <- function(drresults, data, 
+drplot <- function(drresults, data,
         dtype = "std", alpha = 0.95, ctype = "none",
         path = "./", fileprefix = "drplot", overlay = FALSE,
         xlim = c("auto","auto"), ylim = c("auto","auto"),
         xlab = paste("Decadic Logarithm of the dose in ", unit),
         ylab = "Normalized response",
         axes = TRUE, frame.plot = TRUE,
-        postscript = FALSE, pdf = FALSE, png = FALSE, 
+        postscript = FALSE, pdf = FALSE, png = FALSE,
         bw = TRUE,
         pointsize = 12,
         colors = 1:8, ltys = 1:8, pchs = "auto",
@@ -24,7 +24,7 @@ drplot <- function(drresults, data,
     if(is.data.frame(data)) {
         # Get rid of pseudo substance names of controls
         nonzerodata <- subset(data,dose!=0)
-        nonzerodata$substance <- factor(nonzerodata$substance) 
+        nonzerodata$substance <- factor(nonzerodata$substance)
         zerodata <- subset(data,dose==0)
         nc <- length(zerodata$dose)     # Number of control points
         if (nc > 0) {
@@ -44,12 +44,12 @@ drplot <- function(drresults, data,
         hr <- max(nonzerodata$response)
         if (ctype == "std") hr <- max(hr,1 + sdc)
         if (ctype == "conf") hr <- max(hr,1 + controlconf)
-        dsubstances <- levels(nonzerodata$substance)    
+        dsubstances <- levels(nonzerodata$substance)
     } else {
         lld <- min(drresults[["logED50"]],na.rm=TRUE) - 2
         lhd <- max(drresults[["logED50"]],na.rm=TRUE) + 2
         if (length(subset(drresults,mtype=="linlogit")$Substance) != 0) {
-            hr <- 1.8 
+            hr <- 1.8
         } else {
             hr <- 1.0
         }
@@ -70,20 +70,20 @@ drplot <- function(drresults, data,
             postscript(file=filename,
                     paper="special",width=7,height=7,horizontal=FALSE, pointsize=pointsize)
             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)
             message("Created File: ",filename,"\n")
-        } 
+        }
         if (png) {
             filename = paste(path,fileprefix,".png",sep="")
             png(filename=filename,
                 width=500, height=500, pointsize=pointsize)
             message("Created File: ",filename,"\n")
         }
-            
+
         plot(0,type="n",
             xlim = xlim,
             ylim = ylim,
@@ -97,7 +97,7 @@ drplot <- function(drresults, data,
         if (!postscript && !png && !pdf && length(dsubstances) > 1) {
             op <- par(ask=TRUE)
             on.exit(par(op))
-        } 
+        }
     }
     # nl is the overall number of fits to draw by different line types
     nl <- 0
@@ -123,20 +123,20 @@ drplot <- function(drresults, data,
                         postscript(file=filename,
                                 paper="special",width=7,height=7,horizontal=FALSE,pointsize=pointsize)
                         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)
                         message("Created File: ",filename,"\n")
-                    } 
+                    }
                     if (png) {
                         filename = paste(path,fileprefix,sub(" ","_",i),".png",sep="")
                         png(filename=filename,
                             width=500, height=500, pointsize=pointsize)
                         message("Created File: ",filename,"\n")
                     }
-                        
+
                     plot(0,type="n",
                         xlim = xlim,
                         ylim = ylim,
@@ -147,7 +147,7 @@ drplot <- function(drresults, data,
                 }
                 if (!overlay) legend(lpos, i, lty = 1, col = color, pch = pch, inset=0.05)
                 tmp$dosefactor <- factor(tmp$dose)  # necessary because the old
-                                                    # factor has all levels, not 
+                                                    # factor has all levels, not
                                                     # only the ones tested with
                                                     # this substance
 
@@ -157,7 +157,7 @@ drplot <- function(drresults, data,
                     abline(h = 1 + sdc, lty = 2)
                 }
                 if (ctype == "conf") {
-                    abline(h = 1 - controlconf, lty = 2) 
+                    abline(h = 1 - controlconf, lty = 2)
                     abline(h = 1 + controlconf, lty = 2)
                 }
 
@@ -179,7 +179,7 @@ drplot <- function(drresults, data,
                     }
                     if (dtype == "conf")
                     {
-                        confidencedeltas <- qt((1 + alpha)/2, lengths - 1) * sqrt(vars) 
+                        confidencedeltas <- qt((1 + alpha)/2, lengths - 1) * sqrt(vars)
                         tops <- means + confidencedeltas
                         bottoms <- means - confidencedeltas
                     }
@@ -207,13 +207,13 @@ drplot <- function(drresults, data,
                         if (drresults[[fit.row, "mtype"]] %in% c("probit",
                                                                  "logit",
                                                                  "weibull",
-                                                                 "linlogit")) 
+                                                                 "linlogit"))
                         {
                             m <- attr(drresults, "models")[[as.numeric(fit.row)]]
                             of <- function(x) {
                                 predict(m, data.frame(dose = 10^x))
-                            } 
-                            plot(of, lld - 0.5, lhd + 2, 
+                            }
+                            plot(of, lld - 0.5, lhd + 2,
                                  add = TRUE, col = color, lty = lty)
                         }
                     }