Switch to odbc, reformattting of code

to make it more readable. Also remove outdated hyperlinks from
the help files.

5 files changed, 426 insertions, 430 deletions

diff --git a/R/checkcontrols.R b/R/checkcontrols.R
index d996d18..b071769 100644
--- a/R/checkcontrols.R
+++ b/R/checkcontrols.R
@@ -1,145 +1,138 @@
-if(getRversion() >= '2.15.1') utils::globalVariables(c("type", "conc"))
-checkcontrols <- function(last = 10, id = NULL, db = "cytotox",
+utils::globalVariables(c("type", "conc"))
+checkcontrols <- function(last = 10, id = NULL, db = c("cytotox", "enzymes", "ecotox"),
                           celltype = "IPC-81", enzymetype = "AChE",
                           organism = "Vibrio fischeri",
                           endpoint = "%", qcc = c("R", "xbar"))
 {
+  db <- match.arg(db)
 
-    if (!(db %in% c("cytotox", "ecotox", "enzymes"))) stop("Database is not supported")
+  con <- dbConnect(odbc(), "cytotox", database = db)
 
-    if (requireNamespace("RODBC")) {
-      channel <- RODBC::odbcConnect(db, uid="cytotox", pwd="cytotox", case="tolower")
+  if (db %in% c("cytotox","enzymes")) {
+    if (is.null(id[1])) {
+      platequery <- "SELECT plate FROM"
+      if (db == "cytotox") {
+        platequery <- paste0(platequery, " cytotox WHERE celltype like '",
+                             celltype, "'")
+      }
+      if (db == "enzymes") {
+        platequery <- paste0(platequery, " enzymes WHERE enzyme like '",
+                             enzymetype, "'")
+        }
+        platequery <- paste(platequery, 
+          "GROUP BY plate ORDER BY plate DESC LIMIT", last)
+        plates <- dbGetQuery(con, platequery)$plate
     } else {
-      stop("For this function, the RODBC package has to be installed and configured.")
+      plates <- id
     }
-
-    if (db %in% c("cytotox","enzymes")) {
-        if (is.null(id[1])) {
-            platequery <- "SELECT plate FROM"
-            if (db == "cytotox") {
-                platequery <- paste0(platequery, " cytotox WHERE celltype like
-                                     '", celltype, "'")
-            }
-            if (db == "enzymes") {
-                platequery <- paste0(platequery, " enzymes WHERE enzyme like
-                                     '", enzymetype, "'")
-            }
-                platequery <- paste(platequery,
-                    "GROUP BY plate ORDER BY plate DESC LIMIT", last)
-            plates <- RODBC::sqlQuery(channel, platequery)$plate
-        } else {
-            plates <- id
+    controlquery <- paste("SELECT plate, type, location, response FROM controls",
+      "WHERE plate IN (", paste(plates, collapse = ", "), ")")
+    controldata <- dbGetQuery(con,controlquery)
+  } else {
+    if (is.null(id[1])) {
+      lastquery = paste0("SELECT experiment, type FROM ecotox ",
+        "WHERE organism LIKE '", organism, "'",
+        "AND type LIKE '", endpoint, "' ",
+        "GROUP BY experiment ORDER BY experiment DESC LIMIT ", last)
+      res <- dbGetQuery(con, lastquery)
+      if (nrow(res) == 0) {
+        stop("No results for endpoint", endpoint)
+      } else {
+        if (nlevels(res$type) > 1) {
+          stop("Found more than one endpoint type:\n",
+               paste(levels(res$type), collapse = ", "), "\n",
+               "Please specify an endpoint in your call to checkcontrols()")
         }
-        controlquery <- paste("SELECT plate, type, location, response FROM controls",
-            "WHERE plate IN (", paste(plates, collapse = ", "), ")")
-        controldata <- RODBC::sqlQuery(channel,controlquery)
+        experiments <- res$experiment
+      }
     } else {
-        if (is.null(id[1])) {
-            lastquery = paste0("SELECT experiment, type FROM ecotox ",
-                "WHERE organism LIKE '", organism, "'",
-                "AND type LIKE '", endpoint, "' ",
-                "GROUP BY experiment ORDER BY experiment DESC LIMIT ", last)
-            res <- RODBC::sqlQuery(channel, lastquery)
-            if (nrow(res) == 0) {
-                stop("No results for endpoint", endpoint)
-            } else {
-                if (nlevels(res$type) > 1) {
-                    stop("Found more than one endpoint type:\n",
-                         paste(levels(res$type), collapse = ", "), "\n",
-                         "Please specify an endpoint in your call to checkcontrols()")
-                }
-                experiments <- res$experiment
-            }
-        } else {
-            experiments <- id
-        }
-        expquery <- paste0("SELECT ",
-            "experimentator, experiment, substance, organism, type, conc, unit, raw_response, ",
-            "performed, ok ",
-            "FROM ecotox ",
-            "WHERE experiment IN (", paste(experiments, collapse = ", "), ") ",
-            "AND organism LIKE '", organism, "' ",
-            "AND type LIKE '", endpoint, "'")
-        expdata <- RODBC::sqlQuery(channel, expquery)
-        if (nlevels(expdata$type) > 1) {
-            stop("Found more than one endpoint type:\n",
-                 paste(levels(expdata$type), collapse = ", "), "\n",
-                 "Please specify an endpoint in your call to checkcontrols()")
-        }
-        # Use the raw response for QA
-        expdata$response <- expdata$raw_response
+      experiments <- id
     }
+    expquery <- paste0("SELECT ",
+      "experimentator, experiment, substance, organism, type, conc, unit, raw_response, ",
+      "performed, ok ",
+      "FROM ecotox ",
+      "WHERE experiment IN (", paste(experiments, collapse = ", "), ") ",
+      "AND organism LIKE '", organism, "' ",
+      "AND type LIKE '", endpoint, "'")
+    expdata <- dbGetQuery(con, expquery)
+    if (nlevels(expdata$type) > 1) {
+      stop("Found more than one endpoint type:\n",
+        paste(levels(expdata$type), collapse = ", "), "\n",
+        "Please specify an endpoint in your call to checkcontrols()")
+    }
+    # Use the raw response for QA
+    expdata$response <- expdata$raw_response
+  }
 
-    RODBC::odbcClose(channel)
+  if (db %in% c("cytotox","enzymes")) {
+      blinds <- subset(controldata, type == "blind")
+      controls <- subset(controldata, type == "control")
+      QA <- matrix(nrow = 2, ncol = 4,
+          dimnames = list(c("Blind", "Control (conc = 0)"),
+                          c("Number", "Mean", "Std. Dev.", "% Std. Dev")))
 
-    if (db %in% c("cytotox","enzymes")) {
-        blinds <- subset(controldata, type == "blind")
-        controls <- subset(controldata, type == "control")
-        QA <- matrix(nrow = 2, ncol = 4,
-            dimnames = list(c("Blind", "Control (conc = 0)"),
-                            c("Number", "Mean", "Std. Dev.", "% Std. Dev")))
+      QA[1, 1] <- length(blinds$response)
+      QA[1, 2] <- signif(mean(blinds$response), 2)
+      QA[1, 3] <- signif(sd(blinds$response), 2)
+      QA[1, 4] <-signif(QA[1, 3] * 100 / QA[1, 2],2)
+  } else {
+      controls <- subset(expdata, conc == 0)
+      QA <- matrix(nrow = 1, ncol = 4,
+          dimnames = list(c("Control (conc = 0)"),
+                          c("Number", "Mean", "Std. Dev.", "% Std. Dev")))
+  }
 
-        QA[1, 1] <- length(blinds$response)
-        QA[1, 2] <- signif(mean(blinds$response), 2)
-        QA[1, 3] <- signif(sd(blinds$response), 2)
-        QA[1, 4] <-signif(QA[1, 3] * 100 / QA[1, 2],2)
-    } else {
-        controls <- subset(expdata, conc == 0)
-        QA <- matrix(nrow = 1, ncol = 4,
-            dimnames = list(c("Control (conc = 0)"),
-                            c("Number", "Mean", "Std. Dev.", "% Std. Dev")))
-    }
+  numberOfControls <- length(controls$response)
+  QA["Control (conc = 0)", 1] <- numberOfControls
+  if (numberOfControls > 0) {
+      QA["Control (conc = 0)", 2] <- signif(mean(controls$response),2)
+      QA["Control (conc = 0)", 3] <- signif(sd(controls$response),2)
+      QA["Control (conc = 0)", 4] <- signif(QA["Control (conc = 0)", 3] * 100 /
+                                            QA["Control (conc = 0)", 2],2)
+  }
 
-    numberOfControls <- length(controls$response)
-    QA["Control (conc = 0)", 1] <- numberOfControls
-    if (numberOfControls > 0) {
-        QA["Control (conc = 0)", 2] <- signif(mean(controls$response),2)
-        QA["Control (conc = 0)", 3] <- signif(sd(controls$response),2)
-        QA["Control (conc = 0)", 4] <- signif(QA["Control (conc = 0)", 3] * 100 /
-                                              QA["Control (conc = 0)", 2],2)
-    }
+  # The report
+  cat("\nDatabase", db, "\n")
 
-    # The report
-    cat("\nDatabase", db, "\n")
+  if (db == "ecotox") {
+      cat("Organism", organism, "\n")
+      cat("Endpoint", unique(expdata$type), "\n")
+      cat("\nExperiments ", paste(experiments, collapse = ", "), "\n\n")
+  } else {
+      if (db == "cytotox") cat ("Cell type", celltype, "\n")
+      if (db == "enzymes") cat ("Enzyme type", enzymetype, "\n")
+      cat("\nPlates", paste(plates, collapse = ", "), "\n\n")
+  }
+  print(QA)
 
-    if (db == "ecotox") {
-        cat("Organism", organism, "\n")
-        cat("Endpoint", unique(expdata$type), "\n")
-        cat("\nExperiments ", paste(experiments, collapse = ", "), "\n\n")
-    } else {
-        if (db == "cytotox") cat ("Cell type", celltype, "\n")
-        if (db == "enzymes") cat ("Enzyme type", enzymetype, "\n")
-        cat("\nPlates", paste(plates, collapse = ", "), "\n\n")
-    }
-    print(QA)
+  if (!is.na(qcc[1])) {
+      op <- par(ask=TRUE)
+      on.exit(par(op))
+      requireNamespace("reshape2")
+      if (db == "ecotox") {
+          controls$row <- rownames(controls)
+          controls_molten <- melt(controls[c("experiment", "row", "response")],
+                                  id = c("experiment", "row"))
+          controls_wide <- acast(controls_molten, formula = experiment ~ row)
 
-    if (!is.na(qcc[1])) {
-        op <- par(ask=TRUE)
-        on.exit(par(op))
-        requireNamespace("reshape2")
-        if (db == "ecotox") {
-            controls$row <- rownames(controls)
-            controls_molten <- melt(controls[c("experiment", "row", "response")],
-                                    id = c("experiment", "row"))
-            controls_wide <- acast(controls_molten, formula = experiment ~ row)
-
-        } else {
-            controls_molten <- melt(controls[c("plate", "location", "response")],
-                                    id = c("plate", "location"))
-            controls_wide <- acast(controls_molten, formula = plate ~ location)
-        }
-        if ("R" %in% qcc) {
-            qcc(controls_wide, type = "R", nsigmas = 3,
-                title = "Range chart",
-                data.name = "Controls (conc = 0)")
-        }
-        if ("xbar" %in% qcc) {
-            qcc(controls_wide, type = "xbar", nsigmas = 3,
-                title = "Mean chart",
-                data.name = "Controls (conc = 0)")
-        }
-    }
+      } else {
+          controls_molten <- melt(controls[c("plate", "location", "response")],
+                                  id = c("plate", "location"))
+          controls_wide <- acast(controls_molten, formula = plate ~ location)
+      }
+      if ("R" %in% qcc) {
+          qcc(controls_wide, type = "R", nsigmas = 3,
+              title = "Range chart",
+              data.name = "Controls (conc = 0)")
+      }
+      if ("xbar" %in% qcc) {
+          qcc(controls_wide, type = "xbar", nsigmas = 3,
+              title = "Mean chart",
+              data.name = "Controls (conc = 0)")
+      }
+  }
 
-    invisible(controls)
+  invisible(controls)
 }
-# vim: ts=4 sw=4 expandtab:
+# vim: ts=2 sw=2 expandtab:
diff --git a/R/checkexperiment.R b/R/checkexperiment.R
index 2806317..7fa1a60 100644
--- a/R/checkexperiment.R
+++ b/R/checkexperiment.R
@@ -1,190 +1,189 @@
-if(getRversion() >= '2.15.1') utils::globalVariables(c("type", "conc", "substance"))
-checkexperiment <- function(id, db = "ecotox", endpoint = "%")
-{
-    databases <- data.frame(
-        responsename=c("viability","activity","raw_response"),
-        testtype=c("celltype","enzyme","organism"),
-        exptype=c("plate","plate","experiment"))
-    rownames(databases) <- c("cytotox","enzymes","ecotox")
-
-    if (!(db %in% rownames(databases))) stop("Database is not supported")
-
-    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.")
-    }
-
-    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 <- RODBC::sqlQuery(channel,commentquery)
-    comment <- as.character(commentdata[[1]])
-
-    expquery <- paste("SELECT experimentator, substance, ",
-        testtype, ", conc, unit,", responsename, ", type, raw_0, duration, performed, ok",
-        " FROM ",db," WHERE ",exptype,"=", id,
-            sep = "")
-
-    if (db == "ecotox") {
-        expquery <- paste0(expquery, " AND type LIKE '", endpoint, "'") 
-    }
-
-    expdata <- RODBC::sqlQuery(channel,expquery)
-
-    if (db %in% c("cytotox","enzymes")) {
-        controlquery <- paste("SELECT type,response FROM controls
-            WHERE plate=",id)
-        controldata <- RODBC::sqlQuery(channel,controlquery)
-    }
-
-    RODBC::odbcClose(channel)
-
-    op <- par(ask=TRUE)
-    on.exit(par(op))
-
-    if (db %in% c("cytotox","enzymes")) {
-        blinds <- subset(controldata, type == "blind")
-        controls <- subset(controldata, type == "control")
-        QA <- matrix(nrow = 2, ncol = 4,
-            dimnames = list(c("Blind", "Control (conc = 0)"),
-                            c("Number", "Mean", "Std. Dev.", "% Std. Dev")))
-
-        QA[1, 1] <- length(blinds$response)
-        QA[1, 2] <- signif(mean(blinds$response), 2)
-        QA[1, 3] <- signif(sd(blinds$response), 2)
-        QA[1, 4] <-signif(QA[1, 3] * 100 / QA[1, 2],2)
-    } else {
-        # Use raw response for ecotox
-        expdata$response <- expdata$raw_response
-        
-        if (nlevels(expdata$type) > 1) {
-          message("There are data for more than one type of raw response in your data.\n",
-                  "The types are ", paste(levels(expdata$type), collapse = " and "), ".\n",
-                  "You should choose one of these types using 'endpoint = \"$type\"'",
-                  "in your call to checkexperiment\n",
-                  "For now, we are continuing with the data for ", levels(expdata$type)[1])
-        }
-        endpoint <- expdata$type[1]
-        expdata <- subset(expdata, type == endpoint)
-
-        controls <- subset(expdata, conc == 0)
-        expdata <- subset(expdata, conc != 0)
-
-        QA <- matrix(nrow = 1, ncol = 4,
-            dimnames = list(c("Control (conc = 0)"),
-                            c("Number", "Mean", "Std. Dev.", "% Std. Dev")))
-
-    }
-
-    numberOfControls <- length(controls$response)
-    QA["Control (conc = 0)", 1] <- numberOfControls
-    if (numberOfControls > 0) {
-        QA["Control (conc = 0)", 2] <- signif(mean(controls$response),2)
-        QA["Control (conc = 0)", 3] <- signif(sd(controls$response),2)
-        QA["Control (conc = 0)", 4] <- signif(QA["Control (conc = 0)", 3] * 100 /
-                                              QA["Control (conc = 0)", 2],2)
-    }
+utils::globalVariables(c("type", "conc", "substance"))
 
-    if (db == "ecotox") {
-        if (identical(as.character(levels(expdata$organism)), "Vibrio fischeri")) {
-            positive <- subset(expdata, substance == "Na Cl")
-            if (nrow(positive) > 0) {
-                 QA <- rbind(QA,
-                             c(nrow(positive),
-                               signif(mean(positive$raw_response), 2),
-                               signif(sd(positive$raw_response), 2),
-                               signif(100 * sd(positive$raw_response) /
-                                      mean(positive$raw_response), 2)))
-
-                 rownames(QA) <- c("Control (conc = 0)",
-                                   "Positive control (Na Cl)")
-            }
-            expdata <- subset(expdata, substance != "Na Cl", drop = TRUE)
-        }
-    }
-
-    if (length(expdata$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)
-    expdata$type <- factor(expdata[[testtype]])
-    expdata$performed <- factor(as.character(expdata$performed))
-    expdata$substance <- factor(expdata$substance)
-    expdata$unit <- factor(expdata$unit)
-    expdata$ok <- factor(expdata$ok)
-
-    # Info on the experiment
-    cat("\n",exptypestring,id,"from database",db,":\n\n",
-        "\tExperimentator(s):\t",levels(expdata$experimentator),"\n",
-        "\tType(s):\t\t",levels(expdata$type),"\n",
-        "\tPerformed on:\t\t",levels(expdata$performed),"\n",
-        "\tSubstance(s):\t\t",levels(expdata$substance),"\n",
-        "\tConcentration unit(s):\t",levels(expdata$unit),"\n",
-        "\tComment:\t\t",comment,"\n",
-        "\tOK Levels:\t\t",levels(expdata$ok),"\n\n")
-
-    print(QA)
-
-    # Control growth rate for Lemna and algae
-    if (endpoint %in% c("cell count", "frond area", "frond number")) {
-      duration <- unique(expdata$duration) # in hours
-      if (length(duration) > 1) stop("More than one duration in the data")
-      response_0 <- unique(expdata$raw_0)
-      if (length(response_0) > 1) stop("More than one mean response at time 0 in the data")
-      t_days <- duration / 24
-      control_growth_rates <- (log(controls$response) - log(response_0)) / t_days
-      cat("\nMean growth rate in controls:\t", round(mean(control_growth_rates), 3), "per day\n")
-    }
-
-
-    # Box plot of control data
-    if (db == "ecotox") {
-        boxplot(controls$response,
-            names="controls",
-            ylab=endpoint,
-            ylim=range(controls$response, na.rm = TRUE),
-            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))
+checkexperiment <- function(id, 
+  db = c("ecotox", "cytotox", "enzymes"), 
+  endpoint = "%")
+{
+  db = match.arg(db)
+
+  databases <- data.frame(
+    responsename = c("viability", "activity", "raw_response"),
+    testtype = c("celltype", "enzyme", "organism"),
+    exptype = c("plate", "plate", "experiment"),
+    row.names = c("cytotox", "enzymes", "ecotox"),
+    stringsAsFactors = FALSE)
+
+  con <- dbConnect(odbc(), "cytotox", database = db)
+
+  responsename <- databases[db, 1]
+  testtype <- databases[db, 2]
+  exptype <- databases[db, 3]
+
+  exptable <- paste(exptype, "s", sep = "")
+
+  commentquery <- paste0("SELECT comment FROM ", exptable, " ",
+    "WHERE ", exptype, " = ", id)
+  commentdata <- dbGetQuery(con, commentquery)
+  comment <- as.character(commentdata[[1]])
+
+  expquery <- paste0("SELECT ",
+    "experimentator, substance, ", testtype, ", conc, unit,", responsename, ",
+    type, raw_0, duration, performed, ok ",
+    "FROM ", db, " ",
+    "WHERE ", exptype, "=", id)
+
+  if (db == "ecotox") {
+    expquery <- paste0(expquery, " AND type LIKE '", endpoint, "'") 
+  }
+
+  expdata <- dbGetQuery(con, expquery)
+
+  if (db %in% c("cytotox", "enzymes")) {
+    controlquery <- paste0("SELECT type, response FROM controls ",
+      " WHERE plate=", id)
+    controldata <- dbGetQuery(con, controlquery)
+  }
+
+  op <- par(ask=TRUE)
+  on.exit(par(op))
+
+  if (db %in% c("cytotox","enzymes")) {
+    blinds <- subset(controldata, type == "blind")
+    controls <- subset(controldata, type == "control")
+    QA <- matrix(nrow = 2, ncol = 4,
+      dimnames = list(c("Blind", "Control (conc = 0)"),
+                      c("Number", "Mean", "Std. Dev.", "% Std. Dev")))
+
+    QA[1, 1] <- length(blinds$response)
+    QA[1, 2] <- signif(mean(blinds$response), 2)
+    QA[1, 3] <- signif(sd(blinds$response), 2)
+    QA[1, 4] <- signif(QA[1, 3] * 100 / QA[1, 2], 2)
+  } else {
+    # Use raw response for ecotox
+    expdata$response <- expdata$raw_response
+    
+    if (nlevels(expdata$type) > 1) {
+      message("There are data for more than one type of raw response in your data.\n",
+              "The types are ", paste(levels(expdata$type), collapse = " and "), ".\n",
+              "You should choose one of these types using 'endpoint = \"$type\"'",
+              "in your call to checkexperiment\n",
+              "For now, we are continuing with the data for ", levels(expdata$type)[1])
     }
-
-    # Plot of dose response data
-    drdata <- expdata[c(2,4,6)]
-    drdata$substance <- factor(drdata$substance)
-    substances <- levels(drdata$substance)
-
-    lld <- log10(min(subset(drdata,conc!=0)$conc))
-    lhd <- log10(max(drdata$conc))
-
-    ylab <- if (db == "ecotox") endpoint
-            else responsename
-
-    plot(1,type="n",
-        xlim = c(lld - 0.5, lhd + 2),
-        ylim = range(expdata[responsename], na.rm = TRUE),
-        xlab = paste("decadic logarithm of the concentration in ",levels(expdata$unit)),
-        ylab = ylab)
-
-    drdatalist <- split(drdata,drdata$substance)
-
-    for (i in 1:length(drdatalist)) {
-        points(log10(drdatalist[[i]]$conc),drdatalist[[i]][[responsename]],col=i);
+    endpoint <- expdata$type[1]
+    expdata <- subset(expdata, type == endpoint)
+
+    controls <- subset(expdata, conc == 0)
+    expdata <- subset(expdata, conc != 0)
+
+    QA <- matrix(nrow = 1, ncol = 4,
+      dimnames = list(c("Control (conc = 0)"),
+                      c("Number", "Mean", "Std. Dev.", "% Std. Dev")))
+  }
+
+  numberOfControls <- length(controls$response)
+  QA["Control (conc = 0)", 1] <- numberOfControls
+  if (numberOfControls > 0) {
+    QA["Control (conc = 0)", 2] <- signif(mean(controls$response),2)
+    QA["Control (conc = 0)", 3] <- signif(sd(controls$response),2)
+    QA["Control (conc = 0)", 4] <- signif(QA["Control (conc = 0)", 3] * 100 /
+                                          QA["Control (conc = 0)", 2],2)
+  }
+
+  if (db == "ecotox") {
+    if (identical(as.character(levels(expdata$organism)), "Vibrio fischeri")) {
+      positive <- subset(expdata, substance == "Na Cl")
+      if (nrow(positive) > 0) {
+        QA <- rbind(QA,
+          c(nrow(positive),
+            signif(mean(positive$raw_response), 2),
+            signif(sd(positive$raw_response), 2),
+            signif(100 * sd(positive$raw_response) /
+            mean(positive$raw_response), 2)))
+
+            rownames(QA) <- c("Control (conc = 0)",
+                              "Positive control (Na Cl)")
+      }
+      expdata <- subset(expdata, substance != "Na Cl", drop = TRUE)
     }
-
-    legend("topright",substances, pch=1, col=1:length(substances), inset=0.05)
-    title(main=paste(levels(expdata$experimentator),
-        " - ",levels(expdata$type)))
+  }
+
+  if (length(expdata$experimentator) < 1) {
+    stop("There is no response data for ", exptype, " ",
+      id, " in database ", db, "\n")
+  }
+  exptypestring <- paste0(toupper(substring(exptype, 1, 1)),
+      substring(exptype, 2))
+  expdata$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$ok <- factor(expdata$ok)
+
+  # Info on the experiment
+  cat("\n",
+    exptypestring, id, "from database", db, ":\n\n",
+      "\tExperimentator(s):\t",levels(expdata$experimentator),"\n",
+      "\tType(s):\t\t",levels(expdata$type),"\n",
+      "\tPerformed on:\t\t",levels(expdata$performed),"\n",
+      "\tSubstance(s):\t\t",levels(expdata$substance),"\n",
+      "\tConcentration unit(s):\t",levels(expdata$unit),"\n",
+      "\tComment:\t\t",comment,"\n",
+      "\tOK Levels:\t\t",levels(expdata$ok),"\n\n")
+
+  print(QA)
+
+  # Control growth rate for Lemna and algae
+  if (endpoint %in% c("cell count", "frond area", "frond number")) {
+    duration <- as.numeric(unique(expdata$duration)) # in hours
+    if (length(duration) > 1) stop("More than one duration in the data")
+    response_0 <- unique(expdata$raw_0)
+    if (length(response_0) > 1) stop("More than one mean response at time 0 in the data")
+    t_days <- duration / 24
+    control_growth_rates <- (log(controls$response) - log(response_0)) / t_days
+    cat("\nMean growth rate in controls:\t", round(mean(control_growth_rates), 3), "per day\n")
+  }
+
+  # Box plot of control data
+  if (db == "ecotox") {
+      boxplot(controls$response,
+          names="controls",
+          ylab=endpoint,
+          ylim=range(controls$response, na.rm = TRUE),
+          boxwex=0.4,
+          main=paste("Plate ",id))
+  } else {
+      boxplot(blinds$response,controls$response,
+          names=c("blinds","controls"),
+          ylab="Response",
+          boxwex=0.4,
+          main=paste("Plate ",id))
+  }
+
+  # Plot of dose response data
+  drdata <- expdata[c(2,4,6)]
+  drdata$substance <- factor(drdata$substance)
+  substances <- levels(drdata$substance)
+
+  lld <- log10(min(subset(drdata,conc!=0)$conc))
+  lhd <- log10(max(drdata$conc))
+
+  ylab <- if (db == "ecotox") endpoint
+          else responsename
+
+  plot(1,type="n",
+      xlim = c(lld - 0.5, lhd + 2),
+      ylim = range(expdata[responsename], na.rm = TRUE),
+      xlab = paste("decadic logarithm of the concentration in ",levels(expdata$unit)),
+      ylab = ylab)
+
+  drdatalist <- split(drdata,drdata$substance)
+
+  for (i in 1:length(drdatalist)) {
+      points(log10(drdatalist[[i]]$conc),drdatalist[[i]][[responsename]],col=i);
+  }
+
+  legend("topright",substances, pch=1, col=1:length(substances), inset=0.05)
+  title(main=paste(levels(expdata$experimentator),
+      " - ",levels(expdata$type)))
 }
diff --git a/R/checkplate.R b/R/checkplate.R
index 0a56e44..1421179 100644
--- a/R/checkplate.R
+++ b/R/checkplate.R
@@ -1,4 +1,4 @@
-checkplate <- function(id, db = "cytotox")
+checkplate <- function(id, db = c("cytotox", "enzymes"))
 {
-    checkexperiment(id, db = db)
+  checkexperiment(id, db = db)
 }
diff --git a/R/checksubstance.R b/R/checksubstance.R
index f22d4e2..e74ad21 100644
--- a/R/checksubstance.R
+++ b/R/checksubstance.R
@@ -1,97 +1,95 @@
-checksubstance <- function(substance, db = "cytotox", experimentator = "%",
-        celltype = "%", enzymetype = "%", organism = "%",
-        endpoint = "%",
-        whereClause = "1", ok= "%")
+checksubstance <- function(substance, 
+  db = c("cytotox", "enzymes", "ecotox"), 
+  experimentator = "%",
+  celltype = "%", enzymetype = "%", organism = "%",
+  endpoint = "%",
+  whereClause = "1", ok= "%")
 {
-    databases <- data.frame(
-        responsename=c("viability","activity","response"),
-        testtype=c("celltype","enzyme","organism"),
-        exptype=c("plate","plate","experiment"))
-    rownames(databases) <- c("cytotox","enzymes","ecotox")
+  db = match.arg(db)
 
-    if (!(db %in% rownames(databases))) stop("Database is not supported")
+  databases <- data.frame(
+    responsename = c("viability", "activity", "raw_response"),
+    testtype = c("celltype", "enzyme", "organism"),
+    exptype = c("plate", "plate", "experiment"),
+    row.names = c("cytotox", "enzymes", "ecotox"),
+    stringsAsFactors = FALSE)
 
-    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.")
-    }
+  con <- dbConnect(odbc(), "cytotox", database = db)
 
-    responsename = as.character(databases[db,1])
-    testtype = as.character(databases[db,2])
-    exptype = as.character(databases[db,3])
+  responsename <- databases[db, 1]
+  testtype <- databases[db, 2]
+  exptype <- databases[db, 3]
 
-    if (db == "cytotox") {
-        type <- celltype
-    }
-    if (db == "enzymes") {
-        type <- enzymetype
-    }
-    if (db == "ecotox") {
-        type <- organism
-    }
+  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",
-        " FROM ",db," WHERE substance LIKE '",
-        substance,"' AND experimentator LIKE '",
-        experimentator,"' AND ",testtype," LIKE '",
-        type,"' AND ",
-        whereClause," AND ok LIKE '",ok,"'",
-                sep = "")
+  query <- paste("SELECT experimentator,substance,",
+      testtype, ",", exptype, ",conc,unit,",responsename,",ok",
+      " FROM ",db," WHERE substance LIKE '",
+      substance,"' AND experimentator LIKE '",
+      experimentator,"' AND ",testtype," LIKE '",
+      type,"' AND ",
+      whereClause," AND ok LIKE '",ok,"'",
+              sep = "")
 
-    if (db == "ecotox") {
-        query <- paste(query, " AND type LIKE '",
-                endpoint, "'", sep = "")
-    }
+  if (db == "ecotox") {
+      query <- paste(query, " AND type LIKE '",
+              endpoint, "'", sep = "")
+  }
 
-    data <- RODBC::sqlQuery(channel,query)
-    RODBC::odbcClose(channel)
+  data <- dbGetQuery(con, query)
 
-    if (length(data$experimentator) < 1) {
-        stop(paste("\nNo response data for",substance,"in database",
-                db,"found with these parameters\n"))
-    }
+  if (length(data$experimentator) < 1) {
+      stop(paste("\nNo response data for",substance,"in database",
+              db,"found with these parameters\n"))
+  }
 
-    data$experimentator <- factor(data$experimentator)
-    data$substance <- factor(data$substance)
-    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$ok <- factor(data$ok)
+  data$experimentator <- factor(data$experimentator)
+  data$substance <- factor(data$substance)
+  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$ok <- factor(data$ok)
 
-    if (length(experiments)>6) {
-        palette(rainbow(length(experiments)))
-    }
+  if (length(experiments)>6) {
+      palette(rainbow(length(experiments)))
+  }
 
-    plot(log10(data$conc),data[[responsename]],
-        xlim=c(-2.5, 4.5),
-        ylim= range(data[[responsename]], na.rm = TRUE),
-        xlab=paste("decadic logarithm of the concentration in ",levels(data$unit)),
-        ylab=responsename)
+  plot(log10(data$conc),data[[responsename]],
+      xlim=c(-2.5, 4.5),
+      ylim= range(data[[responsename]], na.rm = TRUE),
+      xlab=paste("decadic logarithm of the concentration in ",levels(data$unit)),
+      ylab=responsename)
 
-    explist <- split(data,data[[exptype]])
+  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)))
+  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)),
-        substring(exptype,2), sep = "")
-    experimentators <- paste(levels(data$experimentator), collapse = " ")
-    types <- paste(levels(data$type), collapse = " ")
-    experiments <- paste(levels(data[[exptype]]), collapse = " ")
-    class(experiments)
-    cat("\n\tSubstanz:\t\t",substance,"\n",
-        "\tExperimentator(s):\t", experimentators,"\n",
-        "\tType(s): \t\t",types,"\n",
-        "\tEndpoint: \t\t",endpoint,"\n",
-        "\t", exptypename, "(s):\t\t",experiments,"\n\n", sep = "")
+  exptypename <-  paste(toupper(substring(exptype,1,1)),
+      substring(exptype,2), sep = "")
+  experimentators <- paste(levels(data$experimentator), collapse = " ")
+  types <- paste(levels(data$type), collapse = " ")
+  experiments <- paste(levels(data[[exptype]]), collapse = " ")
+  class(experiments)
+  cat("\n\tSubstanz:\t\t",substance,"\n",
+      "\tExperimentator(s):\t", experimentators,"\n",
+      "\tType(s): \t\t",types,"\n",
+      "\tEndpoint: \t\t",endpoint,"\n",
+      "\t", exptypename, "(s):\t\t",experiments,"\n\n", sep = "")
 }
diff --git a/R/drdata.R b/R/drdata.R
index b7e4761..8f18ebd 100644
--- a/R/drdata.R
+++ b/R/drdata.R
@@ -3,44 +3,50 @@ drdata <- function(substances, experimentator = "%", db = "cytotox",
     organism = "Vibrio fischeri", endpoint = "Luminescence", whereClause = "1",
     ok = "'ok','no fit'")
 {
-  if (requireNamespace("RODBC")) {
-    channel <- RODBC::odbcConnect(db,uid="cytotox",pwd="cytotox",case="tolower")
-    slist <- paste(substances,collapse="','")
-    if (db == "cytotox") {
-        experimenttype <- "plate"
-        responsetype <- "viability"
-        testtype <- "celltype"
-        type <- celltype
-    } else {
-        if (db == "enzymes") {
-            experimenttype <- "plate"
-            responsetype <- "activity"
-            testtype <- "enzyme"
-            type <- enzymetype
-        } else {
-            experimenttype <- "experiment"
-            responsetype <- "response"
-            testtype <- "organism"
-            type <- organism
-        }
-    }
+  # Connect to the correct database via the DSN
+  con <- dbConnect(odbc(), "cytotox", database = db)
 
-    query <- paste("SELECT conc,",responsetype,", unit, experimentator, ",
-        experimenttype, ", substance, ", testtype,
-        ", ok FROM ", db, " WHERE substance IN ('",
-        slist,"') AND experimentator LIKE '",
-        experimentator,"' AND ",testtype," LIKE '",
-        type,"' AND ",
-        whereClause," AND ok in (",
-        ok,")",sep="")
-    if (db == "ecotox") query <- paste(query," AND type LIKE '",endpoint,"'",sep="")
-    data <- RODBC::sqlQuery(channel,query)
-    RODBC::odbcClose(channel)
-    names(data)[[1]] <- "dose"
-    names(data)[[2]] <- "response"
-    data$substance <- factor(data$substance,levels=substances)
-    return(data)
+  # Construct the query
+  slist <- paste(substances, collapse = "','")
+  if (db == "cytotox") {
+    experimenttype <- "plate"
+    responsetype <- "viability"
+    testtype <- "celltype"
+    type <- celltype
   } else {
-    stop("For this function, the RODBC package has to be installed and configured.")
+    if (db == "enzymes") {
+      experimenttype <- "plate"
+      responsetype <- "activity"
+      testtype <- "enzyme"
+      type <- enzymetype
+    } else {
+      experimenttype <- "experiment"
+      responsetype <- "response"
+      testtype <- "organism"
+      type <- organism
+    }
   }
+
+  query <- paste0(
+    "SELECT conc,", responsetype, ", unit, experimentator, ",
+            experimenttype, ", substance, ", testtype,
+            ", ok ",
+      "FROM ", db, " ",
+      "WHERE ",
+        "substance IN ('", slist, "') AND ",
+        "experimentator LIKE '", experimentator,"' AND ",
+        testtype, " LIKE '", type, "' AND ",
+        whereClause, " AND ",
+        "ok in (", ok, ")")
+
+  if (db == "ecotox") query <- paste0(query, " AND type LIKE '", endpoint, "'")
+
+  # Get the data, format and return them
+  data <- dbGetQuery(con, query)
+
+  names(data)[[1]] <- "dose"
+  names(data)[[2]] <- "response"
+  data$substance <- factor(data$substance, levels = substances)
+
+  return(data)
 }