Switch to odbc, reformattting of code

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 Also remove outdated hyperlinks from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

1 files changed, 78 insertions, 80 deletions

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 = "")
 }