Mean control growth rate, y axis labels

Also warn if there is more than one endpoint in the data, and restrict
the data to the first endpoint (e.g. frond area if there is also frond
number data).

1 files changed, 32 insertions, 5 deletions

diff --git a/R/checkexperiment.R b/R/checkexperiment.R
index 02ed706..58868da 100644
--- a/R/checkexperiment.R
+++ b/R/checkexperiment.R
@@ -26,13 +26,12 @@ checkexperiment <- function(id, db = "ecotox", endpoint = "%")
     comment <- as.character(commentdata[[1]])
 
     expquery <- paste("SELECT experimentator, substance, ",
-        testtype, ", conc, unit,", responsename, ", performed, ok",
+        testtype, ", conc, unit,", responsename, ", type, raw_0, duration, performed, ok",
         " FROM ",db," WHERE ",exptype,"=", id,
             sep = "")
 
     if (db == "ecotox") {
-        expquery <- paste(expquery, " AND type LIKE '",
-                endpoint, "'", sep = "")
+        expquery <- paste0(expquery, " AND type LIKE '", endpoint, "'") 
     }
 
     expdata <- RODBC::sqlQuery(channel,expquery)
@@ -62,6 +61,16 @@ checkexperiment <- function(id, db = "ecotox", endpoint = "%")
     } 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)
@@ -112,6 +121,7 @@ checkexperiment <- function(id, db = "ecotox", endpoint = "%")
     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",
@@ -123,10 +133,23 @@ checkexperiment <- function(id, db = "ecotox", endpoint = "%")
 
     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="Response",
+            ylab=endpoint,
             ylim=range(controls$response, na.rm = TRUE),
             boxwex=0.4,
             main=paste("Plate ",id))
@@ -138,6 +161,7 @@ checkexperiment <- function(id, db = "ecotox", endpoint = "%")
             main=paste("Plate ",id))
     }
 
+    # Plot of dose response data
     drdata <- expdata[c(2,4,6)]
     drdata$substance <- factor(drdata$substance)
     substances <- levels(drdata$substance)
@@ -145,11 +169,14 @@ checkexperiment <- function(id, db = "ecotox", endpoint = "%")
     lld <- log10(min(subset(drdata,conc!=0)$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 = responsename)
+        ylab = ylab)
 
     drdatalist <- split(drdata,drdata$substance)