diff options
| -rw-r--r-- | R/checkexperiment.R | 37 |
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) |