aboutsummaryrefslogtreecommitdiff
path: root/R/checkexperiment.R
diff options
context:
space:
mode:
authorJohannes Ranke <jranke@uni-bremen.de>2017-03-24 15:24:04 +0100
committerJohannes Ranke <jranke@uni-bremen.de>2017-03-24 15:24:04 +0100
commit22c11d5dbc118881f9cfd7c9c2ac9711295a0f16 (patch)
treea2c88069b82633027047c60bf656e53c4b561182 /R/checkexperiment.R
parentb05f8438729e8070f4e0cbbf628bbbcbbe3f1a7a (diff)
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
Diffstat (limited to 'R/checkexperiment.R')
-rw-r--r--R/checkexperiment.R30
1 files changed, 15 insertions, 15 deletions
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);
}

Contact - Imprint