From 22c11d5dbc118881f9cfd7c9c2ac9711295a0f16 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Fri, 24 Mar 2017 15:24:04 +0100
Subject: 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
---
 R/checkexperiment.R | 30 +++++++++++++++---------------
 1 file changed, 15 insertions(+), 15 deletions(-)

(limited to 'R/checkexperiment.R')

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);
     }
-- 
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