Maintenance changes for the release of 0.6.4v0.6.4

6 files changed, 51 insertions, 36 deletions

diff --git a/ChangeLog b/ChangeLog
index c29f20a..4ccb21e 100644
--- a/ChangeLog
+++ b/ChangeLog
@@ -1,3 +1,10 @@
+2015-10-07  Johannes Ranke
+
+	* Suggest RODBC instead of depending on it, as it is not available
+	  on all CRAN check systems.
+
+	* Adress various NOTES given by R CMD check
+
 2014-07-28  Johannes Ranke
 
 	* DESCRIPTION: New verson 0.6.3
diff --git a/DESCRIPTION b/DESCRIPTION
index d45a28e..c98693e 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,25 +1,27 @@
 Package: drfit
 Version: 0.6.4
-Date: 2015-07-02
-Title: Dose-response data evaluation
+Date: 2015-10-07
+Title: Dose-Response Data Evaluation
 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre"), 
                     email = "jranke@uni-bremen.de"))
-Imports: graphics, grDevices, MASS, RODBC, drc
-Description: drfit provides basic and easy-to-use functions for fitting
-	dose-response curves to dose-response data, calculating some
-	(eco)toxicological parameters and plotting the results. Functions that are
-	fitted are the cumulative density function of the lognormal distribution
-	(probit fit), of the logistic distribution (logit fit), of the weibull
-	distribution (weibull fit) and a linear-logistic model ("linlogit" fit),
-	derived from the latter, which is used to describe data showing stimulation
-	at low doses (hormesis). In addition, functions checking, plotting and
-	retrieving dose-response data retrieved from a database accessed via RODBC
-	are included. As an alternative to the original fitting methods, the
-  algorithms from the drc package can be used.
+Imports: graphics, grDevices, MASS, drc
+Suggests: RODBC
+Description: A somewhat outdated package of basic and easy-to-use functions for
+  fitting dose-response curves to continuous dose-response data, calculating some
+  (eco)toxicological parameters and plotting the results. Please consider using
+  the more powerful and actively developed 'drc' package.  Functions that are
+  fitted are the cumulative density function of the lognormal distribution
+  (probit fit), of the logistic distribution (logit fit), of the weibull
+  distribution (weibull fit) and a linear-logistic model ("linlogit" fit),
+  derived from the latter, which is used to describe data showing stimulation at
+  low doses (hormesis). In addition, functions checking, plotting and retrieving
+  dose-response data retrieved from a database accessed via RODBC are included.
+  As an alternative to the original fitting methods, the algorithms from the drc
+  package can be used.
 Encoding: latin1
 License: GPL (>= 2)
 LazyLoad: yes
 LazyData: yes
 URL: http://www.r-project.org, 
 	http://www.uft.uni-bremen.de/chemie/ranke?page=drfit,
-	http://kriemhild.uft.uni-bremen.de/viewcvs/?root=drfit
+	http://cgit.jrwb.de/drfit/
diff --git a/NAMESPACE b/NAMESPACE
index e2772d7..91a4d4a 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,16 +1,10 @@
-# Default NAMESPACE created by R
-# Remove the previous line if you edit this file
-
-# Export all names
 exportPattern(".")
 
-# Import all packages listed as Imports or Depends
 import(
   graphics,
   grDevices,
   stats,
-  MASS,
-  RODBC
+  MASS
 )
 
 importFrom("drc", drm, ED, LN.2, LL.2, BC.4, W1.2)
diff --git a/R/checkexperiment.R b/R/checkexperiment.R
index 2bf0ce7..8c2f472 100644
--- a/R/checkexperiment.R
+++ b/R/checkexperiment.R
@@ -9,7 +9,11 @@ checkexperiment <- function(id, db = "ecotox", endpoint = "%")
 
     if (!(db %in% rownames(databases))) stop("Database is not supported")
 
-    channel <- odbcConnect(db,uid="cytotox",pwd="cytotox",case="tolower")
+    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.")
+    }
 
 
     responsename = as.character(databases[db,1])
@@ -19,7 +23,7 @@ checkexperiment <- function(id, db = "ecotox", endpoint = "%")
     exptable <- paste(exptype, "s", sep="")
     commentquery <- paste("SELECT comment FROM ", exptable ,
         " WHERE ", exptype, " = ", id)
-    commentdata <- sqlQuery(channel,commentquery)
+    commentdata <- RODBC::sqlQuery(channel,commentquery)
     comment <- as.character(commentdata[[1]])
         
     expquery <- paste("SELECT experimentator,substance, ",
@@ -32,15 +36,15 @@ checkexperiment <- function(id, db = "ecotox", endpoint = "%")
                 endpoint, "'", sep = "")
     }
 
-    expdata <- sqlQuery(channel,expquery)
+    expdata <- RODBC::sqlQuery(channel,expquery)
 
     if (db %in% c("cytotox","enzymes")) {
         controlquery <- paste("SELECT type,response FROM controls 
             WHERE plate=",id)
-        controldata <- sqlQuery(channel,controlquery)
+        controldata <- RODBC::sqlQuery(channel,controlquery)
     }
 
-    odbcClose(channel)
+    RODBC::odbcClose(channel)
 
     op <- par(ask=TRUE)
     on.exit(par(op))
diff --git a/R/checksubstance.R b/R/checksubstance.R
index b50c3da..3e07f92 100644
--- a/R/checksubstance.R
+++ b/R/checksubstance.R
@@ -11,7 +11,11 @@ checksubstance <- function(substance, db = "cytotox", experimentator = "%",
 
     if (!(db %in% rownames(databases))) stop("Database is not supported")
 
-    channel <- odbcConnect(db,uid="cytotox",pwd="cytotox",case="tolower")
+    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.")
+    }
 
     responsename = as.character(databases[db,1])
     testtype = as.character(databases[db,2])
@@ -41,8 +45,8 @@ checksubstance <- function(substance, db = "cytotox", experimentator = "%",
                 endpoint, "'", sep = "")
     }
 
-    data <- sqlQuery(channel,query)
-    odbcClose(channel)
+    data <- RODBC::sqlQuery(channel,query)
+    RODBC::odbcClose(channel)
 
     if (length(data$experimentator) < 1) {
         stop(paste("\nNo response data for",substance,"in database",
diff --git a/R/drdata.R b/R/drdata.R
index 15c61ac..0bf9597 100644
--- a/R/drdata.R
+++ b/R/drdata.R
@@ -1,9 +1,10 @@
 drdata <- function(substances, experimentator = "%", db = "cytotox",
-    celltype="IPC-81",enzymetype="AChE",
-    organism="Vibrio fischeri",endpoint="Luminescence",whereClause="1",
-    ok="'ok','no fit'")
+    celltype = "IPC-81", enzymetype = "AChE",
+    organism = "Vibrio fischeri", endpoint = "Luminescence", whereClause = "1",
+    ok = "'ok','no fit'")
 {
-    channel <- odbcConnect(db,uid="cytotox",pwd="cytotox",case="tolower")
+  if (requireNamespace("RODBC")) {
+    channel <- RODBC::odbcConnect(db,uid="cytotox",pwd="cytotox",case="tolower")
     slist <- paste(substances,collapse="','")
     if (db == "cytotox") {
         responsetype <- "viability"
@@ -29,10 +30,13 @@ drdata <- function(substances, experimentator = "%", db = "cytotox",
         whereClause," AND ok in (",
         ok,")",sep="")
     if (db == "ecotox") query <- paste(query," AND type LIKE '",endpoint,"'",sep="")
-    data <- sqlQuery(channel,query)
-    odbcClose(channel)
+    data <- RODBC::sqlQuery(channel,query)
+    RODBC::odbcClose(channel)
     names(data)[[1]] <- "dose"
     names(data)[[2]] <- "response"
     data$substance <- factor(data$substance,levels=substances)
     return(data)
+  } else {
+    stop("For this function, the RODBC package has to be installed and configured.")
+  }
 }