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-rw-r--r--ChangeLog7
-rw-r--r--DESCRIPTION32
-rw-r--r--NAMESPACE8
-rw-r--r--R/checkexperiment.R14
-rw-r--r--R/checksubstance.R10
-rw-r--r--R/drdata.R16
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+Description: A somewhat outdated package of basic and easy-to-use functions for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.")
+ }
}

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