Changeset: ff8b818a5a3c for MonetDB
URL: http://dev.monetdb.org/hg/MonetDB?cmd=changeset;node=ff8b818a5a3c
Added Files:
clients/R/MonetDB.R/man/dbApply.Rd
Modified Files:
clients/R/MonetDB.R/NEWS
clients/R/MonetDB.R/R/control.R
clients/R/MonetDB.R/R/dbapply.R
clients/R/MonetDB.R/R/dbi.R
clients/R/MonetDB.R/R/dplyr.R
Branch: default
Log Message:
R Connector: Documentation for dbApply() and CRAN checks
diffs (123 lines):
diff --git a/clients/R/MonetDB.R/NEWS b/clients/R/MonetDB.R/NEWS
--- a/clients/R/MonetDB.R/NEWS
+++ b/clients/R/MonetDB.R/NEWS
@@ -1,11 +1,10 @@
-0.9.9
-- dbWriteTable now quotes table/column names if necessary, and outputs
warnings if it did
-- New dbApply function to automatically create embedded R functions in MonetDB
-
0.9.8
- Added support for esoteric data types such as MONTH_INTERVAL (Thanks, Roman)
- Cleaned up SQL to R type mapping (we had this twice)
- Now creating actual R integers if data fits
+- dbWriteTable now quotes table/column names if necessary, and outputs
warnings if it did
+- New dbApply function to automatically create embedded R functions in MonetDB
+- Fixes for dplyr backend
0.9.7
- Fixed crash on Windows (Sorry, everyone)
diff --git a/clients/R/MonetDB.R/R/control.R b/clients/R/MonetDB.R/R/control.R
--- a/clients/R/MonetDB.R/R/control.R
+++ b/clients/R/MonetDB.R/R/control.R
@@ -5,7 +5,7 @@ monetdb.server.start <-
if( !file.exists( bat.file ) ) stop( paste( bat.file , "does not exist.
Run monetdb.server.setup() to create a batch file." ) )
# uugly, find path of pid file again by parsing shell script.
- sc <- read.table(bat.file,sep="\n",stringsAsFactors=F)
+ sc <- utils::read.table(bat.file,sep="\n",stringsAsFactors=F)
pidfile <- substring(sc[[2,1]],11)
# run script
diff --git a/clients/R/MonetDB.R/R/dbapply.R b/clients/R/MonetDB.R/R/dbapply.R
--- a/clients/R/MonetDB.R/R/dbapply.R
+++ b/clients/R/MonetDB.R/R/dbapply.R
@@ -8,11 +8,12 @@
# TODO: optionally inline serialized context for remote dbs
res <- tempfile()
- save(list=vars,file=res,envir=environment(name),compress=T)
+ save(list=vars,file=res,envir=environment(name), compress=T)
return(res)
}
-if (is.null(getGeneric("dbApply"))) setGeneric("dbApply", function(conn, ...)
+# TOOD: support running this on query results?
+if (is.null(getGeneric("dbApply"))) setGeneric("dbApply", function(conn,
table, rettype, fun)
standardGeneric("dbApply"))
setMethod("dbApply", signature(conn="MonetDBConnection"), def=function(conn,
table, rettype, fun) {
diff --git a/clients/R/MonetDB.R/R/dbi.R b/clients/R/MonetDB.R/R/dbi.R
--- a/clients/R/MonetDB.R/R/dbi.R
+++ b/clients/R/MonetDB.R/R/dbi.R
@@ -22,8 +22,8 @@ setMethod("dbUnloadDriver", "MonetDBDriv
setMethod("dbGetInfo", "MonetDBDriver", def=function(dbObj, ...)
list(name="MonetDBDriver",
- driver.version=packageVersion("MonetDB.R"),
- DBI.version=packageVersion("DBI"),
+ driver.version=utils::packageVersion("MonetDB.R"),
+ DBI.version=utils::packageVersion("DBI"),
client.version="NA",
max.connections=125) # R can only handle 128 connections, three of
which are pre-allocated
)
@@ -624,7 +624,7 @@ monet.read.csv <- monetdb.read.csv <- fu
delim=",", newline="\\n",
quote="\"", create=TRUE, ...){
if (length(na.strings)>1) stop("na.strings must be of length 1")
- headers <- lapply(files, read.csv, sep=delim, na.strings=na.strings,
quote=quote, nrows=nrow.check,
+ headers <- lapply(files, utils::read.csv, sep=delim, na.strings=na.strings,
quote=quote, nrows=nrow.check,
...)
if (!missing(nrows)) {
diff --git a/clients/R/MonetDB.R/R/dplyr.R b/clients/R/MonetDB.R/R/dplyr.R
--- a/clients/R/MonetDB.R/R/dplyr.R
+++ b/clients/R/MonetDB.R/R/dplyr.R
@@ -14,7 +14,8 @@ src_translate_env.src_monetdb <- functio
sd = dplyr::sql_prefix("STDDEV_SAMP"),
var = dplyr::sql_prefix("VAR_SAMP"),
median = dplyr::sql_prefix("MEDIAN"),
- n_distinct = function(x) {build_sql(sql("count(distinct "),x,sql(")"))}
+ n_distinct = function(x) {dplyr::build_sql(dplyr::sql("count(distinct
"),
+ x, dplyr::sql(")"))}
)
)
}
diff --git a/clients/R/MonetDB.R/man/dbApply.Rd
b/clients/R/MonetDB.R/man/dbApply.Rd
new file mode 100644
--- /dev/null
+++ b/clients/R/MonetDB.R/man/dbApply.Rd
@@ -0,0 +1,34 @@
+\name{dbApply}
+\alias{dbApply}
+\alias{dbApply,MonetDBConnection-method}
+
+\title{
+ Apply a R function to a MonetDB table.
+}
+\description{
+\code{dbApply} is used to switch the data from the normal auto-commiting mode
into transactional mode. Here, changes to the database will not be permanent
until \code{dbCommit} is called. If the changes are not to be kept around, you
can use \code{dbRollback} to undo all the changes since \code{dbTransaction}
was called.
+
+}
+\usage{
+ dbApply(conn, table, rettype, fun)
+}
+\arguments{
+ \item{conn}{A MonetDB.R database connection. Created using
\code{\link[DBI]{dbConnect}}
+ with the \code{\link[MonetDB.R]{MonetDB.R}} database driver.}
+ \item{table}{A MonetDB database table. Can also be a view or temporary
table.}
+ \item{rettype}{SQL type the function returns. Case-insensitive. For
example, \code{INTEGER}, \code{DOUBLE}, \code{STRING} etc.}
+ \item{fun}{A R function to be run on the database table. The function gets
passed a single \code{data.frame} argument which represents the database table.
The function needs to return a single vector (for now).}
+ }
+\value{
+ Returns the result of the function applied to the database table.
+}
+\examples{
+\dontrun{
+conn <- dbConnect(MonetDB.R(), "demo")
+data(mtcars)
+dbWriteTable(conn, "mtcars", mtcars)
+
+mpgplus42 <- dbApply(conn, "mtcars", "double", function(d) {
+ d$mpg + 42
+})
+}}
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