[Dplr-commits] r764 - in pkg/dplR: . R man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Apr 4 14:48:38 CEST 2014
Author: mvkorpel
Date: 2014-04-04 14:48:38 +0200 (Fri, 04 Apr 2014)
New Revision: 764
Modified:
pkg/dplR/ChangeLog
pkg/dplR/DESCRIPTION
pkg/dplR/R/write.compact.R
pkg/dplR/R/write.crn.R
pkg/dplR/R/write.rwl.R
pkg/dplR/R/write.tridas.R
pkg/dplR/R/write.tucson.R
pkg/dplR/man/print.redfit.Rd
pkg/dplR/man/write.compact.Rd
pkg/dplR/man/write.crn.Rd
pkg/dplR/man/write.rwl.Rd
pkg/dplR/man/write.tridas.Rd
pkg/dplR/man/write.tucson.Rd
Log:
* The write.* functions now return the name of the output file. This
is useful if the fname argument is a call that creates the file
name, e.g. tempfile(). Previously there was (practically) no return
value. This should not break anything.
* Examples in the write.*.Rd files were modified to use tempfile()s
instead of writing to the working directory, which was potentially
harmful.
Modified: pkg/dplR/ChangeLog
===================================================================
--- pkg/dplR/ChangeLog 2014-04-04 09:13:17 UTC (rev 763)
+++ pkg/dplR/ChangeLog 2014-04-04 12:48:38 UTC (rev 764)
@@ -69,8 +69,8 @@
- New wrapper to plot rwl objects. This is setting the
stage for having plot, summary, etc. methods for rwl
objects. There are still several things to work on. Like
- setting the class() of rwl data objects via read.rwl (and in
- the onboard data sets). And will this class change break any
+ setting the class() of rwl data objects via read.rwl (and in
+ the onboard data sets). And will this class change break any
existing functions?
File: spag.plot.R
@@ -106,6 +106,16 @@
computed
- Optimizations
+Files: write.compact.R, write.crn.R,
+write.rwl.R, write.tridas.R, write.tucson.R
+-------------------------------------------
+
+- The write.* functions now return the name of the output file.
+ Previously it was documented that there was no return value.
+- Examples in the corresponding .Rd files were modified to use
+ tempfile()s instead of writing to the working directory, which was
+ potentially harmful.
+
* CHANGES IN dplR VERSION 1.5.9
Files: dplR.h, rcompact.c, redfit.c
Modified: pkg/dplR/DESCRIPTION
===================================================================
--- pkg/dplR/DESCRIPTION 2014-04-04 09:13:17 UTC (rev 763)
+++ pkg/dplR/DESCRIPTION 2014-04-04 12:48:38 UTC (rev 764)
@@ -3,7 +3,7 @@
Type: Package
Title: Dendrochronology Program Library in R
Version: 1.6.0
-Date: 2014-04-02
+Date: 2014-04-04
Authors at R: c(person("Andy", "Bunn", role = c("aut", "cph",
"cre", "trl"), email = "andy.bunn at wwu.edu"), person("Mikko",
"Korpela", role = c("aut", "trl")), person("Franco", "Biondi",
Modified: pkg/dplR/R/write.compact.R
===================================================================
--- pkg/dplR/R/write.compact.R 2014-04-04 09:13:17 UTC (rev 763)
+++ pkg/dplR/R/write.compact.R 2014-04-04 12:48:38 UTC (rev 764)
@@ -102,4 +102,5 @@
cat(line.str, line.term, file=rwl.out, sep="")
}
}
+ fname
}
Modified: pkg/dplR/R/write.crn.R
===================================================================
--- pkg/dplR/R/write.crn.R 2014-04-04 09:13:17 UTC (rev 763)
+++ pkg/dplR/R/write.crn.R 2014-04-04 12:48:38 UTC (rev 764)
@@ -129,4 +129,5 @@
dec.str <- c(hdr, dec.str)
}
cat(dec.str, file = fname, sep = "\n", append=append)
+ fname
}
Modified: pkg/dplR/R/write.rwl.R
===================================================================
--- pkg/dplR/R/write.rwl.R 2014-04-04 09:13:17 UTC (rev 763)
+++ pkg/dplR/R/write.rwl.R 2014-04-04 12:48:38 UTC (rev 764)
@@ -1,6 +1,8 @@
write.rwl <-
function(rwl.df, fname, format=c("tucson", "compact", "tridas"), ...)
{
+ ## NOTE: This function is documented to return fname. Therefore,
+ ## each branch of the switch must return fname.
switch(match.arg(format),
tucson = write.tucson(rwl.df, fname, ...),
compact = write.compact(rwl.df, fname, ...),
Modified: pkg/dplR/R/write.tridas.R
===================================================================
--- pkg/dplR/R/write.tridas.R 2014-04-04 09:13:17 UTC (rev 763)
+++ pkg/dplR/R/write.tridas.R 2014-04-04 12:48:38 UTC (rev 764)
@@ -1063,4 +1063,5 @@
}
}
doc.closeTag() # </project>
+ fname
}
Modified: pkg/dplR/R/write.tucson.R
===================================================================
--- pkg/dplR/R/write.tucson.R 2014-04-04 09:13:17 UTC (rev 763)
+++ pkg/dplR/R/write.tucson.R 2014-04-04 12:48:38 UTC (rev 764)
@@ -242,4 +242,5 @@
file = rwl.out, sep="")
}
}
+ fname
}
Modified: pkg/dplR/man/print.redfit.Rd
===================================================================
--- pkg/dplR/man/print.redfit.Rd 2014-04-04 09:13:17 UTC (rev 763)
+++ pkg/dplR/man/print.redfit.Rd 2014-04-04 12:48:38 UTC (rev 764)
@@ -75,8 +75,9 @@
redf <- redfit(x[idx], t[idx], "time",
nsim = 100, iwin = 0, ofac = 1, n50 = 1)
print(redf)
-f <- tempfile()
+f <- tempfile(fileext=".csv")
print(redf, csv.out = TRUE, file = f)
redftable <- read.csv(f)
+unlink(f) # remove the file
}
\keyword{ print }
Modified: pkg/dplR/man/write.compact.Rd
===================================================================
--- pkg/dplR/man/write.compact.Rd 2014-04-04 09:13:17 UTC (rev 763)
+++ pkg/dplR/man/write.compact.Rd 2014-04-04 12:48:38 UTC (rev 764)
@@ -47,14 +47,16 @@
list of the renamings (see Arguments).
}
\value{
- None. Invoked for side effect (file is written).
- }
+ \code{\var{fname}}
+}
\author{ Mikko Korpela, based on write.tucson by Andy Bunn }
\seealso{ \code{\link{write.rwl}}, \code{\link{write.tucson}},
\code{\link{write.tridas}}, \code{\link{read.compact}}
}
\examples{data(co021)
-write.compact(rwl.df = co021, fname = "tmp.rwl", append = FALSE,
- prec = 0.001)
+fname <- write.compact(rwl.df = co021,
+ fname = tempfile(fileext=".rwl"),
+ append = FALSE, prec = 0.001)
+unlink(fname) # remove the file
}
\keyword{ IO }
Modified: pkg/dplR/man/write.crn.Rd
===================================================================
--- pkg/dplR/man/write.crn.Rd 2014-04-04 09:13:17 UTC (rev 763)
+++ pkg/dplR/man/write.crn.Rd 2014-04-04 12:48:38 UTC (rev 764)
@@ -70,15 +70,15 @@
than crn files in terms of usefulness on the \acronym{ITRDB}.
}
\value{
- None. Invoked for side effect (file is written).
- }
+ \code{\var{fname}}
+}
\author{ Andy Bunn. Patched and improved by Mikko Korpela. }
\seealso{ \code{\link{chron}}, \code{\link{read.crn}}
}
\examples{data(ca533)
ca533.rwi <- detrend(rwl = ca533, method = "ModNegExp")
ca533.crn <- chron(ca533.rwi, prefix = "CAM")
-write.crn(ca533.crn, "tmp.crn")
+fname1 <- write.crn(ca533.crn, tempfile(fileext=".crn"))
## Put the standard and residual chronologies in a single file
## with ITRDB header info on top. Not reccomended.
ca533.crn <- chron(ca533.rwi, prefix = "CAM", prewhiten = TRUE)
@@ -88,7 +88,9 @@
long = -11813, first.yr = 626, last.yr = 1983,
lead.invs = "Donald A. Graybill, V.C. LaMarche, Jr.",
comp.date = "Nov1983")
-write.crn(ca533.crn[, -2], "tmp.crn", header = ca533.hdr)
-write.crn(ca533.crn[, -1], "tmp.crn", append = TRUE)
+fname2 <- write.crn(ca533.crn[, -2], tempfile(fileext=".crn"),
+ header = ca533.hdr)
+write.crn(ca533.crn[, -1], fname2, append = TRUE)
+unlink(c(fname1, fname2)) # remove the files
}
\keyword{ IO }
Modified: pkg/dplR/man/write.rwl.Rd
===================================================================
--- pkg/dplR/man/write.rwl.Rd 2014-04-04 09:13:17 UTC (rev 763)
+++ pkg/dplR/man/write.rwl.Rd 2014-04-04 12:48:38 UTC (rev 764)
@@ -32,7 +32,7 @@
write operation.
}
\value{
- None. Invoked for side effect (file is written).
+ \code{\var{fname}}
}
\author{ Mikko Korpela }
\seealso{ \code{\link{write.crn}}, \code{\link{write.tucson}},
@@ -46,7 +46,9 @@
spp = "DOUGLAS FIR", elev = 2103, lat = 3712,
long = -10830, first.yr = 1400, last.yr = 1963,
lead.invs = "E. SCHULMAN", comp.date = "")
-write.rwl(rwl.df = co021, fname = "tmp.rwl", format = "tucson",
- header = co021.hdr, append = FALSE, prec = 0.001)
+fname <- write.rwl(rwl.df = co021, fname = tempfile(fileext=".rwl"),
+ format = "tucson", header = co021.hdr,
+ append = FALSE, prec = 0.001)
+unlink(fname) # remove the file
}
\keyword{ IO }
Modified: pkg/dplR/man/write.tridas.Rd
===================================================================
--- pkg/dplR/man/write.tridas.Rd 2014-04-04 09:13:17 UTC (rev 763)
+++ pkg/dplR/man/write.tridas.Rd 2014-04-04 12:48:38 UTC (rev 764)
@@ -335,7 +335,7 @@
}
-\value{ None. Invoked for side effect (file is written). }
+\value{ \code{\var{fname}} }
\references{ TRiDaS \enc{–}{--} The Tree Ring Data Standard,
\url{http://www.tridas.org/} }
@@ -363,11 +363,13 @@
data(ca533)
ca533.rwi <- detrend(rwl = ca533, method = "ModNegExp")
ca533.crn <- chron(ca533.rwi, prefix = "CAM", prewhiten = TRUE)
-write.tridas(crn = ca533.crn, fname = "tmp2.xml",
+fname <- write.tridas(crn = ca533.crn,
+ fname = tempfile(fileext=".xml"),
taxon = "Pinus longaeva D.K. Bailey",
project.info =
list(investigator = "Donald A. Graybill, V.C. LaMarche, Jr.",
title = "Campito Mountain", category = "",
period = "", type = "unknown"))
+unlink(fname) # remove the file
}
\keyword{ IO }
Modified: pkg/dplR/man/write.tucson.Rd
===================================================================
--- pkg/dplR/man/write.tucson.Rd 2014-04-04 09:13:17 UTC (rev 763)
+++ pkg/dplR/man/write.tucson.Rd 2014-04-04 12:48:38 UTC (rev 764)
@@ -93,8 +93,8 @@
incompatibility with other software.
}
\value{
- None. Invoked for side effect (file is written).
- }
+ \code{\var{fname}}
+}
\author{ Andy Bunn. Patched and improved by Mikko Korpela. }
\seealso{ \code{\link{write.crn}}, \code{\link{read.tucson}},
\code{\link{write.rwl}}, \code{\link{write.compact}},
@@ -107,7 +107,8 @@
spp = "DOUGLAS FIR", elev = "2103M", lat = 3712,
long = -10830, first.yr = 1400, last.yr = 1963,
lead.invs = "E. SCHULMAN", comp.date = "")
-write.tucson(rwl.df = co021, fname = "tmp.rwl", header = co021.hdr,
- append = FALSE, prec = 0.001)
+fname <- write.tucson(rwl.df = co021, fname = tempfile(fileext=".rwl"),
+ header = co021.hdr, append = FALSE, prec = 0.001)
+unlink(fname) # remove the file
}
\keyword{ IO }
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