[Dplr-commits] r835 - in pkg/dplR: . man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Apr 24 09:25:44 CEST 2014
Author: mvkorpel
Date: 2014-04-24 09:25:43 +0200 (Thu, 24 Apr 2014)
New Revision: 835
Modified:
pkg/dplR/DESCRIPTION
pkg/dplR/man/detrend.Rd
pkg/dplR/man/fill.internal.NA.Rd
pkg/dplR/man/print.redfit.Rd
pkg/dplR/man/skel.plot.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:
In all examples that create files (even if in \dontrun):
* Use a tempfile()
* Print the filename
* Finally remove the file (command separated by an empty line)
Modified: pkg/dplR/DESCRIPTION
===================================================================
--- pkg/dplR/DESCRIPTION 2014-04-23 13:32:39 UTC (rev 834)
+++ pkg/dplR/DESCRIPTION 2014-04-24 07:25:43 UTC (rev 835)
@@ -3,7 +3,7 @@
Type: Package
Title: Dendrochronology Program Library in R
Version: 1.6.0
-Date: 2014-04-23
+Date: 2014-04-24
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/man/detrend.Rd
===================================================================
--- pkg/dplR/man/detrend.Rd 2014-04-23 13:32:39 UTC (rev 834)
+++ pkg/dplR/man/detrend.Rd 2014-04-24 07:25:43 UTC (rev 835)
@@ -98,10 +98,14 @@
## Detrend using all methods. Returns a list
ca533.rwi <- detrend(rwl = ca533)
## Save a pdf of all series
-pdf("foo.pdf")
+fname <- tempfile(fileext=".pdf")
+print(fname) # tempfile used for output
+pdf(fname)
ca533.rwi <- detrend(rwl = ca533, method = c("Spline", "ModNegExp"),
make.plot = TRUE)
dev.off()
+
+unlink(fname) # remove the file
}
}
\keyword{ manip }
Modified: pkg/dplR/man/fill.internal.NA.Rd
===================================================================
--- pkg/dplR/man/fill.internal.NA.Rd 2014-04-23 13:32:39 UTC (rev 834)
+++ pkg/dplR/man/fill.internal.NA.Rd 2014-04-24 07:25:43 UTC (rev 835)
@@ -34,7 +34,7 @@
caution. For instance, some users code missing rings as \code{NA}
instead of \code{0}. And missing values (i.e., \code{NA}) are
sometimes present in maximum latewood density data when the rings are
- small. A common, but not reccomended, practice is to leave stretches
+ small. A common, but not recommended, practice is to leave stretches
of \code{NA} values in places where it has been impossible to
accurately measure rings (perhaps because of a break in the core). It
is often better to treat that core as two separate series (e.g., "01A"
Modified: pkg/dplR/man/print.redfit.Rd
===================================================================
--- pkg/dplR/man/print.redfit.Rd 2014-04-23 13:32:39 UTC (rev 834)
+++ pkg/dplR/man/print.redfit.Rd 2014-04-24 07:25:43 UTC (rev 835)
@@ -75,9 +75,11 @@
redf <- redfit(x[idx], t[idx], "time",
nsim = 100, iwin = 0, ofac = 1, n50 = 1)
print(redf)
-f <- tempfile(fileext=".csv")
-print(redf, csv.out = TRUE, file = f)
-redftable <- read.csv(f)
-unlink(f) # remove the file
+fname <- tempfile(fileext=".csv")
+print(fname) # tempfile used for output
+print(redf, csv.out = TRUE, file = fname)
+redftable <- read.csv(fname)
+
+unlink(fname) # remove the file
}
\keyword{ print }
Modified: pkg/dplR/man/skel.plot.Rd
===================================================================
--- pkg/dplR/man/skel.plot.Rd 2014-04-23 13:32:39 UTC (rev 834)
+++ pkg/dplR/man/skel.plot.Rd 2014-04-24 07:25:43 UTC (rev 835)
@@ -88,8 +88,11 @@
y <- co021[, 11]
y.yrs <- as.numeric(rownames(co021))
y.name <- colnames(co021)[11]
+
## send to postscript - 3 pages total
-postscript("xdating.examp.ps")
+fname1 <- tempfile(fileext=".ps")
+print(fname1) # tempfile used for PS output
+postscript(fname1)
## "Master series" with correct calendar dates
skel.plot(x, yr.vec = x.yrs, sname = x.name, master = TRUE)
## Undated series, try to align with last plot
@@ -98,12 +101,18 @@
skel.plot(y, yr.vec = y.yrs, sname = y.name)
dev.off()
+unlink(fname1) # remove the PS file
+
## alternatively send to pdf
-pdf("xdating.examp.pdf", width = 10, height = 7.5, paper = "USr")
+fname2 <- tempfile(fileext=".pdf")
+print(fname2) # tempfile used for PDF output
+pdf(fname2, width = 10, height = 7.5, paper = "USr")
skel.plot(x, yr.vec = x.yrs, sname = x.name, master = TRUE)
skel.plot(y)
skel.plot(y, yr.vec = y.yrs, sname = y.name)
dev.off()
+
+unlink(fname2) # remove the PDF file
}
}
\keyword{ hplot }
Modified: pkg/dplR/man/write.compact.Rd
===================================================================
--- pkg/dplR/man/write.compact.Rd 2014-04-23 13:32:39 UTC (rev 834)
+++ pkg/dplR/man/write.compact.Rd 2014-04-24 07:25:43 UTC (rev 835)
@@ -57,6 +57,8 @@
fname <- write.compact(rwl.df = co021,
fname = tempfile(fileext=".rwl"),
append = FALSE, prec = 0.001)
+print(fname) # tempfile used for output
+
unlink(fname) # remove the file
}
\keyword{ IO }
Modified: pkg/dplR/man/write.crn.Rd
===================================================================
--- pkg/dplR/man/write.crn.Rd 2014-04-23 13:32:39 UTC (rev 834)
+++ pkg/dplR/man/write.crn.Rd 2014-04-24 07:25:43 UTC (rev 835)
@@ -79,8 +79,10 @@
ca533.rwi <- detrend(rwl = ca533, method = "ModNegExp")
ca533.crn <- chron(ca533.rwi, prefix = "CAM")
fname1 <- write.crn(ca533.crn, tempfile(fileext=".crn"))
+print(fname1) # tempfile used for output
+
## Put the standard and residual chronologies in a single file
-## with ITRDB header info on top. Not reccomended.
+## with ITRDB header info on top. Not recommended.
ca533.crn <- chron(ca533.rwi, prefix = "CAM", prewhiten = TRUE)
ca533.hdr <- list(site.id = "CAM", site.name = "Campito Mountain",
spp.code = "PILO", state.country = "California",
@@ -91,6 +93,8 @@
fname2 <- write.crn(ca533.crn[, -2], tempfile(fileext=".crn"),
header = ca533.hdr)
write.crn(ca533.crn[, -1], fname2, append = TRUE)
+print(fname2) # tempfile used for output
+
unlink(c(fname1, fname2)) # remove the files
}
\keyword{ IO }
Modified: pkg/dplR/man/write.rwl.Rd
===================================================================
--- pkg/dplR/man/write.rwl.Rd 2014-04-23 13:32:39 UTC (rev 834)
+++ pkg/dplR/man/write.rwl.Rd 2014-04-24 07:25:43 UTC (rev 835)
@@ -49,6 +49,8 @@
fname <- write.rwl(rwl.df = co021, fname = tempfile(fileext=".rwl"),
format = "tucson", header = co021.hdr,
append = FALSE, prec = 0.001)
+print(fname) # tempfile used for output
+
unlink(fname) # remove the file
}
\keyword{ IO }
Modified: pkg/dplR/man/write.tridas.Rd
===================================================================
--- pkg/dplR/man/write.tridas.Rd 2014-04-23 13:32:39 UTC (rev 834)
+++ pkg/dplR/man/write.tridas.Rd 2014-04-24 07:25:43 UTC (rev 835)
@@ -359,6 +359,7 @@
project.info = list(investigator = "E. Schulman",
title = "", category = "",
period = "", type = "unknown"))
+print(fname1) # tempfile used for output
## Write mean value chronology of detrended ring widths
data(ca533)
@@ -371,6 +372,8 @@
list(investigator = "Donald A. Graybill, V.C. LaMarche, Jr.",
title = "Campito Mountain", category = "",
period = "", type = "unknown"))
+print(fname2) # tempfile used for output
+
unlink(c(fname1, fname2)) # remove the files
}
\keyword{ IO }
Modified: pkg/dplR/man/write.tucson.Rd
===================================================================
--- pkg/dplR/man/write.tucson.Rd 2014-04-23 13:32:39 UTC (rev 834)
+++ pkg/dplR/man/write.tucson.Rd 2014-04-24 07:25:43 UTC (rev 835)
@@ -109,6 +109,8 @@
lead.invs = "E. SCHULMAN", comp.date = "")
fname <- write.tucson(rwl.df = co021, fname = tempfile(fileext=".rwl"),
header = co021.hdr, append = FALSE, prec = 0.001)
+print(fname) # tempfile used for output
+
unlink(fname) # remove the file
}
\keyword{ IO }
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