[Dplr-commits] r1090 - in pkg/dplR: . R man vignettes
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri Apr 6 06:48:46 CEST 2018
Author: andybunn
Date: 2018-04-06 06:48:45 +0200 (Fri, 06 Apr 2018)
New Revision: 1090
Added:
pkg/dplR/R/time.rwl.R
pkg/dplR/man/time.rwl.Rd
Modified:
pkg/dplR/ChangeLog
pkg/dplR/DESCRIPTION
pkg/dplR/NAMESPACE
pkg/dplR/R/cms.R
pkg/dplR/R/plotRings.R
pkg/dplR/R/seg.plot.R
pkg/dplR/man/bai.in.Rd
pkg/dplR/man/bai.out.Rd
pkg/dplR/man/fill.internal.NA.Rd
pkg/dplR/man/hanning.Rd
pkg/dplR/man/morlet.Rd
pkg/dplR/man/plotRings.Rd
pkg/dplR/man/print.redfit.Rd
pkg/dplR/man/redfit.Rd
pkg/dplR/man/rwi.stats.running.Rd
pkg/dplR/man/seg.plot.Rd
pkg/dplR/man/skel.plot.Rd
pkg/dplR/man/wavelet.plot.Rd
pkg/dplR/vignettes/chron-dplR.Rnw
pkg/dplR/vignettes/intro-dplR.Rnw
pkg/dplR/vignettes/timeseries-dplR.Rnw
pkg/dplR/vignettes/xdate-dplR.Rnw
Log:
Added time.rwl and time.crn as convenience functions to get years out of crn and rwl. Changes to Rd files to demonstrate.
Modified: pkg/dplR/ChangeLog
===================================================================
--- pkg/dplR/ChangeLog 2018-03-24 21:01:46 UTC (rev 1089)
+++ pkg/dplR/ChangeLog 2018-04-06 04:48:45 UTC (rev 1090)
@@ -2,6 +2,13 @@
- Note that Darwin Alexander Pucha Cofrep has been added as a developer to work on plotRings() etc.
+File: time.rwl.R
+----------------
+
+- Two convenience functions time.rwl and time.crn which extract the row.names of
+ rwl and crn objects as numerics. Used as a S3 method with class rwl and class crn.
+ This resulted in various changes to Rd files to make use of this capability.
+
File: seg.plot.R
----------------
Modified: pkg/dplR/DESCRIPTION
===================================================================
--- pkg/dplR/DESCRIPTION 2018-03-24 21:01:46 UTC (rev 1089)
+++ pkg/dplR/DESCRIPTION 2018-04-06 04:48:45 UTC (rev 1090)
@@ -3,7 +3,7 @@
Type: Package
Title: Dendrochronology Program Library in R
Version: 1.6.8
-Date: 2018-03-24
+Date: 2018-04-05
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", "cph", "trl")), person("Franco", "Biondi",
Modified: pkg/dplR/NAMESPACE
===================================================================
--- pkg/dplR/NAMESPACE 2018-03-24 21:01:46 UTC (rev 1089)
+++ pkg/dplR/NAMESPACE 2018-04-06 04:48:45 UTC (rev 1090)
@@ -52,10 +52,12 @@
write.tucson, plot.rwl, interseries.cor, summary.rwl, plot.crn,
insert.ring, delete.ring, xskel.ccf.plot, xskel.plot, latexify,
latexDate, rasterPlot, treeMean, rwl.report, print.rwl.report,
- plotRings)
+ plotRings,time.rwl,time.crn)
S3method(print, redfit)
S3method(plot, rwl)
S3method(plot, crn)
S3method(summary, rwl)
S3method(print, rwl.report)
+S3method(time, rwl)
+S3method(time, crn)
Modified: pkg/dplR/R/cms.R
===================================================================
--- pkg/dplR/R/cms.R 2018-03-24 21:01:46 UTC (rev 1089)
+++ pkg/dplR/R/cms.R 2018-04-06 04:48:45 UTC (rev 1090)
@@ -26,7 +26,7 @@
## divide each series by c curve and restore to cal years
rwi <- rwl2
- yrs <- as.numeric(row.names(rwi))
+ yrs <- time(rwi)
c.vec <- rep(as.numeric(NA), n.col)
names(c.vec) <- col.names
if(c.hat.t){
Modified: pkg/dplR/R/plotRings.R
===================================================================
--- pkg/dplR/R/plotRings.R 2018-03-24 21:01:46 UTC (rev 1089)
+++ pkg/dplR/R/plotRings.R 2018-04-06 04:48:45 UTC (rev 1090)
@@ -1,7 +1,7 @@
plotRings <- function(year, trwN, trwS = NA_real_,
- trwE = NA_real_, trwW = NA_real_,
+ trwE = NA_real_, trwW = NA_real_,
+ length.unit = "mm",
animation = FALSE,
- length.unit = "100 mm",
sys.sleep = 0.2,
year.labels = TRUE,
d2pith = NA,
Modified: pkg/dplR/R/seg.plot.R
===================================================================
--- pkg/dplR/R/seg.plot.R 2018-03-24 21:01:46 UTC (rev 1089)
+++ pkg/dplR/R/seg.plot.R 2018-04-06 04:48:45 UTC (rev 1090)
@@ -6,6 +6,7 @@
}
yr <- as.numeric(row.names(rwl))
first.year <- as.matrix(apply(rwl, 2, yr.range, yr.vec=yr))[1, ]
+ last.year <- as.matrix(apply(rwl, 2, yr.range, yr.vec=yr))[2, ]
neworder <- order(first.year, decreasing=FALSE)
segs <- rwl[, neworder, drop=FALSE]
n.col <- ncol(segs)
Added: pkg/dplR/R/time.rwl.R
===================================================================
--- pkg/dplR/R/time.rwl.R (rev 0)
+++ pkg/dplR/R/time.rwl.R 2018-04-06 04:48:45 UTC (rev 1090)
@@ -0,0 +1,7 @@
+time.rwl <- function(x,...){
+ as.numeric(rownames(x))
+}
+
+time.crn <- function(x,...){
+ as.numeric(rownames(x))
+}
Property changes on: pkg/dplR/R/time.rwl.R
___________________________________________________________________
Added: svn:eol-style
+ native
Modified: pkg/dplR/man/bai.in.Rd
===================================================================
--- pkg/dplR/man/bai.in.Rd 2018-03-24 21:01:46 UTC (rev 1089)
+++ pkg/dplR/man/bai.in.Rd 2018-04-06 04:48:45 UTC (rev 1090)
@@ -74,10 +74,10 @@
data(gp.d2pith)
foo <- bai.in(rwl = gp.rwl, d2pith = gp.d2pith)
foo.crn <- chron(foo)
-yr <- as.numeric(rownames(foo.crn))
-plot(yr, foo.crn[, 1], type = "n",
+yrs <- time(foo.crn)
+plot(yrs, foo.crn[, 1], type = "n",
xlab = "Year", ylab = expression(mm^2))
-lines(yr, foo.crn[, 1], col = "grey", lty = "dashed")
-lines(yr, ffcsaps(foo.crn[, 1], nyrs = 32), col = "red", lwd = 2)
+lines(yrs, foo.crn[, 1], col = "grey", lty = "dashed")
+lines(yrs, ffcsaps(foo.crn[, 1], nyrs = 32), col = "red", lwd = 2)
}
\keyword{ manip }
Modified: pkg/dplR/man/bai.out.Rd
===================================================================
--- pkg/dplR/man/bai.out.Rd 2018-03-24 21:01:46 UTC (rev 1089)
+++ pkg/dplR/man/bai.out.Rd 2018-04-06 04:48:45 UTC (rev 1090)
@@ -79,10 +79,10 @@
gp.dbh2[, 2] <- (gp.dbh[, 2] - gp.dbh[, 3]) * 10
bar <- bai.out(rwl = gp.rwl, diam = gp.dbh2)
bar.crn <- chron(bar)
-yr <- as.numeric(rownames(bar.crn))
-plot(yr, bar.crn[, 1], type = "n",
+yrs <- time(bar.crn)
+plot(yrs, bar.crn[, 1], type = "n",
xlab = "Year", ylab = expression(mm^2))
-lines(yr, bar.crn[, 1], col = "grey", lty = "dashed")
-lines(yr, ffcsaps(bar.crn[, 1], nyrs = 32), col = "red", lwd = 2)
+lines(yrs, bar.crn[, 1], col = "grey", lty = "dashed")
+lines(yrs, ffcsaps(bar.crn[, 1], nyrs = 32), col = "red", lwd = 2)
}
\keyword{ manip }
Modified: pkg/dplR/man/fill.internal.NA.Rd
===================================================================
--- pkg/dplR/man/fill.internal.NA.Rd 2018-03-24 21:01:46 UTC (rev 1089)
+++ pkg/dplR/man/fill.internal.NA.Rd 2018-04-06 04:48:45 UTC (rev 1090)
@@ -65,14 +65,14 @@
x8=c(rnorm(8), NA, NA),
x9=c(rnorm(5), NA, rnorm(3), NA))
row.names(foo) <- 1901:1910
-
+class(foo) <- c("rwl","data.frame")
fill.internal.NA(foo, fill=0)
bar <- fill.internal.NA(foo, fill="Spline")
baz <- fill.internal.NA(foo, fill="Linear")
## note differences in method "Spline" vs. "Linear"
-yrs <- as.numeric(row.names(foo))
+yrs <- time(foo)
plot(yrs, foo$x7, type="b", lwd=3)
lines(yrs, bar$x7, col="red", lwd=2)
lines(yrs, baz$x7, col="green", lwd=1)
Modified: pkg/dplR/man/hanning.Rd
===================================================================
--- pkg/dplR/man/hanning.Rd 2018-03-24 21:01:46 UTC (rev 1089)
+++ pkg/dplR/man/hanning.Rd 2018-04-06 04:48:45 UTC (rev 1090)
@@ -30,7 +30,7 @@
\examples{library(graphics)
library(utils)
data(ca533)
-yrs <- as.numeric(rownames(ca533))
+yrs <- time(ca533)
y <- ca533[, 1]
not.na <- !is.na(y)
yrs <- yrs[not.na]
Modified: pkg/dplR/man/morlet.Rd
===================================================================
--- pkg/dplR/man/morlet.Rd 2018-03-24 21:01:46 UTC (rev 1089)
+++ pkg/dplR/man/morlet.Rd 2018-04-06 04:48:45 UTC (rev 1090)
@@ -49,7 +49,7 @@
data(ca533)
ca533.rwi <- detrend(rwl = ca533, method = "ModNegExp")
ca533.crn <- chron(ca533.rwi, prefix = "CAM", prewhiten = FALSE)
-Years <- as.numeric(rownames(ca533.crn))
+Years <- time(ca533.crn)
CAMstd <- ca533.crn[, 1]
out.wave <- morlet(y1 = CAMstd, x1 = Years, dj = 0.1, siglvl = 0.99)
}
Modified: pkg/dplR/man/plotRings.Rd
===================================================================
--- pkg/dplR/man/plotRings.Rd 2018-03-24 21:01:46 UTC (rev 1089)
+++ pkg/dplR/man/plotRings.Rd 2018-04-06 04:48:45 UTC (rev 1090)
@@ -110,7 +110,7 @@
# with tree-ring series from Rothenburg data
data("anos1")
-yrs <- as.numeric(rownames(anos1))
+yrs <- time(anos1)
# Plot rings with data of two radii from same individual tree
res <- plotRings(yrs, anos1[,4], trwW = anos1[,5],
species.name = "Cedrela odorata")
@@ -150,16 +150,17 @@
trw01.w = abs(rnorm(100, 10, 2.5)), # West direction
trw01.e = abs(rnorm(100, 10, 2.5)), # East direction
row.names = 1918:2017)
+class(trw) <- c("rwl","data.frame")
-year <- as.numeric(rownames(trw))
+yrs <- time(trw)
# Default plot with 2, 3 and 4 radii
-res <- plotRings(year, trw[,1], trw[,2], trw[,3], trw[,4])
+res <- plotRings(yrs, trw[,1], trw[,2], trw[,3], trw[,4])
# with d2pith values (see the hole before the first rings in the plot)
-res <- plotRings(year, trw[,1], trw[,2], trw[,3], trw[,4],
+res <- plotRings(yrs, trw[,1], trw[,2], trw[,3], trw[,4],
d2pith = 500)
-res <- plotRings(year, trw[,1], trw[,2], trw[,3], trw[,4],
+res <- plotRings(yrs, trw[,1], trw[,2], trw[,3], trw[,4],
d2pith = c(200, NA, NA, 50))
}
Modified: pkg/dplR/man/print.redfit.Rd
===================================================================
--- pkg/dplR/man/print.redfit.Rd 2018-03-24 21:01:46 UTC (rev 1089)
+++ pkg/dplR/man/print.redfit.Rd 2018-04-06 04:48:45 UTC (rev 1090)
@@ -71,17 +71,16 @@
}
\examples{library(utils)
data(ca533)
-t <- as.numeric(row.names(ca533))
+tm <- time(ca533)
x <- ca533[[1]]
idx <- which(!is.na(x))
-redf <- redfit(x[idx], t[idx], "time",
+redf <- redfit(x[idx], tm[idx], "time",
nsim = 100, iwin = 0, ofac = 1, n50 = 1)
print(redf)
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/redfit.Rd
===================================================================
--- pkg/dplR/man/redfit.Rd 2018-03-24 21:01:46 UTC (rev 1089)
+++ pkg/dplR/man/redfit.Rd 2018-04-06 04:48:45 UTC (rev 1090)
@@ -373,7 +373,7 @@
library(utils)
data(cana157)
-yrs <- as.numeric(rownames(cana157))
+yrs <- time(cana157)
x <- cana157[, 1]
redf.x <- redfit(x, nsim = 1000)
Modified: pkg/dplR/man/rwi.stats.running.Rd
===================================================================
--- pkg/dplR/man/rwi.stats.running.Rd 2018-03-24 21:01:46 UTC (rev 1089)
+++ pkg/dplR/man/rwi.stats.running.Rd 2018-04-06 04:48:45 UTC (rev 1090)
@@ -244,7 +244,7 @@
gp.crn <- chron(gp.rwi)
## Running stats on the rwi with an window
foo <- rwi.stats.running(gp.rwi, gp.ids, window.length = 80)
- yrs <- as.numeric(rownames(gp.crn))
+ yrs <- time(gp.crn)
bar <- data.frame(yrs = c(min(yrs), foo$mid.year, max(yrs)),
eps = c(NA, foo$eps, NA))
par(mar = c(2, 2, 2, 2), mgp = c(1.1, 0.1, 0), tcl = 0.25,
Modified: pkg/dplR/man/seg.plot.Rd
===================================================================
--- pkg/dplR/man/seg.plot.Rd 2018-03-24 21:01:46 UTC (rev 1089)
+++ pkg/dplR/man/seg.plot.Rd 2018-04-06 04:48:45 UTC (rev 1090)
@@ -25,6 +25,6 @@
\seealso{ \code{\link{spag.plot}} }
\examples{library(utils)
data(co021)
-seg.plot(co021, main = "Campito Mountain")
+seg.plot(co021)
}
\keyword{ hplot }
Modified: pkg/dplR/man/skel.plot.Rd
===================================================================
--- pkg/dplR/man/skel.plot.Rd 2018-03-24 21:01:46 UTC (rev 1089)
+++ pkg/dplR/man/skel.plot.Rd 2018-04-06 04:48:45 UTC (rev 1090)
@@ -79,7 +79,7 @@
\examples{library(utils)
data(co021)
x <- co021[,33]
-x.yrs <- as.numeric(rownames(co021))
+x.yrs <- time(co021)
x.name <- colnames(co021)[33]
## On a raw ring width series - undated
skel.plot(x)
@@ -89,7 +89,7 @@
library(grDevices)
## Try cross-dating
y <- co021[, 11]
-y.yrs <- as.numeric(rownames(co021))
+y.yrs <- time(co021)
y.name <- colnames(co021)[11]
## send to postscript - 3 pages total
Added: pkg/dplR/man/time.rwl.Rd
===================================================================
--- pkg/dplR/man/time.rwl.Rd (rev 0)
+++ pkg/dplR/man/time.rwl.Rd 2018-04-06 04:48:45 UTC (rev 1090)
@@ -0,0 +1,36 @@
+\encoding{UTF-8}
+\name{time.rwl}
+\alias{time.rwl}
+\alias{time.crn}
+\title{
+ Return time values for rwl and crn objects
+}
+\description{
+ Returns the time values for rwl and crn objects.
+}
+\usage{
+\method{time}{rwl}(x, ...)
+\method{time}{crn}(x, ...)
+}
+\arguments{
+
+ \item{x}{ An object of class \code{"rwl"} or an aboject of class \code{"crn"}. }
+
+ \item{\dots}{ Not used. }
+}
+\value{
+ A \code{numeric} vector of time (typically in years) for the object. This is done via \code{as.numeric(rownames(x))} but has been asked for by users so many times that it is being included as a function.
+}
+\author{
+ Andy Bunn
+}
+\seealso{
+ \code{\link{read.rwl}}
+ \code{\link{read.crn}}
+}
+\examples{
+library(utils)
+data(co021)
+co021.yrs <- time(co021)
+}
+\keyword{ manip }
Property changes on: pkg/dplR/man/time.rwl.Rd
___________________________________________________________________
Added: svn:eol-style
+ native
Modified: pkg/dplR/man/wavelet.plot.Rd
===================================================================
--- pkg/dplR/man/wavelet.plot.Rd 2018-03-24 21:01:46 UTC (rev 1089)
+++ pkg/dplR/man/wavelet.plot.Rd 2018-04-06 04:48:45 UTC (rev 1090)
@@ -99,7 +99,7 @@
data(ca533)
ca533.rwi <- detrend(rwl = ca533, method = "ModNegExp")
ca533.crn <- chron(ca533.rwi, prefix = "CAM", prewhiten = FALSE)
-Years <- as.numeric(rownames(ca533.crn))
+Years <- time(ca533.crn)
CAMstd <- ca533.crn[, 1]
out.wave <- morlet(y1 = CAMstd, x1 = Years, p2 = 9, dj = 0.1,
siglvl = 0.99)
Modified: pkg/dplR/vignettes/chron-dplR.Rnw
===================================================================
--- pkg/dplR/vignettes/chron-dplR.Rnw 2018-03-24 21:01:46 UTC (rev 1089)
+++ pkg/dplR/vignettes/chron-dplR.Rnw 2018-04-06 04:48:45 UTC (rev 1090)
@@ -178,7 +178,7 @@
wa082.ids <- autoread.ids(wa082)
eps.cut <- 0.75 # An arbitrary EPS cutoff for demonstration
wa082.rwi.stats <- rwi.stats.running(wa082.rwi, wa082.ids, window.length = 30)
-yrs <- as.numeric(rownames(wa082.crn))
+yrs <- time(wa082.crn)
bar <- data.frame(yrs = c(min(yrs), wa082.rwi.stats$mid.year, max(yrs)),
eps = c(NA, wa082.rwi.stats$eps, NA))
op <- par(no.readonly=TRUE)
Modified: pkg/dplR/vignettes/intro-dplR.Rnw
===================================================================
--- pkg/dplR/vignettes/intro-dplR.Rnw 2018-03-24 21:01:46 UTC (rev 1089)
+++ pkg/dplR/vignettes/intro-dplR.Rnw 2018-04-06 04:48:45 UTC (rev 1090)
@@ -313,7 +313,7 @@
## based on EPS. Running stats on the rwi with a window.
foo <- rwi.stats.running(ca533.rwi, ca533.ids,
window.length = 80)
-yrs <- as.numeric(rownames(ca533.crn))
+yrs <- time(ca533.crn)
bar <- data.frame(yrs = c(min(yrs), foo$mid.year, max(yrs)),
eps = c(NA, foo$eps, NA))
par(mar = c(2, 2, 2, 2), mgp = c(1.1, 0.1, 0), tcl = 0.25,
Modified: pkg/dplR/vignettes/timeseries-dplR.Rnw
===================================================================
--- pkg/dplR/vignettes/timeseries-dplR.Rnw 2018-03-24 21:01:46 UTC (rev 1089)
+++ pkg/dplR/vignettes/timeseries-dplR.Rnw 2018-04-06 04:48:45 UTC (rev 1090)
@@ -236,7 +236,7 @@
the result via \code{wavelet.plot}.
<<e, fig=TRUE>>=
-yrs <- as.numeric(rownames(co021.crn))
+yrs <- time(co021.crn)
out.wave <- morlet(y1 = dat, x1 = yrs, p2 = 8, dj = 0.1,
siglvl = 0.99)
wavelet.plot(out.wave, useRaster=NA, reverse.y = TRUE)
Modified: pkg/dplR/vignettes/xdate-dplR.Rnw
===================================================================
--- pkg/dplR/vignettes/xdate-dplR.Rnw 2018-03-24 21:01:46 UTC (rev 1089)
+++ pkg/dplR/vignettes/xdate-dplR.Rnw 2018-04-06 04:48:45 UTC (rev 1090)
@@ -186,7 +186,7 @@
<<d, fig=TRUE>>=
win <- 1800:1960
-dat.yrs <- as.numeric(rownames(dat))
+dat.yrs <- time(dat)
dat.trunc <- dat[dat.yrs %in% win, ]
ccf.30 <- ccf.series.rwl(rwl=dat.trunc, series="643114",
seg.length=30, bin.floor=50)
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