[Dplr-commits] r651 - in pkg/dplR: . R man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Oct 2 17:03:11 CEST 2012
Author: mvkorpel
Date: 2012-10-02 17:03:10 +0200 (Tue, 02 Oct 2012)
New Revision: 651
Modified:
pkg/dplR/ChangeLog
pkg/dplR/DESCRIPTION
pkg/dplR/R/corr.rwl.seg.R
pkg/dplR/man/corr.rwl.seg.Rd
Log:
In corr.rwl.seg(), allow the master series to be built from a second set of tree ring series by using a data.frame 'master' argument
Modified: pkg/dplR/ChangeLog
===================================================================
--- pkg/dplR/ChangeLog 2012-08-30 19:57:20 UTC (rev 650)
+++ pkg/dplR/ChangeLog 2012-10-02 15:03:10 UTC (rev 651)
@@ -22,6 +22,8 @@
- Bug fix: series names were not shown (numbers were shown instead)
- Bug fix: there were off-by-one errors in the length of the bars
+- New feature: allow the master series to be built from a second set of
+ tree ring series by using a data.frame 'master' argument
File: DESCRIPTION
---------------
Modified: pkg/dplR/DESCRIPTION
===================================================================
--- pkg/dplR/DESCRIPTION 2012-08-30 19:57:20 UTC (rev 650)
+++ pkg/dplR/DESCRIPTION 2012-10-02 15:03:10 UTC (rev 651)
@@ -3,7 +3,7 @@
Type: Package
Title: Dendrochronology Program Library in R
Version: 1.5.6
-Date: 2012-08-29
+Date: 2012-10-02
Authors at R: c(person(c("Andrew", "G."), "Bunn", role = c("aut", "cph",
"cre", "trl"), email = "andrew.bunn at wwu.edu"), person("Mikko",
"Korpela", role = c("aut", "cph")), person("Franco", "Biondi",
Modified: pkg/dplR/R/corr.rwl.seg.R
===================================================================
--- pkg/dplR/R/corr.rwl.seg.R 2012-08-30 19:57:20 UTC (rev 650)
+++ pkg/dplR/R/corr.rwl.seg.R 2012-10-02 15:03:10 UTC (rev 651)
@@ -2,7 +2,12 @@
prewhiten = TRUE, pcrit=0.05, biweight=TRUE,
make.plot = TRUE, label.cex=1,
floor.plus1 = FALSE, master = NULL,
- master.yrs = as.numeric(names(master)), ...) {
+ master.yrs = as.numeric(if (is.null(dim(master))) {
+ names(master)
+ } else {
+ rownames(master)
+ }),
+ ...) {
## helper function
yr.range <- function(x, yr.vec=as.numeric(names(x))) {
@@ -42,20 +47,52 @@
nrow = max.yr - min.yr + 1,
ncol = nseries,
dimnames = list(as.character(yrs), cnames))
- rwl.tmp <- as.matrix(rwl)
- for (rname in row.names(rwl)) {
- rwl2[rname, ] <- rwl.tmp[rname, ]
- }
+ rwl2[row.names(rwl), ] <- as.matrix(rwl)
rwl2 <- as.data.frame(rwl2)
}
## Pad rwl and master (if present) to same number of years
if (!is.null(master)) {
+ master.dim <- dim(master)
min.master.yr <- min(master.yrs)
max.master.yr <- max(master.yrs)
- master2 <- rep(NA_real_, max.master.yr - min.master.yr + 1)
- names(master2) <- min.master.yr : max.master.yr
- master2[as.character(master.yrs)] <- master
+
+ if (!is.null(master.dim) && length(master.dim) == 2 &&
+ master.dim[2] > 1) {
+ ## A. master is a data.frame or a matrix. Normalize and
+ ## compute master chronology as a mean of series
+ ## (columns).
+
+ ## Ensure that master has consecutive years in increasing order
+ if (!all(diff(master.yrs) == 1)) {
+ char.yrs <- as.character(min.master.yr : max.master.yr)
+ master.inc <- matrix(NA_real_,
+ nrow = max.master.yr - min.master.yr + 1,
+ ncol = master.dim[2],
+ dimnames = list(char.yrs,
+ colnames(master)))
+ master.inc[rownames(master), ] <- as.matrix(master)
+ } else {
+ master.inc <- master
+ }
+
+ ## normalize all series (columns in master matrix)
+ tmp <- normalize1(master.inc, n, prewhiten)
+ master.norm <- tmp$master[, tmp$idx.good, drop=FALSE]
+
+ ## compute master series by normal mean or robust mean
+ if (!biweight) {
+ master2 <- apply(master.norm, 1, exactmean)
+ } else {
+ master2 <- apply(master.norm, 1, tbrm, C=9)
+ }
+ } else {
+ ## B. master is a vector
+ master2 <- rep(NA_real_, max.master.yr - min.master.yr + 1)
+ names(master2) <- as.character(min.master.yr : max.master.yr)
+ master2[as.character(master.yrs)] <- master
+ }
+
if (min.master.yr < min.yr) {
n.pad <- min.yr - min.master.yr
padding <- matrix(NA_real_, n.pad, nseries)
@@ -129,16 +166,10 @@
master.norm <- rwi[, idx.good & idx.noti, drop=FALSE]
## compute master series by normal mean or robust mean
- master2 <- vector(mode="numeric", length=nyrs)
if (!biweight) {
- for (j in seq_len(nyrs)) {
- master2[j] <- exactmean(master.norm[j, ])
- }
+ master2 <- apply(master.norm, 1, exactmean)
} else {
- ## surprisingly, for loop is faster than apply
- for (j in seq_len(nyrs)) {
- master2[j] <- tbrm(master.norm[j, ], C=9)
- }
+ master2 <- apply(master.norm, 1, tbrm, C=9)
}
}
series <- rwi[, i]
Modified: pkg/dplR/man/corr.rwl.seg.Rd
===================================================================
--- pkg/dplR/man/corr.rwl.seg.Rd 2012-08-30 19:57:20 UTC (rev 650)
+++ pkg/dplR/man/corr.rwl.seg.Rd 2012-10-02 15:03:10 UTC (rev 651)
@@ -8,7 +8,12 @@
corr.rwl.seg(rwl, seg.length = 50, bin.floor = 100, n = NULL,
prewhiten = TRUE, pcrit = 0.05, biweight = TRUE,
make.plot = TRUE, label.cex = 1, floor.plus1 = FALSE,
- master = NULL, master.yrs = as.numeric(names(master)),
+ master = NULL,
+ master.yrs = as.numeric(if (is.null(dim(master))) {
+ names(master)
+ } else {
+ rownames(master)
+ }),
\dots)
}
\arguments{
@@ -35,34 +40,41 @@
\item{floor.plus1}{ \code{logical} flag. If \code{TRUE}, one year is
added to the base location of the first segment (e.g., 1601, 1701,
1801 \acronym{AD}). }
- \item{master}{ a \code{numeric} vector. If not \code{NULL}, the
- function uses this as the master chronology. If \code{NULL}, a
- number of master chronologies, one for each series in
- \code{\var{rwl}}, is built from \code{\var{rwl}} using the
- leave-one-out principle. }
+ \item{master}{ \code{NULL}, a \code{numeric} \code{vector} or a
+ \code{matrix}-like object of \code{numeric} values, including a
+ \code{data.frame}. If \code{NULL}, a number of master chronologies,
+ one for each series in \code{\var{rwl}}, is built from
+ \code{\var{rwl}} using the leave-one-out principle. If a
+ \code{vector}, the function uses this as the master chronology. If
+ a \code{matrix} or \code{data.frame}, this object is used for
+ building the master chronology (no leave-one-out). }
\item{master.yrs}{ a \code{numeric} vector giving the years of
- \code{\var{series}}. Defaults to
- \code{as.numeric(names(\var{master}))}. }
+ \code{\var{series}}. Defaults to \code{names} or \code{rownames} of
+ \code{\var{master}} coerced to \code{numeric} type. }
\item{\dots}{ other arguments passed to plot. }
}
\details{
+
This function calculates correlation serially between each tree-ring
series and a master chronology built from all the other series in the
\code{\var{rwl}} object (leave-one-out principle). Optionally, the
- user may give a \code{\var{master}} chronology as an argument. In the
- latter case, the same master chronology is used for all the series in
- the \code{\var{rwl}} object. Correlations are done for each segment
- of the series where segments are lagged by half the segment length
- (e.g., 100-year segments would be overlapped by 50-years). The first
- segment is placed according to \code{\var{bin.floor}}. The minimum
- bin year is calculated as
+ user may give a \code{\var{master}} chronology (a \code{vector}) as an
+ argument. In the latter case, the same master chronology is used for
+ all the series in the \code{\var{rwl}} object. The user can also
+ choose to give a \code{\var{master}} \code{data.frame} (series as
+ columns, years as rows), from which a single master chronology is
+ built.
+
+ Correlations are done for each segment of the series where segments
+ are lagged by half the segment length (e.g., 100-year segments would
+ be overlapped by 50-years). The first segment is placed according to
+ \code{\var{bin.floor}}. The minimum bin year is calculated as
\code{ceiling(\var{min.yr}/\var{bin.floor})*\var{bin.floor}} where
\code{\var{min.yr}} is the first year in either the \code{\var{rwl}}
object or the user-specified \code{\var{master}} chronology, whichever
is smaller. For example if the first year is 626 and
- \code{\var{bin.floor}} is 100 then the first bin would start in
- 700. If \code{\var{bin.floor}} is 10 then the first bin would start in
- 630.
+ \code{\var{bin.floor}} is 100 then the first bin would start in 700.
+ If \code{\var{bin.floor}} is 10 then the first bin would start in 630.
Correlations are calculated for the first segment, then the second
segment and so on. Correlations are only calculated for segments with
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