[Dplr-commits] r973 - in pkg/dplR: . man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Mar 12 09:50:48 CET 2015
Author: mvkorpel
Date: 2015-03-12 09:50:48 +0100 (Thu, 12 Mar 2015)
New Revision: 973
Modified:
pkg/dplR/DESCRIPTION
pkg/dplR/man/anos1.Rd
pkg/dplR/man/bai.in.Rd
pkg/dplR/man/bai.out.Rd
pkg/dplR/man/ca533.Rd
pkg/dplR/man/cana157.Rd
pkg/dplR/man/ccf.series.rwl.Rd
pkg/dplR/man/chron.Rd
pkg/dplR/man/cms.Rd
pkg/dplR/man/combine.rwl.Rd
pkg/dplR/man/common.interval.Rd
pkg/dplR/man/corr.rwl.seg.Rd
pkg/dplR/man/corr.series.seg.Rd
pkg/dplR/man/crn.plot.Rd
pkg/dplR/man/detrend.Rd
pkg/dplR/man/detrend.series.Rd
pkg/dplR/man/dplR-package.Rd
pkg/dplR/man/ffcsaps.Rd
pkg/dplR/man/fill.internal.NA.Rd
pkg/dplR/man/gini.coef.Rd
pkg/dplR/man/glk.Rd
pkg/dplR/man/gp.d2pith.Rd
pkg/dplR/man/gp.dbh.Rd
pkg/dplR/man/gp.po.Rd
pkg/dplR/man/gp.rwl.Rd
pkg/dplR/man/hanning.Rd
pkg/dplR/man/i.detrend.Rd
pkg/dplR/man/i.detrend.series.Rd
pkg/dplR/man/insert.ring.Rd
pkg/dplR/man/interseries.cor.Rd
pkg/dplR/man/latexify.Rd
pkg/dplR/man/morlet.Rd
pkg/dplR/man/net.Rd
pkg/dplR/man/plot.rwl.Rd
pkg/dplR/man/po.to.wc.Rd
pkg/dplR/man/pointer.Rd
pkg/dplR/man/powt.Rd
pkg/dplR/man/print.redfit.Rd
pkg/dplR/man/rcs.Rd
pkg/dplR/man/read.compact.Rd
pkg/dplR/man/read.crn.Rd
pkg/dplR/man/read.fh.Rd
pkg/dplR/man/read.ids.Rd
pkg/dplR/man/read.tridas.Rd
pkg/dplR/man/read.tucson.Rd
pkg/dplR/man/redfit.Rd
pkg/dplR/man/rwi.stats.running.Rd
pkg/dplR/man/rwl.stats.Rd
pkg/dplR/man/sea.Rd
pkg/dplR/man/seg.plot.Rd
pkg/dplR/man/sens1.Rd
pkg/dplR/man/sens2.Rd
pkg/dplR/man/series.rwl.plot.Rd
pkg/dplR/man/skel.plot.Rd
pkg/dplR/man/spag.plot.Rd
pkg/dplR/man/strip.rwl.Rd
pkg/dplR/man/tbrm.Rd
pkg/dplR/man/tridas.vocabulary.Rd
pkg/dplR/man/uuid.gen.Rd
pkg/dplR/man/wavelet.plot.Rd
pkg/dplR/man/wc.to.po.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
pkg/dplR/man/xskel.ccf.plot.Rd
pkg/dplR/man/xskel.plot.Rd
Log:
Many small fixes and formatting changes to .Rd files.
* Fixed typo in xskel.plot.Rd: closing parentheses in code sample
* Edited author info of reference in ca533.Rd: dataset
description page at ITRDB lists two author names, we only had
one. Also added another initial to first author's name.
* Using typographic (curved shape, Unicode) apostrophe instead of
/ in parallel with typewriter apostrophe (straight shape,
ASCII).
* Using en dash instead of ASCII hyphen / minus in some places.
* Formatting changes as recommended ("intended for core
developers but may also be useful for package writers")
in "Guidelines for Rd files" at http://developer.r-project.org/
- References: Added \bold{} formatting to journal volume
numbers. Page numbers are now separated with ", " instead
of ":". More consistent use of comma before "and" in author
lists with at least three names. Other small consistency
adjustments. It would be nice to switch to
some (semi)automatic formatting mechanism. Maybe when there's
more time...
- More consistent use of two spaces after periods ending a
sentence.
* Broke the long lines of bai.in.Rd, bai.out.Rd, cms.Rd, read.fh.Rd.
* Indented the Details section in xskel.plot.Rd and
xskel.ccf.plot.Rd. This makes the two space policy easier to
maintain, not having to add spaces before a newline at the
limit of two sentences.
* Replaced indentation tabs with spaces: detrend.series.Rd,
read.tridas.Rd, redfit.Rd, write.tridas.Rd.
* Other minor formatting adjustments on input or also on the output side
Modified: pkg/dplR/DESCRIPTION
===================================================================
--- pkg/dplR/DESCRIPTION 2015-03-11 11:57:35 UTC (rev 972)
+++ pkg/dplR/DESCRIPTION 2015-03-12 08:50:48 UTC (rev 973)
@@ -3,7 +3,7 @@
Type: Package
Title: Dendrochronology Program Library in R
Version: 1.6.3
-Date: 2015-03-11
+Date: 2015-03-12
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/anos1.Rd
===================================================================
--- pkg/dplR/man/anos1.Rd 2015-03-11 11:57:35 UTC (rev 972)
+++ pkg/dplR/man/anos1.Rd 2015-03-12 08:50:48 UTC (rev 973)
@@ -12,12 +12,12 @@
}
\usage{data(anos1)}
\format{A \code{data.frame} containing 20 tree-ring series from 10 trees
- in columns and 98 years in rows. The correct stc mask for use with
+ in columns and 98 years in rows. The correct stc mask for use with
\code{\link{read.ids}} is \code{c(5, 2, 1)}.}
\references{
Zang, C. (2010) Growth reaction of temperate forest tree species to
summer drought \enc{–}{--} a multispecies tree-ring network
- approach. PhD-Thesis, Technische \enc{Universität}{Universitaet}
+ approach. PhD thesis, Technische \enc{Universität}{Universitaet}
\enc{München}{Muenchen}.
}
\keyword{datasets}
Modified: pkg/dplR/man/bai.in.Rd
===================================================================
--- pkg/dplR/man/bai.in.Rd 2015-03-11 11:57:35 UTC (rev 972)
+++ pkg/dplR/man/bai.in.Rd 2015-03-12 08:50:48 UTC (rev 973)
@@ -3,25 +3,46 @@
\alias{bai.in}
\title{ Basal Area Increment (Inside Out) }
\description{
- Convert multiple ring-width series to basal area increment (i.e., ring area) going from the pith to the bark.
+ Convert multiple ring-width series to basal area increment (i.e., ring
+ area) going from the pith to the bark.
}
\usage{
bai.in(rwl, d2pith = NULL)
}
\arguments{
- \item{rwl}{ a \code{data.frame} with series as columns and years as rows such as that produced by \code{\link{read.rwl}} }
- \item{d2pith}{ an optional \code{vector} containing two variables. If present, then variable one (\code{series} in the example below) gives the series \acronym{ID} as either \code{characters} or \code{factors}. These must exactly match \code{colnames(\var{rwl})}. Variable two (\code{\var{d2pith}} in the example below) gives the distance from the innermost measured ring to the pith of the tree in mm. If \code{\var{d2pith}} is \code{NULL} then the distance to pith is assumed to be zero for each series (column) in \code{\var{rwl}}. }
+ \item{rwl}{ a \code{data.frame} with series as columns and years as
+ rows such as that produced by \code{\link{read.rwl}} }
+ \item{d2pith}{ an optional \code{vector} containing two variables. If
+ present, then variable one (\code{series} in the example below)
+ gives the series \acronym{ID} as either \code{characters} or
+ \code{factors}. These must exactly match
+ \code{colnames(\var{rwl})}. Variable two (\code{\var{d2pith}} in
+ the example below) gives the distance from the innermost measured
+ ring to the pith of the tree in mm. If \code{\var{d2pith}} is
+ \code{NULL} then the distance to pith is assumed to be zero for each
+ series (column) in \code{\var{rwl}}. }
}
\details{
-This converts ring-width series (mm) to ring-area series (mm squared) (aka basal area increments) based on the distance between the innermost measured ring and the pith of the tree. It is related to \code{\link{bai.out}}, which calculates each ring area starting from the outside of the tree and working inward. Both methods assume a circular cross section (Biondi 1999). See the references below for further details.
-
+ This converts ring-width series (mm) to ring-area series (mm squared)
+ (aka basal area increments) based on the distance between the
+ innermost measured ring and the pith of the tree. It is related to
+ \code{\link{bai.out}}, which calculates each ring area starting from
+ the outside of the tree and working inward. Both methods assume a
+ circular cross section (Biondi 1999). See the references below for
+ further details.
}
\value{
- A \code{data.frame} containing the ring areas for each series with column names, row names and dimensions of \code{\var{rwl}}.
+ A \code{data.frame} containing the ring areas for each series with
+ column names, row names and dimensions of \code{\var{rwl}}.
}
-\references{ Biondi, F. (1999) Comparing tree-ring chronologies and repeated timber inventories as forest monitoring tools. \emph{Ecological Applications}, 9(1):216\enc{–}{--}227.
+\references{
+ Biondi, F. (1999) Comparing tree-ring chronologies and repeated timber
+ inventories as forest monitoring tools. \emph{Ecological
+ Applications}, \bold{9}(1), 216\enc{–}{--}227.
-Biondi, F. and Qeadan, F. (2008) A theory-driven approach to tree-ring standardization: Defining the biological trend from expected basal area increment. \emph{Tree-Ring Research}, 64(2):81\enc{–}{--}96.
+ Biondi, F. and Qeadan, F. (2008) A theory-driven approach to tree-ring
+ standardization: Defining the biological trend from expected basal area
+ increment. \emph{Tree-Ring Research}, \bold{64}(2), 81\enc{–}{--}96.
}
\note{ DendroLab website: \url{http://dendrolab.org/} }
\author{ Code by Andy Bunn based on work from DendroLab, University of
Modified: pkg/dplR/man/bai.out.Rd
===================================================================
--- pkg/dplR/man/bai.out.Rd 2015-03-11 11:57:35 UTC (rev 972)
+++ pkg/dplR/man/bai.out.Rd 2015-03-12 08:50:48 UTC (rev 973)
@@ -3,26 +3,47 @@
\alias{bai.out}
\title{ Basal Area Increment (Outside In) }
\description{
- Convert multiple ring-width series to basal area increment (i.e., ring area) going from the bark to the pith.
-
+ Convert multiple ring-width series to basal area increment (i.e., ring
+ area) going from the bark to the pith.
}
\usage{
bai.out(rwl, diam = NULL)
}
\arguments{
- \item{rwl}{ a \code{data.frame} with series as columns and years as rows such as that produced by \code{\link{read.rwl}} }
- \item{diam}{ an optional \code{data.frame} containing two variables. If present, variable one (\code{\var{series}} in the example below) gives the series \acronym{ID} as either \code{character}s or \code{factor}s. These must exactly match \code{colnames(\var{rwl})}. Variable two (\code{\var{diam}} in the example below) gives the diameter of the tree (in mm) up to the outermost ring (e.g., the diameter of the tree where the core was taken minus the thickness of the bark). If \code{\var{diam}} is \code{NULL} then the diameter is taken as twice the sum of the widths for each series (column) in \code{\var{rwl}}. }
+ \item{rwl}{ a \code{data.frame} with series as columns and years as
+ rows such as that produced by \code{\link{read.rwl}} }
+ \item{diam}{ an optional \code{data.frame} containing two variables.
+ If present, variable one (\code{\var{series}} in the example below)
+ gives the series \acronym{ID} as either \code{character}s or
+ \code{factor}s. These must exactly match
+ \code{colnames(\var{rwl})}. Variable two (\code{\var{diam}} in the
+ example below) gives the diameter of the tree (in mm) up to the
+ outermost ring (e.g., the diameter of the tree where the core was
+ taken minus the thickness of the bark). If \code{\var{diam}} is
+ \code{NULL} then the diameter is taken as twice the sum of the
+ widths for each series (column) in \code{\var{rwl}}. }
}
\details{
-This converts ring-width series (mm) to ring-area series (mm squared) (aka basal area increments) based on the diameter of the tree and the width of each ring moving towards the pith of the tree. It is related to \code{\link{bai.in}}, which calculates each ring area starting from the inside of the tree and working outward. Both methods assume a circular cross section (Biondi 1999). See the references below for further details.
-
+ This converts ring-width series (mm) to ring-area series (mm squared)
+ (aka basal area increments) based on the diameter of the tree and the
+ width of each ring moving towards the pith of the tree. It is related
+ to \code{\link{bai.in}}, which calculates each ring area starting from
+ the inside of the tree and working outward. Both methods assume a
+ circular cross section (Biondi 1999). See the references below for
+ further details.
}
\value{
- A \code{data.frame} containing the ring areas for each series with column names, row names and dimensions of \code{\var{rwl}}.
+ A \code{data.frame} containing the ring areas for each series with
+ column names, row names and dimensions of \code{\var{rwl}}.
}
-\references{ Biondi, F. (1999) Comparing tree-ring chronologies and repeated timber inventories as forest monitoring tools. \emph{Ecological Applications}, 9(1):216\enc{–}{--}227.
+\references{
+ Biondi, F. (1999) Comparing tree-ring chronologies and repeated timber
+ inventories as forest monitoring tools. \emph{Ecological
+ Applications}, \bold{9}(1), 216\enc{–}{--}227.
-Biondi, F. and Qeadan, F. (2008) A theory-driven approach to tree-ring standardization: Defining the biological trend from expected basal area increment. \emph{Tree-Ring Research}, 64(2):81\enc{–}{--}96.
+ Biondi, F. and Qeadan, F. (2008) A theory-driven approach to tree-ring
+ standardization: Defining the biological trend from expected basal area
+ increment. \emph{Tree-Ring Research}, \bold{64}(2), 81\enc{–}{--}96.
}
\note{ DendroLab website: \url{http://dendrolab.org/} }
\author{ Code by Andy Bunn based on work from DendroLab, University of
Modified: pkg/dplR/man/ca533.Rd
===================================================================
--- pkg/dplR/man/ca533.Rd 2015-03-11 11:57:35 UTC (rev 972)
+++ pkg/dplR/man/ca533.Rd 2015-03-12 08:50:48 UTC (rev 973)
@@ -20,9 +20,10 @@
\url{ftp://ftp.ncdc.noaa.gov/pub/data/paleo/treering/measurements/northamerica/usa/ca533.rwl}
}
\references{
- Graybill, D. (1983) Campito Mountain Data Set. \acronym{IGBP}
- \acronym{PAGES}/World Data Center for Paleoclimatology Data
- Contribution Series 1983-CA533.RWL. \acronym{NOAA}/\acronym{NCDC}
- Paleoclimatology Program, Boulder, Colorado, \acronym{USA}.
+ Graybill, D. A. and LaMarche, Jr., V. C. (1983) Campito Mountain Data
+ Set. \acronym{IGBP} \acronym{PAGES}/World Data Center for
+ Paleoclimatology Data Contribution Series 1983-CA533.RWL.
+ \acronym{NOAA}/\acronym{NCDC} Paleoclimatology Program, Boulder,
+ Colorado, \acronym{USA}.
}
\keyword{datasets}
Modified: pkg/dplR/man/cana157.Rd
===================================================================
--- pkg/dplR/man/cana157.Rd 2015-03-11 11:57:35 UTC (rev 972)
+++ pkg/dplR/man/cana157.Rd 2015-03-12 08:50:48 UTC (rev 973)
@@ -19,9 +19,9 @@
\url{ftp://ftp.ncdc.noaa.gov/pub/data/paleo/treering/chronologies/northamerica/canada/cana157.crn}
}
\references{
- Jacoby, G., D'Arrigo, R. and Buckley, B. (1992) Twisted Tree Heartrot
- Hill Data Set. \acronym{IGBP} \acronym{PAGES}/World Data Center for
- Paleoclimatology Data Contribution Series 1992-CANA157.CRN.
+ Jacoby, G., D\enc{’}{'}Arrigo, R. and Buckley, B. (1992) Twisted Tree
+ Heartrot Hill Data Set. \acronym{IGBP} \acronym{PAGES}/World Data
+ Center for Paleoclimatology Data Contribution Series 1992-CANA157.CRN.
\acronym{NOAA}/\acronym{NCDC} Paleoclimatology Program, Boulder,
Colorado, \acronym{USA}.
}
Modified: pkg/dplR/man/ccf.series.rwl.Rd
===================================================================
--- pkg/dplR/man/ccf.series.rwl.Rd 2015-03-11 11:57:35 UTC (rev 972)
+++ pkg/dplR/man/ccf.series.rwl.Rd 2015-03-12 08:50:48 UTC (rev 973)
@@ -29,13 +29,13 @@
years (e.g., 20, 50, 100 years). }
\item{bin.floor}{ a non-negative integral value giving the base for
locating the first segment (e.g., 1600, 1700, 1800
- \acronym{AD}). Typically 0, 10, 50, 100, etc. } \item{n}{
- \code{NULL} or an integral value giving the filter length for the
- \code{\link{hanning}} filter used for removal of low frequency
- variation. }
- \item{prewhiten}{ \code{logical} flag. If \code{TRUE} each series is
+ \acronym{AD}). Typically 0, 10, 50, 100, etc. }
+ \item{n}{ \code{NULL} or an integral value giving the filter length
+ for the \code{\link{hanning}} filter used for removal of low
+ frequency variation. }
+ \item{prewhiten}{ \code{logical} flag. If \code{TRUE} each series is
whitened using \code{\link{ar}}. }
- \item{biweight}{ \code{logical} flag. If \code{TRUE} then a robust
+ \item{biweight}{ \code{logical} flag. If \code{TRUE} then a robust
mean is calculated using \code{\link{tbrm}}. }
\item{pcrit}{ a number between 0 and 1 giving the critical value for the
correlation test. }
@@ -43,7 +43,7 @@
calculate the \code{\link{ccf}}. }
\item{make.plot}{ \code{logical} flag indicating whether to make a
plot. }
- \item{floor.plus1}{ \code{logical} flag. If \code{TRUE}, one year is
+ \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{\dots}{ other arguments passed to plot. }
@@ -53,44 +53,44 @@
tree-ring series and a master chronology built from \code{\var{rwl}}
looking at correlations lagged positively and negatively using
\code{\link{ccf}} at overlapping segments set by
- \code{\var{seg.length}}. For instance, with \code{\var{lag.max}} set
+ \code{\var{seg.length}}. For instance, with \code{\var{lag.max}} set
to 5, cross-correlations would be calculated at for each segment with
- the master lagged at \code{\var{k} = -5:5} years.
+ the master lagged at \code{\var{k} = -5:5} years.
The cross correlations are calculated calling
\code{\link{ccf}} as \cr
- \code{ccf(x=series, y=master, lag.max=lag.max, plot=FALSE)}. Note that
+ \code{ccf(x=series, y=master, lag.max=lag.max, plot=FALSE)}. Note that
prior to dplR version 1.60, the \code{master} was set as \code{x} and
- the \code{series} as \code{y}. This was changed to be more in line with
+ the \code{series} as \code{y}. This was changed to be more in line with
user expectations so that a missing ring in a series produces a positive
- lag in the plot rather than a negative lag. This structure of this call
+ lag in the plot rather than a negative lag. This structure of this call
does put the plots at odds with Figure 3 in Bunn (2010) which is unfortunate.
Correlations are calculated for the first segment, then the
- second segment and so on. Correlations are only calculated for segments with
+ second segment and so on. Correlations are only calculated for segments with
complete overlap with the master chronology.
Each series (including those in the \code{\var{rwl}} object) is
optionally detrended as the residuals from a \code{\link{hanning}}
- filter with weight \code{\var{n}}. The filter is not applied if
- \code{\var{n}} is \code{NULL}. Detrending can also be done via
+ filter with weight \code{\var{n}}. The filter is not applied if
+ \code{\var{n}} is \code{NULL}. Detrending can also be done via
prewhitening where the residuals of an \code{\link{ar}} model are
- added to each series mean. This is the default. The master chronology
+ added to each series mean. This is the default. The master chronology
is computed as the mean of the \code{\var{rwl}} object using
\code{\link{tbrm}} if \code{\var{biweight}} is \code{TRUE} and
- \code{rowMeans} if not. Note that detrending typically changes the
+ \code{rowMeans} if not. Note that detrending typically changes the
length of the series. E.g., a \code{\link{hanning}} filter will
- shorten the series on either end by \code{floor(\var{n}/2)}. The
+ shorten the series on either end by \code{floor(\var{n}/2)}. The
prewhitening default will change the series length based on the
- \code{\link{ar}} model fit. The effects of detrending can be seen with
+ \code{\link{ar}} model fit. The effects of detrending can be seen with
\code{\link{series.rwl.plot}}.
}
\value{
A \code{list} containing matrices \code{\var{ccf}} and
- \code{\var{bins}}. Matrix \code{\var{ccf}} contains the correlations
+ \code{\var{bins}}. Matrix \code{\var{ccf}} contains the correlations
between the series and the master chronology at the lags window given
- by \code{\var{lag.max}}. Matrix \code{\var{bins}} contains the years
+ by \code{\var{lag.max}}. Matrix \code{\var{bins}} contains the years
encapsulated by each bin.
}
\author{ Andy Bunn. Patched and improved by Mikko Korpela. }
@@ -98,8 +98,8 @@
\code{\link{skel.plot}}, \code{\link{series.rwl.plot}}
}
\references{ Bunn, A. G. (2010) Statistical and visual crossdating
- in R using the dplR library. \emph{Dendrochronologia},
- 28(4):251\enc{–}{--}258.
+ in R using the dplR library. \emph{Dendrochronologia},
+ \bold{28}(4), 251\enc{–}{--}258.
}
\examples{
data(co021)
Modified: pkg/dplR/man/chron.Rd
===================================================================
--- pkg/dplR/man/chron.Rd 2015-03-11 11:57:35 UTC (rev 972)
+++ pkg/dplR/man/chron.Rd 2015-03-12 08:50:48 UTC (rev 973)
@@ -16,13 +16,13 @@
containing each series \acronym{ID} such as produced by
\code{\link{read.rwl}}}
\item{prefix}{a \code{character} string with less than 4
- characters. Defaults to \code{"xxx"}}
- \item{biweight}{\code{logical} flag. If \acronym{TRUE} then a robust
+ characters. Defaults to \code{"xxx"}}
+ \item{biweight}{\code{logical} flag. If \acronym{TRUE} then a robust
mean is calculated using \code{\link{tbrm}.}}
- \item{prewhiten}{\code{logical} flag. If \acronym{TRUE} each series is
+ \item{prewhiten}{\code{logical} flag. If \acronym{TRUE} each series is
whitened using \code{\link{ar}} prior to averaging.}
\item{\dots}{Arguments passed to \code{\link{ar}} when
- \code{prewhiten} is \code{TRUE}. For example, use \code{aic}
+ \code{prewhiten} is \code{TRUE}. For example, use \code{aic}
and \code{order.max} to control the order of the AR model.}
}
\details{
@@ -35,14 +35,14 @@
prewhitening was performed), and the sample depth.
}
\references{
- Cook, E. R. and Kairiukstis, L. A. (1990) \emph{Methods of
- Dendrochronology: Applications in the Environmental Sciences.}
- Springer. \acronym{ISBN-13}: 978-0-7923-0586-6.
+ Cook, E. R. and Kairiukstis, L. A., editors (1990) \emph{Methods of
+ Dendrochronology: Applications in the Environmental Sciences}.
+ Springer. \acronym{ISBN-13}: 978-0-7923-0586-6.
- Fritts, H. C. (2001) \emph{Tree Rings and Climate.} Blackburn.
+ Fritts, H. C. (2001) \emph{Tree Rings and Climate}. Blackburn.
\acronym{ISBN-13}: 978-1-930665-39-2.
}
-\author{ Andy Bunn. Patched and improved by Mikko Korpela. }
+\author{ Andy Bunn. Patched and improved by Mikko Korpela. }
\seealso{ \code{\link{read.rwl}}, \code{\link{detrend}},
\code{\link{ar}}, \code{\link{crn.plot}}
}
Modified: pkg/dplR/man/cms.Rd
===================================================================
--- pkg/dplR/man/cms.Rd 2015-03-11 11:57:35 UTC (rev 972)
+++ pkg/dplR/man/cms.Rd 2015-03-12 08:50:48 UTC (rev 973)
@@ -9,33 +9,59 @@
cms(rwl, po, c.hat.t = FALSE, c.hat.i = FALSE)
}
\arguments{
- \item{rwl}{ a \code{data.frame} with series as columns and years as rows such as
- that produced by \code{\link{read.rwl}} }
- \item{po}{ a \code{data.frame} containing two variables. Variable one (\code{\var{series}} in the example below) gives the series \acronym{ID} as either \code{character}s or \code{factor}s. These must exactly match \code{colnames(\var{rwl})}. Variable two (\code{\var{pith.offset}} in the example below) must be integral values and give the years from the beginning of the core to the pith (or center) of the tree. }
- \item{c.hat.t}{ a \code{logical} indicating whether to export the C-curves for each tree by biological age. }
- \item{c.hat.i}{ a \code{logical} indicating whether to export the expected ring widths for each series. }
+ \item{rwl}{ a \code{data.frame} with series as columns and years as
+ rows such as that produced by \code{\link{read.rwl}} }
+ \item{po}{ a \code{data.frame} containing two variables. Variable one
+ (\code{\var{series}} in the example below) gives the series
+ \acronym{ID} as either \code{character}s or \code{factor}s. These
+ must exactly match \code{colnames(\var{rwl})}. Variable two
+ (\code{\var{pith.offset}} in the example below) must be integral
+ values and give the years from the beginning of the core to the pith
+ (or center) of the tree. }
+ \item{c.hat.t}{ a \code{logical} indicating whether to export the
+ C-curves for each tree by biological age. }
+ \item{c.hat.i}{ a \code{logical} indicating whether to export the
+ expected ring widths for each series. }
}
\details{
- This method detrends and standardizes tree-ring series by calculating a growth curve based on constant annual basal area increment. The method is based on the \dQuote{assumption that constant growth is expressed by a constant basal area increment distributed over a growing surface} (Biondi and Qeadan 2008). The detrending is the estimation and removal of the tree's natural biological growth trend. The standardization is done by dividing each series by the growth trend to produce units in the dimensionless ring-width index (\acronym{RWI}).
+ This method detrends and standardizes tree-ring series by calculating
+ a growth curve based on constant annual basal area increment. The
+ method is based on the \dQuote{assumption that constant growth is
+ expressed by a constant basal area increment distributed over a
+ growing surface} (Biondi and Qeadan 2008). The detrending is the
+ estimation and removal of the tree\enc{’}{'}s natural biological
+ growth trend. The standardization is done by dividing each series by
+ the growth trend to produce units in the dimensionless ring-width
+ index (\acronym{RWI}).
- This attempts to remove the low frequency variability that is due to biological or stand effects.
+ This attempts to remove the low frequency variability that is due to
+ biological or stand effects.
See the reference below for further details.
}
\value{
- A \code{data.frame} containing the dimensionless and detrended ring-width indices with column names, row names and dimensions of \code{\var{rwl}} if \code{\var{c.hat.t}} is \code{FALSE} and \code{\var{c.hat.i}} is \code{FALSE}.
- Otherwise a \code{list} of length 2 or 3 containing the \acronym{RWI} \code{data.frame}, a \code{data.frame} containing the C-curves for each tree (\code{\var{c.hat.t}}), and/or a vector containing the C-values for each tree (\code{\var{c.hat.i}}) depending on the output flags. See Eq. 12 in Biondi and Qeadan (2008) for more detail on \code{\var{c.hat.t}}, and \code{\var{c.hat.i}}.
+ A \code{data.frame} containing the dimensionless and detrended
+ ring-width indices with column names, row names and dimensions of
+ \code{\var{rwl}} if \code{\var{c.hat.t}} is \code{FALSE} and
+ \code{\var{c.hat.i}} is \code{FALSE}.
+
+ Otherwise a \code{list} of length 2 or 3 containing the \acronym{RWI}
+ \code{data.frame}, a \code{data.frame} containing the C-curves for
+ each tree (\code{\var{c.hat.t}}), and/or a vector containing the
+ C-values for each tree (\code{\var{c.hat.i}}) depending on the output
+ flags. See Eq. 12 in Biondi and Qeadan (2008) for more detail on
+ \code{\var{c.hat.t}}, and \code{\var{c.hat.i}}.
}
\references{
Biondi, F. and Qeadan, F. (2008) A theory-driven approach to tree-ring
- standardization: Defining the biological trend from expected basal
- area increment. \emph{Tree-Ring Research}, 64(2):81\enc{–}{--}96.
+ standardization: Defining the biological trend from expected basal area
+ increment. \emph{Tree-Ring Research}, \bold{64}(2), 81\enc{–}{--}96.
}
\note{ DendroLab website: \url{http://dendrolab.org/} }
\author{
Code provided by DendroLab based on programming by F. Qeadan and
F. Biondi, University of Nevada Reno, \acronym{USA} and adapted for
- dplR by Andy Bunn. Patched and improved by Mikko Korpela.
+ dplR by Andy Bunn. Patched and improved by Mikko Korpela.
}
\seealso{ \code{\link{detrend}}, \code{\link{chron}}, \code{\link{rcs}} }
\examples{library(graphics)
Modified: pkg/dplR/man/combine.rwl.Rd
===================================================================
--- pkg/dplR/man/combine.rwl.Rd 2015-03-11 11:57:35 UTC (rev 972)
+++ pkg/dplR/man/combine.rwl.Rd 2015-03-12 08:50:48 UTC (rev 973)
@@ -28,7 +28,7 @@
rows. The keycodes are the column names and the years are the row
names. }
-\author{ Christian Zang. Patched by Mikko Korpela. }
+\author{ Christian Zang. Patched by Mikko Korpela. }
\examples{data(ca533)
data(co021)
Modified: pkg/dplR/man/common.interval.Rd
===================================================================
--- pkg/dplR/man/common.interval.Rd 2015-03-11 11:57:35 UTC (rev 972)
+++ pkg/dplR/man/common.interval.Rd 2015-03-12 08:50:48 UTC (rev 973)
@@ -16,7 +16,7 @@
containing each series \acronym{ID} such as produced by
\code{\link{read.rwl}}}
\item{type}{a \code{character} string of
- \code{"series"}, \code{"years"}, or \code{"both"}. Argument
+ \code{"series"}, \code{"years"}, or \code{"both"}. Argument
matching is performed. }
\item{make.plot}{a \code{logical} indicating if a plot should be drawn }
}
@@ -25,7 +25,7 @@
This trims an \code{rwl} object to a common interval that maximizes
the number of series (\code{type="series"}), the number of years
(\code{type="years"}), or a compromise between the two
- (\code{type="both"}). A modified \code{\link{seg.plot}} can be drawn
+ (\code{type="both"}). A modified \code{\link{seg.plot}} can be drawn
as well.
}
Modified: pkg/dplR/man/corr.rwl.seg.Rd
===================================================================
--- pkg/dplR/man/corr.rwl.seg.Rd 2015-03-11 11:57:35 UTC (rev 972)
+++ pkg/dplR/man/corr.rwl.seg.Rd 2015-03-12 08:50:48 UTC (rev 973)
@@ -37,7 +37,7 @@
mean is calculated using \code{\link{tbrm}}. }
\item{method}{Can be either \code{"pearson"}, \code{"kendall"}, or
\code{"spearman"} which indicates the correlation coefficient to be
- used. Defaults to \code{"spearman"}. See \code{\link{cor.test}}. }
+ used. Defaults to \code{"spearman"}. See \code{\link{cor.test}}. }
\item{make.plot}{ \code{logical flag} indicating whether to make a
plot. }
\item{label.cex}{ \code{numeric} scalar for the series labels on the
@@ -84,7 +84,7 @@
Correlations are calculated for the first segment, then the second
segment and so on. Correlations are only calculated for segments with
complete overlap with the master chronology. For now, correlations are
- Spearman's rho calculated via \code{\link{cor.test}} using
+ Spearman\enc{’}{'}s rho calculated via \code{\link{cor.test}} using
\code{method = "spearman"}.
Each series (including those in the rwl object) is optionally
@@ -118,7 +118,7 @@
correlations for each series by bin. Matrix \code{\var{p.val}}
contains the p-values on the correlation for each series by
bin. Matrix \code{\var{overall}} contains the average correlation and
- p-value for each series. Matrix \code{\var{bins}} contains the years
+ p-value for each series. Matrix \code{\var{bins}} contains the years
encapsulated by each bin. The vector \code{\var{avg.seg.rho}}
contains the average correlation for each bin.
}
Modified: pkg/dplR/man/corr.series.seg.Rd
===================================================================
--- pkg/dplR/man/corr.series.seg.Rd 2015-03-11 11:57:35 UTC (rev 972)
+++ pkg/dplR/man/corr.series.seg.Rd 2015-03-12 08:50:48 UTC (rev 973)
@@ -30,22 +30,22 @@
years (e.g., 20, 50, 100 years). }
\item{bin.floor}{ a non-negative integral value giving the base for
locating the first segment (e.g., 1600, 1700, 1800
- \acronym{AD}). Typically 0, 10, 50, 100, etc. }
+ \acronym{AD}). Typically 0, 10, 50, 100, etc. }
\item{n}{ \code{NULL} or an integral value giving the filter length
for the \code{\link{hanning}} filter used for removal of low
frequency variation. }
- \item{prewhiten}{ \code{logical} flag. If \code{TRUE} each series is
+ \item{prewhiten}{ \code{logical} flag. If \code{TRUE} each series is
whitened using \code{\link{ar}}. }
- \item{biweight}{ \code{logical} flag. If \code{TRUE} then a robust
+ \item{biweight}{ \code{logical} flag. If \code{TRUE} then a robust
mean is calculated using \code{\link{tbrm}}. }
\item{method}{Can be either \code{"pearson"}, \code{"kendall"}, or
\code{"spearman"} which indicates the correlation coefficient to be
- used. Defaults to \code{"spearman"}. See \code{\link{cor.test}}. }
+ used. Defaults to \code{"spearman"}. See \code{\link{cor.test}}. }
\item{pcrit}{ a number between 0 and 1 giving the critical value for
the correlation test. }
\item{make.plot}{ \code{logical} flag indicating whether to make a
plot. }
- \item{floor.plus1}{ \code{logical} flag. If \code{TRUE}, one year is
+ \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{\dots}{ other arguments passed to plot. }
@@ -65,14 +65,14 @@
\code{\var{p.val}}, and \code{\var{overall}}.
Matrix \code{\var{bins}} contains the years encapsulated by each bin
- (segments). Matrix \code{\var{moving.rho}} contains the moving
+ (segments). Matrix \code{\var{moving.rho}} contains the moving
correlation and p-value for a moving average equal to
\code{\var{seg.length}}. Vector \code{\var{spearman.rho}} contains
the correlations by bin and \code{\var{p.val}} contains
- the p-values. Vector \code{\var{overall}} contains the average
+ the p-values. Vector \code{\var{overall}} contains the average
correlation and p-value.
}
-\author{ Andy Bunn. Patched and improved by Mikko Korpela. }
+\author{ Andy Bunn. Patched and improved by Mikko Korpela. }
\seealso{
\code{\link{corr.series.seg}}, \code{\link{skel.plot}},
\code{\link{series.rwl.plot}}, \code{\link{ccf.series.rwl}}
Modified: pkg/dplR/man/crn.plot.Rd
===================================================================
--- pkg/dplR/man/crn.plot.Rd 2015-03-11 11:57:35 UTC (rev 972)
+++ pkg/dplR/man/crn.plot.Rd 2015-03-12 08:50:48 UTC (rev 973)
@@ -21,18 +21,18 @@
}
\arguments{
\item{x, crn}{ a \code{data.frame} e.g., as produced by
- \code{\link{chron}}. The \code{data.frame} should have the years in
+ \code{\link{chron}}. The \code{data.frame} should have the years in
\code{rownames(\var{crn})}, the chronologies in the columns.
Optionally, the last column can contain the sample depth named
- \code{"samp.depth"}. If the data are produced via \code{\link{chron}}
+ \code{"samp.depth"}. If the data are produced via \code{\link{chron}}
the object will be of class "crn" and the generic plot method can be used }
- \item{add.spline}{ a \code{logical} flag. Will add a line with a
+ \item{add.spline}{ a \code{logical} flag. Will add a line with a
smoothing spline using \code{\link{ffcsaps} } }
\item{nyrs}{ a number giving the rigidity of the smoothing spline.
Defaults to 0.33 times the length of the first chronology if
\code{\var{nyrs}} is \code{NULL} }
\item{f}{ a number between 0 and 1 giving the frequency response or
- wavelength cutoff. Defaults to 0.5 }
+ wavelength cutoff. Defaults to 0.5 }
\item{crn.line.col}{ color for the x line }
\item{spline.line.col}{ color for the spline (if added) }
\item{samp.depth.col}{ color for the sample depth polygon (if present) }
@@ -51,9 +51,9 @@
This makes a plot of one or more tree-ring chronologies.
}
\value{
- None. Invoked for side effect (plot).
+ None. Invoked for side effect (plot).
}
-\author{ Andy Bunn. Patched and improved by Mikko Korpela. }
+\author{ Andy Bunn. Patched and improved by Mikko Korpela. }
\seealso{ \code{\link{chron}}
}
\examples{data(cana157)
Modified: pkg/dplR/man/detrend.Rd
===================================================================
--- pkg/dplR/man/detrend.Rd 2015-03-11 11:57:35 UTC (rev 972)
+++ pkg/dplR/man/detrend.Rd 2015-03-12 08:50:48 UTC (rev 973)
@@ -20,14 +20,14 @@
\item{y.name}{ a \code{character} vector of
\code{length(ncol(\var{rwl}))} that gives the \acronym{ID} of each
- series. Defaults to the column names of \code{\var{rwl}}. }
+ series. Defaults to the column names of \code{\var{rwl}}. }
- \item{make.plot}{ a \code{logical} flag. Makes plots of the raw data
- and detrended data if \code{TRUE}. See details below. }
+ \item{make.plot}{ a \code{logical} flag. Makes plots of the raw data
+ and detrended data if \code{TRUE}. See details below. }
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/dplr -r 973
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