[Dplr-commits] r850 - pkg/dplR/man
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Fri May 2 19:45:21 CEST 2014
Author: mvkorpel
Date: 2014-05-02 19:45:20 +0200 (Fri, 02 May 2014)
New Revision: 850
Modified:
pkg/dplR/man/ccf.series.rwl.Rd
pkg/dplR/man/corr.rwl.seg.Rd
pkg/dplR/man/corr.series.seg.Rd
pkg/dplR/man/dplR-package.Rd
pkg/dplR/man/interseries.cor.Rd
pkg/dplR/man/plot.rwl.Rd
pkg/dplR/man/powt.Rd
pkg/dplR/man/read.tridas.Rd
pkg/dplR/man/rwi.stats.running.Rd
pkg/dplR/man/rwl.stats.Rd
pkg/dplR/man/sea.Rd
pkg/dplR/man/sens1.Rd
pkg/dplR/man/sens2.Rd
pkg/dplR/man/strip.rwl.Rd
pkg/dplR/man/write.tridas.Rd
pkg/dplR/man/xskel.ccf.plot.Rd
Log:
Improved appearance of help pages (text, html, pdf):
* Adjusted line wraps (some lines in dplR.pdf were too long, some
unnecessary line breaks were present in the html)
* Unified the formatting of references
* Shortened the title of interseries.cor.Rd
* Each \keyword entry must be on one line (strip.rwl.Rd created a
spurious empty help topic to the Index of dplR.pdf)
* Fixed some typos, etc.
Modified: pkg/dplR/man/ccf.series.rwl.Rd
===================================================================
--- pkg/dplR/man/ccf.series.rwl.Rd 2014-05-02 14:39:11 UTC (rev 849)
+++ pkg/dplR/man/ccf.series.rwl.Rd 2014-05-02 17:45:20 UTC (rev 850)
@@ -57,7 +57,7 @@
the master lagged at \code{\var{k} = -5:5} years.
The cross correlations are calculated calling
- \code{\link{ccf}} as
+ \code{\link{ccf}} as \cr
\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
@@ -96,8 +96,9 @@
\seealso{ \code{\link{corr.rwl.seg}}, \code{\link{corr.series.seg}},
\code{\link{skel.plot}}, \code{\link{series.rwl.plot}}
}
-\references{ Bunn AG (2010). Statistical and visual crossdating
- in R using the dplR library. Dendrochronologia, 28(4): 251-258.
+\references{ Bunn, A. G. (2010) Statistical and visual crossdating
+ in R using the dplR library. \emph{Dendrochronologia},
+ 28(4):251\enc{–}{--}258.
}
\examples{
data(co021)
Modified: pkg/dplR/man/corr.rwl.seg.Rd
===================================================================
--- pkg/dplR/man/corr.rwl.seg.Rd 2014-05-02 14:39:11 UTC (rev 849)
+++ pkg/dplR/man/corr.rwl.seg.Rd 2014-05-02 17:45:20 UTC (rev 850)
@@ -34,9 +34,9 @@
the correlation test. }
\item{biweight}{ \code{logical} flag. If \code{TRUE} then a robust
mean is calculated using \code{\link{tbrm}}. }
- \item{method}{Can either "pearson", "kendall", or "spearman" which indicates
- the correlation coefficient is to be used. Defaults to "spearman." See
- \code{\link{cor.test}}. }
+ \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}}. }
\item{make.plot}{ \code{logical flag} indicating whether to make a
plot. }
\item{label.cex}{ \code{numeric} scalar for the series labels on the
Modified: pkg/dplR/man/corr.series.seg.Rd
===================================================================
--- pkg/dplR/man/corr.series.seg.Rd 2014-05-02 14:39:11 UTC (rev 849)
+++ pkg/dplR/man/corr.series.seg.Rd 2014-05-02 17:45:20 UTC (rev 850)
@@ -37,9 +37,9 @@
whitened using \code{\link{ar}}. }
\item{biweight}{ \code{logical} flag. If \code{TRUE} then a robust
mean is calculated using \code{\link{tbrm}}. }
- \item{method}{Can either "pearson", "kendall", or "spearman" which indicates
- the correlation coefficient is to be used. Defaults to "spearman." See
- \code{\link{cor.test}}. }
+ \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}}. }
\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
Modified: pkg/dplR/man/dplR-package.Rd
===================================================================
--- pkg/dplR/man/dplR-package.Rd 2014-05-02 14:39:11 UTC (rev 849)
+++ pkg/dplR/man/dplR-package.Rd 2014-05-02 17:45:20 UTC (rev 850)
@@ -13,7 +13,7 @@
\tabular{ll}{
Package: \tab dplR\cr
Type: \tab Package\cr
-License: \tab \acronym{GPL}\cr
+License: \tab \acronym{GPL} (>= 2)\cr
}
\emph{Main Functions}
\describe{
Modified: pkg/dplR/man/interseries.cor.Rd
===================================================================
--- pkg/dplR/man/interseries.cor.Rd 2014-05-02 14:39:11 UTC (rev 849)
+++ pkg/dplR/man/interseries.cor.Rd 2014-05-02 17:45:20 UTC (rev 850)
@@ -1,9 +1,9 @@
\name{interseries.cor}
\alias{interseries.cor}
-\title{ Calculate an indidual series correlation against a master chronology
- in an rwl object }
+\title{ Individual Series Correlation Against a Master Chronology }
\description{
- This function calculates the correlation between a series and a master chronology
+ This function calculates the correlation between a series and a master
+ chronology.
}
\usage{
interseries.cor(rwl,n=NULL,prewhiten=TRUE,biweight=TRUE,
@@ -19,9 +19,9 @@
whitened using \code{\link{ar}}. }
\item{biweight}{ \code{logical} flag. If \code{TRUE} then a robust
mean is calculated using \code{\link{tbrm}}.}
- \item{method}{Can either "pearson", "kendall", or "spearman" which indicates
- the correlation coefficient is to be used. Defaults to "spearman." See
- \code{\link{cor.test}}. }
+ \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}}. }
}
\details{
This function calculates correlation serially between each tree-ring
@@ -42,10 +42,10 @@
series length based on the \code{\link{ar}} model fit. The effects of
detrending can be seen with \code{\link{series.rwl.plot}}.
- This function produces the same output of the "overall" portion of
+ This function produces the same output of the \code{\var{overall}} portion of
\code{\link{corr.rwl.seg}}. The mean correlation value given is sometimes
- referred to as the "overall interseries correlation"" or the "COFECHA
- interseries correlation." This output differs from the \code{rbar}
+ referred to as the \dQuote{overall interseries correlation} or the \dQuote{COFECHA
+ interseries correlation}. This output differs from the \code{rbar}
statistics given by \code{\link{rwi.stats}} in that \code{rbar} is
the average pairwise correlation between series where this is the
correlation between a series and a master chronology.
Modified: pkg/dplR/man/plot.rwl.Rd
===================================================================
--- pkg/dplR/man/plot.rwl.Rd 2014-05-02 14:39:11 UTC (rev 849)
+++ pkg/dplR/man/plot.rwl.Rd 2014-05-02 17:45:20 UTC (rev 850)
@@ -1,10 +1,10 @@
\name{plot.rwl}
\alias{plot.rwl}
\title{
- Plotting rwl objects
+ Plotting Rwl Objects
}
\description{
- Plots rwl objects
+ Plots rwl objects.
}
\usage{
\method{plot}{rwl}(x, plot.type=c("seg","spag"), ...)
@@ -16,7 +16,7 @@
\item{plot.type}{ Character. Type "seg" calls \code{\link{seg.plot}}
while "spag" calls \code{\link{spag.plot}} }
- \item{\dots}{ Additional arguemnts for each \code{type} }
+ \item{\dots}{ Additional arguments for each \code{type} }
}
\value{
Modified: pkg/dplR/man/powt.Rd
===================================================================
--- pkg/dplR/man/powt.Rd 2014-05-02 14:39:11 UTC (rev 849)
+++ pkg/dplR/man/powt.Rd 2014-05-02 17:45:20 UTC (rev 850)
@@ -27,7 +27,7 @@
R_t^{1-b}}{R*_t = R_t^(1-b)}.
}
\references{
- Edward R. Cook and Kenneth Peters (1997) Calculating unbiased
+ Cook, E. R. and Peters, K. (1997) Calculating unbiased
tree-ring indices for the study of climatic and environmental
change. \emph{The Holocene}, 7(3):361\enc{–}{--}370.
}
Modified: pkg/dplR/man/read.tridas.Rd
===================================================================
--- pkg/dplR/man/read.tridas.Rd 2014-05-02 14:39:11 UTC (rev 849)
+++ pkg/dplR/man/read.tridas.Rd 2014-05-02 17:45:20 UTC (rev 850)
@@ -72,36 +72,38 @@
\item{measurements}{A \code{data.frame} or a list of \code{data.frame}s with
the series in columns and the years as rows. Contains measurements
- (\verb{<measurementSeries>}) with known years. The series
+ (\samp{<measurementSeries>}) with known years. The series
\acronym{ID}s are the column names and the years are the row
- names. The series \acronym{ID}s are derived from \verb{<title>}
+ names. The series \acronym{ID}s are derived from \samp{<title>}
elements in the input file. Each unique combination of
- \verb{<project>}, \verb{<object>}, \verb{<unit>}, \verb{<taxon>},
- and \verb{<variable>} gets a separate \code{data.frame}. }
+ \samp{<project>}, \samp{<object>}, \samp{<unit>}, \samp{<taxon>},
+ and \samp{<variable>} gets a separate \code{data.frame}. }
\item{ids}{A \code{data.frame} or a list of \code{data.frame}s with columns
named \code{"tree"}, \code{"core"}, \code{"radius"}, and
\code{"measurement"}, together giving a unique \code{numeric} \acronym{ID}
for each column of the \code{data.frame}(s) in
- \code{\var{measurements}}. If \code{!\var{combine.series} &&
- (\var{ids.from.titles} || \var{ids.from.identifiers})}, some rows
- may be non-unique. }
+ \code{\var{measurements}}.
+
+ If \code{!\var{combine.series} && (\var{ids.from.titles} || \var{ids.from.identifiers})}, some rows may be non-unique. }
\item{titles}{A \code{data.frame} or a list of \code{data.frame}s with
columns named \code{"tree"}, \code{"core"}, \code{"radius"}, and
- \code{"measurement"}, containing the \verb{<title>} hierarchy of
+ \code{"measurement"}, containing the \samp{<title>} hierarchy of
each column of the \code{data.frame}(s) in \code{\var{measurements}}. }
\item{wood.completeness}{A \code{data.frame} or a list of \code{data.frame}s
containing wood completeness information. Column names are a subset
of the following, almost self-explanatory set:
\code{"pith.presence"}, \code{"heartwood.presence"},
- \code{"sapwood.presence"}, \code{"last.ring.presence"},
- \code{"last.ring.details"}, \code{"bark.presence"},
+ \code{"sapwood.presence"},\cr
+ \code{"last.ring.presence"}, \code{"last.ring.details"},
+ \code{"bark.presence"},\cr
\code{"n.sapwood"}, \code{"n.missing.heartwood"},
- \code{"n.missing.sapwood"}, \code{"missing.heartwood.foundation"},
- \code{"missing.sapwood.foundation"}, \code{"n.unmeasured.inner"},
- \code{"n.unmeasured.outer"}. }
+ \code{"n.missing.sapwood"},\cr
+ \code{"missing.heartwood.foundation"},
+ \code{"missing.sapwood.foundation"},\cr
+ \code{"n.unmeasured.inner"}, \code{"n.unmeasured.outer"}. }
\item{unit}{A \code{character} vector giving the unit of the
measurements. Length equals the number of \code{data.frame}s in
@@ -109,7 +111,7 @@
\item{project.id}{A \code{numeric} vector giving the project
\acronym{ID}, i.e. the position of the corresponding
- \verb{<project>} element), of the measurements in each
+ \samp{<project>} element), of the measurements in each
\code{data.frame} in \code{\var{measurements}}. Length equals the
number of \code{data.frame}s. }
@@ -118,15 +120,15 @@
Length equals the number of \code{data.frame}s. }
\item{site.id}{A \code{data.frame} giving the site \acronym{ID}
- (position of \verb{<object>} element(s) within a \verb{<project>})
+ (position of \samp{<object>} element(s) within a \samp{<project>})
of each \code{data.frame} in \code{\var{measurements}}. May have
- several columns to reflect the possibly nested \verb{<object>}
+ several columns to reflect the possibly nested \samp{<object>}
elements. }
\item{site.title}{A \code{data.frame} giving the site
- (\verb{<object>}) title of each \code{data.frame} in
+ (\samp{<object>}) title of each \code{data.frame} in
\code{\var{measurements}}. May have several columns to reflect the
- possibly nested \verb{<object>} elements. }
+ possibly nested \samp{<object>} elements. }
\item{taxon}{A \code{data.frame} showing the taxonomic name for each
\code{data.frame} in \code{\var{measurements}}. Contains some of
@@ -165,7 +167,7 @@
\item{titles}{A \code{data.frame} with columns named
\code{"tree"}, \code{"core"}, \code{"radius"}, and
- \code{"measurement"}, containing the \verb{<title>} hierarchy of
+ \code{"measurement"}, containing the \samp{<title>} hierarchy of
each measurement series in \code{\var{undated}$\var{data}} }
\item{project.id}{A \code{numeric} vector giving the project
@@ -241,14 +243,14 @@
}
\item{type}{A \code{data.frame} containing the type of various
- entities, and metadata related to each \verb{type} element.
+ entities, and metadata related to each \samp{type} element.
Contents are \code{NA} where the metadata is not applicable (e.g.,
- no \code{\var{tree.id}} when the \verb{type} element refers to a
+ no \code{\var{tree.id}} when the \samp{type} element refers to a
project). Columns are a subset of the following:
\describe{
- \item{text}{The text of the \verb{type} element}
+ \item{text}{The text of the \samp{type} element}
\item{lang}{The language of the text}
@@ -262,8 +264,8 @@
\item{project.id}{The \acronym{ID} of the project}
\item{site.id}{One or more columns with this prefix, depending on
- the maximum depth of the \verb{<object>} hierarchy. Gives the
- \acronym{ID} of the site where the \verb{<type>} element
+ the maximum depth of the \samp{<object>} hierarchy. Gives the
+ \acronym{ID} of the site where the \samp{<type>} element
appeared.}
\item{tree.id}{The \acronym{ID} of the tree}
@@ -275,8 +277,8 @@
\item{project.title}{The title of the project}
\item{site.title}{One or more columns with this prefix, depending
- on the maximum depth of the \verb{<object>} hierarchy. Gives the
- title of the site where the \verb{<type>} element appeared.}
+ on the maximum depth of the \samp{<object>} hierarchy. Gives the
+ title of the site where the \samp{<type>} element appeared.}
\item{tree.title}{The title of the tree}
@@ -288,18 +290,18 @@
}
\item{comments}{A \code{data.frame} containing comments to various
- entities, and metadata related to each \verb{comments} element.
+ entities, and metadata related to each \samp{comments} element.
Contents are \code{NA} where the metadata is not applicable. Columns
are a subset of the following:
\describe{
- \item{text}{The text of the \verb{comments} element}
+ \item{text}{The text of the \samp{comments} element}
\item{project.id}{The \acronym{ID} of the project}
\item{site.id}{One or more columns with this prefix, depending on
- the maximum depth of the \verb{<object>} hierarchy. Gives the
+ the maximum depth of the \samp{<object>} hierarchy. Gives the
\acronym{ID} of the site.}
\item{tree.id}{The \acronym{ID} of the tree}
@@ -315,7 +317,7 @@
\item{project.title}{The title of the project}
\item{site.title}{One or more columns with this prefix, depending
- on the maximum depth of the \verb{<object>} hierarchy. Gives the
+ on the maximum depth of the \samp{<object>} hierarchy. Gives the
title of the site.}
\item{tree.title}{The title of the tree}
@@ -332,20 +334,20 @@
}
\item{identifier}{A \code{data.frame} containing identifiers of
- various entities, and metadata related to each \verb{identifier}
+ various entities, and metadata related to each \samp{identifier}
element. Contents are \code{NA} where the metadata is not
applicable. Columns are a subset of the following:
\describe{
- \item{text}{The text of the \verb{identifier} element}
+ \item{text}{The text of the \samp{identifier} element}
\item{domain}{The domain which the identifier is applicable to}
\item{project.id}{The \acronym{ID} of the project}
\item{site.id}{One or more columns with this prefix, depending on
- the maximum depth of the \verb{<object>} hierarchy. Gives the
+ the maximum depth of the \samp{<object>} hierarchy. Gives the
\acronym{ID} of the site.}
\item{tree.id}{The \acronym{ID} of the tree}
@@ -361,7 +363,7 @@
\item{project.title}{The title of the project}
\item{site.title}{One or more columns with this prefix, depending
- on the maximum depth of the \verb{<object>} hierarchy. Gives the
+ on the maximum depth of the \samp{<object>} hierarchy. Gives the
title of the site.}
\item{tree.title}{The title of the tree}
@@ -488,7 +490,7 @@
\item{project.id}{The \acronym{ID} of the project}
\item{site.id}{One or more columns with this prefix, depending on
- the maximum depth of the \verb{<object>} hierarchy. Gives the
+ the maximum depth of the \samp{<object>} hierarchy. Gives the
\acronym{ID} of the site.}
\item{tree.id}{The \acronym{ID} of the tree}
@@ -496,7 +498,7 @@
\item{project.title}{The title of the project}
\item{site.title}{One or more columns with this prefix, depending
- on the maximum depth of the \verb{<object>} hierarchy. Gives the
+ on the maximum depth of the \samp{<object>} hierarchy. Gives the
title of the site.}
\item{tree.title}{The title of the tree}
@@ -521,7 +523,7 @@
\item{project.id}{The \acronym{ID} of the project}
\item{site.id}{One or more columns with this prefix, depending on
- the maximum depth of the \verb{<object>} hierarchy. Gives the
+ the maximum depth of the \samp{<object>} hierarchy. Gives the
\acronym{ID} of the site.}
\item{tree.id}{The \acronym{ID} of the tree}
@@ -529,7 +531,7 @@
\item{project.title}{The title of the project}
\item{site.title}{One or more columns with this prefix, depending on
- the maximum depth of the \verb{<object>} hierarchy. Gives
+ the maximum depth of the \samp{<object>} hierarchy. Gives
the title of the site.}
\item{tree.title}{The title of the tree}
Modified: pkg/dplR/man/rwi.stats.running.Rd
===================================================================
--- pkg/dplR/man/rwi.stats.running.Rd 2014-05-02 14:39:11 UTC (rev 849)
+++ pkg/dplR/man/rwi.stats.running.Rd 2014-05-02 17:45:20 UTC (rev 850)
@@ -36,17 +36,16 @@
\item{ids}{ an optional \code{data.frame} with column one named
\code{"tree"} giving a \code{numeric} \acronym{ID} for each tree and
column two named \code{"core"} giving a \code{numeric} \acronym{ID}
- for each core. Defaults to one core per tree as
- \code{data.frame(tree = 1:ncol(\var{rwi}), core = rep(1,
- ncol(\var{rwi})))}. }
+ for each core. Defaults to one core per tree as\cr
+ \code{data.frame(tree=1:ncol(\var{rwi}), core=rep(1, ncol(\var{rwi})))}. }
\item{period}{ a \code{character} string, either \code{"common"} or
\code{"max"} indicating whether correlations should be limited to
complete observations over the period common to all cores (i.e. rows
common to all samples) or the maximum pairwise overlap. Defaults
to \code{"max"}. }
- \item{method}{Can either "pearson", "kendall", or "spearman" which indicates
- the correlation coefficient is to be used. Defaults to "spearman." See
- \code{\link{cor}}. }
+ \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}}. }
\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. }
@@ -163,10 +162,12 @@
least one non-\code{NA} core in order to be counted). Not returned
in the results of \code{rwi.stats.legacy}}
- \item{n.tot}{total number of correlations calculated as \code{
- \var{n.wt} + \var{n.bt}}. Equal to \code{\var{n.cores} *
- (\var{n.cores}-1)/2} if there is overlap between all samples }
+ \item{n.tot}{total number of correlations calculated as
+ \code{\var{n.wt} + \var{n.bt}}.
+ Equal to \code{\var{n.cores} * (\var{n.cores}-1)/2} if there is
+ overlap between all samples }
+
\item{n.wt}{number of within-tree correlations computed}
\item{n.bt}{number of between-tree correlations computed}
@@ -183,15 +184,16 @@
\item{c.eff}{the effective number of cores (takes into account the
number of within-tree correlations in each tree)}
- \item{rbar.eff}{the effective signal calculated as \code{
- \var{rbar.bt} / (\var{rbar.wt} + (1-\var{rbar.wt}) / \var{c.eff}) }}
+ \item{rbar.eff}{the effective signal calculated as
+ \code{\var{rbar.bt} / (\var{rbar.wt} + (1-\var{rbar.wt}) / \var{c.eff}) }}
\item{eps}{the expressed population signal calculated using the average
- number of trees as \code{\var{n} * \var{rbar.eff} / ((\var{n} - 1) *
- \var{rbar.eff} + 1)} }
+ number of trees as\cr
+ \code{\var{n} * \var{rbar.eff} / ((\var{n} - 1) * \var{rbar.eff} + 1)} }
\item{snr}{the signal to noise ratio calculated using the average
- number of trees as \code{\var{n} * \var{rbar.eff} / (1-\var{rbar.eff})} }
+ number of trees as\cr
+ \code{\var{n} * \var{rbar.eff} / (1-\var{rbar.eff})} }
}
\references{
@@ -199,7 +201,10 @@
Dendrochronology: Applications in the Environmental Sciences}.
Springer. \acronym{ISBN-13}: 978-0-7923-0586-6.
- Cook, E. R. and Pederson, N. (2011) \emph{Uncertainty, Emergence, and Statistics in Dendrochronology} In M.K. Hughes, T.W. Swetnam, and H.F. Diaz (Eds.), \emph{Dendroclimatology}(77-112), \acronym{ISBN-13}: 978-1-4020-4010-8.
+ Cook, E. R. and Pederson, N. (2011) \emph{Uncertainty, Emergence, and
+ Statistics in Dendrochronology} In M.K. Hughes, T.W. Swetnam, and
+ H.F. Diaz (Eds.), \emph{Dendroclimatology} (77\enc{–}{--}112),
+ \acronym{ISBN-13}: 978-1-4020-4010-8.
Fritts, H. C. (2001) \emph{Tree Rings and Climate}. Blackburn.
\acronym{ISBN-13}: 978-1-930665-39-2.
Modified: pkg/dplR/man/rwl.stats.Rd
===================================================================
--- pkg/dplR/man/rwl.stats.Rd 2014-05-02 14:39:11 UTC (rev 849)
+++ pkg/dplR/man/rwl.stats.Rd 2014-05-02 17:45:20 UTC (rev 850)
@@ -50,9 +50,10 @@
}
\references{
- Bunn. A.G., Jansma E., Korpela M., Westfall R.D., and Baldwin J. (2013)
- Using simulations and data to evaluate mean sensitivity (zeta) as a useful
- statistic in dendrochronology Dendrochronologia 31 250–4.
+ Bunn, A. G., Jansma, E., Korpela, M., Westfall, R. D., and Baldwin,
+ J. (2013) Using simulations and data to evaluate mean sensitivity
+ (\eqn{\zeta}{zeta}) as a useful statistic in dendrochronology.
+ \emph{Dendrochronologia}, 31(3):250\enc{–}{--}254.
Cook, E. R. and Kairiukstis, L.A. (1990) \emph{Methods of
Dendrochronology: Applications in the Environmental Sciences}.
Modified: pkg/dplR/man/sea.Rd
===================================================================
--- pkg/dplR/man/sea.Rd 2014-05-02 14:39:11 UTC (rev 849)
+++ pkg/dplR/man/sea.Rd 2014-05-02 17:45:20 UTC (rev 850)
@@ -51,7 +51,7 @@
\references{
- Lough, J. M., Fritts, H. C. (1987) An assessment of the possible
+ Lough, J. M. and Fritts, H. C. (1987) An assessment of the possible
effects of volcanic eruptions on North American climate using
tree-ring data, 1602 to 1900 \acronym{AD}. \emph{Climatic Change},
10(3):219\enc{–}{--}239.
Modified: pkg/dplR/man/sens1.Rd
===================================================================
--- pkg/dplR/man/sens1.Rd 2014-05-02 14:39:11 UTC (rev 849)
+++ pkg/dplR/man/sens1.Rd 2014-05-02 17:45:20 UTC (rev 850)
@@ -26,9 +26,10 @@
Biondi, F. and Qeadan, F. (2008) Inequality in Paleorecords.
\emph{Ecology}, 89(4):1056\enc{–}{--}1067.
- Bunn. A.G., Jansma E., Korpela M., Westfall R.D., and Baldwin J. (2013)
- Using simulations and data to evaluate mean sensitivity (zeta) as a useful
- statistic in dendrochronology Dendrochronologia 31 250–4.
+ Bunn, A. G., Jansma, E., Korpela, M., Westfall, R. D., and Baldwin,
+ J. (2013) Using simulations and data to evaluate mean sensitivity
+ (\eqn{\zeta}{zeta}) as a useful statistic in dendrochronology.
+ \emph{Dendrochronologia}, 31(3):250\enc{–}{--}254.
}
\author{ Mikko Korpela, based on original by Andy Bunn }
Modified: pkg/dplR/man/sens2.Rd
===================================================================
--- pkg/dplR/man/sens2.Rd 2014-05-02 14:39:11 UTC (rev 849)
+++ pkg/dplR/man/sens2.Rd 2014-05-02 17:45:20 UTC (rev 850)
@@ -25,9 +25,10 @@
Biondi, F. and Qeadan, F. (2008) Inequality in Paleorecords.
\emph{Ecology}, 89(4):1056\enc{–}{--}1067.
- Bunn. A.G., Jansma E., Korpela M., Westfall R.D., and Baldwin J. (2013)
- Using simulations and data to evaluate mean sensitivity (zeta) as a useful
- statistic in dendrochronology Dendrochronologia 31 250–4.
+ Bunn, A. G., Jansma, E., Korpela, M., Westfall, R. D., and Baldwin,
+ J. (2013) Using simulations and data to evaluate mean sensitivity
+ (\eqn{\zeta}{zeta}) as a useful statistic in dendrochronology.
+ \emph{Dendrochronologia}, 31(3):250\enc{–}{--}254.
}
\author{ Mikko Korpela, based on original by Andy Bunn }
Modified: pkg/dplR/man/strip.rwl.Rd
===================================================================
--- pkg/dplR/man/strip.rwl.Rd 2014-05-02 14:39:11 UTC (rev 849)
+++ pkg/dplR/man/strip.rwl.Rd 2014-05-02 17:45:20 UTC (rev 850)
@@ -83,6 +83,4 @@
\author{
Christian Zang. Patched and improved by Mikko Korpela.
}
-\keyword{
- manip
-}
+\keyword{ manip }
Modified: pkg/dplR/man/write.tridas.Rd
===================================================================
--- pkg/dplR/man/write.tridas.Rd 2014-05-02 14:39:11 UTC (rev 849)
+++ pkg/dplR/man/write.tridas.Rd 2014-05-02 17:45:20 UTC (rev 850)
@@ -76,9 +76,9 @@
radius, and optional column four named \code{"measurement"} giving
the \code{numeric} \acronym{ID} of the measurement. If column
\code{"measurement"} exists, column \code{"radius"} must also exist.
- Defaults to one core, radius and measurement per tree:
- \code{data.frame(tree = 1:\var{n.col}, core = rep(1,\var{n.col}),
- radius = rep(1,\var{n.col}), measurement = rep(1,\var{n.col}))},
+ Defaults to one core, radius and measurement per tree:\preformatted{
+ data.frame(tree=1:n.col, core=rep(1,n.col),
+ radius=rep(1,n.col), measurement=rep(1,n.col))}
where \code{\var{n.col}} is the number of columns in
\code{\var{rwl.df}}. }
@@ -100,7 +100,7 @@
correct length. After that, the vectors inside the list are
recycled to match the number of derived series in each
\code{data.frame} of \code{\var{crn}}. The default is to write
- empty \verb{<type>} elements. }
+ empty \samp{<type>} elements. }
\item{crn.titles}{ optional \code{character} vector or a \code{list}
of \code{character} vectors giving the titles of the derived series
@@ -113,8 +113,8 @@
\code{character} vectors giving the units of the derived series in
\code{\var{crn}}. The interpretation is the same as with
\code{\var{crn.types}}, except that the default is to mark the
- series as \verb{<unitless>}. Also \code{NA} means
- \verb{<unitless>}. }
+ series as \samp{<unitless>}. Also \code{NA} means
+ \samp{<unitless>}. }
\item{tridas.measuring.method}{ \code{character} vector giving the
measuring method used to acquire each series of \code{\var{rwl.df}}.
@@ -161,14 +161,15 @@
that have not been measured. Typically used to note when rings
are too damaged to measure. Non-negative integral value.}
- \item{pith.presence}{Whether the pith is present or absent. Each
- element must be a partial match with the contents of category
- \code{"complex presence / absence"} in
+ \item{pith.presence}{Whether the pith is present or absent.
+ Each element must be a partial match with the contents of
+ category \code{"complex presence / absence"} in
\code{\link{tridas.vocabulary}}.}
\item{heartwood.presence}{Whether the outer (youngest) heartwood
- is present and if so whether it is complete. Category
- \code{"complex presence / absence"} in
+ is present and if so whether it is complete.
+
+ Category \code{"complex presence / absence"} in
\code{\link{tridas.vocabulary}}.}
\item{n.missing.heartwood}{Estimated number of missing heartwood
@@ -179,14 +180,17 @@
what the certainty is. Free-form string.}
\item{sapwood.presence}{Whether the sapwood is present or not.
+
Category \code{"complex presence / absence"}.}
\item{n.sapwood}{Number of sapwood rings measured. Non-negative
integral value.}
\item{last.ring.presence}{Last ring under the bark is present or
- absent. Category \code{"presence / absence"}.}
+ absent.
+ Category \code{"presence / absence"}.}
+
\item{last.ring.details}{If the last ring under the bark is
present, include information about the completeness of this ring
and/or season of felling. Free-form string.}
@@ -198,9 +202,11 @@
estimation of how many sapwood rings are missing was made and
what the certainty is. Free-form string.}
- \item{bark.presence}{Bark is present or absent. Category
- \code{"presence / absence"} in \code{\link{tridas.vocabulary}}.}
+ \item{bark.presence}{Bark is present or absent.
+ Category \code{"presence / absence"} in
+ \code{\link{tridas.vocabulary}}.}
+
}
}
@@ -303,7 +309,7 @@
}
\item{site.info}{ \code{list} containing information about the site
- (\verb{<object>}). Elements are the following, and all are
+ (\samp{<object>}). Elements are the following, and all are
\code{character} strings:
\describe{
@@ -319,10 +325,10 @@
\item{random.identifiers}{ \code{logical} flag. If \code{TRUE},
unique random identifiers are created with \code{\link{uuid.gen}}
- and attached to each \verb{<project>} (one in the file),
- \verb{object} (site, one in the file), \verb{<element>} (tree),
- \verb{<sample>} (core), \verb{<radius>}, \verb{<measurementSeries>}
- (measurement) and \verb{<derivedSeries>} element in the resulting
+ and attached to each \samp{<project>} (one in the file),
+ \samp{object} (site, one in the file), \samp{<element>} (tree),
+ \samp{<sample>} (core), \samp{<radius>}, \samp{<measurementSeries>}
+ (measurement) and \samp{<derivedSeries>} element in the resulting
TRiDaS file. }
\item{identifier.domain}{ \code{character} string. The domain which
Modified: pkg/dplR/man/xskel.ccf.plot.Rd
===================================================================
--- pkg/dplR/man/xskel.ccf.plot.Rd 2014-05-02 14:39:11 UTC (rev 849)
+++ pkg/dplR/man/xskel.ccf.plot.Rd 2014-05-02 17:45:20 UTC (rev 850)
@@ -49,7 +49,7 @@
The bottom panels show cross correlations for the first half (left) and second
half of the time series using function \code{\link{ccf}} as
-\code{ccf(x=series,y=master,lag.max=5}.
+\code{ccf(x=series,y=master,lag.max=5)}.
The plot is built using the \code{\link[grid]{Grid}} package which allows for
great flexibility in building complicated plots. However, these plots look best
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