From noreply at r-forge.r-project.org Wed Mar 4 15:05:19 2015 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Wed, 4 Mar 2015 15:05:19 +0100 (CET) Subject: [Dplr-commits] r966 - in pkg/dplR: . R Message-ID: <20150304140519.26FF3187872@r-forge.r-project.org> Author: mvkorpel Date: 2015-03-04 15:05:18 +0100 (Wed, 04 Mar 2015) New Revision: 966 Modified: pkg/dplR/ChangeLog pkg/dplR/DESCRIPTION pkg/dplR/NAMESPACE pkg/dplR/R/write.tridas.R Log: Cleaner retrieval of dplR version number in write.tridas() Modified: pkg/dplR/ChangeLog =================================================================== --- pkg/dplR/ChangeLog 2015-02-18 21:08:20 UTC (rev 965) +++ pkg/dplR/ChangeLog 2015-03-04 14:05:18 UTC (rev 966) @@ -32,6 +32,7 @@ - Importing captureOutput() from R.utils. - Importing package Matrix. - Importing various functions from matrixStats. +- Importing packageDescription() from utils, dropped installed.packages(). - Exporting net(). Various .R files @@ -82,6 +83,12 @@ value of the argument. Reported by Daniel Bishop and Neil Pederson. +File: write.tridas.R +-------------------- + +- Implementation detail: When checking the package version, + packageDescription() is now used instead of installed.packages(). + * CHANGES IN dplR VERSION 1.6.2 No functional changes. A unit test was changed so it would not fail Modified: pkg/dplR/DESCRIPTION =================================================================== --- pkg/dplR/DESCRIPTION 2015-02-18 21:08:20 UTC (rev 965) +++ pkg/dplR/DESCRIPTION 2015-03-04 14:05:18 UTC (rev 966) @@ -3,7 +3,7 @@ Type: Package Title: Dendrochronology Program Library in R Version: 1.6.3 -Date: 2015-02-12 +Date: 2015-03-04 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/NAMESPACE =================================================================== --- pkg/dplR/NAMESPACE 2015-02-18 21:08:20 UTC (rev 965) +++ pkg/dplR/NAMESPACE 2015-03-04 14:05:18 UTC (rev 966) @@ -31,7 +31,7 @@ importFrom(stringr, str_pad, str_trim) -importFrom(utils, head, installed.packages, read.fwf, tail, +importFrom(utils, head, packageDescription, read.fwf, tail, packageVersion, write.table) import(Matrix) Modified: pkg/dplR/R/write.tridas.R =================================================================== --- pkg/dplR/R/write.tridas.R 2015-02-18 21:08:20 UTC (rev 965) +++ pkg/dplR/R/write.tridas.R 2015-03-04 14:05:18 UTC (rev 966) @@ -371,16 +371,9 @@ ## TODO: Enable identifiers given by the user if (random.identifiers) { - prefix.stub <- "dplR" - ip <- try(installed.packages(), silent = TRUE) - if (!inherits(ip, "try-error")) { - dplR.index <- which(rownames(ip) == "dplR") - if (length(dplR.index) > 0) { - prefix.stub <- - paste0(prefix.stub, ip[dplR.index[1], "Version"]) - } - } - ugen <- uuid.gen(paste0(prefix.stub, fname)) + ugen <- uuid.gen(paste0("dplR", + packageDescription("dplR", fields = "Version"), + fname)) } ## From noreply at r-forge.r-project.org Wed Mar 4 16:42:14 2015 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Wed, 4 Mar 2015 16:42:14 +0100 (CET) Subject: [Dplr-commits] r967 - in pkg/dplR: . R Message-ID: <20150304154214.A2B24186D47@r-forge.r-project.org> Author: mvkorpel Date: 2015-03-04 16:42:14 +0100 (Wed, 04 Mar 2015) New Revision: 967 Modified: pkg/dplR/ChangeLog pkg/dplR/R/latexify.R Log: Removed an unused variable from latexify() Modified: pkg/dplR/ChangeLog =================================================================== --- pkg/dplR/ChangeLog 2015-03-04 14:05:18 UTC (rev 966) +++ pkg/dplR/ChangeLog 2015-03-04 15:42:14 UTC (rev 967) @@ -64,6 +64,7 @@ terms of lines of code in dplR. See Henrik Bengtsson's notes at http://www.jottr.org/2014/05/captureOutput.html (referenced on 2015-01-07). +- Removed an unused variable. File: net.R ----------- Modified: pkg/dplR/R/latexify.R =================================================================== --- pkg/dplR/R/latexify.R 2015-03-04 14:05:18 UTC (rev 966) +++ pkg/dplR/R/latexify.R 2015-03-04 15:42:14 UTC (rev 967) @@ -25,7 +25,6 @@ if (any(encBytes)) { y[encBytes] <- captureOutput(cat(y[encBytes], sep = "\n")) } - l10n <- l10n_info() Letters <- paste0(c(LETTERS, letters), collapse="") fontenc <- "fontenc" %in% packages textcomp <- "textcomp" %in% packages From noreply at r-forge.r-project.org Wed Mar 4 16:56:51 2015 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Wed, 4 Mar 2015 16:56:51 +0100 (CET) Subject: [Dplr-commits] r968 - pkg/dplR Message-ID: <20150304155651.6F9501878ED@r-forge.r-project.org> Author: mvkorpel Date: 2015-03-04 16:56:51 +0100 (Wed, 04 Mar 2015) New Revision: 968 Modified: pkg/dplR/ChangeLog pkg/dplR/NAMESPACE Log: Added previously missing imports Modified: pkg/dplR/ChangeLog =================================================================== --- pkg/dplR/ChangeLog 2015-03-04 15:42:14 UTC (rev 967) +++ pkg/dplR/ChangeLog 2015-03-04 15:56:51 UTC (rev 968) @@ -34,6 +34,11 @@ - Importing various functions from matrixStats. - Importing packageDescription() from utils, dropped installed.packages(). - Exporting net(). +- Added previously missing imports. From grDevices: + dev.capabilities(), dev.cur(), png(), dev.off(), dev.set(), + devAskNewPage(). From utils: read.table(). As these packages are + attached by default, the missing imports would not have been a + problem in most cases. Various .R files ---------------- Modified: pkg/dplR/NAMESPACE =================================================================== --- pkg/dplR/NAMESPACE 2015-03-04 15:42:14 UTC (rev 967) +++ pkg/dplR/NAMESPACE 2015-03-04 15:56:51 UTC (rev 968) @@ -9,7 +9,8 @@ importFrom(gmp, as.bigq, as.bigz, chooseZ, is.bigq) -importFrom(grDevices, dev.hold, dev.flush, rainbow) +importFrom(grDevices, dev.hold, dev.flush, rainbow, dev.capabilities, + dev.cur, png, dev.off, dev.set, devAskNewPage) importFrom(grid, gpar, grid.lines, grid.newpage, grid.polygon, grid.segments, grid.text, pushViewport, seekViewport, unit, @@ -32,7 +33,7 @@ importFrom(stringr, str_pad, str_trim) importFrom(utils, head, packageDescription, read.fwf, tail, - packageVersion, write.table) + packageVersion, write.table, read.table) import(Matrix) From noreply at r-forge.r-project.org Wed Mar 4 17:02:59 2015 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Wed, 4 Mar 2015 17:02:59 +0100 (CET) Subject: [Dplr-commits] r969 - pkg/dplR Message-ID: <20150304160300.13E8D187504@r-forge.r-project.org> Author: mvkorpel Date: 2015-03-04 17:02:59 +0100 (Wed, 04 Mar 2015) New Revision: 969 Modified: pkg/dplR/ChangeLog pkg/dplR/NAMESPACE Log: One more missing import added Modified: pkg/dplR/ChangeLog =================================================================== --- pkg/dplR/ChangeLog 2015-03-04 15:56:51 UTC (rev 968) +++ pkg/dplR/ChangeLog 2015-03-04 16:02:59 UTC (rev 969) @@ -36,9 +36,9 @@ - Exporting net(). - Added previously missing imports. From grDevices: dev.capabilities(), dev.cur(), png(), dev.off(), dev.set(), - devAskNewPage(). From utils: read.table(). As these packages are - attached by default, the missing imports would not have been a - problem in most cases. + devAskNewPage(). From utils: read.table(), write.csv(). As these + packages are attached by default, the missing imports would not + have been a problem in most cases. Various .R files ---------------- Modified: pkg/dplR/NAMESPACE =================================================================== --- pkg/dplR/NAMESPACE 2015-03-04 15:56:51 UTC (rev 968) +++ pkg/dplR/NAMESPACE 2015-03-04 16:02:59 UTC (rev 969) @@ -33,7 +33,7 @@ importFrom(stringr, str_pad, str_trim) importFrom(utils, head, packageDescription, read.fwf, tail, - packageVersion, write.table, read.table) + packageVersion, write.table, read.table, write.csv) import(Matrix) From noreply at r-forge.r-project.org Mon Mar 9 16:49:52 2015 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Mon, 9 Mar 2015 16:49:52 +0100 (CET) Subject: [Dplr-commits] r970 - in pkg/dplR: . man Message-ID: <20150309154952.E045F18558F@r-forge.r-project.org> Author: mvkorpel Date: 2015-03-09 16:49:52 +0100 (Mon, 09 Mar 2015) New Revision: 970 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/co021.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/latexDate.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/rasterPlot.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.rwl.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: * Small formatting changes to cana157.Rd and write.tridas.Rd. * Added \encoding{UTF-8} to all .Rd files. "Writing R Extensions" reads "So an \encoding{} section must be used to specify the encoding if it is not ASCII." The "must" is pretty clear, although "The encoding declared in the DESCRIPTION file will be used if none is declared in the file." Not all .Rd files in dplR contain non-ASCII characters, but we add the \encoding{} anyway so that it will not be missing when possibly needed in the future. Modified: pkg/dplR/DESCRIPTION =================================================================== --- pkg/dplR/DESCRIPTION 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/DESCRIPTION 2015-03-09 15:49:52 UTC (rev 970) @@ -3,7 +3,7 @@ Type: Package Title: Dendrochronology Program Library in R Version: 1.6.3 -Date: 2015-03-04 +Date: 2015-03-09 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 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/anos1.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{anos1} \docType{data} \alias{anos1} Modified: pkg/dplR/man/bai.in.Rd =================================================================== --- pkg/dplR/man/bai.in.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/bai.in.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{bai.in} \alias{bai.in} \title{ Basal Area Increment (Inside Out) } Modified: pkg/dplR/man/bai.out.Rd =================================================================== --- pkg/dplR/man/bai.out.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/bai.out.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{bai.out} \alias{bai.out} \title{ Basal Area Increment (Outside In) } Modified: pkg/dplR/man/ca533.Rd =================================================================== --- pkg/dplR/man/ca533.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/ca533.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{ca533} \docType{data} \alias{ca533} Modified: pkg/dplR/man/cana157.Rd =================================================================== --- pkg/dplR/man/cana157.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/cana157.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{cana157} \docType{data} \alias{cana157} @@ -11,8 +12,8 @@ \usage{data(cana157)} \format{ A \code{data.frame} containing the standard chronology in column one - and the sample depth in column two. There are 463 years (1530--1992) - in the rows. + and the sample depth in column two. There are 463 years + (1530\enc{?}{--}1992) in the rows. } \source{International tree-ring data bank, Accessed on 27-August-2007 at \url{ftp://ftp.ncdc.noaa.gov/pub/data/paleo/treering/chronologies/northamerica/canada/cana157.crn} Modified: pkg/dplR/man/ccf.series.rwl.Rd =================================================================== --- pkg/dplR/man/ccf.series.rwl.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/ccf.series.rwl.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{ccf.series.rwl} \alias{ccf.series.rwl} \title{ Cross-Correlation between a Series and a Master Chronology } Modified: pkg/dplR/man/chron.Rd =================================================================== --- pkg/dplR/man/chron.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/chron.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{chron} \alias{chron} \title{Build Mean Value Chronology} Modified: pkg/dplR/man/cms.Rd =================================================================== --- pkg/dplR/man/cms.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/cms.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{cms} \alias{cms} \title{ C-Method Standardization } Modified: pkg/dplR/man/co021.Rd =================================================================== --- pkg/dplR/man/co021.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/co021.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{co021} \docType{data} \alias{co021} Modified: pkg/dplR/man/combine.rwl.Rd =================================================================== --- pkg/dplR/man/combine.rwl.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/combine.rwl.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{combine.rwl} \alias{combine.rwl} Modified: pkg/dplR/man/common.interval.Rd =================================================================== --- pkg/dplR/man/common.interval.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/common.interval.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{common.interval} \alias{common.interval} \title{Common Interval} Modified: pkg/dplR/man/corr.rwl.seg.Rd =================================================================== --- pkg/dplR/man/corr.rwl.seg.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/corr.rwl.seg.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{corr.rwl.seg} \alias{corr.rwl.seg} \title{ Compute Correlations between Series } Modified: pkg/dplR/man/corr.series.seg.Rd =================================================================== --- pkg/dplR/man/corr.series.seg.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/corr.series.seg.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{corr.series.seg} \alias{corr.series.seg} \title{ Compute Correlation between a Series and a Master Chronology } Modified: pkg/dplR/man/crn.plot.Rd =================================================================== --- pkg/dplR/man/crn.plot.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/crn.plot.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{crn.plot} \alias{plot.crn} \alias{crn.plot} Modified: pkg/dplR/man/detrend.Rd =================================================================== --- pkg/dplR/man/detrend.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/detrend.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{detrend} \alias{detrend} \title{ Detrend Multiple Ring-Width Series Simultaneously } Modified: pkg/dplR/man/detrend.series.Rd =================================================================== --- pkg/dplR/man/detrend.series.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/detrend.series.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{detrend.series} \alias{detrend.series} \title{ Detrend a Ring-Width Series } Modified: pkg/dplR/man/dplR-package.Rd =================================================================== --- pkg/dplR/man/dplR-package.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/dplR-package.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{dplR-package} \alias{dplR-package} \alias{dplR} Modified: pkg/dplR/man/ffcsaps.Rd =================================================================== --- pkg/dplR/man/ffcsaps.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/ffcsaps.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{ffcsaps} \alias{ffcsaps} \title{ Smoothing Spline with User-Specified Rigidity and Frequency Cutoff } Modified: pkg/dplR/man/fill.internal.NA.Rd =================================================================== --- pkg/dplR/man/fill.internal.NA.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/fill.internal.NA.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{fill.internal.NA} \alias{fill.internal.NA} \title{Fill Internal NA} Modified: pkg/dplR/man/gini.coef.Rd =================================================================== --- pkg/dplR/man/gini.coef.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/gini.coef.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{gini.coef} \alias{gini.coef} \title{ Calculate the Gini Coefficient } Modified: pkg/dplR/man/glk.Rd =================================================================== --- pkg/dplR/man/glk.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/glk.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{glk} \alias{glk} Modified: pkg/dplR/man/gp.d2pith.Rd =================================================================== --- pkg/dplR/man/gp.d2pith.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/gp.d2pith.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{gp.d2pith} \docType{data} \alias{gp.d2pith} Modified: pkg/dplR/man/gp.dbh.Rd =================================================================== --- pkg/dplR/man/gp.dbh.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/gp.dbh.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{gp.dbh} \docType{data} \alias{gp.dbh} Modified: pkg/dplR/man/gp.po.Rd =================================================================== --- pkg/dplR/man/gp.po.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/gp.po.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{gp.po} \docType{data} \alias{gp.po} Modified: pkg/dplR/man/gp.rwl.Rd =================================================================== --- pkg/dplR/man/gp.rwl.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/gp.rwl.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{gp.rwl} \docType{data} \alias{gp.rwl} Modified: pkg/dplR/man/hanning.Rd =================================================================== --- pkg/dplR/man/hanning.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/hanning.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{hanning} \alias{hanning} \title{ Hanning Filter } Modified: pkg/dplR/man/i.detrend.Rd =================================================================== --- pkg/dplR/man/i.detrend.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/i.detrend.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{i.detrend} \alias{i.detrend} \title{ Interactively Detrend Multiple Ring-Width Series } Modified: pkg/dplR/man/i.detrend.series.Rd =================================================================== --- pkg/dplR/man/i.detrend.series.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/i.detrend.series.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{i.detrend.series} \alias{i.detrend.series} \title{ Interactively Detrend a Ring-Width Series } Modified: pkg/dplR/man/insert.ring.Rd =================================================================== --- pkg/dplR/man/insert.ring.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/insert.ring.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{insert.ring} \alias{insert.ring} \alias{delete.ring} Modified: pkg/dplR/man/interseries.cor.Rd =================================================================== --- pkg/dplR/man/interseries.cor.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/interseries.cor.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{interseries.cor} \alias{interseries.cor} \title{ Individual Series Correlation Against a Master Chronology } Modified: pkg/dplR/man/latexDate.Rd =================================================================== --- pkg/dplR/man/latexDate.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/latexDate.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{latexDate} \alias{latexDate} \title{ Modified: pkg/dplR/man/latexify.Rd =================================================================== --- pkg/dplR/man/latexify.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/latexify.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{latexify} \alias{latexify} \title{ Modified: pkg/dplR/man/morlet.Rd =================================================================== --- pkg/dplR/man/morlet.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/morlet.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{morlet} \alias{morlet} \title{ Perform a Continuous Morlet Wavelet Transform } Modified: pkg/dplR/man/net.Rd =================================================================== --- pkg/dplR/man/net.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/net.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{net} \alias{net} \title{ Modified: pkg/dplR/man/plot.rwl.Rd =================================================================== --- pkg/dplR/man/plot.rwl.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/plot.rwl.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{plot.rwl} \alias{plot.rwl} \title{ Modified: pkg/dplR/man/po.to.wc.Rd =================================================================== --- pkg/dplR/man/po.to.wc.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/po.to.wc.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{po.to.wc} \alias{po.to.wc} \title{ Modified: pkg/dplR/man/pointer.Rd =================================================================== --- pkg/dplR/man/pointer.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/pointer.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{pointer} \alias{pointer} Modified: pkg/dplR/man/powt.Rd =================================================================== --- pkg/dplR/man/powt.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/powt.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{powt} \alias{powt} \title{Power Transformation of Tree-Ring Data} Modified: pkg/dplR/man/print.redfit.Rd =================================================================== --- pkg/dplR/man/print.redfit.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/print.redfit.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{print.redfit} \alias{print.redfit} \title{ Modified: pkg/dplR/man/rasterPlot.Rd =================================================================== --- pkg/dplR/man/rasterPlot.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/rasterPlot.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{rasterPlot} \alias{rasterPlot} \title{ Modified: pkg/dplR/man/rcs.Rd =================================================================== --- pkg/dplR/man/rcs.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/rcs.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{rcs} \alias{rcs} \title{ Regional Curve Standardization } Modified: pkg/dplR/man/read.compact.Rd =================================================================== --- pkg/dplR/man/read.compact.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/read.compact.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{read.compact} \alias{read.compact} \title{ Read \acronym{DPL} Compact Format Ring Width File } Modified: pkg/dplR/man/read.crn.Rd =================================================================== --- pkg/dplR/man/read.crn.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/read.crn.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{read.crn} \alias{read.crn} \title{ Read Tucson Format Chronology File } Modified: pkg/dplR/man/read.fh.Rd =================================================================== --- pkg/dplR/man/read.fh.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/read.fh.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{read.fh} \alias{read.fh} \title{ Read Heidelberg Format Ring Width File } Modified: pkg/dplR/man/read.ids.Rd =================================================================== --- pkg/dplR/man/read.ids.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/read.ids.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{read.ids} \alias{read.ids} \alias{autoread.ids} Modified: pkg/dplR/man/read.rwl.Rd =================================================================== --- pkg/dplR/man/read.rwl.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/read.rwl.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{read.rwl} \alias{read.rwl} \title{ Read Ring Width File } Modified: pkg/dplR/man/read.tridas.Rd =================================================================== --- pkg/dplR/man/read.tridas.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/read.tridas.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{read.tridas} \alias{read.tridas} Modified: pkg/dplR/man/read.tucson.Rd =================================================================== --- pkg/dplR/man/read.tucson.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/read.tucson.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{read.tucson} \alias{read.tucson} \title{ Read Tucson Format Ring Width File } Modified: pkg/dplR/man/redfit.Rd =================================================================== --- pkg/dplR/man/redfit.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/redfit.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{redfit} \alias{redfit} \alias{runcrit} Modified: pkg/dplR/man/rwi.stats.running.Rd =================================================================== --- pkg/dplR/man/rwi.stats.running.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/rwi.stats.running.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{rwi.stats.running} \alias{rwi.stats.running} \alias{rwi.stats} Modified: pkg/dplR/man/rwl.stats.Rd =================================================================== --- pkg/dplR/man/rwl.stats.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/rwl.stats.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{rwl.stats} \alias{rwl.stats} \alias{summary.rwl} Modified: pkg/dplR/man/sea.Rd =================================================================== --- pkg/dplR/man/sea.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/sea.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{sea} \alias{sea} Modified: pkg/dplR/man/seg.plot.Rd =================================================================== --- pkg/dplR/man/seg.plot.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/seg.plot.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{seg.plot} \alias{seg.plot} \title{ Segment Plot } Modified: pkg/dplR/man/sens1.Rd =================================================================== --- pkg/dplR/man/sens1.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/sens1.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{sens1} \alias{sens1} \title{ Calculate Mean Sensitivity } Modified: pkg/dplR/man/sens2.Rd =================================================================== --- pkg/dplR/man/sens2.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/sens2.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{sens2} \alias{sens2} \title{ Calculate Mean Sensitivity on Series with a Trend } Modified: pkg/dplR/man/series.rwl.plot.Rd =================================================================== --- pkg/dplR/man/series.rwl.plot.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/series.rwl.plot.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{series.rwl.plot} \alias{series.rwl.plot} \title{ Plot Series and a Master } Modified: pkg/dplR/man/skel.plot.Rd =================================================================== --- pkg/dplR/man/skel.plot.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/skel.plot.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{skel.plot} \alias{skel.plot} \title{ Skeleton Plot } Modified: pkg/dplR/man/spag.plot.Rd =================================================================== --- pkg/dplR/man/spag.plot.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/spag.plot.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{spag.plot} \alias{spag.plot} \title{ Spaghetti Plot } Modified: pkg/dplR/man/strip.rwl.Rd =================================================================== --- pkg/dplR/man/strip.rwl.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/strip.rwl.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{strip.rwl} \alias{strip.rwl} \title{Chronology Stripping by \acronym{EPS}} Modified: pkg/dplR/man/tbrm.Rd =================================================================== --- pkg/dplR/man/tbrm.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/tbrm.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{tbrm} \alias{tbrm} \title{ Calculate Tukey's Biweight Robust Mean } Modified: pkg/dplR/man/tridas.vocabulary.Rd =================================================================== --- pkg/dplR/man/tridas.vocabulary.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/tridas.vocabulary.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{tridas.vocabulary} \alias{tridas.vocabulary} \title{ Modified: pkg/dplR/man/uuid.gen.Rd =================================================================== --- pkg/dplR/man/uuid.gen.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/uuid.gen.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{uuid.gen} \alias{uuid.gen} \title{ Modified: pkg/dplR/man/wavelet.plot.Rd =================================================================== --- pkg/dplR/man/wavelet.plot.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/wavelet.plot.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{wavelet.plot} \alias{wavelet.plot} \title{ Plot a Continuous Wavelet Transform } Modified: pkg/dplR/man/wc.to.po.Rd =================================================================== --- pkg/dplR/man/wc.to.po.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/wc.to.po.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{wc.to.po} \alias{wc.to.po} \title{ Modified: pkg/dplR/man/write.compact.Rd =================================================================== --- pkg/dplR/man/write.compact.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/write.compact.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{write.compact} \alias{write.compact} \title{ Write \acronym{DPL} Compact Format Ring Width File } Modified: pkg/dplR/man/write.crn.Rd =================================================================== --- pkg/dplR/man/write.crn.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/write.crn.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{write.crn} \alias{write.crn} \title{ Write Tucson Format Chronology File } Modified: pkg/dplR/man/write.rwl.Rd =================================================================== --- pkg/dplR/man/write.rwl.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/write.rwl.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{write.rwl} \alias{write.rwl} \title{ Write Chronology File } Modified: pkg/dplR/man/write.tridas.Rd =================================================================== --- pkg/dplR/man/write.tridas.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/write.tridas.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{write.tridas} \alias{write.tridas} @@ -36,7 +37,7 @@ series \acronym{ID}s are the column names and the years are the row names. This type of \code{data.frame} is produced by \code{\link{read.tucson}}, \code{\link{read.compact}} and - \code{\link{read.tridas}}. Defaults to \code{NULL} -- no measurement + \code{\link{read.tridas}}. Defaults to \code{NULL}: no measurement series are written. } \item{fname}{ \code{character} vector giving the file name of the rwl @@ -54,11 +55,11 @@ that the first chronology gets the first sample depth column, second chronology gets the second set of sample depths, etc. If there are less sample depth columns than chronologies, the sample depths are - recycled. Defaults to \code{NULL} -- no chronologies are written. } + recycled. Defaults to \code{NULL}: no chronologies are written. } \item{prec}{ optional \code{numeric} indicating the rounding precision of the output file when writing the data contained in - \code{\var{rwl.df}}. Defaults to \code{NULL} -- no rounding is done + \code{\var{rwl.df}}. Defaults to \code{NULL}: no rounding is done and the measurements are written in (non-integer) millimetres. Possible \code{numeric} values are 0.001, 0.01, 0.05, 0.1, 1, 10, 100 and 1000, which cause the data to be transformed to micrometres, Modified: pkg/dplR/man/write.tucson.Rd =================================================================== --- pkg/dplR/man/write.tucson.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/write.tucson.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{write.tucson} \alias{write.tucson} \title{ Write Tucson Format Chronology File } Modified: pkg/dplR/man/xskel.ccf.plot.Rd =================================================================== --- pkg/dplR/man/xskel.ccf.plot.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/xskel.ccf.plot.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{xskel.ccf.plot} \alias{xskel.ccf.plot} \title{ Skeleton Plot for Series and Master with Cross Correlation } Modified: pkg/dplR/man/xskel.plot.Rd =================================================================== --- pkg/dplR/man/xskel.plot.Rd 2015-03-04 16:02:59 UTC (rev 969) +++ pkg/dplR/man/xskel.plot.Rd 2015-03-09 15:49:52 UTC (rev 970) @@ -1,3 +1,4 @@ +\encoding{UTF-8} \name{xskel.plot} \alias{xskel.plot} \title{ Skeleton Plot for Series and Master } From noreply at r-forge.r-project.org Tue Mar 10 11:18:07 2015 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Tue, 10 Mar 2015 11:18:07 +0100 (CET) Subject: [Dplr-commits] r971 - in pkg/dplR: . man Message-ID: <20150310101807.7784C1859E0@r-forge.r-project.org> Author: mvkorpel Date: 2015-03-10 11:18:07 +0100 (Tue, 10 Mar 2015) New Revision: 971 Modified: pkg/dplR/DESCRIPTION pkg/dplR/man/print.redfit.Rd Log: Updated REDFIT URL in print.redfit.Rd to match the address given in redfit.Rd. Modified: pkg/dplR/DESCRIPTION =================================================================== --- pkg/dplR/DESCRIPTION 2015-03-09 15:49:52 UTC (rev 970) +++ pkg/dplR/DESCRIPTION 2015-03-10 10:18:07 UTC (rev 971) @@ -3,7 +3,7 @@ Type: Package Title: Dendrochronology Program Library in R Version: 1.6.3 -Date: 2015-03-09 +Date: 2015-03-10 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/print.redfit.Rd =================================================================== --- pkg/dplR/man/print.redfit.Rd 2015-03-09 15:49:52 UTC (rev 970) +++ pkg/dplR/man/print.redfit.Rd 2015-03-10 10:18:07 UTC (rev 971) @@ -55,7 +55,7 @@ \references{ This function is based on the Fortran program - \href{http://www.ncdc.noaa.gov/paleo/softlib/redfit/redfit.html}{REDFIT}, + \href{http://www.geo.uni-bremen.de/geomod/staff/mschulz/}{REDFIT}, which is in the public domain. Schulz, M. and Mudelsee, M. (2002) REDFIT: estimating red-noise From noreply at r-forge.r-project.org Wed Mar 11 12:57:35 2015 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Wed, 11 Mar 2015 12:57:35 +0100 (CET) Subject: [Dplr-commits] r972 - in pkg/dplR: . R Message-ID: <20150311115735.CC365187591@r-forge.r-project.org> Author: mvkorpel Date: 2015-03-11 12:57:35 +0100 (Wed, 11 Mar 2015) New Revision: 972 Modified: pkg/dplR/DESCRIPTION pkg/dplR/R/morlet.R pkg/dplR/R/redfit.R Log: M-x untabify (replace tabs with spaces) Modified: pkg/dplR/DESCRIPTION =================================================================== --- pkg/dplR/DESCRIPTION 2015-03-10 10:18:07 UTC (rev 971) +++ pkg/dplR/DESCRIPTION 2015-03-11 11:57:35 UTC (rev 972) @@ -3,7 +3,7 @@ Type: Package Title: Dendrochronology Program Library in R Version: 1.6.3 -Date: 2015-03-10 +Date: 2015-03-11 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/R/morlet.R =================================================================== --- pkg/dplR/R/morlet.R 2015-03-10 10:18:07 UTC (rev 971) +++ pkg/dplR/R/morlet.R 2015-03-11 11:57:35 UTC (rev 972) @@ -1,23 +1,23 @@ morlet <- function(y1, x1=seq_along(y1), p2=NULL, dj=0.25, siglvl=0.95){ morlet.func <- function(k0=6, Scale, k) { - n <- length(k) - expnt <- -(Scale * k - k0) ^ 2 / 2 * as.numeric(k > 0) - Dt <- 2 * pi / (n * k[2]) - norm <- sqrt(2 * pi * Scale / Dt) * (pi ^ (-0.25)) # total energy=N [Eqn(7)] + n <- length(k) + expnt <- -(Scale * k - k0) ^ 2 / 2 * as.numeric(k > 0) + Dt <- 2 * pi / (n * k[2]) + norm <- sqrt(2 * pi * Scale / Dt) * (pi ^ (-0.25)) # total energy=N [Eqn(7)] - morlet <- norm * exp(ifelse(expnt > -100, expnt, 100)) - morlet <- morlet * (as.numeric(expnt > -100)) # Avoid underflow errors - morlet <- morlet * (as.numeric(k > 0)) # Heaviside step function (Morlet is complex) - fourier_factor <- + morlet <- norm * exp(ifelse(expnt > -100, expnt, 100)) + morlet <- morlet * (as.numeric(expnt > -100)) # Avoid underflow errors + morlet <- morlet * (as.numeric(k > 0)) # Heaviside step function (Morlet is complex) + fourier_factor <- (4 * pi) / (k0 + sqrt(2 + k0 ^ 2)) # Scale-->Fourier [Sec.3h] - period <- Scale * fourier_factor - coi <- fourier_factor / sqrt(2) # Cone-of-influence [Sec.3g] - ## dofmin = 2 # Degrees of freedom with no smoothing - ## Cdelta = -1 - ## if(k0 == 6) Cdelta = 0.776 # Reconstruction factor - ## psi0 = pi^(-0.25) - list(psi_fft = morlet, period = period, coi = coi) + period <- Scale * fourier_factor + coi <- fourier_factor / sqrt(2) # Cone-of-influence [Sec.3g] + ## dofmin = 2 # Degrees of freedom with no smoothing + ## Cdelta = -1 + ## if(k0 == 6) Cdelta = 0.776 # Reconstruction factor + ## psi0 = pi^(-0.25) + list(psi_fft = morlet, period = period, coi = coi) } ## Construct optional inputs, these could be passed in as args @@ -84,9 +84,9 @@ psi_fft <- morlet.out$psi_fft coi <- morlet.out$coi # One value per scale wave[, a1] <- fft(yfft * psi_fft, inverse=TRUE) - if(do_daughter) daughter[, a1] <- fft(psi_fft, inverse=TRUE) + if(do_daughter) daughter[, a1] <- fft(psi_fft, inverse=TRUE) period[a1] <- morlet.out$period # Save period - fft_theor[a1] <- sum((abs(psi_fft) ^ 2) * fft_theor_k) / n + fft_theor[a1] <- sum((abs(psi_fft) ^ 2) * fft_theor_k) / n } time.scalar <- c(seq_len(floor(n1 + 1) / 2), seq.int(from=floor(n1 / 2), to=1, by=-1)) * Dt Modified: pkg/dplR/R/redfit.R =================================================================== --- pkg/dplR/R/redfit.R 2015-03-10 10:18:07 UTC (rev 971) +++ pkg/dplR/R/redfit.R 2015-03-11 11:57:35 UTC (rev 972) @@ -1547,17 +1547,17 @@ rhovec <- numeric(n50) twkM <- matrix(1, nseg2, 2) for (i in as.numeric(seq_len(n50))) { - ## copy data of (i+1)'th segment into workspace - iseg <- .Call(dplR.seg50, i, nseg2, segskip2, np) + ## copy data of (i+1)'th segment into workspace + iseg <- .Call(dplR.seg50, i, nseg2, segskip2, np) twk <- t[iseg] twkM[, 2] <- twk xwk <- x[iseg] - ## detrend data + ## detrend data xwk <- do.call(lmfitfun, list(twkM, xwk))[["residuals"]] - ## estimate and sum rho for each segment - rho <- redfitTauest(twk, xwk) - ## bias correction for rho (Kendall & Stuart, 1967; Vol. 3)) - rhovec[i] <- (rho * (nseg2 - 1) + 1) / (nseg2 - 4) + ## estimate and sum rho for each segment + rho <- redfitTauest(twk, xwk) + ## bias correction for rho (Kendall & Stuart, 1967; Vol. 3)) + rhovec[i] <- (rho * (nseg2 - 1) + 1) / (nseg2 - 4) } ## average rho mean(rhovec) @@ -1598,11 +1598,11 @@ xscalMNP <- xscal[-np] rho <- sum(xscalMNP * xscal[-1]) / sum(xscalMNP * xscalMNP) if (rho <= 0) { - rho <- 0.05 - warning("rho estimation: <= 0") + rho <- 0.05 + warning("rho estimation: <= 0") } else if (rho > 1) { - rho <- 0.95 - warning("rho estimation: > 1") + rho <- 0.95 + warning("rho estimation: > 1") } scalt <- -log(rho) / dt tscal <- t * scalt @@ -1612,14 +1612,14 @@ mult <- minRes[["nmu"]] warnings <- FALSE if (mult) { - warning("estimation problem: LS function has > 1 minima") + warning("estimation problem: LS function has > 1 minima") warnings <- TRUE } if (amin <= 0) { - warning("estimation problem: a_min =< 0") + warning("estimation problem: a_min =< 0") warnings <- TRUE } else if (amin >= 1) { - warning("estimation problem: a_min >= 1") + warning("estimation problem: a_min >= 1") warnings <- TRUE } if (!warnings) { From noreply at r-forge.r-project.org Thu Mar 12 09:50:48 2015 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Thu, 12 Mar 2015 09:50:48 +0100 (CET) Subject: [Dplr-commits] r973 - in pkg/dplR: . man Message-ID: <20150312085048.8E334187728@r-forge.r-project.org> 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{Universit?t}{Universitaet} + approach. PhD thesis, Technische \enc{Universit?t}{Universitaet} \enc{M?nchen}{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 From noreply at r-forge.r-project.org Fri Mar 13 11:23:38 2015 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Fri, 13 Mar 2015 11:23:38 +0100 (CET) Subject: [Dplr-commits] r974 - in pkg/dplR: . man Message-ID: <20150313102338.2FE2D187925@r-forge.r-project.org> Author: mvkorpel Date: 2015-03-13 11:23:37 +0100 (Fri, 13 Mar 2015) New Revision: 974 Modified: pkg/dplR/DESCRIPTION pkg/dplR/man/latexify.Rd pkg/dplR/man/read.fh.Rd pkg/dplR/man/read.tridas.Rd pkg/dplR/man/skel.plot.Rd pkg/dplR/man/tridas.vocabulary.Rd pkg/dplR/man/uuid.gen.Rd pkg/dplR/man/write.tridas.Rd Log: * In .Rd files of TRiDaS functions: Added a reference to article by Jansma et al. (2010) * Small formatting change to reference in uuid.gen.Rd * Removed URL prefix from URLs in references, because \url{foo} is formatted as when an .Rd file is formatted as text. URL does not look nice. Modified: pkg/dplR/DESCRIPTION =================================================================== --- pkg/dplR/DESCRIPTION 2015-03-12 08:50:48 UTC (rev 973) +++ pkg/dplR/DESCRIPTION 2015-03-13 10:23:37 UTC (rev 974) @@ -3,7 +3,7 @@ Type: Package Title: Dendrochronology Program Library in R Version: 1.6.3 -Date: 2015-03-12 +Date: 2015-03-13 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/latexify.Rd =================================================================== --- pkg/dplR/man/latexify.Rd 2015-03-12 08:50:48 UTC (rev 973) +++ pkg/dplR/man/latexify.Rd 2015-03-13 10:23:37 UTC (rev 974) @@ -104,7 +104,7 @@ } \references{ INRIA. Tralics: a LaTeX to XML translator, HTML documentation of all - TeX commands. \acronym{URL} \url{http://www-sop.inria.fr/marelle/tralics/}. + TeX commands. \url{http://www-sop.inria.fr/marelle/tralics/}. Levitt, N., Persch, C., and Unicode, Inc. (2013) GNOME Character Map, application version 3.10.1. @@ -114,11 +114,10 @@ second edition. \acronym{ISBN-13}: 978-0-201-36299-2. Pakin, S. (2009) The Comprehensive LaTeX Symbol - List. \acronym{URL} - \url{http://www.ctan.org/tex-archive/info/symbols/comprehensive}. + List. \url{http://www.ctan.org/tex-archive/info/symbols/comprehensive}. The Unicode Consortium. The Unicode Standard. - \acronym{URL} \url{http://www.unicode.org/versions/latest/}. + \url{http://www.unicode.org/versions/latest/}. } \author{ Mikko Korpela Modified: pkg/dplR/man/read.fh.Rd =================================================================== --- pkg/dplR/man/read.fh.Rd 2015-03-12 08:50:48 UTC (rev 973) +++ pkg/dplR/man/read.fh.Rd 2015-03-13 10:23:37 UTC (rev 974) @@ -35,6 +35,6 @@ \seealso{ \code{\link{read.rwl}} } \references{ Rinn, F. (2003) \emph{TSAP-Win User Reference Manual.} - Rinntech, Heidelberg. \acronym{URL} \url{http://www.rinntech.com/}. + Rinntech, Heidelberg. \url{http://www.rinntech.com/}. } \keyword{ IO } Modified: pkg/dplR/man/read.tridas.Rd =================================================================== --- pkg/dplR/man/read.tridas.Rd 2015-03-12 08:50:48 UTC (rev 973) +++ pkg/dplR/man/read.tridas.Rd 2015-03-13 10:23:37 UTC (rev 974) @@ -60,13 +60,21 @@ } -\details{ The parameters used for rearranging - (\code{\var{ids.from.titles}}, \code{\var{ids.from.identifiers}}) and - combining (\code{\var{combine.series}}) measurement series only affect - the four lowest levels of document structure: element, sample, radius, +\details{ + + The Tree Ring Data Standard (TRiDaS) is described in Jansma et. al + (2010). Information about the current version of the standard can be + found from \href{http://www.tridas.org/}{TRiDaS website}. + + The parameters used for rearranging (\code{\var{ids.from.titles}}, + \code{\var{ids.from.identifiers}}) and combining + (\code{\var{combine.series}}) measurement series only affect the four + lowest levels of document structure: element, sample, radius, measurementSeries. Series are not reorganized or combined at the - upper structural levels (project, object). } + upper structural levels (project, object). +} + \value{ A list with a variable number of components according to the contents of the input file. The possible list components are: @@ -541,9 +549,15 @@ } } -\references{ TRiDaS \enc{?}{--} The Tree Ring Data Standard. - \acronym{URL} \url{http://www.tridas.org/}. } +\references{ + Jansma, E., Brewer, P. W., and Zandhuis, I. (2010) TRiDaS 1.1: The + tree-ring data standard. \emph{Dendrochronologia}, \bold{28}(2), + 99--130. + TRiDaS \enc{?}{--} The Tree Ring Data Standard. + \url{http://www.tridas.org/}. +} + \author{ Mikko Korpela } \note{ This is an early version of the function. Bugs are likely to Modified: pkg/dplR/man/skel.plot.Rd =================================================================== --- pkg/dplR/man/skel.plot.Rd 2015-03-12 08:50:48 UTC (rev 973) +++ pkg/dplR/man/skel.plot.Rd 2015-03-13 10:23:37 UTC (rev 974) @@ -66,11 +66,10 @@ \acronym{ISBN-13}: 978-0-8165-1680-3. Sheppard, P. R. (2002) Crossdating Tree Rings Using Skeleton Plotting. - \acronym{URL} \url{http://www.ltrr.arizona.edu/skeletonplot/introcrossdate.htm}. Meko, D. (2002) Tree-Ring MATLAB Toolbox. - \acronym{URL} \url{http://www.mathworks.com/matlabcentral/}. + \url{http://www.mathworks.com/matlabcentral/}. } \author{ Andy Bunn. Patched and improved by Mikko Korpela. } Modified: pkg/dplR/man/tridas.vocabulary.Rd =================================================================== --- pkg/dplR/man/tridas.vocabulary.Rd 2015-03-12 08:50:48 UTC (rev 973) +++ pkg/dplR/man/tridas.vocabulary.Rd 2015-03-13 10:23:37 UTC (rev 974) @@ -30,6 +30,10 @@ \code{FALSE}.} } \details{ + The Tree Ring Data Standard (TRiDaS) is described in Jansma et. al + (2010). Information about the current version of the standard can be + found from \href{http://www.tridas.org/}{TRiDaS website}. + The function has four usage modes: \enumerate{ @@ -65,8 +69,12 @@ } \references{ + Jansma, E., Brewer, P. W., and Zandhuis, I. (2010) TRiDaS 1.1: The + tree-ring data standard. \emph{Dendrochronologia}, \bold{28}(2), + 99--130. + TRiDaS \enc{?}{--} The Tree Ring Data Standard. - \acronym{URL} \url{http://www.tridas.org/}. + \url{http://www.tridas.org/}. } \author{ Mikko Korpela Modified: pkg/dplR/man/uuid.gen.Rd =================================================================== --- pkg/dplR/man/uuid.gen.Rd 2015-03-12 08:50:48 UTC (rev 973) +++ pkg/dplR/man/uuid.gen.Rd 2015-03-13 10:23:37 UTC (rev 974) @@ -71,9 +71,8 @@ } \references{ Leach, P., Mealling, M., and Salz, R. (2005) A Universally Unique - IDentifier (\acronym{UUID}) \acronym{URN} namespace, \acronym{RFC} - 4122, RFC Editor. - \acronym{URL} \url{http://www.rfc-editor.org/rfc/rfc4122.txt}. + IDentifier (\acronym{UUID}) \acronym{URN} namespace. \acronym{RFC} + 4122, RFC Editor. \url{http://www.rfc-editor.org/rfc/rfc4122.txt}. } \author{ Mikko Korpela Modified: pkg/dplR/man/write.tridas.Rd =================================================================== --- pkg/dplR/man/write.tridas.Rd 2015-03-12 08:50:48 UTC (rev 973) +++ pkg/dplR/man/write.tridas.Rd 2015-03-13 10:23:37 UTC (rev 974) @@ -342,11 +342,23 @@ } +\details{ + The Tree Ring Data Standard (TRiDaS) is described in Jansma et. al + (2010). Information about the current version of the standard can be + found from \href{http://www.tridas.org/}{TRiDaS website}. +} + \value{ \code{\var{fname}} } -\references{ TRiDaS \enc{?}{--} The Tree Ring Data Standard. - \acronym{URL} \url{http://www.tridas.org/}. } +\references{ + Jansma, E., Brewer, P. W., and Zandhuis, I. (2010) TRiDaS 1.1: The + tree-ring data standard. \emph{Dendrochronologia}, \bold{28}(2), + 99--130. + TRiDaS \enc{?}{--} The Tree Ring Data Standard. + \url{http://www.tridas.org/}. +} + \author{ Mikko Korpela } \note{ This is an early version of the function. Bugs are likely to From noreply at r-forge.r-project.org Fri Mar 13 12:15:58 2015 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Fri, 13 Mar 2015 12:15:58 +0100 (CET) Subject: [Dplr-commits] r975 - pkg/dplR/man Message-ID: <20150313111558.AF1E5185509@r-forge.r-project.org> Author: mvkorpel Date: 2015-03-13 12:15:58 +0100 (Fri, 13 Mar 2015) New Revision: 975 Modified: pkg/dplR/man/anos1.Rd Log: Small formatting changes to reference Modified: pkg/dplR/man/anos1.Rd =================================================================== --- pkg/dplR/man/anos1.Rd 2015-03-13 10:23:37 UTC (rev 974) +++ pkg/dplR/man/anos1.Rd 2015-03-13 11:15:58 UTC (rev 975) @@ -15,9 +15,9 @@ 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{Universit?t}{Universitaet} + Zang, C. (2010) \emph{Growth reaction of temperate forest tree species + to summer drought \enc{?}{--} a multispecies tree-ring network + approach}. Ph.D. thesis, Technische \enc{Universit?t}{Universitaet} \enc{M?nchen}{Muenchen}. } \keyword{datasets} From noreply at r-forge.r-project.org Mon Mar 23 14:18:32 2015 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Mon, 23 Mar 2015 14:18:32 +0100 (CET) Subject: [Dplr-commits] r976 - in pkg/dplR: . R Message-ID: <20150323131832.B2E29184B54@r-forge.r-project.org> Author: mvkorpel Date: 2015-03-23 14:18:32 +0100 (Mon, 23 Mar 2015) New Revision: 976 Modified: pkg/dplR/ChangeLog pkg/dplR/DESCRIPTION pkg/dplR/R/redfit.R Log: Fixed a bug where redfit() would fail if "stats" was not attached. Modified: pkg/dplR/ChangeLog =================================================================== --- pkg/dplR/ChangeLog 2015-03-13 11:15:58 UTC (rev 975) +++ pkg/dplR/ChangeLog 2015-03-23 13:18:32 UTC (rev 976) @@ -89,6 +89,12 @@ value of the argument. Reported by Daniel Bishop and Neil Pederson. +File: redfit.R +-------------- + +- Fixed a bug where redfit() would fail if the "stats" package was + not attached. + File: write.tridas.R -------------------- Modified: pkg/dplR/DESCRIPTION =================================================================== --- pkg/dplR/DESCRIPTION 2015-03-13 11:15:58 UTC (rev 975) +++ pkg/dplR/DESCRIPTION 2015-03-23 13:18:32 UTC (rev 976) @@ -3,7 +3,7 @@ Type: Package Title: Dendrochronology Program Library in R Version: 1.6.3 -Date: 2015-03-13 +Date: 2015-03-23 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/R/redfit.R =================================================================== --- pkg/dplR/R/redfit.R 2015-03-13 11:15:58 UTC (rev 975) +++ pkg/dplR/R/redfit.R 2015-03-23 13:18:32 UTC (rev 976) @@ -314,8 +314,9 @@ ww[, i] <- redfitWinwgt(twk, iwin2) } ## determine autospectrum of input data - lmfitfun <- tryCatch(match.fun(".lm.fit"), - error = function(...) match.fun("lm.fit")) + lmfitfun <- + tryCatch(getExportedValue("stats", ".lm.fit"), + error = function(...) getExportedValue("stats", "lm.fit")) gxx <- .Call(dplR.spectr, t2, x2, np, ww, tr[[1]], tr[[2]], tr[[3]], nseg, nfreq, avgdt, freq, dn50, segskip, lmfitfun) ## estimate data variance from autospectrum From noreply at r-forge.r-project.org Mon Mar 23 15:22:42 2015 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Mon, 23 Mar 2015 15:22:42 +0100 (CET) Subject: [Dplr-commits] r977 - in pkg/dplR: . R Message-ID: <20150323142242.D3030187539@r-forge.r-project.org> Author: mvkorpel Date: 2015-03-23 15:22:41 +0100 (Mon, 23 Mar 2015) New Revision: 977 Modified: pkg/dplR/ChangeLog pkg/dplR/R/series.rwl.plot.R Log: Worked around a problem in graphics::abline(). Modified: pkg/dplR/ChangeLog =================================================================== --- pkg/dplR/ChangeLog 2015-03-23 13:18:32 UTC (rev 976) +++ pkg/dplR/ChangeLog 2015-03-23 14:22:41 UTC (rev 977) @@ -95,6 +95,14 @@ - Fixed a bug where redfit() would fail if the "stats" package was not attached. +File: series.rwl.plot.R +----------------------- + +- Worked around a problem in graphics::abline(): the function + fails when a linear model is given and the "stats" package is not + attached. The solution is to extract the coefficients of the model + and use those in the call. + File: write.tridas.R -------------------- Modified: pkg/dplR/R/series.rwl.plot.R =================================================================== --- pkg/dplR/R/series.rwl.plot.R 2015-03-23 13:18:32 UTC (rev 976) +++ pkg/dplR/R/series.rwl.plot.R 2015-03-23 14:22:41 UTC (rev 977) @@ -98,7 +98,7 @@ ylab=gettext("Master", domain="R-dplR"), xlab=gettext("Series", domain="R-dplR"), pch=20, sub=bquote(R^2==.(tmp))) - abline(lm1, lwd=2) + abline(coef = coef(lm1), lwd=2) ## plot 3 plot(yrs, series2, type="n", ylim=c(-1, 1), ylab="", From noreply at r-forge.r-project.org Mon Mar 23 15:27:43 2015 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Mon, 23 Mar 2015 15:27:43 +0100 (CET) Subject: [Dplr-commits] r978 - pkg/dplR/man Message-ID: <20150323142743.EFEE9187539@r-forge.r-project.org> Author: mvkorpel Date: 2015-03-23 15:27:43 +0100 (Mon, 23 Mar 2015) New Revision: 978 Modified: pkg/dplR/man/bai.in.Rd pkg/dplR/man/bai.out.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/ffcsaps.Rd pkg/dplR/man/fill.internal.NA.Rd pkg/dplR/man/gini.coef.Rd pkg/dplR/man/glk.Rd pkg/dplR/man/hanning.Rd pkg/dplR/man/insert.ring.Rd pkg/dplR/man/interseries.cor.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/rasterPlot.Rd pkg/dplR/man/rcs.Rd pkg/dplR/man/read.ids.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/skel.plot.Rd pkg/dplR/man/spag.plot.Rd pkg/dplR/man/strip.rwl.Rd pkg/dplR/man/tbrm.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: Added library() calls: examples run even if default packages are detached. Modified: pkg/dplR/man/bai.in.Rd =================================================================== --- pkg/dplR/man/bai.in.Rd 2015-03-23 14:22:41 UTC (rev 977) +++ pkg/dplR/man/bai.in.Rd 2015-03-23 14:27:43 UTC (rev 978) @@ -50,6 +50,8 @@ \seealso{ \code{\link{bai.out}} } \examples{ library(graphics) +library(stats) +library(utils) ## Toy n <- 100 ## Make three fake tree-ring series to show that these funcs work on rwl objects Modified: pkg/dplR/man/bai.out.Rd =================================================================== --- pkg/dplR/man/bai.out.Rd 2015-03-23 14:22:41 UTC (rev 977) +++ pkg/dplR/man/bai.out.Rd 2015-03-23 14:27:43 UTC (rev 978) @@ -50,8 +50,10 @@ Nevada Reno, \acronym{USA}. Patched and improved by Mikko Korpela. } \seealso{ \code{\link{bai.in}} } \examples{ +library(graphics) +library(utils) \dontrun{ -library(graphics) +library(stats) ## Toy n <- 100 ## Make three fake tree-ring series to show that these funcs work on rwl objects Modified: pkg/dplR/man/ccf.series.rwl.Rd =================================================================== --- pkg/dplR/man/ccf.series.rwl.Rd 2015-03-23 14:22:41 UTC (rev 977) +++ pkg/dplR/man/ccf.series.rwl.Rd 2015-03-23 14:27:43 UTC (rev 978) @@ -102,6 +102,7 @@ \bold{28}(4), 251\enc{?}{--}258. } \examples{ +library(utils) data(co021) dat <- co021 ## Create a missing ring by deleting a year of growth in a random series Modified: pkg/dplR/man/chron.Rd =================================================================== --- pkg/dplR/man/chron.Rd 2015-03-23 14:22:41 UTC (rev 977) +++ pkg/dplR/man/chron.Rd 2015-03-23 14:27:43 UTC (rev 978) @@ -46,7 +46,9 @@ \seealso{ \code{\link{read.rwl}}, \code{\link{detrend}}, \code{\link{ar}}, \code{\link{crn.plot}} } -\examples{data(ca533) +\examples{library(graphics) +library(utils) +data(ca533) ca533.rwi <- detrend(rwl = ca533, method = "ModNegExp") ca533.crn <- chron(ca533.rwi, prefix = "CAM") plot(ca533.crn,xlab="Year",ylab="RWI") Modified: pkg/dplR/man/cms.Rd =================================================================== --- pkg/dplR/man/cms.Rd 2015-03-23 14:22:41 UTC (rev 977) +++ pkg/dplR/man/cms.Rd 2015-03-23 14:27:43 UTC (rev 978) @@ -65,6 +65,7 @@ } \seealso{ \code{\link{detrend}}, \code{\link{chron}}, \code{\link{rcs}} } \examples{library(graphics) +library(utils) data(gp.rwl) data(gp.po) gp.rwi <- cms(rwl = gp.rwl, po = gp.po) Modified: pkg/dplR/man/combine.rwl.Rd =================================================================== --- pkg/dplR/man/combine.rwl.Rd 2015-03-23 14:22:41 UTC (rev 977) +++ pkg/dplR/man/combine.rwl.Rd 2015-03-23 14:27:43 UTC (rev 978) @@ -30,7 +30,8 @@ \author{ Christian Zang. Patched by Mikko Korpela. } -\examples{data(ca533) +\examples{library(utils) +data(ca533) data(co021) combi1 <- combine.rwl(list(ca533, co021)) ## or alternatively for data.frames to combine Modified: pkg/dplR/man/common.interval.Rd =================================================================== --- pkg/dplR/man/common.interval.Rd 2015-03-23 14:22:41 UTC (rev 977) +++ pkg/dplR/man/common.interval.Rd 2015-03-23 14:27:43 UTC (rev 978) @@ -37,6 +37,7 @@ \seealso{ \code{\link{seg.plot}} } \examples{ +library(utils) data(co021) co021.s <- common.interval(co021, type="series", make.plot=TRUE) co021.y <- common.interval(co021, type="years", make.plot=TRUE) Modified: pkg/dplR/man/corr.rwl.seg.Rd =================================================================== --- pkg/dplR/man/corr.rwl.seg.Rd 2015-03-23 14:22:41 UTC (rev 977) +++ pkg/dplR/man/corr.rwl.seg.Rd 2015-03-23 14:27:43 UTC (rev 978) @@ -127,7 +127,8 @@ \code{\link{corr.series.seg}}, \code{\link{skel.plot}}, \code{\link{series.rwl.plot}}, \code{\link{ccf.series.rwl}} } -\examples{data(co021) +\examples{library(utils) +data(co021) crs <- corr.rwl.seg(co021, seg.length = 100, label.cex = 1.25) names(crs) ## Average correlation and p-value for the first few series Modified: pkg/dplR/man/corr.series.seg.Rd =================================================================== --- pkg/dplR/man/corr.series.seg.Rd 2015-03-23 14:22:41 UTC (rev 977) +++ pkg/dplR/man/corr.series.seg.Rd 2015-03-23 14:27:43 UTC (rev 978) @@ -77,7 +77,8 @@ \code{\link{corr.series.seg}}, \code{\link{skel.plot}}, \code{\link{series.rwl.plot}}, \code{\link{ccf.series.rwl}} } -\examples{data(co021) +\examples{library(utils) +data(co021) dat <- co021 ## Create a missing ring by deleting a year of growth in a random series flagged <- dat$"641143" Modified: pkg/dplR/man/crn.plot.Rd =================================================================== --- pkg/dplR/man/crn.plot.Rd 2015-03-23 14:22:41 UTC (rev 977) +++ pkg/dplR/man/crn.plot.Rd 2015-03-23 14:27:43 UTC (rev 978) @@ -56,7 +56,9 @@ \author{ Andy Bunn. Patched and improved by Mikko Korpela. } \seealso{ \code{\link{chron}} } -\examples{data(cana157) +\examples{library(graphics) +library(utils) +data(cana157) crn.plot(cana157,xlab='Year',ylab='RWI') plot(cana157,xlab='Year',ylab='RWI', main='Twisted Tree Heartrot Hill') # with added spline Modified: pkg/dplR/man/detrend.Rd =================================================================== --- pkg/dplR/man/detrend.Rd 2015-03-23 14:22:41 UTC (rev 977) +++ pkg/dplR/man/detrend.Rd 2015-03-23 14:27:43 UTC (rev 978) @@ -90,7 +90,8 @@ } \author{ Andy Bunn. Improved by Mikko Korpela. } \seealso{ \code{\link{detrend.series}} } -\examples{data(ca533) +\examples{library(utils) +data(ca533) ## Detrend using modified exponential decay. Returns a data.frame ca533.rwi <- detrend(rwl = ca533, method = "ModNegExp") Modified: pkg/dplR/man/detrend.series.Rd =================================================================== --- pkg/dplR/man/detrend.series.Rd 2015-03-23 14:22:41 UTC (rev 977) +++ pkg/dplR/man/detrend.series.Rd 2015-03-23 14:27:43 UTC (rev 978) @@ -192,6 +192,7 @@ related to negative output values is based on work by Jacob Cecile. } \seealso{ \code{\link{detrend}} } \examples{library(stats) +library(utils) ## Using a plausible representation of a tree-ring series gt <- 0.5 * exp (-0.05 * 1:200) + 0.2 noise <- c(arima.sim(model = list(ar = 0.7), n = 200, sd = 0.5))+2 Modified: pkg/dplR/man/ffcsaps.Rd =================================================================== --- pkg/dplR/man/ffcsaps.Rd 2015-03-23 14:22:41 UTC (rev 977) +++ pkg/dplR/man/ffcsaps.Rd 2015-03-23 14:27:43 UTC (rev 978) @@ -50,14 +50,15 @@ \seealso{ \code{\link{hanning}}, \code{\link{detrend}} } -\examples{docFile <- system.file("doc", "math-dplR.pdf", package="dplR") +\examples{library(graphics) +library(utils) +docFile <- system.file("doc", "math-dplR.pdf", package="dplR") cat("See the following PDF for mathematical details:\n") cat(docFile, sep="\n") \dontrun{ if (interactive() && requireNamespace("Biobase")) { Biobase::openPDF(docFile) } -library(graphics) ## Use series CAM011 from the Campito data set data(ca533) series <- ca533[, "CAM011"] Modified: pkg/dplR/man/fill.internal.NA.Rd =================================================================== --- pkg/dplR/man/fill.internal.NA.Rd 2015-03-23 14:22:41 UTC (rev 977) +++ pkg/dplR/man/fill.internal.NA.Rd 2015-03-23 14:27:43 UTC (rev 978) @@ -54,6 +54,7 @@ } \examples{ library(graphics) +library(stats) foo <- data.frame(x1=c(rnorm(5), NA, NA, rnorm(3)), x2=c(rnorm(10)), x3=c(NA, NA, rnorm(3), NA, rnorm(4)), Modified: pkg/dplR/man/gini.coef.Rd =================================================================== --- pkg/dplR/man/gini.coef.Rd 2015-03-23 14:22:41 UTC (rev 977) +++ pkg/dplR/man/gini.coef.Rd 2015-03-23 14:27:43 UTC (rev 978) @@ -40,6 +40,7 @@ if (interactive() && requireNamespace("Biobase")) { Biobase::openPDF(docFile) }} +library(utils) data(ca533) ca533.rwi <- detrend(rwl = ca533, method = "ModNegExp") ca533.crn <- chron(ca533.rwi, prefix = "CAM") Modified: pkg/dplR/man/glk.Rd =================================================================== --- pkg/dplR/man/glk.Rd 2015-03-23 14:22:41 UTC (rev 977) +++ pkg/dplR/man/glk.Rd 2015-03-23 14:27:43 UTC (rev 978) @@ -56,7 +56,8 @@ Netherlands, 276 p. } -\examples{data(ca533) +\examples{library(utils) +data(ca533) ca533.glk <- glk(ca533) mean(ca533.glk, na.rm = TRUE) } Modified: pkg/dplR/man/hanning.Rd =================================================================== --- pkg/dplR/man/hanning.Rd 2015-03-23 14:22:41 UTC (rev 977) +++ pkg/dplR/man/hanning.Rd 2015-03-23 14:27:43 UTC (rev 978) @@ -28,6 +28,7 @@ \seealso{ \code{\link[stats]{filter} } } \examples{library(graphics) +library(utils) data(ca533) yrs <- as.numeric(rownames(ca533)) y <- ca533[, 1] Modified: pkg/dplR/man/insert.ring.Rd =================================================================== --- pkg/dplR/man/insert.ring.Rd 2015-03-23 14:22:41 UTC (rev 977) +++ pkg/dplR/man/insert.ring.Rd 2015-03-23 14:27:43 UTC (rev 978) @@ -30,7 +30,8 @@ \author{ Andy Bunn. Patched and improved by Mikko Korpela. } \seealso{ \code{\link{dplR}} } -\examples{data(gp.rwl) +\examples{library(utils) +data(gp.rwl) series <- gp.rwl$"50A" names(series) <- rownames(gp.rwl) series <- series[!is.na(series)] Modified: pkg/dplR/man/interseries.cor.Rd =================================================================== --- pkg/dplR/man/interseries.cor.Rd 2015-03-23 14:22:41 UTC (rev 977) +++ pkg/dplR/man/interseries.cor.Rd 2015-03-23 14:27:43 UTC (rev 978) @@ -56,7 +56,8 @@ } \author{ Andy Bunn, patched and improved by Mikko Korpela } \seealso{ \code{\link{rwl.stats}}, \code{\link{rwi.stats}} } -\examples{data(gp.rwl) +\examples{library(utils) +data(gp.rwl) foo <- interseries.cor(gp.rwl) # compare to: # corr.rwl.seg(rwl=gp.rwl,make.plot=FALSE)$overall Modified: pkg/dplR/man/morlet.Rd =================================================================== --- pkg/dplR/man/morlet.Rd 2015-03-23 14:22:41 UTC (rev 977) +++ pkg/dplR/man/morlet.Rd 2015-03-23 14:27:43 UTC (rev 978) @@ -44,7 +44,8 @@ } \author{ Andy Bunn. Patched and improved by Mikko Korpela. } \seealso{ \code{\link{wavelet.plot}} } -\examples{data(ca533) +\examples{library(utils) +data(ca533) ca533.rwi <- detrend(rwl = ca533, method = "ModNegExp") ca533.crn <- chron(ca533.rwi, prefix = "CAM", prewhiten = FALSE) Years <- as.numeric(rownames(ca533.crn)) Modified: pkg/dplR/man/net.Rd =================================================================== --- pkg/dplR/man/net.Rd 2015-03-23 14:22:41 UTC (rev 977) +++ pkg/dplR/man/net.Rd 2015-03-23 14:27:43 UTC (rev 978) @@ -76,7 +76,8 @@ \author{ Mikko Korpela } -\examples{data(ca533) +\examples{library(utils) +data(ca533) ca533.rwi <- detrend(rwl = ca533, method = "ModNegExp") ca533.net <- net(ca533.rwi) tail(ca533.net$all) Modified: pkg/dplR/man/plot.rwl.Rd =================================================================== --- pkg/dplR/man/plot.rwl.Rd 2015-03-23 14:22:41 UTC (rev 977) +++ pkg/dplR/man/plot.rwl.Rd 2015-03-23 14:27:43 UTC (rev 978) @@ -29,7 +29,9 @@ \seealso{ \code{\link{read.rwl}} } -\examples{data(co021) +\examples{library(graphics) +library(utils) +data(co021) plot(co021, plot.type="seg") plot(co021, plot.type="spag") plot(co021, plot.type="spag", zfac=2) Modified: pkg/dplR/man/po.to.wc.Rd =================================================================== --- pkg/dplR/man/po.to.wc.Rd 2015-03-23 14:22:41 UTC (rev 977) +++ pkg/dplR/man/po.to.wc.Rd 2015-03-23 14:27:43 UTC (rev 978) @@ -38,6 +38,7 @@ } \examples{ \dontrun{ +library(utils) data(gp.po) all(wc.to.po(po.to.wc(gp.po)) == gp.po) } Modified: pkg/dplR/man/pointer.Rd =================================================================== --- pkg/dplR/man/pointer.Rd 2015-03-23 14:22:41 UTC (rev 977) +++ pkg/dplR/man/pointer.Rd 2015-03-23 14:27:43 UTC (rev 978) @@ -112,6 +112,7 @@ \seealso{ \code{\link{skel.plot}} } \examples{## Pointer years calculation on ring-width series. Returns a data.frame. +library(utils) data(gp.rwl) py <- pointer(rwl=gp.rwl, rgv.thresh=10, nseries.thresh=75, round.decimals=2) Modified: pkg/dplR/man/powt.Rd =================================================================== --- pkg/dplR/man/powt.Rd 2015-03-23 14:22:41 UTC (rev 977) +++ pkg/dplR/man/powt.Rd 2015-03-23 14:27:43 UTC (rev 978) @@ -34,7 +34,8 @@ } \seealso{\code{\link{rcs}} } -\examples{data(gp.rwl) +\examples{library(utils) +data(gp.rwl) gp.pt <- powt(gp.rwl) } \author{ Modified: pkg/dplR/man/print.redfit.Rd =================================================================== --- pkg/dplR/man/print.redfit.Rd 2015-03-23 14:22:41 UTC (rev 977) +++ pkg/dplR/man/print.redfit.Rd 2015-03-23 14:27:43 UTC (rev 978) @@ -69,7 +69,8 @@ \seealso{ \code{\link{redfit}} } -\examples{data(ca533) +\examples{library(utils) +data(ca533) t <- as.numeric(row.names(ca533)) x <- ca533[[1]] idx <- which(!is.na(x)) Modified: pkg/dplR/man/rasterPlot.Rd =================================================================== --- pkg/dplR/man/rasterPlot.Rd 2015-03-23 14:22:41 UTC (rev 977) +++ pkg/dplR/man/rasterPlot.Rd 2015-03-23 14:27:43 UTC (rev 978) @@ -88,7 +88,9 @@ requires one of the following \code{\link{capabilities}}: \code{"png"}, \code{"aqua"} or \code{"cairo"}. } -\examples{plot(1:5, type = "n") +\examples{library(graphics) +library(stats) +plot(1:5, type = "n") foo <- runif(5, min = 1, max = 5) rasterPlot(quote(points(foo))) } Modified: pkg/dplR/man/rcs.Rd =================================================================== --- pkg/dplR/man/rcs.Rd 2015-03-23 14:22:41 UTC (rev 977) +++ pkg/dplR/man/rcs.Rd 2015-03-23 14:27:43 UTC (rev 978) @@ -90,7 +90,8 @@ } \seealso{ \code{\link{detrend}}, \code{\link{chron}}, \code{\link{cms}}, \code{\link{ffcsaps}} } -\examples{data(gp.rwl) +\examples{library(utils) +data(gp.rwl) data(gp.po) gp.rwi <- rcs(rwl = gp.rwl, po = gp.po, biweight = TRUE, rc.out = TRUE, make.plot = FALSE) Modified: pkg/dplR/man/read.ids.Rd =================================================================== --- pkg/dplR/man/read.ids.Rd 2015-03-23 14:22:41 UTC (rev 977) +++ pkg/dplR/man/read.ids.Rd 2015-03-23 14:27:43 UTC (rev 978) @@ -248,7 +248,8 @@ \author{ Andy Bunn (original version) and Mikko Korpela (patches, \code{\var{stc}="auto"}, \code{\var{fix.typos}}, etc.). } \seealso{ \code{\link{rwi.stats}}, \code{\link{read.rwl}} } -\examples{data(ca533) +\examples{library(utils) +data(ca533) read.ids(ca533, stc = c(3, 2, 3)) autoread.ids(ca533) } Modified: pkg/dplR/man/redfit.Rd =================================================================== --- pkg/dplR/man/redfit.Rd 2015-03-23 14:22:41 UTC (rev 977) +++ pkg/dplR/man/redfit.Rd 2015-03-23 14:27:43 UTC (rev 978) @@ -368,6 +368,7 @@ # Note the long-term low-freq signal in the data. E.g., # crn.plot(cana157) +library(utils) data(cana157) yrs <- as.numeric(rownames(cana157)) x <- cana157[, 1] Modified: pkg/dplR/man/rwi.stats.running.Rd =================================================================== --- pkg/dplR/man/rwi.stats.running.Rd 2015-03-23 14:22:41 UTC (rev 977) +++ pkg/dplR/man/rwi.stats.running.Rd 2015-03-23 14:27:43 UTC (rev 978) @@ -223,7 +223,8 @@ \seealso{ \code{\link{detrend}}, \code{\link{cor}}, \code{\link{read.ids}}, \code{\link{rwi.stats}}, \code{\link{corr.rwl.seg}} } -\examples{data(gp.rwl) +\examples{library(utils) +data(gp.rwl) data(gp.po) gp.rwi <- cms(rwl = gp.rwl, po = gp.po) gp.ids <- read.ids(gp.rwl, stc = c(0, 2, 1)) Modified: pkg/dplR/man/rwl.stats.Rd =================================================================== --- pkg/dplR/man/rwl.stats.Rd 2015-03-23 14:22:41 UTC (rev 977) +++ pkg/dplR/man/rwl.stats.Rd 2015-03-23 14:27:43 UTC (rev 978) @@ -66,7 +66,8 @@ } \author{ Andy Bunn. Slightly improved by Mikko Korpela. } \seealso{ \code{\link{rwi.stats}}, \code{\link{read.rwl}} } -\examples{data(ca533) +\examples{library(utils) +data(ca533) rwl.stats(ca533) summary(ca533) } Modified: pkg/dplR/man/sea.Rd =================================================================== --- pkg/dplR/man/sea.Rd 2015-03-23 14:22:41 UTC (rev 977) +++ pkg/dplR/man/sea.Rd 2015-03-23 14:27:43 UTC (rev 978) @@ -60,6 +60,7 @@ } \examples{library(graphics) +library(utils) data(cana157) event.years <- c(1631, 1742, 1845) cana157.sea <- sea(cana157, event.years) Modified: pkg/dplR/man/seg.plot.Rd =================================================================== --- pkg/dplR/man/seg.plot.Rd 2015-03-23 14:22:41 UTC (rev 977) +++ pkg/dplR/man/seg.plot.Rd 2015-03-23 14:27:43 UTC (rev 978) @@ -23,7 +23,8 @@ } \author{ Andy Bunn. Patched and improved by Mikko Korpela. } \seealso{ \code{\link{spag.plot}} } -\examples{data(co021) +\examples{library(utils) +data(co021) seg.plot(co021, main = "Campito Mountain") } \keyword{ hplot } Modified: pkg/dplR/man/sens1.Rd =================================================================== --- pkg/dplR/man/sens1.Rd 2015-03-23 14:22:41 UTC (rev 977) +++ pkg/dplR/man/sens1.Rd 2015-03-23 14:27:43 UTC (rev 978) @@ -35,7 +35,8 @@ } \author{ Mikko Korpela, based on original by Andy Bunn } \seealso{ \code{\link{sens2}}, \code{\link{rwl.stats}} } -\examples{data(ca533) +\examples{library(utils) +data(ca533) ca533.rwi <- detrend(rwl = ca533, method = "ModNegExp") sens1(ca533.rwi[, 1]) } Modified: pkg/dplR/man/sens2.Rd =================================================================== --- pkg/dplR/man/sens2.Rd 2015-03-23 14:22:41 UTC (rev 977) +++ pkg/dplR/man/sens2.Rd 2015-03-23 14:27:43 UTC (rev 978) @@ -34,7 +34,8 @@ } \author{ Mikko Korpela, based on original by Andy Bunn } \seealso{ \code{\link{sens1}}, \code{\link{rwl.stats}} } -\examples{data(ca533) +\examples{library(utils) +data(ca533) ca533.rwi <- detrend(rwl = ca533, method = "ModNegExp") sens2(ca533.rwi[, 1]) } Modified: pkg/dplR/man/skel.plot.Rd =================================================================== --- pkg/dplR/man/skel.plot.Rd 2015-03-23 14:22:41 UTC (rev 977) +++ pkg/dplR/man/skel.plot.Rd 2015-03-23 14:27:43 UTC (rev 978) @@ -75,7 +75,7 @@ \author{ Andy Bunn. Patched and improved by Mikko Korpela. } \seealso{ \code{\link{Devices}}, \code{\link{hanning}} } -\examples{library(grDevices) +\examples{library(utils) data(co021) x <- co021[,33] x.yrs <- as.numeric(rownames(co021)) @@ -85,6 +85,7 @@ ## On a raw ring width series - dated with names skel.plot(x, yr.vec = x.yrs, sname = x.name, master = TRUE) \dontrun{ +library(grDevices) ## Try cross-dating y <- co021[, 11] y.yrs <- as.numeric(rownames(co021)) Modified: pkg/dplR/man/spag.plot.Rd =================================================================== --- pkg/dplR/man/spag.plot.Rd 2015-03-23 14:22:41 UTC (rev 977) +++ pkg/dplR/man/spag.plot.Rd 2015-03-23 14:27:43 UTC (rev 978) @@ -36,7 +36,8 @@ } \author{ Andy Bunn. Patched and improved by Mikko Korpela. } \seealso{ \code{\link{seg.plot}} } -\examples{data(co021) +\examples{library(utils) +data(co021) spag.plot(co021) spag.plot(co021, zfac = 2) } Modified: pkg/dplR/man/strip.rwl.Rd =================================================================== --- pkg/dplR/man/strip.rwl.Rd 2015-03-23 14:22:41 UTC (rev 977) +++ pkg/dplR/man/strip.rwl.Rd 2015-03-23 14:27:43 UTC (rev 978) @@ -77,6 +77,7 @@ \code{\link{rwi.stats}} } \examples{ +library(utils) data(anos1) anos1.ids <- read.ids(anos1, stc = c(4, 3, 1)) srwl <- strip.rwl(anos1, ids = anos1.ids, verbose = TRUE) Modified: pkg/dplR/man/tbrm.Rd =================================================================== --- pkg/dplR/man/tbrm.Rd 2015-03-23 14:22:41 UTC (rev 977) +++ pkg/dplR/man/tbrm.Rd 2015-03-23 14:27:43 UTC (rev 978) @@ -53,7 +53,8 @@ \author{ Mikko Korpela } \seealso{ \code{\link{chron}} } \examples{ - +library(stats) +library(utils) foo <- rnorm(100) tbrm(foo) mean(foo) Modified: pkg/dplR/man/wavelet.plot.Rd =================================================================== --- pkg/dplR/man/wavelet.plot.Rd 2015-03-23 14:22:41 UTC (rev 977) +++ pkg/dplR/man/wavelet.plot.Rd 2015-03-23 14:27:43 UTC (rev 978) @@ -85,7 +85,9 @@ } \author{ Andy Bunn. Patched and improved by Mikko Korpela. } \seealso{ \code{\link{morlet}}, \code{\link{ffcsaps}}} -\examples{data(ca533) +\examples{library(stats) +library(utils) +data(ca533) ca533.rwi <- detrend(rwl = ca533, method = "ModNegExp") ca533.crn <- chron(ca533.rwi, prefix = "CAM", prewhiten = FALSE) Years <- as.numeric(rownames(ca533.crn)) @@ -96,6 +98,8 @@ \dontrun{ ## Alternative palette with better separation of colors if (require(RColorBrewer)) { + ## RColorBrewer (1.1.2) uses but does not import rgb() + library(grDevices) wavelet.plot(out.wave, key.cols=rev(brewer.pal(10, "Spectral")), useRaster = NA) } Modified: pkg/dplR/man/wc.to.po.Rd =================================================================== --- pkg/dplR/man/wc.to.po.Rd 2015-03-23 14:22:41 UTC (rev 977) +++ pkg/dplR/man/wc.to.po.Rd 2015-03-23 14:27:43 UTC (rev 978) @@ -35,7 +35,8 @@ \seealso{ \code{\link{po.to.wc}}, \code{\link{rcs}}, \code{\link{read.tridas}} } -\examples{data(gp.po) +\examples{library(utils) +data(gp.po) all(wc.to.po(po.to.wc(gp.po)) == gp.po) } \keyword{ manip } Modified: pkg/dplR/man/write.compact.Rd =================================================================== --- pkg/dplR/man/write.compact.Rd 2015-03-23 14:22:41 UTC (rev 977) +++ pkg/dplR/man/write.compact.Rd 2015-03-23 14:27:43 UTC (rev 978) @@ -54,7 +54,8 @@ \seealso{ \code{\link{write.rwl}}, \code{\link{write.tucson}}, \code{\link{write.tridas}}, \code{\link{read.compact}} } -\examples{data(co021) +\examples{library(utils) +data(co021) fname <- write.compact(rwl.df = co021, fname = tempfile(fileext=".rwl"), append = FALSE, prec = 0.001) Modified: pkg/dplR/man/write.crn.Rd =================================================================== --- pkg/dplR/man/write.crn.Rd 2015-03-23 14:22:41 UTC (rev 977) +++ pkg/dplR/man/write.crn.Rd 2015-03-23 14:27:43 UTC (rev 978) @@ -76,7 +76,8 @@ \author{ Andy Bunn. Patched and improved by Mikko Korpela. } \seealso{ \code{\link{chron}}, \code{\link{read.crn}} } -\examples{data(ca533) +\examples{library(utils) +data(ca533) ca533.rwi <- detrend(rwl = ca533, method = "ModNegExp") ca533.crn <- chron(ca533.rwi, prefix = "CAM") fname1 <- write.crn(ca533.crn, tempfile(fileext=".crn")) Modified: pkg/dplR/man/write.rwl.Rd =================================================================== --- pkg/dplR/man/write.rwl.Rd 2015-03-23 14:22:41 UTC (rev 977) +++ pkg/dplR/man/write.rwl.Rd 2015-03-23 14:27:43 UTC (rev 978) @@ -40,7 +40,8 @@ \code{\link{write.compact}}, \code{\link{write.tridas}}, \code{\link{read.rwl}} } -\examples{data(co021) +\examples{library(utils) +data(co021) co021.hdr <- list(site.id = "CO021", site.name = "SCHULMAN OLD TREE NO. 1, MESA VERDE", spp.code = "PSME", state.country = "COLORADO", Modified: pkg/dplR/man/write.tridas.Rd =================================================================== --- pkg/dplR/man/write.tridas.Rd 2015-03-23 14:22:41 UTC (rev 977) +++ pkg/dplR/man/write.tridas.Rd 2015-03-23 14:27:43 UTC (rev 978) @@ -368,7 +368,8 @@ \code{\link{write.compact}}, \code{\link{write.crn}}, \code{\link{read.tridas}} } -\examples{## Write raw ring widths +\examples{library(utils) +## Write raw ring widths data(co021) fname1 <- write.tridas(rwl.df = co021, fname = tempfile(fileext=".xml"), prec = 0.01, Modified: pkg/dplR/man/write.tucson.Rd =================================================================== --- pkg/dplR/man/write.tucson.Rd 2015-03-23 14:22:41 UTC (rev 977) +++ pkg/dplR/man/write.tucson.Rd 2015-03-23 14:27:43 UTC (rev 978) @@ -101,7 +101,8 @@ \code{\link{write.rwl}}, \code{\link{write.compact}}, \code{\link{write.tridas}} } -\examples{data(co021) +\examples{library(utils) +data(co021) co021.hdr <- list(site.id = "CO021", site.name = "SCHULMAN OLD TREE NO. 1, MESA VERDE", spp.code = "PSME", state.country = "COLORADO", Modified: pkg/dplR/man/xskel.ccf.plot.Rd =================================================================== --- pkg/dplR/man/xskel.ccf.plot.Rd 2015-03-23 14:22:41 UTC (rev 977) +++ pkg/dplR/man/xskel.ccf.plot.Rd 2015-03-23 14:27:43 UTC (rev 978) @@ -64,7 +64,8 @@ \author{ Andy Bunn. Patched and improved by Mikko Korpela. } \seealso{ \code{\link{ccf}} } -\examples{data(co021) +\examples{library(utils) +data(co021) dat <- co021 #corrupt a series bad.series <- dat$"641143" Modified: pkg/dplR/man/xskel.plot.Rd =================================================================== --- pkg/dplR/man/xskel.plot.Rd 2015-03-23 14:22:41 UTC (rev 977) +++ pkg/dplR/man/xskel.plot.Rd 2015-03-23 14:27:43 UTC (rev 978) @@ -64,7 +64,8 @@ \author{ Andy Bunn. Patched and improved by Mikko Korpela. } \seealso{ \code{\link{ccf}} } -\examples{data(co021) +\examples{library(utils) +data(co021) dat <- co021 #corrupt a series bad.series <- dat$"641143" From noreply at r-forge.r-project.org Mon Mar 23 15:46:38 2015 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Mon, 23 Mar 2015 15:46:38 +0100 (CET) Subject: [Dplr-commits] r979 - pkg/dplR/man Message-ID: <20150323144638.6DA82184220@r-forge.r-project.org> Author: mvkorpel Date: 2015-03-23 15:46:38 +0100 (Mon, 23 Mar 2015) New Revision: 979 Modified: pkg/dplR/man/morlet.Rd pkg/dplR/man/wavelet.plot.Rd Log: Commented out a dead hyperlink (two instances) Modified: pkg/dplR/man/morlet.Rd =================================================================== --- pkg/dplR/man/morlet.Rd 2015-03-23 14:27:43 UTC (rev 978) +++ pkg/dplR/man/morlet.Rd 2015-03-23 14:46:38 UTC (rev 979) @@ -39,8 +39,8 @@ \bold{79}(1), 61\enc{?}{--}78. } -\note{ This is a port of Torrence\enc{?}{'}s \acronym{IDL} code available at - \url{http://paos.colorado.edu/research/wavelets/software.html} +\note{ This is a port of Torrence\enc{?}{'}s \acronym{IDL} code.% available at +% \url{http://paos.colorado.edu/research/wavelets/software.html} } \author{ Andy Bunn. Patched and improved by Mikko Korpela. } \seealso{ \code{\link{wavelet.plot}} } Modified: pkg/dplR/man/wavelet.plot.Rd =================================================================== --- pkg/dplR/man/wavelet.plot.Rd 2015-03-23 14:27:43 UTC (rev 978) +++ pkg/dplR/man/wavelet.plot.Rd 2015-03-23 14:46:38 UTC (rev 979) @@ -80,8 +80,8 @@ \bold{79}(1), 61\enc{?}{--}78. } \note{ The function \code{morlet} is a port of Torrence\enc{?}{'}s - \acronym{IDL} code available at - \url{http://paos.colorado.edu/research/wavelets/software.html}. + \acronym{IDL} code.% available at +% \url{http://paos.colorado.edu/research/wavelets/software.html}. } \author{ Andy Bunn. Patched and improved by Mikko Korpela. } \seealso{ \code{\link{morlet}}, \code{\link{ffcsaps}}} From noreply at r-forge.r-project.org Mon Mar 23 16:28:40 2015 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Mon, 23 Mar 2015 16:28:40 +0100 (CET) Subject: [Dplr-commits] r980 - pkg/dplR/man Message-ID: <20150323152840.B5D1B1808F5@r-forge.r-project.org> Author: mvkorpel Date: 2015-03-23 16:28:40 +0100 (Mon, 23 Mar 2015) New Revision: 980 Modified: pkg/dplR/man/morlet.Rd pkg/dplR/man/wavelet.plot.Rd Log: Added Wayback Archive link to wavelet code Modified: pkg/dplR/man/morlet.Rd =================================================================== --- pkg/dplR/man/morlet.Rd 2015-03-23 14:46:38 UTC (rev 979) +++ pkg/dplR/man/morlet.Rd 2015-03-23 15:28:40 UTC (rev 980) @@ -39,8 +39,9 @@ \bold{79}(1), 61\enc{?}{--}78. } -\note{ This is a port of Torrence\enc{?}{'}s \acronym{IDL} code.% available at -% \url{http://paos.colorado.edu/research/wavelets/software.html} +\note{ This is a port of Torrence\enc{?}{'}s \acronym{IDL} code, +which can be accessed through the +\href{http://web.archive.org/web/20141216211516/http://paos.colorado.edu/research/wavelets/software.html}{Internet Archive Wayback Machine}. } \author{ Andy Bunn. Patched and improved by Mikko Korpela. } \seealso{ \code{\link{wavelet.plot}} } Modified: pkg/dplR/man/wavelet.plot.Rd =================================================================== --- pkg/dplR/man/wavelet.plot.Rd 2015-03-23 14:46:38 UTC (rev 979) +++ pkg/dplR/man/wavelet.plot.Rd 2015-03-23 15:28:40 UTC (rev 980) @@ -80,8 +80,8 @@ \bold{79}(1), 61\enc{?}{--}78. } \note{ The function \code{morlet} is a port of Torrence\enc{?}{'}s - \acronym{IDL} code.% available at -% \url{http://paos.colorado.edu/research/wavelets/software.html}. + \acronym{IDL} code, which can be accessed through the +\href{http://web.archive.org/web/20141216211516/http://paos.colorado.edu/research/wavelets/software.html}{Internet Archive Wayback Machine}. } \author{ Andy Bunn. Patched and improved by Mikko Korpela. } \seealso{ \code{\link{morlet}}, \code{\link{ffcsaps}}}