From noreply at r-forge.r-project.org Wed Feb 4 12:45:54 2015 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Wed, 4 Feb 2015 12:45:54 +0100 (CET) Subject: [Dplr-commits] r956 - in pkg/dplR: . inst/doc Message-ID: <20150204114555.0EFF6186CEE@r-forge.r-project.org> Author: mvkorpel Date: 2015-02-04 12:45:54 +0100 (Wed, 04 Feb 2015) New Revision: 956 Modified: pkg/dplR/DESCRIPTION pkg/dplR/inst/doc/math-dplR.R pkg/dplR/inst/doc/math-dplR.Rnw.txt pkg/dplR/inst/doc/math-dplR.bib pkg/dplR/inst/doc/math-dplR.pdf Log: Updated math-dplR.pdf to match new (optimized) ffcsaps() Modified: pkg/dplR/DESCRIPTION =================================================================== --- pkg/dplR/DESCRIPTION 2015-01-28 16:10:07 UTC (rev 955) +++ pkg/dplR/DESCRIPTION 2015-02-04 11:45:54 UTC (rev 956) @@ -3,7 +3,7 @@ Type: Package Title: Dendrochronology Program Library in R Version: 1.6.3 -Date: 2015-01-28 +Date: 2015-02-04 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/inst/doc/math-dplR.R =================================================================== --- pkg/dplR/inst/doc/math-dplR.R 2015-01-28 16:10:07 UTC (rev 955) +++ pkg/dplR/inst/doc/math-dplR.R 2015-02-04 11:45:54 UTC (rev 956) @@ -1,4 +1,3 @@ - ## ----"try-matlab", echo=FALSE, results="hide"---------------------------- TRY_MATLAB <- TRUE @@ -11,17 +10,14 @@ library(dichromat) library(graphics) library(stats) +library(Matrix) # ffcsaps uses sparse matrices - - - ## ----"knitr-init-fig", echo=FALSE, cache=FALSE--------------------------- PAGE_WIDTH <- 4.74 PAGE_HEIGHT <- 8.22 opts_template$set(myfigures=list(fig.path = "figure/", fig.pos = "tbp", fig.align = "center", fig.lp = "fig:", dev = "tikz")) - ## ----"response-comp-init"------------------------------------------------ ## Helper function used in ffcsaps2 inc <- function(from, to) { @@ -153,10 +149,10 @@ c(0, 0, odx[-1])), arg2, n) R2[, 1] <- R2[, 1] - 1 - forR <- matrix(0, zz2, zz2) - forR2 <- matrix(0, zz2, n) - forR[R[, 1] + (R[, 2] - 1) * zz2] <- R[, 3] - forR2[R2[, 1] + (R2[, 2] - 1) * zz2] <- R2[, 3] + forR <- Matrix(0, zz2, zz2, sparse = TRUE) + forR2 <- Matrix(0, zz2, n, sparse = TRUE) + forR[R[, 1:2, drop=FALSE]] <- R[, 3] + forR2[R2[, 1:2, drop=FALSE]] <- R2[, 3] if (!missing(p)) { ## NEW: give value of p directly as an argument p.inv <- 1 / p @@ -177,8 +173,8 @@ mplier <- 6 - 6 / p.inv # slightly more accurate than 6*(1-1/p.inv) ## forR*p is faster than forR/p.inv, and a quick test didn't ## show any difference in the final spline - u <- solve(mplier * tcrossprod(forR2) + forR * p, - diff(diff(yi) / diff.xi)) + u <- as.numeric(solve(mplier * tcrossprod(forR2) + forR * p, + diff(diff(yi) / diff.xi))) yi <- yi - mplier * diff(c(0, diff(c(0, u, 0)) / diff.xi, 0)) test0 <- xi[-c(1, n)] c3 <- c(0, u / p.inv, 0) @@ -204,7 +200,6 @@ res } - ## ----"response-init"----------------------------------------------------- ## Cook, E. R. and Kairiukstis, L. A. (1990) Methods of ## Dendrochronology: Applications in the Environmental Sciences. @@ -225,7 +220,6 @@ 1 - 1 / (1 + (p * (cos(pif2) + 2)) / (6 * (cos(pif2) - 1)^2)) } - ## ----"response-comp", message=FALSE, dependson="response-comp-init", cache.vars=c("response1", "response2", "NYRS", "nFreq")---- N <- 1536 K <- 500 @@ -292,7 +286,6 @@ response2[, j] <- rowMeans(ratio2[, , j]) } - ## ----"ffcsaps-caption", cache=FALSE-------------------------------------- FFCSAPS_CAPTION <- paste("Theoretical frequency response of spline filter vs response", @@ -337,7 +330,6 @@ lwd = c(1, 1, LWD)) par(op) - ## ----"smoothed-R", dependson="response-comp-init", cache.vars=c("smoothed.R", "y")---- if (!exists(".Random.seed", globalenv(), mode="numeric")) { foo <- sample(TRUE) @@ -405,7 +397,7 @@ } else { matlabValue <- NULL smoothed.matlab <- NULL - matlabVersion <- "8.3.0.532 (R2014a)" # tested ok on 2014-05-12 + matlabVersion <- "8.4.0.150421 (R2014b)" # tested ok on 2015-02-04 } ## ----"R-matlab-compare", cache=FALSE, error=FALSE------------------------ @@ -425,7 +417,6 @@ stopifnot(all(allEqual)) } - ## ----"smoothed-caption", cache=FALSE------------------------------------- SMOOTHED_CAPTION <- paste("Spline with different values of smoothing parameter", @@ -455,13 +446,11 @@ bty = "n") par(op) - ## ----"matlab-version", cache=FALSE--------------------------------------- if (isTRUE(TRY_MATLAB) && matlabValue == 0) { matlabVersionText <- paste0("(version ", latexify2(matlabVersion), ")") } - ## ----"matlab-note", cache=FALSE, message=FALSE--------------------------- matlabNoteText <- if (!isTRUE(TRY_MATLAB)) { message(paste("Set TRY_MATLAB=TRUE and re-knit the document to repeat the comparison.", @@ -487,7 +476,6 @@ "The result was reproduced when this document was compiled." } - ## ----gini-rmd, echo=TRUE, tidy=FALSE, cache=FALSE------------------------ ## Gini index is one half of relative mean difference. ## x should not have NA values. @@ -495,4 +483,3 @@ mean(abs(outer(x, x, "-"))) / mean(x) * 0.5 } - Modified: pkg/dplR/inst/doc/math-dplR.Rnw.txt =================================================================== --- pkg/dplR/inst/doc/math-dplR.Rnw.txt 2015-01-28 16:10:07 UTC (rev 955) +++ pkg/dplR/inst/doc/math-dplR.Rnw.txt 2015-02-04 11:45:54 UTC (rev 956) @@ -62,6 +62,7 @@ library(dichromat) library(graphics) library(stats) +library(Matrix) # ffcsaps uses sparse matrices @ \usepackage[T1]{fontenc} @@ -255,10 +256,10 @@ c(0, 0, odx[-1])), arg2, n) R2[, 1] <- R2[, 1] - 1 - forR <- matrix(0, zz2, zz2) - forR2 <- matrix(0, zz2, n) - forR[R[, 1] + (R[, 2] - 1) * zz2] <- R[, 3] - forR2[R2[, 1] + (R2[, 2] - 1) * zz2] <- R2[, 3] + forR <- Matrix(0, zz2, zz2, sparse = TRUE) + forR2 <- Matrix(0, zz2, n, sparse = TRUE) + forR[R[, 1:2, drop=FALSE]] <- R[, 3] + forR2[R2[, 1:2, drop=FALSE]] <- R2[, 3] if (!missing(p)) { ## NEW: give value of p directly as an argument p.inv <- 1 / p @@ -279,8 +280,8 @@ mplier <- 6 - 6 / p.inv # slightly more accurate than 6*(1-1/p.inv) ## forR*p is faster than forR/p.inv, and a quick test didn't ## show any difference in the final spline - u <- solve(mplier * tcrossprod(forR2) + forR * p, - diff(diff(yi) / diff.xi)) + u <- as.numeric(solve(mplier * tcrossprod(forR2) + forR * p, + diff(diff(yi) / diff.xi))) yi <- yi - mplier * diff(c(0, diff(c(0, u, 0)) / diff.xi, 0)) test0 <- xi[-c(1, n)] c3 <- c(0, u / p.inv, 0) @@ -339,8 +340,11 @@ The original implementations of the functions covered here were not written by the author of this document. Therefore the functions were -analyzed with a reverse engineering approach. At the time of writing, -dplR was at version 1.6.0. Although any changes affecting the +analyzed with a reverse engineering approach. At the time when this +document was updated, the latest release of dplR was version 1.6.2, +but the performance improvements of (future) version 1.6.3 had already +been applied to \texttt{ffcsaps} in the development version and in the +source code of the document. Although any changes affecting the mathematical details of the functions are unlikely, the reader is advised to check that the document file originated from a current version of dplR. @@ -603,7 +607,7 @@ } else { matlabValue <- NULL smoothed.matlab <- NULL - matlabVersion <- "8.3.0.532 (R2014a)" # tested ok on 2014-05-12 + matlabVersion <- "8.4.0.150421 (R2014b)" # tested ok on 2015-02-04 } @ <<"R-matlab-compare", cache=FALSE, error=FALSE>>= Modified: pkg/dplR/inst/doc/math-dplR.bib =================================================================== --- pkg/dplR/inst/doc/math-dplR.bib 2015-01-28 16:10:07 UTC (rev 955) +++ pkg/dplR/inst/doc/math-dplR.bib 2015-02-04 11:45:54 UTC (rev 956) @@ -105,10 +105,10 @@ @Manual{dplRman, title = {dplR: Dendrochronology Program Library in R}, author = {Andy Bunn and Mikko Korpela and Franco Biondi and Filipe - Campelo and Pierre M?rian and Manfred Mudelsee and - Fares Qeadan and Michael Schulz and Christian Zang}, - year = {2014}, - note = {R package version 1.6.0}, + Campelo and Pierre M?rian and Fares Qeadan and + Christian Zang}, + year = {2015}, + note = {R package version 1.6.3}, url = {http://huxley.wwu.edu/trl/htrl-dplr, http://R-Forge.R-project.org/projects/dplr/}, } @@ -118,6 +118,6 @@ author = {{R Core Team}}, organization = {R Foundation for Statistical Computing}, address = {Vienna, Austria}, - year = {2014}, + year = {2015}, url = {http://www.R-project.org/}, } Modified: pkg/dplR/inst/doc/math-dplR.pdf =================================================================== (Binary files differ) From noreply at r-forge.r-project.org Wed Feb 4 13:08:31 2015 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Wed, 4 Feb 2015 13:08:31 +0100 (CET) Subject: [Dplr-commits] r957 - pkg/dplR/man Message-ID: <20150204120831.1A105186D44@r-forge.r-project.org> Author: mvkorpel Date: 2015-02-04 13:08:30 +0100 (Wed, 04 Feb 2015) New Revision: 957 Modified: pkg/dplR/man/morlet.Rd pkg/dplR/man/wavelet.plot.Rd Log: Updated URL Modified: pkg/dplR/man/morlet.Rd =================================================================== --- pkg/dplR/man/morlet.Rd 2015-02-04 11:45:54 UTC (rev 956) +++ pkg/dplR/man/morlet.Rd 2015-02-04 12:08:30 UTC (rev 957) @@ -39,7 +39,7 @@ } \note{ This is a port of Torrence's \acronym{IDL} code available at - \url{http://atoc.colorado.edu/research/wavelets/software.html} + \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 2015-02-04 11:45:54 UTC (rev 956) +++ pkg/dplR/man/wavelet.plot.Rd 2015-02-04 12:08:30 UTC (rev 957) @@ -78,7 +78,7 @@ } \note{ The function \code{morlet} is a port of Torrence's \acronym{IDL} code available at - \url{http://atoc.colorado.edu/research/wavelets/software.html} + \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 Thu Feb 5 09:48:59 2015 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Thu, 5 Feb 2015 09:48:59 +0100 (CET) Subject: [Dplr-commits] r958 - pkg/dplR Message-ID: <20150205084859.44BDF1861EE@r-forge.r-project.org> Author: mvkorpel Date: 2015-02-05 09:48:58 +0100 (Thu, 05 Feb 2015) New Revision: 958 Modified: pkg/dplR/DESCRIPTION Log: The comma (,) is a valid character in URLs [1], so I guess it should not be used as a separator of two URLs, even though R-exts instructs us to use a comma or white. Let's use plain whitespace instead. [1] http://tools.ietf.org/html/rfc3986#section-2.2 [2] http://cran.r-project.org/doc/manuals/r-release/R-exts.html#The-DESCRIPTION-file Modified: pkg/dplR/DESCRIPTION =================================================================== --- pkg/dplR/DESCRIPTION 2015-02-04 12:08:30 UTC (rev 957) +++ pkg/dplR/DESCRIPTION 2015-02-05 08:48:58 UTC (rev 958) @@ -30,6 +30,6 @@ dendrochronology LazyData: no License: GPL (>= 2) -URL: http://huxley.wwu.edu/trl/htrl-dplr, +URL: http://huxley.wwu.edu/trl/htrl-dplr http://R-Forge.R-project.org/projects/dplr/ MailingList: https://groups.google.com/d/forum/dplr-help From noreply at r-forge.r-project.org Thu Feb 5 10:05:08 2015 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Thu, 5 Feb 2015 10:05:08 +0100 (CET) Subject: [Dplr-commits] r959 - pkg/dplR Message-ID: <20150205090508.9F1B9181371@r-forge.r-project.org> Author: mvkorpel Date: 2015-02-05 10:05:08 +0100 (Thu, 05 Feb 2015) New Revision: 959 Modified: pkg/dplR/DESCRIPTION Log: Oops, I accidentally submitted the last commit with an unfinished message. Here is a better one: Separating two URLs in the URL field of DESCRIPTION with whitespace instead of a comma (and whitespace). Whitespace was previously used at some point, until I switched to comma for some reason (unfortunately not documented). Anyway, here is a reason to ditch the comma: The comma is a valid character in URLs [1, Section 2.2], so I guess it should not be used as a separator of two URLs, even though R-exts [2] instructs us to use a comma or whitespace. In other words, blindly splitting the URL field at every comma is not bulletproof. I don't know if R (CRAN?) is smarter than that, but whitespace seems like a more robust separator. Whitespace is listed as one of the suggested URI (URL) delimiters in, the others being double quotes and angle brackets. Technically, whitespace may have to be introduced in the middle of a URL if its length exceeds the maximum line length of the transport medium (file format), and it is the responsibility of the application to detect such (rare) cases. [1, Appendix C] [1] http://tools.ietf.org/html/rfc3986 [2] http://cran.r-project.org/doc/manuals/r-release/R-exts.html Modified: pkg/dplR/DESCRIPTION =================================================================== --- pkg/dplR/DESCRIPTION 2015-02-05 08:48:58 UTC (rev 958) +++ pkg/dplR/DESCRIPTION 2015-02-05 09:05:08 UTC (rev 959) @@ -3,7 +3,7 @@ Type: Package Title: Dendrochronology Program Library in R Version: 1.6.3 -Date: 2015-02-04 +Date: 2015-02-05 Authors at R: c(person("Andy", "Bunn", role = c("aut", "cph", "cre", "trl"), email = "andy.bunn at wwu.edu"), person("Mikko", "Korpela", role = c("aut", "trl")), person("Franco", "Biondi", From noreply at r-forge.r-project.org Thu Feb 5 13:18:59 2015 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Thu, 5 Feb 2015 13:18:59 +0100 (CET) Subject: [Dplr-commits] r960 - in pkg/dplR: . R man tests/testthat Message-ID: <20150205121900.02E33187977@r-forge.r-project.org> Author: mvkorpel Date: 2015-02-05 13:18:59 +0100 (Thu, 05 Feb 2015) New Revision: 960 Modified: pkg/dplR/ChangeLog pkg/dplR/R/read.tucson.R pkg/dplR/man/read.tucson.Rd pkg/dplR/tests/testthat/test-io.R Log: Fixed bug or misfeature which caused read.tucson() to drop leading or trailing zeros. The old behavior can be restored by setting edge.zeros=FALSE. Modified: pkg/dplR/ChangeLog =================================================================== --- pkg/dplR/ChangeLog 2015-02-05 09:05:08 UTC (rev 959) +++ pkg/dplR/ChangeLog 2015-02-05 12:18:59 UTC (rev 960) @@ -62,6 +62,18 @@ - New function for computing the NET parameter (Esper et al., 2001). +File: read.tucson.R +------------------- + +- New argument 'edge.zeros', TRUE (default) or FALSE. If TRUE, + possible leading and trailing zero values in tree-ring series are + kept. If FALSE, such values are dropped. The latter is how the + function has worked between (pre-)release 1.5.5 and the previoius + release, and may be considered a bug or a misfeature. To + reiterate, the default behavior has changed in some cases. The + alternative, 1.5.5--1.6.2 behavior can be restored by changing the + value of the argument. + * CHANGES IN dplR VERSION 1.6.2 No functional changes. A unit test was changed so it would not fail Modified: pkg/dplR/R/read.tucson.R =================================================================== --- pkg/dplR/R/read.tucson.R 2015-02-05 09:05:08 UTC (rev 959) +++ pkg/dplR/R/read.tucson.R 2015-02-05 12:18:59 UTC (rev 960) @@ -1,5 +1,6 @@ `read.tucson` <- function(fname, header = NULL, long = FALSE, - encoding = getOption("encoding")) + encoding = getOption("encoding"), + edge.zeros = TRUE) { ## Checks that the input is good. The input variables are vectors ## ('series', 'decade.yr') or matrices ('x') containing most of @@ -206,7 +207,7 @@ if (!grepl("\t", data1[length(data1)])) { ## Using a connection instead of a file name in read.fwf and ## read.table allows the function to support different encodings. - if (long) { + if (isTRUE(long)) { ## Reading 11 years per decade allows nonstandard use of stop ## marker at the end of a line that already has 10 ## measurements. Such files exist in ITRDB. @@ -245,8 +246,12 @@ series.fixed <- series decade.fixed <- decade.yr x <- as.matrix(dat[3:12]) - ## Convert values <= 0 (not -9999) to NA - x[x <= 0 & x != -9999] <- NA + ## Convert values <= 0 or < 0 (not -9999) to NA + if (isTRUE(edge.zeros)) { + x[x < 0 & x != -9999] <- NA + } else { + x[x <= 0 & x != -9999] <- NA + } x.fixed <- x fixed.ok <- input.ok(series, decade.yr, x) } else { @@ -285,7 +290,11 @@ series <- dat[[1]] decade.yr <- dat[[2]] x <- as.matrix(dat[3:12]) - x[x <= 0 & x != -9999] <- NA + if (isTRUE(edge.zeros)) { + x[x < 0 & x != -9999] <- NA + } else { + x[x <= 0 & x != -9999] <- NA + } if (!input.ok(series, decade.yr, x)) { if (exists("series.fixed", inherits=FALSE) && exists("decade.fixed", inherits=FALSE) && Modified: pkg/dplR/man/read.tucson.Rd =================================================================== --- pkg/dplR/man/read.tucson.Rd 2015-02-05 09:05:08 UTC (rev 959) +++ pkg/dplR/man/read.tucson.Rd 2015-02-05 12:18:59 UTC (rev 960) @@ -6,7 +6,7 @@ } \usage{ read.tucson(fname, header = NULL, long = FALSE, - encoding = getOption("encoding")) + encoding = getOption("encoding"), edge.zeros = TRUE) } \arguments{ \item{fname}{ a \code{character} vector giving the file name of the @@ -26,6 +26,10 @@ problem. Examples of popular encodings available on many systems are \code{"ASCII"}, \code{"UTF-8"}, and \code{"latin1"} alias \code{"ISO-8859-1"}. See the help of \code{\link{file}}. } + \item{edge.zeros}{ \code{logical} flag indicating whether leading or + trailing zeros in series will be preserved (when the flag is + \code{TRUE}, the default) or discarded, i.e. marked as \code{NA} + (when \code{FALSE}). } } \details{ This reads in a standard rwl file as defined according to the Modified: pkg/dplR/tests/testthat/test-io.R =================================================================== --- pkg/dplR/tests/testthat/test-io.R 2015-02-05 09:05:08 UTC (rev 959) +++ pkg/dplR/tests/testthat/test-io.R 2015-02-05 12:18:59 UTC (rev 960) @@ -188,6 +188,41 @@ expect_equal(0, nrow(read.tucson(tf13, header = FALSE))) }) + tf14 <- tempfile() + fh14 <- file(tf14, "wt") + on.exit(unlink(tf14), add=TRUE) + writeLines(c("TST14A 1906 0 0 100 200", + "TST14A 1910 300 200 100 200 300 999", + "TST14B 1905 300 200 100 200 300", + "TST14B 1910 200 100 0 0 999", + "TST14C 1906 0 200 100 200", + "TST14C 1910 300 200 100 0 999"), fh14) + close(fh14) + test_that("read.tucson (by default) preserves edge zeros", { + res.tf14 <- read.tucson(tf14) + expect_true(is.data.frame(res.tf14)) + expect_named(res.tf14, c("TST14A", "TST14B", "TST14C")) + expect_equal(row.names(res.tf14), as.character(1905:1914)) + expect_equal(res.tf14[[1]], + c(NA_real_, 0, 0, 1, 2, 3, 2, 1, 2, 3)) + expect_equal(res.tf14[[2]], + c(3, 2, 1, 2, 3, 2, 1, 0, 0, NA_real_)) + expect_equal(res.tf14[[3]], + c(NA_real_, 0, 2, 1, 2, 3, 2, 1, 0, NA_real_)) + res.tf14B <- read.tucson(tf14, edge.zeros=FALSE) + expect_true(is.data.frame(res.tf14B)) + expect_named(res.tf14B, c("TST14A", "TST14B", "TST14C")) + expect_equal(row.names(res.tf14B), as.character(1905:1914)) + NA2 <- rep.int(NA_real_, 2) + NA3 <- rep.int(NA_real_, 3) + expect_equal(res.tf14B[[1]], + c(NA3, 1, 2, 3, 2, 1, 2, 3)) + expect_equal(res.tf14B[[2]], + c(3, 2, 1, 2, 3, 2, 1, NA3)) + expect_equal(res.tf14B[[3]], + c(NA2, 2, 1, 2, 3, 2, 1, NA2)) + }) + } test.read.tucson() ### We should write tests for other I/O functions, also From noreply at r-forge.r-project.org Mon Feb 9 12:46:33 2015 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Mon, 9 Feb 2015 12:46:33 +0100 (CET) Subject: [Dplr-commits] r961 - pkg/dplR Message-ID: <20150209114633.BB6E0186E93@r-forge.r-project.org> Author: mvkorpel Date: 2015-02-09 12:46:33 +0100 (Mon, 09 Feb 2015) New Revision: 961 Modified: pkg/dplR/DESCRIPTION Log: Added period to complete the last sentence of Description (R CMD check). Modified: pkg/dplR/DESCRIPTION =================================================================== --- pkg/dplR/DESCRIPTION 2015-02-05 12:18:59 UTC (rev 960) +++ pkg/dplR/DESCRIPTION 2015-02-09 11:46:33 UTC (rev 961) @@ -3,7 +3,7 @@ Type: Package Title: Dendrochronology Program Library in R Version: 1.6.3 -Date: 2015-02-05 +Date: 2015-02-09 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", @@ -27,7 +27,7 @@ Description: This package contains functions for performing tree-ring analyses such as detrending, chronology building, and cross dating. The package reads and writes standard file formats used in - dendrochronology + dendrochronology. LazyData: no License: GPL (>= 2) URL: http://huxley.wwu.edu/trl/htrl-dplr From noreply at r-forge.r-project.org Mon Feb 9 15:41:12 2015 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Mon, 9 Feb 2015 15:41:12 +0100 (CET) Subject: [Dplr-commits] r962 - pkg/dplR Message-ID: <20150209144112.86B51181371@r-forge.r-project.org> Author: mvkorpel Date: 2015-02-09 15:41:12 +0100 (Mon, 09 Feb 2015) New Revision: 962 Modified: pkg/dplR/ChangeLog Log: Credits for reporting the latest issue Modified: pkg/dplR/ChangeLog =================================================================== --- pkg/dplR/ChangeLog 2015-02-09 11:46:33 UTC (rev 961) +++ pkg/dplR/ChangeLog 2015-02-09 14:41:12 UTC (rev 962) @@ -72,7 +72,8 @@ release, and may be considered a bug or a misfeature. To reiterate, the default behavior has changed in some cases. The alternative, 1.5.5--1.6.2 behavior can be restored by changing the - value of the argument. + value of the argument. Reported by Daniel Bishop and Neil + Pederson. * CHANGES IN dplR VERSION 1.6.2 From noreply at r-forge.r-project.org Tue Feb 10 10:55:58 2015 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Tue, 10 Feb 2015 10:55:58 +0100 (CET) Subject: [Dplr-commits] r963 - in pkg/dplR: . R Message-ID: <20150210095558.748D8187858@r-forge.r-project.org> Author: mvkorpel Date: 2015-02-10 10:55:58 +0100 (Tue, 10 Feb 2015) New Revision: 963 Modified: pkg/dplR/ChangeLog pkg/dplR/DESCRIPTION pkg/dplR/R/corr.rwl.seg.R pkg/dplR/R/corr.series.seg.R pkg/dplR/R/series.rwl.plot.R Log: Reduced the number of calls to options() Modified: pkg/dplR/ChangeLog =================================================================== --- pkg/dplR/ChangeLog 2015-02-09 14:41:12 UTC (rev 962) +++ pkg/dplR/ChangeLog 2015-02-10 09:55:58 UTC (rev 963) @@ -39,6 +39,8 @@ column names anymore. - Using base::rowSums and functions from the matrixStats package to speed up some operations on rows or columns of matrices. +- Reduced the number of calls to options() by one when setting and + restoring options File: ffcsaps.R --------------- Modified: pkg/dplR/DESCRIPTION =================================================================== --- pkg/dplR/DESCRIPTION 2015-02-09 14:41:12 UTC (rev 962) +++ pkg/dplR/DESCRIPTION 2015-02-10 09:55:58 UTC (rev 963) @@ -3,7 +3,7 @@ Type: Package Title: Dendrochronology Program Library in R Version: 1.6.3 -Date: 2015-02-09 +Date: 2015-02-10 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/R/corr.rwl.seg.R =================================================================== --- pkg/dplR/R/corr.rwl.seg.R 2015-02-09 14:41:12 UTC (rev 962) +++ pkg/dplR/R/corr.rwl.seg.R 2015-02-10 09:55:58 UTC (rev 963) @@ -15,9 +15,8 @@ ## turn off warnings for this function ## The sig test for spearman's rho often produces warnings. - w <- options("warn") + w <- options(warn = -1) on.exit(options(w)) - options(warn = -1) nseries <- length(rwl) if (is.null(master) && nseries < 2) { Modified: pkg/dplR/R/corr.series.seg.R =================================================================== --- pkg/dplR/R/corr.series.seg.R 2015-02-09 14:41:12 UTC (rev 962) +++ pkg/dplR/R/corr.series.seg.R 2015-02-10 09:55:58 UTC (rev 963) @@ -17,9 +17,8 @@ ## turn off warnings for this function ## The sig test for spearman's rho often produces warnings. - w <- options("warn") + w <- options(warn = -1) on.exit(options(w)) - options(warn = -1) seg.lag <- seg.length / 2 Modified: pkg/dplR/R/series.rwl.plot.R =================================================================== --- pkg/dplR/R/series.rwl.plot.R 2015-02-09 14:41:12 UTC (rev 962) +++ pkg/dplR/R/series.rwl.plot.R 2015-02-10 09:55:58 UTC (rev 963) @@ -14,9 +14,8 @@ ## turn off warnings for this function ## The sig test for spearman's rho often produces warnings. - w <- options("warn") + w <- options(warn = -1) on.exit(options(w)) - options(warn = -1) seg.lag <- seg.length / 2 From noreply at r-forge.r-project.org Thu Feb 12 09:54:54 2015 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Thu, 12 Feb 2015 09:54:54 +0100 (CET) Subject: [Dplr-commits] r964 - pkg/dplR Message-ID: <20150212085454.14E88187567@r-forge.r-project.org> Author: mvkorpel Date: 2015-02-12 09:54:53 +0100 (Thu, 12 Feb 2015) New Revision: 964 Modified: pkg/dplR/DESCRIPTION Log: A Description without NOTE from R CMD check (R-devel r67799) Modified: pkg/dplR/DESCRIPTION =================================================================== --- pkg/dplR/DESCRIPTION 2015-02-10 09:55:58 UTC (rev 963) +++ pkg/dplR/DESCRIPTION 2015-02-12 08:54:53 UTC (rev 964) @@ -3,7 +3,7 @@ Type: Package Title: Dendrochronology Program Library in R Version: 1.6.3 -Date: 2015-02-10 +Date: 2015-02-12 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", @@ -24,10 +24,9 @@ stringi (>= 0.2-2), stringr (>= 0.4), XML (>= 2.1-0) Suggests: Biobase, dichromat (>= 1.2-3), foreach, forecast, iterators, knitr, RColorBrewer, testthat (>= 0.8), tikzDevice, waveslim -Description: This package contains functions for performing tree-ring - analyses such as detrending, chronology building, and cross dating. - The package reads and writes standard file formats used in - dendrochronology. +Description: Perform tree-ring analyses such as detrending, chronology + building, and cross dating. Read and write standard file formats + used in dendrochronology. LazyData: no License: GPL (>= 2) URL: http://huxley.wwu.edu/trl/htrl-dplr From noreply at r-forge.r-project.org Wed Feb 18 22:08:20 2015 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Wed, 18 Feb 2015 22:08:20 +0100 (CET) Subject: [Dplr-commits] r965 - in pkg/dplR: . R Message-ID: <20150218210820.CDA591876F5@r-forge.r-project.org> Author: andybunn Date: 2015-02-18 22:08:20 +0100 (Wed, 18 Feb 2015) New Revision: 965 Modified: pkg/dplR/ChangeLog pkg/dplR/R/spag.plot.R Log: cosmetic change to spag.plot Modified: pkg/dplR/ChangeLog =================================================================== --- pkg/dplR/ChangeLog 2015-02-12 08:54:53 UTC (rev 964) +++ pkg/dplR/ChangeLog 2015-02-18 21:08:20 UTC (rev 965) @@ -1,5 +1,10 @@ * CHANGES IN dplR VERSION 1.6.3 +File: spag.plot.R +-------------- + +- Change to ylim in the plotting area. + File: CITATION -------------- Modified: pkg/dplR/R/spag.plot.R =================================================================== --- pkg/dplR/R/spag.plot.R 2015-02-12 08:54:53 UTC (rev 964) +++ pkg/dplR/R/spag.plot.R 2015-02-18 21:08:20 UTC (rev 965) @@ -12,7 +12,7 @@ op <- par(no.readonly=TRUE) on.exit(par(op)) par(mar=c(2, 5, 2, 5) + 0.1, mgp=c(1.1, 0.1, 0), tcl=0.5, - xaxs="i") + xaxs="i",yaxs="i") ## Set vertical offset for plotting each series for (i in 1:nseries) { rwl2[, i] <- rwl2[, i] + i