From noreply at r-forge.r-project.org Fri Dec 18 14:30:19 2015 From: noreply at r-forge.r-project.org (noreply at r-forge.r-project.org) Date: Fri, 18 Dec 2015 14:30:19 +0100 (CET) Subject: [Dplr-commits] r1008 - in pkg/dplR: . R Message-ID: <20151218133019.2141B1803BD@r-forge.r-project.org> Author: mvkorpel Date: 2015-12-18 14:30:18 +0100 (Fri, 18 Dec 2015) New Revision: 1008 Modified: pkg/dplR/ChangeLog pkg/dplR/DESCRIPTION pkg/dplR/R/common.interval.R pkg/dplR/R/rwi.stats.running.R Log: Using row and column subsetting in matrixStats. Thanks to Henrik Bengtsson. Modified: pkg/dplR/ChangeLog =================================================================== --- pkg/dplR/ChangeLog 2015-11-13 14:31:25 UTC (rev 1007) +++ pkg/dplR/ChangeLog 2015-12-18 13:30:18 UTC (rev 1008) @@ -1,5 +1,10 @@ * CHANGES IN dplR VERSION 1.6.4 +File: DESCRIPTION +----------------- + +- Version number requirement for matrixStats is now (>= 0.50.0). + File: rasterPlot.R ------------------ - rasterPlot() now reverts to normal plotting if png device is unavailable or @@ -35,6 +40,9 @@ nchar(type = "width") and nchar() with default 'type'; format(string, width = w, justify = "left") and stringr::str_pad(string, w, side="right"). +- Using 'rows' and 'cols' arguments of matrixStats functions where + appropriate. This should result in less time and memory being + used. Thanks to Henrik Bengtsson for the tip and code examples. * CHANGES IN dplR VERSION 1.6.3 Modified: pkg/dplR/DESCRIPTION =================================================================== --- pkg/dplR/DESCRIPTION 2015-11-13 14:31:25 UTC (rev 1007) +++ pkg/dplR/DESCRIPTION 2015-12-18 13:30:18 UTC (rev 1008) @@ -3,7 +3,7 @@ Type: Package Title: Dendrochronology Program Library in R Version: 1.6.4 -Date: 2015-11-13 +Date: 2015-12-18 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", @@ -20,7 +20,7 @@ Depends: R (>= 2.15.2) Imports: graphics, grDevices, grid, stats, utils, lattice (>= 0.13-6), Matrix (>= 1.0-3), digest (>= 0.2.3), gmp (>= 0.5-5), - matrixStats (>= 0.9.7), png (>= 0.1-1), R.utils (>= 1.32.0), + matrixStats (>= 0.50.0), png (>= 0.1-1), R.utils (>= 1.32.0), 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 Modified: pkg/dplR/R/common.interval.R =================================================================== --- pkg/dplR/R/common.interval.R 2015-11-13 14:31:25 UTC (rev 1007) +++ pkg/dplR/R/common.interval.R 2015-12-18 13:30:18 UTC (rev 1008) @@ -55,7 +55,7 @@ break } } - tmp <- rowAlls(rwlNotNA[dontkeep.row, keep.col, drop = FALSE]) + tmp <- rowAlls(rwlNotNA, rows = dontkeep.row, cols = keep.col) dontkeep.row[dontkeep.row] <- !tmp nRow <- nRow + sum(tmp) n.years <- nCol * nRow @@ -133,7 +133,7 @@ keep.row <- tmp[[3]] keep.col <- tmp[[4]] } else { # type2 == "both" - keep.col <- colAlls(rwlNotNA[row.idx, , drop = FALSE]) + keep.col <- colAlls(rwlNotNA, rows = row.idx) nCol <- sum(keep.col) } opt <- nRow * nCol Modified: pkg/dplR/R/rwi.stats.running.R =================================================================== --- pkg/dplR/R/rwi.stats.running.R 2015-11-13 14:31:25 UTC (rev 1007) +++ pkg/dplR/R/rwi.stats.running.R 2015-12-18 13:30:18 UTC (rev 1008) @@ -167,7 +167,7 @@ tree.any <- matrix(FALSE, n.years, n.trees) for (i in seq.tree) { tree.any[, i] <- - rowAnys(rwiNotNA[, treeIds == unique.trees[i], drop=FALSE]) + rowAnys(rwiNotNA, cols = treeIds == unique.trees[i]) } n.trees.by.year <- rowSums(tree.any) @@ -305,7 +305,7 @@ rbar.bt <- rsum.bt / n.bt } - coresPresent <- which(colAnys(rwiNotNA[year.idx, , drop = FALSE])) + coresPresent <- which(colAnys(rwiNotNA, rows = year.idx)) treesPresent <- unique(treeIds[coresPresent]) nCores <- length(coresPresent) nTrees <- length(treesPresent)