[Dplr-commits] r954 - pkg/dplR/R
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Jan 28 17:05:48 CET 2015
Author: mvkorpel
Date: 2015-01-28 17:05:48 +0100 (Wed, 28 Jan 2015)
New Revision: 954
Modified:
pkg/dplR/R/i.detrend.series.R
pkg/dplR/R/read.crn.R
pkg/dplR/R/rwi.stats.running.R
pkg/dplR/R/series.rwl.plot.R
pkg/dplR/R/wc.to.po.R
Log:
More matrix stats optimizations
Modified: pkg/dplR/R/i.detrend.series.R
===================================================================
--- pkg/dplR/R/i.detrend.series.R 2015-01-28 14:12:54 UTC (rev 953)
+++ pkg/dplR/R/i.detrend.series.R 2015-01-28 16:05:48 UTC (rev 954)
@@ -4,7 +4,7 @@
fits <- detrend.series(y, y.name, make.plot=TRUE, nyrs = nyrs, f = f,
pos.slope = pos.slope)
## Remove the nec resids if all na
- fits <- fits[, !apply(is.na(fits), 2, all), drop=FALSE]
+ fits <- fits[, !colAlls(is.na(fits)), drop=FALSE]
col.names <- names(fits)
cat(gettextf("\nChoose a detrending method for this series %s.\n",
y.name, domain="R-dplR"))
Modified: pkg/dplR/R/read.crn.R
===================================================================
--- pkg/dplR/R/read.crn.R 2015-01-28 14:12:54 UTC (rev 953)
+++ pkg/dplR/R/read.crn.R 2015-01-28 16:05:48 UTC (rev 954)
@@ -118,7 +118,7 @@
## Clean up NAs
crn.mat[which(crn.mat[, -ncol.crn.mat] == 9990)] <- NA # column-major order
crn.mat <-
- crn.mat[!apply(is.na(crn.mat[, -ncol.crn.mat, drop=FALSE]), 1, all),
+ crn.mat[!rowAlls(is.na(crn.mat[, -ncol.crn.mat, drop=FALSE])),
,
drop=FALSE]
## If samp depth is all 1 then dump it
Modified: pkg/dplR/R/rwi.stats.running.R
===================================================================
--- pkg/dplR/R/rwi.stats.running.R 2015-01-28 14:12:54 UTC (rev 953)
+++ pkg/dplR/R/rwi.stats.running.R 2015-01-28 16:05:48 UTC (rev 954)
@@ -167,13 +167,13 @@
tree.any <- matrix(FALSE, n.years, n.trees)
for (i in seq.tree) {
tree.any[, i] <-
- apply(rwiNotNA[, treeIds == unique.trees[i], drop=FALSE], 1, any)
+ rowAnys(rwiNotNA[, treeIds == unique.trees[i], drop=FALSE])
}
n.trees.by.year <- rowSums(tree.any)
## Easy way to force complete overlap of data
if (period2 == "common") {
- bad.rows <- !apply(rwiNotNA, 1, all)
+ bad.rows <- !rowAlls(rwiNotNA)
rwi3[bad.rows, ] <- NA
rwiNotNA[bad.rows, ] <- FALSE
good.rows.flag <- !bad.rows
@@ -305,8 +305,7 @@
rbar.bt <- rsum.bt / n.bt
}
- coresPresent <-
- which(apply(rwiNotNA[year.idx, , drop = FALSE], 2, any))
+ coresPresent <- which(colAnys(rwiNotNA[year.idx, , drop = FALSE]))
treesPresent <- unique(treeIds[coresPresent])
nCores <- length(coresPresent)
nTrees <- length(treesPresent)
Modified: pkg/dplR/R/series.rwl.plot.R
===================================================================
--- pkg/dplR/R/series.rwl.plot.R 2015-01-28 14:12:54 UTC (rev 953)
+++ pkg/dplR/R/series.rwl.plot.R 2015-01-28 16:05:48 UTC (rev 954)
@@ -20,7 +20,7 @@
seg.lag <- seg.length / 2
- mask <- !apply(as.matrix(is.na(rwl2)), 1, all)
+ mask <- !rowAlls(as.matrix(is.na(rwl2)))
yrs0 <- as.numeric(row.names(rwl2))[mask]
## Normalize.
tmp <- normalize.xdate(rwl2, series2, n, prewhiten, biweight)
Modified: pkg/dplR/R/wc.to.po.R
===================================================================
--- pkg/dplR/R/wc.to.po.R 2015-01-28 14:12:54 UTC (rev 953)
+++ pkg/dplR/R/wc.to.po.R 2015-01-28 16:05:48 UTC (rev 954)
@@ -15,10 +15,8 @@
!is.na(missing))
pith.offset <- rep(as.integer(NA), n)
pith.offset[not.na] <-
- as.integer(apply(cbind(missing[not.na], unmeasured[not.na]),
- 1,
- sum,
- na.rm = TRUE) + 1)
+ as.integer(rowSums(cbind(missing[not.na], unmeasured[not.na]),
+ na.rm = TRUE) + 1)
data.frame(series = row.names(wc),
pith.offset)
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