[Analogue-commits] r250 - in pkg: . inst tests/Examples
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Jan 11 15:29:43 CET 2012
Author: gsimpson
Date: 2012-01-11 15:29:38 +0100 (Wed, 11 Jan 2012)
New Revision: 250
Modified:
pkg/DESCRIPTION
pkg/inst/ChangeLog
pkg/tests/Examples/analogue-Ex.Rout.save
Log:
package ready for 0.8-0 release
Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION 2012-01-11 12:22:25 UTC (rev 249)
+++ pkg/DESCRIPTION 2012-01-11 14:29:38 UTC (rev 250)
@@ -1,7 +1,7 @@
Package: analogue
Type: Package
Title: Analogue and weighted averaging methods for palaeoecology
-Version: 0.7-7
+Version: 0.8-0
Date: $Date$
Depends: R (>= 2.10.0), stats, graphics, vegan (>= 1.17-12), lattice, grid,
MASS, princurve
Modified: pkg/inst/ChangeLog
===================================================================
--- pkg/inst/ChangeLog 2012-01-11 12:22:25 UTC (rev 249)
+++ pkg/inst/ChangeLog 2012-01-11 14:29:38 UTC (rev 250)
@@ -1,5 +1,10 @@
analogue Change Log
+Version 0.8-0
+
+ * Updated Example test checks and packaged for release to CRAN
+ Jan 11, 2012.
+
Version 0.7-7
* mat: new argument `kmax` can be used to limit the number of
Modified: pkg/tests/Examples/analogue-Ex.Rout.save
===================================================================
--- pkg/tests/Examples/analogue-Ex.Rout.save 2012-01-11 12:22:25 UTC (rev 249)
+++ pkg/tests/Examples/analogue-Ex.Rout.save 2012-01-11 14:29:38 UTC (rev 250)
@@ -1,6 +1,6 @@
-R version 2.14.0 Patched (2011-11-04 r57570)
-Copyright (C) 2011 The R Foundation for Statistical Computing
+R version 2.14.1 Patched (2012-01-10 r58088)
+Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -24,31 +24,20 @@
> library('analogue')
Loading required package: vegan
Loading required package: permute
-This is vegan 2.0-2
+This is vegan 2.0-1
Loading required package: lattice
Loading required package: grid
Loading required package: MASS
Loading required package: princurve
-This is analogue 0.7-7
+This is analogue 0.8-0
>
> assign(".oldSearch", search(), pos = 'CheckExEnv')
-> assign(".ExTimings", "analogue-Ex.timings", pos = 'CheckExEnv')
-> cat("name\tuser\tsystem\telapsed\n", file=get(".ExTimings", pos = 'CheckExEnv'))
-> assign(".format_ptime",
-+ function(x) {
-+ if(!is.na(x[4L])) x[1L] <- x[1L] + x[4L]
-+ if(!is.na(x[5L])) x[2L] <- x[2L] + x[5L]
-+ format(x[1L:3L])
-+ },
-+ pos = 'CheckExEnv')
->
> cleanEx()
> nameEx("ImbrieKipp")
> ### * ImbrieKipp
>
> flush(stderr()); flush(stdout())
>
-> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ImbrieKipp
> ### Title: Imbrie and Kipp foraminifera training set
> ### Aliases: ImbrieKipp SumSST WinSST Salinity V12.122
@@ -119,16 +108,12 @@
>
>
>
->
-> assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> cat("ImbrieKipp", get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("Pollen")
> ### * Pollen
>
> flush(stderr()); flush(stdout())
>
-> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Pollen
> ### Title: North American Modern Pollen Database
> ### Aliases: Pollen Biome Climate Location
@@ -146,16 +131,12 @@
>
>
>
->
-> assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> cat("Pollen", get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("RMSEP")
> ### * RMSEP
>
> flush(stderr()); flush(stdout())
>
-> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: RMSEP
> ### Title: Root mean square error of prediction
> ### Aliases: RMSEP RMSEP.default RMSEP.mat RMSEP.bootstrap.mat
@@ -257,16 +238,12 @@
>
>
>
->
-> assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> cat("RMSEP", get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("Stratiplot")
> ### * Stratiplot
>
> flush(stderr()); flush(stdout())
>
-> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Stratiplot
> ### Title: Palaeoecological stratigraphic diagrams
> ### Aliases: Stratiplot Stratiplot.default Stratiplot.formula
@@ -316,16 +293,12 @@
>
>
>
->
-> assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> cat("Stratiplot", get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("abernethy")
> ### * abernethy
>
> flush(stderr()); flush(stdout())
>
-> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: abernethy
> ### Title: Abernethy Forest Pollen Sequence
> ### Aliases: abernethy
@@ -392,16 +365,12 @@
>
>
>
->
-> assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> cat("abernethy", get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("analog")
> ### * analog
>
> flush(stderr()); flush(stdout())
>
-> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: analog
> ### Title: Analogue matching
> ### Aliases: analog analog.default print.analog
@@ -789,16 +758,12 @@
>
>
>
->
-> assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> cat("analog", get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("bayesF")
> ### * bayesF
>
> flush(stderr()); flush(stdout())
>
-> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bayesF
> ### Title: Bayes factors
> ### Aliases: bayesF print.bayesF plot.bayesF
@@ -880,16 +845,12 @@
>
>
>
->
-> assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> cat("bayesF", get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("bootstrap")
> ### * bootstrap
>
> flush(stderr()); flush(stdout())
>
-> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bootstrap
> ### Title: Bootstrap estimation and errors
> ### Aliases: bootstrap bootstrap.default bootstrap.mat print.bootstrap.mat
@@ -1114,16 +1075,12 @@
>
>
>
->
-> assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> cat("bootstrap", get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("bootstrap.wa")
> ### * bootstrap.wa
>
> flush(stderr()); flush(stdout())
>
-> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bootstrap.wa
> ### Title: Bootstrap estimation and errors for WA models
> ### Aliases: bootstrap.wa print.bootstrap.wa
@@ -1181,16 +1138,12 @@
>
>
>
->
-> assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> cat("bootstrap.wa", get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("chooseTaxa")
> ### * chooseTaxa
>
> flush(stderr()); flush(stdout())
>
-> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: chooseTaxa
> ### Title: Select taxa (variables) on basis of maximum abundance attained
> ### and number of occurrences
@@ -1208,16 +1161,12 @@
>
>
>
->
-> assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> cat("chooseTaxa", get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("cma")
> ### * cma
>
> flush(stderr()); flush(stdout())
>
-> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cma
> ### Title: Close modern analogues
> ### Aliases: cma cma.default cma.analog cma.mat cma.predict.mat print.cma
@@ -1679,16 +1628,12 @@
>
>
>
->
-> assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> cat("cma", get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("crossval")
> ### * crossval
>
> flush(stderr()); flush(stdout())
>
-> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: crossval
> ### Title: Cross-validation of palaeoecological transfer function models
> ### Aliases: crossval crossval.wa print.crossval predWA predWAT
@@ -1800,16 +1745,12 @@
>
>
>
->
-> assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> cat("crossval", get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("densityplot.residLen")
> ### * densityplot.residLen
>
> flush(stderr()); flush(stdout())
>
-> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: densityplot.residLen
> ### Title: Lattice density plot for residual lengths
> ### Aliases: densityplot.residLen
@@ -1842,16 +1783,12 @@
>
>
>
->
-> assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> cat("densityplot.residLen", get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("dissimilarities")
> ### * dissimilarities
>
> flush(stderr()); flush(stdout())
>
-> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dissimilarities
> ### Title: Extract dissimilarity coefficients from models
> ### Aliases: dissimilarities dissimilarities.analog dissimilarities.mat
@@ -2243,16 +2180,12 @@
>
>
>
->
-> assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> cat("dissimilarities", get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("distance")
> ### * distance
>
> flush(stderr()); flush(stdout())
>
-> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: distance
> ### Title: Flexibly calculate dissimilarity or distance measures
> ### Aliases: distance distance.default distance.join
@@ -2315,16 +2248,12 @@
>
>
>
->
-> assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> cat("distance", get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("fuse")
> ### * fuse
>
> flush(stderr()); flush(stdout())
>
-> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: fuse
> ### Title: Fused dissimilarities
> ### Aliases: fuse fuse.matrix fuse.dist
@@ -2375,16 +2304,12 @@
>
>
>
->
-> assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> cat("fuse", get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("getK")
> ### * getK
>
> flush(stderr()); flush(stdout())
>
-> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getK
> ### Title: Extract and set the number of analogues
> ### Aliases: getK getK.default getK.mat getK.bootstrap.mat getK.predict.mat
@@ -2439,16 +2364,12 @@
>
>
>
->
-> assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> cat("getK", get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("gradientDist")
> ### * gradientDist
>
> flush(stderr()); flush(stdout())
>
-> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gradientDist
> ### Title: Positions of samples along a unit-length ordination gradient.
> ### Aliases: gradientDist gradientDist.default gradientDist.cca
@@ -2482,16 +2403,12 @@
>
>
>
->
-> assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> cat("gradientDist", get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("hist.residLen")
> ### * hist.residLen
>
> flush(stderr()); flush(stdout())
>
-> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: hist.residLen
> ### Title: Histogram plot for residual lengths
> ### Aliases: hist.residLen
@@ -2524,16 +2441,12 @@
>
>
>
->
-> assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> cat("hist.residLen", get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("histogram.residLen")
> ### * histogram.residLen
>
> flush(stderr()); flush(stdout())
>
-> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: histogram.residLen
> ### Title: Lattice histogram plot for residual lengths
> ### Aliases: histogram.residLen
@@ -2566,16 +2479,12 @@
>
>
>
->
-> assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> cat("histogram.residLen", get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("join")
> ### * join
>
> flush(stderr()); flush(stdout())
>
-> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: join
> ### Title: Merge species data sets on common columns (species)
> ### Aliases: join head.join tail.join
@@ -3265,16 +3174,12 @@
>
>
>
->
-> assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> cat("join", get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("logitreg")
> ### * logitreg
>
> flush(stderr()); flush(stdout())
>
-> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: logitreg
> ### Title: Logistic regression models for assessing analogues/non-analogues
> ### Aliases: logitreg logitreg.default logitreg.analog print.logitreg
@@ -3370,16 +3275,12 @@
>
>
>
->
-> assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> cat("logitreg", get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("mat")
> ### * mat
>
> flush(stderr()); flush(stdout())
>
-> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mat
> ### Title: Modern Analogue Technique transfer function models
> ### Aliases: mat mat.default mat.formula fitted.mat residuals.mat resid.mat
@@ -4232,9 +4133,6 @@
>
>
>
->
-> assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> cat("mat", get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> graphics::par(get("par.postscript", pos = 'CheckExEnv'))
> cleanEx()
> nameEx("mcarlo")
@@ -4242,7 +4140,6 @@
>
> flush(stderr()); flush(stdout())
>
-> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mcarlo
> ### Title: Monte Carlo simulation of dissimilarities
> ### Aliases: mcarlo mcarlo.default mcarlo.mat mcarlo.analog print.mcarlo
@@ -4299,16 +4196,12 @@
>
>
>
->
-> assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> cat("mcarlo", get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("minDC")
> ### * minDC
>
> flush(stderr()); flush(stdout())
>
-> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: minDC
> ### Title: Extract minimum dissimilarities
> ### Aliases: minDC minDC.default minDC.predict.mat minDC.analog minDC.wa
@@ -4416,16 +4309,12 @@
>
>
>
->
-> assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> cat("minDC", get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("optima")
> ### * optima
>
> flush(stderr()); flush(stdout())
>
-> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: optima
> ### Title: Weighted averaging optima and tolerance ranges
> ### Aliases: optima optima.default print.optima print.tolerance
@@ -4529,16 +4418,12 @@
>
>
>
->
-> assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> cat("optima", get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("pcr")
> ### * pcr
>
> flush(stderr()); flush(stdout())
>
-> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pcr
> ### Title: Prinicpal component regression transfer function models
> ### Aliases: pcr pcr.default pcr.formula print.pcr Hellinger ChiSquare
@@ -4770,16 +4655,12 @@
>
>
>
->
-> assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> cat("pcr", get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("performance")
> ### * performance
>
> flush(stderr()); flush(stdout())
>
-> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: performance
> ### Title: Transfer function model performance statistics
> ### Aliases: performance print.performance performance.wa
@@ -4915,16 +4796,12 @@
>
>
>
->
-> assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> cat("performance", get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("plot.dissimilarities")
> ### * plot.dissimilarities
>
> flush(stderr()); flush(stdout())
>
-> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.dissimilarities
> ### Title: Plots the distribution of extracted dissimilarities
> ### Aliases: plot.dissimilarities
@@ -5314,16 +5191,12 @@
>
>
>
->
-> assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> cat("plot.dissimilarities", get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("plot.mat")
> ### * plot.mat
>
> flush(stderr()); flush(stdout())
>
-> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.mat
> ### Title: Plot diagnostics for a mat object
> ### Aliases: plot.mat
@@ -5575,16 +5448,12 @@
>
>
>
->
-> assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> cat("plot.mat", get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("plot.mcarlo")
> ### * plot.mcarlo
>
> flush(stderr()); flush(stdout())
>
-> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.mcarlo
> ### Title: Plot Monte Carlo simulated dissimilarity distributions
> ### Aliases: plot.mcarlo
@@ -5641,16 +5510,12 @@
>
>
>
->
-> assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> cat("plot.mcarlo", get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("plot.minDC")
> ### * plot.minDC
>
> flush(stderr()); flush(stdout())
>
-> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.minDC
> ### Title: Plot of minimum dissimilarity per sample
> ### Aliases: plot.minDC
@@ -5756,16 +5621,12 @@
>
>
>
->
-> assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> cat("plot.minDC", get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("plot.prcurve")
> ### * plot.prcurve
>
> flush(stderr()); flush(stdout())
>
-> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.prcurve
> ### Title: Plot a fitted principal curve in PCA space
> ### Aliases: plot.prcurve
@@ -5800,16 +5661,12 @@
>
>
>
->
-> assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> cat("plot.prcurve", get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("plot.residLen")
> ### * plot.residLen
>
> flush(stderr()); flush(stdout())
>
-> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.residLen
> ### Title: Plot method for residual lengths
> ### Aliases: plot.residLen
@@ -5842,16 +5699,12 @@
>
>
>
->
-> assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> cat("plot.residLen", get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("plot.wa")
> ### * plot.wa
>
> flush(stderr()); flush(stdout())
>
-> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.wa
> ### Title: Plot diagnostics for a weighted averaging model
> ### Aliases: plot.wa
@@ -5987,9 +5840,6 @@
>
>
>
->
-> assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> cat("plot.wa", get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> graphics::par(get("par.postscript", pos = 'CheckExEnv'))
> cleanEx()
> nameEx("prcurve")
@@ -5997,7 +5847,6 @@
>
> flush(stderr()); flush(stdout())
>
-> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: prcurve
> ### Title: Fits a principal curve to m-dimensional data
> ### Aliases: prcurve initCurve smoothSpline
@@ -6052,16 +5901,12 @@
>
>
>
->
-> assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> cat("prcurve", get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("predict.mat")
> ### * predict.mat
>
> flush(stderr()); flush(stdout())
>
-> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: predict.mat
> ### Title: Predict method for Modern Analogue Technique models
> ### Aliases: predict.mat print.predict.mat
@@ -6169,16 +6014,12 @@
>
>
>
->
-> assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> cat("predict.mat", get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("predict.wa")
> ### * predict.wa
>
> flush(stderr()); flush(stdout())
>
-> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: predict.wa
> ### Title: Predict from a weighted average model
> ### Aliases: predict.wa print.predict.wa
@@ -6211,16 +6052,12 @@
>
>
>
->
-> assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> cat("predict.wa", get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("reconPlot")
> ### * reconPlot
>
> flush(stderr()); flush(stdout())
>
-> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: reconPlot
> ### Title: Stratigraphic plots of palaeoenvironmental reconstructions
> ### Aliases: reconPlot reconPlot.default reconPlot.predict.mat
@@ -6301,16 +6138,12 @@
>
>
>
->
-> assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> cat("reconPlot", get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("residLen")
> ### * residLen
>
> flush(stderr()); flush(stdout())
>
-> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: residLen
> ### Title: Squared residual length diagnostics
> ### Aliases: residLen print.residLen fittedY sqrlLinear sqrlUnimodal
@@ -6355,16 +6188,12 @@
>
>
>
->
-> assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> cat("residLen", get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("rlgh")
> ### * rlgh
>
> flush(stderr()); flush(stdout())
>
-> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rlgh
> ### Title: Round Loch of Glenhead Diatoms
> ### Aliases: rlgh
@@ -6376,16 +6205,12 @@
>
>
>
->
-> assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> cat("rlgh", get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("roc")
> ### * roc
>
> flush(stderr()); flush(stdout())
>
-> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: roc
> ### Title: ROC curve analysis
> ### Aliases: roc roc.default roc.mat roc.analog print.roc summary.roc
@@ -6446,16 +6271,12 @@
>
>
>
->
-> assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> cat("roc", get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("screeplot")
> ### * screeplot
>
> flush(stderr()); flush(stdout())
>
-> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: screeplot
> ### Title: Screeplots of model results
> ### Aliases: screeplot.mat screeplot.bootstrap.mat
@@ -6530,16 +6351,12 @@
>
>
>
->
-> assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> cat("screeplot", get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("stdError")
> ### * stdError
>
> flush(stderr()); flush(stdout())
>
-> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: stdError
> ### Title: Standard error of MAT fitted and predicted values
> ### Aliases: stdError stdError.mat stdError.predict.mat
@@ -6636,16 +6453,12 @@
>
>
>
->
-> assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> cat("stdError", get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("summary.analog")
> ### * summary.analog
>
> flush(stderr()); flush(stdout())
>
-> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: summary.analog
> ### Title: Summarise analogue matching results
> ### Aliases: summary.analog print.summary.analog
@@ -6665,16 +6478,12 @@
>
>
>
->
-> assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> cat("summary.analog", get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("summary.bootstrap.mat")
> ### * summary.bootstrap.mat
>
> flush(stderr()); flush(stdout())
>
-> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: summary.bootstrap.mat
> ### Title: Summarise bootstrap resampling for MAT models
> ### Aliases: summary.bootstrap.mat print.summary.bootstrap.mat
@@ -6697,16 +6506,12 @@
>
>
>
->
-> assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> cat("summary.bootstrap.mat", get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("summary.cma")
> ### * summary.cma
>
> flush(stderr()); flush(stdout())
>
-> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: summary.cma
> ### Title: Summarise the extraction of close modern analogues
> ### Aliases: summary.cma print.summary.cma
@@ -6731,16 +6536,12 @@
>
>
>
->
-> assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> cat("summary.cma", get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("summary.mat")
> ### * summary.mat
>
> flush(stderr()); flush(stdout())
>
-> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: summary.mat
> ### Title: Summarise Modern Analogue Technique models
> ### Aliases: summary.mat print.summary.mat
@@ -6766,16 +6567,12 @@
>
>
>
->
-> assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> cat("summary.mat", get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("summary.predict.mat")
> ### * summary.predict.mat
>
> flush(stderr()); flush(stdout())
>
-> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: summary.predict.mat
> ### Title: Summarise MAT model predictions
> ### Aliases: summary.predict.mat print.summary.predict.mat
@@ -6797,16 +6594,12 @@
>
>
>
->
-> assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> cat("summary.predict.mat", get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("swapdiat")
> ### * swapdiat
>
> flush(stderr()); flush(stdout())
>
-> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: swapdiat
> ### Title: SWAP sub-fossil diatom and pH training set
> ### Aliases: swapdiat
@@ -6818,16 +6611,12 @@
>
>
>
->
-> assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> cat("swapdiat", get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("swappH")
> ### * swappH
>
> flush(stderr()); flush(stdout())
>
-> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: swappH
> ### Title: SWAP sub-fossil diatom and pH training set
> ### Aliases: swappH
@@ -6842,16 +6631,12 @@
>
>
>
->
-> assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> cat("swappH", get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("timetrack")
> ### * timetrack
>
> flush(stderr()); flush(stdout())
>
-> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: timetrack
> ### Title: Timetracks of change in species composition
> ### Aliases: timetrack print.timetrack plot.timetrack fitted.timetrack
@@ -6891,16 +6676,12 @@
>
>
>
->
-> assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> cat("timetrack", get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("tran")
> ### * tran
>
> flush(stderr()); flush(stdout())
>
-> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: tran
> ### Title: Common data transformations and standardizations
> ### Aliases: tran tran.default tran.formula
@@ -6936,16 +6717,12 @@
>
>
>
->
-> assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> cat("tran", get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("varExpl")
> ### * varExpl
>
> flush(stderr()); flush(stdout())
>
-> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: varExpl
> ### Title: Variance explained by ordination axes
> ### Aliases: varExpl varExpl.default varExpl.cca varExpl.prcurve
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/analogue -r 250
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