[Analogue-commits] r378 - pkg/tests/Examples
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Tue Oct 8 00:58:25 CEST 2013
Author: gsimpson
Date: 2013-10-08 00:58:25 +0200 (Tue, 08 Oct 2013)
New Revision: 378
Modified:
pkg/tests/Examples/analogue-Ex.Rout.save
Log:
must not copy the reference outputs when checking --as-cran
Modified: pkg/tests/Examples/analogue-Ex.Rout.save
===================================================================
--- pkg/tests/Examples/analogue-Ex.Rout.save 2013-10-07 02:36:50 UTC (rev 377)
+++ pkg/tests/Examples/analogue-Ex.Rout.save 2013-10-07 22:58:25 UTC (rev 378)
@@ -1,5 +1,5 @@
-R version 3.0.2 Patched (2013-09-26 r64005) -- "Frisbee Sailing"
+R version 3.0.2 Patched (2013-10-07 r64035) -- "Frisbee Sailing"
Copyright (C) 2013 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -20,18 +20,6 @@
> pkgname <- "analogue"
> source(file.path(R.home("share"), "R", "examples-header.R"))
> options(warn = 1)
-> base::assign(".ExTimings", "analogue-Ex.timings", pos = 'CheckExEnv')
-> base::cat("name\tuser\tsystem\telapsed\n", file=base::get(".ExTimings", pos = 'CheckExEnv'))
-> base::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]
-+ options(OutDec = '.')
-+ format(x[1L:3L], digits = 7L)
-+ },
-+ pos = 'CheckExEnv')
->
-> ### * </HEADER>
> library('analogue')
Loading required package: vegan
Loading required package: permute
@@ -47,7 +35,6 @@
>
> flush(stderr()); flush(stdout())
>
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: ImbrieKipp
> ### Title: Imbrie and Kipp foraminifera training set
> ### Aliases: ImbrieKipp SumSST WinSST Salinity V12.122
@@ -118,15 +105,12 @@
>
>
>
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("ImbrieKipp", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("Pollen")
> ### * Pollen
>
> flush(stderr()); flush(stdout())
>
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Pollen
> ### Title: North American Modern Pollen Database
> ### Aliases: Pollen Biome Climate Location
@@ -144,15 +128,12 @@
>
>
>
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("Pollen", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("RMSEP")
> ### * RMSEP
>
> flush(stderr()); flush(stdout())
>
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: RMSEP
> ### Title: Root mean square error of prediction
> ### Aliases: RMSEP RMSEP.default RMSEP.mat RMSEP.bootstrap.mat
@@ -254,15 +235,12 @@
>
>
>
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("RMSEP", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("Stratiplot")
> ### * Stratiplot
>
> flush(stderr()); flush(stdout())
>
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: Stratiplot
> ### Title: Palaeoecological stratigraphic diagrams
> ### Aliases: Stratiplot Stratiplot.default Stratiplot.formula
@@ -349,15 +327,12 @@
>
>
>
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("Stratiplot", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("abernethy")
> ### * abernethy
>
> flush(stderr()); flush(stdout())
>
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: abernethy
> ### Title: Abernethy Forest Pollen Sequence
> ### Aliases: abernethy
@@ -424,15 +399,12 @@
>
>
>
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("abernethy", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("analog")
> ### * analog
>
> flush(stderr()); flush(stdout())
>
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: analog
> ### Title: Analogue matching
> ### Aliases: analog analog.default analog.distance print.analog
@@ -860,15 +832,12 @@
>
>
>
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("analog", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("bayesF")
> ### * bayesF
>
> flush(stderr()); flush(stdout())
>
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bayesF
> ### Title: Bayes factors
> ### Aliases: bayesF print.bayesF plot.bayesF
@@ -950,15 +919,12 @@
>
>
>
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("bayesF", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("bootstrap")
> ### * bootstrap
>
> flush(stderr()); flush(stdout())
>
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bootstrap
> ### Title: Bootstrap estimation and errors
> ### Aliases: bootstrap bootstrap.default bootstrap.mat print.bootstrap.mat
@@ -1183,15 +1149,12 @@
>
>
>
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("bootstrap", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("bootstrap.wa")
> ### * bootstrap.wa
>
> flush(stderr()); flush(stdout())
>
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: bootstrap.wa
> ### Title: Bootstrap estimation and errors for WA models
> ### Aliases: bootstrap.wa print.bootstrap.wa
@@ -1249,15 +1212,12 @@
>
>
>
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("bootstrap.wa", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("caterpillarPlot")
> ### * caterpillarPlot
>
> flush(stderr()); flush(stdout())
>
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: caterpillarPlot
> ### Title: Caterpillar plot of species' WA optima and tolerance range.
> ### Aliases: caterpillarPlot caterpillarPlot.default
@@ -1291,15 +1251,12 @@
>
>
>
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("caterpillarPlot", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("chooseTaxa")
> ### * chooseTaxa
>
> flush(stderr()); flush(stdout())
>
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: chooseTaxa
> ### Title: Select taxa (variables) on basis of maximum abundance attained
> ### and number of occurrences.
@@ -1326,15 +1283,12 @@
>
>
>
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("chooseTaxa", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("cma")
> ### * cma
>
> flush(stderr()); flush(stdout())
>
-> base::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
@@ -1796,15 +1750,12 @@
>
>
>
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("cma", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("crossval")
> ### * crossval
>
> flush(stderr()); flush(stdout())
>
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: crossval
> ### Title: Cross-validation of palaeoecological transfer function models
> ### Aliases: crossval crossval.wa print.crossval predWA predWAT
@@ -1916,15 +1867,12 @@
>
>
>
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("crossval", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("densityplot.residLen")
> ### * densityplot.residLen
>
> flush(stderr()); flush(stdout())
>
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: densityplot.residLen
> ### Title: Lattice density plot for residual lengths
> ### Aliases: densityplot.residLen
@@ -1957,15 +1905,12 @@
>
>
>
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("densityplot.residLen", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("dissimilarities")
> ### * dissimilarities
>
> flush(stderr()); flush(stdout())
>
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: dissimilarities
> ### Title: Extract dissimilarity coefficients from models
> ### Aliases: dissimilarities dissimilarities.analog dissimilarities.mat
@@ -2357,15 +2302,12 @@
>
>
>
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("dissimilarities", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("distance")
> ### * distance
>
> flush(stderr()); flush(stdout())
>
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: distance
> ### Title: Flexibly calculate dissimilarity or distance measures
> ### Aliases: distance distance.default distance.join oldDistance
@@ -2433,15 +2375,12 @@
>
>
>
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("distance", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("fuse")
> ### * fuse
>
> flush(stderr()); flush(stdout())
>
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: fuse
> ### Title: Fused dissimilarities
> ### Aliases: fuse fuse.matrix fuse.dist
@@ -2492,15 +2431,12 @@
>
>
>
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("fuse", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("getK")
> ### * getK
>
> flush(stderr()); flush(stdout())
>
-> base::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
@@ -2555,15 +2491,12 @@
>
>
>
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("getK", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("gradientDist")
> ### * gradientDist
>
> flush(stderr()); flush(stdout())
>
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gradientDist
> ### Title: Positions of samples along a unit-length ordination gradient.
> ### Aliases: gradientDist gradientDist.default gradientDist.cca
@@ -2597,15 +2530,12 @@
>
>
>
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("gradientDist", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("hist.residLen")
> ### * hist.residLen
>
> flush(stderr()); flush(stdout())
>
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: hist.residLen
> ### Title: Histogram plot for residual lengths
> ### Aliases: hist.residLen
@@ -2638,15 +2568,12 @@
>
>
>
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("hist.residLen", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("histogram.residLen")
> ### * histogram.residLen
>
> flush(stderr()); flush(stdout())
>
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: histogram.residLen
> ### Title: Lattice histogram plot for residual lengths
> ### Aliases: histogram.residLen
@@ -2679,15 +2606,12 @@
>
>
>
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("histogram.residLen", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("join")
> ### * join
>
> flush(stderr()); flush(stdout())
>
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: join
> ### Title: Merge species data sets on common columns (species)
> ### Aliases: join head.join tail.join
@@ -3377,15 +3301,12 @@
>
>
>
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("join", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("logitreg")
> ### * logitreg
>
> flush(stderr()); flush(stdout())
>
-> base::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
@@ -3498,15 +3419,12 @@
>
>
>
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("logitreg", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("mat")
> ### * mat
>
> flush(stderr()); flush(stdout())
>
-> base::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
@@ -3992,8 +3910,6 @@
>
>
>
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("mat", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> graphics::par(get("par.postscript", pos = 'CheckExEnv'))
> cleanEx()
> nameEx("mcarlo")
@@ -4001,7 +3917,6 @@
>
> flush(stderr()); flush(stdout())
>
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: mcarlo
> ### Title: Monte Carlo simulation of dissimilarities
> ### Aliases: mcarlo mcarlo.default mcarlo.mat mcarlo.analog print.mcarlo
@@ -4058,15 +3973,12 @@
>
>
>
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("mcarlo", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("minDC")
> ### * minDC
>
> flush(stderr()); flush(stdout())
>
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: minDC
> ### Title: Extract minimum dissimilarities
> ### Aliases: minDC minDC.default minDC.predict.mat minDC.analog minDC.wa
@@ -4174,15 +4086,12 @@
>
>
>
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("minDC", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("optima")
> ### * optima
>
> flush(stderr()); flush(stdout())
>
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: optima
> ### Title: Weighted averaging optima and tolerance ranges
> ### Aliases: optima optima.default print.optima print.tolerance
@@ -4289,15 +4198,12 @@
>
>
>
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("optima", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("pcr")
> ### * pcr
>
> flush(stderr()); flush(stdout())
>
-> base::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
@@ -4529,15 +4435,12 @@
>
>
>
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("pcr", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("performance")
> ### * performance
>
> flush(stderr()); flush(stdout())
>
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: performance
> ### Title: Transfer function model performance statistics
> ### Aliases: performance print.performance performance.wa
@@ -4571,19 +4474,16 @@
> ## the model performance statistics
> performance(mod)
RMSE R2 Avg.Bias Max.Bias
- 2.019e+00 9.173e-01 2.854e-15 -3.815e+00
+ 2.019e+00 9.173e-01 2.228e-14 -3.815e+00
>
>
>
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("performance", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("plot.dissimilarities")
> ### * plot.dissimilarities
>
> flush(stderr()); flush(stdout())
>
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.dissimilarities
> ### Title: Plots the distribution of extracted dissimilarities
> ### Aliases: plot.dissimilarities
@@ -4973,15 +4873,12 @@
>
>
>
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("plot.dissimilarities", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("plot.mat")
> ### * plot.mat
>
> flush(stderr()); flush(stdout())
>
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.mat
> ### Title: Plot diagnostics for a mat object
> ### Aliases: plot.mat
@@ -5021,15 +4918,12 @@
>
>
>
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("plot.mat", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("plot.mcarlo")
> ### * plot.mcarlo
>
> flush(stderr()); flush(stdout())
>
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.mcarlo
> ### Title: Plot Monte Carlo simulated dissimilarity distributions
> ### Aliases: plot.mcarlo
@@ -5086,15 +4980,12 @@
>
>
>
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("plot.mcarlo", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("plot.minDC")
> ### * plot.minDC
>
> flush(stderr()); flush(stdout())
>
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.minDC
> ### Title: Plot of minimum dissimilarity per sample
> ### Aliases: plot.minDC
@@ -5200,15 +5091,12 @@
>
>
>
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("plot.minDC", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("plot.prcurve")
> ### * plot.prcurve
>
> flush(stderr()); flush(stdout())
>
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.prcurve
> ### Title: Plot a fitted principal curve in PCA space
> ### Aliases: plot.prcurve lines.prcurve
@@ -5329,15 +5217,12 @@
>
>
>
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("plot.prcurve", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("plot.residLen")
> ### * plot.residLen
>
> flush(stderr()); flush(stdout())
>
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.residLen
> ### Title: Plot method for residual lengths
> ### Aliases: plot.residLen
@@ -5370,15 +5255,12 @@
>
>
>
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("plot.residLen", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("plot.wa")
> ### * plot.wa
>
> flush(stderr()); flush(stdout())
>
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot.wa
> ### Title: Plot diagnostics for a weighted averaging model
> ### Aliases: plot.wa
@@ -5391,15 +5273,12 @@
>
>
>
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("plot.wa", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("plot3d.prcurve")
> ### * plot3d.prcurve
>
> flush(stderr()); flush(stdout())
>
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: plot3d.prcurve
> ### Title: Interactive 3D plof of a principal curve in principal coordinate
> ### space
@@ -5514,15 +5393,12 @@
>
>
>
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("plot3d.prcurve", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("prcurve")
> ### * prcurve
>
> flush(stderr()); flush(stdout())
>
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: prcurve
> ### Title: Fits a principal curve to m-dimensional data
> ### Aliases: prcurve initCurve print.prcurve
@@ -5735,15 +5611,12 @@
>
>
>
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("prcurve", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("predict.mat")
> ### * predict.mat
>
> flush(stderr()); flush(stdout())
>
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: predict.mat
> ### Title: Predict method for Modern Analogue Technique models
> ### Aliases: predict.mat print.predict.mat
@@ -5851,15 +5724,12 @@
>
>
>
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("predict.mat", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("predict.wa")
> ### * predict.wa
>
> flush(stderr()); flush(stdout())
>
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: predict.wa
> ### Title: Predict from a weighted average model
> ### Aliases: predict.wa print.predict.wa
@@ -5910,15 +5780,12 @@
>
>
>
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("predict.wa", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("rankDC")
> ### * rankDC
>
> flush(stderr()); flush(stdout())
>
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rankDC
> ### Title: Rank correlation between environmental and species
> ### dissimilarities.
@@ -5941,15 +5808,12 @@
>
>
>
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("rankDC", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("reconPlot")
> ### * reconPlot
>
> flush(stderr()); flush(stdout())
>
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: reconPlot
> ### Title: Stratigraphic plots of palaeoenvironmental reconstructions
> ### Aliases: reconPlot reconPlot.default reconPlot.predict.mat
@@ -6030,15 +5894,12 @@
>
>
>
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("reconPlot", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("residLen")
> ### * residLen
>
> flush(stderr()); flush(stdout())
>
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: residLen
> ### Title: Squared residual length diagnostics
> ### Aliases: residLen print.residLen fittedY sqrlLinear sqrlUnimodal
@@ -6083,15 +5944,12 @@
>
>
>
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("residLen", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("residuals.prcurve")
> ### * residuals.prcurve
>
> flush(stderr()); flush(stdout())
>
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: residuals.prcurve
> ### Title: Residuals of a principal curve fit.
> ### Aliases: residuals.prcurve resid.prcurve
@@ -6534,15 +6392,12 @@
>
>
>
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("residuals.prcurve", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("rlgh")
> ### * rlgh
>
> flush(stderr()); flush(stdout())
>
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rlgh
> ### Title: Round Loch of Glenhead Diatoms
> ### Aliases: rlgh
@@ -6554,15 +6409,12 @@
>
>
>
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("rlgh", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("roc")
> ### * roc
>
> flush(stderr()); flush(stdout())
>
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: roc
> ### Title: ROC curve analysis
> ### Aliases: roc roc.default roc.mat roc.analog print.roc summary.roc
@@ -6623,15 +6475,12 @@
>
>
>
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("roc", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("scores.prcurve")
> ### * scores.prcurve
>
> flush(stderr()); flush(stdout())
>
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: scores.prcurve
> ### Title: 'scores' method for principal curve objects of class
> ### '"prcurve"'.
@@ -6762,15 +6611,12 @@
>
>
>
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("scores.prcurve", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("screeplot")
> ### * screeplot
>
> flush(stderr()); flush(stdout())
>
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: screeplot
> ### Title: Screeplots of model results
> ### Aliases: screeplot.mat screeplot.bootstrap.mat
@@ -6845,15 +6691,12 @@
>
>
>
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("screeplot", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("splitSample")
> ### * splitSample
>
> flush(stderr()); flush(stdout())
>
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: splitSample
> ### Title: Select samples from along an environmental gradient
> ### Aliases: splitSample
@@ -6909,15 +6752,12 @@
>
>
>
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("splitSample", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("sppResponse.prcurve")
> ### * sppResponse.prcurve
>
> flush(stderr()); flush(stdout())
>
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: sppResponse
> ### Title: Species responses along gradients.
> ### Aliases: sppResponse sppResponse.prcurve
@@ -7032,15 +6872,12 @@
>
>
>
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("sppResponse.prcurve", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("stdError")
> ### * stdError
>
> flush(stderr()); flush(stdout())
>
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: stdError
> ### Title: Standard error of MAT fitted and predicted values
> ### Aliases: stdError stdError.mat stdError.predict.mat
@@ -7179,15 +7016,12 @@
>
>
>
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("stdError", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("summary.analog")
> ### * summary.analog
>
> flush(stderr()); flush(stdout())
>
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: summary.analog
> ### Title: Summarise analogue matching results
> ### Aliases: summary.analog print.summary.analog
@@ -7207,15 +7041,12 @@
>
>
>
-> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
-> base::cat("summary.analog", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
> nameEx("summary.bootstrap.mat")
> ### * summary.bootstrap.mat
>
> flush(stderr()); flush(stdout())
>
-> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: summary.bootstrap.mat
> ### Title: Summarise bootstrap resampling for MAT models
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/analogue -r 378
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