[Analogue-commits] r377 - pkg/tests/Examples
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Oct 7 04:36:50 CEST 2013
Author: gsimpson
Date: 2013-10-07 04:36:50 +0200 (Mon, 07 Oct 2013)
New Revision: 377
Modified:
pkg/tests/Examples/analogue-Ex.Rout.save
Log:
Update reference output for Example checks
Modified: pkg/tests/Examples/analogue-Ex.Rout.save
===================================================================
--- pkg/tests/Examples/analogue-Ex.Rout.save 2013-10-07 02:36:01 UTC (rev 376)
+++ pkg/tests/Examples/analogue-Ex.Rout.save 2013-10-07 02:36:50 UTC (rev 377)
@@ -1,5 +1,5 @@
-R version 3.0.1 RC (2013-05-11 r62732) -- "Good Sport"
+R version 3.0.2 Patched (2013-09-26 r64005) -- "Frisbee Sailing"
Copyright (C) 2013 The R Foundation for Statistical Computing
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -20,14 +20,25 @@
> 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
-This is vegan 2.1-29
-Loading required package: princurve
Loading required package: lattice
+This is vegan 2.0-9
Loading required package: rgl
-This is analogue 0.11-4
+This is analogue 0.11-6
>
> base::assign(".oldSearch", base::search(), pos = 'CheckExEnv')
> cleanEx()
@@ -36,6 +47,7 @@
>
> 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
@@ -106,12 +118,15 @@
>
>
>
+> 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
@@ -129,12 +144,15 @@
>
>
>
+> 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
@@ -236,12 +254,15 @@
>
>
>
+> 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
@@ -328,12 +349,15 @@
>
>
>
+> 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
@@ -400,12 +424,15 @@
>
>
>
+> 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
@@ -833,12 +860,15 @@
>
>
>
+> 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
@@ -920,12 +950,15 @@
>
>
>
+> 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
@@ -1150,12 +1183,15 @@
>
>
>
+> 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
@@ -1213,12 +1249,15 @@
>
>
>
+> 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
@@ -1252,12 +1291,15 @@
>
>
>
+> 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.
@@ -1284,12 +1326,15 @@
>
>
>
+> 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
@@ -1751,12 +1796,15 @@
>
>
>
+> 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
@@ -1868,12 +1916,15 @@
>
>
>
+> 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
@@ -1906,12 +1957,15 @@
>
>
>
+> 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
@@ -2303,15 +2357,19 @@
>
>
>
+> 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
+> ### Aliases: distance distance.default distance.join oldDistance
+> ### oldDistance.default oldDistance.join
> ### Keywords: multivariate methods
>
> ### ** Examples
@@ -2343,11 +2401,12 @@
..$ : chr [1:20] "A" "B" "C" "D" ...
..$ : chr [1:10] "a" "b" "c" "d" ...
- attr(*, "method")= chr "euclidean"
+ - attr(*, "class")= chr [1:2] "distance" "matrix"
- attr(*, "type")= chr "asymmetric"
- - attr(*, "class")= chr [1:2] "distance" "matrix"
>
> ## calculate Gower's general coefficient for mixed data
> ## first, make a couple of variables factors
+>
> fossil[,4] <- factor(sample(rep(1:4, length = 10), 10))
> train[,4] <- factor(sample(rep(1:4, length = 20), 20))
> ## now fit the mixed coefficient
@@ -2358,107 +2417,31 @@
> x2 <- t(c(1,3,3,1,2,2,2,5))
> Rj <- c(1,4,2,4,1,3,2,5) # supplied ranges
>
-> distance(x1, x2, method = "mixed", R = Rj)
-[1] 0.3380952
-attr(,"method")
-[1] "mixed"
-attr(,"type")
-[1] "asymmetric"
-attr(,"class")
-[1] "distance" "matrix"
->
-> ## note this gives 1 - 0.66 (not 0.66 as the answer in
-> ## Legendre & Legendre) as this is expressed as a
-> ## distance whereas Legendre & Legendre describe the
-> ## coefficient as similarity coefficient
->
->
->
-> cleanEx()
-> nameEx("distance3")
-> ### * distance3
->
-> flush(stderr()); flush(stdout())
->
-> ### Name: distance3
-> ### Title: Flexibly calculate dissimilarity or distance measures
-> ### Aliases: distance3 distanceX distance3.default
-> ### Keywords: multivariate methods
->
-> ### ** Examples
->
-> ## simple example using dummy data
-> train <- data.frame(matrix(abs(runif(200)), ncol = 10))
-> rownames(train) <- LETTERS[1:20]
-> colnames(train) <- as.character(1:10)
-> fossil <- data.frame(matrix(abs(runif(100)), ncol = 10))
-> colnames(fossil) <- as.character(1:10)
-> rownames(fossil) <- letters[1:10]
->
-> ## calculate distances/dissimilarities between train and fossil
-> ## samples
-> test <- distance3(train, fossil)
-> test.o <- distance(train, fossil)
-> stopifnot(isTRUE(all.equal(test.o, test)))
->
-> ## using a different coefficient, chi-square distance
-> test <- distance3(train, fossil, method = "chi.distance")
-> test.o <- distance(train, fossil, method = "chi.distance")
-> stopifnot(isTRUE(all.equal(test.o, test)))
->
-> ## calculate pairwise distances/dissimilarities for training
-> ## set samples
-> ##test2 <- distance3(train)
->
-> ## Using distance on an object of class join
-> #dists <- distance3(join(train, fossil))
-> #str(dists)
-> dists <- distance(join(train, fossil))
-> ##distsX <- distanceX(join(train, fossil))
->
-> ## calculate Gower's general coefficient for mixed data
-> ## first, make a couple of variables factors
-> fossil[,4] <- factor(sample(rep(1:4, length = 10), 10))
-> train[,4] <- factor(sample(rep(1:4, length = 20), 20))
-> ## now fit the mixed coefficient
-> test3 <- distance3(train, fossil, "mixed")
->
-> ## Example from page 260 of Legendre & Legendre (1998)
-> x1 <- t(c(2,2,NA,2,2,4,2,6))
-> x2 <- t(c(1,3,3,1,2,2,2,5))
-> Rj <- c(1,4,2,4,1,3,2,5) # supplied ranges
->
-> distance3(x1, x2, method = "mixed", R = Rj)
+> 1 - distance(x1, x2, method = "mixed", R = Rj)
[,1]
-[1,] 0.3380952
+[1,] 0.6619048
attr(,"method")
[1] "mixed"
-attr(,"type")
-[1] "asymmetric"
attr(,"class")
[1] "distance" "matrix"
-> distance(x1, x2, method = "mixed", R = Rj)
-[1] 0.3380952
-attr(,"method")
-[1] "mixed"
attr(,"type")
[1] "asymmetric"
-attr(,"class")
-[1] "distance" "matrix"
>
-> ## note this gives 1 - 0.66 (not 0.66 as the answer in
-> ## Legendre & Legendre) as this is expressed as a
-> ## distance whereas Legendre & Legendre describe the
-> ## coefficient as similarity coefficient
+> ## note this gives ~0.66 as Legendre & Legendre describe the
+> ## coefficient as a similarity coefficient. Hence here we do
+> ## 1 - Dij here to get the same answer.
>
>
>
+> 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
@@ -2509,12 +2492,15 @@
>
>
>
+> 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
@@ -2569,12 +2555,15 @@
>
>
>
+> 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
@@ -2608,12 +2597,15 @@
>
>
>
+> 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
@@ -2646,12 +2638,15 @@
>
>
>
+> 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
@@ -2684,12 +2679,15 @@
>
>
>
+> 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
@@ -3379,12 +3377,15 @@
>
>
>
+> 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
@@ -3497,12 +3498,15 @@
>
>
>
+> 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
@@ -3988,6 +3992,8 @@
>
>
>
+> 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")
@@ -3995,6 +4001,7 @@
>
> 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
@@ -4051,12 +4058,15 @@
>
>
>
+> 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
@@ -4164,12 +4174,15 @@
>
>
>
+> 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
@@ -4276,12 +4289,15 @@
>
>
>
+> 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
@@ -4513,12 +4529,15 @@
>
>
>
+> 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
@@ -4552,16 +4571,19 @@
> ## the model performance statistics
> performance(mod)
RMSE R2 Avg.Bias Max.Bias
- 2.019e+00 9.173e-01 2.228e-14 -3.815e+00
+ 2.019e+00 9.173e-01 2.854e-15 -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
@@ -4951,12 +4973,15 @@
>
>
>
+> 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
@@ -4996,12 +5021,15 @@
>
>
>
+> 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
@@ -5058,12 +5086,15 @@
>
>
>
+> 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
@@ -5169,12 +5200,15 @@
>
>
>
+> 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
@@ -5285,22 +5319,25 @@
>
> ## Plot the curve
-> plot(aber.pc, abernethy2)
+> plot(aber.pc)
>
> ## The lines() method can be used to add the principal curve to an
> ## existing plot
> ord <- rda(abernethy2)
-> plot(ord)
-> lines(aber.pc, data = abernethy2)
+> plot(ord, scaling = 1)
+> lines(aber.pc, scaling = 1)
>
>
>
+> 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
@@ -5333,12 +5370,15 @@
>
>
>
+> 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
@@ -5351,12 +5391,15 @@
>
>
>
+> 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
@@ -5470,12 +5513,16 @@
>
>
>
+>
+> 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
@@ -5688,12 +5735,15 @@
>
>
>
+> 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
@@ -5801,12 +5851,15 @@
>
>
>
+> 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
@@ -5857,12 +5910,15 @@
>
>
>
+> 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.
@@ -5885,12 +5941,15 @@
>
>
>
+> 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
@@ -5971,12 +6030,15 @@
>
>
>
+> 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
@@ -6021,12 +6083,15 @@
>
>
>
+> 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
@@ -6469,12 +6534,15 @@
>
>
>
+> 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
@@ -6486,12 +6554,15 @@
>
>
>
+> 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
[TRUNCATED]
To get the complete diff run:
svnlook diff /svnroot/analogue -r 377
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