[Analogue-commits] r392 - in pkg: . inst man tests/Examples

Fri Dec 13 06:35:21 CET 2013

Author: gsimpson
Date: 2013-12-13 06:35:20 +0100 (Fri, 13 Dec 2013)
New Revision: 392

Modified:
   pkg/DESCRIPTION
   pkg/inst/ChangeLog
   pkg/man/analogue-package.Rd
   pkg/tests/Examples/analogue-Ex.Rout.save
Log:
prepare for 0.12-0 release; update reference material, bump to 0.11-99

Modified: pkg/DESCRIPTION
===================================================================

--- pkg/DESCRIPTION	2013-12-13 04:08:51 UTC (rev 391)
+++ pkg/DESCRIPTION	2013-12-13 05:35:20 UTC (rev 392)
@@ -1,7 +1,7 @@
 Package: analogue
 Type: Package
 Title: Analogue and weighted averaging methods for palaeoecology
-Version: 0.11-6
+Version: 0.11-99
 Date: $Date$
 Depends: R (>= 2.15.0), vegan (>= 1.17-12), lattice, rgl
 Imports: mgcv, MASS, stats, graphics, grid, brglm, princurve

Modified: pkg/inst/ChangeLog
===================================================================
--- pkg/inst/ChangeLog	2013-12-13 04:08:51 UTC (rev 391)
+++ pkg/inst/ChangeLog	2013-12-13 05:35:20 UTC (rev 392)
@@ -1,5 +1,9 @@
 analogue Change Log
 
+Version 0.11-99
+
+	* Preparing for the 0.12-0 release.
+
 Version 0.11-6
 
 	* distance3: removed - redundant attempt to improve `distance()`.

Modified: pkg/man/analogue-package.Rd
===================================================================
--- pkg/man/analogue-package.Rd	2013-12-13 04:08:51 UTC (rev 391)
+++ pkg/man/analogue-package.Rd	2013-12-13 05:35:20 UTC (rev 392)
@@ -14,7 +14,7 @@
 \tabular{ll}{
 Package: \tab analogue\cr
 Type: \tab Package\cr
-Version: \tab 0.11-6\cr
+Version: \tab 0.11-99\cr
 Date: \tab $Date: 2013-10-05 15:11:52 -0600 (Sat, 05 Oct 2013) $\cr
 Depends: \tab R (>= 2.15.0), vegan (>= 1.17-12), lattice, rgl\cr
 Imports: \tab mgcv, MASS, stats, graphics, grid, brglm, princurve\cr
@@ -30,8 +30,8 @@
 License: \tab GPL-2\cr
 ByteCompile: \tab true\cr
 URL: \tab http://analogue.r-forge.r-project.org\cr
-Packaged: \tab 2013-10-14 20:41:41 UTC; gavin\cr
-Built: \tab R 3.0.2; x86_64-unknown-linux-gnu; 2013-10-14 20:41:48 UTC; unix\cr
+Packaged: \tab 2013-12-13 05:23:57 UTC; gavin\cr
+Built: \tab R 3.0.2; x86_64-unknown-linux-gnu; 2013-12-13 05:27:27 UTC; unix\cr
 }
 
 Index:
@@ -42,7 +42,8 @@
 Stratiplot              Palaeoecological stratigraphic diagrams
 abernethy               Abernethy Forest Pollen Sequence
 analog                  Analogue matching
-analogue-package        Analogue methods for palaeoecology
+analogue-package        Analogue and weighted averaging methods for
+                        palaeoecology
 bayesF                  Bayes factors
 bootstrap               Bootstrap estimation and errors
 bootstrap.wa            Bootstrap estimation and errors for WA models

Modified: pkg/tests/Examples/analogue-Ex.Rout.save
===================================================================
--- pkg/tests/Examples/analogue-Ex.Rout.save	2013-12-13 04:08:51 UTC (rev 391)
+++ pkg/tests/Examples/analogue-Ex.Rout.save	2013-12-13 05:35:20 UTC (rev 392)
@@ -24,9 +24,9 @@
 Loading required package: vegan
 Loading required package: permute
 Loading required package: lattice
-This is vegan 2.0-9
+This is vegan 2.0-10
 Loading required package: rgl
-This is analogue 0.11-6
+This is analogue 0.11-99
 > 
 > base::assign(".oldSearch", base::search(), pos = 'CheckExEnv')
 > cleanEx()
@@ -5749,7 +5749,7 @@
 > mod <- pcr(ImbrieKipp[-take, ], SumSST[-take], tranFun = Hellinger)
 > 
 > ## predictions
-> predict(mod, ImbrieKipp[take, ], ncomp = 1:4)
+> predict(mod, ImbrieKipp[take, ], ncomp = 4)
              PC1       PC2       PC3       PC4
 V14.47  10.34383  8.964025  8.816845  8.700079
 V20.7   28.37448 26.720456 26.781783 26.619102
@@ -5762,9 +5762,25 @@
 V23.29  11.45795 11.373413 11.816852 12.136959
 A180.76 28.15434 26.970442 27.221069 27.230316
 > 
+> ## predictions
+> set.seed(123)
+> predict(mod, ImbrieKipp[take, ], ncomp = 4, CV = "bootstrap",
++         nboot = 100)
+             PC1       PC2       PC3       PC4
+V14.47  10.86146  9.108554  8.796106  8.721006
+V20.7   27.93000 26.680977 26.738630 26.619345
+V12.18  26.09875 26.452455 26.273816 26.340640
+V15.164 28.31861 27.344207 27.415372 27.455231
+V22.204 26.44229 26.237016 26.479955 26.523139
+V19.222 22.69438 23.664213 23.651692 23.626940
+V16.189 26.56779 26.665168 26.550892 26.443218
+V20.230 27.67475 26.752244 27.058222 27.096922
+V23.29  12.11350 11.412378 11.789892 12.165228
+A180.76 27.79627 26.907033 27.191718 27.251444
 > 
 > 
 > 
+> 
 > cleanEx()
 > nameEx("predict.wa")
 > ### * predict.wa
@@ -7300,9 +7316,9 @@
 Call: rda(X = X, Y = mf)
 
               Inertia Proportion Rank
-Total         0.61631    1.00000     
-Constrained   0.09743    0.15808    1
-Unconstrained 0.51888    0.84192  165
+Total          0.6163     1.0000     
+Constrained    0.0974     0.1581    1
+Unconstrained  0.5189     0.8419  165
 Inertia is variance 
 
 Eigenvalues for constrained axes:
@@ -7767,7 +7783,7 @@
 > ###
 > options(digits = 7L)
 > base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed:  23.269 0.335 24.256 0.001 0.003 
+Time elapsed:  22.285 0.434 23.459 0.001 0.003 
 > grDevices::dev.off()
 null device 
           1 

