[Analogue-commits] r406 - in pkg: R inst man tests/Examples

[noreply at r-forge.r-project.org]

Author: gsimpson
Date: 2014-02-14 20:27:27 +0100 (Fri, 14 Feb 2014)
New Revision: 406

Modified:
   pkg/R/predict.pcr.R
   pkg/inst/ChangeLog
   pkg/man/predict.pcr.Rd
   pkg/tests/Examples/analogue-Ex.Rout.save
Log:
predict.pcr was setting ncomp incorrectly if not specified by the user.

Modified: pkg/R/predict.pcr.R
===================================================================
--- pkg/R/predict.pcr.R	2014-02-13 22:26:44 UTC (rev 405)
+++ pkg/R/predict.pcr.R	2014-02-14 19:27:27 UTC (rev 406)
@@ -1,4 +1,4 @@
-`predict.pcr` <- function(object, newdata, ncomp = seq_along(object$ncomp),
+`predict.pcr` <- function(object, newdata, ncomp = object$ncomp,
                           CV = c("none", "LOO", "bootstrap", "kfold"),
                           verbose = FALSE, nboot = 100, kfold = 10,
                           folds = 5, ...) {

Modified: pkg/inst/ChangeLog
===================================================================
--- pkg/inst/ChangeLog	2014-02-13 22:26:44 UTC (rev 405)
+++ pkg/inst/ChangeLog	2014-02-14 19:27:27 UTC (rev 406)
@@ -5,6 +5,9 @@
 	* crossval.pcr: Fixed a number of bugs in the method for PCR
 	related to k-fold cross validation, which were causing errors.
 
+	* predict.pcr: would set argument `ncomp` incorrectly (in the
+	wrong form) if not supplied.
+
 Version 0.13-3 Opened 11 Feb 2014
 
 	* timetrack: A number of additions added and improvements made:

Modified: pkg/man/predict.pcr.Rd
===================================================================
--- pkg/man/predict.pcr.Rd	2014-02-13 22:26:44 UTC (rev 405)
+++ pkg/man/predict.pcr.Rd	2014-02-14 19:27:27 UTC (rev 406)
@@ -10,7 +10,7 @@
 }
 
 \usage{
-\method{predict}{pcr}(object, newdata, ncomp = seq_along(object$ncomp),
+\method{predict}{pcr}(object, newdata, ncomp = object$ncomp,
         CV = c("none", "LOO", "bootstrap", "kfold"),
         verbose = FALSE, nboot = 100, kfold = 10, folds = 5,
         \dots)

Modified: pkg/tests/Examples/analogue-Ex.Rout.save
===================================================================
--- pkg/tests/Examples/analogue-Ex.Rout.save	2014-02-13 22:26:44 UTC (rev 405)
+++ pkg/tests/Examples/analogue-Ex.Rout.save	2014-02-14 19:27:27 UTC (rev 406)
@@ -26,7 +26,7 @@
 Loading required package: lattice
 This is vegan 2.0-10
 Loading required package: rgl
-This is analogue 0.13-3
+This is analogue 0.13-4
 > 
 > base::assign(".oldSearch", base::search(), pos = 'CheckExEnv')
 > cleanEx()
@@ -1888,8 +1888,28 @@
 9     9 0.95742 -0.083771 -5.1489 2.0288 2.0585 0.34841 2.0288
 10   10 0.95784 -0.055376 -4.9774 2.0176 2.0499 0.36230 2.0176
 > 
+> crossval(mpcr, method = "bootstrap", nboot = 250, ncomp = 10)
+	Model Cross-validation:
+
+crossval(obj = mpcr, method = "bootstrap", ncomp = 10, nboot = 250)
+
+Method: bootstrap
+No. Bootstraps: 250
+
+   comp      R2   avgBias maxBias  RMSEP RMSEP2      s1     s2
+1     1 0.94633 -0.098164 -6.3331 2.3477 2.7404 1.41352 2.3477
+2     2 0.95203 -0.041775 -5.3330 2.1490 2.2467 0.65548 2.1490
+3     3 0.95520 -0.044662 -4.4128 2.0789 2.1797 0.65524 2.0789
+4     4 0.95557 -0.047229 -4.4156 2.0703 2.1880 0.70792 2.0703
+5     5 0.95740 -0.047406 -4.9908 2.0281 2.1796 0.79856 2.0281
+6     6 0.95716 -0.055633 -4.8585 2.0336 2.2021 0.84479 2.0336
+7     7 0.95816 -0.052451 -4.7913 2.0102 2.1975 0.88769 2.0102
+8     8 0.95978 -0.031075 -4.8303 1.9712 2.1437 0.84254 1.9712
+9     9 0.96015 -0.031626 -4.9102 1.9622 2.1470 0.87149 1.9622
+10   10 0.96116 -0.029623 -4.8634 1.9379 2.1373 0.90148 1.9379
 > 
 > 
+> 
 > cleanEx()
 > nameEx("densityplot.residLen")
 > ### * densityplot.residLen
@@ -7830,7 +7850,7 @@
 > ###
 > options(digits = 7L)
 > base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed:  17.431 0.285 17.846 0 0.003 
+Time elapsed:  17.799 0.401 18.495 0 0.002 
 > grDevices::dev.off()
 null device 
           1