[Analogue-commits] r345 - in pkg: inst man

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

Author: gsimpson
Date: 2013-07-20 23:00:38 +0200 (Sat, 20 Jul 2013)
New Revision: 345

Modified:
   pkg/inst/ChangeLog
   pkg/man/caterpillarPlot.Rd
   pkg/man/mat.Rd
   pkg/man/performance.Rd
   pkg/man/plot.mat.Rd
Log:
streamline some of the examples

Modified: pkg/inst/ChangeLog
===================================================================
--- pkg/inst/ChangeLog	2013-07-20 20:59:03 UTC (rev 344)
+++ pkg/inst/ChangeLog	2013-07-20 21:00:38 UTC (rev 345)
@@ -26,6 +26,9 @@
 	estimates of smooth complexities. Residual variance printed to
 	fewer decimal places.
 
+	* Streamlined some of the documentation to avoid runnning the same
+	code many times.
+
 Version 0.11-3
 
 	* chooseTaxa: new argument `value` controls whether the data for

Modified: pkg/man/caterpillarPlot.Rd
===================================================================
--- pkg/man/caterpillarPlot.Rd	2013-07-20 20:59:03 UTC (rev 344)
+++ pkg/man/caterpillarPlot.Rd	2013-07-20 21:00:38 UTC (rev 345)
@@ -86,20 +86,17 @@
 data(SumSST)
 
 ## default plot
-caterpillarPlot(ImbrieKipp, SumSST)
+caterpillar(ImbrieKipp, SumSST)
 
 ## customisation
 opttol <-
-    caterpillarPlot(ImbrieKipp, SumSST, col = "red2",
-                    bg = "yellow", lcol = "blue",
-                    xlab = expression(Summer ~ Sea ~ Surface ~
-                                      Temperature~(degree*C)))
+    caterpillar(ImbrieKipp, SumSST, col = "red2",
+                bg = "yellow", lcol = "blue",
+                xlab = expression(Summer ~ Sea ~ Surface ~
+                                 Temperature~(degree*C)))
 
 ## invisibly returns the optima and tolerances
 head(opttol)
-
-## The short form name may be easier on the typing fingers
-caterpillar(ImbrieKipp, SumSST)
 }
 
 % Add one or more standard keywords, see file 'KEYWORDS' in the

Modified: pkg/man/mat.Rd
===================================================================
--- pkg/man/mat.Rd	2013-07-20 20:59:03 UTC (rev 344)
+++ pkg/man/mat.Rd	2013-07-20 21:00:38 UTC (rev 345)
@@ -251,7 +251,7 @@
 plot(ik.mat)
 par(mfrow = c(1,1))
 
-## reconstruct for the RLGH core data
+## reconstruct for the V12.122 core data
 coreV12.mat <- predict(ik.mat, V12.122, k = 3)
 coreV12.mat
 summary(coreV12.mat)
@@ -265,29 +265,6 @@
 ik.mat2 <- mat(ImbrieKipp, SumSST, method = "chord", kmax = 20)
 ik.mat2
 
-## model summary
-summary(ik.mat2)
-
-## fitted values
-fitted(ik.mat2)
-
-## model residuals
-resid(ik.mat2)
-
-## draw summary plots of the model
-par(mfrow = c(2,2))
-plot(ik.mat2)
-par(mfrow = c(1,1))
-
-## reconstruct for the V12.122 core data
-coreV12.mat2 <- predict(ik.mat, V12.122, k = 3)
-coreV12.mat2
-summary(coreV12.mat2)
-
-## draw the reconstruction
-reconPlot(coreV12.mat2, use.labels = TRUE, display.error = "bars",
-          xlab = "Depth", ylab = "SumSST")
-
 }
 \keyword{models}% at least one, from doc/KEYWORDS
 \keyword{multivariate}% __ONLY ONE__ keyword per line

Modified: pkg/man/performance.Rd
===================================================================
--- pkg/man/performance.Rd	2013-07-20 20:59:03 UTC (rev 344)
+++ pkg/man/performance.Rd	2013-07-20 21:00:38 UTC (rev 345)
@@ -37,9 +37,13 @@
 \seealso{\code{\link{wa}}, \code{\link{predict.wa}},
   \code{\link{bootstrap.wa}}.}
 \examples{
-## continue the example from ?wa
-example(wa)
+data(ImbrieKipp)
+data(SumSST)
 
+## fit the WA model
+mod <- wa(SumSST ~., data = ImbrieKipp)
+mod
+
 ## the model performance statistics
 performance(mod)
 }

Modified: pkg/man/plot.mat.Rd
===================================================================
--- pkg/man/plot.mat.Rd	2013-07-20 20:59:03 UTC (rev 344)
+++ pkg/man/plot.mat.Rd	2013-07-20 21:00:38 UTC (rev 345)
@@ -92,8 +92,6 @@
 
 ## MAT
 ik.mat <- mat(ImbrieKipp, SumSST, method = "chord")
-ik.mat
-summary(ik.mat)
 
 ## summary plot of MAT model
 layout(matrix(1:4, ncol = 2, byrow = TRUE))