use dontshow instead of testonly

man/residuals.prcurve.Rd

@@ -82,6 +82,7 @@
 }
 
 \examples{
+  \dontshow{od <- options(digits = 4)}
   ## Load Abernethy Forest data set
   data(abernethy)
 
@@ -93,13 +94,16 @@
   aber.pc <- prcurve(abernethy2, method = "ca", keep.data = TRUE)
 
   ## default "distance" residuals
-  resid(aber.pc)
+  res <- resid(aber.pc)
+  head(res)
 
   ## residuals from the underlying smooth models, also illustrates
   ## how to select specific types of residual from the individual
   ## method using argument 'type'
-  resid(aber.pc, which = "smooths", type = "deviance")
-
+  res <- resid(aber.pc, which = "smooths", type = "deviance")
+  dim(res)
+  head(res[, 1:5])		# just show a few species residuals
+  \dontshow{options(od)}
 }
 
 \keyword{ methods }

man/wa.Rd

@@ -162,7 +162,7 @@ waFit(x, y, tol.dw, useN2, deshrink, na.tol, small.tol,
 \author{Gavin L. Simpson and Jari Oksanen}
 \seealso{\code{\link{mat}} for an alternative transfer function method.}
 \examples{
-\testonly{od <- options(digits = 4)}
+\dontshow{od <- options(digits = 4)}
 data(ImbrieKipp)
 data(SumSST)
 
@@ -216,7 +216,7 @@ fitted(mod4)
 ## residuals for the training set
 residuals(mod4)
 
-\testonly{options(od)}
+\dontshow{options(od)}
 }
 \keyword{methods}
 \keyword{models}