[Pomp-commits] r479 - in pkg: . R

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

Author: kingaa
Date: 2011-05-16 16:55:37 +0200 (Mon, 16 May 2011)
New Revision: 479

Modified:
   pkg/DESCRIPTION
   pkg/R/sannbox.R
   pkg/R/sobol.R
   pkg/R/spect-match.R
   pkg/R/spect.R
Log:
- replace some instances of 'sapply' with 'vapply'


Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION	2011-05-13 15:02:48 UTC (rev 478)
+++ pkg/DESCRIPTION	2011-05-16 14:55:37 UTC (rev 479)
@@ -1,8 +1,8 @@
 Package: pomp
 Type: Package
 Title: Statistical inference for partially observed Markov processes
-Version: 0.37-1
-Date: 2011-05-14
+Version: 0.37-2
+Date: 2011-05-16
 Author: Aaron A. King, Edward L. Ionides, Carles Breto, Steve Ellner, Bruce Kendall, Helen Wearing, Matthew J. Ferrari, Michael Lavine, Daniel C. Reuman
 Maintainer: Aaron A. King <kingaa at umich.edu>
 URL: http://pomp.r-forge.r-project.org

Modified: pkg/R/sannbox.R
===================================================================
--- pkg/R/sannbox.R	2011-05-13 15:02:48 UTC (rev 478)
+++ pkg/R/sannbox.R	2011-05-16 14:55:37 UTC (rev 479)
@@ -32,7 +32,7 @@
     control$sched <- function (k) control$temp/log(((k-1)%/%control$tmax)*control$tmax+exp(1))
 
   if (is.function(control$sched))
-    temps <- sapply(seq.int(from=1,to=control$maxit,by=1),control$sched)
+    temps <- vapply(seq_len(control$maxit),control$sched,numeric(1))
   else if (is.numeric(control$sched))
     temps <- control$sched
   

Modified: pkg/R/sobol.R
===================================================================
--- pkg/R/sobol.R	2011-05-13 15:02:48 UTC (rev 478)
+++ pkg/R/sobol.R	2011-05-16 14:55:37 UTC (rev 479)
@@ -5,11 +5,12 @@
     stop("sobol error: each entry in ",sQuote("vars")," must specify a range")
   d <- length(vars)
   x <- .Call("sobol_sequence",as.integer(c(d,n)))
-  y <- sapply(
-              seq(length=d),
+  y <- vapply(
+              seq_len(d),
               function (k) {
                 vars[[k]][1]+(vars[[k]][2]-vars[[k]][1])*x[k,]
-              }
+              },
+              numeric(n)
               )
   colnames(y) <- names(vars)
   as.data.frame(y)

Modified: pkg/R/spect-match.R
===================================================================
--- pkg/R/spect-match.R	2011-05-13 15:02:48 UTC (rev 478)
+++ pkg/R/spect-match.R	2011-05-16 14:55:37 UTC (rev 479)
@@ -151,7 +151,7 @@
     if ((length(weights)!=length(ds$freq)))
       stop("if ",sQuote("weights")," is provided as a vector, it must have length ",length(ds$freq))
   } else if (is.function(weights)) {
-    weights <- sapply(ds$freq,weights)
+    weights <- vapply(ds$freq,weights,numeric(1))
   } else {
     stop(sQuote("weights")," must be specified as a vector or as a function")
   }

Modified: pkg/R/spect.R
===================================================================
--- pkg/R/spect.R	2011-05-13 15:02:48 UTC (rev 478)
+++ pkg/R/spect.R	2011-05-16 14:55:37 UTC (rev 479)
@@ -187,9 +187,10 @@
               ## L-2 distance between data and mean simulated spectrum
               datdist <- sum((datspec[,j]-mean.simspec[,j])^2)
               ## L-2 distance betw. each sim. and mean simulated spectrum
-              simdist <- sapply(
+              simdist <- vapply(
                                 seq_len(nsim),
-                                function(k)sum((simspec[k,,j]-mean.simspec[,j])^2)
+                                function(k)sum((simspec[k,,j]-mean.simspec[,j])^2),
+                                numeric(1)
                                 )
               pvals[j] <- (nsim+1-sum(simdist<datdist))/(nsim+1)
               totdatdist <- totdatdist+datdist