[Vegan-commits] r2893 - pkg/vegan/R

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

Author: jarioksa
Date: 2014-10-07 11:50:19 +0200 (Tue, 07 Oct 2014)
New Revision: 2893

Modified:
   pkg/vegan/R/getPermuteMatrix.R
   pkg/vegan/R/vegan-deprecated.R
Log:
Squashed commit of the following:

commit ea6dcea6a34dc8b52624bb17b08a43de5bb82af7
Author: Jari Oksanen <jari.oksanen at oulu.fi>
Date:   Tue Oct 7 10:48:27 2014 +0300

    Do not yet warn on commsimulator deprecation

    We do not yet warn on commsimulator deprecation in vegan 2.2-0
    but only in the next release to give other packages time to
    adapt. There were thousands of warnings in CRAN packages
    bipartite and metacom.

commit dde0dd6c726f0781b8ffabe8cdc402e939546bb8
Author: Jari Oksanen <jari.oksanen at oulu.fi>
Date:   Mon Oct 6 14:50:11 2014 +0300

    allow missing 'strata' in permutations

    getPermuteMatrix used 'strata=NULL' to define there are no
    strata. Vegan functions were adopted to this, but this broke
    CRAN packages cocorresp and mpmcorrelogram. The fix was so simple
    and obvious that it is almost annoying.

Modified: pkg/vegan/R/getPermuteMatrix.R
===================================================================
--- pkg/vegan/R/getPermuteMatrix.R	2014-10-03 13:15:29 UTC (rev 2892)
+++ pkg/vegan/R/getPermuteMatrix.R	2014-10-07 09:50:19 UTC (rev 2893)
@@ -15,7 +15,7 @@
         perm <- how(nperm = perm) 
     }
     ## apply 'strata'
-    if (!is.null(strata)) {
+    if (!missing(strata) && !is.null(strata)) {
         if (!inherits(perm, "how"))  # 'perm' is a matrix
             stop("'strata' can be used only with simple permutation or with 'how()'")
         if (!is.null(getBlocks(perm)))

Modified: pkg/vegan/R/vegan-deprecated.R
===================================================================
--- pkg/vegan/R/vegan-deprecated.R	2014-10-03 13:15:29 UTC (rev 2892)
+++ pkg/vegan/R/vegan-deprecated.R	2014-10-07 09:50:19 UTC (rev 2893)
@@ -3,7 +3,8 @@
 "commsimulator" <-
 function (x, method, thin = 1) 
 {
-    .Deprecated("nullmodel", package="vegan")
+    ## Do not yet warn on deprecation to allow smooth transition
+    ##.Deprecated("nullmodel", package="vegan")
     method <- match.arg(method, 
                         c("r0","r1","r2","r00","c0","swap", "tswap",
                           "backtrack", "quasiswap"))