[Vegan-commits] r1840 - pkg/vegan/R

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

Author: jarioksa
Date: 2011-09-12 19:16:57 +0200 (Mon, 12 Sep 2011)
New Revision: 1840

Modified:
   pkg/vegan/R/clamtest.R
   pkg/vegan/R/permatswap.R
   pkg/vegan/R/tsallis.R
   pkg/vegan/R/tsallisaccum.R
Log:
warnings() -> warning()

Modified: pkg/vegan/R/clamtest.R
===================================================================
--- pkg/vegan/R/clamtest.R	2011-09-12 14:02:52 UTC (rev 1839)
+++ pkg/vegan/R/clamtest.R	2011-09-12 17:16:57 UTC (rev 1840)
@@ -41,9 +41,9 @@
         stop("zero group totals not allowed")
     ## check if comm contains integer, especially for singletons
     if (any(X[X>0] < 1) || any(Y[Y>0] < 1))
-        warnings("<1 non integer values detected: analysis might not be meaningful")
+        warning("<1 non integer values detected: analysis might not be meaningful")
     if (abs(sum(X,Y) - sum(as.integer(X), as.integer(Y))) > 10^-6)
-        warnings("non integer values detected")
+        warning("non integer values detected")
     C1 <- 1 - sum(X==1)/n
     C2 <- 1 - sum(Y==1)/m
     ## this stands for other than 2/3 cases

Modified: pkg/vegan/R/permatswap.R
===================================================================
--- pkg/vegan/R/permatswap.R	2011-09-12 14:02:52 UTC (rev 1839)
+++ pkg/vegan/R/permatswap.R	2011-09-12 17:16:57 UTC (rev 1840)
@@ -36,10 +36,10 @@
     ## non-sequential algos: no burnin required
     } else {
         if (burnin > 0)
-            warnings("Non sequential algorithm used: 'burnin' argument ignored")
+            warning("Non sequential algorithm used: 'burnin' argument ignored")
         burnin <- 0
         if (thin != 1)
-            warnings("Non sequential algorithm used: 'thin' value set to 1")
+            warning("Non sequential algorithm used: 'thin' value set to 1")
         thin <- 1
         perm <- replicate(times, 
             permatswap1(m, method, fixedmar, shuffle, strata, mtype, thin), 

Modified: pkg/vegan/R/tsallis.R
===================================================================
--- pkg/vegan/R/tsallis.R	2011-09-12 14:02:52 UTC (rev 1839)
+++ pkg/vegan/R/tsallis.R	2011-09-12 17:16:57 UTC (rev 1840)
@@ -36,7 +36,7 @@
             }
         }
     }
-    result <- as.data.frame(result)
+    #result <- as.data.frame(result)
     if (any(dim(result) == 1)) 
         result <- unlist(result, use.names = TRUE)
     class(result) <- c("tsallis", "renyi", class(result))

Modified: pkg/vegan/R/tsallisaccum.R
===================================================================
--- pkg/vegan/R/tsallisaccum.R	2011-09-12 14:02:52 UTC (rev 1839)
+++ pkg/vegan/R/tsallisaccum.R	2011-09-12 17:16:57 UTC (rev 1840)
@@ -1,5 +1,5 @@
-tsallisaccum <-
-function (x, scales = seq(0, 2, 0.2), permutations = 100, raw = FALSE, ...)
+`tsallisaccum` <-
+    function (x, scales = seq(0, 2, 0.2), permutations = 100, raw = FALSE, ...)
 {
     x <- as.matrix(x)
     n <- nrow(x)