[Vegan-commits] r1887 - pkg/vegan/R

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

Author: psolymos
Date: 2011-09-26 08:35:32 +0200 (Mon, 26 Sep 2011)
New Revision: 1887

Modified:
   pkg/vegan/R/permatfull.R
   pkg/vegan/R/permatswap.R
   pkg/vegan/R/print.permat.R
   pkg/vegan/R/print.summary.permat.R
Log:
permat* passes commsim name for transparency

Modified: pkg/vegan/R/permatfull.R
===================================================================
--- pkg/vegan/R/permatfull.R	2011-09-25 18:23:57 UTC (rev 1886)
+++ pkg/vegan/R/permatfull.R	2011-09-26 06:35:32 UTC (rev 1887)
@@ -48,7 +48,7 @@
     out <- list(call=match.call(), orig=m, perm=perm)
     attr(out, "mtype") <- mtype
     attr(out, "ptype") <- "full"
-    attr(out, "method") <- NA
+    attr(out, "method") <- ALGO
     attr(out, "fixedmar") <- fixedmar
     attr(out, "times") <- times
     attr(out, "shuffle") <- shuffle

Modified: pkg/vegan/R/permatswap.R
===================================================================
--- pkg/vegan/R/permatswap.R	2011-09-25 18:23:57 UTC (rev 1886)
+++ pkg/vegan/R/permatswap.R	2011-09-26 06:35:32 UTC (rev 1887)
@@ -80,7 +80,7 @@
     out <- list(call=match.call(), orig=m, perm=perm)
     attr(out, "mtype") <- mtype
     attr(out, "ptype") <- "swap"
-    attr(out, "method") <- method
+    attr(out, "method") <- ALGO
     attr(out, "fixedmar") <- if (method == "swsh") "none" else fixedmar
     attr(out, "times") <- times
     attr(out, "shuffle") <- if (method == "swsh") shuffle else NA

Modified: pkg/vegan/R/print.permat.R
===================================================================
--- pkg/vegan/R/print.permat.R	2011-09-25 18:23:57 UTC (rev 1886)
+++ pkg/vegan/R/print.permat.R	2011-09-26 06:35:32 UTC (rev 1887)
@@ -4,12 +4,12 @@
 {
     cat("Object of class 'permat' with ", attr(x, "times"), " simulations\n", sep="")
     cat("\nMatrix type:", attr(x, "mtype"), "\nPermutation type:", attr(x, "ptype"))
+    cat("\nMethod: ", attr(x, "method"), sep = "")
     if (attr(x, "ptype") == "swap") {
-        cat("\nMethod: ", attr(x, "method"), sep = "")
-        if (attr(x, "method") != "quasiswap") {
+        if (!is.na(attr(x, "burnin")))
             cat(", burnin: ", attr(x, "burnin"), sep = "")
+        if (!is.na(attr(x, "thin")))
             cat(", thin: ", attr(x, "thin"), sep = "")
-        }
     }
     cat("\nRestricted:", attr(x, "is.strat"), "\nFixed margins:", attr(x, "fixedmar"))
     if (!is.na(attr(x, "shuffle"))) {
@@ -20,8 +20,4 @@
     }
     cat("\n")
     invisible(x)
-#    cat("\n\nMatrix dimensions:", nrow(x$orig), "rows,", ncol(x$orig), "columns")
-#    cat("\nSum of original matrix:", sum(x$orig))
-#    cat("\nFill of original matrix:", round(sum(x$orig>0)/(nrow(x$orig)*ncol(x$orig)),digits))
-#    cat("\nNumber of permuted matrices:", attr(x, "times"),"\n")
 }

Modified: pkg/vegan/R/print.summary.permat.R
===================================================================
--- pkg/vegan/R/print.summary.permat.R	2011-09-25 18:23:57 UTC (rev 1886)
+++ pkg/vegan/R/print.summary.permat.R	2011-09-26 06:35:32 UTC (rev 1887)
@@ -6,12 +6,12 @@
     cat("Summary of object of class 'permat'\n\nCall: ")
     print(x$x$call)
     cat("\nMatrix type:", attr(x$x, "mtype"), "\nPermutation type:", attr(x$x, "ptype"))
-    if (attr(x$x, "ptype") == "swap") {
-        cat("\nMethod: ", attr(x$x, "method"), sep = "")
-        if (attr(x$x, "method") != "quasiswap") {
-            cat(", burnin: ", attr(x$x, "burnin"), sep = "")
-            cat(", thin: ", attr(x$x, "thin"), sep = "")
-        }
+    cat("\nMethod: ", attr(x, "method"), sep = "")
+    if (attr(x, "ptype") == "swap") {
+        if (!is.na(attr(x, "burnin")))
+            cat(", burnin: ", attr(x, "burnin"), sep = "")
+        if (!is.na(attr(x, "thin")))
+            cat(", thin: ", attr(x, "thin"), sep = "")
     }
     cat("\nRestricted:", attr(x$x, "is.strat"), "\nFixed margins:", attr(x$x, "fixedmar"))
     if (!is.na(attr(x$x, "shuffle"))) {