[Vegan-commits] r2367 - in pkg/vegan: R tests/Examples

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

Author: jarioksa
Date: 2013-01-14 08:57:24 +0100 (Mon, 14 Jan 2013)
New Revision: 2367

Modified:
   pkg/vegan/R/print.mantel.R
   pkg/vegan/R/summary.anosim.R
   pkg/vegan/tests/Examples/vegan-Ex.Rout.save
Log:
rectify misleading text in printed output (null, not confidence limit in anosim, mantel)

Modified: pkg/vegan/R/print.mantel.R
===================================================================
--- pkg/vegan/R/print.mantel.R	2013-01-13 19:24:26 UTC (rev 2366)
+++ pkg/vegan/R/print.mantel.R	2013-01-14 07:57:24 UTC (rev 2367)
@@ -1,4 +1,4 @@
-"print.mantel" <-
+`print.mantel` <-
   function (x, digits = max(3, getOption("digits") - 3), ...) 
 {
   cat("\n")
@@ -14,7 +14,7 @@
     cat("      Significance:", format.pval(x$signif), 
         "\n\n")
     out <- quantile(x$perm, c(0.9, 0.95, 0.975, 0.99))
-    cat("Empirical upper confidence limits of r:\n")
+    cat("Upper quantiles of permutations (null model):\n")
     print(out, digits = 3)
     cat("\nBased on", nperm, "permutations")
     if (!is.null(x$strata)) 

Modified: pkg/vegan/R/summary.anosim.R
===================================================================
--- pkg/vegan/R/summary.anosim.R	2013-01-13 19:24:26 UTC (rev 2366)
+++ pkg/vegan/R/summary.anosim.R	2013-01-14 07:57:24 UTC (rev 2367)
@@ -1,10 +1,10 @@
-"summary.anosim" <-
+`summary.anosim` <-
 function (object, ...) 
 {
    print(object)
    if (object$permutations) {
      out <- quantile(object$perm, c(0.9, 0.95, 0.975, 0.99))
-     cat("Empirical upper confidence limits of R:\n")
+     cat("Upper quantiles of permutations (null model):\n")
      print(out, digits=3)
    }
    cat("\n")

Modified: pkg/vegan/tests/Examples/vegan-Ex.Rout.save
===================================================================
--- pkg/vegan/tests/Examples/vegan-Ex.Rout.save	2013-01-13 19:24:26 UTC (rev 2366)
+++ pkg/vegan/tests/Examples/vegan-Ex.Rout.save	2013-01-14 07:57:24 UTC (rev 2367)
@@ -1,5 +1,5 @@
 
-R Under development (unstable) (2013-01-09 r61595) -- "Unsuffered Consequences"
+R Under development (unstable) (2013-01-13 r61644) -- "Unsuffered Consequences"
 Copyright (C) 2013 The R Foundation for Statistical Computing
 ISBN 3-900051-07-0
 Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -161,7 +161,7 @@
 
 Formula:
 y ~ poly(x1, 1) + poly(x2, 1)
-<environment: 0x2ca4338>
+<environment: 0x3df5138>
 Total model degrees of freedom 3 
 
 GCV score: 0.04278782
@@ -752,7 +752,7 @@
 
 Based on  999  permutations
 
-Empirical upper confidence limits of R:
+Upper quantiles of permutations (null model):
   90%   95% 97.5%   99% 
 0.116 0.160 0.203 0.233 
 
@@ -3421,7 +3421,7 @@
 Mantel statistic r: 0.3047 
       Significance: 0.001 
 
-Empirical upper confidence limits of r:
+Upper quantiles of permutations (null model):
   90%   95% 97.5%   99% 
 0.107 0.145 0.169 0.200 
 
@@ -3437,7 +3437,7 @@
 Mantel statistic r: 0.2838 
       Significance: 0.001 
 
-Empirical upper confidence limits of r:
+Upper quantiles of permutations (null model):
   90%   95% 97.5%   99% 
 0.108 0.141 0.169 0.196 
 
@@ -4912,7 +4912,7 @@
 
 Formula:
 y ~ s(x1, x2, k = knots)
-<environment: 0x94283c0>
+<environment: 0xb6d08b8>
 
 Estimated degrees of freedom:
 6.45  total = 7.45 
@@ -4928,7 +4928,7 @@
 
 Formula:
 y ~ s(x1, x2, k = knots)
-<environment: 0x9c4f678>
+<environment: 0xb45d698>
 
 Estimated degrees of freedom:
 6.12  total = 7.12 
@@ -5088,7 +5088,7 @@
 
 Formula:
 y ~ s(x1, x2, k = knots)
-<environment: 0x8bcd578>
+<environment: 0x926fa88>
 
 Estimated degrees of freedom:
 8.93  total = 9.93 
@@ -5101,7 +5101,7 @@
 
 Formula:
 y ~ s(x1, x2, k = knots)
-<environment: 0x9370d28>
+<environment: 0xb4d7d30>
 
 Estimated degrees of freedom:
 7.75  total = 8.75 
@@ -5114,7 +5114,7 @@
 
 Formula:
 y ~ s(x1, x2, k = knots)
-<environment: 0x9b14638>
+<environment: 0x9deafc8>
 
 Estimated degrees of freedom:
 8.9  total = 9.9 
@@ -7691,7 +7691,7 @@
 
 Formula:
 y ~ s(x1, x2, k = knots)
-<environment: 0x3ac4fa8>
+<environment: 0xb37bc20>
 
 Estimated degrees of freedom:
 2  total = 3 
@@ -8171,7 +8171,7 @@
 > ### * <FOOTER>
 > ###
 > cat("Time elapsed: ", proc.time() - get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed:  26.573 0.116 26.874 0 0 
+Time elapsed:  26.901 0.172 27.2 0 0 
 > grDevices::dev.off()
 null device 
           1