[Vegan-commits] r919 - in pkg/vegan: R inst man

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

Author: jarioksa
Date: 2009-08-12 18:40:59 +0200 (Wed, 12 Aug 2009)
New Revision: 919

Modified:
   pkg/vegan/R/specaccum.R
   pkg/vegan/R/specpool.R
   pkg/vegan/R/specpool2vect.R
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/specaccum.Rd
   pkg/vegan/man/specpool.Rd
Log:
specpool & friends: (almost) consistent naming of indices in all lower case

Modified: pkg/vegan/R/specaccum.R
===================================================================
--- pkg/vegan/R/specaccum.R	2009-08-12 16:23:46 UTC (rev 918)
+++ pkg/vegan/R/specaccum.R	2009-08-12 16:40:59 UTC (rev 919)
@@ -1,6 +1,6 @@
 `specaccum` <-
     function (comm, method = "exact", permutations = 100, conditioned=TRUE,
-              gamma="Jack.1", ...)
+              gamma="jack1", ...)
 {
     x <- comm
     x <- as.matrix(x)

Modified: pkg/vegan/R/specpool.R
===================================================================
--- pkg/vegan/R/specpool.R	2009-08-12 16:23:46 UTC (rev 918)
+++ pkg/vegan/R/specpool.R	2009-08-12 16:40:59 UTC (rev 919)
@@ -48,9 +48,9 @@
         Zp <- (crossprod(X == 0)/n)^n - outer(pn, pn, "*")
         var.boot[is] <- sum(pn * (1 - pn)) + 2 * sum(Zp[lower.tri(Zp)])
     }
-    out <- list(Species = S, Chao = chao,  Chao.SE = sqrt(var.chao), 
-                Jack.1 = jack.1, Jack1.SE = sqrt(var.jack1), Jack.2 = jack.2, 
-                Boot = bootS, Boot.SE = sqrt(var.boot), n = as.vector(groups))
+    out <- list(Species = S, chao = chao,  chao.se = sqrt(var.chao), 
+                jack1 = jack.1, jack1.se = sqrt(var.jack1), jack2 = jack.2, 
+                boot = bootS, boot.se = sqrt(var.boot), n = as.vector(groups))
     out <- as.data.frame(out)
     attr(out, "pool") <- pool
     out

Modified: pkg/vegan/R/specpool2vect.R
===================================================================
--- pkg/vegan/R/specpool2vect.R	2009-08-12 16:23:46 UTC (rev 918)
+++ pkg/vegan/R/specpool2vect.R	2009-08-12 16:40:59 UTC (rev 919)
@@ -1,5 +1,5 @@
 "specpool2vect" <-
-function(X, index = c("Jack.1","Jack.2", "Chao", "Boot", "Species"))
+function(X, index = c("jack1","jack2", "chao", "boot", "Species"))
 {
     pool <- attr(X, "pool")
     index <- match.arg(index)

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2009-08-12 16:23:46 UTC (rev 918)
+++ pkg/vegan/inst/ChangeLog	2009-08-12 16:40:59 UTC (rev 919)
@@ -6,8 +6,10 @@
 
 	* poolaccum: new function to find the extrapolated richness
 	values (or specpool() estimates) for random accumulation of
-	sites (with summary and plot methods). Arguments (indices) still
-	need consistent naming.
+	sites (with summary and plot methods). 
+
+	* specaccum, specpool, specpool2vect and friends: index names are
+	now all lower-case.
 	
 Version 1.16-22 (closed August 11, 2009)
 

Modified: pkg/vegan/man/specaccum.Rd
===================================================================
--- pkg/vegan/man/specaccum.Rd	2009-08-12 16:23:46 UTC (rev 918)
+++ pkg/vegan/man/specaccum.Rd	2009-08-12 16:40:59 UTC (rev 919)
@@ -13,7 +13,7 @@
 }
 \usage{
 specaccum(comm, method = "exact", permutations = 100,
-          conditioned =TRUE, gamma = "Jack.1",  ...)
+          conditioned =TRUE, gamma = "jack1",  ...)
 \method{plot}{specaccum}(x, add = FALSE, ci = 2, ci.type = c("bar", "line", "polygon"), 
     col = par("fg"), ci.col = col, ci.lty = 1, xlab = "Sites", 
     ylab = x$method, ylim, ...)

Modified: pkg/vegan/man/specpool.Rd
===================================================================
--- pkg/vegan/man/specpool.Rd	2009-08-12 16:23:46 UTC (rev 918)
+++ pkg/vegan/man/specpool.Rd	2009-08-12 16:40:59 UTC (rev 919)
@@ -20,7 +20,7 @@
 \usage{
 specpool(x, pool)
 estimateR(x, ...)
-specpool2vect(X, index = c("Jack.1","Jack.2", "Chao", "Boot","Species"))
+specpool2vect(X, index = c("jack1","jack2", "chao", "boot","Species"))
 poolaccum(x, permutations = 100, minsize = 3)
 \method{summary}{poolaccum}(object, display, alpha = 0.05, ...)
 \method{plot}{poolaccum}(x, alpha = 0.05, type = c("l","g"), ...)