[Analogue-commits] r157 - in pkg: . R inst

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

Author: gsimpson
Date: 2010-01-18 20:04:17 +0100 (Mon, 18 Jan 2010)
New Revision: 157

Modified:
   pkg/DESCRIPTION
   pkg/R/fixUpTol.R
   pkg/R/wa.formula.R
   pkg/inst/ChangeLog
Log:
fix passing tolerance-related arguments from formula to default method in wa and correct a bug in argument matching within fixUpTol

Modified: pkg/DESCRIPTION
===================================================================
--- pkg/DESCRIPTION	2010-01-16 16:53:24 UTC (rev 156)
+++ pkg/DESCRIPTION	2010-01-18 19:04:17 UTC (rev 157)
@@ -1,7 +1,7 @@
 Package: analogue
 Type: Package
 Title: Analogue and weighted averaging methods for palaeoecology
-Version: 0.6-22
+Version: 0.6-23
 Date: $Date$
 Depends: R (>= 2.5.0), stats, graphics, vegan, lattice, MASS
 Author: Gavin L. Simpson, Jari Oksanen

Modified: pkg/R/fixUpTol.R
===================================================================
--- pkg/R/fixUpTol.R	2010-01-16 16:53:24 UTC (rev 156)
+++ pkg/R/fixUpTol.R	2010-01-18 19:04:17 UTC (rev 157)
@@ -1,7 +1,7 @@
 ## fix-up tolerances for use in TF computations
 fixUpTol <- function(tol, na.tol, small.tol, min.tol, f, env) {
     ## first missing tolerances
-    if(any(NA.TOL <- is.na(tol))) {
+    if(any(NA.TOL <- is.na(tol) | is.infinite(tol))) {
         tol[NA.TOL] <-
             switch(na.tol,
                    min = min(tol, na.rm = TRUE),
@@ -10,7 +10,6 @@
     }
     ## second, replace tol < min.tol
     if(!is.null(min.tol) && any(MIN.TOL <- tol < min.tol)) {
-        small.tol <- match.arg(small.tol)
         ## min.tol must be in or on extremesof range(env)
         if(min.tol < min(env) || min.tol > max(env))
             stop("'min.tol' must be >= min(env) and <= max(env)")

Modified: pkg/R/wa.formula.R
===================================================================
--- pkg/R/wa.formula.R	2010-01-16 16:53:24 UTC (rev 156)
+++ pkg/R/wa.formula.R	2010-01-18 19:04:17 UTC (rev 157)
@@ -28,7 +28,9 @@
     mt <- attr(mf, "terms")
     y <- model.response(mf, "numeric")
     x <- model.matrix(mt, mf)
-    res <- wa.default(x, y, deshrink = deshrink, tol.dw = tol.dw, ...)
+    res <- wa.default(x, y, deshrink = deshrink, tol.dw = tol.dw,
+                      na.tol = na.tol, small.tol = small.tol,
+                      min.tol = min.tol, f = f, ...)
     res$na.action <- attr(mf, "na.action")
     res$call <- .call
     if(model) {

Modified: pkg/inst/ChangeLog
===================================================================
--- pkg/inst/ChangeLog	2010-01-16 16:53:24 UTC (rev 156)
+++ pkg/inst/ChangeLog	2010-01-18 19:04:17 UTC (rev 157)
@@ -1,5 +1,19 @@
 analogue Change Log
 
+Version 0.6-23
+
+	* tran: 'rootroot' transformation was same as 'cuberoot' from
+	vhanges made in r140. Now fixed.
+
+	* wa: 'formula' method was not passing tolerance-related arguments
+	to default method. As such, the newer code to handle small
+	tolerance values was not being invoked when using the formula
+	interface to wa().
+
+	Code was also tidied a bit.
+
+	* fixUpTol: was inappropriately matching one of it's arguments.
+
 Version 0.6-22
 
 	* tran.formula: bug in my implementation of the standard