[Vegan-commits] r1038 - in pkg/vegan: R inst man

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

Author: jarioksa
Date: 2009-10-07 19:55:56 +0200 (Wed, 07 Oct 2009)
New Revision: 1038

Added:
   pkg/vegan/R/model.frame.cca.R
   pkg/vegan/R/model.matrix.cca.R
Modified:
   pkg/vegan/inst/ChangeLog
   pkg/vegan/man/cca.Rd
Log:
add model.frame.cca & model.matrix.cca

Added: pkg/vegan/R/model.frame.cca.R
===================================================================
--- pkg/vegan/R/model.frame.cca.R	                        (rev 0)
+++ pkg/vegan/R/model.frame.cca.R	2009-10-07 17:55:56 UTC (rev 1038)
@@ -0,0 +1,15 @@
+`model.frame.cca` <-
+    function (formula, ...) 
+{
+    call <- formula$call
+    m <- match(c("formula", "data", "na.action", "subset"), names(call), 
+        0)
+    call <- call[c(1, m)]
+    call[[1]] <- as.name("ordiParseFormula")
+    out <- eval(call, parent.frame())
+    mf <- out$modelframe
+    attr(mf, "terms") <- out$terms.expand
+    if (!is.null(out$na.action)) 
+        attr(mf, "na.action") <- out$na.action
+    mf
+}

Added: pkg/vegan/R/model.matrix.cca.R
===================================================================
--- pkg/vegan/R/model.matrix.cca.R	                        (rev 0)
+++ pkg/vegan/R/model.matrix.cca.R	2009-10-07 17:55:56 UTC (rev 1038)
@@ -0,0 +1,18 @@
+`model.matrix.cca` <-
+    function (formula, ...) 
+{
+    call <- formula$call
+    m <- match(c("formula", "data", "na.action", "subset"), names(call), 
+        0)
+    call <- call[c(1, m)]
+    call[[1]] <- as.name("ordiParseFormula")
+    out <- eval(call, parent.frame())[c("Z", "Y")]
+    m <- list()
+    if (!is.null(out$Z))
+        m$Conditions <- out$Z
+    if (!is.null(out$Y))
+        m$Constraints <- out$Y
+    if (length(m) == 1)
+        m <- m[[1]]
+    m
+}

Modified: pkg/vegan/inst/ChangeLog
===================================================================
--- pkg/vegan/inst/ChangeLog	2009-10-07 08:25:51 UTC (rev 1037)
+++ pkg/vegan/inst/ChangeLog	2009-10-07 17:55:56 UTC (rev 1038)
@@ -4,6 +4,12 @@
 
 Version 1.16-31 (opened October 3, 2009)
 
+	* model.frame.cca, model.matrix.cca: new support functions to
+	reconstitute the model frame and model matrix (or  a list of
+	condition and constrain model matrices) from a cca/rda/capscale
+	result object. Not yet documentd (don't know where?), but alias is
+	in cca.Rd.
+
 	* constrained ordination (cca, rda, capscale) did not analyse
 	constrained component in model like cca(varespec ~ Al:P +
 	Condition(Al + P)) or in constrained interaction terms if the

Modified: pkg/vegan/man/cca.Rd
===================================================================
--- pkg/vegan/man/cca.Rd	2009-10-07 08:25:51 UTC (rev 1037)
+++ pkg/vegan/man/cca.Rd	2009-10-07 17:55:56 UTC (rev 1038)
@@ -6,6 +6,8 @@
 \alias{rda}
 \alias{rda.default}
 \alias{rda.formula}
+\alias{model.frame.cca} % <- Move to a better help page!!
+\alias{model.matrix.cca} % <- Move to a better help page!
 \concept{ordination}
 
 \title{ [Partial] [Constrained] Correspondence Analysis and Redundancy