[Rcpp-commits] r3065 - in pkg/RcppGSL: . R man src

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

Author: dmbates
Date: 2011-06-15 00:34:50 +0200 (Wed, 15 Jun 2011)
New Revision: 3065

Modified:
   pkg/RcppGSL/DESCRIPTION
   pkg/RcppGSL/R/fastLm.R
   pkg/RcppGSL/man/fastLm.Rd
   pkg/RcppGSL/src/fastLm.cpp
Log:
Change order of arguments in fastLm.cpp and fastLm.R and documentation.  New version.


Modified: pkg/RcppGSL/DESCRIPTION
===================================================================
--- pkg/RcppGSL/DESCRIPTION	2011-06-14 20:18:55 UTC (rev 3064)
+++ pkg/RcppGSL/DESCRIPTION	2011-06-14 22:34:50 UTC (rev 3065)
@@ -1,7 +1,7 @@
 Package: RcppGSL
 Type: Package
 Title: Rcpp integration for GNU GSL vectors and matrices
-Version: 0.1.1.1
+Version: 0.1.2
 Date: $Date$
 Author: Romain Francois and Dirk Eddelbuettel
 Maintainer: Dirk Eddelbuettel and Romain Francois <RomainAndDirk at r-enthusiasts.com>

Modified: pkg/RcppGSL/R/fastLm.R
===================================================================
--- pkg/RcppGSL/R/fastLm.R	2011-06-14 20:18:55 UTC (rev 3064)
+++ pkg/RcppGSL/R/fastLm.R	2011-06-14 22:34:50 UTC (rev 3065)
@@ -17,25 +17,25 @@
 ## You should have received a copy of the GNU General Public License
 ## along with RcppGSL.  If not, see <http://www.gnu.org/licenses/>.
 
-fastLmPure <- function(y, X) {
+fastLmPure <- function(X, y) {
 
     stopifnot(is.matrix(X))
     stopifnot(nrow(y)==nrow(X))
 
-    res <- .Call("fastLm", y, X, package="RcppGSL")
+    res <- .Call("fastLm", X, y, package="RcppGSL")
 }
 
 fastLm <- function(x, ...) UseMethod("fastLm")
 
-fastLm.default <- function(x, y, ...) {
+fastLm.default <- function(X, y, ...) {
 
-    x <- as.matrix(x)
+    X <- as.matrix(X)
     y <- as.numeric(y)
 
-    res <- fastLmPure(y, x)
-    names(res$coefficients) <- colnames(x)
+    res <- fastLmPure(X, y)
+    names(res$coefficients) <- colnames(X)
 
-    res$fitted.values <- as.vector(x %*% res$coefficients)
+    res$fitted.values <- as.vector(X %*% res$coefficients)
     res$residuals <- y - res$fitted.values
     res$call <- match.call()
 
@@ -60,8 +60,8 @@
                  p.value = 2*pt(-abs(tval), df=object$df))
 
     # why do I need this here?
-    rownames(TAB) <- names(object$coefficients)
-    colnames(TAB) <- c("Estimate", "StdErr", "t.value", "p.value")
+#    rownames(TAB) <- names(object$coefficients)
+#    colnames(TAB) <- c("Estimate", "StdErr", "t.value", "p.value")
 
     ## cf src/stats/R/lm.R and case with no weights and an intercept
     f <- object$fitted.values
@@ -94,10 +94,10 @@
 
 fastLm.formula <- function(formula, data=list(), ...) {
     mf <- model.frame(formula=formula, data=data)
-    x <- model.matrix(attr(mf, "terms"), data=mf)
+    X <- model.matrix(attr(mf, "terms"), data=mf)
     y <- model.response(mf)
 
-    res <- fastLm.default(x, y, ...)
+    res <- fastLm.default(X, y, ...)
     res$call <- match.call()
     res$formula <- formula
     res

Modified: pkg/RcppGSL/man/fastLm.Rd
===================================================================
--- pkg/RcppGSL/man/fastLm.Rd	2011-06-14 20:18:55 UTC (rev 3064)
+++ pkg/RcppGSL/man/fastLm.Rd	2011-06-14 22:34:50 UTC (rev 3065)
@@ -10,16 +10,15 @@
   function of the \code{GNU GSL} library.
 }
 \usage{
-fastLmPure(y, X)
+fastLmPure(X, y)
 
-fastLm(x, \dots)
-\method{fastLm}{default}(x, y, \dots)
+fastLm(X, \dots)
+\method{fastLm}{default}(X, y, \dots)
 \method{fastLm}{formula}(formula, data = list(), \dots)
 }
 \arguments{
   \item{y}{a vector containing the explained variable.}
-  \item{X}{a data.frame or matrix containing the explanatory variables.}
-  \item{x}{a numeric design matrix for the model.}
+  \item{X}{a model matrix.}
   \item{formula}{a symbolic description of the model to be fit.}
   \item{data}{an optional data frame containing the variables in the model.}
   \item{\ldots}{not used}

Modified: pkg/RcppGSL/src/fastLm.cpp
===================================================================
--- pkg/RcppGSL/src/fastLm.cpp	2011-06-14 20:18:55 UTC (rev 3064)
+++ pkg/RcppGSL/src/fastLm.cpp	2011-06-14 22:34:50 UTC (rev 3065)
@@ -24,7 +24,7 @@
 #include <gsl/gsl_multifit.h>
 #include <cmath>
 
-extern "C" SEXP fastLm(SEXP ys, SEXP Xs) {
+extern "C" SEXP fastLm(SEXP Xs, SEXP ys) {
 
     try {
 	
@@ -51,8 +51,8 @@
 		std::transform( std_err.begin(), std_err.end(), std_err.begin(), sqrt );
 
 		Rcpp::List res = Rcpp::List::create(Rcpp::Named("coefficients") = coef, 
-											Rcpp::Named("stderr") = std_err,
-											Rcpp::Named("df") = n - k);
+											Rcpp::Named("stderr")       = std_err,
+											Rcpp::Named("df.residual")  = n - k);
 
 		// free all the GSL vectors and matrices -- as these are really C data structures
 		// we cannot take advantage of automatic memory management