[Vegan-commits] r1298 - in pkg/gravy: R inst man

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

Author: jarioksa
Date: 2010-09-03 08:47:15 +0200 (Fri, 03 Sep 2010)
New Revision: 1298

Modified:
   pkg/gravy/R/HOF.default.R
   pkg/gravy/R/residuals.HOF.R
   pkg/gravy/inst/ChangeLog
   pkg/gravy/man/HOF.Rd
Log:
HOF returns 'family' & residuals gain type 'pearson'

Modified: pkg/gravy/R/HOF.default.R
===================================================================
--- pkg/gravy/R/HOF.default.R	2010-09-02 13:28:55 UTC (rev 1297)
+++ pkg/gravy/R/HOF.default.R	2010-09-03 06:47:15 UTC (rev 1298)
@@ -14,9 +14,10 @@
         dev <- sum(dev.resids(y, mu, wt))
         aic(y, n, mu, wt, dev)/2
     }
-    aic <- family()$aic
-    dev.resids <- family()$dev.resids
-    famname <- family()$family
+    fam <- eval(family())
+    aic <- fam$aic
+    dev.resids <- fam$dev.resids
+    famname <- fam$family
     if (!(famname %in% c("binomial", "gaussian", "poisson")))
         stop("Allowed familes: binomial, gaussian, poisson")
     div <- if(famname == "binomial") M else  1
@@ -73,7 +74,7 @@
                    I = I.res)
     out <- list(call = match.call(), x = x.orig, y = spec, x.name = x.name, 
                 y.name = y.name, range = x.range, M = M, nobs = nobs, 
-                models = models)
+                models = models, family = fam)
     class(out) <- "HOF"
     out
 }

Modified: pkg/gravy/R/residuals.HOF.R
===================================================================
--- pkg/gravy/R/residuals.HOF.R	2010-09-02 13:28:55 UTC (rev 1297)
+++ pkg/gravy/R/residuals.HOF.R	2010-09-03 06:47:15 UTC (rev 1298)
@@ -1,14 +1,21 @@
 `residuals.HOF` <-
-    function(object, type = c("deviance", "working", "response"), model, ...)
+    function(object,
+             type = c("deviance", "working", "response", "pearson"),
+             model, ...)
 {
     type <- match.arg(type)
     y <- object$y
+    V <- object$family$variance
+    M <- object$M
+    if (length(M) == 1)
+        M <- rep(M, length(y))
     mu <- sapply(object$models, fitted)
     r <- sapply(object$models, residuals)
     res <- switch(type,
                   deviance = ifelse(sweep(mu, 1, y, "<"), sqrt(r), -sqrt(r)),
                   working = r,
-                  response = -sweep(mu, 1, y, "-"))
+                  response = -sweep(mu, 1, y, "-"),
+                  pearson = -sweep(mu, 1, y, "-")/V(sweep(mu, 1, M, "/")))
     if (!missing(model))
         res <- res[, model]
     res

Modified: pkg/gravy/inst/ChangeLog
===================================================================
--- pkg/gravy/inst/ChangeLog	2010-09-02 13:28:55 UTC (rev 1297)
+++ pkg/gravy/inst/ChangeLog	2010-09-03 06:47:15 UTC (rev 1298)
@@ -1,7 +1,7 @@
 Version 0.1-3 September 2, 2010
-	* HOF: gained residuals() method with (useful) alternatives 'type
-	= "deviance"' and 'type = "response"' plue (useless) 'type =
-	"working"'. 
+	* HOF: gained residuals() method with (useful) 'type's "deviance",
+	"response" and "pearson" plus (useless) 'type = "working"'.
+	* HOF: returns 'family' object.
 Version 0.1-2 March 18, 2010
 	* ssHOF: HOF gave unnecesarry warnings when used with non-integer
 	data. 

Modified: pkg/gravy/man/HOF.Rd
===================================================================
--- pkg/gravy/man/HOF.Rd	2010-09-02 13:28:55 UTC (rev 1297)
+++ pkg/gravy/man/HOF.Rd	2010-09-03 06:47:15 UTC (rev 1298)
@@ -27,8 +27,8 @@
 \method{plot}{HOF}(x, ...)
 \method{plot}{HOF.frame}(x, level = 0.95, test ="F", species, ...) 
 \method{fitted}{HOF}(object, model, ...)
-\method{residuals}{HOF}(object, type = c("deviance", "working", "response"), 
-    model, ...)
+\method{residuals}{HOF}(object, type = c("deviance", "working",
+  "response", "pearson"), model, ...)
 \method{predict}{HOF}(object, newdata, model, ...)
 \method{GaussPara}{HOF}(resp, model, ...)
 }
@@ -48,7 +48,7 @@
   \item{test}{Test for model selection. Alternatives are \code{"F"},
     \code{"Chisq"}, \code{"AIC"}, \code{"BIC"}. }
   \item{type}{the type of residuals which should be returned (see
-    \code{\link{predict.glm}}).}
+    \code{\link{residuals.glm}}).}
   \item{species}{Names of the species displayed in graphs.}
   \item{x, object}{An object from \code{HOF(spec, \dots)}.}
   \item{newdata}{Vector of gradient values for prediction.}