[Mboost-commits] r729 - in pkg/mboostPatch: . tests vignettes

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

Author: thothorn
Date: 2013-09-03 20:59:14 +0200 (Tue, 03 Sep 2013)
New Revision: 729

Modified:
   pkg/mboostPatch/DESCRIPTION
   pkg/mboostPatch/tests/regtest-glmboost.R
   pkg/mboostPatch/vignettes/SurvivalEnsembles.Rnw
Log:
ipred -> TH.data

Modified: pkg/mboostPatch/DESCRIPTION
===================================================================
--- pkg/mboostPatch/DESCRIPTION	2013-09-03 18:58:32 UTC (rev 728)
+++ pkg/mboostPatch/DESCRIPTION	2013-09-03 18:59:14 UTC (rev 729)
@@ -17,7 +17,7 @@
   and interaction models to potentially high-dimensional data.
 Depends: R (>= 2.14.0), methods, stats, parallel
 Imports: Matrix, survival, splines, lattice
-Suggests: party (>= 1.0-3), ipred, MASS, fields,
+Suggests: party (>= 1.0-3), TH.data, MASS, fields,
   BayesX, gbm, mlbench, RColorBrewer, rpart (>= 4.0-3)
 LazyData: yes
 License: GPL-2

Modified: pkg/mboostPatch/tests/regtest-glmboost.R
===================================================================
--- pkg/mboostPatch/tests/regtest-glmboost.R	2013-09-03 18:58:32 UTC (rev 728)
+++ pkg/mboostPatch/tests/regtest-glmboost.R	2013-09-03 18:59:14 UTC (rev 729)
@@ -327,7 +327,7 @@
 coef(mod2, off2int = TRUE)
 stopifnot(all.equal(round(coef(mod), 2), round(coef(mod2, off2int = TRUE), 2)))
 
-data("GlaucomaM", package = "ipred")
+data("GlaucomaM", package = "TH.data")
 coef(mod3 <- glm(Class ~ varg, data = GlaucomaM, family = binomial(link = "probit")))
 coef(mod4 <- glmboost(Class ~ varg, data = GlaucomaM, family = Binomial(link = "probit"))[1000])
 stopifnot(all.equal(round(coef(mod3), 3), round(coef(mod4, off2int = TRUE), 3)))

Modified: pkg/mboostPatch/vignettes/SurvivalEnsembles.Rnw
===================================================================
--- pkg/mboostPatch/vignettes/SurvivalEnsembles.Rnw	2013-09-03 18:58:32 UTC (rev 728)
+++ pkg/mboostPatch/vignettes/SurvivalEnsembles.Rnw	2013-09-03 18:59:14 UTC (rev 729)
@@ -11,7 +11,7 @@
 %%\usepackage{Sweave}
 
 %%\VignetteIndexEntry{Survival Ensembles}
-%%\VignetteDepends{mboost, survival, rpart, ipred}
+%%\VignetteDepends{mboost, survival, rpart, TH.data}
 
 \newcommand{\Rpackage}[1]{{\normalfont\fontseries{b}\selectfont #1}}
 \newcommand{\Robject}[1]{\texttt{#1}}
@@ -100,10 +100,12 @@
 
 <<setup, echo = FALSE, results = hide>>=
 source("setup.R")
-if (!require("ipred"))
-    stop("cannot attach package ", sQuote("ipred"))
+if (!require("TH.data"))
+    stop("cannot attach package ", sQuote("TH.data"))
 if (!require("rpart"))
     stop("cannot attach package ", sQuote("rpart"))
+if (!require("survival"))
+    stop("cannot attach package ", sQuote("survival"))
 if (!require("party"))
     stop("cannot attach package ", sQuote("party"))
 
@@ -226,7 +228,7 @@
 Compute IPC weights and set up learning sample:
 <<GBSG2-dpp, echo = TRUE>>=
 ### attach data
-data("GBSG2", package = "ipred")
+data("GBSG2", package = "TH.data")
 
 ### IPC weights
 GBSG2w <- IPCweights(Surv(GBSG2$time, GBSG2$cens))