[Mboost-commits] r731 - / pkg/mboostDevel pkg/mboostDevel/inst pkg/mboostDevel/tests pkg/mboostDevel/vignettes pkg/mboostPatch/inst pkg/mboostPatch/tests

noreply at r-forge.r-project.org noreply at r-forge.r-project.org
Thu Sep 5 16:59:24 CEST 2013 

Author: hofner
Date: 2013-09-05 16:59:24 +0200 (Thu, 05 Sep 2013)
New Revision: 731

Modified:
   pkg/mboostDevel/DESCRIPTION
   pkg/mboostDevel/inst/CHANGES
   pkg/mboostDevel/tests/regtest-gamboost.R
   pkg/mboostDevel/tests/regtest-glmboost.R
   pkg/mboostDevel/vignettes/SurvivalEnsembles.Rnw
   pkg/mboostPatch/inst/CHANGES
   pkg/mboostPatch/tests/regtest-gamboost.R
   pkg/mboostPatch/tests/regtest-glmboost.R
   svn_release.txt
Log:
- also use TH.data in mboostDevel (dependenciy on ipred removed)


Modified: pkg/mboostDevel/DESCRIPTION
===================================================================
--- pkg/mboostDevel/DESCRIPTION	2013-09-05 14:16:13 UTC (rev 730)
+++ pkg/mboostDevel/DESCRIPTION	2013-09-05 14:59:24 UTC (rev 731)
@@ -16,8 +16,8 @@
   trees as base-learners for fitting generalized linear, additive
   and interaction models to potentially high-dimensional data.
 Depends: R (>= 2.14.0), methods, stats, parallel
-Imports: Matrix, survival, splines, lattice, nnls
-Suggests: party (>= 1.0-3), ipred, MASS, fields, BayesX, gbm, mlbench,
+Imports: Matrix, survival, splines, lattice, nnls, survival
+Suggests: party (>= 1.0-3), TH.data, MASS, fields, BayesX, gbm, mlbench,
         RColorBrewer, rpart (>= 4.0-3)
 LazyData: yes
 License: GPL-2

Modified: pkg/mboostDevel/inst/CHANGES
===================================================================
--- pkg/mboostDevel/inst/CHANGES	2013-09-05 14:16:13 UTC (rev 730)
+++ pkg/mboostDevel/inst/CHANGES	2013-09-05 14:59:24 UTC (rev 731)
@@ -1,6 +1,9 @@
 
                 CHANGES in `mboost' VERSION 2.3-0 (2013-XX-XX)
 
+  o  stabsel was recoded and now uses different terminology and a better
+     tested code base
+
   o  new replacement function mstop<- as an alternative to <mboost>[i]
      (suggested by Achim Zeileis).
 

Modified: pkg/mboostDevel/tests/regtest-gamboost.R
===================================================================
--- pkg/mboostDevel/tests/regtest-gamboost.R	2013-09-05 14:16:13 UTC (rev 730)
+++ pkg/mboostDevel/tests/regtest-gamboost.R	2013-09-05 14:59:24 UTC (rev 731)
@@ -1,5 +1,6 @@
 
 require("mboostDevel")
+require("survival")
 
 set.seed(290875)
 

Modified: pkg/mboostDevel/tests/regtest-glmboost.R
===================================================================
--- pkg/mboostDevel/tests/regtest-glmboost.R	2013-09-05 14:16:13 UTC (rev 730)
+++ pkg/mboostDevel/tests/regtest-glmboost.R	2013-09-05 14:59:24 UTC (rev 731)
@@ -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/mboostDevel/vignettes/SurvivalEnsembles.Rnw
===================================================================
--- pkg/mboostDevel/vignettes/SurvivalEnsembles.Rnw	2013-09-05 14:16:13 UTC (rev 730)
+++ pkg/mboostDevel/vignettes/SurvivalEnsembles.Rnw	2013-09-05 14:59:24 UTC (rev 731)
@@ -11,7 +11,7 @@
 %%\usepackage{Sweave}
 
 %%\VignetteIndexEntry{Survival Ensembles}
-%%\VignetteDepends{mboostDevel, survival, rpart, ipred}
+%%\VignetteDepends{mboostDevel, 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))

Modified: pkg/mboostPatch/inst/CHANGES
===================================================================
--- pkg/mboostPatch/inst/CHANGES	2013-09-05 14:16:13 UTC (rev 730)
+++ pkg/mboostPatch/inst/CHANGES	2013-09-05 14:59:24 UTC (rev 731)
@@ -1,8 +1,5 @@
                 CHANGES in `mboost' VERSION 2.2-3 (2013-XX-XX, rYYY)
 
-  o  stabsel was recoded and now uses different terminology and a better
-     tested code base
-
   o  fixed bugs in survival families:
      -  offset in all survival families was based on max(survtime) instead
      	of max(log(survtime));

Modified: pkg/mboostPatch/tests/regtest-gamboost.R
===================================================================
--- pkg/mboostPatch/tests/regtest-gamboost.R	2013-09-05 14:16:13 UTC (rev 730)
+++ pkg/mboostPatch/tests/regtest-gamboost.R	2013-09-05 14:59:24 UTC (rev 731)
@@ -139,6 +139,7 @@
 stopifnot(max(abs(predict(mod1, newdata = tmp) - predict(mod2, newdata = tmp)))  < sqrt(.Machine$double.eps))
 
 ## Cox model
+
 fit2 <- gamboost(Surv(futime, fustat) ~ bbs(age) +
     bols(resid.ds) + bols(rx) + bols(ecog.ps), data = ovarian,
     family = CoxPH(), control = boost_control(mstop = 1000))

Modified: pkg/mboostPatch/tests/regtest-glmboost.R
===================================================================
--- pkg/mboostPatch/tests/regtest-glmboost.R	2013-09-05 14:16:13 UTC (rev 730)
+++ pkg/mboostPatch/tests/regtest-glmboost.R	2013-09-05 14:59:24 UTC (rev 731)
@@ -38,7 +38,7 @@
 mydf.lm <- lm(y ~ ., data = mydf)
 
 ### compare coefficients
-which(abs(coef(mydf.lm)) < abs(coef(mydf.gb[mstop(aic)])))
+which(abs(coef(mydf.lm, which = "")) < abs(coef(mydf.gb[mstop(aic)], which = "")))
 
 #### check boosting hat matrix and subsetting / predict
 stopifnot(isTRUE(all.equal(drop(attr(ht, "hatmatrix") %*% mydf$y),

Modified: svn_release.txt
===================================================================
--- svn_release.txt	2013-09-05 14:16:13 UTC (rev 730)
+++ svn_release.txt	2013-09-05 14:59:24 UTC (rev 731)
@@ -155,7 +155,8 @@
     ../relative/path/to/R-devel/bin/R
 
   Run
-    install.packages(c("party", "TH.data", "fields", "BayesX", "gbm", "mlbench", "RColorBrewer"))
+    install.packages(c("party", "TH.data", "fields", "BayesX", "gbm",
+                       "mlbench", "RColorBrewer", "mfp", "randomForest"))
 
   Quite R and run
    ../relative/path/to/R-devel/bin/R CMD check --as-cran mboost_XXX.tar.gz

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