[Mboost-commits] r802 - in pkg/mboostDevel: man tests tests/Examples
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Oct 2 11:05:37 CEST 2014
Author: hofner
Date: 2014-10-02 11:05:36 +0200 (Thu, 02 Oct 2014)
New Revision: 802
Modified:
pkg/mboostDevel/man/confint.Rd
pkg/mboostDevel/tests/Examples/mboostDevel-Ex.Rout.save
pkg/mboostDevel/tests/birds_Biometrics.Rout.save
pkg/mboostDevel/tests/bugfixes.Rout.save
pkg/mboostDevel/tests/regtest-baselearner.Rout.save
pkg/mboostDevel/tests/regtest-blackboost.Rout.save
pkg/mboostDevel/tests/regtest-family.Rout.save
pkg/mboostDevel/tests/regtest-gamboost.Rout.save
pkg/mboostDevel/tests/regtest-glmboost.Rout.save
pkg/mboostDevel/tests/regtest-hatmatrix.Rout.save
pkg/mboostDevel/tests/regtest-inference.Rout.save
Log:
- Examples in confint are not tested as this takes too long
- Updated .Rout.save files
Modified: pkg/mboostDevel/man/confint.Rd
===================================================================
--- pkg/mboostDevel/man/confint.Rd 2014-10-02 07:37:30 UTC (rev 801)
+++ pkg/mboostDevel/man/confint.Rd 2014-10-02 09:05:36 UTC (rev 802)
@@ -131,6 +131,7 @@
\code{\link{mboost_methods}} for other methods.
}
\examples{
+\donttest{
### a simple linear example
set.seed(1907)
data <- data.frame(x1 = rnorm(100), x2 = rnorm(100),
@@ -151,7 +152,6 @@
## or print a subset (with point estimates):
print(CI, level = 0.8, pe = TRUE, which = "z")
-
### a simple smooth example
set.seed(1907)
data <- data.frame(x1 = rnorm(100), x2 = rnorm(100))
@@ -170,4 +170,5 @@
## level in the plot or lines function:
lines(CI_gam, which = 2, level = 0.8)
}
+}
\keyword{methods}
Modified: pkg/mboostDevel/tests/Examples/mboostDevel-Ex.Rout.save
===================================================================
--- pkg/mboostDevel/tests/Examples/mboostDevel-Ex.Rout.save 2014-10-02 07:37:30 UTC (rev 801)
+++ pkg/mboostDevel/tests/Examples/mboostDevel-Ex.Rout.save 2014-10-02 09:05:36 UTC (rev 802)
@@ -34,6 +34,7 @@
> ### * </HEADER>
> library('mboostDevel')
Loading required package: parallel
+Loading required package: stabs
This is mboostDevel 2.4-0. See ‘package?mboostDevel’ and the NEWS file
for a complete list of changes.
@@ -961,117 +962,9 @@
>
> ### ** Examples
>
-> ### a simple linear example
-> set.seed(1907)
-> data <- data.frame(x1 = rnorm(100), x2 = rnorm(100),
-+ z = factor(sample(1:3, 100, replace = TRUE)))
-> data$y <- rnorm(100, mean = data$x1 - data$x2 - 1 * (data$z == 2) +
-+ 1 * (data$z == 3), sd = 0.1)
-> linmod <- glmboost(y ~ x1 + x2 + z, data = data,
-+ control = boost_control(mstop = 200))
>
-> ## compute confidence interval from 10 samples. Usually one should use
-> ## at least 1000 samples.
-> CI <- confint(linmod, B = 10, level = 0.9)
-Warning in cvrisk.mboost(mod, folds = cv(model.weights(mod), B = B.mstop), :
- zero weights
-Warning in cvrisk.mboost(mod, folds = cv(model.weights(mod), B = B.mstop), :
- zero weights
-Warning in cvrisk.mboost(mod, folds = cv(model.weights(mod), B = B.mstop), :
- zero weights
-Warning in cvrisk.mboost(mod, folds = cv(model.weights(mod), B = B.mstop), :
- zero weights
-Warning in cvrisk.mboost(mod, folds = cv(model.weights(mod), B = B.mstop), :
- zero weights
-Warning in cvrisk.mboost(mod, folds = cv(model.weights(mod), B = B.mstop), :
- zero weights
-Warning in cvrisk.mboost(mod, folds = cv(model.weights(mod), B = B.mstop), :
- zero weights
-Warning in cvrisk.mboost(mod, folds = cv(model.weights(mod), B = B.mstop), :
- zero weights
-Warning in cvrisk.mboost(mod, folds = cv(model.weights(mod), B = B.mstop), :
- zero weights
-Warning in cvrisk.mboost(mod, folds = cv(model.weights(mod), B = B.mstop), :
- zero weights
-> CI
- Bootstrap Confidence Intervals
- 5% 95%
-(Intercept) -0.01975195 0.02598639
-x1 0.98986917 1.01853830
-x2 -1.00530226 -0.98158388
-z2 -1.04350674 -0.99290512
-z3 0.98234788 1.06652604
>
-> ## to compute a confidence interval for another level simply change the
-> ## level in the print function:
-> print(CI, level = 0.8)
- Bootstrap Confidence Intervals
- 10% 90%
-(Intercept) -0.01105303 0.01607163
-x1 0.99577904 1.01340240
-x2 -1.00234059 -0.98355672
-z2 -1.03767821 -0.99552711
-z3 0.98851355 1.04334685
-> ## or print a subset (with point estimates):
-> print(CI, level = 0.8, pe = TRUE, which = "z")
- Bootstrap Confidence Intervals
- beta 10% 90%
-z2 -1.016220 -1.0376782 -0.9955271
-z3 1.024731 0.9885135 1.0433468
>
->
-> ### a simple smooth example
-> set.seed(1907)
-> data <- data.frame(x1 = rnorm(100), x2 = rnorm(100))
-> data$y <- rnorm(100, mean = data$x1^2 - sin(data$x2), sd = 0.1)
-> gam <- gamboost(y ~ x1 + x2, data = data,
-+ control = boost_control(mstop = 200))
->
-> ## compute confidence interval from 10 samples. Usually one should use
-> ## at least 1000 samples.
-> CI_gam <- confint(gam, B = 10, level = 0.9)
-Start computing bootstrap confidence intervals...
-
-B = 1Warning in cvrisk.mboost(object = list(baselearner = list(`bbs(x1, df = dfbase)` = list( :
- zero weights
-
-B = 2Warning in cvrisk.mboost(object = list(baselearner = list(`bbs(x1, df = dfbase)` = list( :
- zero weights
-
-B = 3Warning in cvrisk.mboost(object = list(baselearner = list(`bbs(x1, df = dfbase)` = list( :
- zero weights
-
-B = 4Warning in cvrisk.mboost(object = list(baselearner = list(`bbs(x1, df = dfbase)` = list( :
- zero weights
-
-B = 5Warning in cvrisk.mboost(object = list(baselearner = list(`bbs(x1, df = dfbase)` = list( :
- zero weights
-
-B = 6Warning in cvrisk.mboost(object = list(baselearner = list(`bbs(x1, df = dfbase)` = list( :
- zero weights
-
-B = 7Warning in cvrisk.mboost(object = list(baselearner = list(`bbs(x1, df = dfbase)` = list( :
- zero weights
-
-B = 8Warning in cvrisk.mboost(object = list(baselearner = list(`bbs(x1, df = dfbase)` = list( :
- zero weights
-
-B = 9Warning in cvrisk.mboost(object = list(baselearner = list(`bbs(x1, df = dfbase)` = list( :
- zero weights
-
-B = 10Warning in cvrisk.mboost(object = list(baselearner = list(`bbs(x1, df = dfbase)` = list( :
- zero weights
-
->
-> par(mfrow = c(1, 2))
-> plot(CI_gam, which = 1)
-> plot(CI_gam, which = 2)
-> ## to compute a confidence interval for another level simply change the
-> ## level in the plot or lines function:
-> lines(CI_gam, which = 2, level = 0.8)
->
->
->
> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
> base::cat("confint", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> graphics::par(get("par.postscript", pos = 'CheckExEnv'))
@@ -1545,8 +1438,6 @@
>
> ### use stability selection for base-learner selection
> library("stabs")
-Note: the specification for class “boost_family” in package ‘mboost’ seems equivalent to one from package ‘mboostDevel’: not turning on duplicate class definitions for this class.
-Note: the specification for class “boost_family_glm” in package ‘mboost’ seems equivalent to one from package ‘mboostDevel’: not turning on duplicate class definitions for this class.
> ## fit a linear model
> # (as this is quicker; also possible with non-linear model from above)
> mod <- glmboost(DEXfat ~ ., data = bodyfat)
@@ -1578,9 +1469,9 @@
> graphics::par(get("par.postscript", pos = 'CheckExEnv'))
> cleanEx()
-detaching ‘package:stabs’, ‘package:party’, ‘package:modeltools’,
- ‘package:stats4’, ‘package:strucchange’, ‘package:sandwich’,
- ‘package:zoo’, ‘package:grid’
+detaching ‘package:party’, ‘package:modeltools’, ‘package:stats4’,
+ ‘package:strucchange’, ‘package:sandwich’, ‘package:zoo’,
+ ‘package:grid’
> nameEx("mboost_package")
> ### * mboost_package
@@ -1588,9 +1479,9 @@
> flush(stderr()); flush(stdout())
>
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
-> ### Name: mboostDevel-package
-> ### Title: mboostDevel: Model-Based Boosting
-> ### Aliases: mboostDevel-package
+> ### Name: mboost-package
+> ### Title: mboost: Model-Based Boosting
+> ### Aliases: mboost-package mboost_package package_mboost package-mboost
> ### Keywords: package smooth nonparametric models
>
> ### ** Examples
@@ -3248,6 +3139,67 @@
> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
> base::cat("methods", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
> cleanEx()
+> nameEx("stabsel")
+> ### * stabsel
+>
+> flush(stderr()); flush(stdout())
+>
+> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
+> ### Name: stabsel
+> ### Title: Stability Selection
+> ### Aliases: stabsel stabsel.mboost stabsel_parameters.mboost
+> ### Keywords: nonparametric
+>
+> ### ** Examples
+>
+> ## make data set available
+> data("bodyfat", package = "TH.data")
+> ## set seed
+> set.seed(1234)
+>
+> ### low-dimensional example
+> mod <- glmboost(DEXfat ~ ., data = bodyfat)
+>
+> ## compute cutoff ahead of running stabsel to see if it is a sensible
+> ## parameter choice.
+> ## p = ncol(bodyfat) - 1 (= Outcome) + 1 ( = Intercept)
+> stabsel_parameters(q = 3, PFER = 1, p = ncol(bodyfat) - 1 + 1,
++ sampling.type = "MB")
+Stability Selection without further assumptions
+Cutoff: 0.95; q: 3; PFER: 1
+> ## the same:
+> stabsel(mod, q = 3, PFER = 1, sampling.type = "MB", eval = FALSE)
+Stability Selection without further assumptions
+Cutoff: 0.95; q: 3; PFER: 1
+>
+> ## now run stability selection
+> (sbody <- stabsel(mod, q = 3, PFER = 1, sampling.type = "MB"))
+ Stability Selection without further assumptions
+
+Selected base-learners:
+hipcirc
+ 4
+
+Selection probabilities:
+ (Intercept) age elbowbreadth kneebreadth anthro3b anthro4
+ 0.00 0.00 0.00 0.01 0.11 0.17
+ anthro3c anthro3a waistcirc hipcirc
+ 0.18 0.60 0.93 1.00
+
+Cutoff: 0.95; q: 3; PFER: 1
+
+> opar <- par(mai = par("mai") * c(1, 1, 1, 2.7))
+> plot(sbody)
+> par(opar)
+>
+> plot(sbody, type = "maxsel", ymargin = 6)
+>
+>
+>
+> base::assign(".dptime", (proc.time() - get(".ptime", pos = "CheckExEnv")), pos = "CheckExEnv")
+> base::cat("stabsel", base::get(".format_ptime", pos = 'CheckExEnv')(get(".dptime", pos = "CheckExEnv")), "\n", file=base::get(".ExTimings", pos = 'CheckExEnv'), append=TRUE, sep="\t")
+> graphics::par(get("par.postscript", pos = 'CheckExEnv'))
+> cleanEx()
> nameEx("survFit")
> ### * survFit
>
@@ -3333,7 +3285,7 @@
> ###
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed: 17.527 0.998 35.294 26.941 1.832
+Time elapsed: 14.895 0.337 17.75 1.39 0.079
> grDevices::dev.off()
null device
1
Modified: pkg/mboostDevel/tests/birds_Biometrics.Rout.save
===================================================================
--- pkg/mboostDevel/tests/birds_Biometrics.Rout.save 2014-10-02 07:37:30 UTC (rev 801)
+++ pkg/mboostDevel/tests/birds_Biometrics.Rout.save 2014-10-02 09:05:36 UTC (rev 802)
@@ -18,6 +18,7 @@
>
> library("mboostDevel")
Loading required package: parallel
+Loading required package: stabs
This is mboostDevel 2.4-0. See 'package?mboostDevel' and the NEWS file
for a complete list of changes.
@@ -314,4 +315,4 @@
>
> proc.time()
user system elapsed
- 19.303 0.336 20.173
+ 18.541 0.565 19.760
Modified: pkg/mboostDevel/tests/bugfixes.Rout.save
===================================================================
--- pkg/mboostDevel/tests/bugfixes.Rout.save 2014-10-02 07:37:30 UTC (rev 801)
+++ pkg/mboostDevel/tests/bugfixes.Rout.save 2014-10-02 09:05:36 UTC (rev 802)
@@ -19,6 +19,7 @@
> require("mboostDevel")
Loading required package: mboostDevel
Loading required package: parallel
+Loading required package: stabs
This is mboostDevel 2.4-0. See 'package?mboostDevel' and the NEWS file
for a complete list of changes.
@@ -703,7 +704,7 @@
missing values are excluded per base-learner, i.e., base-learners may depend on different numbers of observations.
5: In brad(x1, x2, knots = 20) : base-learner contains missing values;
missing values are excluded per base-learner, i.e., base-learners may depend on different numbers of observations.
-6: In cover.design(R = unique(x), nd = knots) :
+6: In fields::cover.design(R = unique(x), nd = knots) :
Number of nearst neighbors (nn) reduced to the actual number of candidates
7: In bmono(x1) : base-learner contains missing values;
missing values are excluded per base-learner, i.e., base-learners may depend on different numbers of observations.
@@ -735,4 +736,4 @@
>
> proc.time()
user system elapsed
- 27.765 0.389 28.560
+ 28.060 0.378 28.861
Modified: pkg/mboostDevel/tests/regtest-baselearner.Rout.save
===================================================================
--- pkg/mboostDevel/tests/regtest-baselearner.Rout.save 2014-10-02 07:37:30 UTC (rev 801)
+++ pkg/mboostDevel/tests/regtest-baselearner.Rout.save 2014-10-02 09:05:36 UTC (rev 802)
@@ -18,6 +18,7 @@
>
> library("mboostDevel")
Loading required package: parallel
+Loading required package: stabs
This is mboostDevel 2.4-0. See 'package?mboostDevel' and the NEWS file
for a complete list of changes.
@@ -29,8 +30,9 @@
IPCweights, Laplace, Loglog, Lognormal, Multinomial, NBinomial,
Poisson, PropOdds, QuantReg, Weibull, bbs, blackboost, bmono, bmrf,
bns, bols, boost_control, brad, brandom, bspatial, bss, btree,
- buser, cv, cvrisk, extract, gamboost, glmboost, mboost, mboost_fit,
- mstop, mstop<-, nuisance, risk, selected, survFit
+ buser, confint.glmboost, confint.mboost, cv, cvrisk, extract,
+ gamboost, glmboost, mboost, mboost_fit, mstop, mstop<-, nuisance,
+ risk, selected, stabsel.mboost, stabsel_parameters.mboost, survFit
> library("MASS")
> library("Matrix")
@@ -1200,4 +1202,4 @@
>
> proc.time()
user system elapsed
- 32.798 0.582 33.944
+ 34.268 1.116 36.222
Modified: pkg/mboostDevel/tests/regtest-blackboost.Rout.save
===================================================================
--- pkg/mboostDevel/tests/regtest-blackboost.Rout.save 2014-10-02 07:37:30 UTC (rev 801)
+++ pkg/mboostDevel/tests/regtest-blackboost.Rout.save 2014-10-02 09:05:36 UTC (rev 802)
@@ -19,6 +19,7 @@
> require("mboostDevel")
Loading required package: mboostDevel
Loading required package: parallel
+Loading required package: stabs
This is mboostDevel 2.4-0. See 'package?mboostDevel' and the NEWS file
for a complete list of changes.
@@ -203,4 +204,4 @@
>
> proc.time()
user system elapsed
- 8.561 0.274 9.109
+ 8.559 0.201 9.020
Modified: pkg/mboostDevel/tests/regtest-family.Rout.save
===================================================================
--- pkg/mboostDevel/tests/regtest-family.Rout.save 2014-10-02 07:37:30 UTC (rev 801)
+++ pkg/mboostDevel/tests/regtest-family.Rout.save 2014-10-02 09:05:36 UTC (rev 802)
@@ -18,6 +18,7 @@
>
> library("mboostDevel")
Loading required package: parallel
+Loading required package: stabs
This is mboostDevel 2.4-0. See 'package?mboostDevel' and the NEWS file
for a complete list of changes.
@@ -403,4 +404,4 @@
>
> proc.time()
user system elapsed
- 15.965 0.154 16.312
+ 16.432 0.143 16.798
Modified: pkg/mboostDevel/tests/regtest-gamboost.Rout.save
===================================================================
--- pkg/mboostDevel/tests/regtest-gamboost.Rout.save 2014-10-02 07:37:30 UTC (rev 801)
+++ pkg/mboostDevel/tests/regtest-gamboost.Rout.save 2014-10-02 09:05:36 UTC (rev 802)
@@ -19,6 +19,7 @@
> require("mboostDevel")
Loading required package: mboostDevel
Loading required package: parallel
+Loading required package: stabs
This is mboostDevel 2.4-0. See 'package?mboostDevel' and the NEWS file
for a complete list of changes.
@@ -507,4 +508,4 @@
>
> proc.time()
user system elapsed
- 10.946 0.189 11.354
+ 11.110 0.250 11.664
Modified: pkg/mboostDevel/tests/regtest-glmboost.Rout.save
===================================================================
--- pkg/mboostDevel/tests/regtest-glmboost.Rout.save 2014-10-02 07:37:30 UTC (rev 801)
+++ pkg/mboostDevel/tests/regtest-glmboost.Rout.save 2014-10-02 09:05:36 UTC (rev 802)
@@ -19,6 +19,7 @@
> require("mboostDevel")
Loading required package: mboostDevel
Loading required package: parallel
+Loading required package: stabs
This is mboostDevel 2.4-0. See 'package?mboostDevel' and the NEWS file
for a complete list of changes.
@@ -597,4 +598,4 @@
>
> proc.time()
user system elapsed
- 16.073 0.217 17.211
+ 16.180 0.229 16.669
Modified: pkg/mboostDevel/tests/regtest-hatmatrix.Rout.save
===================================================================
--- pkg/mboostDevel/tests/regtest-hatmatrix.Rout.save 2014-10-02 07:37:30 UTC (rev 801)
+++ pkg/mboostDevel/tests/regtest-hatmatrix.Rout.save 2014-10-02 09:05:36 UTC (rev 802)
@@ -18,6 +18,7 @@
>
> library("mboostDevel")
Loading required package: parallel
+Loading required package: stabs
This is mboostDevel 2.4-0. See 'package?mboostDevel' and the NEWS file
for a complete list of changes.
@@ -83,4 +84,4 @@
>
> proc.time()
user system elapsed
- 2.209 0.038 2.292
+ 2.130 0.082 2.278
Modified: pkg/mboostDevel/tests/regtest-inference.Rout.save
===================================================================
--- pkg/mboostDevel/tests/regtest-inference.Rout.save 2014-10-02 07:37:30 UTC (rev 801)
+++ pkg/mboostDevel/tests/regtest-inference.Rout.save 2014-10-02 09:05:36 UTC (rev 802)
@@ -18,6 +18,7 @@
> require("mboostDevel")
Loading required package: mboostDevel
Loading required package: parallel
+Loading required package: stabs
This is mboostDevel 2.4-0. See 'package?mboostDevel' and the NEWS file
for a complete list of changes.
@@ -29,8 +30,9 @@
IPCweights, Laplace, Loglog, Lognormal, Multinomial, NBinomial,
Poisson, PropOdds, QuantReg, Weibull, bbs, blackboost, bmono, bmrf,
bns, bols, boost_control, brad, brandom, bspatial, bss, btree,
- buser, cv, cvrisk, extract, gamboost, glmboost, mboost, mboost_fit,
- mstop, mstop<-, nuisance, risk, selected, survFit
+ buser, confint.glmboost, confint.mboost, cv, cvrisk, extract,
+ gamboost, glmboost, mboost, mboost_fit, mstop, mstop<-, nuisance,
+ risk, selected, stabsel.mboost, stabsel_parameters.mboost, survFit
>
> set.seed(1907)
@@ -204,4 +206,4 @@
>
> proc.time()
user system elapsed
- 49.173 5.592 49.202
+ 49.465 5.646 49.896
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