[Mboost-commits] r819 - in pkg/mboostPatch/tests: . Examples
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Dec 15 18:50:30 CET 2014
Author: hofner
Date: 2014-12-15 18:50:29 +0100 (Mon, 15 Dec 2014)
New Revision: 819
Modified:
pkg/mboostPatch/tests/Examples/mboost-Ex.Rout.save
pkg/mboostPatch/tests/birds_Biometrics.Rout.save
pkg/mboostPatch/tests/bugfixes.Rout.save
pkg/mboostPatch/tests/regtest-baselearner.Rout.save
pkg/mboostPatch/tests/regtest-blackboost.Rout.save
pkg/mboostPatch/tests/regtest-family.Rout.save
pkg/mboostPatch/tests/regtest-gamboost.Rout.save
pkg/mboostPatch/tests/regtest-glmboost.Rout.save
pkg/mboostPatch/tests/regtest-hatmatrix.Rout.save
pkg/mboostPatch/tests/regtest-inference.Rout.save
Log:
updated test results (.Rout.save)
Modified: pkg/mboostPatch/tests/Examples/mboost-Ex.Rout.save
===================================================================
--- pkg/mboostPatch/tests/Examples/mboost-Ex.Rout.save 2014-12-15 17:50:28 UTC (rev 818)
+++ pkg/mboostPatch/tests/Examples/mboost-Ex.Rout.save 2014-12-15 17:50:29 UTC (rev 819)
@@ -1,5 +1,5 @@
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
@@ -35,7 +35,7 @@
> library('mboost')
Loading required package: parallel
Loading required package: stabs
-This is mboost 2.4-0. See ‘package?mboost’ and the NEWS file
+This is mboost 2.4-1. See ‘package?mboost’ and the NEWS file
for a complete list of changes.
>
@@ -875,6 +875,13 @@
Loading required package: strucchange
Loading required package: modeltools
Loading required package: stats4
+
+Attaching package: ‘modeltools’
+
+The following object is masked from ‘package:stabs’:
+
+ parameters
+
> cars.gb
Model-based Boosting
@@ -1140,6 +1147,13 @@
Loading required package: strucchange
Loading required package: modeltools
Loading required package: stats4
+
+Attaching package: ‘modeltools’
+
+The following object is masked from ‘package:stabs’:
+
+ parameters
+
> cvtree <- cvrisk(blackbox, papply = lapply)
> plot(cvtree)
>
@@ -1427,6 +1441,13 @@
Loading required package: strucchange
Loading required package: modeltools
Loading required package: stats4
+
+Attaching package: ‘modeltools’
+
+The following object is masked from ‘package:stabs’:
+
+ parameters
+
> layout(matrix(1:6, nc = 3, byrow = TRUE))
> plot(mod, ask = FALSE, main = "formula")
>
@@ -1445,7 +1466,7 @@
> (sbody <- stabsel(mod, q = 3, PFER = 1, sampling.type = "MB"))
Stability Selection without further assumptions
-Selected base-learners:
+Selected variables:
hipcirc
4
@@ -1455,7 +1476,9 @@
anthro3c anthro3a waistcirc hipcirc
0.24 0.61 0.92 0.99
+---
Cutoff: 0.95; q: 3; PFER: 1
+PFER corresponds to signif. level 0.1 (without multiplicity adjustment)
> opar <- par(mai = par("mai") * c(1, 1, 1, 2.7))
> plot(sbody)
@@ -1512,6 +1535,13 @@
Loading required package: strucchange
Loading required package: modeltools
Loading required package: stats4
+
+Attaching package: ‘modeltools’
+
+The following object is masked from ‘package:stabs’:
+
+ parameters
+
>
> ### bootstrap for assessing `optimal' number of boosting iterations
> cvm <- cvrisk(model, papply = lapply)
@@ -1568,8 +1598,8 @@
> ### resid.mboost variable.names.glmboost variable.names.mboost risk
> ### risk.mboost extract extract.mboost extract.gamboost extract.glmboost
> ### extract.blackboost extract.blg extract.bl_lin extract.bl_tree
-> ### logLik.mboost hatvalues.gamboost hatvalues.glmboost selected
-> ### selected.mboost nuisance nuisance.mboost
+> ### logLik.mboost hatvalues.gamboost hatvalues.glmboost selected.mboost
+> ### nuisance nuisance.mboost
> ### Keywords: methods
>
> ### ** Examples
@@ -3165,18 +3195,24 @@
> ## 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
+Stability selection without further assumptions
+
Cutoff: 0.95; q: 3; PFER: 1
+PFER (specified upper bound): 1
+PFER corresponds to signif. level 0.1 (without multiplicity adjustment)
> ## the same:
> stabsel(mod, q = 3, PFER = 1, sampling.type = "MB", eval = FALSE)
-Stability Selection without further assumptions
+Stability selection without further assumptions
+
Cutoff: 0.95; q: 3; PFER: 1
+PFER (specified upper bound): 1
+PFER corresponds to signif. level 0.1 (without multiplicity adjustment)
>
> ## now run stability selection
> (sbody <- stabsel(mod, q = 3, PFER = 1, sampling.type = "MB"))
Stability Selection without further assumptions
-Selected base-learners:
+Selected variables:
hipcirc
4
@@ -3186,7 +3222,9 @@
anthro3c anthro3a waistcirc hipcirc
0.18 0.60 0.93 1.00
+---
Cutoff: 0.95; q: 3; PFER: 1
+PFER corresponds to signif. level 0.1 (without multiplicity adjustment)
> opar <- par(mai = par("mai") * c(1, 1, 1, 2.7))
> plot(sbody)
@@ -3285,7 +3323,7 @@
> ###
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed: 14.895 0.337 17.75 1.39 0.079
+Time elapsed: 15.536 0.68 19.097 2.326 0.227
> grDevices::dev.off()
null device
1
Modified: pkg/mboostPatch/tests/birds_Biometrics.Rout.save
===================================================================
--- pkg/mboostPatch/tests/birds_Biometrics.Rout.save 2014-12-15 17:50:28 UTC (rev 818)
+++ pkg/mboostPatch/tests/birds_Biometrics.Rout.save 2014-12-15 17:50:29 UTC (rev 819)
@@ -1,5 +1,5 @@
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
@@ -19,7 +19,7 @@
> library("mboost")
Loading required package: parallel
Loading required package: stabs
-This is mboost 2.4-0. See 'package?mboost' and the NEWS file
+This is mboost 2.4-1. See 'package?mboost' and the NEWS file
for a complete list of changes.
> data("birds", package = "TH.data")
@@ -315,4 +315,4 @@
>
> proc.time()
user system elapsed
- 18.541 0.565 19.760
+ 19.935 0.696 21.177
Modified: pkg/mboostPatch/tests/bugfixes.Rout.save
===================================================================
--- pkg/mboostPatch/tests/bugfixes.Rout.save 2014-12-15 17:50:28 UTC (rev 818)
+++ pkg/mboostPatch/tests/bugfixes.Rout.save 2014-12-15 17:50:29 UTC (rev 819)
@@ -1,5 +1,5 @@
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
@@ -20,7 +20,7 @@
Loading required package: mboost
Loading required package: parallel
Loading required package: stabs
-This is mboost 2.4-0. See 'package?mboost' and the NEWS file
+This is mboost 2.4-1. See 'package?mboost' and the NEWS file
for a complete list of changes.
> require("Matrix")
@@ -46,6 +46,13 @@
Loading required package: strucchange
Loading required package: modeltools
Loading required package: stats4
+
+Attaching package: 'modeltools'
+
+The following object is masked from 'package:stabs':
+
+ parameters
+
> stopifnot(is.factor(pr) && all(levels(pr) %in% levels(dummy$y)))
>
> ### predict for g{al}mboost.matrix did not work
@@ -736,4 +743,4 @@
>
> proc.time()
user system elapsed
- 28.060 0.378 28.861
+ 27.983 0.489 28.889
Modified: pkg/mboostPatch/tests/regtest-baselearner.Rout.save
===================================================================
--- pkg/mboostPatch/tests/regtest-baselearner.Rout.save 2014-12-15 17:50:28 UTC (rev 818)
+++ pkg/mboostPatch/tests/regtest-baselearner.Rout.save 2014-12-15 17:50:29 UTC (rev 819)
@@ -1,5 +1,5 @@
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
@@ -19,7 +19,7 @@
> library("mboost")
Loading required package: parallel
Loading required package: stabs
-This is mboost 2.4-0. See 'package?mboost' and the NEWS file
+This is mboost 2.4-1. See 'package?mboost' and the NEWS file
for a complete list of changes.
> attach(asNamespace("mboost"))
@@ -32,7 +32,8 @@
bns, bols, boost_control, brad, brandom, bspatial, bss, btree,
buser, confint.glmboost, confint.mboost, cv, cvrisk, extract,
gamboost, glmboost, mboost, mboost_fit, mstop, mstop<-, nuisance,
- risk, selected, stabsel.mboost, stabsel_parameters.mboost, survFit
+ risk, selected.mboost, stabsel.mboost, stabsel_parameters.mboost,
+ survFit
> library("MASS")
> library("Matrix")
@@ -336,7 +337,7 @@
In data.frame(..., check.names = FALSE) :
row names were found from a short variable and have been discarded
> coef(m1)
-$`"bbs(x1) %X% bols(f, df = 5, contrasts.arg = \"contr.dummy\")"`
+$`"bbs(x1) %X% bols(f, df = 5, contrasts.arg = \\"contr.dummy\\")"`
[1] 0.2242693758 0.0244549055 -0.0018236656 -0.0649204417 -0.0158616261
[6] -0.1891022703 0.0633957967 -0.1288712394 -0.3211539316 -0.4271143516
[11] 0.1304389247 -0.1279015955 -0.2844975667 -0.5354756406 0.1377335871
@@ -1202,4 +1203,4 @@
>
> proc.time()
user system elapsed
- 34.268 1.116 36.222
+ 33.789 1.594 35.922
Modified: pkg/mboostPatch/tests/regtest-blackboost.Rout.save
===================================================================
--- pkg/mboostPatch/tests/regtest-blackboost.Rout.save 2014-12-15 17:50:28 UTC (rev 818)
+++ pkg/mboostPatch/tests/regtest-blackboost.Rout.save 2014-12-15 17:50:29 UTC (rev 819)
@@ -1,5 +1,5 @@
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
@@ -20,7 +20,7 @@
Loading required package: mboost
Loading required package: parallel
Loading required package: stabs
-This is mboost 2.4-0. See 'package?mboost' and the NEWS file
+This is mboost 2.4-1. See 'package?mboost' and the NEWS file
for a complete list of changes.
> if (require("party")) {
@@ -144,6 +144,13 @@
Loading required package: strucchange
Loading required package: modeltools
Loading required package: stats4
+
+Attaching package: 'modeltools'
+
+The following object is masked from 'package:stabs':
+
+ parameters
+
[1] 2.367443
Loading required package: gbm
Loading required package: survival
@@ -204,4 +211,4 @@
>
> proc.time()
user system elapsed
- 8.559 0.201 9.020
+ 8.502 0.171 8.888
Modified: pkg/mboostPatch/tests/regtest-family.Rout.save
===================================================================
--- pkg/mboostPatch/tests/regtest-family.Rout.save 2014-12-15 17:50:28 UTC (rev 818)
+++ pkg/mboostPatch/tests/regtest-family.Rout.save 2014-12-15 17:50:29 UTC (rev 819)
@@ -1,5 +1,5 @@
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
@@ -19,7 +19,7 @@
> library("mboost")
Loading required package: parallel
Loading required package: stabs
-This is mboost 2.4-0. See 'package?mboost' and the NEWS file
+This is mboost 2.4-1. See 'package?mboost' and the NEWS file
for a complete list of changes.
>
@@ -404,4 +404,4 @@
>
> proc.time()
user system elapsed
- 16.432 0.143 16.798
+ 16.036 0.203 16.416
Modified: pkg/mboostPatch/tests/regtest-gamboost.Rout.save
===================================================================
--- pkg/mboostPatch/tests/regtest-gamboost.Rout.save 2014-12-15 17:50:28 UTC (rev 818)
+++ pkg/mboostPatch/tests/regtest-gamboost.Rout.save 2014-12-15 17:50:29 UTC (rev 819)
@@ -1,5 +1,5 @@
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
@@ -20,7 +20,7 @@
Loading required package: mboost
Loading required package: parallel
Loading required package: stabs
-This is mboost 2.4-0. See 'package?mboost' and the NEWS file
+This is mboost 2.4-1. See 'package?mboost' and the NEWS file
for a complete list of changes.
> require("survival")
@@ -208,6 +208,13 @@
Loading required package: strucchange
Loading required package: modeltools
Loading required package: stats4
+
+Attaching package: 'modeltools'
+
+The following object is masked from 'package:stabs':
+
+ parameters
+
> mod2 <- gamboost(fm2, data = tmp, base = "btree")
> stopifnot(max(abs(fitted(mod1) - fitted(mod2))) < sqrt(.Machine$double.eps))
> stopifnot(max(abs(predict(mod1, newdata = tmp) - predict(mod2, newdata = tmp))) < sqrt(.Machine$double.eps))
@@ -508,4 +515,4 @@
>
> proc.time()
user system elapsed
- 11.110 0.250 11.664
+ 11.326 0.308 11.928
Modified: pkg/mboostPatch/tests/regtest-glmboost.Rout.save
===================================================================
--- pkg/mboostPatch/tests/regtest-glmboost.Rout.save 2014-12-15 17:50:28 UTC (rev 818)
+++ pkg/mboostPatch/tests/regtest-glmboost.Rout.save 2014-12-15 17:50:29 UTC (rev 819)
@@ -1,5 +1,5 @@
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
@@ -20,7 +20,7 @@
Loading required package: mboost
Loading required package: parallel
Loading required package: stabs
-This is mboost 2.4-0. See 'package?mboost' and the NEWS file
+This is mboost 2.4-1. See 'package?mboost' and the NEWS file
for a complete list of changes.
>
@@ -598,4 +598,4 @@
>
> proc.time()
user system elapsed
- 16.180 0.229 16.669
+ 15.562 0.104 15.815
Modified: pkg/mboostPatch/tests/regtest-hatmatrix.Rout.save
===================================================================
--- pkg/mboostPatch/tests/regtest-hatmatrix.Rout.save 2014-12-15 17:50:28 UTC (rev 818)
+++ pkg/mboostPatch/tests/regtest-hatmatrix.Rout.save 2014-12-15 17:50:29 UTC (rev 819)
@@ -1,5 +1,5 @@
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
@@ -19,7 +19,7 @@
> library("mboost")
Loading required package: parallel
Loading required package: stabs
-This is mboost 2.4-0. See 'package?mboost' and the NEWS file
+This is mboost 2.4-1. See 'package?mboost' and the NEWS file
for a complete list of changes.
>
@@ -84,4 +84,4 @@
>
> proc.time()
user system elapsed
- 2.130 0.082 2.278
+ 2.169 0.100 2.312
Modified: pkg/mboostPatch/tests/regtest-inference.Rout.save
===================================================================
--- pkg/mboostPatch/tests/regtest-inference.Rout.save 2014-12-15 17:50:28 UTC (rev 818)
+++ pkg/mboostPatch/tests/regtest-inference.Rout.save 2014-12-15 17:50:29 UTC (rev 819)
@@ -1,5 +1,5 @@
-R version 3.1.1 (2014-07-10) -- "Sock it to Me"
+R version 3.1.2 (2014-10-31) -- "Pumpkin Helmet"
Copyright (C) 2014 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
@@ -19,7 +19,7 @@
Loading required package: mboost
Loading required package: parallel
Loading required package: stabs
-This is mboost 2.4-0. See 'package?mboost' and the NEWS file
+This is mboost 2.4-1. See 'package?mboost' and the NEWS file
for a complete list of changes.
> attach(asNamespace("mboost"))
@@ -32,7 +32,8 @@
bns, bols, boost_control, brad, brandom, bspatial, bss, btree,
buser, confint.glmboost, confint.mboost, cv, cvrisk, extract,
gamboost, glmboost, mboost, mboost_fit, mstop, mstop<-, nuisance,
- risk, selected, stabsel.mboost, stabsel_parameters.mboost, survFit
+ risk, selected.mboost, stabsel.mboost, stabsel_parameters.mboost,
+ survFit
>
> set.seed(1907)
@@ -98,106 +99,106 @@
>
> confint.gam <- confint(gam, B = 100, B.mstop = 1)
Start computing bootstrap confidence intervals...
-
-B = 1
-B = 2
-B = 3
-B = 4
-B = 5
-B = 6
-B = 7
-B = 8
-B = 9
-B = 10
-B = 11
-B = 12
-B = 13
-B = 14
-B = 15
-B = 16
-B = 17
-B = 18
-B = 19
-B = 20
-B = 21
-B = 22
-B = 23
-B = 24
-B = 25
-B = 26
-B = 27
-B = 28
-B = 29
-B = 30
-B = 31
-B = 32
-B = 33
-B = 34
-B = 35
-B = 36
-B = 37
-B = 38
-B = 39
-B = 40
-B = 41
-B = 42
-B = 43
-B = 44
-B = 45
-B = 46
-B = 47
-B = 48
-B = 49
-B = 50
-B = 51
-B = 52
-B = 53
-B = 54
-B = 55
-B = 56
-B = 57
-B = 58
-B = 59
-B = 60
-B = 61
-B = 62
-B = 63
-B = 64
-B = 65
-B = 66
-B = 67
-B = 68
-B = 69
-B = 70
-B = 71
-B = 72
-B = 73
-B = 74
-B = 75
-B = 76
-B = 77
-B = 78
-B = 79
-B = 80
-B = 81
-B = 82
-B = 83
-B = 84
-B = 85
-B = 86
-B = 87
-B = 88
-B = 89
-B = 90
-B = 91
-B = 92
-B = 93
-B = 94
-B = 95
-B = 96
-B = 97
-B = 98
-B = 99
+
+B = 1
+B = 2
+B = 3
+B = 4
+B = 5
+B = 6
+B = 7
+B = 8
+B = 9
+B = 10
+B = 11
+B = 12
+B = 13
+B = 14
+B = 15
+B = 16
+B = 17
+B = 18
+B = 19
+B = 20
+B = 21
+B = 22
+B = 23
+B = 24
+B = 25
+B = 26
+B = 27
+B = 28
+B = 29
+B = 30
+B = 31
+B = 32
+B = 33
+B = 34
+B = 35
+B = 36
+B = 37
+B = 38
+B = 39
+B = 40
+B = 41
+B = 42
+B = 43
+B = 44
+B = 45
+B = 46
+B = 47
+B = 48
+B = 49
+B = 50
+B = 51
+B = 52
+B = 53
+B = 54
+B = 55
+B = 56
+B = 57
+B = 58
+B = 59
+B = 60
+B = 61
+B = 62
+B = 63
+B = 64
+B = 65
+B = 66
+B = 67
+B = 68
+B = 69
+B = 70
+B = 71
+B = 72
+B = 73
+B = 74
+B = 75
+B = 76
+B = 77
+B = 78
+B = 79
+B = 80
+B = 81
+B = 82
+B = 83
+B = 84
+B = 85
+B = 86
+B = 87
+B = 88
+B = 89
+B = 90
+B = 91
+B = 92
+B = 93
+B = 94
+B = 95
+B = 96
+B = 97
+B = 98
+B = 99
B = 100
There were 50 or more warnings (use warnings() to see the first 50)
> plot(confint.gam, which = 1)
@@ -206,4 +207,4 @@
>
> proc.time()
user system elapsed
- 49.465 5.646 49.896
+ 48.422 5.464 48.206
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