[Robast-commits] r455 - in pkg/RobLoxBioC: . R man tests/Examples
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Jan 16 21:43:56 CET 2012
Author: stamats
Date: 2012-01-16 21:43:47 +0100 (Mon, 16 Jan 2012)
New Revision: 455
Modified:
pkg/RobLoxBioC/DESCRIPTION
pkg/RobLoxBioC/R/0AllGeneric.R
pkg/RobLoxBioC/man/KolmogorovMinDist.Rd
pkg/RobLoxBioC/man/SimStudies.Rd
pkg/RobLoxBioC/man/robloxbioc.Rd
pkg/RobLoxBioC/tests/Examples/RobLoxBioC-Ex.Rout.save
Log:
minor changes to RobLoxBioC to remove check warnings and increase reproducibility of examples
Modified: pkg/RobLoxBioC/DESCRIPTION
===================================================================
--- pkg/RobLoxBioC/DESCRIPTION 2011-09-30 09:13:05 UTC (rev 454)
+++ pkg/RobLoxBioC/DESCRIPTION 2012-01-16 20:43:47 UTC (rev 455)
@@ -1,10 +1,10 @@
Package: RobLoxBioC
-Version: 0.8.1
-Date: 2011-09-30
+Version: 0.8.2
+Date: 2012-01-13
Title: Infinitesimally robust estimators for preprocessing omics data
Description: Functions for the determination of optimally robust influence curves and
estimators for preprocessing omics data, in particular gene expression data.
-Depends: R(>= 2.8.1), methods, Biobase, affy, beadarray, distr, RobLox, lattice, RColorBrewer
+Depends: R(>= 2.14.0), methods, Biobase, affy, beadarray, distr, RobLox, lattice, RColorBrewer
Author: Matthias Kohl <Matthias.Kohl at stamats.de>
Maintainer: Matthias Kohl <Matthias.Kohl at stamats.de>
LazyLoad: yes
Modified: pkg/RobLoxBioC/R/0AllGeneric.R
===================================================================
--- pkg/RobLoxBioC/R/0AllGeneric.R 2011-09-30 09:13:05 UTC (rev 454)
+++ pkg/RobLoxBioC/R/0AllGeneric.R 2012-01-16 20:43:47 UTC (rev 455)
@@ -1,8 +1,4 @@
############# preparations ################
-.onLoad <- function(lib, pkg) {
- require("methods", character = TRUE, quietly = TRUE)
-}
-
if(!isGeneric("robloxbioc")){
setGeneric("robloxbioc",
function(x, ...) standardGeneric("robloxbioc"))
Modified: pkg/RobLoxBioC/man/KolmogorovMinDist.Rd
===================================================================
--- pkg/RobLoxBioC/man/KolmogorovMinDist.Rd 2011-09-30 09:13:05 UTC (rev 454)
+++ pkg/RobLoxBioC/man/KolmogorovMinDist.Rd 2012-01-16 20:43:47 UTC (rev 455)
@@ -61,6 +61,8 @@
%\note{}
\seealso{\code{\link[distrEx]{KolmogorovDist}}, \code{\link[distrMod]{MDEstimator}} }
\examples{
+set.seed(123) # to have reproducible results for package checking
+
## matrix method for KolmogorovMinDist
ind <- rbinom(200, size=1, prob=0.05)
X <- matrix(rnorm(200, mean=ind*3, sd=(1-ind) + ind*9), nrow = 2)
Modified: pkg/RobLoxBioC/man/SimStudies.Rd
===================================================================
--- pkg/RobLoxBioC/man/SimStudies.Rd 2011-09-30 09:13:05 UTC (rev 454)
+++ pkg/RobLoxBioC/man/SimStudies.Rd 2012-01-16 20:43:47 UTC (rev 455)
@@ -59,6 +59,8 @@
%\note{}
\seealso{\code{\link[RobLox]{rowRoblox}}}
\examples{
+set.seed(123) # to have reproducible results for package checking
+
AffySimStudy(n = 11, M = 100, eps = 0.02, contD = Norm(mean = 0, sd = 3),
plot1 = TRUE, plot2 = TRUE, plot3 = TRUE)
IlluminaSimStudy(n = 30, M = 100, eps = 0.02, contD = Norm(mean = 0, sd = 3),
Modified: pkg/RobLoxBioC/man/robloxbioc.Rd
===================================================================
--- pkg/RobLoxBioC/man/robloxbioc.Rd 2011-09-30 09:13:05 UTC (rev 454)
+++ pkg/RobLoxBioC/man/robloxbioc.Rd 2012-01-16 20:43:47 UTC (rev 455)
@@ -127,8 +127,10 @@
\code{\link[Biobase:class.ExpressionSet]{ExpressionSet-class}},
\code{\link[beadarray]{createBeadSummaryData}} }
\examples{
+set.seed(123) # to have reproducible results for package checking
+
## similar to rowRoblox of package RobLox
-ind <- rbinom(200, size=1, prob=0.05)
+ind <- rbinom(200, size=1, prob=0.05)
X <- matrix(rnorm(200, mean=ind*3, sd=(1-ind) + ind*9), nrow = 2)
robloxbioc(X)
robloxbioc(X, steps = 5)
Modified: pkg/RobLoxBioC/tests/Examples/RobLoxBioC-Ex.Rout.save
===================================================================
--- pkg/RobLoxBioC/tests/Examples/RobLoxBioC-Ex.Rout.save 2011-09-30 09:13:05 UTC (rev 454)
+++ pkg/RobLoxBioC/tests/Examples/RobLoxBioC-Ex.Rout.save 2012-01-16 20:43:47 UTC (rev 455)
@@ -1,6 +1,6 @@
-R version 2.12.1 Patched (2011-01-04 r53913)
-Copyright (C) 2011 The R Foundation for Statistical Computing
+R version 2.14.1 Patched (2012-01-12 r58096)
+Copyright (C) 2012 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
Platform: x86_64-unknown-linux-gnu (64-bit)
@@ -27,16 +27,35 @@
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
- 'openVignette()'. To cite Bioconductor, see
- 'citation("Biobase")' and for packages 'citation(pkgname)'.
+ 'browseVignettes()'. To cite Bioconductor, see
+ 'citation("Biobase")' and for packages 'citation("pkgname")'.
Loading required package: affy
Loading required package: beadarray
-Welcome to beadarray version 2.0.2
-There have been major changes to beadarray since Bioconductor 2.6 (April 2010). Please see package vignette for details
+Loading required package: ggplot2
+Loading required package: reshape
+Loading required package: plyr
+
+Attaching package: ‘reshape’
+
+The following object(s) are masked from ‘package:plyr’:
+
+ rename, round_any
+
+Loading required package: grid
+Loading required package: proto
+Welcome to beadarray version 2.4.1
+beadarray versions >= 2.0.0 are substantial updates from beadarray 1.16.0 and earlier. Please see package vignette for details
+
+Attaching package: ‘beadarray’
+
+The following object(s) are masked from ‘package:plyr’:
+
+ summarize
+
Loading required package: distr
Loading required package: startupmsg
-:startupmsg> Utilities for start-up messages (version 0.7.1)
+:startupmsg> Utilities for start-up messages (version 0.7.3)
:startupmsg>
:startupmsg> For more information see ?"startupmsg",
:startupmsg> NEWS("startupmsg")
@@ -44,7 +63,8 @@
Loading required package: sfsmisc
Loading required package: SweaveListingUtils
:SweaveListingUtils> Utilities for Sweave together with
-:SweaveListingUtils> TeX listings package (version 0.5)
+:SweaveListingUtils> TeX listings package (version
+:SweaveListingUtils> 0.5.4)
:SweaveListingUtils>
:SweaveListingUtils> Some functions from package 'base'
:SweaveListingUtils> are intentionally masked ---see
@@ -63,14 +83,14 @@
:SweaveListingUtils> vignette("ExampleSweaveListingUtils").
-Attaching package: 'SweaveListingUtils'
+Attaching package: ‘SweaveListingUtils’
-The following object(s) are masked from 'package:base':
+The following object(s) are masked from ‘package:base’:
library, require
:distr> Object oriented implementation of distributions (version
-:distr> 2.3)
+:distr> 2.3.4)
:distr>
:distr> Attention: Arithmetics on distribution objects are
:distr> understood as operations on corresponding random variables
@@ -89,25 +109,34 @@
:distr> vignette("distr").
-Attaching package: 'distr'
+Attaching package: ‘distr’
-The following object(s) are masked from 'package:stats':
+The following object(s) are masked from ‘package:stats’:
df, qqplot, sd
Loading required package: RobLox
+Loading required package: lattice
+Loading required package: RColorBrewer
Loading required package: distrMod
Loading required package: distrEx
Loading required package: evd
+
+Attaching package: ‘evd’
+
+The following object(s) are masked from ‘package:lattice’:
+
+ qq
+
Loading required package: actuar
-Attaching package: 'actuar'
+Attaching package: ‘actuar’
-The following object(s) are masked from 'package:grDevices':
+The following object(s) are masked from ‘package:grDevices’:
cm
-:distrEx> Extensions of package distr (version 2.3)
+:distrEx> Extensions of package distr (version 2.3.2)
:distrEx>
:distrEx> Note: Packages "e1071", "moments", "fBasics" should be
:distrEx> attached /before/ package "distrEx". See distrExMASK().
@@ -120,14 +149,14 @@
:distrEx> vignette("distr").
-Attaching package: 'distrEx'
+Attaching package: ‘distrEx’
-The following object(s) are masked from 'package:stats':
+The following object(s) are masked from ‘package:stats’:
IQR, mad, median, var
Loading required package: RandVar
-:RandVar> Implementation of random variables (version 0.8)
+:RandVar> Implementation of random variables (version 0.8.1)
:RandVar>
:RandVar> For more information see ?"RandVar", NEWS("RandVar"), as
:RandVar> well as
@@ -138,7 +167,7 @@
Loading required package: MASS
Loading required package: stats4
:distrMod> Object oriented implementation of probability models
-:distrMod> (version 2.3)
+:distrMod> (version 2.3.3)
:distrMod>
:distrMod> Some functions from pkg's 'base' and 'stats' are
:distrMod> intentionally masked ---see distrModMASK().
@@ -157,22 +186,22 @@
:distrMod> vignette("distr").
-Attaching package: 'distrMod'
+Attaching package: ‘distrMod’
-The following object(s) are masked from 'package:stats4':
+The following object(s) are masked from ‘package:stats4’:
confint
-The following object(s) are masked from 'package:stats':
+The following object(s) are masked from ‘package:stats’:
confint
-The following object(s) are masked from 'package:base':
+The following object(s) are masked from ‘package:base’:
norm
Loading required package: RobAStBase
-:RobAStBase> Robust Asymptotic Statistics (version 0.8)
+:RobAStBase> Robust Asymptotic Statistics (version 0.8.1)
:RobAStBase>
:RobAStBase> Some functions from pkg's 'stats' and 'graphics'
:RobAStBase> are intentionally masked ---see RobAStBaseMASK().
@@ -185,25 +214,12 @@
:RobAStBase> http://robast.r-forge.r-project.org/
-Attaching package: 'RobAStBase'
+Attaching package: ‘RobAStBase’
-The following object(s) are masked from 'package:stats':
+The following object(s) are masked from ‘package:graphics’:
- start
-
-The following object(s) are masked from 'package:graphics':
-
clip
-Loading required package: lattice
-
-Attaching package: 'lattice'
-
-The following object(s) are masked from 'package:evd':
-
- qq
-
-Loading required package: RColorBrewer
>
> assign(".oldSearch", search(), pos = 'CheckExEnv')
> cleanEx()
@@ -240,12 +256,14 @@
>
> ### ** Examples
>
+> set.seed(123) # to have reproducible results for package checking
+>
> ## matrix method for KolmogorovMinDist
> ind <- rbinom(200, size=1, prob=0.05)
> X <- matrix(rnorm(200, mean=ind*3, sd=(1-ind) + ind*9), nrow = 2)
> KolmogorovMinDist(X, D = Norm())
$dist
-[1] 0.05032454 0.04616206
+[1] 0.06544843 0.04356402
$n
[1] 100 100
@@ -256,7 +274,7 @@
> probes <- log2(pm(SpikeIn))
> (res <- KolmogorovMinDist(probes, Norm()))
$dist
- [1] 0.1755693 0.1567648 0.1571410 0.1609188 0.1617499 0.1607157 0.1382646
+ [1] 0.1755693 0.1567648 0.1571403 0.1609188 0.1617499 0.1607157 0.1382646
[8] 0.1471997 0.1693088 0.1836652 0.1787724 0.1601283 0.1729001 0.1519412
[15] 0.1682097 0.1662173 0.1547481 0.1716497 0.1751219 0.1671566
@@ -312,27 +330,29 @@
>
> ### ** Examples
>
+> set.seed(123) # to have reproducible results for package checking
+>
> AffySimStudy(n = 11, M = 100, eps = 0.02, contD = Norm(mean = 0, sd = 3),
+ plot1 = TRUE, plot2 = TRUE, plot3 = TRUE)
dev.new(): using pdf(file="Rplots1.pdf")
- ML Med Tukey rmx
-n x empMSE (loc) 1.2837045 1.826711 1.698428 1.399230
-relMSE (loc) 0.9174362 1.305512 1.213830 1.000000
-n x empMSE (scale) 0.6072430 1.573206 1.573206 0.723606
-relMSE (scale) 0.8391900 2.174119 2.174119 1.000000
-n x empMSE (loc + scale) 1.8909475 3.399917 3.271634 2.122836
-relMSE (loc + scale) 0.8907646 1.601592 1.541162 1.000000
+ ML Med Tukey rmx
+n x empMSE (loc) 1.2837045 1.826711 1.698428 1.3992302
+relMSE (loc) 0.9174362 1.305512 1.213830 1.0000000
+n x empMSE (scale) 0.6072430 1.573206 1.573206 0.7236061
+relMSE (scale) 0.8391900 2.174119 2.174119 1.0000000
+n x empMSE (loc + scale) 1.8909475 3.399917 3.271634 2.1228363
+relMSE (loc + scale) 0.8907646 1.601592 1.541162 1.0000000
> IlluminaSimStudy(n = 30, M = 100, eps = 0.02, contD = Norm(mean = 0, sd = 3),
+ plot1 = TRUE, plot2 = TRUE, plot3 = TRUE)
dev.new(): using pdf(file="Rplots2.pdf")
dev.new(): using pdf(file="Rplots3.pdf")
- ML Med Illumina rmx
-n x empMSE (loc) 1.172077 1.591148 1.205941 1.1132052
-relMSE (loc) 1.052885 1.429339 1.083305 1.0000000
-n x empMSE (scale) 1.084569 1.331247 0.816445 0.5927791
-relMSE (scale) 1.829635 2.245773 1.377318 1.0000000
-n x empMSE (loc + scale) 2.256646 2.922395 2.022386 1.7059843
-relMSE (loc + scale) 1.322783 1.713026 1.185466 1.0000000
+ ML Med Illumina rmx
+n x empMSE (loc) 1.172077 1.591148 1.2059413 1.1132052
+relMSE (loc) 1.052885 1.429339 1.0833055 1.0000000
+n x empMSE (scale) 1.084569 1.331247 0.8164451 0.5927791
+relMSE (scale) 1.829635 2.245773 1.3773176 1.0000000
+n x empMSE (loc + scale) 2.256646 2.922395 2.0223864 1.7059843
+relMSE (loc + scale) 1.322783 1.713026 1.1854660 1.0000000
>
>
>
@@ -350,31 +370,33 @@
>
> ### ** Examples
>
+> set.seed(123) # to have reproducible results for package checking
+>
> ## similar to rowRoblox of package RobLox
-> ind <- rbinom(200, size=1, prob=0.05)
+> ind <- rbinom(200, size=1, prob=0.05)
> X <- matrix(rnorm(200, mean=ind*3, sd=(1-ind) + ind*9), nrow = 2)
> robloxbioc(X)
- mean sd
-[1,] -0.014713379 0.9643588
-[2,] 0.003050954 1.0587182
+ mean sd
+[1,] 0.01361094 1.103944
+[2,] -0.13024109 1.023868
> robloxbioc(X, steps = 5)
- mean sd
-[1,] -0.014294296 0.9649008
-[2,] 0.003004433 1.0587286
+ mean sd
+[1,] 0.01454172 1.105150
+[2,] -0.13018096 1.023832
> robloxbioc(X, eps = 0.05)
- mean sd
-[1,] -0.028278572 0.927434
-[2,] -0.001566506 1.051123
+ mean sd
+[1,] -0.02555103 1.042593
+[2,] -0.16758006 1.004678
> robloxbioc(X, eps = 0.05, steps = 5)
- mean sd
-[1,] -0.028227242 0.9276155
-[2,] -0.001567355 1.0511232
+ mean sd
+[1,] -0.02545634 1.042738
+[2,] -0.16757528 1.004658
>
> ## the function is designed for large scale problems
> X <- matrix(rnorm(50000*20, mean = 1), nrow = 50000)
> system.time(robloxbioc(X))
user system elapsed
- 4.380 0.110 4.498
+ 5.597 0.044 5.660
>
> ## using Affymetrix-Data
> ## confer example to generateExprVal.method.mas
@@ -411,10 +433,10 @@
> ### * <FOOTER>
> ###
> cat("Time elapsed: ", proc.time() - get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed: 10.24 0.16 10.423 0 0
+Time elapsed: 16.901 0.156 17.124 0 0
> grDevices::dev.off()
-postscript
- 2
+pdf
+ 2
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
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