[Robast-commits] r447 - in pkg/RobLoxBioC: . R tests/Examples
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Thu Jan 6 10:19:35 CET 2011
Author: stamats
Date: 2011-01-06 10:19:35 +0100 (Thu, 06 Jan 2011)
New Revision: 447
Modified:
pkg/RobLoxBioC/DESCRIPTION
pkg/RobLoxBioC/R/AffySimStudyFunction.R
pkg/RobLoxBioC/R/IlluminaSimStudyFunction.R
pkg/RobLoxBioC/tests/Examples/RobLoxBioC-Ex.Rout.save
Log:
updated RobLoxBioC-Ex.Rout.save files to R 2.12.1 patched, corrected minor bug in functions for simulations studies, updated DESCRIPTION file
Modified: pkg/RobLoxBioC/DESCRIPTION
===================================================================
--- pkg/RobLoxBioC/DESCRIPTION 2011-01-05 19:19:52 UTC (rev 446)
+++ pkg/RobLoxBioC/DESCRIPTION 2011-01-06 09:19:35 UTC (rev 447)
@@ -1,6 +1,6 @@
Package: RobLoxBioC
Version: 0.8
-Date: 2010-12-03
+Date: 2011-01-06
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.
Modified: pkg/RobLoxBioC/R/AffySimStudyFunction.R
===================================================================
--- pkg/RobLoxBioC/R/AffySimStudyFunction.R 2011-01-05 19:19:52 UTC (rev 446)
+++ pkg/RobLoxBioC/R/AffySimStudyFunction.R 2011-01-06 09:19:35 UTC (rev 447)
@@ -38,12 +38,13 @@
if(plot2){
- ind <- sample(1:M, min(M, 20))
+ ind <- if(M <= 20) 1:M else sample(1:M, 20)
if(plot1) dev.new()
+ M1 <- min(M, 20)
print(
- stripplot(rep(1:20, each = 20) ~ as.vector(Mre[ind,]),
+ stripplot(rep(1:M1, each = n) ~ as.vector(Mre[ind,]),
ylab = "samples", xlab = "x", pch = 20,
- main = "Randomly chosen samples")
+ main = ifelse(M <= 20, "Samples", "20 randomly chosen samples"))
)
}
@@ -72,11 +73,10 @@
abline(h = 0)
boxplot(Ergebnis2, col = myCol[c(1,2,4)], pch = 20, main = "Scale")
abline(h = 1)
- op <- par(mar = rep(2, 4), no.readonly = TRUE)
+ op <- par(mar = rep(2, 4))
plot(c(0,1), c(1, 0), type = "n", axes = FALSE)
legend("center", c("ML", "Med/MAD", "biweight", "rmx"),
fill = myCol, ncol = 4, cex = 1.5)
-# op$cin <- op$cra <- op$csi <- op$cxy <- op$din <- NULL
on.exit(par(op))
}
@@ -117,4 +117,6 @@
empMSE
}
+AffySimStudy(n = 11, M = 10, eps = 0.02, contD = Norm(mean = 0, sd = 3),
+ plot1 = TRUE, plot2 = TRUE, plot3 = TRUE)
Modified: pkg/RobLoxBioC/R/IlluminaSimStudyFunction.R
===================================================================
--- pkg/RobLoxBioC/R/IlluminaSimStudyFunction.R 2011-01-05 19:19:52 UTC (rev 446)
+++ pkg/RobLoxBioC/R/IlluminaSimStudyFunction.R 2011-01-06 09:19:35 UTC (rev 447)
@@ -39,12 +39,13 @@
if(plot2){
- ind <- sample(1:M, min(M, 20))
+ ind <- if(M <= 20) 1:M else sample(1:M, 20)
if(plot1) dev.new()
+ M1 <- min(M, 20)
print(
- stripplot(rep(1:20, each = 20) ~ as.vector(Mre[ind,]),
+ stripplot(rep(1:M1, each = n) ~ as.vector(Mre[ind,]),
ylab = "samples", xlab = "x", pch = 20,
- main = "Randomly chosen samples")
+ main = ifelse(M <= 20, "Samples", "20 randomly chosen samples"))
)
}
@@ -79,11 +80,11 @@
abline(h = 0)
boxplot(Ergebnis2, col = myCol, pch = 20, main = "Scale")
abline(h = 1)
- op <- par(mar = rep(2, 4), no.readonly = TRUE)
+ op <- par(mar = rep(2, 4))
plot(c(0,1), c(1, 0), type = "n", axes = FALSE)
legend("center", c("ML", "Med/MAD", "Illumina", "rmx"),
fill = myCol, ncol = 4, cex = 1.5)
-# op$cin <- op$cra <- op$csi <- op$cxy <- op$din <- NULL
+ op$cin <- op$cra <- op$csi <- op$cxy <- op$din <- NULL
on.exit(par(op))
}
Modified: pkg/RobLoxBioC/tests/Examples/RobLoxBioC-Ex.Rout.save
===================================================================
--- pkg/RobLoxBioC/tests/Examples/RobLoxBioC-Ex.Rout.save 2011-01-05 19:19:52 UTC (rev 446)
+++ pkg/RobLoxBioC/tests/Examples/RobLoxBioC-Ex.Rout.save 2011-01-06 09:19:35 UTC (rev 447)
@@ -1,7 +1,8 @@
-R version 2.10.1 Patched (2010-03-27 r51528)
-Copyright (C) 2010 The R Foundation for Statistical Computing
+R version 2.12.1 Patched (2011-01-04 r53913)
+Copyright (C) 2011 The R Foundation for Statistical Computing
ISBN 3-900051-07-0
+Platform: x86_64-unknown-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
@@ -31,16 +32,45 @@
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: distr
Loading required package: startupmsg
-:startupmsg> Utilities for start-up messages (version 0.7)
+:startupmsg> Utilities for start-up messages (version 0.7.1)
:startupmsg>
:startupmsg> For more information see ?"startupmsg",
:startupmsg> NEWS("startupmsg")
Loading required package: sfsmisc
-:distr> Object orientated implementation of distributions (version
-:distr> 2.2.2)
+Loading required package: SweaveListingUtils
+:SweaveListingUtils> Utilities for Sweave together with
+:SweaveListingUtils> TeX listings package (version 0.5)
+:SweaveListingUtils>
+:SweaveListingUtils> Some functions from package 'base'
+:SweaveListingUtils> are intentionally masked ---see
+:SweaveListingUtils> SweaveListingMASK().
+:SweaveListingUtils>
+:SweaveListingUtils> Note that global options are
+:SweaveListingUtils> controlled by
+:SweaveListingUtils> SweaveListingoptions() ---c.f.
+:SweaveListingUtils> ?"SweaveListingoptions".
+:SweaveListingUtils>
+:SweaveListingUtils> For more information see
+:SweaveListingUtils> ?"SweaveListingUtils",
+:SweaveListingUtils> NEWS("SweaveListingUtils")
+:SweaveListingUtils> There is a vignette to this
+:SweaveListingUtils> package; try
+:SweaveListingUtils> vignette("ExampleSweaveListingUtils").
+
+
+Attaching package: 'SweaveListingUtils'
+
+The following object(s) are masked from 'package:base':
+
+ library, require
+
+:distr> Object oriented implementation of distributions (version
+:distr> 2.3)
:distr>
:distr> Attention: Arithmetics on distribution objects are
:distr> understood as operations on corresponding random variables
@@ -61,13 +91,10 @@
Attaching package: 'distr'
+The following object(s) are masked from 'package:stats':
- The following object(s) are masked from package:stats :
+ df, qqplot, sd
- df,
- qqplot,
- sd
-
Loading required package: RobLox
Loading required package: distrMod
Loading required package: distrEx
@@ -76,12 +103,11 @@
Attaching package: 'actuar'
+The following object(s) are masked from 'package:grDevices':
- The following object(s) are masked from package:grDevices :
+ cm
- cm
-
-:distrEx> Extensions of package distr (version 2.2)
+:distrEx> Extensions of package distr (version 2.3)
:distrEx>
:distrEx> Note: Packages "e1071", "moments", "fBasics" should be
:distrEx> attached /before/ package "distrEx". See distrExMASK().
@@ -96,16 +122,12 @@
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
- IQR,
- mad,
- median,
- var
-
Loading required package: RandVar
-:RandVar> Implementation of random variables (version 0.7)
+:RandVar> Implementation of random variables (version 0.8)
:RandVar>
:RandVar> For more information see ?"RandVar", NEWS("RandVar"), as
:RandVar> well as
@@ -115,8 +137,8 @@
Loading required package: MASS
Loading required package: stats4
-:distrMod> Object orientated implementation of probability models
-:distrMod> (version 2.2)
+:distrMod> Object oriented implementation of probability models
+:distrMod> (version 2.3)
:distrMod>
:distrMod> Some functions from pkg's 'base' and 'stats' are
:distrMod> intentionally masked ---see distrModMASK().
@@ -127,25 +149,30 @@
:distrMod> For more information see ?"distrMod",
:distrMod> NEWS("distrMod"), as well as
:distrMod> http://distr.r-forge.r-project.org/
-:distrMod> Package "distrDoc" provides a vignette to this package
+:distrMod> There is a vignette to this package; try
+:distrMod> vignette("distrMod").
+:distrMod> Package "distrDoc" provides a vignette to the other
+:distrMod> distrXXX packages,
:distrMod> as well as to several related packages; try
:distrMod> vignette("distr").
Attaching package: 'distrMod'
+The following object(s) are masked from 'package:stats4':
- The following object(s) are masked from package:stats4 :
+ confint
- confint
+The following object(s) are masked from 'package:stats':
+ confint
- The following object(s) are masked from package:stats :
+The following object(s) are masked from 'package:base':
- confint
+ norm
Loading required package: RobAStBase
-:RobAStBase> Robust Asymptotic Statistics (version 0.7.1)
+:RobAStBase> Robust Asymptotic Statistics (version 0.8)
:RobAStBase>
:RobAStBase> Some functions from pkg's 'stats' and 'graphics'
:RobAStBase> are intentionally masked ---see RobAStBaseMASK().
@@ -160,25 +187,22 @@
Attaching package: 'RobAStBase'
+The following object(s) are masked from 'package:stats':
- The following object(s) are masked from package:stats :
+ start
- start
+The following object(s) are masked from 'package:graphics':
+ clip
- 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':
- The following object(s) are masked from package:evd :
+ qq
- qq
-
Loading required package: RColorBrewer
>
> assign(".oldSearch", search(), pos = 'CheckExEnv')
@@ -232,8 +256,8 @@
> probes <- log2(pm(SpikeIn))
> (res <- KolmogorovMinDist(probes, Norm()))
$dist
- [1] 0.1642185 0.1567706 0.1571387 0.1609188 0.1617499 0.1607157 0.1382646
- [8] 0.1471997 0.1693088 0.1836652 0.1787724 0.1601283 0.1728984 0.1519412
+ [1] 0.1755693 0.1567648 0.1571410 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
$n
@@ -350,7 +374,7 @@
> X <- matrix(rnorm(50000*20, mean = 1), nrow = 50000)
> system.time(robloxbioc(X))
user system elapsed
- 11.692 0.888 14.859
+ 4.380 0.110 4.498
>
> ## using Affymetrix-Data
> ## confer example to generateExprVal.method.mas
@@ -387,7 +411,7 @@
> ### * <FOOTER>
> ###
> cat("Time elapsed: ", proc.time() - get("ptime", pos = 'CheckExEnv'),"\n")
-Time elapsed: 29.937 1.044 35.693 0.016 0.008
+Time elapsed: 10.24 0.16 10.423 0 0
> grDevices::dev.off()
postscript
2
More information about the Robast-commits
mailing list