[Robast-commits] r1035 - in pkg/RobLoxBioC: . inst
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Mon Jul 23 22:28:27 CEST 2018
Author: ruckdeschel
Date: 2018-07-23 22:28:27 +0200 (Mon, 23 Jul 2018)
New Revision: 1035
Modified:
pkg/RobLoxBioC/DESCRIPTION
pkg/RobLoxBioC/NAMESPACE
pkg/RobLoxBioC/inst/NEWS
Log:
[RobLox] merged branch 1.1 into trunk
Modified: pkg/RobLoxBioC/DESCRIPTION
===================================================================
--- pkg/RobLoxBioC/DESCRIPTION 2018-07-23 20:21:14 UTC (rev 1034)
+++ pkg/RobLoxBioC/DESCRIPTION 2018-07-23 20:28:27 UTC (rev 1035)
@@ -1,18 +1,19 @@
-Package: RobLoxBioC
-Version: 0.9
-Date: 2013-09-12
-Title: Infinitesimally robust estimators for preprocessing omics data
+Package: RobLox
+Version: 1.1.0
+Date: 2018-07-17
+Title: Optimally Robust Influence Curves and Estimators for Location and Scale
Description: Functions for the determination of optimally robust influence curves and
- estimators for preprocessing omics data, in particular gene expression data.
-Depends: R(>= 2.14.0), methods, RobLox(>= 0.9), affy
-Imports: BiocGenerics, Biobase, beadarray, lattice, RColorBrewer, distr(>= 2.5.2)
-Author: Matthias Kohl <Matthias.Kohl at stamats.de>
-Maintainer: Matthias Kohl <Matthias.Kohl at stamats.de>
-LazyLoad: yes
+ estimators in case of normal location and/or scale.
+Depends: R(>= 2.14.0), stats, distrMod(>= 2.5.2), RobAStBase(>= 0.9)
+Imports: methods, lattice, RColorBrewer, Biobase, RandVar(>= 0.9.2), distr(>= 2.5.2)
+Suggests: MASS
+Authors at R: c(person("Matthias", "Kohl", role=c("cre", "cph"),
+ email="Matthias.Kohl at stamats.de"), person("Peter", "Ruckdeschel", role=c("aut",
+ "cph")))
ByteCompile: yes
License: LGPL-3
+Encoding: latin1
URL: http://robast.r-forge.r-project.org/
-Encoding: latin1
LastChangedDate: {$LastChangedDate$}
LastChangedRevision: {$LastChangedRevision$}
-SVNRevision: 696
+VCS/SVNRevision: 940
Modified: pkg/RobLoxBioC/NAMESPACE
===================================================================
--- pkg/RobLoxBioC/NAMESPACE 2018-07-23 20:21:14 UTC (rev 1034)
+++ pkg/RobLoxBioC/NAMESPACE 2018-07-23 20:28:27 UTC (rev 1035)
@@ -1,15 +1,48 @@
-import("methods", "distr")
-importMethodsFrom("BiocGenerics","append","annotation")
-importFrom("Biobase","assayDataNew")
+importFrom("Biobase", "rowMedians")
importFrom("lattice","stripplot")
importFrom("RColorBrewer","brewer.pal")
-importClassesFrom("Biobase","ExpressionSet","AssayData","AnnotatedDataFrame")
-importMethodsFrom("Biobase", "rowMedians", "featureNames", "sampleNames",
- "phenoData", "experimentData", "exprs", "exprs<-", "assayData","assayData<-")
-importFrom("affy","bg.correct.mas","getCdfInfo","tukey.biweight")
-importMethodsFrom("affy","intensity")
-import("beadarray")
-importFrom("RobLox", "rowRoblox", "finiteSampleCorrection")
+importFrom("distr", "p", "q", "r", "q.l", "Reals")
+importClassesFrom("distr","Reals")
+importFrom("RandVar", "EuclRandVarList", "RealRandVariable")
+importClassesFrom("RandVar", "EuclRandVarList", "RealRandVariable")
+importFrom("distrMod", "NormLocationFamily", "NormLocationScaleFamily", "symmetricBias", "NormType")
+importClassesFrom("distrMod", "L2LocationFamily", "NormLocationFamily", "NormLocationScaleFamily")
+importMethodsFrom("distrMod", "distribution", "main", "addInfo<-", "Infos", "Infos<-",
+ "normtype", "biastype","normtype<-","biastype<-", "estimate")
+importFrom("RobAStBase","generateIC","ContNeighborhood", "IC")
+importFrom("grDevices", "dev.new")
+importFrom("graphics", "abline", "boxplot", "curve", "layout",
+ "legend", "par", "plot")
+importFrom("methods", "is", "new")
+importFrom("stats", "approx", "complete.cases", "dnorm", "integrate",
+ "mad", "median", "na.omit", "optim", "optimize", "pnorm",
+ "qnorm", "rbinom", "rnorm", "uniroot")
+importClassesFrom("RobAStBase", "HampelWeight", "ALEstimate", "kStepEstimate", "ContNeighborhood")
+importMethodsFrom("RobAStBase", "clip", "cent", "stand", "weight", "clip<-", "cent<-", "stand<-", "weight<-",
+ "getweight", "makeIC", "CallL2Fam", "CallL2Fam<-", "neighborRadius", "modifyIC", "addInfo<-")
-exportMethods("robloxbioc", "KolmogorovMinDist")
-export("AffySimStudy", "IlluminaSimStudy")
+export(finiteSampleCorrection,
+ rlsOptIC.AL,
+ rlsOptIC.M,
+ rlsOptIC.BM,
+ rlsOptIC.Hu1,
+ rlsOptIC.Hu2a,
+ rlsOptIC.Hu2,
+ rlsOptIC.Hu3,
+ rlsOptIC.HuMad,
+ rlsOptIC.Ha3,
+ rlsOptIC.Ha4,
+ rlsOptIC.HaMad,
+ rlsOptIC.An1,
+ rlsOptIC.An2,
+ rlsOptIC.AnMad,
+ rlsOptIC.Tu1,
+ rlsOptIC.Tu2,
+ rlsOptIC.TuMad,
+ rlsOptIC.MM2,
+ rlOptIC,
+ rsOptIC,
+ roblox,
+ rowRoblox,
+ colRoblox,
+ showdown)
Modified: pkg/RobLoxBioC/inst/NEWS
===================================================================
--- pkg/RobLoxBioC/inst/NEWS 2018-07-23 20:21:14 UTC (rev 1034)
+++ pkg/RobLoxBioC/inst/NEWS 2018-07-23 20:28:27 UTC (rev 1035)
@@ -1,5 +1,5 @@
###############################################################################
-## News: to package RobLoxBioC
+## News: to package RobLox
###############################################################################
(first two numbers of package versions do not necessarily reflect
@@ -8,11 +8,27 @@
information)
#######################################
-version 0.9
+version 1.1
#######################################
user-visible CHANGES:
++ DESCRIPTION tag SVNRevision changed to VCS/SVNRevision
+under the hood:
++ wherever possible also use q.l internally instead of q to
+ provide functionality in IRKernel
+
+#######################################
+version 1.0
+#######################################
+
+user-visible CHANGES:
++ title changed to title style / capitalization
+
+#######################################
+version 0.9
+#######################################
+
GENERAL ENHANCEMENTS:
+ cleaned DESCRIPTION and NAMESPACE file as to Imports/Depends
@@ -24,35 +40,38 @@
#######################################
-version 0.8.3
+version 0.8.1
#######################################
-+ update for beadarray versions >= 2.0.0 with support by Mark Dunnings and
- Andy Lynch
-+ some changes for internal functions due to changes in R 2.16.0 regarding
- .C and .Call
++ new internal functions due to changes to .C() and .Call() calls
+
#######################################
version 0.8
#######################################
-+ renamed AffySimStudy.R to AffymetrixSimStudy.R
-+ update of Figure numbers in IlluminaExample.R
-+ added scripts AffymetrixReproducibility.R and IlluminaReproducibility.R
-+ DESCRIPTION files and package-help files gain a tag SVNRevision
+BUG FIX:
++ roblox(): if only sd or mean is to be estimated, starting
+ value mean.sd was not; similarly, in case only mean is of
+ interest, robEst had no component est...
+
+ + DESCRIPTION files and package-help files gain a tag SVNRevision
to be filled by get[All]RevNr.R from utils in distr
#######################################
-## version 0.7.1
-#######################################
-+ corrected bug in AffySimStudy and IlluminaSimStudy
-+ minor modifications of scripts in scripts folder
-
-#######################################
version 0.7
#######################################
+
+user-visible CHANGES:
+
++ Roblox,colRoblox,rowRoblox gain na.rm argument
+ and consistently fill new slot completecases
++ introduction of finite-sample correction
++ handle marginal cases n = 1 or 2 as well as eps = 0 and mad = 0
++ package Rd-file added
+
GENERAL ENHANCEMENTS:
-+ added tests/Examples folder with file RobLoxBioC-Ex.Rout.save to have
++ added tests/Examples folder with file RobLox-Ex.Rout.save to have
some automatic testing
+ added TOBEDONE (sic!) files; in English (for possible collaborators)
+ added keyword robust and made some minor corrections ...
@@ -72,51 +91,21 @@
+ removed pdf-file from version control - Rnw-file is sufficient
-
INTERNALLY:
-+ renamed AllGeneric.R to 0AllGeneric.R to be on first position ...
-+ in robloxAffyBatch.R return se not sd ...
-+ some modifications for Figure 2 in IlluminaExample.R
-+ set default to 3-step estimation ...
-+ changed return value of KolmogorovMinDist, now also returns the corresponding sample sizes.
-+ Added file for Illumina simulation study and renamed file AffySimStudy.Rd to SimStudies.Rd.
-+ reduced the Illumina example code to relevant part ...
++ gains new slots of kStepEstimator
-
BUGFIXES:
-+ code seems to work correctly, affycompTable in AffymetrixExample does
- not work yet (because of missing dilution data).
++ corrected small bug in computation of bias in case of TuMad IC ...
++ small correction in finiteSampleCorrection ...
++ forgot to include correction for 50% or more outliers
#######################################
-version 0.5
+version 0.6.1
#######################################
-+ added example code for Illumina data
-+ function to perform Monte-Carlo studies for comparison with Illumina's
- default method
-
-#######################################
-version 0.4
-#######################################
-+ added finite-sample correction
-+ handle cases with sample size <= 2 and contamination eps = 0
-+ moved function AffySimStudy from folder inst/scripts to folder R as
- exported and documented function to perform Monte-Carlo studies.
-
-#######################################
-version 0.3
-#######################################
-+ added KolmogorovMinDist methods for matrix, AffyBatch and BeadLevelList
-
-#######################################
-version 0.2
-#######################################
-+ robloxbioc methods for AffyBatch and BeadLevelList
-
-#######################################
-version 0.1
-#######################################
-+ start of development
-
++ bug in computation of as. covariance in roblox corrected.
++ bug in rsOptIC corrected.
++ introduction of NEWS-file
++ update of CITATION-file (based on code provided by A. Zeileis on R help)
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