Author: Karl W Broman
Diff between qtlbook versions 0.16-3 dated 2009-03-30 and 0.17-1 dated 2009-04-28
Title: Datasets for the R/qtl book
Description: Datasets for the book, A guide to QTL Mapping with R/qtl
.gitignore |only
DESCRIPTION | 10 +++++-----
inst/LICENSE.txt | 10 ++++------
inst/STATUS.txt | 23 +++++++++++++----------
4 files changed, 22 insertions(+), 21 deletions(-)
Author: Gabriel Rodrigues Alves Margarido
Diff between onemap versions 1.0-0 dated 2009-04-17 and 1.0-1 dated 2009-04-28
Title: Software for constructing genetic maps in outcrossing species
Description: Analysis of molecular marker data from non-model systems
to simultaneously estimate linkage and linkage phases (genetic
map construction)
onemap-1.0-0/onemap/inst/doc/Tutorial_OneMap.Rnw |only
onemap-1.0-0/onemap/inst/doc/Tutorial_OneMap.pdf |only
onemap-1.0-0/onemap/inst/doc/Tutorial_OneMap_with_output.pdf |only
onemap-1.0-1/onemap/DESCRIPTION | 8 -
onemap-1.0-1/onemap/R/comb.ger.R | 58 ++++++++++-
onemap-1.0-1/onemap/R/compare.R | 22 +++-
onemap-1.0-1/onemap/R/rf.graph.table.R | 4
onemap-1.0-1/onemap/R/try.seq.R | 38 ++++++-
onemap-1.0-1/onemap/inst/doc/Turorial_Onemap.Rnw |only
onemap-1.0-1/onemap/inst/doc/Turorial_Onemap.pdf |only
onemap-1.0-1/onemap/inst/doc/Turorial_Onemap_with_output.pdf |only
onemap-1.0-1/onemap/man/onemap-internal.Rd | 4
onemap-1.0-1/onemap/man/rcd.Rd | 2
onemap-1.0-1/onemap/src/hmm_out.c | 5
onemap-1.0-1/onemap/src/twopts.c | 4
onemap-1.0-1/onemap/src/twopts.h | 4
16 files changed, 129 insertions(+), 20 deletions(-)
Author: Sophie Baillargeon
Diff between Rcapture versions 1.1 dated 2008-01-29 and 1.2-0 dated 2009-04-28
Title: Loglinear Models for Capture-Recapture Experiments
Description: Estimation of abundance and other demographic parameters
for closed populations, open populations and the robust design
in capture-recapture experiments using loglinear models.
Rcapture-1.1/Rcapture/R/Xclosedp.r |only
Rcapture-1.1/Rcapture/R/Xomega.0.R |only
Rcapture-1.1/Rcapture/R/Xomega.t.r |only
Rcapture-1.1/Rcapture/R/Zdelta.R |only
Rcapture-1.1/Rcapture/R/histfreq.0.R |only
Rcapture-1.1/Rcapture/R/histfreq.t.R |only
Rcapture-1.1/Rcapture/R/histpos.0.R |only
Rcapture-1.1/Rcapture/R/histpos.t.R |only
Rcapture-1.1/Rcapture/man/histfreq.Rd |only
Rcapture-1.1/Rcapture/man/model.matrices.Rd |only
Rcapture-1.2-0/Rcapture/DESCRIPTION | 28 -
Rcapture-1.2-0/Rcapture/NAMESPACE |only
Rcapture-1.2-0/Rcapture/NEWS |only
Rcapture-1.2-0/Rcapture/R/closedp.Mtb.R | 34 -
Rcapture-1.2-0/Rcapture/R/closedp.R | 583 +++++++++--------------
Rcapture-1.2-0/Rcapture/R/closedp.bc.R | 358 +++++---------
Rcapture-1.2-0/Rcapture/R/closedp.h.r | 30 -
Rcapture-1.2-0/Rcapture/R/closedp.mX.R | 18
Rcapture-1.2-0/Rcapture/R/closedpCI.R |only
Rcapture-1.2-0/Rcapture/R/descriptive.R | 259 +++++-----
Rcapture-1.2-0/Rcapture/R/histfreq.R |only
Rcapture-1.2-0/Rcapture/R/histpos.R |only
Rcapture-1.2-0/Rcapture/R/internal.R |only
Rcapture-1.2-0/Rcapture/R/model.matrices.R |only
Rcapture-1.2-0/Rcapture/R/openp.R | 95 +--
Rcapture-1.2-0/Rcapture/R/periodhist.R | 33 -
Rcapture-1.2-0/Rcapture/R/profileCI.R | 70 +-
Rcapture-1.2-0/Rcapture/R/robustd.0.R | 235 +--------
Rcapture-1.2-0/Rcapture/R/robustd.t.r | 293 +++--------
Rcapture-1.2-0/Rcapture/R/uifit.R | 168 ++----
Rcapture-1.2-0/Rcapture/data/BBS2001.rda |only
Rcapture-1.2-0/Rcapture/data/catb.rda |only
Rcapture-1.2-0/Rcapture/data/mvole.rda |binary
Rcapture-1.2-0/Rcapture/data/rbvole.rda |binary
Rcapture-1.2-0/Rcapture/inst/doc/RcaptureJSS.Rnw |only
Rcapture-1.2-0/Rcapture/inst/doc/RcaptureJSS.pdf |binary
Rcapture-1.2-0/Rcapture/inst/doc/Rplots.pdf |only
Rcapture-1.2-0/Rcapture/inst/doc/biblio |only
Rcapture-1.2-0/Rcapture/inst/doc/fig |only
Rcapture-1.2-0/Rcapture/inst/doc/jss.bst |only
Rcapture-1.2-0/Rcapture/inst/doc/jss.cls |only
Rcapture-1.2-0/Rcapture/man/BBS2001.Rd |only
Rcapture-1.2-0/Rcapture/man/HIV.Rd | 16
Rcapture-1.2-0/Rcapture/man/Rcapture.package.Rd | 59 +-
Rcapture-1.2-0/Rcapture/man/bunting.Rd | 15
Rcapture-1.2-0/Rcapture/man/catb.Rd |only
Rcapture-1.2-0/Rcapture/man/closedp.Mtb.Rd | 10
Rcapture-1.2-0/Rcapture/man/closedp.Rd | 130 +++--
Rcapture-1.2-0/Rcapture/man/closedp.bc.Rd | 46 +
Rcapture-1.2-0/Rcapture/man/closedp.custom.Rd | 26 -
Rcapture-1.2-0/Rcapture/man/closedpCI.Rd |only
Rcapture-1.2-0/Rcapture/man/descriptive.Rd | 63 +-
Rcapture-1.2-0/Rcapture/man/duck.Rd | 15
Rcapture-1.2-0/Rcapture/man/hare.Rd | 20
Rcapture-1.2-0/Rcapture/man/histpos.Rd | 12
Rcapture-1.2-0/Rcapture/man/mvole.Rd | 9
Rcapture-1.2-0/Rcapture/man/openp.Rd | 15
Rcapture-1.2-0/Rcapture/man/periodhist.Rd | 25
Rcapture-1.2-0/Rcapture/man/profileCI.Rd | 24
Rcapture-1.2-0/Rcapture/man/rbvole.Rd | 7
Rcapture-1.2-0/Rcapture/man/robustd.Rd | 33 -
Rcapture-1.2-0/Rcapture/man/uifit.Rd | 4
62 files changed, 1195 insertions(+), 1538 deletions(-)
Author: HUANG Ronggui
Title: R-based Qualitative Data Analysis
Description: R package for Qualitative Data Analysis. Current version
only supports plain text.
Diff between RQDA versions 0.1-6 dated 2008-12-30 and 0.1-7 dated 2009-04-28
RQDA-0.1-6/RQDA/R/Rename.R |only RQDA-0.1-6/RQDA/inst |only RQDA-0.1-6/RQDA/man/RQDA-internal.rd |only RQDA-0.1-7/RQDA/CITATION |only RQDA-0.1-7/RQDA/ChangeLog | 121 +++++++++++++++++ RQDA-0.1-7/RQDA/DESCRIPTION | 34 +++- RQDA-0.1-7/RQDA/KnownBugs | 4 RQDA-0.1-7/RQDA/NAMESPACE |only RQDA-0.1-7/RQDA/R/Attributes.R |only RQDA-0.1-7/RQDA/R/AttributesWidge.R |only RQDA-0.1-7/RQDA/R/CaseButton.R | 69 +++++++-- RQDA-0.1-7/RQDA/R/CaseFun.R | 9 - RQDA-0.1-7/RQDA/R/CodeCatButton.R | 32 ++-- RQDA-0.1-7/RQDA/R/CodesFun.R | 243 ++++++++++++++++++++++++++++++----- RQDA-0.1-7/RQDA/R/Coding_Buttons.R | 142 +++++++++++--------- RQDA-0.1-7/RQDA/R/FileButton.R | 133 +++++++++++++++++-- RQDA-0.1-7/RQDA/R/FileCatButton.R | 189 ++++++++++++++++++++------- RQDA-0.1-7/RQDA/R/FilesFun.R | 164 ++++++++++++++++++----- RQDA-0.1-7/RQDA/R/GUIHandler.R | 77 +++-------- RQDA-0.1-7/RQDA/R/Journal.R |only RQDA-0.1-7/RQDA/R/ProjectButton.R | 27 +++ RQDA-0.1-7/RQDA/R/ProjectFun.R | 78 ++++++++++- RQDA-0.1-7/RQDA/R/RQDAtm.R |only RQDA-0.1-7/RQDA/R/Setting.R | 9 + RQDA-0.1-7/RQDA/R/deletion.R | 2 RQDA-0.1-7/RQDA/R/merger.R |only RQDA-0.1-7/RQDA/R/relation.R | 2 RQDA-0.1-7/RQDA/R/root_gui.R | 41 ++++- RQDA-0.1-7/RQDA/R/sysdata.rda |binary RQDA-0.1-7/RQDA/R/utils.R | 103 +++++++++++++- RQDA-0.1-7/RQDA/R/zzz.R | 3 RQDA-0.1-7/RQDA/man/GetAttr.Rd |only RQDA-0.1-7/RQDA/man/GetCaseId.rd |only RQDA-0.1-7/RQDA/man/GetFileId.rd | 22 ++- RQDA-0.1-7/RQDA/man/GetFileIdSets.Rd |only RQDA-0.1-7/RQDA/man/RQDA-package.Rd | 4 RQDA-0.1-7/RQDA/man/RQDA2tm.Rd |only RQDA-0.1-7/RQDA/man/RQDAQuery.rd |only RQDA-0.1-7/RQDA/man/RQDATables.rd |only RQDA-0.1-7/RQDA/man/gselect.list.rd |only RQDA-0.1-7/RQDA/man/retrieval.Rd |only 41 files changed, 1181 insertions(+), 327 deletions(-)
Author: Delphine Charif and Jean R. Lobry and Anamaria Necsulea and
Leonor Palmeira and Simon Penel
Title: Biological Sequences Retrieval and Analysis
Description: Exploratory data analysis and data visualization for
biological sequence (DNA and protein) data. Include also
utilities for sequence data management under the ACNUC system.
Diff between seqinr versions 2.0-2 dated 2009-02-06 and 2.0-3 dated 2009-04-28
seqinr-2.0-2/seqinr/inst/doc/seqinr_2_0-1.pdf |only seqinr-2.0-3/seqinr/DESCRIPTION | 27 seqinr-2.0-3/seqinr/R/al2bp.R |only seqinr-2.0-3/seqinr/R/getTrans.R | 2 seqinr-2.0-3/seqinr/R/peakabif.R | 7 seqinr-2.0-3/seqinr/R/plotladder.R | 2 seqinr-2.0-3/seqinr/R/readBins.R |only seqinr-2.0-3/seqinr/R/readPanels.R |only seqinr-2.0-3/seqinr/inst/abif/AmpFLSTR_Bins_v1.txt |only seqinr-2.0-3/seqinr/inst/abif/AmpFLSTR_Panels_v1.txt |only seqinr-2.0-3/seqinr/inst/abif/Promega_Bins_v1.txt |only seqinr-2.0-3/seqinr/inst/abif/Promega_Panels_v1.txt |only seqinr-2.0-3/seqinr/inst/doc/seqinr_2_0-3.pdf |only seqinr-2.0-3/seqinr/inst/doc/src/appendix/FAQ.tex | 36 seqinr-2.0-3/seqinr/inst/doc/src/appendix/fdl.tex | 2 seqinr-2.0-3/seqinr/inst/doc/src/appendix/releasenotes.rnw | 43 seqinr-2.0-3/seqinr/inst/doc/src/appendix/releasenotes.tex | 88 + seqinr-2.0-3/seqinr/inst/doc/src/appendix/subsequences.tex | 540 ++++++++--- seqinr-2.0-3/seqinr/inst/doc/src/config/book.bib | 7 seqinr-2.0-3/seqinr/inst/doc/src/config/commonrnw.rnw | 13 seqinr-2.0-3/seqinr/inst/doc/src/config/sessionInfo.rnw | 4 seqinr-2.0-3/seqinr/inst/doc/src/figs/cover.pdf | 8 seqinr-2.0-3/seqinr/inst/doc/src/frontmatter/cover.tex | 20 seqinr-2.0-3/seqinr/inst/doc/src/mainmatter/acnucsocket.tex | 188 +-- seqinr-2.0-3/seqinr/inst/doc/src/mainmatter/chr1.RData |binary seqinr-2.0-3/seqinr/inst/doc/src/mainmatter/dealseq.tex | 24 seqinr-2.0-3/seqinr/inst/doc/src/mainmatter/extractseqs.tex | 56 - seqinr-2.0-3/seqinr/inst/doc/src/mainmatter/getseqacnuc.tex | 110 +- seqinr-2.0-3/seqinr/inst/doc/src/mainmatter/getseqflat.tex | 32 seqinr-2.0-3/seqinr/inst/doc/src/mainmatter/introduction.tex | 51 - seqinr-2.0-3/seqinr/inst/doc/src/mainmatter/multivariate.tex | 24 seqinr-2.0-3/seqinr/inst/doc/src/mainmatter/nonparastats.tex | 24 seqinr-2.0-3/seqinr/inst/doc/src/mainmatter/querylang.tex | 36 seqinr-2.0-3/seqinr/inst/doc/src/tables/aacost.tex | 46 seqinr-2.0-3/seqinr/inst/doc/src/tables/dpqrtable.tex | 44 seqinr-2.0-3/seqinr/inst/doc/src/tables/toyaa.tex | 14 seqinr-2.0-3/seqinr/inst/doc/src/tables/toycodon.tex | 12 seqinr-2.0-3/seqinr/inst/sequences/DarrenObbard.fasta |only seqinr-2.0-3/seqinr/man/al2bp.Rd |only seqinr-2.0-3/seqinr/man/kaks.Rd | 56 - seqinr-2.0-3/seqinr/man/peakabif.Rd | 7 seqinr-2.0-3/seqinr/man/plotladder.Rd | 2 seqinr-2.0-3/seqinr/man/readBins.Rd |only seqinr-2.0-3/seqinr/man/readPanels.Rd |only seqinr-2.0-3/seqinr/src/kaks.c | 272 ++--- 45 files changed, 1099 insertions(+), 698 deletions(-)
Author: Hadley Wickham
Diff between reshape versions 0.8.2 dated 2008-11-04 and 0.8.3 dated 2009-04-28
Title: Flexibly reshape data.
Description: Reshape lets you flexibly restructure and aggregate data
using just two functions: melt and cast.
DESCRIPTION | 9 ++++++---
NEWS | 6 ++++++
R/melt.r | 13 ++++++++-----
R/stamp.r | 2 +-
R/utils.r | 15 ++++++++++++++-
inst/CITATION | 2 +-
man/cast-parse-formula-uw.rd | 6 +++---
man/french-fries.rd | 3 ++-
man/melt-check-j7.rd | 4 ++--
man/melt-data-frame-da.rd | 2 +-
man/rename-au.rd | 15 ++++++++++++++-
man/stamp-fw.rd | 2 +-
man/tips.rd | 5 +++--
13 files changed, 62 insertions(+), 22 deletions(-)
Author: Derek Young Tatiana Benaglia Didier Chauveau Ryan Elmore Tom
Hettmansperger David Hunter Hoben Thomas Fengjuan Xuan
Title: Tools for analyzing finite mixture models
Description: A collection of R functions for analyzing finite mixture
models.
Diff between mixtools versions 0.3.3 dated 2009-01-11 and 0.4.0 dated 2009-04-28
DESCRIPTION | 31 ++++------ R/bootcomp.R | 4 - R/compcdf.R | 94 +++++++++------------------------ R/dmvnorm.R | 13 ++-- R/multmixEM.R | 65 ++++++++++++++-------- R/multmixmodelsel.R | 8 ++ R/normalmixEM.R | 136 +++++++++++++++++++++++++++--------------------- R/regmixMH.R | 4 - R/summary.mixEM.R |only man/compCDF.Rd | 31 +++++++--- man/dmvnorm.Rd | 8 +- man/makemultdata.Rd | 3 - man/multmixEM.Rd | 22 ++++--- man/multmixmodel.sel.Rd | 7 +- man/normalmixEM.Rd | 75 +++++++++++++++++++++----- man/npEM.Rd | 13 ++-- man/spEM.Rd | 9 +-- man/summary.mixEM.Rd |only src/multinompost.c |only src/normpost.c |only src/sd.c | 2 src/z.c | 9 +-- 22 files changed, 297 insertions(+), 237 deletions(-)
Author: Cedric Gouy-Pailler
Diff between jointDiag versions 0.1 dated 2009-03-12 and 0.1-2 dated 2009-04-28
Title: Joint Approximate Diagonalization of a set of square matrices
Description: Different algorithms to perform approximate joint
diagonalization of a finite set of square matrices. Depending
on the algorithm, orthogonal or non-orthogonal diagonalizer is
found. These algorithms are particularly useful in the context
of blind source separation.
jointDiag-0.1-2/jointDiag/DESCRIPTION | 22 +++++++++-------------
jointDiag-0.1-2/jointDiag/man/ajd.Rd | 3 ++-
jointDiag-0.1-2/jointDiag/src/Makevars | 3 +--
jointDiag-0.1-2/jointDiag/src/Makevars.win | 3 +--
jointDiag-0.1/jointDiag/R/lscjadiag.R |only
5 files changed, 13 insertions(+), 18 deletions(-)
Author: Sinnwell JP, Schaid DJ
Title: Statistical Analysis of Haplotypes with Traits and Covariates
when Linkage Phase is Ambiguous
Description: A suite of S-PLUS/R routines for the analysis of
indirectly measured haplotypes. The statistical methods assume
that all subjects are unrelated and that haplotypes are
ambiguous (due to unknown linkage phase of the genetic
markers). The main functions are: haplo.em, haplo.glm,
haplo.score, haplo.power, and seqhap. Copyright: 2003 Mayo
Foundation for Medical Education and Research.
Diff between haplo.stats versions 1.3.8 dated 2008-05-13 and 1.4.3 dated 2009-04-28
DESCRIPTION | 25 ++++++++----- NEWS | 47 +++++++++++++++++++++++- R/haplo.scan.q | 17 +++++++- R/haplo.score.q | 15 +++++-- R/plot.seqhap.q | 59 +++++++++++++++++------------- R/print.haplo.em.q | 25 ++++++++++--- R/print.seqhap.q | 35 +++++++++++------- R/seqhap.q | 17 ++++++-- R/summary.haplo.em.q | 10 +++-- README.haplo.stats | 30 +++++++++------ data/seqhap.dat.tab | 2 - inst/doc/manualHaploStats.pdf |binary man/hapPower.demo.Rd | 38 +++++++++++-------- man/hla.demo.Rd | 80 ++++++++++++++++++++++++------------------ man/plot.seqhap.Rd | 30 ++++++++++++--- man/seqhap.Rd | 37 +++++++++++++------ man/seqhap.dat.Rd | 56 +++++++++++++++++++++-------- src/seqhap.c | 72 +++++++++++++++++++++++++++---------- 18 files changed, 407 insertions(+), 188 deletions(-)
Author: Sebastian Kaiser, Rodrigo Santamaria, Roberto Theron, Luis
Quintales and Friedrich Leisch.
Title: BiCluster Algorithms
Description: The main function biclust provides several algorithms to
find biclusters in two-dimensional data: Cheng and Church,
Spectral, Plaid Model, Xmotifs and Bimax. In addition, the
package provides methods for data preprocessing (normalization
and discretisation), visualisation, and validation of bicluster
solutions.
Diff between biclust versions 0.7.1 dated 2009-03-13 and 0.7.2 dated 2009-04-28
biclust-0.7.1/biclust/R/gibbs.r |only biclust-0.7.1/biclust/R/qhb.r |only biclust-0.7.2/biclust/DESCRIPTION | 14 ++++++++------ biclust-0.7.2/biclust/NAMESPACE | 2 +- biclust-0.7.2/biclust/NEWS | 3 ++- biclust-0.7.2/biclust/R/clustmember.r | 4 ++-- biclust-0.7.2/biclust/R/questmotif.r | 4 ++-- biclust-0.7.2/biclust/man/clustmember.rd | 6 +++--- biclust-0.7.2/biclust/man/plotclust.rd | 6 +++--- 9 files changed, 21 insertions(+), 18 deletions(-)
Author: Hector Corrada Bravo (CSDP by Brian Borchers)
Title: R interface to the CSDP semidefinite programming library
Description: R interface to the CSDP semidefinite programming library.
Installs version 6.0.1 of CSDP from the COIN-OR website if
required. An existing intallation of CSDP may be used by
passing the proper configure arguments to the installation
command. See the INSTALL file for further details.
Diff between Rcsdp versions 0.1-3 dated 2009-03-09 and 0.1-4 dated 2009-04-28
CHANGES |only DESCRIPTION | 15 +++++++++++---- R/sparse.R | 2 +- 3 files changed, 12 insertions(+), 5 deletions(-)