Title: A collection of functions useful for phonetics work.
Diff between phonTools versions 0.1-1 dated 2012-07-24 and 0.1-2 dated 2012-09-14
Description: The functions contained in this package are intended to
facilitate the organization, display, and analysis of the sorts
of data frequently encountered in phonetics research and
experimentation.
Author: Santiago Barreda
Maintainer: Santiago Barreda
DESCRIPTION | 10 +++++-----
LICENSE |only
MD5 | 17 ++++++++++++-----
R/createtemplate.R |only
R/interpolate.R |only
R/spectralslice.R | 8 ++++----
R/spectrogram.R | 9 ++++-----
R/windowfunc.R |only
man/createtemplate.Rd |only
man/interpolate.Rd |only
man/spectralslice.Rd | 7 ++++---
man/spectrogram.Rd | 9 +++++----
man/windowfunc.Rd |only
13 files changed, 34 insertions(+), 26 deletions(-)
Title: Rmetrics - Markets and Basic Statistics
Diff between fBasics versions 2160.83 dated 2012-08-23 and 2160.84 dated 2012-09-14
Description: Environment for teaching "Financial Engineering and
Computational Finance" NOTE: SEVERAL PARTS ARE STILL
PRELIMINARY AND MAY BE CHANGED IN THE FUTURE. THIS TYPICALLY
INCLUDES FUNCTION AND ARGUMENT NAMES, AS WELL AS DEFAULTS FOR
ARGUMENTS AND RETURN VALUES. Please donate, www.rmetrics.org,
to support future activities of the Rmetrics association.
Author: Diethelm Wuertz and Rmetrics core team members, uses code
builtin from the following R contributed packages: gmm from
Pierre Chauss, gld from Robert King, gss from Chong Gu, nortest
from Juergen Gross, HyperbolicDist from David Scott, sandwich
from Thomas Lumley and Achim Zeileis, fortran/C code from
Kersti Aas and akima (0.5-1: R code under GPL) from Albrecht
Gebhardt
Maintainer: Yohan Chalabi
fBasics-2160.83/fBasics/R/utils-Sys.putenv.R |only
fBasics-2160.84/fBasics/ChangeLog | 6 ++++++
fBasics-2160.84/fBasics/DESCRIPTION | 10 +++++-----
fBasics-2160.84/fBasics/MD5 | 5 ++---
4 files changed, 13 insertions(+), 8 deletions(-)
Title: A simple way to fit detection functions to distance sampling
data and calculate abundance/density for biological
populations.
Diff between Distance versions 0.6.1 dated 2012-08-01 and 0.6.2 dated 2012-09-14
Description: A library that provides a simple way of fitting detection
functions to distance sampling data for both line and point
transects. Adjustment term selection, left and right
truncation as well as monotonicity constraints and binning are
supported. Abundance and density estimates can also be
calculated if survey area information is provided.
Author: David L. Miller
Maintainer: David L Miller
DESCRIPTION | 8 ++--
MD5 | 8 ++--
R/ds.R | 75 +++++++++++++++++++++++++++++++---------------
R/print.summary.dsmodel.R | 2 -
man/ds.Rd | 9 +++--
5 files changed, 66 insertions(+), 36 deletions(-)
Title: Tools to make developing R code easier
Diff between devtools versions 0.7.1 dated 2012-07-02 and 0.8 dated 2012-09-14
Description: Collection of package development tools
Author: Hadley Wickham [aut, cre], Winston Chang [aut], R Core team
[ctb] (Namespace related code extracted out of base R)
Maintainer: Hadley Wickham
devtools-0.7.1/devtools/R/load-c.r |only
devtools-0.7.1/devtools/man/clear_pkg_env.Rd |only
devtools-0.7.1/devtools/man/env_name.Rd |only
devtools-0.7.1/devtools/man/load_c.Rd |only
devtools-0.7.1/devtools/man/load_deps.Rd |only
devtools-0.8/devtools/DESCRIPTION | 40 +
devtools-0.8/devtools/MD5 | 210 ++++++----
devtools-0.8/devtools/NAMESPACE | 36 +
devtools-0.8/devtools/NEWS | 149 +++++++
devtools-0.8/devtools/R/bash.r | 2
devtools-0.8/devtools/R/build.r | 23 -
devtools-0.8/devtools/R/check-cran.r | 84 +++-
devtools-0.8/devtools/R/check.r | 40 +
devtools-0.8/devtools/R/check_devtools.r |only
devtools-0.8/devtools/R/compile.r |only
devtools-0.8/devtools/R/create.r |only
devtools-0.8/devtools/R/decompress.r | 35 -
devtools-0.8/devtools/R/dependencies.r | 11
devtools-0.8/devtools/R/dev-example.r |only
devtools-0.8/devtools/R/dev-help.r |only
devtools-0.8/devtools/R/devel-mode.r | 2
devtools-0.8/devtools/R/document.r | 71 +--
devtools-0.8/devtools/R/env-utils.r |only
devtools-0.8/devtools/R/has-devel.r | 12
devtools-0.8/devtools/R/imports-env.r |only
devtools-0.8/devtools/R/inst.r |only
devtools-0.8/devtools/R/install-bitbucket.r | 12
devtools-0.8/devtools/R/install-github.r | 61 ++
devtools-0.8/devtools/R/install-gitorious.r | 13
devtools-0.8/devtools/R/install-url.r | 10
devtools-0.8/devtools/R/install.r | 8
devtools-0.8/devtools/R/load-code.r | 65 +--
devtools-0.8/devtools/R/load-data.r | 6
devtools-0.8/devtools/R/load-dll.r |only
devtools-0.8/devtools/R/load.r | 127 +++++-
devtools-0.8/devtools/R/metadata.r |only
devtools-0.8/devtools/R/missing-s3.r | 6
devtools-0.8/devtools/R/namespace-env.r |only
devtools-0.8/devtools/R/news.r | 2
devtools-0.8/devtools/R/package-deps.r | 89 ++--
devtools-0.8/devtools/R/package-env.r | 127 ++----
devtools-0.8/devtools/R/package.r | 69 ---
devtools-0.8/devtools/R/parent-envs.r |only
devtools-0.8/devtools/R/release.r | 4
devtools-0.8/devtools/R/reload.r | 105 ++++-
devtools-0.8/devtools/R/run-example.r |only
devtools-0.8/devtools/R/run-examples.r | 75 +--
devtools-0.8/devtools/R/run-loadhooks.r |only
devtools-0.8/devtools/R/session-info.r |only
devtools-0.8/devtools/R/system.r | 21 -
devtools-0.8/devtools/R/test.r | 27 +
devtools-0.8/devtools/R/topic-index.r |only
devtools-0.8/devtools/R/utils.r |only
devtools-0.8/devtools/R/vignettes.r | 85 +++-
devtools-0.8/devtools/R/wd.r | 2
devtools-0.8/devtools/README.md | 10
devtools-0.8/devtools/inst/templates |only
devtools-0.8/devtools/inst/tests/check-extrafile |only
devtools-0.8/devtools/inst/tests/depend-missing |only
devtools-0.8/devtools/inst/tests/depend-version |only
devtools-0.8/devtools/inst/tests/dll-load |only
devtools-0.8/devtools/inst/tests/invalid-description/DESCRIPTION | 2
devtools-0.8/devtools/inst/tests/load-hooks |only
devtools-0.8/devtools/inst/tests/namespace |only
devtools-0.8/devtools/inst/tests/test-checks.r |only
devtools-0.8/devtools/inst/tests/test-depend.r |only
devtools-0.8/devtools/inst/tests/test-description.r | 10
devtools-0.8/devtools/inst/tests/test-dll.r |only
devtools-0.8/devtools/inst/tests/test-imports.r |only
devtools-0.8/devtools/inst/tests/test-load-hooks.r |only
devtools-0.8/devtools/inst/tests/test-metadata.r |only
devtools-0.8/devtools/inst/tests/test-namespace.r |only
devtools-0.8/devtools/inst/tests/test-vignettes.r |only
devtools-0.8/devtools/inst/tests/vignettes |only
devtools-0.8/devtools/man/as.envlist.Rd |only
devtools-0.8/devtools/man/as.package.Rd | 2
devtools-0.8/devtools/man/bash.Rd | 2
devtools-0.8/devtools/man/build.Rd | 2
devtools-0.8/devtools/man/build_vignettes.Rd | 11
devtools-0.8/devtools/man/build_win.Rd | 2
devtools-0.8/devtools/man/check.Rd | 6
devtools-0.8/devtools/man/check_cran.Rd | 13
devtools-0.8/devtools/man/check_dep_version.Rd |only
devtools-0.8/devtools/man/check_doc.Rd | 2
devtools-0.8/devtools/man/clean_dll.Rd |only
devtools-0.8/devtools/man/clean_vignettes.Rd |only
devtools-0.8/devtools/man/compile_dll.Rd |only
devtools-0.8/devtools/man/create.Rd |only
devtools-0.8/devtools/man/dev_example.Rd |only
devtools-0.8/devtools/man/dev_help.Rd |only
devtools-0.8/devtools/man/dev_meta.Rd |only
devtools-0.8/devtools/man/dev_packages.Rd |only
devtools-0.8/devtools/man/devtest.Rd |only
devtools-0.8/devtools/man/document.Rd | 14
devtools-0.8/devtools/man/find_code.Rd | 2
devtools-0.8/devtools/man/imports_env.Rd |only
devtools-0.8/devtools/man/inst.Rd |only
devtools-0.8/devtools/man/install.Rd | 2
devtools-0.8/devtools/man/install_bitbucket.Rd | 9
devtools-0.8/devtools/man/install_github.Rd | 20
devtools-0.8/devtools/man/install_gitorious.Rd | 9
devtools-0.8/devtools/man/install_url.Rd | 7
devtools-0.8/devtools/man/load_all.Rd | 71 +++
devtools-0.8/devtools/man/load_code.Rd | 7
devtools-0.8/devtools/man/load_data.Rd | 7
devtools-0.8/devtools/man/load_dll.Rd |only
devtools-0.8/devtools/man/load_imports.Rd |only
devtools-0.8/devtools/man/loaded_packages.Rd |only
devtools-0.8/devtools/man/missing_s3.Rd | 2
devtools-0.8/devtools/man/ns_env.Rd |only
devtools-0.8/devtools/man/parenvs.Rd |only
devtools-0.8/devtools/man/parse_deps.Rd | 4
devtools-0.8/devtools/man/parse_ns_file.Rd |only
devtools-0.8/devtools/man/pkg_env.Rd | 31 +
devtools-0.8/devtools/man/print.envlist.Rd |only
devtools-0.8/devtools/man/release.Rd | 2
devtools-0.8/devtools/man/reload.Rd | 17
devtools-0.8/devtools/man/revdep.Rd | 6
devtools-0.8/devtools/man/run_examples.Rd | 26 -
devtools-0.8/devtools/man/run_onattach.Rd |only
devtools-0.8/devtools/man/run_onload.Rd |only
devtools-0.8/devtools/man/show_news.Rd | 2
devtools-0.8/devtools/man/show_rd.Rd | 5
devtools-0.8/devtools/man/test.Rd | 2
devtools-0.8/devtools/man/unload.Rd |only
devtools-0.8/devtools/man/wd.Rd | 2
devtools-0.8/devtools/src |only
devtools-0.8/devtools/tests/has-devel.R |only
128 files changed, 1377 insertions(+), 561 deletions(-)
Title: Retrieve Oklahoma Mesonet climatological data
Diff between okmesonet versions 0.1.3 dated 2012-05-21 and 0.1.4 dated 2012-09-14
Description: okmesonet retrieves and summarizes Oklahoma (USA) Mesonet
climatological data provided by the Oklahoma Climatological
Survey. Measurements are recorded every five minutes at
approximately 120 stations throughout Oklahoma and are
available in near real-time.
Author: Brady Allred, Torre Hovick, Samuel Fuhlendorf
Maintainer: Brady Allred
DESCRIPTION | 8 ++--
MD5 | 18 +++++----
NAMESPACE | 1
NEWS | 11 +++++
R/okcurobs.R |only
R/okmts.R | 19 ++++++++--
R/retrievemts.R | 6 +--
R/totalprecip.R | 96 ++++++++++++++++++++++++++++------------------------
data/okstations.rda |binary
man/okcurobs.Rd |only
man/okmts.Rd | 11 +++++
11 files changed, 106 insertions(+), 64 deletions(-)
Title: Model-Independent Particle Swarm Optimisation for Environmental
Models
Diff between hydroPSO versions 0.1-57 dated 2012-06-29 and 0.1-58 dated 2012-09-14
Description: This package implements a state-of-the-art version of the
Particle Swarm Optimisation (PSO) algorithm, with a special
focus on the calibration of environmental models. hydroPSO is
model-independent, allowing the user to easily interface any
model code with the calibration engine (PSO). hydroPSO includes
a series of controlling options and PSO variants to fine-tune
the performance of the calibration engine. An advanced
sensitivity analysis function together with user-friendly
plotting summaries facilitate the interpretation and assessment
of the calibration results. Bugs reports/comments/questions are
very welcomed.
Author: Mauricio Zambrano-Bigiarini [aut, cre] and Rodrigo Rojas [ctb]
Maintainer: Mauricio Zambrano-Bigiarini
DESCRIPTION | 16 +--
MD5 | 18 ++--
NAMESPACE | 3
NEWS | 14 +++
R/PSO_v2012.R | 195 ++++++++++++++++++++++++++++++------------------
R/test_functions.R | 13 ++-
man/ReadPlot_results.Rd | 4
man/hydroPSO-package.Rd | 8 -
man/hydroPSO.Rd | 74 +++++++++++++-----
man/test_functions.Rd | 1
10 files changed, 228 insertions(+), 118 deletions(-)
Title: Analysis of Ecological Data : Exploratory and Euclidean methods
in Environmental sciences
Diff between ade4 versions 1.5-0 dated 2012-04-23 and 1.5-1 dated 2012-09-14
Description: Multivariate data analysis and graphical display.
Author: Daniel Chessel, Anne-Beatrice Dufour
Maintainer: Simon Penel
ChangeLog | 76 +++++++++++
DESCRIPTION | 11 -
MD5 | 315 ++++++++++++++++++++++++------------------------
R/bca.rlq.R | 14 --
R/between.R | 14 +-
R/betweencoinertia.R | 14 +-
R/coinertia.R | 37 ++++-
R/corkdist.R | 4
R/discrimin.R | 14 +-
R/dpcoa.R | 14 +-
R/dudi.R | 50 ++++++-
R/dudi.acm.R | 2
R/foucart.R | 12 -
R/kplot.sepan.R | 4
R/ktab.R | 12 -
R/mcoa.R | 10 -
R/mfa.R | 8 -
R/multispati.R | 14 +-
R/niche.R | 18 +-
R/nipals.R | 8 -
R/orthogram.R | 35 ++---
R/pcaiv.R | 65 ++++++---
R/pcaivortho.R | 46 +++++--
R/pta.R | 12 -
R/randtest.cca.R | 20 ---
R/randtest.coinertia.R | 24 +--
R/randtest.discrimin.R | 4
R/randtest.pcaiv.R | 21 +--
R/randtest.pcaivortho.R | 21 +--
R/rlq.R | 32 ++--
R/rtest.between.R | 4
R/rtest.discrimin.R | 10 -
R/scatter.acm.R | 2
R/scatter.fca.R | 2
R/score.acm.R | 2
R/score.coa.R | 12 -
R/score.mix.R | 2
R/score.pca.R | 2
R/sepan.R | 12 -
R/statis.R | 4
R/testdim.R | 4
R/variance.phylog.R | 11 -
R/wca.rlq.R | 16 +-
R/within.R | 8 -
R/withincoinertia.R | 14 +-
R/witwit.R | 18 +-
R/witwitsepan.R | 8 -
data/abouheif.eg.rda |binary
data/acacia.rda |binary
data/aminoacyl.rda |binary
data/apis108.rda |binary
data/ardeche.rda |binary
data/arrival.rda |binary
data/atlas.rda |binary
data/atya.rda |binary
data/avijons.rda |binary
data/avimedi.rda |binary
data/aviurba.rda |binary
data/bacteria.rda |binary
data/banque.rda |binary
data/baran95.rda |binary
data/bf88.rda |binary
data/bordeaux.rda |binary
data/bsetal97.rda |binary
data/buech.rda |binary
data/butterfly.rda |binary
data/capitales.rda |binary
data/carni19.rda |binary
data/carni70.rda |binary
data/carniherbi49.rda |binary
data/casitas.rda |binary
data/chatcat.rda |binary
data/chats.rda |binary
data/chazeb.rda |binary
data/chevaine.rda |binary
data/clementines.rda |binary
data/cnc2003.rda |binary
data/coleo.rda |binary
data/corvus.rda |binary
data/deug.rda |binary
data/doubs.rda |binary
data/dunedata.rda |binary
data/ecg.rda |binary
data/ecomor.rda |binary
data/elec88.rda |binary
data/escopage.rda |binary
data/euro123.rda |binary
data/fission.rda |binary
data/friday87.rda |binary
data/fruits.rda |binary
data/ggtortoises.rda |binary
data/granulo.rda |binary
data/hdpg.rda |binary
data/housetasks.rda |binary
data/humDNAm.rda |binary
data/ichtyo.rda |binary
data/irishdata.rda |binary
data/julliot.rda |binary
data/jv73.rda |binary
data/kcponds.rda |binary
data/lascaux.rda |binary
data/lizards.rda |binary
data/macaca.rda |binary
data/macon.rda |binary
data/macroloire.rda |binary
data/mafragh.rda |binary
data/maples.rda |binary
data/mariages.rda |binary
data/meau.rda |binary
data/meaudret.rda |binary
data/microsatt.rda |binary
data/mjrochet.rda |binary
data/mollusc.rda |binary
data/monde84.rda |binary
data/morphosport.rda |binary
data/newick.eg.rda |binary
data/njplot.rda |binary
data/olympic.rda |binary
data/oribatid.rda |binary
data/ours.rda |binary
data/palm.rda |binary
data/pap.rda |binary
data/perthi02.rda |binary
data/piosphere.rda |binary
data/presid2002.rda |binary
data/procella.rda |binary
data/rankrock.rda |binary
data/rhizobium.rda |binary
data/rhone.rda |binary
data/rpjdl.rda |binary
data/santacatalina.rda |binary
data/sarcelles.rda |binary
data/seconde.rda |binary
data/skulls.rda |binary
data/steppe.rda |binary
data/syndicats.rda |binary
data/t3012.rda |binary
data/tarentaise.rda |binary
data/taxo.eg.rda |binary
data/tintoodiel.rda |binary
data/tithonia.rda |binary
data/tortues.rda |binary
data/toxicity.rda |binary
data/trichometeo.rda |binary
data/ungulates.rda |binary
data/vegtf.rda |binary
data/veuvage.rda |binary
data/westafrica.rda |binary
data/woangers.rda |binary
data/worksurv.rda |binary
data/yanomama.rda |binary
data/zealand.rda |binary
man/ade4-deprecated.Rd |only
man/dudi.Rd | 10 +
man/orthogram.Rd | 3
man/pcaiv.Rd | 14 +-
man/pcaivortho.Rd | 9 +
man/variance.phylog.Rd | 2
src/testdim.c | 2
159 files changed, 632 insertions(+), 470 deletions(-)
Title: Detection of QTL effects in a small mapping population
Diff between WCQ versions 0.1-2 dated 2012-07-29 and 0.2 dated 2012-09-14
Description: The package contains the WCQ method for detection of QTL
effects in a small mapping population. It also contains
implementation of the Chen-Qin two-sample and one-sample test
of means.
Author: Jan Michael Yap
Maintainer: Jan Michael Yap
WCQ-0.1-2/WCQ/R/onesamplemeantest.R |only
WCQ-0.1-2/WCQ/R/twosamplemeantest.R |only
WCQ-0.2/WCQ/DESCRIPTION | 14 +-
WCQ-0.2/WCQ/MD5 | 12 +-
WCQ-0.2/WCQ/R/wcq.R | 212 +++++++++++++++++++++++++++++++++++-
WCQ-0.2/WCQ/man/WCQ-package.Rd | 10 -
WCQ-0.2/WCQ/man/detect.qtl.Rd |only
WCQ-0.2/WCQ/man/wcq.Rd | 9 +
WCQ-0.2/WCQ/man/wcq.fdrc.Rd |only
9 files changed, 234 insertions(+), 23 deletions(-)
Title: Stable isotope analysis
Diff between IsotopeR versions 0.4.3 dated 2012-06-01 and 0.4.4 dated 2012-09-14
Description: Estimates diet contributions from isotopic sources using
JAGS. Includes estimation of concentration dependence and
measurement error.
Author: Jake Ferguson and Jack Hopkins
Maintainer: Jake Ferguson
DESCRIPTION | 8 ++++----
MD5 | 8 ++++----
NEWS | 2 ++
R/Plot_jags.r | 7 ++++++-
inst/doc/IsotopeR.pdf |binary
5 files changed, 16 insertions(+), 9 deletions(-)
Title: Diversity-dependent diversification
Diff between DDD versions 1.2 dated 2012-06-28 and 1.3 dated 2012-09-14
Description: DDD implements maximum likelihood methods based on the
diversity-dependent birth-death process to test whether
speciation or extinction are diversity-dependent. See Etienne
et al. 2012, Proc. Roy. Soc. B 279: 1300-1309, doi:
10.1098/rspb.2011.1439. DDD also implements a maximum
likelihood method to detect key innovations defined as
decoupling of diversity-dependence. See Etienne & Haegeman
2012, Am. Nat. In press, doi: 10.1086/667574.
Author: Rampal S. Etienne & Bart Haegeman
Maintainer: Rampal S. Etienne
DDD-Ex.pdf |only
DDD-manual.pdf |only
DESCRIPTION | 12 ++++++------
MD5 | 12 +++++++-----
R/dd_ML.R | 9 ++++++---
man/DDD-package.Rd | 12 ++++++++----
man/dd_KI_loglik.Rd | 2 ++
man/dd_ML.Rd | 11 ++++++-----
8 files changed, 35 insertions(+), 23 deletions(-)
Title: Conditionally Specified Logistic Regression
Diff between cslogistic versions 0.1-2 dated 2012-01-16 and 0.1-3 dated 2012-09-14
Description: This package contains functions for likelihood and
posterior analysis of conditionally specified logistic
regression models. All calculus and simulation is done in
compiled FORTRAN.
Author: Alejandro Jara [aut, cre], Maria Jose Garcia-Zattera [ctb]
Maintainer: Alejandro Jara
DESCRIPTION | 19 +++++++++----------
MD5 | 2 +-
2 files changed, 10 insertions(+), 11 deletions(-)
Title: Pretty Heatmaps
Diff between pheatmap versions 0.7.2 dated 2012-09-03 and 0.7.3 dated 2012-09-14
Description: A package for drawing pretty heatmaps in R. The ordinary
heatmap function in R has several drawbacks when it comes to
producing publication quality heatmaps. It is hard to produce
pictures with consistent text, cell and overall sizes and
shapes. The function pheatmap tries to alleviate the problems
by offering more fine grained control over heatmap dimensions
and appearance.
Author: Raivo Kolde
Maintainer: Raivo Kolde
DESCRIPTION | 6 +--
MD5 | 8 ++---
NEWS | 5 +++
R/pheatmap.r | 86 ++++++++++++++++++++++++++++----------------------------
man/pheatmap.Rd | 71 +++++++++++++++++++++++-----------------------
5 files changed, 92 insertions(+), 84 deletions(-)
Title: A package for Graphical Markov Models
Diff between ggm versions 1.995-0 dated 2012-08-24 and 1.995-2 dated 2012-09-14
Description: Functions for analyzing and fitting Graphical Markov
models
Author: Giovanni M. Marchetti, Mathias Drton, Kayvan Sadeghi
Maintainer: Giovanni M. Marchetti
DESCRIPTION | 8
MD5 | 14
R/functions.R | 51
R/kayvan.R | 3009 +++++++++++++++++++++++-----------------------
ggm-Ex.R |only
inst/doc/mixed-graphs.pdf |binary
man/makeMG.Rd | 2
man/plotGraph.Rd | 193 +-
vignettes |only
9 files changed, 1648 insertions(+), 1629 deletions(-)
Title: Cox regression with Firth's penalized likelihood
Diff between coxphf versions 1.08 dated 2011-10-27 and 1.09 dated 2012-09-14
Description: Cox regression with Firth's penalized likelihood
Author: R by Meinhard Ploner, Fortran by Georg Heinze
Maintainer:
DESCRIPTION | 10 +++++-----
MD5 | 12 ++++++------
R/coxphf.R | 10 +++++-----
data/breast.txt.gz |binary
man/coxphfplot.Rd | 2 --
man/coxphftest.Rd | 2 --
src/coxphf.f90 | 4 ++--
7 files changed, 18 insertions(+), 22 deletions(-)
Title: Weighted Cox regression
Diff between coxphw versions 2.11 dated 2011-10-26 and 2.12 dated 2012-09-14
Description: Weighted estimation for Cox regression
Author: R by Meinhard Ploner, Fortran by Georg Heinze
Maintainer:
DESCRIPTION | 10 +++++-----
MD5 | 8 ++++----
R/coxphw.fit.R | 2 +-
R/coxphw.r | 8 ++++----
src/coxphw.f90 | 5 +++--
5 files changed, 17 insertions(+), 16 deletions(-)
Title: Fast and light-weight caching (memoization) of objects
Diff between R.cache versions 0.6.2 dated 2012-04-04 and 0.6.3 dated 2012-09-14
Description: Methods for memoization, that is, caching arbitrary R
objects in persistent memory. Objects can be loaded and saved
stratified on a set of hashing objects.
Author: Henrik Bengtsson
Maintainer: Henrik Bengtsson
R.cache-0.6.2/R.cache/inst/.Rcache |only
R.cache-0.6.3/R.cache/DESCRIPTION | 15 ++++-----
R.cache-0.6.3/R.cache/MD5 | 21 ++++++------
R.cache-0.6.3/R.cache/R/999.package.R | 8 +---
R.cache-0.6.3/R.cache/R/getCachePath.R | 5 ++-
R.cache-0.6.3/R.cache/R/loadCache.R | 13 +++----
R.cache-0.6.3/R.cache/R/private.baseLoad.R | 45 +++++++--------------------
R.cache-0.6.3/R.cache/R/readCacheHeader.R | 18 +++-------
R.cache-0.6.3/R.cache/R/setCacheRootPath.R | 5 ++-
R.cache-0.6.3/R.cache/inst/NEWS | 8 ++++
R.cache-0.6.3/R.cache/inst/_Rcache |only
R.cache-0.6.3/R.cache/man/R.cache-package.Rd | 8 +---
R.cache-0.6.3/R.cache/man/loadCache.Rd | 2 -
13 files changed, 64 insertions(+), 84 deletions(-)
Title: Association analysis of CNV data
Diff between CNVassoc versions 1.2 dated 2012-03-26 and 1.4 dated 2012-09-14
Description: This package carries out association analysis of common
copy number variants in population-based studies. This package
includes functions for analysing association under a series of
study designs (case-control, cohort, etc), using several
dependent variables (class status, censored data, counts) as
response, adjusting for covariates and considering various
inheritance models. It also includes functions for inferring
copy number (CNV genotype calling). Various classes and
methods for generic functions (print, summary, plot, anova, ...
) have been created to facilitate the analysis.
Author: Juan R González, Isaac Subirana
Maintainer: Juan R González
CNVassoc-1.2/CNVassoc/R/CNVassoc.r |only
CNVassoc-1.2/CNVassoc/R/CNVtest.r |only
CNVassoc-1.2/CNVassoc/R/EMWeibull.r |only
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CNVassoc-1.2/CNVassoc/R/simCNVdataBinary.r |only
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CNVassoc-1.2/CNVassoc/R/simCNVdataNorm.r |only
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CNVassoc-1.4/CNVassoc/R/getProbs.R |only
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CNVassoc-1.4/CNVassoc/R/getProbsRegions.R | 4
CNVassoc-1.4/CNVassoc/R/getProbsRegions.i.R | 4
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CNVassoc-1.4/CNVassoc/R/getQualityScore.cnv.R |only
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CNVassoc-1.4/CNVassoc/R/hessianWeibull.R |only
CNVassoc-1.4/CNVassoc/R/ifelsem.R |only
CNVassoc-1.4/CNVassoc/R/linear.fit.R |only
CNVassoc-1.4/CNVassoc/R/logLik.CNVassoc.R |only
CNVassoc-1.4/CNVassoc/R/logLik.survreg.R |only
CNVassoc-1.4/CNVassoc/R/logLike.norm.R |only
CNVassoc-1.4/CNVassoc/R/logLike.poisson.R |only
CNVassoc-1.4/CNVassoc/R/logLike.weibull.R |only
CNVassoc-1.4/CNVassoc/R/logistic.fit.R | 2
CNVassoc-1.4/CNVassoc/R/mix.R |only
CNVassoc-1.4/CNVassoc/R/mixture.R |only
CNVassoc-1.4/CNVassoc/R/plot.cnv.R |only
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CNVassoc-1.4/CNVassoc/R/plot.cnv.probabilities.R |only
CNVassoc-1.4/CNVassoc/R/plotSignal.R |only
CNVassoc-1.4/CNVassoc/R/poisson.fit.R |only
CNVassoc-1.4/CNVassoc/R/print.CNVassoc.R |only
CNVassoc-1.4/CNVassoc/R/print.CNVtest.R |only
CNVassoc-1.4/CNVassoc/R/print.QualityScore.R |only
CNVassoc-1.4/CNVassoc/R/print.anova.CNVassoc.R |only
CNVassoc-1.4/CNVassoc/R/print.cnv.R |only
CNVassoc-1.4/CNVassoc/R/print.summary.CNVassoc.R |only
CNVassoc-1.4/CNVassoc/R/signalPlot.R |only
CNVassoc-1.4/CNVassoc/R/simCNVdataBinary.R |only
CNVassoc-1.4/CNVassoc/R/simCNVdataCaseCon.R |only
CNVassoc-1.4/CNVassoc/R/simCNVdataNorm.R |only
CNVassoc-1.4/CNVassoc/R/simCNVdataPois.R |only
CNVassoc-1.4/CNVassoc/R/simCNVdataWeibull.R |only
CNVassoc-1.4/CNVassoc/R/simNormMixt.R |only
CNVassoc-1.4/CNVassoc/R/subset.cnv.R |only
CNVassoc-1.4/CNVassoc/R/summary.CNVassoc.R |only
CNVassoc-1.4/CNVassoc/R/weibull.fit.R |only
CNVassoc-1.4/CNVassoc/R/z[.cnv.R |only
CNVassoc-1.4/CNVassoc/data/NeveCalled.rda |binary
CNVassoc-1.4/CNVassoc/data/NeveRegions.rda |binary
CNVassoc-1.4/CNVassoc/inst/doc/CNVassoc_vignette.pdf |binary
CNVassoc-1.4/CNVassoc/inst/doc/changelog.txt | 10
CNVassoc-1.4/CNVassoc/man/CNVassoc-internal.Rd | 2
CNVassoc-1.4/CNVassoc/man/getProbsRegions.Rd | 3
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CNVassoc-1.4/CNVassoc/vignettes/CNVassoc_vignette.Rnw | 178 +++++++-------
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CNVassoc-1.4/CNVassoc/vignettes/figures/fig2b.pdf |binary
CNVassoc-1.4/CNVassoc/vignettes/make_latex.r | 26 +-
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147 files changed, 232 insertions(+), 176 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-11-17 0.68-27
2011-11-14 0.68-26
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2010-10-09 0.5.0
2010-07-30 0.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-01-19 3.0
2010-04-15 2.1
2008-11-20 2.0.1
2008-11-07 2.0
2006-09-29 1.0.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-06-30 1.0
Title: Probability Models for Ranking Data
Diff between pmr versions 1.1.1 dated 2011-11-25 and 1.1.2 dated 2012-09-14
Description: Fitting probability models for ranking data. Currently,
only complete rankings are supported by this package.
Author: Paul H. Lee and Philip L. H. Yu
Maintainer: Paul H. Lee
DESCRIPTION | 11 ++++++-----
MD5 | 33 +++++++++++++++++----------------
NAMESPACE |only
R/dbm.R | 8 +++++++-
R/destat.R | 4 +++-
R/pl.R | 5 +++--
R/rankplot.R | 4 ++--
R/wdbm.R | 8 +++++++-
man/breasttissue.Rd | 4 ++--
man/dbm.Rd | 5 +++--
man/destat.Rd | 2 +-
man/mdpref.Rd | 2 +-
man/phicom.Rd | 2 +-
man/pl.Rd | 2 +-
man/rankagg.Rd | 4 ++--
man/rankplot.Rd | 2 +-
man/rinv.Rd | 2 +-
man/wdbm.Rd | 5 +++--
18 files changed, 61 insertions(+), 42 deletions(-)
Title: support package for "Programming Graphical User Interfaces in R"
Diff between ProgGUIinR versions 0.0-2 dated 2012-07-03 and 0.0-3 dated 2012-09-14
Description: sample code, appendices and functions for the text
Programming GUIs in R
Author: Michael Lawrence and John Verzani
Maintainer: John Verzani
DESCRIPTION | 6 +++---
MD5 | 7 ++++---
NEWS |only
R/misc.R | 6 ++++--
man/make_graph_icon.Rd | 5 +++--
5 files changed, 14 insertions(+), 10 deletions(-)
Title: Bayesian nonparametric modeling in R
Diff between DPpackage versions 1.1-5 dated 2012-06-15 and 1.1-6 dated 2012-09-14
Description: This package contains functions to perform inference via
simulation from the posterior distributions for Bayesian
nonparametric and semiparametric models. Although the name of
the package was motivated by the Dirichlet Process prior, the
package considers and will consider other priors on functional
spaces. So far, DPpackage includes models considering Dirichlet
Processes, Dependent Dirichlet Processes, Dependent Poisson-
Dirichlet Processes, Hierarchical Dirichlet Processes, Polya
Trees, Linear Dependent Tailfree Processes, Mixtures of
Triangular distributions, Random Bernstein polynomials priors
and Dependent Bernstein Polynomials. The package also includes
models considering Penalized B-Splines. Currently the package
includes semiparametric models for marginal and conditional
density estimation, ROC curve analysis, interval censored data,
binary regression models, generalized linear mixed models, IRT
type models, and generalized additive models. The package also
contains functions to compute Pseudo-Bayes factors for model
comparison, and to elicitate the precision parameter of the
Dirichlet Process. To maximize computational efficiency, the
actual sampling for each model is done in compiled FORTRAN. The
functions return objects which can be subsequently analyzed
with functions provided in the coda package.
Author: Alejandro Jara [aut, cre], Timothy Hanson [ctb], Fernando
Quintana [ctb], Peter Mueller [ctb], Gary Rosner [ctb]
Maintainer: Alejandro Jara
DPpackage-1.1-5/DPpackage/src/DPunimdensity.f |only
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DPpackage-1.1-6/DPpackage/NAMESPACE | 770 ++++++++++++-------------
DPpackage-1.1-6/DPpackage/R/BDPdensity.R | 2
DPpackage-1.1-6/DPpackage/R/CSDPbinary.R | 2
DPpackage-1.1-6/DPpackage/R/DPMdencens.R | 2
DPpackage-1.1-6/DPpackage/R/DPMglmm.R | 2
DPpackage-1.1-6/DPpackage/R/DPMlmm.R | 2
DPpackage-1.1-6/DPpackage/R/DPMmeta.R | 2
DPpackage-1.1-6/DPpackage/R/DPMolmm.R | 2
DPpackage-1.1-6/DPpackage/R/DPMrandom.R | 2
DPpackage-1.1-6/DPpackage/R/DPMrasch.R | 2
DPpackage-1.1-6/DPpackage/R/DPMraschpoisson.R | 2
DPpackage-1.1-6/DPpackage/R/DPbetabinom.R | 2
DPpackage-1.1-6/DPpackage/R/DPbinary.R | 2
DPpackage-1.1-6/DPpackage/R/DPcaterpillar.R | 2
DPpackage-1.1-6/DPpackage/R/DPcdensity.R | 2
DPpackage-1.1-6/DPpackage/R/DPdensity.R | 2
DPpackage-1.1-6/DPpackage/R/DPelicit.R | 2
DPpackage-1.1-6/DPpackage/R/DPglmm.R | 2
DPpackage-1.1-6/DPpackage/R/DPlmm.R | 2
DPpackage-1.1-6/DPpackage/R/DPmeta.R | 2
DPpackage-1.1-6/DPpackage/R/DPmultmeta.R | 14
DPpackage-1.1-6/DPpackage/R/DPolmm.R | 2
DPpackage-1.1-6/DPpackage/R/DPpsBF.R | 2
DPpackage-1.1-6/DPpackage/R/DPrandom.R | 66 ++
DPpackage-1.1-6/DPpackage/R/DPrasch.R | 2
DPpackage-1.1-6/DPpackage/R/DPraschpoisson.R | 2
DPpackage-1.1-6/DPpackage/R/DProc.R | 2
DPpackage-1.1-6/DPpackage/R/DPsurvint.R | 2
DPpackage-1.1-6/DPpackage/R/FPTbinary.R | 18
DPpackage-1.1-6/DPpackage/R/FPTrasch.R | 2
DPpackage-1.1-6/DPpackage/R/FPTraschpoisson.R | 2
DPpackage-1.1-6/DPpackage/R/HDPMcdensity.R | 14
DPpackage-1.1-6/DPpackage/R/HDPMdensity.R | 14
DPpackage-1.1-6/DPpackage/R/LDBDPdensity.R | 2
DPpackage-1.1-6/DPpackage/R/LDDPdensity.R | 10
DPpackage-1.1-6/DPpackage/R/LDDPrasch.R | 2
DPpackage-1.1-6/DPpackage/R/LDDPraschpoisson.R | 2
DPpackage-1.1-6/DPpackage/R/LDDProc.R | 30
DPpackage-1.1-6/DPpackage/R/LDDPsurvival.R | 10
DPpackage-1.1-6/DPpackage/R/LDDPtwopl.R |only
DPpackage-1.1-6/DPpackage/R/LDPDdoublyint.R | 2
DPpackage-1.1-6/DPpackage/R/LDTFPdensity.R | 8
DPpackage-1.1-6/DPpackage/R/LDTFPglmm.R |only
DPpackage-1.1-6/DPpackage/R/LDTFPsurvival.R | 8
DPpackage-1.1-6/DPpackage/R/PSgam.R | 2
DPpackage-1.1-6/DPpackage/R/PTdensity.R | 110 +--
DPpackage-1.1-6/DPpackage/R/PTglmm.R | 18
DPpackage-1.1-6/DPpackage/R/PTlmm.R | 2
DPpackage-1.1-6/DPpackage/R/PTmeta.R | 24
DPpackage-1.1-6/DPpackage/R/PTolmm.R | 18
DPpackage-1.1-6/DPpackage/R/PTrandom.R | 2
DPpackage-1.1-6/DPpackage/R/PTsampler.R | 2
DPpackage-1.1-6/DPpackage/R/Pbinary.R | 2
DPpackage-1.1-6/DPpackage/R/Plm.R | 3
DPpackage-1.1-6/DPpackage/R/TDPdensity.R | 2
DPpackage-1.1-6/DPpackage/R/hidden.R | 2
DPpackage-1.1-6/DPpackage/R/ps.R | 2
DPpackage-1.1-6/DPpackage/man/LDDPrasch.Rd | 2
DPpackage-1.1-6/DPpackage/man/LDDProc.Rd | 30
DPpackage-1.1-6/DPpackage/man/LDDPtwopl.Rd |only
DPpackage-1.1-6/DPpackage/man/LDTFPglmm.Rd |only
DPpackage-1.1-6/DPpackage/src/LDDPdensity.f | 19
DPpackage-1.1-6/DPpackage/src/LDDPsurvival.f | 26
DPpackage-1.1-6/DPpackage/src/LDDPtwopl.f |only
DPpackage-1.1-6/DPpackage/src/LDTFPglmmpois.f |only
DPpackage-1.1-6/DPpackage/src/ToolsLDTFP.f | 247 ++++++++
73 files changed, 1026 insertions(+), 669 deletions(-)