Title: R Code for MARK Analysis
Diff between RMark versions 2.1.7 dated 2013-12-15 and 2.1.8 dated 2014-06-26
Description: This package provides an interface to the
software package MARK developed by Gary White. MARK is
freely available at
(http://www.phidot.org/software/mark/download/) but is
not open source.
Author: Jeff Laake
Maintainer: Jeff Laake
DESCRIPTION | 31
MD5 | 254 +--
NAMESPACE | 9
NEWS | 25
R/adjust.parameter.count.R | 8
R/collect.model.names.R | 4
R/compute.design.data.R | 5
R/compute.real.R | 13
R/covariate.predictions.r | 141 +
R/create.mark.mcmc.R | 16
R/create.model.list.R | 2
R/extract.mark.output.R | 8
R/get.link.R | 2
R/get.real.R | 8
R/make.mark.model.R | 57
R/mark.R | 31
R/mark.wrapper.R | 4
R/mark.wrapper.parallel.r | 2
R/mata.wald.r | 5
R/merge.mark.r | 4
R/model.average.list.r | 24
R/model.average.marklist.R | 15
R/model.table.R | 6
R/popan.r | 2
R/process.data.R | 20
R/read.mark.binary.linux.R | 2
R/rerun.mark.R | 6
R/run.mark.model.R | 43
R/run.models.R | 2
R/summary.mark.R | 6
R/utility.r | 2
R/valid.parameters.R | 4
R/zzz.R | 12
data/Blackduck.rda |binary
data/dipper.rda |binary
data/edwards.eberhardt.rda |binary
data/mstrata.rda |binary
data/robust.rda |binary
inst/MarkModels.pdf |binary
man/ABeginnersGuide.Rd | 277 +--
man/Blackduck.Rd | 33
man/Donovan.7.Rd | 10
man/Donovan.8.Rd | 15
man/IELogitNormalMR.Rd | 5
man/LogitNormalMR.Rd | 4
man/NicholsMSOccupancy.Rd | 13
man/PIMS.Rd | 29
man/PoissonMR.Rd | 3
man/Poisson_twoMR.Rd | 5
man/RDOccupancy.Rd | 206 +-
man/RDSalamander.Rd | 10
man/TransitionMatrix.Rd | 69
man/Whatsnew.Rd | 3053 ++++++++++++++++------------------------
man/add.design.data.Rd | 212 +-
man/adjust.parameter.count.Rd | 70
man/adjust.value.Rd | 79 -
man/brownie.Rd | 32
man/cleanup.Rd | 98 -
man/collect.model.names.Rd | 60
man/collect.models.Rd | 110 -
man/compute.design.data.Rd | 120 -
man/compute.link.Rd | 56
man/compute.links.from.reals.Rd | 70
man/compute.real.Rd | 174 --
man/convert.inp.Rd | 158 --
man/convert.link.to.real.Rd | 43
man/covariate.predictions.Rd | 208 +-
man/crdms.Rd | 14
man/create.mark.mcmc.Rd | 32
man/create.model.list.Rd | 85 -
man/deer.Rd | 128 -
man/deltamethod.special.Rd | 53
man/deriv_inverse.link.Rd | 39
man/dipper.Rd | 97 -
man/edwards.eberhardt.Rd | 31
man/example.data.Rd | 17
man/export.MARK.Rd | 75
man/export.chdata.Rd | 51
man/export.model.Rd | 51
man/extract.indices.Rd | 175 --
man/extract.mark.output.Rd | 75
man/fill.covariates.Rd | 42
man/find.covariates.Rd | 72
man/get.link.Rd | 54
man/get.real.Rd | 145 -
man/import.chdata.Rd | 130 -
man/inverse.link.Rd | 63
man/killdeer.Rd | 53
man/larksparrow.Rd | 16
man/load.model.Rd | 13
man/make.design.data.Rd | 728 ++++-----
man/make.mark.model.Rd | 845 ++++-------
man/make.time.factor.Rd | 65
man/mallard.Rd | 53
man/mark.Rd | 481 ++----
man/mark.wrapper.Rd | 164 --
man/mark.wrapper.parallel.Rd | 167 --
man/mata.wald.Rd | 119 -
man/merge.mark.Rd | 23
man/merge_design.covariates.Rd | 86 -
man/model.average.Rd | 25
man/model.average.list.Rd | 155 --
man/model.average.marklist.Rd | 176 +-
man/model.table.Rd | 111 -
man/mstrata.Rd | 22
man/popan.derived.Rd | 126 -
man/print.mark.Rd | 71
man/process.data.Rd | 333 +---
man/read.mark.binary.Rd | 33
man/release.gof.Rd | 29
man/remove.mark.Rd | 21
man/rerun.mark.Rd | 115 -
man/robust.Rd | 42
man/run.mark.model.Rd | 167 --
man/run.models.Rd | 52
man/salamander.Rd | 15
man/setup.model.Rd | 66
man/setup.parameters.Rd | 149 -
man/splitCH.Rd | 34
man/store.Rd | 24
man/strip.comments.Rd | 23
man/summary.mark.Rd | 164 --
man/summary_ch.Rd | 56
man/valid.parameters.Rd | 20
man/var.components.Rd | 94 -
man/var.components.reml.Rd | 70
man/weta.Rd | 15
man/wwdo.popan.Rd | 133 -
128 files changed, 5584 insertions(+), 6994 deletions(-)
Title: Calls CNV from exome sequence data
Diff between ExomeDepth versions 1.0.0 dated 2014-02-12 and 1.0.5 dated 2014-06-26
Description: Calls copy number variants (CNVs) from targeted sequence data
Author: Vincent Plagnol
Maintainer: Vincent Plagnol
DESCRIPTION | 6 -
MD5 | 26 +++---
R/class_definition.R | 143 ++++++++++++++++++++++++++------------
R/countBamInGranges.R | 16 ++--
R/optimize_reference_set.R | 17 ++--
R/plot_CNVs_method.R | 27 +++++--
R/tools.R | 4 -
inst/doc/ExomeDepth-vignette.R | 2
inst/doc/ExomeDepth-vignette.Rnw | 22 +++++
inst/doc/ExomeDepth-vignette.pdf |binary
man/CallCNVs.Rd | 17 ++--
man/viterbi.hmm.Rd | 4 -
src/hmm.cpp | 30 +++++--
vignettes/ExomeDepth-vignette.Rnw | 22 +++++
14 files changed, 237 insertions(+), 99 deletions(-)
Title: Correspondence Analysis Variants
Diff between CAvariants versions 1.0 dated 2014-05-14 and 2.0 dated 2014-06-26
Description: Six variants of two-way correspondence analysis can be performed,
simple ca
singly ordered ca
doubly ordered ca
non symmetrical ca
singly ordered non symmetrical ca
doubly ordered non symmetrical ca
Author: Rosaria Lombardo and Eric J Beh
Maintainer: Rosaria Lombardo
DESCRIPTION | 8 +-
MD5 | 28 +++++-----
R/CAvariants.R | 46 +++++++++-------
R/cacorporateplus.R | 2
R/caellipse.R | 5 +
R/docabasic.R | 17 +++---
R/donscabasic.R | 4 -
R/emerson.poly.R | 5 +
R/nsca.ellipse.R | 5 -
R/plotcacorporateplus.R | 120 ++++++++++++++++++++++++++++++++-----------
R/plotone.R | 6 +-
R/printcacorporateplus.R | 6 +-
R/socabasic.R | 2
R/sonscabasic.R | 6 +-
man/cacorporateplus-class.Rd | 1
15 files changed, 170 insertions(+), 91 deletions(-)
Title: Provides access to databases through the JDBC interface
Diff between RJDBC versions 0.2-3 dated 2013-12-14 and 0.2-4 dated 2014-06-26
Description: RJDBC is an implementation of R's DBI interface using JDBC as a back-end. This allows R to connect to any DBMS that has a JDBC driver.
Author: Simon Urbanek
Maintainer: Simon Urbanek
RJDBC-0.2-3/RJDBC/test.sh |only
RJDBC-0.2-4/RJDBC/DESCRIPTION | 6 +++---
RJDBC-0.2-4/RJDBC/MD5 | 11 +++++------
RJDBC-0.2-4/RJDBC/NEWS | 10 ++++++++++
RJDBC-0.2-4/RJDBC/R/class.R | 7 ++++++-
RJDBC-0.2-4/RJDBC/inst/java/RJDBC.jar |binary
RJDBC-0.2-4/RJDBC/java-src/JDBCResultPull.java | 1 +
7 files changed, 25 insertions(+), 10 deletions(-)
Title: R graphics device using cairo graphics library for creating
high-quality bitmap (PNG, JPEG, TIFF), vector (PDF, SVG,
PostScript) and display (X11 and Win32) output.
Diff between Cairo versions 1.5-5 dated 2013-12-23 and 1.5-6 dated 2014-06-26
Description: This package provides a Cairo graphics device that can be use to create high-quality vector (PDF, PostScript and SVG) and bitmap output (PNG,JPEG,TIFF), and high-quality rendering in displays (X11 and Win32). Since it uses the same back-end for all output, copying across formats is WYSIWYG. Files are created without the dependence on X11 or other external programs. This device supports alpha channel (semi-transparent drawing) and resulting images can contain transparent and semi-transparent regions. It is ideal for use in server environments (file output) and as a replacement for other devices that don't have Cairo's capabilities such as alpha support or anti-aliasing. Backends are modular such that any subset of backends is supported.
Author: Simon Urbanek
Maintainer: Simon Urbanek
DESCRIPTION | 6 +++---
MD5 | 8 ++++----
NEWS | 4 ++++
src/cairogd.h | 2 +-
src/cairotalk.c | 2 +-
5 files changed, 13 insertions(+), 9 deletions(-)
Title: Tools for base64 encoding
Diff between base64enc versions 0.1-1 dated 2012-11-05 and 0.1-2 dated 2014-06-26
Description: This package provides tools for handling base64 encoding. It is more flexible than the orphaned base64 package.
Author: Simon Urbanek
Maintainer: Simon Urbanek
DESCRIPTION | 10 +++++-----
MD5 | 6 +++---
NEWS | 6 ++++++
R/base64.R | 2 +-
4 files changed, 15 insertions(+), 9 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-06-25 1.1.1
2014-05-10 1.1
2014-02-18 1.0
Title: A Handbook of Statistical Analyses Using R (3rd Edition)
Diff between HSAUR3 versions 1.0-0 dated 2014-04-17 and 1.0-1 dated 2014-06-26
Description: Functions, data sets, analyses and examples from the
third edition of the book
`A Handbook of Statistical Analyses Using R' (Torsten Hothorn and Brian S.
Everitt, Chapman & Hall/CRC, 2014). The first chapter
of the book, which is entitled `An Introduction to R',
is completely included in this package, for all other chapters,
a vignette containing all data analyses is available. In addition,
Sweave source code for slides of selected chapters is included in
this package (see HSAUR3/inst/slides).
Author: Brian S. Everitt and Torsten Hothorn
Maintainer: Torsten Hothorn
DESCRIPTION | 10 +-
MD5 | 124 +++++++++++++-------------
build/vignette.rds |binary
data/BCG.rda |binary
data/CYGOB1.rda |binary
data/Lanza.rda |binary
data/birthdeathrates.rda |binary
data/bladdercancer.rda |binary
data/epilepsy.rda |binary
data/foster.rda |binary
data/heptathlon.rda |binary
data/meteo.rda |binary
data/orallesions.rda |binary
data/phosphate.rda |binary
data/pistonrings.rda |binary
data/planets.rda |binary
data/plasma.rda |binary
data/polyps.rda |binary
data/rearrests.rda |binary
data/roomwidth.rda |binary
data/schizophrenia.rda |binary
data/schizophrenia2.rda |binary
data/smoking.rda |binary
data/students.rda |binary
data/suicides.rda |binary
data/toothpaste.rda |binary
data/voting.rda |binary
data/water.rda |binary
data/watervoles.rda |binary
data/waves.rda |binary
data/weightgain.rda |binary
inst/NEWS | 6 +
inst/doc/Ch_analysing_longitudinal_dataI.pdf |binary
inst/doc/Ch_analysing_longitudinal_dataII.pdf |binary
inst/doc/Ch_analysis_of_variance.pdf |binary
inst/doc/Ch_bayesian_inference.Rnw | 2
inst/doc/Ch_bayesian_inference.pdf |binary
inst/doc/Ch_cluster_analysis.pdf |binary
inst/doc/Ch_conditional_inference.pdf |binary
inst/doc/Ch_density_estimation.pdf |binary
inst/doc/Ch_errata.pdf |binary
inst/doc/Ch_gam.Rnw | 2
inst/doc/Ch_gam.pdf |binary
inst/doc/Ch_graphical_display.pdf |binary
inst/doc/Ch_introduction_to_R.Rnw | 2
inst/doc/Ch_introduction_to_R.pdf |binary
inst/doc/Ch_logistic_regression_glm.pdf |binary
inst/doc/Ch_meta_analysis.pdf |binary
inst/doc/Ch_missing_values.Rnw | 2
inst/doc/Ch_missing_values.pdf |binary
inst/doc/Ch_multidimensional_scaling.pdf |binary
inst/doc/Ch_multiple_linear_regression.pdf |binary
inst/doc/Ch_principal_components_analysis.pdf |binary
inst/doc/Ch_quantile_regression.pdf |binary
inst/doc/Ch_recursive_partitioning.pdf |binary
inst/doc/Ch_simple_inference.pdf |binary
inst/doc/Ch_simultaneous_inference.pdf |binary
inst/doc/Ch_survival_analysis.pdf |binary
vignettes/Ch_bayesian_inference.Rnw | 2
vignettes/Ch_gam.Rnw | 2
vignettes/Ch_introduction_to_R.Rnw | 2
vignettes/Ch_missing_values.Rnw | 2
vignettes/LaTeXBibTeX/HSAUR.in | 4
63 files changed, 83 insertions(+), 77 deletions(-)
Title: Easily Play Notification Sounds on any Platform
Diff between beepr versions 1.0 dated 2014-06-25 and 1.1 dated 2014-06-26
Description: This package contains one function, beep(), with one purpose: To
make it easy to play notification sounds on whatever platform you are on.
It is intended to be useful, for example, if you are running a long analysis
in the background and want to know when it is ready.
Author: Rasmus Bååth
Maintainer: Rasmus Bååth
DESCRIPTION | 8 ++++----
MD5 | 10 +++++-----
NEWS | 5 +++++
R/beepr.R | 42 ++++++++++++++++++++----------------------
README.md | 2 ++
man/beep.Rd | 28 +++++++++++++---------------
6 files changed, 49 insertions(+), 46 deletions(-)
Title: Model-Free Covariate Selection
Diff between CovSel versions 1.0 dated 2013-09-25 and 1.1 dated 2014-06-26
Description: Model-free selection of covariates under unconfoundedness for situations where the parameter of interest is an average causal effect. This package is based on model-free backward elimination algorithms proposed in de Luna, Waernbaum and Richardson (2011). Marginal co-ordinate hypothesis testing is used in situations where all covariates are continuous while kernel-based smoothing appropriate for mixed data is used otherwise.
Author: Jenny Häggström, Emma Persson,
Maintainer: Jenny Häggström
DESCRIPTION | 8 ++++----
MD5 | 8 ++++----
NAMESPACE | 3 ++-
R/cov.sel.np.R | 38 +++++++++++++++++++-------------------
man/cov.sel.Rd | 2 +-
5 files changed, 30 insertions(+), 29 deletions(-)
Title: Affinity Propagation Clustering
Diff between apcluster versions 1.3.4 dated 2014-06-25 and 1.3.5 dated 2014-06-26
Description: The apcluster package implements Frey's and Dueck's
Affinity Propagation clustering in R. The algorithms are
largely analogous to the Matlab code published by Frey and
Dueck. The package further provides leveraged affinity
propagation and an algorithm for exemplar-based agglomerative
clustering that can also be used to join clusters obtained
from affinity propagation. Various plotting functions are
available for analyzing clustering results.
Author: Ulrich Bodenhofer, Andreas Kothmeier, Johannes Palme
Maintainer: Ulrich Bodenhofer
DESCRIPTION | 8 ++++----
MD5 | 16 ++++++++--------
NEWS | 4 ++++
R/apclusterL-methods.R | 11 ++++-------
inst/doc/apcluster.Rnw | 19 +++++++++++--------
inst/doc/apcluster.pdf |binary
man/apclusterL-methods.Rd | 6 +-----
src/apclusterLeveragedC.cpp | 12 +++++-------
vignettes/apcluster.Rnw | 19 +++++++++++--------
9 files changed, 48 insertions(+), 47 deletions(-)
Title: Model-Based Boosting
Diff between mboost versions 2.2-3 dated 2013-09-09 and 2.3-0 dated 2014-06-26
Description: Functional gradient descent algorithm
(boosting) for optimizing general risk functions utilizing
component-wise (penalised) least squares estimates or regression
trees as base-learners for fitting generalized linear, additive
and interaction models to potentially high-dimensional data.
Author: Torsten Hothorn [aut, cre],
Peter Buehlmann [aut],
Thomas Kneib [aut],
Matthias Schmid [aut],
Benjamin Hofner [aut],
Fabian Sobotka [ctb],
Fabian Scheipl [ctb]
Maintainer: Torsten Hothorn
mboost-2.2-3/mboost/data |only
mboost-2.2-3/mboost/man/Westbc.Rd |only
mboost-2.2-3/mboost/man/birds.Rd |only
mboost-2.2-3/mboost/man/bodyfat.Rd |only
mboost-2.2-3/mboost/man/wpbc.Rd |only
mboost-2.3-0/mboost/DESCRIPTION | 12
mboost-2.3-0/mboost/MD5 | 96 +--
mboost-2.3-0/mboost/NAMESPACE | 11
mboost-2.3-0/mboost/NEWS | 40 +
mboost-2.3-0/mboost/R/AAA.R | 16
mboost-2.3-0/mboost/R/bkronecker.R | 36 +
mboost-2.3-0/mboost/R/bl.R | 99 +++
mboost-2.3-0/mboost/R/bmono.R | 225 ++++-----
mboost-2.3-0/mboost/R/bmrf.R | 6
mboost-2.3-0/mboost/R/control.R | 6
mboost-2.3-0/mboost/R/crossvalidation.R | 1
mboost-2.3-0/mboost/R/family.R | 78 +++
mboost-2.3-0/mboost/R/helpers.R | 113 ++++
mboost-2.3-0/mboost/R/inference.R | 425 +++++++++++++++--
mboost-2.3-0/mboost/R/mboost.R | 45 +
mboost-2.3-0/mboost/R/methods.R | 71 ++
mboost-2.3-0/mboost/build |only
mboost-2.3-0/mboost/inst/CHANGES | 40 +
mboost-2.3-0/mboost/inst/CITATION | 8
mboost-2.3-0/mboost/inst/birds_Biometrics.R | 2
mboost-2.3-0/mboost/inst/doc/SurvivalEnsembles.pdf |binary
mboost-2.3-0/mboost/inst/doc/mboost.R | 1
mboost-2.3-0/mboost/inst/doc/mboost.Rnw | 3
mboost-2.3-0/mboost/inst/doc/mboost.pdf |binary
mboost-2.3-0/mboost/inst/doc/mboost_illustrations.R | 2
mboost-2.3-0/mboost/inst/doc/mboost_illustrations.Rnw | 4
mboost-2.3-0/mboost/inst/doc/mboost_illustrations.pdf |binary
mboost-2.3-0/mboost/inst/doc/mboost_tutorial.R | 4
mboost-2.3-0/mboost/inst/doc/mboost_tutorial.Rnw | 10
mboost-2.3-0/mboost/inst/doc/mboost_tutorial.pdf |binary
mboost-2.3-0/mboost/man/FP.Rd | 2
mboost-2.3-0/mboost/man/Family.Rd | 51 +-
mboost-2.3-0/mboost/man/baselearners.Rd | 111 +++-
mboost-2.3-0/mboost/man/control.Rd | 6
mboost-2.3-0/mboost/man/cvrisk.Rd | 5
mboost-2.3-0/mboost/man/gamboost.Rd | 8
mboost-2.3-0/mboost/man/glmboost.Rd | 10
mboost-2.3-0/mboost/man/mboost.Rd | 16
mboost-2.3-0/mboost/man/mboost_package.Rd | 67 ++
mboost-2.3-0/mboost/man/methods.Rd | 42 +
mboost-2.3-0/mboost/man/stabsel.Rd | 151 ++++--
mboost-2.3-0/mboost/vignettes/auto |only
mboost-2.3-0/mboost/vignettes/mboost.Rnw | 3
mboost-2.3-0/mboost/vignettes/mboost_illustrations.Rnw | 4
mboost-2.3-0/mboost/vignettes/mboost_tutorial.Rnw | 10
mboost-2.3-0/mboost/vignettes/setup.R | 4
51 files changed, 1414 insertions(+), 430 deletions(-)
Title: Boosting Methods for GAMLSS
Diff between gamboostLSS versions 1.1-1 dated 2014-06-16 and 1.1-2 dated 2014-06-26
Description: Boosting models for fitting generalized additive models for
location, shape and scale (GAMLSS) to potentially high dimensional
data.
Author: Benjamin Hofner, Andreas Mayr, Nora Fenske, Matthias Schmid
Maintainer: Benjamin Hofner
ChangeLog | 14 ++++++++++++++
DESCRIPTION | 12 ++++++------
MD5 | 22 +++++++++++-----------
NAMESPACE | 1 -
NEWS | 17 ++++++++++++++---
R/families.R | 12 ++++++------
R/helpers.R | 5 +++++
R/mboostLSS.R | 2 ++
R/methods.R | 4 ----
inst/CHANGES | 17 ++++++++++++++---
tests/regtest-families.R | 15 ++++++++++++++-
tests/regtest-glmboostLSS.R | 10 +++++-----
12 files changed, 91 insertions(+), 40 deletions(-)
Title: Rank Estimation for Linear Models
Diff between Rfit versions 0.17 dated 2013-06-30 and 0.18 dated 2014-06-26
Description: R estimation and inference for linear models. Estimation
is for general scores and a library of commonly used score
functions is included.
Author: John Kloke, Joseph McKean
Maintainer: John Kloke
DESCRIPTION | 8 +++---
MD5 | 22 +++++++++++--------
R/kwayr.r | 4 +--
R/print.raov.R | 6 ++---
R/rfit.default.R | 55 +++++++++++++++++-------------------------------
data/logGFscores.rda |only
data/logrank.scores.rda |only
data/serumLH.rda |only
man/Rfit-package.Rd | 4 +--
man/allscores.Rd | 8 +++---
man/print.rfit.Rd | 3 --
man/rfit.Rd | 11 ++-------
man/rstudent.rfit.Rd | 2 -
man/serumLH.Rd |only
14 files changed, 53 insertions(+), 70 deletions(-)
More information about RelValAnalysis at CRAN
Permanent link
Title: provide an easy to use framework to conduct simulation
Diff between ezsim versions 0.5.4 dated 2014-06-05 and 0.5.5 dated 2014-06-26
Description: ezsim provides a handy way to run simulation and examine its result
Author: TszKin Julian Chan
Maintainer: TszKin Julian Chan
DESCRIPTION | 8 ++--
MD5 | 60 ++++++++++++++++++++-----------------
NAMESPACE | 2 +
NEWS |only
R/createSimulationTable.ezsim.r | 3 -
R/ezsim.r | 54 +++++++++++++++++++++++----------
R/generate.parameterDef.r | 2 -
R/generic.r | 18 +++++------
R/getSelectionName.ezsim.r | 2 -
R/getSelectionName.summary.ezsim.r | 2 -
R/merge.ezsim.r | 7 ++--
R/merge.parameterDef.r | 5 +--
R/plot.ezsim.r | 8 +++-
R/plot.summary.ezsim.r | 15 ++++++---
R/print.ezsim.r | 2 -
R/print.parameterDef.r | 2 -
R/print.parameters.r | 2 -
R/print.summary.ezsim.r | 2 -
R/run.ezsim.r | 28 ++++++++++++++---
R/setBanker.parameterDef.r | 2 -
R/setSelection.parameterDef.r | 2 -
R/subset.ezsim.r | 2 -
R/summary.ezsim.r | 2 -
R/test.ezsim.r | 20 ++++++++++--
build |only
inst |only
man/ezsim.Rd | 16 ++++++---
man/merge.ezsim.Rd | 6 ++-
man/merge.parameterDef.Rd | 4 +-
man/run.ezsim.Rd | 1
man/test.ezsim.Rd | 1
vignettes |only
32 files changed, 180 insertions(+), 98 deletions(-)