Title: R Package for Ridge Fusion in Statistical Learning
Diff between RidgeFusion versions 1.0-2 dated 2013-10-11 and 1.0-3 dated 2014-09-18
Description: This package implements ridge fusion methodology for inverse covariance matrix estimation for use in quadratic discriminant analysis. The package also contains function for model based clustering using ridge fusion for inverse matrix estimation, as well as tuning parameter selection functions. We have also implemented QDA using joint inverse covariance estimation.
Author: Bradley S. Price
Maintainer: Bradley S. Price
DESCRIPTION | 14 +++++++-------
LICENSE | 2 +-
MD5 | 10 +++++-----
NAMESPACE | 2 ++
R/RidgeFused.R | 26 ++++++++++++++++----------
man/RidgeFusedCV.Rd | 3 ++-
6 files changed, 33 insertions(+), 24 deletions(-)
Title: Fitting illness-death model for interval-censored data
Diff between SmoothHazard versions 1.2.0 dated 2014-09-18 and 1.2.3 dated 2014-09-18
Description: SmoothHazard is a package for fitting illness-death (and survival)
model with possibly interval-censored data for transition toward transient
state. Left-truncated and right-censored data are also allowed.
Proportional intensities regression models allow for covariates on each of
the 3 transitions. We use either a parametric approach with Weibull
baseline intensities or a semi-parametric approach with M-splines
approximation of baseline intensities in order to obtain smooth estimates.
Estimation of parameters is conducted by likelihood maximization in the
parametric approach or penalized likelihood maximization in the
semi-parametric approach.
Author: Celia Touraine, Pierre Joly, Thomas A. Gerds
Maintainer: Thomas Alexander Gerds
DESCRIPTION | 6 ++--
MD5 | 16 ++++++------
R/lifexpect.R | 3 +-
R/simulateIDM.R | 2 +
man/idmModel.Rd | 2 +
man/lifexpect.Rd | 3 +-
src/Makevars | 4 +--
src/Makevars.win | 70 +++++++++++++++++++++----------------------------------
src/survPl.f90 | 2 -
9 files changed, 48 insertions(+), 60 deletions(-)
Title: Diverse basic statistical and graphical functions
Diff between RVAideMemoire versions 0.9-38 dated 2014-08-12 and 0.9-39 dated 2014-09-18
Description: This package contains diverse more or less complicated functions, written to simplify user's life: simplifications of existing functions, basic but not implemented tests, easy-to-use tools, bridges between functions of different packages... All functions are presented in the French book 'Aide-memoire de statistique appliquee a la biologie', written by the same author and available on CRAN.
Author: Maxime Hervé
Maintainer: Maxime Hervé
DESCRIPTION | 8 ++++----
MD5 | 32 +++++++++++++++++++-------------
NAMESPACE | 23 ++++++++++++++++++++++-
R/DA.var.R | 1 +
R/MVA.synt.R |only
R/cor.sparse.R |only
R/lsm.basis.clm.R | 2 +-
R/lsm.basis.clmm.R | 2 +-
R/scatter.coa2.R |only
R/zzz.R | 2 +-
man/DA.valid.Rd | 4 ++--
man/DA.var.Rd | 4 +++-
man/MVA.synt.Rd |only
man/PLSDA.ncomp.Rd | 2 +-
man/RVAideMemoire-package.Rd | 4 ++--
man/cor.sparse.Rd |only
man/cramer.test.Rd | 3 +--
man/perm.t.test.Rd | 6 ++++--
man/s.corcircle2.Rd | 6 +++---
man/scatter.coa2.Rd |only
20 files changed, 65 insertions(+), 34 deletions(-)
Title: Regression Modeling Strategies
Diff between rms versions 4.2-0 dated 2014-04-13 and 4.2-1 dated 2014-09-18
Description: Regression modeling, testing, estimation, validation,
graphics, prediction, and typesetting by storing enhanced model design
attributes in the fit. rms is a collection of functions that
assist with and streamline modeling. It also contains functions for
binary and ordinal logistic regression models, ordinal models for
continuous Y with a variety of distribution families, and the Buckley-James
multiple regression model for right-censored responses, and implements
penalized maximum likelihood estimation for logistic and ordinary
linear models. rms works with almost any regression model, but it
was especially written to work with binary or ordinal regression
models, Cox regression, accelerated failure time models,
ordinary linear models, the Buckley-James model, generalized least
squares for serially or spatially correlated observations, generalized
linear models, and quantile regression.
Author: Frank E Harrell Jr
Maintainer: Frank E Harrell Jr
DESCRIPTION | 14 -
MD5 | 76 +++----
NAMESPACE | 11 -
NEWS | 18 +
R/Gls.s | 2
R/Rq.s | 2
R/bootcov.s | 2
R/bplot.s | 15 -
R/calibrate.cph.s | 16 -
R/calibrate.psm.s | 16 -
R/contrast.s | 2
R/gendata.s | 17 +
R/lrm.fit.s | 184 +++++++++--------
R/lrm.s | 27 +-
R/npsurv.s | 6
R/ols.s | 69 +++---
R/orm.fit.s | 42 ++--
R/orm.s | 5
R/pentrace.s | 60 ++---
R/plot.Predict.s | 529 ++++++++++++++++++++++++---------------------------
R/predictrms.s | 49 ++--
R/rmsMisc.s | 42 +++-
R/summary.rms.s | 80 +++----
R/val.surv.s | 5
R/validate.rpart.s | 2
man/Gls.Rd | 4
man/bplot.Rd | 10
man/lrm.Rd | 10
man/lrm.fit.Rd | 13 +
man/orm.Rd | 10
man/orm.fit.Rd | 10
man/pentrace.Rd | 10
man/plot.Predict.Rd | 10
man/rmsMisc.Rd | 3
man/summary.rms.Rd | 6
tests/Glm.s | 31 ++
tests/bplot.r |only
tests/cphtdc.r |only
tests/ols.penalty.r |only
tests/qt50.rda |only
tests/scale.r |only
tests/validate.ols.r |only
42 files changed, 795 insertions(+), 613 deletions(-)
Title: Access the Gmail RESTful API from R
Diff between gmailr versions 0.0.1 dated 2014-07-26 and 0.5.0 dated 2014-09-18
Description: An R interface to the Gmail RESTful API. Allows access to your
Gmail messages, threads, drafts and labels from R.
Author: Jim Hester
Maintainer: Jim Hester
gmailr-0.0.1/gmailr/man/body.gmail_message.Rd |only
gmailr-0.0.1/gmailr/man/date.Rd |only
gmailr-0.0.1/gmailr/man/from.Rd |only
gmailr-0.0.1/gmailr/man/print.gmail_draft.Rd |only
gmailr-0.0.1/gmailr/man/print.gmail_message.Rd |only
gmailr-0.0.1/gmailr/man/print.gmail_messages.Rd |only
gmailr-0.0.1/gmailr/man/print.gmail_threads.Rd |only
gmailr-0.0.1/gmailr/man/subject.Rd |only
gmailr-0.0.1/gmailr/man/to.Rd |only
gmailr-0.5.0/gmailr/DESCRIPTION | 12
gmailr-0.5.0/gmailr/MD5 | 106 ++++----
gmailr-0.5.0/gmailr/NAMESPACE | 50 +++
gmailr-0.5.0/gmailr/R/draft.R | 37 ++
gmailr-0.5.0/gmailr/R/gmailr.R | 272 ++++++++++++++-------
gmailr-0.5.0/gmailr/R/label.R | 12
gmailr-0.5.0/gmailr/R/message.R | 92 ++++++-
gmailr-0.5.0/gmailr/R/mime.R |only
gmailr-0.5.0/gmailr/R/quoted_prinable.R |only
gmailr-0.5.0/gmailr/R/thread.R | 10
gmailr-0.5.0/gmailr/R/utils.R | 46 +++
gmailr-0.5.0/gmailr/README.md | 13 -
gmailr-0.5.0/gmailr/build |only
gmailr-0.5.0/gmailr/inst |only
gmailr-0.5.0/gmailr/man/accessors.Rd |only
gmailr-0.5.0/gmailr/man/as.character.mime.Rd |only
gmailr-0.5.0/gmailr/man/attach.Rd |only
gmailr-0.5.0/gmailr/man/attachment.Rd | 2
gmailr-0.5.0/gmailr/man/body.Rd | 11
gmailr-0.5.0/gmailr/man/common_fields.Rd |only
gmailr-0.5.0/gmailr/man/create_draft.Rd |only
gmailr-0.5.0/gmailr/man/create_label.Rd | 2
gmailr-0.5.0/gmailr/man/delete_label.Rd | 2
gmailr-0.5.0/gmailr/man/delete_message.Rd | 2
gmailr-0.5.0/gmailr/man/delete_thread.Rd | 2
gmailr-0.5.0/gmailr/man/draft.Rd | 2
gmailr-0.5.0/gmailr/man/drafts.Rd | 2
gmailr-0.5.0/gmailr/man/format.Rd |only
gmailr-0.5.0/gmailr/man/gmail_auth.Rd | 5
gmailr-0.5.0/gmailr/man/gmailr.Rd | 2
gmailr-0.5.0/gmailr/man/history.Rd | 2
gmailr-0.5.0/gmailr/man/id.Rd | 24 +
gmailr-0.5.0/gmailr/man/import_message.Rd |only
gmailr-0.5.0/gmailr/man/insert_message.Rd |only
gmailr-0.5.0/gmailr/man/label.Rd | 2
gmailr-0.5.0/gmailr/man/labels.Rd | 2
gmailr-0.5.0/gmailr/man/message.Rd | 2
gmailr-0.5.0/gmailr/man/messages.Rd | 2
gmailr-0.5.0/gmailr/man/mime.Rd |only
gmailr-0.5.0/gmailr/man/mime_body.Rd |only
gmailr-0.5.0/gmailr/man/modify_message.Rd | 2
gmailr-0.5.0/gmailr/man/modify_thread.Rd | 2
gmailr-0.5.0/gmailr/man/pipe.Rd |only
gmailr-0.5.0/gmailr/man/print.Rd |only
gmailr-0.5.0/gmailr/man/quoted_printable_encode.Rd |only
gmailr-0.5.0/gmailr/man/save_attachment.Rd | 2
gmailr-0.5.0/gmailr/man/save_attachments.Rd | 2
gmailr-0.5.0/gmailr/man/send_draft.Rd | 2
gmailr-0.5.0/gmailr/man/send_message.Rd |only
gmailr-0.5.0/gmailr/man/thread.Rd | 2
gmailr-0.5.0/gmailr/man/threads.Rd | 2
gmailr-0.5.0/gmailr/man/trash_message.Rd | 2
gmailr-0.5.0/gmailr/man/trash_thread.Rd | 2
gmailr-0.5.0/gmailr/man/untrash_message.Rd | 2
gmailr-0.5.0/gmailr/man/untrash_thread.Rd | 2
gmailr-0.5.0/gmailr/man/update_label.Rd | 2
gmailr-0.5.0/gmailr/tests |only
gmailr-0.5.0/gmailr/vignettes |only
67 files changed, 544 insertions(+), 196 deletions(-)
Title: More powerful unconditional testing of negative binomial means
for Digital Gene Expression Data
Diff between edgeRun versions 1.0.7 dated 2014-08-13 and 1.0.8 dated 2014-09-18
Description: Extends edgeR functionality by improving on exactTest using an unconditional exact test of negative binomial means.
Author: Emmanuel Dimont
Maintainer: Emmanuel Dimont
DESCRIPTION | 10 +++++-----
MD5 | 4 ++--
man/edgeRun-package.Rd | 20 ++++++++++++++------
3 files changed, 21 insertions(+), 13 deletions(-)
Title: Functions for wind resource assessment
Diff between bReeze versions 0.3-2 dated 2014-05-08 and 0.4-0 dated 2014-09-18
Description: A collection of functions to analyse, visualize and interpret wind data
and to calculate the potential energy production of wind turbines.
Author: Christian Graul and Carsten Poppinga
Maintainer: Christian Graul
bReeze-0.3-2/bReeze/R/aepInt.R |only
bReeze-0.3-2/bReeze/R/availabilityInt.R |only
bReeze-0.3-2/bReeze/R/cleanInt.R |only
bReeze-0.3-2/bReeze/R/createMast.R |only
bReeze-0.3-2/bReeze/R/createPC.R |only
bReeze-0.3-2/bReeze/R/createSet.R |only
bReeze-0.3-2/bReeze/R/energyInt.R |only
bReeze-0.3-2/bReeze/R/formatTS.R |only
bReeze-0.3-2/bReeze/R/monthStats.R |only
bReeze-0.3-2/bReeze/R/monthStatsInt.R |only
bReeze-0.3-2/bReeze/R/plotAep.R |only
bReeze-0.3-2/bReeze/R/plotAvailability.R |only
bReeze-0.3-2/bReeze/R/plotDay.R |only
bReeze-0.3-2/bReeze/R/plotEnergy.R |only
bReeze-0.3-2/bReeze/R/plotFrequency.R |only
bReeze-0.3-2/bReeze/R/plotMap.R |only
bReeze-0.3-2/bReeze/R/plotMonthStats.R |only
bReeze-0.3-2/bReeze/R/plotPC.R |only
bReeze-0.3-2/bReeze/R/plotPolar.R |only
bReeze-0.3-2/bReeze/R/plotProfile.R |only
bReeze-0.3-2/bReeze/R/plotTimeSeries.R |only
bReeze-0.3-2/bReeze/R/plotTurbIEC.R |only
bReeze-0.3-2/bReeze/R/plotTurbulence.R |only
bReeze-0.3-2/bReeze/R/plotUncertainty.R |only
bReeze-0.3-2/bReeze/R/plotWbDir.R |only
bReeze-0.3-2/bReeze/R/plotWeibull.R |only
bReeze-0.3-2/bReeze/R/printObject.R |only
bReeze-0.3-2/bReeze/R/readPC.R |only
bReeze-0.3-2/bReeze/R/subsetInt.R |only
bReeze-0.3-2/bReeze/R/weibullInt.R |only
bReeze-0.3-2/bReeze/man/aepInt.Rd |only
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bReeze-0.3-2/bReeze/man/createSet.Rd |only
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bReeze-0.3-2/bReeze/man/formatTS.Rd |only
bReeze-0.3-2/bReeze/man/monthStats.Rd |only
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bReeze-0.3-2/bReeze/man/plotMonthStats.Rd |only
bReeze-0.3-2/bReeze/man/plotPC.Rd |only
bReeze-0.3-2/bReeze/man/plotPolar.Rd |only
bReeze-0.3-2/bReeze/man/plotProfile.Rd |only
bReeze-0.3-2/bReeze/man/plotTimeSeries.Rd |only
bReeze-0.3-2/bReeze/man/plotTurbIEC.Rd |only
bReeze-0.3-2/bReeze/man/plotTurbulence.Rd |only
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bReeze-0.3-2/bReeze/man/plotWbDir.Rd |only
bReeze-0.3-2/bReeze/man/plotWeibull.Rd |only
bReeze-0.3-2/bReeze/man/printObject.Rd |only
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bReeze-0.3-2/bReeze/man/subsetInt.Rd |only
bReeze-0.3-2/bReeze/man/weibullInt.Rd |only
bReeze-0.4-0/bReeze/DESCRIPTION | 12 +-
bReeze-0.4-0/bReeze/MD5 | 163 +++++++++++++---------------
bReeze-0.4-0/bReeze/NAMESPACE | 87 ++++++--------
bReeze-0.4-0/bReeze/R/aep.R | 24 ++--
bReeze-0.4-0/bReeze/R/aep.int.R |only
bReeze-0.4-0/bReeze/R/availability.R | 34 ++---
bReeze-0.4-0/bReeze/R/availability.int.R |only
bReeze-0.4-0/bReeze/R/clean.R | 15 +-
bReeze-0.4-0/bReeze/R/clean.int.R |only
bReeze-0.4-0/bReeze/R/day.plot.R |only
bReeze-0.4-0/bReeze/R/energy.R | 21 ++-
bReeze-0.4-0/bReeze/R/energy.int.R |only
bReeze-0.4-0/bReeze/R/frequency.R | 10 -
bReeze-0.4-0/bReeze/R/map.plot.R |only
bReeze-0.4-0/bReeze/R/mast.R |only
bReeze-0.4-0/bReeze/R/month.stats.R |only
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bReeze-0.4-0/bReeze/R/turbulence.R | 10 -
bReeze-0.4-0/bReeze/R/uncertainty.R | 8 -
bReeze-0.4-0/bReeze/R/weibull.R | 14 +-
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bReeze-0.4-0/bReeze/R/zzz.R | 142 +++++-------------------
bReeze-0.4-0/bReeze/data/winddata.RData |binary
bReeze-0.4-0/bReeze/inst/NEWS | 14 ++
bReeze-0.4-0/bReeze/man/aep.Rd | 100 ++++++++++++++---
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bReeze-0.4-0/bReeze/man/availability.Rd | 65 +++++++++--
bReeze-0.4-0/bReeze/man/availability.int.Rd |only
bReeze-0.4-0/bReeze/man/bReeze-package.Rd | 29 +---
bReeze-0.4-0/bReeze/man/clean.Rd | 24 ++--
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bReeze-0.4-0/bReeze/man/energy.Rd | 83 ++++++++++++--
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bReeze-0.4-0/bReeze/man/frequency.Rd | 74 ++++++++++--
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bReeze-0.4-0/bReeze/man/turbulence.Rd | 70 ++++++++----
bReeze-0.4-0/bReeze/man/uncertainty.Rd | 112 +++++++++++++++++--
bReeze-0.4-0/bReeze/man/weibull.Rd | 137 ++++++++++++++++++++---
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140 files changed, 884 insertions(+), 459 deletions(-)
Title: Identifying unique multilocus genotypes where genotyping error
and missing data may be present
Diff between allelematch versions 2.03 dated 2013-01-14 and 2.5 dated 2014-09-18
Description: This package provides tools for the identification of unique of multilocus genotypes when both genotyping error and missing data may be present. The package is targeted at those working with large datasets and databases containing multiple samples of each individual, a situation that is common in conservation genetics, and particularly in non-invasive wildlife sampling applications. Functions explicitly incorporate missing data, and can tolerate allele mismatches created by genotyping error. If you use this tool, please cite the package using the journal article in Molecular Ecology Resources (Galpern et al., 2012). Please use citation('allelematch') to find this. Due to changing CRAN policy, and the size and compile time of the vignettes, they can no longer be distributed with this package. Please contact the package primary author, or visit the allelematch site for a complete vignette (http://nricaribou.cc.umanitoba.ca/allelematch/). For users with access to academic literature, tutorial material is also available as supplementary material to the article describing this software.
Author: Paul Galpern
Maintainer: Paul Galpern
allelematch-2.03/allelematch/inst/doc |only
allelematch-2.5/allelematch/DESCRIPTION | 19 ++++++-------------
allelematch-2.5/allelematch/MD5 | 4 +---
3 files changed, 7 insertions(+), 16 deletions(-)
Title: Simulating trees under the birth-death model
Diff between TreeSim versions 2.0 dated 2014-07-28 and 2.1 dated 2014-09-18
Description: The package simulates phylogenetic trees where (i) all tips are sampled at one time point or (ii) tips are sampled sequentially through time. (i) For sampling at one time point, simulations are performed under a constant rate birth-death process, conditioned on having a fixed number of final tips (sim.bd.taxa), or a fixed age (sim.bd.age), or a fixed age and number of tips (sim.bd.taxa.age). When conditioning on the number of final tips, the method allows for shifts in rates and mass extinction events during the birth-death process (sim.rateshift.taxa). The function sim.bd.age (and sim.rateshift.taxa without extinction) allow the speciation rate to change in a density-dependent way. The LTT plots of the simulations can be displayed using LTT.plot, LTT.plot.gen and LTT.average.root. TreeSim further samples trees with n final tips from a set of trees generated by the common sampling algorithm stopping when a fixed number m>>n of tips is first reached (sim.gsa.taxa). This latter method is appropriate for m-tip trees generated under a big class of models (details in the sim.gsa.taxa man page). For incomplete phylogeny, the missing speciation events can be added through simulations (corsim). (ii) sim.rateshifts.taxa is generalized to sim.bdsky.stt for serially sampled trees, where the trees are conditioned on either the number of sampled tips or the age. Furthermore, for a multitype-branching process with sequential sampling, trees on a fixed number of tips can be simulated using sim.bdtypes.stt.taxa. This function further allows to simulate under epidemiological models with an exposed class. The function sim.genespeciestree simulates coalescent gene trees within birth-death species trees, and sim.genetree simulates coalescent gene trees.
Author: Tanja Stadler
Maintainer: Tanja Stadler
DESCRIPTION | 10 +++++-----
MD5 | 10 +++++-----
R/sim.bdtypes.stt.taxa.R | 21 +++++++++++++++++----
man/TreeSim-package.Rd | 6 +++---
man/sim.bdsky.stt.Rd | 2 +-
man/sim.bdtypes.stt.taxa.Rd | 24 ++++++++++++++++++++++--
6 files changed, 53 insertions(+), 20 deletions(-)
Title: T-distributed Stochastic Neighbor Embedding using Barnes-Hut
implementation
Diff between Rtsne versions 0.8 dated 2014-07-28 and 0.9 dated 2014-09-18
Description: An R wrapper around the fast T-distributed Stochastic
Neighbor Embedding implementation by Van der Maaten
Author: Jesse Krijthe
Maintainer: Jesse Krijthe
Rtsne-0.8/Rtsne/src/quadtree.cpp |only
Rtsne-0.8/Rtsne/src/quadtree.h |only
Rtsne-0.9/Rtsne/DESCRIPTION | 6 ++--
Rtsne-0.9/Rtsne/MD5 | 22 +++++++++---------
Rtsne-0.9/Rtsne/NAMESPACE | 2 -
Rtsne-0.9/Rtsne/R/Rtsne.R | 17 ++++++++------
Rtsne-0.9/Rtsne/README.md | 2 +
Rtsne-0.9/Rtsne/man/Rtsne.Rd | 12 +++++----
Rtsne-0.9/Rtsne/src/Rtsne.cpp | 16 ++++++++++---
Rtsne-0.9/Rtsne/src/sptree.cpp |only
Rtsne-0.9/Rtsne/src/sptree.h |only
Rtsne-0.9/Rtsne/src/tsne.cpp | 47 ++++++++++++++++++++-------------------
Rtsne-0.9/Rtsne/src/tsne.h | 8 +++---
Rtsne-0.9/Rtsne/src/vptree.h | 7 +++--
14 files changed, 80 insertions(+), 59 deletions(-)
Title: Geostatistics using SpatialPoints and rasters
Diff between geostatsp versions 1.0.0 dated 2014-09-17 and 1.0.1 dated 2014-09-18
Description: This package provides to geostatistical modelling facilities using raster and SpatialPoints objects.
Author: Patrick Brown
Maintainer: Patrick Brown
RFsimulate.R | 6
tmp/cranberry7f8e71ce27be/geostatsp-1.0.1/geostatsp/DESCRIPTION | 20 -
tmp/cranberry7f8e71ce27be/geostatsp-1.0.1/geostatsp/MD5 | 8
tmp/cranberry7f8e71ce27be/geostatsp-1.0.1/geostatsp/R/RFsimulate.R | 174 +++++-----
tmp/cranberry7f8e71ce27be/geostatsp-1.0.1/geostatsp/man/RFsimulate.Rd | 14
5 files changed, 115 insertions(+), 107 deletions(-)
Title: Simulation, estimation and forecasting of Beta-Skew-t-EGARCH
models
Diff between betategarch versions 3.1 dated 2013-12-09 and 3.2 dated 2014-09-18
Description: Simulation, estimation and forecasting of first-order Beta-Skew-t-EGARCH models with leverage (one-component, two-component, skewed versions).
Author: Genaro Sucarrat
Maintainer: Genaro Sucarrat
DESCRIPTION | 8 ++++----
MD5 | 9 +++++----
NAMESPACE | 2 +-
NEWS |only
R/tegarch.R | 24 ++++++++++++++++--------
man/betategarch-package.Rd | 4 ++--
6 files changed, 28 insertions(+), 19 deletions(-)
Title: Biogeography-Based Optimization
Diff between bbo versions 0.1 dated 2013-04-19 and 0.2 dated 2014-09-18
Description: This package provides an R implementation of
Biogeography-Based Optimization (BBO), originally invented by
Prof. Dan Simon, Cleveland State University, Ohio. This method
is an application of the concept of biogeography, a study of
the geographical distribution of biological organisms, to
optimization problems. More information about this method can
be found here: http://academic.csuohio.edu/simond/bbo/.
Author: Sarvesh Nikumbh (BBO originally invented by Prof. Dan Simon,
Cleveland State University, Ohio)
Maintainer: Sarvesh Nikumbh
bbo-0.1/bbo/inst/doc/bbo.bib |only
bbo-0.2/bbo/ChangeLog | 3 +++
bbo-0.2/bbo/DESCRIPTION | 6 +++---
bbo-0.2/bbo/MD5 | 13 +++++++------
bbo-0.2/bbo/man/bbo-methods.Rd | 8 +++++++-
bbo-0.2/bbo/man/bbo.Rd | 7 ++++++-
bbo-0.2/bbo/man/bbo.control.Rd | 6 +++++-
bbo-0.2/bbo/vignettes |only
8 files changed, 31 insertions(+), 12 deletions(-)
Title: Modelling temperature effects using time series data
Diff between modTempEff versions 1.5.1 dated 2012-04-13 and 1.5.2 dated 2014-09-18
Description: Fits a Constrained Segmented Distributed Lag regression model
to epidemiological time series of mortality, temperature, and other confounders.
Author: Vito M.R. Muggeo
Maintainer: Vito M.R. Muggeo
DESCRIPTION | 16 ++++++-------
MD5 | 21 ++++++++++-------
NEWS |only
R/anova.modTempEff.R | 4 ++-
R/plot.modTempEff.R | 55 +++++++++++++++++++++++++++++++++++-----------
R/tempeff.R | 8 +++---
build |only
inst/doc/modTempEff.R |only
inst/doc/modTempEff.pdf |binary
man/modTempEff-package.Rd | 4 +--
man/plot.modTempEff.Rd | 11 +++++++--
man/tempeff.Rd | 6 +++--
vignettes |only
13 files changed, 86 insertions(+), 39 deletions(-)
Title: Dirichlet Regression in R
Diff between DirichletReg versions 0.5-1 dated 2014-09-18 and 0.5-2 dated 2014-09-18
Description: Implements the Dirichlet Regression in R
Author: Marco Johannes Maier [cre, aut]
Maintainer: Marco Johannes Maier
DirichletReg-0.5-1/DirichletReg/inst/tests |only
DirichletReg-0.5-1/DirichletReg/tests/test-all.R |only
DirichletReg-0.5-2/DirichletReg/DESCRIPTION | 13
DirichletReg-0.5-2/DirichletReg/MD5 | 27
DirichletReg-0.5-2/DirichletReg/R/sysdata.rda |binary
DirichletReg-0.5-2/DirichletReg/build/partial.rdb |binary
DirichletReg-0.5-2/DirichletReg/build/vignette.rds |binary
DirichletReg-0.5-2/DirichletReg/data/ArcticLake.RData |binary
DirichletReg-0.5-2/DirichletReg/data/BloodSamples.RData |binary
DirichletReg-0.5-2/DirichletReg/data/GlacialTills.RData |binary
DirichletReg-0.5-2/DirichletReg/data/ReadingSkills.RData |binary
DirichletReg-0.5-2/DirichletReg/data/Rocks.RData |binary
DirichletReg-0.5-2/DirichletReg/inst/NEWSRd2txt.R |only
DirichletReg-0.5-2/DirichletReg/inst/doc/DirichletReg-vig.R | 888 ++++++------
DirichletReg-0.5-2/DirichletReg/tests/testthat |only
DirichletReg-0.5-2/DirichletReg/tests/testthat.R |only
DirichletReg-0.5-2/DirichletReg/vignettes/_compile.bat |only
17 files changed, 463 insertions(+), 465 deletions(-)
Title: Bindings for the Geospatial Data Abstraction Library
Diff between rgdal versions 0.8-16 dated 2014-02-07 and 0.9-1 dated 2014-09-18
Description: Provides bindings to Frank Warmerdam's Geospatial Data Abstraction Library (GDAL) (>= 1.6.3, < 2) and access to projection/transformation operations from the PROJ.4 library. The GDAL and PROJ.4 libraries are external to the package, and, when installing the package from source, must be correctly installed first. Both GDAL raster and OGR vector map data can be imported into R, and GDAL raster data and OGR vector data exported. Use is made of classes defined in the sp package. Windows and Mac Intel OS X binaries (including GDAL, PROJ.4 and Expat) are provided on CRAN.
Author: Roger Bivand [cre, aut],
Tim Keitt [aut],
Barry Rowlingson [aut],
Edzer Pebesma [ctb],
Michael Sumner [ctb],
Robert Hijmans [ctb],
Even Rouault [ctb]
Maintainer: Roger Bivand
ChangeLog | 100 ++++++++++++++++++
DESCRIPTION | 18 +--
MD5 | 41 +++----
R/Class-CRSx.R | 14 ++
R/ogr.R | 57 +++++++---
R/ogr_sp.R | 65 ++++++++++-
R/project.R | 14 +-
build/vignette.rds |binary
configure | 30 +++--
configure.ac | 9 +
inst/ChangeLog | 100 ++++++++++++++++++
inst/LICENSE.TXT |only
inst/SVN_VERSION | 2
inst/doc/OGR_shape_encoding.pdf |binary
man/readOGR.Rd | 7 -
man/spTransform-methods.Rd | 18 +++
src/OGR_write.cpp | 1
src/init.c | 2
src/ogrsource.cpp | 221 ++++++++++++++++++++++++++++++++++++----
src/projectit.cpp | 31 ++---
src/rgdal.h | 2
tests/tests.Rout.save | 10 -
22 files changed, 631 insertions(+), 111 deletions(-)
Title: Gene And Splice Site Annotation Using Annotation Data From
Ensembl And UCSC Genome Browsers
Diff between refGenome versions 1.2.0 dated 2013-12-04 and 1.3.0 dated 2014-09-18
Description: The packge contains functionality for import and managing of downloaded genome annotation Data from Ensembl genome browser (European Bioinformatics Institute) and from UCSC genome browser (University of California, Santa Cruz) and annotation routines for genomic positions and splice site positions.
Author: Wolfgang Kaisers
Maintainer: Wolfgang Kaisers
ChangeLog |only
DESCRIPTION | 14
MD5 | 47
NAMESPACE | 6
NEWS |only
R/refGenome.r | 1999 ++++++++++++++++++++++-------------
build/vignette.rds |binary
inst/doc/refGenome.pdf |binary
inst/extdata/hs.ensembl.76.small.gtf |only
man/addIsCoding.Rd | 19
man/ensemblGenome-class.Rd | 121 +-
man/extractByGeneName.Rd | 30
man/getGenePositions.Rd | 39
man/overlap.Rd | 47
man/overlapJuncs.Rd |only
man/refExons-class.Rd | 48
man/refGenome-class.Rd | 74 -
man/refGenome-package.Rd | 7
man/refJunctions-class.Rd | 41
man/saveGenome.Rd | 42
man/ucscGenome-class.Rd | 113 +
man/unifyJuncs.Rd | 13
man/writeDB.Rd | 40
src/refGenome.c | 573 +++++++++-
src/refGenome.h | 39
tests |only
26 files changed, 2360 insertions(+), 952 deletions(-)
Title: A collection of miscellaneous tools for reproducible research
with R.
Diff between repmis versions 0.2.9 dated 2014-05-11 and 0.3 dated 2014-09-18
Description: The package includes tools to load R packages
and automatically generate BibTeX files citing them as well as load
plain-text and Excel formatted data stored on Dropbox, GitHub, and from
other sources.
Author: Christopher Gandrud
Maintainer: Christopher Gandrud
DESCRIPTION | 8 +--
MD5 | 26 +++++-----
NAMESPACE | 2
NEWS | 4 +
R/LoadandCite.R | 6 +-
R/source_DropboxData.R | 10 +--
R/source_data.R | 78 +++++++++++++++++++++---------
R/utils.R | 117 ++++++++++++++++++++++------------------------
README.md | 56 ++++++++++++++++------
man/InstallOldPackages.Rd | 2
man/LoadandCite.Rd | 2
man/source_DropboxData.Rd | 2
man/source_XlsxData.Rd | 2
man/source_data.Rd | 47 ++++++++++--------
14 files changed, 215 insertions(+), 147 deletions(-)
Title: Visualizing and Analyzing Mass Spectrometry Related Data in
Proteomics
Diff between protViz versions 0.1.98 dated 2014-06-25 and 0.2.06 dated 2014-09-18
Description: This R package helps with quality checks, visualizations
and analysis of mass spectrometry data, coming from proteomics
experiments. The package is developed, tested and used at the Functional
Genomics Center Zurich. We use this package mainly for prototyping,
teaching, and having fun with proteomics data. But it can also be
used to do solid data analysis for small scale data sets.
Author: Christian Panse
Maintainer: Christian Panse
protViz-0.1.98/protViz/R/swath.R |only
protViz-0.1.98/protViz/man/swath.Rd |only
protViz-0.2.06/protViz/DESCRIPTION | 16 +-
protViz-0.2.06/protViz/MD5 | 57 +++++-----
protViz-0.2.06/protViz/NAMESPACE | 28 ++--
protViz-0.2.06/protViz/R/aa2mass.R |only
protViz-0.2.06/protViz/R/peakplot.R | 44 ++-----
protViz-0.2.06/protViz/R/sysdata.rda |only
protViz-0.2.06/protViz/build/vignette.rds |binary
protViz-0.2.06/protViz/data/AA.RData |binary
protViz-0.2.06/protViz/data/HexNAc.RData |binary
protViz-0.2.06/protViz/data/averagine.RData |binary
protViz-0.2.06/protViz/data/fetuinLFQ.RData |binary
protViz-0.2.06/protViz/data/iRTpeptides.RData |binary
protViz-0.2.06/protViz/data/iTRAQ.RData |binary
protViz-0.2.06/protViz/data/msms.RData |binary
protViz-0.2.06/protViz/data/pgLFQfeature.RData |binary
protViz-0.2.06/protViz/data/pgLFQprot.RData |binary
protViz-0.2.06/protViz/data/pressureProfile.RData |binary
protViz-0.2.06/protViz/exec/protViz_bibliospec2RData.py | 54 +++++----
protViz-0.2.06/protViz/exec/protViz_mgf2RData.pl | 10 +
protViz-0.2.06/protViz/inst/doc/PTM_MarkerFinder.pdf |binary
protViz-0.2.06/protViz/inst/doc/protViz.R | 43 ++++---
protViz-0.2.06/protViz/inst/doc/protViz.Rnw | 16 +-
protViz-0.2.06/protViz/inst/doc/protViz.pdf |binary
protViz-0.2.06/protViz/inst/unitTests/test_aa2mass_main.R |only
protViz-0.2.06/protViz/inst/unitTests/test_aa2mass_main__verus__parentIonMass.R |only
protViz-0.2.06/protViz/inst/unitTests/test_findNN_.R | 17 ++
protViz-0.2.06/protViz/man/aa2mass.Rd |only
protViz-0.2.06/protViz/man/peakplot.Rd | 4
protViz-0.2.06/protViz/src/base/ms/deisotoper.h | 4
protViz-0.2.06/protViz/src/findNN_.cpp | 10 +
protViz-0.2.06/protViz/vignettes/protViz.Rnw | 16 +-
33 files changed, 170 insertions(+), 149 deletions(-)
Title: Paleontological and Phylogenetic Analyses of Evolution
Diff between paleotree versions 2.1 dated 2014-08-16 and 2.2 dated 2014-09-18
Description: Analyzes, time-scales and simulates phylogenies of extinct/fossil
lineages, along with calculation of diversity curves. Also fits likelihood
models to estimate sampling rates from stratigraphic ranges.
Author: David W. Bapst
Maintainer: David W. Bapst
paleotree-2.1/paleotree/data/retiolitinae.rda |only
paleotree-2.2/paleotree/CHANGELOG | 10
paleotree-2.2/paleotree/DESCRIPTION | 8
paleotree-2.2/paleotree/MD5 | 121 ++++++-----
paleotree-2.2/paleotree/NAMESPACE | 3
paleotree-2.2/paleotree/R/DiversityCurves.R | 18 +
paleotree-2.2/paleotree/R/graptDisparity.R |only
paleotree-2.2/paleotree/R/multiDiv.R | 14 -
paleotree-2.2/paleotree/R/nearestNeighborDist.R |only
paleotree-2.2/paleotree/R/paleotree-package.R | 6
paleotree-2.2/paleotree/R/retiolitinae.R | 21 +-
paleotree-2.2/paleotree/R/simPaleoTrees.R | 10
paleotree-2.2/paleotree/R/taxa2phylo.R | 1
paleotree-2.2/paleotree/R/termTaxa.R | 2
paleotree-2.2/paleotree/R/timeLadderTree.R | 3
paleotree-2.2/paleotree/R/timePaleoPhy.R | 186 ++++++++++++------
paleotree-2.2/paleotree/R/timeSliceTree.R | 4
paleotree-2.2/paleotree/data/graptDisparity.rdata |only
paleotree-2.2/paleotree/data/retiolitinae.rdata |only
paleotree-2.2/paleotree/man/DiversityCurves.Rd | 23 +-
paleotree-2.2/paleotree/man/SamplingConv.Rd | 12 -
paleotree-2.2/paleotree/man/binTimeData.Rd | 2
paleotree-2.2/paleotree/man/branchClasses.Rd | 2
paleotree-2.2/paleotree/man/cal3TimePaleoPhy.Rd | 71 +++---
paleotree-2.2/paleotree/man/cladogeneticTraitCont.Rd | 2
paleotree-2.2/paleotree/man/compareTimescaling.Rd | 2
paleotree-2.2/paleotree/man/constrainParPaleo.Rd | 2
paleotree-2.2/paleotree/man/dateNodes.Rd | 2
paleotree-2.2/paleotree/man/degradeTree.Rd | 2
paleotree-2.2/paleotree/man/depthRainbow.Rd | 2
paleotree-2.2/paleotree/man/durationFreq.Rd | 24 +-
paleotree-2.2/paleotree/man/expandTaxonTree.Rd | 2
paleotree-2.2/paleotree/man/footeValues.Rd | 2
paleotree-2.2/paleotree/man/freqRat.Rd | 2
paleotree-2.2/paleotree/man/getSampProbDisc.Rd | 2
paleotree-2.2/paleotree/man/getSampRateCont.Rd | 2
paleotree-2.2/paleotree/man/graptDisparity.Rd |only
paleotree-2.2/paleotree/man/horizonSampRate.Rd | 2
paleotree-2.2/paleotree/man/inverseSurv.Rd | 58 ++---
paleotree-2.2/paleotree/man/modelMethods.Rd | 2
paleotree-2.2/paleotree/man/modifyTerminalBranches.Rd | 2
paleotree-2.2/paleotree/man/multiDiv.Rd | 41 ++-
paleotree-2.2/paleotree/man/nearestNeighborDist.Rd |only
paleotree-2.2/paleotree/man/optimPaleo.Rd | 2
paleotree-2.2/paleotree/man/paleotree-package.Rd | 8
paleotree-2.2/paleotree/man/perCapitaRates.Rd | 8
paleotree-2.2/paleotree/man/perfectParsCharTree.Rd | 2
paleotree-2.2/paleotree/man/plotTraitgram.Rd | 2
paleotree-2.2/paleotree/man/pqr2Ps.Rd | 10
paleotree-2.2/paleotree/man/probAnc.Rd | 18 -
paleotree-2.2/paleotree/man/retiolitinae.Rd | 24 +-
paleotree-2.2/paleotree/man/reverseList.Rd | 2
paleotree-2.2/paleotree/man/rootSplit.Rd | 2
paleotree-2.2/paleotree/man/sampleRanges.Rd | 2
paleotree-2.2/paleotree/man/seqTimeList.Rd | 2
paleotree-2.2/paleotree/man/simFossilTaxa.Rd | 2
paleotree-2.2/paleotree/man/simFossilTaxa_SRCond.Rd | 2
paleotree-2.2/paleotree/man/simPaleoTrees.Rd | 50 ++--
paleotree-2.2/paleotree/man/taxa2cladogram.Rd | 2
paleotree-2.2/paleotree/man/taxa2phylo.Rd | 3
paleotree-2.2/paleotree/man/termTaxa.Rd | 4
paleotree-2.2/paleotree/man/timeLadderTree.Rd | 3
paleotree-2.2/paleotree/man/timePaleoPhy.Rd | 141 ++++++++-----
paleotree-2.2/paleotree/man/timeSliceTree.Rd | 2
paleotree-2.2/paleotree/man/unitLengthTree.Rd | 2
65 files changed, 571 insertions(+), 390 deletions(-)
Title: Conditioned Latin Hypercube Sampling
Diff between clhs versions 0.5-1 dated 2012-09-10 and 0.5-4 dated 2014-09-18
Description: This package implements the conditioned Latin hypercube sampling, as published by Minasny and McBratney (2006). This method proposes to stratify sampling in presence of ancillary data. An extension of this method, which propose to associate a cost to each individual and take it into account during the optimisation process, is also proposed (Roudier et al., 2012).
Author: Pierre Roudier
Maintainer: Pierre Roudier
DESCRIPTION | 19 +++++++------------
MD5 | 21 ++++++++++++---------
NAMESPACE | 2 ++
NEWS | 8 +++++++-
R/clhs.R | 2 +-
R/plot.R | 3 ---
build |only
inst/doc/vignette.R |only
inst/doc/vignette.pdf |binary
man/clhs-package.Rd | 6 +++++-
man/clhs.Rd | 6 +++++-
man/plot.cLHS_result.Rd | 6 +++++-
vignettes |only
13 files changed, 44 insertions(+), 29 deletions(-)
Title: Bayesian Ordination and Regression AnaLysis
Diff between boral versions 0.4 dated 2014-08-25 and 0.5 dated 2014-09-18
Description: Bayesian approaches for analyzing multivariate data in ecology. Estimation is performed using Markov Chain Monte Carlo (MCMC) methods via JAGS. Three types of models may be fitted: 1) With explanatory variables only, boral fits independent column GLMs to each column of the response matrix; 2) With latent variables only, boral fits a purely latent variable model for model-based unconstrained ordination; 3) With explanatory and latent variables, boral fits correlated column GLMs with latent variables to account for any residual correlation between the columns of the response matrix.
Author: Francis K.C. Hui
Maintainer: Francis Hui
DESCRIPTION | 10 -
MD5 | 46 ++---
NAMESPACE | 6
R/auxilaryfunctions.R | 360 ++++++++++++++++++++++++++---------------
R/boral.jags.R | 202 +++++++++++------------
inst |only
man/boral-package.Rd | 11 -
man/boral.Rd | 101 +++++++----
man/calc.condlogLik.Rd | 16 -
man/calc.logLik.lv0.Rd | 14 -
man/calc.marglogLik.Rd | 16 -
man/create.life.Rd | 16 -
man/ds.residuals.Rd | 8
man/fitted.boral.Rd | 2
man/get.dic.Rd | 6
man/get.enviro.cor.Rd |only
man/get.hpdintervals.Rd | 14 -
man/get.measures.Rd | 34 ++-
man/get.more.measures.Rd | 39 ++--
man/get.residual.cor.Rd | 16 +
man/lvsplot.Rd | 8
man/make.jagsboralmodel.Rd | 27 +--
man/make.jagsboralnullmodel.Rd | 24 +-
man/plot.boral.Rd | 6
man/summary.boral.Rd | 4
25 files changed, 582 insertions(+), 404 deletions(-)
Title: Various R programming tools for plotting data
Diff between gplots versions 2.14.1 dated 2014-06-30 and 2.14.2 dated 2014-09-18
Description: Various R programming tools for plotting data
Author: Gregory R. Warnes, Ben Bolker, Lodewijk Bonebakker, Robert
Gentleman, Wolfgang Huber Andy Liaw, Thomas Lumley, Martin
Maechler, Arni Magnusson, Steffen Moeller, Marc Schwartz, Bill
Venables
Maintainer: Gregory R. Warnes
ChangeLog | 39 ++++++++++++++++++++++++
DESCRIPTION | 8 ++---
MD5 | 25 ++++++++-------
NAMESPACE | 26 ++++++++--------
NEWS | 22 +++++++++++++
R/heatmap.2.R | 57 +++++++++++++++++++++++++++---------
R/plotNode.R |only
build/vignette.rds |binary
inst/ChangeLog | 39 ++++++++++++++++++++++++
inst/NEWS | 22 +++++++++++++
inst/doc/venn.pdf |binary
man/heatmap.2.Rd | 6 +--
tests/dat.csv |only
tests/heatmap2Test.Rout.save | 10 ++----
tests/test_plottingDeepDendrogram.R |only
15 files changed, 203 insertions(+), 51 deletions(-)
Title: Dirichlet Regression in R
Diff between DirichletReg versions 0.4-0 dated 2012-09-06 and 0.5-1 dated 2014-09-18
Description: Implements the Dirichlet Regression in R
Author: Marco Johannes Maier [cre, aut]
Maintainer: Marco Johannes Maier
DirichletReg-0.4-0/DirichletReg/R/AIC.DirichletRegMixture.R |only
DirichletReg-0.4-0/DirichletReg/R/CIspline3d.R |only
DirichletReg-0.4-0/DirichletReg/R/DirichMixture.R |only
DirichletReg-0.4-0/DirichletReg/R/dirichlet_misc.R |only
DirichletReg-0.5-1/DirichletReg/.Rinstignore |only
DirichletReg-0.5-1/DirichletReg/DESCRIPTION | 32 -
DirichletReg-0.5-1/DirichletReg/MD5 | 112 ++---
DirichletReg-0.5-1/DirichletReg/NAMESPACE | 27 -
DirichletReg-0.5-1/DirichletReg/NEWS | 93 +++-
DirichletReg-0.5-1/DirichletReg/R/DR_LL_alt.R | 70 +--
DirichletReg-0.5-1/DirichletReg/R/DR_LL_common.R | 95 ++--
DirichletReg-0.5-1/DirichletReg/R/DR_data.R | 131 +++---
DirichletReg-0.5-1/DirichletReg/R/DirichReg.R | 187 +++++----
DirichletReg-0.5-1/DirichletReg/R/DirichReg_fit.R | 14
DirichletReg-0.5-1/DirichletReg/R/Dirichlet.R |only
DirichletReg-0.5-1/DirichletReg/R/anova.DirichletRegModel.R | 91 ++--
DirichletReg-0.5-1/DirichletReg/R/cmyk2rgb.R | 6
DirichletReg-0.5-1/DirichletReg/R/coef.DirichletRegModel.R | 24 -
DirichletReg-0.5-1/DirichletReg/R/confint.DirichletRegModel.R | 2
DirichletReg-0.5-1/DirichletReg/R/coord.trafo.R | 2
DirichletReg-0.5-1/DirichletReg/R/fitted.DirichletRegModel.R | 2
DirichletReg-0.5-1/DirichletReg/R/lines.DirichletRegData.R | 2
DirichletReg-0.5-1/DirichletReg/R/make.VT.R | 16
DirichletReg-0.5-1/DirichletReg/R/plot.DirichletRegData.R | 22 -
DirichletReg-0.5-1/DirichletReg/R/plot.DirichletRegModel.R | 8
DirichletReg-0.5-1/DirichletReg/R/plot_DRdata_3d.R | 71 ++-
DirichletReg-0.5-1/DirichletReg/R/plot_DRdata_4d.R | 22 -
DirichletReg-0.5-1/DirichletReg/R/predict.DirichletRegModel.R | 64 +--
DirichletReg-0.5-1/DirichletReg/R/print.DirichletRegModel.R | 107 ++---
DirichletReg-0.5-1/DirichletReg/R/residuals.DirichletRegModel.R | 8
DirichletReg-0.5-1/DirichletReg/R/summary.DirichletRegData.R | 14
DirichletReg-0.5-1/DirichletReg/R/summary.DirichletRegModel.R | 204 +++++-----
DirichletReg-0.5-1/DirichletReg/R/sysdata.rda |binary
DirichletReg-0.5-1/DirichletReg/R/terms.DirichletRegModel.R |only
DirichletReg-0.5-1/DirichletReg/R/toTernaryQuaternary.R |only
DirichletReg-0.5-1/DirichletReg/R/zzz.R | 42 +-
DirichletReg-0.5-1/DirichletReg/build |only
DirichletReg-0.5-1/DirichletReg/data/ArcticLake.RData |binary
DirichletReg-0.5-1/DirichletReg/data/BloodSamples.RData |binary
DirichletReg-0.5-1/DirichletReg/data/GlacialTills.RData |binary
DirichletReg-0.5-1/DirichletReg/data/ReadingSkills.RData |binary
DirichletReg-0.5-1/DirichletReg/data/Rocks.RData |binary
DirichletReg-0.5-1/DirichletReg/inst/CITATION | 54 +-
DirichletReg-0.5-1/DirichletReg/inst/NEWS.Rd |only
DirichletReg-0.5-1/DirichletReg/inst/doc/DirichletReg-vig.R |only
DirichletReg-0.5-1/DirichletReg/inst/doc/DirichletReg-vig.Rnw | 187 +++++----
DirichletReg-0.5-1/DirichletReg/inst/doc/DirichletReg-vig.pdf |binary
DirichletReg-0.5-1/DirichletReg/inst/tests |only
DirichletReg-0.5-1/DirichletReg/man/ArcticLake.Rd | 13
DirichletReg-0.5-1/DirichletReg/man/BloodSamples.Rd | 24 -
DirichletReg-0.5-1/DirichletReg/man/DR_data.Rd | 102 +++--
DirichletReg-0.5-1/DirichletReg/man/Dirichlet.Rd | 24 -
DirichletReg-0.5-1/DirichletReg/man/DirichletReg-package.Rd | 22 -
DirichletReg-0.5-1/DirichletReg/man/DirichletRegModel.Rd | 45 +-
DirichletReg-0.5-1/DirichletReg/man/GlacialTills.Rd | 1
DirichletReg-0.5-1/DirichletReg/man/ReadingSkills.Rd | 11
DirichletReg-0.5-1/DirichletReg/man/Rocks.Rd | 25 -
DirichletReg-0.5-1/DirichletReg/man/anova.DirichletRegModel.Rd | 11
DirichletReg-0.5-1/DirichletReg/man/dirichreg.Rd | 9
DirichletReg-0.5-1/DirichletReg/man/plot.DirichletRegData.Rd | 21 -
DirichletReg-0.5-1/DirichletReg/man/toTernaryQuaternary.Rd |only
DirichletReg-0.5-1/DirichletReg/src |only
DirichletReg-0.5-1/DirichletReg/tests |only
DirichletReg-0.5-1/DirichletReg/vignettes/DirichletReg-vig.Rnw | 187 +++++----
64 files changed, 1307 insertions(+), 897 deletions(-)
Title: Analysis of binary character evolution
Diff between corHMM versions 1.14 dated 2014-07-11 and 1.15 dated 2014-09-18
Description: Fits a hidden rates model that allows different transition rate classes on different portions of a phylogeny by treating rate classes as hidden states in a Markov process and various other functions for evaluating models of binary character evolution.
Author: Jeremy M. Beaulieu
Maintainer: Jeremy Beaulieu
DESCRIPTION | 12 ++++++------
MD5 | 10 +++++-----
NAMESPACE | 3 ++-
R/corHMM.R | 14 +++++++-------
R/rayDISC.R | 13 +++++++++----
man/rayDISC.Rd | 1 +
6 files changed, 30 insertions(+), 23 deletions(-)