Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-08-06 0.1-2
2012-01-18 0.1-1
Title: Simulating trees under the birth-death model
Diff between TreeSim versions 1.9.1 dated 2013-12-10 and 2.0 dated 2014-07-28
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. 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 | 14 -
MD5 | 58 ++--
NAMESPACE | 5
R/getx.R | 18 +
R/reconstructed.age.R | 3
R/sim.bd.age.help.R | 2
R/sim.bd.taxa.R | 8
R/sim.bd.taxa.age.help.R | 1
R/sim.bdsky.stt.R | 579 ++++++++++++++++++++++++++++++--------------
R/sim.bdtypes.stt.taxa.R | 5
R/sim.genespeciestree.R |only
R/sim.genetree.R |only
R/sim.rateshift.taxa.R | 8
R/sim2.bd.R | 1
R/sim2.bd.fast.single.R | 9
R/sim2.bd.mrca.R | 8
R/sim2.bd.mrca.reconst.R | 2
R/stats.R |only
man/LTT.plot.Rd | 21 -
man/LTT.plot.gen.Rd | 27 +-
man/TreeSim-package.Rd | 18 -
man/corsim.Rd | 14 -
man/cuttree.Rd |only
man/getx.Rd | 35 ++
man/sim.bd.age.Rd | 31 +-
man/sim.bd.taxa.Rd | 29 --
man/sim.bd.taxa.age.Rd | 20 -
man/sim.bdsky.stt.Rd | 57 +++-
man/sim.bdtypes.stt.taxa.Rd | 9
man/sim.genespeciestree.Rd |only
man/sim.genetree.Rd |only
man/sim.gsa.taxa.Rd | 25 -
man/sim.rateshift.taxa.Rd | 19 -
33 files changed, 668 insertions(+), 358 deletions(-)
Title: Estimating birth and death rates based on phylogenies
Diff between TreePar versions 2.5 dated 2013-06-09 and 3.0 dated 2014-07-28
Description: (i) For a given species phylogeny on present day data which is calibrated to calendar-time, a method for estimating maximum likelihood speciation and extinction processes is provided. The method allows for non-constant rates. Rates may change (1) as a function of time, i.e. rate shifts at specified times or mass extinction events (likelihood implemented as LikShifts, optimization as bd.shifts.optim and visualized as bd.shifts.plot) or (2) as a function of the number of species, i.e. density-dependence (likelihood implemented as LikDD and optimization as bd.densdep.optim). Note that the methods take into account the whole phylogeny, in particular it accounts for the "pull of the present" effect. Both (1) and (2) can take into account incomplete species sampling, as long as each species has the same probability of being sampled. For a given phylogeny on higher taxa (i.e. all but one species per taxa are missing), where the number of species is known within each higher taxa, speciation and extinction rates can be estimated under model (1) (implemented within LikShifts and bd.shifts.optim with groups !=0). (ii) For a given phylogeny with sequentially sampled tips, e.g. a virus phylogeny, rates can be estimated under a model where rates vary across time using bdsky.stt.optim based on likelihood LikShiftsSTT (extending LikShifts and bd.shifts.optim). Furthermore, rates may vary as a function of host types using LikTypesSTT (multitype branching process extending functions in R package diversitree).
Author: Tanja Stadler
Maintainer: Tanja Stadler
TreePar-2.5/TreePar/R/BDSSsky.R |only
TreePar-2.5/TreePar/R/LikComp2.R |only
TreePar-2.5/TreePar/R/bdtypes.stt.lik.R |only
TreePar-2.5/TreePar/R/treemrcashifts.R |only
TreePar-2.5/TreePar/man/bdtypes.stt.lik.Rd |only
TreePar-2.5/TreePar/man/treemrcashifts.Rd |only
TreePar-3.0/TreePar/DESCRIPTION | 39 ++---------
TreePar-3.0/TreePar/MD5 | 77 ++++++++++++++--------
TreePar-3.0/TreePar/NAMESPACE | 8 --
TreePar-3.0/TreePar/R/BDSSanal.R | 1
TreePar-3.0/TreePar/R/BDSSnum.help-orig.R |only
TreePar-3.0/TreePar/R/BDSSnum.help.R | 35 +++++++---
TreePar-3.0/TreePar/R/Fderifuncshift.R |only
TreePar-3.0/TreePar/R/Fderifuncshifth.R |only
TreePar-3.0/TreePar/R/Ffuncshift.R | 4 -
TreePar-3.0/TreePar/R/HelpShiftsPPn.R |only
TreePar-3.0/TreePar/R/LikConstant.R |only
TreePar-3.0/TreePar/R/LikConstantn.R |only
TreePar-3.0/TreePar/R/LikDD.R |only
TreePar-3.0/TreePar/R/LikShifts.R |only
TreePar-3.0/TreePar/R/LikShiftsPP.R |only
TreePar-3.0/TreePar/R/LikShiftsSTT.R |only
TreePar-3.0/TreePar/R/LikTypesSTT.R |only
TreePar-3.0/TreePar/R/addroot.R |only
TreePar-3.0/TreePar/R/bd.ME.optim.R | 4 -
TreePar-3.0/TreePar/R/bd.ME.optim.rho.R | 2
TreePar-3.0/TreePar/R/bd.ME.optim.rho.all.R | 2
TreePar-3.0/TreePar/R/bd.MEyule.optim.R | 2
TreePar-3.0/TreePar/R/bd.densdep.optim.R | 5 -
TreePar-3.0/TreePar/R/bd.densdep.optim.discrete.R | 2
TreePar-3.0/TreePar/R/bd.shifts.optim.R | 4 -
TreePar-3.0/TreePar/R/bdsky.stt.optim.R | 7 --
TreePar-3.0/TreePar/R/bdtypes.stt.lik.orig.R |only
TreePar-3.0/TreePar/R/integrator-orig.R |only
TreePar-3.0/TreePar/R/integrator.R | 14 +++-
TreePar-3.0/TreePar/R/integrator2-orig.R |only
TreePar-3.0/TreePar/R/integrator2.R | 11 ++-
TreePar-3.0/TreePar/R/p0.R |only
TreePar-3.0/TreePar/R/p1.R |only
TreePar-3.0/TreePar/R/pn.R |only
TreePar-3.0/TreePar/R/pnshift.R | 9 +-
TreePar-3.0/TreePar/R/qhelp.R |only
TreePar-3.0/TreePar/man/LikConstant.Rd |only
TreePar-3.0/TreePar/man/LikConstantn.Rd |only
TreePar-3.0/TreePar/man/LikDD.Rd |only
TreePar-3.0/TreePar/man/LikShifts.Rd |only
TreePar-3.0/TreePar/man/LikShiftsPP.Rd |only
TreePar-3.0/TreePar/man/LikShiftsSTT.Rd |only
TreePar-3.0/TreePar/man/LikTypesSTT.Rd |only
TreePar-3.0/TreePar/man/TreePar-package.Rd | 18 +----
TreePar-3.0/TreePar/man/addroot.Rd |only
TreePar-3.0/TreePar/man/bd.densdep.optim.Rd | 40 +++++++----
TreePar-3.0/TreePar/man/bd.shifts.optim.Rd | 60 ++++++++++-------
TreePar-3.0/TreePar/man/bd.shifts.plot.Rd | 20 ++---
TreePar-3.0/TreePar/man/bdsky.stt.optim.Rd | 20 +++--
TreePar-3.0/TreePar/man/get.groups.Rd | 15 ++--
56 files changed, 227 insertions(+), 172 deletions(-)
Title: General network (HTTP/FTP/...) client interface for R
Diff between RCurl versions 1.95-4.1 dated 2013-03-06 and 1.95-4.2 dated 2014-07-28
Description: The package allows one to compose general HTTP requests
and provides convenient functions to fetch URIs, get & post
forms, etc. and process the results returned by the Web server.
This provides a great deal of control over the HTTP/FTP/...
connection and the form of the request while providing a
higher-level interface than is available just using R socket
connections. Additionally, the underlying implementation is
robust and extensive, supporting FTP/FTPS/TFTP (uploads and
downloads), SSL/HTTPS, telnet, dict, ldap, and also supports
cookies, redirects, authentication, etc.
Author: Duncan Temple Lang
Maintainer: Duncan Temple Lang
DESCRIPTION | 6
MD5 | 10
configure | 7467 ++++++++++++++++----------------------------
configure.in | 4
data/mimeTypeExtensions.rda |binary
src/CURLOptTable.h | 2
6 files changed, 2761 insertions(+), 4728 deletions(-)
Title: Multiple Precision Arithmetic
Diff between gmp versions 0.5-11 dated 2013-12-04 and 0.5-12 dated 2014-07-28
Description: Multiple Precision Arithmetic (big integers and rationals,
prime number tests, matrix computation), "arithmetic without limitations"
using the C library GMP (GNU Multiple Precision Arithmetic).
Author: Antoine Lucas, Immanuel Scholz, Rainer Boehme
Maintainer: Antoine Lucas
gmp-0.5-11/gmp/inst |only
gmp-0.5-12/gmp/ChangeLog | 4 +
gmp-0.5-12/gmp/DESCRIPTION | 8 +--
gmp-0.5-12/gmp/MD5 | 35 ++++-----------
gmp-0.5-12/gmp/R/biginteger.R | 12 ++---
gmp-0.5-12/gmp/TODO | 3 -
gmp-0.5-12/gmp/src/bigmod.cc | 22 ++++++++-
gmp-0.5-12/gmp/src/bigmod.h | 10 +++-
gmp-0.5-12/gmp/src/bigrational.cc | 3 -
gmp-0.5-12/gmp/tests/arith-ex.R | 11 ++++
gmp-0.5-12/gmp/tests/gmp-test.R | 3 -
gmp-0.5-12/gmp/tests/gmp-test.Rout.save | 73 ++++++++++++++++----------------
12 files changed, 108 insertions(+), 76 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-05-29 1.0
2012-05-29 1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-01-25 1.0.1
2009-02-18 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-03-14 1.0-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2010-08-16 1.1-2
2010-02-12 1.1-0
2010-01-27 1.0-1
2010-01-26 1.0-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-03-26 2.0-1
2011-11-18 2.0-0
2010-04-15 1.2-0
2007-04-11 1.1-0
Title: Tools for estimating and predicting the cosinor model
Diff between cosinor versions 1.0 dated 2014-07-25 and 1.1 dated 2014-07-28
Description: cosinor is a set of simple functions that transforms longitudinal
data to estimate the cosinor linear model as described in Tong (1976).
Methods are given to summarize the mean, amplitude and acrophase, to
predict the mean annual outcome value, and to test the coefficients.
Author: Michael Sachs
Maintainer: Michael Sachs
DESCRIPTION | 19 +++++++++--------
MD5 | 27 +++++++++++++++----------
NAMESPACE | 4 +++
NEWS | 7 ++++++
R/cosinor.lm.R | 20 +++++++++++++++---
R/cosinor_analyzer.R |only
R/plot.cosinor.lm.R | 8 ++++++-
R/summary.cosinor.lm.R | 43 +++++++++++++++++++++++++++++++++-------
build |only
data/vitamind.RData |binary
inst |only
man/cosinor.lm.Rd | 3 ++
man/cosinor_analyzer.Rd |only
man/print.summary.cosinor.lm.Rd |only
man/update_covnames.Rd | 1
vignettes/Intro.Rmd | 24 ++++++++++++++++------
16 files changed, 119 insertions(+), 37 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2009-10-28 0.0-10
2009-09-18 0.0-8
2009-09-08 0.0-6
2009-09-07 0.0-5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2009-10-20 1.1-1
2009-09-30 1.0-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2006-06-19 0.8-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-06-21 1.0-4
2012-06-02 1.0-3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-09-11 1.0-10
2011-04-04 1.0-9
2010-09-30 1.0-8
2010-09-09 1.0-7
2010-08-20 1.0-6
2010-03-25 1.0-5
2010-03-08 1.0-4
2010-03-05 1.0-3
2010-02-14 1.0-2
2010-02-08 1.0-1
2010-02-04 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-03-29 0.2.2
2010-05-07 0.2.1.1
2008-02-11 0.2.1
2007-11-22 0.2
2007-08-14 0.1-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2008-02-11 0.1.2
2007-12-07 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2009-02-11 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-10-27 0.3
2011-04-24 0.2
2011-04-23 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-10-17 1.0-2
2010-05-18 1.0-1
2009-10-30 1.0-0
Title: Shrinkage Discriminant Analysis and CAT Score Variable Selection
Diff between sda versions 1.3.3 dated 2014-04-18 and 1.3.4 dated 2014-07-28
Description: This package provides an efficient framework for
high-dimensional linear and diagonal discriminant analysis with
variable selection. The classifier is trained using James-Stein-type
shrinkage estimators and predictor variables are ranked using
correlation-adjusted t-scores (CAT scores). Variable selection error
is controlled using false non-discovery rates or higher criticism.
Author: Miika Ahdesmaki, Verena Zuber, Sebastian Gibb, and Korbinian Strimmer
Maintainer: Korbinian Strimmer
DESCRIPTION | 12 ++++++------
MD5 | 6 +++---
NEWS | 6 ++++++
inst/doc/index.html | 20 ++++++++++++--------
4 files changed, 27 insertions(+), 17 deletions(-)
Title: T-distributed Stochastic Neighbor Embedding using Barnes-Hut
implementation
Diff between Rtsne versions 0.6 dated 2014-06-23 and 0.8 dated 2014-07-28
Description: An R wrapper around the fast T-distributed Stochastic
Neighbor Embedding implementation by Van der Maaten
Author: Jesse Krijthe
Maintainer: Jesse Krijthe
DESCRIPTION | 6 +++---
MD5 | 22 +++++++++++-----------
NAMESPACE | 2 +-
R/RcppExports.R | 4 ++--
R/Rtsne.R | 15 ++++++++-------
README.md | 11 +++++++----
man/Rtsne.Rd | 16 +++++++++-------
src/RcppExports.cpp | 7 ++++---
src/Rtsne.cpp | 10 ++--------
src/quadtree.cpp | 1 +
src/tsne.cpp | 5 ++++-
src/vptree.h | 3 ++-
12 files changed, 54 insertions(+), 48 deletions(-)
Title: Serialize R objects to JSON, JavaScript Object Notation
Diff between RJSONIO versions 1.2-0.2 dated 2014-04-29 and 1.3-0 dated 2014-07-28
Description: This is a package that allows conversion to and from
data in Javascript object notation (JSON) format.
This allows R objects to be inserted into Javascript/ECMAScript/ActionScript code
and allows R programmers to read and convert JSON content to R objects.
This is an alternative to rjson package. Originally, that was too slow for converting large R objects to JSON
and was not extensible. rjson's performance is now similar to this package, and perhaps slightly faster in some cases.
This package uses methods and is readily extensible by defining methods for different classes,
vectorized operations, and C code and callbacks to R functions for deserializing JSON objects to R.
The two packages intentionally share the same basic interface. This package (RJSONIO) has many additional
options to allow customizing the generation and processing of JSON content.
This package uses libjson rather than implementing yet another JSON parser. The aim is to support
other general projects by building on their work, providing feedback and benefit from their ongoing development.
Author: Duncan Temple Lang
Maintainer: Duncan Temple Lang
RJSONIO-1.2-0.2/RJSONIO/inst/sampleData/web.json |only
RJSONIO-1.2-0.2/RJSONIO/src/JSONAllocator.cpp |only
RJSONIO-1.2-0.2/RJSONIO/src/JSONChildren.cpp |only
RJSONIO-1.2-0.2/RJSONIO/src/JSONDebug.cpp |only
RJSONIO-1.2-0.2/RJSONIO/src/JSONIterators.cpp |only
RJSONIO-1.2-0.2/RJSONIO/src/JSONMemory.cpp |only
RJSONIO-1.2-0.2/RJSONIO/src/JSONNode.cpp |only
RJSONIO-1.2-0.2/RJSONIO/src/JSONNode_Mutex.cpp |only
RJSONIO-1.2-0.2/RJSONIO/src/JSONOptions.h |only
RJSONIO-1.2-0.2/RJSONIO/src/JSONPreparse.cpp |only
RJSONIO-1.2-0.2/RJSONIO/src/JSONStream.cpp |only
RJSONIO-1.2-0.2/RJSONIO/src/JSONValidator.cpp |only
RJSONIO-1.2-0.2/RJSONIO/src/JSONWorker.cpp |only
RJSONIO-1.2-0.2/RJSONIO/src/JSONWriter.cpp |only
RJSONIO-1.2-0.2/RJSONIO/src/internalJSONNode.cpp |only
RJSONIO-1.2-0.2/RJSONIO/src/libjson.cpp |only
RJSONIO-1.3-0/RJSONIO/Changes | 8 ++
RJSONIO-1.3-0/RJSONIO/Changes.html | 14 ++++
RJSONIO-1.3-0/RJSONIO/DESCRIPTION | 23 +++----
RJSONIO-1.3-0/RJSONIO/MD5 | 43 ++++----------
RJSONIO-1.3-0/RJSONIO/R/json.R | 14 ++--
RJSONIO-1.3-0/RJSONIO/configure.win | 4 -
RJSONIO-1.3-0/RJSONIO/src/Makevars.in | 5 -
RJSONIO-1.3-0/RJSONIO/src/Makevars.win | 7 +-
RJSONIO-1.3-0/RJSONIO/src/libjson/JSONOptions.h | 6 -
RJSONIO-1.3-0/RJSONIO/src/libjson/Source/JSONChildren.cpp | 2
RJSONIO-1.3-0/RJSONIO/src/libjson/Source/JSONDefs/GNU_C.h | 2
RJSONIO-1.3-0/RJSONIO/src/libjson/Source/JSONWorker.cpp | 14 +---
RJSONIO-1.3-0/RJSONIO/src/rlibjson.c | 12 +++
RJSONIO-1.3-0/RJSONIO/tests/toJSON.R | 10 +++
RJSONIO-1.3-0/RJSONIO/tests/utf8.R |only
31 files changed, 100 insertions(+), 64 deletions(-)
Title: Simulation-Based Bayesian Inference for Latent Traits of Item
Response Models
Diff between ltbayes versions 0.2 dated 2014-05-15 and 0.3 dated 2014-07-28
Description: Functions for simulating realizations from the posterior distribution of
a latent trait of an item response model. Distributions are conditional on one or
a subset of response patterns (e.g., sum scores). Functions for computing likelihoods,
Fisher and observed information, posterior modes, and profile likelihood confidence
intervals are also included. These functions are designed to be easily amenable to
user-specified models.
Author: Timothy R. Johnson
Maintainer: Timothy R. Johnson
DESCRIPTION | 13 ++--
MD5 | 59 +++++++++++---------
R/fmodelrsm.R | 2
R/information.R | 4 -
R/postmode.R | 2
R/posttrace.R | 16 +----
R/profileci.R | 44 +++++++--------
build |only
inst |only
man/fmodel1pl.Rd | 119 ++++++++++++++++++++++++----------------
man/fmodel1pp.Rd | 119 ++++++++++++++++++++++++----------------
man/fmodel2pl.Rd | 31 ++++++++++
man/fmodel2pp.Rd | 31 ++++++++++
man/fmodel3pl.Rd | 32 ++++++++++
man/fmodel3pp.Rd | 138 ++++++++++++++++++++++++++++-------------------
man/fmodel4pl.Rd | 155 +++++++++++++++++++++++++++++++----------------------
man/fmodel4pp.Rd | 152 +++++++++++++++++++++++++++++++--------------------
man/fmodelgrl.Rd | 39 ++++++++++---
man/fmodelgrp.Rd | 149 +++++++++++++++++++++++++++++---------------------
man/fmodelnrm.Rd | 127 +++++++++++++++++++++++++------------------
man/fmodelpcm.Rd | 129 +++++++++++++++++++++++++-------------------
man/fmodelrsm.Rd | 141 ++++++++++++++++++++++++++++--------------------
man/fmodelseq.Rd | 121 ++++++++++++++++++++++++-----------------
man/information.Rd | 122 +++++++++++++++++++++++------------------
man/postmode.Rd | 18 +++---
man/postsamp.Rd | 112 +++++++++++++++++++-------------------
man/posttrace.Rd | 29 +++++----
man/profileci.Rd | 11 ++-
vignettes |only
29 files changed, 1153 insertions(+), 762 deletions(-)
Title: A Fast Parameter Estimation Method for Evolutionary Biology
Diff between jaatha versions 2.4 dated 2014-06-03 and 2.5 dated 2014-07-28
Description: Jaatha is a composite likelihood method for inferring evolutionary
parameters using genetic data. Given a model of the evolutionary history of
two biological populations as well as SNP data from multiple individuals
from each population, it estimates model parameters like the time of
separation of both species.
Author: Paul R. Staab, Lisha Mathew and Dirk Metzler
Maintainer: Paul R. Staab
jaatha-2.4/jaatha/inst/unitTests/runit.calc_likelihood.R |only
jaatha-2.4/jaatha/inst/unitTests/runit.confidence_intervals.R |only
jaatha-2.4/jaatha/inst/unitTests/runit.custom_simulator.R |only
jaatha-2.4/jaatha/inst/unitTests/runit.dm-ms.R |only
jaatha-2.4/jaatha/inst/unitTests/runit.dm-seqgen.R |only
jaatha-2.4/jaatha/inst/unitTests/runit.estimate_likelihood.R |only
jaatha-2.4/jaatha/inst/unitTests/runit.fit_glm.R |only
jaatha-2.4/jaatha/inst/unitTests/runit.initial_search.R |only
jaatha-2.4/jaatha/inst/unitTests/runit.read_fasta.R |only
jaatha-2.4/jaatha/inst/unitTests/runit.refined_search.R |only
jaatha-2.4/jaatha/inst/unitTests/runit.sim_likelihood.R |only
jaatha-2.4/jaatha/inst/unitTests/runit.sim_program.R |only
jaatha-2.4/jaatha/inst/unitTests/runit.simulate_dm.R |only
jaatha-2.4/jaatha/inst/unitTests/runit.simulate_within_block.R |only
jaatha-2.4/jaatha/inst/unitTests/test_setup.R |only
jaatha-2.4/jaatha/inst/unitTests/test_setup.Rda |only
jaatha-2.4/jaatha/man/getLogFile.Rd |only
jaatha-2.4/jaatha/man/getLogLevel.Rd |only
jaatha-2.4/jaatha/src/msFile2jsfs.cc |only
jaatha-2.4/jaatha/src/seqgenFile2jsfs.cc |only
jaatha-2.5/jaatha/DESCRIPTION | 26
jaatha-2.5/jaatha/MD5 | 112 +--
jaatha-2.5/jaatha/NAMESPACE | 4
jaatha-2.5/jaatha/NEWS | 36 +
jaatha-2.5/jaatha/R/Block.R | 15
jaatha-2.5/jaatha/R/DemographicModel.R | 327 +++++-----
jaatha-2.5/jaatha/R/Jaatha.R | 126 ++-
jaatha-2.5/jaatha/R/RcppExports.R |only
jaatha-2.5/jaatha/R/fit_glm.R | 25
jaatha-2.5/jaatha/R/helper_functions.R | 60 -
jaatha-2.5/jaatha/R/initial_search.R | 24
jaatha-2.5/jaatha/R/package_info.R |only
jaatha-2.5/jaatha/R/refined_search.R | 39 -
jaatha-2.5/jaatha/R/sim_program.R | 163 ----
jaatha-2.5/jaatha/R/sim_program_ms.R | 164 +----
jaatha-2.5/jaatha/R/sim_program_msms.R |only
jaatha-2.5/jaatha/R/sim_program_seqgen.R | 81 +-
jaatha-2.5/jaatha/R/sum_stat_fpc.R |only
jaatha-2.5/jaatha/README | 4
jaatha-2.5/jaatha/inst/integrationTests/it.initial_search.R | 18
jaatha-2.5/jaatha/inst/integrationTests/it.one_par_model.R | 4
jaatha-2.5/jaatha/inst/integrationTests/it.refined_search.R | 21
jaatha-2.5/jaatha/inst/integrationTests/it.sim_prog_seqgen.R | 39 -
jaatha-2.5/jaatha/inst/unitTests/runit.calc-likelihood.R |only
jaatha-2.5/jaatha/inst/unitTests/runit.confidence-intervals.R |only
jaatha-2.5/jaatha/inst/unitTests/runit.cpp-parse-output.R |only
jaatha-2.5/jaatha/inst/unitTests/runit.cpp-parse-seqgen.R |only
jaatha-2.5/jaatha/inst/unitTests/runit.cpp-sumstat-fpc.R |only
jaatha-2.5/jaatha/inst/unitTests/runit.cpp-sumstat-jsfs.R |only
jaatha-2.5/jaatha/inst/unitTests/runit.custom-simulator.R |only
jaatha-2.5/jaatha/inst/unitTests/runit.dm.R | 126 ++-
jaatha-2.5/jaatha/inst/unitTests/runit.estimate-likelihood.R |only
jaatha-2.5/jaatha/inst/unitTests/runit.fit-glm.R |only
jaatha-2.5/jaatha/inst/unitTests/runit.fixed-bugs.R | 6
jaatha-2.5/jaatha/inst/unitTests/runit.initial-search.R |only
jaatha-2.5/jaatha/inst/unitTests/runit.jaatha.R | 62 +
jaatha-2.5/jaatha/inst/unitTests/runit.read-fasta.R |only
jaatha-2.5/jaatha/inst/unitTests/runit.refined-search.R |only
jaatha-2.5/jaatha/inst/unitTests/runit.sim-likelihood.R |only
jaatha-2.5/jaatha/inst/unitTests/runit.sim-prog-ms.R |only
jaatha-2.5/jaatha/inst/unitTests/runit.sim-prog-seqgen.R |only
jaatha-2.5/jaatha/inst/unitTests/runit.sim-program.R |only
jaatha-2.5/jaatha/inst/unitTests/runit.sim_program_msms.r |only
jaatha-2.5/jaatha/inst/unitTests/runit.simulate-dm.R |only
jaatha-2.5/jaatha/inst/unitTests/runit.simulate-within-block.R |only
jaatha-2.5/jaatha/inst/unitTests/runit.sum-stat-fpc.R |only
jaatha-2.5/jaatha/inst/unitTests/test-setup.R |only
jaatha-2.5/jaatha/inst/unitTests/test-setup.Rda |only
jaatha-2.5/jaatha/man/Jaatha.initialSearch.Rd | 2
jaatha-2.5/jaatha/man/dm.addMigration.Rd | 3
jaatha-2.5/jaatha/man/dm.addMutation.Rd | 6
jaatha-2.5/jaatha/man/dm.addOutgroup.Rd | 2
jaatha-2.5/jaatha/man/dm.addRecombination.Rd | 3
jaatha-2.5/jaatha/man/dm.addSizeChange.Rd | 2
jaatha-2.5/jaatha/man/dm.addSpeciationEvent.Rd | 6
jaatha-2.5/jaatha/man/dm.createDemographicModel.Rd | 12
jaatha-2.5/jaatha/man/setLogging.Rd | 4
jaatha-2.5/jaatha/src/RcppExports.cpp |only
jaatha-2.5/jaatha/src/parse_output.cpp |only
jaatha-2.5/jaatha/src/sum_stat_fpc.cpp |only
jaatha-2.5/jaatha/src/sum_stat_jsfs.cpp |only
jaatha-2.5/jaatha/tests/doRUnit.R | 11
82 files changed, 782 insertions(+), 751 deletions(-)
Title: Tools for working with URLs and HTTP
Diff between httr versions 0.3 dated 2014-03-19 and 0.4 dated 2014-07-28
Description: Provides useful tools for working with HTTP. The API is based
around http verbs (GET(), POST(), etc) with pluggable components to control
the request (authenticate(), add_headers() and so on).
Author: Hadley Wickham
Maintainer: Hadley Wickham
httr-0.3/httr/R/request-bin.r |only
httr-0.3/httr/man/new_bin.Rd |only
httr-0.4/httr/DESCRIPTION | 20 +-
httr-0.4/httr/MD5 | 209 +++++++++++++++-------------
httr-0.4/httr/NAMESPACE | 21 ++
httr-0.4/httr/R/authenticate.r | 6
httr-0.4/httr/R/body.R | 125 ++++++++++------
httr-0.4/httr/R/config.r | 99 +++++++++++--
httr-0.4/httr/R/content-parse.r | 5
httr-0.4/httr/R/content.r | 11 +
httr-0.4/httr/R/cookies.r | 31 +++-
httr-0.4/httr/R/envvar.R |only
httr-0.4/httr/R/handle.r | 10 -
httr-0.4/httr/R/headers.r | 90 ++++++++++--
httr-0.4/httr/R/hmac.r | 2
httr-0.4/httr/R/http--request.r | 41 ++---
httr-0.4/httr/R/http-delete.r | 3
httr-0.4/httr/R/http-get.r | 22 +-
httr-0.4/httr/R/http-patch.r | 11 +
httr-0.4/httr/R/http-post.r | 49 ++++--
httr-0.4/httr/R/http-put.r | 19 +-
httr-0.4/httr/R/httr.r | 2
httr-0.4/httr/R/media-guess.r | 2
httr-0.4/httr/R/oauth-app.r | 10 -
httr-0.4/httr/R/oauth-endpoint.r | 3
httr-0.4/httr/R/oauth-init.R | 20 +-
httr-0.4/httr/R/oauth-listener.r | 5
httr-0.4/httr/R/oauth-refresh.R | 2
httr-0.4/httr/R/oauth-signature.r | 38 +++--
httr-0.4/httr/R/oauth-token-utils.R | 6
httr-0.4/httr/R/perform.R | 75 +++++++---
httr-0.4/httr/R/progress.R |only
httr-0.4/httr/R/proxy.r | 4
httr-0.4/httr/R/response-status.r | 52 +++---
httr-0.4/httr/R/response.r | 48 ++++--
httr-0.4/httr/R/upload-file.r | 6
httr-0.4/httr/R/url-query.r | 24 ++-
httr-0.4/httr/R/url.r | 19 +-
httr-0.4/httr/R/utils.r | 11 +
httr-0.4/httr/R/verbose.r | 68 ++++++++-
httr-0.4/httr/R/zzz.R | 4
httr-0.4/httr/README.md | 38 ++---
httr-0.4/httr/build |only
httr-0.4/httr/demo/00Index | 1
httr-0.4/httr/demo/connection-sharing.r | 9 -
httr-0.4/httr/demo/oauth1-twitter.r | 6
httr-0.4/httr/demo/oauth1-yahoo.r |only
httr-0.4/httr/demo/oauth2-github.r | 8 -
httr-0.4/httr/inst/cacert.pem | 133 ++++++++++++++---
httr-0.4/httr/inst/doc |only
httr-0.4/httr/man/BROWSE.Rd | 7
httr-0.4/httr/man/DELETE.Rd | 10 -
httr-0.4/httr/man/GET.Rd | 24 +--
httr-0.4/httr/man/HEAD.Rd | 7
httr-0.4/httr/man/PATCH.Rd | 35 +++-
httr-0.4/httr/man/POST.Rd | 47 ++++--
httr-0.4/httr/man/PUT.Rd | 39 +++--
httr-0.4/httr/man/Token-class.Rd | 2
httr-0.4/httr/man/add_headers.Rd | 26 +--
httr-0.4/httr/man/authenticate.Rd | 9 -
httr-0.4/httr/man/config.Rd | 23 +--
httr-0.4/httr/man/content.Rd | 2
httr-0.4/httr/man/content_type.Rd |only
httr-0.4/httr/man/cookies.Rd |only
httr-0.4/httr/man/guess_media.Rd | 2
httr-0.4/httr/man/handle.Rd | 2
httr-0.4/httr/man/handle_pool.Rd | 2
httr-0.4/httr/man/has_content.Rd |only
httr-0.4/httr/man/headers.Rd |only
httr-0.4/httr/man/hmac_sha1.Rd | 2
httr-0.4/httr/man/http_condition.Rd | 2
httr-0.4/httr/man/http_error.Rd | 2
httr-0.4/httr/man/http_status.Rd | 2
httr-0.4/httr/man/httr.Rd | 2
httr-0.4/httr/man/httr_options.Rd |only
httr-0.4/httr/man/init_oauth1.0.Rd | 7
httr-0.4/httr/man/init_oauth2.0.Rd | 6
httr-0.4/httr/man/insensitive.Rd | 2
httr-0.4/httr/man/modify_url.Rd | 2
httr-0.4/httr/man/new_token.Rd | 2
httr-0.4/httr/man/oauth1.0_token.Rd | 2
httr-0.4/httr/man/oauth2.0_token.Rd | 2
httr-0.4/httr/man/oauth_app.Rd | 2
httr-0.4/httr/man/oauth_callback.Rd | 2
httr-0.4/httr/man/oauth_endpoint.Rd | 2
httr-0.4/httr/man/oauth_endpoints.Rd | 2
httr-0.4/httr/man/oauth_exchanger.Rd | 2
httr-0.4/httr/man/oauth_listener.Rd | 6
httr-0.4/httr/man/oauth_signature.Rd |only
httr-0.4/httr/man/parse_media.Rd | 2
httr-0.4/httr/man/parse_url.Rd | 2
httr-0.4/httr/man/progress.Rd |only
httr-0.4/httr/man/response.Rd | 2
httr-0.4/httr/man/set_config.Rd | 4
httr-0.4/httr/man/set_cookies.Rd | 7
httr-0.4/httr/man/sign_oauth.Rd | 2
httr-0.4/httr/man/status_code.Rd |only
httr-0.4/httr/man/timeout.Rd | 5
httr-0.4/httr/man/upload_file.Rd | 7
httr-0.4/httr/man/url_ok.Rd | 2
httr-0.4/httr/man/url_success.Rd | 2
httr-0.4/httr/man/use_proxy.Rd | 7
httr-0.4/httr/man/user_agent.Rd | 5
httr-0.4/httr/man/verbose.Rd | 60 +++++++-
httr-0.4/httr/man/with_config.Rd | 10 +
httr-0.4/httr/tests/testthat/test-body.r | 71 ++++-----
httr-0.4/httr/tests/testthat/test-config.r | 3
httr-0.4/httr/tests/testthat/test-content.R |only
httr-0.4/httr/tests/testthat/test-header.r | 33 ++++
httr-0.4/httr/tests/testthat/test-url.r | 6
httr-0.4/httr/vignettes |only
111 files changed, 1275 insertions(+), 609 deletions(-)
Title: Differential analysis of RNA-seq data with Poisson mixture
models
Diff between HTSDiff versions 1.0.1 dated 2013-12-10 and 1.0.2 dated 2014-07-28
Description: This package implements a Poisson mixture model to identify differentially expressed genes from RNA-seq data.
Author: Andrea Rau, Marie-Laure Martin-Magniette, Cathy Maugis-Rabusseau
Maintainer: Andrea Rau
DESCRIPTION | 17 +++++++----------
MD5 | 27 ++++++++++++++++++---------
NAMESPACE | 3 ++-
R/HTSDiff.R | 6 ++++--
R/nullModelLogLike.R | 6 ++++--
build |only
inst/CITATION | 4 ++--
inst/NEWS | 10 ++++++++++
inst/doc |only
man/HTSDiff-package.Rd | 4 ++--
man/HTSDiff.Rd | 10 ++++++++--
man/nullModelLogLike.Rd | 2 +-
vignettes |only
13 files changed, 58 insertions(+), 31 deletions(-)
Title: Clustering high throughput sequencing (HTS) data
Diff between HTSCluster versions 2.0.1 dated 2013-12-10 and 2.0.3 dated 2014-07-28
Description: This package implements a Poisson mixture model to cluster observations (e.g., genes) in high throughput sequencing data. Parameter estimation is performed using either the EM or CEM algorithm, and the ICL criterion is used for model selection (i.e., to choose the number of clusters).
Author: Andrea Rau, Gilles Celeux, Marie-Laure Martin-Magniette, Cathy Maugis-Rabusseau
Maintainer: Andrea Rau
HTSCluster-2.0.1/HTSCluster/R/logLikePoisMix.R |only
HTSCluster-2.0.1/HTSCluster/man/logLikePoisMix.Rd |only
HTSCluster-2.0.3/HTSCluster/DESCRIPTION | 15 +---
HTSCluster-2.0.3/HTSCluster/MD5 | 33 ++++++----
HTSCluster-2.0.3/HTSCluster/NAMESPACE | 4 -
HTSCluster-2.0.3/HTSCluster/R/PoisMixClus.R | 22 ++++--
HTSCluster-2.0.3/HTSCluster/R/PoisMixClusWrapper.R | 14 ++--
HTSCluster-2.0.3/HTSCluster/R/mylogLikePoisMixObs.R |only
HTSCluster-2.0.3/HTSCluster/R/probaPostInit.R | 2
HTSCluster-2.0.3/HTSCluster/R/splitEMInit.R | 59 +++++++-----------
HTSCluster-2.0.3/HTSCluster/build |only
HTSCluster-2.0.3/HTSCluster/inst/NEWS | 25 +++++++
HTSCluster-2.0.3/HTSCluster/inst/doc |only
HTSCluster-2.0.3/HTSCluster/man/HTSCluster-package.Rd | 4 -
HTSCluster-2.0.3/HTSCluster/man/Init.Rd | 7 --
HTSCluster-2.0.3/HTSCluster/man/PoisMixClus.Rd | 20 ++++--
HTSCluster-2.0.3/HTSCluster/man/logLikePoisMixDiff.Rd |only
HTSCluster-2.0.3/HTSCluster/vignettes |only
18 files changed, 120 insertions(+), 85 deletions(-)
Title: High-Dimensional Penalized Regression.
Diff between HDPenReg versions 0.89.7 dated 2014-07-17 and 0.89.8 dated 2014-07-28
Description: This package contains algorithms for lasso and fused-lasso
problems. It contains an implementation of the lars algorithm [1], for the
lasso and fusion penalization and EM-based algorithms for (logistic) lasso
and fused-lasso.
Author: Quentin Grimonprez [aut, cre],
Serge Iovleff [ctb]
Maintainer: Quentin Grimonprez
DESCRIPTION | 8 +--
MD5 | 30 +++++------
R/HDPenReg-package.R | 4 -
R/LarsPath.R | 2
R/simulation.R | 2
inst/doc/vignette.Rnw | 3 -
inst/doc/vignette.pdf |binary
man/HDPenReg-package.Rd | 4 -
man/coeff.Rd | 2
man/simul.Rd | 2
src/HDPenReg/lars/Fusion.cpp | 2
src/HDPenReg/lars/Path.cpp | 3 -
src/larsR.cpp | 18 ++++--
src/stkpp/makevars | 4 -
src/stkpp/projects/STatistiK/include/MersenneTwister.h | 44 ++++++++---------
vignettes/vignette.Rnw | 3 -
16 files changed, 69 insertions(+), 62 deletions(-)
Title: Modeling and Inferring Gene Networks
Diff between GeneNet versions 1.2.9 dated 2014-04-15 and 1.2.10 dated 2014-07-28
Description: GeneNet is a package for analyzing gene expression
(time series) data with focus on the inference of gene networks.
In particular, GeneNet implements the methods of Schaefer and
Strimmer (2005a,b,c) and Opgen-Rhein and Strimmer (2006, 2007)
for learning large-scale gene association networks (including
assignment of putative directions).
Author: Juliane Schaefer, Rainer Opgen-Rhein, and
Korbinian Strimmer.
Maintainer: Korbinian Strimmer
DESCRIPTION | 10 +++++-----
MD5 | 6 +++---
NEWS | 7 +++++++
inst/doc/index.html | 20 ++++++++++++--------
4 files changed, 27 insertions(+), 16 deletions(-)
Title: R Interface to C API of IBM ILOG CPLEX
Diff between cplexAPI versions 1.2.9 dated 2013-05-23 and 1.2.11 dated 2014-07-28
Description: R Interface to C API of IBM ILOG CPLEX, depends on IBM ILOG CPLEX (>= 12.1)
Author: Gabriel Gelius-Dietrich [aut, cre]
Maintainer: Gabriel Gelius-Dietrich
DESCRIPTION | 17 +-
MD5 | 65 ++++----
NAMESPACE | 176 +++++++++++++++++++++++
R/cplex.R | 4
R/cplexAPI.R | 139 ++++++++++++++++++
R/cplexConst.R | 190 +++++++++++++++++++++++-
R/cplexErrorClass.R | 4
R/cplexPtrClass.R | 4
R/cplex_checkAPI.R | 4
R/cplex_longparamAPI.R | 4
R/generics.R | 4
R/zzz.R | 4
build |only
configure | 209 ++++++++++++++-------------
configure.ac | 2
inst/NEWS.Rd | 21 ++
inst/c2r.map | 6
inst/doc/cplexAPI.Rnw | 4
inst/doc/cplexAPI.pdf |binary
man/addIndConstrCPLEX.Rd |only
man/addQConstrCPLEX.Rd |only
man/cplexConstants.Rd | 350 +++++++++++++++++++++++++++++++++++++++++++++-
man/delIndConstrsCPLEX.Rd |only
man/delQConstrsCPLEX.Rd |only
man/getIndConstrCPLEX.Rd |only
man/getQConstrCPLEX.Rd |only
src/Makevars.win | 2
src/cplexAPI.c | 292 ++++++++++++++++++++++++++++++++++++++
src/cplexAPI.h | 27 +++
src/cplexR.c | 4
src/cplexR.h | 4
src/cplex_checkAPI.c | 4
src/cplex_checkAPI.h | 4
src/cplex_longparamAPI.c | 4
src/cplex_longparamAPI.h | 4
src/init.c | 10 +
vignettes/cplexAPI.Rnw | 4
37 files changed, 1372 insertions(+), 194 deletions(-)
Title: High-Dimensional Regression and CAR Score Variable Selection
Diff between care versions 1.1.4 dated 2014-04-18 and 1.1.5 dated 2014-07-28
Description: The "care" package implements the regression approach
of Zuber and Strimmer (2011) "High-dimensional regression and variable
selection using CAR scores" SAGMB 10: 34.
CAR scores measure the correlation between the response and the
Mahalanobis-decorrelated predictors. The squared CAR score is a
natural measure of variable importance and provides a canonical
ordering of variables. This package provides functions for estimating
CAR scores, for variable selection using CAR scores, and for estimating
corresponding regression coefficients. Both shrinkage as well as
empirical estimators are available.
Author: Verena Zuber and Korbinian Strimmer.
Maintainer: Korbinian Strimmer
DESCRIPTION | 10 +++++-----
MD5 | 6 +++---
NEWS | 6 ++++++
inst/doc/index.html | 20 ++++++++++++--------
4 files changed, 26 insertions(+), 16 deletions(-)
Title: Evaluation of diversity in nucleotide libraries
Diff between peptider versions 0.1.4 dated 2014-05-19 and 0.1.5 dated 2014-07-28
Description: Functions for evaluating diversity in peptide libraries, including
NNN, NNB, NNK/S, and trimer schemes. This includes expected coverage,
relative efficiency, and functional diversity of the library.
Author: Heike Hofmann, Eric Hare, ggobi Foundation
Maintainer: Eric Hare
DESCRIPTION | 10
MD5 | 53 +-
NAMESPACE | 37 -
R/peptider.r | 1095 +++++++++++++++++++++++---------------------
R/tabulate.r | 392 ++++++---------
README.md | 8
man/BLOSUM80.Rd | 30 -
man/codons.Rd | 50 +-
man/coverage.Rd | 58 +-
man/detect.Rd | 52 +-
man/diversity.Rd | 56 +-
man/efficiency.Rd | 58 +-
man/encodingReduce.Rd | 38 -
man/genNeighbors.Rd |only
man/genNeighbors_reduced.Rd |only
man/generateCustom.Rd | 62 +-
man/generateCustomLib.Rd | 42 -
man/generateCustomNei.Rd |only
man/generateCustomProbs.Rd | 40 -
man/getChoices.Rd | 34 -
man/getCounts.Rd | 38 -
man/getNeighbors.Rd | 54 +-
man/getNofNeighbors.Rd | 62 +-
man/libBuild.Rd | 56 +-
man/libscheme.Rd | 54 +-
man/makowski.Rd | 54 +-
man/ppeptide.Rd | 50 +-
man/scheme.Rd | 46 -
man/schemes.Rd | 56 +-
29 files changed, 1308 insertions(+), 1277 deletions(-)
Title: Functions to create and manipulate discrete random variables
Diff between discreteRV versions 1.1 dated 2014-04-01 and 1.1.2 dated 2014-07-28
Description: discreteRV implements a set of functions that allow computations
involving discrete random variables. It uses a syntax which is familiar to
that which is used in mathematical statistics and probability courses.
Author: Andreas Buja
Maintainer: Eric Hare
DESCRIPTION | 6 +--
MD5 | 58 +++++++++++++++++-----------------
NAMESPACE | 6 +++
R/discreteRV-Probabilities.r | 72 ++++++++++++++++++++++++++++---------------
man/Conditional.Rd | 5 +-
man/E.Rd | 3 +
man/KURT.Rd | 3 +
man/P.Rd | 3 +
man/Prop.Rd | 7 +---
man/SD.Rd | 3 +
man/SKEW.Rd | 3 +
man/SofI.Rd | 6 +--
man/SofIID.Rd | 10 ++---
man/V.Rd | 3 +
man/as.RV.Rd | 11 ++----
man/grapes-AND-grapes.Rd | 5 +-
man/grapes-OR-grapes.Rd | 5 +-
man/grapes-in-grapes.Rd |only
man/make.RV.Rd | 21 +++++-------
man/margins.Rd | 9 ++---
man/mult.Rd | 11 ++----
man/multN.Rd | 13 +++----
man/outcomes.Rd |only
man/plot.RV.Rd | 27 +++++-----------
man/plot.RVsim.Rd | 7 +---
man/print.RV.Rd | 17 ++++------
man/probs.Rd | 9 ++---
man/props.Rd | 7 +---
man/qqnorm.RV.Rd | 26 +++++----------
man/rsim.Rd | 5 +-
man/skewSim.Rd | 4 +-
31 files changed, 190 insertions(+), 175 deletions(-)
Title: Dose-response data evaluation
Diff between drfit versions 0.6.1 dated 2014-03-20 and 0.6.3 dated 2014-07-28
Description: drfit provides basic and easy-to-use functions for fitting
dose-response curves to dose-response data, calculating some
(eco)toxicological parameters and plotting the results. Functions that are
fitted are the cumulative density function of the lognormal distribution
(probit fit), of the logistic distribution (logit fit), of the weibull
distribution (weibull fit) and a linear-logistic model ("linlogit" fit),
derived from the latter, which is used to describe data showing stimulation
at low doses (hormesis). In addition, functions checking, plotting and
retrieving dose-response data retrieved from a database accessed via RODBC
are included. As an alternative to the original fitting methods, the
algorithms from the drc package can be used.
Author: Johannes Ranke [aut, cre]
Maintainer: Johannes Ranke
drfit-0.6.1/drfit/ChangeLog |only
drfit-0.6.3/drfit/DESCRIPTION | 8 +--
drfit-0.6.3/drfit/MD5 | 21 ++++----
drfit-0.6.3/drfit/data/XY.rda |binary
drfit-0.6.3/drfit/inst/doc/drfit-Rnews.pdf |binary
drfit-0.6.3/drfit/inst/doc/index.html | 4 +
drfit-0.6.3/drfit/tests/IM1xIPC81.Rout.save | 9 +--
drfit-0.6.3/drfit/tests/IM1xVibrio.Rout.save | 9 +--
drfit-0.6.3/drfit/tests/XY.Rout.save | 11 ++--
drfit-0.6.3/drfit/tests/antifoul.Rout.save | 11 ++--
drfit-0.6.3/drfit/tests/pyrithione.R | 2
drfit-0.6.3/drfit/tests/pyrithione.Rout.save | 67 ++++++++++++---------------
12 files changed, 68 insertions(+), 74 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-07-16 1.0
Title: Collection of functions for plotting relations, generating
tables, and more.
Diff between Gmisc versions 0.6.4 dated 2014-06-16 and 0.6.7 dated 2014-07-28
Description: This is a collection of functions for tables, plots, and more. For
tables you'll find the convenient htmlTable() that I use for advanced
markdown table layout. A major focus has been to have it compatible with
LibreOffice and MS Word - you can now copy-paste most tables directly into
your document from the viewer. The main plots in the package are the
transitionPlot() and forestplot2(), see the examples for demo. Apart from
those it is worth mentioning the getDescriptionStatsBy() and its associated
function that help you generate a descriptive table (i.e. the Table 1 in
most journals), the pvalueFormatter() that formats p-values, and
mergeLists() that provides a complex recursive list merge.
Author: Max Gordon
Maintainer: Max Gordon
Gmisc-0.6.4/Gmisc/man/Gmisc.Rd |only
Gmisc-0.6.7/Gmisc/DESCRIPTION | 13
Gmisc-0.6.7/Gmisc/MD5 | 178 +-
Gmisc-0.6.7/Gmisc/NAMESPACE | 8
Gmisc-0.6.7/Gmisc/NEWS | 45
Gmisc-0.6.7/Gmisc/R/Gmisc.R | 93 -
Gmisc-0.6.7/Gmisc/R/bezierArrowGradient.R | 183 +-
Gmisc-0.6.7/Gmisc/R/bezierArrowSmpl.R | 147 -
Gmisc-0.6.7/Gmisc/R/bezier_private_functions.R | 288 +--
Gmisc-0.6.7/Gmisc/R/copyAllNewAttributes.R | 15
Gmisc-0.6.7/Gmisc/R/descriptionStats.R | 230 +--
Gmisc-0.6.7/Gmisc/R/figCaptionNo.R |only
Gmisc-0.6.7/Gmisc/R/forestplot2.R | 345 ++--
Gmisc-0.6.7/Gmisc/R/forestplot2_helpers.R | 762 +++++-----
Gmisc-0.6.7/Gmisc/R/getDescriptionStatsBy.R | 189 +-
Gmisc-0.6.7/Gmisc/R/getSvdMostInfluential.R | 83 -
Gmisc-0.6.7/Gmisc/R/getTicks.R | 37
Gmisc-0.6.7/Gmisc/R/grid_helpers.R | 15
Gmisc-0.6.7/Gmisc/R/htmlTable.R | 555 +++----
Gmisc-0.6.7/Gmisc/R/insertRowAndKeepAttr.R | 18
Gmisc-0.6.7/Gmisc/R/mergeLists.R | 60
Gmisc-0.6.7/Gmisc/R/outputInt.R | 21
Gmisc-0.6.7/Gmisc/R/private_functions.R | 141 -
Gmisc-0.6.7/Gmisc/R/pvalueFormatter.R | 29
Gmisc-0.6.7/Gmisc/R/transitionPlot.R | 215 +-
Gmisc-0.6.7/Gmisc/R/transitionPlot_helpers.R | 260 +--
Gmisc-0.6.7/Gmisc/inst/examples/forestplot2_example.R | 27
Gmisc-0.6.7/Gmisc/inst/examples/getDescriptionStatsBy_example.R | 37
Gmisc-0.6.7/Gmisc/inst/examples/htmlTable_example.R | 92 -
Gmisc-0.6.7/Gmisc/man/Gmisc-package.Rd |only
Gmisc-0.6.7/Gmisc/man/bezierArrowGradient.Rd | 17
Gmisc-0.6.7/Gmisc/man/bezierArrowSmpl.Rd | 5
Gmisc-0.6.7/Gmisc/man/copyAllNewAttributes.Rd | 5
Gmisc-0.6.7/Gmisc/man/describeFactors.Rd | 5
Gmisc-0.6.7/Gmisc/man/describeMean.Rd | 5
Gmisc-0.6.7/Gmisc/man/describeMedian.Rd | 5
Gmisc-0.6.7/Gmisc/man/describeProp.Rd | 5
Gmisc-0.6.7/Gmisc/man/figCapNo.Rd |only
Gmisc-0.6.7/Gmisc/man/figCapNoLast.Rd |only
Gmisc-0.6.7/Gmisc/man/figCapNoNext.Rd |only
Gmisc-0.6.7/Gmisc/man/forestplot2.Rd | 44
Gmisc-0.6.7/Gmisc/man/fpColors.Rd | 22
Gmisc-0.6.7/Gmisc/man/fpDrawCI.Rd | 5
Gmisc-0.6.7/Gmisc/man/getDescriptionStatsBy.Rd | 44
Gmisc-0.6.7/Gmisc/man/getGridVal.Rd | 5
Gmisc-0.6.7/Gmisc/man/getLines.Rd | 13
Gmisc-0.6.7/Gmisc/man/getLinesWithArrow.Rd | 5
Gmisc-0.6.7/Gmisc/man/getSvdMostInfluential.Rd | 5
Gmisc-0.6.7/Gmisc/man/getTicks.Rd | 5
Gmisc-0.6.7/Gmisc/man/getVectorAngle.Rd | 5
Gmisc-0.6.7/Gmisc/man/heightDetails.xaxis.Rd | 11
Gmisc-0.6.7/Gmisc/man/htmlTable.Rd | 219 +-
Gmisc-0.6.7/Gmisc/man/insertRowAndKeepAttr.Rd | 4
Gmisc-0.6.7/Gmisc/man/isHorizontal.Rd | 5
Gmisc-0.6.7/Gmisc/man/mergeLists.Rd | 5
Gmisc-0.6.7/Gmisc/man/mergeLists_internal.Rd | 5
Gmisc-0.6.7/Gmisc/man/outputInt.Rd | 5
Gmisc-0.6.7/Gmisc/man/prConvertShowMissing.Rd | 5
Gmisc-0.6.7/Gmisc/man/prFpDrawLegend.Rd | 5
Gmisc-0.6.7/Gmisc/man/prFpFetchRowLabel.Rd | 5
Gmisc-0.6.7/Gmisc/man/prFpFindWidestGrob.Rd | 6
Gmisc-0.6.7/Gmisc/man/prFpGetConfintFnList.Rd | 5
Gmisc-0.6.7/Gmisc/man/prFpGetGraphTicksAndClips.Rd | 5
Gmisc-0.6.7/Gmisc/man/prFpGetLabels.Rd | 5
Gmisc-0.6.7/Gmisc/man/prFpGetLayoutVP.Rd | 5
Gmisc-0.6.7/Gmisc/man/prFpGetLegendBoxPosition.Rd | 5
Gmisc-0.6.7/Gmisc/man/prFpGetLegendGrobs.Rd | 5
Gmisc-0.6.7/Gmisc/man/prFpPrepareLegendMarker.Rd | 5
Gmisc-0.6.7/Gmisc/man/prFpPrintLabels.Rd | 5
Gmisc-0.6.7/Gmisc/man/prFpPrintXaxis.Rd | 5
Gmisc-0.6.7/Gmisc/man/prFpValidateLabelList.Rd | 5
Gmisc-0.6.7/Gmisc/man/prFpXrange.Rd | 5
Gmisc-0.6.7/Gmisc/man/prGetAndValidateDefaultRef.Rd | 5
Gmisc-0.6.7/Gmisc/man/prGetStatistics.Rd | 5
Gmisc-0.6.7/Gmisc/man/prGetTextGrobCex.Rd | 2
Gmisc-0.6.7/Gmisc/man/prGridPlotTitle.Rd | 5
Gmisc-0.6.7/Gmisc/man/prPushMarginViewport.Rd | 5
Gmisc-0.6.7/Gmisc/man/prTpGetBoxPositions.Rd | 5
Gmisc-0.6.7/Gmisc/man/prTpGetBoxPropClr.Rd | 5
Gmisc-0.6.7/Gmisc/man/prTpGetBoxSizedTextGrob.Rd | 5
Gmisc-0.6.7/Gmisc/man/prTpGetColors.Rd | 5
Gmisc-0.6.7/Gmisc/man/prTpPlotArrows.Rd | 5
Gmisc-0.6.7/Gmisc/man/prTpPlotBox.Rd | 5
Gmisc-0.6.7/Gmisc/man/prTpPlotBoxes.Rd | 5
Gmisc-0.6.7/Gmisc/man/pvalueFormatter.Rd | 5
Gmisc-0.6.7/Gmisc/man/rotateWidthAccAngle.Rd | 8
Gmisc-0.6.7/Gmisc/man/rotateWidthAccVector.Rd | 5
Gmisc-0.6.7/Gmisc/man/splitLines4Table.Rd | 7
Gmisc-0.6.7/Gmisc/man/transitionPlot.Rd | 7
Gmisc-0.6.7/Gmisc/man/validateAndConvertVectorInputs.Rd | 5
Gmisc-0.6.7/Gmisc/tests/testthat/test-figCapNo.R |only
Gmisc-0.6.7/Gmisc/tests/testthat/test-getDescriptionStats.R | 129 +
Gmisc-0.6.7/Gmisc/tests/testthat/test-htmlTable.R | 42
Gmisc-0.6.7/Gmisc/tests/visual_tests/htmlTable_markdown.Rmd |only
94 files changed, 2493 insertions(+), 2388 deletions(-)
Title: Splitting methods for convex clustering
Diff between cvxclustr versions 1.1.0 dated 2014-07-26 and 1.1.1 dated 2014-07-28
Description: Alternating Minimization Algorithm (AMA) and Alternating Direction
Method of Multipliers (ADMM) splitting methods for convex clustering.
Author: Eric C. Chi, Kenneth Lange
Maintainer: Eric C. Chi
DESCRIPTION | 8 ++++----
MD5 | 6 ++++--
NEWS | 6 ++++++
src/Makevars |only
src/Makevars.win |only
5 files changed, 14 insertions(+), 6 deletions(-)