Mon, 28 Jul 2014

Package RMendeley (with last version 0.1-2) was removed from CRAN

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

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Package TreeSim updated to version 2.0 with previous version 1.9.1 dated 2013-12-10

Title: Simulating trees under the birth-death model
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

Diff between TreeSim versions 1.9.1 dated 2013-12-10 and 2.0 dated 2014-07-28

 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 
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 R/sim.rateshift.taxa.R      |    8 
 R/sim2.bd.R                 |    1 
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 33 files changed, 668 insertions(+), 358 deletions(-)

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Package TreePar updated to version 3.0 with previous version 2.5 dated 2013-06-09

Title: Estimating birth and death rates based on phylogenies
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

Diff between TreePar versions 2.5 dated 2013-06-09 and 3.0 dated 2014-07-28

 TreePar-2.5/TreePar/R/BDSSsky.R                   |only
 TreePar-2.5/TreePar/R/LikComp2.R                  |only
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 TreePar-3.0/TreePar/R/BDSSanal.R                  |    1 
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 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(-)

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Package RCurl updated to version 1.95-4.2 with previous version 1.95-4.1 dated 2013-03-06

Title: General network (HTTP/FTP/...) client interface for R
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

Diff between RCurl versions 1.95-4.1 dated 2013-03-06 and 1.95-4.2 dated 2014-07-28

 DESCRIPTION                 |    6 
 MD5                         |   10 
 configure                   | 7467 ++++++++++++++++----------------------------
 configure.in                |    4 
 data/mimeTypeExtensions.rda |binary
 src/CURLOptTable.h          |    2 
 6 files changed, 2761 insertions(+), 4728 deletions(-)

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Package gmp updated to version 0.5-12 with previous version 0.5-11 dated 2013-12-04

Title: Multiple Precision Arithmetic
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 , Sylvain Jasson , Martin Maechler
Maintainer: Antoine Lucas

Diff between gmp versions 0.5-11 dated 2013-12-04 and 0.5-12 dated 2014-07-28

 gmp-0.5-11/gmp/inst                     |only
 gmp-0.5-12/gmp/ChangeLog                |    4 +
 gmp-0.5-12/gmp/DESCRIPTION              |    8 +--
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 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 +++-
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 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(-)

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Package longclust (with last version 1.1) was removed from CRAN

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

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Package mvtBinaryEP (with last version 1.0.1) was removed from CRAN

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

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Package rocplus (with last version 1.0-0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2011-03-14 1.0-0

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Package lmPerm (with last version 1.1-2) was removed from CRAN

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

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Package ldDesign (with last version 2.0-1) was removed from CRAN

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

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Package cosinor updated to version 1.1 with previous version 1.0 dated 2014-07-25

Title: Tools for estimating and predicting the cosinor model
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

Diff between cosinor versions 1.0 dated 2014-07-25 and 1.1 dated 2014-07-28

 DESCRIPTION                     |   19 +++++++++--------
 MD5                             |   27 +++++++++++++++----------
 NAMESPACE                       |    4 +++
 NEWS                            |    7 ++++++
 R/cosinor.lm.R                  |   20 +++++++++++++++---
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 16 files changed, 119 insertions(+), 37 deletions(-)

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Package ant (with last version 0.0-10) was removed from CRAN

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

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Package RelativeRisk (with last version 1.1-1) was removed from CRAN

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

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Package cramer (with last version 0.8-1) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2006-06-19 0.8-1

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Package jmec (with last version 1.0-4) was removed from CRAN

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

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Package ipw (with last version 1.0-10) was removed from CRAN

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

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Package biOps (with last version 0.2.2) was removed from CRAN

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

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Package biOpsGUI (with last version 0.1.2) was removed from CRAN

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

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Package NMRS (with last version 1.0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2009-02-11 1.0

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Package FRBData (with last version 0.3) was removed from CRAN

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

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Package BayesQTLBIC (with last version 1.0-2) was removed from CRAN

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

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Package sda updated to version 1.3.4 with previous version 1.3.3 dated 2014-04-18

Title: Shrinkage Discriminant Analysis and CAT Score Variable Selection
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

Diff between sda versions 1.3.3 dated 2014-04-18 and 1.3.4 dated 2014-07-28

 DESCRIPTION         |   12 ++++++------
 MD5                 |    6 +++---
 NEWS                |    6 ++++++
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 4 files changed, 27 insertions(+), 17 deletions(-)

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New package rYoutheria with initial version 1.0.0
Package: rYoutheria
Type: Package
Title: Access to the YouTheria mammal trait database
Description: A programmatic interface to web-services of Youtheria. Youtheria is an online database of mammalian trait data.
Version: 1.0.0
Date: 2014-07-24
Author: Tom August
Maintainer: Tom August
VignetteBuilder: knitr
URL: https://github.com/biologicalrecordscentre/rYoutheria
BugReports: https://github.com/biologicalrecordscentre/rYoutheria/issues
Depends: R (>= 3.0.0)
Imports: plyr, RJSONIO, reshape2, RCurl
Suggests: knitr, testthat, roxygen2
License: MIT + file LICENSE
Packaged: 2014-07-28 14:04:59 UTC; tomaug
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-07-28 17:46:15

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Package Rtsne updated to version 0.8 with previous version 0.6 dated 2014-06-23

Title: T-distributed Stochastic Neighbor Embedding using Barnes-Hut implementation
Description: An R wrapper around the fast T-distributed Stochastic Neighbor Embedding implementation by Van der Maaten
Author: Jesse Krijthe
Maintainer: Jesse Krijthe

Diff between Rtsne versions 0.6 dated 2014-06-23 and 0.8 dated 2014-07-28

 DESCRIPTION         |    6 +++---
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 12 files changed, 54 insertions(+), 48 deletions(-)

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Package RJSONIO updated to version 1.3-0 with previous version 1.2-0.2 dated 2014-04-29

Title: Serialize R objects to JSON, JavaScript Object Notation
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

Diff between RJSONIO versions 1.2-0.2 dated 2014-04-29 and 1.3-0 dated 2014-07-28

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 RJSONIO-1.3-0/RJSONIO/src/libjson/Source/JSONWorker.cpp   |   14 +---
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 31 files changed, 100 insertions(+), 64 deletions(-)

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Package ltbayes updated to version 0.3 with previous version 0.2 dated 2014-05-15

Title: Simulation-Based Bayesian Inference for Latent Traits of Item Response Models
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

Diff between ltbayes versions 0.2 dated 2014-05-15 and 0.3 dated 2014-07-28

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 MD5                |   59 +++++++++++---------
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Permanent link

Package jaatha updated to version 2.5 with previous version 2.4 dated 2014-06-03

Title: A Fast Parameter Estimation Method for Evolutionary Biology
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

Diff between jaatha versions 2.4 dated 2014-06-03 and 2.5 dated 2014-07-28

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Package httr updated to version 0.4 with previous version 0.3 dated 2014-03-19

Title: Tools for working with URLs and HTTP
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

Diff between httr versions 0.3 dated 2014-03-19 and 0.4 dated 2014-07-28

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Package HTSDiff updated to version 1.0.2 with previous version 1.0.1 dated 2013-12-10

Title: Differential analysis of RNA-seq data with Poisson mixture models
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

Diff between HTSDiff versions 1.0.1 dated 2013-12-10 and 1.0.2 dated 2014-07-28

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Package HTSCluster updated to version 2.0.3 with previous version 2.0.1 dated 2013-12-10

Title: Clustering high throughput sequencing (HTS) data
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

Diff between HTSCluster versions 2.0.1 dated 2013-12-10 and 2.0.3 dated 2014-07-28

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Package HDPenReg updated to version 0.89.8 with previous version 0.89.7 dated 2014-07-17

Title: High-Dimensional Penalized Regression.
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

Diff between HDPenReg versions 0.89.7 dated 2014-07-17 and 0.89.8 dated 2014-07-28

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Package GeneNet updated to version 1.2.10 with previous version 1.2.9 dated 2014-04-15

Title: Modeling and Inferring Gene Networks
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

Diff between GeneNet versions 1.2.9 dated 2014-04-15 and 1.2.10 dated 2014-07-28

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Permanent link

Package cplexAPI updated to version 1.2.11 with previous version 1.2.9 dated 2013-05-23

Title: R Interface to C API of IBM ILOG CPLEX
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

Diff between cplexAPI versions 1.2.9 dated 2013-05-23 and 1.2.11 dated 2014-07-28

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Package care updated to version 1.1.5 with previous version 1.1.4 dated 2014-04-18

Title: High-Dimensional Regression and CAR Score Variable Selection
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

Diff between care versions 1.1.4 dated 2014-04-18 and 1.1.5 dated 2014-07-28

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More information about care at CRAN
Permanent link

Package peptider updated to version 0.1.5 with previous version 0.1.4 dated 2014-05-19

Title: Evaluation of diversity in nucleotide libraries
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

Diff between peptider versions 0.1.4 dated 2014-05-19 and 0.1.5 dated 2014-07-28

 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(-)

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Package discreteRV updated to version 1.1.2 with previous version 1.1 dated 2014-04-01

Title: Functions to create and manipulate discrete random variables
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

Diff between discreteRV versions 1.1 dated 2014-04-01 and 1.1.2 dated 2014-07-28

 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(-)

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Package drfit updated to version 0.6.3 with previous version 0.6.1 dated 2014-03-20

Title: Dose-response data evaluation
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

Diff between drfit versions 0.6.1 dated 2014-03-20 and 0.6.3 dated 2014-07-28

 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(-)

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Package trimTrees (with last version 1.0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2014-07-16 1.0

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Package Gmisc updated to version 0.6.7 with previous version 0.6.4 dated 2014-06-16

Title: Collection of functions for plotting relations, generating tables, and more.
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

Diff between Gmisc versions 0.6.4 dated 2014-06-16 and 0.6.7 dated 2014-07-28

 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(-)

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Package cvxclustr updated to version 1.1.1 with previous version 1.1.0 dated 2014-07-26

Title: Splitting methods for convex clustering
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

Diff between cvxclustr versions 1.1.0 dated 2014-07-26 and 1.1.1 dated 2014-07-28

 DESCRIPTION      |    8 ++++----
 MD5              |    6 ++++--
 NEWS             |    6 ++++++
 src/Makevars     |only
 src/Makevars.win |only
 5 files changed, 14 insertions(+), 6 deletions(-)

More information about cvxclustr at CRAN
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