Sun, 24 Sep 2017

Package spacetime updated to version 1.2-1 with previous version 1.2-0 dated 2016-09-03

Title: Classes and Methods for Spatio-Temporal Data
Description: Classes and methods for spatio-temporal data, including space-time regular lattices, sparse lattices, irregular data, and trajectories; utility functions for plotting data as map sequences (lattice or animation) or multiple time series; methods for spatial and temporal selection and subsetting, as well as for spatial/temporal/spatio-temporal matching or aggregation, retrieving coordinates, print, summary, etc.
Author: Edzer Pebesma [cre, aut], Benedikt Graeler [ctb], Tom Gottfried [ctb], Robert J. Hijmans [ctb]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>

Diff between spacetime versions 1.2-0 dated 2016-09-03 and 1.2-1 dated 2017-09-24

 DESCRIPTION                 |    6 
 MD5                         |   58 +--
 R/bind.R                    |   35 +-
 R/mnf.R                     |   90 +----
 R/stconstruct.R             |    5 
 build/vignette.rds          |binary
 data/air.rda                |binary
 data/fires.rda              |binary
 inst/ChangeLog              |  736 ++++++++++++++++++++++++++++++++++++++++++++
 inst/doc/jss816.Rnw         |    4 
 inst/doc/jss816.pdf         |binary
 inst/doc/stgvis.R           |    2 
 inst/doc/stgvis.Rmd         |   16 
 inst/doc/stgvis.html        |  282 ++++++++--------
 inst/doc/sto.Rnw            |    2 
 inst/doc/sto.pdf            |binary
 inst/doc/stpg.Rnw           |    4 
 inst/doc/stpg.pdf           |binary
 inst/doc/stsubs.pdf         |binary
 man/eof.Rd                  |   10 
 man/mnf.Rd                  |    6 
 tests/rw.Rout.save          |   12 
 tests/stconstruct.R         |    3 
 tests/stconstruct.Rout.save |   21 +
 tests/wind.Rout.save        |   12 
 vignettes/jss816.Rnw        |    4 
 vignettes/jss816.bib        |   16 
 vignettes/stgvis.Rmd        |   16 
 vignettes/sto.Rnw           |    2 
 vignettes/stpg.Rnw          |    4 
 30 files changed, 1036 insertions(+), 310 deletions(-)

More information about spacetime at CRAN
Permanent link

Package msaenet updated to version 2.7 with previous version 2.6 dated 2017-04-24

Title: Multi-Step Adaptive Estimation Methods for Sparse Regressions
Description: Multi-step adaptive elastic-net (MSAENet) algorithm for feature selection in high-dimensional regressions proposed in Xiao and Xu (2015) <DOI:10.1080/00949655.2015.1016944>, with additional support for multi-step adaptive MCP-net (MSAMNet) and multi-step adaptive SCAD-net (MSASNet) methods.
Author: Nan Xiao [aut, cre]
Maintainer: Nan Xiao <me@nanx.me>

Diff between msaenet versions 2.6 dated 2017-04-24 and 2.7 dated 2017-09-24

 msaenet-2.6/msaenet/vignettes/header.html             |only
 msaenet-2.7/msaenet/DESCRIPTION                       |    8 -
 msaenet-2.7/msaenet/MD5                               |   81 ++++++++----------
 msaenet-2.7/msaenet/NEWS.md                           |    6 +
 msaenet-2.7/msaenet/R/amnet.R                         |    1 
 msaenet-2.7/msaenet/R/asnet.R                         |    1 
 msaenet-2.7/msaenet/R/msamnet.R                       |    1 
 msaenet-2.7/msaenet/R/msasnet.R                       |    1 
 msaenet-2.7/msaenet/README.md                         |    8 +
 msaenet-2.7/msaenet/build/vignette.rds                |binary
 msaenet-2.7/msaenet/inst/doc/msaenet.Rmd              |    2 
 msaenet-2.7/msaenet/inst/doc/msaenet.html             |    9 --
 msaenet-2.7/msaenet/man/aenet.Rd                      |    7 -
 msaenet-2.7/msaenet/man/amnet.Rd                      |    1 
 msaenet-2.7/msaenet/man/asnet.Rd                      |    1 
 msaenet-2.7/msaenet/man/coef.msaenet.Rd               |    1 
 msaenet-2.7/msaenet/man/msaenet-package.Rd            |    7 -
 msaenet-2.7/msaenet/man/msaenet.Rd                    |    7 -
 msaenet-2.7/msaenet/man/msaenet.fn.Rd                 |    1 
 msaenet-2.7/msaenet/man/msaenet.fp.Rd                 |    1 
 msaenet-2.7/msaenet/man/msaenet.mae.Rd                |    1 
 msaenet-2.7/msaenet/man/msaenet.mse.Rd                |    1 
 msaenet-2.7/msaenet/man/msaenet.nzv.Rd                |    1 
 msaenet-2.7/msaenet/man/msaenet.nzv.all.Rd            |    1 
 msaenet-2.7/msaenet/man/msaenet.rmse.Rd               |    1 
 msaenet-2.7/msaenet/man/msaenet.rmsle.Rd              |    1 
 msaenet-2.7/msaenet/man/msaenet.sim.binomial.Rd       |    1 
 msaenet-2.7/msaenet/man/msaenet.sim.cox.Rd            |    7 -
 msaenet-2.7/msaenet/man/msaenet.sim.gaussian.Rd       |    7 -
 msaenet-2.7/msaenet/man/msaenet.sim.poisson.Rd        |    1 
 msaenet-2.7/msaenet/man/msaenet.tp.Rd                 |    1 
 msaenet-2.7/msaenet/man/msaenet.tune.glmnet.Rd        |    7 -
 msaenet-2.7/msaenet/man/msaenet.tune.ncvreg.Rd        |    7 -
 msaenet-2.7/msaenet/man/msaenet.tune.nsteps.glmnet.Rd |    1 
 msaenet-2.7/msaenet/man/msaenet.tune.nsteps.ncvreg.Rd |    1 
 msaenet-2.7/msaenet/man/msamnet.Rd                    |    1 
 msaenet-2.7/msaenet/man/msasnet.Rd                    |    1 
 msaenet-2.7/msaenet/man/plot.msaenet.Rd               |    1 
 msaenet-2.7/msaenet/man/predict.msaenet.Rd            |    1 
 msaenet-2.7/msaenet/man/print.msaenet.Rd              |    1 
 msaenet-2.7/msaenet/vignettes/msaenet.Rmd             |    2 
 msaenet-2.7/msaenet/vignettes/msaenet.css             |    3 
 42 files changed, 89 insertions(+), 104 deletions(-)

More information about msaenet at CRAN
Permanent link

Package MatrixCorrelation updated to version 0.9.2 with previous version 0.9.1 dated 2017-05-05

Title: Matrix Correlation Coefficients
Description: Computation and visualization of matrix correlation coefficients. The main method is the Similarity of Matrices Index, while various related measures like r1, r2, r3, r4, Yanai's GCD, RV, RV2 and adjusted RV are included for comparison.
Author: Kristian Hovde Liland [aut, cre], Tormod NŠs [ctb], Ulf Geir Indahl [ctb]
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>

Diff between MatrixCorrelation versions 0.9.1 dated 2017-05-05 and 0.9.2 dated 2017-09-24

 DESCRIPTION              |   12 ++++++------
 MD5                      |    6 +++---
 R/RcppExports.R          |    6 +++---
 man/MatrixCorrelation.Rd |    2 +-
 4 files changed, 13 insertions(+), 13 deletions(-)

More information about MatrixCorrelation at CRAN
Permanent link

Package HelpersMG updated to version 2.0 with previous version 1.9 dated 2017-03-12

Title: Tools for Earth Meteorological Analysis
Description: Contains many functions useful for managing 'NetCDF' files (see <http://en.wikipedia.org/wiki/NetCDF>), get tide levels on any point of the globe, get moon phase and time for sun rise and fall, analyse and reconstruct periodic time series of temperature with irregular sinusoidal pattern, show scales and wind rose in plot with change of color of text, Metropolis-Hastings algorithm for Bayesian MCMC analysis, plot graphs or boxplot with error bars, search files in disk by there names or their content, read the contents of all files from a folder at one time.
Author: Marc Girondot
Maintainer: Marc Girondot <marc.girondot@u-psud.fr>

Diff between HelpersMG versions 1.9 dated 2017-03-12 and 2.0 dated 2017-09-24

 DESCRIPTION              |   10 ++++-----
 MD5                      |   48 ++++++++++++++++++++++++++++-------------------
 NAMESPACE                |    5 ++++
 NEWS                     |   13 +++++++++++-
 R/BinomialConfidence.R   |    1 
 R/Ellipse.R              |only
 R/HelpersMG-package.R    |    4 +--
 R/SEfromHessian.R        |only
 R/asc.R                  |    1 
 R/compare.R              |    3 +-
 R/compare_AIC.R          |    1 
 R/compare_AICc.R         |   13 ++++++++++--
 R/compare_BIC.R          |    3 +-
 R/extractAIC.R           |only
 R/index.periodic.R       |    2 -
 R/invlogit.R             |only
 R/logit.R                |only
 R/merge.mcmcComposite.R  |    3 +-
 R/modeled.hist.R         |    2 -
 R/read_folder.R          |   11 +++++-----
 man/ExtractAIC.glm.Rd    |only
 man/HelpersMG-package.Rd |    4 +--
 man/SEfromHessian.Rd     |only
 man/compare.Rd           |    7 +++++-
 man/compare_AIC.Rd       |    5 ++++
 man/compare_AICc.Rd      |    9 +++++++-
 man/compare_BIC.Rd       |    7 +++++-
 man/ellipse.Rd           |only
 man/invlogit.Rd          |only
 man/logit.Rd             |only
 30 files changed, 107 insertions(+), 45 deletions(-)

More information about HelpersMG at CRAN
Permanent link

Package phenology updated to version 6.0 with previous version 5.4 dated 2017-03-12

Title: Tools to Manage a Parametric Function that Describes Phenology
Description: Functions used to fit and test the phenology of species based on counts.
Author: Marc Girondot
Maintainer: Marc Girondot <marc.girondot@u-psud.fr>

Diff between phenology versions 5.4 dated 2017-03-12 and 6.0 dated 2017-09-24

 DESCRIPTION              |   12 +++---
 MD5                      |   46 ++++++++++++++++++-------
 NAMESPACE                |    8 ++++
 NEWS                     |   18 +++++++++-
 R/Gratiot.R              |    2 -
 R/Tagloss_L.R            |only
 R/Tagloss_LengthObs.R    |only
 R/Tagloss_Lind.R         |only
 R/Tagloss_daymax.R       |only
 R/Tagloss_fit.R          |only
 R/Tagloss_format.R       |only
 R/Tagloss_model.R        |only
 R/Tagloss_simulate.R     |only
 R/add_phenology.R        |    6 +--
 R/fit_phenology.R        |   45 +++++++++++++++----------
 R/outLR.R                |only
 R/par_init.R             |   84 ++++++++++++++++++++++++++---------------------
 R/phenology-package.R    |   23 +++++++-----
 R/plot.Tagloss.R         |only
 data/outLR.rda           |only
 inst/shiny/ui.R          |   79 ++++++++++++++++++++++++++++++++++++++++++--
 man/Gratiot.Rd           |    2 -
 man/Tagloss_L.Rd         |only
 man/Tagloss_LengthObs.Rd |only
 man/Tagloss_daymax.Rd    |only
 man/Tagloss_fit.Rd       |only
 man/Tagloss_format.Rd    |only
 man/Tagloss_model.Rd     |only
 man/Tagloss_simulate.Rd  |only
 man/fit_phenology.Rd     |   17 +++++++++
 man/outLR.Rd             |only
 man/par_init.Rd          |    5 +-
 man/phenology-package.Rd |   24 ++++++++-----
 man/plot.Tagloss.Rd      |only
 34 files changed, 267 insertions(+), 104 deletions(-)

More information about phenology at CRAN
Permanent link

Package ICBayes updated to version 1.1 with previous version 1.0 dated 2015-11-28

Title: Bayesian Semiparametric Models for Interval-Censored Data
Description: Contains functions to fit Bayesian semiparametric regression survival models (proportional hazards model, proportional odds model, and probit model) to interval-censored time-to-event data.
Author: Chun Pan, Bo Cai, Lianming Wang, and Xiaoyan Lin
Maintainer: Chun Pan <chunpan2003@hotmail.com>

Diff between ICBayes versions 1.0 dated 2015-11-28 and 1.1 dated 2017-09-24

 ICBayes-1.0/ICBayes/R/print.ICBayes.R      |only
 ICBayes-1.0/ICBayes/man/print.ICBayes.Rd   |only
 ICBayes-1.1/ICBayes/DESCRIPTION            |   10 ++--
 ICBayes-1.1/ICBayes/MD5                    |   34 +++++++++-------
 ICBayes-1.1/ICBayes/NAMESPACE              |    6 +-
 ICBayes-1.1/ICBayes/R/ICBayes.default.R    |   61 +++++++++++++++--------------
 ICBayes-1.1/ICBayes/R/case1ph.R            |   28 +++++++------
 ICBayes-1.1/ICBayes/R/case1po.R            |   40 ++++++++++---------
 ICBayes-1.1/ICBayes/R/case2ph.R            |   29 +++++++------
 ICBayes-1.1/ICBayes/R/case2probit.R        |   37 +++++++++--------
 ICBayes-1.1/ICBayes/R/coef.ICBayes.R       |only
 ICBayes-1.1/ICBayes/R/logLik.ICBayes.R     |only
 ICBayes-1.1/ICBayes/R/summary.ICBayes.R    |only
 ICBayes-1.1/ICBayes/man/ICBayes-package.Rd |    4 -
 ICBayes-1.1/ICBayes/man/ICBayes.Rd         |   16 +++----
 ICBayes-1.1/ICBayes/man/case1ph.Rd         |    7 ++-
 ICBayes-1.1/ICBayes/man/case1po.Rd         |    8 ++-
 ICBayes-1.1/ICBayes/man/case2ph.Rd         |    7 ++-
 ICBayes-1.1/ICBayes/man/case2probit.Rd     |    9 +++-
 ICBayes-1.1/ICBayes/man/coef.ICBayes.Rd    |only
 ICBayes-1.1/ICBayes/man/logLik.ICBayes.Rd  |only
 ICBayes-1.1/ICBayes/man/summary.ICBayes.Rd |only
 22 files changed, 169 insertions(+), 127 deletions(-)

More information about ICBayes at CRAN
Permanent link

Package smoothSurv updated to version 2.0 with previous version 1.6 dated 2015-07-27

Title: Survival Regression with Smoothed Error Distribution
Description: Contains, as a main contribution, a function to fit a regression model with possibly right, left or interval censored observations and with the error distribution expressed as a mixture of G-splines. Core part of the computation is done in compiled C++ written using the Scythe Statistical Library Version 0.3.
Author: Arnošt Komárek <arnost.komarek@mff.cuni.cz>
Maintainer: Arnošt Komárek <arnost.komarek@mff.cuni.cz>

Diff between smoothSurv versions 1.6 dated 2015-07-27 and 2.0 dated 2017-09-24

 DESCRIPTION               |    8 +++----
 MD5                       |   19 +++++++++---------
 NAMESPACE                 |    2 -
 NEWS                      |    7 +++++-
 R/estimTdiff.R            |    7 +++---
 R/minPenalty.R            |    2 -
 R/smoothSurvReg.fit.R     |    2 -
 inst/CITATION             |   12 +++++++----
 man/smoothSurvReg.Rd      |    1 
 src/00smoothSurv_init.cpp |only
 src/smoothSurvReg84.h     |   47 ++++++++++++++++++++++++++++++++++++++++++++++
 11 files changed, 83 insertions(+), 24 deletions(-)

More information about smoothSurv at CRAN
Permanent link

Package RcppGSL updated to version 0.3.3 with previous version 0.3.2 dated 2017-03-04

Title: 'Rcpp' Integration for 'GNU GSL' Vectors and Matrices
Description: 'Rcpp' integration for 'GNU GSL' vectors and matrices The 'GNU Scientific Library' (or 'GSL') is a collection of numerical routines for scientific computing. It is particularly useful for C and C++ programs as it provides a standard C interface to a wide range of mathematical routines. There are over 1000 functions in total with an extensive test suite. The 'RcppGSL' package provides an easy-to-use interface between 'GSL' data structures and R using concepts from 'Rcpp' which is itself a package that eases the interfaces between R and C++. This package also serves as a prime example of how to build a package that uses 'Rcpp' to connect to another third-party library. The 'autoconf' script, 'inline' plugin and example package can all be used as a stanza to write a similar package against another library.
Author: Dirk Eddelbuettel and Romain Francois
Maintainer: Dirk Eddelbuettel <edd@debian.org>

Diff between RcppGSL versions 0.3.2 dated 2017-03-04 and 0.3.3 dated 2017-09-24

 RcppGSL-0.3.2/RcppGSL/inst/doc/RcppGSL-intro.Rnw     |only
 RcppGSL-0.3.2/RcppGSL/vignettes/RcppGSL-intro.Rnw    |only
 RcppGSL-0.3.2/RcppGSL/vignettes/buildVig.R           |only
 RcppGSL-0.3.2/RcppGSL/vignettes/buildVignette.R      |only
 RcppGSL-0.3.3/RcppGSL/ChangeLog                      |   24 +++++
 RcppGSL-0.3.3/RcppGSL/DESCRIPTION                    |   12 +-
 RcppGSL-0.3.3/RcppGSL/MD5                            |   26 ++---
 RcppGSL-0.3.3/RcppGSL/R/inline.R                     |   23 ++---
 RcppGSL-0.3.3/RcppGSL/build/vignette.rds             |binary
 RcppGSL-0.3.3/RcppGSL/cleanup                        |    5 -
 RcppGSL-0.3.3/RcppGSL/inst/NEWS.Rd                   |    8 +
 RcppGSL-0.3.3/RcppGSL/inst/doc/RcppGSL-intro.R       |   86 ++-----------------
 RcppGSL-0.3.3/RcppGSL/inst/doc/RcppGSL-intro.Rmd     |only
 RcppGSL-0.3.3/RcppGSL/inst/doc/RcppGSL-intro.pdf     |binary
 RcppGSL-0.3.3/RcppGSL/inst/doc/RcppGSL-unitTests.pdf |binary
 RcppGSL-0.3.3/RcppGSL/tests/doRUnit.R                |   43 ++++-----
 RcppGSL-0.3.3/RcppGSL/vignettes/RcppGSL-intro.Rmd    |only
 17 files changed, 97 insertions(+), 130 deletions(-)

More information about RcppGSL at CRAN
Permanent link

New package editData with initial version 0.1.0
Package: editData
Type: Package
Title: 'RStudio' Addin for Editing a 'data.frame'
Version: 0.1.0
Imports: shiny (>= 0.13), miniUI (>= 0.1.1), rstudioapi (>= 0.5), DT, tibble
Authors@R: person("Keon-Woong", "Moon", email = "cardiomoon@gmail.com", role = c("aut", "cre"))
Description: An 'RStudio' addin for editing a 'data.frame' or a 'tibble'. You can delete, add or update a 'data.frame' without coding. You can get resultant data as a 'tibble' or 'data.frame'.
URL: https://github.com/cardiomoon/editData
BugReports: https://github.com/cardiomoon/editData/issues
License: GPL-3
Encoding: UTF-8
Depends: R (>= 2.10)
LazyData: true
RoxygenNote: 6.0.1
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2017-09-23 02:13:06 UTC; cardiomoon
Author: Keon-Woong Moon [aut, cre]
Maintainer: Keon-Woong Moon <cardiomoon@gmail.com>
Repository: CRAN
Date/Publication: 2017-09-24 14:50:49 UTC

More information about editData at CRAN
Permanent link

Package bayesSurv updated to version 3.1 with previous version 3.0 dated 2017-05-29

Title: Bayesian Survival Regression with Flexible Error and Random Effects Distributions
Description: Contains Bayesian implementations of Mixed-Effects Accelerated Failure Time (MEAFT) models for censored data. Those can be not only right-censored but also interval-censored, doubly-interval-censored or misclassified interval-censored.
Author: Arnošt Komárek <arnost.komarek@mff.cuni.cz>
Maintainer: Arnošt Komárek <arnost.komarek@mff.cuni.cz>

Diff between bayesSurv versions 3.0 dated 2017-05-29 and 3.1 dated 2017-09-24

 CHANGES       |    4 ++++
 DESCRIPTION   |    8 ++++----
 MD5           |    6 +++---
 inst/CITATION |   27 +++++++++++++++++----------
 4 files changed, 28 insertions(+), 17 deletions(-)

More information about bayesSurv at CRAN
Permanent link

Package scam updated to version 1.2-2 with previous version 1.2-1 dated 2017-02-16

Title: Shape Constrained Additive Models
Description: Routines for generalized additive modelling under shape constraints on the component functions of the linear predictor (Pya and Wood, 2015) <doi:10.1007/s11222-013-9448-7>. Models can contain multiple shape constrained (univariate and/or bivariate) and unconstrained terms. The routines of gam() in package 'mgcv' are used for setting up the model matrix, printing and plotting the results. Penalized likelihood maximization based on Newton-Raphson method is used to fit a model with multiple smoothing parameter selection by GCV or UBRE/AIC.
Author: Natalya Pya <nat.pya@gmail.com>
Maintainer: Natalya Pya <nat.pya@gmail.com>

Diff between scam versions 1.2-1 dated 2017-02-16 and 1.2-2 dated 2017-09-24

 ChangeLog                               |   15 +++++++++++
 DESCRIPTION                             |    8 +++---
 MD5                                     |   23 +++++++++--------
 NAMESPACE                               |    4 +++
 R/plot.r                                |    4 ---
 R/print.scam.R                          |    7 +++--
 R/scam-v1.r                             |only
 R/scam.check.R                          |    3 +-
 R/scam.r                                |   27 +++++++++++++++++++-
 R/summary.scam.R                        |   28 ++++++++++++---------
 man/formula.scam.Rd                     |only
 man/logLik.scam.Rd                      |only
 man/scam.Rd                             |    7 +++--
 man/smooth.construct.mpi.smooth.spec.Rd |   42 ++++++++++++++++++++++++++++----
 14 files changed, 127 insertions(+), 41 deletions(-)

More information about scam at CRAN
Permanent link

Package JGR updated to version 1.8-4 with previous version 1.8-3 dated 2017-09-22

Title: Java GUI for R
Description: Java GUI for R - cross-platform, universal and unified Graphical User Interface for R. For full functionality on Windows and Mac OS X JGR requires a start application which depends on your OS.
Author: Markus Helbig <info@markushelbig.de>, Simon Urbanek, Ian Fellows
Maintainer: Markus Helbig <info@markushelbig.de>

Diff between JGR versions 1.8-3 dated 2017-09-22 and 1.8-4 dated 2017-09-24

 DESCRIPTION       |    8 ++++----
 MD5               |    8 ++++----
 NEWS              |    3 +++
 R/JGR.R           |    2 +-
 inst/java/JGR.jar |binary
 5 files changed, 12 insertions(+), 9 deletions(-)

More information about JGR at CRAN
Permanent link

New package LMfilteR with initial version 0.1.0
Package: LMfilteR
Type: Package
Title: Filter Methods for Parameter Estimation in Linear Regression Models
Version: 0.1.0
Authors@R: c( person("Christian", "Llano Robayo", email = "cxl985@miami.edu", role = c("aut","cre")), person("Nazrul", "Shaikh", email = "n.shaikh@miami.edu", role = "aut") )
Description: We present a method based on filtering algorithms to estimate the parameters of linear regressions, i.e. the coefficients and the variance of the error term. The proposed algorithm makes use of Particle Filters following Ristic, B., Arulampalam, S., Gordon, N. (2004, ISBN: 158053631X) resampling methods.
License: GPL (>= 2)
Imports: MASS (>= 7.3-45), stats (>= 3.3.3)
Depends: R (>= 3.3.3)
Encoding: UTF-8
LazyData: true
BugReports: https://github.com/ChrissCod/LMfilteR/issues
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2017-09-23 15:24:31 UTC; cp
Author: Christian Llano Robayo [aut, cre], Nazrul Shaikh [aut]
Maintainer: Christian Llano Robayo <cxl985@miami.edu>
Repository: CRAN
Date/Publication: 2017-09-24 10:34:27 UTC

More information about LMfilteR at CRAN
Permanent link

Package castor updated to version 1.2.1 with previous version 1.2 dated 2017-09-23

Title: Efficient Phylogenetics on Large Trees
Description: Efficient tree manipulation functions including pruning, rerooting, calculation of most-recent common ancestors, calculating distances from the tree root and calculating pairwise distance matrices. Calculation of phylogenetic signal and mean trait depth (trait conservatism). Ancestral state reconstruction and hidden character prediction of discrete characters, using Maximum Likelihood and Maximum Parsimony methods. Simulating and fitting models of trait evolution, and generating random trees using birth-death models.
Author: Stilianos Louca
Maintainer: Stilianos Louca <louca@zoology.ubc.ca>

Diff between castor versions 1.2 dated 2017-09-23 and 1.2.1 dated 2017-09-24

 DESCRIPTION                        |    8 -
 MD5                                |    8 -
 R/RcppExports.R                    |  124 +++++++++++------------
 src/RcppExports.cpp                |  195 +++++++++++++++++++++++++------------
 src/phylogenetics_cpp_routines.cpp |    2 
 5 files changed, 204 insertions(+), 133 deletions(-)

More information about castor at CRAN
Permanent link

Package rwalkr updated to version 0.3.1 with previous version 0.3.0 dated 2017-09-02

Title: API to Melbourne Pedestrian Data
Description: Provides API to Melbourne pedestrian data in tidy data form.
Author: Earo Wang [aut, cre]
Maintainer: Earo Wang <earo.wang@gmail.com>

Diff between rwalkr versions 0.3.0 dated 2017-09-02 and 0.3.1 dated 2017-09-24

 DESCRIPTION           |    6 +++---
 MD5                   |   18 +++++++++---------
 NEWS.md               |   13 +++++++++++++
 R/scrape.R            |    8 ++++++--
 R/shiny.R             |    6 +++---
 R/soda.R              |    3 ++-
 R/sysdata.rda         |binary
 man/figure/plot-1.png |binary
 man/run_melb.Rd       |    2 +-
 man/shine_melb.Rd     |    4 ++--
 10 files changed, 39 insertions(+), 21 deletions(-)

More information about rwalkr at CRAN
Permanent link

Package Rdimtools updated to version 0.1.1 with previous version 0.1.0 dated 2017-09-21

Title: Dimension Reduction and Estimation Methods
Description: We provide a rich collection of linear and nonlinear dimension reduction techniques implemented using 'RcppArmadillo'. The question on what we should use as the target dimension is addressed by intrinsic dimension estimation methods introduced as well. For more details on dimensionality techniques, see the paper by Ma and Zhu (2013) <doi:10.1111/j.1751-5823.2012.00182.x> if you are interested in statistical approach, or Engel, Huttenberger, and Hamann (2012) <doi:10.4230/OASIcs.VLUDS.2011.135> for a broader cross-disciplinary overview.
Author: Kisung You [aut, cre], Donggun Kim [aut], Yoon Mo Jung [rev]
Maintainer: Kisung You <kyou@nd.edu>

Diff between Rdimtools versions 0.1.0 dated 2017-09-21 and 0.1.1 dated 2017-09-24

 DESCRIPTION                 |    6 +--
 MD5                         |   68 +++++++++++++++++++++++---------------------
 NAMESPACE                   |    2 +
 R/auxiliary.R               |   16 +++++-----
 R/init.R                    |    2 -
 R/linear_FA.R               |    4 +-
 R/linear_LPP.R              |    2 -
 R/linear_NPE.R              |    2 -
 R/linear_PCA.R              |    4 +-
 R/nonlinear_CISOMAP.R       |    2 -
 R/nonlinear_ISOMAP.R        |    2 -
 R/nonlinear_KECA.R          |only
 R/nonlinear_LAPEIG.R        |    2 -
 R/nonlinear_LISOMAP.R       |    2 -
 R/nonlinear_LLE.R           |    2 -
 R/nonlinear_LTSA.R          |only
 R/nonlinear_MVU.R           |    4 +-
 R/nonlinear_PLP.R           |    2 -
 R/package-Rdimtools.R       |    2 +
 man/Rdimtools.Rd            |    2 +
 man/aux_graphnbd.Rd         |   10 +++---
 man/aux_preprocess.Rd       |    6 +--
 man/linear_FA.Rd            |    4 +-
 man/linear_LPP.Rd           |    2 -
 man/linear_NPE.Rd           |    2 -
 man/linear_PCA.Rd           |    4 +-
 man/nonlinear_CISOMAP.Rd    |    2 -
 man/nonlinear_ISOMAP.Rd     |    2 -
 man/nonlinear_KECA.Rd       |only
 man/nonlinear_LAPEIG.Rd     |    2 -
 man/nonlinear_LISOMAP.Rd    |    2 -
 man/nonlinear_LLE.Rd        |    2 -
 man/nonlinear_LTSA.Rd       |only
 man/nonlinear_MVU.Rd        |    4 +-
 man/nonlinear_PLP.Rd        |    2 -
 src/Rdimtools_auxiliary.cpp |    7 ++--
 src/methods_nonlinear.cpp   |    1 
 37 files changed, 94 insertions(+), 84 deletions(-)

More information about Rdimtools at CRAN
Permanent link

Package dparser updated to version 0.1.5 with previous version 0.1.4 dated 2017-09-22

Title: Port of Dparser Package
Description: A Scannerless GLR parser/parser generator. Note that GLR standing for "generalized LR", where L stands for "left-to-right" and R stands for "rightmost (derivation)". For more information see <https://en.wikipedia.org/wiki/GLR_parser>. This parser is based on the Tomita (1987) algorithm. (Paper can be found at <http://acl-arc.comp.nus.edu.sg/archives/acl-arc-090501d3/data/pdf/anthology-PDF/J/J87/J87-1004.pdf>). The original dparser package documentation can be found at <http://dparser.sourceforge.net/>. This allows you to add mini-languages to R (like RxODE's ODE mini-language Wang, Hallow, and James 2015 <DOI:10.1002/psp4.12052>) or to parse other languages like 'NONMEM' to automatically translate them to R code. To use this in your code, add a LinkingTo dparser in your DESCRIPTION file and instead of using #include <dparse.h> use #include <dparser.h>. This also provides a R-based port of the make_dparser <http://dparser.sourceforge.net/d/make_dparser.cat> command called mkdparser(). Additionally you can parse an arbitrary grammar within R using the dparse() function, which works on most OSes and is mainly for grammar testing. The fastest parsing, of course, occurs at the C level, and is suggested.
Author: Matthew Fidler [aut, cre], John Plevyak [aut]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>

Diff between dparser versions 0.1.4 dated 2017-09-22 and 0.1.5 dated 2017-09-24

 DESCRIPTION        |   15 ++++++++-------
 MD5                |   16 +++++++++-------
 R/dparser.R        |   31 +++++++++++++++++++++++++++++++
 R/version.R        |    2 +-
 inst               |only
 man/dparse.Rd      |   28 ++++++++++++++++++++++++++++
 man/mkdparse.Rd    |    5 +++++
 src/dparser.h      |   10 +++++-----
 src/write_tables.c |    8 ++++----
 9 files changed, 91 insertions(+), 24 deletions(-)

More information about dparser at CRAN
Permanent link


Built and running on Debian GNU/Linux using R, littler and blosxom. Styled with Bootstrap.