Mon, 01 Dec 2014

Package YplantQMC updated to version 0.6-3 with previous version 0.5 dated 2013-03-03

Title: Plant Architectural Analysis with Yplant and QuasiMC
Description: An R implementation of Yplant, combined with the QuasiMC raytracer. Calculate radiation absorption, transmission and scattering, photosynthesis and transpiration of virtual 3D plants.
Author: Remko Duursma. QuasiMC by Mik Cieslak. Uses code by Robert Pearcy (Yplant) and Belinda Medlyn (MAESTRA)
Maintainer: Remko Duursma

Diff between YplantQMC versions 0.5 dated 2013-03-03 and 0.6-3 dated 2014-12-01

 YplantQMC-0.5/YplantQMC/R/STARbar.plant3dlist.R         |only
 YplantQMC-0.5/YplantQMC/R/UNLOAD.R                      |only
 YplantQMC-0.5/YplantQMC/R/YplantDay.plant3d.R           |only
 YplantQMC-0.5/YplantQMC/R/YplantDay.plant3dlist.R       |only
 YplantQMC-0.5/YplantQMC/R/changeinternodes.R            |only
 YplantQMC-0.5/YplantQMC/R/makereport.R                  |only
 YplantQMC-0.5/YplantQMC/R/modifypfile.R                 |only
 YplantQMC-0.5/YplantQMC/R/plot.plant3dlist.R            |only
 YplantQMC-0.5/YplantQMC/R/plot.stand3d.R                |only
 YplantQMC-0.5/YplantQMC/R/readplantlist.R               |only
 YplantQMC-0.5/YplantQMC/R/runYplant.stand3d.R           |only
 YplantQMC-0.5/YplantQMC/R/ypaddonMessage.R              |only
 YplantQMC-0.5/YplantQMC/man/makereport.Rd               |only
 YplantQMC-0.6-3/YplantQMC/CHANGELOG                     |    7 
 YplantQMC-0.6-3/YplantQMC/DESCRIPTION                   |   24 
 YplantQMC-0.6-3/YplantQMC/MD5                           |  288 ++---
 YplantQMC-0.6-3/YplantQMC/NAMESPACE                     |  121 +-
 YplantQMC-0.6-3/YplantQMC/R/DAPA.R                      |    6 
 YplantQMC-0.6-3/YplantQMC/R/DAPA.plant3d.R              |   94 -
 YplantQMC-0.6-3/YplantQMC/R/DAPAQMC.R                   |   50 -
 YplantQMC-0.6-3/YplantQMC/R/Farquhar.R                  |  264 +++--
 YplantQMC-0.6-3/YplantQMC/R/GramSchmidt.R               |only
 YplantQMC-0.6-3/YplantQMC/R/KE.R                        |   72 -
 YplantQMC-0.6-3/YplantQMC/R/Kn.R                        |   97 -
 YplantQMC-0.6-3/YplantQMC/R/STARbar.R                   |  521 ++++++----
 YplantQMC-0.6-3/YplantQMC/R/Silhouette.R                |   66 -
 YplantQMC-0.6-3/YplantQMC/R/VPDTdiurnal.R               |   78 -
 YplantQMC-0.6-3/YplantQMC/R/VPDtoRH.R                   |   12 
 YplantQMC-0.6-3/YplantQMC/R/YplantDay.R                 |  302 +++++-
 YplantQMC-0.6-3/YplantQMC/R/acosangle.R                 |   26 
 YplantQMC-0.6-3/YplantQMC/R/areapoly.R                  |    9 
 YplantQMC-0.6-3/YplantQMC/R/as.data.frame.STARbarlist.R |   18 
 YplantQMC-0.6-3/YplantQMC/R/calcparhrly.R               |  104 +-
 YplantQMC-0.6-3/YplantQMC/R/checkHemi.R                 |   17 
 YplantQMC-0.6-3/YplantQMC/R/checkInstallation.R         |   28 
 YplantQMC-0.6-3/YplantQMC/R/constructplant.R            |  799 +++++++++-------
 YplantQMC-0.6-3/YplantQMC/R/crownhull.R                 |   99 +
 YplantQMC-0.6-3/YplantQMC/R/esat.R                      |   20 
 YplantQMC-0.6-3/YplantQMC/R/evalHemi.R                  |   89 -
 YplantQMC-0.6-3/YplantQMC/R/getR.R                      |  133 +-
 YplantQMC-0.6-3/YplantQMC/R/getangles.R                 |  101 +-
 YplantQMC-0.6-3/YplantQMC/R/getleafnormal.R             |   18 
 YplantQMC-0.6-3/YplantQMC/R/getpsil.R                   |  440 ++++----
 YplantQMC-0.6-3/YplantQMC/R/gridtrace.R                 |  286 ++---
 YplantQMC-0.6-3/YplantQMC/R/includePhy.R                |  107 +-
 YplantQMC-0.6-3/YplantQMC/R/installQuasiMC.R            |  116 +-
 YplantQMC-0.6-3/YplantQMC/R/leafdata.R                  |   81 -
 YplantQMC-0.6-3/YplantQMC/R/leafdispersion.R            |  132 +-
 YplantQMC-0.6-3/YplantQMC/R/lightresponse.R             |   35 
 YplantQMC-0.6-3/YplantQMC/R/madeleafdirection.R         |   80 -
 YplantQMC-0.6-3/YplantQMC/R/makeQMCinput.R              |   99 +
 YplantQMC-0.6-3/YplantQMC/R/makeStand.R                 |  168 ++-
 YplantQMC-0.6-3/YplantQMC/R/makesolarvec.R              |   20 
 YplantQMC-0.6-3/YplantQMC/R/makevector.R                |    2 
 YplantQMC-0.6-3/YplantQMC/R/makeviewplane.R             |   22 
 YplantQMC-0.6-3/YplantQMC/R/pathlen.R                   |  263 ++---
 YplantQMC-0.6-3/YplantQMC/R/photosyn.R                  |  284 ++---
 YplantQMC-0.6-3/YplantQMC/R/plot.leaffile.R             |   72 +
 YplantQMC-0.6-3/YplantQMC/R/plot.plant3d.R              |  428 +++++---
 YplantQMC-0.6-3/YplantQMC/R/plot.projectedplant3d.R     |  109 +-
 YplantQMC-0.6-3/YplantQMC/R/plot.tracedplant.R          |   56 -
 YplantQMC-0.6-3/YplantQMC/R/plot.yphemi.R               |  191 +--
 YplantQMC-0.6-3/YplantQMC/R/plot.yplantsim.R            |  196 +--
 YplantQMC-0.6-3/YplantQMC/R/plot.yplocation.R           |   20 
 YplantQMC-0.6-3/YplantQMC/R/plot.ypmet.R                |   88 -
 YplantQMC-0.6-3/YplantQMC/R/plot3dcylinder.R            |   62 -
 YplantQMC-0.6-3/YplantQMC/R/plotstemsections.R          |   50 -
 YplantQMC-0.6-3/YplantQMC/R/print.STAR.R                |   28 
 YplantQMC-0.6-3/YplantQMC/R/print.plant3d.R             |   36 
 YplantQMC-0.6-3/YplantQMC/R/print.plant3dlist.R         |   16 
 YplantQMC-0.6-3/YplantQMC/R/print.projectedplant3d.R    |   15 
 YplantQMC-0.6-3/YplantQMC/R/print.stand3d.R             |   19 
 YplantQMC-0.6-3/YplantQMC/R/print.summary.plant3d.R     |   68 -
 YplantQMC-0.6-3/YplantQMC/R/print.yplantsim.R           |   43 
 YplantQMC-0.6-3/YplantQMC/R/print.yplantsimlist.R       |   20 
 YplantQMC-0.6-3/YplantQMC/R/print.yplocation.R          |   27 
 YplantQMC-0.6-3/YplantQMC/R/print.ypmet.R               |   48 
 YplantQMC-0.6-3/YplantQMC/R/print.ypphy.R               |   23 
 YplantQMC-0.6-3/YplantQMC/R/projectplant.R              |  173 ++-
 YplantQMC-0.6-3/YplantQMC/R/psrdata.R                   |   24 
 YplantQMC-0.6-3/YplantQMC/R/randomplant.R               |  258 +++--
 YplantQMC-0.6-3/YplantQMC/R/readCAN.R                   |   74 -
 YplantQMC-0.6-3/YplantQMC/R/readQMCout.R                |   57 -
 YplantQMC-0.6-3/YplantQMC/R/readl.R                     |  203 ++--
 YplantQMC-0.6-3/YplantQMC/R/readp.R                     |  110 +-
 YplantQMC-0.6-3/YplantQMC/R/replaceangles.R             |  266 ++++-
 YplantQMC-0.6-3/YplantQMC/R/runQMCUOC.R                 |   85 -
 YplantQMC-0.6-3/YplantQMC/R/runYplant.R                 |  516 ++++++----
 YplantQMC-0.6-3/YplantQMC/R/runquasimc.R                |   59 -
 YplantQMC-0.6-3/YplantQMC/R/setHemi.R                   |  171 ++-
 YplantQMC-0.6-3/YplantQMC/R/setLocation.R               |  115 +-
 YplantQMC-0.6-3/YplantQMC/R/setMet.R                    |  451 +++++----
 YplantQMC-0.6-3/YplantQMC/R/setPhy.R                    |   93 +
 YplantQMC-0.6-3/YplantQMC/R/shiftplant.R                |  138 +-
 YplantQMC-0.6-3/YplantQMC/R/summary.plant3d.R           |  369 ++++---
 YplantQMC-0.6-3/YplantQMC/R/summary.plant3dlist.R       |  155 +--
 YplantQMC-0.6-3/YplantQMC/R/summary.yplantsimlist.R     |  181 +--
 YplantQMC-0.6-3/YplantQMC/R/viewplot.R                  |  143 +-
 YplantQMC-0.6-3/YplantQMC/R/writeOUTfile.R              |   26 
 YplantQMC-0.6-3/YplantQMC/R/writePSRfile.R              |  119 +-
 YplantQMC-0.6-3/YplantQMC/R/writecfg.R                  |  182 +--
 YplantQMC-0.6-3/YplantQMC/R/writerandomdiffuse.R        |    4 
 YplantQMC-0.6-3/YplantQMC/R/writeturtlediffuse.R        |   47 
 YplantQMC-0.6-3/YplantQMC/R/xmastime.R                  |   69 -
 YplantQMC-0.6-3/YplantQMC/R/xprod.R                     |   12 
 YplantQMC-0.6-3/YplantQMC/R/yplantqmc-package.R         |only
 YplantQMC-0.6-3/YplantQMC/R/ypreport.R                  |only
 YplantQMC-0.6-3/YplantQMC/R/zenaz.R                     |  433 ++++----
 YplantQMC-0.6-3/YplantQMC/R/zzz.R                       |   62 -
 YplantQMC-0.6-3/YplantQMC/README.md                     |only
 YplantQMC-0.6-3/YplantQMC/data/hemiphotos.RData         |binary
 YplantQMC-0.6-3/YplantQMC/data/plantexamples.RData      |binary
 YplantQMC-0.6-3/YplantQMC/data/turtle.RData             |binary
 YplantQMC-0.6-3/YplantQMC/data/turtle244.RData          |binary
 YplantQMC-0.6-3/YplantQMC/data/turtle482.RData          |binary
 YplantQMC-0.6-3/YplantQMC/data/yplantaltaz.RData        |binary
 YplantQMC-0.6-3/YplantQMC/man/Farquhar.Rd               |  203 ++--
 YplantQMC-0.6-3/YplantQMC/man/ModifyPfiles.Rd           |  131 +-
 YplantQMC-0.6-3/YplantQMC/man/STARbar.Rd                |  158 +--
 YplantQMC-0.6-3/YplantQMC/man/Silhouette.Rd             |   43 
 YplantQMC-0.6-3/YplantQMC/man/YplantDay.Rd              |  169 +--
 YplantQMC-0.6-3/YplantQMC/man/constructplant.Rd         |  150 +--
 YplantQMC-0.6-3/YplantQMC/man/crownhull.Rd              |   71 -
 YplantQMC-0.6-3/YplantQMC/man/examplehemi.Rd            |   24 
 YplantQMC-0.6-3/YplantQMC/man/getR.Rd                   |   28 
 YplantQMC-0.6-3/YplantQMC/man/getangles.Rd              |   41 
 YplantQMC-0.6-3/YplantQMC/man/installQuasiMC.Rd         |   42 
 YplantQMC-0.6-3/YplantQMC/man/leafdispersion.Rd         |   81 -
 YplantQMC-0.6-3/YplantQMC/man/lightresponse.Rd          |   44 
 YplantQMC-0.6-3/YplantQMC/man/makeStand.Rd              |   62 -
 YplantQMC-0.6-3/YplantQMC/man/plantexamples.Rd          |   24 
 YplantQMC-0.6-3/YplantQMC/man/plot.leaffile.Rd          |   47 
 YplantQMC-0.6-3/YplantQMC/man/plot.plant3d.Rd           |  149 +-
 YplantQMC-0.6-3/YplantQMC/man/projectplant.Rd           |   86 -
 YplantQMC-0.6-3/YplantQMC/man/psrdata.Rd                |   34 
 YplantQMC-0.6-3/YplantQMC/man/randomplant.Rd            |  115 +-
 YplantQMC-0.6-3/YplantQMC/man/readl.Rd                  |   37 
 YplantQMC-0.6-3/YplantQMC/man/readp.Rd                  |   50 -
 YplantQMC-0.6-3/YplantQMC/man/runYplant.Rd              |  189 ++-
 YplantQMC-0.6-3/YplantQMC/man/setHemi.Rd                |   90 -
 YplantQMC-0.6-3/YplantQMC/man/setLocation.Rd            |   56 -
 YplantQMC-0.6-3/YplantQMC/man/setMet.Rd                 |  171 +--
 YplantQMC-0.6-3/YplantQMC/man/setPhy.Rd                 |  110 +-
 YplantQMC-0.6-3/YplantQMC/man/summary.plant3d.Rd        |  149 +-
 YplantQMC-0.6-3/YplantQMC/man/turtle.Rd                 |   35 
 YplantQMC-0.6-3/YplantQMC/man/turtle244.Rd              |   33 
 YplantQMC-0.6-3/YplantQMC/man/turtle482.Rd              |   36 
 YplantQMC-0.6-3/YplantQMC/man/viewplot.Rd               |   60 -
 YplantQMC-0.6-3/YplantQMC/man/xmastime.Rd               |   36 
 YplantQMC-0.6-3/YplantQMC/man/yplantaltaz.Rd            |   19 
 YplantQMC-0.6-3/YplantQMC/man/ypreport.Rd               |only
 YplantQMC-0.6-3/YplantQMC/man/zenaz.Rd                  |  114 +-
 YplantQMC-0.6-3/YplantQMC/src/bristospitters.f90        |   76 -
 YplantQMC-0.6-3/YplantQMC/src/kn.f                      |    2 
 154 files changed, 8431 insertions(+), 6342 deletions(-)

More information about YplantQMC at CRAN
Permanent link

Package yaImpute updated to version 1.0-23 with previous version 1.0-22 dated 2014-07-10

Title: yaImpute: An R Package for k-NN Imputation
Description: Performs nearest neighbor-based imputation using one or more alternative approaches to processing multivariate data. These include methods based on canonical correlation analysis, canonical correspondence analysis, and a multivariate adaptation of the random forest classification and regression techniques of Leo Breiman and Adele Cutler. Additional methods are also offered. The package includes functions for comparing the results from running alternative techniques, detecting imputation targets that are notably distant from reference observations, detecting and correcting for bias, bootstrapping and building ensemble imputations, and mapping results.
Author: Nicholas L. Crookston, Andrew O. Finley, John Coulston (Sunil Arya and David Mount for ANN)
Maintainer: Nicholas L. Crookston

Diff between yaImpute versions 1.0-22 dated 2014-07-10 and 1.0-23 dated 2014-12-01

 DESCRIPTION              |   14 ++--
 MD5                      |   26 +++----
 NEWS                     |    9 ++
 R/asciigridimpute.R      |   25 +++++--
 R/errorstats.R           |    7 +-
 R/varSelection.R         |   22 +++---
 R/yai.R                  |  157 ++++++++++++++++++++++++++++++-----------------
 R/yaiVarImp.R            |   16 +++-
 data/MoscowMtStJoe.RData |binary
 data/TallyLake.RData     |binary
 man/applyMask.Rd         |    2 
 man/bestVars.Rd          |    2 
 man/notablydifferent.Rd  |    2 
 man/varSelection.Rd      |    4 -
 14 files changed, 183 insertions(+), 103 deletions(-)

More information about yaImpute at CRAN
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New package wrassp with initial version 0.1.3
Package: wrassp
Version: 0.1.3
Title: Interface to the ASSP Library
Authors@R: as.person(c( "Raphael Winkelmann [aut, cre]", "Lasse Bombien [aut]", "Michel Scheffers [aut]"))
Description: wrassp is a wrapper around Michel Scheffers's libassp (Advanced Speech Signal Processor). The libassp library aims at providing functionality for handling speech signal files in most common audio formats and for performing analyses common in phonetic science/speech science. This includes the calculation of formants, fundamental frequency, root mean square, auto correlation, a variety of spectral analyses, zero crossing rate, filtering etc. This wrapper provides R with a large subset of libassp's signal processing functions and provides them to the user in a (hopefully) user-friendly manner.
Depends: R (>= 3.1.1)
VignetteBuilder: knitr
Suggests: compare(>= 0.2.4), knitr(>= 1.7), testthat(>= 0.7.1.99)
License: GPL (>= 3)
URL: https://github.com/IPS-LMU/wrassp
BugReports: https://github.com/IPS-LMU/wrassp/issues
Packaged: 2014-12-01 17:13:26 UTC; raphaelwinkelmann
Author: Raphael Winkelmann [aut, cre], Lasse Bombien [aut], Michel Scheffers [aut]
Maintainer: Raphael Winkelmann
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-12-02 00:17:08

More information about wrassp at CRAN
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Package plgp updated to version 1.1-7 with previous version 1.1-5 dated 2012-07-24

Title: Particle Learning of Gaussian Processes
Description: Sequential Monte Carlo inference for fully Bayesian Gaussian process (GP) regression and classification models by particle learning (PL). The sequential nature of inference and the active learning (AL) hooks provided facilitate thrifty sequential design (by entropy) and optimization (by improvement) for classification and regression models, respectively. This package essentially provides a generic PL interface, and functions (arguments to the interface) which implement the GP models and AL heuristics. Functions for a special, linked, regression/classification GP model and an integrated expected conditional improvement (IECI) statistic is provides for optimization in the presence of unknown constraints. Separable and isotropic Gaussian, and single-index correlation functions are supported. See the examples section of ?plgp and demo(package="plgp") for an index of demos
Author: Robert B. Gramacy
Maintainer: Robert B. Gramacy

Diff between plgp versions 1.1-5 dated 2012-07-24 and 1.1-7 dated 2014-12-01

 plgp-1.1-5/plgp/LICENSE                  |only
 plgp-1.1-7/plgp/ChangeLog                |   21 +++
 plgp-1.1-7/plgp/DESCRIPTION              |   42 +++----
 plgp-1.1-7/plgp/MD5                      |   47 ++++----
 plgp-1.1-7/plgp/NAMESPACE                |    4 
 plgp-1.1-7/plgp/R/covar.R                |    3 
 plgp-1.1-7/plgp/R/ieci.R                 |    2 
 plgp-1.1-7/plgp/R/pl.R                   |   61 +++++-----
 plgp-1.1-7/plgp/R/plcgp.R                |   77 ++++++-------
 plgp-1.1-7/plgp/R/plconstgp.R            |   72 ++++++------
 plgp-1.1-7/plgp/R/plgp.R                 |  177 ++++++++++++++++---------------
 plgp-1.1-7/plgp/demo/plcgp_cush.R        |    7 -
 plgp-1.1-7/plgp/demo/plcgp_exp.R         |    7 -
 plgp-1.1-7/plgp/demo/plcgp_exp_entropy.R |   13 +-
 plgp-1.1-7/plgp/demo/plconstgp_1d_ieci.R |   15 +-
 plgp-1.1-7/plgp/demo/plconstgp_2d_ieci.R |   17 +-
 plgp-1.1-7/plgp/demo/plgp_1d_ieci.R      |   17 +-
 plgp-1.1-7/plgp/demo/plgp_exp_ei.R       |   17 +-
 plgp-1.1-7/plgp/demo/plgp_sin1d.R        |   13 +-
 plgp-1.1-7/plgp/man/PL.Rd                |   20 ++-
 plgp-1.1-7/plgp/man/data.GP.Rd           |   14 +-
 plgp-1.1-7/plgp/man/plgp-internal.Rd     |    4 
 plgp-1.1-7/plgp/src/covar.c              |    6 -
 plgp-1.1-7/plgp/src/ieci.c               |    9 +
 plgp-1.1-7/plgp/src/matrix.c             |   18 +--
 25 files changed, 376 insertions(+), 307 deletions(-)

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Package pedometrics updated to version 0.4-1 with previous version 0.3-0 dated 2014-11-19

Title: Pedometric Tools and Techniques
Description: This package contains functions to employ many tools and techniques used in the field of pedometrics (see http://en.wikipedia.org/wiki/Pedometrics for definition of pedometrics). These functions were developed to fulfil the demands created by the PhD research project (2012-2016) entitled Contribution to the Construction of Models for Predicting Soil Properties, developed by Alessandro Samuel-Rosa under the supervision of Dr Lucia HC Anjos (Universidade Federal Rural do Rio de Janeiro, Brazil), Dr Gustavo M Vasques (Embrapa Solos, Brazil), and Dr Gerard BM Heuvelink (ISRIC - World Soil Information, the Netherlands). The project is supported by the CAPES, Ministério da Educação, Brasília - DF 70040-020, Brazil, process ID BEX 11677/13-9. Several functions are simple wrapper functions that extend the functionalities of other functions commonly used for the analysis of pedometric data. It should be noted that changes are likely to occur quite often and using this package as a dependency for other packages is strongly discouraged.
Author: Alessandro Samuel-Rosa [aut, cre], Lucia Helena Cunha dos Anjos [ths], Gustavo de Mattos Vasques [ths], Gerard B. M. Heuvelink [ths], Tony Olsen [ctb], Tom Kincaid [ctb], Juan Carlos Ruiz Cuetos [ctb], Maria Eugenia Polo Garcia [ctb], Pablo Garcia Rodriguez [ctb], Edzer Pebesma [ctb], Jon Skoien [ctb], Joshua French [ctb]
Maintainer: Alessandro Samuel-Rosa

Diff between pedometrics versions 0.3-0 dated 2014-11-19 and 0.4-1 dated 2014-12-01

 pedometrics-0.3-0/pedometrics/R/objMSSD.R                |only
 pedometrics-0.3-0/pedometrics/R/objectiveLags.R          |only
 pedometrics-0.3-0/pedometrics/man/objMSSD.Rd             |only
 pedometrics-0.3-0/pedometrics/man/objectiveLags.Rd       |only
 pedometrics-0.3-0/pedometrics/man/spJitter.Rd            |only
 pedometrics-0.3-0/pedometrics/man/spSANN.Rd              |only
 pedometrics-0.4-1/pedometrics/DESCRIPTION                |   67 +-
 pedometrics-0.4-1/pedometrics/MD5                        |   88 +--
 pedometrics-0.4-1/pedometrics/NAMESPACE                  |   80 +--
 pedometrics-0.4-1/pedometrics/R/RcppExports.R            |only
 pedometrics-0.4-1/pedometrics/R/adjR2.R                  |   41 +
 pedometrics-0.4-1/pedometrics/R/bbox2sp.R                |   42 +
 pedometrics-0.4-1/pedometrics/R/buildMS.R                |  114 +++-
 pedometrics-0.4-1/pedometrics/R/cdfPlot.R                |  148 ++++-
 pedometrics-0.4-1/pedometrics/R/cdfStats.R               |   75 +-
 pedometrics-0.4-1/pedometrics/R/cdfTable.R               |  101 ++-
 pedometrics-0.4-1/pedometrics/R/coordenadas.R            |   48 +
 pedometrics-0.4-1/pedometrics/R/gcpDiff.R                |  127 +++-
 pedometrics-0.4-1/pedometrics/R/gcpVector.R              |   63 +-
 pedometrics-0.4-1/pedometrics/R/pedometrics.R            |only
 pedometrics-0.4-1/pedometrics/R/plotESDA.R               |   75 ++
 pedometrics-0.4-1/pedometrics/R/plotHD.R                 |   89 +++
 pedometrics-0.4-1/pedometrics/R/plotMS.R                 |  229 ++++++++
 pedometrics-0.4-1/pedometrics/R/spJitter.R               |  243 +++++----
 pedometrics-0.4-1/pedometrics/R/spSANN.R                 |  397 ++++-----------
 pedometrics-0.4-1/pedometrics/R/spsannMSSD.R             |only
 pedometrics-0.4-1/pedometrics/R/spsannPPL.R              |only
 pedometrics-0.4-1/pedometrics/R/statsMS.R                |  119 ++++
 pedometrics-0.4-1/pedometrics/R/stepVIF.R                |  115 +++-
 pedometrics-0.4-1/pedometrics/inst/NEWS.Rd               |   19 
 pedometrics-0.4-1/pedometrics/man/adjR2.Rd               |   57 --
 pedometrics-0.4-1/pedometrics/man/bbox2sp.Rd             |   64 +-
 pedometrics-0.4-1/pedometrics/man/buildMS.Rd             |  183 +++---
 pedometrics-0.4-1/pedometrics/man/cdfPlot.Rd             |  249 ++++-----
 pedometrics-0.4-1/pedometrics/man/cdfStats.Rd            |   81 +--
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Package GlobalOptions updated to version 0.0.4 with previous version 0.0.3 dated 2014-11-02

Title: Generate Functions to Get or Set Global Options
Description: Generate functions to get or set global options
Author: Zuguang Gu
Maintainer: Zuguang Gu

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Package GGally updated to version 0.5.0 with previous version 0.4.8 dated 2014-08-26

Title: Extension to ggplot2.
Description: GGally is designed to be a helper to ggplot2. It contains templates for different plots to be combined into a plot matrix, a parallel coordinate plot function, as well as a function for making a network plot.
Author: Barret Schloerke , Jason Crowley , Di Cook , Heike Hofmann , Hadley Wickham , and Francois Briatte , Moritz Marbach , and Edwin Thoen
Maintainer: Barret Schloerke

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Package DOBAD updated to version 1.0.4 with previous version 1.0.3 dated 2014-03-10

Title: Analysis of Discretely Observed linear Birth-And-Death(-and-immigration) Markov Chains
Description: Frequentist (EM) and Bayesian (MCMC) Methods for Inference of Birth-Death-Immigration Markov Chains
Author: Charles Doss, Vladimir Minin, Marc Suchard
Maintainer: Charles Doss

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Package blocksdesign updated to version 1.3 with previous version 1.2 dated 2014-11-02

Title: Nested Block Designs for Unstructured Treatments
Description: Nested block designs for unstructured treatment sets where blocks can be repeatedly nested and treatments can have different levels of replication. Blocks strata are optimized hierarchically with each set of nested blocks optimized within the levels of the preceding set. Block sizes are equal if the number of blocks exactly divides the number of plots, otherwise they differ by at most one plot. The design output is a data table giving a randomised allocation of treatments to blocks together with a plan table showing treatments in blocks and a set of blocks-by-treatments incidence matrices, one for each blocks stratum.
Author: R. N. Edmondson
Maintainer: Rodney Edmondson

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Package alabama updated to version 2014.12-1 with previous version 2011.9-1 dated 2011-09-16

Title: Constrained Nonlinear Optimization
Description: Augmented Lagrangian Adaptive Barrier Minimization Algorithm for optimizing smooth nonlinear objective functions with constraints. Linear or nonlinear equality and inequality constraints are allowed.
Author: Ravi Varadhan (with contributions from Gabor Grothendieck)
Maintainer: Ravi Varadhan

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Package traj updated to version 1.1 with previous version 1.0 dated 2014-10-22

Title: Trajectory Analysis
Description: Implements the three-step procedure proposed by Leffondree et al. (2004) to identify clusters of individual longitudinal trajectories. The procedure involves (1) calculating 24 measures describing the features of the trajectories; (2) using factor analysis to select a subset of the 24 measures and (3) using cluster analysis to identify clusters of trajectories, and classify each individual trajectory in one of the clusters.
Author: Marie-Pierre Sylvestre, Dan Vatnik
Maintainer: Dan Vatnik

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New package RegressionFactory with initial version 0.7
Package: RegressionFactory
Type: Package
Title: Expander Functions for Generating Full Gradient and Hessian from Single- and Multi-Slot Base Distributions
Version: 0.7
Date: 2014-12-01
Author: Alireza S. Mahani, Mansour T.A. Sharabiani
Maintainer: Alireza S. Mahani
Description: The expander functions rely on the mathematics developed for the Hessian-definiteness invariance theorem for linear projection transformations of variables, described in authors' paper, to generate the full, high-dimensional gradient and Hessian from the lower-dimensional derivative objects. This greatly relieves the computational burden of generating the regression-function derivatives, which in turn can be fed into any optimization routine that utilizes such derivatives. The theorem guarantees that Hessian definiteness is preserved, meaning that reasoning about this property can be performed in the low-dimensional space of the base distribution. This is often a much easier task than its equivalent in the full, high-dimensional space. Definiteness of Hessian can be useful in selecting optimization/sampling algorithms such as Newton-Raphson optimization or its sampling equivalent, the Stochastic Newton Sampler. Finally, in addition to being a computational tool, the regression expansion framework is of conceptual value by offering new opportunities to generate novel regression problems.
License: GPL (>= 2)
Suggests: sns
Packaged: 2014-12-01 17:23:57 UTC; amahani
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-01 22:00:48

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Package EpiModel updated to version 1.1.2 with previous version 1.1.1 dated 2014-11-02

Title: Mathematical Modeling of Infectious Disease
Description: Tools for simulating mathematical models of infectious disease. Epidemic model classes include deterministic compartmental models, stochastic individual contact models, and stochastic network models. Disease types include SI, SIR, and SIS epidemics with and without demography, with tools available for expansion to model complex epidemic processes.
Author: Samuel Jenness [cre, aut], Steven M. Goodreau [aut], Martina Morris [aut], Li Wang [ctb]
Maintainer: Samuel Jenness

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Package apcluster updated to version 1.4.0 with previous version 1.3.5 dated 2014-06-26

Title: Affinity Propagation Clustering
Description: The apcluster package implements Frey's and Dueck's Affinity Propagation clustering in R. The algorithms are largely analogous to the Matlab code published by Frey and Dueck. The package further provides leveraged affinity propagation and an algorithm for exemplar-based agglomerative clustering that can also be used to join clusters obtained from affinity propagation. Various plotting functions are available for analyzing clustering results.
Author: Ulrich Bodenhofer, Johannes Palme, Chrats Melkonian, Andreas Kothmeier
Maintainer: Ulrich Bodenhofer

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Package multcomp updated to version 1.3-8 with previous version 1.3-7 dated 2014-10-02

Title: Simultaneous Inference in General Parametric Models
Description: Simultaneous tests and confidence intervals for general linear hypotheses in parametric models, including linear, generalized linear, linear mixed effects, and survival models. The package includes demos reproducing analyzes presented in the book "Multiple Comparisons Using R" (Bretz, Hothorn, Westfall, 2010, CRC Press).
Author: Torsten Hothorn [aut, cre], Frank Bretz [aut], Peter Westfall [aut], Richard M. Heiberger [ctb], Andre Schuetzenmeister [ctb]
Maintainer: Torsten Hothorn

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New package paleofire with initial version 1.1.5
Package: paleofire
Type: Package
Title: Analysis of Charcoal Records from the Global Charcoal Database
Version: 1.1.5
Date: 2014-11-24
Author: Global Paleofire Working Group
Maintainer: Olivier Blarquez
Description: Tools to extract and analyse charcoal sedimentary data stored in the Global Charcoal Database. Main functionalities includes data extraction and sites selection, transformation and interpolation of the charcoal records as well as compositing.
URL: http://gpwg.org
License: GPL (>= 2)
Imports: locfit, raster, ggplot2, plyr, rgdal, lattice
Suggests: gtools,caTools,pscl,agricolae,Imap,sp,rworldmap,RColorBrewer
Depends: R(>= 2.10.0), methods, GCD
LazyLoad: yes
LazyData: no
Encoding: UTF-8
Packaged: 2014-11-30 18:41:01 UTC; Olivier
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-01 18:09:29

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Package kriging updated to version 1.1 with previous version 1.0.1 dated 2011-12-21

Title: Ordinary Kriging
Description: Simple and highly optimized ordinary kriging algorithm to plot geographical data
Author: Omar E. Olmedo
Maintainer: Omar E. Olmedo

Diff between kriging versions 1.0.1 dated 2011-12-21 and 1.1 dated 2014-12-01

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New package GCPM with initial version 1.1.1
Package: GCPM
Type: Package
Title: Generalized Credit Portfolio Model
Version: 1.1.1
Date: 2014-12-01
Author: Kevin Jakob
Maintainer: Kevin Jakob
Description: The package helps to analyze the default risk of credit portfolios. Commonly known models, like CreditRisk+ or the CreditMetrics model are implemented in their very basic settings. The portfolio loss distribution can be achieved either by simulation or analytically in case of the classic CreditRisk+ model. Models are only implemented to respect losses caused by defaults, i.e. migration risk is not included. The package structure is kept flexible especially with respect to distributional assumptions in order to quantify the sensitivity of risk figures with respect to several assumptions. Therefore the package can be used to determine the credit risk of a given portfolio as well as to quantify model sensitivities.
License: GPL-2
Imports: Rcpp (>= 0.11.2), methods, RcppProgress(>= 0.1)
LinkingTo: Rcpp, RcppProgress
SystemRequirements: Windows, Linux, OS X
Packaged: 2014-12-01 09:43:48 UTC; Kevin_Jakob
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-12-01 18:13:42

More information about GCPM at CRAN
Permanent link

Package jiebaR updated to version 0.3 with previous version 0.2 dated 2014-11-23

Title: Chinese Text Segmentation
Description: Chinese text segmentation, keyword extraction and speech tagging For R.
Author: Qin Wenfeng, and the authors of CppJieba for the included version of CppJieba
Maintainer: Qin Wenfeng

Diff between jiebaR versions 0.2 dated 2014-11-23 and 0.3 dated 2014-12-01

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Package HTMLUtils updated to version 0.1.6 with previous version 0.1.5 dated 2012-05-18

Title: Facilitates Automated HTML Report Creation
Description: Facilitates automated HTML report creation, in particular framed HTML pages and dynamically sortable tables.
Author: "Markus Loecher, Berlin School of Economics and Law (BSEL)"
Maintainer: "Markus Loecher, Berlin School of Economics and Law (BSEL)"

Diff between HTMLUtils versions 0.1.5 dated 2012-05-18 and 0.1.6 dated 2014-12-01

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More information about HTMLUtils at CRAN
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Package fda.usc updated to version 1.2.1 with previous version 1.2.0 dated 2014-05-29

Title: Functional Data Analysis and Utilities for Statistical Computing
Description: Routines for exploratory and descriptive analysis of functional data such as depth measurements, atypical curves detection, regression models, supervised classification, unsupervised classification and functional analysis of variance.
Author: Manuel Febrero Bande [aut], Manuel Oviedo de la Fuente [aut, cre], Pedro Galeano [ctb], Alicia Nieto [ctb], Eduardo Garcia-Portugues [ctb]
Maintainer: Manuel Oviedo de la Fuente

Diff between fda.usc versions 1.2.0 dated 2014-05-29 and 1.2.1 dated 2014-12-01

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Permanent link

Package nodiv updated to version 1.0.0 with previous version 0.9.3 dated 2014-11-21

Title: Compares the Distribution of Sister Clades Through a Phylogeny
Description: An implementation of the nodiv algorithm, (see Borregaard, M.K., Rahbek, C., Fjeldsaa, J., Parra, J.L., Whittaker, R.J. & Graham, C.H. 2014. Node-based analysis of species distributions. Methods in Ecology and Evolution 5(11): 1225-1235. DOI: 10.1111/2041-210X.12283. Package for phylogenetic analysis of species distributions. The main function goes through each node in the phylogeny, compares the distributions of the two descendant nodes, and compares the result to a null model. This highlights nodes where major distributional divergence have occurred. The distributional divergence for these nodes is mapped using the SOS statistic.
Author: Michael Krabbe Borregaard
Maintainer: Michael Krabbe Borregaard

Diff between nodiv versions 0.9.3 dated 2014-11-21 and 1.0.0 dated 2014-12-01

 DESCRIPTION                    |   10 +++++-----
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Permanent link

New package ssd with initial version 0.3
Package: ssd
Type: Package
Title: Sample Size Determination (SSD) for Unordered Categorical Data
Version: 0.3
Date: 2014-11-30
Author: Junheng Ma and Jiayang Sun
Maintainer: Junheng Ma
Description: ssd calculates the sample size needed to detect the differences between two sets of unordered categorical data.
License: GPL-2
Packaged: 2014-12-01 05:48:18 UTC; Junheng Ma
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-01 09:28:44

More information about ssd at CRAN
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New package rngSetSeed with initial version 0.3-1
Package: rngSetSeed
Type: Package
Title: Seeding the Default RNG With a Numeric Vector
Version: 0.3-1
Date: 2014-12-01
Author: Petr Savicky
Maintainer: Petr Savicky
Description: A function setVectorSeed() is provided. Its argument is a numeric vector of an arbitrary nonzero length, whose components have integer values from [0, 2^32-1]. The input vector is transformed using AES (Advanced Encryption Standard) algorithm into an initial state of Mersenne-Twister random number generator. The function provides a better alternative to the R base function set.seed() if the input vector is a single integer. Initializing a stream of random numbers with a vector is a convenient way to obtain several streams, each of which is identified by several integer indices.
License: GPL-3
Packaged: 2014-12-01 08:01:26 UTC; petr
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2014-12-01 11:07:13

More information about rngSetSeed at CRAN
Permanent link

Package plotKML updated to version 0.4-7 with previous version 0.4-5 dated 2014-07-31

Title: Visualization of spatial and spatio-temporal objects in Google Earth
Description: Writes sp-class, spacetime-class, raster-class and similar spatial and spatio-temporal objects to KML following some basic cartographic rules.
Author: Tomislav Hengl [cre, aut], Pierre Roudier [ctb], Dylan Beaudette [ctb], Edzer Pebesma [ctb], Michael Blaschek [ctb]
Maintainer: Tomislav Hengl

Diff between plotKML versions 0.4-5 dated 2014-07-31 and 0.4-7 dated 2014-12-01

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New package mipfp with initial version 1.0
Package: mipfp
Type: Package
Title: Multidimensional Iterative Proportional Fitting
Version: 1.0
Date: 2014-11-26
Authors@R: c(person("Johan", "Barthelemy", role = c("aut", "cre"),email = "johan@uow.edu.au"),person("Thomas", "Suesse", role = "aut"),person("Mohammad", "Namazi-Rad", role = "ctb"))
Author: Johan Barthelemy [aut, cre], Thomas Suesse [aut], Mohammad Namazi-Rad [ctb]
Maintainer: Johan Barthelemy
Description: An implementation of the iterative proportional fitting procedure for updating a N-dimensional array with respect to given target marginal distributions (which, in turn can be multi-dimensional)
License: GPL-2
URL: www.r-project.org
Packaged: 2014-12-01 00:10:22 UTC; johan
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-01 09:10:27

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Package MindOnStats updated to version 0.11 with previous version 0.8 dated 2012-11-01

Title: Data sets included in Utts and Heckard's Mind on Statistics
Description: 66 data sets that were imported using read.table() where appropriate but more commonly after converting to a csv file for importing via read.csv().
Author: A. Jonathan R. Godfrey [aut, cre]
Maintainer: A. Jonathan R. Godfrey

Diff between MindOnStats versions 0.8 dated 2012-11-01 and 0.11 dated 2014-12-01

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 MindOnStats-0.11/MindOnStats/man/Asia-Pacific.Rd         |    6 
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 MindOnStats-0.11/MindOnStats/man/MindOnStats-package.Rd  |   10 
 MindOnStats-0.8/MindOnStats/doc                          |only
 97 files changed, 126 insertions(+), 108 deletions(-)

More information about MindOnStats at CRAN
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New package lintr with initial version 0.2.0
Package: lintr
Title: Static R Code Analysis
Version: 0.2.0
Authors@R: "Jim Hester [aut, cre]"
URL: https://github.com/jimhester/lintr
BugReports: https://github.com/jimhester/lintr/issues
Description: Checks adherence to a given style, syntax errors and possible semantic issues. Supports on the fly checking of R code edited with Emacs, Vim and Sublime Text.
Depends: R (>= 3.1.1)
Imports: rex, crayon, codetools, stringdist, testthat, digest, igraph
License: MIT + file LICENSE
LazyData: true
Suggests: knitr
VignetteBuilder: knitr
Packaged: 2014-12-01 02:53:22 UTC; james.hester
Author: "Jim Hester" [aut, cre]
Maintainer: "Jim Hester"
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2014-12-01 09:09:24

More information about lintr at CRAN
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Package jsonlite updated to version 0.9.14 with previous version 0.9.13 dated 2014-10-21

Title: A Robust, High Performance JSON Parser and Generator for R
Description: A fast JSON parser and generator optimized for statistical data and the web. Started out as a fork of RJSONIO, but has been completely rewritten in recent versions. The package offers flexible, robust, high performance tools for working with JSON in R and is particularly powerful for building pipelines and interacting with web APIs. The implementation is based on the mapping described in the vignette of the package (Ooms, 2014). In addition to drop-in replacements for toJSON and fromJSON, jsonlite contains functions to stream, validate, and prettify JSON data. The unit tests included with the package verify that all edge cases are encoded and decoded consistently for use with dynamic data in systems and applications.
Author: Jeroen Ooms, Duncan Temple Lang, Lloyd Hilaiel
Maintainer: Jeroen Ooms

Diff between jsonlite versions 0.9.13 dated 2014-10-21 and 0.9.14 dated 2014-12-01

 DESCRIPTION                     |   32 +--
 LICENSE                         |only
 MD5                             |   61 +++--
 NAMESPACE                       |    1 
 NEWS                            |    9 
 R/asJSON.data.frame.R           |   15 +
 R/asJSON.int64.R                |    2 
 R/asJSON.numeric.R              |   15 +
 R/download.R                    |   16 +
 R/fromJSON.R                    |   30 +-
 R/num_to_char.R                 |    9 
 R/prettify.R                    |   19 -
 R/stream.R                      |   13 -
 R/toJSON.R                      |   25 --
 R/unbox.R                       |   17 +
 build/vignette.rds              |binary
 inst/CITATION                   |only
 inst/doc/json-aaquickstart.Rmd  |    8 
 inst/doc/json-aaquickstart.html |  416 ++++++++++++----------------------------
 inst/doc/json-mapping.pdf       |binary
 inst/doc/json-opencpu.pdf       |binary
 man/fromJSON.Rd                 |   32 +--
 man/prettify.Rd                 |    4 
 man/stream_in.Rd                |   13 -
 man/unbox.Rd                    |   14 -
 src/Makevars                    |    7 
 src/integer64_to_na.c           |only
 src/modp_numtoa.c               |   10 
 src/num_to_char.c               |   10 
 src/parse.c                     |   19 +
 src/prettify.c                  |   11 -
 src/validate.c                  |   19 +
 vignettes/json-aaquickstart.Rmd |    8 
 33 files changed, 384 insertions(+), 451 deletions(-)

More information about jsonlite at CRAN
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Package sn updated to version 1.1-2 with previous version 1.1-1 dated 2014-10-30

Title: The skew-normal and skew-t distributions
Description: Define and manipulate probability distributions of the skew-normal family and some related ones (notably the skew-t family) and provide related statistical methods for data fitting and diagnostics, in the univariate and the multivariate case.
Author: Adelchi Azzalini
Maintainer: Adelchi Azzalini

Diff between sn versions 1.1-1 dated 2014-10-30 and 1.1-2 dated 2014-12-01

 ChangeLog             |   13 ++-
 DESCRIPTION           |    8 +-
 MD5                   |   32 ++++-----
 NAMESPACE             |   14 ++--
 R/sn-funct.R          |  174 +++++++++++++++++++++++++++++---------------------
 R/sn_S4.R             |   22 +-----
 data/ais.rda          |binary
 data/barolo.rda       |binary
 data/frontier.rda     |binary
 data/wines.rda        |binary
 inst/CITATION         |    4 -
 man/coef.selm.Rd      |only
 man/dmst.Rd           |    5 -
 man/plot.selm.Rd      |   13 +--
 man/residuals.selm.Rd |only
 man/selm-class.Rd     |   20 +++--
 man/selm.Rd           |   16 ++--
 man/summary.selm.Rd   |   33 ++++++---
 18 files changed, 195 insertions(+), 159 deletions(-)

More information about sn at CRAN
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Package curl updated to version 0.3 with previous version 0.2 dated 2014-11-20

Title: A Connection Interface to Libcurl
Description: The curl() function provides a drop-in replacement for base url() with better performance and support for http 2.0, ssl (https://, ftps://), gzip, deflate and other libcurl goodies. This interface is implemented using the RConnection API in order to support incremental processing of both binary and text streams. If you are looking for a more-user-friendly http client, try the RCurl or httr packages instead.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms

Diff between curl versions 0.2 dated 2014-11-20 and 0.3 dated 2014-12-01

 DESCRIPTION          |   23 +++---
 MD5                  |   22 +++--
 NAMESPACE            |    3 
 NEWS                 |   10 ++
 R/curl.R             |    5 -
 R/curl_download.R    |only
 configure            |only
 man/curl_download.Rd |only
 src/Makevars         |    4 -
 src/Makevars.win     |    2 
 src/curl.c           |  190 ++++++++++++++++++++++-----------------------------
 src/download.c       |only
 src/utils.c          |only
 src/utils.h          |only
 tools/winlibs.R      |   13 ++-
 15 files changed, 134 insertions(+), 138 deletions(-)

More information about curl at CRAN
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