Sun, 27 Jul 2014

Package stsm updated to version 1.4 with previous version 1.3 dated 2014-05-30

Title: Structural Time Series Models
Description: This package provides algorithms to fit structural time series models by maximum likelihood.
Author: Javier López-de-Lacalle
Maintainer: Javier López-de-Lacalle

Diff between stsm versions 1.3 dated 2014-05-30 and 1.4 dated 2014-07-27

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 stsm-1.4/stsm/DESCRIPTION                              |    8 
 stsm-1.4/stsm/MD5                                      |   64 +++--
 stsm-1.4/stsm/R/logLik.R                               |    4 
 stsm-1.4/stsm/R/maxclik-fd-scoring.R                   |   13 -
 stsm-1.4/stsm/R/maxlik-fd-optim.R                      |  142 ++++--------
 stsm-1.4/stsm/R/maxlik-fd-scoring.R                    |  142 ++++--------
 stsm-1.4/stsm/R/maxlik-td-optim.R                      |  111 ++-------
 stsm-1.4/stsm/R/maxlik-td-scoring.R                    |  140 ++++--------
 stsm-1.4/stsm/R/mcloglik-fd.R                          |    8 
 stsm-1.4/stsm/R/methods-stsmFit.R                      |   65 ++++-
 stsm-1.4/stsm/R/methods-vcov-confint.R                 |   21 +
 stsm-1.4/stsm/R/mloglik-fd.R                           |  193 +++++++++++++----
 stsm-1.4/stsm/R/mloglik-td.R                           |  125 +++++++----
 stsm-1.4/stsm/R/stsmFit.R                              |   16 +
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 stsm-1.4/stsm/inst/sims/datagen-llm.R                  |    7 
 stsm-1.4/stsm/inst/sims/datagen-llmseas.R              |   11 
 stsm-1.4/stsm/inst/sims/sim-llm-mcl-fd.R               |   58 -----
 stsm-1.4/stsm/inst/sims/sim-llm-ml-fd.R                |   13 -
 stsm-1.4/stsm/inst/sims/sim-llm-ml-td.R                |    9 
 stsm-1.4/stsm/inst/sims/sim-llmseas-mcl-fd.R           |   23 +-
 stsm-1.4/stsm/inst/sims/sim-llmseas-ml-fd.R            |   15 -
 stsm-1.4/stsm/inst/sims/sim-llmseas-ml-td.R            |   83 -------
 stsm-1.4/stsm/inst/sims/test-derivatives-mcloglik-fd.R |    1 
 stsm-1.4/stsm/inst/sims/test-derivatives-mloglik-fd.R  |   59 -----
 stsm-1.4/stsm/man/maxlik-fd.Rd                         |   23 --
 stsm-1.4/stsm/man/maxlik-td.Rd                         |   17 -
 stsm-1.4/stsm/man/methods-stsmFit.Rd                   |   15 +
 stsm-1.4/stsm/man/mloglik-fd.Rd                        |   45 +++
 stsm-1.4/stsm/man/mloglik-td.Rd                        |   15 -
 33 files changed, 695 insertions(+), 751 deletions(-)

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Package migest updated to version 1.6 with previous version 1.5 dated 2014-03-27

Title: Useful R code for the Estimation of Migration
Description: The migest package contains a collection of R functions that are useful to estimate migration when there is missing data. Included is the ffs routine to estimate migration flows from stock data, as well as various other functions to indirectly estimate flows where marginal totals are known. Functions are illustrated with dummy data.
Author: Guy J. Abel
Maintainer: Guy J. Abel

Diff between migest versions 1.5 dated 2014-03-27 and 1.6 dated 2014-07-27

 DESCRIPTION           |    8 -
 MD5                   |   28 ++---
 R/ffs.R               |   23 +++-
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 demo/cfplot_reg.R     |    6 -
 man/cm2.Rd            |    2 
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 man/ipf2.Rd           |    3 
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 15 files changed, 198 insertions(+), 160 deletions(-)

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Package GrapheR updated to version 1.9-84 with previous version 1.9-83 dated 2014-06-28

Title: A multi-platform GUI for drawing customizable graphs in R
Description: GrapheR is a multi-platform user interface for drawing highly customizable graphs in R. It aims to be a valuable help to quickly draw publishable graphs without any knowledge of R commands. Six kinds of graph are available: histogram, box-and-whisker plot, bar plot, pie chart, curve and scatter plot.
Author: Maxime Herv
Maintainer: Maxime Herv

Diff between GrapheR versions 1.9-83 dated 2014-06-28 and 1.9-84 dated 2014-07-27

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 6 files changed, 24 insertions(+), 20 deletions(-)

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Package DatABEL updated to version 0.9-4.1 with previous version 0.9-4 dated 2013-03-12

Title: file-based access to large matrices stored on HDD in binary format
Description: a package providing an interface to the C++ FILEVECTOR library facilitating analysis of large (giga- to tera-bytes) matrices; matrix storage is organized in a way that either columns or rows are quickly accessible; primarily aimed to support genome-wide association analyses e.g. using GenABEL, MixABEL and ProbABEL
Author: Yurii Aulchenko, Stepan Yakovenko, Erik Roos, Marcel Kempenaar
Maintainer: Yurii Aulchenko

Diff between DatABEL versions 0.9-4 dated 2013-03-12 and 0.9-4.1 dated 2014-07-27

 DESCRIPTION         |    6 +++---
 MD5                 |   10 +++++-----
 R/zzz.R             |    6 ++++--
 man/apply2dfo.Rd    |    6 ++++--
 man/text2databel.Rd |    8 ++++----
 src/CastUtils.cpp   |    7 ++++---
 6 files changed, 24 insertions(+), 19 deletions(-)

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Package poppr updated to version 1.1.1 with previous version 1.1.0 dated 2014-07-24

Title: an R package for genetic analysis of populations with mixed reproduction
Description: Population genetic analyses for hierarchical analysis of partially clonal populations built upon the architecture of the adegenet package.
Author: Zhian N. Kamvar , Javier F. Tabima , Niklaus J. Grunwald
Maintainer: Zhian N. Kamvar

Diff between poppr versions 1.1.0 dated 2014-07-24 and 1.1.1 dated 2014-07-27

 DESCRIPTION                             |    8 
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 NEWS                                    |    7 
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 src/poppr_distance.c                    |  470 ++++++++++++++------------------
 tests/testthat/test-values.R            |    4 
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 32 files changed, 314 insertions(+), 359 deletions(-)

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Package openxlsx updated to version 2.0.15 with previous version 2.0.1 dated 2014-05-29

Title: .xlsx reading, writing and editing.
Description: This package simplifies the creation of .xlsx files by providing a high level interface to writing, styling and editing worksheets. Through the use of Rcpp, read/write times are comparable to the xlsx and XLConnect packages with the added benefit of removing the dependency on Java.
Author: Alexander Walker [aut, cre], Luca Braglia [ctb]
Maintainer: Alexander Walker

Diff between openxlsx versions 2.0.1 dated 2014-05-29 and 2.0.15 dated 2014-07-27

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 openxlsx-2.0.15/openxlsx/NAMESPACE                  |    3 
 openxlsx-2.0.15/openxlsx/NEWS                       |   43 
 openxlsx-2.0.15/openxlsx/R/RcppExports.R            |   20 
 openxlsx-2.0.15/openxlsx/R/StyleClass.R             |   10 
 openxlsx-2.0.15/openxlsx/R/WorkbookClass.R          |  750 ++--
 openxlsx-2.0.15/openxlsx/R/baseXML.R                |    7 
 openxlsx-2.0.15/openxlsx/R/borderFunctions.R        |  701 +++-
 openxlsx-2.0.15/openxlsx/R/helperFunctions.R        |  381 ++
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Package KFKSDS updated to version 1.5 with previous version 1.4 dated 2014-06-15

Title: Kalman Filter, Smoother and Disturbance Smoother
Description: Naive implementation of the Kalman filter, smoother and disturbance smoother for state space models. An interface to other implementations of the filter that are available in other packages is also provided.
Author: Javier López-de-Lacalle
Maintainer: Javier López-de-Lacalle

Diff between KFKSDS versions 1.4 dated 2014-06-15 and 1.5 dated 2014-07-27

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 KFKSDS-1.5/KFKSDS/MD5                         |   15 +--
 KFKSDS-1.5/KFKSDS/R/KF.R                      |  113 ++++++++++++++++++--------
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 KFKSDS-1.5/KFKSDS/man/KF.Rd                   |   23 ++++-
 KFKSDS-1.5/KFKSDS/man/predict-stsmSS.Rd       |    3 
 KFKSDS-1.5/KFKSDS/src/KF-deriv.cpp            |   89 +++++++++++++++-----
 10 files changed, 183 insertions(+), 70 deletions(-)

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Package HiClimR updated to version 1.1.2 with previous version 1.1.1 dated 2014-07-14

Title: Hierarchical Climate Regionalization: An Improved Hierarchical Clustering in R for Climate Regionalization
Description: HiClimR package modifies and improves hierarchical clustering in R ('hclust' function in 'stats' library), for climate regionalization. It adds a new clustering method (called, regional linkage) to the set of available methods together with several features including regridding, coarsening spatial resolution, geographic masking, data thresholds, detrending and standardization preprocessing, faster correlation function, hybrid hierarchical clustering, and cluster validation. Badr et. al (2014) describes the regionalization algorithms and data processing tools included in the package and presents a demonstration application in which the package is used to regionalize Africa on the basis of interannual precipitation variability. It is applicable to any correlation-based clustering.
Author: Hamada S. Badr [aut, cre], Benjamin F. Zaitchik [aut], Amin K. Dezfuli [aut]
Maintainer: Hamada S. Badr

Diff between HiClimR versions 1.1.1 dated 2014-07-14 and 1.1.2 dated 2014-07-27

 Changelog       |   23 +++++++++++++++++------
 DESCRIPTION     |    8 ++++----
 MD5             |   22 +++++++++++-----------
 R/HiClimR.R     |   11 +++++++++--
 R/coarseR.R     |    5 +++--
 R/fastCor.R     |    5 +++--
 R/geogMask.R    |    5 +++--
 R/grid2D.R      |    5 +++--
 R/minSigCor.R   |    5 +++--
 R/validClimR.R  |    5 +++--
 inst/CITATION   |    8 ++++----
 src/HiClimR.f90 |    3 ++-
 12 files changed, 65 insertions(+), 40 deletions(-)

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