Mon, 18 Jul 2016

Package table1xls updated to version 0.3.2 with previous version 0.3.1 dated 2014-06-13

Title: Produces Summary Tables and Exports Them to Multi-Tab Spreadsheet Format (.xls or .xlsx)
Description: A collection of time-saving wrappers for producing and exporting summary tables commonly used in scientific articles, to .xls/.xlsx multi-tab spreadsheets, while controlling spreadsheet layout. Powered by 'XLConnect'/'rJava' utilities.
Author: Assaf P. Oron
Maintainer: Assaf P. Oron <assaf.oron@seattlechildrens.org>

Diff between table1xls versions 0.3.1 dated 2014-06-13 and 0.3.2 dated 2016-07-18

 table1xls-0.3.1/table1xls/man/XLuniVariate.Rd       |only
 table1xls-0.3.2/table1xls/DESCRIPTION               |   16 +-
 table1xls-0.3.2/table1xls/MD5                       |   36 +++---
 table1xls-0.3.2/table1xls/NAMESPACE                 |   12 --
 table1xls-0.3.2/table1xls/NEWS                      |   15 ++
 table1xls-0.3.2/table1xls/R/XLoneWay.r              |    8 -
 table1xls-0.3.2/table1xls/R/exploratoryUtils.r      |   56 +++++----
 table1xls-0.3.2/table1xls/R/regressionSummaries.r   |   10 -
 table1xls-0.3.2/table1xls/R/utilities.r             |   10 -
 table1xls-0.3.2/table1xls/inst/examples/Ex2way.r    |    4 
 table1xls-0.3.2/table1xls/inst/examples/ExRegress.r |    4 
 table1xls-0.3.2/table1xls/man/XLaddText.Rd          |   31 +----
 table1xls-0.3.2/table1xls/man/XLgeneric.Rd          |   73 ++++--------
 table1xls-0.3.2/table1xls/man/XLoneWay.Rd           |   68 +++--------
 table1xls-0.3.2/table1xls/man/XLregresSummary.Rd    |  119 ++++++--------------
 table1xls-0.3.2/table1xls/man/XLtwoWay.Rd           |  117 ++++++-------------
 table1xls-0.3.2/table1xls/man/XLunivariate.Rd       |only
 table1xls-0.3.2/table1xls/man/XLwriteOpen.Rd        |   32 +----
 table1xls-0.3.2/table1xls/man/rangeString.Rd        |   69 +++--------
 table1xls-0.3.2/table1xls/man/table1xls-package.Rd  |    6 -
 20 files changed, 255 insertions(+), 431 deletions(-)

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Permanent link

New package tranSurv with initial version 1.0-0
Package: tranSurv
Type: Package
Title: Estimating a Survival Distribution in the Presence of Dependent Left Truncation and Right Censoring
Version: 1.0-0
Date: 2016-07-18
Author: Sy Han (Steven) Chiou
Maintainer: Sy Han (Steven) Chiou <schiou@hsph.harvard.edu>
Description: A structural transformation model for a latent, quasi-independent truncation time as a function of the observed dependent truncation time and the event time, and an unknown dependence parameter. The dependence parameter is chosen to minimize the conditional Kendall's tau. The marginal distribution for the truncation time and the event time are completely left unspecified.
License: GPL (>= 3)
LazyLoad: yes
Imports: survival, SQUAREM
Packaged: 2016-07-18 22:01:39 UTC; steven
NeedsCompilation: yes
Repository: CRAN
Date/Publication: 2016-07-19 02:33:36

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New package SuperRanker with initial version 1.0.1
Package: SuperRanker
Type: Package
Title: Sequential Rank Agreement
Version: 1.0.1
Date: 2016-07-19
Author: Claus Thorn Ekstrøm and Thomas Alexander Gerds
Maintainer: Claus Thorn Ekstrøm <ekstrom@sund.ku.dk>
Description: Tools for analysing the aggreement of two or more rankings of the same items. Examples are importance rankings of predictor variables and risk predictions of subjects. Benchmarks for agreement are computed based on random permutation and bootstrap.
License: GPL (>= 2)
Imports: stats, graphics, Rcpp (>= 0.11.5), prodlim (>= 1.5.7)
LinkingTo: Rcpp
RoxygenNote: 5.0.1
Encoding: UTF-8
NeedsCompilation: yes
Packaged: 2016-07-19 00:02:06 UTC; cld189
Repository: CRAN
Date/Publication: 2016-07-19 02:45:01

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Package logbin updated to version 2.0.1 with previous version 2.0 dated 2016-07-18

Title: Relative Risk Regression Using the Log-Binomial Model
Description: Methods for fitting log-link GLMs and GAMs to binomial data, including EM-type algorithms with more stable convergence properties than standard methods.
Author: Mark W. Donoghoe [aut, cre], Ian C. Marschner [ths], Alexandra C. Gillett [ctb] (wrote an initial version of the nplbin function)
Maintainer: Mark W. Donoghoe <markdonoghoe@gmail.com>

Diff between logbin versions 2.0 dated 2016-07-18 and 2.0.1 dated 2016-07-18

 DESCRIPTION           |   12 ++++++------
 MD5                   |    8 ++++----
 README.md             |   14 +++++++-------
 inst/CITATION         |    2 +-
 man/logbin-package.Rd |    4 ++--
 5 files changed, 20 insertions(+), 20 deletions(-)

More information about logbin at CRAN
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Package embryogrowth updated to version 6.3 with previous version 6.2 dated 2016-01-08

Title: Tools to Analyze the Thermal Reaction Norm of Embryo Growth
Description: Tools to analyze the embryo growth and the sexualisation thermal reaction norms.
Author: Marc Girondot <marc.girondot@u-psud.fr>
Maintainer: Marc Girondot <marc.girondot@u-psud.fr>

Diff between embryogrowth versions 6.2 dated 2016-01-08 and 6.3 dated 2016-07-18

 embryogrowth-6.2/embryogrowth/R/STSRE_NestingArea.R        |only
 embryogrowth-6.2/embryogrowth/R/STSRE_TSD.R                |only
 embryogrowth-6.2/embryogrowth/R/fonctionMCMC.R             |only
 embryogrowth-6.2/embryogrowth/R/web.embryogrowth.R         |only
 embryogrowth-6.2/embryogrowth/data/STSRE_NestingArea.rda   |only
 embryogrowth-6.2/embryogrowth/data/STSRE_TSD.rda           |only
 embryogrowth-6.2/embryogrowth/inst                         |only
 embryogrowth-6.2/embryogrowth/man/STSRE_NestingArea.Rd     |only
 embryogrowth-6.2/embryogrowth/man/STSRE_TSD.Rd             |only
 embryogrowth-6.3/embryogrowth/DESCRIPTION                  |    8 
 embryogrowth-6.3/embryogrowth/MD5                          |  126 +-
 embryogrowth-6.3/embryogrowth/NAMESPACE                    |    4 
 embryogrowth-6.3/embryogrowth/NEWS                         |   44 +
 embryogrowth-6.3/embryogrowth/R/ChangeSSM.R                |   12 
 embryogrowth-6.3/embryogrowth/R/DatabaseNestingArea.R      |only
 embryogrowth-6.3/embryogrowth/R/DatabaseTSD.R              |only
 embryogrowth-6.3/embryogrowth/R/GRTRN_MHmcmc.R             |   31 
 embryogrowth-6.3/embryogrowth/R/MovingIncubation.R         |   47 -
 embryogrowth-6.3/embryogrowth/R/SEforR.R                   |only
 embryogrowth-6.3/embryogrowth/R/SSM.R                      |  214 ++--
 embryogrowth-6.3/embryogrowth/R/STRN.R                     |  154 ++-
 embryogrowth-6.3/embryogrowth/R/STRN_fit.R                 |   11 
 embryogrowth-6.3/embryogrowth/R/embryogrowth-package.R     |    4 
 embryogrowth-6.3/embryogrowth/R/fitSSM.R                   |    2 
 embryogrowth-6.3/embryogrowth/R/fonctiontsdMCMC.R          |    5 
 embryogrowth-6.3/embryogrowth/R/hist.Nests.R               |    1 
 embryogrowth-6.3/embryogrowth/R/info.nests.R               |  259 ++++-
 embryogrowth-6.3/embryogrowth/R/modelTSD.R                 |   17 
 embryogrowth-6.3/embryogrowth/R/plot.NestsResult.R         |   56 -
 embryogrowth-6.3/embryogrowth/R/plot.tsd.R                 |   21 
 embryogrowth-6.3/embryogrowth/R/plotR.R                    |  569 +++++++------
 embryogrowth-6.3/embryogrowth/R/plotR_hist.R               |   35 
 embryogrowth-6.3/embryogrowth/R/predict.tsd.R              |   32 
 embryogrowth-6.3/embryogrowth/R/searchR.R                  |  111 +-
 embryogrowth-6.3/embryogrowth/R/tempConst.R                |    5 
 embryogrowth-6.3/embryogrowth/R/tsd.R                      |   32 
 embryogrowth-6.3/embryogrowth/R/tsd_MHmcmc.R               |   19 
 embryogrowth-6.3/embryogrowth/R/tsd_fit.R                  |   16 
 embryogrowth-6.3/embryogrowth/data/DatabaseNestingArea.rda |only
 embryogrowth-6.3/embryogrowth/data/DatabaseTSD.rda         |only
 embryogrowth-6.3/embryogrowth/data/TSP.list.rda            |binary
 embryogrowth-6.3/embryogrowth/data/stages.rda              |binary
 embryogrowth-6.3/embryogrowth/man/ChangeSSM.Rd             |    6 
 embryogrowth-6.3/embryogrowth/man/DatabaseNestingArea.Rd   |only
 embryogrowth-6.3/embryogrowth/man/DatabaseTSD.Rd           |only
 embryogrowth-6.3/embryogrowth/man/GRTRN_MHmcmc.Rd          |    7 
 embryogrowth-6.3/embryogrowth/man/MovingIncubation.Rd      |   31 
 embryogrowth-6.3/embryogrowth/man/SEforR.Rd                |only
 embryogrowth-6.3/embryogrowth/man/STRN.Rd                  |   66 +
 embryogrowth-6.3/embryogrowth/man/TSP.list.Rd              |    2 
 embryogrowth-6.3/embryogrowth/man/embryogrowth-package.Rd  |    4 
 embryogrowth-6.3/embryogrowth/man/info.nests.Rd            |   29 
 embryogrowth-6.3/embryogrowth/man/plot.NestsResult.Rd      |   38 
 embryogrowth-6.3/embryogrowth/man/plot.tsd.Rd              |   10 
 embryogrowth-6.3/embryogrowth/man/plotR.Rd                 |   75 +
 embryogrowth-6.3/embryogrowth/man/plotR_hist.Rd            |   10 
 embryogrowth-6.3/embryogrowth/man/predict.tsd.Rd           |    8 
 embryogrowth-6.3/embryogrowth/man/searchR.Rd               |   20 
 embryogrowth-6.3/embryogrowth/man/stages.Rd                |    2 
 embryogrowth-6.3/embryogrowth/man/tempConst.Rd             |    5 
 embryogrowth-6.3/embryogrowth/man/tsd.Rd                   |    8 
 embryogrowth-6.3/embryogrowth/man/tsd_MHmcmc.Rd            |   12 
 embryogrowth-6.3/embryogrowth/man/tsd_MHmcmc_p.Rd          |    2 
 63 files changed, 1390 insertions(+), 780 deletions(-)

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Package FSAdata updated to version 0.3.3 with previous version 0.3.2 dated 2015-10-22

Title: Data to Support Fish Stock Assessment (FSA) Package
Description: The datasets to support the Fish Stock Assessment (FSA) package.
Author: Derek Ogle [aut, cre]
Maintainer: Derek Ogle <derek@derekogle.com>

Diff between FSAdata versions 0.3.2 dated 2015-10-22 and 0.3.3 dated 2016-07-18

 DESCRIPTION               |    9 -
 MD5                       |  352 +++++++++++++++++++++++-----------------------
 NAMESPACE                 |    2 
 R/Bonito.R                |only
 R/Mosquitofish.R          |only
 R/RWhitefishAI.R          |    4 
 R/RWhitefishIR.R          |    4 
 R/SnapperHG2.R            |    2 
 R/StripedBass2.R          |    2 
 R/YPerchSB1.R             |    2 
 R/YPerchTL.R              |    4 
 data/Bonito.rdata         |only
 data/Mosquitofish.rdata   |only
 man/AHerringChile.Rd      |    5 
 man/AfricanRivers.Rd      |    3 
 man/AlewifeLH.Rd          |    5 
 man/AnchovetaChile.Rd     |   11 -
 man/BGHRfish.Rd           |    3 
 man/BGHRsample.Rd         |    3 
 man/BSkateGB.Rd           |    3 
 man/BassFL.Rd             |   11 -
 man/BlackDrum2001.Rd      |    3 
 man/BloaterLH.Rd          |    5 
 man/BlueCatfish.Rd        |    3 
 man/BlueCrab.Rd           |    3 
 man/BluefishAge.Rd        |    5 
 man/BluegillLM.Rd         |    2 
 man/BluntnoseIL1.Rd       |    7 
 man/Bonito.Rd             |only
 man/BrookTroutNC.Rd       |    5 
 man/BrookTroutNEWP.Rd     |   13 -
 man/BrookTroutNEWP1.Rd    |   11 -
 man/BrookTroutOnt.Rd      |    5 
 man/BrownTroutVC1.Rd      |    3 
 man/BullTroutRML1.Rd      |    3 
 man/BullTroutRML2.Rd      |   11 -
 man/BullTroutTC.Rd        |    5 
 man/CCatfishNB.Rd         |    7 
 man/Cabezon.Rd            |   17 +-
 man/Casselman1990.Rd      |    9 -
 man/ChinookKR.Rd          |    5 
 man/CiscoTL.Rd            |    9 -
 man/CrappieARMS.Rd        |    5 
 man/CreekChub.Rd          |    3 
 man/CreelMN.Rd            |   13 -
 man/Croaker1.Rd           |    9 -
 man/Croaker2.Rd           |    7 
 man/CutthroatALf.Rd       |    5 
 man/DarterMahon.Rd        |   13 -
 man/DarterOnt.Rd          |    9 -
 man/Deckeretal1999.Rd     |    3 
 man/EuroPerchTJ.Rd        |    7 
 man/FHCatfish.Rd          |    7 
 man/FHCatfishATL.Rd       |    9 -
 man/FSAdata-internals.Rd  |    2 
 man/FSAdata.Rd            |    9 -
 man/FWDrumLE1.Rd          |    7 
 man/FWDrumLE2.Rd          |   11 -
 man/Ghats.Rd              |    5 
 man/GreensCreekMine.Rd    |    3 
 man/Hake.Rd               |    9 -
 man/HalibutPAC.Rd         |    3 
 man/Herman.Rd             |    7 
 man/HerringBWE.Rd         |    3 
 man/HerringISS.Rd         |    3 
 man/HumpbackWFCR.Rd       |    3 
 man/InchLake1.Rd          |   11 -
 man/InchLake2.Rd          |    5 
 man/JobfishSIO.Rd         |   15 +
 man/JonesStockwell.Rd     |    3 
 man/Jonubi1.Rd            |    7 
 man/Jonubi2.Rd            |    3 
 man/KingCrabAK.Rd         |    3 
 man/LJCisco.Rd            |    7 
 man/LMBassBL.Rd           |    5 
 man/LMBassLCB.Rd          |    5 
 man/LakeTroutALTER.Rd     |   23 +--
 man/LakeTroutEggs.Rd      |    5 
 man/LakeTroutGIS.Rd       |    3 
 man/LakeTroutMI.Rd        |    5 
 man/Lizardfish.Rd         |    3 
 man/LobsterHI.Rd          |   19 +-
 man/LobsterPEI.Rd         |   15 +
 man/Menhaden1.Rd          |    8 -
 man/Morwong1.Rd           |    7 
 man/Morwong2.Rd           |    7 
 man/Morwong3.Rd           |    5 
 man/Morwong4.Rd           |    5 
 man/Morwong4a.Rd          |    5 
 man/Mosquitofish.Rd       |only
 man/MulletBS.Rd           |    7 
 man/MuskieSLR.Rd          |    7 
 man/MuskieWI06MR.Rd       |    3 
 man/PSalmonAK.Rd          |    3 
 man/Pallid.Rd             |   17 +-
 man/Pathfinder.Rd         |   18 +-
 man/PikeHL.Rd             |    3 
 man/PikeIL.Rd             |   17 +-
 man/PikeNYPartial2.Rd     |    3 
 man/PikeWindermere.Rd     |    4 
 man/PygmyWFBC.Rd          |    3 
 man/RBSmeltErie.Rd        |    9 -
 man/RBSmeltLM.Rd          |    7 
 man/RBTroutKenai.Rd       |   15 +
 man/RBTroutUNSP.Rd        |    7 
 man/RWhitefishAI.Rd       |    9 -
 man/RWhitefishIR.Rd       |    9 -
 man/RedDrum.Rd            |    7 
 man/Riffleshell.Rd        |    3 
 man/RockBassCL.Rd         |    5 
 man/RockBassLO1.Rd        |    9 -
 man/RockBassLO2.Rd        |    3 
 man/RuffeSLRH92.Rd        |   13 -
 man/RuffeTL89.Rd          |    5 
 man/SLampreyGL.Rd         |    5 
 man/SalmonADP.Rd          |    7 
 man/SalmonidsMCCA.Rd      |    3 
 man/SardineChile.Rd       |   15 +
 man/SardineLK.Rd          |    5 
 man/SardinesPacific.Rd    |    3 
 man/SculpinALTER.Rd       |    7 
 man/ShadCR.Rd             |    4 
 man/ShrimpGuam.Rd         |   17 +-
 man/SimonsonLyons.Rd      |    3 
 man/SiscowetMI2004.Rd     |    3 
 man/Snapper.Rd            |    3 
 man/SnapperHG1.Rd         |    3 
 man/SnapperHG2.Rd         |    7 
 man/SockeyeKL.Rd          |    5 
 man/SockeyeSR.Rd          |    7 
 man/SpotVA2.Rd            |    7 
 man/SpottedSucker1.Rd     |    5 
 man/StripedBass1.Rd       |    9 -
 man/StripedBass2.Rd       |    7 
 man/StripedBass3.Rd       |    9 -
 man/StripedBass4.Rd       |    5 
 man/StripedBass5.Rd       |    9 -
 man/StripedBass6.Rd       |    5 
 man/SturgeonBL.Rd         |    5 
 man/SturgeonGB.Rd         |    3 
 man/SunfishIN.Rd          |    8 -
 man/SunfishLP.Rd          |    5 
 man/TPrawnsEG.Rd          |    6 
 man/TroutADP.Rd           |    7 
 man/TroutBR.Rd            |   13 -
 man/TroutperchLM1.Rd      |    9 -
 man/TroutperchLM2.Rd      |    7 
 man/TroutperchLM3.Rd      |    7 
 man/VendaceLP.Rd          |    5 
 man/VendaceLP2.Rd         |    3 
 man/WShrimpGA.Rd          |    3 
 man/WalleyeConsumption.Rd |    7 
 man/WalleyeEL.Rd          |    3 
 man/WalleyeErie.Rd        |    9 -
 man/WalleyeErie2.Rd       |    7 
 man/WalleyeKS.Rd          |    9 -
 man/WalleyeML.Rd          |   17 +-
 man/WalleyeMN06a.Rd       |    5 
 man/WalleyeMN06b.Rd       |    5 
 man/WalleyePL.Rd          |    3 
 man/WalleyePS.Rd          |    9 -
 man/WalleyeRL.Rd          |   19 +-
 man/WalleyeWad.Rd         |    3 
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 man/WhiteGrunt1.Rd        |    9 -
 man/WhiteGrunt2.Rd        |    3 
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 man/WhitefishMB.Rd        |   13 -
 man/WhitefishTB.Rd        |    3 
 man/YERockfish.Rd         |   15 +
 man/YPerchCB1.Rd          |    7 
 man/YPerchCB2.Rd          |    3 
 man/YPerchGB.Rd           |    9 -
 man/YPerchGL.Rd           |    3 
 man/YPerchRL.Rd           |    7 
 man/YPerchSB.Rd           |    3 
 man/YPerchSB1.Rd          |    9 -
 man/YPerchTL.Rd           |   11 -
 man/YTFlounder.Rd         |   11 -
 180 files changed, 846 insertions(+), 680 deletions(-)

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Package FSA updated to version 0.8.8 with previous version 0.8.7 dated 2016-05-08

Title: Simple Fisheries Stock Assessment Methods
Description: A variety of simple fish stock assessment methods. Detailed vignettes are available on the fishR website <http://derekogle.com/fishR/>.
Author: Derek Ogle [aut, cre]
Maintainer: Derek Ogle <derek@derekogle.com>

Diff between FSA versions 0.8.7 dated 2016-05-08 and 0.8.8 dated 2016-07-18

 DESCRIPTION                          |    8 -
 MD5                                  |   20 +-
 NEWS.md                              |    5 
 R/growthModels.R                     |   65 +++++++-
 R/vbStarts.R                         |  256 +++++++++++++++++++++++------------
 man/Schnute.Rd                       |    2 
 man/growthModels.Rd                  |   10 -
 man/vbStarts.Rd                      |   25 ++-
 tests/testthat/Rplots.pdf            |binary
 tests/testthat/test_VonBertalanffy.R |   84 +++++++++++
 tests/testthat/test_growthFuns.R     |    4 
 11 files changed, 362 insertions(+), 117 deletions(-)

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New package simPATHy with initial version 0.1
Package: simPATHy
Type: Package
Title: Simulation Model of Expression Data for Pathway Analysis
Version: 0.1
Date: 2016-07-18
Authors@R: c(person("Elisa", "Salviato", email = "elisa.salviato.88@gmail.com", role = c("aut", "cre")), person("Vera", "Djordjilovic", email = "djordjilovic@stat.unipd.it", role = "aut"), person("Chiara","Romualdi",email="chiara.romualdi@unipd.it",role="aut"), person("Monica","Chiogna",email="monica@stat.unipd.it",role="aut"))
Description: Simulate data from a Gaussian graphical model or a Gaussian Bayesian network in two conditions. Given a covariance matrix of a reference condition simulate plausible dysregulations.
Depends: R (>= 2.10)
Imports: mvtnorm, gRbase, graph, igraph, ggm, qpgraph, R.utils, htmlwidgets, shiny, shinydashboard ,grDevices, graphics, stats
License: AGPL-3
LazyData: TRUE
RoxygenNote: 5.0.1
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2016-07-18 16:10:47 UTC; Elisetta
Author: Elisa Salviato [aut, cre], Vera Djordjilovic [aut], Chiara Romualdi [aut], Monica Chiogna [aut]
Maintainer: Elisa Salviato <elisa.salviato.88@gmail.com>
Repository: CRAN
Date/Publication: 2016-07-18 20:08:47

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New package sensiPhy with initial version 0.5.0
Package: sensiPhy
Title: Sensitivity Analysis for Comparative Methods
Version: 0.5.0
Date: 2016-07-18
Authors@R: c( person("Gustavo","Paterno", email = "paternogbc@gmail.com", role = c("cre","aut")), person("Gijsbert", "Werner", email = "gijsbert.werner@zoo.ox.ac.uk", role = "aut"), person("Caterina", "Penone", email = "caterina.penone@gmail.com", role = "aut"))
Maintainer: Gustavo Paterno <paternogbc@gmail.com>
Description: An implementation of sensitivity analysis in phylogenetic regression models, for both linear and logistic phylogenetic regressions. The package is an umbrella of statistical and graphical methods that estimate and report different types of uncertainty in PGLS models: (i) Sampling uncertainty (sample size; influential species and clades). (ii) Phylogenetic uncertainty. (iii) Data uncertainty (intraspecific variation and measurement error).
Depends: R (>= 3.1.0), ape (>= 3.3), phylolm (>= 2.4), ggplot2 (>= 2.1.0)
License: GPL-2
URL: https://github.com/paternogbc/sensiPhy
BugReports: https://github.com/paternogbc/sensiPhy/issues
LazyData: true
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-07-18 16:10:15 UTC; gugab
Author: Gustavo Paterno [cre, aut], Gijsbert Werner [aut], Caterina Penone [aut]
Repository: CRAN
Date/Publication: 2016-07-18 20:37:24

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Package permPATH updated to version 0.9 with previous version 0.8 dated 2016-07-13

Title: Permutation Based Gene Expression Pathway Analysis
Description: Can be used to carry out permutation based gene expression pathway analysis. This work was supported by a National Institute of Allergy and Infectious Disease/National Institutes of Health contract (No. HHSN272200900059C).
Author: Ivo D. Shterev [aut, cre], Kouros Owzar [aut], Gregory D. Sempowski [aut], Kenneth Wilder [ctb, cph] (wrote original version of ranker.h)
Maintainer: Ivo D. Shterev <i.shterev@duke.edu>

Diff between permPATH versions 0.8 dated 2016-07-13 and 0.9 dated 2016-07-18

 DESCRIPTION                  |    8 ++++----
 MD5                          |   14 +++++++-------
 inst/doc/permPATHmanual.R    |   40 ++++++++++++++++++++++++++++++++++++++--
 inst/doc/permPATHmanual.Rnw  |   40 ++++++++++++++++++++++++++++++++++++++--
 inst/doc/permPATHmanual.pdf  |binary
 man/perm.path.Rd             |   13 ++++++++-----
 src/permPATH.cpp             |    2 +-
 vignettes/permPATHmanual.Rnw |   40 ++++++++++++++++++++++++++++++++++++++--
 8 files changed, 134 insertions(+), 23 deletions(-)

More information about permPATH at CRAN
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Package lsmeans updated to version 2.23-5 with previous version 2.23 dated 2016-03-10

Title: Least-Squares Means
Description: Obtain least-squares means for many linear, generalized linear, and mixed models. Compute contrasts or linear functions of least-squares means, and comparisons of slopes. Plots and compact letter displays.
Author: Russell Lenth [aut, cre]
Maintainer: Russell Lenth <russell-lenth@uiowa.edu>

Diff between lsmeans versions 2.23 dated 2016-03-10 and 2.23-5 dated 2016-07-18

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 tests/tests1.Rout.save     |   18 +++++-----
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Package iRegression updated to version 1.2.1 with previous version 1.2 dated 2012-07-26

Title: Regression Methods for Interval-Valued Variables
Description: Contains some important regression methods for interval-valued variables. For each method, it is available the fitted values, residuals and some goodness-of-fit measures.
Author: Eufrasio de A. Lima Neto / Claudio A. V. de Souza Filho / Pedro R. D. Marinho
Maintainer: Eufrasio de A. Lima Neto <eufrasio@de.ufpb.br>

Diff between iRegression versions 1.2 dated 2012-07-26 and 1.2.1 dated 2016-07-18

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 R/ccrm.r                   |  327 ++++++++++++------------
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 man/Cardiological.CR.Rd    |   94 +++----
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 man/iRegression-package.Rd |   98 +++----
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Package HDoutliers updated to version 0.5 with previous version 0.2 dated 2016-06-22

Title: Leland Wilkinson's Algorithm for Detecting Multidimensional Outliers
Description: An implementation of an algorithm for outlier detection that can handle a) data with a mixed categorical and continuous variables, b) many columns of data, c) many rows of data, d) outliers that mask other outliers, and e) both unidimensional and multidimensional datasets. Unlike ad hoc methods found in many machine learning papers, HDoutliers is based on a distributional model that uses probabilities to determine outliers.
Author: Leland Wilkinson [aut], Chris Fraley [cre]
Maintainer: Chris Fraley <cfraley@tableau.com>

Diff between HDoutliers versions 0.2 dated 2016-06-22 and 0.5 dated 2016-07-18

 DESCRIPTION |   11 +++++------
 LICENSE     |only
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 3 files changed, 7 insertions(+), 7 deletions(-)

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New package Chaos01 with initial version 1.0.0
Package: Chaos01
Title: 0-1 Test for Chaos
Version: 1.0.0
Authors@R: person("Tomas", "Martinovic", email = "tomas.martinovic@vsb.cz", role = c("aut", "cre"))
Description: Computes and plot the results of the 0-1 test for chaos proposed by Gottwald and Melbourne (2004) <DOI:10.1137/080718851>. The algorithm is available in parallel for the independent values of parameter c.
Depends: R (>= 3.1.0)
License: GPL-3
Encoding: UTF-8
LazyData: true
NeedsCompilation: yes
Imports: graphics, stats
Suggests: parallel, Rmpi
RoxygenNote: 5.0.1.9000
Packaged: 2016-07-18 15:43:34 UTC; martinovic
Author: Tomas Martinovic [aut, cre]
Maintainer: Tomas Martinovic <tomas.martinovic@vsb.cz>
Repository: CRAN
Date/Publication: 2016-07-18 20:33:42

More information about Chaos01 at CRAN
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New package BoardGames with initial version 1.0.0
Package: BoardGames
Type: Package
Title: Board Games and Tools for Building Board Games
Version: 1.0.0
Authors@R: c(person("Derek", "Qiu", role = c("aut", "cre"), email = "qiu.derek.d@gmail.com"))
Description: Tools for constructing board/grid based games, as well as readily available game(s) for your entertainment.
Depends: R (>= 3.0.2)
License: GPL (>= 2)
LazyData: TRUE
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-07-18 18:25:23 UTC; admin123
Author: Derek Qiu [aut, cre]
Maintainer: Derek Qiu <qiu.derek.d@gmail.com>
Repository: CRAN
Date/Publication: 2016-07-18 20:37:26

More information about BoardGames at CRAN
Permanent link

Package strptimer (with last version 0.1.0) was removed from CRAN

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

2015-12-13 0.1.0

Permanent link
Package sprintfr (with last version 0.1.0) was removed from CRAN

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

2016-01-05 0.1.0

Permanent link
Package lgcp updated to version 1.3-15 with previous version 1.3-14 dated 2016-01-11

Title: Log-Gaussian Cox Process
Description: Spatial and spatio-temporal modelling of point patterns using the log-Gaussian Cox process. Bayesian inference for spatial, spatiotemporal, multivariate and aggregated point processes using Markov chain Monte Carlo.
Author: Benjamin M. Taylor, Tilman M. Davies, Barry S. Rowlingson, Peter J. Diggle. Additional code contributions from Edzer Pebesma.
Maintainer: Benjamin M. Taylor <b.taylor1@lancaster.ac.uk>

Diff between lgcp versions 1.3-14 dated 2016-01-11 and 1.3-15 dated 2016-07-18

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 man/txtProgressBar2.Rd                                   |    2 
 man/updateAMCMC.Rd                                       |    2 
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 man/updateAMCMC.constanth.Rd                             |    2 
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 man/varfield.lgcpPredict.Rd                              |    4 
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 man/window.lgcpPredict.Rd                                |    4 
 man/xvals.Rd                                             |    2 
 man/xvals.SpatialGridDataFrame.Rd                        |    2 
 man/xvals.default.Rd                                     |    2 
 man/xvals.fromXYZ.Rd                                     |    2 
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More information about lgcp at CRAN
Permanent link

New package statTarget with initial version 1.2.0
Package: statTarget
Type: Package
Title: Statistical Analysis of Metabolite Profile
Version: 1.2.0
Date: 2016-07-014
Author: Hemi Luan
Maintainer: Hemi Luan <hemi.luan@gmail.com>
Depends: R (>= 3.3.0),gWidgets2
Imports: randomForest,plyr,LMGene,pracma,pROC,robustbase,utils, grDevices,graphics,stats,rrcov, RGtk2,pls
Suggests: car, pdist, testthat, impute, gWidgetsRGtk2
Description: A easy to use tool provides a graphical user interface for quality control based signal correction, integration of metabolomic data from multiple batches, and the comprehensive statistic analysis for non-targeted and targeted approaches.
License: GPL (>= 2)
URL: https://github.com/13479776
biocViews: Metabolomics, MassSpectrometry
RoxygenNote: 5.0.1
LazyData: true
NeedsCompilation: no
Packaged: 2016-07-18 00:32:38 UTC; Hees
Repository: CRAN
Date/Publication: 2016-07-18 16:15:52

More information about statTarget at CRAN
Permanent link

New package shinyTime with initial version 0.1.0
Package: shinyTime
Type: Package
Title: A Time Input Widget for Shiny
Version: 0.1.0
Authors@R: person("Gerhard", "Burger", email = "burger.ga@gmail.com", role = c("aut", "cre"))
Description: Provides a time input widget for Shiny. This widget allows intuitive time input in the '[hh]:[mm]:[ss]' (24H) format by using a separate numeric input for each part of the time. The interface with R uses 'DateTimeClasses' objects. See the project page for more information and examples.
License: GPL-3 | file LICENSE
LazyData: TRUE
Imports: htmltools, shiny
URL: https://github.com/burgerga/shinyTime
BugReports: https://github.com/burgerga/shinyTime/issues
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-07-18 13:46:10 UTC; gerhard
Author: Gerhard Burger [aut, cre]
Maintainer: Gerhard Burger <burger.ga@gmail.com>
Repository: CRAN
Date/Publication: 2016-07-18 16:05:11

More information about shinyTime at CRAN
Permanent link

Package numOSL updated to version 2.0 with previous version 1.9 dated 2016-01-23

Title: Numeric Routines for Optically Stimulated Luminescence Dating
Description: Package for optimizing regular numeric problems in optically stimulated luminescence dating, such as: equivalent dose calculation, annual dose rate determination, growth curve fitting, decay curve decomposition, statistical age model optimization, and statistical plot visualization.
Author: Jun Peng [aut, cre], Bo Li [aut], Jorge More [ctb], Burton Garbow [ctb], Kenneth Hillstrom [ctb], John Burkardt [ctb], Paul Gilbert [ctb], Ravi Varadhan [ctb]
Maintainer: Jun Peng <pengjun10@mails.ucas.ac.cn>

Diff between numOSL versions 1.9 dated 2016-01-23 and 2.0 dated 2016-07-18

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 59 files changed, 1433 insertions(+), 1491 deletions(-)

More information about numOSL at CRAN
Permanent link

Package nat updated to version 1.8.4 with previous version 1.8.1 dated 2015-12-30

Title: NeuroAnatomy Toolbox for Analysis of 3D Image Data
Description: NeuroAnatomy Toolbox (nat) enables analysis and visualisation of 3D biological image data, especially traced neurons. Reads and writes 3D images in NRRD and 'Amira' AmiraMesh formats and reads surfaces in 'Amira' hxsurf format. Traced neurons can be imported from and written to SWC and 'Amira' LineSet and SkeletonGraph formats. These data can then be visualised in 3D via 'rgl', manipulated including applying calculated registrations, e.g. using the 'CMTK' registration suite, and analysed. There is also a simple representation for neurons that have been subjected to 3D skeletonisation but not formally traced; this allows morphological comparison between neurons including searches and clustering (via the 'nat.nblast' extension package).
Author: Greg Jefferis and James Manton
Maintainer: Greg Jefferis <jefferis@gmail.com>

Diff between nat versions 1.8.1 dated 2015-12-30 and 1.8.4 dated 2016-07-18

 DESCRIPTION                                         |   17 
 MD5                                                 |  346 ++++++++++----------
 NAMESPACE                                           |   19 -
 NEWS                                                |   41 ++
 R/cmtkreg.R                                         |   33 +
 R/dotprops.R                                        |   13 
 R/graph-nodes.R                                     |    5 
 R/hxsurf.R                                          |   24 +
 R/im3d.R                                            |   67 +++
 R/nat-data.R                                        |    5 
 R/nat-package.R                                     |   23 +
 R/neuron-io.R                                       |   87 +++--
 R/neuron-plot.R                                     |   18 -
 R/neuron.R                                          |   67 +++
 R/neuronlist.R                                      |   31 +
 R/neuronlist_interactive_3d.R                       |    2 
 R/ngraph.R                                          |  160 +++++++--
 R/potential_synapses.R                              |    1 
 R/reglist.R                                         |only
 R/summary.R                                         |    1 
 R/xform.R                                           |   65 ++-
 R/xformimage.R                                      |    9 
 R/xformpoints.R                                     |   45 ++
 R/zzz.R                                             |   10 
 README.md                                           |   21 +
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 man/MBL.surf.Rd                                     |    7 
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 man/all.equal.neuron.Rd                             |    6 
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 177 files changed, 2647 insertions(+), 2021 deletions(-)

More information about nat at CRAN
Permanent link

Package polysat updated to version 1.5-0 with previous version 1.4-1 dated 2015-08-18

Title: Tools for Polyploid Microsatellite Analysis
Description: A collection of tools to handle microsatellite data of any ploidy (and samples of mixed ploidy) where allele copy number is not known in partially heterozygous genotypes. It can import and export data in ABI 'GeneMapper', 'Structure', 'ATetra', 'Tetrasat'/'Tetra', 'GenoDive', 'SPAGeDi', 'POPDIST', 'STRand', and binary presence/absence formats. It can calculate pairwise distances between individuals using a stepwise mutation model or infinite alleles model, with or without taking ploidies and allele frequencies into account. These distances can be used for the calculation of clonal diversity statistics or used for further analysis in R. Allelic diversity statistics are also available. polysat can assist the user in estimating the ploidy of samples, and it can estimate allele frequencies in populations, calculate pairwise Fst values based on those frequencies, and export allele frequencies to 'SPAGeDi' and 'adegenet'. Functions are also included for assigning alleles to isoloci in cases where one pair of microsatellite primers amplifies alleles from two or more independently segregating isoloci.
Author: Lindsay V. Clark [aut, cre]
Maintainer: Lindsay V. Clark <lvclark@illinois.edu>

Diff between polysat versions 1.4-1 dated 2015-08-18 and 1.5-0 dated 2016-07-18

 DESCRIPTION                    |   34 +-
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 NAMESPACE                      |    9 
 NEWS                           |   24 +
 R/allopolyploidy.R             |  319 ++++++++++++++++++++++--
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 39 files changed, 2154 insertions(+), 1441 deletions(-)

More information about polysat at CRAN
Permanent link

Package phenology updated to version 5.2 with previous version 5.1 dated 2016-05-03

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 5.1 dated 2016-05-03 and 5.2 dated 2016-07-18

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 phenology-5.2/phenology/R/Lnegbin.R                    |   67 +++++---
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 phenology-5.2/phenology/R/fit_phenology.R              |    2 
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 31 files changed, 324 insertions(+), 250 deletions(-)

More information about phenology at CRAN
Permanent link

Package mason updated to version 0.2.5 with previous version 0.2.4 dated 2016-07-15

Title: Build Data Structures for Common Statistical Analysis
Description: Use a consistent syntax to create data structures of common statistical techniques that can be continued in a pipe chain. Design the analysis, add settings and variables, construct the results, and polish the final structure. Rinse and repeat for any number of statistical techniques.
Author: Luke Johnston [aut, cre]
Maintainer: Luke Johnston <lwjohnst@gmail.com>

Diff between mason versions 0.2.4 dated 2016-07-15 and 0.2.5 dated 2016-07-18

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Package logbin updated to version 2.0 with previous version 1.2 dated 2015-05-12

Title: Relative Risk Regression Using the Log-Binomial Model
Description: Methods for fitting log-link GLMs and GAMs to binomial data, including EM-type algorithms with more stable convergence properties than standard methods.
Author: Mark W. Donoghoe [aut, cre], Ian C. Marschner [ths], Alexandra C. Gillett [ctb] (Wrote an initial version of the nplbin function)
Maintainer: Mark W. Donoghoe <markdonoghoe@gmail.com>

Diff between logbin versions 1.2 dated 2015-05-12 and 2.0 dated 2016-07-18

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Package HelpersMG updated to version 1.6 with previous version 1.5 dated 2016-05-01

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 1.5 dated 2016-05-01 and 1.6 dated 2016-07-18

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New package funData with initial version 1.0
Package: funData
Type: Package
Title: An S4 Class for Functional Data
Version: 1.0
Date: 2016-07-18
Authors@R: person("Clara", "Happ", email = "clara.happ@stat.uni-muenchen.de", role = c("aut", "cre"))
Author: Clara Happ [aut, cre]
Maintainer: Clara Happ <clara.happ@stat.uni-muenchen.de>
Description: S4 classes for univariate and multivariate functional data with utility functions.
License: GPL-2
Depends: methods
Imports: abind, fields, foreach, graphics, grDevices, stats
Suggests: zoo, testthat
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-07-18 09:03:34 UTC; happ
Repository: CRAN
Date/Publication: 2016-07-18 13:59:36

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Package epiR updated to version 0.9-79 with previous version 0.9-77 dated 2016-05-13

Title: Tools for the Analysis of Epidemiological Data
Description: Tools for the analysis of epidemiological data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on the basis of single or multiple strata of count data presented in a contingency table, and computing confidence intervals around incidence risk and incidence rate estimates. Miscellaneous functions for use in meta-analysis, diagnostic test interpretation, and sample size calculations.
Author: Mark Stevenson <mark.stevenson1@unimelb.edu.au> with contributions from Telmo Nunes, Cord Heuer, Jonathon Marshall, Javier Sanchez, Ron Thornton, Jeno Reiczigel, Jim Robison-Cox, Paola Sebastiani, Peter Solymos, Kazuki Yoshida, Geoff Jones, Sarah Pirikahu, Simon Firestone and Ryan Kyle
Maintainer: Mark Stevenson <mark.stevenson1@unimelb.edu.au>

Diff between epiR versions 0.9-77 dated 2016-05-13 and 0.9-79 dated 2016-07-18

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Package SinIW updated to version 0.2 with previous version 0.1 dated 2016-07-17

Title: The SinIW Distribution
Description: Density, distribution function, quantile function, random generation and survival function for the Sine Inverse Weibull Distribution as defined by SOUZA, L. New Trigonometric Class of Probabilistic Distributions. 219 p. Thesis (Doctorate in Biometry and Applied Statistics) - Department of Statistics and Information, Federal Rural University of Pernambuco, Recife, Pernambuco, 2015 (available at <http://www.openthesis.org/documents/New-trigonometric-classes-probabilistic-distributions-602633.html>) and BRITO, C. C. R. Method Distributions generator and Probability Distributions Classes. 241 p. Thesis (Doctorate in Biometry and Applied Statistics) - Department of Statistics and Information, Federal Rural University of Pernambuco, Recife, Pernambuco, 2014 (available upon request).
Author: Luciano Souza <lcnsza@gmail.com>, Lucas Gallindo <lgallindo@gmail.com>, Luciano Serafim de Souza <lucianoserafimdesouza@gmail.com>
Maintainer: Lucas Gallindo <lgallindo@gmail.com>

Diff between SinIW versions 0.1 dated 2016-07-17 and 0.2 dated 2016-07-18

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Package SecKW updated to version 0.2 with previous version 0.1 dated 2016-07-17

Title: The SecKW Distribution
Description: Density, distribution function, quantile function, random generation and survival function for the Secant Kumaraswamy Weibull Distribution as defined by SOUZA, L. New Trigonometric Class of Probabilistic Distributions. 219 p. Thesis (Doctorate in Biometry and Applied Statistics) - Department of Statistics and Information, Federal Rural University of Pernambuco, Recife, Pernambuco, 2015 (available at <http://www.openthesis.org/documents/New-trigonometric-classes-probabilistic-distributions-602633.html>) and BRITO, C. C. R. Method Distributions generator and Probability Distributions Classes. 241 p. Thesis (Doctorate in Biometry and Applied Statistics) - Department of Statistics and Information, Federal Rural University of Pernambuco, Recife, Pernambuco, 2014 (available upon request).
Author: Luciano Souza <lcnsza@gmail.com>, Lucas Gallindo <lgallindo@gmail.com>, Luciano Serafim de Souza <lucianoserafimdesouza@gmail.com>
Maintainer: Lucas Gallindo <lgallindo@gmail.com>

Diff between SecKW versions 0.1 dated 2016-07-17 and 0.2 dated 2016-07-18

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Package DWreg updated to version 2.0 with previous version 1.0 dated 2015-12-09

Title: Parametric Regression for Discrete Response
Description: Regression for a discrete response, where the conditional distribution is modelled via a discrete Weibull distribution.
Author: Veronica Vinciotti <veronica.vinciotti@brunel.ac.uk>
Maintainer: Veronica Vinciotti<veronica.vinciotti@brunel.ac.uk>

Diff between DWreg versions 1.0 dated 2015-12-09 and 2.0 dated 2016-07-18

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