Tue, 16 Aug 2016

New package multigraph with initial version 0.30
Package: multigraph
Type: Package
Title: Plot and Manipulate Multigraphs
Version: 0.30
Depends: R (>= 3.3.1), multiplex (>= 2.0)
Imports: methods
Date: 2016-08-16
Authors@R: person(given = "Antonio", family = "Rivero Ostoic", role = c("aut", "cre"), email = "jaro@econ.au.dk")
Author: Antonio Rivero Ostoic [aut, cre]
Maintainer: Antonio Rivero Ostoic <jaro@econ.au.dk>
Description: Functions to plot and manipulate multigraphs and bipartite graphs with different layout options.
URL: http://github.com/mplex/multigraph/
BugReports: https://github.com/mplex/multigraph/issues/new/
Repository: CRAN
License: GPL-3
NeedsCompilation: no
Packaged: 2016-08-16 10:51:42 UTC; jari
Date/Publication: 2016-08-17 02:17:10

More information about multigraph at CRAN
Permanent link

Package spsurvey updated to version 3.2 with previous version 3.1 dated 2015-10-23

Title: Spatial Survey Design and Analysis
Description: This group of functions implements algorithms for design and analysis of probability surveys. The functions are tailored for Generalized Random Tessellation Stratified survey designs.
Author: Tom Kincaid [aut, cre], Tony Olsen [aut], Don Stevens [ctb], Christian Platt [ctb], Denis White [ctb], Richard Remington [ctb]
Maintainer: Tom Kincaid <Kincaid.Tom@epa.gov>

Diff between spsurvey versions 3.1 dated 2015-10-23 and 3.2 dated 2016-08-16

 DESCRIPTION                        |   13 
 MD5                                |  260 ++++-----
 NAMESPACE                          |    1 
 R/AAA.R                            |    2 
 R/attisk.est.R                     |    8 
 R/attrisk.analysis.R               |    9 
 R/attrisk.var.R                    |    6 
 R/cat.analysis.R                   |   11 
 R/category.est.R                   |    8 
 R/catvar.prop.R                    |    6 
 R/catvar.size.R                    |    6 
 R/cdf.decon.R                      |    8 
 R/cdf.est.R                        |    8 
 R/cdf.test.R                       |   41 +
 R/cdf.test.prop.R                  |   19 
 R/cdf.test.size.prop.R             |    5 
 R/cdfvar.prop.R                    |    6 
 R/cdfvar.size.prop.R               |    6 
 R/cdfvar.size.total.R              |    6 
 R/cdfvar.test.R                    |    6 
 R/cdfvar.total.R                   |    6 
 R/change.analysis.R                |  175 +++++-
 R/change.est.R                     | 1008 +++++++++++++++++++++++++++++++++----
 R/changevar.mean.R                 |    6 
 R/changevar.prop.R                 |    6 
 R/changevar.size.R                 |    6 
 R/cont.analysis.R                  |    9 
 R/cont.cdftest.R                   |   19 
 R/dcdfvar.prop.R                   |    6 
 R/dcdfvar.size.prop.R              |    6 
 R/dcdfvar.size.total.R             |    6 
 R/dcdfvar.total.R                  |    6 
 R/examine.R                        |only
 R/grts.R                           |   44 -
 R/grtsarea.R                       |    2 
 R/grtslin.R                        |    2 
 R/input.check.R                    |   27 
 R/input.format.R                   |    2 
 R/irs.R                            |   44 -
 R/read.dbf.R                       |    6 
 R/read.sas.R                       |    3 
 R/relrisk.analysis.R               |    9 
 R/relrisk.est.R                    |    8 
 R/relrisk.var.R                    |    6 
 R/sp2shape.R                       |   35 +
 R/spsurvey.analysis.R              |   13 
 R/total.est.R                      |    8 
 R/total.var.R                      |    6 
 R/write.dbf.R                      |   12 
 build/vignette.rds                 |binary
 data/FL_lakes.rda                  |binary
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 inst/CITATION                      |   10 
 inst/NEWS.Rd                       |   55 ++
 inst/doc/Area_Analysis.R           |    6 
 inst/doc/Area_Analysis.Rnw         |   16 
 inst/doc/Area_Analysis.pdf         |binary
 inst/doc/Area_Design.Rnw           |    2 
 inst/doc/Area_Design.pdf           |binary
 inst/doc/CDF_Analysis.R            |    5 
 inst/doc/CDF_Analysis.Rnw          |   16 
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 inst/doc/CDF_Deconvolution.Rnw     |    2 
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 inst/doc/Linear_Analysis.pdf       |binary
 inst/doc/Linear_Design.Rnw         |    2 
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 man/cat.analysis.Rd                |    9 
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 man/cdf.est.Rd                     |    6 
 man/cdf.test.Rd                    |   24 
 man/change.analysis.Rd             |   35 -
 man/change.est.Rd                  |   41 -
 man/cont.analysis.Rd               |    9 
 man/cont.cdftest.Rd                |   11 
 man/examine.Rd                     |only
 man/grts.Rd                        |   36 -
 man/irs.Rd                         |   36 -
 man/read.sas.Rd                    |    5 
 man/relrisk.analysis.Rd            |    9 
 man/relrisk.est.Rd                 |    6 
 man/sp2shape.Rd                    |   13 
 man/spsurvey.analysis.Rd           |    9 
 man/total.est.Rd                   |    8 
 src/dbfFileParser.c                |   31 -
 src/grts.c                         |   48 +
 src/grtsarea.c                     |    2 
 src/grtslin.c                      |    2 
 src/insideAreaGridCell.c           |   40 +
 src/insideLinearGridCell.c         |   40 +
 src/irsarea.c                      |    2 
 src/irslin.c                       |    2 
 src/order.h                        |only
 src/pickAreaSamplePoints.c         |   27 
 src/pickGridCells.c                |   10 
 src/pickLinearSamplePoints.c       |   24 
 src/shapeParser.c                  |  439 ++++------------
 vignettes/Area_Analysis.Rnw        |   16 
 vignettes/Area_Design.Rnw          |    2 
 vignettes/CDF_Analysis.Rnw         |   16 
 vignettes/CDF_Deconvolution.Rnw    |    2 
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 vignettes/Change_Analysis_plot.pdf |only
 vignettes/Finite_Analysis.Rnw      |   21 
 vignettes/Finite_Design.Rnw        |    2 
 vignettes/Linear_Analysis.Rnw      |   23 
 vignettes/Linear_Design.Rnw        |    2 
 vignettes/Risk_Analysis.Rnw        |   12 
 vignettes/spsurvey.bib             |   21 
 136 files changed, 2228 insertions(+), 968 deletions(-)

More information about spsurvey at CRAN
Permanent link

Package spBayesSurv updated to version 1.0.4 with previous version 1.0.3 dated 2015-09-01

Title: Bayesian Modeling and Analysis of Spatially Correlated Survival Data
Description: Provides several Bayesian survival models for spatial/non-spatial survival data: marginal Bayesian Nonparametric models, marginal Bayesian proportional hazards models, generalized accelerated failure time frailty models, and standard semiparametric frailty models within the context of proportional hazards, proportional odds and accelerated failure time.
Author: Haiming Zhou <zhouh@niu.edu> and Tim Hanson <hansont@stat.sc.edu>
Maintainer: Haiming Zhou <zhouh@niu.edu>

Diff between spBayesSurv versions 1.0.3 dated 2015-09-01 and 1.0.4 dated 2016-08-16

 spBayesSurv-1.0.3/spBayesSurv/src/spSurv_AFT.cpp               |only
 spBayesSurv-1.0.3/spBayesSurv/src/spSurv_AH.cpp                |only
 spBayesSurv-1.0.3/spBayesSurv/src/spSurv_MPT_tools.cpp         |only
 spBayesSurv-1.0.3/spBayesSurv/src/spSurv_MPT_tools.h           |only
 spBayesSurv-1.0.3/spBayesSurv/src/spSurv_PH.cpp                |only
 spBayesSurv-1.0.3/spBayesSurv/src/spSurv_PO.cpp                |only
 spBayesSurv-1.0.3/spBayesSurv/src/spSurv_anovaDDP.h            |only
 spBayesSurv-1.0.3/spBayesSurv/src/spSurv_frailtyLDTFP.h        |only
 spBayesSurv-1.0.3/spBayesSurv/src/spSurv_indeptCoxph.h         |only
 spBayesSurv-1.0.3/spBayesSurv/src/spSurv_nonfrailtyLDTFP.h     |only
 spBayesSurv-1.0.3/spBayesSurv/src/spSurv_spCopulaCoxph.h       |only
 spBayesSurv-1.0.3/spBayesSurv/src/spSurv_spCopulaDDP.h         |only
 spBayesSurv-1.0.4/spBayesSurv/DESCRIPTION                      |   10 
 spBayesSurv-1.0.4/spBayesSurv/MD5                              |   89 
 spBayesSurv-1.0.4/spBayesSurv/NAMESPACE                        |   10 
 spBayesSurv-1.0.4/spBayesSurv/R/SuperSurvRegBayes2.R           |only
 spBayesSurv-1.0.4/spBayesSurv/R/frailtyGAFT.R                  |  412 ++-
 spBayesSurv-1.0.4/spBayesSurv/R/survregbayes.R                 | 1058 ++++------
 spBayesSurv-1.0.4/spBayesSurv/R/survregbayes2.R                |only
 spBayesSurv-1.0.4/spBayesSurv/R/wrappers.R                     |   54 
 spBayesSurv-1.0.4/spBayesSurv/man/GetCurves.Rd                 |    2 
 spBayesSurv-1.0.4/spBayesSurv/man/SuperSurvRegBayes2.Rd        |only
 spBayesSurv-1.0.4/spBayesSurv/man/anovaDDP.Rd                  |    2 
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 spBayesSurv-1.0.4/spBayesSurv/man/indeptCoxph.Rd               |    2 
 spBayesSurv-1.0.4/spBayesSurv/man/spBayesSurv-package.Rd       |   12 
 spBayesSurv-1.0.4/spBayesSurv/man/spCopulaCoxph.Rd             |    4 
 spBayesSurv-1.0.4/spBayesSurv/man/spCopulaDDP.Rd               |    2 
 spBayesSurv-1.0.4/spBayesSurv/man/survregbayes.Rd              |  161 -
 spBayesSurv-1.0.4/spBayesSurv/man/survregbayes2.Rd             |only
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 spBayesSurv-1.0.4/spBayesSurv/src/spSurv_BP_tools.cpp          |only
 spBayesSurv-1.0.4/spBayesSurv/src/spSurv_BP_tools.h            |only
 spBayesSurv-1.0.4/spBayesSurv/src/spSurv_Coxph_tools.cpp       |   26 
 spBayesSurv-1.0.4/spBayesSurv/src/spSurv_Coxph_tools.h         |    1 
 spBayesSurv-1.0.4/spBayesSurv/src/spSurv_DDP_tools.cpp         |   25 
 spBayesSurv-1.0.4/spBayesSurv/src/spSurv_DDP_tools.h           |    1 
 spBayesSurv-1.0.4/spBayesSurv/src/spSurv_LDTFP_tools.cpp       |   75 
 spBayesSurv-1.0.4/spBayesSurv/src/spSurv_LDTFP_tools.h         |    5 
 spBayesSurv-1.0.4/spBayesSurv/src/spSurv_MPT_tools_single.cpp  |only
 spBayesSurv-1.0.4/spBayesSurv/src/spSurv_MPT_tools_single.h    |only
 spBayesSurv-1.0.4/spBayesSurv/src/spSurv_MPT_tools_super.cpp   |only
 spBayesSurv-1.0.4/spBayesSurv/src/spSurv_MPT_tools_super.h     |only
 spBayesSurv-1.0.4/spBayesSurv/src/spSurv_PHPOAFT_BP.cpp        |only
 spBayesSurv-1.0.4/spBayesSurv/src/spSurv_PH_BP.cpp             |only
 spBayesSurv-1.0.4/spBayesSurv/src/spSurv_PH_MPT.cpp            |only
 spBayesSurv-1.0.4/spBayesSurv/src/spSurv_PO_BP.cpp             |only
 spBayesSurv-1.0.4/spBayesSurv/src/spSurv_PO_MPT.cpp            |only
 spBayesSurv-1.0.4/spBayesSurv/src/spSurv_anovaDDP.cpp          |    9 
 spBayesSurv-1.0.4/spBayesSurv/src/spSurv_common.cpp            |  225 --
 spBayesSurv-1.0.4/spBayesSurv/src/spSurv_common.h              |   42 
 spBayesSurv-1.0.4/spBayesSurv/src/spSurv_frailtyLDTFP.cpp      |  177 +
 spBayesSurv-1.0.4/spBayesSurv/src/spSurv_frailty_GRF_LDTFP.cpp |only
 spBayesSurv-1.0.4/spBayesSurv/src/spSurv_indeptCoxph.cpp       |   15 
 spBayesSurv-1.0.4/spBayesSurv/src/spSurv_nonfrailtyLDTFP.cpp   |    7 
 spBayesSurv-1.0.4/spBayesSurv/src/spSurv_spCopulaCoxph.cpp     |   15 
 spBayesSurv-1.0.4/spBayesSurv/src/spSurv_spCopulaDDP.cpp       |   13 
 spBayesSurv-1.0.4/spBayesSurv/src/spSurv_spatialtools.cpp      |only
 spBayesSurv-1.0.4/spBayesSurv/src/spSurv_spatialtools.h        |only
 62 files changed, 1173 insertions(+), 1319 deletions(-)

More information about spBayesSurv at CRAN
Permanent link

Package rr updated to version 1.4 with previous version 1.3.1 dated 2016-05-14

Title: Statistical Methods for the Randomized Response Technique
Description: Enables researchers to conduct multivariate statistical analyses of survey data with randomized response technique items from several designs, including mirrored question, forced question, and unrelated question. This includes regression with the randomized response as the outcome and logistic regression with the randomized response item as a predictor. In addition, tools for conducting power analysis for designing randomized response items are included. The package implements methods described in Blair, Imai, and Zhou (2015) ''Design and Analysis of the Randomized Response Technique,'' Journal of the American Statistical Association <http://graemeblair.com/papers/randresp.pdf>.
Author: Graeme Blair [aut, cre], Yang-Yang Zhou [aut, cre], Kosuke Imai [aut, cre], Winston Chou [ctb]
Maintainer: Graeme Blair <graeme.blair@ucla.edu>

Diff between rr versions 1.3.1 dated 2016-05-14 and 1.4 dated 2016-08-16

 ChangeLog            |   13 +--
 DESCRIPTION          |   23 ++---
 MD5                  |   16 +--
 NAMESPACE            |    6 +
 R/rr.R               |  218 +++++++++++++++++++++++++++++++++++++++++++++++++--
 R/rrBayes.R          |    8 +
 man/predict.rrreg.Rd |    2 
 man/rrreg.Rd         |   20 +++-
 man/rrreg.bayes.Rd   |    5 -
 9 files changed, 271 insertions(+), 40 deletions(-)

More information about rr at CRAN
Permanent link

New package optimr with initial version 2016-8.16
Package: optimr
Version: 2016-8.16
Date: 2016-08-16
Title: A Replacement and Extension of the 'optim' Function
Authors@R: c( person(given = c("John", "C"), family = "Nash", role = c("aut", "cre"), email = "nashjc@uottawa.ca"), person(given = "Ravi", family = "Varadhan", role = "aut", email = "RVaradhan@jhmi.edu"), person(given = "Gabor", family = "Grothendieck", role = "ctb", email = "ggrothendieck@gmail.com") )
Author: John C Nash [aut, cre], Ravi Varadhan [aut], Gabor Grothendieck [ctb]
Maintainer: John C Nash <nashjc@uottawa.ca>
Description: Provides a test of replacement and extension of the optim() function to unify and streamline optimization capabilities in R for smooth, possibly box constrained functions of several or many parameters. This version has a reduced set of methods and is intended to be on CRAN.
License: GPL-2
LazyLoad: Yes
Imports: optextras, numDeriv, setRNG, Rvmmin, Rcgmin
NeedsCompilation: no
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
Packaged: 2016-08-16 21:05:26 UTC; john
Repository: CRAN
Date/Publication: 2016-08-17 00:31:27

More information about optimr at CRAN
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Package multiplex updated to version 2.0 with previous version 1.9.3 dated 2016-06-16

Title: Algebraic Tools for the Analysis of Multiple Social Networks
Description: Algebraic procedures for the analysis of multiple social networks are delivered with this package. Among other things, it is possible to create and manipulate multivariate network data with different formats, and there are effective ways available to treat multiple networks with routines that combine algebraic systems like the partially ordered semigroup or the semiring structure together with the relational bundles occurring in different types of multivariate network data sets. As well an algebraic approach for two-mode networks is made through Galois derivations between families of the pair of subsets.
Author: Antonio Rivero Ostoic [aut, cre]
Maintainer: Antonio Rivero Ostoic <multiplex@post.com>

Diff between multiplex versions 1.9.3 dated 2016-06-16 and 2.0 dated 2016-08-16

 multiplex-1.9.3/multiplex/R/symclos.R                 |only
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 multiplex-2.0/multiplex/DESCRIPTION                   |   17 
 multiplex-2.0/multiplex/MD5                           |   90 +--
 multiplex-2.0/multiplex/R/bundle.census.R             |  428 ++++++++----------
 multiplex-2.0/multiplex/R/bundles.R                   |  102 ++--
 multiplex-2.0/multiplex/R/cngr.R                      |   13 
 multiplex-2.0/multiplex/R/dhc.R                       |    3 
 multiplex-2.0/multiplex/R/iinc.R                      |   15 
 multiplex-2.0/multiplex/R/jnt.R                       |    3 
 multiplex-2.0/multiplex/R/men.R                       |    3 
 multiplex-2.0/multiplex/R/pacnet.R                    |   13 
 multiplex-2.0/multiplex/R/rbox.R                      |  139 +++++
 multiplex-2.0/multiplex/R/read.dl.R                   |only
 multiplex-2.0/multiplex/R/rel.sys.R                   |  121 +++--
 multiplex-2.0/multiplex/R/semiring.R                  |  106 ++++
 multiplex-2.0/multiplex/R/summaryBundles.R            |   17 
 multiplex-2.0/multiplex/R/swp.R                       |    7 
 multiplex-2.0/multiplex/R/transf.R                    |   87 +--
 multiplex-2.0/multiplex/R/transl.R                    |    7 
 multiplex-2.0/multiplex/R/zbind.R                     |   15 
 multiplex-2.0/multiplex/inst/CHANGELOG                |   23 
 multiplex-2.0/multiplex/inst/doc/TwoModeNetworks.Rnw  |   59 --
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 multiplex-2.0/multiplex/man/dhc.Rd                    |    2 
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 multiplex-2.0/multiplex/man/galois.Rd                 |   14 
 multiplex-2.0/multiplex/man/iinc.Rd                   |    7 
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 multiplex-2.0/multiplex/man/rel.sys.Rd                |   20 
 multiplex-2.0/multiplex/man/summaryBundles.Rd         |    9 
 multiplex-2.0/multiplex/man/swp.Rd                    |    2 
 multiplex-2.0/multiplex/man/transf.Rd                 |   24 -
 multiplex-2.0/multiplex/man/transl.Rd                 |    2 
 multiplex-2.0/multiplex/man/write.dl.Rd               |    2 
 multiplex-2.0/multiplex/man/zbind.Rd                  |    4 
 multiplex-2.0/multiplex/vignettes/TwoModeNetworks.Rnw |   59 --
 50 files changed, 822 insertions(+), 647 deletions(-)

More information about multiplex at CRAN
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New package ModelMetrics with initial version 1.0.0
Package: ModelMetrics
Title: Rapid Calculation of Model Metrics
Version: 1.0.0
Authors@R: person("Tyler", "Hunt", email = "thunt@snapfinance.com", role = c("aut", "cre"))
Description: Collection of metrics for evaluating models written in C++ using 'Rcpp'.
Depends: R (>= 3.2.2)
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
LinkingTo: Rcpp
Imports: Rcpp
RoxygenNote: 5.0.1
Suggests: testthat
NeedsCompilation: yes
Packaged: 2016-08-16 22:47:34 UTC; snapadmin
Author: Tyler Hunt [aut, cre]
Maintainer: Tyler Hunt <thunt@snapfinance.com>
Repository: CRAN
Date/Publication: 2016-08-17 01:11:51

More information about ModelMetrics at CRAN
Permanent link

Package FFTrees updated to version 1.1.3 with previous version 1.1.1 dated 2016-07-21

Title: Generate, Visualise, and Compare Fast and Frugal Decision Trees
Description: Contains several functions that allow users to create, visualize, and test Fast and Frugal Trees (FFTs). FFts are very simple decision trees for classifying cases (i.e.; breast cancer patients) into one of two classes (e.g.; no cancer vs. true cancer) based on a small number of cues (e.g.; test results). FFTs can be preferable to more complex algorithms (such as logistic regression) because they are easy to communicate and implement, and are robust against noisy data.
Author: Nathaniel Phillips [aut, cre]
Maintainer: Nathaniel Phillips <Nathaniel.D.Phillips.is@gmail.com>

Diff between FFTrees versions 1.1.1 dated 2016-07-21 and 1.1.3 dated 2016-08-16

 FFTrees-1.1.1/FFTrees/R/hello.R                  |only
 FFTrees-1.1.1/FFTrees/vignettes/fft_examples.md  |only
 FFTrees-1.1.3/FFTrees/DESCRIPTION                |   16 
 FFTrees-1.1.3/FFTrees/MD5                        |   84 ++--
 FFTrees-1.1.3/FFTrees/NAMESPACE                  |    3 
 FFTrees-1.1.3/FFTrees/R/auc_function.R           |   11 
 FFTrees-1.1.3/FFTrees/R/blood_doc.R              |   12 
 FFTrees-1.1.3/FFTrees/R/breastcancer_doc.R       |   22 -
 FFTrees-1.1.3/FFTrees/R/cartpred_function.R      |   53 +-
 FFTrees-1.1.3/FFTrees/R/classtable_function.R    |   16 
 FFTrees-1.1.3/FFTrees/R/factclean_function.R     |only
 FFTrees-1.1.3/FFTrees/R/fft_function.R           |  415 ++++++++++++++---------
 FFTrees-1.1.3/FFTrees/R/growffts_function.R      |   28 +
 FFTrees-1.1.3/FFTrees/R/heartdisease_doc.R       |   30 -
 FFTrees-1.1.3/FFTrees/R/lrpred_function.R        |   29 +
 FFTrees-1.1.3/FFTrees/R/plotfft_function.R       |  295 ++++++++++------
 FFTrees-1.1.3/FFTrees/R/predictfft_function.R    |  161 ++++++++
 FFTrees-1.1.3/FFTrees/R/printfft_function.R      |only
 FFTrees-1.1.3/FFTrees/R/showcues_function.R      |only
 FFTrees-1.1.3/FFTrees/R/summaryfft_function.R    |    2 
 FFTrees-1.1.3/FFTrees/build/vignette.rds         |binary
 FFTrees-1.1.3/FFTrees/data/heartdisease.RData    |binary
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New package fastcmh with initial version 0.1.9
Package: fastcmh
Title: Significant Interval Discovery with Categorical Covariates
Version: 0.1.9
Author: Felipe Llinares Lopez, Dean Bodenham
Maintainer: Dean Bodenham <deanbodenhambsse@gmail.com>
Description: A method which uses the Cochran-Mantel-Haenszel test with significant pattern mining to detect intervals in binary genotype data which are significantly associated with a particular phenotype, while accounting for categorical covariates.
Depends: bindata
License: GPL-2 | GPL-3
LinkingTo: Rcpp
Imports: Rcpp
RoxygenNote: 5.0.1
NeedsCompilation: yes
Packaged: 2016-08-16 08:25:27 UTC; dean
Repository: CRAN
Date/Publication: 2016-08-17 01:05:14

More information about fastcmh at CRAN
Permanent link

Package cda updated to version 2.0.0 with previous version 1.5.1 dated 2014-01-19

Title: Coupled-Dipole Approximation for Electromagnetic Scattering by Three-Dimensional Clusters of Sub-Wavelength Particles
Description: Coupled-dipole simulations for electromagnetic scattering of light by sub-wavelength particles in arbitrary 3-dimensional configurations. Scattering and absorption spectra are simulated by inversion of the interaction matrix, or by an order-of-scattering approximation scheme. High-level functions are provided to simulate spectra with varying angles of incidence, as well as with full angular averaging.
Author: Baptiste Auguie [aut, cre]
Maintainer: Baptiste Auguie <baptiste.auguie@gmail.com>

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Package ApacheLogProcessor updated to version 0.1.6 with previous version 0.1.5 dated 2015-06-10

Title: Process the Apache Web Server Access Log Files
Description: Provides a function to process Apache Log Common or Combined files. The main functionality is to extract data from log files to data frames.
Author: Diogo Silveira Mendonca
Maintainer: Diogo Silveira Mendonca <diogosmendonca@gmail.com>

Diff between ApacheLogProcessor versions 0.1.5 dated 2015-06-10 and 0.1.6 dated 2016-08-16

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New package timelineS with initial version 0.1.0
Package: timelineS
Type: Package
Title: Timeline and Time Duration-Related Tools
Version: 0.1.0
Date: 2016-08-15
Author: Dahee Lee [aut, cre], Dustin Tingley [aut]
Maintainer: Dahee Lee <dhlee99@gmail.com>
Description: An easy tool for plotting annotated timelines, grouped timelines, and exploratory graphics (boxplot/histogram/density plot/scatter plot/line plot). Filter, summarize date data by duration and convert to calendar units.
License: GPL-2
LazyData: TRUE
Imports: base, graphics, magrittr, dplyr, lubridate, ggplot2, stats
Depends: R (>= 3.1.0)
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-08-16 00:56:44 UTC; Dahee
Repository: CRAN
Date/Publication: 2016-08-16 19:14:03

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New package SqlRender with initial version 1.1.7
Package: SqlRender
Type: Package
Title: Rendering Parameterized SQL and Translation to Dialects
Version: 1.1.7
Date: 2016-08-15
Author: Martijn J. Schuemie [aut, cre], Marc A. Suchard [aut],
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>
Description: A rendering tool for parameterized SQL that also translates into different SQL dialects. These dialects include Sql Server, Oracle, PostgreSql, Amazon RedShift, and Microsoft PDW.
License: Apache License 2.0
VignetteBuilder: knitr
URL: https://github.com/OHDSI/SqlRender
BugReports: https://github.com/OHDSI/SqlRender/issues
Imports: rJava
Suggests: testthat, knitr, rmarkdown
LazyData: false
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-08-16 11:23:26 UTC; mschuemi
Repository: CRAN
Date/Publication: 2016-08-16 19:47:24

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Package SimReg updated to version 2.1 with previous version 1.4 dated 2016-03-06

Title: Similarity Regression Functions
Description: Functions for performing Bayesian `similarity regression', specialised for modelling the association between a HPO-encoded phenotype and binary genotype. A `no association' model is compared with one in which the log odds of having a rare genotype is linked to the semantic similarity between patient phenotype and a latent characteristic phenotype. The method estimates the probability of an association together with an HPO-coded phenotype characteristic of the disease.
Author: Daniel Greene
Maintainer: Daniel Greene <dg333@cam.ac.uk>

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Package SIDES updated to version 1.4 with previous version 1.3 dated 2016-07-26

Title: Subgroup Identification Based on Differential Effect Search
Description: Provides function to apply "Subgroup Identification based on Differential Effect Search" (SIDES) method proposed by Lipkovich et al. (2011) <doi:10.1002/sim.4289>.
Author: Marie-Karelle Riviere
Maintainer: Marie-Karelle Riviere <eldamjh@gmail.com>

Diff between SIDES versions 1.3 dated 2016-07-26 and 1.4 dated 2016-08-16

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Package sem updated to version 3.1-8 with previous version 3.1-7 dated 2016-04-06

Title: Structural Equation Models
Description: Functions for fitting general linear structural equation models (with observed and latent variables) using the RAM approach, and for fitting structural equations in observed-variable models by two-stage least squares.
Author: John Fox [aut, cre], Zhenghua Nie [aut], Jarrett Byrnes [aut], Michael Culbertson [ctb], Saikat DebRoy [ctb], Michael Friendly [ctb], Benjamin Goodrich [ctb], Richard H. Jones [ctb], Adam Kramer [ctb], Georges Monette [ctb], R-Core [ctb]
Maintainer: John Fox <jfox@mcmaster.ca>

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Package sdcMicroGUI updated to version 1.3.0 with previous version 1.2.0 dated 2015-05-06

Title: Graphical User Interface for Package sdcMicro
Description: A point and click graphical user interface based on top of the 'sdcMicro' package to create anonymized data set. The graphical user interface provides full reproducibility of any result via the script menu in the GUI.
Author: Alexander Kowarik, Matthias Templ, Bernhard Meindl, Francois Fonteneau
Maintainer: Alexander Kowarik <alexander.kowarik@statistik.gv.at>

Diff between sdcMicroGUI versions 1.2.0 dated 2015-05-06 and 1.3.0 dated 2016-08-16

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Package rtfbs updated to version 0.3.5 with previous version 0.3.4 dated 2015-02-09

Title: Transcription Factor Binding Site Identification Tool
Description: Identifies and scores possible Transcription Factor Binding Sites and allows for FDR analysis and pruning. It supports splitting of sequences based on size or a specified GFF, grouping by G+C content, and specification of Markov model order. The heavy lifting is done in C while all results are made available via R.
Author: Nicholas Peterson, Andre Martins, Melissa Hubisz, and Adam Siepel
Maintainer: Melissa Hubisz <mjhubisz@cornell.edu>

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Package Rfit updated to version 0.23.0 with previous version 0.22.0 dated 2015-08-26

Title: Rank Estimation for Linear Models
Description: R estimation and inference for linear models. Estimation is for general scores and a library of commonly used score functions is included.
Author: John Kloke, Joseph McKean
Maintainer: John Kloke <kloke@biostat.wisc.edu>

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Package RcppParallel updated to version 4.3.20 with previous version 4.3.19 dated 2016-05-04

Title: Parallel Programming Tools for 'Rcpp'
Description: High level functions for parallel programming with 'Rcpp'. For example, the 'parallelFor()' function can be used to convert the work of a standard serial "for" loop into a parallel one and the 'parallelReduce()' function can be used for accumulating aggregate or other values.
Author: JJ Allaire [aut], Romain Francois [aut, cph], Kevin Ushey [aut, cre], Gregory Vandenbrouck [aut], Marcus Geelnard [aut, cph] (TinyThread library, http://tinythreadpp.bitsnbites.eu/), RStudio [cph], Intel [aut, cph] (Intel TBB library, https://www.threadingbuildingblocks.org/), Microsoft [cph]
Maintainer: Kevin Ushey <kevin@rstudio.com>

Diff between RcppParallel versions 4.3.19 dated 2016-05-04 and 4.3.20 dated 2016-08-16

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Package RcmdrPlugin.survival updated to version 1.1-1 with previous version 1.1-0 dated 2016-04-06

Title: R Commander Plug-in for the 'survival' Package
Description: An R Commander plug-in for the survival package, with dialogs for Cox models, parametric survival regression models, estimation of survival curves, and testing for differences in survival curves, along with data-management facilities and a variety of tests, diagnostics and graphs.
Author: John Fox
Maintainer: John Fox <jfox@mcmaster.ca>

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Package MVar.pt updated to version 1.9.4 with previous version 1.9.3 dated 2016-07-26

Title: Analise multivariada (brazilian portuguese)
Description: Pacote para analise multivariada, que possui funcoes que executam analise de correspondencia simples (CA) e multipla (MCA), analise de componentes principais (PCA), analise de correlacao canonica (CCA), analise fatorial (FA), escalonamento multidimensional (MDS), analise de cluster hierarquico e nao hierarquico, regressao linear, analise de multiplos fatores (MFA) para dados quantitativos, qualitativos, de frequencia (MFACT) e dados mistos. Tambem possui outras funcoes uteis para a analise multivariada.
Author: Paulo Cesar Ossani <ossanipc@hotmail.com> Marcelo Angelo Cirillo <macufla@dex.ufla.br>
Maintainer: Paulo Cesar Ossani <ossanipc@hotmail.com>

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New package IMFData with initial version 0.1.0
Package: IMFData
Type: Package
Title: R Interface for International Monetary Fund(IMF) Data API
Version: 0.1.0
Date: 2016-08-15
Authors@R: person("Ming-Jer", "Lee", email = "mingjerli@gmail.com", role = c("aut", "cre"))
Depends: R (>= 3.3.0)
Imports: httr, jsonlite, plyr
Description: Search, extract and formulate IMF's datasets.
License: MIT + file LICENSE
LazyData: TRUE
KeepSource: TRUE
URL: https://github.com/mingjerli/IMFData
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-08-16 02:17:36 UTC; mingjerli
Author: Ming-Jer Lee [aut, cre]
Maintainer: Ming-Jer Lee <mingjerli@gmail.com>
Repository: CRAN
Date/Publication: 2016-08-16 19:13:56

More information about IMFData at CRAN
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New package getlandsat with initial version 0.1.0
Package: getlandsat
Type: Package
Title: Get Landsat 8 Data from Amazon Public Data Sets
Description: Get Landsat 8 Data from Amazon Web Services ('AWS') public data sets (<https://aws.amazon.com/public-data-sets/landsat/>). Includes functions for listing images and fetching them, and handles caching to prevent unnecessary additional requests.
Version: 0.1.0
Authors@R: c(person("Scott", "Chamberlain", role = c("aut", "cre"), email = "myrmecocystus@gmail.com"))
License: MIT + file LICENSE
URL: https://github.com/ropenscilabs/getlandsat
BugReports: https://github.com/ropenscilabs/getlandsat/issues
Imports: methods, readr (>= 1.0.0), httr (>= 1.2.0), xml2 (>= 1.0.0), data.table, tibble, rappdirs
Suggests: roxygen2 (>= 5.0.1), testthat, knitr, covr, raster
VignetteBuilder: knitr
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-08-16 00:32:42 UTC; sacmac
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Repository: CRAN
Date/Publication: 2016-08-16 19:14:01

More information about getlandsat at CRAN
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Package gesis updated to version 0.2 with previous version 0.1 dated 2015-11-30

Title: R Client for GESIS Data Catalogue (DBK)
Description: Provides programmatic access to the GESIS - Leibniz-Institute for the Social Sciences Data Catalogue/Datenbestandkatalog (DBK), which maintains a large repository of data sets related to the social sciences.
Author: Eric Persson [aut, cre]
Maintainer: Eric Persson <expersso5@gmail.com>

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Package enveomics.R updated to version 1.1.1 with previous version 1.1.0 dated 2016-05-14

Title: Various R Functions from the Kostas Lab
Description: A collection of R functions of common use in the Kostas Lab for microbial ecology.
Author: Luis M. Rodriguez-R [aut, cre]
Maintainer: Luis M. Rodriguez-R <lmrodriguezr@gmail.com>

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Package EmpiricalCalibration updated to version 1.2.0 with previous version 1.1.0 dated 2016-02-15

Title: Routines for Performing Empirical Calibration of Observational Study Estimates
Description: Routines for performing empirical calibration of observational study estimates. By using a set of negative control hypotheses we can estimate the empirical null distribution of a particular observational study setup. This empirical null distribution can be used to compute a calibrated p-value, which reflects the probability of observing an estimated effect size when the null hypothesis is true taking both random and systematic error into account.
Author: Martijn Schuemie, Marc Suchard
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>

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Package DiffusionRjgqd updated to version 0.1.1 with previous version 0.1.0 dated 2016-01-24

Title: Inference and Analysis for Jump Generalized Quadratic Diffusions
Description: Tools for performing inference and analysis on a class of quadratic jump diffusion processes.
Author: Etienne A.D. Pienaar [aut, cre], Melvin M. Varughese [ctb]
Maintainer: Etienne A.D. Pienaar <etiennead@gmail.com>

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Package DiffusionRimp updated to version 0.1.1 with previous version 0.1.0 dated 2016-06-13

Title: Inference and Analysis for Diffusion Processes via Data Imputation and Method of Lines
Description: Tools for performing inference and analysis using a data-imputation scheme and the method of lines.
Author: Etienne A.D. Pienaar [aut, cre], Melvin M. Varughese [ctb]
Maintainer: Etienne A.D. Pienaar <etiennead@gmail.com>

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Package dggridR updated to version 0.1.10 with previous version 0.1.8 dated 2016-07-27

Title: Discrete Global Grids for R
Description: Spatial analyses involving binning require that every bin have the same area, but this is impossible using a rectangular grid laid over the Earth or over any projection of the Earth. Discrete global grids use hexagons, triangles, and diamonds to overcome this issue, overlaying the Earth with equally-sized bins. This package provides utilities for working with discrete global grids, along with utilities to aid in plotting such data.
Author: Richard Barnes [aut, cre], Kevin Sahr [ctb], Gerald Evenden [ctb], Angus Johnson [ctb], Frank Warmerdam [ctb]
Maintainer: Richard Barnes <rbarnes@umn.edu>

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New package ctmcd with initial version 0.9
Package: ctmcd
Type: Package
Title: Estimating the Parameters of a Continuous-Time Markov Chain from Discrete-Time Data
Version: 0.9
Date: 2016-08-08
Author: Marius Pfeuffer
Maintainer: Marius Pfeuffer <marius.pfeuffer@fau.de>
Description: Functions for estimating Markov generator matrices from discrete-time observations. The implemented approaches comprise diagonal adjustment, weighted adjustment and quasi-optimization of matrix logarithm based candidate solutions, an expectation-maximization algorithm as well as a Gibbs sampler.
License: GPL-3
Imports: Rcpp (>= 0.12.6), expm, numDeriv
Suggests: knitr, rmarkdown
LinkingTo: Rcpp, RcppArmadillo
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2016-08-13 13:41:55 UTC; Stefan
Repository: CRAN
Date/Publication: 2016-08-16 19:47:33

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New package complexplus with initial version 1.0
Package: complexplus
Type: Package
Title: Functions of Complex or Real Variable
Version: 1.0
Date: 2016-08-16
Author: Albert Dorador and Uffe Høgsbro Thygesen
Maintainer: Albert Dorador <albert.dorador@estudiant.upc.edu>
Description: Extension of several functions to the complex domain, including the matrix exponential and logarithm, and the determinant.
Depends: R (>= 3.1.0)
Imports: expm (>= 0.999-0)
License: GPL-2
ByteCompile: true
Encoding: UTF-8
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-08-16 06:01:26 UTC; Albert
Repository: CRAN
Date/Publication: 2016-08-16 19:14:00

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Package cdfquantreg updated to version 1.0.5 with previous version 1.0.4 dated 2016-04-05

Title: Quantile Regression for Random Variables on the Unit Interval
Description: Employs a two-parameter family of distributions for modelling random variables on the (0, 1) interval by applying the cumulative distribution function (cdf) of one parent distribution to the quantile function of another.
Author: Yiyun Shou [aut, cre], Michael Smithson [aut]
Maintainer: Yiyun Shou <yiyun.shou@anu.edu.au>

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Package caschrono updated to version 2.0 with previous version 1.4 dated 2014-03-21

Title: Séries Temporelles Avec R
Description: Functions, data sets and exercises solutions for the book 'Séries Temporelles Avec R' (Yves Aragon, edp sciences, 2016). For all chapters, a vignette is available with some additional material and exercises solutions.
Author: Yves Aragon
Maintainer: Thibault Laurent <Thibault.Laurent@univ-tlse1.fr>

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Package Boruta updated to version 5.1.0 with previous version 5.0.0 dated 2015-09-13

Title: Wrapper Algorithm for All Relevant Feature Selection
Description: An all relevant feature selection wrapper algorithm. It finds relevant features by comparing original attributes' importance with importance achievable at random, estimated using their permuted copies.
Author: Miron B. Kursa [aut, cre], Witold R. Rudnicki [aut]
Maintainer: Miron B. Kursa <M.Kursa@icm.edu.pl>

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Package admixturegraph updated to version 1.0.1 with previous version 1.0.0 dated 2016-06-13

Title: Admixture Graph Manipulation and Fitting
Description: Implements tools for building and visualising admixture graphs and for extracting equations from them. These equations can be compared to f- statistics obtained from data to test the consistency of a graph against data -- for example by comparing the sign of f_4-statistics with the signs predicted by the graph -- and graph parameters (edge lengths and admixture proportions) can be fitted to observed statistics.
Author: Thomas Mailund [cre, aut], Kalle Leppala [aut], Svend Nielsen [aut]
Maintainer: Thomas Mailund <mailund@birc.au.dk>

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Package neuralnet updated to version 1.33 with previous version 1.32 dated 2012-09-20

Title: Training of Neural Networks
Description: Training of neural networks using backpropagation, resilient backpropagation with (Riedmiller, 1994) or without weight backtracking (Riedmiller and Braun, 1993) or the modified globally convergent version by Anastasiadis et al. (2005). The package allows flexible settings through custom-choice of error and activation function. Furthermore, the calculation of generalized weights (Intrator O & Intrator N, 1993) is implemented.
Author: Stefan Fritsch [aut], Frauke Guenther [aut, cre], Marc Suling [ctb], Sebastian M. Mueller [ctb]
Maintainer: Frauke Guenther <guenther@leibniz-bips.de>

Diff between neuralnet versions 1.32 dated 2012-09-20 and 1.33 dated 2016-08-16

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Package mplot updated to version 0.7.8 with previous version 0.7.7 dated 2015-11-18

Title: Graphical Model Stability and Variable Selection Procedures
Description: Model stability and variable inclusion plots [Mueller and Welsh (2010, <doi:10.1111/j.1751-5823.2010.00108.x>); Murray, Heritier and Mueller (2013, <doi:10.1002/sim.5855>)] as well as the adaptive fence [Jiang et al. (2008, <doi:10.1214/07-AOS517>); Jiang et al. (2009, <doi:10.1016/j.spl.2008.10.014>)] for linear and generalised linear models.
Author: Garth Tarr [aut, cre], Samuel Mueller [aut], Alan Welsh [aut]
Maintainer: Garth Tarr <garth.tarr@gmail.com>

Diff between mplot versions 0.7.7 dated 2015-11-18 and 0.7.8 dated 2016-08-16

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Package rcbalance updated to version 1.8.3 with previous version 1.8.2 dated 2016-02-11

Title: Large, Sparse Optimal Matching with Refined Covariate Balance
Description: Tools for large, sparse optimal matching of treated units and control units in observational studies. Provisions are made for refined covariate balance constraints, which include fine and near-fine balance as special cases. Matches are optimal in the sense that they are computed as solutions to network optimization problems rather than greedy algorithms.
Author: Samuel D. Pimentel
Maintainer: Samuel D. Pimentel <spi@wharton.upenn.edu>

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Package PGEE updated to version 1.4 with previous version 1.3 dated 2016-07-30

Title: Penalized Generalized Estimating Equations in High-Dimension
Description: Fits penalized generalized estimating equations to longitudinal data with high-dimensional covariates.
Author: Gul Inan (Visiting scholar, University of Minnesota), Jianhui Zhou (Associate Professor, University of Virginia) and Lan Wang (Professor, University of Minnesota)
Maintainer: Gul Inan <inanx002@umn.edu>

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Package list updated to version 8.2 with previous version 8.1 dated 2016-07-27

Title: Statistical Methods for the Item Count Technique and List Experiment
Description: Allows researchers to conduct multivariate statistical analyses of survey data with list experiments. This survey methodology is also known as the item count technique or the unmatched count technique and is an alternative to the commonly used randomized response method. The package implements the methods developed by Imai (2011), Blair and Imai (2012), Blair, Imai, and Lyall (2013), Imai, Park, and Greene (2014), and Aronow, Coppock, Crawford, and Green (2015). This includes a Bayesian MCMC implementation of regression for the standard and multiple sensitive item list experiment designs and a random effects setup, a Bayesian MCMC hierarchical regression model with up to three hierarchical groups, the combined list experiment and endorsement experiment regression model, a joint model of the list experiment that enables the analysis of the list experiment as a predictor in outcome regression models, and a method for combining list experiments with direct questions. In addition, the package implements the statistical test that is designed to detect certain failures of list experiments, and a placebo test for the list experiment using data from direct questions.
Author: Graeme Blair [aut, cre], Kosuke Imai [aut, cre], Bethany Park [ctb], Alexander Coppock [ctb], Winston Chou [ctb]
Maintainer: Graeme Blair <graeme.blair@ucla.edu>

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Package boxr updated to version 0.3.3 with previous version 0.3.2 dated 2016-01-31

Title: Interface for the 'Box.com API'
Description: An R interface for the remote file hosting service 'Box' (<https://www.box.com/>). In addition to uploading and downloading files, this package includes functions which mirror base R operations for local files, (e.g. box_load(), box_save(), box_read(), box_setwd(), etc.), as well as 'git' style functions for entire directories (e.g. box_fetch(), box_push()).
Author: Brendan Rocks [aut, cre]
Maintainer: Brendan Rocks <foss@brendanrocks.com>

Diff between boxr versions 0.3.2 dated 2016-01-31 and 0.3.3 dated 2016-08-16

 DESCRIPTION                         |   25 ++---
 MD5                                 |   84 +++++++++---------
 NEWS.md                             |    2 
 R/boxr__internal_dir_comparison.R   |    2 
 R/boxr__internal_misc.R             |   19 +++-
 R/boxr__internal_package_homepage.R |    2 
 R/boxr__internal_update_upload.R    |    2 
 R/boxr__internal_verb_exit.R        |  160 ++++++++++++++++++------------------
 R/boxr_add_description.R            |    2 
 R/boxr_auth.R                       |    6 -
 R/boxr_delete_restore.R             |    2 
 R/boxr_dir_verbs.R                  |    6 -
 R/boxr_file_versions.R              |   30 +++++-
 R/boxr_misc.R                       |   17 ++-
 R/boxr_read.R                       |    2 
 R/boxr_s3_classes.R                 |  116 ++++++++++++++------------
 R/boxr_save_load.R                  |    2 
 R/boxr_search.R                     |    2 
 R/boxr_source.R                     |    2 
 R/boxr_upload_download.R            |    2 
 R/boxr_write.R                      |    2 
 build/vignette.rds                  |binary
 inst/doc/boxr.html                  |   35 ++++---
 man/box_add_description.Rd          |    2 
 man/box_auth.Rd                     |    4 
 man/box_auth_on_attach.Rd           |    2 
 man/box_delete_file.Rd              |    2 
 man/box_dir_create.Rd               |    2 
 man/box_dir_diff.Rd                 |    2 
 man/box_dl.Rd                       |    2 
 man/box_fetch.Rd                    |    2 
 man/box_ls.Rd                       |    2 
 man/box_previous_versions.Rd        |    2 
 man/box_read.Rd                     |    2 
 man/box_save.Rd                     |    2 
 man/box_search.Rd                   |    2 
 man/box_setwd.Rd                    |    2 
 man/box_source.Rd                   |    2 
 man/box_upload_new.Rd               |    2 
 man/box_write.Rd                    |    2 
 man/boxr-package.Rd                 |    2 
 man/boxr_S3_classes.Rd              |    2 
 man/boxr_options.Rd                 |    2 
 43 files changed, 315 insertions(+), 249 deletions(-)

More information about boxr at CRAN
Permanent link

Package bdots updated to version 0.1.9 with previous version 0.1.7 dated 2016-02-23

Title: Bootstrapped Differences of Time Series
Description: Analyze differences among time series curves with p-value adjustment for multiple comparisons introduced in Oleson et al (2015) <DOI:10.1177/0962280215607411>.
Author: Michael Seedorff, Jacob Oleson, Grant Brown, Joseph Cavanaugh, and Bob McMurray
Maintainer: Michael Seedorff <michael-seedorff@uiowa.edu>

Diff between bdots versions 0.1.7 dated 2016-02-23 and 0.1.9 dated 2016-08-16

 DESCRIPTION         |    8 ++++----
 MD5                 |   24 +++++++++++++-----------
 NAMESPACE           |    3 ++-
 R/doubleGaussBoot.r |    9 +++++++--
 R/logisticBoot.r    |    1 -
 R/printFits.r       |only
 R/writeCSV.r        |   47 +++++++++++++++++++++++++++++++++++++----------
 build/vignette.rds  |binary
 inst/doc/bdots.R    |   16 +++++++++++-----
 inst/doc/bdots.Rnw  |    7 +++++++
 inst/doc/bdots.pdf  |binary
 man/printFits.Rd    |only
 man/writeCSV.Rd     |    8 +++++---
 vignettes/bdots.Rnw |    7 +++++++
 14 files changed, 93 insertions(+), 37 deletions(-)

More information about bdots at CRAN
Permanent link


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