Title: Detecting Election Fraud from Irregularities in Vote-Share
Distributions
Description: Applies re-sampled kernel density method to detect vote fraud. It estimates the proportion of coarse vote-shares in the observed data relative to the null hypothesis of no fraud.
Author: Arturas Rozenas
Maintainer: Arturas Rozenas <ar199@nyu.edu>
Diff between spikes versions 1.0 dated 2016-09-06 and 1.1 dated 2016-09-21
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/plot.out.R | 12 +++++------- R/spikes-internal.R | 1 + man/plot.out.Rd | 5 ++++- 5 files changed, 18 insertions(+), 16 deletions(-)
Title: Interface to the 'Orcid.org' 'API'
Description: Client for the 'Orcid.org' 'API' (http://orcid.org/).
Functions included for searching for people, searching by 'DOI',
and searching by 'Orcid' 'ID'.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rorcid versions 0.2.2 dated 2016-02-09 and 0.3.0 dated 2016-09-21
rorcid-0.2.2/rorcid/R/truncmat.R |only rorcid-0.2.2/rorcid/man/type_summ.Rd |only rorcid-0.2.2/rorcid/tests/testthat/test-trunc.R |only rorcid-0.3.0/rorcid/DESCRIPTION | 11 rorcid-0.3.0/rorcid/MD5 | 62 - rorcid-0.3.0/rorcid/NAMESPACE | 24 rorcid-0.3.0/rorcid/NEWS.md | 30 rorcid-0.3.0/rorcid/R/as.orcid.R | 78 - rorcid-0.3.0/rorcid/R/browse.R | 2 rorcid-0.3.0/rorcid/R/deprecated-defunct.R |only rorcid-0.3.0/rorcid/R/identifiers.R | 7 rorcid-0.3.0/rorcid/R/orcid.r | 151 +-- rorcid-0.3.0/rorcid/R/orcid_doi.r | 38 rorcid-0.3.0/rorcid/R/orcid_id.r | 40 rorcid-0.3.0/rorcid/R/rorcid-package.R | 13 rorcid-0.3.0/rorcid/R/works.R | 23 rorcid-0.3.0/rorcid/R/zzz.R | 10 rorcid-0.3.0/rorcid/README.md | 786 ++++++------------ rorcid-0.3.0/rorcid/build |only rorcid-0.3.0/rorcid/inst |only rorcid-0.3.0/rorcid/man/as.orcid.Rd | 31 rorcid-0.3.0/rorcid/man/identifiers.Rd | 1 rorcid-0.3.0/rorcid/man/orcid.Rd | 123 +- rorcid-0.3.0/rorcid/man/orcid_doi.Rd | 22 rorcid-0.3.0/rorcid/man/orcid_id.Rd | 31 rorcid-0.3.0/rorcid/man/rorcid-defunct.Rd |only rorcid-0.3.0/rorcid/man/summary.or_cid-defunct.Rd |only rorcid-0.3.0/rorcid/man/works.Rd | 22 rorcid-0.3.0/rorcid/tests/testthat/test-as.orcid.R | 26 rorcid-0.3.0/rorcid/tests/testthat/test-identifiers.R | 4 rorcid-0.3.0/rorcid/tests/testthat/test-orcid.R | 22 rorcid-0.3.0/rorcid/tests/testthat/test-orcid_doi.R | 22 rorcid-0.3.0/rorcid/tests/testthat/test-orcid_id.R | 36 rorcid-0.3.0/rorcid/tests/testthat/test-works.R | 4 rorcid-0.3.0/rorcid/vignettes |only 35 files changed, 764 insertions(+), 855 deletions(-)
Title: Online Principal Component Analysis
Description: Online PCA for multivariate and functional data using perturbation methods, low-rank incremental methods, and stochastic optimization methods.
Author: David Degras [aut, cre], Herve Cardot [ctb]
Maintainer: David Degras <ddegrasv@gmail.com>
Diff between onlinePCA versions 1.3 dated 2015-10-29 and 1.3.1 dated 2016-09-21
DESCRIPTION | 12 ++++++------ MD5 | 12 ++++++------ NAMESPACE | 2 +- man/batchpca.Rd | 2 +- man/onlinePCA-package.Rd | 2 +- src/Makevars | 26 -------------------------- src/Makevars.win | 3 ++- 7 files changed, 17 insertions(+), 42 deletions(-)
Title: Nested Association Mapping
Description: Designed for association studies in nested association mapping (NAM) panels, also handling experimental and random panels. It includes tools for genome-wide associations of multiple populations, marker quality control, population genetics analysis, genome-wide prediction, solving mixed models and finding variance components through likelihood and Bayesian methods.
Author: Alencar Xavier, William Muir, Katy Rainey, Shizhong Xu.
Maintainer: Alencar Xavier <alenxav@gmail.com>
Diff between NAM versions 1.4.7 dated 2016-09-14 and 1.4.8 dated 2016-09-21
DESCRIPTION | 10 - MD5 | 47 +++-- R/RcppExports.R | 26 ++- R/gmm.R | 14 - R/snp.R | 6 R/wgr.R | 256 ++++++++++++++---------------- inst/add/cvNAM.R | 46 +++-- inst/add/modelSelect.R | 361 ++++++++++++------------------------------- inst/add/sparseGMM.R | 14 - inst/doc/gwa_description.pdf |binary inst/doc/vignette1.Rmd | 20 ++ inst/doc/vignette1.html | 24 ++ inst/doc/vignette2.html | 4 man/Internals.Rd | 11 + man/NAM-package.Rd | 4 man/gibbs.Rd | 4 man/gmm.Rd | 4 man/reml.Rd | 2 man/wgr.Rd | 11 - src/KMUP.cpp | 56 +++--- src/KMUP2.cpp |only src/RcppExports.cpp | 151 +++++++++++++---- src/emBA.cpp |only src/emBB.cpp |only src/emBC.cpp |only src/emRR.cpp |only vignettes/vignette1.Rmd | 20 ++ 27 files changed, 549 insertions(+), 542 deletions(-)
Title: Extractive Summarization of Text with the LexRank Algorithm
Description: An R implementation of the LexRank algorithm described by G. Erkan and D. R. Radev (2004) <DOI:10.1613/jair.1523>.
Author: Adam Spannbauer <spannbaueradam@gmail.com>
Maintainer: Adam Spannbauer <spannbaueradam@gmail.com>
Diff between lexRankr versions 0.1.0 dated 2016-07-28 and 0.2.0 dated 2016-09-21
DESCRIPTION | 7 ++++--- LICENSE | 2 +- MD5 | 18 ++++++++++-------- NEWS.md |only R/lexRank.R | 5 +++-- R/lexRankFromSimil.R | 1 + R/sentenceSimil.R | 11 ++++++++--- R/tokenize.R | 2 +- README.md |only man/lexRank.Rd | 9 ++++++--- man/sentenceSimil.Rd | 4 ++-- 11 files changed, 36 insertions(+), 23 deletions(-)
Title: Generalised Linear Mixed Models with BUGS and JAGS
Description: Automates running Generalized Linear Mixed Models, including
spatial models, with WinBUGS, OpenBUGS and JAGS. Models are specified with
formulas, with the package writings model files, arranging unbalanced data
in ragged arrays, and creating starting values. The model is re-parameterized,
and functions are provided for converting model outputs to the original
parameterization.
Author: Patrick Brown, Lutong Zhou
Maintainer: Patrick Brown <patrick.brown@utoronto.ca>
Diff between glmmBUGS versions 2.3 dated 2014-01-02 and 2.4.0 dated 2016-09-21
glmmBUGS-2.3/glmmBUGS/man/rongelapResult.Rd |only glmmBUGS-2.4.0/glmmBUGS/DESCRIPTION | 33 +++++---- glmmBUGS-2.4.0/glmmBUGS/MD5 | 60 ++++++++++------ glmmBUGS-2.4.0/glmmBUGS/NAMESPACE | 27 ++++--- glmmBUGS-2.4.0/glmmBUGS/R/addSpatial.R | 5 - glmmBUGS-2.4.0/glmmBUGS/R/binToBinom.R | 1 glmmBUGS-2.4.0/glmmBUGS/R/checkChain.R | 5 - glmmBUGS-2.4.0/glmmBUGS/R/cholInvArray.R | 1 glmmBUGS-2.4.0/glmmBUGS/R/getDesignMatrix.R | 13 +-- glmmBUGS-2.4.0/glmmBUGS/R/getRaggedSeq.R | 1 glmmBUGS-2.4.0/glmmBUGS/R/getStartingValues.R | 3 glmmBUGS-2.4.0/glmmBUGS/R/glmmBUGS.R | 3 glmmBUGS-2.4.0/glmmBUGS/R/glmmPQLstrings.R | 10 +- glmmBUGS-2.4.0/glmmBUGS/R/mergeBugsData.R |only glmmBUGS-2.4.0/glmmBUGS/R/restoreParams.R | 13 ++- glmmBUGS-2.4.0/glmmBUGS/R/startingFunction.R | 1 glmmBUGS-2.4.0/glmmBUGS/R/summaryChain.R | 5 - glmmBUGS-2.4.0/glmmBUGS/R/winBugsRaggedArray.R | 1 glmmBUGS-2.4.0/glmmBUGS/R/writeBugsModel.R | 1 glmmBUGS-2.4.0/glmmBUGS/build |only glmmBUGS-2.4.0/glmmBUGS/inst |only glmmBUGS-2.4.0/glmmBUGS/man/glmmBUGS.Rd | 79 +++++++++++++--------- glmmBUGS-2.4.0/glmmBUGS/man/mergeBugsData.Rd |only glmmBUGS-2.4.0/glmmBUGS/man/popDataAdjMat.Rd | 20 +++-- glmmBUGS-2.4.0/glmmBUGS/man/rongelapUTM.Rd | 71 +++++++++++++++---- glmmBUGS-2.4.0/glmmBUGS/man/winBugsRaggedArray.Rd | 2 glmmBUGS-2.4.0/glmmBUGS/man/writeBugsModel.Rd | 13 ++- glmmBUGS-2.4.0/glmmBUGS/tests/bym.R |only glmmBUGS-2.4.0/glmmBUGS/tests/openbugs.R | 78 +++++++++++---------- glmmBUGS-2.4.0/glmmBUGS/vignettes |only 30 files changed, 281 insertions(+), 165 deletions(-)
Title: Image Registration Using the NiftyReg Library
Description: Provides an R interface to the NiftyReg image registration tools
<http://sourceforge.net/projects/niftyreg/>. Linear and nonlinear registration
are supported, in two and three dimensions.
Author: Jon Clayden, based on original code by Marc Modat, Pankaj Daga and
others
Maintainer: Jon Clayden <code@clayden.org>
Diff between RNiftyReg versions 2.3.0 dated 2016-05-06 and 2.4.0 dated 2016-09-21
RNiftyReg-2.3.0/RNiftyReg/R/xform.R |only RNiftyReg-2.3.0/RNiftyReg/man/dumpNifti.Rd |only RNiftyReg-2.3.0/RNiftyReg/man/internalImage.Rd |only RNiftyReg-2.3.0/RNiftyReg/man/ndim.Rd |only RNiftyReg-2.3.0/RNiftyReg/man/pixdim.Rd |only RNiftyReg-2.3.0/RNiftyReg/man/updateNifti.Rd |only RNiftyReg-2.3.0/RNiftyReg/man/voxelToWorld.Rd |only RNiftyReg-2.3.0/RNiftyReg/man/writeNifti.Rd |only RNiftyReg-2.3.0/RNiftyReg/man/xform.Rd |only RNiftyReg-2.3.0/RNiftyReg/src/NiftiImage.cpp |only RNiftyReg-2.3.0/RNiftyReg/src/NiftiImage.h |only RNiftyReg-2.3.0/RNiftyReg/src/niftilib |only RNiftyReg-2.3.0/RNiftyReg/src/print.h |only RNiftyReg-2.3.0/RNiftyReg/src/zlib |only RNiftyReg-2.3.0/RNiftyReg/src/znzlib |only RNiftyReg-2.3.0/RNiftyReg/tests/testthat/test-05-nifti.R |only RNiftyReg-2.3.0/RNiftyReg/tests/testthat/test-10-xform.R |only RNiftyReg-2.4.0/RNiftyReg/DESCRIPTION | 13 RNiftyReg-2.4.0/RNiftyReg/MD5 | 107 +---- RNiftyReg-2.4.0/RNiftyReg/NAMESPACE | 12 RNiftyReg-2.4.0/RNiftyReg/NEWS | 12 RNiftyReg-2.4.0/RNiftyReg/R/affine.R | 10 RNiftyReg-2.4.0/RNiftyReg/R/image.R | 196 ---------- RNiftyReg-2.4.0/RNiftyReg/R/nifti.R | 106 ----- RNiftyReg-2.4.0/RNiftyReg/R/niftyreg.R | 28 - RNiftyReg-2.4.0/RNiftyReg/R/zzz.R | 38 + RNiftyReg-2.4.0/RNiftyReg/README.md | 53 -- RNiftyReg-2.4.0/RNiftyReg/man/niftyreg.Rd | 16 RNiftyReg-2.4.0/RNiftyReg/man/niftyreg.linear.Rd | 16 RNiftyReg-2.4.0/RNiftyReg/man/niftyreg.nonlinear.Rd | 16 RNiftyReg-2.4.0/RNiftyReg/man/readNifti.Rd | 9 RNiftyReg-2.4.0/RNiftyReg/man/reexports.Rd |only RNiftyReg-2.4.0/RNiftyReg/src/AffineMatrix.h | 2 RNiftyReg-2.4.0/RNiftyReg/src/DeformationField.h | 3 RNiftyReg-2.4.0/RNiftyReg/src/Makevars | 8 RNiftyReg-2.4.0/RNiftyReg/src/RNifti.cpp |only RNiftyReg-2.4.0/RNiftyReg/src/aladin.h | 2 RNiftyReg-2.4.0/RNiftyReg/src/f3d.h | 3 RNiftyReg-2.4.0/RNiftyReg/src/main.cpp | 186 ++------- RNiftyReg-2.4.0/RNiftyReg/src/reg-lib/ConvolutionKernel.h | 4 RNiftyReg-2.4.0/RNiftyReg/src/reg-lib/Kernels.h | 4 RNiftyReg-2.4.0/RNiftyReg/src/reg-lib/ResampleImageKernel.h | 4 RNiftyReg-2.4.0/RNiftyReg/src/reg-lib/cpu/CPUBlockMatchingKernel.h | 4 RNiftyReg-2.4.0/RNiftyReg/src/reg-lib/cpu/CPUOptimiseKernel.h | 4 RNiftyReg-2.4.0/RNiftyReg/src/reg-lib/cpu/_reg_KLdivergence.h | 4 RNiftyReg-2.4.0/RNiftyReg/src/reg-lib/cpu/_reg_femTrans.h | 4 RNiftyReg-2.4.0/RNiftyReg/src/reg-lib/cpu/_reg_globalTrans.h | 4 RNiftyReg-2.4.0/RNiftyReg/src/reg-lib/cpu/_reg_maths.cpp | 16 RNiftyReg-2.4.0/RNiftyReg/src/reg-lib/cpu/_reg_maths.h | 4 RNiftyReg-2.4.0/RNiftyReg/src/reg-lib/cpu/_reg_resampling.h | 4 50 files changed, 261 insertions(+), 631 deletions(-)
Title: Add a Scale Bar to 'OpenStreetMap' Plots
Description: Functionality to handle and project lat-long coordinates, easily download background maps
and add a correct scale bar to 'OpenStreetMap' plots in any map projection.
Author: Berry Boessenkool
Maintainer: Berry Boessenkool <berry-b@gmx.de>
Diff between OSMscale versions 0.2.9 dated 2016-08-21 and 0.3.5 dated 2016-09-21
DESCRIPTION | 10 +-- MD5 | 40 +++++++------- NAMESPACE | 3 - NEWS | 15 ++++- R/OSMscale-package.R | 5 + R/checkLL.R | 46 +++++++++------- R/degree.R | 22 +++---- R/earthDist.R | 52 ++++++++++-------- R/pointsMap.R | 74 ++++++++++++++------------ R/proj.R | 2 R/projectPoints.R | 29 +++++++--- R/scaleBar.R | 135 ++++++++++++++++++++++++++---------------------- R/triangleArea.R | 13 ++-- README.md | 43 ++++++--------- man/OSMscale-package.Rd | 5 + man/checkLL.Rd | 26 ++++++--- man/degree.Rd | 16 ++--- man/earthDist.Rd | 25 +++++--- man/pointsMap.Rd | 33 ++++++----- man/projectPoints.Rd | 22 ++++--- man/scaleBar.Rd | 25 ++++---- 21 files changed, 359 insertions(+), 282 deletions(-)
Title: Fast Truncated SVD, PCA and Symmetric Eigendecomposition for
Large Dense and Sparse Matrices
Description: Fast and memory efficient methods for truncated singular and
eigenvalue decompositions and principal component analysis of large sparse or
dense matrices.
Author: Jim Baglama [aut, cph],
Lothar Reichel [aut, cph],
B. W. Lewis [aut, cre, cph]
Maintainer: B. W. Lewis <blewis@illposed.net>
Diff between irlba versions 2.1.1 dated 2016-08-27 and 2.1.2 dated 2016-09-21
DESCRIPTION | 8 ++--- MD5 | 26 +++++++++-------- R/eigen.R | 3 ++ R/irlba.R | 48 +++++++++++++++++++++++--------- README.md | 28 ++++++++++-------- build/vignette.rds |binary demo |only inst/doc/irlba.pdf |binary man/irlba.Rd | 20 ++++++++++--- man/partial_eigen.Rd | 3 ++ src/irlb.c | 76 ++++++++++++++++++++++++++++++++++++++------------- src/utility.c | 9 +++--- tests/edge.R | 32 ++++++++++++++++++++- tests/test.R | 30 +++++++++++++++----- 14 files changed, 206 insertions(+), 77 deletions(-)
Title: Exploratory and Descriptive Event-Based Data Analysis
Description: Functions for exploratory and descriptive analysis of event based
data. Can be used to import and export Xes-files, the IEEE eXtensible Event
Stream standard. Provides methods for describing and selecting process data,
and for preparing event log data for process mining.
Author: Gert Janssenswillen
Maintainer: Gert Janssenswillen <gert.janssenswillen@uhasselt.be>
Diff between edeaR versions 0.4.3 dated 2016-08-25 and 0.4.4 dated 2016-09-21
DESCRIPTION | 8 - MD5 | 54 ++++--- NAMESPACE | 5 R/activities.R | 2 R/activity_specialization.R | 5 R/activity_type_frequency_resource.R | 4 R/edeaR.R | 2 R/eventlog.R | 10 - R/filter_case.R |only R/filter_resource.R |only R/mapping.R | 21 +- R/n_resources.R | 2 R/print.mapping.R |only R/re_map.R |only R/traces_light.R | 3 README.md | 2 inst/doc/descriptives.html | 127 ++++++++++------- inst/doc/potential.html | 247 +++++++++++++++++------------------ inst/doc/preprocessing.R | 4 inst/doc/preprocessing.Rmd | 4 inst/doc/preprocessing.html | 67 ++++----- inst/doc/selection.R | 6 inst/doc/selection.Rmd | 6 inst/doc/selection.html | 125 ++++++++++------- man/activities.Rd | 2 man/activity_specialization.Rd | 4 man/eventlog.Rd | 7 man/filter_case.Rd |only man/filter_resource.Rd |only man/print.eventlog_mapping.Rd |only man/re_map.Rd |only vignettes/preprocessing.Rmd | 4 32 files changed, 387 insertions(+), 334 deletions(-)
Title: Distance Covariance and Correlation for Time Series Analysis
Description: Computing and plotting the distance covariance and correlation
function of a univariate or a multivariate time series. Both versions
of biased and unbiased estimators of distance covariance and correlation are provided.
Test statistics for testing pairwise independence are also implemented.
Some data sets are also included.
Author: Maria Pitsillou [aut, cre],
Konstantinos Fokianos [aut]
Maintainer: Maria Pitsillou <pitsillou.maria@ucy.ac.cy>
Diff between dCovTS versions 1.0 dated 2016-03-08 and 1.1 dated 2016-09-21
dCovTS-1.0/dCovTS/R/mADCFplot.r |only dCovTS-1.1/dCovTS/DESCRIPTION | 14 +++--- dCovTS-1.1/dCovTS/MD5 | 67 ++++++++++++++++--------------- dCovTS-1.1/dCovTS/NAMESPACE | 3 - dCovTS-1.1/dCovTS/R/ADCF.R | 16 ++++--- dCovTS-1.1/dCovTS/R/ADCFplot.R | 39 +++++++++--------- dCovTS-1.1/dCovTS/R/ADCV.R | 18 +++++--- dCovTS-1.1/dCovTS/R/ATilde.R | 3 - dCovTS-1.1/dCovTS/R/OrdinaryBoot.R |only dCovTS-1.1/dCovTS/R/OrdinaryBoot1.R |only dCovTS-1.1/dCovTS/R/OrdinaryBoot2.R |only dCovTS-1.1/dCovTS/R/OrdinaryBootCV.R |only dCovTS-1.1/dCovTS/R/RbootCV.R | 33 +++++---------- dCovTS-1.1/dCovTS/R/SubsCV.R | 15 ++++--- dCovTS-1.1/dCovTS/R/TstarBoot.R | 41 +++++++------------ dCovTS-1.1/dCovTS/R/TstarBoot1.R | 7 +-- dCovTS-1.1/dCovTS/R/TstarBoot2.R | 12 ++--- dCovTS-1.1/dCovTS/R/UnivTest.R | 44 ++++++++++++-------- dCovTS-1.1/dCovTS/R/crossDist.R | 10 ++-- dCovTS-1.1/dCovTS/R/kernelFun.R | 6 +- dCovTS-1.1/dCovTS/R/mADCF.R | 11 +++-- dCovTS-1.1/dCovTS/R/mADCFplot.R |only dCovTS-1.1/dCovTS/R/mADCFtest.R | 23 +++++++--- dCovTS-1.1/dCovTS/R/mADCV.R | 10 +++- dCovTS-1.1/dCovTS/R/mADCVtest.R | 23 +++++++--- dCovTS-1.1/dCovTS/R/mOrdinaryBootCV.R |only dCovTS-1.1/dCovTS/R/mRbootCV.R | 8 +-- dCovTS-1.1/dCovTS/man/ADCF.Rd | 49 ++++++++++++++--------- dCovTS-1.1/dCovTS/man/ADCFplot.Rd | 43 +++++++++++--------- dCovTS-1.1/dCovTS/man/ADCV.Rd | 68 +++++++++++++++++++------------- dCovTS-1.1/dCovTS/man/UnivTest.Rd | 37 ++++++++++++++--- dCovTS-1.1/dCovTS/man/dCovTS-package.Rd | 43 ++++++++++++++------ dCovTS-1.1/dCovTS/man/kernelFun.Rd | 4 - dCovTS-1.1/dCovTS/man/mADCF.Rd | 42 ++++++++++++++----- dCovTS-1.1/dCovTS/man/mADCFplot.Rd | 38 +++++++++++++---- dCovTS-1.1/dCovTS/man/mADCFtest.Rd | 40 ++++++++++++++---- dCovTS-1.1/dCovTS/man/mADCV.Rd | 35 +++++++++++----- dCovTS-1.1/dCovTS/man/mADCVtest.Rd | 42 +++++++++++++------ 38 files changed, 523 insertions(+), 321 deletions(-)
Title: Sequential Full Factorial-Based Latin Hypercube Design
Description: Gives design points from a sequential full factorial-based
Latin hypercube design, as described in Duan, Ankenman, Sanchez,
and Sanchez (2015, Technometrics,
<doi:10.1080/00401706.2015.1108233>).
Author: Collin Erickson
Maintainer: Collin Erickson <collinberickson@gmail.com>
Diff between sFFLHD versions 0.1.0 dated 2016-08-27 and 0.1.1 dated 2016-09-21
DESCRIPTION | 9 MD5 | 14 - NAMESPACE | 17 - NEWS.md | 16 + R/sFFLHD.R | 505 ++++++++++++++++++++++++++-------------------------- README.md | 42 ++-- man/sFFLHD-class.Rd | 138 +++++++------- man/split_matrix.Rd | 64 +++--- 8 files changed, 410 insertions(+), 395 deletions(-)
Title: R API for Mixpanel
Description: Provides an interface to many endpoints of Mixpanel's Data Export, Engage and JQL API. The R functions allow for event and profile data export as well as for segmentation, retention and addiction analysis. Results are always parsed into convenient R objects. Furthermore it is possible to load and update profiles.
Author: Meinhard Ploner [aut, cre, cph],
ProSiebenSat.1 Digital GmbH [cph]
Maintainer: Meinhard Ploner <meinhard.ploner@gmail.net>
Diff between RMixpanel versions 0.4-0 dated 2016-08-11 and 0.4-1 dated 2016-09-21
RMixpanel-0.4-0/RMixpanel/R/mixpanelGetDataDeprecated.R |only RMixpanel-0.4-1/RMixpanel/DESCRIPTION | 18 ++-- RMixpanel-0.4-1/RMixpanel/LICENSE | 2 RMixpanel-0.4-1/RMixpanel/MD5 | 13 +-- RMixpanel-0.4-1/RMixpanel/R/mixpanelJQLQuery.R | 50 +++++++++--- RMixpanel-0.4-1/RMixpanel/README.md | 62 ++++++++++++++-- RMixpanel-0.4-1/RMixpanel/build/partial.rdb |binary RMixpanel-0.4-1/RMixpanel/man/mixpanelJQLQuery.Rd | 4 - 8 files changed, 115 insertions(+), 34 deletions(-)
Title: Calculation of the Integrated Flow of Particles Between Polygons
Description: Calculate the flow of particles between polygons by two integration methods: integration by a cubature method and integration on a grid of points.
Author: Annie Bouvier, Kien Kieu, Kasia Adamczyk, and Herve Monod
Maintainer: Annie Bouvier <Annie.Bouvier@inra.fr>
Diff between RCALI versions 0.2-15 dated 2015-01-13 and 0.2-17 dated 2016-09-21
RCALI-0.2-15/RCALI/LICENSE |only RCALI-0.2-17/RCALI/DESCRIPTION | 16 +-- RCALI-0.2-17/RCALI/LICENSE.note |only RCALI-0.2-17/RCALI/MD5 | 101 +++++++++++++++++++++--- RCALI-0.2-17/RCALI/NAMESPACE | 2 RCALI-0.2-17/RCALI/NEWS | 13 +++ RCALI-0.2-17/RCALI/inst/doc/RCALIvignette.pdf |binary RCALI-0.2-17/RCALI/inst/doc/RCALIvignette.tex |only RCALI-0.2-17/RCALI/inst/doc/VignetteDir |only RCALI-0.2-17/RCALI/inst/doc/art_ems2008.pdf |binary RCALI-0.2-17/RCALI/man/RCALI-package.Rd | 2 RCALI-0.2-17/RCALI/src/Vector.cc | 1 RCALI-0.2-17/RCALI/tests/cte.Rout.save | 9 -- RCALI-0.2-17/RCALI/tests/disppollen.Rout.save | 9 -- RCALI-0.2-17/RCALI/tests/dispseed.Rout.save | 9 -- RCALI-0.2-17/RCALI/tests/fdispersions.Rout.save | 9 -- 16 files changed, 130 insertions(+), 41 deletions(-)
More information about neuropsychology at CRAN
Permanent link
Title: Multi-Parameter Regression (MPR)
Description: Package for fitting Multi-Parameter Regression (MPR) models to right-censored survival data. These are flexible parametric regression models which extend standard models, for example, proportional hazards.
Author: Kevin Burke
Maintainer: Kevin Burke <kevin.burke@ul.ie>
Diff between mpr versions 1.0.2 dated 2016-08-11 and 1.0.3 dated 2016-09-21
DESCRIPTION | 10 +++++----- MD5 | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-)
Title: Penalized Likelihood Estimation and Dynamic Prediction under the
Joint Frailty-Copula Models Between Tumour Progression and
Death for Meta-Analysis
Description: Perform the Cox regression and dynamic prediction under the joint frailty-copula model between tumour progression and death for meta-analysis.
The method is applicable for meta-analytic data combining several studies. The data should have information on both terminal event time (time-to-death) and non-terminal event time (time-to-tumour progression).
Author: Takeshi Emura
Maintainer: Takeshi Emura <takeshiemura@gmail.com>
Diff between joint.Cox versions 2.6 dated 2016-06-04 and 2.7 dated 2016-09-21
DESCRIPTION | 8 ++++---- MD5 | 12 +++++++----- R/F.prediction.R |only R/F.windows.R | 6 +++--- man/F.prediction.Rd |only man/F.window.Rd | 12 +++++++----- man/F.windows.Rd | 13 ++++++++----- man/joint.Cox-package.Rd | 7 +++++-- 8 files changed, 34 insertions(+), 24 deletions(-)
Title: Event History Analysis
Description: Sampling of risk sets in Cox regression, selections in
the Lexis diagram, bootstrapping. Parametric proportional
hazards fitting with left truncation and right censoring for
common families of distributions, piecewise constant hazards,
and discrete models. AFT regression for left truncated and
right censored data. Binary and Poisson regression for
clustered data, fixed and random effects with bootstrapping.
Author: Göran Broström [aut, cre]
Maintainer: Göran Broström <goran.brostrom@umu.se>
Diff between eha versions 2.4-3 dated 2015-05-05 and 2.4-4 dated 2016-09-21
ChangeLog | 10 +++++ DESCRIPTION | 8 ++-- MD5 | 16 ++++----- R/Pch.R | 2 - R/plot.coxreg.R | 16 +++++++-- R/plot.phreg.R | 88 +++++++++++++++++++++++++++++++++++++--------------- man/plot.phreg.Rd | 11 ++++-- man/plot.weibreg.Rd | 5 +- man/weibreg.Rd | 10 +++-- 9 files changed, 114 insertions(+), 52 deletions(-)
Title: Bagging Whole-Genome Regression
Description: Designed for whole-genome regressions using Bayesian models fitted via EM or Gibbs sampling with optional resampling techniques (Bagging) and polygenic term with reduced dimensionality.
Author: Alencar Xavier, William Muir, Katy Rainey.
Maintainer: Alencar Xavier <alenxav@gmail.com>
Diff between bWGR versions 1.3.1 dated 2016-03-17 and 1.3.2 dated 2016-09-21
bWGR-1.3.1/bWGR/R/bmen.R |only bWGR-1.3.1/bWGR/R/wGELA.R |only bWGR-1.3.1/bWGR/R/wgr2.R |only bWGR-1.3.1/bWGR/inst/doc/BagMEN.pdf |only bWGR-1.3.1/bWGR/man/bmen.Rd |only bWGR-1.3.1/bWGR/man/wgr2.Rd |only bWGR-1.3.2/bWGR/DESCRIPTION | 10 - bWGR-1.3.2/bWGR/MD5 | 35 +++--- bWGR-1.3.2/bWGR/NAMESPACE | 4 bWGR-1.3.2/bWGR/R/RcppExports.R | 26 +++- bWGR-1.3.2/bWGR/R/ben.R |only bWGR-1.3.2/bWGR/R/mkr.R | 12 +- bWGR-1.3.2/bWGR/R/wgr.R | 193 ++++++++---------------------------- bWGR-1.3.2/bWGR/man/bWGR.Rd | 10 - bWGR-1.3.2/bWGR/man/ben.Rd |only bWGR-1.3.2/bWGR/man/em.Rd |only bWGR-1.3.2/bWGR/man/tpod.Rd | 1 bWGR-1.3.2/bWGR/man/wgr.Rd | 38 ++----- bWGR-1.3.2/bWGR/src/KMUP.cpp | 52 +++++---- bWGR-1.3.2/bWGR/src/KMUP2.cpp | 78 ++++++++------ bWGR-1.3.2/bWGR/src/RcppExports.cpp | 102 +++++++++++++++---- bWGR-1.3.2/bWGR/src/emBA.cpp |only bWGR-1.3.2/bWGR/src/emBB.cpp |only bWGR-1.3.2/bWGR/src/emBC.cpp |only bWGR-1.3.2/bWGR/src/emRR.cpp |only 25 files changed, 279 insertions(+), 282 deletions(-)
Title: Gradient Boosting
Description: Functional gradient descent algorithm for a variety of convex and non-convex loss functions, for both classical and robust regression and classification problems.
Author: Zhu Wang [aut, cre],
Torsten Hothorn [ctb]
Maintainer: Zhu Wang <zwang@connecticutchildrens.org>
Diff between bst versions 0.3-13 dated 2016-02-28 and 0.3-14 dated 2016-09-21
DESCRIPTION | 12 MD5 | 56 +- NAMESPACE | 6 NEWS | 7 R/bst.R | 178 +++++- R/mbst.R | 1049 +++++++++++++++++++-------------------- R/rbst.R | 42 + R/rmbst.R | 36 - build/vignette.rds |binary inst/CITATION |only inst/doc/cancer.R |only inst/doc/cancer.Rnw |only inst/doc/cancer.pdf |only inst/doc/index.html | 13 inst/doc/khan.pdf |binary inst/doc/mcl.pdf |binary inst/doc/pros.pdf |binary inst/doc/static_cancer.pdf |only inst/doc/static_cancer.pdf.asis |only man/bfunc.Rd |only man/bst-internal.Rd | 1 man/bst.Rd | 7 man/bst_control.Rd | 11 man/cv.bst.Rd | 7 man/cv.mbst.Rd | 2 man/cv.rbst.Rd | 6 man/cv.rmbst.Rd | 6 man/evalerr.Rd |only man/mbst.Rd | 4 man/rbst.Rd | 10 man/rmbst.Rd | 8 vignettes/bst.bib | 52 + vignettes/cancer.Rnw |only vignettes/static_cancer.pdf.asis |only 34 files changed, 862 insertions(+), 651 deletions(-)
Title: Function Collection Related to Plotting and Hydrology
Description: Draw horizontal histograms, color scattered points by 3rd dimension,
enhance date- and log-axis plots, zoom in X11 graphics,
use the unit hydrograph in a linear storage cascade, convert lists to data.frames,
fit multiple functions by regression (power, reciprocal, exponential, logarithmic,
polynomial, rational).
Author: Berry Boessenkool
Maintainer: Berry Boessenkool <berry-b@gmx.de>
Diff between berryFunctions versions 1.11.0 dated 2016-08-18 and 1.12.2 dated 2016-09-21
berryFunctions-1.11.0/berryFunctions/R/nse.R |only berryFunctions-1.11.0/berryFunctions/R/randomPoints.R |only berryFunctions-1.11.0/berryFunctions/R/rmse.R |only berryFunctions-1.11.0/berryFunctions/R/rsquare.R |only berryFunctions-1.11.0/berryFunctions/R/triangleArea.R |only berryFunctions-1.11.0/berryFunctions/man/nse.Rd |only berryFunctions-1.11.0/berryFunctions/man/randomPoints.Rd |only berryFunctions-1.11.0/berryFunctions/man/rmse.Rd |only berryFunctions-1.11.0/berryFunctions/man/rsquare.Rd |only berryFunctions-1.11.0/berryFunctions/man/triangleArea.Rd |only berryFunctions-1.12.2/berryFunctions/DESCRIPTION | 8 berryFunctions-1.12.2/berryFunctions/MD5 | 90 +-- berryFunctions-1.12.2/berryFunctions/NAMESPACE | 8 berryFunctions-1.12.2/berryFunctions/NEWS | 17 berryFunctions-1.12.2/berryFunctions/R/betaPlot.R | 3 berryFunctions-1.12.2/berryFunctions/R/checkFile.R | 15 berryFunctions-1.12.2/berryFunctions/R/classify.R | 3 berryFunctions-1.12.2/berryFunctions/R/colPoints.R | 12 berryFunctions-1.12.2/berryFunctions/R/createDoc.R | 2 berryFunctions-1.12.2/berryFunctions/R/dataDWD.R | 62 +- berryFunctions-1.12.2/berryFunctions/R/getColumn.R |only berryFunctions-1.12.2/berryFunctions/R/getName.R |only berryFunctions-1.12.2/berryFunctions/R/gof.R |only berryFunctions-1.12.2/berryFunctions/R/logSpaced.R | 3 berryFunctions-1.12.2/berryFunctions/R/mReg.R | 23 berryFunctions-1.12.2/berryFunctions/R/normPlot.R | 4 berryFunctions-1.12.2/berryFunctions/R/quantileBands.R | 3 berryFunctions-1.12.2/berryFunctions/R/seasonality.R | 244 ++++++-- berryFunctions-1.12.2/berryFunctions/R/seqPal.R | 22 berryFunctions-1.12.2/berryFunctions/R/smallPlot.R | 2 berryFunctions-1.12.2/berryFunctions/R/sortDF.R | 14 berryFunctions-1.12.2/berryFunctions/R/spiralDate.R | 16 berryFunctions-1.12.2/berryFunctions/R/textField.R | 3 berryFunctions-1.12.2/berryFunctions/R/traceCall.R |only berryFunctions-1.12.2/berryFunctions/build/vignette.rds |binary berryFunctions-1.12.2/berryFunctions/inst/doc/berryFunctions.R | 24 berryFunctions-1.12.2/berryFunctions/inst/doc/berryFunctions.Rmd | 33 - berryFunctions-1.12.2/berryFunctions/inst/doc/berryFunctions.html | 288 +++++----- berryFunctions-1.12.2/berryFunctions/man/betaPlot.Rd | 3 berryFunctions-1.12.2/berryFunctions/man/checkFile.Rd | 4 berryFunctions-1.12.2/berryFunctions/man/createDoc.Rd | 2 berryFunctions-1.12.2/berryFunctions/man/dataDWD.Rd | 60 +- berryFunctions-1.12.2/berryFunctions/man/getColumn.Rd |only berryFunctions-1.12.2/berryFunctions/man/getName.Rd |only berryFunctions-1.12.2/berryFunctions/man/gof.Rd |only berryFunctions-1.12.2/berryFunctions/man/mReg.Rd | 9 berryFunctions-1.12.2/berryFunctions/man/normPlot.Rd | 4 berryFunctions-1.12.2/berryFunctions/man/quantileBands.Rd | 3 berryFunctions-1.12.2/berryFunctions/man/seasonality.Rd | 74 +- berryFunctions-1.12.2/berryFunctions/man/seqPal.Rd | 14 berryFunctions-1.12.2/berryFunctions/man/sortDF.Rd | 13 berryFunctions-1.12.2/berryFunctions/man/spiralDate.Rd | 7 berryFunctions-1.12.2/berryFunctions/man/textField.Rd | 3 berryFunctions-1.12.2/berryFunctions/man/traceCall.Rd |only berryFunctions-1.12.2/berryFunctions/vignettes/berryFunctions.Rmd | 33 - 55 files changed, 680 insertions(+), 448 deletions(-)
More information about berryFunctions at CRAN
Permanent link
Title: Collate Gene Annotation Data from Uniprot and NIH Gene Databases
Description: Taking a list of genes, the package collates together the summary
information about those genes from the publicly available resources at Uniprot
and NCBI. Additionally, the package is able to collate publication information
from a search of the NCBI Pubmed database.
Author: I. Richard Thompson [aut, cre]
Maintainer: I. Richard Thompson <ithompson@qf.org.qa>
Diff between ungeneanno versions 0.1.4 dated 2016-07-24 and 0.1.6 dated 2016-09-21
DESCRIPTION | 8 MD5 | 56 +++-- NAMESPACE | 1 NEWS | 21 +- R/GeneAnno.R | 359 +++---------------------------------- R/GeneAnnoClasses.R |only R/NCBI.R |only R/Pubmed.R |only R/Uniprot.R |only build/vignette.rds |binary inst/doc/Complete_examples.R |only inst/doc/Complete_examples.Rmd | 76 ++++--- inst/doc/Complete_examples.html | 103 +++++++--- inst/doc/PubMed_Query_Example.Rmd | 19 + inst/doc/PubMed_Query_Example.html | 21 +- man/gene-class.Rd | 2 man/geneanno-class.Rd | 2 man/getNihQuery.Rd | 2 man/getNihSummary.Rd | 2 man/getPublicationList.Rd | 2 man/getUniprotSummary.Rd | 2 man/produceOutputFiles.Rd | 15 + man/pubmed-class.Rd | 2 man/query-class.Rd | 2 man/searchPublications.Rd |only tests |only vignettes/Complete_examples.Rmd | 76 ++++--- vignettes/PubMed_Query_Example.Rmd | 19 + 28 files changed, 305 insertions(+), 485 deletions(-)
Title: Template Model Builder: A General Random Effect Tool Inspired by
'ADMB'
Description: With this tool, a user should be able to quickly implement complex
random effect models through simple C++ templates. The package combines
'CppAD' (C++ automatic differentiation), 'Eigen' (templated matrix-vector
library) and 'CHOLMOD' (sparse matrix routines available from R) to obtain an
efficient implementation of the applied Laplace approximation with exact
derivatives. Key features are: Automatic sparseness detection, parallelism
through 'BLAS' and parallel user templates.
Author: Kasper Kristensen [aut, cre, cph],
Brad Bell [cph],
Hans Skaug [ctb],
Arni Magnusson [ctb],
Casper Berg [ctb],
Anders Nielsen [ctb],
Martin Maechler [ctb],
Theo Michelot [ctb],
Mollie Brooks [ctb],
Cole Monnahan [ctb]
Maintainer: Kasper Kristensen <kaskr@dtu.dk>
Diff between TMB versions 1.7.2 dated 2016-08-09 and 1.7.4 dated 2016-09-21
DESCRIPTION | 16 +- MD5 | 67 ++++++++--- NAMESPACE | 2 NEWS | 33 +++++ R/TMB.R | 2 R/examples.R | 4 R/sdreport.R | 6 - R/zzz.R | 27 ++++ inst/include/TMB.hpp | 9 + inst/include/atomic_macro.hpp | 16 ++ inst/include/atomic_math.hpp | 111 +++++++++++++----- inst/include/convenience.hpp | 16 -- inst/include/distributions_R.hpp | 134 ++++++++++++++++++++++ inst/include/expm.hpp | 22 +-- inst/include/lgamma.hpp | 1 inst/include/tiny_ad |only inst/include/tmb_core.hpp | 226 ++++++++++++++++++++++++-------------- inst/include/tmbutils/density.hpp | 36 ++++-- man/MakeADFun.Rd | 2 19 files changed, 544 insertions(+), 186 deletions(-)
Title: ABC-SMC Inference of STEPCAM
Description: Collection of model estimation, and model plotting functions
related to the STEPCAM family of community assembly models.
STEPCAM is a STEPwise Community Assembly Model that infers
the relative contribution of Dispersal Assembly, Habitat Filtering
and Limiting Similarity from a dataset consisting of the
combination of trait and abundance data. See also <http://onlinelibrary.wiley.com/wol1/doi/10.1890/14-0454.1/abstract> for more information.
Author: Thijs Janzen [aut, cre],
Fons van der Plas [aut],
Thorsten Hauffe [ctb]
Maintainer: Thijs Janzen <thijsjanzen@gmail.com>
Diff between STEPCAM versions 1.1.2 dated 2016-04-26 and 1.2 dated 2016-09-21
DESCRIPTION | 28 + MD5 | 56 ++- R/ABC_SMC.R | 545 ++++++++++++++---------------- R/Preparation.R | 375 +++++++++++---------- R/STEPCAM.R | 208 ++++++----- R/generateArtificialData.R | 173 ++++----- R/main.R | 334 ++++++++---------- R/modified_dbFD.R | 706 ++++++++++++++++++++-------------------- R/ternPlot.R | 213 +++++------- README.md |only build |only inst |only man/STEPCAM-internal.Rd | 50 +- man/STEPCAM-package.Rd | 83 ++-- man/STEPCAM_ABC.Rd | 134 ++++--- man/TernPlot.Rd | 61 +-- man/generate.Artificial.Data.Rd | 68 +-- man/plotSMC.Rd | 72 ++-- man/plotSTEPCAM.Rd | 65 +-- tests |only vignettes |only 21 files changed, 1626 insertions(+), 1545 deletions(-)
Title: Spatial Dependence: Weighting Schemes, Statistics and Models
Description: A collection of functions to create spatial weights matrix
objects from polygon contiguities, from point patterns by distance and
tessellations, for summarizing these objects, and for permitting their
use in spatial data analysis, including regional aggregation by minimum
spanning tree; a collection of tests for spatial autocorrelation,
including global Moran's I, APLE, Geary's C, Hubert/Mantel general cross
product statistic, Empirical Bayes estimates and Assunção/Reis Index,
Getis/Ord G and multicoloured join count statistics, local Moran's I
and Getis/Ord G, saddlepoint approximations and exact tests for global
and local Moran's I; and functions for estimating spatial simultaneous
autoregressive (SAR) lag and error models, impact measures for lag
models, weighted and unweighted SAR and CAR spatial regression models,
semi-parametric and Moran eigenvector spatial filtering, GM SAR error
models, and generalized spatial two stage least squares models.
Author: Roger Bivand [cre, aut],
Micah Altman [ctb],
Luc Anselin [ctb],
Renato Assunção [ctb],
Olaf Berke [ctb],
Andrew Bernat [ctb],
Guillaume Blanchet [ctb],
Eric Blankmeyer [ctb],
Marilia Carvalho [ctb],
Bjarke Christensen [ctb],
Yongwan Chun [ctb],
Carsten Dormann [ctb],
Stéphane Dray [ctb],
Virgilio Gómez-Rubio [ctb],
Martin Gubri [ctb],
Rein Halbersma [ctb],
Elias Krainski [ctb],
Pierre Legendre [ctb],
Nicholas Lewin-Koh [ctb],
Hongfei Li [ctb],
Jielai Ma [ctb],
Abhirup Mallik [ctb, trl],
Giovanni Millo [ctb],
Werner Mueller [ctb],
Hisaji Ono [ctb],
Pedro Peres-Neto [ctb],
Gianfranco Piras [ctb],
Markus Reder [ctb],
Michael Tiefelsdorf [ctb],
Danlin Yu [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between spdep versions 0.6-6 dated 2016-07-30 and 0.6-8 dated 2016-09-21
ChangeLog | 33 +++++++++++++++++++++++++++++++++ DESCRIPTION | 8 ++++---- MD5 | 36 ++++++++++++++++++------------------ R/error.spsarlm.R | 22 ++++++++++++---------- R/knearneigh.R | 7 +++++-- R/nb2blocknb.R | 8 +++++++- inst/ChangeLog | 33 +++++++++++++++++++++++++++++++++ inst/doc/CO69.pdf |binary inst/doc/SpatialFiltering.pdf |binary inst/doc/nb.pdf |binary inst/doc/nb_igraph.html | 4 ++-- inst/doc/sids.pdf |binary man/COL.OLD.Rd | 2 +- man/baltimore.Rd | 2 +- man/columbus.Rd | 2 +- man/errorsarlm.Rd | 1 + man/nc.sids.Rd | 2 +- man/read.gal.Rd | 2 +- man/read.gwt2nb.Rd | 2 +- 19 files changed, 121 insertions(+), 43 deletions(-)
Title: Analyze Shot Group Data
Description: Analyzes shooting data with respect to group shape,
precision, and accuracy. This includes graphical methods,
descriptive statistics, and inference tests using standard,
but also non-parametric and robust statistical methods.
Implements distributions for radial error in bivariate normal
variables. Works with files exported by OnTarget PC/TDS or
Taran, as well as with custom data files in text format.
Supports inference from range statistics like extreme spread.
Includes a set of web-based graphical user interfaces.
Author: Daniel Wollschlaeger
Maintainer: Daniel Wollschlaeger <dwoll@kuci.org>
Diff between shotGroups versions 0.7.1 dated 2016-04-15 and 0.7.2 dated 2016-09-21
DESCRIPTION | 12 ++++++------ MD5 | 12 ++++++------ R/hoyt.R | 37 ++++++++++++++++++++++++++++++++----- R/mvnEll.R | 2 +- inst/ChangeLog | 7 ++++++- inst/doc/shotGroups.pdf |binary man/shotGroups-package.Rd | 6 +++--- 7 files changed, 54 insertions(+), 22 deletions(-)
Title: N-Gram Analysis of Biological Sequences
Description: Tools for extraction and analysis of various
n-grams (k-mers) derived from biological sequences (proteins
or nucleic acids). Contains QuiPT (quick permutation test) for fast
feature-filtering of the n-gram data.
Author: Michal Burdukiewicz [cre, aut],
Piotr Sobczyk [aut],
Chris Lauber [aut]
Maintainer: Michal Burdukiewicz <michalburdukiewicz@gmail.com>
Diff between biogram versions 1.2 dated 2015-06-22 and 1.3 dated 2016-09-21
biogram-1.2/biogram/R/add_ngrams.R |only biogram-1.3/biogram/CHANGELOG | 8 biogram-1.3/biogram/DESCRIPTION | 22 +- biogram-1.3/biogram/MD5 | 148 +++++++++-------- biogram-1.3/biogram/NAMESPACE | 24 ++ biogram-1.3/biogram/R/aaprop.R |only biogram-1.3/biogram/R/add_remove_ngrams.R |only biogram-1.3/biogram/R/biogram.R | 46 +++-- biogram-1.3/biogram/R/calc_ed.R |only biogram-1.3/biogram/R/calc_si.R |only biogram-1.3/biogram/R/chi_square.R |only biogram-1.3/biogram/R/cluster_reg_exp.R |only biogram-1.3/biogram/R/construct_ngrams.R | 82 +++++---- biogram-1.3/biogram/R/count_multigrams.R | 8 biogram-1.3/biogram/R/count_ngrams.R | 53 +++--- biogram-1.3/biogram/R/count_specified.R | 89 ++++------ biogram-1.3/biogram/R/criterion_distribution.R | 2 biogram-1.3/biogram/R/criterions.R | 47 ++--- biogram-1.3/biogram/R/data_manipulation.R | 96 +++++------ biogram-1.3/biogram/R/degenerate.R | 43 +++- biogram-1.3/biogram/R/distr_crit.R | 18 +- biogram-1.3/biogram/R/feature_test_class.R | 113 ++++++++---- biogram-1.3/biogram/R/indices_and_positions.R | 33 +-- biogram-1.3/biogram/R/information_gain.R | 34 +-- biogram-1.3/biogram/R/is_ngram.R | 15 + biogram-1.3/biogram/R/kl_divergence.R | 22 +- biogram-1.3/biogram/R/ngram_coding.R | 24 +- biogram-1.3/biogram/R/ngrams.R | 78 +------- biogram-1.3/biogram/R/position_ngrams.R | 18 +- biogram-1.3/biogram/R/seq2matrix.R |only biogram-1.3/biogram/R/table_ngrams.R | 23 +- biogram-1.3/biogram/R/test_features.R | 63 +++++-- biogram-1.3/biogram/R/utilities.R | 47 ++++- biogram-1.3/biogram/README.md | 10 - biogram-1.3/biogram/build |only biogram-1.3/biogram/data/aaprop.rda |only biogram-1.3/biogram/inst/CITATION | 24 ++ biogram-1.3/biogram/inst/doc |only biogram-1.3/biogram/man/aaprop.Rd |only biogram-1.3/biogram/man/add_1grams.Rd | 33 ++- biogram-1.3/biogram/man/as.data.frame.feature_test.Rd |only biogram-1.3/biogram/man/binarize.Rd |only biogram-1.3/biogram/man/biogram-package.Rd | 67 ++++--- biogram-1.3/biogram/man/calc_criterion.Rd | 39 ++-- biogram-1.3/biogram/man/calc_cs.Rd |only biogram-1.3/biogram/man/calc_ed.Rd |only biogram-1.3/biogram/man/calc_ig.Rd | 31 +-- biogram-1.3/biogram/man/calc_kl.Rd | 29 +-- biogram-1.3/biogram/man/calc_si.Rd |only biogram-1.3/biogram/man/cluster_reg_exp.Rd |only biogram-1.3/biogram/man/code_ngrams.Rd | 2 biogram-1.3/biogram/man/construct_ngrams.Rd | 32 ++- biogram-1.3/biogram/man/count_multigrams.Rd | 22 +- biogram-1.3/biogram/man/count_ngrams.Rd | 20 +- biogram-1.3/biogram/man/count_specified.Rd | 8 biogram-1.3/biogram/man/count_total.Rd | 19 +- biogram-1.3/biogram/man/create_feature_target.Rd | 10 - biogram-1.3/biogram/man/create_ngrams.Rd | 20 +- biogram-1.3/biogram/man/criterion_distribution.Rd | 2 biogram-1.3/biogram/man/cut.feature_test.Rd | 14 - biogram-1.3/biogram/man/decode_ngrams.Rd | 2 biogram-1.3/biogram/man/degenerate.Rd | 19 +- biogram-1.3/biogram/man/distr_crit.Rd | 8 biogram-1.3/biogram/man/encoding2df.Rd |only biogram-1.3/biogram/man/fast_crosstable.Rd | 14 - biogram-1.3/biogram/man/feature_test.Rd | 13 + biogram-1.3/biogram/man/gap_ngrams.Rd | 14 + biogram-1.3/biogram/man/get_ngrams_ind.Rd | 12 - biogram-1.3/biogram/man/human_cleave.Rd | 6 biogram-1.3/biogram/man/is_ngram.Rd | 6 biogram-1.3/biogram/man/l2n.Rd | 6 biogram-1.3/biogram/man/list2matrix.Rd |only biogram-1.3/biogram/man/n2l.Rd | 6 biogram-1.3/biogram/man/ngrams2df.Rd | 2 biogram-1.3/biogram/man/plot.criterion_distribution.Rd | 25 +- biogram-1.3/biogram/man/position_ngrams.Rd | 14 - biogram-1.3/biogram/man/print.feature_test.Rd | 2 biogram-1.3/biogram/man/seq2ngrams.Rd | 8 biogram-1.3/biogram/man/summary.feature_test.Rd | 4 biogram-1.3/biogram/man/table_ngrams.Rd | 25 +- biogram-1.3/biogram/man/test_features.Rd | 65 +++++-- biogram-1.3/biogram/man/validate_encoding.Rd |only biogram-1.3/biogram/tests/testthat/test_calc_ed.R |only biogram-1.3/biogram/tests/testthat/test_is_ngram.R | 7 biogram-1.3/biogram/tests/testthat/test_table_ngrams.R |only biogram-1.3/biogram/vignettes |only 86 files changed, 1013 insertions(+), 783 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-02-04 0.0.11
2015-11-19 0.0.10
2015-10-02 0.0.9
Title: A Method for Simulating Data from Perturbed Biological Pathways
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.
Author: Elisa Salviato [aut, cre],
Vera Djordjilovic [aut],
Chiara Romualdi [aut],
Monica Chiogna [aut]
Maintainer: Elisa Salviato <elisa.salviato.88@gmail.com>
Diff between simPATHy versions 0.1 dated 2016-07-18 and 0.2 dated 2016-09-21
DESCRIPTION | 14 ++--- MD5 | 14 ++--- R/graphNELD3.R | 20 ++++---- inst/doc/simPATHy.R | 30 ++++++++++-- inst/doc/simPATHy.Rmd | 120 ++++++++++++++++++++++++++++++++++++++++--------- inst/doc/simPATHy.html | 119 +++++++++++++++++++++++++++++++++++++++++------- vignettes/biblio.bib | 20 ++++++++ vignettes/simPATHy.Rmd | 120 ++++++++++++++++++++++++++++++++++++++++--------- 8 files changed, 371 insertions(+), 86 deletions(-)
Title: Coefficient of Determination
Description: Calculates a newly defined coefficient of determination, aka R^2, and coefficient of partial determination, aka partial R^2 by Zhang (2016) for generalized linear models (including quasi models with well defined variance functions). It also avoids overstatement of variation proportion explained by the model or a group of covariates.
Author: Dabao Zhang
Maintainer: Dabao Zhang <zhangdb@stat.purdue.edu>
Diff between rsq versions 0.5 dated 2016-06-02 and 0.6 dated 2016-09-21
DESCRIPTION | 8 ++++---- MD5 | 12 +++++++----- R/rsq.R | 20 +++++++++----------- data/hschool.rda |only man/hcrabs.Rd | 2 -- man/hschool.Rd |only man/lifetime.Rd | 2 +- man/rsq.partial.Rd | 4 ---- 8 files changed, 21 insertions(+), 27 deletions(-)
Title: Time Dependent Point Process Modelling
Description: Fits and analyses time dependent marked point process models with an emphasis on earthquake modelling. For a more detailed introduction to the package, see the topic "PtProcess". A list of recent changes can be found in the topic "Change Log".
Author: David Harte
Maintainer: David Harte <d.s.harte@gmail.com>
Diff between PtProcess versions 3.3-10 dated 2015-07-02 and 3.3-12 dated 2016-09-21
PtProcess-3.3-10/PtProcess/R/etas_normal0.R |only PtProcess-3.3-10/PtProcess/man/etas_normal0.Rd |only PtProcess-3.3-12/PtProcess/DESCRIPTION | 12 +++--- PtProcess-3.3-12/PtProcess/MD5 | 22 +++++------ PtProcess-3.3-12/PtProcess/NAMESPACE | 1 PtProcess-3.3-12/PtProcess/R/plot.mpp.R | 6 ++- PtProcess-3.3-12/PtProcess/data/NthChina.rda |binary PtProcess-3.3-12/PtProcess/data/Ogata.rda |binary PtProcess-3.3-12/PtProcess/data/Phuket.rda |binary PtProcess-3.3-12/PtProcess/data/Tangshan.rda |binary PtProcess-3.3-12/PtProcess/inst/doc/index.html | 5 -- PtProcess-3.3-12/PtProcess/man/Changes.Rd | 12 ++++-- PtProcess-3.3-12/PtProcess/man/PtProcess.Rd | 46 +++++++++++++------------ 13 files changed, 54 insertions(+), 50 deletions(-)
Title: Graph-Constrained Estimation and Hypothesis Tests
Description: Use the graph-constrained estimation (Grace) procedure to estimate graph-guided linear regression coefficients and use the Grace/GraceI/GraceR tests to perform graph-guided hypothesis tests on the association between the response and the predictors.
Author: Sen Zhao
Maintainer: Sen Zhao <senz@uw.edu>
Diff between Grace versions 0.4 dated 2016-09-11 and 0.4.1 dated 2016-09-21
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/cvGrace.R | 25 ++++++++++++++++--------- R/grace.R | 19 +++++++++++-------- R/grace.test.R | 9 ++++++--- 5 files changed, 41 insertions(+), 28 deletions(-)
Title: Wrappers Around Stanford CoreNLP Tools
Description: Provides a minimal interface for applying
annotators from the 'Stanford CoreNLP' java library. Methods
are provided for tasks such as tokenisation, part of speech
tagging, lemmatisation, named entity recognition, coreference
detection and sentiment analysis.
Author: Taylor Arnold, Lauren Tilton
Maintainer: Taylor Arnold <taylor.arnold@acm.org>
Diff between coreNLP versions 0.4-1 dated 2015-06-03 and 0.4-2 dated 2016-09-21
coreNLP-0.4-1/coreNLP/R/plot.R |only coreNLP-0.4-1/coreNLP/inst/extdata/config.properties |only coreNLP-0.4-1/coreNLP/inst/extdata/config_fast.properties |only coreNLP-0.4-1/coreNLP/man/plot.annotation.Rd |only coreNLP-0.4-2/coreNLP/DESCRIPTION | 19 - coreNLP-0.4-2/coreNLP/MD5 | 53 +-- coreNLP-0.4-2/coreNLP/NAMESPACE | 9 coreNLP-0.4-2/coreNLP/R/download.R | 41 +- coreNLP-0.4-2/coreNLP/R/nlp.R | 148 +++++++--- coreNLP-0.4-2/coreNLP/README.md | 7 coreNLP-0.4-2/coreNLP/inst/extdata/StanfordCoreNLP-arabic.properties |only coreNLP-0.4-2/coreNLP/inst/extdata/StanfordCoreNLP-chinese.properties |only coreNLP-0.4-2/coreNLP/inst/extdata/StanfordCoreNLP-english-all.properties |only coreNLP-0.4-2/coreNLP/inst/extdata/StanfordCoreNLP-english-fast.properties |only coreNLP-0.4-2/coreNLP/inst/extdata/StanfordCoreNLP-french.properties |only coreNLP-0.4-2/coreNLP/inst/extdata/StanfordCoreNLP-german.properties |only coreNLP-0.4-2/coreNLP/inst/extdata/StanfordCoreNLP-spanish.properties |only coreNLP-0.4-2/coreNLP/inst/extdata/StanfordCoreNLP.properties |only coreNLP-0.4-2/coreNLP/man/annoEtranger.rda.Rd | 2 coreNLP-0.4-2/coreNLP/man/annoHp.rda.Rd | 2 coreNLP-0.4-2/coreNLP/man/annotateFile.Rd | 2 coreNLP-0.4-2/coreNLP/man/annotateString.Rd | 2 coreNLP-0.4-2/coreNLP/man/downloadCoreNLP.Rd | 15 - coreNLP-0.4-2/coreNLP/man/getCoreference.Rd | 3 coreNLP-0.4-2/coreNLP/man/getDependency.Rd | 3 coreNLP-0.4-2/coreNLP/man/getOpenIE.Rd |only coreNLP-0.4-2/coreNLP/man/getParse.Rd | 3 coreNLP-0.4-2/coreNLP/man/getSentiment.Rd | 3 coreNLP-0.4-2/coreNLP/man/getToken.Rd | 3 coreNLP-0.4-2/coreNLP/man/initCoreNLP.Rd | 13 coreNLP-0.4-2/coreNLP/man/loadXMLAnnotation.Rd | 2 coreNLP-0.4-2/coreNLP/man/parseAnnoXML.Rd | 2 coreNLP-0.4-2/coreNLP/man/print.annotation.Rd | 3 coreNLP-0.4-2/coreNLP/man/universalTagset.Rd | 3 34 files changed, 219 insertions(+), 119 deletions(-)
Title: Bayesian Survival Model with Lasso Shrinkage Using Generalized
Weibull Regression
Description: Bayesian survival model using Weibull regression on both scale and shape parameters. Dependence of shape parameter on covariates permits deviation from proportional-hazard assumption, leading to dynamic - i.e. non-constant with time - hazard ratios between subjects. Bayesian Lasso shrinkage in the form of two Laplace priors - one for scale and one for shape coefficients - allows for many covariates to be included. Cross-validation helper functions can be used to tune the shrinkage parameters. Monte Carlo Markov Chain (MCMC) sampling using a Gibbs wrapper around Radford Neal's univariate slice sampler (R package MfUSampler) is used for coefficient estimation.
Author: Alireza S. Mahani, Mansour T.A. Sharabiani
Maintainer: Alireza S. Mahani <alireza.s.mahani@gmail.com>
Diff between BSGW versions 0.9.1 dated 2015-09-07 and 0.9.2 dated 2016-09-21
ChangeLog | 9 +++++++++ DESCRIPTION | 13 ++++++------- MD5 | 20 ++++++++++---------- NAMESPACE | 7 ++++--- R/BSGW.R | 50 +++++++++++++++++++++++++++++++++++++++----------- R/Sample.R | 19 ++++++++++++++----- man/bsgw.Rd | 10 ++++++---- man/crossval_bsgw.Rd | 6 ++++-- man/plot_bsgw.Rd | 5 +++-- man/predict_bsgw.Rd | 4 +++- man/summary_bsgw.Rd | 4 +++- 11 files changed, 101 insertions(+), 46 deletions(-)