Title: Facilitates Analysis of CDC NHANES Data
Description: Tools for downloading and analyzing CDC NHANES data, with a focus
on analytical laboratory data.
Author: Herb Susmann [cre, aut],
Silent Spring Institute [cph]
Maintainer: Herb Susmann <susmann@silentspring.org>
Diff between RNHANES versions 1.0 dated 2016-09-27 and 1.1.0 dated 2016-11-28
DESCRIPTION | 8 +-- MD5 | 23 ++++----- NEWS.md |only R/import.R | 2 R/lookup_table.R | 5 ++ R/quantiles.R | 2 R/sample_size.R | 2 R/variables.R | 6 +- R/vcov.R | 4 - inst/doc/introduction.html | 112 ++++++++++++++++++++++++++------------------- man/nhanes_quantile.Rd | 2 man/nhanes_sample_size.Rd | 2 man/nhanes_vcov.Rd | 6 +- 13 files changed, 99 insertions(+), 75 deletions(-)
Title: Learning Sparse Bayesian Networks from High-Dimensional Data
Description: Fast methods for learning sparse Bayesian networks from high-dimensional data using sparse regularization. Designed to incorporate mixed experimental and observational data with thousands of variables with either continuous or discrete observations.
Author: Bryon Aragam [aut, cre]
Maintainer: Bryon Aragam <sparsebn@gmail.com>
Diff between sparsebn versions 0.0.1 dated 2016-08-19 and 0.0.2 dated 2016-11-28
DESCRIPTION | 12 MD5 | 39 +- NAMESPACE | 7 NEWS.md |only R/sparsebn-main.R | 9 R/sparsebn-plotting.R |only R/zzz.R | 4 README.md | 2 build/vignette.rds |binary data/cytometryContinuous.rda |binary data/cytometryDiscrete.rda |binary data/pathfinder.rda |binary inst/doc/sparsebn-vignette.R | 143 +++++----- inst/doc/sparsebn-vignette.Rmd | 229 ++++++++-------- inst/doc/sparsebn-vignette.html | 232 +++++++++-------- man/estimate.covariance.Rd | 2 man/estimate.dag.Rd | 7 man/plotDAG.Rd |only tests/testthat/Rplots.pdf |only tests/testthat/helper-sparsebnUtils-generate_objects.R | 90 +++++- tests/testthat/test-dag.R | 1 tests/testthat/test-plotDAG.R |only vignettes/sparsebn-vignette.Rmd | 229 ++++++++-------- 23 files changed, 575 insertions(+), 431 deletions(-)
Title: Raw Accelerometer Data Analysis
Description: A tool to process and analyse data collected with wearable raw acceleration sensors. The package has been developed and tested for binary data from GENEActiv and GENEA devices and .csv-export data from Actigraph devices. These devices are currently widely used in research on human daily physical activity.
Author: Vincent T van Hees [aut, cre],
Zhou Fang [ctb],
Jing Hua Zhao [ctb],
Severine Sabia [ctb]
Maintainer: Vincent T van Hees <vincentvanhees@gmail.com>
Diff between GGIR versions 1.2-11 dated 2016-08-31 and 1.3-2 dated 2016-11-28
DESCRIPTION | 9 MD5 | 40 NAMESPACE | 6 R/CLS_time.R |only R/g.analyse.R | 1738 +++++++++++++++++++-------------------- R/g.calibrate.R | 1021 +++++++++++------------ R/g.getbout.R | 177 ++-- R/g.getmeta.R | 2270 +++++++++++++++++++++++++--------------------------- R/g.inspectfile.R | 424 ++++----- R/g.part1.R | 7 R/g.part3.R | 158 +-- R/g.part4.R | 1630 ++++++++++++++++++------------------- R/g.part5.R |only R/g.report.part5.R |only R/g.shell.GGIR.R | 96 +- R/g.sib.det.R | 320 +++---- R/g.wavread.R | 47 + inst/NEWS.Rd | 8 man/GGIR-package.Rd | 9 man/g.analyse.Rd | 2 man/g.getbout.Rd | 3 man/g.part5.Rd |only man/g.shell.GGIR.Rd | 2 23 files changed, 4016 insertions(+), 3951 deletions(-)
Title: Computes R Squared for Mixed (Multilevel) Models
Description: The model R squared and semi-partial R squared for the linear and
generalized linear mixed model (LMM and GLMM) are computed with confidence
limits. The R squared measure from Edwards et.al (2008) <DOI:10.1002/sim.3429>
is extended to the GLMM using penalized quasi-likelihood (PQL) estimation
(see Jaeger et al. 2016 <DOI:10.1080/02664763.2016.1193725>). Three methods
of computation are provided and described as follows. Firstly, The
Kenward-Roger approach. Due to some inconsistency between the 'pbkrtest'
package and the 'glmmPQL' function, the Kenward-Roger approach in the
'r2glmm' package is limited to the LMM. Secondly, The method introduced
by Nakagawa and Schielzeth (2013) <DOI:10.1111/j.2041-210x.2012.00261.x>
and later extended by Johnson (2014) <DOI:10.1111/2041-210X.12225>.
The 'r2glmm' package only computes marginal R squared for the LMM and does
not generalize the statistic to the GLMM; however, confidence limits and
semi-partial R squared for fixed effects are useful additions. Lastly, an
approach using standardized generalized variance (SGV) can be used for
covariance model selection. Package installation instructions can be found
in the readme file.
Author: Byron Jaeger [aut, cre]
Maintainer: Byron Jaeger <byron.jaeger@gmail.com>
Diff between r2glmm versions 0.1.0 dated 2016-09-15 and 0.1.1 dated 2016-11-28
r2glmm-0.1.0/r2glmm/man/plot_r2.Rd |only r2glmm-0.1.1/r2glmm/DESCRIPTION | 8 r2glmm-0.1.1/r2glmm/MD5 | 43 ++- r2glmm-0.1.1/r2glmm/NAMESPACE | 6 r2glmm-0.1.1/r2glmm/R/cmpR2_Function.R | 1 r2glmm-0.1.1/r2glmm/R/glm_PQL_Function.R | 13 + r2glmm-0.1.1/r2glmm/R/mpc_Function.R | 8 r2glmm-0.1.1/r2glmm/R/plot_r2_Function.R | 152 +++++++++++-- r2glmm-0.1.1/r2glmm/R/r2_sgv_est_Function.R | 159 +++++++++++--- r2glmm-0.1.1/r2glmm/R/r2beta_Function.R | 246 +--------------------- r2glmm-0.1.1/r2glmm/R/r2beta_glm_Function.R | 5 r2glmm-0.1.1/r2glmm/R/r2beta_glmerMod_Function.R |only r2glmm-0.1.1/r2glmm/R/r2beta_glmmPQL_Function.R | 38 +++ r2glmm-0.1.1/r2glmm/R/r2beta_lm_Function.R | 5 r2glmm-0.1.1/r2glmm/R/r2beta_lme_Function.R | 115 +++++----- r2glmm-0.1.1/r2glmm/R/r2beta_lmerMod_Function.R | 185 ++++++++-------- r2glmm-0.1.1/r2glmm/R/r2dt_Function.R |only r2glmm-0.1.1/r2glmm/README.md | 253 +++++++++++++++++++---- r2glmm-0.1.1/r2glmm/man/calc_sgv.Rd | 7 r2glmm-0.1.1/r2glmm/man/glmPQL.Rd | 6 r2glmm-0.1.1/r2glmm/man/make.partial.C.Rd | 1 r2glmm-0.1.1/r2glmm/man/plot.R2.Rd |only r2glmm-0.1.1/r2glmm/man/pqlmer.Rd |only r2glmm-0.1.1/r2glmm/man/print.R2.Rd |only r2glmm-0.1.1/r2glmm/man/r2beta.Rd | 11 - r2glmm-0.1.1/r2glmm/man/r2dt.Rd |only 26 files changed, 750 insertions(+), 512 deletions(-)
Title: Bayesian Non-Homogenous Markov and Mixture Models (Multiple Time
Series)
Description: Bayesian HMM and NHMM modeling for multiple time series. The
emission distribution can be mixtures of Gammas, Poissons, Normals and zero
inflation is possible.
Author: Tracy Holsclaw
Maintainer: Tracy Holsclaw <iamrandom@iamrandom.com>
Diff between NHMM versions 3.6 dated 2016-09-27 and 3.7 dated 2016-11-28
DESCRIPTION | 15 +- MD5 | 32 ++--- R/HMM.R | 2 R/NHMM.R | 2 R/RcppExports.R | 2 R/RgetPoissontheta.R | 5 man/HMM.Rd | 258 +++++++++++++++++++------------------------- man/NHMM.Rd | 297 ++++++++++++++++++++++----------------------------- man/NHMM_MVN.Rd | 208 ++++++++++++++++------------------- man/OBIC.Rd | 34 ++--- man/OQQ.Rd | 27 ++-- man/OWcoef.Rd | 41 +++---- man/OXcoef.Rd | 38 ++---- man/Oemparams.Rd | 57 +++------ man/Oz.Rd | 25 ++-- src/RcppExports.cpp | 260 ++++++++++++++++++++++---------------------- src/rcpp_rdmix0.cpp | 14 +- 17 files changed, 604 insertions(+), 713 deletions(-)
Title: Multiple Imputation for Interval Censored Data
Description: Implements multiple imputation for proportional hazards regression
with interval censored data or proportional sub-distribution hazards
regression for interval censored competing risks data. The main functions
allow to estimate survival function, cumulative incidence function, Cox
and Fine & Gray regression coefficients and associated variance-covariance
matrix. 'MIICD' functions call 'Surv', 'survfit' and 'coxph' from the
'survival' package, 'crprep' from the 'mstate' package, and 'mvrnorm' from
the 'MASS' package.
Author: Marc Delord [aut, cre]
Maintainer: Marc Delord <mdelord@gmail.com>
Diff between MIICD versions 2.2 dated 2015-12-17 and 2.3 dated 2016-11-28
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- R/ANDA.crreg.R | 2 +- R/MI.ci.R | 2 +- R/MI.ci_1.R | 2 +- R/MI.surv.R | 2 +- R/MI.surv_1.R | 2 +- R/PMDA.coxph.R | 2 +- R/PMDA.crreg.R | 2 +- R/get_est_mi.R | 2 +- R/get_est_mi_surv.R | 2 +- 11 files changed, 22 insertions(+), 22 deletions(-)
Title: Item Response Theory Implemented in R and Cpp
Description: Provides a C++ implementation of the Multidimensional Item Response Theory (MIRT) capable of performing parameter and traits estimations. It also provides a list of options to perform an optimal analysis and obtain useful information about the resulting model. This package is a work of SICS Research Group, Universidad Nacional de Colombia.
Author: Milder Hernandez Cagua [aut],
Jhonatan Javier Guzman del Rio [aut],
Camilo Antonio Suarez Bolanos [cre],
Alvaro Mauricio Montenegro [aut],
Sergio Paez Moncaleano [aut],
Juan David Cortes Castillo [aut],
Campo Elias Pardo Turriago [aut],
Luisa Fernanda Parra Arboleda [aut],
Emilio Pablo Berdugo Camacho [aut],
SICS Research Group [cph]
Maintainer: Camilo Antonio Suarez Bolanos <caasuarezbo@unal.edu.co>
Diff between LatentREGpp versions 0.1.1 dated 2016-10-27 and 0.2.2 dated 2016-11-28
LatentREGpp-0.1.1/LatentREGpp/R/inivalsMultiPoly.R |only LatentREGpp-0.1.1/LatentREGpp/R/inivalsMultiUni.R |only LatentREGpp-0.1.1/LatentREGpp/man/LatentREGpp.Rd |only LatentREGpp-0.1.1/LatentREGpp/man/inivals_MultiPoly.Rd |only LatentREGpp-0.1.1/LatentREGpp/man/inivals_MultiUni_NOHARM.Rd |only LatentREGpp-0.1.1/LatentREGpp/man/standarize.Rd |only LatentREGpp-0.2.2/LatentREGpp/DESCRIPTION | 13 LatentREGpp-0.2.2/LatentREGpp/LICENSE | 2 LatentREGpp-0.2.2/LatentREGpp/MD5 | 150 LatentREGpp-0.2.2/LatentREGpp/NAMESPACE | 45 LatentREGpp-0.2.2/LatentREGpp/R/RcppExports.R | 26 LatentREGpp-0.2.2/LatentREGpp/R/eeitems.R |only LatentREGpp-0.2.2/LatentREGpp/R/exploratory.R |only LatentREGpp-0.2.2/LatentREGpp/R/findClusters.R | 248 - LatentREGpp-0.2.2/LatentREGpp/R/findim_hcpc.R |only LatentREGpp-0.2.2/LatentREGpp/R/goodness_of_fit.R |only LatentREGpp-0.2.2/LatentREGpp/R/gpc.R |only LatentREGpp-0.2.2/LatentREGpp/R/isdatadicho.R | 20 LatentREGpp-0.2.2/LatentREGpp/R/itemfit.R | 165 LatentREGpp-0.2.2/LatentREGpp/R/itemfitbayesian.R |only LatentREGpp-0.2.2/LatentREGpp/R/itemfix.R |only LatentREGpp-0.2.2/LatentREGpp/R/personfit.R | 238 - LatentREGpp-0.2.2/LatentREGpp/R/quadpoints.R | 9 LatentREGpp-0.2.2/LatentREGpp/R/rtnorm.r | 160 LatentREGpp-0.2.2/LatentREGpp/R/simulate_dichotomous.R | 26 LatentREGpp-0.2.2/LatentREGpp/R/simulate_poly_multi.R | 372 - LatentREGpp-0.2.2/LatentREGpp/R/simulate_poly_uni.R | 106 LatentREGpp-0.2.2/LatentREGpp/R/simulate_polytomous.R | 9 LatentREGpp-0.2.2/LatentREGpp/R/standarize.R | 5 LatentREGpp-0.2.2/LatentREGpp/R/utils.R |only LatentREGpp-0.2.2/LatentREGpp/inst/dataset/1D/dicho/1000x50-1.csv | 2000 +++++----- LatentREGpp-0.2.2/LatentREGpp/inst/dataset/1D/dicho/1000x50-parameters.csv | 200 - LatentREGpp-0.2.2/LatentREGpp/inst/dataset/1D/poly/1000x50-1.csv | 2000 +++++----- LatentREGpp-0.2.2/LatentREGpp/inst/dataset/1D/poly/1000x50-parameters.csv | 400 +- LatentREGpp-0.2.2/LatentREGpp/inst/dataset/3D/dicho/1000x55-1.csv | 2000 +++++----- LatentREGpp-0.2.2/LatentREGpp/inst/dataset/3D/dicho/1000x55-parameters.csv | 110 LatentREGpp-0.2.2/LatentREGpp/inst/dataset/3D/poly/1000x60-1.csv | 2000 +++++----- LatentREGpp-0.2.2/LatentREGpp/inst/dataset/3D/poly/1000x60-parameters.csv | 120 LatentREGpp-0.2.2/LatentREGpp/inst/dataset/TUN.txt |only LatentREGpp-0.2.2/LatentREGpp/inst/include/dlibUsedHeaders.txt |only LatentREGpp-0.2.2/LatentREGpp/inst/include/script.ps1 |only LatentREGpp-0.2.2/LatentREGpp/man/LatentREGpp-Description.Rd |only LatentREGpp-0.2.2/LatentREGpp/man/Yule.Rd |only LatentREGpp-0.2.2/LatentREGpp/man/alpha_cronbach.Rd |only LatentREGpp-0.2.2/LatentREGpp/man/alpha_curve.Rd |only LatentREGpp-0.2.2/LatentREGpp/man/an_parallel.Rd |only LatentREGpp-0.2.2/LatentREGpp/man/biserial_cor.Rd |only LatentREGpp-0.2.2/LatentREGpp/man/eap_gpc.Rd |only LatentREGpp-0.2.2/LatentREGpp/man/envelope_itemf.Rd |only LatentREGpp-0.2.2/LatentREGpp/man/estim_gpc.Rd |only LatentREGpp-0.2.2/LatentREGpp/man/findim_hcpc.Rd |only LatentREGpp-0.2.2/LatentREGpp/man/gutt.Rd |only LatentREGpp-0.2.2/LatentREGpp/man/itemfit.Rd | 30 LatentREGpp-0.2.2/LatentREGpp/man/itemfit_bayesian.Rd |only LatentREGpp-0.2.2/LatentREGpp/man/map_gpc.Rd |only LatentREGpp-0.2.2/LatentREGpp/man/orlando_itemf.Rd |only LatentREGpp-0.2.2/LatentREGpp/man/personfit.Rd | 95 LatentREGpp-0.2.2/LatentREGpp/man/phi.Rd |only LatentREGpp-0.2.2/LatentREGpp/man/polyserial_cor.Rd |only LatentREGpp-0.2.2/LatentREGpp/man/quadpoints.Rd | 8 LatentREGpp-0.2.2/LatentREGpp/man/simulate_dichotomous.Rd | 27 LatentREGpp-0.2.2/LatentREGpp/man/simulate_polytomous.Rd | 12 LatentREGpp-0.2.2/LatentREGpp/man/x2_itemf.Rd |only LatentREGpp-0.2.2/LatentREGpp/man/z3_itemf.Rd |only LatentREGpp-0.2.2/LatentREGpp/man/z3_personf.Rd |only LatentREGpp-0.2.2/LatentREGpp/src/Makevars | 82 LatentREGpp-0.2.2/LatentREGpp/src/Makevars.win | 4 LatentREGpp-0.2.2/LatentREGpp/src/RcppExports.cpp | 28 LatentREGpp-0.2.2/LatentREGpp/src/dichotomous/estimation/estep.cpp | 6 LatentREGpp-0.2.2/LatentREGpp/src/dichotomous/estimation/estep.h | 4 LatentREGpp-0.2.2/LatentREGpp/src/dichotomous/estimation/estimation.cpp | 233 - LatentREGpp-0.2.2/LatentREGpp/src/dichotomous/estimation/estimation.h | 13 LatentREGpp-0.2.2/LatentREGpp/src/dichotomous/estimation/mstep.cpp | 60 LatentREGpp-0.2.2/LatentREGpp/src/dichotomous/model/bayesian.cpp |only LatentREGpp-0.2.2/LatentREGpp/src/dichotomous/model/bayesian.h |only LatentREGpp-0.2.2/LatentREGpp/src/dichotomous/model/model.cpp | 14 LatentREGpp-0.2.2/LatentREGpp/src/dichotomous/model/model.h | 7 LatentREGpp-0.2.2/LatentREGpp/src/dichotomous/model/onepl.cpp | 6 LatentREGpp-0.2.2/LatentREGpp/src/dichotomous/model/onepl.h | 2 LatentREGpp-0.2.2/LatentREGpp/src/dichotomous/model/threepl.cpp | 6 LatentREGpp-0.2.2/LatentREGpp/src/dichotomous/model/threepl.h | 2 LatentREGpp-0.2.2/LatentREGpp/src/dichotomous/model/twopl.cpp | 6 LatentREGpp-0.2.2/LatentREGpp/src/dichotomous/model/twopl.h | 2 LatentREGpp-0.2.2/LatentREGpp/src/dichotomous/type/estimationdata.h | 4 LatentREGpp-0.2.2/LatentREGpp/src/latentregpp.cpp | 158 LatentREGpp-0.2.2/LatentREGpp/src/latentregpp.h | 21 LatentREGpp-0.2.2/LatentREGpp/src/polytomous/estimation/estep.cpp | 4 LatentREGpp-0.2.2/LatentREGpp/src/polytomous/estimation/estep.h | 2 LatentREGpp-0.2.2/LatentREGpp/src/polytomous/estimation/estimation.cpp | 50 LatentREGpp-0.2.2/LatentREGpp/src/polytomous/estimation/estimation.h | 8 LatentREGpp-0.2.2/LatentREGpp/src/polytomous/estimation/mstep.cpp | 4 LatentREGpp-0.2.2/LatentREGpp/src/polytomous/estimation/mstep.h | 2 LatentREGpp-0.2.2/LatentREGpp/src/polytomous/type/estimationdata.h | 2 LatentREGpp-0.2.2/LatentREGpp/src/util/constants.h | 4 LatentREGpp-0.2.2/LatentREGpp/src/util/helper.h | 40 95 files changed, 6064 insertions(+), 5306 deletions(-)
Title: Leland Wilkinson's Algorithm for Detecting Multidimensional
Outliers
Description: An implementation of an algorithm for outlier detection that can handle a) data with a mixed categorical and continuous variables, b) many columns of data, c) many rows of data, d) outliers that mask other outliers, and e) both unidimensional and multidimensional datasets. Unlike ad hoc methods found in many machine learning papers, HDoutliers is based on a distributional model that uses probabilities to determine outliers. See <https://www.cs.uic.edu/~wilkinson/Publications/outliers.pdf>.
Author: Chris Fraley [aut, cre],
Leland Wilkinson [ctb]
Maintainer: Chris Fraley <cfraley@tableau.com>
Diff between HDoutliers versions 0.12 dated 2016-11-17 and 0.14 dated 2016-11-28
CHANGELOG | 1 + DESCRIPTION | 18 ++++++++++-------- MD5 | 10 +++++----- man/dots.Rd | 3 ++- man/getHDmembers.Rd | 3 ++- man/getHDoutliers.Rd | 1 + 6 files changed, 21 insertions(+), 15 deletions(-)
Title: Computation of Parameters Used in Preliminary Assessment of
Conservation Status
Description: Multi-species estimation of geographical range parameters
for preliminary assessment of conservation status following Criterion B of the
International Union for Conservation of Nature (IUCN,
see <http://www.iucnredlist.org>).
Author: Gilles Dauby
Maintainer: Gilles Dauby <gildauby@gmail.com>
Diff between ConR versions 1.0 dated 2016-10-31 and 1.1 dated 2016-11-28
DESCRIPTION | 6 ++-- MD5 | 16 ++++++------ R/IUCNeval.functionv11.R | 13 ++++++--- build/partial.rdb |binary build/vignette.rds |binary inst/doc/my-vignette.R | 6 +++- inst/doc/my-vignette.Rmd | 61 +++++++++++++++++++++------------------------- inst/doc/my-vignette.html | 58 ++++++++++++++++++++----------------------- vignettes/my-vignette.Rmd | 61 +++++++++++++++++++++------------------------- 9 files changed, 109 insertions(+), 112 deletions(-)
Title: Embedded JavaScript Engine for R
Description: An R interface to Google's open source JavaScript engine.
V8 is written in C++ and implements ECMAScript as specified in ECMA-262,
5th edition. In addition, this package implements typed arrays as
specified in ECMA 6 used for high-performance computing and libraries
compiled with 'emscripten'.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between V8 versions 1.1 dated 2016-07-16 and 1.2 dated 2016-11-28
DESCRIPTION | 11 ++++---- MD5 | 12 ++++----- NEWS | 4 +++ R/RcppExports.R | 2 - build/vignette.rds |binary configure | 58 +++++++++++++++++++++++++-------------------- src/RcppExports.cpp | 66 ++++++++++++++++++++++++++-------------------------- 7 files changed, 82 insertions(+), 71 deletions(-)
Title: Detect Text Reuse and Document Similarity
Description: Tools for measuring similarity among documents and detecting
passages which have been reused. Implements shingled n-gram, skip n-gram,
and other tokenizers; similarity/dissimilarity functions; pairwise
comparisons; minhash and locality sensitive hashing algorithms; and a
version of the Smith-Waterman local alignment algorithm suitable for
natural language.
Author: Lincoln Mullen [aut, cre]
Maintainer: Lincoln Mullen <lincoln@lincolnmullen.com>
Diff between textreuse versions 0.1.3 dated 2016-03-28 and 0.1.4 dated 2016-11-28
DESCRIPTION | 11 ++++++----- MD5 | 26 +++++++++++++------------- NEWS.md | 5 +++++ R/RcppExports.R | 2 +- README.md | 30 ++++++++++++++---------------- build/vignette.rds |binary inst/doc/textreuse-alignment.html | 11 +++++------ inst/doc/textreuse-introduction.Rmd | 2 +- inst/doc/textreuse-introduction.html | 19 +++++++++---------- inst/doc/textreuse-minhash.html | 25 ++++++++++--------------- inst/doc/textreuse-pairwise.html | 14 ++++++-------- src/RcppExports.cpp | 34 +++++++++++++++++----------------- tests/testthat/test-lsh.R | 2 +- vignettes/textreuse-introduction.Rmd | 2 +- 14 files changed, 89 insertions(+), 94 deletions(-)
Title: Raster Time Series Analysis
Description: This framework aims to provide classes and methods for manipulating and processing of raster time series data (e.g. a time series of satellite images).
Author: Babak Naimi
Maintainer: Babak Naimi <naimi.b@gmail.com>
Diff between rts versions 1.0-12 dated 2016-07-01 and 1.0-18 dated 2016-11-28
DESCRIPTION | 12 +-- MD5 | 9 +- R/AAAClasses.R | 81 ++++++++++++++-------- R/ModisDownload.R | 182 ++++++++++++++++++++++++++++++++++++++++++++------- R/zzz.R |only man/ModisDownload.Rd | 15 +++- 6 files changed, 237 insertions(+), 62 deletions(-)
Title: Accelerating 'ggplot2'
Description: The aim of 'ggplot2' is to aid in visual data investigations. This
focus has led to a lack of facilities for composing specialised plots.
'ggforce' aims to be a collection of mainly new stats and geoms that fills
this gap. All additional functionality is aimed to come through the official
extension system so using 'ggforce' should be a stable experience.
Author: Thomas Lin Pedersen
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>
Diff between ggforce versions 0.1.0 dated 2016-11-22 and 0.1.1 dated 2016-11-28
DESCRIPTION | 14 ++-- MD5 | 22 +++---- NEWS.md | 52 +++++++++++------ R/facet_grid_paginate.R | 6 + R/facet_wrap_paginate.R | 6 + R/facet_zoom.R | 101 +++++++++++++++++++++++---------- README.md | 136 +++++++++++++++++---------------------------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/Visual_Guide.Rmd | 2 inst/doc/Visual_Guide.html | 24 ++++--- vignettes/Visual_Guide.Rmd | 2 12 files changed, 206 insertions(+), 159 deletions(-)
Title: Robust Geostatistical Analysis of Spatial Data
Description: Provides functions for efficiently fitting linear models with
spatially correlated errors by robust and Gaussian (Restricted)
Maximum Likelihood and for computing robust and customary point
and block external-drift Kriging predictions, along with utility
functions for variogram modelling in ad hoc geostatistical analyses,
model building, model evaluation by cross-validation and for
unbiased back-transformation of Kriging predictions of
log-transformed data.
Author: Andreas Papritz [cre, aut],
Cornelia Schwierz [ctb]
Maintainer: Andreas Papritz <andreas.papritz@env.ethz.ch>
Diff between georob versions 0.3-1 dated 2016-09-09 and 0.3-2 dated 2016-11-28
ChangeLog | 9 ++++ DESCRIPTION | 8 ++-- MD5 | 18 ++++----- R/georob.predict.R | 24 +++++++----- R/georob.private.functions.R | 80 ++++++++++++++++++++++++++++++------------ build/vignette.rds |binary inst/doc/georob_vignette.Rnw | 9 ++-- inst/doc/georob_vignette.pdf |binary man/georob-package.Rd | 12 +++--- vignettes/georob_vignette.Rnw | 9 ++-- 10 files changed, 109 insertions(+), 60 deletions(-)
Title: Tools for CM SAF NetCDF Data
Description: The Satellite Application Facility on Climate Monitoring (CM SAF)
is a ground segment of the European Organization for the Exploitation of
Meteorological Satellites (EUMETSAT) and one of EUMETSATs Satellite Application
Facilities. The CM SAF contributes to the sustainable observing of the climate
system by providing Essential Climate Variables related to the energy and water
cycle of the atmosphere (<http://www.cmsaf.eu>). It is a joint cooperation of seven
National Meteorological and Hydrological Services, including the Deutscher
Wetterdienst (DWD).
The 'cmsaf' R-package provides a small collection of R-functions, which are
inspired by the Climate Data Operators ('cdo'). This gives the opportunity to
analyse and manipulate CM SAF data without the need of installing cdo.
The 'cmsaf' R-package is tested for CM SAF NetCDF data, which are structured
in three-dimensional arrays (longitude, latitude, time) on a rectangular grid.
Layered CM SAF data have to be converted with the provided 'levbox_mergetime()'
function. The 'cmsaf' R-package functions have only minor checks for deviations
from the recommended data structure, and give only few specific error messages.
Thus, there is no warranty of accurate results.
Scripts for an easy application of the functions are provided at the CM SAF homepage
(<http://www.cmsaf.eu/EN/Products/Tools/Tools_node.html>).
Author: Steffen Kothe <Steffen.Kothe@dwd.de>
Maintainer: Steffen Kothe <Steffen.Kothe@dwd.de>
Diff between cmsaf versions 1.7.0 dated 2016-10-12 and 1.7.1 dated 2016-11-28
DESCRIPTION | 24 +++---- MD5 | 156 ++++++++++++++++++++++++------------------------ R/box_mergetime.R | 14 ++-- R/extract.period.R | 6 + R/fldmax.R | 12 ++- R/fldmin.R | 6 + R/levbox_mergetime.R | 6 + R/monmax.R | 8 +- R/monmin.R | 8 +- R/sellonlatbox.R | 6 + R/selmon.R | 6 + R/selperiod.R | 6 + R/selpoint.R | 6 + R/seltime.R | 6 + R/selyear.R | 6 + R/timmax.R | 6 + R/timmin.R | 6 + R/ymonmax.R | 6 + R/ymonmin.R | 6 + R/yseasmax.R | 6 + R/yseasmin.R | 6 + man/box_mergetime.Rd | 56 ++++++++--------- man/change_att.Rd | 43 ++++++------- man/checkfile.Rd | 10 +-- man/cmsaf-package.Rd | 17 ++--- man/cmsaf.add.Rd | 51 ++++++++------- man/cmsaf.addc.Rd | 40 ++++++------ man/cmsaf.div.Rd | 51 ++++++++------- man/cmsaf.divc.Rd | 40 ++++++------ man/cmsaf.mul.Rd | 51 ++++++++------- man/cmsaf.mulc.Rd | 40 ++++++------ man/cmsaf.sub.Rd | 51 ++++++++------- man/cmsaf.subc.Rd | 40 ++++++------ man/dayrange.Rd | 39 ++++++------ man/divdpm.Rd | 39 ++++++------ man/extract.period.Rd | 45 +++++++------ man/fldmax.Rd | 41 ++++++------ man/fldmean.Rd | 41 ++++++------ man/fldmin.Rd | 41 ++++++------ man/get_time.Rd | 2 man/levbox_mergetime.Rd | 63 +++++++++---------- man/mon.anomaly.Rd | 40 ++++++------ man/monmax.Rd | 43 ++++++------- man/monmean.Rd | 41 ++++++------ man/monmin.Rd | 43 ++++++------- man/monsd.Rd | 43 ++++++------- man/monsum.Rd | 41 ++++++------ man/muldpm.Rd | 39 ++++++------ man/multimonmean.Rd | 45 +++++++------ man/multimonsum.Rd | 49 +++++++-------- man/ncinfo.Rd | 39 ++++++------ man/read_nc.Rd | 41 ++++++------ man/remapbil.Rd | 55 ++++++++-------- man/seas.anomaly.Rd | 44 +++++++------ man/seasmean.Rd | 41 ++++++------ man/sellonlatbox.Rd | 47 +++++++------- man/selmon.Rd | 42 ++++++------ man/selperiod.Rd | 45 +++++++------ man/selpoint.Rd | 47 +++++++------- man/seltime.Rd | 45 +++++++------ man/selyear.Rd | 43 ++++++------- man/timmax.Rd | 43 ++++++------- man/timmean.Rd | 41 ++++++------ man/timmin.Rd | 43 ++++++------- man/timsd.Rd | 45 +++++++------ man/trend.Rd | 41 ++++++------ man/wfldmean.Rd | 39 ++++++------ man/year.anomaly.Rd | 40 ++++++------ man/yearmean.Rd | 42 ++++++------ man/yearsum.Rd | 42 ++++++------ man/ymonmax.Rd | 41 ++++++------ man/ymonmean.Rd | 42 ++++++------ man/ymonmin.Rd | 43 ++++++------- man/ymonsd.Rd | 45 +++++++------ man/ymonsum.Rd | 41 ++++++------ man/yseasmax.Rd | 43 ++++++------- man/yseasmean.Rd | 42 ++++++------ man/yseasmin.Rd | 44 +++++++------ man/yseassd.Rd | 44 +++++++------ 79 files changed, 1447 insertions(+), 1300 deletions(-)
Title: Mean and Variance Modeling of Binary Data
Description: Modeling under- and over-dispersed binary data using extended Poisson process models (EPPM).
Author: David M Smith, Malcolm J Faddy
Maintainer: David M. Smith <david.m.smith@truvenhealth.com>
Diff between BinaryEPPM versions 1.0 dated 2015-05-14 and 2.0 dated 2016-11-28
BinaryEPPM-1.0/BinaryEPPM/R/BinaryEPPM.distribution.R |only BinaryEPPM-1.0/BinaryEPPM/R/BinaryEPPM.summary.R |only BinaryEPPM-1.0/BinaryEPPM/R/F.Regression.Binary.R |only BinaryEPPM-1.0/BinaryEPPM/data/Titanic.survivors.rda |only BinaryEPPM-1.0/BinaryEPPM/data/herons.case.rda |only BinaryEPPM-1.0/BinaryEPPM/man/BinaryEPPM.distribution.Rd |only BinaryEPPM-1.0/BinaryEPPM/man/BinaryEPPM.summary.Rd |only BinaryEPPM-1.0/BinaryEPPM/man/F.Regression.Binary.Rd |only BinaryEPPM-1.0/BinaryEPPM/man/Titanic.survivors.Rd |only BinaryEPPM-1.0/BinaryEPPM/man/herons.case.Rd |only BinaryEPPM-2.0/BinaryEPPM/DESCRIPTION | 10 BinaryEPPM-2.0/BinaryEPPM/MD5 | 135 - BinaryEPPM-2.0/BinaryEPPM/NAMESPACE | 22 BinaryEPPM-2.0/BinaryEPPM/R/BBprob.R | 57 BinaryEPPM-2.0/BinaryEPPM/R/BinaryEPPM.R | 1052 ++++++----- BinaryEPPM-2.0/BinaryEPPM/R/CBprob.R | 55 BinaryEPPM-2.0/BinaryEPPM/R/EPPMprob.R | 10 BinaryEPPM-2.0/BinaryEPPM/R/GBprob.R | 17 BinaryEPPM-2.0/BinaryEPPM/R/LL.Regression.Binary.R | 35 BinaryEPPM-2.0/BinaryEPPM/R/LL.gradient.R |only BinaryEPPM-2.0/BinaryEPPM/R/Model.BCBinProb.R | 180 + BinaryEPPM-2.0/BinaryEPPM/R/Model.Binary.R | 26 BinaryEPPM-2.0/BinaryEPPM/R/Model.GB.R | 33 BinaryEPPM-2.0/BinaryEPPM/R/Model.JMVGB.R | 73 BinaryEPPM-2.0/BinaryEPPM/R/coef.BinaryEPPM.R |only BinaryEPPM-2.0/BinaryEPPM/R/cooks.distance.BinaryEPPM.R |only BinaryEPPM-2.0/BinaryEPPM/R/doubexp.R |only BinaryEPPM-2.0/BinaryEPPM/R/doubrecip.R |only BinaryEPPM-2.0/BinaryEPPM/R/fitted.BinaryEPPM.R |only BinaryEPPM-2.0/BinaryEPPM/R/hatvalues.BinaryEPPM.R |only BinaryEPPM-2.0/BinaryEPPM/R/logLik.BinaryEPPM.R |only BinaryEPPM-2.0/BinaryEPPM/R/loglog.R |only BinaryEPPM-2.0/BinaryEPPM/R/plot.BinaryEPPM.R |only BinaryEPPM-2.0/BinaryEPPM/R/powerlogit.R |only BinaryEPPM-2.0/BinaryEPPM/R/predict.BinaryEPPM.R |only BinaryEPPM-2.0/BinaryEPPM/R/print.BinaryEPPM.R |only BinaryEPPM-2.0/BinaryEPPM/R/print.summaryBinaryEPPM.R |only BinaryEPPM-2.0/BinaryEPPM/R/residuals.BinaryEPPM.R |only BinaryEPPM-2.0/BinaryEPPM/R/summary.BinaryEPPM.R |only BinaryEPPM-2.0/BinaryEPPM/R/vcov.BinaryEPPM.R |only BinaryEPPM-2.0/BinaryEPPM/build |only BinaryEPPM-2.0/BinaryEPPM/data/Berkshires.litters.rda |binary BinaryEPPM-2.0/BinaryEPPM/data/GasolineYield.rda |only BinaryEPPM-2.0/BinaryEPPM/data/Hiroshima.case.rda |only BinaryEPPM-2.0/BinaryEPPM/data/Hiroshima.grouped.rda |only BinaryEPPM-2.0/BinaryEPPM/data/KupperHaseman.case.rda |binary BinaryEPPM-2.0/BinaryEPPM/data/Luningetal.litters.rda |binary BinaryEPPM-2.0/BinaryEPPM/data/Parkes.litters.rda |binary BinaryEPPM-2.0/BinaryEPPM/data/Titanic.survivors.case.rda |binary BinaryEPPM-2.0/BinaryEPPM/data/Titanic.survivors.grouped.rda |only BinaryEPPM-2.0/BinaryEPPM/data/Williams.litters.rda |binary BinaryEPPM-2.0/BinaryEPPM/data/Yorkshires.litters.rda |binary BinaryEPPM-2.0/BinaryEPPM/data/foodstamp.case.rda |only BinaryEPPM-2.0/BinaryEPPM/data/foodstamp.grouped.rda |only BinaryEPPM-2.0/BinaryEPPM/data/ropespores.case.rda |binary BinaryEPPM-2.0/BinaryEPPM/data/ropespores.grouped.rda |binary BinaryEPPM-2.0/BinaryEPPM/man/BBprob.Rd | 22 BinaryEPPM-2.0/BinaryEPPM/man/Berkshires.litters.Rd | 12 BinaryEPPM-2.0/BinaryEPPM/man/BinaryEPPM-package.Rd | 67 BinaryEPPM-2.0/BinaryEPPM/man/BinaryEPPM.Rd | 228 +- BinaryEPPM-2.0/BinaryEPPM/man/CBprob.Rd | 16 BinaryEPPM-2.0/BinaryEPPM/man/EPPMprob.Rd | 17 BinaryEPPM-2.0/BinaryEPPM/man/GBprob.Rd | 17 BinaryEPPM-2.0/BinaryEPPM/man/GasolineYield.Rd |only BinaryEPPM-2.0/BinaryEPPM/man/Hiroshima.case.Rd |only BinaryEPPM-2.0/BinaryEPPM/man/Hiroshima.grouped.Rd |only BinaryEPPM-2.0/BinaryEPPM/man/KupperHaseman.case.Rd | 1 BinaryEPPM-2.0/BinaryEPPM/man/LL.Regression.Binary.Rd | 48 BinaryEPPM-2.0/BinaryEPPM/man/LL.gradient.Rd |only BinaryEPPM-2.0/BinaryEPPM/man/Luningetal.litters.Rd | 4 BinaryEPPM-2.0/BinaryEPPM/man/Model.BCBinProb.Rd | 26 BinaryEPPM-2.0/BinaryEPPM/man/Model.Binary.Rd | 29 BinaryEPPM-2.0/BinaryEPPM/man/Model.GB.Rd | 26 BinaryEPPM-2.0/BinaryEPPM/man/Model.JMVGB.Rd | 32 BinaryEPPM-2.0/BinaryEPPM/man/Parkes.litters.Rd | 12 BinaryEPPM-2.0/BinaryEPPM/man/Titanic.survivors.case.Rd | 4 BinaryEPPM-2.0/BinaryEPPM/man/Titanic.survivors.grouped.Rd |only BinaryEPPM-2.0/BinaryEPPM/man/Williams.litters.Rd | 9 BinaryEPPM-2.0/BinaryEPPM/man/Yorkshires.litters.Rd | 11 BinaryEPPM-2.0/BinaryEPPM/man/coef.BinaryEPPM.Rd |only BinaryEPPM-2.0/BinaryEPPM/man/cooks.distance.BinaryEPPM.Rd |only BinaryEPPM-2.0/BinaryEPPM/man/doubexp.Rd |only BinaryEPPM-2.0/BinaryEPPM/man/doubrecip.Rd |only BinaryEPPM-2.0/BinaryEPPM/man/fitted.BinaryEPPM.Rd |only BinaryEPPM-2.0/BinaryEPPM/man/foodstamp.case.Rd |only BinaryEPPM-2.0/BinaryEPPM/man/foodstamp.grouped.Rd |only BinaryEPPM-2.0/BinaryEPPM/man/hatvalues.BinaryEPPM.Rd |only BinaryEPPM-2.0/BinaryEPPM/man/logLik.BinaryEPPM.Rd |only BinaryEPPM-2.0/BinaryEPPM/man/loglog.Rd |only BinaryEPPM-2.0/BinaryEPPM/man/plot.BinaryEPPM.Rd |only BinaryEPPM-2.0/BinaryEPPM/man/powerlogit.Rd |only BinaryEPPM-2.0/BinaryEPPM/man/predict.BinaryEPPM.Rd |only BinaryEPPM-2.0/BinaryEPPM/man/print.BinaryEPPM.Rd |only BinaryEPPM-2.0/BinaryEPPM/man/print.summaryBinaryEPPM.Rd |only BinaryEPPM-2.0/BinaryEPPM/man/residuals.BinaryEPPM.Rd |only BinaryEPPM-2.0/BinaryEPPM/man/summary.BinaryEPPM.Rd |only BinaryEPPM-2.0/BinaryEPPM/man/vcov.BinaryEPPM.Rd |only 97 files changed, 1361 insertions(+), 925 deletions(-)
Title: SA Counterparty Credit Risk under Basel III
Description: Computes the Exposure-At-Default based on standardized approach
of the Basel III Regulatory framework (SA-CCR). Currently, trade types of all
the five major asset classes have been created and, given the inheritance-
based structure of the application, the addition of further trade types
is straightforward. The application returns a list of trees (one per CSA) after
automatically separating the trades based on the CSAs, the hedging sets, the
netting sets and the risk factors. The basis and volatility transactions are
also identified and treated in specific hedging sets whereby the corresponding
penalty factors are applied. All the examples appearing on the
regulatory paper (including the margined and the un-margined workflow) have been
implemented.
Author: Tasos Grivas
Maintainer: Tasos Grivas <info@openriskcalculator.com>
Diff between SACCR versions 2.0 dated 2016-11-22 and 2.1 dated 2016-11-28
DESCRIPTION | 10 ++++----- MD5 | 46 +++++++++++++++++++++--------------------- NAMESPACE | 1 R/CalcAddon.R | 43 ++++++++++++++++++++++++++++++--------- R/CreateTradeGraph.R | 2 - R/ExampleBasisVol.R | 13 ++++++++++- R/ExampleComm.R | 13 ++++++++++- R/ExampleCredit.R | 13 ++++++++++- R/ExampleFX.R | 13 ++++++++++- R/ExampleIRD.R | 16 +++++++++++--- R/ExampleIRDCommMargined.R | 15 ++++++++++--- R/ExampleIRDCredit.R | 16 +++++++++++--- R/GroupFXTrades.R | 2 - R/SACCRCalculator.R | 19 +++++++++++++---- R/SingleTradeAddon.R | 6 ++--- R/runExampleCalcs.R | 2 - man/ExampleBasisVol.Rd | 5 +++- man/ExampleComm.Rd | 5 +++- man/ExampleCredit.Rd | 5 +++- man/ExampleFX.Rd | 5 +++- man/ExampleIRD.Rd | 5 +++- man/ExampleIRDCommMargined.Rd | 5 +++- man/ExampleIRDCredit.Rd | 5 +++- man/SACCRCalculator.Rd | 4 ++- 24 files changed, 196 insertions(+), 73 deletions(-)
Title: Quality Improvement Charts
Description: Functions for making run charts and basic Shewhart control
charts for measure and count data.
The main function, qic(), creates run and control charts and has a
simple interface with a rich set of options to control data analysis
and plotting, including options for automatic data aggregation by
subgroups, easy analysis of before-and-after data, exclusion of one
or more data points from analysis, and splitting charts into
sequential time periods.
Missing values and empty subgroups are handled gracefully.
Author: Jacob Anhoej [aut, cre],
Timo Roeder [ctb]
Maintainer: Jacob Anhoej <jacob@anhoej.net>
Diff between qicharts versions 0.5.1 dated 2016-03-24 and 0.5.3 dated 2016-11-28
DESCRIPTION | 8 +-- MD5 | 16 +++---- NEWS | 11 ++++ R/paretochart.R | 5 +- R/qic.R | 2 R/tcc.R | 2 build/vignette.rds |binary inst/doc/controlcharts.html | 98 +++++++++++++++----------------------------- inst/doc/runcharts.html | 62 ++++++++++----------------- 9 files changed, 87 insertions(+), 117 deletions(-)
Title: A Laboratory for Recursive Partytioning
Description: A computational toolbox for recursive partitioning.
The core of the package is ctree(), an implementation of
conditional inference trees which embed tree-structured
regression models into a well defined theory of conditional
inference procedures. This non-parametric class of regression
trees is applicable to all kinds of regression problems, including
nominal, ordinal, numeric, censored as well as multivariate response
variables and arbitrary measurement scales of the covariates.
Based on conditional inference trees, cforest() provides an
implementation of Breiman's random forests. The function mob()
implements an algorithm for recursive partitioning based on
parametric models (e.g. linear models, GLMs or survival
regression) employing parameter instability tests for split
selection. Extensible functionality for visualizing tree-structured
regression models is available.
Author: Torsten Hothorn [aut, cre],
Kurt Hornik [aut],
Carolin Strobl [aut],
Achim Zeileis [aut]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between party versions 1.1-1 dated 2016-11-23 and 1.1-2 dated 2016-11-28
party-1.1-1/party/R/Memory.R |only party-1.1-1/party/tests/IndependenceTest-regtest.R |only party-1.1-1/party/tests/IndependenceTest-regtest.Rout.save |only party-1.1-1/party/tests/Node-regtest.R |only party-1.1-1/party/tests/Node-regtest.Rout.save |only party-1.1-1/party/tests/Splits-regtest.R |only party-1.1-1/party/tests/Splits-regtest.Rout.save |only party-1.1-2/party/DESCRIPTION | 8 - party-1.1-2/party/MD5 | 35 +--- party-1.1-2/party/inst/NEWS | 5 party-1.1-2/party/inst/doc/MOB.pdf |binary party-1.1-2/party/inst/doc/party.pdf |binary party-1.1-2/party/tests/Distributions.R | 2 party-1.1-2/party/tests/Distributions.Rout.save | 92 ++++++------- party-1.1-2/party/tests/LinearStatistic-regtest.Rout.save | 2 party-1.1-2/party/tests/Predict-regtest.Rout.save | 2 party-1.1-2/party/tests/RandomForest-regtest.Rout.save | 2 party-1.1-2/party/tests/TestStatistic-regtest.Rout.save | 2 party-1.1-2/party/tests/TreeGrow-regtest.Rout.save | 2 party-1.1-2/party/tests/Utils-regtest.Rout.save | 2 party-1.1-2/party/tests/bugfixes.Rout.save | 2 party-1.1-2/party/tests/mob.Rout.save | 2 22 files changed, 80 insertions(+), 78 deletions(-)
Title: Applied Latent Semantic Analysis (LSA) Functions
Description: Provides functions that allow for convenient working
with Latent Semantic Analysis. For actually building an LSA space, use the
package 'lsa' or other specialized software.
Author: Fritz Guenther [aut, cre]
Maintainer: Fritz Guenther <fritz.guenther@uni-tuebingen.de>
Diff between LSAfun versions 0.5 dated 2016-02-23 and 0.5.1 dated 2016-11-28
ChangeLog | 7 +++++++ DESCRIPTION | 8 ++++---- MD5 | 38 +++++++++++++++++++------------------- NAMESPACE | 6 +++--- R/Cosine.r | 8 ++++++++ R/Predication.r | 8 ++++++++ R/asym.R | 8 ++++++++ R/choose.target.r | 8 ++++++++ R/coherence.r | 8 ++++++++ R/compose.r | 10 ++++++++++ R/conSIM.r | 8 ++++++++ R/costring.r | 8 ++++++++ R/distance.r | 8 ++++++++ R/multicos.r | 8 ++++++++ R/multicostring.r | 8 ++++++++ R/neighbors.r | 8 ++++++++ R/pairwise.r | 8 ++++++++ R/plausibility.r | 7 +++++++ R/plot_neighbors.r | 15 +++++++++++++++ R/plot_wordlist.r | 15 +++++++++++++++ 20 files changed, 176 insertions(+), 26 deletions(-)
Title: Transcriptomic Dynamics Models in Field Conditions
Description: Provides functionality for constructing
statistical models of transcriptomic dynamics in field conditions.
It further offers the function to predict expression of a gene given
the attributes of samples and meteorological data.
Author: Koji Iwayama [cre],
Yuri Aisaka [aut]
Maintainer: Koji Iwayama <fieldtranscriptome@gmail.com>
Diff between FIT versions 0.0.3 dated 2016-11-24 and 0.0.4 dated 2016-11-28
DESCRIPTION | 6 +++--- MD5 | 10 ++++++---- NAMESPACE | 1 + build/vignette.rds |binary src/Makevars |only src/Makevars.win |only src/prep.h | 2 +- 7 files changed, 11 insertions(+), 8 deletions(-)
Title: Implementation of 2D Correlation Analysis in R
Description: Implementation of two-dimensional (2D) correlation analysis based
on the Fourier-transformation approach described by Isao Noda (I. Noda
(1993) <DOI:10.1366/0003702934067694>). Additionally there are two plot
functions for the resulting correlation matrix: The first one creates
colored 2D plots, while the second one generates 3D plots.
Author: Robert Geitner [cre, aut],
Robby Fritzsch [aut],
Thomas Bocklitz [aut],
Juergen Popp [ctb, cph]
Maintainer: Robert Geitner <robert.geitner@uni-jena.de>
Diff between corr2D versions 0.1.11 dated 2016-10-17 and 0.1.12 dated 2016-11-28
DESCRIPTION | 10 ++-- MD5 | 16 +++---- NAMESPACE | 2 R/corr2d.R | 4 + R/corr2d_plot.R | 109 +++++++++++++++++++++++++++++-------------------- build/vignette.rds |binary inst/doc/corr2D.html | 8 +-- man/plot_corr2d.Rd | 7 ++- man/plot_corr2din3d.Rd | 8 ++- 9 files changed, 99 insertions(+), 65 deletions(-)
Title: Estimation and Gene Selection Based on the Compound Covariate
Method Under the Cox Proportional Hazard Model
Description: Cox regression for survival data with high-dimensional gene expressions.
Available are statistical methods in Emura et al (2012 PLoS ONE) <DOI:10.1371/journal.pone.0047627> and
Emura & Chen (2016 Stat Methods Med Res) <DOI:10.1177/0962280214533378>
and a survival dataset for non-small-cell lung cancer patients in Chen et al (2007 New Engl J Med) <DOI:10.1056/NEJMoa060096>.
Author: Takeshi Emura, Hsuan-Yu Chen, Yi-Hau Chen
Maintainer: Takeshi Emura <takeshiemura@gmail.com>
Diff between compound.Cox versions 2.1 dated 2016-10-21 and 3.0 dated 2016-11-28
DESCRIPTION | 19 +++++++++++-------- MD5 | 18 +++++++++++------- R/CG.Clayton.R |only data/Lung.rda |only man/CG.Clayton.Rd |only man/Lung.Rd |only man/X.pathway.Rd | 6 +++--- man/X.tag.Rd | 6 +++--- man/cindex.CV.Rd | 4 ++-- man/compound.Cox-package.Rd | 20 +++++++++++--------- man/dependCox.reg.CV.Rd | 6 +++--- man/dependCox.reg.Rd | 8 ++++---- 12 files changed, 48 insertions(+), 39 deletions(-)
Title: Conditional Inference Procedures in a Permutation Test Framework
Description: Conditional inference procedures for the general independence
problem including two-sample, K-sample (non-parametric ANOVA), correlation,
censored, ordered and multivariate problems.
Author: Torsten Hothorn [aut, cre],
Kurt Hornik [aut],
Mark A. van de Wiel [aut],
Henric Winell [aut],
Achim Zeileis [aut]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between coin versions 1.1-2 dated 2015-11-16 and 1.1-3 dated 2016-11-28
DESCRIPTION | 12 MD5 | 106 R/Classes.R | 8 R/Confints.R | 30 R/IndependenceTest.R | 2 R/InitMethods.R | 48 R/MTP.R | 2 R/SymmetryTest.R | 2 R/SymmetryTests.R | 12 R/Transformations.R | 51 R/helpers.R | 22 R/zAccess.R | 5 build/vignette.rds |binary inst/NEWS.Rd | 513 +- inst/doc/LegoCondInf.pdf |binary inst/doc/MAXtest.pdf |binary inst/doc/coin.pdf |binary inst/doc/coin_implementation.pdf |binary inst/doxygen.cfg | 56 man/ContingencyTests.Rd | 27 man/CorrelationTests.Rd | 2 man/IndependenceProblem-class.Rd | 2 man/LocationTests.Rd | 16 man/MarginalHomogeneityTests.Rd | 38 man/MaximallySelectedStatisticsTests.Rd | 2 man/NullDistribution.Rd | 80 man/PermutationDistribution-methods.Rd | 8 man/ScaleTests.Rd | 2 man/SurvivalTests.Rd | 2 man/Transformations.Rd | 3 src/Helpers.c | 10 src/LinearStatistic.c | 10 src/StreitbergRoehmel.c | 4 src/vandeWiel.c | 10 tests/Examples/coin-Ex.Rout.save | 6006 ++++++++++++++++---------------- tests/bugfixes.R | 36 tests/bugfixes.Rout.save | 67 tests/comparisons.R | 1 tests/comparisons.Rout.save | 7 tests/regtest_2sample.R | 3 tests/regtest_2sample.Rout.save | 9 tests/regtest_Ksample.R | 3 tests/regtest_Ksample.Rout.save | 9 tests/regtest_MTP.R | 3 tests/regtest_MTP.Rout.save | 9 tests/regtest_contingency.R | 4 tests/regtest_contingency.Rout.save | 10 tests/regtest_correlation.R | 3 tests/regtest_correlation.Rout.save | 9 tests/regtest_distribution.Rout.save | 8 tests/regtest_trafo.R | 1 tests/regtest_trafo.Rout.save | 7 vignettes/LegoCondInf.Rout.save | 4 vignettes/coin.Rout.save | 5 54 files changed, 3716 insertions(+), 3573 deletions(-)
Title: Animal Social Network Inference and Permutations for Ecologists
Description: Implements several tools that are used in animal social network analysis. In particular, this package provides the tools to infer groups and generate networks from observation data, perform permutation tests on the data, calculate lagged association rates, and performed multiple regression analysis on social network data.
Author: Damien R. Farine <dfarine@orn.mpg.de>
Maintainer: Damien R. Farine <dfarine@orn.mpg.de>
Diff between asnipe versions 1.0 dated 2016-09-13 and 1.1 dated 2016-11-28
DESCRIPTION | 8 ++--- MD5 | 10 +++---- R/get_network.R | 1 R/gmmevents.R | 71 +++++++++++++++++++++++++++++++++++++++++++++++--- man/asnipe-package.Rd | 4 +- man/gmmevents.Rd | 15 ++++++---- 6 files changed, 89 insertions(+), 20 deletions(-)
Title: Two Stage Hazard Rate Comparison
Description: Two-stage procedure compares hazard rate functions,
which may or may not cross each other.
Author: Jun Sheng, Peihua Qiu <qiu@stat.umn.edu>, and Charles J. Geyer
<charlie@stat.umn.edu>
Maintainer: Charles J. Geyer <charlie@stat.umn.edu>
Diff between TSHRC versions 0.1-3 dated 2013-03-30 and 0.1-4 dated 2016-11-28
DESCRIPTION | 14 +++++++------- LICENSE | 23 ++--------------------- MD5 | 16 ++++++++-------- tests/bar.R | 2 ++ tests/bar.Rout.save | 23 ++++++++++++++--------- tests/foo.R | 2 ++ tests/foo.Rout.save | 23 ++++++++++++++--------- tests/rats.R | 2 ++ tests/rats.Rout.save | 15 ++++++++++----- 9 files changed, 61 insertions(+), 59 deletions(-)
Title: Nonlinear Nonparametric Statistics
Description: Nonlinear nonparametric statistics using partial moments. Partial moments are the elements of variance and asymptotically approximate the area of f(x). These robust statistics provide the basis for nonlinear analysis while retaining linear equivalences.
Author: Fred Viole
Maintainer: Fred Viole <viole.nawrocki@gmail.com>
Diff between NNS versions 0.2.3 dated 2016-10-21 and 0.2.4 dated 2016-11-28
NNS-0.2.3/NNS/man/Feature.probability.Rd |only NNS-0.2.4/NNS/DESCRIPTION | 8 NNS-0.2.4/NNS/MD5 | 58 +++---- NNS-0.2.4/NNS/NAMESPACE | 4 NNS-0.2.4/NNS/R/ARMA.R | 2 NNS-0.2.4/NNS/R/Causation.R | 23 -- NNS-0.2.4/NNS/R/Correlation.R | 12 - NNS-0.2.4/NNS/R/Dependence.R | 39 ++-- NNS-0.2.4/NNS/R/Feature_probability.R | 18 +- NNS-0.2.4/NNS/R/Multivariate_Regression.R | 159 +++++++++++++------ NNS-0.2.4/NNS/R/NNS_term_matrix.R | 74 +++++++-- NNS-0.2.4/NNS/R/Partial_Moments.R | 100 ++++-------- NNS-0.2.4/NNS/R/Partition_Map.R | 151 ++++++++++++++---- NNS-0.2.4/NNS/R/Regression.R | 245 +++++++++++++++++++----------- NNS-0.2.4/NNS/R/dy_d_wrt.R | 67 +++++--- NNS-0.2.4/NNS/R/dy_dx.R | 30 +-- NNS-0.2.4/NNS/man/Co.LPM.Rd | 14 - NNS-0.2.4/NNS/man/Co.UPM.Rd | 14 - NNS-0.2.4/NNS/man/D.LPM.Rd | 14 - NNS-0.2.4/NNS/man/D.UPM.Rd | 14 - NNS-0.2.4/NNS/man/LPM.Rd | 5 NNS-0.2.4/NNS/man/NNS.Feature.prob.Rd |only NNS-0.2.4/NNS/man/NNS.term.matrix.Rd | 17 +- NNS-0.2.4/NNS/man/UPM.Rd | 6 NNS-0.2.4/NNS/man/VN.M.reg.Rd | 18 +- NNS-0.2.4/NNS/man/VN.cor.Rd | 6 NNS-0.2.4/NNS/man/VN.dep.Rd | 6 NNS-0.2.4/NNS/man/VN.reg.Rd | 25 ++- NNS-0.2.4/NNS/man/dy.d_.Rd | 31 ++- NNS-0.2.4/NNS/man/dy.dx.Rd | 10 - NNS-0.2.4/NNS/man/partition.map.Rd | 13 + 31 files changed, 754 insertions(+), 429 deletions(-)
Title: Get or Set UNIX Niceness
Description: Get or set UNIX priority (niceness) of running R process.
Author: Charles J. Geyer <charlie@stat.umn.edu>.
Maintainer: Charles J. Geyer <charlie@stat.umn.edu>
Diff between nice versions 0.4 dated 2013-03-31 and 0.4-1 dated 2016-11-28
nice-0.4-1/nice/DESCRIPTION | 13 ++++++------- nice-0.4-1/nice/LICENSE | 23 ++--------------------- nice-0.4-1/nice/MD5 | 7 +++---- nice-0.4-1/nice/tests/foo.Rout.save | 9 +++++---- nice-0.4/nice/foompter |only 5 files changed, 16 insertions(+), 36 deletions(-)
Title: A Text Mining Toolkit for Chinese Document
Description: The CTM package is designed to solve problems of text mining and is specific for Chinese document.
Author: Jim Liu, Quan Gu
Maintainer: Jim Liu <jimliu741523@gmail.com>
Diff between CTM versions 0.1 dated 2016-08-23 and 0.2 dated 2016-11-28
DESCRIPTION | 12 +- MD5 | 12 +- NAMESPACE | 1 R/CTM.R | 240 +++++++++++++++++++++++++++++++++---------------------- man/CDTM.Rd | 32 ++++--- man/CTDM.Rd | 30 ++++-- man/termCount.Rd | 21 ++-- 7 files changed, 207 insertions(+), 141 deletions(-)
Title: Authoring Books and Technical Documents with R Markdown
Description: Output formats and utilities for authoring books and technical documents with R Markdown.
Author: Yihui Xie [aut, cre],
JJ Allaire [ctb],
RStudio Inc [cph],
Bartek Szopka [ctb] (The jQuery Highlight plugin),
jQuery Foundation [cph] (jQuery library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/resources/AUTHORS),
MathQuill contributors [ctb] (The MathQuill library; authors listed in
inst/resources/AUTHORS),
FriendCode Inc [cph, ctb] (The gitbook style, with modifications)
Maintainer: Yihui Xie <xie@yihui.name>
Diff between bookdown versions 0.2 dated 2016-11-12 and 0.3 dated 2016-11-28
DESCRIPTION | 16 ++++++------ MD5 | 23 +++++++++-------- NAMESPACE | 4 --- NEWS.md | 18 ++++++++++++++ R/addins.R | 36 ---------------------------- R/gitbook.R | 4 +-- R/html.R | 27 ++++++++++++++------- R/latex.R | 18 ++++++++++---- R/publish.R | 2 - R/utils.R | 8 ------ README.md | 2 - inst/resources/gitbook/js/plugin-sharing.js | 12 ++++++++- inst/scripts/mathquill.R |only 13 files changed, 86 insertions(+), 84 deletions(-)
Title: A New Link Function that Blends Two Specified Link Functions
Description: A new link function that equals one specified link function up to a cutover then a linear rescaling of another specified link function. For use in glm() or glm2(). The intended use is in binary regression, in which case the first link should be set to "log" and the second to "logit". This ensures that fitted probabilities are between 0 and 1 and that exponentiated coefficients can be interpreted as relative risks for probabilities up to the cutoff.
Author: Robert Clark
Maintainer: "Robert Clark" <rclark@uow.edu.au>
Diff between blendedLink versions 0.1 dated 2016-05-30 and 0.2 dated 2016-11-28
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/pvalue.cutover.R | 21 ++++++++++++++++----- inst/CITATION | 2 +- inst/blendedLink.pdf |binary man/pvalue.cutover.Rd | 6 +++++- 6 files changed, 31 insertions(+), 16 deletions(-)
Title: Gene Regulatory Network Inference with Bc3net
Description: Implementation of the BC3NET algorithm for gene regulatory network inference (de Matos Simoes and Frank Emmert-Streib, Bagging Statistical Network Inference from Large-Scale Gene Expression Data, PLoS ONE 7(3): e33624, <doi:10.1371/journal.pone.0033624>).
Author: Ricardo de Matos Simoes [aut, cre],
Frank Emmert-Streib [aut]
Maintainer: Ricardo de Matos Simoes <ricardo_dematossimoes@dfci.harvard.edu>
Diff between bc3net versions 1.0.3 dated 2015-12-30 and 1.0.4 dated 2016-11-28
DESCRIPTION | 12 ++++++------ MD5 | 16 +++++++++++++--- NAMESPACE | 2 +- R/enrichment.R |only R/getgcc.R |only R/gpea.R |only data/exanet.rda |only data/exgensets.rda |only man/bc3net.Rd | 5 +++-- man/enrichment.Rd |only man/exanet.Rd |only man/exgensets.Rd |only man/getgcc.Rd |only man/gpea.Rd |only 14 files changed, 23 insertions(+), 12 deletions(-)