Title: Finding Unique or Duplicated Rows or Columns for Atomic Matrices
Description: An alternative implementation and extension (grpDuplicated) of base::duplicated.matrix, base:anyDuplicated.matrix and base::unique.matrix for matrices of atomic mode, avoiding the time consuming collapse of the matrix into a character vector.
Author: Long Qu [aut, cre]
Maintainer: Long Qu <long.qu@wright.edu>
Diff between uniqueAtomMat versions 0.1-1 dated 2016-02-29 and 0.1-2 dated 2016-03-01
DESCRIPTION | 8 MD5 | 28 +-- NAMESPACE | 32 +-- R/duplicated.matrix.R | 216 ++++++++++++------------ cleanup | 3 cleanup.win | 3 configure | 18 -- configure.win | 15 - man/grpDuplicated.Rd | 178 +++++++++---------- man/unique.Rd | 282 +++++++++++++++---------------- src/dupAtomMat.cpp | 4 src/dupAtomMatHash.cpp | 7 src/rcSetHash.h | 1 tests/testGrpDup.R | 440 ++++++++++++++++++++++++------------------------- tests/testUnique.R | 118 ++++++------- 15 files changed, 678 insertions(+), 675 deletions(-)
Title: An R Interface to the Oniguruma Regular Expression Library
Description: Provides an alternative to R's built-in functionality for handling
regular expressions, based on the Oniguruma library. Offers first-class
compiled regex objects, partial matching and function-based substitutions,
amongst other features.
Author: Jon Clayden, based on Onigmo by K. Kosako and K. Takata
Maintainer: Jon Clayden <code@clayden.org>
Diff between ore versions 1.2.2 dated 2016-01-27 and 1.3.0 dated 2016-03-01
DESCRIPTION | 10 +- MD5 | 77 ++++++++++++----- NAMESPACE | 3 NEWS | 15 +++ R/file.R |only R/match.R | 59 ++++++++++--- R/zzz.R | 8 + README.md | 39 ++++++++ man/matches.Rd | 13 ++ man/ore.file.Rd |only man/ore.ismatch.Rd | 7 + man/ore.search.Rd | 4 src/Makevars | 4 src/compile.c | 134 ++++++++++++++++++++++++------ src/compile.h | 8 + src/match.c | 179 +++++++++++++++++++++++++++++++++++------ src/match.h | 13 ++ src/onig/enc/big5.c |only src/onig/enc/cp1251.c |only src/onig/enc/cp932.c |only src/onig/enc/euc_jp.c |only src/onig/enc/euc_kr.c |only src/onig/enc/euc_tw.c |only src/onig/enc/gb18030.c |only src/onig/enc/iso8859_10.c |only src/onig/enc/iso8859_11.c |only src/onig/enc/iso8859_13.c |only src/onig/enc/iso8859_14.c |only src/onig/enc/iso8859_15.c |only src/onig/enc/iso8859_16.c |only src/onig/enc/iso8859_2.c |only src/onig/enc/iso8859_3.c |only src/onig/enc/iso8859_4.c |only src/onig/enc/iso8859_5.c |only src/onig/enc/iso8859_6.c |only src/onig/enc/iso8859_7.c |only src/onig/enc/iso8859_8.c |only src/onig/enc/iso8859_9.c |only src/onig/enc/jis |only src/onig/enc/koi8.c |only src/onig/enc/koi8_r.c |only src/onig/enc/sjis.c |only src/onig/enc/utf16_be.c |only src/onig/enc/utf16_le.c |only src/onig/enc/utf32_be.c |only src/onig/enc/utf32_le.c |only src/onig/oniguruma.h | 125 +++++++++++++--------------- src/print.c | 88 +++++++++++--------- src/print.h | 4 src/split.c | 4 src/subst.c | 16 +-- src/wcwidth.c |only src/wcwidth.h |only src/zzz.c | 4 tests/testthat/hello.bin |only tests/testthat/sjis.txt |only tests/testthat/test-10-match.R | 18 ++++ 57 files changed, 611 insertions(+), 221 deletions(-)
Title: Matrix Analysis and Normalization by Concordant Information
Enhancement
Description: High-dimensional data integration is a critical but difficult problem in genomics research because of potential biases from high-throughput experiments. We present MANCIE, a computational method for integrating two genomic data sets with homogenous dimensions from different sources based on a PCA procedure as an approximation to a Bayesian approach.
Author: Tao Wang, Chongzhi Zang
Maintainer: Tao Wang <tao.wang@utsouthwestern.edu>
Diff between MANCIE versions 1.2 dated 2015-09-25 and 1.4 dated 2016-03-01
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS | 4 ++++ R/summarize_mat.R | 13 ++++++++++--- man/summarize_mat.Rd | 7 +++++-- 5 files changed, 27 insertions(+), 13 deletions(-)
Title: Gaussian Processes for Pareto Front Estimation and Optimization
Description: Gaussian process regression models, a.k.a. kriging models, are
applied to global multiobjective optimization of black-box functions.
Multiobjective Expected Improvement and Step-wise Uncertainty Reduction
sequential infill criteria are available. A quantification of uncertainty
on Pareto fronts is provided using conditional simulations.
Author: Mickael Binois, Victor Picheny
Maintainer: Mickael Binois <mickael.binois@mines-stetienne.fr>
Diff between GPareto versions 1.0.1 dated 2015-07-03 and 1.0.2 dated 2016-03-01
DESCRIPTION | 18 - MD5 | 89 ++++--- NAMESPACE | 132 +++++----- NEWS | 33 ++ R/CPF.R | 45 +-- R/EHI_2d.R | 12 R/GPareto-package.R | 153 +++++------- R/GParetoptim.R | 134 +++++++--- R/ParetoSetDensity.R |only R/SAA_MEI.R | 27 +- R/TestFunctions.R | 72 +++-- R/checkPredict.R | 30 +- R/crit_EHI.R | 9 R/crit_EMI.R | 6 R/crit_SMS.R | 103 ++++---- R/crit_SUR.R | 12 R/crit_optimizer.R | 71 ++++- R/easyGParetoptim.R |only R/fastfun.R | 56 +++- R/getDesign.R |only R/integration_design_optim.R | 2 R/plotGPareto.R |only R/plotParetoEmp.R | 6 R/plotParetoGrid.R | 17 - R/plotSymDevFun.R | 3 R/plot_uncertainty.R |only build |only inst |only man/CPF.Rd | 225 ++++++++--------- man/GPareto.Rd | 373 ++++++++++++++--------------- man/GParetoptim.Rd | 331 +++++++++++++------------- man/ParetoSetDensity.Rd |only man/TestFunctions.Rd | 205 ++++++++-------- man/checkPredict.Rd | 72 ++--- man/crit_EHI.Rd | 162 ++++++------ man/crit_EMI.Rd | 152 ++++++------ man/crit_SMS.Rd | 153 ++++++------ man/crit_SUR.Rd | 201 ++++++++------- man/crit_optimizer.Rd | 503 ++++++++++++++++++++-------------------- man/easyGParetoptim.Rd |only man/fastfun-class.Rd | 125 +++++---- man/fastfun.Rd | 176 ++++++------- man/getDesign.Rd |only man/integration_design_optim.Rd | 144 +++++------ man/plotGPareto.Rd |only man/plotParetoEmp.Rd | 78 +++--- man/plotParetoGrid.Rd | 62 ++-- man/plotSymDevFun.Rd | 129 +++++----- man/plotSymDifRNP.Rd | 76 +++--- man/plot_uncertainty.Rd |only vignettes |only 51 files changed, 2221 insertions(+), 1976 deletions(-)
Title: Variable Selection for Generalized Linear Mixed Models by
L1-Penalized Estimation
Description: A variable selection approach for generalized linear mixed models by L1-penalized estimation is provided.
Author: Andreas Groll
Maintainer: Andreas Groll <groll@mathematik.uni-muenchen.de>
Diff between glmmLasso versions 1.4.0 dated 2016-03-01 and 1.4.1 dated 2016-03-01
DESCRIPTION | 8 +-- MD5 | 20 +++---- R/glmmLasso_RE.R | 94 ++++++++++++++++++++++--------------- R/glmmLasso_noRE.R | 82 ++++++++++++++++++++------------ R/glmm_final.r | 2 R/glmm_final.smooth.r | 2 R/glmm_final.smooth_noRE.R | 2 R/glmm_final_multi_random.r | 2 R/glmm_final_multi_random_smooth.r | 2 R/glmm_final_noRE.R | 2 man/glmmLasso.rd | 4 - 11 files changed, 130 insertions(+), 90 deletions(-)
Title: Flexible Modelling Functions for Epidemiological Data Analysis
Description: Provides flexible model fitting used in epidemiological data
analysis by a unified model specification, along with some data manipulation
functions. This package covers fitting of variety models including Cox
regression models, linear regression models, Poisson regression models, logistic
models and others whose likelihood is expressed in negative binomial, gamma and
Weibull distributions.
Author: Kazutaka Doi [aut,cre],
Kei Sakabe [ctb],
Masataka Taruri [ctb]
Maintainer: Kazutaka Doi <kztkdi@gmail.com>
Diff between epifit versions 0.0.5 dated 2016-02-01 and 0.0.6 dated 2016-03-01
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS | 6 ++++++ R/calcAge.R | 30 +++++++++++++++++++++--------- R/modes.R | 2 +- R/pullOneValue.R | 17 +++++++++++++++-- man/calcAge.Rd | 2 +- man/modes.Rd | 2 +- man/pullOneValue.Rd | 5 ++++- 9 files changed, 61 insertions(+), 27 deletions(-)
Title: Identify Similar Cases for Qualitative Case Studies
Description: Allows users to identify similar cases for qualitative case studies using statistical matching methods.
Author: Rich Nielsen
Maintainer: Rich Nielsen <rnielsen@mit.edu>
Diff between caseMatch versions 1.0.5 dated 2016-02-02 and 1.0.6 dated 2016-03-01
DESCRIPTION | 8 MD5 | 4 R/case.match.R | 541 ++++++++++++++++++++++++--------------------------------- 3 files changed, 243 insertions(+), 310 deletions(-)
Title: Bayesian Optimal INterval (BOIN) Design for Single-Agent and
Drug- Combination Phase I Clinical Trials
Description: The Bayesian optimal interval (BOIN) design is a novel phase I
clinical trial design for finding the maximum tolerated dose (MTD). It can be
used to design both single-agent and drug-combination trials. The BOIN design
is motivated by the top priority and concern of clinicians when testing a new
drug, which is to effectively treat patients and minimize the chance of exposing
them to subtherapeutic or overly toxic doses. The prominent advantage of the
BOIN design is that it achieves simplicity and superior performance at the same
time. The BOIN design is algorithm-based and can be implemented in a simple
way similar to the traditional 3+3 design. The BOIN design yields an average
performance that is comparable to that of the continual reassessment method
(CRM, one of the best model-based designs) in terms of selecting the MTD, but
has a substantially lower risk of assigning patients to subtherapeutic or overly
toxic doses.
Author: Ying Yuan and Suyu Liu
Maintainer: Ying Yuan <yyuan@mdanderson.org>
Diff between BOIN versions 2.0 dated 2015-09-04 and 2.1 dated 2016-03-01
BOIN-2.0/BOIN/R/conduct.comb.R |only BOIN-2.0/BOIN/man/BOIN-package.Rd |only BOIN-2.0/BOIN/man/conduct.comb.Rd |only BOIN-2.1/BOIN/DESCRIPTION | 35 - BOIN-2.1/BOIN/MD5 | 35 - BOIN-2.1/BOIN/NAMESPACE | 13 BOIN-2.1/BOIN/R/BOIN.R | 3 BOIN-2.1/BOIN/R/get.boundary.R | 299 +++++++++----- BOIN-2.1/BOIN/R/get.oc.R | 281 ++++++++----- BOIN-2.1/BOIN/R/get.oc.comb.R | 631 +++++++++++++++++++++++++++++-- BOIN-2.1/BOIN/R/get.oc.comb.phase12.R |only BOIN-2.1/BOIN/R/next.comb.R |only BOIN-2.1/BOIN/R/next.subtrial.R |only BOIN-2.1/BOIN/R/select.mtd.R | 235 +++++++---- BOIN-2.1/BOIN/R/select.mtd.comb.R | 196 +++++++-- BOIN-2.1/BOIN/man/get.boundary.Rd | 237 +++++------ BOIN-2.1/BOIN/man/get.oc.Rd | 216 ++++------ BOIN-2.1/BOIN/man/get.oc.comb.Rd | 246 ++++++------ BOIN-2.1/BOIN/man/get.oc.comb.phase12.Rd |only BOIN-2.1/BOIN/man/next.comb.Rd |only BOIN-2.1/BOIN/man/next.subtrial.Rd |only BOIN-2.1/BOIN/man/select.mtd.Rd | 153 +++---- BOIN-2.1/BOIN/man/select.mtd.comb.Rd | 186 ++++----- 23 files changed, 1820 insertions(+), 946 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-02-27 0.2.1
Title: Single and Multi-Objective Optimization Test Functions
Description: Provides generators for a high number of both single- and multi-
objective test functions which are frequently used for the benchmarking of
(numerical) optimization algorithms. Moreover, it offers a set of convenient
functions to generate, plot and work with objective functions.
Author: Jakob Bossek [aut, cre],
Pascal Kerschke [ctb]
Maintainer: Jakob Bossek <j.bossek@gmail.com>
Diff between smoof versions 1.2 dated 2016-01-22 and 1.3 dated 2016-03-01
DESCRIPTION | 14 MD5 | 60 +- NAMESPACE | 11 NEWS | 13 R/getLocalOptimum.R |only R/getMeanFunction.R |only R/getRefPoint.R |only R/makeMultiObjectiveFunction.R | 16 R/makeObjectiveFunction.R | 23 R/makeSingleObjectiveFunction.R | 12 R/mof.dtlz1.R | 3 R/mof.dtlz2.R | 3 R/mof.dtlz3.R | 3 R/mof.dtlz4.R | 3 R/mof.dtlz5.R | 3 R/mof.dtlz6.R | 3 R/mof.zdt1.R | 5 R/mof.zdt2.R | 3 R/mof.zdt3.R | 3 R/mof.zdt4.R | 3 R/mof.zdt6.R | 3 R/sof.mpm2.R | 42 + inst/mpm2.py | 604 +++++++++++----------- man/getLocalOptimum.Rd |only man/getMeanFunction.Rd |only man/getRefPoint.Rd |only man/makeMPM2Function.Rd | 21 man/makeMultiObjectiveFunction.Rd | 13 man/makeSingleObjectiveFunction.Rd | 12 tests/testthat/Rplots.pdf |binary tests/testthat/test_helpers.R | 31 + tests/testthat/test_isMultiobjective.R | 6 tests/testthat/test_makeSingleObjectiveFunction.R | 18 tests/testthat/test_soofuns.R | 13 34 files changed, 568 insertions(+), 376 deletions(-)
Title: Less Code, More Results
Description: Each function accomplishes the work of several or more standard R functions. For example, two function calls, Read() and CountAll(), read the data and generate summary statistics for all variables in the data frame, plus histograms and bar charts as appropriate. Other functions provide for descriptive statistics, a comprehensive regression analysis, analysis of variance and t-test, plotting, bar chart, histogram, box plot, density curves, calibrated power curve, reading multiple data formats with the same function call, variable labels, color themes, and a built-in help system. A confirmatory factor analysis of multiple indicator measurement models is available, as are pedagogical routines for data simulation such as for the Central Limit Theorem. Compatible with 'RStudio' and 'knitr' including generation of 'knitr' instructions for interpretative output.
Author: David W. Gerbing, School of Business Administration, Portland State University
Maintainer: David W. Gerbing <gerbing@pdx.edu>
Diff between lessR versions 3.4 dated 2015-12-27 and 3.4.4 dated 2016-03-01
lessR-3.4.4/lessR/DESCRIPTION | 10 lessR-3.4.4/lessR/MD5 | 164 ++++---- lessR-3.4.4/lessR/NAMESPACE | 7 lessR-3.4.4/lessR/NEWS | 97 +++++ lessR-3.4.4/lessR/R/ANOVA.R | 28 + lessR-3.4.4/lessR/R/ANOVAz1.R | 12 lessR-3.4.4/lessR/R/BarChart.R | 50 +- lessR-3.4.4/lessR/R/BoxPlot.R | 41 +- lessR-3.4.4/lessR/R/Density.R | 40 +- lessR-3.4.4/lessR/R/Help.R | 202 +++++----- lessR-3.4.4/lessR/R/Histogram.R | 57 ++- lessR-3.4.4/lessR/R/LineChart.R | 21 - lessR-3.4.4/lessR/R/Merge.R | 2 lessR-3.4.4/lessR/R/PieChart.R | 4 lessR-3.4.4/lessR/R/Plot.R | 2 lessR-3.4.4/lessR/R/Read.R | 43 +- lessR-3.4.4/lessR/R/Regression.R | 48 +- lessR-3.4.4/lessR/R/ScatterPlot.R | 344 ++++++++++++------ lessR-3.4.4/lessR/R/SummaryStats.R | 21 - lessR-3.4.4/lessR/R/VariableLabels.R | 25 + lessR-3.4.4/lessR/R/anova.Rmd.R |only lessR-3.4.4/lessR/R/bc.data.frame.R | 10 lessR-3.4.4/lessR/R/bc.zmain.R | 225 +++++++---- lessR-3.4.4/lessR/R/bx.zmain.R | 39 +- lessR-3.4.4/lessR/R/corCFA.R | 29 - lessR-3.4.4/lessR/R/corEFA.R | 13 lessR-3.4.4/lessR/R/corFA.Rmd.R |only lessR-3.4.4/lessR/R/corScree.R | 8 lessR-3.4.4/lessR/R/cr.data.frame.R | 56 +- lessR-3.4.4/lessR/R/details.R | 7 lessR-3.4.4/lessR/R/dist.Rmd.R |only lessR-3.4.4/lessR/R/dn.zmain.R | 44 +- lessR-3.4.4/lessR/R/dp.zmain.R | 69 +++ lessR-3.4.4/lessR/R/dpmat.zmain.R |only lessR-3.4.4/lessR/R/hst.zmain.R | 37 + lessR-3.4.4/lessR/R/lc.zmain.R | 75 ++- lessR-3.4.4/lessR/R/logit.z4Pred.R | 20 - lessR-3.4.4/lessR/R/pc.zmain.R | 89 +--- lessR-3.4.4/lessR/R/plt.zmain.R | 546 +++++++++++++++++++---------- lessR-3.4.4/lessR/R/reg.z1bckBasic.R | 11 lessR-3.4.4/lessR/R/reg.z3dnResidual.R | 4 lessR-3.4.4/lessR/R/reg.z3resfitResidual.R | 14 lessR-3.4.4/lessR/R/reg.z5Plot.R | 55 +- lessR-3.4.4/lessR/R/reg.zRmd.R |only lessR-3.4.4/lessR/R/set.R | 2 lessR-3.4.4/lessR/R/simCImean.R | 3 lessR-3.4.4/lessR/R/simCLT.R | 10 lessR-3.4.4/lessR/R/simFlips.R | 8 lessR-3.4.4/lessR/R/simMeans.R | 15 lessR-3.4.4/lessR/R/ss.zdata.frame.R | 6 lessR-3.4.4/lessR/R/ss.zfactor.R | 19 - lessR-3.4.4/lessR/R/ss.znumeric.R | 17 lessR-3.4.4/lessR/R/tt.z1group.R | 5 lessR-3.4.4/lessR/R/tt.z2group.R | 14 lessR-3.4.4/lessR/R/tt.zformula.R | 39 +- lessR-3.4.4/lessR/R/ttest.R | 32 + lessR-3.4.4/lessR/R/ttp2zgraph.R | 43 +- lessR-3.4.4/lessR/R/zzz.R | 401 +++++++++++++++------ lessR-3.4.4/lessR/man/ANOVA.Rd | 15 lessR-3.4.4/lessR/man/BarChart.Rd | 57 ++- lessR-3.4.4/lessR/man/BoxPlot.Rd | 39 +- lessR-3.4.4/lessR/man/Correlation.Rd | 2 lessR-3.4.4/lessR/man/Density.Rd | 38 +- lessR-3.4.4/lessR/man/Help.Rd | 6 lessR-3.4.4/lessR/man/Histogram.Rd | 50 +- lessR-3.4.4/lessR/man/LineChart.Rd | 32 + lessR-3.4.4/lessR/man/Merge.Rd | 4 lessR-3.4.4/lessR/man/Nest.Rd | 2 lessR-3.4.4/lessR/man/PieChart.Rd | 5 lessR-3.4.4/lessR/man/Read.Rd | 10 lessR-3.4.4/lessR/man/Regression.Rd | 58 +-- lessR-3.4.4/lessR/man/ScatterPlot.Rd | 268 +++++++------- lessR-3.4.4/lessR/man/Subset.Rd | 17 lessR-3.4.4/lessR/man/SummaryStats.Rd | 2 lessR-3.4.4/lessR/man/Transform.Rd | 6 lessR-3.4.4/lessR/man/VariableLabels.Rd | 4 lessR-3.4.4/lessR/man/corCFA.Rd | 57 +-- lessR-3.4.4/lessR/man/corEFA.Rd | 13 lessR-3.4.4/lessR/man/dataMach4.Rd | 2 lessR-3.4.4/lessR/man/print_outpiece.Rd | 2 lessR-3.4.4/lessR/man/set.Rd | 2 lessR-3.4.4/lessR/man/to.Rd | 6 lessR-3.4/lessR/R/DotPlot.R |only lessR-3.4/lessR/R/anova.zknitr.R |only lessR-3.4/lessR/R/corFA.zknitr.R |only lessR-3.4/lessR/R/dist.zknitr.R |only lessR-3.4/lessR/R/dp.R |only lessR-3.4/lessR/R/hl.R |only lessR-3.4/lessR/R/reg.zknitr.R |only 89 files changed, 2477 insertions(+), 1403 deletions(-)
Title: Ensemble Platform for Species Distribution Modeling
Description: Functions for species distribution modeling, calibration and
evaluation, ensemble of models.
Author: Wilfried Thuiller [aut, cre],
Damien Georges [aut, cre],
Robin Engler [aut],
Frank Breiner [aut]
Maintainer: Damien Georges <damien.georges2@gmail.com>
Diff between biomod2 versions 3.1-64 dated 2014-12-10 and 3.3-7 dated 2016-03-01
biomod2-3.1-64/biomod2/man/BinaryTransformation.Rd |only biomod2-3.3-7/biomod2/DESCRIPTION | 30 biomod2-3.3-7/biomod2/MD5 | 80 +- biomod2-3.3-7/biomod2/NAMESPACE | 32 biomod2-3.3-7/biomod2/NEWS | 31 biomod2-3.3-7/biomod2/R/BIOMOD_EnsembleForecasting.R | 36 biomod2-3.3-7/biomod2/R/BIOMOD_EnsembleModeling.R | 42 - biomod2-3.3-7/biomod2/R/BIOMOD_FormatingData.R | 4 biomod2-3.3-7/biomod2/R/BIOMOD_Modeling.R | 87 +- biomod2-3.3-7/biomod2/R/BIOMOD_ModelingOptions.R | 67 + biomod2-3.3-7/biomod2/R/BIOMOD_Projection.R | 13 biomod2-3.3-7/biomod2/R/BIOMOD_RangeSize.R | 25 biomod2-3.3-7/biomod2/R/BIOMOD_cv.R |only biomod2-3.3-7/biomod2/R/BIOMOD_presenceonly.R |only biomod2-3.3-7/biomod2/R/BIOMOD_tuning.R |only biomod2-3.3-7/biomod2/R/BinaryTransformation.R | 80 +- biomod2-3.3-7/biomod2/R/Biomod.Models_RE.R | 222 ++++- biomod2-3.3-7/biomod2/R/BiomodClass.R | 409 ++++------ biomod2-3.3-7/biomod2/R/CustomIndexMaker.R | 34 biomod2-3.3-7/biomod2/R/Evaluate.models.R | 126 ++- biomod2-3.3-7/biomod2/R/FilteringTransformation.R | 2 biomod2-3.3-7/biomod2/R/Prepare.Maxent.WorkDir.R | 113 ++ biomod2-3.3-7/biomod2/R/Projection.R | 36 biomod2-3.3-7/biomod2/R/Rescaler4.R | 1 biomod2-3.3-7/biomod2/R/biomod2_models-class.R | 534 ++++++++++---- biomod2-3.3-7/biomod2/R/deprecated_functions.R | 10 biomod2-3.3-7/biomod2/R/pseudo.abs.R | 248 ++++-- biomod2-3.3-7/biomod2/R/sample.factor.levels.R |only biomod2-3.3-7/biomod2/R/scope.R | 3 biomod2-3.3-7/biomod2/R/sre.R | 25 biomod2-3.3-7/biomod2/R/testnull.R | 1 biomod2-3.3-7/biomod2/R/transform.outputs.R | 4 biomod2-3.3-7/biomod2/R/variables_importance.R | 2 biomod2-3.3-7/biomod2/inst/doc/html/00Index.html | 15 biomod2-3.3-7/biomod2/man/BIOMOD.Model.Options-class.Rd | 3 biomod2-3.3-7/biomod2/man/BIOMOD.models.out-methods.Rd | 5 biomod2-3.3-7/biomod2/man/BIOMOD_FormatingData.Rd | 2 biomod2-3.3-7/biomod2/man/BIOMOD_Modeling.Rd | 23 biomod2-3.3-7/biomod2/man/BIOMOD_ModelingOptions.Rd | 45 - biomod2-3.3-7/biomod2/man/BIOMOD_cv.Rd |only biomod2-3.3-7/biomod2/man/BIOMOD_presenceonly.Rd |only biomod2-3.3-7/biomod2/man/BIOMOD_tuning.Rd |only biomod2-3.3-7/biomod2/man/BinaryTransformation-methods.Rd |only biomod2-3.3-7/biomod2/man/Find.Optim.Stat.Rd | 90 +- biomod2-3.3-7/biomod2/man/biomod2_model-class.Rd | 12 biomod2-3.3-7/biomod2/man/sample.factor.levels.Rd |only 46 files changed, 1620 insertions(+), 872 deletions(-)
Title: Calculate Accurate Precision-Recall and Receiver Operator
Characteristics Curves
Description: Accurate calculations and visualization of Precision-Recall and Receiver Operator Characteristics
curves.
Author: Takaya Saito [aut, cre],
Marc Rehmsmeier [aut]
Maintainer: Takaya Saito <takaya.saito@outlook.com>
Diff between precrec versions 0.2.0 dated 2015-12-21 and 0.3.1 dated 2016-03-01
DESCRIPTION | 15 +- MD5 | 15 +- NEWS.md |only README.md | 17 +-- inst/doc/introduction.Rmd | 7 + inst/doc/introduction.html | 165 +++++++++++++++++-------------- tests/testthat/test_g_autoplot2_curves.R | 8 - tests/testthat/test_g_autoplot3_points.R | 8 - vignettes/introduction.Rmd | 7 + 9 files changed, 139 insertions(+), 103 deletions(-)
Title: Dental Surface Complexity Measurement Tools
Description: Surface topography calculations of Dirichlet's normal energy,
relief index, and orientation patch count for teeth using scans of enamel caps.
Importantly, for the relief index and orientation patch count calculations to
work, the scanned tooth files must be oriented with the occlusal plane parallel
to the x and y axes, and perpendicular to the z axis. The files should also be
simplified, and smoothed in some other software prior to uploading into R.
Author: James D. Pampush [aut, cre, cph],
Julia M. Winchester [aut, cph],
Paul E. Morse [aut, cph],
Alexander Q. Vining [aut, cph]
Maintainer: James D. Pampush <jdpampush@gmail.com>
Diff between molaR versions 2.0 dated 2016-02-22 and 2.1 dated 2016-03-01
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/RFI.R | 10 ++++++++-- 3 files changed, 13 insertions(+), 7 deletions(-)
Title: Lattice Options and Add-Ins
Description: Various plots and functions that make use of the lattice/trellis plotting framework.
The plots (which include 'loaPlot', 'GoogleMap' and 'trianglePlot') use panelPal(), a function that
extends 'lattice' and 'hexbin' package methods to automate plot subscript and panel-to-panel
and panel-to-key synchronization/management.
Author: Karl Ropkins
Maintainer: Karl Ropkins <k.ropkins@its.leeds.ac.uk>
Diff between loa versions 0.2.22 dated 2015-01-20 and 0.2.38 dated 2016-03-01
DESCRIPTION | 28 +-- MD5 | 48 +++-- NAMESPACE | 23 ++ NEWS | 73 ++++++++- R/formulaHandler.R | 147 +++++++++++++++++- R/key.handlers.R | 75 +++++++++ R/lims.and.scales.handlers.R | 70 +++++++- R/loaPlot.R | 21 ++ R/other.panel.functions.R | 8 R/panelPal.R | 76 ++++++++- R/plot.argument.handlers.R | 11 - R/specialist.panels.01.R | 292 +++++++++++++++++++++++++++++++++++- R/stackPlot.R |only R/trianglePlot.R | 11 + data/lat.lon.meuse.RData |binary data/roadmap.meuse.RData |binary inst/CITATION | 19 ++ man/1.1.loaPlot.Rd | 4 man/1.2.googleMap.Rd | 2 man/1.3.trianglePlot.Rd | 2 man/1.4.stackPlot.Rd |only man/2.1.specialist.panels.Rd | 224 ++++++++++++++++++--------- man/4.2.plot.structure.handlers.Rd | 33 +++- man/4.3.lims.and.scales.handlers.Rd | 20 +- man/4.6.key.handlers.Rd | 14 + man/loa-package.Rd | 6 26 files changed, 1047 insertions(+), 160 deletions(-)
Title: An Implementation of the Grammar of Graphics
Description: An implementation of the grammar of graphics in R. It combines the
advantages of both base and lattice graphics: conditioning and shared axes
are handled automatically, and you can still build up a plot step by step
from multiple data sources. It also implements a sophisticated
multidimensional conditioning system and a consistent interface to map
data to aesthetic attributes. See http://ggplot2.org for more information,
documentation and examples.
Author: Hadley Wickham [aut, cre],
Winston Chang [aut],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between ggplot2 versions 2.0.0 dated 2015-12-18 and 2.1.0 dated 2016-03-01
ggplot2-2.0.0/ggplot2/R/translate-qplot-base.r |only ggplot2-2.0.0/ggplot2/man/translate_qplot_base.Rd |only ggplot2-2.1.0/ggplot2/DESCRIPTION | 49 - ggplot2-2.1.0/ggplot2/MD5 | 344 ++++++------- ggplot2-2.1.0/ggplot2/NAMESPACE | 11 ggplot2-2.1.0/ggplot2/NEWS.md |only ggplot2-2.1.0/ggplot2/R/aes.r | 2 ggplot2-2.1.0/ggplot2/R/annotation-custom.r | 17 ggplot2-2.1.0/ggplot2/R/annotation.r | 3 ggplot2-2.1.0/ggplot2/R/bin.R |only ggplot2-2.1.0/ggplot2/R/data.R | 6 ggplot2-2.1.0/ggplot2/R/facet-grid-.r | 142 +---- ggplot2-2.1.0/ggplot2/R/facet-wrap.r | 29 - ggplot2-2.1.0/ggplot2/R/fortify.r | 9 ggplot2-2.1.0/ggplot2/R/geom-.r | 5 ggplot2-2.1.0/ggplot2/R/geom-abline.r | 9 ggplot2-2.1.0/ggplot2/R/geom-bar.r | 12 ggplot2-2.1.0/ggplot2/R/geom-bin2d.r | 10 ggplot2-2.1.0/ggplot2/R/geom-blank.r | 24 ggplot2-2.1.0/ggplot2/R/geom-boxplot.r | 32 - ggplot2-2.1.0/ggplot2/R/geom-contour.r | 15 ggplot2-2.1.0/ggplot2/R/geom-count.r | 10 ggplot2-2.1.0/ggplot2/R/geom-crossbar.r | 10 ggplot2-2.1.0/ggplot2/R/geom-curve.r | 15 ggplot2-2.1.0/ggplot2/R/geom-density.r | 10 ggplot2-2.1.0/ggplot2/R/geom-density2d.r | 15 ggplot2-2.1.0/ggplot2/R/geom-dotplot.r | 24 ggplot2-2.1.0/ggplot2/R/geom-errorbar.r | 9 ggplot2-2.1.0/ggplot2/R/geom-errorbarh.r | 10 ggplot2-2.1.0/ggplot2/R/geom-freqpoly.r | 20 ggplot2-2.1.0/ggplot2/R/geom-hex.r | 10 ggplot2-2.1.0/ggplot2/R/geom-histogram.r | 16 ggplot2-2.1.0/ggplot2/R/geom-hline.r | 3 ggplot2-2.1.0/ggplot2/R/geom-jitter.r | 11 ggplot2-2.1.0/ggplot2/R/geom-label.R | 16 ggplot2-2.1.0/ggplot2/R/geom-linerange.r | 10 ggplot2-2.1.0/ggplot2/R/geom-map.r | 10 ggplot2-2.1.0/ggplot2/R/geom-path.r | 18 ggplot2-2.1.0/ggplot2/R/geom-point.r | 42 - ggplot2-2.1.0/ggplot2/R/geom-pointrange.r | 10 ggplot2-2.1.0/ggplot2/R/geom-polygon.r | 12 ggplot2-2.1.0/ggplot2/R/geom-quantile.r | 14 ggplot2-2.1.0/ggplot2/R/geom-raster.r | 13 ggplot2-2.1.0/ggplot2/R/geom-rect.r | 11 ggplot2-2.1.0/ggplot2/R/geom-ribbon.r | 16 ggplot2-2.1.0/ggplot2/R/geom-rug.r | 11 ggplot2-2.1.0/ggplot2/R/geom-segment.r | 13 ggplot2-2.1.0/ggplot2/R/geom-smooth.r | 21 ggplot2-2.1.0/ggplot2/R/geom-spoke.r | 10 ggplot2-2.1.0/ggplot2/R/geom-text.r | 16 ggplot2-2.1.0/ggplot2/R/geom-tile.r | 14 ggplot2-2.1.0/ggplot2/R/geom-violin.r | 15 ggplot2-2.1.0/ggplot2/R/geom-vline.r | 3 ggplot2-2.1.0/ggplot2/R/ggproto.r | 7 ggplot2-2.1.0/ggplot2/R/guide-legend.r | 45 + ggplot2-2.1.0/ggplot2/R/hexbin.R |only ggplot2-2.1.0/ggplot2/R/labels.r | 10 ggplot2-2.1.0/ggplot2/R/layer.r | 70 ++ ggplot2-2.1.0/ggplot2/R/margins.R | 4 ggplot2-2.1.0/ggplot2/R/panel.r | 4 ggplot2-2.1.0/ggplot2/R/plot-build.r | 4 ggplot2-2.1.0/ggplot2/R/plot-construction.r | 2 ggplot2-2.1.0/ggplot2/R/plot.r | 2 ggplot2-2.1.0/ggplot2/R/position-jitterdodge.R | 15 ggplot2-2.1.0/ggplot2/R/position-nudge.R | 4 ggplot2-2.1.0/ggplot2/R/save.r | 2 ggplot2-2.1.0/ggplot2/R/scale-.r | 5 ggplot2-2.1.0/ggplot2/R/scale-discrete-.r | 34 - ggplot2-2.1.0/ggplot2/R/scale-shape.r | 2 ggplot2-2.1.0/ggplot2/R/scale-size.r | 16 ggplot2-2.1.0/ggplot2/R/scale-type.R |only ggplot2-2.1.0/ggplot2/R/scales-.r | 57 -- ggplot2-2.1.0/ggplot2/R/stat-bin.r | 171 +++--- ggplot2-2.1.0/ggplot2/R/stat-bin2d.r | 19 ggplot2-2.1.0/ggplot2/R/stat-bindot.r | 19 ggplot2-2.1.0/ggplot2/R/stat-binhex.r | 59 -- ggplot2-2.1.0/ggplot2/R/stat-boxplot.r | 10 ggplot2-2.1.0/ggplot2/R/stat-contour.r | 9 ggplot2-2.1.0/ggplot2/R/stat-count.r | 10 ggplot2-2.1.0/ggplot2/R/stat-density-2d.r | 19 ggplot2-2.1.0/ggplot2/R/stat-density.r | 24 ggplot2-2.1.0/ggplot2/R/stat-ecdf.r | 41 - ggplot2-2.1.0/ggplot2/R/stat-ellipse.R | 18 ggplot2-2.1.0/ggplot2/R/stat-function.r | 37 - ggplot2-2.1.0/ggplot2/R/stat-identity.r | 28 - ggplot2-2.1.0/ggplot2/R/stat-qq.r | 17 ggplot2-2.1.0/ggplot2/R/stat-quantile.r | 18 ggplot2-2.1.0/ggplot2/R/stat-smooth-methods.r | 6 ggplot2-2.1.0/ggplot2/R/stat-smooth.r | 19 ggplot2-2.1.0/ggplot2/R/stat-sum.r | 12 ggplot2-2.1.0/ggplot2/R/stat-summary-2d.r | 29 - ggplot2-2.1.0/ggplot2/R/stat-summary-bin.R | 18 ggplot2-2.1.0/ggplot2/R/stat-summary-hex.r | 55 -- ggplot2-2.1.0/ggplot2/R/stat-summary.r | 57 -- ggplot2-2.1.0/ggplot2/R/stat-unique.r | 14 ggplot2-2.1.0/ggplot2/R/stat-ydensity.r | 27 - ggplot2-2.1.0/ggplot2/R/theme-defaults.r | 35 + ggplot2-2.1.0/ggplot2/R/theme.r | 59 +- ggplot2-2.1.0/ggplot2/R/translate-qplot-lattice.r | 13 ggplot2-2.1.0/ggplot2/R/utilities-grid.r | 8 ggplot2-2.1.0/ggplot2/R/zxx.r | 29 + ggplot2-2.1.0/ggplot2/build/partial.rdb |binary ggplot2-2.1.0/ggplot2/build/vignette.rds |binary ggplot2-2.1.0/ggplot2/inst/CITATION | 4 ggplot2-2.1.0/ggplot2/inst/doc/extending-ggplot2.Rmd | 12 ggplot2-2.1.0/ggplot2/inst/doc/extending-ggplot2.html | 196 ++++--- ggplot2-2.1.0/ggplot2/inst/doc/ggplot2-specs.Rmd | 6 ggplot2-2.1.0/ggplot2/inst/doc/ggplot2-specs.html | 97 ++- ggplot2-2.1.0/ggplot2/inst/staticdocs/index.r | 3 ggplot2-2.1.0/ggplot2/man/aes_.Rd | 2 ggplot2-2.1.0/ggplot2/man/annotate.Rd | 6 ggplot2-2.1.0/ggplot2/man/annotation_custom.Rd | 17 ggplot2-2.1.0/ggplot2/man/discrete_scale.Rd | 5 ggplot2-2.1.0/ggplot2/man/facet_grid.Rd | 142 +---- ggplot2-2.1.0/ggplot2/man/geom_abline.Rd | 38 - ggplot2-2.1.0/ggplot2/man/geom_bar.Rd | 40 - ggplot2-2.1.0/ggplot2/man/geom_bin2d.Rd | 44 - ggplot2-2.1.0/ggplot2/man/geom_blank.Rd | 53 -- ggplot2-2.1.0/ggplot2/man/geom_boxplot.Rd | 56 +- ggplot2-2.1.0/ggplot2/man/geom_contour.Rd | 45 - ggplot2-2.1.0/ggplot2/man/geom_count.Rd | 44 - ggplot2-2.1.0/ggplot2/man/geom_density.Rd | 50 + ggplot2-2.1.0/ggplot2/man/geom_density_2d.Rd | 45 - ggplot2-2.1.0/ggplot2/man/geom_dotplot.Rd | 40 - ggplot2-2.1.0/ggplot2/man/geom_errorbarh.Rd | 40 - ggplot2-2.1.0/ggplot2/man/geom_hex.Rd | 44 - ggplot2-2.1.0/ggplot2/man/geom_histogram.Rd | 86 +-- ggplot2-2.1.0/ggplot2/man/geom_jitter.Rd | 54 +- ggplot2-2.1.0/ggplot2/man/geom_linerange.Rd | 48 - ggplot2-2.1.0/ggplot2/man/geom_map.Rd | 46 - ggplot2-2.1.0/ggplot2/man/geom_path.Rd | 46 - ggplot2-2.1.0/ggplot2/man/geom_point.Rd | 40 - ggplot2-2.1.0/ggplot2/man/geom_polygon.Rd | 40 - ggplot2-2.1.0/ggplot2/man/geom_quantile.Rd | 47 - ggplot2-2.1.0/ggplot2/man/geom_ribbon.Rd | 40 - ggplot2-2.1.0/ggplot2/man/geom_rug.Rd | 40 - ggplot2-2.1.0/ggplot2/man/geom_segment.Rd | 44 - ggplot2-2.1.0/ggplot2/man/geom_smooth.Rd | 59 +- ggplot2-2.1.0/ggplot2/man/geom_spoke.Rd | 40 - ggplot2-2.1.0/ggplot2/man/geom_text.Rd | 41 - ggplot2-2.1.0/ggplot2/man/geom_tile.Rd | 49 + ggplot2-2.1.0/ggplot2/man/geom_violin.Rd | 57 +- ggplot2-2.1.0/ggplot2/man/gg-add.Rd | 2 ggplot2-2.1.0/ggplot2/man/ggtheme.Rd | 1 ggplot2-2.1.0/ggplot2/man/guide_legend.Rd | 29 - ggplot2-2.1.0/ggplot2/man/layer.Rd | 41 + ggplot2-2.1.0/ggplot2/man/margin.Rd | 4 ggplot2-2.1.0/ggplot2/man/presidential.Rd | 6 ggplot2-2.1.0/ggplot2/man/scale_discrete.Rd | 6 ggplot2-2.1.0/ggplot2/man/scale_gradient.Rd | 4 ggplot2-2.1.0/ggplot2/man/scale_shape.Rd | 4 ggplot2-2.1.0/ggplot2/man/scale_size.Rd | 2 ggplot2-2.1.0/ggplot2/man/stat_ecdf.Rd | 44 + ggplot2-2.1.0/ggplot2/man/stat_ellipse.Rd | 41 + ggplot2-2.1.0/ggplot2/man/stat_function.Rd | 45 + ggplot2-2.1.0/ggplot2/man/stat_identity.Rd | 39 - ggplot2-2.1.0/ggplot2/man/stat_qq.Rd | 45 + ggplot2-2.1.0/ggplot2/man/stat_summary.Rd | 92 +-- ggplot2-2.1.0/ggplot2/man/stat_summary_2d.Rd | 53 +- ggplot2-2.1.0/ggplot2/man/stat_unique.Rd | 41 + ggplot2-2.1.0/ggplot2/man/theme.Rd | 29 - ggplot2-2.1.0/ggplot2/man/theme_update.Rd | 25 ggplot2-2.1.0/ggplot2/man/translate_qplot_lattice.Rd | 13 ggplot2-2.1.0/ggplot2/tests/testthat/Rplots.pdf |only ggplot2-2.1.0/ggplot2/tests/testthat/test-aes-setting.r | 19 ggplot2-2.1.0/ggplot2/tests/testthat/test-boxplot.r | 37 - ggplot2-2.1.0/ggplot2/tests/testthat/test-empty-data.r | 8 ggplot2-2.1.0/ggplot2/tests/testthat/test-facet-strips.r |only ggplot2-2.1.0/ggplot2/tests/testthat/test-geom-boxplot.R |only ggplot2-2.1.0/ggplot2/tests/testthat/test-geom-freqpoly.R |only ggplot2-2.1.0/ggplot2/tests/testthat/test-geom-ribbon.R |only ggplot2-2.1.0/ggplot2/tests/testthat/test-geom-tile.R |only ggplot2-2.1.0/ggplot2/tests/testthat/test-grid-utils.R |only ggplot2-2.1.0/ggplot2/tests/testthat/test-layer.r | 13 ggplot2-2.1.0/ggplot2/tests/testthat/test-scale-discrete.R |only ggplot2-2.1.0/ggplot2/tests/testthat/test-stat-bin.R | 84 +++ ggplot2-2.1.0/ggplot2/tests/testthat/test-stat-bin2d.R | 4 ggplot2-2.1.0/ggplot2/tests/testthat/test-stats-function.r | 11 ggplot2-2.1.0/ggplot2/vignettes/extending-ggplot2.Rmd | 12 ggplot2-2.1.0/ggplot2/vignettes/ggplot2-specs.Rmd | 6 180 files changed, 2732 insertions(+), 2154 deletions(-)
Title: Network Meta-Analysis Using Bayesian Methods
Description: Network meta-analyses (mixed treatment comparisons) in the Bayesian
framework using JAGS. Includes methods to assess heterogeneity and
inconsistency, and a number of standard visualizations.
Author: Gert van Valkenhoef, Joel Kuiper
Maintainer: Gert van Valkenhoef <g.h.m.van.valkenhoef@rug.nl>
Diff between gemtc versions 0.7-1 dated 2015-10-12 and 0.8 dated 2016-03-01
gemtc-0.7-1/gemtc/inst/extdata/cipriani-efficacy.gemtc |only gemtc-0.7-1/gemtc/inst/extdata/luades-thrombolytic.gemtc |only gemtc-0.7-1/gemtc/inst/gemtc.study.baseline.priors.txt |only gemtc-0.7-1/gemtc/man/mtc.network.xml.Rd |only gemtc-0.7-1/gemtc/tests/data/fat-survival.data.txt |only gemtc-0.7-1/gemtc/tests/data/fat-survival.summaries.txt |only gemtc-0.7-1/gemtc/tests/data/luades-smoking.txt |only gemtc-0.7-1/gemtc/tests/data/parkinson-diff.data.txt |only gemtc-0.7-1/gemtc/tests/data/parkinson-shared.data-ab.txt |only gemtc-0.7-1/gemtc/tests/data/parkinson-shared.data-re.txt |only gemtc-0.7-1/gemtc/tests/data/parkinson.txt |only gemtc-0.7-1/gemtc/tests/testthat/test-unit-mtc.model_data.re.R |only gemtc-0.7-1/gemtc/tests/testthat/test-unit-write.mtc.network.R |only gemtc-0.8/gemtc/DESCRIPTION | 33 gemtc-0.8/gemtc/MD5 | 152 ++- gemtc-0.8/gemtc/NAMESPACE | 5 gemtc-0.8/gemtc/NEWS | 27 gemtc-0.8/gemtc/R/anohe.R | 4 gemtc-0.8/gemtc/R/arrayize.R |only gemtc-0.8/gemtc/R/code.R | 35 gemtc-0.8/gemtc/R/data.R | 40 gemtc-0.8/gemtc/R/deviance.R | 42 - gemtc-0.8/gemtc/R/inits.R | 404 ++++++---- gemtc-0.8/gemtc/R/likelihoods.R | 31 gemtc-0.8/gemtc/R/ll.binom.cloglog.R | 7 gemtc-0.8/gemtc/R/ll.binom.log.R | 7 gemtc-0.8/gemtc/R/ll.binom.logit.R | 7 gemtc-0.8/gemtc/R/ll.normal.identity.R | 8 gemtc-0.8/gemtc/R/ll.poisson.log.R | 10 gemtc-0.8/gemtc/R/mtc.hy.prior.R |only gemtc-0.8/gemtc/R/mtc.model.R | 73 - gemtc-0.8/gemtc/R/mtc.model.regression.R |only gemtc-0.8/gemtc/R/mtc.network.R | 10 gemtc-0.8/gemtc/R/mtc.network.xml.R | 50 - gemtc-0.8/gemtc/R/mtc.result.R | 34 gemtc-0.8/gemtc/R/plotCovariateEffect.R |only gemtc-0.8/gemtc/R/rank.probability.R | 8 gemtc-0.8/gemtc/R/regression.R |only gemtc-0.8/gemtc/R/relative.effect.R | 46 - gemtc-0.8/gemtc/R/relative.effect.table.R | 5 gemtc-0.8/gemtc/R/solveLP.R |only gemtc-0.8/gemtc/R/stopIfNotConsistent.R |only gemtc-0.8/gemtc/R/template.R | 15 gemtc-0.8/gemtc/data/atrialFibrillation.rdata |only gemtc-0.8/gemtc/data/blocker.rdata |only gemtc-0.8/gemtc/data/certolizumab.rdata |only gemtc-0.8/gemtc/data/dietfat.rdata |only gemtc-0.8/gemtc/data/hfPrevention.rdata |only gemtc-0.8/gemtc/data/parkinson-diff.rdata |only gemtc-0.8/gemtc/data/parkinson-shared.rdata |only gemtc-0.8/gemtc/inst/gemtc.armeffect.likelihood.txt | 2 gemtc-0.8/gemtc/inst/gemtc.fixedeffect.txt | 2 gemtc-0.8/gemtc/inst/gemtc.likelihood.binom.power.txt |only gemtc-0.8/gemtc/inst/gemtc.likelihood.binom.txt |only gemtc-0.8/gemtc/inst/gemtc.likelihood.normal.power.txt |only gemtc-0.8/gemtc/inst/gemtc.likelihood.normal.txt |only gemtc-0.8/gemtc/inst/gemtc.likelihood.poisson.power.txt |only gemtc-0.8/gemtc/inst/gemtc.likelihood.poisson.txt |only gemtc-0.8/gemtc/inst/gemtc.model.template.txt | 5 gemtc-0.8/gemtc/inst/gemtc.model.use.template.txt | 4 gemtc-0.8/gemtc/inst/gemtc.randomeffects.txt | 2 gemtc-0.8/gemtc/inst/gemtc.releffect.likelihood.power.r2.txt |only gemtc-0.8/gemtc/inst/gemtc.releffect.likelihood.power.rm.txt |only gemtc-0.8/gemtc/inst/gemtc.releffect.likelihood.r2.txt | 11 gemtc-0.8/gemtc/inst/gemtc.releffect.likelihood.rm.txt | 11 gemtc-0.8/gemtc/man/atrialFibrillation.Rd |only gemtc-0.8/gemtc/man/blocker.Rd |only gemtc-0.8/gemtc/man/certolizumab.Rd |only gemtc-0.8/gemtc/man/dietfat.Rd |only gemtc-0.8/gemtc/man/gemtc-package.Rd | 26 gemtc-0.8/gemtc/man/hfPrevention.Rd |only gemtc-0.8/gemtc/man/ll.call.Rd | 2 gemtc-0.8/gemtc/man/mtc.hy.prior.Rd | 4 gemtc-0.8/gemtc/man/mtc.model.Rd | 59 + gemtc-0.8/gemtc/man/mtc.network.Rd | 8 gemtc-0.8/gemtc/man/mtc.nodesplit.Rd | 2 gemtc-0.8/gemtc/man/mtc.run.Rd | 8 gemtc-0.8/gemtc/man/parkinson.Rd | 8 gemtc-0.8/gemtc/man/plotCovariateEffect.Rd |only gemtc-0.8/gemtc/man/rank.probability.Rd | 13 gemtc-0.8/gemtc/man/read.mtc.network.Rd |only gemtc-0.8/gemtc/man/relative.effect.Rd | 5 gemtc-0.8/gemtc/man/relative.effect.table.Rd | 3 gemtc-0.8/gemtc/tests/data/dietfat.fe.summaries.txt |only gemtc-0.8/gemtc/tests/data/dietfat.re.summaries.txt |only gemtc-0.8/gemtc/tests/data/parkinson-diff.summaries.txt | 75 - gemtc-0.8/gemtc/tests/data/parkinson-shared.summaries.txt | 76 - gemtc-0.8/gemtc/tests/data/parkinson.summaries.txt | 71 - gemtc-0.8/gemtc/tests/data/riskratio.summaries.txt | 2 gemtc-0.8/gemtc/tests/testthat/helper-regress.R | 17 gemtc-0.8/gemtc/tests/testthat/helper-validate.R | 42 - gemtc-0.8/gemtc/tests/testthat/test-regress-models.R | 129 ++- gemtc-0.8/gemtc/tests/testthat/test-unit-arrayize.R |only gemtc-0.8/gemtc/tests/testthat/test-unit-mtc.model_data.R | 107 +- gemtc-0.8/gemtc/tests/testthat/test-unit-mtc.model_inits.R | 292 +++++++ gemtc-0.8/gemtc/tests/testthat/test-unit-read.mtc.network.R | 6 gemtc-0.8/gemtc/tests/testthat/test-unit-regression.R |only gemtc-0.8/gemtc/tests/testthat/test-validate-dietfat-fe.R |only gemtc-0.8/gemtc/tests/testthat/test-validate-dietfat-re.R |only gemtc-0.8/gemtc/tests/testthat/test-validate-parkinson-diff.R | 3 gemtc-0.8/gemtc/tests/testthat/test-validate-parkinson-shared.R | 4 101 files changed, 1374 insertions(+), 678 deletions(-)
Title: Solvers for Initial Value Problems of Differential Equations
(ODE, DAE, DDE)
Description: Functions that solve initial value problems of a system
of first-order ordinary differential equations (ODE), of
partial differential equations (PDE), of differential
algebraic equations (DAE), and of delay differential
equations. The functions provide an interface to the FORTRAN
functions lsoda, lsodar, lsode, lsodes of the ODEPACK
collection, to the FORTRAN functions dvode and daspk and a
C-implementation of solvers of the Runge-Kutta family with
fixed or variable time steps. The package contains routines
designed for solving ODEs resulting from 1-D, 2-D and 3-D
partial differential equations (PDE) that have been converted
to ODEs by numerical differencing.
Author: Karline Soetaert [aut],
Thomas Petzoldt [aut, cre],
R. Woodrow Setzer [aut],
odepack authors [cph]
Maintainer: Thomas Petzoldt <thomas.petzoldt@tu-dresden.de>
Diff between deSolve versions 1.12 dated 2015-07-06 and 1.13 dated 2016-03-01
DESCRIPTION | 6 MD5 | 72 - NEWS | 14 R/Utilities.R | 16 R/checkevents.R | 4 R/daspk.R | 6 R/diagnostics.R | 360 ++++--- R/euler.R | 295 +++--- R/lsoda.R | 5 R/lsodar.R | 6 R/lsode.R | 6 R/matplot.R | 4 R/radau.R | 5 R/rk.R | 447 +++++---- R/rk4.R | 203 ++-- R/vode.R | 6 build/vignette.rds |binary data/ccl4data.rda |binary inst/CITATION | 48 - inst/doc/compiledCode.R | 708 +++++++-------- inst/doc/compiledCode.pdf |binary inst/doc/deSolve.R | 2074 +++++++++++++++++++++++----------------------- inst/doc/deSolve.pdf |binary man/deSolve.Rd | 14 man/events.Rd | 26 man/plot.deSolve.Rd | 2 man/rk.Rd | 4 man/rkMethod.Rd | 54 - src/call_daspk.c | 4 src/call_lsoda.c | 11 src/call_radau.c | 2 src/ex_SCOC.c | 8 src/forcings.c | 7 src/rk_auto.c | 24 src/rk_fixed.c | 21 src/rk_implicit.c | 81 - vignettes/.install_extras | 2 vignettes/integration.bib | 446 ++++----- 38 files changed, 2573 insertions(+), 2418 deletions(-)
Title: Query 'Team Cymru' 'IP' Address, Autonomous System Number
('ASN'), Border Gateway Protocol ('BGP'), Bogon and 'Malware'
Hash Data Services
Description: A toolkit for querying 'Team Cymru' <http://team-cymru.org> 'IP'
address, Autonomous System Number ('ASN'), Border Gateway Protocol ('BGP'), Bogon
and 'Malware' Hash Data Services.
Author: Bob Rudis [aut, cre]
Maintainer: Bob Rudis <bob@rudis.net>
Diff between cymruservices versions 0.1.1 dated 2015-07-27 and 0.2.0 dated 2016-03-01
DESCRIPTION | 21 ++--- MD5 | 32 ++++---- NAMESPACE | 3 NEWS |only R/asn.R | 141 +++++++++++++++++++++++++++--------- R/bogons.R | 121 ++++++++++++++++++++++-------- R/cymruservices-package.r | 1 R/malwarehash.R | 37 ++++++--- R/utils.R | 2 README.md |only man/bulk_origin.Rd | 13 ++- man/bulk_origin_asn.Rd | 13 ++- man/bulk_peer.Rd | 13 ++- man/cymruservices.Rd | 2 man/ipv4_bogons.Rd | 6 + man/ipv6_bogons.Rd | 6 + man/malware_hash.Rd | 13 ++- tests/testthat/test-cymruservices.R | 31 +++++-- 18 files changed, 328 insertions(+), 127 deletions(-)
Title: A Compression Format Optimized for the Web
Description: A lossless compressed data format that uses a combination of the
LZ77 algorithm and Huffman coding. Brotli is similar in speed to deflate (gzip)
but offers more dense compression.
Author: Jeroen Ooms [aut, cre],
Google, Inc [aut, cph] (Brotli C++ library)
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between brotli versions 0.5 dated 2016-01-23 and 0.6 dated 2016-03-01
brotli-0.5/brotli/src/dec/streams.c |only brotli-0.5/brotli/src/dec/streams.h |only brotli-0.6/brotli/DESCRIPTION | 13 brotli-0.6/brotli/MD5 | 82 +- brotli-0.6/brotli/NAMESPACE | 2 brotli-0.6/brotli/NEWS | 4 brotli-0.6/brotli/inst/doc/benchmarks.html | 8 brotli-0.6/brotli/man/brotli.Rd | 2 brotli-0.6/brotli/src/Makevars | 14 brotli-0.6/brotli/src/dec/bit_reader.c | 6 brotli-0.6/brotli/src/dec/bit_reader.h | 46 - brotli-0.6/brotli/src/dec/context.h | 8 brotli-0.6/brotli/src/dec/decode.c | 473 ++++++---------- brotli-0.6/brotli/src/dec/decode.h | 136 +--- brotli-0.6/brotli/src/dec/dictionary.c | 2 brotli-0.6/brotli/src/dec/dictionary.h | 15 brotli-0.6/brotli/src/dec/huffman.c | 207 +++---- brotli-0.6/brotli/src/dec/huffman.h | 23 brotli-0.6/brotli/src/dec/port.h | 50 - brotli-0.6/brotli/src/dec/prefix.h | 2 brotli-0.6/brotli/src/dec/state.c | 26 brotli-0.6/brotli/src/dec/state.h | 23 brotli-0.6/brotli/src/dec/transform.h | 82 +- brotli-0.6/brotli/src/dec/types.h | 4 brotli-0.6/brotli/src/enc/backward_references.cc | 88 +- brotli-0.6/brotli/src/enc/backward_references.h | 2 brotli-0.6/brotli/src/enc/bit_cost.h | 2 brotli-0.6/brotli/src/enc/block_splitter.h | 2 brotli-0.6/brotli/src/enc/brotli_bit_stream.cc | 6 brotli-0.6/brotli/src/enc/brotli_bit_stream.h | 1 brotli-0.6/brotli/src/enc/command.h | 10 brotli-0.6/brotli/src/enc/compress_fragment.cc | 1 brotli-0.6/brotli/src/enc/compress_fragment_two_pass.cc | 1 brotli-0.6/brotli/src/enc/encode.cc | 17 brotli-0.6/brotli/src/enc/encode.h | 9 brotli-0.6/brotli/src/enc/encode_parallel.cc | 5 brotli-0.6/brotli/src/enc/hash.h | 312 +++++++++- brotli-0.6/brotli/src/enc/histogram.h | 4 brotli-0.6/brotli/src/enc/metablock.h | 2 brotli-0.6/brotli/src/enc/ringbuffer.h | 13 brotli-0.6/brotli/src/enc/streams.cc | 2 brotli-0.6/brotli/src/enc/streams.h | 10 brotli-0.6/brotli/src/wrapper.cc | 52 - 43 files changed, 907 insertions(+), 860 deletions(-)
Title: Analysis of Ecological Data : Exploratory and Euclidean Methods
in Environmental Sciences
Description: Multivariate data analysis and graphical display.
Author: Stéphane Dray <stephane.dray@univ-lyon1.fr>, Anne-Béatrice Dufour <anne-beatrice.dufour@univ-lyon1.fr>, and Jean Thioulouse <jean.thioulouse@univ-lyon1.fr>, with contributions from Thibaut Jombart, Sandrine Pavoine, Jean R. Lobry, Sébastien Ollier, and Aurélie Siberchicot. Based on earlier work by Daniel Chessel.
Maintainer: Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Diff between ade4 versions 1.7-3 dated 2015-11-22 and 1.7-4 dated 2016-03-01
ChangeLog | 67 ++++++++++++++++++++++++++++++++++++++++++++++++++ DESCRIPTION | 8 ++--- MD5 | 18 +++++++------ NAMESPACE | 1 R/dpcoa.R | 6 ++-- R/mfa.R | 2 - R/plot.4thcorner.R | 6 ++-- R/randtest.dpcoa.R |only man/randtest.dpcoa.Rd |only man/testdim.Rd | 4 +- src/fourthcorner.c | 2 - 11 files changed, 94 insertions(+), 20 deletions(-)
Title: Manage Massive Matrices with Shared Memory and Memory-Mapped
Files
Description: Create, store, access, and manipulate massive matrices.
Matrices are allocated to shared memory and may use memory-mapped
files. Packages 'biganalytics', 'bigtabulate', 'synchronicity', and
'bigalgebra' provide advanced functionality.
Author: Michael J. Kane <kaneplusplus@gmail.com>, John W. Emerson
<jayemerson@gmail.com>, Peter Haverty <haverty.peter@gene.com>, and Charles
Determan Jr. <cdetermanjr@gmail.com>
Maintainer: Michael J. Kane <bigmemoryauthors@gmail.com>
Diff between bigmemory versions 4.5.11 dated 2016-02-22 and 4.5.17 dated 2016-03-01
DESCRIPTION | 8 +-- MD5 | 28 +++++----- NEWS | 2 R/bigmemory.R | 105 ++++++++++++++++++++++------------------- R/hello-bigmemory.R | 2 man/attach.big.matrix.Rd | 7 -- man/big.matrix.Rd | 22 -------- man/bigmemory-package.Rd | 2 man/flush-methods.Rd | 5 + man/sub.big.matrix.Rd | 4 - man/write.big.matrix.Rd | 21 +++++--- src/BigMatrix.cpp | 7 +- tests/testthat/test_create.R | 8 +-- tests/testthat/test_misc.R | 9 +-- tests/testthat/test_readonly.R | 54 ++++++++++----------- 15 files changed, 138 insertions(+), 146 deletions(-)
Title: 'Rcpp' Integration for the 'Eigen' Templated Linear Algebra
Library
Description: R and 'Eigen' integration using 'Rcpp'.
'Eigen' is a C++ template library for linear algebra: matrices,
vectors, numerical solvers and related algorithms. It supports dense
and sparse matrices on integer, floating point and complex numbers,
decompositions of such matrices, and solutions of linear systems. Its
performance on many algorithms is comparable with some of the best
implementations based on 'Lapack' and level-3 'BLAS'.
The 'RcppEigen' package includes the header files from the 'Eigen' C++
template library (currently version 3.2.8). Thus users do not need to
install 'Eigen' itself in order to use 'RcppEigen'.
Since version 3.1.1, 'Eigen' is licensed under the Mozilla Public License
(version 2); earlier version were licensed under the GNU LGPL version 3 or
later. 'RcppEigen' (the 'Rcpp' bindings/bridge to 'Eigen') is licensed under
the GNU GPL version 2 or later, as is the rest of 'Rcpp'.
Author: Douglas Bates, Dirk Eddelbuettel, Romain Francois, and Yixuan Qiu;
the authors of Eigen for the included version of Eigen
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppEigen versions 0.3.2.8.0 dated 2016-02-23 and 0.3.2.8.1 dated 2016-03-01
ChangeLog | 15 DESCRIPTION | 8 MD5 | 18 inst/NEWS.Rd | 9 inst/doc/RcppEigen-Introduction.pdf |binary inst/include/Eigen/src/SparseCore/CompressedStorage.h | 5 inst/include/Eigen/src/SparseCore/SparseBlock.h | 1077 ++++++++---------- inst/include/Eigen/src/SparseCore/SparseMatrix.h | 12 inst/include/Eigen/src/SparseCore/SparseRedux.h | 4 inst/include/Eigen/src/SparseCore/SparseVector.h | 10 10 files changed, 592 insertions(+), 566 deletions(-)
Title: Variable Selection for Generalized Linear Mixed Models by
L1-Penalized Estimation
Description: A variable selection approach for generalized linear mixed models by L1-penalized estimation is provided.
Author: Andreas Groll
Maintainer: Andreas Groll <groll@mathematik.uni-muenchen.de>
Diff between glmmLasso versions 1.3.7 dated 2015-11-20 and 1.4.0 dated 2016-03-01
DESCRIPTION | 10 MD5 | 43 NAMESPACE | 19 R/family_acat.R |only R/family_cumulative.R |only R/glmmLasso.r | 107 - R/glmmLassoControl.r | 4 R/glmmLasso_RE.R | 2048 ++++++++++++++++++------------------- R/glmmLasso_noRE.R | 1858 ++++++++++++++------------------- R/glmm_final.r | 245 +--- R/glmm_final.smooth.r | 269 ++-- R/glmm_final.smooth_noRE.R | 196 +-- R/glmm_final_multi_random.r | 190 ++- R/glmm_final_multi_random_smooth.r | 206 ++- R/glmm_final_noRE.R | 185 +-- R/helpers.R |only R/likelihood.r | 33 R/logLik.glmmLasso.r | 67 - data/knee.RData |only demo/glmmLasso-soccer.r | 6 man/acat.Rd |only man/cumulative.Rd |only man/glmmLasso.rd | 45 man/glmmLassoControl.rd | 9 man/knee.Rd |only man/soccer.Rd | 6 26 files changed, 2617 insertions(+), 2929 deletions(-)
Title: Tools for Parsing and Generating XML Within R and S-Plus
Description: Many approaches for both reading and
creating XML (and HTML) documents (including DTDs), both local
and accessible via HTTP or FTP. Also offers access to an
'XPath' "interpreter".
Author: Duncan Temple Lang and the CRAN Team
Maintainer: Duncan Temple Lang <duncan@r-project.org>
Diff between XML versions 3.98-1.3 dated 2015-06-30 and 3.98-1.4 dated 2016-03-01
DESCRIPTION | 8 - DESCRIPTION.in | 2 Docs/CreatingXML.xml | 2 Docs/MemoryManagement.html | 42 +++---- Docs/MemoryManagement.pdf |binary Docs/ModernDoc.Rdb | 4 Docs/ModernDoc.html | 16 +- Docs/ModernDoc.pdf |binary Docs/WritingXML.html | 2 Docs/description.nw | 2 Docs/description.xml | 4 Docs/htmlTable.xml | 2 Docs/shortIntro.xml | 6 - FAQ.html | 6 - GNUmakefile.admin | 2 MD5 | 182 +++++++++++++++++----------------- R/XMLClasses.R | 4 R/getRelativeURL.R | 20 +-- R/xmlInternalSource.R | 4 Rsamples/addChildren.R | 4 Rsamples/ns.R | 10 - Rsamples/tt.R | 2 Todo.xml | 6 - index.html | 14 +- index.html.in | 14 +- inst/exampleData/catalog.xml | 6 - inst/exampleData/cleanNamespace.xml | 4 inst/exampleData/longitudinalData.xml | 2 inst/exampleData/namespaces.xml | 4 inst/exampleData/namespaces2.xml | 4 inst/exampleData/redundantNS.xml | 4 inst/exampleData/tagnames.xml | 4 inst/exampleData/test.xml | 2 inst/exampleData/writeRS.xml | 2 inst/exampleData/xpathTest.xml | 4 inst/examples/GNUmakefile | 2 inst/examples/HTMLText.R | 2 inst/examples/RhelpInfo.xml | 2 inst/examples/catalog.R | 2 inst/examples/foo.html | 2 inst/examples/getElements.S | 4 inst/examples/gettingStarted.html | 38 +++---- inst/examples/newNodes.R | 2 inst/examples/prompt.xml | 2 inst/examples/xmlTags.xml | 4 man/AssignXMLNode.Rd | 2 man/addChildren.Rd | 4 man/append.XMLNode.Rd | 2 man/asXMLNode.Rd | 2 man/catalogResolve.Rd | 8 - man/catalogs.Rd | 4 man/dtdElement.Rd | 2 man/dtdElementValidEntry.Rd | 2 man/dtdIsAttribute.Rd | 2 man/dtdValidElement.Rd | 2 man/genericSAXHandlers.Rd | 2 man/getHTMLLinks.Rd | 6 - man/getNodeSet.Rd | 22 ++-- man/getRelativeURL.Rd | 2 man/getXMLErrors.Rd | 2 man/length.XMLNode.Rd | 2 man/libxmlVersion.Rd | 2 man/names.XMLNode.Rd | 2 man/newXMLDoc.Rd | 14 +- man/parseDTD.Rd | 2 man/parseURI.Rd | 14 +- man/parseXMLAndAdd.Rd | 4 man/print.Rd | 2 man/readHTMLList.Rd | 2 man/readHTMLTable.Rd | 2 man/saveXML.Rd | 2 man/supportsExpat.Rd | 2 man/xmlApply.Rd | 2 man/xmlAttributeType.Rd | 2 man/xmlContainsEntity.Rd | 2 man/xmlDOMApply.Rd | 2 man/xmlElementsByTagName.Rd | 4 man/xmlEventHandler.Rd | 2 man/xmlEventParse.Rd | 2 man/xmlGetAttr.Rd | 2 man/xmlHandler.Rd | 2 man/xmlName.Rd | 2 man/xmlNamespace.Rd | 4 man/xmlNode.Rd | 4 man/xmlOutput.Rd | 8 - man/xmlParseDoc.Rd | 4 man/xmlRoot.Rd | 2 man/xmlSize.Rd | 2 man/xmlSubset.Rd | 2 man/xmlTree.Rd | 12 +- man/xmlTreeParse.Rd | 2 man/xmlValue.Rd | 2 92 files changed, 316 insertions(+), 316 deletions(-)
Title: Split-Population Duration (Cure) Regression
Description: Functions for estimating split-duration regression models and
various associated generic function methods.
Author: Andreas Beger [aut, cre],
Daina Chiba [aut],
Daniel Hill [aut],
Nils Metternich [aut],
Shahryar Minhas [aut],
Michael Ward [cph]
Maintainer: Andreas Beger <adbeger@gmail.com>
Diff between spduration versions 0.14.0 dated 2015-10-27 and 0.15.0 dated 2016-03-01
spduration-0.14.0/spduration/man/logLik.spdur.Rd |only spduration-0.14.0/spduration/man/nobs.spdur.Rd |only spduration-0.15.0/spduration/DESCRIPTION | 12 spduration-0.15.0/spduration/MD5 | 93 ++--- spduration-0.15.0/spduration/NAMESPACE | 11 spduration-0.15.0/spduration/NEWS |only spduration-0.15.0/spduration/NEWS.md |only spduration-0.15.0/spduration/R/accessors.spdur.R | 167 ++++++---- spduration-0.15.0/spduration/R/fit-stats.R |only spduration-0.15.0/spduration/R/plot.spdur.R | 80 ++-- spduration-0.15.0/spduration/R/predict.spdur.R | 58 ++- spduration-0.15.0/spduration/R/spdur.R | 57 ++- spduration-0.15.0/spduration/R/summary.spdur.R | 50 +- spduration-0.15.0/spduration/README.md | 5 spduration-0.15.0/spduration/data/model.coups.rda |binary spduration-0.15.0/spduration/man/AIC.spdur.Rd | 5 spduration-0.15.0/spduration/man/BIC.spdur.Rd | 5 spduration-0.15.0/spduration/man/accessors.Rd |only spduration-0.15.0/spduration/man/add_duration.Rd | 55 +-- spduration-0.15.0/spduration/man/as.data.frame.spdur.Rd | 11 spduration-0.15.0/spduration/man/attempt_date.Rd | 2 spduration-0.15.0/spduration/man/bscoup.Rd | 4 spduration-0.15.0/spduration/man/coups.Rd | 8 spduration-0.15.0/spduration/man/expand.call.Rd | 8 spduration-0.15.0/spduration/man/forecast.Rd | 2 spduration-0.15.0/spduration/man/forecast.default.Rd | 2 spduration-0.15.0/spduration/man/forecast.spdur.Rd | 9 spduration-0.15.0/spduration/man/hazard.Rd | 2 spduration-0.15.0/spduration/man/loglog.Rd | 2 spduration-0.15.0/spduration/man/loglog_lnl.Rd | 2 spduration-0.15.0/spduration/man/model.coups.Rd | 4 spduration-0.15.0/spduration/man/panel_lag.Rd | 13 spduration-0.15.0/spduration/man/plot.spdur.Rd | 7 spduration-0.15.0/spduration/man/plot_hazard.Rd | 30 + spduration-0.15.0/spduration/man/plot_hazard1.Rd | 2 spduration-0.15.0/spduration/man/plot_hazard2.Rd | 2 spduration-0.15.0/spduration/man/predict.spdur.Rd | 48 +- spduration-0.15.0/spduration/man/print.summary.spdur.Rd | 5 spduration-0.15.0/spduration/man/separationplot.spdur.Rd | 17 - spduration-0.15.0/spduration/man/spdur.Rd | 33 + spduration-0.15.0/spduration/man/spduration.Rd | 26 - spduration-0.15.0/spduration/man/sploglog.Rd | 2 spduration-0.15.0/spduration/man/sploglog_lnl.Rd | 2 spduration-0.15.0/spduration/man/spweib_lnl.Rd | 2 spduration-0.15.0/spduration/man/spweibull.Rd | 2 spduration-0.15.0/spduration/man/summary.spdur.Rd | 5 spduration-0.15.0/spduration/man/weib_lnl.Rd | 2 spduration-0.15.0/spduration/man/weibull.Rd | 2 spduration-0.15.0/spduration/man/xtable.spdur.Rd | 3 spduration-0.15.0/spduration/tests/testthat/Rplots.pdf |only spduration-0.15.0/spduration/tests/testthat/test_predict.spdur.R | 19 + 51 files changed, 524 insertions(+), 352 deletions(-)
Title: Exemplar Data Sets for SGP Analyses
Description: Data sets utilized by the SGP Package as exemplars for users to conduct their own SGP analyses.
Author: Damian W. Betebenner [aut, cre],
Adam Van Iwaarden [aut],
Ben Domingue [aut]
Maintainer: Damian W. Betebenner <dbetebenner@nciea.org>
Diff between SGPdata versions 12.0-0.0 dated 2015-12-04 and 13.0-0.0 dated 2016-03-01
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- R/zzz.R | 2 +- data/sgpData.rda |binary data/sgpData_INSTRUCTOR_NUMBER.rda |binary data/sgpData_LONG.rda |binary inst/CITATION | 8 ++++---- inst/NEWS | 6 ++++++ man/SGPdata-package.Rd | 4 ++-- man/sgpData.Rd | 20 ++++++++++---------- 10 files changed, 37 insertions(+), 31 deletions(-)
Title: Useful Tools for Structural Equation Modeling
Description: Provides useful tools for structural equation modeling packages.
Author: Sunthud Pornprasertmanit [aut, cre],
Patrick Miller [aut],
Alexander Schoemann [aut],
Yves Rosseel [aut],
Corbin Quick [ctb],
Mauricio Garnier-Villarreal [ctb],
James Selig [ctb],
Aaron Boulton [ctb],
Kristopher Preacher [ctb],
Donna Coffman [ctb],
Mijke Rhemtulla [ctb],
Alexander Robitzsch [ctb],
Craig Enders [ctb],
Ruber Arslan [ctb],
Bell Clinton [ctb],
Pavel Panko [ctb],
Edgar Merkle [ctb],
Terry Jorgensen [ctb],
Steven Chesnut [ctb],
Jarrett Byrnes [ctb],
Jason Rights [ctb]
Maintainer: Sunthud Pornprasertmanit <psunthud@gmail.com>
Diff between semTools versions 0.4-9 dated 2015-06-28 and 0.4-11 dated 2016-03-01
DESCRIPTION | 22 - MD5 | 144 ++++---- NAMESPACE | 13 R/NET.R | 8 R/PAVranking.R |only R/ci.reliability.R |only R/efa.R | 12 R/fitIndices.R | 2 R/imposeStart.R | 4 R/lavSpatialCorrect.R | 8 R/missingBootstrap.R | 276 ++++++++-------- R/monteCarloMed.R | 4 R/partialInvariance.R | 56 +-- R/partialInvarianceCat.R | 38 +- R/permuteMeasEq.R | 639 +++++++++++++++++++++++---------------- R/probeInteraction.R | 8 R/reliability.R | 10 R/runMI.R | 63 ++- R/wald.R | 6 build/vignette.rds |binary data/simParcel.rda |binary man/BootMiss-class.Rd | 10 man/EFA-class.Rd | 3 man/FitDiff-class.Rd | 2 man/PAVranking.Rd |only man/auxiliary.Rd | 4 man/bsBootMiss.Rd | 28 + man/ci.reliability.Rd |only man/clipboard.Rd | 2 man/combinequark.Rd | 2 man/compareFit.Rd | 2 man/efaUnrotate.Rd | 2 man/findRMSEApower.Rd | 2 man/findRMSEApowernested.Rd | 2 man/findRMSEAsamplesize.Rd | 2 man/findRMSEAsamplesizenested.Rd | 2 man/fitMeasuresMx.Rd | 2 man/impliedFactorStat.Rd | 2 man/imposeStart.Rd | 2 man/indProd.Rd | 2 man/kurtosis.Rd | 2 man/lavaanStar-class.Rd | 2 man/loadingFromAlpha.Rd | 2 man/longInvariance.Rd | 2 man/mardiaKurtosis.Rd | 2 man/mardiaSkew.Rd | 2 man/maximalRelia.Rd | 2 man/measurementInvariance.Rd | 2 man/measurementInvarianceCat.Rd | 4 man/miPowerFit.Rd | 2 man/moreFitIndices.Rd | 2 man/mvrnonnorm.Rd | 2 man/net.Rd | 3 man/nullMx.Rd | 2 man/partialInvariance.Rd | 2 man/permuteMeasEq-class.Rd | 18 - man/permuteMeasEq.Rd | 173 ++++------ man/plotProbe.Rd | 2 man/plotRMSEAdist.Rd | 2 man/plotRMSEApowernested.Rd | 2 man/probe2WayMC.Rd | 2 man/probe2WayRC.Rd | 2 man/probe3WayMC.Rd | 2 man/probe3WayRC.Rd | 2 man/quark.Rd | 2 man/reliability.Rd | 2 man/reliabilityL2.Rd | 2 man/residualCovariate.Rd | 2 man/rotate.Rd | 2 man/runMI.Rd | 15 man/saturateMx.Rd | 2 man/singleParamTest.Rd | 2 man/skew.Rd | 2 man/standardizeMx.Rd | 2 man/wald.Rd | 2 75 files changed, 912 insertions(+), 745 deletions(-)
Title: General Network (HTTP/FTP/...) Client Interface for R
Description: A wrapper for 'libcurl' <http://curl.haxx.se/libcurl/>
Provides functions to allow one to compose general HTTP requests
and provides convenient functions to fetch URIs, get & post
forms, etc. and process the results returned by the Web server.
This provides a great deal of control over the HTTP/FTP/...
connection and the form of the request while providing a
higher-level interface than is available just using R socket
connections. Additionally, the underlying implementation is
robust and extensive, supporting FTP/FTPS/TFTP (uploads and
downloads), SSL/HTTPS, telnet, dict, ldap, and also supports
cookies, redirects, authentication, etc.
Author: Duncan Temple Lang and the CRAN team
Maintainer: Duncan Temple Lang <duncan@r-project.org>
Diff between RCurl versions 1.95-4.7 dated 2015-06-30 and 1.95-4.8 dated 2016-03-01
Changes.html | 2 DESCRIPTION | 10 ++-- MD5 | 88 ++++++++++++++++++++--------------------- NAMESPACE | 1 R/getFormParams.R | 2 Todo.html | 2 getURL.html | 34 +++++++-------- inst/doc/FAQ.html | 6 +- inst/doc/RCurl.tex | 10 ++-- inst/doc/philosophy.html | 46 ++++++++++----------- inst/doc/philosophy.xml | 48 +++++++++++----------- inst/doc/withCookies.Rdb | 4 - inst/doc/withCookies.html | 22 +++++----- inst/examples/chunks.S | 2 inst/examples/concurrent.S | 2 inst/examples/concurrent.html | 14 +++--- inst/examples/concurrent.xml | 18 ++++---- inst/examples/curl.c | 2 inst/examples/encoding.R | 2 inst/examples/multi.S | 8 +-- inst/examples/nestedHTML.html | 6 +- inst/examples/nestedHTML.xml | 8 +-- inst/examples/omg.netrc | 2 inst/examples/postFormPasswd.R | 6 +- inst/examples/progress.S | 2 inst/examples/xmlParse.html | 4 - inst/examples/xmlParse.xml | 8 +-- man/MultiCURLHandle-class.Rd | 2 man/basicHeaderGatherer.Rd | 4 - man/basicTextGatherer.Rd | 20 ++++----- man/binaryBuffer.Rd | 4 - man/chunkToLineReader.Rd | 4 - man/curlPerform.Rd | 8 +-- man/curlSetOpt.Rd | 4 - man/dynCurlReader.Rd | 8 +-- man/getBinaryURL.Rd | 2 man/getCurlHandle.Rd | 6 +- man/getCurlInfo.Rd | 4 - man/getFormParams.Rd | 4 - man/getURIAsynchronous.Rd | 6 +- man/getURL.Rd | 36 ++++++++-------- man/url.exists.Rd | 4 - src/curl.c | 2 src/curl.c-expt | 2 tests/jpeg.R | 2 45 files changed, 241 insertions(+), 240 deletions(-)
Title: Statistical Toolbox for Sedimentary Provenance Analysis
Description: Bundles a number of established statistical methods to facilitate
the visual interpretation of large datasets in sedimentary geology. Includes
functionality for adaptive kernel density estimation, multidimensional scaling,
generalised procrustes analysis and individual differences scaling using a
variety of dissimilarity measures. Univariate provenance proxies, such as
single-grain ages or (isotopic) compositions are compared with the Kolmogorov-
Smirnov dissimilarity and Sircombe-Hazelton L2-norm. Categorical provenance
proxies, such as mineralogical, petrographic or chemical compositions are
compared with the Aitchison and Bray-Curtis distances. Also included are tools
to plot compositional data on ternary diagrams, to calculate the sample size
required for specified levels of statistical precision, and to assess the
effects of hydraulic sorting on detrital compositions. Includes an intuitive
query-based user interface for users who are not proficient in R.
Author: Pieter Vermeesch [aut, cre]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>
Diff between provenance versions 1.3 dated 2016-02-12 and 1.4 dated 2016-03-01
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/gui.R | 22 +++++++++++----------- R/provenance.R | 7 ++++--- man/plot.ternary.Rd | 2 +- 5 files changed, 23 insertions(+), 22 deletions(-)
Title: Density Estimation with a Penalized Mixture Approach
Description: Estimation of univariate (conditional) densities using penalized B-splines with automatic selection of optimal smoothing parameter.
Author: Christian Schellhase
Maintainer: Christian Schellhase <cschellhase@wiwi.uni-bielefeld.de>
Diff between pendensity versions 0.2.8 dated 2015-04-08 and 0.2.9 dated 2016-03-01
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NAMESPACE | 2 ++ R/plot.pendensity.R | 23 ++++++++++++----------- build/vignette.rds |binary man/pendensity-package.Rd | 4 ++-- man/plot.pendensity.Rd | 3 ++- 7 files changed, 28 insertions(+), 24 deletions(-)
Title: Adding Progress Bar to '*apply' Functions
Description: A lightweight package that adds
progress bar to vectorized R functions
('*apply'). The implementation can easily be added
to functions where showing the progress is
useful (e.g. bootstrap). The type and style of the
progress bar (with percentages or remaining time)
can be set through options.
Author: Peter Solymos [aut, cre], Zygmunt Zawadzki [aut]
Maintainer: Peter Solymos <solymos@ualberta.ca>
Diff between pbapply versions 1.1-3 dated 2015-11-24 and 1.2-0 dated 2016-03-01
DESCRIPTION | 17 +- MD5 | 44 ++--- NAMESPACE | 16 + R/closepb.R | 13 - R/pbapply.R | 198 +++++++++++------------ R/pblapply.R | 38 ++-- R/pboptions.R | 32 +-- R/pbreplicate.R | 8 R/pbsapply.R | 22 +- R/timerProgressBar.R |only R/unix/dopb.R | 25 +- R/unix/getpb.R | 27 +-- R/unix/setpb.R | 27 +-- R/unix/startpb.R | 36 ++-- R/windows/dopb.R | 25 +- R/windows/getpb.R | 29 +-- R/windows/setpb.R | 29 +-- R/windows/startpb.R | 42 +++- R/zzz.R | 32 ++- inst/ChangeLog | 121 +++++++------- man/pbapply.Rd | 404 ++++++++++++++++++++++++------------------------ man/pboptions.Rd | 276 ++++++++++++++++---------------- man/timerProgressBar.Rd |only tests/tests.R | 82 ++++----- 24 files changed, 809 insertions(+), 734 deletions(-)
Title: Tools for the Analysis of Air Pollution Data
Description: Tools to analyse, interpret and understand air
pollution data. Data are typically hourly time series
and both monitoring data and dispersion model output
can be analysed. Many functions can also be applied to
other data, including meteorological and traffic data.
Author: David Carslaw [aut, cre],
Karl Ropkins [aut]
Maintainer: David Carslaw <david.carslaw@york.ac.uk>
Diff between openair versions 1.7 dated 2016-02-22 and 1.7-3 dated 2016-03-01
DESCRIPTION | 8 MD5 | 38 - R/TaylorDiagram.R | 4 R/TheilSen.R | 1004 +++++++++++++++++++++++++++------------------------- R/checkPrep.R | 3 R/conditionalEval.R | 11 R/modStats.R | 20 - R/polarFreq.R | 2 R/scatterPlot.R | 9 R/smoothTrend.R | 846 +++++++++++++++++++++++-------------------- R/timeAverage.R | 30 + R/timePlot.R | 12 R/timeProp.R | 5 R/trajCluster.R | 34 + R/utilities.R | 191 ++++----- R/windRose.R | 2 man/TheilSen.Rd | 249 ++++++------ man/smoothTrend.Rd | 271 +++++++------- man/timeAverage.Rd | 22 - man/trajCluster.Rd | 12 20 files changed, 1460 insertions(+), 1313 deletions(-)
Title: Multivariate Data Handling with S4 Classes and Sparse Matrices
Description: An S4 update of the 'mefa' package
using sparse matrices for enhanced efficiency.
Sparse array-like objects are supported via
lists of sparse matrices.
Author: Peter Solymos
Maintainer: Peter Solymos <solymos@ualberta.ca>
Diff between mefa4 versions 0.3-2 dated 2015-11-22 and 0.3-3 dated 2016-03-01
mefa4-0.3-2/mefa4/R/mefa4extras.R |only mefa4-0.3-2/mefa4/inst/extras |only mefa4-0.3-3/mefa4/DESCRIPTION | 11 +++--- mefa4-0.3-3/mefa4/MD5 | 13 +++---- mefa4-0.3-3/mefa4/NAMESPACE | 3 + mefa4-0.3-3/mefa4/R/mefa4plus.R |only mefa4-0.3-3/mefa4/R/mefa4utilities.R | 47 ++++++++++++++++++++++++++ mefa4-0.3-3/mefa4/inst/ChangeLog | 61 ++++++++++++++++++++++++----------- mefa4-0.3-3/mefa4/man/nameAlnum.Rd | 26 +++++++++++++- 9 files changed, 128 insertions(+), 33 deletions(-)
Title: Sparse and Dense Matrix Classes and Methods
Description: Classes and methods for dense and sparse matrices and
operations on them using 'LAPACK' and 'SuiteSparse'.
Author: Douglas Bates <bates@stat.wisc.edu> and Martin Maechler
Maintainer: Martin Maechler <mmaechler+Matrix@gmail.com>
Diff between Matrix versions 1.2-3 dated 2015-11-28 and 1.2-4 dated 2016-03-01
DESCRIPTION | 8 +++--- MD5 | 54 ++++++++++++++++++++++---------------------- R/diagMatrix.R | 2 + R/sparseMatrix.R | 27 ++++++++++++++++------ TODO | 4 +++ build/vignette.rds |binary inst/NEWS.Rd | 21 +++++++++++++++++ inst/doc/Comparisons.pdf |binary inst/doc/Design-issues.pdf |binary inst/doc/Intro2Matrix.pdf |binary inst/doc/Introduction.pdf |binary inst/doc/sparseModels.pdf |binary inst/test-tools-Matrix.R | 3 -- man/Matrix-class.Rd | 7 ++++- man/bdiag.Rd | 11 +++++++++ man/spMatrix.Rd | 17 ++++++++----- man/sparseMatrix-class.Rd | 3 +- man/sparseMatrix.Rd | 17 ++++++++++++- src/CHOLMOD/Lib/Makefile | 5 ++++ src/Csparse.c | 6 ++++ src/Mutils.c | 9 ++++--- src/chm_common.c | 4 +-- src/dense.h | 2 - src/dgCMatrix.c | 2 - src/dgTMatrix.c | 55 ++++++++++++++++++++++++++++++++++++--------- src/factorizations.c | 21 +++++++++-------- src/init.c | 2 - tests/Simple.R | 28 +++++++++++++++++++++- 28 files changed, 227 insertions(+), 81 deletions(-)