Title: Prediction Intervals for Random-Effects Meta-Analysis
Description: An implementation of prediction intervals for random-effects meta-analysis:
Higgins et al. (2009) <doi:10.1111/j.1467-985X.2008.00552.x>, Partlett and Riley (2017)
<doi:10.1002/sim.7140>, and Nagashima et al. (2018) <doi:10.1177/0962280218773520>,
<arXiv:1804.01054>.
Author: Kengo Nagashima [aut, cre] (<https://orcid.org/0000-0003-4529-9045>),
Hisashi Noma [aut],
Toshi A. Furukawa [aut]
Maintainer: Kengo Nagashima <nshi1201@gmail.com>
Diff between pimeta versions 1.1.0 dated 2018-09-14 and 1.1.1 dated 2018-09-14
DESCRIPTION | 6 +-- MD5 | 28 +++++++-------- NEWS.md | 5 ++ R/pima-.r | 93 ++++++++++++++++++++++++++++++++++++-------------- R/pima-boot.r | 37 ++++++++++++++++---- R/pima-hts.r | 50 +++++++++++++++++---------- R/pima-htsreml.r | 63 +++++++++++++++++++++++----------- build/vignette.rds |binary inst/doc/pimeta.Rmd | 73 +++++++++++++++++++++++++++++++++++++-- inst/doc/pimeta.html | 76 +++++++++++++++++++++++++++++++++++++---- man/pima.Rd | 94 +++++++++++++++++++++++++++++++++++++-------------- man/pima_boot.Rd | 32 ++++++++++++++--- man/pima_hts.Rd | 43 +++++++++++++++-------- man/pima_htsreml.Rd | 51 ++++++++++++++++++--------- vignettes/pimeta.Rmd | 73 +++++++++++++++++++++++++++++++++++++-- 15 files changed, 560 insertions(+), 164 deletions(-)
Title: High Performance Tools for Combinatorics and Computational
Mathematics
Description: Provides optimized functions implemented in C++ with 'Rcpp'
for solving problems in combinatorics and computational mathematics.
There are combination/permutation functions that are both flexible as
well as efficient with respect to speed and memory. Constraint
parameters allow for generation of all combinations/permutations of a
vector meeting specific criteria (e.g. finding all combinations such
that the sum is less than a bound). Capable of generating specific
combinations/permutations (e.g. retrieve only the nth lexicographical
result) which sets up nicely for parallelization as well as random
sampling. Gmp support permits exploration where the total number of
results is large (e.g. comboSample(10000, 500, n = 4)). Additionally,
there are several highly efficient number theoretic functions that
are useful for problems common in computational mathematics. Some of
these functions make use of the fast integer division library
'libdivide' by <http://ridiculousfish.com>. The primeSieve function
is based on the segmented sieve of Eratosthenes implementation by
Kim Walisch. It is capable of generating all primes less than a
billion in just over 1 second. It can also quickly generate prime
numbers over a range (e.g. primeSieve(10^13, 10^13+10^9)). Finally,
there is a prime counting function that implements a simple variations
of Legendre's formula based on the algorithm by Kim Walisch.
Author: Joseph Wood
Maintainer: Joseph Wood <jwood000@gmail.com>
Diff between RcppAlgos versions 2.1.0 dated 2018-09-11 and 2.2.0 dated 2018-09-14
RcppAlgos-2.1.0/RcppAlgos/tests/testthat/testParallel.R |only RcppAlgos-2.2.0/RcppAlgos/DESCRIPTION | 8 RcppAlgos-2.2.0/RcppAlgos/MD5 | 36 - RcppAlgos-2.2.0/RcppAlgos/R/Combinatorics.R | 12 RcppAlgos-2.2.0/RcppAlgos/R/RcppExports.R | 8 RcppAlgos-2.2.0/RcppAlgos/README.md | 6 RcppAlgos-2.2.0/RcppAlgos/inst/NEWS.Rd | 15 RcppAlgos-2.2.0/RcppAlgos/inst/include/Combinations.h | 10 RcppAlgos-2.2.0/RcppAlgos/inst/include/ComboResults.h | 4 RcppAlgos-2.2.0/RcppAlgos/inst/include/Permutations.h | 21 RcppAlgos-2.2.0/RcppAlgos/inst/include/PermuteResults.h | 2 RcppAlgos-2.2.0/RcppAlgos/man/RcppAlgos-package.Rd | 3 RcppAlgos-2.2.0/RcppAlgos/man/combinatoricsGeneral.Rd | 33 RcppAlgos-2.2.0/RcppAlgos/man/combinatoricsSample.Rd | 24 RcppAlgos-2.2.0/RcppAlgos/src/Combinatorics.cpp | 331 ++-------- RcppAlgos-2.2.0/RcppAlgos/src/RcppExports.cpp | 18 RcppAlgos-2.2.0/RcppAlgos/src/SampleContainer.cpp | 108 --- RcppAlgos-2.2.0/RcppAlgos/tests/testthat/testCombPermResults.R |only RcppAlgos-2.2.0/RcppAlgos/tests/testthat/testComboGeneral.R | 58 - RcppAlgos-2.2.0/RcppAlgos/tests/testthat/testSample.R | 88 -- 20 files changed, 182 insertions(+), 603 deletions(-)
Title: Generalized Boosted Regression Models
Description: An implementation of extensions to Freund and Schapire's AdaBoost
algorithm and Friedman's gradient boosting machine. Includes regression
methods for least squares, absolute loss, t-distribution loss, quantile
regression, logistic, multinomial logistic, Poisson, Cox proportional hazards
partial likelihood, AdaBoost exponential loss, Huberized hinge loss, and
Learning to Rank measures (LambdaMart). Originally developed by Greg Ridgeway.
Author: Brandon Greenwell [aut, cre] (<https://orcid.org/0000-0002-8120-0084>),
Bradley Boehmke [aut] (<https://orcid.org/0000-0002-3611-8516>),
Jay Cunningham [aut],
GBM Developers [aut] (https://github.com/gbm-developers)
Maintainer: ORPHANED
Diff between gbm versions 2.1.3 dated 2017-03-21 and 2.1.4 dated 2018-09-14
gbm-2.1.3/gbm/R/checks.R |only gbm-2.1.3/gbm/R/gbm.loss.R |only gbm-2.1.3/gbm/R/gbmCluster.R |only gbm-2.1.3/gbm/R/gbmDoFold.R |only gbm-2.1.3/gbm/R/getCVgroup.R |only gbm-2.1.3/gbm/R/getStratify.R |only gbm-2.1.3/gbm/R/guessDist.R |only gbm-2.1.3/gbm/R/permutation.test.gbm.R |only gbm-2.1.3/gbm/inst/doc/gbm.Sweave |only gbm-2.1.3/gbm/inst/doc/gbm.tex |only gbm-2.1.3/gbm/inst/doc/index.html |only gbm-2.1.3/gbm/inst/doc/oobperf2.eps |only gbm-2.1.3/gbm/inst/doc/oobperf2.pdf |only gbm-2.1.3/gbm/inst/doc/shrinkage-v-iterations.eps |only gbm-2.1.3/gbm/inst/doc/shrinkage-v-iterations.pdf |only gbm-2.1.3/gbm/inst/doc/srcltx.sty |only gbm-2.1.3/gbm/man/gbm-internal.Rd |only gbm-2.1.3/gbm/man/validate.Rd |only gbm-2.1.3/gbm/src/init.c |only gbm-2.1.4/gbm/DESCRIPTION | 61 - gbm-2.1.4/gbm/LICENSE | 2 gbm-2.1.4/gbm/MD5 | 125 +- gbm-2.1.4/gbm/NAMESPACE | 119 ++ gbm-2.1.4/gbm/NEWS.md |only gbm-2.1.4/gbm/R/basehaz.gbm.R | 111 +- gbm-2.1.4/gbm/R/calibrate.plot.R | 273 ++++-- gbm-2.1.4/gbm/R/gbm-internals.R |only gbm-2.1.4/gbm/R/gbm-package.R |only gbm-2.1.4/gbm/R/gbm.R | 648 ++++++++++---- gbm-2.1.4/gbm/R/gbm.fit.R | 981 +++++++++++++--------- gbm-2.1.4/gbm/R/gbm.more.R | 132 ++ gbm-2.1.4/gbm/R/gbm.object.R |only gbm-2.1.4/gbm/R/gbm.perf.R | 278 ++---- gbm-2.1.4/gbm/R/gbmCrossVal.R | 206 +++- gbm-2.1.4/gbm/R/interact.gbm.R | 42 gbm-2.1.4/gbm/R/ir.measures.R | 115 ++ gbm-2.1.4/gbm/R/plot.gbm.R | 741 +++++++--------- gbm-2.1.4/gbm/R/predict.gbm.R | 52 + gbm-2.1.4/gbm/R/pretty.gbm.tree.R | 28 gbm-2.1.4/gbm/R/print.gbm.R | 101 ++ gbm-2.1.4/gbm/R/reconstructGBMdata.R | 13 gbm-2.1.4/gbm/R/relative.influence.R | 146 +++ gbm-2.1.4/gbm/R/shrink.gbm.R | 38 gbm-2.1.4/gbm/R/shrink.gbm.pred.R | 17 gbm-2.1.4/gbm/R/test.gbm.R | 75 + gbm-2.1.4/gbm/R/utils.R |only gbm-2.1.4/gbm/R/zzz.R |only gbm-2.1.4/gbm/README.md |only gbm-2.1.4/gbm/build |only gbm-2.1.4/gbm/inst/doc/gbm.Rnw |only gbm-2.1.4/gbm/inst/doc/gbm.pdf |binary gbm-2.1.4/gbm/man/basehaz.gbm.Rd | 76 + gbm-2.1.4/gbm/man/calibrate.plot.Rd | 114 +- gbm-2.1.4/gbm/man/gbm-internals.Rd |only gbm-2.1.4/gbm/man/gbm-package.Rd | 84 - gbm-2.1.4/gbm/man/gbm.Rd | 559 ++++++------ gbm-2.1.4/gbm/man/gbm.fit.Rd |only gbm-2.1.4/gbm/man/gbm.more.Rd |only gbm-2.1.4/gbm/man/gbm.object.Rd | 69 - gbm-2.1.4/gbm/man/gbm.perf.Rd | 74 - gbm-2.1.4/gbm/man/gbm.roc.area.Rd | 89 + gbm-2.1.4/gbm/man/gbmCrossVal.Rd | 106 +- gbm-2.1.4/gbm/man/grid.arrange.Rd |only gbm-2.1.4/gbm/man/interact.gbm.Rd | 76 - gbm-2.1.4/gbm/man/plot.gbm.Rd | 128 +- gbm-2.1.4/gbm/man/predict.gbm.Rd | 80 + gbm-2.1.4/gbm/man/pretty.gbm.tree.Rd | 58 - gbm-2.1.4/gbm/man/print.gbm.Rd | 85 - gbm-2.1.4/gbm/man/quantile.rug.Rd | 35 gbm-2.1.4/gbm/man/reconstructGBMdata.Rd | 29 gbm-2.1.4/gbm/man/relative.influence.Rd | 82 + gbm-2.1.4/gbm/man/shrink.gbm.Rd | 67 - gbm-2.1.4/gbm/man/shrink.gbm.pred.Rd | 53 - gbm-2.1.4/gbm/man/summary.gbm.Rd | 103 +- gbm-2.1.4/gbm/man/test.gbm.Rd |only gbm-2.1.4/gbm/src/gbm-init.c |only gbm-2.1.4/gbm/src/gbmentry.cpp | 2 gbm-2.1.4/gbm/src/locationm.cpp | 5 gbm-2.1.4/gbm/vignettes |only 79 files changed, 3926 insertions(+), 2352 deletions(-)
Title: Visualization and Analysis of Statistical Measures of Confidence
Description: Enables: (1) plotting two-dimensional confidence regions, (2) coverage analysis
of confidence region simulations and (3) calculating confidence intervals and the associated
actual coverage for binomial proportions. Each is given in greater detail next.
(1) Plots the two-dimensional confidence region for probability distribution parameters
(supported distribution suffixes: gamma, invgauss, llogis, lnorm, norm, unif, weibull)
corresponding to a user given dataset and level of significance. The crplot() algorithm plots
more points in areas of greater curvature to ensure a smooth appearance throughout the
confidence region boundary. An alternative heuristic plots a specified number of points at
roughly uniform intervals along its boundary. Both heuristics build upon the radial profile
log-likelihood ratio technique for plotting two-dimensional confidence regions given by Jaeger
(2016) <doi:10.1080/00031305.2016.1182946>. (2) Performs confidence region coverage simulations
for a random sample drawn from a user-specified parametric population distribution, or for a
user-specified dataset and point of interest with coversim(). (3) Calculates confidence
interval bounds for a binomial proportion with binomTest(), calculates the actual coverage
with binomTestCoverage(), and plots the actual coverage with binomTestCoveragePlot().
Calculates confidence interval bounds for the binomial proportion using an ensemble of
constituent confidence intervals with binomTestEnsemble().
Author: Christopher Weld [aut, cre] (<https://orcid.org/0000-0001-5902-9738>),
Hayeon Park [aut],
Lawrence Leemis [aut],
Andrew Loh [ctb],
Yuan Chang [ctb],
Brock Crook [ctb],
Xin Zhang [ctb]
Maintainer: Christopher Weld <ceweld@email.wm.edu>
Diff between conf versions 1.3.2 dated 2018-09-10 and 1.3.3 dated 2018-09-14
DESCRIPTION | 38 +++++++++--------- MD5 | 28 ++++++------- R/conf-package.R | 9 +++- R/coversim.R | 100 ++++++++++++++++++++++++++++++++----------------- R/crplot.R | 6 +- inst/doc/coversim.R | 12 +++++ inst/doc/coversim.Rmd | 23 ++++++++++- inst/doc/coversim.html | 65 ++++++++++++++++++++++++++++++- inst/doc/crplot.Rmd | 2 inst/doc/crplot.html | 30 ++++++++++---- man/conf.Rd | 11 ++++- man/coversim.Rd | 48 +++++++++++++---------- man/crplot.Rd | 3 - vignettes/coversim.Rmd | 23 ++++++++++- vignettes/crplot.Rmd | 2 15 files changed, 294 insertions(+), 106 deletions(-)
Title: Applied Statistical Hypothesis Tests
Description: Gives some hypothesis test functions (sign test, median and other quantile tests,
Wilcoxon signed rank test, coefficient of variation test, test of normal variance,
test on weighted sums of Poisson [see Fay and Kim <doi:10.1002/bimj.201600111>],
sample size for t-tests with different variances
and non-equal n per arm, Behrens-Fisher test, nonparametric ABC intervals,
Wilcoxon-Mann-Whitney test [with effect estimates and confidence intervals,
see Fay and Malinovsky <doi:10.1002/sim.7890>], two-sample melding tests
[see Fay, Proschan, and Brittain <doi:10.1111/biom.12231>],
one-way ANOVA allowing var.equal=FALSE [see Brown and Forsythe, 1974, Biometrics]).
The focus is on methods that have compatible confidence intervals.
Author: Michael P. Fay
Maintainer: Michael P. Fay <mfay@niaid.nih.gov>
Diff between asht versions 0.9.3 dated 2017-10-14 and 0.9.4 dated 2018-09-14
DESCRIPTION | 19 ++++++++++++++----- MD5 | 26 ++++++++++++++++++-------- NAMESPACE | 8 ++++++-- R/anovaOneWay.R |only R/bfTest.R | 7 +++++-- R/meldCD.R |only R/meldtTest.R |only R/tukeyWelsch.R |only R/wmwTest.R | 15 +++++++++++++-- data |only inst/NEWS.Rd | 17 +++++++++++++++++ man/ama1c1cpg.Rd |only man/anovaOneWay.Rd |only man/bfTest.Rd | 12 ++++++++---- man/meldCD.Rd |only man/meldtTest.Rd |only man/tukeyWelsch.Rd |only man/wmwTest.Rd | 16 ++++++++++++---- man/wsrTest.Rd | 6 +++--- 19 files changed, 96 insertions(+), 30 deletions(-)
Title: Statistical Tools for Covariance Analysis
Description: Covariance is of universal prevalence across various disciplines within statistics.
We provide a rich collection of geometric and inferential tools for convenient analysis of
covariance structures, topics including distance measures, mean covariance estimator,
covariance hypothesis test for one-sample and two-sample cases, and covariance estimation.
For an introduction to covariance in multivariate statistical analysis,
see Schervish (1987) <doi:10.1214/ss/1177013111>.
Author: Kyoungjae Lee [aut],
Lizhen Lin [ctb],
Kisung You [aut, cre] (<https://orcid.org/0000-0002-8584-459X>)
Maintainer: Kisung You <kyou@nd.edu>
Diff between CovTools versions 0.4.0 dated 2018-09-01 and 0.5.0 dated 2018-09-14
CovTools-0.4.0/CovTools/man/CovTools-package.Rd |only CovTools-0.5.0/CovTools/DESCRIPTION | 8 +- CovTools-0.5.0/CovTools/MD5 | 36 +++++---- CovTools-0.5.0/CovTools/NAMESPACE | 3 CovTools-0.5.0/CovTools/R/BayesTest1.R |only CovTools-0.5.0/CovTools/R/CovDist.R | 2 CovTools-0.5.0/CovTools/R/CovMean.R | 5 + CovTools-0.5.0/CovTools/R/CovTest1.R | 22 ++++- CovTools-0.5.0/CovTools/R/DiagTest1.R |only CovTools-0.5.0/CovTools/R/auxiliary.R | 3 CovTools-0.5.0/CovTools/R/fns.bayestest1.R |only CovTools-0.5.0/CovTools/R/fns.diagtest1.R |only CovTools-0.5.0/CovTools/R/fns.test1.R | 34 ++++++-- CovTools-0.5.0/CovTools/R/init.R | 25 ++++++ CovTools-0.5.0/CovTools/R/package-CovTools.R | 21 ++++- CovTools-0.5.0/CovTools/build/partial.rdb |binary CovTools-0.5.0/CovTools/inst/REFERENCES.bib | 91 ++++++++++++++++-------- CovTools-0.5.0/CovTools/man/BayesTest1.Rd |only CovTools-0.5.0/CovTools/man/CovDist.Rd | 2 CovTools-0.5.0/CovTools/man/CovMean.Rd | 4 - CovTools-0.5.0/CovTools/man/CovTest1.Rd | 11 ++ CovTools-0.5.0/CovTools/man/DiagTest1.Rd |only CovTools-0.5.0/CovTools/man/package-CovTools.Rd |only 23 files changed, 193 insertions(+), 74 deletions(-)
Title: Analysis of Age-Structured Demographic Models
Description: Construction and analysis of matrix population models in R.
Author: James Holland Jones [aut] <jhj1@stanford.edu>, Jim Oeppen [ctb]
Maintainer: Hana Sevcikova <hanas@uw.edu>
Diff between demogR versions 0.5.1 dated 2018-08-03 and 0.6.0 dated 2018-09-14
ChangeLog | 8 DESCRIPTION | 10 - MD5 | 16 - R/cdmlte.R | 493 +++++++++++++++++++++++--------------------------- R/cdmltn.R | 473 +++++++++++++++++++++++------------------------ R/cdmlts.R | 453 +++++++++++++++++++++------------------------ R/cdmltw.R | 472 ++++++++++++++++++++++------------------------- man/cdmltw.Rd | 11 - man/demogR-package.Rd | 8 9 files changed, 934 insertions(+), 1010 deletions(-)
Title: Computing F-Statistics from Pool-Seq Data
Description: Functions for the computation of F-statistics from Pool-Seq data in population genomics studies. The package also includes several utilities to manipulate Pool-Seq data stored in standard format ('vcf' and 'rsync' files as obtained from the popular software 'VarScan' and 'PoPoolation' respectively) and perform conversion to alternative format (as used in the 'BayPass' and 'SelEstim' software).
Author: Mathieu Gautier, Valentin Hivert and Renaud Vitalis
Maintainer: Mathieu Gautier <mathieu.gautier@inra.fr>
Diff between poolfstat versions 0.0.1 dated 2018-03-14 and 1.0.0 dated 2018-09-14
DESCRIPTION | 8 +++--- MD5 | 20 +++++++++------ NAMESPACE | 2 + R/computeFST.R | 52 ++++++++++++++++++++-------------------- R/computePairwiseFSTmatrix.R |only R/genobaypass2pooldata.R | 2 - R/genoselestim2pooldata.R | 2 - R/is.pooldata.R | 2 - R/pooldata.subset.R |only man/computeFST.Rd | 4 +-- man/computePairwiseFSTmatrix.Rd |only man/pooldata-class.Rd | 4 +-- man/pooldata.subset.Rd |only 13 files changed, 51 insertions(+), 45 deletions(-)
Title: Kinetic Evaluation of Chemical Degradation Data
Description: Calculation routines based on the FOCUS Kinetics Report (2006,
2014). Includes a function for conveniently defining differential equation
models, model solution based on eigenvalues if possible or using numerical
solvers and a choice of the optimisation methods made available by the 'FME'
package. If a C compiler (on windows: 'Rtools') is installed, differential
equation models are solved using compiled C functions. Please note that no
warranty is implied for correctness of results or fitness for a particular
purpose.
Author: Johannes Ranke [aut, cre, cph]
(<https://orcid.org/0000-0003-4371-6538>),
Katrin Lindenberger [ctb],
René Lehmann [ctb],
Eurofins Regulatory AG [cph]
Maintainer: Johannes Ranke <jranke@uni-bremen.de>
Diff between mkin versions 0.9.47.2 dated 2018-07-19 and 0.9.47.5 dated 2018-09-14
mkin-0.9.47.2/mkin/inst/doc/FOCUS_Z.R |only mkin-0.9.47.2/mkin/inst/doc/FOCUS_Z.Rmd |only mkin-0.9.47.2/mkin/inst/doc/FOCUS_Z.pdf |only mkin-0.9.47.2/mkin/inst/doc/compiled_models.R |only mkin-0.9.47.2/mkin/inst/doc/compiled_models.Rmd |only mkin-0.9.47.2/mkin/inst/doc/compiled_models.html |only mkin-0.9.47.2/mkin/vignettes/FOCUS_Z.Rmd |only mkin-0.9.47.2/mkin/vignettes/FOCUS_Z.html |only mkin-0.9.47.2/mkin/vignettes/compiled_models.Rmd |only mkin-0.9.47.5/mkin/DESCRIPTION | 8 mkin-0.9.47.5/mkin/MD5 | 69 mkin-0.9.47.5/mkin/NEWS.md | 18 mkin-0.9.47.5/mkin/R/mkinfit.R | 36 mkin-0.9.47.5/mkin/README.md | 2 mkin-0.9.47.5/mkin/build/vignette.rds |binary mkin-0.9.47.5/mkin/inst/doc/FOCUS_D.html | 310 +- mkin-0.9.47.5/mkin/inst/doc/FOCUS_L.html | 1333 +++++++++ mkin-0.9.47.5/mkin/inst/doc/mkin.html | 1340 +++++++++- mkin-0.9.47.5/mkin/inst/doc/twa.html | 188 + mkin-0.9.47.5/mkin/man/mccall81_245T.Rd | 12 mkin-0.9.47.5/mkin/man/mkinerrmin.Rd | 6 mkin-0.9.47.5/mkin/man/mkinfit.Rd | 18 mkin-0.9.47.5/mkin/man/mkinparplot.Rd | 3 mkin-0.9.47.5/mkin/tests/testthat/test_FOCUS_D_UBA_expertise.R | 70 mkin-0.9.47.5/mkin/tests/testthat/test_FOCUS_chi2_error_level.R | 3 mkin-0.9.47.5/mkin/tests/testthat/test_irls.R | 6 mkin-0.9.47.5/mkin/tests/testthat/test_mkinpredict_SFO_SFO.R | 4 mkin-0.9.47.5/mkin/tests/testthat/test_parent_only.R | 7 mkin-0.9.47.5/mkin/tests/testthat/test_synthetic_data_for_UBA_2014.R | 1 mkin-0.9.47.5/mkin/tests/testthat/test_twa.R | 14 mkin-0.9.47.5/mkin/vignettes/FOCUS_D_cache/html/fit_2985a0533271a8bb42f83d1f2e76e1de.rdb |binary mkin-0.9.47.5/mkin/vignettes/FOCUS_D_cache/html/fit_2985a0533271a8bb42f83d1f2e76e1de.rdx |binary mkin-0.9.47.5/mkin/vignettes/FOCUS_D_cache/html/model_95fdb0128acdf550cddff2cd16326bdd.rdb |binary mkin-0.9.47.5/mkin/vignettes/FOCUS_D_cache/html/model_95fdb0128acdf550cddff2cd16326bdd.rdx |binary mkin-0.9.47.5/mkin/vignettes/FOCUS_D_cache/html/unnamed-chunk-2_3588001d6da0ec2a11482b64e1495c95.RData |binary mkin-0.9.47.5/mkin/vignettes/mkin_cache/html/__packages | 1 mkin-0.9.47.5/mkin/vignettes/mkin_cache/html/unnamed-chunk-2_7ae000e6f50efde9fcf617528f8e0f41.rdb |binary mkin-0.9.47.5/mkin/vignettes/mkin_cache/html/unnamed-chunk-2_7ae000e6f50efde9fcf617528f8e0f41.rdx |binary mkin-0.9.47.5/mkin/vignettes/web_only |only 39 files changed, 3219 insertions(+), 230 deletions(-)
Title: Spectral Response of Water Wells to Harmonic Strain and Pressure
Signals
Description: Provides tools to calculate the theoretical hydrodynamic response
of an aquifer undergoing harmonic straining or pressurization, or analyze
measured responses. There are
two classes of models here: (1) for sealed wells, based on the model of
Kitagawa et al (2011, <doi:10.1029/2010JB007794>),
and (2) for open wells, based on the models of
Cooper et al (1965, <doi:10.1029/JZ070i016p03915>),
Hsieh et al (1987, <doi:10.1029/WR023i010p01824>),
Rojstaczer (1988, <doi:10.1029/JB093iB11p13619>), and
Liu et al (1989, <doi:10.1029/JB094iB07p09453>). These models treat
strain (or aquifer head) as an input to the
physical system, and fluid-pressure (or water height) as the output. The
applicable frequency band of these models is characteristic of seismic
waves, atmospheric pressure fluctuations, and solid earth tides.
Author: Andrew J Barbour
Maintainer: Andrew J Barbour <andy.barbour@gmail.com>
Diff between kitagawa versions 2.1-0 dated 2013-10-04 and 2.2-2 dated 2018-09-14
DESCRIPTION | 41 ++++---- MD5 | 68 +++++++------ NAMESPACE | 26 ++++- R/alpha_constants.R | 6 - R/cross.R |only R/kitagawa-package.R | 7 - R/methods.R | 72 ++++---------- R/omega_constants.R | 4 R/open_well_response.R | 20 +-- R/utilities.R | 15 -- R/well_response.R | 15 +- README.md |only build/vignette.rds |binary inst/NEWS.Rd | 63 ++++++++++-- inst/doc/REFS.bib | 145 +++++++++++++++------------- inst/doc/ResponseModels.R | 39 ++----- inst/doc/ResponseModels.Rnw | 55 +++++----- inst/doc/ResponseModels.pdf |binary inst/doc/Tohoku.R |only inst/doc/Tohoku.Rmd |only inst/doc/Tohoku.html |only man/alpha_constants.Rd | 81 +++++++-------- man/cross_spectrum.Rd |only man/kitagawa-constants.Rd | 48 ++++----- man/kitagawa-package.Rd | 183 +++++++++++++++++------------------- man/kitagawa-utilities.Rd | 50 ++++----- man/logsmoo.Rd |only man/logticks.Rd | 83 +++++++--------- man/omega_constants.Rd | 123 ++++++++++++------------ man/omega_norm.Rd | 44 ++++---- man/open_well_response.Rd | 161 +++++++++++++++---------------- man/owrsp-methods.Rd | 88 ++++++++--------- man/sensing_volume.Rd | 62 +++++------- man/well_response.Rd | 135 ++++++++++++-------------- man/wrsp-methods.Rd | 111 ++++++++++----------- vignettes/REFS.bib | 145 +++++++++++++++------------- vignettes/ResponseModels.Rnw | 55 +++++----- vignettes/ResponseModels.synctex.gz |only vignettes/ResponseModels.tex |only vignettes/Tohoku.Rmd |only 40 files changed, 983 insertions(+), 962 deletions(-)
Title: Fit Continuous-Time Correlated Random Walk Models to Animal
Movement Data
Description: Fit continuous-time correlated random walk models with time indexed
covariates to animal telemetry data. The model is fit using the Kalman-filter on
a state space version of the continuous-time stochastic movement process.
Author: Devin S. Johnson [aut, cre],
Josh London [aut],
Kenady Wilson [ctb]
Maintainer: Devin S. Johnson <devin.johnson@noaa.gov>
Diff between crawl versions 2.2.0 dated 2018-08-25 and 2.2.1 dated 2018-09-14
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/crawl-package.R | 4 ++-- R/crwMLE.R | 27 ++++++++------------------- R/crwPredict.R | 4 ++-- man/crawl-package.Rd | 4 ++-- man/crwMLE.Rd | 32 ++++++++++---------------------- 7 files changed, 34 insertions(+), 57 deletions(-)
Title: Simulation-Based Regularized Logistic Regression
Description: Regularized (polychotomous) logistic regression
by Gibbs sampling. The package implements subtly different
MCMC schemes with varying efficiency depending on the data type
(binary v. binomial, say) and the desired estimator (regularized maximum
likelihood, or Bayesian maximum a posteriori/posterior mean, etc.) through a
unified interface.
Author: Robert B. Gramacy <rbg@vt.edu>
Maintainer: Robert B. Gramacy <rbg@vt.edu>
Diff between reglogit versions 1.2-5 dated 2017-11-19 and 1.2-6 dated 2018-09-14
reglogit-1.2-5/reglogit/man/reglogit-package.Rd |only reglogit-1.2-6/reglogit/ChangeLog | 8 ++++++++ reglogit-1.2-6/reglogit/DESCRIPTION | 8 ++++---- reglogit-1.2-6/reglogit/MD5 | 5 ++--- 4 files changed, 14 insertions(+), 7 deletions(-)
Title: Estimation for Multivariate Normal and Student-t Data with
Monotone Missingness
Description: Estimation of multivariate normal and student-t data of
arbitrary dimension where the pattern of missing data is monotone.
Through the use of parsimonious/shrinkage regressions
(plsr, pcr, lasso, ridge, etc.), where standard regressions fail,
the package can handle a nearly arbitrary amount of missing data.
The current version supports maximum likelihood inference and
a full Bayesian approach employing scale-mixtures for Gibbs sampling.
Monotone data augmentation extends this Bayesian approach to arbitrary
missingness patterns. A fully functional standalone interface to the
Bayesian lasso (from Park & Casella), Normal-Gamma (from Griffin & Brown),
Horseshoe (from Carvalho, Polson, & Scott), and ridge regression
with model selection via Reversible Jump, and student-t errors
(from Geweke) is also provided.
Author: Robert B. Gramacy <rbg@vt.edu>
Maintainer: Robert B. Gramacy <rbg@vt.edu>
Diff between monomvn versions 1.9-7 dated 2017-01-08 and 1.9-8 dated 2018-09-14
ChangeLog | 11 +++++++++++ DESCRIPTION | 33 ++++++++++++++++----------------- MD5 | 21 +++++++++++---------- R/blasso.R | 7 ++++++- data/cement.rda |binary man/blasso.Rd | 2 +- src/blasso.cc | 26 ++++++++++++++------------ src/blasso.h | 9 +++++---- src/bmonomvn.cc | 10 +++++----- src/monomvn_init.c |only src/nu.c | 36 +++++++++++++++++++++++++----------- src/nu.h | 12 +++++++----- 12 files changed, 101 insertions(+), 66 deletions(-)
Title: Unconstrained Numerical Optimization Algorithms
Description: Optimization algorithms implemented in R, including
conjugate gradient (CG), Broyden-Fletcher-Goldfarb-Shanno (BFGS) and the
limited memory BFGS (L-BFGS) methods. Most internal parameters can be set
through the call interface. The solvers hold up quite well for
higher-dimensional problems.
Author: James Melville [aut, cre]
Maintainer: James Melville <jlmelville@gmail.com>
Diff between mize versions 0.1.1 dated 2017-07-14 and 0.2.0 dated 2018-09-14
DESCRIPTION | 11 LICENSE | 4 MD5 | 128 - NAMESPACE | 16 NEWS.md | 44 R/DONTCHECKMEIN.R |only R/adaptive_restart.R | 222 +- R/convergence.R | 204 - R/gradient.R | 1578 ++++++++++----- R/hager_zhang.R | 1418 ++++++------- R/learning_rate.R | 238 +- R/life_cycle.R | 678 +++--- R/mize.R | 3681 ++++++++++++++++++----------------- R/momentum.R | 366 +-- R/more_thuente.R | 1738 ++++++++-------- R/nesterov.R | 482 ++-- R/optimize.R | 1018 ++++----- R/polation.R | 390 +-- R/rasmussen.R | 588 ++--- R/schmidt.R | 1954 +++++++++--------- R/step_size.R | 475 ++-- R/util.R | 226 +- R/validate.R | 184 - R/wolfe.R | 1720 ++++++++-------- build/vignette.rds |binary inst/doc/convergence.R | 166 - inst/doc/convergence.Rmd | 450 ++-- inst/doc/convergence.html | 742 ++++--- inst/doc/mize.R | 546 ++--- inst/doc/mize.Rmd | 1796 ++++++++--------- inst/doc/mize.html | 1224 ++++++----- inst/doc/mmds.R | 236 +- inst/doc/mmds.Rmd | 542 ++--- inst/doc/mmds.html | 704 ++++-- inst/doc/stateful.R | 338 +-- inst/doc/stateful.Rmd | 742 +++---- inst/doc/stateful.html | 872 +++++--- man/check_mize_convergence.Rd | 98 man/make_mize.Rd | 457 ++-- man/mize.Rd | 1388 ++++++------- man/mize_init.Rd | 186 - man/mize_step.Rd | 184 - man/mize_step_summary.Rd | 164 - tests/testthat.R | 8 tests/testthat/helper_util.R | 757 +++---- tests/testthat/test_api.R | 697 +++--- tests/testthat/test_cg.R |only tests/testthat/test_hager_zhang.R | 238 +- tests/testthat/test_loop_api.R | 142 - tests/testthat/test_minfunc_armijo.R | 854 ++++---- tests/testthat/test_minfunc_wolfe.R | 604 ++--- tests/testthat/test_mizer.R | 2806 +++++++++++++------------- tests/testthat/test_mmds.R | 120 - tests/testthat/test_momentum.R | 144 - tests/testthat/test_more_thuente.R | 257 +- tests/testthat/test_nesterov.R | 122 - tests/testthat/test_newton.R | 114 - tests/testthat/test_polation.R | 14 tests/testthat/test_quadposdef.R | 136 - tests/testthat/test_rasmussen.R | 224 +- tests/testthat/test_rasmussen_cg.R | 178 - tests/testthat/test_tn.R |only vignettes/DONTCHECKMEIN.md |only vignettes/convergence.Rmd | 450 ++-- vignettes/mize.Rmd | 1796 ++++++++--------- vignettes/mmds.Rmd | 542 ++--- vignettes/stateful.Rmd | 742 +++---- 67 files changed, 20574 insertions(+), 18569 deletions(-)
Title: Importing and Manipulating Symmetric Input-Output Tables
Description: Pre-processing tasks related to working with Eurostat's symmetric input-output
tables and provide basic input-output economics calculations. The package is
a part of rOpenGov <http://ropengov.github.io/> to open source open government initiatives.
Author: Daniel Antal [aut, cre]
Maintainer: Daniel Antal <daniel.antal@ceemid.eu>
Diff between iotables versions 0.3.3 dated 2018-09-10 and 0.3.4 dated 2018-09-14
DESCRIPTION | 9 - MD5 | 54 ++++++---- NAMESPACE | 3 NEWS.md | 8 + R/backward_linkages.R | 4 R/direct_effects_create.R |only R/employment_get.R | 2 R/forward_linkages.R | 6 - R/input_coefficient_matrix_create.R | 31 ++++- R/input_multipliers_create.R |only R/iotables_download.R | 56 +++++----- R/output_coefficient_matrix_create.R | 10 + R/use_table_get.R | 77 +++++++------- README.md | 130 +++---------------------- build/vignette.rds |binary inst/doc/germany_1990.R | 32 +++++- inst/doc/germany_1990.Rmd | 43 +++++++- inst/doc/germany_1990.html | 84 +++++++++++++--- inst/doc/try_load.R |only inst/doc/try_load.Rmd |only inst/doc/try_load.html |only inst/doc/working_with_eurostat.R |only inst/doc/working_with_eurostat.Rmd |only inst/doc/working_with_eurostat.html |only inst/extdata |only man/direct_effects_create.Rd |only man/employment_get.Rd | 2 man/forward_linkages.Rd | 4 man/input_multipliers_create.Rd |only man/iotables_download.Rd | 27 ++--- tests/testthat/test_backward_linkages.R | 6 - tests/testthat/test_direct_effects.R |only tests/testthat/test_input_multipliers_create.R |only vignettes/germany_1990.Rmd | 43 +++++++- vignettes/working_with_eurostat.Rmd |only 35 files changed, 365 insertions(+), 266 deletions(-)
Title: Interface to Climatic Research Unit Time-Series Version 3.21
Data
Description: Functions for reading in and manipulating CRU TS3.21: Climatic
Research Unit (CRU) Time-Series (TS) Version 3.21 data.
Author: Benjamin M. Taylor
Additional contributions
Bikash Parida
Jacob Davies
Maintainer: Benjamin M. Taylor <b.taylor1@lancaster.ac.uk>
Diff between cruts versions 0.4 dated 2018-05-22 and 0.5 dated 2018-09-14
DESCRIPTION | 7 ++++--- MD5 | 8 ++++---- NEWS | 22 ++++++++++++++++++---- R/import-export.R | 52 ++++++++++++++++++++++++---------------------------- build/partial.rdb |binary 5 files changed, 50 insertions(+), 39 deletions(-)
Title: Analysis of Codon Data under Stationarity using a Bayesian
Framework
Description: Is a collection of models to analyze genome scale codon
data using a Bayesian framework. Provides visualization
routines and checkpointing for model fittings. Currently
published models to analyze gene data for selection on codon
usage based on Ribosome Overhead Cost (ROC) are: ROC (Gilchrist
et al. (2015) <doi:10.1093/gbe/evv087>), and ROC with phi
(Wallace & Drummond (2013) <doi:10.1093/molbev/mst051>). In
addition 'AnaCoDa' contains three currently unpublished models.
The FONSE (First order approximation On NonSense Error) model
analyzes gene data for selection on codon usage against of
nonsense error rates. The PA (PAusing time) and PANSE (PAusing
time + NonSense Error) models use ribosome footprinting data to
analyze estimate ribosome pausing times with and without
nonsense error rate from ribosome footprinting data.
Author: Cedric Landerer [aut, cre],
Gabriel Hanas [ctb],
Jeremy Rogers [ctb],
Alex Cope [ctb],
Denizhan Pak [ctb]
Maintainer: Cedric Landerer <cedric.landerer@gmail.com>
Diff between AnaCoDa versions 0.1.1 dated 2018-02-12 and 0.1.2 dated 2018-09-14
AnaCoDa-0.1.1/AnaCoDa/inst/doc/anacoda.bib |only AnaCoDa-0.1.1/AnaCoDa/inst/doc/expression_trace.png |only AnaCoDa-0.1.1/AnaCoDa/inst/doc/logpost_trace.png |only AnaCoDa-0.1.1/AnaCoDa/inst/doc/model_fit.png |only AnaCoDa-0.1.1/AnaCoDa/inst/doc/param_comp.png |only AnaCoDa-0.1.1/AnaCoDa/inst/doc/sel_cai_comp.png |only AnaCoDa-0.1.1/AnaCoDa/inst/doc/selection_trace.png |only AnaCoDa-0.1.2/AnaCoDa/DESCRIPTION | 22 AnaCoDa-0.1.2/AnaCoDa/MD5 | 110 - AnaCoDa-0.1.2/AnaCoDa/NAMESPACE | 7 AnaCoDa-0.1.2/AnaCoDa/NEWS.md | 7 AnaCoDa-0.1.2/AnaCoDa/R/genomeObject.R | 126 + AnaCoDa-0.1.2/AnaCoDa/R/parameterObject.R | 585 ++++-- AnaCoDa-0.1.2/AnaCoDa/R/plotParameterObject.R | 87 AnaCoDa-0.1.2/AnaCoDa/R/plotTraceObject.R | 100 + AnaCoDa-0.1.2/AnaCoDa/README.md | 8 AnaCoDa-0.1.2/AnaCoDa/build |only AnaCoDa-0.1.2/AnaCoDa/inst/doc/anacoda.R |only AnaCoDa-0.1.2/AnaCoDa/inst/doc/anacoda.html | 890 ++++++---- AnaCoDa-0.1.2/AnaCoDa/man/calculateSCUO.Rd |only AnaCoDa-0.1.2/AnaCoDa/man/findOptimalCodon.Rd |only AnaCoDa-0.1.2/AnaCoDa/man/geomMean.Rd |only AnaCoDa-0.1.2/AnaCoDa/man/getCAI.Rd | 4 AnaCoDa-0.1.2/AnaCoDa/man/getCAIweights.Rd | 4 AnaCoDa-0.1.2/AnaCoDa/man/getCSPEstimates.Rd | 19 AnaCoDa-0.1.2/AnaCoDa/man/getCodonCounts.Rd |only AnaCoDa-0.1.2/AnaCoDa/man/getCodonCountsForAA.Rd | 10 AnaCoDa-0.1.2/AnaCoDa/man/initializeGenomeObject.Rd | 5 AnaCoDa-0.1.2/AnaCoDa/man/plotCodonSpecificHyperParameters.Rd |only AnaCoDa-0.1.2/AnaCoDa/src/Default |only AnaCoDa-0.1.2/AnaCoDa/src/FONSEParameter.cpp | 18 AnaCoDa-0.1.2/AnaCoDa/src/Gene.cpp | 8 AnaCoDa-0.1.2/AnaCoDa/src/Genome.cpp | 92 - AnaCoDa-0.1.2/AnaCoDa/src/MCMCAlgorithm.cpp | 19 AnaCoDa-0.1.2/AnaCoDa/src/PAModel.cpp | 60 AnaCoDa-0.1.2/AnaCoDa/src/PANSEModel.cpp | 20 AnaCoDa-0.1.2/AnaCoDa/src/PAParameter.cpp | 27 AnaCoDa-0.1.2/AnaCoDa/src/Parameter.cpp | 1 AnaCoDa-0.1.2/AnaCoDa/src/ROCModel.cpp | 26 AnaCoDa-0.1.2/AnaCoDa/src/ROCParameter.cpp | 5 AnaCoDa-0.1.2/AnaCoDa/src/SequenceSummary.cpp | 60 AnaCoDa-0.1.2/AnaCoDa/src/Testing.cpp | 150 - AnaCoDa-0.1.2/AnaCoDa/src/Trace.cpp | 27 AnaCoDa-0.1.2/AnaCoDa/src/include/Genome.h | 7 AnaCoDa-0.1.2/AnaCoDa/src/include/PA/PAModel.h | 3 AnaCoDa-0.1.2/AnaCoDa/src/include/PA/PAParameter.h | 1 AnaCoDa-0.1.2/AnaCoDa/src/include/ROC/ROCParameter.h | 2 AnaCoDa-0.1.2/AnaCoDa/src/include/SequenceSummary.h | 23 AnaCoDa-0.1.2/AnaCoDa/src/include/base/Parameter.h | 5 AnaCoDa-0.1.2/AnaCoDa/src/include/base/Trace.h | 27 AnaCoDa-0.1.2/AnaCoDa/src/main.cpp | 38 AnaCoDa-0.1.2/AnaCoDa/tests/testthat/UnitTestingData/testMCMCROCFiles/simulatedAllUniqueR_phi_withPhiSet.csv | 4 AnaCoDa-0.1.2/AnaCoDa/tests/testthat/UnitTestingData/writeSimulatedGenome.csv | 18 AnaCoDa-0.1.2/AnaCoDa/tests/testthat/UnitTestingOut/testMCMCROCLogPhi.txt | 20 AnaCoDa-0.1.2/AnaCoDa/tests/testthat/testGene.R | 134 - AnaCoDa-0.1.2/AnaCoDa/tests/testthat/testGenome.R | 70 AnaCoDa-0.1.2/AnaCoDa/tests/testthat/testMCMCROC.R | 2 AnaCoDa-0.1.2/AnaCoDa/tests/testthat/testPAModel.R | 406 ++-- AnaCoDa-0.1.2/AnaCoDa/vignettes |only 59 files changed, 2009 insertions(+), 1248 deletions(-)
Title: Immunoglobulin Clonal Lineage and Diversity Analysis
Description: Provides methods for high-throughput adaptive immune
receptor repertoire sequencing (AIRR-Seq; Rep-Seq) analysis. In
particular, immunoglobulin (Ig) sequence lineage reconstruction,
lineage topology analysis, diversity profiling, amino acid property
analysis and gene usage.
Citations:
Gupta and Vander Heiden, et al (2017) <doi:10.1093/bioinformatics/btv359>,
Stern, Yaari and Vander Heiden, et al (2014) <doi:10.1126/scitranslmed.3008879>.
Author: Jason Vander Heiden [aut, cre],
Namita Gupta [aut],
Susanna Marquez [ctb],
Daniel Gadala-Maria [ctb],
Ruoyi Jiang [ctb],
Nima Nouri [ctb],
Steven Kleinstein [aut, cph]
Maintainer: Jason Vander Heiden <jason.vanderheiden@yale.edu>
Diff between alakazam versions 0.2.10 dated 2018-03-30 and 0.2.11 dated 2018-09-14
alakazam-0.2.10/alakazam/inst/markr |only alakazam-0.2.11/alakazam/DESCRIPTION | 24 + alakazam-0.2.11/alakazam/MD5 | 85 +++--- alakazam-0.2.11/alakazam/NAMESPACE | 7 alakazam-0.2.11/alakazam/NEWS.md | 31 ++ alakazam-0.2.11/alakazam/R/Alakazam.R | 3 alakazam-0.2.11/alakazam/R/Core.R | 95 ++++-- alakazam-0.2.11/alakazam/R/Diversity.R | 191 +++++++++----- alakazam-0.2.11/alakazam/R/Gene.R | 120 ++++++++ alakazam-0.2.11/alakazam/R/Lineage.R | 16 + alakazam-0.2.11/alakazam/R/RcppExports.R | 4 alakazam-0.2.11/alakazam/R/Sequence.R | 39 ++ alakazam-0.2.11/alakazam/R/Topology.R | 23 - alakazam-0.2.11/alakazam/build/vignette.rds |binary alakazam-0.2.11/alakazam/inst/doc/AminoAcids-Vignette.pdf |binary alakazam-0.2.11/alakazam/inst/doc/Diversity-Vignette.pdf |binary alakazam-0.2.11/alakazam/inst/doc/GeneUsage-Vignette.pdf |binary alakazam-0.2.11/alakazam/inst/doc/Lineage-Vignette.pdf |binary alakazam-0.2.11/alakazam/inst/doc/Topology-Vignette.pdf |binary alakazam-0.2.11/alakazam/man/AbundanceCurve-class.Rd | 1 alakazam-0.2.11/alakazam/man/DiversityCurve-class.Rd | 1 alakazam-0.2.11/alakazam/man/DiversityTest-class.Rd | 1 alakazam-0.2.11/alakazam/man/EdgeTest-class.Rd | 1 alakazam-0.2.11/alakazam/man/MRCATest-class.Rd | 1 alakazam-0.2.11/alakazam/man/alakazam.Rd | 2 alakazam-0.2.11/alakazam/man/aminoAcidProperties.Rd | 6 alakazam-0.2.11/alakazam/man/baseTheme.Rd |only alakazam-0.2.11/alakazam/man/buildPhylipLineage.Rd | 2 alakazam-0.2.11/alakazam/man/checkColumns.Rd |only alakazam-0.2.11/alakazam/man/countGenes.Rd | 9 alakazam-0.2.11/alakazam/man/countPatterns.Rd | 3 alakazam-0.2.11/alakazam/man/cpuCount.Rd |only alakazam-0.2.11/alakazam/man/estimateAbundance.Rd | 10 alakazam-0.2.11/alakazam/man/extractVRegion.Rd | 3 alakazam-0.2.11/alakazam/man/getPathLengths.Rd | 3 alakazam-0.2.11/alakazam/man/getSegment.Rd | 8 alakazam-0.2.11/alakazam/man/groupGenes.Rd |only alakazam-0.2.11/alakazam/man/makeChangeoClone.Rd | 5 alakazam-0.2.11/alakazam/man/nonsquareDist.Rd |only alakazam-0.2.11/alakazam/man/plotAbundanceCurve.Rd | 4 alakazam-0.2.11/alakazam/man/plotDiversityCurve.Rd | 6 alakazam-0.2.11/alakazam/man/plotDiversityTest.Rd | 4 alakazam-0.2.11/alakazam/man/plotSubtrees.Rd | 21 - alakazam-0.2.11/alakazam/man/progressBar.Rd |only alakazam-0.2.11/alakazam/man/testDiversity.Rd | 4 alakazam-0.2.11/alakazam/src/RcppDistance.cpp | 42 +++ alakazam-0.2.11/alakazam/src/RcppExports.cpp | 14 + 47 files changed, 580 insertions(+), 209 deletions(-)
Title: Stochastic Gradient Markov Chain Monte Carlo
Description: Provides functions that performs popular stochastic gradient Markov chain Monte Carlo (SGMCMC) methods on user specified models. The required gradients are automatically calculated using 'TensorFlow' <https://www.tensorflow.org/>, an efficient library for numerical computation. This means only the log likelihood and log prior functions need to be specified. The methods implemented include stochastic gradient Langevin dynamics (SGLD), stochastic gradient Hamiltonian Monte Carlo (SGHMC), stochastic gradient Nose-Hoover thermostat (SGNHT) and their respective control variate versions for increased efficiency. References: M. Welling, Y. W. Teh (2011) <http://www.icml-2011.org/papers/398_icmlpaper.pdf>; T. Chen, E. B. Fox, C. E. Guestrin (2014) <arXiv:1402.4102>; N. Ding, Y. Fang, R. Babbush, C. Chen, R. D. Skeel, H. Neven (2014) <https://papers.nips.cc/paper/5592-bayesian-sampling-using-stochastic-gradient-thermostats>; J. Baker, P. Fearnhead, E. B. Fox, C. Nemeth (2017) <arXiv:1706.05439>.
Author: Jack Baker [aut, cre, cph],
Christopher Nemeth [aut, cph],
Paul Fearnhead [aut, cph],
Emily B. Fox [aut, cph],
STOR-i [cph]
Maintainer: Jack Baker <j.baker1@lancaster.ac.uk>
Diff between sgmcmc versions 0.2.2 dated 2018-04-11 and 0.2.3 dated 2018-09-14
DESCRIPTION | 12 +++--- MD5 | 47 ++++++++++++------------ NAMESPACE | 1 NEWS.md | 4 ++ R/install.R |only R/setup.R | 9 +--- R/tfErrors.R |only R/zzz.R | 76 +++++++++++++++++++++++++-------------- README.md | 8 ++-- inst/doc/gaussMixture.Rmd | 2 - inst/doc/gaussMixture.html | 4 +- inst/doc/logisticRegression.Rmd | 2 - inst/doc/logisticRegression.html | 4 +- inst/doc/mvGauss.Rmd | 2 - inst/doc/mvGauss.html | 4 +- inst/doc/nn.Rmd | 2 - inst/doc/nn.html | 2 - inst/doc/sgmcmc.Rmd | 4 +- inst/doc/sgmcmc.html | 4 +- man/installTF.Rd |only tests/testthat/testMatrixParam.R | 2 - vignettes/gaussMixture.Rmd | 2 - vignettes/logisticRegression.Rmd | 2 - vignettes/mvGauss.Rmd | 2 - vignettes/nn.Rmd | 2 - vignettes/sgmcmc.Rmd | 4 +- 26 files changed, 116 insertions(+), 85 deletions(-)
Title: Movement Data Visualization
Description: Tools to visualize movement data (e.g. from GPS tracking) and temporal changes of environmental data (e.g. from remote sensing) by creating video animations.
Author: Jakob Schwalb-Willmann [aut, cre]
Maintainer: Jakob Schwalb-Willmann <movevis@schwalb-willmann.de>
Diff between moveVis versions 0.9.7 dated 2018-09-10 and 0.9.8 dated 2018-09-14
DESCRIPTION | 9 ++++--- MD5 | 23 ++++++++++--------- NEWS.md | 41 +++++++++++++++++++++++++++++++++-- R/animate_move.R | 16 +++++++++++-- R/animate_raster.R | 14 +++++------ R/basemap_data.R | 2 - README.md | 10 ++++---- man/animate_raster.Rd | 12 ++++------ man/basemap_data.Rd | 2 - tests/testthat/helper-vars.R | 3 ++ tests/testthat/test-animate_move.R | 32 +++++++++++++++------------ tests/testthat/test-animate_raster.R |only tests/testthat/test-get_libraries.R | 4 --- 13 files changed, 110 insertions(+), 58 deletions(-)
Title: Statistics for Long-Memory Processes (Book Jan Beran), and
Related Functionality
Description: Datasets and Functionality from
'Jan Beran' (1994). Statistics for Long-Memory Processes; Chapman & Hall.
Estimation of Hurst (and more) parameters for fractional Gaussian noise,
'fARIMA' and 'FEXP' models.
Author: S scripts originally by Jan Beran <jan.beran@uni-konstanz.de>;
Datasets via Brandon Whitcher <brandon@stat.washington.edu>.
Toplevel R functions and much more by Martin Maechler.
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between longmemo versions 1.0-0 dated 2011-06-15 and 1.1-1 dated 2018-09-14
longmemo-1.0-0/longmemo/Done |only longmemo-1.0-0/longmemo/INDEX-MM |only longmemo-1.0-0/longmemo/README |only longmemo-1.0-0/longmemo/R_README |only longmemo-1.1-1/longmemo/ChangeLog | 20 +++ longmemo-1.1-1/longmemo/DESCRIPTION | 23 ++- longmemo-1.1-1/longmemo/MD5 |only longmemo-1.1-1/longmemo/NAMESPACE | 20 ++- longmemo-1.1-1/longmemo/R/WhittleEst.R | 145 ++++++++++++++++++++---- longmemo-1.1-1/longmemo/R/polyFEXP.R | 5 longmemo-1.1-1/longmemo/README.md |only longmemo-1.1-1/longmemo/TODO | 24 +++ longmemo-1.1-1/longmemo/build |only longmemo-1.1-1/longmemo/data/ethernetTraffic.R |only longmemo-1.1-1/longmemo/inst |only longmemo-1.1-1/longmemo/man/Qeta.Rd | 8 - longmemo-1.1-1/longmemo/man/WhittleEst.Rd | 9 + longmemo-1.1-1/longmemo/man/simGauss.Rd | 25 +++- longmemo-1.1-1/longmemo/man/specFGN.Rd | 68 +++++++++-- longmemo-1.1-1/longmemo/tests/ceta-ex.Rout.save | 66 +++++----- longmemo-1.1-1/longmemo/tests/spec-ex.R |only longmemo-1.1-1/longmemo/vignettes |only 22 files changed, 321 insertions(+), 92 deletions(-)
Title: Produce Charts that you See on the Fingertips Website
Description: Use Fingertips charts to recreate the visualisations
that are displayed on the Fingertips website (<http://fingertips.phe.org.uk/>).
Author: Sebastian Fox [aut, cre]
Maintainer: Sebastian Fox <sebastian.fox@phe.gov.uk>
Diff between fingertipscharts versions 0.0.1 dated 2018-07-28 and 0.0.2 dated 2018-09-14
DESCRIPTION | 12 MD5 | 58 - NAMESPACE | 6 NEWS.md | 6 R/dummy_data.R |only R/fingertipscharts.R | 12 R/quick_charts.R | 80 + R/spine_chart_utils.R | 9 inst/doc/quick_charts.R | 7 inst/doc/quick_charts.Rmd | 7 inst/doc/quick_charts.html | 29 man/area_profiles.Rd | 13 man/compare_areas.Rd | 2 man/create_test_data.Rd |only man/spine_rescaler.Rd | 2 tests/figs/area-profiles/domains-included-area-profiles.svg | 208 ++-- tests/figs/compare-indicators-example/compare-indicators-example.svg | 382 ++++----- tests/figs/map-example/map-example.svg | 420 ++++------ tests/figs/map/map.svg | 374 ++++---- tests/figs/population/full-pop-pyramid.svg | 104 +- tests/figs/population/no-comparator-pop-pyramid.svg | 96 +- tests/figs/population/one-comparator-pop-pyramid.svg | 100 +- tests/testthat.R | 86 -- tests/testthat/test-area-profiles.R | 2 tests/testthat/test-box-plots.R | 2 tests/testthat/test-compare-areas.R | 4 tests/testthat/test-compare-indicators.R | 4 tests/testthat/test-overview.R | 2 tests/testthat/test-population.R | 1 tests/testthat/test-trends.R | 2 vignettes/quick_charts.Rmd | 7 31 files changed, 963 insertions(+), 1074 deletions(-)
More information about fingertipscharts at CRAN
Permanent link
Title: Simple Network of Workstations
Description: Support for simple parallel computing in R.
Author: Luke Tierney, A. J. Rossini, Na Li, H. Sevcikova
Maintainer: Luke Tierney <luke-tierney@uiowa.edu>
Diff between snow versions 0.4-2 dated 2016-10-13 and 0.4-3 dated 2018-09-14
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NAMESPACE | 1 + R/snow.R | 11 ++++++----- R/sock.R | 24 +++++++++++++++++++----- man/snow-internal.Rd | 2 -- 6 files changed, 34 insertions(+), 20 deletions(-)
Title: Graphing for Markov, Hidden Markov, and Mixture Transition
Distribution Models
Description: Produces parallel coordinate plots of probability transition matrices from Markov, hidden Markov, and mixture transition distribution models.
Author: Pauline Adamopoulou [aut, cre, cph],
Gilbert Ritschard [ths],
Andre Berchtold [ths],
Reto Buergin [ctb],
Ogier Maitre [ctb]
Maintainer: Pauline Adamopoulou <padamopo@gmail.com>
Diff between MmgraphR versions 0.3 dated 2018-07-25 and 0.3-1 dated 2018-09-14
DESCRIPTION | 13 ++++++++----- MD5 | 12 ++++++------ NEWS | 22 ++++++++++++++++++++-- R/trmatplot.default.R | 25 ++++++++++++++++--------- R/trmatplot.march.Dcmm.R | 28 ++++++++++++++++++---------- ToDo | 3 +++ man/MmgraphR-package.Rd | 4 ++-- 7 files changed, 73 insertions(+), 34 deletions(-)
Title: R Interface to C API of GLPK
Description: R Interface to C API of GLPK, depends on GLPK Version >= 4.42.
Author: Mayo Roettger [cre],
Gabriel Gelius-Dietrich [aut],
Louis Luangkesorn [ctb]
Maintainer: Mayo Roettger <mayo.roettger@hhu.de>
Diff between glpkAPI versions 1.3.0 dated 2015-01-06 and 1.3.1 dated 2018-09-14
DESCRIPTION | 18 +- MD5 | 328 ++++++++++++++++++++--------------------- build/vignette.rds |binary inst/INSTALL | 6 inst/NEWS.Rd | 11 + inst/doc/glpk-gmpl-intro.pdf |binary inst/doc/glpkAPI.pdf |binary man/addColsGLPK.Rd | 2 man/addRowsGLPK.Rd | 2 man/advBasisGLPK.Rd | 2 man/bfExistsGLPK.Rd | 2 man/bfUpdatedGLPK.Rd | 2 man/checkDupGLPK.Rd | 2 man/copyProbGLPK.Rd | 2 man/cpxBasisGLPK.Rd | 2 man/createIndexGLPK.Rd | 2 man/delColsGLPK.Rd | 2 man/delProbGLPK.Rd | 2 man/delRowsGLPK.Rd | 2 man/deleteIndexGLPK.Rd | 2 man/eraseProbGLPK.Rd | 2 man/factorizeGLPK.Rd | 2 man/findColGLPK.Rd | 2 man/findRowGLPK.Rd | 2 man/getBfcpGLPK.Rd | 2 man/getBheadGLPK.Rd | 2 man/getCbindGLPK.Rd | 2 man/getColDualGLPK.Rd | 2 man/getColDualIptGLPK.Rd | 2 man/getColKindGLPK.Rd | 2 man/getColLowBndGLPK.Rd | 2 man/getColNameGLPK.Rd | 2 man/getColPrimGLPK.Rd | 2 man/getColPrimIptGLPK.Rd | 2 man/getColStatGLPK.Rd | 2 man/getColTypeGLPK.Rd | 2 man/getColUppBndGLPK.Rd | 2 man/getColsDualGLPK.Rd | 2 man/getColsDualIptGLPK.Rd | 2 man/getColsKindGLPK.Rd | 2 man/getColsLowBndsGLPK.Rd | 2 man/getColsPrimGLPK.Rd | 2 man/getColsPrimIptGLPK.Rd | 2 man/getColsStatGLPK.Rd | 2 man/getColsUppBndsGLPK.Rd | 2 man/getDualStatGLPK.Rd | 2 man/getInteriorParmGLPK.Rd | 2 man/getMIPParmGLPK.Rd | 2 man/getMatColGLPK.Rd | 2 man/getMatRowGLPK.Rd | 2 man/getNumBinGLPK.Rd | 2 man/getNumColsGLPK.Rd | 2 man/getNumIntGLPK.Rd | 2 man/getNumNnzGLPK.Rd | 2 man/getNumRowsGLPK.Rd | 2 man/getObjCoefGLPK.Rd | 2 man/getObjCoefsGLPK.Rd | 2 man/getObjDirGLPK.Rd | 2 man/getObjNameGLPK.Rd | 2 man/getObjValGLPK.Rd | 2 man/getObjValIptGLPK.Rd | 2 man/getPrimStatGLPK.Rd | 2 man/getProbNameGLPK.Rd | 2 man/getRbindGLPK.Rd | 2 man/getRiiGLPK.Rd | 2 man/getRowDualGLPK.Rd | 2 man/getRowDualIptGLPK.Rd | 2 man/getRowLowBndGLPK.Rd | 2 man/getRowNameGLPK.Rd | 2 man/getRowPrimGLPK.Rd | 2 man/getRowPrimIptGLPK.Rd | 2 man/getRowStatGLPK.Rd | 2 man/getRowTypeGLPK.Rd | 2 man/getRowUppBndGLPK.Rd | 2 man/getRowsDualGLPK.Rd | 2 man/getRowsDualIptGLPK.Rd | 2 man/getRowsLowBndsGLPK.Rd | 2 man/getRowsPrimGLPK.Rd | 2 man/getRowsPrimIptGLPK.Rd | 2 man/getRowsStatGLPK.Rd | 2 man/getRowsTypesGLPK.Rd | 2 man/getRowsUppBndsGLPK.Rd | 2 man/getSimplexParmGLPK.Rd | 2 man/getSjjGLPK.Rd | 2 man/getSolStatGLPK.Rd | 2 man/getSolStatIptGLPK.Rd | 2 man/getUnbndRayGLPK.Rd | 2 man/glpkAPI-package.Rd | 2 man/glpkConstants.Rd | 2 man/glpkPtr-class.Rd | 2 man/initProbGLPK.Rd | 2 man/loadMatrixGLPK.Rd | 2 man/mipColValGLPK.Rd | 2 man/mipColsValGLPK.Rd | 2 man/mipObjValGLPK.Rd | 2 man/mipRowValGLPK.Rd | 2 man/mipRowsValGLPK.Rd | 2 man/mipStatusGLPK.Rd | 2 man/mplAllocWkspGLPK.Rd | 2 man/mplBuildProbGLPK.Rd | 2 man/mplFreeWkspGLPK.Rd | 2 man/mplGenerateGLPK.Rd | 2 man/mplPostsolveGLPK.Rd | 2 man/mplReadDataGLPK.Rd | 2 man/mplReadModelGLPK.Rd | 2 man/printIptGLPK.Rd | 2 man/printMIPGLPK.Rd | 2 man/printRangesGLPK.Rd | 2 man/printSolGLPK.Rd | 2 man/readIptGLPK.Rd | 2 man/readLPGLPK.Rd | 2 man/readMIPGLPK.Rd | 2 man/readMPSGLPK.Rd | 2 man/readProbGLPK.Rd | 2 man/readSolGLPK.Rd | 2 man/return_codeGLPK.Rd | 2 man/scaleProbGLPK.Rd | 2 man/setBfcpGLPK.Rd | 2 man/setColBndGLPK.Rd | 2 man/setColKindGLPK.Rd | 2 man/setColNameGLPK.Rd | 2 man/setColStatGLPK.Rd | 2 man/setColsBndsGLPK.Rd | 2 man/setColsBndsObjCoefsGLPK.Rd | 2 man/setColsKindGLPK.Rd | 2 man/setColsNamesGLPK.Rd | 2 man/setDefaultIptParmGLPK.Rd | 2 man/setDefaultMIPParmGLPK.Rd | 2 man/setDefaultSmpParmGLPK.Rd | 2 man/setInteriorParmGLPK.Rd | 2 man/setMIPParmGLPK.Rd | 2 man/setMatColGLPK.Rd | 2 man/setMatRowGLPK.Rd | 2 man/setObjCoefGLPK.Rd | 2 man/setObjCoefsGLPK.Rd | 2 man/setObjDirGLPK.Rd | 2 man/setObjNameGLPK.Rd | 2 man/setProbNameGLPK.Rd | 2 man/setRhsZeroGLPK.Rd | 2 man/setRiiGLPK.Rd | 2 man/setRowBndGLPK.Rd | 2 man/setRowNameGLPK.Rd | 2 man/setRowStatGLPK.Rd | 2 man/setRowsBndsGLPK.Rd | 2 man/setRowsNamesGLPK.Rd | 2 man/setSimplexParmGLPK.Rd | 2 man/setSjjGLPK.Rd | 2 man/solveInteriorGLPK.Rd | 2 man/solveMIPGLPK.Rd | 2 man/solveSimplexExactGLPK.Rd | 2 man/solveSimplexGLPK.Rd | 2 man/sortMatrixGLPK.Rd | 2 man/status_codeGLPK.Rd | 2 man/stdBasisGLPK.Rd | 2 man/termOutGLPK.Rd | 2 man/unscaleProbGLPK.Rd | 2 man/versionGLPK.Rd | 2 man/warmUpGLPK.Rd | 2 man/writeIptGLPK.Rd | 2 man/writeLPGLPK.Rd | 2 man/writeMIPGLPK.Rd | 2 man/writeMPSGLPK.Rd | 2 man/writeProbGLPK.Rd | 2 man/writeSolGLPK.Rd | 2 src/glpkR.h | 3 165 files changed, 346 insertions(+), 334 deletions(-)
Title: A Small Message Queue for Parallel Processes
Description: This queue is a data structure that lets
parallel processes send and receive messages,
and it can help coordinate the work
of complicated parallel tasks.
Processes can push new messages to the queue,
pop old messages, and obtain a
log of all the messages ever pushed. File locking
preserves the integrity of the data even when
multiple processes access the queue simultaneously.
Author: William Michael Landau [aut, cre],
Eli Lilly and Company [cph]
Maintainer: William Michael Landau <will.landau@gmail.com>
Diff between txtq versions 0.0.4 dated 2018-06-15 and 0.1.0 dated 2018-09-14
DESCRIPTION | 8 +- MD5 | 14 ++-- NAMESPACE | 1 NEWS.md |only R/txtq.R | 74 +++++++++++++++++++----- README.md | 134 ++++++++++++++++++++++++++++++++++++--------- man/R6_txtq.Rd |only man/txtq.Rd | 20 ++++++ tests/testthat/test-txtq.R | 50 ++++++++++++++++ 9 files changed, 248 insertions(+), 53 deletions(-)
Title: R Interface for H2O Sparkling Water
Description: An extension package for 'sparklyr' that provides an R interface to
H2O Sparkling Water machine learning library (see <https://github.com/h2oai/sparkling-water> for more information).
Author: Jakub Hava [aut, cre],
Navdeep Gill [aut],
Erin LeDell [aut],
Michal Malohlava [aut],
JJ Allaire [aut],
H2O.ai [cph],
RStudio [cph]
Maintainer: Jakub Hava <jakub@h2o.ai>
Diff between rsparkling versions 0.2.5 dated 2018-08-03 and 0.2.8 dated 2018-09-14
rsparkling-0.2.5/rsparkling/tests/testthat/h2ologs |only rsparkling-0.2.8/rsparkling/DESCRIPTION | 6 +-- rsparkling-0.2.8/rsparkling/MD5 | 36 +-------------------- rsparkling-0.2.8/rsparkling/R/h2o_context.R | 11 +++++- rsparkling-0.2.8/rsparkling/R/sysdata.rda |binary 5 files changed, 16 insertions(+), 37 deletions(-)
Title: Prediction Intervals for Random-Effects Meta-Analysis
Description: An implementation of prediction intervals for random-effects meta-analysis:
Higgins et al. (2009) <doi:10.1111/j.1467-985X.2008.00552.x>, Partlett and Riley (2017)
<doi:10.1002/sim.7140>, and Nagashima et al. (2018) <doi:10.1177/0962280218773520>,
<arXiv:1804.01054>.
Author: Kengo Nagashima [aut, cre] (<https://orcid.org/0000-0003-4529-9045>),
Hisashi Noma [aut],
Toshi A. Furukawa [aut]
Maintainer: Kengo Nagashima <nshi1201@gmail.com>
Diff between pimeta versions 1.0.1 dated 2018-05-10 and 1.1.0 dated 2018-09-14
pimeta-1.0.1/pimeta/R/RcppExports.r |only pimeta-1.0.1/pimeta/R/stat-PI.r |only pimeta-1.0.1/pimeta/man/bootPI.Rd |only pimeta-1.0.1/pimeta/man/htsdl.Rd |only pimeta-1.0.1/pimeta/man/htsreml.Rd |only pimeta-1.0.1/pimeta/src/bootPI.cpp |only pimeta-1.1.0/pimeta/DESCRIPTION | 11 + pimeta-1.1.0/pimeta/MD5 | 37 ++++-- pimeta-1.1.0/pimeta/NAMESPACE | 5 pimeta-1.1.0/pimeta/NEWS.md | 6 + pimeta-1.1.0/pimeta/R/RcppExports.R |only pimeta-1.1.0/pimeta/R/data.r | 180 ++++++++++++++++---------------- pimeta-1.1.0/pimeta/R/package.r | 24 ++-- pimeta-1.1.0/pimeta/R/pima-.r |only pimeta-1.1.0/pimeta/R/pima-boot.r |only pimeta-1.1.0/pimeta/R/pima-hts.r |only pimeta-1.1.0/pimeta/R/pima-htsreml.r |only pimeta-1.1.0/pimeta/README.md | 52 ++++----- pimeta-1.1.0/pimeta/build |only pimeta-1.1.0/pimeta/inst/CITATION | 48 ++++---- pimeta-1.1.0/pimeta/inst/doc |only pimeta-1.1.0/pimeta/man/pima.Rd |only pimeta-1.1.0/pimeta/man/pima_boot.Rd |only pimeta-1.1.0/pimeta/man/pima_hts.Rd |only pimeta-1.1.0/pimeta/man/pima_htsreml.Rd |only pimeta-1.1.0/pimeta/man/print.pima.Rd |only pimeta-1.1.0/pimeta/src/pi-boot.cpp |only pimeta-1.1.0/pimeta/src/pimeta.h | 27 +++- pimeta-1.1.0/pimeta/vignettes |only 29 files changed, 212 insertions(+), 178 deletions(-)
Title: Omnibus Test for Genetic Association Analysis using the Rank
Normal Transformation
Description: Implementation of genetic association tests for continuous outcomes utilizing the rank-based inverse normal transformation (INT). For outcomes whose residual distribution is heavily skewed or enriched for outliers, INT-based tests provided valid inference and improved power. The primary contribution is a rank normal omnibus test (RNOmni), which synthesizes two complementary INT-based approaches. In simulations against non-normal phenotypes, the omnibus test controlled the type I error in the absence of genetic associations, and improved power in the presence of genetic associations. Under the same settings, standard linear regression variously failed to control the type I error in the absence of associations, and was underpowered in the presence of associations.
Author: Zachary McCaw [aut, cre]
Maintainer: Zachary McCaw <zmccaw@g.harvard.edu>
Diff between RNOmni versions 0.4.0 dated 2018-05-16 and 0.5.0 dated 2018-09-14
RNOmni-0.4.0/RNOmni/R/BasicTest.R |only RNOmni-0.4.0/RNOmni/R/DataDesc.R |only RNOmni-0.4.0/RNOmni/R/DirectMethod.R |only RNOmni-0.4.0/RNOmni/R/IndirectMethod.R |only RNOmni-0.4.0/RNOmni/R/InputCheck.R |only RNOmni-0.4.0/RNOmni/R/RankNormal.R |only RNOmni-0.4.0/RNOmni/data |only RNOmni-0.4.0/RNOmni/man/G.Rd |only RNOmni-0.4.0/RNOmni/man/Resid.Rd |only RNOmni-0.4.0/RNOmni/man/S.Rd |only RNOmni-0.4.0/RNOmni/man/X.Rd |only RNOmni-0.4.0/RNOmni/man/Y.Rd |only RNOmni-0.4.0/RNOmni/man/fastDet.Rd |only RNOmni-0.4.0/RNOmni/man/fastIP.Rd |only RNOmni-0.4.0/RNOmni/man/fastInv.Rd |only RNOmni-0.4.0/RNOmni/man/fastMMp.Rd |only RNOmni-0.4.0/RNOmni/man/fastQF.Rd |only RNOmni-0.4.0/RNOmni/man/fastT.Rd |only RNOmni-0.4.0/RNOmni/man/fitNorm.Rd |only RNOmni-0.4.0/RNOmni/man/inCheck.Rd |only RNOmni-0.4.0/RNOmni/man/olsB.Rd |only RNOmni-0.4.0/RNOmni/man/rankNormal.Rd |only RNOmni-0.4.0/RNOmni/man/vecCor.Rd |only RNOmni-0.4.0/RNOmni/src/RNOmni.cpp |only RNOmni-0.4.0/RNOmni/vignettes/RNOmni_cache |only RNOmni-0.4.0/RNOmni/vignettes/RNOmni_files |only RNOmni-0.5.0/RNOmni/DESCRIPTION | 14 - RNOmni-0.5.0/RNOmni/MD5 | 110 +++------- RNOmni-0.5.0/RNOmni/NAMESPACE | 16 - RNOmni-0.5.0/RNOmni/R/BAT.R |only RNOmni-0.5.0/RNOmni/R/DINT.R |only RNOmni-0.5.0/RNOmni/R/IINT.R |only RNOmni-0.5.0/RNOmni/R/Omnibus.R |only RNOmni-0.5.0/RNOmni/R/PackageHelp.R |only RNOmni-0.5.0/RNOmni/R/RN.R |only RNOmni-0.5.0/RNOmni/R/RcppExports.R | 125 ++++------- RNOmni-0.5.0/RNOmni/inst/doc/RNOmni.R | 144 ++++++++----- RNOmni-0.5.0/RNOmni/inst/doc/RNOmni.Rmd | 179 +++++++++------- RNOmni-0.5.0/RNOmni/inst/doc/RNOmni.html | 308 ++++++++++++++++------------- RNOmni-0.5.0/RNOmni/man/AvgCorr.Rd | 6 RNOmni-0.5.0/RNOmni/man/BAT.Rd | 32 +-- RNOmni-0.5.0/RNOmni/man/BootCorr.Rd | 9 RNOmni-0.5.0/RNOmni/man/DINT.Rd | 35 +-- RNOmni-0.5.0/RNOmni/man/IINT.Rd | 40 ++- RNOmni-0.5.0/RNOmni/man/MMP.Rd |only RNOmni-0.5.0/RNOmni/man/OmniP.Rd | 4 RNOmni-0.5.0/RNOmni/man/RNOmni-help.Rd |only RNOmni-0.5.0/RNOmni/man/RNOmni.Rd | 83 ++++--- RNOmni-0.5.0/RNOmni/man/SchurC.Rd | 13 - RNOmni-0.5.0/RNOmni/man/cov.Rd |only RNOmni-0.5.0/RNOmni/man/det.Rd |only RNOmni-0.5.0/RNOmni/man/fitOLS.Rd |only RNOmni-0.5.0/RNOmni/man/matIP.Rd |only RNOmni-0.5.0/RNOmni/man/matInv.Rd |only RNOmni-0.5.0/RNOmni/man/matQF.Rd |only RNOmni-0.5.0/RNOmni/man/rankNorm.Rd |only RNOmni-0.5.0/RNOmni/src/Covariance.cpp |only RNOmni-0.5.0/RNOmni/src/MatrixOps.cpp | 94 ++------ RNOmni-0.5.0/RNOmni/src/RcppExports.cpp | 125 ++++------- RNOmni-0.5.0/RNOmni/src/Regression.cpp |only RNOmni-0.5.0/RNOmni/vignettes/RNOmni.Rmd | 179 +++++++++------- 61 files changed, 755 insertions(+), 761 deletions(-)
Title: Identification, Tuning, Visualisation and Analysis of Labour
Market Areas
Description: Produces Labour Market Areas from commuting flows available at elementary territorial units. It provides tools for automatic tuning based on spatial contiguity. It also allows for statistical analyses and visualisation of the new functional geography.
Author: Daniela Ichim, Luisa Franconi, Michele D'Alo', Guido van den Heuvel
Maintainer: Luisa Franconi <franconi@istat.it>
Diff between LabourMarketAreas versions 3.2 dated 2017-12-07 and 3.2.2 dated 2018-09-14
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/LabourMarketAreas.R | 20 +++++++++++++++----- man/LabourMarketAreas-package.Rd | 4 ++-- 4 files changed, 24 insertions(+), 14 deletions(-)
More information about LabourMarketAreas at CRAN
Permanent link
Title: Access iTunes App Store Ratings and Reviews using R
Description: To enable 'iOS' App Developers to access iTunes App Store Ratings and Reviews using R to extract Basic App Information and Reviews submitted by their App users, Since Apple Store does not provide this straightforward.
Author: AbdulMajedRaja RS [aut, cre]
Maintainer: AbdulMajedRaja RS <amrrs.data@gmail.com>
Diff between itunesr versions 0.1.1 dated 2018-03-05 and 0.1.2 dated 2018-09-14
DESCRIPTION | 14 ++++++------ MD5 | 14 ++++++------ NAMESPACE | 12 +++++----- R/iTunesR.R | 59 +++++++++++++++++++++++++++++++++++++++------------ README.md | 32 +++++++++++++++++++-------- man/getAttributes.Rd | 45 +++++++++++++++++++------------------- man/getLogo.Rd | 45 +++++++++++++++++++------------------- man/getReviews.Rd | 49 ++++++++++++++++++++---------------------- 8 files changed, 157 insertions(+), 113 deletions(-)
Title: R Interface to 'tslib' (a Time Series Library in C++)
Description: Fast operations for time series objects.
Author: Whit Armstrong <armstrong.whit@gmail.com>
Maintainer: Whit Armstrong <armstrong.whit@gmail.com>
Diff between fts versions 0.9.9.1 dated 2018-07-29 and 0.9.9.2 dated 2018-09-14
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- src/diff.cpp | 2 +- src/lag.cpp | 2 +- src/lead.cpp | 2 +- src/pad.cpp | 2 +- 6 files changed, 12 insertions(+), 12 deletions(-)
Title: Time Series Regression Models with Distributed Lag Models
Description: Provides time series regression models with one predictor using finite distributed lag models, polynomial (Almon) distributed lag models, geometric distributed lag models with Koyck transformation, and autoregressive distributed lag models. It also consists of functions for computation of h-step ahead forecasts from these models. See Baltagi (2011) <doi:10.1007/978-3-642-20059-5> for more information.
Author: Haydar Demirhan [aut, cre, cph] (<https://orcid.org/0000-0002-8565-4710>)
Maintainer: Haydar Demirhan <haydar.demirhan@rmit.edu.au>
Diff between dLagM versions 1.0.2 dated 2018-01-17 and 1.0.6 dated 2018-09-14
dLagM-1.0.2/dLagM/R/MASE.default.R |only dLagM-1.0.2/dLagM/R/ardlDlmForecast.R |only dLagM-1.0.2/dLagM/R/ardlDlmForecast.default.R |only dLagM-1.0.2/dLagM/R/dlmForecast.R |only dLagM-1.0.2/dLagM/R/dlmForecast.default.R |only dLagM-1.0.2/dLagM/R/koyckDlmForecast.R |only dLagM-1.0.2/dLagM/R/koyckDlmForecast.default.R |only dLagM-1.0.2/dLagM/R/polyDlmForecast.R |only dLagM-1.0.2/dLagM/R/polyDlmForecast.default.R |only dLagM-1.0.2/dLagM/man/ardlDlmForecast.Rd |only dLagM-1.0.2/dLagM/man/dlmForecast.Rd |only dLagM-1.0.2/dLagM/man/koyckDlmForecast.Rd |only dLagM-1.0.2/dLagM/man/polyDlmForecast.Rd |only dLagM-1.0.6/dLagM/DESCRIPTION | 11 +-- dLagM-1.0.6/dLagM/MD5 | 84 ++++++++++++------------- dLagM-1.0.6/dLagM/NAMESPACE | 20 ++--- dLagM-1.0.6/dLagM/NEWS.md |only dLagM-1.0.6/dLagM/R/MASE.R | 54 +++++++++++++++- dLagM-1.0.6/dLagM/R/ardlDlm.R | 3 dLagM-1.0.6/dLagM/R/ardlDlm.default.R | 18 ++--- dLagM-1.0.6/dLagM/R/ardlDlm.main.R | 30 ++++++-- dLagM-1.0.6/dLagM/R/ardlDlmForecast.main.R | 17 +++-- dLagM-1.0.6/dLagM/R/dlm.R | 3 dLagM-1.0.6/dLagM/R/dlm.default.R | 11 +-- dLagM-1.0.6/dLagM/R/dlm.main.R | 70 ++++++++++++++------ dLagM-1.0.6/dLagM/R/dlmForecast.main.R | 8 +- dLagM-1.0.6/dLagM/R/finiteDLMauto.R | 1 dLagM-1.0.6/dLagM/R/finiteDLMauto.default.R | 1 dLagM-1.0.6/dLagM/R/finiteDLMauto.main.R | 41 +++++------- dLagM-1.0.6/dLagM/R/forecast.R |only dLagM-1.0.6/dLagM/R/forecast.ardlDlm.R |only dLagM-1.0.6/dLagM/R/forecast.dlm.R |only dLagM-1.0.6/dLagM/R/forecast.koyckDlm.R |only dLagM-1.0.6/dLagM/R/forecast.polyDlm.R |only dLagM-1.0.6/dLagM/R/koyckDlm.R | 3 dLagM-1.0.6/dLagM/R/koyckDlm.default.R | 5 - dLagM-1.0.6/dLagM/R/koyckDlm.main.R | 12 +-- dLagM-1.0.6/dLagM/R/poly.dlm.tests.R | 23 ------ dLagM-1.0.6/dLagM/R/polyDlm.R | 3 dLagM-1.0.6/dLagM/R/polyDlm.default.R | 5 - dLagM-1.0.6/dLagM/R/polyDlm.main.R | 7 -- dLagM-1.0.6/dLagM/R/sortScore.R | 1 dLagM-1.0.6/dLagM/R/sortScore.default.R | 1 dLagM-1.0.6/dLagM/R/summary.ardlDlm.R |only dLagM-1.0.6/dLagM/R/summary.dlm.R |only dLagM-1.0.6/dLagM/R/summary.koyckDlm.R |only dLagM-1.0.6/dLagM/R/summary.polyDlm.R |only dLagM-1.0.6/dLagM/man/MASE.Rd | 6 - dLagM-1.0.6/dLagM/man/ardlDlm.Rd | 53 ++++++++------- dLagM-1.0.6/dLagM/man/dLagM-package.Rd | 16 ++-- dLagM-1.0.6/dLagM/man/dlm.Rd | 48 ++++++++++---- dLagM-1.0.6/dLagM/man/forecast.Rd |only dLagM-1.0.6/dLagM/man/koyckDlm.Rd | 11 +-- dLagM-1.0.6/dLagM/man/polyDlm.Rd | 11 +-- dLagM-1.0.6/dLagM/man/sort.score.Rd | 6 - 55 files changed, 344 insertions(+), 239 deletions(-)
Title: Bayesian Model Averaging
Description: Package for Bayesian model averaging and variable selection for linear models,
generalized linear models and survival models (cox
regression).
Author: Adrian Raftery <raftery@uw.edu>, Jennifer Hoeting,
Chris Volinsky, Ian Painter, Ka Yee Yeung
Maintainer: Hana Sevcikova <hanas@uw.edu>
Diff between BMA versions 3.18.8 dated 2018-03-22 and 3.18.9 dated 2018-09-14
ChangeLog | 3 +++ DESCRIPTION | 10 +++++----- MD5 | 4 ++-- 3 files changed, 10 insertions(+), 7 deletions(-)
Title: To Inspect, Impute, Encode, and Partition Data; and to Keep
Track of This Process
Description: Functions to work with data frames to prepare data for further analysis.
The functions for imputation, encoding, and Partitioning can produce log files to keep track of data manipulation process.
Author: Sherry Zhao
Maintainer: Sherry Zhao <sxzhao@gwu.edu>
Diff between cleandata versions 0.1.0 dated 2018-07-21 and 0.2.0 dated 2018-09-14
DESCRIPTION | 17 ++++++++++------- MD5 | 31 ++++++++++++++++++++----------- NAMESPACE | 2 +- R/encoders.R | 40 ++++++++++++++++++++-------------------- R/imputers.R | 24 +++--------------------- R/inspecters.R | 21 ++++++++++++++++++++- R/internal.R |only R/partitioners.R |only build |only inst |only man/encode.Rd | 4 +++- man/encode_binary.Rd | 12 +++++++++--- man/encode_onehot.Rd |only man/encode_ordinal.Rd | 12 +++++++++--- man/impute.Rd | 12 +++++++++--- man/inspect_map.Rd | 3 +++ man/inspect_na.Rd | 4 ++++ man/inspect_smap.Rd |only man/partition_random.Rd |only vignettes |only 20 files changed, 111 insertions(+), 71 deletions(-)
Title: Markov Chain Monte Carlo (MCMC) Package
Description: Contains functions to perform Bayesian
inference using posterior simulation for a number of
statistical models. Most simulation is done in compiled C++
written in the Scythe Statistical Library Version 1.0.3. All
models return 'coda' mcmc objects that can then be summarized
using the 'coda' package. Some useful
utility functions such as density functions,
pseudo-random number generators for statistical
distributions, a general purpose Metropolis sampling algorithm,
and tools for visualization are provided.
Author: Andrew D. Martin [aut], Kevin M. Quinn [aut], Jong Hee Park [aut,cre], Ghislain Vieilledent [ctb], Michael Malecki[ctb], Matthew Blackwell [ctb], Keith Poole [ctb], Craig Reed [ctb], Ben Goodrich [ctb], Ross Ihaka [cph], The R Development Core Team [cph], The R Foundation [cph], Pierre L'Ecuyer [cph], Makoto Matsumoto [cph], Takuji Nishimura [cph]
Maintainer: Jong Hee Park <jongheepark@snu.ac.kr>
Diff between MCMCpack versions 1.4-3 dated 2018-05-15 and 1.4-4 dated 2018-09-14
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- src/cHDPHMMpoisson.cc | 2 +- src/rng.h | 4 +++- 4 files changed, 11 insertions(+), 9 deletions(-)
Title: Multi-Category Classification Accuracy
Description: It contains six common multi-category classification accuracy evaluation measures:
Hypervolume Under Manifold (HUM), described in
Li and Fine (2008) <doi:10.1093/biostatistics/kxm050>.
Correct Classification Percentage (CCP), Integrated Discrimination Improvement (IDI), Net Reclassification Improvement (NRI), R-Squared Value (RSQ), described in
Li, Jiang and Fine (2013) <doi:10.1093/biostatistics/kxs047>.
Polytomous Discrimination Index (PDI), described in
Van Calster et al. (2012) <doi:10.1007/s10654-012-9733-3>.
Li et al. (2018) <doi:10.1177/0962280217692830>.
Author: Ming Gao, Jialiang Li
Maintainer: Ming Gao <gaoming96@sjtu.edu.cn>
Diff between mcca versions 0.3.0 dated 2018-04-09 and 0.4.0 dated 2018-09-14
DESCRIPTION | 6 - MD5 | 6 - R/ccp.R | 138 ++++++++++++++++++++-------------------- R/nri.R | 202 ++---------------------------------------------------------- 4 files changed, 83 insertions(+), 269 deletions(-)