Title: Robust Instrumental Variables Estimator
Description: Finds a robust instrumental variables estimator using a
high breakdown point S-estimator of multivariate location
and scatter matrix.
Author: Gabriela Cohen-Freue and Davor Cubranic,
with contributions from B. Kaufmann and R.H. Zamar
Maintainer: Gabriela Cohen-Freue <gcohen@stat.ubc.ca>
Diff between riv versions 2.0-4 dated 2013-10-03 and 2.0-5 dated 2018-05-23
DESCRIPTION | 11 ++++++----- MD5 | 6 +++--- NAMESPACE | 1 + man/riv.package.Rd | 11 ++--------- 4 files changed, 12 insertions(+), 17 deletions(-)
Title: Stationarity Test Based on Unsystematic Sub-Sampling
Description: Performs a test for second-order stationarity of time series based
on unsystematic sub-samples.
Author: Haeran Cho [aut, cre]
Maintainer: Haeran Cho <haeran.cho@bristol.ac.uk>
Diff between unsystation versions 0.1.1 dated 2016-11-03 and 0.2.0 dated 2018-05-23
unsystation-0.1.1/unsystation/man/funcApplyVar.Rd |only unsystation-0.1.1/unsystation/man/funcRes.Rd |only unsystation-0.1.1/unsystation/man/funcResVar.Rd |only unsystation-0.1.1/unsystation/man/funcSimX.Rd |only unsystation-0.1.1/unsystation/man/func_coef.Rd |only unsystation-0.1.1/unsystation/src/Makevars.win |only unsystation-0.2.0/unsystation/DESCRIPTION | 13 - unsystation-0.2.0/unsystation/MD5 | 22 -- unsystation-0.2.0/unsystation/NAMESPACE | 18 + unsystation-0.2.0/unsystation/R/RcppExports.R | 56 +++-- unsystation-0.2.0/unsystation/R/stat_code.R | 155 ++++++++------- unsystation-0.2.0/unsystation/man/unsys.station.test.Rd | 94 +++------ unsystation-0.2.0/unsystation/man/unsystation-package.Rd | 74 +++---- unsystation-0.2.0/unsystation/src/RcppExports.cpp | 82 +++++-- unsystation-0.2.0/unsystation/src/sim12.cpp | 7 15 files changed, 279 insertions(+), 242 deletions(-)
Title: Dendrochronology Program Library in R
Description: Perform tree-ring analyses such as detrending, chronology
building, and cross dating. Read and write standard file formats
used in dendrochronology.
Author: Andy Bunn [aut, cph, cre, trl],
Mikko Korpela [aut, cph, trl],
Franco Biondi [aut, cph],
Filipe Campelo [aut, cph],
Pierre Mérian [aut, cph],
Fares Qeadan [aut, cph],
Christian Zang [aut, cph],
Allan Buras [ctb],
Jacob Cecile [ctb],
Manfred Mudelsee [ctb],
Michael Schulz [ctb],
Darwin Pucha-Cofrep [aut, cph],
Jakob Wernicke [aut, cph]
Maintainer: Andy Bunn <andy.bunn@wwu.edu>
Diff between dplR versions 1.6.7 dated 2018-01-29 and 1.6.8 dated 2018-05-23
ChangeLog | 48 +++++++ DESCRIPTION | 21 +-- MD5 | 78 ++++++----- NAMESPACE | 6 R/cms.R | 2 R/csv2rwl.R |only R/plotRings.R | 280 ++++++++++++++++++++++++------------------ R/read.crn.R | 86 +++++++++--- R/read.rwl.R | 108 +++++++++------- R/seg.plot.R | 5 R/time.rwl.R |only build/vignette.rds |binary inst/COPYRIGHTS | 3 inst/doc/chron-dplR.R | 2 inst/doc/chron-dplR.pdf |binary inst/doc/intro-dplR.R | 2 inst/doc/intro-dplR.pdf |binary inst/doc/timeseries-dplR.R | 22 +-- inst/doc/timeseries-dplR.pdf |binary inst/doc/xdate-dplR.R | 2 inst/doc/xdate-dplR.pdf |binary man/bai.in.Rd | 8 - man/bai.out.Rd | 8 - man/csv2rwl.Rd |only man/fill.internal.NA.Rd | 4 man/hanning.Rd | 2 man/morlet.Rd | 2 man/plotRings.Rd | 90 +++++++------ man/print.redfit.Rd | 5 man/read.crn.Rd | 10 + man/read.rwl.Rd | 13 + man/read.tucson.Rd | 2 man/redfit.Rd | 2 man/rwi.stats.running.Rd | 2 man/seg.plot.Rd | 2 man/skel.plot.Rd | 4 man/time.rwl.Rd |only man/wavelet.plot.Rd | 2 vignettes/chron-dplR.Rnw | 2 vignettes/intro-dplR.Rnw | 2 vignettes/timeseries-dplR.Rnw | 22 +-- vignettes/xdate-dplR.Rnw | 6 42 files changed, 516 insertions(+), 337 deletions(-)
Title: Research Project Directory Generator
Description: Create a project directory structure, along with typical files
for that project. This allows projects to be quickly and easily created,
as well as for them to be standardized. Designed specifically with scientists
in mind (mainly bio-medical researchers, but likely applies to other fields).
Author: Luke Johnston [aut, cre] (<https://orcid.org/0000-0003-4169-2616>)
Maintainer: Luke Johnston <lwjohnst@gmail.com>
Diff between prodigenr versions 0.3.0 dated 2016-07-29 and 0.4.0 dated 2018-05-23
prodigenr-0.3.0/prodigenr/inst/doc/introduction.R |only prodigenr-0.3.0/prodigenr/inst/doc/introduction.Rmd |only prodigenr-0.3.0/prodigenr/inst/doc/introduction.html |only prodigenr-0.3.0/prodigenr/inst/templates/R |only prodigenr-0.3.0/prodigenr/inst/templates/abstract |only prodigenr-0.3.0/prodigenr/inst/templates/manuscript |only prodigenr-0.3.0/prodigenr/inst/templates/poster |only prodigenr-0.3.0/prodigenr/inst/templates/readme |only prodigenr-0.3.0/prodigenr/inst/templates/rfigshare |only prodigenr-0.3.0/prodigenr/inst/templates/slides |only prodigenr-0.3.0/prodigenr/man/include_mit_license.Rd |only prodigenr-0.3.0/prodigenr/man/include_rfigshare_script.Rd |only prodigenr-0.3.0/prodigenr/man/include_strobe.Rd |only prodigenr-0.3.0/prodigenr/vignettes/introduction.Rmd |only prodigenr-0.4.0/prodigenr/DESCRIPTION | 27 - prodigenr-0.4.0/prodigenr/LICENSE | 2 prodigenr-0.4.0/prodigenr/MD5 | 76 ++-- prodigenr-0.4.0/prodigenr/NAMESPACE | 9 prodigenr-0.4.0/prodigenr/NEWS.md | 24 + prodigenr-0.4.0/prodigenr/R/create_doc.R |only prodigenr-0.4.0/prodigenr/R/includes.R | 86 ----- prodigenr-0.4.0/prodigenr/R/prodigen.R | 47 -- prodigenr-0.4.0/prodigenr/R/prodigenr-package.R |only prodigenr-0.4.0/prodigenr/R/setup_project.R |only prodigenr-0.4.0/prodigenr/R/utils.R | 55 ++- prodigenr-0.4.0/prodigenr/README.md | 87 +++-- prodigenr-0.4.0/prodigenr/build/vignette.rds |binary prodigenr-0.4.0/prodigenr/inst/doc/prodigenr.R |only prodigenr-0.4.0/prodigenr/inst/doc/prodigenr.Rmd |only prodigenr-0.4.0/prodigenr/inst/doc/prodigenr.html |only prodigenr-0.4.0/prodigenr/inst/rmarkdown |only prodigenr-0.4.0/prodigenr/inst/templates/R-README.md |only prodigenr-0.4.0/prodigenr/inst/templates/README.md |only prodigenr-0.4.0/prodigenr/inst/templates/data-README.md |only prodigenr-0.4.0/prodigenr/inst/templates/doc-README.md |only prodigenr-0.4.0/prodigenr/inst/templates/fetch_data.R |only prodigenr-0.4.0/prodigenr/inst/templates/setup.R |only prodigenr-0.4.0/prodigenr/man/create_doc.Rd |only prodigenr-0.4.0/prodigenr/man/figures |only prodigenr-0.4.0/prodigenr/man/prodigen.Rd | 23 - prodigenr-0.4.0/prodigenr/man/prodigenr-package.Rd |only prodigenr-0.4.0/prodigenr/man/setup_project.Rd |only prodigenr-0.4.0/prodigenr/man/template_list.Rd | 1 prodigenr-0.4.0/prodigenr/tests/testthat/test-files.R |only prodigenr-0.4.0/prodigenr/tests/testthat/test-projects.R | 167 ---------- prodigenr-0.4.0/prodigenr/vignettes/file_structure.txt | 14 prodigenr-0.4.0/prodigenr/vignettes/file_structure_with_doc.txt |only prodigenr-0.4.0/prodigenr/vignettes/manifesto.R |only prodigenr-0.4.0/prodigenr/vignettes/manifesto.html |only prodigenr-0.4.0/prodigenr/vignettes/prodigenr.Rmd |only 50 files changed, 247 insertions(+), 371 deletions(-)
Title: Constrained Inference for Linear Mixed Effects Models
Description: Estimation and inference for linear models where some or all of the
fixed-effects coefficients are subject to order restrictions. This package uses
the robust residual bootstrap methodology for inference, and can handle some
structure in the residual variance matrix.
Author: Casey M. Jelsema [aut, cre],
Shyamal D. Peddada [aut]
Maintainer: Casey M. Jelsema <jelsema.casey@gmail.com>
Diff between CLME versions 2.0-9 dated 2018-02-01 and 2.0-10 dated 2018-05-23
CLME-2.0-10/CLME/DESCRIPTION | 15 ++++++++----- CLME-2.0-10/CLME/MD5 | 22 +++++++++---------- CLME-2.0-10/CLME/NEWS | 25 +++++++++++++++------- CLME-2.0-10/CLME/R/00Package.r | 29 ++++++++------------------ CLME-2.0-10/CLME/R/clme.r | 5 ++-- CLME-2.0-10/CLME/R/utilities.r | 10 +++++++-- CLME-2.0-10/CLME/data/rat.blood.csv |only CLME-2.0-10/CLME/man/CLME-package.Rd | 32 +++++++++++++++-------------- CLME-2.0-10/CLME/man/clme.Rd | 5 ---- CLME-2.0-10/CLME/man/fibroid.Rd | 2 - CLME-2.0-10/CLME/man/print.varcorr_clme.Rd | 2 - CLME-2.0-10/CLME/man/rat.blood.Rd | 2 - CLME-2.0-9/CLME/data/rat.blood.csv.gz |only 13 files changed, 78 insertions(+), 71 deletions(-)
Title: Create Hyperlinks to Biological Databases and Resources
Description: Generate urls and hyperlinks to commonly used biological databases
and resources based on standard identifiers. This is primarily useful when
writing dynamic reports that reference things like gene symbols in text or
tables, allowing you to, for example, convert gene identifiers to hyperlinks
pointing to their entry in the NCBI Gene database. Currently supports NCBI
Gene, PubMed, Gene Ontology, CRAN and Bioconductor.
Author: Aaron Wolen [aut, cre]
Maintainer: Aaron Wolen <aaron@wolen.com>
Diff between biolink versions 0.1.4 dated 2018-04-20 and 0.1.5 dated 2018-05-23
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 4 ++++ README.md | 1 + tests/testthat/test-tags-entrez.r | 2 ++ tests/testthat/test-tags-go.r | 2 ++ tests/testthat/test-tags-pubmed.r | 2 ++ 7 files changed, 21 insertions(+), 10 deletions(-)
Title: Fitting Frailty Models with the EM Algorithm
Description: Contains functions for fitting shared frailty models with a semi-parametric
baseline hazard with the Expectation-Maximization algorithm. Supported data formats
include clustered failures with left truncation and recurrent events in gap-time
or Andersen-Gill format. Several frailty distributions, such as the the gamma, positive stable
and the Power Variance Family are supported.
Author: Theodor Adrian Balan, Hein Putter
Maintainer: Theodor Adrian Balan <t.a.balan@lumc.nl>
Diff between frailtyEM versions 0.8.7 dated 2018-04-23 and 0.8.8 dated 2018-05-23
DESCRIPTION | 6 MD5 | 79 - NAMESPACE | 133 +-- NEWS.md | 430 +++++----- R/RcppExports.R | 72 - R/autoplot.emfrail.R | 763 ++++++++--------- R/ca_test_cph.R | 872 ++++++++++---------- R/ca_test_fit.R | 256 ++--- R/em_fit.R | 1122 +++++++++++++------------- R/emfrail.R | 1762 ++++++++++++++++++++--------------------- R/emfrail_arguments.R | 306 +++---- R/emfrail_aux.R | 404 ++++----- R/emfrail_methods.R | 154 +-- R/fast_Estep.R | 108 +- R/plot.emfrail.R | 630 +++++++------- R/predict.emfrail.R | 668 +++++++-------- R/print.emfrail.R | 114 +- R/print.emfrail_summary.R | 324 +++---- R/summary.emfrail.R | 870 ++++++++++---------- build/vignette.rds |binary inst/doc/frailtyEM_manual.R | 454 +++++----- inst/doc/frailtyEM_manual.Rnw | 1736 ++++++++++++++++++++-------------------- inst/doc/frailtyEM_manual.pdf |binary man/Estep.Rd | 64 - man/autoplot.Rd |only man/autoplot.emfrail.Rd | 179 ++-- man/ca_test.Rd | 72 - man/dist_to_pars.Rd | 44 - man/emfrail.Rd | 448 +++++----- man/emfrail_control.Rd | 142 +-- man/emfrail_dist.Rd | 84 - man/emfrail_pll.Rd | 170 +-- man/fast_Estep.Rd | 66 - man/laplace_transform.Rd | 52 - man/logLik.emfrail.Rd | 64 - man/plot.emfrail.Rd | 152 +-- man/predict.emfrail.Rd | 248 ++--- man/residuals.emfrail.Rd | 58 - man/summary.emfrail.Rd | 198 ++-- vignettes/frailtyEM_manual.Rnw | 1736 ++++++++++++++++++++-------------------- vignettes/mybib.bib | 1050 ++++++++++++------------ 41 files changed, 8046 insertions(+), 8044 deletions(-)
Title: Manipulate and Explore UK Biobank Data
Description: A set of tools to create a UK Biobank <http://www.ukbiobank.ac.uk/> dataset from a UKB fileset (.tab, .r, .html),
visualize primary demographic data for a sample subset, query ICD diagnoses,
retrieve genetic metadata, read and write standard file formats for genetic analyses.
Author: Ken Hanscombe [aut, cre]
Maintainer: Ken Hanscombe <ken.hanscombe@gmail.com>
Diff between ukbtools versions 0.10.1 dated 2018-02-05 and 0.11.0 dated 2018-05-23
DESCRIPTION | 8 MD5 | 49 ++--- NAMESPACE | 6 NEWS.md | 19 ++ R/context.R | 57 ++++-- R/genetics_qc.R |only R/metadata.R | 360 ++++++++++++++++----------------------- R/readwrite.R | 31 +-- R/ukb_dataset.R | 114 +++++++----- README.md | 20 +- build/vignette.rds |binary inst/doc/explore-ukb-data.html | 4 man/ukb_centre.Rd | 6 man/ukb_context.Rd | 24 +- man/ukb_defunct.Rd |only man/ukb_df.Rd | 4 man/ukb_gen_excl.Rd | 5 man/ukb_gen_excl_to_na.Rd | 3 man/ukb_gen_het.Rd | 3 man/ukb_gen_meta.Rd | 2 man/ukb_gen_pcs.Rd | 4 man/ukb_gen_rel.Rd | 2 man/ukb_gen_rel_count.Rd | 21 +- man/ukb_gen_related_with_data.Rd |only man/ukb_gen_samples_to_remove.Rd |only man/ukb_gen_sqc_names.Rd |only man/ukb_gen_write_bgenie.Rd | 12 - man/ukb_gen_write_plink_excl.Rd | 1 28 files changed, 404 insertions(+), 351 deletions(-)
Title: Evolutionary Transcriptomics
Description: Investigate the evolution of biological processes by capturing evolutionary signatures in transcriptomes (Drost et al. (2017) <doi:10.1093/bioinformatics/btx835>). The aim of this tool is to provide a transcriptome analysis environment for answering questions regarding the evolution of biological processes (Drost et al. (2016) <doi:10.1101/051565>).
Author: Hajk-Georg Drost [aut, cre] (<https://orcid.org/0000-0002-1567-306X>)
Maintainer: Hajk-Georg Drost <hgd23@cam.ac.uk>
Diff between myTAI versions 0.7.0 dated 2018-04-11 and 0.8.0 dated 2018-05-23
DESCRIPTION | 8 ++-- MD5 | 80 ++++++++++++++++++++-------------------- NEWS.md | 8 ++++ R/CollapseReplicates.R | 1 R/DiffGenes.R | 1 R/EnrichmentTest.R | 4 +- R/Expressed.R | 2 + R/GroupDiffs.R | 2 - R/PlotBarRE.R | 13 +++--- R/PlotCIRatio.R | 2 - R/PlotCategoryExpr.R | 13 +++--- R/PlotContribution.R | 4 +- R/PlotCorrelation.R | 2 + R/PlotDistribution.R | 2 - R/PlotGeneSet.R | 7 ++- R/PlotGroupDiffs.R | 11 +++-- R/PlotMeans.R | 1 R/PlotMedians.R | 1 R/PlotPattern.R | 1 R/PlotRE.R | 3 + R/PlotReplicateQuality.R | 6 +-- R/PlotSelectedAgeDistr.R | 3 + R/PlotVars.R | 1 R/SelectGeneSet.R | 1 R/age.apply.R | 6 +-- R/combinatorialSignificance.R | 13 +++--- R/geom.mean.R | 4 +- R/harm.mean.R | 4 +- R/omitMatrix.R | 4 +- R/tf.R | 1 README.md | 18 ++++----- inst/doc/Advanced.html | 4 +- inst/doc/Enrichment.html | 4 +- inst/doc/Expression.html | 4 +- inst/doc/Intermediate.html | 52 +++++++++++++------------- inst/doc/Introduction.R | 6 +++ inst/doc/Introduction.Rmd | 20 +++++----- inst/doc/Introduction.html | 17 ++++---- inst/doc/Taxonomy.html | 4 +- tests/testthat/test-Expressed.R | 3 - vignettes/Introduction.Rmd | 20 +++++----- 41 files changed, 199 insertions(+), 162 deletions(-)
Title: Ratios of Coefficients in the General Linear Model
Description: Performs (simultaneous) inferences for ratios of linear combinations of coefficients in the general linear model. Multiple comparisons and simultaneous confidence interval estimations can be performed for ratios of treatment means in the normal one-way layout with homogeneous and heterogeneous treatment variances, according to Dilba et al. (2007) <https://cran.r-project.org/doc/Rnews/Rnews_2007-1.pdf> and Hasler and Hothorn (2008) <doi:10.1002/bimj.200710466>. Confidence interval estimations for ratios of linear combinations of linear model parameters like in (multiple) slope ratio and parallel line assays can be carried out. Moreover, it is possible to calculate the sample sizes required in comparisons with a control based on relative margins. For the simple two-sample problem, functions for a t-test for ratio-formatted hypotheses and the corresponding confidence interval are provided assuming homogeneous or heterogeneous group variances.
Author: Gemechis Djira [aut],
Mario Hasler [aut],
Daniel Gerhard [aut],
Frank Schaarschmidt [aut, cre]
Maintainer: Frank Schaarschmidt <schaarschmidt@biostat.uni-hannover.de>
Diff between mratios versions 1.3.17 dated 2012-11-02 and 1.4.0 dated 2018-05-23
mratios-1.3.17/mratios/R/t.test.ratio.R |only mratios-1.3.17/mratios/R/t.test.ratio.default.R |only mratios-1.3.17/mratios/R/t.test.ratio.formula.R |only mratios-1.3.17/mratios/man/t.test.ratio.Rd |only mratios-1.4.0/mratios/DESCRIPTION | 39 +-- mratios-1.4.0/mratios/MD5 | 67 ++--- mratios-1.4.0/mratios/NAMESPACE | 9 mratios-1.4.0/mratios/NEWS |only mratios-1.4.0/mratios/R/contrMatRatio.R | 4 mratios-1.4.0/mratios/R/gsci.ratio.R | 240 ++++++++++++--------- mratios-1.4.0/mratios/R/plot.sci.ratio.R | 23 +- mratios-1.4.0/mratios/R/print.sci.ratio.R | 4 mratios-1.4.0/mratios/R/ratioVH.R | 70 +++--- mratios-1.4.0/mratios/R/sci.ratio.R | 4 mratios-1.4.0/mratios/R/sci.ratio.gen.R | 73 +++--- mratios-1.4.0/mratios/R/sci.ratioI.R | 60 +++-- mratios-1.4.0/mratios/R/summary.sci.ratio.R | 5 mratios-1.4.0/mratios/R/ttestratio.R |only mratios-1.4.0/mratios/data/ASAT.rda |binary mratios-1.4.0/mratios/data/BW.rda |binary mratios-1.4.0/mratios/data/Mutagenicity.rda |binary mratios-1.4.0/mratios/data/SRAssay.rda |binary mratios-1.4.0/mratios/data/angina.rda |binary mratios-1.4.0/mratios/data/rat.weight.rda |binary mratios-1.4.0/mratios/man/contrMatRatio.Rd | 4 mratios-1.4.0/mratios/man/gsci.ratio.Rd | 16 - mratios-1.4.0/mratios/man/mratios.package.Rd | 27 -- mratios-1.4.0/mratios/man/plot.sci.ratio.Rd | 5 mratios-1.4.0/mratios/man/print.sci.ratio.Rd | 5 mratios-1.4.0/mratios/man/print.simtest.ratio.Rd | 7 mratios-1.4.0/mratios/man/rat.weight.rd | 1 mratios-1.4.0/mratios/man/sci.ratio.Rd | 34 +- mratios-1.4.0/mratios/man/sci.ratio.gen.Rd | 2 mratios-1.4.0/mratios/man/sci.ratioVH.Rd | 5 mratios-1.4.0/mratios/man/simtest.ratio.Rd | 4 mratios-1.4.0/mratios/man/simtest.ratioVH.Rd | 5 mratios-1.4.0/mratios/man/summary.simtest.ratio.Rd | 6 mratios-1.4.0/mratios/man/ttestratio.Rd |only 38 files changed, 408 insertions(+), 311 deletions(-)
Title: Interface to 'MLeap'
Description: A 'sparklyr' <https://spark.rstudio.com> extension that provides
an interface to 'MLeap' <https://github.com/combust/mleap>, an open source library
that enables exporting and serving of 'Apache Spark' pipelines.
Author: Kevin Kuo [aut, cre] (<https://orcid.org/0000-0001-7803-7901>)
Maintainer: Kevin Kuo <kevin.kuo@rstudio.com>
Diff between mleap versions 0.1.1 dated 2018-05-10 and 0.1.2 dated 2018-05-23
DESCRIPTION | 12 ++++++------ MD5 | 20 ++++++++++---------- NEWS.md | 4 ++++ R/installers.R | 6 +++--- inst/extdata/config.json | 2 +- inst/java/mleap-2.0-2.11.jar |binary inst/java/mleap-2.1-2.11.jar |binary inst/java/mleap-2.2-2.11.jar |binary inst/java/mleap-2.3-2.11.jar |binary tests/testthat/helpers-initialize.R | 2 +- tests/testthat/test-serving.R | 11 +++++++++-- 11 files changed, 34 insertions(+), 23 deletions(-)
Title: A Most Informative Histogram-Like Model
Description: Using the MDL principle, it is possible to estimate
parameters for a histogram-like model. The package contains
the implementation of such an estimation method.
Author: Jouke Witteveen
Maintainer: Jouke Witteveen <j.witteveen@gmail.com>
Diff between histmdl versions 0.6-1 dated 2016-09-28 and 0.7-1 dated 2018-05-23
histmdl-0.6-1/histmdl/man/histmdl-package.Rd |only histmdl-0.7-1/histmdl/DESCRIPTION | 8 ++++---- histmdl-0.7-1/histmdl/MD5 | 7 +++---- histmdl-0.7-1/histmdl/NAMESPACE | 2 +- histmdl-0.7-1/histmdl/src/histmdl.c | 15 ++++++++++++++- 5 files changed, 22 insertions(+), 10 deletions(-)
Title: Query 'HaploReg' and 'RegulomeDB'
Description: A set of utilities for querying
'HaploReg' <http://archive.broadinstitute.org/mammals/haploreg/haploreg.php>
and 'RegulomeDB' <http://www.regulomedb.org> web-based tools. The package connects to
'HaploReg' or 'RegulomeDB', searches and downloads results, without
opening web pages, directly from R environment.
Results are stored in a data frame that can be directly used in various
kinds of downstream analyses.
Author: Ilya Y. Zhbannikov [aut, cre]
Maintainer: Ilya Y. Zhbannikov <ilya.zhbannikov@duke.edu>
Diff between haploR versions 1.6.2 dated 2017-10-31 and 1.6.4 dated 2018-05-23
DESCRIPTION | 15 -- MD5 | 14 +- R/regulome.R | 6 build/vignette.rds |binary inst/NEWS | 4 inst/doc/haplor-vignette.Rmd | 3 inst/doc/haplor-vignette.html | 262 +++++++++++++++++++++--------------------- vignettes/haplor-vignette.Rmd | 3 8 files changed, 153 insertions(+), 154 deletions(-)
Title: Synthetic Likelihood Methods for Intractable Likelihoods
Description: Framework to perform synthetic likelihood inference
for models where the likelihood function is unavailable or
intractable.
Author: Matteo Fasiolo and Simon Wood
Maintainer: Matteo Fasiolo <matteo.fasiolo@gmail.com>
Diff between synlik versions 0.1.1 dated 2014-06-08 and 0.1.2 dated 2018-05-23
DESCRIPTION | 16 +++--- MD5 | 89 +++++++++++++++++---------------- NAMESPACE | 46 +++++++++++------ R/Class_definitions.R | 9 +-- R/Generic_functions.R | 2 R/I_clean.R | 2 R/I_slick.R | 2 R/continue_smcmc.R | 11 ++++ R/internal_docs.R |only R/paramsSimulator.R | 3 - R/plot_smcmc.R | 4 + R/plot_synlik.R | 1 R/simulators.R | 7 +- R/summary_statistics.R | 8 +-- build/vignette.rds |binary inst/doc/synlik.R | 29 ----------- inst/doc/synlik.Rmd | 2 inst/doc/synlik.html | 89 +++++++++++++++++---------------- man/ANYOrNULL-class.Rd | 4 + man/blowSimul.Rd | 56 +++++++++------------ man/blow_sl.Rd | 25 ++++----- man/checkNorm.Rd | 78 +++++++++++------------------ man/continue-generic.Rd | 56 ++++++++++++++------- man/extractCorr.Rd | 10 ++- man/functionOrNULL-class.Rd | 4 + man/internal_C.Rd |only man/nlar.Rd | 27 ++++------ man/numericOrNULL-class.Rd | 4 + man/orderDist.Rd | 24 ++++----- man/plot-smcmc.Rd | 53 +++++++++----------- man/plot-synlik.Rd | 29 ++++++----- man/rickerSimul.Rd | 55 ++++++++------------ man/ricker_sl.Rd | 25 ++++----- man/robCov.Rd | 57 +++++++++------------ man/simulate-synlik.Rd | 70 +++++++++++--------------- man/slAcf.Rd | 22 +++----- man/slice.Rd | 101 ++++++++++++++++---------------------- man/slik.Rd | 53 ++++++++------------ man/smcmc-class.Rd | 116 +++++++++++++++++++------------------------- man/smcmc.Rd | 56 +++++++++------------ man/synlik-class.Rd | 60 +++++++++------------- man/synlik-package.Rd | 8 +-- src/Makevars | 2 src/init.c |only src/summ_stats.h | 2 src/synlik.h | 6 -- vignettes/synlik.Rmd | 2 47 files changed, 629 insertions(+), 696 deletions(-)
Title: Locally Stationary Two-Dimensional Wavelet Process Estimation
Scheme
Description: Estimates two-dimensional local wavelet spectra.
Author: Idris Eckley [aut, cre],
Guy Nason [aut],
Sarah Taylor [ctb],
Matthew Nunes [ctb]
Maintainer: Idris Eckley <i.eckley@lancaster.ac.uk>
Diff between LS2W versions 1.3-3 dated 2013-07-12 and 1.3.4 dated 2018-05-23
DESCRIPTION | 22 +++++++++++++--------- MD5 | 19 ++++++++++--------- NAMESPACE | 42 ++++++++++++++++++++++++++++++++++++++++-- R/PhiJ.R | 2 +- R/PsiJ.R | 2 +- R/zzz.R | 25 ------------------------- man/LS2W-package.Rd | 8 -------- man/LS2Wsim.cddews.Rd | 2 +- src/functionsIE.c | 2 +- src/init.c |only src/phij.c | 2 +- 11 files changed, 68 insertions(+), 58 deletions(-)
Title: Bayesian Inference of Non-Linear and Non-Gaussian State Space
Models
Description: Efficient methods for Bayesian inference of state space models
via particle Markov chain Monte Carlo and parallel importance sampling type weighted
Markov chain Monte Carlo (Vihola, Helske, and Franks, 2017, <arXiv:1609.02541>).
Gaussian, Poisson, binomial, or negative binomial
observation densities and basic stochastic volatility models with Gaussian state
dynamics, as well as general non-linear Gaussian models and discretised diffusion models
are supported.
Author: Jouni Helske, Matti Vihola
Maintainer: Jouni Helske <jouni.helske@iki.fi>
Diff between bssm versions 0.1.4 dated 2018-02-04 and 0.1.5 dated 2018-05-23
DESCRIPTION | 12 MD5 | 118 +- NAMESPACE | 296 +++---- NEWS | 114 +- R/RcppExports.R | 438 +++++------ R/as_gssm.R | 9 R/kfilter.R | 11 R/run_mcmc.R | 1654 +++++++++++++++++++++--------------------- R/smoother.R | 12 build/vignette.rds |binary inst/doc/bssm.R | 154 +-- inst/doc/bssm.pdf |binary inst/doc/growth_model.R | 140 +-- inst/doc/growth_model.pdf |binary man/ar1.Rd | 58 - man/as_gssm.Rd | 56 - man/autoplot.predict_bssm.Rd | 62 - man/bootstrap_filter.Rd | 86 +- man/bsm.Rd | 120 +-- man/bssm.Rd | 32 man/drownings.Rd | 32 man/ekf.Rd | 52 - man/ekf_smoother.Rd | 50 - man/ekpf_filter.Rd | 64 - man/exchange.Rd | 36 man/expand_sample.Rd | 58 - man/gaussian_approx.Rd | 48 - man/gssm.Rd | 114 +- man/importance_sample.Rd | 100 +- man/kfilter.Rd | 60 - man/lgg_ssm.Rd | 108 +- man/logLik.Rd | 72 - man/mv_gssm.Rd | 106 +- man/ng_ar1.Rd | 74 - man/ng_bsm.Rd | 164 ++-- man/ngssm.Rd | 124 +-- man/nlg_ssm.Rd | 122 +-- man/particle_smoother.Rd | 114 +- man/poisson_series.Rd | 34 man/predict.Rd | 184 ++-- man/print.mcmc_output.Rd | 54 - man/priors.Rd | 74 - man/run_mcmc.Rd | 56 - man/run_mcmc_g.Rd | 142 +-- man/run_mcmc_ng.Rd | 276 +++---- man/sde_ssm.Rd | 84 +- man/sim_smoother.Rd | 70 - man/smoother.Rd | 56 - man/summary.mcmc_output.Rd | 58 - man/svm.Rd | 90 +- man/ukf.Rd | 50 - src/R_kfilter.cpp | 6 src/R_smoother.cpp | 2 src/RcppExports.cpp | 48 - src/mgg_ssm.cpp | 98 +- src/nlg_ssm.cpp | 111 +- src/ugg_ssm.cpp | 1 src/ung_ssm.cpp | 4 tests/testthat/test_as_gssm.R | 2 tests/testthat/test_basics.R | 34 60 files changed, 3282 insertions(+), 3122 deletions(-)
Title: Variance Estimation for Sample Surveys by the Ultimate Cluster
Method
Description: Generation of domain variables, linearization of several nonlinear population statistics (the ratio of two totals, weighted income percentile, relative median income ratio, at-risk-of-poverty rate, at-risk-of-poverty threshold, Gini coefficient, gender pay gap, the aggregate replacement ratio, the relative median income ratio, median income below at-risk-of-poverty gap, income quintile share ratio, relative median at-risk-of-poverty gap), computation of regression residuals in case of weight calibration, variance estimation of sample surveys by the ultimate cluster method (Hansen, Hurwitz and Madow,Theory, vol. I: Methods and Applications; vol. II: Theory. 1953, New York: John Wiley and Sons), variance estimation for longitudinal, cross-sectional measures and measures of change for single and multistage stage cluster sampling designs (Berger, Y. G., 2015, <doi:10.1111/rssa.12116>). Several other precision measures are derived - standard error, the coefficient of variation, the margin of error, confidence interval, design effect.
Author: Juris Breidaks [aut, cre],
Martins Liberts [aut],
Santa Ivanova [aut]
Maintainer: Juris Breidaks <Juris.Breidaks@csb.gov.lv>
Diff between vardpoor versions 0.9.11 dated 2017-11-07 and 0.10.0 dated 2018-05-23
DESCRIPTION | 10 - MD5 | 76 ++++++------ NAMESPACE | 2 R/domain.R | 9 - R/incPercentile.R | 4 R/linarpr.R | 4 R/linarpt.R | 15 +- R/linarr.R | 4 R/linpoormed.R | 4 R/linrmir.R | 4 R/linrmpg.R | 4 R/residual_est.R | 5 R/vardannual.R | 32 +++-- R/vardchanges.R | 153 ++++++++++++++----------- R/vardchangespoor.R | 288 +++++++++++++----------------------------------- R/vardchangstrs.R |only R/vardcros.R | 38 +++--- R/vardcrospoor.R | 19 +-- R/vardom.R | 33 +++-- R/vardom_othstr.R | 43 ++++--- R/vardomh.R | 41 ++++-- R/varpoord.R | 33 +++-- inst/NEWS | 4 man/incPercentile.Rd | 4 man/linarpr.Rd | 4 man/linarpt.Rd | 4 man/linarr.Rd | 2 man/linpoormed.Rd | 4 man/linrmir.Rd | 2 man/linrmpg.Rd | 4 man/residual_est.Rd | 8 + man/vardchangespoor.Rd | 4 man/vardchangstrs.Rd |only man/vardcrospoor.Rd | 4 man/vardom.Rd | 2 man/vardom_othstr.Rd | 2 man/vardomh.Rd | 4 man/vardpoor-package.Rd | 7 - man/variance_othstr.Rd | 2 man/varpoord.Rd | 8 - 40 files changed, 429 insertions(+), 461 deletions(-)
More information about ODEsensitivity at CRAN
Permanent link
Title: Convenient Data Exchange with Microsoft Excel
Description: Allows access to data in running instance of Microsoft Excel
(e. g. 'xl[a1] = xl[b2]*3' and so on). Graphics can be transferred with
'xl[a1] = current.graphics()'. Additionally there are function for reading/writing
'Excel' files - 'xl.read.file'/'xl.save.file'. They are not fast but able to read/write
'*.xlsb'-files and password-protected files. There is an Excel workbook with
examples of calling R from Excel in the 'doc' folder. It tries to keep things as
simple as possible - there are no needs in any additional
installations besides R, only 'VBA' code in the Excel workbook.
Microsoft Excel is required for this package.
Author: Gregory Demin <excel.link.feedback@gmail.com>. To comply CRAN policy
includes source code from 'RDCOMClient' (http://www.omegahat.net/RDCOMClient) by
Duncan Temple Lang <duncan@wald.ucdavis.edu>.
Maintainer: Gregory Demin <excel.link.feedback@gmail.com>
Diff between excel.link versions 0.9.7 dated 2017-05-01 and 0.9.8-1 dated 2018-05-23
DESCRIPTION | 14 ++--- MD5 | 36 ++++++------- NAMESPACE | 9 ++- NEWS | 9 +++ R/0zzzCOMLists.R | 23 ++++---- R/0zzzrunTime.R | 14 +---- R/excel.link.R | 5 + R/utils.R | 16 +++++ R/xl.read.file.R | 78 +++++++++++++++++----------- R/xl.sheet.add.R | 99 ++++++++++++++++++++++++++++++++---- R/xl.workbooks.R | 50 +++++++++++++----- build/vignette.rds |binary inst/doc/CallingRFromExcel.html | 6 +- inst/doc/R_connection_examples.xlsm |binary man/RDCOMClient.Rd | 6 -- man/xl.read.file.Rd | 12 +++- man/xl.sheet.add.Rd | 31 +++++++++-- man/xl.workbook.add.Rd | 12 +++- src/Makevars.win | 1 19 files changed, 304 insertions(+), 117 deletions(-)
Title: Multivariate Multiscale Spatial Analysis
Description: Tools for the multiscale spatial analysis of multivariate data.
Several methods are based on the use of a spatial weighting matrix and its
eigenvector decomposition (Moran's Eigenvectors Maps, MEM).
Author: Stéphane Dray, David Bauman, Guillaume Blanchet, Daniel Borcard, Sylvie Clappe, Guillaume Guenard,
Thibaut Jombart, Guillaume Larocque, Pierre Legendre, Naima Madi, Helene H Wagner
Maintainer: Stéphane Dray <stephane.dray@univ-lyon1.fr>
Diff between adespatial versions 0.1-1 dated 2018-01-16 and 0.2-0 dated 2018-05-23
adespatial-0.1-1/adespatial/R/createlistw.R |only adespatial-0.1-1/adespatial/R/ortho.AIC.R |only adespatial-0.1-1/adespatial/R/test.W.R |only adespatial-0.1-1/adespatial/inst/createlistw |only adespatial-0.1-1/adespatial/man/createlistw.Rd |only adespatial-0.1-1/adespatial/man/ortho.AIC.Rd |only adespatial-0.1-1/adespatial/man/test.W.Rd |only adespatial-0.2-0/adespatial/DESCRIPTION | 14 adespatial-0.2-0/adespatial/MD5 | 44 adespatial-0.2-0/adespatial/NAMESPACE | 15 adespatial-0.2-0/adespatial/R/forward.sel.R | 9 adespatial-0.2-0/adespatial/R/listw.candidates.R |only adespatial-0.2-0/adespatial/R/listw.explore.R |only adespatial-0.2-0/adespatial/R/listw.select.R |only adespatial-0.2-0/adespatial/R/mem.select.R |only adespatial-0.2-0/adespatial/R/scores.listw.R | 14 adespatial-0.2-0/adespatial/build/vignette.rds |binary adespatial-0.2-0/adespatial/inst/doc/tutorial.R | 74 - adespatial-0.2-0/adespatial/inst/doc/tutorial.Rmd | 131 -- adespatial-0.2-0/adespatial/inst/doc/tutorial.html | 1140 ++++++++++---------- adespatial-0.2-0/adespatial/inst/listw.explore |only adespatial-0.2-0/adespatial/man/forward.sel.Rd | 5 adespatial-0.2-0/adespatial/man/listw.candidates.Rd |only adespatial-0.2-0/adespatial/man/listw.explore.Rd |only adespatial-0.2-0/adespatial/man/listw.select.Rd |only adespatial-0.2-0/adespatial/man/mem.Rd | 13 adespatial-0.2-0/adespatial/man/mem.select.Rd |only adespatial-0.2-0/adespatial/src/forward.c | 9 adespatial-0.2-0/adespatial/src/init.c | 2 adespatial-0.2-0/adespatial/vignettes/tutorial.Rmd | 131 -- 30 files changed, 666 insertions(+), 935 deletions(-)
Title: Adaptive Semiparametric Additive Regression with Simultaneous
Confidence Bands and Specification Tests
Description: Fits semiparametric additive regression models with spatially adaptive penalized splines and computes simultaneous confidence bands and associated specification (lack-of-fit) tests. Simultaneous confidence bands cover the entire curve with a prescribed level of confidence and allow us to assess the estimation uncertainty for the whole curve. In contrast to pointwise confidence bands, they permit statements about the statistical significance of certain features (e.g. bumps) in the underlying curve.The method allows for handling of spatially heterogeneous functions and their derivatives as well as heteroscedasticity in the data. See Wiesenfarth et al (2012) <doi:10.1080/01621459.2012.682809>.
Author: Manuel Wiesenfarth and Tatyana Krivobokova
Maintainer: Manuel Wiesenfarth <m.wiesenfarth@dkfz.de>
Diff between AdaptFitOS versions 0.65 dated 2017-09-22 and 0.67 dated 2018-05-23
DESCRIPTION | 14 ++-- MD5 | 21 +++---- R/aspmFormReadOS.r | 2 R/aspmPenReadOS.R | 134 +++++++++++++++++++++++----------------------- R/spmArgReadOS.r | 2 build |only man/AdaptFitOS-package.Rd | 59 +++++++++----------- man/asp2.Rd | 31 ++++++++-- man/aspHetero.Rd | 4 - man/plot.asp.Rd | 2 man/scbM.Rd | 2 man/summary.asp.Rd | 8 +- 12 files changed, 149 insertions(+), 130 deletions(-)
Title: Gene Set Enrichment Analysis in R
Description: R-interface to C++ implementation of the rank/score permutation based GSEA test (Subramanian et al 2005 <doi: 10.1073/pnas.0506580102>).
Author: Daniel Greene
Maintainer: Daniel Greene <dg333@cam.ac.uk>
Diff between gsEasy versions 1.1 dated 2016-08-06 and 1.3 dated 2018-05-23
gsEasy-1.1/gsEasy/src/RcppExports.h |only gsEasy-1.3/gsEasy/DESCRIPTION | 10 gsEasy-1.3/gsEasy/MD5 | 36 + gsEasy-1.3/gsEasy/NAMESPACE | 22 - gsEasy-1.3/gsEasy/NEWS.md | 4 gsEasy-1.3/gsEasy/R/Interface.R |only gsEasy-1.3/gsEasy/R/RcppExports.R | 144 ------- gsEasy-1.3/gsEasy/build/vignette.rds |binary gsEasy-1.3/gsEasy/data/GO_gene_sets.RData |binary gsEasy-1.3/gsEasy/data/datalist | 2 gsEasy-1.3/gsEasy/inst/doc/gsEasy-guide.R | 70 +-- gsEasy-1.3/gsEasy/inst/doc/gsEasy-guide.Rmd | 6 gsEasy-1.3/gsEasy/inst/doc/gsEasy-guide.html | 396 ++++++++++----------- gsEasy-1.3/gsEasy/man/GO_gene_sets.Rd | 27 - gsEasy-1.3/gsEasy/man/get_GO_gene_sets.Rd | 55 +- gsEasy-1.3/gsEasy/man/get_ontological_gene_sets.Rd | 53 +- gsEasy-1.3/gsEasy/man/gset.Rd | 77 ++-- gsEasy-1.3/gsEasy/src/Interface.cpp |only gsEasy-1.3/gsEasy/src/Interface.h |only gsEasy-1.3/gsEasy/src/RcppExports.cpp | 128 ++---- gsEasy-1.3/gsEasy/vignettes/gsEasy-guide.Rmd | 6 21 files changed, 443 insertions(+), 593 deletions(-)
Title: Beyond the Border - Kernel Density Estimation for Urban
Geography
Description: The kernelSmoothing() function allows you to square and smooth geolocated data. It calculates a classical kernel smoothing (conservative) or a geographically weighted median. There are four major call modes of the function.
The first call mode is kernelSmoothing(obs, epsg, cellsize, bandwith) for a classical kernel smoothing and automatic grid.
The second call mode is kernelSmoothing(obs, epsg, cellsize, bandwith, quantiles) for a geographically weighted median and automatic grid.
The third call mode is kernelSmoothing(obs, epsg, cellsize, bandwith, centroids) for a classical kernel smoothing and user grid.
The fourth call mode is kernelSmoothing(obs, epsg, cellsize, bandwith, quantiles, centroids) for a geographically weighted median and user grid.
Geographically weighted summary statistics : a framework for localised exploratory data analysis, C.Brunsdon & al., in Computers, Environment and Urban Systems C.Brunsdon & al. (2002) <doi:10.1016/S0198-9715(01)00009-6>,
Statistical Analysis of Spatial and Spatio-Temporal Point Patterns, Third Edition, Diggle, pp. 83-86, (2003) <doi:10.1080/13658816.2014.937718>.
Author: Arlindo Dos Santos [cre],
Francois Semecurbe [drt, aut],
Auriane Renaud [ctb],
Cynthia Faivre [ctb],
Thierry Cornely [ctb],
Farida Marouchi [ctb],
Farida Marouchi [ctb]
Maintainer: Arlindo Dos Santos <Arlindo.Dos-Santos@insee.fr>
Diff between btb versions 0.1.25 dated 2018-05-17 and 0.1.30 dated 2018-05-23
DESCRIPTION | 31 ++- MD5 | 24 +- inst/testsUnitaires/documentationLissageMedian.R | 2 man/constituerGrappes.Rd | 3 man/constituerMatriceEffectifs.Rd | 9 man/dfPrix_SP95_2016.Rd | 6 man/dfRestaurantParis.Rd | 2 man/dfToGrid.Rd | 4 man/kernelSmoothing.Rd | 96 +++++----- man/pixel_france.Rd | 6 man/reunion.Rd | 13 - src/constituerGrappes.cpp | 132 +++++++------- src/rcppLissageMedianGrappe.cpp | 212 +++++++++++------------ 13 files changed, 274 insertions(+), 266 deletions(-)
Title: Test for Monotonicity in Expected Asset Returns, Sorted by
Portfolios
Description: Test for monotonicity in financial variables sorted by portfolios. It is conventional practice in empirical research to form portfolios of assets ranked by a certain sort variable. A t-test is then used to consider the mean return spread between the portfolios with the highest and lowest values of the sort variable. Yet comparing only the average returns on the top and bottom portfolios does not provide a sufficient way to test for a monotonic relation between expected returns and the sort variable. This package provides nonparametric tests for the full set of monotonic patterns by Patton, A. and Timmermann, A. (2010) <doi:10.1016/0304-4076(89)90094-8> and compares the proposed results with extant alternatives such as t-tests, Bonferroni bounds, and multivariate inequality tests through empirical applications and simulations.
Author: Siegfried Köstlmeier [aut, cre, trl]
Maintainer: Siegfried Köstlmeier <siegfried.koestlmeier@gmail.com>
Diff between monotonicity versions 1.0 dated 2018-04-18 and 1.1 dated 2018-05-23
DESCRIPTION | 7 ++++--- LICENSE | 10 +++++++--- MD5 | 19 +++++++++++++------ R/monoSummary.R | 13 +++++++++---- R/wolak.R | 10 +++++++++- build/partial.rdb |binary man/monoSummary.Rd | 2 +- tests |only 8 files changed, 43 insertions(+), 18 deletions(-)
Title: Analyse Citation Data from Google Scholar
Description: Provides functions to extract citation data from Google
Scholar. Convenience functions are also provided for comparing
multiple scholars and predicting future h-index values.
Author: Guangchuang Yu [aut, cre] (<https://orcid.org/0000-0002-6485-8781>),
James Keirstead [aut],
Gregory Jefferis [ctb]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between scholar versions 0.1.4 dated 2015-11-21 and 0.1.6 dated 2018-05-23
DESCRIPTION | 21 ++++++++++----- MD5 | 49 +++++++++++++++++++----------------- NAMESPACE | 2 - NEWS | 5 +++ R/compare.r | 23 ++++++++-------- R/publications.r | 53 +++++++++++++++++++++------------------ R/scholar.r | 16 +++++++++++ R/zzz.r | 4 +- README.md | 2 + build |only inst/CITATION | 6 ++-- inst/doc |only man/compare_scholar_careers.Rd | 9 +++--- man/compare_scholars.Rd | 10 +++---- man/get_article_cite_history.Rd | 4 +- man/get_citation_history.Rd | 4 +- man/get_num_articles.Rd | 4 +- man/get_num_distinct_journals.Rd | 4 +- man/get_num_top_journals.Rd | 4 +- man/get_oldest_article.Rd | 4 +- man/get_profile.Rd | 4 +- man/get_publications.Rd | 4 +- man/predict_h_index.Rd | 4 +- man/scholar.Rd | 4 +- man/tidy_id.Rd | 4 +- vignettes |only 26 files changed, 142 insertions(+), 102 deletions(-)
Title: Draws Diagrams Useful for Checking Latent Scales
Description: A graph
proposed by Rosenbaum is useful
for checking some properties of various
sorts of latent scale, this program generates commands
to obtain the graph using 'dot' from 'graphviz'.
Author: Michael Dewey
Maintainer: Michael Dewey <lists@dewey.myzen.co.uk>
Diff between latdiag versions 0.2-3 dated 2016-10-19 and 0.2-4 dated 2018-05-23
DESCRIPTION | 8 ++++---- MD5 | 7 ++++--- NEWS | 3 +++ build |only man/latdiag-package.Rd | 24 +++++------------------- 5 files changed, 16 insertions(+), 26 deletions(-)
Title: Evolutionary Learning of Globally Optimal Trees
Description: Commonly used classification and regression tree methods like the CART algorithm
are recursive partitioning methods that build the model in a forward stepwise search.
Although this approach is known to be an efficient heuristic, the results of recursive
tree methods are only locally optimal, as splits are chosen to maximize homogeneity at
the next step only. An alternative way to search over the parameter space of trees is
to use global optimization methods like evolutionary algorithms. The 'evtree' package
implements an evolutionary algorithm for learning globally optimal classification and
regression trees in R. CPU and memory-intensive tasks are fully computed in C++ while
the 'partykit' package is leveraged to represent the resulting trees in R, providing
unified infrastructure for summaries, visualizations, and predictions.
Author: Thomas Grubinger [aut, cre],
Achim Zeileis [aut] (<https://orcid.org/0000-0003-0918-3766>>),
Karl-Peter Pfeiffer [aut]
Maintainer: Thomas Grubinger <ThomasGrubinger@gmail.com>
Diff between evtree versions 1.0-6 dated 2017-12-15 and 1.0-7 dated 2018-05-23
DESCRIPTION | 18 +++++++++--------- MD5 | 24 ++++++++++++------------ NEWS | 5 +++++ build/vignette.rds |binary data/BBBClub.rda |binary data/ContraceptiveChoice.RData |binary data/GermanCredit.RData |binary data/MAGICGammaTelescope.RData |binary data/StatlogHeart.RData |binary inst/doc/evtree.R | 8 ++++---- inst/doc/evtree.Rnw | 4 ++-- inst/doc/evtree.pdf |binary vignettes/evtree.Rnw | 4 ++-- 13 files changed, 34 insertions(+), 29 deletions(-)
Title: Project MOSAIC Statistics and Mathematics Teaching Utilities
Description: Data sets and utilities from Project MOSAIC (<http://mosaic-web.org>) used
to teach mathematics, statistics, computation and modeling. Funded by the
NSF, Project MOSAIC is a community of educators working to tie together
aspects of quantitative work that students in science, technology,
engineering and mathematics will need in their professional lives, but
which are usually taught in isolation, if at all.
Author: Randall Pruim <rpruim@calvin.edu>, Daniel T. Kaplan
<kaplan@macalester.edu>, Nicholas J. Horton <nhorton@amherst.edu>
Maintainer: Randall Pruim <rpruim@calvin.edu>
Diff between mosaic versions 1.1.1 dated 2017-11-28 and 1.2.0 dated 2018-05-23
mosaic-1.1.1/mosaic/R/dfapply.R |only mosaic-1.1.1/mosaic/R/ediff.R |only mosaic-1.1.1/mosaic/R/evalFormula.R |only mosaic-1.1.1/mosaic/R/inspect.R |only mosaic-1.1.1/mosaic/R/logit.R |only mosaic-1.1.1/mosaic/R/msummary.R |only mosaic-1.1.1/mosaic/R/nmissing.R |only mosaic-1.1.1/mosaic/R/tally.R |only mosaic-1.1.1/mosaic/inst/doc/plotModel-vignette.R |only mosaic-1.1.1/mosaic/inst/doc/plotModel-vignette.Rmd |only mosaic-1.1.1/mosaic/inst/doc/plotModel-vignette.html |only mosaic-1.1.1/mosaic/man/columns.Rd |only mosaic-1.1.1/mosaic/man/dfapply.Rd |only mosaic-1.1.1/mosaic/man/ediff.Rd |only mosaic-1.1.1/mosaic/man/evalFormula.Rd |only mosaic-1.1.1/mosaic/man/evalSubFormula.Rd |only mosaic-1.1.1/mosaic/man/inspect.Rd |only mosaic-1.1.1/mosaic/man/joinFrames.Rd |only mosaic-1.1.1/mosaic/man/logical2factor.Rd |only mosaic-1.1.1/mosaic/man/logit.Rd |only mosaic-1.1.1/mosaic/man/msummary.Rd |only mosaic-1.1.1/mosaic/man/n_missing.Rd |only mosaic-1.1.1/mosaic/man/prop.Rd |only mosaic-1.1.1/mosaic/man/tally.Rd |only mosaic-1.1.1/mosaic/tests/testthat/test-evalFormula.R |only mosaic-1.1.1/mosaic/tests/testthat/test-tabulation.R |only mosaic-1.1.1/mosaic/vignettes/plotModel-vignette.Rmd |only mosaic-1.2.0/mosaic/DESCRIPTION | 14 - mosaic-1.2.0/mosaic/MD5 | 130 ++++------ mosaic-1.2.0/mosaic/NAMESPACE | 76 +++--- mosaic-1.2.0/mosaic/NEWS.md | 8 mosaic-1.2.0/mosaic/R/aggregatingAux.R | 14 - mosaic-1.2.0/mosaic/R/aggregatingMeta.R | 9 mosaic-1.2.0/mosaic/R/cdist.R | 160 ++++++++---- mosaic-1.2.0/mosaic/R/compareMean.R | 4 mosaic-1.2.0/mosaic/R/compareProportion.R | 4 mosaic-1.2.0/mosaic/R/cor-test.R | 6 mosaic-1.2.0/mosaic/R/dpqrdist.R | 209 ++++++++-------- mosaic-1.2.0/mosaic/R/interval.R | 2 mosaic-1.2.0/mosaic/R/mPlots.R | 68 +++-- mosaic-1.2.0/mosaic/R/mosaic-package.R | 5 mosaic-1.2.0/mosaic/R/mplot.R | 8 mosaic-1.2.0/mosaic/R/perctable.R | 4 mosaic-1.2.0/mosaic/R/plotFun.R | 40 ++- mosaic-1.2.0/mosaic/R/plotModel.R | 4 mosaic-1.2.0/mosaic/R/pqrdata.R | 20 + mosaic-1.2.0/mosaic/R/reexports.R | 27 ++ mosaic-1.2.0/mosaic/R/statTally.R | 22 + mosaic-1.2.0/mosaic/R/ttest.R | 2 mosaic-1.2.0/mosaic/R/xpnorm.R | 222 +++++++++++++----- mosaic-1.2.0/mosaic/build/vignette.rds |binary mosaic-1.2.0/mosaic/inst/doc/MinimalR.pdf |binary mosaic-1.2.0/mosaic/inst/doc/MinimalRgg.pdf |binary mosaic-1.2.0/mosaic/inst/doc/Resampling.pdf |binary mosaic-1.2.0/mosaic/inst/doc/ggformula-lattice.R | 10 mosaic-1.2.0/mosaic/inst/doc/ggformula-lattice.Rmd | 26 ++ mosaic-1.2.0/mosaic/inst/doc/ggformula-lattice.pdf |binary mosaic-1.2.0/mosaic/inst/doc/mosaic-resources.Rmd | 13 - mosaic-1.2.0/mosaic/inst/doc/mosaic-resources.html | 17 - mosaic-1.2.0/mosaic/man/FunctionsFromData.Rd | 3 mosaic-1.2.0/mosaic/man/MAD.Rd | 9 mosaic-1.2.0/mosaic/man/aggregating.Rd | 11 mosaic-1.2.0/mosaic/man/as-xtabs.Rd | 2 mosaic-1.2.0/mosaic/man/cdist.Rd | 58 ++++ mosaic-1.2.0/mosaic/man/cnorm.Rd |only mosaic-1.2.0/mosaic/man/compareMean.Rd | 2 mosaic-1.2.0/mosaic/man/compareProportion.Rd | 2 mosaic-1.2.0/mosaic/man/cor.test.Rd | 7 mosaic-1.2.0/mosaic/man/findZeros.Rd | 2 mosaic-1.2.0/mosaic/man/mosaic.options.Rd | 1 mosaic-1.2.0/mosaic/man/mplot.Rd | 7 mosaic-1.2.0/mosaic/man/panel.plotFun.Rd | 9 mosaic-1.2.0/mosaic/man/panel.plotFun1.Rd | 6 mosaic-1.2.0/mosaic/man/perctable.Rd | 2 mosaic-1.2.0/mosaic/man/qdist.Rd | 31 +- mosaic-1.2.0/mosaic/man/reexports.Rd | 23 + mosaic-1.2.0/mosaic/man/rfun.Rd | 1 mosaic-1.2.0/mosaic/man/xpnorm.Rd | 12 mosaic-1.2.0/mosaic/vignettes/ggformula-lattice.Rmd | 26 ++ mosaic-1.2.0/mosaic/vignettes/mosaic-resources.Rmd | 13 - 80 files changed, 879 insertions(+), 472 deletions(-)