Title: Variable Descriptions
Description: Abstract descriptions of (yet) unobserved variables.
Author: Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>)
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between variables versions 1.0-0 dated 2018-03-08 and 1.0-1 dated 2018-09-17
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- inst/NEWS.Rd | 7 +++++++ 3 files changed, 13 insertions(+), 6 deletions(-)
Title: Most Likely Transformations
Description: Likelihood-based estimation of conditional transformation
models via the most likely transformation approach described in
Hothorn et al. (2018) <DOI:10.1111/sjos.12291>.
Author: Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>)
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mlt versions 1.0-2 dated 2018-06-22 and 1.0-3 dated 2018-09-17
DESCRIPTION | 8 +-- MD5 | 26 ++++++------ NAMESPACE | 4 + R/ctm.R | 2 R/distr.R | 23 ++++++++++ R/mlt.R | 7 +-- R/plot.R | 8 ++- build/partial.rdb |binary inst/NEWS.Rd | 8 +++ man/ctm.Rd | 11 ++++- man/predict.Rd | 5 +- tests/polr-Ex.R | 55 +++++++++++++++++++++++++ tests/polr-Ex.Rout.save | 102 +++++++++++++++++++++++++++++++++++++++++++++++- tests/surv-Ex.Rout.save | 30 +++++++------- 14 files changed, 244 insertions(+), 45 deletions(-)
Title: Succinct and Correct Statistical Summaries for Reports
Description: Succinctly and correctly format statistical summaries of
various models and tests (F-test, Chi-Sq-test, Fisher-test, T-test, and rank-significance). The main purpose is unified reporting
of experimental results, working around issue such as the difficulty of
extracting model summary facts (such as with 'lm'/'glm'). This package also
includes empirical tests, such as bootstrap estimates.
Author: John Mount [aut, cre],
Nina Zumel [aut],
Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>
Diff between sigr versions 0.2.8 dated 2018-07-19 and 1.0.0 dated 2018-09-17
DESCRIPTION | 14 +++++++------- MD5 | 32 ++++++++++++++++---------------- NEWS.md | 4 ++++ inst/doc/lmExample.html | 4 ++-- inst/doc/sigrFormatting.html | 4 ++-- man/reexports.Rd | 24 ------------------------ man/render.sigr_aucresamptest.Rd | 5 +++-- man/render.sigr_significance.Rd | 5 +++-- man/testAUCpair.Rd | 5 +++-- man/wrapChiSqTest.data.frame.Rd | 3 ++- man/wrapCorTest.data.frame.Rd | 6 +++--- man/wrapFTest.data.frame.Rd | 5 +++-- man/wrapFTest.summary.lm.Rd | 4 ++-- man/wrapFisherTest.data.frame.Rd | 7 ++++--- man/wrapFisherTest.table.Rd | 7 ++++--- man/wrapTTest.data.frame.Rd | 7 ++++--- man/wrapTTest.numeric.Rd | 5 +++-- 17 files changed, 65 insertions(+), 76 deletions(-)
Title: Process Map Token Replay Animation
Description: Token replay animation for process maps created with
'processmapR' by using SVG animations ('SMIL') and the 'htmlwidget' package.
Author: Felix Mannhardt [aut, cre],
Gert Janssenswillen [ctb]
Maintainer: Felix Mannhardt <felix.mannhardt@sintef.no>
Diff between processanimateR versions 0.1.1 dated 2018-04-20 and 0.2.0 dated 2018-09-17
processanimateR-0.1.1/processanimateR/R/iprocessanimateR.R |only processanimateR-0.1.1/processanimateR/inst/htmlwidgets/lib/d3/API.md |only processanimateR-0.1.1/processanimateR/inst/htmlwidgets/lib/d3/CHANGES.md |only processanimateR-0.1.1/processanimateR/inst/htmlwidgets/lib/d3/README.md |only processanimateR-0.1.1/processanimateR/inst/htmlwidgets/lib/d3/d3.js |only processanimateR-0.1.1/processanimateR/inst/htmlwidgets/lib/viz/viz-lite.js |only processanimateR-0.1.1/processanimateR/inst/processanimateR-banner.png |only processanimateR-0.1.1/processanimateR/man/ianimate_process.Rd |only processanimateR-0.2.0/processanimateR/DESCRIPTION | 23 processanimateR-0.2.0/processanimateR/LICENSE | 2 processanimateR-0.2.0/processanimateR/MD5 | 50 processanimateR-0.2.0/processanimateR/NAMESPACE | 2 processanimateR-0.2.0/processanimateR/R/processanimateR.R | 211 processanimateR-0.2.0/processanimateR/README.md | 32 processanimateR-0.2.0/processanimateR/build |only processanimateR-0.2.0/processanimateR/inst/doc |only processanimateR-0.2.0/processanimateR/inst/htmlwidgets/lib/d3-selection-multi |only processanimateR-0.2.0/processanimateR/inst/htmlwidgets/lib/d3-simple-slider |only processanimateR-0.2.0/processanimateR/inst/htmlwidgets/lib/fakesmil/smil.user.js | 3158 +++++----- processanimateR-0.2.0/processanimateR/inst/htmlwidgets/lib/momentjs |only processanimateR-0.2.0/processanimateR/inst/htmlwidgets/processanimateR.js | 231 processanimateR-0.2.0/processanimateR/inst/htmlwidgets/processanimateR.yaml | 14 processanimateR-0.2.0/processanimateR/man/add_token_color.Rd | 4 processanimateR-0.2.0/processanimateR/man/add_token_size.Rd | 4 processanimateR-0.2.0/processanimateR/man/animate_process.Rd | 42 processanimateR-0.2.0/processanimateR/man/figures |only processanimateR-0.2.0/processanimateR/man/processanimaterOutput.Rd | 11 processanimateR-0.2.0/processanimateR/man/renderProcessanimater.Rd | 6 processanimateR-0.2.0/processanimateR/tests |only processanimateR-0.2.0/processanimateR/vignettes |only 30 files changed, 1961 insertions(+), 1829 deletions(-)
More information about processanimateR at CRAN
Permanent link
Title: Group Animal Relocation Data by Spatial and Temporal
Relationship
Description: Detects spatial and temporal groups in GPS relocations.
It can be used to convert GPS relocations to
gambit-of-the-group format to build proximity-based social networks.
In addition, the randomizations function provides data-stream
randomization methods suitable for GPS data.
Author: Alec L. Robitaille [aut, cre],
Quinn Webber [aut],
Eric Vander Wal [aut]
Maintainer: Alec L. Robitaille <robit.alec@gmail.com>
Diff between spatsoc versions 0.1.0 dated 2018-07-20 and 0.1.1 dated 2018-09-17
spatsoc-0.1.0/spatsoc/NEWS.md |only spatsoc-0.1.0/spatsoc/README.md |only spatsoc-0.1.0/spatsoc/tests/testdata/buffalo.csv |only spatsoc-0.1.1/spatsoc/DESCRIPTION | 8 spatsoc-0.1.1/spatsoc/MD5 | 74 spatsoc-0.1.1/spatsoc/NAMESPACE | 14 spatsoc-0.1.1/spatsoc/R/build_lines.R | 66 spatsoc-0.1.1/spatsoc/R/build_polys.R | 64 spatsoc-0.1.1/spatsoc/R/extdata.R |only spatsoc-0.1.1/spatsoc/R/group_lines.R | 94 spatsoc-0.1.1/spatsoc/R/group_polys.R | 56 spatsoc-0.1.1/spatsoc/R/group_pts.R | 41 spatsoc-0.1.1/spatsoc/R/group_times.R | 70 spatsoc-0.1.1/spatsoc/R/randomizations.R | 185 spatsoc-0.1.1/spatsoc/R/spatsoc.R |only spatsoc-0.1.1/spatsoc/build/vignette.rds |binary spatsoc-0.1.1/spatsoc/inst/doc/faq.R |only spatsoc-0.1.1/spatsoc/inst/doc/faq.Rmd |only spatsoc-0.1.1/spatsoc/inst/doc/faq.html |only spatsoc-0.1.1/spatsoc/inst/doc/intro-spatsoc.R | 17 spatsoc-0.1.1/spatsoc/inst/doc/intro-spatsoc.Rmd | 37 spatsoc-0.1.1/spatsoc/inst/doc/intro-spatsoc.html | 1606 - spatsoc-0.1.1/spatsoc/inst/doc/using-in-sna.R |only spatsoc-0.1.1/spatsoc/inst/doc/using-in-sna.Rmd |only spatsoc-0.1.1/spatsoc/inst/doc/using-in-sna.html |only spatsoc-0.1.1/spatsoc/inst/extdata/DT.csv |16097 ++++++++++++++-- spatsoc-0.1.1/spatsoc/man/DT.Rd |only spatsoc-0.1.1/spatsoc/man/build_lines.Rd | 54 spatsoc-0.1.1/spatsoc/man/build_polys.Rd | 71 spatsoc-0.1.1/spatsoc/man/group_lines.Rd | 77 spatsoc-0.1.1/spatsoc/man/group_polys.Rd | 41 spatsoc-0.1.1/spatsoc/man/group_pts.Rd | 39 spatsoc-0.1.1/spatsoc/man/group_times.Rd | 54 spatsoc-0.1.1/spatsoc/man/randomizations.Rd | 118 spatsoc-0.1.1/spatsoc/man/spatsoc.Rd |only spatsoc-0.1.1/spatsoc/tests/testdata/DT.csv |only spatsoc-0.1.1/spatsoc/tests/testthat/test-build-lines.R | 212 spatsoc-0.1.1/spatsoc/tests/testthat/test-build-polys.R | 5 spatsoc-0.1.1/spatsoc/tests/testthat/test-group-lines.R | 86 spatsoc-0.1.1/spatsoc/tests/testthat/test-group-polys.R | 29 spatsoc-0.1.1/spatsoc/tests/testthat/test-pts.R | 4 spatsoc-0.1.1/spatsoc/tests/testthat/test-random.R | 260 spatsoc-0.1.1/spatsoc/tests/testthat/test-time.R | 16 spatsoc-0.1.1/spatsoc/vignettes/faq.Rmd |only spatsoc-0.1.1/spatsoc/vignettes/intro-spatsoc.Rmd | 37 spatsoc-0.1.1/spatsoc/vignettes/using-in-sna.Rmd |only 46 files changed, 16715 insertions(+), 2817 deletions(-)
Title: Common Plots for Analysis
Description: Select data analysis plots, under a standardized calling interface implemented on top of 'ggplot2' and 'plotly'.
Plots of interest include: 'ROC', gain curve, scatter plot with marginal distributions,
conditioned scatter plot with marginal densities,
box and stem with matching theoretical distribution, and density with matching theoretical distribution.
Author: John Mount [aut, cre],
Nina Zumel [aut],
Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>
Diff between WVPlots versions 1.0.2 dated 2018-07-20 and 1.0.3 dated 2018-09-17
DESCRIPTION | 16 +++---- MD5 | 60 ++++++++++++++-------------- NEWS.md | 6 ++ R/BinaryYScatterPlot.R | 11 ++--- R/ClevelandDotPlot.R | 11 ++--- R/ConditionalSmoothedScatterPlot.R | 11 ++--- R/DiscreteDistribution.R | 11 ++--- R/DistributionPlot.R | 48 ++++++++++++---------- R/DoubleDensity.R | 51 ++++++++++++------------ R/DoubleHistogram.R | 71 +++++++++++++++++----------------- R/LogLogPlot.R | 27 ++++++------ R/ScatterBoxPlot.R | 22 +++++----- R/ScatterHist.R | 43 ++++++++++---------- R/ScatterHistC.R | 32 ++++++++------- R/ShadedDensity.R | 52 ++++++++++++++++-------- R/ShadowHist.R | 13 +++--- R/ShadowPlot.R | 11 ++--- R/sharedFunctions.R | 4 - inst/doc/WVPlots_concept.html | 4 - inst/doc/WVPlots_examples.html | 4 - man/ConditionalSmoothedScatterPlot.Rd | 4 - man/GainCurvePlotWithNotation.Rd | 4 - man/PRPlot.Rd | 3 - man/ROCPlot.Rd | 5 +- man/ROCPlotPair2.Rd | 4 - man/ShadedDensity.Rd | 4 + man/ShadedDensityCenter.Rd | 4 + man/ShadowHist.Rd | 2 man/plot_Keras_fit_trajectory.Rd | 4 - man/plot_fit_trajectory.Rd | 6 +- man/reexports.Rd | 12 ----- 31 files changed, 299 insertions(+), 261 deletions(-)
Title: Infrastructure for Computing with Basis Functions
Description: Some very simple infrastructure for basis functions.
Author: Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>)
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between basefun versions 1.0-1 dated 2018-03-29 and 1.0-2 dated 2018-09-17
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/bernstein.R | 31 ++++++++++++++++++++++++++++--- inst/NEWS.Rd | 9 +++++++++ man/Bernstein_basis.Rd | 7 ++++++- 5 files changed, 51 insertions(+), 12 deletions(-)
Title: Spatial Association Between Regionalizations
Description: Calculates a degree of spatial association between regionalizations
or categorical maps using the information-theoretical V-measure
(Nowosad and Stepinski (2018) <doi:10.1080/13658816.2018.1511794>). It also
offers an R implementation of the MapCurve method
(Hargrove et al. (2006) <doi:10.1007/s10109-006-0025-x>).
Author: Jakub Nowosad [aut, cre] (<https://orcid.org/0000-0002-1057-3721>),
Tomasz Stepinski [aut],
Space Informatics Lab [cph]
Maintainer: Jakub Nowosad <nowosad.jakub@gmail.com>
Diff between sabre versions 0.2.0 dated 2018-04-23 and 0.2.1 dated 2018-09-17
DESCRIPTION | 10 MD5 | 29 +- R/vmeasure_calc.R | 15 - README.md | 42 ++- build/vignette.rds |binary inst/CITATION |only inst/doc/sabre.Rmd | 2 inst/doc/sabre.html | 342 +++++++++++++++++++++++++------ man/figures/README-unnamed-chunk-2-1.png |binary man/figures/README-unnamed-chunk-2-2.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/figures/README-unnamed-chunk-6-2.png |binary man/sabre-package.Rd | 10 man/vmeasure_calc.Rd | 7 tests/testthat/test-eco-us.R | 2 vignettes/sabre.Rmd | 2 16 files changed, 345 insertions(+), 116 deletions(-)
Title: Tools to Work with Google's 'DNS-over-HTTPS' ('DoH') 'API'
Description: To address the problem of insecurity of 'UDP'-based 'DNS' requests,
'Google Public DNS' offers 'DNS' resolution over an encrypted 'HTTPS'
connection. 'DNS-over-HTTPS' greatly enhances privacy and security
between a client and a recursive resolver, and complements 'DNSSEC'
to provide end-to-end authenticated 'DNS' lookups. Functions that enable
querying individual requests that bulk requests that return detailed
responses and bulk requests are both provided. Support for reverse
lookups is also provided. See <https://developers.google.com/speed/public-dns/docs/dns-over-https>
for more information.
Author: Bob Rudis [aut, cre] (<https://orcid.org/0000-0001-5670-2640>)
Maintainer: Bob Rudis <bob@rud.is>
Diff between gdns versions 0.2.1 dated 2017-07-02 and 0.3.1 dated 2018-09-17
gdns-0.2.1/gdns/LICENSE |only gdns-0.2.1/gdns/R/gdns.r |only gdns-0.3.1/gdns/DESCRIPTION | 31 + gdns-0.3.1/gdns/MD5 | 27 - gdns-0.3.1/gdns/NAMESPACE | 10 gdns-0.3.1/gdns/NEWS.md | 10 gdns-0.3.1/gdns/R/gdns-package.r | 19 - gdns-0.3.1/gdns/R/spf.r | 12 gdns-0.3.1/gdns/R/utils-mappers.R |only gdns-0.3.1/gdns/R/utils-safely.R |only gdns-0.3.1/gdns/R/utils.R |only gdns-0.3.1/gdns/R/zbulk-query.R |only gdns-0.3.1/gdns/R/zgdns.r |only gdns-0.3.1/gdns/README.md | 480 ++++++++++------------------- gdns-0.3.1/gdns/data |only gdns-0.3.1/gdns/man/bulk_query.Rd | 4 gdns-0.3.1/gdns/man/query.Rd | 2 gdns-0.3.1/gdns/man/resource_record_tbl.Rd |only gdns-0.3.1/gdns/tests/testthat/test-gdns.R | 2 19 files changed, 236 insertions(+), 361 deletions(-)
Title: General Frailty Models: Shared, Joint and Nested Frailty Models
with Prediction
Description: The following several classes of frailty models using a penalized likelihood estimation on the hazard function but also a parametric estimation can be fit using this R package:
1) A shared frailty model (with gamma or log-normal frailty distribution) and Cox proportional hazard model. Clustered and recurrent survival times can be studied.
2) Additive frailty models for proportional hazard models with two correlated random effects (intercept random effect with random slope).
3) Nested frailty models for hierarchically clustered data (with 2 levels of clustering) by including two iid gamma random effects.
4) Joint frailty models in the context of the joint modelling for recurrent events with terminal event for clustered data or not. A joint frailty model for two semi-competing risks and clustered data is also proposed.
5) Joint general frailty models in the context of the joint modelling for recurrent events with terminal event data with two independent frailty terms.
6) Joint Nested frailty models in the context of the joint modelling for recurrent events with terminal event, for hierarchically clustered data (with two levels of clustering) by including two iid gamma random effects.
7) Multivariate joint frailty models for two types of recurrent events and a terminal event.
8) Joint models for longitudinal data and a terminal event.
9) Trivariate joint models for longitudinal data, recurrent events and a terminal event.
Prediction values are available (for a terminal event or for a new recurrent event). Left-truncated (not for Joint model), right-censored data, interval-censored data (only for Cox proportional hazard and shared frailty model) and strata are allowed. In each model, the random effects have the gamma or normal distribution. Now, you can also consider time-varying covariates effects in Cox, shared and joint frailty models (1-5). The package includes concordance measures for Cox proportional hazards models and for shared frailty models.
Author: Virginie Rondeau, Juan R. Gonzalez, Yassin Mazroui, Audrey
Mauguen, Agnieszka Krol, Amadou Diakite, Alexandre Laurent and Myriam Lopez
Maintainer: Virginie Rondeau <Virginie.Rondeau@inserm.fr>
Diff between frailtypack versions 2.12.7 dated 2018-07-30 and 2.13.1 dated 2018-09-17
DESCRIPTION | 8 MD5 | 38 +- NAMESPACE | 2 NEWS | 7 R/frailtyPenal.R | 81 +++-- R/print.jointPenal.R | 1 R/wts.R |only data/dataNCC.rda |only inst/CITATION | 2 man/dataNCC.Rd |only man/frailtyPenal.Rd | 27 + man/trivPenalNL.Rd | 4 man/wts.Rd |only src/Aparameters.f90 | 3 src/aaOptim.f90 | 575 +++++++++++++++++++++++++++++++++++++++- src/frailtypack.h | 10 src/funcpajsplines.f90 | 6 src/funcpajsplinesIndiv.f90 |only src/funcpajsplines_log.f90 | 6 src/funcpajsplines_logIndiv.f90 |only src/init.c | 2 src/joint.f90 | 55 ++- src/predictionfam.f90 | 10 23 files changed, 744 insertions(+), 93 deletions(-)
Title: Bayesian Meta-Analysis of Diagnostic Test Data
Description: Functions for Bayesian meta-analysis of diagnostic test data which
are based on a scale mixtures bivariate random-effects model.
Author: Pablo Emilio Verde [aut, cre]
Maintainer: Pablo Emilio Verde <pabloemilio.verde@hhu.de>
Diff between bamdit versions 3.2.0 dated 2018-08-24 and 3.2.1 dated 2018-09-17
bamdit-3.2.0/bamdit/R/testing_march_2017.R |only bamdit-3.2.1/bamdit/ChangeLog | 3 +++ bamdit-3.2.1/bamdit/DESCRIPTION | 11 ++++++----- bamdit-3.2.1/bamdit/MD5 | 25 ++++++++++++------------- bamdit-3.2.1/bamdit/R/bamdit-package.R | 11 +++++++---- bamdit-3.2.1/bamdit/R/bsroc.R | 9 +++++++++ bamdit-3.2.1/bamdit/R/metadiag.R | 6 +++--- bamdit-3.2.1/bamdit/inst/CITATION | 15 +++++++++------ bamdit-3.2.1/bamdit/man/bamdit-package.Rd | 10 ++++++---- bamdit-3.2.1/bamdit/man/bsroc.Rd | 17 +++++++++++++---- bamdit-3.2.1/bamdit/man/metadiag.Rd | 13 +++++++------ bamdit-3.2.1/bamdit/man/plot.metadiag.Rd | 9 +++++---- bamdit-3.2.1/bamdit/man/plotcompare.Rd | 3 ++- bamdit-3.2.1/bamdit/man/summary.metadiag.Rd | 4 ++-- 14 files changed, 84 insertions(+), 52 deletions(-)
Title: Use 'Python' from Within 'R'
Description: Interact with 'Python' <https://www.python.org/> from within 'R'.
Author: Florian Schwendinger [aut, cre],
Kimyen Truong [ctb]
Maintainer: Florian Schwendinger <FlorianSchwendinger@gmx.at>
Diff between PythonInR versions 0.1-4 dated 2018-01-17 and 0.1-6 dated 2018-09-17
ChangeLog | 4 +++ DESCRIPTION | 6 ++--- MD5 | 16 +++++++-------- README.md | 9 -------- configure | 56 +++++++++++++++++++++++++++++++++++++++++------------ src/CastRObjects.c | 10 ++++++--- src/PyCall.c | 8 ++++--- src/PythonInR.c | 2 - src/PythonInR.h | 2 - 9 files changed, 74 insertions(+), 39 deletions(-)
Title: Gaussian Process Laboratory
Description: Gaussian Process models with customised covariance kernels.
Author: Yves Deville, David Ginsbourger, Olivier Roustant. Contributors: Nicolas Durrande.
Maintainer: Olivier Roustant <roustant@emse.fr>
Diff between kergp versions 0.2.0 dated 2015-12-23 and 0.4.0 dated 2018-09-17
kergp-0.2.0/kergp/ChangeLog |only kergp-0.4.0/kergp/DESCRIPTION | 24 kergp-0.4.0/kergp/MD5 | 158 +- kergp-0.4.0/kergp/NAMESPACE | 48 kergp-0.4.0/kergp/R/CovFormulas.R |only kergp-0.4.0/kergp/R/allGenerics.R | 16 kergp-0.4.0/kergp/R/checkGrad.R |only kergp-0.4.0/kergp/R/covComp.R |only kergp-0.4.0/kergp/R/covMan.R | 148 +- kergp-0.4.0/kergp/R/covQual.R |only kergp-0.4.0/kergp/R/covQualNested.R |only kergp-0.4.0/kergp/R/covRadial.R |only kergp-0.4.0/kergp/R/covTS.R | 68 kergp-0.4.0/kergp/R/covZZAll.R | 140 + kergp-0.4.0/kergp/R/gp.R | 103 - kergp-0.4.0/kergp/R/kFuns.R |only kergp-0.4.0/kergp/R/kernelNorm.R |only kergp-0.4.0/kergp/R/kernels1d_Call.R | 72 kergp-0.4.0/kergp/R/logLikFuns.R | 14 kergp-0.4.0/kergp/R/methodGLS.R | 27 kergp-0.4.0/kergp/R/methodMLE.R | 498 ++++-- kergp-0.4.0/kergp/R/miscUtils.R |only kergp-0.4.0/kergp/R/prinKrige.R |only kergp-0.4.0/kergp/R/q1CompSymm.R |only kergp-0.4.0/kergp/R/q1Diag.R |only kergp-0.4.0/kergp/R/q1Symm.R |only kergp-0.4.0/kergp/R/simulate_gp.R |only kergp-0.4.0/kergp/build |only kergp-0.4.0/kergp/inst |only kergp-0.4.0/kergp/man/MLE-methods.Rd | 803 ++++++----- kergp-0.4.0/kergp/man/MLE.Rd | 4 kergp-0.4.0/kergp/man/checkGrad.Rd |only kergp-0.4.0/kergp/man/checkPar.Rd |only kergp-0.4.0/kergp/man/checkX-methods.Rd | 23 kergp-0.4.0/kergp/man/checkX.Rd | 4 kergp-0.4.0/kergp/man/coef-methods.Rd | 5 kergp-0.4.0/kergp/man/coefLower.Rd | 2 kergp-0.4.0/kergp/man/coefReplace.Rd | 4 kergp-0.4.0/kergp/man/contr.helmod.Rd |only kergp-0.4.0/kergp/man/corLevCompSymm.Rd |only kergp-0.4.0/kergp/man/corLevDiag.Rd |only kergp-0.4.0/kergp/man/corLevSymm.Rd |only kergp-0.4.0/kergp/man/covAll-class.Rd | 19 kergp-0.4.0/kergp/man/covComp-class.Rd |only kergp-0.4.0/kergp/man/covComp.Rd |only kergp-0.4.0/kergp/man/covMan-class.Rd | 28 kergp-0.4.0/kergp/man/covMan.Rd | 20 kergp-0.4.0/kergp/man/covMat-methods.Rd | 10 kergp-0.4.0/kergp/man/covMat.Rd | 4 kergp-0.4.0/kergp/man/covQual-class.Rd |only kergp-0.4.0/kergp/man/covQualNested-class.Rd |only kergp-0.4.0/kergp/man/covQualNested.Rd |only kergp-0.4.0/kergp/man/covRadial-class.Rd |only kergp-0.4.0/kergp/man/covRadial.Rd |only kergp-0.4.0/kergp/man/covTS-class.Rd | 9 kergp-0.4.0/kergp/man/covTS.Rd | 336 ++-- kergp-0.4.0/kergp/man/gls-methods.Rd | 358 ++-- kergp-0.4.0/kergp/man/gls.Rd | 4 kergp-0.4.0/kergp/man/gp.Rd | 71 kergp-0.4.0/kergp/man/influence.gp.Rd | 2 kergp-0.4.0/kergp/man/inputNames.Rd | 37 kergp-0.4.0/kergp/man/k1Funs.Rd |only kergp-0.4.0/kergp/man/k1Kerns.Rd |only kergp-0.4.0/kergp/man/kGauss.Rd |only kergp-0.4.0/kergp/man/kMatern.Rd |only kergp-0.4.0/kergp/man/kergp-package.Rd | 16 kergp-0.4.0/kergp/man/kernelName.Rd | 2 kergp-0.4.0/kergp/man/npar-methods.Rd | 7 kergp-0.4.0/kergp/man/npar.Rd | 2 kergp-0.4.0/kergp/man/optimMethods.Rd |only kergp-0.4.0/kergp/man/parMap-methods.Rd | 10 kergp-0.4.0/kergp/man/parMap.Rd | 4 kergp-0.4.0/kergp/man/parNamesSymm.Rd |only kergp-0.4.0/kergp/man/parseCovFormula.Rd |only kergp-0.4.0/kergp/man/plot.gp.Rd | 2 kergp-0.4.0/kergp/man/plot.simulate.Rd |only kergp-0.4.0/kergp/man/predict.gp.Rd | 12 kergp-0.4.0/kergp/man/prinKrige.Rd |only kergp-0.4.0/kergp/man/q1CompSymm.Rd |only kergp-0.4.0/kergp/man/q1Diag.Rd |only kergp-0.4.0/kergp/man/q1Symm.Rd |only kergp-0.4.0/kergp/man/scores.Rd | 2 kergp-0.4.0/kergp/man/shapeSlot.Rd | 2 kergp-0.4.0/kergp/man/simulPar-covAll-method.Rd |only kergp-0.4.0/kergp/man/simulPar.Rd | 4 kergp-0.4.0/kergp/man/simulate.covAll.Rd |only kergp-0.4.0/kergp/man/simulate.gp.Rd |only kergp-0.4.0/kergp/man/symIndices.Rd |only kergp-0.4.0/kergp/man/translude.Rd |only kergp-0.4.0/kergp/man/varVec-methods.Rd |only kergp-0.4.0/kergp/man/varVec.Rd |only kergp-0.4.0/kergp/src/covMan.c | 137 + kergp-0.4.0/kergp/src/covMan2.c | 10 kergp-0.4.0/kergp/src/covTS.c | 176 ++ kergp-0.4.0/kergp/src/covWhiteNoise.c | 3 kergp-0.4.0/kergp/src/init.c |only kergp-0.4.0/kergp/src/k1Funs.c |only kergp-0.4.0/kergp/src/kergp.h |only kergp-0.4.0/kergp/src/kern1d_Call.c | 50 kergp-0.4.0/kergp/src/q1CompSymm.c |only kergp-0.4.0/kergp/src/q1Symm.c |only kergp-0.4.0/kergp/tests/testthat/test-SK-OrnsteinUhlenbeck.R | 6 kergp-0.4.0/kergp/tests/testthat/test-covMat.R | 8 kergp-0.4.0/kergp/tests/testthat/test-covTSGrad.R | 7 kergp-0.4.0/kergp/tests/testthat/test-interp.R | 4 kergp-0.4.0/kergp/tests/testthat/test-loo.R | 2 106 files changed, 2280 insertions(+), 1245 deletions(-)
Title: Parse Data of 'R' Code as an 'XML' Tree
Description: Convert the output of 'utils::getParseData()' to an 'XML'
tree, that one can search via 'XPath', and easier to manipulate in
general.
Author: Gábor Csárdi
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between xmlparsedata versions 1.0.1 dated 2016-06-18 and 1.0.2 dated 2018-09-17
DESCRIPTION | 17 +++++++++-------- MD5 | 16 ++++++++-------- NEWS.md | 7 +++++++ R/package.R | 17 +++++++++++++++-- README.md | 8 ++++---- man/xml_parse_data.Rd | 5 ++--- man/xml_parse_token_map.Rd | 1 - man/xmlparsedata.Rd | 1 - tests/testthat/test.R | 22 ++++++++++++++++++---- 9 files changed, 63 insertions(+), 31 deletions(-)
Title: Bayesian Variable Selection and Model Choice for Generalized
Additive Mixed Models
Description: Bayesian variable selection, model choice, and regularized
estimation for (spatial) generalized additive mixed regression models
via stochastic search variable selection with spike-and-slab priors.
Author: Fabian Scheipl [aut, cre],
Bettina Gruen [ctb]
Maintainer: Fabian Scheipl <fabian.scheipl@stat.uni-muenchen.de>
Diff between spikeSlabGAM versions 1.1-11 dated 2016-02-29 and 1.1-14 dated 2018-09-17
spikeSlabGAM-1.1-11/spikeSlabGAM/R/zzz.R |only spikeSlabGAM-1.1-14/spikeSlabGAM/DESCRIPTION | 21 spikeSlabGAM-1.1-14/spikeSlabGAM/MD5 | 68 spikeSlabGAM-1.1-14/spikeSlabGAM/NAMESPACE | 2 spikeSlabGAM-1.1-14/spikeSlabGAM/NEWS | 9 spikeSlabGAM-1.1-14/spikeSlabGAM/R/bugs.R | 43 spikeSlabGAM-1.1-14/spikeSlabGAM/R/plot.R | 973 ++++++---- spikeSlabGAM-1.1-14/spikeSlabGAM/R/predict.R | 172 + spikeSlabGAM-1.1-14/spikeSlabGAM/R/spikeAndSlab.R | 684 ++++--- spikeSlabGAM-1.1-14/spikeSlabGAM/R/spikeSlabGAM.R | 38 spikeSlabGAM-1.1-14/spikeSlabGAM/R/ssGAMDesign.R | 224 +- spikeSlabGAM-1.1-14/spikeSlabGAM/R/summary.R | 189 + spikeSlabGAM-1.1-14/spikeSlabGAM/R/terms.R | 257 +- spikeSlabGAM-1.1-14/spikeSlabGAM/R/utils.R | 466 ++-- spikeSlabGAM-1.1-14/spikeSlabGAM/build/vignette.rds |binary spikeSlabGAM-1.1-14/spikeSlabGAM/inst/doc/UsingSpikeSlabGAM.pdf |binary spikeSlabGAM-1.1-14/spikeSlabGAM/man/evalTerm.Rd | 1 spikeSlabGAM-1.1-14/spikeSlabGAM/man/fct.Rd | 1 spikeSlabGAM-1.1-14/spikeSlabGAM/man/getPosteriorTerm.Rd | 1 spikeSlabGAM-1.1-14/spikeSlabGAM/man/lin.Rd | 1 spikeSlabGAM-1.1-14/spikeSlabGAM/man/mrf.Rd | 10 spikeSlabGAM-1.1-14/spikeSlabGAM/man/plot.spikeSlabGAM.Rd | 11 spikeSlabGAM-1.1-14/spikeSlabGAM/man/plotTerm.Rd | 6 spikeSlabGAM-1.1-14/spikeSlabGAM/man/predict.spikeSlabGAM.Rd | 8 spikeSlabGAM-1.1-14/spikeSlabGAM/man/print.summary.spikeSlabGAM.Rd | 7 spikeSlabGAM-1.1-14/spikeSlabGAM/man/rnd.Rd | 1 spikeSlabGAM-1.1-14/spikeSlabGAM/man/sm.Rd | 13 spikeSlabGAM-1.1-14/spikeSlabGAM/man/spikeAndSlab.Rd | 7 spikeSlabGAM-1.1-14/spikeSlabGAM/man/spikeSlabGAM.Rd | 7 spikeSlabGAM-1.1-14/spikeSlabGAM/man/srf.Rd | 11 spikeSlabGAM-1.1-14/spikeSlabGAM/man/ssGAM2Bugs.Rd | 1 spikeSlabGAM-1.1-14/spikeSlabGAM/man/ssGAMDesign.Rd | 5 spikeSlabGAM-1.1-14/spikeSlabGAM/man/summary.spikeSlabGAM.Rd | 7 spikeSlabGAM-1.1-14/spikeSlabGAM/man/u.Rd | 1 spikeSlabGAM-1.1-14/spikeSlabGAM/src/spikeSlabGAM_init.c |only spikeSlabGAM-1.1-14/spikeSlabGAM/vignettes/UsingSpikeSlabGAM.bib | 4 36 files changed, 1888 insertions(+), 1361 deletions(-)
Title: Accesses Google Maps APIs to Retrieve Data and Plot Maps
Description: Provides a mechanism to plot a 'Google Map' from 'R' and overlay
it with shapes and markers. Also provides access to 'Google Maps' APIs,
including places, directions, roads, distances, geocoding, elevation and
timezone.
Author: David Cooley [aut, cre],
Paulo Barcelos [ctb] (Author of c++ decode_pl),
Rstudio [ctb] (Functions written for the Leaflet pacakge)
Maintainer: David Cooley <dcooley@symbolix.com.au>
Diff between googleway versions 2.7.0 dated 2018-05-25 and 2.7.1 dated 2018-09-17
DESCRIPTION | 10 MD5 | 87 ++-- NAMESPACE | 2 R/google_directions.R | 24 - R/google_distance.R | 24 - R/google_keys.R | 3 R/google_map.R | 6 R/google_map_layer_marker.R | 1 R/google_map_layer_polyline.R | 7 R/google_places.R | 242 +++++++++--- R/google_utilities.R | 1 R/googleway-package.R | 12 R/legend.R | 2 R/onLoad.R | 1 R/parameter_checks.R | 140 +++++-- inst/doc/googleway-vignette.Rmd | 5 inst/doc/googleway-vignette.html | 10 inst/htmlwidgets/google_map.js | 61 +-- inst/htmlwidgets/google_map.yaml | 1 inst/htmlwidgets/lib/circles/circles.js | 2 inst/htmlwidgets/lib/drawing/drawing.js | 22 - inst/htmlwidgets/lib/geojson/geojson.js | 6 inst/htmlwidgets/lib/heatmap/heatmap.js | 24 - inst/htmlwidgets/lib/map/charts.js | 85 ++-- inst/htmlwidgets/lib/map/geolocation.js |only inst/htmlwidgets/lib/map/legend.js | 34 - inst/htmlwidgets/lib/map/map_events.js | 595 ++++++++++++++---------------- inst/htmlwidgets/lib/map/map_layers.js | 2 inst/htmlwidgets/lib/overlay/overlay.js | 2 inst/htmlwidgets/lib/polygons/polygons.js | 2 man/google_directions.Rd | 26 - man/google_distance.Rd | 31 - man/google_find_place.Rd |only man/google_map.Rd | 5 man/google_places.Rd | 38 - man/place_fields.Rd |only man/set_key.Rd | 4 tests/manual_tests.R | 44 ++ tests/testthat/test-google_directions.R | 3 tests/testthat/test-google_distances.R | 17 tests/testthat/test-google_keys.R | 63 --- tests/testthat/test-google_map.R | 3 tests/testthat/test-google_places.R | 38 + tests/testthat/test-onLoad.R | 2 tests/testthat/test-parameter_checks.R | 25 + vignettes/googleway-vignette.Rmd | 5 46 files changed, 970 insertions(+), 747 deletions(-)
Title: Phylogenetic Tree Manipulation Class and Methods
Description: S4 class and methods for intuitive and efficient phylogenetic tree manipulation.
Author: D.J. Bennett
Maintainer: D.J. Bennett <dominic.john.bennett@gmail.com>
Diff between treeman versions 1.1.2 dated 2018-04-06 and 1.1.3 dated 2018-09-17
DESCRIPTION | 6 +-- MD5 | 21 +++++++------ NAMESPACE | 1 R/calc-methods.R | 39 ++++++------------------- R/get-spcl-methods.R | 50 +++++++++++++++++++++++++++++++++ R/server-methods.R | 15 +++++++-- man/calcDstRF.Rd | 7 ---- man/getBiprts.Rd |only man/searchTxnyms.Rd | 1 man/taxaResolve.Rd | 1 tests/testthat/test-get-spcl-methods.R | 19 ++++++++++++ tests/testthat/test_server_methods.R | 6 +-- 12 files changed, 111 insertions(+), 55 deletions(-)
Title: Port of the 'Scilab' 'n1qn1' and 'qnbd' Modules for
(Un)constrained BFGS Optimization
Description: Provides 'Scilab' 'n1qn1', or Quasi-Newton BFGS
"qn" without constraints and 'qnbd' or Quasi-Newton BFGS with constraints.
This takes more memory than traditional L-BFGS. The n1qn1 routine is useful since it allows prespecification of a Hessian.
If the Hessian is near enough the truth in optimization it can speed up the optimization problem. Both algorithms are described in the
'Scilab' optimization documentation located at
<http://www.scilab.org/content/download/250/1714/file/optimization_in_scilab.pdf>.
Author: Matthew Fidler [aut, cre],
Wenping Wang [aut],
Claude Lemarechal [aut, ctb],
Joseph Bonnans [ctb],
Jean-Charles Gilbert [ctb],
Claudia Sagastizabal [ctb],
Stephen L. Campbell, [ctb],
Jean-Philippe Chancelier [ctb],
Ramine Nikoukhah [ctb],
Dirk Eddelbuettel [ctb],
Bruno Jofret [ctb],
INRIA [cph]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between n1qn1 versions 6.0.0-1 dated 2017-10-30 and 6.0.1-3 dated 2018-09-17
DESCRIPTION | 17 +- MD5 | 24 ++- NAMESPACE | 1 R/n1qn1.R | 338 +++++++++++++++++++++++++++++++---------------------- README.md | 2 man/qnbd.Rd |only src/Makevars | 2 src/RcppExpMod.cpp | 281 ++++++++++++++++++++++++++++++++++++++------ src/ajour.f |only src/calmaj.f |only src/init.c | 18 ++ src/n1qn1_all.f | 1 src/proj.f |only src/qnbd.f |only src/rlbd.f |only src/satur.f |only src/zqnbd.f |only 17 files changed, 490 insertions(+), 194 deletions(-)
Title: Create and Investigate Magic Squares
Description: A collection of efficient, vectorized algorithms for the
creation and investigation of magic squares and hypercubes, including
a variety of functions for the manipulation and analysis of
arbitrarily dimensioned arrays. The package includes methods for
creating normal magic squares of any order greater than 2. The
ultimate intention is for the package to be a computerized embodiment
all magic square knowledge, including direct numerical verification
of properties of magic squares (such as recent results on the
determinant of odd-ordered semimagic squares). Some antimagic
functionality is included. The package also
serves as a rebuttal to the often-heard comment "I thought R
was just for statistics".
Author: Robin K. S. Hankin
Maintainer: "Robin K. S. Hankin" <hankin.robin@gmail.com>
Diff between magic versions 1.5-8 dated 2018-01-26 and 1.5-9 dated 2018-09-17
DESCRIPTION | 8 ++++---- MD5 | 38 +++++++++++++++++++------------------- R/magic.R | 6 ++++-- build/vignette.rds |binary data/Frankenstein.rda |binary data/Ollerenshaw.rda |binary data/cube2.rda |binary data/hendricks.rda |binary data/magiccubes.rda |binary data/perfectcube5.rda |binary data/perfectcube6.rda |binary inst/doc/magicpaper.pdf |binary man/adiag.Rd | 10 +++++----- man/allsubhypercubes.Rd | 5 +++-- man/aplus.Rd | 15 ++++++++++----- man/arev.Rd | 4 ++-- man/arow.Rd | 4 ++++ man/circulant.Rd | 9 +++++---- man/do.index.Rd | 9 ++++++--- man/hudson.Rd | 2 +- 20 files changed, 63 insertions(+), 47 deletions(-)
Title: Dependencies for the 'jamovi' Framework
Description: A framework for creating rich interactive analyses for the jamovi
platform (see <https://www.jamovi.org> for more information).
Author: Jonathon Love
Maintainer: Jonathon Love <jon@thon.cc>
Diff between jmvcore versions 0.9.2.0 dated 2018-08-12 and 0.9.4 dated 2018-09-17
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/group.R | 5 +++++ R/options.R | 6 ++---- 4 files changed, 14 insertions(+), 11 deletions(-)
Title: Magnitude-Based Inferences
Description: Allows practitioners and researchers a wholesale approach for deriving magnitude-based inferences from raw data. A major goal of 'mbir' is to programmatically detect appropriate statistical tests to run in lieu of relying on practitioners to determine correct stepwise procedures independently.
Author: Kyle Peterson [aut, cre],
Aaron Caldwell [aut]
Maintainer: Kyle Peterson <petersonkdon@gmail.com>
Diff between mbir versions 1.3.2 dated 2018-07-06 and 1.3.4 dated 2018-09-17
DESCRIPTION | 14 +++++++------- MD5 | 24 ++++++++++++------------ R/aipe_smd.R | 5 +++++ R/boot_test.R | 16 ++++++++++++++-- R/es_convert.R | 2 ++ R/prop.R | 1 + R/smd.R | 32 +++++++++++++++++--------------- R/ss_corr.R | 11 +++++++++++ R/ss_odds.R | 11 +++++++++++ R/ss_smd.R | 11 +++++++++++ R/swc_ind.R | 1 + build/vignette.rds |binary inst/doc/mbir-vignette.html | 12 ++++++------ 13 files changed, 98 insertions(+), 42 deletions(-)
Title: Identify Global Objects in R Expressions
Description: Identifies global ("unknown" or "free") objects in R expressions
by code inspection using various strategies, e.g. conservative or liberal.
The objective of this package is to make it as simple as possible to
identify global objects for the purpose of exporting them in distributed
compute environments.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between globals versions 0.12.2 dated 2018-08-25 and 0.12.3 dated 2018-09-17
DESCRIPTION | 6 +-- MD5 | 20 +++++----- NEWS | 108 ++++++++++++++++++++++++++++++------------------------ R/Globals-class.R | 20 +++++----- R/cleanup.R | 2 - R/findGlobals.R | 40 +++++++++----------- R/globalsOf.R | 64 +++++++++++++++++--------------- R/packagesOf.R | 6 +-- R/utils.R | 3 + R/where.R | 19 ++++----- tests/globalsOf.R | 29 ++++++++++++++ 11 files changed, 181 insertions(+), 136 deletions(-)