Title: Exploring Heterogeneity in Meta-Analysis using Random Forests
Description: Conduct random forests-based meta-analysis, obtain partial dependence plots for metaforest and classic meta-analyses, and cross-validate and tune metaforest- and classic meta-analyses in conjunction with the caret package. A requirement of classic meta-analysis is that the studies being aggregated are conceptually similar, and ideally, close replications. However, in many fields, there is substantial heterogeneity between studies on the same topic. Classic meta-analysis lacks the power to assess more than a handful of univariate moderators. MetaForest, by contrast, has substantial power to explore heterogeneity in meta-analysis. It can identify important moderators from a larger set of potential candidates, even with as little as 20 studies (Van Lissa, in preparation). This is an appealing quality, because many meta-analyses have small sample sizes. Moreover, MetaForest yields a measure of variable importance which can be used to identify important moderators, and offers partial prediction plots to explore the shape of the marginal relationship between moderators and effect size.
Author: Caspar J. van Lissa
Maintainer: Caspar J. van Lissa <c.j.vanlissa@gmail.com>
Diff between metaforest versions 0.1.2 dated 2018-05-31 and 0.1.3 dated 2020-01-07
metaforest-0.1.2/metaforest/R/ClusterMF.R |only metaforest-0.1.2/metaforest/man/ClusterMF.Rd |only metaforest-0.1.2/metaforest/man/print.MetaForest.Rd |only metaforest-0.1.2/metaforest/man/summary.MetaForest.Rd |only metaforest-0.1.3/metaforest/DESCRIPTION | 13 metaforest-0.1.3/metaforest/MD5 | 74 - metaforest-0.1.3/metaforest/NAMESPACE | 18 metaforest-0.1.3/metaforest/NEWS.md | 18 metaforest-0.1.3/metaforest/R/MF.R |only metaforest-0.1.3/metaforest/R/MF_cluster.R |only metaforest-0.1.3/metaforest/R/MetaForest.R | 105 + metaforest-0.1.3/metaforest/R/ModelInfo_mf.R | 90 - metaforest-0.1.3/metaforest/R/ModelInfo_rma.R | 1 metaforest-0.1.3/metaforest/R/PartialDependence.R | 790 ++++++++------- metaforest-0.1.3/metaforest/R/VarImpPlot.R | 19 metaforest-0.1.3/metaforest/R/WeightedScatter.R | 4 metaforest-0.1.3/metaforest/R/coef_test.R |only metaforest-0.1.3/metaforest/R/curry.R |only metaforest-0.1.3/metaforest/R/deprecated_functions.R |only metaforest-0.1.3/metaforest/R/fukkink_lont.R |only metaforest-0.1.3/metaforest/R/helpers.R |only metaforest-0.1.3/metaforest/R/marginal_predictions.R |only metaforest-0.1.3/metaforest/R/metaforest-deprecated.r |only metaforest-0.1.3/metaforest/R/plot.MetaForest.R | 38 metaforest-0.1.3/metaforest/R/preselect.R |only metaforest-0.1.3/metaforest/R/print.MetaForest.R | 17 metaforest-0.1.3/metaforest/R/print.summary.MetaForest.R | 11 metaforest-0.1.3/metaforest/R/summary.MetaForest.R | 39 metaforest-0.1.3/metaforest/README.md | 129 +- metaforest-0.1.3/metaforest/build |only metaforest-0.1.3/metaforest/data |only metaforest-0.1.3/metaforest/inst |only metaforest-0.1.3/metaforest/man/ClusterMF-deprecated.Rd |only metaforest-0.1.3/metaforest/man/MetaForest.Rd | 53 - metaforest-0.1.3/metaforest/man/PartialDependence.Rd | 54 - metaforest-0.1.3/metaforest/man/SimulateSMD.Rd | 4 metaforest-0.1.3/metaforest/man/VarImpPlot.Rd | 4 metaforest-0.1.3/metaforest/man/WeightedScatter.Rd | 7 metaforest-0.1.3/metaforest/man/coef_test.Rd |only metaforest-0.1.3/metaforest/man/curry.Rd |only metaforest-0.1.3/metaforest/man/fukkink_lont.Rd |only metaforest-0.1.3/metaforest/man/metaforest-deprecated.Rd |only metaforest-0.1.3/metaforest/man/predict.MetaForest.Rd | 3 metaforest-0.1.3/metaforest/man/preselect.Rd |only metaforest-0.1.3/metaforest/man/preselect_vars.Rd |only metaforest-0.1.3/metaforest/man/report.Rd |only metaforest-0.1.3/metaforest/tests |only metaforest-0.1.3/metaforest/vignettes |only 48 files changed, 888 insertions(+), 603 deletions(-)
Title: Fast Implementation of (Local) Population Stratification Methods
Description: Fast and fully sparse 'cpp' implementations to compute the genetic covariance matrix, the genomic relationship matrix, the Jaccard matrix, and the s-matrix of an input matrix. Full support for sparse matrices from the R-package 'Matrix'. Additionally, a 'cpp' implementation of the power method (von Mises iteration) algorithm to compute the largest eigenvector of a matrix is included, and a function to compute sliding windows.
Author: Georg Hahn [aut,cre], Sharon M. Lutz [ctb], Christoph Lange [ctb]
Maintainer: Georg Hahn <ghahn@hsph.harvard.edu>
Diff between locStra versions 1.1 dated 2019-11-26 and 1.2 dated 2020-01-07
DESCRIPTION | 8 ++++---- MD5 | 10 +++++++--- R/localStrat.r | 23 +++++++++++++++++++---- R/testdata.R |only data |only man/figures |only man/fullscan.Rd | 22 ++++++++++++++++++---- man/testdata-data.Rd |only 8 files changed, 48 insertions(+), 15 deletions(-)
Title: Interface with General Bikeshare Feed Specification Files
Description: Supplies a set of functions to interface with General Bikeshare
Feed Specification .json feeds in R, allowing users to save and accumulate
tidy .rds datasets for specified cities/bikeshare programs.
Author: Kaelyn Rosenberg [aut],
Simon P. Couch [aut, cre],
Mark Padgham [ctb]
Maintainer: Simon P. Couch <simonpatrickcouch@gmail.com>
Diff between gbfs versions 1.2.0 dated 2019-09-10 and 1.3.0 dated 2020-01-07
gbfs-1.2.0/gbfs/README.md |only gbfs-1.3.0/gbfs/DESCRIPTION | 12 gbfs-1.3.0/gbfs/MD5 | 44 - gbfs-1.3.0/gbfs/NAMESPACE | 1 gbfs-1.3.0/gbfs/NEWS.md | 22 gbfs-1.3.0/gbfs/R/gbfs_description.R | 54 + gbfs-1.3.0/gbfs/R/get_dynamic_feeds.R | 301 ++-------- gbfs-1.3.0/gbfs/R/get_gbfs.R | 315 ++++------- gbfs-1.3.0/gbfs/R/get_static_feeds.R | 664 +++++++----------------- gbfs-1.3.0/gbfs/R/utils.R |only gbfs-1.3.0/gbfs/man/gbfs.Rd | 69 ++ gbfs-1.3.0/gbfs/man/get_free_bike_status.Rd | 75 ++ gbfs-1.3.0/gbfs/man/get_gbfs.Rd | 59 +- gbfs-1.3.0/gbfs/man/get_station_information.Rd | 65 +- gbfs-1.3.0/gbfs/man/get_station_status.Rd | 72 +- gbfs-1.3.0/gbfs/man/get_system_alerts.Rd | 66 +- gbfs-1.3.0/gbfs/man/get_system_calendar.Rd | 66 +- gbfs-1.3.0/gbfs/man/get_system_hours.Rd | 67 +- gbfs-1.3.0/gbfs/man/get_system_information.Rd | 64 +- gbfs-1.3.0/gbfs/man/get_system_pricing_plans.Rd | 64 +- gbfs-1.3.0/gbfs/man/get_system_regions.Rd | 64 +- gbfs-1.3.0/gbfs/man/get_which_gbfs_feeds.Rd |only gbfs-1.3.0/gbfs/tests |only 23 files changed, 1055 insertions(+), 1089 deletions(-)
Title: Dominance Analysis
Description: Dominance analysis is a method that allows to compare the
relative importance of predictors in multiple regression models:
ordinary least squares, generalized linear models,
hierarchical linear models, beta regression and dynamic linear models.
The main principles and methods of
dominance analysis are described in
Budescu, D. V. (1993) <doi:10.1037/0033-2909.114.3.542> and
Azen, R., & Budescu, D. V. (2003) <doi:10.1037/1082-989X.8.2.129>
for ordinary least squares regression. Subsequently, the extensions
for multivariate regression, logistic regression and
hierarchical linear models were described in
Azen, R., & Budescu, D. V. (2006) <doi:10.3102/10769986031002157>,
Azen, R., & Traxel, N. (2009) <doi:10.3102/1076998609332754> and
Luo, W., & Azen, R. (2013) <doi:10.3102/1076998612458319>,
respectively.
Author: Claudio Bustos Navarrete [aut, cre]
(<https://orcid.org/0000-0003-3478-9858>),
Filipa Coutinho Soares [aut] (<https://orcid.org/0000-0002-7579-2538>)
Maintainer: Claudio Bustos Navarrete <clbustos@gmail.com>
Diff between dominanceanalysis versions 1.2.0 dated 2019-09-22 and 1.3.0 dated 2020-01-07
DESCRIPTION | 16 MD5 | 87 +-- NAMESPACE | 2 NEWS.md | 7 R/daFitFunctions.r | 70 ++ R/daRawResults.r | 23 R/daUtils.r | 6 R/dominanceAnalysis.r | 26 - R/dominanceMatrix.r | 32 - R/dominanceanalysis-package.r | 3 R/plot.dominanceAnalysis.R |only README.md | 460 ++++++++---------- build/vignette.rds |binary inst/WORDLIST | 7 inst/doc/da-logistic-regression.R | 92 ++- inst/doc/da-logistic-regression.Rmd | 71 ++ inst/doc/da-logistic-regression.html | 352 ++++++------- inst/extdata/bootavemodpres100.rds |binary inst/extdata/bootmodpres100.rds |binary inst/extdata/da-lr-test.rds |only inst/extdata/da-lr-train.rds |only man/averageContribution.Rd | 8 man/bootAverageDominanceAnalysis.Rd | 11 man/bootDominanceAnalysis.Rd | 11 man/contributionByLevel.Rd | 8 man/da.betareg.fit.Rd |only man/da.dynlm.fit.Rd | 11 man/da.glm.fit.Rd | 11 man/da.lm.fit.Rd | 11 man/da.lmWithCov.fit.Rd | 11 man/da.lmerMod.fit.Rd | 11 man/da.mlmWithCov.fit.Rd | 11 man/daCompleteDominance.Rd | 5 man/daConditionalDominance.Rd | 5 man/daGeneralDominance.Rd | 5 man/daRawResults.Rd | 12 man/dominanceAnalysis.Rd | 35 + man/dominanceBriefing.Rd | 8 man/dominanceMatrix.Rd | 28 - man/dominanceanalysis-package.Rd | 3 man/getFits.Rd | 9 man/plot.dominanceAnalysis.Rd |only man/summary.bootAverageDominanceAnalysis.Rd | 3 man/summary.bootDominanceAnalysis.Rd | 3 tests/testthat/test-beta-with-gasolineyield-example.R |only tests/testthat/test-dominance-analysis-plots.R |only tests/testthat/test-dominanceMatrix.R | 33 + vignettes/da-logistic-regression.Rmd | 71 ++ 48 files changed, 963 insertions(+), 615 deletions(-)
More information about dominanceanalysis at CRAN
Permanent link
Title: Distance-Based Measures of Spatial Structures
Description: Simple computation of spatial statistic functions of distance to characterize the spatial structures of mapped objects, following Marcon, Traissac, Puech, and Lang (2015) <doi:10.18637/jss.v067.c03>.
Includes classical functions (Ripley's K and others) and more recent ones used by spatial economists (Duranton and Overman's Kd, Marcon and Puech's M).
Relies on 'spatstat' for some core calculation.
Author: Eric Marcon [aut, cre] (<https://orcid.org/0000-0002-5249-321X>),
Gabriel Lang [aut] (<https://orcid.org/0000-0002-4325-6044>),
Stephane Traissac [aut],
Florence Puech [aut] (<https://orcid.org/0000-0002-5279-6878>)
Maintainer: Eric Marcon <eric.marcon@ecofog.gf>
Diff between dbmss versions 2.7-0 dated 2019-03-25 and 2.7-1 dated 2020-01-07
DESCRIPTION | 8 - MD5 | 28 ++-- NEWS.md | 15 ++ R/CheckdbmssArguments.R | 15 +- R/KEnvelope.R | 4 R/LEnvelope.R | 7 - R/rRandomPositionK.R | 9 + R/wmppp.R | 2 README.md | 2 build/vignette.rds |binary inst/doc/dbmss.R | 10 - inst/doc/dbmss.html | 333 +++++++++++++++++++++++++++++++++++++++--------- man/KEnvelope.Rd | 5 man/LEnvelope.Rd | 5 man/rRandomPositionK.Rd | 9 + 15 files changed, 353 insertions(+), 99 deletions(-)
Title: High Dimensional Numerical and Symbolic Calculus
Description: Efficient C++ optimized functions for numerical and symbolic calculus. It includes basic symbolic arithmetic, tensor calculus, Einstein summing convention, fast computation of the Levi-Civita symbol and generalized Kronecker delta, Taylor series expansion, multivariate Hermite polynomials, accurate high-order derivatives, differential operators (Gradient, Jacobian, Hessian, Divergence, Curl, Laplacian) and numerical integration in arbitrary orthogonal coordinate systems: cartesian, polar, spherical, cylindrical, parabolic or user defined by custom scale factors.
Author: Emanuele Guidotti [aut, cre] (<https://orcid.org/0000-0002-8961-6623>)
Maintainer: Emanuele Guidotti <emanuele.guidotti@unine.ch>
Diff between calculus versions 0.1.1 dated 2019-11-11 and 0.2.0 dated 2020-01-07
DESCRIPTION | 13 MD5 | 21 - NEWS.md |only R/det.R | 2 R/einstein.R | 4 R/integral.R | 196 ++++++++---- R/operators.R | 16 - R/package.R | 27 + R/utilities.R | 2 README.md | 869 +++++++++++++++++++++++++++++++++++++++++++++++++++++++- man/integral.Rd | 49 ++- man/wrap.Rd | 2 12 files changed, 1092 insertions(+), 109 deletions(-)
Title: Model Butcher
Description: Provides a set of five S3 generics to axe components of fitted model objects and help reduce the size of model objects saved to disk.
Author: Joyce Cahoon [aut, cre] (<https://orcid.org/0000-0001-7217-4702>),
Davis Vaughan [aut],
Max Kuhn [aut],
Alex Hayes [aut]
Maintainer: Joyce Cahoon <joyceyu48@gmail.com>
Diff between butcher versions 0.1.0 dated 2019-08-09 and 0.1.1 dated 2020-01-07
butcher-0.1.0/butcher/R/cv.R |only butcher-0.1.0/butcher/R/stanreg.R |only butcher-0.1.0/butcher/man/axe-cv.glmnet.Rd |only butcher-0.1.0/butcher/man/axe-stanreg.Rd |only butcher-0.1.0/butcher/tests/testthat/test-cv.R |only butcher-0.1.0/butcher/tests/testthat/test-stanreg.R |only butcher-0.1.1/butcher/DESCRIPTION | 20 - butcher-0.1.1/butcher/MD5 | 92 +++---- butcher-0.1.1/butcher/NAMESPACE | 5 butcher-0.1.1/butcher/NEWS.md |only butcher-0.1.1/butcher/R/axe-generics.R | 2 butcher-0.1.1/butcher/R/elnet.R | 15 - butcher-0.1.1/butcher/R/flexsurvreg.R | 2 butcher-0.1.1/butcher/R/formula.R | 2 butcher-0.1.1/butcher/R/glmnet.R | 14 - butcher-0.1.1/butcher/R/model_fit.R | 8 butcher-0.1.1/butcher/R/multnet.R | 15 - butcher-0.1.1/butcher/R/recipe.R | 5 butcher-0.1.1/butcher/R/train.recipe.R | 1 butcher-0.1.1/butcher/R/weigh.R | 11 butcher-0.1.1/butcher/R/xgb.R | 2 butcher-0.1.1/butcher/README.md | 15 - butcher-0.1.1/butcher/build/butcher.pdf |binary butcher-0.1.1/butcher/build/vignette.rds |binary butcher-0.1.1/butcher/inst/doc/adding-models-to-butcher.R | 12 - butcher-0.1.1/butcher/inst/doc/available-axe-methods.R | 4 butcher-0.1.1/butcher/inst/doc/available-axe-methods.html | 164 ++++++-------- butcher-0.1.1/butcher/inst/doc/butcher.R | 32 +- butcher-0.1.1/butcher/inst/doc/butcher.html | 100 +++----- butcher-0.1.1/butcher/man/axe-elnet.Rd | 19 - butcher-0.1.1/butcher/man/axe-flexsurvreg.Rd | 4 butcher-0.1.1/butcher/man/axe-function.Rd | 2 butcher-0.1.1/butcher/man/axe-glmnet.Rd | 18 - butcher-0.1.1/butcher/man/axe-ksvm.Rd | 4 butcher-0.1.1/butcher/man/axe-model_fit.Rd | 8 butcher-0.1.1/butcher/man/axe-multnet.Rd | 19 - butcher-0.1.1/butcher/man/axe-recipe.Rd | 1 butcher-0.1.1/butcher/man/axe-spark.Rd | 2 butcher-0.1.1/butcher/man/axe-train.recipe.Rd | 9 butcher-0.1.1/butcher/man/axe_env.Rd | 2 butcher-0.1.1/butcher/man/butcher-package.Rd | 2 butcher-0.1.1/butcher/tests/testthat/helper-objects.R |only butcher-0.1.1/butcher/tests/testthat/test-earth.R | 2 butcher-0.1.1/butcher/tests/testthat/test-elnet.R | 17 - butcher-0.1.1/butcher/tests/testthat/test-flexsurvreg.R | 8 butcher-0.1.1/butcher/tests/testthat/test-glmnet.R | 10 butcher-0.1.1/butcher/tests/testthat/test-multnet.R | 14 - butcher-0.1.1/butcher/tests/testthat/test-recipe.R | 22 + butcher-0.1.1/butcher/tests/testthat/test-train.R | 2 butcher-0.1.1/butcher/tests/testthat/test-train.recipe.R | 3 butcher-0.1.1/butcher/tests/testthat/test-weigh.R | 14 - 51 files changed, 291 insertions(+), 412 deletions(-)
Title: (Permuted) Brunner-Munzel Test
Description: Provides the functions for Brunner-Munzel test and
permuted Brunner-Munzel test,
which enable to use formula, matrix, and table as argument.
These functions are based on Brunner and Munzel (2000)
<doi:10.1002/(SICI)1521-4036(200001)42:1%3C17::AID-BIMJ17%3E3.0.CO;2-U>
and Neubert and Brunner (2007) <doi:10.1016/j.csda.2006.05.024>,
and are written with FORTRAN.
Author: Toshiaki Ara [aut, cre]
Maintainer: Toshiaki Ara <toshiaki.ara@gmail.com>
Diff between brunnermunzel versions 1.3.5 dated 2019-05-30 and 1.4.1 dated 2020-01-07
brunnermunzel-1.3.5/brunnermunzel/R/brunnermunzel.perutation.test.R |only brunnermunzel-1.4.1/brunnermunzel/DESCRIPTION | 10 brunnermunzel-1.4.1/brunnermunzel/MD5 | 24 brunnermunzel-1.4.1/brunnermunzel/NEWS.md | 8 brunnermunzel-1.4.1/brunnermunzel/R/brunnermunzel.permutation.test.R |only brunnermunzel-1.4.1/brunnermunzel/R/brunnermunzel.test.R | 89 ++ brunnermunzel-1.4.1/brunnermunzel/build/vignette.rds |binary brunnermunzel-1.4.1/brunnermunzel/inst/doc/usage.R | 43 - brunnermunzel-1.4.1/brunnermunzel/inst/doc/usage.Rmd | 21 brunnermunzel-1.4.1/brunnermunzel/inst/doc/usage.html | 302 +++++----- brunnermunzel-1.4.1/brunnermunzel/man/brunnermunzel.permutation.test.Rd | 74 +- brunnermunzel-1.4.1/brunnermunzel/man/brunnermunzel.test.Rd | 63 +- brunnermunzel-1.4.1/brunnermunzel/src/bm_permutation_test.f | 21 brunnermunzel-1.4.1/brunnermunzel/vignettes/usage.Rmd | 21 14 files changed, 448 insertions(+), 228 deletions(-)
Title: Australian Government Bureau of Meteorology ('BOM') Data Client
Description: Provides functions to interface with Australian Government Bureau
of Meteorology ('BOM') data, fetching data and returning a tidy data frame
of precis forecasts, historical and current weather data from stations,
agriculture bulletin data, 'BOM' 0900 or 1500 weather bulletins and
downloading and importing radar and satellite imagery files. Data (c)
Australian Government Bureau of Meteorology Creative Commons (CC)
Attribution 3.0 licence or Public Access Licence (PAL) as appropriate. See
<http://www.bom.gov.au/other/copyright.shtml> for further details.
Author: Adam H. Sparks [aut, cre] (<https://orcid.org/0000-0002-0061-8359>),
Jonathan Carroll [aut] (<https://orcid.org/0000-0002-1404-5264>),
James Goldie [aut] (<https://orcid.org/0000-0002-5024-6207>),
Dean Marchiori [aut],
Paul Melloy [aut] (<https://orcid.org/0000-0003-4253-7167>),
Mark Padgham [aut, rev] (<https://orcid.org/0000-0003-2172-5265>),
Hugh Parsonage [aut] (<https://orcid.org/0000-0003-4055-0835>),
Keith Pembleton [aut] (<https://orcid.org/0000-0002-1896-4516>),
James Balamuta [ctb] (<https://orcid.org/0000-0003-2826-8458>),
Brooke Anderson [rev] (<https://orcid.org/0000-0002-5012-9035>)
Maintainer: Adam H. Sparks <adamhsparks@gmail.com>
Diff between bomrang versions 0.6.0 dated 2019-07-04 and 0.6.1 dated 2020-01-07
bomrang-0.6.0/bomrang/inst/doc/bomrang.R |only bomrang-0.6.1/bomrang/DESCRIPTION | 30 bomrang-0.6.1/bomrang/MD5 | 91 bomrang-0.6.1/bomrang/NEWS.md | 22 bomrang-0.6.1/bomrang/R/bomrang.r | 7 bomrang-0.6.1/bomrang/R/bomrang_tbl.R | 5 bomrang-0.6.1/bomrang/R/dplyr.R | 6 bomrang-0.6.1/bomrang/R/get_ag_bulletin.R | 4 bomrang-0.6.1/bomrang/R/get_coastal_forecast.R | 3 bomrang-0.6.1/bomrang/R/get_current_weather.R | 22 bomrang-0.6.1/bomrang/R/get_historical.R | 1 bomrang-0.6.1/bomrang/R/get_precis_forecast.R | 2 bomrang-0.6.1/bomrang/R/get_radar_imagery.R | 1 bomrang-0.6.1/bomrang/R/get_satellite_imagery.R | 1 bomrang-0.6.1/bomrang/R/get_weather_bulletins.R | 2 bomrang-0.6.1/bomrang/R/sweep_for_forecast_towns.R | 12 bomrang-0.6.1/bomrang/R/sweep_for_stations.R | 5 bomrang-0.6.1/bomrang/R/update_forecast_towns.R | 5 bomrang-0.6.1/bomrang/R/update_station_locations.R | 55 bomrang-0.6.1/bomrang/R/zzz.R | 3 bomrang-0.6.1/bomrang/build/vignette.rds |binary bomrang-0.6.1/bomrang/inst/CITATION | 10 bomrang-0.6.1/bomrang/inst/doc/bomrang.Rmd | 506 ++++- bomrang-0.6.1/bomrang/inst/doc/bomrang.html | 967 ++++++---- bomrang-0.6.1/bomrang/inst/doc/use_case.R | 12 bomrang-0.6.1/bomrang/inst/doc/use_case.html | 49 bomrang-0.6.1/bomrang/inst/extdata/AAC_codes.rda |binary bomrang-0.6.1/bomrang/inst/extdata/JSONurl_site_list.rda |binary bomrang-0.6.1/bomrang/inst/extdata/current_stations_site_list.rda |binary bomrang-0.6.1/bomrang/inst/extdata/marine_AAC_codes.rda |binary bomrang-0.6.1/bomrang/inst/extdata/radar_locations.rda |binary bomrang-0.6.1/bomrang/man/bomrang.Rd | 9 bomrang-0.6.1/bomrang/man/get_current_weather.Rd | 29 bomrang-0.6.1/bomrang/man/get_historical.Rd | 7 bomrang-0.6.1/bomrang/man/get_weather_bulletin.Rd | 2 bomrang-0.6.1/bomrang/man/reexports.Rd | 2 bomrang-0.6.1/bomrang/man/sweep_for_forecast_towns.Rd | 2 bomrang-0.6.1/bomrang/man/sweep_for_stations.Rd | 2 bomrang-0.6.1/bomrang/man/update_station_locations.Rd | 2 bomrang-0.6.1/bomrang/tests/testthat/test-get_current_weather.R | 22 bomrang-0.6.1/bomrang/tests/testthat/test-get_precis_forecast.R | 5 bomrang-0.6.1/bomrang/tests/testthat/test-update_station_locations.R | 4 bomrang-0.6.1/bomrang/vignettes/bomrang.Rmd | 506 ++++- bomrang-0.6.1/bomrang/vignettes/bomrang.Rmd.orig |only bomrang-0.6.1/bomrang/vignettes/completeness_map-1.png |only bomrang-0.6.1/bomrang/vignettes/get_radar_imagery-1.png |only bomrang-0.6.1/bomrang/vignettes/get_satellite_imagery-1.png |binary bomrang-0.6.1/bomrang/vignettes/precompile.R |only bomrang-0.6.1/bomrang/vignettes/station-locations-map-1.png |only bomrang-0.6.1/bomrang/vignettes/years_available-1.png |only 50 files changed, 1803 insertions(+), 610 deletions(-)
Title: Simulating Realistic Gene Expression Data
Description: The Ultimate Microrray Prediction, Reality and Inference
Engine (UMPIRE) is a package to facilitate the simulation of realistic
microarray data sets with link to associate outcomes. See Zhang and
Coombes (2012) <doi:10.1186/1471-2105-13-S13-S1>.
Author: Kevin R. Coombes, Jiexin Zhang
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between Umpire versions 1.3.7 dated 2019-05-06 and 1.3.8 dated 2020-01-07
DESCRIPTION | 8 MD5 | 10 TODO | 50 + inst/doc/Umpire.pdf |binary tests/t02-indLogNorm.R | 4 tests/t02-indLogNorm.Rout.save | 1449 ++++++++++++++++++++--------------------- 6 files changed, 782 insertions(+), 739 deletions(-)
Title: Optimum Threshold Estimation
Description: Functions that provide point and interval estimations of optimum thresholds for continuous diagnostic tests. The methodology used is based on minimizing an overall cost function in the two- and three-state settings. The package also provides functions for sample size determination and estimation of diagnostic accuracy measures. It also includes graphical tools.
Author: Sara Perez-Jaume, Natalia Pallares, Konstantina Skaltsa
Maintainer: Sara Perez-Jaume <spjaume@gmail.com>
Diff between ThresholdROC versions 2.7 dated 2019-02-26 and 2.8 dated 2020-01-07
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/ThresholdROC-2states.R | 22 +++++++++++----------- man/ThresholdROC-package.Rd | 4 ++-- man/thres2.Rd | 8 ++++++-- 5 files changed, 27 insertions(+), 23 deletions(-)
Title: Inference in Regressions with Shift-Share Structure
Description: Provides confidence intervals in least-squares regressions when the
variable of interest has a shift-share structure, and in instrumental
variables regressions when the instrument has a shift-share structure. The
confidence intervals implement the AKM and AKM0 methods developed in Adão,
Kolesár, and Morales (2019) <doi:10.1093/qje/qjz025>.
Author: Michal Kolesár [aut, cre] (<https://orcid.org/0000-0002-2482-7796>),
Eduardo Morales [ctb],
Rodrigo Adão [ctb]
Maintainer: Michal Kolesár <kolesarmi@googlemail.com>
Diff between ShiftShareSE versions 1.0.0 dated 2019-08-24 and 1.0.1 dated 2020-01-07
ShiftShareSE-1.0.0/ShiftShareSE/vignettes/auto/bartik_library.el |only ShiftShareSE-1.0.1/ShiftShareSE/DESCRIPTION | 8 - ShiftShareSE-1.0.1/ShiftShareSE/MD5 | 40 ++--- ShiftShareSE-1.0.1/ShiftShareSE/NEWS.md | 8 + ShiftShareSE-1.0.1/ShiftShareSE/R/documentation.R | 4 ShiftShareSE-1.0.1/ShiftShareSE/R/iv.R | 63 ++++---- ShiftShareSE-1.0.1/ShiftShareSE/R/ols.R | 78 +++++----- ShiftShareSE-1.0.1/ShiftShareSE/build/vignette.rds |binary ShiftShareSE-1.0.1/ShiftShareSE/inst/WORDLIST | 6 ShiftShareSE-1.0.1/ShiftShareSE/inst/doc/ShiftShareSE.R | 11 - ShiftShareSE-1.0.1/ShiftShareSE/inst/doc/ShiftShareSE.Rmd | 26 ++- ShiftShareSE-1.0.1/ShiftShareSE/inst/doc/ShiftShareSE.pdf |binary ShiftShareSE-1.0.1/ShiftShareSE/man/ADH.Rd | 4 ShiftShareSE-1.0.1/ShiftShareSE/man/ivreg_ss.Rd | 77 ++++++--- ShiftShareSE-1.0.1/ShiftShareSE/man/ivreg_ss.fit.Rd | 49 ++++-- ShiftShareSE-1.0.1/ShiftShareSE/man/reg_ss.Rd | 54 ++++-- ShiftShareSE-1.0.1/ShiftShareSE/man/reg_ss.fit.Rd | 42 +++-- ShiftShareSE-1.0.1/ShiftShareSE/tests/testthat/test_adh.R | 7 ShiftShareSE-1.0.1/ShiftShareSE/tests/testthat/test_se.R | 14 + ShiftShareSE-1.0.1/ShiftShareSE/vignettes/ShiftShareSE.Rmd | 26 ++- ShiftShareSE-1.0.1/ShiftShareSE/vignettes/auto/library.el |only ShiftShareSE-1.0.1/ShiftShareSE/vignettes/library.bib | 8 - 22 files changed, 338 insertions(+), 187 deletions(-)
Title: Mixture Models with Heterogeneous and (Partially) Missing Data
Description: Mixture Composer <https://github.com/modal-inria/MixtComp> is a project to build mixture models with
heterogeneous data sets and partially missing data management.
It includes 8 models for real, categorical, counting, functional and ranking data.
Author: Vincent Kubicki [aut],
Christophe Biernacki [aut],
Quentin Grimonprez [aut, cre],
Matthieu Marbac-Lourdelle [ctb],
Étienne Goffinet [ctb],
Serge Iovleff [ctb]
Maintainer: Quentin Grimonprez <quentin.grimonprez@inria.fr>
Diff between RMixtComp versions 4.0.2 dated 2019-09-16 and 4.1.0 dated 2020-01-07
RMixtComp-4.0.2/RMixtComp/R/MIXTCOMP_models.R |only RMixtComp-4.1.0/RMixtComp/DESCRIPTION | 17 - RMixtComp-4.1.0/RMixtComp/MD5 | 70 ++++-- RMixtComp-4.1.0/RMixtComp/NAMESPACE | 6 RMixtComp-4.1.0/RMixtComp/NEWS | 7 RMixtComp-4.1.0/RMixtComp/R/MIXTCOMP_datasets.R | 2 RMixtComp-4.1.0/RMixtComp/R/MIXTCOMP_formatData.R | 2 RMixtComp-4.1.0/RMixtComp/R/MIXTCOMP_hierarchical.R | 2 RMixtComp-4.1.0/RMixtComp/R/MIXTCOMP_methods.R | 9 RMixtComp-4.1.0/RMixtComp/R/MIXTCOMP_mixtCompLearn.R | 7 RMixtComp-4.1.0/RMixtComp/R/PLOT_plotCrit.R | 24 -- RMixtComp-4.1.0/RMixtComp/R/RMixtComp-package.R | 16 + RMixtComp-4.1.0/RMixtComp/R/miscellaneous.R |only RMixtComp-4.1.0/RMixtComp/R/slopeHeuristic.R |only RMixtComp-4.1.0/RMixtComp/build |only RMixtComp-4.1.0/RMixtComp/data/CanadianWeather.rda |binary RMixtComp-4.1.0/RMixtComp/data/prostate.rda |binary RMixtComp-4.1.0/RMixtComp/data/simData.rda |binary RMixtComp-4.1.0/RMixtComp/data/titanic.rda |binary RMixtComp-4.1.0/RMixtComp/inst |only RMixtComp-4.1.0/RMixtComp/man/CanadianWeather.Rd | 8 RMixtComp-4.1.0/RMixtComp/man/RMixtComp-package.Rd | 9 RMixtComp-4.1.0/RMixtComp/man/extractMixtCompObject.Rd |only RMixtComp-4.1.0/RMixtComp/man/mixtCompLearn.Rd | 28 ++ RMixtComp-4.1.0/RMixtComp/man/plot.MixtCompLearn.Rd | 17 + RMixtComp-4.1.0/RMixtComp/man/plotCrit.Rd | 3 RMixtComp-4.1.0/RMixtComp/man/print.MixtCompLearn.Rd | 3 RMixtComp-4.1.0/RMixtComp/man/prostate.Rd | 6 RMixtComp-4.1.0/RMixtComp/man/simData.Rd | 6 RMixtComp-4.1.0/RMixtComp/man/slopeHeuristic.Rd |only RMixtComp-4.1.0/RMixtComp/man/titanic.Rd | 6 RMixtComp-4.1.0/RMixtComp/tests/testthat/test.hierarchical.R | 4 RMixtComp-4.1.0/RMixtComp/tests/testthat/test.miscellaneous.R |only RMixtComp-4.1.0/RMixtComp/tests/testthat/test.parameterPretreatment.R | 28 +- RMixtComp-4.1.0/RMixtComp/tests/testthat/test.run.R | 40 ++- RMixtComp-4.1.0/RMixtComp/tests/testthat/test.runWrapper.R | 102 +++++----- RMixtComp-4.1.0/RMixtComp/tests/testthat/test.slopeHeuristic.R |only RMixtComp-4.1.0/RMixtComp/vignettes |only 38 files changed, 250 insertions(+), 172 deletions(-)
Title: Connect to 'AWS Athena' using 'Boto3' ('DBI' Interface)
Description: Designed to be compatible with the R package 'DBI' (Database Interface)
when connecting to Amazon Web Service ('AWS') Athena <https://aws.amazon.com/athena/>.
To do this 'Python' 'Boto3' Software Development Kit ('SDK')
<https://boto3.amazonaws.com/v1/documentation/api/latest/index.html> is used as a driver.
Author: Dyfan Jones [aut, cre]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>
Diff between RAthena versions 1.6.0 dated 2019-12-19 and 1.7.0 dated 2020-01-07
RAthena-1.6.0/RAthena/tests/testthat/test-datatransfer.R |only RAthena-1.7.0/RAthena/DESCRIPTION | 13 - RAthena-1.7.0/RAthena/MD5 | 71 ++++---- RAthena-1.7.0/RAthena/NAMESPACE | 3 RAthena-1.7.0/RAthena/NEWS.md | 25 ++ RAthena-1.7.0/RAthena/R/Connection.R | 84 ++++++++-- RAthena-1.7.0/RAthena/R/DataTypes.R | 73 ++++++-- RAthena-1.7.0/RAthena/R/Driver.R | 3 RAthena-1.7.0/RAthena/R/File_Parser.R |only RAthena-1.7.0/RAthena/R/Options.R |only RAthena-1.7.0/RAthena/R/Result.R | 35 +--- RAthena-1.7.0/RAthena/R/View.R |only RAthena-1.7.0/RAthena/R/table.R | 6 RAthena-1.7.0/RAthena/R/util.R | 52 +----- RAthena-1.7.0/RAthena/inst |only RAthena-1.7.0/RAthena/man/AthenaWriteTables.Rd | 61 +++++-- RAthena-1.7.0/RAthena/man/Query.Rd | 11 - RAthena-1.7.0/RAthena/man/RAthena_options.Rd |only RAthena-1.7.0/RAthena/man/assume_role.Rd | 11 - RAthena-1.7.0/RAthena/man/dbConnect-AthenaDriver-method.Rd | 27 ++- RAthena-1.7.0/RAthena/man/dbDisconnect.Rd | 2 RAthena-1.7.0/RAthena/man/dbExistsTable.Rd | 2 RAthena-1.7.0/RAthena/man/dbFetch.Rd | 2 RAthena-1.7.0/RAthena/man/dbGetPartition.Rd | 2 RAthena-1.7.0/RAthena/man/dbGetQuery.Rd | 5 RAthena-1.7.0/RAthena/man/dbGetTables.Rd |only RAthena-1.7.0/RAthena/man/dbListFields.Rd | 2 RAthena-1.7.0/RAthena/man/dbListTables.Rd | 8 RAthena-1.7.0/RAthena/man/dbQuote.Rd | 2 RAthena-1.7.0/RAthena/man/dbRemoveTable.Rd | 5 RAthena-1.7.0/RAthena/man/dbShow.Rd | 2 RAthena-1.7.0/RAthena/man/db_copy_to.Rd | 18 +- RAthena-1.7.0/RAthena/man/db_save_query.Rd | 11 + RAthena-1.7.0/RAthena/man/install_boto.Rd | 9 - RAthena-1.7.0/RAthena/man/session_token.Rd | 9 - RAthena-1.7.0/RAthena/man/sqlCreateTable.Rd | 21 +- RAthena-1.7.0/RAthena/man/sqlData.Rd | 10 - RAthena-1.7.0/RAthena/man/work_group.Rd | 28 ++- RAthena-1.7.0/RAthena/tests/testthat/test-datatransfer-datatable.R |only RAthena-1.7.0/RAthena/tests/testthat/test-datatransfer-vroom.R |only 40 files changed, 401 insertions(+), 212 deletions(-)
Title: Parallel GLM
Description: Provides a parallel estimation method for generalized
linear models without compiling with a multithreaded LAPACK or BLAS.
Author: Benjamin Christoffersen [cre, aut],
Anthony Williams [cph],
Boost developers [cph]
Maintainer: Benjamin Christoffersen <boennecd@gmail.com>
Diff between parglm versions 0.1.3 dated 2019-03-18 and 0.1.4 dated 2020-01-07
DESCRIPTION | 6 +++--- MD5 | 24 ++++++++++++------------ NEWS.md | 8 ++++++++ R/parglm.R | 16 ++++++++++++++-- README.md | 6 +++--- build/vignette.rds |binary man/parglm.Rd | 13 +++++++++++-- src/Makevars | 1 + src/R_BLAS_LAPACK.cpp | 22 +++++++++++++++++----- src/arma_n_rcpp.h | 7 ------- src/parallel_glm.cpp | 16 ++++++++++++++-- src/parallel_qr.cpp | 5 ++++- tests/testthat/test_parglm_fams.R | 24 +++++++++++++++++++++++- 13 files changed, 110 insertions(+), 38 deletions(-)
Title: Recursive Partitioning for Structural Equation Models
Description: SEM Trees and SEM Forests -- an extension of model-based decision
trees and forests to Structural Equation Models (SEM). SEM trees hierarchically
split empirical data into homogeneous groups sharing similar data patterns
with respect to a SEM by recursively selecting optimal predictors of these
differences. SEM forests are an extension of SEM trees. They are ensembles of
SEM trees each built on a random sample of the original data. By aggregating
over a forest, we obtain measures of variable importance that are more robust
than measures from single trees.
Author: Andreas M. Brandmaier [aut, cre],
John J. Prindle [aut],
Manuel Arnold [aut]
Maintainer: Andreas M. Brandmaier <andy@brandmaier.de>
Diff between semtree versions 0.9.13 dated 2018-11-05 and 0.9.14 dated 2020-01-07
DESCRIPTION | 25 ++++++----- MD5 | 93 ++++++++++++++++++++++++++---------------- NAMESPACE | 24 ++++++++-- NEWS.md | 9 ++++ R/biodiversity.R | 6 +- R/coef.R |only R/contributions.R |only R/fitSubmodels.R | 4 - R/getHeight.R | 4 + R/getLeafs.R |only R/growTree.R | 45 ++++++++++++++++---- R/indexing.R |only R/isLeaf.R |only R/kl.R | 3 - R/logLik.R |only R/mergeForests.R | 1 R/naiveSplitScoreTest.R |only R/nobs.R |only R/plot.semforest.varimp.R | 4 - R/plot.semtree.R | 12 ----- R/plusOperator.R |only R/print.semforest.control.R | 2 R/print.semforest.varimp.R | 2 R/print.semtree.control.R | 6 ++ R/print.semtreeControl.R | 3 - R/safeRunAndEvaluate.R | 4 - R/scoreTest.R |only R/scoreTestcensored.R |only R/semtree.R | 24 +++++++++- R/semtree.control.R | 11 ++++ R/setData.R | 10 +--- R/stoppingRuleDefault.R | 4 + R/traverse.R | 2 R/traverseConditional.R | 8 --- R/varimp.R | 4 + README.md | 50 +++++++++------------- build |only inst/doc |only man/evaluateDataLikelihood.Rd | 5 -- man/evaluateTree.Rd | 5 -- man/getDepth.Rd |only man/getLeafs.Rd |only man/getNodeById.Rd | 5 -- man/getNumNodes.Rd | 5 -- man/getTerminalNodes.Rd | 5 -- man/isLeaf.Rd |only man/outliers.Rd | 4 - man/proximity.Rd | 5 -- man/semtree.control.Rd | 14 +++++- man/subforest.Rd | 5 -- man/varimp.Rd | 10 +--- tests/vim.R | 2 vignettes |only 53 files changed, 242 insertions(+), 183 deletions(-)
Title: Iterative Extrapolation of Species' Haplotype Accumulation
Curves for Genetic Diversity Assessment
Description: Performs iterative extrapolation of species' haplotype accumulation curves using a nonparametric stochastic (Monte Carlo) optimization method for assessment of specimen sampling completeness based on the approach of Phillips et al. (2015) <doi:10.1515/dna-2015-0008>, Phillips et al. (2019) <doi:10.1002/ece3.4757> and Phillips et al. (2020) <doi: 10.7717/peerj-cs.243>. Any genomic marker can be targeted to assess likely required specimen sample sizes. The method is well-suited to assess sampling sufficiency for DNA barcoding initiatives.
Author: Jarrett D. Phillips [aut, cre], Steven H. French [ctb]
Maintainer: Jarrett D. Phillips <phillipsjarrett1@gmail.com>
Diff between HACSim versions 1.0.4 dated 2019-09-14 and 1.0.5 dated 2020-01-07
DESCRIPTION | 12 - MD5 | 20 +-- R/HAC.object.R | 179 ++++++++++++++------------- R/HAC.sim.R | 316 ++++++++++++++++++++++++------------------------- R/HAC.simrep.R | 163 +++++++++++++------------ R/zzz.R | 8 - build/partial.rdb |binary man/HACHypothetical.Rd | 6 man/HACReal.Rd | 6 man/HACSim-package.Rd | 4 man/envr.Rd | 1 11 files changed, 376 insertions(+), 339 deletions(-)
Title: Apply Function to Elements in Parallel using Futures
Description: Implementations of apply(), by(), eapply(), lapply(), Map(), mapply(), replicate(), sapply(), tapply(), and vapply() that can be resolved using any future-supported backend, e.g. parallel on the local machine or distributed on a compute cluster. These future_*apply() functions come with the same pros and cons as the corresponding base-R *apply() functions but with the additional feature of being able to be processed via the future framework.
Author: Henrik Bengtsson [aut, cre, cph],
R Core Team [cph, ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between future.apply versions 1.3.0 dated 2019-06-18 and 1.4.0 dated 2020-01-07
DESCRIPTION | 14 +- MD5 | 55 ++++--- NAMESPACE | 1 NEWS | 21 +++ R/future.apply-package.R | 1 R/future_Map.R | 4 R/future_apply.R | 60 +++++++- R/future_by.R | 4 R/future_eapply.R | 4 R/future_lapply.R | 289 +++++++----------------------------------- R/future_mapply.R | 288 ++++++++--------------------------------- R/future_replicate.R | 5 R/future_sapply.R | 4 R/future_tapply.R | 5 R/future_vapply.R | 4 R/future_xapply.R |only R/rng.R | 7 - R/utils.R | 26 +++ build/vignette.rds |binary man/future.apply.Rd | 26 +-- man/future_apply.Rd | 23 +++ man/future_lapply.Rd | 104 ++++++++++++--- man/future_mapply.Rd | 34 +++- man/makeChunks.Rd | 8 - man/make_rng_seeds.Rd | 3 tests/future_lapply,RNG.R | 2 tests/future_lapply,globals.R | 27 +++ tests/future_lapply.R | 21 +++ tests/future_mapply.R | 13 + 29 files changed, 476 insertions(+), 577 deletions(-)
Title: Fingertips Data for Public Health
Description: Fingertips (<http://fingertips.phe.org.uk/>) contains data for many indicators of public health in England. The underlying data is now more easily accessible by making use of the API.
Author: Sebastian Fox [aut, cre],
Julian Flowers [aut, ctb],
Simon Thelwall [ctb] (<https://orcid.org/0000-0002-0434-2724>),
Duncan Gormansway [ctb],
Carl Ganz [ctb],
David Whiting [ctb],
Crown Copyright 2018 [cph]
Maintainer: Sebastian Fox <sebastian.fox@phe.gov.uk>
Diff between fingertipsR versions 0.2.9 dated 2019-09-25 and 1.0.0 dated 2020-01-07
fingertipsR-0.2.9/fingertipsR/tests/a-e.R |only fingertipsR-0.2.9/fingertipsR/vignettes/fingertips_paper_captions.R |only fingertipsR-1.0.0/fingertipsR/DESCRIPTION | 13 fingertipsR-1.0.0/fingertipsR/MD5 | 93 ++--- fingertipsR-1.0.0/fingertipsR/NAMESPACE | 5 fingertipsR-1.0.0/fingertipsR/NEWS.md | 11 fingertipsR-1.0.0/fingertipsR/R/area_types.R | 42 ++ fingertipsR-1.0.0/fingertipsR/R/deprivation_decile.R | 83 ++-- fingertipsR-1.0.0/fingertipsR/R/enhancements.R | 5 fingertipsR-1.0.0/fingertipsR/R/fingertipsR.R | 3 fingertipsR-1.0.0/fingertipsR/R/fingertips_data.R | 93 ++--- fingertipsR-1.0.0/fingertipsR/R/indicator_metadata.R | 2 fingertipsR-1.0.0/fingertipsR/R/indicators.R | 2 fingertipsR-1.0.0/fingertipsR/R/retrieve_data.R | 46 ++ fingertipsR-1.0.0/fingertipsR/README.md | 118 +++--- fingertipsR-1.0.0/fingertipsR/build/vignette.rds |binary fingertipsR-1.0.0/fingertipsR/inst/doc/lifeExpectancy.R | 18 - fingertipsR-1.0.0/fingertipsR/inst/doc/lifeExpectancy.html | 127 +++++-- fingertipsR-1.0.0/fingertipsR/inst/doc/selectIndicatorsRedRed.R | 12 fingertipsR-1.0.0/fingertipsR/inst/doc/selectIndicatorsRedRed.Rmd | 2 fingertipsR-1.0.0/fingertipsR/inst/doc/selectIndicatorsRedRed.html | 11 fingertipsR-1.0.0/fingertipsR/man/add_timestamp.Rd | 26 - fingertipsR-1.0.0/fingertipsR/man/area_types.Rd | 130 +++---- fingertipsR-1.0.0/fingertipsR/man/category_types.Rd | 88 ++--- fingertipsR-1.0.0/fingertipsR/man/deprivation_decile.Rd | 118 +++--- fingertipsR-1.0.0/fingertipsR/man/fingertipsR.Rd | 41 +- fingertipsR-1.0.0/fingertipsR/man/fingertips_data.Rd | 173 +++++----- fingertipsR-1.0.0/fingertipsR/man/fingertips_endpoint.Rd | 26 - fingertipsR-1.0.0/fingertipsR/man/fingertips_ensure_api_available.Rd | 32 - fingertipsR-1.0.0/fingertipsR/man/fingertips_redred.Rd | 65 +-- fingertipsR-1.0.0/fingertipsR/man/fingertips_stats.Rd | 40 +- fingertipsR-1.0.0/fingertipsR/man/get_fingertips_api.Rd | 26 - fingertipsR-1.0.0/fingertipsR/man/indicator_areatypes.Rd | 96 ++--- fingertipsR-1.0.0/fingertipsR/man/indicator_metadata.Rd | 129 +++---- fingertipsR-1.0.0/fingertipsR/man/indicator_order.Rd | 109 +++--- fingertipsR-1.0.0/fingertipsR/man/indicators.Rd | 104 +++--- fingertipsR-1.0.0/fingertipsR/man/indicators_unique.Rd | 95 ++--- fingertipsR-1.0.0/fingertipsR/man/nearest_neighbours.Rd | 128 +++---- fingertipsR-1.0.0/fingertipsR/man/profiles.Rd | 109 +++--- fingertipsR-1.0.0/fingertipsR/man/select_indicators.Rd | 40 +- fingertipsR-1.0.0/fingertipsR/tests/a-c.R |only fingertipsR-1.0.0/fingertipsR/tests/d.R |only fingertipsR-1.0.0/fingertipsR/tests/e.R |only fingertipsR-1.0.0/fingertipsR/tests/testthat/test-area_types.R | 9 fingertipsR-1.0.0/fingertipsR/tests/testthat/test-deprivation.R | 163 ++++++++- fingertipsR-1.0.0/fingertipsR/tests/testthat/test-enhancements.R | 8 fingertipsR-1.0.0/fingertipsR/tests/testthat/test-extract.R | 47 +- fingertipsR-1.0.0/fingertipsR/tests/testthat/test-indicators.R | 6 fingertipsR-1.0.0/fingertipsR/tests/testthat/test-metadata.R | 10 fingertipsR-1.0.0/fingertipsR/vignettes/selectIndicatorsRedRed.Rmd | 2 50 files changed, 1415 insertions(+), 1091 deletions(-)
Title: Mathematical Modeling of Infectious Disease Dynamics
Description: Tools for simulating mathematical models of infectious disease dynamics.
Epidemic model classes include deterministic compartmental models, stochastic
individual-contact models, and stochastic network models. Network models use the
robust statistical methods of exponential-family random graph models (ERGMs)
from the Statnet suite of software packages in R. Standard templates for epidemic
modeling include SI, SIR, and SIS disease types. EpiModel features
an API for extending these templates to address novel scientific research aims.
Author: Samuel Jenness [cre, aut],
Steven M. Goodreau [aut],
Martina Morris [aut],
Emily Beylerian [ctb],
Skye Bender-deMoll [ctb],
Kevin Weiss [ctb],
Shawnee Anderson [ctb]
Maintainer: Samuel Jenness <samuel.m.jenness@emory.edu>
Diff between EpiModel versions 1.7.3 dated 2019-08-29 and 1.7.5 dated 2020-01-07
DESCRIPTION | 12 ++++---- MD5 | 62 +++++++++++++++++++++--------------------- NEWS.md | 15 ++++++++++ R/EpiModel-package.r | 4 +- R/ErgmTerms.R | 21 +++++++------- R/net.mod.init.R | 6 +++- R/net.utils.R | 66 ++++++++++++++++++++++++++++++++++++++++----- R/plot.R | 7 +++- R/print.r | 52 ++++++++++++++++++++++++++++++++++- inst/doc/Intro.R | 4 +- inst/doc/Intro.html | 8 ++--- man/EpiModel-package.Rd | 4 +- man/as.data.frame.dcm.Rd | 3 -- man/as.data.frame.icm.Rd | 14 ++++++--- man/as.data.frame.netdx.Rd | 3 -- man/color_tea.Rd | 15 ++++++++-- man/control.dcm.Rd | 15 ++++++++-- man/control.icm.Rd | 24 ++++++++++++---- man/control.net.Rd | 50 +++++++++++++++++++++++++--------- man/dissolution_coefs.Rd | 66 ++++++++++++++++++++++++++++++++++++++++----- man/init.net.Rd | 3 -- man/merge.netsim.Rd | 12 ++++++-- man/netdx.Rd | 19 ++++++++++-- man/netest.Rd | 15 ++++++++-- man/param.dcm.Rd | 23 +++++++++++++-- man/param.icm.Rd | 23 +++++++++++++-- man/param.net.Rd | 21 ++++++++++++-- man/plot.dcm.Rd | 20 +++++++++++-- man/plot.icm.Rd | 30 +++++++++++++++++--- man/plot.netdx.Rd | 33 ++++++++++++++++++---- man/plot.netsim.Rd | 44 ++++++++++++++++++++++++------ man/plot.transmat.Rd | 3 -- 32 files changed, 548 insertions(+), 149 deletions(-)
Title: Distance Measure Based Judgment and Learning
Description: Implements various decision support tools related to the Econometrics & Technometrics.
Subroutines include correlation reliability test, Mahalanobis distance measure for outlier detection, combinatorial search (all possible subset regression), non-parametric efficiency analysis measures: DDF (directional distance function), DEA (data envelopment analysis), HDF (hyperbolic distance function), SBM (slack-based measure), and SF (shortage function), benchmarking, Malmquist productivity analysis, risk analysis, technology adoption model, new product target setting, etc.
Author: Dong-Joon Lim, PhD
Maintainer: Dong-Joon Lim <tgno3.com@gmail.com>
Diff between DJL versions 3.1 dated 2019-11-16 and 3.2 dated 2020-01-07
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS | 15 +++++++++++++++ R/target.arrival.dea.R | 33 +++++++++++++++++++++++++-------- R/target.arrival.hdf.R | 28 +++++++++++++++++++++++----- R/target.arrival.sf.R | 29 +++++++++++++++++++++++------ man/target.arrival.dea.Rd | 4 +++- man/target.arrival.hdf.Rd | 4 +++- man/target.arrival.sf.Rd | 4 +++- 9 files changed, 107 insertions(+), 34 deletions(-)
Title: Automate Data Exploration and Treatment
Description: Automated data exploration process for analytic tasks and predictive modeling, so
that users could focus on understanding data and extracting insights. The package scans and
analyzes each variable, and visualizes them with typical graphical techniques. Common
data processing methods are also available to treat and format data.
Author: Boxuan Cui [aut, cre]
Maintainer: Boxuan Cui <boxuancui@gmail.com>
Diff between DataExplorer versions 0.8.0 dated 2019-03-17 and 0.8.1 dated 2020-01-07
DataExplorer-0.8.0/DataExplorer/inst/rmd_template/d3.min.js |only DataExplorer-0.8.0/DataExplorer/vignettes/d3.min.js |only DataExplorer-0.8.1/DataExplorer/DESCRIPTION | 17 DataExplorer-0.8.1/DataExplorer/LICENSE | 2 DataExplorer-0.8.1/DataExplorer/MD5 | 124 DataExplorer-0.8.1/DataExplorer/NEWS.md | 15 DataExplorer-0.8.1/DataExplorer/R/configure_report.r | 2 DataExplorer-0.8.1/DataExplorer/R/create_report.r | 33 DataExplorer-0.8.1/DataExplorer/R/dummify.r | 150 DataExplorer-0.8.1/DataExplorer/R/plot_bar.r | 16 DataExplorer-0.8.1/DataExplorer/R/plot_boxplot.r | 113 DataExplorer-0.8.1/DataExplorer/R/plot_correlation.r | 8 DataExplorer-0.8.1/DataExplorer/R/plot_density.r | 101 DataExplorer-0.8.1/DataExplorer/R/plot_histogram.r | 95 DataExplorer-0.8.1/DataExplorer/R/plot_intro.r | 3 DataExplorer-0.8.1/DataExplorer/R/plot_missing.r | 16 DataExplorer-0.8.1/DataExplorer/R/plot_prcomp.r | 20 DataExplorer-0.8.1/DataExplorer/R/plot_qq.r | 126 DataExplorer-0.8.1/DataExplorer/R/plot_scatterplot.r | 99 DataExplorer-0.8.1/DataExplorer/R/split_columns.r | 2 DataExplorer-0.8.1/DataExplorer/README.md | 4 DataExplorer-0.8.1/DataExplorer/build/vignette.rds |binary DataExplorer-0.8.1/DataExplorer/inst/doc/dataexplorer-intro.R | 118 DataExplorer-0.8.1/DataExplorer/inst/doc/dataexplorer-intro.Rmd | 27 DataExplorer-0.8.1/DataExplorer/inst/doc/dataexplorer-intro.html | 1848 ++++++++-- DataExplorer-0.8.1/DataExplorer/inst/rmd_template/report.rmd | 81 DataExplorer-0.8.1/DataExplorer/man/configure_report.Rd | 45 DataExplorer-0.8.1/DataExplorer/man/create_report.Rd | 35 DataExplorer-0.8.1/DataExplorer/man/figures/README-plot-bar-1.png |binary DataExplorer-0.8.1/DataExplorer/man/figures/README-plot-bar-prepare-1.png |binary DataExplorer-0.8.1/DataExplorer/man/figures/README-plot-bar-prepare-2.png |binary DataExplorer-0.8.1/DataExplorer/man/figures/README-plot-density-1.png |binary DataExplorer-0.8.1/DataExplorer/man/figures/README-plot-histogram-1.png |binary DataExplorer-0.8.1/DataExplorer/man/figures/README-plot-intro-1.png |binary DataExplorer-0.8.1/DataExplorer/man/figures/README-plot-missing-1.png |binary DataExplorer-0.8.1/DataExplorer/man/figures/README-plot-qq-1.png |binary DataExplorer-0.8.1/DataExplorer/man/figures/README-plot-qq-cut-1.png |binary DataExplorer-0.8.1/DataExplorer/man/figures/README-plot_boxplot-1.png |binary DataExplorer-0.8.1/DataExplorer/man/figures/README-plot_correlation-1.png |binary DataExplorer-0.8.1/DataExplorer/man/figures/README-plot_prcomp-1.png |binary DataExplorer-0.8.1/DataExplorer/man/figures/README-plot_prcomp-2.png |binary DataExplorer-0.8.1/DataExplorer/man/figures/README-plot_scatterplot-1.png |binary DataExplorer-0.8.1/DataExplorer/man/group_category.Rd | 11 DataExplorer-0.8.1/DataExplorer/man/plotDataExplorer.grid.Rd | 12 DataExplorer-0.8.1/DataExplorer/man/plotDataExplorer.multiple.Rd | 11 DataExplorer-0.8.1/DataExplorer/man/plotDataExplorer.single.Rd | 3 DataExplorer-0.8.1/DataExplorer/man/plot_bar.Rd | 16 DataExplorer-0.8.1/DataExplorer/man/plot_boxplot.Rd | 26 DataExplorer-0.8.1/DataExplorer/man/plot_correlation.Rd | 16 DataExplorer-0.8.1/DataExplorer/man/plot_density.Rd | 32 DataExplorer-0.8.1/DataExplorer/man/plot_histogram.Rd | 27 DataExplorer-0.8.1/DataExplorer/man/plot_intro.Rd | 9 DataExplorer-0.8.1/DataExplorer/man/plot_missing.Rd | 16 DataExplorer-0.8.1/DataExplorer/man/plot_prcomp.Rd | 22 DataExplorer-0.8.1/DataExplorer/man/plot_qq.Rd | 20 DataExplorer-0.8.1/DataExplorer/man/plot_scatterplot.Rd | 30 DataExplorer-0.8.1/DataExplorer/man/plot_str.Rd | 9 DataExplorer-0.8.1/DataExplorer/tests/testthat/test-configure-report.r | 4 DataExplorer-0.8.1/DataExplorer/tests/testthat/test-create-report.r | 59 DataExplorer-0.8.1/DataExplorer/tests/testthat/test-dummify.r | 33 DataExplorer-0.8.1/DataExplorer/tests/testthat/test-plot-boxplot.r |only DataExplorer-0.8.1/DataExplorer/tests/testthat/test-plot-prcomp.r | 16 DataExplorer-0.8.1/DataExplorer/tests/testthat/test-plot-scatterplot.r |only DataExplorer-0.8.1/DataExplorer/tests/testthat/test-split-columns.r | 44 DataExplorer-0.8.1/DataExplorer/vignettes/dataexplorer-intro.Rmd | 27 65 files changed, 2626 insertions(+), 917 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-07-21 1.0.2-2.1
Title: Utilities for Handling Strings and Text
Description: Utilities for handling character vectors
that store human-readable text (either plain or with
markup, such as HTML or LaTeX). The package provides,
in particular, functions that help with the
preparation of plain-text reports, e.g. for expanding
and aligning strings that form the lines of such
reports. The package also provides generic functions for
transforming R objects to HTML and to plain text.
Author: Enrico Schumann [aut, cre] (<https://orcid.org/0000-0001-7601-6576>)
Maintainer: Enrico Schumann <es@enricoschumann.net>
Diff between textutils versions 0.1-11 dated 2019-05-01 and 0.2-0 dated 2020-01-07
textutils-0.1-11/textutils/README.md |only textutils-0.1-11/textutils/inst/unitTests |only textutils-0.2-0/textutils/DESCRIPTION | 13 ++-- textutils-0.2-0/textutils/MD5 | 27 ++++----- textutils-0.2-0/textutils/NEWS | 12 ++++ textutils-0.2-0/textutils/R/functions.R | 58 +++++++++++++++----- textutils-0.2-0/textutils/build/partial.rdb |binary textutils-0.2-0/textutils/build/vignette.rds |binary textutils-0.2-0/textutils/inst/doc/btable.pdf |binary textutils-0.2-0/textutils/inst/tinytest |only textutils-0.2-0/textutils/man/HTMLdecode.Rd | 42 +++++++++++--- textutils-0.2-0/textutils/man/here.Rd | 2 textutils-0.2-0/textutils/man/toLatex.data.frame.Rd | 11 ++- textutils-0.2-0/textutils/man/trim.Rd | 4 - textutils-0.2-0/textutils/tests |only 15 files changed, 121 insertions(+), 48 deletions(-)
Title: Sequentially-Allocated Latent Structure Optimization
Description: Point estimation for partition distributions using the sequentially-allocated latent structure optimization (SALSO) method to minimize the expectation of the Binder loss or the lower bound of the expectation of the variation of information loss. The SALSO method was presented at the workshop "Bayesian Nonparametric Inference: Dependence Structures and their Applications" in Oaxaca, Mexico on December 6, 2017. See <https://www.birs.ca/events/2017/5-day-workshops/17w5060/schedule>.
Author: David B. Dahl
Maintainer: David B. Dahl <dahl@stat.byu.edu>
Diff between salso versions 0.1.9 dated 2019-11-29 and 0.1.11 dated 2020-01-07
DESCRIPTION | 8 +++---- MD5 | 8 +++---- NEWS | 3 ++ src/rustlib/Cargo.lock | 51 ++++++++++++++++++++++++------------------------- src/rustlib/Cargo.toml | 5 ++-- 5 files changed, 40 insertions(+), 35 deletions(-)
Title: Testing and Plotting Procedures for Biostatistics
Description: Contains miscellaneous functions useful in biostatistics, mostly univariate and multivariate testing procedures with a special emphasis on permutation tests. Many functions intend to simplify user's life by shortening existing procedures or by implementing plotting functions that can be used with as many methods from different packages as possible.
Author: Maxime Herv<e9>
Maintainer: Maxime Herv<e9> <maxime.herve@univ-rennes1.fr>
Diff between RVAideMemoire versions 0.9-73 dated 2019-03-26 and 0.9-74 dated 2020-01-07
RVAideMemoire-0.9-73/RVAideMemoire/R/CvM.test.R |only RVAideMemoire-0.9-73/RVAideMemoire/man/CvM.test.Rd |only RVAideMemoire-0.9-74/RVAideMemoire/DESCRIPTION | 16 +- RVAideMemoire-0.9-74/RVAideMemoire/MD5 | 36 +++--- RVAideMemoire-0.9-74/RVAideMemoire/NAMESPACE | 11 - RVAideMemoire-0.9-74/RVAideMemoire/NEWS | 7 + RVAideMemoire-0.9-74/RVAideMemoire/R/MVA.ident.R | 21 +++ RVAideMemoire-0.9-74/RVAideMemoire/R/MVA.pairplot.R | 6 - RVAideMemoire-0.9-74/RVAideMemoire/R/MVA.scoreplot.R | 8 - RVAideMemoire-0.9-74/RVAideMemoire/R/MVA.trajplot.R | 6 - RVAideMemoire-0.9-74/RVAideMemoire/R/byf.hist.R | 34 +++--- RVAideMemoire-0.9-74/RVAideMemoire/R/deprecated.R | 6 - RVAideMemoire-0.9-74/RVAideMemoire/R/dhist.R | 13 -- RVAideMemoire-0.9-74/RVAideMemoire/R/multtest.gp.bin.R |only RVAideMemoire-0.9-74/RVAideMemoire/R/pairwise.perm.manova.R | 56 ++++++++-- RVAideMemoire-0.9-74/RVAideMemoire/R/zzz.R | 2 RVAideMemoire-0.9-74/RVAideMemoire/man/RVAideMemoire-package.Rd | 4 RVAideMemoire-0.9-74/RVAideMemoire/man/byf.hist.Rd | 6 - RVAideMemoire-0.9-74/RVAideMemoire/man/deprecated.Rd | 4 RVAideMemoire-0.9-74/RVAideMemoire/man/multtest.gp.bin.Rd |only RVAideMemoire-0.9-74/RVAideMemoire/man/pairwise.perm.manova.Rd | 10 + 21 files changed, 173 insertions(+), 73 deletions(-)
Title: Preprocessing Tools to Create Design Matrices
Description: An extensible framework to create and preprocess
design matrices. Recipes consist of one or more data manipulation
and analysis "steps". Statistical parameters for the steps can
be estimated from an initial data set and then applied to
other data sets. The resulting design matrices can then be used
as inputs into statistical or machine learning models.
Author: Max Kuhn [aut, cre],
Hadley Wickham [aut],
RStudio [cph]
Maintainer: Max Kuhn <max@rstudio.com>
Diff between recipes versions 0.1.8 dated 2019-12-18 and 0.1.9 dated 2020-01-07
DESCRIPTION | 8 MD5 | 25 +- NAMESPACE | 4 NEWS.md | 6 R/relevel.R |only R/zzz.R | 9 inst/doc/Custom_Steps.html | 450 +++++++++++++++++++----------------- inst/doc/Dummies.html | 474 ++++++++++++++++++++------------------ inst/doc/Ordering.html | 27 ++ inst/doc/Roles.html | 370 +++++++++++++++-------------- inst/doc/Selecting_Variables.html | 176 ++++++++------ inst/doc/Simple_Example.html | 338 ++++++++++++++------------- inst/doc/Skipping.html | 110 +++++--- man/step_relevel.Rd |only tests/testthat/test_relevel.R |only 15 files changed, 1105 insertions(+), 892 deletions(-)
Title: A Common API to Modeling and Analysis Functions
Description: A common interface is provided to allow users to specify a model without having to remember the different argument names across different functions or computational engines (e.g. 'R', 'Spark', 'Stan', etc).
Author: Max Kuhn [aut, cre],
Davis Vaughan [aut],
RStudio [cph]
Maintainer: Max Kuhn <max@rstudio.com>
Diff between parsnip versions 0.0.4 dated 2019-11-02 and 0.0.5 dated 2020-01-07
parsnip-0.0.4/parsnip/R/data.R |only parsnip-0.0.4/parsnip/data |only parsnip-0.0.4/parsnip/man/check_times.Rd |only parsnip-0.0.4/parsnip/man/lending_club.Rd |only parsnip-0.0.4/parsnip/man/wa_churn.Rd |only parsnip-0.0.5/parsnip/DESCRIPTION | 12 parsnip-0.0.5/parsnip/MD5 | 149 ++++------ parsnip-0.0.5/parsnip/NAMESPACE | 7 parsnip-0.0.5/parsnip/NEWS.md | 21 + parsnip-0.0.5/parsnip/R/arguments.R | 7 parsnip-0.0.5/parsnip/R/boost_tree_data.R | 2 parsnip-0.0.5/parsnip/R/descriptors.R | 1 parsnip-0.0.5/parsnip/R/fit.R | 11 parsnip-0.0.5/parsnip/R/linear_reg_data.R | 9 parsnip-0.0.5/parsnip/R/logistic_reg_data.R | 6 parsnip-0.0.5/parsnip/R/misc.R | 20 + parsnip-0.0.5/parsnip/R/mlp.R | 20 - parsnip-0.0.5/parsnip/R/mlp_data.R | 4 parsnip-0.0.5/parsnip/R/multinom_reg.R | 13 parsnip-0.0.5/parsnip/R/multinom_reg_data.R | 90 +++++- parsnip-0.0.5/parsnip/R/predict.R | 9 parsnip-0.0.5/parsnip/R/varying.R | 14 parsnip-0.0.5/parsnip/build/parsnip.pdf |binary parsnip-0.0.5/parsnip/inst/doc/parsnip_Intro.R | 14 parsnip-0.0.5/parsnip/inst/doc/parsnip_Intro.html | 131 +++++--- parsnip-0.0.5/parsnip/man/C5.0_train.Rd | 3 parsnip-0.0.5/parsnip/man/add_on_exports.Rd |only parsnip-0.0.5/parsnip/man/boost_tree.Rd | 29 + parsnip-0.0.5/parsnip/man/decision_tree.Rd | 20 + parsnip-0.0.5/parsnip/man/descriptors.Rd | 1 parsnip-0.0.5/parsnip/man/fit.Rd | 7 parsnip-0.0.5/parsnip/man/keras_mlp.Rd | 20 - parsnip-0.0.5/parsnip/man/linear_reg.Rd | 10 parsnip-0.0.5/parsnip/man/logistic_reg.Rd | 10 parsnip-0.0.5/parsnip/man/mars.Rd | 19 + parsnip-0.0.5/parsnip/man/mlp.Rd | 24 + parsnip-0.0.5/parsnip/man/model_spec.Rd | 2 parsnip-0.0.5/parsnip/man/multi_predict.Rd | 21 - parsnip-0.0.5/parsnip/man/multinom_reg.Rd | 16 - parsnip-0.0.5/parsnip/man/nearest_neighbor.Rd | 8 parsnip-0.0.5/parsnip/man/predict.model_fit.Rd | 3 parsnip-0.0.5/parsnip/man/rand_forest.Rd | 18 - parsnip-0.0.5/parsnip/man/rpart_train.Rd | 11 parsnip-0.0.5/parsnip/man/surv_reg.Rd | 3 parsnip-0.0.5/parsnip/man/svm_poly.Rd | 22 + parsnip-0.0.5/parsnip/man/svm_rbf.Rd | 14 parsnip-0.0.5/parsnip/man/type_sum.model_spec.Rd | 6 parsnip-0.0.5/parsnip/man/xgb_train.Rd | 15 - parsnip-0.0.5/parsnip/tests/testthat/helper-objects.R |only parsnip-0.0.5/parsnip/tests/testthat/test_boost_tree_C50.R | 6 parsnip-0.0.5/parsnip/tests/testthat/test_boost_tree_spark.R | 5 parsnip-0.0.5/parsnip/tests/testthat/test_boost_tree_xgboost.R | 9 parsnip-0.0.5/parsnip/tests/testthat/test_failed_models.R | 2 parsnip-0.0.5/parsnip/tests/testthat/test_fit_interfaces.R | 4 parsnip-0.0.5/parsnip/tests/testthat/test_linear_reg.R | 5 parsnip-0.0.5/parsnip/tests/testthat/test_linear_reg_glmnet.R | 11 parsnip-0.0.5/parsnip/tests/testthat/test_linear_reg_keras.R | 1 parsnip-0.0.5/parsnip/tests/testthat/test_linear_reg_spark.R | 5 parsnip-0.0.5/parsnip/tests/testthat/test_logistic_reg.R | 5 parsnip-0.0.5/parsnip/tests/testthat/test_logistic_reg_glmnet.R | 14 parsnip-0.0.5/parsnip/tests/testthat/test_logistic_reg_keras.R | 1 parsnip-0.0.5/parsnip/tests/testthat/test_logistic_reg_spark.R | 5 parsnip-0.0.5/parsnip/tests/testthat/test_logistic_reg_stan.R | 2 parsnip-0.0.5/parsnip/tests/testthat/test_mars.R | 7 parsnip-0.0.5/parsnip/tests/testthat/test_mlp_keras.R | 9 parsnip-0.0.5/parsnip/tests/testthat/test_mlp_nnet.R | 9 parsnip-0.0.5/parsnip/tests/testthat/test_multinom_reg_glmnet.R | 11 parsnip-0.0.5/parsnip/tests/testthat/test_multinom_reg_nnet.R |only parsnip-0.0.5/parsnip/tests/testthat/test_multinom_reg_spark.R | 5 parsnip-0.0.5/parsnip/tests/testthat/test_nearest_neighbor_kknn.R | 5 parsnip-0.0.5/parsnip/tests/testthat/test_predict_formats.R | 3 parsnip-0.0.5/parsnip/tests/testthat/test_rand_forest_randomForest.R | 10 parsnip-0.0.5/parsnip/tests/testthat/test_rand_forest_ranger.R | 10 parsnip-0.0.5/parsnip/tests/testthat/test_rand_forest_spark.R | 5 parsnip-0.0.5/parsnip/tests/testthat/test_surv_reg_flexsurv.R | 5 parsnip-0.0.5/parsnip/tests/testthat/test_surv_reg_survreg.R | 6 parsnip-0.0.5/parsnip/vignettes/articles/Models.Rmd | 65 +++- parsnip-0.0.5/parsnip/vignettes/articles/Scratch.Rmd | 6 78 files changed, 670 insertions(+), 383 deletions(-)
Title: A Toolkit for Year-Quarter, Year-Month and Year-Isoweek Dates
Description: S3 classes and methods to create and work
with year-quarter, year-month and year-isoweek vectors. Basic
arithmetic operations (such as adding and subtracting) are supported,
as well as formatting and converting to and from standard R date
types.
Author: Stefan Fleck [aut, cre] (<https://orcid.org/0000-0003-3344-9851>)
Maintainer: Stefan Fleck <stefan.b.fleck@gmail.com>
Diff between dint versions 2.1.1 dated 2019-12-02 and 2.1.2 dated 2020-01-07
DESCRIPTION | 8 ++--- MD5 | 18 ++++++------ NEWS.md | 5 +++ R/scale_date_xx.R | 16 ++++++++-- R/zoo-compat.R | 6 ++-- README.md | 39 ++++++++++++++++---------- inst/WORDLIST | 2 + inst/doc/dint.R | 34 +++++++++++----------- inst/doc/dint.html | 29 ++++++++++--------- tests/testthat/manual_tests/ggplot_scales.Rmd | 3 +- 10 files changed, 96 insertions(+), 64 deletions(-)
Title: Classification and Regression Training
Description: Misc functions for training and plotting classification and
regression models.
Author: Max Kuhn [aut, cre],
Jed Wing [ctb],
Steve Weston [ctb],
Andre Williams [ctb],
Chris Keefer [ctb],
Allan Engelhardt [ctb],
Tony Cooper [ctb],
Zachary Mayer [ctb],
Brenton Kenkel [ctb],
R Core Team [ctb],
Michael Benesty [ctb],
Reynald Lescarbeau [ctb],
Andrew Ziem [ctb],
Luca Scrucca [ctb],
Yuan Tang [ctb],
Can Candan [ctb],
Tyler Hunt [ctb]
Maintainer: Max Kuhn <mxkuhn@gmail.com>
Diff between caret versions 6.0-84 dated 2019-04-27 and 6.0-85 dated 2020-01-07
DESCRIPTION | 58 ++- MD5 | 172 ++++----- NAMESPACE | 1 R/adaptive.R | 10 R/bag.R | 2 R/bagEarth.R | 30 - R/bagFDA.R | 2 R/calibration.R | 2 R/caret-package.R | 12 R/classDist.R | 4 R/confusionMatrix.R | 2 R/createDataPartition.R | 20 - R/gafs.R | 8 R/modelLookup.R | 40 +- R/postResample.R | 36 - R/preProcess.R | 16 R/resamples.R | 6 R/safs.R | 6 R/sampling.R | 133 +++---- R/train.default.R | 10 build/vignette.rds |binary inst/NEWS.Rd | 14 inst/doc/caret.html | 608 ++++++++++++++++---------------- inst/models/models.RData |binary man/BoxCoxTrans.Rd | 10 man/avNNet.Rd | 30 + man/bag.Rd | 16 man/bagEarth.Rd | 17 man/bagFDA.Rd | 15 man/calibration.Rd | 11 man/caret-internal.Rd | 24 - man/caretFuncs.Rd | 8 man/cars.Rd | 8 man/classDist.Rd | 3 man/confusionMatrix.Rd | 21 - man/confusionMatrix.train.Rd | 8 man/createDataPartition.Rd | 12 man/diff.resamples.Rd | 14 man/dotplot.diff.resamples.Rd | 3 man/downSample.Rd | 2 man/dummyVars.Rd | 3 man/featurePlot.Rd | 9 man/findCorrelation.Rd | 9 man/gafs.default.Rd | 36 + man/gafs_initial.Rd | 2 man/icr.formula.Rd | 3 man/knn3.Rd | 3 man/learning_curve_dat.Rd | 10 man/lift.Rd | 25 + man/maxDissim.Rd | 12 man/modelLookup.Rd | 2 man/nearZeroVar.Rd | 11 man/panel.needle.Rd | 18 man/pcaNNet.Rd | 15 man/plot.gafs.Rd | 15 man/plot.rfe.Rd | 11 man/plot.train.Rd | 26 + man/plot.varImp.train.Rd | 9 man/plsda.Rd | 6 man/postResample.Rd | 2 man/prcomp.resamples.Rd | 3 man/preProcess.Rd | 27 + man/predict.bagEarth.Rd | 2 man/predict.train.Rd | 23 - man/print.confusionMatrix.Rd | 9 man/print.train.Rd | 10 man/recall.Rd | 19 - man/resamples.Rd | 6 man/rfe.Rd | 36 + man/rfeControl.Rd | 22 - man/safs.Rd | 6 man/safsControl.Rd | 45 +- man/sbf.Rd | 3 man/sbfControl.Rd | 18 man/sensitivity.Rd | 39 +- man/train.Rd | 35 + man/trainControl.Rd | 42 +- man/twoClassSim.Rd | 34 + man/varImp.Rd | 6 man/varImp.gafs.Rd | 8 man/xyplot.resamples.Rd | 65 ++- tests/testthat/test_misc.R | 36 + tests/testthat/test_models_bagEarth.R | 2 tests/testthat/test_multiclassSummary.R | 78 +++- tests/testthat/test_resamples.R | 43 +- tests/testthat/test_spatialSign.R | 16 tests/testthat/test_twoClassSummary.R | 6 87 files changed, 1398 insertions(+), 862 deletions(-)
Title: Bayesian Linear Regression
Description: Bayesian Linear Regression.
Author: Gustavo de los Campos, Paulino Perez Rodriguez,
Maintainer: Paulino Perez Rodriguez <perpdgo@colpos.mx>
Diff between BLR versions 1.5 dated 2018-08-23 and 1.6 dated 2020-01-07
DESCRIPTION | 10 +++---- MD5 | 10 +++---- NAMESPACE | 1 R/BLRw_c.R | 78 +++++++++++++++++++++++++++++++++++++++++++------------ inst/history.txt | 9 +++++- man/wheat.Rd | 2 - 6 files changed, 81 insertions(+), 29 deletions(-)
Title: Multiple Hypothesis Testing
Description: Seven different methods for multiple testing problems. The SGoF-type methods and the BH and BY false discovery rate controlling procedures.
Author: Irene Castro Conde and Jacobo de Una Alvarez
Maintainer: Irene Castro Conde <irene.castro@uvigo.es>
Diff between sgof versions 2.3 dated 2016-04-18 and 2.3.1 dated 2020-01-07
DESCRIPTION | 10 +++---- MD5 | 10 +++---- NAMESPACE | 1 R/Discrete.SGoF.R | 65 ++++++++++++++++++++++++++++++++++++++++++++++++++- man/Discrete.SGoF.Rd | 9 +++---- man/sgof-package.Rd | 5 +-- 6 files changed, 80 insertions(+), 20 deletions(-)
Title: Fit and Compare Species-Area Relationship Models Using
Multimodel Inference
Description: Implements the basic elements of the multi-model
inference paradigm for up to twenty species-area relationship models (SAR), using simple
R list-objects and functions, as in Triantis et al. 2012 <DOI:10.1111/j.1365-2699.2011.02652.x>.
The package is scalable and users can easily create their own model and data objects. Additional
SAR related functions are provided.
Author: Thomas J. Matthews [aut, cre] (<https://orcid.org/0000-0002-7624-244X>),
Francois Guilhaumon [aut] (<https://orcid.org/0000-0003-4707-8932>),
Kevin Cazelles [rev] (<https://orcid.org/0000-0001-6619-9874>)
Maintainer: Thomas J. Matthews <txm676@gmail.com>
Diff between sars versions 1.2.0 dated 2019-07-25 and 1.2.1 dated 2020-01-07
DESCRIPTION | 6 MD5 | 62 +-- NEWS.md | 4 R/class_plot.R | 70 ++- R/mod_linear_power.R | 16 R/sar_asymp.R | 9 R/sar_betap.R | 9 R/sar_chapman.R | 9 R/sar_epm1.R | 9 R/sar_epm2.R | 9 R/sar_gompertz.R | 9 R/sar_heleg.R | 9 R/sar_koba.R | 9 R/sar_loga.R | 9 R/sar_mmf.R | 9 R/sar_monod.R | 9 R/sar_negexpo.R | 9 R/sar_p1.R | 9 R/sar_p2.R | 9 R/sar_power.R | 9 R/sar_powerR.R | 9 R/sar_ratio.R | 9 R/sar_weibull3.R | 9 R/sar_weibull4.R | 9 README.md | 117 ++---- build/vignette.rds |binary inst/doc/sars-r-package.R | 16 inst/doc/sars-r-package.html | 765 +++++++++++++++--------------------------- inst/model_factory.R | 13 man/plot.multi.Rd | 48 +- tests/testthat/test_lin_pow.R | 11 tests/testthat/test_power.R | 9 32 files changed, 658 insertions(+), 650 deletions(-)
Title: Log Rotation and Conditional Backups
Description: Conditionally rotate or back-up files based on
their size or the date of the last backup; inspired by the 'Linux'
utility 'logrotate'.
Author: Stefan Fleck [aut, cre] (<https://orcid.org/0000-0003-3344-9851>)
Maintainer: Stefan Fleck <stefan.b.fleck@gmail.com>
Diff between rotor versions 0.2.3 dated 2019-06-17 and 0.2.4 dated 2020-01-07
DESCRIPTION | 8 +- MD5 | 18 ++--- NEWS.md | 7 +- R/utils-sfmisc.R | 41 +++++++++++ README.md | 58 ++++++++-------- man/BackupQueue.Rd | 14 ++-- man/rotate.Rd | 131 +++++++++++++++++++++++++++----------- man/rotor-package.Rd | 2 tests/testthat/test_BackupQueue.R | 8 +- tests/testthat/test_rotate_date.R | 6 - 10 files changed, 196 insertions(+), 97 deletions(-)
Title: Download DBnomics Data
Description: R access to hundreds of millions data series from DBnomics API
(<https://db.nomics.world/>).
Author: Sebastien Galais [cre, ctb],
Thomas Brand [aut]
Maintainer: Sebastien Galais <s915.stem@gmail.com>
Diff between rdbnomics versions 0.5.0 dated 2019-09-23 and 0.5.1 dated 2020-01-07
rdbnomics-0.5.0/rdbnomics/tests/testthat/test-rdb_by_api_link.R |only rdbnomics-0.5.1/rdbnomics/DESCRIPTION | 8 rdbnomics-0.5.1/rdbnomics/MD5 | 46 - rdbnomics-0.5.1/rdbnomics/NAMESPACE | 3 rdbnomics-0.5.1/rdbnomics/NEWS.md | 8 rdbnomics-0.5.1/rdbnomics/R/dbnomics.R |only rdbnomics-0.5.1/rdbnomics/R/dot_rdb.R |only rdbnomics-0.5.1/rdbnomics/R/rdb.R | 249 ++++- rdbnomics-0.5.1/rdbnomics/R/rdb_by_api_link.R | 434 ---------- rdbnomics-0.5.1/rdbnomics/R/rdb_last_updates.R | 1 rdbnomics-0.5.1/rdbnomics/R/rdb_providers.R | 1 rdbnomics-0.5.1/rdbnomics/R/rdbnomics.R | 5 rdbnomics-0.5.1/rdbnomics/R/sysdata.rda |binary rdbnomics-0.5.1/rdbnomics/README.md | 149 +-- rdbnomics-0.5.1/rdbnomics/build/vignette.rds |binary rdbnomics-0.5.1/rdbnomics/inst/doc/rdbnomics.R | 355 +++++--- rdbnomics-0.5.1/rdbnomics/inst/doc/rdbnomics.Rmd | 257 ++++- rdbnomics-0.5.1/rdbnomics/inst/doc/rdbnomics.html | 374 +++++--- rdbnomics-0.5.1/rdbnomics/man/dbnomics.Rd |only rdbnomics-0.5.1/rdbnomics/man/rdb.Rd | 409 +++++---- rdbnomics-0.5.1/rdbnomics/man/rdb_by_api_link.Rd | 301 +++--- rdbnomics-0.5.1/rdbnomics/man/rdb_last_updates.Rd | 115 +- rdbnomics-0.5.1/rdbnomics/man/rdb_providers.Rd | 117 +- rdbnomics-0.5.1/rdbnomics/man/rdbnomics.Rd | 17 rdbnomics-0.5.1/rdbnomics/tests/testthat/test-rdb.R | 36 rdbnomics-0.5.1/rdbnomics/vignettes/rdbnomics.Rmd | 257 ++++- 26 files changed, 1754 insertions(+), 1388 deletions(-)
Title: Interface to the 'PM4py' Process Mining Library
Description: Interface to 'PM4py' <http://pm4py.org>, a process mining library
in 'Python'. This package uses the 'reticulate' package to act as a bridge
between 'PM4Py' and the 'R' package 'bupaR'. It provides several process
discovery algorithms, evaluation measures, and alignments.
Author: Felix Mannhardt [aut, cre]
Maintainer: Felix Mannhardt <felix.mannhardt@sintef.no>
Diff between pm4py versions 1.0.1 dated 2019-03-10 and 1.2.7 dated 2020-01-07
DESCRIPTION | 8 MD5 | 53 ++-- NAMESPACE | 8 NEWS.md | 7 R/conformance.R | 6 R/discovery.R | 20 + R/install.R | 8 R/package.R | 31 ++ R/petrinet.R | 80 ++++++ R/pm4py.R | 6 R/utils.R | 1 R/version.R | 11 README.md | 10 inst/python/pm4pytools/__pycache__/__init__.cpython-36.pyc |only inst/python/pm4pytools/__pycache__/log.cpython-36.pyc |only man/as_pm4py_marking.Rd | 58 ++-- man/conformance.Rd | 131 +++++----- man/discovery.Rd | 144 ++++++----- man/evaluation.Rd | 160 +++++++------ man/install_pm4py.Rd | 70 +++-- man/parameters.Rd | 86 +++--- man/petrinet_check_relaxed_soundness.Rd |only man/petrinet_check_wfnet.Rd |only man/petrinet_synchronous_product.Rd | 108 ++++---- man/pm4py.Rd | 76 +++--- man/pm4py_available.Rd | 38 +-- man/pm4py_version.Rd |only man/reexports.Rd | 32 +- man/version.Rd | 31 +- man/write_pnml.Rd | 81 +++--- 30 files changed, 733 insertions(+), 531 deletions(-)
Title: Protein Quantification in Mass Spectrometry-Based Proteomics
Description: An implementation of the maximal
peptide ratio extraction module of the MaxLFQ algorithm by
Cox et al. (2014) <doi:10.1074/mcp.M113.031591> in a complete
pipeline for processing proteomics data in data-independent acquisition mode.
It offers additional options for protein quantification using the N most intense
fragment ions, using all
fragment ions, and a wrapper for the median polish algorithm by Tukey (1977, ISBN:0201076160).
Author: Thang Pham [aut, cre, cph, ctb]
(<https://orcid.org/0000-0003-0333-2492>),
Alex Henneman [ctb] (<https://orcid.org/0000-0002-3746-4410>)
Maintainer: Thang Pham <t.pham@amsterdamumc.nl>
Diff between iq versions 1.0 dated 2019-11-15 and 1.3 dated 2020-01-07
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NAMESPACE | 2 +- R/iq.R | 27 ++++++++++++++++----------- inst/doc/iq.html | 4 ++-- 5 files changed, 26 insertions(+), 21 deletions(-)
Title: Functions to Support the ICES Transparent Assessment Framework
Description: Functions to support the ICES Transparent Assessment Framework
<https://taf.ices.dk> to organize data, methods, and results used in ICES
assessments. ICES is an organization facilitating international collaboration
in marine science.
Author: Arni Magnusson [aut, cre],
Colin Millar [aut],
Alexandros Kokkalis [ctb],
Ibrahim Umar [ctb]
Maintainer: Arni Magnusson <arni.magnusson@ices.dk>
Diff between icesTAF versions 3.3-1 dated 2019-12-11 and 3.3-2 dated 2020-01-07
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NEWS | 8 ++++++++ R/process.bib.R | 19 +++++++++++-------- data/catage.long.rda |binary data/catage.taf.rda |binary data/catage.xtab.rda |binary data/summary.taf.rda |binary data/taf.colors.rda |binary man/process.bib.Rd | 7 +++---- 10 files changed, 35 insertions(+), 25 deletions(-)
Title: Extra Recipes for Encoding Categorical Predictors
Description: Predictors can be converted to one or more numeric representations using simple generalized linear models <arXiv:1611.09477> or nonlinear models <arXiv:1604.06737>. All encoding methods are supervised.
Author: Max Kuhn [aut, cre],
RStudio [cph]
Maintainer: Max Kuhn <max@rstudio.com>
Diff between embed versions 0.0.4 dated 2019-09-15 and 0.0.5 dated 2020-01-07
DESCRIPTION | 19 +++++----- MD5 | 43 +++++++++++++----------- NAMESPACE | 4 +- NEWS.md | 12 ++++++ R/bayes.R | 1 R/glm.R | 1 R/lme.R | 1 R/tf.R | 16 ++++++--- R/tunable.R |only R/woe.R | 34 +++++++++---------- man/step_embed.Rd | 47 ++++++++++++++++++-------- man/step_lencode_bayes.Rd | 17 +++++++-- man/step_lencode_glm.Rd | 14 ++++++- man/step_lencode_mixed.Rd | 15 ++++++-- man/step_umap.Rd | 23 ++++++++++--- man/step_woe.Rd | 17 +++++++-- man/tunable.step_embed.Rd |only tests/testthat/test_helpers.R |only tests/testthat/test_mixed.R | 11 ++---- tests/testthat/test_no_pooling.R | 14 +++---- tests/testthat/test_pooling.R | 69 ++++++++++++++++++++++----------------- tests/testthat/test_tf.R | 15 +++----- tests/testthat/test_umap.R | 10 +---- tests/testthat/test_woe.R | 9 ++--- 24 files changed, 241 insertions(+), 151 deletions(-)
Title: Estimate Quantitative Genetics Parameters from Generalised
Linear Mixed Models
Description: Compute various quantitative genetics parameters from a Generalised Linear Mixed Model (GLMM) estimates. Especially, it yields the observed phenotypic mean, phenotypic variance and additive genetic variance.
Author: Pierre de Villemereuil <bonamy@horus.ens.fr>
Maintainer: Pierre de Villemereuil <bonamy@horus.ens.fr>
Diff between QGglmm versions 0.7.3 dated 2019-12-06 and 0.7.4 dated 2020-01-07
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 1 + build/partial.rdb |binary build/vignette.rds |binary inst/doc/QGglmmHowTo.Rnw | 2 +- inst/doc/QGglmmHowTo.pdf |binary vignettes/QGglmmHowTo.Rnw | 2 +- 8 files changed, 14 insertions(+), 13 deletions(-)
Title: 'DataRobot' Predictive Modeling API
Description: For working with the 'DataRobot' predictive modeling platform's API <https://www.datarobot.com/>.
Author: Ron Pearson [aut], Zachary Deane-Mayer [aut], David Chudzicki [aut], Dallin Akagi [aut], Sergey Yurgenson [aut], Thakur Raj Anand [aut], Peter Hurford [aut]
Maintainer: Peter Hurford <api-maintainer@datarobot.com>
Diff between datarobot versions 2.15.0 dated 2019-11-18 and 2.16.0 dated 2020-01-07
DESCRIPTION | 6 - MD5 | 115 ++++++++++++++-------------- NAMESPACE | 4 NEWS | 27 ++++++ R/Blueprints.R | 4 R/ComplianceDocumentation.R | 7 + R/ConnectToDataRobot.R | 4 R/DataRobotRequests.R | 4 R/Enums.R | 6 - R/GetPredictions.R | 75 +++++++++++------- R/ModelRecommendations.R | 3 R/Models.R | 96 ++++++++++++++--------- R/ParetoFront.R | 2 R/Partitions.R | 8 - R/PauseQueue.R | 2 R/PredictionDatasets.R | 33 ++++++-- R/PredictionExplanations.R | 2 R/PrimeModels.R | 2 R/SeriesAccuracy.R |only R/UnpauseQueue.R | 2 R/ViewWebModel.R | 22 +++-- R/ViewWebProject.R | 22 ----- inst/doc/AdvancedTuning.html | 4 inst/doc/AdvancedVignette.html | 6 - inst/doc/Calendars.html | 4 inst/doc/ComparingSubsets.html | 4 inst/doc/ComplianceDocumentation.html | 4 inst/doc/DatetimePartitionedProjects.html | 4 inst/doc/IntroductionToDataRobot.html | 4 inst/doc/Multiclass.html | 4 inst/doc/PartialDependence.html | 4 inst/doc/PredictionExplanations.html | 4 inst/doc/RatingTables.html | 4 inst/doc/TimeSeries.Rmd | 16 +++ inst/doc/TimeSeries.html | 16 +++ inst/doc/TrainingPredictions.html | 4 inst/doc/VariableImportance.Rmd | 2 inst/doc/VariableImportance.html | 6 - man/CreateDatetimePartitionSpecification.Rd | 4 man/DownloadComplianceDocumentation.Rd | 5 - man/DownloadPredictionExplanations.Rd | 2 man/DownloadSeriesAccuracy.Rd |only man/GenerateDatetimePartition.Rd | 4 man/GetBlueprintDocumentation.Rd | 2 man/GetDatetimeModel.Rd | 86 ++++++++++++-------- man/GetDatetimePartition.Rd | 4 man/GetParetoFront.Rd | 2 man/GetPredictions.Rd | 14 ++- man/GetPrimeModelFromJobId.Rd | 2 man/GetSeriesAccuracy.Rd |only man/GetSeriesAccuracyForModel.Rd |only man/JobType.Rd | 2 man/ListPredictions.Rd | 4 man/Predict.Rd | 45 +++++++--- man/RecommendedModelType.Rd | 4 man/RequestFrozenModel.Rd | 2 man/RequestPredictions.Rd | 30 ++++++- man/RequestSeriesAccuracy.Rd |only tests/testthat/test-StartAutopilot.R | 2 vignettes/TimeSeries.Rmd | 16 +++ vignettes/VariableImportance.Rmd | 2 61 files changed, 482 insertions(+), 286 deletions(-)
Title: Fast Implementation of Dijkstra Algorithm
Description: Calculation of distances, shortest paths and isochrones on weighted graphs using several variants of Dijkstra algorithm.
Proposed algorithms are unidirectional Dijkstra (Dijkstra, E. W. (1959) <doi:10.1007/BF01386390>),
bidirectional Dijkstra (Goldberg, Andrew & Fonseca F. Werneck, Renato (2005) <https://pdfs.semanticscholar.org/0761/18dfbe1d5a220f6ac59b4de4ad07b50283ac.pdf>),
A* search (P. E. Hart, N. J. Nilsson et B. Raphael (1968) <doi:10.1109/TSSC.1968.300136>),
new bidirectional A* (Pijls & Post (2009) <http://repub.eur.nl/pub/16100/ei2009-10.pdf>),
Contraction hierarchies (R. Geisberger, P. Sanders, D. Schultes and D. Delling (2008) <doi:10.1007/978-3-540-68552-4_24>),
PHAST (D. Delling, A.Goldberg, A. Nowatzyk, R. Werneck (2011) <doi:10.1016/j.jpdc.2012.02.007>).
Author: Vincent Larmet
Maintainer: Vincent Larmet <larmet.vincent@gmail.com>
Diff between cppRouting versions 1.2 dated 2019-09-30 and 2.0 dated 2020-01-07
cppRouting-1.2/cppRouting/src/simplify3.cpp |only cppRouting-2.0/cppRouting/DESCRIPTION | 24 cppRouting-2.0/cppRouting/MD5 | 104 ++-- cppRouting-2.0/cppRouting/NAMESPACE | 4 cppRouting-2.0/cppRouting/NEWS.md | 18 cppRouting-2.0/cppRouting/R/RcppExports.R | 88 ++- cppRouting-2.0/cppRouting/R/contract.R |only cppRouting-2.0/cppRouting/R/get_detour.R | 61 +- cppRouting-2.0/cppRouting/R/get_distance_mat.R | 116 +++- cppRouting-2.0/cppRouting/R/get_distance_pair.R | 168 ++---- cppRouting-2.0/cppRouting/R/get_isochrone.R | 48 + cppRouting-2.0/cppRouting/R/get_multi_paths.R | 32 + cppRouting-2.0/cppRouting/R/get_path_pair.R | 125 +++-- cppRouting-2.0/cppRouting/R/graphs.R | 21 cppRouting-2.0/cppRouting/R/simplify.R | 74 -- cppRouting-2.0/cppRouting/R/to_df.R | 3 cppRouting-2.0/cppRouting/inst/CITATION |only cppRouting-2.0/cppRouting/inst/doc/cpprouting.R | 2 cppRouting-2.0/cppRouting/inst/doc/cpprouting.Rmd | 53 +- cppRouting-2.0/cppRouting/inst/doc/cpprouting.html | 62 +- cppRouting-2.0/cppRouting/man/cppRouting-package.Rd | 15 cppRouting-2.0/cppRouting/man/cpp_contract.Rd |only cppRouting-2.0/cppRouting/man/cpp_simplify.Rd | 17 cppRouting-2.0/cppRouting/man/get_detour.Rd | 18 cppRouting-2.0/cppRouting/man/get_distance_matrix.Rd | 16 cppRouting-2.0/cppRouting/man/get_distance_pair.Rd | 22 cppRouting-2.0/cppRouting/man/get_isochrone.Rd | 14 cppRouting-2.0/cppRouting/man/get_multi_paths.Rd | 10 cppRouting-2.0/cppRouting/man/get_path_pair.Rd | 27 - cppRouting-2.0/cppRouting/man/makegraph.Rd | 7 cppRouting-2.0/cppRouting/src/Astar.cpp | 20 cppRouting-2.0/cppRouting/src/Astar_path.cpp | 28 - cppRouting-2.0/cppRouting/src/RcppExports.cpp | 323 +++++++++++-- cppRouting-2.0/cppRouting/src/bidir.cpp | 19 cppRouting-2.0/cppRouting/src/bidir_astar2.cpp | 40 - cppRouting-2.0/cppRouting/src/bidir_astar_path.cpp | 42 - cppRouting-2.0/cppRouting/src/bidir_mat3.cpp |only cppRouting-2.0/cppRouting/src/bidir_mod3.cpp |only cppRouting-2.0/cppRouting/src/bidir_mod_path.cpp |only cppRouting-2.0/cppRouting/src/bidir_path.cpp | 41 - cppRouting-2.0/cppRouting/src/contract_ED4.cpp |only cppRouting-2.0/cppRouting/src/detour.cpp | 22 cppRouting-2.0/cppRouting/src/dijkstra_early_stop.cpp | 10 cppRouting-2.0/cppRouting/src/dijkstra_early_stop_path.cpp | 17 cppRouting-2.0/cppRouting/src/dijkstra_mat.cpp | 11 cppRouting-2.0/cppRouting/src/dijkstra_multi_path.cpp | 17 cppRouting-2.0/cppRouting/src/duplicated.cpp | 15 cppRouting-2.0/cppRouting/src/functions_one_to_all_ED4.cpp |only cppRouting-2.0/cppRouting/src/functions_one_to_all_ED4.h |only cppRouting-2.0/cppRouting/src/isochrone.cpp | 15 cppRouting-2.0/cppRouting/src/isochrone_multi.cpp | 29 - cppRouting-2.0/cppRouting/src/par_NBA.cpp |only cppRouting-2.0/cppRouting/src/par_astar.cpp |only cppRouting-2.0/cppRouting/src/par_bidir2.cpp |only cppRouting-2.0/cppRouting/src/par_bidir_mat2.cpp |only cppRouting-2.0/cppRouting/src/par_bidir_mod.cpp |only cppRouting-2.0/cppRouting/src/par_dijkstra.cpp |only cppRouting-2.0/cppRouting/src/par_dijkstra_mat.cpp |only cppRouting-2.0/cppRouting/src/phast3.cpp |only cppRouting-2.0/cppRouting/src/phast_par.cpp |only cppRouting-2.0/cppRouting/src/simp.cpp |only cppRouting-2.0/cppRouting/src/simp.h |only cppRouting-2.0/cppRouting/src/simplify5.cpp |only cppRouting-2.0/cppRouting/vignettes/cpprouting.Rmd | 53 +- 64 files changed, 1177 insertions(+), 674 deletions(-)
Title: Cox Proportional Hazards Regression for Right-Truncated Data
Description: Fits Cox regression based on retrospectively ascertained times-to-event. The method uses Inverse-Probability-Weighting estimating equations.
Author: Bella Vakulenko-Lagun, Micha Mandel, Rebecca A. Betensky
Maintainer: Bella Vakulenko-Lagun <bella.vakulenko-lagun@mail.huji.ac.il>
Diff between coxrt versions 1.0.2 dated 2019-07-31 and 1.0.3 dated 2020-01-07
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NAMESPACE | 1 + R/coxrt.R | 1 + R/coxrt_functions.R | 4 ++-- inst/doc/coxrt-vignette.Rmd | 2 +- inst/doc/coxrt-vignette.html | 15 ++++++++------- man/coxph.RT.Rd | 2 +- vignettes/coxrt-vignette.Rmd | 2 +- vignettes/references.bib | 3 ++- 10 files changed, 30 insertions(+), 26 deletions(-)
Title: Logging for 'dplyr' and 'tidyr' Functions
Description: Provides feedback about 'dplyr' and 'tidyr' operations.
Author: Benjamin Elbers [aut, cre] (<https://orcid.org/0000-0001-5392-3448>),
Damiano Oldoni [ctb] (<https://orcid.org/0000-0003-3445-7562>)
Maintainer: Benjamin Elbers <elbersb@gmail.com>
Diff between tidylog versions 0.2.0 dated 2019-09-02 and 1.0.0 dated 2020-01-07
tidylog-0.2.0/tidylog/R/gather_spread.R |only tidylog-0.2.0/tidylog/man/gather.Rd |only tidylog-0.2.0/tidylog/man/spread.Rd |only tidylog-0.2.0/tidylog/tests/testthat/test_gather_spread.R |only tidylog-0.2.0/tidylog/tests/testthat/test_lintr.R |only tidylog-1.0.0/tidylog/DESCRIPTION | 21 +-- tidylog-1.0.0/tidylog/MD5 | 47 +++--- tidylog-1.0.0/tidylog/NAMESPACE | 12 + tidylog-1.0.0/tidylog/NEWS.md | 14 +- tidylog-1.0.0/tidylog/R/filter.R | 26 +++ tidylog-1.0.0/tidylog/R/group_by.R | 20 ++ tidylog-1.0.0/tidylog/R/longer_wider.R |only tidylog-1.0.0/tidylog/R/mutate.R | 13 + tidylog-1.0.0/tidylog/R/rename.R |only tidylog-1.0.0/tidylog/R/summarize.R | 6 tidylog-1.0.0/tidylog/README.md | 35 +++-- tidylog-1.0.0/tidylog/man/filter.Rd | 12 + tidylog-1.0.0/tidylog/man/group_by.Rd | 7 - tidylog-1.0.0/tidylog/man/pivot_longer.Rd |only tidylog-1.0.0/tidylog/man/rename.Rd |only tidylog-1.0.0/tidylog/man/summarize.Rd | 3 tidylog-1.0.0/tidylog/tests/testthat/test_filter.R | 32 ++++ tidylog-1.0.0/tidylog/tests/testthat/test_group_by.R | 18 ++ tidylog-1.0.0/tidylog/tests/testthat/test_join.R | 97 ++++++++++---- tidylog-1.0.0/tidylog/tests/testthat/test_longer_wider.R |only tidylog-1.0.0/tidylog/tests/testthat/test_mutate.R | 23 +++ tidylog-1.0.0/tidylog/tests/testthat/test_rename.R |only tidylog-1.0.0/tidylog/tests/testthat/test_select.R | 2 tidylog-1.0.0/tidylog/tests/testthat/test_summarize.R | 11 + tidylog-1.0.0/tidylog/tests/testthat/test_tidylog.R | 5 30 files changed, 312 insertions(+), 92 deletions(-)
Title: 'SQLite' Interface for R
Description: Embeds the 'SQLite' database engine in R and
provides an interface compliant with the 'DBI' package. The source for
the 'SQLite' engine is included.
Author: Kirill Müller [aut, cre] (<https://orcid.org/0000-0002-1416-3412>),
Hadley Wickham [aut],
David A. James [aut],
Seth Falcon [aut],
SQLite Authors [ctb] (for the included SQLite sources),
Liam Healy [ctb] (for the included SQLite sources),
R Consortium [fnd],
RStudio [cph]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>
Diff between RSQLite versions 2.1.5 dated 2019-12-18 and 2.2.0 dated 2020-01-07
DESCRIPTION | 14 +++++++------- MD5 | 11 ++++++----- NEWS.md | 5 +++++ R/names.R | 9 +-------- R/pkgconfig.R |only build/vignette.rds |binary tests/testthat/helper-DBItest.R | 2 ++ 7 files changed, 21 insertions(+), 20 deletions(-)
Title: Analyzing Case-Parent Triad and/or Case-Control Data with SNP
Haplotypes
Description: Performs genetic association analyses of case-parent triad (trio) data with multiple markers. It can also incorporate complete or incomplete control triads, for instance independent control children. Estimation is based on haplotypes, for instance SNP haplotypes, even though phase is not known from the genetic data. 'Haplin' estimates relative risk (RR + conf.int.) and p-value associated with each haplotype. It uses maximum likelihood estimation to make optimal use of data from triads with missing genotypic data, for instance if some SNPs has not been typed for some individuals. 'Haplin' also allows estimation of effects of maternal haplotypes and parent-of-origin effects, particularly appropriate in perinatal epidemiology. 'Haplin' allows special models, like X-inactivation, to be fitted on the X-chromosome. A GxE analysis allows testing interactions between environment and all estimated genetic effects. The models were originally described in Gjessing, HK and Lie, RT (2006) <doi:10.1111/j.1529-8817.2005.00218.x>.
Author: Hakon K. Gjessing [aut, cre],
Miriam Gjerdevik [ctb] (functions 'lineByLine' and 'convertPed'),
Julia Romanowska [ctb] (<https://orcid.org/0000-0001-6733-1953>, new
data format, parallelisation, new documentation),
Oivind Skare [ctb] (TDT tests)
Maintainer: Hakon K. Gjessing <hakon.gjessing@uib.no>
Diff between Haplin versions 7.1.0 dated 2019-04-17 and 7.2.2 dated 2020-01-07
Haplin-7.1.0/Haplin/inst/doc/hapRelEff.R |only Haplin-7.1.0/Haplin/inst/doc/hapRelEff.Rmd |only Haplin-7.1.0/Haplin/inst/doc/hapRelEff.html |only Haplin-7.1.0/Haplin/vignettes/hapRelEff.Rmd |only Haplin-7.1.0/Haplin/vignettes/submit_haplin_cluster_rmpi.sh |only Haplin-7.2.2/Haplin/DESCRIPTION | 27 Haplin-7.2.2/Haplin/MD5 | 201 Haplin-7.2.2/Haplin/NAMESPACE | 11 Haplin-7.2.2/Haplin/R/JohnsonFit.R |only Haplin-7.2.2/Haplin/R/convertPed.R | 2 Haplin-7.2.2/Haplin/R/f.a.asymp.R | 2 Haplin-7.2.2/Haplin/R/f.b.asymp.R | 2 Haplin-7.2.2/Haplin/R/f.beta.haplo.freq.asymp.R | 2 Haplin-7.2.2/Haplin/R/f.check.pars.R | 4 Haplin-7.2.2/Haplin/R/f.check.pars0.R | 2 Haplin-7.2.2/Haplin/R/f.check.unique.ids.R |only Haplin-7.2.2/Haplin/R/f.coefnames.R | 2 Haplin-7.2.2/Haplin/R/f.create.snp.names.R |only Haplin-7.2.2/Haplin/R/f.data.R | 2 Haplin-7.2.2/Haplin/R/f.debug.pvalues.R | 2 Haplin-7.2.2/Haplin/R/f.get.data.R | 2 Haplin-7.2.2/Haplin/R/f.get.gen.data.cols.R | 4 Haplin-7.2.2/Haplin/R/f.get.marker.names.R | 2 Haplin-7.2.2/Haplin/R/f.grid.asymp.R | 2 Haplin-7.2.2/Haplin/R/f.hapArg.R | 2 Haplin-7.2.2/Haplin/R/f.hapTests.R | 2 Haplin-7.2.2/Haplin/R/f.insert.row.R | 4 Haplin-7.2.2/Haplin/R/f.make.ff.data.out.R | 1 Haplin-7.2.2/Haplin/R/f.make.out.filename.R | 16 Haplin-7.2.2/Haplin/R/f.mat.asymp.R | 1 Haplin-7.2.2/Haplin/R/f.match.R | 2 Haplin-7.2.2/Haplin/R/f.ped.to.mfc.new.R | 21 Haplin-7.2.2/Haplin/R/f.prob.asymp.R | 2 Haplin-7.2.2/Haplin/R/f.var.covar.asymp.R | 2 Haplin-7.2.2/Haplin/R/genDataGetPart.R | 35 Haplin-7.2.2/Haplin/R/genDataLoad.R | 6 Haplin-7.2.2/Haplin/R/genDataPreprocess.R | 66 Haplin-7.2.2/Haplin/R/genDataRead.R | 44 Haplin-7.2.2/Haplin/R/getChildren.R |only Haplin-7.2.2/Haplin/R/getDyads_or_Triads.R |only Haplin-7.2.2/Haplin/R/getFathers.R |only Haplin-7.2.2/Haplin/R/getMothers.R |only Haplin-7.2.2/Haplin/R/gxe.R | 4 Haplin-7.2.2/Haplin/R/hapCovar.R | 12 Haplin-7.2.2/Haplin/R/hapPower.R | 2 Haplin-7.2.2/Haplin/R/hapPowerAsymp.R | 2 Haplin-7.2.2/Haplin/R/hapRun.R | 2 Haplin-7.2.2/Haplin/R/hapSim.R | 2 Haplin-7.2.2/Haplin/R/haplin.R | 2 Haplin-7.2.2/Haplin/R/haplinSlide.R | 33 Haplin-7.2.2/Haplin/R/haplinSlide0.R | 30 Haplin-7.2.2/Haplin/R/haplinStrat.R | 4 Haplin-7.2.2/Haplin/R/haptable.gxe.R | 2 Haplin-7.2.2/Haplin/R/nfam.R | 3 Haplin-7.2.2/Haplin/R/nindiv.R | 3 Haplin-7.2.2/Haplin/R/nsnps.R | 3 Haplin-7.2.2/Haplin/R/output.R | 2 Haplin-7.2.2/Haplin/R/postTest.R | 2 Haplin-7.2.2/Haplin/R/print.gxe.R | 2 Haplin-7.2.2/Haplin/R/print.haplin.data.R | 6 Haplin-7.2.2/Haplin/R/showGen.R | 26 Haplin-7.2.2/Haplin/R/showPheno.R | 3 Haplin-7.2.2/Haplin/R/showSNPnames.R |only Haplin-7.2.2/Haplin/R/suest.R | 2 Haplin-7.2.2/Haplin/R/zzz.R | 2 Haplin-7.2.2/Haplin/build/vignette.rds |binary Haplin-7.2.2/Haplin/inst/doc/A_Haplin_intro_installation.R | 24 Haplin-7.2.2/Haplin/inst/doc/A_Haplin_intro_installation.html | 548 -- Haplin-7.2.2/Haplin/inst/doc/B_Reading_data.R | 154 Haplin-7.2.2/Haplin/inst/doc/B_Reading_data.Rmd | 73 Haplin-7.2.2/Haplin/inst/doc/B_Reading_data.html | 1094 +--- Haplin-7.2.2/Haplin/inst/doc/C_Running_Haplin.R | 199 Haplin-7.2.2/Haplin/inst/doc/C_Running_Haplin.Rmd | 39 Haplin-7.2.2/Haplin/inst/doc/C_Running_Haplin.html | 2500 ++++------ Haplin-7.2.2/Haplin/inst/doc/D_Running_Haplin_on_cluster.R | 66 Haplin-7.2.2/Haplin/inst/doc/D_Running_Haplin_on_cluster.html | 594 -- Haplin-7.2.2/Haplin/inst/doc/E_hapRelEff.R |only Haplin-7.2.2/Haplin/inst/doc/E_hapRelEff.Rmd |only Haplin-7.2.2/Haplin/inst/doc/E_hapRelEff.html |only Haplin-7.2.2/Haplin/inst/extdata/submit_haplin_cluster_rmpi.sh |only Haplin-7.2.2/Haplin/man/create.missingness.matrix.Rd |only Haplin-7.2.2/Haplin/man/f.check.unique.ids.Rd |only Haplin-7.2.2/Haplin/man/f.convert.matrix.ff.Rd | 76 Haplin-7.2.2/Haplin/man/f.create.snp.names.Rd |only Haplin-7.2.2/Haplin/man/f.extract.ff.numeric.Rd | 44 Haplin-7.2.2/Haplin/man/f.get.gen.data.cols.Rd | 44 Haplin-7.2.2/Haplin/man/finishParallelRun.Rd | 26 Haplin-7.2.2/Haplin/man/genDataGetPart.Rd | 188 Haplin-7.2.2/Haplin/man/genDataLoad.Rd | 62 Haplin-7.2.2/Haplin/man/genDataPreprocess.Rd | 165 Haplin-7.2.2/Haplin/man/genDataRead.Rd | 205 Haplin-7.2.2/Haplin/man/getChildren.Rd |only Haplin-7.2.2/Haplin/man/getDyads.Rd |only Haplin-7.2.2/Haplin/man/getFathers.Rd |only Haplin-7.2.2/Haplin/man/getFullTriads.Rd |only Haplin-7.2.2/Haplin/man/getMothers.Rd |only Haplin-7.2.2/Haplin/man/hapPowerAsymp.Rd | 3 Haplin-7.2.2/Haplin/man/haplin.Rd | 7 Haplin-7.2.2/Haplin/man/haplinSlide.Rd | 4 Haplin-7.2.2/Haplin/man/haplinStrat.Rd | 5 Haplin-7.2.2/Haplin/man/initParallelRun.Rd | 34 Haplin-7.2.2/Haplin/man/nfam.Rd | 38 Haplin-7.2.2/Haplin/man/nindiv.Rd | 50 Haplin-7.2.2/Haplin/man/nsnps.Rd | 50 Haplin-7.2.2/Haplin/man/pJohnson.Rd |only Haplin-7.2.2/Haplin/man/plot.haplinSlide.Rd | 104 Haplin-7.2.2/Haplin/man/plot.haplinStrat.Rd | 102 Haplin-7.2.2/Haplin/man/plotPValues.Rd | 90 Haplin-7.2.2/Haplin/man/showGen.Rd | 78 Haplin-7.2.2/Haplin/man/showPheno.Rd | 56 Haplin-7.2.2/Haplin/man/showSNPnames.Rd |only Haplin-7.2.2/Haplin/src |only Haplin-7.2.2/Haplin/vignettes/B_Reading_data.Rmd | 73 Haplin-7.2.2/Haplin/vignettes/C_Running_Haplin.Rmd | 39 Haplin-7.2.2/Haplin/vignettes/E_hapRelEff.Rmd |only 115 files changed, 3407 insertions(+), 4049 deletions(-)
Title: Read and Write 'FreeSurfer' Neuroimaging File Formats
Description: Provides functions to read and write data from neuroimaging files in 'FreeSurfer' <http://freesurfer.net/> binary formats. This includes the following file formats: 1) MGH/MGZ format files, which can contain multi-dimensional images or other data. Typically they contain time-series of three-dimensional brain scans acquired by magnetic resonance imaging (MRI). They can also contain vertex-wise measures of surface morphometry data. The MGH format is named after the Massachusetts General Hospital, and the MGZ format is a compressed version of the same format. 2) 'FreeSurfer' morphometry data files in binary 'curv' format. These contain vertex-wise surface measures, i.e., one scalar value for each vertex of a brain surface mesh. These are typically values like the cortical thickness or brain surface area at each vertex. 3) Annotation file format. This contains a brain surface parcellation derived from a cortical atlas. 4) Surface file format. Contains a brain surface mesh, given by a list of vertices and a list of faces.
Author: Tim Schäfer [aut, cre] (<https://orcid.org/0000-0002-3683-8070>)
Maintainer: Tim Schäfer <ts+code@rcmd.org>
Diff between freesurferformats versions 0.1.6 dated 2019-11-27 and 0.1.7 dated 2020-01-07
DESCRIPTION | 6 +- MD5 | 56 ++++++++++++--------- NAMESPACE | 7 ++ R/read_fs_annot.R | 45 +++++++++++++++-- R/read_fs_label.R | 59 +++++++++++++++++++++- R/read_fs_mgh.R | 9 +++ R/read_fs_surface.R | 33 +++++++++++- R/write_fs_annot.R | 85 ++++++++++++++++++++------------- R/write_fs_label.R | 25 ++++++++- R/write_fs_mgh.R | 4 - R/write_fs_surface.R | 11 ++++ build/vignette.rds |binary man/is.fs.annot.Rd |only man/is.fs.label.Rd |only man/is.fs.surface.Rd |only man/print.fs.annot.Rd |only man/print.fs.label.Rd |only man/print.fs.surface.Rd |only man/read.fs.annot.Rd | 8 ++- man/read.fs.label.Rd | 9 ++- man/read.fs.mgh.Rd | 4 + man/read.fs.surface.Rd | 4 + man/write.fs.annot.Rd | 31 +++++++++--- man/write.fs.label.Rd | 17 +++++- man/write.fs.surface.Rd | 12 ++++ tests/testthat.R | 10 +++ tests/testthat/test-read-fs-annot.R | 3 + tests/testthat/test-read-fs-label.R | 30 +++++++++++ tests/testthat/test-read-fs-surface.R | 26 +++++++--- tests/testthat/test-write-fs-annot.R | 14 +++++ tests/testthat/test-write-fs-label.R | 19 +++++++ tests/testthat/test-write-fs-surface.R | 3 + 32 files changed, 428 insertions(+), 102 deletions(-)
More information about freesurferformats at CRAN
Permanent link
Title: Distance Metrics for Trees Generated by Congreve and Lamsdell
Description: Includes the 100 datasets simulated by Congreve and Lamsdell (2016)
<doi:10.1111/pala.12236>, and analyses of the partition and quartet distance of
reconstructed trees from the generative tree, as analysed by Smith (2019)
<doi:10.1098/rsbl.2018.0632>.
Author: Martin R. Smith [aut, cre, cph]
(<https://orcid.org/0000-0001-5660-1727>),
Curtis R. Congreve [cph, dtc],
James C. Lamsdell [cph, dtc]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between CongreveLamsdell2016 versions 1.0.1 dated 2019-02-07 and 1.0.2 dated 2020-01-07
DESCRIPTION | 11 - MD5 | 36 +++--- NEWS.md | 4 R/data.R | 3 R/plots.R | 1 R/points.R | 4 README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/Compare-methods.R | 204 +++++++++++++++++------------------- inst/doc/Compare-methods.Rmd | 204 +++++++++++++++++------------------- inst/doc/Compare-methods.pdf |binary inst/doc/Compare-node-supports.R | 44 ++++--- inst/doc/Compare-node-supports.Rmd | 44 ++++--- inst/doc/Compare-node-supports.pdf |binary inst/doc/Conduct-analyses.pdf |binary man/clReferenceTree.Rd | 3 vignettes/Compare-methods.Rmd | 204 +++++++++++++++++------------------- vignettes/Compare-node-supports.Rmd | 44 ++++--- 19 files changed, 404 insertions(+), 404 deletions(-)
More information about CongreveLamsdell2016 at CRAN
Permanent link
Title: Antarctic Spatial Data Manipulation
Description: Loads and creates spatial data, including layers and tools that are relevant
to the activities of the Commission for the Conservation of Antarctic Marine Living
Resources. Provides two categories of functions: load functions and create functions.
Load functions are used to import existing spatial layers from the online CCAMLR GIS
such as the ASD boundaries. Create functions are used to create layers from user data
such as polygons and grids.
Author: Stephane Thanassekos [aut, cre],
Keith Reid [aut],
Lucy Robinson [aut],
Michael D. Sumner [ctb],
Roger Bivand [ctb]
Maintainer: Stephane Thanassekos <stephane.thanassekos@ccamlr.org>
Diff between CCAMLRGIS versions 3.0.0 dated 2019-12-18 and 3.0.1 dated 2020-01-07
DESCRIPTION | 14 ++++--- MD5 | 44 +++++++++++----------- NEWS.md | 4 ++ R/CCAMLRGIS_DataDescription.R | 12 +++++- R/load.R | 27 +++++++++---- README.md | 31 ++++++++++++++- build/vignette.rds |binary data/Coast.RData |binary data/SmallBathy.RData |binary inst/doc/CCAMLRGIS.R | 4 +- inst/doc/CCAMLRGIS.Rmd | 4 +- inst/doc/CCAMLRGIS.html | 84 +++++++++++++++++++++++++++--------------- man/CCAMLRp.Rd | 3 + man/Coast.Rd | 3 + man/Depth_cols.Rd | 3 + man/Depth_cuts.Rd | 3 + man/GridData.Rd | 3 + man/Labels.Rd | 5 ++ man/LineData.Rd | 3 + man/PointData.Rd | 3 + man/PolyData.Rd | 3 + man/SmallBathy.Rd | 3 + vignettes/CCAMLRGIS.Rmd | 4 +- 23 files changed, 184 insertions(+), 76 deletions(-)
Title: Gene Set Enrichment Analysis via Integration of Metabolic
Networks and RNA-Seq Data
Description: Integrates metabolic networks and RNA-seq data to construct condition-specific series of metabolic sub-networks and applies to gene set enrichment analysis (Tran et al. (2018) <doi:10.1093/bioinformatics/bty929>).
Author: Van Du T. Tran [aut, cre], Marco Pagni [aut]
Maintainer: Van Du T. Tran <thuong.tran@sib.swiss>
Diff between metaboGSE versions 1.2.2 dated 2019-12-12 and 1.2.3 dated 2020-01-07
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NAMESPACE | 1 + R/metaboGSE.R | 3 +-- inst/NEWS.Rd | 8 ++++++++ inst/doc/metaboGSE.pdf |binary 6 files changed, 19 insertions(+), 11 deletions(-)
Title: Interfaces for Loading Datasets
Description: Visual interface for loading datasets in RStudio from all installed (unloaded) packages, also includes command line interfaces.
Author: Bastiaan quast [aut, cre]
Maintainer: Bastiaan quast <bquast@gmail.com>
Diff between datasets.load versions 1.0.0 dated 2019-12-12 and 1.2.0 dated 2020-01-07
DESCRIPTION | 8 ++++---- MD5 | 19 ++++++++++--------- R/datasets.load.R | 2 +- README.md | 2 ++ man/alldata.Rd | 3 +-- man/browseDatasets.Rd | 8 ++++++-- man/datasets.Rd | 3 +-- man/figures |only man/getDatasetInfo.Rd | 8 ++++++-- man/printDatasets.Rd | 8 ++++++-- man/promptDatasets.Rd | 8 ++++++-- 11 files changed, 43 insertions(+), 26 deletions(-)
Title: Linguistic Phonetic Fieldwork Tools
Description: There are a lot of different typical tasks that have to be solved during phonetic research and experiments. This includes creating a presentation that will contain all stimuli, renaming and concatenating multiple sound files recorded during a session, automatic annotation in 'Praat' TextGrids (this is one of the sound annotation standards provided by 'Praat' software, see Boersma & Weenink 2018 <http://www.fon.hum.uva.nl/praat/>), creating an html table with annotations and spectrograms, and converting multiple formats ('Praat' TextGrid, 'EXMARaLDA' and 'ELAN'). All of these tasks can be solved by a mixture of different tools (any programming language has programs for automatic renaming, and Praat contains scripts for concatenating and renaming files, etc.). `phonfieldwork` provides a functionality that will make it easier to solve those tasks independently of any additional tools. You can also compare the functionality with other packages: 'rPraat' <https://CRAN.R-project.org/package=rPraat>, 'textgRid' <https://CRAN.R-project.org/package=textgRid>.
Author: George Moroz
Maintainer: George Moroz <agricolamz@gmail.com>
Diff between phonfieldwork versions 0.0.2 dated 2019-09-23 and 0.0.3 dated 2020-01-07
DESCRIPTION | 15 - MD5 | 30 +- NAMESPACE | 3 NEWS | 15 + R/create_image_look_up.R |only R/create_presentation.R | 31 ++- R/create_sound_play.R |only R/create_viewer.R | 30 ++ R/rename_videofiles.R |only inst/rmarkdown/templates/annotation_viewer/skeleton/skeleton.Rmd | 102 +++++++--- man/annotate_textgrid.Rd | 10 man/create_image_look_up.Rd |only man/create_presentation.Rd | 16 + man/create_sound_play.Rd |only man/create_viewer.Rd | 22 +- man/draw_sound.Rd | 23 +- man/extract_intervals.Rd | 11 - man/rename_soundfiles.Rd | 11 - man/rename_videofiles.Rd |only 19 files changed, 246 insertions(+), 73 deletions(-)
Title: Model and Analyse Interval Data
Description: Implements methodologies for modelling interval data by Normal
and Skew-Normal distributions, considering appropriate parameterizations of
the variance-covariance matrix that takes into account the intrinsic nature of
interval data, and lead to four different possible configuration structures.
The Skew-Normal parameters can be estimated by maximum likelihood, while Normal
parameters may be estimated by maximum likelihood or robust trimmed maximum
likelihood methods.
Author: Pedro Duarte Silva <psilva@porto.ucp.pt>, Paula Brito
<mpbrito.fep.up.pt>
Maintainer: Pedro Duarte Silva <psilva@porto.ucp.pt>
Diff between MAINT.Data versions 2.3.0 dated 2019-08-19 and 2.3.1 dated 2020-01-07
CHANGELOG | 2 DESCRIPTION | 8 MD5 | 42 +-- R/AgrMcDt.R | 6 R/Azzalini_sn_code.R | 35 ++- R/CPLogLik.grads.R | 15 + R/CPMaxLik.R | 31 ++ R/ClasGenMetDef.R | 395 +++++++++++++++++----------------- R/DACrossVal.R | 6 R/IData.R | 30 +- R/IdtMaxLikSN.R | 66 +++-- R/Idtmclust.R | 14 - R/RepLOptim.R | 19 + R/SNmle.R | 6 R/fasttle.R | 3 R/fulltle.R | 521 +++++++++++++++++++++++----------------------- R/lqda.R | 7 R/mle.R | 15 - R/pdwt.solve.R | 44 +-- R/sknda.R | 7 man/MAINT.Data-package.Rd | 400 +++++++++++++++++------------------ man/fulltle-methods.Rd | 236 ++++++++++---------- 22 files changed, 1011 insertions(+), 897 deletions(-)
Title: Analysis of Diversity
Description: Functions, data sets and examples for the calculation of various indices of biodiversity including species, functional and phylogenetic diversity. Part of the indices are expressed in terms of equivalent numbers of species. The package also provides ways to partition biodiversity across spatial or temporal scales (alpha, beta, gamma diversities). In addition to the quantification of biodiversity, ordination approaches are available which rely on diversity indices and allow the detailed identification of species, functional or phylogenetic differences between communities.
Author: Sandrine Pavoine
Maintainer: Sandrine Pavoine <sandrine.pavoine@mnhn.fr>
Diff between adiv versions 1.3 dated 2019-10-18 and 1.4 dated 2020-01-07
DESCRIPTION | 10 +++++----- MD5 | 23 ++++++++++++++--------- NAMESPACE | 15 ++++++++------- R/barp4d.R |only R/dotp4d.R |only R/gridp4d.R |only R/plot.phylo4d.R |only R/plot.rlqESLTP.R | 18 +++++++++++++----- build/partial.rdb |binary man/crossdpcoa.Rd | 30 +++++++++++++++++++++++------- man/distinctTopo.Rd | 9 ++++----- man/distinctTree.Rd | 9 +++++---- man/distinctUltra.Rd | 10 +++++----- man/plot.phylo4d.Rd |only man/rlqESLTP.Rd | 4 ++-- 15 files changed, 79 insertions(+), 49 deletions(-)
Title: Spatio-Temporal Modeling of Large Data Using a Spectral SPDE
Approach
Description: Functionality for spatio-temporal modeling of large data sets is provided. A Gaussian process in space and time is defined through a stochastic partial differential equation (SPDE). The SPDE is solved in the spectral space, and after discretizing in time and space, a linear Gaussian state space model is obtained. When doing inference, the main computational difficulty consists in evaluating the likelihood and in sampling from the full conditional of the spectral coefficients, or equivalently, the latent space-time process. In comparison to the traditional approach of using a spatio-temporal covariance function, the spectral SPDE approach is computationally advantageous. See Sigrist, Kuensch, and Stahel (2015) <doi:10.1111/rssb.12061> for more information on the methodology. This package aims at providing tools for two different modeling approaches. First, the SPDE based spatio-temporal model can be used as a component in a customized hierarchical Bayesian model (HBM). The functions of the package then provide parameterizations of the process part of the model as well as computationally efficient algorithms needed for doing inference with the HBM. Alternatively, the adaptive MCMC algorithm implemented in the package can be used as an algorithm for doing inference without any additional modeling. The MCMC algorithm supports data that follow a Gaussian or a censored distribution with point mass at zero. Covariates can be included in the model through a regression term.
Author: Fabio Sigrist, Hans R. Kuensch, Werner A. Stahel
Maintainer: Fabio Sigrist <fabiosigrist@gmail.com>
Diff between spate versions 1.6 dated 2019-09-24 and 1.7 dated 2020-01-07
DESCRIPTION | 8 MD5 | 4 R/spateFcts.R | 2874 +++++++++++++++++++++++++++++----------------------------- 3 files changed, 1443 insertions(+), 1443 deletions(-)
Title: Processing various types of data on GEO and TCGA
Description: Gene Expression Omnibus(GEO) and The Cancer Genome Atlas (TCGA)
provide us with a wealth of data, such as RNA-seq, DNA Methylation,
and Copy number variation data. It's easy to download data from TCGA using the
gdc tool, but processing these data into a format suitable for bioinformatics
analysis requires more work. This R package was developed to handle these data.
Author: Erqiang Hu [aut, cre]
Maintainer: Erqiang Hu <13766876214@163.com>
Diff between GeoTcgaData versions 0.2.0 dated 2019-09-23 and 0.2.2 dated 2020-01-07
GeoTcgaData-0.2.0/GeoTcgaData/inst/extdata/methy/0a0 |only GeoTcgaData-0.2.0/GeoTcgaData/inst/extdata/methy/0a6 |only GeoTcgaData-0.2.2/GeoTcgaData/DESCRIPTION | 8 GeoTcgaData-0.2.2/GeoTcgaData/MD5 | 84 +-- GeoTcgaData-0.2.2/GeoTcgaData/NAMESPACE | 2 GeoTcgaData-0.2.2/GeoTcgaData/R/Merge_methylation.R | 33 - GeoTcgaData-0.2.2/GeoTcgaData/R/ann_merge.r | 2 GeoTcgaData-0.2.2/GeoTcgaData/R/fpkm_count_conversion.r | 6 GeoTcgaData-0.2.2/GeoTcgaData/R/id_conversion_all.r | 2 GeoTcgaData-0.2.2/GeoTcgaData/R/kegg_diff_gene.R | 5 GeoTcgaData-0.2.2/GeoTcgaData/R/prepareChi.r | 5 GeoTcgaData-0.2.2/GeoTcgaData/README.md | 307 ++++-------- GeoTcgaData-0.2.2/GeoTcgaData/inst/doc/GeoTcgaData.R | 244 ++-------- GeoTcgaData-0.2.2/GeoTcgaData/inst/doc/GeoTcgaData.Rmd | 292 ++++-------- GeoTcgaData-0.2.2/GeoTcgaData/inst/doc/GeoTcgaData.html | 339 ++++---------- GeoTcgaData-0.2.2/GeoTcgaData/inst/extdata/methy/0a0b4 |only GeoTcgaData-0.2.2/GeoTcgaData/inst/extdata/methy/0a6b |only GeoTcgaData-0.2.2/GeoTcgaData/inst/extdata/methy/0ae7 |only GeoTcgaData-0.2.2/GeoTcgaData/inst/extdata/methy/0b32 |only GeoTcgaData-0.2.2/GeoTcgaData/man/GSE66705_sample2.Rd | 32 - GeoTcgaData-0.2.2/GeoTcgaData/man/Merge_methy_tcga.Rd | 42 - GeoTcgaData-0.2.2/GeoTcgaData/man/ann_merge.Rd | 48 - GeoTcgaData-0.2.2/GeoTcgaData/man/cal_mean_module.Rd | 46 - GeoTcgaData-0.2.2/GeoTcgaData/man/classify_sample.Rd | 38 - GeoTcgaData-0.2.2/GeoTcgaData/man/countToFpkm_matrix.Rd | 48 - GeoTcgaData-0.2.2/GeoTcgaData/man/countToTpm_matrix.Rd | 48 - GeoTcgaData-0.2.2/GeoTcgaData/man/diff_gene.Rd | 42 - GeoTcgaData-0.2.2/GeoTcgaData/man/differential_cnv.Rd | 58 +- GeoTcgaData-0.2.2/GeoTcgaData/man/fpkmToTpm_matrix.Rd | 48 - GeoTcgaData-0.2.2/GeoTcgaData/man/geneExpress.Rd | 32 - GeoTcgaData-0.2.2/GeoTcgaData/man/gene_ave.Rd | 52 +- GeoTcgaData-0.2.2/GeoTcgaData/man/hgnc.Rd | 26 - GeoTcgaData-0.2.2/GeoTcgaData/man/id_conversion.Rd | 38 - GeoTcgaData-0.2.2/GeoTcgaData/man/id_conversion_vector.Rd | 48 - GeoTcgaData-0.2.2/GeoTcgaData/man/kegg_liver.Rd | 32 - GeoTcgaData-0.2.2/GeoTcgaData/man/module.Rd | 26 - GeoTcgaData-0.2.2/GeoTcgaData/man/prepare_chi.Rd | 56 +- GeoTcgaData-0.2.2/GeoTcgaData/man/profile.Rd | 32 - GeoTcgaData-0.2.2/GeoTcgaData/man/rep1.Rd | 54 +- GeoTcgaData-0.2.2/GeoTcgaData/man/rep2.Rd | 54 +- GeoTcgaData-0.2.2/GeoTcgaData/man/tcga_cli_deal.Rd | 40 - GeoTcgaData-0.2.2/GeoTcgaData/man/ventricle.Rd | 32 - GeoTcgaData-0.2.2/GeoTcgaData/vignettes/GeoTcgaData.Rmd | 292 ++++-------- 43 files changed, 1046 insertions(+), 1547 deletions(-)
Title: Time Series Forecasting with Machine Learning Methods
Description: The purpose of 'forecastML' is to simplify the process of multi-step-ahead direct forecasting with standard machine learning algorithms. 'forecastML' supports lagged, dynamic, static, and grouping features for modeling single and grouped numeric or factor/sequence time series. In addition, simple wrapper functions are used to support model-building with most R packages. This approach to forecasting is inspired by Bergmeir, Hyndman, and Koo's (2018) paper "A note on the validity of cross-validation for evaluating autoregressive time series prediction" <doi:10.1016/j.csda.2017.11.003>.
Author: Nickalus Redell
Maintainer: Nickalus Redell <nickalusredell@gmail.com>
Diff between forecastML versions 0.6.0 dated 2019-11-23 and 0.7.0 dated 2020-01-07
DESCRIPTION | 12 MD5 | 79 +-- NAMESPACE | 2 R/combine_forecasts.R |only R/create_windows.R | 94 +++ R/data_seatbelts.R | 4 R/examples/example_combine_forecasts.R |only R/lagged_df.R | 11 R/return_error.R | 242 ++++++---- R/train_model.R | 647 +++++++++++++++++++++------ R/zzz.R | 24 + README.md | 254 +++++++++- inst/doc/custom_functions.html | 18 inst/doc/grouped_forecast.R | 57 -- inst/doc/grouped_forecast.Rmd | 232 +++++---- inst/doc/grouped_forecast.html | 557 +++++++++++------------ inst/doc/lagged_features.R | 32 - inst/doc/lagged_features.Rmd | 60 +- inst/doc/lagged_features.html | 107 ++-- inst/doc/package_overview.R | 183 +++++-- inst/doc/package_overview.Rmd | 443 +++++++++++------- inst/doc/package_overview.html | 762 +++++++++++++++++--------------- man/combine_forecasts.Rd |only man/create_windows.Rd | 6 man/data_seatbelts.Rd | 4 man/plot.forecastML.Rd |only man/plot.windows.Rd | 2 man/predict.forecast_model.Rd | 12 man/return_error.Rd | 10 man/train_model.Rd | 2 tests/testthat/test_combine_forecasts.R |only tests/testthat/test_fill_gaps.R | 26 + tests/testthat/test_return_error.R | 50 ++ tools/forecastML_cheat_sheet.png |binary tools/forecastML_cheat_sheet_data.png |binary tools/forecastML_cheat_sheet_model.png |binary tools/forecastML_factor_plot.png |only tools/forecastML_plot.png |only tools/sequence_forecast_level.png |only tools/sequence_forecast_prob.png |only tools/sequence_valid_level.png |only tools/sequence_valid_prob.png |only tools/sequence_windows.png |only vignettes/forecastML_plot.png |only vignettes/grouped_forecast.Rmd | 232 +++++---- vignettes/lagged_features.Rmd | 60 +- vignettes/package_overview.Rmd | 443 +++++++++++------- 47 files changed, 2979 insertions(+), 1688 deletions(-)
Title: Mean and Covariance Matrix Estimation under Heavy Tails
Description: Robust estimation methods for the mean vector and covariance matrix
from data (possibly containing NAs) under multivariate heavy-tailed
distributions such as angular Gaussian (via Tyler's method), Cauchy,
and Student's t.
Additionally, a factor model structure can be specified for the covariance
matrix.
The package is based on the papers: Sun, Babu, and Palomar (2014),
Sun, Babu, and Palomar (2015), Liu and Rubin (1995), and
Zhou, Liu, Kumar, and Palomar (2019).
Author: Daniel P. Palomar [cre, aut],
Rui Zhou [aut]
Maintainer: Daniel P. Palomar <daniel.p.palomar@gmail.com>
Diff between fitHeavyTail versions 0.1.1 dated 2019-11-22 and 0.1.2 dated 2020-01-07
fitHeavyTail-0.1.1/fitHeavyTail/tests/testthat/fitted_mvt_regnu_check.RData |only fitHeavyTail-0.1.2/fitHeavyTail/DESCRIPTION | 33 fitHeavyTail-0.1.2/fitHeavyTail/MD5 | 45 - fitHeavyTail-0.1.2/fitHeavyTail/NEWS.md | 18 fitHeavyTail-0.1.2/fitHeavyTail/R/fitHeavyTail-package.R | 12 fitHeavyTail-0.1.2/fitHeavyTail/R/fit_TylerCauchy.R | 49 - fitHeavyTail-0.1.2/fitHeavyTail/R/fit_mvt.R | 334 +++++++--- fitHeavyTail-0.1.2/fitHeavyTail/R/plotting.R | 27 fitHeavyTail-0.1.2/fitHeavyTail/README.md | 91 +- fitHeavyTail-0.1.2/fitHeavyTail/inst/CITATION | 46 + fitHeavyTail-0.1.2/fitHeavyTail/inst/doc/CovarianceEstimationHeavyTail.html | 131 ++- fitHeavyTail-0.1.2/fitHeavyTail/man/figures/README-ellipses-1.png |binary fitHeavyTail-0.1.2/fitHeavyTail/man/fitHeavyTail-package.Rd | 12 fitHeavyTail-0.1.2/fitHeavyTail/man/fit_Cauchy.Rd | 27 fitHeavyTail-0.1.2/fitHeavyTail/man/fit_Tyler.Rd | 27 fitHeavyTail-0.1.2/fitHeavyTail/man/fit_mvt.Rd | 78 +- fitHeavyTail-0.1.2/fitHeavyTail/tests/testthat/fitted_Cauchy_check.RData |binary fitHeavyTail-0.1.2/fitHeavyTail/tests/testthat/fitted_Tyler_check.RData |binary fitHeavyTail-0.1.2/fitHeavyTail/tests/testthat/fitted_mvt_check.RData |binary fitHeavyTail-0.1.2/fitHeavyTail/tests/testthat/fitted_mvt_fixednu_kurtosis_check.RData |only fitHeavyTail-0.1.2/fitHeavyTail/tests/testthat/fitted_mvt_fixednu_mle_check.RData |only fitHeavyTail-0.1.2/fitHeavyTail/tests/testthat/fitted_mvt_wNA_check.RData |binary fitHeavyTail-0.1.2/fitHeavyTail/tests/testthat/test-fit_Cauchy.R | 27 fitHeavyTail-0.1.2/fitHeavyTail/tests/testthat/test-fit_Tyler.R | 27 fitHeavyTail-0.1.2/fitHeavyTail/tests/testthat/test-fit_mvt.R | 56 - 25 files changed, 686 insertions(+), 354 deletions(-)
Title: Enhancements for 'broom' Package Family
Description: Collection of functions to assist 'broom' and
'broom.mixed' package-related data analysis workflows. In particular,
the generic functions tidy(), glance(), and augment() choose
appropriate S3 methods from these two packages depending on which
package exports the needed method. Additionally, 'grouped_' variants
of the generics provides a convenient way to execute functions across
a combination of grouping variable(s) in a dataframe.
Author: Indrajeet Patil [aut, cre, ctb]
(<https://orcid.org/0000-0003-1995-6531>)
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>
Diff between broomExtra versions 1.0.0 dated 2019-12-17 and 1.0.1 dated 2020-01-07
DESCRIPTION | 19 +++---- MD5 | 44 ++++++++--------- NAMESPACE | 6 -- NEWS.md | 4 + R/grouped_generics.R | 82 +++++++++------------------------ README.md | 43 ++++------------- build/broomExtra.pdf |binary build/vignette.rds |binary inst/doc/available_methods.R | 13 +++-- inst/doc/available_methods.Rmd | 14 +++-- inst/doc/available_methods.html | 4 - inst/doc/tests_and_coverage.Rmd | 18 +++---- inst/doc/tests_and_coverage.html | 20 ++++---- man/augment.Rd | 2 man/glance.Rd | 2 man/grouped_augment.Rd | 4 - man/grouped_glance.Rd | 4 - man/grouped_tidy.Rd | 4 - man/tidy.Rd | 2 tests/README.md | 20 ++++---- tests/testthat/test-grouped_generics.R | 6 +- vignettes/available_methods.Rmd | 14 +++-- vignettes/tests_and_coverage.Rmd | 18 +++---- 23 files changed, 147 insertions(+), 196 deletions(-)
Title: Sequential Pairwise Online Rating Techniques
Description: Calculates ratings for two-player or
multi-player challenges. Methods included in package such as are able to
estimate ratings (players strengths) and their evolution in time, also able to
predict output of challenge. Algorithms are based on Bayesian Approximation
Method, and they don't involve any matrix inversions nor likelihood estimation.
Parameters are updated sequentially, and computation doesn't require any
additional RAM to make estimation feasible. Additionally, base of the package
is written in C++ what makes sport computation even faster. Methods used in the
package refers to Mark E. Glickman (1999)
<http://www.glicko.net/research/glicko.pdf>;
Mark E. Glickman (2001) <doi:10.1080/02664760120059219>;
Ruby C. Weng, Chih-Jen Lin (2011)
<http://jmlr.csail.mit.edu/papers/volume12/weng11a/weng11a.pdf>;
W. Penny, Stephen J. Roberts (1999) <doi:10.1109/IJCNN.1999.832603>.
Author: Dawid Kałędkowski [aut, cre] (<https://orcid.org/0000-0001-9533-457X>)
Maintainer: Dawid Kałędkowski <dawid.kaledkowski@gmail.com>
Diff between sport versions 0.1.2 dated 2019-01-07 and 0.2.0 dated 2020-01-07
sport-0.1.2/sport/R/bbt_run.R |only sport-0.1.2/sport/R/createTermMatrix.R |only sport-0.1.2/sport/R/dbl_run.R |only sport-0.1.2/sport/R/errors.R |only sport-0.1.2/sport/R/glicko2_run.R |only sport-0.1.2/sport/R/glicko_run.R |only sport-0.1.2/sport/src/bbt.cpp |only sport-0.1.2/sport/src/dbl.cpp |only sport-0.1.2/sport/src/dbl.h |only sport-0.1.2/sport/src/factor2dummy.cpp |only sport-0.1.2/sport/src/factor2dummy.h |only sport-0.1.2/sport/src/glicko.cpp |only sport-0.1.2/sport/src/glicko.h |only sport-0.1.2/sport/tests/testthat/test_bbt_run.R |only sport-0.1.2/sport/tests/testthat/test_glicko2_run.R |only sport-0.1.2/sport/tests/testthat/test_glicko_run.R |only sport-0.2.0/sport/DESCRIPTION | 28 sport-0.2.0/sport/MD5 | 99 - sport-0.2.0/sport/NAMESPACE | 40 sport-0.2.0/sport/NEWS.md | 22 sport-0.2.0/sport/R/RcppExports.R | 42 sport-0.2.0/sport/R/data.R | 88 - sport-0.2.0/sport/R/output.R | 278 ++- sport-0.2.0/sport/R/package-init.R | 13 sport-0.2.0/sport/R/predict.R | 272 +-- sport-0.2.0/sport/R/rating_run.R |only sport-0.2.0/sport/R/terms.R |only sport-0.2.0/sport/R/utils.R |only sport-0.2.0/sport/build/vignette.rds |binary sport-0.2.0/sport/data/gpheats.rda |binary sport-0.2.0/sport/data/gpsquads.rda |binary sport-0.2.0/sport/inst/WORDLIST |only sport-0.2.0/sport/inst/doc/sport_in_r.R | 210 +- sport-0.2.0/sport/inst/doc/sport_in_r.Rmd | 550 ++++--- sport-0.2.0/sport/inst/doc/sport_in_r.html | 986 ++++++++----- sport-0.2.0/sport/inst/doc/the_theory.R |only sport-0.2.0/sport/inst/doc/the_theory.Rmd |only sport-0.2.0/sport/inst/doc/the_theory.html |only sport-0.2.0/sport/man/bbt_run.Rd | 182 +- sport-0.2.0/sport/man/dbl_run.Rd | 154 +- sport-0.2.0/sport/man/figures/README-unnamed-chunk-7-1.png |binary sport-0.2.0/sport/man/figures/README-unnamed-chunk-7-2.png |binary sport-0.2.0/sport/man/glicko2_run.Rd | 202 +- sport-0.2.0/sport/man/glicko_run.Rd | 177 +- sport-0.2.0/sport/man/gpheats.Rd | 52 sport-0.2.0/sport/man/gpsquads.Rd | 48 sport-0.2.0/sport/man/plot.rating.Rd | 41 sport-0.2.0/sport/man/predict.rating.Rd | 51 sport-0.2.0/sport/man/rating_run.Rd |only sport-0.2.0/sport/man/summary.rating.Rd | 75 sport-0.2.0/sport/src/Makevars |only sport-0.2.0/sport/src/Makevars.win |only sport-0.2.0/sport/src/RcppExports.cpp | 121 - sport-0.2.0/sport/src/bbt.h | 18 sport-0.2.0/sport/src/calc_ratings.h |only sport-0.2.0/sport/src/ratings.cpp |only sport-0.2.0/sport/src/ratings.h |only sport-0.2.0/sport/src/utils.h |only sport-0.2.0/sport/tests/spelling.R |only sport-0.2.0/sport/tests/testthat.R | 7 sport-0.2.0/sport/tests/testthat/test_dbl_run.R | 221 +- sport-0.2.0/sport/tests/testthat/test_output.R | 79 - sport-0.2.0/sport/tests/testthat/test_predict.R | 184 +- sport-0.2.0/sport/tests/testthat/test_rating.R |only sport-0.2.0/sport/tests/testthat/test_terms.R |only sport-0.2.0/sport/tests/testthat/test_utils.R |only sport-0.2.0/sport/vignettes/sport_in_r.Rmd | 550 ++++--- sport-0.2.0/sport/vignettes/the_theory.Rmd |only 68 files changed, 2791 insertions(+), 1999 deletions(-)
Title: R Interface to the 'Yacas' Computer Algebra System
Description: Interface to the 'yacas' computer algebra system (<http://www.yacas.org/>).
Author: Mikkel Meyer Andersen [aut, cre, cph],
Rob Goedman [aut, cph],
Gabor Grothendieck [aut, cph],
Søren Højsgaard [aut, cph],
Grzegorz Mazur [aut, cph],
Ayal Pinkus [aut, cph],
Nemanja Trifunovic [cph] (UTF-8 part of yacas
(src/yacas/include/yacas/utf8*))
Maintainer: Mikkel Meyer Andersen <mikl@math.aau.dk>
Diff between Ryacas versions 1.1.1 dated 2019-10-31 and 1.1.2 dated 2020-01-07
DESCRIPTION | 12 MD5 | 69 +- NAMESPACE | 7 R/converters.R | 4 R/print.R | 7 R/yac-symbol.R | 240 +++++++++ build/vignette.rds |binary inst/NEWS | 14 inst/doc/arbitrary-precision.R | 22 inst/doc/arbitrary-precision.html | 175 +++--- inst/doc/getting-started.R | 40 - inst/doc/getting-started.Rmd | 2 inst/doc/getting-started.html | 227 ++++---- inst/doc/high-level.R | 34 - inst/doc/high-level.Rmd | 38 + inst/doc/high-level.html | 304 ++++++----- inst/doc/latent-variable-model.R | 16 inst/doc/latent-variable-model.html | 77 +- inst/doc/low-level.R | 62 +- inst/doc/low-level.html | 245 ++++----- inst/doc/ssm-matrix.R | 20 inst/doc/ssm-matrix.html | 133 ++--- inst/doc/yacas-rules.R | 16 inst/doc/yacas-rules.html | 27 - inst/yacas-custom/ryacasinit.ys | 3 inst/yacas/orthopoly.rep/code.ys | 928 ++++++++++++++++++------------------ inst/yacas/texform.rep/code.ys | 4 man/cbind.yac_symbol.Rd |only man/diag-set.Rd | 2 man/prod.yac_symbol.Rd |only man/rbind.yac_symbol.Rd |only man/sum.yac_symbol.Rd | 5 man/with_value.Rd |only man/yac_cli.Rd | 2 man/ysym_ls.Rd |only tests/testthat/test-symbol.R | 145 +++++ vignettes/getting-started.Rmd | 2 vignettes/high-level.Rmd | 38 + 38 files changed, 1696 insertions(+), 1224 deletions(-)
Title: Powerful Algorithm for Maximal Eigenpair
Description: An implementation for using powerful algorithm to compute the
maximal eigenpair of Hermitizable tridiagonal matrices in R. It
provides two algorithms to find the maximal and the next to maximal
eigenpairs under the tridiagonal matrix. Besides, it also provides
two auxiliary algorithms to generate tridiagonal matrix and solve
the linear equation by Thomas algorithm. Several examples are included
in the vignettes to illustrate the usage of the functions.
Author: Yueshuang Li <liyueshuang@mail.bnu.edu.cn> and Xiaojun Mao <maoxj@fudan.edu.cn>
Maintainer: Xiaojun Mao <maoxj@fudan.edu.cn>
Diff between PowerfulMaxEigenpair versions 0.1.0 dated 2019-06-03 and 0.1.1 dated 2020-01-07
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NAMESPACE | 13 +++++++------ build/vignette.rds |binary inst/doc/Powerful_MaxEigenpair.R | 32 ++++++++++++++++---------------- vignettes/Powerful_MaxEigenpair.html | 9 ++++----- 6 files changed, 37 insertions(+), 37 deletions(-)
More information about PowerfulMaxEigenpair at CRAN
Permanent link
Title: Standardize Plant Names According to World Flora Online
Taxonomic Backbone
Description: World Flora Online is an online flora of all known plants, available from <http://www.worldfloraonline.org/>. Methods are provided of matching a list of plant names (scientific names, taxonomic names, botanical names) against a static copy of the World Flora Online Taxonomic Backbone data that can be downloaded from the World Flora Online website. The World Flora Online Taxonomic Backbone is an updated version of The Plant List (<http://www.theplantlist.org/>), a working list of plant names that has become static since 2013.
Author: Roeland Kindt
Maintainer: Roeland Kindt <R.KINDT@CGIAR.ORG>
Diff between WorldFlora versions 1.1 dated 2019-12-17 and 1.2 dated 2020-01-07
DESCRIPTION | 8 +-- MD5 | 11 ++--- NAMESPACE | 2 R/WFO.match.R | 116 +++++++++++++++++++++++++++++++++++++++++++++++++------ R/WFO.one.R |only inst/ChangeLog | 41 ++++++++++++++++++- man/WFO.match.Rd | 53 ++++++++++++++++++++----- 7 files changed, 198 insertions(+), 33 deletions(-)
Title: Download and Manage Data from Tehran Stock Exchange
Description: Tools for downloading and organizing data from Tehran Stock Exchange (TSE) <http://new.tse.ir/en/>. It also performs some descriptive data analysis for assets.
Author: Ali Saeb
Maintainer: Ali Saeb <ali.saeb@gmail.com>
Diff between TSEtools versions 0.1.3 dated 2019-04-04 and 0.1.4 dated 2020-01-07
DESCRIPTION | 6 - MD5 | 10 +-- R/getTSE.R | 108 +++++++++++++++++--------------- R/mcPrt.R | 158 +++++++++++++++++++++++++----------------------- README.md | 6 + inst/extdata/sample.csv | 3 6 files changed, 156 insertions(+), 135 deletions(-)
Title: Feature Ordering by Conditional Independence
Description: Feature Ordering by Conditional Independence (FOCI) is a variable selection algorithm based on the measure of conditional dependence.
For more information, see the paper: Azadkia and Chatterjee (2019),"A simple measure of conditional dependence" <arXiv:1910.12327>.
Author: Mona Azadkia [aut, cre],
Sourav Chatterjee [aut, ctb]
Maintainer: Mona Azadkia <monaazadkia@gmail.com>
Diff between FOCI versions 0.1.0 dated 2019-12-17 and 0.1.1 dated 2020-01-07
DESCRIPTION | 7 ++++--- MD5 | 6 +++--- inst/doc/codec.html | 14 +++++++------- inst/doc/foci.html | 2 +- 4 files changed, 15 insertions(+), 14 deletions(-)
Title: Fast Kernel Sums
Description: Implements the method of Hofmeyr, D.P. (2019) <DOI:10.1109/TPAMI.2019.2930501> for fast evaluation of univariate kernel smoothers based on recursive computations.
Applications to the basic problems of density and regression function estimation are provided, as well as some projection pursuit methods
for which the objective is based on non-parametric functionals of the projected density, or conditional density of a response given projected
covariates.
Author: David P. Hofmeyr
Maintainer: David P. Hofmeyr <dhofmeyr@sun.ac.za>
Diff between FKSUM versions 0.1.2 dated 2019-12-08 and 0.1.3 dated 2020-01-07
DESCRIPTION | 8 - MD5 | 22 +- R/PPR_WORKS.R | 327 +++++++++++++++++++++++++++++++++----------- R/fk_ICA.R | 44 ++--- R/fk_density.R | 6 R/fk_regression.R | 21 ++ R/fk_sum.R | 97 +++++++++---- build/partial.rdb |binary man/FKSUM-package.Rd | 2 man/fk_ICA.Rd | 2 man/fk_ppr.Rd | 9 - src/FKSUM_CPP_FUNCTIONS.cpp | 6 12 files changed, 387 insertions(+), 157 deletions(-)
Title: Directional Statistics
Description: A collection of functions for directional data (including massive, with millions of observations, data) analysis. Hypothesis testing, discriminant and regression analysis, MLE of distributions and more are included. The standard textbook for such data is the "Directional Statistics" by Mardia, K. V. and Jupp, P. E. (2000). Other references include a) Phillip J. Paine, Simon P. Preston Michail Tsagris and Andrew T. A. Wood (2018). An elliptically symmetric angular Gaussian distribution. Statistics and Computing 28(3): 689-697. <doi:10.1007/s11222-017-9756-4>. b) Tsagris M. and Alenazi A. (2019). Comparison of discriminant analysis methods on the sphere. Communications in Statistics: Case Studies, Data Analysis and Applications 5(4):467--491. <doi:10.1080/23737484.2019.1684854>. c) P. J. Paine, S. P. Preston, M. Tsagris and Andrew T. A. Wood (2019). Spherical regression models with general covariates and anisotropic errors. Statistics and Computing (to appear). <doi:10.1007/s11222-019-09872-2>.
Author: Michail Tsagris, Giorgos Athineou, Anamul Sajib, Eli Amson, Micah J. Waldstein
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between Directional versions 4.0 dated 2019-09-14 and 4.1 dated 2020-01-07
Directional-4.0/Directional/man/acg.Rd |only Directional-4.0/Directional/man/iag.mle.Rd |only Directional-4.1/Directional/DESCRIPTION | 14 - Directional-4.1/Directional/MD5 | 206 ++++++++--------- Directional-4.1/Directional/NAMESPACE | 18 - Directional-4.1/Directional/R/ESAGsim.R | 8 Directional-4.1/Directional/R/embed.circaov.R | 25 -- Directional-4.1/Directional/R/hcf.circaov.R | 30 -- Directional-4.1/Directional/R/het.circaov.R | 20 - Directional-4.1/Directional/R/iag.mle.R | 4 Directional-4.1/Directional/R/lr.circaov.R | 20 - Directional-4.1/Directional/R/makefolds.R | 15 - Directional-4.1/Directional/R/multispml.mle.R |only Directional-4.1/Directional/R/multivm.mle.R |only Directional-4.1/Directional/R/multivmf.R |only Directional-4.1/Directional/R/rayleigh.R | 2 Directional-4.1/Directional/R/rvmf.R | 7 Directional-4.1/Directional/R/spml.fbed.R |only Directional-4.1/Directional/R/spml.nb.R |only Directional-4.1/Directional/R/spml.regs.R |only Directional-4.1/Directional/R/spmlnb.pred.R |only Directional-4.1/Directional/R/vm.nb.R |only Directional-4.1/Directional/R/vmf.R | 1 Directional-4.1/Directional/R/vmnb.pred.R |only Directional-4.1/Directional/man/Arotation.Rd | 2 Directional-4.1/Directional/man/Directional-package.Rd | 10 Directional-4.1/Directional/man/ESAG.da.Rd | 2 Directional-4.1/Directional/man/ESAGda.pred.Rd | 2 Directional-4.1/Directional/man/ESAGmle.Rd | 2 Directional-4.1/Directional/man/ESAGsim.Rd | 2 Directional-4.1/Directional/man/bic.mixvmf.Rd | 2 Directional-4.1/Directional/man/circ.cor1.Rd | 8 Directional-4.1/Directional/man/circ.cors1.Rd | 10 Directional-4.1/Directional/man/circ.summary.Rd | 2 Directional-4.1/Directional/man/circlin.cor.Rd | 2 Directional-4.1/Directional/man/conc.test.Rd | 2 Directional-4.1/Directional/man/dirda.cv.Rd | 2 Directional-4.1/Directional/man/dirknn.Rd | 2 Directional-4.1/Directional/man/dirknn.tune.Rd | 2 Directional-4.1/Directional/man/euclid.Rd | 2 Directional-4.1/Directional/man/euclid.inv.Rd | 2 Directional-4.1/Directional/man/eul2rot.Rd | 4 Directional-4.1/Directional/man/f.rbing.Rd | 2 Directional-4.1/Directional/man/fb.saddle.Rd | 2 Directional-4.1/Directional/man/fishkent.Rd | 2 Directional-4.1/Directional/man/ggvm.Rd | 2 Directional-4.1/Directional/man/group.gof.Rd | 2 Directional-4.1/Directional/man/group.vm.Rd | 2 Directional-4.1/Directional/man/habeck.rot.Rd | 4 Directional-4.1/Directional/man/hcf.aov.Rd | 2 Directional-4.1/Directional/man/hcf.circaov.Rd | 2 Directional-4.1/Directional/man/iag.reg.Rd | 2 Directional-4.1/Directional/man/iagesag.Rd | 2 Directional-4.1/Directional/man/kent.contour.Rd | 2 Directional-4.1/Directional/man/kent.datacontour.Rd | 2 Directional-4.1/Directional/man/kent.density.Rd | 2 Directional-4.1/Directional/man/kent.logcon.Rd | 2 Directional-4.1/Directional/man/kent.mle.Rd | 2 Directional-4.1/Directional/man/knn.reg.Rd | 2 Directional-4.1/Directional/man/knnreg.tune.Rd | 2 Directional-4.1/Directional/man/kuiper.Rd | 2 Directional-4.1/Directional/man/lambert.Rd | 2 Directional-4.1/Directional/man/lambert.inv.Rd | 2 Directional-4.1/Directional/man/makefolds.Rd | 2 Directional-4.1/Directional/man/matrixfisher.mle.Rd | 2 Directional-4.1/Directional/man/meandir.test.Rd | 2 Directional-4.1/Directional/man/mediandir.Rd | 2 Directional-4.1/Directional/man/mix.vmf.Rd | 2 Directional-4.1/Directional/man/mixvmf.contour.Rd | 2 Directional-4.1/Directional/man/multivm.mle.Rd |only Directional-4.1/Directional/man/purka.mle.Rd | 2 Directional-4.1/Directional/man/pvm.Rd | 2 Directional-4.1/Directional/man/quat2rot.Rd | 2 Directional-4.1/Directional/man/racg.Rd | 2 Directional-4.1/Directional/man/rayleigh.Rd | 2 Directional-4.1/Directional/man/rbingham.Rd | 2 Directional-4.1/Directional/man/rfb.Rd | 2 Directional-4.1/Directional/man/rkent.Rd | 2 Directional-4.1/Directional/man/rmatrixfisher.Rd | 2 Directional-4.1/Directional/man/rmixvmf.Rd | 2 Directional-4.1/Directional/man/rot.matrix.Rd | 2 Directional-4.1/Directional/man/rot2eul.Rd | 4 Directional-4.1/Directional/man/rot2quat.Rd | 2 Directional-4.1/Directional/man/rotation.Rd | 2 Directional-4.1/Directional/man/rsop.Rd | 2 Directional-4.1/Directional/man/rvmf.Rd | 2 Directional-4.1/Directional/man/rvonmises.Rd | 2 Directional-4.1/Directional/man/spher.cor.Rd | 2 Directional-4.1/Directional/man/spher.reg.Rd | 2 Directional-4.1/Directional/man/spherconc.test.Rd | 2 Directional-4.1/Directional/man/sphereplot.Rd | 2 Directional-4.1/Directional/man/spml.fbed.Rd |only Directional-4.1/Directional/man/spml.mle.Rd | 2 Directional-4.1/Directional/man/spml.reg.Rd | 2 Directional-4.1/Directional/man/spml.regs.Rd |only Directional-4.1/Directional/man/tang.conc.Rd | 2 Directional-4.1/Directional/man/vec.Rd | 2 Directional-4.1/Directional/man/visual.check.Rd | 4 Directional-4.1/Directional/man/vm.density.Rd | 2 Directional-4.1/Directional/man/vm.kde.Rd | 2 Directional-4.1/Directional/man/vm.nb.Rd |only Directional-4.1/Directional/man/vmf.Rd | 103 ++++++-- Directional-4.1/Directional/man/vmf.contour.Rd | 2 Directional-4.1/Directional/man/vmf.da.Rd | 2 Directional-4.1/Directional/man/vmf.density.Rd | 2 Directional-4.1/Directional/man/vmf.kde.Rd | 2 Directional-4.1/Directional/man/vmf.kerncontour.Rd | 2 Directional-4.1/Directional/man/vmfda.pred.Rd | 2 Directional-4.1/Directional/man/vmfkde.tune.Rd | 2 Directional-4.1/Directional/man/vmkde.tune.Rd | 2 Directional-4.1/Directional/man/vmnb.pred.Rd |only Directional-4.1/Directional/man/wood.mle.Rd | 2 112 files changed, 323 insertions(+), 344 deletions(-)
Title: Linear and Nonlinear Methods for Analyzing Daily and Monthly
Dendroclimatological Data
Description: Provides novel dendroclimatological methods, primarily used by the
Tree-ring research community. There are four core functions. The first one is
daily_response(), which finds the optimal sequence of days that are related
to one or more tree-ring proxy records. Similar function is daily_response_seascorr(),
which implements partial correlations in the analysis of daily response functions.
For the enthusiast of monthly data, there is monthly_response() function.
The last core function is compare_methods(), which effectively compares several
linear and nonlinear regression algorithms on the task of climate reconstruction.
Author: Jernej Jevsenak [aut, cre]
Maintainer: Jernej Jevsenak <jernej.jevsenak@gmail.com>
Diff between dendroTools versions 1.0.6 dated 2019-07-20 and 1.0.7 dated 2020-01-07
dendroTools-1.0.6/dendroTools/R/KNMI_daily_transform.R |only dendroTools-1.0.6/dendroTools/R/boot_f.R |only dendroTools-1.0.6/dendroTools/R/swit272_monthly_temperatures.R |only dendroTools-1.0.6/dendroTools/data/swit272_monthly_temperatures.rda |only dendroTools-1.0.6/dendroTools/man/KNMI_daily_transform.Rd |only dendroTools-1.0.6/dendroTools/man/boot_f.Rd |only dendroTools-1.0.6/dendroTools/man/swit272_monthly_temperatures.Rd |only dendroTools-1.0.7/dendroTools/DESCRIPTION | 9 dendroTools-1.0.7/dendroTools/MD5 | 97 - dendroTools-1.0.7/dendroTools/NAMESPACE | 11 dendroTools-1.0.7/dendroTools/NEWS.md | 8 dendroTools-1.0.7/dendroTools/R/boot_f_brnn.R |only dendroTools-1.0.7/dendroTools/R/boot_f_cor.R |only dendroTools-1.0.7/dendroTools/R/boot_f_lm.R |only dendroTools-1.0.7/dendroTools/R/boot_f_pcor.R |only dendroTools-1.0.7/dendroTools/R/compare_methods.R | 40 dendroTools-1.0.7/dendroTools/R/daily_response.R | 838 +++++++--- dendroTools-1.0.7/dendroTools/R/daily_response_seascorr.R | 376 ++-- dendroTools-1.0.7/dendroTools/R/data_MVA.R | 2 dendroTools-1.0.7/dendroTools/R/data_TRW.R | 6 dendroTools-1.0.7/dendroTools/R/data_TRW_1.R | 2 dendroTools-1.0.7/dendroTools/R/data_transform.R |only dendroTools-1.0.7/dendroTools/R/dataset_MVA_individual.R | 2 dendroTools-1.0.7/dendroTools/R/example_dataset_1.R | 2 dendroTools-1.0.7/dendroTools/R/example_proxies_1.R | 2 dendroTools-1.0.7/dendroTools/R/example_proxies_individual.R | 2 dendroTools-1.0.7/dendroTools/R/generics.R | 25 dendroTools-1.0.7/dendroTools/R/generics2.R |only dendroTools-1.0.7/dendroTools/R/glimpse_daily_data.R | 6 dendroTools-1.0.7/dendroTools/R/monthly_response.R | 808 +++++++-- dendroTools-1.0.7/dendroTools/R/monthly_response_seascorr.R | 422 +++-- dendroTools-1.0.7/dendroTools/R/plot_extreme.R | 18 dendroTools-1.0.7/dendroTools/R/plot_heatmap.R | 72 dendroTools-1.0.7/dendroTools/R/smooth_matrix.R | 3 dendroTools-1.0.7/dendroTools/R/swit272_daily_precipitation.R |only dendroTools-1.0.7/dendroTools/R/swit272_daily_temperatures.R | 15 dendroTools-1.0.7/dendroTools/data/swit272_daily_precipitation.rda |only dendroTools-1.0.7/dendroTools/data/swit272_daily_temperatures.rda |binary dendroTools-1.0.7/dendroTools/inst/doc/Examples_daily_response.html | 189 +- dendroTools-1.0.7/dendroTools/inst/doc/compare_methods_vignette.html | 37 dendroTools-1.0.7/dendroTools/man/boot_f_brnn.Rd |only dendroTools-1.0.7/dendroTools/man/boot_f_cor.Rd |only dendroTools-1.0.7/dendroTools/man/boot_f_lm.Rd |only dendroTools-1.0.7/dendroTools/man/boot_f_pcor.Rd |only dendroTools-1.0.7/dendroTools/man/compare_methods.Rd | 40 dendroTools-1.0.7/dendroTools/man/daily_response.Rd | 158 + dendroTools-1.0.7/dendroTools/man/daily_response_seascorr.Rd | 70 dendroTools-1.0.7/dendroTools/man/data_MVA.Rd | 2 dendroTools-1.0.7/dendroTools/man/data_TRW.Rd | 5 dendroTools-1.0.7/dendroTools/man/data_TRW_1.Rd | 2 dendroTools-1.0.7/dendroTools/man/data_transform.Rd |only dendroTools-1.0.7/dendroTools/man/dataset_MVA_individual.Rd | 2 dendroTools-1.0.7/dendroTools/man/example_dataset_1.Rd | 2 dendroTools-1.0.7/dendroTools/man/example_proxies_1.Rd | 2 dendroTools-1.0.7/dendroTools/man/example_proxies_individual.Rd | 2 dendroTools-1.0.7/dendroTools/man/glimpse_daily_data.Rd | 6 dendroTools-1.0.7/dendroTools/man/monthly_response.Rd | 137 - dendroTools-1.0.7/dendroTools/man/monthly_response_seascorr.Rd | 125 - dendroTools-1.0.7/dendroTools/man/swit272_daily_precipitation.Rd |only dendroTools-1.0.7/dendroTools/man/swit272_daily_temperatures.Rd | 15 60 files changed, 2399 insertions(+), 1161 deletions(-)
Title: Camera Trap Data Management and Preparation of Occupancy and
Spatial Capture-Recapture Analyses
Description: Management of and data extraction from camera trap photographs in wildlife studies. The package provides a workflow for storing and sorting camera trap photos, tabulates records of species and individuals, and creates detection/non-detection matrices for occupancy and spatial capture-recapture analyses with great flexibility. In addition, it provides simple mapping functions (number of species, number of independent species detections by station including GIS export) and can visualise species activity data.
Author: Juergen Niedballa [aut, cre],
Alexandre Courtiol [aut],
Rahel Sollmann [aut],
John Mathai [ctb],
Seth Timothy Wong [ctb],
An The Truong Nguyen [ctb],
Azlan bin Mohamed [ctb],
Andrew Tilker [ctb],
Andreas Wilting [ctb, ths]
Maintainer: Juergen Niedballa <camtrapr@gmail.com>
Diff between camtrapR versions 1.2.1 dated 2019-12-17 and 1.2.2 dated 2020-01-07
DESCRIPTION | 12 +-- MD5 | 42 ++++++------ NAMESPACE | 2 NEWS | 13 +++ R/addCopyrightTag.R | 2 R/cameraOperation.R | 10 ++ R/exifTagNames.R | 2 R/getSpeciesImages.R | 6 - R/imageRename.R | 5 - R/recordTable.R | 57 ++++++++-------- R/recordTableIndividual.R | 48 +++++++------ R/timeShiftImages.R | 3 R/variousOtherHelperFunctions.R | 5 - inst/doc/DataExploration.html | 12 +-- inst/doc/DataExtraction.html | 58 ++++++++-------- inst/doc/ImageOrganisation.html | 58 ++++++++-------- inst/doc/SpeciesIndividualIdentification.R | 2 inst/doc/SpeciesIndividualIdentification.Rmd | 2 inst/doc/SpeciesIndividualIdentification.html | 90 +++++++++++++------------- man/recordTable.Rd | 2 tests |only vignettes/SpeciesIndividualIdentification.Rmd | 2 22 files changed, 233 insertions(+), 200 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 [aut, cre] (<https://orcid.org/0000-0001-7130-793X>),
Matti Vihola [aut] (<https://orcid.org/0000-0002-8041-7222>)
Maintainer: Jouni Helske <jouni.helske@iki.fi>
Diff between bssm versions 0.1.8 dated 2019-09-25 and 0.1.8-1 dated 2020-01-07
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS | 4 ++++ R/predict.R | 4 ++-- inst/CITATION | 2 +- inst/doc/bssm.html | 16 +++++++++------- inst/doc/growth_model.html | 4 ++-- man/predict.Rd | 4 ++-- tests/testthat/test_mcmc.R | 34 +++++++++++++++++----------------- 9 files changed, 49 insertions(+), 43 deletions(-)
Title: Australia Maps
Description: Maps of Australian coastline and administrative regions. Data
can be drawn or accessed directly as simple features objects. Includes
simple functions for country or state maps of Australia and in-built data
sets of administrative regions from the Australian Bureau of Statistics
<https://www.abs.gov.au/>. Layers include electoral divisions and local
government areas, simplified from the original sources but with sufficient
detail to allow mapping of a local municipality.
Author: Michael Sumner [aut, cre],
Dianne Cook [ctb],
Edzer Pebesma [ctb] (sf plot)
Maintainer: Michael Sumner <mdsumner@gmail.com>
Diff between ozmaps versions 0.2.0 dated 2019-11-06 and 0.3.0 dated 2020-01-07
DESCRIPTION | 11 ++--- MD5 | 38 ++++++++++++----- NEWS.md |only R/ozmap.R | 3 - R/ozmaps-package.R | 11 ++++- README.md | 68 +++++++++++++++++++++++++------ build |only inst/doc |only inst/examples/awesome-colRoz.R |only man/abs-data.Rd | 11 ++++- man/figures/README-abs-1.png |only man/figures/README-abs-2.png |only man/figures/README-add-plot-1.png |only man/figures/README-country-1.png |only man/figures/README-detail-1.png |only man/figures/README-ochRe-1.png |only man/figures/README-ochRe-2.png |only man/figures/README-ozmap-1.png |only man/figures/README-unnamed-chunk-4-1.png |binary man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-6-1.png |only man/figures/README-unnamed-chunk-8-1.png |binary man/figures/README-unnamed-chunk-8-2.png |binary man/figures/README-unnamed-chunk-9-1.png |only man/figures/README-unnamed-chunk-9-2.png |only man/ozmap_data.Rd | 3 - vignettes |only 27 files changed, 113 insertions(+), 32 deletions(-)
Title: 'sf'-Based Interface to the 'HERE' REST APIs
Description: Interface to the 'HERE' REST APIs <https://developer.here.com/develop/rest-apis>:
(1) geocode and autocomplete addresses or reverse geocode POIs using the 'Geocoder' API;
(2) route directions, travel distance or time matrices and isolines using the 'Routing' API;
(3) request real-time traffic flow and incident information from the 'Traffic' API;
(4) find request public transport connections and nearby stations from the 'Public Transit' API;
(5) get weather forecasts, reports on current weather conditions, astronomical
information and alerts at a specific location from the 'Destination Weather' API.
Locations, routes and isolines are returned as 'sf' objects.
Author: Merlin Unterfinger [aut, cre]
Maintainer: Merlin Unterfinger <info@munterfinger.ch>
Diff between hereR versions 0.2.1 dated 2019-12-16 and 0.3.0 dated 2020-01-07
hereR-0.2.1/hereR/man/set_auth.Rd |only hereR-0.2.1/hereR/man/unset_auth.Rd |only hereR-0.3.0/hereR/DESCRIPTION | 15 hereR-0.3.0/hereR/MD5 | 138 - hereR-0.3.0/hereR/NAMESPACE | 5 hereR-0.3.0/hereR/NEWS.md | 20 hereR-0.3.0/hereR/R/authentication.R | 162 - hereR-0.3.0/hereR/R/autocomplete.R | 19 hereR-0.3.0/hereR/R/checks.R | 42 hereR-0.3.0/hereR/R/connection.R |only hereR-0.3.0/hereR/R/data.R | 74 hereR-0.3.0/hereR/R/defunct.R |only hereR-0.3.0/hereR/R/geocode.R | 21 hereR-0.3.0/hereR/R/isoline.R | 68 hereR-0.3.0/hereR/R/package.R |only hereR-0.3.0/hereR/R/reverse_geocode.R | 21 hereR-0.3.0/hereR/R/route.R | 82 hereR-0.3.0/hereR/R/route_matrix.R | 112 hereR-0.3.0/hereR/R/station.R |only hereR-0.3.0/hereR/R/sysdata.rda |binary hereR-0.3.0/hereR/R/traffic.R | 85 hereR-0.3.0/hereR/R/utils.R | 23 hereR-0.3.0/hereR/R/weather.R | 27 hereR-0.3.0/hereR/README.md | 94 hereR-0.3.0/hereR/build/vignette.rds |binary hereR-0.3.0/hereR/inst/doc/authentication.R | 12 hereR-0.3.0/hereR/inst/doc/authentication.Rmd | 20 hereR-0.3.0/hereR/inst/doc/authentication.html | 21 hereR-0.3.0/hereR/inst/doc/geocoder.R | 20 hereR-0.3.0/hereR/inst/doc/geocoder.html | 1085 ++++---- hereR-0.3.0/hereR/inst/doc/routing.R | 31 hereR-0.3.0/hereR/inst/doc/routing.Rmd | 24 hereR-0.3.0/hereR/inst/doc/routing.html | 1277 +++++----- hereR-0.3.0/hereR/inst/doc/traffic.R | 17 hereR-0.3.0/hereR/inst/doc/traffic.Rmd | 9 hereR-0.3.0/hereR/inst/doc/traffic.html | 1080 ++++---- hereR-0.3.0/hereR/inst/doc/transit.R |only hereR-0.3.0/hereR/inst/doc/transit.Rmd |only hereR-0.3.0/hereR/inst/doc/transit.html |only hereR-0.3.0/hereR/inst/doc/weather.R | 38 hereR-0.3.0/hereR/inst/doc/weather.Rmd | 26 hereR-0.3.0/hereR/inst/doc/weather.html | 1256 +++++---- hereR-0.3.0/hereR/man/aoi.Rd | 2 hereR-0.3.0/hereR/man/autocomplete.Rd | 9 hereR-0.3.0/hereR/man/connection.Rd |only hereR-0.3.0/hereR/man/geocode.Rd | 9 hereR-0.3.0/hereR/man/hereR-defunct.Rd |only hereR-0.3.0/hereR/man/hereR-package.Rd |only hereR-0.3.0/hereR/man/isoline.Rd | 43 hereR-0.3.0/hereR/man/poi.Rd | 2 hereR-0.3.0/hereR/man/reverse_geocode.Rd | 12 hereR-0.3.0/hereR/man/route.Rd | 49 hereR-0.3.0/hereR/man/route_matrix.Rd | 45 hereR-0.3.0/hereR/man/set_auth-defunct.Rd |only hereR-0.3.0/hereR/man/set_key.Rd |only hereR-0.3.0/hereR/man/station.Rd |only hereR-0.3.0/hereR/man/traffic.Rd | 29 hereR-0.3.0/hereR/man/unset_auth-defunct.Rd |only hereR-0.3.0/hereR/man/unset_key.Rd |only hereR-0.3.0/hereR/man/weather.Rd | 11 hereR-0.3.0/hereR/tests/testthat/test-authentication.R | 19 hereR-0.3.0/hereR/tests/testthat/test-autocomplete.R | 9 hereR-0.3.0/hereR/tests/testthat/test-connection.R |only hereR-0.3.0/hereR/tests/testthat/test-geocode.R | 7 hereR-0.3.0/hereR/tests/testthat/test-isoline.R | 10 hereR-0.3.0/hereR/tests/testthat/test-reverse_geocode.R | 9 hereR-0.3.0/hereR/tests/testthat/test-route.R | 22 hereR-0.3.0/hereR/tests/testthat/test-route_matrix.R | 26 hereR-0.3.0/hereR/tests/testthat/test-station.R |only hereR-0.3.0/hereR/tests/testthat/test-traffic_flow.R | 16 hereR-0.3.0/hereR/tests/testthat/test-traffic_incidents.R | 11 hereR-0.3.0/hereR/tests/testthat/test-weather_alerts.R | 7 hereR-0.3.0/hereR/tests/testthat/test-weather_forecast_astronomy.R | 37 hereR-0.3.0/hereR/tests/testthat/test-weather_forecast_hourly.R | 37 hereR-0.3.0/hereR/tests/testthat/test-weather_observation.R | 37 hereR-0.3.0/hereR/vignettes/authentication.Rmd | 20 hereR-0.3.0/hereR/vignettes/routing.Rmd | 24 hereR-0.3.0/hereR/vignettes/traffic.Rmd | 9 hereR-0.3.0/hereR/vignettes/transit.Rmd |only hereR-0.3.0/hereR/vignettes/weather.Rmd | 26 80 files changed, 3490 insertions(+), 2971 deletions(-)