Title: Run Predictions Inside the Database
Description: It parses a fitted 'R' model object, and returns a formula
in 'Tidy Eval' code that calculates the predictions.
It works with several databases back-ends because it leverages 'dplyr'
and 'dbplyr' for the final 'SQL' translation of the algorithm. It currently
supports lm(), glm(), randomForest(), ranger(), earth(), xgb.Booster.complete(),
cubist(), and ctree() models.
Author: Edgar Ruiz [aut, cre]
Maintainer: Edgar Ruiz <edgar@rstudio.com>
Diff between tidypredict versions 0.3.0 dated 2019-01-10 and 0.4.0 dated 2019-07-12
tidypredict-0.3.0/tidypredict/man/figures/howitworks.PNG |only tidypredict-0.4.0/tidypredict/DESCRIPTION | 21 tidypredict-0.4.0/tidypredict/MD5 | 140 ++ tidypredict-0.4.0/tidypredict/NAMESPACE | 111 +- tidypredict-0.4.0/tidypredict/NEWS.md | 94 +- tidypredict-0.4.0/tidypredict/R/acceptable.R | 161 +-- tidypredict-0.4.0/tidypredict/R/as-parsed-model.R |only tidypredict-0.4.0/tidypredict/R/model-cubist.R |only tidypredict-0.4.0/tidypredict/R/model-earth.R | 165 +-- tidypredict-0.4.0/tidypredict/R/model-lm.R | 470 +++++----- tidypredict-0.4.0/tidypredict/R/model-partykit.R |only tidypredict-0.4.0/tidypredict/R/model-ranger.R | 182 ++- tidypredict-0.4.0/tidypredict/R/model-rf.R | 232 ++-- tidypredict-0.4.0/tidypredict/R/model-xgboost.R |only tidypredict-0.4.0/tidypredict/R/parsemodel.R | 39 tidypredict-0.4.0/tidypredict/R/predict-column.R | 83 - tidypredict-0.4.0/tidypredict/R/predict-fit.R | 53 - tidypredict-0.4.0/tidypredict/R/predict-interval.R | 69 - tidypredict-0.4.0/tidypredict/R/test-predictions.R | 405 +++++--- tidypredict-0.4.0/tidypredict/R/tidymodels.R |only tidypredict-0.4.0/tidypredict/R/tidypredict.R | 39 tidypredict-0.4.0/tidypredict/R/to_sql.R | 93 - tidypredict-0.4.0/tidypredict/README.md | 205 +++- tidypredict-0.4.0/tidypredict/build |only tidypredict-0.4.0/tidypredict/inst |only tidypredict-0.4.0/tidypredict/man/acceptable_formula.Rd | 45 tidypredict-0.4.0/tidypredict/man/as_parsed_model.Rd |only tidypredict-0.4.0/tidypredict/man/figures/howitworks.png |only tidypredict-0.4.0/tidypredict/man/figures/logo.png |binary tidypredict-0.4.0/tidypredict/man/knit_print.tidypredict_test.Rd | 24 tidypredict-0.4.0/tidypredict/man/parse_model.Rd | 49 - tidypredict-0.4.0/tidypredict/man/print.tidypredict_test.Rd | 24 tidypredict-0.4.0/tidypredict/man/reexports.Rd |only tidypredict-0.4.0/tidypredict/man/tidy.pm_regression.Rd |only tidypredict-0.4.0/tidypredict/man/tidypredict-package.Rd | 59 - tidypredict-0.4.0/tidypredict/man/tidypredict_fit.Rd | 41 tidypredict-0.4.0/tidypredict/man/tidypredict_interval.Rd | 53 - tidypredict-0.4.0/tidypredict/man/tidypredict_sql.Rd | 49 - tidypredict-0.4.0/tidypredict/man/tidypredict_sql_interval.Rd | 53 - tidypredict-0.4.0/tidypredict/man/tidypredict_test.Rd | 77 - tidypredict-0.4.0/tidypredict/man/tidypredict_to_column.Rd | 54 - tidypredict-0.4.0/tidypredict/tests/testthat.R | 16 tidypredict-0.4.0/tidypredict/tests/testthat/test-acceptable.R | 18 tidypredict-0.4.0/tidypredict/tests/testthat/test-cubist.R |only tidypredict-0.4.0/tidypredict/tests/testthat/test-earth.R | 250 +++-- tidypredict-0.4.0/tidypredict/tests/testthat/test-list.R | 32 tidypredict-0.4.0/tidypredict/tests/testthat/test-party.R |only tidypredict-0.4.0/tidypredict/tests/testthat/test-ranger.R | 77 + tidypredict-0.4.0/tidypredict/tests/testthat/test-rf.R | 66 - tidypredict-0.4.0/tidypredict/tests/testthat/test-sql.R | 26 tidypredict-0.4.0/tidypredict/tests/testthat/test-tester.R | 71 - tidypredict-0.4.0/tidypredict/tests/testthat/test_glm.R | 52 - tidypredict-0.4.0/tidypredict/tests/testthat/test_lm.R | 62 + tidypredict-0.4.0/tidypredict/tests/testthat/test_xgboost.R |only tidypredict-0.4.0/tidypredict/vignettes |only 55 files changed, 2162 insertions(+), 1598 deletions(-)
Title: General Resampling Infrastructure
Description: Classes and functions to create and summarize different types of resampling objects (e.g. bootstrap, cross-validation).
Author: Max Kuhn [aut, cre],
Fanny Chow [aut],
Hadley Wickham [aut],
RStudio [cph]
Maintainer: Max Kuhn <max@rstudio.com>
Diff between rsample versions 0.0.4 dated 2019-01-07 and 0.0.5 dated 2019-07-12
DESCRIPTION | 15 +- MD5 | 76 +++++++------- NAMESPACE | 25 ++++ NEWS.md | 8 + R/apparent.R | 20 +-- R/boot.R | 90 +++++++++++------ R/bootci.R |only R/groups.R | 12 +- R/initial_split.R | 34 ++++-- R/lables.R | 59 ++++++++++- R/loo.R | 10 + R/make_strata.R | 78 ++++++++------ R/mc.R | 87 ++++++++++------ R/nest.R | 18 +-- R/rolling_origin.R | 34 ++++-- R/tidy.R | 72 ++++++++----- R/vfold.R | 55 ++++++++-- build/vignette.rds |binary inst/doc/Basics.html | 93 +++++++++++------ inst/doc/Working_with_rsets.html | 141 ++++++++++++++++----------- man/add_resample_id.Rd |only man/apparent.Rd | 4 man/bootstraps.Rd | 48 +++++++-- man/figures |only man/group_vfold_cv.Rd | 4 man/initial_split.Rd | 25 +++- man/int_pctl.Rd |only man/labels.rsplit.Rd | 3 man/loo_cv.Rd | 9 + man/make_strata.Rd | 9 + man/mc_cv.Rd | 32 ++++-- man/rolling_origin.Rd | 32 ++++-- man/tidy.rsplit.Rd | 39 ++++--- man/vfold_cv.Rd | 40 ++++++- tests/testthat/test_boot.R | 3 tests/testthat/test_bootci.R |only tests/testthat/test_labels.R | 46 ++++++++ tests/testthat/test_mc.R | 3 tests/testthat/test_strata.R | 2 tests/testthat/test_vfold.R | 3 vignettes/Applications/Intervals.Rmd |only vignettes/Applications/Survival_Analysis.Rmd | 7 - 42 files changed, 848 insertions(+), 388 deletions(-)
Title: Manipulation Testing Based on Density Discontinuity
Description: Density discontinuity test (a.k.a. manipulation test) is commonly employed in regression discontinuity designs and other program evaluation settings to detect whether there is evidence of perfect self-selection (manipulation) around a cutoff where a treatment/policy assignment changes. This package provides tools for conducting the aforementioned statistical test: rddensity() to construct local polynomial based density discontinuity test given a prespecified cutoff, rdbwdensity() to perform bandwidth selection, and rdplotdensity() to construct density plot near the cutoff.
Author: Matias D. Cattaneo, Michael Jansson, Xinwei Ma
Maintainer: Xinwei Ma <x1ma@ucsd.edu>
Diff between rddensity versions 0.2.2 dated 2017-08-03 and 1.0 dated 2019-07-12
DESCRIPTION | 12 ++++++------ MD5 | 26 +++++++++++++------------- R/rdbwdensity.R | 36 ++++++++++++++++++++---------------- R/rddensity-package.R | 16 ++++++++-------- R/rddensity.R | 29 +++++++++++++++++++---------- R/rddensity_fun.R | 10 ---------- R/rddensity_senate.R | 6 +++--- R/rdplotdensity.R | 29 +++++++++++++++++++++-------- man/h_opt_density.Rd | 3 ++- man/rdbwdensity.Rd | 24 +++++++++++++----------- man/rddensity-package.Rd | 16 ++++++++-------- man/rddensity.Rd | 21 +++++++++++---------- man/rddensity_senate.Rd | 6 +++--- man/rdplotdensity.Rd | 31 ++++++++++++++++++------------- 14 files changed, 145 insertions(+), 120 deletions(-)
Title: Local Polynomial Density Estimation and Inference
Description: Without imposing stringent distributional assumptions or shape restrictions, nonparametric density estimation has been popular in economics and other social sciences for counterfactual analysis, program evaluation, and policy recommendations. This package implements a novel density estimator based on local polynomial regressions, documented in Cattaneo, Jansson and Ma (2019a, b) <arXiv:1811.11512, arXiv:1906.06529>: lpdensity() to construct local polynomial based density (and derivatives) estimator; lpbwdensity() to perform data-driven bandwidth selection; and lpdensity.plot() for density plot with robust confidence interval.
Author: Matias D. Cattaneo, Michael Jansson, Xinwei Ma
Maintainer: Xinwei Ma <x1ma@ucsd.edu>
Diff between lpdensity versions 0.2.3 dated 2019-04-15 and 1.0 dated 2019-07-12
DESCRIPTION | 10 +++++----- MD5 | 22 +++++++++++----------- R/lpbwdensity.R | 29 ++++++++++++++++------------- R/lpbwdensity_fn.R | 17 ++--------------- R/lpdensity-package.R | 18 +++++++++--------- R/lpdensity.R | 21 ++++++++++++--------- R/lpdensity.plot.R | 23 +++++++++++++++-------- R/lpdensity_fn.R | 21 --------------------- man/lpbwdensity.Rd | 19 +++++++++++-------- man/lpdensity-package.Rd | 18 +++++++++--------- man/lpdensity.Rd | 19 +++++++++++-------- man/lpdensity.plot.Rd | 23 +++++++++++++++-------- 12 files changed, 116 insertions(+), 124 deletions(-)
Title: Airborne LiDAR Data Manipulation and Visualization for Forestry
Applications
Description: Airborne LiDAR (Light Detection and Ranging) interface for data
manipulation and visualization. Read/write 'las' and 'laz' files, computation
of metrics in area based approach, point filtering, artificial point reduction,
classification from geographic data, normalization, individual tree segmentation
and other manipulations.
Author: Jean-Romain Roussel [aut, cre, cph],
David Auty [aut, ctb] (Reviews the documentation),
Florian De Boissieu [ctb] (Fixed bugs and improved catalog features),
Andrew Sánchez Meador [ctb] (Implemented lassnags)
Maintainer: Jean-Romain Roussel <jean-romain.roussel.1@ulaval.ca>
Diff between lidR versions 2.0.3 dated 2019-05-09 and 2.1.0 dated 2019-07-12
lidR-2.0.3/lidR/R/LASmethods-LAS.r |only lidR-2.0.3/lidR/R/LASmethods-LAScatalog.r |only lidR-2.0.3/lidR/R/LASmethods-LAScluster.r |only lidR-2.0.3/lidR/R/LASmethods-LASheader.r |only lidR-2.0.3/lidR/R/LASmethods-generic.r |only lidR-2.0.3/lidR/R/algo_digital_surface_model.r |only lidR-2.0.3/lidR/R/algo_ground_segmentation.r |only lidR-2.0.3/lidR/R/algo_points_decimation.r |only lidR-2.0.3/lidR/R/algo_snags_segmentation.r |only lidR-2.0.3/lidR/R/algo_spatial_interpolations.r |only lidR-2.0.3/lidR/R/algo_tree_detection.R |only lidR-2.0.3/lidR/R/algo_tree_segmentation.r |only lidR-2.0.3/lidR/R/lidR-package.r |only lidR-2.0.3/lidR/R/utils_match_chm_and_seeds.r |only lidR-2.0.3/lidR/man/catalog.Rd |only lidR-2.0.3/lidR/man/epsg.Rd |only lidR-2.0.3/lidR/man/is.empty.Rd |only lidR-2.0.3/lidR/tests/testthat/test-catalog_select.R |only lidR-2.1.0/lidR/DESCRIPTION | 67 - lidR-2.1.0/lidR/MD5 | 357 +++-- lidR-2.1.0/lidR/NAMESPACE | 31 lidR-2.1.0/lidR/NEWS.md | 122 + lidR-2.1.0/lidR/R/Class-LAScatalog.r | 15 lidR-2.1.0/lidR/R/Class-LASheader.r | 53 lidR-2.1.0/lidR/R/RcppExports.R | 44 lidR-2.1.0/lidR/R/algorithm-dsm.r |only lidR-2.1.0/lidR/R/algorithm-gnd.r |only lidR-2.1.0/lidR/R/algorithm-itd.R |only lidR-2.1.0/lidR/R/algorithm-its.r |only lidR-2.1.0/lidR/R/algorithm-points-decimation.r |only lidR-2.1.0/lidR/R/algorithm-shp.r |only lidR-2.1.0/lidR/R/algorithm-snag.r |only lidR-2.1.0/lidR/R/algorithm-spatial-interpolations.r |only lidR-2.1.0/lidR/R/catalog_apply.r | 141 +- lidR-2.1.0/lidR/R/catalog_fakerun.r | 14 lidR-2.1.0/lidR/R/catalog_retile.r | 4 lidR-2.1.0/lidR/R/catalog_select.r | 140 +- lidR-2.1.0/lidR/R/clusters_apply.r | 281 ++-- lidR-2.1.0/lidR/R/doc-drivers.R |only lidR-2.1.0/lidR/R/doc-lidR.R |only lidR-2.1.0/lidR/R/doc-parallelism.R |only lidR-2.1.0/lidR/R/grid_hexametrics.r | 8 lidR-2.1.0/lidR/R/grid_metrics.r | 107 + lidR-2.1.0/lidR/R/grid_metrics3d.r | 10 lidR-2.1.0/lidR/R/grid_terrain.r | 10 lidR-2.1.0/lidR/R/io_readLAS.r | 86 - lidR-2.1.0/lidR/R/io_readLAScatalog.r |only lidR-2.1.0/lidR/R/lascheck.r | 492 ++----- lidR-2.1.0/lidR/R/lasclip.r | 12 lidR-2.1.0/lidR/R/lasdetectshape.r |only lidR-2.1.0/lidR/R/lasfilter.r | 13 lidR-2.1.0/lidR/R/lasfilterdecimate.r | 4 lidR-2.1.0/lidR/R/lasfilterduplicates.r | 2 lidR-2.1.0/lidR/R/lasfiltersurfacepoints.r | 2 lidR-2.1.0/lidR/R/lasground.r | 33 lidR-2.1.0/lidR/R/lasindentify.r | 46 lidR-2.1.0/lidR/R/lasmergespatial.r | 2 lidR-2.1.0/lidR/R/lasmetrics.r | 8 lidR-2.1.0/lidR/R/lasnormalize.r | 6 lidR-2.1.0/lidR/R/lassmooth.r | 9 lidR-2.1.0/lidR/R/lassnags.r | 2 lidR-2.1.0/lidR/R/lastransform.r | 32 lidR-2.1.0/lidR/R/lastrees.r | 9 lidR-2.1.0/lidR/R/lasvoxelize.r | 4 lidR-2.1.0/lidR/R/methods-LAS.r |only lidR-2.1.0/lidR/R/methods-LAScatalog.r |only lidR-2.1.0/lidR/R/methods-LAScluster.r |only lidR-2.1.0/lidR/R/methods-LASheader.r |only lidR-2.1.0/lidR/R/plot.r |only lidR-2.1.0/lidR/R/print.r |only lidR-2.1.0/lidR/R/projection.r |only lidR-2.1.0/lidR/R/tree_detection.r | 39 lidR-2.1.0/lidR/R/tree_hulls.r | 118 - lidR-2.1.0/lidR/R/tree_metrics.r | 59 lidR-2.1.0/lidR/R/utils_assertive.r | 74 - lidR-2.1.0/lidR/R/utils_catalog_options.r | 22 lidR-2.1.0/lidR/R/utils_define_constant.R | 61 lidR-2.1.0/lidR/R/utils_geometry.r | 128 +- lidR-2.1.0/lidR/R/utils_is.r | 95 + lidR-2.1.0/lidR/R/utils_metrics.r | 628 +++++----- lidR-2.1.0/lidR/R/utils_misc.r | 93 - lidR-2.1.0/lidR/R/utils_raster.r |only lidR-2.1.0/lidR/R/utils_threads.r |only lidR-2.1.0/lidR/R/zzz.r | 24 lidR-2.1.0/lidR/build/vignette.rds |binary lidR-2.1.0/lidR/inst/doc/lidR-LAS-class.R | 14 lidR-2.1.0/lidR/inst/doc/lidR-LAS-class.Rmd | 24 lidR-2.1.0/lidR/inst/doc/lidR-LAS-class.html | 62 lidR-2.1.0/lidR/inst/doc/lidR-LAScatalog-class.Rmd | 4 lidR-2.1.0/lidR/inst/doc/lidR-LAScatalog-class.html | 17 lidR-2.1.0/lidR/inst/doc/lidR-catalog-apply-examples.Rmd | 4 lidR-2.1.0/lidR/inst/doc/lidR-catalog-apply-examples.html | 4 lidR-2.1.0/lidR/inst/doc/lidR-computation-speed-LAScatalog.R | 27 lidR-2.1.0/lidR/inst/doc/lidR-computation-speed-LAScatalog.Rmd | 48 lidR-2.1.0/lidR/inst/doc/lidR-computation-speed-LAScatalog.html | 86 - lidR-2.1.0/lidR/man/LAS-class.Rd | 2 lidR-2.1.0/lidR/man/LAScatalog-class.Rd | 13 lidR-2.1.0/lidR/man/LASheader.Rd | 2 lidR-2.1.0/lidR/man/area.Rd | 44 lidR-2.1.0/lidR/man/as.list.LASheader.Rd | 2 lidR-2.1.0/lidR/man/catalog_apply.Rd | 31 lidR-2.1.0/lidR/man/catalog_options_tools.Rd | 2 lidR-2.1.0/lidR/man/catalog_retile.Rd | 2 lidR-2.1.0/lidR/man/catalog_select.Rd |only lidR-2.1.0/lidR/man/csf.Rd | 2 lidR-2.1.0/lidR/man/dalponte2016.Rd | 2 lidR-2.1.0/lidR/man/dsmtin.Rd | 2 lidR-2.1.0/lidR/man/extent.Rd | 2 lidR-2.1.0/lidR/man/grid_canopy.Rd | 2 lidR-2.1.0/lidR/man/grid_density.Rd | 2 lidR-2.1.0/lidR/man/grid_hexametrics.Rd | 8 lidR-2.1.0/lidR/man/grid_metrics.Rd | 61 lidR-2.1.0/lidR/man/grid_metrics3d.Rd | 8 lidR-2.1.0/lidR/man/grid_terrain.Rd | 2 lidR-2.1.0/lidR/man/highest.Rd | 2 lidR-2.1.0/lidR/man/homogenize.Rd | 2 lidR-2.1.0/lidR/man/is.Rd |only lidR-2.1.0/lidR/man/knnidw.Rd | 2 lidR-2.1.0/lidR/man/kriging.Rd | 2 lidR-2.1.0/lidR/man/lascheck.Rd | 5 lidR-2.1.0/lidR/man/lasclip.Rd | 3 lidR-2.1.0/lidR/man/lasdetectshape.Rd |only lidR-2.1.0/lidR/man/lasfilterdecimate.Rd | 2 lidR-2.1.0/lidR/man/lasfilterduplicates.Rd | 2 lidR-2.1.0/lidR/man/lasfiltersurfacepoints.Rd | 2 lidR-2.1.0/lidR/man/lasground.Rd | 13 lidR-2.1.0/lidR/man/lasidentify.Rd | 11 lidR-2.1.0/lidR/man/lasmetrics.Rd | 8 lidR-2.1.0/lidR/man/lasnormalize.Rd | 2 lidR-2.1.0/lidR/man/lassnags.Rd | 2 lidR-2.1.0/lidR/man/lastransform.Rd | 13 lidR-2.1.0/lidR/man/lasvoxelize.Rd | 2 lidR-2.1.0/lidR/man/li2012.Rd | 2 lidR-2.1.0/lidR/man/lidR-LAScatalog-drivers.Rd |only lidR-2.1.0/lidR/man/lidR-package.Rd | 12 lidR-2.1.0/lidR/man/lidR-parallelism.Rd |only lidR-2.1.0/lidR/man/lmf.Rd | 56 lidR-2.1.0/lidR/man/lmfauto.Rd |only lidR-2.1.0/lidR/man/manual.Rd | 14 lidR-2.1.0/lidR/man/p2r.Rd | 2 lidR-2.1.0/lidR/man/pitfree.Rd | 2 lidR-2.1.0/lidR/man/plot.Rd | 42 lidR-2.1.0/lidR/man/pmf.Rd | 2 lidR-2.1.0/lidR/man/print.Rd | 3 lidR-2.1.0/lidR/man/projection.Rd |only lidR-2.1.0/lidR/man/random.Rd | 2 lidR-2.1.0/lidR/man/readLAS.Rd | 26 lidR-2.1.0/lidR/man/readLAScatalog.Rd |only lidR-2.1.0/lidR/man/readLASheader.Rd |only lidR-2.1.0/lidR/man/redefined_behaviors.Rd | 2 lidR-2.1.0/lidR/man/set_lidr_threads.Rd |only lidR-2.1.0/lidR/man/shape_detection.Rd |only lidR-2.1.0/lidR/man/silva2016.Rd | 2 lidR-2.1.0/lidR/man/stdmetrics.Rd | 76 - lidR-2.1.0/lidR/man/tin.Rd | 2 lidR-2.1.0/lidR/man/tree_detection.Rd | 5 lidR-2.1.0/lidR/man/tree_hulls.Rd | 25 lidR-2.1.0/lidR/man/tree_metrics.Rd | 25 lidR-2.1.0/lidR/man/util_makeZhangParam.Rd | 2 lidR-2.1.0/lidR/man/watershed.Rd | 2 lidR-2.1.0/lidR/man/wing2015.Rd | 4 lidR-2.1.0/lidR/src/C_Rfast.cpp | 15 lidR-2.1.0/lidR/src/C_knn.cpp | 37 lidR-2.1.0/lidR/src/C_lasdetectshape.cpp |only lidR-2.1.0/lidR/src/C_lassmooth.cpp | 25 lidR-2.1.0/lidR/src/C_li2012.cpp | 8 lidR-2.1.0/lidR/src/C_lmf.cpp | 27 lidR-2.1.0/lidR/src/C_morphology.cpp | 12 lidR-2.1.0/lidR/src/C_points_in_polygons_wkt.cpp | 25 lidR-2.1.0/lidR/src/C_search.cpp |only lidR-2.1.0/lidR/src/C_tsearch.cpp | 26 lidR-2.1.0/lidR/src/C_wing2015.cpp | 43 lidR-2.1.0/lidR/src/Makevars |only lidR-2.1.0/lidR/src/Makevars.win |only lidR-2.1.0/lidR/src/Progress.cpp | 49 lidR-2.1.0/lidR/src/Progress.h | 4 lidR-2.1.0/lidR/src/QuadTree.cpp | 58 lidR-2.1.0/lidR/src/QuadTree.h | 4 lidR-2.1.0/lidR/src/RcppExports.cpp | 121 + lidR-2.1.0/lidR/src/lidr.h |only lidR-2.1.0/lidR/src/myomp.h |only lidR-2.1.0/lidR/src/openmputils.cpp |only lidR-2.1.0/lidR/tests/testthat/Rplots.pdf |binary lidR-2.1.0/lidR/tests/testthat/test-LAS.R | 149 +- lidR-2.1.0/lidR/tests/testthat/test-LAScatalog.R | 38 lidR-2.1.0/lidR/tests/testthat/test-algorithm-dispatch.R |only lidR-2.1.0/lidR/tests/testthat/test-catalog_errors.R | 5 lidR-2.1.0/lidR/tests/testthat/test-catalog_index.R | 48 lidR-2.1.0/lidR/tests/testthat/test-catalog_intersect.R |only lidR-2.1.0/lidR/tests/testthat/test-catalog_makeclusters.R | 585 ++------- lidR-2.1.0/lidR/tests/testthat/test-catalog_retile.R | 20 lidR-2.1.0/lidR/tests/testthat/test-grid_canopy.R | 80 - lidR-2.1.0/lidR/tests/testthat/test-grid_density.R | 17 lidR-2.1.0/lidR/tests/testthat/test-grid_hexametrics.R | 19 lidR-2.1.0/lidR/tests/testthat/test-grid_metrics.R | 117 + lidR-2.1.0/lidR/tests/testthat/test-grid_metrics3d.R | 18 lidR-2.1.0/lidR/tests/testthat/test-grid_terrain.R | 104 - lidR-2.1.0/lidR/tests/testthat/test-internal_quadtree.R | 18 lidR-2.1.0/lidR/tests/testthat/test-lasclip.R | 253 ++-- lidR-2.1.0/lidR/tests/testthat/test-lasground.R | 2 lidR-2.1.0/lidR/tests/testthat/test-lasnormalize.R | 2 lidR-2.1.0/lidR/tests/testthat/test-lastrees.R | 4 lidR-2.1.0/lidR/tests/testthat/test-projection.R |only lidR-2.1.0/lidR/tests/testthat/test-tree_detection.R | 2 lidR-2.1.0/lidR/tests/testthat/test-tree_metrics.R | 8 lidR-2.1.0/lidR/tests/testthat/test-utils_geometry.R | 24 lidR-2.1.0/lidR/vignettes/lidR-LAS-class.Rmd | 24 lidR-2.1.0/lidR/vignettes/lidR-LAScatalog-class.Rmd | 4 lidR-2.1.0/lidR/vignettes/lidR-catalog-apply-examples.Rmd | 4 lidR-2.1.0/lidR/vignettes/lidR-computation-speed-LAScatalog.Rmd | 48 210 files changed, 3334 insertions(+), 3080 deletions(-)
Title: Randomization Tests
Description: A collection of randomization tests, data sets and examples. The current version focuses on three testing problems and their implementation in empirical work. First, it facilitates the empirical researcher to test for particular hypotheses, such as comparisons of means, medians, and variances from k populations using robust permutation tests, which asymptotic validity holds under very weak assumptions, while retaining the exact rejection probability in finite samples when the underlying distributions are identical. Second, the description and implementation of a permutation test for testing the continuity assumption of the baseline covariates in the sharp regression discontinuity design (RDD) as in Canay and Kamat (2017) <https://goo.gl/UZFqt7>. More specifically, it allows the user to select a set of covariates and test the aforementioned hypothesis using a permutation test based on the Cramer-von Miss test statistic. Graphical inspection of the empirical CDF and histograms for the variables of interest is also supported in the package. Third, it provides the practitioner with an effortless implementation of a permutation test based on the martingale decomposition of the empirical process for the goodness-of-fit testing problem with an estimated nuisance parameter. An application of this testing problem is the one of testing for heterogeneous treatment effects in a randomized control trial.
Author: Mauricio Olivares-Gonzalez [aut, cre],
Ignacio Sarmiento-Barbieri [aut]
Maintainer: Mauricio Olivares-Gonzalez <maurice.olivares@gmail.com>
Diff between RATest versions 0.1.4 dated 2018-11-30 and 0.1.5 dated 2019-07-12
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/PT.Khmaladze.fit.R | 2 +- R/RPT.R | 2 +- build/vignette.rds |binary inst/doc/RDperm.pdf |binary 6 files changed, 10 insertions(+), 10 deletions(-)
Title: Perform Phylogenetic Path Analysis
Description: A comprehensive and easy to use R implementation of confirmatory
phylogenetic path analysis as described by Von Hardenberg and Gonzalez-Voyer
(2012) <doi:10.1111/j.1558-5646.2012.01790.x>.
Author: Wouter van der Bijl [aut, cre]
Maintainer: Wouter van der Bijl <wouter@zoology.ubc.ca>
Diff between phylopath versions 1.0.2 dated 2019-01-02 and 1.1.0 dated 2019-07-12
DESCRIPTION | 15 MD5 | 73 +- NAMESPACE | 38 - NEWS.md | 349 +++++++------ R/DAG.R | 407 ++++++++-------- R/internal.R | 521 ++++++++++---------- R/phylopath.R | 626 +++++++++++++----------- R/print_and_plot.R | 746 ++++++++++++++--------------- build/vignette.rds |binary inst/doc/binary_models.R | 80 +-- inst/doc/binary_models.Rmd | 238 ++++----- inst/doc/binary_models.html | 875 +++++++++++++++++----------------- inst/doc/intro_to_phylopath.R | 154 +++--- inst/doc/intro_to_phylopath.Rmd | 422 ++++++++-------- inst/doc/intro_to_phylopath.html | 992 +++++++++++++++++++-------------------- man/DAG.Rd | 80 +-- man/average.Rd | 131 ++--- man/average_DAGs.Rd | 99 ++- man/best.Rd | 69 +- man/choice.Rd | 71 +- man/cichlids.Rd | 46 - man/cichlids_tree.Rd | 42 - man/coef_plot.Rd | 88 +-- man/define_model_set.Rd | 70 +- man/est_DAG.Rd | 114 ++-- man/phylo_path.Rd | 183 +++---- man/plot.DAG.Rd | 146 ++--- man/plot.fitted_DAG.Rd | 152 ++--- man/plot_model_set.Rd | 140 ++--- man/red_list.Rd | 50 - man/red_list_tree.Rd | 58 +- man/rhino.Rd | 46 - man/rhino_tree.Rd | 42 - man/show_warnings.Rd | 32 - tests |only vignettes/binary_models.Rmd | 238 ++++----- vignettes/intro_to_phylopath.Rmd | 422 ++++++++-------- 37 files changed, 3987 insertions(+), 3868 deletions(-)
Title: Odds Ratios, Contingency Table, and Model Significance from a
Generalized Linear Model Object
Description: Computes odds ratios and 95% confidence intervals from a generalized linear model object. It also computes model significance with the chi-squared statistic and p-value and it computes model fit using a contingency table to determine the percent of observations for which the model correctly predicts the value of the outcome. Calculates model sensitivity and specificity.
Author: Jenine Harris [aut, cre]
Maintainer: Jenine Harris <harrisj@wustl.edu>
Diff between odds.n.ends versions 0.1.0 dated 2019-01-20 and 0.1.1 dated 2019-07-12
DESCRIPTION | 18 +++++++++++------- MD5 | 6 +++--- NAMESPACE | 2 +- R/or_function.R | 40 ++++++++++++++++++++++++++++------------ 4 files changed, 43 insertions(+), 23 deletions(-)
Title: Native R Kernel for the 'Jupyter Notebook'
Description: The R kernel for the 'Jupyter' environment executes R code which the front-end
('Jupyter Notebook' or other front-ends) submits to the kernel via the network.
Author: Thomas Kluyver [aut, cph],
Philipp Angerer [aut, cph, cre]
(<https://orcid.org/0000-0002-0369-2888>),
Jan Schulz [aut, cph],
Karthik Ram [aut, cph]
Maintainer: Philipp Angerer <phil.angerer@gmail.com>
Diff between IRkernel versions 1.0.1 dated 2019-05-02 and 1.0.2 dated 2019-07-12
IRkernel-1.0.1/IRkernel/tests/testthat/__pycache__/test_ir.cpython-35.pyc |only IRkernel-1.0.1/IRkernel/tests/testthat/__pycache__/test_ir.cpython-36.pyc |only IRkernel-1.0.1/IRkernel/tests/testthat/jkt/jupyter_kernel_test/__pycache__/__init__.cpython-36.pyc |only IRkernel-1.0.1/IRkernel/tests/testthat/jkt/jupyter_kernel_test/__pycache__/messagespec.cpython-36.pyc |only IRkernel-1.0.1/IRkernel/tests/testthat/jkt/jupyter_kernel_test/__pycache__/messagespec_common.cpython-36.pyc |only IRkernel-1.0.2/IRkernel/DESCRIPTION | 6 +- IRkernel-1.0.2/IRkernel/MD5 | 21 +++------- IRkernel-1.0.2/IRkernel/R/completion.r | 2 IRkernel-1.0.2/IRkernel/R/kernel.r | 6 +- IRkernel-1.0.2/IRkernel/tests/testthat/__pycache__/test_ir.cpython-37.pyc |binary IRkernel-1.0.2/IRkernel/tests/testthat/jkt/jupyter_kernel_test/__pycache__/__init__.cpython-37.pyc |binary IRkernel-1.0.2/IRkernel/tests/testthat/jkt/jupyter_kernel_test/__pycache__/messagespec.cpython-37.pyc |binary IRkernel-1.0.2/IRkernel/tests/testthat/jkt/jupyter_kernel_test/__pycache__/messagespec_common.cpython-37.pyc |binary IRkernel-1.0.2/IRkernel/tests/testthat/test_ir.py | 4 + 14 files changed, 20 insertions(+), 19 deletions(-)
Title: Functions to Analyze Single System Data
Description: Functions to visually and statistically analyze single system data.
Author: Charles Auerbach [aut, cre],
Wendy Zeitlin [aut]
Maintainer: Charles Auerbach <auerbach@yu.edu>
Diff between SSDforR versions 1.5.6 dated 2019-06-24 and 1.5.7 dated 2019-07-12
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/SD1.R | 2 +- R/SD1legend.R | 7 ++++--- R/SD2legend.R | 9 +++++---- R/XRchart.R | 2 +- R/sd1bandgraph.R | 8 +++++--- R/sd2bandgraph.R | 7 ++++--- 8 files changed, 31 insertions(+), 26 deletions(-)
Title: Correlations in R
Description: A tool for exploring correlations.
It makes it possible to easily perform routine tasks when
exploring correlation matrices such as ignoring the diagonal,
focusing on the correlations of certain variables against others,
or rearranging and visualizing the matrix in terms of the
strength of the correlations.
Author: Edgar Ruiz [aut, cre],
Simon Jackson [aut],
Jorge Cimentada [aut]
Maintainer: Edgar Ruiz <edgararuiz@gmail.com>
Diff between corrr versions 0.3.2 dated 2019-04-20 and 0.4.0 dated 2019-07-12
corrr-0.3.2/corrr/R/corrr-package.R |only corrr-0.3.2/corrr/R/zzz.R |only corrr-0.4.0/corrr/DESCRIPTION | 48 - corrr-0.4.0/corrr/LICENSE | 2 corrr-0.4.0/corrr/MD5 | 101 +- corrr-0.4.0/corrr/NAMESPACE | 103 +- corrr-0.4.0/corrr/NEWS.md | 188 ++-- corrr-0.4.0/corrr/R/cor_df.R | 577 ++++++------- corrr-0.4.0/corrr/R/correlate.R | 341 +++---- corrr-0.4.0/corrr/R/corrr.R |only corrr-0.4.0/corrr/R/dataframe.R | 20 corrr-0.4.0/corrr/R/internal.R | 78 - corrr-0.4.0/corrr/R/matrix.R | 13 corrr-0.4.0/corrr/R/output.R | 281 +++--- corrr-0.4.0/corrr/R/reshape.R | 250 +++-- corrr-0.4.0/corrr/R/retract.R |only corrr-0.4.0/corrr/R/utility.R | 175 ++-- corrr-0.4.0/corrr/README.md | 330 ++++--- corrr-0.4.0/corrr/build/vignette.rds |binary corrr-0.4.0/corrr/inst/doc/databases.R |only corrr-0.4.0/corrr/inst/doc/databases.Rmd |only corrr-0.4.0/corrr/inst/doc/databases.html |only corrr-0.4.0/corrr/inst/doc/using-corrr.R | 108 +- corrr-0.4.0/corrr/inst/doc/using-corrr.Rmd | 246 ++--- corrr-0.4.0/corrr/inst/doc/using-corrr.html | 949 +++++++++++----------- corrr-0.4.0/corrr/man/as_cordf.Rd | 54 - corrr-0.4.0/corrr/man/as_matrix.Rd | 46 - corrr-0.4.0/corrr/man/correlate.Rd | 148 +-- corrr-0.4.0/corrr/man/corrr-package.Rd | 62 - corrr-0.4.0/corrr/man/dice.Rd |only corrr-0.4.0/corrr/man/fashion.Rd | 74 - corrr-0.4.0/corrr/man/first_col.Rd | 44 - corrr-0.4.0/corrr/man/focus.Rd | 120 +- corrr-0.4.0/corrr/man/focus_if.Rd | 78 - corrr-0.4.0/corrr/man/network_plot.Rd | 84 - corrr-0.4.0/corrr/man/pair_n.Rd | 50 - corrr-0.4.0/corrr/man/rearrange.Rd | 64 - corrr-0.4.0/corrr/man/retract.Rd |only corrr-0.4.0/corrr/man/rplot.Rd | 76 - corrr-0.4.0/corrr/man/shave.Rd | 52 - corrr-0.4.0/corrr/man/stretch.Rd | 66 - corrr-0.4.0/corrr/tests/testthat.R | 10 corrr-0.4.0/corrr/tests/testthat/test-as_cordf.R | 37 corrr-0.4.0/corrr/tests/testthat/test-correlate.R | 39 corrr-0.4.0/corrr/tests/testthat/test-dataframe.R |only corrr-0.4.0/corrr/tests/testthat/test-fashion.R | 149 +-- corrr-0.4.0/corrr/tests/testthat/test-focus.R | 102 +- corrr-0.4.0/corrr/tests/testthat/test-focus_.R | 84 - corrr-0.4.0/corrr/tests/testthat/test-plots.R |only corrr-0.4.0/corrr/tests/testthat/test-rearrange.R | 67 - corrr-0.4.0/corrr/tests/testthat/test-shave.R | 52 - corrr-0.4.0/corrr/tests/testthat/test-stretch.R | 72 - corrr-0.4.0/corrr/tests/testthat/test-tbl_sql.R | 82 - corrr-0.4.0/corrr/tests/testthat/test-utilities.R |only corrr-0.4.0/corrr/tools/readme/combination-1.png |binary corrr-0.4.0/corrr/tools/readme/combination-2.png |binary corrr-0.4.0/corrr/vignettes/databases.Rmd |only corrr-0.4.0/corrr/vignettes/using-corrr.Rmd | 246 ++--- 58 files changed, 2953 insertions(+), 2815 deletions(-)
Title: Regression Models and Utilities for Repeated Measures and Panel
Data
Description: Provides an object type and associated tools for storing and
wrangling panel data. Implements several methods for creating regression
models that take advantage of the unique aspects of
panel data. Among other capabilities, automates the "within-between"
(also known as "between-within" and "hybrid") panel regression specification
that combines the desirable aspects of both fixed effects and random effects
econometric models and fits them as multilevel models
(Allison, 2009 <doi:10.4135/9781412993869.d33>;
Bell & Jones, 2015 <doi:10.1017/psrm.2014.7>). These models can also be
estimated via generalized estimating equations
(GEE; McNeish, 2019 <doi:10.1080/00273171.2019.1602504>) and Bayesian
estimation is (optionally) supported via 'Stan'.
Supports estimation of asymmetric effects models via first differences
(Allison, 2019 <doi:10.1177/2378023119826441>) as well as a generalized
linear model extension thereof using GEE.
Author: Jacob A. Long [aut, cre] (<https://orcid.org/0000-0002-1582-6214>)
Maintainer: Jacob A. Long <long.1377@osu.edu>
Diff between panelr versions 0.7.0 dated 2019-05-16 and 0.7.1 dated 2019-07-12
DESCRIPTION | 6 - MD5 | 48 +++++++------- NAMESPACE | 8 ++ NEWS.md | 14 ++++ R/panel_data.R | 7 +- R/panel_methods.R | 24 ++++++- R/utils.R | 148 +++++++++++++++++++++++++++++++++----------- R/wb_data_prep.R | 10 ++ R/wb_gee.R | 15 +++- R/wb_lmer.R | 6 + R/wb_utils.R | 32 +++++---- README.md | 35 ++-------- inst/doc/reshape.html | 4 - inst/doc/wbm.Rmd | 7 -- inst/doc/wbm.html | 33 +++++---- man/fdm_tidiers.Rd | 4 - man/make_wb_data.Rd | 19 +++++ man/predict.wbm.Rd | 2 man/wbgee.Rd | 6 + man/wbgee_tidiers.Rd | 6 - man/wbm_tidiers.Rd | 7 +- tests/testthat/test-utils.R | 1 tests/testthat/test_wbgee.R | 58 ++++++++++++++++- tests/testthat/test_wbm.R | 78 ++++++++++++++++++++++- vignettes/wbm.Rmd | 7 -- 25 files changed, 431 insertions(+), 154 deletions(-)
Title: Functions for Optimal Matching
Description: Distance based bipartite matching using the RELAX-IV minimum cost flow solver,
oriented to matching of treatment and control groups in observational
studies. Routines are provided to generate distances from generalised linear models (propensity
score matching), formulas giving variables on which to limit matched distances, stratified or
exact matching directives, or calipers, alone or in combination.
Author: Ben B. Hansen <ben.hansen@umich.edu>, Mark Fredrickson
<mark.m.fredrickson@gmail.com>, Josh Buckner, Josh Errickson,
Adam Rauh and Peter Solenberger, with embedded Fortran code due to
Dimitri P. Bertsekas <dimitrib@mit.edu> and Paul Tseng
Maintainer: Mark M. Fredrickson <mark.m.fredrickson@gmail.com>
Diff between optmatch versions 0.9-10 dated 2018-07-12 and 0.9-11 dated 2019-07-12
optmatch-0.9-10/optmatch/README.md |only optmatch-0.9-10/optmatch/inst/doc/fullmatch-vignette.html |only optmatch-0.9-10/optmatch/inst/doc/matching-from-foreign-software.html |only optmatch-0.9-10/optmatch/tests/mahal-dist.R |only optmatch-0.9-11/optmatch/DESCRIPTION | 20 optmatch-0.9-11/optmatch/MD5 | 103 +- optmatch-0.9-11/optmatch/NAMESPACE | 2 optmatch-0.9-11/optmatch/NEWS | 14 optmatch-0.9-11/optmatch/R/InfinitySparseMatrix.R | 30 optmatch-0.9-11/optmatch/R/Optmatch.R | 111 +- optmatch-0.9-11/optmatch/R/fill.NAs.R | 5 optmatch-0.9-11/optmatch/R/fullmatch.R | 52 - optmatch-0.9-11/optmatch/R/makedist.R | 4 optmatch-0.9-11/optmatch/R/match_on.R | 85 + optmatch-0.9-11/optmatch/R/matchfailed.R | 4 optmatch-0.9-11/optmatch/R/pairmatch.R | 5 optmatch-0.9-11/optmatch/R/stratumStructure.R | 22 optmatch-0.9-11/optmatch/R/utilities.R | 6 optmatch-0.9-11/optmatch/build/vignette.rds |binary optmatch-0.9-11/optmatch/inst/doc/fullmatch-vignette.pdf |only optmatch-0.9-11/optmatch/inst/doc/matching-from-foreign-software.R | 8 optmatch-0.9-11/optmatch/inst/doc/matching-from-foreign-software.Rmd | 37 optmatch-0.9-11/optmatch/inst/doc/matching-from-foreign-software.pdf |only optmatch-0.9-11/optmatch/inst/doc/matching-within-subgroups.R |only optmatch-0.9-11/optmatch/inst/doc/matching-within-subgroups.Rmd |only optmatch-0.9-11/optmatch/inst/doc/matching-within-subgroups.pdf |only optmatch-0.9-11/optmatch/man/BlockedInfinitySparseMatrix-class.Rd |only optmatch-0.9-11/optmatch/man/InfinitySparseMatrix-class.Rd | 20 optmatch-0.9-11/optmatch/man/c.optmatch.Rd |only optmatch-0.9-11/optmatch/man/caliper-methods.Rd | 4 optmatch-0.9-11/optmatch/man/fullmatch.Rd | 9 optmatch-0.9-11/optmatch/man/match_on-methods.Rd | 37 optmatch-0.9-11/optmatch/man/mdist.Rd | 4 optmatch-0.9-11/optmatch/man/optmatch-defunct.Rd | 11 optmatch-0.9-11/optmatch/man/optmatch.Rd | 3 optmatch-0.9-11/optmatch/man/pairmatch.Rd | 9 optmatch-0.9-11/optmatch/man/predict.CBPS.Rd | 3 optmatch-0.9-11/optmatch/man/stratumStructure.Rd | 21 optmatch-0.9-11/optmatch/man/summary.ism.Rd | 6 optmatch-0.9-11/optmatch/man/update.optmatch.Rd | 8 optmatch-0.9-11/optmatch/tests/testthat/test.InfinitySparseMatrix.R | 18 optmatch-0.9-11/optmatch/tests/testthat/test.Optmatch.R | 512 +++++++--- optmatch-0.9-11/optmatch/tests/testthat/test.compute_mahal.R | 22 optmatch-0.9-11/optmatch/tests/testthat/test.fill.NAs.R | 3 optmatch-0.9-11/optmatch/tests/testthat/test.fmatch.R | 32 optmatch-0.9-11/optmatch/tests/testthat/test.fullmatch.R | 14 optmatch-0.9-11/optmatch/tests/testthat/test.fullmatch.infeasible.recovery.R | 6 optmatch-0.9-11/optmatch/tests/testthat/test.mahal-dist.R | 2 optmatch-0.9-11/optmatch/tests/testthat/test.match_on.R | 81 + optmatch-0.9-11/optmatch/tests/testthat/test.maxControlsCap.old.R | 4 optmatch-0.9-11/optmatch/tests/testthat/test.optimality.R |only optmatch-0.9-11/optmatch/tests/testthat/test.pairmatch.R | 15 optmatch-0.9-11/optmatch/tests/testthat/test.scores.R | 38 optmatch-0.9-11/optmatch/tests/testthat/test.stratumStructure.old.R | 4 optmatch-0.9-11/optmatch/tests/testthat/test.summary.optmatch.R | 4 optmatch-0.9-11/optmatch/tests/testthat/test.summary.optmatch.old.R | 4 optmatch-0.9-11/optmatch/tests/testthat/test.utilities.R | 10 optmatch-0.9-11/optmatch/vignettes/matching-from-foreign-software.Rmd | 37 optmatch-0.9-11/optmatch/vignettes/matching-within-subgroups.Rmd |only 59 files changed, 1008 insertions(+), 441 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 0.0.2 dated 2018-11-19 and 0.0.3 dated 2019-07-12
DESCRIPTION | 12 ++++++------ MD5 | 29 +++++++++++++++++++---------- NAMESPACE | 17 +++++++++++++++++ NEWS.md | 8 ++++++++ R/bayes.R | 27 +++++++++++++++++++-------- R/glm.R | 11 +++++++++-- R/umap.R |only R/woe.R |only man/add_woe.Rd |only man/dictionary.Rd |only man/step_embed.Rd | 14 +++++++------- man/step_umap.Rd |only man/step_woe.Rd |only man/woe_table.Rd |only tests/testthat/test_mixed.R | 9 ++++++--- tests/testthat/test_no_pooling.R | 9 ++++++--- tests/testthat/test_pooling.R | 11 +++++++---- tests/testthat/test_tf.R | 9 ++++++--- tests/testthat/test_umap.R |only tests/testthat/test_woe.R |only 20 files changed, 110 insertions(+), 46 deletions(-)
Title: Exploring Genomic Relations for Enhanced Interpretation Through
Enrichment, Similarity, Network and Annotation Analysis
Description: The central goal of XGR by Fang et al. (2016) <doi:10.1186/s13073-016-0384-y> is to provide a data interpretation system necessary to do "big data" science. It is designed to make a user-defined gene or SNP list (or genomic regions) more interpretable by comprehensively utilising ontology annotations and interaction networks to reveal relationships and enhance opportunities for biological discovery. XGR is unique in supporting a broad range of ontologies (including knowledge of biological and molecular functions, pathways, diseases and phenotypes - in both human and mouse) and different types of networks (including functional, physical and pathway interactions). There are two core functionalities of XGR. The first is to provide basic infrastructures for easy access to built-in ontologies and networks. The second is to support data interpretations via 1) enrichment analysis using either built-in or custom ontologies, 2) similarity analysis for calculating semantic similarity between genes (or SNPs) based on their ontology annotation profiles, 3) network analysis for identification of gene networks given a query list of (significant) genes, SNPs or genomic regions, and 4) annotation analysis for interpreting genomic regions using co-localised functional genomic annotations (such as open chromatin, epigenetic marks, TF binding sites and genomic segments) and using nearby gene annotations (by ontologies). Together with its web app, XGR aims to provide a user-friendly tool for exploring genomic relations at the gene, SNP and genomic region level.
Author: Hai Fang, Bogdan Knezevic, Katie L Burnham, Julian C Knight
Maintainer: Hai Fang <hfang@well.ox.ac.uk>
Diff between XGR versions 1.1.5 dated 2019-03-29 and 1.1.6 dated 2019-07-12
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- R/xDefineEQTL.r | 2 +- R/xEnrichForest.r | 4 +++- R/xSNPscores.r | 6 +++--- data/Haploid_regulators.RData |binary data/ImmunoBase.RData |binary data/JKscience_TS2A.RData |binary inst/xEnrichForest.html | 2 +- man/xEnrichForest.Rd | 2 +- 10 files changed, 22 insertions(+), 20 deletions(-)
Title: Mesh Generation and Surface Tessellation
Description: Makes the 'Qhull' library <http://www.qhull.org>
available in R, in a similar manner as in Octave and MATLAB. Qhull
computes convex hulls, Delaunay triangulations, halfspace
intersections about a point, Voronoi diagrams, furthest-site
Delaunay triangulations, and furthest-site Voronoi diagrams. It
runs in 2D, 3D, 4D, and higher dimensions. It implements the
Quickhull algorithm for computing the convex hull. Qhull does not
support constrained Delaunay triangulations, or mesh generation of
non-convex objects, but the package does include some R functions
that allow for this.
Author: Jean-Romain Roussel [cph, ctb] (wrote tsearch function with QuadTrees),
C. B. Barber [cph],
Kai Habel [cph, aut],
Raoul Grasman [cph, aut],
Robert B. Gramacy [cph, aut],
Pavlo Mozharovskyi [cph, aut],
David C. Sterratt [cph, aut, cre]
(<https://orcid.org/0000-0001-9092-9099>)
Maintainer: David C. Sterratt <david.c.sterratt@ed.ac.uk>
Diff between geometry versions 0.4.1.1 dated 2019-07-02 and 0.4.2 dated 2019-07-12
DESCRIPTION | 12 - MD5 | 39 +++-- NAMESPACE | 4 NEWS | 21 ++- R/convhulln.R | 80 +++++++---- R/delaunayn.R | 38 ++--- R/inhulln.R | 5 R/intersectn.R | 167 ++++++++++++++++++++++-- R/polyarea.R | 2 build/vignette.rds |binary inst/doc/qhull-eg.pdf |binary inst/extdata/error_15_620.RData |only inst/extdata/intersectn4D.RData |only inst/extdata/issue35-intersectn.RData |only inst/extdata/overlap260-5034.RData |only inst/extdata/save-overlap149-9428.RData |only inst/extdata/save-overlap32-176.RData |only inst/extdata/save-overlap68-557.RData |only man/convhulln.Rd | 74 ++++++----- man/delaunayn.Rd | 38 ++--- man/inhulln.Rd | 4 man/intersectn.Rd | 18 ++ src/geometry_init.c | 4 tests/testthat/test-intersectn.R | 215 +++++++++++--------------------- 24 files changed, 433 insertions(+), 288 deletions(-)
Title: Relationship Matrices for Diploid and Autopolyploid Species
Description: Computation of A (pedigree), G (genomic-base), and H (A corrected
by G) relationship matrices for diploid and autopolyploid species. Several methods
are implemented considering additive and non-additive models.
Author: Rodrigo Amadeu [aut, cre],
Catherine Cellon [ctb],
Leticia Lara [ctb],
Marcio Resende [ctb],
Ivone Oliveira [ctb],
Luis Ferrao [ctb],
Patricio Munoz [ctb],
Augusto Garcia [ctb]
Maintainer: Rodrigo Amadeu <rramadeu@ufl.edu>
Diff between AGHmatrix versions 0.0.5 dated 2019-03-26 and 1.0.0 dated 2019-07-12
AGHmatrix-0.0.5/AGHmatrix/R/snp.table-data.R |only AGHmatrix-0.0.5/AGHmatrix/data/snp.table.rdata |only AGHmatrix-0.0.5/AGHmatrix/inst/doc/Tutorial_AGHmatrix.html |only AGHmatrix-0.0.5/AGHmatrix/man/snp.table.Rd |only AGHmatrix-1.0.0/AGHmatrix/DESCRIPTION | 13 AGHmatrix-1.0.0/AGHmatrix/MD5 | 48 +- AGHmatrix-1.0.0/AGHmatrix/NAMESPACE | 2 AGHmatrix-1.0.0/AGHmatrix/R/Amatrix.R | 21 - AGHmatrix-1.0.0/AGHmatrix/R/Gmatrix.R | 17 AGHmatrix-1.0.0/AGHmatrix/R/Hmatrix.R | 190 ++++++--- AGHmatrix-1.0.0/AGHmatrix/R/ped.mrode-data.R | 2 AGHmatrix-1.0.0/AGHmatrix/R/ped.sol-data.R |only AGHmatrix-1.0.0/AGHmatrix/R/snp.pine-data.R | 8 AGHmatrix-1.0.0/AGHmatrix/R/snp.sol-data.R |only AGHmatrix-1.0.0/AGHmatrix/build/vignette.rds |binary AGHmatrix-1.0.0/AGHmatrix/data/datalist | 3 AGHmatrix-1.0.0/AGHmatrix/data/ped.sol.rdata |only AGHmatrix-1.0.0/AGHmatrix/data/snp.sol.rdata |only AGHmatrix-1.0.0/AGHmatrix/inst/doc/Tutorial_AGHmatrix.R | 143 +++---- AGHmatrix-1.0.0/AGHmatrix/inst/doc/Tutorial_AGHmatrix.Rmd | 264 ++++++------- AGHmatrix-1.0.0/AGHmatrix/inst/doc/Tutorial_AGHmatrix.pdf |only AGHmatrix-1.0.0/AGHmatrix/inst/misc/Tutorial_AGHmatrix.R |only AGHmatrix-1.0.0/AGHmatrix/inst/misc/Tutorial_AGHmatrix.Rmd |only AGHmatrix-1.0.0/AGHmatrix/inst/misc/Tutorial_AGHmatrix.pdf |only AGHmatrix-1.0.0/AGHmatrix/man/Amatrix.Rd | 21 - AGHmatrix-1.0.0/AGHmatrix/man/Gmatrix.Rd | 24 - AGHmatrix-1.0.0/AGHmatrix/man/Hmatrix.Rd | 51 +- AGHmatrix-1.0.0/AGHmatrix/man/ped.mrode.Rd | 2 AGHmatrix-1.0.0/AGHmatrix/man/ped.sol.Rd |only AGHmatrix-1.0.0/AGHmatrix/man/snp.pine.Rd | 7 AGHmatrix-1.0.0/AGHmatrix/man/snp.sol.Rd |only AGHmatrix-1.0.0/AGHmatrix/vignettes/Tutorial_AGHmatrix.Rmd | 264 ++++++------- 32 files changed, 573 insertions(+), 507 deletions(-)
Title: Log-Concave Density Estimation in Arbitrary Dimensions
Description: Software for computing a log-concave (maximum likelihood) estimator for i.i.d. data in any number of dimensions. For a detailed description of the method see Cule, Samworth and Stewart (2010, Journal of Royal Statistical Society Series B, <doi:10.1111/j.1467-9868.2010.00753.x>).
Author: Madeleine Cule, Robert Gramacy, Richard Samworth, Yining Chen
Maintainer: Yining Chen <Y.Chen101@lse.ac.uk>
Diff between LogConcDEAD versions 1.6-1 dated 2018-04-13 and 1.6-3 dated 2019-07-12
DESCRIPTION | 11 ++++++----- MD5 | 20 ++++++++++---------- NAMESPACE | 4 ++-- NEWS | 4 +++- R/plot.LogConcDEAD.R | 14 +++++++------- build/vignette.rds |binary inst/doc/LogConcDEAD.pdf |binary man/EMmixlcd.Rd | 2 +- src/io.c | 8 ++++---- src/qset.h | 2 +- src/solvoptweights.c | 17 +++++++++++------ 11 files changed, 45 insertions(+), 37 deletions(-)
Title: 'ggplot2' Based Plots with Statistical Details
Description: Extension of 'ggplot2', 'ggstatsplot' creates
graphics with details from statistical tests included in the plots
themselves. It is targeted primarily at behavioral sciences community
to provide a one-line code to generate information-rich plots for
statistical analysis of continuous (violin plots, scatterplots,
histograms, dot plots, dot-and-whisker plots) or categorical (pie and
bar charts) data. Currently, it supports only the most common types of
statistical tests: parametric, nonparametric, robust, and bayesian
versions of t-test/anova, correlation analyses, contingency table
analysis, and regression analyses.
Author: Indrajeet Patil [cre, aut, ctb]
(<https://orcid.org/0000-0003-1995-6531>),
Chuck Powell [aut, ctb] (<https://orcid.org/0000-0002-3606-2188>)
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>
Diff between ggstatsplot versions 0.0.11 dated 2019-06-14 and 0.0.12 dated 2019-07-12
ggstatsplot-0.0.11/ggstatsplot/R/helpers_ggcorrmat.R |only ggstatsplot-0.0.11/ggstatsplot/man/bf_one_sample_ttest.Rd |only ggstatsplot-0.0.11/ggstatsplot/man/bf_two_sample_ttest.Rd |only ggstatsplot-0.0.11/ggstatsplot/man/kw_eta_h_ci.Rd |only ggstatsplot-0.0.11/ggstatsplot/man/matrix_to_tibble.Rd |only ggstatsplot-0.0.11/ggstatsplot/man/numdf_summary.Rd |only ggstatsplot-0.0.11/ggstatsplot/man/subtitle_onesample_proptest.Rd |only ggstatsplot-0.0.11/ggstatsplot/tests/testthat/test_kw_eta_h_ci.R |only ggstatsplot-0.0.11/ggstatsplot/tests/testthat/test_matrix_to_tibble.R |only ggstatsplot-0.0.11/ggstatsplot/tests/testthat/test_numdf_summary.R |only ggstatsplot-0.0.12/ggstatsplot/DESCRIPTION | 28 ggstatsplot-0.0.12/ggstatsplot/MD5 | 283 ++--- ggstatsplot-0.0.12/ggstatsplot/NAMESPACE | 18 ggstatsplot-0.0.12/ggstatsplot/NEWS.md | 39 ggstatsplot-0.0.12/ggstatsplot/R/effsize_t_parametric.R |only ggstatsplot-0.0.12/ggstatsplot/R/ggbarstats.R | 180 +-- ggstatsplot-0.0.12/ggstatsplot/R/ggbetweenstats.R | 57 - 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ggstatsplot-0.0.12/ggstatsplot/R/helpers_gghistostats_subtitles.R | 79 - ggstatsplot-0.0.12/ggstatsplot/R/helpers_ggpiestats_subtitles.R | 502 ++++---- ggstatsplot-0.0.12/ggstatsplot/R/helpers_ggscatterstats_subtitles.R | 168 +-- ggstatsplot-0.0.12/ggstatsplot/R/helpers_grouped_functions.R | 4 ggstatsplot-0.0.12/ggstatsplot/R/helpers_messages.R | 24 ggstatsplot-0.0.12/ggstatsplot/R/helpers_pairwise_comparison.R | 84 - ggstatsplot-0.0.12/ggstatsplot/R/subtitle_maker_templates.R | 43 ggstatsplot-0.0.12/ggstatsplot/R/switch_functions.R | 24 ggstatsplot-0.0.12/ggstatsplot/R/theme_ggstatsplot.R | 16 ggstatsplot-0.0.12/ggstatsplot/README.md | 378 ++++-- ggstatsplot-0.0.12/ggstatsplot/build/vignette.rds |binary ggstatsplot-0.0.12/ggstatsplot/inst/CITATION | 4 ggstatsplot-0.0.12/ggstatsplot/inst/WORDLIST | 28 ggstatsplot-0.0.12/ggstatsplot/inst/doc/additional.Rmd | 3 ggstatsplot-0.0.12/ggstatsplot/inst/doc/additional.html | 9 ggstatsplot-0.0.12/ggstatsplot/man/bf_contingency_tab.Rd | 40 ggstatsplot-0.0.12/ggstatsplot/man/bf_corr_test.Rd | 2 ggstatsplot-0.0.12/ggstatsplot/man/bf_extractor.Rd | 9 ggstatsplot-0.0.12/ggstatsplot/man/bf_meta_message.Rd | 41 ggstatsplot-0.0.12/ggstatsplot/man/bf_oneway_anova.Rd | 2 ggstatsplot-0.0.12/ggstatsplot/man/bf_ttest.Rd |only ggstatsplot-0.0.12/ggstatsplot/man/cat_counter.Rd | 7 ggstatsplot-0.0.12/ggstatsplot/man/effsize_t_parametric.Rd | 4 ggstatsplot-0.0.12/ggstatsplot/man/figures/README-ggbarstats1-1.png |binary ggstatsplot-0.0.12/ggstatsplot/man/figures/README-ggbarstats2-1.png |binary ggstatsplot-0.0.12/ggstatsplot/man/figures/README-ggbetweenstats1-1.png |binary ggstatsplot-0.0.12/ggstatsplot/man/figures/README-ggbetweenstats2-1.png |binary ggstatsplot-0.0.12/ggstatsplot/man/figures/README-ggbetweenstats3-1.png |binary ggstatsplot-0.0.12/ggstatsplot/man/figures/README-ggcoefstats1-1.png |binary ggstatsplot-0.0.12/ggstatsplot/man/figures/README-ggcoefstats2-1.png |binary ggstatsplot-0.0.12/ggstatsplot/man/figures/README-ggcorrmat1-1.png |binary ggstatsplot-0.0.12/ggstatsplot/man/figures/README-ggcorrmat3-1.png |binary ggstatsplot-0.0.12/ggstatsplot/man/figures/README-ggdotplotstats1-1.png |binary ggstatsplot-0.0.12/ggstatsplot/man/figures/README-ggdotplotstats2-1.png |binary ggstatsplot-0.0.12/ggstatsplot/man/figures/README-gghistostats1-1.png |binary ggstatsplot-0.0.12/ggstatsplot/man/figures/README-gghistostats2-1.png |binary ggstatsplot-0.0.12/ggstatsplot/man/figures/README-gghistostats4-1.png |binary ggstatsplot-0.0.12/ggstatsplot/man/figures/README-ggpiestats1-1.png |binary ggstatsplot-0.0.12/ggstatsplot/man/figures/README-ggpiestats2-1.png |binary ggstatsplot-0.0.12/ggstatsplot/man/figures/README-ggpiestats3-1.png |binary ggstatsplot-0.0.12/ggstatsplot/man/figures/README-ggpiestats4-1.png |binary ggstatsplot-0.0.12/ggstatsplot/man/figures/README-ggscatterstats1-1.png |binary ggstatsplot-0.0.12/ggstatsplot/man/figures/README-ggscatterstats2-1.png |binary ggstatsplot-0.0.12/ggstatsplot/man/figures/README-ggscatterstats3-1.png |binary ggstatsplot-0.0.12/ggstatsplot/man/figures/README-ggwithinstats1-1.png |binary ggstatsplot-0.0.12/ggstatsplot/man/figures/README-ggwithinstats2-1.png |binary ggstatsplot-0.0.12/ggstatsplot/man/figures/README-pirateplot-1.png |binary ggstatsplot-0.0.12/ggstatsplot/man/figures/README-theme_ggstatsplot-1.png |binary ggstatsplot-0.0.12/ggstatsplot/man/ggbarstats.Rd | 41 ggstatsplot-0.0.12/ggstatsplot/man/ggbetweenstats.Rd | 9 ggstatsplot-0.0.12/ggstatsplot/man/ggbetweenstats_switch.Rd | 3 ggstatsplot-0.0.12/ggstatsplot/man/ggcoefstats.Rd | 29 ggstatsplot-0.0.12/ggstatsplot/man/ggcorrmat.Rd | 59 - 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ggstatsplot-0.0.12/ggstatsplot/tests/testthat/test_subtitle_contingency_tab_paired.R | 6 ggstatsplot-0.0.12/ggstatsplot/tests/testthat/test_subtitle_ggscatterstats.R | 2 ggstatsplot-0.0.12/ggstatsplot/tests/testthat/test_subtitle_t_bayes.R | 4 ggstatsplot-0.0.12/ggstatsplot/tests/testthat/test_subtitle_t_onesample.R | 4 ggstatsplot-0.0.12/ggstatsplot/vignettes/additional.Rmd | 3 ggstatsplot-0.0.12/ggstatsplot/vignettes/web_only/effsize_interpretation.Rmd |only ggstatsplot-0.0.12/ggstatsplot/vignettes/web_only/faq.Rmd | 26 ggstatsplot-0.0.12/ggstatsplot/vignettes/web_only/ggbetweenstats.Rmd | 5 ggstatsplot-0.0.12/ggstatsplot/vignettes/web_only/ggcoefstats.Rmd | 247 +++- ggstatsplot-0.0.12/ggstatsplot/vignettes/web_only/ggcorrmat.Rmd | 74 - ggstatsplot-0.0.12/ggstatsplot/vignettes/web_only/gghistostats.Rmd | 5 ggstatsplot-0.0.12/ggstatsplot/vignettes/web_only/ggpiestats.Rmd | 5 ggstatsplot-0.0.12/ggstatsplot/vignettes/web_only/ggscatterstats.Rmd | 5 ggstatsplot-0.0.12/ggstatsplot/vignettes/web_only/ggstatsplot_paper.Rmd | 39 ggstatsplot-0.0.12/ggstatsplot/vignettes/web_only/ggwithinstats.Rmd | 5 149 files changed, 3661 insertions(+), 3267 deletions(-)
Title: Solving Differential Equations (ODEs, SDEs, DDEs, DAEs)
Description: An interface to 'DifferentialEquations.jl' <http://docs.juliadiffeq.org/latest/> from the R programming language.
It has unique high performance methods for solving ordinary differential equations (ODE), stochastic differential equations (SDE),
delay differential equations (DDE), differential-algebraic equations (DAE), and more. Much of the functionality,
including features like adaptive time stepping in SDEs, are unique and allow for multiple orders of magnitude speedup over more common methods.
'diffeqr' attaches an R interface onto the package, allowing seamless use of this tooling by R users.
Author: Christopher Rackauckas [aut, cre]
Maintainer: Christopher Rackauckas <me@chrisrackauckas.com>
Diff between diffeqr versions 0.1.1 dated 2018-04-27 and 0.1.2 dated 2019-07-12
DESCRIPTION | 8 LICENSE | 4 MD5 | 55 +-- NEWS.md | 30 - R/diffeqr.R | 843 +++++++++++++++++++++++----------------------- README.md | 742 ++++++++++++++++++++-------------------- build/vignette.rds |binary inst/CITATION |only inst/doc/dae.Rmd | 118 +++--- inst/doc/dae.html | 359 ++++++++++++++++--- inst/doc/dde.Rmd | 96 ++--- inst/doc/dde.html | 339 +++++++++++++++--- inst/doc/ode.Rmd | 312 ++++++++--------- inst/doc/ode.html | 389 ++++++++++++++++----- inst/doc/sde.Rmd | 240 ++++++------- inst/doc/sde.html | 439 ++++++++++++++++++----- man/dae.solve.Rd | 10 man/dde.solve.Rd | 8 man/ode.solve.Rd | 7 man/sde.solve.Rd | 10 tests/testthat.R | 4 tests/testthat/test_dae.R | 64 +-- tests/testthat/test_dde.R | 48 +- tests/testthat/test_ode.R | 122 +++--- tests/testthat/test_sde.R | 180 ++++----- vignettes/dae.Rmd | 118 +++--- vignettes/dde.Rmd | 96 ++--- vignettes/ode.Rmd | 312 ++++++++--------- vignettes/sde.Rmd | 240 ++++++------- 29 files changed, 3075 insertions(+), 2118 deletions(-)
Title: Set of Tools to Compute Various Climate Indices
Description: Set of tools to compute metrics and indices for climate analysis.
The package provides functions to compute extreme indices, evaluate the
agreement between models and combine theses models into an ensemble. Multi-model
time series of climate indices can be computed either after averaging the 2-D
fields from different models provided they share a common grid or by combining
time series computed on the model native grid. Indices can be assigned weights
and/or combined to construct new indices.
Author: BSC-CNS [aut, cph],
Alasdair Hunter [aut],
Nuria Perez-Zanon [aut, cre],
Nicolau Manubens [ctb],
Louis-Philippe Caron [ctb]
Maintainer: Nuria Perez-Zanon <nuria.perez@bsc.es>
Diff between ClimProjDiags versions 0.0.3 dated 2019-04-30 and 0.0.4 dated 2019-07-12
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/Threshold.R | 17 +++++++++++++---- man/Threshold.Rd | 4 +++- 4 files changed, 22 insertions(+), 11 deletions(-)
Title: Curriculum Vitae for R Markdown
Description: Provides templates and functions to simplify the production and maintenance of curriculum vitae.
Author: Mitchell O'Hara-Wild [aut, cre]
(<https://orcid.org/0000-0001-6729-7695>),
Rob Hyndman [aut] (<https://orcid.org/0000-0002-2140-5352>)
Maintainer: Mitchell O'Hara-Wild <mail@mitchelloharawild.com>
Diff between vitae versions 0.1.0 dated 2019-01-08 and 0.2.0 dated 2019-07-12
vitae-0.1.0/vitae/inst/rmarkdown/templates/moderncv/resources/moderncv.log |only vitae-0.1.0/vitae/inst/rmarkdown/templates/moderncv/skeleton/moderncvcompatibility.sty |only vitae-0.2.0/vitae/DESCRIPTION | 8 vitae-0.2.0/vitae/MD5 | 89 + vitae-0.2.0/vitae/NAMESPACE | 1 vitae-0.2.0/vitae/NEWS.md | 19 vitae-0.2.0/vitae/R/bibliography.R | 41 vitae-0.2.0/vitae/R/cv_document.R | 11 vitae-0.2.0/vitae/R/detailed.R | 7 vitae-0.2.0/vitae/R/formats.R | 25 vitae-0.2.0/vitae/README.md | 61 - vitae-0.2.0/vitae/build/vignette.rds |binary vitae-0.2.0/vitae/inst/doc/data.R |only vitae-0.2.0/vitae/inst/doc/data.Rmd |only vitae-0.2.0/vitae/inst/doc/data.html |only vitae-0.2.0/vitae/inst/doc/extending.html | 3 vitae-0.2.0/vitae/inst/doc/vitae.Rmd | 2 vitae-0.2.0/vitae/inst/doc/vitae.html | 51 - vitae-0.2.0/vitae/inst/rmarkdown/templates/awesomecv/resources/awesome-cv.tex | 7 vitae-0.2.0/vitae/inst/rmarkdown/templates/awesomecv/skeleton/awesome-cv.cls | 19 vitae-0.2.0/vitae/inst/rmarkdown/templates/awesomecv/skeleton/skeleton.Rmd | 47 + vitae-0.2.0/vitae/inst/rmarkdown/templates/hyndman/resources/hyndmantemplate.tex | 20 vitae-0.2.0/vitae/inst/rmarkdown/templates/hyndman/skeleton/skeleton.Rmd | 47 + vitae-0.2.0/vitae/inst/rmarkdown/templates/latexcv |only vitae-0.2.0/vitae/inst/rmarkdown/templates/moderncv/resources/moderncv.tex | 105 +- vitae-0.2.0/vitae/inst/rmarkdown/templates/moderncv/skeleton/moderncv.cls | 453 +++++++--- vitae-0.2.0/vitae/inst/rmarkdown/templates/moderncv/skeleton/moderncvbodyi.sty |only vitae-0.2.0/vitae/inst/rmarkdown/templates/moderncv/skeleton/moderncvbodyiii.sty |only vitae-0.2.0/vitae/inst/rmarkdown/templates/moderncv/skeleton/moderncvbodyiv.sty |only vitae-0.2.0/vitae/inst/rmarkdown/templates/moderncv/skeleton/moderncvbodyv.sty |only vitae-0.2.0/vitae/inst/rmarkdown/templates/moderncv/skeleton/moderncvcollection.sty |only vitae-0.2.0/vitae/inst/rmarkdown/templates/moderncv/skeleton/moderncvfooti.sty |only vitae-0.2.0/vitae/inst/rmarkdown/templates/moderncv/skeleton/moderncvheadi.sty |only vitae-0.2.0/vitae/inst/rmarkdown/templates/moderncv/skeleton/moderncvheadii.sty |only vitae-0.2.0/vitae/inst/rmarkdown/templates/moderncv/skeleton/moderncvheadiii.sty |only vitae-0.2.0/vitae/inst/rmarkdown/templates/moderncv/skeleton/moderncvheadiv.sty |only vitae-0.2.0/vitae/inst/rmarkdown/templates/moderncv/skeleton/moderncvheadv.sty |only vitae-0.2.0/vitae/inst/rmarkdown/templates/moderncv/skeleton/moderncvstylebanking.sty |only vitae-0.2.0/vitae/inst/rmarkdown/templates/moderncv/skeleton/moderncvstylecasual.sty | 195 ---- vitae-0.2.0/vitae/inst/rmarkdown/templates/moderncv/skeleton/moderncvstyleclassic.sty | 286 ------ vitae-0.2.0/vitae/inst/rmarkdown/templates/moderncv/skeleton/moderncvstylefancy.sty |only vitae-0.2.0/vitae/inst/rmarkdown/templates/moderncv/skeleton/moderncvstyleoldstyle.sty |only vitae-0.2.0/vitae/inst/rmarkdown/templates/moderncv/skeleton/skeleton.Rmd | 47 + vitae-0.2.0/vitae/inst/rmarkdown/templates/moderncv/skeleton/tweaklist.sty | 2 vitae-0.2.0/vitae/inst/rmarkdown/templates/twentyseconds/resources/twentysecondstemplate.tex | 4 vitae-0.2.0/vitae/inst/rmarkdown/templates/twentyseconds/skeleton/skeleton.Rmd | 47 + vitae-0.2.0/vitae/man/bibliography_entries.Rd | 9 vitae-0.2.0/vitae/man/cv_document.Rd | 8 vitae-0.2.0/vitae/man/cv_formats.Rd | 9 vitae-0.2.0/vitae/man/vitae-package.Rd | 2 vitae-0.2.0/vitae/tests/testthat/test-entries.R | 4 vitae-0.2.0/vitae/tests/testthat/test-template.R |only vitae-0.2.0/vitae/vignettes/data.Rmd |only vitae-0.2.0/vitae/vignettes/sample.txt | 17 vitae-0.2.0/vitae/vignettes/vitae.Rmd | 2 55 files changed, 898 insertions(+), 750 deletions(-)
Title: A Collection of Efficient and Extremely Fast R Functions
Description: A collection of fast (utility) functions for data analysis. Column- and row- wise means, medians, variances, minimums, maximums, many t, F and G-square tests, many regressions (normal, logistic, Poisson), are some of the many fast functions. Reference: Tsagris M, Papadakis M. (2018). Taking R to its limits: 70+ tips. PeerJ Preprints 6:e26605v1 <doi:10.7287/peerj.preprints.26605v1>.
Author: Manos Papadakis, Michail Tsagris, Marios Dimitriadis, Stefanos Fafalios, Ioannis Tsamardinos, Matteo Fasiolo, Giorgos Borboudakis, John Burkardt, Changliang Zou, Kleanthi Lakiotaki and Christina Chatzipantsiou.
Maintainer: Manos Papadakis <rfastofficial@gmail.com>
Diff between Rfast versions 1.9.4 dated 2019-05-24 and 1.9.5 dated 2019-07-12
DESCRIPTION | 8 - MD5 | 84 +++++++------- NAMESPACE | 2 NEWS.md | 38 ++++++ R/bic.corfsreg.R | 4 R/binom.mle.R | 6 - R/cor.fbed.R | 13 -- R/cor.fsreg.R | 11 - R/dirknn.cv.R | 3 R/gammanb.R | 2 R/group.all.R | 1 R/group.any.R | 1 R/group.mad.R | 1 R/group.max.R | 1 R/group.mean.R | 1 R/group.med.R | 1 R/group.min.R | 1 R/group.min_max.R | 1 R/group.sum.R | 1 R/group.var.R | 1 R/groupcolVars.R | 16 +- R/omp.R | 17 --- R/poly.cor.R | 3 R/regression.R | 10 + R/sort_mat.R | 5 R/vm.mle.R | 2 R/vmf.mle.R | 47 ++++---- man/AddToNamespace.Rd | 2 man/Dist.Rd | 4 man/Rfast-package.Rd | 4 man/checkNamespace.Rd | 3 man/dirknn.Rd | 3 man/regression.Rd | 5 man/zip.mle.Rd | 1 src/add_to_namespace.cpp | 2 src/check.cpp | 19 +-- src/col_row_utilities.cpp | 2 src/dir_knn.cpp | 13 -- src/dists.cpp | 260 +++++++++++++++++++++++++--------------------- src/glm.cpp | 115 +++++++++++--------- src/reg_lib.cpp | 13 +- src/spml.cpp | 2 src/system_files.h | 45 +++++++ 43 files changed, 453 insertions(+), 321 deletions(-)
Title: Multiple Testing Procedures with Adaptation for Discrete Tests
Description: Multiple testing procedures described in the paper Döhler, Durand and Roquain (2018) "New FDR bounds for discrete and heterogeneous tests" <doi:10.1214/18-EJS1441>. The main procedures of the paper (HSU and HSD), their adaptive counterparts (AHSU and AHSD), and the HBR variant are available and are coded to take as input a set of observed p-values and their discrete support under the null. A function to compute such p-values and supports for Fisher's exact tests is also provided, along with a wrapper allowing to apply discrete procedures directly from contingency tables.
Author: Sebastian Döhler [ctb],
Guillermo Durand [aut, ctb],
Florian Junge [aut, cre],
Etienne Roquain [ctb]
Maintainer: Florian Junge <florian.junge@h-da.de>
Diff between DiscreteFDR versions 1.2 dated 2019-01-07 and 1.3 dated 2019-07-12
DiscreteFDR-1.2/DiscreteFDR/R/kernel_fun.R |only DiscreteFDR-1.2/DiscreteFDR/man/DiscreteFDR-package.Rd |only DiscreteFDR-1.2/DiscreteFDR/man/build.stepfuns.Rd |only DiscreteFDR-1.2/DiscreteFDR/man/kernel.DBR.Rd |only DiscreteFDR-1.2/DiscreteFDR/man/short.eff.Rd |only DiscreteFDR-1.3/DiscreteFDR/DESCRIPTION | 22 DiscreteFDR-1.3/DiscreteFDR/MD5 | 50 +- DiscreteFDR-1.3/DiscreteFDR/NAMESPACE | 52 +- DiscreteFDR-1.3/DiscreteFDR/R/Aux_fun.R | 108 ---- DiscreteFDR-1.3/DiscreteFDR/R/DBR_fun.R | 71 +-- DiscreteFDR-1.3/DiscreteFDR/R/DiscreteFDR.R | 8 DiscreteFDR-1.3/DiscreteFDR/R/RcppExports.R |only DiscreteFDR-1.3/DiscreteFDR/R/discreteBH_fun.R | 124 ++--- DiscreteFDR-1.3/DiscreteFDR/R/fast_appli.R | 24 - DiscreteFDR-1.3/DiscreteFDR/R/plot_funs.R |only DiscreteFDR-1.3/DiscreteFDR/R/print_funs.R |only DiscreteFDR-1.3/DiscreteFDR/R/summary_funs.R |only DiscreteFDR-1.3/DiscreteFDR/R/support.R | 328 +++++++------- DiscreteFDR-1.3/DiscreteFDR/build |only DiscreteFDR-1.3/DiscreteFDR/inst |only DiscreteFDR-1.3/DiscreteFDR/man/DBR.Rd | 143 +++--- DiscreteFDR-1.3/DiscreteFDR/man/DiscreteFDR.Rd |only DiscreteFDR-1.3/DiscreteFDR/man/amnesia.Rd | 70 +- DiscreteFDR-1.3/DiscreteFDR/man/discrete.BH.Rd | 182 ++++--- DiscreteFDR-1.3/DiscreteFDR/man/fast.Discrete.Rd | 137 +++-- DiscreteFDR-1.3/DiscreteFDR/man/fisher.pvalues.support.Rd | 211 ++++----- DiscreteFDR-1.3/DiscreteFDR/man/hist.DiscreteFDR.Rd |only DiscreteFDR-1.3/DiscreteFDR/man/kernel.Rd | 220 ++++----- DiscreteFDR-1.3/DiscreteFDR/man/match.pvals.Rd | 98 ++-- DiscreteFDR-1.3/DiscreteFDR/man/plot.DiscreteFDR.Rd |only DiscreteFDR-1.3/DiscreteFDR/man/print.DiscreteFDR.Rd |only DiscreteFDR-1.3/DiscreteFDR/man/summary.DiscreteFDR.Rd |only DiscreteFDR-1.3/DiscreteFDR/src |only DiscreteFDR-1.3/DiscreteFDR/vignettes |only 34 files changed, 926 insertions(+), 922 deletions(-)
Title: Article Formats for R Markdown
Description: A suite of custom R Markdown formats and templates for
authoring journal articles and conference submissions.
Author: JJ Allaire [aut],
Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>),
R Foundation [aut, cph],
Hadley Wickham [aut],
Journal of Statistical Software [aut, cph],
RStudio [cph],
Ramnath Vaidyanathan [aut, cph],
Association for Computing Machinery [aut, cph],
Carl Boettiger [aut, cph],
Elsevier [aut, cph],
Karl Broman [aut, cph],
Kirill Mueller [aut, cph],
Bastiaan Quast [aut, cph],
Randall Pruim [aut, cph],
Ben Marwick [aut, cph],
Charlotte Wickham [aut, cph],
Oliver Keyes [aut, cph],
Miao Yu [aut, cph],
Daniel Emaasit [aut, cph],
Thierry Onkelinx [aut, cph],
Alessandro Gasparini [aut, cph]
(<https://orcid.org/0000-0002-8319-7624>),
Marc-Andre Desautels [aut, cph],
Dominik Leutnant [aut, cph] (<https://orcid.org/0000-0003-3293-2315>),
MDPI [aut, cph],
Taylor and Francis [aut, cph],
Oğuzhan Öğreden [aut] (<https://orcid.org/0000-0002-9949-3348>),
Dalton Hance [aut],
Daniel Nüst [aut, cph] (<https://orcid.org/0000-0002-0024-5046>),
Petter Uvesten [aut, cph],
Elio Campitelli [aut, cph] (<https://orcid.org/0000-0002-7742-9230>),
John Muschelli [aut, cph] (<https://orcid.org/0000-0001-6469-1750>)
Maintainer: Yihui Xie <xie@yihui.name>
Diff between rticles versions 0.8 dated 2019-05-14 and 0.9 dated 2019-07-12
rticles-0.8/rticles/inst/rmarkdown/templates/copernicus_article/resources/README_copernicus_package_5_0.txt |only rticles-0.8/rticles/inst/rmarkdown/templates/elsevier_article/resources/elsevier-harvard-without-titles.csl |only rticles-0.8/rticles/inst/rmarkdown/templates/elsevier_article/resources/elsevier-harvard.csl |only rticles-0.8/rticles/inst/rmarkdown/templates/elsevier_article/resources/elsevier-vancouver.csl |only rticles-0.8/rticles/inst/rmarkdown/templates/elsevier_article/resources/elsevier-with-titles-alphabetical.csl |only rticles-0.8/rticles/inst/rmarkdown/templates/elsevier_article/resources/elsevier-with-titles.csl |only rticles-0.8/rticles/inst/rmarkdown/templates/elsevier_article/resources/elsevier-without-titles.csl |only rticles-0.9/rticles/DESCRIPTION | 11 rticles-0.9/rticles/MD5 | 50 - rticles-0.9/rticles/NEWS.md | 11 rticles-0.9/rticles/R/copernicus_article.R | 4 rticles-0.9/rticles/README.md | 2 rticles-0.9/rticles/inst/rmarkdown/templates/copernicus_article/resources/README_copernicus_package_5_3.txt |only rticles-0.9/rticles/inst/rmarkdown/templates/copernicus_article/resources/template.tex | 9 rticles-0.9/rticles/inst/rmarkdown/templates/copernicus_article/skeleton/copernicus.cfg | 95 ++ rticles-0.9/rticles/inst/rmarkdown/templates/copernicus_article/skeleton/copernicus.cls | 134 ++-- rticles-0.9/rticles/inst/rmarkdown/templates/copernicus_article/skeleton/skeleton.Rmd | 4 rticles-0.9/rticles/inst/rmarkdown/templates/elsevier_article/resources/template.tex | 1 rticles-0.9/rticles/inst/rmarkdown/templates/elsevier_article/skeleton/elsevier-harvard-without-titles.csl |only rticles-0.9/rticles/inst/rmarkdown/templates/elsevier_article/skeleton/elsevier-harvard.csl |only rticles-0.9/rticles/inst/rmarkdown/templates/elsevier_article/skeleton/elsevier-vancouver.csl |only rticles-0.9/rticles/inst/rmarkdown/templates/elsevier_article/skeleton/elsevier-with-titles-alphabetical.csl |only rticles-0.9/rticles/inst/rmarkdown/templates/elsevier_article/skeleton/elsevier-with-titles.csl |only rticles-0.9/rticles/inst/rmarkdown/templates/elsevier_article/skeleton/elsevier-without-titles.csl |only rticles-0.9/rticles/inst/rmarkdown/templates/elsevier_article/skeleton/skeleton.Rmd | 3 rticles-0.9/rticles/inst/rmarkdown/templates/ieee_article/resources/template.tex | 7 rticles-0.9/rticles/inst/rmarkdown/templates/ieee_article/skeleton/skeleton.Rmd | 1 rticles-0.9/rticles/inst/rmarkdown/templates/jss_article/resources/template.tex | 7 rticles-0.9/rticles/inst/rmarkdown/templates/jss_article/skeleton/skeleton.Rmd | 1 rticles-0.9/rticles/inst/rmarkdown/templates/sim_article/skeleton/WileyNJD-AMA.bst | 333 +++++----- rticles-0.9/rticles/inst/rmarkdown/templates/sim_article/skeleton/WileyNJD-v2.cls | 111 +-- rticles-0.9/rticles/inst/rmarkdown/templates/sim_article/skeleton/bibfile.bib | 44 - rticles-0.9/rticles/man/copernicus_article.Rd | 2 33 files changed, 488 insertions(+), 342 deletions(-)
Title: Interface Between R and the OpenStreetMap-Based Routing Service
OSRM
Description: An interface between R and the OSRM API. OSRM is a routing
service based on OpenStreetMap data. See <http://project-osrm.org/> for more
information. This package allows to compute distances (travel time and
kilometric distance) between points and travel time matrices.
Author: Timothée Giraud [cre, aut] (<https://orcid.org/0000-0002-1932-3323>),
Robin Cura [ctb],
Matthieu Viry [ctb]
Maintainer: Timothée Giraud <timothee.giraud@cnrs.fr>
Diff between osrm versions 3.3.0 dated 2019-04-29 and 3.3.1 dated 2019-07-12
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS | 9 +++++++++ R/osrmIsochrone.R | 34 ++++++++++++++++++++++------------ R/osrmRoute.R | 5 ++++- R/osrmTrip.R | 19 +++++++++++-------- R/utils.R | 18 ++++++++++++++---- inst/forReadme.R | 6 +++--- inst/test.r | 1 + 9 files changed, 75 insertions(+), 39 deletions(-)
Title: Analyze Cricketers and Cricket Teams Based on ESPN Cricinfo
Statsguru
Description: Tools for analyzing performances of cricketers based on stats in
ESPN Cricinfo Statsguru. The toolset can be used for analysis of Tests,ODIs
and Twenty20 matches of both batsmen and bowlers. The package can also be used to
analyze team performances.
Author: Tinniam V Ganesh
Maintainer: Tinniam V Ganesh <tvganesh.85@gmail.com>
Diff between cricketr versions 0.0.21 dated 2019-07-01 and 0.0.22 dated 2019-07-12
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++++---- R/clean.R | 3 +++ R/cleanBowlerData.R | 3 +++ R/getPlayerDataHA.R |only R/getPlayerDataOppnHA.R |only build/partial.rdb |binary man/getPlayerDataHA.Rd |only man/getPlayerDataOppnHA.Rd |only 9 files changed, 18 insertions(+), 8 deletions(-)
Title: Create Reproducible Research Projects
Description: Creates reproducible academic projects with integrated academic elements, including datasets, references, codes, images, manuscripts, dissertations, slides and so on. These elements are well connected so that they can be easily synchronized and updated.
Author: Peng Zhao [aut, cre]
Maintainer: Peng Zhao <pzhao@pzhao.net>
Diff between rosr versions 0.0.7 dated 2019-05-02 and 0.0.8 dated 2019-07-12
DESCRIPTION | 8 MD5 | 18 NAMESPACE | 1 R/rmd.R | 8 inst/rmarkdown/templates/article_svm/resources/template.tex | 547 ++++----- inst/rmarkdown/templates/beamer_zh |only inst/rmarkdown/templates/manuscript_svm/resources/template.tex | 594 +++++----- inst/rmarkdown/templates/statement_svm/resources/template.tex | 18 man/rmd_template.Rd | 3 9 files changed, 615 insertions(+), 582 deletions(-)
Title: Qualitative Interaction Trees
Description: Grows a qualitative interaction tree. Quint is a tool for subgroup analysis, suitable for data from a two-arm randomized controlled trial.
Author: Elise Dusseldorp [aut, cre, cph],
Lisa Doove [aut],
Jeanne van de Put [aut],
Cor Ninaber [ctb] (supported with the plot function),
Iven Van Mechelen [aut, cph],
Juan Claramunt Gonzalez [aut]
Maintainer: Elise Dusseldorp <elise.dusseldorp@fsw.leidenuniv.nl>
Diff between quint versions 2.0.0 dated 2018-09-28 and 2.0.1 dated 2019-07-12
DESCRIPTION | 18 ++- MD5 | 47 +++++---- NAMESPACE | 94 +++++++++---------- NEWS | 208 +++++++++++++++++++++++--------------------- R/SimData_1.R | 8 - R/bcrp.R | 14 +- R/nodeinfo.R | 18 ++- R/prune.quint.R | 16 ++- R/quint-package.R | 18 +-- R/quint.R | 43 +++++---- R/quint.control.R | 43 ++++++--- R/quint.validate.R | 192 +++++++++++++++++++++------------------- build |only inst |only man/SimData_1.Rd | 94 +++++++++---------- man/bcrp.Rd | 124 +++++++++++++------------- man/plot.quint.Rd | 90 +++++++++---------- man/predict.quint.Rd | 118 ++++++++++++------------- man/prune.quint.Rd | 128 +++++++++++++-------------- man/quint-package.Rd | 142 +++++++++++++++--------------- man/quint.Rd | 236 +++++++++++++++++++++++++------------------------- man/quint.control.Rd | 154 ++++++++++++++++---------------- man/quint.validate.Rd | 170 ++++++++++++++++++------------------ man/summary.quint.Rd | 98 ++++++++++---------- vignettes |only 25 files changed, 1072 insertions(+), 1001 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-07-09 1.1-3
Title: Presentation Ninja
Description: Create HTML5 slides with R Markdown and the JavaScript library
'remark.js' (<https://remarkjs.com>).
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>),
Benjie Gillam [ctb],
Claus Thorn Ekstrøm [ctb],
Daniel Anderson [ctb],
Dawei Lang [ctb],
Garrick Aden-Buie [ctb],
John Little [ctb],
Joseph Casillas [ctb],
Michael Wayne Kearney [ctb],
Nan-Hung Hsieh [ctb],
Ole Petter Bang [ctb] (CSS in
rmarkdown/templates/xaringan/resources/default.css),
Patrick Schratz [ctb],
Paul Lemmens [ctb],
Sean Lopp [ctb],
Lucy D'Agostino McGowan [ctb] (<https://orcid.org/0000-0001-7297-9359>),
Emi Tanaka [ctb],
Yongfu Liao [ctb],
Malcolm Barrett [ctb] (<https://orcid.org/0000-0003-0299-5825>),
Alessandro Gasparini [ctb] (<https://orcid.org/0000-0002-8319-7624>),
Yue Jiang [ctb] (<https://orcid.org/0000-0002-9798-5517>)
Maintainer: Yihui Xie <xie@yihui.name>
Diff between xaringan versions 0.10 dated 2019-05-14 and 0.11 dated 2019-07-12
DESCRIPTION | 6 ++-- MD5 | 8 ++--- R/utils.R | 6 ++-- build/vignette.rds |binary tests/testit/test-utils.R | 64 ++++++++++++++++++++++------------------------ 5 files changed, 41 insertions(+), 43 deletions(-)
Title: Dynamic Documents for R
Description: Convert R Markdown documents into a variety of formats.
Author: JJ Allaire [aut],
Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>),
Jonathan McPherson [aut],
Javier Luraschi [aut],
Kevin Ushey [aut],
Aron Atkins [aut],
Hadley Wickham [aut],
Joe Cheng [aut],
Winston Chang [aut],
Richard Iannone [aut] (<https://orcid.org/0000-0003-3925-190X>),
Barret Schloerke [ctb],
Christophe Dervieux [ctb],
Frederik Aust [ctb] (<https://orcid.org/0000-0003-4900-788X>),
Jeff Allen [ctb],
Malcolm Barrett [ctb],
Rob Hyndman [ctb],
Romain Lesur [ctb],
Roy Storey [ctb],
Ruben Arslan [ctb],
RStudio, Inc. [cph],
jQuery Foundation [cph] (jQuery library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/rmd/h/jquery-AUTHORS.txt),
jQuery UI contributors [ctb, cph] (jQuery UI library; authors listed in
inst/rmd/h/jqueryui-AUTHORS.txt),
Mark Otto [ctb] (Bootstrap library),
Jacob Thornton [ctb] (Bootstrap library),
Bootstrap contributors [ctb] (Bootstrap library),
Twitter, Inc [cph] (Bootstrap library),
Alexander Farkas [ctb, cph] (html5shiv library),
Scott Jehl [ctb, cph] (Respond.js library),
Ivan Sagalaev [ctb, cph] (highlight.js library),
Greg Franko [ctb, cph] (tocify library),
John MacFarlane [ctb, cph] (Pandoc templates),
Google, Inc. [ctb, cph] (ioslides library),
Dave Raggett [ctb] (slidy library),
W3C [cph] (slidy library),
Dave Gandy [ctb, cph] (Font-Awesome),
Ben Sperry [ctb] (Ionicons),
Drifty [cph] (Ionicons),
Aidan Lister [ctb, cph] (jQuery StickyTabs)
Maintainer: Yihui Xie <xie@yihui.name>
Diff between rmarkdown versions 1.13 dated 2019-05-22 and 1.14 dated 2019-07-12
DESCRIPTION | 37 ++++---- MD5 | 28 ++++-- NEWS.md | 16 +++ R/pandoc.R | 4 R/pdf_document.R | 4 R/util.R | 2 README.md |only build |only inst/doc |only inst/rmd/h/default.html | 125 +++++++++++++++------------- inst/rmd/ioslides/ioslides_presentation.lua | 2 man/pdf_document.Rd | 8 + tests/testthat/test-ioslides.R | 4 vignettes |only 14 files changed, 136 insertions(+), 94 deletions(-)