Title: Variable Importance Plots
Description: A general framework for constructing variable importance plots from
various types machine learning models in R. Aside from some standard model-
based variable importance measures, this package also provides a novel
approach based on partial dependence plots (PDPs) and individual conditional
expectation (ICE) curves as described in Greenwell et al. (2018)
<arXiv:1805.04755>.
Author: Brandon Greenwell [aut, cre] (<https://orcid.org/0000-0002-8120-0084>),
Brad Boehmke [aut] (<https://orcid.org/0000-0002-3611-8516>),
Bernie Gray [aut]
Maintainer: Brandon Greenwell <greenwell.brandon@gmail.com>
Diff between vip versions 0.1.1 dated 2018-09-27 and 0.1.2 dated 2018-09-30
DESCRIPTION | 10 +++++----- MD5 | 19 ++++++++++--------- NAMESPACE | 6 ++++++ NEWS.md | 7 +++++++ R/utils.R | 26 ++++++++++++++++++++++++++ R/vi.R | 3 +++ R/vi_model.R | 50 ++++++++++++++++++++++++++++++++++++++++++++++++++ R/vip.R | 47 +++++++++++++++++++++++++++++++++++++---------- man/pipe.Rd |only man/vi_model.Rd | 6 ++++++ man/vip.Rd | 17 ++++++++++++++--- 11 files changed, 164 insertions(+), 27 deletions(-)
Title: Landscape Metrics for Categorical Map Patterns
Description: Calculates landscape metrics for categorical landscape patterns in
a tidy workflow. 'landscapemetrics' reimplements the most common metrics from
'FRAGSTATS' (<https://www.umass.edu/landeco/research/fragstats/fragstats.html>)
and new ones from the current literature on landscape metrics.
This package supports 'raster' spatial objects and takes
RasterLayer, RasterStacks, RasterBricks or lists of RasterLayer from the
'raster' package as input arguments. It further provides utility functions
to visualize patches, select metrics and building blocks to develop new
metrics.
Author: Maximillian H.K. Hesselbarth [aut, cre]
(<https://orcid.org/0000-0003-1125-9918>),
Marco Sciaini [aut] (<https://orcid.org/0000-0002-3042-5435>),
Jakub Nowosad [aut] (<https://orcid.org/0000-0002-1057-3721>),
Laura J. Graham [ctb] (<https://orcid.org/0000-0002-1057-3721>),
Kimberly A. With [ctb] (<https://orcid.org/0000-0001-5570-1515>),
Jeffrey Hollister [ctb] (<https://orcid.org/0000-0002-3611-7281>),
Matt Strimas-Mackey [ctb] (<https://orcid.org/0000-0001-8929-7776>),
Jeremy VanDerWal [ctb] (Original author of underlying C code for
get_patches() function),
Florian Privé [ctb] (Original author of underlying C++ code for
get_nearestneighbour() function)
Maintainer: Maximillian H.K. Hesselbarth <maximilian.hesselbarth@uni-goettingen.de>
Diff between landscapemetrics versions 0.1.1 dated 2018-08-14 and 0.2 dated 2018-09-30
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landscapemetrics-0.2/landscapemetrics/tests/testthat/test-lsm-l-dcad.R | 30 landscapemetrics-0.2/landscapemetrics/tests/testthat/test-lsm-l-dcore-cv.R | 31 landscapemetrics-0.2/landscapemetrics/tests/testthat/test-lsm-l-dcore-mn.R | 31 landscapemetrics-0.2/landscapemetrics/tests/testthat/test-lsm-l-dcore-sd.R | 29 landscapemetrics-0.2/landscapemetrics/tests/testthat/test-lsm-l-division.R | 30 landscapemetrics-0.2/landscapemetrics/tests/testthat/test-lsm-l-ed.R | 30 landscapemetrics-0.2/landscapemetrics/tests/testthat/test-lsm-l-enn-cv.R | 34 landscapemetrics-0.2/landscapemetrics/tests/testthat/test-lsm-l-enn-mn.R | 31 landscapemetrics-0.2/landscapemetrics/tests/testthat/test-lsm-l-enn-sd.R | 34 landscapemetrics-0.2/landscapemetrics/tests/testthat/test-lsm-l-ent.R | 24 landscapemetrics-0.2/landscapemetrics/tests/testthat/test-lsm-l-frac-cv.R | 34 landscapemetrics-0.2/landscapemetrics/tests/testthat/test-lsm-l-frac-mn.R | 31 landscapemetrics-0.2/landscapemetrics/tests/testthat/test-lsm-l-frac-sd.R | 34 landscapemetrics-0.2/landscapemetrics/tests/testthat/test-lsm-l-gyrate-cv.R | 29 landscapemetrics-0.2/landscapemetrics/tests/testthat/test-lsm-l-gyrate-mn.R | 31 landscapemetrics-0.2/landscapemetrics/tests/testthat/test-lsm-l-gyrate-sd.R | 30 landscapemetrics-0.2/landscapemetrics/tests/testthat/test-lsm-l-iji.R |only landscapemetrics-0.2/landscapemetrics/tests/testthat/test-lsm-l-joinent.R | 24 landscapemetrics-0.2/landscapemetrics/tests/testthat/test-lsm-l-lpi.R | 30 landscapemetrics-0.2/landscapemetrics/tests/testthat/test-lsm-l-lsi.R | 30 landscapemetrics-0.2/landscapemetrics/tests/testthat/test-lsm-l-mesh.R | 30 landscapemetrics-0.2/landscapemetrics/tests/testthat/test-lsm-l-msidi.R | 29 landscapemetrics-0.2/landscapemetrics/tests/testthat/test-lsm-l-msiei.R | 30 landscapemetrics-0.2/landscapemetrics/tests/testthat/test-lsm-l-mutinf.R | 24 landscapemetrics-0.2/landscapemetrics/tests/testthat/test-lsm-l-ndca.R | 29 landscapemetrics-0.2/landscapemetrics/tests/testthat/test-lsm-l-np.R | 30 landscapemetrics-0.2/landscapemetrics/tests/testthat/test-lsm-l-pafrac.R | 36 landscapemetrics-0.2/landscapemetrics/tests/testthat/test-lsm-l-para-cv.R | 32 landscapemetrics-0.2/landscapemetrics/tests/testthat/test-lsm-l-para-mn.R | 30 landscapemetrics-0.2/landscapemetrics/tests/testthat/test-lsm-l-para-sd.R | 34 landscapemetrics-0.2/landscapemetrics/tests/testthat/test-lsm-l-pd.R | 30 landscapemetrics-0.2/landscapemetrics/tests/testthat/test-lsm-l-pladj.R | 38 landscapemetrics-0.2/landscapemetrics/tests/testthat/test-lsm-l-pr.R | 30 landscapemetrics-0.2/landscapemetrics/tests/testthat/test-lsm-l-prd.R | 30 landscapemetrics-0.2/landscapemetrics/tests/testthat/test-lsm-l-rpr.R | 30 landscapemetrics-0.2/landscapemetrics/tests/testthat/test-lsm-l-shape-cv.R | 40 landscapemetrics-0.2/landscapemetrics/tests/testthat/test-lsm-l-shape-mn.R | 31 landscapemetrics-0.2/landscapemetrics/tests/testthat/test-lsm-l-shape-sd.R | 34 landscapemetrics-0.2/landscapemetrics/tests/testthat/test-lsm-l-shdi.R | 30 landscapemetrics-0.2/landscapemetrics/tests/testthat/test-lsm-l-shei.R | 30 landscapemetrics-0.2/landscapemetrics/tests/testthat/test-lsm-l-sidi.R | 30 landscapemetrics-0.2/landscapemetrics/tests/testthat/test-lsm-l-siei.R | 30 landscapemetrics-0.2/landscapemetrics/tests/testthat/test-lsm-l-split.R | 30 landscapemetrics-0.2/landscapemetrics/tests/testthat/test-lsm-l-ta.R | 30 landscapemetrics-0.2/landscapemetrics/tests/testthat/test-lsm-l-tca.R | 30 landscapemetrics-0.2/landscapemetrics/tests/testthat/test-lsm-l-te.R | 39 landscapemetrics-0.2/landscapemetrics/tests/testthat/test-lsm-p-area.R | 29 landscapemetrics-0.2/landscapemetrics/tests/testthat/test-lsm-p-cai.R | 29 landscapemetrics-0.2/landscapemetrics/tests/testthat/test-lsm-p-circle.R | 29 landscapemetrics-0.2/landscapemetrics/tests/testthat/test-lsm-p-contig.R | 29 landscapemetrics-0.2/landscapemetrics/tests/testthat/test-lsm-p-core.R | 33 landscapemetrics-0.2/landscapemetrics/tests/testthat/test-lsm-p-enn.R | 29 landscapemetrics-0.2/landscapemetrics/tests/testthat/test-lsm-p-frac.R | 29 landscapemetrics-0.2/landscapemetrics/tests/testthat/test-lsm-p-gyrate.R | 29 landscapemetrics-0.2/landscapemetrics/tests/testthat/test-lsm-p-nca.R | 31 landscapemetrics-0.2/landscapemetrics/tests/testthat/test-lsm-p-para.R | 29 landscapemetrics-0.2/landscapemetrics/tests/testthat/test-lsm-p-perim.R | 33 landscapemetrics-0.2/landscapemetrics/tests/testthat/test-lsm-p-shape.R | 29 landscapemetrics-0.2/landscapemetrics/tests/testthat/test-pad-raster.R |only landscapemetrics-0.2/landscapemetrics/tests/testthat/test-sample-lsm.R |only landscapemetrics-0.2/landscapemetrics/tests/testthat/test-show-cores.R |only landscapemetrics-0.2/landscapemetrics/tests/testthat/test-show-correlation.R | 6 landscapemetrics-0.2/landscapemetrics/tests/testthat/test-show-patches.R | 22 landscapemetrics-0.2/landscapemetrics/tests/testthat/test_fragstats.R |only landscapemetrics-0.2/landscapemetrics/vignettes/getstarted.Rmd | 6 494 files changed, 32157 insertions(+), 28622 deletions(-)
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Title: Predicts Oomycete Effectors
Description: Predicts cytoplasmic effector proteins using genomic data by searching for motifs of interest using regular expression searches and hidden Markov models (HMM) based in Haas et al. (2009) <doi:10.1038/nature08358>.
Author: Javier Tabima [aut, cre],
Niklaus J. Grunwald [ths]
Maintainer: Javier Tabima <tabimaj@oregonstate.edu>
Diff between effectR versions 1.0.1 dated 2018-04-25 and 1.0.2 dated 2018-09-30
DESCRIPTION | 14 +-- MD5 | 28 +++--- README.md | 8 - build/vignette.rds |binary inst/doc/effectR.R | 2 inst/doc/effectR.Rmd | 6 - inst/doc/effectR.html | 62 +++++++-------- inst/extdata/REGEX.fasta | 2 inst/extdata/test_infestans.fasta | 136 +++++++++++++-------------------- man/get_hmmer_path.Rd | 3 tests/testthat/test_HMM.R | 6 - tests/testthat/test_HMM_logo.R | 14 +-- tests/testthat/test_effector_summary.R | 17 +--- tests/testthat/test_regex.R | 4 vignettes/effectR.Rmd | 6 - 15 files changed, 142 insertions(+), 166 deletions(-)
Title: Interactive Statistical Data Visualization
Description: An extendable toolkit for interactive data visualization and exploration.
Author: Adrian Waddell [aut, cre],
R. Wayne Oldford [aut],
Zehao Xu [ctb]
Maintainer: Adrian Waddell <adrian@waddell.ch>
Diff between loon versions 1.1.1 dated 2018-03-01 and 1.2.0 dated 2018-09-30
loon-1.1.1/loon/demo/l_map_sp.R |only loon-1.1.1/loon/inst/doc/Intro.R |only loon-1.1.1/loon/inst/doc/Intro.Rmd |only loon-1.1.1/loon/inst/doc/Intro.html |only loon-1.1.1/loon/vignettes/Intro.Rmd |only loon-1.2.0/loon/DESCRIPTION | 35 loon-1.2.0/loon/MD5 | 243 +++--- loon-1.2.0/loon/NAMESPACE | 77 + loon-1.2.0/loon/NEWS.md | 36 loon-1.2.0/loon/R/datasets.R | 2 loon-1.2.0/loon/R/l_ColorList.R | 78 + loon-1.2.0/loon/R/l_cget.R | 17 loon-1.2.0/loon/R/l_compound.R |only loon-1.2.0/loon/R/l_configure.R | 17 loon-1.2.0/loon/R/l_context2d.R | 2 loon-1.2.0/loon/R/l_create_handle.R | 104 +- loon-1.2.0/loon/R/l_data.R | 2 loon-1.2.0/loon/R/l_export.R | 2 loon-1.2.0/loon/R/l_generics.R | 52 + loon-1.2.0/loon/R/l_getOption.R |only loon-1.2.0/loon/R/l_glyph_image.R | 6 loon-1.2.0/loon/R/l_glyphs.R | 100 +- loon-1.2.0/loon/R/l_graph.R | 15 loon-1.2.0/loon/R/l_graphswitch.R | 6 loon-1.2.0/loon/R/l_hexcolor.R | 5 loon-1.2.0/loon/R/l_hist.R | 7 loon-1.2.0/loon/R/l_info.R | 40 loon-1.2.0/loon/R/l_isLoonWidget.R | 14 loon-1.2.0/loon/R/l_ladder.R | 4 loon-1.2.0/loon/R/l_layer.R | 5 loon-1.2.0/loon/R/l_layer_contourLines.R | 7 loon-1.2.0/loon/R/l_layer_map.R | 3 loon-1.2.0/loon/R/l_layer_rasterImage.R | 21 loon-1.2.0/loon/R/l_navgraph.R | 20 loon-1.2.0/loon/R/l_navigator.R | 25 loon-1.2.0/loon/R/l_ng_plots.R | 25 loon-1.2.0/loon/R/l_ng_ranges.R | 15 loon-1.2.0/loon/R/l_pairs.R | 403 ++++++++-- loon-1.2.0/loon/R/l_plot.R | 8 loon-1.2.0/loon/R/l_plot_decomposed_ts.R |only loon-1.2.0/loon/R/l_plot_density.R |only loon-1.2.0/loon/R/l_plot_stl.R | 71 + loon-1.2.0/loon/R/l_plot_ts.R |only loon-1.2.0/loon/R/l_serialaxes.R | 15 loon-1.2.0/loon/R/l_setTitleFont.R | 21 loon-1.2.0/loon/R/l_state_names.R |only loon-1.2.0/loon/R/l_throwErrorIfNotLoonWidget.R | 2 loon-1.2.0/loon/R/loonGrob.R |only loon-1.2.0/loon/R/loonGrob_l_compound.R |only loon-1.2.0/loon/R/loonGrob_l_layer_graph.R |only loon-1.2.0/loon/R/loonGrob_l_layer_histogram.R |only loon-1.2.0/loon/R/loonGrob_l_layer_scatterplot.R |only loon-1.2.0/loon/R/loonGrob_l_navgraph.R |only loon-1.2.0/loon/R/loonGrob_l_navigator.R |only loon-1.2.0/loon/R/loonGrob_l_pairs.R |only loon-1.2.0/loon/R/loonGrob_l_serialaxes.R |only loon-1.2.0/loon/R/loonGrob_l_ts.R |only loon-1.2.0/loon/R/loonPlotFactory.R | 3 loon-1.2.0/loon/R/loonobject.R | 41 - loon-1.2.0/loon/R/onLoad.R | 39 loon-1.2.0/loon/R/tkcolors.R | 2 loon-1.2.0/loon/build/vignette.rds |binary loon-1.2.0/loon/demo/00Index | 2 loon-1.2.0/loon/demo/l_add_regressions.R | 8 loon-1.2.0/loon/demo/l_glyph_sizes.R | 8 loon-1.2.0/loon/demo/l_knn.R | 16 loon-1.2.0/loon/demo/l_layers.R | 2 loon-1.2.0/loon/demo/l_linkPrimitiveGlyphs.R | 13 loon-1.2.0/loon/demo/l_linking.R | 46 - loon-1.2.0/loon/demo/l_polygons_sp.R |only loon-1.2.0/loon/demo/l_scagnostics.R | 6 loon-1.2.0/loon/inst/doc/minorities.R | 42 - loon-1.2.0/loon/inst/doc/minorities.Rmd | 39 loon-1.2.0/loon/inst/doc/minorities.html | 50 - loon-1.2.0/loon/inst/doc/teaching-example-smoothing.R | 2 loon-1.2.0/loon/inst/doc/teaching-example-smoothing.Rmd | 2 loon-1.2.0/loon/inst/doc/teaching-example-smoothing.html | 6 loon-1.2.0/loon/inst/tcl/loon/library/oo_Configurable.tcl | 82 +- loon-1.2.0/loon/inst/tcl/loon/library/oo_Navigator.tcl | 4 loon-1.2.0/loon/inst/tcl/loon/library/oo_ScalesGuidesVisual.tcl | 176 ++-- loon-1.2.0/loon/inst/tcl/loon/pkgIndex.tcl | 4 loon-1.2.0/loon/man/UsAndThem.Rd | 2 loon-1.2.0/loon/man/color_loon.Rd | 4 loon-1.2.0/loon/man/figures/gestures_move.png |binary loon-1.2.0/loon/man/figures/gestures_select.png |binary loon-1.2.0/loon/man/figures/gestures_zoom_pan.png |binary loon-1.2.0/loon/man/grid.loon.Rd |only loon-1.2.0/loon/man/hex12tohex6.Rd |only loon-1.2.0/loon/man/l_colRemoveAlpha.Rd |only loon-1.2.0/loon/man/l_createCompoundGrob.Rd |only loon-1.2.0/loon/man/l_getLocations.Rd |only loon-1.2.0/loon/man/l_getOption.Rd |only loon-1.2.0/loon/man/l_getOptionNames.Rd |only loon-1.2.0/loon/man/l_getPlots.Rd |only loon-1.2.0/loon/man/l_get_arrangeGrobArgs.Rd |only loon-1.2.0/loon/man/l_glyph_add_pointrange.Rd | 3 loon-1.2.0/loon/man/l_graph.Rd | 2 loon-1.2.0/loon/man/l_graph.default.Rd | 4 loon-1.2.0/loon/man/l_graphswitch_add.graph.Rd | 4 loon-1.2.0/loon/man/l_hist.Rd | 1 loon-1.2.0/loon/man/l_info_states.Rd | 11 loon-1.2.0/loon/man/l_layer.SpatialLinesDataFrame.Rd | 3 loon-1.2.0/loon/man/l_layer.SpatialPointsDataFrame.Rd | 3 loon-1.2.0/loon/man/l_layer.SpatialPolygonsDataFrame.Rd | 4 loon-1.2.0/loon/man/l_layer_contourLines.Rd | 9 loon-1.2.0/loon/man/l_layer_heatImage.Rd | 9 loon-1.2.0/loon/man/l_layer_polygon.Rd | 3 loon-1.2.0/loon/man/l_layer_polygons.Rd | 3 loon-1.2.0/loon/man/l_layer_rasterImage.Rd | 21 loon-1.2.0/loon/man/l_layer_rectangle.Rd | 3 loon-1.2.0/loon/man/l_layer_rectangles.Rd | 3 loon-1.2.0/loon/man/l_layer_text.Rd | 4 loon-1.2.0/loon/man/l_layer_texts.Rd | 4 loon-1.2.0/loon/man/l_navgraph.Rd | 2 loon-1.2.0/loon/man/l_navigator_getPath.Rd |only loon-1.2.0/loon/man/l_navigator_ids.Rd | 2 loon-1.2.0/loon/man/l_nestedTclList2Rlist.Rd | 3 loon-1.2.0/loon/man/l_ng_plots.default.Rd | 3 loon-1.2.0/loon/man/l_ng_ranges.default.Rd | 2 loon-1.2.0/loon/man/l_pairs.Rd | 23 loon-1.2.0/loon/man/l_plot.decomposed.ts.Rd |only loon-1.2.0/loon/man/l_plot.default.Rd | 4 loon-1.2.0/loon/man/l_plot.density.Rd |only loon-1.2.0/loon/man/l_plot.stl.Rd |only loon-1.2.0/loon/man/l_plot_ts.Rd |only loon-1.2.0/loon/man/l_primitiveGlyphs.Rd |only loon-1.2.0/loon/man/l_serialaxes.Rd | 4 loon-1.2.0/loon/man/l_setColorList.Rd | 2 loon-1.2.0/loon/man/l_setColorList_ColorBrewer.Rd | 10 loon-1.2.0/loon/man/l_setColorList_baseR.Rd | 4 loon-1.2.0/loon/man/l_setColorList_ggplot2.Rd |only loon-1.2.0/loon/man/l_setColorList_hcl.Rd | 4 loon-1.2.0/loon/man/l_setColorList_loon.Rd | 4 loon-1.2.0/loon/man/l_setOption.Rd |only loon-1.2.0/loon/man/l_setTitleFont.Rd |only loon-1.2.0/loon/man/l_state_names.Rd |only loon-1.2.0/loon/man/l_userOptionDefault.Rd |only loon-1.2.0/loon/man/l_userOptions.Rd |only loon-1.2.0/loon/man/loon.Rd | 6 loon-1.2.0/loon/man/loonGrob.Rd |only loon-1.2.0/loon/man/loonGrob_layoutType.Rd |only loon-1.2.0/loon/man/names.loon.Rd |only loon-1.2.0/loon/man/tkcolors.Rd | 2 loon-1.2.0/loon/tests/test_loonGrob.R |only loon-1.2.0/loon/vignettes/minorities.Rmd | 39 loon-1.2.0/loon/vignettes/teaching-example-smoothing.Rmd | 2 146 files changed, 1616 insertions(+), 698 deletions(-)
Title: Read Data from JSTOR/DfR
Description: Functions and helpers to import metadata, ngrams and full-texts
delivered by Data for Research by JSTOR.
Author: Thomas Klebel [aut, cre] (<https://orcid.org/0000-0002-7331-4751>)
Maintainer: Thomas Klebel <t.klebel@hotmail.com>
Diff between jstor versions 0.3.2 dated 2018-07-20 and 0.3.3 dated 2018-09-30
DESCRIPTION | 14 +-- MD5 | 78 +++++++++--------- NEWS.md | 24 +++++ R/augmentations.R | 20 ++++ R/batch_import_fun.R | 6 - R/deprecated.R | 132 ++++++++++++++++++++----------- R/footnotes.R | 2 R/helpers.R | 6 - R/import_spec.R | 139 +++++++++++++++++++++++++++------ R/journal_info.R | 61 ++++++++------ R/re-import.R | 12 +- R/references.R | 2 R/sysdata.rda |binary R/utils.R |only inst/CITATION |only inst/doc/automating-file-import.R | 2 inst/doc/automating-file-import.Rmd | 4 inst/doc/automating-file-import.html | 33 ++----- inst/doc/introduction.html | 4 inst/doc/known-quirks.html | 4 inst/extdata/sample_ngram.txt |only inst/pkgdown |only man/find_article.Rd | 8 + man/find_authors.Rd | 7 + man/find_book.Rd | 8 + man/find_chapters.Rd | 12 ++ man/find_footnotes.Rd | 9 +- man/find_references.Rd | 9 +- man/get_basename.Rd | 6 + man/jst_combine_outputs.Rd | 8 - man/jst_define_import.Rd | 2 man/jst_get_footnotes.Rd | 2 man/jst_get_journal_overview.Rd | 8 + man/jst_import.Rd | 2 man/jst_re_import.Rd | 2 man/jst_unify_journal_id.Rd | 20 ++++ man/jstor_example.Rd | 11 +- man/jstor_import.Rd | 19 ++-- man/read_full_text.Rd | 6 + tests/testthat/test-import-spec.R | 5 + tests/testthat/test-journal-overview.R | 12 ++ vignettes/automating-file-import.Rmd | 4 42 files changed, 477 insertions(+), 226 deletions(-)
Title: Read, Validate, Analyze, and Map Files in the General Transit
Feed Specification
Description: Read General Transit Feed Specification (GTFS) zipfiles into a list of R dataframes. Perform validation of the data structure against the specification. Analyze the headways and frequencies at routes and stops. Create maps and perform spatial analysis on the routes and stops. Please see the GTFS documentation here for more detail: <http://gtfs.org/>.
Author: Tom Buckley [aut, cre],
Danton Noriega-Goodwin [aut],
Flavio Poletti [aut],
Angela Li [aut],
Patrick Hausmann [ctb],
Bob Rudis [ctb],
Mark Padgham [ctb],
Kearey Smith [ctb],
Dave Vautin [ctb],
Kyle Walker [ctb],
Elaine McVey [cph],
Charles Hans Thompson [cph],
Michael Sumner [cph]
Maintainer: Tom Buckley <tom@tbuckl.com>
Diff between tidytransit versions 0.3.2 dated 2018-09-03 and 0.3.4 dated 2018-09-30
tidytransit-0.3.2/tidytransit/inst/doc/tidytransit-introduction.R |only tidytransit-0.3.2/tidytransit/inst/doc/tidytransit-introduction.Rmd |only tidytransit-0.3.2/tidytransit/inst/doc/tidytransit-introduction.html |only tidytransit-0.3.2/tidytransit/man/list_files.Rd |only tidytransit-0.3.2/tidytransit/man/stops_for_service.Rd |only tidytransit-0.3.2/tidytransit/man/validate_gtfs_structure.Rd |only tidytransit-0.3.4/tidytransit/DESCRIPTION | 14 tidytransit-0.3.4/tidytransit/MD5 | 53 - tidytransit-0.3.4/tidytransit/NAMESPACE | 3 tidytransit-0.3.4/tidytransit/R/globals.R | 8 tidytransit-0.3.4/tidytransit/R/import.R | 261 +++---- tidytransit-0.3.4/tidytransit/R/joins.R | 34 tidytransit-0.3.4/tidytransit/R/service.R | 19 tidytransit-0.3.4/tidytransit/R/spec.R | 243 +++--- tidytransit-0.3.4/tidytransit/R/time.R | 95 ++ tidytransit-0.3.4/tidytransit/R/validate.R | 364 +++------- tidytransit-0.3.4/tidytransit/build/vignette.rds |binary tidytransit-0.3.4/tidytransit/inst/doc/GTFS-table-relationships.R |only tidytransit-0.3.4/tidytransit/inst/doc/GTFS-table-relationships.Rmd |only tidytransit-0.3.4/tidytransit/inst/doc/GTFS-table-relationships.html |only tidytransit-0.3.4/tidytransit/inst/doc/introduction.R | 4 tidytransit-0.3.4/tidytransit/inst/doc/introduction.Rmd | 9 tidytransit-0.3.4/tidytransit/inst/doc/introduction.html | 38 - tidytransit-0.3.4/tidytransit/man/filter_stops.Rd |only tidytransit-0.3.4/tidytransit/man/get_date_service_table.Rd |only tidytransit-0.3.4/tidytransit/man/import_gtfs.Rd | 4 tidytransit-0.3.4/tidytransit/man/read_gtfs.Rd | 9 tidytransit-0.3.4/tidytransit/man/set_hms_times.Rd |only tidytransit-0.3.4/tidytransit/man/shapes_for_routes.Rd | 6 tidytransit-0.3.4/tidytransit/man/unzip_file.Rd | 4 tidytransit-0.3.4/tidytransit/tests/testthat/test-import-gtfs.R | 44 - tidytransit-0.3.4/tidytransit/tests/testthat/test_headways.R | 2 tidytransit-0.3.4/tidytransit/vignettes/GTFS-table-relationships.Rmd |only tidytransit-0.3.4/tidytransit/vignettes/introduction.Rmd | 9 34 files changed, 594 insertions(+), 629 deletions(-)
Title: Remote Sensing for Movement Ecology
Description: Tools that support the combined use of animal movement and remote sensing data. Based on the paper on the paper by Remelgado et al. (2015) <doi:10.1002/rse2.70>.
Author: Ruben Remelgado [aut, cre]
Maintainer: Ruben Remelgado <ruben.remelgado@uni-wuerzburg.de>
Diff between rsMove versions 0.2.4 dated 2018-07-04 and 0.2.5 dated 2018-09-30
rsMove-0.2.4/rsMove/R/poly2sample.R |only rsMove-0.2.4/rsMove/inst/doc/rsMove.R |only rsMove-0.2.4/rsMove/inst/doc/rsMove.Rmd |only rsMove-0.2.4/rsMove/inst/doc/rsMove.html |only rsMove-0.2.4/rsMove/man/poly2sample.Rd |only rsMove-0.2.4/rsMove/vignettes/rsMove.Rmd |only rsMove-0.2.5/rsMove/DESCRIPTION | 13 - rsMove-0.2.5/rsMove/MD5 | 98 ++++------ rsMove-0.2.5/rsMove/NAMESPACE | 7 rsMove-0.2.5/rsMove/R/backSample.R | 25 +- rsMove-0.2.5/rsMove/R/checkOverlap.R | 25 +- rsMove-0.2.5/rsMove/R/dataQuery.R | 23 -- rsMove-0.2.5/rsMove/R/hotMove.R | 73 ++++--- rsMove-0.2.5/rsMove/R/hotMoveStats.R | 161 ++++++----------- rsMove-0.2.5/rsMove/R/imgInt.R | 25 +- rsMove-0.2.5/rsMove/R/labelSample.R | 80 +++----- rsMove-0.2.5/rsMove/R/moveCloud.R | 60 +++--- rsMove-0.2.5/rsMove/R/moveReduce.R | 23 -- rsMove-0.2.5/rsMove/R/moveSeg.R | 95 ++++++---- rsMove-0.2.5/rsMove/R/plausibilityTest.R | 18 - rsMove-0.2.5/rsMove/R/plotMove.R | 6 rsMove-0.2.5/rsMove/R/predictResources.R | 37 ++- rsMove-0.2.5/rsMove/R/rsComposite.R | 113 +++++------ rsMove-0.2.5/rsMove/R/sampleMove.R | 30 ++- rsMove-0.2.5/rsMove/R/segRaster.R | 29 +-- rsMove-0.2.5/rsMove/R/spaceDir.R | 123 ++++++------ rsMove-0.2.5/rsMove/R/specVar.R | 46 ++-- rsMove-0.2.5/rsMove/R/timeDir.R | 49 ++--- rsMove-0.2.5/rsMove/README.md | 2 rsMove-0.2.5/rsMove/build/vignette.rds |binary rsMove-0.2.5/rsMove/inst/doc/resource_suitability.R | 21 +- rsMove-0.2.5/rsMove/inst/doc/resource_suitability.Rmd | 42 ++-- rsMove-0.2.5/rsMove/inst/doc/resource_suitability.html | 100 ++++------ rsMove-0.2.5/rsMove/inst/extdata/roi.qpj | 2 rsMove-0.2.5/rsMove/man/backSample.Rd | 25 +- rsMove-0.2.5/rsMove/man/checkOverlap.Rd | 7 rsMove-0.2.5/rsMove/man/dataQuery.Rd | 23 -- rsMove-0.2.5/rsMove/man/hotMove.Rd | 29 +-- rsMove-0.2.5/rsMove/man/hotMoveStats.Rd | 30 +-- rsMove-0.2.5/rsMove/man/labelSample.Rd | 30 +-- rsMove-0.2.5/rsMove/man/moveCloud.Rd | 26 +- rsMove-0.2.5/rsMove/man/moveReduce.Rd | 11 - rsMove-0.2.5/rsMove/man/moveSeg.Rd | 36 ++- rsMove-0.2.5/rsMove/man/plausibilityTest.Rd | 18 - rsMove-0.2.5/rsMove/man/plotMove.Rd | 4 rsMove-0.2.5/rsMove/man/predictResources.Rd | 32 +-- rsMove-0.2.5/rsMove/man/rsComposite.Rd | 36 +-- rsMove-0.2.5/rsMove/man/sampleMove.Rd | 28 +- rsMove-0.2.5/rsMove/man/segRaster.Rd | 11 - rsMove-0.2.5/rsMove/man/spaceDir.Rd | 33 +-- rsMove-0.2.5/rsMove/man/specVar.Rd | 18 - rsMove-0.2.5/rsMove/man/timeDir.Rd | 26 +- rsMove-0.2.5/rsMove/vignettes/resource_suitability.Rmd | 42 ++-- 53 files changed, 880 insertions(+), 911 deletions(-)
Title: Nanosecond-Resolution Time for R
Description: Full 64-bit resolution date and time support with resolution up
to nanosecond granularity is provided, with easy transition to and from the
standard 'POSIXct' type.
Author: Dirk Eddelbuettel and Leonardo Silvestri
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between nanotime versions 0.2.2 dated 2018-07-18 and 0.2.3 dated 2018-09-30
ChangeLog | 17 +++ DESCRIPTION | 8 - MD5 | 10 +- inst/NEWS.Rd | 8 + inst/unitTests/test_nanotime.R | 201 ++++++++++++++++++++++------------------- inst/unitTests/test_zoo.R | 4 6 files changed, 147 insertions(+), 101 deletions(-)
More information about linguisticsdown at CRAN
Permanent link
Title: HTML Widgets for R
Description: A framework for creating HTML widgets that render in various
contexts including the R console, 'R Markdown' documents, and 'Shiny'
web applications.
Author: Ramnath Vaidyanathan [aut, cph],
Yihui Xie [aut],
JJ Allaire [aut],
Joe Cheng [aut, cre],
Kenton Russell [aut, cph],
RStudio [cph]
Maintainer: Joe Cheng <joe@rstudio.com>
Diff between htmlwidgets versions 1.2 dated 2018-04-19 and 1.3 dated 2018-09-30
DESCRIPTION | 18 +++++----- MD5 | 24 ++++++------- R/htmlwidgets.R | 22 ++++++++---- R/utils.R | 10 ++--- build/vignette.rds |binary inst/NEWS | 15 ++++++++ inst/doc/develop_advanced.html | 71 ++++++++++++++++++++++++++++++++++++++- inst/doc/develop_intro.Rmd | 2 - inst/doc/develop_intro.html | 73 ++++++++++++++++++++++++++++++++++++++--- inst/doc/develop_sizing.html | 71 ++++++++++++++++++++++++++++++++++++++- inst/www/htmlwidgets.js | 5 ++ man/htmlwidgets-shiny.Rd | 3 + vignettes/develop_intro.Rmd | 2 - 13 files changed, 269 insertions(+), 47 deletions(-)
Title: Companion to Applied Regression Data Sets
Description: Datasets to Accompany J. Fox and S. Weisberg,
An R Companion to Applied Regression, Third Edition, Sage (forthcoming).
Author: John Fox [aut, cre],
Sanford Weisberg [aut],
Brad Price [aut]
Maintainer: John Fox <jfox@mcmaster.ca>
Diff between carData versions 3.0-1 dated 2018-03-28 and 3.0-2 dated 2018-09-30
DESCRIPTION | 13 ++-- MD5 | 130 ++++++++++++++++++++++++----------------------- NEWS | 4 + data/AMSsurvey.rda |binary data/Adler.rda |binary data/Angell.rda |binary data/Anscombe.rda |binary data/Arrests.rda |binary data/BEPS.rda |binary data/Baumann.rda |binary data/Bfox.rda |binary data/Blackmore.rda |binary data/Burt.rda |binary data/CES11.rda |only data/CanPop.rda |binary data/Chile.rda |binary data/Chirot.rda |binary data/Cowles.rda |binary data/Davis.rda |binary data/DavisThin.rda |binary data/Depredations.rda |binary data/Duncan.rda |binary data/Ericksen.rda |binary data/Florida.rda |binary data/Freedman.rda |binary data/Friendly.rda |binary data/GSSvocab.rda |binary data/Ginzberg.rda |binary data/Greene.rda |binary data/Guyer.rda |binary data/Hartnagel.rda |binary data/Highway1.rda |binary data/KosteckiDillon.rda |binary data/Leinhardt.rda |binary data/LoBD.rda |binary data/Mandel.rda |binary data/Migration.rda |binary data/Moore.rda |binary data/MplsDemo.rda |binary data/MplsStops.rda |binary data/Mroz.rda |binary data/OBrienKaiser.rda |binary data/Ornstein.rda |binary data/Pottery.rda |binary data/Prestige.rda |binary data/Quartet.rda |binary data/Robey.rda |binary data/Rossi.rda |only data/SLID.rda |binary data/Sahlins.rda |binary data/Salaries.rda |binary data/Soils.rda |binary data/States.rda |binary data/TitanicSurvival.rda |binary data/Transact.rda |binary data/UN.rda |binary data/UN98.rda |only data/USPop.rda |binary data/Vocab.rda |binary data/WVS.rda |binary data/WeightLoss.rda |binary data/Wells.rda |binary data/Womenlf.rda |binary data/Wong.rda |binary data/Wool.rda |binary data/datalist | 121 ++++++++++++++++++++++--------------------- man/CES11.Rd |only man/Rossi.Rd |only man/UN98.Rd |only 69 files changed, 142 insertions(+), 126 deletions(-)
Title: Expanded Replacement and Extension of the 'optim' Function
Description: Provides a replacement and extension of the optim()
function to call to several function minimization codes in R in a single
statement. These methods handle smooth, possibly box constrained functions
of several or many parameters. Note that function 'optimr()' was prepared to
simplify the incorporation of minimization codes going forward. Also implements some
utility codes and some extra solvers, including safeguarded Newton methods.
Many methods previously separate are now included here.
Author: John C Nash [aut, cre],
Ravi Varadhan [aut],
Gabor Grothendieck [ctb]
Maintainer: John C Nash <nashjc@uottawa.ca>
Diff between optimx versions 2013.8.7 dated 2014-11-13 and 2018-7.10 dated 2018-09-30
optimx-2013.8.7/optimx/inst/unitTests |only optimx-2013.8.7/optimx/man/coef.optimx.Rd |only optimx-2018-7.10/optimx/DESCRIPTION | 29 optimx-2018-7.10/optimx/MD5 | 129 +++ optimx-2018-7.10/optimx/NAMESPACE | 59 + optimx-2018-7.10/optimx/NEWS | 467 ++++++++++++- optimx-2018-7.10/optimx/R/Rcgmin.R |only optimx-2018-7.10/optimx/R/Rcgminb.R |only optimx-2018-7.10/optimx/R/Rcgminu.R |only optimx-2018-7.10/optimx/R/Rtnmin-package.R |only optimx-2018-7.10/optimx/R/Rvmmin.R |only optimx-2018-7.10/optimx/R/Rvmminb.R |only optimx-2018-7.10/optimx/R/Rvmminu.R |only optimx-2018-7.10/optimx/R/axsearch.R |only optimx-2018-7.10/optimx/R/bmchk.R |only optimx-2018-7.10/optimx/R/bmstep.R |only optimx-2018-7.10/optimx/R/checksolver.R |only optimx-2018-7.10/optimx/R/ctrldefault.R |only optimx-2018-7.10/optimx/R/fnchk.R |only optimx-2018-7.10/optimx/R/gHgen.R |only optimx-2018-7.10/optimx/R/gHgenb.R |only optimx-2018-7.10/optimx/R/grback.R |only optimx-2018-7.10/optimx/R/grcentral.R |only optimx-2018-7.10/optimx/R/grchk.R |only optimx-2018-7.10/optimx/R/grfwd.R |only optimx-2018-7.10/optimx/R/grnd.R |only optimx-2018-7.10/optimx/R/hesschk.R |only optimx-2018-7.10/optimx/R/hjn.R |only optimx-2018-7.10/optimx/R/kktchk.R |only optimx-2018-7.10/optimx/R/multistart.R |only optimx-2018-7.10/optimx/R/opm.R |only optimx-2018-7.10/optimx/R/optchk.R |only optimx-2018-7.10/optimx/R/optimr.R |only optimx-2018-7.10/optimx/R/optimx-package.R | 14 optimx-2018-7.10/optimx/R/optimx.check.R | 9 optimx-2018-7.10/optimx/R/optimx.run.R | 202 +++-- optimx-2018-7.10/optimx/R/optimx.setup.R | 7 optimx-2018-7.10/optimx/R/polyopt.R |only optimx-2018-7.10/optimx/R/proptimr.R |only optimx-2018-7.10/optimx/R/scalechk.R |only optimx-2018-7.10/optimx/R/snewton.R |only optimx-2018-7.10/optimx/R/snewtonm.R |only optimx-2018-7.10/optimx/R/tn.R |only optimx-2018-7.10/optimx/R/tnbc.R |only optimx-2018-7.10/optimx/R/zzz.R |only optimx-2018-7.10/optimx/TODO |only optimx-2018-7.10/optimx/build |only optimx-2018-7.10/optimx/demo/00Index | 2 optimx-2018-7.10/optimx/demo/cyq_test.R |only optimx-2018-7.10/optimx/demo/genrose_test.R |only optimx-2018-7.10/optimx/demo/ox.R | 1 optimx-2018-7.10/optimx/inst/doc |only optimx-2018-7.10/optimx/man/Rcgmin.Rd |only optimx-2018-7.10/optimx/man/Rcgminb.Rd |only optimx-2018-7.10/optimx/man/Rcgminu.Rd |only optimx-2018-7.10/optimx/man/Rvmmin.Rd |only optimx-2018-7.10/optimx/man/Rvmminb.Rd |only optimx-2018-7.10/optimx/man/Rvmminu.Rd |only optimx-2018-7.10/optimx/man/axsearch.Rd |only optimx-2018-7.10/optimx/man/bmchk.Rd |only optimx-2018-7.10/optimx/man/bmstep.Rd |only optimx-2018-7.10/optimx/man/checksolver.Rd |only optimx-2018-7.10/optimx/man/coef.opm.Rd |only optimx-2018-7.10/optimx/man/ctrldefault.Rd |only optimx-2018-7.10/optimx/man/fnchk.Rd |only optimx-2018-7.10/optimx/man/gHgen.Rd |only optimx-2018-7.10/optimx/man/gHgenb.Rd |only optimx-2018-7.10/optimx/man/grback.Rd |only optimx-2018-7.10/optimx/man/grcentral.Rd |only optimx-2018-7.10/optimx/man/grchk.Rd |only optimx-2018-7.10/optimx/man/grfwd.Rd |only optimx-2018-7.10/optimx/man/grnd.Rd |only optimx-2018-7.10/optimx/man/hesschk.Rd |only optimx-2018-7.10/optimx/man/hjn.Rd |only optimx-2018-7.10/optimx/man/kktchk.Rd |only optimx-2018-7.10/optimx/man/multistart.Rd |only optimx-2018-7.10/optimx/man/opm.Rd |only optimx-2018-7.10/optimx/man/optchk.Rd |only optimx-2018-7.10/optimx/man/optimr.Rd |only optimx-2018-7.10/optimx/man/optimx-package.Rd | 48 + optimx-2018-7.10/optimx/man/optimx.Rd | 930 +++++++++++++------------- optimx-2018-7.10/optimx/man/polyopt.Rd |only optimx-2018-7.10/optimx/man/proptimr.Rd |only optimx-2018-7.10/optimx/man/scalechk.Rd |only optimx-2018-7.10/optimx/man/snewton.Rd |only optimx-2018-7.10/optimx/man/tn.Rd |only optimx-2018-7.10/optimx/man/tnbc.Rd |only optimx-2018-7.10/optimx/po |only optimx-2018-7.10/optimx/tests |only optimx-2018-7.10/optimx/vignettes |only 90 files changed, 1313 insertions(+), 584 deletions(-)
Title: R Interface to NLopt
Description: Solve optimization problems using an R interface to NLopt. NLopt is a
free/open-source library for nonlinear optimization, providing a common
interface for a number of different free optimization routines available
online as well as original implementations of various other algorithms.
See <http://ab-initio.mit.edu/wiki/index.php/NLopt_Introduction> for more
information on the available algorithms. During installation of nloptr on
Unix-based systems, the installer checks whether the NLopt library is
installed on the system. If the NLopt library cannot be found, the code
is compiled using the NLopt source included in the nloptr package.
Author: Jelmer Ypma <uctpjyy@ucl.ac.uk>, with contributions by
Hans W. Borchers <hwborchers@googlemail.com> and
Dirk Eddelbuettel <edd@debian.org>
Maintainer: Jelmer Ypma <uctpjyy@ucl.ac.uk>
Diff between nloptr versions 1.0.4 dated 2014-08-04 and 1.2.0 dated 2018-09-30
nloptr-1.0.4/nloptr/inst/doc/nloptr.Rnw |only nloptr-1.0.4/nloptr/man/gradients.Rd |only nloptr-1.0.4/nloptr/man/nloptions.Rd |only nloptr-1.0.4/nloptr/vignettes/nloptr.Rnw |only nloptr-1.2.0/nloptr/CHANGELOG | 199 +- nloptr-1.2.0/nloptr/DESCRIPTION | 30 nloptr-1.2.0/nloptr/INSTALL.windows | 4 nloptr-1.2.0/nloptr/MD5 | 381 ++++ nloptr-1.2.0/nloptr/NAMESPACE | 43 nloptr-1.2.0/nloptr/R/PkgFlags.R |only nloptr-1.2.0/nloptr/R/PkgFlags.R.in |only nloptr-1.2.0/nloptr/R/auglag.R | 312 ++- nloptr-1.2.0/nloptr/R/check.derivatives.R | 301 ++- nloptr-1.2.0/nloptr/R/cobyla.R | 310 +++ nloptr-1.2.0/nloptr/R/direct.R | 236 ++- nloptr-1.2.0/nloptr/R/global.R | 429 ++++- nloptr-1.2.0/nloptr/R/gradients.R | 143 + nloptr-1.2.0/nloptr/R/is.nloptr.R | 411 ++--- nloptr-1.2.0/nloptr/R/lbfgs.R | 136 + nloptr-1.2.0/nloptr/R/mlsl.R | 201 +- nloptr-1.2.0/nloptr/R/mma.R | 204 +- nloptr-1.2.0/nloptr/R/nloptions.R | 112 - nloptr-1.2.0/nloptr/R/nloptr-package.R |only nloptr-1.2.0/nloptr/R/nloptr.R | 865 +++++++---- nloptr-1.2.0/nloptr/R/nloptr.add.default.options.R | 62 nloptr-1.2.0/nloptr/R/nloptr.get.default.options.R | 295 ++- nloptr-1.2.0/nloptr/R/nloptr.print.options.R | 132 + nloptr-1.2.0/nloptr/R/nm.R | 215 ++ nloptr-1.2.0/nloptr/R/onLoad.R |only nloptr-1.2.0/nloptr/R/onUnLoad.R |only nloptr-1.2.0/nloptr/R/print.nloptr.R | 161 +- nloptr-1.2.0/nloptr/R/slsqp.R | 217 +- nloptr-1.2.0/nloptr/R/tnewton.R | 154 + nloptr-1.2.0/nloptr/R/varmetric.R | 138 + nloptr-1.2.0/nloptr/README.md | 124 - nloptr-1.2.0/nloptr/build/vignette.rds |binary nloptr-1.2.0/nloptr/cleanup | 17 nloptr-1.2.0/nloptr/configure | 203 +- nloptr-1.2.0/nloptr/configure.ac | 172 +- nloptr-1.2.0/nloptr/inst/doc/nloptr.R | 124 - nloptr-1.2.0/nloptr/inst/doc/nloptr.Rmd |only nloptr-1.2.0/nloptr/inst/doc/nloptr.pdf |binary nloptr-1.2.0/nloptr/inst/include |only nloptr-1.2.0/nloptr/man/auglag.Rd | 153 + nloptr-1.2.0/nloptr/man/bobyqa.Rd | 69 nloptr-1.2.0/nloptr/man/check.derivatives.Rd | 90 - nloptr-1.2.0/nloptr/man/cobyla.Rd | 87 - nloptr-1.2.0/nloptr/man/crs2lm.Rd | 95 - nloptr-1.2.0/nloptr/man/direct.Rd | 120 - nloptr-1.2.0/nloptr/man/is.nloptr.Rd | 34 nloptr-1.2.0/nloptr/man/isres.Rd | 99 - nloptr-1.2.0/nloptr/man/lbfgs.Rd | 101 - nloptr-1.2.0/nloptr/man/mlsl.Rd | 124 - nloptr-1.2.0/nloptr/man/mma.Rd | 100 - nloptr-1.2.0/nloptr/man/neldermead.Rd | 78 nloptr-1.2.0/nloptr/man/newuoa.Rd | 65 nloptr-1.2.0/nloptr/man/nl.grad.Rd |only nloptr-1.2.0/nloptr/man/nl.opts.Rd |only nloptr-1.2.0/nloptr/man/nloptr-package.Rd | 149 - nloptr-1.2.0/nloptr/man/nloptr.Rd | 311 +-- nloptr-1.2.0/nloptr/man/nloptr.get.default.options.Rd | 43 nloptr-1.2.0/nloptr/man/nloptr.print.options.Rd | 47 nloptr-1.2.0/nloptr/man/print.nloptr.Rd | 42 nloptr-1.2.0/nloptr/man/sbplx.Rd | 76 nloptr-1.2.0/nloptr/man/slsqp.Rd | 104 - nloptr-1.2.0/nloptr/man/stogo.Rd | 78 nloptr-1.2.0/nloptr/man/tnewton.Rd | 85 - nloptr-1.2.0/nloptr/man/varmetric.Rd | 93 - nloptr-1.2.0/nloptr/src/Makevars.in | 4 nloptr-1.2.0/nloptr/src/Makevars.win | 46 nloptr-1.2.0/nloptr/src/init_nloptr.c |only nloptr-1.2.0/nloptr/src/nlopt_src |only nloptr-1.2.0/nloptr/src/nloptr.h |only nloptr-1.2.0/nloptr/tests/testthat/test-C-api.R |only nloptr-1.2.0/nloptr/tests/testthat/test-derivative-checker.R | 11 nloptr-1.2.0/nloptr/tests/testthat/test-hs023.R | 192 +- nloptr-1.2.0/nloptr/tests/testthat/test-options-maxtime.R |only nloptr-1.2.0/nloptr/vignettes/nloptr.Rmd |only nloptr-1.2.0/nloptr/vignettes/reflist.bib | 44 79 files changed, 5507 insertions(+), 3364 deletions(-)
Title: Test Analysis Modules
Description: Includes marginal maximum likelihood estimation and joint maximum
likelihood estimation for unidimensional and multidimensional
item response models. The package functionality covers the
Rasch model, 2PL model, 3PL model, generalized partial credit model,
multi-faceted Rasch model, nominal item response model,
structured latent class model, mixture distribution IRT models,
and located latent class models. Latent regression models and
plausible value imputation are also supported. For details see
Adams, Wilson and Wang, 1997 <doi:10.1177/0146621697211001>,
Adams, Wilson and Wu, 1997 <doi:10.3102/10769986022001047>,
Formann, 1982 <doi:10.1002/bimj.4710240209>,
Formann, 1992 <doi:10.1080/01621459.1992.10475229>.
Author: Alexander Robitzsch [aut, cre], Thomas Kiefer [aut], Margaret Wu [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between TAM versions 2.12-18 dated 2018-05-25 and 2.13-15 dated 2018-09-30
DESCRIPTION | 13 +- MD5 | 141 +++++++++++------------ NAMESPACE | 17 +- R/IRT.RISE.R |only R/IRT.expectedCounts.tam.R | 15 ++ R/IRT.irfprob.tam.R | 3 R/IRT.likelihood.TAM.R | 4 R/IRT.residuals.R | 17 +- R/RcppExports.R | 6 R/designMatrices.mfr.R | 4 R/designMatrices.mfr2.R | 4 R/lavaanify.IRT.R | 41 +++--- R/lavpartable.grep.underbrace.R | 36 ++--- R/summary.tam.R | 8 - R/summary.tam.jml.R | 8 - R/summary.tam.mml.3pl.R | 10 - R/summary_tamaan_3pl_intro.R | 10 - R/tam.mml.wle.R | 5 R/tam.np.R |only R/tam_jml_version2.R | 32 ++--- R/tam_jml_wle.R | 4 R/tam_latent_regression_standardized_solution.R | 7 - R/tam_mml_progress_em.R | 7 - R/tam_np_inits.R |only R/tam_print_call.R | 10 + R/tamaan.R | 17 +- R/tamaanify.R | 25 +--- R/tamaanify.proc.itemtype.R | 25 +--- R/tamaanify.proc.lavaanmodel.R | 7 - R/tamaanify.tam.mml.3pl.designMatrices.MIXTURE.R | 14 -- R/tamaanify.tam.mml.3pl.designMatrices.R | 6 data/data.cqc01.rda |binary data/data.cqc02.rda |binary data/data.cqc03.rda |binary data/data.cqc04.rda |binary data/data.cqc05.rda |binary data/data.ctest1.rda |binary data/data.ctest2.rda |binary data/data.ex08.rda |binary data/data.ex10.rda |binary data/data.ex11.rda |binary data/data.ex12.rda |binary data/data.ex14.rda |binary data/data.ex15.rda |binary data/data.ex16.rda |binary data/data.ex17.rda |binary data/data.exJ03.rda |binary data/data.fims.Aus.Jpn.raw.rda |binary data/data.fims.Aus.Jpn.scored.rda |binary data/data.geiser.rda |binary data/data.gpcm.rda |binary data/data.janssen.rda |binary data/data.janssen2.rda |binary data/data.mc.rda |binary data/data.numeracy.rda |binary data/data.sim.facets.rda |binary data/data.sim.mfr.rda |binary data/data.sim.rasch.missing.rda |binary data/data.sim.rasch.pweights.rda |binary data/data.sim.rasch.rda |binary data/data.timssAusTwn.rda |binary data/data.timssAusTwn.scored.rda |binary inst/NEWS | 22 +++ man/IRT.expectedCounts.tam.Rd | 7 - man/IRT.irfprob.tam.Rd | 7 - man/IRT.likelihood.tam.Rd | 9 + man/IRT.residuals.Rd | 7 - man/tam.linking.Rd | 53 ++++++++ man/tam.np.Rd |only man/tam.wle.Rd | 17 +- man/tamaan.Rd | 6 src/RcppExports.cpp | 18 ++ src/init.c | 4 src/tam_rcpp_tam_np.cpp |only 74 files changed, 384 insertions(+), 262 deletions(-)
Title: Data-Driven Plot Design
Description: Designs plots in terms of core structure. See 'example(metaplot)'.
Primary arguments are (unquoted) column names; order and type (numeric or not)
dictate the resulting plot. Specify any y variables, x variable, any groups variable,
and any conditioning variables to metaplot() to generate density plots, boxplots,
mosaic plots, scatterplots, scatterplot matrices, or conditioned plots. Use multiplot()
to arrange plots in grids. Wherever present, scalar column attributes 'label' and 'guide'
are honored, producing fully annotated plots with minimal effort. Attribute 'guide'
is typically units, but may be encoded() to provide interpretations of categorical
values (see '?encode'). Utility unpack() transforms scalar column attributes to row
values and pack() does the reverse, supporting tool-neutral storage of metadata along
with primary data. The package supports customizable aesthetics such as such as reference
lines, unity lines, smooths, log transformation, and linear fits. The user may choose
between trellis and ggplot output. Compact syntax and integrated metadata promote workflow
scalability.
Author: Tim Bergsma
Maintainer: Tim Bergsma <bergsmat@gmail.com>
Diff between metaplot versions 0.7.0 dated 2018-08-09 and 0.8.0 dated 2018-09-30
DESCRIPTION | 10 - MD5 | 87 ++++---- NAMESPACE | 6 R/box.R | 74 ++++--- R/categorical.R | 104 ++++++---- R/corsplom.R | 196 +++++++++++-------- R/density.R | 149 +++++++++----- R/metaplot.R | 19 - R/multiplot.R | 26 -- R/scatter.R | 379 +++++++++++++++++++++++--------------- R/utils.R | 135 +++++++++---- man/boxplot.data.frame.Rd | 5 man/boxplot_data_frame.Rd | 50 ++--- man/boxplot_panel.Rd | 4 man/categorical.data.frame.Rd | 6 man/categorical_data_frame.Rd | 53 ++--- man/categorical_panel.Rd | 16 + man/corsplom.data.frame.Rd | 4 man/corsplom_data_frame.Rd | 65 +++--- man/corsplom_gg_correlation.Rd | 8 man/corsplom_gg_diagonal.Rd | 25 +- man/corsplom_gg_scatter.Rd | 13 - man/corsplom_panel_correlation.Rd | 5 man/corsplom_panel_diagonal.Rd | 25 +- man/corsplom_panel_scatter.Rd | 14 - man/dens_panel.Rd | 5 man/densplot.data.frame.Rd | 4 man/densplot_data_frame.Rd | 58 +++-- man/diag_label.Rd | 11 - man/metOption.Rd | 25 +- man/metaplot.Rd | 7 man/metaplot.data.frame.Rd | 13 - man/metaplot_key.Rd | 4 man/model.Rd | 1 man/multiplot.Rd | 5 man/panel.meta_densityplot.Rd | 4 man/panel_tile.Rd | 4 man/plot.metaplot_gtable.Rd | 16 - man/print.metaplot_gtable.Rd | 8 man/region.Rd | 1 man/scatter.data.frame.Rd | 9 man/scatter_data_frame.Rd | 126 ++++++------ man/scatter_panel.Rd | 73 +++---- man/setOption.Rd |only man/tiles.Rd | 4 45 files changed, 1075 insertions(+), 781 deletions(-)
Title: Fast 'Rcpp' Implementation of Gauss-Hermite Quadrature
Description: Fast, numerically-stable Gauss-Hermite quadrature rules and
utility functions for adaptive GH quadrature. See Liu, Q. and Pierce, D. A.
(1994) <doi:10.2307/2337136> for a reference on these methods.
Author: Alexander W Blocker
Maintainer: Alexander W Blocker <ablocker@gmail.com>
Diff between fastGHQuad versions 0.2 dated 2014-08-14 and 1.0 dated 2018-09-30
fastGHQuad-0.2/fastGHQuad/README |only fastGHQuad-1.0/fastGHQuad/DESCRIPTION | 15 +++++--- fastGHQuad-1.0/fastGHQuad/MD5 | 34 ++++++++++---------- fastGHQuad-1.0/fastGHQuad/NAMESPACE | 2 - fastGHQuad-1.0/fastGHQuad/R/integrate.R | 2 - fastGHQuad-1.0/fastGHQuad/R/lib.R | 3 + fastGHQuad-1.0/fastGHQuad/README.md |only fastGHQuad-1.0/fastGHQuad/inst |only fastGHQuad-1.0/fastGHQuad/man/aghQuad.Rd | 15 +++++--- fastGHQuad-1.0/fastGHQuad/man/evalHermitePoly.Rd | 10 ++--- fastGHQuad-1.0/fastGHQuad/man/fastGHQuad-package.Rd | 16 +++++---- fastGHQuad-1.0/fastGHQuad/man/findPolyRoots.Rd | 10 ++--- fastGHQuad-1.0/fastGHQuad/man/gaussHermiteData.Rd | 10 ++--- fastGHQuad-1.0/fastGHQuad/man/ghQuad.Rd | 13 ++++--- fastGHQuad-1.0/fastGHQuad/man/hermitePolyCoef.Rd | 10 ++--- fastGHQuad-1.0/fastGHQuad/src/Makevars | 2 - fastGHQuad-1.0/fastGHQuad/src/Makevars.win | 2 - fastGHQuad-1.0/fastGHQuad/src/init.cpp |only fastGHQuad-1.0/fastGHQuad/src/lib.cpp | 9 ++--- fastGHQuad-1.0/fastGHQuad/src/lib.h | 6 +-- 20 files changed, 88 insertions(+), 71 deletions(-)
Title: Extension of `data.frame`
Description: Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group using no copies at all, list columns, friendly and fast character-separated-value read/write. Offers a natural and flexible syntax, for faster development.
Author: Matt Dowle [aut, cre],
Arun Srinivasan [aut],
Jan Gorecki [ctb],
Michael Chirico [ctb],
Pasha Stetsenko [ctb],
Tom Short [ctb],
Steve Lianoglou [ctb],
Eduard Antonyan [ctb],
Markus Bonsch [ctb],
Hugh Parsonage [ctb]
Maintainer: Matt Dowle <mattjdowle@gmail.com>
Diff between data.table versions 1.11.6 dated 2018-09-19 and 1.11.8 dated 2018-09-30
data.table-1.11.6/data.table/inst/tests/allchar.csv |only data.table-1.11.6/data.table/inst/tests/grr.csv |only data.table-1.11.6/data.table/inst/tests/issue_2157_sampling_overlap.txt |only data.table-1.11.6/data.table/inst/tests/issue_2157_sampling_reached_eof_early.txt |only data.table-1.11.6/data.table/inst/tests/winallquoted.csv |only data.table-1.11.8/data.table/DESCRIPTION | 8 data.table-1.11.8/data.table/MD5 | 60 data.table-1.11.8/data.table/NAMESPACE | 33 data.table-1.11.8/data.table/NEWS.md | 110 data.table-1.11.8/data.table/R/data.table.R | 32 data.table-1.11.8/data.table/R/fcast.R | 12 data.table-1.11.8/data.table/R/fmelt.R | 19 data.table-1.11.8/data.table/R/fread.R | 15 data.table-1.11.8/data.table/R/setkey.R | 2 data.table-1.11.8/data.table/inst/doc/datatable-benchmarking.html | 425 -- data.table-1.11.8/data.table/inst/doc/datatable-faq.Rmd | 2 data.table-1.11.8/data.table/inst/doc/datatable-faq.html | 1419 +++----- data.table-1.11.8/data.table/inst/doc/datatable-importing.Rmd | 81 data.table-1.11.8/data.table/inst/doc/datatable-importing.html | 478 +- data.table-1.11.8/data.table/inst/doc/datatable-intro.html | 1609 ++++------ data.table-1.11.8/data.table/inst/doc/datatable-keys-fast-subset.html | 1228 +++---- data.table-1.11.8/data.table/inst/doc/datatable-reference-semantics.html | 928 ++--- data.table-1.11.8/data.table/inst/doc/datatable-reshape.html | 816 ++--- data.table-1.11.8/data.table/inst/doc/datatable-secondary-indices-and-auto-indexing.html | 845 ++--- data.table-1.11.8/data.table/inst/tests/allchar.csv.gz |only data.table-1.11.8/data.table/inst/tests/grr.csv.gz |only data.table-1.11.8/data.table/inst/tests/issue_2157_sampling_overlap.txt.gz |only data.table-1.11.8/data.table/inst/tests/issue_2157_sampling_reached_eof_early.txt.bz2 |only data.table-1.11.8/data.table/inst/tests/tests.Rraw | 127 data.table-1.11.8/data.table/inst/tests/winallquoted.csv.bz2 |only data.table-1.11.8/data.table/man/fread.Rd | 2 data.table-1.11.8/data.table/src/assign.c | 6 data.table-1.11.8/data.table/src/subset.c | 6 data.table-1.11.8/data.table/src/uniqlist.c | 15 data.table-1.11.8/data.table/vignettes/datatable-faq.Rmd | 2 data.table-1.11.8/data.table/vignettes/datatable-importing.Rmd | 81 36 files changed, 3632 insertions(+), 4729 deletions(-)
Title: High Performance CommonMark and Github Markdown Rendering in R
Description: The CommonMark specification defines a rationalized version of markdown
syntax. This package uses the 'cmark' reference implementation for converting
markdown text into various formats including html, latex and groff man. In
addition it exposes the markdown parse tree in xml format. Also inlcudes opt-in
support for GFM extensions including tables, autolinks, and strikethrough text.
Author: Jeroen Ooms [aut, cre],
John MacFarlane [cph] (Author of cmark)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between commonmark versions 1.5 dated 2018-04-28 and 1.6 dated 2018-09-30
commonmark-1.5/commonmark/src/cmark/cmark.h |only commonmark-1.5/commonmark/src/cmark/cmark_export.h |only commonmark-1.5/commonmark/src/cmark/cmark_extension_api.h |only commonmark-1.5/commonmark/src/cmark/cmark_version.h |only commonmark-1.5/commonmark/src/extensions/cmarkextensions_export.h |only commonmark-1.5/commonmark/src/extensions/core-extensions.h |only commonmark-1.6/commonmark/DESCRIPTION | 14 commonmark-1.6/commonmark/MD5 | 101 commonmark-1.6/commonmark/NEWS | 3 commonmark-1.6/commonmark/src/cmark/arena.c | 4 commonmark-1.6/commonmark/src/cmark/blocks.c | 36 commonmark-1.6/commonmark/src/cmark/buffer.h | 46 commonmark-1.6/commonmark/src/cmark/chunk.h | 2 commonmark-1.6/commonmark/src/cmark/cmark-gfm-extension_api.h |only commonmark-1.6/commonmark/src/cmark/cmark-gfm.h |only commonmark-1.6/commonmark/src/cmark/cmark-gfm_export.h |only commonmark-1.6/commonmark/src/cmark/cmark-gfm_version.h |only commonmark-1.6/commonmark/src/cmark/cmark.c | 6 commonmark-1.6/commonmark/src/cmark/cmark_ctype.h | 12 commonmark-1.6/commonmark/src/cmark/commonmark.c | 12 commonmark-1.6/commonmark/src/cmark/footnotes.c | 2 commonmark-1.6/commonmark/src/cmark/houdini.h | 12 commonmark-1.6/commonmark/src/cmark/houdini_href_e.c | 4 commonmark-1.6/commonmark/src/cmark/html.c | 14 commonmark-1.6/commonmark/src/cmark/inlines.c | 41 commonmark-1.6/commonmark/src/cmark/inlines.h | 2 commonmark-1.6/commonmark/src/cmark/iterator.c | 2 commonmark-1.6/commonmark/src/cmark/iterator.h | 2 commonmark-1.6/commonmark/src/cmark/latex.c | 2 commonmark-1.6/commonmark/src/cmark/linked_list.c | 2 commonmark-1.6/commonmark/src/cmark/main.c | 56 commonmark-1.6/commonmark/src/cmark/man.c | 2 commonmark-1.6/commonmark/src/cmark/node.c | 20 commonmark-1.6/commonmark/src/cmark/node.h | 8 commonmark-1.6/commonmark/src/cmark/plugin.h | 4 commonmark-1.6/commonmark/src/cmark/references.c | 2 commonmark-1.6/commonmark/src/cmark/registry.c | 2 commonmark-1.6/commonmark/src/cmark/registry.h | 8 commonmark-1.6/commonmark/src/cmark/render.c | 2 commonmark-1.6/commonmark/src/cmark/scanners.c |28601 +++------- commonmark-1.6/commonmark/src/cmark/scanners.h | 2 commonmark-1.6/commonmark/src/cmark/syntax_extension.c | 12 commonmark-1.6/commonmark/src/cmark/syntax_extension.h | 6 commonmark-1.6/commonmark/src/cmark/utf8.h | 12 commonmark-1.6/commonmark/src/cmark/xml.c | 13 commonmark-1.6/commonmark/src/extensions.c | 12 commonmark-1.6/commonmark/src/extensions/autolink.h | 6 commonmark-1.6/commonmark/src/extensions/cmark-gfm-core-extensions.h |only commonmark-1.6/commonmark/src/extensions/cmark-gfm-extensions_export.h |only commonmark-1.6/commonmark/src/extensions/core-extensions.c | 4 commonmark-1.6/commonmark/src/extensions/ext_scanners.h | 2 commonmark-1.6/commonmark/src/extensions/strikethrough.c | 13 commonmark-1.6/commonmark/src/extensions/strikethrough.h | 6 commonmark-1.6/commonmark/src/extensions/table.c | 97 commonmark-1.6/commonmark/src/extensions/table.h | 10 commonmark-1.6/commonmark/src/extensions/tagfilter.h | 6 commonmark-1.6/commonmark/src/init.c |only commonmark-1.6/commonmark/src/wrapper.c | 7 58 files changed, 10955 insertions(+), 18277 deletions(-)
Title: Statistical Inference and Sure Independence Screening via Ball
Statistics
Description: Hypothesis tests and sure independence screening (SIS) procedure based on ball statistics, including ball divergence <doi:10.1214/17-AOS1579>, ball covariance, and ball correlation <doi:10.1080/01621459.2018.1462709>, are developed to analyze complex data. The ball divergence and ball covariance based distribution-free tests are implemented to examine equality of multivariate distributions and independence between random vectors of arbitrary dimensions. Furthermore, a generic non-parametric SIS procedure based on ball correlation and all of its variants are implemented to tackle the challenge in the context of ultra high dimensional data.
Author: Xueqin Wang, Wenliang Pan, Heping Zhang, Hongtu Zhu, Yuan Tian, Weinan Xiao, Chengfeng Liu, Jin Zhu
Maintainer: Jin Zhu <zhuj37@mail2.sysu.edu.cn>
Diff between Ball versions 1.2.0 dated 2018-06-17 and 1.3.0 dated 2018-09-30
DESCRIPTION | 10 MD5 | 48 - NAMESPACE | 1 NEWS.md | 5 R/bcorsis.R | 2 R/bcov.R | 2 R/bd.R | 18 R/data.R | 1 R/wrap_c.R | 8 README.md | 2 inst/doc/Ball.html | 12 man/bcorsis.Rd | 2 man/bcov.test.Rd | 2 man/bd.Rd | 2 man/bd.test.Rd | 2 src/BD.c | 1995 ++++++++++++++++++++++++------------------ src/BD.h | 3 src/BI.c | 1449 ++++++++++++++---------------- src/Ball_omp.h |only src/utilities.c | 30 src/utilities.h | 2 src/utilize_R.c | 11 src/utilize_R.h | 1 tests/testthat/test_bcorsis.R |only tests/testthat/test_bcov.R | 21 tests/testthat/test_bd.R | 92 + 26 files changed, 2059 insertions(+), 1662 deletions(-)
Title: Cognitive Diagnosis Modeling
Description: Functions for cognitive diagnosis modeling and multidimensional item response modeling
for dichotomous and polytomous item responses. This package enables the estimation of
the DINA and DINO model (Junker & Sijtsma, 2001, <doi:10.1177/01466210122032064>),
the multiple group (polytomous) GDINA model (de la Torre, 2011,
<doi:10.1007/s11336-011-9207-7>), the multiple choice DINA model (de la Torre, 2009,
<doi:10.1177/0146621608320523>), the general diagnostic model (GDM; von Davier, 2008,
<doi:10.1348/000711007X193957>), the structured latent class model (SLCA; Formann, 1992,
<doi:10.1080/01621459.1992.10475229>) and regularized latent class analysis
(Chen, Li, Liu, & Ying, 2017, <doi:10.1007/s11336-016-9545-6>).
See George, Robitzsch, Kiefer, Gross, and Uenlue (2017) <doi:10.18637/jss.v074.i02>
for further details on estimation and the package structure.
For tutorials on how to use the CDM package see
George and Robitzsch (2015, <doi:10.20982/tqmp.11.3.p189>) as well as
Ravand and Robitzsch (2015).
Author: Alexander Robitzsch [aut, cre], Thomas Kiefer [aut],
Ann Cathrice George [aut], Ali Uenlue [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between CDM versions 6.5-12 dated 2018-08-16 and 6.6-5 dated 2018-09-30
DESCRIPTION | 8 MD5 | 50 ++--- R/IRT_RMSD_calc_rmsd.R | 8 R/RcppExports.R | 2 R/cdm_replace_inf.R | 4 R/gdina.R | 6 R/gdina_mstep_item_ml.R | 8 R/gdina_mstep_item_ml_update_parameter.R | 8 R/gdina_mstep_item_ml_update_parameter_regularization.R | 6 R/gdina_mstep_item_parameters.R | 8 R/gdina_mstep_item_uls.R | 4 R/reglca.R | 5 R/reglca_calc_deviance.R | 4 R/reglca_fit_probabilities.R | 4 R/reglca_freq_ll.R | 5 R/reglca_mstep_item_parameters.R | 13 - R/reglca_progress_em_algorithm.R | 8 R/reglca_threshold_parameter.R | 4 R/reglca_update_parameter.R | 15 + R/rrum.param.R | 4 R/sim.din.R | 41 ---- R/summary.din.R | 148 +++++++--------- inst/NEWS | 12 + man/CDM-utilities.Rd | 8 src/RcppExports.cpp | 2 src/init.c | 2 26 files changed, 189 insertions(+), 198 deletions(-)
Title: Penalized Composite Link Model for Efficient Estimation of
Smooth Distributions from Coarsely Binned Data
Description: Versatile method for ungrouping histograms (binned count data)
assuming that counts are Poisson distributed and that the underlying sequence
on a fine grid to be estimated is smooth. The method is based on the composite
link model and estimation is achieved by maximizing a penalized likelihood.
Smooth detailed sequences of counts and rates are so estimated from the binned
counts. Ungrouping binned data can be desirable for many reasons: Bins can be
too coarse to allow for accurate analysis; comparisons can be hindered when
different grouping approaches are used in different histograms; and the last
interval is often wide and open-ended and, thus, covers a lot of information
in the tail area. Age-at-death distributions grouped in age classes and
abridged life tables are examples of binned data. Because of modest assumptions,
the approach is suitable for many demographic and epidemiological applications.
For a detailed description of the method and applications see
Rizzi et al. (2015) <doi:10.1093/aje/kwv020>.
Author: Marius D. Pascariu [aut, cre] (<https://orcid.org/0000-0002-2568-6489>),
Silvia Rizzi [aut],
Jonas Schoeley [aut] (<https://orcid.org/0000-0002-3340-8518>),
Maciej J. Danko [aut] (<https://orcid.org/0000-0002-7924-9022>)
Maintainer: Marius D. Pascariu <rpascariu@outlook.com>
Diff between ungroup versions 1.0.0 dated 2018-09-03 and 1.1.0 dated 2018-09-30
ungroup-1.0.0/ungroup/R/zzz.R |only ungroup-1.1.0/ungroup/DESCRIPTION | 11 +-- ungroup-1.1.0/ungroup/MD5 | 45 ++++++------ ungroup-1.1.0/ungroup/NAMESPACE | 1 ungroup-1.1.0/ungroup/NEWS | 7 + ungroup-1.1.0/ungroup/R/pclm_1D.R | 15 ++-- ungroup-1.1.0/ungroup/R/pclm_2D.R | 18 ++-- ungroup-1.1.0/ungroup/R/pclm_CI.R | 3 ungroup-1.1.0/ungroup/R/pclm_fit.R | 13 ++- ungroup-1.1.0/ungroup/R/pclm_graphics.R | 77 +++++++++++++-------- ungroup-1.1.0/ungroup/R/pclm_optim.R | 7 - ungroup-1.1.0/ungroup/R/ungroup-package.r | 1 ungroup-1.1.0/ungroup/R/utils.R | 47 +++++------- ungroup-1.1.0/ungroup/README.md | 22 ++++-- ungroup-1.1.0/ungroup/THANKS | 6 + ungroup-1.1.0/ungroup/build/partial.rdb |binary ungroup-1.1.0/ungroup/inst/CITATION |only ungroup-1.1.0/ungroup/inst/doc/Intro.Rmd | 14 +-- ungroup-1.1.0/ungroup/inst/doc/Intro.pdf |binary ungroup-1.1.0/ungroup/man/pclm.Rd | 5 + ungroup-1.1.0/ungroup/man/pclm2D.Rd | 1 ungroup-1.1.0/ungroup/man/ungroup.Rd | 2 ungroup-1.1.0/ungroup/tests/testthat/test_pclm.R | 63 +---------------- ungroup-1.1.0/ungroup/tests/testthat/test_pclm2D.R |only ungroup-1.1.0/ungroup/vignettes/Intro.Rmd | 14 +-- 25 files changed, 188 insertions(+), 184 deletions(-)
Title: Create and Evaluate NONMEM Models in a Project Context
Description: Systematically creates and modifies NONMEM(R) control streams. Harvests
NONMEM output, builds run logs, creates derivative data, generates diagnostics.
NONMEM (ICON Development Solutions <http://www.iconplc.com/>) is software for
nonlinear mixed effects modeling. See 'package?nonmemica'.
Author: Tim Bergsma
Maintainer: Tim Bergsma <bergsmat@gmail.com>
Diff between nonmemica versions 0.8.2 dated 2018-03-29 and 0.8.3 dated 2018-09-30
DESCRIPTION | 6 - MD5 | 29 ++++++-- NAMESPACE | 15 ++++ R/halfmatrix.R | 133 ++++++++++++++++++++++++++++++++++++++++ R/likebut.R | 2 R/model.R | 3 build/vignette.rds |binary inst/doc/parameter-table.html | 16 ++-- man/as.data.frame.halfmatrix.Rd |only man/as.halfmatrix.Rd |only man/as.halfmatrix.default.Rd |only man/as.halfmatrix.halfmatrix.Rd |only man/as.matrix.halfmatrix.Rd |only man/half.Rd |only man/half.matrix.Rd |only man/is.square.Rd |only man/is.square.matrix.Rd |only man/offdiag.Rd |only man/offdiag.halfmatrix.Rd |only man/ord.Rd |only man/ord.halfmatrix.Rd |only man/ord.matrix.Rd |only man/print.halfmatrix.Rd |only 23 files changed, 186 insertions(+), 18 deletions(-)
Title: Maximum Likelihood Estimation of DNA Methylation and
Hydroxymethylation Proportions
Description: Maximum likelihood estimates (MLE) of the proportions
of 5-mC and 5-hmC in the DNA using information from BS-conversion,
TAB-conversion, and oxBS-conversion methods. One can use information from all three methods
or any combination of two of them. Estimates are based on Binomial model by
Qu et al. (2013) <doi:10.1093/bioinformatics/btt459> and
Kiihl et al. (2018, to appear).
Author: Samara Kiihl [aut, cre],
Maria Jose Martinez-Garrido [aut],
Arce Domingo-Relloso [aut],
Jose Bermudez [aut],
Maria Tellez-Plaza [aut]
Maintainer: Samara Kiihl <samara@ime.unicamp.br>
Diff between MLML2R versions 0.2.1 dated 2018-05-16 and 0.3.0 dated 2018-09-30
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Title: A Toolkit for Using Whole Building Simulation Program
'EnergyPlus'
Description: A rich toolkit of using the whole building simulation program
'EnergyPlus'(<https://energyplus.net>), which enables programmatic
navigation, modification of 'EnergyPlus' models and makes it less painful to
do parametric simulations and analysis.
Author: Hongyuan Jia [aut, cre] (<https://orcid.org/0000-0002-0075-8183>)
Maintainer: Hongyuan Jia <hongyuanjia@cqu.edu.cn>
Diff between eplusr versions 0.9.1 dated 2018-08-29 and 0.9.2 dated 2018-09-30
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Title: A Pipeline Toolkit for Reproducible Computation at Scale
Description: A general-purpose computational engine for data analysis,
drake rebuilds intermediate data objects when their dependencies change,
and it skips work when the results are already up to date.
Not every execution starts from scratch,
and completed projects have tangible evidence
that they are reproducible.
Extensive documentation, from beginner-friendly tutorials
to practical examples and more, is available at the reference website
<https://ropensci.github.io/drake/> and the online manual
<https://ropenscilabs.github.io/drake-manual/>.
Author: William Michael Landau [aut, cre],
Alex Axthelm [ctb],
Jasper Clarkberg [ctb],
Kirill Müller [ctb],
Ben Marwick [rev],
Peter Slaughter [rev],
Eli Lilly and Company [cph]
Maintainer: William Michael Landau <will.landau@gmail.com>
Diff between drake versions 5.4.0 dated 2018-08-07 and 6.0.0 dated 2018-09-30
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