Title: Vector Helpers
Description: Defines new notions of prototype and size that are
used to provide tools for consistent and well-founded type-coercion
and size-recycling, and are in turn connected to ideas of type- and
size-stability useful for analysing function interfaces.
Author: Hadley Wickham [aut],
Lionel Henry [aut, cre],
Davis Vaughan [aut],
RStudio [cph]
Maintainer: Lionel Henry <lionel@rstudio.com>
Diff between vctrs versions 0.3.2 dated 2020-07-15 and 0.3.3 dated 2020-08-27
DESCRIPTION | 8 MD5 | 247 +++++++++--------- NAMESPACE | 25 + NEWS.md | 81 +++++ R/assert.R | 2 R/cast.R | 2 R/compare.R | 102 ++++--- R/equal.R | 5 R/faq-developer.R | 7 R/faq.R | 16 + R/numeric.R | 6 R/proxy.R | 11 R/slice.R | 32 +- R/type-bare.R | 49 +++ R/type-data-frame.R | 185 ++++++++++++- R/type-date-time.R | 2 R/type-rcrd.R | 93 +----- R/type-table.R | 53 +-- R/type-vctr.R | 2 R/utils.R | 64 ++++ build/vctrs.pdf |binary inst/doc/pillar.html | 39 +- inst/doc/s3-vector.Rmd | 2 inst/doc/s3-vector.html | 9 inst/doc/stability.html | 4 man/data_frame.Rd |only man/df_list.Rd |only man/faq-compatibility-types.Rd |only man/faq-error-scalar-type.Rd |only man/faq/developer/howto-faq-fix-scalar-type-error.Rmd |only man/faq/setup.Rmd | 2 man/faq/user |only man/howto-faq-fix-scalar-type-error.Rd |only man/new_data_frame.Rd | 22 - man/new_rcrd.Rd | 12 man/table.Rd | 7 man/vctrs-data-frame.Rd |only man/vec_data.Rd | 4 man/vec_is_list.Rd | 3 man/vec_math.Rd | 6 man/vec_order.Rd | 4 man/vec_proxy_compare.Rd | 52 ++- src/altrep-rle.c | 2 src/altrep-rle.h | 2 src/altrep.h | 10 src/bind.c | 134 ++++----- src/c-unchop.c | 110 +++----- src/c.c | 64 ++-- src/c.h | 2 src/dictionary.c | 12 src/init.c | 10 src/names.c | 99 ++++--- src/names.h | 3 src/proxy-restore.c | 8 src/proxy.c | 229 +++++++++++----- src/size.c | 8 src/slice-assign.c | 43 +-- src/slice-assign.h | 1 src/slice-chop.c | 2 src/slice.c | 5 src/translate.c | 5 src/type-data-frame.c | 231 +++++++++++++++- src/type-data-frame.h | 6 src/type-info.c | 40 -- src/utils-rlang.c |only src/utils-rlang.h |only src/utils.c | 104 +++++-- src/utils.h | 59 +++- src/vctrs.h | 11 src/version.c | 2 tests/testthat/helper-cast.R | 2 tests/testthat/helper-expectations.R | 4 tests/testthat/helper-performance.R | 32 ++ tests/testthat/helper-rational.R | 2 tests/testthat/helper-s3.R | 6 tests/testthat/helper-size.R | 5 tests/testthat/helper-types.R | 7 tests/testthat/helper-vctrs.R | 46 +++ tests/testthat/performance |only tests/testthat/test-arith.R | 1 tests/testthat/test-assert.R | 25 + tests/testthat/test-bind.R | 123 ++++++++ tests/testthat/test-c.R | 130 +++++++++ tests/testthat/test-cast-list.R | 1 tests/testthat/test-cast.R | 1 tests/testthat/test-compare.R | 67 +++- tests/testthat/test-conditions.R | 1 tests/testthat/test-dictionary.R | 2 tests/testthat/test-dim.R | 1 tests/testthat/test-empty.R | 1 tests/testthat/test-equal.R | 2 tests/testthat/test-fields.R | 1 tests/testthat/test-group.R | 3 tests/testthat/test-hash.R | 1 tests/testthat/test-names.R | 44 +++ tests/testthat/test-partial-factor.R | 1 tests/testthat/test-partial-frame.R | 1 tests/testthat/test-print-str-mtcars.txt | 23 - tests/testthat/test-print-str.R | 1 tests/testthat/test-proxy-restore.R | 7 tests/testthat/test-proxy.R | 15 + tests/testthat/test-ptype-abbr-full.R | 1 tests/testthat/test-recycle.R | 1 tests/testthat/test-s4.R | 1 tests/testthat/test-shape.R | 1 tests/testthat/test-size.R | 1 tests/testthat/test-slice-assign.R | 53 +-- tests/testthat/test-slice-chop.R | 4 tests/testthat/test-slice.R | 24 + tests/testthat/test-split.R | 1 tests/testthat/test-translate.R | 1 tests/testthat/test-type-bare.R | 6 tests/testthat/test-type-data-frame.R | 112 +++++++- tests/testthat/test-type-date-time.R | 1 tests/testthat/test-type-factor.R | 1 tests/testthat/test-type-integer64.R | 1 tests/testthat/test-type-list-of.R | 1 tests/testthat/test-type-rational.R | 1 tests/testthat/test-type-rcrd.R | 100 +++++-- tests/testthat/test-type-sclr.R | 1 tests/testthat/test-type-table.R | 116 +++++--- tests/testthat/test-type-tibble.R | 1 tests/testthat/test-type-unspecified.R | 1 tests/testthat/test-type-vctr.R | 11 tests/testthat/test-type.R | 7 tests/testthat/test-type2.R | 1 tests/testthat/test-utils.R | 1 tests/testthat/test-vctrs.R | 1 vignettes/s3-vector.Rmd | 2 129 files changed, 2392 insertions(+), 977 deletions(-)
Title: Photobiological Calculations
Description: Definitions of classes, methods, operators and functions for use
in photobiology and radiation meteorology and climatology. Calculation of
effective (weighted) and not-weighted irradiances/doses, fluence rates,
transmittance, reflectance, absorptance, absorbance and diverse ratios and
other derived quantities from spectral data. Local maxima and minima: peaks,
valleys and spikes. Conversion between energy-and photon-based units.
Wavelength interpolation. Astronomical calculations related solar angles and
day length. Colours and vision. This package is part of the 'r4photobiology'
suite, Aphalo, P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.
Author: Pedro J. Aphalo [aut, cre] (<https://orcid.org/0000-0003-3385-972X>),
Titta K. Kotilainen [ctb] (<https://orcid.org/0000-0002-2822-9734>),
Glenn Davis [ctb],
Agnese Fazio [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between photobiology versions 0.10.4 dated 2020-06-07 and 0.10.5 dated 2020-08-27
photobiology-0.10.4/photobiology/data/colors-spct.rda |only photobiology-0.10.4/photobiology/man/uncollect.Rd |only photobiology-0.10.4/photobiology/man/wl_colors.spct.Rd |only photobiology-0.10.5/photobiology/DESCRIPTION | 15 photobiology-0.10.5/photobiology/MD5 | 188 - photobiology-0.10.5/photobiology/NAMESPACE | 35 photobiology-0.10.5/photobiology/NEWS | 27 photobiology-0.10.5/photobiology/R/calc.multipliers.r | 24 photobiology-0.10.5/photobiology/R/calc.source.output.r | 12 photobiology-0.10.5/photobiology/R/color.of.R | 52 photobiology-0.10.5/photobiology/R/copy.attr.R | 7 photobiology-0.10.5/photobiology/R/fel.spectrum.r | 6 photobiology-0.10.5/photobiology/R/interpolate.spectrum.r | 4 photobiology-0.10.5/photobiology/R/irradiance.r | 15 photobiology-0.10.5/photobiology/R/join.mspct.R | 10 photobiology-0.10.5/photobiology/R/mspct.methods.R | 275 -- photobiology-0.10.5/photobiology/R/normalized.diff.idx.r | 6 photobiology-0.10.5/photobiology/R/print.waveband.r | 10 photobiology-0.10.5/photobiology/R/rbindspct.r | 14 photobiology-0.10.5/photobiology/R/s.e.irrad2rgb.r | 14 photobiology-0.10.5/photobiology/R/spct.absorbance.R | 2 photobiology-0.10.5/photobiology/R/spct.absorptance.R | 2 photobiology-0.10.5/photobiology/R/spct.classes.r | 1199 +--------- photobiology-0.10.5/photobiology/R/spct.clean.r | 8 photobiology-0.10.5/photobiology/R/spct.compare.r | 26 photobiology-0.10.5/photobiology/R/spct.conversion.R | 16 photobiology-0.10.5/photobiology/R/spct.fscale.r | 20 photobiology-0.10.5/photobiology/R/spct.integrate.r | 2 photobiology-0.10.5/photobiology/R/spct.irrad.r | 2 photobiology-0.10.5/photobiology/R/spct.metadata.r |only photobiology-0.10.5/photobiology/R/spct.new.r | 17 photobiology-0.10.5/photobiology/R/spct.normalize.r | 21 photobiology-0.10.5/photobiology/R/spct.operators.r | 36 photobiology-0.10.5/photobiology/R/spct.peaks.r | 8 photobiology-0.10.5/photobiology/R/spct.reflectance.r | 2 photobiology-0.10.5/photobiology/R/spct.response.R | 4 photobiology-0.10.5/photobiology/R/spct.rgb.spct.r | 2 photobiology-0.10.5/photobiology/R/spct.smooth.spct.r | 750 +++--- photobiology-0.10.5/photobiology/R/spct.spikes.R | 2 photobiology-0.10.5/photobiology/R/spct.summaries.r | 4 photobiology-0.10.5/photobiology/R/spct.tag.r | 17 photobiology-0.10.5/photobiology/R/spct.transmittance.r | 2 photobiology-0.10.5/photobiology/R/spct.utils.r | 261 ++ photobiology-0.10.5/photobiology/R/sun.calc.r | 12 photobiology-0.10.5/photobiology/R/sysdata.rda |only photobiology-0.10.5/photobiology/R/trim.waveband.r | 22 photobiology-0.10.5/photobiology/R/waveband.class.r | 16 photobiology-0.10.5/photobiology/R/waveband.ratio.r | 6 photobiology-0.10.5/photobiology/README.md | 4 photobiology-0.10.5/photobiology/build/vignette.rds |binary photobiology-0.10.5/photobiology/inst/doc/userguide1-intro.html | 22 photobiology-0.10.5/photobiology/inst/doc/userguide2-radiation.R | 9 photobiology-0.10.5/photobiology/inst/doc/userguide2-radiation.Rmd | 30 photobiology-0.10.5/photobiology/inst/doc/userguide2-radiation.html | 659 ++--- photobiology-0.10.5/photobiology/inst/doc/userguide3-astronomy.html | 42 photobiology-0.10.5/photobiology/man/adaptive_smoothing.Rd |only photobiology-0.10.5/photobiology/man/add_attr2tb.Rd | 134 - photobiology-0.10.5/photobiology/man/as.response_spct.Rd | 4 photobiology-0.10.5/photobiology/man/as.source_spct.Rd | 4 photobiology-0.10.5/photobiology/man/collect2mspct.Rd |only photobiology-0.10.5/photobiology/man/day_night.Rd | 6 photobiology-0.10.5/photobiology/man/drop_user_cols.Rd |only photobiology-0.10.5/photobiology/man/extract.Rd | 4 photobiology-0.10.5/photobiology/man/fit_peaks.Rd | 2 photobiology-0.10.5/photobiology/man/getFilterProperties.Rd | 4 photobiology-0.10.5/photobiology/man/getHowMeasured.Rd | 4 photobiology-0.10.5/photobiology/man/getInstrDesc.Rd | 4 photobiology-0.10.5/photobiology/man/getInstrSettings.Rd | 4 photobiology-0.10.5/photobiology/man/getNormalized.Rd | 11 photobiology-0.10.5/photobiology/man/getResponseType.Rd |only photobiology-0.10.5/photobiology/man/getScaled.Rd | 5 photobiology-0.10.5/photobiology/man/getWhatMeasured.Rd | 4 photobiology-0.10.5/photobiology/man/getWhenMeasured.Rd | 4 photobiology-0.10.5/photobiology/man/getWhereMeasured.Rd | 14 photobiology-0.10.5/photobiology/man/get_attributes.Rd | 2 photobiology-0.10.5/photobiology/man/isValidInstrDesc.Rd | 4 photobiology-0.10.5/photobiology/man/isValidInstrSettings.Rd | 4 photobiology-0.10.5/photobiology/man/normalized_diff_ind.Rd | 2 photobiology-0.10.5/photobiology/man/photobiology-package.Rd | 2 photobiology-0.10.5/photobiology/man/select_spct_attributes.Rd | 2 photobiology-0.10.5/photobiology/man/setFilterProperties.Rd | 17 photobiology-0.10.5/photobiology/man/setGenericSpct.Rd | 14 photobiology-0.10.5/photobiology/man/setHowMeasured.Rd | 4 photobiology-0.10.5/photobiology/man/setInstrDesc.Rd | 4 photobiology-0.10.5/photobiology/man/setInstrSettings.Rd | 4 photobiology-0.10.5/photobiology/man/setResponseType.Rd |only photobiology-0.10.5/photobiology/man/setTimeUnit.Rd | 5 photobiology-0.10.5/photobiology/man/setWhatMeasured.Rd | 4 photobiology-0.10.5/photobiology/man/setWhenMeasured.Rd | 4 photobiology-0.10.5/photobiology/man/setWhereMeasured.Rd | 4 photobiology-0.10.5/photobiology/man/smooth_spct.Rd | 68 photobiology-0.10.5/photobiology/man/source_spct.Rd | 3 photobiology-0.10.5/photobiology/man/spct_attr2tb.Rd | 2 photobiology-0.10.5/photobiology/man/spct_metadata.Rd |only photobiology-0.10.5/photobiology/man/sun_angles.Rd | 6 photobiology-0.10.5/photobiology/man/thin_wl.Rd | 4 photobiology-0.10.5/photobiology/man/trimInstrDesc.Rd | 4 photobiology-0.10.5/photobiology/man/trimInstrSettings.Rd | 4 photobiology-0.10.5/photobiology/man/uncollect2spct.Rd |only photobiology-0.10.5/photobiology/man/using_Tfr.Rd | 2 photobiology-0.10.5/photobiology/vignettes/userguide2-radiation.Rmd | 30 101 files changed, 1979 insertions(+), 2367 deletions(-)
Title: CSS Animations for 'shiny' Elements
Description: A wrapper around a CSS library called 'vov.css', intended for use
in 'shiny' applications. Simply wrap a UI element in one of the animation
functions to see it move.
Author: Tyler Littlefield [aut, cre] (Creator of Shiny Wrapper),
Vaibhav Tandon [ctb, cph] (Author of included CSS code),
Danube Huynhle [ctb]
Maintainer: Tyler Littlefield <tylerlittlefield@hey.com>
Diff between vov versions 0.1.1 dated 2020-08-02 and 0.1.2 dated 2020-08-27
DESCRIPTION | 10 MD5 | 120 +- NAMESPACE | 12 NEWS.md | 8 R/utils.R | 84 + R/vov.R | 537 ++++++++++-- README.md | 65 - inst/extdata/app.R | 33 inst/extdata/vov.css | 1771 ---------------------------------------- man/blur_in.Rd | 18 man/blur_out.Rd | 18 man/fade_in.Rd | 18 man/fade_in_bottom_left.Rd | 24 man/fade_in_bottom_right.Rd | 24 man/fade_in_down.Rd | 18 man/fade_in_left.Rd | 18 man/fade_in_right.Rd | 24 man/fade_in_top_left.Rd | 24 man/fade_in_top_right.Rd | 24 man/fade_in_up.Rd | 18 man/fade_out.Rd | 18 man/fade_out_bottom_left.Rd | 24 man/fade_out_bottom_right.Rd | 24 man/fade_out_down.Rd | 24 man/fade_out_left.Rd | 24 man/fade_out_right.Rd | 24 man/fade_out_top_left.Rd | 24 man/fade_out_top_right.Rd | 24 man/fade_out_up.Rd | 18 man/figures/vov-logo.png |only man/flash.Rd | 18 man/i_throb.Rd | 18 man/roll_in_left.Rd | 18 man/roll_in_right.Rd | 24 man/roll_out_left.Rd | 24 man/roll_out_right.Rd | 24 man/shake_diagonally.Rd |only man/shake_horizontal.Rd | 24 man/shake_i_diagonally.Rd |only man/shake_vertical.Rd | 24 man/slide_in_down.Rd | 24 man/slide_in_left.Rd | 24 man/slide_in_right.Rd | 24 man/slide_in_up.Rd | 18 man/slide_out_down.Rd | 24 man/slide_out_left.Rd | 24 man/slide_out_right.Rd | 24 man/slide_out_up.Rd | 18 man/swivel_horizontal.Rd | 24 man/swivel_horizontal_double.Rd | 24 man/swivel_vertical.Rd | 24 man/swivel_vertical_double.Rd | 24 man/throb.Rd | 18 man/wheel_in_left.Rd | 24 man/wheel_in_right.Rd | 24 man/wheel_out_left.Rd | 24 man/wheel_out_right.Rd | 24 man/zoom_in.Rd |only man/zoom_in_down.Rd |only man/zoom_in_left.Rd |only man/zoom_in_right.Rd |only man/zoom_in_up.Rd |only man/zoom_out.Rd |only man/zoom_out_down.Rd |only man/zoom_out_left.Rd |only man/zoom_out_right.Rd |only man/zoom_out_up.Rd |only tests/testthat/test-parsers.R |only 68 files changed, 1527 insertions(+), 2109 deletions(-)
Title: Microbiome Regression-Based Analysis Tests
Description: Test for overall association between microbiome composition data and phenotypes via phylogenetic kernels.
The phenotype can be univariate continuous or binary (Zhao et al. (2015) <doi:10.1016/j.ajhg.2015.04.003>),
survival outcomes (Plantinga et al. (2017) <doi:10.1186/s40168-017-0239-9>),
multivariate (Zhan et al. (2017) <doi:10.1002/gepi.22030>) and
structured phenotypes (Zhan et al. (2017) <doi:10.1111/biom.12684>).
The package can also use robust and quantile regression (Fu et al. (2020+), in preparation).
In each case, the microbiome community effect is modeled nonparametrically through a kernel function,
which can incorporate phylogenetic tree information.
Author: Anna Plantinga [aut, cre],
Nehemiah Wilson [aut, ctb],
Haotian Zheng [aut, ctb],
Xiang Zhan [aut, ctb],
Michael Wu [aut],
Ni Zhao [aut, ctb],
Jun Chen [aut]
Maintainer: Anna Plantinga <amp9@williams.edu>
Diff between MiRKAT versions 1.1.0 dated 2020-04-14 and 1.1.1 dated 2020-08-27
MiRKAT-1.1.0/MiRKAT/R/helperFunctions1.R |only MiRKAT-1.1.1/MiRKAT/DESCRIPTION | 10 MiRKAT-1.1.1/MiRKAT/MD5 | 71 ++--- MiRKAT-1.1.1/MiRKAT/R/CSKAT.R | 83 +++--- MiRKAT-1.1.1/MiRKAT/R/CSKAT_helper.R | 2 MiRKAT-1.1.1/MiRKAT/R/CSKAT_support.R |only MiRKAT-1.1.1/MiRKAT/R/GLMMMiRKAT.R | 49 ++- MiRKAT-1.1.1/MiRKAT/R/KRV.R | 52 ++- MiRKAT-1.1.1/MiRKAT/R/KRV_helper.R | 18 - MiRKAT-1.1.1/MiRKAT/R/MMiRKAT.R | 10 MiRKAT-1.1.1/MiRKAT/R/MiRKAT.R | 19 - MiRKAT-1.1.1/MiRKAT/R/MiRKATS.R | 103 +++++-- MiRKAT-1.1.1/MiRKAT/R/MiRKATS_helper.R | 15 - MiRKAT-1.1.1/MiRKAT/R/MiRKAT_Binary.R | 156 ++++------- MiRKAT-1.1.1/MiRKAT/R/MiRKAT_Continuous.R | 181 +++++-------- MiRKAT-1.1.1/MiRKAT/R/MiRKAT_Q.R | 45 ++- MiRKAT-1.1.1/MiRKAT/R/MiRKAT_R.R | 51 +++ MiRKAT-1.1.1/MiRKAT/R/MiRKAT_support.R |only MiRKAT-1.1.1/MiRKAT/build/vignette.rds |binary MiRKAT-1.1.1/MiRKAT/inst/doc/MiRKAT_Vignette.R | 20 - MiRKAT-1.1.1/MiRKAT/inst/doc/MiRKAT_Vignette.Rmd | 30 +- MiRKAT-1.1.1/MiRKAT/inst/doc/MiRKAT_Vignette.html | 288 ++++++++++------------ MiRKAT-1.1.1/MiRKAT/man/CSKAT.Rd | 5 MiRKAT-1.1.1/MiRKAT/man/GLMMMiRKAT.Rd | 4 MiRKAT-1.1.1/MiRKAT/man/KRV.Rd | 4 MiRKAT-1.1.1/MiRKAT/man/MiRKAT.Q.Rd | 5 MiRKAT-1.1.1/MiRKAT/man/MiRKAT.R.Rd | 9 MiRKAT-1.1.1/MiRKAT/man/MiRKAT.Rd | 4 MiRKAT-1.1.1/MiRKAT/man/MiRKATS.Rd | 6 MiRKAT-1.1.1/MiRKAT/man/MiRKAT_binary.Rd | 6 MiRKAT-1.1.1/MiRKAT/man/MiRKAT_continuous.Rd | 6 MiRKAT-1.1.1/MiRKAT/man/bindata.Rd | 6 MiRKAT-1.1.1/MiRKAT/man/nordata.Rd | 6 MiRKAT-1.1.1/MiRKAT/man/poisdata.Rd | 6 MiRKAT-1.1.1/MiRKAT/man/throat.meta.Rd | 6 MiRKAT-1.1.1/MiRKAT/man/throat.otu.tab.Rd | 4 MiRKAT-1.1.1/MiRKAT/man/throat.tree.Rd | 4 MiRKAT-1.1.1/MiRKAT/vignettes/MiRKAT_Vignette.Rmd | 30 +- 38 files changed, 719 insertions(+), 595 deletions(-)
Title: An Interface for Content-Based Identifiers
Description: An interface for creating, registering, and resolving content-based
identifiers for data management. Content-based identifiers rely on
the 'cryptographic' hashes to refer to the files they identify, thus,
anyone possessing the file can compute the identifier using a
well-known standard algorithm, such as 'SHA256'. By registering
a URL at which the content is accessible to a public archive, such
as <https://hash-archive.org>, the content identifier can serve
many functions typically associated with A Digital Object Identifier
('DOI'). Unlike location-based identifiers like 'DOIs', content-based
identifiers permit the same content to be registered in many locations.
Author: Carl Boettiger [aut, cre] (<https://orcid.org/0000-0002-1642-628X>),
Jorrit Poelen [aut] (<https://orcid.org/0000-0003-3138-4118>),
NSF OAC 1839201 [fnd]
(https://www.nsf.gov/awardsearch/showAward?AWD_ID=1839201)
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between contentid versions 0.0.4 dated 2020-08-12 and 0.0.5 dated 2020-08-27
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++----------- NAMESPACE | 1 + NEWS.md | 6 +++++- R/local_registry.R | 2 +- R/query_sources.R | 7 +++++-- R/register.R | 17 ++++++++++------- R/resolve.R | 3 ++- R/utils.R | 1 + tests/testthat/test-pin.R | 4 ++++ tests/testthat/test-register-query.R | 1 + tests/testthat/test-software-heritage.R | 29 ++++++++++++++++++++--------- 12 files changed, 64 insertions(+), 35 deletions(-)
Title: Analysis of Multivariate Event Times
Description: Implementation of various statistical models for multivariate
event history data <doi:10.1007/s10985-013-9244-x>. Including multivariate
cumulative incidence models <doi:10.1002/sim.6016>, and bivariate random
effects probit models (Liability models) <doi:10.1016/j.csda.2015.01.014>.
Also contains two-stage binomial modelling that can do pairwise odds-ratio
dependence modelling based marginal logistic regression models. This is an
alternative to the alternating logistic regression approach (ALR).
Author: Klaus K. Holst [aut, cre],
Thomas Scheike [aut]
Maintainer: Klaus K. Holst <klaus@holst.it>
Diff between mets versions 1.2.7.1 dated 2020-03-04 and 1.2.8 dated 2020-08-27
mets-1.2.7.1/mets/NEWS |only mets-1.2.7.1/mets/inst/devel |only mets-1.2.7.1/mets/inst/doc/basic-dutils.ltx |only mets-1.2.7.1/mets/inst/doc/basic-dutils.pdf |only mets-1.2.7.1/mets/inst/doc/binomial-case-control-ascertainment.ltx |only mets-1.2.7.1/mets/inst/doc/binomial-case-control-ascertainment.pdf |only mets-1.2.7.1/mets/inst/doc/binomial-family.ltx |only mets-1.2.7.1/mets/inst/doc/binomial-family.pdf |only mets-1.2.7.1/mets/inst/doc/binomial-twin.ltx |only mets-1.2.7.1/mets/inst/doc/binomial-twin.pdf |only mets-1.2.7.1/mets/inst/doc/competing.ltx |only mets-1.2.7.1/mets/inst/doc/competing.pdf |only mets-1.2.7.1/mets/inst/doc/marginal-cox.ltx |only mets-1.2.7.1/mets/inst/doc/marginal-cox.pdf |only mets-1.2.7.1/mets/inst/doc/quantitative-twin.ltx |only mets-1.2.7.1/mets/inst/doc/quantitative-twin.pdf |only mets-1.2.7.1/mets/inst/doc/recurrent-events.ltx |only mets-1.2.7.1/mets/inst/doc/recurrent-events.pdf |only mets-1.2.7.1/mets/inst/doc/twostage-survival-case-control.ltx |only 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mets-1.2.8/mets/man/fast.reshape.Rd | 21 mets-1.2.8/mets/man/figures |only mets-1.2.8/mets/man/gof.phreg.Rd | 19 mets-1.2.8/mets/man/gofM.phreg.Rd | 14 mets-1.2.8/mets/man/gofZ.phreg.Rd | 14 mets-1.2.8/mets/man/haplo.surv.discrete.Rd | 35 mets-1.2.8/mets/man/internal.Rd | 2 mets-1.2.8/mets/man/interval.logitsurv.discrete.Rd | 25 mets-1.2.8/mets/man/ipw.Rd | 19 mets-1.2.8/mets/man/ipw2.Rd | 31 mets-1.2.8/mets/man/km.Rd | 10 mets-1.2.8/mets/man/lifecourse.Rd | 28 mets-1.2.8/mets/man/logitSurv.Rd | 8 mets-1.2.8/mets/man/mlogit.Rd | 2 mets-1.2.8/mets/man/phreg.Rd | 3 mets-1.2.8/mets/man/phregR.Rd | 2 mets-1.2.8/mets/man/predict.phreg.Rd | 27 mets-1.2.8/mets/man/prob.exceed.recurrent.Rd | 19 mets-1.2.8/mets/man/random.cif.Rd | 30 mets-1.2.8/mets/man/simAalenFrailty.Rd | 12 mets-1.2.8/mets/man/simClaytonOakes.Rd | 14 mets-1.2.8/mets/man/simClaytonOakesWei.Rd | 13 mets-1.2.8/mets/man/simMultistate.Rd | 24 mets-1.2.8/mets/man/simRecurrent.Rd | 17 mets-1.2.8/mets/man/simRecurrentII.Rd | 18 mets-1.2.8/mets/man/simRecurrentTS.Rd | 21 mets-1.2.8/mets/man/summary.cor.Rd | 3 mets-1.2.8/mets/man/survival.iterative.Rd | 100 mets-1.2.8/mets/man/survival.twostage.Rd | 167 mets-1.2.8/mets/man/twin.clustertrunc.Rd | 13 mets-1.2.8/mets/man/twinbmi.Rd | 6 mets-1.2.8/mets/man/twinlm.Rd | 26 mets-1.2.8/mets/man/twinsim.Rd | 16 mets-1.2.8/mets/man/twinstut.Rd | 6 mets-1.2.8/mets/man/twostageMLE.Rd | 30 mets-1.2.8/mets/src/RcppExports.cpp | 13 mets-1.2.8/mets/src/binomial-twostage.cpp | 738 -- mets-1.2.8/mets/src/fastcox.cpp | 754 +- mets-1.2.8/mets/src/init.c | 95 mets-1.2.8/mets/src/mvn.cpp | 309 mets-1.2.8/mets/src/survival-twostage.cpp | 595 - mets-1.2.8/mets/src/tools.cpp | 159 mets-1.2.8/mets/src/tools.h | 12 mets-1.2.8/mets/vignettes/basic-dutils.Rmd |only mets-1.2.8/mets/vignettes/basic-dutils.org | 3 mets-1.2.8/mets/vignettes/binomial-family.Rmd |only mets-1.2.8/mets/vignettes/binomial-twin.Rmd |only mets-1.2.8/mets/vignettes/cifreg.Rmd |only 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Title: Construct Complex Table with 'kable' and Pipe Syntax
Description: Build complex HTML or 'LaTeX' tables using 'kable()' from 'knitr'
and the piping syntax from 'magrittr'. Function 'kable()' is a light weight
table generator coming from 'knitr'. This package simplifies the way to
manipulate the HTML or 'LaTeX' codes generated by 'kable()' and allows
users to construct complex tables and customize styles using a readable
syntax.
Author: Hao Zhu [aut, cre] (<https://orcid.org/0000-0002-3386-6076>),
Thomas Travison [ctb],
Timothy Tsai [ctb],
Will Beasley [ctb],
Yihui Xie [ctb],
GuangChuang Yu [ctb],
Stéphane Laurent [ctb],
Rob Shepherd [ctb],
Yoni Sidi [ctb],
Brian Salzer [ctb],
George Gui [ctb],
Yeliang Fan [ctb],
Duncan Murdoch [ctb]
Maintainer: Hao Zhu <haozhu233@gmail.com>
Diff between kableExtra versions 1.1.0 dated 2019-03-16 and 1.2.1 dated 2020-08-27
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Title: Subnational Data for the Covid-19 Outbreak
Description: An interface to subnational and national level Covid-19 data.
For all countries supported, this includes a daily time-series of cases.
Wherever available we also provide data on deaths, hospitalisations, and tests.
National level data is also supported using a range of data sources as well as
linelist data and links to intervention data sets. Data sources included:
WHO <https://covid19.who.int>;
ACAPS interventions <https://data.humdata.org/dataset/acaps-covid19-government-measures-dataset>;
patient linelist: <https://github.com/beoutbreakprepared/nCoV2019>),
regional data (Afghanistan: <https://data.humdata.org/dataset/afghanistan-covid-19-statistics-per-province>;
Belgium: <https://epistat.wiv-isp.be/covid/>; Brazil: <https://github.com/wcota/covid19br>;
Canada: <https://health-infobase.canada.ca/>; Colombia: <https://github.com/danielcs88/colombia_covid-19>;
Germany: <https://npgeo-corona-npgeo-de.hub.arcgis.com/datasets/dd4580c810204019a7b8eb3e0b329dd6_0>;
India: <https://api.covid19india.org/>; Italy: <https://github.com/pcm-dpc/COVID-19>;
Russia: <https://github.com/grwlf/COVID-19_plus_Russia>; UK: <https://coronavirus.data.gov.uk>;
USA: <https://github.com/nytimes/covid-19-data>),
and geocoding data (Colombia: <https://en.wikipedia.org/wiki/ISO_3166-2:CO>; Russia: <https://en.wikipedia.org/wiki/ISO_3166-2:RU>).
Author: Sam Abbott [aut, cre] (<https://orcid.org/0000-0001-8057-8037>),
Katharine Sherratt [aut] (<https://orcid.org/0000-0003-4413-453X>),
Jonnie Bevan [aut],
Hamish Gibbs [aut] (<https://orcid.org/0000-0003-4413-453X>),
Joel Hellewell [aut] (<https://orcid.org/0000-0003-2683-0849>),
James Munday [aut],
Patrick Barks [ctb],
Paul Campbell [aut],
Flavio Finger [ctb] (<https://orcid.org/0000-0002-8613-5170>),
Sebastian Funk [aut]
Maintainer: Sam Abbott <sam.abbott@lshtm.ac.uk>
Diff between covidregionaldata versions 0.5.0 dated 2020-07-24 and 0.6.0 dated 2020-08-27
DESCRIPTION | 21 +- MD5 | 39 ++- NAMESPACE | 8 NEWS.md | 9 R/afghanistan.R | 6 R/covid19R_wrappers.R | 14 + R/get_national_data.R | 5 R/get_region_codes.R | 8 R/get_regional_data.R | 79 ++++--- R/national.R | 44 +--- R/uk.R | 280 +++++++++++++++++++--------- R/utils.R | 12 - README.md | 10 - man/get_regional_data.Rd | 9 man/get_uk_data.Rd |only man/get_uk_regional_cases_only_level_1.Rd | 6 man/get_uk_regional_cases_with_level_2.Rd | 10 - man/get_who_cases.Rd | 2 tests/testthat/test-get_national_data.R | 39 +++ tests/testthat/test-get_regional_data.R | 25 ++ tests/testthat/test-get_uk_regional_cases.R | 35 +-- 21 files changed, 430 insertions(+), 231 deletions(-)
More information about covidregionaldata at CRAN
Permanent link
Title: Load Data from Facebook API Marketing
Description: Load data by campaigns, ads, ad sets and insights, ad account and business manager
from Facebook Marketing API into R. For more details see official documents by Facebook
Marketing API <https://developers.facebook.com/docs/marketing-apis/>.
Author: Alexey Seleznev [aut, cre] (<https://orcid.org/0000-0003-0410-7385>)
Maintainer: Alexey Seleznev <selesnow@gmail.com>
Diff between rfacebookstat versions 2.1.1 dated 2020-05-29 and 2.1.7 dated 2020-08-27
DESCRIPTION | 10 MD5 | 44 ++-- NAMESPACE | 1 NEWS.md | 39 +++ R/authorization.R | 6 R/fbActions.R | 47 +++- R/fbGetAdCreative.R | 40 +++ R/fbGetAdSets.R | 5 R/fbGetAds.R | 2 R/fbGetCampaigns.R | 2 R/fbParsers.R | 25 +- R/zzz.R | 2 README.md | 292 ++++++++++++++--------------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/rfacebookstat-authorization.html | 58 +++-- inst/doc/rfacebookstat-cost-data.html | 74 ++++--- inst/doc/rfacebookstat-get-statistics.Rmd | 4 inst/doc/rfacebookstat-get-statistics.html | 244 ++++++++++++------------ man/fbAuth.Rd | 8 man/fbGetAdCreative.Rd | 11 - man/fbGetCostData.Rd | 6 vignettes/rfacebookstat-get-statistics.Rmd | 4 23 files changed, 532 insertions(+), 392 deletions(-)
Title: Presentation-Ready Data Summary and Analytic Result Tables
Description: Creates presentation-ready tables summarizing data
sets, regression models, and more. The code to create the tables is
concise and highly customizable. Data frames can be summarized with
any function, e.g. mean(), median(), even user-written functions.
Regression models are summarized and include the reference rows for
categorical variables. Common regression models, such as logistic
regression and Cox proportional hazards regression, are automatically
identified and the tables are pre-filled with appropriate column
headers.
Author: Daniel D. Sjoberg [aut, cre] (<https://orcid.org/0000-0003-0862-2018>),
Margie Hannum [aut] (<https://orcid.org/0000-0002-2953-0449>),
Karissa Whiting [aut] (<https://orcid.org/0000-0002-4683-1868>),
Emily C. Zabor [aut] (<https://orcid.org/0000-0002-1402-4498>),
Michael Curry [ctb] (<https://orcid.org/0000-0002-0261-4044>),
Esther Drill [ctb] (<https://orcid.org/0000-0002-3315-4538>),
Jessica Flynn [ctb] (<https://orcid.org/0000-0001-8310-6684>),
Joseph Larmarange [ctb] (<https://orcid.org/0000-0001-7097-700X>),
Stephanie Lobaugh [ctb],
Gustavo Zapata Wainberg [ctb] (<https://orcid.org/0000-0002-2524-3637>)
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>
Diff between gtsummary versions 1.3.3 dated 2020-08-11 and 1.3.4 dated 2020-08-27
DESCRIPTION | 6 MD5 | 43 NEWS.md | 10 R/tbl_cross.R | 6 R/tbl_survfit.R | 7 R/where.R |only README.md | 4 build/gtsummary.pdf | 5326 +++++++++++----------- inst/WORDLIST | 1 inst/doc/gallery.html | 792 +-- inst/doc/global_options.html | 72 inst/doc/inline_text.html | 144 inst/doc/rmarkdown.html | 274 - inst/doc/tbl_regression.html | 288 - inst/doc/tbl_summary.html | 576 +- inst/doc/themes.html | 432 - man/figures/README-tbl_merge_ex1-1.png |binary man/figures/README-tbl_regression_printa-1.png |binary man/figures/README-tbl_summary_print_extra-1.png |binary man/figures/README-tbl_summary_print_simple-1.png |binary man/tbl_cross.Rd | 3 man/tbl_survfit.Rd | 6 tests/testthat/test-tbl_cross.R | 34 23 files changed, 4039 insertions(+), 3985 deletions(-)
Title: Mediation Analysis using Interventional Effects
Description: Implementing the interventional effects for mediation analysis for up to 3 mediators.
The methods used are based on VanderWeele, Vansteelandt and Robins (2014) <doi:10.1097/ede.0000000000000034>,
Vansteelandt and Daniel (2017) <doi:10.1097/ede.0000000000000596> and Chan and Leung (2020; unpublished manuscript, available on request from the author of this package).
Linear regression, logistic regression and Poisson regression are used for continuous, binary
and count mediator/outcome variables respectively.
Author: Gary Chan [aut, cre, cph]
Maintainer: Gary Chan <c.chan4@uq.edu.au>
Diff between intmed versions 0.1.1 dated 2020-03-01 and 0.1.2 dated 2020-08-27
DESCRIPTION | 11 ++++------ MD5 | 27 ++++++++++++------------ NEWS.md |only R/gen_html_results.R | 4 +-- R/impute.R | 3 ++ R/intmed.R | 1 R/mediate.R | 46 +++++++++++++++++++++++++++--------------- R/utility_function.R | 8 +++++-- build/vignette.rds |binary inst/doc/intmed-vignette.html | 24 +++++++++++++++++---- man/intmed.Rd | 2 - man/mediate.Rd | 9 +++++--- man/sim_data.Rd | 6 +++-- man/substance.Rd | 6 +++-- tests/testthat/test-mediate.R | 8 +++---- 15 files changed, 99 insertions(+), 56 deletions(-)
Title: Advanced and Fast Data Transformation
Description: A C/C++ based package for advanced data transformation and
statistical computing in R that is extremely fast, flexible and
parsimonious to code with and programmer friendly.
It is well integrated with 'dplyr', 'plm' and 'data.table'.
--- Key Features: ---
(1) Advanced statistical programming: A full set of fast statistical functions
supporting grouped and weighted computations on vectors, matrices and
data frames. Fast and programmable grouping, ordering, unique values / rows,
factor generation and interactions. Fast and flexible functions for data
manipulation and data object conversions.
(2) Advanced aggregation: Fast and easy multi-data-type, multi-function,
weighted, parallelized and fully customized data aggregation.
(3) Advanced transformations: Fast (grouped) replacing and sweeping out of
statistics, and (grouped, weighted) scaling / standardizing, between
(averaging) and (quasi-)within (centering / demeaning) transformations,
higher-dimensional centering (i.e. multiple fixed effects transformations),
linear prediction and partialling-out.
(4) Advanced time-computations: Fast (sequences of) lags / leads, and
(lagged / leaded, iterated, quasi-, log-) differences and growth
rates on (unordered) time series and panel data. Multivariate auto-,
partial- and cross-correlation functions for panel data.
Panel data to (ts-)array conversions.
(5) List processing: (Recursive) list search / identification, extraction /
subsetting, data-apply, and generalized row-binding / unlisting in 2D.
(6) Advanced data exploration: Fast (grouped, weighted, panel-decomposed)
summary statistics for complex multilevel / panel data.
Author: Sebastian Krantz [aut, cre],
Matt Dowle [ctb],
Arun Srinivasan [ctb],
Simen Gaure [ctb],
Dirk Eddelbuettel [ctb],
R Core Team and contributors worldwide [ctb],
Martyn Plummer [cph],
1999-2016 The R Core Team [cph]
Maintainer: Sebastian Krantz <sebastian.krantz@graduateinstitute.ch>
Diff between collapse versions 1.3.0 dated 2020-08-11 and 1.3.1 dated 2020-08-27
DESCRIPTION | 8 MD5 | 20 - NEWS.md | 3 inst/doc/collapse_and_dplyr.html | 363 ++++++++++++++++---------------- inst/doc/collapse_and_plm.html | 114 +++++----- inst/doc/collapse_intro.html | 92 ++++---- man/collapse-package.Rd | 88 +++---- tests/testthat/test-fmedian.R | 20 - tests/testthat/test-fmode.R | 24 +- tests/testthat/test-fscale-STD.R | 432 +++++++++++++++++++-------------------- tests/testthat/test-fvar-fsd.R | 16 - 11 files changed, 594 insertions(+), 586 deletions(-)
Title: Minimization Tool for Pharmacokinetic-Pharmacodynamic Data
Analysis
Description: This is a set of minimization tools (maximum likelihood estimation and least square fitting) to solve examples in the Johan Gabrielsson and Dan Weiner's book "Pharmacokinetic and Pharmacodynamic Data Analysis - Concepts and Applications" 5th ed. (ISBN:9198299107). Examples include linear and nonlinear compartmental model, turn-over model, single or multiple dosing bolus/infusion/oral models, allometry, toxicokinetics, reversible metabolism, in-vitro/in-vivo extrapolation, enterohepatic circulation, metabolite modeling, Emax model, inhibitory model, tolerance model, oscillating response model, enantiomer interaction model, effect compartment model, drug-drug interaction model, receptor occupancy model, and rebound phenomena model.
Author: Kyun-Seop Bae [aut]
Maintainer: Kyun-Seop Bae <k@acr.kr>
Diff between wnl versions 0.6.0 dated 2020-07-16 and 0.6.1 dated 2020-08-27
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/nlr.R | 4 ++-- inst/NEWS.Rd | 7 +++++++ inst/doc/wnl-manual.pdf |binary man/nlr.Rd | 3 ++- 6 files changed, 19 insertions(+), 11 deletions(-)
Title: Most Likely Transformations: Documentation and Regression Tests
Description: Additional documentation, a package vignette and
regression tests for package mlt.
Author: Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>)
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mlt.docreg versions 1.0-5 dated 2020-02-13 and 1.0-6 dated 2020-08-27
DESCRIPTION | 26 +++++++++++++------------- MD5 | 16 ++++++++-------- NAMESPACE | 14 +++++++++++--- build/vignette.rds |binary inst/NEWS.Rd | 7 +++++++ inst/doc/mlt.R | 12 ++++++++++-- inst/doc/mlt.Rnw | 13 +++++++++++-- inst/doc/mlt.pdf |binary vignettes/mlt.Rnw | 13 +++++++++++-- 9 files changed, 71 insertions(+), 30 deletions(-)
Title: Cross-Platform 'zip' Compression
Description: Cross-Platform 'zip' Compression Library. A replacement
for the 'zip' function, that does not require any additional
external tools on any platform.
Author: Gábor Csárdi, Kuba Podgórski, Rich Geldreich
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between zip versions 2.1.0 dated 2020-08-10 and 2.1.1 dated 2020-08-27
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ tests/testthat/test-paths.R | 6 ++++++ 4 files changed, 16 insertions(+), 6 deletions(-)
Title: Alt String Implementation
Description: Provides an extendable, performant and multithreaded 'alt-string' implementation backed by 'C++' vectors and strings.
Author: Travers Ching [aut, cre, cph],
Phillip Hazel [ctb] (Bundled PCRE2 code),
Zoltan Herczeg [ctb, cph] (Bundled PCRE2 code),
University of Cambridge [cph] (Bundled PCRE2 code),
Tilera Corporation [cph] (Stack-less Just-In-Time compiler bundled with
PCRE2),
Yann Collet [ctb, cph] (Yann Collet is the author of the bundled xxHash
code)
Maintainer: Travers Ching <traversc@gmail.com>
Diff between stringfish versions 0.13.3 dated 2020-07-09 and 0.14.1 dated 2020-08-27
stringfish-0.13.3/stringfish/R/help_files.R |only stringfish-0.14.1/stringfish/ChangeLog | 6 stringfish-0.14.1/stringfish/DESCRIPTION | 16 stringfish-0.14.1/stringfish/MD5 | 84 - stringfish-0.14.1/stringfish/NAMESPACE | 12 stringfish-0.14.1/stringfish/R/RcppExports.R | 44 stringfish-0.14.1/stringfish/R/sf_functions.r | 13 stringfish-0.14.1/stringfish/R/zz_help_files.R |only stringfish-0.14.1/stringfish/R/zzz.R | 2 stringfish-0.14.1/stringfish/README.md | 55 stringfish-0.14.1/stringfish/inst/doc/vignette.html | 35 stringfish-0.14.1/stringfish/inst/doc/vignette.rmd | 33 stringfish-0.14.1/stringfish/inst/include/sf_internal.h | 18 stringfish-0.14.1/stringfish/man/convert_to_sf.Rd | 5 stringfish-0.14.1/stringfish/man/get_string_type.Rd | 2 stringfish-0.14.1/stringfish/man/materialize.Rd | 2 stringfish-0.14.1/stringfish/man/random_strings.Rd | 2 stringfish-0.14.1/stringfish/man/sf_assign.Rd | 2 stringfish-0.14.1/stringfish/man/sf_collapse.Rd | 2 stringfish-0.14.1/stringfish/man/sf_compare.Rd |only stringfish-0.14.1/stringfish/man/sf_concat.Rd |only stringfish-0.14.1/stringfish/man/sf_ends.Rd | 2 stringfish-0.14.1/stringfish/man/sf_grepl.Rd | 6 stringfish-0.14.1/stringfish/man/sf_gsub.Rd | 6 stringfish-0.14.1/stringfish/man/sf_iconv.Rd | 6 stringfish-0.14.1/stringfish/man/sf_match.Rd | 6 stringfish-0.14.1/stringfish/man/sf_nchar.Rd | 6 stringfish-0.14.1/stringfish/man/sf_paste.Rd | 6 stringfish-0.14.1/stringfish/man/sf_readLines.Rd | 2 stringfish-0.14.1/stringfish/man/sf_split.Rd | 6 stringfish-0.14.1/stringfish/man/sf_starts.Rd | 2 stringfish-0.14.1/stringfish/man/sf_substr.Rd | 6 stringfish-0.14.1/stringfish/man/sf_tolower.Rd | 2 stringfish-0.14.1/stringfish/man/sf_toupper.Rd | 2 stringfish-0.14.1/stringfish/man/sf_trim.Rd | 2 stringfish-0.14.1/stringfish/man/sf_vector.Rd | 2 stringfish-0.14.1/stringfish/man/sf_writeLines.Rd | 2 stringfish-0.14.1/stringfish/man/string_identical.Rd | 2 stringfish-0.14.1/stringfish/src/Makevars.in | 2 stringfish-0.14.1/stringfish/src/Makevars.win | 3 stringfish-0.14.1/stringfish/src/RcppExports.cpp | 108 + stringfish-0.14.1/stringfish/src/sf_altrep.h | 39 stringfish-0.14.1/stringfish/src/sf_functions.cpp | 1120 ++++++++++++---- stringfish-0.14.1/stringfish/vignettes/bench_v2.png |binary stringfish-0.14.1/stringfish/vignettes/vignette.rmd | 33 45 files changed, 1290 insertions(+), 414 deletions(-)
Title: Sustainable Transport Planning
Description: Tools for transport planning with an emphasis on spatial transport
data and non-motorized modes. Enables common transport planning tasks including:
downloading and cleaning transport datasets; creating geographic "desire lines"
from origin-destination (OD) data; route assignment, locally and via
interfaces to routing services such as <https://cyclestreets.net/>;
calculation of route segment attributes such as bearing and aggregate flow;
and 'travel watershed' analysis.
See Lovelace and Ellison (2018) <doi:10.32614/RJ-2018-053>.
Author: Robin Lovelace [aut, cre] (<https://orcid.org/0000-0001-5679-6536>),
Richard Ellison [aut],
Malcolm Morgan [aut] (<https://orcid.org/0000-0002-9488-9183>),
Barry Rowlingson [ctb] (Author of overline),
Nick Bearman [ctb] (Co-author of gclip),
Nikolai Berkoff [ctb] (Co-author of line2route),
Scott Chamberlain [rev] (Scott reviewed the package for rOpenSci, see
https://github.com/ropensci/onboarding/issues/10),
Mark Padgham [ctb],
Andrea Gilardi [ctb] (<https://orcid.org/0000-0002-9424-7439>)
Maintainer: Robin Lovelace <rob00x@gmail.com>
Diff between stplanr versions 0.6.2 dated 2020-07-08 and 0.7.0 dated 2020-08-27
stplanr-0.6.2/stplanr/R/line_match.R |only stplanr-0.6.2/stplanr/man/gtfs2sldf.Rd |only stplanr-0.6.2/stplanr/man/od_aggregate.Rd |only stplanr-0.6.2/stplanr/man/od_radiation.Rd |only stplanr-0.6.2/stplanr/man/onewayid.Rd |only stplanr-0.6.2/stplanr/man/route_graphhopper.Rd |only stplanr-0.6.2/stplanr/man/sp_aggregate.Rd |only stplanr-0.6.2/stplanr/vignettes/rsconnect |only stplanr-0.7.0/stplanr/DESCRIPTION | 10 stplanr-0.7.0/stplanr/MD5 | 230 +- stplanr-0.7.0/stplanr/NAMESPACE | 11 stplanr-0.7.0/stplanr/NEWS.md | 14 stplanr-0.7.0/stplanr/R/SpatialLinesNetwork.R | 20 stplanr-0.7.0/stplanr/R/data.R | 6 stplanr-0.7.0/stplanr/R/deprecated.R | 882 +--------- stplanr-0.7.0/stplanr/R/geo-functions.R | 174 - stplanr-0.7.0/stplanr/R/geo_projected.R | 2 stplanr-0.7.0/stplanr/R/google-functions.R | 2 stplanr-0.7.0/stplanr/R/linefuns.R | 2 stplanr-0.7.0/stplanr/R/od-funs.R | 31 stplanr-0.7.0/stplanr/R/overline.R | 267 +-- stplanr-0.7.0/stplanr/R/route-transport-api.R | 2 stplanr-0.7.0/stplanr/R/route_local.R | 2 stplanr-0.7.0/stplanr/README.md | 37 stplanr-0.7.0/stplanr/build/vignette.rds |binary stplanr-0.7.0/stplanr/data/ca_local.rda |binary stplanr-0.7.0/stplanr/data/cents.rda |binary stplanr-0.7.0/stplanr/data/cents_sf.rda |binary stplanr-0.7.0/stplanr/data/destination_zones.rda |binary stplanr-0.7.0/stplanr/data/destinations.rda |binary stplanr-0.7.0/stplanr/data/destinations_sf.rda |binary stplanr-0.7.0/stplanr/data/flowlines.rda |binary stplanr-0.7.0/stplanr/data/flowlines_sf.rda |binary stplanr-0.7.0/stplanr/data/l_poly.rda |binary stplanr-0.7.0/stplanr/data/osm_net_example.rda |binary stplanr-0.7.0/stplanr/data/rnet_cycleway_intersection.rda |binary stplanr-0.7.0/stplanr/data/rnet_overpass.rda |binary stplanr-0.7.0/stplanr/data/rnet_roundabout.rda |binary stplanr-0.7.0/stplanr/data/route_network.rda |binary stplanr-0.7.0/stplanr/data/route_network_sf.rda |binary stplanr-0.7.0/stplanr/data/routes_fast.rda |binary stplanr-0.7.0/stplanr/data/routes_fast_sf.rda |binary stplanr-0.7.0/stplanr/data/routes_slow.rda |binary stplanr-0.7.0/stplanr/data/routes_slow_sf.rda |binary stplanr-0.7.0/stplanr/data/zones.rda |binary stplanr-0.7.0/stplanr/data/zones_sf.rda |binary stplanr-0.7.0/stplanr/inst/doc/stplanr-od.R | 2 stplanr-0.7.0/stplanr/inst/doc/stplanr-od.Rmd | 10 stplanr-0.7.0/stplanr/inst/doc/stplanr-od.html | 48 stplanr-0.7.0/stplanr/inst/doc/stplanr-paper.Rmd | 6 stplanr-0.7.0/stplanr/inst/doc/stplanr-paper.html | 36 stplanr-0.7.0/stplanr/inst/doc/stplanr-parallel.html | 26 stplanr-0.7.0/stplanr/inst/doc/stplanr-route-nets.R | 2 stplanr-0.7.0/stplanr/inst/doc/stplanr-route-nets.Rmd | 4 stplanr-0.7.0/stplanr/inst/doc/stplanr-route-nets.html | 60 stplanr-0.7.0/stplanr/inst/doc/stplanr-routing.R | 37 stplanr-0.7.0/stplanr/inst/doc/stplanr-routing.Rmd | 52 stplanr-0.7.0/stplanr/inst/doc/stplanr-routing.html | 84 stplanr-0.7.0/stplanr/inst/doc/stplanr.R | 24 stplanr-0.7.0/stplanr/inst/doc/stplanr.Rmd | 96 - stplanr-0.7.0/stplanr/inst/doc/stplanr.html | 146 - stplanr-0.7.0/stplanr/man/SpatialLinesNetwork.Rd | 20 stplanr-0.7.0/stplanr/man/angle_diff.Rd | 1 stplanr-0.7.0/stplanr/man/destination_zones.Rd | 4 stplanr-0.7.0/stplanr/man/dist_google.Rd | 7 stplanr-0.7.0/stplanr/man/figures/README-plot1-1.png |binary stplanr-0.7.0/stplanr/man/figures/README-unnamed-chunk-6-1.png |binary stplanr-0.7.0/stplanr/man/flow.Rd | 2 stplanr-0.7.0/stplanr/man/gclip.Rd | 13 stplanr-0.7.0/stplanr/man/geo_bb.Rd | 8 stplanr-0.7.0/stplanr/man/geo_select_aeq.Rd | 2 stplanr-0.7.0/stplanr/man/geo_toptail.Rd | 1 stplanr-0.7.0/stplanr/man/is_linepoint.Rd | 1 stplanr-0.7.0/stplanr/man/line2df.Rd | 1 stplanr-0.7.0/stplanr/man/line2points.Rd | 17 stplanr-0.7.0/stplanr/man/line2route.Rd | 1 stplanr-0.7.0/stplanr/man/line2routeRetry.Rd | 1 stplanr-0.7.0/stplanr/man/line_bearing.Rd | 1 stplanr-0.7.0/stplanr/man/line_match.Rd | 5 stplanr-0.7.0/stplanr/man/line_midpoint.Rd | 1 stplanr-0.7.0/stplanr/man/line_sample.Rd | 1 stplanr-0.7.0/stplanr/man/line_segment.Rd | 1 stplanr-0.7.0/stplanr/man/line_via.Rd | 1 stplanr-0.7.0/stplanr/man/mapshape.Rd | 2 stplanr-0.7.0/stplanr/man/mapshape_available.Rd | 4 stplanr-0.7.0/stplanr/man/mats2line.Rd | 1 stplanr-0.7.0/stplanr/man/n_sample_length.Rd | 1 stplanr-0.7.0/stplanr/man/n_vertices.Rd | 3 stplanr-0.7.0/stplanr/man/od2line.Rd | 5 stplanr-0.7.0/stplanr/man/od2odf.Rd | 5 stplanr-0.7.0/stplanr/man/od_aggregate_from.Rd | 5 stplanr-0.7.0/stplanr/man/od_aggregate_to.Rd | 5 stplanr-0.7.0/stplanr/man/od_coords.Rd | 5 stplanr-0.7.0/stplanr/man/od_coords2line.Rd | 5 stplanr-0.7.0/stplanr/man/od_dist.Rd | 5 stplanr-0.7.0/stplanr/man/od_id.Rd | 5 stplanr-0.7.0/stplanr/man/od_oneway.Rd | 5 stplanr-0.7.0/stplanr/man/od_to_odmatrix.Rd | 5 stplanr-0.7.0/stplanr/man/odmatrix_to_od.Rd | 5 stplanr-0.7.0/stplanr/man/onewaygeo.Rd | 1 stplanr-0.7.0/stplanr/man/overline.Rd | 37 stplanr-0.7.0/stplanr/man/overline_intersection.Rd | 8 stplanr-0.7.0/stplanr/man/points2flow.Rd | 5 stplanr-0.7.0/stplanr/man/points2line.Rd | 1 stplanr-0.7.0/stplanr/man/points2odf.Rd | 5 stplanr-0.7.0/stplanr/man/route.Rd | 1 stplanr-0.7.0/stplanr/man/route_dodgr.Rd | 1 stplanr-0.7.0/stplanr/man/route_local.Rd | 10 stplanr-0.7.0/stplanr/man/route_transportapi_public.Rd | 1 stplanr-0.7.0/stplanr/man/toptail_buff.Rd | 1 stplanr-0.7.0/stplanr/man/toptailgs.Rd | 1 stplanr-0.7.0/stplanr/man/update_line_geometry.Rd | 1 stplanr-0.7.0/stplanr/tests/testthat/test-od2line.R | 7 stplanr-0.7.0/stplanr/tests/testthat/test-overline.R | 4 stplanr-0.7.0/stplanr/vignettes/references.bib | 4 stplanr-0.7.0/stplanr/vignettes/stplanr-od.Rmd | 10 stplanr-0.7.0/stplanr/vignettes/stplanr-paper.Rmd | 6 stplanr-0.7.0/stplanr/vignettes/stplanr-route-nets.Rmd | 4 stplanr-0.7.0/stplanr/vignettes/stplanr-routing.Rmd | 52 stplanr-0.7.0/stplanr/vignettes/stplanr.Rmd | 96 - 120 files changed, 930 insertions(+), 1806 deletions(-)
Title: Landscape Meteorology Tools
Description: Functions to estimate weather variables at any position of a landscape [De Caceres et al. (2018) <doi:10.1016/j.envsoft.2018.08.003>].
Author: Miquel De Cáceres [aut, cre],
Nicolas Martin [aut],
Víctor Granda [aut],
Antoine Cabon [aut]
Maintainer: Miquel De Cáceres <miquelcaceres@gmail.com>
Diff between meteoland versions 0.9.3 dated 2020-06-09 and 0.9.4 dated 2020-08-27
DESCRIPTION | 10 MD5 | 222 +- NAMESPACE | 162 +- NEWS.md | 318 ++-- R/DefineProcedureClasses.R | 306 +-- R/DefineSpatialDataClasses.R | 12 R/MeteorologyInterpolationData.R | 286 +-- R/MeteorologyUncorrectedData.R | 34 R/NetCDFutils.R | 48 R/RcppExports.R | 454 ++--- R/SpatialGridMeteorology-methods.R | 277 +-- R/SpatialGridTopography-methods.R | 246 +-- R/SpatialPixelsMeteorology-methods.R | 281 +-- R/SpatialPixelsTopography-methods.R | 256 +-- R/SpatialPointsMeteorology-methods.R | 247 +-- R/SpatialPointsTopography-methods.R | 214 +- R/averagearea.R | 56 R/bias_correction_internals.R | 582 +++---- R/correctionpoints.R | 414 ++--- R/correctionpoints.errors.R | 560 +++---- R/defaultCorrectionParams.R | 32 R/defaultGenerationParams.R | 28 R/defaultInterpolationParams.R | 48 R/download_currentday.R | 582 +++---- R/download_historical.R | 880 +++++------ R/download_historicalstationlist.R | 218 +- R/extractNetCDF.R | 434 ++--- R/extractdates.R | 266 +-- R/extractgridpoints.R | 182 +- R/interpolation.calibration.R | 584 +++---- R/interpolation.coverage.R | 54 R/interpolation.cv.R | 524 +++--- R/interpolationgrid.R | 376 ++-- R/interpolationpixels.R | 376 ++-- R/interpolationpoints.R | 458 ++--- R/mergegrids.R | 240 +-- R/meteocomplete.R | 172 +- R/meteoplot.R | 146 - R/ncdf_internals.R | 1632 ++++++++++---------- R/plot.interpolation.cv.R | 144 + R/precipitationconcentration.R | 154 - R/readmeteorologygrid.R | 358 ++-- R/readmeteorologypoints.R | 160 +- R/reshapeweathercan.R | 312 +-- R/reshapeworldmet.R | 234 +- R/summary.interpolation.cv.R | 228 +- R/summarygridpixels.R | 184 +- R/summaryinterpolationdata.R | 92 - R/summarypoints.R | 264 +-- R/utils.R | 228 +- R/weathergeneration.R | 788 +++++----- R/writemeteorologygrid.R | 102 - R/writemeteorologypoints.R | 134 - build/vignette.rds |binary data/examplecorrectiondata.rda |binary data/examplegridtopography.rda |binary data/exampleinterpolationdata.rda |binary inst/CITATION | 36 inst/doc/UserGuide.R | 488 +++--- inst/doc/UserGuide.Rmd | 946 ++++++------ inst/doc/UserGuide.html | 2341 +++++++++++++++--------------- man/MeteorologyInterpolationData-class.Rd | 114 - man/MeteorologyInterpolationData.Rd | 118 - man/MeteorologyProcedureData-class.Rd | 76 man/MeteorologyUncorrectedData-class.Rd | 88 - man/MeteorologyUncorrectedData.Rd | 68 man/NetCDFutils.Rd | 76 man/SpatialGridMeteorology-class.Rd | 98 - man/SpatialGridTopography-class.Rd | 96 - man/SpatialGridTopography.Rd | 140 - man/SpatialPixelsMeteorology-class.Rd | 106 - man/SpatialPixelsMeteorology.Rd | 68 man/SpatialPixelsTopography-class.Rd | 108 - man/SpatialPixelsTopography.Rd | 108 - man/SpatialPointsMeteorology-class.Rd | 94 - man/SpatialPointsMeteorology.Rd | 62 man/SpatialPointsTopography-class.Rd | 90 - man/SpatialPointsTopography.Rd | 92 - man/averagearea.Rd | 90 - man/correction_lowlevel.Rd | 68 man/correctionpoints.Rd | 254 +-- man/defaultCorrectionParams.Rd | 80 - man/defaultGenerationParams.Rd | 68 man/defaultInterpolationParams.Rd | 92 - man/downloadAEMET.Rd | 112 - man/downloadMG.Rd | 84 - man/downloadSMC.Rd | 122 - man/examplecorrectiondata.Rd | 42 man/extractNetCDF.Rd | 106 - man/extractdates.Rd | 86 - man/humidity.Rd | 60 man/interpolation.coverage.Rd | 78 man/interpolation.cv.Rd | 264 +-- man/interpolation_lowlevel.Rd | 156 - man/interpolationpoints.Rd | 202 +- man/mergegrids.Rd | 66 man/meteocomplete.Rd | 116 - man/meteoplot.Rd | 120 - man/penman.Rd | 112 - man/precipitationconcentration.Rd | 76 man/radiation.Rd | 220 +- man/readmeteorologygrid.Rd | 102 - man/readmeteorologypoint.Rd | 86 - man/reshapeworldmet.Rd | 86 - man/spplot.Rd | 80 - man/subsample.Rd | 76 man/summarypoints.Rd | 156 - man/utils.Rd | 122 - man/weathergeneration.Rd | 120 - man/writemeteorologygrid.Rd | 98 - man/writemeteorologypoint.Rd | 86 - vignettes/UserGuide.Rmd | 946 ++++++------ 112 files changed, 12862 insertions(+), 12782 deletions(-)
Title: Routing with GTFS (General Transit Feed Specification) Data
Description: Use GTFS (General Transit Feed Specification) data
for routing from nominated start and end stations, and for extracting
isochrones from nominated start station.
Author: Mark Padgham [aut, cre],
Marcin Stepniak [aut] (<https://orcid.org/0000-0002-6489-5443>),
Alexandra Kapp [ctb]
Maintainer: Mark Padgham <mark.padgham@email.com>
Diff between gtfsrouter versions 0.0.1 dated 2019-03-22 and 0.0.3 dated 2020-08-27
gtfsrouter-0.0.1/gtfsrouter/tests/testthat/test-summary.R |only gtfsrouter-0.0.3/gtfsrouter/DESCRIPTION | 50 + gtfsrouter-0.0.3/gtfsrouter/MD5 | 69 +- gtfsrouter-0.0.3/gtfsrouter/NAMESPACE | 3 gtfsrouter-0.0.3/gtfsrouter/NEWS.md |only gtfsrouter-0.0.3/gtfsrouter/R/RcppExports.R | 5 gtfsrouter-0.0.3/gtfsrouter/R/extract-gtfs.R | 158 ++++- gtfsrouter-0.0.3/gtfsrouter/R/frequencies_to_stop_times.R |only gtfsrouter-0.0.3/gtfsrouter/R/go_home_work.R | 27 gtfsrouter-0.0.3/gtfsrouter/R/gtfsrouter-package.R | 8 gtfsrouter-0.0.3/gtfsrouter/R/isochrone.R | 82 +- gtfsrouter-0.0.3/gtfsrouter/R/methods.R | 30 + gtfsrouter-0.0.3/gtfsrouter/R/router.R | 156 ++++- gtfsrouter-0.0.3/gtfsrouter/R/timetable.R | 111 +++ gtfsrouter-0.0.3/gtfsrouter/R/transfers.R |only gtfsrouter-0.0.3/gtfsrouter/R/utils.R | 7 gtfsrouter-0.0.3/gtfsrouter/README.md | 257 ++++++++ gtfsrouter-0.0.3/gtfsrouter/build/vignette.rds |binary gtfsrouter-0.0.3/gtfsrouter/inst/doc/gtfsrouter.R | 54 - gtfsrouter-0.0.3/gtfsrouter/inst/doc/gtfsrouter.Rmd | 4 gtfsrouter-0.0.3/gtfsrouter/inst/doc/gtfsrouter.html | 291 +++++----- gtfsrouter-0.0.3/gtfsrouter/man/berlin_gtfs.Rd | 12 gtfsrouter-0.0.3/gtfsrouter/man/extract_gtfs.Rd | 15 gtfsrouter-0.0.3/gtfsrouter/man/frequencies_to_stop_times.Rd |only gtfsrouter-0.0.3/gtfsrouter/man/go_home.Rd | 4 gtfsrouter-0.0.3/gtfsrouter/man/go_to_work.Rd | 6 gtfsrouter-0.0.3/gtfsrouter/man/gtfs_isochrone.Rd | 26 gtfsrouter-0.0.3/gtfsrouter/man/gtfs_route.Rd | 40 + gtfsrouter-0.0.3/gtfsrouter/man/gtfs_timetable.Rd | 15 gtfsrouter-0.0.3/gtfsrouter/man/gtfs_transfer_table.Rd |only gtfsrouter-0.0.3/gtfsrouter/man/gtfsrouter.Rd | 5 gtfsrouter-0.0.3/gtfsrouter/man/plot.gtfs_ischrone.Rd | 2 gtfsrouter-0.0.3/gtfsrouter/src/csa-isochrone.cpp | 66 +- gtfsrouter-0.0.3/gtfsrouter/tests/testthat/test-extract.R |only gtfsrouter-0.0.3/gtfsrouter/tests/testthat/test-frequencies.R |only gtfsrouter-0.0.3/gtfsrouter/tests/testthat/test-isochrone.R | 7 gtfsrouter-0.0.3/gtfsrouter/tests/testthat/test-route.R | 71 +- gtfsrouter-0.0.3/gtfsrouter/tests/testthat/test-time-formats.R | 4 gtfsrouter-0.0.3/gtfsrouter/tests/testthat/test-transfers.R |only gtfsrouter-0.0.3/gtfsrouter/vignettes/gtfsrouter.Rmd | 4 40 files changed, 1148 insertions(+), 441 deletions(-)
Title: Raw Accelerometer Data Analysis
Description: A tool to process and analyse data collected with wearable raw acceleration sensors as described in Migueles and colleagues (JMPB 2019), and van Hees and colleagues (JApplPhysiol 2014; PLoSONE 2015). The package has been developed and tested for binary data from 'GENEActiv' <https://www.activinsights.com/> and GENEA devices (not for sale), .csv-export data from 'Actigraph' <https://actigraphcorp.com> devices, and .cwa and .wav-format data from 'Axivity' <https://axivity.com>. These devices are currently widely used in research on human daily physical activity. Further, the package can handle accelerometer data file from any other sensor brand providing that the data is stored in csv format and has either no header or a two column header. Also the package allows for external function embedding.
Author: Vincent T van Hees [aut, cre],
Zhou Fang [ctb],
Jing Hua Zhao [ctb],
Joe Heywood [ctb],
Evgeny Mirkes [ctb],
Severine Sabia [ctb],
Joan Capdevila Pujol [ctb],
Jairo H Migueles [ctb],
Matthew R Patterson [ctb],
Dan Jackson [ctb]
Maintainer: Vincent T van Hees <v.vanhees@accelting.com>
Diff between GGIR versions 2.0-0 dated 2020-05-01 and 2.1-0 dated 2020-08-27
DESCRIPTION | 18 MD5 | 214 ++-- NAMESPACE | 2 R/g.analyse.R | 35 R/g.analyse.perday.R | 14 R/g.analyse.perfile.R | 11 R/g.applymetrics.R | 245 +++- R/g.calibrate.R | 40 R/g.extractheadervars.R | 23 R/g.getM5L5.R | 2 R/g.getidfromheaderobject.R | 4 R/g.getmeta.R | 267 +++-- R/g.getstarttime.R | 5 R/g.impute.R | 22 R/g.inspectfile.R | 29 R/g.metric.R | 32 R/g.part1.R | 72 - R/g.part2.R | 3 R/g.part4.R | 17 R/g.part5.R | 1264 ++++++++++++------------ R/g.part5.addfirstwake.R | 32 R/g.part5.definedays.R | 63 - R/g.part5.fixmissingnight.R | 22 R/g.part5.savetimeseries.R | 37 R/g.part5.wakesleepwindows.R | 25 R/g.plot5.R | 169 +-- R/g.readaccfile.R | 46 R/g.readtemp_movisens.R |only R/g.report.part4.R | 89 + R/g.report.part5.R | 9 R/g.shell.GGIR.R | 57 - R/g.sib.det.R | 20 R/get_nw_clip_block_params.R | 9 R/get_starttime_weekday_meantemp_truncdata.R | 21 R/ismovisens.R |only R/read.myacc.csv.R | 23 build/vignette.rds |binary inst/CITATION | 8 inst/NEWS.Rd | 41 inst/doc/ExternalFunction.Rmd | 10 inst/doc/ExternalFunction.pdf |binary inst/doc/GGIR.Rmd | 39 inst/doc/GGIR.html | 223 ++-- man/GGIR-package.Rd | 6 man/POSIXtime2iso8601.Rd | 2 man/applyExtFunction.Rd | 2 man/check_myfun.Rd | 2 man/createConfigFile.Rd | 2 man/datadir2fnames.Rd | 2 man/g.IVIS.Rd | 2 man/g.abr.day.names.Rd | 2 man/g.analyse.Rd | 2 man/g.analyse.avday.Rd | 2 man/g.analyse.perday.Rd | 2 man/g.analyse.perfile.Rd | 5 man/g.applymetrics.Rd | 7 man/g.binread.Rd | 82 - man/g.calibrate.Rd | 2 man/g.create.sp.mat.Rd | 2 man/g.createcoordinates.Rd | 2 man/g.cwaread.Rd | 1 man/g.detecmidnight.Rd | 2 man/g.dotorcomma.Rd | 2 man/g.downsample.Rd | 2 man/g.extractheadervars.Rd | 2 man/g.getM5L5.Rd | 2 man/g.getbout.Rd | 2 man/g.getidfromheaderobject.Rd | 2 man/g.getmeta.Rd | 36 man/g.getstarttime.Rd | 2 man/g.impute.Rd | 2 man/g.inspectfile.Rd | 2 man/g.intensitygradient.Rd | 2 man/g.loadlog.Rd | 2 man/g.metric.Rd | 2 man/g.part1.Rd | 25 man/g.part2.Rd | 2 man/g.part3.Rd | 2 man/g.part4.Rd | 30 man/g.part5.Rd | 14 man/g.part5.addfirstwake.Rd | 2 man/g.part5.addsib.Rd | 2 man/g.part5.definedays.Rd | 2 man/g.part5.fixmissingnight.Rd | 2 man/g.part5.ontsetwaketiming.Rd | 2 man/g.part5.savetimeseries.Rd | 21 man/g.part5.wakesleepwindows.Rd | 2 man/g.plot.Rd | 106 +- man/g.plot5.Rd | 2 man/g.readaccfile.Rd | 2 man/g.readtemp_movisens.Rd |only man/g.report.part2.Rd | 2 man/g.report.part4.Rd | 7 man/g.report.part5.Rd | 2 man/g.shell.GGIR.Rd | 2 man/g.sib.det.Rd | 2 man/g.sib.plot.Rd | 2 man/g.sib.sum.Rd | 2 man/g.wavread.Rd | 2 man/g.weardec.Rd | 2 man/get_nw_clip_block_params.Rd | 2 man/get_starttime_weekday_meantemp_truncdata.Rd | 2 man/ismovisens.Rd |only man/read.myacc.csv.Rd | 7 tests/testthat/test_MCS_functions.R |only tests/testthat/test_chainof5parts.R | 78 + tests/testthat/test_gmetric.R | 53 - tests/testthat/test_part1_with_allmetrics.R | 10 tests/testthat/test_part5_fixmissingnight.R |only vignettes/ExternalFunction.Rmd | 10 vignettes/GGIR.Rmd | 39 111 files changed, 2391 insertions(+), 1500 deletions(-)
Title: Feature Extraction and Statistics for Time Series
Description: Provides a collection of features, decomposition methods,
statistical summaries and graphics functions for the analysing tidy time
series data. The package name 'feasts' is an acronym comprising of its key
features: Feature Extraction And Statistics for Time Series.
Author: Mitchell O'Hara-Wild [aut, cre],
Rob Hyndman [aut],
Earo Wang [aut],
Di Cook [ctb],
Thiyanga Talagala [ctb] (Correlation features),
Leanne Chhay [ctb] (Guerrero's method)
Maintainer: Mitchell O'Hara-Wild <mail@mitchelloharawild.com>
Diff between feasts versions 0.1.4 dated 2020-06-17 and 0.1.5 dated 2020-08-27
feasts-0.1.4/feasts/man/n_flat_spots.Rd |only feasts-0.1.5/feasts/DESCRIPTION | 11 +- feasts-0.1.5/feasts/MD5 | 47 +++++----- feasts-0.1.5/feasts/NAMESPACE | 2 feasts-0.1.5/feasts/NEWS.md | 25 +++++ feasts-0.1.5/feasts/R/acf.R | 5 - feasts-0.1.5/feasts/R/features.R | 21 +++- feasts-0.1.5/feasts/R/graphics.R | 43 +++++++-- feasts-0.1.5/feasts/R/guerrero.R | 5 + feasts-0.1.5/feasts/R/utils.R | 5 - feasts-0.1.5/feasts/build/vignette.rds |binary feasts-0.1.5/feasts/inst/doc/feasts.html | 33 +++++-- feasts-0.1.5/feasts/man/feat_spectral.Rd | 2 feasts-0.1.5/feasts/man/figures/lifecycle-archived.svg |only feasts-0.1.5/feasts/man/figures/lifecycle-defunct.svg |only feasts-0.1.5/feasts/man/figures/lifecycle-deprecated.svg |only feasts-0.1.5/feasts/man/figures/lifecycle-experimental.svg |only feasts-0.1.5/feasts/man/figures/lifecycle-maturing.svg |only feasts-0.1.5/feasts/man/figures/lifecycle-questioning.svg |only feasts-0.1.5/feasts/man/figures/lifecycle-soft-deprecated.svg |only feasts-0.1.5/feasts/man/figures/lifecycle-stable.svg |only feasts-0.1.5/feasts/man/figures/lifecycle-superseded.svg |only feasts-0.1.5/feasts/man/gg_season.Rd | 5 - feasts-0.1.5/feasts/man/gg_subseries.Rd | 2 feasts-0.1.5/feasts/man/gg_tsdisplay.Rd | 2 feasts-0.1.5/feasts/man/gg_tsresiduals.Rd | 2 feasts-0.1.5/feasts/man/guerrero.Rd | 6 + feasts-0.1.5/feasts/man/longest_flat_spot.Rd |only feasts-0.1.5/feasts/tests/testthat/Rplots.pdf |binary feasts-0.1.5/feasts/tests/testthat/test-features.R | 4 30 files changed, 164 insertions(+), 56 deletions(-)
Title: Poisson-Tweedie Generalized Linear Mixed Model
Description: Fits the Poisson-Tweedie generalized linear mixed
model described in Signorelli et al. (2020,
<doi:10.1177/1471082X20936017>). Likelihood approximation based on
adaptive Gauss Hermite quadrature rule.
Author: Mirko Signorelli [aut, cre] (<https://orcid.org/0000-0002-8102-3356>),
Pietro Spitali [aut],
Roula Tsonaka [aut]
Maintainer: Mirko Signorelli <msignorelli.rpackages@gmail.com>
Diff between ptmixed versions 0.5.4 dated 2020-06-13 and 1.0.0 dated 2020-08-27
DESCRIPTION | 22 ++-- MD5 | 66 ++++++------- R/df1.R | 3 R/loglik.R | 3 R/makespaghetti.R | 21 +++- R/nbglm.R | 3 R/nbmixed.R | 3 R/pmf.R | 3 R/ptglm.R | 3 R/ptmixed.R | 3 R/ranef.R | 3 R/simulate_ptglmm.R | 3 R/summary-ptglm.R | 3 R/summary-ptglmm.R | 3 R/wald-test.R | 3 build/vignette.rds |binary inst/CITATION | 9 + inst/NEWS.md | 23 +++- inst/doc/Overview_functionalities_ptmixed.Rmd | 25 ++++- inst/doc/Overview_functionalities_ptmixed.html | 124 +++++++++++++++---------- man/df1.Rd | 5 + man/loglik.pt.1re.Rd | 5 + man/make.spaghetti.Rd | 16 ++- man/nbglm.Rd | 5 + man/nbmixed.Rd | 5 + man/pmf.Rd | 5 + man/ptglm.Rd | 5 + man/ptmixed.Rd | 5 + man/ranef.Rd | 5 + man/simulate_ptglmm.Rd | 5 + man/summary.ptglm.Rd | 5 + man/summary.ptglmm.Rd | 5 + man/wald.test.Rd | 5 + vignettes/Overview_functionalities_ptmixed.Rmd | 25 ++++- 34 files changed, 315 insertions(+), 112 deletions(-)
Title: Propensity to Cycle Tool
Description: Functions and example data to teach and
increase the reproducibility of the methods and code underlying
the Propensity to Cycle Tool (PCT), a research project and web application
hosted at <https://www.pct.bike/>.
For an academic paper on the methods,
see Lovelace et al (2017) <doi:10.5198/jtlu.2016.862>.
Author: Robin Lovelace [aut, cre] (<https://orcid.org/0000-0001-5679-6536>),
Layik Hama [aut] (<https://orcid.org/0000-0003-1912-4890>)
Maintainer: Robin Lovelace <rob00x@gmail.com>
Diff between pct versions 0.4.1 dated 2020-06-15 and 0.5.0 dated 2020-08-27
DESCRIPTION | 8 - MD5 | 79 +++++---- NAMESPACE | 3 NEWS.md | 7 R/get_pct.R | 52 ++++-- R/model.R |only R/msoa_centroids.R | 2 R/uptake.R | 186 +++++++++++++++++++++-- README.md | 263 +++++++++++++++++++++------------ build/vignette.rds |binary inst/doc/cycling-potential-uk.R | 41 ++++- inst/doc/cycling-potential-uk.Rmd | 53 +++++- inst/doc/cycling-potential-uk.html | 74 +++++---- inst/doc/pct-international.html | 72 ++++----- inst/doc/pct.Rmd | 6 inst/doc/pct.html | 78 +++++---- inst/doc/pct_training.Rmd | 4 inst/doc/pct_training.html | 96 ++++++------ inst/pct_training_solutions.Rmd | 2 inst/rmd/pct-slides.Rmd | 10 - man/figures/README-centroids-1.png |binary man/figures/README-decay-1.png |binary man/figures/README-desire-1.png |binary man/figures/README-get_pct_lines-1.png |binary man/figures/README-rnetgove-1.png |binary man/figures/README-routes_fast-1.png |only man/get_centroids_ew.Rd | 2 man/get_pct.Rd | 6 man/get_pct_centroids.Rd | 11 - man/get_pct_lines.Rd | 11 - man/get_pct_rnet.Rd | 7 man/get_pct_routes_fast.Rd | 11 - man/get_pct_routes_quiet.Rd | 11 - man/get_pct_zones.Rd | 7 man/model_pcycle_pct_2020.Rd |only man/uptake_pct_godutch.Rd | 45 ++++- man/uptake_pct_govtarget.Rd | 85 ++++++++++ tests/testthat/test-get-pct.R | 4 tests/testthat/test-scenarios.R | 4 vignettes/cycling-potential-uk.Rmd | 53 +++++- vignettes/pct.Rmd | 6 vignettes/pct_training.Rmd | 4 42 files changed, 907 insertions(+), 396 deletions(-)
Title: Interface to the 'g:Profiler' Toolset
Description: A toolset for functional enrichment analysis and visualization, gene/protein/SNP identifier conversion and mapping orthologous genes across species via 'g:Profiler' (<https://biit.cs.ut.ee/gprofiler>).
The main tools are:
(1) 'g:GOSt' - functional enrichment analysis and visualization of gene lists;
(2) 'g:Convert' - gene/protein/transcript identifier conversion across various namespaces;
(3) 'g:Orth' - orthology search across species;
(4) 'g:SNPense' - mapping SNP rs identifiers to chromosome positions, genes and variant effects
This package is an R interface corresponding to the 2019 update of 'g:Profiler' and provides access to 'g:Profiler' for versions 'e94_eg41_p11' and higher. See the package 'gProfileR' for accessing older versions from the 'g:Profiler' toolset.
Author: Liis Kolberg <liis.kolberg@ut.ee>, Uku Raudvere <uku.raudvere@ut.ee>
Maintainer: Liis Kolberg <liis.kolberg@ut.ee>
Diff between gprofiler2 versions 0.1.9 dated 2020-04-23 and 0.2.0 dated 2020-08-27
DESCRIPTION | 10 +- MD5 | 16 +-- R/gprofiler2.R | 65 +++++++++++-- inst/doc/gprofiler2.Rmd | 2 inst/doc/gprofiler2.html | 219 +++++++++++++++++++++++++---------------------- man/gconvert.Rd | 2 man/gorth.Rd | 2 man/gost.Rd | 6 - vignettes/gprofiler2.Rmd | 2 9 files changed, 193 insertions(+), 131 deletions(-)
Title: Interpreted String Literals
Description: An implementation of interpreted string literals, inspired by
Python's Literal String Interpolation <https://www.python.org/dev/peps/pep-0498/> and Docstrings
<https://www.python.org/dev/peps/pep-0257/> and Julia's Triple-Quoted String Literals
<https://docs.julialang.org/en/v1.3/manual/strings/#Triple-Quoted-String-Literals-1>.
Author: Jim Hester [aut, cre]
Maintainer: Jim Hester <james.f.hester@gmail.com>
Diff between glue versions 1.4.1 dated 2020-05-13 and 1.4.2 dated 2020-08-27
DESCRIPTION | 10 +++++----- MD5 | 26 +++++++++++++------------- NEWS.md | 6 ++++++ R/glue.R | 2 +- R/safe.R | 2 +- R/sql.R | 3 +++ R/utils.R | 2 +- README.md | 8 ++++---- build/vignette.rds |binary inst/doc/speed.html | 16 ++++++++++++++++ inst/doc/transformers.html | 16 ++++++++++++++++ man/glue.Rd | 2 +- man/glue_safe.Rd | 10 ++++++++++ tests/testthat/test-sql.R | 4 ++++ 14 files changed, 81 insertions(+), 26 deletions(-)
Title: Extreme Risk Measures
Description: A set of procedures for estimating risks related to extreme events via risk measures such as Expectile, Value-at-Risk, etc. is provided. Estimation methods for univariate independent observations and temporal dependent observations are available. The methodology is extended to the case of independent multidimensional observations. The statistical inference is performed through parametric and non-parametric estimators. Inferential procedures such as confidence intervals, confidence regions and hypothesis testing are obtained by exploiting the asymptotic theory. Adapts the methodologies derived in Padoan and Stupfler (2020) <arxiv:2004.04078>, Padoan and Stupfler (2020) <arxiv:2007.08944>, Daouia et al. (2018) <doi:10.1111/rssb.12254>, Drees (2000) <doi:10.1214/aoap/1019487617>, Drees (2003) <doi:10.3150/bj/1066223272>, de Haan and Ferreira (2006) <doi:10.1007/0-387-34471-3>, de Haan et al. (2016) <doi:10.1007/s00780-015-0287-6>.
Author: Simone Padoan [cre, aut],
Gilles Stupfler [aut],
Bocconi Institute for Data Science and Analytics [fnd],
French National Research [fnd] (grant ANR-19-CE40-0013-01/ExtremReg)
Maintainer: Simone Padoan <simone.padoan@unibocconi.it>
Diff between ExtremeRisks versions 0.0.3 dated 2020-05-07 and 0.0.4 dated 2020-08-27
DESCRIPTION | 24 ++-- MD5 | 40 ++++---- NAMESPACE | 15 ++- R/Expectiles.r | 53 ++++++++-- R/MultiEstimation.r |only R/Simulation.r | 218 ++++++++++++++++++++++++++++++++++++++++----- R/UniEstimation.r |only man/EBTailIndex.Rd | 2 man/ExpectMES.Rd | 2 man/HTailIndex.Rd | 2 man/HypoTesting.Rd |only man/MLTailIndex.Rd | 2 man/MultiHTailIndex.Rd |only man/QuantMES.Rd | 2 man/estExpectiles.Rd | 6 - man/estExtLevel.Rd | 2 man/estMultiExpectiles.Rd |only man/expectiles.Rd | 2 man/extMultiQuantile.Rd |only man/extQuantile.Rd | 4 man/predExpectiles.Rd | 4 man/predMultiExpectiles.Rd |only man/rbtimeseries.Rd | 2 man/rmdata.Rd |only man/rtimeseries.Rd | 2 25 files changed, 303 insertions(+), 79 deletions(-)
Title: Efficient Phylogenetics on Large Trees
Description: Efficient phylogenetic analyses on massive phylogenies comprising up to millions of tips. Functions include pruning, rerooting, calculation of most-recent common ancestors, calculating distances from the tree root and calculating pairwise distances. Calculation of phylogenetic signal and mean trait depth (trait conservatism), ancestral state reconstruction and hidden character prediction of discrete characters, simulating and fitting models of trait evolution, fitting and simulating diversification models, dating trees, comparing trees, and reading/writing trees in Newick format. Citation: Louca, Stilianos and Doebeli, Michael (2017) <doi:10.1093/bioinformatics/btx701>.
Author: Stilianos Louca
Maintainer: Stilianos Louca <louca@zoology.ubc.ca>
Diff between castor versions 1.6.2 dated 2020-07-19 and 1.6.3 dated 2020-08-27
DESCRIPTION | 8 MD5 | 46 ++-- R/asr_max_parsimony.R | 1 R/auxiliary_routines.R | 7 R/fit_and_compare_sbm_const.R | 2 R/fit_hbd_model_on_grid.R | 34 ++- R/fit_hbd_model_parametric.R | 21 +- R/fit_hbd_pdr_and_grid.R | 10 R/fit_hbd_pdr_on_grid.R | 19 + R/fit_hbd_pdr_parametric.R | 31 +-- R/fit_hbd_psr_on_grid.R | 8 R/fit_hbds_model_on_grid.R | 10 R/fit_hbds_model_parametric.R | 18 + R/fit_sbm_const.R | 69 ++++-- R/fit_sbm_const_biased_sampling_unfinished.R | 22 +- R/read_tree.R | 9 R/tree_distance.R | 34 ++- man/asr_max_parsimony.Rd | 8 man/fit_hbd_pdr_parametric.Rd | 2 man/fit_sbm_const.Rd | 4 man/read_tree.Rd | 6 man/reconstruct_past_diversification.Rd | 16 - man/tree_distance.Rd | 16 - src/phylogenetics_cpp_routines.cpp | 273 ++++++++++++++++++--------- 24 files changed, 449 insertions(+), 225 deletions(-)
Title: Tidy Messy Data
Description: Tools to help to create tidy data, where each column is a
variable, each row is an observation, and each cell contains a single value.
'tidyr' contains tools for changing the shape (pivoting) and hierarchy
(nesting and 'unnesting') of a dataset, turning deeply nested lists
into rectangular data frames ('rectangling'), and extracting values out
of string columns. It also includes tools for working with missing values
(both implicit and explicit).
Author: Hadley Wickham [aut, cre],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between tidyr versions 1.1.1 dated 2020-07-31 and 1.1.2 dated 2020-08-27
DESCRIPTION | 13 +-- MD5 | 85 ++++++++++++------------- NEWS.md | 9 ++ R/cpp11.R | 1 R/doc-params.R | 32 +-------- R/nest-legacy.R | 2 R/nest.R | 10 +- R/pivot-long.R | 6 - R/separate-rows.R | 2 README.md | 24 +++---- build/tidyr.pdf |binary inst/doc/in-packages.R | 12 +-- inst/doc/in-packages.Rmd | 14 ++-- inst/doc/in-packages.html | 18 ++--- inst/doc/nest.Rmd | 2 inst/doc/nest.html | 2 inst/doc/pivot.R | 14 ++-- inst/doc/pivot.Rmd | 18 ++--- inst/doc/pivot.html | 122 ++++++++++++++++++------------------ inst/doc/programming.R | 6 - inst/doc/programming.Rmd | 12 +-- inst/doc/programming.html | 14 ++-- inst/doc/rectangle.R | 2 inst/doc/rectangle.Rmd | 4 - inst/doc/rectangle.html | 4 - inst/doc/tidy-data.R | 4 - inst/doc/tidy-data.Rmd | 4 - inst/doc/tidy-data.html | 4 - man/nest.Rd | 10 +- man/nest_legacy.Rd | 2 man/pivot_longer.Rd | 2 man/pivot_longer_spec.Rd | 4 - man/rmd |only man/tidyr-package.Rd | 5 - man/tidyr_tidy_select.Rd | 62 ++++++++++++------ src/cpp11.cpp | 10 +- tests/testthat/test-separate-rows.R | 8 ++ tests/testthat/test-unite.R | 2 vignettes/in-packages.Rmd | 14 ++-- vignettes/nest.Rmd | 2 vignettes/pivot.Rmd | 18 ++--- vignettes/programming.Rmd | 12 +-- vignettes/rectangle.Rmd | 4 - vignettes/tidy-data.Rmd | 4 - 44 files changed, 300 insertions(+), 299 deletions(-)
Title: Transformed Additive Gaussian Processes
Description: Implement the transformed additive Gaussian (TAG) process and the transformed approximately additive Gaussian (TAAG) process proposed in Lin and Joseph (2019+) <DOI:10.1080/00401706.2019.1665592>. These functions can be used to model deterministic computer experiments, obtain predictions at new inputs, and quantify the uncertainty of the predictions. This research is supported by a U.S. National Science Foundation grant DMS-1712642 and a U.S. Army Research Office grant W911NF-17-1-0007.
Author: Li-Hsiang Lin and V. Roshan Joseph
Maintainer: Li-Hsiang Lin <llin79@gatech.edu>
Diff between TAG versions 0.2.0 dated 2020-01-09 and 0.2.1 dated 2020-08-27
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- R/Initial_TAG.R | 18 +++++++++++++++--- 3 files changed, 22 insertions(+), 10 deletions(-)
Title: Working with 'Sapfluxnet' Project Data
Description: Access, modify, aggregate and plot data from the 'Sapfluxnet' project
(<http://sapfluxnet.creaf.cat>), the first global database of sap flow measurements.
Author: Victor Granda [aut, cre] (<https://orcid.org/0000-0002-0469-1991>),
Rafael Poyatos [aut] (<https://orcid.org/0000-0003-0521-2523>),
Victor Flo [aut] (<https://orcid.org/0000-0003-1908-4577>),
Jacob Nelson [ctb] (<https://orcid.org/0000-0002-4663-2420>),
Sapfluxnet Core Team [cph]
Maintainer: Victor Granda <victorgrandagarcia@gmail.com>
Diff between sapfluxnetr versions 0.1.0 dated 2020-05-11 and 0.1.1 dated 2020-08-27
DESCRIPTION | 8 MD5 | 80 +- NEWS.md | 8 R/getters.R | 6 R/helpers.R | 15 R/visualizations.R | 22 build/vignette.rds |binary data/ARG_MAZ.rda |binary data/ARG_TRE.rda |binary data/AUS_CAN_ST2_MIX.rda |binary data/sfn_metadata_ex.rda |binary inst/doc/custom-aggregation.R | 3 inst/doc/custom-aggregation.Rmd | 9 inst/doc/custom-aggregation.html | 418 +++++------ inst/doc/data-flags.html | 4 inst/doc/memory-and-parallelization.R | 8 inst/doc/memory-and-parallelization.Rmd | 14 inst/doc/memory-and-parallelization.html | 168 ++-- inst/doc/metadata-and-data-units.html | 99 +- inst/doc/sapfluxnetr-quick-guide.R | 24 inst/doc/sapfluxnetr-quick-guide.Rmd | 65 - inst/doc/sapfluxnetr-quick-guide.html | 1052 ++++++++++++++--------------- inst/doc/sfn-data-classes.R | 2 inst/doc/sfn-data-classes.Rmd | 16 inst/doc/sfn-data-classes.html | 1084 +++++++++++++++--------------- man/filter_sites_by_md.Rd | 6 tests/testthat/ARG_MAZ.RData |binary tests/testthat/ARG_TRE.RData |binary tests/testthat/AUS_CAN_ST2_MIX.RData |binary tests/testthat/Data/ARG_MAZ.RData |binary tests/testthat/Data/ARG_TRE.RData |binary tests/testthat/Data/AUS_CAN_ST2_MIX.RData |binary tests/testthat/test-getters.R | 3 tests/testthat/test-metrics.R | 28 vignettes/custom-aggregation.Rmd | 9 vignettes/memory-and-parallelization.Rmd | 14 vignettes/resources/ARG_MAZ.RData |binary vignettes/resources/ARG_TRE.RData |binary vignettes/resources/AUS_CAN_ST2_MIX.RData |binary vignettes/sapfluxnetr-quick-guide.Rmd | 65 - vignettes/sfn-data-classes.Rmd | 16 41 files changed, 1666 insertions(+), 1580 deletions(-)
Title: Access the 'Public Transport Victoria' Timetable API
Description: Access the 'Public Transport Victoria' Timetable API
<https://www.ptv.vic.gov.au/footer/data-and-reporting/datasets/ptv-timetable-api/>,
with results returned as familiar R data structures. Retrieve information on
stops, routes, disruptions, departures, and more.
Author: David Neuzerling [aut, cre, cph]
Maintainer: David Neuzerling <david@neuzerling.com>
Diff between ptvapi versions 1.1.2 dated 2020-06-03 and 1.1.3 dated 2020-08-27
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- README.md | 12 +++++++++++- tests/testthat/test-filter-departures.R | 10 +++++----- 4 files changed, 23 insertions(+), 13 deletions(-)
Title: Tools for Case 1 Best-Worst Scaling
Description: Provides basic functions that support an implementation of object case (Case 1) best-worst scaling: a function for converting a two-level orthogonal main-effect design/balanced incomplete block design into questions; two functions for creating a data set suitable for analysis; a function for calculating count-based scores; a function for calculating shares of preference; and a function for generating artificial responses to questions. For details on best-worst scaling, see Louviere et al. (2015) <doi:10.1017/CBO9781107337855>.
Author: Hideo Aizaki
Maintainer: Hideo Aizaki <azk-r@spa.nifty.com>
Diff between support.BWS versions 0.4-1 dated 2020-04-12 and 0.4-2 dated 2020-08-27
DESCRIPTION | 10 ++++---- MD5 | 10 ++++---- NEWS | 4 +++ R/bws.sp.R | 52 ++++++++++++++++++++++++++++++++++++++++++--- man/bws.sp.Rd | 4 +-- man/support.BWS-package.Rd | 6 ++--- 6 files changed, 68 insertions(+), 18 deletions(-)
Title: Extract, Analyze and Visualize Signatures for Genomic Variations
Description: Genomic alterations including single nucleotide
substitution, copy number alteration, etc. are the major force for
cancer initialization and development. Due to the specificity of
molecular lesions caused by genomic alterations, we can generate
characteristic alteration spectra, called 'signature' (Wang, Shixiang,
et al. (2020) <DOI:10.1101/2020.04.27.20082404> & Alexandrov, Ludmil
B., et al. (2020) <DOI:10.1038/s41586-020-1943-3> & Macintyre, Geoff,
et al. (2018) <DOI:10.1038/s41588-018-0179-8>). This package helps
users to extract, analyze and visualize signatures from genomic
alteration records, thus providing new insight into cancer study.
Author: Shixiang Wang [aut, cre] (<https://orcid.org/0000-0001-9855-7357>),
Xue-Song Liu [aut, ctb] (<https://orcid.org/0000-0002-7736-0077>),
Tao Wu [aut, ctb],
Ziyu Tao [aut, ctb],
Geoffrey Macintyre [ctb],
Anand Mayakonda [ctb]
Maintainer: Shixiang Wang <w_shixiang@163.com>
Diff between sigminer versions 1.0.7 dated 2020-06-17 and 1.0.13 dated 2020-08-27
DESCRIPTION | 23 +- MD5 | 150 +++++++++------ NAMESPACE | 14 + NEWS.md | 42 ++++ R/CN-mutex-classification-methed.R | 301 +++++++++++++++++++++++++++++-- R/RcppExports.R |only R/cosine.R |only R/data.R | 38 +++ R/generate_matrices.R | 63 ++++-- R/get.R | 292 +++++++++++++++++++++--------- R/get_bayesian_result.R | 2 R/get_cn_freq_table.R |only R/get_genome_annotation.R | 88 +-------- R/get_groups.R | 35 ++- R/get_sig_similarity.R | 110 +++++++---- R/globalVariables.R |only R/helper_create_chunks.R |only R/helper_derive_cn_features.R | 85 ++++++-- R/helper_join_segments.R | 123 ++++++++++++ R/helper_sort_signature.R | 17 - R/read_copynumber.R | 79 +++++--- R/read_copynumber_seqz.R |only R/read_maf.R | 2 R/read_vcf.R |only R/show_cn_circos.R | 5 R/show_cn_features.R | 15 - R/show_cn_freq_circos.R |only R/show_cn_group_profile.R | 283 +++++++++++++++++++++-------- R/show_cn_profile.R | 88 ++------- R/show_cosmic_signatures.R | 23 -- R/show_sig_exposure.R | 14 + R/show_sig_fit.R | 13 - R/show_sig_number_survey.R | 11 - R/show_sig_profile.R | 74 +++++-- R/show_sig_profile_heatmap.R |only R/show_sig_profile_loop.R |only R/sig_auto_extract.R | 9 R/sig_estimate.R | 2 R/sig_extract.R | 2 R/sig_extract_WTSI.R |only R/sig_fit.R | 23 -- R/sig_fit_bootstrap_batch.R | 2 R/sig_tally.R | 157 +++++++--------- R/sigminer.R | 10 + R/sigprofiler.R |only R/transform_seg_table.R |only R/utils.R | 47 ++-- README.md | 6 build/vignette.rds |binary data/centromeres.mm10.rda |only data/chromsize.mm10.rda |only data/cytobands.mm10.rda |only data/transcript.mm10.rda |only inst/CITATION | 2 inst/extdata/mouse_mm10_gene_info.rds |only inst/extdata/test1.vcf |only inst/extdata/test2.vcf |only inst/extdata/test3.vcf |only man/CN.features.Rd | 4 man/centromeres.mm10.Rd |only man/chromsize.mm10.Rd |only man/cosine.Rd |only man/cytobands.mm10.Rd |only man/figures/README-unnamed-chunk-1-1.png |binary man/figures/README-unnamed-chunk-3-1.png |binary man/figures/README-unnamed-chunk-4-1.png |binary man/figures/README-unnamed-chunk-7-1.png |binary man/get_cn_freq_table.Rd |only man/get_genome_annotation.Rd | 9 man/get_sig_db.Rd |only man/get_sig_similarity.Rd | 5 man/read_copynumber.Rd | 13 - man/read_copynumber_seqz.Rd |only man/read_maf.Rd | 2 man/read_vcf.Rd |only man/show_catalogue.Rd | 2 man/show_cn_circos.Rd | 2 man/show_cn_components.Rd | 2 man/show_cn_features.Rd | 2 man/show_cn_freq_circos.Rd |only man/show_cn_group_profile.Rd |only man/show_cn_profile.Rd | 7 man/show_sig_bootstrap.Rd | 19 - man/show_sig_fit.Rd | 19 - man/show_sig_number_survey.Rd | 7 man/show_sig_profile.Rd | 14 - man/show_sig_profile_heatmap.Rd |only man/show_sig_profile_loop.Rd |only man/sig_tally.Rd | 15 - man/sigprofiler.Rd |only man/transcript.mm10.Rd |only man/transform_seg_table.Rd |only man/use_color_style.Rd | 8 src |only 94 files changed, 1606 insertions(+), 774 deletions(-)
Title: Seasonal Analysis of Health Data
Description: Routines for the seasonal analysis of health data,
including regression models, time-stratified case-crossover,
plotting functions and residual checks, see Barnett and Dobson (2010) ISBN 978-3-642-10748-1. Thanks to Yuming Guo
for checking the case-crossover code.
Author: Adrian Barnett and Peter Baker
Maintainer: Adrian Barnett <a.barnett@qut.edu.au>
Diff between season versions 0.3.11 dated 2020-05-25 and 0.3.12 dated 2020-08-27
DESCRIPTION | 6 ++-- MD5 | 18 +++++++------- R/invyrfraction.R | 4 +-- build/vignette.rds |binary inst/doc/season-vignette.html | 20 ++++++++++++++- man/AFL.Rd | 50 +++++++++++++++++++------------------- man/invyrfraction.Rd | 39 +++++++++++++++--------------- man/plot.monthglm.Rd | 46 +++++++++++++++++------------------ man/seasrescheck.Rd | 38 ++++++++++++++--------------- man/stillbirth.Rd | 54 +++++++++++++++++++++--------------------- 10 files changed, 146 insertions(+), 129 deletions(-)
Title: A Versatile Cutting Tool
Description: A tool for cutting data into intervals. Allows singleton intervals.
Always includes the whole range of data by default. Flexible labelling.
Convenience functions for cutting by quantiles etc. Handles dates and times.
Author: David Hugh-Jones [aut, cre]
Maintainer: David Hugh-Jones <davidhughjones@gmail.com>
Diff between santoku versions 0.4.1 dated 2020-06-16 and 0.5.0 dated 2020-08-27
DESCRIPTION | 8 MD5 | 22 - NEWS.md | 6 R/breaks.R | 47 ++- R/chop.R | 14 build/santoku.pdf |binary build/vignette.rds |binary inst/doc/santoku.html | 562 ++++++++++++++++++------------------ man/chop_width.Rd | 14 tests/testthat/test-Date-DateTime.R | 19 + tests/testthat/test-breaks.R | 15 tests/testthat/test-tab.R | 5 12 files changed, 402 insertions(+), 310 deletions(-)
Title: Database Interface and 'MariaDB' Driver
Description: Implements a 'DBI'-compliant interface to 'MariaDB'
(<https://mariadb.org/>) and 'MySQL' (<https://www.mysql.com/>)
databases.
Author: Kirill Müller [aut, cre] (<https://orcid.org/0000-0002-1416-3412>),
Jeroen Ooms [aut] (<https://orcid.org/0000-0002-4035-0289>),
David James [aut],
Saikat DebRoy [aut],
Hadley Wickham [aut],
Jeffrey Horner [aut],
R Consortium [fnd],
RStudio [cph]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>
Diff between RMariaDB versions 1.0.9 dated 2020-07-03 and 1.0.10 dated 2020-08-27
DESCRIPTION | 6 +++--- MD5 | 32 ++++++++++++++++---------------- NEWS.md | 16 ++++++++++++++++ R/RcppExports.R | 4 ++-- R/connect.R | 14 ++++++++++++-- R/query.R | 3 +++ R/table.R | 8 ++++++-- README.md | 8 +++++++- man/dbConnect-MariaDBDriver-method.Rd | 6 +++++- src/DbConnection.cpp | 7 ++++++- src/DbConnection.h | 3 ++- src/MariaBinding.cpp | 13 ++++++++++--- src/MariaBinding.h | 2 +- src/RcppExports.cpp | 9 +++++---- src/connection.cpp | 5 +++-- tests/testthat/test-dbWriteTable.R | 6 ++---- tests/testthat/test-queries.R | 27 ++++++++++++++++++++++++++- 17 files changed, 125 insertions(+), 44 deletions(-)
Title: Validation of Local and Remote Data Tables
Description: Validate data in data frames, 'tibble' objects, and in database
tables (e.g., 'PostgreSQL' and 'MySQL'). Validation pipelines can be made
using easily-readable, consecutive validation steps. Upon execution of the
validation plan, several reporting options are available. User-defined
thresholds for failure rates allow for the determination of appropriate
reporting actions.
Author: Richard Iannone [aut, cre] (<https://orcid.org/0000-0003-3925-190X>),
Mauricio Vargas [aut] (<https://orcid.org/0000-0003-1017-7574>)
Maintainer: Richard Iannone <riannone@me.com>
Diff between pointblank versions 0.5.0 dated 2020-08-12 and 0.5.1 dated 2020-08-27
DESCRIPTION | 18 ++- MD5 | 185 ++++++++++++++++++++++++--------------- NEWS.md | 20 +++- R/col_exists.R | 3 R/col_is_character.R | 3 R/col_is_date.R | 3 R/col_is_factor.R | 3 R/col_is_integer.R | 3 R/col_is_logical.R | 3 R/col_is_numeric.R | 3 R/col_is_posix.R | 3 R/col_schema_match.R | 3 R/col_vals_between.R | 3 R/col_vals_equal.R | 3 R/col_vals_expr.R | 3 R/col_vals_gt.R | 10 +- R/col_vals_gte.R | 3 R/col_vals_in_set.R | 3 R/col_vals_lt.R | 3 R/col_vals_lte.R | 3 R/col_vals_not_between.R | 3 R/col_vals_not_equal.R | 3 R/col_vals_not_in_set.R | 3 R/col_vals_not_null.R | 3 R/col_vals_null.R | 3 R/col_vals_regex.R | 3 R/conjointly.R | 3 R/create_agent.R | 1 R/get_agent_report.R | 123 ++++++++++++++++--------- R/get_agent_x_list.R | 4 R/get_sundered_data.R | 57 +++++++++--- R/interrogate.R | 83 ++++++++++++----- R/print.R | 4 R/rows_distinct.R | 3 R/steps_and_briefs.R | 2 R/utils.R | 46 ++++++++- R/zzz.R | 1 inst/img/function_icons |only man/col_exists.Rd | 3 man/col_is_character.Rd | 3 man/col_is_date.Rd | 3 man/col_is_factor.Rd | 3 man/col_is_integer.Rd | 3 man/col_is_logical.Rd | 3 man/col_is_numeric.Rd | 3 man/col_is_posix.Rd | 3 man/col_schema_match.Rd | 3 man/col_vals_between.Rd | 7 + man/col_vals_equal.Rd | 7 + man/col_vals_expr.Rd | 3 man/col_vals_gt.Rd | 9 + man/col_vals_gte.Rd | 7 + man/col_vals_in_set.Rd | 3 man/col_vals_lt.Rd | 7 + man/col_vals_lte.Rd | 7 + man/col_vals_not_between.Rd | 7 + man/col_vals_not_equal.Rd | 7 + man/col_vals_not_in_set.Rd | 3 man/col_vals_not_null.Rd | 3 man/col_vals_null.Rd | 3 man/col_vals_regex.Rd | 7 + man/conjointly.Rd | 3 man/get_sundered_data.Rd | 37 +++++-- man/rows_distinct.Rd | 3 tests/testthat.R | 2 tests/testthat/sqlserver.R |only tests/testthat/test-mysql-2.R | 4 tests/testthat/test-mysql.R | 6 + tests/testthat/test-postgres-2.R | 4 tests/testthat/test-postgres.R | 6 + tests/testthat/test-sundering.R | 137 ++++++++++++++++++++++++++++ tests/testthat/test-x_list.R | 8 + tests/testthat/tests |only 73 files changed, 739 insertions(+), 204 deletions(-)
Title: Estimation of Recombination Rate and Maternal LD in Half-Sibs
Description: Paternal recombination rate and maternal linkage disequilibrium
(LD) are estimated for pairs of biallelic markers such as single nucleotide
polymorphisms (SNPs) from progeny genotypes and sire haplotypes. At least
one sire has to be double heterozygous at the investigated pairs of SNPs.
The implementation relies on paternal half-sib families. If maternal half-
sib families are used, the roles of sire/dam are swapped. Multiple families
can be considered.
Hampel, Teuscher, Gomez-Raya, Doschoris, Wittenburg (2018) "Estimation of
recombination rate and maternal linkage disequilibrium in half-sibs"
<doi:10.3389/fgene.2018.00186>.
Gomez-Raya (2012) "Maximum likelihood estimation of linkage disequilibrium
in half-sib families" <doi:10.1534/genetics.111.137521>.
Author: Dörte Wittenburg [aut, cre]
Maintainer: Dörte Wittenburg <wittenburg@fbn-dummerstorf.de>
Diff between hsrecombi versions 0.3.0 dated 2020-05-28 and 0.3.1 dated 2020-08-27
DESCRIPTION | 9 ++++++--- MD5 | 21 +++++++++++++-------- NEWS.md | 4 ++++ R/functions.R | 4 ++-- R/hsrecombi.R | 4 ++-- build |only inst |only man/checkCandidates.Rd | 2 +- man/editraw.Rd | 2 +- man/geneticPosition.Rd | 2 +- man/hsrecombi.Rd | 2 +- vignettes |only 12 files changed, 31 insertions(+), 19 deletions(-)
Title: Multiple Fill and Colour Scales in 'ggplot2'
Description: Use multiple fill and colour scales in 'ggplot2'.
Author: Elio Campitelli [cre, aut] (<https://orcid.org/0000-0002-7742-9230>)
Maintainer: Elio Campitelli <elio.campitelli@cima.fcen.uba.ar>
Diff between ggnewscale versions 0.4.2 dated 2020-08-01 and 0.4.3 dated 2020-08-27
DESCRIPTION | 8 ++++---- MD5 | 11 +++++++---- NEWS.md | 7 +++++++ R/new-scale.R | 10 +++++----- tests/figs |only tests/testthat/test-newscale.R | 39 ++++++++++++++++++++++++++++++++++----- 6 files changed, 57 insertions(+), 18 deletions(-)
Title: Analysis of Doubly-Truncated Data
Description: Likelihood-based inference methods with doubly-truncated data are developed under various models.
Nonparametric models are based on Efron and Petrosian (1999) <doi:10.1080/01621459.1999.10474187> and
Emura, Konno, and Michimae (2015) <doi:10.1007/s10985-014-9297-5>.
Parametric models from the special exponential family (SEF) are based on
Hu and Emura (2015) <doi:10.1007/s00180-015-0564-z> and
Emura, Hu and Konno (2017) <doi:10.1007/s00362-015-0730-y>.
The parametric location-scale models are based on Dorre et al. (2020-).
Author: Takeshi Emura, Ya-Hsuan Hu, Chung-Yan Huang
Maintainer: Takeshi Emura <takeshiemura@gmail.com>
Diff between double.truncation versions 1.5 dated 2020-07-16 and 1.6 dated 2020-08-27
DESCRIPTION | 9 +++++---- MD5 | 4 +++- R/simu.Weibull.R |only man/simu.Weibull.Rd |only 4 files changed, 8 insertions(+), 5 deletions(-)
More information about double.truncation at CRAN
Permanent link
Title: Anything to 'POSIXct' or 'Date' Converter
Description: Convert input in any one of character, integer, numeric, factor,
or ordered type into 'POSIXct' (or 'Date') objects, using one of a number of
predefined formats, and relying on Boost facilities for date and time parsing.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between anytime versions 0.3.8 dated 2020-07-24 and 0.3.9 dated 2020-08-27
ChangeLog | 12 ++++++++++++ DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- R/anytime.R | 2 +- README.md | 26 +++++++++++++------------- build/partial.rdb |binary inst/NEWS.Rd | 8 ++++++++ inst/doc/anytime-introduction.pdf |binary inst/tinytest/test_simple.R | 16 +++++++++++++--- inst/tinytest/test_utilities.R | 3 ++- man/anytime-package.Rd | 12 ++++++------ man/anytime.Rd | 2 +- 12 files changed, 71 insertions(+), 40 deletions(-)
Title: Bayesian Estimation using Bernstein Polynomial Fits Rate Matrix
Description: Smoothed lexis diagrams with Bayesian method specifically tailored to cancer
incidence data. Providing to calculating slope and constructing credible interval.
LC Chien et al. (2015) <doi:10.1080/01621459.2015.1042106>.
LH Chien et al. (2017) <doi:10.1002/cam4.1102>.
Author: Li-Syuan Hong [aut, cre]
Maintainer: Li-Syuan Hong <lisyuan@nhri.org.tw>
Diff between BayesBP versions 1.0 dated 2019-10-02 and 1.1 dated 2020-08-27
BayesBP-1.0/BayesBP/R/BPFhat_pd_ages.R |only BayesBP-1.0/BayesBP/R/BPFhat_pd_years.R |only BayesBP-1.0/BayesBP/R/BPbasis_pd_ages.R |only BayesBP-1.0/BayesBP/R/BPbasis_pd_years.R |only BayesBP-1.0/BayesBP/R/Credible_interval_pd_ages.R |only BayesBP-1.0/BayesBP/R/Credible_interval_pd_years.R |only BayesBP-1.0/BayesBP/R/mapping_to_01.R |only BayesBP-1.0/BayesBP/man/BPFhat_pd_ages.Rd |only BayesBP-1.0/BayesBP/man/BPFhat_pd_years.Rd |only BayesBP-1.0/BayesBP/man/BPbasis_pd_ages.Rd |only BayesBP-1.0/BayesBP/man/BPbasis_pd_years.Rd |only BayesBP-1.0/BayesBP/man/Credible_interval_pd_ages.Rd |only BayesBP-1.0/BayesBP/man/Credible_interval_pd_years.Rd |only BayesBP-1.0/BayesBP/man/mapping_to_01.Rd |only BayesBP-1.1/BayesBP/DESCRIPTION | 10 BayesBP-1.1/BayesBP/MD5 | 65 +-- BayesBP-1.1/BayesBP/NAMESPACE | 14 BayesBP-1.1/BayesBP/R/BP2D.R | 380 +++++++----------- BayesBP-1.1/BayesBP/R/BP2Dcoef.R | 9 BayesBP-1.1/BayesBP/R/BP2Dtable.R | 6 BayesBP-1.1/BayesBP/R/BPFhat.R | 31 - BayesBP-1.1/BayesBP/R/BPbasis.R | 52 -- BayesBP-1.1/BayesBP/R/Credible_interval.R | 47 -- BayesBP-1.1/BayesBP/R/PD_BPFhat.R |only BayesBP-1.1/BayesBP/R/PD_BPbasis.R |only BayesBP-1.1/BayesBP/R/PD_Credible_interval.R |only BayesBP-1.1/BayesBP/R/scale_to_01.R |only BayesBP-1.1/BayesBP/R/simulated_data.R | 125 ++--- BayesBP-1.1/BayesBP/R/writeBP.R | 1 BayesBP-1.1/BayesBP/data/simulated_data_1.rda |binary BayesBP-1.1/BayesBP/data/simulated_data_2.rda |binary BayesBP-1.1/BayesBP/man/BP2D.Rd | 112 ++--- BayesBP-1.1/BayesBP/man/BP2D_coef.Rd | 5 BayesBP-1.1/BayesBP/man/BP2D_table.Rd | 5 BayesBP-1.1/BayesBP/man/BPFhat.Rd | 21 BayesBP-1.1/BayesBP/man/BPbasis.Rd | 18 BayesBP-1.1/BayesBP/man/Credible_interval.Rd | 6 BayesBP-1.1/BayesBP/man/M.Rd |only BayesBP-1.1/BayesBP/man/PD_BPFhat.Rd |only BayesBP-1.1/BayesBP/man/PD_BPbasis.Rd |only BayesBP-1.1/BayesBP/man/PD_Credible_interval.Rd |only BayesBP-1.1/BayesBP/man/bin.Rd |only BayesBP-1.1/BayesBP/man/gen_data.Rd |only BayesBP-1.1/BayesBP/man/scale_to_01.Rd |only BayesBP-1.1/BayesBP/man/simulated_data_1.Rd | 43 -- BayesBP-1.1/BayesBP/man/simulated_data_2.Rd | 69 +-- 46 files changed, 457 insertions(+), 562 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-08-19 1.9-2.1
2014-04-23 1.9-2
2013-11-08 1.9-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-11-12 2.3
2018-02-08 2.1
2017-09-06 1.16
2017-07-19 1.14.2
2017-07-10 1.14
Title: Enhanced Database Interactivity
Description: Facilitates interaction with ODBC data sources, by remembering and hiding communication settings and supporting parameterised multi-statement SQL with embedded R.
Author: Mike Lee
Maintainer: Mike Lee <random.deviate@gmail.com>
Diff between SQRL versions 0.7.2 dated 2020-05-13 and 0.7.3 dated 2020-08-27
DESCRIPTION | 8 - MD5 | 14 - R/SQRL.R | 373 ++++++++++++++++++++++++++++++++++++++++++++++------ man/SQRL-package.Rd | 9 - man/sqrlConfig.Rd | 8 + man/sqrlParams.Rd | 8 - man/sqrlScript.Rd | 302 +++++++++++++++++++++++------------------- man/sqrlSource.Rd | 20 +- 8 files changed, 545 insertions(+), 197 deletions(-)
Title: Mixed GAM Computation Vehicle with Automatic Smoothness
Estimation
Description: Generalized additive (mixed) models, some of their extensions and
other generalized ridge regression with multiple smoothing
parameter estimation by (Restricted) Marginal Likelihood,
Generalized Cross Validation and similar, or using iterated
nested Laplace approximation for fully Bayesian inference. See
Wood (2017) <doi:10.1201/9781315370279> for an overview.
Includes a gam() function, a wide variety of smoothers, 'JAGS'
support and distributions beyond the exponential family.
Author: Simon Wood <simon.wood@r-project.org>
Maintainer: Simon Wood <simon.wood@r-project.org>
Diff between mgcv versions 1.8-32 dated 2020-08-19 and 1.8-33 dated 2020-08-27
ChangeLog | 5 +++++ DESCRIPTION | 6 +++--- MD5 | 10 +++++----- src/mat.c | 8 ++++---- src/matrix.c | 2 +- src/sparse.c | 2 +- 6 files changed, 19 insertions(+), 14 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-08-25 4.4.4
2020-06-25 4.4.3
2020-03-19 4.4.1
2019-09-19 4.2.0
2019-05-27 4.1.0
2018-11-02 4.0.0
2018-05-18 3.4.0
2018-04-22 3.3.4
2018-01-29 3.3.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-03-02 1.0.3
2018-01-03 1.0.2
2017-08-29 1.0.1
2017-04-18 1.0
2015-02-02 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-02-04 0.2.1
2015-06-11 0.2.0
2015-02-08 0.1.2
2015-01-10 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-12-11 0.10.11
2016-04-04 0.10.8
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-08-09 4.12.1
2012-05-10 4.12.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-04-15 1.0.0
Title: Taxometric Analysis
Description: We provide functions to perform taxometric analyses. This package contains 44 functions, but only 5 should be called directly by users. CheckData() should be run prior to any taxometric analysis to ensure that the data are appropriate for taxometric analysis. RunTaxometrics() performs taxometric analyses for a sample of data. RunCCFIProfile() performs a series of taxometric analyses to generate a CCFI profile. CreateData() generates a sample of categorical or dimensional data. ClassifyCases() assigns cases to groups using the base-rate classification method.
Author: John Ruscio <ruscio@tcnj.edu> and Shirley Wang <shirleywang@g.harvard.edu>
Maintainer: John Ruscio <ruscio@tcnj.edu>
Diff between RTaxometrics versions 2.3 dated 2017-09-09 and 2.4 dated 2020-08-27
DESCRIPTION | 12 ++-- LICENSE | 2 MD5 | 108 +++++++++++++++++++++---------------------- NAMESPACE | 2 R/DisplayBaseRates.R | 2 R/DisplayCCFIs.R | 15 +++-- R/DisplayPanels.R | 20 +++++++ R/DisplayProfiles.R | 20 +++++++ R/DisplayTextOutput.R | 7 ++ R/RunCCFIProfile.R | 36 ++++++++++++-- R/RunTaxometrics.R | 41 +++++++++++++--- man/AddVariance.Rd | 2 man/AssignMAMBAC.Rd | 2 man/AssignMAXEIG.Rd | 2 man/CalculateCCFI.Rd | 2 man/CalculateCCFIs.Rd | 2 man/CalculateFitDensities.Rd | 2 man/CalculateKurtosis.Rd | 2 man/CalculateLModeCCFI.Rd | 2 man/CalculateMAMBAC.Rd | 2 man/CalculateMAXEIG.Rd | 2 man/CalculateMAXSLOPE.Rd | 2 man/CalculateSkew.Rd | 2 man/CalculateValidity.Rd | 2 man/CheckClassification.Rd | 2 man/CheckData.Rd | 2 man/CheckParameters.Rd | 2 man/ClassifyCases.Rd | 2 man/CreateData.Rd | 2 man/CreateSample.Rd | 2 man/CreateVariable.Rd | 2 man/DisplayBaseRates.Rd | 6 +- man/DisplayCCFIs.Rd | 4 - man/DisplayPanels.Rd | 2 man/DisplayProfiles.Rd | 2 man/DisplaySpecifications.Rd | 2 man/DisplayTextOutput.Rd | 4 - man/EstimateLMode.Rd | 2 man/EstimateMAMBAC.Rd | 2 man/EstimateMAXEIG.Rd | 2 man/EstimateMAXSLOPE.Rd | 2 man/GenerateData.Rd | 2 man/PlotPanel.Rd | 2 man/ProcessProfile.Rd | 2 man/RemoveMissingData.Rd | 2 man/RunCCFIProfile.Rd | 20 +++++-- man/RunFactorAnalysis.Rd | 2 man/RunLMode.Rd | 2 man/RunMAMBAC.Rd | 2 man/RunMAXEIG.Rd | 2 man/RunMAXSLOPE.Rd | 2 man/RunProcedures.Rd | 2 man/RunProceduresComp.Rd | 2 man/RunTaxometrics.Rd | 16 +++++- man/SummarizeDist.Rd | 2 55 files changed, 255 insertions(+), 138 deletions(-)
Title: Public Economic Data and Quantitative Analysis
Description: Provides an interface to access public economic and financial data for
economic research and quantitative analysis. The data sources including
NBS, FRED, Yahoo Finance, 163 Finance and etc.
Author: Shichen Xie [aut, cre]
Maintainer: Shichen Xie <xie@shichen.name>
Diff between pedquant versions 0.1.5 dated 2020-04-09 and 0.1.6 dated 2020-08-27
DESCRIPTION | 10 MD5 | 80 ++-- NAMESPACE | 11 NEWS.md | 6 R/condition_helper_fun.R | 9 R/dim_admin_div_cn.R | 99 ++++ R/ed_code.R | 45 -- R/ed_fred.R | 2 R/ed_nbs.R | 6 R/md_0cate.R | 2 R/md_future.R | 4 R/md_stock1_.R | 28 + R/md_stock1_yahoo.R | 23 - R/md_stock_adj.R | 6 R/md_stock_fs.R | 15 R/md_stock_symbol.R | 2 R/pq_addti.R | 231 +++++++---- R/pq_backtest.R | 3 R/pq_index.R | 6 R/pq_perf.R | 2 R/pq_plot.R | 779 +++++++++++++++++++++++++++++++++++---- R/pq_return.R | 1 R/pq_to_freq.R | 1 README.md | 17 data |only man/ed_code.Rd | 2 man/ed_fred_symbol.Rd | 2 man/ed_nbs.Rd | 2 man/ed_nbs_subregion.Rd | 2 man/ed_nbs_symbol.Rd | 2 man/figures/README-charts1-1.png |binary man/figures/README-charts2-1.png |binary man/md_cate.Rd | 2 man/md_future.Rd | 2 man/md_future_symbol.Rd | 2 man/md_stock.Rd | 4 man/md_stock_adjust.Rd | 2 man/md_stock_financials.Rd | 2 man/md_stock_symbol.Rd | 2 man/pq_addti.Rd | 14 man/pq_plot.Rd | 7 man/ssec.Rd |only 42 files changed, 1115 insertions(+), 320 deletions(-)
Title: Sparse Canonical Correlation Analysis for High-Dimensional Mixed
Data
Description: Semi-parametric approach for sparse canonical correlation analysis
which can handle mixed data types: continuous, binary and truncated continuous.
Bridge functions are provided to connect Kendall's tau to latent correlation
under the Gaussian copula model. The methods are described in
Yoon, Carroll and Gaynanova (2020) <doi:10.1093/biomet/asaa007>.
Author: Grace Yoon [aut, cre] (<https://orcid.org/0000-0003-3263-1352>),
Irina Gaynanova [aut] (<https://orcid.org/0000-0002-4116-0268>)
Maintainer: Grace Yoon <gyoon@stat.tamu.edu>
Diff between mixedCCA versions 1.3.0 dated 2020-08-26 and 1.3.1 dated 2020-08-27
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NAMESPACE | 1 + R/bridgeInv.R | 2 ++ R/fromKtoR_ipol.R | 2 +- src/RcppExports.cpp | 4 ++-- src/find_w1w2.cpp | 4 ++-- 7 files changed, 18 insertions(+), 15 deletions(-)
Title: Multivariate Autoregressive State-Space Modeling
Description: The MARSS package provides maximum-likelihood parameter estimation for constrained and unconstrained linear multivariate autoregressive state-space (MARSS) models fit to multivariate time-series data. Fitting is primarily via an Expectation-Maximization (EM) algorithm, although fitting via the BFGS algorithm (using the optim function) is also provided. MARSS models are a class of dynamic linear model (DLM) and vector autoregressive model (VAR) model. Functions are provided for parametric and innovations bootstrapping, Kalman filtering and smoothing, bootstrap model selection criteria (AICb), confidences intervals via the Hessian approximation and via bootstrapping and calculation of auxiliary residuals for detecting outliers and shocks. The user guide shows examples of using MARSS for parameter estimation for a variety of applications, model selection, dynamic factor analysis, outlier and shock detection, and addition of covariates. Type RShowDoc("UserGuide", package="MARSS") at the R command line to open the MARSS user guide. Online workshops (lectures and computer labs) at <https://nwfsc-timeseries.github.io/> See the NEWS file for update information.
Author: Eli Holmes, Eric Ward, Mark Scheuerell, and Kellie Wills, NOAA, Seattle, USA
Maintainer: Elizabeth Holmes - NOAA Federal <eli.holmes@noaa.gov>
Diff between MARSS versions 3.10.12 dated 2020-02-04 and 3.11.1 dated 2020-08-27
MARSS-3.10.12/MARSS/R/augment_marssMLE.R |only MARSS-3.10.12/MARSS/inst/doc/versiontest.R |only MARSS-3.10.12/MARSS/man/augment_marssMLE.Rd |only MARSS-3.11.1/MARSS/DESCRIPTION | 14 MARSS-3.11.1/MARSS/MD5 | 311 MARSS-3.11.1/MARSS/NAMESPACE | 160 MARSS-3.11.1/MARSS/NEWS.md | 1054 +- MARSS-3.11.1/MARSS/R/CSEGriskfigure.R | 396 MARSS-3.11.1/MARSS/R/CSEGtmufigure.R | 182 MARSS-3.11.1/MARSS/R/MARSS.R | 498 - MARSS-3.11.1/MARSS/R/MARSSFisherI.r | 48 MARSS-3.11.1/MARSS/R/MARSS_dfa.r | 454 - MARSS-3.11.1/MARSS/R/MARSS_marss.R | 1396 +-- MARSS-3.11.1/MARSS/R/MARSS_marxss.R | 2546 ++--- MARSS-3.11.1/MARSS/R/MARSSaic.R | 186 MARSS-3.11.1/MARSS/R/MARSSapplynames.R | 55 MARSS-3.11.1/MARSS/R/MARSSboot.R | 398 MARSS-3.11.1/MARSS/R/MARSSharveyobsFI.R | 508 - MARSS-3.11.1/MARSS/R/MARSShatyt.r | 302 MARSS-3.11.1/MARSS/R/MARSShessian.R | 76 MARSS-3.11.1/MARSS/R/MARSShessian_numerical.R | 74 MARSS-3.11.1/MARSS/R/MARSSinfo.R | 590 - MARSS-3.11.1/MARSS/R/MARSSinits.R | 240 MARSS-3.11.1/MARSS/R/MARSSinnovationsboot.R | 210 MARSS-3.11.1/MARSS/R/MARSSkem.r | 2498 ++--- MARSS-3.11.1/MARSS/R/MARSSkemcheck.r | 572 - MARSS-3.11.1/MARSS/R/MARSSkf.r | 44 MARSS-3.11.1/MARSS/R/MARSSkfas.r | 528 - MARSS-3.11.1/MARSS/R/MARSSkfss.R | 944 +- MARSS-3.11.1/MARSS/R/MARSSoptim.r | 390 MARSS-3.11.1/MARSS/R/MARSSparamCIs.R | 150 MARSS-3.11.1/MARSS/R/MARSSresiduals.R |only MARSS-3.11.1/MARSS/R/MARSSresiduals.tT.R | 556 - MARSS-3.11.1/MARSS/R/MARSSresiduals_tt.R |only MARSS-3.11.1/MARSS/R/MARSSresiduals_tt1.R | 291 MARSS-3.11.1/MARSS/R/MARSSsimulate.R | 388 MARSS-3.11.1/MARSS/R/MARSSvectorizeparam.R | 170 MARSS-3.11.1/MARSS/R/accuracy_marssMLE.R |only MARSS-3.11.1/MARSS/R/autoplot_marssMLE.R | 733 - MARSS-3.11.1/MARSS/R/autoplot_marssPredict.R |only MARSS-3.11.1/MARSS/R/checkMARSSInputs.r | 282 MARSS-3.11.1/MARSS/R/checkModelList.r | 206 MARSS-3.11.1/MARSS/R/coef_marssMLE.r | 200 MARSS-3.11.1/MARSS/R/describe_marssMODEL.R | 32 MARSS-3.11.1/MARSS/R/fitted_marssMLE.r | 348 MARSS-3.11.1/MARSS/R/forecast_marssMLE.R |only MARSS-3.11.1/MARSS/R/glance_marssMLE.R | 42 MARSS-3.11.1/MARSS/R/is_marssMLE.r | 362 MARSS-3.11.1/MARSS/R/is_marssMODEL.R | 578 - MARSS-3.11.1/MARSS/R/logLik_marssMLE.R | 28 MARSS-3.11.1/MARSS/R/model_frame_marssMODEL.R | 80 MARSS-3.11.1/MARSS/R/onLoad.R | 82 MARSS-3.11.1/MARSS/R/plot.marssMLE.R | 584 - MARSS-3.11.1/MARSS/R/plot_marssMLE.R |only MARSS-3.11.1/MARSS/R/plot_marssPredict.R |only MARSS-3.11.1/MARSS/R/predict_marssMLE.R |only MARSS-3.11.1/MARSS/R/print_marssMLE.r | 740 - MARSS-3.11.1/MARSS/R/print_marssMODEL.R | 56 MARSS-3.11.1/MARSS/R/print_marssPredict.R |only MARSS-3.11.1/MARSS/R/progressBar.R | 52 MARSS-3.11.1/MARSS/R/residuals_marssMLE.R | 120 MARSS-3.11.1/MARSS/R/summary_marssMLE.R | 39 MARSS-3.11.1/MARSS/R/summary_marssMODEL.R | 78 MARSS-3.11.1/MARSS/R/sysdata.rda |only MARSS-3.11.1/MARSS/R/tidy_marssMLE.R | 250 MARSS-3.11.1/MARSS/R/toLatex_marssMODEL.R | 912 +- MARSS-3.11.1/MARSS/R/tsSmooth_marssMLE.R |only MARSS-3.11.1/MARSS/R/utility_functions.R | 1947 ++-- MARSS-3.11.1/MARSS/build/vignette.rds |binary MARSS-3.11.1/MARSS/inst/CITATION | 70 MARSS-3.11.1/MARSS/inst/WORDLIST |only MARSS-3.11.1/MARSS/inst/doc/Chapter_AnimalTracking.R | 667 - MARSS-3.11.1/MARSS/inst/doc/Chapter_CombiningTrendData.R | 302 MARSS-3.11.1/MARSS/inst/doc/Chapter_Covariates.R | 681 - MARSS-3.11.1/MARSS/inst/doc/Chapter_DFA.R | 856 + MARSS-3.11.1/MARSS/inst/doc/Chapter_KFAS.R |only MARSS-3.11.1/MARSS/inst/doc/Chapter_MARp.R | 646 - MARSS-3.11.1/MARSS/inst/doc/Chapter_MLR.R | 688 - MARSS-3.11.1/MARSS/inst/doc/Chapter_PVA.R | 330 MARSS-3.11.1/MARSS/inst/doc/Chapter_SealPopStructure.R | 554 - MARSS-3.11.1/MARSS/inst/doc/Chapter_SealTrend.R | 246 MARSS-3.11.1/MARSS/inst/doc/Chapter_SpeciesInteractions.R | 789 - MARSS-3.11.1/MARSS/inst/doc/Chapter_StructuralBreaks.R | 321 MARSS-3.11.1/MARSS/inst/doc/Chapter_Structural_TS.R |only MARSS-3.11.1/MARSS/inst/doc/Chapter_UnivariateDLM.R | 382 MARSS-3.11.1/MARSS/inst/doc/Chapter_inits.R | 430 MARSS-3.11.1/MARSS/inst/doc/EMDerivation.Rnw | 6092 +++++++------- MARSS-3.11.1/MARSS/inst/doc/EMDerivation.pdf |binary MARSS-3.11.1/MARSS/inst/doc/Quick_Examples.R |only MARSS-3.11.1/MARSS/inst/doc/Quick_Start.Rnw | 410 MARSS-3.11.1/MARSS/inst/doc/Quick_Start.pdf |binary MARSS-3.11.1/MARSS/inst/doc/Residuals.Rnw | 1494 +-- MARSS-3.11.1/MARSS/inst/doc/Residuals.pdf |binary MARSS-3.11.1/MARSS/inst/doc/UserGuide.Rnw | 16 MARSS-3.11.1/MARSS/inst/doc/UserGuide.pdf |binary MARSS-3.11.1/MARSS/inst/doc/index.html | 22 MARSS-3.11.1/MARSS/man/CSEGriskfigure.Rd | 108 MARSS-3.11.1/MARSS/man/CSEGtmufigure.Rd | 78 MARSS-3.11.1/MARSS/man/MARSS-package.Rd | 188 MARSS-3.11.1/MARSS/man/MARSS.Rd | 401 MARSS-3.11.1/MARSS/man/MARSSFisherI.Rd | 130 MARSS-3.11.1/MARSS/man/MARSS_dfa.Rd | 159 MARSS-3.11.1/MARSS/man/MARSS_marss.Rd | 103 MARSS-3.11.1/MARSS/man/MARSS_marxss.Rd | 156 MARSS-3.11.1/MARSS/man/MARSS_vectorized.Rd | 96 MARSS-3.11.1/MARSS/man/MARSSaic.Rd | 112 MARSS-3.11.1/MARSS/man/MARSSapplynames.Rd | 56 MARSS-3.11.1/MARSS/man/MARSSboot.Rd | 156 MARSS-3.11.1/MARSS/man/MARSSharveyobsFI.Rd | 86 MARSS-3.11.1/MARSS/man/MARSShatyt.Rd | 104 MARSS-3.11.1/MARSS/man/MARSShessian.Rd | 112 MARSS-3.11.1/MARSS/man/MARSShessian_numerical.Rd | 66 MARSS-3.11.1/MARSS/man/MARSSinfo.Rd | 50 MARSS-3.11.1/MARSS/man/MARSSinits.Rd | 86 MARSS-3.11.1/MARSS/man/MARSSinnovationsboot.Rd | 80 MARSS-3.11.1/MARSS/man/MARSSkem.Rd | 199 MARSS-3.11.1/MARSS/man/MARSSkemcheck.Rd | 48 MARSS-3.11.1/MARSS/man/MARSSkf.Rd | 186 MARSS-3.11.1/MARSS/man/MARSSoptim.Rd | 142 MARSS-3.11.1/MARSS/man/MARSSparamCIs.Rd | 98 MARSS-3.11.1/MARSS/man/MARSSresiduals.Rd |only MARSS-3.11.1/MARSS/man/MARSSresiduals_tT.Rd | 324 MARSS-3.11.1/MARSS/man/MARSSresiduals_tt1.Rd | 209 MARSS-3.11.1/MARSS/man/MARSSresiduals_ttt.Rd |only MARSS-3.11.1/MARSS/man/MARSSsimulate.Rd | 104 MARSS-3.11.1/MARSS/man/MARSSvectorizeparam.Rd | 72 MARSS-3.11.1/MARSS/man/SalmonSurvCUI.Rd | 44 MARSS-3.11.1/MARSS/man/accuracy_marssMLE.Rd |only MARSS-3.11.1/MARSS/man/allowed.Rd | 30 MARSS-3.11.1/MARSS/man/as_marssMODEL.Rd | 72 MARSS-3.11.1/MARSS/man/checkMARSSInputs.Rd | 88 MARSS-3.11.1/MARSS/man/checkModelList.Rd | 66 MARSS-3.11.1/MARSS/man/coef_marssMLE.Rd | 90 MARSS-3.11.1/MARSS/man/datasets.Rd | 36 MARSS-3.11.1/MARSS/man/describe_marssMODEL.Rd | 58 MARSS-3.11.1/MARSS/man/fitted_marssMLE.Rd | 226 MARSS-3.11.1/MARSS/man/forecast_marssMLE.Rd |only MARSS-3.11.1/MARSS/man/glance_marssMLE.Rd | 68 MARSS-3.11.1/MARSS/man/graywhales.Rd | 108 MARSS-3.11.1/MARSS/man/harborSeal.Rd | 72 MARSS-3.11.1/MARSS/man/is_marssMLE.Rd | 154 MARSS-3.11.1/MARSS/man/is_marssMODEL.Rd | 134 MARSS-3.11.1/MARSS/man/isleRoyal.Rd | 56 MARSS-3.11.1/MARSS/man/ldiag.Rd |only MARSS-3.11.1/MARSS/man/logLik_marssMLE.Rd | 60 MARSS-3.11.1/MARSS/man/loggerhead.Rd | 72 MARSS-3.11.1/MARSS/man/marssMLE-class.Rd | 74 MARSS-3.11.1/MARSS/man/marssMODEL-class.Rd | 134 MARSS-3.11.1/MARSS/man/marssPredict-class.Rd |only MARSS-3.11.1/MARSS/man/marssResiduals-class.Rd |only MARSS-3.11.1/MARSS/man/model_frame_marssMODEL.Rd | 54 MARSS-3.11.1/MARSS/man/plankton.Rd | 80 MARSS-3.11.1/MARSS/man/plot_marssMLE.Rd | 129 MARSS-3.11.1/MARSS/man/plot_marssPredict.Rd |only MARSS-3.11.1/MARSS/man/predict_help.Rd |only MARSS-3.11.1/MARSS/man/predict_marssMLE.Rd |only MARSS-3.11.1/MARSS/man/print_marssMLE.Rd | 136 MARSS-3.11.1/MARSS/man/print_marssMODEL.Rd | 80 MARSS-3.11.1/MARSS/man/print_marssPredict.Rd |only MARSS-3.11.1/MARSS/man/residuals_marssMLE.Rd | 229 MARSS-3.11.1/MARSS/man/stdInnov.Rd | 76 MARSS-3.11.1/MARSS/man/sysdata.Rd |only MARSS-3.11.1/MARSS/man/tidy_marssMLE.Rd | 196 MARSS-3.11.1/MARSS/man/toLatex_marssMLE.Rd | 94 MARSS-3.11.1/MARSS/man/tsSmooth_marssMLE.Rd |only MARSS-3.11.1/MARSS/man/utility_functions.Rd | 244 MARSS-3.11.1/MARSS/man/zscore.Rd | 72 MARSS-3.11.1/MARSS/vignettes/EMDerivation.Rnw | 6092 +++++++------- MARSS-3.11.1/MARSS/vignettes/EMDerivation.bib | 414 MARSS-3.11.1/MARSS/vignettes/Quick_Start.Rnw | 410 MARSS-3.11.1/MARSS/vignettes/Residuals.Rnw | 1494 +-- MARSS-3.11.1/MARSS/vignettes/UserGuide.Rnw | 16 172 files changed, 27544 insertions(+), 26599 deletions(-)
Title: Integrative Conditional Autoregressive Horseshoe Model
Description: Implements the integrative conditional autoregressive horseshoe model
discussed in Jendoubi, T., Ebbels, T.M. Integrative analysis of time course metabolic data and biomarker discovery.
BMC Bioinformatics 21, 11 (2020) <doi:10.1186/s12859-019-3333-0>.
The model consists in three levels: Metabolic pathways level modeling interdependencies between
variables via a conditional auto-regressive (CAR) component, integrative analysis level to identify
potential associations between heterogeneous omic variables via a Horseshoe prior and experimental
design level to capture experimental design conditions through a mixed-effects model.
The package also provides functions to simulate data from the model, construct pathway matrices,
post process and plot model parameters.
Author: Takoua Jendoubi [aut, cre],
Timothy M.D. Ebbels [aut]
Maintainer: Takoua Jendoubi <t.jendoubi14@imperial.ac.uk>
Diff between iCARH versions 2.0.2.0 dated 2020-06-16 and 2.0.2.1 dated 2020-08-27
DESCRIPTION | 11 - MD5 | 30 ++-- R/iCARH.model.R | 12 + R/iCARH.parameters.R | 2 R/pathways.R | 11 - R/postprocessing.R | 2 R/summary-method.R | 2 build/vignette.rds |binary inst/doc/example.R | 30 ++-- inst/doc/example.Rmd | 34 ++--- inst/doc/example.html | 294 +++----------------------------------------- man/iCARH.getBeta.Rd | 2 man/iCARH.getPathwaysMat.Rd | 6 man/iCARH.params.Rd | 2 man/iCARH.plotBeta.Rd | 2 vignettes/example.Rmd | 34 ++--- 16 files changed, 125 insertions(+), 349 deletions(-)
Title: Build Error Correction Models
Description: Functions for easy building of error correction models (ECM) for time series regression.
Author: Gaurav Bansal
Maintainer: Gaurav Bansal <gaurbans@gmail.com>
Diff between ecm versions 4.5.0 dated 2020-06-27 and 5.0.0 dated 2020-08-27
DESCRIPTION | 8 ++++---- MD5 | 26 +++++++++++++------------- NAMESPACE | 1 + R/ecm.R | 33 ++++++++++++++++++--------------- R/ecmave.R | 29 +++++++++++++++-------------- R/ecmaveback.r | 27 +++++++++++++-------------- R/ecmback.r | 27 +++++++++++++-------------- R/ecmpredict.r | 28 +++++++++++++--------------- README.md | 2 +- man/ecm.Rd | 6 +++++- man/ecmave.Rd | 3 +++ man/ecmaveback.Rd | 3 +++ man/ecmback.Rd | 3 +++ man/ecmpredict.Rd | 4 ++-- 14 files changed, 107 insertions(+), 93 deletions(-)
Title: Connector to the Objective Revision Evaluation Service (ORES)
Description: A connector to ORES (<https://ores.wmflabs.org/>), an AI project to provide edit scoring for content
on Wikipedia and other Wikimedia projects. This lets a researcher identify
if edits are likely to be reverted, damaging, or made in good faith.
Author: Os Keyes [aut, cre], Aaron Halfaker [ctb], Yuvi Panda [ctb]
Maintainer: Os Keyes <ironholds@gmail.com>
Diff between ores versions 0.3.1 dated 2017-11-17 and 0.3.2 dated 2020-08-27
DESCRIPTION | 16 - MD5 | 14 - README.md | 2 build/vignette.rds |binary inst/doc/introduction.R | 2 inst/doc/introduction.html | 364 +++++++++++++++++++++++++++++++++++++------ man/ores.Rd | 1 tests/testthat/test_checks.R | 37 ++-- 8 files changed, 353 insertions(+), 83 deletions(-)
Title: Manipulating Labelled Data
Description: Work with labelled data imported from 'SPSS'
or 'Stata' with 'haven' or 'foreign'. This package
provides useful functions to deal with "haven_labelled" and
"haven_labelled_spss" classes introduced by 'haven' package.
Author: Joseph Larmarange [aut, cre] (<https://orcid.org/0000-0001-7097-700X>),
Daniel Ludecke [ctb],
Hadley Wickham [ctb],
Michal Bojanowski [ctb],
François Briatte [ctb]
Maintainer: Joseph Larmarange <joseph@larmarange.net>
Diff between labelled versions 2.5.0 dated 2020-06-17 and 2.6.0 dated 2020-08-27
DESCRIPTION | 12 MD5 | 85 - NAMESPACE | 277 +-- NEWS.md | 262 +-- R/copy_labels.R | 148 - R/drop_unused_value_labels.R | 72 R/labelled-package.R |only R/labelled.R | 32 R/lookfor.R | 363 +++- R/na_values.R | 398 ++--- R/recode.R | 168 +- R/remove_attributes.R | 72 R/remove_labels.R | 258 +-- R/retrocompatibility.R | 140 - R/tagged_na.R | 38 R/to_character.R | 86 - R/to_factor.R | 388 ++-- R/to_labelled.R | 452 ++--- R/to_na.R | 138 - R/val_labels.R | 769 +++++---- R/var_label.R | 286 +-- README.md | 109 - build/vignette.rds |binary inst/doc/intro_labelled.R | 558 +++---- inst/doc/intro_labelled.Rmd | 1072 ++++++------- inst/doc/intro_labelled.html | 2378 +++++++++++++++--------------- inst/doc/look_for.R |only inst/doc/look_for.Rmd |only inst/doc/look_for.html |only man/figures/labelled.svg | 312 +-- man/figures/lifecycle-archived.svg |only man/figures/lifecycle-defunct.svg |only man/figures/lifecycle-deprecated.svg |only man/figures/lifecycle-experimental.svg |only man/figures/lifecycle-maturing.svg |only man/figures/lifecycle-questioning.svg |only man/figures/lifecycle-soft-deprecated.svg |only man/figures/lifecycle-stable.svg |only man/figures/lifecycle-superseded.svg |only man/look_for.Rd | 86 - man/na_values.Rd | 2 man/names_prefixed_by_values.Rd |only man/nolabel_to_na.Rd | 36 man/reexports.Rd | 52 man/val_labels.Rd | 2 man/val_labels_to_na.Rd | 42 man/var_label.Rd | 2 tests/testthat.R | 6 tests/testthat/test-labelled.r | 804 +++++----- vignettes/intro_labelled.Rmd | 1072 ++++++------- vignettes/look_for.Rmd |only 51 files changed, 5636 insertions(+), 5341 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-08-12 1.8.2
2018-04-11 1.7.9
2016-04-05 1.7.7
2016-02-23 1.7.6
2015-08-14 1.7.1
2014-09-04 1.6.11
2013-12-06 1.6.8
2013-01-17 1.6.3
2013-01-15 1.6.1
2012-11-20 1.5.8
2012-09-28 1.5.6
2012-02-25 1.5.5
2011-12-13 1.5.2
2009-10-01 1.4.4
2009-04-28 1.4.3
2008-05-13 1.3.8
2007-06-14 1.3.1
Title: Weighting for Covariate Balance in Observational Studies
Description: Generates weights to form equivalent groups in observational studies with point or longitudinal treatments by easing and extending the functionality of the R packages 'twang' for generalized boosted modeling (McCaffrey, Ridgeway & Morral, 2004) <doi:10.1037/1082-989X.9.4.403>, 'CBPS' for covariate balancing propensity score weighting (Imai & Ratkovic, 2014) <doi:10.1111/rssb.12027>, 'ebal' for entropy balancing (Hainmueller, 2012) <doi:10.1093/pan/mpr025>, 'optweight' for optimization-based weights (Zubizarreta, 2015) <doi:10.1080/01621459.2015.1023805>, 'ATE' for empirical balancing calibration weighting (Chan, Yam, & Zhang, 2016) <doi:10.1111/rssb.12129>, and 'SuperLearner' for stacked machine learning-based propensity scores (Pirracchio, Petersen, & van der Laan, 2015) <doi:10.1093/aje/kwu253>. Also allows for assessment of weights and checking of covariate balance by interfacing directly with 'cobalt'.
Author: Noah Greifer [aut, cre] (<https://orcid.org/0000-0003-3067-7154>)
Maintainer: Noah Greifer <noah.greifer@gmail.com>
Diff between WeightIt versions 0.10.1 dated 2020-08-12 and 0.10.2 dated 2020-08-27
WeightIt-0.10.1/WeightIt/inst/doc/WeightIt_A0_basic_use.R |only WeightIt-0.10.1/WeightIt/inst/doc/WeightIt_A0_basic_use.Rmd |only WeightIt-0.10.1/WeightIt/inst/doc/WeightIt_A0_basic_use.html |only WeightIt-0.10.1/WeightIt/vignettes/WeightIt_A0_basic_use.Rmd |only WeightIt-0.10.2/WeightIt/DESCRIPTION | 6 WeightIt-0.10.2/WeightIt/MD5 | 20 +- WeightIt-0.10.2/WeightIt/NEWS.md | 4 WeightIt-0.10.2/WeightIt/R/SHARED.R | 28 ++-- WeightIt-0.10.2/WeightIt/R/weightit2method.R | 76 +++++------ WeightIt-0.10.2/WeightIt/build/partial.rdb |binary WeightIt-0.10.2/WeightIt/build/vignette.rds |binary WeightIt-0.10.2/WeightIt/inst/doc/WeightIt.R |only WeightIt-0.10.2/WeightIt/inst/doc/WeightIt.Rmd |only WeightIt-0.10.2/WeightIt/inst/doc/WeightIt.html |only WeightIt-0.10.2/WeightIt/vignettes/WeightIt.Rmd |only 15 files changed, 75 insertions(+), 59 deletions(-)
Title: Read and Write Rectangular Text Data Quickly
Description: The goal of 'vroom' is to read and write data (like
'csv', 'tsv' and 'fwf') quickly. When reading it uses a quick initial
indexing step, then reads the values lazily , so only the data you
actually use needs to be read. The writer formats the data in
parallel and writes to disk asynchronously from formatting.
Author: Jim Hester [aut, cre] (<https://orcid.org/0000-0002-2739-7082>),
Hadley Wickham [aut] (<https://orcid.org/0000-0003-4757-117X>),
https://github.com/mandreyel/ [cph] (mio library),
R Core Team [ctb] (localtime.c code adapted from R),
Jukka Jylänki [cph] (grisu3 implementation),
Mikkel Jørgensen [cph] (grisu3 implementation),
RStudio [cph, fnd]
Maintainer: Jim Hester <james.f.hester@gmail.com>
Diff between vroom versions 1.3.0 dated 2020-08-14 and 1.3.1 dated 2020-08-27
DESCRIPTION | 6 ++-- MD5 | 33 +++++++++++++------------ NEWS.md | 8 ++++++ R/vroom.R | 10 ++++++- README.md | 4 ++- build/vroom.pdf |binary inst/WORDLIST | 1 inst/doc/vroom.html | 2 - inst/extdata/mtcars-4.csv |only inst/extdata/mtcars-6.csv |only inst/extdata/mtcars-8.csv |only man/vroom.Rd | 10 ++++++- src/delimited_index_connection.cc | 8 ++++-- src/vroom_dttm.h | 50 ++++++++++++++++---------------------- src/vroom_fct.h | 14 ++-------- src/vroom_vec.h | 44 +++++++++++++++++++++++++-------- tests/testthat/test-datetime.R | 32 +++++++++++++++--------- tests/testthat/test-factor.R | 9 ++++++ tests/testthat/test-vroom.R | 8 ++++++ 19 files changed, 155 insertions(+), 84 deletions(-)
Title: Species Trait Data from Around the Web
Description: Species trait data from many different sources, including
sequence data from 'NCBI' (<https://www.ncbi.nlm.nih.gov/>),
plant trait data from 'BETYdb', data from 'EOL' 'Traitbank',
'Birdlife' International, and more.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>),
Zachary Foster [aut],
Ignasi Bartomeus [aut],
David LeBauer [aut],
Chris Black [aut],
David Harris [aut],
Rupert Collins [ctb]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between traits versions 0.4.2 dated 2019-06-29 and 0.5.0 dated 2020-08-27
traits-0.4.2/traits/inst/vign |only traits-0.4.2/traits/man/coral.Rd |only traits-0.4.2/traits/man/tr_usda.Rd |only traits-0.5.0/traits/DESCRIPTION | 29 traits-0.5.0/traits/LICENSE | 2 traits-0.5.0/traits/MD5 | 88 - traits-0.5.0/traits/NEWS.md | 18 traits-0.5.0/traits/R/betydb.R | 2 traits-0.5.0/traits/R/birdlife.R | 6 traits-0.5.0/traits/R/coral.R | 99 - traits-0.5.0/traits/R/defunct.R | 27 traits-0.5.0/traits/R/leda.R | 78 - traits-0.5.0/traits/R/ncbi_byid.R | 55 - traits-0.5.0/traits/R/ncbi_byname.R | 65 - traits-0.5.0/traits/R/ncbi_searcher.R | 97 + traits-0.5.0/traits/R/taxa_search.R | 2 traits-0.5.0/traits/R/tr_usda.R | 38 traits-0.5.0/traits/R/traits-package.r | 41 traits-0.5.0/traits/R/zzz.R | 2 traits-0.5.0/traits/README.md | 205 --- traits-0.5.0/traits/build/vignette.rds |binary traits-0.5.0/traits/inst/doc/betydb.Rmd | 163 --- traits-0.5.0/traits/inst/doc/betydb.html | 684 ++++++------- traits-0.5.0/traits/inst/doc/traits.Rmd | 212 +--- traits-0.5.0/traits/inst/doc/traits.html | 1037 ++++++++++---------- traits-0.5.0/traits/man/betydb.Rd | 102 + traits-0.5.0/traits/man/betydb_query.Rd | 20 traits-0.5.0/traits/man/birdlife_habitat.Rd | 5 traits-0.5.0/traits/man/birdlife_threats.Rd | 3 traits-0.5.0/traits/man/coral-defunct.Rd |only traits-0.5.0/traits/man/leda.Rd | 7 traits-0.5.0/traits/man/ncbi_byid.Rd | 38 traits-0.5.0/traits/man/ncbi_byname.Rd | 28 traits-0.5.0/traits/man/ncbi_searcher.Rd | 36 traits-0.5.0/traits/man/taxa_search.Rd | 2 traits-0.5.0/traits/man/tr_ernest.Rd | 2 traits-0.5.0/traits/man/tr_usda-defunct.Rd |only traits-0.5.0/traits/man/tr_zanne.Rd | 2 traits-0.5.0/traits/man/traits-defunct.Rd | 25 traits-0.5.0/traits/man/traits-package.Rd | 41 traits-0.5.0/traits/man/traits_cache.Rd | 28 traits-0.5.0/traits/tests/testthat/test-betydb.R | 34 traits-0.5.0/traits/tests/testthat/test-traitbank.R | 2 traits-0.5.0/traits/vignettes/betydb.Rmd | 163 --- traits-0.5.0/traits/vignettes/betydb.Rmd.og |only traits-0.5.0/traits/vignettes/traits.Rmd | 212 +--- traits-0.5.0/traits/vignettes/traits.Rmd.og |only 47 files changed, 1642 insertions(+), 2058 deletions(-)
Title: Tests for Rotational Symmetry on the Hypersphere
Description: Implementation of the tests for rotational symmetry on the hypersphere
proposed in García-Portugués, Paindaveine and Verdebout (2020)
<doi:10.1080/01621459.2019.1665527>. The package also implements the
proposed distributions on the hypersphere, based on the tangent-normal
decomposition, and allows for the replication of the data application
considered in the paper.
Author: Eduardo García-Portugués [aut, cre]
(<https://orcid.org/0000-0002-9224-4111>),
Davy Paindaveine [aut],
Thomas Verdebout [aut]
Maintainer: Eduardo García-Portugués <edgarcia@est-econ.uc3m.es>
Diff between rotasym versions 1.0.8 dated 2020-07-29 and 1.0.9 dated 2020-08-27
DESCRIPTION | 14 ++++++++------ MD5 | 36 ++++++++++++++++++------------------ NEWS.md | 4 ++++ R/TE.R | 2 +- R/TM.R | 2 +- R/cosines-signs.R | 2 +- R/estimators.R | 2 +- R/rotasym-package.R | 2 +- R/tang-norm.R | 2 +- R/tests.R | 2 +- inst/CITATION | 21 ++++++++++----------- man/cosines-signs.Rd | 2 +- man/estimators.Rd | 2 +- man/rotasym-package.Rd | 2 +- man/tang-norm-decomp.Rd | 2 +- man/tangent-elliptical.Rd | 2 +- man/tangent-vMF.Rd | 2 +- man/test_rotasym.Rd | 2 +- src/vMF.cpp | 2 +- 19 files changed, 55 insertions(+), 50 deletions(-)
Title: Straightforward 'NetCDF' Metadata
Description: Extract metadata from 'NetCDF' data sources, these can be files, file handles or
servers. This package leverages and extends the lower level functions of the 'RNetCDF' package
providing a consistent set of functions that all return data frames. We introduce named concepts
of 'grid', 'axis' and 'source' which are all meaningful entities without formal definition in the
'NetCDF' library <https://www.unidata.ucar.edu/software/netcdf/>. 'RNetCDF' matches the library
itself with only the named concepts of 'variables', 'dimensions' and 'attributes'.
Author: Michael Sumner [aut, cre],
Tomas Remenyi [ctb],
Ben Raymond [ctb],
David Blodgett [ctb]
Maintainer: Michael Sumner <mdsumner@gmail.com>
Diff between ncmeta versions 0.2.5 dated 2020-05-12 and 0.3.0 dated 2020-08-27
DESCRIPTION | 11 MD5 | 46 +- NAMESPACE | 138 +++---- NEWS.md | 130 +++---- R/nc-gridmapping.R | 768 +++++++++++++++++++++---------------------- R/nc_coord.R | 416 +++++++++++------------ R/nc_sources.R | 39 +- README.md | 186 +++++----- man/nc_att.Rd | 78 ++-- man/nc_atts.Rd | 66 +-- man/nc_axes.Rd | 56 +-- man/nc_axis.Rd | 52 +- man/nc_coord_var.Rd | 98 ++--- man/nc_dim.Rd | 66 +-- man/nc_dims.Rd | 50 +- man/nc_gm_to_prj.Rd | 92 ++--- man/nc_grid_mapping_atts.Rd | 70 +-- man/nc_grids.Rd | 70 +-- man/nc_inq.Rd | 102 ++--- man/nc_meta.Rd | 76 ++-- man/nc_prj_to_gridmapping.Rd | 72 ++-- man/nc_sources.Rd | 38 +- man/nc_var.Rd | 58 +-- man/nc_vars.Rd | 50 +- 24 files changed, 1418 insertions(+), 1410 deletions(-)
Title: Lightning Fast Serialization of Data Frames
Description: Multithreaded serialization of compressed data frames using the
'fst' format. The 'fst' format allows for random access of stored data and
compression with the LZ4 and ZSTD compressors created by Yann Collet. The ZSTD
compression library is owned by Facebook Inc.
Author: Mark Klik [aut, cre, cph],
Yann Collet [ctb, cph] (Yann Collet is author of the bundled LZ4 and
ZSTD code and copyright holder of LZ4),
Facebook, Inc. [cph] (Bundled ZSTD code)
Maintainer: Mark Klik <markklik@gmail.com>
Diff between fst versions 0.9.2 dated 2020-04-01 and 0.9.4 dated 2020-08-27
DESCRIPTION | 14 +- MD5 | 28 ++-- R/RcppExports.R | 8 - R/compress.R | 6 src/RcppExports.cpp | 14 -- src/fst_compress.cpp | 53 +++++--- src/fst_compress.h | 4 src/init.c | 8 - tests/testthat.R | 4 tests/testthat/test_fst.R | 28 +--- tests/testthat/test_integer64.R | 17 ++ tests/testthat/test_lintr.R | 22 +-- tests/testthat/test_meta.R | 222 +++++++++++++++++++++-------------- tests/testthat/test_nanotime.R | 11 - tests/testthat/test_special_tables.R | 2 15 files changed, 249 insertions(+), 192 deletions(-)
Title: Convolution-Type Smoothed Quantile Regression
Description: Fast and accurate convolution-type smoothed quantile regression. Implemented using Barzilai-Borwein gradient descent with a Huber regression warm start. Construct confidence intervals for regression coefficients using multiplier bootstrap.
Author: Xuming He [aut],
Xiaoou Pan [aut, cre],
Kean Ming Tan [aut],
Wen-Xin Zhou [aut]
Maintainer: Xiaoou Pan <xip024@ucsd.edu>
Diff between conquer versions 1.0.1 dated 2020-05-06 and 1.0.2 dated 2020-08-27
DESCRIPTION | 14 +++++++------- MD5 | 10 +++++----- R/RcppExports.R | 12 ------------ README.md | 13 ++++++++----- src/RcppExports.cpp | 43 ------------------------------------------- src/smqr.cpp | 43 ------------------------------------------- 6 files changed, 20 insertions(+), 115 deletions(-)
Title: Bayesian Network Meta-Analysis using 'JAGS'
Description: Network meta-analyses using Bayesian framework following Dias et al. (2013) <DOI:10.1177/0272989X12458724>. Based on the data input, creates prior, model file, and initial values needed to run models in 'rjags'. Able to handle binomial, normal and multinomial arm-based data. Can handle multi-arm trials and includes methods to incorporate covariate and baseline risk effects. Includes standard diagnostics and visualization tools to evaluate the results.
Author: Michael Seo [aut, cre],
Christopher Schmid [aut]
Maintainer: Michael Seo <swj8874@gmail.com>
Diff between bnma versions 1.2.0 dated 2020-07-06 and 1.3.0 dated 2020-08-27
DESCRIPTION | 8 MD5 | 26 +- NEWS.md | 5 R/network.data.R | 4 R/network.rjags.R | 7 R/network.run.R | 21 +- R/ume.network.R | 2 inst/doc/my-vignette.R | 18 + inst/doc/my-vignette.Rmd | 24 ++ inst/doc/my-vignette.html | 431 ++++++++++++++++++++++++++++------------------ man/network.data.Rd | 4 man/network.run.Rd | 4 man/ume.network.run.Rd | 2 vignettes/my-vignette.Rmd | 24 ++ 14 files changed, 386 insertions(+), 194 deletions(-)
Title: Header-Only C++ Mathematical Optimization Library for
'Armadillo'
Description: 'Ensmallen' is a templated C++ mathematical optimization library
(by the 'MLPACK' team) that provides a simple set of abstractions for writing an
objective function to optimize. Provided within are various standard and
cutting-edge optimizers that include full-batch gradient descent techniques,
small-batch techniques, gradient-free optimizers, and constrained optimization.
The 'RcppEnsmallen' package includes the header files from the 'Ensmallen' library
and pairs the appropriate header files from 'armadillo' through the
'RcppArmadillo' package. Therefore, users do not need to install 'Ensmallen' nor
'Armadillo' to use 'RcppEnsmallen'. Note that 'Ensmallen' is licensed under
3-Clause BSD, 'Armadillo' starting from 7.800.0 is licensed under Apache License 2,
'RcppArmadillo' (the 'Rcpp' bindings/bridge to 'Armadillo') is licensed under
the GNU GPL version 2 or later. Thus, 'RcppEnsmallen' is also licensed under
similar terms. Note that 'Ensmallen' requires a compiler that supports
'C++11' and 'Armadillo' 8.400 or later.
Author: James Joseph Balamuta [aut, cre, cph]
(<https://orcid.org/0000-0003-2826-8458>),
Dirk Eddelbuettel [aut, cph] (<https://orcid.org/0000-0001-6419-907X>)
Maintainer: James Joseph Balamuta <balamut2@illinois.edu>
Diff between RcppEnsmallen versions 0.2.13.0.1 dated 2020-07-24 and 0.2.14.1.1 dated 2020-08-27
ChangeLog | 31 ++++++++++ DESCRIPTION | 8 +- MD5 | 24 ++++--- NEWS.md | 18 +++++ README.md | 6 - inst/doc/using-rcppensmallen.html | 20 +++--- inst/include/ensmallen.hpp | 5 + inst/include/ensmallen_bits/aug_lagrangian/aug_lagrangian_impl.hpp | 17 ++++- inst/include/ensmallen_bits/ens_version.hpp | 4 - inst/include/ensmallen_bits/lbfgs/lbfgs_impl.hpp | 2 inst/include/ensmallen_bits/nsga2 |only inst/include/ensmallen_bits/problems/fonseca_fleming_function.hpp |only inst/include/ensmallen_bits/problems/problems.hpp | 2 inst/include/ensmallen_bits/problems/schaffer_function_n1.hpp |only 14 files changed, 104 insertions(+), 33 deletions(-)
Title: Interactively Visualize Genetic Mutation Data using a
Lollipop-Diagram
Description: R interface for 'g3-lollipop' JavaScript library.
Visualize genetic mutation data using an interactive lollipop diagram in RStudio or your browser.
Author: Xin Guo [aut, cre]
Maintainer: Xin Guo <g3viz.group@gmail.com>
Diff between g3viz versions 1.1.2 dated 2019-05-29 and 1.1.3 dated 2020-08-27
DESCRIPTION | 10 MD5 | 42 +- NEWS.md | 5 R/g3Lollipop.R | 37 + R/zzz.R | 7 build/vignette.rds |binary data/hgnc2pfam.df.rda |binary inst/doc/chart_themes.R | 22 - inst/doc/chart_themes.html | 411 ++++++++++++-------- inst/doc/introduction.R | 24 - inst/doc/introduction.Rmd | 7 inst/doc/introduction.html | 672 +++++++++++++++++++--------------- man/g3Lollipop.Rd | 18 man/g3Lollipop.options.Rd | 76 ++- man/g3Lollipop.theme.Rd | 8 man/getMutationsFromCbioportal.Rd | 9 man/hgnc2pfam.Rd | 3 man/hgnc2pfam.df.Rd | 6 man/mapMutationTypeToMutationClass.Rd | 6 man/mutation.table.df.Rd | 6 man/readMAF.Rd | 16 vignettes/introduction.Rmd | 7 22 files changed, 833 insertions(+), 559 deletions(-)