Title: Fitting Frailty Models with the EM Algorithm
Description: Contains functions for fitting shared frailty models with a semi-parametric
baseline hazard with the Expectation-Maximization algorithm. Supported data formats
include clustered failures with left truncation and recurrent events in gap-time
or Andersen-Gill format. Several frailty distributions, such as the the gamma, positive stable
and the Power Variance Family are supported.
Author: Theodor Adrian Balan [aut, cre],
Hein Putter [aut]
Maintainer: Theodor Adrian Balan <hello@tbalan.com>
Diff between frailtyEM versions 1.0.1 dated 2019-09-22 and 1.0.2 dated 2026-10-30
DESCRIPTION | 21 ++++++--- MD5 | 45 ++++++++++---------- NAMESPACE | 90 ++++++++++++++++++++++------------------- NEWS.md | 5 ++ R/ca_test_fit.R | 3 - R/emfrail.R | 6 +- R/emfrail_arguments.R | 18 ++++---- build/vignette.rds |binary inst/CITATION | 34 +++++++-------- inst/doc/frailtyEM_manual.R | 1 inst/doc/frailtyEM_manual.Rnw | 2 inst/doc/frailtyEM_manual.pdf |binary man/autoplot.emfrail.Rd | 17 +++++-- man/ca_test_fit.Rd |only man/emfrail.Rd | 12 ++++- man/emfrail_control.Rd | 38 ++++++++++------- man/emfrail_dist.Rd | 9 +++- man/frailtyEM-package.Rd | 6 -- man/plot.emfrail.Rd | 17 +++++-- man/predict.emfrail.Rd | 16 +++++-- man/summary.emfrail.Rd | 10 +++- src/RcppExports.cpp | 5 ++ vignettes/frailtyEM_manual.Rnw | 2 vignettes/mybib.bib | 24 +++++----- 24 files changed, 226 insertions(+), 155 deletions(-)
Title: GeoZarr Conventions for Geospatial Data in Zarr Stores
Description: Large-scale gridded data stores are increasingly using the Zarr
format. GeoZarr is defined in terms of a number of community conventions
built on top of the Zarr specification. These conventions specify how Zarr
metadata is to be interpreted to attach semantic meaning to the data in the
Zarr array providing the metadata. This package implements a number of
community conventions on top of the 'zarr' package, enabling the R community
to use geospatial data stored in Zarr.
Author: Patrick Van Laake [aut, cre]
Maintainer: Patrick Van Laake <patrick@vanlaake.net>
Diff between geozarr versions 0.2.0 dated 2026-09-15 and 0.3.0 dated 2026-10-30
DESCRIPTION | 8 MD5 | 81 ++++--- NAMESPACE | 2 NEWS.md | 12 + R/api.R | 116 +++------- R/axis.R | 83 ++----- R/convention_cs.R | 26 +- R/convention_proj.R | 33 +- R/convention_spatial.R | 52 ++-- R/coordinate_system.R | 20 + R/coordinates.R | 330 ++++++++++++++++++----------- R/domain_geozarr.R | 111 +++++---- R/geozarr_array.R | 237 +++++++++++--------- R/geozarr_group.R | 5 R/identified_object.R | 2 R/utils.R | 147 +++++++++++- R/zzz.R | 16 - README.md | 86 +++---- man/CoordinateSystemAxis.Rd | 102 -------- man/Coordinates.Rd | 92 -------- man/CoordinatesIrregular.Rd |only man/CoordinatesOrdinal.Rd | 25 -- man/CoordinatesPacked.Rd | 5 man/CoordinatesString.Rd | 5 man/CoordinatesTime.Rd | 30 ++ man/as_geozarr.Rd | 27 -- man/create_geozarr_array.Rd | 14 - man/geozarr_array.Rd | 39 +-- man/geozarr_group.Rd | 4 man/set_convention.Rd | 18 - man/zarr_conv_proj.Rd | 28 -- man/zarr_conv_spatial.Rd | 28 -- man/zarr_convention_cs.Rd | 6 man/zarr_domain_geozarr.Rd | 5 tests/testthat/helper-geozarr.R |only tests/testthat/test-api.R | 54 +++- tests/testthat/test-axis.R |only tests/testthat/test-convention_cs.R |only tests/testthat/test-convention_proj.R |only tests/testthat/test-convention_spatial.R |only tests/testthat/test-coordinate_system.R |only tests/testthat/test-coordinates.R |only tests/testthat/test-create_geozarr_array.R |only tests/testthat/test-domain.R |only tests/testthat/test-geozarr_array.R |only tests/testthat/test-identified_object.R |only tests/testthat/test-print.R |only tests/testthat/test-set_convention.R |only tests/testthat/test-utils.R |only 49 files changed, 941 insertions(+), 908 deletions(-)
Title: Computes Proximity in Large Matrices
Description: Computes proximity between rows or columns of large matrices efficiently in C++.
Functions are optimised for large matrices using the Armadillo and Intel TBB libraries.
Among various built-in similarity/distance measures, computation of correlation,
cosine similarity, Dice coefficient and Euclidean distance is particularly fast.
Author: Kohei Watanabe [cre, aut, cph] ,
Robrecht Cannoodt [aut]
Maintainer: Kohei Watanabe <watanabe.kohei@gmail.com>
Diff between proxyC versions 0.5.2 dated 2025-04-25 and 0.6.0 dated 2026-10-30
DESCRIPTION | 19 +- MD5 | 70 +++++--- NAMESPACE | 6 NEWS.md | 11 + R/RcppExports.R | 36 ++-- R/crossprod.R |only R/mask.R | 2 R/proxy.R | 122 ++++++++------ R/utils.R | 192 +++++++++++++++++------ README.md | 32 ++- build/vignette.rds |binary inst/doc/measures.html | 4 man/colMaxs.Rd |only man/colSds.Rd | 14 + man/colZeros.Rd | 7 man/crossprod.Rd | 16 + man/figures/unnamed-chunk-5-1.png |binary man/figures/unnamed-chunk-6-1.png |binary man/figures/unnamed-chunk-7-1.png |only man/figures/unnamed-chunk-8-1.png |binary man/figures/unnamed-chunk-9-1.png |only man/maxCol.Rd |only man/simil.Rd | 21 +- src/RcppExports.cpp | 121 +++++++++----- src/linear.cpp | 198 +++-------------------- src/linear.h |only src/mask.cpp | 4 src/pair.cpp | 314 +++----------------------------------- src/pair.h |only src/proxyc.h | 34 +++- src/utility.cpp | 68 ++++++++ src/utility.h |only tests/misc |only tests/testthat/test-crossprod.R | 71 ++++++-- tests/testthat/test-dense.R |only tests/testthat/test-dist.R | 4 tests/testthat/test-mask.R | 5 tests/testthat/test-proxy.R | 137 ++++++++++++---- tests/testthat/test-utils.R |only 39 files changed, 784 insertions(+), 724 deletions(-)
Title: Parsing Glycan Structure Text Representations
Description: Provides functions to parse glycan structure text representations
into 'glyrepr' glycan structures. Currently, it supports StrucGP-style,
pGlyco-style, IUPAC-condensed, IUPAC-extended, IUPAC-short, IUPAC-compact,
WURCS, LINUCS, Linear Code, GlycoCT, KCF, and GlycoWorkbench formats. It
also provides an automatic parser to detect the format and parse the
structure string.
Author: Bin Fu [aut, cre, cph]
Maintainer: Bin Fu <23110220018@m.fudan.edu.cn>
Diff between glyparse versions 0.8.1 dated 2026-08-28 and 1.0.0 dated 2026-10-30
glyparse-0.8.1/glyparse/R/furanose.R |only glyparse-0.8.1/glyparse/R/utils.R |only glyparse-1.0.0/glyparse/DESCRIPTION | 16 glyparse-1.0.0/glyparse/MD5 | 91 glyparse-1.0.0/glyparse/NAMESPACE | 2 glyparse-1.0.0/glyparse/NEWS.md | 15 glyparse-1.0.0/glyparse/R/RcppExports.R |only glyparse-1.0.0/glyparse/R/auto-parse.R | 82 glyparse-1.0.0/glyparse/R/native.R |only glyparse-1.0.0/glyparse/R/parse-glycam-iupac.R | 273 glyparse-1.0.0/glyparse/R/parse-glycoct.R | 2756 ---------- glyparse-1.0.0/glyparse/R/parse-gwb.R | 641 -- glyparse-1.0.0/glyparse/R/parse-iupac-compact.R | 351 - glyparse-1.0.0/glyparse/R/parse-iupac-condensed.R | 6 glyparse-1.0.0/glyparse/R/parse-iupac-extended.R | 174 glyparse-1.0.0/glyparse/R/parse-iupac-short.R | 80 glyparse-1.0.0/glyparse/R/parse-kcf.R | 596 -- glyparse-1.0.0/glyparse/R/parse-linear-code.R | 49 glyparse-1.0.0/glyparse/R/parse-linucs.R | 637 -- glyparse-1.0.0/glyparse/R/parse-pglyco.R | 73 glyparse-1.0.0/glyparse/R/parse-strucgp.R | 82 glyparse-1.0.0/glyparse/R/parse-wurcs.R | 1336 ---- glyparse-1.0.0/glyparse/R/struc-parser-wrapper.R | 195 glyparse-1.0.0/glyparse/README.md | 21 glyparse-1.0.0/glyparse/inst/doc/glyparse.html | 464 - glyparse-1.0.0/glyparse/man/glyparse_options.Rd |only glyparse-1.0.0/glyparse/man/parse_glycoct.Rd | 11 glyparse-1.0.0/glyparse/man/parse_kcf.Rd | 11 glyparse-1.0.0/glyparse/man/parse_linucs.Rd | 11 glyparse-1.0.0/glyparse/man/parse_pglyco_struc.Rd | 11 glyparse-1.0.0/glyparse/man/parse_strucgp_struc.Rd | 11 glyparse-1.0.0/glyparse/man/parse_wurcs.Rd | 11 glyparse-1.0.0/glyparse/src |only glyparse-1.0.0/glyparse/tests/testthat/_snaps/performance.md |only glyparse-1.0.0/glyparse/tests/testthat/fixtures |only glyparse-1.0.0/glyparse/tests/testthat/helper-native.R |only glyparse-1.0.0/glyparse/tests/testthat/test-auto-parse.R | 38 glyparse-1.0.0/glyparse/tests/testthat/test-native.R |only glyparse-1.0.0/glyparse/tests/testthat/test-parse-glycoct.R | 5 glyparse-1.0.0/glyparse/tests/testthat/test-parse-pglyco.R | 10 glyparse-1.0.0/glyparse/tests/testthat/test-parse-strucgp.R | 10 glyparse-1.0.0/glyparse/tests/testthat/test-parse-wurcs.R | 18 glyparse-1.0.0/glyparse/tests/testthat/test-parser-arrays.R |only glyparse-1.0.0/glyparse/tests/testthat/test-parser-batch-performance.R |only glyparse-1.0.0/glyparse/tests/testthat/test-performance.R | 122 glyparse-1.0.0/glyparse/tests/testthat/test-progress.R | 87 glyparse-1.0.0/glyparse/tests/testthat/test-struc-parser-wrapper.R | 23 47 files changed, 750 insertions(+), 7569 deletions(-)