Title: Calculate Concentration and Dispersion in Ordered Rating Scales
Description: Calculates concentration and dispersion in ordered rating scales. It implements various measures of concentration and dispersion to describe what researchers variably call agreement, concentration, consensus, dispersion, or polarization among respondents in ordered data. It also implements other related measures to classify distributions. In addition to a generic city-block based concentration measure and a generic dispersion measure, the package implements various measures, including van der Eijk's (2001) <DOI: 10.1023/A:1010374114305> measure of agreement A, measures of concentration by Leik, Tatsle and Wierman, Blair and Lacy, Kvalseth, Berry and Mielke, Reardon, and Garcia-Montalvo and Reynal-Querol. Furthermore, the package provides an implementation of Galtungs AJUS-system to classify distributions, as well as a function to identify the position of multiple modes.
Author: Didier Ruedin [aut, cre]
Clem Aeppli [ctb]
Maintainer: Didier Ruedin <didier.ruedin@unine.ch>
Diff between agrmt versions 1.42.4 dated 2020-08-31 and 1.42.7 dated 2021-07-17
DESCRIPTION | 12 ++++++------ LICENSE | 2 +- MD5 | 14 +++++++------- NEWS | 12 ++++++++++++ R/collapse.R | 15 +++++++++++++-- build/vignette.rds |binary inst/doc/agrmt.pdf |binary man/collapse.Rd | 18 +++++++++++++++--- 8 files changed, 54 insertions(+), 19 deletions(-)
Title: Radiomics Image Analysis Toolbox for Medial Images
Description: Radiomics image analysis toolbox for 2D and 3D radiological images. RIA supports DICOM, NIfTI,
nrrd and npy (numpy array) file formats.
RIA calculates first-order, gray level co-occurrence matrix, gray level run length matrix and
geometry-based statistics. Almost all calculations are done using vectorized formulas to
optimize run speeds. Calculation of several thousands of parameters only takes minutes
on a single core of a conventional PC.
Author: Marton Kolossvary [aut, cre]
Maintainer: Marton Kolossvary <marton.kolossvary@gmail.com>
Diff between RIA versions 1.5.1 dated 2021-06-30 and 1.6.0 dated 2021-07-17
DESCRIPTION | 22 ++++++++++++---------- MD5 | 33 ++++++++++++++++++--------------- NAMESPACE | 1 + R/create_header_npy.R |only R/load_dicom.R | 42 +++++++++++++++++++++++++++++++----------- R/load_nifti.R | 42 +++++++++++++++++++++++++++++++----------- R/load_npy.R |only R/load_nrrd.R | 42 +++++++++++++++++++++++++++++++----------- R/radiomics_all.R | 6 +++--- README.md | 14 +++++++------- inst/doc/RIA.R | 3 +-- inst/doc/RIA.Rmd | 18 ++++++++++-------- inst/doc/RIA.html | 41 ++++++++++++++++++++--------------------- man/load_dicom.Rd | 16 ++++++++++++---- man/load_nifti.Rd | 16 ++++++++++++---- man/load_npy.Rd |only man/load_nrrd.Rd | 16 ++++++++++++---- man/radiomics_all.Rd | 6 +++--- vignettes/RIA.Rmd | 18 ++++++++++-------- 19 files changed, 214 insertions(+), 122 deletions(-)
Title: Access USPTO Bulk Data in Tidy Rectangular Format
Description: Converts TXT and XML data curated by the United States Patent and
Trademark Office (USPTO). Allows conversion of bulk data after downloading
directly from the USPTO bulk data website, eliminating need for users to
wrangle multiple data formats to get large patent databases in tidy,
rectangular format. Data details can be found on the USPTO website
<https://bulkdata.uspto.gov/>. Currently, all 3 formats: 1. TXT data
(1976-2001); 2. XML format 1 data (2002-2004); and 3. XML format 2 data
(2005-current) can be converted to rectangular, CSV format.
Relevant literature that uses data from USPTO includes Wada (2020)
<doi:10.1007/s11192-020-03674-4> and Plaza & Albert (2008)
<doi:10.1007/s11192-007-1763-3>.
Author: Raoul Wadhwa [aut, cre] (<https://orcid.org/0000-0003-0503-9580>),
James Yu [aut],
Hayley Beltz [aut],
Milind Desai [aut],
Jacob Scott [aut],
Peter Erdi [aut]
Maintainer: Raoul Wadhwa <raoulwadhwa@gmail.com>
Diff between patentr versions 0.1.0 dated 2021-02-08 and 0.1.2 dated 2021-07-17
DESCRIPTION | 41 +++-- MD5 | 36 +++- NAMESPACE | 2 R/RcppExports.R | 4 R/acquire.R | 45 +++-- R/convert_txt.R | 162 ++++---------------- R/convert_xml1.R |only R/convert_xml2.R |only R/data.R |only R/utility.R | 288 ++++++++++++++++++++++++++++++++++++ build |only data |only inst |only man/get_bulk_patent_data.Rd | 6 man/wku_to_pno.Rd |only man/y1976w1.Rd |only src/RcppExports.cpp | 17 ++ src/convert_funcs.cpp | 140 +++++++++++++++-- tests/testthat/TXT-sample-2 |only tests/testthat/XML1-sample-14 |only tests/testthat/XML2-sample-10 |only tests/testthat/test-acquire.R |only tests/testthat/test-convert.R |only tests/testthat/test-utility-funcs.R | 18 ++ vignettes |only 25 files changed, 578 insertions(+), 181 deletions(-)
Title: Comprehensive Statistical Analysis of Plant Breeding Experiments
Description: Performs statistical data analysis of various Plant Breeding experiments. Contains functions for Line by Tester analysis as per Arunachalam, V.(1974) <http://repository.ias.ac.in/89299/> and Diallel analysis as per Griffing, B. (1956) <https://www.publish.csiro.au/bi/pdf/BI9560463>.
Author: Nandan Patil [cre, aut] (<https://orcid.org/0000-0003-0100-9931>),
Lakshmi R. Gangavati [aut, ctb]
Maintainer: Nandan Patil <tryanother609@gmail.com>
Diff between gpbStat versions 0.3.2 dated 2021-06-16 and 0.3.3 dated 2021-07-17
gpbStat-0.3.2/gpbStat/R/on-attach.R |only gpbStat-0.3.3/gpbStat/DESCRIPTION | 12 gpbStat-0.3.3/gpbStat/MD5 | 47 - gpbStat-0.3.3/gpbStat/R/alphaltc.R | 3 gpbStat-0.3.3/gpbStat/R/alphaltcchk.R | 1 gpbStat-0.3.3/gpbStat/R/dm2.R | 2 gpbStat-0.3.3/gpbStat/R/dm2alpha.R | 12 gpbStat-0.3.3/gpbStat/R/ltcchk.R | 2 gpbStat-0.3.3/gpbStat/R/sysdata.rda |only gpbStat-0.3.3/gpbStat/README.md | 9 gpbStat-0.3.3/gpbStat/build/vignette.rds |binary gpbStat-0.3.3/gpbStat/data/alphaltc.rda |binary gpbStat-0.3.3/gpbStat/data/alphaltcchk.rda |binary gpbStat-0.3.3/gpbStat/data/dm2alpha.rda |binary gpbStat-0.3.3/gpbStat/inst/doc/dm2.R | 4 gpbStat-0.3.3/gpbStat/inst/doc/dm2.Rmd | 4 gpbStat-0.3.3/gpbStat/inst/doc/dm2.html | 829 ++++++++++------------------- gpbStat-0.3.3/gpbStat/inst/doc/ltc.html | 698 +++++++----------------- gpbStat-0.3.3/gpbStat/inst/doc/ltcchk.html | 706 +++++++----------------- gpbStat-0.3.3/gpbStat/man/alphaltc.Rd | 3 gpbStat-0.3.3/gpbStat/man/alphaltcchk.Rd | 1 gpbStat-0.3.3/gpbStat/man/dm2.Rd | 2 gpbStat-0.3.3/gpbStat/man/dm2alpha.Rd | 12 gpbStat-0.3.3/gpbStat/man/ltcchk.Rd | 2 gpbStat-0.3.3/gpbStat/vignettes/dm2.Rmd | 4 gpbStat-0.3.3/gpbStat/vignettes/rsconnect |only 26 files changed, 804 insertions(+), 1549 deletions(-)
Title: Exploratory Analysis of Genetic and Genomic Data
Description: Toolset for the exploration of genetic and genomic
data. Adegenet provides formal (S4) classes for storing and handling
various genetic data, including genetic markers with varying ploidy
and hierarchical population structure ('genind' class), alleles counts
by populations ('genpop'), and genome-wide SNP data ('genlight'). It
also implements original multivariate methods (DAPC, sPCA), graphics,
statistical tests, simulation tools, distance and similarity measures,
and several spatial methods. A range of both empirical and simulated
datasets is also provided to illustrate various methods.
Author: Thibaut Jombart [aut] (<https://orcid.org/0000-0003-2226-8692>),
Zhian N. Kamvar [aut, cre] (<https://orcid.org/0000-0003-1458-7108>),
Caitlin Collins [ctb],
Roman Lustrik [ctb],
Marie-Pauline Beugin [ctb],
Brian J. Knaus [ctb],
Peter Solymos [ctb],
Vladimir Mikryukov [ctb],
Klaus Schliep [ctb],
Tiago Maié [ctb],
Libor Morkovsky [ctb],
Ismail Ahmed [ctb],
Anne Cori [ctb],
Federico Calboli [ctb],
RJ Ewing [ctb],
Frédéric Michaud [ctb],
Rebecca DeCamp [ctb],
Alexandre Courtiol [ctb] (<https://orcid.org/0000-0003-0637-2959>)
Maintainer: Zhian N. Kamvar <zkamvar@gmail.com>
Diff between adegenet versions 2.1.3 dated 2020-05-10 and 2.1.4 dated 2021-07-17
ChangeLog | 7 +++++++ DESCRIPTION | 8 ++++---- MD5 | 35 ++++++++++++++++++----------------- R/snapclust.R | 21 ++++++++++++++++++--- R/snapclust.choose.k.R | 17 ++++++++++++++--- README.md | 9 +++++---- build |only data/H3N2.rda |binary data/dapcIllus.rda |binary data/eHGDP.rda |binary data/hybridtoy.RData |binary data/microbov.rda |binary data/nancycats.rda |binary data/rupica.RData |binary data/sim2pop.rda |binary data/spcaIllus.rda |binary data/swallowtails.rda |binary man/snapclust.Rd | 21 +++++++++++++++++++-- man/snapclust.choose.k.Rd | 16 ++++++++++++++-- 19 files changed, 99 insertions(+), 35 deletions(-)
Title: Flexible Framework for Simulating Community Assembly
Description: Flexible framework for trait-based simulation of community assembly, where components could be replaced by user-defined function and that
allows variation of traits within species.
Author: Zoltan Botta-Dukat
Maintainer: Zoltan Botta-Dukat <botta-dukat.zoltan@okologia.mta.hu>
Diff between comsimitv versions 0.1.4 dated 2020-10-22 and 0.1.5 dated 2021-07-17
DESCRIPTION | 9 - MD5 | 44 ++++---- R/Gaussian.competition.kernel.R | 10 + R/Gaussian.tolerance.R | 8 - R/Gener.species.pool.R | 57 ++++++---- R/MetaCom.Dispersal.R | 9 + R/SeedProduction.R | 18 ++- R/asymmetric.competition.kernel.R | 12 +- R/comm.simul.R | 40 +++---- R/randomITV.R | 70 ++++++------- build/partial.rdb |only build/vignette.rds |binary inst/doc/competition.R | 184 +++++++++++++++++------------------ inst/doc/competition.Rmd | 2 inst/doc/competition.pdf |binary man/Gaussian.competition.kernel.Rd | 13 +- man/Gaussian.tolerance.Rd | 12 +- man/Gener.species.pool.Rd | 18 +-- man/SeedProduction.Rd | 12 +- man/asymmetric.competition.kernel.Rd | 9 + man/comm.simul.Rd | 5 man/randomITV.Rd | 10 + vignettes/competition.Rmd | 2 vignettes/competition.html |only 24 files changed, 299 insertions(+), 245 deletions(-)
Title: Neat and Painless Statistical Reporting
Description: User-friendly, clear and simple statistics, primarily for
publication in psychological science. The main functions are wrappers for
other packages, but there are various additions as well. Every relevant step
from data aggregation to reportable printed statistics is covered for basic
experimental designs.
Author: Gáspár Lukács [aut, cre] (<https://orcid.org/0000-0001-9401-4830>),
Bennett Kleinberg [ctb] (<https://orcid.org/0000-0003-1658-9086>),
Johnny van Doorn [ctb] (<https://orcid.org/0000-0003-0270-096X>)
Maintainer: Gáspár Lukács <lkcsgaspar@gmail.com>
Diff between neatStats versions 1.5.1 dated 2020-10-08 and 1.7.2 dated 2021-07-17
DESCRIPTION | 17 - MD5 | 40 +-- R/anova_neat.R | 24 +- R/dems_neat.R | 127 ++++++++-- R/internal.R | 61 ++++- R/plot_neat.R | 54 +++- R/props_neat.R | 633 +++++++++++++++++++++++++++++++++++++++++++----------- R/rbind_loop.R | 6 R/roc_neat.R | 190 +++++++++++++--- R/t_neat.R | 190 ++++++++++------ R/var_tests.R | 2 README.md | 13 - build/partial.rdb |binary man/anova_neat.Rd | 9 man/dems_neat.Rd | 50 +++- man/plot_neat.Rd | 16 - man/props_neat.Rd | 223 ++++++++++++++++--- man/rbind_loop.Rd | 2 man/roc_neat.Rd | 50 +++- man/t_neat.Rd | 64 +++-- man/var_tests.Rd | 2 21 files changed, 1382 insertions(+), 391 deletions(-)
Title: Simulate and Estimate Close-Kin Dispersal Kernels
Description: Functions for simulating and estimating kinship-related dispersal. Based
on the methods described in M. Jasper, T.L. Schmidt., N.W. Ahmad, S.P. Sinkins & A.A.
Hoffmann (2019) <doi:10.1111/1755-0998.13043> "A genomic approach to inferring kinship
reveals limited intergenerational dispersal in the yellow fever mosquito".
Assumes an additive variance model of dispersal in two dimensions, compatible with
Wright's neighbourhood area. Simple and composite dispersal simulations are supplied,
as well as the functions needed to estimate parent-offspring dispersal for simulated or
empirical data, and to undertake sampling design for future field studies of dispersal.
For ease of use an integrated Shiny app is also included.
Author: Moshe-Elijah Jasper [aut, cre]
(<https://orcid.org/0000-0003-4541-3223>)
Maintainer: Moshe-Elijah Jasper <moshe.jasper@unimelb.edu.au>
Diff between kindisperse versions 0.9.2 dated 2021-03-31 and 0.10.1 dated 2021-07-17
kindisperse-0.10.1/kindisperse/DESCRIPTION | 13 kindisperse-0.10.1/kindisperse/MD5 | 178 +- kindisperse-0.10.1/kindisperse/NAMESPACE | 31 kindisperse-0.10.1/kindisperse/NEWS.md | 18 kindisperse-0.10.1/kindisperse/R/DispersalModel.R |only kindisperse-0.10.1/kindisperse/R/KinPairData.R | 132 + kindisperse-0.10.1/kindisperse/R/KinPairSimulation.R | 392 +++-- kindisperse-0.10.1/kindisperse/R/app.R | 22 kindisperse-0.10.1/kindisperse/R/app_ports.R | 93 + kindisperse-0.10.1/kindisperse/R/axial_helper_functions.R | 132 + kindisperse-0.10.1/kindisperse/R/axials_standard.R | 183 ++ kindisperse-0.10.1/kindisperse/R/dispersal_model.R |only kindisperse-0.10.1/kindisperse/R/export_functions.R | 65 kindisperse-0.10.1/kindisperse/R/import_kinpairs.R | 34 kindisperse-0.10.1/kindisperse/R/sample_kindist.R | 83 + kindisperse-0.10.1/kindisperse/R/simgraph_data.R | 1 kindisperse-0.10.1/kindisperse/R/simgraph_graph.R | 1 kindisperse-0.10.1/kindisperse/R/simulate_kindist_composite.R | 71 - kindisperse-0.10.1/kindisperse/R/simulate_kindist_custom.R |only kindisperse-0.10.1/kindisperse/R/simulate_kindist_simple.R | 57 kindisperse-0.10.1/kindisperse/README.md | 673 +++++++++- kindisperse-0.10.1/kindisperse/build/partial.rdb |binary kindisperse-0.10.1/kindisperse/build/vignette.rds |binary kindisperse-0.10.1/kindisperse/inst/doc/using-kindisperse.R | 57 kindisperse-0.10.1/kindisperse/inst/doc/using-kindisperse.Rmd | 213 +++ kindisperse-0.10.1/kindisperse/inst/doc/using-kindisperse.html | 621 ++++++--- kindisperse-0.10.1/kindisperse/man/DispersalModel-class.Rd |only kindisperse-0.10.1/kindisperse/man/KinPairData-class.Rd | 177 +- kindisperse-0.10.1/kindisperse/man/KinPairSimulation-class.Rd | 417 ++---- kindisperse-0.10.1/kindisperse/man/KinPairSimulation_composite.Rd | 5 kindisperse-0.10.1/kindisperse/man/KinPairSimulation_custom.Rd |only kindisperse-0.10.1/kindisperse/man/KinPairSimulation_simple.Rd | 5 kindisperse-0.10.1/kindisperse/man/access_sigmas.Rd |only kindisperse-0.10.1/kindisperse/man/axials.Rd | 15 kindisperse-0.10.1/kindisperse/man/axials_add.Rd | 9 kindisperse-0.10.1/kindisperse/man/axials_decompose.Rd | 13 kindisperse-0.10.1/kindisperse/man/axials_standard.Rd | 71 - kindisperse-0.10.1/kindisperse/man/axials_subtract.Rd | 9 kindisperse-0.10.1/kindisperse/man/axpermute.Rd | 15 kindisperse-0.10.1/kindisperse/man/axpermute_standard.Rd | 71 - kindisperse-0.10.1/kindisperse/man/axpermute_subtract.Rd | 16 kindisperse-0.10.1/kindisperse/man/breeding_cycle.Rd |only kindisperse-0.10.1/kindisperse/man/breeding_stage.Rd |only kindisperse-0.10.1/kindisperse/man/check_valid_kinship.Rd | 4 kindisperse-0.10.1/kindisperse/man/check_valid_lifestage.Rd | 4 kindisperse-0.10.1/kindisperse/man/csv_to_kinpair.Rd | 20 kindisperse-0.10.1/kindisperse/man/df_to_kinpair.Rd | 20 kindisperse-0.10.1/kindisperse/man/dispersal_model.Rd |only kindisperse-0.10.1/kindisperse/man/dispersal_vector.Rd |only kindisperse-0.10.1/kindisperse/man/display_appdata.Rd | 20 kindisperse-0.10.1/kindisperse/man/distances.Rd | 22 kindisperse-0.10.1/kindisperse/man/elongate.Rd | 6 kindisperse-0.10.1/kindisperse/man/figures/README-graphical_simulation-1.png |binary kindisperse-0.10.1/kindisperse/man/figures/README-simgraphhist-1.png |binary kindisperse-0.10.1/kindisperse/man/figures/README-simgraphpin-1.png |binary kindisperse-0.10.1/kindisperse/man/filter_methods.Rd |only kindisperse-0.10.1/kindisperse/man/filtertype.Rd | 23 kindisperse-0.10.1/kindisperse/man/fs.Rd |only kindisperse-0.10.1/kindisperse/man/get_dispersal_model.Rd |only kindisperse-0.10.1/kindisperse/man/hs.Rd |only kindisperse-0.10.1/kindisperse/man/is.DispersalModel.Rd |only kindisperse-0.10.1/kindisperse/man/kernelshape.Rd | 24 kindisperse-0.10.1/kindisperse/man/kerneltype.Rd | 31 kindisperse-0.10.1/kindisperse/man/kin_pair_data.Rd |only kindisperse-0.10.1/kindisperse/man/kin_pair_simulation.Rd |only kindisperse-0.10.1/kindisperse/man/kinpair_to_csv.Rd | 17 kindisperse-0.10.1/kindisperse/man/kinpair_to_tibble.Rd | 10 kindisperse-0.10.1/kindisperse/man/kinpair_to_tsv.Rd | 17 kindisperse-0.10.1/kindisperse/man/kinship.Rd | 33 kindisperse-0.10.1/kindisperse/man/lifestage.Rd | 29 kindisperse-0.10.1/kindisperse/man/mount_appdata.Rd | 25 kindisperse-0.10.1/kindisperse/man/read_kindata.Rd | 18 kindisperse-0.10.1/kindisperse/man/rebase_dims.Rd | 2 kindisperse-0.10.1/kindisperse/man/reset_appdata.Rd | 19 kindisperse-0.10.1/kindisperse/man/reset_tempdata.Rd | 19 kindisperse-0.10.1/kindisperse/man/retrieve_appdata.Rd | 26 kindisperse-0.10.1/kindisperse/man/retrieve_tempdata.Rd | 22 kindisperse-0.10.1/kindisperse/man/retrieveall_appdata.Rd | 27 kindisperse-0.10.1/kindisperse/man/sample_kindist.Rd | 74 - kindisperse-0.10.1/kindisperse/man/sampling_stage.Rd |only kindisperse-0.10.1/kindisperse/man/simdims.Rd | 23 kindisperse-0.10.1/kindisperse/man/simgraph_data.Rd | 5 kindisperse-0.10.1/kindisperse/man/simgraph_graph.Rd | 5 kindisperse-0.10.1/kindisperse/man/simtype.Rd | 31 kindisperse-0.10.1/kindisperse/man/simulate_kindist_composite.Rd | 66 kindisperse-0.10.1/kindisperse/man/simulate_kindist_custom.Rd |only kindisperse-0.10.1/kindisperse/man/simulate_kindist_simple.Rd | 58 kindisperse-0.10.1/kindisperse/man/stages.Rd |only kindisperse-0.10.1/kindisperse/man/tsv_to_kinpair.Rd | 20 kindisperse-0.10.1/kindisperse/man/unmount_appdata.Rd | 23 kindisperse-0.10.1/kindisperse/man/vector_to_kinpair.Rd | 14 kindisperse-0.10.1/kindisperse/man/visible_stage.Rd |only kindisperse-0.10.1/kindisperse/man/write_kindata.Rd | 18 kindisperse-0.10.1/kindisperse/vignettes/using-kindisperse.Rmd | 213 +++ kindisperse-0.9.2/kindisperse/man/KinPairData.Rd |only kindisperse-0.9.2/kindisperse/man/KinPairSimulation.Rd |only kindisperse-0.9.2/kindisperse/man/breedsigma-set.Rd |only kindisperse-0.9.2/kindisperse/man/filtertype-set.Rd |only kindisperse-0.9.2/kindisperse/man/gravsigma-set.Rd |only kindisperse-0.9.2/kindisperse/man/initsigma-set.Rd |only kindisperse-0.9.2/kindisperse/man/kerneltype-set.Rd |only kindisperse-0.9.2/kindisperse/man/ovisigma-set.Rd |only kindisperse-0.9.2/kindisperse/man/posigma-set.Rd |only kindisperse-0.9.2/kindisperse/man/posigma.Rd |only kindisperse-0.9.2/kindisperse/man/simdims-set.Rd |only kindisperse-0.9.2/kindisperse/man/simtype-set.Rd |only kindisperse-0.9.2/kindisperse/man/upper.Rd |only 107 files changed, 3875 insertions(+), 1006 deletions(-)
Title: Simple Fisheries Stock Assessment Methods
Description: A variety of simple fish stock assessment methods.
Detailed vignettes are available on the fishR website <http://derekogle.com/fishR/>.
Author: Derek Ogle [aut, cre] (<https://orcid.org/0000-0002-0370-9299>),
Jason Doll [aut],
Powell Wheeler [aut],
Alexis Dinno [aut] (Provided base functionality of dunnTest())
Maintainer: Derek Ogle <derek@derekogle.com>
Diff between FSA versions 0.9.0 dated 2021-06-09 and 0.9.1 dated 2021-07-17
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 3 +++ inst/CITATION | 5 +++-- tests/testthat/testthat_catchCurve.R | 22 +++++++++++----------- 5 files changed, 25 insertions(+), 21 deletions(-)
Title: Bias Reduction in Generalized Linear Models
Description: Estimation and inference from generalized linear models based on various methods for bias reduction and maximum penalized likelihood with powers of the Jeffreys prior as penalty. The 'brglmFit' fitting method can achieve reduction of estimation bias by solving either the mean bias-reducing adjusted score equations in Firth (1993) <doi:10.1093/biomet/80.1.27> and Kosmidis and Firth (2009) <doi:10.1093/biomet/asp055>, or the median bias-reduction adjusted score equations in Kenne et al. (2017) <doi:10.1093/biomet/asx046>, or through the direct subtraction of an estimate of the bias of the maximum likelihood estimator from the maximum likelihood estimates as in Cordeiro and McCullagh (1991) <https://www.jstor.org/stable/2345592>. See Kosmidis et al (2020) <doi:10.1007/s11222-019-09860-6> for more details. Estimation in all cases takes place via a quasi Fisher scoring algorithm, and S3 methods for the construction of of confidence intervals for the reduced-bias estimates are provided. In the special case of generalized linear models for binomial and multinomial responses (both ordinal and nominal), the adjusted score approaches to mean and media bias reduction have been found to return estimates with improved frequentist properties, that are also always finite, even in cases where the maximum likelihood estimates are infinite (e.g. complete and quasi-complete separation; see Kosmidis and Firth, 2020 <doi:10.1093/biomet/asaa052>, for a proof for mean bias reduction in logistic regression).
Author: Ioannis Kosmidis [aut, cre] (<https://orcid.org/0000-0003-1556-0302>),
Euloge Clovis Kenne Pagui [aut],
Kjell Konis [ctb],
Nicola Sartori [ctb]
Maintainer: Ioannis Kosmidis <ioannis.kosmidis@warwick.ac.uk>
Diff between brglm2 versions 0.7.1 dated 2021-01-22 and 0.8.0 dated 2021-07-17
brglm2-0.7.1/brglm2/R/check_infinite_estimates.R |only brglm2-0.7.1/brglm2/R/detect_separation.R |only brglm2-0.7.1/brglm2/R/separator.R |only brglm2-0.7.1/brglm2/inst/doc/separation.R |only brglm2-0.7.1/brglm2/inst/doc/separation.Rmd |only brglm2-0.7.1/brglm2/inst/doc/separation.html |only brglm2-0.7.1/brglm2/man/check_infinite_estimates.Rd |only brglm2-0.7.1/brglm2/man/check_infinite_estimates.glm.Rd |only brglm2-0.7.1/brglm2/man/detect_separation.Rd |only brglm2-0.7.1/brglm2/man/detect_separation_control.Rd |only brglm2-0.7.1/brglm2/vignettes/separation.Rmd |only brglm2-0.8.0/brglm2/DESCRIPTION | 14 brglm2-0.8.0/brglm2/MD5 | 94 +- brglm2-0.8.0/brglm2/NAMESPACE | 19 brglm2-0.8.0/brglm2/NEWS.md | 31 brglm2-0.8.0/brglm2/R/bracl.R | 72 -- brglm2-0.8.0/brglm2/R/brglm2-defunct.R |only brglm2-0.8.0/brglm2/R/brglm2-package.R | 96 ++ brglm2-0.8.0/brglm2/R/brglmControl.R | 12 brglm2-0.8.0/brglm2/R/brglmFit.R | 34 brglm2-0.8.0/brglm2/R/brmultinom.R | 119 ++- brglm2-0.8.0/brglm2/R/brnb.R |only brglm2-0.8.0/brglm2/R/data.R | 4 brglm2-0.8.0/brglm2/R/mis-link.R | 15 brglm2-0.8.0/brglm2/R/ordinal_superiority.R |only brglm2-0.8.0/brglm2/R/utils.R | 2 brglm2-0.8.0/brglm2/R/warnings.R | 40 + brglm2-0.8.0/brglm2/R/zzz_conventions.R | 26 brglm2-0.8.0/brglm2/build/partial.rdb |binary brglm2-0.8.0/brglm2/build/vignette.rds |binary brglm2-0.8.0/brglm2/inst/CITATION | 2 brglm2-0.8.0/brglm2/inst/doc/adjacent.R | 6 brglm2-0.8.0/brglm2/inst/doc/adjacent.Rmd | 14 brglm2-0.8.0/brglm2/inst/doc/adjacent.html | 503 ++++---------- brglm2-0.8.0/brglm2/inst/doc/iteration.Rmd | 12 brglm2-0.8.0/brglm2/inst/doc/iteration.html | 292 +------- brglm2-0.8.0/brglm2/inst/doc/multinomial.R | 3 brglm2-0.8.0/brglm2/inst/doc/multinomial.Rmd | 11 brglm2-0.8.0/brglm2/inst/doc/multinomial.html | 567 +++++----------- brglm2-0.8.0/brglm2/inst/doc/negativeBinomial.R |only brglm2-0.8.0/brglm2/inst/doc/negativeBinomial.Rmd |only brglm2-0.8.0/brglm2/inst/doc/negativeBinomial.html |only brglm2-0.8.0/brglm2/man/brglm2-defunct.Rd |only brglm2-0.8.0/brglm2/man/brglm2.Rd | 4 brglm2-0.8.0/brglm2/man/brglmControl.Rd | 10 brglm2-0.8.0/brglm2/man/brglmFit.Rd | 20 brglm2-0.8.0/brglm2/man/brnb.Rd |only brglm2-0.8.0/brglm2/man/coef.brnb.Rd |only brglm2-0.8.0/brglm2/man/confint.brnb.Rd |only brglm2-0.8.0/brglm2/man/endometrial.Rd | 4 brglm2-0.8.0/brglm2/man/ordinal_superiority.Rd |only brglm2-0.8.0/brglm2/man/print.summary.brnb.Rd |only brglm2-0.8.0/brglm2/man/simulate.brmultinom.Rd |only brglm2-0.8.0/brglm2/man/simulate.brnb.Rd |only brglm2-0.8.0/brglm2/man/summary.brnb.Rd |only brglm2-0.8.0/brglm2/man/vcov.brnb.Rd |only brglm2-0.8.0/brglm2/src |only brglm2-0.8.0/brglm2/vignettes/adjacent.Rmd | 14 brglm2-0.8.0/brglm2/vignettes/brglm2.bib | 26 brglm2-0.8.0/brglm2/vignettes/iteration.Rmd | 12 brglm2-0.8.0/brglm2/vignettes/multinomial.Rmd | 11 brglm2-0.8.0/brglm2/vignettes/negativeBinomial.Rmd |only 62 files changed, 902 insertions(+), 1187 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-02-16 0.0-4
2019-03-29 0.0-3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-01-16 0.0-7
2018-09-13 0.0-6
2018-08-05 0.0-5.1
2018-03-11 0.0-5
Title: Extend 'tinytest' with 'diffobj'
Description: The 'tinytest' package offers a light-weight zero-dependency unit-testing
framework to which this package adds support of the 'diffobj' package for 'diff'-style
comparison of R objects.
Author: Dirk Eddelbuettel and Alton Barbehenn
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between ttdo versions 0.0.7 dated 2021-07-06 and 0.0.8 dated 2021-07-17
ChangeLog | 9 +++++++++ DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/expectations_xl.R | 1 + inst/NEWS.Rd | 6 ++++++ 5 files changed, 24 insertions(+), 8 deletions(-)
Title: Identification and Classification of the Most Influential Nodes
Description: Contains functions for the classification and ranking of top candidate features, reconstruction of networks from
adjacency matrices and data frames, analysis of the topology of the network
and calculation of centrality measures, and identification of the most
influential nodes. Also, a function is provided for running SIRIR model, which
is the combination of leave-one-out cross validation technique and the conventional SIR model, on a network to unsupervisedly rank the true influence of vertices. Additionally, some functions have been provided for the assessment
of dependence and correlation of two network centrality measures as well as
the conditional probability of deviation from their corresponding means in opposite direction.
Fred Viole and David Nawrocki (2013, ISBN:1490523995).
Csardi G, Nepusz T (2006). "The igraph software package for complex network research." InterJournal, Complex Systems, 1695.
Adopted algorithms and sources are referenced in function document.
Author: Adrian (Abbas) Salavaty [aut, cre], Mirana Ramialison [ths], Peter D. Currie [ths]
Maintainer: Adrian Salavaty <abbas.salavaty@gmail.com>
Diff between influential versions 2.2.2 dated 2021-04-30 and 2.2.3 dated 2021-07-17
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 7 +++++-- R/functions.R | 22 ++++++++-------------- README.md | 1 - inst/ShinyApps/ExIR/app.R | 18 ++++++------------ inst/doc/Vignettes.html | 4 ++-- man/influential-package.Rd | 4 ++-- 8 files changed, 33 insertions(+), 43 deletions(-)
Title: Plot a Model's Residuals, Response, and Partial Dependence Plots
Description: Plot model surfaces for a wide variety of models
using partial dependence plots and other techniques.
Also plot model residuals and other information on the model.
Author: Stephen Milborrow
Maintainer: Stephen Milborrow <milbo@sonic.net>
Diff between plotmo versions 3.6.0 dated 2020-09-13 and 3.6.1 dated 2021-07-17
DESCRIPTION | 7 MD5 | 99 ++++++------ NEWS | 6 R/lib.R | 2 R/singles.R | 4 R/stop.if.dots.R | 9 - R/xy.R | 2 inst/doc/modguide.pdf |binary inst/doc/plotmo-notes.pdf |binary inst/doc/plotres-notes.pdf |binary inst/slowtests/make.README.bat | 2 inst/slowtests/makeclean.bat |only inst/slowtests/test.c50.bat | 2 inst/slowtests/test.caret.Rout.save | 3 inst/slowtests/test.caret.bat | 2 inst/slowtests/test.center.bat | 2 inst/slowtests/test.degree.bat | 2 inst/slowtests/test.dots.bat | 2 inst/slowtests/test.fac.bat | 2 inst/slowtests/test.gbm.bat | 2 inst/slowtests/test.glmnet.Rout.save | 5 inst/slowtests/test.glmnet.bat | 2 inst/slowtests/test.glmnetUtils.bat | 2 inst/slowtests/test.linmod.R | 4 inst/slowtests/test.linmod.Rout.save | 24 +-- inst/slowtests/test.linmod.bat | 2 inst/slowtests/test.mlr.R | 1 inst/slowtests/test.mlr.Rout.save | 7 inst/slowtests/test.mlr.bat | 2 inst/slowtests/test.modguide.bat | 2 inst/slowtests/test.non.earth.R | 2 inst/slowtests/test.non.earth.Rout.save | 32 +++- inst/slowtests/test.non.earth.bat | 2 inst/slowtests/test.parsnip.R | 33 ++-- inst/slowtests/test.parsnip.Rout.save | 90 +++-------- inst/slowtests/test.parsnip.bat | 2 inst/slowtests/test.partdep.bat | 2 inst/slowtests/test.partykit.bat | 2 inst/slowtests/test.plotmo.Rout.save | 2 inst/slowtests/test.plotmo.args.bat | 2 inst/slowtests/test.plotmo.bat | 2 inst/slowtests/test.plotmo.dots.bat | 2 inst/slowtests/test.plotmo.x.bat | 2 inst/slowtests/test.plotmo3.R | 134 ++++++++-------- inst/slowtests/test.plotmo3.Rout.save | 255 +++++++++++++++++++------------- inst/slowtests/test.plotmo3.bat | 2 inst/slowtests/test.plotres.bat | 2 inst/slowtests/test.pre.Rout.save | 2 inst/slowtests/test.pre.bat | 2 inst/slowtests/test.printcall.bat | 2 inst/slowtests/test.unusual.vars.bat | 2 51 files changed, 424 insertions(+), 351 deletions(-)
Title: Curve Text Elements in 'Shiny' Using 'CircleType.js'
Description: Enables curving text elements in 'Shiny' apps.
Author: Etienne Bacher [aut, cre, cph]
Maintainer: Etienne Bacher <etienne.bacher@protonmail.com>
Diff between circletyper versions 1.0.0 dated 2021-01-20 and 1.0.1 dated 2021-07-17
DESCRIPTION | 7 +++---- MD5 | 5 +++-- NEWS.md |only README.md | 12 ++++++++---- 4 files changed, 14 insertions(+), 10 deletions(-)
Title: Download and Explore Datasets from UCSC Xena Data Hubs
Description: Download and explore datasets from UCSC Xena data hubs, which are
a collection of UCSC-hosted public databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others.
Databases are normalized so they can be combined, linked, filtered, explored and downloaded.
Author: Shixiang Wang [aut, cre] (<https://orcid.org/0000-0001-9855-7357>),
Xue-Song Liu [aut] (<https://orcid.org/0000-0002-7736-0077>),
Martin Morgan [ctb],
Christine Stawitz [rev] (Christine reviewed the package for ropensci,
see <https://github.com/ropensci/software-review/issues/315>),
Carl Ganz [rev] (Carl reviewed the package for ropensci, see
<https://github.com/ropensci/software-review/issues/315>)
Maintainer: Shixiang Wang <w_shixiang@163.com>
Diff between UCSCXenaTools versions 1.4.5 dated 2021-05-27 and 1.4.6 dated 2021-07-17
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- NEWS.md | 7 ++++++- R/XenaDownload.R | 3 ++- R/XenaQuery.R | 17 ++++++++++++++++- R/fetch.R | 13 +++++++++++++ README.md | 14 +++++++------- build/vignette.rds |binary inst/doc/USCSXenaTools.Rmd | 2 +- inst/doc/USCSXenaTools.html | 13 +++++++------ vignettes/USCSXenaTools.Rmd | 2 +- 11 files changed, 66 insertions(+), 31 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-06-09 1.1
2011-09-20 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-06-18 1.0.5
2017-11-13 1.0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-04-12 0.1-2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-02-08 2.0.9
2017-01-16 2.0.8
2015-01-30 2.0.6
2014-06-23 2.0.5
2014-02-25 2.0.4
2013-08-23 2.0.3
2013-01-14 1.9.9
2012-08-31 1.9.8
2012-04-19 1.9.7
2011-11-07 1.9.4
2011-09-06 1.9.3
2011-06-02 1.9.1
2011-05-30 1.9
2011-04-06 1.8
2011-02-08 1.7
2011-01-14 1.6
2010-11-08 1.5
2009-01-22 1.4
2007-05-16 1.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-11-18 2.3.0
2020-02-11 2.2.1
2020-01-14 2.2.0
2019-04-15 2.1.0
2019-02-19 2.0.10
2018-11-08 2.0.9
2018-05-29 2.0.8
2018-04-08 2.0.7
2017-08-14 2.0.6
2017-07-12 2.0.5
2017-01-11 2.0.3
2016-08-22 2.0.2
2016-02-08 2.0.0
2015-05-06 1.9.1
2014-08-18 1.9.0
2014-03-16 1.8.0
2014-02-07 1.7.0
2013-11-26 1.6.4
2013-02-27 1.6.3
2013-01-11 1.6.2
2012-05-15 1.6.0
2011-05-06 1.5.0
2011-01-11 1.4.4
2010-08-16 1.4.3
2010-07-05 1.4.2
2010-06-21 1.4.1
2010-04-06 1.4.0
2010-01-18 1.3.3
2009-11-29 1.3.2
2009-05-08 1.2.2
2009-03-06 1.2
2009-01-20 1.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-05-28 2.1.0
2021-01-21 2.0.1
Title: Helpers for Developing Command Line Interfaces
Description: A suite of tools to build attractive command line interfaces
('CLIs'), from semantic elements: headings, lists, alerts, paragraphs,
etc. Supports custom themes via a 'CSS'-like language. It also contains a
number of lower level 'CLI' elements: rules, boxes, trees, and
'Unicode' symbols with 'ASCII' alternatives. It support ANSI colors and
text styles as well.
Author: Gábor Csárdi [aut, cre],
Hadley Wickham [ctb],
Kirill Müller [ctb],
RStudio [cph]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between cli versions 3.0.0 dated 2021-06-30 and 3.0.1 dated 2021-07-17
DESCRIPTION | 6 ++--- MD5 | 31 ++++++++++++++-------------- NEWS.md | 5 ++++ R/ansiex.R | 4 +-- R/cli.R | 5 ++-- R/onload.R | 13 +++++++---- R/progress-server.R | 9 +++++++- R/rlang.R | 2 - R/test.R | 9 +++++--- man/cli_abort.Rd | 2 - man/format_inline.Rd | 4 ++- man/test_that_cli.Rd | 9 +++++--- src/thread.c | 31 ++++++++++++++++++++++------ tests/testthat/_snaps/progress-variables.md | 5 +++- tests/testthat/_snaps/rlang-errors.new.md |only tests/testthat/test-progress-c.R | 3 ++ tests/testthat/test-progress-message.R | 8 +++++++ 17 files changed, 102 insertions(+), 44 deletions(-)
Title: Linear Networks Functionality of the 'spatstat' Family
Description: Defines types of spatial data on a linear network
and provides functionality for geometrical operations,
data analysis and modelling of data on a linear network,
in the 'spatstat' family of packages.
Contains definitions and support for linear networks, including creation of networks, geometrical measurements, topological connectivity, geometrical operations such as inserting and deleting vertices, intersecting a network with another object, and interactive editing of networks.
Data types defined on a network include point patterns, pixel images, functions, and tessellations.
Exploratory methods include kernel estimation of intensity on a network, K-functions and pair correlation functions on a network, simulation envelopes, nearest neighbour distance and empty space distance, relative risk estimation with cross-validated bandwidth selection. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Monte Carlo, Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Monte Carlo) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov, ANOVA) are also supported.
Parametric models can be fitted to point pattern data using the function lppm() similar to glm(). Only Poisson models are implemented so far. Models may involve dependence on covariates and dependence on marks. Models are fitted by maximum likelihood.
Fitted point process models can be simulated, automatically. Formal hypothesis tests of a fitted model are supported (likelihood ratio test, analysis of deviance, Monte Carlo tests) along with basic tools for model selection (stepwise(), AIC()) and variable selection (sdr). Tools for validating the fitted model include simulation envelopes, residuals, residual plots and Q-Q plots, leverage and influence diagnostics, partial residuals, and added variable plots.
Random point patterns on a network can be generated using a variety of models.
Author: Adrian Baddeley [aut, cre],
Rolf Turner [aut],
Ege Rubak [aut],
Ottmar Cronie [ctb],
Tilman Davies [ctb],
Greg McSwiggan [ctb],
Suman Rakshit [ctb]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.linnet versions 2.2-1 dated 2021-06-22 and 2.3-0 dated 2021-07-17
DESCRIPTION | 12 ++++++------ MD5 | 30 ++++++++++++++++++------------ NAMESPACE | 10 +++++++++- NEWS | 44 ++++++++++++++++++++++++++++++++++++++++++++ R/Math.linim.R | 8 ++++++-- R/Math.linimlist.R | 4 +++- R/densitylppVoronoi.R | 4 ++-- R/lppm.R | 1 + R/perspex.R |only R/sdr.R |only inst/doc/packagesizes.txt | 1 + man/methods.lppm.Rd | 34 ++++++++++++++++++++-------------- man/persp.linfun.Rd |only man/persp.linim.Rd |only man/sdr.lpp.Rd |only src/depthrel.c |only src/init.c | 9 ++++++++- src/proto.h | 1 + tests/testsL.R | 9 ++++++++- 19 files changed, 127 insertions(+), 40 deletions(-)
More information about spatstat.linnet at CRAN
Permanent link
Title: Dot-and-Whisker Plots of Regression Results
Description: Quick and easy dot-and-whisker plots of regression results.
Author: Frederick Solt [aut],
Yue Hu [aut, cre],
Os Keyes [ctb],
Ben Bolker [ctb],
Stefan Müller [ctb],
Thomas Leeper [ctb],
Chris Wallace [ctb],
Christopher Warshaw [ctb]
Maintainer: Yue Hu <yuehu@tsinghua.edu.cn>
Diff between dotwhisker versions 0.6.0 dated 2021-02-17 and 0.7.0 dated 2021-07-17
DESCRIPTION | 11 LICENSE | 4 MD5 | 44 +- NAMESPACE | 3 NEWS.md | 12 R/add_brackets.R | 10 R/by_2sd.R | 2 R/dwplot.R | 39 +- R/relabel_predictors.R | 4 R/secret_weapon.R | 6 R/small_multiple.R | 8 build/vignette.rds |binary inst/doc/dotwhisker-vignette.R | 502 +++++++++++++++++++------------- inst/doc/dotwhisker-vignette.Rmd | 511 ++++++++++++++++++++------------- inst/doc/dotwhisker-vignette.html | 585 ++++++++++++++++++++++---------------- inst/doc/kl2007_examples.html | 20 - man/add_brackets.Rd | 9 man/by_2sd.Rd | 2 man/dwplot.Rd | 22 - man/relabel_predictors.Rd | 2 man/secret_weapon.Rd | 6 man/small_multiple.Rd | 8 vignettes/dotwhisker-vignette.Rmd | 511 ++++++++++++++++++++------------- 23 files changed, 1410 insertions(+), 911 deletions(-)
Title: The Complete R6 Probability Distributions Interface
Description: An R6 object oriented distributions package. Unified interface for 42 probability distributions and 11 kernels including functionality for multiple scientific types. Additionally functionality for composite distributions and numerical imputation. Design patterns including wrappers and decorators are described in Gamma et al. (1994, ISBN:0-201-63361-2). For quick reference of probability distributions including d/p/q/r functions and results we refer to McLaughlin, M. P. (2001). Additionally Devroye (1986, ISBN:0-387-96305-7) for sampling the Dirichlet distribution, Gentle (2009) <doi:10.1007/978-0-387-98144-4> for sampling the Multivariate Normal distribution and Michael et al. (1976) <doi:10.2307/2683801> for sampling the Wald distribution.
Author: Raphael Sonabend [aut, cre] (<https://orcid.org/0000-0001-9225-4654>),
Franz Kiraly [aut],
Peter Ruckdeschel [ctb] (Author of distr),
Matthias Kohl [ctb] (Author of distr),
Nurul Ain Toha [ctb],
Shen Chen [ctb],
Jordan Deenichin [ctb],
Chengyang Gao [ctb],
Chloe Zhaoyuan Gu [ctb],
Yunjie He [ctb],
Xiaowen Huang [ctb],
Shuhan Liu [ctb],
Runlong Yu [ctb],
Chijing Zeng [ctb],
Qian Zhou [ctb]
Maintainer: Raphael Sonabend <raphaelsonabend@gmail.com>
Diff between distr6 versions 1.5.4 dated 2021-07-14 and 1.5.6 dated 2021-07-17
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 8 ++++++++ inst/doc/distr6.html | 4 ++-- tests/testthat/test_asDistribution.R | 13 +++---------- 5 files changed, 20 insertions(+), 19 deletions(-)
Title: Isolation-Based Outlier Detection
Description: Fast and multi-threaded implementation of
isolation forest (Liu, Ting, Zhou (2008) <doi:10.1109/ICDM.2008.17>),
extended isolation forest (Hariri, Kind, Brunner (2018) <arXiv:1811.02141>),
SCiForest (Liu, Ting, Zhou (2010) <doi:10.1007/978-3-642-15883-4_18>),
and fair-cut forest (Cortes (2019) <arXiv:1911.06646>),
for isolation-based outlier detection, clustered outlier detection, distance or similarity
approximation (Cortes (2019) <arXiv:1910.12362>),
and imputation of missing values (Cortes (2019) <arXiv:1911.06646>),
based on random or guided decision tree splitting. Provides simple heuristics for fitting the model to
categorical columns and handling missing data, and offers options for varying between random and guided
splits, and for using different splitting criteria.
Author: David Cortes
Maintainer: David Cortes <david.cortes.rivera@gmail.com>
Diff between isotree versions 0.2.8 dated 2021-07-11 and 0.2.10 dated 2021-07-17
DESCRIPTION | 6 MD5 | 44 +-- R/RcppExports.R | 4 R/isoforest.R | 17 + man/isolation.forest.Rd | 4 man/predict.isolation_forest.Rd | 3 src/RcppExports.cpp | 15 + src/Rwrapper.cpp | 39 +-- src/crit.h | 44 ++- src/dist.h | 104 ++++++-- src/extended.h | 41 ++- src/fit_model.h | 233 ++++++++++-------- src/helpers_iforest.h | 65 ++--- src/impute.h | 134 ++++++---- src/instantiate_model.h | 4 src/isoforest.h | 157 +++++++++--- src/isotree.h | 66 +++-- src/merge_models.cpp | 72 +++-- src/mult.h | 36 +- src/other_helpers.h | 5 src/predict.h | 509 ++++++++++++++++++++++++++-------------- src/sql.cpp | 123 ++++++--- src/utils.h | 66 +++-- 23 files changed, 1187 insertions(+), 604 deletions(-)
Title: Get Swiss Federal and Cantonal Vote Results from Opendata.swiss
Description: Builds upon the real time data service as well as the archive for national votes <https://opendata.swiss/api/3/action/package_show?id=echtzeitdaten-am-abstimmungstag-zu-eidgenoessischen-abstimmungsvorlagen> and cantonal votes <https://opendata.swiss/api/3/action/package_show?id=echtzeitdaten-am-abstimmungstag-zu-kantonalen-abstimmungsvorlagen>. It brings the results of Swiss popular votes, aggregated at the geographical level of choice, into R. Additionally, it allows to retrieve data from the Swissvotes-Database, one of the most comprehensive data platforms on Swiss referendums and initiatives <https://swissvotes.ch/page/dataset/swissvotes_dataset.csv>.
Author: Thomas Lo Russo [cre, aut],
Thomas Willi [aut]
Maintainer: Thomas Lo Russo <th.lorusso@gmail.com>
Diff between swissdd versions 1.1.3 dated 2021-06-29 and 1.1.4 dated 2021-07-17
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/get_geodata.R | 11 ++++++----- 3 files changed, 12 insertions(+), 11 deletions(-)
Title: Species Distribution Model Selection
Description: User-friendly framework that enables the training and the
evaluation of species distribution models (SDMs). The package implements
functions for data driven variable selection and model tuning and includes
numerous utilities to display the results. All the functions used to select
variables or to tune model hyperparameters have an interactive real-time
chart displayed in the 'RStudio' viewer pane during their execution.
Author: Sergio Vignali [aut, cre] (<https://orcid.org/0000-0002-3390-5442>),
Arnaud Barras [aut] (<https://orcid.org/0000-0003-0850-6965>),
Veronika Braunisch [aut] (<https://orcid.org/0000-0001-7035-4662>),
Conservation Biology - University of Bern [fnd]
Maintainer: Sergio Vignali <sergio.vignali@iee.unibe.ch>
Diff between SDMtune versions 1.1.4 dated 2021-03-14 and 1.1.5 dated 2021-07-17
DESCRIPTION | 10 +++---- MD5 | 26 +++++++++---------- NEWS.md | 6 +++- R/convertFolds.R | 11 ++++---- R/maxentVarImp.R | 2 + R/plotResponse.R | 12 ++------ R/train.R | 6 ++-- R/trainMaxent.R | 2 - R/trainMaxnet.R | 2 - README.md | 50 ++++++++++++++++++------------------- inst/WORDLIST | 1 man/maxentVarImp.Rd | 2 + man/train.Rd | 6 ++-- tests/testthat/test-convertFolds.R | 29 ++++++++++++++++++++- 14 files changed, 101 insertions(+), 64 deletions(-)
Title: Single- And Multiple-Group Penalized Factor Analysis
Description: Fits single- and multiple-group penalized factor analysis models
via a trust-region algorithm with integrated automatic multiple tuning
parameter selection (Geminiani et al., 2021 <doi:10.1007/s11336-021-09751-8>).
Available penalties include lasso, adaptive lasso, scad, mcp, and ridge.
Author: Elena Geminiani [aut, cre] (<https://orcid.org/0000-0001-5992-9728>),
Giampiero Marra [aut] (<https://orcid.org/0000-0002-9010-2646>),
Irini Moustaki [aut] (<https://orcid.org/0000-0001-8371-1251>)
Maintainer: Elena Geminiani <geminianielena@gmail.com>
Diff between penfa versions 0.1.0 dated 2021-07-12 and 0.1.1 dated 2021-07-17
penfa-0.1.0/penfa/inst/doc/multiple-group-analysis.R |only penfa-0.1.0/penfa/inst/doc/multiple-group-analysis.Rmd |only penfa-0.1.0/penfa/inst/doc/multiple-group-analysis.html |only penfa-0.1.0/penfa/vignettes/multiple-group-analysis.Rmd |only penfa-0.1.1/penfa/DESCRIPTION | 6 - penfa-0.1.1/penfa/MD5 | 30 +++----- penfa-0.1.1/penfa/NEWS.md | 5 + penfa-0.1.1/penfa/R/penfa-package.R | 3 penfa-0.1.1/penfa/R/penfa.R | 7 ++ penfa-0.1.1/penfa/README.md | 38 ++++++----- penfa-0.1.1/penfa/build/partial.rdb |binary penfa-0.1.1/penfa/build/vignette.rds |binary penfa-0.1.1/penfa/inst/doc/automatic-tuning-selection.html | 8 +- penfa-0.1.1/penfa/inst/doc/grid-search-tuning-selection.Rmd | 5 - penfa-0.1.1/penfa/inst/doc/grid-search-tuning-selection.html | 8 +- penfa-0.1.1/penfa/man/penfa-package.Rd | 3 penfa-0.1.1/penfa/man/penfa.Rd | 9 ++ penfa-0.1.1/penfa/vignettes/grid-search-tuning-selection.Rmd | 5 - 18 files changed, 74 insertions(+), 53 deletions(-)
Title: Locally Induced Gaussian Process Regression
Description: Performs locally induced approximate GP regression for large computer experiments and spatial datasets following Cole D.A., Christianson, R., Gramacy, R.B. (2021) Statistics and Computing, 31(3), 1-21, <arXiv:2008.12857>. The approximation is based on small local designs combined with a set of inducing points (latent design points) for predictions at particular inputs. Parallelization is supported for generating predictions over an immense out-of-sample testing set. Local optimization of the inducing points design is provided based on variance-based criteria. Inducing point template schemes, including scaling of space-filling designs, are also provided.
Author: D. Austin Cole [aut, cre],
Ryan B Christianson [cph],
Robert B. Gramacy [cph]
Maintainer: D. Austin Cole <austin.cole8@vt.edu>
Diff between liGP versions 1.0.0 dated 2021-07-01 and 1.0.1 dated 2021-07-17
DESCRIPTION | 6 +++--- MD5 | 9 +++++---- NEWS |only R/template.R | 2 +- man/loiGP.Rd | 4 ++-- src/init.c | 4 ++-- 6 files changed, 13 insertions(+), 12 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-07-16 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-04-03 1.1.0
2021-01-18 1.0.0
Title: Analyse Biological Time-Series Data
Description: Compiles functions to trim, bin, visualise, and analyse activity/sleep time-series data collected from the Drosophila Activity Monitor (DAM) system (Trikinetics, USA). The following methods were used to compute periodograms - Chi-square periodogram: Sokolove and Bushell (1978) <doi:10.1016/0022-5193(78)90022-X>, Lomb-Scargle periodogram: Lomb (1976) <doi:10.1007/BF00648343>, Scargle (1982) <doi:10.1086/160554> and Ruf (1999) <doi:10.1076/brhm.30.2.178.1422>, and Autocorrelation: Eijzenbach et al. (1986) <doi:10.1111/j.1440-1681.1986.tb00943.x>. Identification of activity peaks is done after using a Savitzky-Golay filter (Savitzky and Golay (1964) <doi:10.1021/ac60214a047>) to smooth raw activity data. Three methods to estimate anticipation of activity are used based on the following papers - Slope method: Fernandez et al. (2020) <doi:10.1016/j.cub.2020.04.025>, Harrisingh method: Harrisingh et al. (2007) <doi:10.1523/JNEUROSCI.3680-07.2007>, and Stoleru method: Stoleru et al. (2004) <doi:10.1038/nature02926>. Rose plots and circular analysis are based on methods from - Batschelet (1981) <ISBN:0120810506> and Zar (2010) <ISBN:0321656865>.
Author: Lakshman Abhilash [aut, cre] (<https://orcid.org/0000-0002-9933-8989>)
Maintainer: Lakshman Abhilash <labhilash@gc.cuny.edu>
Diff between phase versions 1.1.1 dated 2021-07-02 and 1.1.2 dated 2021-07-17
DESCRIPTION | 10 +++++----- LICENSE | 2 +- MD5 | 20 ++++++++++---------- R/indActogram.R | 9 +++++++-- R/indActogramWake.R | 5 ++++- R/indSomnogram.R | 5 ++++- R/peakIdentifier.R | 4 ++-- man/indActogram.Rd | 2 ++ man/indActogramWake.Rd | 2 ++ man/indSomnogram.Rd | 2 ++ man/peakIdentifier.Rd | 4 ++-- 11 files changed, 41 insertions(+), 24 deletions(-)
Title: Sampling from k-th Order Statistics of New Families of
Distributions
Description: Set of tools to generate samples of k-th order statistics and others quantities of interest from new families of distributions.
The main references for this package are: C. Kleiber and S. Kotz (2003) Statistical size distributions in economics and actuarial sciences; Gentle, J. (2009), Computational Statistics, Springer-Verlag;
Naradajah, S. and Rocha, R. (2016), <DOI:10.18637/jss.v069.i10> and Stasinopoulos, M. and Rigby, R. (2015), <DOI:10.1111/j.1467-9876.2005.00510.x>.
The families of distributions are: Burr distributions, Feller-Pareto distributions, Generalized Pareto Distributions, The Inverse Paralogistic Distributions, Marshall-Olkin G distributions, exponentiated G distributions, beta G distributions,
gamma G distributions, Kumaraswamy G distributions, generalized beta G distributions,
beta extended G distributions, gamma G distributions, gamma uniform G distributions, beta exponential G distributions, Weibull G distributions, log gamma G I distributions, log gamma G II distributions,
exponentiated generalized G distributions, exponentiated Kumaraswamy G distributions, geometric exponential Poisson G distributions, truncated-exponential skew-symmetric G distributions, modified beta G distributions,
exponentiated exponential Poisson G distributions, Poisson-inverse gaussian distribution, Skew normal type 1 distributions, Skew student t distribution, Sinh-Arcsinh distribution, Sichel distribution, Zero inflated Poisson.
Author: Carlos Alberto Cardozo Delgado
Maintainer: Carlos Alberto Cardozo Delgado <cardozorpackages@gmail.com>
Diff between orders versions 0.1.5 dated 2021-03-29 and 0.1.6 dated 2021-07-17
DESCRIPTION | 21 ++++++++++----------- MD5 | 12 ++++++++++-- NAMESPACE | 12 ++++++++++++ R/order_burr.R |only R/order_fellerpareto.R |only R/order_gpareto.R |only R/order_iparalogistic.R |only man/order_burr.Rd |only man/order_fellerpareto.Rd |only man/order_gpareto.Rd |only man/order_iparalogistic.Rd |only 11 files changed, 32 insertions(+), 13 deletions(-)
Title: The 'jamovi' Analyses
Description: A suite of common statistical methods such as descriptives,
t-tests, ANOVAs, regression, correlation matrices, proportion tests,
contingency tables, and factor analysis. This package is also useable from
the 'jamovi' statistical spreadsheet (see <https://www.jamovi.org> for more
information).
Author: Ravi Selker, Jonathon Love, Damian Dropmann, Victor Moreno
Maintainer: Jonathon Love <jon@thon.cc>
Diff between jmv versions 1.2.23 dated 2020-06-26 and 2.0 dated 2021-07-17
jmv-1.2.23/jmv/R/html.b.R |only jmv-1.2.23/jmv/R/html.h.R |only jmv-2.0/jmv/DESCRIPTION | 17 jmv-2.0/jmv/MD5 | 166 +-- jmv-2.0/jmv/NAMESPACE | 1 jmv-2.0/jmv/R/00jmv.R | 21 jmv-2.0/jmv/R/00meta.R |only jmv-2.0/jmv/R/ancova.b.R | 136 ++ jmv-2.0/jmv/R/ancova.h.R | 105 +- jmv-2.0/jmv/R/anova.b.R | 2 jmv-2.0/jmv/R/anova.h.R | 90 + jmv-2.0/jmv/R/anovanp.h.R | 26 jmv-2.0/jmv/R/anovaonew.h.R | 24 jmv-2.0/jmv/R/anovarm.b.R | 35 jmv-2.0/jmv/R/anovarm.h.R | 63 + jmv-2.0/jmv/R/anovarmnp.h.R | 20 jmv-2.0/jmv/R/cfa.h.R | 20 jmv-2.0/jmv/R/constants.R |only jmv-2.0/jmv/R/conttables.b.R | 275 +++++ jmv-2.0/jmv/R/conttables.h.R | 290 +++++- jmv-2.0/jmv/R/conttablespaired.h.R | 38 jmv-2.0/jmv/R/corrmatrix.h.R | 20 jmv-2.0/jmv/R/corrpart.b.R |only jmv-2.0/jmv/R/corrpart.h.R |only jmv-2.0/jmv/R/descriptives.b.R | 965 ++++++++++++++------ jmv-2.0/jmv/R/descriptives.h.R | 160 ++- jmv-2.0/jmv/R/efa.h.R | 30 jmv-2.0/jmv/R/empty.b.R |only jmv-2.0/jmv/R/empty.h.R |only jmv-2.0/jmv/R/errors.R |only jmv-2.0/jmv/R/linreg.b.R | 1076 +++++++++++++---------- jmv-2.0/jmv/R/linreg.h.R | 110 +- jmv-2.0/jmv/R/loglinear.h.R | 22 jmv-2.0/jmv/R/logregbin.b.R | 1209 ++++++++++++++------------ jmv-2.0/jmv/R/logregbin.h.R | 78 + jmv-2.0/jmv/R/logregmulti.h.R | 22 jmv-2.0/jmv/R/logregord.h.R | 20 jmv-2.0/jmv/R/mancova.h.R | 20 jmv-2.0/jmv/R/pca.b.R | 475 ++++++---- jmv-2.0/jmv/R/pca.h.R | 49 - jmv-2.0/jmv/R/proptest2.h.R | 20 jmv-2.0/jmv/R/proptestn.h.R | 28 jmv-2.0/jmv/R/reliability.b.R | 229 +++- jmv-2.0/jmv/R/reliability.h.R | 58 - jmv-2.0/jmv/R/ttestis.b.R | 41 jmv-2.0/jmv/R/ttestis.h.R | 59 - jmv-2.0/jmv/R/ttestones.b.R | 20 jmv-2.0/jmv/R/ttestones.h.R | 47 - jmv-2.0/jmv/R/ttestps.b.R | 13 jmv-2.0/jmv/R/ttestps.h.R | 45 jmv-2.0/jmv/R/utils.R | 28 jmv-2.0/jmv/build/vignette.rds |binary jmv-2.0/jmv/inst/doc/new-syntax.html | 366 +++---- jmv-2.0/jmv/man/ANOVA.Rd | 38 jmv-2.0/jmv/man/ancova.Rd | 39 jmv-2.0/jmv/man/anovaOneW.Rd | 24 jmv-2.0/jmv/man/anovaRM.Rd | 39 jmv-2.0/jmv/man/anovaRMNP.Rd | 10 jmv-2.0/jmv/man/bugs.Rd | 7 jmv-2.0/jmv/man/cfa.Rd | 29 jmv-2.0/jmv/man/contTables.Rd | 67 - jmv-2.0/jmv/man/contTablesPaired.Rd | 15 jmv-2.0/jmv/man/corrMatrix.Rd | 20 jmv-2.0/jmv/man/corrPart.Rd |only jmv-2.0/jmv/man/descriptives.Rd | 68 - jmv-2.0/jmv/man/efa.Rd | 27 jmv-2.0/jmv/man/linReg.Rd | 51 - jmv-2.0/jmv/man/linRegClass.Rd |only jmv-2.0/jmv/man/logLinear.Rd | 30 jmv-2.0/jmv/man/logRegBin.Rd | 49 - jmv-2.0/jmv/man/logRegBinClass.Rd |only jmv-2.0/jmv/man/logRegMulti.Rd | 32 jmv-2.0/jmv/man/logRegOrd.Rd | 25 jmv-2.0/jmv/man/mancova.Rd | 13 jmv-2.0/jmv/man/pca.Rd | 24 jmv-2.0/jmv/man/propTest2.Rd | 19 jmv-2.0/jmv/man/propTestN.Rd | 3 jmv-2.0/jmv/man/reliability.Rd | 21 jmv-2.0/jmv/man/ttestIS.Rd | 30 jmv-2.0/jmv/man/ttestOneS.Rd | 27 jmv-2.0/jmv/man/ttestPS.Rd | 25 jmv-2.0/jmv/tests/testthat/testanovarm.R | 45 jmv-2.0/jmv/tests/testthat/testcorrpart.R |only jmv-2.0/jmv/tests/testthat/testdescriptives.R | 117 ++ jmv-2.0/jmv/tests/testthat/testerrors.R |only jmv-2.0/jmv/tests/testthat/testlinreg.R | 109 ++ jmv-2.0/jmv/tests/testthat/testlogregbin.R | 119 ++ jmv-2.0/jmv/tests/testthat/testpca.R | 15 jmv-2.0/jmv/tests/testthat/testttestis.R | 15 jmv-2.0/jmv/tests/testthat/testttestones.R | 18 jmv-2.0/jmv/tests/testthat/testttestps.R | 15 91 files changed, 4853 insertions(+), 2871 deletions(-)
Title: 'grid' Pattern Grobs
Description: Provides 'grid' grobs that fill in a user-defined area with various patterns. Includes enhanced versions of the geometric and image-based patterns originally contained in the 'ggpattern' package as well as original 'pch', 'polygon_tiling', 'regular_polygon', 'rose', 'text', 'wave', and 'weave' patterns plus support for custom user-defined patterns.
Author: Mike FC [aut] (Patterns extracted from ggpattern),
Trevor L Davis [aut, cre],
Thomas Lin Pedersen [ctb] (new_data_frame() copied from ggplot2)
Maintainer: Trevor L Davis <trevor.l.davis@gmail.com>
Diff between gridpattern versions 0.1.2 dated 2021-06-17 and 0.2.1 dated 2021-07-17
gridpattern-0.1.2/gridpattern/R/pattern-array-gradient.R |only gridpattern-0.1.2/gridpattern/tests/figs/deps.txt |only gridpattern-0.1.2/gridpattern/tests/figs/geometry |only gridpattern-0.1.2/gridpattern/tests/figs/pch |only gridpattern-0.1.2/gridpattern/tests/figs/tiling |only gridpattern-0.2.1/gridpattern/DESCRIPTION | 10 gridpattern-0.2.1/gridpattern/MD5 | 123 +++++----- gridpattern-0.2.1/gridpattern/NAMESPACE | 6 gridpattern-0.2.1/gridpattern/NEWS.md | 59 ++++ gridpattern-0.2.1/gridpattern/R/clippingPathGrob.R |only gridpattern-0.2.1/gridpattern/R/grid-pattern.R | 89 ++++++- gridpattern-0.2.1/gridpattern/R/gridpattern-package.R |only gridpattern-0.2.1/gridpattern/R/pattern-both-gradient.R |only gridpattern-0.2.1/gridpattern/R/pattern-both-rose.R |only gridpattern-0.2.1/gridpattern/R/pattern-both-text.R |only gridpattern-0.2.1/gridpattern/R/pattern-geometry-circle.R | 2 gridpattern-0.2.1/gridpattern/R/pattern-geometry-regular_polygon.R | 30 +- gridpattern-0.2.1/gridpattern/R/pattern-geometry-wave.R |only gridpattern-0.2.1/gridpattern/R/utils-array.R | 24 - gridpattern-0.2.1/gridpattern/R/utils-grid.R | 8 gridpattern-0.2.1/gridpattern/R/utils-magick-read.R | 7 gridpattern-0.2.1/gridpattern/R/utils-params.R | 53 +++- gridpattern-0.2.1/gridpattern/R/utils-polygon_df.R | 4 gridpattern-0.2.1/gridpattern/README.md | 108 +++++++- gridpattern-0.2.1/gridpattern/inst/doc/tiling.html | 1 gridpattern-0.2.1/gridpattern/man/clippingPathGrob.Rd |only gridpattern-0.2.1/gridpattern/man/figures/README-piecepackr-1.png |only gridpattern-0.2.1/gridpattern/man/figures/README-rose-1.png |only gridpattern-0.2.1/gridpattern/man/figures/README-text-1.png |only gridpattern-0.2.1/gridpattern/man/figures/README-wave-1.png |only gridpattern-0.2.1/gridpattern/man/grid.pattern.Rd | 16 + gridpattern-0.2.1/gridpattern/man/grid.pattern_circle.Rd | 2 gridpattern-0.2.1/gridpattern/man/grid.pattern_gradient.Rd | 20 + gridpattern-0.2.1/gridpattern/man/grid.pattern_rose.Rd |only gridpattern-0.2.1/gridpattern/man/grid.pattern_text.Rd |only gridpattern-0.2.1/gridpattern/man/grid.pattern_wave.Rd |only gridpattern-0.2.1/gridpattern/man/gridpattern-package.Rd |only gridpattern-0.2.1/gridpattern/tests/figs/array/clipGrob.png |only gridpattern-0.2.1/gridpattern/tests/figs/array/plasma_zero.png |only gridpattern-0.2.1/gridpattern/tests/figs/array/rose.png |only gridpattern-0.2.1/gridpattern/tests/figs/array/text.png |only gridpattern-0.2.1/gridpattern/tests/testthat/_snaps |only gridpattern-0.2.1/gridpattern/tests/testthat/test_array.R | 40 +++ gridpattern-0.2.1/gridpattern/tests/testthat/test_geometry.R | 17 + gridpattern-0.2.1/gridpattern/tests/testthat/test_pch.R | 2 gridpattern-0.2.1/gridpattern/tests/testthat/test_tiling.R | 3 gridpattern-0.2.1/gridpattern/tests/testthat/test_utils.R | 19 + 47 files changed, 498 insertions(+), 145 deletions(-)
Title: Fasano-Franceschini Test: A 2-D Kolmogorov-Smirnov Two-Sample
Test
Description: An implementation of the 2-D Kolmogorov-Smirnov (KS) two-sample test as defined by Fasano and Franceschini (Fasano and Franceschini 1987). The 'fasano.franceschini.test' package provides three improvements over the current 2-D KS test on the Comprehensive R Archive Network (CRAN): (i) the Fasano and Franceschini test has been shown to run in O(n^2) versus the Peacock implementation which runs in O(n^3); (ii) the package implements a procedure for handling ties in the data; and (iii) the package implements a parallelized bootstrapping procedure for improved significance testing. Ultimately, the 'fasano.franceschini.test' package presents a robust statistical test for analyzing random samples defined in 2-dimensions.
Author: Elan Ness-Cohn [aut, cre] (<https://orcid.org/0000-0002-3935-6667>),
Rosemary Braun [ctb, ths] (<https://orcid.org/0000-0001-9668-9866>)
Maintainer: Elan Ness-Cohn <elanness-cohn2017@u.northwestern.edu>
Diff between fasano.franceschini.test versions 1.0.0 dated 2021-06-22 and 1.0.1 dated 2021-07-17
DESCRIPTION | 6 +- MD5 | 17 ++++---- NAMESPACE | 3 - NEWS.md |only R/fasano_franceschini_test.R | 51 +++++++++++-------------- R/interal_functions_FasFran.R | 32 +++++++++------ README.md | 39 +++++++++---------- build/partial.rdb |binary inst/doc/fasano-franceschini-test.html | 22 +++++----- tests/testthat/test-fasano_franceschini_test.R | 13 ++++-- 10 files changed, 95 insertions(+), 88 deletions(-)
More information about fasano.franceschini.test at CRAN
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