Title: Supervised Compression of Big Data
Description: A supervised compression method that incorporates the response for reducing big data to a carefully selected subset. Please see Joseph and Mak (2021) <doi:10.1002/sam.11508>. This research is supported by a U.S. National Science Foundation (NSF) grant CMMI-1921646.
Author: Chaofan Huang [aut, cre],
V. Roshan Joseph [aut]
Maintainer: Chaofan Huang <chaofan.huang@gatech.edu>
Diff between supercompress versions 1.0 dated 2021-10-20 and 1.1 dated 2022-01-13
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/supercompress.R | 8 ++++---- 3 files changed, 9 insertions(+), 9 deletions(-)
Title: Pedigree, Genetic Merit, Phenotype, and Genotype Simulation
Description: Simulate pedigree, genetic merits and phenotypes with random/non-random matings followed by random/non-random selection with different intensities and patterns in males and females. Genotypes can be simulated for a given pedigree, or an appended pedigree to an existing pedigree with genotypes.
Bijma, P. & Rutten, M. (2002) <https://www.wur.nl/en/Research-Results/Chair-groups/Animal-Sciences/Animal-Breeding-and-Genomics-Group/Research/Software.htm>.
Author: Mohammad Ali Nilforooshan [aut, cre]
(<https://orcid.org/0000-0003-0339-5442>)
Maintainer: Mohammad Ali Nilforooshan <m.a.nilforooshan@gmail.com>
Diff between pedSimulate versions 1.3.0 dated 2021-12-08 and 1.3.1 dated 2022-01-13
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/appendPed.R | 3 ++- R/simulatePed.R | 3 ++- 5 files changed, 15 insertions(+), 9 deletions(-)
Title: Integrative Pathway Enrichment Analysis of Multivariate Omics
Data
Description: Framework for analysing multiple omics datasets in the context of molecular pathways, biological processes and other types of gene sets. The package uses p-value merging to combine gene- or protein-level signals, followed by ranked hypergeometric tests to determine enriched pathways and processes. This approach allows researchers to interpret a series of omics datasets in the context of known biology and gene function, and discover associations that are only apparent when several datasets are combined. The package is part of the following publication: Integrative Pathway Enrichment Analysis of Multivariate Omics Data. Paczkowska M^, Barenboim J^, Sintupisut N, Fox NS, Zhu H, Abd-Rabbo D, Mee MW, Boutros PC, PCAWG Drivers and Functional Interpretation Working Group; Reimand J, PCAWG Consortium. Nature Communications (2020) <doi:10.1038/s41467-019-13983-9>.
Author: Juri Reimand [aut, cre],
Jonathan Barenboim [aut],
Mykhaylo Slobodyanyuk [ctb]
Maintainer: Juri Reimand <juri.reimand@utoronto.ca>
Diff between ActivePathways versions 1.0.3 dated 2021-12-03 and 1.0.4 dated 2022-01-13
DESCRIPTION | 14 ++++++++------ MD5 | 30 ++++++++++++++++-------------- NEWS.md | 11 +++++++++-- R/ActivePathways.r | 31 +++++++++++++++++++++++++++++-- R/cytoscape.r | 26 +++++++++++++++++++------- inst/doc/ActivePathways-vignette.R | 6 ++++++ inst/doc/ActivePathways-vignette.Rmd | 20 ++++++++++++++++++++ inst/doc/ActivePathways-vignette.html | 21 ++++++++++++++++----- man/ActivePathways.Rd | 13 ++++++++++++- man/prepareCytoscape.Rd | 17 ++++++++++++++++- tests/testthat/test_validation.r | 24 ++++++++++++++++++++++++ vignettes/ActivePathways-vignette.Rmd | 20 ++++++++++++++++++++ vignettes/LegendView.png |binary vignettes/LegendView_Custom.png |only vignettes/LegendView_RColorBrewer.png |only vignettes/NetworkStep1_V2.png |binary vignettes/NetworkStep2_V2.png |binary 17 files changed, 195 insertions(+), 38 deletions(-)
More information about ActivePathways at CRAN
Permanent link
Title: Tidy Interface to 'data.table'
Description: A tidy interface to 'data.table' that is 'rlang' compatible,
giving users the speed of 'data.table' with the clean syntax of the tidyverse.
Author: Mark Fairbanks [aut, cre],
Abdessabour Moutik [ctb],
Matt Carlson [ctb],
Ivan Leung [ctb],
Ross Kennedy [ctb]
Maintainer: Mark Fairbanks <mark.t.fairbanks@gmail.com>
Diff between tidytable versions 0.6.6 dated 2021-12-10 and 0.6.7 dated 2022-01-13
tidytable-0.6.6/tidytable/R/first-last.R |only tidytable-0.6.6/tidytable/tests/testthat/test-first-last.R |only tidytable-0.6.7/tidytable/DESCRIPTION | 8 tidytable-0.6.7/tidytable/MD5 | 212 +++++----- tidytable-0.6.7/tidytable/NAMESPACE | 9 tidytable-0.6.7/tidytable/NEWS.md | 15 tidytable-0.6.7/tidytable/R/across.R | 8 tidytable-0.6.7/tidytable/R/arrange.R | 12 tidytable-0.6.7/tidytable/R/arrange_across.R | 6 tidytable-0.6.7/tidytable/R/as_tidytable.R | 4 tidytable-0.6.7/tidytable/R/between.R | 8 tidytable-0.6.7/tidytable/R/c_across.R | 4 tidytable-0.6.7/tidytable/R/case.R | 4 tidytable-0.6.7/tidytable/R/case_when.R | 4 tidytable-0.6.7/tidytable/R/complete.R | 6 tidytable-0.6.7/tidytable/R/count.R | 12 tidytable-0.6.7/tidytable/R/cur_group.R | 6 tidytable-0.6.7/tidytable/R/desc.R | 10 tidytable-0.6.7/tidytable/R/distinct.R | 6 tidytable-0.6.7/tidytable/R/dt.R | 4 tidytable-0.6.7/tidytable/R/expand.R | 6 tidytable-0.6.7/tidytable/R/fill.R | 10 tidytable-0.6.7/tidytable/R/filter.R | 12 tidytable-0.6.7/tidytable/R/first-last-nth.R |only tidytable-0.6.7/tidytable/R/get_dummies.R | 17 tidytable-0.6.7/tidytable/R/group_split.R | 12 tidytable-0.6.7/tidytable/R/ifelse.R | 4 tidytable-0.6.7/tidytable/R/join.R | 4 tidytable-0.6.7/tidytable/R/lag-lead.R | 4 tidytable-0.6.7/tidytable/R/mutate.R | 34 - tidytable-0.6.7/tidytable/R/mutate_across.R | 12 tidytable-0.6.7/tidytable/R/mutate_rowwise.R | 6 tidytable-0.6.7/tidytable/R/n.R | 6 tidytable-0.6.7/tidytable/R/nest.R | 6 tidytable-0.6.7/tidytable/R/nest_by.R | 10 tidytable-0.6.7/tidytable/R/notin.R | 4 tidytable-0.6.7/tidytable/R/pivot_longer.R | 6 tidytable-0.6.7/tidytable/R/pivot_wider.R | 6 tidytable-0.6.7/tidytable/R/pull.R | 8 tidytable-0.6.7/tidytable/R/relocate.R | 8 tidytable-0.6.7/tidytable/R/rename_with.R | 8 tidytable-0.6.7/tidytable/R/replace_na.R | 26 - tidytable-0.6.7/tidytable/R/row_number.R | 6 tidytable-0.6.7/tidytable/R/select.R | 14 tidytable-0.6.7/tidytable/R/separate.R | 8 tidytable-0.6.7/tidytable/R/separate_rows.R | 6 tidytable-0.6.7/tidytable/R/slice.R | 16 tidytable-0.6.7/tidytable/R/summarize.R | 14 tidytable-0.6.7/tidytable/R/summarize_across.R | 12 tidytable-0.6.7/tidytable/R/tidytable-package.R | 24 + tidytable-0.6.7/tidytable/R/top_n.R | 6 tidytable-0.6.7/tidytable/R/transmute.R | 6 tidytable-0.6.7/tidytable/R/unite.R | 18 tidytable-0.6.7/tidytable/R/utils-prep_exprs.R | 53 +- tidytable-0.6.7/tidytable/README.md | 107 +---- tidytable-0.6.7/tidytable/man/across..Rd | 8 tidytable-0.6.7/tidytable/man/arrange..Rd | 6 tidytable-0.6.7/tidytable/man/arrange_across..Rd | 6 tidytable-0.6.7/tidytable/man/as_tidytable.Rd | 4 tidytable-0.6.7/tidytable/man/between..Rd | 8 tidytable-0.6.7/tidytable/man/c_across..Rd | 4 tidytable-0.6.7/tidytable/man/case..Rd | 4 tidytable-0.6.7/tidytable/man/case_when..Rd | 4 tidytable-0.6.7/tidytable/man/complete..Rd | 6 tidytable-0.6.7/tidytable/man/count..Rd | 12 tidytable-0.6.7/tidytable/man/cur_group_id..Rd | 6 tidytable-0.6.7/tidytable/man/desc..Rd | 10 tidytable-0.6.7/tidytable/man/distinct..Rd | 6 tidytable-0.6.7/tidytable/man/dt.Rd | 4 tidytable-0.6.7/tidytable/man/expand..Rd | 6 tidytable-0.6.7/tidytable/man/fill..Rd | 10 tidytable-0.6.7/tidytable/man/filter..Rd | 6 tidytable-0.6.7/tidytable/man/first..Rd | 20 tidytable-0.6.7/tidytable/man/get_dummies..Rd | 17 tidytable-0.6.7/tidytable/man/grapes-notin-grapes.Rd | 4 tidytable-0.6.7/tidytable/man/group_split..Rd | 12 tidytable-0.6.7/tidytable/man/ifelse..Rd | 4 tidytable-0.6.7/tidytable/man/lags..Rd | 4 tidytable-0.6.7/tidytable/man/left_join..Rd | 4 tidytable-0.6.7/tidytable/man/mutate..Rd | 10 tidytable-0.6.7/tidytable/man/mutate_across..Rd | 12 tidytable-0.6.7/tidytable/man/mutate_rowwise..Rd | 6 tidytable-0.6.7/tidytable/man/n..Rd | 6 tidytable-0.6.7/tidytable/man/nest..Rd | 6 tidytable-0.6.7/tidytable/man/nest_by..Rd | 10 tidytable-0.6.7/tidytable/man/pivot_longer..Rd | 6 tidytable-0.6.7/tidytable/man/pivot_wider..Rd | 6 tidytable-0.6.7/tidytable/man/pull..Rd | 8 tidytable-0.6.7/tidytable/man/reexports.Rd | 10 tidytable-0.6.7/tidytable/man/relocate..Rd | 8 tidytable-0.6.7/tidytable/man/rename_with..Rd | 8 tidytable-0.6.7/tidytable/man/replace_na..Rd | 6 tidytable-0.6.7/tidytable/man/row_number..Rd | 6 tidytable-0.6.7/tidytable/man/select..Rd | 14 tidytable-0.6.7/tidytable/man/separate..Rd | 6 tidytable-0.6.7/tidytable/man/separate_rows..Rd | 6 tidytable-0.6.7/tidytable/man/slice..Rd | 16 tidytable-0.6.7/tidytable/man/summarize..Rd | 10 tidytable-0.6.7/tidytable/man/summarize_across..Rd | 12 tidytable-0.6.7/tidytable/man/top_n..Rd | 6 tidytable-0.6.7/tidytable/man/transmute..Rd | 6 tidytable-0.6.7/tidytable/man/unite..Rd | 18 tidytable-0.6.7/tidytable/tests/testthat/test-across.R | 10 tidytable-0.6.7/tidytable/tests/testthat/test-arrange.R | 8 tidytable-0.6.7/tidytable/tests/testthat/test-filter.R | 21 tidytable-0.6.7/tidytable/tests/testthat/test-first-last-nth.R |only tidytable-0.6.7/tidytable/tests/testthat/test-mutate.R | 52 ++ tidytable-0.6.7/tidytable/tests/testthat/test-separate.R | 21 tidytable-0.6.7/tidytable/tests/testthat/test-summarize.R | 22 + 109 files changed, 769 insertions(+), 579 deletions(-)
Title: Creates Log Files
Description: Contains functions to help create log files. The
package aims to overcome the difficulty of the base R sink() command. The
log_print() function will print to both the console and the file log,
without interfering in other write operations.
Author: David Bosak [aut, cre]
Maintainer: David Bosak <dbosak01@gmail.com>
Diff between logr versions 1.2.7 dated 2021-11-16 and 1.2.8 dated 2022-01-13
DESCRIPTION | 6 +++--- MD5 | 30 +++++++++++++++--------------- NEWS.md | 5 ++++- R/utilities.R | 2 +- inst/doc/logr-example1.Rmd | 7 ++++++- inst/doc/logr-example1.html | 11 ++++++++++- inst/doc/logr-faq.Rmd | 14 +++++++------- inst/doc/logr-faq.html | 10 +++++----- inst/doc/logr-tidylog.Rmd | 3 +-- inst/doc/logr-tidylog.html | 1 + inst/doc/logr.Rmd | 1 + inst/doc/logr.html | 1 + vignettes/logr-example1.Rmd | 7 ++++++- vignettes/logr-faq.Rmd | 14 +++++++------- vignettes/logr-tidylog.Rmd | 3 +-- vignettes/logr.Rmd | 1 + 16 files changed, 70 insertions(+), 46 deletions(-)
Title: Possible Adverse Events/Reactions from the
Vaccinations/Experimental Gene Therapies
Description: Provides data about the possible adverse events/reactions
resulting from being injected with a vaccine/experimental gene therapy.
Currently, this data set only includes information from six reference
sources. Refer to the CITATION.cff file for the complete citations of
the reference sources. For information about vaccination$/immunization$
hazards, visit <https://www.questionuniverse.com/rethink.html#vaccine>,
<https://www.ecoccs.com/healing.html#vaccines>,
<https://www.questionuniverse.com/rethink_current_crisis.html#cov_vaccin>,
and <https://www.questionuniverse.com/vaccination.html>.
Author: Irucka Embry [aut, cre]
Maintainer: Irucka Embry <iembry@ecoccs.com>
Diff between jab.adverse.reactions versions 1.0.0 dated 2022-01-12 and 1.0.1 dated 2022-01-13
jab.adverse.reactions-1.0.0/jab.adverse.reactions/inst/pdf |only jab.adverse.reactions-1.0.0/jab.adverse.reactions/inst/public |only jab.adverse.reactions-1.0.1/jab.adverse.reactions/DESCRIPTION | 16 +- jab.adverse.reactions-1.0.1/jab.adverse.reactions/MD5 | 19 +-- jab.adverse.reactions-1.0.1/jab.adverse.reactions/NEWS.md | 10 + jab.adverse.reactions-1.0.1/jab.adverse.reactions/README.md | 63 ++++++++-- jab.adverse.reactions-1.0.1/jab.adverse.reactions/data/jab_adverse_reactions.RData |binary jab.adverse.reactions-1.0.1/jab.adverse.reactions/inst/CITATION |only jab.adverse.reactions-1.0.1/jab.adverse.reactions/inst/data-raw/jab.adverse.reactions.create.R | 56 ++++++-- jab.adverse.reactions-1.0.1/jab.adverse.reactions/inst/references/Data_References.bib | 35 +++++ 10 files changed, 158 insertions(+), 41 deletions(-)
More information about jab.adverse.reactions at CRAN
Permanent link
Title: A friendly MCMC framework
Description: Provides a friendly (flexible) Markov Chain Monte Carlo (MCMC)
framework for implementing Metropolis-Hastings algorithm in a modular way
allowing users to specify automatic convergence checker, personalized
transition kernels, and out-of-the-box multiple MCMC chains using
parallel computing. Most of the methods implemented in this package can
be found in Brooks et al. (2011, ISBN 9781420079425). Among the methods
included, we have: Haario (2001) <doi:10.1007/s11222-011-9269-5>
Adaptive Metropolis, Vihola (2012) <doi:10.1007/s11222-011-9269-5>
Robust Adaptive Metropolis, and Thawornwattana et
al. (2018) <doi:10.1214/17-BA1084> Mirror transition kernels.
Author: George Vega Yon [aut, cre] (<https://orcid.org/0000-0002-3171-0844>),
Paul Marjoram [ctb, ths] (<https://orcid.org/0000-0003-0824-7449>),
National Cancer Institute (NCI) [fnd] (Grant Number 5P01CA196569-02),
Fabian Scheipl [rev] (JOSS reviewer,
<https://orcid.org/0000-0001-8172-3603>)
Maintainer: George Vega Yon <g.vegayon@gmail.com>
Diff between fmcmc versions 0.5-0 dated 2021-09-03 and 0.5-1 dated 2022-01-13
DESCRIPTION | 10 - MD5 | 26 +- NEWS.md | 7 R/convergence.R | 16 - R/kernel.R | 4 R/mcmc.R | 6 R/mcmc_info.R | 9 - build/partial.rdb |binary build/vignette.rds |binary inst/NEWS | 10 + inst/doc/advanced-features.html | 332 +++++++++++++++++-------------------- inst/doc/user-defined-kernels.html | 170 ++++++++---------- inst/doc/workflow-with-fmcmc.html | 326 +++++++++++++++++------------------- man/convergence-checker.Rd | 2 14 files changed, 441 insertions(+), 477 deletions(-)
Title: Simulating Survival Data from Change-Point Hazard Distributions
Description: Simulates time-to-event data
with type I right censoring using two methods: the inverse CDF
method and our proposed memoryless method. The latter method
takes advantage of the memoryless property of survival and
simulates a separate distribution between change-points. We
include two parametric distributions: exponential and Weibull.
Inverse CDF method draws on the work of Rainer Walke (2010),
<https://www.demogr.mpg.de/papers/technicalreports/tr-2010-003.pdf>.
Author: Camille Hochheimer [aut, cre]
Maintainer: Camille Hochheimer <dochoch19@gmail.com>
Diff between cpsurvsim versions 1.2.0 dated 2020-01-20 and 1.2.1 dated 2022-01-13
DESCRIPTION | 19 ++++++------- MD5 | 12 ++++---- R/expfns.R | 45 ++++++++++++++++++++++++++++++++ R/weibullfns.R | 54 +++++++++++++++++++++++++++++++++++++++ build/vignette.rds |binary inst/CITATION | 12 ++++---- inst/doc/cpsurvsim-vignette.html | 26 +++++++++++++----- 7 files changed, 138 insertions(+), 30 deletions(-)
Title: Easily Apply Formats to Data
Description: Contains a set of functions that can be used to apply
formats to data frames or vectors. The package aims to provide to
functionality similar to that of SAS® formats. Formats are assigned to
the format attribute on data frame columns. Then when the fdata()
function is called, a new data frame is created with the column data
formatted as specified. The package also contains a value() function
to create a user-defined format, similar to a SAS® user-defined format.
Author: David Bosak
Maintainer: David Bosak <dbosak01@gmail.com>
Diff between fmtr versions 1.5.4 dated 2021-11-18 and 1.5.5 dated 2022-01-13
fmtr-1.5.4/fmtr/vignettes/output |only fmtr-1.5.5/fmtr/DESCRIPTION | 6 +- fmtr-1.5.5/fmtr/MD5 | 47 ++++++++-------- fmtr-1.5.5/fmtr/NEWS.md | 54 +++++++++++-------- fmtr-1.5.5/fmtr/R/fmt.R | 14 ++++- fmtr-1.5.5/fmtr/R/helpers.R | 9 ++- fmtr-1.5.5/fmtr/README.md | 2 fmtr-1.5.5/fmtr/inst/doc/fmtr-convenience.html | 4 - fmtr-1.5.5/fmtr/inst/doc/fmtr-example1.R | 3 - fmtr-1.5.5/fmtr/inst/doc/fmtr-example1.Rmd | 10 ++- fmtr-1.5.5/fmtr/inst/doc/fmtr-example1.html | 70 ++++++++++++++----------- fmtr-1.5.5/fmtr/inst/doc/fmtr-fapply.html | 4 - fmtr-1.5.5/fmtr/inst/doc/fmtr-faq.R | 6 +- fmtr-1.5.5/fmtr/inst/doc/fmtr-faq.Rmd | 8 +- fmtr-1.5.5/fmtr/inst/doc/fmtr-faq.html | 8 +- fmtr-1.5.5/fmtr/inst/doc/fmtr-fcat.html | 4 - fmtr-1.5.5/fmtr/inst/doc/fmtr-fdata.html | 4 - fmtr-1.5.5/fmtr/inst/doc/fmtr-helpers.html | 4 - fmtr-1.5.5/fmtr/man/fmt_mean_sd.Rd | 6 +- fmtr-1.5.5/fmtr/man/images/example1.png |binary fmtr-1.5.5/fmtr/tests/testthat/test-fdata.R | 2 fmtr-1.5.5/fmtr/tests/testthat/test-fmt.R | 25 ++++++++ fmtr-1.5.5/fmtr/tests/testthat/test-helpers.R | 3 + fmtr-1.5.5/fmtr/vignettes/fmtr-example1.Rmd | 10 ++- fmtr-1.5.5/fmtr/vignettes/fmtr-faq.Rmd | 8 +- 25 files changed, 195 insertions(+), 116 deletions(-)
Title: Cumulative History Analysis for Bistable Perception Time Series
Description: Estimates cumulative history for time-series for continuously
viewed bistable perceptual rivalry displays. Computes cumulative history
via a homogeneous first order differential process. I.e., it assumes
exponential growth/decay of the history as a function time and perceptually
dominant state, Pastukhov & Braun (2011) <doi:10.1167/11.10.12>.
Supports Gamma, log normal, and normal distribution families.
Provides a method to compute history directly and example of using the
computation on a custom Stan code.
Author: Alexander Pastukhov [aut, cre]
(<https://orcid.org/0000-0002-8738-8591>)
Maintainer: Alexander Pastukhov <pastukhov.alexander@gmail.com>
Diff between bistablehistory versions 1.0.0 dated 2021-09-28 and 1.1.0 dated 2022-01-13
bistablehistory-1.0.0/bistablehistory/man/history_mix.Rd |only bistablehistory-1.0.0/bistablehistory/tests/testthat/test-history_paramter.R |only bistablehistory-1.1.0/bistablehistory/DESCRIPTION | 8 bistablehistory-1.1.0/bistablehistory/MD5 | 118 - bistablehistory-1.1.0/bistablehistory/NAMESPACE | 7 bistablehistory-1.1.0/bistablehistory/NEWS.md |only bistablehistory-1.1.0/bistablehistory/R/RcppExports.R | 41 bistablehistory-1.1.0/bistablehistory/R/bayes_R2.R | 4 bistablehistory-1.1.0/bistablehistory/R/check_fixed_history_parameter.R | 9 bistablehistory-1.1.0/bistablehistory/R/check_normal_prior.R |only bistablehistory-1.1.0/bistablehistory/R/coef.R | 5 bistablehistory-1.1.0/bistablehistory/R/compute_history.R | 5 bistablehistory-1.1.0/bistablehistory/R/data.R | 2 bistablehistory-1.1.0/bistablehistory/R/evaluate_history_parameter.R | 215 +- bistablehistory-1.1.0/bistablehistory/R/extract_history.R | 2 bistablehistory-1.1.0/bistablehistory/R/extract_history_parameter.R |only bistablehistory-1.1.0/bistablehistory/R/extract_term.R |only bistablehistory-1.1.0/bistablehistory/R/fit_cumhist.R | 458 +++--- bistablehistory-1.1.0/bistablehistory/R/fixef.R | 7 bistablehistory-1.1.0/bistablehistory/R/history_parameter.R | 375 ++-- bistablehistory-1.1.0/bistablehistory/R/predict.R | 108 + bistablehistory-1.1.0/bistablehistory/R/print.R | 4 bistablehistory-1.1.0/bistablehistory/R/summary.R | 3 bistablehistory-1.1.0/bistablehistory/README.md | 76 - bistablehistory-1.1.0/bistablehistory/build/partial.rdb |binary bistablehistory-1.1.0/bistablehistory/build/vignette.rds |binary bistablehistory-1.1.0/bistablehistory/inst/doc/cumulative-history.R | 14 bistablehistory-1.1.0/bistablehistory/inst/doc/cumulative-history.Rmd | 187 +- bistablehistory-1.1.0/bistablehistory/inst/doc/cumulative-history.html | 73 bistablehistory-1.1.0/bistablehistory/inst/doc/usage-examples.R | 19 bistablehistory-1.1.0/bistablehistory/inst/doc/usage-examples.Rmd | 82 - bistablehistory-1.1.0/bistablehistory/inst/doc/usage-examples.html | 149 + bistablehistory-1.1.0/bistablehistory/inst/doc/writing-stan-code.R | 3 bistablehistory-1.1.0/bistablehistory/inst/doc/writing-stan-code.Rmd | 317 ++-- bistablehistory-1.1.0/bistablehistory/inst/doc/writing-stan-code.html | 19 bistablehistory-1.1.0/bistablehistory/inst/stan/historylm.stan | 95 - bistablehistory-1.1.0/bistablehistory/man/bayes_R2.Rd | 2 bistablehistory-1.1.0/bistablehistory/man/br_contrast.Rd | 50 bistablehistory-1.1.0/bistablehistory/man/check_normal_prior.Rd |only bistablehistory-1.1.0/bistablehistory/man/coef.cumhist.Rd | 5 bistablehistory-1.1.0/bistablehistory/man/compute_history.Rd | 5 bistablehistory-1.1.0/bistablehistory/man/evaluate_history_init.Rd | 2 bistablehistory-1.1.0/bistablehistory/man/extract_history.Rd | 2 bistablehistory-1.1.0/bistablehistory/man/extract_history_parameter.Rd |only bistablehistory-1.1.0/bistablehistory/man/extract_replicate_term_to_matrix.Rd |only bistablehistory-1.1.0/bistablehistory/man/extract_term_to_matrix.Rd |only bistablehistory-1.1.0/bistablehistory/man/fast_history_compute.Rd | 2 bistablehistory-1.1.0/bistablehistory/man/fit_cumhist.Rd | 43 bistablehistory-1.1.0/bistablehistory/man/fixef.Rd | 5 bistablehistory-1.1.0/bistablehistory/man/history_parameter.Rd | 3 bistablehistory-1.1.0/bistablehistory/man/kde_two_observers.Rd | 4 bistablehistory-1.1.0/bistablehistory/man/predict.cumhist.Rd | 14 bistablehistory-1.1.0/bistablehistory/man/predict_samples.Rd |only bistablehistory-1.1.0/bistablehistory/man/print.cumhist.Rd | 6 bistablehistory-1.1.0/bistablehistory/man/summary.cumhist.Rd | 2 bistablehistory-1.1.0/bistablehistory/src/RcppExports.cpp | 29 bistablehistory-1.1.0/bistablehistory/src/fast_history_compute.cpp | 121 + bistablehistory-1.1.0/bistablehistory/src/stanExports_historylm.h | 754 +++------- bistablehistory-1.1.0/bistablehistory/tests/testthat/fit-fixed.RDS |only bistablehistory-1.1.0/bistablehistory/tests/testthat/fit.RDS |only bistablehistory-1.1.0/bistablehistory/tests/testthat/test-check_fixed_history_parameter.R |only bistablehistory-1.1.0/bistablehistory/tests/testthat/test-check_normal_prior.R |only bistablehistory-1.1.0/bistablehistory/tests/testthat/test-fit_and_post_fit_utilities.R |only bistablehistory-1.1.0/bistablehistory/tests/testthat/test-fit_cumhist.R |only bistablehistory-1.1.0/bistablehistory/tests/testthat/test-history_parameter.R |only bistablehistory-1.1.0/bistablehistory/vignettes/cumulative-history.Rmd | 187 +- bistablehistory-1.1.0/bistablehistory/vignettes/cumulative-history.bib |only bistablehistory-1.1.0/bistablehistory/vignettes/usage-examples.Rmd | 82 - bistablehistory-1.1.0/bistablehistory/vignettes/usage-examples.bib |only bistablehistory-1.1.0/bistablehistory/vignettes/writing-stan-code.Rmd | 317 ++-- 70 files changed, 2147 insertions(+), 1893 deletions(-)
More information about bistablehistory at CRAN
Permanent link
Title: Seamless R and C++ Integration
Description: The 'Rcpp' package provides R functions as well as C++ classes which
offer a seamless integration of R and C++. Many R data types and objects can be
mapped back and forth to C++ equivalents which facilitates both writing of new
code as well as easier integration of third-party libraries. Documentation
about 'Rcpp' is provided by several vignettes included in this package, via the
'Rcpp Gallery' site at <https://gallery.rcpp.org>, the paper by Eddelbuettel and
Francois (2011, <doi:10.18637/jss.v040.i08>), the book by Eddelbuettel (2013,
<doi:10.1007/978-1-4614-6868-4>) and the paper by Eddelbuettel and Balamuta (2018,
<doi:10.1080/00031305.2017.1375990>); see 'citation("Rcpp")' for details.
Author: Dirk Eddelbuettel, Romain Francois, JJ Allaire, Kevin Ushey, Qiang Kou,
Nathan Russell, Inaki Ucar, Douglas Bates and John Chambers
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between Rcpp versions 1.0.7 dated 2021-07-07 and 1.0.8 dated 2022-01-13
ChangeLog | 150 +++++++++++++++++++++++++++ DESCRIPTION | 8 - MD5 | 87 ++++++++------- R/RcppLdpath.R | 5 README.md | 26 +++- build/partial.rdb |only build/vignette.rds |binary cleanup | 4 inst/CITATION | 15 +- inst/NEWS.Rd | 38 ++++++ inst/bib/Rcpp.bib | 130 ++++++++++++----------- inst/doc/Rcpp-FAQ.pdf |binary inst/doc/Rcpp-attributes.pdf |binary inst/doc/Rcpp-extending.pdf |binary inst/doc/Rcpp-introduction.pdf |binary inst/doc/Rcpp-jss-2011.pdf |binary inst/doc/Rcpp-libraries.pdf |binary inst/doc/Rcpp-modules.pdf |binary inst/doc/Rcpp-package.pdf |binary inst/doc/Rcpp-quickref.pdf |binary inst/doc/Rcpp-sugar.pdf |binary inst/examples/Misc/piSugar.cpp | 9 - inst/examples/RcppGibbs/RcppGibbs.R | 14 +- inst/examples/RcppGibbs/timeRNGs.R | 181 +++++++++++++++++---------------- inst/include/Rcpp/Light |only inst/include/Rcpp/Lighter |only inst/include/Rcpp/Lightest |only inst/include/Rcpp/Rcpp |only inst/include/Rcpp/XPtr.h | 7 + inst/include/Rcpp/config.h | 10 - inst/include/Rcpp/r/headers.h | 6 - inst/tinytest/testRcppAttributePackage |only inst/tinytest/test_attribute_package.R |only inst/tinytest/test_xptr.R | 33 +++++- man/Rcpp-package.Rd | 2 man/RcppLdFlags.Rd | 2 src/attributes.cpp | 105 +++++++++++++++++-- vignettes/pdf/Rcpp-FAQ.pdf |binary vignettes/pdf/Rcpp-attributes.pdf |binary vignettes/pdf/Rcpp-extending.pdf |binary vignettes/pdf/Rcpp-introduction.pdf |binary vignettes/pdf/Rcpp-jss-2011.pdf |binary vignettes/pdf/Rcpp-libraries.pdf |binary vignettes/pdf/Rcpp-modules.pdf |binary vignettes/pdf/Rcpp-package.pdf |binary vignettes/pdf/Rcpp-quickref.pdf |binary vignettes/pdf/Rcpp-sugar.pdf |binary 47 files changed, 583 insertions(+), 249 deletions(-)
Title: Project Environments
Description: A dependency management toolkit for R. Using 'renv', you can create
and manage project-local R libraries, save the state of these libraries to
a 'lockfile', and later restore your library as required. Together, these
tools can help make your projects more isolated, portable, and reproducible.
Author: Kevin Ushey [aut, cre],
RStudio, PBC [cph]
Maintainer: Kevin Ushey <kevin@rstudio.com>
Diff between renv versions 0.15.0 dated 2022-01-04 and 0.15.1 dated 2022-01-13
DESCRIPTION | 6 - MD5 | 59 +++++++++--------- NEWS.md | 25 +++++++ R/cache.R | 2 R/config-defaults.R | 2 R/dcf.R | 46 +++++++++----- R/dependencies.R | 68 ++++----------------- R/install.R | 4 - R/knitr.R | 100 +++++++++++++++++++++++++++++++ R/load.R | 9 +- R/project.R | 19 ++++- R/retrieve.R | 48 +++++++++++++- R/sandbox.R | 42 ++++++++----- R/settings.R | 2 R/tests.R | 1 inst/config.yml | 3 inst/doc/docker.html | 4 - inst/doc/profiles.Rmd | 32 +++++++-- inst/doc/profiles.html | 10 ++- inst/doc/renv.html | 6 - inst/resources/activate.R | 5 - man/settings.Rd | 2 tests/testthat/resources/yaml-chunks.Rmd |only tests/testthat/test-dcf.R | 69 +++++++++++++++++++++ tests/testthat/test-dependencies.R | 6 + tests/testthat/test-install.R | 24 +++++++ tests/testthat/test-knitr.R |only tests/testthat/test-profile.R | 21 ++++++ tests/testthat/test-rmd.R | 25 +++++++ tests/testthat/test-sandbox.R | 16 ++++ vignettes/profiles.Rmd | 32 +++++++-- vignettes/renv.md |only 32 files changed, 521 insertions(+), 167 deletions(-)
More information about PoissonMultinomial at CRAN
Permanent link
Title: Modeling Phylogenetic Signals using Eigenvector Maps
Description: Computational tools to represent phylogenetic signals using adapted eigenvector maps.
Author: Guillaume Guenard, with contribution from Pierre Legendre
Maintainer: Guillaume Guenard <guillaume.guenard@gmail.com>
Diff between MPSEM versions 0.3-6 dated 2019-06-03 and 0.4-1 dated 2022-01-13
MPSEM-0.3-6/MPSEM/R/GraphFunctions.R |only MPSEM-0.3-6/MPSEM/R/MPSEM.R |only MPSEM-0.3-6/MPSEM/R/OUSim.R |only MPSEM-0.3-6/MPSEM/R/PEM.R |only MPSEM-0.3-6/MPSEM/R/lmutils.R |only MPSEM-0.3-6/MPSEM/inst/doc/MPSEM.R |only MPSEM-0.3-6/MPSEM/inst/doc/MPSEM.Rnw |only MPSEM-0.3-6/MPSEM/inst/doc/MPSEM.pdf |only MPSEM-0.3-6/MPSEM/man/GraphFunctions.Rd |only MPSEM-0.3-6/MPSEM/man/OUSim.Rd |only MPSEM-0.3-6/MPSEM/man/PEM.Rd |only MPSEM-0.3-6/MPSEM/man/lmutils.Rd |only MPSEM-0.3-6/MPSEM/src/registerDynamicSymbol.c |only MPSEM-0.3-6/MPSEM/vignettes/MPSEM.Rnw |only MPSEM-0.4-1/MPSEM/DESCRIPTION | 17 +- MPSEM-0.4-1/MPSEM/MD5 | 51 +++--- MPSEM-0.4-1/MPSEM/NAMESPACE | 57 +++++-- MPSEM-0.4-1/MPSEM/R/MPSEM-package.R |only MPSEM-0.4-1/MPSEM/R/PEM-class.R |only MPSEM-0.4-1/MPSEM/R/PEM-functions.R |only MPSEM-0.4-1/MPSEM/R/graph-class.R |only MPSEM-0.4-1/MPSEM/R/graph-functions.R |only MPSEM-0.4-1/MPSEM/R/lm-utils.R |only MPSEM-0.4-1/MPSEM/R/trait-simulator.R |only MPSEM-0.4-1/MPSEM/README.md |only MPSEM-0.4-1/MPSEM/build/partial.rdb |binary MPSEM-0.4-1/MPSEM/build/vignette.rds |binary MPSEM-0.4-1/MPSEM/inst/doc/PEM_with_MPSEM.R |only MPSEM-0.4-1/MPSEM/inst/doc/PEM_with_MPSEM.Rnw |only MPSEM-0.4-1/MPSEM/inst/doc/PEM_with_MPSEM.pdf |only MPSEM-0.4-1/MPSEM/man/MPSEM-package.Rd | 126 +++++++--------- MPSEM-0.4-1/MPSEM/man/PEM-class.Rd | 194 ++++++++++++++----------- MPSEM-0.4-1/MPSEM/man/PEM-functions.Rd |only MPSEM-0.4-1/MPSEM/man/graph-class.Rd | 70 +++++---- MPSEM-0.4-1/MPSEM/man/graph-functions.Rd |only MPSEM-0.4-1/MPSEM/man/lm-utils.Rd |only MPSEM-0.4-1/MPSEM/man/trait-simulator.Rd |only MPSEM-0.4-1/MPSEM/src/MPSEM.c | 183 +++++++++++++++-------- MPSEM-0.4-1/MPSEM/src/MPSEM.h | 144 +++++++++++------- MPSEM-0.4-1/MPSEM/src/init.c |only MPSEM-0.4-1/MPSEM/vignettes/PEM_with_MPSEM.Rnw |only MPSEM-0.4-1/MPSEM/vignettes/PEM_with_MPSEM.lyx | 4 42 files changed, 501 insertions(+), 345 deletions(-)
Title: Make Static HTML Documentation for a Package
Description: Generate an attractive and useful website from a source
package. 'pkgdown' converts your documentation, vignettes, 'README',
and more to 'HTML' making it easy to share information about your
package online.
Author: Hadley Wickham [aut, cre] (<https://orcid.org/0000-0003-4757-117X>),
Jay Hesselberth [aut] (<https://orcid.org/0000-0002-6299-179X>),
Maëlle Salmon [aut] (<https://orcid.org/0000-0002-2815-0399>),
RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between pkgdown versions 2.0.1 dated 2021-12-03 and 2.0.2 dated 2022-01-13
pkgdown-2.0.1/pkgdown/tests/testthat/assets/news-bad-nesting |only pkgdown-2.0.1/pkgdown/tests/testthat/assets/news-github-links |only pkgdown-2.0.1/pkgdown/tests/testthat/assets/news-multi-page |only pkgdown-2.0.2/pkgdown/DESCRIPTION | 16 - pkgdown-2.0.2/pkgdown/MD5 | 160 +++++----- pkgdown-2.0.2/pkgdown/NEWS.md | 55 +++ pkgdown-2.0.2/pkgdown/R/build-articles.R | 12 pkgdown-2.0.2/pkgdown/R/build-footer.R | 10 pkgdown-2.0.2/pkgdown/R/build-home-authors.R | 36 -- pkgdown-2.0.2/pkgdown/R/build-home-citation.R | 6 pkgdown-2.0.2/pkgdown/R/build-home-index.R | 5 pkgdown-2.0.2/pkgdown/R/build-home-md.R | 6 pkgdown-2.0.2/pkgdown/R/build-news.R | 53 +-- pkgdown-2.0.2/pkgdown/R/build-redirects.R | 7 pkgdown-2.0.2/pkgdown/R/build-reference-index.R | 38 +- pkgdown-2.0.2/pkgdown/R/build-reference.R | 3 pkgdown-2.0.2/pkgdown/R/build.R | 11 pkgdown-2.0.2/pkgdown/R/deploy-site.R | 23 + pkgdown-2.0.2/pkgdown/R/markdown.R | 22 - pkgdown-2.0.2/pkgdown/R/pkgdown.R | 15 pkgdown-2.0.2/pkgdown/R/rd-html.R | 3 pkgdown-2.0.2/pkgdown/R/test.R | 2 pkgdown-2.0.2/pkgdown/R/theme.R | 18 + pkgdown-2.0.2/pkgdown/R/tweak-page.R | 8 pkgdown-2.0.2/pkgdown/R/tweak-tags.R | 2 pkgdown-2.0.2/pkgdown/build/pkgdown.pdf |binary pkgdown-2.0.2/pkgdown/build/vignette.rds |binary pkgdown-2.0.2/pkgdown/inst/BS5/assets/pkgdown.js | 10 pkgdown-2.0.2/pkgdown/inst/BS5/assets/pkgdown.scss | 15 pkgdown-2.0.2/pkgdown/inst/BS5/templates/navbar.html | 2 pkgdown-2.0.2/pkgdown/inst/doc/customise.Rmd | 6 pkgdown-2.0.2/pkgdown/inst/doc/customise.html | 4 pkgdown-2.0.2/pkgdown/inst/doc/pkgdown.Rmd | 14 pkgdown-2.0.2/pkgdown/inst/doc/pkgdown.html | 14 pkgdown-2.0.2/pkgdown/inst/po/de/LC_MESSAGES/R-pkgdown.mo |binary pkgdown-2.0.2/pkgdown/inst/po/dk |only pkgdown-2.0.2/pkgdown/inst/po/es/LC_MESSAGES/R-pkgdown.mo |binary pkgdown-2.0.2/pkgdown/inst/po/fr/LC_MESSAGES/R-pkgdown.mo |binary pkgdown-2.0.2/pkgdown/inst/po/ko |only pkgdown-2.0.2/pkgdown/inst/po/kr |only pkgdown-2.0.2/pkgdown/inst/po/pt/LC_MESSAGES/R-pkgdown.mo |binary pkgdown-2.0.2/pkgdown/inst/po/tr/LC_MESSAGES/R-pkgdown.mo |binary pkgdown-2.0.2/pkgdown/inst/po/zh_CN/LC_MESSAGES/R-pkgdown.mo |binary pkgdown-2.0.2/pkgdown/man/build_home.Rd | 2 pkgdown-2.0.2/pkgdown/man/build_site.Rd | 7 pkgdown-2.0.2/pkgdown/man/deploy_to_branch.Rd | 9 pkgdown-2.0.2/pkgdown/man/rmd-fragments/home-configuration.Rmd | 2 pkgdown-2.0.2/pkgdown/man/test-verbatim.Rd | 2 pkgdown-2.0.2/pkgdown/po/R-de.po | 28 + pkgdown-2.0.2/pkgdown/po/R-dk.po |only pkgdown-2.0.2/pkgdown/po/R-es.po | 30 + pkgdown-2.0.2/pkgdown/po/R-fr.po | 28 + pkgdown-2.0.2/pkgdown/po/R-ko.po |only pkgdown-2.0.2/pkgdown/po/R-pkgdown.pot | 30 + pkgdown-2.0.2/pkgdown/po/R-pt.po | 28 + pkgdown-2.0.2/pkgdown/po/R-tr.po | 28 + pkgdown-2.0.2/pkgdown/po/R-zh_CN.po | 28 + pkgdown-2.0.2/pkgdown/tests/testthat/_snaps/build-home-authors.md | 6 pkgdown-2.0.2/pkgdown/tests/testthat/_snaps/build-home-index.md | 10 pkgdown-2.0.2/pkgdown/tests/testthat/_snaps/build-news.md | 38 ++ pkgdown-2.0.2/pkgdown/tests/testthat/_snaps/build-reference-index.md | 16 - pkgdown-2.0.2/pkgdown/tests/testthat/_snaps/build-search-docs/search-no-url.json | 2 pkgdown-2.0.2/pkgdown/tests/testthat/_snaps/build-search-docs/search.json | 2 pkgdown-2.0.2/pkgdown/tests/testthat/_snaps/markdown.md | 3 pkgdown-2.0.2/pkgdown/tests/testthat/_snaps/navbar.md | 2 pkgdown-2.0.2/pkgdown/tests/testthat/_snaps/rd-html.md | 5 pkgdown-2.0.2/pkgdown/tests/testthat/_snaps/render.md | 3 pkgdown-2.0.2/pkgdown/tests/testthat/assets/articles/vignettes/html-deps.Rmd |only pkgdown-2.0.2/pkgdown/tests/testthat/assets/news/DESCRIPTION | 1 pkgdown-2.0.2/pkgdown/tests/testthat/assets/reference-html-dep |only pkgdown-2.0.2/pkgdown/tests/testthat/test-build-articles.R | 44 ++ pkgdown-2.0.2/pkgdown/tests/testthat/test-build-home-authors.R | 2 pkgdown-2.0.2/pkgdown/tests/testthat/test-build-news.R | 154 +++++++-- pkgdown-2.0.2/pkgdown/tests/testthat/test-build-redirects.R | 1 pkgdown-2.0.2/pkgdown/tests/testthat/test-build-reference-index.R | 15 pkgdown-2.0.2/pkgdown/tests/testthat/test-build-reference.R | 25 + pkgdown-2.0.2/pkgdown/tests/testthat/test-navbar.R | 25 + pkgdown-2.0.2/pkgdown/tests/testthat/test-tweak-page.R | 30 + pkgdown-2.0.2/pkgdown/tests/testthat/test-tweak-tags.R | 15 pkgdown-2.0.2/pkgdown/vignettes/customise.Rmd | 6 pkgdown-2.0.2/pkgdown/vignettes/pkgdown.Rmd | 14 pkgdown-2.0.2/pkgdown/vignettes/test/rendering.Rmd | 6 82 files changed, 832 insertions(+), 391 deletions(-)
Title: Translate English Words into Chinese, or Translate Chinese Words
into English
Description: If translate English words into Chinese, there is a faster
way for R user. 'RYoudaoTranslate' package provides interface to
'Youdao' <http://youdao.com/> translation open API for R user. 'entcn'
package also provides similar features. But it does not support Chinese
words translation into English, I have made some improvements on the basis
of this software. You can pass in a words or a vector consisting of multiple
words, ecce package support both English and Chinese translation. It also
support browse translation results in website.
Author: Xinyuan Chu [aut, cre]
Maintainer: Xinyuan Chu <chuxinyuan@outlook.com>
Diff between ecce versions 1.0.7 dated 2020-06-29 and 1.0.8 dated 2022-01-13
ecce-1.0.7/ecce/man/figures/logo.png |only ecce-1.0.8/ecce/DESCRIPTION | 15 ecce-1.0.8/ecce/LICENSE | 4 ecce-1.0.8/ecce/MD5 | 30 - ecce-1.0.8/ecce/NAMESPACE | 10 ecce-1.0.8/ecce/R/translate.R | 150 ++--- ecce-1.0.8/ecce/R/translate_full.R | 168 +++--- ecce-1.0.8/ecce/R/translate_view.R | 116 ++-- ecce-1.0.8/ecce/README.md | 98 +-- ecce-1.0.8/ecce/build/vignette.rds |binary ecce-1.0.8/ecce/inst/doc/ecce.R | 94 +-- ecce-1.0.8/ecce/inst/doc/ecce.Rmd | 208 +++---- ecce-1.0.8/ecce/inst/doc/ecce.html | 671 ++++++++---------------- ecce-1.0.8/ecce/man/figures/logo.PNG |only ecce-1.0.8/ecce/tests/testthat.R | 8 ecce-1.0.8/ecce/tests/testthat/test-translate.R | 38 - ecce-1.0.8/ecce/vignettes/ecce.Rmd | 208 +++---- 17 files changed, 821 insertions(+), 997 deletions(-)
Title: Plane Geometry
Description: An extensive set of plane geometry routines. Provides R6 classes representing triangles, circles, circular arcs, ellipses, elliptical arcs and lines, and their plot methods. Also provides R6 classes representing transformations: rotations, reflections, homotheties, scalings, general affine transformations, inversions, Möbius transformations.
Author: Stéphane Laurent
Maintainer: Stéphane Laurent <laurent_step@outlook.fr>
Diff between PlaneGeometry versions 1.3.0 dated 2021-12-23 and 1.3.1 dated 2022-01-13
DESCRIPTION | 9 +++++---- MD5 | 15 ++++++++------- NAMESPACE | 2 ++ NEWS.md | 6 ++++++ R/Ellipse.R | 46 ++++++++++++++++++++++++++++++++++++++++++++++ inst/doc/examples.Rmd | 9 +++++---- inst/doc/examples.html | 6 +++--- man/fitEllipse.Rd |only vignettes/examples.Rmd | 9 +++++---- 9 files changed, 80 insertions(+), 22 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 1.1-2 dated 2021-12-16 and 1.1-3 dated 2022-01-13
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- inst/NEWS.Rd | 8 ++++++++ inst/doc/mlt.pdf |binary tests/GBSG2.R | 2 +- 5 files changed, 18 insertions(+), 10 deletions(-)
Title: Omics Data Integration Using Kernel Methods
Description: Kernel-based methods are powerful methods for integrating
heterogeneous types of data. mixKernel aims at providing methods to combine
kernel for unsupervised exploratory analysis. Different solutions are
provided to compute a meta-kernel, in a consensus way or in a way that
best preserves the original topology of the data. mixKernel also integrates
kernel PCA to visualize similarities between samples in a non linear space
and from the multiple source point of view. Functions to assess and display
important variables are also provided in the package. Ref: Jerome Mariette
and Nathalie Villa-Vialaneix (2018) <doi:10.1093/bioinformatics/btx682>.
Author: Jerome Mariette [aut, cre],
Celine Brouard [aut],
Remi Flamary [aut],
Nathalie Vialaneix [aut]
Maintainer: Jerome Mariette <jerome.mariette@inrae.fr>
Diff between mixKernel versions 0.7 dated 2021-06-15 and 0.8 dated 2022-01-13
DESCRIPTION | 19 ++++++----- MD5 | 25 +++++++++----- NEWS | 9 ++++- build |only inst/CITATION | 14 +++++++- inst/doc |only inst/python/center_scale.py | 2 - inst/python/kokfs.py | 2 - inst/python/ukfs.py | 2 - man/center.scale.Rd | 2 - man/select.features.Rd | 76 ++++++++++++++++++++++---------------------- vignettes |only 12 files changed, 92 insertions(+), 59 deletions(-)
Title: Treatment of Zeros, Left-Censored and Missing Values in
Compositional Data Sets
Description: Principled methods for the imputation of zeros, left-censored and missing data in
compositional data sets (Palarea-Albaladejo and Martin-Fernandez (2015) <doi:10.1016/j.chemolab.2015.02.019>).
Author: Javier Palarea-Albaladejo [cre, aut]
(<https://orcid.org/0000-0003-0162-669X>),
Josep Antoni Martin-Fernandez [aut]
(<https://orcid.org/0000-0003-2366-1592>)
Maintainer: Javier Palarea-Albaladejo <javier.palarea@udg.edu>
Diff between zCompositions versions 1.3.4 dated 2020-03-04 and 1.4.0 dated 2022-01-13
DESCRIPTION | 29 +++++-- MD5 | 63 +++++++++------- NEWS | 15 ++++ R/cmultRepl.R | 161 +++++++++++++++++++++++++------------------ R/lrDA.R | 45 +++++++++--- R/lrEM.R | 52 ++++++++++--- R/lrEMplus.R | 38 ++++++++-- R/lrSVD.R |only R/lrSVDplus.R |only R/multKM.R | 28 ++++++- R/multLN.R | 28 ++++++- R/multRepl.R | 36 ++++++++- R/multReplus.R | 38 ++++++++-- R/splineKM.R | 2 R/zVarArray.R | 2 R/zVarArrayError.R | 2 R/zVarArrayTest.R | 2 README.md | 5 + build |only man/cmultRepl.Rd | 25 ++++-- man/lcTest.Rd | 18 ++-- man/lrDA.Rd | 19 +++-- man/lrEM.Rd | 27 ++++--- man/lrEMplus.Rd | 19 +++-- man/lrSVD.Rd |only man/lrSVDplus.Rd |only man/multKM.Rd | 9 +- man/multLN.Rd | 11 +- man/multRepl.Rd | 22 +++-- man/multReplus.Rd | 17 ++-- man/zCompositions-package.Rd | 6 - man/zPatterns.Rd | 2 man/zVarArray.Rd | 5 - man/zVarArrayError.Rd | 14 ++- man/zVarArrayTest.Rd | 5 - 35 files changed, 518 insertions(+), 227 deletions(-)
Title: Identifiability of Linear Structural Equation Models
Description: Provides routines to check identifiability or non-identifiability
of linear structural equation models as described in Drton, Foygel, and
Sullivant (2011) <doi:10.1214/10-AOS859>, Foygel, Draisma, and Drton (2012)
<doi:10.1214/12-AOS1012>, and other works. The routines are based on the graphical
representation of structural equation models.
Author: Rina Foygel Barber [aut],
Mathias Drton [aut],
Luca Weihs [aut],
Nils Sturma [cre, aut]
Maintainer: Nils Sturma <nils.sturma@tum.de>
Diff between SEMID versions 0.3.2 dated 2019-05-21 and 0.4.0 dated 2022-01-13
SEMID-0.3.2/SEMID/man/MixedGraphFixedOrder.Rd |only SEMID-0.3.2/SEMID/man/createHalfTrekFlowGraph.Rd |only SEMID-0.3.2/SEMID/man/createHtrGraph.Rd |only SEMID-0.3.2/SEMID/man/stronglyConnectedComponents.Rd |only SEMID-0.4.0/SEMID/DESCRIPTION | 30 SEMID-0.4.0/SEMID/MD5 | 215 +- SEMID-0.4.0/SEMID/NAMESPACE | 222 +- SEMID-0.4.0/SEMID/NEWS.md |only SEMID-0.4.0/SEMID/R/FlowGraph.R | 280 +- SEMID-0.4.0/SEMID/R/LatentDigraph.R |only SEMID-0.4.0/SEMID/R/MixedGraph.R | 1278 ++++-------- SEMID-0.4.0/SEMID/R/SEMID.R | 206 - SEMID-0.4.0/SEMID/R/ancestralID.R | 1012 ++++----- SEMID-0.4.0/SEMID/R/edgewiseID.R | 348 +-- SEMID-0.4.0/SEMID/R/graphID.R | 1002 ++++----- SEMID-0.4.0/SEMID/R/htcID.R | 638 ++--- SEMID-0.4.0/SEMID/R/lfhtcID.R |only SEMID-0.4.0/SEMID/R/plotting.R | 114 - SEMID-0.4.0/SEMID/R/trekSepId.R | 282 +- SEMID-0.4.0/SEMID/R/utils.R | 1160 +++++----- SEMID-0.4.0/SEMID/README.md | 616 +++-- SEMID-0.4.0/SEMID/demo/00Index | 2 SEMID-0.4.0/SEMID/demo/SEMID.R | 564 ++--- SEMID-0.4.0/SEMID/man/FlowGraph.Rd | 52 SEMID-0.4.0/SEMID/man/L.Rd | 42 SEMID-0.4.0/SEMID/man/LatentDigraph.Rd |only SEMID-0.4.0/SEMID/man/LatentDigraphFixedOrder.Rd |only SEMID-0.4.0/SEMID/man/MixedGraph.Rd | 91 SEMID-0.4.0/SEMID/man/O.Rd | 36 SEMID-0.4.0/SEMID/man/SEMID-package.Rd | 200 - SEMID-0.4.0/SEMID/man/ancestors.Rd | 58 SEMID-0.4.0/SEMID/man/ancestralID.Rd | 52 SEMID-0.4.0/SEMID/man/ancestralIdentifyStep.Rd | 113 - SEMID-0.4.0/SEMID/man/children.Rd |only SEMID-0.4.0/SEMID/man/createAncestralIdentifier.Rd | 91 SEMID-0.4.0/SEMID/man/createEdgewiseIdentifier.Rd | 80 SEMID-0.4.0/SEMID/man/createHtcIdentifier.Rd | 80 SEMID-0.4.0/SEMID/man/createIdentifierBaseCase.Rd | 74 SEMID-0.4.0/SEMID/man/createLFHtcIdentifier.Rd |only SEMID-0.4.0/SEMID/man/createLFIdentifierBaseCase.Rd |only SEMID-0.4.0/SEMID/man/createSimpleBiDirIdentifier.Rd | 38 SEMID-0.4.0/SEMID/man/createTrGraph.Rd | 36 SEMID-0.4.0/SEMID/man/createTrekFlowGraph.Rd | 36 SEMID-0.4.0/SEMID/man/createTrekSeparationIdentifier.Rd | 80 SEMID-0.4.0/SEMID/man/descendants.Rd | 55 SEMID-0.4.0/SEMID/man/edgewiseID.Rd | 68 SEMID-0.4.0/SEMID/man/edgewiseIdentifyStep.Rd | 123 - SEMID-0.4.0/SEMID/man/edgewiseTSID.Rd | 90 SEMID-0.4.0/SEMID/man/flowBetween.Rd | 54 SEMID-0.4.0/SEMID/man/generalGenericID.Rd | 116 - SEMID-0.4.0/SEMID/man/getAncestors.Rd | 40 SEMID-0.4.0/SEMID/man/getDescendants.Rd | 42 SEMID-0.4.0/SEMID/man/getHalfTrekSystem.Rd | 95 SEMID-0.4.0/SEMID/man/getMaxFlow.Rd | 98 SEMID-0.4.0/SEMID/man/getMixedCompForNode.Rd | 62 SEMID-0.4.0/SEMID/man/getMixedGraph.Rd |only SEMID-0.4.0/SEMID/man/getParents.Rd | 40 SEMID-0.4.0/SEMID/man/getSiblings.Rd | 40 SEMID-0.4.0/SEMID/man/getTrekSystem.Rd | 95 SEMID-0.4.0/SEMID/man/graphID.Rd | 209 + SEMID-0.4.0/SEMID/man/graphID.ancestralID.Rd | 68 SEMID-0.4.0/SEMID/man/graphID.decompose.Rd | 100 SEMID-0.4.0/SEMID/man/graphID.genericID.Rd | 76 SEMID-0.4.0/SEMID/man/graphID.globalID.Rd | 64 SEMID-0.4.0/SEMID/man/graphID.htcID.Rd | 64 SEMID-0.4.0/SEMID/man/graphID.main.Rd | 79 SEMID-0.4.0/SEMID/man/graphID.nonHtcID.Rd | 66 SEMID-0.4.0/SEMID/man/htcID.Rd | 72 SEMID-0.4.0/SEMID/man/htcIdentifyStep.Rd | 132 - SEMID-0.4.0/SEMID/man/htr.Rd | 52 SEMID-0.4.0/SEMID/man/htrFrom.Rd | 59 SEMID-0.4.0/SEMID/man/inducedSubgraph.Rd | 43 SEMID-0.4.0/SEMID/man/isSibling.Rd | 53 SEMID-0.4.0/SEMID/man/latentDigraphHasSimpleNumbering.Rd |only SEMID-0.4.0/SEMID/man/latentNodes.Rd |only SEMID-0.4.0/SEMID/man/lfhtcID.Rd |only SEMID-0.4.0/SEMID/man/lfhtcIdentifyStep.Rd |only SEMID-0.4.0/SEMID/man/mixedGraphHasSimpleNumbering.Rd | 30 SEMID-0.4.0/SEMID/man/nodes.Rd | 36 SEMID-0.4.0/SEMID/man/numLatents.Rd |only SEMID-0.4.0/SEMID/man/numNodes.Rd | 45 SEMID-0.4.0/SEMID/man/numObserved.Rd |only SEMID-0.4.0/SEMID/man/observedNodes.Rd |only SEMID-0.4.0/SEMID/man/observedParents.Rd |only SEMID-0.4.0/SEMID/man/parents.Rd | 60 SEMID-0.4.0/SEMID/man/plot.Rd | 37 SEMID-0.4.0/SEMID/man/plotLatentDigraph.Rd |only SEMID-0.4.0/SEMID/man/plotMixedGraph.Rd | 56 SEMID-0.4.0/SEMID/man/print.GenericIDResult.Rd | 36 SEMID-0.4.0/SEMID/man/print.LfhtcIDResult.Rd |only SEMID-0.4.0/SEMID/man/print.SEMIDResult.Rd | 36 SEMID-0.4.0/SEMID/man/semID.Rd | 167 - SEMID-0.4.0/SEMID/man/siblings.Rd | 49 SEMID-0.4.0/SEMID/man/stronglyConnectedComponent.Rd | 50 SEMID-0.4.0/SEMID/man/subsetsOfSize.Rd | 40 SEMID-0.4.0/SEMID/man/tianComponent.Rd | 38 SEMID-0.4.0/SEMID/man/tianDecompose.Rd | 50 SEMID-0.4.0/SEMID/man/tianIdentifier.Rd | 44 SEMID-0.4.0/SEMID/man/tianSigmaForComponent.Rd | 68 SEMID-0.4.0/SEMID/man/toEx.Rd | 43 SEMID-0.4.0/SEMID/man/toIn.Rd | 43 SEMID-0.4.0/SEMID/man/trFrom.Rd | 80 SEMID-0.4.0/SEMID/man/trekSeparationIdentifyStep.Rd | 117 - SEMID-0.4.0/SEMID/man/updateEdgeCapacities.Rd | 44 SEMID-0.4.0/SEMID/man/updateVertexCapacities.Rd | 42 SEMID-0.4.0/SEMID/man/validateLatentNodesAreSources.Rd |only SEMID-0.4.0/SEMID/man/validateMatrices.Rd | 44 SEMID-0.4.0/SEMID/man/validateMatrix.Rd |only SEMID-0.4.0/SEMID/man/validateNodes.Rd |only SEMID-0.4.0/SEMID/man/validateVarArgsEmpty.Rd |only SEMID-0.4.0/SEMID/tests/testthat.R | 26 SEMID-0.4.0/SEMID/tests/testthat/graphExamples.R | 583 +++-- SEMID-0.4.0/SEMID/tests/testthat/helperFunctions.R | 124 - SEMID-0.4.0/SEMID/tests/testthat/test_LatentDigraph.R |only SEMID-0.4.0/SEMID/tests/testthat/test_ancestral.R | 397 +-- SEMID-0.4.0/SEMID/tests/testthat/test_edgewiseID.R | 80 SEMID-0.4.0/SEMID/tests/testthat/test_graphID.ancestralID.R | 74 SEMID-0.4.0/SEMID/tests/testthat/test_graphID.globalID.R | 42 SEMID-0.4.0/SEMID/tests/testthat/test_graphID.htcID.R | 44 SEMID-0.4.0/SEMID/tests/testthat/test_graphID.nonID.R | 42 SEMID-0.4.0/SEMID/tests/testthat/test_lfhtcID.R |only SEMID-0.4.0/SEMID/tests/testthat/test_tianDecompose.R | 89 SEMID-0.4.0/SEMID/tests/testthat/test_trekSepID.R | 62 123 files changed, 7147 insertions(+), 6954 deletions(-)
Title: k-Nearest Neighbor Join for Spatial Data
Description: K-nearest neighbor search for projected and non-projected 'sf' spatial layers. Nearest neighbor search uses (1) C code from 'GeographicLib' for lon-lat point layers, (2) function knn() from package 'nabor' for projected point layers, or (3) function st_distance() from package 'sf' for line or polygon layers. The package also includes several other utility functions for spatial analysis.
Author: Michael Dorman [aut, cre],
Johnathan Rush [ctb],
Ian Hough [ctb],
Dominic Russel [ctb],
Luigi Ranghetti [ctb],
Attilio Benini [ctb],
Arnaud Tarroux [ctb],
Charles F.F Karney [ctb, cph] (Author of included C code from
'GeographicLib' for geodesic distance)
Maintainer: Michael Dorman <dorman@post.bgu.ac.il>
Diff between nngeo versions 0.4.4 dated 2021-09-06 and 0.4.5 dated 2022-01-13
nngeo-0.4.4/nngeo/data/cities.RData |only nngeo-0.4.4/nngeo/data/line.RData |only nngeo-0.4.4/nngeo/data/pnt.RData |only nngeo-0.4.4/nngeo/data/towns.RData |only nngeo-0.4.4/nngeo/data/water.RData |only nngeo-0.4.5/nngeo/DESCRIPTION | 6 +++--- nngeo-0.4.5/nngeo/MD5 | 20 ++++++++++---------- nngeo-0.4.5/nngeo/NEWS.md | 6 +++++- nngeo-0.4.5/nngeo/R/st_nn_pnt_proj.R | 27 ++++++++++++++++++++++++++- nngeo-0.4.5/nngeo/build/vignette.rds |binary nngeo-0.4.5/nngeo/data/cities.rda |only nngeo-0.4.5/nngeo/data/line.rda |only nngeo-0.4.5/nngeo/data/pnt.rda |only nngeo-0.4.5/nngeo/data/towns.rda |only nngeo-0.4.5/nngeo/data/water.rda |only nngeo-0.4.5/nngeo/inst/doc/intro.pdf |binary 16 files changed, 44 insertions(+), 15 deletions(-)
Title: Computations Around Bayesian Predictive Power
Description: Implements functions to update Bayesian Predictive Power Computations after not stopping a clinical trial at an interim analysis. Such an interim analysis can either be blinded or unblinded. Code is provided for Normally distributed endpoints with known variance, with a prominent example being the hazard ratio.
Author: Kaspar Rufibach, Paul Jordan, Markus Abt
Maintainer: Kaspar Rufibach <kaspar.rufibach@roche.com>
Diff between bpp versions 1.0.3 dated 2021-11-30 and 1.0.4 dated 2022-01-13
DESCRIPTION | 8 ++-- MD5 | 20 +++++------ NEWS | 4 ++ R/NormalNormalPosterior.r | 7 +--- inst/doc/bpp.R | 4 +- inst/doc/bpp.Rmd | 4 +- inst/doc/bpp.html | 73 +++++++++++++++++++++---------------------- man/NormalNormalPosterior.Rd | 8 ++-- man/bpp-package.Rd | 4 +- man/bpp_1interim.Rd | 6 +-- vignettes/bpp.Rmd | 4 +- 11 files changed, 73 insertions(+), 69 deletions(-)
Title: Bayesian Functional Linear Regression with Sparse Step Functions
Description: A method for the Bayesian functional linear regression model (scalar-on-function),
including two estimators of the coefficient function and an estimator of its support.
A representation of the posterior distribution is also available. Grollemund P-M., Abraham C.,
Baragatti M., Pudlo P. (2019) <doi:10.1214/18-BA1095>.
Author: Paul-Marie Grollemund [aut, cre],
Isabelle Sanchez [ctr],
Meili Baragatti [ctr]
Maintainer: Paul-Marie Grollemund <paul.marie.grollemund@gmail.com>
Diff between bliss versions 1.0.2 dated 2021-05-17 and 1.0.3 dated 2022-01-13
DESCRIPTION | 10 MD5 | 43 +- NEWS.md |only R/Bliss_Gibbs_Sampler.R | 32 + R/Bliss_method.R | 30 + R/basic_functions.R | 6 build/vignette.rds |binary inst/doc/BlissIntro.R | 54 ++ inst/doc/BlissIntro.Rmd | 198 ++++++++-- inst/doc/BlissIntro.html | 512 ++++++++++----------------- man/Bliss_Gibbs_Sampler.Rd | 2 man/Bliss_Simulated_Annealing.Rd | 8 man/bliss.Rd | 1 man/build_Fourier_basis.Rd | 2 man/data1.Rd | 6 man/fit_Bliss.Rd | 13 man/interpretation_plot.Rd | 3 man/param1.Rd | 6 man/plot_bliss.Rd | 3 man/res_bliss1.Rd | 6 src/RcppExports.cpp | 5 src/bliss_rcpp_functions.cpp | 722 ++++++++++++++++++++------------------- vignettes/BlissIntro.Rmd | 198 ++++++++-- 23 files changed, 1045 insertions(+), 815 deletions(-)
Title: 'sf'-Compatible Interface to 'Google Maps' APIs
Description: Interface to the 'Google Maps' APIs: (1) routing directions based on the 'Directions' API, returned as 'sf' objects, either as single feature per alternative route, or a single feature per segment per alternative route; (2) travel distance or time matrices based on the 'Distance Matrix' API; (3) geocoded locations based on the 'Geocode' API, returned as 'sf' objects, either points or bounds; (4) map images using the 'Maps Static' API, returned as 'stars' objects.
Author: Michael Dorman [aut, cre],
Tom Buckley [ctb],
Alex Dannenberg [ctb],
Mihir Bhaskar [ctb],
Juan P. Fonseca-Zamora [ctb]
Maintainer: Michael Dorman <dorman@post.bgu.ac.il>
Diff between mapsapi versions 0.5.0 dated 2021-09-06 and 0.5.3 dated 2022-01-13
DESCRIPTION | 10 MD5 | 42 NAMESPACE | 7 NEWS.md | 12 R/check_inputs.R | 6 R/data.R | 4 R/decode_line.R | 6 R/encode_locations.R | 11 R/mp_directions.R | 20 R/mp_geocode.R | 12 R/mp_get_bounds.R | 67 R/mp_get_matrix.R | 67 R/mp_get_points.R | 29 R/mp_get_routes.R | 316 +- R/mp_get_segments.R | 301 +- R/mp_map.R | 16 R/mp_matrix.R | 29 build/vignette.rds |binary inst/doc/intro.html | 6237 ++++++++++++++++++++++++++++++++++++++++++++++++++- man/mp_directions.Rd | 5 man/mp_geocode.Rd | 5 man/mp_matrix.Rd | 19 22 files changed, 6728 insertions(+), 493 deletions(-)
Title: Spatial Data Analysis
Description: Methods for spatial data analysis with raster and vector data. Raster methods allow for low-level data manipulation as well as high-level global, local, zonal, and focal computation. The predict and interpolate methods facilitate the use of regression type (interpolation, machine learning) models for spatial prediction, including with satellite remote sensing data. Processing of very large files is supported. See the manual and tutorials on <https://rspatial.org/terra/> to get started. 'terra' is very similar to the 'raster' package; but 'terra' can do more, is easier to use, and it is faster.
Author: Robert J. Hijmans [cre, aut] (<https://orcid.org/0000-0001-5872-2872>),
Roger Bivand [ctb] (<https://orcid.org/0000-0003-2392-6140>),
Jacob van Etten [ctb] (<https://orcid.org/0000-0001-7554-2558>),
Karl Forner [ctb],
Jeroen Ooms [ctb] (<https://orcid.org/0000-0002-4035-0289>),
Edzer Pebesma [ctb] (<https://orcid.org/0000-0001-8049-7069>)
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between terra versions 1.4-22 dated 2021-11-24 and 1.5-12 dated 2022-01-13
terra-1.4-22/terra/man/copy.Rd |only terra-1.4-22/terra/man/isLonLat.Rd |only terra-1.4-22/terra/man/math.Rd |only terra-1.5-12/terra/DESCRIPTION | 13 terra-1.5-12/terra/MD5 | 386 +++--- terra-1.5-12/terra/NAMESPACE | 7 terra-1.5-12/terra/NEWS.md | 144 +- terra-1.5-12/terra/R/Agenerics.R | 39 terra-1.5-12/terra/R/Arith_generics.R | 91 + terra-1.5-12/terra/R/RGB.R |only terra-1.5-12/terra/R/RcppExports.R | 50 terra-1.5-12/terra/R/SpatRasterDataset.R | 25 terra-1.5-12/terra/R/Zdeprecated.R | 15 terra-1.5-12/terra/R/aggregate.R | 14 terra-1.5-12/terra/R/app.R | 14 terra-1.5-12/terra/R/approximate.R |only terra-1.5-12/terra/R/autocor.R | 24 terra-1.5-12/terra/R/click.R | 2 terra-1.5-12/terra/R/coerce.R | 383 ------ terra-1.5-12/terra/R/colors.R | 20 terra-1.5-12/terra/R/connect.R | 12 terra-1.5-12/terra/R/crs.R | 29 terra-1.5-12/terra/R/distance.R | 31 terra-1.5-12/terra/R/expand.R | 2 terra-1.5-12/terra/R/extract.R | 170 +- terra-1.5-12/terra/R/focal.R | 357 +++++- terra-1.5-12/terra/R/focalMat.R | 16 terra-1.5-12/terra/R/gdal.R | 24 terra-1.5-12/terra/R/generics.R | 204 ++- terra-1.5-12/terra/R/geom.R | 18 terra-1.5-12/terra/R/gridDistance.R |only terra-1.5-12/terra/R/ifelse.R | 10 terra-1.5-12/terra/R/init.R | 2 terra-1.5-12/terra/R/inset.R | 35 terra-1.5-12/terra/R/lapp.R | 6 terra-1.5-12/terra/R/layerCor.R |only terra-1.5-12/terra/R/levels.R | 35 terra-1.5-12/terra/R/lines.R | 18 terra-1.5-12/terra/R/makeVRT.R |only terra-1.5-12/terra/R/match.R | 29 terra-1.5-12/terra/R/math.R | 44 terra-1.5-12/terra/R/merge.R | 5 terra-1.5-12/terra/R/mergeTime.R |only terra-1.5-12/terra/R/messages.R | 7 terra-1.5-12/terra/R/names.R | 6 terra-1.5-12/terra/R/ncdf.R | 6 terra-1.5-12/terra/R/options.R | 11 terra-1.5-12/terra/R/pack.R | 25 terra-1.5-12/terra/R/plot.R | 23 terra-1.5-12/terra/R/plot2rasters.R | 2 terra-1.5-12/terra/R/plotExtent.R | 18 terra-1.5-12/terra/R/plotRGB.R | 230 --- terra-1.5-12/terra/R/plot_legend.R | 14 terra-1.5-12/terra/R/plot_raster.R | 100 + terra-1.5-12/terra/R/plot_scale.R | 189 ++- terra-1.5-12/terra/R/plot_vector.R | 106 + terra-1.5-12/terra/R/predict.R | 4 terra-1.5-12/terra/R/rast.R | 85 - terra-1.5-12/terra/R/rasterize.R | 55 terra-1.5-12/terra/R/readsvg.R | 22 terra-1.5-12/terra/R/relate.R | 8 terra-1.5-12/terra/R/replace.R | 51 terra-1.5-12/terra/R/sample.R | 124 +- terra-1.5-12/terra/R/show.R | 45 terra-1.5-12/terra/R/spatDF.R | 4 terra-1.5-12/terra/R/spatvec.R | 43 terra-1.5-12/terra/R/tapp.R | 4 terra-1.5-12/terra/R/tempfiles.R | 2 terra-1.5-12/terra/R/tiles.R | 2 terra-1.5-12/terra/R/time.R | 5 terra-1.5-12/terra/R/values.R | 172 +- terra-1.5-12/terra/R/vect.R | 26 terra-1.5-12/terra/R/write.R | 13 terra-1.5-12/terra/R/zonal.R | 10 terra-1.5-12/terra/R/zoom.R | 2 terra-1.5-12/terra/R/zzz.R | 27 terra-1.5-12/terra/configure | 33 terra-1.5-12/terra/configure.ac | 11 terra-1.5-12/terra/inst/tinytest/test_classify.R | 2 terra-1.5-12/terra/inst/tinytest/test_extract.R | 20 terra-1.5-12/terra/inst/tinytest/test_focal.R | 45 terra-1.5-12/terra/inst/tinytest/test_patches.R |only terra-1.5-12/terra/man/RGB.Rd | 40 terra-1.5-12/terra/man/all.equal.Rd |only terra-1.5-12/terra/man/app.Rd | 2 terra-1.5-12/terra/man/approximate.Rd |only terra-1.5-12/terra/man/arith-generic.Rd |only terra-1.5-12/terra/man/arrow.Rd |only terra-1.5-12/terra/man/as.data.frame.Rd | 9 terra-1.5-12/terra/man/boxplot.Rd | 6 terra-1.5-12/terra/man/buffer.Rd | 4 terra-1.5-12/terra/man/c.Rd | 5 terra-1.5-12/terra/man/cellSize.Rd | 4 terra-1.5-12/terra/man/cells.Rd | 8 terra-1.5-12/terra/man/classify.Rd | 22 terra-1.5-12/terra/man/coerce.Rd | 8 terra-1.5-12/terra/man/compare-generics.Rd |only terra-1.5-12/terra/man/contour.Rd | 10 terra-1.5-12/terra/man/cover.Rd | 13 terra-1.5-12/terra/man/crop.Rd | 5 terra-1.5-12/terra/man/deepcopy.Rd |only terra-1.5-12/terra/man/densify.Rd |only terra-1.5-12/terra/man/describe.Rd | 4 terra-1.5-12/terra/man/direction.Rd |only terra-1.5-12/terra/man/distance.Rd | 12 terra-1.5-12/terra/man/dots.Rd | 7 terra-1.5-12/terra/man/expanse.Rd | 5 terra-1.5-12/terra/man/extract.Rd | 29 terra-1.5-12/terra/man/factors.Rd | 6 terra-1.5-12/terra/man/fillTime.Rd |only terra-1.5-12/terra/man/focal.Rd | 45 terra-1.5-12/terra/man/focal3D.Rd |only terra-1.5-12/terra/man/focalCor.Rd |only terra-1.5-12/terra/man/focalCpp.Rd | 6 terra-1.5-12/terra/man/focalMat.Rd | 3 terra-1.5-12/terra/man/focalReg.Rd | 8 terra-1.5-12/terra/man/gdal.Rd | 11 terra-1.5-12/terra/man/geometry.Rd | 4 terra-1.5-12/terra/man/global.Rd | 4 terra-1.5-12/terra/man/gridDistance.Rd |only terra-1.5-12/terra/man/ifelse.Rd | 2 terra-1.5-12/terra/man/impose.Rd |only terra-1.5-12/terra/man/inset.Rd | 26 terra-1.5-12/terra/man/is.bool.Rd |only terra-1.5-12/terra/man/is.lonlat.Rd |only terra-1.5-12/terra/man/isvalid.Rd | 15 terra-1.5-12/terra/man/layerCor.Rd |only terra-1.5-12/terra/man/lines.Rd | 14 terra-1.5-12/terra/man/makeVRT.Rd |only terra-1.5-12/terra/man/math-generics.Rd |only terra-1.5-12/terra/man/mergeTime.Rd |only terra-1.5-12/terra/man/minmax.Rd | 9 terra-1.5-12/terra/man/mosaic.Rd | 4 terra-1.5-12/terra/man/patches.Rd | 29 terra-1.5-12/terra/man/plot.Rd | 22 terra-1.5-12/terra/man/project.Rd | 5 terra-1.5-12/terra/man/quantile.Rd | 19 terra-1.5-12/terra/man/rast.Rd | 39 terra-1.5-12/terra/man/rasterize.Rd | 31 terra-1.5-12/terra/man/readwrite.Rd | 8 terra-1.5-12/terra/man/replace.Rd | 6 terra-1.5-12/terra/man/sample.Rd | 19 terra-1.5-12/terra/man/sbar.Rd | 35 terra-1.5-12/terra/man/sds.Rd | 10 terra-1.5-12/terra/man/setValues.Rd | 3 terra-1.5-12/terra/man/sources.Rd | 9 terra-1.5-12/terra/man/stretch.Rd | 12 terra-1.5-12/terra/man/summarize-generics.Rd | 6 terra-1.5-12/terra/man/terra-package.Rd | 122 +- terra-1.5-12/terra/man/terraOptions.Rd | 4 terra-1.5-12/terra/man/terrain.Rd | 9 terra-1.5-12/terra/man/union.Rd | 13 terra-1.5-12/terra/man/values.Rd | 9 terra-1.5-12/terra/man/vect.Rd | 8 terra-1.5-12/terra/man/vrt.Rd | 3 terra-1.5-12/terra/man/writeRaster.Rd | 6 terra-1.5-12/terra/src/Makevars.ucrt | 26 terra-1.5-12/terra/src/RcppExports.cpp | 179 +++ terra-1.5-12/terra/src/RcppFunctions.cpp | 131 +- terra-1.5-12/terra/src/RcppModule.cpp | 106 + terra-1.5-12/terra/src/arith.cpp | 298 +++-- terra-1.5-12/terra/src/crs.cpp | 11 terra-1.5-12/terra/src/date.h | 2 terra-1.5-12/terra/src/distRaster.cpp | 1336 +++++++++++------------ terra-1.5-12/terra/src/distance.cpp | 127 -- terra-1.5-12/terra/src/distance.h | 4 terra-1.5-12/terra/src/extract.cpp | 124 +- terra-1.5-12/terra/src/file_utils.cpp | 35 terra-1.5-12/terra/src/file_utils.h | 4 terra-1.5-12/terra/src/focal.cpp | 221 ++- terra-1.5-12/terra/src/gcp.cpp | 4 terra-1.5-12/terra/src/gdal_algs.cpp | 667 +++++++---- terra-1.5-12/terra/src/gdal_multidimensional.cpp | 26 terra-1.5-12/terra/src/gdalio.cpp | 124 +- terra-1.5-12/terra/src/geos_methods.cpp | 439 +++++-- terra-1.5-12/terra/src/geos_spat.h | 27 terra-1.5-12/terra/src/geosphere.cpp |only terra-1.5-12/terra/src/math_utils.cpp | 8 terra-1.5-12/terra/src/mediancut.cpp | 10 terra-1.5-12/terra/src/memory.cpp | 25 terra-1.5-12/terra/src/ram.cpp | 2 terra-1.5-12/terra/src/raster_methods.cpp | 1194 ++++++++++++-------- terra-1.5-12/terra/src/raster_stats.cpp | 52 terra-1.5-12/terra/src/rasterize.cpp | 138 +- terra-1.5-12/terra/src/read.cpp | 80 - terra-1.5-12/terra/src/read_gdal.cpp | 429 +++++-- terra-1.5-12/terra/src/read_ogr.cpp | 34 terra-1.5-12/terra/src/sample.cpp | 52 terra-1.5-12/terra/src/spatBase.cpp | 21 terra-1.5-12/terra/src/spatBase.h | 30 terra-1.5-12/terra/src/spatDataframe.cpp | 30 terra-1.5-12/terra/src/spatDataframe.h | 10 terra-1.5-12/terra/src/spatFactor.h | 2 terra-1.5-12/terra/src/spatRaster.cpp | 189 ++- terra-1.5-12/terra/src/spatRaster.h | 119 +- terra-1.5-12/terra/src/spatRasterMultiple.h | 31 terra-1.5-12/terra/src/spatSources.cpp | 97 + terra-1.5-12/terra/src/spatTime.cpp | 41 terra-1.5-12/terra/src/spatTime.h | 1 terra-1.5-12/terra/src/spatVector.cpp | 311 ++++- terra-1.5-12/terra/src/spatVector.h | 36 terra-1.5-12/terra/src/string_utils.cpp | 14 terra-1.5-12/terra/src/string_utils.h | 4 terra-1.5-12/terra/src/vecmath.cpp | 15 terra-1.5-12/terra/src/vecmath.h | 39 terra-1.5-12/terra/src/vector_methods.cpp | 16 terra-1.5-12/terra/src/write.cpp | 231 ++- terra-1.5-12/terra/src/write_gdal.cpp | 274 +++- terra-1.5-12/terra/src/write_ogr.cpp | 63 - 209 files changed, 7813 insertions(+), 4279 deletions(-)
Title: Identify Rogue Taxa in Sets of Phylogenetic Trees
Description: Rogue ("wildcard") taxa are leaves with uncertain phylogenetic
position.
Their position may vary from tree to tree under inference methods that yield a
tree set (e.g. bootstrapping, Bayesian tree searches, maximum parsimony).
The presence of rogue taxa in a tree set can potentially remove all
information from a consensus tree. The information content of a consensus
tree - a function of its resolution and branch support values - can often be
increased by removing rogue taxa.
'Rogue' provides an explicitly information-theoretic approach to rogue
detection (Smith 2022) <doi:10.1093/sysbio/syab099>,
and an interface to 'RogueNaRok' (Aberer et al. 2013)
<doi:10.1093/sysbio/sys078>.
Author: Martin R. Smith [aut, cre, cph]
(<https://orcid.org/0000-0001-5660-1727>),
Andre J. Aberer [aut, cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between Rogue versions 2.0.0 dated 2021-09-13 and 2.1.0 dated 2022-01-13
Rogue-2.0.0/Rogue/R/RogueNaRok.R |only Rogue-2.0.0/Rogue/man/Cophenetic.Rd |only Rogue-2.0.0/Rogue/src/cophenetic.c |only Rogue-2.0.0/Rogue/tests/testthat/RogueNaRok_droppedRogues.tmp |only Rogue-2.0.0/Rogue/tests/testthat/RogueNaRok_info.tmp |only Rogue-2.1.0/Rogue/DESCRIPTION | 22 - Rogue-2.1.0/Rogue/MD5 | 58 ++-- Rogue-2.1.0/Rogue/NAMESPACE | 4 Rogue-2.1.0/Rogue/NEWS.md | 20 + Rogue-2.1.0/Rogue/R/Rogue-package.R | 6 Rogue-2.1.0/Rogue/R/RogueTaxa.R | 37 ++ Rogue-2.1.0/Rogue/R/SPIC.R | 75 +++-- Rogue-2.1.0/Rogue/R/stability.R | 73 +++-- Rogue-2.1.0/Rogue/R/zz_RogueNaRok.R |only Rogue-2.1.0/Rogue/build/partial.rdb |binary Rogue-2.1.0/Rogue/build/vignette.rds |only Rogue-2.1.0/Rogue/inst/CITATION | 41 ++ Rogue-2.1.0/Rogue/inst/REFERENCES.bib | 140 +++++++++- Rogue-2.1.0/Rogue/inst/WORDLIST | 3 Rogue-2.1.0/Rogue/inst/apa-old-doi-prefix.csl |only Rogue-2.1.0/Rogue/inst/doc |only Rogue-2.1.0/Rogue/man/GraphGeodesic.Rd |only Rogue-2.1.0/Rogue/man/Rogue-package.Rd | 6 Rogue-2.1.0/Rogue/man/RogueTaxa.Rd | 138 +++++---- Rogue-2.1.0/Rogue/man/TipInstability.Rd | 22 + Rogue-2.1.0/Rogue/man/TipVolatility.Rd | 7 Rogue-2.1.0/Rogue/man/figures |only Rogue-2.1.0/Rogue/src/Makevars | 2 Rogue-2.1.0/Rogue/src/Rogue_init.c | 8 Rogue-2.1.0/Rogue/src/graph_geodesic.c |only Rogue-2.1.0/Rogue/tests/spelling.R |only Rogue-2.1.0/Rogue/tests/testthat/test-RogueNaRok.R | 8 Rogue-2.1.0/Rogue/tests/testthat/test-RogueTaxa.R | 2 Rogue-2.1.0/Rogue/tests/testthat/test-spic.R | 4 Rogue-2.1.0/Rogue/tests/testthat/test-stability.R | 16 - Rogue-2.1.0/Rogue/vignettes |only 36 files changed, 499 insertions(+), 193 deletions(-)
Title: A 'DBI' Interface to the 'Yandex Clickhouse' Database Providing
Basic 'dplyr' Support
Description: 'Yandex Clickhouse' (<https://clickhouse.com/>) is a high-performance relational column-store database to enable
big data exploration and 'analytics' scaling to petabytes of data. Methods are
provided that enable working with 'Yandex Clickhouse' databases via
'DBI' methods and using 'dplyr'/'dbplyr' idioms.
Author: Christian Hotz-Behofsits [aut, cre],
Daniel Winkler [aut],
Luca Rauchenberger [aut],
Peter Knaus [aut],
Clemens Danninger [aut],
Simon Stiebellehner [aut],
Dan Egnor [aut],
Vlad Losev [aut],
Keith Ray [aut],
Zhanyong Wan [aut],
Markus Heule [aut],
Oliver Flasch [aut],
Google [cph],
Yann Collet [cph]
Maintainer: Christian Hotz-Behofsits <christian.hotz-behofsits@wu.ac.at>
Diff between RClickhouse versions 0.5.2 dated 2020-03-06 and 0.6.0 dated 2022-01-13
DESCRIPTION | 11 - MD5 | 33 ++-- NAMESPACE | 7 R/ClickhouseConnection.R | 116 +++++++++++++++- R/ClickhouseDriver.R | 9 - R/dplyr.R | 68 ++------- man/ClickhouseDriver-class.Rd | 6 src/connection.cpp | 2 src/vendor/clickhouse-cpp/clickhouse/client.cpp | 37 ++++- tests/testthat/test-DBI_methods__ClickhouseConnection.R |only tests/testthat/test-DBI_methods__ClickhouseDriver.R |only tests/testthat/test-DBI_methods__ClickhouseResult.R |only tests/testthat/test-agg.R | 2 tests/testthat/test-array.R | 37 +++++ tests/testthat/test-escape.R |only tests/testthat/test-insert_fetch_types.R |only tests/testthat/test-int64.R | 2 tests/testthat/test-prefix.R | 2 tests/testthat/test-uuid.R | 5 tests/testthat/utils.R | 21 ++ 20 files changed, 260 insertions(+), 98 deletions(-)
Title: Linear and Nonlinear Mixed Effects Models
Description: Fit and compare Gaussian linear and nonlinear mixed-effects models.
Author: José Pinheiro [aut] (S version),
Douglas Bates [aut] (up to 2007),
Saikat DebRoy [ctb] (up to 2002),
Deepayan Sarkar [ctb] (up to 2005),
EISPACK authors [ctb] (src/rs.f),
Siem Heisterkamp [ctb] (Author fixed sigma),
Bert Van Willigen [ctb] (Programmer fixed sigma),
Johannes Ranke [ctb] (varConstProp()),
R-core [aut, cre]
Maintainer: R-core <R-core@R-project.org>
Diff between nlme versions 3.1-153 dated 2021-09-07 and 3.1-155 dated 2022-01-13
ChangeLog | 29 +++++++++ DESCRIPTION | 8 +- MD5 | 41 +++++++------- R/gls.R | 3 - R/gnls.R | 4 - R/lme.R | 1 R/nlme.R | 17 ++--- R/nlsList.R | 9 +-- build/partial.rdb |binary man/Quinidine.Rd | 4 - man/glsObject.Rd | 6 +- man/pdCompSymm.Rd | 2 src/corStruct.c | 126 ++++++++++++++++++++++--------------------- src/gnls.c | 28 +++++---- src/matrix.c | 36 ++++++------ src/nlme.c | 88 +++++++++++++++--------------- src/nlmefit.c | 154 ++++++++++++++++++++++++++--------------------------- src/pdMat.c | 14 ++-- tests/anova.gls.R | 10 ++- tests/nlme-stall.R | 16 ++++- tests/nlme.R | 11 +++ tests/scoping.R |only 22 files changed, 335 insertions(+), 272 deletions(-)
Title: Performance Measures for 'mlr3'
Description: Implements multiple performance measures for
supervised learning. Includes over 40 measures for regression and
classification. Additionally, meta information about the performance
measures can be queried, e.g. what the best and worst possible
performances scores are.
Author: Michel Lang [cre, aut] (<https://orcid.org/0000-0001-9754-0393>),
Martin Binder [ctb]
Maintainer: Michel Lang <michellang@gmail.com>
Diff between mlr3measures versions 0.4.0 dated 2021-09-26 and 0.4.1 dated 2022-01-13
DESCRIPTION | 6 - MD5 | 196 ++++++++++++++++++++++---------------------- NEWS.md | 10 +- R/binary_auc.R | 2 R/binary_bbrier.R | 4 R/binary_dor.R | 4 R/binary_fbeta.R | 19 +--- R/binary_fdr.R | 4 R/binary_fn.R | 4 R/binary_fnr.R | 4 R/binary_fomr.R | 4 R/binary_fp.R | 4 R/binary_fpr.R | 4 R/binary_mcc.R | 4 R/binary_npv.R | 4 R/binary_ppv.R | 4 R/binary_prauc.R | 2 R/binary_tn.R | 4 R/binary_tnr.R | 4 R/binary_tp.R | 4 R/binary_tpr.R | 4 R/classif_acc.R | 4 R/classif_auc.R | 2 R/classif_bacc.R | 4 R/classif_ce.R | 4 R/classif_logloss.R | 4 R/classif_mbrier.R | 2 R/regr_bias.R | 4 R/regr_ktau.R | 4 R/regr_mae.R | 4 R/regr_mape.R | 4 R/regr_maxae.R | 4 R/regr_maxse.R | 4 R/regr_medae.R | 4 R/regr_medse.R | 4 R/regr_mse.R | 4 R/regr_msle.R | 4 R/regr_pbias.R | 4 R/regr_rae.R | 4 R/regr_rmse.R | 4 R/regr_rmsle.R | 4 R/regr_rrse.R | 4 R/regr_rse.R | 4 R/regr_rsq.R | 4 R/regr_sae.R | 4 R/regr_smape.R | 4 R/regr_srho.R | 4 R/regr_sse.R | 4 R/similarity_jaccard.R | 5 - R/similarity_phi.R | 5 - build/partial.rdb |binary man/acc.Rd | 7 + man/auc.Rd | 8 + man/bacc.Rd | 7 + man/bbrier.Rd | 7 + man/bias.Rd | 5 - man/ce.Rd | 7 + man/dor.Rd | 10 +- man/fbeta.Rd | 17 +-- man/fdr.Rd | 10 +- man/fn.Rd | 7 + man/fnr.Rd | 10 +- man/fomr.Rd | 10 +- man/fp.Rd | 7 + man/fpr.Rd | 10 +- man/jaccard.Rd | 7 - man/ktau.Rd | 5 - man/logloss.Rd | 7 + man/mae.Rd | 5 - man/mape.Rd | 8 + man/mauc_aunu.Rd | 5 + man/maxae.Rd | 5 - man/maxse.Rd | 5 - man/mbrier.Rd | 5 + man/mcc.Rd | 10 +- man/medae.Rd | 5 - man/medse.Rd | 5 - man/mlr3measures-package.Rd | 6 - man/mse.Rd | 5 - man/msle.Rd | 8 + man/npv.Rd | 10 +- man/pbias.Rd | 5 - man/phi.Rd | 7 - man/ppv.Rd | 10 +- man/prauc.Rd | 8 + man/rae.Rd | 8 + man/rmse.Rd | 5 - man/rmsle.Rd | 8 + man/rrse.Rd | 8 + man/rse.Rd | 8 + man/rsq.Rd | 8 + man/sae.Rd | 5 - man/smape.Rd | 8 + man/srho.Rd | 5 - man/sse.Rd | 5 - man/tn.Rd | 7 + man/tnr.Rd | 10 +- man/tp.Rd | 7 + man/tpr.Rd | 10 +- 99 files changed, 459 insertions(+), 305 deletions(-)
Title: Read Data Stored by 'Minitab', 'S', 'SAS', 'SPSS', 'Stata',
'Systat', 'Weka', 'dBase', ...
Description: Reading and writing data stored by some versions of
'Epi Info', 'Minitab', 'S', 'SAS', 'SPSS', 'Stata', 'Systat', 'Weka',
and for reading and writing some 'dBase' files.
Author: R Core Team [aut, cph, cre],
Roger Bivand [ctb, cph],
Vincent J. Carey [ctb, cph],
Saikat DebRoy [ctb, cph],
Stephen Eglen [ctb, cph],
Rajarshi Guha [ctb, cph],
Swetlana Herbrandt [ctb],
Nicholas Lewin-Koh [ctb, cph],
Mark Myatt [ctb, cph],
Michael Nelson [ctb],
Ben Pfaff [ctb],
Brian Quistorff [ctb],
Frank Warmerdam [ctb, cph],
Stephen Weigand [ctb, cph],
Free Software Foundation, Inc. [cph]
Maintainer: R Core Team <R-core@R-project.org>
Diff between foreign versions 0.8-81 dated 2020-12-22 and 0.8-82 dated 2022-01-13
ChangeLog | 10 + DESCRIPTION | 8 - MD5 | 60 +++++----- inst/po/de/LC_MESSAGES/R-foreign.mo |binary inst/po/de/LC_MESSAGES/foreign.mo |binary inst/po/en@quot/LC_MESSAGES/R-foreign.mo |binary inst/po/en@quot/LC_MESSAGES/foreign.mo |binary inst/po/fr/LC_MESSAGES/R-foreign.mo |binary inst/po/fr/LC_MESSAGES/foreign.mo |binary inst/po/it/LC_MESSAGES/R-foreign.mo |binary inst/po/it/LC_MESSAGES/foreign.mo |binary inst/po/pl/LC_MESSAGES/R-foreign.mo |binary inst/po/pl/LC_MESSAGES/foreign.mo |binary man/lookup.xport.Rd | 2 man/read.xport.Rd | 2 po/R-foreign.pot | 4 po/R-fr.po | 42 ++----- po/de.po | 158 ++++++++++++++-------------- po/foreign.pot | 152 +++++++++++++-------------- po/fr.po | 170 ++++++++++++++++--------------- po/it.po | 150 +++++++++++++-------------- po/pl.po | 150 +++++++++++++-------------- src/SASxport.c | 32 ++--- src/avl.c | 14 +- src/dbfopen.c | 2 src/file-handle.c | 18 +-- src/minitab.c | 18 +-- src/pfm-read.c | 32 ++--- src/sfm-read.c | 94 ++++++++--------- src/spss.c | 12 +- src/stataread.c | 12 +- 31 files changed, 573 insertions(+), 569 deletions(-)
Title: Conventional and Fuzzy Data Envelopment Analysis
Description: Set of functions for Data Envelopment Analysis. It runs both classic and fuzzy DEA models.See: Banker, R.; Charnes, A.; Cooper, W.W. (1984). <doi:10.1287/mnsc.30.9.1078>, Charnes, A.; Cooper, W.W.; Rhodes, E. (1978). <doi:10.1016/0377-2217(78)90138-8> and Charnes, A.; Cooper, W.W.; Rhodes, E. (1981). <doi:10.1287/mnsc.27.6.668>.
Author: Vicente Coll-Serrano, Vicente Bolos, Rafael Benitez Suarez <rabesua@uv.es>
Maintainer: Vicente Bolos <vicente.bolos@uv.es>
Diff between deaR versions 1.2.4 dated 2021-11-16 and 1.2.5 dated 2022-01-13
DESCRIPTION | 6 MD5 | 16 +- R/cross_efficiency.R | 296 ++++++++++++++++++++++++++++----------------- R/cross_efficiency_fuzzy.R | 74 ++++++----- R/model_basic.R | 45 +++++- R/model_multiplier.R | 62 ++++++--- R/modelfuzzy_guotanaka.R | 8 - build/partial.rdb |binary man/cross_efficiency.Rd | 16 +- 9 files changed, 335 insertions(+), 188 deletions(-)
Title: API Client for CHIRPS and CHIRTS
Description: API Client for the Climate Hazards Center 'CHIRPS' and 'CHIRTS'.
The 'CHIRPS' data is a quasi-global (50°S – 50°N) high-resolution
(0.05 arc-degrees) rainfall data set, which incorporates satellite imagery
and in-situ station data to create gridded rainfall time series for trend
analysis and seasonal drought monitoring. 'CHIRTS' is a quasi-global
(60°S – 70°N), high-resolution data set of daily maximum and minimum
temperatures. For more details on 'CHIRPS' and 'CHIRTS' data please visit
its official home page <https://www.chc.ucsb.edu/data>.
Author: Kauê de Sousa [aut, cre] (<https://orcid.org/0000-0002-7571-7845>),
Adam H. Sparks [aut] (<https://orcid.org/0000-0002-0061-8359>),
Aniruddha Ghosh [aut] (<https://orcid.org/0000-0003-3667-8019>),
Pete Peterson [ctb] (API Client implementation),
William Ashmall [ctb] (API Client implementation),
Jacob van Etten [ths] (<https://orcid.org/0000-0001-7554-2558>),
Svein Ø. Solberg [ths] (<https://orcid.org/0000-0002-4491-4483>)
Maintainer: Kauê de Sousa <kaue.desousa@inn.no>
Diff between chirps versions 0.1.2 dated 2020-07-13 and 0.1.4 dated 2022-01-13
chirps-0.1.2/chirps/man/figures |only chirps-0.1.4/chirps/DESCRIPTION | 37 + chirps-0.1.4/chirps/MD5 | 65 +-- chirps-0.1.4/chirps/NAMESPACE | 13 chirps-0.1.4/chirps/NEWS.md | 29 + chirps-0.1.4/chirps/R/GET.R | 2 chirps-0.1.4/chirps/R/as.geojson.R | 37 - chirps-0.1.4/chirps/R/chirps.R | 24 - chirps-0.1.4/chirps/R/get_chirps.R | 480 +++++++++++++++++------ chirps-0.1.4/chirps/R/get_chirts.R |only chirps-0.1.4/chirps/R/get_esi.R | 10 chirps-0.1.4/chirps/R/get_imerg.R | 11 chirps-0.1.4/chirps/R/internal_functions.R | 120 +++-- chirps-0.1.4/chirps/R/precip_indices.R | 9 chirps-0.1.4/chirps/R/tapajos.R | 4 chirps-0.1.4/chirps/build/partial.rdb |only chirps-0.1.4/chirps/build/vignette.rds |binary chirps-0.1.4/chirps/data/tapajos.rda |binary chirps-0.1.4/chirps/inst/CITATION | 2 chirps-0.1.4/chirps/inst/doc/Overview.Rmd | 92 +--- chirps-0.1.4/chirps/inst/doc/Overview.html | 86 +--- chirps-0.1.4/chirps/inst/paper/paper.bib | 4 chirps-0.1.4/chirps/inst/paper/paper.log |only chirps-0.1.4/chirps/inst/paper/paper.pdf |binary chirps-0.1.4/chirps/man/as.geojson.Rd | 14 chirps-0.1.4/chirps/man/chirps.Rd | 35 - chirps-0.1.4/chirps/man/get_chirps.Rd | 97 +++- chirps-0.1.4/chirps/man/get_chirts.Rd |only chirps-0.1.4/chirps/man/get_esi.Rd | 15 chirps-0.1.4/chirps/man/get_imerg.Rd | 16 chirps-0.1.4/chirps/man/precip_indices.Rd | 8 chirps-0.1.4/chirps/man/tapajos.Rd | 4 chirps-0.1.4/chirps/vignettes/Overview.Rmd | 92 +--- chirps-0.1.4/chirps/vignettes/chirps.bib | 17 chirps-0.1.4/chirps/vignettes/citation_style.csl | 130 ------ 35 files changed, 816 insertions(+), 637 deletions(-)
Title: Reshape Disorganised Messy Data
Description: Helps the user to build and register schema descriptions of
disorganised (messy) tables. Disorganised tables are tables that are
not in a topologically coherent form, where packages such as 'tidyr' could
be used for reshaping. The schema description documents the arrangement of
input tables and is used to reshape them into a standardised (tidy) output
format.
Author: Steffen Ehrmann [aut, cre] (<https://orcid.org/0000-0002-2958-0796>),
Carsten Meyer [aut] (<https://orcid.org/0000-0003-3927-5856>),
Abdualmaged Alhemiary [ctb],
Amelie Haas [ctb],
Annika Ertel [ctb],
Arne Rümmler [ctb] (<https://orcid.org/0000-0001-8637-9071>),
Caroline Busse [ctb],
Tsvetelina Tomova [ctb]
Maintainer: Steffen Ehrmann <steffen@funroll-loops.de>
Diff between tabshiftr versions 0.3.0 dated 2021-07-01 and 0.3.2 dated 2022-01-13
tabshiftr-0.3.0/tabshiftr/tests/testthat/test-03_clusters.R |only tabshiftr-0.3.0/tabshiftr/tests/testthat/test-04_wide_id.R |only tabshiftr-0.3.0/tabshiftr/tests/testthat/test-05_listed_measured.R |only tabshiftr-0.3.2/tabshiftr/DESCRIPTION | 17 tabshiftr-0.3.2/tabshiftr/MD5 | 76 tabshiftr-0.3.2/tabshiftr/NAMESPACE | 4 tabshiftr-0.3.2/tabshiftr/NEWS.md | 11 tabshiftr-0.3.2/tabshiftr/R/find.R | 9 tabshiftr-0.3.2/tabshiftr/R/getClusterVar.R | 21 tabshiftr-0.3.2/tabshiftr/R/getIDVars.R | 54 tabshiftr-0.3.2/tabshiftr/R/getObsVars.R | 112 tabshiftr-0.3.2/tabshiftr/R/helpers.R | 354 + tabshiftr-0.3.2/tabshiftr/R/reorganise.R | 38 tabshiftr-0.3.2/tabshiftr/R/schema.R | 105 tabshiftr-0.3.2/tabshiftr/R/setClusters.R | 4 tabshiftr-0.3.2/tabshiftr/R/setFilter.R | 4 tabshiftr-0.3.2/tabshiftr/R/setIDVar.R | 16 tabshiftr-0.3.2/tabshiftr/R/setObsVar.R | 18 tabshiftr-0.3.2/tabshiftr/R/validateSchema.R | 18 tabshiftr-0.3.2/tabshiftr/README.md | 44 tabshiftr-0.3.2/tabshiftr/build/vignette.rds |binary tabshiftr-0.3.2/tabshiftr/data/tabs2shift.rda |binary tabshiftr-0.3.2/tabshiftr/inst/doc/tabshiftr.R | 10 tabshiftr-0.3.2/tabshiftr/inst/doc/tabshiftr.Rmd | 47 tabshiftr-0.3.2/tabshiftr/inst/doc/tabshiftr.html | 1938 +--------- tabshiftr-0.3.2/tabshiftr/man/dot-eval_find.Rd | 2 tabshiftr-0.3.2/tabshiftr/man/dot-find.Rd | 8 tabshiftr-0.3.2/tabshiftr/man/dot-tidyVars.Rd | 6 tabshiftr-0.3.2/tabshiftr/man/setFilter.Rd | 2 tabshiftr-0.3.2/tabshiftr/man/setIDVar.Rd | 12 tabshiftr-0.3.2/tabshiftr/man/setObsVar.Rd | 7 tabshiftr-0.3.2/tabshiftr/man/validateSchema.Rd | 2 tabshiftr-0.3.2/tabshiftr/tests/testthat/test-02_column_mismatch.R | 33 tabshiftr-0.3.2/tabshiftr/tests/testthat/test-03_wide_id.R |only tabshiftr-0.3.2/tabshiftr/tests/testthat/test-04_listed_measured.R |only tabshiftr-0.3.2/tabshiftr/tests/testthat/test-05-implicit_variables.R |only tabshiftr-0.3.2/tabshiftr/tests/testthat/test-06-nested_variables.R |only tabshiftr-0.3.2/tabshiftr/tests/testthat/test-07_clusters.R |only tabshiftr-0.3.2/tabshiftr/tests/testthat/test-filter.R | 44 tabshiftr-0.3.2/tabshiftr/tests/testthat/test-find.R | 17 tabshiftr-0.3.2/tabshiftr/tests/testthat/test-validateSchema.R | 1 tabshiftr-0.3.2/tabshiftr/vignettes/references.bib | 491 -- tabshiftr-0.3.2/tabshiftr/vignettes/tabshiftr.Rmd | 47 43 files changed, 1084 insertions(+), 2488 deletions(-)
Title: Relational Data Modeler
Description: The aim of this package is to manipulate relational
data models in R.
It provides functions to create, modify and export data models
in json format.
It also allows importing models created
with 'MySQL Workbench' (<https://www.mysql.com/products/workbench/>).
These functions are accessible through a graphical user
interface made with 'shiny'.
Constraints such as types, keys, uniqueness and mandatory fields are
automatically checked and corrected when editing a model.
Finally, real data can be confronted to a model to check their compatibility.
Author: Patrice Godard [aut, cre, cph]
Maintainer: Patrice Godard <patrice.godard@gmail.com>
Diff between ReDaMoR versions 0.4.3 dated 2020-12-14 and 0.5.2 dated 2022-01-13
DESCRIPTION | 35 MD5 | 45 NAMESPACE | 28 R/RelDataModel.R | 499 +- R/RelTableModel.R | 275 + R/TYPEDEF.R | 46 R/df_to_model.R | 84 R/json_data_model.R | 8 R/model_relational_data.R | 1946 +++++----- R/namespace.R |only R/plot.RelDataModel.R | 47 R/readSQLDataModel.R | 22 build/vignette.rds |binary inst/doc/ReDaMoR.R | 41 inst/doc/ReDaMoR.Rmd | 136 inst/doc/ReDaMoR.html | 6809 +----------------------------------- inst/examples/GE-model.json |only inst/www/interactions.js | 84 man/RelTableModel.Rd | 7 man/SUPPTYPES.Rd | 2 man/confront_table_data.Rd | 2 man/is.MatrixModel.Rd |only man/is.RelTableModel.Rd | 4 vignettes/ReDaMoR.Rmd | 136 vignettes/img/Add-key-button.png |only vignettes/img/Add-key-interface.png |only 26 files changed, 2370 insertions(+), 7886 deletions(-)
Title: Simple Scraping and Tidy Webpage Summaries
Description: Simple tools for scraping webpages, extracting common html tags and parsing contents to a tidy, tabular format. Tools help with extraction of page titles, links, images, rss feeds, social media handles and page metadata.
Author: Alastair Rushworth
Maintainer: Alastair Rushworth <alastairmrushworth@gmail.com>
Diff between htmldf versions 0.4.0 dated 2021-08-17 and 0.5.0 dated 2022-01-13
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- NAMESPACE | 1 + NEWS.md | 11 ++++++++++- R/chrome_read_html.R | 36 ++++++++++++++++++++++++++++-------- R/fetch_page.R | 27 ++++++++++++--------------- R/get_generator.R | 1 - R/get_tables.R | 9 +-------- R/get_time.R | 4 +++- R/html_df.R | 35 ++++++++++++++++++++++++----------- README.md | 49 +++++++++++++++++++++++++++++++------------------ man/html_df.Rd | 15 ++++++++++++--- 12 files changed, 137 insertions(+), 81 deletions(-)
Title: Tools for Highfrequency Data Analysis
Description: Provide functionality to manage, clean and match highfrequency
trades and quotes data, calculate various liquidity measures, estimate and
forecast volatility, detect price jumps and investigate microstructure noise and intraday
periodicity.
Author: Kris Boudt [aut, cre] (<https://orcid.org/0000-0002-1000-5142>),
Jonathan Cornelissen [aut],
Scott Payseur [aut],
Giang Nguyen [ctb],
Onno Kleen [aut] (<https://orcid.org/0000-0003-4731-4640>),
Emil Sjoerup [aut]
Maintainer: Kris Boudt <kris.boudt@ugent.be>
Diff between highfrequency versions 0.9.1 dated 2021-11-02 and 0.9.2 dated 2022-01-13
DESCRIPTION | 47 +++++++++++++++++------------------------------ MD5 | 12 ++++++------ NAMESPACE | 1 + NEWS.md | 4 ++++ R/dataHandling.R | 1 + R/realizedMeasures.R | 13 ++++++++----- man/rBACov.Rd | 13 ++++++++----- 7 files changed, 45 insertions(+), 46 deletions(-)
Title: Client for Dataverse 4+ Repositories
Description: Provides access to Dataverse APIs <https://dataverse.org/> (versions 4-5),
enabling data search, retrieval, and deposit. For Dataverse versions <= 3.0,
use the archived 'dvn' package <https://cran.r-project.org/package=dvn>.
Author: Shiro Kuriwaki [aut, cre] (<https://orcid.org/0000-0002-5687-2647>),
Will Beasley [aut] (<https://orcid.org/0000-0002-5613-5006>),
Thomas J. Leeper [aut] (<https://orcid.org/0000-0003-4097-6326>),
Philip Durbin [aut] (<https://orcid.org/0000-0002-9528-9470>),
Sebastian Karcher [aut] (<https://orcid.org/0000-0001-8249-7388>),
Jan Kanis [ctb],
Edward Jee [ctb]
Maintainer: Shiro Kuriwaki <shirokuriwaki@gmail.com>
Diff between dataverse versions 0.3.9 dated 2021-07-26 and 0.3.10 dated 2022-01-13
DESCRIPTION | 11 MD5 | 109 ++--- NEWS.md | 9 R/get_dataframe.R | 88 ++-- R/get_dataset.R | 15 R/get_file.R | 26 - R/get_file_by_id.R | 40 + R/get_file_metadata.R | 9 R/native_user.R | 12 R/utils.R | 301 ++++++++------ README.md | 75 ++- build/vignette.rds |binary inst/constants.yml | 4 inst/doc/A-introduction.html | 13 inst/doc/B-search.html | 108 ++--- inst/doc/C-download.R | 7 inst/doc/C-download.Rmd | 16 inst/doc/C-download.html | 80 ++- inst/expected-dataverse-root.yml | 2 inst/expected-dataverse.yml | 4 man/add_dataset_file.Rd | 11 man/add_file.Rd | 11 man/create_dataset.Rd | 11 man/create_dataverse.Rd | 11 man/dataset_atom.Rd | 11 man/dataset_versions.Rd | 11 man/dataverse_metadata.Rd | 11 man/dataverse_search.Rd | 11 man/delete_dataset.Rd | 11 man/delete_dataverse.Rd | 11 man/delete_file.Rd | 11 man/delete_sword_dataset.Rd | 11 man/files.Rd | 48 +- man/get_dataframe.Rd | 101 +++- man/get_dataset.Rd | 27 - man/get_dataverse.Rd | 11 man/get_facets.Rd | 11 man/get_file_metadata.Rd | 24 - man/get_filesize.Rd |only man/get_user_key.Rd | 10 man/initiate_sword_dataset.Rd | 11 man/is_ingested.Rd | 39 + man/list_datasets.Rd | 11 man/publish_dataset.Rd | 11 man/publish_dataverse.Rd | 11 man/publish_sword_dataset.Rd | 11 man/service_document.Rd | 11 man/set_dataverse_metadata.Rd | 11 tests/testthat.R | 19 tests/testthat/tests-dataset_metadata.R | 6 tests/testthat/tests-dataverse_contents.R | 1 tests/testthat/tests-get_dataframe-dataframe-basketball.R | 24 + tests/testthat/tests-get_dataverse.R | 1 tests/testthat/tests-get_file.R | 3 tests/testthat/tests-list_datasets.R | 3 vignettes/C-download.Rmd | 16 56 files changed, 930 insertions(+), 552 deletions(-)
Title: Nonlinear Nonparametric Statistics
Description: Nonlinear nonparametric statistics using partial moments. Partial moments are the elements of variance and asymptotically approximate the area of f(x). These robust statistics provide the basis for nonlinear analysis while retaining linear equivalences. NNS offers: Numerical integration, Numerical differentiation, Clustering, Correlation, Dependence, Causal analysis, ANOVA, Regression, Classification, Seasonality, Autoregressive modeling, Normalization and Stochastic dominance. All routines based on: Viole, F. and Nawrocki, D. (2013), Nonlinear Nonparametric Statistics: Using Partial Moments (ISBN: 1490523995).
Author: Fred Viole
Maintainer: Fred Viole <ovvo.financial.systems@gmail.com>
Diff between NNS versions 0.8.4 dated 2022-01-12 and 0.8.4.1 dated 2022-01-13
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/ARMA_optim.R | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Estimation of Model-Based Predictions, Contrasts and Means
Description: Implements a general interface for model-based estimations
for a wide variety of models (see list of supported models using the
function 'insight::supported_models()'), used in the computation of
marginal means, contrast analysis and predictions.
Author: Dominique Makowski [aut, cre] (<https://orcid.org/0000-0001-5375-9967>,
@Dom_Makowski),
Daniel Lüdecke [aut] (<https://orcid.org/0000-0002-8895-3206>,
@strengejacke),
Mattan S. Ben-Shachar [aut] (<https://orcid.org/0000-0002-4287-4801>,
@mattansb),
Indrajeet Patil [aut] (<https://orcid.org/0000-0003-1995-6531>,
@patilindrajeets)
Maintainer: Dominique Makowski <dom.makowski@gmail.com>
Diff between modelbased versions 0.7.0 dated 2021-06-06 and 0.7.1 dated 2022-01-13
modelbased-0.7.0/modelbased/R/reshape_random.R |only modelbased-0.7.0/modelbased/R/visualisation_recipe.R |only modelbased-0.7.0/modelbased/man/visualisation_recipe.Rd |only modelbased-0.7.1/modelbased/DESCRIPTION | 30 - modelbased-0.7.1/modelbased/MD5 | 103 +-- modelbased-0.7.1/modelbased/NAMESPACE | 31 - modelbased-0.7.1/modelbased/NEWS.md | 33 - modelbased-0.7.1/modelbased/R/describe_nonlinear.R | 41 - modelbased-0.7.1/modelbased/R/estimate_contrasts.R | 79 +- modelbased-0.7.1/modelbased/R/estimate_grouplevel.R | 42 + modelbased-0.7.1/modelbased/R/estimate_means.R | 93 +-- modelbased-0.7.1/modelbased/R/estimate_predicted.R | 189 +++++- modelbased-0.7.1/modelbased/R/estimate_slopes.R | 191 ++++-- modelbased-0.7.1/modelbased/R/model_emcontrasts.R |only modelbased-0.7.1/modelbased/R/model_emmeans.R | 286 +++++----- modelbased-0.7.1/modelbased/R/model_emtrends.R |only modelbased-0.7.1/modelbased/R/plot.R | 5 modelbased-0.7.1/modelbased/R/print.R | 1 modelbased-0.7.1/modelbased/R/reexports.R |only modelbased-0.7.1/modelbased/R/reshape_grouplevel.R |only modelbased-0.7.1/modelbased/R/smoothing.R | 10 modelbased-0.7.1/modelbased/R/standardize_methods.R | 15 modelbased-0.7.1/modelbased/R/visualisation_matrix.data.frame.R | 185 +++--- modelbased-0.7.1/modelbased/R/visualisation_matrix.models.R | 41 + modelbased-0.7.1/modelbased/R/visualisation_recipe.estimate_grouplevel.R | 27 modelbased-0.7.1/modelbased/R/visualisation_recipe.estimate_means.R | 26 modelbased-0.7.1/modelbased/R/visualisation_recipe.estimate_predicted.R | 124 +++- modelbased-0.7.1/modelbased/R/visualisation_recipe.estimate_slopes.R |only modelbased-0.7.1/modelbased/R/zero_crossings.R | 8 modelbased-0.7.1/modelbased/README.md | 199 +++++- modelbased-0.7.1/modelbased/inst/CITATION | 2 modelbased-0.7.1/modelbased/inst/WORDLIST | 36 - modelbased-0.7.1/modelbased/man/describe_nonlinear.Rd | 6 modelbased-0.7.1/modelbased/man/estimate_contrasts.Rd | 85 +- modelbased-0.7.1/modelbased/man/estimate_expectation.Rd | 136 ++++ modelbased-0.7.1/modelbased/man/estimate_grouplevel.Rd | 119 ++-- modelbased-0.7.1/modelbased/man/estimate_means.Rd | 85 +- modelbased-0.7.1/modelbased/man/estimate_slopes.Rd | 67 +- modelbased-0.7.1/modelbased/man/figures/unnamed-chunk-10-1.png |binary modelbased-0.7.1/modelbased/man/figures/unnamed-chunk-11-1.png |binary modelbased-0.7.1/modelbased/man/figures/unnamed-chunk-12-1.png |binary modelbased-0.7.1/modelbased/man/figures/unnamed-chunk-13-1.png |binary modelbased-0.7.1/modelbased/man/figures/unnamed-chunk-15-1.png |only modelbased-0.7.1/modelbased/man/figures/unnamed-chunk-16-1.png |only modelbased-0.7.1/modelbased/man/figures/unnamed-chunk-17-1.png |only modelbased-0.7.1/modelbased/man/figures/unnamed-chunk-18-1.png |only modelbased-0.7.1/modelbased/man/figures/unnamed-chunk-5-1.png |binary modelbased-0.7.1/modelbased/man/figures/unnamed-chunk-7-1.png |binary modelbased-0.7.1/modelbased/man/model_emmeans.Rd | 117 +++- modelbased-0.7.1/modelbased/man/smoothing.Rd | 2 modelbased-0.7.1/modelbased/man/visualisation_matrix.Rd | 36 - modelbased-0.7.1/modelbased/man/visualisation_recipe.estimate_predicted.Rd |only modelbased-0.7.1/modelbased/tests/testthat/test-attributes_visualisation.R | 26 modelbased-0.7.1/modelbased/tests/testthat/test-estimate_contrasts.R | 36 - modelbased-0.7.1/modelbased/tests/testthat/test-estimate_means.R | 73 +- modelbased-0.7.1/modelbased/tests/testthat/test-estimate_predicted.R | 16 modelbased-0.7.1/modelbased/tests/testthat/test-estimate_slopes.R | 19 modelbased-0.7.1/modelbased/tests/testthat/test-glmmTMB.R | 2 modelbased-0.7.1/modelbased/tests/testthat/test-signal.R | 4 59 files changed, 1668 insertions(+), 958 deletions(-)
Title: Individual-Level, Summary-Level and Single-Step Bayesian
Regression Model
Description: A user-friendly tool to fit Bayesian regression models. It can fit 3 types of Bayesian models using individual-level, summary-level, and individual plus pedigree-level (single-step) data for both Genomic prediction/selection (GS) and Genome-Wide Association Study (GWAS), it was designed to estimate joint effects and genetic parameters for a complex trait, including:
(1) fixed effects and coefficients of covariates,
(2) environmental random effects, and its corresponding variance,
(3) genetic variance,
(4) residual variance,
(5) heritability,
(6) genomic estimated breeding values (GEBV) for both genotyped and non-genotyped individuals,
(7) SNP effect size,
(8) phenotype/genetic variance explained (PVE) for single or multiple SNPs,
(9) posterior probability of association of the genomic window (WPPA),
(10) posterior inclusive probability (PIP).
The functions are not limited, we will keep on going in enriching it with more features.
References: Meuwissen et al. (2001) <doi:10.1093/genetics/157.4.1819>; Gustavo et al. (2013) <doi:10.1534/genetics.112.143313>; Habier et al. (2011) <doi:10.1186/1471-2105-12-186>; Yi et al. (2008) <doi:10.1534/genetics.107.085589>; Zhou et al. (2013) <doi:10.1371/journal.pgen.1003264>; Moser et al. (2015) <doi:10.1371/journal.pgen.1004969>; Lloyd-Jones et al. (2019) <doi:10.1038/s41467-019-12653-0>; Henderson (1976) <doi:10.2307/2529339>; Fernando et al. (2014) <doi:10.1186/1297-9686-46-50>.
Author: Lilin Yin [aut, cre, cph],
Haohao Zhang [aut, cph],
Xiaolei Liu [aut, cph]
Maintainer: Lilin Yin <ylilin@163.com>
Diff between hibayes versions 1.0.0 dated 2021-12-10 and 1.0.1 dated 2022-01-13
DESCRIPTION | 8 MD5 | 30 R/RcppExports.R | 24 R/bayes.r | 51 R/sbayes.r | 48 R/ssbayes.r | 58 inst/extdata/example.fam | 9596 +++++++++++++++++++++++------------------------ man/bayes.Rd | 9 man/sbayes.Rd | 11 man/ssbayes.Rd | 11 src/Bayes.cpp | 76 src/RcppExports.cpp | 66 src/SBayesD.cpp | 26 src/SBayesS.cpp | 26 src/cutwind.cpp | 32 src/rm.cpp | 18 16 files changed, 5068 insertions(+), 5022 deletions(-)
Title: Automated Grading of R Scripts
Description: Tools for grading the coding style and documentation of R
scripts. This is the R component of Roger the Omni Grader, an
automated grading system for computer programming projects based on
Unix shell scripts; see <https://gitlab.com/roger-project>. The
package also provides an R interface to the shell scripts. Inspired by
the lintr package.
Author: Vincent Goulet [aut, cre],
Samuel Fréchette [aut],
Jean-Christophe Langlois [aut],
Jim Hester [ctb]
Maintainer: Vincent Goulet <vincent.goulet@act.ulaval.ca>
Diff between roger versions 0.99-1 dated 2021-10-20 and 0.99-2 dated 2022-01-13
DESCRIPTION | 8 +- MD5 | 17 +++--- NAMESPACE | 4 + R/nomagic_style.R | 8 +- R/roger_interface.R | 135 +++++++++++++++++++++++++++++++++++------------- inst/NEWS.Rd | 35 ++++++++++++ man/nomagic_style.Rd | 1 man/roger-interface.Rd | 69 +++++++++++++++--------- tests/interface-tests.R |only tests/style-tests.R | 10 +++ 10 files changed, 208 insertions(+), 79 deletions(-)
Title: Circle Manhattan Plot
Description: Manhattan plot, a type of scatter plot, was widely used to display the association results. However, it is usually time-consuming and laborious for a non-specialist user to write scripts and adjust parameters of an elaborate plot. Moreover, the ever-growing traits measured have necessitated the integration of results from different Genome-wide association study researches. Circle Manhattan Plot is the first open R package that can lay out. Genome-wide association study P-value results in both traditional rectangular patterns, QQ-plot and novel circular ones. United in only one bull's eye style plot, association results from multiple traits can be compared interactively, thereby to reveal both similarities and differences between signals. Additional functions include: highlight signals, a group of SNPs, chromosome visualization and candidate genes around SNPs.
Author: LiLin-Yin
Maintainer: LiLin-Yin <ylilin@163.com>
Diff between CMplot versions 3.7.0 dated 2021-10-20 and 4.0.0 dated 2022-01-13
DESCRIPTION | 8 +++--- MD5 | 6 ++-- R/CMplot.r | 66 ++++++++++++++++++++++++++++++++++---------------- man/CMplot-package.Rd | 9 ++++-- 4 files changed, 58 insertions(+), 31 deletions(-)
Title: Functions for Kriging and Point Pattern Analysis
Description: Functions for kriging and point pattern analysis.
Author: Brian Ripley [aut, cre, cph],
Roger Bivand [ctb],
William Venables [cph]
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>
Diff between spatial versions 7.3-14 dated 2021-05-03 and 7.3-15 dated 2022-01-13
DESCRIPTION | 8 +++--- MD5 | 4 +-- src/krc.c | 78 ++++++++++++++++++++++++++++++------------------------------ 3 files changed, 45 insertions(+), 45 deletions(-)
Title: Variance Stabilizing Transformations for Single Cell UMI Data
Description: A normalization method for single-cell UMI count data using a
variance stabilizing transformation. The transformation is based on a
negative binomial regression model with regularized parameters. As part of the
same regression framework, this package also provides functions for
batch correction, and data correction. See Hafemeister and Satija (2019)
<doi:10.1186/s13059-019-1874-1>, and Choudhary and Satija (2021) <doi:10.1101/2021.07.07.451498>
for more details.
Author: Christoph Hafemeister [aut] (<https://orcid.org/0000-0001-6365-8254>),
Saket Choudhary [aut, cre] (<https://orcid.org/0000-0001-5202-7633>),
Rahul Satija [ctb] (<https://orcid.org/0000-0001-9448-8833>)
Maintainer: Saket Choudhary <schoudhary@nygenome.org>
Diff between sctransform versions 0.3.2 dated 2020-12-16 and 0.3.3 dated 2022-01-13
DESCRIPTION | 37 ++- MD5 | 46 ++-- NAMESPACE | 13 + NEWS.md | 32 ++ R/data.R | 10 R/denoise.R | 29 ++ R/differential_expression.R | 403 ++++++++++++++++++++++++++++++------- R/fit.R | 59 +++++ R/plotting.R | 17 - R/umify.R |only R/utils.R | 157 ++++++++++++-- R/vst.R | 434 +++++++++++++++++++++++++++++++++++----- README.md | 62 +++-- build |only data/umify_data.rda |only man/correct.Rd | 6 man/correct_counts.Rd | 4 man/diff_mean_test.Rd | 18 + man/diff_mean_test_conserved.Rd |only man/get_nz_median.Rd |only man/get_nz_median2.Rd |only man/plot_model_pars.Rd | 3 man/umify.Rd |only man/umify_data.Rd |only man/vst.Rd | 39 ++- src/RcppExports.cpp | 5 tests/testthat/test_generate.R | 2 tests/testthat/test_vst.R | 61 +++++ 28 files changed, 1200 insertions(+), 237 deletions(-)
Title: Statistical Inference for Partially Observed Markov Processes
Description: Tools for data analysis with partially observed Markov process (POMP) models (also known as stochastic dynamical systems, hidden Markov models, and nonlinear, non-Gaussian, state-space models). The package provides facilities for implementing POMP models, simulating them, and fitting them to time series data by a variety of frequentist and Bayesian methods. It is also a versatile platform for implementation of inference methods for general POMP models.
Author: Aaron A. King [aut, cre],
Edward L. Ionides [aut],
Carles Breto [aut],
Stephen P. Ellner [ctb],
Matthew J. Ferrari [ctb],
Sebastian Funk [ctb],
Steven G. Johnson [ctb],
Bruce E. Kendall [ctb],
Michael Lavine [ctb],
Dao Nguyen [ctb],
Eamon B. O'Dea [ctb],
Daniel C. Reuman [ctb],
Helen Wearing [ctb],
Simon N. Wood [ctb]
Maintainer: Aaron A. King <kingaa@umich.edu>
Diff between pomp versions 3.6 dated 2021-09-03 and 4.1 dated 2022-01-13
DESCRIPTION | 39 ++-- MD5 | 270 +++++++++++++++-------------- NAMESPACE | 12 + R/abc.R | 8 R/as_data_frame.R | 2 R/bake.R | 10 - R/basic_components.R | 4 R/betabinom.R |only R/bsflu.R | 1 R/ebola.R | 4 R/emeasure_spec.R |only R/flow.R | 11 - R/forecast.R | 40 +++- R/gompertz.R | 12 - R/kalman.R | 400 ++++++++++++++++++++++++++------------------ R/kf.R |only R/listie.R | 8 R/mcap.R |only R/nlf.R | 2 R/objfun.R | 12 + R/ou2.R | 2 R/parmat.R | 121 +++++++++++-- R/parus.R | 1 R/pfilter.R | 2 R/plot.R | 95 ++++++---- R/pmcmc.R | 9 R/pomp.R | 66 ++++++- R/pomp_class.R | 4 R/probe.R | 10 - R/profile_design.R | 1 R/pstop.R | 11 + R/ricker.R | 5 R/rmeasure_spec.R | 4 R/rprocess_spec.R | 2 R/rw2.R | 8 R/show.R | 4 R/simulate.R | 4 R/sir.R | 64 +++---- R/skeleton_spec.R | 5 R/spect_match.R | 2 R/spy.R | 6 R/templates.R | 50 +++++ R/traj_match.R | 2 R/trajectory.R | 177 +++++++++++++++---- R/verhulst.R | 6 R/vmeasure_spec.R |only R/workhorses.R | 150 ++++++++++++++++ build/partial.rdb |binary data/LondonYorke.rda |binary data/bsflu.rda |binary data/ebolaWA2014.rda |binary data/ewcitmeas.rda |binary data/ewmeas.rda |binary inst/NEWS | 100 +++++++++++ inst/NEWS.Rd | 46 +++++ inst/include/pomp.h | 8 inst/include/pomp_defines.h | 6 man/abc.Rd | 8 man/accumulators.Rd | 5 man/bake.Rd | 2 man/basic_components.Rd | 9 man/betabinom.Rd |only man/blowflies.Rd | 2 man/bsflu.Rd | 15 - man/childhood.Rd | 2 man/coef.Rd | 3 man/covariate_table.Rd | 5 man/csnippet.Rd | 5 man/dacca.Rd | 2 man/design.Rd | 1 man/distributions.Rd | 5 man/dmeasure.Rd | 4 man/dmeasure_spec.Rd | 5 man/dprior.Rd | 4 man/dprocess.Rd | 4 man/dprocess_spec.Rd | 5 man/ebola.Rd | 6 man/emeasure.Rd |only man/emeasure_spec.Rd |only man/flow.Rd | 4 man/forecast.Rd | 3 man/gompertz.Rd | 12 - man/kalman.Rd | 37 ++-- man/kf.Rd |only man/macros/citations.Rd | 2 man/mcap.Rd |only man/ou2.Rd | 2 man/pStop.Rd | 6 man/parameter_trans.Rd | 5 man/parmat.Rd | 27 ++ man/partrans.Rd | 4 man/parus.Rd | 15 - man/pmcmc.Rd | 9 man/pomp-package.Rd | 7 man/pomp.Rd | 19 +- man/pomp_examp.Rd | 2 man/prior_spec.Rd | 5 man/probe.Rd | 8 man/ricker.Rd | 15 + man/rinit.Rd | 4 man/rinit_spec.Rd | 5 man/rmeasure.Rd | 4 man/rmeasure_spec.Rd | 9 man/rprior.Rd | 4 man/rprocess.Rd | 4 man/rprocess_spec.Rd | 7 man/rw2.Rd | 2 man/sir.Rd | 9 man/skeleton.Rd | 4 man/skeleton_spec.Rd | 23 +- man/traj_match.Rd | 2 man/trajectory.Rd | 152 ++++++++++++++-- man/transformations.Rd | 5 man/userdata.Rd | 5 man/verhulst.Rd | 4 man/vmeasure.Rd |only man/vmeasure_spec.Rd |only man/workhorses.Rd | 6 src/distributions.c | 41 ++++ src/dmeasure.c | 2 src/dprocess.c | 2 src/emeasure.c |only src/euler.c | 2 src/gompertz.c | 21 ++ src/init.c | 4 src/ou2.c | 29 +++ src/pfilter.c | 2 src/pomp.h | 8 src/pomp_decls.h | 16 + src/pomp_defines.h | 6 src/pomp_fun.c | 2 src/pomp_mat.h | 17 + src/probe.c | 2 src/rinit.c | 2 src/rmeasure.c | 4 src/rprior.c | 2 src/rprocess.c | 2 src/simulate.c | 2 src/skeleton.c | 2 src/synth_lik.c | 6 src/trajectory.c | 11 - src/vmeasure.c |only src/wpfilter.c | 2 143 files changed, 1857 insertions(+), 659 deletions(-)
Title: Feed-Forward Neural Networks and Multinomial Log-Linear Models
Description: Software for feed-forward neural networks with a single
hidden layer, and for multinomial log-linear models.
Author: Brian Ripley [aut, cre, cph],
William Venables [cph]
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>
Diff between nnet versions 7.3-16 dated 2021-05-03 and 7.3-17 dated 2022-01-13
DESCRIPTION | 8 +++---- MD5 | 4 +-- src/nnet.c | 62 ++++++++++++++++++++++++++++++------------------------------ 3 files changed, 37 insertions(+), 37 deletions(-)
Title: Interface to 'Neptune' Experiment Tracking and Management Tool
Description: Interface to 'Neptune', experiment tracking tool that helps you organize
your machine learning experiments. You can log your hyperparameter, metrics, model binaries and
performance charts, organize them with tags and names and share everything easily in the app.
For more information see <https://neptune.ai/>.
Author: Mateusz Dominiak [aut],
Rafal Jankowski [aut, cre]
Maintainer: Rafal Jankowski <rafal.jankowski@neptune.ai>
Diff between neptune versions 0.1.2 dated 2021-01-11 and 0.2.0 dated 2022-01-13
neptune-0.1.2/neptune/R/neptune.R |only neptune-0.1.2/neptune/man/append_tag.Rd |only neptune-0.1.2/neptune/man/create_experiment.Rd |only neptune-0.1.2/neptune/man/get_neptune.Rd |only neptune-0.1.2/neptune/man/init_neptune.Rd |only neptune-0.1.2/neptune/man/install_neptune.Rd |only neptune-0.1.2/neptune/man/log_artifact.Rd |only neptune-0.1.2/neptune/man/log_image.Rd |only neptune-0.1.2/neptune/man/log_metric.Rd |only neptune-0.1.2/neptune/man/set_neptune_token.Rd |only neptune-0.1.2/neptune/man/set_property.Rd |only neptune-0.1.2/neptune/man/stop_experiment.Rd |only neptune-0.2.0/neptune/DESCRIPTION | 22 ++-- neptune-0.2.0/neptune/LICENSE |only neptune-0.2.0/neptune/MD5 | 89 +++++++++++++++--- neptune-0.2.0/neptune/NAMESPACE | 23 ++-- neptune-0.2.0/neptune/R/check_handler.R |only neptune-0.2.0/neptune/R/check_handler_or_run.R |only neptune-0.2.0/neptune/R/check_run.R |only neptune-0.2.0/neptune/R/get_neptune.R |only neptune-0.2.0/neptune/R/neptune-internal.R |only neptune-0.2.0/neptune/R/neptune_add.R |only neptune-0.2.0/neptune/R/neptune_assign.R |only neptune-0.2.0/neptune/R/neptune_clear.R |only neptune-0.2.0/neptune/R/neptune_delete_files.R |only neptune-0.2.0/neptune/R/neptune_download.R |only neptune-0.2.0/neptune/R/neptune_download_last.R |only neptune-0.2.0/neptune/R/neptune_exists.R |only neptune-0.2.0/neptune/R/neptune_fetch.R |only neptune-0.2.0/neptune/R/neptune_fetch_files_list.R |only neptune-0.2.0/neptune/R/neptune_fetch_hash.R |only neptune-0.2.0/neptune/R/neptune_fetch_last.R |only neptune-0.2.0/neptune/R/neptune_fetch_runs_table.R |only neptune-0.2.0/neptune/R/neptune_fetch_values.R |only neptune-0.2.0/neptune/R/neptune_file_as_html.R |only neptune-0.2.0/neptune/R/neptune_file_as_image.R |only neptune-0.2.0/neptune/R/neptune_get_run_url.R |only neptune-0.2.0/neptune/R/neptune_get_structure.R |only neptune-0.2.0/neptune/R/neptune_init.R |only neptune-0.2.0/neptune/R/neptune_install.R |only neptune-0.2.0/neptune/R/neptune_log.R |only neptune-0.2.0/neptune/R/neptune_pop.R |only neptune-0.2.0/neptune/R/neptune_print_structure.R |only neptune-0.2.0/neptune/R/neptune_remove.R |only neptune-0.2.0/neptune/R/neptune_set_api_token.R |only neptune-0.2.0/neptune/R/neptune_stop.R |only neptune-0.2.0/neptune/R/neptune_sync.R |only neptune-0.2.0/neptune/R/neptune_track_files.R |only neptune-0.2.0/neptune/R/neptune_upload.R |only neptune-0.2.0/neptune/R/neptune_upload_files.R |only neptune-0.2.0/neptune/R/neptune_wait.R |only neptune-0.2.0/neptune/R/parse_neptune_version.R |only neptune-0.2.0/neptune/R/process_value.R |only neptune-0.2.0/neptune/R/z[.neptune.new.run.Run.R |only neptune-0.2.0/neptune/R/z[_-.neptune.new.run.Run.R |only neptune-0.2.0/neptune/README.md |only neptune-0.2.0/neptune/man/neptune_add.Rd |only neptune-0.2.0/neptune/man/neptune_assign.Rd |only neptune-0.2.0/neptune/man/neptune_clear.Rd |only neptune-0.2.0/neptune/man/neptune_delete_files.Rd |only neptune-0.2.0/neptune/man/neptune_download.Rd |only neptune-0.2.0/neptune/man/neptune_download_last.Rd |only neptune-0.2.0/neptune/man/neptune_exists.Rd |only neptune-0.2.0/neptune/man/neptune_fetch.Rd |only neptune-0.2.0/neptune/man/neptune_fetch_files_list.Rd |only neptune-0.2.0/neptune/man/neptune_fetch_hash.Rd |only neptune-0.2.0/neptune/man/neptune_fetch_last.Rd |only neptune-0.2.0/neptune/man/neptune_fetch_runs_table.Rd |only neptune-0.2.0/neptune/man/neptune_fetch_values.Rd |only neptune-0.2.0/neptune/man/neptune_file_as_html.Rd |only neptune-0.2.0/neptune/man/neptune_file_as_image.Rd |only neptune-0.2.0/neptune/man/neptune_get_run_url.Rd |only neptune-0.2.0/neptune/man/neptune_get_structure.Rd |only neptune-0.2.0/neptune/man/neptune_init.Rd |only neptune-0.2.0/neptune/man/neptune_install.Rd |only neptune-0.2.0/neptune/man/neptune_log.Rd |only neptune-0.2.0/neptune/man/neptune_pop.Rd |only neptune-0.2.0/neptune/man/neptune_print_structure.Rd |only neptune-0.2.0/neptune/man/neptune_remove.Rd |only neptune-0.2.0/neptune/man/neptune_set_api_token.Rd |only neptune-0.2.0/neptune/man/neptune_stop.Rd |only neptune-0.2.0/neptune/man/neptune_sync.Rd |only neptune-0.2.0/neptune/man/neptune_track_files.Rd |only neptune-0.2.0/neptune/man/neptune_upload.Rd |only neptune-0.2.0/neptune/man/neptune_upload_files.Rd |only neptune-0.2.0/neptune/man/neptune_wait.Rd |only neptune-0.2.0/neptune/man/z[.neptune.new.run.Run.Rd |only neptune-0.2.0/neptune/man/z[_-.neptune.new.run.Run.Rd |only 88 files changed, 97 insertions(+), 37 deletions(-)
Title: Support Functions and Datasets for Venables and Ripley's MASS
Description: Functions and datasets to support Venables and Ripley,
"Modern Applied Statistics with S" (4th edition, 2002).
Author: Brian Ripley [aut, cre, cph],
Bill Venables [ctb],
Douglas M. Bates [ctb],
Kurt Hornik [trl] (partial port ca 1998),
Albrecht Gebhardt [trl] (partial port ca 1998),
David Firth [ctb]
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>
Diff between MASS versions 7.3-54 dated 2021-05-03 and 7.3-55 dated 2022-01-13
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- R/area.R | 2 +- build/partial.rdb |binary inst/po/de/LC_MESSAGES/R-MASS.mo |binary po/R-de.po | 8 ++++---- src/MASS.c | 36 ++++++++++++++++++------------------ src/lqs.c | 3 ++- 8 files changed, 37 insertions(+), 36 deletions(-)
Title: Functions for Classification
Description: Various functions for classification, including k-nearest
neighbour, Learning Vector Quantization and Self-Organizing Maps.
Author: Brian Ripley [aut, cre, cph],
William Venables [cph]
Maintainer: Brian Ripley <ripley@stats.ox.ac.uk>
Diff between class versions 7.3-19 dated 2021-05-03 and 7.3-20 dated 2022-01-13
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- src/class.c | 26 +++++++++++++------------- 3 files changed, 19 insertions(+), 19 deletions(-)
Title: Risk Measure Calculation in Financial TS
Description: Enables the user to calculate Value at Risk (VaR) and Expected
Shortfall (ES) by means of various parametric and semiparametric
GARCH-type models. For the latter the estimation of the nonparametric scale
function is carried out by means of a data-driven smoothing approach. Model
quality, in terms of forecasting VaR and ES, can be assessed by means of
various backtesting methods such as the traffic light test for VaR and a
newly developed traffic light test for ES. The approaches implemented in
this package are described in e.g. Feng Y., Beran J., Letmathe S. and
Ghosh S. <https://ideas.repec.org/p/pdn/ciepap/137.html> as well as
Letmathe S., Feng Y. and Uhde A. (2021)
<https://ideas.repec.org/p/pdn/ciepap/141.html>.
Author: Yuanhua Feng [aut] (Paderborn University, Germany),
Xuehai Zhang [aut] (Ernst & Young, Germany),
Christian Peitz [aut] (Paderborn University, Germany),
Dominik Schulz [aut] (Paderborn University, Germany),
Shujie Li [aut] (Paderborn Universtiy, Germany),
Sebastian Letmathe [aut, cre] (Paderborn University, Germany)
Maintainer: Sebastian Letmathe <sebastian.letmathe@uni-paderborn.de>
Diff between ufRisk versions 1.0.0 dated 2022-01-11 and 1.0.1 dated 2022-01-13
DESCRIPTION | 6 +++--- MD5 | 13 +++++++------ NEWS.md |only R/varcast.R | 10 +++++----- README.md | 8 ++++---- man/figures/README-unnamed-chunk-4-1.png |binary man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary 8 files changed, 19 insertions(+), 18 deletions(-)
Title: Fun with Fractions and Number Sequences
Description: A collection of toys to do things like generate Collatz sequences, convert a fraction to "continued fraction" form, calculate a fraction which is a close approximation to some value (e.g., 22/7 or 355/113 for pi), and so on.
Author: Carl Witthoft
Maintainer: Carl Witthoft <carl@witthoft.com>
Diff between FunWithNumbers versions 1.0 dated 2020-10-05 and 1.1 dated 2022-01-13
ChangeLog |only DESCRIPTION | 10 +++++----- MD5 | 11 +++++++---- NAMESPACE | 5 ++--- R/bpp.R |only build/partial.rdb |binary data/preciseNumbersAsChar.rda |binary man/bpp.Rd |only 8 files changed, 14 insertions(+), 12 deletions(-)
More information about FunWithNumbers at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-09-28 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-04-26 0.9-0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-06-25 1.0.8
2016-12-02 1.0.2