Title: Discretization and Grouping for Logistic Regression
Description: A Stochastic-Expectation-Maximization (SEM) algorithm (Celeux et al. (1995) <https://hal.inria.fr/inria-00074164>) associated with a Gibbs sampler which purpose is to learn a constrained representation for logistic regression that is called quantization (Ehrhardt et al. (2019) <arXiv:1903.08920>). Continuous features are discretized and categorical features' values are grouped to produce a better logistic regression model. Pairwise interactions between quantized features are dynamically added to the model through a Metropolis-Hastings algorithm (Hastings, W. K. (1970) <doi:10.1093/biomet/57.1.97>).
Author: Adrien Ehrhardt [aut, cre],
Vincent Vandewalle [aut],
Christophe Biernacki [ctb],
Philippe Heinrich [ctb]
Maintainer: Adrien Ehrhardt <adrien.ehrhardt@centraliens-lille.org>
Diff between glmdisc versions 0.5 dated 2020-03-22 and 0.6 dated 2020-09-30
DESCRIPTION | 23 MD5 | 70 + NAMESPACE | 1 R/cut.dataset.R | 70 + R/discretize.link.R | 106 +- R/generic_cutpoints.R | 2 R/generic_discretize.R | 2 R/glmdisc.R | 12 R/initialization.R |only R/method_cutpoints.R | 74 +- R/method_discretize.R | 31 R/method_plot.R | 100 +- R/method_predict.R | 93 +- R/methods_disc.R | 30 R/normalizedGini.R | 28 R/semDiscretization.R | 1188 +++++++++++++++------------------ inst/CITATION |only inst/doc/glmdisc.R | 4 inst/doc/glmdisc.Rmd | 6 inst/doc/glmdisc.html | 134 +-- inst/document.R |only inst/lint.R |only inst/rhubcheck.R |only man/cutpoints-method.Rd | 23 man/discretize.Rd | 25 man/glmdisc.Rd | 23 man/normalizedGini.Rd | 2 man/plot.Rd | 23 man/predict.Rd | 23 src/rcpp_predictlogisticRegression.cpp | 2 tests/testthat/test-all-classes.R |only tests/testthat/test-cut-dataset.R | 62 - tests/testthat/test-discretize-link.R | 104 ++ tests/testthat/test-discretize.R |only tests/testthat/test-glmdisc.R |only tests/testthat/test-method_cutpoints.R | 87 ++ tests/testthat/test-method_predict.R | 89 ++ tests/testthat/test-methods-disc.R |only tests/testthat/test-normalizedgini.R | 6 tests/testthat/test-plot.R |only vignettes/glmdisc.Rmd | 6 41 files changed, 1308 insertions(+), 1141 deletions(-)
Title: Comprehensive Automatized Evaluation of Distribution Models for
Count Data
Description: A large number of measurements generate count data. This is a statistical data type
that only assumes non-negative integer values and is generated by counting. Typically, counting
data can be found in biomedical applications, such as the analysis of DNA double-strand breaks.
The number of DNA double-strand breaks can be counted in individual cells using various
bioanalytical methods. For diagnostic applications, it is relevant to record the distribution of
the number data in order to determine their biomedical significance (Roediger, S. et al., 2018.
Journal of Laboratory and Precision Medicine. <doi:10.21037/jlpm.2018.04.10>). The software
offers functions for a comprehensive automated evaluation of distribution models of count
data. In addition to programmatic interaction, a graphical user interface (web server)
is included, which enables fast and interactive data-scientific analyses. The user is supported
in selecting the most suitable counting distribution for his own data set.
Author: Jaroslaw Chilimoniuk [cre, ctb]
(<https://orcid.org/0000-0001-5467-018X>),
Alicja Gosiewska [ctb] (<https://orcid.org/0000-0001-6563-5742>),
Jadwiga Słowik [ctb] (<https://orcid.org/0000-0003-3466-8933>),
Michal Burdukiewicz [aut] (<https://orcid.org/0000-0001-8926-582X>),
Stefan Roediger [ctb] (<https://orcid.org/0000-0002-1441-6512>)
Maintainer: Jaroslaw Chilimoniuk <jaroslaw.chilimoniuk@gmail.com>
Diff between countfitteR versions 1.3 dated 2020-09-02 and 1.4 dated 2020-09-30
DESCRIPTION | 14 - MD5 | 24 +- NAMESPACE | 3 R/countfitteR_gui.R | 9 R/validate_data.R |only README.md | 14 - inst/countfitteR/readmes/about.md | 6 inst/countfitteR/readmes/manual.html | 252 ++++++++++++++++--------- inst/countfitteR/readmes/manual.md | 2 inst/countfitteR/report/countfitter_report.Rmd | 2 inst/countfitteR/server.R | 69 +----- inst/countfitteR/ui.R | 5 inst/doc/countfitteR.html | 4 man/validate_counts.Rd |only 14 files changed, 235 insertions(+), 169 deletions(-)
Title: Create Area-Proportional Venn Diagrams from Biological Lists
Description: Creates an area-proportional Venn diagram of 2 or 3 circles. 'BioVenn' is the only R package that can automatically generate an accurate area-proportional Venn diagram by having only lists of (biological) identifiers as input. Also offers the option to map Entrez and/or Affymetrix IDs to Ensembl IDs. In SVG mode, text and numbers can be dragged and dropped. Based on the BioVenn web interface available at <https://www.biovenn.nl>. Hulsen et al. (2008) <doi:10.1186/1471-2164-9-488>.
Author: Tim Hulsen [aut, cre] (<https://orcid.org/0000-0002-0208-8443>)
Maintainer: Tim Hulsen <thulsen@gmail.com>
Diff between BioVenn versions 1.0.1 dated 2020-09-07 and 1.0.2 dated 2020-09-30
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/draw.venn.R | 23 +++++++++++++++++------ 3 files changed, 22 insertions(+), 11 deletions(-)
Title: Binned Data Analysis
Description: Algorithms developed for binned data analysis,
gene expression data analysis and
measurement error models for ordinal data analysis.
Author: Bin Wang <bwang831@gmail.com>
Maintainer: Bin Wang <bwang831@gmail.com>
Diff between bda versions 15.0.2 dated 2020-07-27 and 15.1.7 dated 2020-09-30
DESCRIPTION | 8 MD5 | 19 - NAMESPACE | 2 R/lpsmooth.R | 123 +++------- R/npr.R |only R/vas.R | 2 data/Pain.RData |binary man/lpsmooth.Rd | 19 + man/lpsvariance.Rd | 7 src/init.c | 26 ++ src/npr.c | 620 ++++++++++++++++++++++++++++++++++++++++++++++++++++- 11 files changed, 713 insertions(+), 113 deletions(-)
Title: Stubbing and Setting Expectations on 'HTTP' Requests
Description: Stubbing and setting expectations on 'HTTP' requests.
Includes tools for stubbing 'HTTP' requests, including expected
request conditions and response conditions. Match on
'HTTP' method, query parameters, request body, headers and
more. Can be used for unit tests or outside of a testing
context.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>),
Aaron Wolen [ctb] (<https://orcid.org/0000-0003-2542-2202>),
rOpenSci [fnd] (https://ropensci.org)
Maintainer: Scott Chamberlain <myrmecocystus+r@gmail.com>
Diff between webmockr versions 0.6.2 dated 2020-03-24 and 0.7.0 dated 2020-09-30
DESCRIPTION | 15 - MD5 | 83 ++++---- NAMESPACE | 2 NEWS.md | 22 ++ R/RequestPattern.R | 155 +++++++++++---- R/RequestRegistry.R | 100 +++++++--- R/StubRegistry.R | 4 R/StubbedRequest.R | 177 ++++++++++++------ R/adapter-crul.R | 10 - R/adapter-httr.R | 12 - R/adapter.R | 76 +++++-- R/onload.R | 9 R/stub_registry_clear.R | 9 R/stub_request.R | 42 +++- R/to_return.R | 55 ++++- R/webmockr.R | 1 R/webmockr_reset.R |only R/wi_th.R | 46 +++- R/zzz.R | 14 + README.md | 9 man/HashCounter.Rd | 26 +- man/RequestPattern.Rd | 14 + man/RequestRegistry.Rd | 67 ++++++ man/StubbedRequest.Rd | 45 +++- man/UriPattern.Rd | 130 +++++++++++-- man/stub_registry_clear.Rd | 7 man/stub_request.Rd | 45 ++++ man/to_return.Rd | 48 ++++ man/webmockr_reset.Rd |only man/wi_th.Rd | 37 ++- tests/testthat/test-HashCounter.R | 25 +- tests/testthat/test-RequestPattern.R | 27 ++ tests/testthat/test-RequestRegistry.R | 12 - tests/testthat/test-StubbedRequest.R | 17 + tests/testthat/test-request_registry.R | 2 tests/testthat/test-stub_registry.R | 11 + tests/testthat/test-to_raise.R | 14 - tests/testthat/test-to_return.R | 10 - tests/testthat/test-to_return_body.R | 2 tests/testthat/test-to_return_then.R |only tests/testthat/test-to_timeout.R | 4 tests/testthat/test-uri_regex.R |only tests/testthat/test-webmockr_reset.R |only tests/testthat/test-wi_th.R | 130 +++++++++++++ tests/testthat/test-writing-to-disk-write_disk_path.R | 72 +++++++ 45 files changed, 1248 insertions(+), 338 deletions(-)
Title: Read and Write Rectangular Text Data Quickly
Description: The goal of 'vroom' is to read and write data (like
'csv', 'tsv' and 'fwf') quickly. When reading it uses a quick initial
indexing step, then reads the values lazily , so only the data you
actually use needs to be read. The writer formats the data in
parallel and writes to disk asynchronously from formatting.
Author: Jim Hester [aut, cre] (<https://orcid.org/0000-0002-2739-7082>),
Hadley Wickham [aut] (<https://orcid.org/0000-0003-4757-117X>),
https://github.com/mandreyel/ [cph] (mio library),
R Core Team [ctb] (localtime.c code adapted from R),
Jukka Jylänki [cph] (grisu3 implementation),
Mikkel Jørgensen [cph] (grisu3 implementation),
RStudio [cph, fnd]
Maintainer: Jim Hester <james.f.hester@gmail.com>
Diff between vroom versions 1.3.1 dated 2020-08-27 and 1.3.2 dated 2020-09-30
vroom-1.3.1/vroom/inst/bench/all_character-long/data.table-data.table.tsv |only vroom-1.3.1/vroom/inst/bench/all_character-long/read.delim-base.tsv |only vroom-1.3.1/vroom/inst/bench/all_character-long/readr-dplyr.tsv |only vroom-1.3.1/vroom/inst/bench/all_character-long/vroom-base.tsv |only vroom-1.3.1/vroom/inst/bench/all_character-long/vroom-dplyr.tsv |only vroom-1.3.1/vroom/inst/bench/all_character-long/vroom_no_altrep-dplyr.tsv |only vroom-1.3.1/vroom/inst/bench/all_character-wide/data.table-data.table.tsv |only vroom-1.3.1/vroom/inst/bench/all_character-wide/read.delim-base.tsv |only vroom-1.3.1/vroom/inst/bench/all_character-wide/readr-dplyr.tsv |only vroom-1.3.1/vroom/inst/bench/all_character-wide/vroom-base.tsv |only vroom-1.3.1/vroom/inst/bench/all_character-wide/vroom-dplyr.tsv |only vroom-1.3.1/vroom/inst/bench/all_character-wide/vroom_no_altrep-dplyr.tsv |only vroom-1.3.1/vroom/inst/bench/all_numeric-long/data.table-data.table.tsv |only vroom-1.3.1/vroom/inst/bench/all_numeric-long/read.delim-base.tsv |only vroom-1.3.1/vroom/inst/bench/all_numeric-long/readr-dplyr.tsv |only vroom-1.3.1/vroom/inst/bench/all_numeric-long/vroom-base.tsv |only vroom-1.3.1/vroom/inst/bench/all_numeric-long/vroom-dplyr.tsv |only vroom-1.3.1/vroom/inst/bench/all_numeric-long/vroom_no_altrep-base.tsv |only vroom-1.3.1/vroom/inst/bench/all_numeric-long/vroom_no_altrep-dplyr.tsv |only vroom-1.3.1/vroom/inst/bench/all_numeric-wide/data.table-data.table.tsv |only vroom-1.3.1/vroom/inst/bench/all_numeric-wide/read.delim-base.tsv |only vroom-1.3.1/vroom/inst/bench/all_numeric-wide/readr-dplyr.tsv |only vroom-1.3.1/vroom/inst/bench/all_numeric-wide/vroom-base.tsv |only vroom-1.3.1/vroom/inst/bench/all_numeric-wide/vroom-dplyr.tsv |only vroom-1.3.1/vroom/inst/bench/all_numeric-wide/vroom_no_altrep-base.tsv |only vroom-1.3.1/vroom/inst/bench/all_numeric-wide/vroom_no_altrep-dplyr.tsv |only vroom-1.3.1/vroom/inst/bench/fwf/read.delim-base.tsv |only vroom-1.3.1/vroom/inst/bench/fwf/readr-dplyr.tsv |only vroom-1.3.1/vroom/inst/bench/fwf/vroom-base.tsv |only vroom-1.3.1/vroom/inst/bench/fwf/vroom-dplyr.tsv |only vroom-1.3.1/vroom/inst/bench/fwf/vroom_no_altrep-dplyr.tsv |only vroom-1.3.1/vroom/inst/bench/taxi/data.table-data.table.tsv |only vroom-1.3.1/vroom/inst/bench/taxi/read.delim-base.tsv |only vroom-1.3.1/vroom/inst/bench/taxi/readr-dplyr.tsv |only vroom-1.3.1/vroom/inst/bench/taxi/vroom-base.tsv |only vroom-1.3.1/vroom/inst/bench/taxi/vroom-dplyr.tsv |only vroom-1.3.1/vroom/inst/bench/taxi/vroom_no_altrep-dplyr.tsv |only vroom-1.3.1/vroom/inst/bench/taxi_multiple/data.table-data.table.tsv |only vroom-1.3.1/vroom/inst/bench/taxi_multiple/readr-dplyr.tsv |only vroom-1.3.1/vroom/inst/bench/taxi_multiple/vroom-base.tsv |only vroom-1.3.1/vroom/inst/bench/taxi_multiple/vroom-dplyr.tsv |only vroom-1.3.1/vroom/inst/bench/taxi_multiple/vroom_no_altrep-dplyr.tsv |only vroom-1.3.1/vroom/inst/bench/taxi_writing/base-gzip.tsv |only vroom-1.3.1/vroom/inst/bench/taxi_writing/base-multithreaded_gzip.tsv |only vroom-1.3.1/vroom/inst/bench/taxi_writing/base-uncompressed.tsv |only vroom-1.3.1/vroom/inst/bench/taxi_writing/base-zstandard.tsv |only vroom-1.3.1/vroom/inst/bench/taxi_writing/data.table-gzip.tsv |only vroom-1.3.1/vroom/inst/bench/taxi_writing/data.table-multithreaded_gzip.tsv |only vroom-1.3.1/vroom/inst/bench/taxi_writing/data.table-uncompressed.tsv |only vroom-1.3.1/vroom/inst/bench/taxi_writing/readr-gzip.tsv |only vroom-1.3.1/vroom/inst/bench/taxi_writing/readr-multithreaded_gzip.tsv |only vroom-1.3.1/vroom/inst/bench/taxi_writing/readr-uncompressed.tsv |only vroom-1.3.1/vroom/inst/bench/taxi_writing/readr-zstandard.tsv |only vroom-1.3.1/vroom/inst/bench/taxi_writing/vroom-gzip.tsv |only vroom-1.3.1/vroom/inst/bench/taxi_writing/vroom-multithreaded_gzip.tsv |only vroom-1.3.1/vroom/inst/bench/taxi_writing/vroom-uncompressed.tsv |only vroom-1.3.1/vroom/inst/bench/taxi_writing/vroom-zstandard.tsv |only vroom-1.3.1/vroom/src/mio/CMakeLists.txt |only vroom-1.3.1/vroom/src/mio/cmake |only vroom-1.3.1/vroom/src/mio/include/mio/CMakeLists.txt |only vroom-1.3.1/vroom/src/mio/include/mio/detail/CMakeLists.txt |only vroom-1.3.1/vroom/src/mio/single_include |only vroom-1.3.1/vroom/src/mio/test |only vroom-1.3.2/vroom/DESCRIPTION | 10 vroom-1.3.2/vroom/MD5 | 133 ++-------- vroom-1.3.2/vroom/NEWS.md | 6 vroom-1.3.2/vroom/R/col_types.R | 7 vroom-1.3.2/vroom/R/cpp11.R | 26 - vroom-1.3.2/vroom/R/utils.R | 7 vroom-1.3.2/vroom/R/zzz.R | 1 vroom-1.3.2/vroom/README.md | 2 vroom-1.3.2/vroom/build/vignette.rds |binary vroom-1.3.2/vroom/build/vroom.pdf |binary vroom-1.3.2/vroom/inst/doc/benchmarks.R | 3 vroom-1.3.2/vroom/inst/doc/benchmarks.Rmd | 5 vroom-1.3.2/vroom/inst/doc/benchmarks.html | 18 - vroom-1.3.2/vroom/inst/doc/vroom.html | 2 vroom-1.3.2/vroom/src/connection.h | 6 vroom-1.3.2/vroom/src/vroom_fct.cc | 43 +-- vroom-1.3.2/vroom/src/vroom_fct.h | 8 vroom-1.3.2/vroom/src/vroom_lgl.h | 5 vroom-1.3.2/vroom/tests/testthat/helper.R | 8 vroom-1.3.2/vroom/tests/testthat/test-big-int.R | 2 vroom-1.3.2/vroom/tests/testthat/test-chr.R | 6 vroom-1.3.2/vroom/tests/testthat/test-connection.R | 20 - vroom-1.3.2/vroom/tests/testthat/test-datetime.R | 23 - vroom-1.3.2/vroom/tests/testthat/test-factor.R | 4 vroom-1.3.2/vroom/tests/testthat/test-int.R | 2 vroom-1.3.2/vroom/tests/testthat/test-logical.R | 2 vroom-1.3.2/vroom/tests/testthat/test-multi-byte.R | 4 vroom-1.3.2/vroom/tests/testthat/test-multi-file.R | 17 - vroom-1.3.2/vroom/tests/testthat/test-num.R | 2 vroom-1.3.2/vroom/tests/testthat/test-path.R | 20 - vroom-1.3.2/vroom/tests/testthat/test-select.R | 33 +- vroom-1.3.2/vroom/tests/testthat/test-vroom.R | 99 ++++--- vroom-1.3.2/vroom/tests/testthat/test-vroom_fwf.R | 10 vroom-1.3.2/vroom/tests/testthat/test-vroom_write.R | 16 - vroom-1.3.2/vroom/vignettes/benchmarks.Rmd | 5 98 files changed, 259 insertions(+), 296 deletions(-)
Title: Download and Explore Datasets from UCSC Xena Data Hubs
Description: Download and explore datasets from UCSC Xena data hubs, which are
a collection of UCSC-hosted public databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others.
Databases are normalized so they can be combined, linked, filtered, explored and downloaded.
Author: Shixiang Wang [aut, cre] (<https://orcid.org/0000-0001-9855-7357>),
Xue-Song Liu [aut] (<https://orcid.org/0000-0002-7736-0077>),
Martin Morgan [ctb],
Christine Stawitz [rev] (Christine reviewed the package for ropensci,
see <https://github.com/ropensci/software-review/issues/315>),
Carl Ganz [rev] (Carl reviewed the package for ropensci, see
<https://github.com/ropensci/software-review/issues/315>)
Maintainer: Shixiang Wang <w_shixiang@163.com>
Diff between UCSCXenaTools versions 1.3.3 dated 2020-08-05 and 1.3.4 dated 2020-09-30
DESCRIPTION | 8 MD5 | 12 - NEWS.md | 4 README.md | 31 +-- build/vignette.rds |binary data/XenaData.rda |binary inst/doc/USCSXenaTools.html | 357 +++++++++++++++++++++++--------------------- 7 files changed, 216 insertions(+), 196 deletions(-)
Title: Output Analysis and Diagnostics for MCMC
Description: Provides functions for summarizing and plotting the
output from Markov Chain Monte Carlo (MCMC) simulations, as
well as diagnostic tests of convergence to the equilibrium
distribution of the Markov chain.
Author: Martyn Plummer [aut, cre, trl],
Nicky Best [aut],
Kate Cowles [aut],
Karen Vines [aut],
Deepayan Sarkar [aut],
Douglas Bates [aut],
Russell Almond [aut],
Arni Magnusson [aut]
Maintainer: Martyn Plummer <martyn.plummer@gmail.com>
Diff between coda versions 0.19-3 dated 2019-07-05 and 0.19-4 dated 2020-09-30
CHANGELOG | 7 +++++-- DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/cumuplot.R | 2 +- 4 files changed, 13 insertions(+), 10 deletions(-)
Title: Kuhn-Tucker and Multiple Discrete-Continuous Extreme Value
Models
Description: Estimates and simulates Kuhn-Tucker demand models with individual heterogeneity. The package implements the multiple-discrete continuous extreme value (MDCEV) model and the Kuhn-Tucker specification common in the environmental economics literature on recreation demand. Latent class and random parameters specifications can be implemented and the models are fit using maximum likelihood estimation or Bayesian estimation. All models are implemented in Stan, which is a C++ package for performing full Bayesian inference (see Stan Development Team, 2019) <https://mc-stan.org/>. The package also implements demand forecasting (Pinjari and Bhat (2011) <https://repositories.lib.utexas.edu/handle/2152/23880>) and welfare calculation (Lloyd-Smith (2018) <doi:10.1016/j.jocm.2017.12.002>) for policy simulation.
Author: Patrick Lloyd-Smith [aut, cre],
Trustees of Columbia University [cph]
Maintainer: Patrick Lloyd-Smith <patrick.lloydsmith@usask.ca>
Diff between rmdcev versions 1.2.3 dated 2020-09-23 and 1.2.4 dated 2020-09-30
rmdcev-1.2.3/rmdcev/man/BayesMDCEV.Rd |only rmdcev-1.2.3/rmdcev/man/CreateListsCol.Rd |only rmdcev-1.2.3/rmdcev/man/CreateListsRow.Rd |only rmdcev-1.2.3/rmdcev/man/CreateParmInfo.Rd |only rmdcev-1.2.3/rmdcev/man/CreatePsi.Rd |only rmdcev-1.2.3/rmdcev/man/CreatePsiMatrix.Rd |only rmdcev-1.2.3/rmdcev/man/DoCbind.Rd |only rmdcev-1.2.3/rmdcev/man/GenClassNames.Rd |only rmdcev-1.2.3/rmdcev/man/GrabIndividualParms.Rd |only rmdcev-1.2.3/rmdcev/man/GrabParms.Rd |only rmdcev-1.2.3/rmdcev/man/MultiplyMatrix.Rd |only rmdcev-1.2.3/rmdcev/man/ProcessSimulationData.Rd |only rmdcev-1.2.3/rmdcev/man/ReduceStanFitSize.Rd |only rmdcev-1.2.3/rmdcev/man/RunStanSampling.Rd |only rmdcev-1.2.3/rmdcev/man/StanSimulate.Rd |only rmdcev-1.2.3/rmdcev/man/maxlikeMDCEV.Rd |only rmdcev-1.2.3/rmdcev/man/mdcev.datacheck.Rd |only rmdcev-1.2.3/rmdcev/man/processMDCEVdata.Rd |only rmdcev-1.2.4/rmdcev/DESCRIPTION | 8 rmdcev-1.2.4/rmdcev/MD5 | 72 +-- rmdcev-1.2.4/rmdcev/NAMESPACE | 3 rmdcev-1.2.4/rmdcev/NEWS | 12 rmdcev-1.2.4/rmdcev/R/BayesMDCEV.R | 51 -- rmdcev-1.2.4/rmdcev/R/CreateParmInfo.R | 12 rmdcev-1.2.4/rmdcev/R/PrepareSimulationData.R | 11 rmdcev-1.2.4/rmdcev/R/StanSimulate.R | 2 rmdcev-1.2.4/rmdcev/R/helperFunctions.R | 47 +- rmdcev-1.2.4/rmdcev/R/maxLikeMDCEV.R | 33 - rmdcev-1.2.4/rmdcev/R/mdcev.R | 47 -- rmdcev-1.2.4/rmdcev/R/mdcev.data.R | 21 rmdcev-1.2.4/rmdcev/R/mdcev.datacheck.R | 9 rmdcev-1.2.4/rmdcev/R/processMDCEVdata.R | 27 - rmdcev-1.2.4/rmdcev/README.md | 25 - rmdcev-1.2.4/rmdcev/inst/stan/common/mdcev_tdata.stan | 7 rmdcev-1.2.4/rmdcev/inst/stan/mdcev.stan | 33 + rmdcev-1.2.4/rmdcev/inst/stan/mdcev_rp.stan | 9 rmdcev-1.2.4/rmdcev/man/mdcev.Rd | 6 rmdcev-1.2.4/rmdcev/man/mdcev.data.Rd | 4 rmdcev-1.2.4/rmdcev/src/stanExports_mdcev.h | 404 ++++++++++-------- rmdcev-1.2.4/rmdcev/src/stanExports_mdcev_rp.h | 374 ++++++++-------- rmdcev-1.2.4/rmdcev/tests/testthat/test-bayes.R | 6 rmdcev-1.2.4/rmdcev/tests/testthat/test-choice.R | 9 rmdcev-1.2.4/rmdcev/tests/testthat/test-data.R | 94 ++-- rmdcev-1.2.4/rmdcev/tests/testthat/test-kt_ee.R | 22 rmdcev-1.2.4/rmdcev/tests/testthat/test-lc.R | 3 rmdcev-1.2.4/rmdcev/tests/testthat/test-simulations.R | 18 46 files changed, 736 insertions(+), 633 deletions(-)
Title: Dynamic Documents for R
Description: Convert R Markdown documents into a variety of formats.
Author: JJ Allaire [aut],
Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>),
Jonathan McPherson [aut],
Javier Luraschi [aut],
Kevin Ushey [aut],
Aron Atkins [aut],
Hadley Wickham [aut],
Joe Cheng [aut],
Winston Chang [aut],
Richard Iannone [aut] (<https://orcid.org/0000-0003-3925-190X>),
Andrew Dunning [ctb] (<https://orcid.org/0000-0003-0464-5036>),
Atsushi Yasumoto [ctb, cph] (<https://orcid.org/0000-0002-8335-495X>,
Number sections Lua filter),
Barret Schloerke [ctb],
Christophe Dervieux [ctb],
Frederik Aust [ctb] (<https://orcid.org/0000-0003-4900-788X>),
Jeff Allen [ctb],
JooYoung Seo [ctb] (<https://orcid.org/0000-0002-4064-6012>),
Malcolm Barrett [ctb],
Rob Hyndman [ctb],
Romain Lesur [ctb],
Roy Storey [ctb],
Ruben Arslan [ctb],
Sergio Oller [ctb],
RStudio, PBC [cph],
jQuery Foundation [cph] (jQuery library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/rmd/h/jquery-AUTHORS.txt),
jQuery UI contributors [ctb, cph] (jQuery UI library; authors listed in
inst/rmd/h/jqueryui-AUTHORS.txt),
Mark Otto [ctb] (Bootstrap library),
Jacob Thornton [ctb] (Bootstrap library),
Bootstrap contributors [ctb] (Bootstrap library),
Twitter, Inc [cph] (Bootstrap library),
Alexander Farkas [ctb, cph] (html5shiv library),
Scott Jehl [ctb, cph] (Respond.js library),
Ivan Sagalaev [ctb, cph] (highlight.js library),
Greg Franko [ctb, cph] (tocify library),
John MacFarlane [ctb, cph] (Pandoc templates),
Google, Inc. [ctb, cph] (ioslides library),
Dave Raggett [ctb] (slidy library),
W3C [cph] (slidy library),
Dave Gandy [ctb, cph] (Font-Awesome),
Ben Sperry [ctb] (Ionicons),
Drifty [cph] (Ionicons),
Aidan Lister [ctb, cph] (jQuery StickyTabs),
Benct Philip Jonsson [ctb, cph] (pagebreak Lua filter),
Albert Krewinkel [ctb, cph] (pagebreak Lua filter)
Maintainer: Yihui Xie <xie@yihui.name>
Diff between rmarkdown versions 2.3 dated 2020-06-18 and 2.4 dated 2020-09-30
rmarkdown-2.3/rmarkdown/inst/doc/pandoc.R |only rmarkdown-2.3/rmarkdown/inst/doc/pandoc.Rmd |only rmarkdown-2.3/rmarkdown/inst/doc/pandoc.html |only rmarkdown-2.3/rmarkdown/inst/rmd/lua |only rmarkdown-2.3/rmarkdown/vignettes/pandoc.Rmd |only rmarkdown-2.4/rmarkdown/DESCRIPTION | 31 +- rmarkdown-2.4/rmarkdown/MD5 | 149 ++++------ rmarkdown-2.4/rmarkdown/NAMESPACE | 2 rmarkdown-2.4/rmarkdown/NEWS.md | 36 ++ rmarkdown-2.4/rmarkdown/R/base64.R | 23 - rmarkdown-2.4/rmarkdown/R/beamer_presentation.R | 15 - rmarkdown-2.4/rmarkdown/R/context_document.R | 18 - rmarkdown-2.4/rmarkdown/R/github_document.R | 12 rmarkdown-2.4/rmarkdown/R/html_document.R | 11 rmarkdown-2.4/rmarkdown/R/html_document_base.R | 8 rmarkdown-2.4/rmarkdown/R/html_fragment.R | 2 rmarkdown-2.4/rmarkdown/R/html_notebook.R | 2 rmarkdown-2.4/rmarkdown/R/html_notebook_output.R | 2 rmarkdown-2.4/rmarkdown/R/html_resources.R | 2 rmarkdown-2.4/rmarkdown/R/html_vignette.R | 2 rmarkdown-2.4/rmarkdown/R/ioslides_presentation.R | 18 - rmarkdown-2.4/rmarkdown/R/md_document.R | 16 - rmarkdown-2.4/rmarkdown/R/odt_document.R | 18 - rmarkdown-2.4/rmarkdown/R/output_format.R | 17 - rmarkdown-2.4/rmarkdown/R/pandoc.R | 17 - rmarkdown-2.4/rmarkdown/R/pdf_document.R | 20 - rmarkdown-2.4/rmarkdown/R/powerpoint_presentation.R | 6 rmarkdown-2.4/rmarkdown/R/render.R | 55 ++- rmarkdown-2.4/rmarkdown/R/render_site.R | 51 ++- rmarkdown-2.4/rmarkdown/R/rtf_document.R | 12 rmarkdown-2.4/rmarkdown/R/shiny_prerendered.R | 2 rmarkdown-2.4/rmarkdown/R/slidy_presentation.R | 16 - rmarkdown-2.4/rmarkdown/R/tufte_handout.R | 2 rmarkdown-2.4/rmarkdown/R/util.R | 53 ++- rmarkdown-2.4/rmarkdown/R/word_document.R | 26 + rmarkdown-2.4/rmarkdown/README.md | 6 rmarkdown-2.4/rmarkdown/build/vignette.rds |binary rmarkdown-2.4/rmarkdown/inst/CITATION | 16 + rmarkdown-2.4/rmarkdown/inst/doc/lua-filters.R | 26 + rmarkdown-2.4/rmarkdown/inst/doc/lua-filters.Rmd | 79 ++++- rmarkdown-2.4/rmarkdown/inst/doc/lua-filters.html | 139 ++++++++- rmarkdown-2.4/rmarkdown/inst/doc/rmarkdown.Rmd | 2 rmarkdown-2.4/rmarkdown/inst/doc/rmarkdown.html | 11 rmarkdown-2.4/rmarkdown/inst/rmarkdown/lua |only rmarkdown-2.4/rmarkdown/inst/rmd/h/default.html | 18 + rmarkdown-2.4/rmarkdown/inst/rmd/h/navigation-1.1/codefolding.js | 8 rmarkdown-2.4/rmarkdown/inst/rmd/ioslides/default.html | 16 + rmarkdown-2.4/rmarkdown/inst/rmd/slidy/default.html | 18 + rmarkdown-2.4/rmarkdown/man/beamer_presentation.Rd | 4 rmarkdown-2.4/rmarkdown/man/compile_notebook.Rd | 2 rmarkdown-2.4/rmarkdown/man/context_document.Rd | 4 rmarkdown-2.4/rmarkdown/man/github_document.Rd | 3 rmarkdown-2.4/rmarkdown/man/html_document.Rd | 6 rmarkdown-2.4/rmarkdown/man/html_fragment.Rd | 2 rmarkdown-2.4/rmarkdown/man/html_vignette.Rd | 2 rmarkdown-2.4/rmarkdown/man/ioslides_presentation.Rd | 9 rmarkdown-2.4/rmarkdown/man/md_document.Rd | 7 rmarkdown-2.4/rmarkdown/man/odt_document.Rd | 7 rmarkdown-2.4/rmarkdown/man/pandoc_args.Rd | 6 rmarkdown-2.4/rmarkdown/man/pandoc_convert.Rd | 2 rmarkdown-2.4/rmarkdown/man/pandoc_exec.Rd | 2 rmarkdown-2.4/rmarkdown/man/pandoc_options.Rd | 8 rmarkdown-2.4/rmarkdown/man/pdf_document.Rd | 4 rmarkdown-2.4/rmarkdown/man/pkg_file_lua.Rd |only rmarkdown-2.4/rmarkdown/man/powerpoint_presentation.Rd | 3 rmarkdown-2.4/rmarkdown/man/render.Rd | 18 + rmarkdown-2.4/rmarkdown/man/rmarkdown_format.Rd | 2 rmarkdown-2.4/rmarkdown/man/rtf_document.Rd | 5 rmarkdown-2.4/rmarkdown/man/slidy_presentation.Rd | 7 rmarkdown-2.4/rmarkdown/man/tufte_handout.Rd | 2 rmarkdown-2.4/rmarkdown/man/word_document.Rd | 5 rmarkdown-2.4/rmarkdown/tests/testthat/resources/rmarkdown.Rmd | 1 rmarkdown-2.4/rmarkdown/tests/testthat/test-lua-filters.R | 46 ++- rmarkdown-2.4/rmarkdown/tests/testthat/test-output_format.R | 20 + rmarkdown-2.4/rmarkdown/tests/testthat/test-render.R |only rmarkdown-2.4/rmarkdown/tests/testthat/test-resources.R | 14 rmarkdown-2.4/rmarkdown/vignettes/lua-filters.Rmd | 79 ++++- rmarkdown-2.4/rmarkdown/vignettes/rmarkdown.Rmd | 2 78 files changed, 924 insertions(+), 331 deletions(-)
Title: Create Interactive Linked Charts with Minimal Code
Description: An easy-to-use tool to employ interactivity in every-day exploratory analysis. It contains
a collection of most commonly used types of charts (such as scatter plots, line plots, heatmaps, bar charts),
which can be linked to each other or to other interactive elements with just few lines of code.
Author: Svetlana Ovchinnikova [aut, cre],
Simon Anders [aut]
Maintainer: Svetlana Ovchinnikova <s.ovchinnikova@zmbh.uni-heidelberg.de>
Diff between rlc versions 0.2.0 dated 2020-01-17 and 0.3.0 dated 2020-09-30
DESCRIPTION | 15 - MD5 | 37 +-- NAMESPACE | 1 NEWS.md | 33 +++ R/lc.R | 386 +++++++++++++++++++++++++++++------- README.md | 12 - inst/http_root/linked-charts.css | 7 inst/http_root/linked-charts.min.js | 2 inst/http_root/rlc.js | 45 ++-- man/lc_bars.Rd | 14 + man/lc_colourSlider.Rd | 17 + man/lc_heatmap.Rd | 15 + man/lc_hist.Rd | 6 man/lc_html.Rd | 6 man/lc_image.Rd |only man/lc_input.Rd | 6 man/lc_line.Rd | 37 ++- man/lc_scatter.Rd | 24 +- man/mark.Rd | 4 man/setProperties.Rd | 6 20 files changed, 526 insertions(+), 147 deletions(-)
Title: Bayesian Global Vector Autoregressions
Description: Estimation of Bayesian Global Vector Autoregressions (BGVAR) with different prior setups and the possibility to introduce stochastic volatility. Built-in priors include the Minnesota, the stochastic search variable selection and Normal-Gamma (NG) prior. For a reference see also Crespo Cuaresma, J., Feldkircher, M. and F. Huber (2016) "Forecasting with Global Vector Autoregressive Models: a Bayesian Approach", Journal of Applied Econometrics, Vol. 31(7), pp. 1371-1391 <doi:10.1002/jae.2504>. Post-processing functions allow for doing predictions, structurally identify the model with short-run or sign-restrictions and compute impulse response functions, historical decompositions and forecast error variance decompositions. Plotting functions are also available.
Author: Maximilian Boeck [aut, cre] (<https://orcid.org/0000-0001-6024-8305>),
Martin Feldkircher [aut] (<https://orcid.org/0000-0002-5511-9215>),
Florian Huber [aut] (<https://orcid.org/0000-0002-2896-7921>),
Christopher Sims [ctb]
Maintainer: Maximilian Boeck <maximilian.boeck@wu.ac.at>
Diff between BGVAR versions 2.1.2 dated 2020-09-14 and 2.1.3 dated 2020-09-30
DESCRIPTION | 6 MD5 | 16 - NEWS | 3 R/bgvar.R | 2 R/predict.R | 1 inst/doc/examples.R | 2 inst/doc/examples.Rmd | 2 inst/doc/examples.html | 497 ++++++++++++++++++++++++------------------------- vignettes/examples.Rmd | 2 9 files changed, 270 insertions(+), 261 deletions(-)
Title: Mendelian Randomization Package
Description: Encodes several methods for performing Mendelian randomization
analyses with summarized data. Summarized data on genetic associations with the
exposure and with the outcome can be obtained from large consortia. These data
can be used for obtaining causal estimates using instrumental variable methods.
Author: Olena Yavorska <olena.yavorska@ludwig.ox.ac.uk>
James Staley <james.staley@bristol.ac.uk>
Maintainer: Stephen Burgess <sb452@medschl.cam.ac.uk>
Diff between MendelianRandomization versions 0.4.3 dated 2020-08-11 and 0.5.0 dated 2020-09-30
DESCRIPTION | 11 - MD5 | 143 +++++++------- NAMESPACE | 12 + NEWS | 11 + R/AllClasses.R | 112 +++++++++++ R/AllGenerics.R | 239 +++++++++++++++++++++++ R/extract.pheno.csv-function.R | 2 R/getter-methods.R | 15 + R/mr_forest-methods.R |only R/mr_funnel-methods.R |only R/mr_lasso-methods.R |only R/mr_loo-methods.R |only R/mr_mbe-methods.R | 5 R/mr_median-methods.R | 5 R/mr_mvivw-methods.R | 11 + R/mr_mvlasso-methods.R |only R/mr_mvmedian-methods.R |only R/mr_plot-methods.R | 148 ++++++++++++++ R/new-methods.R | 1 R/pheno_input-function.R | 2 R/show-methods.R | 83 ++++++++ man/Egger-class.Rd | 122 ++++++------ man/IVW-class.Rd | 86 ++++---- man/MRAll-class.Rd | 38 +-- man/MRConMix-class.Rd | 86 ++++---- man/MRHetPen-class.Rd | 74 +++---- man/MRInput-class.Rd | 84 ++++---- man/MRLasso-class.Rd |only man/MRMBE-class.Rd | 74 +++---- man/MRMVInput-class.Rd | 76 +++---- man/MVEgger-class.Rd | 102 +++++----- man/MVIVW-class.Rd | 80 ++++---- man/MVLasso-class.Rd |only man/MVMedian-class.Rd |only man/MaxLik-class.Rd | 82 ++++---- man/WeightedMedian-class.Rd | 66 +++--- man/calcium.Rd | 88 ++++---- man/ci_normal.Rd | 62 +++--- man/ci_t.Rd | 66 +++--- man/decimals.Rd | 54 ++--- man/egger.bounds.Rd | 78 +++---- man/extract.pheno.csv.Rd | 176 ++++++++--------- man/getter.Rd | 113 ++++++----- man/het.weight.Rd | 62 +++--- man/ldlc.Rd | 146 +++++++------- man/loglikelihood.Rd | 58 ++--- man/loglikelihoodcorrel.Rd | 58 ++--- man/loglikelihoodrhocorrel.Rd | 54 ++--- man/mbe_boot.Rd | 64 +++--- man/mbe_est.Rd | 58 ++--- man/model.prior.Rd | 58 ++--- man/mr_allmethods.Rd | 86 ++++---- man/mr_conmix.Rd | 124 ++++++------ man/mr_egger.Rd | 204 ++++++++++---------- man/mr_forest.Rd |only man/mr_funnel.Rd |only man/mr_hetpen.Rd | 150 +++++++-------- man/mr_input.Rd | 138 ++++++------- man/mr_ivw.Rd | 226 +++++++++++----------- man/mr_lasso.Rd |only man/mr_loo.Rd |only man/mr_maxlik.Rd | 174 ++++++++--------- man/mr_mbe.Rd | 168 ++++++++-------- man/mr_median.Rd | 198 +++++++++---------- man/mr_mvegger.Rd | 154 +++++++-------- man/mr_mvinput.Rd | 132 ++++++------- man/mr_mvivw.Rd | 161 ++++++++-------- man/mr_mvlasso.Rd |only man/mr_mvmedian.Rd |only man/mr_plot.Rd | 137 +++++++------ man/penalised.weights.Rd | 66 +++--- man/penalised.weights.delta.Rd | 70 +++---- man/pheno_input.Rd | 126 ++++++------ man/phenoscanner.Rd | 118 +++++------ man/r.weights.Rd | 58 ++--- man/r.weights.delta.Rd | 76 +++---- man/values.Rd | 46 ++-- man/weighted.median.Rd | 54 ++--- man/weighted.median.boot.se.Rd | 76 +++---- vignettes/Vignette_MR.html | 409 +++++++++++++++++++++-------------------- 80 files changed, 3390 insertions(+), 2726 deletions(-)
More information about MendelianRandomization at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-08-10 0.5-0
2020-06-02 0.4-0
2020-03-20 0.3-1
2020-01-31 0.2-0
Title: Create Simple Yet Powerful HTML Documents with Light Weight CSS
Frameworks
Description: Create minimal, responsive, and style-agnostic HTML documents with
the lightweight CSS frameworks such as 'sakura', 'Water.css', and 'mini.css'.
Powerful features include floating table of contents as a sidebar,
code folding of source, output, message, warning, and error, and accordion
menus. They work without JavaScript.
Author: Atsushi Yasumoto [aut, cph, cre]
(<https://orcid.org/0000-0002-8335-495X>),
Angelos Chalaris [aut] (mini.css),
Mitesh Shah [aut] (sakura),
Kognise [aut] (Water.css)
Maintainer: Atsushi Yasumoto <atusy.rpkg@gmail.com>
Diff between minidown versions 0.0.1 dated 2020-05-04 and 0.0.2 dated 2020-09-30
minidown-0.0.1/minidown/R/dependencies.R |only minidown-0.0.1/minidown/R/includes.R |only minidown-0.0.1/minidown/R/pandoc-args.R |only minidown-0.0.1/minidown/tests/testthat/test-dependencies.R |only minidown-0.0.1/minidown/tests/testthat/test-includes.R |only minidown-0.0.2/minidown/DESCRIPTION | 10 +- minidown-0.0.2/minidown/MD5 | 46 ++++++---- minidown-0.0.2/minidown/NAMESPACE | 1 minidown-0.0.2/minidown/NEWS.md |only minidown-0.0.2/minidown/R/download-rmd.R |only minidown-0.0.2/minidown/R/hook-results-folding.R |only minidown-0.0.2/minidown/R/hook.R | 11 -- minidown-0.0.2/minidown/R/mini-document.R | 41 ++++++-- minidown-0.0.2/minidown/R/pandoc.R |only minidown-0.0.2/minidown/R/spec-dependencies.R |only minidown-0.0.2/minidown/R/spec-includes.R |only minidown-0.0.2/minidown/R/spec-knitr-knit-hooks.R |only minidown-0.0.2/minidown/R/spec-knitr-opts-chunk.R |only minidown-0.0.2/minidown/R/spec-knitr-opts-hooks.R |only minidown-0.0.2/minidown/R/spec-pandoc-args.R |only minidown-0.0.2/minidown/R/spec-pre-knit.R |only minidown-0.0.2/minidown/R/spec-pre-processor.R |only minidown-0.0.2/minidown/R/spec-template.R |only minidown-0.0.2/minidown/R/template.R | 36 +++++-- minidown-0.0.2/minidown/README.md | 3 minidown-0.0.2/minidown/inst/WORDLIST | 4 minidown-0.0.2/minidown/inst/rmarkdown/templates/mini_document/resources/css/common.css |only minidown-0.0.2/minidown/inst/rmarkdown/templates/mini_document/resources/css/feat-toc-float.css | 9 - minidown-0.0.2/minidown/inst/rmarkdown/templates/mini_document/resources/default.html | 2 minidown-0.0.2/minidown/inst/rmarkdown/templates/mini_document/resources/html/math-katex.html | 2 minidown-0.0.2/minidown/man/download_rmd_button.Rd |only minidown-0.0.2/minidown/man/frameworks.Rd | 4 minidown-0.0.2/minidown/man/mini_document.Rd | 27 ++++- minidown-0.0.2/minidown/tests/testthat/test-spec-dependencies.R |only minidown-0.0.2/minidown/tests/testthat/test-spec-includes.R |only 35 files changed, 127 insertions(+), 69 deletions(-)
Title: Spatial and Network Based Individual Level Models for Epidemics
Description: Provides tools for simulating from discrete-time individual level models for infectious disease data analysis. This epidemic model class contains spatial and contact-network based models with two disease types: Susceptible-Infectious (SI) and Susceptible-Infectious-Removed (SIR).
Author: Vineetha Warriyar. K. V., Waleed Almutiry, and Rob Deardon
Maintainer: Waleed Almutiry <wkmtierie@qu.edu.sa>
Diff between EpiILM versions 1.5.1 dated 2020-06-29 and 1.5.2 dated 2020-09-30
DESCRIPTION | 10 +- MD5 | 14 +-- R/epiplot.r | 217 +++++++++++++++++++++++++++++++++++++++++--------- build/partial.rdb |binary inst/doc/Predict.R | 28 ++---- inst/doc/Predict.Rnw | 24 ++++- inst/doc/Predict.pdf |binary vignettes/Predict.Rnw | 24 ++++- 8 files changed, 244 insertions(+), 73 deletions(-)
Title: Biodiversity Assessment Tools
Description: Includes algorithms to assess alpha and beta
diversity in all their dimensions (taxon, phylogenetic and functional
diversity), whether communities are completely sampled or not. It allows
performing a number of analyses based on either species identities or
phylogenetic/functional trees or functional kernel n-dimensional hypervolumes
depicting species relationships.
Author: Pedro Cardoso, Stefano Mammola, Francois Rigal, Jose Carlos Carvalho
Maintainer: Pedro Cardoso <pedro.cardoso@helsinki.fi>
Diff between BAT versions 2.1.1 dated 2020-08-29 and 2.2.0 dated 2020-09-30
DESCRIPTION | 8 +- MD5 | 28 +++---- NAMESPACE | 2 R/BAT.R | 177 +++++++++++++++++++++++++++++++++++++++------ man/cwd.Rd |only man/cwe.Rd |only man/cwm.Rd | 2 man/gdm.Rd | 2 man/iaor.Rd | 2 man/kernel.alpha.Rd | 2 man/kernel.beta.Rd | 4 - man/kernel.contribution.Rd | 2 man/kernel.dispersion.Rd | 4 - man/kernel.evenness.Rd | 8 +- man/kernel.originality.Rd | 2 man/kernel.similarity.Rd | 2 16 files changed, 192 insertions(+), 53 deletions(-)
Title: Data and Methods Around Reference Values in Pediatrics
Description: Calculation of standard deviation scores and percentiles adduced from different
growth standards (WHO, UK, Germany, Italy, China, etc). Therefore, the calculation of SDS-values
for different measures like BMI, weight, height, head circumference, different
ratios, etc. are easy to carry out. Also, references for laboratory values in
children and adults are available, e.g., serum lipids, iron-related blood parameters, IGF, liver enzymes. In the
new version, there are also functions combining the lms() function from package 'gamlss' with
resampling methods for using with repeated measurements and family dependencies. A searchable list
of items can be found here: <https://github.com/mvogel78/childsds/wiki>.
Author: Mandy Vogel [aut, cre]
Maintainer: Mandy Vogel <mandy.vogel@googlemail.com>
Diff between childsds versions 0.7.4 dated 2019-03-26 and 0.7.6 dated 2020-09-30
DESCRIPTION | 8 ++-- MD5 | 76 ++++++++++++++++++++++----------------- NEWS.md | 9 ++++ R/createlms.R | 12 +++--- R/data.R | 82 +++++++++++++++++++++++++++++++++---------- data/bone.ref.rda |only data/cn.ref.rda |only data/life_thyr.ref.rda |only data/metabolom.ref.rda |only data/motor.ref.rda |only man/aga_15.ref.Rd | 2 - man/belgium.ref.Rd | 2 - man/bone.ref.Rd |only man/calc_confints.Rd | 8 +++- man/cn.ref.Rd |only man/colombia_sf.ref.Rd | 2 - man/do_iterations.Rd | 32 +++++++++++++--- man/doyon_age.ref.Rd | 2 - man/doyon_height.ref.Rd | 2 - man/duran_bf.ref.Rd | 2 - man/ethiop.ref.Rd | 2 - man/fit_gamlss.Rd | 21 +++++++++-- man/fit_gamlss1.Rd | 17 ++++++-- man/fit_vgam.Rd | 15 ++++++- man/international_lab.ref.Rd | 4 +- man/japan_lab.ref.Rd | 2 - man/life_thyr.ref.Rd |only man/make_percentile_tab.Rd | 12 +++++- man/metabolom.ref.Rd |only man/motor.ref.Rd |only man/nl3.ref.Rd | 4 +- man/one_iteration.Rd | 29 ++++++++++++--- man/prepare_data.Rd | 12 +++++- man/preterm.ref.Rd | 2 - man/saudi.ref.Rd | 2 - man/sds.Rd | 3 - man/sds_2d.Rd | 13 +++++- man/sdsold.Rd | 12 +++++- man/show-ParTab-method.Rd | 1 man/show-RefGroup-method.Rd | 1 man/turkish.ref.Rd | 4 +- man/uk1990.ref.Rd | 4 +- man/who2007.ref.Rd | 2 - man/wormplot_gg.Rd | 9 +++- 44 files changed, 291 insertions(+), 119 deletions(-)
More information about treedata.table at CRAN
Permanent link
Title: Generates Networks from BTS Data
Description: A flexible tool that allows generating bespoke
air transport statistics for urban studies based on publicly available
data from the Bureau of Transport Statistics (BTS) in the United States
<https://www.transtats.bts.gov/databases.asp?Mode_ID=1&Mode_Desc=Aviation&Subject_ID2=0>.
Author: Filipe Teixeira [aut, cre]
Maintainer: Filipe Teixeira <Filipe.MarquesTeixeira@Ugent.be>
Diff between skynet versions 1.3.8 dated 2020-06-02 and 1.3.9 dated 2020-09-30
DESCRIPTION | 12 ++++++------ MD5 | 26 +++++++++++++------------- NEWS.md | 5 +++++ R/download_t100.R | 6 +++++- R/import_db1b.R | 2 +- R/import_ontime.R | 2 +- R/import_t100.R | 4 ++-- README.md | 5 ++--- build/vignette.rds |binary inst/doc/skynet.html | 28 ++++++++++++++++++++++------ man/import_db1b.Rd | 2 +- man/import_ontime.Rd | 2 +- man/import_t100.Rd | 2 +- man/skynet-package.Rd | 4 ++-- 14 files changed, 62 insertions(+), 38 deletions(-)
Title: Kernel Density Estimation with Parametric Starts and Asymmetric
Kernels
Description: Handles univariate non-parametric density estimation with
parametric starts and asymmetric kernels in a simple and flexible way.
Kernel density estimation with parametric starts involves fitting a
parametric density to the data before making a correction with kernel
density estimation, see Hjort & Glad (1995) <doi:10.1214/aos/1176324627>.
Asymmetric kernels make kernel density estimation more efficient on bounded
intervals such as (0, 1) and the positive half-line. Supported asymmetric
kernels are the gamma kernel of Chen (2000) <doi:10.1023/A:1004165218295>,
the beta kernel of Chen (1999) <doi:10.1016/S0167-9473(99)00010-9>, and the
copula kernel of Jones & Henderson (2007) <doi:10.1093/biomet/asm068>.
User-supplied kernels, parametric starts, and bandwidths are supported.
Author: Jonas Moss, Martin Tveten
Maintainer: Jonas Moss <jonas.gjertsen@gmail.com>
Diff between kdensity versions 1.0.1 dated 2019-07-11 and 1.1.0 dated 2020-09-30
kdensity-1.0.1/kdensity/R/builtin_starts_estimation.R |only kdensity-1.0.1/kdensity/man/mlbeta.Rd |only kdensity-1.0.1/kdensity/man/mlgamma.Rd |only kdensity-1.0.1/kdensity/man/mlgumbel.Rd |only kdensity-1.0.1/kdensity/man/mlkumar.Rd |only kdensity-1.0.1/kdensity/man/mlweibull.Rd |only kdensity-1.0.1/kdensity/tests/testthat/test_ml.R |only kdensity-1.1.0/kdensity/DESCRIPTION | 15 kdensity-1.1.0/kdensity/MD5 | 61 +-- kdensity-1.1.0/kdensity/NEWS.md | 6 kdensity-1.1.0/kdensity/R/builtin_bandwidths.R | 36 - kdensity-1.1.0/kdensity/R/builtin_bandwidths_get_bw.R | 2 kdensity-1.1.0/kdensity/R/builtin_kernels.R | 54 +- kdensity-1.1.0/kdensity/R/builtin_kernels_get_kernel.R | 2 kdensity-1.1.0/kdensity/R/builtin_starts_get_start.R | 4 kdensity-1.1.0/kdensity/R/builtin_starts_list.R | 180 +++------ kdensity-1.1.0/kdensity/R/generics.R | 32 + kdensity-1.1.0/kdensity/R/kdensity.R | 73 ++-- kdensity-1.1.0/kdensity/R/kdensity_helpers.R | 4 kdensity-1.1.0/kdensity/R/utility_functions.R | 4 kdensity-1.1.0/kdensity/README.md | 80 +++- kdensity-1.1.0/kdensity/build/vignette.rds |binary kdensity-1.1.0/kdensity/inst/doc/tutorial.R | 26 - kdensity-1.1.0/kdensity/inst/doc/tutorial.Rmd | 17 kdensity-1.1.0/kdensity/inst/doc/tutorial.html | 235 ++++++------- kdensity-1.1.0/kdensity/man/bandwidths.Rd | 48 +- kdensity-1.1.0/kdensity/man/figures/README-example-1.png |binary kdensity-1.1.0/kdensity/man/kdensity.Rd | 57 +-- kdensity-1.1.0/kdensity/man/kernels.Rd | 65 +-- kdensity-1.1.0/kdensity/man/parametric_starts.Rd | 40 -- kdensity-1.1.0/kdensity/man/plot.kdensity.Rd | 13 kdensity-1.1.0/kdensity/man/plot_helper.Rd | 10 kdensity-1.1.0/kdensity/tests/testthat/Rplots.pdf |only kdensity-1.1.0/kdensity/tests/testthat/test_kdensity.R | 14 kdensity-1.1.0/kdensity/tests/testthat/test_univariateML.R |only kdensity-1.1.0/kdensity/vignettes/tutorial.Rmd | 17 36 files changed, 564 insertions(+), 531 deletions(-)
Title: Tests for General Factorial Designs
Description: Implemented are the Wald-type statistic,
a permuted version thereof as well as the ANOVA-type statistic
for general factorial designs, even with non-normal error terms
and/or heteroscedastic variances, for crossed designs with an
arbitrary number of factors and nested designs with up to three factors.
Author: Sarah Friedrich, Frank Konietschke, Markus Pauly
Maintainer: Sarah Friedrich <sarah.friedrich@med.uni-goettingen.de>
Diff between GFD versions 0.2.6 dated 2018-09-29 and 0.2.8 dated 2020-09-30
GFD-0.2.6/GFD/vignettes/IntroductionToGFD.md |only GFD-0.2.8/GFD/DESCRIPTION | 14 GFD-0.2.8/GFD/MD5 | 25 - GFD-0.2.8/GFD/R/Data.R | 4 GFD-0.2.8/GFD/R/GFD-function.R | 5 GFD-0.2.8/GFD/R/calculate_statistics.R | 2 GFD-0.2.8/GFD/build/vignette.rds |binary GFD-0.2.8/GFD/inst/NEWS.md | 3 GFD-0.2.8/GFD/inst/doc/IntroductionToGFD.html | 416 +++++++++++++++++--------- GFD-0.2.8/GFD/man/GFD.Rd | 3 GFD-0.2.8/GFD/man/calculateGUI.Rd | 3 GFD-0.2.8/GFD/man/curdies.Rd | 3 GFD-0.2.8/GFD/man/pizza.Rd | 1 GFD-0.2.8/GFD/man/startup.Rd | 3 14 files changed, 304 insertions(+), 178 deletions(-)
Title: Main Package of the EMU Speech Database Management System
Description: An R package that provides the EMU Speech
Database Management System (EMU-SDMS) with database management, data
extraction, data preparation and data visualization facilities.
Author: Raphael Winkelmann [aut, cre],
Klaus Jaensch [aut, ctb],
Steve Cassidy [aut, ctb],
Jonathan Harrington [aut, ctb]
Maintainer: Raphael Winkelmann <raphael@phonetik.uni-muenchen.de>
Diff between emuR versions 2.1.0 dated 2020-06-15 and 2.1.1 dated 2020-09-30
DESCRIPTION | 13 MD5 | 196 - NEWS.md | 693 +-- R/bayesdist.R | 2 R/classplot.R | 192 - R/dplot.R | 7 R/emuR-annotations_crud.R | 1323 +++---- R/emuR-bas_webservices.R | 1313 +++---- R/emuR-bas_webservicesDBI.R | 5046 +++++++++++++-------------- R/emuR-bundleList.R | 132 R/emuR-convert_TextGridCollection.R | 460 +- R/emuR-create_seglists.R | 1130 +++--- R/emuR-crud-helpers.R | 674 +-- R/emuR-database.R | 212 + R/emuR-database.caching.R | 20 R/emuR-database.files.R | 666 +-- R/emuR-databaseGit.R | 126 R/emuR-emuRtrackdata.R | 616 +-- R/emuR-export_TextGridCollection.R | 4 R/emuR-get_trackdata.R | 1146 +++--- R/emuR-query.database.R | 5122 ++++++++++++++-------------- R/emuR-requery.database.R | 1338 +++---- R/emusegs.R | 2 R/epg.class.R | 1392 +++---- R/eplot.R | 6 R/euclidean.R | 72 README.md | 2 man/bridge.Rd | 26 man/coutts.Rd | 28 man/coutts.epg.Rd | 26 man/coutts.l.Rd | 26 man/coutts.rms.Rd | 36 man/coutts.sam.Rd | 26 man/coutts2.Rd | 26 man/coutts2.epg.Rd | 26 man/coutts2.l.Rd | 26 man/coutts2.sam.Rd | 26 man/create_itemsInLevel.Rd | 7 man/delete_itemsInLevel.Rd | 11 man/demo.all.Rd | 44 man/demo.all.f0.Rd | 52 man/demo.all.fm.Rd | 50 man/demo.all.rms.Rd | 50 man/demo.vowels.Rd | 44 man/demo.vowels.f0.Rd | 50 man/demo.vowels.fm.Rd | 48 man/dip.Rd | 28 man/dip.fdat.Rd | 26 man/dip.l.Rd | 26 man/dip.spkr.Rd | 26 man/dplot.Rd | 6 man/dur.emusegs.Rd | 2 man/e.dft.Rd | 28 man/emuRsegs.Rd | 132 man/emuRtrackdata.Rd | 90 man/engassim.Rd | 30 man/engassim.epg.Rd | 26 man/engassim.l.Rd | 28 man/engassim.w.Rd | 26 man/eplot.Rd | 6 man/fric.Rd | 28 man/fric.dft.Rd | 26 man/fric.l.Rd | 26 man/fric.w.Rd | 26 man/isol.Rd | 28 man/isol.fdat.Rd | 26 man/isol.l.Rd | 26 man/polhom.Rd | 26 man/polhom.epg.Rd | 26 man/polhom.l.Rd | 26 man/runBASwebservice_chunker.Rd | 168 man/runBASwebservice_g2pForPronunciation.Rd | 136 man/runBASwebservice_g2pForTokenization.Rd | 130 man/runBASwebservice_maus.Rd | 156 man/runBASwebservice_minni.Rd | 138 man/runBASwebservice_pho2sylCanonical.Rd | 124 man/runBASwebservice_pho2sylSegmental.Rd | 154 man/segmentlist.Rd | 60 man/trackdata.Rd | 118 man/vowlax.Rd | 28 man/vowlax.df.Rd | 26 man/vowlax.dft.5.Rd | 28 man/vowlax.fdat.5.Rd | 28 man/vowlax.fdat.Rd | 26 man/vowlax.fund.5.Rd | 28 man/vowlax.fund.Rd | 26 man/vowlax.l.Rd | 26 man/vowlax.left.Rd | 26 man/vowlax.right.Rd | 26 man/vowlax.rms.5.Rd | 28 man/vowlax.rms.Rd | 26 man/vowlax.spkr.Rd | 26 man/vowlax.word.Rd | 26 man/wordlax.l.Rd | 26 tests/testthat/test_emuR-annotations_crud.R | 55 tests/testthat/test_emuR-autobuild.R | 1768 ++++----- tests/testthat/test_emuR-bas_webservices.R | 122 tests/testthat/test_emuR-query.database.R | 1234 +++--- tests/testthat/test_emuR-requery.database.R | 677 +-- 99 files changed, 14565 insertions(+), 14152 deletions(-)
Title: Analyzing Dichotomous Choice Contingent Valuation Data
Description: Functions for analyzing dichotomous choice contingent
valuation (CV) data. It provides functions for estimating parametric and
nonparametric models for single-, one-and-one-half-, and double-bounded
CV data. For details, see Aizaki et al. (2014) <doi:10.1201/b17292>.
Author: Tomoaki Nakatani [aut, cph] (original developer),
Hideo Aizaki [aut, cre] (code patches),
Kazuo Sato [ctb] (theoretical part of the manual)
Maintainer: Hideo Aizaki <azk-r@spa.nifty.com>
Diff between DCchoice versions 0.0.16 dated 2020-02-21 and 0.0.17 dated 2020-09-30
DESCRIPTION | 32 +++++++++++++++++--------------- MD5 | 18 +++++++++--------- R/dbchoice.R | 5 +++++ R/oohbchoice.R | 17 ++++++++++++++--- R/sbchoice.R | 5 +++++ R/turnbull_db.R | 15 +++++++++++++-- R/turnbull_sb.R | 18 ++++++++++++++---- man/Carson.Rd | 2 +- man/DCchoice-package.Rd | 2 +- man/turnbull.Rd | 9 +++++---- 10 files changed, 84 insertions(+), 39 deletions(-)
Title: Vehicular Emissions Inventories
Description: Elaboration of vehicular emissions inventories,
consisting in four stages, pre-processing activity data, preparing
emissions factors, estimating the emissions and post-processing of emissions
in maps and databases. More details in Ibarra-Espinosa et al (2018) <doi:10.5194/gmd-11-2209-2018>.
Before using VEIN you need to know the vehicular composition of your study area, in other words,
the combination of of type of vehicles, size and fuel of the fleet. Then, it is recommended to
start with the project to download a template to create a structure of directories and scripts.
Author: Sergio Ibarra-Espinosa [aut, cre, wdc]
(<https://orcid.org/0000-0002-3162-1905>)
Maintainer: Sergio Ibarra-Espinosa <sergio.ibarra@usp.br>
Diff between vein versions 0.8.9 dated 2020-06-11 and 0.9.0 dated 2020-09-30
vein-0.8.9/vein/R/emis_order2.R |only vein-0.8.9/vein/R/matvect.R |only vein-0.8.9/vein/man/emis_order2.Rd |only vein-0.8.9/vein/src/e2d.f95 |only vein-0.8.9/vein/src/e3d.f95 |only vein-0.8.9/vein/src/e4d.f95 |only vein-0.8.9/vein/src/etd1.f95 |only vein-0.8.9/vein/src/etd2.f95 |only vein-0.8.9/vein/src/etd2cold.f95 |only vein-0.8.9/vein/src/etd3.f95 |only vein-0.8.9/vein/src/etd3cold.f95 |only vein-0.8.9/vein/src/etd4.f95 |only vein-0.8.9/vein/src/etd4cold.f95 |only vein-0.8.9/vein/src/etd5.f95 |only vein-0.8.9/vein/src/etd5cold.f95 |only vein-0.8.9/vein/src/etd6.f95 |only vein-0.8.9/vein/src/etd6cold.f95 |only vein-0.8.9/vein/src/etd7.f95 |only vein-0.8.9/vein/tests/testthat/test-emis_order2.R |only vein-0.8.9/vein/tests/testthat/test-get_project.R |only vein-0.9.0/vein/DESCRIPTION | 18 vein-0.9.0/vein/MD5 | 191 ++--- vein-0.9.0/vein/NAMESPACE | 8 vein-0.9.0/vein/NEWS.md | 208 +++--- vein-0.9.0/vein/R/GriddedEmissionsArray.R | 4 vein-0.9.0/vein/R/Vehicles.R | 5 vein-0.9.0/vein/R/age_hdv.R | 8 vein-0.9.0/vein/R/age_ldv.R | 8 vein-0.9.0/vein/R/age_moto.R | 8 vein-0.9.0/vein/R/aw.R | 2 vein-0.9.0/vein/R/check_nt.R |only vein-0.9.0/vein/R/colplot.R |only vein-0.9.0/vein/R/ef_cetesb.R | 98 ++ vein-0.9.0/vein/R/ef_ldv_speed.R | 107 +-- vein-0.9.0/vein/R/emis.R | 134 +++- vein-0.9.0/vein/R/emis_cold_td.R | 312 +++++++-- vein-0.9.0/vein/R/emis_grid.R | 4 vein-0.9.0/vein/R/emis_hot_td.R | 400 +++++++++--- vein-0.9.0/vein/R/emis_merge.R | 18 vein-0.9.0/vein/R/emis_order.R | 17 vein-0.9.0/vein/R/emis_post.R | 4 vein-0.9.0/vein/R/emis_source.R | 8 vein-0.9.0/vein/R/emis_wrf.R | 4 vein-0.9.0/vein/R/get_project.R | 86 +- vein-0.9.0/vein/R/grid_emis.R | 14 vein-0.9.0/vein/R/long_to_wide.R | 4 vein-0.9.0/vein/R/make_grid.R | 7 vein-0.9.0/vein/R/my_age.R | 2 vein-0.9.0/vein/R/netspeed.R | 4 vein-0.9.0/vein/R/speciate.R | 47 + vein-0.9.0/vein/R/split_emis.R | 6 vein-0.9.0/vein/R/sysdata.rda |binary vein-0.9.0/vein/R/temp_fact.R | 2 vein-0.9.0/vein/R/vein_notes.R | 306 ++++----- vein-0.9.0/vein/build |only vein-0.9.0/vein/inst/CITATION | 2 vein-0.9.0/vein/inst/README.Rmd | 125 ++- vein-0.9.0/vein/inst/doc |only vein-0.9.0/vein/man/aw.Rd | 2 vein-0.9.0/vein/man/check_nt.Rd |only vein-0.9.0/vein/man/colplot.Rd |only vein-0.9.0/vein/man/ef_cetesb.Rd | 37 - vein-0.9.0/vein/man/emis.Rd | 6 vein-0.9.0/vein/man/emis_cold_td.Rd | 6 vein-0.9.0/vein/man/emis_hot_td.Rd | 28 vein-0.9.0/vein/man/emis_merge.Rd | 5 vein-0.9.0/vein/man/emis_order.Rd | 3 vein-0.9.0/vein/man/fe2015.Rd | 6 vein-0.9.0/vein/man/fkm.Rd | 6 vein-0.9.0/vein/man/get_project.Rd | 23 vein-0.9.0/vein/man/make_grid.Rd | 2 vein-0.9.0/vein/man/net.Rd | 6 vein-0.9.0/vein/man/pc_cold.Rd | 6 vein-0.9.0/vein/man/pc_profile.Rd | 6 vein-0.9.0/vein/man/pollutants.Rd | 6 vein-0.9.0/vein/man/profiles.Rd | 6 vein-0.9.0/vein/man/speciate.Rd | 7 vein-0.9.0/vein/man/split_emis.Rd | 2 vein-0.9.0/vein/man/vein-deprecated.Rd | 22 vein-0.9.0/vein/man/vein-package.Rd | 2 vein-0.9.0/vein/man/vein_notes.Rd | 5 vein-0.9.0/vein/src/Makevars | 9 vein-0.9.0/vein/src/check_nt.f95 |only vein-0.9.0/vein/src/e_bottomup.f95 |only vein-0.9.0/vein/src/e_topdown.f95 |only vein-0.9.0/vein/src/init.c | 62 + vein-0.9.0/vein/tests/testthat/Rplots.pdf |binary vein-0.9.0/vein/tests/testthat/test-GriddedEmissionsArray.R | 50 - vein-0.9.0/vein/tests/testthat/test-Vehicles.R | 6 vein-0.9.0/vein/tests/testthat/test-add_polid.R | 27 vein-0.9.0/vein/tests/testthat/test-adt.R | 2 vein-0.9.0/vein/tests/testthat/test-age.R | 2 vein-0.9.0/vein/tests/testthat/test-age_hdv.R | 11 vein-0.9.0/vein/tests/testthat/test-age_ldv.R | 10 vein-0.9.0/vein/tests/testthat/test-age_moto.R | 11 vein-0.9.0/vein/tests/testthat/test-aw.R | 2 vein-0.9.0/vein/tests/testthat/test-colplot.R |only vein-0.9.0/vein/tests/testthat/test-ef_cetesb.R | 10 vein-0.9.0/vein/tests/testthat/test-ef_china.R | 1 vein-0.9.0/vein/tests/testthat/test-ef_ldv_speed.R | 9 vein-0.9.0/vein/tests/testthat/test-emis.R | 60 + vein-0.9.0/vein/tests/testthat/test-emis_cold_td.R | 234 ++++++- vein-0.9.0/vein/tests/testthat/test-emis_grid.R | 11 vein-0.9.0/vein/tests/testthat/test-emis_hot_td.R | 171 +++++ vein-0.9.0/vein/tests/testthat/test-emis_post.R | 13 vein-0.9.0/vein/tests/testthat/test-emis_wear.R | 37 - vein-0.9.0/vein/tests/testthat/test-grid_emis.R | 11 vein-0.9.0/vein/tests/testthat/test-make_grid.R | 6 vein-0.9.0/vein/tests/testthat/test-speciate.R | 22 vein-0.9.0/vein/tests/testthat/test-split_emis.R | 2 vein-0.9.0/vein/vignettes |only 111 files changed, 2197 insertions(+), 945 deletions(-)
Title: Solving Mixed Model Equations in R
Description: Structural multivariate-univariate linear mixed model solver for estimation of multiple random effects and unknown variance-covariance structures (i.e. heterogeneous and unstructured variance models) (Covarrubias-Pazaran, 2016 <doi:10.1371/journal.pone.0156744>; Maier et al., 2015 <doi:10.1016/j.ajhg.2014.12.006>). ML/REML estimates can be obtained using the Direct-Inversion Newton-Raphson and Direct-Inversion Average Information algorithms. Designed for genomic prediction and genome wide association studies (GWAS), particularly focused in the p > n problem (more coefficients than observations) and dense known covariance structures for levels of random effects. Spatial models can also be fitted using i.e. the two-dimensional spline functionality available in sommer.
Author: Giovanny Covarrubias-Pazaran
Maintainer: Giovanny Covarrubias-Pazaran <cova_ruber@live.com.mx>
Diff between sommer versions 4.1.0 dated 2020-06-16 and 4.1.1 dated 2020-09-30
sommer-4.1.0/sommer/inst/doc/sommer.FAQ.R |only sommer-4.1.0/sommer/inst/doc/sommer.FAQ.Rmd |only sommer-4.1.0/sommer/inst/doc/sommer.FAQ.pdf |only sommer-4.1.0/sommer/inst/doc/sommer.GxE.models.R |only sommer-4.1.0/sommer/inst/doc/sommer.GxE.models.Rmd |only sommer-4.1.0/sommer/inst/doc/sommer.GxE.models.pdf |only sommer-4.1.0/sommer/inst/doc/sommer.R |only sommer-4.1.0/sommer/inst/doc/sommer.Rmd |only sommer-4.1.0/sommer/inst/doc/sommer.changes.Rmd |only sommer-4.1.0/sommer/inst/doc/sommer.changes.pdf |only sommer-4.1.0/sommer/inst/doc/sommer.pdf |only sommer-4.1.0/sommer/inst/doc/sommer.start.R |only sommer-4.1.0/sommer/inst/doc/sommer.start.Rmd |only sommer-4.1.0/sommer/inst/doc/sommer.start.pdf |only sommer-4.1.0/sommer/inst/doc/special.topics.in.QG.R |only sommer-4.1.0/sommer/inst/doc/special.topics.in.QG.Rmd |only sommer-4.1.0/sommer/inst/doc/special.topics.in.QG.pdf |only sommer-4.1.0/sommer/man/unsBLUP.Rd |only sommer-4.1.0/sommer/vignettes/sommer.FAQ.Rmd |only sommer-4.1.0/sommer/vignettes/sommer.FAQ.html |only sommer-4.1.0/sommer/vignettes/sommer.GxE.models.Rmd |only sommer-4.1.0/sommer/vignettes/sommer.GxE.models.html |only sommer-4.1.0/sommer/vignettes/sommer.Rmd |only sommer-4.1.0/sommer/vignettes/sommer.changes.Rmd |only sommer-4.1.0/sommer/vignettes/sommer.changes.html |only sommer-4.1.0/sommer/vignettes/sommer.html |only sommer-4.1.0/sommer/vignettes/sommer.start.Rmd |only sommer-4.1.0/sommer/vignettes/sommer.start.html |only sommer-4.1.0/sommer/vignettes/special.topics.in.QG.Rmd |only sommer-4.1.0/sommer/vignettes/special.topics.in.QG.html |only sommer-4.1.1/sommer/CHANGELOG | 18 sommer-4.1.1/sommer/DESCRIPTION | 10 sommer-4.1.1/sommer/MD5 | 84 - sommer-4.1.1/sommer/NAMESPACE | 6 sommer-4.1.1/sommer/R/FUN_spatial.R | 381 +++++++ sommer-4.1.1/sommer/R/FUN_special.R | 506 +--------- sommer-4.1.1/sommer/R/FUN_stats.R | 79 + sommer-4.1.1/sommer/R/FUN_utils.R | 316 ------ sommer-4.1.1/sommer/R/mmer.R | 64 - sommer-4.1.1/sommer/R/predict.R |only sommer-4.1.1/sommer/build/vignette.rds |binary sommer-4.1.1/sommer/inst/doc/v1.sommer.quick.start.R |only sommer-4.1.1/sommer/inst/doc/v1.sommer.quick.start.Rmd |only sommer-4.1.1/sommer/inst/doc/v1.sommer.quick.start.pdf |only sommer-4.1.1/sommer/inst/doc/v2.sommer.changes.and.faqs.R |only sommer-4.1.1/sommer/inst/doc/v2.sommer.changes.and.faqs.Rmd |only sommer-4.1.1/sommer/inst/doc/v2.sommer.changes.and.faqs.pdf |only sommer-4.1.1/sommer/inst/doc/v3.sommer.qg.R |only sommer-4.1.1/sommer/inst/doc/v3.sommer.qg.Rmd |only sommer-4.1.1/sommer/inst/doc/v3.sommer.qg.pdf |only sommer-4.1.1/sommer/inst/doc/v4.sommer.gxe.R |only sommer-4.1.1/sommer/inst/doc/v4.sommer.gxe.Rmd |only sommer-4.1.1/sommer/inst/doc/v4.sommer.gxe.pdf |only sommer-4.1.1/sommer/man/DT_technow.Rd | 2 sommer-4.1.1/sommer/man/GWAS.Rd | 41 sommer-4.1.1/sommer/man/mmer.Rd | 65 - sommer-4.1.1/sommer/man/predict.Rd | 24 sommer-4.1.1/sommer/man/spl2D.Rd | 2 sommer-4.1.1/sommer/man/vs.Rd | 32 sommer-4.1.1/sommer/man/wald.Rd |only sommer-4.1.1/sommer/src/MNR.cpp | 193 +-- sommer-4.1.1/sommer/vignettes/v1.sommer.quick.start.Rmd |only sommer-4.1.1/sommer/vignettes/v1.sommer.quick.start.html |only sommer-4.1.1/sommer/vignettes/v2.sommer.changes.and.faqs.Rmd |only sommer-4.1.1/sommer/vignettes/v2.sommer.changes.and.faqs.html |only sommer-4.1.1/sommer/vignettes/v3.sommer.qg.Rmd |only sommer-4.1.1/sommer/vignettes/v3.sommer.qg.html |only sommer-4.1.1/sommer/vignettes/v4.sommer.gxe.Rmd |only sommer-4.1.1/sommer/vignettes/v4.sommer.gxe.html |only 69 files changed, 873 insertions(+), 950 deletions(-)
Title: 'SQLite' Interface for R
Description: Embeds the 'SQLite' database engine in R and
provides an interface compliant with the 'DBI' package. The source for
the 'SQLite' engine is included.
Author: Kirill Müller [aut, cre] (<https://orcid.org/0000-0002-1416-3412>),
Hadley Wickham [aut],
David A. James [aut],
Seth Falcon [aut],
SQLite Authors [ctb] (for the included SQLite sources),
Liam Healy [ctb] (for the included SQLite sources),
R Consortium [fnd],
RStudio [cph]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>
Diff between RSQLite versions 2.2.0 dated 2020-01-07 and 2.2.1 dated 2020-09-30
DESCRIPTION | 10 MD5 | 53 NEWS.md | 34 R/connect.R | 6 R/copy.R | 2 R/deprecated.R | 2 R/extensions.R | 2 R/table.R | 15 README.md | 226 build/vignette.rds |binary inst/WORDLIST |only inst/doc/RSQLite.Rmd | 4 inst/doc/RSQLite.html | 178 man/SQLite.Rd | 8 man/SQLiteConnection-class.Rd | 3 man/initExtension.Rd | 2 man/sqlite-transaction.Rd | 4 man/sqliteBuildTableDefinition.Rd | 4 man/sqliteCopyDatabase.Rd | 2 src/Makevars | 3 src/SqliteResultImpl.cpp | 10 src/vendor/sqlite3/regexp.c | 6 src/vendor/sqlite3/sqlite3.c |36427 +++++++++++++++++++++----------------- src/vendor/sqlite3/sqlite3.h | 2093 +- src/vendor/sqlite3/sqlite3ext.h | 25 tests/testthat/test-blob.R | 18 tests/testthat/test-error.R | 12 vignettes/RSQLite.Rmd | 4 28 files changed, 22509 insertions(+), 16644 deletions(-)
Title: DBI Package for the DuckDB Database Management System
Description: The DuckDB project is an embedded analytical data
management system with support for the Structured Query Language (SQL). This package includes all of
DuckDB and a R Database Interface (DBI) connector.
Author: Hannes Mühleisen [aut, cre] (<https://orcid.org/0000-0001-8552-0029>),
Mark Raasveldt [aut] (<https://orcid.org/0000-0001-5005-6844>),
DuckDB Contributors [aut],
Apache Software Foundation [cph],
PostgreSQL Global Development Group [cph],
The Regents of the University of California [cph],
Cameron Desrochers [cph],
Victor Zverovich [cph],
RAD Game Tools [cph],
Valve Software [cph],
Rich Geldreich [cph],
Tenacious Software LLC [cph],
The RE2 Authors [cph],
Google Inc. [cph],
Steven G. Johnson [cph],
Jiahao Chen [cph],
Tony Kelman [cph],
Jonas Fonseca [cph],
Lukas Fittl [cph]
Maintainer: Hannes Mühleisen <hannes@cwi.nl>
Diff between duckdb versions 0.2.1 dated 2020-09-10 and 0.2.1-2 dated 2020-09-30
duckdb-0.2.1-2/duckdb/DESCRIPTION | 8 duckdb-0.2.1-2/duckdb/MD5 | 552 duckdb-0.2.1-2/duckdb/src/Makevars | 2 duckdb-0.2.1-2/duckdb/src/duckdb/amalgamation-1.cpp | 79 duckdb-0.2.1-2/duckdb/src/duckdb/amalgamation-2.cpp | 99 duckdb-0.2.1-2/duckdb/src/duckdb/amalgamation-3.cpp | 111 duckdb-0.2.1-2/duckdb/src/duckdb/amalgamation-4.cpp | 99 duckdb-0.2.1-2/duckdb/src/duckdb/amalgamation-5.cpp | 87 duckdb-0.2.1-2/duckdb/src/duckdb/amalgamation-6.cpp | 95 duckdb-0.2.1-2/duckdb/src/duckdb/amalgamation-7.cpp | 95 duckdb-0.2.1-2/duckdb/src/duckdb/amalgamation-8.cpp | 38 duckdb-0.2.1-2/duckdb/src/duckdb/extension/parquet/include/parquet_reader.hpp |only duckdb-0.2.1-2/duckdb/src/duckdb/extension/parquet/include/parquet_timestamp.hpp |only duckdb-0.2.1-2/duckdb/src/duckdb/extension/parquet/include/parquet_writer.hpp |only duckdb-0.2.1-2/duckdb/src/duckdb/extension/parquet/include/resizable_buffer.hpp |only duckdb-0.2.1-2/duckdb/src/duckdb/extension/parquet/parquet-extension.cpp | 1431 duckdb-0.2.1-2/duckdb/src/duckdb/extension/parquet/parquet_reader.cpp |only duckdb-0.2.1-2/duckdb/src/duckdb/extension/parquet/parquet_timestamp.cpp |only duckdb-0.2.1-2/duckdb/src/duckdb/extension/parquet/parquet_writer.cpp |only duckdb-0.2.1-2/duckdb/src/duckdb/src/catalog/catalog.cpp | 31 duckdb-0.2.1-2/duckdb/src/duckdb/src/catalog/catalog_entry/copy_function_catalog_entry.cpp | 4 duckdb-0.2.1-2/duckdb/src/duckdb/src/catalog/catalog_entry/pragma_function_catalog_entry.cpp |only duckdb-0.2.1-2/duckdb/src/duckdb/src/catalog/catalog_entry/schema_catalog_entry.cpp | 29 duckdb-0.2.1-2/duckdb/src/duckdb/src/catalog/catalog_entry/view_catalog_entry.cpp | 15 duckdb-0.2.1-2/duckdb/src/duckdb/src/common/enums/catalog_type.cpp | 11 duckdb-0.2.1-2/duckdb/src/duckdb/src/common/enums/logical_operator_type.cpp | 8 duckdb-0.2.1-2/duckdb/src/duckdb/src/common/enums/physical_operator_type.cpp | 14 duckdb-0.2.1-2/duckdb/src/duckdb/src/common/enums/statement_type.cpp | 2 duckdb-0.2.1-2/duckdb/src/duckdb/src/common/file_buffer.cpp | 4 duckdb-0.2.1-2/duckdb/src/duckdb/src/common/file_system.cpp | 71 duckdb-0.2.1-2/duckdb/src/duckdb/src/common/limits.cpp | 20 duckdb-0.2.1-2/duckdb/src/duckdb/src/common/operator/cast_operators.cpp | 17 duckdb-0.2.1-2/duckdb/src/duckdb/src/common/serializer.cpp | 8 duckdb-0.2.1-2/duckdb/src/duckdb/src/common/types/data_chunk.cpp | 23 duckdb-0.2.1-2/duckdb/src/duckdb/src/common/types/date.cpp | 9 duckdb-0.2.1-2/duckdb/src/duckdb/src/common/types/hugeint.cpp | 4 duckdb-0.2.1-2/duckdb/src/duckdb/src/common/types/null_value.cpp | 14 duckdb-0.2.1-2/duckdb/src/duckdb/src/common/types/string_type.cpp | 18 duckdb-0.2.1-2/duckdb/src/duckdb/src/common/types/timestamp.cpp | 19 duckdb-0.2.1-2/duckdb/src/duckdb/src/common/types/value.cpp | 16 duckdb-0.2.1-2/duckdb/src/duckdb/src/common/types/vector.cpp | 6 duckdb-0.2.1-2/duckdb/src/duckdb/src/common/vector_operations/boolean_operators.cpp | 14 duckdb-0.2.1-2/duckdb/src/duckdb/src/common/vector_operations/gather.cpp | 6 duckdb-0.2.1-2/duckdb/src/duckdb/src/common/vector_operations/numeric_inplace_operators.cpp | 3 duckdb-0.2.1-2/duckdb/src/duckdb/src/common/vector_operations/vector_cast.cpp | 30 duckdb-0.2.1-2/duckdb/src/duckdb/src/execution/aggregate_hashtable.cpp | 75 duckdb-0.2.1-2/duckdb/src/duckdb/src/execution/expression_executor.cpp | 11 duckdb-0.2.1-2/duckdb/src/duckdb/src/execution/expression_executor/execute_between.cpp | 13 duckdb-0.2.1-2/duckdb/src/duckdb/src/execution/expression_executor/execute_case.cpp | 5 duckdb-0.2.1-2/duckdb/src/duckdb/src/execution/expression_executor/execute_cast.cpp | 4 duckdb-0.2.1-2/duckdb/src/duckdb/src/execution/expression_executor/execute_comparison.cpp | 11 duckdb-0.2.1-2/duckdb/src/duckdb/src/execution/expression_executor/execute_conjunction.cpp | 4 duckdb-0.2.1-2/duckdb/src/duckdb/src/execution/expression_executor/execute_function.cpp | 28 duckdb-0.2.1-2/duckdb/src/duckdb/src/execution/expression_executor/execute_operator.cpp | 5 duckdb-0.2.1-2/duckdb/src/duckdb/src/execution/expression_executor_state.cpp | 7 duckdb-0.2.1-2/duckdb/src/duckdb/src/execution/index/art/art.cpp | 175 duckdb-0.2.1-2/duckdb/src/duckdb/src/execution/join_hashtable.cpp | 35 duckdb-0.2.1-2/duckdb/src/duckdb/src/execution/operator/aggregate/physical_hash_aggregate.cpp | 8 duckdb-0.2.1-2/duckdb/src/duckdb/src/execution/operator/aggregate/physical_window.cpp | 5 duckdb-0.2.1-2/duckdb/src/duckdb/src/execution/operator/filter/physical_filter.cpp | 5 duckdb-0.2.1-2/duckdb/src/duckdb/src/execution/operator/helper/physical_limit.cpp | 8 duckdb-0.2.1-2/duckdb/src/duckdb/src/execution/operator/helper/physical_pragma.cpp | 207 duckdb-0.2.1-2/duckdb/src/duckdb/src/execution/operator/join/physical_blockwise_nl_join.cpp | 7 duckdb-0.2.1-2/duckdb/src/duckdb/src/execution/operator/join/physical_cross_product.cpp | 6 duckdb-0.2.1-2/duckdb/src/duckdb/src/execution/operator/join/physical_delim_join.cpp | 55 duckdb-0.2.1-2/duckdb/src/duckdb/src/execution/operator/join/physical_hash_join.cpp | 7 duckdb-0.2.1-2/duckdb/src/duckdb/src/execution/operator/join/physical_nested_loop_join.cpp | 8 duckdb-0.2.1-2/duckdb/src/duckdb/src/execution/operator/join/physical_piecewise_merge_join.cpp | 6 duckdb-0.2.1-2/duckdb/src/duckdb/src/execution/operator/order/physical_order.cpp | 5 duckdb-0.2.1-2/duckdb/src/duckdb/src/execution/operator/order/physical_top_n.cpp | 5 duckdb-0.2.1-2/duckdb/src/duckdb/src/execution/operator/persistent/buffered_csv_reader.cpp | 303 duckdb-0.2.1-2/duckdb/src/duckdb/src/execution/operator/projection/physical_projection.cpp | 6 duckdb-0.2.1-2/duckdb/src/duckdb/src/execution/operator/projection/physical_unnest.cpp | 6 duckdb-0.2.1-2/duckdb/src/duckdb/src/execution/operator/scan/physical_chunk_scan.cpp | 4 duckdb-0.2.1-2/duckdb/src/duckdb/src/execution/operator/scan/physical_expression_scan.cpp | 5 duckdb-0.2.1-2/duckdb/src/duckdb/src/execution/operator/scan/physical_table_scan.cpp | 123 duckdb-0.2.1-2/duckdb/src/duckdb/src/execution/operator/set/physical_recursive_cte.cpp | 39 duckdb-0.2.1-2/duckdb/src/duckdb/src/execution/operator/set/physical_union.cpp | 4 duckdb-0.2.1-2/duckdb/src/duckdb/src/execution/physical_operator.cpp | 14 duckdb-0.2.1-2/duckdb/src/duckdb/src/execution/physical_plan/plan_dummy_scan.cpp |only duckdb-0.2.1-2/duckdb/src/duckdb/src/execution/physical_plan/plan_get.cpp | 80 duckdb-0.2.1-2/duckdb/src/duckdb/src/execution/physical_plan/plan_pragma.cpp |only duckdb-0.2.1-2/duckdb/src/duckdb/src/execution/physical_plan/plan_recursive_cte.cpp | 2 duckdb-0.2.1-2/duckdb/src/duckdb/src/execution/physical_plan/plan_simple.cpp | 3 duckdb-0.2.1-2/duckdb/src/duckdb/src/execution/physical_plan_generator.cpp | 11 duckdb-0.2.1-2/duckdb/src/duckdb/src/function/aggregate/distributive/first.cpp | 4 duckdb-0.2.1-2/duckdb/src/duckdb/src/function/aggregate/distributive/string_agg.cpp | 85 duckdb-0.2.1-2/duckdb/src/duckdb/src/function/aggregate/nested/list.cpp | 2 duckdb-0.2.1-2/duckdb/src/duckdb/src/function/function.cpp | 72 duckdb-0.2.1-2/duckdb/src/duckdb/src/function/pragma |only duckdb-0.2.1-2/duckdb/src/duckdb/src/function/pragma_function.cpp |only duckdb-0.2.1-2/duckdb/src/duckdb/src/function/scalar/date/strftime.cpp | 43 duckdb-0.2.1-2/duckdb/src/duckdb/src/function/scalar/math/numeric.cpp | 12 duckdb-0.2.1-2/duckdb/src/duckdb/src/function/scalar/pragma_functions.cpp |only duckdb-0.2.1-2/duckdb/src/duckdb/src/function/scalar/string/like.cpp | 91 duckdb-0.2.1-2/duckdb/src/duckdb/src/function/scalar/string/nfc_normalize.cpp |only duckdb-0.2.1-2/duckdb/src/duckdb/src/function/scalar/string/strip_accents.cpp | 4 duckdb-0.2.1-2/duckdb/src/duckdb/src/function/scalar/string_functions.cpp | 1 duckdb-0.2.1-2/duckdb/src/duckdb/src/function/table/arrow.cpp | 59 duckdb-0.2.1-2/duckdb/src/duckdb/src/function/table/copy_csv.cpp | 253 duckdb-0.2.1-2/duckdb/src/duckdb/src/function/table/glob.cpp |only duckdb-0.2.1-2/duckdb/src/duckdb/src/function/table/information_schema |only duckdb-0.2.1-2/duckdb/src/duckdb/src/function/table/information_schema_functions.cpp |only duckdb-0.2.1-2/duckdb/src/duckdb/src/function/table/range.cpp | 98 duckdb-0.2.1-2/duckdb/src/duckdb/src/function/table/read_csv.cpp | 124 duckdb-0.2.1-2/duckdb/src/duckdb/src/function/table/repeat.cpp | 39 duckdb-0.2.1-2/duckdb/src/duckdb/src/function/table/sqlite/pragma_collations.cpp | 44 duckdb-0.2.1-2/duckdb/src/duckdb/src/function/table/sqlite/pragma_database_list.cpp | 18 duckdb-0.2.1-2/duckdb/src/duckdb/src/function/table/sqlite/pragma_table_info.cpp | 54 duckdb-0.2.1-2/duckdb/src/duckdb/src/function/table/sqlite/sqlite_master.cpp | 39 duckdb-0.2.1-2/duckdb/src/duckdb/src/function/table/sqlite_functions.cpp | 24 duckdb-0.2.1-2/duckdb/src/duckdb/src/function/table/table_scan.cpp |only duckdb-0.2.1-2/duckdb/src/duckdb/src/function/table/version/pragma_version.cpp | 26 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb.h | 67 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/catalog/catalog.hpp | 10 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/catalog/catalog_entry/list.hpp | 2 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/catalog/catalog_entry/pragma_function_catalog_entry.hpp |only duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/catalog/catalog_entry/schema_catalog_entry.hpp | 5 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/catalog/catalog_entry/view_catalog_entry.hpp | 2 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/common/enums/catalog_type.hpp | 22 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/common/enums/logical_operator_type.hpp | 91 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/common/enums/physical_operator_type.hpp | 8 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/common/enums/statement_type.hpp | 1 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/common/enums/undo_flags.hpp | 2 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/common/file_system.hpp | 4 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/common/helper.hpp | 16 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/common/mutex.hpp | 3 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/common/operator/comparison_operators.hpp | 4 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/common/serializer.hpp | 13 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/common/types/date.hpp | 6 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/common/types/string_type.hpp | 60 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/common/vector_operations/binary_executor.hpp | 7 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/common/vector_operations/unary_executor.hpp | 6 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/execution/aggregate_hashtable.hpp | 2 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/execution/executor.hpp | 3 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/execution/expression_executor_state.hpp | 3 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/execution/index/art/art.hpp | 27 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/execution/operator/helper/physical_pragma.hpp | 11 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/execution/operator/join/physical_delim_join.hpp | 3 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/execution/operator/list.hpp | 4 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/execution/operator/persistent/buffered_csv_reader.hpp | 17 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/execution/operator/persistent/physical_delete.hpp | 2 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/execution/operator/scan/physical_table_scan.hpp | 27 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/execution/operator/set/physical_recursive_cte.hpp | 8 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/execution/physical_operator.hpp | 17 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/execution/physical_plan_generator.hpp | 5 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/function/copy_function.hpp | 7 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/function/function.hpp | 11 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/function/pragma |only duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/function/pragma_function.hpp |only duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/function/scalar/strftime.hpp | 93 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/function/scalar/string_functions.hpp | 7 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/function/table/information_schema_functions.hpp |only duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/function/table/range.hpp | 4 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/function/table/read_csv.hpp | 42 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/function/table/table_scan.hpp |only duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/function/table_function.hpp | 131 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/main/client_context.hpp | 11 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/main/connection.hpp | 17 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/main/database.hpp | 1 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/main/relation/read_csv_relation.hpp | 4 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/optimizer/filter_combiner.hpp | 3 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/parallel/parallel_state.hpp |only duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/parallel/pipeline.hpp | 23 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/parallel/task_context.hpp | 9 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/parser/parsed_data/alter_table_info.hpp | 12 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/parser/parsed_data/create_aggregate_function_info.hpp | 3 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/parser/parsed_data/create_copy_function_info.hpp | 2 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/parser/parsed_data/create_function_info.hpp | 3 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/parser/parsed_data/create_info.hpp | 8 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/parser/parsed_data/create_pragma_function_info.hpp |only duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/parser/parsed_data/create_scalar_function_info.hpp | 3 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/parser/parsed_data/pragma_info.hpp | 2 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/parser/qualified_name.hpp |only duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/parser/query_node/recursive_cte_node.hpp | 2 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/parser/statement/call_statement.hpp |only duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/parser/statement/list.hpp | 1 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/parser/statement/select_statement.hpp | 7 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/parser/tokens.hpp | 1 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/parser/transformer.hpp | 11 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/planner/bind_context.hpp | 6 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/planner/binder.hpp | 8 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/planner/logical_tokens.hpp | 5 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/planner/operator/list.hpp | 5 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/planner/operator/logical_dummy_scan.hpp |only duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/planner/operator/logical_get.hpp | 24 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/planner/operator/logical_pragma.hpp |only duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/planner/pragma_handler.hpp |only duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/planner/table_binding.hpp | 51 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/planner/tableref/bound_basetableref.hpp | 4 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/planner/tableref/bound_table_function.hpp | 22 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/storage/data_table.hpp | 39 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/storage/index.hpp | 12 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/storage/table/chunk_info.hpp | 21 duckdb-0.2.1-2/duckdb/src/duckdb/src/include/duckdb/storage/table/scan_state.hpp | 16 duckdb-0.2.1-2/duckdb/src/duckdb/src/main/client_context.cpp | 53 duckdb-0.2.1-2/duckdb/src/duckdb/src/main/connection.cpp | 18 duckdb-0.2.1-2/duckdb/src/duckdb/src/main/database.cpp | 4 duckdb-0.2.1-2/duckdb/src/duckdb/src/main/duckdb-c.cpp | 9 duckdb-0.2.1-2/duckdb/src/duckdb/src/main/query_profiler.cpp | 5 duckdb-0.2.1-2/duckdb/src/duckdb/src/main/query_result.cpp | 9 duckdb-0.2.1-2/duckdb/src/duckdb/src/main/relation/create_table_relation.cpp | 2 duckdb-0.2.1-2/duckdb/src/duckdb/src/main/relation/create_view_relation.cpp | 2 duckdb-0.2.1-2/duckdb/src/duckdb/src/main/relation/read_csv_relation.cpp | 26 duckdb-0.2.1-2/duckdb/src/duckdb/src/optimizer/expression_heuristics.cpp | 2 duckdb-0.2.1-2/duckdb/src/duckdb/src/optimizer/filter_combiner.cpp | 39 duckdb-0.2.1-2/duckdb/src/duckdb/src/optimizer/join_order_optimizer.cpp | 6 duckdb-0.2.1-2/duckdb/src/duckdb/src/optimizer/optimizer.cpp | 7 duckdb-0.2.1-2/duckdb/src/duckdb/src/optimizer/pushdown/pushdown_get.cpp | 71 duckdb-0.2.1-2/duckdb/src/duckdb/src/optimizer/remove_unused_columns.cpp | 32 duckdb-0.2.1-2/duckdb/src/duckdb/src/parallel/executor.cpp | 58 duckdb-0.2.1-2/duckdb/src/duckdb/src/parallel/pipeline.cpp | 54 duckdb-0.2.1-2/duckdb/src/duckdb/src/parser/parsed_data/alter_table_info.cpp | 8 duckdb-0.2.1-2/duckdb/src/duckdb/src/parser/parser.cpp | 25 duckdb-0.2.1-2/duckdb/src/duckdb/src/parser/query_node/recursive_cte_node.cpp | 3 duckdb-0.2.1-2/duckdb/src/duckdb/src/parser/statement/select_statement.cpp | 21 duckdb-0.2.1-2/duckdb/src/duckdb/src/parser/tableref/subqueryref.cpp | 13 duckdb-0.2.1-2/duckdb/src/duckdb/src/parser/tableref/table_function.cpp | 5 duckdb-0.2.1-2/duckdb/src/duckdb/src/parser/transform/helpers/nodetype_to_string.cpp | 2 duckdb-0.2.1-2/duckdb/src/duckdb/src/parser/transform/helpers/transform_cte.cpp | 34 duckdb-0.2.1-2/duckdb/src/duckdb/src/parser/transform/statement/transform_alter_table.cpp | 15 duckdb-0.2.1-2/duckdb/src/duckdb/src/parser/transform/statement/transform_call.cpp |only duckdb-0.2.1-2/duckdb/src/duckdb/src/parser/transform/statement/transform_create_index.cpp | 2 duckdb-0.2.1-2/duckdb/src/duckdb/src/parser/transform/statement/transform_create_schema.cpp | 2 duckdb-0.2.1-2/duckdb/src/duckdb/src/parser/transform/statement/transform_create_sequence.cpp | 12 duckdb-0.2.1-2/duckdb/src/duckdb/src/parser/transform/statement/transform_create_table.cpp | 2 duckdb-0.2.1-2/duckdb/src/duckdb/src/parser/transform/statement/transform_create_table_as.cpp | 12 duckdb-0.2.1-2/duckdb/src/duckdb/src/parser/transform/statement/transform_create_view.cpp | 2 duckdb-0.2.1-2/duckdb/src/duckdb/src/parser/transform/statement/transform_import.cpp | 2 duckdb-0.2.1-2/duckdb/src/duckdb/src/parser/transform/statement/transform_insert.cpp | 10 duckdb-0.2.1-2/duckdb/src/duckdb/src/parser/transform/statement/transform_pragma.cpp | 6 duckdb-0.2.1-2/duckdb/src/duckdb/src/parser/transform/statement/transform_rename.cpp | 19 duckdb-0.2.1-2/duckdb/src/duckdb/src/parser/transform/statement/transform_select.cpp | 14 duckdb-0.2.1-2/duckdb/src/duckdb/src/parser/transform/statement/transform_show.cpp | 4 duckdb-0.2.1-2/duckdb/src/duckdb/src/parser/transform/tableref/transform_base_tableref.cpp | 21 duckdb-0.2.1-2/duckdb/src/duckdb/src/parser/transformer.cpp | 2 duckdb-0.2.1-2/duckdb/src/duckdb/src/planner/bind_context.cpp | 14 duckdb-0.2.1-2/duckdb/src/duckdb/src/planner/binder.cpp | 12 duckdb-0.2.1-2/duckdb/src/duckdb/src/planner/binder/query_node/bind_recursive_cte_node.cpp | 38 duckdb-0.2.1-2/duckdb/src/duckdb/src/planner/binder/statement/bind_call.cpp |only duckdb-0.2.1-2/duckdb/src/duckdb/src/planner/binder/statement/bind_copy.cpp | 13 duckdb-0.2.1-2/duckdb/src/duckdb/src/planner/binder/statement/bind_create.cpp | 4 duckdb-0.2.1-2/duckdb/src/duckdb/src/planner/binder/statement/bind_delete.cpp | 10 duckdb-0.2.1-2/duckdb/src/duckdb/src/planner/binder/statement/bind_pragma.cpp |only duckdb-0.2.1-2/duckdb/src/duckdb/src/planner/binder/statement/bind_simple.cpp | 24 duckdb-0.2.1-2/duckdb/src/duckdb/src/planner/binder/statement/bind_update.cpp | 7 duckdb-0.2.1-2/duckdb/src/duckdb/src/planner/binder/tableref/bind_basetableref.cpp | 26 duckdb-0.2.1-2/duckdb/src/duckdb/src/planner/binder/tableref/bind_table_function.cpp | 39 duckdb-0.2.1-2/duckdb/src/duckdb/src/planner/binder/tableref/plan_dummytableref.cpp | 4 duckdb-0.2.1-2/duckdb/src/duckdb/src/planner/binder/tableref/plan_expressionlistref.cpp | 4 duckdb-0.2.1-2/duckdb/src/duckdb/src/planner/binder/tableref/plan_joinref.cpp | 95 duckdb-0.2.1-2/duckdb/src/duckdb/src/planner/binder/tableref/plan_table_function.cpp | 9 duckdb-0.2.1-2/duckdb/src/duckdb/src/planner/joinside.cpp | 5 duckdb-0.2.1-2/duckdb/src/duckdb/src/planner/operator/logical_get.cpp | 34 duckdb-0.2.1-2/duckdb/src/duckdb/src/planner/planner.cpp | 1 duckdb-0.2.1-2/duckdb/src/duckdb/src/planner/pragma_handler.cpp |only duckdb-0.2.1-2/duckdb/src/duckdb/src/planner/table_binding.cpp | 113 duckdb-0.2.1-2/duckdb/src/duckdb/src/storage/checkpoint/table_data_writer.cpp | 4 duckdb-0.2.1-2/duckdb/src/duckdb/src/storage/checkpoint_manager.cpp | 2 duckdb-0.2.1-2/duckdb/src/duckdb/src/storage/column_data.cpp | 4 duckdb-0.2.1-2/duckdb/src/duckdb/src/storage/data_table.cpp | 146 duckdb-0.2.1-2/duckdb/src/duckdb/src/storage/meta_block_reader.cpp | 2 duckdb-0.2.1-2/duckdb/src/duckdb/src/storage/meta_block_writer.cpp | 2 duckdb-0.2.1-2/duckdb/src/duckdb/src/storage/single_file_block_manager.cpp | 34 duckdb-0.2.1-2/duckdb/src/duckdb/src/storage/string_segment.cpp | 21 duckdb-0.2.1-2/duckdb/src/duckdb/src/storage/table/chunk_info.cpp | 65 duckdb-0.2.1-2/duckdb/src/duckdb/src/storage/table/version_manager.cpp | 16 duckdb-0.2.1-2/duckdb/src/duckdb/src/storage/uncompressed_segment.cpp | 56 duckdb-0.2.1-2/duckdb/src/duckdb/src/transaction/cleanup_state.cpp | 2 duckdb-0.2.1-2/duckdb/src/duckdb/src/transaction/commit_state.cpp | 9 duckdb-0.2.1-2/duckdb/src/duckdb/src/transaction/rollback_state.cpp | 2 duckdb-0.2.1-2/duckdb/src/duckdb/src/transaction/transaction.cpp | 4 duckdb-0.2.1-2/duckdb/src/duckdb/src/transaction/undo_buffer.cpp | 18 duckdb-0.2.1-2/duckdb/src/duckdb/third_party/libpg_query/include/nodes/nodes.hpp | 1 duckdb-0.2.1-2/duckdb/src/duckdb/third_party/libpg_query/include/nodes/parsenodes.hpp | 16 duckdb-0.2.1-2/duckdb/src/duckdb/third_party/libpg_query/include/parser/gram.hpp | 1610 duckdb-0.2.1-2/duckdb/src/duckdb/third_party/libpg_query/include/parser/kwlist.hpp | 2 duckdb-0.2.1-2/duckdb/src/duckdb/third_party/libpg_query/pg_functions.cpp | 8 duckdb-0.2.1-2/duckdb/src/duckdb/third_party/libpg_query/src_backend_parser_gram.cpp |25758 +++++----- duckdb-0.2.1-2/duckdb/src/duckdb/third_party/miniz/miniz.hpp | 2 duckdb-0.2.1-2/duckdb/src/duckdb/third_party/re2/re2/prog.h | 24 duckdb-0.2.1-2/duckdb/src/duckdb/third_party/re2/re2/regexp.h | 46 duckdb-0.2.1-2/duckdb/src/duckdb/third_party/re2/re2/walker-inl.h | 9 duckdb-0.2.1-2/duckdb/src/duckdbr.cpp | 57 duckdb-0.2.1/duckdb/src/duckdb/src/execution/operator/persistent/physical_copy_from_file.cpp |only duckdb-0.2.1/duckdb/src/duckdb/src/execution/operator/scan/physical_index_scan.cpp |only duckdb-0.2.1/duckdb/src/duckdb/src/execution/operator/scan/physical_table_function.cpp |only duckdb-0.2.1/duckdb/src/duckdb/src/execution/physical_plan/plan_copy_from_file.cpp |only duckdb-0.2.1/duckdb/src/duckdb/src/execution/physical_plan/plan_index_scan.cpp |only duckdb-0.2.1/duckdb/src/duckdb/src/execution/physical_plan/plan_table_function.cpp |only duckdb-0.2.1/duckdb/src/duckdb/src/include/duckdb/execution/operator/persistent/physical_copy_from_file.hpp |only duckdb-0.2.1/duckdb/src/duckdb/src/include/duckdb/execution/operator/scan/physical_index_scan.hpp |only duckdb-0.2.1/duckdb/src/duckdb/src/include/duckdb/execution/operator/scan/physical_table_function.hpp |only duckdb-0.2.1/duckdb/src/duckdb/src/include/duckdb/optimizer/index_scan.hpp |only duckdb-0.2.1/duckdb/src/duckdb/src/include/duckdb/parser/pragma_handler.hpp |only duckdb-0.2.1/duckdb/src/duckdb/src/include/duckdb/planner/operator/logical_copy_from_file.hpp |only duckdb-0.2.1/duckdb/src/duckdb/src/include/duckdb/planner/operator/logical_index_scan.hpp |only duckdb-0.2.1/duckdb/src/duckdb/src/include/duckdb/planner/operator/logical_table_function.hpp |only duckdb-0.2.1/duckdb/src/duckdb/src/optimizer/index_scan.cpp |only duckdb-0.2.1/duckdb/src/duckdb/src/parser/pragma_handler.cpp |only duckdb-0.2.1/duckdb/src/duckdb/src/planner/operator/logical_table_function.cpp |only 301 files changed, 17560 insertions(+), 18023 deletions(-)
Title: Functions for Visualising Simple Graphs (Networks), Plotting
Flow Diagrams
Description: Visualises simple graphs (networks) based on a transition matrix, utilities to plot flow diagrams,
visualising webs, electrical networks, etc.
Support for the book "A practical guide to ecological modelling -
using R as a simulation platform"
by Karline Soetaert and Peter M.J. Herman (2009), Springer.
and the book "Solving Differential Equations in R"
by Karline Soetaert, Jeff Cash and Francesca Mazzia (2012), Springer.
Includes demo(flowchart), demo(plotmat), demo(plotweb).
Author: Karline Soetaert <karline.soetaert@nioz.nl>
Maintainer: Karline Soetaert <karline.soetaert@nioz.nl>
Diff between diagram versions 1.6.4 dated 2017-08-16 and 1.6.5 dated 2020-09-30
diagram-1.6.4/diagram/inst/doc/changes.txt.r |only diagram-1.6.4/diagram/man/eNetwork.Rd |only diagram-1.6.5/diagram/DESCRIPTION | 11 diagram-1.6.5/diagram/MD5 | 43 diagram-1.6.5/diagram/NAMESPACE | 1 diagram-1.6.5/diagram/R/circuitplot.r | 2 diagram-1.6.5/diagram/R/curvedarrow.R | 2 diagram-1.6.5/diagram/R/plotmat.R | 13 diagram-1.6.5/diagram/R/plotweb.R | 2 diagram-1.6.5/diagram/build/vignette.rds |binary diagram-1.6.5/diagram/data/Teasel.rda |binary diagram-1.6.5/diagram/data/rigaweb.rda |binary diagram-1.6.5/diagram/data/takapotoweb.rda |binary diagram-1.6.5/diagram/inst/doc/diagram.R | 1373 ++++++++++++------------- diagram-1.6.5/diagram/inst/doc/diagram.pdf |binary diagram-1.6.5/diagram/man/bentarrow.Rd | 12 diagram-1.6.5/diagram/man/curvedarrow.Rd | 12 diagram-1.6.5/diagram/man/electricalnetwork.Rd |only diagram-1.6.5/diagram/man/plotmat.Rd | 820 +++++++------- diagram-1.6.5/diagram/man/segmentarrow.Rd | 12 diagram-1.6.5/diagram/man/selfarrow.Rd | 12 diagram-1.6.5/diagram/man/splitarrow.Rd | 10 diagram-1.6.5/diagram/man/straightarrow.Rd | 12 diagram-1.6.5/diagram/man/treearrow.Rd | 10 24 files changed, 1200 insertions(+), 1147 deletions(-)
Title: Change-in-Estimate Approach to Assess Confounding Effects
Description: Applies the change-in-effect estimate method to assess confounding
effects in medical and epidemiological research (Greenland & Pearce (2016)
<doi:10.1146/annurev-publhealth-031914-122559> ). It starts with a crude model
including only the outcome and exposure variables. At each of the subsequent
steps, one variable which creates the largest change among the remaining variables
is selected. This process is repeated until all variables have been entered into
the model (Wang Z (2007) <doi:10.1177/1536867X0700700203> ). Currently, the 'chest'
package has functions for linear regression, logistic regression, negative
binomial regression, Cox proportional hazards model and conditional logistic
regression.
Author: Zhiqiang Wang [aut, cre]
Maintainer: Zhiqiang Wang <zhiqiang.wang@menzies.edu.au>
Diff between chest versions 0.3.3 dated 2020-07-12 and 0.3.4 dated 2020-09-30
DESCRIPTION | 6 +- MD5 | 38 +++++++------- NEWS.md | 3 + R/chest.R | 4 - R/chest_clogit.R | 95 +++++++++++++++++++++---------------- R/chest_cox.R | 93 +++++++++++++++++++----------------- R/chest_forest.R | 48 ++++++++++-------- R/chest_glm.R | 107 ++++++++++++++++++++++++----------------- R/chest_lm.R | 96 ++++++++++++++++++++----------------- R/chest_nb.R | 99 ++++++++++++++++++++++---------------- R/chest_plot.R | 109 +++++++++++++++++++++++------------------- R/chest_speedglm.R | 110 +++++++++++++++++++++++-------------------- inst/doc/chest-vignette.html | 40 +++++++-------- man/chest.Rd | 1 man/chest_clogit.Rd | 6 +- man/chest_cox.Rd | 1 man/chest_glm.Rd | 6 +- man/chest_lm.Rd | 2 man/chest_plot.Rd | 8 +-- man/chest_speedglm.Rd | 15 ++--- 20 files changed, 494 insertions(+), 393 deletions(-)
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],
Tyson Barrett [ctb],
Ivan Leung [ctb],
Ross Kennedy [ctb],
Lionel Henry [ctb],
Matt Carlson [ctb],
Abdessabour Moutik [ctb]
Maintainer: Mark Fairbanks <mark.t.fairbanks@gmail.com>
Diff between tidytable versions 0.5.5 dated 2020-09-02 and 0.5.6 dated 2020-09-30
DESCRIPTION | 6 - MD5 | 195 +++++++++++++++++----------------- NAMESPACE | 8 + NEWS.md | 27 ++++ R/arrange.R | 25 +++- R/arrange_across.R |only R/bind.R | 9 - R/case.R | 29 ++--- R/case_when.R |only R/complete.R | 2 R/count.R | 2 R/desc.R |only R/distinct.R | 2 R/drop_na.R | 2 R/expand.R | 4 R/fill.R | 19 +-- R/filter.R | 13 -- R/get_dummies.R | 4 R/group_split.R | 2 R/ifelse.R | 2 R/join.R | 10 - R/map.R | 16 +- R/map2.R | 16 +- R/mutate.R | 12 -- R/mutate_across.R | 13 -- R/mutate_variants.R | 33 ++--- R/n.R | 2 R/nest.R | 2 R/pivot_longer.R | 2 R/pivot_wider.R | 2 R/print.R | 38 ++++-- R/pull.R | 2 R/relocate.R | 2 R/rename.R | 2 R/rename_variants.R | 16 ++ R/rename_with.R | 2 R/replace_na.R | 2 R/row_number.R | 2 R/select.R | 2 R/separate.R | 2 R/slice.R | 83 +++++--------- R/summarize.R | 22 +-- R/summarize_across.R | 8 - R/tidytable-package.R | 2 R/tidytable.R | 2 R/top_n.R | 13 -- R/transmute.R | 14 +- R/unite.R | 2 R/unnest.R | 48 ++++++-- R/utils-general.R | 13 -- README.md | 2 man/arrange..Rd | 5 man/arrange_across..Rd |only man/bind_cols..Rd | 4 man/case..Rd | 20 +-- man/case_when..Rd |only man/desc..Rd |only man/dt_verb.Rd | 41 +++---- man/expand..Rd | 2 man/fill..Rd | 13 -- man/filter..Rd | 4 man/get_dummies..Rd | 2 man/knit_print.tidytable.Rd |only man/mutate..Rd | 4 man/mutate_across..Rd | 12 -- man/mutate_if..Rd | 14 +- man/rename_all..Rd | 2 man/slice..Rd | 12 -- man/summarize..Rd | 6 - man/summarize_across..Rd | 8 - man/top_n..Rd | 6 - man/transmute..Rd | 4 man/unnest..Rd | 23 +++- tests/testthat/test-arrange.R | 57 ++++----- tests/testthat/test-arrange_across.R |only tests/testthat/test-bind.R | 39 ------ tests/testthat/test-case.R |only tests/testthat/test-case_when.R | 66 +++-------- tests/testthat/test-count.R | 11 - tests/testthat/test-distinct.R | 12 -- tests/testthat/test-drop_na.R | 11 - tests/testthat/test-fill.R | 19 --- tests/testthat/test-filter.R | 10 - tests/testthat/test-get_dummies.R | 35 ------ tests/testthat/test-group_split.R | 10 - tests/testthat/test-ifelse.R | 16 -- tests/testthat/test-join.R | 25 ---- tests/testthat/test-mutate.R | 11 - tests/testthat/test-mutate_variants.R | 12 -- tests/testthat/test-pivot_longer.R | 14 -- tests/testthat/test-pivot_wider.R | 9 - tests/testthat/test-pull.R | 7 - tests/testthat/test-purrr.R | 35 ------ tests/testthat/test-relocate.R | 8 - tests/testthat/test-rename.R | 20 --- tests/testthat/test-replace_na.R | 9 - tests/testthat/test-select.R | 11 - tests/testthat/test-separate.R | 13 -- tests/testthat/test-slice.R | 43 +------ tests/testthat/test-summarize.R | 11 - tests/testthat/test-top_n.R | 13 -- tests/testthat/test-unite.R | 13 -- tests/testthat/test-unnest.R | 62 ++-------- 103 files changed, 554 insertions(+), 968 deletions(-)
Title: Build MultiClass Pair-Based Classifiers using TSPs or RF
Description: A toolbox to train a single sample classifier that uses in-sample feature relationships. The relationships are represented as feature1 < feature2 (e.g. gene1 < gene2). We provide two options to go with. First is based on 'switchBox' package which uses Top-score pairs algorithm. Second is a novel implementation based on random forest algorithm. For simple problems we recommend to use one-vs-rest using TSP option due to its simplicity and for being easy to interpret. For complex problems RF performs better. Both lines filter the features first then combine the filtered features to make the list of all the possible rules (i.e. rule1: feature1 < feature2, rule2: feature1 < feature3, etc...). Then the list of rules will be filtered and the most important and informative rules will be kept. The informative rules will be assembled in an one-vs-rest model or in an RF model. We provide a detailed description with each function in this package to explain the filtration and training methodology in each line.
Author: Nour-al-dain Marzouka
Maintainer: Nour-al-dain Marzouka <Nour-al-dain.Marzouka@med.lu.se>
Diff between multiclassPairs versions 0.2.0 dated 2020-09-28 and 0.2.1 dated 2020-09-30
DESCRIPTION | 13 +-- MD5 | 16 +-- NAMESPACE | 7 - NEWS.md | 21 ++++- R/functions.R | 168 ++++++++++++++++++++++++++++++++--------- man/filter_genes_TSP.Rd | 9 ++ man/plot_binary_TSP.Rd | 9 ++ man/predict_one_vs_rest_TSP.Rd | 9 ++ man/train_one_vs_rest_TSP.Rd | 9 ++ 9 files changed, 204 insertions(+), 57 deletions(-)
More information about multiclassPairs at CRAN
Permanent link
Title: Utilities for Fundamental Geo-Spatial Data
Description: Read and Parse for Fundamental Geo-Spatial Data (FGD) which downloads XML file
from providing site (<https://fgd.gsi.go.jp/download/menu.php>). The JPGIS format file
provided by FGD so that it can be handled as an R spatial object such as 'sf' and
'raster', 'terra' or 'stars'.
Supports the FGD version 4.1, and accepts fundamental items and digital elevation models.
Author: Shinya Uryu [aut, cre] (<https://orcid.org/0000-0002-0493-6186>)
Maintainer: Shinya Uryu <suika1127@gmail.com>
Diff between fgdr versions 1.0.1 dated 2020-05-06 and 1.1.0 dated 2020-09-30
DESCRIPTION | 20 ++--- MD5 | 28 +++---- NAMESPACE | 2 NEWS.md | 10 ++ R/commons.R | 28 ++++--- R/read_fdg_dem.R | 81 ++++++++++++++-------- R/util.R | 32 +++++++- README.md | 48 +++++-------- inst/extdata/FG-GML-0000-00-00-DEM5A-dummy.xml | 2 inst/extdata/FG-GML-0000-10-dem10b-dummy.xml | 12 +-- man/figures/README-read_fgd_dem_raster_plot-1.png |binary man/read_fgd.Rd | 2 man/read_fgd_dem.Rd | 23 +++--- tests/testthat/test-read_fgd_dem.R | 52 +++++++++++--- tests/testthat/test-util.R | 2 15 files changed, 223 insertions(+), 119 deletions(-)
Title: Visualization Package for CanvasXpress in R
Description: Enables creation of visualizations using the CanvasXpress framework
in R. CanvasXpress is a standalone JavaScript library for reproducible research
with complete tracking of data and end-user modifications stored in a single
PNG image that can be played back. See <https://www.canvasxpress.org> for more
information.
Author: Isaac Neuhaus [aut],
Connie Brett [aut, cre]
Maintainer: Connie Brett <connie@aggregate-genius.com>
Diff between canvasXpress versions 1.27.6-1 dated 2020-04-11 and 1.29.6 dated 2020-09-30
canvasXpress-1.27.6-1/canvasXpress/inst/extdata |only canvasXpress-1.27.6-1/canvasXpress/tests/README-known_issues.md |only canvasXpress-1.29.6/canvasXpress/DESCRIPTION | 19 canvasXpress-1.29.6/canvasXpress/MD5 | 258 --- canvasXpress-1.29.6/canvasXpress/NEWS.md | 7 canvasXpress-1.29.6/canvasXpress/R/canvasXpress.R | 10 canvasXpress-1.29.6/canvasXpress/R/internal_functionality.R | 4 canvasXpress-1.29.6/canvasXpress/README.md | 34 canvasXpress-1.29.6/canvasXpress/build/vignette.rds |binary canvasXpress-1.29.6/canvasXpress/inst/README-known_issues.md |only canvasXpress-1.29.6/canvasXpress/inst/doc/additional_examples.Rmd | 2 canvasXpress-1.29.6/canvasXpress/inst/doc/additional_examples.html | 216 +- canvasXpress-1.29.6/canvasXpress/inst/doc/getting_started.Rmd | 30 canvasXpress-1.29.6/canvasXpress/inst/doc/getting_started.html | 240 +-- canvasXpress-1.29.6/canvasXpress/inst/htmlwidgets/canvasXpress.js | 8 canvasXpress-1.29.6/canvasXpress/inst/htmlwidgets/canvasXpress.yaml | 2 canvasXpress-1.29.6/canvasXpress/inst/htmlwidgets/lib/canvasXpress/canvasXpress.css | 38 canvasXpress-1.29.6/canvasXpress/inst/htmlwidgets/lib/canvasXpress/canvasXpress.min.js | 8 canvasXpress-1.29.6/canvasXpress/inst/shiny-examples/example1/server.R | 4 canvasXpress-1.29.6/canvasXpress/inst/shiny-examples/example2/global.R | 36 canvasXpress-1.29.6/canvasXpress/inst/shiny-examples/example2/server.R | 64 canvasXpress-1.29.6/canvasXpress/inst/shiny-examples/example2/ui.R | 4 canvasXpress-1.29.6/canvasXpress/inst/ui-examples |only canvasXpress-1.29.6/canvasXpress/man/canvasXpress-package.Rd | 2 canvasXpress-1.29.6/canvasXpress/tests/cX-ui-functions.R | 791 +++++++++- canvasXpress-1.29.6/canvasXpress/tests/cx-get-ui-generated-test-setup.R | 18 canvasXpress-1.29.6/canvasXpress/tests/testthat.R | 7 canvasXpress-1.29.6/canvasXpress/tests/testthat/helper-functions.R | 7 canvasXpress-1.29.6/canvasXpress/tests/testthat/test-manual-transform.R | 5 canvasXpress-1.29.6/canvasXpress/tests/testthat/test-other-color-setting.R |only canvasXpress-1.29.6/canvasXpress/tests/testthat/test-other-data-url.R | 3 canvasXpress-1.29.6/canvasXpress/tests/testthat/test-other-decorations.R | 129 + canvasXpress-1.29.6/canvasXpress/tests/testthat/test-other-differentiated-groups.R | 1 canvasXpress-1.29.6/canvasXpress/tests/testthat/test-other-legend-position.R | 2 canvasXpress-1.29.6/canvasXpress/tests/testthat/test-other-segregation-violin.R | 1 canvasXpress-1.29.6/canvasXpress/tests/testthat/test-other-webshot-print.R | 2 canvasXpress-1.29.6/canvasXpress/tests/testthat/test-ui-bar.R | 2 canvasXpress-1.29.6/canvasXpress/tests/testthat/test-ui-barline.R | 7 canvasXpress-1.29.6/canvasXpress/tests/testthat/test-ui-boxplot.R | 4 canvasXpress-1.29.6/canvasXpress/tests/testthat/test-ui-circular.R | 2 canvasXpress-1.29.6/canvasXpress/tests/testthat/test-ui-contour.R | 16 canvasXpress-1.29.6/canvasXpress/tests/testthat/test-ui-density.R | 16 canvasXpress-1.29.6/canvasXpress/tests/testthat/test-ui-dotplot.R | 2 canvasXpress-1.29.6/canvasXpress/tests/testthat/test-ui-facet.R |only canvasXpress-1.29.6/canvasXpress/tests/testthat/test-ui-heatmap.R | 5 canvasXpress-1.29.6/canvasXpress/tests/testthat/test-ui-histogram.R | 6 canvasXpress-1.29.6/canvasXpress/tests/testthat/test-ui-kaplanmeier.R | 18 canvasXpress-1.29.6/canvasXpress/tests/testthat/test-ui-layout.R | 5 canvasXpress-1.29.6/canvasXpress/tests/testthat/test-ui-map.R | 5 canvasXpress-1.29.6/canvasXpress/tests/testthat/test-ui-network.R | 10 canvasXpress-1.29.6/canvasXpress/tests/testthat/test-ui-oncoprint.R | 10 canvasXpress-1.29.6/canvasXpress/tests/testthat/test-ui-radar.R | 2 canvasXpress-1.29.6/canvasXpress/tests/testthat/test-ui-scatter2D.R | 7 canvasXpress-1.29.6/canvasXpress/tests/testthat/test-ui-scatter3D.R | 2 canvasXpress-1.29.6/canvasXpress/tests/testthat/test-ui-splom.R |only canvasXpress-1.29.6/canvasXpress/tests/testthat/test-ui-tcga.R | 36 canvasXpress-1.29.6/canvasXpress/tests/testthat/test-ui-violin.R | 4 canvasXpress-1.29.6/canvasXpress/vignettes/additional_examples.Rmd | 2 canvasXpress-1.29.6/canvasXpress/vignettes/getting_started.Rmd | 30 59 files changed, 1487 insertions(+), 656 deletions(-)