Title: Ordinal Regression Analysis for Continuous Scales
Description: A regression framework for response variables which are continuous
self-rating scales such as the Visual Analog Scale (VAS) used in pain
assessment, or the Linear Analog Self-Assessment (LASA) scales in quality
of life studies. These scales measure subjects' perception of an intangible
quantity, and cannot be handled as ratio variables because of their inherent
non-linearity. We treat them as ordinal variables, measured on a continuous
scale. A function (the g function) connects the scale with an underlying
continuous latent variable. The link function is the inverse of the CDF of the
assumed underlying distribution of the latent variable. A variety of
link functions are currently implemented. Such models are described in Manuguerra et al (2020) <doi:10.18637/jss.v096.i08>.
Author: Maurizio Manuguerra [aut, cre],
Gillian Heller [aut]
Maintainer: Maurizio Manuguerra <maurizio.manuguerra@mq.edu.au>
Diff between ordinalCont versions 2.0.1 dated 2019-02-13 and 2.0.2 dated 2020-12-02
DESCRIPTION | 10 +++++----- MD5 | 31 ++++++++++++++++--------------- R/ocm.R | 3 ++- R/ocm.methods.R | 12 ++++++------ R/ordinalCont.R | 8 +++++--- inst |only man/ANZ0001.Rd | 6 ++++-- man/ANZ0001.sub.Rd | 6 ++++-- man/anova.ocm.Rd | 2 +- man/neck_pain.Rd | 6 ++++-- man/ocm.Rd | 22 +++++++++++++++------- man/ordinalCont-package.Rd | 4 +++- man/plot.ocm.Rd | 19 +++++++++++++------ man/predict.ocm.Rd | 14 ++++++++++---- man/print.anova.ocm.Rd | 11 +++++++---- man/print.ocm.Rd | 3 +-- man/summary.ocm.Rd | 2 +- 17 files changed, 97 insertions(+), 62 deletions(-)
Title: Spatial Analysis and Modelling Utilities
Description: Utilities to support spatial data manipulation, query, sampling
and modelling. Functions include models for species population density, download
utilities for climate and global deforestation spatial products, spatial
smoothing, multivariate separability, point process model for creating pseudo-
absences and sub-sampling, polygon and point-distance landscape metrics,
auto-logistic model, sampling models, cluster optimization, statistical
exploratory tools and raster-based metrics.
Author: Jeffrey S. Evans [aut, cre],
Melanie A. Murphy [ctb],
Karthik Ram [ctb]
Maintainer: Jeffrey S. Evans <jeffrey_evans@tnc.org>
Diff between spatialEco versions 1.3-2 dated 2020-06-04 and 1.3-3 dated 2020-12-02
DESCRIPTION | 12 +++--- MD5 | 81 ++++++++++++++++++++++++++----------------- NAMESPACE | 9 ++++ R/bearing.distance.R | 5 ++ R/built.index.R |only R/chae.R |only R/collinear.R |only R/cross.tab.R | 3 - R/crossCorrelation.R | 39 -------------------- R/dahi.R |only R/date_seq.R |only R/daymet.tiles.R | 69 +++++------------------------------- R/download.prism.R | 4 +- R/geo.buffer.R | 2 - R/hli.R | 2 - R/impute.loess.R |only R/max_extent.R |only R/oli.aws.R | 4 +- R/parea.sample.R | 36 ++++++++++--------- R/partial.cor.R | 2 - R/quadrats.R |only R/raster.change.R | 2 - R/rotate.polygon.R |only R/separability.R | 16 ++++---- R/smooth.time.series.R | 43 ++++++++++++++-------- R/spectral.separability.R |only R/swvi.R | 1 inst/CITATION | 2 - inst/NEWS | 22 +++++++++++ man/bearing.distance.Rd | 6 ++- man/built.index.Rd |only man/chae.Rd |only man/collinear.Rd | 34 +++++++++++++++++- man/cross.tab.Rd | 3 - man/crossCorrelation.Rd | 39 -------------------- man/dahi.Rd |only man/date.seq.Rd |only man/daymet.tiles.Rd | 39 +------------------- man/download.prism.Rd | 4 +- man/geo.buffer.Rd | 2 - man/impute.loess.Rd |only man/max_extent.Rd |only man/oli.asw.Rd | 4 +- man/parea.sample.Rd | 7 ++- man/partial.cor.Rd | 2 - man/quadrats.Rd |only man/raster.change.Rd | 2 - man/rotate.polygon.Rd |only man/separability.Rd | 4 +- man/smooth.time.series.Rd | 23 +++++++++--- man/spectral.separability.Rd |only 51 files changed, 242 insertions(+), 281 deletions(-)
Title: 'Rcpp' Bindings to Parser for Tom's Obvious Markup Language
Description: The configuration format defined by 'TOML' (which expands to
"Tom's Obvious Markup Language") specifies an excellent format
(described at <https://toml.io/en/>) suitable for both human editing
as well as the common uses of a machine-readable format. This package
uses 'Rcpp' to connect the 'cpptoml' parser written by Chase Geigle
(in C++11) to R.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppTOML versions 0.1.6 dated 2019-06-25 and 0.1.7 dated 2020-12-02
ChangeLog | 43 ++++++++++++++++++++++++++++++++++++++++--- DESCRIPTION | 19 ++++++++++--------- MD5 | 16 ++++++++-------- README.md | 26 +++++++++++++++----------- cleanup | 2 +- inst/NEWS.Rd | 22 +++++++++++++++------- inst/include/cpptoml.h | 1 + man/RcppTOML-package.Rd | 4 ++-- man/parseTOML.Rd | 2 +- 9 files changed, 93 insertions(+), 42 deletions(-)
Title: Testing Pleiotropy in Multiparental Populations
Description: We implement an
adaptation of Jiang & Zeng's (1995) <https://www.genetics.org/content/140/3/1111> likelihood ratio test for testing
the null hypothesis of pleiotropy against the alternative hypothesis,
two separate quantitative trait loci. The test differs from that in Jiang & Zeng (1995) <https://www.genetics.org/content/140/3/1111>
and that in Tian et al. (2016) <doi:10.1534/genetics.115.183624> in
that our test accommodates multiparental populations.
Author: Frederick J Boehm [aut, cre] (<https://orcid.org/0000-0002-1644-5931>)
Maintainer: Frederick J Boehm <frederick.boehm@gmail.com>
Diff between qtl2pleio versions 1.4.1 dated 2020-10-29 and 1.4.3 dated 2020-12-02
qtl2pleio-1.4.1/qtl2pleio/R/catch-routine-registration.R |only qtl2pleio-1.4.1/qtl2pleio/src/test-example.cpp |only qtl2pleio-1.4.1/qtl2pleio/src/test-runner.cpp |only qtl2pleio-1.4.1/qtl2pleio/tests/testthat/test-cpp.R |only qtl2pleio-1.4.3/qtl2pleio/DESCRIPTION | 8 qtl2pleio-1.4.3/qtl2pleio/MD5 | 20 - qtl2pleio-1.4.3/qtl2pleio/NAMESPACE | 1 qtl2pleio-1.4.3/qtl2pleio/NEWS.md | 26 ++ qtl2pleio-1.4.3/qtl2pleio/R/convert_to_scan1_output.R |only qtl2pleio-1.4.3/qtl2pleio/R/qtl2pleio-package.r | 2 qtl2pleio-1.4.3/qtl2pleio/inst/doc/bootstrap-cluster.html | 155 +++++++++----- qtl2pleio-1.4.3/qtl2pleio/man/convert_to_scan1_output.Rd |only qtl2pleio-1.4.3/qtl2pleio/src/RcppExports.cpp | 3 qtl2pleio-1.4.3/qtl2pleio/src/rcpp_ols.cpp | 8 14 files changed, 148 insertions(+), 75 deletions(-)
Title: Analysis and Visualization Tools for Genetic Barcode Data
Description: Provides the necessary functions to identify and extract a selection of already available barcode constructs (Cornils, K. et al. (2014) <doi:10.1093/nar/gku081>) and freely choosable barcode designs from next generation sequence (NGS) data. Furthermore, it offers the possibility to account for sequence errors, the calculation of barcode similarities and provides a variety of visualisation tools (Thielecke, L. et al. (2017) <doi:10.1038/srep43249>).
Author: Lars Thielecke <lars.thielecke@tu-dresden.de>
Maintainer: Lars Thielecke <lars.thielecke@tu-dresden.de>
Diff between genBaRcode versions 1.2.3 dated 2020-05-08 and 1.2.4 dated 2020-12-02
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/plot_functions.R | 3 ++- R/raw_data_processing.R | 11 +++++++---- build/vignette.rds |binary inst/doc/genBaRcode_GUI_Vignette.pdf |binary inst/doc/genBaRcode_Vignette.pdf |binary 7 files changed, 19 insertions(+), 15 deletions(-)
Title: Formal Concept Analysis
Description: Provides tools to perform fuzzy formal concept
analysis, presented in Wille (1982) <doi:10.1007/978-3-642-01815-2_23>
and in Ganter and Obiedkov (2016) <doi:10.1007/978-3-662-49291-8>. It
provides functions to load and save a formal context, extract its
concept lattice and implications. In addition, one can use the
implications to compute semantic closures of fuzzy sets and, thus,
build recommendation systems.
Author: Domingo Lopez Rodriguez [aut, cre]
(<https://orcid.org/0000-0002-0172-1585>),
Angel Mora [aut],
Jesus Dominguez [aut],
Ana Villalon [aut],
Ian Johnson [ctb]
Maintainer: Domingo Lopez Rodriguez <dominlopez@uma.es>
Diff between fcaR versions 1.0.6 dated 2020-11-18 and 1.0.7 dated 2020-12-02
DESCRIPTION | 14 +- MD5 | 87 +++++++------- NAMESPACE | 4 NEWS.md | 10 + R/concept_lattice.R | 154 ++------------------------ R/context_to_latex.R |only R/equivalences_registry.R | 1 R/fcaR-package.R | 3 R/formal_context.R | 184 +++++++++---------------------- R/implication_set.R | 32 ----- R/imps_to_arules.R |only R/lattice_plot.R |only R/plot_context.R |only R/reorder_layout.R |only R/to_fraction.R | 61 ++++++++++ R/utils-pipe.R |only README.md | 34 +++-- inst/doc/arules.R | 5 inst/doc/arules.Rmd | 5 inst/doc/arules.html | 59 ++-------- inst/doc/concept_lattice.R | 3 inst/doc/concept_lattice.Rmd | 3 inst/doc/concept_lattice.html | 149 +++++++++++-------------- inst/doc/extending_equivalence.R | 3 inst/doc/extending_equivalence.Rmd | 3 inst/doc/extending_equivalence.html | 18 +-- inst/doc/implications.R | 3 inst/doc/implications.Rmd | 3 inst/doc/implications.html | 4 man/ConceptLattice.Rd | 3 man/FormalContext.Rd | 3 man/fcaR.Rd | 3 man/pipe.Rd |only src/aux_functions.cpp | 4 src/implication_tree.cpp | 20 +++ src/implication_tree.h | 2 src/nextclosure.cpp | 28 +++- src/set_operations_galois.cpp | 38 ++++++ src/set_operations_galois.h | 4 src/vector_operations.cpp | 10 + tests/testthat/Rplots.pdf |binary tests/testthat/test-concept_lattice.R | 1 tests/testthat/test-formal_context.R | 23 ++- tests/testthat/test-implication_set.R | 200 +++++++++++++++++++++++++++++----- vignettes/arules.Rmd | 5 vignettes/concept_lattice.Rmd | 3 vignettes/extending_equivalence.Rmd | 3 vignettes/implications.Rmd | 3 48 files changed, 625 insertions(+), 570 deletions(-)
Title: Bayesian Test Reliability Estimation
Description: When samples contain missing data, are small, or are suspected of bias,
estimation of scale reliability may not be trustworthy. A recommended solution
for this common problem has been Bayesian model estimation. Bayesian methods
rely on user specified information from historical data or researcher intuition
to more accurately estimate the parameters. This package provides a user friendly
interface for estimating test reliability. Here, reliability is modeled as a beta
distributed random variable with shape parameters alpha=true score variance and
beta=error variance (Tanzer & Harlow, 2020) <doi:10.1080/00273171.2020.1854082>.
Author: Joshua Ray Tanzer
Maintainer: Joshua Ray Tanzer <jtanzer@lifespan.org>
Diff between brxx versions 0.1.0 dated 2020-11-11 and 0.1.1 dated 2020-12-02
DESCRIPTION | 8 ++++---- MD5 | 32 ++++++++++++++++---------------- NEWS.md | 3 +++ R/bcor.R | 1 + R/bcov.R | 2 ++ R/bomega.R | 11 ++++++----- R/bomega_general.R | 1 + R/brxx_Cor.R | 7 +++++-- R/brxx_Cor_general.R | 7 ++++--- R/brxx_ICC.R | 13 ++++++++----- R/brxx_ICC_general.R | 13 ++++++++----- R/brxx_general.R | 13 ++++++++----- R/standardize.R | 7 ++++--- man/bomega.Rd | 2 +- man/brxx_ICC.Rd | 6 ++++-- man/brxx_ICC_general.Rd | 6 ++++-- man/brxx_general.Rd | 6 ++++-- 17 files changed, 83 insertions(+), 55 deletions(-)
Title: Generalized Price and Quantity Indexes
Description: A small package for calculating lots of different price indexes, and by extension quantity indexes. Provides tools to build and work with any type of generalized bilateral index (of which most price indexes are), along with a few important indexes that don't belong to the generalized family. Implements and extends many of the methods in Balk (2008, ISBN:978-1-107-40496-0) and ILO, IMF, OECD, Eurostat, UN, and World Bank (2004, ISBN:92-2-113699-X) for bilateral price indexes.
Author: Steve Martin [aut, cre, cph]
Maintainer: Steve Martin <stevemartin041@gmail.com>
Diff between gpindex versions 0.2.1 dated 2020-11-03 and 0.2.3 dated 2020-12-02
gpindex-0.2.1/gpindex/R/means.R |only gpindex-0.2.1/gpindex/R/price_indexes.R |only gpindex-0.2.1/gpindex/R/quantity_index.R |only gpindex-0.2.1/gpindex/R/weights.R |only gpindex-0.2.3/gpindex/DESCRIPTION | 6 gpindex-0.2.3/gpindex/MD5 | 45 +- gpindex-0.2.3/gpindex/NAMESPACE | 3 gpindex-0.2.3/gpindex/NEWS | 8 gpindex-0.2.3/gpindex/R/0_helper_functions.R |only gpindex-0.2.3/gpindex/R/1_means.R |only gpindex-0.2.3/gpindex/R/2_weights.R |only gpindex-0.2.3/gpindex/R/3_price_indexes.R |only gpindex-0.2.3/gpindex/R/4_quantity_index.R |only gpindex-0.2.3/gpindex/README.md | 12 gpindex-0.2.3/gpindex/inst/doc/gpindex.R | 2 gpindex-0.2.3/gpindex/inst/doc/gpindex.Rnw | 2 gpindex-0.2.3/gpindex/inst/doc/gpindex.pdf |binary gpindex-0.2.3/gpindex/man/generalized_mean.Rd | 89 ++-- gpindex-0.2.3/gpindex/man/lehmer_mean.Rd |only gpindex-0.2.3/gpindex/man/logarithmic_means.Rd | 33 + gpindex-0.2.3/gpindex/man/nested_contributions.Rd |only gpindex-0.2.3/gpindex/man/price_indexes.Rd | 23 - gpindex-0.2.3/gpindex/man/transform_weights.Rd | 9 gpindex-0.2.3/gpindex/tests/Examples/gpindex-Ex.Rout.save | 272 ++++++++++---- gpindex-0.2.3/gpindex/tests/test_means.R | 236 ++++++------ gpindex-0.2.3/gpindex/tests/test_price_indexes.R | 2 gpindex-0.2.3/gpindex/tests/test_weights.R | 119 ++---- gpindex-0.2.3/gpindex/tests/vignette_gpindex.R |only gpindex-0.2.3/gpindex/tests/vignette_gpindex.Rout.save |only gpindex-0.2.3/gpindex/vignettes/gpindex.Rnw | 2 30 files changed, 524 insertions(+), 339 deletions(-)
Title: 'ggplot2' Extension for Seasonal and Trading Day Adjustment with
'RJDemetra'
Description: Provides 'ggplot2' functions to return the results of seasonal and trading day adjustment
made by 'RJDemetra'. 'RJDemetra' is an 'R' interface around 'JDemetra+' (<https://github.com/jdemetra/jdemetra-app>),
the seasonal adjustment software officially recommended to the members of the European Statistical System and
the European System of Central Banks.
Author: Alain Quartier-la-Tente [aut, cre]
(<https://orcid.org/0000-0001-7890-3857>)
Maintainer: Alain Quartier-la-Tente <alain.quartier@yahoo.fr>
Diff between ggdemetra versions 0.2.1 dated 2019-09-12 and 0.2.2 dated 2020-12-02
DESCRIPTION | 12 - MD5 | 46 +++-- NAMESPACE | 3 NEWS.md | 8 + R/geom_outliers.R | 1 R/ipi_c_eu.R | 34 ++-- R/ts2df.R |only README.md | 30 ++- build/vignette.rds |binary data/ipi_c_eu.rda |binary data/ipi_c_eu_df.rda |binary inst/doc/ggdemetra.R | 30 ++- inst/doc/ggdemetra.Rmd | 19 +- inst/doc/ggdemetra.html | 243 +++++++++++++++++++------------ man/figures/README-unnamed-chunk-3-1.png |binary man/figures/README-unnamed-chunk-4-1.png |binary man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/geom_arima.Rd | 23 ++ man/geom_diagnostics.Rd | 25 ++- man/geom_outlier.Rd | 32 ++-- man/geom_sa.Rd | 36 +++- man/ipi_c_eu.Rd | 12 - man/ts2df.Rd |only vignettes/ggdemetra.Rmd | 19 +- 25 files changed, 370 insertions(+), 203 deletions(-)
Title: 'R Markdown' Format for Scientific and Technical Writing
Description: Scientific and technical article format for the web. 'Distill' articles
feature attractive, reader-friendly typography, flexible layout options
for visualizations, and full support for footnotes and citations.
Author: JJ Allaire [aut, cre] (<https://orcid.org/0000-0003-0174-9868>),
Rich Iannone [aut],
Alison Presmanes Hill [aut] (<https://orcid.org/0000-0002-8082-1890>),
Yihui Xie [aut] (<https://orcid.org/0000-0003-0645-5666>),
RStudio, Inc. [cph],
Google LLC [ctb, cph] (https://distill.pub/guide/),
Nick Williams [ctb, cph] (https://wicky.nillia.ms/headroom.js/),
Denis Demchenko [ctb, cph] (https://github.com/lancedikson/bowser),
The Polymer Authors [ctb, cph]
(https://www.webcomponents.org/polyfills/),
Gábor Csárdi [ctb, cph] (whoami),
JooYoung Seo [ctb] (<https://orcid.org/0000-0002-4064-6012>)
Maintainer: JJ Allaire <jj@rstudio.com>
Diff between distill versions 1.0 dated 2020-10-22 and 1.1 dated 2020-12-02
distill-1.0/distill/inst/rmarkdown/templates/distill_article/resources/a11y.theme |only distill-1.0/distill/tests/testthat/utils.R |only distill-1.1/distill/DESCRIPTION | 12 +-- distill-1.1/distill/MD5 | 39 +++++----- distill-1.1/distill/NEWS.md | 9 ++ distill-1.1/distill/R/collections.R | 2 distill-1.1/distill/R/distill_article.R | 2 distill-1.1/distill/R/import.R | 12 ++- distill-1.1/distill/R/theme.R | 18 ++++ distill-1.1/distill/R/utils.R | 11 ++ distill-1.1/distill/inst/rmarkdown/templates/distill_article/resources/arrow.theme |only distill-1.1/distill/inst/rmarkdown/templates/distill_article/resources/base-style.css | 3 distill-1.1/distill/inst/rmarkdown/templates/distill_article/resources/distill.html | 2 distill-1.1/distill/inst/rmarkdown/templates/distill_article/resources/navbar.html | 1 distill-1.1/distill/inst/rmarkdown/templates/distill_article/resources/search.html | 29 ++----- distill-1.1/distill/man/create_theme.Rd | 33 ++++++++ distill-1.1/distill/man/rmd-fragments |only distill-1.1/distill/tests/testthat.R | 3 distill-1.1/distill/tests/testthat/_snaps |only distill-1.1/distill/tests/testthat/setup.R |only distill-1.1/distill/tests/testthat/test-article.R | 4 - distill-1.1/distill/tests/testthat/test-blog.R | 12 --- distill-1.1/distill/tests/testthat/test-theme.R |only distill-1.1/distill/tests/testthat/test-website.R | 4 - 24 files changed, 123 insertions(+), 73 deletions(-)
Title: Log-Concave Density Estimation in Arbitrary Dimensions
Description: Software for computing a log-concave (maximum likelihood) estimator for i.i.d. data in any number of dimensions. For a detailed description of the method see Cule, Samworth and Stewart (2010, Journal of Royal Statistical Society Series B, <doi:10.1111/j.1467-9868.2010.00753.x>).
Author: Madeleine Cule, Robert Gramacy, Richard Samworth, Yining Chen
Maintainer: Yining Chen <Y.Chen101@lse.ac.uk>
Diff between LogConcDEAD versions 1.6-3 dated 2019-07-12 and 1.6-4 dated 2020-12-02
DESCRIPTION | 12 ++-- MD5 | 30 ++++++------ NAMESPACE | 3 - NEWS | 5 +- R/interactive2D.R | 110 ++++++++++++++++++++++----------------------- R/plot.LogConcDEAD.R | 2 build/vignette.rds |binary inst/CITATION | 4 - inst/doc/LogConcDEAD.pdf |binary man/LogConcDEAD-package.Rd | 4 - man/cov.LogConcDEAD.Rd | 2 man/dslcd.Rd | 2 man/hatA.Rd | 2 man/interactive2D.Rd | 4 - man/mlelcd.Rd | 16 ++++-- man/rslcd.Rd | 2 16 files changed, 104 insertions(+), 94 deletions(-)
Title: Directory of Open Access Journals Client
Description: Client for the Directory of Open Access Journals ('DOAJ')
(<https://doaj.org/>). API documentation at
<https://doaj.org/api/v1/docs>. Methods included for working with
all 'DOAJ' API routes: fetch article information by identifier,
search for articles, fetch journal information by identifier,
and search for journals.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>),
rOpenSci [fnd] (https://ropensci.org/)
Maintainer: Scott Chamberlain <myrmecocystus+r@gmail.com>
Diff between jaod versions 0.2.0 dated 2019-09-04 and 0.3.0 dated 2020-12-02
jaod-0.2.0/jaod/README.md |only jaod-0.2.0/jaod/build |only jaod-0.2.0/jaod/inst |only jaod-0.2.0/jaod/vignettes |only jaod-0.3.0/jaod/DESCRIPTION | 25 jaod-0.3.0/jaod/LICENSE | 4 jaod-0.3.0/jaod/MD5 | 52 jaod-0.3.0/jaod/NEWS.md | 9 jaod-0.3.0/jaod/R/jaod-package.R | 6 jaod-0.3.0/jaod/R/jaod_article_search.R | 3 jaod-0.3.0/jaod/R/jaod_journal_search.R | 4 jaod-0.3.0/jaod/R/zzz.R | 2 jaod-0.3.0/jaod/man/jaod-package.Rd | 6 jaod-0.3.0/jaod/man/jaod_article_search.Rd | 2 jaod-0.3.0/jaod/man/jaod_journal_search.Rd | 6 jaod-0.3.0/jaod/tests/fixtures/jaod_article.yml | 52 jaod-0.3.0/jaod/tests/fixtures/jaod_article_many_inputs.yml | 137 jaod-0.3.0/jaod/tests/fixtures/jaod_article_search.yml | 692 +- jaod-0.3.0/jaod/tests/fixtures/jaod_article_search_params.yml | 2640 +++++----- jaod-0.3.0/jaod/tests/fixtures/jaod_journal.yml | 81 jaod-0.3.0/jaod/tests/fixtures/jaod_journal_many_inputs.yml | 165 jaod-0.3.0/jaod/tests/fixtures/jaod_journal_search.yml | 532 -- jaod-0.3.0/jaod/tests/fixtures/jaod_journal_search_params.yml | 1742 +++--- jaod-0.3.0/jaod/tests/testthat/helper-jaod.R | 2 jaod-0.3.0/jaod/tests/testthat/test-jaod_article.R | 28 jaod-0.3.0/jaod/tests/testthat/test-jaod_article_search.R | 33 jaod-0.3.0/jaod/tests/testthat/test-jaod_journal.R | 28 jaod-0.3.0/jaod/tests/testthat/test-jaod_journal_search.R | 38 28 files changed, 3119 insertions(+), 3170 deletions(-)
Title: Multiple Fill and Colour Scales in 'ggplot2'
Description: Use multiple fill and colour scales in 'ggplot2'.
Author: Elio Campitelli [cre, aut] (<https://orcid.org/0000-0002-7742-9230>)
Maintainer: Elio Campitelli <elio.campitelli@cima.fcen.uba.ar>
Diff between ggnewscale versions 0.4.3 dated 2020-08-27 and 0.4.4 dated 2020-12-02
DESCRIPTION | 8 ++--- MD5 | 14 +++++---- NEWS.md | 6 ++++ R/new-scale.R | 34 +++++++++++++++++------ README.md | 11 +++++-- tests/figs/deps.txt | 2 - tests/figs/tests/many-layers.svg |only tests/testthat/Rplots.pdf |only tests/testthat/test-newscale.R | 56 ++++++++++++++++++++++++++++++++++++++- 9 files changed, 107 insertions(+), 24 deletions(-)
Title: Generalized Fiducial Inference for Normal Linear Mixed Models
Description: Simulation of the generalized fiducial distribution for normal linear mixed models with interval data. Fiducial inference is somehow similar to Bayesian inference, in the sense that it is based on a distribution that represents the uncertainty about the parameters, like the posterior distribution in Bayesian statistics. It does not require a prior distribution, and it yields results close to frequentist results. Reference: Cisewski and Hannig (2012) <doi:10.1214/12-AOS1030>.
Author: Stéphane Laurent [aut, cre],
Jessi Cisewski [aut, ctb] (author of the original Matlab code,
<https://orcid.org/0000-0002-9656-2272>)
Maintainer: Stéphane Laurent <laurent_step@outlook.fr>
Diff between gfilmm versions 2.0.0 dated 2020-12-01 and 2.0.1 dated 2020-12-02
DESCRIPTION | 6 ++--- MD5 | 12 +++++------ NAMESPACE | 1 NEWS.md | 5 ++++ R/gfilmm.R | 1 inst/doc/the-gfilmm-package.html | 42 +++++++++++++++++++-------------------- src/gfilmm.cpp | 2 - 7 files changed, 38 insertions(+), 31 deletions(-)
Title: Estimation Methods for Causal Inference Based on Inverse
Probability Weighting
Description: Various estimators of causal effects based on inverse probability weighting, doubly robust estimation, and double machine learning. Specifically, the package includes methods for estimating average treatment effects, direct and indirect effects in causal mediation analysis, and dynamic treatment effects. The models refer to studies of Froelich (2007) <doi:10.1016/j.jeconom.2006.06.004>, Huber (2012) <doi:10.3102/1076998611411917>, Huber (2014) <doi:10.1080/07474938.2013.806197>, Huber (2014) <doi:10.1002/jae.2341>, Froelich and Huber (2017) <doi:10.1111/rssb.12232>, Hsu, Huber, Lee, and Lettry (2020) <doi:10.1002/jae.2765>, and others.
Author: Hugo Bodory [aut, cre] (<https://orcid.org/0000-0002-3645-1204>),
Martin Huber [aut] (<https://orcid.org/0000-0002-8590-9402>)
Maintainer: Hugo Bodory <hugo.bodory@unisg.ch>
Diff between causalweight versions 0.2.1 dated 2020-06-15 and 1.0.0 dated 2020-12-02
DESCRIPTION | 33 ++++++++++++++++++++++----------- MD5 | 33 +++++++++++++++++++-------------- NAMESPACE | 3 ++- R/functions.R | 34 ++++++++++++++++++++++++++++++++++ R/games.R |only R/medDML.R | 2 +- R/medweightcont.R | 2 +- R/swissexper.R | 2 -- R/treatDML.R | 2 +- R/treatselDML.R |only R/treatweight.R | 2 +- data/games.RData |only inst/doc/bodory-huber.pdf |binary man/games.Rd |only man/medDML.Rd | 2 +- man/medweightcont.Rd | 2 +- man/swissexper.Rd | 1 - man/treatDML.Rd | 2 +- man/treatselDML.Rd |only man/treatweight.Rd | 2 +- 20 files changed, 85 insertions(+), 37 deletions(-)
Title: Auto-Adaptive Parentage Inference Software Tolerant to Missing
Parents
Description: Parentage assignment package.
Parentage assignment is performed based on observed average Mendelian transmission probability distributions.
The main function of this package is the function APIS(), which is the parentage assignment function.
Author: Ronan Griot, François Allal, Romain Morvezen, Sophie Brard-Fudulea, Pierrick Haffray, Florence Phocas and Marc Vandeputte
Maintainer: Ronan Griot <ronan.griot@gmail.com>
Diff between APIS versions 1.0.0 dated 2019-12-12 and 1.0.1 dated 2020-12-02
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/APIS_functions.R | 5 ++++- inst/doc/APIS_vignette.html | 30 ++++++++++++++++-------------- 4 files changed, 26 insertions(+), 21 deletions(-)
Title: Rasch Model Parameters by Pairwise Algorithm
Description: Performs the explicit calculation
-- not estimation! -- of the Rasch item parameters for dichotomous and
polytomous item responses, using a pairwise comparison approach. Person
parameters (WLE) are calculated according to Warm's weighted likelihood
approach.
Author: Joerg-Henrik Heine <jhheine@googlemail.com>
Maintainer: Joerg-Henrik Heine <jhheine@googlemail.com>
Diff between pairwise versions 0.4.5-1 dated 2020-06-05 and 0.5.0-1 dated 2020-12-02
DESCRIPTION | 8 +-- MD5 | 40 +++++++++-------- NAMESPACE | 2 NEWS | 8 +++ R/i.dataprep1.R | 40 +++++++++++++++++ R/pair.R | 76 +++++++++------------------------- R/residuals.pers.R |only R/summary.pair.R | 46 ++++++++++---------- build/vignette.rds |binary data/DEU_PISA2012.RData |binary data/Neoffi5.RData |binary data/bfiN.RData |binary data/bfiN_miss.RData |binary data/bfi_cov.RData |binary data/cog.RData |binary data/cogBOOKLET.RData |binary data/kft5.RData |binary data/sim200x3.RData |binary inst/doc/DEU_PISA2012_description.R | 1 inst/doc/DEU_PISA2012_description.pdf |binary man/pair.Rd | 7 +-- man/residuals.pers.Rd |only 22 files changed, 123 insertions(+), 105 deletions(-)
Title: Prototype of Multiple Latent Dirichlet Allocation Runs
Description: Determine a Prototype from a number of runs of Latent Dirichlet Allocation (LDA) measuring its similarities with S-CLOP: A procedure to select the LDA run with highest mean pairwise similarity, which is measured by S-CLOP (Similarity of multiple sets by Clustering with Local Pruning), to all other runs. LDA runs are specified by its assignments leading to estimators for distribution parameters. Repeated runs lead to different results, which we encounter by choosing the most representative LDA run as prototype.
Author: Jonas Rieger [aut, cre] (<https://orcid.org/0000-0002-0007-4478>)
Maintainer: Jonas Rieger <jonas.rieger@tu-dortmund.de>
Diff between ldaPrototype versions 0.2.0 dated 2020-07-16 and 0.3.0 dated 2020-12-02
DESCRIPTION | 8 - MD5 | 91 +++++++++-------- NAMESPACE | 4 R/LDA.R | 23 ++++ R/LDABatch.R | 18 +-- R/LDAPrototype.R | 3 R/LDARep.R | 12 ++ R/SCLOP.R | 24 ++-- R/as.LDABatch.R | 1 R/as.LDARep.R | 37 ++++--- R/cosineTopics.R |only R/data.R | 4 R/dendTopics.R | 41 +++++++ R/getJob.R | 8 + R/getPrototype.R | 64 ++++++------ R/getSCLOP.R | 13 ++ R/jaccardTopics.R | 48 +++++++-- R/jsTopics.R |only R/ldaPrototype-package.R | 19 ++- R/mergeBatchTopics.R | 7 + R/mergeRepTopics.R | 6 + R/pruneSCLOP.R | 2 R/rboTopics.R |only README.md | 25 ++++ man/LDA.Rd | 190 ++++++++++++++++++------------------ man/LDABatch.Rd | 3 man/LDAPrototype.Rd | 12 +- man/LDARep.Rd | 3 man/SCLOP.Rd | 182 +++++++++++++++++----------------- man/cosineTopics.Rd |only man/dendTopics.Rd | 10 + man/getJob.Rd | 140 +++++++++++++------------- man/getPrototype.Rd | 21 ++- man/getSCLOP.Rd | 3 man/getSimilarity.Rd | 5 man/jaccardTopics.Rd | 20 +++ man/jsTopics.Rd |only man/ldaPrototype-package.Rd | 21 ++- man/mergeBatchTopics.Rd | 122 +++++++++++------------ man/mergeRepTopics.Rd | 114 ++++++++++----------- man/pruneSCLOP.Rd | 114 ++++++++++----------- man/rboTopics.Rd |only man/reuters.Rd | 4 tests/testthat/test_LDABatch.R | 22 ++-- tests/testthat/test_LDARep.R | 11 +- tests/testthat/test_Prototype.R | 11 +- tests/testthat/test_cosineTopics.R |only tests/testthat/test_jaccardTopics.R | 40 +++++-- tests/testthat/test_jsTopics.R |only tests/testthat/test_mergeTopics.R | 4 tests/testthat/test_rboTopics.R |only 51 files changed, 889 insertions(+), 621 deletions(-)
Title: Mock the Unix Make Utility
Description: Use R as a minimal build system. This might come in
handy if you are developing R packages and can not use a proper build
system. Stay away if you can (use a proper build system).
Author: Andreas Dominik Cullmann [aut, cre]
Maintainer: Andreas Dominik Cullmann <fvafrcu@mailbox.org>
Diff between fakemake versions 1.8.1 dated 2020-11-02 and 1.9.0 dated 2020-12-02
fakemake-1.8.1/fakemake/inst/doc/An_Introduction_to_fakemake.Rmd |only fakemake-1.8.1/fakemake/vignettes/An_Introduction_to_fakemake.Rmd |only fakemake-1.9.0/fakemake/DESCRIPTION | 12 fakemake-1.9.0/fakemake/MD5 | 20 fakemake-1.9.0/fakemake/NEWS.md | 4 fakemake-1.9.0/fakemake/build/vignette.rds |binary fakemake-1.9.0/fakemake/inst/doc/An_Introduction_to_fakemake.R | 25 fakemake-1.9.0/fakemake/inst/doc/An_Introduction_to_fakemake.Rasciidoc |only fakemake-1.9.0/fakemake/inst/doc/An_Introduction_to_fakemake.html | 1888 ++++++---- fakemake-1.9.0/fakemake/inst/doc/Building_Packages.Rmd | 6 fakemake-1.9.0/fakemake/inst/doc/Building_Packages.html | 194 - fakemake-1.9.0/fakemake/vignettes/An_Introduction_to_fakemake.Rasciidoc |only fakemake-1.9.0/fakemake/vignettes/Building_Packages.Rmd | 6 13 files changed, 1394 insertions(+), 761 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-08-14 1.0.2
2020-03-12 1.0.1.1
2020-03-09 1.0.0.1
2019-12-18 0.1.5.0
Title: Create, Build and Maintain Packages
Description: Helper functions for package creation, building and
maintenance. Designed to work with a build system such as 'GNU make' or
package 'fakemake' to help you to conditionally work through the stages of
package development (such as spell checking, linting, testing, before
building and checking a package).
Author: Andreas Dominik Cullmann [aut, cre]
Maintainer: Andreas Dominik Cullmann <fvafrcu@mailbox.org>
Diff between packager versions 1.7.0 dated 2020-11-17 and 1.8.0 dated 2020-12-02
packager-1.7.0/packager/inst/doc/An_Introduction_to_packager.Rmd |only packager-1.7.0/packager/vignettes/An_Introduction_to_packager.Rmd |only packager-1.8.0/packager/DESCRIPTION | 16 packager-1.8.0/packager/MD5 | 29 packager-1.8.0/packager/NEWS.md | 16 packager-1.8.0/packager/R/cran_comments.R | 160 packager-1.8.0/packager/R/rhub.R |only packager-1.8.0/packager/R/throw.R | 1 packager-1.8.0/packager/R/tools.R | 5 packager-1.8.0/packager/build/vignette.rds |binary packager-1.8.0/packager/inst/doc/An_Introduction_to_packager.R | 40 packager-1.8.0/packager/inst/doc/An_Introduction_to_packager.Rasciidoc |only packager-1.8.0/packager/inst/doc/An_Introduction_to_packager.html | 2356 ++++++---- packager-1.8.0/packager/inst/templates/nomakefile | 28 packager-1.8.0/packager/man/add_github_url_to_desc.Rd | 1 packager-1.8.0/packager/man/provide_cran_comments.Rd | 7 packager-1.8.0/packager/man/use_template.Rd | 4 packager-1.8.0/packager/vignettes/An_Introduction_to_packager.Rasciidoc |only 18 files changed, 1763 insertions(+), 900 deletions(-)
Title: Data Language Engine for 'knitr' / 'rmarkdown'
Description: Implements a data language engine for incorporating data directly in
'rmarkdown' documents so that they can be made completely standalone.
Author: David M. Kaplan [aut, cre, cph]
(<https://orcid.org/0000-0001-6087-359X>, dmkaplan2000)
Maintainer: David M. Kaplan <dmkaplan2000@gmail.com>
Diff between knitrdata versions 0.5.2 dated 2020-10-23 and 0.6.0 dated 2020-12-02
DESCRIPTION | 10 - MD5 | 37 ++- NAMESPACE | 3 NEWS.md | 14 + R/create_chunks.R | 259 ++++++++++++++++++--------- R/data_engine.R | 11 - R/extra_data_engines.R |only R/rstudio_addins.R | 89 +++++---- R/utils.R | 126 +++++++++++-- R/zzz.R | 6 inst/doc/data_language_engine_vignette.Rmd | 135 ++++++++++---- inst/doc/data_language_engine_vignette.html | 265 ++++++++++++++-------------- man/create_chunk.Rd | 103 ++++++---- man/is.file.binary.Rd | 60 ++++-- man/list_rmd_chunks.Rd | 161 +++++++---------- man/platform.newline.Rd | 3 man/unlock_gpg_key_passphrase.Rd |only tests/test.create_chunks.R | 39 ++-- tests/test.csv_rds_chunks.R |only tests/test.md5sum_chunks.R | 66 ++++++ vignettes/data_language_engine_vignette.Rmd | 135 ++++++++++---- 21 files changed, 998 insertions(+), 524 deletions(-)
More information about allcontributors at CRAN
Permanent link
More information about threesixtygiving at CRAN
Permanent link
Title: Fast and Easy Data Cleaning
Description: Data cleaning functions for classes logical,
factor, numeric, character, currency and Date to make
data cleaning fast and easy. Relying on very few dependencies, it
provides smart guessing, but with user options to override
anything if needed.
Author: Matthijs S. Berends [aut, cre]
(<https://orcid.org/0000-0001-7620-1800>)
Maintainer: Matthijs S. Berends <m.s.berends@umcg.nl>
Diff between cleaner versions 1.5.0 dated 2020-06-01 and 1.5.1 dated 2020-12-02
cleaner-1.5.0/cleaner/tests/testthat/test-is.Date.R |only cleaner-1.5.1/cleaner/DESCRIPTION | 12 - cleaner-1.5.1/cleaner/MD5 | 29 ++-- cleaner-1.5.1/cleaner/NAMESPACE | 1 cleaner-1.5.1/cleaner/NEWS.md | 13 ++ cleaner-1.5.1/cleaner/R/clean.R | 15 +- cleaner-1.5.1/cleaner/R/currency.R | 23 ++- cleaner-1.5.1/cleaner/R/format_names.R | 2 cleaner-1.5.1/cleaner/R/format_p_value.R |only cleaner-1.5.1/cleaner/R/na_replace.R | 2 cleaner-1.5.1/cleaner/R/zzz.R |only cleaner-1.5.1/cleaner/README.md | 129 ++++++++++++++------ cleaner-1.5.1/cleaner/man/clean.Rd | 2 cleaner-1.5.1/cleaner/man/currency.Rd | 6 cleaner-1.5.1/cleaner/man/format_names.Rd | 2 cleaner-1.5.1/cleaner/man/format_p_value.Rd |only cleaner-1.5.1/cleaner/tests/testthat/test-clean.R | 4 cleaner-1.5.1/cleaner/tests/testthat/test-rdate.R |only 18 files changed, 166 insertions(+), 74 deletions(-)
More information about AnchorRegression at CRAN
Permanent link
Title: Datasets for the 'canvasXpress' Package
Description: Contains the prepared data that is needed for the 'shiny' application examples in the
'canvasXpress' package. This package also includes datasets used for automated 'testthat' tests.
Scotto L, Narayan G, Nandula SV, Arias-Pulido H et al. (2008) <doi:10.1002/gcc.20577>.
Davis S, Meltzer PS (2007) <doi:10.1093/bioinformatics/btm254>.
Author: Isaac Neuhaus [aut],
Connie Brett [aut, cre],
Ger Inberg [aut]
Maintainer: Connie Brett <connie@aggregate-genius.com>
Diff between canvasXpress.data versions 1.29.0 dated 2020-08-04 and 1.30.5 dated 2020-12-02
DESCRIPTION | 8 - MD5 | 84 ++++++++++---------- NEWS.md | 4 inst/extdata/cX-basic-dat.txt.gz |binary inst/extdata/cX-basic2-dat.txt.gz |binary inst/extdata/cX-body2-dat.txt.gz |only inst/extdata/cX-body2-var.txt.gz |only inst/extdata/cX-generic-dat.txt.gz |binary inst/extdata/cX-generic-smp.txt.gz |binary inst/extdata/cX-generic-var.txt.gz |binary inst/extdata/cX-generic2-dat.txt.gz |binary inst/extdata/cX-generic2-smp.txt.gz |binary inst/extdata/cX-generic2-var.txt.gz |binary inst/extdata/cX-heatmapR-dat.txt.gz |binary inst/extdata/cX-heatmapR-smp.txt.gz |binary inst/extdata/cX-heatmapR-var.txt.gz |binary inst/extdata/cX-lincoln-dat.txt.gz |only inst/extdata/cX-lincoln-var.txt.gz |only inst/extdata/cX-lollipop-dat.txt.gz |binary inst/extdata/cX-multidimensionalheatmap-dat.txt.gz |binary inst/extdata/cX-multidimensionalheatmap-dat2.txt.gz |binary inst/extdata/cX-multidimensionalheatmap-dat3.txt.gz |binary inst/extdata/cX-multidimensionalheatmap-dat4.txt.gz |binary inst/extdata/cX-multidimensionalheatmap-smp.txt.gz |binary inst/extdata/cX-multidimensionalheatmap-var.txt.gz |binary inst/extdata/cX-multidimensionalheatmap2-dat.txt.gz |binary inst/extdata/cX-networkbasic-nodes.txt.gz |binary inst/extdata/cX-nonlinearfit-dat.txt.gz |binary inst/extdata/cX-oncoprint-dat.txt.gz |binary inst/extdata/cX-oncoprint-dat2.txt.gz |binary inst/extdata/cX-oncoprint-dat3.txt.gz |binary inst/extdata/cX-oncoprint-dat4.txt.gz |binary inst/extdata/cX-oncoprint-smp.txt.gz |binary inst/extdata/cX-oncoprint-var.txt.gz |binary inst/extdata/cX-overlays-dat.txt.gz |binary inst/extdata/cX-overlays-smp.txt.gz |binary inst/extdata/cX-overlays-var.txt.gz |binary inst/extdata/cX-petallength-dat.txt.gz |only inst/extdata/cX-petallength-var.txt.gz |only inst/extdata/cX-scatter3d-dat.txt.gz |binary inst/extdata/cX-scatterR4-dat.txt.gz |binary inst/extdata/cX-simple-dat.txt.gz |binary inst/extdata/cX-simple-smp.txt.gz |binary inst/extdata/cX-tree2-dat.txt.gz |only inst/extdata/cX-tree2-smp.txt.gz |only inst/extdata/cX-wpapoptosis-edges.txt.gz |binary tests/cx-get-ui-generated-test-datasets.R | 2 47 files changed, 55 insertions(+), 43 deletions(-)
More information about canvasXpress.data at CRAN
Permanent link
Title: Infrastructure for Data Stream Mining
Description: A framework for data stream modeling and associated data mining tasks such as clustering and classification. The development of this package was supported in part by NSF IIS-0948893 and NIH R21HG005912. Hahsler et al (2017) <doi:10.18637/jss.v076.i14>.
Author: Michael Hahsler [aut, cre, cph],
Matthew Bolanos [aut, cph],
John Forrest [ctb],
Matthias Carnein [ctb],
Dennis Assenmacher [ctb],
Dalibor Krleža [ctb]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between stream versions 1.3-2 dated 2020-05-04 and 1.4-0 dated 2020-12-02
DESCRIPTION | 18 - MD5 | 98 +++---- NAMESPACE | 24 + NEWS.md | 9 R/DSC.R | 157 +++++++++-- R/DSC_DStream.R | 2 R/DSC_R.R | 29 +- R/DSC_TwoStage.R | 71 +++-- R/DSD.R | 29 +- R/DSD_BarsAndGaussians.R | 41 +- R/DSD_Cubes.R | 52 +-- R/DSD_Gaussians.R | 267 +++++++++++++++---- R/DSD_MG.R | 66 ++-- R/DSD_Memory.R | 31 +- R/DSD_ReadCSV.R | 64 +++- R/DSD_ReadDB.R | 35 +- R/DSD_ScaleStream.R | 49 +-- R/DSD_Target.R | 18 - R/DSD_UniformNoise.R | 2 R/DSD_mlbenchGenerator.R | 28 +- R/evaluate.R | 378 ++++++++++++++++++++------- R/write_stream.R | 39 +- README.md | 2 build/vignette.rds |binary inst/doc/stream.R | 284 ++++++++++++++++---- inst/doc/stream.Rnw | 483 +++++++++++++++++++++++++++++++---- inst/doc/stream.pdf |binary inst/doc/stream_extension.R | 70 ++++- inst/doc/stream_extension.Rnw | 282 +++++++++++++------- inst/doc/stream_extension.pdf |binary man/DSC_Micro.Rd | 2 man/DSC_Outlier.Rd |only man/DSC_SinglePass.Rd |only man/DSD.Rd | 16 - man/DSD_Gaussians.Rd | 89 ++++-- man/DSD_Memory.Rd | 49 +-- man/DSD_ReadCSV.Rd | 30 +- man/DSD_ReadDB.Rd | 41 +- man/DefaultEvalCallback.Rd |only man/EvalCallback.Rd |only man/clean_outliers.Rd |only man/evaluate.Rd | 66 ++++ man/plot.Rd | 34 +- man/write_stream.Rd | 18 - vignettes/dst_uml.odg |binary vignettes/dst_uml.pdf |binary vignettes/interaction.odg |binary vignettes/interaction.pdf |binary vignettes/interaction_singlepass.odg |only vignettes/interaction_singlepass.pdf |only vignettes/outlier_assignment.RDS |only vignettes/stream.Rnw | 483 +++++++++++++++++++++++++++++++---- vignettes/stream.bib | 104 ++++--- vignettes/stream_extension.Rnw | 282 +++++++++++++------- 54 files changed, 2856 insertions(+), 986 deletions(-)
Title: Interface to the National 'Phenology' Network 'API'
Description: Programmatic interface to the
Web Service methods provided by the National 'Phenology' Network
(<https://usanpn.org/>), which includes data on various life history
events that occur at specific times.
Author: Lee Marsh [aut, cre],
Scott Chamberlain [aut],
Alyssa Rosemartin [aut],
Kevin Wong [aut]
Maintainer: Lee Marsh <lee@usanpn.org>
Diff between rnpn versions 0.1.0 dated 2016-04-20 and 1.1.1 dated 2020-12-02
rnpn-0.1.0/rnpn/R/globals.R |only rnpn-0.1.0/rnpn/R/npn_allobssp.R |only rnpn-0.1.0/rnpn/R/npn_indsatstations.R |only rnpn-0.1.0/rnpn/R/npn_indspatstations.R |only rnpn-0.1.0/rnpn/R/npn_obsspbyday.R |only rnpn-0.1.0/rnpn/R/npn_stationsbystate.R |only rnpn-0.1.0/rnpn/R/npn_stationswithspp.R |only rnpn-0.1.0/rnpn/data |only rnpn-0.1.0/rnpn/inst/ignore |only rnpn-0.1.0/rnpn/inst/img |only rnpn-0.1.0/rnpn/man/lookup_names.Rd |only rnpn-0.1.0/rnpn/man/npn_allobssp.Rd |only rnpn-0.1.0/rnpn/man/npn_indsatstations.Rd |only rnpn-0.1.0/rnpn/man/npn_indspatstations.Rd |only rnpn-0.1.0/rnpn/man/npn_obsspbyday.Rd |only rnpn-0.1.0/rnpn/man/npn_stationsbystate.Rd |only rnpn-0.1.0/rnpn/man/npn_stationswithspp.Rd |only rnpn-0.1.0/rnpn/man/taxonlist.Rd |only rnpn-0.1.0/rnpn/tests/testthat/test-npn_indsatstations.R |only rnpn-0.1.0/rnpn/tests/testthat/test-npn_indspatstations.R |only rnpn-0.1.0/rnpn/tests/testthat/test-npn_obsspbyday.R |only rnpn-0.1.0/rnpn/tests/testthat/test-npn_stationsbystate.R |only rnpn-0.1.0/rnpn/tests/testthat/test-npn_stationswithspp.R |only rnpn-1.1.1/rnpn/DESCRIPTION | 33 rnpn-1.1.1/rnpn/LICENSE | 4 rnpn-1.1.1/rnpn/MD5 | 181 ++++- rnpn-1.1.1/rnpn/NAMESPACE | 77 +- rnpn-1.1.1/rnpn/NEWS.md | 25 rnpn-1.1.1/rnpn/R/defunct.R |only rnpn-1.1.1/rnpn/R/lookup_names.R | 48 - rnpn-1.1.1/rnpn/R/npn_data_download.R |only rnpn-1.1.1/rnpn/R/npn_dataset.R |only rnpn-1.1.1/rnpn/R/npn_geoserver.R |only rnpn-1.1.1/rnpn/R/npn_get_species.R | 199 +++-- rnpn-1.1.1/rnpn/R/npn_partner_groups.R |only rnpn-1.1.1/rnpn/R/npn_phenophases.R |only rnpn-1.1.1/rnpn/R/npn_stations.R |only rnpn-1.1.1/rnpn/R/rnpn-package.R | 44 - rnpn-1.1.1/rnpn/R/zzz.R | 106 ++- rnpn-1.1.1/rnpn/README.md | 418 ++++-------- rnpn-1.1.1/rnpn/build |only rnpn-1.1.1/rnpn/inst/doc |only rnpn-1.1.1/rnpn/man/get_additional_rasters.Rd |only rnpn-1.1.1/rnpn/man/npn_abundance_categories.Rd |only rnpn-1.1.1/rnpn/man/npn_allobssp-defunct.Rd |only rnpn-1.1.1/rnpn/man/npn_check_point_cached.Rd |only rnpn-1.1.1/rnpn/man/npn_datasets.Rd |only rnpn-1.1.1/rnpn/man/npn_download_geospatial.Rd |only rnpn-1.1.1/rnpn/man/npn_download_individual_phenometrics.Rd |only rnpn-1.1.1/rnpn/man/npn_download_magnitude_phenometrics.Rd |only rnpn-1.1.1/rnpn/man/npn_download_site_phenometrics.Rd |only rnpn-1.1.1/rnpn/man/npn_download_status_data.Rd |only rnpn-1.1.1/rnpn/man/npn_get_agdd_point_data.Rd |only rnpn-1.1.1/rnpn/man/npn_get_common_query_vars.Rd |only rnpn-1.1.1/rnpn/man/npn_get_custom_agdd_raster.Rd |only rnpn-1.1.1/rnpn/man/npn_get_custom_agdd_time_series.Rd |only rnpn-1.1.1/rnpn/man/npn_get_data.Rd |only rnpn-1.1.1/rnpn/man/npn_get_data_by_year.Rd |only rnpn-1.1.1/rnpn/man/npn_get_download_url.Rd |only rnpn-1.1.1/rnpn/man/npn_get_layer_details.Rd |only rnpn-1.1.1/rnpn/man/npn_get_phenophases_for_taxon.Rd |only rnpn-1.1.1/rnpn/man/npn_get_point_data.Rd |only rnpn-1.1.1/rnpn/man/npn_groups.Rd |only rnpn-1.1.1/rnpn/man/npn_indsatstations-defunct.Rd |only rnpn-1.1.1/rnpn/man/npn_indspatstations-defunct.Rd |only rnpn-1.1.1/rnpn/man/npn_lookup_names.Rd |only rnpn-1.1.1/rnpn/man/npn_merge_geo_data.Rd |only rnpn-1.1.1/rnpn/man/npn_obsspbyday-defunct.Rd |only rnpn-1.1.1/rnpn/man/npn_pheno_classes.Rd |only rnpn-1.1.1/rnpn/man/npn_phenophase_definitions.Rd |only rnpn-1.1.1/rnpn/man/npn_phenophase_details.Rd |only rnpn-1.1.1/rnpn/man/npn_phenophases.Rd |only rnpn-1.1.1/rnpn/man/npn_phenophases_by_species.Rd |only rnpn-1.1.1/rnpn/man/npn_set_env.Rd |only rnpn-1.1.1/rnpn/man/npn_species.Rd | 143 +--- rnpn-1.1.1/rnpn/man/npn_species_types.Rd |only rnpn-1.1.1/rnpn/man/npn_stations.Rd |only rnpn-1.1.1/rnpn/man/npn_stations_by_location.Rd |only rnpn-1.1.1/rnpn/man/npn_stations_by_state.Rd |only rnpn-1.1.1/rnpn/man/npn_stations_with_spp.Rd |only rnpn-1.1.1/rnpn/man/npn_stationsbystate-defunct.Rd |only rnpn-1.1.1/rnpn/man/npn_stationswithspp-defunct.Rd |only rnpn-1.1.1/rnpn/man/resolve_six_raster.Rd |only rnpn-1.1.1/rnpn/man/rnpn-defunct.Rd |only rnpn-1.1.1/rnpn/man/rnpn-package.Rd | 24 rnpn-1.1.1/rnpn/tests/fixtures |only rnpn-1.1.1/rnpn/tests/test-all.R | 8 rnpn-1.1.1/rnpn/tests/testthat/helper-rnpn.R |only rnpn-1.1.1/rnpn/tests/testthat/test-npn-datasets.R |only rnpn-1.1.1/rnpn/tests/testthat/test-npn-defunct.R |only rnpn-1.1.1/rnpn/tests/testthat/test-npn-geoserver.R |only rnpn-1.1.1/rnpn/tests/testthat/test-npn-get-species.R |only rnpn-1.1.1/rnpn/tests/testthat/test-npn-observations.R |only rnpn-1.1.1/rnpn/tests/testthat/test-npn-partners.R |only rnpn-1.1.1/rnpn/tests/testthat/test-npn-phenophases.R |only rnpn-1.1.1/rnpn/tests/testthat/test-npn-stations.R |only rnpn-1.1.1/rnpn/vignettes |only 97 files changed, 701 insertions(+), 609 deletions(-)
Title: Installing and Loading R Packages for Reproducible Workflows
Description: A single key function, 'Require' that wraps 'install.packages',
'remotes::install_github', 'versions::install.versions', and 'base::require'
that allows for reproducible workflows. As with other functions in a
reproducible workflow, this package emphasizes functions that return the
same result whether it is the first or subsequent times running the function.
Maturing.
Author: Eliot J B McIntire [aut, cre] (<https://orcid.org/0000-0002-6914-8316>),
Her Majesty the Queen in Right of Canada, as represented by the
Minister of Natural Resources Canada [cph]
Maintainer: Eliot J B McIntire <eliot.mcintire@canada.ca>
Diff between Require versions 0.0.9 dated 2020-11-30 and 0.0.10 dated 2020-12-02
DESCRIPTION | 8 MD5 | 12 NEWS.md | 7 R/Require.R | 2 R/pkgDep.R | 4 man/Require.Rd | 1 tests/testit/packageVersions.txt | 584 +++++++++++++-------------------------- 7 files changed, 218 insertions(+), 400 deletions(-)
Title: R Markdown Templates to Preregister Scientific Studies
Description: Provides a collection of templates to author preregistration documents for scientific studies in PDF format.
Author: Frederik Aust [aut, cre] (<https://orcid.org/0000-0003-4900-788X>),
Lisa Spitzer [aut]
Maintainer: Frederik Aust <frederik.aust@uni-koeln.de>
Diff between prereg versions 0.4.0 dated 2019-01-09 and 0.5.0 dated 2020-12-02
DESCRIPTION | 19 +- MD5 | 25 ++- NAMESPACE | 2 R/prereg.R | 14 - R/psyquant_prereg.R |only R/rr_prereg.R |only README.md | 113 ++++++++++---- inst/NEWS.md | 5 inst/rmarkdown/templates/cos_prereg/skeleton/skeleton.Rmd | 4 inst/rmarkdown/templates/psyquant_prereg |only inst/rmarkdown/templates/rr_prereg |only man/prereg.Rd | 15 - man/psyquant_prereg.Rd |only man/rr_prereg.Rd |only tools/images/unnamed-chunk-1-1.png |binary 15 files changed, 135 insertions(+), 62 deletions(-)
Title: Fast Implementation of (Local) Population Stratification Methods
Description: Fast implementations to compute the genetic covariance matrix, the Jaccard similarity matrix, the s-matrix (the weighted Jaccard similarity matrix), and the (classic or robust) genomic relationship matrix of a (dense or sparse) input matrix. Full support for sparse matrices from the R-package 'Matrix'. Additionally, an implementation of the power method (von Mises iteration) to compute the largest eigenvector of a matrix is included, a function to perform an automated full run of global and local correlations in population stratification data, and a function to compute sliding windows. New functionality in locStra allows one to extract the k leading eigenvectors of the genetic covariance matrix, Jaccard similarity matrix, s-matrix, and genomic relationship matrix without actually computing the similarity matrices.
Author: Georg Hahn [aut,cre], Sharon M. Lutz [ctb], Christoph Lange [ctb]
Maintainer: Georg Hahn <ghahn@hsph.harvard.edu>
Diff between locStra versions 1.4 dated 2020-06-14 and 1.5 dated 2020-12-02
locStra-1.4/locStra/R/localStrat.r |only locStra-1.4/locStra/inst |only locStra-1.5/locStra/DESCRIPTION | 14 locStra-1.5/locStra/MD5 | 31 - locStra-1.5/locStra/NAMESPACE | 8 locStra-1.5/locStra/R/RcppExports.R | 60 +- locStra-1.5/locStra/R/locStra.r |only locStra-1.5/locStra/man/covMatrix.Rd | 12 locStra-1.5/locStra/man/fastCovEVs.Rd |only locStra-1.5/locStra/man/fastGrmEVs.Rd |only locStra-1.5/locStra/man/fastJaccardEVs.Rd |only locStra-1.5/locStra/man/fastSMatrixEVs.Rd |only locStra-1.5/locStra/man/fullscan.Rd | 10 locStra-1.5/locStra/man/grMatrix.Rd | 14 locStra-1.5/locStra/man/jaccardMatrix.Rd | 12 locStra-1.5/locStra/man/makeWindows.Rd | 6 locStra-1.5/locStra/man/powerMethod.Rd | 6 locStra-1.5/locStra/man/sMatrix.Rd | 25 - locStra-1.5/locStra/src/RcppExports.cpp | 220 +++++++-- locStra-1.5/locStra/src/auxcode.cpp | 714 +++++++++++++++++++++--------- 20 files changed, 810 insertions(+), 322 deletions(-)
Title: Generalized Correlations and Various Causal Paths
Description: Since causal paths from data are important for all sciences, the
package provides many sophisticated functions. causeSummBlk()
gives easy-to-interpret causal paths. Let Z denote control variables and compare
two flipped kernel regressions: X=f(Y, Z)+e1 and Y=g(X,Z)+e2. Our criterion Cr1
says that if |e1*Y|>|e2*X| then variation in X is more "exogenous or independent"
than in Y and causal path is X to Y. Criterion Cr2 requires |e2|<|e1|. These
inequalities between many absolute values are quantified by four orders of
stochastic dominance. Our third criterion Cr3 for the causal path X to Y
requires new generalized partial correlations to satisfy |r*(x|y,z)|< |r*(y|x,z)|.
The function parcorBMany() reports generalized partials between the first
variable and all others. The package provides several R functions including
get0outliers() for outlier detection, bigfp() for numerical integration by the
trapezoidal rule, stochdom2() for stochastic dominance, pillar3D() for 3D charts,
canonRho() for generalized canonical correlations, depMeas() measures nonlinear
dependence, and causeSummary(mtx) reports summary of causal paths among matrix columns
is easiest to use. Several functions whose names begin with 'boot' provide bootstrap
statistical inference including a new bootGcRsq() test for "Granger-causality"
allowing nonlinear relations. See Vinod (2019) <doi:10.1080/03610918.2015.1122048>.
Author: Prof. H. D. Vinod, Fordham University, NY.
Maintainer: H. D. Vinod <vinod@fordham.edu>
Diff between generalCorr versions 1.1.7 dated 2020-11-29 and 1.1.8 dated 2020-12-02
DESCRIPTION | 10 +++++----- MD5 | 20 ++++++++++---------- NEWS | 4 ++++ R/bootGcLC.R | 24 ++++++++++++++++-------- R/bootGcRsq.R | 26 ++++++++++++++++++-------- inst/doc/generalCorr-vignette.pdf |binary inst/doc/generalCorr-vignette2.pdf |binary inst/doc/generalCorr-vignette3.pdf |binary inst/doc/generalCorr-vignette5.pdf |binary man/bootGcLC.Rd | 17 +++++++++++------ man/bootGcRsq.Rd | 17 +++++++++++------ 11 files changed, 75 insertions(+), 43 deletions(-)
Title: Bayesian Meta Analysis for Studying Cross-Phenotype Genetic
Associations
Description: A Bayesian meta-analysis method for studying cross-phenotype
genetic associations. It uses summary-level data across multiple phenotypes to
simultaneously measure the evidence of aggregate-level pleiotropic association
and estimate an optimal subset of traits associated with the risk locus. CPBayes
is based on a spike and slab prior. The methodology is available from: A Majumdar, T Haldar, S Bhattacharya, JS Witte (2018) <doi:10.1371/journal.pgen.1007139>.
Author: Arunabha Majumdar <statgen.arunabha@gmail.com> [aut, cre],
Tanushree Haldar <tanushree.haldar@gmail.com> [aut],
John Witte [ctb]
Maintainer: Arunabha Majumdar <statgen.arunabha@gmail.com>
Diff between CPBayes versions 1.0.0 dated 2019-01-12 and 1.1.0 dated 2020-12-02
DESCRIPTION | 12 MD5 | 46 - NEWS.md | 13 R/FuncUserCor.R | 10 R/FuncUserUncor.R | 10 R/corln_estimation.R | 64 +- R/help.R | 15 R/summary_functions.R | 4 build/vignette.rds |binary inst/doc/cpbayes.R | 50 - inst/doc/cpbayes.Rmd | 12 inst/doc/cpbayes.html | 890 +++++++++++++++++++++++------------ man/CPBayes.Rd | 1 man/ExampleDataCor.Rd | 6 man/ExampleDataUncor.Rd | 6 man/SampleOverlapMatrix.Rd | 6 man/cpbayes_cor.Rd | 22 man/cpbayes_uncor.Rd | 21 man/estimate_corln.Rd | 13 man/forest_cpbayes.Rd | 2 man/post_summaries.Rd | 2 tests/testthat/test-InputRestCor.R | 14 tests/testthat/test-InputRestUnCor.R | 14 vignettes/cpbayes.Rmd | 12 24 files changed, 800 insertions(+), 445 deletions(-)
Title: Methods for Correlation Analysis
Description: Lightweight package for computing different kinds of correlations, such as partial correlations, Bayesian correlations, multilevel correlations, polychoric correlations, biweight correlations, distance correlations and more. Relies on the easystats ecosystem (Lüdecke, Waggoner & Makowski (2019) <doi:10.21105/joss.01412>).
Author: Dominique Makowski [aut, cre] (<https://orcid.org/0000-0001-5375-9967>),
Daniel Lüdecke [aut] (<https://orcid.org/0000-0002-8895-3206>),
Mattan S. Ben-Shachar [ctb] (<https://orcid.org/0000-0002-4287-4801>),
Indrajeet Patil [ctb] (<https://orcid.org/0000-0003-1995-6531>)
Maintainer: Dominique Makowski <dom.makowski@gmail.com>
Diff between correlation versions 0.4.0 dated 2020-09-27 and 0.5.0 dated 2020-12-02
DESCRIPTION | 16 - MD5 | 85 +++--- NAMESPACE | 22 + NEWS.md | 52 +++ R/cor_test.R | 46 ++- R/cor_test_bayes.R | 54 +++ R/cor_test_biserial.R | 2 R/cor_test_freq.R | 48 +++ R/cor_test_somers.R |only R/cor_to_ci.R | 5 R/cor_to_p.R | 2 R/cor_to_pcor.R | 11 R/correlation.R | 167 ++++++++++-- R/display.R |only R/mahalanobis.R | 4 R/methods.easycorrelation.R | 5 R/print.easycormatrix.R | 17 - R/print_md.R |only R/utils_create_diagonal.R | 1 R/utils_find_correlationtype.R | 9 R/utils_remove_redundant.R | 14 - R/winsorize.R |only build/vignette.rds |binary inst/WORDLIST |only inst/doc/multilevel.R | 22 - inst/doc/multilevel.Rmd | 26 + inst/doc/multilevel.html | 60 ++-- inst/doc/types.R | 40 +- inst/doc/types.Rmd | 44 +-- inst/doc/types.html | 123 ++++---- man/cor_test.Rd | 20 + man/cor_to_p.Rd | 4 man/correlation.Rd | 20 - man/display.easycormatrix.Rd |only man/distance_mahalanobis.Rd | 4 man/reexports.Rd |only man/winsorize.Rd |only tests/spelling.R |only tests/testthat/test-cor_multilevel.R | 13 tests/testthat/test-cor_test.R | 73 ++--- tests/testthat/test-cor_to_pcor.R | 27 - tests/testthat/test-correlation.R | 83 +++-- tests/testthat/test-misc.R | 6 vignettes/multilevel.Rmd | 26 + vignettes/multilevel_files/figure-gfm/unnamed-chunk-3-1.png |binary vignettes/multilevel_files/figure-gfm/unnamed-chunk-5-1.png |binary vignettes/types.Rmd | 44 +-- vignettes/types_files/figure-gfm/unnamed-chunk-4-1.png |binary 48 files changed, 776 insertions(+), 419 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-11-06 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-08-24 0.7.2
2019-02-13 0.7.1
2018-10-19 0.7.0
2017-11-15 0.6.5
2017-03-21 0.6.4
2016-01-15 0.6.3
2015-04-22 0.6.2
2015-01-13 0.6.1
2014-03-15 0.6
Title: Tufte's Styles for R Markdown Documents
Description: Provides R Markdown output formats to use Tufte styles for PDF and HTML output.
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>),
JJ Allaire [aut],
Andrzej Oles [ctb],
Dave Liepmann [ctb] (Tufte CSS in
inst/rmarkdown/templates/tufte_html/resources),
RStudio, PBC [cph]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between tufte versions 0.8 dated 2020-10-30 and 0.9 dated 2020-12-02
DESCRIPTION | 6 +-- MD5 | 10 ++--- R/handout.R | 1 inst/rmarkdown/templates/tufte_ctex/skeleton/skeleton.Rmd | 2 - inst/rmarkdown/templates/tufte_handout/resources/tufte-handout.tex | 20 ++++++++++ inst/rmarkdown/templates/tufte_html/skeleton/skeleton.Rmd | 2 - 6 files changed, 30 insertions(+), 11 deletions(-)