Title: 'Dang' Associated New Goodies
Description: A collection of utility functions.
Author: Dirk Eddelbuettel with contributions by Brodie Gaslam, Kevin Denny,
Kabira Namit, Colin Gillespie, R Core, Josh Ulrich, Jordan Mark Barbone,
and others.
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between dang versions 0.0.14 dated 2021-10-17 and 0.0.15 dated 2021-10-29
ChangeLog | 8 +++++- DESCRIPTION | 8 +++--- MD5 | 8 +++--- inst/NEWS.Rd | 9 ++++++ src/rollMinMax.cpp | 69 ++++++++++++++++++++++++++--------------------------- 5 files changed, 57 insertions(+), 45 deletions(-)
Title: Colored Terminal Output
Description: Colored terminal output on terminals that support 'ANSI'
color and highlight codes. It also works in 'Emacs' 'ESS'. 'ANSI'
color support is automatically detected. Colors and highlighting can
be combined and nested. New styles can also be created easily.
This package was inspired by the 'chalk' 'JavaScript' project.
Author: Gábor Csárdi [aut, cre],
Brodie Gaslam [ctb]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between crayon versions 1.4.1 dated 2021-02-08 and 1.4.2 dated 2021-10-29
DESCRIPTION | 12 +- MD5 | 20 ++- NEWS.md | 6 + R/aaa-rstudio-detect.R | 24 ++++ R/aab-num-ansi-colors.R | 244 +++++++++++++++++++++--------------------- R/aac-num-ansi-colors.R |only R/ansi-palette.R |only R/machinery.r | 18 ++- R/styles.r | 57 ++++++--- man/num_ansi_colors.Rd | 48 ++++++-- tests/testthat/test-combine.R | 4 tools |only 12 files changed, 267 insertions(+), 166 deletions(-)
Title: Learning Discrete Bayesian Network Classifiers from Data
Description: State-of-the art algorithms for learning discrete Bayesian network classifiers from data, including a number of those described in Bielza & Larranaga (2014) <doi:10.1145/2576868>, with functions for prediction, model evaluation and inspection.
Author: Mihaljevic Bojan [aut, cre],
Bielza Concha [aut],
Larranaga Pedro [aut],
Wickham Hadley [ctb] (some code extracted from memoise package)
Maintainer: Mihaljevic Bojan <boki.mihaljevic@gmail.com>
Diff between bnclassify versions 0.4.5 dated 2020-03-12 and 0.4.6 dated 2021-10-29
DESCRIPTION | 10 +-- MD5 | 40 ++++++------ NEWS.md | 5 - R/0bnclassify-doc.R | 4 - R/learn-params-wanbia.R | 2 R/wrap-gRain.R | 78 +++++++++++-------------- inst/doc/methods.pdf |binary inst/doc/overview.pdf |binary inst/doc/usage.R | 6 - inst/doc/usage.pdf |binary inst/doc/usage.rmd | 6 - man/car.Rd | 2 man/compute_wanbia_weights.Rd | 4 - man/voting.Rd | 2 tests/testthat/test-anb-bn.R | 5 - tests/testthat/test-cpp-table.R | 1 tests/testthat/test-cv.R | 7 -- tests/testthat/test-wrap-grain.R | 19 +++--- vignettes/bnclassify.bib | 4 - vignettes/includes/impl-related-conclusion.rmd | 6 - vignettes/usage.rmd | 6 - 21 files changed, 100 insertions(+), 107 deletions(-)
Title: Automatic Processing of TLS Point Cloud Data for Forestry
Purposes
Description: Process automation of Terrestrial Laser Scanner (TLS) point cloud data derived from single scans. 'FORTLS' enables (i) detection of trees and estimation of diameter at breast height (dbh), (ii) estimation of some stand variables (e.g. density, basal area, mean and dominant height), (iii) computation of metrics related to important forest attributes estimated in Forest Inventories (FIs) at stand level and (iv) optimization of plot design for combining TLS data and field measured data. Documentation about 'FORTLS' is described in Molina-Valero et al. (2020, <doi:10.3390/IECF2020-08066>).
Author: Juan Alberto Molina-Valero [aut, cph, cre],
María José Ginzo Villamayor [aut, com],
Manuel Antonio Novo Pérez [aut, com],
Adela Martínez-Calvo [aut, com],
Juan Gabriel Álvarez-González [aut, ths],
Fernando Montes [aut],
César Pérez-Cruzado [aut, ths]
Maintainer: Juan Alberto Molina-Valero <juanalberto.molina.valero@usc.es>
Diff between FORTLS versions 1.0.4 dated 2021-10-25 and 1.0.5 dated 2021-10-29
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NAMESPACE | 1 + build/partial.rdb |binary man/correlations.Rd | 11 +++++++---- man/metrics.variables.Rd | 4 ++-- man/optimize.plot.design.Rd | 7 ++++++- 7 files changed, 26 insertions(+), 17 deletions(-)
Title: Extensible Markov Model for Modelling Temporal Relationships
Between Clusters
Description: Implements TRACDS (Temporal Relationships
between Clusters for Data Streams), a generalization of
Extensible Markov Model (EMM). TRACDS adds a temporal or order model
to data stream clustering by superimposing a dynamically adapting
Markov Chain. Also provides an implementation of EMM (TRACDS on top of tNN
data stream clustering). Development of this
package was supported in part by NSF IIS-0948893 and R21HG005912 from
the National Human Genome Research Institute. Hahsler and Dunham (2010) <doi:10.18637/jss.v035.i05>.
Author: Michael Hahsler [aut, cre, cph],
Margaret H. Dunham [aut, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between rEMM versions 1.0-11 dated 2015-07-24 and 1.1.0 dated 2021-10-29
rEMM-1.0-11/rEMM/R/conversion.R |only rEMM-1.0-11/rEMM/inst/NEWS |only rEMM-1.0-11/rEMM/inst/tests |only rEMM-1.0-11/rEMM/man/conversion.Rd |only rEMM-1.1.0/rEMM/DESCRIPTION | 12 rEMM-1.1.0/rEMM/MD5 | 43 - rEMM-1.1.0/rEMM/NAMESPACE | 2 rEMM-1.1.0/rEMM/NEWS.md |only rEMM-1.1.0/rEMM/R/TRAC.R |only rEMM-1.1.0/rEMM/R/plot.R | 1242 +++++++++++++++++++----------------- rEMM-1.1.0/rEMM/README.md |only rEMM-1.1.0/rEMM/build/partial.rdb |only rEMM-1.1.0/rEMM/build/vignette.rds |binary rEMM-1.1.0/rEMM/data/16S.rda |binary rEMM-1.1.0/rEMM/data/Derwent.rda |binary rEMM-1.1.0/rEMM/data/EMMTraffic.rda |binary rEMM-1.1.0/rEMM/data/EMMsim.rda |binary rEMM-1.1.0/rEMM/inst/CITATION | 13 rEMM-1.1.0/rEMM/inst/doc/rEMM.R | 1 rEMM-1.1.0/rEMM/inst/doc/rEMM.pdf |binary rEMM-1.1.0/rEMM/man/Derwent.Rd | 8 rEMM-1.1.0/rEMM/man/TRAC-class.Rd |only rEMM-1.1.0/rEMM/man/TRACDS-class.Rd | 10 rEMM-1.1.0/rEMM/man/combine.Rd | 10 rEMM-1.1.0/rEMM/man/remove.Rd | 10 rEMM-1.1.0/rEMM/src/dll.c |only rEMM-1.1.0/rEMM/tests/testthat |only 27 files changed, 734 insertions(+), 617 deletions(-)
Title: REST API Client for the 'PGS' Catalog
Description: Programmatic access to the 'PGS' Catalog.
This package provides easy access to 'PGS' Catalog data by
accessing the REST API <https://www.pgscatalog.org/rest/>.
Author: Ramiro Magno [aut, cre] (<https://orcid.org/0000-0001-5226-3441>),
Isabel Duarte [aut] (<https://orcid.org/0000-0003-0060-2936>),
Ana-Teresa Maia [aut] (<https://orcid.org/0000-0002-0454-9207>),
CINTESIS [cph, fnd]
Maintainer: Ramiro Magno <ramiro.magno@gmail.com>
Diff between quincunx versions 0.1.1 dated 2021-10-08 and 0.1.2 dated 2021-10-29
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/read_pgs_scoring_file.R | 12 +++++++++++- README.md | 16 +++++++++++++++- build/partial.rdb |binary 5 files changed, 33 insertions(+), 9 deletions(-)
Title: Generative Mechanism Estimation in Temporal Complex Networks
Description: Statistical methods for estimating preferential attachment and node fitness generative mechanisms in temporal complex networks are provided. Thong Pham et al. (2015) <doi:10.1371/journal.pone.0137796>. Thong Pham et al. (2016) <doi:10.1038/srep32558>. Thong Pham et al. (2020) <doi:10.18637/jss.v092.i03>. Thong Pham et al. (2021) <doi:10.1093/comnet/cnab024>.
Author: Thong Pham, Paul Sheridan, Hidetoshi Shimodaira
Maintainer: Thong Pham <thongphamthe@gmail.com>
Diff between PAFit versions 1.1.0.4 dated 2021-07-22 and 1.2.1 dated 2021-10-29
DESCRIPTION | 10 +++++----- MD5 | 20 ++++++++++---------- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 25 +++++++++++++++++++++---- inst/NEWS.Rd | 8 ++++++++ man/PAFit-package.Rd | 10 ++++++---- man/PAFit_oneshot.rd | 13 ++++++------- man/generate_BA.rd | 2 +- src/Cpp_code.cpp | 2 +- src/RcppExports.cpp | 5 +++++ 11 files changed, 63 insertions(+), 32 deletions(-)
Title: Plotting Field Plans for Agricultural Experiments
Description: A function for plotting maps of agricultural field experiments that
are laid out in grids.
Author: Kevin Wright [aut, cre] (<https://orcid.org/0000-0002-0617-8673>)
Maintainer: Kevin Wright <kw.stat@gmail.com>
Diff between desplot versions 1.8 dated 2020-10-21 and 1.9 dated 2021-10-29
DESCRIPTION | 11 - MD5 | 10 - NEWS.md | 5 R/ggdesplot.R | 7 build/vignette.rds |binary inst/doc/desplot_examples.html | 358 ++++++----------------------------------- 6 files changed, 78 insertions(+), 313 deletions(-)
Title: Convolution-Type Smoothed Quantile Regression
Description: Estimation and inference for conditional linear quantile regression models using a convolution smoothed approach. In the low-dimensional setting, efficient gradient-based methods are employed for fitting both a single model and a regression process over a quantile range. Normal-based and (multiplier) bootstrap confidence intervals for all slope coefficients are constructed. In high dimensions, the conquer methods complemented with l_1-penalization and iteratively reweighted l_1-penalization are used to fit sparse models.
Author: Xuming He [aut],
Xiaoou Pan [aut, cre],
Kean Ming Tan [aut],
Wen-Xin Zhou [aut]
Maintainer: Xiaoou Pan <xip024@ucsd.edu>
Diff between conquer versions 1.0.2 dated 2020-08-27 and 1.2.0 dated 2021-10-29
conquer-1.0.2/conquer/README.md |only conquer-1.2.0/conquer/DESCRIPTION | 12 conquer-1.2.0/conquer/MD5 | 24 conquer-1.2.0/conquer/NAMESPACE | 7 conquer-1.2.0/conquer/R/RcppExports.R | 316 +++- conquer-1.2.0/conquer/R/conquer-package.R | 10 conquer-1.2.0/conquer/R/generate_ns.R | 5 conquer-1.2.0/conquer/R/smqr.R | 346 ++++ conquer-1.2.0/conquer/man/conquer-package.Rd | 12 conquer-1.2.0/conquer/man/conquer.Rd | 33 conquer-1.2.0/conquer/man/conquer.cv.reg.Rd |only conquer-1.2.0/conquer/man/conquer.process.Rd |only conquer-1.2.0/conquer/man/conquer.reg.Rd |only conquer-1.2.0/conquer/src/RcppExports.cpp | 1604 +++++++++++++++++++- conquer-1.2.0/conquer/src/smqr.cpp | 2130 ++++++++++++++++++++++++++- 15 files changed, 4341 insertions(+), 158 deletions(-)
Title: 'systemPipeShiny' Utility Functions
Description: The systemPipeShiny (SPS) framework comes with many useful utility functions. However, installing the whole framework is heavy and takes some time. If you like only a few useful utility functions from SPS, install this package is enough.
Author: Le Zhang [aut, cre]
Maintainer: Le Zhang <lezhang100@gmail.com>
Diff between spsUtil versions 0.2.0 dated 2021-08-11 and 0.2.1 dated 2021-10-29
DESCRIPTION | 11 ++++++----- MD5 | 12 +++++++----- NAMESPACE | 2 ++ NEWS.md | 10 ++++++++++ R/spsUtil.R | 7 +++++-- R/str_uniquefy.R |only man/msg.Rd | 3 ++- man/strUniquefy.Rd |only 8 files changed, 32 insertions(+), 13 deletions(-)
Title: L1-Norm PCA Methods
Description: Implementations of several methods for principal component analysis
using the L1 norm. The package depends on COIN-OR Clp version >=
1.17.4. The methods implemented are
PCA-L1 (Kwak 2008) <DOI:10.1109/TPAMI.2008.114>,
L1-PCA (Ke and Kanade 2003, 2005) <DOI:10.1109/CVPR.2005.309>,
L1-PCA* (Brooks, Dula, and Boone 2013) <DOI:10.1016/j.csda.2012.11.007>,
L1-PCAhp (Visentin, Prestwich and Armagan 2016)
<DOI:10.1007/978-3-319-46227-1_37>,
wPCA (Park and Klabjan 2016) <DOI: 10.1109/ICDM.2016.0054>,
awPCA (Park and Klabjan 2016) <DOI: 10.1109/ICDM.2016.0054>,
PCA-Lp (Kwak 2014) <DOI:10.1109/TCYB.2013.2262936>, and
SharpEl1-PCA (Brooks and Dula, submitted).
Author: Sapan Jot <sapan.madaan@gmail.com>, Paul Brooks
<jpbrooks@vcu.edu>,
Andrea Visentin <andrea.visentin@insight-centre.org>,
Young Woong Park <ywpark@mail.smu.edu>,
and Yi-Hui Zhou <yihui_zhou@ncsu.edu>
Maintainer: Paul Brooks <jpbrooks@vcu.edu>
Diff between pcaL1 versions 1.5.4 dated 2020-02-11 and 1.5.5 dated 2021-10-29
ChangeLog | 6 DESCRIPTION | 14 MD5 | 10 configure | 2484 +++++++++++++++++++++++++++------------------------ configure.ac | 15 man/pcaL1-package.Rd | 6 6 files changed, 1378 insertions(+), 1157 deletions(-)
Title: Perform Pharmacokinetic Non-Compartmental Analysis
Description: Compute standard Non-Compartmental Analysis (NCA) parameters for
typical pharmacokinetic analyses and summarize them.
Author: Bill Denney [aut, cre] (<https://orcid.org/0000-0002-5759-428X>),
Clare Buckeridge [aut],
Sridhar Duvvuri [ctb]
Maintainer: Bill Denney <wdenney@humanpredictions.com>
Diff between PKNCA versions 0.9.4 dated 2020-06-01 and 0.9.5 dated 2021-10-29
PKNCA-0.9.4/PKNCA/R/merge.R |only PKNCA-0.9.4/PKNCA/inst/doc/Data-Cleaning-in-PKNCA.Rmd |only PKNCA-0.9.4/PKNCA/inst/doc/Data-Cleaning-in-PKNCA.html |only PKNCA-0.9.4/PKNCA/man/merge.splitlist.Rd |only PKNCA-0.9.4/PKNCA/man/split.PKNCAconc.Rd |only PKNCA-0.9.4/PKNCA/tests/testthat/test-merge.R |only PKNCA-0.9.4/PKNCA/vignettes/Data-Cleaning-in-PKNCA.Rmd |only PKNCA-0.9.5/PKNCA/DESCRIPTION | 16 PKNCA-0.9.5/PKNCA/MD5 | 182 - PKNCA-0.9.5/PKNCA/NAMESPACE | 13 PKNCA-0.9.5/PKNCA/NEWS.md | 22 PKNCA-0.9.5/PKNCA/R/001-add.interval.col.R | 14 PKNCA-0.9.5/PKNCA/R/AIC.list.R | 3 PKNCA-0.9.5/PKNCA/R/PKNCA.options.R | 14 PKNCA-0.9.5/PKNCA/R/auc.R | 4 PKNCA-0.9.5/PKNCA/R/check.intervals.R | 22 PKNCA-0.9.5/PKNCA/R/class-PKNCAconc.R | 99 PKNCA-0.9.5/PKNCA/R/class-PKNCAdata.R | 137 - PKNCA-0.9.5/PKNCA/R/class-PKNCAdose.R | 13 PKNCA-0.9.5/PKNCA/R/cleaners.R | 12 PKNCA-0.9.5/PKNCA/R/exclude.R | 18 PKNCA-0.9.5/PKNCA/R/half.life.R | 20 PKNCA-0.9.5/PKNCA/R/pk.calc.all.R | 338 +-- PKNCA-0.9.5/PKNCA/R/prepare_data.R |only PKNCA-0.9.5/PKNCA/R/superposition.R | 29 PKNCA-0.9.5/PKNCA/R/time.above.R |only PKNCA-0.9.5/PKNCA/README.md | 6 PKNCA-0.9.5/PKNCA/build/vignette.rds |binary PKNCA-0.9.5/PKNCA/inst/doc/AUC-Calculation-with-PKNCA.html | 560 +---- PKNCA-0.9.5/PKNCA/inst/doc/Example-theophylline.Rmd | 2 PKNCA-0.9.5/PKNCA/inst/doc/Example-theophylline.html | 1042 +++++----- PKNCA-0.9.5/PKNCA/inst/doc/Half-Life-Calculation.R |only PKNCA-0.9.5/PKNCA/inst/doc/Half-Life-Calculation.Rmd |only PKNCA-0.9.5/PKNCA/inst/doc/Half-Life-Calculation.html |only PKNCA-0.9.5/PKNCA/inst/doc/Introduction-and-Usage.html | 643 ++---- PKNCA-0.9.5/PKNCA/inst/doc/Methods-for-Dose-Aware-Interpolation-and-Extrapolation.html | 202 - PKNCA-0.9.5/PKNCA/inst/doc/Options-for-Controlling-PKNCA.html | 309 +- PKNCA-0.9.5/PKNCA/inst/doc/PKNCA-validation.html | 252 -- PKNCA-0.9.5/PKNCA/inst/doc/Post-Processing.R |only PKNCA-0.9.5/PKNCA/inst/doc/Post-Processing.Rmd |only PKNCA-0.9.5/PKNCA/inst/doc/Post-Processing.html |only PKNCA-0.9.5/PKNCA/inst/doc/Selection-of-Calculation-Intervals.html | 432 +--- PKNCA-0.9.5/PKNCA/inst/doc/Superposition.R | 2 PKNCA-0.9.5/PKNCA/inst/doc/Superposition.Rmd | 2 PKNCA-0.9.5/PKNCA/inst/doc/Superposition.html | 302 -- PKNCA-0.9.5/PKNCA/inst/doc/Writing-Parameter-Functions.html | 196 - PKNCA-0.9.5/PKNCA/man/PKNCA.Rd | 76 PKNCA-0.9.5/PKNCA/man/PKNCA.options.Rd | 128 - PKNCA-0.9.5/PKNCA/man/PKNCA.set.summary.Rd | 132 - PKNCA-0.9.5/PKNCA/man/PKNCAconc.Rd | 10 PKNCA-0.9.5/PKNCA/man/PKNCAdata.Rd | 150 - PKNCA-0.9.5/PKNCA/man/PKNCAdose.Rd | 164 - PKNCA-0.9.5/PKNCA/man/PKNCAresults.Rd | 68 PKNCA-0.9.5/PKNCA/man/add.interval.col.Rd | 206 - PKNCA-0.9.5/PKNCA/man/addProvenance.Rd | 52 PKNCA-0.9.5/PKNCA/man/checkProvenance.Rd | 44 PKNCA-0.9.5/PKNCA/man/clean.conc.blq.Rd | 150 - PKNCA-0.9.5/PKNCA/man/clean.conc.na.Rd | 74 PKNCA-0.9.5/PKNCA/man/exclude.Rd | 124 - PKNCA-0.9.5/PKNCA/man/exclude_nca.Rd | 118 - PKNCA-0.9.5/PKNCA/man/fit_half_life.Rd | 60 PKNCA-0.9.5/PKNCA/man/get.parameter.deps.Rd | 56 PKNCA-0.9.5/PKNCA/man/getAttributeColumn.Rd | 48 PKNCA-0.9.5/PKNCA/man/getColumnValueOrNot.Rd | 62 PKNCA-0.9.5/PKNCA/man/getGroups.PKNCAconc.Rd | 96 PKNCA-0.9.5/PKNCA/man/group_vars.PKNCAconc.Rd |only PKNCA-0.9.5/PKNCA/man/interp.extrap.conc.Rd | 354 +-- PKNCA-0.9.5/PKNCA/man/parseFormula.Rd | 102 PKNCA-0.9.5/PKNCA/man/pk.business.Rd | 74 PKNCA-0.9.5/PKNCA/man/pk.calc.aucint.Rd | 296 +- PKNCA-0.9.5/PKNCA/man/pk.calc.aucpext.Rd | 52 PKNCA-0.9.5/PKNCA/man/pk.calc.auxc.Rd | 352 +-- PKNCA-0.9.5/PKNCA/man/pk.calc.ceoi.Rd | 50 PKNCA-0.9.5/PKNCA/man/pk.calc.cl.Rd | 68 PKNCA-0.9.5/PKNCA/man/pk.calc.half.life.Rd | 224 +- PKNCA-0.9.5/PKNCA/man/pk.calc.mrt.md.Rd | 72 PKNCA-0.9.5/PKNCA/man/pk.calc.time_above.Rd |only PKNCA-0.9.5/PKNCA/man/pk.calc.vd.Rd | 70 PKNCA-0.9.5/PKNCA/man/pk.nca.intervals.Rd |only PKNCA-0.9.5/PKNCA/man/setAttributeColumn.Rd | 96 PKNCA-0.9.5/PKNCA/man/setExcludeColumn.Rd | 46 PKNCA-0.9.5/PKNCA/man/summary.PKNCAresults.Rd | 140 - PKNCA-0.9.5/PKNCA/tests/testthat/test-PKNCA.options.R | 3 PKNCA-0.9.5/PKNCA/tests/testthat/test-auc.R | 2 PKNCA-0.9.5/PKNCA/tests/testthat/test-check.intervals.R | 42 PKNCA-0.9.5/PKNCA/tests/testthat/test-class-PKNCAconc.R | 57 PKNCA-0.9.5/PKNCA/tests/testthat/test-class-PKNCAdata.R | 45 PKNCA-0.9.5/PKNCA/tests/testthat/test-class-PKNCAdose.R | 14 PKNCA-0.9.5/PKNCA/tests/testthat/test-class-PKNCAresults.R | 114 - PKNCA-0.9.5/PKNCA/tests/testthat/test-cleaners.R | 20 PKNCA-0.9.5/PKNCA/tests/testthat/test-exclude.R | 46 PKNCA-0.9.5/PKNCA/tests/testthat/test-interpolate.conc.R | 10 PKNCA-0.9.5/PKNCA/tests/testthat/test-parseFormula.R | 4 PKNCA-0.9.5/PKNCA/tests/testthat/test-pk.calc.all.R | 143 - PKNCA-0.9.5/PKNCA/tests/testthat/test-prepare_data.R |only PKNCA-0.9.5/PKNCA/tests/testthat/test-provenance.R | 8 PKNCA-0.9.5/PKNCA/tests/testthat/test-superpostion.R | 22 PKNCA-0.9.5/PKNCA/tests/testthat/test-time.above.R |only PKNCA-0.9.5/PKNCA/tests/testthat/test-time.to.steady.state.R | 16 PKNCA-0.9.5/PKNCA/vignettes/Example-theophylline.Rmd | 2 PKNCA-0.9.5/PKNCA/vignettes/Half-Life-Calculation.Rmd |only PKNCA-0.9.5/PKNCA/vignettes/Post-Processing.Rmd |only PKNCA-0.9.5/PKNCA/vignettes/Superposition.Rmd | 2 103 files changed, 4160 insertions(+), 5110 deletions(-)
Title: Extra Methods for Sparse Matrices
Description: Extends sparse matrix and vector classes from the 'Matrix' package by providing:
(a) Methods and operators that work natively on CSR formats (compressed sparse row,
a.k.a. 'RsparseMatrix') such as slicing/sub-setting, assignment, rbind(),
mathematical operators for CSR and COO such as addition ("+") or sqrt(), and methods such as diag();
(b) Multi-threaded matrix multiplication and cross-product for many <sparse, dense> types,
including the 'float32' type from 'float';
(c) Coercion methods between pairs of classes which are not present in 'Matrix',
such as 'dgCMatrix' -> 'ngRMatrix', as well as convenience conversion functions;
(d) Utility functions for sparse matrices such as sorting the indices or removing
zero-valued entries;
(e) Fast transposes that work by outputting in the opposite storage format;
(f) Faster replacements for many 'Matrix' methods for all sparse types, such as
slicing and elementwise multiplication.
(g) Convenience functions for sparse objects, such as 'mapSparse' or a shorter 'show' method.
Author: David Cortes [aut, cre, cph],
Dmitry Selivanov [cph],
Thibaut Goetghebuer-Planchon [cph] (Copyright holder of included
robinmap library),
Martin Maechler [cph] (Copyright holder of 'Matrix' package from which
some code was taken)
Maintainer: David Cortes <david.cortes.rivera@gmail.com>
Diff between MatrixExtra versions 0.1.7 dated 2021-09-26 and 0.1.8 dated 2021-10-29
DESCRIPTION | 17 + MD5 | 52 +++--- NAMESPACE | 2 R/MatrixExtra.R | 2 R/RcppExports.R | 12 + R/assignment.R | 44 +++-- R/operators.R | 5 R/rbind.R | 1 R/scalar_funs.R | 1 R/show.R |only R/utils.R | 2 R/zzz.R | 17 + configure | 24 +- configure.ac | 6 inst/doc/Introducing_MatrixExtra.html | 283 +++++++++++++++++---------------- man/MatrixExtra-options.Rd | 15 + man/MatrixExtra.Rd | 2 man/assignment.Rd | 2 man/mapSparse.Rd | 2 man/mathematical-functions.Rd | 1 man/operators.Rd | 5 man/rbind_csr.Rd | 1 man/show.Rd |only src/RcppExports.cpp | 40 ++++ src/assignment.cpp | 45 +++++ tests/testthat/test-assignment.R | 94 ++++++++++ vignettes/Introducing_MatrixExtra.Rmd | 21 ++ vignettes/Introducing_MatrixExtra.html | 283 +++++++++++++++++---------------- 28 files changed, 653 insertions(+), 326 deletions(-)
Title: Manipulating Labelled Data
Description: Work with labelled data imported from 'SPSS'
or 'Stata' with 'haven' or 'foreign'. This package
provides useful functions to deal with "haven_labelled" and
"haven_labelled_spss" classes introduced by 'haven' package.
Author: Joseph Larmarange [aut, cre] (<https://orcid.org/0000-0001-7097-700X>),
Daniel Ludecke [ctb],
Hadley Wickham [ctb],
Michal Bojanowski [ctb],
François Briatte [ctb]
Maintainer: Joseph Larmarange <joseph@larmarange.net>
Diff between labelled versions 2.8.0 dated 2021-03-08 and 2.9.0 dated 2021-10-29
DESCRIPTION | 13 MD5 | 80 +++-- NAMESPACE | 28 ++ NEWS.md | 364 ++++++++++++++------------ R/data.R |only R/is_prefixed.R | 2 R/labelled.R | 3 R/lookfor.R | 32 ++ R/na_values.R | 109 +++++++- R/remove_labels.R | 127 +++++++-- R/tagged_na.R | 206 +++++++++++++++ R/to_character.R | 19 + R/to_factor.R | 28 +- R/to_labelled.R | 31 +- R/val_labels.R | 50 ++- README.md | 6 build/vignette.rds |binary data |only inst/WORDLIST | 6 inst/doc/intro_labelled.R | 3 inst/doc/intro_labelled.Rmd | 43 +-- inst/doc/intro_labelled.html | 289 ++++++++++----------- inst/doc/look_for.html | 150 +++++------ inst/doc/missing_values.R |only inst/doc/missing_values.Rmd |only inst/doc/missing_values.html |only man/look_for.Rd | 25 + man/na_values.Rd | 54 +++ man/reexports.Rd | 3 man/remove_labels.Rd | 107 ++++--- man/tagged_na_to_user_na.Rd |only man/test_datasets.Rd |only man/to_character.Rd | 94 +++--- man/to_factor.Rd | 260 +++++++++---------- man/to_labelled.Rd | 3 man/unique_tagged_na.Rd |only man/val_labels.Rd | 2 tests/testthat/test-labelled.r | 503 ++++++++++++++++++++++++++++++++++++- tests/testthat/test-miscellanous.R |only tests/testthat/test-na_values.R |only tests/testthat/test-recode_if.r | 4 tests/testthat/test-tagged_na.r |only tests/testthat/test-to_labelled.r | 95 ++++++ tests/testthat/test_lookfor.R |only vignettes/intro_labelled.Rmd | 43 +-- vignettes/missing_values.Rmd |only 46 files changed, 2000 insertions(+), 782 deletions(-)
Title: Syntax Highlighting and Automatic Linking
Description: Syntax highlighting of R code, specifically designed for the
needs of 'RMarkdown' packages like 'pkgdown', 'hugodown', and
'bookdown'. It includes linking of function calls to their
documentation on the web, and automatic translation of ANSI escapes in
output to the equivalent HTML.
Author: Hadley Wickham [aut, cre],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between downlit versions 0.2.1 dated 2020-11-04 and 0.4.0 dated 2021-10-29
downlit-0.2.1/downlit/tests/testthat/test-evaluate.txt |only downlit-0.4.0/downlit/DESCRIPTION | 41 +- downlit-0.4.0/downlit/MD5 | 62 +-- downlit-0.4.0/downlit/NAMESPACE | 9 downlit-0.4.0/downlit/NEWS.md | 60 +++ downlit-0.4.0/downlit/R/article-index.R | 2 downlit-0.4.0/downlit/R/downlit-html.R | 21 - downlit-0.4.0/downlit/R/downlit-md.R | 2 downlit-0.4.0/downlit/R/downlit-package.R | 24 - downlit-0.4.0/downlit/R/evaluate.R | 216 ++++++++----- downlit-0.4.0/downlit/R/highlight.R | 57 ++- downlit-0.4.0/downlit/R/link.R | 170 +++++----- downlit-0.4.0/downlit/R/metadata.R | 47 ++ downlit-0.4.0/downlit/R/packages.R | 36 ++ downlit-0.4.0/downlit/R/utils.R | 27 + downlit-0.4.0/downlit/R/zzz.R |only downlit-0.4.0/downlit/README.md | 6 downlit-0.4.0/downlit/man/autolink.Rd | 19 + downlit-0.4.0/downlit/man/downlit-package.Rd | 27 - downlit-0.4.0/downlit/man/evaluate_and_highlight.Rd | 37 +- downlit-0.4.0/downlit/man/highlight.Rd | 19 + downlit-0.4.0/downlit/man/href_topic.Rd | 10 downlit-0.4.0/downlit/man/is_low_change.Rd |only downlit-0.4.0/downlit/tests/testthat/_snaps/evaluate.md |only downlit-0.4.0/downlit/tests/testthat/_snaps/highlight.md | 8 downlit-0.4.0/downlit/tests/testthat/autolink.html | 1 downlit-0.4.0/downlit/tests/testthat/fake-repo |only downlit-0.4.0/downlit/tests/testthat/test-downlit-html.txt | 2 downlit-0.4.0/downlit/tests/testthat/test-evaluate.R | 108 ++++-- downlit-0.4.0/downlit/tests/testthat/test-highlight.R | 14 downlit-0.4.0/downlit/tests/testthat/test-highlight.txt | 2 downlit-0.4.0/downlit/tests/testthat/test-link.R | 26 + downlit-0.4.0/downlit/tests/testthat/test-metadata.R | 24 + downlit-0.4.0/downlit/tests/testthat/test-packages.R | 10 downlit-0.4.0/downlit/tests/testthat/test-utils.R |only 35 files changed, 744 insertions(+), 343 deletions(-)
Title: Explainable Outlier Detection Through Decision Tree Conditioning
Description: Outlier detection method that flags suspicious values within observations,
constrasting them against the normal values in a user-readable format, potentially
describing conditions within the data that make a given outlier more rare.
Full procedure is described in Cortes (2020) <arXiv:2001.00636>.
Loosely based on the 'GritBot' <https://www.rulequest.com/gritbot-info.html> software.
Author: David Cortes
Maintainer: David Cortes <david.cortes.rivera@gmail.com>
Diff between outliertree versions 1.7.6 dated 2021-09-25 and 1.7.6-1 dated 2021-10-29
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- configure | 6 +++--- configure.ac | 4 ++-- inst/doc/Introducing_OutlierTree.html | 8 ++++---- 5 files changed, 16 insertions(+), 16 deletions(-)
Title: Interface to 'Zenodo' REST API
Description: Provides an Interface to 'Zenodo' (<https://zenodo.org>) REST API,
including management of depositions, attribution of DOIs by 'Zenodo' and
upload and download of files.
Author: Emmanuel Blondel [aut, cre] (<https://orcid.org/0000-0002-5870-5762>),
Julien Barde [ctb] (<https://orcid.org/0000-0002-3519-6141>),
Stephen Eglen [ctb] (<https://orcid.org/0000-0001-8607-8025>),
Hans Van Calster [ctb] (<https://orcid.org/0000-0001-8595-8426>),
Floris Vanderhaeghe [ctb] (<https://orcid.org/0000-0002-6378-6229>)
Maintainer: Emmanuel Blondel <emmanuel.blondel1@gmail.com>
Diff between zen4R versions 0.5 dated 2021-09-15 and 0.5-1 dated 2021-10-29
DESCRIPTION | 8 +-- MD5 | 26 ++++++------ NEWS.md | 9 ++++ R/ZenodoManager.R | 24 ++++++++--- R/ZenodoRecord.R | 41 ++++++++++++------- R/ZenodoRequest.R | 2 R/zen4R.R | 4 - README.md | 4 - man/zen4R.Rd | 4 - tests/testthat/test_communities.R | 3 + tests/testthat/test_funders.R | 3 + tests/testthat/test_grants.R | 1 tests/testthat/test_licenses.R | 3 + tests/testthat/test_records.R | 79 +++++++++++++++++++++++++++----------- 14 files changed, 144 insertions(+), 67 deletions(-)
Title: Functional Data Analysis
Description: These functions were developed to support functional data
analysis as described in Ramsay, J. O. and Silverman, B. W.
(2005) Functional Data Analysis. New York: Springer and in
Ramsay, J. O., Hooker, Giles, and Graves, Spencer (2009).
Functional Data Analysis with R and Matlab (Springer).
The package includes data sets and script files working many examples
including all but one of the 76 figures in this latter book. Matlab versions
are available by ftp from
<https://www.psych.mcgill.ca/misc/fda/downloads/FDAfuns/>.
Author: J. O. Ramsay <ramsay@psych.mcgill.ca> [aut,cre],
Spencer Graves <spencer.graves@effectivedefense.org> [ctb],
Giles Hooker <gjh27@cornell.edu> [ctb]
Maintainer: J. O. Ramsay <ramsay@psych.mcgill.ca>
Diff between fda versions 5.4.0 dated 2021-09-28 and 5.5.0 dated 2021-10-29
fda-5.4.0/fda/NEWS |only fda-5.5.0/fda/DESCRIPTION | 8 - fda-5.5.0/fda/MD5 | 31 ++++--- fda-5.5.0/fda/NAMESPACE | 4 fda-5.5.0/fda/R/density.fd.R | 14 +-- fda-5.5.0/fda/R/lnsrch.R | 20 ++++ fda-5.5.0/fda/R/polintmat.R | 2 fda-5.5.0/fda/R/smooth.morph2.R |only fda-5.5.0/fda/R/smooth.surp.R | 10 +- fda-5.5.0/fda/R/surp.fit.R | 17 ++-- fda-5.5.0/fda/inst/NEWS.Rd |only fda-5.5.0/fda/man/Data2fd.Rd | 2 fda-5.5.0/fda/man/density.fd.Rd | 2 fda-5.5.0/fda/man/monfn.Rd | 156 ++++++++++++++++++++----------------- fda-5.5.0/fda/man/mongrad.Rd |only fda-5.5.0/fda/man/monhess.Rd |only fda-5.5.0/fda/man/polintmat.Rd |only fda-5.5.0/fda/man/smooth.morph.Rd | 5 - fda-5.5.0/fda/man/smooth.morph2.Rd |only fda-5.5.0/fda/man/surp.fit.Rd | 4 20 files changed, 161 insertions(+), 114 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-10-15 0.1.1
2021-09-20 0.1.0
Title: Likelihood Analyses for Common Statistical Tests
Description: A collection of functions that calculate the log likelihood
(support) for a range of statistical tests. Where possible the likelihood
function and likelihood interval for the observed data are displayed. The
evidential approach used here is based on the book "Likelihood" by A.W.F.
Edwards (1992, ISBN-13 : 978-0801844430), "Statistical Evidence" by R.
Royall (1997, ISBN-13 : 978-0412044113), S.N. Goodman & R. Royall
(2011) <doi:10.2105/AJPH.78.12.1568>, "Understanding
Psychology as a Science" by Z. Dienes (2008, ISBN-13 : 978-0230542310),
S. Glover & P. Dixon <https://link.springer.com/article/10.3758/BF03196706>
and others. This package accompanies "Evidence-Based Statistics" by
P. Cahusac (2020, ISBN-13 : 978-1119549802).
Author: Peter Cahusac [aut, cre] (<https://orcid.org/0000-0003-4976-2834>)
Maintainer: Peter Cahusac <peteqsac@gmail.com>
Diff between likelihoodR versions 1.0.5 dated 2021-10-13 and 1.0.6 dated 2021-10-29
DESCRIPTION | 6 - MD5 | 18 +-- R/L_OR.R | 4 man/L_1way_ANOVA.Rd | 198 +++++++++++++++++----------------- man/L_2way_Factorial_ANOVA.Rd | 242 +++++++++++++++++++++--------------------- man/L_OR.Rd | 198 +++++++++++++++++----------------- man/L_RR.Rd | 200 +++++++++++++++++----------------- man/L_corr.Rd | 164 ++++++++++++++-------------- man/L_efficacy.Rd | 174 +++++++++++++++--------------- man/L_logistic_regress.Rd | 146 ++++++++++++------------- 10 files changed, 675 insertions(+), 675 deletions(-)
Title: Memory-Efficient Storage of Large Data on Disk and Fast Access
Functions
Description: The ff package provides data structures that are stored on
disk but behave (almost) as if they were in RAM by transparently
mapping only a section (pagesize) in main memory - the effective
virtual memory consumption per ff object. ff supports R's standard
atomic data types 'double', 'logical', 'raw' and 'integer' and
non-standard atomic types boolean (1 bit), quad (2 bit unsigned),
nibble (4 bit unsigned), byte (1 byte signed with NAs), ubyte (1 byte
unsigned), short (2 byte signed with NAs), ushort (2 byte unsigned),
single (4 byte float with NAs). For example 'quad' allows efficient
storage of genomic data as an 'A','T','G','C' factor. The unsigned
types support 'circular' arithmetic. There is also support for
close-to-atomic types 'factor', 'ordered', 'POSIXct', 'Date' and
custom close-to-atomic types.
ff not only has native C-support for vectors, matrices and arrays
with flexible dimorder (major column-order, major row-order and
generalizations for arrays). There is also a ffdf class not unlike
data.frames and import/export filters for csv files.
ff objects store raw data in binary flat files in native encoding,
and complement this with metadata stored in R as physical and virtual
attributes. ff objects have well-defined hybrid copying semantics,
which gives rise to certain performance improvements through
virtualization. ff objects can be stored and reopened across R
sessions. ff files can be shared by multiple ff R objects
(using different data en/de-coding schemes) in the same process
or from multiple R processes to exploit parallelism. A wide choice of
finalizer options allows to work with 'permanent' files as well as
creating/removing 'temporary' ff files completely transparent to the
user. On certain OS/Filesystem combinations, creating the ff files
works without notable delay thanks to using sparse file allocation.
Several access optimization techniques such as Hybrid Index
Preprocessing and Virtualization are implemented to achieve good
performance even with large datasets, for example virtual matrix
transpose without touching a single byte on disk. Further, to reduce
disk I/O, 'logicals' and non-standard data types get stored native and
compact on binary flat files i.e. logicals take up exactly 2 bits to
represent TRUE, FALSE and NA.
Beyond basic access functions, the ff package also provides
compatibility functions that facilitate writing code for ff and ram
objects and support for batch processing on ff objects (e.g. as.ram,
as.ff, ffapply). ff interfaces closely with functionality from package
'bit': chunked looping, fast bit operations and coercions between
different objects that can store subscript information ('bit',
'bitwhich', ff 'boolean', ri range index, hi hybrid index). This allows
to work interactively with selections of large datasets and quickly
modify selection criteria.
Further high-performance enhancements can be made available upon request.
Author: Daniel Adler [aut],
Christian Gläser [aut],
Oleg Nenadic [aut],
Jens Oehlschlägel [aut, cre],
Martijn Schuemie [aut],
Walter Zucchini [aut]
Maintainer: Jens Oehlschlägel <Jens.Oehlschlaegel@truecluster.com>
Diff between ff versions 4.0.4 dated 2020-10-13 and 4.0.5 dated 2021-10-29
DESCRIPTION | 8 +- MD5 | 18 ++--- NAMESPACE | 18 +++-- NEWS | 15 ++++ R/ff.R | 124 ++++++++++++++++++------------------- R/generics.R | 3 R/zzz.R | 26 +------ man/ff.rd | 2 tests/testthat/test-zeroRows.R | 47 +++++++------- tests/testthat/test-zero_lengths.R | 6 - 10 files changed, 135 insertions(+), 132 deletions(-)
Title: Data Mining and R Programming for Beginners
Description: Contains functions to simplify the use of data mining methods (classification, regression, clustering, etc.), for students and beginners in R programming. Various R packages are used and wrappers are built around the main functions, to standardize the use of data mining methods (input/output): it brings a certain loss of flexibility, but also a gain of simplicity. The package name came from the French "Fouille de Données en Master 2 Informatique Décisionnelle".
Author: Alexandre Blansché [aut, cre]
Maintainer: Alexandre Blansché <alexandre.blansche@univ-lorraine.fr>
Diff between fdm2id versions 0.9.5 dated 2021-01-04 and 0.9.6 dated 2021-10-29
DESCRIPTION | 6 +++--- MD5 | 24 ++++++++++++------------ NAMESPACE | 2 +- R/clustering.R | 6 +++--- R/dataset.R | 4 ++-- R/misc.R | 3 +++ R/regression.R | 21 +++++++++++++++------ R/text.R | 36 ++++++++++++++++++++++++++++-------- man/cookplot.Rd | 4 +++- man/data.diag.Rd | 5 ++--- man/leverageplot.Rd | 4 +++- man/loadtext.Rd | 12 +++++++++++- man/resplot.Rd | 4 +++- 13 files changed, 89 insertions(+), 42 deletions(-)
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 'spcss'.
Powerful features include table of contents floating as a sidebar,
folding codes and results, and more.
Author: Atsushi Yasumoto [aut, cph, cre]
(<https://orcid.org/0000-0002-8335-495X>),
Angelos Chalaris [aut] (mini.css),
Susam Pal [aut] (spcss),
Mitesh Shah [aut] (sakura),
Kognise [aut] (Water.css)
Maintainer: Atsushi Yasumoto <atusy.rpkg@gmail.com>
Diff between minidown versions 0.2.0 dated 2021-09-06 and 0.3.0 dated 2021-10-29
DESCRIPTION | 6 ++-- MD5 | 14 +++++------ NEWS.md | 6 ++++ R/mini-document.R | 16 ++++++++++-- R/spec-dependencies.R | 29 ++++++++++++----------- inst/doc/Writing-vignettes-with-minidown.html | 6 ++-- inst/rmarkdown/html/highlightToC/highlightToC.js | 2 - man/mini_document.Rd | 7 +++-- 8 files changed, 53 insertions(+), 33 deletions(-)
Title: Download Data from Bank of Spain
Description: Tools to download data series from 'Banco de España' ('BdE')
on 'tibble' format. 'Banco de España' is the national central bank
and, within the framework of the Single Supervisory Mechanism ('SSM'),
the supervisor of the Spanish banking system along with the European
Central Bank. This package is in no way sponsored endorsed or
administered by 'Banco de España'.
Author: Diego H. Herrero [aut, cre, cph]
(<https://orcid.org/0000-0001-8457-4658>, rOpenSpain)
Maintainer: Diego H. Herrero <dev.dieghernan@gmail.com>
Diff between tidyBdE versions 0.2.1 dated 2021-10-07 and 0.2.2 dated 2021-10-29
tidyBdE-0.2.1/tidyBdE/inst/doc/tidyBdE.R |only tidyBdE-0.2.2/tidyBdE/DESCRIPTION | 6 - tidyBdE-0.2.2/tidyBdE/MD5 | 33 +++-- tidyBdE-0.2.2/tidyBdE/NEWS.md | 84 +++++++++------ tidyBdE-0.2.2/tidyBdE/R/bde_check_access.R |only tidyBdE-0.2.2/tidyBdE/R/bde_pals.R | 6 - tidyBdE-0.2.2/tidyBdE/R/catalogs.R | 23 ++-- tidyBdE-0.2.2/tidyBdE/R/indicators.R | 2 tidyBdE-0.2.2/tidyBdE/R/series.R | 3 tidyBdE-0.2.2/tidyBdE/R/utils.R | 89 +++++----------- tidyBdE-0.2.2/tidyBdE/README.md | 47 +++----- tidyBdE-0.2.2/tidyBdE/build/vignette.rds |binary tidyBdE-0.2.2/tidyBdE/man/bde_catalog_load.Rd | 21 ++- tidyBdE-0.2.2/tidyBdE/man/bde_check_access.Rd | 2 tidyBdE-0.2.2/tidyBdE/man/bde_parse_dates.Rd | 20 ++- tidyBdE-0.2.2/tidyBdE/tests/testthat/test-catalogs.R | 27 +--- tidyBdE-0.2.2/tidyBdE/tests/testthat/test-indicators.R | 31 ++++- tidyBdE-0.2.2/tidyBdE/tests/testthat/test-parse_dates.R |only tidyBdE-0.2.2/tidyBdE/tests/testthat/test-series.R | 2 19 files changed, 207 insertions(+), 189 deletions(-)
Title: Bioinformatics Analysis of T-Cell and B-Cell Immune Repertoires
Description: A comprehensive framework for bioinformatics exploratory analysis of bulk and single-cell
T-cell receptor and antibody repertoires. It provides seamless data loading, analysis and
visualisation for AIRR (Adaptive Immune Receptor Repertoire) data, both bulk immunosequencing (RepSeq)
and single-cell sequencing (scRNAseq). It implements most of the widely used AIRR analysis methods,
such as: clonality analysis, estimation of repertoire similarities in distribution of clonotypes
and gene segments, repertoire diversity analysis, annotation of clonotypes using external immune receptor
databases and clonotype tracking in vaccination and cancer studies. A successor to our
previously published 'tcR' immunoinformatics package (Nazarov 2015) <doi:10.1186/s12859-015-0613-1>.
Author: Vadim I. Nazarov [aut, cre],
Vasily O. Tsvetkov [aut],
Eugene Rumynskiy [aut],
Aleksandr A. Popov [aut],
Ivan Balashov [aut],
Anna Lorenc [ctb],
Daniel J. Moore [ctb],
Victor Greiff [ctb],
ImmunoMind [cph, fnd]
Maintainer: Vadim I. Nazarov <support@immunomind.io>
Diff between immunarch versions 0.6.6 dated 2021-07-07 and 0.6.7 dated 2021-10-29
DESCRIPTION | 38 ++-- MD5 | 102 ++++++------ NAMESPACE | 11 + R/RcppExports.R | 5 R/diversity.R | 6 R/dynamics.R | 4 R/explore.R | 6 R/filters.R |only R/gene_usage.R | 3 R/immunr_data_format.R | 4 R/io-parsers.R | 261 +++++++++++++++++++++++-------- R/io-savers.R | 6 R/io-utility.R | 90 +++++++++- R/io.R | 26 +-- R/overlap.R | 11 - R/public.R | 33 ++- R/shiny.R | 12 - R/singlecell.R | 8 R/spectratyping.R | 2 R/tools.R | 14 + R/vis.R | 59 +++---- README.md | 6 inst/doc/v1_introduction.Rmd | 30 +-- inst/doc/v1_introduction.html | 15 - inst/doc/v2_data.Rmd | 10 - inst/doc/v2_data.html | 26 +-- man/inc_overlap.Rd | 1 man/pubRep.Rd | 2 man/pubRepApply.Rd | 2 man/pubRepFilter.Rd | 2 man/pubRepStatistics.Rd | 2 man/public_matrix.Rd | 2 man/repFilter.Rd |only man/repOverlap.Rd | 8 man/repSave.Rd | 2 man/spectratype.Rd | 2 man/vis.immunr_clonal_prop.Rd | 2 man/vis_heatmap2.Rd | 10 - src/RcppExports.cpp | 5 vignettes/v1_introduction.Rmd | 30 +-- vignettes/v2_data.Rmd | 10 - vignettes/web_only/load_10x.Rmd | 22 +- vignettes/web_only/load_mixcr.Rmd | 44 ++--- vignettes/web_only/v10_prop.Rmd | 4 vignettes/web_only/v11_db.Rmd | 10 - vignettes/web_only/v21_singlecell.Rmd | 5 vignettes/web_only/v3_basic_analysis.Rmd | 6 vignettes/web_only/v4_overlap.Rmd | 6 vignettes/web_only/v5_gene_usage.Rmd | 4 vignettes/web_only/v6_diversity.Rmd | 4 vignettes/web_only/v7_fixvis.Rmd | 4 vignettes/web_only/v8_tracking.Rmd | 8 vignettes/web_only/v9_kmers.Rmd | 6 53 files changed, 608 insertions(+), 383 deletions(-)
Title: Kernel k Nearest Neighbors
Description: Extends the simple k-nearest neighbors algorithm by incorporating numerous kernel functions and a variety of distance metrics. The package takes advantage of 'RcppArmadillo' to speed up the calculation of distances between observations.
Author: Lampros Mouselimis [aut, cre] (<https://orcid.org/0000-0002-8024-1546>),
Matthew Parks [ctb] (Github Contributor)
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>
Diff between KernelKnn versions 1.1.3 dated 2021-09-29 and 1.1.4 dated 2021-10-29
DESCRIPTION | 15 - MD5 | 18 - NEWS.md | 5 R/dist_kernelknn.R | 19 - R/kernelknn.R | 38 +-- README.md | 3 build/vignette.rds |binary inst/doc/binary_classification_using_the_ionosphere_data.html | 102 +++++++--- inst/doc/image_classification_using_MNIST_CIFAR_data.html | 4 inst/doc/regression_using_the_housing_data.html | 4 10 files changed, 132 insertions(+), 76 deletions(-)
Title: Programming with Big Data -- Interface to 'ZeroMQ'
Description: 'ZeroMQ' is a well-known library for high-performance
asynchronous messaging in scalable, distributed applications. This
package provides high level R wrapper functions to easily utilize
'ZeroMQ'. We mainly focus on interactive client/server programming
frameworks. For convenience, a minimal 'ZeroMQ' library (4.2.2)
is shipped with 'pbdZMQ', which can be used if no system installation
of 'ZeroMQ' is available. A few wrapper functions compatible with
'rzmq' are also provided.
Author: Wei-Chen Chen [aut, cre],
Drew Schmidt [aut],
Christian Heckendorf [aut] (file transfer),
George Ostrouchov [aut] (Mac OSX),
Whit Armstrong [ctb] (some functions are modified from the rzmq package
for backwards compatibility),
Brian Ripley [ctb] (C code of shellexec, and Solaris),
R Core team [ctb] (some functions are modified from the R source code),
Philipp A. [ctb] (Fedora),
Elliott Sales de Andrade [ctb] (sprintf),
Spencer Aiello [ctb] (windows conf),
Paul Andrey [ctb] (Mac OSX conf),
Panagiotis Cheilaris [ctb] (add serialize version)
Maintainer: Wei-Chen Chen <wccsnow@gmail.com>
Diff between pbdZMQ versions 0.3-5 dated 2021-02-10 and 0.3-6 dated 2021-10-29
ChangeLog | 13 +++++++ DESCRIPTION | 9 ++-- MD5 | 20 +++++----- R/111_control.r | 91 +++++++++++++++++++++++++++++++++++++++++++++++-- R/get_conf_zmq.r | 35 +++++++++++++++++- configure | 77 ++++++++++++++++++++++++++++++++++++++++- configure.ac | 22 ++++++++--- man/zz_zmq_control.Rd | 45 +++++++++++++++++++++++- src/Makevars.in | 1 tests/send_recv.R | 33 +++++++++++++---- tests/send_recv_rzmq.R | 27 ++++++++++---- 11 files changed, 328 insertions(+), 45 deletions(-)
Title: Process GPX Files into R Data Structures
Description: Process open standard GPX files into data.frames for further use and analysis in R.
Author: Mark Ewing [aut, cre]
Maintainer: Mark Ewing <b.mark@ewingsonline.com>
Diff between gpx versions 1.0.0 dated 2021-10-25 and 1.0.1 dated 2021-10-29
gpx-1.0.0/gpx/tests/testthat/test-bayes.R |only gpx-1.0.0/gpx/tests/testthat/test-beauty.R |only gpx-1.0.0/gpx/tests/testthat/test-cotswold.R |only gpx-1.0.0/gpx/tests/testthat/test-cranberry.R |only gpx-1.0.0/gpx/tests/testthat/test-greasy.R |only gpx-1.0.0/gpx/tests/testthat/test-palmetto.R |only gpx-1.0.0/gpx/tests/testthat/test-salins.R |only gpx-1.0.1/gpx/DESCRIPTION | 8 +- gpx-1.0.1/gpx/MD5 | 20 ++---- gpx-1.0.1/gpx/NEWS.md | 5 - gpx-1.0.1/gpx/R/helpers.R | 81 +++++++++++++++----------- gpx-1.0.1/gpx/R/read_gpx.R | 6 - gpx-1.0.1/gpx/README.md | 2 gpx-1.0.1/gpx/tests/testthat/test-files.R |only gpx-1.0.1/gpx/tests/testthat/test-gpx.R | 10 +-- 15 files changed, 73 insertions(+), 59 deletions(-)
Title: A Collection of R Functions for Directional Data Analysis
Description: A collection of functions for directional data (including massive data, with millions of observations) analysis. Hypothesis testing, discriminant and regression analysis, MLE of distributions and more are included. The standard textbook for such data is the "Directional Statistics" by Mardia, K. V. and Jupp, P. E. (2000). Other references include a) Phillip J. Paine, Simon P. Preston Michail Tsagris and Andrew T. A. Wood (2018). An elliptically symmetric angular Gaussian distribution. Statistics and Computing 28(3): 689-697. <doi:10.1007/s11222-017-9756-4>. b) Tsagris M. and Alenazi A. (2019). Comparison of discriminant analysis methods on the sphere. Communications in Statistics: Case Studies, Data Analysis and Applications 5(4):467--491. <doi:10.1080/23737484.2019.1684854>. c) P. J. Paine, S. P. Preston, M. Tsagris and Andrew T. A. Wood (2020). Spherical regression models with general covariates and anisotropic errors. Statistics and Computing 30(1): 153--165. <doi:10.1007/s11222-019-09872-2>.
Author: Michail Tsagris, Giorgos Athineou, Christos Adam, Anamul Sajib, Eli Amson, Micah J. Waldstein
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between Directional versions 5.0 dated 2021-05-26 and 5.1 dated 2021-10-29
DESCRIPTION | 15 ++++++++------- MD5 | 18 +++++++++++++----- NAMESPACE | 6 ++++++ R/africa.R |only R/asia.R |only R/europe.R |only R/hclr.boot.R | 4 ++-- R/hclr.perm.R | 2 -- R/north.america.R |only R/oceania.R |only R/south.america.R |only R/worldmap.R |only man/Directional-package.Rd | 4 ++-- man/oceania.Rd |only 14 files changed, 31 insertions(+), 18 deletions(-)
Title: Construct and Compare scGRN from Single-Cell Transcriptomic Data
Description: A workflow based on machine learning methods to construct and compare single-cell gene regulatory networks (scGRN) using single-cell RNA-seq (scRNA-seq) data collected from different conditions. Uses principal component regression, tensor decomposition, and manifold alignment, to accurately identify even subtly shifted gene expression programs. See <doi:10.1016/j.patter.2020.100139> for more details.
Author: Daniel Osorio [aut, cre] (<https://orcid.org/0000-0003-4424-8422>),
Yan Zhong [aut, ctb],
Guanxun Li [aut, ctb],
Jianhua Huang [aut, ctb],
James Cai [aut, ctb, ths] (<https://orcid.org/0000-0002-8081-6725>)
Maintainer: Daniel Osorio <dcosorioh@utexas.edu>
Diff between scTenifoldNet versions 1.2.4 dated 2020-11-17 and 1.3 dated 2021-10-29
DESCRIPTION | 16 ++++++++-------- MD5 | 24 ++++++++++++------------ NAMESPACE | 2 ++ R/dRegulation.R | 14 +++++++++----- R/makeNetworks.R | 5 +++-- R/manifoldAlignment.R | 8 +++++++- R/pcNet.R | 8 +++++++- R/scTenifoldNet.R | 22 ++++++++++++++-------- README.md | 2 +- man/makeNetworks.Rd | 5 ++++- man/manifoldAlignment.Rd | 4 +++- man/pcNet.Rd | 5 ++++- man/scTenifoldNet.Rd | 8 +++++++- 13 files changed, 81 insertions(+), 42 deletions(-)
Title: R Time Series Intelligent Data Storage
Description: A tool that allows to download and save historical time series data
for future use offline. The intelligent updating functionality will only download
the new available information; thus, saving you time and Internet bandwidth.
It will only re-download the full data-set if any inconsistencies are detected.
This package supports following data provides: 'Yahoo' (<https://finance.yahoo.com>),
'FRED' (<https://fred.stlouisfed.org>), 'Quandl' (<https://data.nasdaq.com>),
'AlphaVantage' (<https://www.alphavantage.co>), 'Tiingo' (<https://www.tiingo.com>).
Author: RTSVizTeam [aut, cph],
Irina Kapler [cre]
Maintainer: Irina Kapler <irkapler@gmail.com>
Diff between rtsdata versions 0.1.2 dated 2020-01-24 and 0.1.3 dated 2021-10-29
DESCRIPTION | 14 +++++++------- MD5 | 22 +++++++++++----------- NAMESPACE | 2 +- NEWS.md | 4 ++++ R/data.r | 7 +++---- R/rtsdata.r | 2 +- R/storage.r | 2 +- R/utils.r | 2 +- README.md | 5 +++-- man/ds.get.url.Rd | 2 +- man/ds.storage.database.Rd | 2 +- man/rtsdata.Rd | 2 +- 12 files changed, 35 insertions(+), 31 deletions(-)
Title: Find Related Items and Lexical Dimensions in a Lexicon
Description: Implements code to identify lexical competitors in a given list
of words. We include many of the standard competitor types used in spoken word
recognition research, such as functions to find cohorts, neighbors, and
rhymes, amongst many others. The package includes documentation for using a
variety of lexicon files, including those with form codes made up of multiple
letters (i.e., phoneme codes) and also basic orthographies. Importantly, the
code makes use of multiple CPU cores and vectorization when possible, making
it extremely fast and able to handle large lexicons. Additionally, the package
contains documentation for users to easily write new functions, allowing
researchers to examine other relationships within a lexicon.
Preprint: <https://psyarxiv.com/8dyru/>. Open access: <https://link.springer.com/epdf/10.3758/s13428-021-01667-6?sharing_token=9WlO9soCc9y0uSuwWSUYfJAH0g46feNdnc402WrhzyrdKcK8uzZx_hDEtgbYzn3gvxdG5Cuj0j0cC4lVMFBqYCGTQmE2blN2Gwo74LJ8ro1pEOAYDRFy6Lhf1nc719vD-zU7GDvKOQxDAwPbrisvPBeXSIu0NkqXF7Jx3IuUwIs%3D>.
Citation: Li, Z., Crinnion, A.M. & Magnuson, J.S. (2021).
<doi:10.3758/s13428-021-01667-6>.
Author: ZhaoBin Li [aut, cre],
Anne Marie Crinnion [aut],
James S. Magnuson [aut, cph]
Maintainer: ZhaoBin Li <bzilplj@gmail.com>
Diff between LexFindR versions 1.0.1 dated 2021-08-21 and 1.0.2 dated 2021-10-29
LexFindR-1.0.1/LexFindR/vignettes/my-vignette_cache/html/parallelize_f8b10b8b3be82e281b148b3e2a0f322a.RData |only LexFindR-1.0.1/LexFindR/vignettes/my-vignette_cache/html/parallelize_f8b10b8b3be82e281b148b3e2a0f322a.rdb |only LexFindR-1.0.1/LexFindR/vignettes/my-vignette_cache/html/parallelize_f8b10b8b3be82e281b148b3e2a0f322a.rdx |only LexFindR-1.0.2/LexFindR/DESCRIPTION | 13 +++-- LexFindR-1.0.2/LexFindR/MD5 | 13 ++--- LexFindR-1.0.2/LexFindR/README.md | 13 ++++- LexFindR-1.0.2/LexFindR/inst/CITATION |only LexFindR-1.0.2/LexFindR/inst/doc/my-vignette.html | 26 +++++----- LexFindR-1.0.2/LexFindR/vignettes/my-vignette_cache/html/parallelize_ea26456423a2aa2d0ecec38fc1cb2f26.RData |only LexFindR-1.0.2/LexFindR/vignettes/my-vignette_cache/html/parallelize_ea26456423a2aa2d0ecec38fc1cb2f26.rdb |only LexFindR-1.0.2/LexFindR/vignettes/my-vignette_cache/html/parallelize_ea26456423a2aa2d0ecec38fc1cb2f26.rdx |only 11 files changed, 40 insertions(+), 25 deletions(-)
Title: Joint Frailty-Copula Models for Tumour Progression and Death in
Meta-Analysis
Description: Fit survival data and perform dynamic prediction under joint frailty-copula models for tumour progression and death.
Likelihood-based methods are employed for estimating model parameters, where the baseline hazard functions are modeled by the cubic M-spline or the Weibull model.
The methods are applicable for meta-analytic data containing individual-patient information from several studies.
Survival outcomes need information on both terminal event time (e.g., time-to-death) and non-terminal event time (e.g., time-to-tumour progression).
Methodologies were published in
Emura et al. (2017) <doi:10.1177/0962280215604510>, Emura et al. (2018) <doi:10.1177/0962280216688032>,
Emura et al. (2020) <doi:10.1177/0962280219892295>, Shinohara et al. (2020) <doi:10.1080/03610918.2020.1855449>,
Wu et al. (2020) <doi:10.1007/s00180-020-00977-1>, and Emura et al. (2021) <doi:10.1177/09622802211046390>.
See also the book of Emura et al. (2019) <doi:10.1007/978-981-13-3516-7>.
Survival data from ovarian cancer patients are also available.
Author: Takeshi Emura
Maintainer: Takeshi Emura <takeshiemura@gmail.com>
Diff between joint.Cox versions 3.14 dated 2021-07-03 and 3.15 dated 2021-10-29
DESCRIPTION | 12 ++++++------ MD5 | 16 ++++++++-------- man/I.spline.Rd | 4 ++-- man/M.spline.Rd | 4 ++-- man/Weibull.simu.Rd | 27 ++++++++++++++++++++------- man/cmprskCox.reg.Rd | 6 +++--- man/condCox.reg.Rd | 32 +++++++++++++++++++++++++++----- man/joint.Cox-package.Rd | 11 +++++++---- man/splineCox.reg.Rd | 8 ++++---- 9 files changed, 79 insertions(+), 41 deletions(-)
Title: Simplify Access to Data from the Amazon Region
Description: Functions to download and treat data regarding the Brazilian Amazon region from a variety of official sources.
Author: DataZoom (PUC-Rio) [aut, cre],
Francisco de Lima Cavalcanti [aut],
Guilherme Jardim [aut],
Daniel AC Barbosa [aut],
Bruno Alcantara Duarte [aut],
Fredie Didier [aut],
Tito Bruni [aut],
Victor Aliende da Matta [aut],
Anna Carolina Dutra Saraiva [aut],
Arthur Carvalho Brito [aut],
Igor Rigolon Veiga [aut],
Maria Mittelbach [aut]
Maintainer: DataZoom (PUC-Rio) <datazoom@econ.puc-rio.br>
Diff between datazoom.amazonia versions 0.1.0 dated 2021-09-07 and 0.2.0 dated 2021-10-29
DESCRIPTION | 10 MD5 | 134 +-- NEWS.md | 85 +- R/IPS.R | 354 +++++----- R/cempre.R | 324 +++++++++ R/comex.R | 612 ++++++++--------- R/degrad.R | 295 ++++---- R/deter.R | 541 ++++++--------- R/dictionary.R | 155 ++++ R/download.R | 1661 ++++++++++++++++++++++++------------------------ R/ibama.R | 248 +++---- R/pam.R | 656 +++++++++--------- R/pevs.R | 666 +++++++++---------- R/pibmunic.R | 136 +++ R/ppm.R | 948 +++++++++++++-------------- R/prodes.R | 391 +++++------ R/seeg.R | 1411 ++++++++++++++++++++++++++++++++++++++++ R/sigmine.R | 288 +++----- README.md | 147 ++-- inst/doc/CEMPRE.R | 29 inst/doc/CEMPRE.Rmd | 29 inst/doc/CEMPRE.html | 29 inst/doc/COMEX.Rmd | 84 +- inst/doc/DEGRAD.R | 13 inst/doc/DEGRAD.Rmd | 85 +- inst/doc/DEGRAD.html | 17 inst/doc/DETER.R | 11 inst/doc/DETER.Rmd | 69 + inst/doc/DETER.html | 14 inst/doc/IBAMA.R | 13 inst/doc/IBAMA.Rmd | 73 +- inst/doc/IBAMA.html | 13 inst/doc/IPS.R | 9 inst/doc/IPS.Rmd | 73 +- inst/doc/IPS.html | 9 inst/doc/MAPBIOMAS.Rmd | 56 - inst/doc/PAM.Rmd | 88 +- inst/doc/PEVS.Rmd | 98 +- inst/doc/PIBMUNIC.R | 23 inst/doc/PIBMUNIC.Rmd | 84 +- inst/doc/PIBMUNIC.html | 23 inst/doc/PPM.Rmd | 72 +- inst/doc/PRODES.R | 15 inst/doc/PRODES.Rmd | 81 +- inst/doc/PRODES.html | 15 inst/doc/SEEG.R | 19 inst/doc/SEEG.Rmd | 93 +- inst/doc/SEEG.html | 25 inst/doc/SIGMINE.R | 10 inst/doc/SIGMINE.Rmd | 68 + inst/doc/SIGMINE.html | 10 man/load_degrad.Rd | 18 man/load_deter.Rd | 18 man/load_seeg.Rd | 6 vignettes/CEMPRE.Rmd | 29 vignettes/COMEX.Rmd | 84 +- vignettes/DEGRAD.Rmd | 85 +- vignettes/DETER.Rmd | 69 + vignettes/IBAMA.Rmd | 73 +- vignettes/IPS.Rmd | 73 +- vignettes/MAPBIOMAS.Rmd | 56 - vignettes/PAM.Rmd | 88 +- vignettes/PEVS.Rmd | 98 +- vignettes/PIBMUNIC.Rmd | 84 +- vignettes/PPM.Rmd | 72 +- vignettes/PRODES.Rmd | 81 +- vignettes/SEEG.Rmd | 93 +- vignettes/SIGMINE.Rmd | 68 + 68 files changed, 6874 insertions(+), 4633 deletions(-)
More information about datazoom.amazonia at CRAN
Permanent link
Title: Date-Time Types and Tools
Description: Provides a comprehensive library for date-time manipulations
using a new family of orthogonal date-time classes (durations, time
points, zoned-times, and calendars) that partition responsibilities so
that the complexities of time zones are only considered when they are
really needed. Capabilities include: date-time parsing, formatting,
arithmetic, extraction and updating of components, and rounding.
Author: Davis Vaughan [aut, cre],
RStudio [cph, fnd]
Maintainer: Davis Vaughan <davis@rstudio.com>
Diff between clock versions 0.4.1 dated 2021-09-21 and 0.5.0 dated 2021-10-29
clock-0.4.1/clock/man/sys_time_parse.Rd |only clock-0.5.0/clock/DESCRIPTION | 10 clock-0.5.0/clock/MD5 | 126 +-- clock-0.5.0/clock/NAMESPACE | 2 clock-0.5.0/clock/NEWS.md | 57 + clock-0.5.0/clock/R/date.R | 26 clock-0.5.0/clock/R/gregorian-year-month-day.R | 15 clock-0.5.0/clock/R/naive-time.R | 11 clock-0.5.0/clock/R/posixt.R | 110 ++ clock-0.5.0/clock/R/sys-time.R | 136 +++ clock-0.5.0/clock/R/time-point.R | 12 clock-0.5.0/clock/R/zoned-time.R | 31 clock-0.5.0/clock/README.md | 2 clock-0.5.0/clock/build/vignette.rds |binary clock-0.5.0/clock/inst/doc/clock.R | 16 clock-0.5.0/clock/inst/doc/clock.Rmd | 47 + clock-0.5.0/clock/inst/doc/clock.html | 409 +++++----- clock-0.5.0/clock/inst/doc/faq.R | 4 clock-0.5.0/clock/inst/doc/faq.Rmd | 4 clock-0.5.0/clock/inst/doc/faq.html | 36 clock-0.5.0/clock/inst/doc/recipes.R | 8 clock-0.5.0/clock/inst/doc/recipes.Rmd | 8 clock-0.5.0/clock/inst/doc/recipes.html | 58 - clock-0.5.0/clock/man/clock-package.Rd | 7 clock-0.5.0/clock/man/date-time-parse.Rd | 97 ++ clock-0.5.0/clock/man/date_parse.Rd | 25 clock-0.5.0/clock/man/format.clock_zoned_time.Rd | 7 clock-0.5.0/clock/man/naive_time_parse.Rd | 11 clock-0.5.0/clock/man/posixt-formatting.Rd | 11 clock-0.5.0/clock/man/sys-parsing.Rd |only clock-0.5.0/clock/man/year_month_day_parse.Rd | 9 clock-0.5.0/clock/man/zoned-parsing.Rd | 20 clock-0.5.0/clock/src/calendar.h | 3 clock-0.5.0/clock/src/cpp11.cpp | 129 --- clock-0.5.0/clock/src/duration.cpp | 3 clock-0.5.0/clock/src/format.cpp | 27 clock-0.5.0/clock/src/gregorian-year-day.h | 2 clock-0.5.0/clock/src/gregorian-year-month-day.h | 2 clock-0.5.0/clock/src/gregorian-year-month-weekday.h | 2 clock-0.5.0/clock/src/iso-year-week-day.h | 2 clock-0.5.0/clock/src/parse.h | 12 clock-0.5.0/clock/src/quarterly-year-quarter-day.h | 2 clock-0.5.0/clock/src/sys-time.cpp | 3 clock-0.5.0/clock/tests/testthat/_snaps/gregorian-year-day.md | 28 clock-0.5.0/clock/tests/testthat/_snaps/gregorian-year-month-day.md | 28 clock-0.5.0/clock/tests/testthat/_snaps/gregorian-year-month-weekday.md | 28 clock-0.5.0/clock/tests/testthat/_snaps/iso-year-week-day.md | 28 clock-0.5.0/clock/tests/testthat/_snaps/naive-time.md | 7 clock-0.5.0/clock/tests/testthat/_snaps/posixt.md | 7 clock-0.5.0/clock/tests/testthat/_snaps/quarterly-year-quarter-day.md | 28 clock-0.5.0/clock/tests/testthat/_snaps/sys-time.md | 55 + clock-0.5.0/clock/tests/testthat/_snaps/zoned-time.md | 38 clock-0.5.0/clock/tests/testthat/test-date.R | 8 clock-0.5.0/clock/tests/testthat/test-gregorian-year-day.R | 10 clock-0.5.0/clock/tests/testthat/test-gregorian-year-month-day.R | 16 clock-0.5.0/clock/tests/testthat/test-gregorian-year-month-weekday.R | 10 clock-0.5.0/clock/tests/testthat/test-iso-year-week-day.R | 10 clock-0.5.0/clock/tests/testthat/test-naive-time.R | 22 clock-0.5.0/clock/tests/testthat/test-posixt.R | 58 + clock-0.5.0/clock/tests/testthat/test-quarterly-year-quarter-day.R | 10 clock-0.5.0/clock/tests/testthat/test-sys-time.R | 89 ++ clock-0.5.0/clock/tests/testthat/test-zoned-time.R | 42 - clock-0.5.0/clock/vignettes/clock.Rmd | 47 + clock-0.5.0/clock/vignettes/faq.Rmd | 4 clock-0.5.0/clock/vignettes/recipes.Rmd | 8 65 files changed, 1417 insertions(+), 666 deletions(-)
Title: Extract, Analyze and Visualize Mutational Signatures for Genomic
Variations
Description: Genomic alterations including single nucleotide
substitution, copy number alteration, etc. are the major force for
cancer initialization and development. Due to the specificity of
molecular lesions caused by genomic alterations, we can generate
characteristic alteration spectra, called 'signature' (Wang, Shixiang,
et al. (2020) <DOI:10.1371/journal.pgen.1009557> & Alexandrov, Ludmil
B., et al. (2020) <DOI:10.1038/s41586-020-1943-3>). This package helps
users to extract, analyze and visualize signatures from genomic
alteration records, thus providing new insight into cancer study.
Author: Shixiang Wang [aut, cre] (<https://orcid.org/0000-0001-9855-7357>),
Ziyu Tao [aut] (<https://orcid.org/0000-0003-3272-1227>),
Huimin Li [aut] (<https://orcid.org/0000-0003-1683-9057>),
Tao Wu [aut] (<https://orcid.org/0000-0002-8999-9628>),
Xue-Song Liu [aut, ctb] (<https://orcid.org/0000-0002-7736-0077>),
Anand Mayakonda [ctb]
Maintainer: Shixiang Wang <w_shixiang@163.com>
Diff between sigminer versions 2.1.0 dated 2021-09-22 and 2.1.1 dated 2021-10-29
sigminer-2.1.0/sigminer/inst/extdata/human_hg19_gene_info.rds |only sigminer-2.1.0/sigminer/inst/extdata/mouse_mm9_gene_info.rds |only sigminer-2.1.1/sigminer/DESCRIPTION | 6 sigminer-2.1.1/sigminer/MD5 | 24 +-- sigminer-2.1.1/sigminer/NEWS.md | 8 - sigminer-2.1.1/sigminer/R/get_genome_annotation.R | 8 - sigminer-2.1.1/sigminer/R/get_pLOH_score.R | 13 + sigminer-2.1.1/sigminer/R/output.R | 76 +++++----- sigminer-2.1.1/sigminer/build/partial.rdb |binary sigminer-2.1.1/sigminer/build/vignette.rds |binary sigminer-2.1.1/sigminer/inst/doc/sigminer.html | 6 sigminer-2.1.1/sigminer/man/output_bootstrap.Rd | 21 ++ sigminer-2.1.1/sigminer/man/output_fit.Rd | 21 ++ sigminer-2.1.1/sigminer/man/output_sig.Rd | 21 ++ 14 files changed, 144 insertions(+), 60 deletions(-)
Title: Time Series Plot
Description: A fast and elegant time series visualization package. In addition to the
standard R plot types, this package supports candle sticks, open-high-low-close, and
volume plots. Useful for visualizing any time series data, e.g., stock prices and
technical indicators.
Author: RTSVizTeam [aut, cph],
Irina Kapler [cre]
Maintainer: Irina Kapler <irkapler@gmail.com>
Diff between rtsplot versions 0.1.3 dated 2020-03-29 and 0.1.4 dated 2021-10-29
DESCRIPTION | 11 - MD5 | 56 ++++----- NAMESPACE | 3 NEWS.md | 4 R/rtsplot.r | 55 ++++++++ README.md | 203 +++++++++++++++++--------------- man/Colors.Rd | 38 +++--- man/Themes.Rd | 112 +++++++++--------- man/figures |only man/rtsplot.Rd | 255 ++++++++++++++++++++--------------------- man/rtsplot.candle.Rd | 72 +++++------ man/rtsplot.corner.label.Rd | 108 ++++++++--------- man/rtsplot.fake.stock.data.Rd | 94 +++++++-------- man/rtsplot.format.Rd | 46 +++---- man/rtsplot.grid.Rd | 42 +++--- man/rtsplot.hl.Rd | 64 +++++----- man/rtsplot.layout.Rd | 36 ++--- man/rtsplot.legend.Rd | 112 +++++++++--------- man/rtsplot.lines.Rd | 74 +++++------ man/rtsplot.matplot.Rd | 68 +++++----- man/rtsplot.ohlc.Rd | 64 +++++----- man/rtsplot.polygon.Rd |only man/rtsplot.scale.volume.Rd | 32 ++--- man/rtsplot.stacked.Rd | 74 +++++------ man/rtsplot.text.Rd | 60 ++++----- man/rtsplot.volume.Rd | 48 +++---- man/rtsplot.x.highlight.Rd | 42 +++--- man/rtsplot.y.highlight.Rd | 86 ++++++------- man/rtsplot2Y.Rd | 100 ++++++++-------- 29 files changed, 1021 insertions(+), 938 deletions(-)
Title: Quantal Response Analysis for Dose-Mortality Data
Description: Functions are provided that implement the
use of the Fieller's formula methodology, for
calculating a confidence interval for a ratio of
(commonly, correlated) means. See Fieller (1954)
<doi:10.1111/j.2517-6161.1954.tb00159.x>. Here,
the application of primary interest is to studies
of insect mortality response to increasing doses
of a fumigant, or, e.g., to time in coolstorage.
The formula is used to calculate a confidence
interval for the dose or time required to achieve
a specified mortality proportion, commonly 0.5
or 0.99. Vignettes demonstrate link functions
that may be considered, checks on fitted models,
and alternative choices of error family. Note
in particular the betabinomial error family.
See also Maindonald, Waddell, and Petry (2001)
<doi:10.1016/S0925-5214(01)00082-5>.
Author: John Maindonald [aut, cre] (<https://orcid.org/0000-0002-0106-9224>)
Maintainer: John Maindonald <john@statsresearch.co.nz>
Diff between qra versions 0.2.6 dated 2021-10-17 and 0.2.7 dated 2021-10-29
DESCRIPTION | 17 ++-- MD5 | 31 ++++---- R/Untitled.R |only R/getRho.R | 20 ++++- build/vignette.rds |binary inst/doc/MeBrPlot.html | 4 - inst/doc/countDists.R | 36 +++------- inst/doc/countDists.Rmd | 61 ++++++++--------- inst/doc/countDists.html | 157 ++++++++++++++++++++++---------------------- inst/doc/timeMortality.R | 2 inst/doc/timeMortality.Rmd | 70 ------------------- inst/doc/timeMortality.html | 88 +++--------------------- man/getRho.Rd | 20 ++++- vignettes/countDists.Rmd | 61 ++++++++--------- vignettes/discrete-code.R | 11 --- vignettes/qra.bib | 18 ++--- vignettes/timeMortality.Rmd | 70 ------------------- 17 files changed, 238 insertions(+), 428 deletions(-)
Title: Quiver Plots for 'ggplot2'
Description: An extension of 'ggplot2' to provide quiver plots to visualise vector fields.
This functionality is implemented using a geom to produce a new graphical layer, which
allows aesthetic options. This layer can be overlaid on a map to improve visualisation
of mapped data.
Author: Mitchell O'Hara-Wild [aut, cre]
Maintainer: Mitchell O'Hara-Wild <mail@mitchelloharawild.com>
Diff between ggquiver versions 0.2.0 dated 2019-02-05 and 0.3.0 dated 2021-10-29
ggquiver-0.2.0/ggquiver/man/reexports.Rd |only ggquiver-0.3.0/ggquiver/DESCRIPTION | 16 +-- ggquiver-0.3.0/ggquiver/MD5 | 27 ++--- ggquiver-0.3.0/ggquiver/NAMESPACE | 4 ggquiver-0.3.0/ggquiver/NEWS.md | 5 ggquiver-0.3.0/ggquiver/R/geom-quiver.r | 27 ++--- ggquiver-0.3.0/ggquiver/R/ggquiver.R | 4 ggquiver-0.3.0/ggquiver/R/stat-quiver.r | 25 +--- ggquiver-0.3.0/ggquiver/README.md | 34 +++--- ggquiver-0.3.0/ggquiver/man/figures/README-quiverplot-1.png |binary ggquiver-0.3.0/ggquiver/man/figures/README-sealplot-1.png |binary ggquiver-0.3.0/ggquiver/man/figures/README-windplot-1.png |binary ggquiver-0.3.0/ggquiver/man/geom_quiver.Rd | 64 ++++++++---- ggquiver-0.3.0/ggquiver/man/ggquiver-package.Rd | 5 ggquiver-0.3.0/ggquiver/tests/testthat/test-geom_quiver.R | 2 15 files changed, 112 insertions(+), 101 deletions(-)