Title: Diverse Cluster Ensemble in R
Description: Performs cluster analysis using an ensemble
clustering framework, Chiu & Talhouk (2018)
<doi:10.1186/s12859-017-1996-y>. Results from a diverse set of
algorithms are pooled together using methods such as majority voting,
K-Modes, LinkCluE, and CSPA. There are options to compare cluster
assignments across algorithms using internal and external indices,
visualizations such as heatmaps, and significance testing for the
existence of clusters.
Author: Derek Chiu [aut, cre],
Aline Talhouk [aut],
Johnson Liu [ctb, com]
Maintainer: Derek Chiu <dchiu@bccrc.ca>
Diff between diceR versions 1.2.0 dated 2022-05-13 and 1.2.1 dated 2022-08-16
DESCRIPTION | 12 LICENSE | 4 MD5 | 139 +- NAMESPACE | 76 - NEWS.md | 354 ++--- R/PAC.R | 90 - R/RcppExports.R | 22 R/algorithms.R | 426 +++--- R/consensus_cluster.R | 660 ++++----- R/consensus_combine.R | 110 - R/consensus_evaluate.R | 712 +++++----- R/consensus_funs.R | 360 ++--- R/consensus_matrix.R | 100 - R/data.R | 20 R/dice.R | 274 ++-- R/diceR-package.R | 18 R/external_validity.R | 144 +- R/graphs.R | 474 +++--- R/impute.R | 166 +- R/pcn.R | 146 +- R/prepare_data.R | 140 +- R/sigclust.R | 244 +-- R/similarity.R | 376 ++--- R/utils.R | 266 +-- R/zzz.R | 8 README.md | 214 +-- build/partial.rdb |only build/vignette.rds |binary inst/doc/overview.R | 200 +- inst/doc/overview.Rmd | 534 +++---- inst/doc/overview.html | 2187 ++++++++++++++++---------------- man/CSPA.Rd | 81 - man/LCA.Rd | 90 - man/LCE.Rd | 102 - man/PAC.Rd | 102 - man/compactness.Rd | 78 - man/consensus_cluster.Rd | 340 ++-- man/consensus_combine.Rd | 96 - man/consensus_evaluate.Rd | 194 +- man/consensus_matrix.Rd | 106 - man/dice.Rd | 272 +-- man/diceR-package.Rd | 72 - man/external_validity.Rd | 142 +- man/graphs.Rd | 166 +- man/hgsc.Rd | 40 man/impute_knn.Rd | 84 - man/impute_missing.Rd | 110 - man/k_modes.Rd | 103 - man/majority_voting.Rd | 92 - man/min_fnorm.Rd | 78 - man/pcn.Rd | 106 - man/prepare_data.Rd | 104 - man/relabel_class.Rd | 58 man/sigclust.Rd | 120 - man/similarity.Rd | 90 - tests/testthat.R | 8 tests/testthat/test-PAC.R | 22 tests/testthat/test-consensus_cluster.R | 120 - tests/testthat/test-consensus_combine.R | 110 - tests/testthat/test-consensus_funs.R | 110 - tests/testthat/test-consensus_matrix.R | 60 tests/testthat/test-dice.R | 108 - tests/testthat/test-external_validity.R | 26 tests/testthat/test-graphs.R | 110 - tests/testthat/test-impute.R | 52 tests/testthat/test-pcn.R | 22 tests/testthat/test-prepare_data.R | 30 tests/testthat/test-sigclust.R | 54 tests/testthat/test-similarity.R | 90 - tests/testthat/test-utils.R | 64 vignettes/overview.Rmd | 534 +++---- 71 files changed, 6430 insertions(+), 6392 deletions(-)
Title: Mining Association Rules and Frequent Itemsets
Description: Provides the infrastructure for representing, manipulating and analyzing
transaction data and patterns (frequent itemsets and association rules).
Also provides C implementations of the association mining algorithms Apriori and Eclat.
Hahsler, Gruen and Hornik (2005) <doi:10.18637/jss.v014.i15>.
Author: Michael Hahsler [aut, cre, cph]
,
Christian Buchta [aut, cph],
Bettina Gruen [aut, cph],
Kurt Hornik [aut, cph],
Christian Borgelt [ctb, cph],
Ian Johnson [ctb],
Makhlouf Ledmi [ctb]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between arules versions 1.7-3 dated 2022-01-09 and 1.7-4 dated 2022-08-16
DESCRIPTION | 20 +++++---- MD5 | 89 +++++++++++++++++++++---------------------- NEWS.md | 13 +++++- R/Income.R | 4 - R/appearance.R | 6 +- R/control.R | 10 ++-- R/eclat.R | 4 - R/fim4r.R | 28 +++++++------ R/hierarchy.R | 7 +-- R/image.R | 6 +- R/itemMatrix.R | 45 ++++++++++++++------- R/itemsets.R | 4 - R/parameter.R | 10 ++-- R/pmml.R | 2 R/read_write.R | 2 R/rules.R | 6 +- R/setsItemwise.R | 6 +- R/tidLists.R | 16 +++---- R/transactions.R | 51 ++++++++++++++---------- README.md | 35 ++++++++-------- build/partial.rdb |binary build/vignette.rds |binary data/Adult.rda |binary data/AdultUCI.rda |binary data/Epub.rda |binary data/Groceries.rda |binary data/Income.rda |binary data/IncomeESL.rda |binary data/Mushroom.rda |binary data/SunBai.rda |binary inst/doc/arules.pdf |binary man/APappearance-class.Rd | 6 +- man/AScontrol-classes.Rd | 10 ++-- man/ASparameter-classes.Rd | 10 ++-- man/Income.Rd | 3 - man/associations-class.Rd | 20 ++++----- man/c.Rd | 4 - man/figures |only man/fim4r.Rd | 6 +- man/itemMatrix-class.Rd | 68 +++++++++++++++++++------------- man/itemsets-class.Rd | 26 ++++++------ man/pmml.Rd | 2 man/rules-class.Rd | 32 +++++++-------- man/tidLists-class.Rd | 42 ++++++++++---------- man/transactions-class.Rd | 67 +++++++++++++++++--------------- tests/testthat/test-matrix.R | 10 ++-- 46 files changed, 366 insertions(+), 304 deletions(-)
Title: Numerical Estimation of Sparse Hessians
Description: Estimates Hessian of a scalar-valued function, and returns it
in a sparse Matrix format. The sparsity pattern must be known in advance. The
algorithm is especially efficient for hierarchical models with a large number of
heterogeneous units. See Braun, M. (2017) <doi:10.18637/jss.v082.i10>.
Author: Michael Braun [aut, cre, cph]
Maintainer: Michael Braun <braunm@smu.edu>
Diff between sparseHessianFD versions 0.3.3.5 dated 2021-09-24 and 0.3.3.6 dated 2022-08-16
DESCRIPTION | 14 ++++++------- MD5 | 14 ++++++------- NEWS.md | 5 ++++ R/matrices.R | 44 ++++++++++++++++++++--------------------- R/sparseHessianFD.R | 3 +- build/vignette.rds |binary inst/doc/sparseHessianFD.pdf |binary tests/testthat/test_matrices.R | 14 +++++++++---- 8 files changed, 53 insertions(+), 41 deletions(-)
More information about sparseHessianFD at CRAN
Permanent link
Title: Functions and Datasets to Accompany Hollander, Wolfe, and
Chicken - Nonparametric Statistical Methods, Third Edition
Description: Designed to replace the tables which were in the back of the first two editions of Hollander and Wolfe - Nonparametric Statistical Methods. Exact procedures are performed when computationally possible. Monte Carlo and Asymptotic procedures are performed otherwise. For those procedures included in the base packages, our code simply provides a wrapper to standardize the output with the other procedures in the package.
Author: Grant Schneider, Eric Chicken, Rachel Becvarik
Maintainer: Grant Schneider <gschneidz@gmail.com>
Diff between NSM3 versions 1.16 dated 2021-04-06 and 1.17 dated 2022-08-16
DESCRIPTION | 8 +- MD5 | 46 +++++------ R/cAnsBrad.R | 134 +++++++++++++++++----------------- R/cBohnWolfe.R | 94 ++++++++++++------------ R/cDurSkiMa.R | 2 R/cFligPoli.R | 2 R/cFrd.R | 2 R/cHaySton.R | 2 R/cHollBivSym.R | 2 R/cJCK.R | 2 R/cKW.R | 2 R/cKolSmirn.R | 2 R/cLepage.R | 2 R/cMackSkil.R | 2 R/cNDWol.R | 2 R/cNWWM.R | 2 R/cPage.R | 2 R/cSDCFlig.R | 2 R/cSkilMack.R | 2 R/cUmbrPK.R | 2 R/cUmbrPU.R | 2 R/cWNMT.R | 2 R/pWNMT.R | 215 +++++++++++++++++++++++++++++--------------------------- man/pWNMT.Rd | 99 +++++++++++++------------ 24 files changed, 323 insertions(+), 309 deletions(-)
Title: Sieve Analysis Methods for Proportional Hazards Models
Description: Implements semiparametric estimation and testing procedures for a continuous, possibly multivariate, mark-specific hazard ratio (treatment/placebo) of an event of interest in a randomized treatment efficacy trial with a time-to-event endpoint, as described in Juraska M and Gilbert PB (2013), Mark-specific hazard ratio model with multivariate continuous marks: an application to vaccine efficacy. Biometrics 69(2):328 337 <doi:10.1111/biom.12016>, and in Juraska M and Gilbert PB (2016), Mark-specific hazard ratio model with missing multivariate marks. Lifetime Data Analysis 22(4): 606-25 <doi:10.1007/s10985-015-9353-9>. The former considers continuous multivariate marks fully observed in all subjects who experience the event of interest, whereas the latter extends the previous work to allow multivariate marks that are subject to missingness-at-random. For models with missing marks, two estimators are implemented based on (i) inverse probability weighting (IPW) of complete case [...truncated...]
Author: Michal Juraska [aut, cre],
Stephanie Wu [ctb]
Maintainer: Michal Juraska <mjuraska@fredhutch.org>
Diff between sievePH versions 1.0.1 dated 2019-12-06 and 1.0.3 dated 2022-08-16
DESCRIPTION | 11 +++++------ MD5 | 22 +++++++++++----------- NAMESPACE | 2 +- NEWS |binary R/plot.summary.sievePH.R | 6 +++--- R/sievePH.R | 6 ++++-- R/sievePHaipw.R | 13 +++++++------ R/sievePHipw.R | 13 +++++++------ README.md | 2 +- man/sievePH.Rd | 4 +++- man/sievePHaipw.Rd | 6 ++++-- man/sievePHipw.Rd | 15 ++++++++++++--- 12 files changed, 58 insertions(+), 42 deletions(-)
Title: Utilities for Scoring and Assessing Predictions
Description: Provides a collection of metrics and proper scoring rules
(Tilmann Gneiting & Adrian E Raftery (2007)
<doi:10.1198/016214506000001437>, Jordan, A., Krüger, F., & Lerch, S. (2019)
<doi:10.18637/jss.v090.i12>) within a consistent framework for
evaluation, comparison and visualisation of forecasts.
In addition to proper scoring rules, functions are provided to assess
bias, sharpness and calibration
(Sebastian Funk, Anton Camacho, Adam J. Kucharski, Rachel Lowe, Rosalind
M. Eggo, W. John Edmunds (2019) <doi:10.1371/journal.pcbi.1006785>) of
forecasts.
Several types of predictions (e.g. binary, discrete, continuous) which may
come in different formats (e.g. forecasts represented by predictive samples
or by quantiles of the predictive distribution) can be evaluated.
Scoring metrics can be used either through a convenient data.frame format,
or can be applied as individual functions in a vector / matrix format.
All functionality has been implemented with a focus on pe [...truncated...]
Author: Nikos Bosse [aut, cre] ,
Sam Abbott [aut] ,
Hugo Gruson [aut] ,
Johannes Bracher [ctb] ,
Sebastian Funk [ctb]
Maintainer: Nikos Bosse <nikosbosse@gmail.com>
Diff between scoringutils versions 1.0.0 dated 2022-05-13 and 1.0.1 dated 2022-08-16
DESCRIPTION | 8 - MD5 | 44 ++++---- R/bias.R | 2 R/check_forecasts.R | 11 +- R/input-check-helpers.R | 4 R/score_quantile.R | 2 R/summarise_scores.R | 2 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 23 ++-- inst/create-metric-tables.R | 22 ++-- inst/doc/getting-started.html | 4 inst/doc/metric-details.html | 145 ++++++++++++++--------------- inst/doc/scoring-forecasts-directly.html | 69 +++++++------ inst/manuscript/manuscript.Rmd | 4 inst/manuscript/manuscript.log | 6 - inst/manuscript/manuscript.pdf |binary inst/manuscript/manuscript.tex | 26 ++--- inst/metrics-overview/metrics-detailed.Rda |binary man/bias_quantile.Rd | 2 man/scoringutils-package.Rd | 2 tests/testthat/test-input-check-helpers.R | 11 ++ tests/testthat/test-score.R | 16 +++ 23 files changed, 220 insertions(+), 183 deletions(-)
Title: Functions for Nonlinear Least Squares Solutions - Updated 2022
Description: Provides tools for working with nonlinear least squares problems.
For the estimation of models reliable and robust tools than nls(), where the
the Gauss-Newton method frequently stops with 'singular gradient' messages.
This is accomplished by using, where possible, analytic derivatives to compute
the matrix of derivatives and a stabilization of the solution of the estimation
equations. Tools for approximate or externally supplied derivative matrices
are included. Bounds and masks on parameters are handled properly.
Author: John C Nash [aut, cre],
Duncan Murdoch [aut]
Maintainer: John C Nash <nashjc@uottawa.ca>
Diff between nlsr versions 2021.8.19 dated 2021-08-20 and 2022.8.16 dated 2022-08-16
nlsr-2021.8.19/nlsr/R/nlsr-package.R |only nlsr-2021.8.19/nlsr/R/resgr.R |only nlsr-2021.8.19/nlsr/R/resss.R |only nlsr-2021.8.19/nlsr/R/rjfundoc.R |only nlsr-2021.8.19/nlsr/inst/dev-files |only nlsr-2021.8.19/nlsr/inst/doc/150507ideas.txt |only nlsr-2021.8.19/nlsr/inst/doc/161231todo.txt |only nlsr-2021.8.19/nlsr/inst/doc/model2rjfun.pdf |only nlsr-2021.8.19/nlsr/inst/doc/nlsr-nls-nlsLM.R |only nlsr-2021.8.19/nlsr/inst/doc/nlsr-nls-nlsLM.Rmd |only nlsr-2021.8.19/nlsr/inst/doc/nlsr-nls-nlsLM.pdf |only nlsr-2021.8.19/nlsr/man/Simplify.Rd |only nlsr-2021.8.19/nlsr/man/nlsr-package.Rd |only nlsr-2021.8.19/nlsr/man/res.Rd |only nlsr-2021.8.19/nlsr/man/rjfundoc.Rd |only nlsr-2021.8.19/nlsr/tests/derivs.Rout.save |only nlsr-2021.8.19/nlsr/tests/derivsJN.R |only nlsr-2021.8.19/nlsr/vignettes/nlpd.bib |only nlsr-2021.8.19/nlsr/vignettes/nlsr-nls-nlsLM.Rmd |only nlsr-2022.8.16/nlsr/DESCRIPTION | 28 nlsr-2022.8.16/nlsr/MD5 | 151 nlsr-2022.8.16/nlsr/NAMESPACE | 97 nlsr-2022.8.16/nlsr/NEWS | 109 nlsr-2022.8.16/nlsr/R/derivs.R | 427 + nlsr-2022.8.16/nlsr/R/model2rjfun.R | 155 nlsr-2022.8.16/nlsr/R/nlfb.R | 682 +- nlsr-2022.8.16/nlsr/R/nlsr.package.R |only nlsr-2022.8.16/nlsr/R/nlxb.R | 287 - nlsr-2022.8.16/nlsr/R/numericDerivR.R |only nlsr-2022.8.16/nlsr/R/resJacFns.R |only nlsr-2022.8.16/nlsr/R/wrapnlsr.R | 155 nlsr-2022.8.16/nlsr/build/vignette.rds |binary nlsr-2022.8.16/nlsr/inst/doc/FixedParameters.R | 51 nlsr-2022.8.16/nlsr/inst/doc/FixedParameters.Rmd | 158 nlsr-2022.8.16/nlsr/inst/doc/FixedParameters.pdf |binary nlsr-2022.8.16/nlsr/inst/doc/R-analytic-derivatives.R |only nlsr-2022.8.16/nlsr/inst/doc/R-analytic-derivatives.Rmd |only nlsr-2022.8.16/nlsr/inst/doc/R-analytic-derivatives.pdf |only nlsr-2022.8.16/nlsr/inst/doc/nlsr-derivs.R | 21 nlsr-2022.8.16/nlsr/inst/doc/nlsr-derivs.Rmd | 59 nlsr-2022.8.16/nlsr/inst/doc/nlsr-derivs.pdf |binary nlsr-2022.8.16/nlsr/inst/doc/nlsr-devdoc.R | 1728 ++++-- nlsr-2022.8.16/nlsr/inst/doc/nlsr-devdoc.Rmd | 3957 ++++++++++----- nlsr-2022.8.16/nlsr/inst/doc/nlsr-devdoc.pdf |binary nlsr-2022.8.16/nlsr/man/coef.nlsr.Rd | 36 nlsr-2022.8.16/nlsr/man/dex.Rd | 102 nlsr-2022.8.16/nlsr/man/findSubexprs.Rd | 61 nlsr-2022.8.16/nlsr/man/fitted.nlsr.Rd |only nlsr-2022.8.16/nlsr/man/isCALL.Rd |only nlsr-2022.8.16/nlsr/man/isMINUSONE.Rd |only nlsr-2022.8.16/nlsr/man/isONE.Rd |only nlsr-2022.8.16/nlsr/man/isZERO.Rd |only nlsr-2022.8.16/nlsr/man/jaback.Rd |only nlsr-2022.8.16/nlsr/man/jacentral.Rd |only nlsr-2022.8.16/nlsr/man/jafwd.Rd |only nlsr-2022.8.16/nlsr/man/jand.Rd |only nlsr-2022.8.16/nlsr/man/model2rjfun.Rd | 119 nlsr-2022.8.16/nlsr/man/newDeriv.Rd |only nlsr-2022.8.16/nlsr/man/newSimplification.Rd |only nlsr-2022.8.16/nlsr/man/nlfb.Rd | 236 nlsr-2022.8.16/nlsr/man/nlsDeriv.Rd | 323 - nlsr-2022.8.16/nlsr/man/nlsSimplify.Rd |only nlsr-2022.8.16/nlsr/man/nlsr.Rd |only nlsr-2022.8.16/nlsr/man/nlsr.control.Rd |only nlsr-2022.8.16/nlsr/man/nlxb.Rd | 276 - nlsr-2022.8.16/nlsr/man/numericDerivR.Rd |only nlsr-2022.8.16/nlsr/man/nvec.Rd |only nlsr-2022.8.16/nlsr/man/pctrl.Rd |only nlsr-2022.8.16/nlsr/man/pnlm0.Rd |only nlsr-2022.8.16/nlsr/man/pnls0.Rd |only nlsr-2022.8.16/nlsr/man/predict.nlsr.Rd | 50 nlsr-2022.8.16/nlsr/man/print.nlsr.Rd | 39 nlsr-2022.8.16/nlsr/man/pshort.Rd |only nlsr-2022.8.16/nlsr/man/rawres.nlsr.Rd |only nlsr-2022.8.16/nlsr/man/resgr.Rd | 90 nlsr-2022.8.16/nlsr/man/resid.nlsr.Rd |only nlsr-2022.8.16/nlsr/man/residuals.nlsr.Rd |only nlsr-2022.8.16/nlsr/man/resss.Rd | 85 nlsr-2022.8.16/nlsr/man/summary.nlsr.Rd | 53 nlsr-2022.8.16/nlsr/man/sysDerivs.Rd |only nlsr-2022.8.16/nlsr/man/sysSimplifications.Rd |only nlsr-2022.8.16/nlsr/man/wrapnlsr.Rd | 134 nlsr-2022.8.16/nlsr/tests/bndmask.R | 6 nlsr-2022.8.16/nlsr/tests/boundnlxb.R | 4 nlsr-2022.8.16/nlsr/tests/controltst.R |only nlsr-2022.8.16/nlsr/tests/derivs.R | 31 nlsr-2022.8.16/nlsr/tests/scaledxtests.R | 5 nlsr-2022.8.16/nlsr/vignettes/BellX.R |only nlsr-2022.8.16/nlsr/vignettes/FixedParameters.Rmd | 158 nlsr-2022.8.16/nlsr/vignettes/ImproveNLS.bib |only nlsr-2022.8.16/nlsr/vignettes/R-analytic-derivatives.Rmd |only nlsr-2022.8.16/nlsr/vignettes/nlsr-derivs.Rmd | 59 nlsr-2022.8.16/nlsr/vignettes/nlsr-devdoc.Rmd | 3957 ++++++++++----- 93 files changed, 9191 insertions(+), 4698 deletions(-)
Title: Minimalist Async Evaluation Framework for R
Description: Extremely simple and lightweight method for concurrent /
parallel code execution, built on 'nanonext' and 'NNG' (Nanomsg Next Gen)
technology.
Author: Charlie Gao [aut, cre] ,
Hibiki AI Limited [cph]
Maintainer: Charlie Gao <charlie.gao@shikokuchuo.net>
Diff between mirai versions 0.5.2 dated 2022-07-21 and 0.5.3 dated 2022-08-16
mirai-0.5.2/mirai/man/reexports.Rd |only mirai-0.5.3/mirai/DESCRIPTION | 8 - mirai-0.5.3/mirai/MD5 | 24 ++-- mirai-0.5.3/mirai/NAMESPACE | 6 - mirai-0.5.3/mirai/NEWS.md | 7 + mirai-0.5.3/mirai/R/mirai-package.R | 10 - mirai-0.5.3/mirai/R/mirai.R | 169 ++++++++++++++++++++++++++------ mirai-0.5.3/mirai/README.md | 115 +++++++++++++++++---- mirai-0.5.3/mirai/man/call_mirai.Rd | 19 ++- mirai-0.5.3/mirai/man/eval_mirai.Rd | 27 +++-- mirai-0.5.3/mirai/man/is_error_value.Rd |only mirai-0.5.3/mirai/man/is_mirai_error.Rd |only mirai-0.5.3/mirai/man/stop_mirai.Rd | 4 mirai-0.5.3/mirai/man/unresolved.Rd |only mirai-0.5.3/mirai/tests/tests.R | 12 +- 15 files changed, 301 insertions(+), 100 deletions(-)
Title: R Interface to Apache Spark
Description: R interface to Apache Spark, a fast and general
engine for big data processing, see <https://spark.apache.org/>. This
package supports connecting to local and remote Apache Spark clusters,
provides a 'dplyr' compatible back-end, and provides an interface to
Spark's built-in machine learning algorithms.
Author: Javier Luraschi [aut],
Kevin Kuo [aut] ,
Kevin Ushey [aut],
JJ Allaire [aut],
Samuel Macedo [ctb],
Hossein Falaki [aut],
Lu Wang [aut],
Andy Zhang [aut],
Yitao Li [aut] ,
Jozef Hajnala [ctb],
Maciej Szymkiewicz [ctb] ,
Wil Davis [ctb],
Edgar Ruiz [au [...truncated...]
Maintainer: Edgar Ruiz <edgar@rstudio.com>
Diff between sparklyr versions 1.7.7 dated 2022-06-07 and 1.7.8 dated 2022-08-16
sparklyr-1.7.7/sparklyr/R/dbplyr-compat.R |only sparklyr-1.7.7/sparklyr/R/dbplyr_utils.R |only sparklyr-1.7.7/sparklyr/R/dplyr_spark_connection.R |only sparklyr-1.7.7/sparklyr/R/ml_feature_sql_transformer_utils.R |only sparklyr-1.7.7/sparklyr/R/partial_eval.R |only sparklyr-1.7.8/sparklyr/DESCRIPTION | 70 +-- sparklyr-1.7.8/sparklyr/MD5 | 171 ++++---- sparklyr-1.7.8/sparklyr/NAMESPACE | 96 +--- sparklyr-1.7.8/sparklyr/NEWS.md | 68 +++ sparklyr-1.7.8/sparklyr/R/core_arrow.R | 24 - sparklyr-1.7.8/sparklyr/R/data_interface.R | 49 ++ sparklyr-1.7.8/sparklyr/R/dbi_spark_connection.R | 7 sparklyr-1.7.8/sparklyr/R/do_spark.R | 23 - sparklyr-1.7.8/sparklyr/R/dplyr_join.R | 82 ---- sparklyr-1.7.8/sparklyr/R/dplyr_spark.R | 134 +----- sparklyr-1.7.8/sparklyr/R/dplyr_spark_table.R | 24 - sparklyr-1.7.8/sparklyr/R/dplyr_sql.R | 204 +--------- sparklyr-1.7.8/sparklyr/R/dplyr_sql_translation.R |only sparklyr-1.7.8/sparklyr/R/dplyr_verbs.R |only sparklyr-1.7.8/sparklyr/R/imports.R | 1 sparklyr-1.7.8/sparklyr/R/install_spark.R | 131 ++++-- sparklyr-1.7.8/sparklyr/R/install_spark_versions.R | 51 +- sparklyr-1.7.8/sparklyr/R/ml_constructor_utils.R | 2 sparklyr-1.7.8/sparklyr/R/ml_feature_dplyr_transformer.R | 16 sparklyr-1.7.8/sparklyr/R/ml_mapping_tables.R | 9 sparklyr-1.7.8/sparklyr/R/ml_metrics.R |only sparklyr-1.7.8/sparklyr/R/ml_param_utils.R | 8 sparklyr-1.7.8/sparklyr/R/ml_regression_aft_survival_regression.R | 53 +- sparklyr-1.7.8/sparklyr/R/ml_regression_decision_tree_regressor.R | 27 - sparklyr-1.7.8/sparklyr/R/ml_regression_gbt_regressor.R | 35 - sparklyr-1.7.8/sparklyr/R/ml_regression_generalized_linear_regression.R | 51 +- sparklyr-1.7.8/sparklyr/R/ml_regression_isotonic_regression.R | 13 sparklyr-1.7.8/sparklyr/R/ml_regression_linear_regression.R | 27 - sparklyr-1.7.8/sparklyr/R/ml_regression_random_forest_regressor.R | 31 - sparklyr-1.7.8/sparklyr/R/ml_tuning.R | 11 sparklyr-1.7.8/sparklyr/R/ml_utils.R | 35 + sparklyr-1.7.8/sparklyr/R/ml_validator_utils.R | 21 - sparklyr-1.7.8/sparklyr/R/mutation.R | 6 sparklyr-1.7.8/sparklyr/R/params_validator.R |only sparklyr-1.7.8/sparklyr/R/sdf_wrapper.R | 2 sparklyr-1.7.8/sparklyr/R/spark_apply_bundle.R | 7 sparklyr-1.7.8/sparklyr/R/spark_compile.R | 181 ++++---- sparklyr-1.7.8/sparklyr/R/spark_extensions.R | 7 sparklyr-1.7.8/sparklyr/R/spark_globals.R | 99 ++++ sparklyr-1.7.8/sparklyr/R/spark_sql.R | 3 sparklyr-1.7.8/sparklyr/R/stream_operations.R | 12 sparklyr-1.7.8/sparklyr/R/tidyr_fill.R | 20 sparklyr-1.7.8/sparklyr/R/utils.R | 4 sparklyr-1.7.8/sparklyr/R/zzz.R | 2 sparklyr-1.7.8/sparklyr/build/partial.rdb |binary sparklyr-1.7.8/sparklyr/inst/extdata/versions.json | 40 + sparklyr-1.7.8/sparklyr/inst/java/sparklyr-1.5-2.10.jar |binary sparklyr-1.7.8/sparklyr/inst/java/sparklyr-1.6-2.10.jar |binary sparklyr-1.7.8/sparklyr/inst/java/sparklyr-2.0-2.11.jar |binary sparklyr-1.7.8/sparklyr/inst/java/sparklyr-2.3-2.11.jar |binary sparklyr-1.7.8/sparklyr/inst/java/sparklyr-2.4-2.11.jar |binary sparklyr-1.7.8/sparklyr/inst/java/sparklyr-2.4-2.12.jar |binary sparklyr-1.7.8/sparklyr/inst/java/sparklyr-master-2.12.jar |binary sparklyr-1.7.8/sparklyr/java/embedded_sources.R | 24 - sparklyr-1.7.8/sparklyr/man/collect_from_rds.Rd | 1 sparklyr-1.7.8/sparklyr/man/join.tbl_spark.Rd | 4 sparklyr-1.7.8/sparklyr/man/ml_default_stop_words.Rd | 5 sparklyr-1.7.8/sparklyr/man/ml_metrics_binary.Rd |only sparklyr-1.7.8/sparklyr/man/ml_metrics_multiclass.Rd |only sparklyr-1.7.8/sparklyr/man/ml_metrics_regression.Rd |only sparklyr-1.7.8/sparklyr/man/spark_insert_table.Rd |only sparklyr-1.7.8/sparklyr/man/spark_load_table.Rd | 1 sparklyr-1.7.8/sparklyr/man/spark_read.Rd | 1 sparklyr-1.7.8/sparklyr/man/spark_read_avro.Rd | 1 sparklyr-1.7.8/sparklyr/man/spark_read_binary.Rd | 1 sparklyr-1.7.8/sparklyr/man/spark_read_csv.Rd | 1 sparklyr-1.7.8/sparklyr/man/spark_read_delta.Rd | 1 sparklyr-1.7.8/sparklyr/man/spark_read_image.Rd | 1 sparklyr-1.7.8/sparklyr/man/spark_read_jdbc.Rd | 1 sparklyr-1.7.8/sparklyr/man/spark_read_json.Rd | 1 sparklyr-1.7.8/sparklyr/man/spark_read_libsvm.Rd | 1 sparklyr-1.7.8/sparklyr/man/spark_read_orc.Rd | 1 sparklyr-1.7.8/sparklyr/man/spark_read_parquet.Rd | 1 sparklyr-1.7.8/sparklyr/man/spark_read_source.Rd | 1 sparklyr-1.7.8/sparklyr/man/spark_read_table.Rd | 1 sparklyr-1.7.8/sparklyr/man/spark_read_text.Rd | 1 sparklyr-1.7.8/sparklyr/man/spark_save_table.Rd | 1 sparklyr-1.7.8/sparklyr/man/spark_write_avro.Rd | 1 sparklyr-1.7.8/sparklyr/man/spark_write_csv.Rd | 1 sparklyr-1.7.8/sparklyr/man/spark_write_delta.Rd | 1 sparklyr-1.7.8/sparklyr/man/spark_write_jdbc.Rd | 1 sparklyr-1.7.8/sparklyr/man/spark_write_json.Rd | 1 sparklyr-1.7.8/sparklyr/man/spark_write_orc.Rd | 1 sparklyr-1.7.8/sparklyr/man/spark_write_parquet.Rd | 1 sparklyr-1.7.8/sparklyr/man/spark_write_source.Rd | 1 sparklyr-1.7.8/sparklyr/man/spark_write_table.Rd | 1 sparklyr-1.7.8/sparklyr/man/spark_write_text.Rd | 1 sparklyr-1.7.8/sparklyr/man/stream_lag.Rd | 6 93 files changed, 946 insertions(+), 977 deletions(-)
Title: Fits Models Inside the Database
Description: Uses 'dplyr' and 'tidyeval' to fit statistical models inside
the database. It currently supports KMeans and linear regression
models.
Author: Max Kuhn [aut, cre]
Maintainer: Max Kuhn <max@rstudio.com>
Diff between modeldb versions 0.2.2 dated 2020-02-10 and 0.2.3 dated 2022-08-16
DESCRIPTION | 30 ++-- LICENSE |only MD5 | 21 +- NAMESPACE | 3 NEWS.md | 4 R/kmeans.R | 7 R/modeldb.R | 4 README.md | 92 ++++++++---- build/vignette.rds |binary inst/doc/kmeans.html | 231 +++++++++++++++++++++---------- inst/doc/linear-regression.html | 295 ++++++++++++++++++++++++---------------- man/modeldb-package.Rd | 3 12 files changed, 436 insertions(+), 254 deletions(-)
Title: Correlations in R
Description: A tool for exploring correlations. It makes it possible to
easily perform routine tasks when exploring correlation matrices such
as ignoring the diagonal, focusing on the correlations of certain
variables against others, or rearranging and visualizing the matrix in
terms of the strength of the correlations.
Author: Max Kuhn [aut, cre],
Simon Jackson [aut],
Jorge Cimentada [aut]
Maintainer: Max Kuhn <max@rstudio.com>
Diff between corrr versions 0.4.3 dated 2020-11-24 and 0.4.4 dated 2022-08-16
corrr-0.4.3/corrr/R/corrr.R |only corrr-0.4.4/corrr/DESCRIPTION | 56 +- corrr-0.4.4/corrr/MD5 | 90 ++-- corrr-0.4.4/corrr/NAMESPACE | 3 corrr-0.4.4/corrr/NEWS.md | 10 corrr-0.4.4/corrr/R/colpair.R | 33 - corrr-0.4.4/corrr/R/cor_df.R | 234 ++++++++--- corrr-0.4.4/corrr/R/correlate.R | 146 ++++--- corrr-0.4.4/corrr/R/corrr-package.R |only corrr-0.4.4/corrr/R/dataframe.R | 13 corrr-0.4.4/corrr/R/internal.R | 10 corrr-0.4.4/corrr/R/matrix.R | 4 corrr-0.4.4/corrr/R/output.R | 12 corrr-0.4.4/corrr/R/reshape.R | 41 - corrr-0.4.4/corrr/R/retract.R | 4 corrr-0.4.4/corrr/R/utility.R | 17 corrr-0.4.4/corrr/README.md | 113 +++-- corrr-0.4.4/corrr/build/vignette.rds |binary corrr-0.4.4/corrr/inst/doc/databases.html | 174 +++----- corrr-0.4.4/corrr/inst/doc/using-corrr.html | 352 ++++++++--------- corrr-0.4.4/corrr/man/autoplot.cor_df.Rd |only corrr-0.4.4/corrr/man/colpair_map.Rd | 5 corrr-0.4.4/corrr/man/correlate.Rd | 18 corrr-0.4.4/corrr/man/corrr-package.Rd | 11 corrr-0.4.4/corrr/man/dice.Rd | 1 corrr-0.4.4/corrr/man/figures/README-combination-1.png |binary corrr-0.4.4/corrr/man/figures/README-combination-2.png |binary corrr-0.4.4/corrr/man/focus.Rd | 8 corrr-0.4.4/corrr/man/network_plot.Rd | 11 corrr-0.4.4/corrr/man/rearrange.Rd | 4 corrr-0.4.4/corrr/man/reexports.Rd |only corrr-0.4.4/corrr/man/shave.Rd | 4 corrr-0.4.4/corrr/man/stretch.Rd | 10 corrr-0.4.4/corrr/tests/testthat.R | 1 corrr-0.4.4/corrr/tests/testthat/test-as_cordf.R | 2 corrr-0.4.4/corrr/tests/testthat/test-as_matrix.R | 4 corrr-0.4.4/corrr/tests/testthat/test-colpair.R | 34 + corrr-0.4.4/corrr/tests/testthat/test-correlate.R | 34 + corrr-0.4.4/corrr/tests/testthat/test-dataframe.R | 2 corrr-0.4.4/corrr/tests/testthat/test-fashion.R | 2 corrr-0.4.4/corrr/tests/testthat/test-focus.R | 2 corrr-0.4.4/corrr/tests/testthat/test-focus_.R | 2 corrr-0.4.4/corrr/tests/testthat/test-plots.R | 10 corrr-0.4.4/corrr/tests/testthat/test-rearrange.R | 10 corrr-0.4.4/corrr/tests/testthat/test-shave.R | 6 corrr-0.4.4/corrr/tests/testthat/test-stretch.R | 4 corrr-0.4.4/corrr/tests/testthat/test-tbl_sql.R | 16 corrr-0.4.4/corrr/tests/testthat/test-utilities.R | 2 48 files changed, 860 insertions(+), 655 deletions(-)
Title: Dataset Shift with Outlier Scores
Description: Test for no adverse shift in two-sample comparison when we
have a training set, the reference distribution, and a test set. The
approach is flexible (extensible) and relies on a robust and powerful test
statistic, the weighted AUC. See Kamulete, V. M. (2021) <arXiv:2107.02990>
for details. Outlier scores such as trust scores and prediction uncertainty
can be used as the basis for comparison for example.
Author: Vathy M. Kamulete [aut, cre] ,
Royal Bank of Canada [cph]
Maintainer: Vathy M. Kamulete <vathymut@gmail.com>
Diff between dsos versions 0.1.0 dated 2022-01-18 and 0.1.1 dated 2022-08-16
dsos-0.1.0/dsos/R/dsos-plot.R |only dsos-0.1.0/dsos/R/null-distributions.R |only dsos-0.1.0/dsos/R/rf-helpers.R |only dsos-0.1.0/dsos/R/sampling-helpers.R |only dsos-0.1.0/dsos/R/score-class-probability.R |only dsos-0.1.0/dsos/R/score-outlier-detection.R |only dsos-0.1.0/dsos/R/score-resampling-uncertainty.R |only dsos-0.1.0/dsos/R/score-residual-diagnostic.R |only dsos-0.1.0/dsos/R/statistic-wauc.R |only dsos-0.1.0/dsos/man/cp_at.Rd |only dsos-0.1.0/dsos/man/cp_pt.Rd |only dsos-0.1.0/dsos/man/cp_ss.Rd |only dsos-0.1.0/dsos/man/od_pt.Rd |only dsos-0.1.0/dsos/man/rd_pt.Rd |only dsos-0.1.0/dsos/man/rue_pt.Rd |only dsos-0.1.0/dsos/vignettes/images/combined_dsos_vignette.png |only dsos-0.1.0/dsos/vignettes/images/combined_pca_vignette.png |only dsos-0.1.1/dsos/DESCRIPTION | 26 dsos-0.1.1/dsos/MD5 | 88 dsos-0.1.1/dsos/NAMESPACE | 17 dsos-0.1.1/dsos/NEWS.md |only dsos-0.1.1/dsos/R/bayesian-bootstrap.R |only dsos-0.1.1/dsos/R/datatable-aware.R | 1 dsos-0.1.1/dsos/R/dsos-s3.R |only dsos-0.1.1/dsos/R/pvalue-asymptotic.R |only dsos-0.1.1/dsos/R/pvalue-permutations.R |only dsos-0.1.1/dsos/R/score-permutations.R |only dsos-0.1.1/dsos/R/score-splitting.R |only dsos-0.1.1/dsos/R/utils-rf.R |only dsos-0.1.1/dsos/R/utils-sampling.R |only dsos-0.1.1/dsos/R/wauc-statistic.R |only dsos-0.1.1/dsos/build/vignette.rds |binary dsos-0.1.1/dsos/inst/doc/dependencies.html | 261 + dsos-0.1.1/dsos/inst/doc/diy-score.R | 6 dsos-0.1.1/dsos/inst/doc/diy-score.Rmd | 55 dsos-0.1.1/dsos/inst/doc/diy-score.html | 1394 +++++++++ dsos-0.1.1/dsos/inst/doc/motivation.R | 5 dsos-0.1.1/dsos/inst/doc/motivation.Rmd | 115 dsos-0.1.1/dsos/inst/doc/motivation.html | 1467 +++++++++- dsos-0.1.1/dsos/man/at_from_os.Rd |only dsos-0.1.1/dsos/man/at_oob.Rd |only dsos-0.1.1/dsos/man/dsos-package.Rd | 16 dsos-0.1.1/dsos/man/figures/README-example-1.png |binary dsos-0.1.1/dsos/man/figures/README-iris-1.png |only dsos-0.1.1/dsos/man/figures/README-null_at-1.png |only dsos-0.1.1/dsos/man/figures/README-null_pt-1.png |only dsos-0.1.1/dsos/man/figures/README-shift_at-1.png |only dsos-0.1.1/dsos/man/figures/README-shift_pt-1.png |only dsos-0.1.1/dsos/man/plot.outlier.test.Rd | 23 dsos-0.1.1/dsos/man/print.outlier.test.Rd |only dsos-0.1.1/dsos/man/pt_from_os.Rd |only dsos-0.1.1/dsos/man/pt_oob.Rd |only dsos-0.1.1/dsos/man/pt_refit.Rd |only dsos-0.1.1/dsos/man/score_cp.Rd |only dsos-0.1.1/dsos/man/score_od.Rd |only dsos-0.1.1/dsos/man/score_rd.Rd |only dsos-0.1.1/dsos/man/score_rue.Rd |only dsos-0.1.1/dsos/man/split_cp.Rd |only dsos-0.1.1/dsos/man/wauc_from_os.Rd | 19 dsos-0.1.1/dsos/tests/testthat/test-asymptotic-null.R | 8 dsos-0.1.1/dsos/tests/testthat/test-false-discoveries.R | 34 dsos-0.1.1/dsos/tests/testthat/test-inliers-versus-outliers.R | 12 dsos-0.1.1/dsos/tests/testthat/test-iris.R | 116 dsos-0.1.1/dsos/vignettes/diy-score.Rmd | 55 dsos-0.1.1/dsos/vignettes/images/combined_dsos.png |only dsos-0.1.1/dsos/vignettes/motivation.Rmd | 115 dsos-0.1.1/dsos/vignettes/vignettes.bib | 109 67 files changed, 3378 insertions(+), 564 deletions(-)
Title: Spatial Regression Analysis
Description: A collection of all the estimation functions for spatial cross-sectional models (on lattice/areal data using spatial weights matrices) contained up to now in 'spdep', 'sphet' and 'spse'. These model fitting functions include maximum likelihood methods for cross-sectional models proposed by 'Cliff' and 'Ord' (1973, ISBN:0850860369) and (1981, ISBN:0850860814), fitting methods initially described by 'Ord' (1975) <doi:10.1080/01621459.1975.10480272>. The models are further described by 'Anselin' (1988) <doi:10.1007/978-94-015-7799-1>. Spatial two stage least squares and spatial general method of moment models initially proposed by 'Kelejian' and 'Prucha' (1998) <doi:10.1023/A:1007707430416> and (1999) <doi:10.1111/1468-2354.00027> are provided. Impact methods and MCMC fitting methods proposed by 'LeSage' and 'Pace' (2009) <doi:10.1201/9781420064254> are implemented for the family of cross-sectional spatial regression models. Methods for fitting the log determ [...truncated...]
Author: Roger Bivand [cre, aut] ,
Gianfranco Piras [aut],
Luc Anselin [ctb],
Andrew Bernat [ctb],
Eric Blankmeyer [ctb],
Yongwan Chun [ctb],
Virgilio Gomez-Rubio [ctb],
Daniel Griffith [ctb],
Martin Gubri [ctb],
Rein Halbersma [ctb],
James LeSage [ctb],
Ange [...truncated...]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between spatialreg versions 1.2-3 dated 2022-04-18 and 1.2-5 dated 2022-08-16
DESCRIPTION | 8 ++--- MD5 | 40 ++++++++++++++--------------- NEWS.md | 8 +++++ R/AAA.R | 4 ++ R/jacobian.R | 6 ++-- R/sparse_mat.R | 12 ++++---- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 2 - inst/doc/nb_igraph.R | 51 ++++++++++++++++++++----------------- inst/doc/nb_igraph.Rmd | 51 ++++++++++++++++++++----------------- inst/doc/nb_igraph.html | 62 +++++++++++++++++++++++----------------------- inst/doc/sids_models.html | 6 ++-- man/aple.Rd | 16 +++++------ man/aple.mc.Rd | 12 ++++---- man/aple.plot.Rd | 12 ++++---- man/similar.listw.Rd | 2 - man/sparse_mat.Rd | 1 man/spautolm.Rd | 6 +--- man/trW.Rd | 2 - vignettes/nb_igraph.Rmd | 51 ++++++++++++++++++++----------------- 21 files changed, 186 insertions(+), 166 deletions(-)
Title: Repertoire Analysis of the Detected Clonotype
Description: The 'TRUST4' or 'MiXCR' is used to identify the clonotypes.
The goal of 'rTCRBCRr' is to process the results from these clonotyping tools,
and analyze the clonotype repertoire metrics based on chain names and IGH isotypes.
The manuscript is still under preparation for publication for now.
The references describing the methods in this package will be added later.
Author: Lizhong Ding [aut, cre]
Maintainer: Lizhong Ding <z82xh3f4r@mozmail.com>
Diff between rTCRBCRr versions 0.1.0 dated 2022-06-27 and 0.1.1 dated 2022-08-16
DESCRIPTION | 8 +++---- MD5 | 15 +++++++------ R/globals.R | 4 ++- README.md | 49 ++++++++++++-------------------------------- inst/doc/Quick_Start.Rmd | 8 +++---- inst/doc/Quick_Start.html | 8 +++---- man/rTCRBCRr-package.Rd | 2 - man/the-global-variables.Rd |only vignettes/Quick_Start.Rmd | 8 +++---- 9 files changed, 42 insertions(+), 60 deletions(-)
Title: Dynamic Documents for R
Description: Convert R Markdown documents into a variety of formats.
Author: JJ Allaire [aut],
Yihui Xie [aut, cre] ,
Jonathan McPherson [aut],
Javier Luraschi [aut],
Kevin Ushey [aut],
Aron Atkins [aut],
Hadley Wickham [aut],
Joe Cheng [aut],
Winston Chang [aut],
Richard Iannone [aut] ,
Andrew Dunning [ctb] ,
Atsushi Yasumot [...truncated...]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between rmarkdown versions 2.14 dated 2022-04-25 and 2.15 dated 2022-08-16
DESCRIPTION | 8 MD5 | 48 ++--- NEWS.md | 12 + R/github_document.R | 52 ++++- R/html_document.R | 9 R/html_document_base.R | 5 R/ioslides_presentation.R | 2 R/md_document.R | 2 R/render.R | 4 R/shiny_prerendered.R | 8 R/tufte_handout.R | 5 build/vignette.rds |binary inst/doc/lua-filters.html | 13 + inst/rmarkdown/templates/github_document/resources/preview.html | 4 inst/rmd/h/default.html | 27 ++ man/github_document.Rd | 22 +- man/html_document.Rd | 30 ++- man/html_document_base.Rd | 4 man/html_notebook.Rd | 13 - man/html_vignette.Rd | 7 man/ioslides_presentation.Rd | 91 +++++++--- man/slidy_presentation.Rd | 4 man/tufte_handout.Rd | 1 tests/testthat/test-formats.R | 2 tests/testthat/test-github_document.R | 41 ++++ 25 files changed, 293 insertions(+), 121 deletions(-)
Title: 'grid' Pattern Grobs
Description: Provides 'grid' grobs that fill in a user-defined area with various patterns. Includes enhanced versions of the geometric and image-based patterns originally contained in the 'ggpattern' package as well as original 'pch', 'polygon_tiling', 'regular_polygon', 'rose', 'text', 'wave', and 'weave' patterns plus support for custom user-defined patterns.
Author: Mike FC [aut] ,
Trevor L Davis [aut, cre] ,
Thomas Lin Pedersen [ctb] copied from ggplot2)
Maintainer: Trevor L Davis <trevor.l.davis@gmail.com>
Diff between gridpattern versions 0.5.3 dated 2022-03-22 and 1.0.1 dated 2022-08-16
DESCRIPTION | 13 ++-- MD5 | 73 +++++++++++++------------- NEWS.md | 21 +++++++ R/alphaMaskGrob.R | 2 R/grid-pattern.R | 2 R/guess_has_R_4.1_features.R |only R/pattern-both-rose.R | 10 ++- R/pattern-both-text.R | 1 R/pattern-geometry-circle.R | 10 ++- R/pattern-geometry-crosshatch.R | 9 ++- R/pattern-geometry-pch.R | 12 ++-- R/pattern-geometry-regular_polygon.R | 10 ++- R/pattern-geometry-stripe.R | 7 +- R/pattern-geometry-tiling.R | 10 ++- R/pattern-geometry-wave.R | 9 ++- R/pattern-geometry-weave.R | 10 ++- R/utils-params.R | 95 ----------------------------------- build/vignette.rds |binary inst/doc/developing-patterns.R | 2 inst/doc/developing-patterns.Rmd | 5 + inst/doc/developing-patterns.html | 37 ++++++++----- inst/doc/tiling.html | 1 man/alphaMaskGrob.Rd | 2 man/grid.pattern.Rd | 2 man/grid.pattern_circle.Rd | 7 +- man/grid.pattern_crosshatch.Rd | 7 +- man/grid.pattern_pch.Rd | 7 +- man/grid.pattern_polygon_tiling.Rd | 7 +- man/grid.pattern_regular_polygon.Rd | 7 +- man/grid.pattern_rose.Rd | 7 +- man/grid.pattern_stripe.Rd | 7 +- man/grid.pattern_text.Rd | 2 man/grid.pattern_wave.Rd | 7 +- man/grid.pattern_weave.Rd | 7 +- man/gridpattern-package.Rd | 4 - man/guess_has_R4.1_features.Rd | 2 tests/testthat/test_utils.R | 2 vignettes/developing-patterns.Rmd | 5 + 38 files changed, 209 insertions(+), 212 deletions(-)
Title: Template Model Builder: A General Random Effect Tool Inspired by
'ADMB'
Description: With this tool, a user should be able to quickly implement
complex random effect models through simple C++ templates. The package combines
'CppAD' (C++ automatic differentiation), 'Eigen' (templated matrix-vector
library) and 'CHOLMOD' (sparse matrix routines available from R) to obtain
an efficient implementation of the applied Laplace approximation with exact
derivatives. Key features are: Automatic sparseness detection, parallelism
through 'BLAS' and parallel user templates.
Author: Kasper Kristensen [aut, cre, cph],
Brad Bell [cph],
Hans Skaug [ctb],
Arni Magnusson [ctb],
Casper Berg [ctb],
Anders Nielsen [ctb],
Martin Maechler [ctb],
Theo Michelot [ctb],
Mollie Brooks [ctb],
Alex Forrence [ctb],
Christoffer Moesgaard Albertsen [...truncated...]
Maintainer: Kasper Kristensen <kaskr@dtu.dk>
Diff between TMB versions 1.9.0 dated 2022-05-27 and 1.9.1 dated 2022-08-16
DESCRIPTION | 8 MD5 | 76 +-- NAMESPACE | 2 NEWS | 16 R/TMB.R | 19 R/sdreport.R | 12 R/validation.R | 42 +- inst/examples/simple.R | 4 inst/include/TMBad/TMBad.cpp | 179 -------- inst/include/TMBad/TMBad.hpp | 197 ++++----- inst/include/TMBad/ad_blas.hpp | 37 - inst/include/TMBad/checkpoint.hpp | 538 +++++++++----------------- inst/include/TMBad/code_generator.hpp | 49 -- inst/include/TMBad/compile.hpp | 37 - inst/include/TMBad/compression.hpp | 37 - inst/include/TMBad/config.hpp |only inst/include/TMBad/eigen_numtraits.hpp | 37 - inst/include/TMBad/global.hpp | 250 ++++-------- inst/include/TMBad/graph2dot.hpp | 45 -- inst/include/TMBad/graph_transform.hpp | 147 +++++-- inst/include/TMBad/integrate.hpp | 37 - inst/include/TMBad/radix.hpp | 1 inst/include/TMBad/tmbad_allow_comparison.hpp | 37 - inst/include/tiny_ad/mask.hpp | 47 +- inst/include/tmbutils/autodiff.hpp | 4 inst/include/tmbutils/density.hpp | 9 inst/include/tmbutils/interpol.hpp |only inst/include/tmbutils/kronecker.hpp | 4 inst/include/tmbutils/matexp.hpp | 4 inst/include/tmbutils/newton.hpp | 43 +- inst/include/tmbutils/order.hpp | 13 inst/include/tmbutils/romberg.hpp | 4 inst/include/tmbutils/splines.hpp | 10 inst/include/tmbutils/spmat.hpp | 4 inst/include/tmbutils/tmbutils_extra.hpp | 26 - man/FreeADFun.Rd | 2 man/compile.Rd | 10 man/oneStepPredict.Rd | 40 + man/openmp.Rd | 4 man/sdreport.Rd | 12 40 files changed, 788 insertions(+), 1255 deletions(-)
Title: Converting Transport Data from GTFS Format to GPS-Like Records
Description: Convert general transit feed specification (GTFS) data to global positioning system (GPS) records in 'data.table' format. It also has some functions to subset GTFS data in time and space and to convert both representations to simple feature format.
Author: Rafael H. M. Pereira [aut] ,
Pedro R. Andrade [aut, cre] ,
Joao Bazzo [aut] ,
Daniel Herszenhut [ctb] ,
Marcin Stepniak [ctb],
Marcus Saraiva [ctb] ,
Ipea - Institue for Applied Economic Research [cph, fnd]
Maintainer: Pedro R. Andrade <pedro.andrade@inpe.br>
Diff between gtfs2gps versions 2.0-2 dated 2022-03-10 and 2.1-0 dated 2022-08-16
gtfs2gps-2.0-2/gtfs2gps/R/filter_day_period.R |only gtfs2gps-2.0-2/gtfs2gps/R/merge_gtfs_feeds.R |only gtfs2gps-2.0-2/gtfs2gps/man/cpp_snap_points_nearest1.Rd |only gtfs2gps-2.0-2/gtfs2gps/man/cpp_snap_points_nearest2.Rd |only gtfs2gps-2.0-2/gtfs2gps/man/filter_by_agency_id.Rd |only gtfs2gps-2.0-2/gtfs2gps/man/filter_by_day.Rd |only gtfs2gps-2.0-2/gtfs2gps/man/filter_by_route_id.Rd |only gtfs2gps-2.0-2/gtfs2gps/man/filter_by_route_type.Rd |only gtfs2gps-2.0-2/gtfs2gps/man/filter_by_shape_id.Rd |only gtfs2gps-2.0-2/gtfs2gps/man/filter_day_period.Rd |only gtfs2gps-2.0-2/gtfs2gps/man/filter_week_days.Rd |only gtfs2gps-2.0-2/gtfs2gps/man/merge_gtfs_feeds.Rd |only gtfs2gps-2.0-2/gtfs2gps/man/remove_by_route_id.Rd |only gtfs2gps-2.0-2/gtfs2gps/tests/testthat/test_filter_day_period.R |only gtfs2gps-2.0-2/gtfs2gps/tests/testthat/test_merge_gtfs_feeds.R |only gtfs2gps-2.1-0/gtfs2gps/DESCRIPTION | 16 gtfs2gps-2.1-0/gtfs2gps/MD5 | 109 +- gtfs2gps-2.1-0/gtfs2gps/NAMESPACE | 16 gtfs2gps-2.1-0/gtfs2gps/NEWS.md | 20 gtfs2gps-2.1-0/gtfs2gps/R/RcppExports.R | 29 gtfs2gps-2.1-0/gtfs2gps/R/adjust_arrival_departure.R | 6 gtfs2gps-2.1-0/gtfs2gps/R/adjust_speed.R | 58 - gtfs2gps-2.1-0/gtfs2gps/R/append_height.R | 4 gtfs2gps-2.1-0/gtfs2gps/R/filter_gtfs.R | 264 ------ gtfs2gps-2.1-0/gtfs2gps/R/gps_as_sflinestring.R | 65 + gtfs2gps-2.1-0/gtfs2gps/R/gps_as_sfpoints.R | 6 gtfs2gps-2.1-0/gtfs2gps/R/gtfs2gps.R | 243 +++-- gtfs2gps-2.1-0/gtfs2gps/R/mod_updates.R | 47 - gtfs2gps-2.1-0/gtfs2gps/R/read_gtfs.R | 15 gtfs2gps-2.1-0/gtfs2gps/R/simplify_shapes.R | 15 gtfs2gps-2.1-0/gtfs2gps/R/test_gtfs_freq.R | 7 gtfs2gps-2.1-0/gtfs2gps/R/utils.R |only gtfs2gps-2.1-0/gtfs2gps/R/write_gtfs.R | 6 gtfs2gps-2.1-0/gtfs2gps/R/zzz.R | 14 gtfs2gps-2.1-0/gtfs2gps/build/vignette.rds |binary gtfs2gps-2.1-0/gtfs2gps/demo/fortaleza.R | 2 gtfs2gps-2.1-0/gtfs2gps/demo/poa.R | 2 gtfs2gps-2.1-0/gtfs2gps/demo/sp.R | 2 gtfs2gps-2.1-0/gtfs2gps/inst/doc/intro_to_gtfs2gps.R | 34 gtfs2gps-2.1-0/gtfs2gps/inst/doc/intro_to_gtfs2gps.Rmd | 54 - gtfs2gps-2.1-0/gtfs2gps/inst/doc/intro_to_gtfs2gps.html | 407 +++++++--- gtfs2gps-2.1-0/gtfs2gps/man/adjust_speed.Rd | 5 gtfs2gps-2.1-0/gtfs2gps/man/append_height.Rd | 4 gtfs2gps-2.1-0/gtfs2gps/man/gps_as_sflinestring.Rd | 8 gtfs2gps-2.1-0/gtfs2gps/man/gps_as_sfpoints.Rd | 6 gtfs2gps-2.1-0/gtfs2gps/man/gtfs2gps.Rd | 241 +++-- gtfs2gps-2.1-0/gtfs2gps/man/read_gtfs.Rd | 1 gtfs2gps-2.1-0/gtfs2gps/man/simplify_shapes.Rd | 5 gtfs2gps-2.1-0/gtfs2gps/man/test_gtfs_freq.Rd | 7 gtfs2gps-2.1-0/gtfs2gps/man/write_gtfs.Rd | 4 gtfs2gps-2.1-0/gtfs2gps/src/snap_points.cpp | 54 - gtfs2gps-2.1-0/gtfs2gps/tests/testthat.R | 1 gtfs2gps-2.1-0/gtfs2gps/tests/testthat/test_adjust_arrival_departure.R | 4 gtfs2gps-2.1-0/gtfs2gps/tests/testthat/test_adjust_speed.R | 12 gtfs2gps-2.1-0/gtfs2gps/tests/testthat/test_append_height.R | 2 gtfs2gps-2.1-0/gtfs2gps/tests/testthat/test_filter_gtfs.R | 157 --- gtfs2gps-2.1-0/gtfs2gps/tests/testthat/test_gps_as_sflinestring.R | 20 gtfs2gps-2.1-0/gtfs2gps/tests/testthat/test_gps_as_sfpoints.R | 4 gtfs2gps-2.1-0/gtfs2gps/tests/testthat/test_gtfs2gps.R | 95 +- gtfs2gps-2.1-0/gtfs2gps/tests/testthat/test_read_gtfs.R | 8 gtfs2gps-2.1-0/gtfs2gps/tests/testthat/test_snap_points.R | 4 gtfs2gps-2.1-0/gtfs2gps/tests/testthat/test_write_gtfs.R | 21 gtfs2gps-2.1-0/gtfs2gps/vignettes/intro_to_gtfs2gps.Rmd | 54 - gtfs2gps-2.1-0/gtfs2gps/vignettes/poa_small.zip |only 64 files changed, 999 insertions(+), 1159 deletions(-)
Title: Statistics Norway's Miscellaneous Tools
Description: Functions used by other packages from Statistics Norway are gathered. General data manipulation functions, and functions for hierarchical computations are included (Langsrud, 2020) <doi:10.13140/RG.2.2.27313.61283>. The hierarchy specification functions are useful within statistical disclosure control.
Author: Oyvind Langsrud [aut, cre],
Daniel Lupp [aut],
Bjoern-Helge Mevik [ctb]
Maintainer: Oyvind Langsrud <oyl@ssb.no>
Diff between SSBtools versions 1.3.3 dated 2022-06-23 and 1.3.4 dated 2022-08-16
DESCRIPTION | 10 +++++----- MD5 | 21 +++++++++++++-------- NAMESPACE | 5 +++++ R/As_TsparseMatrix.R |only R/DummyApply.R |only R/DummyDuplicated.R | 26 +++++++++++++------------- R/HierarchyCompute.R | 2 +- R/Matrix2list.R | 4 ++-- R/Reduce0exact.R | 2 +- man/As_TsparseMatrix.Rd |only man/DummyApply.Rd |only tests/testthat/test-DummyApply.R |only tests/testthat/test-HierarchyCompute.R | 2 +- tests/testthat/test-Reduce0exact.R | 8 ++++---- 14 files changed, 45 insertions(+), 35 deletions(-)
Title: Sparse Family and Selection Index
Description: Here we provide tools for the estimation of coefficients in
penalized regressions when the (co)variance matrix of predictors
and the covariance vector between predictors and response, are
provided. These methods are extended to the context of a Selection Index
(commonly used for breeding value prediction). The approaches offer
opportunities such as the integration of high-throughput traits in genetic
evaluations ('Lopez-Cruz et al., 2020') <doi:10.1038/s41598-020-65011-2>
and solutions for training set optimization in Genomic Prediction
('Lopez-Cruz & de los Campos, 2021') <doi:10.1093/genetics/iyab030>.
Author: Marco Lopez-Cruz [aut, cre],
Gustavo de los Campos [aut],
Paulino Perez-Rodriguez [ctb]
Maintainer: Marco Lopez-Cruz <maraloc@gmail.com>
Diff between SFSI versions 1.1.0 dated 2022-03-10 and 1.2.0 dated 2022-08-16
DESCRIPTION | 12 MD5 | 95 +-- NAMESPACE | 1 NEWS.md | 10 R/LARS.R | 284 +++++++---- R/Prune.R |only R/SSI.CV.R | 34 - R/SSI.R | 168 +++--- R/collect.R | 25 - R/cov2cor.R | 27 - R/cov2dist.R | 27 - R/fitBLUP.R | 16 R/getGenCov.R | 4 R/methods.R | 272 ++++++++--- R/net.plot.R | 55 +- R/path.plot.R | 176 +++++-- R/readBinary.R | 30 - R/rrr_functions.R | 71 +- R/saveBinary.R | 31 - R/solveEN.R | 197 ++++++-- data/datalist | 2 data/wheatHTP.RData |binary demo/LARS.R | 4 demo/SSI.CV.R | 9 demo/SSI.R | 14 demo/fitBLUP.R | 7 demo/solveEN.R | 4 inst/doc/PSI-documentation.R | 8 inst/doc/PSI-documentation.Rmd | 18 inst/doc/PSI-documentation.html | 18 inst/doc/SSI-documentation.R | 4 inst/doc/SSI-documentation.Rmd | 12 inst/doc/SSI-documentation.html | 12 man/BinaryFiles.Rd | 16 man/LARS.Rd | 25 - man/Methods_LASSO.Rd | 17 man/Methods_SSI.Rd | 28 - man/SSI.Rd | 50 +- man/collect.Rd | 17 man/fitBLUP.Rd | 17 man/getGenCov.Rd | 11 man/net.plot.Rd | 21 man/path.plot.Rd | 31 - man/solveEN.Rd | 37 + man/wheat.Rd | 32 - src/c_utils.c | 971 ++++++++++++++++++++-------------------- src/init.c | 14 vignettes/PSI-documentation.Rmd | 18 vignettes/SSI-documentation.Rmd | 12 49 files changed, 1728 insertions(+), 1236 deletions(-)
Title: Nonparametric Kernel Smoothing Methods for Mixed Data Types
Description: Nonparametric (and semiparametric) kernel methods that seamlessly handle a mix of continuous, unordered, and ordered factor data types. We would like to gratefully acknowledge support from the Natural Sciences and Engineering Research Council of Canada (NSERC, <https://www.nserc-crsng.gc.ca/>), the Social Sciences and Humanities Research Council of Canada (SSHRC, <https://www.sshrc-crsh.gc.ca/>), and the Shared Hierarchical Academic Research Computing Network (SHARCNET, <https://sharcnet.ca/>).
Author: Jeffrey S. Racine [aut, cre],
Tristen Hayfield [aut]
Maintainer: Jeffrey S. Racine <racinej@mcmaster.ca>
Diff between np versions 0.60-11 dated 2021-06-14 and 0.60-13 dated 2022-08-16
CHANGELOG | 18 +++++++++++++++++- DESCRIPTION | 8 ++++---- MD5 | 46 +++++++++++++++++++++++----------------------- R/np.copula.R | 6 ++++-- R/np.kernel.R | 3 ++- R/np.quantile.R | 6 ++++-- R/np.sigtest.R | 3 ++- R/zzz.R | 2 +- build/vignette.rds |binary data/cps71.rda |binary inst/CITATION | 8 ++++---- inst/doc/entropy_np.R | 2 +- inst/doc/entropy_np.Rnw | 4 ++-- inst/doc/entropy_np.pdf |binary inst/doc/np.R | 2 +- inst/doc/np.Rnw | 10 +++++----- inst/doc/np.pdf |binary inst/doc/np_faq.Rnw | 32 +++++++++++++++++++++++++++++--- inst/doc/np_faq.pdf |binary vignettes/entropy_np.Rnw | 4 ++-- vignettes/entropy_np.bib | 20 ++++++++++++-------- vignettes/np.Rnw | 10 +++++----- vignettes/np.bib | 19 +++++++++++-------- vignettes/np_faq.Rnw | 32 +++++++++++++++++++++++++++++--- 24 files changed, 158 insertions(+), 77 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 'm [...truncated...]
Author: David Cortes [aut, cre, cph],
Dmitry Selivanov [cph],
Thibaut Goetghebuer-Planchon [cph] ,
Martin Maechler [cph] ,
Robert Gentleman [cph] ,
Ross Ihaka [cph]
Maintainer: David Cortes <david.cortes.rivera@gmail.com>
Diff between MatrixExtra versions 0.1.11 dated 2022-08-06 and 0.1.12 dated 2022-08-16
DESCRIPTION | 9 MD5 | 20 NAMESPACE | 1 R/conversions.R | 275 +++++++++++ inst/doc/Introducing_MatrixExtra.html | 799 +++++++++++++++++++++++---------- src/matmul.cpp | 8 tests/testthat/test-conversions.R | 297 ++++++++++++ tests/testthat/test-matmul.R | 1 tests/testthat/test-slice.R | 18 vignettes/Introducing_MatrixExtra.Rmd | 10 vignettes/Introducing_MatrixExtra.html | 799 +++++++++++++++++++++++---------- 11 files changed, 1746 insertions(+), 491 deletions(-)
Title: Jacobi Theta Functions and Related Functions
Description: Evaluation of the Jacobi theta functions and related
functions: Weierstrass elliptic function, Weierstrass sigma function,
Weierstrass zeta function, Klein j-function, Dedekind eta function,
lambda modular function, Jacobi elliptic functions, Neville theta
functions, and Eisenstein series. Complex values of the variable are
supported.
Author: Stephane Laurent [aut, cre],
Mikael Fremling [aut]
Maintainer: Stephane Laurent <laurent_step@outlook.fr>
Diff between jacobi versions 2.0.0 dated 2022-07-19 and 2.0.1 dated 2022-08-16
DESCRIPTION | 6 MD5 | 72 ++--- NAMESPACE | 70 ++--- NEWS.md | 37 +-- R/CostaMesh.R | 174 +++++++------- R/RcppExports.R | 246 ++++++++++---------- R/aaa.R | 8 R/agm.R | 40 +-- R/am.R | 38 +-- R/eisenstein.R | 90 +++---- R/eta-dedekind.R | 36 +- R/internal.R | 190 +++++++-------- R/jellip.R | 92 +++---- R/jtheta.R | 344 ++++++++++++++-------------- R/jtheta1derivatives.R | 58 ++-- R/klein-j.R | 110 ++++----- R/lambda.R | 96 +++---- R/theta-neville.R | 162 ++++++------- R/weierstrassStuff.R | 94 +++---- R/wp.R | 440 ++++++++++++++++++------------------ R/wpinv.R | 112 ++++----- R/wsigma.R | 142 +++++------ R/wzeta.R | 136 +++++------ README.md | 74 +++--- src/jacobi.cpp | 4 tests/testthat/test-agm.R | 12 tests/testthat/test-am.R | 18 - tests/testthat/test-eta.R | 8 tests/testthat/test-jellip.R | 14 - tests/testthat/test-jtheta.R | 6 tests/testthat/test-kleinj.R | 64 ++--- tests/testthat/test-lambda.R | 20 - tests/testthat/test-theta-neville.R | 12 tests/testthat/test-wp.R | 70 ++--- tests/testthat/test-wpinv.R | 12 tests/testthat/test-wsigma.R | 20 - tests/testthat/test-wzeta.R | 58 ++-- 37 files changed, 1595 insertions(+), 1590 deletions(-)
Title: Adaptive Multivariate Integration over Hypercubes
Description: R wrappers around the cubature C library of Steven
G. Johnson for adaptive multivariate integration over hypercubes
and the Cuba C library of Thomas Hahn for deterministic and
Monte Carlo integration. Scalar and vector interfaces for
cubature and Cuba routines are provided; the vector interfaces
are highly recommended as demonstrated in the package
vignette.
Author: Balasubramanian Narasimhan [aut, cre],
Manuel Koller [ctb],
Steven G. Johnson [aut],
Thomas Hahn [aut],
Annie Bouvier [aut],
Kien Kieu [aut],
Simen Gaure [ctb]
Maintainer: Balasubramanian Narasimhan <naras@stat.stanford.edu>
Diff between cubature versions 2.0.4.4 dated 2022-03-22 and 2.0.4.5 dated 2022-08-16
DESCRIPTION | 8 MD5 | 40 +-- NEWS.md | 5 R/cubintegrate.R | 18 - R/cuhre.R | 77 ++---- R/divonne.R | 94 ++++---- R/hcubature.R | 24 +- R/suave.R | 14 - R/vegas.R | 22 - build/vignette.rds |binary inst/doc/cubature.html | 506 ++++++++++++++++++++++----------------------- inst/doc/version2.html | 26 +- man/cubintegrate.Rd | 10 man/cuhre.Rd | 64 +---- man/divonne.Rd | 93 +++----- man/hcubature.Rd | 2 man/suave.Rd | 59 +---- man/vegas.Rd | 57 +---- src/Cuba-4.2/config.log | 175 ++++++++------- src/Cuba-4.2/config.status | 16 - src/Cuba-4.2/makefile | 2 21 files changed, 603 insertions(+), 709 deletions(-)
Title: Tidy Verbs for Fast Data Manipulation
Description: A toolkit of tidy data manipulation verbs with 'data.table' as the backend.
Combining the merits of syntax elegance from 'dplyr' and computing performance from 'data.table',
'tidyfst' intends to provide users with state-of-the-art data manipulation tools with least pain.
This package is an extension of 'data.table'. While enjoying a tidy syntax,
it also wraps combinations of efficient functions to facilitate frequently-used data operations.
Author: Tian-Yuan Huang [aut, cre]
Maintainer: Tian-Yuan Huang <huang.tian-yuan@qq.com>
Diff between tidyfst versions 1.7.0 dated 2022-08-06 and 1.7.1 dated 2022-08-16
DESCRIPTION | 8 ++++---- MD5 | 19 ++++++++++--------- NAMESPACE | 4 ++++ R/pkg_load.R | 4 ++-- R/summarise_dt.R | 20 -------------------- R/sys_time_print.R | 1 + inst/doc/benchmark.html | 32 ++++++++++++++++---------------- inst/doc/chinese_tutorial.html | 20 ++++++++++---------- man/grapes-notin-grapes.Rd |only man/reexports.Rd | 4 +++- man/sys_time_print.Rd | 3 +++ 11 files changed, 53 insertions(+), 62 deletions(-)
Title: R Templates from the University of Miami
Description: This holds some r markdown templates and a template to create a
research project in RStudio.
Author: Raymond Balise [aut, cre] ,
Gabriel Odom [aut] ,
Kyle Grealis [aut] ,
Francisco Cardozo [aut] ,
Frank Gutierrez [ctb]
Maintainer: Raymond Balise <balise@miami.edu>
Diff between rUM versions 0.3.1 dated 2021-11-22 and 1.0.1 dated 2022-08-16
rUM-0.3.1/rUM/inst/doc/make_research_project.R |only rUM-0.3.1/rUM/inst/doc/make_research_project.Rmd |only rUM-0.3.1/rUM/inst/doc/make_research_project.html |only rUM-0.3.1/rUM/vignettes/make_research_project.Rmd |only rUM-1.0.1/rUM/DESCRIPTION | 38 + rUM-1.0.1/rUM/LICENSE | 4 rUM-1.0.1/rUM/MD5 | 68 ++- rUM-1.0.1/rUM/NAMESPACE | 17 rUM-1.0.1/rUM/NEWS.md | 102 ++-- rUM-1.0.1/rUM/R/make_project.R | 221 ++++------ rUM-1.0.1/rUM/README.md | 146 ++++-- rUM-1.0.1/rUM/build/vignette.rds |binary rUM-1.0.1/rUM/inst/bookFiles/bibliography.bib | 16 rUM-1.0.1/rUM/inst/bookFiles/style.css | 20 rUM-1.0.1/rUM/inst/doc/O1_make_research_project.R |only rUM-1.0.1/rUM/inst/doc/O1_make_research_project.Rmd |only rUM-1.0.1/rUM/inst/doc/O1_make_research_project.html |only rUM-1.0.1/rUM/inst/doc/O2_make_research_project_markdown.R |only rUM-1.0.1/rUM/inst/doc/O2_make_research_project_markdown.Rmd |only rUM-1.0.1/rUM/inst/doc/O2_make_research_project_markdown.html |only rUM-1.0.1/rUM/inst/doc/O3_R_Markdown_Templates.R |only rUM-1.0.1/rUM/inst/doc/O3_R_Markdown_Templates.Rmd |only rUM-1.0.1/rUM/inst/doc/O3_R_Markdown_Templates.html |only rUM-1.0.1/rUM/inst/rmarkdown/templates/bookdown_siteWithRum/skeleton/skeleton.Rmd | 108 ++-- rUM-1.0.1/rUM/inst/rmarkdown/templates/bookdown_siteWithRum/template.yaml | 4 rUM-1.0.1/rUM/inst/rmarkdown/templates/html2DetailsWithRum/skeleton/skeleton.Rmd | 90 ++-- rUM-1.0.1/rUM/inst/rmarkdown/templates/html2DetailsWithRum/template.yaml | 4 rUM-1.0.1/rUM/inst/rmarkdown/templates/html2WithRum/skeleton/skeleton.Rmd | 70 +-- rUM-1.0.1/rUM/inst/rmarkdown/templates/html2WithRum/template.yaml | 4 rUM-1.0.1/rUM/inst/rmarkdown/templates/pdf2ShowingLatex/skeleton/skeleton.Rmd | 94 ++-- rUM-1.0.1/rUM/inst/rmarkdown/templates/pdf2ShowingLatex/template.yaml | 4 rUM-1.0.1/rUM/inst/rstudio/templates/project/research_project.dcf | 12 rUM-1.0.1/rUM/man/figures/r.png |only rUM-1.0.1/rUM/man/make_project.Rd | 75 +-- rUM-1.0.1/rUM/vignettes/O1_make_research_project.Rmd |only rUM-1.0.1/rUM/vignettes/O2_make_research_project_markdown.Rmd |only rUM-1.0.1/rUM/vignettes/O3_R_Markdown_Templates.Rmd |only rUM-1.0.1/rUM/vignettes/analysis_Rmd_file.jpg |only rUM-1.0.1/rUM/vignettes/analysis_quarto_file.png |only rUM-1.0.1/rUM/vignettes/created_rUM_markdown_files.png |only rUM-1.0.1/rUM/vignettes/created_rUM_quarto_files.png |only rUM-1.0.1/rUM/vignettes/existing_directory.png |only rUM-1.0.1/rUM/vignettes/from_template.png |only rUM-1.0.1/rUM/vignettes/newfile_markdown.jpg |only rUM-1.0.1/rUM/vignettes/package-logo.jpg |only rUM-1.0.1/rUM/vignettes/project_template.png |only rUM-1.0.1/rUM/vignettes/save_markdown_project_here.png |only rUM-1.0.1/rUM/vignettes/save_quarto_project_here.png |only rUM-1.0.1/rUM/vignettes/template1.png |only rUM-1.0.1/rUM/vignettes/template2.png |only 50 files changed, 617 insertions(+), 480 deletions(-)
Title: Identify Rogue Taxa in Sets of Phylogenetic Trees
Description: Rogue ("wildcard") taxa are leaves with uncertain phylogenetic
position.
Their position may vary from tree to tree under inference methods that yield a
tree set (e.g. bootstrapping, Bayesian tree searches, maximum parsimony).
The presence of rogue taxa in a tree set can potentially remove all
information from a consensus tree. The information content of a consensus
tree - a function of its resolution and branch support values - can often be
increased by removing rogue taxa.
'Rogue' provides an explicitly information-theoretic approach to rogue
detection (Smith 2022) <doi:10.1093/sysbio/syab099>,
and an interface to 'RogueNaRok' (Aberer et al. 2013)
<doi:10.1093/sysbio/sys078>.
Author: Martin R. Smith [aut, cre, cph]
,
Andre J. Aberer [aut, cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between Rogue versions 2.1.1 dated 2022-07-20 and 2.1.2 dated 2022-08-16
DESCRIPTION | 8 ++-- MD5 | 24 ++++++------ NEWS.md | 7 +++ R/RogueTaxa.R | 68 +++++++++++++++++------------------- R/SPIC.R | 55 ++++++++++++++--------------- R/utilities.R | 7 +++ build/partial.rdb |binary inst/CITATION | 8 ++-- inst/REFERENCES.bib | 5 +- inst/doc/Bayesian.html | 79 ++++++++++++++++------------------------- man/RogueTaxa.Rd | 14 +++---- tests/spelling.R | 2 - tests/testthat/test-spic.R | 85 +++++++++++++++++++++++---------------------- 13 files changed, 182 insertions(+), 180 deletions(-)
Title: Implement Download Buttons in 'rmarkdown'
Description: Implement download buttons in HTML output from 'rmarkdown' without the need for 'runtime:shiny'.
Author: Felipe Mattioni Maturana [aut, cre]
,
John Coene [ctb]
Maintainer: Felipe Mattioni Maturana <felipe.mattioni@med.uni-tuebingen.de>
Diff between downloadthis versions 0.3.1 dated 2022-02-23 and 0.3.2 dated 2022-08-16
DESCRIPTION | 8 - MD5 | 12 +- NEWS.md | 4 inst/doc/button_types.html | 224 +++++++++++++++++++++++++++++++++++++++-- inst/doc/customization.html | 226 +++++++++++++++++++++++++++++++++++++++-- inst/doc/downloadthis.html | 237 +++++++++++++++++++++++++++++++++++++++++--- man/downloadthis-package.Rd | 2 7 files changed, 665 insertions(+), 48 deletions(-)
Title: Multi-Action Conservation Planning
Description: This uses a mixed integer mathematical programming (MIP)
approach for building and solving multi-action planning problems,
where the goal is to find an optimal combination of management actions that
abate threats, in an efficient way while accounting for spatial aspects.
Thus, optimizing the connectivity and conservation effectiveness of
the prioritized units and of the deployed actions. The package is capable of
handling different commercial (gurobi, CPLEX) and non-commercial (symphony) MIP solvers.
Gurobi optimization solver can be installed using comprehensive instructions in
the gurobi installation vignette of the prioritizr package (available in
<https://prioritizr.net/articles/gurobi_installation_guide.html>). Instead, CPLEX
optimization solver can be obtain from IBM CPLEX web page (available here
<https://www.ibm.com/es-es/products/ilog-cplex-optimization-studio>). Methods used in the
package refers to Salgado-Rojas et al. (2020) <doi:10.1016/j.ecolmodel.2019.1089 [...truncated...]
Author: Jose Salgado-Rojas [aut, cre],
Irlanda Ceballos-Fuentealba [aut],
Virgilio Hermoso [aut],
Eduardo Alvarez-Miranda [aut],
Jordi Garcia-Gonzalo [aut]
Maintainer: Jose Salgado-Rojas <jose.salgroj@gmail.com>
Diff between prioriactions versions 0.4 dated 2022-02-09 and 0.4.1 dated 2022-08-16
DESCRIPTION | 29 - MD5 | 53 +-- NEWS.md | 83 ++-- R/getActions.R | 3 R/getCost.R | 1 R/getSolutionBenefit.R | 2 R/inputData.R | 20 - R/internal.R | 142 +++++++- R/presolve.R | 8 R/solve.R | 116 ++++++ R/writeOutputs.R | 36 +- build/vignette.rds |binary inst/doc/objectives.html | 322 +++++++++++++++++-- inst/doc/sensitivities.html | 450 ++++++++++++++++++++++++--- man/inputData.Rd | 2 man/solve.Rd | 22 + src/functions.h | 5 tests/testthat.R | 1 tests/testthat/helper_skip.R |only tests/testthat/test_evalBlm.R | 2 tests/testthat/test_evalBudget.R | 2 tests/testthat/test_evalTarget.R | 2 tests/testthat/test_getActions.R | 5 tests/testthat/test_getConnectivityPenalty.R | 3 tests/testthat/test_getCost.R | 3 tests/testthat/test_getPerformance.R | 3 tests/testthat/test_getSolutionBenefit.R | 6 tests/testthat/test_solve.R | 7 28 files changed, 1116 insertions(+), 212 deletions(-)
Title: Gravitational N-Body Simulation
Description: Tools to run simple direct gravitational N-body simulations. It can access different external N-body simulators, but also has a simple built-in default simulator. This default simulator uses a variable block time step and lets the user choose between a range of integrators, including 4th and 6th order integrators for high-accuracy simulations. Basic top-hat smoothing is available as an option. The code also allows the definition of background particles that are fixed or in uniform motion, not subject to acceleration by other particles.
Author: Danail Obreschkow
Maintainer: Danail Obreschkow <danail.obreschkow@gmail.com>
Diff between nbody versions 1.31 dated 2022-03-04 and 1.33 dated 2022-08-16
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/run.simulation.R | 4 +++- man/run.simulation.Rd | 2 +- src/energypot.cpp | 2 +- 5 files changed, 13 insertions(+), 11 deletions(-)
Title: Fairness Auditing and Debiasing for 'mlr3'
Description: Integrates fairness auditing and bias mitigation methods for the 'mlr3' ecosystem.
This includes fairness metrics, reporting tools, visualizations and bias mitigation techniques such as
"Reweighing" described in 'Kamiran, Calders' (2012) <doi:10.1007/s10115-011-0463-8> and
"Equalized Odds" described in 'Hardt et al.' (2016) <https://papers.nips.cc/paper/2016/file/9d2682367c3935defcb1f9e247a97c0d-Paper.pdf>.
Integration with 'mlr3' allows for auditing of ML models as well as convenient joint tuning of
machine learning algorithms and debiasing methods.
Author: Florian Pfisterer [cre, aut] ,
Wei Siyi [aut],
Michel Lang [aut]
Maintainer: Florian Pfisterer <pfistererf@googlemail.com>
Diff between mlr3fairness versions 0.3.0 dated 2022-05-12 and 0.3.1 dated 2022-08-16
DESCRIPTION | 12 ++-- MD5 | 65 ++++++++++++------------ NEWS.md | 4 + R/fairness_accuracy_tradeoff.R | 18 +++--- R/zzz.R | 4 - build/partial.rdb |only inst/doc/debiasing-vignette.html | 20 +++---- inst/doc/measures-vignette.html | 20 +++---- inst/doc/visualization-vignette.html | 28 +++++----- man/MeasureFairness.Rd | 34 ++++++------- man/MeasureFairnessComposite.Rd | 34 ++++++------- man/MeasureFairnessConstraint.Rd | 34 ++++++------- man/MeasureSubgroup.Rd | 34 ++++++------- man/compas.Rd | 12 +++- man/fairness_accuracy_tradeoff.Rd | 18 +++--- man/mlr3fairness-package.Rd | 2 man/mlr_learners_classif.fairfgrrm.Rd | 46 +++++++++-------- man/mlr_learners_classif.fairzlrm.Rd | 46 +++++++++-------- man/mlr_learners_regr.fairfrrm.Rd | 51 ++++++++++--------- man/mlr_learners_regr.fairnclm.Rd | 46 +++++++++-------- man/mlr_learners_regr.fairzlm.Rd | 46 +++++++++-------- man/mlr_measures_positive_probability.Rd | 34 ++++++------- man/mlr_pipeops_equalized_odds.Rd | 37 +++++++------- man/mlr_pipeops_explicit_pta.Rd | 37 +++++++------- man/mlr_pipeops_reweighing.Rd | 68 +++++++++++++------------- tests/testthat/helper_data.R | 10 +-- tests/testthat/helper_test.R | 13 ++-- tests/testthat/test_datasets.R | 1 tests/testthat/test_learners_fairml.R | 1 tests/testthat/test_measure_subgroup.R | 1 tests/testthat/test_measures.R | 4 - tests/testthat/test_pipeop_reweighing.R | 8 +-- tests/testthat/test_use_modelcard_datasheet.R | 3 + tests/testthat/test_visualizations.R | 18 ++++-- 34 files changed, 428 insertions(+), 381 deletions(-)
Title: KMunicate-Style Kaplan–Meier Plots
Description: Produce Kaplan–Meier plots in the style recommended
following the KMunicate study by Morris et al. (2019)
<doi:10.1136/bmjopen-2019-030215>. The KMunicate style consists of
Kaplan-Meier curves with confidence intervals to quantify uncertainty
and an extended risk table (per treatment arm) depicting the number of
study subjects at risk, events, and censored observations over time.
The resulting plots are built using 'ggplot2' and can be further
customised to a certain extent, including themes, fonts, and colour
scales.
Author: Alessandro Gasparini [aut, cre, cph]
,
Ary Serpa Neto [ctb]
Maintainer: Alessandro Gasparini <alessandro@ellessenne.xyz>
Diff between KMunicate versions 0.2.1 dated 2021-04-23 and 0.2.2 dated 2022-08-16
DESCRIPTION | 12 LICENSE | 2 MD5 | 24 - NEWS.md | 5 README.md | 6 build/partial.rdb |binary build/vignette.rds |binary inst/doc/KMunicate.html | 403 +++++++++++++++++++++------- man/figures/README-brcancer-1.png |binary man/figures/README-brcancer-KMunicate-1.png |binary man/figures/README-brcancer-NULL-1.png |binary man/figures/README-brcancer-reverse-1.png |binary man/figures/README-brcancer-survfit-1.png |binary 13 files changed, 338 insertions(+), 114 deletions(-)
Title: Infix Functions For Vector Operations
Description: Vector operations between grapes: An infix-only package! The 'invctr' functions perform common and less common operations on vectors, data frames matrices and list objects:
- Extracting a value (range), or, finding the indices of a value (range).
- Trimming, or padding a vector with a value of your choice.
- Simple polynomial regression.
- Set and membership operations.
- General check & replace function for NAs, Inf and other values.
Author: Fred Hasselman [aut, cre]
Maintainer: Fred Hasselman <fred.hasselman@ru.nl>
Diff between invctr versions 0.1.0 dated 2019-03-07 and 0.2.0 dated 2022-08-16
DESCRIPTION | 15 INDEX | 18 - MD5 | 22 - R/invictor.R | 30 - README.md | 2 build/vignette.rds |binary inst/doc/insiders.R | 18 - inst/doc/insiders.html | 831 +++++++++++++++++++++++++++++++----------------- inst/doc/padders.R | 14 inst/doc/padders.html | 684 +++++++++++++++++++++++++++------------ man/grapes-00-grapes.Rd | 2 man/invctr-package.Rd | 11 12 files changed, 1088 insertions(+), 559 deletions(-)
Title: Collecting Social Media Data and Generating Networks for
Analysis
Description: A suite of easy to use functions for collecting social media
data and generating networks for analysis. Supports Twitter, YouTube,
Reddit and web site data sources.
Author: Bryan Gertzel [aut, cre],
Robert Ackland [aut] ,
Timothy Graham [aut] ,
Francisca Borquez [ctb]
Maintainer: Bryan Gertzel <bryan.gertzel@anu.edu.au>
Diff between vosonSML versions 0.29.13 dated 2020-07-18 and 0.32.7 dated 2022-08-16
vosonSML-0.29.13/vosonSML/R/Collect.twitter.R |only vosonSML-0.29.13/vosonSML/R/ImportData.R |only vosonSML-0.29.13/vosonSML/R/Utils.reddit.R |only vosonSML-0.29.13/vosonSML/R/Utils.twitter.R |only vosonSML-0.29.13/vosonSML/R/Utils.youtube.R |only vosonSML-0.29.13/vosonSML/man/Collect.twitter.Rd |only vosonSML-0.29.13/vosonSML/man/vosonSML-colon-colon-AddText.Rd |only vosonSML-0.29.13/vosonSML/man/vosonSML-colon-colon-AddText.activity.reddit.Rd |only vosonSML-0.29.13/vosonSML/man/vosonSML-colon-colon-AddText.actor.reddit.Rd |only vosonSML-0.29.13/vosonSML/man/vosonSML-colon-colon-AddText.actor.youtube.Rd |only vosonSML-0.29.13/vosonSML/man/vosonSML-colon-colon-AddUserData.Rd |only vosonSML-0.29.13/vosonSML/man/vosonSML-colon-colon-AddUserData.actor.twitter.Rd |only vosonSML-0.29.13/vosonSML/man/vosonSML-colon-colon-AddVideoData.Rd |only vosonSML-0.29.13/vosonSML/man/vosonSML-colon-colon-AddVideoData.actor.youtube.Rd |only vosonSML-0.29.13/vosonSML/man/vosonSML-colon-colon-GetYoutubeVideoIDs.Rd |only vosonSML-0.29.13/vosonSML/man/vosonSML-colon-colon-Graph.Rd |only vosonSML-0.29.13/vosonSML/man/vosonSML-colon-colon-ImportData.Rd |only vosonSML-0.29.13/vosonSML/tests |only vosonSML-0.32.7/vosonSML/DESCRIPTION | 46 vosonSML-0.32.7/vosonSML/MD5 | 160 vosonSML-0.32.7/vosonSML/NAMESPACE | 114 vosonSML-0.32.7/vosonSML/NEWS.md | 160 vosonSML-0.32.7/vosonSML/R/AddText.R | 501 +- vosonSML-0.32.7/vosonSML/R/AddText.twitter.R |only vosonSML-0.32.7/vosonSML/R/AddUserData.R | 418 +- vosonSML-0.32.7/vosonSML/R/AddVideoData.R | 299 - vosonSML-0.32.7/vosonSML/R/Authenticate.R | 34 vosonSML-0.32.7/vosonSML/R/Authenticate.reddit.R | 26 vosonSML-0.32.7/vosonSML/R/Authenticate.twitter.R | 221 - vosonSML-0.32.7/vosonSML/R/Authenticate.web.R |only vosonSML-0.32.7/vosonSML/R/Authenticate.youtube.R | 36 vosonSML-0.32.7/vosonSML/R/Collect.R | 82 vosonSML-0.32.7/vosonSML/R/Collect.reddit.R | 518 +- vosonSML-0.32.7/vosonSML/R/Collect.search.twitter.R |only vosonSML-0.32.7/vosonSML/R/Collect.timeline.twitter.R |only vosonSML-0.32.7/vosonSML/R/Collect.web.R |only vosonSML-0.32.7/vosonSML/R/Collect.youtube.R | 770 ++- vosonSML-0.32.7/vosonSML/R/Create.R | 75 vosonSML-0.32.7/vosonSML/R/Create.activity.reddit.R | 148 vosonSML-0.32.7/vosonSML/R/Create.activity.twitter.R | 293 - vosonSML-0.32.7/vosonSML/R/Create.activity.web.R |only vosonSML-0.32.7/vosonSML/R/Create.activity.youtube.R | 199 - vosonSML-0.32.7/vosonSML/R/Create.actor.reddit.R | 166 vosonSML-0.32.7/vosonSML/R/Create.actor.twitter.R | 497 +- vosonSML-0.32.7/vosonSML/R/Create.actor.web.R |only vosonSML-0.32.7/vosonSML/R/Create.actor.youtube.R | 146 vosonSML-0.32.7/vosonSML/R/Create.semantic.twitter.R | 571 +- vosonSML-0.32.7/vosonSML/R/Create.twomode.twitter.R | 274 - vosonSML-0.32.7/vosonSML/R/Graph.R | 345 + vosonSML-0.32.7/vosonSML/R/Merge.R |only vosonSML-0.32.7/vosonSML/R/Utils.R | 649 ++- vosonSML-0.32.7/vosonSML/R/import_rtweet.R |only vosonSML-0.32.7/vosonSML/R/tokens_twitter.R |only vosonSML-0.32.7/vosonSML/R/utils_reddit.R |only vosonSML-0.32.7/vosonSML/R/utils_twitter.R |only vosonSML-0.32.7/vosonSML/R/utils_web.R |only vosonSML-0.32.7/vosonSML/R/utils_youtube.R |only vosonSML-0.32.7/vosonSML/R/vosonSML-package.R | 49 vosonSML-0.32.7/vosonSML/R/wrappers.R |only vosonSML-0.32.7/vosonSML/README.md | 1151 ++++- vosonSML-0.32.7/vosonSML/build/vignette.rds |binary vosonSML-0.32.7/vosonSML/inst/CITATION |only vosonSML-0.32.7/vosonSML/inst/doc/Intro-to-vosonSML.R | 478 +- vosonSML-0.32.7/vosonSML/inst/doc/Intro-to-vosonSML.Rmd | 1098 +++-- vosonSML-0.32.7/vosonSML/inst/doc/Intro-to-vosonSML.html | 1926 ++++++---- vosonSML-0.32.7/vosonSML/man/AddText.Rd |only vosonSML-0.32.7/vosonSML/man/AddText.activity.reddit.Rd |only vosonSML-0.32.7/vosonSML/man/AddText.activity.twitter.Rd |only vosonSML-0.32.7/vosonSML/man/AddText.actor.reddit.Rd |only vosonSML-0.32.7/vosonSML/man/AddText.actor.twitter.Rd |only vosonSML-0.32.7/vosonSML/man/AddText.actor.youtube.Rd |only vosonSML-0.32.7/vosonSML/man/AddText.semantic.twitter.Rd |only vosonSML-0.32.7/vosonSML/man/AddText.twomode.twitter.Rd |only vosonSML-0.32.7/vosonSML/man/AddUserData.Rd |only vosonSML-0.32.7/vosonSML/man/AddUserData.actor.twitter.Rd |only vosonSML-0.32.7/vosonSML/man/AddUserData.twomode.twitter.Rd |only vosonSML-0.32.7/vosonSML/man/AddVideoData.Rd |only vosonSML-0.32.7/vosonSML/man/AddVideoData.actor.youtube.Rd |only vosonSML-0.32.7/vosonSML/man/Authenticate.Rd | 49 vosonSML-0.32.7/vosonSML/man/Authenticate.reddit.Rd | 64 vosonSML-0.32.7/vosonSML/man/Authenticate.twitter.Rd | 165 vosonSML-0.32.7/vosonSML/man/Authenticate.web.Rd |only vosonSML-0.32.7/vosonSML/man/Authenticate.youtube.Rd | 64 vosonSML-0.32.7/vosonSML/man/Collect.Rd | 44 vosonSML-0.32.7/vosonSML/man/Collect.reddit.Rd | 116 vosonSML-0.32.7/vosonSML/man/Collect.search.twitter.Rd |only vosonSML-0.32.7/vosonSML/man/Collect.timeline.twitter.Rd |only vosonSML-0.32.7/vosonSML/man/Collect.web.Rd |only vosonSML-0.32.7/vosonSML/man/Collect.youtube.Rd | 59 vosonSML-0.32.7/vosonSML/man/Create.Rd | 67 vosonSML-0.32.7/vosonSML/man/Create.activity.reddit.Rd | 70 vosonSML-0.32.7/vosonSML/man/Create.activity.twitter.Rd | 82 vosonSML-0.32.7/vosonSML/man/Create.activity.web.Rd |only vosonSML-0.32.7/vosonSML/man/Create.activity.youtube.Rd | 70 vosonSML-0.32.7/vosonSML/man/Create.actor.reddit.Rd | 66 vosonSML-0.32.7/vosonSML/man/Create.actor.twitter.Rd | 109 vosonSML-0.32.7/vosonSML/man/Create.actor.web.Rd |only vosonSML-0.32.7/vosonSML/man/Create.actor.youtube.Rd | 70 vosonSML-0.32.7/vosonSML/man/Create.semantic.twitter.Rd | 105 vosonSML-0.32.7/vosonSML/man/Create.twomode.twitter.Rd | 40 vosonSML-0.32.7/vosonSML/man/Graph.Rd |only vosonSML-0.32.7/vosonSML/man/ImportRtweet.Rd |only vosonSML-0.32.7/vosonSML/man/Merge.Rd |only vosonSML-0.32.7/vosonSML/man/MergeFiles.Rd |only vosonSML-0.32.7/vosonSML/man/auth_twitter_app.Rd |only vosonSML-0.32.7/vosonSML/man/auth_twitter_dev.Rd |only vosonSML-0.32.7/vosonSML/man/auth_twitter_user.Rd |only vosonSML-0.32.7/vosonSML/man/vosonSML-package.Rd | 62 vosonSML-0.32.7/vosonSML/vignettes/Intro-to-vosonSML.Rmd | 1098 +++-- 109 files changed, 8622 insertions(+), 5228 deletions(-)
Title: The Uniform Manifold Approximation and Projection (UMAP) Method
for Dimensionality Reduction
Description: An implementation of the Uniform Manifold Approximation and
Projection dimensionality reduction by McInnes et al. (2018)
<arXiv:1802.03426>. It also provides means to transform new data and to
carry out supervised dimensionality reduction. An implementation of the
related LargeVis method of Tang et al. (2016) <arXiv:1602.00370> is also
provided. This is a complete re-implementation in R (and C++, via the 'Rcpp'
package): no Python installation is required. See the uwot website
(<https://github.com/jlmelville/uwot>) for more documentation and examples.
Author: James Melville [aut, cre],
Aaron Lun [ctb],
Mohamed Nadhir Djekidel [ctb],
Yuhan Hao [ctb]
Maintainer: James Melville <jlmelville@gmail.com>
Diff between uwot versions 0.1.11 dated 2021-12-02 and 0.1.13 dated 2022-08-16
uwot-0.1.11/uwot/inst/include/uwot/matrix.h |only uwot-0.1.13/uwot/DESCRIPTION | 12 uwot-0.1.13/uwot/MD5 | 100 - uwot-0.1.13/uwot/NEWS.md | 94 + uwot-0.1.13/uwot/R/RcppExports.R | 82 - uwot-0.1.13/uwot/R/affinity.R | 227 +++ uwot-0.1.13/uwot/R/bigstatsr_init.R | 4 uwot-0.1.13/uwot/R/init.R | 188 ++- uwot-0.1.13/uwot/R/neighbors.R | 13 uwot-0.1.13/uwot/R/rspectra_init.R | 11 uwot-0.1.13/uwot/R/supervised.R | 342 ++--- uwot-0.1.13/uwot/R/transform.R | 329 +++-- uwot-0.1.13/uwot/R/util.R | 147 ++ uwot-0.1.13/uwot/R/uwot.R | 715 ++++++++---- uwot-0.1.13/uwot/build |only uwot-0.1.13/uwot/inst/include/RcppPerpendicular.h | 19 uwot-0.1.13/uwot/inst/include/uwot/gradient.h | 130 +- uwot-0.1.13/uwot/inst/include/uwot/perplexity.h | 223 +-- uwot-0.1.13/uwot/inst/include/uwot/smooth_knn.h | 301 ++--- uwot-0.1.13/uwot/inst/include/uwot/transform.h | 129 -- uwot-0.1.13/uwot/inst/include/uwot/update.h | 4 uwot-0.1.13/uwot/man/lvish.Rd | 56 uwot-0.1.13/uwot/man/tumap.Rd | 63 - uwot-0.1.13/uwot/man/umap.Rd | 95 + uwot-0.1.13/uwot/man/umap_transform.Rd | 42 uwot-0.1.13/uwot/man/unload_uwot.Rd | 124 +- uwot-0.1.13/uwot/src/RcppExports.cpp | 56 uwot-0.1.13/uwot/src/nn_parallel.h | 10 uwot-0.1.13/uwot/src/perplexity.cpp | 44 uwot-0.1.13/uwot/src/r_uwot.cpp | 43 uwot-0.1.13/uwot/src/smooth_knn.cpp | 72 - uwot-0.1.13/uwot/src/transform.cpp | 63 - uwot-0.1.13/uwot/tests/testthat/helper_data.R | 127 +- uwot-0.1.13/uwot/tests/testthat/helper_fuzzy_sets.R | 272 ++-- uwot-0.1.13/uwot/tests/testthat/test_curve.R | 24 uwot-0.1.13/uwot/tests/testthat/test_epochs.R | 42 uwot-0.1.13/uwot/tests/testthat/test_errors.R | 27 uwot-0.1.13/uwot/tests/testthat/test_fuzzy_simplicial_set.R | 296 ++-- uwot-0.1.13/uwot/tests/testthat/test_knn_aff.R | 98 - uwot-0.1.13/uwot/tests/testthat/test_mixed_distances.R | 208 +-- uwot-0.1.13/uwot/tests/testthat/test_neighbors.R | 73 - uwot-0.1.13/uwot/tests/testthat/test_normlaplacian.R | 73 + uwot-0.1.13/uwot/tests/testthat/test_output.R | 209 +++ uwot-0.1.13/uwot/tests/testthat/test_pca.R | 4 uwot-0.1.13/uwot/tests/testthat/test_perplexity.R | 372 +++--- uwot-0.1.13/uwot/tests/testthat/test_rand_init.R | 22 uwot-0.1.13/uwot/tests/testthat/test_saveload.R | 253 ++-- uwot-0.1.13/uwot/tests/testthat/test_scale.R | 58 uwot-0.1.13/uwot/tests/testthat/test_smooth_knn_dists.R | 495 +++++--- uwot-0.1.13/uwot/tests/testthat/test_spectral.R | 4 uwot-0.1.13/uwot/tests/testthat/test_supervised.R | 256 ++-- uwot-0.1.13/uwot/tests/testthat/test_transform.R | 98 + 52 files changed, 4197 insertions(+), 2552 deletions(-)
Title: 'SAS' Markdown
Description: Settings and functions to extend the 'knitr' 'SAS' engine.
Author: Doug Hemken [aut, cre] ,
Chao Cheng [ctb]
Maintainer: Doug Hemken <dehemken@wisc.edu>
Diff between SASmarkdown versions 0.4.3 dated 2017-11-30 and 0.7.2 dated 2022-08-16
SASmarkdown-0.4.3/SASmarkdown/inst/doc/SASloghooks.html |only SASmarkdown-0.4.3/SASmarkdown/inst/doc/basicuse.html |only SASmarkdown-0.4.3/SASmarkdown/inst/doc/collectcode.html |only SASmarkdown-0.4.3/SASmarkdown/inst/doc/index.html |only SASmarkdown-0.4.3/SASmarkdown/inst/doc/saserrors.html |only SASmarkdown-0.4.3/SASmarkdown/inst/doc/saveSASfiles.html |only SASmarkdown-0.4.3/SASmarkdown/inst/doc/spinSASmarkdown.html |only SASmarkdown-0.4.3/SASmarkdown/inst/doc/vigsource |only SASmarkdown-0.7.2/SASmarkdown/DESCRIPTION | 23 - SASmarkdown-0.7.2/SASmarkdown/LICENSE | 2 SASmarkdown-0.7.2/SASmarkdown/MD5 | 60 +--- SASmarkdown-0.7.2/SASmarkdown/NAMESPACE | 1 SASmarkdown-0.7.2/SASmarkdown/R/find_sas.r |only SASmarkdown-0.7.2/SASmarkdown/R/misc.r | 51 +++ SASmarkdown-0.7.2/SASmarkdown/R/sas_enginesetup.r | 2 SASmarkdown-0.7.2/SASmarkdown/R/sashtml.r | 26 + SASmarkdown-0.7.2/SASmarkdown/R/saslog.r | 36 ++ SASmarkdown-0.7.2/SASmarkdown/R/saslog_hookset.r | 2 SASmarkdown-0.7.2/SASmarkdown/R/sasloghook.r | 40 +- SASmarkdown-0.7.2/SASmarkdown/R/spinsas.r | 137 +++++++++- SASmarkdown-0.7.2/SASmarkdown/R/utils.R |only SASmarkdown-0.7.2/SASmarkdown/README.md | 7 SASmarkdown-0.7.2/SASmarkdown/inst/NEWS.Rd | 43 +++ SASmarkdown-0.7.2/SASmarkdown/inst/doc/1_Basic_Use_of_SASmarkdown.html |only SASmarkdown-0.7.2/SASmarkdown/inst/doc/2_Linking_SAS_Code_Chunks.html |only SASmarkdown-0.7.2/SASmarkdown/inst/doc/3_Cleaning_Up_SAS_Logs.html |only SASmarkdown-0.7.2/SASmarkdown/inst/doc/4_SAS_Errors.html |only SASmarkdown-0.7.2/SASmarkdown/inst/doc/5_Saving_Intermediate_SAS_Files.html |only SASmarkdown-0.7.2/SASmarkdown/inst/doc/7_Spinning_SASmarkdown.html |only SASmarkdown-0.7.2/SASmarkdown/man/find_sas.Rd |only SASmarkdown-0.7.2/SASmarkdown/man/sas_collectcode.Rd | 10 SASmarkdown-0.7.2/SASmarkdown/man/sas_enginesetup.rd | 11 SASmarkdown-0.7.2/SASmarkdown/man/sas_output.Rd | 10 SASmarkdown-0.7.2/SASmarkdown/man/saslog_hookset.rd | 12 SASmarkdown-0.7.2/SASmarkdown/man/spinsas.Rd | 5 35 files changed, 356 insertions(+), 122 deletions(-)
Title: Toolbox for Pseudo and Quasi Random Number Generation and Random
Generator Tests
Description: Provides (1) pseudo random generators - general linear congruential generators,
multiple recursive generators and generalized feedback shift register (SF-Mersenne Twister
algorithm and WELL generators); (2) quasi random generators - the Torus algorithm, the
Sobol sequence, the Halton sequence (including the Van der Corput sequence) and (3) some
generator tests - the gap test, the serial test, the poker test.
See e.g. Gentle (2003) <doi:10.1007/b97336>. The package can be provided
without the rngWELL dependency on demand.
Take a look at the Distribution task view of types and tests of random number generators.
Package in Memoriam of Diethelm and Barbara Wuertz.
Author: R port by Yohan Chalabi, Christophe Dutang, Petr Savicky and Diethelm Wuertz with some underlying C codes of the SFMT algorithm from M. Matsumoto and M. Saito, the Knuth-TAOCP RNG from D. Knuth.
Maintainer: Christophe Dutang <dutangc@gmail.com>
Diff between randtoolbox versions 2.0.1 dated 2022-06-09 and 2.0.2 dated 2022-08-16
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- build/vignette.rds |binary inst/NEWS | 10 +++++++++- inst/doc/fullpres.pdf |binary inst/doc/shortintro.pdf |binary man/colltest.Rd | 4 ++-- man/colltestsparse.Rd | 4 ++-- man/pseudoRNG.Rd | 2 +- 9 files changed, 25 insertions(+), 17 deletions(-)
Title: Linear Models for Panel Data
Description: A set of estimators for models and (robust) covariance matrices, and tests for panel data
econometrics, including within/fixed effects, random effects, between, first-difference,
nested random effects as well as instrumental-variable (IV) and Hausman-Taylor-style models,
panel generalized method of moments (GMM) and general FGLS models,
mean groups (MG), demeaned MG, and common correlated effects (CCEMG) and pooled (CCEP) estimators
with common factors, variable coefficients and limited dependent variables models.
Test functions include model specification, serial correlation, cross-sectional dependence,
panel unit root and panel Granger (non-)causality. Typical references are general econometrics
text books such as Baltagi (2021), Econometric Analysis of Panel Data (<doi:10.1007/978-3-030-53953-5>),
Hsiao (2014), Analysis of Panel Data (<doi:10.1017/CBO9781139839327>), and Croissant and Millo (2018),
Panel Data Econometrics with R (<doi:10.1002/9781119504641>).
Author: Yves Croissant [aut],
Giovanni Millo [aut],
Kevin Tappe [aut, cre],
Ott Toomet [ctb],
Christian Kleiber [ctb],
Achim Zeileis [ctb],
Arne Henningsen [ctb],
Liviu Andronic [ctb],
Nina Schoenfelder [ctb]
Maintainer: Kevin Tappe <kevin.tappe@bwi.uni-stuttgart.de>
Diff between plm versions 2.6-1 dated 2022-03-05 and 2.6-2 dated 2022-08-16
plm-2.6-1/plm/R/is.pconsecutive_pbalanced.R |only plm-2.6-2/plm/DESCRIPTION | 28 plm-2.6-2/plm/MD5 | 159 plm-2.6-2/plm/NEWS.md | 50 plm-2.6-2/plm/R/deprecated.R | 64 plm-2.6-2/plm/R/detect_lin_dep_alias.R | 9 plm-2.6-2/plm/R/est_cce.R | 297 - plm-2.6-2/plm/R/est_ggls.R | 61 plm-2.6-2/plm/R/est_gmm.R | 71 plm-2.6-2/plm/R/est_ldv.R | 44 plm-2.6-2/plm/R/est_mg.R | 85 plm-2.6-2/plm/R/est_pi.R | 29 plm-2.6-2/plm/R/est_plm.R | 6 plm-2.6-2/plm/R/est_plm.list.R | 14 plm-2.6-2/plm/R/est_vcm.R | 41 plm-2.6-2/plm/R/is.pconsecutive.R |only plm-2.6-2/plm/R/test_cd.R | 122 plm-2.6-2/plm/R/test_cips.R | 50 plm-2.6-2/plm/R/test_general.R | 6 plm-2.6-2/plm/R/test_granger.R | 7 plm-2.6-2/plm/R/test_serial.R | 85 plm-2.6-2/plm/R/test_uroot.R | 125 plm-2.6-2/plm/R/tool_argvalues.R | 1 plm-2.6-2/plm/R/tool_ercomp.R | 8 plm-2.6-2/plm/R/tool_methods.R | 182 plm-2.6-2/plm/R/tool_misc.R | 40 plm-2.6-2/plm/R/tool_model.extract.R | 2 plm-2.6-2/plm/R/tool_pdata.frame.R | 161 plm-2.6-2/plm/R/tool_ranfixef.R | 30 plm-2.6-2/plm/R/tool_transformations.R | 33 plm-2.6-2/plm/R/tool_transformations_collapse.R | 2 plm-2.6-2/plm/R/tool_vcovG.R | 104 plm-2.6-2/plm/build/partial.rdb |binary plm-2.6-2/plm/build/vignette.rds |binary plm-2.6-2/plm/inst/REFERENCES.bib | 55 plm-2.6-2/plm/inst/WORDLIST |only plm-2.6-2/plm/inst/doc/A_plmPackage.Rmd | 4 plm-2.6-2/plm/inst/doc/A_plmPackage.html | 2438 +++++++++-- plm-2.6-2/plm/inst/doc/B_plmFunction.Rmd | 2 plm-2.6-2/plm/inst/doc/B_plmFunction.html | 534 ++ plm-2.6-2/plm/inst/doc/C_plmModelComponents.html | 316 + plm-2.6-2/plm/inst/removed/unused.R | 4 plm-2.6-2/plm/inst/tests/test_Estimators.R | 25 plm-2.6-2/plm/inst/tests/test_Estimators.Rout.save | 226 - plm-2.6-2/plm/inst/tests/test_EstimatorsIV.Rout.save | 28 plm-2.6-2/plm/inst/tests/test_FD_models.R | 25 plm-2.6-2/plm/inst/tests/test_FD_models.Rout.save | 141 plm-2.6-2/plm/inst/tests/test_fixef.R | 10 plm-2.6-2/plm/inst/tests/test_fixef.Rout.save | 19 plm-2.6-2/plm/inst/tests/test_fixef_comp_lm_plm.R | 8 plm-2.6-2/plm/inst/tests/test_fixef_comp_lm_plm.Rout.save | 14 plm-2.6-2/plm/inst/tests/test_pbsytest_unbalanced.Rout.save | 28 plm-2.6-2/plm/inst/tests/test_pcce_pmg.R |only plm-2.6-2/plm/inst/tests/test_pcce_pmg.Rout.save |only plm-2.6-2/plm/inst/tests/test_pcdtest.Rout.save | 6 plm-2.6-2/plm/inst/tests/test_pdiff_fd.Rout.save | 14 plm-2.6-2/plm/inst/tests/test_pggls.R | 44 plm-2.6-2/plm/inst/tests/test_pggls.Rout.save | 203 plm-2.6-2/plm/inst/tests/test_pgmm.Rout.save | 6 plm-2.6-2/plm/inst/tests/test_pht.R | 2 plm-2.6-2/plm/inst/tests/test_pht.Rout.save | 8 plm-2.6-2/plm/inst/tests/test_plmtest_unbalanced.R | 4 plm-2.6-2/plm/inst/tests/test_plmtest_unbalanced.Rout.save | 116 plm-2.6-2/plm/inst/tests/test_predict.R |only plm-2.6-2/plm/inst/tests/test_predict.Rout.save |only plm-2.6-2/plm/inst/tests/test_pvcm.Rout.save | 742 --- plm-2.6-2/plm/inst/tests/test_pwfdtest_pwartest.R | 77 plm-2.6-2/plm/inst/tests/test_pwfdtest_pwartest.Rout.save |only plm-2.6-2/plm/inst/tests/test_residuals_overall_fitted_exp.R | 1 plm-2.6-2/plm/man/is.pbalanced.Rd | 2 plm-2.6-2/plm/man/is.pconsecutive.Rd | 2 plm-2.6-2/plm/man/pcce.Rd | 2 plm-2.6-2/plm/man/plm.Rd | 8 plm-2.6-2/plm/man/plm.fast.Rd | 2 plm-2.6-2/plm/man/predict.plm.Rd |only plm-2.6-2/plm/man/purtest.Rd | 371 - plm-2.6-2/plm/man/pvcm.Rd | 2 plm-2.6-2/plm/man/summary.plm.Rd | 2 plm-2.6-2/plm/man/vcovBK.Rd | 6 plm-2.6-2/plm/man/vcovDC.Rd | 2 plm-2.6-2/plm/man/vcovHC.plm.Rd | 2 plm-2.6-2/plm/man/vcovNW.Rd | 2 plm-2.6-2/plm/man/vcovSCC.Rd | 2 plm-2.6-2/plm/vignettes/A_plmPackage.Rmd | 4 plm-2.6-2/plm/vignettes/B_plmFunction.Rmd | 2 85 files changed, 4678 insertions(+), 2749 deletions(-)
Title: Perceptual Analysis, Visualization and Organization of Spectral
Colour Data
Description: A cohesive framework for the spectral and spatial analysis of
colour described in Maia, Eliason, Bitton, Doucet & Shawkey (2013)
<doi:10.1111/2041-210X.12069> and Maia, Gruson, Endler & White (2019)
<doi:10.1111/2041-210X.13174>.
Author: Thomas White [aut, cre] ,
Rafael Maia [aut] ,
Hugo Gruson [aut] ,
John Endler [aut],
Chad Eliason [aut],
Pierre-Paul Bitton [aut]
Maintainer: Thomas White <thomas.white026@gmail.com>
Diff between pavo versions 2.7.1 dated 2021-09-21 and 2.8.0 dated 2022-08-16
DESCRIPTION | 13 MD5 | 95 +++--- NAMESPACE | 2 NEWS.md | 540 +++++++++++++++++---------------------- R/aggplot.R | 2 R/as.rspec.R | 6 R/coldist.R | 358 +++++++++++-------------- R/data-bgandilum.R | 2 R/data-transmissiondata.R | 2 R/data-ttvertex.R | 2 R/data-vissyst.R | 2 R/find_astar.R | 12 R/getspec.R | 6 R/plot.colspace.R | 30 +- R/procimg.R | 8 R/procspec.R | 18 - R/summary.colspace.R | 9 R/tcsplot.R | 37 +- R/vismodel.R | 5 R/vol.R | 3 R/voloverlap.R | 9 README.md | 4 build/partial.rdb |binary build/vignette.rds |binary inst/doc/pavo.html | 239 ++++++++++++++++- man/as.rspec.Rd | 4 man/bgandilum.Rd | 1 man/cieplot.Rd | 6 man/coldist.Rd | 10 man/diplot.Rd | 6 man/find_astar.Rd | 13 man/getspec.Rd | 4 man/hexplot.Rd | 6 man/legendtetra.Rd | 6 man/pavo-package.Rd | 6 man/plot.colspace.Rd | 30 +- man/procimg.Rd | 8 man/sensdata.Rd | 4 man/summary.colspace.Rd | 9 man/tcsplot.Rd | 43 +-- man/transmissiondata.Rd | 1 man/ttvertex.Rd | 1 man/vismodel.Rd | 4 man/vissyst.Rd | 1 man/vol.Rd | 9 man/voloverlap.Rd | 9 tests/testthat/_snaps |only tests/testthat/test-coldist.R | 1 tests/testthat/test-processing.R | 13 49 files changed, 870 insertions(+), 729 deletions(-)
Title: Generalized Estimating Equation Package
Description: Generalized estimating equations solver for parameters in
mean, scale, and correlation structures, through mean link,
scale link, and correlation link. Can also handle clustered
categorical responses. See e.g. Halekoh and Højsgaard, (2005,
<doi:10.18637/jss.v015.i02>), for details.
Author: Soeren Hoejsgaard [aut, cre, cph],
Ulrich Halekoh [aut, cph],
Jun Yan [aut, cph],
Claus Thorn Ekstroem [ctb]
Maintainer: Soeren Hoejsgaard <sorenh@math.aau.dk>
Diff between geepack versions 1.3.4 dated 2022-05-31 and 1.3.9 dated 2022-08-16
geepack-1.3.4/geepack/R/qic.R |only geepack-1.3.9/geepack/DESCRIPTION | 12 - geepack-1.3.9/geepack/MD5 | 20 - geepack-1.3.9/geepack/NEWS.md | 247 ++------------------- geepack-1.3.9/geepack/R/geeglm-anova.R | 109 ++++----- geepack-1.3.9/geepack/R/genZcor.R | 2 geepack-1.3.9/geepack/R/qic-ce.R |only geepack-1.3.9/geepack/build/vignette.rds |binary geepack-1.3.9/geepack/inst/doc/geepack-manual.Rnw | 22 - geepack-1.3.9/geepack/inst/doc/geepack-manual.pdf |binary geepack-1.3.9/geepack/man/QIC.Rd | 31 +- geepack-1.3.9/geepack/vignettes/geepack-manual.Rnw | 22 - 12 files changed, 143 insertions(+), 322 deletions(-)
Title: Functional Data Analysis and Empirical Dynamics
Description: A versatile package that provides implementation of various
methods of Functional Data Analysis (FDA) and Empirical Dynamics. The core of this
package is Functional Principal Component Analysis (FPCA), a key technique for
functional data analysis, for sparsely or densely sampled random trajectories
and time courses, via the Principal Analysis by Conditional Estimation
(PACE) algorithm. This core algorithm yields covariance and mean functions,
eigenfunctions and principal component (scores), for both functional data and
derivatives, for both dense (functional) and sparse (longitudinal) sampling designs.
For sparse designs, it provides fitted continuous trajectories with confidence bands,
even for subjects with very few longitudinal observations. PACE is a viable and
flexible alternative to random effects modeling of longitudinal data. There is also a
Matlab version (PACE) that contains some methods not available on fdapace and vice
versa. Updates to fdapace were supported by grants from [...truncated...]
Author: Yidong Zhou [aut, cre],
Satarupa Bhattacharjee [aut],
Cody Carroll [aut] ,
Yaqing Chen [aut],
Xiongtao Dai [aut],
Jianing Fan [aut],
Alvaro Gajardo [aut],
Pantelis Z. Hadjipantelis [aut],
Kyunghee Han [aut],
Hao Ji [aut],
Changbo Zhu [aut],
Shu-Chin [...truncated...]
Maintainer: Yidong Zhou <ydzhou@ucdavis.edu>
Diff between fdapace versions 0.5.8 dated 2021-11-22 and 0.5.9 dated 2022-08-16
DESCRIPTION | 18 + MD5 | 50 ++--- NAMESPACE | 1 NEWS | 9 R/CheckData.R | 6 R/CreateBWPlot.R | 2 R/CreateCovPlot.R | 2 R/CreateDesignPlot.R | 2 R/CreateStringingPlot.R | 2 R/FCReg.R | 42 ++-- R/FLM.R | 87 +++++++-- R/FLM1.R |only R/FPCA.R | 2 R/FitEigenValues.R | 4 R/GCVLwls2DV2.R | 2 R/GetCEScores.R | 2 R/Lwls2D.R | 11 + R/SetOptions.R | 4 R/predict.FPCA.R | 2 build/vignette.rds |binary inst/doc/dynFPCA.html | 212 ++++++++++++++++++++++- inst/doc/fdapaceVig.Rmd | 2 inst/doc/fdapaceVig.html | 425 ++++++++++++++++++++++++++++++++++++++++++----- man/FLM.Rd | 10 - man/FLM1.Rd |only man/Lwls2D.Rd | 4 vignettes/fdapaceVig.Rmd | 2 27 files changed, 767 insertions(+), 136 deletions(-)
Title: End-to-End Automated Machine Learning and Model Evaluation
Description: Single unified interface for end-to-end modelling of regression,
categorical and time-to-event (survival) outcomes. Models created using
familiar are self-containing, and their use does not require additional
information such as baseline survival, feature clustering, or feature
transformation and normalisation parameters. Model performance,
calibration, risk group stratification, (permutation) variable importance,
individual conditional expectation, partial dependence, and more, are
assessed automatically as part of the evaluation process and exported in
tabular format and plotted, and may also be computed manually using export
and plot functions. Where possible, metrics and values obtained during the
evaluation process come with confidence intervals.
Author: Alex Zwanenburg [aut, cre] ,
Steffen Loeck [aut],
Stefan Leger [ctb],
Iram Shahzadi [ctb],
Asier Rabasco Meneghetti [ctb],
Sebastian Starke [ctb],
Technische Universitaet Dresden [cph],
German Cancer Research Center [cph]
Maintainer: Alex Zwanenburg <alexander.zwanenburg@nct-dresden.de>
Diff between familiar versions 1.1.0 dated 2022-04-07 and 1.2.0 dated 2022-08-16
familiar-1.1.0/familiar/tests/testthat/test-1_plot_ice_a.R |only familiar-1.1.0/familiar/tests/testthat/test-1_plot_ice_b.R |only familiar-1.1.0/familiar/tests/testthat/test-normalisation.R |only familiar-1.1.0/familiar/tests/testthat/test-plot_calibration.R |only familiar-1.1.0/familiar/tests/testthat/test-vimp_rfsrc_S4.R |only familiar-1.2.0/familiar/DESCRIPTION | 39 familiar-1.2.0/familiar/MD5 | 444 +- familiar-1.2.0/familiar/NAMESPACE | 8 familiar-1.2.0/familiar/NEWS.md | 70 familiar-1.2.0/familiar/R/BatchNormalisation.R | 768 ++-- familiar-1.2.0/familiar/R/CheckArguments.R | 7 familiar-1.2.0/familiar/R/CheckHyperparameters.R | 6 familiar-1.2.0/familiar/R/ClusterRepresentation.R |only familiar-1.2.0/familiar/R/Clustering.R | 1549 ++------- familiar-1.2.0/familiar/R/ClusteringMethod.R |only familiar-1.2.0/familiar/R/CombatNormalisation.R | 264 + familiar-1.2.0/familiar/R/DataObject.R | 517 ++- familiar-1.2.0/familiar/R/DataParameterChecks.R | 1 familiar-1.2.0/familiar/R/DataPreProcessing.R | 533 ++- familiar-1.2.0/familiar/R/DataProcessing.R | 4 familiar-1.2.0/familiar/R/DataServerBackend.R | 6 familiar-1.2.0/familiar/R/ErrorMessages.R | 6 familiar-1.2.0/familiar/R/Evaluation.R | 5 familiar-1.2.0/familiar/R/ExperimentData.R |only familiar-1.2.0/familiar/R/ExperimentSetup.R | 4 familiar-1.2.0/familiar/R/Familiar.R | 500 ++- familiar-1.2.0/familiar/R/FamiliarCollection.R | 11 familiar-1.2.0/familiar/R/FamiliarCollectionExport.R | 134 familiar-1.2.0/familiar/R/FamiliarData.R | 5 familiar-1.2.0/familiar/R/FamiliarDataComputation.R | 8 familiar-1.2.0/familiar/R/FamiliarDataComputationAUCCurves.R | 3 familiar-1.2.0/familiar/R/FamiliarDataComputationCalibrationData.R | 3 familiar-1.2.0/familiar/R/FamiliarDataComputationCalibrationInfo.R | 3 familiar-1.2.0/familiar/R/FamiliarDataComputationConfusionMatrix.R | 3 familiar-1.2.0/familiar/R/FamiliarDataComputationDecisionCurveAnalysis.R | 3 familiar-1.2.0/familiar/R/FamiliarDataComputationFeatureExpression.R | 3 familiar-1.2.0/familiar/R/FamiliarDataComputationFeatureSimilarity.R | 165 - familiar-1.2.0/familiar/R/FamiliarDataComputationHyperparameters.R | 3 familiar-1.2.0/familiar/R/FamiliarDataComputationICE.R | 6 familiar-1.2.0/familiar/R/FamiliarDataComputationModelPerformance.R | 3 familiar-1.2.0/familiar/R/FamiliarDataComputationPermutationVimp.R | 116 familiar-1.2.0/familiar/R/FamiliarDataComputationPredictionData.R | 4 familiar-1.2.0/familiar/R/FamiliarDataComputationRiskStratificationData.R | 3 familiar-1.2.0/familiar/R/FamiliarDataComputationRiskStratificationInfo.R | 3 familiar-1.2.0/familiar/R/FamiliarDataComputationSampleSimilarity.R | 103 familiar-1.2.0/familiar/R/FamiliarDataComputationUnivariateAnalysis.R | 3 familiar-1.2.0/familiar/R/FamiliarDataComputationVimp.R | 210 - familiar-1.2.0/familiar/R/FamiliarDataElement.R | 2 familiar-1.2.0/familiar/R/FamiliarEnsemble.R | 7 familiar-1.2.0/familiar/R/FamiliarHyperparameterLearner.R | 8 familiar-1.2.0/familiar/R/FamiliarModel.R | 78 familiar-1.2.0/familiar/R/FamiliarNoveltyDetector.R | 11 familiar-1.2.0/familiar/R/FamiliarObjectConversion.R | 13 familiar-1.2.0/familiar/R/FamiliarObjectUpdate.R | 463 ++ familiar-1.2.0/familiar/R/FamiliarS4Classes.R | 204 + familiar-1.2.0/familiar/R/FamiliarS4Generics.R | 56 familiar-1.2.0/familiar/R/FamiliarSharedS4Methods.R | 37 familiar-1.2.0/familiar/R/FamiliarVimpMethod.R | 101 familiar-1.2.0/familiar/R/FeatureInfo.R | 882 +---- familiar-1.2.0/familiar/R/FeatureInfoParameters.R |only familiar-1.2.0/familiar/R/FeatureSelection.R | 150 familiar-1.2.0/familiar/R/HyperparameterOptimisation.R | 57 familiar-1.2.0/familiar/R/HyperparameterOptimisationUtilities.R | 26 familiar-1.2.0/familiar/R/Imputation.R | 1085 ++++-- familiar-1.2.0/familiar/R/Iterations.R | 30 familiar-1.2.0/familiar/R/LearnerMain.R | 11 familiar-1.2.0/familiar/R/LearnerS4Cox.R | 21 familiar-1.2.0/familiar/R/LearnerS4GLM.R | 20 familiar-1.2.0/familiar/R/LearnerS4GLMnet.R | 16 familiar-1.2.0/familiar/R/LearnerS4MBoost.R | 16 familiar-1.2.0/familiar/R/LearnerS4RFSRC.R | 232 + familiar-1.2.0/familiar/R/LearnerS4Ranger.R | 126 familiar-1.2.0/familiar/R/LearnerS4SurvivalRegression.R | 16 familiar-1.2.0/familiar/R/LearnerS4XGBoost.R | 47 familiar-1.2.0/familiar/R/ModelBuilding.R | 52 familiar-1.2.0/familiar/R/Normalisation.R | 1129 ++++++- familiar-1.2.0/familiar/R/NoveltyDetectorMain.R | 3 familiar-1.2.0/familiar/R/NoveltyDetectorS4IsolationTree.R | 2 familiar-1.2.0/familiar/R/PairwiseSimilarity.R | 31 familiar-1.2.0/familiar/R/ParallelFunctions.R | 4 familiar-1.2.0/familiar/R/ParseData.R | 30 familiar-1.2.0/familiar/R/ParseSettings.R | 224 - familiar-1.2.0/familiar/R/PlotAUCcurves.R | 6 familiar-1.2.0/familiar/R/PlotAll.R | 3 familiar-1.2.0/familiar/R/PlotCalibration.R | 7 familiar-1.2.0/familiar/R/PlotConfusionMatrix.R | 3 familiar-1.2.0/familiar/R/PlotDecisionCurves.R | 10 familiar-1.2.0/familiar/R/PlotFeatureRanking.R | 115 familiar-1.2.0/familiar/R/PlotFeatureSimilarity.R | 17 familiar-1.2.0/familiar/R/PlotICE.R | 2 familiar-1.2.0/familiar/R/PlotKaplanMeier.R | 3 familiar-1.2.0/familiar/R/PlotModelPerformance.R | 5 familiar-1.2.0/familiar/R/PlotPermutationVariableImportance.R | 3 familiar-1.2.0/familiar/R/PlotSampleClustering.R | 22 familiar-1.2.0/familiar/R/PlotUnivariateImportance.R | 34 familiar-1.2.0/familiar/R/PlotUtilities.R | 2 familiar-1.2.0/familiar/R/PredictS4Methods.R | 7 familiar-1.2.0/familiar/R/RankBordaAggregation.R | 45 familiar-1.2.0/familiar/R/RankMain.R | 560 --- familiar-1.2.0/familiar/R/RankSimpleAggregation.R | 77 familiar-1.2.0/familiar/R/RankStabilityAggregation.R | 44 familiar-1.2.0/familiar/R/TestDataCreators.R | 318 + familiar-1.2.0/familiar/R/TestFunctions.R | 620 ++- familiar-1.2.0/familiar/R/TrainS4Methods.R | 23 familiar-1.2.0/familiar/R/Transformation.R | 641 +++- familiar-1.2.0/familiar/R/Utilities.R | 76 familiar-1.2.0/familiar/R/UtilitiesS4.R | 85 familiar-1.2.0/familiar/R/VimpMain.R | 36 familiar-1.2.0/familiar/R/VimpS4Concordance.R | 32 familiar-1.2.0/familiar/R/VimpS4CoreLearn.R | 13 familiar-1.2.0/familiar/R/VimpS4Correlation.R | 20 familiar-1.2.0/familiar/R/VimpS4MutualInformation.R | 26 familiar-1.2.0/familiar/R/VimpS4Regression.R | 26 familiar-1.2.0/familiar/R/VimpTable.R |only familiar-1.2.0/familiar/build/vignette.rds |binary familiar-1.2.0/familiar/inst/config.xml | 6 familiar-1.2.0/familiar/inst/doc/evaluation_and_explanation_precompiled.Rmd | 4 familiar-1.2.0/familiar/inst/doc/evaluation_and_explanation_precompiled.html | 82 familiar-1.2.0/familiar/inst/doc/feature_selection_precompiled.Rmd | 60 familiar-1.2.0/familiar/inst/doc/feature_selection_precompiled.html | 197 - familiar-1.2.0/familiar/inst/doc/introduction_precompiled.Rmd | 50 familiar-1.2.0/familiar/inst/doc/introduction_precompiled.html | 79 familiar-1.2.0/familiar/inst/doc/learners_precompiled.Rmd | 3 familiar-1.2.0/familiar/inst/doc/learners_precompiled.html | 89 familiar-1.2.0/familiar/inst/doc/performance_metrics_precompiled.Rmd | 2 familiar-1.2.0/familiar/inst/doc/performance_metrics_precompiled.html | 84 familiar-1.2.0/familiar/inst/doc/prospective_use_precompiled.Rmd | 88 familiar-1.2.0/familiar/inst/doc/prospective_use_precompiled.html | 120 familiar-1.2.0/familiar/man/aggregate_vimp_table-methods.Rd |only familiar-1.2.0/familiar/man/as_familiar_collection-methods.Rd | 60 familiar-1.2.0/familiar/man/as_familiar_data-methods.Rd | 60 familiar-1.2.0/familiar/man/dot-get_iteration_data.Rd | 6 familiar-1.2.0/familiar/man/dot-parse_general_settings.Rd | 50 familiar-1.2.0/familiar/man/dot-parse_hyperparameter_optimisation_settings.Rd | 52 familiar-1.2.0/familiar/man/experimentData-class.Rd |only familiar-1.2.0/familiar/man/export_all-methods.Rd | 60 familiar-1.2.0/familiar/man/export_auc_data-methods.Rd | 14 familiar-1.2.0/familiar/man/export_calibration_data-methods.Rd | 24 familiar-1.2.0/familiar/man/export_confusion_matrix_data-methods.Rd | 14 familiar-1.2.0/familiar/man/export_feature_expressions-methods.Rd | 14 familiar-1.2.0/familiar/man/export_ice_data-methods.Rd | 24 familiar-1.2.0/familiar/man/export_model_performance-methods.Rd | 32 familiar-1.2.0/familiar/man/export_partial_dependence_data-methods.Rd | 24 familiar-1.2.0/familiar/man/export_permutation_vimp-methods.Rd | 44 familiar-1.2.0/familiar/man/export_prediction_data-methods.Rd | 22 familiar-1.2.0/familiar/man/export_risk_stratification_data-methods.Rd | 12 familiar-1.2.0/familiar/man/export_univariate_analysis_data-methods.Rd | 30 familiar-1.2.0/familiar/man/familiar.Rd | 2 familiar-1.2.0/familiar/man/familiarCollection-class.Rd | 16 familiar-1.2.0/familiar/man/familiarDataElement-class.Rd | 130 familiar-1.2.0/familiar/man/familiarEnsemble-class.Rd | 2 familiar-1.2.0/familiar/man/familiarHyperparameterLearner-class.Rd | 12 familiar-1.2.0/familiar/man/familiarModel-class.Rd | 8 familiar-1.2.0/familiar/man/familiarNoveltyDetector-class.Rd | 10 familiar-1.2.0/familiar/man/featureInfo-class.Rd | 10 familiar-1.2.0/familiar/man/featureInfoParameters-class.Rd |only familiar-1.2.0/familiar/man/get_vimp_table-methods.Rd |only familiar-1.2.0/familiar/man/outcomeInfo-class.Rd | 2 familiar-1.2.0/familiar/man/plot_auc_roc_curve-methods.Rd | 14 familiar-1.2.0/familiar/man/plot_calibration_data-methods.Rd | 24 familiar-1.2.0/familiar/man/plot_confusion_matrix-methods.Rd | 14 familiar-1.2.0/familiar/man/plot_decision_curve-methods.Rd | 24 familiar-1.2.0/familiar/man/plot_feature_similarity-methods.Rd | 36 familiar-1.2.0/familiar/man/plot_ice-methods.Rd | 24 familiar-1.2.0/familiar/man/plot_kaplan_meier-methods.Rd | 12 familiar-1.2.0/familiar/man/plot_model_performance-methods.Rd | 32 familiar-1.2.0/familiar/man/plot_pd-methods.Rd | 24 familiar-1.2.0/familiar/man/plot_permutation_variable_importance-methods.Rd | 44 familiar-1.2.0/familiar/man/plot_univariate_importance-methods.Rd | 12 familiar-1.2.0/familiar/man/plot_variable_importance-methods.Rd | 58 familiar-1.2.0/familiar/man/precompute_data_assignment.Rd |only familiar-1.2.0/familiar/man/precompute_feature_info.Rd |only familiar-1.2.0/familiar/man/precompute_vimp.Rd |only familiar-1.2.0/familiar/man/summon_familiar.Rd | 58 familiar-1.2.0/familiar/man/train_familiar.Rd | 61 familiar-1.2.0/familiar/man/update_object-methods.Rd | 18 familiar-1.2.0/familiar/man/vimpTable-class.Rd |only familiar-1.2.0/familiar/tests/testthat/test-0_plot_calibration.R |only familiar-1.2.0/familiar/tests/testthat/test-0_plot_ice_a.R |only familiar-1.2.0/familiar/tests/testthat/test-0_plot_ice_b.R |only familiar-1.2.0/familiar/tests/testthat/test-0_preprocessing_clustering.R |only familiar-1.2.0/familiar/tests/testthat/test-0_vimp_rfsrc_S4.R |only familiar-1.2.0/familiar/tests/testthat/test-batch_normalisation.R | 1593 ++++++---- familiar-1.2.0/familiar/tests/testthat/test-experiment_data.R |only familiar-1.2.0/familiar/tests/testthat/test-general_normalisation.R |only familiar-1.2.0/familiar/tests/testthat/test-hyperparameter_optimisation.R | 10 familiar-1.2.0/familiar/tests/testthat/test-imputation.R |only familiar-1.2.0/familiar/tests/testthat/test-learner_cox_s4.R | 12 familiar-1.2.0/familiar/tests/testthat/test-learner_glm_S4.R | 32 familiar-1.2.0/familiar/tests/testthat/test-learner_glmnet_S4.R | 30 familiar-1.2.0/familiar/tests/testthat/test-learner_knn_S4.R | 20 familiar-1.2.0/familiar/tests/testthat/test-learner_mboost_lm_S4.R | 16 familiar-1.2.0/familiar/tests/testthat/test-learner_mboost_tree_S4.R | 8 familiar-1.2.0/familiar/tests/testthat/test-learner_naive_bayes_S4.R | 8 familiar-1.2.0/familiar/tests/testthat/test-learner_ranger_s4.R | 20 familiar-1.2.0/familiar/tests/testthat/test-learner_rfsrc_s4.R | 25 familiar-1.2.0/familiar/tests/testthat/test-learner_survival_regression_S4.R | 4 familiar-1.2.0/familiar/tests/testthat/test-learner_svm_S4.R | 16 familiar-1.2.0/familiar/tests/testthat/test-learner_xgboost_dart_S4.R | 20 familiar-1.2.0/familiar/tests/testthat/test-learner_xgboost_lm_S4.R | 20 familiar-1.2.0/familiar/tests/testthat/test-learner_xgboost_tree_S4.R | 20 familiar-1.2.0/familiar/tests/testthat/test-rank_aggregation_methods.R | 158 familiar-1.2.0/familiar/tests/testthat/test-train_familiar.R | 121 familiar-1.2.0/familiar/tests/testthat/test-transformation.R | 615 ++- familiar-1.2.0/familiar/tests/testthat/test-update_object.R |only familiar-1.2.0/familiar/tests/testthat/test-vimp_concordance_S4.R | 12 familiar-1.2.0/familiar/tests/testthat/test-vimp_corelearn_S4.R | 26 familiar-1.2.0/familiar/tests/testthat/test-vimp_correlation_S4.R | 6 familiar-1.2.0/familiar/tests/testthat/test-vimp_mutual_information_S4.R | 30 familiar-1.2.0/familiar/tests/testthat/test-vimp_ranger_S4.R | 33 familiar-1.2.0/familiar/tests/testthat/test-vimp_regression_S4.R | 10 familiar-1.2.0/familiar/tests/testthat/test-vimp_table.R |only familiar-1.2.0/familiar/vignettes/eval_and_explain/auc-pr-curve-bci-1.png |binary familiar-1.2.0/familiar/vignettes/eval_and_explain/auc-pr-curve-point-1.png |binary familiar-1.2.0/familiar/vignettes/eval_and_explain/auc-roc-curve-bci-1.png |binary familiar-1.2.0/familiar/vignettes/eval_and_explain/auc-roc-curve-point-1.png |binary familiar-1.2.0/familiar/vignettes/eval_and_explain/calibration-data-bci-1.png |binary familiar-1.2.0/familiar/vignettes/eval_and_explain/calibration-data-point-1.png |binary familiar-1.2.0/familiar/vignettes/eval_and_explain/confusion-matrix-1.png |binary familiar-1.2.0/familiar/vignettes/eval_and_explain/decision-curve-bci-1.png |binary familiar-1.2.0/familiar/vignettes/eval_and_explain/feature-similarity-1.png |binary familiar-1.2.0/familiar/vignettes/eval_and_explain/ice-2d-1.png |binary familiar-1.2.0/familiar/vignettes/eval_and_explain/ice-2d-anchored-1.png |binary familiar-1.2.0/familiar/vignettes/eval_and_explain/ice-cell-shap-uniformity-1.png |binary familiar-1.2.0/familiar/vignettes/eval_and_explain/ice-cell-shape-uniformity-anchored-1.png |binary familiar-1.2.0/familiar/vignettes/eval_and_explain/model-performance-plot-1.png |binary familiar-1.2.0/familiar/vignettes/eval_and_explain/model-variable-importance-1.png |binary familiar-1.2.0/familiar/vignettes/eval_and_explain/permutation-variable-importance-bc-1.png |binary familiar-1.2.0/familiar/vignettes/eval_and_explain/permutation-variable-importance-bc-spearman-1.png |binary familiar-1.2.0/familiar/vignettes/eval_and_explain/sample-similarity-1.png |binary familiar-1.2.0/familiar/vignettes/eval_and_explain/sample-similarity-unnormalised-1.png |binary familiar-1.2.0/familiar/vignettes/evaluation_and_explanation_precompiled.Rmd | 4 familiar-1.2.0/familiar/vignettes/feature_selection_precompiled.Rmd | 60 familiar-1.2.0/familiar/vignettes/introduction_precompiled.Rmd | 50 familiar-1.2.0/familiar/vignettes/learners_precompiled.Rmd | 3 familiar-1.2.0/familiar/vignettes/performance_metrics_precompiled.Rmd | 2 familiar-1.2.0/familiar/vignettes/prospective_use_precompiled.Rmd | 88 237 files changed, 11575 insertions(+), 7147 deletions(-)
Title: Categorical Functional Data Analysis
Description: Package for the analysis of categorical functional data.
The main purpose is to compute an encoding (real functional variable) for each state <doi:10.3390/math9233074>.
It also provides functions to perform basic statistical analysis on categorical functional data.
Author: Cristian Preda [aut],
Quentin Grimonprez [aut, cre],
Vincent Vandewalle [ctb]
Maintainer: Quentin Grimonprez <quentingrim@yahoo.fr>
Diff between cfda versions 0.10.0 dated 2022-07-19 and 0.10.1 dated 2022-08-16
cfda-0.10.0/cfda/R/cfd.R |only cfda-0.10.1/cfda/DESCRIPTION | 10 - cfda-0.10.1/cfda/MD5 | 31 ++--- cfda-0.10.1/cfda/NEWS | 7 + cfda-0.10.1/cfda/R/cfda-package.R | 2 cfda-0.10.1/cfda/R/dataPlot.R | 13 -- cfda-0.10.1/cfda/R/datasets.R | 6 cfda-0.10.1/cfda/R/estimation.R | 20 +-- cfda-0.10.1/cfda/R/pretreatment.R | 6 cfda-0.10.1/cfda/inst/doc/cfda.html | 28 ++-- cfda-0.10.1/cfda/man/biofam2.Rd | 3 cfda-0.10.1/cfda/man/care.Rd | 3 cfda-0.10.1/cfda/man/cfda-package.Rd | 2 cfda-0.10.1/cfda/man/cut_data.Rd | 3 cfda-0.10.1/cfda/tests/testthat/test.estimation.R | 52 ++++++++ cfda-0.10.1/cfda/tests/testthat/test.pretreatment.R | 15 ++ cfda-0.10.1/cfda/tests/testthat/test.stat.R | 122 ++++++++++++++++++-- 17 files changed, 251 insertions(+), 72 deletions(-)
Title: Adaptive Trial Simulator
Description: Package that simulates adaptive clinical trials using adaptive
stopping, adaptive arm dropping, and/or adaptive randomisation.
Developed as part of the INCEPT (Intensive Care Platform Trial) project
(<https://incept.dk/>), which is primarily supported by a grant
from Sygeforsikringen "danmark" (<https://www.sygeforsikring.dk/>).
Author: Anders Granholm [aut, cre] ,
Benjamin Skov Kaas-Hansen [aut]
,
Aksel Karl Georg Jensen [ctb] ,
Theis Lange [ctb]
Maintainer: Anders Granholm <andersgran@gmail.com>
Diff between adaptr versions 1.1.0 dated 2022-06-17 and 1.1.1 dated 2022-08-16
DESCRIPTION | 10 MD5 | 26 NEWS.md | 48 R/adaptr-package.R | 127 +- R/print.R | 652 ++++++------- R/setup_trial.R | 2026 ++++++++++++++++++++--------------------- README.md | 8 build/partial.rdb |binary build/vignette.rds |binary inst/doc/Advanced-example.html | 430 +++++++- inst/doc/Basic-examples.html | 263 ++++- inst/doc/Overview.html | 297 +++++- man/adaptr-package.Rd | 5 man/print.Rd | 10 14 files changed, 2368 insertions(+), 1534 deletions(-)
Title: Twang Causal Mediation Modeling via Weighting
Description: Provides functions for estimating natural direct and indirect effects for mediation analysis. It uses weighting where the weights are functions of estimates of the probability of exposure or treatment assignment (Hong, G (2010). <https://cepa.stanford.edu/sites/default/files/workshops/GH_JSM%20Proceedings%202010.pdf> Huber, M. (2014). <doi:10.1002/jae.2341>). Estimation of probabilities can use generalized boosting or logistic regression. Additional functions provide diagnostics of the model fit and weights. The vignette provides details and examples.
Author: Dan McCaffrey [aut, cre],
Katherine Castellano [aut],
Donna Coffman [aut],
Brian Vegetabile [aut],
Megan Schuler [aut],
Haoyu Zhou [aut]
Maintainer: Dan McCaffrey <dmccaffrey@ets.org>
Diff between twangMediation versions 1.1 dated 2021-12-13 and 1.2 dated 2022-08-16
twangMediation-1.1/twangMediation/inst/doc/twangMediation_tutorialimport.Rnw |only twangMediation-1.1/twangMediation/inst/doc/twangMediation_tutorialimport.pdf |only twangMediation-1.1/twangMediation/vignettes/twangMediation.pdf |only twangMediation-1.1/twangMediation/vignettes/twangMediation_tutorialimport.Rnw |only twangMediation-1.2/twangMediation/DESCRIPTION | 8 - twangMediation-1.2/twangMediation/MD5 | 29 ++-- twangMediation-1.2/twangMediation/R/bal.table.mediation.R | 41 +++++ twangMediation-1.2/twangMediation/R/desc.effects.mediation.R | 13 + twangMediation-1.2/twangMediation/R/plot.mediation.R | 14 ++ twangMediation-1.2/twangMediation/R/print.bal.table.mediation.R | 57 +++++++- twangMediation-1.2/twangMediation/R/print.mediation.R | 66 ++++++++- twangMediation-1.2/twangMediation/R/summary.mediation.R | 70 ++++++++-- twangMediation-1.2/twangMediation/R/vignettename.R |only twangMediation-1.2/twangMediation/R/wgtmed.R | 41 ++++- twangMediation-1.2/twangMediation/build/vignette.rds |binary twangMediation-1.2/twangMediation/inst/doc/twangMediation.Rnw |only twangMediation-1.2/twangMediation/inst/doc/twangMediation.pdf |only twangMediation-1.2/twangMediation/man/wgtmed.Rd | 5 twangMediation-1.2/twangMediation/vignettes/twangMediation.Rnw |only twangMediation-1.2/twangMediation/vignettes/twangMediation_tutorial.pdf |only 20 files changed, 280 insertions(+), 64 deletions(-)
More information about twangMediation at CRAN
Permanent link
Title: Nonnegative Integer Solutions of Linear Diophantine Equations
with Applications
Description: Routines for enumerating all existing nonnegative integer solutions of a linear Diophantine equation. The package provides routines for solving 0-1, bounded and unbounded knapsack problems; 0-1, bounded and unbounded subset sum problems; additive partitioning of natural numbers; and one-dimensional bin-packing problem.
Author: Natalya Pya Arnqvist[aut, cre],
Vassilly Voinov [aut],
Rashid Makarov [aut],
Yevgeniy Voinov [aut]
Maintainer: Natalya Pya Arnqvist <nat.pya@gmail.com>
Diff between nilde versions 1.1-6 dated 2021-12-17 and 1.1-7 dated 2022-08-16
ChangeLog | 4 ++++ DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- build/partial.rdb |binary man/tsp_solver.Rd | 2 +- 5 files changed, 13 insertions(+), 9 deletions(-)
Title: Crosstables for Descriptive Analyses
Description: Create descriptive tables for continuous and categorical variables.
Apply summary statistics and counting function, with or without a grouping variable, and create beautiful reports using 'rmarkdown' or 'officer'.
You can also compute effect sizes and statistical tests if needed.
Author: Dan Chaltiel [aut, cre] ,
David Hajage [ccp]
Maintainer: Dan Chaltiel <dan.chaltiel@gmail.com>
Diff between crosstable versions 0.4.1 dated 2022-02-25 and 0.5.0 dated 2022-08-16
crosstable-0.4.1/crosstable/man/compact.Rd |only crosstable-0.4.1/crosstable/man/rename_dataframe_with_labels.Rd |only crosstable-0.5.0/crosstable/DESCRIPTION | 21 crosstable-0.5.0/crosstable/MD5 | 160 crosstable-0.5.0/crosstable/NAMESPACE | 31 crosstable-0.5.0/crosstable/NEWS.md | 412 crosstable-0.5.0/crosstable/R/burgled.R | 154 crosstable-0.5.0/crosstable/R/compact.R | 304 crosstable-0.5.0/crosstable/R/cross_by.R | 200 crosstable-0.5.0/crosstable/R/cross_categorical.R | 595 - crosstable-0.5.0/crosstable/R/cross_numeric.R | 361 crosstable-0.5.0/crosstable/R/cross_survival.R | 332 crosstable-0.5.0/crosstable/R/crosstable-package.R | 21 crosstable-0.5.0/crosstable/R/crosstable.R | 952 - crosstable-0.5.0/crosstable/R/effect.R | 793 - crosstable-0.5.0/crosstable/R/flextable.R | 645 - crosstable-0.5.0/crosstable/R/funs.R | 564 - crosstable-0.5.0/crosstable/R/gt.R | 256 crosstable-0.5.0/crosstable/R/labels.R | 714 - crosstable-0.5.0/crosstable/R/officer.R | 1688 +-- crosstable-0.5.0/crosstable/R/openxlsx.R | 329 crosstable-0.5.0/crosstable/R/options.R | 296 crosstable-0.5.0/crosstable/R/test.R | 849 - crosstable-0.5.0/crosstable/R/utils.R | 1209 +- crosstable-0.5.0/crosstable/README.md | 360 crosstable-0.5.0/crosstable/build/vignette.rds |binary crosstable-0.5.0/crosstable/inst/WORDLIST | 3 crosstable-0.5.0/crosstable/inst/doc/crosstable-install.Rmd | 184 crosstable-0.5.0/crosstable/inst/doc/crosstable-install.html | 228 crosstable-0.5.0/crosstable/inst/doc/crosstable-report.html | 341 crosstable-0.5.0/crosstable/inst/doc/crosstable-selection.Rmd | 352 crosstable-0.5.0/crosstable/inst/doc/crosstable-selection.html | 522 crosstable-0.5.0/crosstable/inst/doc/crosstable.html | 572 - crosstable-0.5.0/crosstable/man/apply_labels.Rd | 2 crosstable-0.5.0/crosstable/man/as_flextable.Rd | 16 crosstable-0.5.0/crosstable/man/as_gt.Rd | 8 crosstable-0.5.0/crosstable/man/as_workbook.Rd | 4 crosstable-0.5.0/crosstable/man/body_add_crosstable.Rd | 12 crosstable-0.5.0/crosstable/man/body_add_crosstable_list.Rd | 16 crosstable-0.5.0/crosstable/man/body_add_gg2.Rd | 4 crosstable-0.5.0/crosstable/man/body_add_img2.Rd | 5 crosstable-0.5.0/crosstable/man/body_add_legend.Rd | 8 crosstable-0.5.0/crosstable/man/body_add_list.Rd | 2 crosstable-0.5.0/crosstable/man/body_add_normal.Rd | 22 crosstable-0.5.0/crosstable/man/body_add_title.Rd | 6 crosstable-0.5.0/crosstable/man/clean_names_with_labels.Rd |only crosstable-0.5.0/crosstable/man/crosstable-package.Rd | 4 crosstable-0.5.0/crosstable/man/crosstable.Rd | 30 crosstable-0.5.0/crosstable/man/crosstable_effect_args.Rd | 32 crosstable-0.5.0/crosstable/man/crosstable_options.Rd | 220 crosstable-0.5.0/crosstable/man/crosstable_reset_options.Rd |only crosstable-0.5.0/crosstable/man/crosstable_test_args.Rd | 32 crosstable-0.5.0/crosstable/man/ct_compact.Rd |only crosstable-0.5.0/crosstable/man/effect_summary.Rd | 8 crosstable-0.5.0/crosstable/man/format_fixed.Rd | 3 crosstable-0.5.0/crosstable/man/get_label.Rd | 2 crosstable-0.5.0/crosstable/man/import_labels.Rd | 20 crosstable-0.5.0/crosstable/man/narm.Rd |only crosstable-0.5.0/crosstable/man/rename_with_labels.Rd |only crosstable-0.5.0/crosstable/man/set_label.Rd | 10 crosstable-0.5.0/crosstable/man/summaryFunctions.Rd | 12 crosstable-0.5.0/crosstable/man/write_and_open.Rd | 4 crosstable-0.5.0/crosstable/tests/testthat.R | 14 crosstable-0.5.0/crosstable/tests/testthat/_snaps/by_factor.md | 5261 ++++------ crosstable-0.5.0/crosstable/tests/testthat/_snaps/by_numeric.md | 362 crosstable-0.5.0/crosstable/tests/testthat/_snaps/crosstable.md |only crosstable-0.5.0/crosstable/tests/testthat/_snaps/effects.md | 1225 +- crosstable-0.5.0/crosstable/tests/testthat/_snaps/flextable.md | 318 crosstable-0.5.0/crosstable/tests/testthat/_snaps/labels.md | 134 crosstable-0.5.0/crosstable/tests/testthat/_snaps/officer.md |only crosstable-0.5.0/crosstable/tests/testthat/_snaps/options.md |only crosstable-0.5.0/crosstable/tests/testthat/_snaps/selection.md |only crosstable-0.5.0/crosstable/tests/testthat/_snaps/tests.md | 226 crosstable-0.5.0/crosstable/tests/testthat/helper-init_dataset.R | 242 crosstable-0.5.0/crosstable/tests/testthat/test-by_factor.R | 569 - crosstable-0.5.0/crosstable/tests/testthat/test-by_numeric.R | 419 crosstable-0.5.0/crosstable/tests/testthat/test-compact.R | 187 crosstable-0.5.0/crosstable/tests/testthat/test-crosstable.R | 196 crosstable-0.5.0/crosstable/tests/testthat/test-effects.R | 396 crosstable-0.5.0/crosstable/tests/testthat/test-flextable.R | 215 crosstable-0.5.0/crosstable/tests/testthat/test-labels.R | 397 crosstable-0.5.0/crosstable/tests/testthat/test-officer.R | 635 - crosstable-0.5.0/crosstable/tests/testthat/test-options.R |only crosstable-0.5.0/crosstable/tests/testthat/test-selection.R | 564 - crosstable-0.5.0/crosstable/tests/testthat/todo_test-1-crosstable-v2.R | 998 - crosstable-0.5.0/crosstable/vignettes/crosstable-install.Rmd | 184 crosstable-0.5.0/crosstable/vignettes/crosstable-selection.Rmd | 352 87 files changed, 14301 insertions(+), 12523 deletions(-)
Title: Accrual Plots and Predictions for Clinical Trials
Description: Tracking accrual in clinical trials is important for trial success.
If accrual is too slow, the trial will take too long and be too expensive. If
accrual is much faster than expected, time sensitive tasks such as the writing
of statistical analysis plans might need to be rushed. 'accrualPlot' provides
functions to aid the tracking of accrual and predict when a trial will reach
it's intended sample size.
Author: Lukas Buetikofer [cre, aut],
Alan G. Haynes [aut]
Maintainer: Lukas Buetikofer <lukas.buetikofer@ctu.unibe.ch>
Diff between accrualPlot versions 1.0.1 dated 2022-05-09 and 1.0.7 dated 2022-08-16
DESCRIPTION | 12 - MD5 | 60 +++--- NAMESPACE | 1 NEWS.md | 25 ++ R/accrual_create_df.R | 24 +- R/accrual_linear_model.R | 17 - R/accrual_plots.r | 143 +++++++++------ R/accrual_predict.R | 66 ++++-- R/accrual_table.R | 17 - R/accrual_time_unit.R | 11 - R/data.R |only R/gg_accrual_plots.R | 188 +++++++++---------- R/helpers.R | 75 +++++-- R/methods.R | 54 ++++- data |only inst/doc/accrualPlot.R | 82 +++++--- inst/doc/accrualPlot.Rmd | 104 +++++++--- inst/doc/accrualPlot.html | 295 +++++++++++++++++-------------- man/accrual_create_df.Rd | 13 - man/accrual_linear_model.Rd | 16 - man/accrual_plot_abs.Rd | 22 -- man/accrual_plot_cum.Rd | 27 +- man/accrual_plot_predict.Rd | 109 +++++------ man/accrual_predict.Rd | 29 +-- man/accrual_table.Rd | 13 - man/accrual_time_unit.Rd | 5 man/accrualdemo.Rd |only man/as.data.frame.accrual_list.Rd |only man/figures/README-unnamed-chunk-3-1.png |binary man/plot.accrual_df.Rd | 9 man/print.accrual_df.Rd | 5 man/summary.accrual_df.Rd | 6 vignettes/accrualPlot.Rmd | 104 +++++++--- 33 files changed, 898 insertions(+), 634 deletions(-)
Title: Additional Tools for Developing Spatially Explicit Discrete
Event Simulation (SpaDES) Models
Description: Provides GIS and map utilities, plus additional modeling tools for
developing cellular automata, dynamic raster models, and agent based models
in 'SpaDES'.
Included are various methods for spatial spreading, spatial agents, GIS
operations, random map generation, and others.
See '?SpaDES.tools' for an categorized overview of these additional tools.
Author: Alex M Chubaty [aut, cre] ,
Eliot J B McIntire [aut] ,
Yong Luo [ctb],
Steve Cumming [ctb],
Jean Marchal [ctb],
Her Majesty the Queen in Right of Canada, as represented by the
Minister of Natural Resources Canada [cph]
Maintainer: Alex M Chubaty <achubaty@for-cast.ca>
Diff between SpaDES.tools versions 0.3.10 dated 2022-02-03 and 1.0.0 dated 2022-08-16
SpaDES.tools-0.3.10/SpaDES.tools/tests/testthat/test-gaussMap.R |only SpaDES.tools-1.0.0/SpaDES.tools/DESCRIPTION | 26 SpaDES.tools-1.0.0/SpaDES.tools/MD5 | 132 ++-- SpaDES.tools-1.0.0/SpaDES.tools/NAMESPACE | 3 SpaDES.tools-1.0.0/SpaDES.tools/NEWS.md | 15 SpaDES.tools-1.0.0/SpaDES.tools/R/SELES.R | 63 -- SpaDES.tools-1.0.0/SpaDES.tools/R/distanceFromEachPoint.R | 124 +-- SpaDES.tools-1.0.0/SpaDES.tools/R/environment.R | 2 SpaDES.tools-1.0.0/SpaDES.tools/R/initialize.R | 119 +-- SpaDES.tools-1.0.0/SpaDES.tools/R/mapReduce.R | 24 SpaDES.tools-1.0.0/SpaDES.tools/R/mergeRaster.R | 159 +++-- SpaDES.tools-1.0.0/SpaDES.tools/R/movement.R | 26 SpaDES.tools-1.0.0/SpaDES.tools/R/neighbourhood.R | 170 ++--- SpaDES.tools-1.0.0/SpaDES.tools/R/numerical-comparisons.R | 8 SpaDES.tools-1.0.0/SpaDES.tools/R/probability.R | 5 SpaDES.tools-1.0.0/SpaDES.tools/R/resample.R | 20 SpaDES.tools-1.0.0/SpaDES.tools/R/rings.R | 24 SpaDES.tools-1.0.0/SpaDES.tools/R/spades-tools-deprecated.R | 6 SpaDES.tools-1.0.0/SpaDES.tools/R/spades-tools-package.R | 71 +- SpaDES.tools-1.0.0/SpaDES.tools/R/splitRaster.R | 27 SpaDES.tools-1.0.0/SpaDES.tools/R/spread.R | 303 ++++----- SpaDES.tools-1.0.0/SpaDES.tools/R/spread2.R | 311 +++++----- SpaDES.tools-1.0.0/SpaDES.tools/R/spread3.R | 47 - SpaDES.tools-1.0.0/SpaDES.tools/R/studyArea.R | 8 SpaDES.tools-1.0.0/SpaDES.tools/inst/WORDLIST | 2 SpaDES.tools-1.0.0/SpaDES.tools/inst/examples/example_cir.R | 158 ++--- SpaDES.tools-1.0.0/SpaDES.tools/inst/examples/example_initiateAgents.R | 11 SpaDES.tools-1.0.0/SpaDES.tools/inst/examples/example_spread3.R | 70 +- SpaDES.tools-1.0.0/SpaDES.tools/inst/extdata |only SpaDES.tools-1.0.0/SpaDES.tools/man/SELESagentLocation.Rd | 4 SpaDES.tools-1.0.0/SpaDES.tools/man/SELESprobInit.Rd | 4 SpaDES.tools-1.0.0/SpaDES.tools/man/SELEStransitions.Rd | 4 SpaDES.tools-1.0.0/SpaDES.tools/man/SpaDES.tools-package.Rd | 67 +- SpaDES.tools-1.0.0/SpaDES.tools/man/adj.Rd | 44 - SpaDES.tools-1.0.0/SpaDES.tools/man/cir.Rd | 166 ++--- SpaDES.tools-1.0.0/SpaDES.tools/man/crw.Rd | 18 SpaDES.tools-1.0.0/SpaDES.tools/man/directions.Rd | 18 SpaDES.tools-1.0.0/SpaDES.tools/man/distanceFromEachPoint.Rd | 18 SpaDES.tools-1.0.0/SpaDES.tools/man/dwrpnorm2.Rd | 4 SpaDES.tools-1.0.0/SpaDES.tools/man/findFactors.Rd | 2 SpaDES.tools-1.0.0/SpaDES.tools/man/gaussMap.Rd | 6 SpaDES.tools-1.0.0/SpaDES.tools/man/inRange.Rd | 4 SpaDES.tools-1.0.0/SpaDES.tools/man/initiateAgents.Rd | 15 SpaDES.tools-1.0.0/SpaDES.tools/man/randomPolygons.Rd | 10 SpaDES.tools-1.0.0/SpaDES.tools/man/rasterizeReduced.Rd | 2 SpaDES.tools-1.0.0/SpaDES.tools/man/resample.Rd | 6 SpaDES.tools-1.0.0/SpaDES.tools/man/rings.Rd | 8 SpaDES.tools-1.0.0/SpaDES.tools/man/splitRaster.Rd | 31 SpaDES.tools-1.0.0/SpaDES.tools/man/spokes.Rd | 2 SpaDES.tools-1.0.0/SpaDES.tools/man/spread.Rd | 129 ++-- SpaDES.tools-1.0.0/SpaDES.tools/man/spread2.Rd | 126 ++-- SpaDES.tools-1.0.0/SpaDES.tools/man/spread3.Rd | 85 +- SpaDES.tools-1.0.0/SpaDES.tools/man/wrap.Rd | 6 SpaDES.tools-1.0.0/SpaDES.tools/tests/testthat/test-mergeRaster.R | 19 SpaDES.tools-1.0.0/SpaDES.tools/tests/testthat/test-randomPolygon.R | 5 SpaDES.tools-1.0.0/SpaDES.tools/tests/testthat/test-splitRaster.R | 43 - SpaDES.tools-1.0.0/SpaDES.tools/tests/testthat/test-spread.R | 15 SpaDES.tools-1.0.0/SpaDES.tools/tests/testthat/test-spread2.R | 11 58 files changed, 1411 insertions(+), 1395 deletions(-)
Title: Helper Functions to Install and Maintain TeX Live, and Compile
LaTeX Documents
Description: Helper functions to install and maintain the 'LaTeX' distribution
named 'TinyTeX' (<https://yihui.org/tinytex/>), a lightweight, cross-platform,
portable, and easy-to-maintain version of 'TeX Live'. This package also
contains helper functions to compile 'LaTeX' documents, and install missing
'LaTeX' packages automatically.
Author: Yihui Xie [aut, cre, cph] ,
RStudio, PBC [cph],
Christophe Dervieux [ctb] ,
Devon Ryan [ctb] ,
Ethan Heinzen [ctb],
Fernando Cagua [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between tinytex versions 0.40 dated 2022-06-15 and 0.41 dated 2022-08-16
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/latex.R | 4 +++- inst/CITATION | 2 +- 4 files changed, 11 insertions(+), 9 deletions(-)
Title: Pac-Man Visualization Package
Description: Provides a broad-view perspective on data via
linear mapping of data onto a radial coordinate system. The package
contains functions to visualize the residual values of linear
regression and Cartesian data in the defined radial scheme. See the
'pacviz' documentation page for more information:
<https://pacviz.sriley.dev/>.
Author: Spencer Riley [aut, cre]
Maintainer: Spencer Riley <academic@sriley.dev>
Diff between pacviz versions 1.0.1 dated 2021-03-04 and 1.0.2 dated 2022-08-16
DESCRIPTION | 13 ++++++------- MD5 | 20 ++++++++++---------- NAMESPACE | 3 ++- R/regression.r | 7 ------- README.md | 2 +- build/vignette.rds |binary inst/doc/pacviz.Rmd | 2 +- inst/doc/pacviz.html | 2 +- man/pac.resid.Rd | 1 - man/svm.partition.Rd | 2 +- vignettes/pacviz.Rmd | 2 +- 11 files changed, 23 insertions(+), 31 deletions(-)
Title: Unidimensional Item Response Theory Modeling
Description: Fit unidimensional item response theory (IRT) models to a mixture
of dichotomous and polytomous data, calibrate online item parameters
(i.e., pretest and operational items), estimate examinees' abilities,
and examine the IRT model-data fit on item-level in different ways
as well as provide useful functions related to unidimensional IRT models.
For the item parameter estimation, the marginal maximum likelihood estimation
via the expectation-maximization (MMLE-EM) algorithm
(Bock & Aitkin (1981) <doi:10.1007/BF02294168>) is used.
For the online calibration, the fixed item parameter calibration method
(Kim (2006) <doi:10.1111/j.1745-3984.2006.00021.x>) and
the fixed ability parameter calibration method
(Ban, Hanson, Wang, Yi, & Harris (2011) <doi:10.1111/j.1745-3984.2001.tb01123.x>)
are provided. For the ability estimation, several popular scoring methods
(e.g., MLE, EAP, and MAP) are implemented. In terms of assessing the IRT
model-data fit, one of distinguished [...truncated...]
Author: Hwanggyu Lim [aut, cre],
Craig S. Wells [ctb]
Maintainer: Hwanggyu Lim <hglim83@gmail.com>
Diff between irtplay versions 1.6.4 dated 2022-03-30 and 1.6.5 dated 2022-08-16
irtplay-1.6.4/irtplay/data/datalist |only irtplay-1.6.5/irtplay/DESCRIPTION | 13 irtplay-1.6.5/irtplay/MD5 | 41 - irtplay-1.6.5/irtplay/NEWS.md | 164 +++--- irtplay-1.6.5/irtplay/R/covirt.R | 3 irtplay-1.6.5/irtplay/R/est_irt.R | 19 irtplay-1.6.5/irtplay/R/est_item.R | 3 irtplay-1.6.5/irtplay/R/est_score.R | 3 irtplay-1.6.5/irtplay/R/estimation.R | 2 irtplay-1.6.5/irtplay/R/irtfit.R | 3 irtplay-1.6.5/irtplay/R/irtplay-package.R | 9 irtplay-1.6.5/irtplay/R/print.R | 97 +++ irtplay-1.6.5/irtplay/R/rdif.R | 11 irtplay-1.6.5/irtplay/README.md | 74 +- irtplay-1.6.5/irtplay/build |only irtplay-1.6.5/irtplay/inst/CITATION |only irtplay-1.6.5/irtplay/man/covirt.Rd | 3 irtplay-1.6.5/irtplay/man/est_irt.Rd | 5 irtplay-1.6.5/irtplay/man/est_item.Rd | 3 irtplay-1.6.5/irtplay/man/est_score.Rd | 3 irtplay-1.6.5/irtplay/man/irtfit.Rd | 3 irtplay-1.6.5/irtplay/man/irtplay-package.Rd | 9 irtplay-1.6.5/irtplay/man/rdif.Rd | 685 +++++++++++++-------------- 23 files changed, 664 insertions(+), 489 deletions(-)
Title: Hardy-Weinberg Equilibrium in Polyploids
Description: Inference concerning equilibrium and random mating in
autopolyploids. Methods are available to test for equilibrium
and random mating at any even ploidy level (>2) in the presence
of double reduction at biallelic loci. For autopolyploid populations
in equilibrium, methods are available to estimate the degree of
double reduction. We also provide functions to calculate genotype
frequencies at equilibrium, or after one or several rounds of
random mating, given rates of double reduction. The main function is
hwefit(). This material is based upon work supported by the
National Science Foundation under Grant No. 2132247. The opinions,
findings, and conclusions or recommendations expressed are those of
the author and do not necessarily reflect the views of the National
Science Foundation. For details of these methods, see
Gerard (2022a) <doi:10.1111/biom.13722> and
Gerard (2022b) <doi:10.1101/2022.08.11.503635>.
Author: David Gerard [aut, cre] ,
NSF DBI 2132247 [fnd]
Maintainer: David Gerard <gerard.1787@gmail.com>
Diff between hwep versions 0.0.2 dated 2022-05-02 and 2.0.0 dated 2022-08-16
DESCRIPTION | 23 - MD5 | 112 +++-- NAMESPACE | 15 NEWS.md | 9 R/RcppExports.R |only R/bayes.R |only R/boot.R | 310 +++++++-------- R/gmm.R | 798 ++++++++++++++++++++-------------------- R/grad.R | 506 ++++++++++++------------- R/hwe.R | 574 ++++++++++++++-------------- R/hwep-package.R | 161 ++++---- R/like.R | 38 + R/nodr.R | 122 +++--- R/plots.R | 13 R/stanmodels.R |only R/tetra.R | 468 +++++++++++------------ R/theo.R | 756 ++++++++++++++++++------------------- R/ustat.R | 602 +++++++++++++++--------------- R/utils.R | 46 ++ README.md | 51 ++ build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 49 +- inst/doc/introduction.Rmd | 4 inst/doc/introduction.html | 343 +++++++++++++++-- inst/include |only inst/stan |only man/all_multinom.Rd |only man/dgamete.Rd | 92 ++-- man/drbounds.Rd | 78 +-- man/figures |only man/gibbs_gl.Rd |only man/gibbs_gl_alt.Rd |only man/gibbs_known.Rd |only man/gsegmat.Rd | 86 ++-- man/gsegmat_symb.Rd | 72 +-- man/hweboot.Rd | 112 ++--- man/hwep-package.Rd | 3 man/menbayesgl.Rd |only man/p_from_alpha.Rd | 72 +-- man/qqpvalue.Rd | 6 man/rmbayes.Rd |only man/rmbayesgl.Rd |only man/rmlike.Rd | 119 +++-- man/simgl.Rd |only man/zsegarray.Rd | 100 ++--- man/zygdist.Rd | 84 ++-- src |only tests/testthat.R | 8 tests/testthat/glshir.RData |only tests/testthat/nvec_hard.RDS |only tests/testthat/test-bayes.R |only tests/testthat/test-grad.R | 460 +++++++++++------------ tests/testthat/test-hwe.R | 22 - tests/testthat/test-llike.R | 102 +++-- tests/testthat/test-seg.R | 618 +++++++++++++++--------------- tests/testthat/test-tetra.R | 96 ++-- tests/testthat/test-ustat.R | 112 ++--- tests/testthat/test-utils.R | 141 +++---- tests/testthat/test-utils_cpp.R |only vignettes/introduction.Rmd | 4 61 files changed, 3942 insertions(+), 3445 deletions(-)
Title: A Lightweight and Flexible Web Framework
Description: A very flexible framework for building server side logic in R. The
framework is unopinionated when it comes to how HTTP requests and WebSocket
messages are handled and supports all levels of app complexity; from serving
static content to full-blown dynamic web-apps. Fiery does not hold your hand
as much as e.g. the shiny package does, but instead sets you free to create
your web app the way you want.
Author: Thomas Lin Pedersen [cre, aut]
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>
Diff between fiery versions 1.1.3 dated 2020-12-15 and 1.1.4 dated 2022-08-16
DESCRIPTION | 8 MD5 | 20 +- NEWS.md | 4 README.md | 40 +--- build/vignette.rds |binary inst/doc/delayed.html | 335 ++++++++++++++++++++++++++++++-------- inst/doc/events.html | 434 ++++++++++++++++++++++++++++++++++++++++---------- inst/doc/plugins.html | 322 ++++++++++++++++++++++++++++--------- man/Fire.Rd | 204 +++++++++++------------ man/fiery-package.Rd | 9 - man/loggers.Rd | 36 ++-- 11 files changed, 1022 insertions(+), 390 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-10-03 0.5.0
2017-09-29 0.4.0
2017-02-01 0.3.1
2016-10-16 0.3.0
2016-09-10 0.2.0
Title: An Automated Cell Type Annotation Tool for Single-Cell
RNA-Sequencing Data
Description: An entirely data-driven cell type annotation tools, which requires training data to learn the classifier, but not biological knowledge to make subjective decisions. It consists of three steps: preprocessing training and test data, model fitting on training data, and cell classification on test data. See Xiangling Ji,Danielle Tsao, Kailun Bai, Min Tsao, Li Xing, Xuekui Zhang.(2022)<doi:10.1101/2022.02.19.481159> for more details.
Author: Xiangling Ji [aut],
Danielle Tsao [aut],
Kailun Bai [ctb],
Min Tsao [aut],
Li Xing [aut],
Xuekui Zhang [aut, cre]
Maintainer: Xuekui Zhang <xuekui@uvic.ca>
Diff between scAnnotate versions 0.0.3 dated 2022-08-09 and 0.0.4 dated 2022-08-16
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/scAnnotate.R | 12 ++++++------ inst/doc/Introduction.Rmd | 12 ++++++------ inst/doc/Introduction.html | 40 +++++++++++++++++++++------------------- man/scAnnotate.Rd | 10 +++++----- vignettes/Introduction.Rmd | 12 ++++++------ 7 files changed, 53 insertions(+), 51 deletions(-)