Title: Validation of Arguments and Objects in User-Defined Functions
Description: Utility functions that implement and automate common sets of validation tasks.
These functions are particularly useful to validate inputs, intermediate objects and output
values in user-defined functions, resulting in tidier and less verbose functions.
Author: Pedro Fonseca [aut, cre] (<https://orcid.org/0000-0002-5708-081X>),
FCT [fnd]
Maintainer: Pedro Fonseca <pedro.teles.fonseca@phd.iseg.ulisboa.pt>
Diff between inspector versions 1.0.2 dated 2020-11-16 and 1.0.3 dated 2021-06-17
inspector-1.0.2/inspector/man/inspect_data_cat_as_dichotomous.Rd |only inspector-1.0.3/inspector/DESCRIPTION | 7 inspector-1.0.3/inspector/MD5 | 64 inspector-1.0.3/inspector/NAMESPACE | 2 inspector-1.0.3/inspector/NEWS.md | 12 inspector-1.0.3/inspector/R/inspect_.R | 813 ++++++---- inspector-1.0.3/inspector/R/inspect_data_.R | 566 ++++-- inspector-1.0.3/inspector/R/inspect_par_.R | 308 ++- inspector-1.0.3/inspector/R/inspector.R | 13 inspector-1.0.3/inspector/R/internal.R | 3 inspector-1.0.3/inspector/README.md | 92 - inspector-1.0.3/inspector/inst/CITATION | 8 inspector-1.0.3/inspector/man/inspect_bfactor.Rd | 51 inspector-1.0.3/inspector/man/inspect_bfactor_log.Rd | 54 inspector-1.0.3/inspector/man/inspect_bfactor_scale.Rd | 39 inspector-1.0.3/inspector/man/inspect_categories.Rd | 34 inspector-1.0.3/inspector/man/inspect_character.Rd | 40 inspector-1.0.3/inspector/man/inspect_character_match.Rd | 38 inspector-1.0.3/inspector/man/inspect_data_cat_as_dichotom.Rd |only inspector-1.0.3/inspector/man/inspect_data_categorical.Rd | 57 inspector-1.0.3/inspector/man/inspect_data_dichotomous.Rd | 69 inspector-1.0.3/inspector/man/inspect_log_base.Rd | 25 inspector-1.0.3/inspector/man/inspect_par_bernoulli.Rd | 36 inspector-1.0.3/inspector/man/inspect_par_beta.Rd | 33 inspector-1.0.3/inspector/man/inspect_par_dirichlet.Rd | 36 inspector-1.0.3/inspector/man/inspect_par_haldane.Rd | 33 inspector-1.0.3/inspector/man/inspect_par_multinomial.Rd | 39 inspector-1.0.3/inspector/man/inspect_prob.Rd | 47 inspector-1.0.3/inspector/man/inspect_true_or_false.Rd | 18 inspector-1.0.3/inspector/man/inspector-package.Rd | 10 inspector-1.0.3/inspector/tests/testthat/test-inspect_.R | 559 ++++-- inspector-1.0.3/inspector/tests/testthat/test-inspect_data_.R | 275 ++- inspector-1.0.3/inspector/tests/testthat/test-inspect_par_.R | 369 ++-- inspector-1.0.3/inspector/tests/testthat/test-internals.R | 12 34 files changed, 2418 insertions(+), 1344 deletions(-)
Title: Spillover Index Based on VAR Modelling
Description: A user-friendly tool for estimating both total and directional volatility spillovers based on Diebold and Yilmaz (2009, 2012). It also provides the user with rolling estimation for total and net indices. User can find both orthogonalized and generalized versions for each kind of measures. See Diebold and Yilmaz (2009, 2012) find them at <doi:10.1111/j.1468-0297.2008.02208.x> and <doi:10.1016/j.ijforecast.2011.02.006>.
Author: Jilber Urbina
Maintainer: Jilber Urbina <jurbina@cipadla.com>
Diff between Spillover versions 0.1 dated 2020-09-29 and 0.1.0.1 dated 2021-06-17
DESCRIPTION | 10 +++++----- MD5 | 22 +++++++++++----------- R/G.spillover.R | 2 +- R/O.spillover.R | 2 +- R/g.fevd.R | 2 +- R/roll_net.R | 5 +++-- R/roll_spillover.R | 2 +- man/G.spillover.Rd | 2 +- man/O.spillover.Rd | 2 +- man/g.fevd.Rd | 2 +- man/roll.net.Rd | 2 +- man/roll.spillover.Rd | 2 +- 12 files changed, 28 insertions(+), 27 deletions(-)
Title: Multiple Imputation of Covariates by Substantive Model
Compatible Fully Conditional Specification
Description: Implements multiple imputation of missing covariates by
Substantive Model Compatible Fully Conditional Specification.
This is a modification of the popular FCS/chained equations
multiple imputation approach, and allows imputation of missing
covariate values from models which are compatible with the user
specified substantive model.
Author: Jonathan Bartlett [aut, cre],
Ruth Keogh [aut],
Edouard F. Bonneville [aut],
Claus Thorn Ekstrøm [ctb]
Maintainer: Jonathan Bartlett <j.w.bartlett@bath.ac.uk>
Diff between smcfcs versions 1.5.0 dated 2021-04-01 and 1.6.0 dated 2021-06-17
DESCRIPTION | 16 MD5 | 73 - NAMESPACE | 20 R/data.r | 286 ++-- R/plot_convergence.R | 412 +++-- R/smcfcs.r | 2328 ++++++++++++++++----------------- R/smcfcs_parallel.r |only README.md | 22 build/partial.rdb |binary build/vignette.rds |binary inst/doc/smcfcs-vignette.R | 96 - inst/doc/smcfcs-vignette.Rmd | 278 +-- inst/doc/smcfcs-vignette.html | 733 +++++----- inst/doc/smcfcs_coverror-vignette.R | 168 +- inst/doc/smcfcs_coverror-vignette.Rmd | 262 +-- inst/doc/smcfcs_coverror-vignette.html | 681 ++++----- man/ex_cc.Rd | 50 man/ex_compet.Rd | 48 man/ex_coxquad.Rd | 50 man/ex_lininter.Rd | 44 man/ex_linquad.Rd | 48 man/ex_logisticquad.Rd | 48 man/ex_ncc.Rd | 52 man/ex_poisson.Rd | 46 man/plot.smcfcs.Rd | 122 - man/smcfcs.Rd | 440 +++--- man/smcfcs.casecohort.Rd | 202 +- man/smcfcs.nestedcc.Rd | 216 +-- man/smcfcs.parallel.Rd |only tests/testthat/test_casecohort.r | 166 +- tests/testthat/test_coxph.r | 96 - tests/testthat/test_dtsam.r | 878 ++++++------ tests/testthat/test_errorchecks.R | 434 +++--- tests/testthat/test_measerror.r | 170 +- tests/testthat/test_nestedcc.R | 272 +-- tests/testthat/test_parallel.r |only tests/testthat/test_weibull.r | 126 - vignettes/smcfcs-vignette.Rmd | 278 +-- vignettes/smcfcs_coverror-vignette.Rmd | 262 +-- 39 files changed, 4723 insertions(+), 4700 deletions(-)
Title: Lightweight Reproducible Reporting
Description: Order, create and store reports from R. By defining a
lightweight interface around the inputs and outputs of an
analysis, a lot of the repetitive work for reproducible research
can be automated. We define a simple format for organising and
describing work that facilitates collaborative reproducible
research and acknowledges that all analyses are run multiple
times over their lifespans.
Author: Rich FitzJohn [aut, cre],
Robert Ashton [aut],
Alex Hill [aut],
Martin Eden [aut],
Wes Hinsley [aut],
Emma Russell [aut],
James Thompson [aut],
Imperial College of Science, Technology and Medicine [cph]
Maintainer: Rich FitzJohn <rich.fitzjohn@gmail.com>
Diff between orderly versions 1.0.4 dated 2020-01-12 and 1.3.0 dated 2021-06-17
orderly-1.0.4/orderly/R/recipe_read.R |only orderly-1.0.4/orderly/R/runner.R |only orderly-1.0.4/orderly/inst/examples/interactive |only orderly-1.0.4/orderly/man/orderly_runner.Rd |only orderly-1.0.4/orderly/tests/testthat/helper-runner.R |only orderly-1.0.4/orderly/tests/testthat/test-recipe-read.R |only orderly-1.0.4/orderly/tests/testthat/test-z-runner.R |only orderly-1.3.0/orderly/DESCRIPTION | 14 orderly-1.3.0/orderly/MD5 | 282 + orderly-1.3.0/orderly/NAMESPACE | 24 orderly-1.3.0/orderly/NEWS.md | 258 + orderly-1.3.0/orderly/R/batch.R |only orderly-1.3.0/orderly/R/bundle.R |only orderly-1.3.0/orderly/R/changelog.R | 26 orderly-1.3.0/orderly/R/cleanup.R | 18 orderly-1.3.0/orderly/R/config.R | 506 ++- orderly-1.3.0/orderly/R/db.R | 104 orderly-1.3.0/orderly/R/db2.R | 115 orderly-1.3.0/orderly/R/deduplicate.R | 2 orderly-1.3.0/orderly/R/dependencies.R |only orderly-1.3.0/orderly/R/dependencies_src.R |only orderly-1.3.0/orderly/R/develop.R |only orderly-1.3.0/orderly/R/envir.R | 28 orderly-1.3.0/orderly/R/file_store.R | 21 orderly-1.3.0/orderly/R/git.R | 19 orderly-1.3.0/orderly/R/helpers.R |only orderly-1.3.0/orderly/R/info.R |only orderly-1.3.0/orderly/R/logging.R | 15 orderly-1.3.0/orderly/R/main.R | 238 + orderly-1.3.0/orderly/R/migrate.R | 6 orderly-1.3.0/orderly/R/new.R | 3 orderly-1.3.0/orderly/R/orderly_recipe.R |only orderly-1.3.0/orderly/R/orderly_recipe_artefacts.R |only orderly-1.3.0/orderly/R/orderly_recipe_depends.R |only orderly-1.3.0/orderly/R/orderly_version.R |only orderly-1.3.0/orderly/R/paths.R | 25 orderly-1.3.0/orderly/R/publish.R | 2 orderly-1.3.0/orderly/R/query.R | 170 - orderly-1.3.0/orderly/R/query_search.R |only orderly-1.3.0/orderly/R/recipe_commit.R | 24 orderly-1.3.0/orderly/R/recipe_run.R | 539 --- orderly-1.3.0/orderly/R/recipe_test.R | 62 orderly-1.3.0/orderly/R/remote.R | 321 +- orderly-1.3.0/orderly/R/remote_path.R | 35 orderly-1.3.0/orderly/R/report_tree.R |only orderly-1.3.0/orderly/R/slack.R | 150 - 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Title: Summary Tables and Plots for Statistical Models and Data:
Beautiful, Customizable, and Publication-Ready
Description: Create beautiful and customizable tables to summarize several
statistical models side-by-side. Draw coefficient plots, multi-level
cross-tabs, dataset summaries, balance tables (a.k.a. "Table 1s"), and
correlation matrices. This package supports dozens of statistical models,
and it can produce tables in HTML, LaTeX, Word, Markdown, PDF, PowerPoint,
Excel, RTF, JPG, or PNG. Tables can easily be embedded in 'Rmarkdown' or
'knitr' dynamic documents.
Author: Vincent Arel-Bundock [aut, cre]
(<https://orcid.org/0000-0003-2042-7063>),
Joachim Gassen [ctb] (<https://orcid.org/0000-0003-4364-2911>),
Nathan Eastwood [ctb],
Nick Huntington-Klein [ctb] (<https://orcid.org/0000-0002-7352-3991>),
Moritz Schwarz [ctb] (<https://orcid.org/0000-0003-0340-3780>),
Benjamin Elbers [ctb] (0000-0001-5392-3448)
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Diff between modelsummary versions 0.8.0 dated 2021-05-21 and 0.8.1 dated 2021-06-17
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Title: Statistics for Matrix Distributions
Description: Tools for homogeneous and in-homogeneous phase-type distributions.
Methods for functional evaluation, simulation and estimation using the
expectation-maximization (EM) algorithm are provided.
The methods of this package are based on the following references.
Asmussen, S., Nerman, O., & Olsson, M. (1996) <https://www.jstor.org/stable/4616418>,
Olsson, M. (1996) <https://www.jstor.org/stable/4616419>.
Albrecher, H., & Bladt, M. (2019) <doi:10.1017/jpr.2019.60>
Albrecher, H., Bladt, M., & Yslas, J. (2020) <doi:10.1111/sjos.12505>
Bladt, M., & Yslas, J. (2020) <arXiv:2011.03219>.
Author: Martin Bladt [aut, cre],
Jorge Yslas [aut]
Maintainer: Martin Bladt <martinbladt@gmail.com>
Diff between matrixdist versions 1.0.2 dated 2021-02-26 and 1.1.0 dated 2021-06-17
DESCRIPTION | 10 MD5 | 109 +++- NAMESPACE | 20 R/0.generics.R | 54 ++ R/1.ph.R | 151 ++++- R/2.iph.R | 43 + R/2b.iph_regression.R |only R/6.sph.R |only R/RcppExports.R | 666 +++++++++++++++++++++++++ man/EMstep_PADE.Rd |only man/EMstep_UNI.Rd |only man/Fisher-sph-method.Rd |only man/Fisher.Rd |only man/LRT-ph-ph-method.Rd |only man/LRT.Rd |only man/cdf-iph-method.Rd | 2 man/cdf-ph-method.Rd | 2 man/coef-sph-method.Rd |only man/dens-iph-method.Rd | 2 man/dens-ph-method.Rd | 2 man/evaluate-sph-method.Rd |only man/evaluate.Rd |only man/fit-ph-method.Rd | 11 man/haz-ph-method.Rd | 2 man/logLikelihoodMgev_PADE.Rd |only man/logLikelihoodMgev_UNI.Rd |only man/logLikelihoodMgompertz_PADE.Rd |only man/logLikelihoodMgompertz_PADEs.Rd |only man/logLikelihoodMgompertz_RKs.Rd |only man/logLikelihoodMgompertz_UNI.Rd |only man/logLikelihoodMgompertz_UNIs.Rd |only man/logLikelihoodMloglogistic_PADE.Rd |only man/logLikelihoodMloglogistic_PADEs.Rd |only man/logLikelihoodMloglogistic_RKs.Rd |only man/logLikelihoodMloglogistic_UNI.Rd |only man/logLikelihoodMloglogistic_UNIs.Rd |only man/logLikelihoodMlognormal_PADE.Rd |only man/logLikelihoodMlognormal_PADEs.Rd |only man/logLikelihoodMlognormal_RKs.Rd |only man/logLikelihoodMlognormal_UNI.Rd |only man/logLikelihoodMlognormal_UNIs.Rd |only man/logLikelihoodMpareto_PADE.Rd |only man/logLikelihoodMpareto_PADEs.Rd |only man/logLikelihoodMpareto_RKs.Rd |only man/logLikelihoodMpareto_UNI.Rd |only man/logLikelihoodMpareto_UNIs.Rd |only man/logLikelihoodMweibull_PADE.Rd |only man/logLikelihoodMweibull_PADEs.Rd |only man/logLikelihoodMweibull_RKs.Rd |only man/logLikelihoodMweibull_UNI.Rd |only man/logLikelihoodMweibull_UNIs.Rd |only man/logLikelihoodPH_PADE.Rd |only man/logLikelihoodPH_PADEs.Rd |only man/logLikelihoodPH_RKs.Rd |only man/logLikelihoodPH_UNI.Rd |only man/logLikelihoodPH_UNIs.Rd |only man/matrixExpSum_arma.Rd |only man/matrix_VanLoanArma.Rd |only man/matrix_exponential.Rd | 4 man/matrix_exponential_slow.Rd |only man/matrix_inverse_slow.Rd |only man/matrix_product.Rd | 8 man/matrix_product_slow.Rd |only man/quan-ph-method.Rd | 2 man/reg-ph-method.Rd |only man/reg.Rd |only man/show-sph-method.Rd |only man/sph-class.Rd |only man/sph.Rd |only man/vectorOfMatrices_arma.Rd |only man/vectorOfMatrices_arma2.Rd |only src/EM_LL.cpp | 394 ++++++++++++++- src/EM_LL_PADE.cpp |only src/EM_LL_UNI.cpp |only src/Makevars |only src/Makevars.win |only src/RcppExports.cpp | 854 ++++++++++++++++++++++++++++++++- src/Simulation.cpp | 1 src/auxilliary.cpp |only src/auxilliary.h |only src/distributions.cpp | 1 src/exp_arm.cpp |only src/exp_arm.h |only src/matrix_functions.cpp | 7 src/matrix_functions.h | 6 src/operations.cpp | 1 src/structure_parameters.cpp | 1 87 files changed, 2244 insertions(+), 109 deletions(-)
Title: Analysis of Ecological Data: Exploratory and Euclidean Methods
in Environmental Sciences
Description: Tools for multivariate data analysis. Several methods are provided for the analysis (i.e., ordination) of one-table (e.g., principal component analysis, correspondence analysis), two-table (e.g., coinertia analysis, redundancy analysis), three-table (e.g., RLQ analysis) and K-table (e.g., STATIS, multiple coinertia analysis). The philosophy of the package is described in Dray and Dufour (2007) <doi:10.18637/jss.v022.i04>.
Author: Stéphane Dray <stephane.dray@univ-lyon1.fr>, Anne-Béatrice Dufour <anne-beatrice.dufour@univ-lyon1.fr>, and Jean Thioulouse <jean.thioulouse@univ-lyon1.fr>, with contributions from Thibaut Jombart, Sandrine Pavoine, Jean R. Lobry, Sébastien Ollier, Daniel Borcard, Pierre Legendre, Stéphanie Bougeard and Aurélie Siberchicot. Based on earlier work by Daniel Chessel.
Maintainer: Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
Diff between ade4 versions 1.7-16 dated 2020-10-28 and 1.7-17 dated 2021-06-17
ChangeLog | 133 +++++++++++++++++++++++++++ DESCRIPTION | 12 +- MD5 | 39 ++++---- NAMESPACE | 1 R/fourthcorner.R | 4 R/fourthcorner2.R | 4 R/loocv.R | 217 +++++++++++++++++++++++++++++++++++---------- R/mcoa.R | 2 build |only man/bwca.dpcoa.Rd | 2 man/dist.ktab.Rd | 6 + man/fourthcorner.Rd | 10 +- man/loocv.bca.Rd | 84 +++++++++++++---- man/loocv.discrimin.Rd | 67 ++++++++++--- man/loocv.dudi.Rd | 16 ++- man/mbpcaiv.Rd | 2 man/mbpls.Rd | 2 man/multiblock.Rd | 2 man/randboot.multiblock.Rd | 2 man/supdist.Rd | 2 man/testdim.multiblock.Rd | 2 21 files changed, 482 insertions(+), 127 deletions(-)
Title: Assessing Normality of Stationary Process
Description: Despite that several tests for normality in stationary processes have been proposed
in the literature, consistent implementations of these tests in programming languages are limited.
Four normality test are implemented. The Lobato and Velasco's, Epps, Psaradakis and Vavra, and the
random projections tests for stationary process. Some other diagnostics such as, unit root test for
stationarity, seasonal tests for seasonality, and arch effect test for volatility; are also performed.
The package also offers residual diagnostic for linear time series models developed in several packages.
Author: Asael Alonzo Matamoros [aut, cre],
Alicia Nieto-Reyes [aut],
Rob Hyndman [ctb],
Mitchell O'Hara-Wild [ctb],
Trapletti A. [ctb]
Maintainer: Asael Alonzo Matamoros <asael.alonzo@gmail.com>
Diff between nortsTest versions 1.0.0 dated 2020-07-27 and 1.0.1 dated 2021-06-17
DESCRIPTION | 13 +++++++------ MD5 | 32 ++++++++++++++++---------------- NEWS.md | 24 ++++++++++++++++++++++-- R/Lm_test.R | 2 +- R/check_residuals.R | 2 +- R/epps_test.R | 2 +- R/lobato_test.R | 4 ++-- R/rejection_rates.R | 2 +- R/rp_test.R | 25 ++++++++----------------- R/test.R | 34 ++++++++++++++++++++++------------ R/vavra_test.R | 6 +++--- README.md | 15 +++++---------- man/arch.test.Rd | 2 +- man/normal.test.Rd | 3 ++- man/rp.test.Rd | 4 ++-- man/seasonal.test.Rd | 2 +- man/uroot.test.Rd | 2 +- 17 files changed, 96 insertions(+), 78 deletions(-)
Title: Tidy IP Addresses
Description: Classes and functions for working with IP (Internet Protocol)
addresses and networks, inspired by the Python 'ipaddress' module.
Offers full support for both IPv4 and IPv6 (Internet Protocol versions
4 and 6) address spaces. It is specifically designed to work well with
the 'tidyverse'.
Author: David Hall [aut, cre] (<https://orcid.org/0000-0002-2193-0480>)
Maintainer: David Hall <david.hall.physics@gmail.com>
Diff between ipaddress versions 0.5.1 dated 2020-09-12 and 0.5.2 dated 2021-06-17
ipaddress-0.5.1/ipaddress/src/ip_to_integer.cpp |only ipaddress-0.5.2/ipaddress/DESCRIPTION | 23 ipaddress-0.5.2/ipaddress/MD5 | 45 - ipaddress-0.5.2/ipaddress/NAMESPACE | 2 ipaddress-0.5.2/ipaddress/NEWS.md | 179 ++-- ipaddress-0.5.2/ipaddress/R/RcppExports.R | 16 ipaddress-0.5.2/ipaddress/R/ip_to_binary.R | 4 ipaddress-0.5.2/ipaddress/R/ip_to_bytes.R | 6 ipaddress-0.5.2/ipaddress/R/ip_to_hex.R |only ipaddress-0.5.2/ipaddress/R/ip_to_integer.R | 78 -- ipaddress-0.5.2/ipaddress/R/operators.R | 12 ipaddress-0.5.2/ipaddress/README.md | 20 ipaddress-0.5.2/ipaddress/build/vignette.rds |binary ipaddress-0.5.2/ipaddress/inst/doc/ipaddress-classes.html | 292 +------ ipaddress-0.5.2/ipaddress/inst/doc/ipaddress-examples.html | 386 ++-------- ipaddress-0.5.2/ipaddress/man/ip_to_binary.Rd | 9 ipaddress-0.5.2/ipaddress/man/ip_to_bytes.Rd | 12 ipaddress-0.5.2/ipaddress/man/ip_to_hex.Rd |only ipaddress-0.5.2/ipaddress/man/ip_to_integer.Rd | 55 - ipaddress-0.5.2/ipaddress/man/ipaddress-package.Rd | 10 ipaddress-0.5.2/ipaddress/src/RcppExports.cpp | 39 - ipaddress-0.5.2/ipaddress/src/ip_to_hex.cpp |only ipaddress-0.5.2/ipaddress/tests/testthat/test-ip_to_hex.R |only ipaddress-0.5.2/ipaddress/tests/testthat/test-ip_to_hostname.R | 12 ipaddress-0.5.2/ipaddress/tests/testthat/test-ip_to_integer.R | 37 ipaddress-0.5.2/ipaddress/tests/testthat/test-pillar.txt | 6 26 files changed, 400 insertions(+), 843 deletions(-)
Title: Biclustering with Missing Data
Description: Biclustering is a statistical learning technique that simultaneously
partitions and clusters rows and columns of a data matrix. Since the solution
space of biclustering is in infeasible to completely search with current
computational mechanisms, this package uses a greedy heuristic. The algorithm
featured in this package is, to the best our knowledge, the first biclustering
algorithm to work on data with missing values. Li, J., Reisner, J., Pham, H.,
Olafsson, S., and Vardeman, S. (2020) Biclustering with Missing Data. Information
Sciences, 510, 304–316.
Author: John Reisner [cre, aut, cph],
Hieu Pham [ctb, cph],
Jing Li [ctb, cph]
Maintainer: John Reisner <johntreisner@gmail.com>
Diff between biclustermd versions 0.2.2 dated 2020-04-15 and 0.2.3 dated 2021-06-17
DESCRIPTION | 18 ++-- MD5 | 34 ++++--- NAMESPACE | 1 R/biclustermd-package.R |only R/biclustermd.R | 16 ++- R/compare_biclusters.R | 7 - R/jaccard.R |only R/rep_biclustermd.R | 2 inst/doc/Airports.html | 179 ++++++++++++++++++++-------------------- man/autoplot.biclustermd.Rd | 14 ++- man/autoplot.biclustermd_sim.Rd | 3 man/biclustermd-package.Rd |only man/biclustermd.Rd | 26 +++-- man/gather.biclustermd.Rd | 11 ++ man/jaccard_similarity.Rd |only man/rep_biclustermd.Rd | 24 ++++- man/results_heatmap.Rd | 13 ++ man/runtimes.Rd | 4 man/synthetic.Rd | 6 - man/tune_biclustermd.Rd | 9 +- 20 files changed, 212 insertions(+), 155 deletions(-)
Title: Assignment of Haplotypes Based on SNP Dosages in Diploids and
Polyploids
Description: Infer the genetic composition of individuals
in terms of haplotype dosages for a haploblock, based
on bi-allelic marker dosages, for any ploidy level.
Reference: Voorrips and Tumino: PolyHaplotyper: haplotyping in polyploids based on bi-allelic marker dosage data.
Submitted to BMC Bioinformatics (2021).
Author: Roeland E. Voorrips
Maintainer: Roeland E. Voorrips <roeland.voorrips@wur.nl>
Diff between PolyHaplotyper versions 1.0.0 dated 2021-02-10 and 1.0.1 dated 2021-06-17
DESCRIPTION | 11 MD5 | 12 NAMESPACE | 1 R/PolyHaplotyper.R | 792 +++++++++++++++++++++++-------------------- build/vignette.rds |binary inst/doc/PolyHaplotyper.html | 2 man/inferHaplotypes.Rd | 12 7 files changed, 451 insertions(+), 379 deletions(-)
More information about PolyHaplotyper at CRAN
Permanent link
Title: Mixed-Frequency GARCH Models
Description: Estimating GARCH-MIDAS (MIxed-DAta-Sampling) models (Engle, Ghysels, Sohn, 2013, <doi:10.1162/REST_a_00300>) and related statistical inference, accompanying the paper "Two are better than one: Volatility forecasting using multiplicative component GARCH models" by Conrad and Kleen (2020, <doi:10.1002/jae.2742>). The GARCH-MIDAS model decomposes the conditional variance of (daily) stock returns into a short- and long-term component, where the latter may depend on an exogenous covariate sampled at a lower frequency.
Author: Onno Kleen [aut, cre] (<https://orcid.org/0000-0003-4731-4640>)
Maintainer: Onno Kleen <r@onnokleen.de>
Diff between mfGARCH versions 0.2.0 dated 2020-05-12 and 0.2.1 dated 2021-06-17
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS.md | 3 +++ R/data.R | 4 ++-- R/fit_mfgarch.R | 42 ++++++++++++++---------------------------- R/generic_functions.R | 10 +++++----- R/helper_functions.R | 6 +++--- man/df_financial.Rd | 2 +- man/df_mfgarch.Rd | 2 +- 9 files changed, 41 insertions(+), 52 deletions(-)
Title: Visualization and Tools for Ichimoku Kinko Hyo Strategies
Description: An implementation of 'Ichimoku Kinko Hyo', also commonly known as
'cloud charts'. Static and interactive visualizations with tools for
creating, backtesting and development of quantitative 'ichimoku' strategies.
As described in Sasaki (1996, ISBN:4925152009), the technique is a refinement
on candlestick charting originating from Japan, now in widespread use in
technical analysis worldwide. Translating as 'one-glance equilibrium chart',
it allows the price action and market structure of financial securities to
be determined 'at-a-glance'.
Author: Charlie Gao [aut, cre]
Maintainer: Charlie Gao <charlie.gao@shikokuchuo.net>
Diff between ichimoku versions 0.1.2 dated 2021-05-19 and 0.2.0 dated 2021-06-17
DESCRIPTION | 28 +- MD5 | 69 ++++--- NAMESPACE | 21 +- NEWS.md | 24 ++ R/RcppExports.R |only R/data.R | 6 R/ichimoku-package.R | 39 ++-- R/ichimoku.R | 398 ++++++++++++++++++++--------------------- R/mltools.R |only R/strat.R |only R/sysdata.rda |binary R/utils.R |only README.md | 74 +++++-- build/vignette.rds |binary data/sample_ohlc_data.rda |binary inst/doc/reference.R | 28 +- inst/doc/reference.Rmd | 201 ++++++++++++-------- inst/doc/reference.html | 275 +++++++++++++++++----------- inst/doc/strategies.R |only inst/doc/strategies.Rmd |only inst/doc/strategies.html |only man/autoplot.ichimoku.Rd | 31 ++- man/autostrat.Rd |only man/duplicate.Rd |only man/figures/README-plot-1.png |binary man/hasStrat.Rd |only man/ichimoku-package.Rd | 30 ++- man/ichimoku.Rd | 36 +-- man/iplot.Rd | 28 +- man/maxOver.Rd |only man/minOver.Rd |only man/mlgrid.Rd |only man/plot.ichimoku.Rd | 57 +++-- man/print.ichimoku.Rd | 10 - man/sample_ohlc_data.Rd | 6 man/strat.Rd |only man/stratcombine.Rd |only man/summary.ichimoku.Rd |only man/tradingDays.Rd |only man/trimdf.Rd |only man/writeMatrix.Rd |only man/writeStrat.Rd |only src |only tests/testthat/test-ichimoku.R | 60 +++++- vignettes/reference.Rmd | 201 ++++++++++++-------- vignettes/strategies.Rmd |only 46 files changed, 990 insertions(+), 632 deletions(-)
Title: Continuous Time Structural Equation Modelling
Description: Hierarchical continuous time state space modelling, for linear
and nonlinear systems measured by continuous variables, with limited support for
binary data. The subject specific dynamic system is modelled as a stochastic
differential equation (SDE), measurement models are typically multivariate normal factor models.
Linear mixed effects SDE's estimated via maximum likelihood and optimization are the default.
Nonlinearities, (state dependent parameters) and random effects on all parameters
are possible, using either max likelihood / max a posteriori optimization
(with optional importance sampling) or
Stan's Hamiltonian Monte Carlo sampling. See <https://github.com/cdriveraus/ctsem/raw/master/vignettes/hierarchicalmanual.pdf>
for details. Priors may be used. For the conceptual
overview of the hierarchical Bayesian linear SDE approach, see <https://www.researchgate.net/publication/324093594_Hierarchical_Bayesian_Continuous_Time_Dynamic_Modeling>.
Exogenous inputs may also be included, for an overview of such possibilities see <https://www.researchgate.net/publication/328221807_Understanding_the_Time_Course_of_Interventions_with_Continuous_Time_Dynamic_Models> .
Stan based functions are not available on 32 bit Windows systems at present.
<https://cdriver.netlify.app/> contains some tutorial blog posts.
Author: Charles Driver [aut, cre, cph],
Manuel Voelkle [aut, cph],
Han Oud [aut, cph],
Trustees of Columbia University [cph]
Maintainer: Charles Driver <charles.driver@ibe.uzh.ch>
Diff between ctsem versions 3.5.2 dated 2021-06-17 and 3.5.3 dated 2021-06-17
DESCRIPTION | 8 ++++---- MD5 | 13 +++++++------ R/ctStanModelWriter.R | 4 ++-- inst/doc/hierarchicalmanual.pdf |binary src/stan_files/ctsm.stan | 4 ++-- src/stan_files/ctsmgen.stan | 4 ++-- tests/testthat/test-corrcheck.R |only tests/testthat/test-knownFits.R | 2 +- 8 files changed, 18 insertions(+), 17 deletions(-)
Title: Core Functionality of the 'spatstat' Family
Description: Functionality for data analysis and modelling of
spatial data, mainly spatial point patterns,
in the 'spatstat' family of packages.
(Excludes analysis of spatial data on a linear network,
which is covered by the separate package 'spatstat.linnet'.)
Exploratory methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Monte Carlo, Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Monte Carlo) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov, ANOVA) are also supported.
Parametric models can be fitted to point pattern data using the functions ppm(), kppm(), slrm(), dppm() similar to glm(). Types of models include Poisson, Gibbs and Cox point processes, Neyman-Scott cluster processes, and determinantal point processes. Models may involve dependence on covariates, inter-point interaction, cluster formation and dependence on marks. Models are fitted by maximum likelihood, logistic regression, minimum contrast, and composite likelihood methods.
A model can be fitted to a list of point patterns (replicated point pattern data) using the function mppm(). The model can include random effects and fixed effects depending on the experimental design, in addition to all the features listed above.
Fitted point process models can be simulated, automatically. Formal hypothesis tests of a fitted model are supported (likelihood ratio test, analysis of deviance, Monte Carlo tests) along with basic tools for model selection (stepwise(), AIC()) and variable selection (sdr). Tools for validating the fitted model include simulation envelopes, residuals, residual plots and Q-Q plots, leverage and influence diagnostics, partial residuals, and added variable plots.
Author: Adrian Baddeley [aut, cre],
Rolf Turner [aut],
Ege Rubak [aut],
Kasper Klitgaard Berthelsen [ctb],
Achmad Choiruddin [ctb],
Jean-Francois Coeurjolly [ctb],
Ottmar Cronie [ctb],
Tilman Davies [ctb],
Julian Gilbey [ctb],
Yongtao Guan [ctb],
Ute Hahn [ctb],
Kassel Hingee [ctb],
Abdollah Jalilian [ctb],
Marie-Colette van Lieshout [ctb],
Greg McSwiggan [ctb],
Tuomas Rajala [ctb],
Suman Rakshit [ctb],
Dominic Schuhmacher [ctb],
Rasmus Plenge Waagepetersen [ctb],
Hangsheng Wang [ctb]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.core versions 2.1-2 dated 2021-04-18 and 2.2-0 dated 2021-06-17
DESCRIPTION | 12 +- MD5 | 51 ++++++----- NAMESPACE | 9 ++ NEWS | 51 +++++++++++ R/distcdf.R | 62 +++++++------ R/ic.kppm.R | 2 R/rPSNCP.R |only R/rhohat.R | 185 +++++++++++++++++++++++++++++++---------- R/slrm.R | 53 ++++++++++- R/spatcov.R |only inst/doc/packagesizes.txt | 2 man/cdf.test.mppm.Rd | 6 - man/density.ppp.Rd | 189 +++++++++++++++++++++++------------------- man/distcdf.Rd | 14 +-- man/leverage.ppm.Rd | 7 + man/methods.slrm.Rd | 6 - man/pairMean.Rd |only man/plot.leverage.ppm.Rd | 4 man/plot.profilepl.Rd | 6 - man/psst.Rd | 10 +- man/psstA.Rd | 13 ++ man/psstG.Rd | 10 ++ man/rHardcore.Rd | 7 - man/rPSNCP.Rd |only man/rStrauss.Rd | 3 man/rhohat.Rd | 37 ++++++-- man/slrm.Rd | 4 man/spatcov.Rd |only man/spatstat.core-internal.Rd | 10 +- 29 files changed, 522 insertions(+), 231 deletions(-)
Title: R Interface to Apache Spark
Description: R interface to Apache Spark, a fast and general
engine for big data processing, see <http://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] (<https://orcid.org/0000-0001-7803-7901>),
Kevin Ushey [aut],
JJ Allaire [aut],
Samuel Macedo [ctb],
Hossein Falaki [aut],
Lu Wang [aut],
Andy Zhang [aut],
Yitao Li [aut, cre] (<https://orcid.org/0000-0002-1261-905X>),
Jozef Hajnala [ctb],
Maciej Szymkiewicz [ctb] (<https://orcid.org/0000-0003-1469-9396>),
Wil Davis [ctb],
RStudio [cph],
The Apache Software Foundation [aut, cph]
Maintainer: Yitao Li <yitao@rstudio.com>
Diff between sparklyr versions 1.7.0 dated 2021-06-10 and 1.7.1 dated 2021-06-17
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 6 ++++++ R/spark_extensions.R | 5 +++-- build/partial.rdb |binary 5 files changed, 16 insertions(+), 9 deletions(-)
Title: Extract, Analyze and Visualize Mutational Signatures for Genomic
Variations
Description: Genomic alterations including single nucleotide
substitution, copy number alteration, etc. are the major force for
cancer initialization and development. Due to the specificity of
molecular lesions caused by genomic alterations, we can generate
characteristic alteration spectra, called 'signature' (Wang, Shixiang,
et al. (2020) <DOI:10.1101/2020.04.27.20082404> & Alexandrov, Ludmil
B., et al. (2020) <DOI:10.1038/s41586-020-1943-3>). This package helps
users to extract, analyze and visualize signatures from genomic
alteration records, thus providing new insight into cancer study.
Author: Shixiang Wang [aut, cre] (<https://orcid.org/0000-0001-9855-7357>),
Ziyu Tao [aut] (<https://orcid.org/0000-0003-3272-1227>),
Huimin Li [aut] (<https://orcid.org/0000-0003-1683-9057>),
Tao Wu [aut] (<https://orcid.org/0000-0002-8999-9628>),
Xue-Song Liu [aut, ctb] (<https://orcid.org/0000-0002-7736-0077>),
Anand Mayakonda [ctb]
Maintainer: Shixiang Wang <w_shixiang@163.com>
Diff between sigminer versions 2.0.1 dated 2021-05-19 and 2.0.2 dated 2021-06-17
DESCRIPTION | 6 ++-- MD5 | 12 ++++---- NEWS.md | 5 +++ R/output.R | 69 +++++++++++++++++++++++++++++++++++++------------ build/partial.rdb |binary build/vignette.rds |binary inst/doc/sigminer.html | 16 ++++++----- 7 files changed, 76 insertions(+), 32 deletions(-)
Title: Spherical Geometry Operators Using the S2 Geometry Library
Description: Provides R bindings for Google's s2 library for geometric calculations on
the sphere. High-performance constructors and exporters provide high compatibility
with existing spatial packages, transformers construct new geometries from existing
geometries, predicates provide a means to select geometries based on spatial
relationships, and accessors extract information about geometries.
Author: Dewey Dunnington [aut] (<https://orcid.org/0000-0002-9415-4582>),
Edzer Pebesma [aut, cre] (<https://orcid.org/0000-0001-8049-7069>),
Ege Rubak [aut],
Jeroen Ooms [ctb] (configure script),
Google, Inc. [cph] (Original s2geometry.io source code)
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between s2 versions 1.0.5 dated 2021-06-01 and 1.0.6 dated 2021-06-17
DESCRIPTION | 6 +++--- MD5 | 19 ++++++++++--------- NEWS.md | 8 ++++++++ README.md | 14 ++++++++++---- build/partial.rdb |binary src/Makevars.in | 2 +- src/Makevars.ucrt |only src/Makevars.win | 33 ++++++++++++--------------------- src/s2-transformers.cpp | 4 ++-- tests/testthat/test-s2-transformers.R | 18 ++++++++++++++++++ tools/winlibs.R | 4 ++-- 11 files changed, 66 insertions(+), 42 deletions(-)
Title: Variable Descriptions
Description: Abstract descriptions of (yet) unobserved variables.
Author: Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>)
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between variables versions 1.1-0 dated 2021-03-08 and 1.1-1 dated 2021-06-17
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/variables.R | 8 ++++++-- inst/NEWS.Rd | 8 ++++++++ man/mkgrid.Rd | 4 +++- tests/regtests.R | 14 ++++++++++++++ tests/regtests.Rout.save | 41 +++++++++++++++++++++++++++++++++++++---- 7 files changed, 78 insertions(+), 17 deletions(-)
Title: Relative Survival
Description: Contains functions for analysing relative survival data, including nonparametric estimators of net (marginal relative) survival, relative survival ratio, crude mortality, methods for fitting and checking additive and multiplicative regression models, transformation approach, methods for dealing with population mortality tables. Work has been described in Pohar Perme, Pavlic (2018) <doi:10.18637/jss.v087.i08>.
Author: Maja Pohar Perme [aut],
Damjan Manevski [aut, cre]
Maintainer: Damjan Manevski <damjan.manevski@mf.uni-lj.si>
Diff between relsurv versions 2.2-3 dated 2018-11-30 and 2.2-4 dated 2021-06-17
DESCRIPTION | 19 - MD5 | 17 R/Rcode.r | 914 ++++++++++++++++++++++++++-------------------------- data/slopop.rda |binary inst/CITATION | 8 inst/news.Rd | 12 src/init.c | 4 src/netfastpinter.c | 2 src/netwei.c | 490 +++++++++++++-------------- src/netweiDM.c |only 10 files changed, 742 insertions(+), 724 deletions(-)
Title: Multivariate Model Based Inference for Domains
Description: Allows users to produce estimates and MSE for multivariate variables using Linear Mixed Model. The package follows the approach of Datta, Day and Basawa (1999) <doi:10.1016/S0378-3758(98)00147-5>.
Author: Michele D'Alo' [aut],
Stefano Falorsi [aut],
Andrea Fasulo [aut, cre]
Maintainer: Andrea Fasulo <fasulo@istat.it>
Diff between mind versions 0.1.0 dated 2021-05-21 and 0.1.1 dated 2021-06-17
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/mind.unit.R | 37 ++++++++++++++++++++----------------- man/mind.unit.Rd | 4 ++-- 4 files changed, 28 insertions(+), 25 deletions(-)
Title: Handling HL7 FHIR Resources in R
Description: Useful tools for conveniently downloading FHIR resources in xml format
and converting them to R data frames. The package uses FHIR-search to download bundles
from a FHIR server, provides functions to save and read xml-files containing such bundles
and allows flattening the bundles to data.frames using XPath expressions.
Author: Thomas Peschel [aut, cre],
Julia Palm [aut] (<https://orcid.org/0000-0003-1568-5893>),
Jens Przybilla [aut],
Frank Meineke [aut] (<https://orcid.org/0000-0002-9256-7543>)
Maintainer: Thomas Peschel <tpeschel@imise.uni-leipzig.de>
Diff between fhircrackr versions 1.0.0 dated 2021-06-16 and 1.0.1 dated 2021-06-17
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 7 ++----- R/design.R | 4 ++-- 4 files changed, 11 insertions(+), 14 deletions(-)
Title: Cross-Validation for Model Selection
Description: Cross-validate one or multiple regression and classification models
and get relevant evaluation metrics in a tidy format. Validate the
best model on a test set and compare it to a baseline evaluation.
Alternatively, evaluate predictions from an external model. Currently
supports regression and classification (binary and multiclass).
Described in chp. 5 of Jeyaraman, B. P., Olsen, L. R.,
& Wambugu M. (2019, ISBN: 9781838550134).
Author: Ludvig Renbo Olsen [aut, cre],
Hugh Benjamin Zachariae [aut],
Indrajeet Patil [ctb] (<https://orcid.org/0000-0003-1995-6531>,
@patilindrajeets)
Maintainer: Ludvig Renbo Olsen <r-pkgs@ludvigolsen.dk>
Diff between cvms versions 1.3.0 dated 2021-06-07 and 1.3.1 dated 2021-06-17
DESCRIPTION | 6 +-- MD5 | 20 +++++----- NEWS.md | 4 ++ R/plot_confusion_matrix.R | 2 - build/cvms.pdf |binary inst/doc/Creating_a_confusion_matrix.html | 4 +- inst/doc/available_metrics.html | 4 +- inst/doc/cross_validating_custom_functions.html | 8 ++-- inst/doc/evaluate_by_id.html | 4 +- inst/doc/picking_the_number_of_folds_for_cross-validation.html | 4 +- tests/testthat/test_plotting_functions.R | 6 +-- 11 files changed, 33 insertions(+), 29 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-06-16 0.1.3
Title: Optimal Distribution Preserving Down-Sampling of Bio-Medical
Data
Description: An optimized method for distribution-preserving class-proportional down-sampling of bio-medical data.
Author: Jorn Lotsch[aut,cre], Sebastian Malkusch[aut], Alfred Ultsch[aut]
Maintainer: Jorn Lotsch <j.lotsch@em.uni-frankfurt.de>
Diff between opdisDownsampling versions 0.1.0 dated 2021-03-25 and 0.5.0 dated 2021-06-17
DESCRIPTION | 6 +++--- MD5 | 15 ++++++++------- R/EucDist.R | 6 +++--- R/KullbLeiblKLD2.R | 2 +- R/SmoothDensHist1dim.R | 8 ++++---- R/amrdd.R | 6 +++--- R/opdisDownsampling.R | 46 ++++++++++++++++++++++++++++++---------------- R/relevant_PCAvariables.R |only man/opdisDownsampling.Rd | 3 ++- 9 files changed, 54 insertions(+), 38 deletions(-)
More information about opdisDownsampling at CRAN
Permanent link
Title: Tools for Descriptive Statistics
Description: A collection of miscellaneous basic statistic functions and convenience wrappers for efficiently describing data. The author's intention was to create a toolbox, which facilitates the (notoriously time consuming) first descriptive tasks in data analysis, consisting of calculating descriptive statistics, drawing graphical summaries and reporting the results. The package contains furthermore functions to produce documents using MS Word (or PowerPoint) and functions to import data from Excel. Many of the included functions can be found scattered in other packages and other sources written partly by Titans of R. The reason for collecting them here, was primarily to have them consolidated in ONE instead of dozens of packages (which themselves might depend on other packages which are not needed at all), and to provide a common and consistent interface as far as function and arguments naming, NA handling, recycling rules etc. are concerned. Google style guides were used as naming rules (in absence of convincing alternatives). The 'BigCamelCase' style was consequently applied to functions borrowed from contributed R packages as well.
Author: Andri Signorell [aut, cre],
Ken Aho [ctb],
Andreas Alfons [ctb],
Nanina Anderegg [ctb],
Tomas Aragon [ctb],
Chandima Arachchige [ctb],
Antti Arppe [ctb],
Adrian Baddeley [ctb],
Kamil Barton [ctb],
Ben Bolker [ctb],
Hans W. Borchers [ctb],
Frederico Caeiro [ctb],
Stephane Champely [ctb],
Daniel Chessel [ctb],
Leanne Chhay [ctb],
Nicholas Cooper [ctb],
Clint Cummins [ctb],
Michael Dewey [ctb],
Harold C. Doran [ctb],
Stephane Dray [ctb],
Charles Dupont [ctb],
Dirk Eddelbuettel [ctb],
Claus Ekstrom [ctb],
Martin Elff [ctb],
Jeff Enos [ctb],
Richard W. Farebrother [ctb],
John Fox [ctb],
Romain Francois [ctb],
Michael Friendly [ctb],
Tal Galili [ctb],
Matthias Gamer [ctb],
Joseph L. Gastwirth [ctb],
Vilmantas Gegzna [ctb],
Yulia R. Gel [ctb],
Sereina Graber [ctb],
Juergen Gross [ctb],
Gabor Grothendieck [ctb],
Frank E. Harrell Jr [ctb],
Richard Heiberger [ctb],
Michael Hoehle [ctb],
Christian W. Hoffmann [ctb],
Soeren Hojsgaard [ctb],
Torsten Hothorn [ctb],
Markus Huerzeler [ctb],
Wallace W. Hui [ctb],
Pete Hurd [ctb],
Rob J. Hyndman [ctb],
Christopher Jackson [ctb],
Matthias Kohl [ctb],
Mikko Korpela [ctb],
Max Kuhn [ctb],
Detlew Labes [ctb],
Friederich Leisch [ctb],
Jim Lemon [ctb],
Dong Li [ctb],
Martin Maechler [ctb],
Arni Magnusson [ctb],
Ben Mainwaring [ctb],
Daniel Malter [ctb],
George Marsaglia [ctb],
John Marsaglia [ctb],
Alina Matei [ctb],
David Meyer [ctb],
Weiwen Miao [ctb],
Giovanni Millo [ctb],
Yongyi Min [ctb],
David Mitchell [ctb],
Franziska Mueller [ctb],
Markus Naepflin [ctb],
Daniel Navarro [ctb],
Henric Nilsson [ctb],
Klaus Nordhausen [ctb],
Derek Ogle [ctb],
Hong Ooi [ctb],
Nick Parsons [ctb],
Sandrine Pavoine [ctb],
Tony Plate [ctb],
Luke Prendergast [ctb],
Roland Rapold [ctb],
William Revelle [ctb],
Tyler Rinker [ctb],
Brian D. Ripley [ctb],
Caroline Rodriguez [ctb],
Nathan Russell [ctb],
Nick Sabbe [ctb],
Ralph Scherer [ctb],
Venkatraman E. Seshan [ctb],
Michael Smithson [ctb],
Greg Snow [ctb],
Karline Soetaert [ctb],
Werner A. Stahel [ctb],
Alec Stephenson [ctb],
Mark Stevenson [ctb],
Ralf Stubner [ctb],
Matthias Templ [ctb],
Duncan Temple Lang [ctb],
Terry Therneau [ctb],
Yves Tille [ctb],
Luis Torgo [ctb],
Adrian Trapletti [ctb],
Joshua Ulrich [ctb],
Kevin Ushey [ctb],
Jeremy VanDerWal [ctb],
Bill Venables [ctb],
John Verzani [ctb],
Pablo J. Villacorta Iglesias [ctb],
Gregory R. Warnes [ctb],
Stefan Wellek [ctb],
Hadley Wickham [ctb],
Rand R. Wilcox [ctb],
Peter Wolf [ctb],
Daniel Wollschlaeger [ctb],
Joseph Wood [ctb],
Ying Wu [ctb],
Thomas Yee [ctb],
Achim Zeileis [ctb]
Maintainer: Andri Signorell <andri@signorell.net>
Diff between DescTools versions 0.99.41 dated 2021-04-10 and 0.99.42 dated 2021-06-17
DescTools-0.99.41/DescTools/man/DenseRank.Rd |only DescTools-0.99.42/DescTools/DESCRIPTION | 8 DescTools-0.99.42/DescTools/MD5 | 36 +- DescTools-0.99.42/DescTools/NAMESPACE | 6 DescTools-0.99.42/DescTools/NEWS | 28 ++ DescTools-0.99.42/DescTools/R/Desc.R | 8 DescTools-0.99.42/DescTools/R/DescTools.r | 214 +++++++++++++++-- DescTools-0.99.42/DescTools/R/LinMod.R | 13 - DescTools-0.99.42/DescTools/R/StatsAndCIs.r | 66 ++--- DescTools-0.99.42/DescTools/R/Tables.r | 3 DescTools-0.99.42/DescTools/README.md | 5 DescTools-0.99.42/DescTools/man/ABCCoords.Rd |only DescTools-0.99.42/DescTools/man/AndersonDarlingTest.Rd | 5 DescTools-0.99.42/DescTools/man/Bg.Rd |only DescTools-0.99.42/DescTools/man/BoxedText.Rd | 6 DescTools-0.99.42/DescTools/man/PercentRank.Rd |only DescTools-0.99.42/DescTools/man/PlotDot.Rd | 30 +- DescTools-0.99.42/DescTools/man/Rank.Rd | 3 DescTools-0.99.42/DescTools/man/RunsTest.Rd | 2 DescTools-0.99.42/DescTools/man/TMod.Rd | 4 DescTools-0.99.42/DescTools/man/lines.lm.Rd | 15 - 21 files changed, 350 insertions(+), 102 deletions(-)
Title: Bayesian Time Series Modeling with Stan
Description: Fit Bayesian time series models using 'Stan' for full Bayesian inference. A wide range
of distributions and models are supported, allowing users to fit Seasonal ARIMA, ARIMAX, Dynamic
Harmonic Regression, GARCH, t-student innovation GARCH models, asymmetric GARCH, Random Walks, stochastic
volatility models for univariate time series. Prior specifications are flexible and explicitly encourage
users to apply prior distributions that actually reflect their beliefs. Model fit can easily be assessed
and compared with typical visualization methods, information criteria such as loglik, AIC, BIC WAIC, Bayes
factor and leave-one-out cross-validation methods. References: Hyndman (2017)
<doi:10.18637/jss.v027.i03>; Carpenter et al. (2017) <doi:10.18637/jss.v076.i01>.
Author: Asael Alonzo Matamoros [aut, cre],
Cristian Cruz Torres [aut],
Andres Dala [ctb],
Rob Hyndman [ctb],
Mitchell O'Hara-Wild [ctb]
Maintainer: Asael Alonzo Matamoros <asael.alonzo@gmail.com>
Diff between bayesforecast versions 0.0.1 dated 2021-01-22 and 1.0.1 dated 2021-06-17
bayesforecast-0.0.1/bayesforecast/R/ipc.R |only bayesforecast-1.0.1/bayesforecast/DESCRIPTION | 13 bayesforecast-1.0.1/bayesforecast/MD5 | 132 ++- bayesforecast-1.0.1/bayesforecast/NAMESPACE | 18 bayesforecast-1.0.1/bayesforecast/NEWS.md | 57 + bayesforecast-1.0.1/bayesforecast/R/Birth.R | 126 ++- bayesforecast-1.0.1/bayesforecast/R/Misc.R | 3 bayesforecast-1.0.1/bayesforecast/R/Sarima.R | 2 bayesforecast-1.0.1/bayesforecast/R/auto_sarima.R | 14 bayesforecast-1.0.1/bayesforecast/R/autoplot.R | 77 + bayesforecast-1.0.1/bayesforecast/R/bayes_factor.R | 8 bayesforecast-1.0.1/bayesforecast/R/ets.R |only bayesforecast-1.0.1/bayesforecast/R/forecast.R | 4 bayesforecast-1.0.1/bayesforecast/R/garch.R | 1 bayesforecast-1.0.1/bayesforecast/R/get_params.R | 5 bayesforecast-1.0.1/bayesforecast/R/log_lik.R | 28 bayesforecast-1.0.1/bayesforecast/R/model.R | 395 +++++----- bayesforecast-1.0.1/bayesforecast/R/posterior_predict.R | 9 bayesforecast-1.0.1/bayesforecast/R/predictive_error.R | 240 +++--- bayesforecast-1.0.1/bayesforecast/R/print.R | 45 + bayesforecast-1.0.1/bayesforecast/R/report.R | 86 ++ bayesforecast-1.0.1/bayesforecast/R/ssm.R | 2 bayesforecast-1.0.1/bayesforecast/R/stan_models.R | 389 +++++++++ bayesforecast-1.0.1/bayesforecast/R/varstan.R | 11 bayesforecast-1.0.1/bayesforecast/README.md | 56 - bayesforecast-1.0.1/bayesforecast/build |only bayesforecast-1.0.1/bayesforecast/data/air.RData |only bayesforecast-1.0.1/bayesforecast/data/aust.RData |only bayesforecast-1.0.1/bayesforecast/data/demgbp.RData |only bayesforecast-1.0.1/bayesforecast/data/oildata.RData |only bayesforecast-1.0.1/bayesforecast/inst/doc |only bayesforecast-1.0.1/bayesforecast/inst/stan/ets.stan | 11 bayesforecast-1.0.1/bayesforecast/man/AICc.Rd | 4 bayesforecast-1.0.1/bayesforecast/man/Holt.Rd |only bayesforecast-1.0.1/bayesforecast/man/Hw.Rd |only bayesforecast-1.0.1/bayesforecast/man/LocalLevel.Rd |only bayesforecast-1.0.1/bayesforecast/man/aic.Rd | 4 bayesforecast-1.0.1/bayesforecast/man/air.Rd |only bayesforecast-1.0.1/bayesforecast/man/as.stan.Rd | 2 bayesforecast-1.0.1/bayesforecast/man/aust.Rd |only bayesforecast-1.0.1/bayesforecast/man/auto.sarima.Rd | 243 +++--- bayesforecast-1.0.1/bayesforecast/man/autoplot.varstan.Rd | 2 bayesforecast-1.0.1/bayesforecast/man/bayes_factor.varstan.Rd | 4 bayesforecast-1.0.1/bayesforecast/man/bic.Rd | 4 bayesforecast-1.0.1/bayesforecast/man/bridge_sampler.varstan.Rd | 4 bayesforecast-1.0.1/bayesforecast/man/check_residuals.Rd | 2 bayesforecast-1.0.1/bayesforecast/man/demgbp.Rd |only bayesforecast-1.0.1/bayesforecast/man/extract_stan.Rd | 2 bayesforecast-1.0.1/bayesforecast/man/figures/fig3-1.png |binary bayesforecast-1.0.1/bayesforecast/man/figures/unnamed-chunk-6-1.png |binary bayesforecast-1.0.1/bayesforecast/man/figures/unnamed-chunk-7-1.png |only bayesforecast-1.0.1/bayesforecast/man/forecast.varstan.Rd | 4 bayesforecast-1.0.1/bayesforecast/man/fourier.Rd | 2 bayesforecast-1.0.1/bayesforecast/man/get_parameters.Rd | 2 bayesforecast-1.0.1/bayesforecast/man/ipc.Rd | 2 bayesforecast-1.0.1/bayesforecast/man/log_lik.varstan.Rd | 4 bayesforecast-1.0.1/bayesforecast/man/loglik.Rd | 4 bayesforecast-1.0.1/bayesforecast/man/loo.varstan.Rd | 4 bayesforecast-1.0.1/bayesforecast/man/mcmc_plot.varstan.Rd |only bayesforecast-1.0.1/bayesforecast/man/oildata.Rd |only bayesforecast-1.0.1/bayesforecast/man/plot.varstan.Rd | 2 bayesforecast-1.0.1/bayesforecast/man/print.Holt.Rd |only bayesforecast-1.0.1/bayesforecast/man/print.Hw.Rd |only bayesforecast-1.0.1/bayesforecast/man/print.LocalLevel.Rd |only bayesforecast-1.0.1/bayesforecast/man/stan_Holt.Rd |only bayesforecast-1.0.1/bayesforecast/man/stan_Hw.Rd |only bayesforecast-1.0.1/bayesforecast/man/stan_LocalLevel.Rd |only bayesforecast-1.0.1/bayesforecast/man/stan_SVM.Rd | 4 bayesforecast-1.0.1/bayesforecast/man/stan_garch.Rd | 6 bayesforecast-1.0.1/bayesforecast/man/stan_naive.Rd | 4 bayesforecast-1.0.1/bayesforecast/man/stan_sarima.Rd | 8 bayesforecast-1.0.1/bayesforecast/man/stan_ssm.Rd | 8 bayesforecast-1.0.1/bayesforecast/man/varstan.Rd | 4 bayesforecast-1.0.1/bayesforecast/man/waic.varstan.Rd | 4 bayesforecast-1.0.1/bayesforecast/src/stanExports_ets.h | 314 ++++--- bayesforecast-1.0.1/bayesforecast/vignettes |only 76 files changed, 1626 insertions(+), 753 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-04-25 0.0.3
2018-03-15 0.0.2
More information about TailClassifier at CRAN
Permanent link
Title: Simple 'ggplot2' Visualisation with Less Brainpower and Typing
Description: Wrapper functions to make 'ggplot2' visualisation easier with less brainpower and typing.
Author: David Hodge [aut, cre] (<https://orcid.org/0000-0002-3868-7501>),
Statistics New Zealand [cph]
Maintainer: David Hodge <davidhodge931@gmail.com>
Diff between simplevis versions 4.0.0 dated 2021-06-04 and 4.1.0 dated 2021-06-17
simplevis-4.0.0/simplevis/man/sv_pal.Rd |only simplevis-4.1.0/simplevis/DESCRIPTION | 12 - simplevis-4.1.0/simplevis/MD5 | 96 +++++----- simplevis-4.1.0/simplevis/NAMESPACE | 2 simplevis-4.1.0/simplevis/NEWS.md | 7 simplevis-4.1.0/simplevis/R/gg_bar.R | 60 +++--- simplevis-4.1.0/simplevis/R/gg_boxplot.R | 56 ++--- simplevis-4.1.0/simplevis/R/gg_hbar.R | 70 +++---- simplevis-4.1.0/simplevis/R/gg_line.R | 56 ++--- simplevis-4.1.0/simplevis/R/gg_point.R | 68 +++---- simplevis-4.1.0/simplevis/R/gg_sf.R | 72 +++---- simplevis-4.1.0/simplevis/R/internal.R | 13 - simplevis-4.1.0/simplevis/R/leaflet_sf.R | 18 - simplevis-4.1.0/simplevis/R/pal.R |only simplevis-4.1.0/simplevis/README.md | 2 simplevis-4.1.0/simplevis/inst/doc/simplevis.R | 11 - simplevis-4.1.0/simplevis/inst/doc/simplevis.Rmd | 17 - simplevis-4.1.0/simplevis/inst/doc/simplevis.html | 49 ++--- simplevis-4.1.0/simplevis/inst/shiny/template1/data/template1.zip |binary simplevis-4.1.0/simplevis/inst/shiny/template1/make_app_vis.R | 22 +- simplevis-4.1.0/simplevis/inst/shiny/template1/server.R | 25 +- simplevis-4.1.0/simplevis/inst/shiny/template2/data/template2.zip |binary simplevis-4.1.0/simplevis/inst/shiny/template2/make_app_vis.R | 35 +-- simplevis-4.1.0/simplevis/inst/shiny/template2/server.R | 60 ++---- simplevis-4.1.0/simplevis/man/gg_bar.Rd | 8 simplevis-4.1.0/simplevis/man/gg_bar_col.Rd | 8 simplevis-4.1.0/simplevis/man/gg_bar_col_facet.Rd | 8 simplevis-4.1.0/simplevis/man/gg_bar_facet.Rd | 8 simplevis-4.1.0/simplevis/man/gg_boxplot.Rd | 8 simplevis-4.1.0/simplevis/man/gg_boxplot_col.Rd | 8 simplevis-4.1.0/simplevis/man/gg_boxplot_col_facet.Rd | 8 simplevis-4.1.0/simplevis/man/gg_boxplot_facet.Rd | 8 simplevis-4.1.0/simplevis/man/gg_hbar.Rd | 8 simplevis-4.1.0/simplevis/man/gg_hbar_col.Rd | 8 simplevis-4.1.0/simplevis/man/gg_hbar_col_facet.Rd | 8 simplevis-4.1.0/simplevis/man/gg_hbar_facet.Rd | 8 simplevis-4.1.0/simplevis/man/gg_line.Rd | 8 simplevis-4.1.0/simplevis/man/gg_line_col.Rd | 8 simplevis-4.1.0/simplevis/man/gg_line_col_facet.Rd | 8 simplevis-4.1.0/simplevis/man/gg_line_facet.Rd | 8 simplevis-4.1.0/simplevis/man/gg_point.Rd | 8 simplevis-4.1.0/simplevis/man/gg_point_col.Rd | 8 simplevis-4.1.0/simplevis/man/gg_point_col_facet.Rd | 8 simplevis-4.1.0/simplevis/man/gg_point_facet.Rd | 8 simplevis-4.1.0/simplevis/man/gg_sf.Rd | 8 simplevis-4.1.0/simplevis/man/gg_sf_col.Rd | 8 simplevis-4.1.0/simplevis/man/gg_sf_col_facet.Rd | 8 simplevis-4.1.0/simplevis/man/gg_sf_facet.Rd | 8 simplevis-4.1.0/simplevis/man/pal_d3_reorder.Rd |only simplevis-4.1.0/simplevis/man/pal_viridis_reorder.Rd |only simplevis-4.1.0/simplevis/vignettes/simplevis.Rmd | 17 - 51 files changed, 464 insertions(+), 496 deletions(-)
Title: Read 'Bibtex' Files and Convert Between Bibliography Formats
Description: Read and write 'Bibtex' files. Convert between bibliography
formats, including 'Bibtex', 'Biblatex', 'Endnote', and 'Bibentry'.
Includes a port of the 'bibutils' utilities by Chris Putnam
<https://sourceforge.net/projects/bibutils/>. Supports all
bibliography formats and character encodings implemented in
'bibutils'.
Author: Georgi N. Boshnakov [aut, cre] (R port, R code, new C code and
modifications to bibutils' C code, conversion to Bibentry (R and C
code)),
Chris Putman [aut] (src/*, author of the bibutils libraries,
https://sourceforge.net/projects/bibutils/),
Richard Mathar [ctb] (src/addsout.c),
Johannes Wilm [ctb] (src/biblatexin.c, src/bltypes.c)
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>
Diff between rbibutils versions 2.2 dated 2021-06-10 and 2.2.1 dated 2021-06-17
DESCRIPTION | 8 - MD5 | 27 ++--- NEWS.md | 7 + build/partial.rdb |binary inst/bib/bib_from_medin.bib |only src/bib2be.c | 5 src/bibcore.c | 5 src/bibprog.c | 1 src/bibtexdirectin.c | 19 ++- src/latex_parse.c | 39 ++++++- src/name.c | 10 + src/str.c | 39 +++++++ src/xml2any.c | 8 + tests/testthat/test-convert.R | 211 ++++++++++++++++++++++++------------------ tests/testthat/test-https.R | 6 - 15 files changed, 257 insertions(+), 128 deletions(-)
Title: Bayesian Optimization of Hyperparameters
Description: A Pure R implementation of Bayesian Global Optimization with Gaussian Processes.
Author: Yachen Yan [aut, cre]
Maintainer: Yachen Yan <yanyachen21@gmail.com>
Diff between rBayesianOptimization versions 1.1.0 dated 2016-09-14 and 1.2.0 dated 2021-06-17
DESCRIPTION | 13 - MD5 | 33 +- NAMESPACE | 52 ++-- R/BayesianOptimization.R | 436 +++++++++++++++++++-------------------- R/KFold.R | 88 +++---- R/Utility.R | 68 +++--- R/Utility_Max.R | 86 +++---- R/Utils.R | 130 +++++------ R/rBayesianOptimization.R | 14 - README.md |only man/BayesianOptimization.Rd | 227 ++++++++++---------- man/KFold.Rd | 47 ++-- man/Matrix_runif.Rd | 45 +--- man/Min_Max_Inverse_Scale_Vec.Rd | 45 +--- man/Min_Max_Scale_Mat.Rd | 45 +--- man/Utility.Rd | 57 ++--- man/Utility_Max.Rd | 57 ++--- man/rBayesianOptimization.Rd | 20 - 18 files changed, 732 insertions(+), 731 deletions(-)
More information about rBayesianOptimization at CRAN
Permanent link
More information about Randomuseragent at CRAN
Permanent link
Title: Maximal Information-Based Nonparametric Exploration for Variable
Analysis
Description: Wrapper for 'minepy' implementation of Maximal
Information-based Nonparametric Exploration statistics (MIC and
MINE family). Detailed information of the ANSI C implementation of
'minepy' can be found at <http://minepy.readthedocs.io/en/latest>.
Author: Michele Filosi [aut, cre],
Roberto Visintainer [aut],
Davide Albanese [aut],
Samantha Riccadonna [ctb],
Giuseppe Jurman [ctb],
Cesare Furlanello [ctb]
Maintainer: Michele Filosi <michele.filosi@gmail.com>
Diff between minerva versions 1.5.8 dated 2019-05-27 and 1.5.10 dated 2021-06-17
DESCRIPTION | 11 +++++---- MD5 | 24 ++++++++++----------- NEWS | 4 +++ R/mictools.R | 8 +++---- R/mine.R | 2 - README.md | 57 ++++++++++++++++++++++++++++++++++----------------- build/partial.rdb |binary man/mic_strength.Rd | 7 ++---- man/mictools.Rd | 5 +--- man/mine.Rd | 20 ++++++++++++++--- man/mine_stat.Rd | 13 +++++++++-- src/mine_int.cpp | 35 ++++++++++++++++++++++++++----- src/mine_interface.c | 22 +++++++++---------- 13 files changed, 139 insertions(+), 69 deletions(-)
Title: Generalized Mortality Estimator
Description: Command-line and 'shiny' GUI implementation of the GenEst models for estimating bird and bat mortality at wind and solar power facilities, following Dalthorp, et al. (2018) <doi:10.3133/tm7A2>.
Author: Daniel Dalthorp [aut, cre],
Juniper Simonis [aut],
Lisa Madsen [aut],
Manuela Huso [aut],
Paul Rabie [aut],
Jeffrey Mintz [aut],
Robert Wolpert [aut],
Jared Studyvin [aut],
Franzi Korner-Nievergelt [aut]
Maintainer: Daniel Dalthorp <ddalthorp@protonmail.com>
Diff between GenEst versions 1.4.5.1 dated 2021-02-13 and 1.4.6 dated 2021-06-17
DESCRIPTION | 8 +- MD5 | 37 +++++++------ R/app_table_functions.R | 15 +++-- R/carcass_persistence_functions.R | 3 - build/vignette.rds |binary inst/doc/GenEstGUI.R |only inst/doc/GenEstGUI.Rmd | 8 ++ inst/doc/GenEstGUI.html | 8 +- inst/doc/command-line-example.R | 2 inst/doc/command-line-example.Rmd | 6 +- inst/doc/command-line-example.html | 99 +++++++++++++++++++------------------ inst/doc/solar-examples.R | 2 inst/doc/solar-examples.Rmd | 6 +- inst/doc/solar-examples.html | 17 ++++-- inst/doc/wind-examples.Rmd | 5 - inst/doc/wind-examples.html | 19 ++++--- vignettes/GenEstGUI.Rmd | 8 ++ vignettes/command-line-example.Rmd | 6 +- vignettes/solar-examples.Rmd | 6 +- vignettes/wind-examples.Rmd | 5 - 20 files changed, 151 insertions(+), 109 deletions(-)
Title: Arbitrary-Precision Integer and Floating-Point Mathematics
Description: Classes for storing and manipulating arbitrary-precision
integer vectors and high-precision floating-point vectors. These
extend the range and precision of the 'integer' and 'double' data
types found in R. This package utilizes the 'Boost.Multiprecision' C++
library. It is specifically designed to work well with the 'tidyverse'
collection of R packages.
Author: David Hall [aut, cre, cph] (<https://orcid.org/0000-0002-2193-0480>)
Maintainer: David Hall <david.hall.physics@gmail.com>
Diff between bignum versions 0.2.0 dated 2021-06-13 and 0.2.1 dated 2021-06-17
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/format.R | 2 -- tests/testthat/_snaps/format.md | 20 -------------------- tests/testthat/test-format.R | 4 ---- 6 files changed, 13 insertions(+), 35 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-01-08 1.1.0
2020-08-26 1.0.0
2019-09-22 0.1.3
2019-07-12 0.1.2
2018-04-27 0.1.1
2018-04-24 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-12-17 0.2.0
2020-11-11 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-07-11 1.1.3
2016-06-22 1.1.2
2015-08-05 1.1.1
2015-04-30 1.1
2014-11-28 1.0
2014-11-22 0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-04-18 1.6
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-10-12 1.2-2
2020-07-26 1.2-1
2019-02-27 1.2-0
2016-01-15 1.1-1
2015-08-06 1.1-0
2015-02-11 1.0-0
2014-11-07 0.9-0
Title: High Mach Finds Routes for Supersonic Aircraft
Description: For supersonic aircraft, flying subsonic over land,
High Mach finds the best route between airports. Allows for coastal buffer and
potentially closed regions. Uses a minimal model of aircraft
performance: the focus is on time saved versus subsonic flight, rather
than on vertical flight profile. For modelling and forecasting, not for planning your
flight!
Author: David Marsh [aut, cre],
EUROCONTROL [fnd, cph]
Maintainer: David Marsh <david.marsh@eurocontrol.int>
Diff between himach versions 0.1.2 dated 2021-04-30 and 0.2.1 dated 2021-06-17
DESCRIPTION | 12 - MD5 | 54 ++++---- NEWS.md | 9 + R/maps.R | 27 +++- R/routes.R | 2 R/utils.R | 4 R/zzz.R | 2 README.md | 134 +++++++++++++++++---- build/vignette.rds |binary inst/doc/Supersonic_Routes.R | 12 + inst/doc/Supersonic_Routes.Rmd | 12 + inst/doc/Supersonic_Routes.html | 34 +++-- inst/doc/Supersonic_Routes_in_depth.R | 8 - inst/doc/Supersonic_Routes_in_depth.Rmd | 8 - inst/doc/Supersonic_Routes_in_depth.html | 24 ++- man/make_airports.Rd | 2 man/map_routes.Rd | 15 ++ tests/testthat/known/ac_default_load |binary tests/testthat/known/ac_load |binary tests/testthat/known/test_multiroute |binary tests/testthat/known/test_multiroute_nofly |binary tests/testthat/known/test_route_subsonic_NZGS_NZDN |binary tests/testthat/test-zzz.R | 8 - vignettes/EDDF_KBOS_speed.png |only vignettes/EDDF_KBOS_time.png |only vignettes/Supersonic_Routes.Rmd | 12 + vignettes/Supersonic_Routes_in_depth.Rmd | 8 - vignettes/polar_examples.png |only vignettes/refuel_examples_pacific.png |only vignettes/three_routes.png |binary 30 files changed, 280 insertions(+), 107 deletions(-)
Title: Weighted BACON Algorithms
Description: The BACON algorithms are methods for multivariate outlier
nomination (detection) and robust linear regression by Billor, Hadi,
and Velleman (2000) <doi:10.1016/S0167-9473(99)00101-2>. The extension
to weighted problems is due to Beguin and Hulliger (2008)
<https://www150.statcan.gc.ca/n1/en/catalogue/12-001-X200800110616>.
Author: Tobias Schoch [aut, cre] (<https://orcid.org/0000-0002-1640-3395>),
R-core [cph] (plot.wbaconlm derives from plot.lm)
Maintainer: Tobias Schoch <tobias.schoch@gmail.com>
Diff between wbacon versions 0.5 dated 2021-06-15 and 0.5-1 dated 2021-06-17
DESCRIPTION | 6 +++--- MD5 | 24 ++++++++++++------------ inst/NEWS.Rd | 18 ++++++++++++++++-- inst/doc/doc_c_functions.pdf |binary inst/doc/methods.pdf |binary man/predict_wbaconlm.Rd | 5 ----- src/median.c | 13 ++----------- src/partial_sort.c | 4 ++-- src/wbacon.c | 5 ++++- src/wbacon.h | 7 +++++-- src/wbacon_reg.c | 4 ++++ src/wbacon_reg.h | 7 +++++-- src/wquantile.c | 4 ++-- 13 files changed, 55 insertions(+), 42 deletions(-)
Title: Visual Regression Testing and Graphical Diffing
Description: An extension to the 'testthat' package that makes it easy
to add graphical unit tests. It provides a Shiny application to
manage the test cases.
Author: Lionel Henry [cre, aut],
Thomas Lin Pedersen [aut] (<https://orcid.org/0000-0002-5147-4711>),
RStudio [cph],
T Jake Luciani [aut] (svglite),
Matthieu Decorde [aut] (svglite),
Vaudor Lise [aut] (svglite),
Tony Plate [ctb] (svglite: Early line dashing code),
David Gohel [ctb] (svglite: Line dashing code and raster code),
Yixuan Qiu [ctb] (svglite: Improved styles; polypath implementation),
Håkon Malmedal [ctb] (svglite: Opacity code)
Maintainer: Lionel Henry <lionel@rstudio.com>
Diff between vdiffr versions 1.0.0 dated 2021-06-08 and 1.0.1 dated 2021-06-17
DESCRIPTION | 10 +++++----- MD5 | 11 +++++++---- NEWS.md | 7 +++++++ R/expect-doppelganger.R | 15 ++++++++++----- tests/testthat/test-expect-doppelganger.R | 18 ++++++++++++++++++ tests/testthat/test-snapshot |only 6 files changed, 47 insertions(+), 14 deletions(-)
Title: Power and Sample Size for Health Researchers via Shiny
Description: Power and Sample Size for Health Researchers is a Shiny application that brings together a
series of functions related to sample size and power calculations for common analysis in the healthcare
field. There are functionalities to calculate the power, sample size to estimate or test hypotheses for means and
proportions (including test for correlated groups, equivalence, non-inferiority and superiority), association, correlations coefficients,
regression coefficients (linear, logistic and Cox), linear mixed model,
Cronbach's alpha, interobserver agreement, intraclass correlation coefficients,
limit of agreement on Bland-Altman plots,
area under the curve, sensitivity and specificity incorporating the prevalence of disease.
You can also use the online version at <https://hcpa-unidade-bioestatistica.shinyapps.io/PSS_Health/>.
Author: Rogério Boff Borges [aut, cre]
(<https://orcid.org/0000-0002-2548-1889>),
Guilherme Serpa Azambuja [aut]
(<https://orcid.org/0000-0001-6246-4538>),
Aline Castello Branco Mancuso [aut]
(<https://orcid.org/0000-0001-6033-8335>),
Vanessa Bielefeldt Leotti [aut]
(<https://orcid.org/0000-0003-3860-9367>),
Vânia Naomi Hirakata [aut] (<https://orcid.org/0000-0003-4645-2080>),
Suzi Alves Camey [aut] (<https://orcid.org/0000-0002-5564-081X>),
Stela Maris de Jezus Castro [aut]
(<https://orcid.org/0000-0001-5862-6709>),
Hospital de Clínicas de Porto Alegre [fnd]
Maintainer: Rogério Boff Borges <roborges@hcpa.edu.br>
Diff between PSS.Health versions 0.1.6 dated 2021-04-08 and 0.2.1 dated 2021-06-17
DESCRIPTION | 18 +++- MD5 | 14 +-- R/PSS_Health.R | 13 --- inst/PSS.Health/global.R | 123 ++++++++++++++++++++++++++++--- inst/PSS.Health/server.R | 149 +++++++++++++++++++++++++++----------- inst/PSS.Health/ui.R | 107 ++++++++++++++++++++++++++- inst/PSS.Health/www/theme_pss.css | 2 man/PSS_Health.Rd | 13 --- 8 files changed, 345 insertions(+), 94 deletions(-)
Title: Pedigree, Genetic Merit and Phenotype Simulation
Description: Simulate pedigree, genetic merits and phenotypes with random/non-random matings followed by random/non-random selection with different intensities and patterns in males and females.
Bijma, P. & Rutten, M. (2002) <https://www.wur.nl/en/Research-Results/Chair-groups/Animal-Sciences/Animal-Breeding-and-Genomics-Group/Research/Software.htm>.
Author: Mohammad Ali Nilforooshan [aut, cre]
(<https://orcid.org/0000-0003-0339-5442>)
Maintainer: Mohammad Ali Nilforooshan <m.a.nilforooshan@gmail.com>
Diff between pedSimulate versions 0.1.2 dated 2021-02-22 and 1.0.0 dated 2021-06-17
pedSimulate-0.1.2/pedSimulate/R/assortative.R |only pedSimulate-0.1.2/pedSimulate/man/assortative.Rd |only pedSimulate-1.0.0/pedSimulate/DESCRIPTION | 9 pedSimulate-1.0.0/pedSimulate/MD5 | 26 +- pedSimulate-1.0.0/pedSimulate/NAMESPACE | 13 - pedSimulate-1.0.0/pedSimulate/NEWS.md | 8 pedSimulate-1.0.0/pedSimulate/R/appendPed.R |only pedSimulate-1.0.0/pedSimulate/R/fs_mate_finder.R | 32 ++- pedSimulate-1.0.0/pedSimulate/R/hs_mate_finder.R |only pedSimulate-1.0.0/pedSimulate/R/pedSimulate.R | 22 -- pedSimulate-1.0.0/pedSimulate/R/pp_mate_finder.R | 31 ++- pedSimulate-1.0.0/pedSimulate/R/simulatePed.R | 149 +++++----------- pedSimulate-1.0.0/pedSimulate/man/appendPed.Rd |only pedSimulate-1.0.0/pedSimulate/man/fs_mate_finder.Rd |only pedSimulate-1.0.0/pedSimulate/man/hs_mate_finder.Rd |only pedSimulate-1.0.0/pedSimulate/man/pedSimulte-package.Rd | 22 -- pedSimulate-1.0.0/pedSimulate/man/pp_mate_finder.Rd |only pedSimulate-1.0.0/pedSimulate/man/simulatePed.Rd | 67 ++----- 18 files changed, 176 insertions(+), 203 deletions(-)
Title: Descriptive Statistics
Description: Exploratory analysis of a data base. Using the functions of this package is possible to filter the data set detecting atypical values (outliers) and to perform exploratory analysis through visual inspection or dispersion measures. With this package you can explore the structure of your data using several parameters at the same time joining statistical parameters with different graphics. Finally, this package aid to confirm or reject the hypothesis that your data structure presents a normal distribution. Therefore this package is useful to get a previous insight of your data before to carry out statistical analysis.
Author: William Herrera-Caceres [aut, cre]
Maintainer: William Herrera-Caceres <williamandresh@hotmail.com>
Diff between DescriptiveWH versions 1.0.2 dated 2021-06-13 and 1.0.3 dated 2021-06-17
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/destatWH.R | 4 ++-- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: When Expectations Meet Reality: Realistic Unit Testing
Description: A framework for unit testing for realistic minimalists,
where we distinguish between expected, acceptable, current, fallback,
ideal, or regressive behaviour. It can also be used for monitoring
third-party software projects for changes.
Author: Marek Gagolewski [aut, cre, cph]
(<https://orcid.org/0000-0003-0637-6028>)
Maintainer: Marek Gagolewski <marek@gagolewski.com>
Diff between realtest versions 0.1.2 dated 2021-06-04 and 0.2.1 dated 2021-06-17
realtest-0.1.2/realtest/tests/realtest-basic.R |only realtest-0.1.2/realtest/tests/realtest-fails.R |only realtest-0.1.2/realtest/tests/realtest-named.R |only realtest-0.1.2/realtest/tests/realtest-postprocessors.R |only realtest-0.2.1/realtest/DESCRIPTION | 12 +- realtest-0.2.1/realtest/MD5 | 40 ++++--- realtest-0.2.1/realtest/NAMESPACE | 3 realtest-0.2.1/realtest/NEWS | 28 +++++ realtest-0.2.1/realtest/R/E.R | 31 +++-- realtest-0.2.1/realtest/R/P.R | 62 +++++------ realtest-0.2.1/realtest/R/R.R | 18 +++ realtest-0.2.1/realtest/R/comparers.R | 83 ++++++++++------ realtest-0.2.1/realtest/R/tools.R | 21 ++-- realtest-0.2.1/realtest/R/validators.R | 21 ---- realtest-0.2.1/realtest/inst |only realtest-0.2.1/realtest/man/E.Rd | 30 +++-- realtest-0.2.1/realtest/man/P.Rd | 38 +++---- realtest-0.2.1/realtest/man/R.Rd | 17 +++ realtest-0.2.1/realtest/man/comparers.Rd | 36 +++--- realtest-0.2.1/realtest/man/summary.realtest_results.Rd | 4 realtest-0.2.1/realtest/man/test_dir.Rd | 4 realtest-0.2.1/realtest/tests/realtest.R |only 22 files changed, 261 insertions(+), 187 deletions(-)
Title: Quantile Regression for Nonlinear Mixed-Effects Models
Description: Quantile regression (QR) for Nonlinear
Mixed-Effects Models via the asymmetric Laplace distribution (ALD).
It uses the Stochastic Approximation of the EM (SAEM) algorithm for
deriving exact maximum likelihood estimates and full inference results
for the fixed-effects and variance components.
It also provides graphical summaries for assessing the algorithm
convergence and fitting results.
Author: Christian E. Galarza <cgalarza88@gmail.com> and Victor H. Lachos <hlachos@ime.unicamp.br>
Maintainer: Christian E. Galarza <cgalarza88@gmail.com>
Diff between qrNLMM versions 2.1 dated 2021-05-20 and 2.2 dated 2021-06-17
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/HelpfulFunctions.R | 23 +++++++++++++++++++++++ R/QRNLMM.R | 14 ++++++++------ build/partial.rdb |binary 5 files changed, 39 insertions(+), 14 deletions(-)
Title: Continuous Time Structural Equation Modelling
Description: Hierarchical continuous time state space modelling, for linear
and nonlinear systems measured by continuous variables, with limited support for
binary data. The subject specific dynamic system is modelled as a stochastic
differential equation (SDE), measurement models are typically multivariate normal factor models.
Linear mixed effects SDE's estimated via maximum likelihood and optimization are the default.
Nonlinearities, (state dependent parameters) and random effects on all parameters
are possible, using either max likelihood / max a posteriori optimization
(with optional importance sampling) or
Stan's Hamiltonian Monte Carlo sampling. See <https://github.com/cdriveraus/ctsem/raw/master/vignettes/hierarchicalmanual.pdf>
for details. Priors may be used. For the conceptual
overview of the hierarchical Bayesian linear SDE approach, see <https://www.researchgate.net/publication/324093594_Hierarchical_Bayesian_Continuous_Time_Dynamic_Modeling>.
Exogenous inputs may also be included, for an overview of such possibilities see <https://www.researchgate.net/publication/328221807_Understanding_the_Time_Course_of_Interventions_with_Continuous_Time_Dynamic_Models> .
Stan based functions are not available on 32 bit Windows systems at present.
<https://cdriver.netlify.app/> contains some tutorial blog posts.
Author: Charles Driver [aut, cre, cph],
Manuel Voelkle [aut, cph],
Han Oud [aut, cph],
Trustees of Columbia University [cph]
Maintainer: Charles Driver <charles.driver@ibe.uzh.ch>
Diff between ctsem versions 3.5.0 dated 2021-06-01 and 3.5.2 dated 2021-06-17
ctsem-3.5.0/ctsem/tests/testthat/test-discretepars.R |only ctsem-3.5.0/ctsem/tests/versioncompare.R |only ctsem-3.5.2/ctsem/DESCRIPTION | 8 ctsem-3.5.2/ctsem/MD5 | 50 +-- ctsem-3.5.2/ctsem/NEWS | 5 ctsem-3.5.2/ctsem/R/covml.R | 34 +- ctsem-3.5.2/ctsem/R/ctKalman.R | 9 ctsem-3.5.2/ctsem/R/ctStanGenerate.R | 4 ctsem-3.5.2/ctsem/R/ctStanModelWriter.R | 61 +++ ctsem-3.5.2/ctsem/R/ctSummarise.R | 3 ctsem-3.5.2/ctsem/R/ctTransforms.R | 22 + ctsem-3.5.2/ctsem/R/extract.ctStanFit.R | 2 ctsem-3.5.2/ctsem/R/plot.ctStanFit.R | 3 ctsem-3.5.2/ctsem/R/sgd.R | 23 - ctsem-3.5.2/ctsem/R/stanoptimis.R | 210 ++++++++----- ctsem-3.5.2/ctsem/data/ctstantestdat.rda |binary ctsem-3.5.2/ctsem/data/ctstantestfit.rda |binary ctsem-3.5.2/ctsem/inst/doc/hierarchicalmanual.pdf |binary ctsem-3.5.2/ctsem/src/Makevars.win | 2 ctsem-3.5.2/ctsem/src/stan_files/cov.stan | 84 +++-- ctsem-3.5.2/ctsem/src/stan_files/ctsm.stan | 61 +++ ctsem-3.5.2/ctsem/src/stan_files/ctsmgen.stan | 59 +++ ctsem-3.5.2/ctsem/tests/testthat/test-ctLOO.R | 2 ctsem-3.5.2/ctsem/tests/testthat/test-ctRaschExampleTest.R | 32 + ctsem-3.5.2/ctsem/tests/testthat/test-knownFits.R | 4 ctsem-3.5.2/ctsem/tests/testthat/test-sunspots.R | 2 ctsem-3.5.2/ctsem/tests/testthat/test-ukfpoptest.R | 2 27 files changed, 469 insertions(+), 213 deletions(-)
Title: Tools for Reading and Visualizing CIFTI Brain Files
Description: CIFTI files contain brain imaging data in "gray-ordinates", which
represent the gray matter as cortical surface vertices (left and right) and
subcortical voxels (cerebellum, basal ganglia, and other deep gray matter).
'ciftiTools' uses the Connectome Workbench to read CIFTI files into R and
apply common pre-processing steps (e.g. smoothing, resampling). It also
provides tools for visualizing the cortical surface with GIFTI files, and
for visualizing the subcortical volume.
Author: Amanda Mejia [aut, cre],
Damon Pham [aut] (<https://orcid.org/0000-0001-7563-4727>)
Maintainer: Amanda Mejia <mandy.mejia@gmail.com>
Diff between ciftiTools versions 0.2.2 dated 2021-03-16 and 0.3.1 dated 2021-06-17
ciftiTools-0.2.2/ciftiTools/R/convert_intent.R |only ciftiTools-0.2.2/ciftiTools/man/concat_xifti.Rd |only ciftiTools-0.2.2/ciftiTools/man/convert_to_dlabel.Rd |only ciftiTools-0.2.2/ciftiTools/man/convert_to_dscalar.Rd |only ciftiTools-0.3.1/ciftiTools/DESCRIPTION | 11 - ciftiTools-0.3.1/ciftiTools/MD5 | 77 ++++---- ciftiTools-0.3.1/ciftiTools/NAMESPACE | 14 + ciftiTools-0.3.1/ciftiTools/NEWS.md | 39 ++++ ciftiTools-0.3.1/ciftiTools/R/combine_xifti.R |only ciftiTools-0.3.1/ciftiTools/R/concat_xifti.R | 6 ciftiTools-0.3.1/ciftiTools/R/convert_xifti.R |only ciftiTools-0.3.1/ciftiTools/R/is.xifti.R | 46 +++-- ciftiTools-0.3.1/ciftiTools/R/make_xifti.R | 17 + ciftiTools-0.3.1/ciftiTools/R/make_xifti_components.R | 2 ciftiTools-0.3.1/ciftiTools/R/newdata_xifti.R | 22 ++ ciftiTools-0.3.1/ciftiTools/R/read_cifti.R | 2 ciftiTools-0.3.1/ciftiTools/R/read_xifti2.R |only ciftiTools-0.3.1/ciftiTools/R/resample_gifti.R | 18 +- ciftiTools-0.3.1/ciftiTools/R/select_xifti.R | 2 ciftiTools-0.3.1/ciftiTools/R/smooth_cifti.R | 5 ciftiTools-0.3.1/ciftiTools/R/smooth_gifti.R |only ciftiTools-0.3.1/ciftiTools/R/transform_xifti.R | 6 ciftiTools-0.3.1/ciftiTools/R/utils_volume.R | 2 ciftiTools-0.3.1/ciftiTools/R/utils_xifti.R | 81 ++++++++- ciftiTools-0.3.1/ciftiTools/R/view_xifti_surface.R | 90 +++++++--- ciftiTools-0.3.1/ciftiTools/R/view_xifti_volume.R | 2 ciftiTools-0.3.1/ciftiTools/R/write_cifti.R | 18 ++ ciftiTools-0.3.1/ciftiTools/R/write_gifti.R | 4 ciftiTools-0.3.1/ciftiTools/README.md | 6 ciftiTools-0.3.1/ciftiTools/inst/extdata/ones_1k.dscalar.nii |binary ciftiTools-0.3.1/ciftiTools/man/as.matrix.xifti.Rd |only ciftiTools-0.3.1/ciftiTools/man/combine_xifti.Rd |only ciftiTools-0.3.1/ciftiTools/man/convert_xifti.Rd |only ciftiTools-0.3.1/ciftiTools/man/dim.xifti.Rd |only ciftiTools-0.3.1/ciftiTools/man/make_surf.Rd | 4 ciftiTools-0.3.1/ciftiTools/man/merge_xifti.Rd |only ciftiTools-0.3.1/ciftiTools/man/ncol_xifti.Rd |only ciftiTools-0.3.1/ciftiTools/man/nrow_xifti.Rd |only ciftiTools-0.3.1/ciftiTools/man/read_xifti2.Rd |only ciftiTools-0.3.1/ciftiTools/man/resample_gifti.Rd | 2 ciftiTools-0.3.1/ciftiTools/man/smooth_cifti.Rd | 5 ciftiTools-0.3.1/ciftiTools/man/smooth_gifti.Rd |only ciftiTools-0.3.1/ciftiTools/man/view_xifti_surface.Rd | 14 + ciftiTools-0.3.1/ciftiTools/man/view_xifti_surface.cleg.Rd | 12 - ciftiTools-0.3.1/ciftiTools/tests/testthat/test-misc.R | 79 +++++++- ciftiTools-0.3.1/ciftiTools/tests/testthat/test-plotting_surf.R | 41 ++-- ciftiTools-0.3.1/ciftiTools/tests/testthat/test-reading.R | 4 ciftiTools-0.3.1/ciftiTools/tests/testthat/test-writing.R | 21 +- 48 files changed, 494 insertions(+), 158 deletions(-)
Title: Spatial and Environmental Blocking for K-Fold Cross-Validation
Description: Creating spatially or environmentally separated folds for cross-validation to provide a robust error estimation in spatially structured environments; Investigating and visualising the effective range of spatial autocorrelation in continuous raster covariates to find an initial realistic distance band to separate training and testing datasets spatially described in Valavi, R. et al. (2019) <doi:10.1111/2041-210X.13107>.
Author: Roozbeh Valavi [aut, cre],
Jane Elith [aut],
José Lahoz-Monfort [aut],
Gurutzeta Guillera-Arroita [aut]
Maintainer: Roozbeh Valavi <valavi.r@gmail.com>
Diff between blockCV versions 2.1.1 dated 2020-02-23 and 2.1.4 dated 2021-06-17
DESCRIPTION | 15 MD5 | 28 - NEWS.md | 12 R/blocking.R | 55 ++- R/helper_functions.R | 4 R/spatialAutoRange.R | 4 README.md | 15 build/vignette.rds |binary inst/doc/BlockCV_for_SDM.R | 54 +-- inst/doc/BlockCV_for_SDM.Rmd | 12 inst/doc/BlockCV_for_SDM.html | 632 +++++++++++++++++++++++------------------- inst/extdata/awt.grd | 24 - inst/extdata/awt.gri |binary man/spatialBlock.Rd | 19 - vignettes/BlockCV_for_SDM.Rmd | 12 15 files changed, 519 insertions(+), 367 deletions(-)