Title: Check User-Supplied Function Arguments
Description: For developers to check user-supplied function arguments. It
is designed to be simple, fast and customizable. Error messages
follow the tidyverse style guide.
Author: Joe Thorley [aut, cre] (<https://orcid.org/0000-0002-7683-4592>),
Kirill Müller [aut] (<https://orcid.org/0000-0002-1416-3412>),
Ayla Pearson [ctb] (<https://orcid.org/0000-0001-7388-1222>),
Nadine Hussein [ctb] (<https://orcid.org/0000-0003-4470-8361>),
Poisson Consulting [cph, fnd]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>
Diff between chk versions 0.6.0 dated 2021-07-04 and 0.7.0 dated 2021-09-03
chk-0.6.0/chk/tests/testthat/test-date-time.R |only chk-0.6.0/chk/tests/testthat/test-environment.R |only chk-0.6.0/chk/tests/testthat/test-not-empty.R |only chk-0.6.0/chk/tests/testthat/test-setequal.R |only chk-0.7.0/chk/DESCRIPTION | 9 chk-0.7.0/chk/MD5 | 269 ++++++------ chk-0.7.0/chk/NAMESPACE | 3 chk-0.7.0/chk/NEWS.md | 21 chk-0.7.0/chk/R/check-dim.R | 4 chk-0.7.0/chk/R/check-dirs.R | 8 chk-0.7.0/chk/R/check-files.R | 8 chk-0.7.0/chk/R/check-key.R | 4 chk-0.7.0/chk/R/check-values.R | 6 chk-0.7.0/chk/R/chk-all-equal.R | 1 chk-0.7.0/chk/R/chk-all-equivalent.R | 1 chk-0.7.0/chk/R/chk-all-identical.R | 1 chk-0.7.0/chk/R/chk-array.R | 1 chk-0.7.0/chk/R/chk-character-or-factor.R | 1 chk-0.7.0/chk/R/chk-chr.R | 23 - chk-0.7.0/chk/R/chk-count.R |only chk-0.7.0/chk/R/chk-date.R | 1 chk-0.7.0/chk/R/chk-datetime.R | 25 - chk-0.7.0/chk/R/chk-dbl.R | 25 - chk-0.7.0/chk/R/chk-dir.R | 1 chk-0.7.0/chk/R/chk-double.R | 1 chk-0.7.0/chk/R/chk-environment.R | 1 chk-0.7.0/chk/R/chk-equal.R | 5 chk-0.7.0/chk/R/chk-equivalent.R | 4 chk-0.7.0/chk/R/chk-ext.R | 4 chk-0.7.0/chk/R/chk-false.R | 1 chk-0.7.0/chk/R/chk-file.R | 2 chk-0.7.0/chk/R/chk-flag.R | 1 chk-0.7.0/chk/R/chk-function.R | 2 chk-0.7.0/chk/R/chk-gte.R | 1 chk-0.7.0/chk/R/chk-identical.R | 5 chk-0.7.0/chk/R/chk-integer.R | 1 chk-0.7.0/chk/R/chk-is.R | 2 chk-0.7.0/chk/R/chk-join.R | 9 chk-0.7.0/chk/R/chk-length.R |only chk-0.7.0/chk/R/chk-lgl.R | 1 chk-0.7.0/chk/R/chk-list.R | 1 chk-0.7.0/chk/R/chk-logical.R | 1 chk-0.7.0/chk/R/chk-lt.R | 1 chk-0.7.0/chk/R/chk-lte.R | 4 chk-0.7.0/chk/R/chk-match.R | 1 chk-0.7.0/chk/R/chk-named.R | 1 chk-0.7.0/chk/R/chk-not-empty.R | 1 chk-0.7.0/chk/R/chk-not-null.R | 1 chk-0.7.0/chk/R/chk-not-subset.R | 1 chk-0.7.0/chk/R/chk-null-or.R | 40 + chk-0.7.0/chk/R/chk-orderset.R | 4 chk-0.7.0/chk/R/chk-range.R | 1 chk-0.7.0/chk/R/chk-s3-class.R | 1 chk-0.7.0/chk/R/chk-scalar.R | 1 chk-0.7.0/chk/R/chk-sorted.R | 1 chk-0.7.0/chk/R/chk-string.R | 1 chk-0.7.0/chk/R/chk-subset.R | 1 chk-0.7.0/chk/R/chk-superset.R | 1 chk-0.7.0/chk/R/chk-true.R | 1 chk-0.7.0/chk/R/chk-tz.R | 1 chk-0.7.0/chk/R/chk-vector.R | 1 chk-0.7.0/chk/R/chk-whole-number.R | 4 chk-0.7.0/chk/R/chk-whole-numeric.R | 7 chk-0.7.0/chk/R/chk-wnum.R | 23 - 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chk-0.7.0/chk/tests/testthat/test-chk-integer.R | 1 chk-0.7.0/chk/tests/testthat/test-chk-is.R | 2 chk-0.7.0/chk/tests/testthat/test-chk-join.R | 12 chk-0.7.0/chk/tests/testthat/test-chk-length.R |only chk-0.7.0/chk/tests/testthat/test-chk-matrix.R | 1 chk-0.7.0/chk/tests/testthat/test-chk-not-any-na.R | 1 chk-0.7.0/chk/tests/testthat/test-chk-not-empty.R |only chk-0.7.0/chk/tests/testthat/test-chk-not-subset.R | 2 chk-0.7.0/chk/tests/testthat/test-chk-null-or.R | 23 - chk-0.7.0/chk/tests/testthat/test-chk-null.R | 2 chk-0.7.0/chk/tests/testthat/test-chk-number.R | 15 chk-0.7.0/chk/tests/testthat/test-chk-numeric.R | 1 chk-0.7.0/chk/tests/testthat/test-chk-orderset.R | 1 chk-0.7.0/chk/tests/testthat/test-chk-range.R | 1 chk-0.7.0/chk/tests/testthat/test-chk-setequal.R |only chk-0.7.0/chk/tests/testthat/test-chk-sorted.R | 2 chk-0.7.0/chk/tests/testthat/test-chk-string.R | 1 chk-0.7.0/chk/tests/testthat/test-chk-subset.R | 18 chk-0.7.0/chk/tests/testthat/test-chk-superset.R |only chk-0.7.0/chk/tests/testthat/test-chk-true.R | 1 chk-0.7.0/chk/tests/testthat/test-chk-type.R | 6 chk-0.7.0/chk/tests/testthat/test-chk-unique.R | 1 chk-0.7.0/chk/tests/testthat/test-chk-whole-number.R |only chk-0.7.0/chk/tests/testthat/test-chk-wnum.R | 9 chk-0.7.0/chk/tests/testthat/test-chkor-vld.R |only chk-0.7.0/chk/tests/testthat/test-chkor.R | 2 chk-0.7.0/chk/tests/testthat/test-expect-chk-error.R | 2 145 files changed, 652 insertions(+), 553 deletions(-)
Title: Estimation for Scale-Shape Mixtures of Skew-Normal Distributions
Description: Provide data generation and estimation tools for the multivariate scale mixtures of normal
presented in Lange and Sinsheimer (1993) <doi:10.2307/1390698>, the multivariate scale
mixtures of skew-normal presented in Zeller, Lachos and Vilca (2011)
<doi:10.1080/02664760903406504>, the multivariate skew scale mixtures of normal
presented in Louredo, Zeller and Ferreira (2021) <doi:10.1007/s13571-021-00257-y>
and the multivariate scale mixtures of skew-normal-Cauchy presented in Kahrari et al. (2020)
<doi:10.1080/03610918.2020.1804582>.
Author: Clecio Ferreira [aut],
Diego Gallardo [aut, cre],
Camila Zeller [aut]
Maintainer: Diego Gallardo <diego.gallardo@uda.cl>
Diff between skewMLRM versions 1.0 dated 2021-06-11 and 1.1 dated 2021-09-03
skewMLRM-1.0/skewMLRM/R/plotMahal.R |only skewMLRM-1.0/skewMLRM/R/se.est.R |only skewMLRM-1.0/skewMLRM/man/plotMahal.Rd |only skewMLRM-1.0/skewMLRM/man/se.est.Rd |only skewMLRM-1.1/skewMLRM/DESCRIPTION | 10 skewMLRM-1.1/skewMLRM/INDEX | 11 skewMLRM-1.1/skewMLRM/MD5 | 100 +++--- skewMLRM-1.1/skewMLRM/NAMESPACE | 9 skewMLRM-1.1/skewMLRM/NEWS.md |only skewMLRM-1.1/skewMLRM/R/FI.MCN.R | 9 skewMLRM-1.1/skewMLRM/R/FI.MSCEC.R | 7 skewMLRM-1.1/skewMLRM/R/FI.MSCN2.R | 26 - skewMLRM-1.1/skewMLRM/R/FI.MSL.R | 9 skewMLRM-1.1/skewMLRM/R/FI.MSN.R | 9 skewMLRM-1.1/skewMLRM/R/FI.MSSL2.R | 9 skewMLRM-1.1/skewMLRM/R/FI.MSSLEC.R | 7 skewMLRM-1.1/skewMLRM/R/FI.MSTEC.R | 7 skewMLRM-1.1/skewMLRM/R/FI.MSTN.R | 9 skewMLRM-1.1/skewMLRM/R/FI.MSTT.R | 9 skewMLRM-1.1/skewMLRM/R/FI.MT.R | 9 skewMLRM-1.1/skewMLRM/R/choose.MSMN.R | 83 +++++ skewMLRM-1.1/skewMLRM/R/choose.MSMSN.R | 98 ++++++ skewMLRM-1.1/skewMLRM/R/choose.MSMSNC.R | 110 ++++++- skewMLRM-1.1/skewMLRM/R/choose.MSSMN.R | 83 +++++ skewMLRM-1.1/skewMLRM/R/choose.models.R | 163 +++++++++-- skewMLRM-1.1/skewMLRM/R/choose2.R | 176 +++++++++++- skewMLRM-1.1/skewMLRM/R/distMahal.R |only skewMLRM-1.1/skewMLRM/R/estimate.MCN.R | 16 - skewMLRM-1.1/skewMLRM/R/estimate.MN.R | 16 - skewMLRM-1.1/skewMLRM/R/estimate.MSCEC.R | 152 ++++++++++ skewMLRM-1.1/skewMLRM/R/estimate.MSCN.R | 16 - skewMLRM-1.1/skewMLRM/R/estimate.MSCN2.R | 312 +++++++++++++++++++++ skewMLRM-1.1/skewMLRM/R/estimate.MSL.R | 26 + skewMLRM-1.1/skewMLRM/R/estimate.MSN.R | 17 - skewMLRM-1.1/skewMLRM/R/estimate.MSNC.R | 25 + skewMLRM-1.1/skewMLRM/R/estimate.MSSL.R | 26 + skewMLRM-1.1/skewMLRM/R/estimate.MSSL2.R | 128 ++++++++ skewMLRM-1.1/skewMLRM/R/estimate.MSSLEC.R | 56 +++ skewMLRM-1.1/skewMLRM/R/estimate.MSTEC.R | 53 +++ skewMLRM-1.1/skewMLRM/R/estimate.MSTN.R | 26 + skewMLRM-1.1/skewMLRM/R/estimate.MSTT.R | 116 +++++++- skewMLRM-1.1/skewMLRM/R/estimate.MT.R | 29 +- skewMLRM-1.1/skewMLRM/R/mbackcrit.R | 386 +++++++++++++++++++-------- skewMLRM-1.1/skewMLRM/R/mbacksign.R | 206 ++++++++++---- skewMLRM-1.1/skewMLRM/R/plot.skewMLRM.R |only skewMLRM-1.1/skewMLRM/R/print.skewMLRM.R |only skewMLRM-1.1/skewMLRM/R/rMSL.R | 1 skewMLRM-1.1/skewMLRM/R/summary.skewMLRM.R |only skewMLRM-1.1/skewMLRM/man/FIM.Rd | 9 skewMLRM-1.1/skewMLRM/man/choose2.Rd | 46 +-- skewMLRM-1.1/skewMLRM/man/chooseM.Rd | 30 +- skewMLRM-1.1/skewMLRM/man/distMahal.Rd |only skewMLRM-1.1/skewMLRM/man/estimateM.Rd | 90 ++++-- skewMLRM-1.1/skewMLRM/man/mbackcrit.Rd | 50 ++- skewMLRM-1.1/skewMLRM/man/mbacksign.Rd | 56 ++- skewMLRM-1.1/skewMLRM/man/plotskewMLRM.Rd |only skewMLRM-1.1/skewMLRM/man/summaryskewMLRM.Rd |only 57 files changed, 2315 insertions(+), 526 deletions(-)
Title: A Fast Clustering Algorithm for High Dimensional Data Based on
the Gram Matrix Decomposition
Description: Clustering algorithm for high dimensional data. Assuming that P feature measurements on N objects are arranged in an N×P matrix X, this package provides clustering based on the left Gram matrix XX^T. To simulate test data, type "help('simulate_HD_data')" and to learn how to use the clustering algorithm, type "help('RJclust')". To cite this package, type 'citation("RJcluster")'.
Author: Shahina Rahman [aut],
Valen E. Johnson [aut],
Suhasini Subba Rao [aut],
Rachael Shudde [aut, cre, trl]
Maintainer: Rachael Shudde <rachael.shudde@gmail.com>
Diff between RJcluster versions 3.2.1 dated 2021-09-02 and 3.2.2 dated 2021-09-03
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/FUNC_RJ_calls_scale.R | 2 +- build/partial.rdb |binary inst/doc/RJclust_Vignette.pdf |binary man/RJcluster-package.Rd | 2 +- 6 files changed, 10 insertions(+), 10 deletions(-)
Title: Fitting Linear Models with Endogenous Regressors using Latent
Instrumental Variables
Description: Fits linear models with endogenous regressor using latent instrumental variable approaches.
The methods included in the package are Lewbel's (1997) <doi:10.2307/2171884> higher moments approach as well as
Lewbel's (2012) <doi:10.1080/07350015.2012.643126> heteroscedasticity approach, Park and Gupta's (2012) <doi:10.1287/mksc.1120.0718> joint estimation method
that uses Gaussian copula and Kim and Frees's (2007) <doi:10.1007/s11336-007-9008-1> multilevel generalized
method of moment approach that deals with endogeneity in a multilevel setting.
These are statistical techniques to address the endogeneity problem where no external instrumental variables are needed.
Note that with version 2.0.0 sweeping changes were introduced which greatly improve functionality and usability but break backwards compatibility.
Author: Raluca Gui [cre, aut],
Markus Meierer [aut],
Rene Algesheimer [aut],
Patrik Schilter [aut]
Maintainer: Raluca Gui <raluca.gui@business.uzh.ch>
Diff between REndo versions 2.4.2 dated 2021-02-10 and 2.4.3 dated 2021-09-03
DESCRIPTION | 8 +++---- MD5 | 17 ++++++++-------- NEWS.md | 7 ++++++ R/f_multilevel_2levels.R | 4 +-- R/f_multilevel_3levels.R | 10 +++++---- R/f_multilevel_omittedvar.R | 6 +++-- build/vignette.rds |binary src/RcppExports.cpp | 5 ++++ tests/testthat/pinson06_rankdeficient_samesizegroup.csv |only tests/testthat/test-runability_multilevel.R | 14 +++++++++++++ 10 files changed, 51 insertions(+), 20 deletions(-)
Title: Simple Tools for Defining Species Ranges
Description: A collection of tools to create species range maps based on
occurrence data, statistics, and spatial objects. Other tools in this
collection can be used to analyze the environmental characteristics of
the species ranges. Plotting options to represent results in various
manners are also available. Results obtained using these tools can be
used to explore the distribution of species and define areas of occupancy
and extent of occurrence of species. Other packages help to explore species
distributions using distinct methods, but options presented in this set of
tools (e.g., using trend surface analysis and concave hull polygons) are
exclusive. Description of methods, approaches, and comments for some of the
tools implemented here can be found in:
IUCN (2001) <https://portals.iucn.org/library/node/10315>,
Peterson et al. (2011) <https://www.degruyter.com/princetonup/view/title/506966>,
and Graham and Hijmans (2006) <doi:10.1111/j.1466-8238.2006.00257.x>.
Author: Marlon E. Cobos [aut, cre] (<https://orcid.org/0000-0002-2611-1767>),
Vijay Barve [aut] (<https://orcid.org/0000-0002-4852-2567>),
Narayani Barve [aut] (<https://orcid.org/0000-0002-7893-8774>),
Alberto Jimenez-Valverde [aut]
(<https://orcid.org/0000-0001-9962-2106>),
Claudia Nuñez-Penichet [aut] (<https://orcid.org/0000-0001-7442-8593>)
Maintainer: Marlon E. Cobos <manubio13@gmail.com>
Diff between rangemap versions 0.1.17 dated 2021-06-26 and 0.1.18 dated 2021-09-03
DESCRIPTION | 8 - MD5 | 36 ++++---- NEWS.md | 6 + R/rangemap.R | 2 R/rangemap_explore.R | 19 +++- R/rangemap_fig.R | 4 R/ranges_espace.R | 58 +++++++++---- README.md | 125 ++++++++++++++---------------- build/vignette.rds |binary inst/doc/rangemap_short_tutorial_I.html | 10 +- inst/doc/rangemap_short_tutorial_II.html | 6 - inst/doc/rangemap_short_tutorial_III.html | 8 - inst/doc/rangemap_short_tutorial_IV.R | 5 - inst/doc/rangemap_short_tutorial_IV.Rmd | 5 - inst/doc/rangemap_short_tutorial_IV.html | 17 ++-- man/rangemap.Rd | 2 man/rangemap_explore.Rd | 11 ++ man/ranges_espace.Rd | 12 +- vignettes/rangemap_short_tutorial_IV.Rmd | 5 - 19 files changed, 196 insertions(+), 143 deletions(-)
Title: Statistical Inference for Partially Observed Markov Processes
Description: Tools for data analysis with partially observed Markov process (POMP) models (also known as stochastic dynamical systems, hidden Markov models, and nonlinear, non-Gaussian, state-space models). The package provides facilities for implementing POMP models, simulating them, and fitting them to time series data by a variety of frequentist and Bayesian methods. It is also a versatile platform for implementation of inference methods for general POMP models.
Author: Aaron A. King [aut, cre],
Edward L. Ionides [aut],
Carles Breto [aut],
Stephen P. Ellner [ctb],
Matthew J. Ferrari [ctb],
Sebastian Funk [ctb],
Steven G. Johnson [ctb],
Bruce E. Kendall [ctb],
Michael Lavine [ctb],
Dao Nguyen [ctb],
Eamon B. O'Dea [ctb],
Daniel C. Reuman [ctb],
Helen Wearing [ctb],
Simon N. Wood [ctb]
Maintainer: Aaron A. King <kingaa@umich.edu>
Diff between pomp versions 3.5 dated 2021-07-28 and 3.6 dated 2021-09-03
pomp-3.5/pomp/R/measles.R |only pomp-3.5/pomp/man/measles.Rd |only pomp-3.6/pomp/DESCRIPTION | 42 +-- pomp-3.6/pomp/MD5 | 356 ++++++++++++++--------------- pomp-3.6/pomp/R/abc.R | 16 - pomp-3.6/pomp/R/accumulators.R | 8 pomp-3.6/pomp/R/bake.R | 10 pomp-3.6/pomp/R/basic_components.R | 29 +- pomp-3.6/pomp/R/basic_probes.R | 35 -- pomp-3.6/pomp/R/blowflies.R | 6 pomp-3.6/pomp/R/bsflu.R | 6 pomp-3.6/pomp/R/bsmc2.R | 8 pomp-3.6/pomp/R/bsplines.R | 2 pomp-3.6/pomp/R/builder.R | 2 pomp-3.6/pomp/R/childhood.R |only pomp-3.6/pomp/R/coef.R | 3 pomp-3.6/pomp/R/cond_logLik.R | 3 pomp-3.6/pomp/R/covariate_table.R | 11 pomp-3.6/pomp/R/covmat.R | 1 pomp-3.6/pomp/R/csnippet.R | 3 pomp-3.6/pomp/R/dacca.R | 6 pomp-3.6/pomp/R/design.R | 2 pomp-3.6/pomp/R/distributions.R | 2 pomp-3.6/pomp/R/dmeasure_spec.R | 16 - pomp-3.6/pomp/R/dprocess_spec.R | 12 pomp-3.6/pomp/R/ebola.R | 4 pomp-3.6/pomp/R/eff_sample_size.R | 3 pomp-3.6/pomp/R/elementary_algorithms.R | 10 pomp-3.6/pomp/R/estimation_algorithms.R | 16 - pomp-3.6/pomp/R/filter_mean.R | 3 pomp-3.6/pomp/R/filter_traj.R | 3 pomp-3.6/pomp/R/flow.R | 19 - pomp-3.6/pomp/R/forecast.R | 1 pomp-3.6/pomp/R/gompertz.R | 4 pomp-3.6/pomp/R/kalman.R | 5 pomp-3.6/pomp/R/loglik.R | 1 pomp-3.6/pomp/R/lookup.R | 4 pomp-3.6/pomp/R/mif2.R | 9 pomp-3.6/pomp/R/nlf.R | 15 - pomp-3.6/pomp/R/obs.R | 11 pomp-3.6/pomp/R/ou2.R | 4 pomp-3.6/pomp/R/package.R | 78 +++--- pomp-3.6/pomp/R/parameter_trans.R | 10 pomp-3.6/pomp/R/parus.R | 32 -- pomp-3.6/pomp/R/pfilter.R | 5 pomp-3.6/pomp/R/pmcmc.R | 19 + pomp-3.6/pomp/R/pomp.R | 39 +-- pomp-3.6/pomp/R/pomp_examp.R | 7 pomp-3.6/pomp/R/pred_mean.R | 3 pomp-3.6/pomp/R/pred_var.R | 3 pomp-3.6/pomp/R/print.R | 2 pomp-3.6/pomp/R/prior_spec.R | 30 +- pomp-3.6/pomp/R/probe.R | 11 pomp-3.6/pomp/R/probe_match.R | 20 - pomp-3.6/pomp/R/proposals.R | 3 pomp-3.6/pomp/R/resample.R | 1 pomp-3.6/pomp/R/ricker.R | 4 pomp-3.6/pomp/R/rinit_spec.R | 11 pomp-3.6/pomp/R/rmeasure_spec.R | 16 - pomp-3.6/pomp/R/rprocess_spec.R | 20 - pomp-3.6/pomp/R/rw2.R | 17 - pomp-3.6/pomp/R/sannbox.R | 17 - pomp-3.6/pomp/R/saved_states.R | 3 pomp-3.6/pomp/R/simulate.R | 23 + pomp-3.6/pomp/R/sir.R | 6 pomp-3.6/pomp/R/skeleton_spec.R | 10 pomp-3.6/pomp/R/spect.R | 4 pomp-3.6/pomp/R/spect_match.R | 15 - pomp-3.6/pomp/R/spy.R | 2 pomp-3.6/pomp/R/states.R | 12 pomp-3.6/pomp/R/summary.R | 3 pomp-3.6/pomp/R/time.R | 16 - pomp-3.6/pomp/R/timezero.R | 3 pomp-3.6/pomp/R/traces.R | 3 pomp-3.6/pomp/R/traj_match.R | 47 ++- pomp-3.6/pomp/R/trajectory.R | 4 pomp-3.6/pomp/R/transformations.R | 2 pomp-3.6/pomp/R/userdata.R | 4 pomp-3.6/pomp/R/verhulst.R | 2 pomp-3.6/pomp/R/workhorses.R | 45 +-- pomp-3.6/pomp/R/wpfilter.R | 5 pomp-3.6/pomp/build/partial.rdb |binary pomp-3.6/pomp/data/LondonYorke.rda |binary pomp-3.6/pomp/data/bsflu.rda |binary pomp-3.6/pomp/data/ebolaWA2014.rda |binary pomp-3.6/pomp/data/ewcitmeas.rda |binary pomp-3.6/pomp/data/ewmeas.rda |binary pomp-3.6/pomp/inst/CITATION | 102 ++++---- pomp-3.6/pomp/inst/NEWS | 29 ++ pomp-3.6/pomp/inst/NEWS.Rd | 14 + pomp-3.6/pomp/inst/doc/index.html | 5 pomp-3.6/pomp/man/abc.Rd | 64 +++-- pomp-3.6/pomp/man/accumulators.Rd | 156 ++++++------ pomp-3.6/pomp/man/bake.Rd | 11 pomp-3.6/pomp/man/basic_components.Rd | 52 ++-- pomp-3.6/pomp/man/basic_probes.Rd | 16 - pomp-3.6/pomp/man/blowflies.Rd | 13 - pomp-3.6/pomp/man/bsflu.Rd | 14 - pomp-3.6/pomp/man/bsmc2.Rd | 51 ++-- pomp-3.6/pomp/man/bsplines.Rd | 7 pomp-3.6/pomp/man/childhood.Rd |only pomp-3.6/pomp/man/coef.Rd | 23 + pomp-3.6/pomp/man/cond_logLik.Rd | 24 + pomp-3.6/pomp/man/covariate_table.Rd | 36 +- pomp-3.6/pomp/man/covmat.Rd | 20 + pomp-3.6/pomp/man/csnippet.Rd | 29 +- pomp-3.6/pomp/man/dacca.Rd | 25 +- pomp-3.6/pomp/man/design.Rd | 2 pomp-3.6/pomp/man/distributions.Rd | 25 +- pomp-3.6/pomp/man/dmeasure.Rd | 5 pomp-3.6/pomp/man/dmeasure_spec.Rd | 64 +++-- pomp-3.6/pomp/man/dprior.Rd | 13 - pomp-3.6/pomp/man/dprocess.Rd | 5 pomp-3.6/pomp/man/dprocess_spec.Rd | 33 +- pomp-3.6/pomp/man/ebola.Rd | 58 ++-- pomp-3.6/pomp/man/eff_sample_size.Rd | 24 + pomp-3.6/pomp/man/elementary_algorithms.Rd | 13 - pomp-3.6/pomp/man/estimation_algorithms.Rd | 27 +- pomp-3.6/pomp/man/filter_mean.Rd | 24 + pomp-3.6/pomp/man/filter_traj.Rd | 24 + pomp-3.6/pomp/man/flow.Rd | 23 + pomp-3.6/pomp/man/forecast.Rd | 21 + pomp-3.6/pomp/man/gompertz.Rd | 9 pomp-3.6/pomp/man/hitch.Rd | 2 pomp-3.6/pomp/man/kalman.Rd | 37 +-- pomp-3.6/pomp/man/loglik.Rd | 21 + pomp-3.6/pomp/man/logmeanexp.Rd | 14 - pomp-3.6/pomp/man/lookup.Rd | 5 pomp-3.6/pomp/man/mif2.Rd | 51 ++-- pomp-3.6/pomp/man/nlf.Rd | 52 ++-- pomp-3.6/pomp/man/obs.Rd | 24 + pomp-3.6/pomp/man/ou2.Rd | 9 pomp-3.6/pomp/man/parameter_trans.Rd | 34 +- pomp-3.6/pomp/man/parmat.Rd | 12 pomp-3.6/pomp/man/partrans.Rd | 3 pomp-3.6/pomp/man/parus.Rd | 60 ++-- pomp-3.6/pomp/man/pfilter.Rd | 31 +- pomp-3.6/pomp/man/pmcmc.Rd | 69 +++-- pomp-3.6/pomp/man/pomp-package.Rd | 132 ++++++---- pomp-3.6/pomp/man/pomp.Rd | 56 +++- pomp-3.6/pomp/man/pomp_examp.Rd | 14 - pomp-3.6/pomp/man/pred_mean.Rd | 24 + pomp-3.6/pomp/man/pred_var.Rd | 24 + pomp-3.6/pomp/man/print.Rd | 2 pomp-3.6/pomp/man/prior_spec.Rd | 120 +++++++-- pomp-3.6/pomp/man/probe.Rd | 36 +- pomp-3.6/pomp/man/probe_match.Rd | 58 ++-- pomp-3.6/pomp/man/proposals.Rd | 5 pomp-3.6/pomp/man/resample.Rd | 1 pomp-3.6/pomp/man/ricker.Rd | 9 pomp-3.6/pomp/man/rinit.Rd | 5 pomp-3.6/pomp/man/rinit_spec.Rd | 83 +++--- pomp-3.6/pomp/man/rmeasure.Rd | 5 pomp-3.6/pomp/man/rmeasure_spec.Rd | 63 +++-- pomp-3.6/pomp/man/rprior.Rd | 13 - pomp-3.6/pomp/man/rprocess.Rd | 5 pomp-3.6/pomp/man/rprocess_spec.Rd | 33 +- pomp-3.6/pomp/man/rw2.Rd | 29 +- pomp-3.6/pomp/man/sannbox.Rd | 17 - pomp-3.6/pomp/man/saved_states.Rd | 24 + pomp-3.6/pomp/man/simulate.Rd | 27 +- pomp-3.6/pomp/man/sir.Rd | 34 +- pomp-3.6/pomp/man/skeleton.Rd | 12 pomp-3.6/pomp/man/skeleton_spec.Rd | 98 ++++++- pomp-3.6/pomp/man/spect.Rd | 34 +- pomp-3.6/pomp/man/spect_match.Rd | 55 ++-- pomp-3.6/pomp/man/spy.Rd | 23 + pomp-3.6/pomp/man/states.Rd | 24 + pomp-3.6/pomp/man/summary.Rd | 23 + pomp-3.6/pomp/man/time.Rd | 25 +- pomp-3.6/pomp/man/timezero.Rd | 23 + pomp-3.6/pomp/man/traces.Rd | 23 + pomp-3.6/pomp/man/traj_match.Rd | 43 ++- pomp-3.6/pomp/man/trajectory.Rd | 23 + pomp-3.6/pomp/man/transformations.Rd | 25 +- pomp-3.6/pomp/man/userdata.Rd | 129 +++++----- pomp-3.6/pomp/man/verhulst.Rd | 24 + pomp-3.6/pomp/man/workhorses.Rd | 9 pomp-3.6/pomp/man/wpfilter.Rd | 31 +- pomp-3.6/pomp/src/pomp_decls.h | 6 pomp-3.6/pomp/src/rinit.c | 4 181 files changed, 2628 insertions(+), 1558 deletions(-)
Title: Algorithm to Compute Monitor Independent Movement Summary Unit
(MIMS-Unit)
Description: The MIMS-unit algorithm is developed to compute Monitor Independent
Movement Summary Unit, a measurement to summarize raw accelerometer data
while ensuring harmonized results across different devices. It also includes
scripts to reproduce results in the related publication
(John, D., Tang. Q., Albinali, F. and Intille, S. (2019) <doi:10.1123/jmpb.2018-0068>).
Author: Qu Tang [aut, cre] (<https://orcid.org/0000-0001-5415-0205>),
Dinesh John [aut],
Stephen Intille [aut],
mHealth Research Group [cph] (https://www.mhealthgroup.org)
Maintainer: Qu Tang <tang.q@northeastern.edu>
Diff between MIMSunit versions 0.10.0 dated 2021-04-29 and 0.11.0 dated 2021-09-03
DESCRIPTION | 8 MD5 | 19 - NEWS.md | 17 + R/import_data.R | 167 ++++++++------- R/mims_unit.R | 34 ++- data/rest_on_table.rda |binary inst/extdata/actigraph_no_timestamp.csv |only man/custom_mims_unit.Rd | 345 ++++++++++++++++---------------- man/import_actigraph_csv.Rd | 26 ++ man/import_actigraph_csv_chunked.Rd | 4 man/mims_unit.Rd | 278 +++++++++++++------------ 11 files changed, 500 insertions(+), 398 deletions(-)
Title: Epidemiological Tool for Contact Tracing
Description: Routines for epidemiological contact tracing
and visualisation of network of contacts.
Author: Maria Noremark [aut] (<https://orcid.org/0000-0003-2555-8476>),
Stefan Widgren [aut, cre] (<https://orcid.org/0000-0001-5745-2284>)
Maintainer: Stefan Widgren <stefan.widgren@gmail.com>
Diff between EpiContactTrace versions 0.15.0 dated 2020-12-12 and 0.16.0 dated 2021-09-03
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS.md | 7 +++++++ R/in-degree.R | 6 +++--- R/ingoing-contact-chain.R | 6 +++--- R/out-degree.R | 6 +++--- man/InDegree-methods.Rd | 4 ++-- man/IngoingContactChain-methods.Rd | 4 ++-- man/OutDegree-methods.Rd | 4 ++-- 9 files changed, 33 insertions(+), 26 deletions(-)
More information about EpiContactTrace at CRAN
Permanent link
Title: Plot Shipboard DAS Data
Description: A utility program oriented to create maps, plot data, and do basic data summaries
of 'DAS' data <https://swfsc-publications.fisheries.noaa.gov/publications/TM/SWFSC/NOAA-TM-NMFS-SWFSC-305.PDF>
produced by 'WinCruz' from the Southwest Fisheries Science Center.
<https://www.fisheries.noaa.gov/west-coast/science-data/california-current-marine-mammal-assessment-program>.
Author: Sam Woodman [aut, cre] (<https://orcid.org/0000-0001-6071-8186>),
Tim Gerrodette [aut]
Maintainer: Sam Woodman <sam.woodman@noaa.gov>
Diff between CruzPlot versions 1.4.5 dated 2021-03-01 and 1.4.6 dated 2021-09-03
CruzPlot-1.4.5/CruzPlot/inst/shiny/server_2_das/cruzDasInteractiveEffort.R |only CruzPlot-1.4.5/CruzPlot/inst/shiny/server_2_das/cruzDasInteractiveSight.R |only CruzPlot-1.4.5/CruzPlot/inst/shiny/server_draw_local |only CruzPlot-1.4.6/CruzPlot/DESCRIPTION | 7 CruzPlot-1.4.6/CruzPlot/MD5 | 26 - CruzPlot-1.4.6/CruzPlot/NEWS.md | 7 CruzPlot-1.4.6/CruzPlot/README.md | 16 CruzPlot-1.4.6/CruzPlot/inst/shiny/app.R | 30 - CruzPlot-1.4.6/CruzPlot/inst/shiny/server_1_map/cruzMapRange.R | 111 ++--- CruzPlot-1.4.6/CruzPlot/inst/shiny/server_2_das/cruzDasInteractive.R | 192 ++++++++++ CruzPlot-1.4.6/CruzPlot/inst/shiny/server_files/drawInteractive.R |only CruzPlot-1.4.6/CruzPlot/inst/shiny/server_files/drawStatic.R |only CruzPlot-1.4.6/CruzPlot/inst/shiny/server_files/server_render.R | 6 CruzPlot-1.4.6/CruzPlot/inst/shiny/ui_files/ui_createMap.R | 2 CruzPlot-1.4.6/CruzPlot/inst/shiny/www/CruzPlot_Manual_app.pdf |binary 15 files changed, 290 insertions(+), 107 deletions(-)
Title: Decorate a 'ggplot' with Associated Information
Description: For many times, we are not just aligning plots as what 'cowplot' and 'patchwork' did. Users would like to align associated information that requires axes to be exactly matched in subplots, e.g. hierarchical clustering with a heatmap. This package provides utilities to aligns associated subplots to a main plot at different sides (left, right, top and bottom) with axes exactly matched.
Author: Guangchuang Yu [aut, cre, cph]
(<https://orcid.org/0000-0002-6485-8781>)
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between aplot versions 0.0.7 dated 2021-09-01 and 0.1.0 dated 2021-09-03
DESCRIPTION | 8 - MD5 | 26 ++-- NAMESPACE | 83 +++++++------ NEWS.md | 88 ++++++++------ R/aplot.R | 148 ++++++++++++------------ R/axis.R | 270 ++++++++++++++++++++++---------------------- R/insertion.R | 336 +++++++++++++++++++++++++++---------------------------- R/plot-list.R | 117 ++++++++++++++----- R/re-export.R | 14 +- R/utilities.R | 96 +++++++-------- man/ggrange.Rd | 46 +++---- man/is.ggtree.Rd | 40 +++--- man/plot_list.Rd | 82 ++++++++----- man/reexports.Rd | 38 +++--- 14 files changed, 753 insertions(+), 639 deletions(-)
Title: Analyzing Partial Rankings in Networks
Description: Implements methods for centrality related analyses of networks.
While the package includes the possibility to build more than 20 indices,
its main focus lies on index-free assessment of centrality via partial
rankings obtained by neighborhood-inclusion or positional dominance. These
partial rankings can be analyzed with different methods, including
probabilistic methods like computing expected node ranks and relative
rank probabilities (how likely is it that a node is more central than another?).
The methodology is described in depth in the vignettes and in
Schoch (2018) <doi:10.1016/j.socnet.2017.12.003>.
Author: David Schoch [aut, cre],
Julian Müller [ctb]
Maintainer: David Schoch <david.schoch@manchester.ac.uk>
Diff between netrankr versions 1.0.0 dated 2021-07-16 and 1.1.0 dated 2021-09-03
DESCRIPTION | 8 MD5 | 170 ++++++------- NAMESPACE | 6 NEWS.md | 15 + R/RcppExports.R | 12 R/aggregate.index.R | 84 +++--- R/approximate.ranks.R | 361 +++++++++++++--------------- R/bradley.terry.R | 18 - R/check.preservation.R | 20 - R/comparable.pairs.R | 22 + R/compare.ranks.R | 27 +- R/data.R | 4 R/distance.index.R | 12 R/dominance.graph.R | 24 + R/get.rankings.R | 61 ++-- R/hyperbolic.index.R | 70 ++--- R/index.builder.R | 383 +++++++++++++++++------------- R/indirect.relations.R | 198 ++++++++------- R/majorization.gap.R | 96 ++++--- R/mcmc.rank.R | 119 +++++---- R/neighborhood.inclusion.R | 88 ++++--- R/netrankr.R | 38 +-- R/plot.rank.intervals.R | 27 +- R/positional.dominance.R | 67 ++--- R/rank.analysis.R | 389 ++++++++++++++++--------------- R/rank.interval.R | 52 ++-- R/spectral.gap.R | 29 +- R/threshold.graph.R | 52 +--- R/transform.relations.R | 86 +++--- R/transitive.reduction.R | 12 R/utils.R | 335 ++++++++++++++++++++------ build/vignette.rds |binary inst/doc/benchmarks.html | 8 inst/doc/neighborhood_inclusion.R | 5 inst/doc/neighborhood_inclusion.Rmd | 6 inst/doc/neighborhood_inclusion.html | 2 inst/doc/partial_centrality.R | 11 inst/doc/partial_centrality.Rmd | 12 inst/doc/partial_centrality.html | 14 - inst/doc/probabilistic_cent.R | 5 inst/doc/probabilistic_cent.Rmd | 8 inst/doc/probabilistic_cent.html | 4 inst/doc/threshold_graph.R | 3 inst/doc/threshold_graph.Rmd | 5 inst/doc/use_case.Rmd | 2 inst/doc/use_case.html | 2 man/aggregate_positions.Rd | 40 +-- man/approx_rank_expected.Rd | 8 man/approx_rank_relative.Rd | 6 man/as.matrix.netrankr_full.Rd |only man/comparable_pairs.Rd | 4 man/compare_ranks.Rd | 10 man/dominance_graph.Rd | 10 man/exact_rank_prob.Rd | 6 man/get_rankings.Rd | 5 man/hyperbolic_index.Rd | 4 man/incomparable_pairs.Rd | 4 man/indirect_relations.Rd | 16 - man/is_preserved.Rd | 6 man/majorization_gap.Rd | 12 man/mcmc_rank_prob.Rd | 4 man/neighborhood_inclusion.Rd | 14 - man/plot.netrankr_interval.Rd | 4 man/plot_rank_intervals.Rd | 17 - man/positional_dominance.Rd | 13 - man/print.netrankr_full.Rd | 2 man/rank_intervals.Rd | 2 man/spectral_gap.Rd | 7 man/summary.netrankr_full.Rd |only man/threshold_graph.Rd | 8 man/transitive_reduction.Rd | 2 src/RcppExports.cpp | 34 +- src/mcmc_rank.cpp | 61 ++++ src/nialgo.cpp | 15 - src/pdalgo.cpp | 5 tests/testthat/test_approximations.R | 71 ++--- tests/testthat/test_dominance.R | 112 ++++---- tests/testthat/test_exact_rank_prob.R | 44 +-- tests/testthat/test_helpers.R | 113 ++++----- tests/testthat/test_indices.R | 158 ++++++------ tests/testthat/test_indirect_relations.R | 175 +++++++------ tests/testthat/test_threshold_graph.R | 30 +- vignettes/neighborhood_inclusion.Rmd | 6 vignettes/partial_centrality.Rmd | 12 vignettes/probabilistic_cent.Rmd | 8 vignettes/threshold_graph.Rmd | 5 vignettes/use_case.Rmd | 2 87 files changed, 2237 insertions(+), 1790 deletions(-)
Title: Southwest Fisheries Science Center Shipboard DAS Data Processing
Description: Process and summarize shipboard
'DAS' <https://swfsc-publications.fisheries.noaa.gov/publications/TM/SWFSC/NOAA-TM-NMFS-SWFSC-305.PDF> data
produced by the Southwest Fisheries Science Center (SWFSC) program 'WinCruz'
<https://www.fisheries.noaa.gov/west-coast/science-data/california-current-marine-mammal-assessment-program>.
This package standardizes and streamlines basic DAS data processing,
and includes a PDF with the DAS data format requirements.
Author: Sam Woodman [aut, cre] (<https://orcid.org/0000-0001-6071-8186>)
Maintainer: Sam Woodman <sam.woodman@noaa.gov>
Diff between swfscDAS versions 0.5.1 dated 2021-05-27 and 0.6.0 dated 2021-09-03
DESCRIPTION | 6 MD5 | 80 +++---- NAMESPACE | 3 NEWS.md | 7 R/as_das_df.R | 1 R/das_check.R | 27 +- R/das_effort.R | 19 + R/das_process.R | 70 +++++- R/das_read.R | 17 - R/swfscDAS-package.R | 11 - build/vignette.rds |binary inst/das_sample_randpicks.csv | 22 +- inst/doc/swfscDAS.R | 2 inst/doc/swfscDAS.Rmd | 6 inst/doc/swfscDAS.html | 369 ++++++++++++++++----------------- man/as_das_df.Rd | 64 ++--- man/as_das_dfr.Rd | 64 ++--- man/das_check.Rd | 228 ++++++++++---------- man/das_chop_condition.Rd | 202 +++++++++--------- man/das_chop_equallength.Rd | 240 +++++++++++----------- man/das_chop_section.Rd | 114 +++++----- man/das_comments.Rd | 96 ++++---- man/das_df-class.Rd | 146 ++++++------- man/das_dfr-class.Rd | 106 ++++----- man/das_effort_sight.Rd | 148 ++++++------- man/das_format_pdf.Rd | 66 +++--- man/das_process.Rd | 311 +++++++++++++++------------- man/das_read.Rd | 160 +++++++------- man/das_segdata.Rd | 184 ++++++++-------- man/das_sight.Rd | 424 +++++++++++++++++++-------------------- man/distance_greatcircle.Rd | 52 ++-- man/randpicks_convert.Rd | 60 ++--- man/subsetting.Rd | 152 ++++++------- man/swfscAirDAS-internals.Rd | 194 ++++++++--------- man/swfscDAS-package.Rd | 44 ++-- tests/testthat.R | 8 tests/testthat/test-class.R | 80 +++---- tests/testthat/test-output.R | 3 tests/testthat/test-process.R | 20 - tests/testthat/test-subsetting.R | 58 ++--- vignettes/swfscDAS.Rmd | 6 41 files changed, 1983 insertions(+), 1887 deletions(-)
Title: Experimental Statistics and Graphics for Agricultural Sciences
Description: Performs the analysis of completely randomized experimental designs (CRD), randomized blocks (RBD) and Latin square (LSD), experiments in double and triple factorial scheme (in CRD and RBD), experiments in subdivided plot scheme (in CRD and RBD), subdivided and joint analysis of experiments in CRD and RBD, linear regression analysis, test for two samples. The package performs analysis of variance, ANOVA assumptions and multiple comparison test of means or regression, according to Pimentel-Gomes (2009, ISBN: 978-85-7133-055-9), nonparametric test (Conover, 1999, ISBN: 0471160687), test for two samples, joint analysis of experiments according to Ferreira (2018, ISBN: 978-85-7269-566-4), Anova of aligned ranks (Wobbrock, JO, Findlater, L., Gergle, D., Higgins , JJ (2011), <doi: 10.1145/1978942.1978963>) and generalized linear model (glm) for binomial and Poisson family in CRD and RBD (Carvalho, FJ (2019), <doi: 10.14393/ufu.te.2019.1244>). It can also be used to obtain descriptive measures and graphics, in addition to correlations and creative graphics used in agricultural sciences (Agronomy, Zootechnics, Food Science and related areas).
Author: Gabriel Danilo Shimizu [aut, cre]
(<https://orcid.org/0000-0001-8524-508X>),
Rodrigo Yudi Palhaci Marubayashi [aut, ctb]
(<https://orcid.org/0000-0003-2778-8654>),
Leandro Simoes Azeredo Goncalves [aut, ctb]
(<https://orcid.org/0000-0001-9700-9375>)
Maintainer: Gabriel Danilo Shimizu <shimizu@uel.br>
Diff between AgroR versions 1.2.2 dated 2021-07-16 and 1.2.3 dated 2021-09-03
DESCRIPTION | 10 - MD5 | 221 ++++++++++++++++++++++-------------------- NAMESPACE | 1 NEWS.md | 24 ++++ R/DBCglm_function.R | 14 ++ R/DICglm_function.R | 8 + R/FAT2DBC_function.R | 44 +++++--- R/FAT2DBCad_function.R | 55 +++++----- R/FAT2DBCart_function.R | 3 R/FAT2DIC_function.R | 75 ++++++++++---- R/FAT2DICad_function.R | 54 +++++----- R/FAT2DICart_function.R | 3 R/FAT3DBC_function.R | 44 ++++---- R/FAT3DIC_function.R | 43 +++----- R/PSUBDBC_function.R | 51 +++++++-- R/PSUBDIC_function.R | 46 ++++++-- R/PSUBSUB_function.R | 3 R/bargraph_function.R | 5 R/barplot_positive_function.R | 4 R/bean_dataset.R |only R/conjdbc_function.R | 40 +++++-- R/conjdic_function.R | 44 +++++--- R/corn_dataset.R |only R/covercrops_dataset.R |only R/croqui_function.R | 203 +++++++++++++++++++++++++++++++------- R/dbc_function.R | 43 +++++--- R/dbct_function.R | 9 + R/desc2fat_function.R | 3 R/desc3fat_function.R | 3 R/desc_function.R | 3 R/dic_function.R | 44 ++++---- R/dict_function.R | 13 +- R/dql_function.R | 24 ++-- R/dqlt_function.R | 13 +- R/dunnet_function.R | 4 R/logistic_function.R | 5 R/orchard_dataset.R |only R/pca_function.R | 47 ++++++-- R/pepper_dataset.R |only R/plot_TH1_function.R | 3 R/plot_TH_function.R | 3 R/plot_interaction_function.R | 48 +++++++-- R/plotcor_function.R | 3 R/polynomial2_function.R | 2 R/polynomial2color_function.R | 2 R/polynomial_function.R | 67 +++++++----- R/radargraph_function.R | 3 R/seggraph_function.R | 5 R/sensorial.R | 1 R/simulate1.R | 1 R/simulate2.R | 1 R/simulate3.R | 1 R/sk_graph_function.R | 35 ++++-- R/soybean_dataset.R |only R/spider_graph_function.R | 3 R/summarise_function.R |only R/tbarplotreverse_function.R | 7 - R/test_two_function.R | 19 +-- R/tomate.R | 1 R/transf_function.R | 3 R/weather.R | 1 README.md |only data/bean.RData |only data/corn.RData |only data/covercrops.RData |only data/orchard.RData |only data/pepper.RData |only data/soybean.RData |only man/AgroR-package.Rd | 2 man/DBC.Rd | 17 ++- man/DBCT.Rd | 4 man/DIC.Rd | 28 ++--- man/DICT.Rd | 8 + man/DQL.Rd | 3 man/DQLT.Rd | 8 + man/FAT2DBC.Rd | 13 ++ man/FAT2DBC.ad.Rd | 5 man/FAT2DBC.art.Rd | 3 man/FAT2DIC.Rd | 14 ++ man/FAT2DIC.ad.Rd | 5 man/FAT2DIC.art.Rd | 3 man/FAT3DBC.Rd | 3 man/FAT3DIC.Rd | 3 man/PCA_function.Rd | 7 - man/PSUBDBC.Rd | 14 ++ man/PSUBDIC.Rd | 8 + man/PSUBSUBDBC.Rd | 3 man/TBARPLOT.reverse.Rd | 3 man/bar_graph.Rd | 5 man/barplot_positive.Rd | 4 man/bean.Rd |only man/conjdbc.Rd | 3 man/conjdic.Rd | 3 man/corn.Rd |only man/covercrops.Rd |only man/desc.Rd | 3 man/desc2fat.Rd | 3 man/desc3fat.Rd | 3 man/dunnett.Rd | 5 man/logistic.Rd | 4 man/orchard.Rd |only man/pepper.Rd |only man/plot_TH.Rd | 3 man/plot_TH1.Rd | 3 man/plot_cor.Rd | 3 man/plot_interaction.Rd | 25 ++++ man/polynomial.Rd | 14 +- man/radargraph.Rd | 3 man/seg_graph.Rd | 5 man/sensorial.Rd | 1 man/simulate1.Rd | 1 man/simulate2.Rd | 1 man/simulate3.Rd | 1 man/sk_graph.Rd | 5 man/sketch.Rd | 20 ++- man/soybean.Rd |only man/spider_graph.Rd | 3 man/summarise_anova.Rd |only man/test_two.Rd | 2 man/tomate.Rd | 1 man/transf.Rd | 3 man/weather.Rd | 1 122 files changed, 1081 insertions(+), 616 deletions(-)
Title: Combination of Independent P-Values
Description: Provides access to six fundamental statistics that can be used for the purpose of combination p-values. All methods used can referenced here: Heard & Rubin-Delanchy (2017) <arXiv:1707.06897>.
Author: Breya McGlown [cre, aut]
Maintainer: Breya McGlown <bswlker2@memphis.edu>
Diff between combinationpvalues versions 0.1.3 dated 2021-07-05 and 0.1.4 dated 2021-09-03
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 4 ++++ R/GeorgeMethod.r | 2 +- R/PearsonsMethod.r | 2 +- 5 files changed, 13 insertions(+), 9 deletions(-)
More information about combinationpvalues at CRAN
Permanent link
Title: Species Sensitivity Distributions
Description: Species sensitivity distributions are
cumulative probability distributions which are fitted to
toxicity concentrations for different species as described by
Posthuma et al.(2001) <isbn:9781566705783>.
The ssdtools package uses Maximum Likelihood to fit distributions
such as the log-normal, gamma, log-logistic,
log-Gumbel, Gompertz and Weibull.
The user can provide custom distributions.
Multiple distributions can be averaged using Information Criteria.
Confidence intervals on hazard concentrations and proportions are produced by
parametric bootstrapping.
Author: Joe Thorley [aut, cre, ctr] (<https://orcid.org/0000-0002-7683-4592>),
Carl Schwarz [aut, ctr],
Angeline Tillmanns [ctb],
Ali Azizishirazi [ctb],
Rebecca Fisher [ctb],
David Fox [ctb],
Kathleen McTavish [ctb],
Heather Thompson [ctb],
Andy Teucher [ctb],
Emilie Doussantousse [ctb],
Stephanie Hazlitt [ctb],
Nadine Hussein [ctb],
Nan-Hung Hsieh [ctb],
Sergio Ibarra Espinosa [ctb],
Province of British Columbia [cph]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>
Diff between ssdtools versions 0.3.4 dated 2021-05-14 and 0.3.5 dated 2021-09-03
DESCRIPTION | 8 +-- MD5 | 22 ++++----- NEWS.md | 8 ++- build/vignette.rds |binary inst/doc/distributions.html | 4 - inst/doc/exposure-plots.html | 86 ++++++++++++++++++++++++------------ inst/doc/faqs.html | 53 ++++++++++++++++++++-- inst/doc/small-sample-bias-ref.html | 4 - inst/doc/ssdtools.html | 52 +++++++++++++++++---- src/RcppExports.cpp | 5 ++ tests/testthat/test-fit.R | 6 -- tests/testthat/test-gompertz.R | 6 -- 12 files changed, 182 insertions(+), 72 deletions(-)
Title: Datasets to Measure the Alignment of Corporate Loan Books with
Climate Goals
Description: These datasets support the implementation in R of the
software 'PACTA' (Paris Agreement Capital Transition Assessment),
which is a free tool that calculates the alignment between corporate
lending portfolios and climate scenarios
(<https://2degrees-investing.org/>). Financial institutions use
'PACTA' to study how their capital allocation decisions align with
climate change mitigation goals. Because both financial institutions
and market data providers keep their data private, this package
provides fake, public data to enable the development and use of
'PACTA' in R.
Author: Mauro Lepore [aut, cre, ctr] (<https://orcid.org/0000-0002-1986-7988>),
Jackson Hoffart [aut, dtc] (<https://orcid.org/0000-0002-8600-5042>),
Klaus Hagedorn [aut],
2 Degrees Investing Initiative [cph, fnd]
Maintainer: Mauro Lepore <maurolepore@gmail.com>
Diff between r2dii.data versions 0.2.1 dated 2021-07-09 and 0.2.2 dated 2021-09-03
DESCRIPTION | 6 +- MD5 | 50 +++++++++++----------- NEWS.md | 5 ++ README.md | 10 ---- data/ald_demo.rda |binary data/cnb_classification.rda |binary data/co2_intensity_scenario_demo.rda |binary data/data_dictionary.rda |binary data/gics_classification.rda |binary data/green_or_brown.rda |binary data/isic_classification.rda |binary data/iso_codes.rda |binary data/loanbook_demo.rda |binary data/nace_classification.rda |binary data/naics_classification.rda |binary data/overwrite_demo.rda |binary data/psic_classification.rda |binary data/region_isos.rda |binary data/region_isos_demo.rda |binary data/scenario_demo_2020.rda |binary data/sector_classifications.rda |binary data/sic_classification.rda |binary man/region_isos.Rd | 2 tests/testthat/_snaps/region_isos.md | 8 +-- tests/testthat/test-classification_bridge.R | 1 tests/testthat/test-region_isos.R | 61 ++++++++++++++++++++++++++++ 26 files changed, 100 insertions(+), 43 deletions(-)
Title: Pacote Para Analise Multivariada
Description: Package with multivariate analysis methodologies for experiment evaluation.
The package estimates dissimilarity measures, builds dendrograms, obtains MANOVA,
principal components, canonical variables, etc. (Pacote com metodologias de analise
multivariada para avaliação de experimentos. O pacote estima medidas de dissimilaridade,
construi de dendogramas, obtem a MANOVA, componentes principais, variáveis canônicas, etc.)
Author: Alcinei Mistico Azevedo [aut, cre]
(<https://orcid.org/0000-0001-5196-0851>)
Maintainer: Alcinei Mistico Azevedo <alcineimistico@hotmail.com>
Diff between MultivariateAnalysis versions 0.4.0 dated 2021-08-05 and 0.4.1 dated 2021-09-03
DESCRIPTION | 9 MD5 | 118 +++--- NAMESPACE | 11 NEWS.md | 8 R/ApplyDissimilaridade.R | 1 R/ComponentesPrincipais.Misto.R | 229 ++++++------- R/CompontesPrincipais.R | 30 - R/CoordenadasPrincipais.R | 5 R/CorrelacaoMantel.R | 59 ++- R/Dendograma.R | 46 +- R/Distancia.R | 45 ++ R/HeatPlot.R |only R/MANOVA.R | 29 + R/MediaDistancia.R | 11 R/Normatiza.R | 3 R/SummaryDistancia.R | 70 +++- R/Tocher.R | 188 ++++++++-- R/VariaveisCanonicas.R | 48 ++ R/VariaveisCanonicas2.R | 4 R/zzz.R | 37 ++ inst/doc/Exemplo_dados_DBC_Misto.R | 6 inst/doc/Exemplo_dados_DBC_Misto.Rmd | 6 inst/doc/Exemplo_dados_DBC_Misto.html | 377 ++++++---------------- inst/doc/Exemplo_dados_Qualitativos_FMI.R | 2 inst/doc/Exemplo_dados_Qualitativos_FMI.Rmd | 2 inst/doc/Exemplo_dados_Qualitativos_FMI.html | 183 +++++----- inst/doc/Exemplo_dados_binarios.html | 130 +++---- inst/doc/Exemplo_dados_misto.R | 6 inst/doc/Exemplo_dados_misto.Rmd | 6 inst/doc/Exemplo_dados_misto.html | 133 ++----- inst/doc/Exemplo_dados_multicategoricos.R | 2 inst/doc/Exemplo_dados_multicategoricos.Rmd | 2 inst/doc/Exemplo_dados_multicategoricos.html | 182 ++++------ inst/doc/Exemplo_dados_quantitativos_DBC.R | 2 inst/doc/Exemplo_dados_quantitativos_DBC.Rmd | 2 inst/doc/Exemplo_dados_quantitativos_DBC.html | 372 ++++++--------------- inst/doc/Exemplo_dados_quantitativos_DIC.R | 2 inst/doc/Exemplo_dados_quantitativos_DIC.Rmd | 2 inst/doc/Exemplo_dados_quantitativos_DIC.html | 183 ++++------ inst/doc/Exemplo_dados_quantitativos_FAT_DBC.Rmd | 1 inst/doc/Exemplo_dados_quantitativos_FAT_DBC.html | 155 +++------ inst/doc/Exemplo_dados_quantitativos_Med.R | 4 inst/doc/Exemplo_dados_quantitativos_Med.Rmd | 5 inst/doc/Exemplo_dados_quantitativos_Med.html | 170 +++------ man/ComponentesPrincipais.Misto.Rd | 7 man/ComponentesPrincipais.Rd | 22 - man/CoordenadasPrincipais.Rd | 2 man/CorrelacaoMantel.Rd | 17 man/HeatPlot.Rd |only man/MultivariateAnalysis-package.Rd | 60 +-- man/SummaryDistancia.Rd | 13 man/Tocher.Rd | 30 + man/VariaveisCanonicas.Rd | 20 - vignettes/Exemplo_dados_DBC_Misto.Rmd | 6 vignettes/Exemplo_dados_Qualitativos_FMI.Rmd | 2 vignettes/Exemplo_dados_misto.Rmd | 6 vignettes/Exemplo_dados_multicategoricos.Rmd | 2 vignettes/Exemplo_dados_quantitativos_DBC.Rmd | 2 vignettes/Exemplo_dados_quantitativos_DIC.Rmd | 2 vignettes/Exemplo_dados_quantitativos_FAT_DBC.Rmd | 1 vignettes/Exemplo_dados_quantitativos_Med.Rmd | 5 61 files changed, 1503 insertions(+), 1580 deletions(-)
More information about MultivariateAnalysis at CRAN
Permanent link
Title: Helps Grade Assignment Submissions that are R Scripts
Description: After being given the location of your students' submissions and a test file, the function runs each .R file, and evaluates the results from all the given tests. Results are neatly returned in a data frame that has a row for each student, and a column for each test.
Author: Taylor Brown [aut, cre]
Maintainer: Taylor Brown <trb5me@virginia.edu>
Diff between gradeR versions 1.0.9 dated 2020-09-07 and 1.0.10 dated 2021-09-03
DESCRIPTION | 7 LICENSE | 4 MD5 | 16 +- NEWS.md | 6 R/grade.r | 172 ++++++++++++---------- README.md | 21 +- build/vignette.rds |binary inst/doc/gradeR.html | 218 +++-------------------------- inst/doc/using_gradeR_with_Gradescope.html | 193 +------------------------ 9 files changed, 169 insertions(+), 468 deletions(-)
Title: Automatic Processing of TLS Point Cloud Data for Forestry
Purposes
Description: Process automation of Terrestrial Laser Scanner (TLS) point cloud data derived from single scans. 'FORTLS' enables (i) detection of trees and estimation of diameter at breast height (dbh), (ii) estimation of some stand variables (e.g. density, basal area, mean and dominant height), (iii) computation of metrics related to important forest attributes estimated in Forest Inventories (FIs) at stand level and (iv) optimization of plot design for combining TLS data and field measured data. Documentation about 'FORTLS' is described in Molina-Valero et al. (2020, <doi:10.3390/IECF2020-08003>).
Author: Juan Alberto Molina-Valero [aut, cph, cre],
María José Ginzo Villamayor [aut, com],
Manuel Antonio Novo Pérez [aut, com],
Adela Martínez-Calvo [aut, com],
Juan Gabriel Álvarez-González [aut, ths],
Fernando Montes [aut],
César Pérez-Cruzado [aut, ths]
Maintainer: Juan Alberto Molina-Valero <juanalberto.molina.valero@usc.es>
Diff between FORTLS versions 1.0.2 dated 2021-04-21 and 1.0.3 dated 2021-09-03
DESCRIPTION | 15 - MD5 | 37 ++-- NAMESPACE | 1 R/auxiliary.functions.R | 223 ++++++++++++++++++++++----- R/correlations.R | 15 + R/estimation.plot.size.R | 24 +- R/metrics.variables.R | 118 +++++++------- R/normalize.R | 37 +++- R/optimize.plot.design.R | 8 R/simulations.R | 302 ++++++++++++++++++++++++++----------- R/tree.detection.R | 337 ++++++++++++++++++++++++++---------------- R/tree.detection.multiple.R | 33 +++- build/partial.rdb |binary man/distance.sampling.Rd | 2 man/estimation.plot.size.Rd | 3 man/figures |only man/normalize.Rd | 16 + src/RcppExports.cpp | 5 src/simulations_1.5.cpp | 7 src/surface_variation_1.3.cpp | 2 20 files changed, 820 insertions(+), 365 deletions(-)
Title: Adaptive Best Subset Selection in Polynomial Time
Description: Extremely efficient toolkit for solving the best subset selection problem in linear regression, logistic regression, Poisson regression, Cox proportional hazard model, multiple-response regression, multinomial logistic regression, and (sequential) principal component analysis. It implements and generalizes algorithms designed in <doi:10.1073/pnas.2014241117> that exploits a novel sequencing-and-splicing technique to guarantee exact support recovery and globally optimal solution in polynomial times.
Author: Jin Zhu [aut, cre] (<https://orcid.org/0000-0001-8550-5822>),
Liyuan Hu [aut],
Junhao Huang [aut],
Kangkang Jiang [aut],
Yanhang Zhang [aut],
Shiyun Lin [aut],
Junxian Zhu [aut],
Canhong Wen [aut],
Heping Zhang [aut] (<https://orcid.org/0000-0002-0688-4076>),
Xueqin Wang [aut] (<https://orcid.org/0000-0001-5205-9950>),
spectra contributors [cph] (Spectra implementation)
Maintainer: Jin Zhu <zhuj37@mail2.sysu.edu.cn>
Diff between abess versions 0.2.0 dated 2021-07-31 and 0.3.0 dated 2021-09-03
abess-0.2.0/abess/src/Algorithm.cpp |only abess-0.2.0/abess/src/Data.cpp |only abess-0.2.0/abess/src/Metric.cpp |only abess-0.2.0/abess/src/model_fit.cpp |only abess-0.2.0/abess/src/path.cpp |only abess-0.2.0/abess/src/screening.cpp |only abess-0.2.0/abess/vignettes/readmeTiming.png |only abess-0.3.0/abess/DESCRIPTION | 22 abess-0.3.0/abess/MD5 | 202 abess-0.3.0/abess/NEWS.md | 5 abess-0.3.0/abess/R/RcppExports.R | 4 abess-0.3.0/abess/R/abess.R | 516 +- abess-0.3.0/abess/R/abesspca.R | 246 abess-0.3.0/abess/R/coef.abess.R | 43 abess-0.3.0/abess/R/coef.abesspca.R | 54 abess-0.3.0/abess/R/deviance.abess.R | 29 abess-0.3.0/abess/R/extract.abess.R | 68 abess-0.3.0/abess/R/omit/plot.abesspca.R | 110 abess-0.3.0/abess/R/plot.abess.R | 134 abess-0.3.0/abess/R/predict.abess.R | 43 abess-0.3.0/abess/R/print.abess.R | 35 abess-0.3.0/abess/R/print.abesspca.R | 35 abess-0.3.0/abess/R/tmp/abess.R | 476 - abess-0.3.0/abess/R/utility.R | 172 abess-0.3.0/abess/README.md | 75 abess-0.3.0/abess/inst/COPYRIGHTS |only abess-0.3.0/abess/inst/doc/v01-abess-guide.html | 48 abess-0.3.0/abess/inst/include/Spectra/DavidsonSymEigsSolver.h |only abess-0.3.0/abess/inst/include/Spectra/GenEigsBase.h | 216 abess-0.3.0/abess/inst/include/Spectra/GenEigsComplexShiftSolver.h | 88 abess-0.3.0/abess/inst/include/Spectra/GenEigsRealShiftSolver.h | 58 abess-0.3.0/abess/inst/include/Spectra/GenEigsSolver.h | 59 abess-0.3.0/abess/inst/include/Spectra/JDSymEigsBase.h |only abess-0.3.0/abess/inst/include/Spectra/LinAlg/Arnoldi.h | 121 abess-0.3.0/abess/inst/include/Spectra/LinAlg/BKLDLT.h | 103 abess-0.3.0/abess/inst/include/Spectra/LinAlg/DoubleShiftQR.h | 214 abess-0.3.0/abess/inst/include/Spectra/LinAlg/Lanczos.h | 58 abess-0.3.0/abess/inst/include/Spectra/LinAlg/Orthogonalization.h |only abess-0.3.0/abess/inst/include/Spectra/LinAlg/RitzPairs.h |only abess-0.3.0/abess/inst/include/Spectra/LinAlg/SearchSpace.h |only abess-0.3.0/abess/inst/include/Spectra/LinAlg/TridiagEigen.h | 77 abess-0.3.0/abess/inst/include/Spectra/LinAlg/UpperHessenbergEigen.h | 47 abess-0.3.0/abess/inst/include/Spectra/LinAlg/UpperHessenbergQR.h | 422 + abess-0.3.0/abess/inst/include/Spectra/LinAlg/UpperHessenbergSchur.h |only abess-0.3.0/abess/inst/include/Spectra/MatOp/DenseCholesky.h | 55 abess-0.3.0/abess/inst/include/Spectra/MatOp/DenseGenComplexShiftSolve.h | 56 abess-0.3.0/abess/inst/include/Spectra/MatOp/DenseGenMatProd.h | 58 abess-0.3.0/abess/inst/include/Spectra/MatOp/DenseGenRealShiftSolve.h | 42 abess-0.3.0/abess/inst/include/Spectra/MatOp/DenseSymMatProd.h | 60 abess-0.3.0/abess/inst/include/Spectra/MatOp/DenseSymShiftSolve.h | 50 abess-0.3.0/abess/inst/include/Spectra/MatOp/SparseCholesky.h | 51 abess-0.3.0/abess/inst/include/Spectra/MatOp/SparseGenComplexShiftSolve.h |only abess-0.3.0/abess/inst/include/Spectra/MatOp/SparseGenMatProd.h | 61 abess-0.3.0/abess/inst/include/Spectra/MatOp/SparseGenRealShiftSolve.h | 45 abess-0.3.0/abess/inst/include/Spectra/MatOp/SparseRegularInverse.h | 63 abess-0.3.0/abess/inst/include/Spectra/MatOp/SparseSymMatProd.h | 63 abess-0.3.0/abess/inst/include/Spectra/MatOp/SparseSymShiftSolve.h | 47 abess-0.3.0/abess/inst/include/Spectra/MatOp/SymShiftInvert.h |only abess-0.3.0/abess/inst/include/Spectra/MatOp/internal/ArnoldiOp.h | 56 abess-0.3.0/abess/inst/include/Spectra/MatOp/internal/SymGEigsBucklingOp.h |only abess-0.3.0/abess/inst/include/Spectra/MatOp/internal/SymGEigsCayleyOp.h |only abess-0.3.0/abess/inst/include/Spectra/MatOp/internal/SymGEigsCholeskyOp.h | 48 abess-0.3.0/abess/inst/include/Spectra/MatOp/internal/SymGEigsRegInvOp.h | 48 abess-0.3.0/abess/inst/include/Spectra/MatOp/internal/SymGEigsShiftInvertOp.h |only abess-0.3.0/abess/inst/include/Spectra/SymEigsBase.h | 253 abess-0.3.0/abess/inst/include/Spectra/SymEigsShiftSolver.h | 79 abess-0.3.0/abess/inst/include/Spectra/SymEigsSolver.h | 65 abess-0.3.0/abess/inst/include/Spectra/SymGEigsShiftSolver.h |only abess-0.3.0/abess/inst/include/Spectra/SymGEigsSolver.h | 202 abess-0.3.0/abess/inst/include/Spectra/Util/CompInfo.h | 33 abess-0.3.0/abess/inst/include/Spectra/Util/GEigsMode.h | 24 abess-0.3.0/abess/inst/include/Spectra/Util/SelectionRule.h | 259 - abess-0.3.0/abess/inst/include/Spectra/Util/SimpleRandom.h | 40 abess-0.3.0/abess/inst/include/Spectra/Util/TypeTraits.h | 52 abess-0.3.0/abess/inst/include/Spectra/Util/Version.h |only abess-0.3.0/abess/inst/include/Spectra/contrib/LOBPCGSolver.h | 51 abess-0.3.0/abess/inst/include/Spectra/contrib/PartialSVDSolver.h | 99 abess-0.3.0/abess/man/abess-package.Rd | 7 abess-0.3.0/abess/man/abess.Rd | 172 abess-0.3.0/abess/man/abesspca.Rd | 67 abess-0.3.0/abess/man/coef.abess.Rd | 16 abess-0.3.0/abess/man/coef.abesspca.Rd | 22 abess-0.3.0/abess/man/deviance.abess.Rd | 14 abess-0.3.0/abess/man/extract.abess.Rd | 20 abess-0.3.0/abess/man/generate.data.Rd | 61 abess-0.3.0/abess/man/plot.abess.Rd | 26 abess-0.3.0/abess/man/predict.abess.Rd | 12 abess-0.3.0/abess/man/print.abess.Rd | 8 abess-0.3.0/abess/man/print.abesspca.Rd | 4 abess-0.3.0/abess/src/Algorithm.h | 2546 +--------- abess-0.3.0/abess/src/AlgorithmGLM.h |only abess-0.3.0/abess/src/AlgorithmPCA.h |only abess-0.3.0/abess/src/Data.h | 2 abess-0.3.0/abess/src/Metric.h | 20 abess-0.3.0/abess/src/RcppExports.cpp | 14 abess-0.3.0/abess/src/abess.cpp | 421 - abess-0.3.0/abess/src/abess.h | 110 abess-0.3.0/abess/src/model_fit.h | 1485 ++--- abess-0.3.0/abess/src/normalize.cpp | 4 abess-0.3.0/abess/src/normalize.h | 6 abess-0.3.0/abess/src/path.h | 123 abess-0.3.0/abess/src/screening.h | 23 abess-0.3.0/abess/src/utilities.cpp | 160 abess-0.3.0/abess/src/utilities.h | 18 abess-0.3.0/abess/tests/testthat/Rplots.pdf |binary abess-0.3.0/abess/tests/testthat/test-abess-group.R | 153 abess-0.3.0/abess/tests/testthat/test-abess.R | 375 - abess-0.3.0/abess/tests/testthat/test-abesspca.R | 24 abess-0.3.0/abess/tests/testthat/test-exception.R | 91 abess-0.3.0/abess/tests/testthat/test-generic.R | 135 abess-0.3.0/abess/tests/testthat/test-screening.R | 137 abess-0.3.0/abess/tests/testthat/test-sparse.R | 43 abess-0.3.0/abess/tests/testthat/utility.R | 1152 ++-- abess-0.3.0/abess/vignettes/Rtimings.png |only 114 files changed, 6188 insertions(+), 7023 deletions(-)
Title: 'RStudio' Addin for Network Analysis and Visualization
Description: 'RStudio' addin which provides a GUI to visualize and analyse networks.
After finishing a session, the code to produce the plot is inserted in the current script.
Alternatively, the function SNAhelperGadget() can be used directly from the console.
Additional addins include the Netreader() for reading network files, Netbuilder() to create
small networks via point and click, and the Componentlayouter() to layout networks with many components manually.
Author: David Schoch [aut, cre]
Maintainer: David Schoch <david.schoch@manchester.ac.uk>
Diff between snahelper versions 1.2.0 dated 2020-09-13 and 1.3.0 dated 2021-09-03
DESCRIPTION | 7 +++---- MD5 | 12 ++++++------ NEWS.md | 6 ++++++ R/Netreader.R | 2 +- R/SNAhelper.R | 6 +++++- R/constants.R | 4 ++-- README.md | 5 ++--- 7 files changed, 25 insertions(+), 17 deletions(-)
Title: NeuroAnatomy Toolbox for Analysis of 3D Image Data
Description: NeuroAnatomy Toolbox (nat) enables analysis and visualisation of 3D
biological image data, especially traced neurons. Reads and writes 3D images
in NRRD and 'Amira' AmiraMesh formats and reads surfaces in 'Amira' hxsurf
format. Traced neurons can be imported from and written to SWC and 'Amira'
LineSet and SkeletonGraph formats. These data can then be visualised in 3D
via 'rgl', manipulated including applying calculated registrations, e.g.
using the 'CMTK' registration suite, and analysed. There is also a simple
representation for neurons that have been subjected to 3D skeletonisation
but not formally traced; this allows morphological comparison between
neurons including searches and clustering (via the 'nat.nblast' extension
package).
Author: Gregory Jefferis [aut, cre] (<https://orcid.org/0000-0002-0587-9355>),
James Manton [aut] (<https://orcid.org/0000-0001-9260-3156>)
Maintainer: Gregory Jefferis <jefferis@gmail.com>
Diff between nat versions 1.8.16 dated 2020-09-22 and 1.8.17 dated 2021-09-03
DESCRIPTION | 13 MD5 | 51 NEWS | 6 R/amiralandmarks-io.R | 2 R/dotprops.R | 14 R/nat-data.R | 24 R/neuron-io-fiji.R | 4 R/neuron-io.R | 9 R/potential_synapses.R | 24 README.md | 70 build/partial.rdb |only build/vignette.rds |binary inst/doc/Installation.Rmd | 5 inst/doc/Installation.html | 252 -- inst/doc/neurons-intro.R | 7 inst/doc/neurons-intro.Rmd | 7 inst/doc/neurons-intro.html | 4816 +------------------------------------------- man/Cell07PNs.Rd | 19 man/dotprops.Rd | 14 man/fileformats.Rd | 4 man/nlapply.Rd | 5 man/potential_synapses.Rd | 18 man/read.landmarks.Rd | 2 man/read.neuron.Rd | 4 man/read.neuron.fiji.Rd | 4 vignettes/Installation.Rmd | 5 vignettes/neurons-intro.Rmd | 7 27 files changed, 352 insertions(+), 5034 deletions(-)
Title: R Markdown and Bookdown Templates to Publish Documents
Description: Producing high-quality documents suitable for publication directly from R is made possible by the R Markdown ecosystem.
'memoiR' makes it easy.
It provides templates to knit memoirs, articles and slideshows with helpers to publish the documents on GitHub Pages and activate continuous integration.
Author: Eric Marcon [aut, cre] (<https://orcid.org/0000-0002-5249-321X>)
Maintainer: Eric Marcon <eric.marcon@agroparistech.fr>
Diff between memoiR versions 1.1-0 dated 2021-07-26 and 1.1-2 dated 2021-09-03
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS.md | 7 +++++++ R/memoiR.R | 5 +++++ README.md | 2 +- build/vignette.rds |binary man/add_font.Rd | 38 +++++++++++++++++++------------------- man/add_hyphen.Rd | 38 +++++++++++++++++++------------------- tests/testthat/test_build.R | 7 ++++++- 9 files changed, 68 insertions(+), 51 deletions(-)
Title: Wavelet Routines for Global and Local Multiple Regression and
Correlation
Description: Wavelet routines that calculate single sets of wavelet
multiple regressions and correlations, and cross-regressions and
cross-correlations from a multivariate time series. Dynamic versions
of the routines allow the wavelet local multiple (cross-)regressions
and (cross-)correlations to evolve over time.
Author: Javier Fernandez-Macho [aut, cre]
(<https://orcid.org/0000-0002-5970-4382>)
Maintainer: Javier Fernandez-Macho <javier.fernandezmacho@ehu.es>
Diff between wavemulcor versions 3.1.0 dated 2020-05-17 and 3.1.2 dated 2021-09-03
wavemulcor-3.1.0/wavemulcor/inst/doc/wavemulcor-vignette.pdf |only wavemulcor-3.1.2/wavemulcor/DESCRIPTION | 31 ++-- wavemulcor-3.1.2/wavemulcor/MD5 | 74 +++++----- wavemulcor-3.1.2/wavemulcor/NEWS | 2 wavemulcor-3.1.2/wavemulcor/R/heatmap_wave.local.multiple.correlation.R | 8 - wavemulcor-3.1.2/wavemulcor/R/heatmap_wave.local.multiple.cross.correlation.R | 42 +++-- wavemulcor-3.1.2/wavemulcor/R/heatmap_wave.multiple.cross.correlation.R | 2 wavemulcor-3.1.2/wavemulcor/R/local.multiple.cross.correlation.R | 2 wavemulcor-3.1.2/wavemulcor/R/local.multiple.cross.regression.R | 2 wavemulcor-3.1.2/wavemulcor/R/plot_local.multiple.cross.correlation.R | 8 - wavemulcor-3.1.2/wavemulcor/R/plot_local.multiple.cross.regression.R | 14 + wavemulcor-3.1.2/wavemulcor/R/plot_local.multiple.regression.R | 4 wavemulcor-3.1.2/wavemulcor/R/plot_wave.local.multiple.correlation.R | 13 + wavemulcor-3.1.2/wavemulcor/R/plot_wave.local.multiple.cross.correlation.R | 5 wavemulcor-3.1.2/wavemulcor/R/plot_wave.local.multiple.cross.regression.R | 6 wavemulcor-3.1.2/wavemulcor/R/plot_wave.local.multiple.regression.R | 22 +- wavemulcor-3.1.2/wavemulcor/R/plot_wave.multiple.cross.regression.R | 8 - wavemulcor-3.1.2/wavemulcor/R/plot_wave.multiple.regression.R | 4 wavemulcor-3.1.2/wavemulcor/R/wave.multiple.cross.correlation.R | 2 wavemulcor-3.1.2/wavemulcor/R/wave.multiple.cross.regression.R | 2 wavemulcor-3.1.2/wavemulcor/README.md |only wavemulcor-3.1.2/wavemulcor/build/partial.rdb |binary wavemulcor-3.1.2/wavemulcor/build/vignette.rds |binary wavemulcor-3.1.2/wavemulcor/inst/doc/wavemulcor-vignette.R | 10 - wavemulcor-3.1.2/wavemulcor/inst/doc/wavemulcor-vignette.Rmd | 23 +-- wavemulcor-3.1.2/wavemulcor/inst/doc/wavemulcor-vignette.html |only wavemulcor-3.1.2/wavemulcor/man/local.multiple.cross.correlation.Rd | 2 wavemulcor-3.1.2/wavemulcor/man/local.multiple.cross.regression.Rd | 2 wavemulcor-3.1.2/wavemulcor/man/local.multiple.regression.Rd | 4 wavemulcor-3.1.2/wavemulcor/man/wave.local.multiple.cross.correlation.Rd | 13 - wavemulcor-3.1.2/wavemulcor/man/wave.multiple.correlation.Rd | 13 - wavemulcor-3.1.2/wavemulcor/man/wave.multiple.cross.correlation.Rd | 11 - wavemulcor-3.1.2/wavemulcor/man/wave.multiple.regression.Rd | 2 wavemulcor-3.1.2/wavemulcor/tests |only wavemulcor-3.1.2/wavemulcor/vignettes/jfbib4wavemulcor.bib | 6 wavemulcor-3.1.2/wavemulcor/vignettes/wavemulcor-vignette.Rmd | 23 +-- 36 files changed, 200 insertions(+), 160 deletions(-)
Title: Facilities for Simulating from ODE-Based Models
Description: Facilities for running simulations from ordinary
differential equation ('ODE') models, such as pharmacometrics and other
compartmental models. A compilation manager translates the ODE model
into C, compiles it, and dynamically loads the object code into R for
improved computational efficiency. An event table object facilitates
the specification of complex dosing regimens (optional) and sampling
schedules. NB: The use of this package requires both C and
Fortran compilers, for details on their use with R please see
Section 6.3, Appendix A, and Appendix D in the "R Administration and
Installation" manual. Also the code is mostly released under GPL. The
'VODE' and 'LSODA' are in the public domain. The information is available
in the inst/COPYRIGHTS.
Author: Matthew L. Fidler [aut] (<https://orcid.org/0000-0001-8538-6691>),
Melissa Hallow [aut],
Wenping Wang [aut, cre],
Zufar Mulyukov [ctb],
Alan Hindmarsh [ctb],
Awad H. Al-Mohy [ctb],
Matt Dowle [ctb],
Cleve Moler [ctb],
David Cooley [ctb],
Drew Schmidt [ctb],
Arun Srinivasan [ctb],
Ernst Hairer [ctb],
Gerhard Wanner [ctb],
Goro Fuji [ctb],
Hadley Wickham [ctb],
Jack Dongarra [ctb],
Linda Petzold [ctb],
Martin Maechler [ctb],
Matteo Fasiolo [ctb],
Morwenn [ctb],
Nicholas J. Higham [ctb],
Roger B. Sidje [ctb],
Simon Frost [ctb],
Kevin Ushey [ctb],
Yu Feng [ctb]
Maintainer: Wenping Wang <wwang8198@gmail.com>
Diff between RxODE versions 1.1.0 dated 2021-08-06 and 1.1.1 dated 2021-09-03
RxODE-1.1.0/RxODE/src/getTime.cpp |only RxODE-1.1.1/RxODE/DESCRIPTION | 6 - RxODE-1.1.1/RxODE/MD5 | 39 +++++------ RxODE-1.1.1/RxODE/NEWS.md | 10 ++ RxODE-1.1.1/RxODE/R/RxODE_md5.R | 2 RxODE-1.1.1/RxODE/build/partial.rdb |binary RxODE-1.1.1/RxODE/build/vignette.rds |binary RxODE-1.1.1/RxODE/inst/doc/RxODE-syntax.html | 14 ++-- RxODE-1.1.1/RxODE/src/Makevars.in | 4 - RxODE-1.1.1/RxODE/src/etTran.cpp | 6 - RxODE-1.1.1/RxODE/src/forder.cpp | 2 RxODE-1.1.1/RxODE/src/getTime.h | 67 +++++-------------- RxODE-1.1.1/RxODE/src/init.c | 4 - RxODE-1.1.1/RxODE/src/lincmt.c | 43 +++++------- RxODE-1.1.1/RxODE/src/lincmtB.cpp | 2 RxODE-1.1.1/RxODE/src/ode.h | 4 - RxODE-1.1.1/RxODE/src/par_solve.cpp | 91 ++++++++++++++++++++++++++- RxODE-1.1.1/RxODE/src/rxthreefry.cpp | 2 RxODE-1.1.1/RxODE/src/rxvandercorput.cpp | 2 RxODE-1.1.1/RxODE/src/seed.cpp | 2 RxODE-1.1.1/RxODE/tests/testthat/test-445.R | 4 - 21 files changed, 182 insertions(+), 122 deletions(-)
Title: Correlation and Regression Analyses for Randomized Response Data
Description: Univariate and multivariate methods to analyze randomized response
(RR) survey designs (e.g., Warner, S. L. (1965). Randomized response: A
survey technique for eliminating evasive answer bias. Journal of the
American Statistical Association, 60, 63–69, <doi:10.2307/2283137>).
Besides univariate estimates of true proportions, RR variables can be used
for correlations, as dependent variable in a logistic regression (with or
without random effects), or as predictors in a linear regression
(Heck, D. W., & Moshagen, M. (2018). RRreg: An R package for correlation and
regression analyses of randomized response data. Journal of Statistical
Software, 85(2), 1–29, <doi:10.18637/jss.v085.i02>). For simulations and
the estimation of statistical power, RR data can be generated according to
several models. The implemented methods also allow to test the link between
continuous covariates and dishonesty in cheating paradigms such as the
coin-toss or dice-roll task (Moshagen, M., & Hilbig, B. E. (2017).
The statistical analysis of cheating paradigms. Behavior Research Methods,
49, 724–732, <doi:10.3758/s13428-016-0729-x>).
Author: Daniel W. Heck [aut, cre] (<https://orcid.org/0000-0002-6302-9252>),
Morten Moshagen [aut]
Maintainer: Daniel W. Heck <dheck@uni-marburg.de>
Diff between RRreg versions 0.7.1 dated 2019-12-04 and 0.7.3 dated 2021-09-03
DESCRIPTION | 18 - MD5 | 32 +- NAMESPACE | 2 NEWS | 12 R/RRcor.R | 2 R/RRlin.R | 2 R/RRlog.R | 2 R/RRuni.R | 2 build/vignette.rds |binary inst/doc/Heck_Moshagen_2018_JSS.pdf |binary inst/doc/RRreg.html | 510 ++++++++++++------------------------ man/RRcor.Rd | 2 man/RRlin.Rd | 2 man/RRlog.Rd | 2 man/RRuni.Rd | 2 man/minarets.Rd | 4 man/plot.powerplot.Rd | 30 +- 17 files changed, 239 insertions(+), 385 deletions(-)
Title: A Toolbox for Non-Tabular Data Manipulation
Description: Provides a set of functions for data manipulation with
list objects, including mapping, filtering, grouping, sorting,
updating, searching, and other useful functions. Most functions
are designed to be pipeline friendly so that data processing with
lists can be chained.
Author: Kun Ren <ken@renkun.me>
Maintainer: Kun Ren <ken@renkun.me>
Diff between rlist versions 0.4.6.1 dated 2016-04-04 and 0.4.6.2 dated 2021-09-03
DESCRIPTION | 18 LICENSE | 4 MD5 | 269 +++++++------- NAMESPACE | 166 ++++---- NEWS | 250 ++++++------- R/List.R | 404 ++++++++++----------- R/data.R | 28 - R/functions.R | 195 +++++----- R/internal.R | 316 ++++++++--------- R/lambda.R | 28 - R/list.all.R | 110 ++--- R/list.clean.R | 90 ++-- R/list.common.R | 64 +-- R/list.count.R | 36 - R/list.do.R | 116 +++--- R/list.expand.R | 52 +- R/list.extract.R | 14 R/list.filter.R | 54 +- R/list.find.R | 74 +-- R/list.first.R | 70 +-- R/list.flatten.R | 62 +-- R/list.group.R | 256 ++++++------- R/list.insert.R | 124 +++--- R/list.is.R | 44 +- R/list.join.R | 106 ++--- R/list.load.R | 204 +++++------ R/list.map.R | 180 ++++----- R/list.match.R | 30 - R/list.merge.R | 66 +-- R/list.names.R | 40 +- R/list.order.R | 76 ++-- R/list.parse.R | 148 +++---- R/list.remove.R | 78 ++-- R/list.reverse.R | 20 - R/list.sample.R | 46 +- R/list.save.R | 98 ++--- R/list.search.R | 192 +++++----- R/list.select.R | 36 - R/list.serialize.R | 128 +++--- R/list.skip.R | 90 ++-- R/list.stack.R | 56 +-- R/list.subset.R | 26 - R/list.table.R | 52 +- R/list.take.R | 88 ++-- R/list.update.R | 58 +-- R/list.which.R | 32 - R/list.zip.R | 176 ++++----- R/rlist.R | 32 - R/subset.list.R | 50 +- R/utils.R | 72 +-- README.md | 387 ++++++++++---------- man/List.Rd | 97 ++--- man/args_env.Rd |only man/args_list.Rd |only man/callwith.Rd |only man/contains.Rd |only man/dot-evalwith.Rd |only man/dots.Rd |only man/getnames.Rd |only man/is.empty.Rd |only man/list.all.Rd | 71 +-- man/list.any.Rd | 71 +-- man/list.append.Rd | 53 +- man/list.apply.Rd | 37 - man/list.cases.Rd | 65 +-- man/list.cbind.Rd | 51 +- man/list.class.Rd | 83 ++-- man/list.clean.Rd | 91 ++-- man/list.common.Rd | 59 +-- man/list.count.Rd | 57 +-- man/list.do.Rd | 49 +- man/list.exclude.Rd | 47 +- man/list.expand.Rd | 55 +- man/list.extract.Rd | 33 - man/list.filter.Rd | 67 +-- man/list.find.Rd | 63 +-- man/list.findi.Rd | 63 +-- man/list.first.Rd | 53 +- man/list.flatten.Rd | 69 +-- man/list.group.Rd | 69 +-- man/list.insert.Rd | 59 +-- man/list.is.Rd | 61 +-- man/list.iter.Rd | 57 +-- man/list.join.Rd | 71 +-- man/list.last.Rd | 53 +- man/list.load.Rd | 112 +++--- man/list.map.Rd | 59 +-- man/list.maps.Rd | 53 +- man/list.mapv.Rd | 69 +-- man/list.match.Rd | 51 +- man/list.merge.Rd | 73 +-- man/list.names.Rd | 49 +- man/list.order.Rd | 69 +-- man/list.parse.Rd | 115 +++--- man/list.prepend.Rd | 49 +- man/list.rbind.Rd | 53 +- man/list.remove.Rd | 49 +- man/list.reverse.Rd | 37 - man/list.sample.Rd | 59 +-- man/list.save.Rd | 67 +-- man/list.search.Rd | 193 +++++----- man/list.select.Rd | 51 +- man/list.serialize.Rd | 63 +-- man/list.skip.Rd | 53 +- man/list.skipWhile.Rd | 61 +-- man/list.sort.Rd | 59 +-- man/list.stack.Rd | 69 +-- man/list.subset.Rd | 43 +- man/list.table.Rd | 59 +-- man/list.take.Rd | 57 +-- man/list.takeWhile.Rd | 61 +-- man/list.ungroup.Rd | 96 ++--- man/list.unserialize.Rd | 57 +-- man/list.unzip.Rd | 112 +++--- man/list.update.Rd | 69 +-- man/list.which.Rd | 57 +-- man/list.zip.Rd | 57 +-- man/nyweather.Rd | 49 +- man/rlist-package.Rd | 42 +- man/set_argnames.Rd |only man/subset.list.Rd | 63 +-- man/tryEval.Rd | 47 +- man/tryGet.Rd | 61 +-- tests/testthat.R | 4 tests/testthat/test-List.R | 178 ++++----- tests/testthat/test-basic.R | 760 ++++++++++++++++++++--------------------- tests/testthat/test-class.R | 32 - tests/testthat/test-filter.R | 74 +-- tests/testthat/test-find.R | 60 +-- tests/testthat/test-group.R | 92 ++-- tests/testthat/test-internal.R | 14 tests/testthat/test-io.R | 132 +++---- tests/testthat/test-join.R | 28 - tests/testthat/test-map.R | 110 ++--- tests/testthat/test-search.R | 132 +++---- tests/testthat/test-select.R | 40 +- tests/testthat/test-sort.R | 90 ++-- tests/testthat/test-subset.R | 142 +++---- tests/testthat/test-update.R | 42 +- tests/testthat/test-utils.R | 42 +- 140 files changed, 5697 insertions(+), 5733 deletions(-)
Title: R Bayesian Evidence Synthesis Tools
Description: Tool-set to support Bayesian evidence synthesis. This
includes meta-analysis, (robust) prior derivation from historical
data, operating characteristics and analysis (1 and 2 sample
cases). Please refer to Neuenschwander et al. (2010)
<doi:10.1177/1740774509356002> and Schmidli et al. (2014)
<doi:10.1111/biom.12242> for details on the methodology.
Author: Novartis Pharma AG [cph],
Sebastian Weber [aut, cre],
Beat Neuenschwander [ctb],
Heinz Schmidli [ctb],
Baldur Magnusson [ctb],
Yue Li [ctb],
Satrajit Roychoudhury [ctb],
Trustees of Columbia University [cph] (R/stanmodels.R, configure,
configure.win)
Maintainer: Sebastian Weber <sebastian.weber@novartis.com>
Diff between RBesT versions 1.6-1 dated 2020-05-28 and 1.6-2 dated 2021-09-03
DESCRIPTION | 25 ++-- MD5 | 124 ++++++++++---------- NAMESPACE | 3 R/RBesT-package.R | 4 R/sysdata.rda |binary build/vignette.rds |binary data/AS.rda |binary data/colitis.rda |binary data/crohn.rda |binary data/transplant.rda |binary inst/NEWS | 5 inst/doc/PoS_codata.R | 96 +++++++-------- inst/doc/PoS_codata.html | 83 +++++++------ inst/doc/PoS_interim.R | 20 +-- inst/doc/PoS_interim.html | 68 +++++------ inst/doc/RBesT.pdf |binary inst/doc/customizing_plots.R | 26 ++-- inst/doc/customizing_plots.Rmd | 2 inst/doc/customizing_plots.html | 92 +++++++-------- inst/doc/introduction.R | 30 ++-- inst/doc/introduction.html | 78 ++++++------ inst/doc/introduction_normal.R | 28 ++-- inst/doc/introduction_normal.html | 76 ++++++------ inst/doc/robustMAP.R | 24 +-- inst/doc/robustMAP.html | 233 +++++++++++++++++++------------------- inst/doc/variances_MAP.R | 20 +-- inst/doc/variances_MAP.html | 85 +++++++------ inst/sbc/calibration.md5 | 6 inst/sbc/sbc_report.html | 153 ++++++++++++------------ man/AS.Rd | 6 man/SimSum.Rd | 10 + man/automixfit.Rd | 3 man/colitis.Rd | 6 man/crohn.Rd | 6 man/decision1S.Rd | 6 man/decision1S_boundary.Rd | 12 - man/decision2S.Rd | 24 ++- man/decision2S_boundary.Rd | 26 ++-- man/ess.Rd | 9 - man/forest_plot.Rd | 14 +- man/gMAP.Rd | 35 ++++- man/integrate_density_log.Rd | 9 + man/knn.Rd | 3 man/mix.Rd | 9 - man/mixbeta.Rd | 12 + man/mixcombine.Rd | 9 - man/mixfit.Rd | 6 man/mixgamma.Rd | 15 +- man/mixnorm.Rd | 9 - man/oc1S.Rd | 6 man/oc2S.Rd | 23 ++- man/plot.EM.Rd | 8 - man/plot.gMAP.Rd | 2 man/plot.mix.Rd | 14 +- man/pos1S.Rd | 6 man/pos2S.Rd | 23 ++- man/predict.gMAP.Rd | 11 + man/transplant.Rd | 6 man/uniroot_int.Rd | 10 + src/Makevars | 10 - src/Makevars.win | 11 - tools/build.sh | 6 vignettes/customizing_plots.Rmd | 2 63 files changed, 879 insertions(+), 769 deletions(-)
Title: Nucleic Acid Melting Curve Analysis
Description: Lightweight utilities for nucleic acid melting curve analysis are
important in life sciences and diagnostics. This software can be used for
the analysis and presentation of melting curve data from microbead-based
assays (surface melting curve analysis) and reactions in solution (e.g.,
quantitative PCR (qPCR), real-time isothermal Amplification). Further
information are described in detail in two publications in The R Journal [
<https://journal.r-project.org/archive/2013-2/roediger-bohm-schimke.pdf>;
<https://journal.r-project.org/archive/2015-1/RJ-2015-1.pdf>].
Author: Stefan Roediger [cre, aut] (<https://orcid.org/0000-0002-1441-6512>),
Michal Burdukiewicz [aut] (<https://orcid.org/0000-0001-8926-582X>)
Maintainer: Stefan Roediger <stefan_roediger@gmx.de>
Diff between MBmca versions 1.0.1-2 dated 2021-09-02 and 1.0.1-3 dated 2021-09-03
CHANGELOG | 3 +++ DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ inst/doc/MBmca.Rmd | 2 +- inst/doc/MBmca.pdf |binary vignettes/MBmca.Rmd | 2 +- vignettes/MBmca.bib | 16 ---------------- 7 files changed, 15 insertions(+), 28 deletions(-)
Title: Geographic Networks
Description: Provides classes and methods for handling networks or
graphs whose nodes are geographical (i.e. locations in the globe).
The functionality includes the creation of objects of class geonetwork
as a graph with node coordinates, the computation of network measures,
the support of spatial operations (projection to different Coordinate
Reference Systems, handling of bounding boxes, etc.) and the plotting of
the geonetwork object combined with supplementary cartography for spatial
representation.
Author: Facundo Muñoz [aut, cre] (<https://orcid.org/0000-0002-5061-4241>)
Maintainer: Facundo Muñoz <facundo.munoz@cirad.fr>
Diff between geonetwork versions 0.3 dated 2019-04-05 and 0.4.1 dated 2021-09-03
DESCRIPTION | 18 +++--- MD5 | 16 ++--- NAMESPACE | 1 NEWS.md | 15 +++++ R/geonetwork.R | 1 README.md | 105 +++++++++++++++++++------------------- man/eurodist.Rd | 4 + man/figures/README-plotting-1.png |binary man/geonetwork.Rd | 3 - 9 files changed, 92 insertions(+), 71 deletions(-)
Title: Advanced Forest Plot Using 'grid' Graphics
Description: A forest plot that allows for
multiple confidence intervals per row,
custom fonts for each text element,
custom confidence intervals,
text mixed with expressions, and more.
The aim is to extend the use of forest plots beyond meta-analyses.
This is a more general version of the original 'rmeta' package's forestplot()
function and relies heavily on the 'grid' package.
Author: Max Gordon [aut, cre],
Thomas Lumley [aut, ctb]
Maintainer: Max Gordon <max@gforge.se>
Diff between forestplot versions 2.0.0 dated 2021-08-10 and 2.0.1 dated 2021-09-03
DESCRIPTION | 6 - MD5 | 21 +-- NEWS.md | 6 + R/forestplot.default.R | 2 R/prFpGetGraphTicksAndClips.R |only R/private.R | 233 --------------------------------------- build/vignette.rds |binary inst/doc/forestplot.R | 12 +- inst/doc/forestplot.Rmd | 14 +- inst/doc/forestplot.html | 74 ++++++------ man/prFpGetGraphTicksAndClips.Rd | 2 vignettes/forestplot.Rmd | 14 +- 12 files changed, 90 insertions(+), 294 deletions(-)
Title: Easy Dockerfile Creation from R
Description: Build a Dockerfile straight from your R session.
'dockerfiler' allows you to create step by step a Dockerfile, and
provide convenient tools to wrap R code inside this Dockerfile.
Author: Colin Fay [cre, aut] (<https://orcid.org/0000-0001-7343-1846>),
Vincent Guyader [aut] (<https://orcid.org/0000-0003-0671-9270>)
Maintainer: Colin Fay <contact@colinfay.me>
Diff between dockerfiler versions 0.1.3 dated 2019-03-19 and 0.1.4 dated 2021-09-03
dockerfiler-0.1.3/dockerfiler/man/dock_from_desc.Rd |only dockerfiler-0.1.4/dockerfiler/DESCRIPTION | 39 dockerfiler-0.1.4/dockerfiler/MD5 | 36 dockerfiler-0.1.4/dockerfiler/NAMESPACE | 17 dockerfiler-0.1.4/dockerfiler/NEWS.md | 8 dockerfiler-0.1.4/dockerfiler/R/add.R | 55 - dockerfiler-0.1.4/dockerfiler/R/dock_from_desc.R | 368 ++++++- dockerfiler-0.1.4/dockerfiler/R/dockerfile.R | 259 ++--- dockerfiler-0.1.4/dockerfiler/R/dockerignore.R |only dockerfiler-0.1.4/dockerfiler/R/get_sysreqs.R |only dockerfiler-0.1.4/dockerfiler/R/rthis.R | 6 dockerfiler-0.1.4/dockerfiler/R/utils.R |only dockerfiler-0.1.4/dockerfiler/build/vignette.rds |binary dockerfiler-0.1.4/dockerfiler/inst/doc/dockerfiler.R | 26 dockerfiler-0.1.4/dockerfiler/inst/doc/dockerfiler.html | 379 ++----- dockerfiler-0.1.4/dockerfiler/man/Dockerfile.Rd | 510 +++++++++- dockerfiler-0.1.4/dockerfiler/man/docker_ignore_add.Rd |only dockerfiler-0.1.4/dockerfiler/man/dockerfiles.Rd |only dockerfiler-0.1.4/dockerfiler/man/get_sysreqs.Rd |only dockerfiler-0.1.4/dockerfiler/tests/testthat/DESC_ |only dockerfiler-0.1.4/dockerfiler/tests/testthat/test-dock_from_desc.R |only dockerfiler-0.1.4/dockerfiler/tests/testthat/test-dockerignore.R |only dockerfiler-0.1.4/dockerfiler/tests/testthat/test-r.R | 8 dockerfiler-0.1.4/dockerfiler/tests/testthat/test-r6.R | 12 24 files changed, 1161 insertions(+), 562 deletions(-)
Title: Data Quality in Epidemiological Research
Description: A set of functions to assess data quality issues in
studies. See 'TMF' <https://www.tmf-ev.de/EnglishSite/Home.aspx>
guideline and 'DFG' <https://www.dfg.de/en/index.jsp> project at
<https://dataquality.ship-med.uni-greifswald.de>.
Author: University Medicine Greifswald [cph],
Adrian Richter [aut],
Carsten Oliver Schmidt [aut],
Stephan Struckmann [aut, cre]
Maintainer: Stephan Struckmann <stephan.struckmann@uni-greifswald.de>
Diff between dataquieR versions 1.0.8 dated 2021-08-12 and 1.0.9 dated 2021-09-03
dataquieR-1.0.8/dataquieR/inst/sort_heatmap_dt.js |only dataquieR-1.0.8/dataquieR/inst/vertical-dt-style.css |only dataquieR-1.0.9/dataquieR/DESCRIPTION | 8 dataquieR-1.0.9/dataquieR/MD5 | 96 ++++----- dataquieR-1.0.9/dataquieR/NEWS.md | 9 dataquieR-1.0.9/dataquieR/R/acc_margins.R | 12 - dataquieR-1.0.9/dataquieR/R/acc_multivariate_outlier.R | 2 dataquieR-1.0.9/dataquieR/R/acc_univariate_outlier.R | 5 dataquieR-1.0.9/dataquieR/R/com_segment_missingness.R | 10 dataquieR-1.0.9/dataquieR/R/con_contradictions.R | 8 dataquieR-1.0.9/dataquieR/R/dq_report.R | 1 dataquieR-1.0.9/dataquieR/R/html_dependency_vert_dt.R |only dataquieR-1.0.9/dataquieR/R/print.ReportSummaryTable.R | 44 ++-- dataquieR-1.0.9/dataquieR/R/rbind.R | 2 dataquieR-1.0.9/dataquieR/R/util_detect_cores.R |only dataquieR-1.0.9/dataquieR/R/util_looks_like_missing.R | 25 +- dataquieR-1.0.9/dataquieR/R/util_par_pmap.R | 1 dataquieR-1.0.9/dataquieR/R/util_sigmagap.R | 12 - dataquieR-1.0.9/dataquieR/R/util_tukey.R | 6 dataquieR-1.0.9/dataquieR/README.md | 4 dataquieR-1.0.9/dataquieR/inst/doc/DQ-report-example.R | 4 dataquieR-1.0.9/dataquieR/inst/doc/DQ-report-example.Rmd | 4 dataquieR-1.0.9/dataquieR/inst/doc/DQ-report-example.html | 101 ++++++++-- dataquieR-1.0.9/dataquieR/inst/vertical-dt-style |only dataquieR-1.0.9/dataquieR/man/acc_robust_univariate_outlier.Rd | 3 dataquieR-1.0.9/dataquieR/man/acc_univariate_outlier.Rd | 3 dataquieR-1.0.9/dataquieR/man/com_segment_missingness.Rd | 6 dataquieR-1.0.9/dataquieR/man/dq_report.Rd | 3 dataquieR-1.0.9/dataquieR/man/html_dependency_vert_dt.Rd |only dataquieR-1.0.9/dataquieR/man/print.ReportSummaryTable.Rd | 12 + dataquieR-1.0.9/dataquieR/man/util_detect_cores.Rd |only dataquieR-1.0.9/dataquieR/man/util_looks_like_missing.Rd | 2 dataquieR-1.0.9/dataquieR/man/util_par_pmap.Rd | 3 dataquieR-1.0.9/dataquieR/tests/testthat/test-acc_distributions.R | 1 dataquieR-1.0.9/dataquieR/tests/testthat/test-acc_end_digits.R | 1 dataquieR-1.0.9/dataquieR/tests/testthat/test-acc_loess.R | 6 dataquieR-1.0.9/dataquieR/tests/testthat/test-acc_margins.R | 1 dataquieR-1.0.9/dataquieR/tests/testthat/test-acc_multivariate_outlier.R | 1 dataquieR-1.0.9/dataquieR/tests/testthat/test-acc_shape_or_scale.R | 1 dataquieR-1.0.9/dataquieR/tests/testthat/test-acc_univariate_outlier.R | 6 dataquieR-1.0.9/dataquieR/tests/testthat/test-com_item_missingness.R | 1 dataquieR-1.0.9/dataquieR/tests/testthat/test-com_segment_missingness.R | 1 dataquieR-1.0.9/dataquieR/tests/testthat/test-con_contradictions.R | 1 dataquieR-1.0.9/dataquieR/tests/testthat/test-con_limit_deviations.R | 6 dataquieR-1.0.9/dataquieR/tests/testthat/test-int_datatype_matrix.R | 1 dataquieR-1.0.9/dataquieR/tests/testthat/test-prep_study2meta.R | 26 +- dataquieR-1.0.9/dataquieR/tests/testthat/test-print.R | 1 dataquieR-1.0.9/dataquieR/tests/testthat/test-pro_applicability_matrix.R | 1 dataquieR-1.0.9/dataquieR/tests/testthat/test-summary.R | 6 dataquieR-1.0.9/dataquieR/tests/testthat/test-util_heatmap_1th.R | 1 dataquieR-1.0.9/dataquieR/tests/testthat/test-util_looks_like_missing.R | 2 dataquieR-1.0.9/dataquieR/vignettes/DQ-report-example.Rmd | 4 52 files changed, 309 insertions(+), 145 deletions(-)
Title: Phylogenetic Ridge Regression Methods for Comparative Studies
Description: Functions for phylogenetic analysis (Castiglione et al, 2018 <doi:10.1111/2041-210X.12954>). The functions perform the estimation of phenotypic evolutionary rates, identification of phenotypic evolutionary rate shifts, quantification of direction and size of evolutionary change in multivariate traits, the computation of ontogenetic shape vectors and test for morphological convergence.
Author: Pasquale Raia, Silvia Castiglione, Carmela Serio, Alessandro Mondanaro, Marina Melchionna, Mirko Di Febbraro, Antonio Profico, Francesco Carotenuto
Maintainer: Pasquale Raia <pasquale.raia@unina.it>
Diff between RRphylo versions 2.5.7 dated 2021-07-16 and 2.5.8 dated 2021-09-03
DESCRIPTION | 12 MD5 | 72 +- NAMESPACE | 1 R/fix.poly.R | 200 +++----- R/node.paths.R |only R/overfitRR.R | 90 ++- R/scaleTree.R | 2 R/search.trend.R | 983 +++++++++++++++++++++------------------- R/tree.merger.R | 6 build/vignette.rds |binary inst/doc/RRphylo.R | 6 inst/doc/RRphylo.Rmd | 6 inst/doc/Tree-Manipulation.R | 6 inst/doc/Tree-Manipulation.Rmd | 6 inst/doc/Tree-Manipulation.html | 4 inst/doc/overfitRR.R | 6 inst/doc/overfitRR.Rmd | 6 inst/doc/search.conv.R | 6 inst/doc/search.conv.Rmd | 6 inst/doc/search.conv.html | 34 - inst/doc/search.shift.R | 6 inst/doc/search.shift.Rmd | 6 inst/doc/search.trend.R | 127 +---- inst/doc/search.trend.Rmd | 129 +---- inst/doc/search.trend.html | 4 inst/doc/swapONE.R | 6 inst/doc/swapONE.Rmd | 6 man/fix.poly.Rd | 28 - man/node.paths.Rd |only man/overfitRR.Rd | 22 man/search.trend.Rd | 179 +++---- vignettes/RRphylo.Rmd | 6 vignettes/Tree-Manipulation.Rmd | 6 vignettes/overfitRR.Rmd | 6 vignettes/search.conv.Rmd | 6 vignettes/search.shift.Rmd | 6 vignettes/search.trend.Rmd | 129 +---- vignettes/swapONE.Rmd | 6 38 files changed, 1140 insertions(+), 990 deletions(-)
Title: Penalized Regression Calibration (PRC)
Description: Computes penalized regression calibration (PRC), a
statistical method that allows to predict survival from
high-dimensional longitudinal predictors. PRC is described in
Signorelli et al. (2021, arXiv preprint: <doi:10.1002/sim.9178>)).
Author: Mirko Signorelli [aut, cre, cph]
(<https://orcid.org/0000-0002-8102-3356>),
Pietro Spitali [ctb],
Roula Tsonaka [ctb]
Maintainer: Mirko Signorelli <msignorelli.rpackages@gmail.com>
Diff between pencal versions 0.4.2 dated 2021-05-28 and 1.0.0 dated 2021-09-03
DESCRIPTION | 8 +- MD5 | 82 ++++++++++++------------ R/datasets.R | 3 R/draw_cluster_bootstrap.R | 3 R/fit_lmms.R | 6 - R/fit_mlpmms.R | 6 - R/fit_prclmm.R | 6 - R/fit_prcmlpmm.R | 6 - R/pencox_baseline.R | 3 R/performance_pencox_baseline.R | 5 - R/performance_prc.R | 5 - R/prepare_longdata.R | 3 R/simulate_prclmm_data.R | 5 - R/simulate_prcmlpmm_data.R | 5 - R/simulate_t_weibull.R | 3 R/summarize_lmms.R | 6 - R/summarize_mlpmms.R | 6 - R/survpred_prclmm.R | 5 - R/survpred_prcmlpmm.R | 5 - data/fitted_prclmm.RData |binary inst/CITATION | 12 +-- inst/NEWS.md | 14 ++++ inst/doc/pencal-vignette.Rmd | 10 +-- inst/doc/pencal-vignette.html | 123 +++++++++++++++++++++++++++++++++---- man/draw_cluster_bootstrap.Rd | 3 man/fit_lmms.Rd | 6 - man/fit_mlpmms.Rd | 6 - man/fit_prclmm.Rd | 6 - man/fit_prcmlpmm.Rd | 6 - man/fitted_prclmm.Rd | 3 man/pencox_baseline.Rd | 3 man/performance_pencox_baseline.Rd | 5 - man/performance_prc.Rd | 5 - man/prepare_longdata.Rd | 3 man/simulate_prclmm_data.Rd | 5 - man/simulate_prcmlpmm_data.Rd | 5 - man/simulate_t_weibull.Rd | 3 man/summarize_lmms.Rd | 6 - man/summarize_mlpmms.Rd | 6 - man/survpred_prclmm.Rd | 5 - man/survpred_prcmlpmm.Rd | 5 - vignettes/pencal-vignette.Rmd | 10 +-- 42 files changed, 278 insertions(+), 143 deletions(-)
Title: Distance Based Cell Lineage Reconstruction
Description: R codes for distance based cell lineage reconstruction. Our methods won both sub-challenges 2 and 3 of the Allen Institute Cell Lineage Reconstruction DREAM Challenge in 2020. The challenge paper is Gong et al. (2021) <doi:10.1016/j.cels.2021.05.008>.
Author: Il-Youp Kwak [aut, cre],
Wuming Gong [aut]
Maintainer: Il-Youp Kwak <ikwak2@cau.ac.kr>
Diff between DCLEAR versions 1.0.0 dated 2021-07-15 and 1.0.8 dated 2021-09-03
DCLEAR-1.0.0/DCLEAR/man/simulate-lineage_tree_config-method.Rd |only DCLEAR-1.0.8/DCLEAR/DESCRIPTION | 12 DCLEAR-1.0.8/DCLEAR/MD5 | 77 ++-- DCLEAR-1.0.8/DCLEAR/NAMESPACE | 17 DCLEAR-1.0.8/DCLEAR/R/AllGeneric.r | 49 ++ DCLEAR-1.0.8/DCLEAR/R/DCLEAR.r | 3 DCLEAR-1.0.8/DCLEAR/R/WH_train.r | 112 ++++- DCLEAR-1.0.8/DCLEAR/R/as_igraph.r |only DCLEAR-1.0.8/DCLEAR/R/as_lineage_tree.r |only DCLEAR-1.0.8/DCLEAR/R/as_phylo.r | 54 +- DCLEAR-1.0.8/DCLEAR/R/downsample.r |only DCLEAR-1.0.8/DCLEAR/R/get_leaves.r |only DCLEAR-1.0.8/DCLEAR/R/process_sequence.r | 5 DCLEAR-1.0.8/DCLEAR/R/prune.r |only DCLEAR-1.0.8/DCLEAR/R/rbind.r |only DCLEAR-1.0.8/DCLEAR/R/simulate.r | 192 +++++++--- DCLEAR-1.0.8/DCLEAR/R/subtract.r |only DCLEAR-1.0.8/DCLEAR/R/subtree.r |only DCLEAR-1.0.8/DCLEAR/R/summarize_kmer.r | 5 DCLEAR-1.0.8/DCLEAR/inst/doc/PrepC3.html | 4 DCLEAR-1.0.8/DCLEAR/inst/doc/WHhowto.Rmd | 2 DCLEAR-1.0.8/DCLEAR/inst/doc/WHhowto.html | 18 DCLEAR-1.0.8/DCLEAR/man/WH_train.Rd | 8 DCLEAR-1.0.8/DCLEAR/man/as_igraph-phylo-method.Rd |only DCLEAR-1.0.8/DCLEAR/man/as_igraph.Rd |only DCLEAR-1.0.8/DCLEAR/man/as_lineage_tree-phyDat-phylo-lineage_tree_config-method.Rd |only DCLEAR-1.0.8/DCLEAR/man/as_lineage_tree.Rd |only DCLEAR-1.0.8/DCLEAR/man/as_phylo-igraph-method.Rd | 2 DCLEAR-1.0.8/DCLEAR/man/as_phylo.Rd | 3 DCLEAR-1.0.8/DCLEAR/man/dist_replacement.Rd | 3 DCLEAR-1.0.8/DCLEAR/man/dist_weighted_hamming.Rd | 3 DCLEAR-1.0.8/DCLEAR/man/downsample-igraph-method.Rd |only DCLEAR-1.0.8/DCLEAR/man/downsample-lineage_tree-method.Rd |only DCLEAR-1.0.8/DCLEAR/man/downsample.Rd |only DCLEAR-1.0.8/DCLEAR/man/get_leaves-lineage_tree-method.Rd |only DCLEAR-1.0.8/DCLEAR/man/get_leaves.Rd |only DCLEAR-1.0.8/DCLEAR/man/positional_mutation_prob.Rd |only DCLEAR-1.0.8/DCLEAR/man/process_sequence.Rd | 3 DCLEAR-1.0.8/DCLEAR/man/prune-igraph-method.Rd |only DCLEAR-1.0.8/DCLEAR/man/prune-lineage_tree-method.Rd |only DCLEAR-1.0.8/DCLEAR/man/prune.Rd |only DCLEAR-1.0.8/DCLEAR/man/rbind-phyDat-method.Rd |only DCLEAR-1.0.8/DCLEAR/man/simulate-lineage_tree_config-missing-method.Rd |only DCLEAR-1.0.8/DCLEAR/man/simulate-lineage_tree_config-phyDat-method.Rd |only DCLEAR-1.0.8/DCLEAR/man/simulate.Rd | 7 DCLEAR-1.0.8/DCLEAR/man/simulate_core.Rd |only DCLEAR-1.0.8/DCLEAR/man/substr_kmer.Rd | 3 DCLEAR-1.0.8/DCLEAR/man/subtract-lineage_tree-lineage_tree-method.Rd |only DCLEAR-1.0.8/DCLEAR/man/subtract.Rd |only DCLEAR-1.0.8/DCLEAR/man/subtree-lineage_tree-method.Rd |only DCLEAR-1.0.8/DCLEAR/man/subtree-phylo-method.Rd |only DCLEAR-1.0.8/DCLEAR/man/subtree.Rd |only DCLEAR-1.0.8/DCLEAR/man/summarize_kmer.Rd | 3 DCLEAR-1.0.8/DCLEAR/src/RcppExports.cpp | 5 DCLEAR-1.0.8/DCLEAR/vignettes/WHhowto.Rmd | 2 55 files changed, 393 insertions(+), 199 deletions(-)
Title: Simple Process-Led Algorithms for Simulating Habitats
Description: This program calculates bioclimatic indices and fluxes (radiation,
evapotranspiration, soil moisture) for use in studies of ecosystem function,
species distribution, and vegetation dynamics under changing climate
scenarios. Predictions are based on a minimum of required inputs: latitude,
precipitation, air temperature, and cloudiness.
Davis et al. (2017) <doi:10.5194/gmd-10-689-2017>.
Author: Tyler W. Davis [aut] (<https://orcid.org/0000-0003-4312-919X>),
Iain Colin Prentice [aut] (<https://orcid.org/0000-0002-1296-6764>),
Benjamin D. Stocker [aut] (<https://orcid.org/0000-0003-2697-9096>),
Rebecca T. Thomas [aut],
Rhys J. Whitley [aut],
Han Wang [aut] (<https://orcid.org/0000-0003-2482-1818>),
Bradley J. Evans [aut],
Angela V. Gallego-Sala [aut],
Martin T. Sykes [aut],
Wolfgang Cramer [aut] (<https://orcid.org/0000-0002-9205-5812>),
Roberto Villegas-Diaz [cre] (<https://orcid.org/0000-0001-5036-8661>)
Maintainer: Roberto Villegas-Diaz <r.villegas-diaz@reading.ac.uk>
Diff between splash versions 1.0.0 dated 2021-09-02 and 1.0.1 dated 2021-09-03
DESCRIPTION | 8 ++++---- MD5 | 33 +++++++++++++++++---------------- NEWS.md | 5 +++++ R/evap.R | 20 ++++++++++---------- R/solar.R | 14 +++++++------- R/splash.R | 8 ++++---- build |only man/berger_tls.Rd | 2 +- man/calc_daily_evap.Rd | 4 ++-- man/calc_daily_solar.Rd | 12 ++++++------ man/density_h2o.Rd | 2 +- man/elv2pres.Rd | 6 +++--- man/enthalpy_vap.Rd | 2 +- man/quick_run.Rd | 4 ++-- man/run_one_day.Rd | 4 ++-- man/sat_slope.Rd | 2 +- man/specific_heat.Rd | 2 +- man/splash-package.Rd | 2 +- 18 files changed, 68 insertions(+), 62 deletions(-)
Title: Reading FRE Corporate Data of Public Traded Companies from B3
Description: Reads corporate data such as board composition and compensation for companies traded at B3,
the Brazilian exchange <http://www.b3.com.br/>. All data is downloaded and imported from the ftp site <http://dados.cvm.gov.br/dados/CIA_ABERTA/DOC/FRE/>.
Author: Marcelo Perlin [aut, cre],
Guilherme Kirch [aut]
Maintainer: Marcelo Perlin <marceloperlin@gmail.com>
Diff between GetFREData versions 0.6 dated 2021-04-06 and 0.7 dated 2021-09-03
DESCRIPTION | 16 +++++++-------- MD5 | 26 +++++++++++++------------ NEWS.md | 8 +++++++ R/fct_download_file.R | 3 +- R/fct_get_fre_data.R | 7 +++--- R/fct_get_fre_links.R | 23 +++++++++++++++++++--- R/fct_read_fre_zip_file.R | 5 +--- R/fcts_xml.R | 9 ++++++-- README.md | 2 - build/vignette.rds |binary inst/doc/GetFREData-vignette-introduction.Rmd | 2 - inst/doc/GetFREData-vignette-introduction.html | 4 +-- tests |only vignettes/GetFREData-vignette-introduction.Rmd | 2 - 14 files changed, 70 insertions(+), 37 deletions(-)
Title: Multiple Testing Procedures with Adaptation for Discrete Tests
Description: Multiple testing procedures described in the paper Döhler, Durand and Roquain (2018) "New FDR bounds for discrete and heterogeneous tests" <doi:10.1214/18-EJS1441>. The main procedures of the paper (HSU and HSD), their adaptive counterparts (AHSU and AHSD), and the HBR variant are available and are coded to take as input a set of observed p-values and their discrete support under the null. A function to compute such p-values and supports for Fisher's exact tests is also provided, along with a wrapper allowing to apply discrete procedures directly from contingency tables.
Author: Sebastian Döhler [ctb],
Guillermo Durand [aut, ctb],
Florian Junge [aut, cre],
Etienne Roquain [ctb]
Maintainer: Florian Junge <florian.junge@h-da.de>
Diff between DiscreteFDR versions 1.3.5 dated 2021-05-25 and 1.3.6 dated 2021-09-03
DiscreteFDR-1.3.5/DiscreteFDR/LICENSE |only DiscreteFDR-1.3.6/DiscreteFDR/DESCRIPTION | 12 DiscreteFDR-1.3.6/DiscreteFDR/MD5 | 37 - DiscreteFDR-1.3.6/DiscreteFDR/NEWS.md | 7 DiscreteFDR-1.3.6/DiscreteFDR/R/support.R | 6 DiscreteFDR-1.3.6/DiscreteFDR/build/partial.rdb |binary DiscreteFDR-1.3.6/DiscreteFDR/build/vignette.rds |binary DiscreteFDR-1.3.6/DiscreteFDR/man/DBR.Rd | 160 ++++---- DiscreteFDR-1.3.6/DiscreteFDR/man/DiscreteFDR.Rd | 132 +++--- DiscreteFDR-1.3.6/DiscreteFDR/man/amnesia.Rd | 74 +-- DiscreteFDR-1.3.6/DiscreteFDR/man/discrete.BH.Rd | 230 ++++++------ DiscreteFDR-1.3.6/DiscreteFDR/man/fast.Discrete.Rd | 160 ++++---- DiscreteFDR-1.3.6/DiscreteFDR/man/fisher.pvalues.support.Rd | 228 +++++------ DiscreteFDR-1.3.6/DiscreteFDR/man/hist.DiscreteFDR.Rd | 98 ++--- DiscreteFDR-1.3.6/DiscreteFDR/man/kernel.Rd | 224 +++++------ DiscreteFDR-1.3.6/DiscreteFDR/man/match.pvals.Rd | 98 ++--- DiscreteFDR-1.3.6/DiscreteFDR/man/plot.DiscreteFDR.Rd | 160 ++++---- DiscreteFDR-1.3.6/DiscreteFDR/man/print.DiscreteFDR.Rd | 80 ++-- DiscreteFDR-1.3.6/DiscreteFDR/man/summary.DiscreteFDR.Rd | 124 +++--- DiscreteFDR-1.3.6/DiscreteFDR/src/RcppExports.cpp | 5 20 files changed, 928 insertions(+), 907 deletions(-)
Title: Bayes Factors for Informative Hypotheses
Description: Computes approximated adjusted fractional Bayes factors for
equality, inequality, and about equality constrained hypotheses. S3 methods
are available for specific types of lm() models, namely ANOVA, ANCOVA, and
multiple regression, and for the t_test(). The statistical underpinnings are
described in
Gu, Mulder, and Hoijtink, (2018) <DOI:10.1111/bmsp.12110>,
Hoijtink, Gu, and Mulder, (2018) <DOI:10.1111/bmsp.12145>, and
Hoijtink, Gu, Mulder, and Rosseel, (2018) <DOI:10.1037/met0000187>.
Author: Xin Gu [aut],
Herbert Hoijtink [aut],
Joris Mulder [aut],
Caspar J van Lissa [aut, cre],
Van Zundert Camiel [ctb],
Jeff Jones [ctb],
Niels Waller [ctb]
Maintainer: Caspar J van Lissa <c.j.vanlissa@uu.nl>
Diff between bain versions 0.2.4 dated 2020-03-09 and 0.2.6 dated 2021-09-03
DESCRIPTION | 11 MD5 | 35 NAMESPACE | 2 R/bain_methods.R | 4 R/create_matrices.R | 10 R/get_estimates.R | 13 R/t.test.default.R | 10 README.md | 67 + build/vignette.rds |binary inst/doc/Introduction_to_bain.Rmd | 3 inst/doc/Introduction_to_bain.html | 1780 ++++++++++++++++--------------------- man/bain.Rd | 220 ++-- man/bain_sensitivity.Rd | 113 +- man/flip_inequality.Rd | 38 man/order_terms.Rd | 36 man/sesamesim.Rd | 124 +- src/Bain.f90 | 6 tests/testthat/test-parser2.R |only vignettes/Introduction_to_bain.Rmd | 3 19 files changed, 1187 insertions(+), 1288 deletions(-)
Title: Loading Data from 'Google Ads API'
Description: Interface for loading data from 'Google Ads API',
see <https://developers.google.com/google-ads/api/docs/start>.
Package provide function for authorization and loading reports.
Author: Alexey Seleznev [aut, cre] (<https://orcid.org/0000-0003-0410-7385>),
Netpeak [cph]
Maintainer: Alexey Seleznev <selesnow@gmail.com>
Diff between rgoogleads versions 0.2.0 dated 2021-08-02 and 0.3.0 dated 2021-09-03
DESCRIPTION | 10 ++++++---- MD5 | 17 +++++++++++++---- NEWS.md | 16 ++++++++++++++++ R/gads_get_report_helper.R | 8 +++++++- README.md | 14 ++++++++++++++ build |only inst |only vignettes |only 8 files changed, 56 insertions(+), 9 deletions(-)
Title: Reddit Data Extraction Toolkit
Description: A collection of tools for extracting structured data from <https://www.reddit.com/>.
Author: Ivan Rivera <ivan.s.rivera@gmail.com>
Maintainer: Ivan Rivera <ivan.s.rivera@gmail.com>
Diff between RedditExtractoR versions 3.0.1 dated 2021-08-23 and 3.0.3 dated 2021-09-03
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ NEWS.md | 14 ++++++++++++-- R/get_user_content.R | 19 ++++++++++++------- R/url_to_json.R | 1 + README.md | 11 +++++++---- man/get_user_content.Rd | 15 ++++++++------- 7 files changed, 51 insertions(+), 31 deletions(-)
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Title: Hierarchical and Variation Partitioning for Canonical Analysis
Description: This function conducts variation partitioning and hierarchical partitioning to calculate the unique, shared (referred as to "common") and individual contributions of each predictor (or matrix) towards explained variation (R-square and adjusted R-square) on canonical analysis (RDA,CCA and db-RDA), applying the algorithm of Chevan, A. and Sutherland, M. 1991 Hierarchical Partitioning.The American Statistician, 90-96 <doi:10.1080/00031305.1991.10475776>.
Author: Jiangshan Lai,Pedro Peres-Neto
Maintainer: Jiangshan Lai <lai@ibcas.ac.cn>
Diff between rdacca.hp versions 1.0-1 dated 2021-08-11 and 1.0-2 dated 2021-09-03
rdacca.hp-1.0-1/rdacca.hp/R/simpleRDA2.R |only rdacca.hp-1.0-1/rdacca.hp/man/simpleRDA2.Rd |only rdacca.hp-1.0-2/rdacca.hp/DESCRIPTION | 8 ++++---- rdacca.hp-1.0-2/rdacca.hp/MD5 | 14 +++++++------- rdacca.hp-1.0-2/rdacca.hp/R/permu.hp.r | 14 ++++++-------- rdacca.hp-1.0-2/rdacca.hp/R/rdacca.hp.r | 10 +++++----- rdacca.hp-1.0-2/rdacca.hp/R/rdar2.R |only rdacca.hp-1.0-2/rdacca.hp/man/permu.hp.Rd | 6 ++---- rdacca.hp-1.0-2/rdacca.hp/man/rdacca.hp.Rd | 4 ++-- rdacca.hp-1.0-2/rdacca.hp/man/rdar2.Rd |only 10 files changed, 26 insertions(+), 30 deletions(-)
Title: Display and Analyze ROC Curves
Description: Tools for visualizing, smoothing and comparing receiver operating characteristic (ROC curves). (Partial) area under the curve (AUC) can be compared with statistical tests based on U-statistics or bootstrap. Confidence intervals can be computed for (p)AUC or ROC curves.
Author: Xavier Robin [cre, aut] (<https://orcid.org/0000-0002-6813-3200>),
Natacha Turck [aut],
Alexandre Hainard [aut],
Natalia Tiberti [aut],
Frédérique Lisacek [aut],
Jean-Charles Sanchez [aut],
Markus Müller [aut],
Stefan Siegert [ctb] (Fast DeLong code),
Matthias Doering [ctb] (Hand & Till Multiclass),
Zane Billings [ctb] (DeLong paired test CI)
Maintainer: Xavier Robin <pROC-cran@xavier.robin.name>
Diff between pROC versions 1.17.0.1 dated 2021-01-13 and 1.18.0 dated 2021-09-03
DESCRIPTION | 15 + MD5 | 32 ++-- NEWS | 8 - R/delong.R | 79 ++++++---- R/roc.test.R | 23 ++ R/roc.utils.R | 30 +++ README.md | 4 build/partial.rdb |binary man/pROC-package.Rd | 2 man/roc.Rd | 2 man/roc.test.Rd | 21 +- tests/testthat/helper-expectations.R | 4 tests/testthat/print_output/roc.test-venkatraman.paired | 2 tests/testthat/print_output/roc.test-venkatraman.unpaired | 2 tests/testthat/print_output/roc.test-venkatraman.unpaired.unstratified | 2 tests/testthat/print_output/roc.test-venkatraman.unstratified | 2 tests/testthat/test-roc.test.R | 18 ++ 17 files changed, 177 insertions(+), 69 deletions(-)
Title: Miscellaneous Extensions to 'ggplot2'
Description: Extensions to 'ggplot2' respecting the grammar of graphics
paradigm. Statistics: locate and tag peaks and valleys; label plot with the
equation of a fitted polynomial or other types of models; labels
with P-value, R^2 or adjusted R^2 or information criteria for fitted models;
label with ANOVA table for fitted models; label with summary for fitted
models. Model fit classes for which suitable methods are provided by package
'broom' and 'broom.mixed' are supported. Scales and stats to build volcano
and quadrant plots based on outcomes, fold changes, p-values and false
discovery rates.
Author: Pedro J. Aphalo [aut, cre] (<https://orcid.org/0000-0003-3385-972X>),
Kamil Slowikowski [ctb] (<https://orcid.org/0000-0002-2843-6370>),
Samer Mouksassi [ctb] (<https://orcid.org/0000-0002-7152-6654>)
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between ggpmisc versions 0.4.2-1 dated 2021-08-15 and 0.4.3 dated 2021-09-03
DESCRIPTION | 17 MD5 | 44 + NAMESPACE | 7 NEWS.md | 25 R/lmodel2-util.R |only R/stat-ma-eq.R |only R/stat-ma-line.R |only R/stat-poly-eq.R | 43 - R/stat-poly-line.R | 10 R/stat-quant-band.r | 6 R/stat-quant-eq.R | 6 R/stat-quant-line.r | 2 build/vignette.rds |binary inst/doc/model-based-annotations.R | 15 inst/doc/model-based-annotations.Rmd | 32 + inst/doc/model-based-annotations.html | 779 ++++++++++++++++--------------- man/coef.lmodel2.Rd |only man/confint.lmodel2.Rd |only man/figures/README-unnamed-chunk-1-1.png |binary man/ggpmisc-ggproto.Rd | 10 man/ggpmisc-package.Rd | 2 man/predict.lmodel2.Rd |only man/stat_ma_eq.Rd |only man/stat_ma_line.Rd |only man/stat_poly_eq.Rd | 17 man/stat_poly_line.Rd | 384 +++++++-------- vignettes/model-based-annotations.Rmd | 32 + 27 files changed, 786 insertions(+), 645 deletions(-)
Title: Geodesic Regression
Description: Provides a gradient descent algorithm to find a geodesic relationship between real-valued independent variables and a manifold-valued dependent variable (i.e. geodesic regression). Available manifolds are Euclidean space, the sphere, hyperbolic space, and Kendall's 2-dimensional shape space. Besides the standard least-squares loss, the least absolute deviations, Huber, and Tukey biweight loss functions can also be used to perform robust geodesic regression. Functions to help choose appropriate cutoff parameters to maintain high efficiency for the Huber and Tukey biweight estimators are included, as are functions for generating random tangent vectors from the Riemannian normal distributions on the sphere and hyperbolic space. The n-sphere is a n-dimensional manifold: we represent it as a sphere of radius 1 and center 0 embedded in (n+1)-dimensional space. Using the hyperboloid model of hyperbolic space, n-dimensional hyperbolic space is embedded in (n+1)-dimensional Minkowski space as the upper sheet of a hyperboloid of two sheets. Kendall's 2D shape space with K landmarks is of real dimension 2K-4; preshapes are represented as complex K-vectors with mean 0 and magnitude 1. Details are described in Shin, H.-Y. and Oh, H.-S. (2020) <arXiv:2007.04518>. Also see Fletcher, P. T. (2013) <doi:10.1007/s11263-012-0591-y>.
Author: Ha-Young Shin [aut, cre],
Hee-Seok Oh [aut]
Maintainer: Ha-Young Shin <hayoung.shin@gmail.com>
Diff between GeodRegr versions 0.1.0 dated 2020-08-24 and 0.2.0 dated 2021-09-03
DESCRIPTION | 12 - MD5 | 36 ++-- NAMESPACE | 27 +-- R/GeodRegr.R | 372 +++++++++++++++++++++++++++++++++------------- R/data.R | 248 +++++++++++++++--------------- R/efficiency.R | 60 +++---- R/normal.R |only R/others.R | 196 +++++++++++++++++------- man/are.Rd | 4 man/are_nr.Rd | 4 man/calvaria.Rd | 2 man/exp_map.Rd | 10 - man/geo_dist.Rd | 4 man/geo_reg.Rd | 196 ++++++++++++------------ man/intrinsic_location.Rd | 156 +++++++++---------- man/log_map.Rd | 11 - man/loss.Rd | 98 ++++++------ man/onmanifold.Rd | 12 - man/par_trans.Rd | 8 man/rnormtangents.Rd |only 20 files changed, 866 insertions(+), 590 deletions(-)
Title: Interface for the 'Finnish Biodiversity Information Facility'
API
Description: A programmatic interface to the 'Finnish Biodiversity Information
Facility' ('FinBIF') API (<https://api.laji.fi>). 'FinBIF' aggregates
Finnish biodiversity data from multiple sources in a single open access
portal for researchers, citizen scientists, industry and government.
'FinBIF' allows users of biodiversity information to find, access, combine
and visualise data on Finnish plants, animals and microorganisms. The
'finbif' package makes the publicly available data in 'FinBIF' easily
accessible to programmers. Biodiversity information is available on taxonomy
and taxon occurrence. Occurrence data can be filtered by taxon, time,
location and other variables. The data accessed are conveniently
preformatted for subsequent analyses.
Author: Finnish Museum of Natural History - Luomus [cph],
William K. Morris [aut, cre] (<https://orcid.org/0000-0002-8686-4154>)
Maintainer: William K. Morris <willi@mmorris.email>
Diff between finbif versions 0.6.1 dated 2021-07-26 and 0.6.2 dated 2021-09-03
finbif-0.6.1/finbif/tests/testthat/test-finbif_request_token.R |only finbif-0.6.2/finbif/DESCRIPTION | 8 finbif-0.6.2/finbif/MD5 | 62 +- finbif-0.6.2/finbif/NEWS.md | 26 + finbif-0.6.2/finbif/R/api_get.R | 14 finbif-0.6.2/finbif/R/finbif-package.R | 4 finbif-0.6.2/finbif/R/finbif_collections.R | 76 +++ finbif-0.6.2/finbif/R/finbif_occurrence_load.R | 9 finbif-0.6.2/finbif/R/finbif_records.R | 74 ++- finbif-0.6.2/finbif/R/finbif_request_token.R | 24 - finbif-0.6.2/finbif/R/methods.R | 2 finbif-0.6.2/finbif/R/sysdata.rda |binary finbif-0.6.2/finbif/R/utils.R | 8 finbif-0.6.2/finbif/R/zzz.R | 6 finbif-0.6.2/finbif/README.md | 11 finbif-0.6.2/finbif/build/vignette.rds |binary finbif-0.6.2/finbif/data/finland_map.rda |binary finbif-0.6.2/finbif/inst/NEWS.Rd | 28 + finbif-0.6.2/finbif/man/finbif-package.Rd | 4 finbif-0.6.2/finbif/man/finbif_occurrence.Rd | 8 finbif-0.6.2/finbif/man/finbif_records.Rd | 8 finbif-0.6.2/finbif/man/finbif_request_token.Rd | 4 finbif-0.6.2/finbif/man/to_dwc.Rd | 2 finbif-0.6.2/finbif/tests/api-dev-cassettes/finbif_occurrence.yml | 212 +++++----- finbif-0.6.2/finbif/tests/api-dev-cassettes/finbif_occurrence_aggregate_documents.yml |only finbif-0.6.2/finbif/tests/api-dev-cassettes/finbif_occurrence_collection.yml | 41 + finbif-0.6.2/finbif/tests/cassettes/finbif_occurrence.yml | 204 +++++---- finbif-0.6.2/finbif/tests/cassettes/finbif_occurrence_aggregate_documents.yml |only finbif-0.6.2/finbif/tests/testthat/_snaps/local-finbif_occurrence_load.md | 52 +- finbif-0.6.2/finbif/tests/testthat/helper-finbif.R | 4 finbif-0.6.2/finbif/tests/testthat/test-finbif_occurrence.R | 24 + finbif-0.6.2/finbif/tests/testthat/test-local-finbif_occurrence_load.R | 11 finbif-0.6.2/finbif/tests/testthat/test-local-finbif_request_token.R |only finbif-0.6.2/finbif/tests/testthat/test-zzz-finbif.R | 4 34 files changed, 628 insertions(+), 302 deletions(-)
Title: A Toolbox for Manipulating Biological Sequences
Description: Classes and functions to work with biological sequences (DNA, RNA and amino acid sequences).
Implements S3 infrastructure to work with biological sequences as described in Keck (2020) <doi:10.1111/2041-210X.13490>.
Provides a collection of functions to perform biological conversion among classes
(transcription, translation) and basic operations on sequences
(detection, selection and replacement based on positions or patterns).
The package also provides functions to import and export sequences from and to other package formats.
Author: Francois Keck [aut, cre, cph] (<https://orcid.org/0000-0002-3323-4167>)
Maintainer: Francois Keck <francois.keck@gmail.com>
Diff between bioseq versions 0.1.2 dated 2020-11-25 and 0.1.3 dated 2021-09-03
bioseq-0.1.2/bioseq/R/experimental.R |only bioseq-0.1.3/bioseq/DESCRIPTION | 10 bioseq-0.1.3/bioseq/MD5 | 48 ++-- bioseq-0.1.3/bioseq/NEWS.md | 8 bioseq-0.1.3/bioseq/R/seq_biological_operations.R | 1 bioseq-0.1.3/bioseq/R/seq_fuzzy_operations.R |only bioseq-0.1.3/bioseq/R/seq_misc_operations.R | 3 bioseq-0.1.3/bioseq/R/seq_string_operation.R | 73 +++++- bioseq-0.1.3/bioseq/build/vignette.rds |binary bioseq-0.1.3/bioseq/inst/doc/intro-bioseq.html | 62 +---- bioseq-0.1.3/bioseq/inst/doc/ref_database.R | 2 bioseq-0.1.3/bioseq/inst/doc/ref_database.Rmd | 4 bioseq-0.1.3/bioseq/inst/doc/ref_database.html | 180 ++++++--------- bioseq-0.1.3/bioseq/man/figures/bioseq_bio_op.gddraw | 2 bioseq-0.1.3/bioseq/man/figures/bioseq_format_fig.gddraw | 2 bioseq-0.1.3/bioseq/man/figures/old_bioseq_fig.gddraw | 2 bioseq-0.1.3/bioseq/man/seq-replace.Rd | 4 bioseq-0.1.3/bioseq/man/seq_count_pattern.Rd | 4 bioseq-0.1.3/bioseq/man/seq_crop_pattern.Rd | 34 ++ bioseq-0.1.3/bioseq/man/seq_detect_pattern.Rd | 25 +- bioseq-0.1.3/bioseq/man/seq_extract_pattern.Rd | 4 bioseq-0.1.3/bioseq/man/seq_remove_pattern.Rd | 4 bioseq-0.1.3/bioseq/man/seq_split_pattern.Rd | 4 bioseq-0.1.3/bioseq/tests/testthat/test-op-misc.R | 10 bioseq-0.1.3/bioseq/tests/testthat/test-op-string.R | 39 +++ bioseq-0.1.3/bioseq/vignettes/ref_database.Rmd | 4 26 files changed, 323 insertions(+), 206 deletions(-)
Title: Commodore Amiga File Format Handler
Description: Modern software often poorly support older file formats. This
package intends to handle many file formats that were native to the
antiquated Commodore Amiga machine. This package focuses on file types from
the older Amiga operating systems (<= 3.0). It will read and write specific
file formats and coerces them into more contemporary data.
Author: Pepijn de Vries [aut, cre, dtc]
Maintainer: Pepijn de Vries <pepijn.devries@outlook.com>
Diff between AmigaFFH versions 0.3.1 dated 2019-03-31 and 0.4.1 dated 2021-09-03
DESCRIPTION | 12 MD5 | 152 ++++--- NAMESPACE | 31 + NEWS | 14 R/AmigaFFH.r | 10 R/basic.r |only R/bitmapfont.r | 63 +- R/data.r | 40 + R/generic_support.r | 8 R/iff.0.r | 16 R/iff.8svx.r | 2 R/iff.ilbm.r | 13 R/system_configuration.r | 6 R/workbench_icon.r | 20 inst/ball.shp |only inst/demo.bas |only inst/r_logo.shp |only man/AmigaBasic-files.Rd |only man/AmigaBasic.Rd |only man/AmigaBasic.reserved.Rd |only man/AmigaBasicBMAP-io.Rd |only man/AmigaBasicBMAP.Rd |only man/AmigaBasicShape.Rd |only man/AmigaBitmapFont.Rd | 342 ++++++++------- man/AmigaFFH.Rd | 185 ++++---- man/AmigaIcon.Rd | 126 ++--- man/ExtractBasic.Rd |only man/IFFChunk-class.Rd | 185 ++++---- man/IFFChunk.Rd | 886 ++++++++++++++++++++--------------------- man/SysConfig.Rd | 126 ++--- man/WaveToIFF.Rd | 174 ++++---- man/amiga_display_keys.Rd | 60 +- man/amiga_display_modes.Rd | 90 ++-- man/amiga_monitors.Rd | 60 +- man/amiga_palettes.Rd | 66 +-- man/as.AmigaBasic.Rd |only man/as.AmigaBasicBMAP.Rd |only man/as.character.Rd |only man/as.raster.Rd | 283 +++++++------ man/as.raw.Rd | 178 ++++---- man/availableFontSizes.Rd | 95 ++-- man/bitmapToRaster.Rd | 203 ++++----- man/c.Rd | 161 ++++--- man/check.names.AmigaBasic.Rd |only man/colourToAmigaRaw.Rd | 167 ++++--- man/deltaFibonacciCompress.Rd | 222 +++++----- man/dither.Rd | 233 +++++----- man/fontName.Rd | 125 ++--- man/font_example.Rd | 72 +-- man/getAmigaBitmapFont.Rd | 108 ++-- man/getIFFChunk.Rd | 187 ++++---- man/hardwareSprite-class.Rd | 144 +++--- man/ilbm8lores.iff.Rd | 72 +-- man/index.colours.Rd | 235 +++++----- man/interpretIFFChunk.Rd | 151 +++--- man/names.AmigaBasic.Rd |only man/packBitmap.Rd | 181 ++++---- man/play.Rd | 106 ++-- man/plot.Rd | 220 +++++----- man/rasterToAmigaBasicShape.Rd |only man/rasterToAmigaBitmapFont.Rd | 393 +++++++++--------- man/rasterToBitmap.Rd | 258 ++++++----- man/rasterToHWSprite.Rd | 140 +++--- man/rasterToIFF.Rd | 188 ++++---- man/rawToAmigaBasic.Rd |only man/rawToAmigaBasicBMAP.Rd |only man/rawToAmigaBasicShape.Rd |only man/rawToAmigaBitmapFont.Rd | 134 +++--- man/rawToAmigaBitmapFontSet.Rd | 160 +++---- man/rawToAmigaIcon.Rd | 126 +++-- man/rawToHWSprite.Rd | 165 ++++--- man/rawToIFFChunk.Rd | 139 +++--- man/rawToSysConfig.Rd | 122 +++-- man/read.AmigaBasic.Rd |only man/read.AmigaBasicShape.Rd |only man/read.AmigaBitmapFont.Rd | 165 ++++--- man/read.AmigaBitmapFontSet.Rd | 169 ++++--- man/read.AmigaIcon.Rd | 137 +++--- man/read.SysConfig.Rd | 121 +++-- man/read.iff.Rd | 134 +++--- man/simpleAmigaIcon.Rd | 149 +++--- man/simpleSysConfig.Rd | 102 ++-- man/timeval.Rd | 84 +-- man/write.AmigaBasic.Rd |only man/write.AmigaBasicShape.Rd |only man/write.AmigaBitmapFont.Rd | 213 +++++---- man/write.AmigaIcon.Rd | 137 +++--- man/write.SysConfig.Rd | 125 +++-- man/write.iff.Rd | 146 +++--- 89 files changed, 4955 insertions(+), 4382 deletions(-)
Title: Interface to the World Database on Protected Areas
Description: Fetch and clean data from the World Database on Protected
Areas (WDPA). Data is obtained from Protected Planet
<https://www.protectedplanet.net/en>.
Author: Jeffrey O Hanson [aut, cre]
Maintainer: Jeffrey O Hanson <jeffrey.hanson@uqconnect.edu.au>
Diff between wdpar versions 1.0.6 dated 2020-12-18 and 1.3.1 dated 2021-09-03
DESCRIPTION | 19 - MD5 | 42 +-- NEWS.md | 42 +++ R/geo.R | 13 - R/internal.R | 42 ++- R/wdpa_clean.R | 107 +++++++-- R/wdpa_fetch.R | 29 +- R/wdpa_read.R | 26 +- R/wdpa_url.R | 2 README.md | 134 ++++++++--- build/vignette.rds |binary inst/doc/wdpar.Rmd | 9 inst/doc/wdpar.html | 421 +++++++++++++++++++++--------------- man/figures/README-readme-map-1.png |binary man/wdpa_clean.Rd | 29 ++ man/wdpa_fetch.Rd | 23 + tests/testthat/test_geo.R | 2 tests/testthat/test_internal.R | 7 tests/testthat/test_wdpa_clean.R | 74 ++++++ tests/testthat/test_wdpa_fetch.R | 17 + tests/testthat/test_wdpa_read.R | 3 vignettes/wdpar.Rmd | 9 22 files changed, 737 insertions(+), 313 deletions(-)
Title: Extract, Analyze and Visualize Mutational Signatures for Genomic
Variations
Description: Genomic alterations including single nucleotide
substitution, copy number alteration, etc. are the major force for
cancer initialization and development. Due to the specificity of
molecular lesions caused by genomic alterations, we can generate
characteristic alteration spectra, called 'signature' (Wang, Shixiang,
et al. (2020) <DOI:10.1371/journal.pgen.1009557> & Alexandrov, Ludmil
B., et al. (2020) <DOI:10.1038/s41586-020-1943-3>). This package helps
users to extract, analyze and visualize signatures from genomic
alteration records, thus providing new insight into cancer study.
Author: Shixiang Wang [aut, cre] (<https://orcid.org/0000-0001-9855-7357>),
Ziyu Tao [aut] (<https://orcid.org/0000-0003-3272-1227>),
Huimin Li [aut] (<https://orcid.org/0000-0003-1683-9057>),
Tao Wu [aut] (<https://orcid.org/0000-0002-8999-9628>),
Xue-Song Liu [aut, ctb] (<https://orcid.org/0000-0002-7736-0077>),
Anand Mayakonda [ctb]
Maintainer: Shixiang Wang <w_shixiang@163.com>
Diff between sigminer versions 2.0.4 dated 2021-08-03 and 2.0.5 dated 2021-09-03
sigminer-2.0.4/sigminer/inst/extdata/human_hg19_gene_info.rds |only sigminer-2.0.5/sigminer/DESCRIPTION | 6 sigminer-2.0.5/sigminer/LICENSE | 4 sigminer-2.0.5/sigminer/MD5 | 434 - sigminer-2.0.5/sigminer/NAMESPACE | 311 - sigminer-2.0.5/sigminer/NEWS.md | 718 +- sigminer-2.0.5/sigminer/R/CN-mutex-classification-method.R | 1262 ++-- sigminer-2.0.5/sigminer/R/RcppExports.R | 26 sigminer-2.0.5/sigminer/R/add_h_arrow.R | 102 sigminer-2.0.5/sigminer/R/add_labels.R | 176 sigminer-2.0.5/sigminer/R/assert.R | 14 sigminer-2.0.5/sigminer/R/bayesianNMF.R | 558 +- sigminer-2.0.5/sigminer/R/best_practice.R | 2674 +++++----- sigminer-2.0.5/sigminer/R/best_practice_helper.R | 1944 +++---- sigminer-2.0.5/sigminer/R/class.R | 262 sigminer-2.0.5/sigminer/R/cosine.R | 64 sigminer-2.0.5/sigminer/R/data.R | 348 - sigminer-2.0.5/sigminer/R/enrich_component_strand_bias.R | 202 sigminer-2.0.5/sigminer/R/find_enriched_signature.R | 106 sigminer-2.0.5/sigminer/R/generate_matrices.R | 1784 +++--- sigminer-2.0.5/sigminer/R/get.R | 1010 +-- sigminer-2.0.5/sigminer/R/get_Aneuploidy_score.R | 218 sigminer-2.0.5/sigminer/R/get_adj_p.R | 204 sigminer-2.0.5/sigminer/R/get_bayesian_result.R | 162 sigminer-2.0.5/sigminer/R/get_cn_freq_table.R | 166 sigminer-2.0.5/sigminer/R/get_cn_ploidy.R | 100 sigminer-2.0.5/sigminer/R/get_genome_annotation.R | 112 sigminer-2.0.5/sigminer/R/get_group_comparison.R | 260 sigminer-2.0.5/sigminer/R/get_groups.R | 474 - sigminer-2.0.5/sigminer/R/get_intersect_size.R |only sigminer-2.0.5/sigminer/R/get_pLOH_score.R |only sigminer-2.0.5/sigminer/R/get_reconstructed_similarity.R | 146 sigminer-2.0.5/sigminer/R/get_shannon_diversity_index.R | 100 sigminer-2.0.5/sigminer/R/get_sig_cancer_type_index.R | 244 sigminer-2.0.5/sigminer/R/get_sig_db.R | 348 - sigminer-2.0.5/sigminer/R/get_sig_exposure.R | 140 sigminer-2.0.5/sigminer/R/get_sig_feature_association.R | 522 - sigminer-2.0.5/sigminer/R/get_sig_optimal_exposure.R | 104 sigminer-2.0.5/sigminer/R/get_sig_similarity.R | 602 +- sigminer-2.0.5/sigminer/R/get_sv.R | 594 +- sigminer-2.0.5/sigminer/R/get_tidy_association.R | 134 sigminer-2.0.5/sigminer/R/globalVariables.R | 20 sigminer-2.0.5/sigminer/R/group_enrichment.R | 498 - sigminer-2.0.5/sigminer/R/handle_hyper_mutation.R | 108 sigminer-2.0.5/sigminer/R/hello.R | 38 sigminer-2.0.5/sigminer/R/helper_create_chunks.R | 22 sigminer-2.0.5/sigminer/R/helper_create_colormap.R | 42 sigminer-2.0.5/sigminer/R/helper_derive_cn_features.R | 822 +-- sigminer-2.0.5/sigminer/R/helper_join_segments.R | 408 - 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Title: Mechanical Loading Prediction Through Accelerometer Data
Description: Functions to read, process and analyse accelerometer
data related to mechanical loading variables. This package is
developed and tested for use with raw accelerometer data from
triaxial 'ActiGraph' <https://actigraphcorp.com> accelerometers.
Author: Lucas Veras [aut, cre] (<https://orcid.org/0000-0003-0562-5803>)
Maintainer: Lucas Veras <lucasdsveras@gmail.com>
Diff between impactr versions 0.1.0 dated 2021-07-01 and 0.2.0 dated 2021-09-03
DESCRIPTION | 6 +-- MD5 | 29 +++++++------- NEWS.md |only R/predict.R | 20 ++++++++++ R/signal_processing.R | 6 +++ R/utils.R | 63 +++++++++++++++++++------------- README.md | 4 +- build/partial.rdb |binary inst/doc/impactr.R | 4 +- inst/doc/impactr.Rmd | 4 +- inst/doc/impactr.html | 46 ++++++++++++----------- man/define_region.Rd | 8 ++-- tests/testthat/test-read_acc.R | 4 +- tests/testthat/test-signal_processing.R | 7 +++ tests/testthat/test-utils.R | 29 +++++++++----- vignettes/impactr.Rmd | 4 +- 16 files changed, 151 insertions(+), 83 deletions(-)
Title: R Interface to Yandex Metrica API
Description: Allows work with 'Management API' for load counters, segments, filters,
user permissions and goals list from Yandex Metrica, 'Reporting API' allows you to get
information about the statistics of site visits and other data without
using the web interface, 'Logs API' allows to receive non-aggregated data and
'Compatible with Google Analytics Core Reporting API v3' allows
receive information about site traffic and other data using field names
from Google Analytics Core API. For more information see official
documents <https://yandex.ru/dev/metrika/doc/api2/concept/about-docpage>.
Author: Alexey Seleznev [aut, cre] (<https://orcid.org/0000-0003-0410-7385>),
Netpeak [cph]
Maintainer: Alexey Seleznev <selesnow@gmail.com>
Diff between rym versions 1.0.3 dated 2020-08-12 and 1.0.5 dated 2021-09-03
DESCRIPTION | 17 - MD5 | 68 +++--- NEWS.md | 9 R/rym_auth.R | 11 - R/rym_get_data.R | 20 + README.md | 11 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/intro-to-rym.Rmd | 10 inst/doc/intro-to-rym.html | 242 +++-------------------- inst/doc/rym-calls.html | 246 +++--------------------- inst/doc/rym-ga-api.Rmd | 4 inst/doc/rym-ga-api.html | 242 +++-------------------- inst/doc/rym-load-expense.html | 290 +++++----------------------- inst/doc/rym-load-offline-conversion.html | 260 ++++--------------------- inst/doc/rym-logs-api.Rmd | 2 inst/doc/rym-logs-api.html | 240 +++-------------------- inst/doc/rym-management-api.Rmd | 2 inst/doc/rym-management-api.html | 304 ++++++------------------------ inst/doc/rym-reporting-api.Rmd | 8 inst/doc/rym-reporting-api.html | 250 +++--------------------- man/rym-package.Rd | 8 man/rym_get_data.Rd | 2 man/rym_get_direct_clients.Rd | 2 man/rym_get_filters.Rd | 2 man/rym_get_ga.Rd | 6 man/rym_get_goals.Rd | 2 man/rym_get_logs.Rd | 6 man/rym_get_segments.Rd | 2 man/rym_users_grants.Rd | 2 vignettes/intro-to-rym.Rmd | 10 vignettes/rym-ga-api.Rmd | 4 vignettes/rym-logs-api.Rmd | 2 vignettes/rym-management-api.Rmd | 2 vignettes/rym-reporting-api.Rmd | 8 35 files changed, 469 insertions(+), 1825 deletions(-)
Title: Encode "License-Plates" from Sequences and Decode Them Back
Description: It can be used to create/encode molecular "license-plates" from sequences and to also decode the "license-plates" back to sequences. While initially created for transfer RNA-derived small fragments (tRFs), this tool can be used for any genomic sequences including but not limited to: tRFs, microRNAs, etc. The detailed information can reference to Pliatsika V, Loher P, Telonis AG, Rigoutsos I (2016) <doi:10.1093/bioinformatics/btw194>. It can also be used to annotate tRFs. The detailed information can reference to Loher P, Telonis AG, Rigoutsos I (2017) <doi:10.1038/srep41184>.
Author: Shanliang Zhong [aut, cre]
Maintainer: Shanliang Zhong <slzhong@foxmail.com>
Diff between MINTplates versions 1.0.0 dated 2021-08-13 and 1.0.1 dated 2021-09-03
MINTplates-1.0.0/MINTplates/man/deseq.Rd |only MINTplates-1.0.0/MINTplates/man/enseq.Rd |only MINTplates-1.0.1/MINTplates/DESCRIPTION | 8 MINTplates-1.0.1/MINTplates/MD5 | 19 - MINTplates-1.0.1/MINTplates/NAMESPACE | 7 MINTplates-1.0.1/MINTplates/R/MINTplates.R | 303 ++++++++++++++++-------- MINTplates-1.0.1/MINTplates/R/sysdata.rda |binary MINTplates-1.0.1/MINTplates/man/annotate_tRF.Rd |only MINTplates-1.0.1/MINTplates/man/deseqs.Rd | 2 MINTplates-1.0.1/MINTplates/man/enseqs.Rd | 2 MINTplates-1.0.1/MINTplates/man/exclusive.Rd |only MINTplates-1.0.1/MINTplates/man/source_tRNA.Rd |only MINTplates-1.0.1/MINTplates/man/source_tRNA2.Rd |only MINTplates-1.0.1/MINTplates/man/tRFtype.Rd |only 14 files changed, 225 insertions(+), 116 deletions(-)
Title: A friendly MCMC framework
Description: Provides a friendly (flexible) Markov Chain Monte Carlo (MCMC)
framework for implementing Metropolis-Hastings algorithm in a modular way
allowing users to specify automatic convergence checker, personalized
transition kernels, and out-of-the-box multiple MCMC chains using
parallel computing. Most of the methods implemented in this package can
be found in Brooks et al. (2011, ISBN 9781420079425). Among the methods
included, we have: Haario (2001) <doi:10.1007/s11222-011-9269-5>
Adaptive Metropolis, Vihola (2012) <doi:10.1007/s11222-011-9269-5>
Robust Adaptive Metropolis, and Thawornwattana et
al. (2018) <doi:10.1214/17-BA1084> Mirror transition kernels.
Author: George Vega Yon [aut, cre] (<https://orcid.org/0000-0002-3171-0844>),
Paul Marjoram [ctb, ths] (<https://orcid.org/0000-0003-0824-7449>),
National Cancer Institute (NCI) [fnd] (Grant Number 5P01CA196569-02),
Fabian Scheipl [rev] (JOSS reviewer,
<https://orcid.org/0000-0001-8172-3603>)
Maintainer: George Vega Yon <g.vegayon@gmail.com>
Diff between fmcmc versions 0.4-0 dated 2020-09-01 and 0.5-0 dated 2021-09-03
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Title: Event Prediction for Time-to-Event Endpoints
Description: Implements the hybrid framework for event prediction described in Fang & Zheng (2011, <doi:10.1016/j.cct.2011.05.013>). To estimate the survival function the event prediction is based on, a piecewise exponential hazard function is fit to the time-to-event data to infer the potential change points. Prior to the last identified change point, the survival function is estimated using Kaplan-Meier, and the tail after the change point is fit using piecewise exponential.
Author: Kaspar Rufibach
Maintainer: Kaspar Rufibach <kaspar.rufibach@roche.com>
Diff between eventTrack versions 1.0.0 dated 2021-05-10 and 1.0.1 dated 2021-09-03
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eventTrack-1.0.1/eventTrack/vignettes/eventTrack_cache/html/unnamed-chunk-9_da38a677daf09df84d59c7a710ecdcfd.rdx |only 109 files changed, 108 insertions(+), 94 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-04-24 3.0-1
2018-02-22 3.0-0
2013-10-10 2.1-2
2012-05-20 2.1-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-08-03 1.3.1
2021-06-15 1.3
2020-10-21 1.2.3
2020-07-13 1.2.2
2020-07-11 1.2.1
2020-07-10 1.2.0
2020-03-21 1.1.2
2019-11-06 1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-08-20 0.8.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-12-05 1.1-1
2016-11-17 1.1-0
2015-01-26 1.0-0
2013-08-19 0.3-1
2013-03-19 0.1-2
2012-05-20 0.1-1
Title: Tidy Interface to 'data.table'
Description: A tidy interface to 'data.table' that is 'rlang' compatible,
giving users the speed of 'data.table' with the clean syntax of the tidyverse.
Author: Mark Fairbanks [aut, cre],
Abdessabour Moutik [ctb],
Matt Carlson [ctb],
Ivan Leung [ctb],
Ross Kennedy [ctb]
Maintainer: Mark Fairbanks <mark.t.fairbanks@gmail.com>
Diff between tidytable versions 0.6.4 dated 2021-07-31 and 0.6.5 dated 2021-09-03
DESCRIPTION | 6 ++-- MD5 | 29 +++++++++++---------- NAMESPACE | 2 + NEWS.md | 9 ++++++ R/dt.R | 2 - R/enframe.R | 10 +++---- R/filter.R | 6 +--- R/fread-fwrite.R |only R/n_distinct.R | 2 - R/pivot_wider.R | 2 - R/slice.R | 38 +++------------------------ R/utils-general.R | 49 +++++++++++++++++++----------------- man/dt.Rd | 2 - man/fread..Rd |only tests/testthat/test-fread.R |only tests/testthat/test-slice.R | 9 +++++- tests/testthat/test-unnest_longer.R | 21 +++++++++++++++ 17 files changed, 101 insertions(+), 86 deletions(-)
Title: Joint Feature Screening via Sparse MLE
Description: Feature screening is a powerful tool in processing ultrahigh dimensional data. It attempts to screen out most irrelevant features in preparation for a more elaborate analysis. Xu and Chen (2014)<doi:10.1080/01621459.2013.879531> proposed an effective screening method SMLE, which naturally incorporates the joint effects among features in the screening process. This package provides an efficient implementation of SMLE-screening for high-dimensional linear, logistic, and Poisson models. The package also provides a function for conducting accurate post-screening feature selection based on an iterative hard-thresholding procedure and a user-specified selection criterion.
Author: Qianxiang Zang [aut, cre],
Chen Xu [aut],
Kelly Burkett [aut],
Maintainer: Qianxiang Zang <qzang023@uottawa.ca>
Diff between SMLE versions 1.1.1 dated 2021-05-09 and 1.2.3 dated 2021-09-03
DESCRIPTION | 15 + MD5 | 61 +++--- NAMESPACE | 123 +++++++------ R/Gen_Data.R | 45 +++-- R/SMLE.R | 248 ++++++++++++++------------- R/coef.R | 50 ++++- R/ctg_fit.R | 264 ++++++++++++++--------------- R/dummy.R | 256 ++++++++++++++-------------- R/ebicc.r | 2 R/logLik.R | 29 ++- R/plot.selection.R | 9 - R/plot.smle.R | 82 ++++----- R/predict.R | 68 +++---- R/print.R | 181 +++++++++----------- R/smle_select.R | 147 +++++++++------- R/standardize.R | 28 +-- R/summary.R | 94 ++++------ R/synSNP.R |only R/ult.R | 444 +++++++++++++++++++++++++------------------------- R/vote.R |only data |only man/Gen_Data.Rd | 221 ++++++++++++------------ man/SMLE-package.Rd | 12 - man/SMLE.Rd | 96 ++++++---- man/coef.Rd | 19 +- man/logLik.Rd | 15 + man/plot.selection.Rd | 55 +++--- man/plot.smle.Rd | 74 ++++---- man/predict.Rd | 20 +- man/print.Rd | 18 +- man/smle_select.Rd | 244 ++++++++++++++------------- man/summary.Rd | 11 - man/synSNP.Rd |only man/vote.Rd |only 34 files changed, 1533 insertions(+), 1398 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-08-18 1.1.0
2020-07-07 1.0.1
2020-06-23 1.0.0
2019-01-25 0.1.2
2018-12-17 0.1.1
2018-10-19 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-03-26 0.4.2
2019-02-20 0.4.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-08-16 0.7.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-08-15 0.1.1
2021-02-26 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-08-09 4.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-02-14 1.0-4
2018-10-16 1.0-3
2017-07-03 1.0-2
2016-11-17 1.0-1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-08-16 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-06-29 1.2.1
2021-06-07 1.2.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-08-12 3.1.0
2021-06-18 3.0.7
2020-09-10 3.0.6
2020-07-30 3.0.5
2020-06-07 3.0.4
2020-03-23 3.0.3
2020-03-16 3.0.2
2020-01-07 3.0.1
2019-12-18 3.0.0
Title: PKPD, PBPK, and Systems Pharmacology Modeling Tools
Description: Complete work flow for the analysis of pharmacokinetic pharmacodynamic (PKPD), physiologically-based pharmacokinetic (PBPK) and systems pharmacology models including: creation of ordinary differential equation-based models, pooled parameter estimation, individual/population based simulations, rule-based simulations for clinical trial design and modeling assays, deployment with a customizable 'Shiny' app, and non-compartmental analysis. System-specific analysis templates can be generated and each element includes integrated reporting with 'PowerPoint' and 'Word'.
Author: John Harrold [aut, cre] (<https://orcid.org/0000-0003-2052-4373>)
Maintainer: John Harrold <john.m.harrold@gmail.com>
Diff between ubiquity versions 1.0.5 dated 2021-04-25 and 2.0.0 dated 2021-09-03
ubiquity-1.0.5/ubiquity/inst/ubinc/templates/org_functions.R |only ubiquity-1.0.5/ubiquity/inst/ubinc/templates/system.png |only ubiquity-1.0.5/ubiquity/man/md_to_officer.Rd |only ubiquity-1.0.5/ubiquity/man/md_to_oo.Rd |only ubiquity-1.0.5/ubiquity/man/system_fetch_report.Rd |only ubiquity-1.0.5/ubiquity/man/system_fetch_report_format.Rd |only ubiquity-1.0.5/ubiquity/man/system_glp_save.Rd |only ubiquity-1.0.5/ubiquity/man/system_report_doc_add_content.Rd |only ubiquity-1.0.5/ubiquity/man/system_report_doc_format_section.Rd |only ubiquity-1.0.5/ubiquity/man/system_report_doc_set_ph.Rd |only ubiquity-1.0.5/ubiquity/man/system_report_estimation.Rd |only ubiquity-1.0.5/ubiquity/man/system_report_glp.Rd |only ubiquity-1.0.5/ubiquity/man/system_report_init.Rd |only ubiquity-1.0.5/ubiquity/man/system_report_nca.Rd |only ubiquity-1.0.5/ubiquity/man/system_report_ph_content.Rd |only ubiquity-1.0.5/ubiquity/man/system_report_save.Rd |only ubiquity-1.0.5/ubiquity/man/system_report_set.Rd |only ubiquity-1.0.5/ubiquity/man/system_report_slide_content.Rd |only ubiquity-1.0.5/ubiquity/man/system_report_slide_section.Rd |only ubiquity-1.0.5/ubiquity/man/system_report_slide_title.Rd |only ubiquity-1.0.5/ubiquity/man/system_report_slide_two_col.Rd |only ubiquity-1.0.5/ubiquity/man/system_report_view_layout.Rd |only ubiquity-1.0.5/ubiquity/vignettes/report_template_layout.png |only ubiquity-2.0.0/ubiquity/DESCRIPTION | 15 ubiquity-2.0.0/ubiquity/MD5 | 152 ubiquity-2.0.0/ubiquity/NAMESPACE | 67 ubiquity-2.0.0/ubiquity/NEWS.md |only ubiquity-2.0.0/ubiquity/R/ubiquity.r | 4394 ++-------- ubiquity-2.0.0/ubiquity/README.md | 38 ubiquity-2.0.0/ubiquity/build/partial.rdb |binary ubiquity-2.0.0/ubiquity/build/vignette.rds |binary ubiquity-2.0.0/ubiquity/inst/CITATION |only ubiquity-2.0.0/ubiquity/inst/doc/Deployment.Rmd | 7 ubiquity-2.0.0/ubiquity/inst/doc/Deployment.html | 8 ubiquity-2.0.0/ubiquity/inst/doc/Estimation.R | 14 ubiquity-2.0.0/ubiquity/inst/doc/Estimation.Rmd | 55 ubiquity-2.0.0/ubiquity/inst/doc/Estimation.html | 56 ubiquity-2.0.0/ubiquity/inst/doc/Language.R | 9 ubiquity-2.0.0/ubiquity/inst/doc/Language.Rmd | 47 ubiquity-2.0.0/ubiquity/inst/doc/Language.html | 34 ubiquity-2.0.0/ubiquity/inst/doc/NCA.R | 42 ubiquity-2.0.0/ubiquity/inst/doc/NCA.Rmd | 70 ubiquity-2.0.0/ubiquity/inst/doc/NCA.html | 211 ubiquity-2.0.0/ubiquity/inst/doc/Reporting.R | 665 - ubiquity-2.0.0/ubiquity/inst/doc/Reporting.Rmd | 1009 -- ubiquity-2.0.0/ubiquity/inst/doc/Reporting.html | 1011 -- ubiquity-2.0.0/ubiquity/inst/doc/Simulation.R | 13 ubiquity-2.0.0/ubiquity/inst/doc/Simulation.Rmd | 19 ubiquity-2.0.0/ubiquity/inst/doc/Simulation.html | 142 ubiquity-2.0.0/ubiquity/inst/doc/Titration.Rmd | 19 ubiquity-2.0.0/ubiquity/inst/doc/Titration.html | 142 ubiquity-2.0.0/ubiquity/inst/ubinc/scripts/analysis_nca_md.R | 64 ubiquity-2.0.0/ubiquity/inst/ubinc/scripts/analysis_nca_sd.R | 31 ubiquity-2.0.0/ubiquity/inst/ubinc/scripts/analysis_nca_sparse.R | 32 ubiquity-2.0.0/ubiquity/inst/ubinc/scripts/analysis_parent.r | 12 ubiquity-2.0.0/ubiquity/inst/ubinc/scripts/analysis_parent_metabolite.r | 13 ubiquity-2.0.0/ubiquity/inst/ubinc/scripts/analysis_parent_metabolite_global.r | 13 ubiquity-2.0.0/ubiquity/inst/ubinc/scripts/analysis_parent_metabolite_nm_data.r | 15 ubiquity-2.0.0/ubiquity/inst/ubinc/scripts/make_report_PowerPoint.R | 442 - ubiquity-2.0.0/ubiquity/inst/ubinc/scripts/make_report_Word.R | 580 - ubiquity-2.0.0/ubiquity/inst/ubinc/scripts/ubiquity_fcns.R | 4394 ++-------- ubiquity-2.0.0/ubiquity/inst/ubinc/templates/jl_components.jl |only ubiquity-2.0.0/ubiquity/inst/ubinc/templates/r_analysis_estimation.R | 13 ubiquity-2.0.0/ubiquity/inst/ubinc/templates/r_nca.R | 27 ubiquity-2.0.0/ubiquity/inst/ubinc/templates/report.yaml |only ubiquity-2.0.0/ubiquity/inst/ubinc/templates/ubiquity_app.R | 10 ubiquity-2.0.0/ubiquity/inst/ubinc/templates/ubiquity_app_custom.R | 9 ubiquity-2.0.0/ubiquity/inst/ubinc/templates/ubiquity_server.R | 2 ubiquity-2.0.0/ubiquity/man/AUC_Bailers_method.Rd | 3 ubiquity-2.0.0/ubiquity/man/system_fetch_rpt_officer_object.Rd |only ubiquity-2.0.0/ubiquity/man/system_fetch_rpt_onbrand_object.Rd |only ubiquity-2.0.0/ubiquity/man/system_glp_scenario.Rd | 2 ubiquity-2.0.0/ubiquity/man/system_rpt_add_doc_content.Rd |only ubiquity-2.0.0/ubiquity/man/system_rpt_add_slide.Rd |only ubiquity-2.0.0/ubiquity/man/system_rpt_estimation.Rd |only ubiquity-2.0.0/ubiquity/man/system_rpt_nca.Rd |only ubiquity-2.0.0/ubiquity/man/system_rpt_read_template.Rd |only ubiquity-2.0.0/ubiquity/man/system_rpt_save_report.Rd |only ubiquity-2.0.0/ubiquity/man/system_rpt_template_details.Rd |only ubiquity-2.0.0/ubiquity/man/system_set_rpt_officer_object.Rd |only ubiquity-2.0.0/ubiquity/man/system_set_rpt_onbrand_object.Rd |only ubiquity-2.0.0/ubiquity/vignettes/Deployment.Rmd | 7 ubiquity-2.0.0/ubiquity/vignettes/Estimation-parent-op.png |binary ubiquity-2.0.0/ubiquity/vignettes/Estimation-parent-tc.png |binary ubiquity-2.0.0/ubiquity/vignettes/Estimation.Rmd | 55 ubiquity-2.0.0/ubiquity/vignettes/Language.Rmd | 47 ubiquity-2.0.0/ubiquity/vignettes/NCA.Rmd | 70 ubiquity-2.0.0/ubiquity/vignettes/NCA_presim.RData |binary ubiquity-2.0.0/ubiquity/vignettes/Reporting.RData |only ubiquity-2.0.0/ubiquity/vignettes/Reporting.Rmd | 1009 -- ubiquity-2.0.0/ubiquity/vignettes/Simulation.Rmd | 19 ubiquity-2.0.0/ubiquity/vignettes/Simulation_cfg_orig.RData |only ubiquity-2.0.0/ubiquity/vignettes/Simulation_som_multiple.RData |binary ubiquity-2.0.0/ubiquity/vignettes/Simulation_som_single.RData |binary ubiquity-2.0.0/ubiquity/vignettes/Titration.Rmd | 19 ubiquity-2.0.0/ubiquity/vignettes/myOrg.yaml |only ubiquity-2.0.0/ubiquity/vignettes/nca_reporting-sparse.png |binary ubiquity-2.0.0/ubiquity/vignettes/ubiquity_hex.png |only 98 files changed, 5323 insertions(+), 9804 deletions(-)
Title: Drop-in Replacements for Base String Functions Powered by
'stringi'
Description: English is the native language for only 5% of the World population.
Also, only 17% of us can understand this text. Moreover, the Latin alphabet
is the main one for merely 36% of the total.
The early computer era, now a very long time ago, was dominated by the US.
Due to the proliferation of the internet, smartphones, social media, and
other technologies and communication platforms, this is no longer the case.
This package replaces base R string functions (such as grep(),
tolower(), sprintf(), and strptime()) with ones that fully
support the Unicode standards related to natural language and
date-time processing. It also fixes some long-standing inconsistencies,
and introduces some new, useful features.
Thanks to 'ICU' (International Components for Unicode) and 'stringi',
they are fast, reliable, and portable across different platforms.
Author: Marek Gagolewski [aut, cre, cph]
(<https://orcid.org/0000-0003-0637-6028>)
Maintainer: Marek Gagolewski <marek@gagolewski.com>
Diff between stringx versions 0.1.3 dated 2021-08-05 and 0.2.2 dated 2021-09-03
DESCRIPTION | 16 +- MD5 | 25 +-- NAMESPACE | 27 +++ NEWS | 26 +++ R/ISOdatetime.R |only R/about_stringx.R | 2 R/strptime.R | 287 ++++++++++++++++++++++++++++++++++----- inst/realtest/ISOdatetime-all.R |only inst/realtest/casemap-all.R | 31 ++-- inst/realtest/casemap-stringx.R | 11 + inst/realtest/strptime-all.R | 26 ++- inst/realtest/strptime-stringx.R | 60 ++++++++ man/ISOdatetime.Rd |only man/about_stringx.Rd | 2 man/strptime.Rd | 120 ++++++++++++++-- 15 files changed, 546 insertions(+), 87 deletions(-)
Title: A Lightweight Wrapper for 'Slurm'
Description: 'Slurm', Simple Linux Utility for Resource Management
<https://slurm.schedmd.com/>, is a popular 'Linux' based software used to
schedule jobs in 'HPC' (High Performance Computing) clusters. This R package
provides a specialized lightweight wrapper of 'Slurm' with a syntax similar to
that found in the 'parallel' R package. The package also includes a method for
creating socket cluster objects spanning multiple nodes that can be used with
the 'parallel' package.
Author: George Vega Yon [aut, cre] (<https://orcid.org/0000-0002-3171-0844>),
Paul Marjoram [ctb, ths] (<https://orcid.org/0000-0003-0824-7449>),
National Cancer Institute (NCI) [fnd] (Grant Number 5P01CA196569-02),
Michael Schubert [rev] (JOSS reviewer,
<https://orcid.org/0000-0002-6862-5221>),
Michel Lang [rev] (JOSS reviewer,
<https://orcid.org/0000-0001-9754-0393>)
Maintainer: George Vega Yon <g.vegayon@gmail.com>
Diff between slurmR versions 0.4-1 dated 2020-04-22 and 0.5-1 dated 2021-09-03
DESCRIPTION | 11 MD5 | 91 ++--- NAMESPACE | 7 NEWS.md | 86 +++- R/Slurm_EvalQ.R | 17 R/Slurm_Map.R | 5 R/Slurm_collect.R | 21 - R/Slurm_lapply.R | 7 R/bash.R | 17 R/docker.R |only R/expand_array_indexes.R | 12 R/makeSlurmCluster.R | 40 +- R/options.R | 232 ++++++++----- R/rscript.R | 32 + R/sacct_safe.R |only R/sbatch.R | 23 - R/slurmR.R | 15 R/slurm_job.R | 52 ++ R/sourceSlurm.R | 18 - R/status.R | 3 R/utils.R | 39 +- R/wait.R | 4 README.md | 602 ++++++++++++++++++---------------- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 15 inst/NEWS |only inst/doc/debugging-re-submission.html | 37 +- inst/doc/getting-started.html | 43 ++ inst/doc/working-with-slurm.Rmd | 2 inst/doc/working-with-slurm.html | 41 ++ inst/docker |only inst/tinytest/test-Slurm_collect.R | 10 inst/tinytest/test-makeSlurmCluster.R | 11 inst/tinytest/test-slurm_job-class.R | 16 inst/tinytest/test-sourceSlurm.R | 2 inst/tinytest/test-utils.R | 5 man/JOB_STATE_CODES.Rd | 4 man/Slurm_EvalQ.Rd | 7 man/Slurm_lapply.Rd | 12 man/makeSlurmCluster.Rd | 19 - man/opts_slurmR.Rd | 20 + man/sbatch.Rd | 10 man/slurmR.Rd | 8 man/slurmr_docker.Rd |only man/sourceSlurm.Rd | 2 tests/tinytest.R | 11 vignettes/working-with-slurm.Rmd | 2 48 files changed, 1060 insertions(+), 551 deletions(-)
Title: r Client for OpenRefine API
Description: 'OpenRefine' (formerly 'Google Refine') is a popular, open source data cleaning software. This package enables users to programmatically trigger data transfer between R and 'OpenRefine'. Available functionality includes project import, export and deletion.
Author: VP Nagraj [aut, cre]
Maintainer: VP Nagraj <nagraj@nagraj.net>
Diff between rrefine versions 1.1.0 dated 2020-10-07 and 1.1.1 dated 2021-09-03
DESCRIPTION | 10 - MD5 | 10 - NEWS.md | 4 R/utils.R | 8 - build/vignette.rds |binary inst/doc/rrefine-vignette.html | 306 +++-------------------------------------- 6 files changed, 44 insertions(+), 294 deletions(-)
Title: Simple Interactive Controls for R using the 'tcltk' Package
Description: A set of functions to build simple
GUI controls for R functions. These are built on the 'tcltk' package.
Uses could include changing a parameter on a graph by animating it
with a slider or a "doublebutton", up to more sophisticated control
panels.
Some functions for specific graphical tasks, referred to as 'cartoons',
are provided.
Author: Bowman, Bowman, Gibson and Crawford
Maintainer: Adrian Bowman <adrian.bowman@glasgow.ac.uk>
Diff between rpanel versions 1.1-4 dated 2018-05-07 and 1.1-5 dated 2021-09-03
rpanel-1.1-4/rpanel/demo/rp.table.r |only rpanel-1.1-5/rpanel/ChangeLog | 60 +++---- rpanel-1.1-5/rpanel/DESCRIPTION | 9 - rpanel-1.1-5/rpanel/MD5 | 84 +++++----- rpanel-1.1-5/rpanel/NAMESPACE | 170 ++++++++++---------- rpanel-1.1-5/rpanel/NEWS.md |only rpanel-1.1-5/rpanel/R/combo.r | 183 +++++++++++----------- rpanel-1.1-5/rpanel/R/notebook.r | 65 ++++--- rpanel-1.1-5/rpanel/R/rp-anova.R | 73 ++++---- rpanel-1.1-5/rpanel/R/rp-colour-key.r | 4 rpanel-1.1-5/rpanel/R/rp-plot4d.r | 2 rpanel-1.1-5/rpanel/R/rp-regression.r | 12 - rpanel-1.1-5/rpanel/R/rp-regression2.r | 247 ++++++++++++++---------------- rpanel-1.1-5/rpanel/R/rp-tables.r | 4 rpanel-1.1-5/rpanel/R/rpanel.r | 8 rpanel-1.1-5/rpanel/demo/00Index | 41 ++-- rpanel-1.1-5/rpanel/demo/rp.assign.r | 9 - rpanel-1.1-5/rpanel/demo/rp.block.r | 4 rpanel-1.1-5/rpanel/demo/rp.image.r | 36 ++-- rpanel-1.1-5/rpanel/inst/CITATION | 82 ++++----- rpanel-1.1-5/rpanel/inst/history.txt | 3 rpanel-1.1-5/rpanel/man/CofE.Rd | 51 +++--- rpanel-1.1-5/rpanel/man/SO2.Rd | 40 ++-- rpanel-1.1-5/rpanel/man/luthor.Rd | 66 ++++---- rpanel-1.1-5/rpanel/man/rp.block.Rd | 94 +++++------ rpanel-1.1-5/rpanel/man/rp.bubbleplot.Rd | 74 ++++---- rpanel-1.1-5/rpanel/man/rp.colour.key.Rd | 66 ++++---- rpanel-1.1-5/rpanel/man/rp.combo.Rd | 142 ++++++++--------- rpanel-1.1-5/rpanel/man/rp.do.Rd | 102 ++++++------ rpanel-1.1-5/rpanel/man/rp.geosim.Rd | 6 rpanel-1.1-5/rpanel/man/rp.likelihood.Rd | 76 ++++----- rpanel-1.1-5/rpanel/man/rp.notebook.Rd | 5 rpanel-1.1-5/rpanel/man/rp.plot4d.Rd | 6 rpanel-1.1-5/rpanel/man/rp.power.Rd | 72 ++++---- rpanel-1.1-5/rpanel/man/rp.radiogroup.Rd | 150 +++++++++--------- rpanel-1.1-5/rpanel/man/rp.rmplot.Rd | 98 +++++------ rpanel-1.1-5/rpanel/man/rp.surface.Rd | 76 ++++----- rpanel-1.1-5/rpanel/man/rp.tables.Rd | 4 rpanel-1.1-5/rpanel/man/rp.textentry.Rd | 182 +++++++++++----------- rpanel-1.1-5/rpanel/man/rp.timer.Rd | 90 +++++----- rpanel-1.1-5/rpanel/man/rp.var.get.Rd | 54 +++--- rpanel-1.1-5/rpanel/man/rp.var.put.Rd | 54 +++--- rpanel-1.1-5/rpanel/man/rpanel.package.Rd | 4 rpanel-1.1-5/rpanel/man/worldbank.Rd | 34 ++-- 44 files changed, 1328 insertions(+), 1314 deletions(-)
Title: Partial Least Squares and Principal Component Regression
Description: Multivariate regression methods
Partial Least Squares Regression (PLSR), Principal Component
Regression (PCR) and Canonical Powered Partial Least Squares (CPPLS).
Author: Kristian Hovde Liland [aut, cre],
Bjørn-Helge Mevik [aut],
Ron Wehrens [aut],
Paul Hiemstra [ctb]
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>
Diff between pls versions 2.7-3 dated 2020-08-07 and 2.8-0 dated 2021-09-03
DESCRIPTION | 31 MD5 | 159 - NAMESPACE | 197 +- R/cppls.fit.R | 894 ++++++----- R/crossval.R | 861 ++++++---- R/cvsegments.R | 287 ++- R/data.R |only R/extract.R | 627 +++++-- R/jackknife.R | 314 ++- R/kernelpls.fit.R | 357 ++-- R/msc.R | 98 - R/mvr.R | 484 ++++- R/mvrVal.R | 568 ++++-- R/mvr_wrappers.R | 76 R/ncomp.R | 230 +- R/oscorespls.fit.R | 404 ++-- R/plots.R | 2271 +++++++++++++++++---------- R/pls-package.R |only R/pls.options.R | 150 + R/predict.mvr.R | 201 +- R/simpls.fit.R | 313 ++- R/stdize.R | 160 + R/summaries.R | 207 +- R/svdpc.fit.R | 205 +- R/widekernelpls.fit.R | 401 ++-- build/vignette.rds |binary inst/NEWS.Rd | 848 +++++----- inst/doc/pls-manual.R | 564 +++--- inst/doc/pls-manual.Rnw | 2518 +++++++++++++++---------------- inst/doc/pls-manual.pdf |binary man/biplot.mvr.Rd | 80 man/coef.mvr.Rd | 212 +- man/coefplot.Rd | 273 +-- man/cppls.fit.Rd | 215 +- man/crossval.Rd | 199 +- man/cvsegments.Rd | 126 - man/delete.intercept.Rd | 26 man/gasoline.Rd | 32 man/jack.test.Rd | 114 - man/kernelpls.fit.Rd | 134 - man/mayonnaise.Rd | 38 man/msc.Rd | 73 man/mvr.Rd | 371 ++-- man/mvrCv.Rd | 247 +-- man/mvrVal.Rd | 260 +-- man/naExcludeMvr.Rd | 61 man/oliveoil.Rd | 38 man/oscorespls.fit.Rd | 143 - man/plot.mvr.Rd | 67 man/pls.Rd |only man/pls.options.Rd | 148 - man/predict.mvr.Rd | 128 - man/predplot.Rd | 228 +- man/scoreplot.Rd | 382 ++-- man/scores.Rd | 71 man/selectNcomp.Rd | 148 + man/simpls.fit.Rd | 126 - man/stdize.Rd | 94 - man/summary.mvr.Rd | 72 man/svdpc.fit.Rd | 112 - man/validationplot.Rd | 221 +- man/var.jack.Rd | 158 - man/widekernelpls.fit.Rd | 175 +- man/yarn.Rd | 36 tests/RUnit/common/create_refmodels.R | 54 tests/RUnit/common/runit.CV.R | 356 ++-- tests/RUnit/common/runit.algorithms.R | 136 - tests/RUnit/common/runit.jackknife.R | 158 - tests/RUnit/common/runit.mvrVal.R | 862 +++++----- tests/RUnit/common/runit.options.R | 110 - tests/RUnit/common/runit.predict.R | 254 +-- tests/RUnit/common/utils.R | 40 tests/RUnit/import/runit.fit.R | 42 tests/RUnit/import/runit.options.R | 36 tests/RUnit/library/runit.CV.R | 226 +- tests/RUnit/library/runit.mvr_wrappers.R | 90 - tests/test_import.R | 64 tests/test_library.R | 60 tests/testthat.R | 8 tests/testthat/test_basic_pls.R | 246 +-- vignettes/pls-manual.Rnw | 2518 +++++++++++++++---------------- vignettes/pls-manual.bib | 488 +++--- 82 files changed, 13445 insertions(+), 10536 deletions(-)
Title: Amazon Web Services Software Development Kit
Description: Interface to Amazon Web Services <https://aws.amazon.com>,
including storage, database, and compute services, such as 'Simple
Storage Service' ('S3'), 'DynamoDB' 'NoSQL' database, and 'Lambda'
functions-as-a-service.
Author: David Kretch [aut, cre],
Adam Banker [aut],
Amazon.com, Inc. [cph]
Maintainer: David Kretch <david.kretch@gmail.com>
Diff between paws versions 0.1.11 dated 2021-03-13 and 0.1.12 dated 2021-09-03
DESCRIPTION | 21 MD5 | 283 +-- NAMESPACE | 279 +-- NEWS.md | 16 R/paws.R | 2652 ++++++++++++++++++++++++++++++++- man/acm.Rd | 134 - man/acmpca.Rd | 172 +- man/apigateway.Rd | 348 ++-- man/apigatewaymanagementapi.Rd | 118 - man/apigatewayv2.Rd | 244 +-- man/applicationautoscaling.Rd | 218 +- man/applicationinsights.Rd | 180 +- man/appmesh.Rd | 204 +- man/appstream.Rd |only man/athena.Rd | 186 +- man/autoscaling.Rd | 242 +-- man/autoscalingplans.Rd | 158 + man/backup.Rd | 206 +- man/batch.Rd | 174 +- man/budgets.Rd | 224 +- man/cloud9.Rd |only man/clouddirectory.Rd | 246 +-- man/cloudformation.Rd | 248 +-- man/cloudfront.Rd | 256 +-- man/cloudhsm.Rd | 154 - man/cloudhsmv2.Rd | 130 - man/cloudsearch.Rd | 174 +- man/cloudsearchdomain.Rd | 130 - man/cloudtrail.Rd | 178 +- man/cloudwatch.Rd | 190 +- man/cloudwatchevents.Rd | 216 +- man/cloudwatchlogs.Rd | 246 +-- man/codebuild.Rd |only man/codecommit.Rd |only man/codedeploy.Rd |only man/codepipeline.Rd |only man/codestar.Rd |only man/cognitoidentity.Rd | 178 +- man/cognitoidentityprovider.Rd | 314 +-- man/cognitosync.Rd | 170 +- man/comprehend.Rd | 226 +- man/comprehendmedical.Rd | 146 - man/configservice.Rd | 306 +-- man/connect.Rd | 308 +-- man/costandusagereportservice.Rd | 140 - man/costexplorer.Rd | 188 +- man/datapipeline.Rd | 182 +- man/dax.Rd | 154 - man/directconnect.Rd | 230 +- man/directoryservice.Rd | 248 +-- man/dlm.Rd | 128 - man/docdb.Rd | 184 +- man/dynamodb.Rd | 300 +-- man/dynamodbstreams.Rd | 120 - man/ec2.Rd | 1008 ++++++------ man/ec2instanceconnect.Rd | 118 - man/ecr.Rd | 198 +- man/ecs.Rd | 242 +-- man/efs.Rd | 176 +- man/eks.Rd | 204 +- man/elasticache.Rd | 252 +-- man/elasticbeanstalk.Rd | 228 +- man/elasticsearchservice.Rd | 198 +- man/elb.Rd | 236 +- man/elbv2.Rd | 246 +-- man/emr.Rd | 200 +- man/eventbridge.Rd | 216 +- man/firehose.Rd | 134 - man/fms.Rd | 168 +- man/fsx.Rd | 150 - man/glacier.Rd | 236 +- man/globalaccelerator.Rd | 540 +++--- man/glue.Rd | 414 ++--- man/guardduty.Rd | 254 +-- man/health.Rd | 206 +- man/iam.Rd | 396 ++-- man/inspector.Rd | 198 +- man/kafka.Rd | 158 + man/kinesis.Rd | 160 + man/kinesisanalytics.Rd | 156 + man/kinesisanalyticsv2.Rd | 162 +- man/kms.Rd | 334 ++-- man/lambda.Rd | 238 +- man/lexmodelbuildingservice.Rd | 190 +- man/lexruntimeservice.Rd | 132 - man/licensemanager.Rd | 182 +- man/lightsail.Rd | 418 ++--- man/machinelearning.Rd | 156 + man/macie.Rd | 140 - man/marketplacecommerceanalytics.Rd | 104 - man/marketplaceentitlementservice.Rd | 126 - man/marketplacemetering.Rd | 200 +- man/mq.Rd | 152 - man/mturk.Rd | 178 +- man/neptune.Rd | 266 +-- man/opsworks.Rd | 366 ++-- man/opsworkscm.Rd | 252 +-- man/organizations.Rd | 210 +- man/personalize.Rd | 188 +- man/personalizeevents.Rd | 112 - man/personalizeruntime.Rd | 104 - man/pi.Rd | 152 - man/pinpoint.Rd | 324 ++-- man/pinpointemail.Rd | 250 +-- man/pinpointsmsvoice.Rd | 116 - man/polly.Rd | 132 - man/pricing.Rd | 164 +- man/quicksight.Rd | 310 +-- man/ram.Rd | 162 +- man/rds.Rd | 446 ++--- man/rdsdataservice.Rd | 132 - man/redshift.Rd | 330 ++-- man/rekognition.Rd | 224 +- man/resourcegroups.Rd | 192 +- man/resourcegroupstaggingapi.Rd | 468 ++--- man/route53.Rd | 244 +-- man/route53domains.Rd | 158 + man/route53resolver.Rd | 242 +-- man/s3.Rd | 297 +-- man/s3control.Rd | 178 +- man/sagemaker.Rd | 578 +++---- man/sagemakerruntime.Rd | 102 - man/secretsmanager.Rd | 10 man/securityhub.Rd | 274 +-- man/serverlessapplicationrepository.Rd | 194 +- man/servicecatalog.Rd | 280 +-- man/servicediscovery.Rd | 166 +- man/servicequotas.Rd | 144 - man/ses.Rd | 258 +-- man/sfn.Rd | 182 +- man/shield.Rd | 172 +- man/simpledb.Rd | 156 + man/sns.Rd | 200 +- man/sqs.Rd | 208 +- man/ssm.Rd | 402 ++--- man/storagegateway.Rd | 6 man/sts.Rd | 168 +- man/support.Rd | 256 +-- man/swf.Rd | 202 +- man/textract.Rd | 116 - man/transcribeservice.Rd | 154 - man/translate.Rd | 130 - man/waf.Rd | 292 +-- man/wafregional.Rd | 306 +-- man/workdocs.Rd |only man/worklink.Rd |only man/workspaces.Rd |only man/xray.Rd |only 148 files changed, 17802 insertions(+), 14326 deletions(-)
Title: Non-Negative Tensor Decomposition
Description: Some functions for performing non-negative matrix factorization, non-negative CANDECOMP/PARAFAC (CP) decomposition, non-negative Tucker decomposition, and generating toy model data. See Andrzej Cichock et al (2009) <doi:10.1002/9780470747278> and the reference section of GitHub README.md <https://github.com/rikenbit/nnTensor>, for details of the methods.
Author: Koki Tsuyuzaki [aut, cre],
Manabu Ishii [aut],
Itoshi Nikaido [aut]
Maintainer: Koki Tsuyuzaki <k.t.the-answer@hotmail.co.jp>
Diff between nnTensor versions 1.1.4 dated 2021-08-17 and 1.1.5 dated 2021-09-03
DESCRIPTION | 6 ++--- MD5 | 14 +++++++----- NAMESPACE | 3 +- R/plotTensor2D.R |only R/plotTensor3D.R | 59 +++++++++++++++++++++++++++++++++++++--------------- build/partial.rdb |binary inst/NEWS | 5 ++++ man/plotTensor2D.Rd |only man/plotTensor3D.Rd | 14 ++++++++++-- 9 files changed, 72 insertions(+), 29 deletions(-)
Title: Maximum Likelihood Analysis of Animal Movement Behavior Using
Multivariate Hidden Markov Models
Description: Extended tools for analyzing telemetry data using generalized hidden Markov models. Features of momentuHMM (pronounced ``momentum'') include data pre-processing and visualization, fitting HMMs to location and auxiliary biotelemetry or environmental data, biased and correlated random walk movement models, hierarchical HMMs, multiple imputation for incorporating location measurement error and missing data, user-specified design matrices and constraints for covariate modelling of parameters, random effects, decoding of the state process, visualization of fitted models, model checking and selection, and simulation. See McClintock and Michelot (2018) <doi:10.1111/2041-210X.12995>.
Author: Brett McClintock, Theo Michelot
Maintainer: Brett McClintock <brett.mcclintock@noaa.gov>
Diff between momentuHMM versions 1.5.3 dated 2021-07-07 and 1.5.4 dated 2021-09-03
DESCRIPTION | 8 ++--- MD5 | 24 ++++++++--------- NEWS | 17 ++++++++++++ R/CIreal.R | 22 +++++++++++----- R/momentuHMM_utils.R | 7 +++-- build/partial.rdb |binary inst/doc/momentuHMM.pdf |binary man/CIreal.Rd | 2 - src/RcppExports.cpp | 4 +- src/XBloop.cpp | 4 +- src/densities.h | 65 ++++++++++++++++++++++++++++-------------------- src/getDM.cpp | 2 - src/nLogLike.cpp | 16 +++++++---- 13 files changed, 109 insertions(+), 62 deletions(-)
Title: Matrices in Data Frames
Description: Provides functions to collapse a tidy data frame into matrices in a data frame
and expand a data frame of matrices into a tidy data frame.
Author: Matthew Heun [aut, cre] (<https://orcid.org/0000-0002-7438-214X>)
Maintainer: Matthew Heun <matthew.heun@me.com>
Diff between matsindf versions 0.3.6 dated 2020-08-24 and 0.3.8 dated 2021-09-03
matsindf-0.3.6/matsindf/tests/testthat/test_collapse.R |only matsindf-0.3.6/matsindf/tests/testthat/test_expand.R |only matsindf-0.3.6/matsindf/tests/testthat/test_matsindf_apply.R |only matsindf-0.3.6/matsindf/tests/testthat/test_utilities.R |only matsindf-0.3.6/matsindf/vignettes/matsindf.md |only matsindf-0.3.8/matsindf/DESCRIPTION | 10 matsindf-0.3.8/matsindf/LICENSE | 2 matsindf-0.3.8/matsindf/MD5 | 35 matsindf-0.3.8/matsindf/NEWS.md | 26 matsindf-0.3.8/matsindf/R/matsindf_apply.R | 2 matsindf-0.3.8/matsindf/README.md | 23 matsindf-0.3.8/matsindf/build/vignette.rds |binary matsindf-0.3.8/matsindf/inst/CITATION | 8 matsindf-0.3.8/matsindf/inst/WORDLIST |only matsindf-0.3.8/matsindf/inst/doc/matsindf.R | 2 matsindf-0.3.8/matsindf/inst/doc/matsindf.Rmd | 4 matsindf-0.3.8/matsindf/inst/doc/matsindf.html | 727 ++++------ matsindf-0.3.8/matsindf/inst/doc/midf_apply_primer.html | 734 ++++------- matsindf-0.3.8/matsindf/tests/spelling.R |only matsindf-0.3.8/matsindf/tests/testthat/test-collapse.R |only matsindf-0.3.8/matsindf/tests/testthat/test-expand.R |only matsindf-0.3.8/matsindf/tests/testthat/test-matsindf_apply.R |only matsindf-0.3.8/matsindf/tests/testthat/test-utilities.R |only matsindf-0.3.8/matsindf/vignettes/matsindf.Rmd | 4 24 files changed, 632 insertions(+), 945 deletions(-)
Title: Linking Geographic Information Systems, Remote Sensing and Other
Command Line Tools
Description: Functions to simplify the linking of open source GIS and remote sensing related command line interfaces.
Author: Chris Reudenbach [cre, aut],
Tim Appelhans [ctb]
Maintainer: Chris Reudenbach <reudenbach@uni-marburg.de>
Diff between link2GI versions 0.4-5 dated 2020-12-07 and 0.4-7 dated 2021-09-03
DESCRIPTION | 10 +-- MD5 | 30 +++++----- NEWS | 9 +++ NEWS.md | 10 +++ R/gdalControls.R | 4 + R/linkOTB.R | 1 R/otbControls.R | 5 + R/parseOTB.R | 133 +++++++++++++++++++++++++++++++++------------- build/vignette.rds |binary data/rgb.rda |binary inst/doc/link2GI6.Rmd | 1 inst/doc/link2GI6.html | 3 - man/parseOTBAlgorithms.Rd | 6 +- man/parseOTBFunction.Rd | 8 +- man/runOTB.Rd | 46 +++++++++++++-- vignettes/link2GI6.Rmd | 1 16 files changed, 190 insertions(+), 77 deletions(-)
Title: Analysis and Presentation of Social Scientific Data
Description: This is a collection of tools that the author (Jacob) has written
for the purpose of more efficiently understanding and sharing the results of
(primarily) regression analyses. There are also a number of miscellaneous
functions for statistical and programming purposes. Just about everything
supports models from the survey package.
Author: Jacob A. Long [aut, cre] (<https://orcid.org/0000-0002-1582-6214>)
Maintainer: Jacob A. Long <jacob.long@sc.edu>
Diff between jtools versions 2.1.3 dated 2021-03-12 and 2.1.4 dated 2021-09-03
DESCRIPTION | 6 MD5 | 14 NEWS.md | 4 build/partial.rdb |binary inst/doc/effect_plot.html | 24 - inst/doc/summ.html | 66 +-- inst/doc/svycor.html | 20 - tests/testthat/test-export-summs.R | 616 ++++++++++++++++++------------------- 8 files changed, 372 insertions(+), 378 deletions(-)
Title: Full Reporting of Interaction Analyses
Description: Produces a publication-ready table that includes all effect estimates necessary for full reporting effect modification and interaction analysis as recommended by Knol and Vanderweele (2012) [<doi:10.1093/ije/dyr218>].
It also estimates confidence interval for the trio of additive interaction measures using the delta method (see Hosmer and Lemeshow (1992), [<doi:10.1097/00001648-199209000-00012>]), variance recovery method (see Zou (2008), [<doi:10.1093/aje/kwn104>]), or percentile bootstrapping (see Assmann et al. (1996), [<doi:10.1097/00001648-199605000-00012>]).
Author: Babatunde Alli
Maintainer: Babatunde Alli <babatunde.alli@mail.mcgill.ca>
Diff between interactionR versions 0.1.2 dated 2021-05-09 and 0.1.3 dated 2021-09-03
DESCRIPTION | 8 - MD5 | 23 ++-- NEWS.md | 5 + R/interactionR.R | 29 +++++- R/interactionR_boot.R | 21 ++++ R/interactionR_delta.R | 26 +++++ R/interactionR_mover.R | 26 +++++ R/interactionR_table.R | 190 +++++++++++++++++++++++++++-------------- README.md | 212 ++++++++++++++++++++++++++++++++++++++-------- build/partial.rdb |binary man/figures |only man/interactionR_table.Rd | 4 12 files changed, 423 insertions(+), 121 deletions(-)
Title: Learning Interactions via Hierarchical Group-Lasso
Regularization
Description: Group-Lasso INTERaction-NET. Fits linear pairwise-interaction models that satisfy strong hierarchy: if an interaction coefficient is estimated to be nonzero, then its two associated main effects also have nonzero estimated coefficients. Accommodates categorical variables (factors) with arbitrary numbers of levels, continuous variables, and combinations thereof. Implements the machinery described in the paper "Learning interactions via hierarchical group-lasso regularization" (JCGS 2015, Volume 24, Issue 3). Michael Lim & Trevor Hastie (2015) <DOI:10.1080/10618600.2014.938812>.
Author: Michael Lim, Trevor Hastie
Maintainer: Michael Lim <michael626@gmail.com>
Diff between glinternet versions 1.0.11 dated 2020-10-10 and 1.0.12 dated 2021-09-03
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- src/c_routines.c | 5 +++-- 3 files changed, 9 insertions(+), 8 deletions(-)