Title: A Minimal Tool Set for Gathering USDA Quick Stat Data for
Analysis and Visualization
Description: Provides a consistent API to pull United States
Department of Agriculture census and survey data from the National
Agricultural Statistics Service (NASS) QuickStats service
<https://quickstats.nass.usda.gov>.
Author: Brad Lindblad [aut, cre],
Michael Thomas [ctb],
Alex Mindeman [ctb]
Maintainer: Brad Lindblad <bradley.lindblad@gmail.com>
Diff between tidyUSDA versions 0.2.8 dated 2020-06-30 and 0.2.9 dated 2020-07-24
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 3 +++ R/getQuickstat.R | 2 +- inst/doc/using_tidyusda.html | 4 ++-- 5 files changed, 14 insertions(+), 11 deletions(-)
Title: Radiation Safety
Description: Provides functions for radiation safety, also known as "radiation protection" and "radiological control". The science of radiation protection is called "health physics" and its engineering functions are called "radiological engineering". Functions in this package cover many of the computations needed by radiation safety professionals. Examples include: obtaining updated calibration and source check values for radiation monitors to account for radioactive decay in a reference source, simulating instrument readings to better understand measurement uncertainty, correcting instrument readings for geometry and ambient atmospheric conditions. Many of these functions are described in Johnson and Kirby (2011, ISBN-13: 978-1609134198). Utilities are also included for developing inputs and processing outputs with radiation transport codes, such as MCNP, a general-purpose Monte Carlo N-Particle code that can be used for neutron, photon, electron, or coupled neutron/photon/electron transport (Werner et. al. (2018) <doi:10.2172/1419730>).
Author: Mark Hogue <mark.hogue.chp@gmail.com>
Maintainer: Mark Hogue <mark.hogue.chp@gmail.com>
Diff between radsafer versions 2.2.1 dated 2020-06-10 and 2.2.2 dated 2020-07-24
DESCRIPTION | 6 ++--- MD5 | 18 +++++++-------- R/RN_search_phot_by_E.R | 2 - R/mcnp_si_sp_RD.R | 38 ++++++++++++++++++++++----------- R/mcnp_si_sp_hist.R | 13 ++++++++++- R/mcnp_si_sp_hist_scan.R | 8 ++++++ build/vignette.rds |binary inst/doc/Introduction_to_radsafer.html | 36 ++++++++++++++++++++++--------- man/RN_search_phot_by_E.Rd | 2 - man/mcnp_si_sp_RD.Rd | 11 ++++++--- 10 files changed, 93 insertions(+), 41 deletions(-)
Title: A Model Comparison Perspective
Description: Accompanies "Designing experiments and
analyzing data: A model comparison perspective" (3rd ed.) by
Maxwell, Delaney, & Kelley (2018; Routledge).
Contains all of the data sets in the book's chapters and
end-of-chapter exercises. Information about the book is available at
<http://www.DesigningExperiments.com>.
Author: Scott Maxwell [aut],
Harold Delaney [aut],
Ken Kelley [aut, cre]
Maintainer: Ken Kelley <kkelley@nd.edu>
Diff between AMCP versions 1.0.0 dated 2020-02-13 and 1.0.1 dated 2020-07-24
DESCRIPTION | 11 MD5 | 283 +- R/AMCP.R | 56 R/documentation.R | 3386 ++++++++++++++--------------- README.md |only man/AMCP-package.Rd | 28 man/chapter_10_exercise_14.Rd | 14 man/chapter_10_exercise_7.Rd | 14 man/chapter_10_exercise_9.Rd | 14 man/chapter_10_table_5.Rd | 12 man/chapter_10_table_9.Rd | 12 man/chapter_11_exercise_17.Rd | 14 man/chapter_11_exercise_18.Rd | 14 man/chapter_11_exercise_19.Rd | 14 man/chapter_11_exercise_21.Rd | 12 man/chapter_11_exercise_22.Rd | 12 man/chapter_11_exercise_23.Rd | 12 man/chapter_11_exercise_24.Rd | 12 man/chapter_11_exercise_3.Rd | 14 man/chapter_11_exercise_5.Rd | 14 man/chapter_11_table_1.Rd | 12 man/chapter_11_table_19.Rd | 12 man/chapter_11_table_20.Rd | 12 man/chapter_11_table_4.Rd | 12 man/chapter_11_table_5.Rd | 12 man/chapter_12_exercise_17.Rd | 12 man/chapter_12_exercise_18.Rd | 12 man/chapter_12_exercise_19.Rd | 12 man/chapter_12_exercise_21.Rd | 12 man/chapter_12_exercise_9.Rd | 12 man/chapter_12_table_1.Rd | 14 man/chapter_12_table_11.Rd | 12 man/chapter_12_table_15.Rd | 12 man/chapter_12_table_21.Rd | 12 man/chapter_12_table_7.Rd | 12 man/chapter_12_table_9.Rd | 12 man/chapter_13_exercise_10.Rd | 12 man/chapter_13_exercise_13.Rd | 12 man/chapter_13_exercise_14.Rd | 12 man/chapter_13_exercise_22.Rd | 12 man/chapter_13_exercise_23.Rd | 12 man/chapter_13_exercise_24.Rd | 12 man/chapter_13_exercise_25.Rd | 12 man/chapter_13_exercise_7.Rd | 12 man/chapter_13_table_1.Rd | 12 man/chapter_13_table_12.Rd | 22 man/chapter_13_table_14.Rd | 12 man/chapter_13_table_2.Rd | 12 man/chapter_13_table_5.Rd | 12 man/chapter_14_exercise_10.Rd | 12 man/chapter_14_exercise_14.Rd | 12 man/chapter_14_exercise_15.Rd | 12 man/chapter_14_exercise_21.Rd | 12 man/chapter_14_exercise_22.Rd | 12 man/chapter_14_table_1.Rd | 12 man/chapter_14_table_10.Rd | 12 man/chapter_14_table_3.Rd | 14 man/chapter_14_table_4.Rd | 12 man/chapter_14_table_5.Rd | 12 man/chapter_14_table_8.Rd | 14 man/chapter_15_exercise_16.Rd | 12 man/chapter_15_exercise_17.Rd | 12 man/chapter_15_exercise_18.Rd | 12 man/chapter_15_exercise_18_univariate.Rd | 12 man/chapter_15_exercise_19.Rd | 12 man/chapter_15_exercise_19_univariate.Rd | 12 man/chapter_15_table_1.Rd | 12 man/chapter_16_exercise_5.Rd | 12 man/chapter_16_exercise_7.Rd | 12 man/chapter_16_exercise_9.Rd | 12 man/chapter_16_table_1.Rd | 12 man/chapter_16_table_4.Rd | 12 man/chapter_1_exercise_18.Rd | 16 man/chapter_1_exercise_19.Rd | 14 man/chapter_1_exercise_21.Rd | 14 man/chapter_1_exercise_22.Rd | 14 man/chapter_1_exercise_23.Rd | 19 man/chapter_1_table_1.Rd | 14 man/chapter_3_exercise_10.Rd | 14 man/chapter_3_exercise_11.Rd | 14 man/chapter_3_exercise_19.Rd | 14 man/chapter_3_exercise_20.Rd | 14 man/chapter_3_exercise_21.Rd | 14 man/chapter_3_exercise_22.Rd | 14 man/chapter_3_exercise_9.Rd | 14 man/chapter_3_table_1.Rd | 12 man/chapter_3_table_3.Rd | 12 man/chapter_3_table_7_raw.Rd | 12 man/chapter_3_table_9_raw.Rd | 12 man/chapter_4_exercise_11.Rd | 12 man/chapter_4_exercise_12.Rd | 14 man/chapter_4_exercise_13.Rd | 14 man/chapter_4_table_1.Rd | 12 man/chapter_4_table_7.Rd | 12 man/chapter_5_exercise_10.Rd | 14 man/chapter_5_exercise_16.Rd | 14 man/chapter_5_exercise_5.Rd | 14 man/chapter_5_table_4.Rd | 12 man/chapter_6_exercise_10.Rd | 14 man/chapter_6_exercise_14.Rd | 14 man/chapter_6_exercise_16.Rd | 14 man/chapter_6_table_1.Rd | 12 man/chapter_7_exercise_12.Rd | 14 man/chapter_7_exercise_13.Rd | 14 man/chapter_7_exercise_14.Rd | 14 man/chapter_7_exercise_15.Rd | 14 man/chapter_7_exercise_18.Rd | 14 man/chapter_7_exercise_19.Rd | 14 man/chapter_7_exercise_22.Rd | 14 man/chapter_7_exercise_23.Rd | 14 man/chapter_7_exercise_24.Rd | 14 man/chapter_7_exercise_25.Rd | 14 man/chapter_7_exercise_6.Rd | 14 man/chapter_7_exercise_9.Rd | 14 man/chapter_7_table_1.Rd | 12 man/chapter_7_table_11.Rd | 12 man/chapter_7_table_15.Rd | 26 man/chapter_7_table_23.Rd | 14 man/chapter_7_table_5.Rd | 12 man/chapter_7_table_9.Rd | 12 man/chapter_8_exercise_15.Rd | 14 man/chapter_8_exercise_16.Rd | 14 man/chapter_8_exercise_17.Rd | 14 man/chapter_8_exercise_18.Rd | 14 man/chapter_8_exercise_19.Rd | 14 man/chapter_8_table_12.Rd | 12 man/chapter_9_exercise_14.Rd | 14 man/chapter_9_exercise_15.Rd | 14 man/chapter_9_exercise_16.Rd | 14 man/chapter_9_exercise_4.Rd | 14 man/chapter_9_extension_exercise_1.Rd | 12 man/chapter_9_extension_exercise_2.Rd | 26 man/chapter_9_extension_figures_4_and_5.Rd | 12 man/chapter_9_extension_table_1.Rd | 12 man/chapter_9_table_1.Rd | 12 man/chapter_9_table_11.Rd | 12 man/chapter_9_table_7.Rd | 12 man/tutorial_1_table_1.Rd | 14 man/tutorial_2_table_1.Rd | 26 man/tutorial_3a_table_1.Rd | 14 man/tutorial_3a_table_2.Rd | 14 man/tutorial_3a_table_4.Rd | 12 man/tutorial_3a_table_5.Rd | 12 143 files changed, 2933 insertions(+), 2648 deletions(-)
Title: Average Bioequivalence with Expanding Limits (ABEL)
Description: Performs comparative bioavailability calculations for Average Bioequivalence with
Expanding Limits (ABEL). Implemented are 'Method A' and 'Method B' and the detection of outliers.
If the design allows, assessment of the empiric Type I Error and iteratively adjusting alpha to
control the consumer risk.
Average Bioequivalence - optionally with a tighter (narrow therapeutic index drugs) or wider
acceptance range (Gulf Cooperation Council, South Africa: Cmax) - is implemented as well.
Author: Helmut Schütz [aut, cre] (<https://orcid.org/0000-0002-1167-7880>),
Michael Tomashevskiy [ctb],
Detlew Labes [ctb] (<https://orcid.org/0000-0003-2169-426X>)
Maintainer: Helmut Schütz <helmut.schuetz@bebac.at>
Diff between replicateBE versions 1.0.14 dated 2020-04-09 and 1.0.15 dated 2020-07-24
DESCRIPTION | 8 MD5 | 37 +- NAMESPACE | 2 NEWS.md | 116 ++------- R/ABE.R | 10 R/CV.calc.R | 24 + R/get.data.R | 38 +- R/info.env.R | 9 R/method.A.R | 14 - R/method.B.R | 14 - README.md | 81 +++--- build/partial.rdb |binary build/vignette.rds |binary inst/doc/vignette.Rmd | 64 ++--- inst/doc/vignette.html | 627 +++++++++++++++++++++++++------------------------ man/ABE.Rd | 26 -- man/figures |only man/method.A.Rd | 40 +-- man/method.B.Rd | 37 +- vignettes/vignette.Rmd | 64 ++--- 20 files changed, 592 insertions(+), 619 deletions(-)
Title: Processing of Model Parameters
Description: Utilities for processing the parameters of various
statistical models. Beyond computing p values, CIs, and other indices
for a wide variety of models (see support list of insight; Lüdecke,
Waggoner & Makowski (2019) <doi:10.21105/joss.01412>), this package
implements features like bootstrapping or simulating of parameters and
models, feature reduction (feature extraction and variable selection)
as well as functions to describe data and variable characteristics
(e.g. skewness, kurtosis, smoothness or distribution).
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>),
Dominique Makowski [aut] (<https://orcid.org/0000-0001-5375-9967>),
Mattan S. Ben-Shachar [aut] (<https://orcid.org/0000-0002-4287-4801>),
Indrajeet Patil [aut] (<https://orcid.org/0000-0003-1995-6531>),
Søren Højsgaard [aut],
Zen J. Lau [ctb]
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between parameters versions 0.8.0 dated 2020-06-08 and 0.8.2 dated 2020-07-24
parameters-0.8.0/parameters/R/format_bf.R |only parameters-0.8.0/parameters/R/format_number.R |only parameters-0.8.0/parameters/R/format_p.R |only parameters-0.8.0/parameters/R/format_pd.R |only parameters-0.8.0/parameters/R/format_rope.R |only parameters-0.8.0/parameters/man/format_bf.Rd |only parameters-0.8.0/parameters/man/format_number.Rd |only parameters-0.8.0/parameters/man/format_p.Rd |only parameters-0.8.0/parameters/man/format_pd.Rd |only parameters-0.8.0/parameters/man/format_rope.Rd |only parameters-0.8.2/parameters/DESCRIPTION | 19 parameters-0.8.2/parameters/MD5 | 199 ++++------ parameters-0.8.2/parameters/NAMESPACE | 26 + parameters-0.8.2/parameters/NEWS.md | 25 + parameters-0.8.2/parameters/R/bootstrap_model.R | 2 parameters-0.8.2/parameters/R/bootstrap_parameters.R | 2 parameters-0.8.2/parameters/R/check_clusterstructure.R | 2 parameters-0.8.2/parameters/R/check_heterogeneity.R | 12 parameters-0.8.2/parameters/R/check_multimodal.R | 13 parameters-0.8.2/parameters/R/ci.R | 44 ++ parameters-0.8.2/parameters/R/ci_wald.R | 13 parameters-0.8.2/parameters/R/convert_efa_to_cfa.R | 7 parameters-0.8.2/parameters/R/demean.R | 20 - parameters-0.8.2/parameters/R/dof.R | 61 ++- parameters-0.8.2/parameters/R/dof_kenward.R | 8 parameters-0.8.2/parameters/R/equivalence_test.R | 31 + parameters-0.8.2/parameters/R/extract_parameters.R | 62 +-- parameters-0.8.2/parameters/R/factor_analysis.R | 22 - parameters-0.8.2/parameters/R/format_order.R | 8 parameters-0.8.2/parameters/R/format_parameters.R | 78 ++- parameters-0.8.2/parameters/R/model_parameters.R | 3 parameters-0.8.2/parameters/R/model_parameters.aov.R | 4 parameters-0.8.2/parameters/R/model_parameters.gam.R | 10 parameters-0.8.2/parameters/R/model_parameters.glht.R |only parameters-0.8.2/parameters/R/model_parameters.psych.R | 46 +- parameters-0.8.2/parameters/R/model_parameters.rma.R | 67 +++ parameters-0.8.2/parameters/R/model_parameters_default.R | 37 + parameters-0.8.2/parameters/R/model_parameters_mixed.R | 22 + parameters-0.8.2/parameters/R/n_clusters.R | 2 parameters-0.8.2/parameters/R/n_factors.R | 2 parameters-0.8.2/parameters/R/p_value.R | 116 ++++- parameters-0.8.2/parameters/R/p_value_betwithin.R | 4 parameters-0.8.2/parameters/R/parameters_table.R | 10 parameters-0.8.2/parameters/R/parameters_type.R | 22 + parameters-0.8.2/parameters/R/principal_components.R | 27 - parameters-0.8.2/parameters/R/print.parameters_model.R | 10 parameters-0.8.2/parameters/R/re-exports.R |only parameters-0.8.2/parameters/R/rescale_weights.R | 14 parameters-0.8.2/parameters/R/robust_estimation.R | 40 -- parameters-0.8.2/parameters/R/select_parameters.R | 35 + parameters-0.8.2/parameters/R/select_parameters.stanreg.R | 4 parameters-0.8.2/parameters/R/standard_error.R | 127 ++++-- parameters-0.8.2/parameters/README.md | 12 parameters-0.8.2/parameters/build/partial.rdb |binary parameters-0.8.2/parameters/build/vignette.rds |binary parameters-0.8.2/parameters/inst/WORDLIST | 15 parameters-0.8.2/parameters/inst/doc/demean.R | 35 + parameters-0.8.2/parameters/inst/doc/demean.Rmd | 48 ++ parameters-0.8.2/parameters/inst/doc/demean.html | 48 ++ parameters-0.8.2/parameters/inst/doc/efa_cfa.html | 2 parameters-0.8.2/parameters/inst/doc/model_parameters.Rmd | 2 parameters-0.8.2/parameters/inst/doc/model_parameters.html | 48 +- parameters-0.8.2/parameters/inst/doc/parameters_reduction.Rmd | 2 parameters-0.8.2/parameters/inst/doc/parameters_reduction.html | 2 parameters-0.8.2/parameters/inst/doc/parameters_selection.R | 19 parameters-0.8.2/parameters/inst/doc/parameters_selection.Rmd | 31 + parameters-0.8.2/parameters/inst/doc/parameters_selection.html | 98 +++- parameters-0.8.2/parameters/man/bootstrap_parameters.Rd | 2 parameters-0.8.2/parameters/man/check_clusterstructure.Rd | 2 parameters-0.8.2/parameters/man/degrees_of_freedom.Rd | 123 +++--- parameters-0.8.2/parameters/man/demean.Rd | 11 parameters-0.8.2/parameters/man/equivalence_test.lm.Rd | 22 - parameters-0.8.2/parameters/man/factor_analysis.Rd | 163 ++++---- parameters-0.8.2/parameters/man/format_order.Rd | 2 parameters-0.8.2/parameters/man/model_parameters.Rd | 101 ++--- parameters-0.8.2/parameters/man/model_parameters.default.Rd | 16 parameters-0.8.2/parameters/man/model_parameters.gam.Rd | 10 parameters-0.8.2/parameters/man/model_parameters.glht.Rd |only parameters-0.8.2/parameters/man/model_parameters.merMod.Rd | 1 parameters-0.8.2/parameters/man/model_parameters.principal.Rd | 46 +- parameters-0.8.2/parameters/man/n_factors.Rd | 166 ++++---- parameters-0.8.2/parameters/man/p_value.Rd | 4 parameters-0.8.2/parameters/man/p_value_betwithin.Rd | 4 parameters-0.8.2/parameters/man/principal_components.Rd | 25 - parameters-0.8.2/parameters/man/reexports.Rd | 9 parameters-0.8.2/parameters/man/rescale_weights.Rd | 10 parameters-0.8.2/parameters/man/select_parameters.Rd | 20 - parameters-0.8.2/parameters/man/standard_error_robust.Rd | 168 ++++---- parameters-0.8.2/parameters/tests/testthat/test-gee.R | 10 parameters-0.8.2/parameters/tests/testthat/test-glmer.R | 23 - parameters-0.8.2/parameters/tests/testthat/test-lme.R | 116 ++--- parameters-0.8.2/parameters/tests/testthat/test-model_parameters.BFBayesFactor.R | 34 + parameters-0.8.2/parameters/tests/testthat/test-model_parameters.glht.R |only parameters-0.8.2/parameters/tests/testthat/test-model_parameters.lme.R | 28 - parameters-0.8.2/parameters/tests/testthat/test-model_parameters.mfx.R | 116 ++--- parameters-0.8.2/parameters/tests/testthat/test-model_parameters_robust.R | 1 parameters-0.8.2/parameters/tests/testthat/test-model_parameters_std.R | 2 parameters-0.8.2/parameters/tests/testthat/test-model_parameters_std_mixed.R | 3 parameters-0.8.2/parameters/tests/testthat/test-n_factors.R | 2 parameters-0.8.2/parameters/tests/testthat/test-p_value.R | 4 parameters-0.8.2/parameters/tests/testthat/test-panelr.R |only parameters-0.8.2/parameters/tests/testthat/test-pca.R | 2 parameters-0.8.2/parameters/tests/testthat/test-plm.R | 37 + parameters-0.8.2/parameters/tests/testthat/test-quantreg.R |only parameters-0.8.2/parameters/tests/testthat/test-rstanarm.R |only parameters-0.8.2/parameters/vignettes/demean.Rmd | 48 ++ parameters-0.8.2/parameters/vignettes/model_parameters.Rmd | 2 parameters-0.8.2/parameters/vignettes/parameters_reduction.Rmd | 2 parameters-0.8.2/parameters/vignettes/parameters_selection.Rmd | 31 + 109 files changed, 1961 insertions(+), 1023 deletions(-)
Title: Biochemically Intuitive Generalized Loewe Model
Description: Response surface methods for drug synergy analysis. Available
methods include generalized and classical Loewe formulations as well as Highest
Single Agent methodology. Response surfaces can be plotted in an interactive
3-D plot and formal statistical tests for presence of synergistic effects are
available. Implemented methods and tests are described in the article
"BIGL: Biochemically Intuitive Generalized Loewe null model for prediction
of the expected combined effect compatible with partial agonism and antagonism"
by Koen Van der Borght, Annelies Tourny, Rytis Bagdziunas, Olivier Thas,
Maxim Nazarov, Heather Turner, Bie Verbist & Hugo Ceulemans (2017)
<doi:10.1038/s41598-017-18068-5>.
Author: Heather Turner, Annelies Tourny, Olivier Thas, Maxim Nazarov, Rytis Bagdziunas
Maintainer: Maxim Nazarov <maxim.nazarov@openanalytics.eu>
Diff between BIGL versions 1.5.1 dated 2020-07-07 and 1.5.2 dated 2020-07-24
DESCRIPTION | 8 ++--- MD5 | 10 +++--- R/MarginalFit-methods.R | 23 ++++++++------- inst/NEWS | 2 + inst/doc/analysis.html | 68 +++++++++++++++++++++++----------------------- inst/doc/methodology.html | 4 +- 6 files changed, 59 insertions(+), 56 deletions(-)
Title: Bayesian Gaussian Graphical Models
Description: Fit Bayesian Gaussian graphical models. The methods are separated into
two Bayesian approaches for inference: hypothesis testing and estimation. There are
extensions for confirmatory hypothesis testing, comparing Gaussian graphical models,
and node wise predictability. These methods were recently introduced in the Gaussian
graphical model literature, including
Williams (2019) <doi:10.31234/osf.io/x8dpr>,
Williams and Mulder (2019) <doi:10.31234/osf.io/ypxd8>,
Williams, Rast, Pericchi, and Mulder (2019) <doi:10.31234/osf.io/yt386>.
Author: Donald Williams [aut, cre],
Joris Mulder [aut]
Maintainer: Donald Williams <drwwilliams@ucdavis.edu>
Diff between BGGM versions 2.0.1 dated 2020-07-23 and 2.0.2 dated 2020-07-24
DESCRIPTION | 9 MD5 | 12 R/estimate.R | 1640 +++++++++++++++++++++++------------------------ R/explore.default.R | 1498 +++++++++++++++++++++--------------------- build/partial.rdb |binary inst/doc/ppc_custom.html | 12 src/bggm_fast.cpp | 2 7 files changed, 1586 insertions(+), 1587 deletions(-)
Title: Univariate and Bivariate Latent Change Score Modeling
Description: Helper functions to implement univariate and bivariate latent change score models in R using the 'lavaan' package.
For details about Latent Change Score Modeling (LCSM) see McArdle (2009) <doi:10.1146/annurev.psych.60.110707.163612> and Grimm, An, McArdle, Zonderman and Resnick (2012) <doi:10.1080/10705511.2012.659627>.
The package automatically generates 'lavaan' syntax for different model specifications and varying timepoints.
The 'lavaan' syntax generated by this package can be returned and further specifications can be added manually.
Longitudinal plots as well as simplified path diagrams can be created to visualise data and model specifications.
Estimated model parameters and fit statistics can be extracted as data frames.
Data for different univariate and bivariate LCSM can be simulated by specifying estimates for model parameters to explore their effects.
This package combines the strengths of other R packages like 'lavaan', 'broom', and 'semPlot' by generating 'lavaan' syntax that helps these packages work together.
Author: Milan Wiedemann [aut, cre] (<https://orcid.org/0000-0003-1991-282X>),
Anke Ehlers [ths] (<https://orcid.org/0000-0002-8742-0192>),
Mental Health Research UK [fnd]
Maintainer: Milan Wiedemann <milan.wiedemann@gmail.com>
Diff between lcsm versions 0.1.1 dated 2020-06-05 and 0.1.2 dated 2020-07-24
DESCRIPTION | 12 - MD5 | 56 ++++---- NAMESPACE | 1 NEWS.md | 5 R/extract_fit.R | 7 - R/plot_lcsm.R | 5 R/plot_trajectories.R | 6 R/rename_vars.R | 6 README.md | 19 ++ build/vignette.rds |binary inst/CITATION | 4 inst/doc/v0-longitudinal-plots.html | 16 ++ inst/doc/v1-lavaan-syntax.R | 48 +++++-- inst/doc/v1-lavaan-syntax.Rmd | 57 ++++++-- inst/doc/v1-lavaan-syntax.html | 234 +++++++++++++++++++++++++++++++++--- inst/doc/v2-path-diagrams.R | 4 inst/doc/v2-path-diagrams.Rmd | 4 inst/doc/v2-path-diagrams.html | 22 ++- inst/doc/v3-extract-tutorial.R | 7 - inst/doc/v3-extract-tutorial.Rmd | 7 - inst/doc/v3-extract-tutorial.html | 181 ++++++++++++++------------- inst/doc/v4-simulate-data.html | 36 ++++- man/extract_fit.Rd | 3 man/plot_lcsm.Rd | 4 man/plot_trajectories.Rd | 6 man/rename_lcsm_vars.Rd | 8 - vignettes/v1-lavaan-syntax.Rmd | 57 ++++++-- vignettes/v2-path-diagrams.Rmd | 4 vignettes/v3-extract-tutorial.Rmd | 7 - 29 files changed, 598 insertions(+), 228 deletions(-)
Title: Enhancements for 'broom' and 'easystats' Package Families
Description: Provides helper functions that assist in data
analysis workflows involving regression analyses. The goal is to
combine the functionality offered by different set of packages
('broom', 'broom.mixed', 'parameters', and 'performance') through a
common syntax to return tidy dataframes containing model parameters
and performance measure summaries. The 'grouped_' variants of the
generics provides a convenient way to execute functions across a
combination of grouping variable(s) in a dataframe.
Author: Indrajeet Patil [aut, cre, cph]
(<https://orcid.org/0000-0003-1995-6531>)
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>
Diff between broomExtra versions 4.0.3 dated 2020-06-19 and 4.0.4 dated 2020-07-24
DESCRIPTION | 8 ++--- MD5 | 12 ++++---- NEWS.md | 4 ++ R/easystats_to_tidy_names.R | 2 + README.md | 50 +++++++++++++++++----------------- build/broomExtra.pdf |binary tests/testthat/test-hybrid_generics.R | 2 - 7 files changed, 42 insertions(+), 36 deletions(-)
Title: Compare the Goodness of Fit of Benford's and Blondeau Da Silva's
Digit Distributions to a Given Dataset
Description: Allows to compare the goodness of fit of Benford's and Blondeau Da Silva's digit distributions in a dataset. It is used to check whether the data distribution is consistent with theoretical distributions highlighted by Blondeau Da Silva or not (through the dat.distr() function): this ideal theoretical distribution must be at least approximately followed by the data for the use of Blondeau Da Silva's model to be well-founded. It also enables to plot histograms of digit distributions, both observed in the dataset and given by the two theoretical approaches (with the digit.ditr() function). Finally, it proposes to quantify the goodness of fit via Pearson's chi-squared test (with the chi2() function).
Author: Blondeau Da Silva Stephane
Maintainer: Blondeau Da Silva Stephane <Stephane.Blondeau-Da-Silva@ac-limoges.fr>
Diff between BeyondBenford versions 1.3 dated 2020-04-11 and 1.4 dated 2020-07-24
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ R/Blon.val.R | 2 +- R/Blon.val.sd.R | 2 +- R/chi2.R | 4 ++-- R/dat.distr.R | 2 +- build/partial.rdb |binary man/BeyondBenford-package.Rd | 2 +- man/Blon.val.Rd | 4 ++-- man/Blon.val.sd.Rd | 2 +- man/dat.distr.Rd | 2 +- man/digit.distr.Rd | 2 +- man/theor.distr.val.Rd | 2 +- 13 files changed, 28 insertions(+), 28 deletions(-)
More information about covidregionaldata at CRAN
Permanent link
Title: Bootstrap Unit Root Tests
Description: Set of functions to perform various bootstrap unit root tests for both individual time series
(including augmented Dickey-Fuller test and union tests), multiple time series and panel data; see
Palm, Smeekes and Urbain (2008) <doi:10.1111/j.1467-9892.2007.00565.x>,
Palm, Smeekes and Urbain (2011) <doi:10.1016/j.jeconom.2010.11.010>,
Moon and Perron (2012) <doi:10.1016/j.jeconom.2012.01.008>,
Smeekes and Taylor (2012) <doi:10.1017/S0266466611000387> and
Smeekes (2015) <doi:10.1111/jtsa.12110> for key references.
Author: Stephan Smeekes [cre, aut] (<https://orcid.org/0000-0002-0157-639X>),
Ines Wilms [aut]
Maintainer: Stephan Smeekes <s.smeekes@maastrichtuniversity.nl>
Diff between bootUR versions 0.1.0 dated 2020-06-25 and 0.2.0 dated 2020-07-24
DESCRIPTION | 10 - MD5 | 59 +++--- NAMESPACE | 4 NEWS.md |only R/RcppExports.R | 4 R/auxiliary.R | 69 +++++-- R/bootURtests.R | 336 +++++++++++++++++++++++++++++++---- README.md | 141 +++++++++++--- build/vignette.rds |binary inst/doc/bootUR-intro.R | 18 + inst/doc/bootUR-intro.Rmd | 47 ++++ inst/doc/bootUR-intro.html | 263 ++++++++++++++++----------- man/BSQTtest.Rd | 15 + man/bFDRtest.Rd | 12 - man/boot_df.Rd | 12 - man/boot_union.Rd | 13 - man/check_inputs.Rd | 6 man/check_missing_insample_values.Rd | 2 man/diff_mult.Rd |only man/do_tests_and_bootstrap.Rd | 7 man/find_nonmissing_subsample.Rd | 2 man/iADFtest.Rd | 15 + man/order_integration.Rd |only man/paneltest.Rd | 14 - man/plot_missing_values.Rd |only man/plot_order_integration.Rd |only src/Makevars | 7 src/Makevars.win | 3 src/RcppExports.cpp | 14 - src/bootURfunctions.cpp | 180 ++++++++++-------- tests/testthat/test_diff.R |only tests/testthat/test_inputs.R | 1 tests/testthat/test_replicability.R |only vignettes/bootUR-intro.Rmd | 47 ++++ 34 files changed, 941 insertions(+), 360 deletions(-)
Title: Estimators of Multiple-Site Dissimilarity Indices for the
Assessment of Beta Diversity
Description: Implement the multiple-site dissimilarity indices of Simpson, Sorensen
and nestedness, which can be used to assess the beta diversity of a population.
These indices were adapted from those developed by Baselga (2010)
<doi:10.1111/j.1466-8238.2009.00490.x> in order to have them population
size-independent. All the details behind the calculation and estimation of
these adapted indices can be found in Fortin et al. (2020) <doi:10.1111/geb.13080>.
Author: Mathieu Fortin, Anna Kondratyeva, Rosalinde Van Couwenberghe
Maintainer: Mathieu Fortin <mathieu.fortin.re@gmail.com>
Diff between betadiv versions 1.0.0 dated 2020-06-05 and 1.0.1 dated 2020-07-24
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- R/connectionFunctions.R | 11 ++--------- R/dissimilarityIndicesFunctions.R | 4 ++-- man/getDissimilarityEstimates.Rd | 4 ++-- tests/testthat/testDissimilarityIndices.R | 3 +++ 6 files changed, 19 insertions(+), 23 deletions(-)
Title: Monte Carlo Option Pricing Algorithms for Jump Diffusion Models
with Correlational Companies
Description: Option is a one of the financial derivatives and its pricing is an important problem in practice. The process of stock prices are represented as Geometric Brownian motion [Black (1973) <doi:10.1086/260062>] or jump diffusion processes [Kou (2002) <doi:10.1287/mnsc.48.8.1086.166>]. In this package, algorithms and visualizations are implemented by Monte Carlo method in order to calculate European option price for three equations by Geometric Brownian motion and jump diffusion processes and furthermore a model that presents jumps among companies affect each other.
Author: Masashi Okada [aut, cre]
Maintainer: Masashi Okada <okadaalgorithm@gmail.com>
Diff between Jdmbs versions 1.3 dated 2018-05-01 and 1.4 dated 2020-07-24
DESCRIPTION | 16 +- MD5 | 23 ++-- NAMESPACE | 2 NEWS |only R/Jdmbs.R | 162 ++++++++++++++++------------- R/JdmbsJump.R | 245 ++++++++++++++++++++++++-------------------- R/JdmbsNewJump.R | 237 +++++++++++++++++++++++------------------- build/vignette.rds |binary inst/doc/Jdmbs-vignette.pdf |binary man/data.Rd | 4 man/jdm_bs.Rd | 29 ++--- man/jdm_new_bs.Rd | 36 +++--- man/normal_bs.Rd | 20 ++- 13 files changed, 429 insertions(+), 345 deletions(-)
Title: Comprehensive TIFF I/O with Full Support for 'ImageJ' TIFF Files
Description: General purpose TIFF file I/O for R users.
Currently the only such package with read and write support for TIFF
files with floating point (real-numbered) pixels, and the only package
that can correctly import TIFF files that were saved from 'ImageJ' and
write TIFF files than can be correctly read by 'ImageJ'
<https://imagej.nih.gov/ij/>. Also supports text image I/O.
Author: Rory Nolan [aut, cre] (<https://orcid.org/0000-0002-5239-4043>),
Kent Johnson [aut],
Simon Urbanek [ctb],
Sergi Padilla-Parra [ths] (<https://orcid.org/0000-0002-8010-9481>),
Jeroen Ooms [rev, ctb] (<https://orcid.org/0000-0002-4035-0289>),
Jon Clayden [rev] (<https://orcid.org/0000-0002-6608-0619>)
Maintainer: Rory Nolan <rorynoolan@gmail.com>
Diff between ijtiff versions 2.1.1 dated 2020-07-05 and 2.1.2 dated 2020-07-24
ijtiff-2.1.1/ijtiff/inst/img/ropensci_footer.png |only ijtiff-2.1.2/ijtiff/DESCRIPTION | 6 +- ijtiff-2.1.2/ijtiff/MD5 | 23 ++++---- ijtiff-2.1.2/ijtiff/NEWS.md | 8 ++- ijtiff-2.1.2/ijtiff/inst/WORDLIST | 2 ijtiff-2.1.2/ijtiff/inst/doc/reading-and-writing-images.Rmd | 6 +- ijtiff-2.1.2/ijtiff/inst/doc/reading-and-writing-images.html | 29 ++++------- ijtiff-2.1.2/ijtiff/inst/doc/text-images.html | 4 - ijtiff-2.1.2/ijtiff/inst/doc/the-imagej-problem.R | 2 ijtiff-2.1.2/ijtiff/inst/doc/the-imagej-problem.Rmd | 2 ijtiff-2.1.2/ijtiff/inst/doc/the-imagej-problem.html | 27 +++------- ijtiff-2.1.2/ijtiff/vignettes/reading-and-writing-images.Rmd | 6 +- ijtiff-2.1.2/ijtiff/vignettes/the-imagej-problem.Rmd | 2 13 files changed, 57 insertions(+), 60 deletions(-)
Title: Header-Only C++ Mathematical Optimization Library for
'Armadillo'
Description: 'Ensmallen' is a templated C++ mathematical optimization library
(by the 'MLPACK' team) that provides a simple set of abstractions for writing an
objective function to optimize. Provided within are various standard and
cutting-edge optimizers that include full-batch gradient descent techniques,
small-batch techniques, gradient-free optimizers, and constrained optimization.
The 'RcppEnsmallen' package includes the header files from the 'Ensmallen' library
and pairs the appropriate header files from 'armadillo' through the
'RcppArmadillo' package. Therefore, users do not need to install 'Ensmallen' nor
'Armadillo' to use 'RcppEnsmallen'. Note that 'Ensmallen' is licensed under
3-Clause BSD, 'Armadillo' starting from 7.800.0 is licensed under Apache License 2,
'RcppArmadillo' (the 'Rcpp' bindings/bridge to 'Armadillo') is licensed under
the GNU GPL version 2 or later. Thus, 'RcppEnsmallen' is also licensed under
similar terms. Note that 'Ensmallen' requires a compiler that supports
'C++11' and 'Armadillo' 8.400 or later.
Author: James Joseph Balamuta [aut, cre, cph]
(<https://orcid.org/0000-0003-2826-8458>),
Dirk Eddelbuettel [aut, cph] (<https://orcid.org/0000-0001-6419-907X>)
Maintainer: James Joseph Balamuta <balamut2@illinois.edu>
Diff between RcppEnsmallen versions 0.2.12.1.1 dated 2020-04-24 and 0.2.13.0.1 dated 2020-07-24
ChangeLog | 9 + DESCRIPTION | 6 MD5 | 16 +- NEWS.md | 8 + build/vignette.rds |binary inst/doc/using-rcppensmallen.html | 68 +++++----- inst/include/ensmallen.hpp | 16 +- inst/include/ensmallen_bits/callbacks/early_stop_at_min_loss.hpp | 56 +++++++- inst/include/ensmallen_bits/ens_version.hpp | 6 9 files changed, 125 insertions(+), 60 deletions(-)
Title: Compute, Handle, Plot and Model Incidence of Dated Events
Description: Provides functions and classes to compute, handle and visualise incidence from dated events for a defined time interval. Dates can be provided in various standard formats. The class 'incidence' is used to store computed incidence and can be easily manipulated, subsetted, and plotted. In addition, log-linear models can be fitted to 'incidence' objects using 'fit'. This package is part of the RECON (<http://www.repidemicsconsortium.org/>) toolkit for outbreak analysis.
Author: Thibaut Jombart [aut],
Zhian N. Kamvar [aut, cre] (<https://orcid.org/0000-0003-1458-7108>),
Rich FitzJohn [aut],
Jun Cai [ctb] (<https://orcid.org/0000-0001-9495-1226>),
Sangeeta Bhatia [ctb],
Jakob Schumacher [ctb],
Juliet R.C. Pulliam [ctb] (<https://orcid.org/0000-0003-3314-8223>)
Maintainer: Zhian N. Kamvar <zkamvar@gmail.com>
Diff between incidence versions 1.7.1 dated 2020-03-25 and 1.7.2 dated 2020-07-24
DESCRIPTION | 10 +-- MD5 | 26 ++++----- NEWS.md | 10 +++ R/plot.R | 3 - build/vignette.rds |binary inst/doc/conversions.html | 52 ++++++++++--------- inst/doc/customize_plot.html | 100 ++++++++++++++++++-------------------- inst/doc/incidence_class.html | 49 +++++++++--------- inst/doc/incidence_fit_class.html | 58 +++++++++++----------- inst/doc/overview.html | 84 ++++++++++++++++--------------- man/bootstrap.Rd | 2 man/estimate_peak.Rd | 6 +- man/incidence.Rd | 12 ++-- man/plot.incidence.Rd | 4 - 14 files changed, 216 insertions(+), 200 deletions(-)
Title: Goodness-of-Fit Tests for Functional Data
Description: Implementation of several goodness-of-fit tests for functional
data. Currently, mostly related with the functional linear model with
functional/scalar response and functional/scalar predictor. The package
allows for the replication of the data applications considered in
García-Portugués, Álvarez-Liébana, Álvarez-Pérez and González-Manteiga
(2019) <arXiv:1909.07686>.
Author: Eduardo García-Portugués [aut, cre],
Javier Álvarez-Liébana [aut],
Gonzalo Álvarez-Pérez [ctb],
Manuel Febrero-Bande [ctb]
Maintainer: Eduardo García-Portugués <edgarcia@est-econ.uc3m.es>
Diff between goffda versions 0.0.6 dated 2019-12-17 and 0.0.7 dated 2020-07-24
DESCRIPTION | 12 ++-- MD5 | 28 +++++----- NEWS.md | 11 +++- R/auxiliary.R | 2 R/data.R | 2 R/flm_est.R | 2 R/flm_test.R | 134 +++++++++++++++++++++++++++++++++++++++------------- R/scenarios-fr.R | 5 + data/aemet_temp.rda |binary man/aemet_temp.Rd | 6 +- man/fda.usc_efic.Rd | 2 man/flm_est.Rd | 2 man/flm_test.Rd | 15 ++++- man/ontario.Rd | 8 +-- man/sim-frmfr.Rd | 5 + 15 files changed, 163 insertions(+), 71 deletions(-)
Title: Alternative Meta-Analysis Methods
Description: Provides alternative statistical methods for meta-analysis, including:
- new heterogeneity tests and measures that are robust to outliers
(Lin et al., 2017 <doi:10.1111/biom.12543>);
- measures, tests, and visualization tools for publication bias or small-study effects
(Lin and Chu, 2018 <doi:10.1111/biom.12817>; Lin, 2019 <doi:10.1002/jrsm.1340>;
Lin, 2020 <doi:10.1177/0962280220910172>; Shi et al., 2020 <doi:10.1002/jrsm.1415>);
- meta-analysis methods for synthesizing proportions
(Lin and Chu, 2020 <doi:10.1097/ede.0000000000001232>);
- models for multivariate meta-analysis
(Lin and Chu, 2018 <doi:10.1002/jrsm.1293>).
Author: Lifeng Lin [aut, cre] (<https://orcid.org/0000-0002-3562-9816>),
Linyu Shi [ctb],
Haitao Chu [aut] (<https://orcid.org/0000-0003-0932-598X>)
Maintainer: Lifeng Lin <linl@stat.fsu.edu>
Diff between altmeta versions 3.0 dated 2020-04-24 and 3.1 dated 2020-07-24
DESCRIPTION | 23 +++++++++++++++++------ MD5 | 38 ++++++++++++++++++++++++-------------- NAMESPACE | 2 +- R/maprop.glmm.R | 3 ++- R/mvma.bayesian.R | 12 +++++------- R/mvma.hybrid.bayesian.R | 12 +++++------- R/pb.bay.R |only R/pb.bayesian.binary.R |only R/pb.reg.bay.R |only build/partial.rdb |binary data/dat.ducharme.rda |only data/dat.henry.rda |only data/dat.poole.rda |only man/dat.ducharme.Rd |only man/dat.henry.Rd |only man/dat.poole.Rd |only man/maprop.glmm.Rd | 27 ++++++++++++++------------- man/maprop.twostep.Rd | 25 +++++++++++++------------ man/metapb.Rd | 2 +- man/mvma.bayesian.Rd | 17 +++++++++-------- man/mvma.hybrid.bayesian.Rd | 15 ++++++++------- man/pb.bayesian.binary.Rd |only man/pb.hybrid.binary.Rd | 8 +------- man/pb.hybrid.generic.Rd | 14 +------------- man/plot.metaoutliers.Rd | 2 +- 25 files changed, 102 insertions(+), 98 deletions(-)
Title: A Collection of DIF Tests for Multistage Tests
Description: A collection of statistical tests for the detection of differential
item functioning (DIF) in multistage tests. Methods entail logistic regression,
an adaptation of the simultaneous item bias test (SIBTEST), and various score-based tests.
The presented tests provide itemwise test for DIF along categorical, ordinal or metric covariates. Methods for uniform and non-uniform
DIF effects are available depending on which method is used.
Author: Rudolf Debelak [aut, cre],
Dries Debeer [aut],
Sebastian Appelbaum [ctb],
Mark J. Gierl [ctb]
Maintainer: Rudolf Debelak <rudolf.debelak@gmail.com>
Diff between mstDIF versions 0.1.5 dated 2020-07-20 and 0.1.6 dated 2020-07-24
DESCRIPTION | 10 - MD5 | 8 - NEWS.md | 4 inst/doc/mstDIF.html | 274 ++++++++++++++++++++++++------------------------- tests/testthat/test1.R | 220 +++++++++++++++++++-------------------- 5 files changed, 260 insertions(+), 256 deletions(-)
Title: Tidy Temporal Data Frames and Tools
Description: Provides a 'tbl_ts' class (the 'tsibble') for
temporal data in an data- and model-oriented format. The 'tsibble'
provides tools to easily manipulate and analyse temporal data, such as
filling in time gaps and aggregating over calendar periods.
Author: Earo Wang [aut, cre] (<https://orcid.org/0000-0001-6448-5260>),
Di Cook [aut, ths] (<https://orcid.org/0000-0002-3813-7155>),
Rob Hyndman [aut, ths] (<https://orcid.org/0000-0002-2140-5352>),
Mitchell O'Hara-Wild [aut] (<https://orcid.org/0000-0001-6729-7695>)
Maintainer: Earo Wang <earo.wang@gmail.com>
Diff between tsibble versions 0.9.1 dated 2020-06-20 and 0.9.2 dated 2020-07-24
tsibble-0.9.1/tsibble/R/deprecated.R |only tsibble-0.9.2/tsibble/DESCRIPTION | 14 - tsibble-0.9.2/tsibble/MD5 | 101 +++++----- tsibble-0.9.2/tsibble/NAMESPACE | 22 +- tsibble-0.9.2/tsibble/NEWS.md | 8 tsibble-0.9.2/tsibble/R/as-tsibble.R | 26 ++ tsibble-0.9.2/tsibble/R/dplyr-verbs.R | 12 - tsibble-0.9.2/tsibble/R/gaps.R | 68 +++---- tsibble-0.9.2/tsibble/R/index-valid.R | 15 + tsibble-0.9.2/tsibble/R/interval.R | 59 ++++-- tsibble-0.9.2/tsibble/R/new-data.R | 7 tsibble-0.9.2/tsibble/R/scales.R | 4 tsibble-0.9.2/tsibble/R/tidyr-verbs.R | 12 - tsibble-0.9.2/tsibble/R/ts2tsibble.R | 4 tsibble-0.9.2/tsibble/R/tsibble-package.R | 35 +-- tsibble-0.9.2/tsibble/R/utils.R | 5 tsibble-0.9.2/tsibble/R/vctrs-tsibble.R | 2 tsibble-0.9.2/tsibble/R/yearmonth.R | 10 - tsibble-0.9.2/tsibble/R/yearquarter.R | 115 ++++++++---- tsibble-0.9.2/tsibble/R/yearweek.R | 153 +++++++++++----- tsibble-0.9.2/tsibble/build/tsibble.pdf |binary tsibble-0.9.2/tsibble/build/vignette.rds |binary tsibble-0.9.2/tsibble/data/tourism.rda |binary tsibble-0.9.2/tsibble/inst/doc/faq.R | 2 tsibble-0.9.2/tsibble/inst/doc/faq.Rmd | 2 tsibble-0.9.2/tsibble/inst/doc/faq.html | 82 +++----- tsibble-0.9.2/tsibble/inst/doc/implicit-na.html | 60 ++---- tsibble-0.9.2/tsibble/inst/doc/intro-tsibble.html | 66 ++---- tsibble-0.9.2/tsibble/man/as-tsibble.Rd | 38 ++- tsibble-0.9.2/tsibble/man/build_tsibble.Rd | 4 tsibble-0.9.2/tsibble/man/deprecated.Rd | 14 - tsibble-0.9.2/tsibble/man/duplicates.Rd | 4 tsibble-0.9.2/tsibble/man/index_valid.Rd | 2 tsibble-0.9.2/tsibble/man/interval-pull.Rd | 5 tsibble-0.9.2/tsibble/man/new-interval.Rd | 6 tsibble-0.9.2/tsibble/man/tsibble-package.Rd | 34 +-- tsibble-0.9.2/tsibble/man/tsibble.Rd | 38 ++- tsibble-0.9.2/tsibble/man/unnest_tsibble.Rd | 2 tsibble-0.9.2/tsibble/man/update_tsibble.Rd | 4 tsibble-0.9.2/tsibble/man/year-month.Rd | 3 tsibble-0.9.2/tsibble/man/year-quarter.Rd | 17 + tsibble-0.9.2/tsibble/man/year-week.Rd | 21 +- tsibble-0.9.2/tsibble/tests/testthat/test-append.R | 5 tsibble-0.9.2/tsibble/tests/testthat/test-dplyr.R | 2 tsibble-0.9.2/tsibble/tests/testthat/test-gaps.R | 4 tsibble-0.9.2/tsibble/tests/testthat/test-interval.R | 13 + tsibble-0.9.2/tsibble/tests/testthat/test-subset.R | 14 - tsibble-0.9.2/tsibble/tests/testthat/test-tsibble.R | 12 + tsibble-0.9.2/tsibble/tests/testthat/test-tsibble2ts.R | 4 tsibble-0.9.2/tsibble/tests/testthat/test-yearquarter.R | 25 ++ tsibble-0.9.2/tsibble/tests/testthat/test-yearweek.R | 38 +++ tsibble-0.9.2/tsibble/vignettes/faq.Rmd | 2 52 files changed, 708 insertions(+), 487 deletions(-)
Title: Miscellaneous Functions by 'Yihui Xie'
Description: Miscellaneous functions commonly used in other packages maintained by 'Yihui Xie'.
Author: Yihui Xie [aut, cre, cph] (<https://orcid.org/0000-0003-0645-5666>),
Wush Wu [ctb],
Daijiang Li [ctb],
Xianying Tan [ctb],
Salim Brüggemann [ctb] (<https://orcid.org/0000-0002-5329-5987>)
Maintainer: Yihui Xie <xie@yihui.name>
Diff between xfun versions 0.15 dated 2020-06-21 and 0.16 dated 2020-07-24
DESCRIPTION | 8 +- MD5 | 32 ++++----- NAMESPACE | 2 NEWS.md | 4 + R/base64.R | 38 ++++++++--- R/markdown.R | 4 - R/paths.R | 16 ++++ R/revcheck.R | 8 +- build/vignette.rds |binary inst/doc/xfun.html | 8 +- man/base64_encode.Rd | 24 +++++-- man/base64_uri.Rd | 2 man/embed_file.Rd | 4 - man/rev_check.Rd | 2 src/base64.c | 146 +++++++++++++++++++++++++++++++++++++++++++++ src/init.c | 2 tests/testit/test-base64.R | 18 +++++ 17 files changed, 270 insertions(+), 48 deletions(-)
Title: Summarizes Provenance Related to Inputs and Outputs of a Script
or Console Commands
Description: Reads the provenance collected by the 'rdt' or
'rdtLite' packages, or other tools providing compatible PROV JSON output
created by the execution of a script, and provides a human-readable
summary identifying the input and output files, the script used
(if any), errors and warnings produced, and the environment in
which it was executed. It can also optionally package all the
files into a zip file. The exact format of the JSON created by
'rdt' and 'rdtLite' is described in
<https://github.com/End-to-end-provenance/ExtendedProvJson>.
More information about 'rdtLite' and associated tools is available
at <https://github.com/End-to-end-provenance/> and Barbara Lerner,
Emery Boose, and Luis Perez (2018), Using Introspection to Collect
Provenance in R, Informatics, <doi: 10.3390/informatics5010012>.
Author: Barbara Lerner [cre],
Emery Boose [aut]
Maintainer: Barbara Lerner <blerner@mtholyoke.edu>
Diff between provSummarizeR versions 1.4.1 dated 2020-07-16 and 1.4.2 dated 2020-07-24
DESCRIPTION | 8 ++++---- MD5 | 21 +++++++++++---------- NEWS.md | 4 ++++ inst/testdata/console.json | 12 ++++++------ inst/testdata/files.json | 30 +++++++++++++++--------------- inst/testdata/prov.json | 22 +++++++++++----------- inst/testdata/warnings.json |only inst/testsummaries/console.expected | 4 ++-- inst/testsummaries/files.expected | 12 ++++++------ inst/testsummaries/prov.expected | 6 +++--- inst/testsummaries/warnings.expected | 32 ++++++++++++++------------------ tests/testthat/test_provSummarize.R | 31 ++++++++++++++++++------------- 12 files changed, 94 insertions(+), 88 deletions(-)
More information about provSummarizeR at CRAN
Permanent link
Title: Unbiased Estimators for Cumulant Products
Description: Tools for estimate (joint) cumulants and products of (joint) cumulants of a given population distribution using (multivariate) k-statistics and (multivariate) polykays, unbiased estimators with minimum variance. Tools for generating univariate and multivariate Faa di Bruno's formula and related polynomials, such as Bell polynomials, generalized complete Bell polynomials, partition polynomials, generalized partition polynomials. For more details see Di Nardo E., Guarino G., Senato D. (2009) <arXiv:0807.5008>, <arXiv:1012.6008>.
Author: Elvira Di Nardo <elvira.dinardo@unito.it>, Giuseppe Guarino <giuseppe.guarino@rete.basilicata.it>
Maintainer: Giuseppe Guarino <giuseppe.guarino@rete.basilicata.it>
Diff between kStatistics versions 1.0 dated 2019-08-05 and 2.0 dated 2020-07-24
DESCRIPTION | 10 +- MD5 | 70 +++++++++++++------ R/BellPol.R |only R/GCBellPol.R |only R/MFB.R |only R/MFB2Set.R |only R/Set2expr.R |only R/cum2mom.R |only R/e_GCBellPol.R |only R/e_MFB.R |only R/gpPart.R |only R/mkT.R |only R/mom2cum.R |only R/nPerm.R |only R/pPart.R |only build/partial.rdb |binary man/BellPol.Rd |only man/GCBellPol.Rd |only man/MFB.Rd |only man/MFB2Set.Rd |only man/Set2expr.Rd |only man/countP.Rd | 29 ++++---- man/cum2mom.Rd |only man/e_GCBellPol.Rd |only man/e_MFB.Rd |only man/ff.Rd | 10 +- man/gpPart.Rd |only man/intPart.Rd | 20 +++-- man/kStatistics-package.Rd | 163 +++++++++++++++++++++++++++++++++++++++------ man/list2Set.Rd | 20 +++-- man/list2m.Rd | 24 +++--- man/m2Set.Rd | 15 ++-- man/mCoeff.Rd | 30 ++++---- man/mkT.Rd |only man/mkmSet.Rd | 22 +++--- man/mom2cum.Rd |only man/mpCart.Rd | 31 ++++---- man/nKM.Rd | 49 +++++++------ man/nKS.Rd | 25 +++--- man/nPM.Rd | 38 +++++----- man/nPS.Rd | 20 +++-- man/nPerm.Rd |only man/nPolyk.Rd | 37 +++++----- man/nStirling2.Rd | 3 man/pCart.Rd | 23 +++--- man/pPart.Rd |only man/pPoly.Rd | 12 +-- man/powS.Rd | 24 +++--- man/umSet.Rd | 9 +- 49 files changed, 432 insertions(+), 252 deletions(-)
More information about InformativeCensoring at CRAN
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Title: Tools for Imaging Flow Cytometry
Description: Contains several tools to treat imaging flow cytometry data from 'ImageStream®' and 'FlowSight®' cytometers ('Amnis®', part of 'Luminex®'). Provides an easy and simple way to read, write and subset .rif, .cif and .daf files. Information such as masks, features, regions and populations set within these files can be retrieved. In addition, raw data such as images stored can also be accessed. Users, may hopefully increase their productivity thanks to dedicated functions to extract, visualize and export 'IFC' data. Toy data example can be installed through the 'IFCdata' package of approximately 32 MB, which is available in a 'drat' repository <https://gitdemont.github.io/IFCdata>. See file 'COPYRIGHTS' and file 'AUTHORS' for a list of copyright holders and authors.
Author: Yohann Demont [aut, cre],
Gautier Stoll [ctb],
Guido Kroemer [ldr],
Jean-Pierre Marolleau [ldr],
Loïc Garçon [ldr]
Maintainer: Yohann Demont <git.demont@gmail.com>
Diff between IFC versions 0.0.8 dated 2020-07-13 and 0.0.9 dated 2020-07-24
IFC-0.0.8/IFC/man/cpp_gray_Decomp2.Rd |only IFC-0.0.8/IFC/man/cpp_num_to_string.Rd |only IFC-0.0.9/IFC/DESCRIPTION | 8 IFC-0.0.9/IFC/MD5 | 50 +- IFC-0.0.9/IFC/NAMESPACE | 6 IFC-0.0.9/IFC/R/ExportToDAF.R | 8 IFC-0.0.9/IFC/R/RcppExports.R | 62 -- IFC-0.0.9/IFC/R/buildGraph.R | 578 ++++++++++++------------ IFC-0.0.9/IFC/R/data_to_DAF.R | 68 +- IFC-0.0.9/IFC/R/getAborted.R | 444 +++++++++--------- IFC-0.0.9/IFC/R/graphs_utils.R | 745 ++++++++++++++++++++++--------- IFC-0.0.9/IFC/R/objectParam.R | 6 IFC-0.0.9/IFC/R/plotGraph.R | 74 +-- IFC-0.0.9/IFC/R/strings_utils.R | 12 IFC-0.0.9/IFC/R/toXML2_graphs.R | 114 ++-- IFC-0.0.9/IFC/R/toXML2_images.R | 130 ++--- IFC-0.0.9/IFC/R/toXML2_pops.R | 236 ++++----- IFC-0.0.9/IFC/R/toXML2_regions.R | 110 ++-- IFC-0.0.9/IFC/R/whoami.R | 328 ++++++------- IFC-0.0.9/IFC/R/zzz.R | 100 ++-- IFC-0.0.9/IFC/inst/CITATION | 2 IFC-0.0.9/IFC/inst/include/trans.hpp | 4 IFC-0.0.9/IFC/man/base_axis_constr.Rd |only IFC-0.0.9/IFC/man/base_hist_constr.Rd |only IFC-0.0.9/IFC/man/convert_to_baseplot.Rd |only IFC-0.0.9/IFC/man/num_to_string.Rd |only IFC-0.0.9/IFC/src/RcppExports.cpp | 31 - IFC-0.0.9/IFC/src/ifc.cpp | 125 ----- IFC-0.0.9/IFC/src/trans.cpp | 48 - 29 files changed, 1693 insertions(+), 1596 deletions(-)
Title: Tools for Working with XML Files as R Dataframes
Description: On import, the XML information is converted to a dataframe that reflects the hierarchical XML structure. Intuitive functions allow to navigate within this transparent XML data structure (without any knowledge of 'XPath'). 'flatXML' also provides tools to extract data from the XML into a flat dataframe that can be used to perform statistical operations. It also supports converting dataframes to XML.
Author: Joachim Zuckarelli [aut, cre]
Maintainer: Joachim Zuckarelli <joachim@zuckarelli.de>
Diff between flatxml versions 0.0.2 dated 2018-07-08 and 0.1.0 dated 2020-07-24
DESCRIPTION | 12 +++--- MD5 | 13 ++++--- NAMESPACE | 1 R/flatxml.r | 82 ++++++++++++++++++++++++++++++++++++++++++---- README.md | 84 +++++++++++++++++++++++++++++++++++++++++++++--- man/flatxml.Rd | 17 +++++---- man/fxml_toDataFrame.Rd | 20 ++++++++--- man/fxml_toXML.Rd |only 8 files changed, 193 insertions(+), 36 deletions(-)
Title: Extension of `data.frame`
Description: Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group using no copies at all, list columns, friendly and fast character-separated-value read/write. Offers a natural and flexible syntax, for faster development.
Author: Matt Dowle [aut, cre],
Arun Srinivasan [aut],
Jan Gorecki [ctb],
Michael Chirico [ctb],
Pasha Stetsenko [ctb],
Tom Short [ctb],
Steve Lianoglou [ctb],
Eduard Antonyan [ctb],
Markus Bonsch [ctb],
Hugh Parsonage [ctb],
Scott Ritchie [ctb],
Kun Ren [ctb],
Xianying Tan [ctb],
Rick Saporta [ctb],
Otto Seiskari [ctb],
Xianghui Dong [ctb],
Michel Lang [ctb],
Watal Iwasaki [ctb],
Seth Wenchel [ctb],
Karl Broman [ctb],
Tobias Schmidt [ctb],
David Arenburg [ctb],
Ethan Smith [ctb],
Francois Cocquemas [ctb],
Matthieu Gomez [ctb],
Philippe Chataignon [ctb],
Nello Blaser [ctb],
Dmitry Selivanov [ctb],
Andrey Riabushenko [ctb],
Cheng Lee [ctb],
Declan Groves [ctb],
Daniel Possenriede [ctb],
Felipe Parages [ctb],
Denes Toth [ctb],
Mus Yaramaz-David [ctb],
Ayappan Perumal [ctb],
James Sams [ctb],
Martin Morgan [ctb],
Michael Quinn [ctb],
@javrucebo [ctb],
@marc-outins [ctb],
Roy Storey [ctb],
Manish Saraswat [ctb],
Morgan Jacob [ctb],
Michael Schubmehl [ctb],
Davis Vaughan [ctb],
Toby Hocking [ctb],
Leonardo Silvestri [ctb],
Tyson Barrett [ctb],
Jim Hester [ctb],
Anthony Damico [ctb],
Sebastian Freundt [ctb],
David Simons [ctb],
Elliott Sales de Andrade [ctb],
Cole Miller [ctb],
Jens Peder Meldgaard [ctb],
Vaclav Tlapak [ctb],
Kevin Ushey [ctb]
Maintainer: Matt Dowle <mattjdowle@gmail.com>
Diff between data.table versions 1.12.8 dated 2019-12-09 and 1.13.0 dated 2020-07-24
data.table-1.12.8/data.table/man/set2key.Rd |only data.table-1.12.8/data.table/src/Makevars |only data.table-1.13.0/data.table/DESCRIPTION | 45 data.table-1.13.0/data.table/MD5 | 233 +- data.table-1.13.0/data.table/NAMESPACE | 6 data.table-1.13.0/data.table/NEWS.md | 185 + data.table-1.13.0/data.table/R/IDateTime.R | 34 data.table-1.13.0/data.table/R/as.data.table.R | 4 data.table-1.13.0/data.table/R/between.R | 6 data.table-1.13.0/data.table/R/data.table.R | 273 +- data.table-1.13.0/data.table/R/devel.R | 33 data.table-1.13.0/data.table/R/duplicated.R | 26 data.table-1.13.0/data.table/R/fcast.R | 21 data.table-1.13.0/data.table/R/fmelt.R | 2 data.table-1.13.0/data.table/R/foverlaps.R | 3 data.table-1.13.0/data.table/R/frank.R | 15 data.table-1.13.0/data.table/R/fread.R | 18 data.table-1.13.0/data.table/R/groupingsets.R | 6 data.table-1.13.0/data.table/R/last.R | 99 data.table-1.13.0/data.table/R/merge.R | 6 data.table-1.13.0/data.table/R/onAttach.R | 12 data.table-1.13.0/data.table/R/onLoad.R | 12 data.table-1.13.0/data.table/R/openmp-utils.R | 6 data.table-1.13.0/data.table/R/print.data.table.R | 83 data.table-1.13.0/data.table/R/setkey.R | 26 data.table-1.13.0/data.table/R/setops.R | 20 data.table-1.13.0/data.table/R/shift.R | 8 data.table-1.13.0/data.table/R/test.data.table.R | 102 data.table-1.13.0/data.table/R/utils.R | 18 data.table-1.13.0/data.table/R/wrappers.R | 1 data.table-1.13.0/data.table/R/xts.R | 13 data.table-1.13.0/data.table/build/vignette.rds |binary data.table-1.13.0/data.table/cleanup |only data.table-1.13.0/data.table/configure | 57 data.table-1.13.0/data.table/inst/cc |only data.table-1.13.0/data.table/inst/doc/datatable-benchmarking.html | 356 ++- data.table-1.13.0/data.table/inst/doc/datatable-faq.html | 710 ++++-- data.table-1.13.0/data.table/inst/doc/datatable-importing.Rmd | 8 data.table-1.13.0/data.table/inst/doc/datatable-importing.html | 404 ++- data.table-1.13.0/data.table/inst/doc/datatable-intro.Rmd | 2 data.table-1.13.0/data.table/inst/doc/datatable-intro.html | 1028 ++++++---- data.table-1.13.0/data.table/inst/doc/datatable-keys-fast-subset.html | 816 ++++--- data.table-1.13.0/data.table/inst/doc/datatable-reference-semantics.html | 676 ++++-- data.table-1.13.0/data.table/inst/doc/datatable-reshape.html | 656 ++++-- data.table-1.13.0/data.table/inst/doc/datatable-sd-usage.html | 900 +++++--- data.table-1.13.0/data.table/inst/doc/datatable-secondary-indices-and-auto-indexing.R | 2 data.table-1.13.0/data.table/inst/doc/datatable-secondary-indices-and-auto-indexing.Rmd | 30 data.table-1.13.0/data.table/inst/doc/datatable-secondary-indices-and-auto-indexing.html | 629 ++++-- data.table-1.13.0/data.table/inst/po |only data.table-1.13.0/data.table/inst/tests/benchmark.Rraw.bz2 |binary data.table-1.13.0/data.table/inst/tests/nafill.Rraw.bz2 |binary data.table-1.13.0/data.table/inst/tests/other.Rraw.bz2 |binary data.table-1.13.0/data.table/inst/tests/tests.Rraw.bz2 |binary data.table-1.13.0/data.table/man/IDateTime.Rd | 21 data.table-1.13.0/data.table/man/all.equal.data.table.Rd | 7 data.table-1.13.0/data.table/man/as.data.table.xts.Rd | 2 data.table-1.13.0/data.table/man/cdt.Rd |only data.table-1.13.0/data.table/man/data.table.Rd | 10 data.table-1.13.0/data.table/man/deprecated.Rd |only data.table-1.13.0/data.table/man/fcase.Rd |only data.table-1.13.0/data.table/man/frank.Rd | 10 data.table-1.13.0/data.table/man/fread.Rd | 18 data.table-1.13.0/data.table/man/melt.data.table.Rd | 3 data.table-1.13.0/data.table/man/nafill.Rd | 10 data.table-1.13.0/data.table/man/openmp-utils.Rd | 23 data.table-1.13.0/data.table/man/print.data.table.Rd | 28 data.table-1.13.0/data.table/man/setattr.Rd | 2 data.table-1.13.0/data.table/man/special-symbols.Rd | 4 data.table-1.13.0/data.table/man/test.Rd | 3 data.table-1.13.0/data.table/man/update.dev.pkg.Rd | 17 data.table-1.13.0/data.table/po |only data.table-1.13.0/data.table/src/Makevars.in |only data.table-1.13.0/data.table/src/Makevars.win |only data.table-1.13.0/data.table/src/assign.c | 290 +- data.table-1.13.0/data.table/src/between.c | 48 data.table-1.13.0/data.table/src/bmerge.c | 56 data.table-1.13.0/data.table/src/chmatch.c | 70 data.table-1.13.0/data.table/src/cj.c | 16 data.table-1.13.0/data.table/src/coalesce.c | 30 data.table-1.13.0/data.table/src/data.table.h | 74 data.table-1.13.0/data.table/src/dogroups.c | 315 +-- data.table-1.13.0/data.table/src/fastmean.c | 8 data.table-1.13.0/data.table/src/fcast.c | 20 data.table-1.13.0/data.table/src/fifelse.c | 242 ++ data.table-1.13.0/data.table/src/fmelt.c | 163 - 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data.table-1.13.0/data.table/src/shift.c | 105 - data.table-1.13.0/data.table/src/snprintf.c |only data.table-1.13.0/data.table/src/subset.c | 103 - data.table-1.13.0/data.table/src/transpose.c | 14 data.table-1.13.0/data.table/src/types.c | 6 data.table-1.13.0/data.table/src/uniqlist.c | 41 data.table-1.13.0/data.table/src/utils.c | 40 data.table-1.13.0/data.table/src/vecseq.c | 14 data.table-1.13.0/data.table/src/wrappers.c | 14 data.table-1.13.0/data.table/vignettes/datatable-importing.Rmd | 8 data.table-1.13.0/data.table/vignettes/datatable-intro.Rmd | 2 data.table-1.13.0/data.table/vignettes/datatable-secondary-indices-and-auto-indexing.Rmd | 30 121 files changed, 7520 insertions(+), 4499 deletions(-)
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>),
Poisson Consulting [cph, fnd]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>
Diff between chk versions 0.5.0 dated 2020-05-29 and 0.5.1 dated 2020-07-24
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NEWS.md | 30 +++++++++++++++++------------- build/chk.pdf |binary build/vignette.rds |binary inst/doc/chk-families.html | 16 ++++++++++++++++ inst/doc/chk.html | 16 ++++++++++++++++ man/err.Rd | 4 ++-- man/p.Rd | 2 +- tests/testthat/test-chk-join.R | 7 ++++++- 10 files changed, 71 insertions(+), 30 deletions(-)
Title: CRISPR Pooled Screen Analysis using Beta-Binomial Test
Description: Provides functions for hit gene identification and quantification of sgRNA (single-guided RNA) abundances for CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) pooled screen data analysis.
Details are in Jeong et al. (2019) <doi:10.1101/gr.245571.118> and Baggerly et al. (2003) <doi:10.1093/bioinformatics/btg173>.
Author: Hyun-Hwan Jeong [aut, cre]
Maintainer: Hyun-Hwan Jeong <jeong.hyunhwan@gmail.com>
Diff between CB2 versions 1.3.3 dated 2020-05-26 and 1.3.4 dated 2020-07-24
DESCRIPTION | 14 MD5 | 17 NAMESPACE | 2 R/helpers.R | 42 +- README.md | 2 build/vignette.rds |binary inst/doc/cb2-input-handling.html | 566 ++++++++++++------------------ inst/doc/cb2-tutorial.html | 719 +++++++++++++++++++-------------------- man/figures |only tests/testthat/test.toydata.R | 26 - 10 files changed, 638 insertions(+), 750 deletions(-)
Title: Anything to 'POSIXct' or 'Date' Converter
Description: Convert input in any one of character, integer, numeric, factor,
or ordered type into 'POSIXct' (or 'Date') objects, using one of a number of
predefined formats, and relying on Boost facilities for date and time parsing.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between anytime versions 0.3.7 dated 2020-01-20 and 0.3.8 dated 2020-07-24
ChangeLog | 33 +++++++++++++++++++++++++++++++++ DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++------------ NAMESPACE | 2 +- R/init.R | 17 ++++++++++++++++- README.md | 4 ++-- build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 10 +++++++++- inst/doc/anytime-introduction.pdf |binary inst/tinytest/test_simple.R | 9 +++++++-- inst/tinytest/test_utilities.R | 3 +++ tests/tinytest.R | 7 +++---- 13 files changed, 90 insertions(+), 27 deletions(-)
Title: Analyze Experimental High-Throughput (Omics) Data
Description: The efficient treatment and convenient analysis of experimental high-throughput (omics) data gets facilitated through this collection of diverse functions. Several functions address advanced object-conversions, like manipulating lists of lists or lists of arrays, reorganizing lists to arrays or into separate vectors, merging of multiple entries, etc. Another set of functions provides speed-optimized calculation of standard deviation (sd), coefficient of variance (CV) or standard error of the mean (SEM) for data in matrixes or means per line with respect to additional grouping (eg n groups of replicates). Other functions facilitate dealing with non-redundant information, by indexing unique, adding counters to redundant or eliminating lines with respect redundancy in a given reference-column, etc. Help is provided to identify very closely matching numeric values to generate (partial) distance matrixes for very big data in a memory efficient manner or to reduce the complexity of large data-sets by combining very close values. Many times large experimental datasets need some additional filtering, adequate functions are provided. Batch reading (or writing) of sets of files and combining data to arrays is supported, too. Convenient data normalization is supported in various different modes, parameter estimation via permutations or boot-strap as well as flexible testing of multiple pair-wise combinations using the framework of 'limma' is provided, too.
Author: Wolfgang Raffelsberger [aut, cre]
Maintainer: Wolfgang Raffelsberger <w.raffelsberger@unistra.fr>
Diff between wrMisc versions 1.2.4 dated 2020-07-03 and 1.3.0 dated 2020-07-24
DESCRIPTION | 8 ++++---- MD5 | 40 ++++++++++++++++++++++------------------ NAMESPACE | 2 ++ R/asSepList.R | 2 +- R/combinatIntTable.R |only R/conv01toColNa.R | 20 ++++++++++---------- R/correctWinPath.R |only R/filterList.R | 18 ++++++++++-------- R/firstOfRepeated.R | 8 +++++--- R/moderTest2grp.R | 2 +- R/moderTestXgrp.R | 8 ++++---- R/pVal2lfdr.R | 4 ++-- R/readVarColumns.R | 2 +- inst/doc/wrMiscVignette1.html | 22 +++++++++++----------- man/asSepList.Rd | 2 +- man/combinatIntTable.Rd |only man/conv01toColNa.Rd | 12 ++++++------ man/correctWinPath.Rd |only man/filterList.Rd | 11 ++++++----- man/firstOfRepeated.Rd | 4 +++- man/moderTest2grp.Rd | 2 +- man/moderTestXgrp.Rd | 2 +- man/readVarColumns.Rd | 8 ++++---- 23 files changed, 95 insertions(+), 82 deletions(-)
Title: Gene Set Analysis Toolkit WebGestaltR
Description: The web version WebGestalt <http://www.webgestalt.org> supports 12 organisms, 354 gene identifiers and 321,251 function categories. Users can upload the data and functional categories with their own gene identifiers. In addition to the Over-Representation Analysis, WebGestalt also supports Gene Set Enrichment Analysis and Network Topology Analysis. The user-friendly output report allows interactive and efficient exploration of enrichment results. The WebGestaltR package not only supports all above functions but also can be integrated into other pipeline or simultaneously analyze multiple gene lists.
Author: Jing Wang [aut],
Yuxing Liao [aut, cre],
Eric Jaehnig [ctb],
Zhiao Shi [ctb],
Quanhu Sheng [ctb]
Maintainer: Yuxing Liao <yuxingliao@gmail.com>
Diff between WebGestaltR versions 0.4.3 dated 2020-01-16 and 0.4.4 dated 2020-07-24
DESCRIPTION | 8 MD5 | 168 NAMESPACE | 150 NEWS.md | 34 R/RcppExports.R | 62 R/WebGestaltR.R | 480 R/WebGestaltRBatch.R | 120 R/WebGestaltRGsea.R | 298 R/WebGestaltRNta.R | 164 R/WebGestaltROra.R | 304 R/affinityPropagation.R | 206 R/cacheFile.R | 104 R/createNtaReport.R | 240 R/createReport.R | 270 R/dagUtils.R | 284 R/enrichResultSection.R | 70 R/errorMessage.R | 792 R/formatCheck.R | 162 R/goSlimReport.R | 12 R/goSlimSummary.R | 246 R/gseaEnrichment.R | 306 R/idMapping.R | 138 R/idMappingGene.R | 220 R/idMappingPhosphosite.R | 310 R/idMappingUtils.R | 146 R/idToSymbol.R | 208 R/linkModification.R | 96 R/listArchiveURL.R | 42 R/listGeneSet.R | 104 R/listIdType.R | 64 R/listOrganism.R | 50 R/listReferenceSet.R | 50 R/loadGeneList.R | 250 R/loadGeneSet.R | 428 R/oraEnrichment.R | 136 R/randomWalkEnrichment.R | 382 R/readGmt.R | 168 R/reportUtils.R | 226 R/summaryDescription.R | 262 R/weightedSetCover.R | 252 README.md | 6 inst/extdata/GOSlimExample.txt | 956 - inst/extdata/GeneRankList.rnk |23906 ++++++++++++++-------------- inst/extdata/exampleGMT.gmt | 708 inst/extdata/interestingGenes.txt | 974 - inst/extdata/referenceGenes.txt |23040 +++++++++++++------------- inst/templates/enrichResultSection.mustache | 270 inst/templates/footer.mustache | 10 inst/templates/goSlimReport.mustache | 38 inst/templates/header.mustache | 16 inst/templates/networkContent.mustache | 166 inst/templates/ntaTemplate.mustache | 110 inst/templates/summary.mustache | 126 inst/templates/summaryGsea.mustache | 68 inst/templates/summaryOra.mustache | 106 inst/templates/template.mustache | 244 man/WebGestaltR.Rd | 596 man/affinityPropagation.Rd | 54 man/cacheUrl.Rd | 44 man/createNtaReport.Rd | 46 man/createReport.Rd | 100 man/enrichResultSection.Rd | 40 man/expandDag.Rd | 24 man/fillInputDataFrame.Rd | 50 man/formatCheck.Rd | 46 man/goSlimSummary.Rd | 86 man/gseaPermutation.Rd | 50 man/idMapping.Rd | 146 man/jaccardSim.Rd | 46 man/keepRep.Rd | 24 man/linkModification.Rd | 24 man/listArchiveUrl.Rd | 30 man/listGeneSet.Rd | 60 man/listIdType.Rd | 62 man/listOrganism.Rd | 38 man/listReferenceSet.Rd | 60 man/loadGeneSet.Rd | 124 man/prepareGseaInput.Rd | 38 man/prepareInputMatrixGsea.Rd | 38 man/readGmt.Rd | 38 man/specificParameterSummaryGsea.Rd | 52 man/specificParameterSummaryOra.Rd | 64 man/summaryDescription.Rd | 86 man/swGsea.Rd | 216 man/weightedSetCover.Rd | 62 85 files changed, 30551 insertions(+), 30549 deletions(-)
Title: Helper Functions to Install and Maintain TeX Live, and Compile
LaTeX Documents
Description: Helper functions to install and maintain the 'LaTeX' distribution
named 'TinyTeX' (<https://yihui.org/tinytex/>), a lightweight, cross-platform,
portable, and easy-to-maintain version of 'TeX Live'. This package also
contains helper functions to compile 'LaTeX' documents, and install missing
'LaTeX' packages automatically.
Author: Yihui Xie [aut, cre, cph] (<https://orcid.org/0000-0003-0645-5666>),
RStudio, PBC [cph],
Fernando Cagua [ctb],
Ethan Heinzen [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between tinytex versions 0.24 dated 2020-06-20 and 0.25 dated 2020-07-24
DESCRIPTION | 12 ++++++------ MD5 | 10 +++++----- R/install.R | 6 +++++- R/latex.R | 2 +- R/tlmgr.R | 15 +++++++++++++-- man/tlmgr.Rd | 5 +++++ 6 files changed, 35 insertions(+), 15 deletions(-)
Title: Easy Web Scraping
Description: The goal of 'ralger' is to facilitate web scraping in R.
The user has the ability to extract a vector with scrap(), a tidy dataframe using tidy_scrap(), a table with table_scrap() and web links with weblink_scrap().
Author: Mohamed El Fodil Ihaddaden [aut, cre],
Ezekiel Ogundepo [ctb]
Maintainer: Mohamed El Fodil Ihaddaden <ihaddaden.fodeil@gmail.com>
Diff between ralger versions 2.0.0 dated 2020-04-12 and 2.0.1 dated 2020-07-24
DESCRIPTION | 14 ++- MD5 | 24 +++--- NEWS.md | 21 ++++- R/table_scrap.R | 7 + README.md | 187 +++++++++++++++++++++++++++++------------------- build/vignette.rds |binary inst/doc/ralger.html | 28 +++++-- man/paragraphs_scrap.Rd | 64 ++++++++-------- man/scrap.Rd | 66 ++++++++-------- man/table_scrap.Rd | 64 ++++++++-------- man/tidy_scrap.Rd | 72 +++++++++--------- man/titles_scrap.Rd | 60 +++++++-------- man/weblink_scrap.Rd | 60 +++++++-------- 13 files changed, 371 insertions(+), 296 deletions(-)