Title: Statistical Toolbox for Sedimentary Provenance Analysis
Description: Bundles a number of established statistical methods to facilitate the visual interpretation of large datasets in sedimentary geology. Includes functionality for adaptive kernel density estimation, principal component analysis, correspondence analysis, multidimensional scaling, generalised procrustes analysis and individual differences scaling using a variety of dissimilarity measures. Univariate provenance proxies, such as single-grain ages or (isotopic) compositions are compared with the Kolmogorov-Smirnov, Kuiper or Sircombe-Hazelton L2 distances. Categorical provenance proxies such as chemical compositions are compared with the Aitchison and Bray-Curtis distances, and point-counting data with the chi-square distance. Also included are tools to plot compositional and point-counting data on ternary diagrams and point-counting data on radial plots, to calculate the sample size required for specified levels of statistical precision, and to assess the effects of hydraulic sorting on detrital compositions. Includes an intuitive query-based user interface for users who are not proficient in R.
Author: Pieter Vermeesch [aut, cre]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>
Diff between provenance versions 2.3 dated 2019-06-06 and 2.4 dated 2020-03-19
DESCRIPTION | 8 - MD5 | 76 +++++++------- NAMESPACE | 2 R/documentation.R | 38 +++---- R/indscal.R | 26 ++--- R/io.R | 92 ++++++++++++++--- R/kde.R | 65 ++++++------ R/minsorting.R | 18 ++- R/plot.R | 234 ++++++++++++++++++++++++++++++++------------- R/radialplot.R | 4 R/ternary.R | 21 ++-- R/toolbox.R | 136 ++++++++++++++++---------- man/CA.Rd | 2 man/GPA.Rd | 9 - man/KDE.Rd | 24 ++-- man/KDEs.Rd | 29 ++--- man/MDS.Rd | 38 +++++-- man/Namib.Rd | 20 +-- man/PCA.Rd | 2 man/amalgamate.Rd | 3 man/as.compositional.Rd | 5 man/as.counts.Rd | 4 man/bray.diss.Rd | 3 man/central.Rd | 4 man/combine.Rd | 3 man/endmembers.Rd | 16 +-- man/get.f.Rd | 5 man/get.n.Rd | 4 man/get.p.Rd | 13 +- man/indscal.Rd | 26 ++--- man/minsorting.Rd | 18 ++- man/plot.CA.Rd | 8 + man/plot.MDS.Rd | 2 man/plot.PCA.Rd | 18 +++ man/read.compositional.Rd | 23 ++++ man/read.counts.Rd | 23 ++++ man/read.densities.Rd | 17 ++- man/read.distributional.Rd | 17 ++- man/subset.Rd | 2 39 files changed, 691 insertions(+), 367 deletions(-)
Title: Mixed-Frequency Bayesian VAR Models
Description: Estimation of mixed-frequency Bayesian vector autoregressive (VAR) models. The package implements a state space-based VAR model that handles mixed frequencies of the data. The model is estimated using Markov Chain Monte Carlo to numerically approximate the posterior distribution. Prior distributions that can be used include normal-inverse Wishart and normal-diffuse priors as well as steady-state priors. Stochastic volatility can be handled by common or factor stochastic volatility models.
Author: Sebastian Ankargren [cre, aut]
(<https://orcid.org/0000-0003-4415-8734>),
Yukai Yang [aut] (<https://orcid.org/0000-0002-2623-8549>),
Gregor Kastner [ctb] (<https://orcid.org/0000-0002-8237-8271>)
Maintainer: Sebastian Ankargren <sebastian.ankargren@statistics.uu.se>
Diff between mfbvar versions 0.5.2 dated 2020-01-09 and 0.5.3 dated 2020-03-19
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- NEWS.md | 3 +++ R/interface.R | 8 +++++--- inst/doc/mfbvar_jss.Rnw | 4 ++-- inst/doc/mfbvar_jss.pdf |binary vignettes/mfbvar_jss.Rnw | 4 ++-- vignettes/refs.bib | 20 +++++++++++++------- 8 files changed, 37 insertions(+), 26 deletions(-)
Title: Meta-Analysis Package for R
Description: A comprehensive collection of functions for conducting meta-analyses in R. The package includes functions to calculate various effect sizes or outcome measures, fit fixed-, random-, and mixed-effects models to such data, carry out moderator and meta-regression analyses, and create various types of meta-analytical plots (e.g., forest, funnel, radial, L'Abbe, Baujat, GOSH plots). For meta-analyses of binomial and person-time data, the package also provides functions that implement specialized methods, including the Mantel-Haenszel method, Peto's method, and a variety of suitable generalized linear (mixed-effects) models (i.e., mixed-effects logistic and Poisson regression models). Finally, the package provides functionality for fitting meta-analytic multivariate/multilevel models that account for non-independent sampling errors and/or true effects (e.g., due to the inclusion of multiple treatment studies, multiple endpoints, or other forms of clustering). Network meta-analyses and meta-analyses accounting for known correlation structures (e.g., due to phylogenetic relatedness) can also be conducted.
Author: Wolfgang Viechtbauer [aut, cre]
(<https://orcid.org/0000-0003-3463-4063>)
Maintainer: Wolfgang Viechtbauer <wvb@metafor-project.org>
Diff between metafor versions 2.1-0 dated 2019-05-14 and 2.4-0 dated 2020-03-19
metafor-2.1-0/metafor/R/misc.func.exported.r |only metafor-2.1-0/metafor/tests/testthat/test_misc_to_long_to_table.r |only metafor-2.4-0/metafor/DESCRIPTION | 17 metafor-2.4-0/metafor/MD5 | 427 - metafor-2.4-0/metafor/NEWS | 66 metafor-2.4-0/metafor/NEWS.md | 48 metafor-2.4-0/metafor/R/addpoly.default.r | 12 metafor-2.4-0/metafor/R/anova.rma.r | 123 metafor-2.4-0/metafor/R/baujat.rma.r | 15 metafor-2.4-0/metafor/R/bldiag.r | 2 metafor-2.4-0/metafor/R/confint.rma.glmm.r | 2 metafor-2.4-0/metafor/R/confint.rma.mh.r | 10 metafor-2.4-0/metafor/R/confint.rma.mv.r | 26 metafor-2.4-0/metafor/R/confint.rma.peto.r | 10 metafor-2.4-0/metafor/R/confint.rma.uni.r | 26 metafor-2.4-0/metafor/R/contrmat.r |only metafor-2.4-0/metafor/R/cooks.distance.rma.mv.r | 21 metafor-2.4-0/metafor/R/cumul.rma.mh.r | 10 metafor-2.4-0/metafor/R/cumul.rma.peto.r | 10 metafor-2.4-0/metafor/R/cumul.rma.uni.r | 10 metafor-2.4-0/metafor/R/dfbetas.rma.mv.r | 21 metafor-2.4-0/metafor/R/escalc.r | 185 metafor-2.4-0/metafor/R/forest.cumul.rma.r | 136 metafor-2.4-0/metafor/R/forest.default.r | 141 metafor-2.4-0/metafor/R/forest.rma.r | 151 metafor-2.4-0/metafor/R/funnel.default.r | 6 metafor-2.4-0/metafor/R/funnel.rma.r | 2 metafor-2.4-0/metafor/R/gosh.rma.r | 44 metafor-2.4-0/metafor/R/influence.rma.uni.r | 10 metafor-2.4-0/metafor/R/labbe.rma.r | 8 metafor-2.4-0/metafor/R/leave1out.rma.mh.r | 10 metafor-2.4-0/metafor/R/leave1out.rma.peto.r | 10 metafor-2.4-0/metafor/R/leave1out.rma.uni.r | 10 metafor-2.4-0/metafor/R/llplot.r | 4 metafor-2.4-0/metafor/R/methods.escalc.r | 2 metafor-2.4-0/metafor/R/methods.list.rma.r | 2 metafor-2.4-0/metafor/R/misc.func.hidden.escalc.r |only metafor-2.4-0/metafor/R/misc.func.hidden.glmm.r |only metafor-2.4-0/metafor/R/misc.func.hidden.mv.r |only metafor-2.4-0/metafor/R/misc.func.hidden.prof.r |only metafor-2.4-0/metafor/R/misc.func.hidden.r | 2370 +--------- metafor-2.4-0/metafor/R/misc.func.hidden.uni.r |only metafor-2.4-0/metafor/R/permutest.rma.uni.r | 30 metafor-2.4-0/metafor/R/plot.cumul.rma.r | 4 metafor-2.4-0/metafor/R/plot.gosh.rma.r | 18 metafor-2.4-0/metafor/R/plot.infl.rma.uni.r | 36 metafor-2.4-0/metafor/R/plot.profile.rma.r | 24 metafor-2.4-0/metafor/R/predict.rma.r | 6 metafor-2.4-0/metafor/R/print.anova.rma.r | 3 metafor-2.4-0/metafor/R/print.escalc.r | 12 metafor-2.4-0/metafor/R/print.infl.rma.uni.r | 26 metafor-2.4-0/metafor/R/print.list.rma.r | 10 metafor-2.4-0/metafor/R/print.rma.glmm.r | 15 metafor-2.4-0/metafor/R/print.rma.mh.r | 24 metafor-2.4-0/metafor/R/print.rma.mv.r | 39 metafor-2.4-0/metafor/R/print.rma.peto.r | 24 metafor-2.4-0/metafor/R/print.rma.uni.r | 60 metafor-2.4-0/metafor/R/profile.rma.mv.r | 46 metafor-2.4-0/metafor/R/profile.rma.uni.r | 34 metafor-2.4-0/metafor/R/qqnorm.rma.mh.r | 2 metafor-2.4-0/metafor/R/qqnorm.rma.peto.r | 2 metafor-2.4-0/metafor/R/qqnorm.rma.uni.r | 23 metafor-2.4-0/metafor/R/radial.rma.r | 18 metafor-2.4-0/metafor/R/ranef.rma.mv.r | 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metafor-2.4-0/metafor/man/dat.senn2013.Rd | 50 metafor-2.4-0/metafor/man/escalc.Rd | 21 metafor-2.4-0/metafor/man/fitstats.Rd | 2 metafor-2.4-0/metafor/man/fitted.rma.Rd | 2 metafor-2.4-0/metafor/man/forest.Rd | 2 metafor-2.4-0/metafor/man/forest.cumul.rma.Rd | 5 metafor-2.4-0/metafor/man/forest.default.Rd | 8 metafor-2.4-0/metafor/man/forest.rma.Rd | 42 metafor-2.4-0/metafor/man/formula.rma.Rd | 6 metafor-2.4-0/metafor/man/fsn.Rd | 4 metafor-2.4-0/metafor/man/funnel.Rd | 4 metafor-2.4-0/metafor/man/gosh.Rd | 2 metafor-2.4-0/metafor/man/hc.Rd | 2 metafor-2.4-0/metafor/man/influence.rma.mv.Rd | 2 metafor-2.4-0/metafor/man/influence.rma.uni.Rd | 5 metafor-2.4-0/metafor/man/labbe.Rd | 2 metafor-2.4-0/metafor/man/leave1out.Rd | 2 metafor-2.4-0/metafor/man/llplot.Rd | 4 metafor-2.4-0/metafor/man/metafor-package.Rd | 11 metafor-2.4-0/metafor/man/metafor.news.Rd | 2 metafor-2.4-0/metafor/man/methods.escalc.Rd | 2 metafor-2.4-0/metafor/man/methods.list.rma.Rd | 2 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2 metafor-2.4-0/metafor/man/radial.Rd | 2 metafor-2.4-0/metafor/man/ranef.Rd | 2 metafor-2.4-0/metafor/man/ranktest.Rd | 4 metafor-2.4-0/metafor/man/regtest.Rd | 4 metafor-2.4-0/metafor/man/reporter.Rd | 6 metafor-2.4-0/metafor/man/residuals.rma.Rd | 4 metafor-2.4-0/metafor/man/rma.glmm.Rd | 10 metafor-2.4-0/metafor/man/rma.mh.Rd | 4 metafor-2.4-0/metafor/man/rma.mv.Rd | 16 metafor-2.4-0/metafor/man/rma.peto.Rd | 4 metafor-2.4-0/metafor/man/rma.uni.Rd | 12 metafor-2.4-0/metafor/man/robust.Rd | 4 metafor-2.4-0/metafor/man/simulate.rma.Rd | 2 metafor-2.4-0/metafor/man/to.long.Rd | 6 metafor-2.4-0/metafor/man/to.table.Rd | 8 metafor-2.4-0/metafor/man/to.wide.Rd |only metafor-2.4-0/metafor/man/transf.Rd | 2 metafor-2.4-0/metafor/man/trimfill.Rd | 2 metafor-2.4-0/metafor/man/update.rma.Rd | 4 metafor-2.4-0/metafor/man/vcov.rma.Rd | 2 metafor-2.4-0/metafor/man/vif.Rd | 2 metafor-2.4-0/metafor/man/weights.rma.Rd | 2 metafor-2.4-0/metafor/tests/testthat/test_analysis_example_law2016.r | 17 metafor-2.4-0/metafor/tests/testthat/test_analysis_example_miller1978.r | 7 metafor-2.4-0/metafor/tests/testthat/test_analysis_example_rothman2008.r | 65 metafor-2.4-0/metafor/tests/testthat/test_analysis_example_vanhouwelingen2002.r | 4 metafor-2.4-0/metafor/tests/testthat/test_misc_anova.r | 6 metafor-2.4-0/metafor/tests/testthat/test_misc_escalc.r | 49 metafor-2.4-0/metafor/tests/testthat/test_misc_handling_nas.r | 22 metafor-2.4-0/metafor/tests/testthat/test_misc_influence.r | 13 metafor-2.4-0/metafor/tests/testthat/test_misc_setlab.r | 166 metafor-2.4-0/metafor/tests/testthat/test_misc_to_long_table_wide.r |only metafor-2.4-0/metafor/tests/testthat/test_misc_update.r | 12 metafor-2.4-0/metafor/tests/testthat/test_plots_cumulative_forest_plot.r | 27 metafor-2.4-0/metafor/tests/testthat/test_plots_forest_plot_with_subgroups.r | 4 222 files changed, 2974 insertions(+), 3733 deletions(-)
Title: Non-Astonishing Results in R
Description: Simple tools for converting columns to new data types. Intuitive functions for columns with missing values.
Author: David Sjoberg
Maintainer: David Sjoberg <dav.sjob@gmail.com>
Diff between hablar versions 0.2.0 dated 2019-06-09 and 0.3.0 dated 2020-03-19
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Title: Analyze Dose-Volume Histograms and Check Constraints
Description: Functionality for analyzing dose-volume histograms (DVH)
in radiation oncology: Read DVH text files, calculate DVH
metrics as well as generalized equivalent uniform dose (gEUD),
biologically effective dose (BED), equivalent dose in 2 Gy
fractions (EQD2), normal tissue complication probability
(NTCP), and tumor control probability (TCP). Show DVH
diagrams, check and visualize quality assurance constraints
for the DVH. Includes web-based graphical user interface.
Author: Daniel Wollschlaeger [aut, cre],
Heiko Karle [aut],
Heinz Schmidberger [ctb]
Maintainer: Daniel Wollschlaeger <wollschlaeger@uni-mainz.de>
Diff between DVHmetrics versions 0.3.9 dated 2019-07-15 and 0.3.10 dated 2020-03-19
DESCRIPTION | 10 +++++----- MD5 | 36 ++++++++++++++++++------------------ R/parseHiArt.R | 19 +++++++++++++++---- R/parseMonaco.R | 20 ++++++++++++++------ R/runGUI.R | 6 +++++- R/showDVH.R | 27 ++++++++++++++++----------- R/unix/parseDVH.R | 4 ++++ R/windows/parseDVH.R | 4 ++++ build/vignette.rds |binary data/dataConstr.rda |binary data/dataMZ.rda |binary inst/ChangeLog | 14 +++++++++++++- inst/DVHshiny/ABOUT.md | 11 ++++++----- inst/DVHshiny/server.R | 6 ++++-- inst/DVHshiny/ui.R | 7 ++++--- inst/doc/DVHmetrics.pdf |binary inst/doc/DVHshiny.pdf |binary man/DVHmetrics-package.Rd | 4 ++-- man/readDVH.Rd | 4 +++- 19 files changed, 113 insertions(+), 59 deletions(-)
Title: Tools for Computation on Batch Systems
Description: As a successor of the packages 'BatchJobs' and 'BatchExperiments',
this package provides a parallel implementation of the Map function for high
performance computing systems managed by schedulers 'IBM Spectrum LSF'
(<https://www.ibm.com/us-en/marketplace/hpc-workload-management>),
'OpenLava' (<http://www.openlava.org/>), 'Univa Grid Engine'/'Oracle Grid
Engine' (<http://www.univa.com/>), 'Slurm' (<http://slurm.schedmd.com/>),
'TORQUE/PBS'
(<https://adaptivecomputing.com/cherry-services/torque-resource-manager/>),
or 'Docker Swarm' (<https://docs.docker.com/swarm/>).
A multicore and socket mode allow the parallelization on a local machines,
and multiple machines can be hooked up via SSH to create a makeshift
cluster. Moreover, the package provides an abstraction mechanism to define
large-scale computer experiments in a well-organized and reproducible way.
Author: Michel Lang [cre, aut] (<https://orcid.org/0000-0001-9754-0393>),
Bernd Bischl [aut],
Dirk Surmann [ctb] (<https://orcid.org/0000-0003-0873-137X>)
Maintainer: Michel Lang <michellang@gmail.com>
Diff between batchtools versions 0.9.12 dated 2020-01-10 and 0.9.13 dated 2020-03-19
DESCRIPTION | 6 ++--- MD5 | 34 ++++++++++++++++----------------- NEWS.md | 4 +++ R/Registry.R | 9 ++++++-- R/addExperiments.R | 5 ++-- R/chunkIds.R | 12 +++++++++-- R/estimateRuntimes.R | 4 ++- R/killJobs.R | 3 +- R/loadRegistry.R | 5 +++- R/syncRegistry.R | 14 ++++++------- R/testJob.R | 3 +- R/waitForJobs.R | 5 +++- build/vignette.rds |binary inst/doc/batchtools.pdf |binary inst/templates/testJob.tmpl | 2 - man/addExperiments.Rd | 3 +- tests/testthat/test_addExperiments.R | 22 +++++++++++---------- tests/testthat/test_estimateRuntimes.R | 5 +++- 18 files changed, 85 insertions(+), 51 deletions(-)
Title: Quantitative Fatty Acid Signature Analysis in R
Description: An implementation of Quantitative Fatty Acid Signature
Analysis (QFASA) in R. QFASA is a method of estimating the diet
composition of predators. The fundamental unit of information in
QFASA is a fatty acid signature (signature), which is a vector of
proportions describing the composition of fatty acids within lipids.
Signature data from at least one predator and from samples of all
potential prey types are required. Calibration coefficients, which
adjust for the differential metabolism of individual fatty acids by
predators, are also required. Given those data inputs, a predator
signature is modeled as a mixture of prey signatures and its diet
estimate is obtained as the mixture that minimizes a measure of
distance between the observed and modeled signatures. A variety of
estimation options and simulation capabilities are implemented.
Please refer to the vignette for additional details and references.
Author: Jeffrey F. Bromaghin [aut, cre]
Maintainer: Jeffrey F. Bromaghin <jbromaghin@usgs.gov>
Diff between qfasar versions 1.2.0 dated 2017-01-09 and 1.2.1 dated 2020-03-19
DESCRIPTION | 10 MD5 | 58 +-- R/est_diet.R | 15 build/vignette.rds |binary inst/doc/qfasar.R | 4 inst/doc/qfasar.Rmd | 127 ++++---- inst/doc/qfasar.html | 532 +++++++++++++++++++++++++---------- man/add_cc_err.Rd | 2 man/adj_diet_fat.Rd | 2 man/cc_aug.Rd | 2 man/comp_chi_gamma.Rd | 2 man/diet_pool.Rd | 2 man/dimac.Rd | 2 man/est_diet.Rd | 36 +- man/find_boot_ss.Rd | 2 man/gof.Rd | 15 man/lopo.Rd | 2 man/lopo_pool.Rd | 2 man/make_diet_grid.Rd | 2 man/make_diet_rand.Rd | 2 man/make_ghost.Rd | 2 man/make_pred_sigs.Rd | 2 man/make_prey_part.Rd | 2 man/pred_beyond_prey.Rd | 2 man/prep_fa.Rd | 2 man/prep_sig.Rd | 2 tests/testthat/test_make_prey_part.R | 3 tests/testthat/test_prep_fa.R | 3 tests/testthat/test_prep_sig.R | 3 vignettes/qfasar.Rmd | 127 ++++---- 30 files changed, 625 insertions(+), 342 deletions(-)
Title: The Integration Between 'IBM COGNOS TM1' and R
Description: Useful functions to connect to 'TM1' <https://www.ibm.com/uk-en/marketplace/planning-and-analytics> instance from R via REST API. With the functions in the package, data can be imported from 'TM1' via mdx view or native view, data can be sent to 'TM1', processes and chores can be executed, and cube and dimension metadata information can be taken.
Author: Muhammed Ali Onder
Maintainer: Muhammed Ali Onder <muhammedalionder@gmail.com>
Diff between tm1r versions 1.1.3 dated 2019-09-28 and 1.1.4 dated 2020-03-19
DESCRIPTION | 6 MD5 | 60 +++--- R/tm1_api_request.R | 60 +++--- R/tm1_connection.R | 63 +++--- R/tm1_create_element.R | 232 ++++++++++++------------ R/tm1_create_subset.R | 363 +++++++++++++++++++-------------------- R/tm1_create_view.R | 154 ++++++++-------- R/tm1_delete_element.R | 235 ++++++++++++------------- R/tm1_delete_subset.R | 110 ++++++----- R/tm1_delete_view.R | 116 ++++++------ R/tm1_get_config.R | 93 +++++---- R/tm1_get_cube_dimensions.R | 104 +++++------ R/tm1_get_cubes.R | 101 +++++----- R/tm1_get_data.R | 114 ++++++------ R/tm1_get_dimension_attributes.R | 98 +++++----- R/tm1_get_dimension_elements.R | 100 +++++----- R/tm1_get_dimension_subsets.R | 110 ++++++----- R/tm1_get_dimensions.R | 101 +++++----- R/tm1_get_element.R | 178 +++++++++---------- R/tm1_get_instances.R | 60 +++--- R/tm1_get_log.R | 86 ++++----- R/tm1_get_mdx_view.R | 220 +++++++++++------------ R/tm1_get_native_view.R | 228 ++++++++++++------------ R/tm1_get_subset_elements.R | 104 +++++------ R/tm1_logout.R | 52 ++--- R/tm1_run_chore.R | 108 +++++------ R/tm1_run_process.R | 188 ++++++++++---------- R/tm1_send_data.R | 234 ++++++++++++------------- R/tm1_send_dataset.R | 310 ++++++++++++++++----------------- man/tm1_connection.Rd | 55 +++-- man/tm1_get_instances.Rd | 51 ++--- 31 files changed, 2079 insertions(+), 2015 deletions(-)
Title: Tools for Case 1 Best-Worst Scaling (MaxDiff) Designs
Description: Tools to design best-worst scaling designs (i.e., balanced incomplete block designs) and
to analyze data from these designs, using aggregate and individual methods such as: difference
scores, Louviere, Lings, Islam, Gudergan, & Flynn (2013) <doi:10.1016/j.ijresmar.2012.10.002>;
analytical estimation, Lipovetsky & Conklin (2014) <doi:10.1016/j.jocm.2014.02.001>; empirical
Bayes, Lipovetsky & Conklin (2015) <doi:10.1142/S1793536915500028>; Elo, Hollis (2018)
<doi:10.3758/s13428-017-0898-2>; and network-based measures.
Author: Mark White [aut, cre]
Maintainer: Mark White <markhwhiteii@gmail.com>
Diff between bwsTools versions 1.0.1 dated 2019-12-04 and 1.1.0 dated 2020-03-19
bwsTools-1.0.1/bwsTools/R/get_prscrores.R |only bwsTools-1.0.1/bwsTools/man/get_M.Rd |only bwsTools-1.0.1/bwsTools/man/get_b.Rd |only bwsTools-1.0.1/bwsTools/man/get_b0.Rd |only bwsTools-1.0.1/bwsTools/man/get_checks.Rd |only bwsTools-1.0.1/bwsTools/man/get_choice_p.Rd |only bwsTools-1.0.1/bwsTools/man/get_eloresults.Rd |only bwsTools-1.0.1/bwsTools/man/get_eloscores.Rd |only bwsTools-1.0.1/bwsTools/man/get_prscores.Rd |only bwsTools-1.0.1/bwsTools/man/get_walkscores.Rd |only bwsTools-1.1.0/bwsTools/DESCRIPTION | 12 ++-- bwsTools-1.1.0/bwsTools/MD5 | 76 +++++++++++++++++--------- bwsTools-1.1.0/bwsTools/NAMESPACE | 1 bwsTools-1.1.0/bwsTools/NEWS.md | 2 bwsTools-1.1.0/bwsTools/R/ae_mnl.R | 9 +++ bwsTools-1.1.0/bwsTools/R/data.R | 15 +++++ bwsTools-1.1.0/bwsTools/R/elo.R |only bwsTools-1.1.0/bwsTools/R/get_M.R | 1 bwsTools-1.1.0/bwsTools/R/get_b.R | 1 bwsTools-1.1.0/bwsTools/R/get_b0.R | 10 +++ bwsTools-1.1.0/bwsTools/R/get_checks.R | 14 +++- bwsTools-1.1.0/bwsTools/R/get_choice_p.R | 1 bwsTools-1.1.0/bwsTools/R/get_eloresults.R | 12 +++- bwsTools-1.1.0/bwsTools/R/get_eloscores.R | 1 bwsTools-1.1.0/bwsTools/R/get_prscores.R |only bwsTools-1.1.0/bwsTools/R/get_walkscores.R | 1 bwsTools-1.1.0/bwsTools/R/make_bibd.R | 3 + bwsTools-1.1.0/bwsTools/README.md | 14 +++- bwsTools-1.1.0/bwsTools/build |only bwsTools-1.1.0/bwsTools/data/agg.rda |only bwsTools-1.1.0/bwsTools/data/vdata.rda |only bwsTools-1.1.0/bwsTools/inst |only bwsTools-1.1.0/bwsTools/man/agg.Rd |only bwsTools-1.1.0/bwsTools/man/elo.Rd |only bwsTools-1.1.0/bwsTools/man/vdata.Rd |only bwsTools-1.1.0/bwsTools/tests |only bwsTools-1.1.0/bwsTools/vignettes |only 37 files changed, 132 insertions(+), 41 deletions(-)
Title: Descriptive Analysis by Groups
Description: Create data summaries for quality control, extensive reports for exploring data, as well as publication-ready univariate or bivariate tables in several formats (plain text, HTML,LaTeX, PDF, Word or Excel. Create figures to quickly visualise the distribution of your data (boxplots, barplots, normality-plots, etc.). Display statistics (mean, median, frequencies, incidences, etc.). Perform the appropriate tests (t-test, Analysis of variance, Kruskal-Wallis, Fisher, log-rank, ...) depending on the nature of the described variable (normal, non-normal or qualitative). Summarize genetic data (Single Nucleotide Polymorphisms) data displaying Allele Frequencies and performing Hardy-Weinberg Equilibrium tests among other typical statistics and tests for these kind of data.
Author: Isaac Subirana [aut, cre] (<https://orcid.org/0000-0003-1676-0197>),
Joan Salvador [ctb]
Maintainer: Isaac Subirana <isubirana@imim.es>
Diff between compareGroups versions 4.2.0 dated 2019-09-19 and 4.4.1 dated 2020-03-19
DESCRIPTION | 12 MD5 | 63 +-- NAMESPACE | 27 + NEWS.md | 23 + R/cGroupsGUI.R | 20 - R/compare.i.R | 52 +- R/compareGroups.R | 5 R/compareGroups.fit.R | 9 R/confinterval.R | 12 R/createTable.R | 4 R/descrTable.R | 11 R/epitools_functions.R |only R/export2md.R | 8 R/export2mdcbind.R | 4 R/export2pdf.R | 75 ++-- R/export2word.R | 15 R/prepare.r | 26 + R/rbind.createTable.R | 2 R/summ.i.R | 2 R/table.i.R | 41 +- R/z[.createTable.R | 4 inst/app/server.R | 22 - inst/app/ui.R | 3 inst/doc/compareGroups_vignette.html | 614 +++++++++++++++++------------------ man/compareGroups-internal.Rd | 22 + man/compareGroups-package.Rd | 4 man/compareGroups.Rd | 25 - man/createTable.Rd | 6 man/descrTable.Rd | 19 - man/export2pdf.Rd | 42 +- man/export2word.Rd | 27 + man/figures/logo.png |binary man/figures/subplot.png |binary 33 files changed, 711 insertions(+), 488 deletions(-)
Title: Create Full Text Browsers from Annotated Token Lists
Description: Create browsers for reading full texts from a token list format.
Information obtained from text analyses (e.g., topic modeling, word scaling)
can be used to annotate the texts.
Author: Kasper Welbers and Wouter van Atteveldt
Maintainer: Kasper Welbers <kasperwelbers@gmail.com>
Diff between tokenbrowser versions 0.1.2 dated 2020-01-28 and 0.1.4 dated 2020-03-19
DESCRIPTION | 8 ++++---- MD5 | 26 +++++++++++++------------- R/quick_view.r | 8 ++++++-- R/wrap_documents.r | 12 ++++++++++-- man/categorical_browser.Rd | 16 +++++++++++++--- man/category_highlight_tokens.Rd | 10 ++++++++-- man/colorscale_tokens.Rd | 9 +++++++-- man/colorscaled_browser.Rd | 18 ++++++++++++++---- man/create_browser.Rd | 24 +++++++++++++++++++----- man/highlighted_browser.Rd | 16 +++++++++++++--- man/html_template.Rd | 3 +-- man/rescale_var.Rd | 3 +-- man/wrap_documents.Rd | 13 ++++++++++--- tests/testthat/test_tokenvis.r | 14 +++++++------- 14 files changed, 126 insertions(+), 54 deletions(-)
Title: Converts Between R Objects and Simple Feature Objects
Description: Converts between R and Simple Feature 'sf' objects, without depending
on the Simple Feature library. Conversion functions are available at both the R level,
and through 'Rcpp'.
Author: David Cooley [aut, cre]
Maintainer: David Cooley <david.cooley.au@gmail.com>
Diff between sfheaders versions 0.1.0 dated 2020-01-20 and 0.2.1 dated 2020-03-19
DESCRIPTION | 12 MD5 | 162 ++++--- NAMESPACE | 10 NEWS.md | 10 R/RcppExports.R | 28 + R/cast.R |only R/sfc.R | 133 ++++++ R/utils.R | 54 ++ README.md | 3 inst/include/sfheaders/cast |only inst/include/sfheaders/df/sf.hpp | 118 ++++- inst/include/sfheaders/df/sfc.hpp | 201 ++++++--- inst/include/sfheaders/df/sfg.hpp | 212 ++++++++-- inst/include/sfheaders/df/utils.hpp | 39 + inst/include/sfheaders/sf/polygon/sf_polygon.hpp | 6 inst/include/sfheaders/sf/sf_utils.hpp | 14 inst/include/sfheaders/sfc/bbox.hpp | 53 ++ inst/include/sfheaders/sfc/linestring/sfc_linestring.hpp | 10 inst/include/sfheaders/sfc/linestring/sfc_linestrings.hpp | 2 inst/include/sfheaders/sfc/m_range.hpp | 5 inst/include/sfheaders/sfc/multilinestring/sfc_multilinestring.hpp | 70 +-- inst/include/sfheaders/sfc/multilinestring/sfc_multilinestrings.hpp | 3 inst/include/sfheaders/sfc/multipoint/sfc_multipoint.hpp | 8 inst/include/sfheaders/sfc/multipoint/sfc_multipoints.hpp | 2 inst/include/sfheaders/sfc/multipolygon/sfc_multipolygon.hpp | 142 ++---- inst/include/sfheaders/sfc/multipolygon/sfc_multipolygons.hpp | 2 inst/include/sfheaders/sfc/point/sfc_point.hpp | 12 inst/include/sfheaders/sfc/point/sfc_points.hpp | 2 inst/include/sfheaders/sfc/polygon/sfc_polygon.hpp | 92 +--- inst/include/sfheaders/sfc/polygon/sfc_polygons.hpp | 2 inst/include/sfheaders/sfc/sfc_attributes.hpp | 117 ++++- inst/include/sfheaders/sfc/z_range.hpp | 5 inst/include/sfheaders/sfg/linestring/sfg_linestrings.hpp | 3 inst/include/sfheaders/sfg/multilinestring/sfg_multilinestrings.hpp | 2 inst/include/sfheaders/sfg/multipoint/sfg_multipoints.hpp | 2 inst/include/sfheaders/sfg/multipolygon/sfg_multipolygon.hpp | 41 + inst/include/sfheaders/sfg/multipolygon/sfg_multipolygons.hpp | 2 inst/include/sfheaders/sfg/point/sfg_points.hpp | 19 inst/include/sfheaders/sfg/polygon/close_polygon.hpp | 10 inst/include/sfheaders/sfg/polygon/sfg_polygon.hpp | 9 inst/include/sfheaders/sfg/polygon/sfg_polygons.hpp | 2 inst/include/sfheaders/sfg/sfg_attributes.hpp | 19 inst/include/sfheaders/sfg/sfg_types.hpp | 5 inst/include/sfheaders/sfheaders.hpp | 2 inst/include/sfheaders/shapes/list_list_mat/list_list_mat.hpp | 29 - inst/include/sfheaders/shapes/list_mat/list_mat.hpp | 16 inst/include/sfheaders/shapes/mat/mat.hpp | 16 inst/include/sfheaders/shapes/vec/vec.hpp | 8 inst/include/sfheaders/utils/columns/columns.hpp | 19 inst/include/sfheaders/utils/lines/lines.hpp | 6 inst/include/sfheaders/utils/matrix/matrix.hpp | 6 inst/include/sfheaders/utils/subset/subset.hpp | 6 inst/include/sfheaders/utils/vectors/vectors.hpp | 25 - man/sf_bbox.Rd |only man/sf_cast.Rd |only man/sf_linestring.Rd | 11 man/sf_multilinestring.Rd | 13 man/sf_multipoint.Rd | 11 man/sf_multipolygon.Rd | 15 man/sf_point.Rd | 3 man/sf_polygon.Rd | 14 man/sf_remove_holes.Rd |only man/sfc_cast.Rd |only man/sfc_linestring.Rd | 10 man/sfc_multilinestring.Rd | 11 man/sfc_multipoint.Rd | 10 man/sfc_multipolygon.Rd | 16 man/sfc_polygon.Rd | 12 man/sfg_multilinestring.Rd | 10 man/sfg_multipolygon.Rd | 12 man/sfg_polygon.Rd | 11 src/RcppExports.cpp | 92 ++++ src/bbox.cpp | 7 src/cast.cpp |only src/to_df.cpp | 26 + src/to_sfc.cpp | 32 + src/to_sfg.cpp | 18 src/utils.cpp | 3 tests/testthat/test-bbox.R | 88 ++++ tests/testthat/test-cast.R |only tests/testthat/test-df.R | 45 +- tests/testthat/test-df_attributes.R |only tests/testthat/test-holes.R |only tests/testthat/test-sfc_multipolygon.R | 27 + tests/testthat/test-sfg_multipolygon.R | 60 ++ tests/testthat/test-utils.R | 4 86 files changed, 1756 insertions(+), 581 deletions(-)
Title: Client for Various 'CrossRef' 'APIs'
Description: Client for various 'CrossRef' 'APIs', including 'metadata' search
with their old and newer search 'APIs', get 'citations' in various formats
(including 'bibtex', 'citeproc-json', 'rdf-xml', etc.), convert 'DOIs'
to 'PMIDs', and 'vice versa', get citations for 'DOIs', and get links to
full text of articles when available.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>),
Hao Zhu [aut],
Najko Jahn [aut],
Carl Boettiger [aut],
Karthik Ram [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rcrossref versions 0.9.2 dated 2019-05-04 and 1.0.0 dated 2020-03-19
rcrossref-0.9.2/rcrossref/inst/doc/crossref_vignette.Rmd |only rcrossref-0.9.2/rcrossref/inst/doc/crossref_vignette.html |only rcrossref-0.9.2/rcrossref/inst/vign |only rcrossref-0.9.2/rcrossref/vignettes/crossref_vignette.Rmd |only rcrossref-1.0.0/rcrossref/DESCRIPTION | 14 rcrossref-1.0.0/rcrossref/LICENSE | 2 rcrossref-1.0.0/rcrossref/MD5 | 74 - rcrossref-1.0.0/rcrossref/NEWS.md | 16 rcrossref-1.0.0/rcrossref/R/crAddins.R | 3 rcrossref-1.0.0/rcrossref/R/cr_fundref.r | 8 rcrossref-1.0.0/rcrossref/R/cr_journals.r | 8 rcrossref-1.0.0/rcrossref/R/cr_members.r | 8 rcrossref-1.0.0/rcrossref/R/cr_prefixes.r | 8 rcrossref-1.0.0/rcrossref/R/cr_types.R | 10 rcrossref-1.0.0/rcrossref/R/cr_works.R | 12 rcrossref-1.0.0/rcrossref/R/id_converter.R | 3 rcrossref-1.0.0/rcrossref/R/rcrossref-package.R | 10 rcrossref-1.0.0/rcrossref/R/requestor.R | 12 rcrossref-1.0.0/rcrossref/R/zzz.R | 1 rcrossref-1.0.0/rcrossref/README.md | 255 ++--- rcrossref-1.0.0/rcrossref/build/vignette.rds |binary rcrossref-1.0.0/rcrossref/inst/doc/crossref_filters.Rmd | 17 rcrossref-1.0.0/rcrossref/inst/doc/crossref_filters.html | 480 +++++----- rcrossref-1.0.0/rcrossref/inst/doc/rcrossref.R |only rcrossref-1.0.0/rcrossref/inst/doc/rcrossref.Rmd |only rcrossref-1.0.0/rcrossref/inst/doc/rcrossref.html |only rcrossref-1.0.0/rcrossref/man/cr_agency.Rd | 2 rcrossref-1.0.0/rcrossref/man/cr_citation_count.Rd | 9 rcrossref-1.0.0/rcrossref/man/cr_cn.Rd | 22 rcrossref-1.0.0/rcrossref/man/cr_funders.Rd | 113 +- rcrossref-1.0.0/rcrossref/man/cr_journals.Rd | 114 +- rcrossref-1.0.0/rcrossref/man/cr_licenses.Rd | 37 rcrossref-1.0.0/rcrossref/man/cr_members.Rd | 114 +- rcrossref-1.0.0/rcrossref/man/cr_prefixes.Rd | 113 +- rcrossref-1.0.0/rcrossref/man/cr_types.Rd | 115 +- rcrossref-1.0.0/rcrossref/man/cr_works.Rd | 118 +- rcrossref-1.0.0/rcrossref/man/id_converter.Rd | 3 rcrossref-1.0.0/rcrossref/man/rcrossref-package.Rd | 12 rcrossref-1.0.0/rcrossref/tests/testthat/test-field_queries.R |only rcrossref-1.0.0/rcrossref/vignettes/crossref_filters.Rmd | 17 rcrossref-1.0.0/rcrossref/vignettes/rcrossref.Rmd |only 41 files changed, 1071 insertions(+), 659 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)
Maintainer: Xavier Robin <pROC-cran@xavier.robin.name>
Diff between pROC versions 1.16.1 dated 2020-01-14 and 1.16.2 dated 2020-03-19
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 3 +++ tests/testthat/test-onload.R | 1 + 4 files changed, 11 insertions(+), 7 deletions(-)
Title: Bayesian Logistic Regression for Oncology Dose-Escalation Trials
Description: Bayesian logistic regression model with optional
EXchangeability-NonEXchangeability parameter modelling for flexible
borrowing from historical or concurrent data-sources. The safety model
can guide dose-escalation decisions for adaptive oncology Phase I
dose-escalation trials which involve an arbitrary number of
drugs. Please refer to Neuenschwander et al. (2008)
<doi:10.1002/sim.3230> and Neuenschwander et al. (2016)
<doi:10.1080/19466315.2016.1174149> for details on the methodology.
Author: Novartis Pharma AG [cph],
Sebastian Weber [aut, cre],
Lukas A. Widmer [aut],
Andrew Bean [aut],
Trustees of Columbia University [cph] (R/stanmodels.R, configure,
configure.win)
Maintainer: Sebastian Weber <sebastian.weber@novartis.com>
Diff between OncoBayes2 versions 0.6-0 dated 2020-02-11 and 0.6-3 dated 2020-03-19
DESCRIPTION | 12 MD5 | 26 - R/sysdata.rda |binary inst/NEWS | 15 inst/doc/OncoBayes2.pdf |binary inst/doc/introduction.R | 2 inst/doc/introduction.Rmd | 2 inst/doc/introduction.html | 282 ++++++------ inst/sbc/calibration.md5 | 6 inst/sbc/sbc_report.html | 490 ++++++++++----------- inst/stan/blrm_exnex.stan | 92 ++- src/stanExports_blrm_exnex.h | 907 +++++++++++++++++++-------------------- tests/testthat/test-blrm_exnex.R | 12 vignettes/introduction.Rmd | 2 14 files changed, 929 insertions(+), 919 deletions(-)
Title: Discovery of Process Models with the Heuristics Miner
Description: Provides the heuristics miner algorithm for process discovery
as proposed by Weijters et al. (2011) <doi:10.1109/CIDM.2011.5949453>. The
algorithm builds a causal net from an event log created with the 'bupaR'
package. Event logs are a set of ordered sequences of events for which
'bupaR' provides the S3 class eventlog(). The discovered causal nets
can be visualised as 'htmlwidgets' and it is possible to annotate them with
the occurrence frequency or processing and waiting time of process
activities.
Author: Felix Mannhardt [aut, cre]
Maintainer: Felix Mannhardt <felix.mannhardt@sintef.no>
Diff between heuristicsmineR versions 0.2.2 dated 2020-02-26 and 0.2.3 dated 2020-03-19
DESCRIPTION | 8 +++---- MD5 | 30 +++++++++++++-------------- NAMESPACE | 2 - NEWS.md | 4 +++ R/causal_net.R | 5 ++-- man/L_heur_1.Rd | 4 ++- man/L_heur_2.Rd | 4 ++- man/as.petrinet.Rd | 40 ++++++++++++++++++------------------- man/causal_net.Rd | 5 ++-- man/causal_performance.Rd | 4 +-- man/hospital_multi_perspective.Rd | 4 ++- man/parallel_matrix_lifecycle.Rd | 34 +++++++++++++++---------------- man/pipe.Rd | 22 ++++++++++---------- man/precedence_matrix_lifecycle.Rd | 34 +++++++++++++++---------------- man/print.causal_net.Rd | 30 +++++++++++++-------------- man/print.dependency_matrix.Rd | 30 +++++++++++++-------------- 16 files changed, 136 insertions(+), 124 deletions(-)
More information about heuristicsmineR at CRAN
Permanent link
Title: Tools for Modelling of Animal Flight Performance
Description: Allows estimation and modelling of flight costs in animal (vertebrate) flight,
implementing the aerodynamic power model described in Klein Heerenbrink et al.
(2015) <doi:10.1098/rspa.2014.0952>. Taking inspiration from the program
'Flight', developed by Colin Pennycuick (Pennycuick (2008) "Modelling the flying
bird". Amsterdam: Elsevier. ISBN 0-19-857721-4), flight performance is estimated
based on basic morphological measurements such as body mass, wingspan and wing
area. 'afpt' can be used to make predictions on how animals should adjust their
flight behaviour and wingbeat kinematics to varying flight conditions.
Author: Marco KleinHeerenbrink [aut, cre],
Anders Hedenström [fnd]
Maintainer: Marco KleinHeerenbrink <Marco.KleinHeerenbrink@zoo.ox.ac.uk>
Diff between afpt versions 1.1.0.0 dated 2020-03-17 and 1.1.0.1 dated 2020-03-19
afpt-1.1.0.0/afpt/inst/doc/afpt-advanced-usage.R |only afpt-1.1.0.0/afpt/inst/doc/afpt-advanced-usage.Rmd |only afpt-1.1.0.0/afpt/inst/doc/afpt-advanced-usage.html |only afpt-1.1.0.0/afpt/vignettes/afpt-advanced-usage.Rmd |only afpt-1.1.0.1/afpt/DESCRIPTION | 8 +- afpt-1.1.0.1/afpt/MD5 | 19 ++----- afpt-1.1.0.1/afpt/build/partial.rdb |binary afpt-1.1.0.1/afpt/build/vignette.rds |binary afpt-1.1.0.1/afpt/inst/doc/afpt-aerodynamic-model.html | 4 - afpt-1.1.0.1/afpt/inst/doc/afpt-basic-usage.html | 4 - afpt-1.1.0.1/afpt/inst/doc/afpt-multiple-birds.html | 4 - afpt-1.1.0.1/afpt/tests/testthat/Rplots.pdf |only afpt-1.1.0.1/afpt/vignettes/references.bib | 46 ----------------- 13 files changed, 18 insertions(+), 67 deletions(-)
Title: Develop Actuarial Models
Description: Actuarial reports are prepared for the last day of a specific
period, such as a month, a quarter or a year. Actuarial models assume that
certain events happen at the beginning or end of periods. The package
contains functions to easily refer to the first or last (working) day
within a specific period relative to a base date to facilitate actuarial
reporting and to compare results.
Author: Zuzanna Chmielewska [aut, cre]
(<https://orcid.org/0000-0001-7622-3321>)
Maintainer: Zuzanna Chmielewska <zchmielewska@gmail.com>
Diff between actuaryr versions 1.0.0 dated 2020-03-06 and 1.1.0 dated 2020-03-19
DESCRIPTION | 12 +-- MD5 | 37 +++++++--- NAMESPACE | 5 + NEWS.md | 5 + R/compare.R |only R/dref_mtd.R |only R/dref_qtd.R |only R/dref_ytd.R |only R/globals.R |only R/utils.R |only README.md | 82 +++++++---------------- inst/doc/actuaryr-vignette.R | 51 ++++++++++++++ inst/doc/actuaryr-vignette.Rmd | 142 ++++++++++++++++++++++++++++++++++++---- inst/doc/actuaryr-vignette.html | 96 ++++++++++++++++++++++++--- man/as.Rd |only man/coerceToCharacter.Rd |only man/compare.Rd |only man/dref_mtd.Rd |only man/dref_qtd.Rd |only man/dref_ytd.Rd |only man/getCommonColumns.Rd |only man/getCommonNrRows.Rd |only man/getCommonTypes.Rd |only tests/testthat/test_compare.R |only tests/testthat/test_dref.R | 18 +++++ vignettes/actuaryr-vignette.Rmd | 142 ++++++++++++++++++++++++++++++++++++---- vignettes/img/dref_mtd.png |only vignettes/img/dref_qtd.png |only vignettes/img/dref_ytd.png |only 29 files changed, 484 insertions(+), 106 deletions(-)
Title: Easily Carry Out Latent Profile Analysis (LPA) Using Open-Source
or Commercial Software
Description: An interface to the 'mclust' package to easily
carry out latent profile analysis ("LPA"). Provides functionality to
estimate commonly-specified models. Follows a tidy approach, in that
output is in the form of a data frame that can subsequently be
computed on. Also has functions to interface to the commercial 'MPlus'
software via the 'MplusAutomation' package.
Author: Joshua M Rosenberg [aut, cre],
Caspar van Lissa [aut],
Jennifer A Schmidt [ctb],
Patrick N Beymer [ctb],
Daniel Anderson [ctb],
Matthew J. Schell [ctb]
Maintainer: Joshua M Rosenberg <jmichaelrosenberg@gmail.com>
Diff between tidyLPA versions 1.0.5 dated 2020-02-09 and 1.0.6 dated 2020-03-19
tidyLPA-1.0.5/tidyLPA/man/tidyLPA-deprecated.Rd |only tidyLPA-1.0.6/tidyLPA/DESCRIPTION | 6 tidyLPA-1.0.6/tidyLPA/MD5 | 15 -- tidyLPA-1.0.6/tidyLPA/NEWS.md | 3 tidyLPA-1.0.6/tidyLPA/inst/CITATION | 2 tidyLPA-1.0.6/tidyLPA/inst/doc/Introduction_to_tidyLPA.Rmd | 2 tidyLPA-1.0.6/tidyLPA/inst/doc/Introduction_to_tidyLPA.html | 74 +++++----- tidyLPA-1.0.6/tidyLPA/inst/doc/benchmarking-mclust-and-mplus.html | 4 tidyLPA-1.0.6/tidyLPA/vignettes/Introduction_to_tidyLPA.Rmd | 2 9 files changed, 55 insertions(+), 53 deletions(-)
Title: Tidy Data and 'Geoms' for Bayesian Models
Description: Compose data for and extract, manipulate, and visualize posterior draws from Bayesian models
('JAGS', 'Stan', 'rstanarm', 'brms', 'MCMCglmm', 'coda', ...) in a tidy data format. Functions are provided
to help extract tidy data frames of draws from Bayesian models and that generate point
summaries and intervals in a tidy format. In addition, 'ggplot2' 'geoms' and 'stats' are provided for
common visualization primitives like points with multiple uncertainty intervals, eye plots (intervals plus
densities), and fit curves with multiple, arbitrary uncertainty bands.
Author: Matthew Kay [aut, cre],
Timothy Mastny [ctb]
Maintainer: Matthew Kay <mjskay@umich.edu>
Diff between tidybayes versions 2.0.1 dated 2020-01-28 and 2.0.2 dated 2020-03-19
DESCRIPTION | 10 MD5 | 127 NAMESPACE | 684 ++--- NEWS.md | 10 R/binning_methods.R | 2 R/compare_levels.R | 6 R/gather_variables.R | 4 R/parse_dist.R | 2 R/predicted_draws.R | 15 R/stat_sample_slabinterval.R | 29 build/partial.rdb |binary inst/doc/freq-uncertainty-vis.html | 18 inst/doc/slabinterval.R | 10 inst/doc/slabinterval.Rmd | 13 inst/doc/slabinterval.html | 282 +- inst/doc/tidy-brms.R | 2 inst/doc/tidy-brms.Rmd | 2 inst/doc/tidy-brms.html | 1285 +++++----- inst/doc/tidy-rstanarm.html | 42 inst/doc/tidybayes-residuals.html | 50 inst/doc/tidybayes.html | 305 +- man/gather_variables.Rd | 2 man/scales.Rd | 3 man/stat_sample_slabinterval.Rd | 5 tests/figs/geom-lineribbon/basic-stat-dist-lineribbon.svg | 128 tests/figs/geom-lineribbon/one-group-geom-lineribbon-manual-aes-in-ggplot-call.svg | 130 - tests/figs/geom-lineribbon/one-group-geom-lineribbon-reverse-order.svg | 130 - tests/figs/geom-lineribbon/one-group-geom-lineribbon.svg | 130 - tests/figs/geom-lineribbon/one-group-stat-lineribbon-reverse-order-mean-qi.svg | 132 - tests/figs/geom-lineribbon/one-group-stat-lineribbon.svg | 132 - tests/figs/geom-lineribbon/two-group-stat-dist-lineribbon.svg | 138 - tests/figs/geom-lineribbon/two-group-stat-lineribbons-grouped-by-color-and-linetype.svg | 156 - tests/figs/geom-lineribbon/two-group-stat-lineribbons-grouped-by-group.svg | 140 - tests/figs/geom-pointinterval/grouped-pointintervals-h.svg | 166 - tests/figs/geom-slabinterval/halfeye-with-normalize-all.svg | 260 +- tests/figs/geom-slabinterval/halfeye-with-normalize-groups.svg | 260 +- tests/figs/geom-slabinterval/halfeye-with-normalize-none.svg | 260 +- tests/figs/geom-slabinterval/halfeye-with-normalize-panels.svg | 260 +- tests/figs/geom-slabinterval/halfeye-with-normalize-xy.svg | 260 +- tests/figs/parse-dist/lkj-marginalization-works.svg | 96 tests/figs/scales/direct-scale-setting.svg | 100 tests/figs/scales/interval-color-continuous-mapping.svg | 148 - tests/figs/scales/point-color-continuous-mapping.svg | 148 - tests/figs/scales/point-fill-continuous-mapping.svg | 148 - tests/figs/scales/slab-color-continuous-mapping.svg | 154 - tests/figs/scales/slab-fill-continuous-mapping.svg | 148 - tests/figs/stat-dist/dist-ccdfintervalh-log-scale-transform.svg | 120 tests/figs/stat-dist/dist-ccdfintervalh-reverse-scale-transform.svg | 104 tests/figs/stat-dist/dist-halfeyeh-log-scale-transform.svg | 120 tests/figs/stat-dist/dist-halfeyeh-reverse-scale-transform.svg | 104 tests/figs/stat-dist/gradient-fill-color-halfeye.svg | 188 - tests/figs/stat-eye/two-parameter-numeric-horizontal-half-eye-fill.svg | 132 - tests/models/models.brms.m_multinom.rds |only tests/testthat/test.add_draws.R | 5 tests/testthat/test.compare_levels.R | 36 tests/testthat/test.fitted_draws.R | 69 tests/testthat/test.gather_draws.R | 2 tests/testthat/test.gather_emmeans_draws.R | 12 tests/testthat/test.gather_variables.R | 2 tests/testthat/test.point_interval.R | 7 tests/testthat/test.predicted_draws.R | 60 tests/testthat/test.residual_draws.R | 5 tests/testthat/test.spread_draws.R | 51 vignettes/slabinterval.Rmd | 13 vignettes/tidy-brms.Rmd | 2 65 files changed, 3881 insertions(+), 3683 deletions(-)
Title: Temporal and Spatio-Temporal Modeling and Monitoring of Epidemic
Phenomena
Description: Statistical methods for the modeling and monitoring of time series
of counts, proportions and categorical data, as well as for the modeling
of continuous-time point processes of epidemic phenomena.
The monitoring methods focus on aberration detection in count data time
series from public health surveillance of communicable diseases, but
applications could just as well originate from environmetrics,
reliability engineering, econometrics, or social sciences. The package
implements many typical outbreak detection procedures such as the
(improved) Farrington algorithm, or the negative binomial GLR-CUSUM
method of H<f6>hle and Paul (2008) <doi:10.1016/j.csda.2008.02.015>.
A novel CUSUM approach combining logistic and multinomial logistic
modeling is also included. The package contains several real-world data
sets, the ability to simulate outbreak data, and to visualize the
results of the monitoring in a temporal, spatial or spatio-temporal
fashion. A recent overview of the available monitoring procedures is
given by Salmon et al. (2016) <doi:10.18637/jss.v070.i10>.
For the retrospective analysis of epidemic spread, the package provides
three endemic-epidemic modeling frameworks with tools for visualization,
likelihood inference, and simulation. hhh4() estimates models for
(multivariate) count time series following Paul and Held (2011)
<doi:10.1002/sim.4177> and Meyer and Held (2014) <doi:10.1214/14-AOAS743>.
twinSIR() models the susceptible-infectious-recovered (SIR) event
history of a fixed population, e.g, epidemics across farms or networks,
as a multivariate point process as proposed by H<f6>hle (2009)
<doi:10.1002/bimj.200900050>. twinstim() estimates self-exciting point
process models for a spatio-temporal point pattern of infective events,
e.g., time-stamped geo-referenced surveillance data, as proposed by
Meyer et al. (2012) <doi:10.1111/j.1541-0420.2011.01684.x>.
A recent overview of the implemented space-time modeling frameworks
for epidemic phenomena is given by Meyer et al. (2017)
<doi:10.18637/jss.v077.i11>.
Author: Michael H<f6>hle [aut, ths] (<https://orcid.org/0000-0002-0423-6702>),
Sebastian Meyer [aut, cre] (<https://orcid.org/0000-0002-1791-9449>),
Michaela Paul [aut],
Leonhard Held [ctb, ths],
Howard Burkom [ctb],
Thais Correa [ctb],
Mathias Hofmann [ctb],
Christian Lang [ctb],
Juliane Manitz [ctb],
Andrea Riebler [ctb],
Daniel Saban<e9>s Bov<e9> [ctb],
Ma<eb>lle Salmon [ctb],
Dirk Schumacher [ctb],
Stefan Steiner [ctb],
Mikko Virtanen [ctb],
Wei Wei [ctb],
Valentin Wimmer [ctb],
R Core Team [ctb] (A few code segments are modified versions of code
from base R)
Maintainer: Sebastian Meyer <seb.meyer@fau.de>
Diff between surveillance versions 1.17.3 dated 2019-12-16 and 1.18.0 dated 2020-03-19
surveillance-1.17.3/surveillance/R/algo_hhh.R |only surveillance-1.17.3/surveillance/R/sim_HHH.R |only surveillance-1.17.3/surveillance/man/algo.hhh.Rd |only surveillance-1.17.3/surveillance/man/algo.hhh.grid.Rd |only surveillance-1.17.3/surveillance/man/create.grid.Rd |only surveillance-1.17.3/surveillance/man/loglikelihood.Rd |only surveillance-1.17.3/surveillance/man/make.design.Rd |only surveillance-1.17.3/surveillance/man/meanResponse.Rd |only surveillance-1.17.3/surveillance/man/predict.ah.Rd |only surveillance-1.17.3/surveillance/man/residuals.ah.Rd |only surveillance-1.17.3/surveillance/man/simHHH.Rd |only surveillance-1.17.3/surveillance/tests/testthat/test-hhh4+algo.hhh.R |only surveillance-1.18.0/surveillance/DESCRIPTION | 8 surveillance-1.18.0/surveillance/MD5 | 110 surveillance-1.18.0/surveillance/NAMESPACE | 26 surveillance-1.18.0/surveillance/R/algo_outbreakP.R | 43 surveillance-1.18.0/surveillance/R/epidata.R | 9 surveillance-1.18.0/surveillance/R/hhh4.R | 17 surveillance-1.18.0/surveillance/R/hhh4_amplitudeShift.R |only surveillance-1.18.0/surveillance/R/hhh4_methods.R | 15 surveillance-1.18.0/surveillance/R/hhh4_plot.R | 14 surveillance-1.18.0/surveillance/R/nowcast.R | 2297 +++++----- surveillance-1.18.0/surveillance/R/pairedbinCUSUM.R | 52 surveillance-1.18.0/surveillance/R/plapply.R | 16 surveillance-1.18.0/surveillance/R/twinstim_siaf_exponential.R |only surveillance-1.18.0/surveillance/R/twinstim_siaf_polyCub_iso.R | 8 surveillance-1.18.0/surveillance/build/partial.rdb |binary surveillance-1.18.0/surveillance/build/vignette.rds |binary surveillance-1.18.0/surveillance/inst/NEWS.Rd | 40 surveillance-1.18.0/surveillance/inst/doc/glrnb.pdf |binary surveillance-1.18.0/surveillance/inst/doc/hhh4.R | 12 surveillance-1.18.0/surveillance/inst/doc/hhh4.Rnw | 6 surveillance-1.18.0/surveillance/inst/doc/hhh4.pdf |binary surveillance-1.18.0/surveillance/inst/doc/hhh4_spacetime.R | 3 surveillance-1.18.0/surveillance/inst/doc/hhh4_spacetime.Rnw | 4 surveillance-1.18.0/surveillance/inst/doc/hhh4_spacetime.pdf |binary surveillance-1.18.0/surveillance/inst/doc/monitoringCounts.pdf |binary surveillance-1.18.0/surveillance/inst/doc/surveillance.R | 75 surveillance-1.18.0/surveillance/inst/doc/surveillance.Rnw | 124 surveillance-1.18.0/surveillance/inst/doc/surveillance.pdf |binary surveillance-1.18.0/surveillance/inst/doc/twinSIR.Rnw | 1 surveillance-1.18.0/surveillance/inst/doc/twinSIR.pdf |binary surveillance-1.18.0/surveillance/inst/doc/twinstim.R | 16 surveillance-1.18.0/surveillance/inst/doc/twinstim.Rnw | 57 surveillance-1.18.0/surveillance/inst/doc/twinstim.pdf |binary surveillance-1.18.0/surveillance/man/algo.rogerson.Rd | 13 surveillance-1.18.0/surveillance/man/hhh4.Rd | 5 surveillance-1.18.0/surveillance/man/hhh4_plot.Rd | 17 surveillance-1.18.0/surveillance/man/permutationTest.Rd | 10 surveillance-1.18.0/surveillance/man/surveillance-defunct.Rd | 24 surveillance-1.18.0/surveillance/man/twinstim.Rd | 5 surveillance-1.18.0/surveillance/man/twinstim_iaf.Rd | 31 surveillance-1.18.0/surveillance/man/twinstim_siaf_simulatePC.Rd | 2 surveillance-1.18.0/surveillance/src/twinstim_siaf_polyCub_iso.c | 19 surveillance-1.18.0/surveillance/tests/testthat/test-siafs.R | 12 surveillance-1.18.0/surveillance/vignettes/hhh4.Rnw | 6 surveillance-1.18.0/surveillance/vignettes/hhh4_spacetime.Rnw | 4 surveillance-1.18.0/surveillance/vignettes/surveillance-cache.RData |binary surveillance-1.18.0/surveillance/vignettes/surveillance-hmm.pdf |binary surveillance-1.18.0/surveillance/vignettes/surveillance.Rnw | 124 surveillance-1.18.0/surveillance/vignettes/twinSIR.Rnw | 1 surveillance-1.18.0/surveillance/vignettes/twinstim-cache.RData |binary surveillance-1.18.0/surveillance/vignettes/twinstim.Rnw | 57 63 files changed, 1545 insertions(+), 1738 deletions(-)
Title: Fitting RT-MPT Models
Description: Fit response-time extended multinomial processing tree (RT-MPT) models by Klauer and
Kellen (2018) <doi:10.1016/j.jmp.2017.12.003>. The RT-MPT class not only incorporate
frequencies like traditional multinomial processing tree (MPT) models, but also latencies. This enables it
to estimate process completion times and encoding plus motor execution times next to the process probabilities
of traditional MPTs. 'rtmpt' is a Bayesian framework and posterior samples are sampled using a Metropolis-Gibbs
sampler like the one described in the Klauer and Kellen (2018), but with some modifications. Other than in
the original C++ program we use the free and open source GNU Scientific Library (GSL). There is also the
possibility to suppress single process completion times.
Author: Raphael Hartmann [aut, cre],
Karl C. Klauer [cph, aut, ctb, ths],
Henrik Singmann [aut, ctb, cph],
Jean Marie Linhart [cph]
Maintainer: Raphael Hartmann <raphael.hartmann@protonmail.com>
Diff between rtmpt versions 0.1-18 dated 2020-02-04 and 0.1-19 dated 2020-03-19
DESCRIPTION | 6 MD5 | 34 - NAMESPACE | 2 build/vignette.rds |binary inst/doc/rtmpt_intro.R | 364 +++++----- inst/doc/rtmpt_intro.html | 1561 ++++++++++++++++++++++------------------------ man/SimData.Rd | 110 +-- man/fit_rtmpt.Rd | 309 ++++----- man/fit_rtmpt_SBC.Rd | 305 ++++---- man/set_params.Rd | 154 ++-- man/set_resps.Rd | 114 +-- man/sim_rtmpt_data.Rd | 288 ++++---- man/sim_rtmpt_data_SBC.Rd | 212 +++--- man/to_rtmpt_data.Rd | 112 +-- man/to_rtmpt_model.Rd | 216 +++--- src/mvtimes.cpp | 6 src/r_wrapper.cpp | 2 src/rts.h | 2 18 files changed, 1878 insertions(+), 1919 deletions(-)
Title: Translation of Base R-Like Functions for 'data.table' Objects
Description: Some heavily used base R functions are reconstructed to also be compliant to data.table objects. Also, some general helper functions that could be of interest for working with data.table objects are included.
Author: Robin Van Oirbeek
Maintainer: Robin Van Oirbeek <robin.vanoirbeek@gmail.com>
Diff between R2DT versions 0.1 dated 2018-01-26 and 0.2 dated 2020-03-19
DESCRIPTION | 6 +++--- MD5 | 40 ++++++++++++++++++++-------------------- R/funcDT.R | 24 ++++++++++++++++++++++++ man/asCharacterDT.Rd | 1 + man/asFactorDT.Rd | 1 + man/asIntegerDT.Rd | 1 + man/asLogicalDT.Rd | 1 + man/checkDT.Rd | 1 + man/detectWeirdLevelNamesDT.Rd | 2 ++ man/extractLevelDT.Rd | 2 ++ man/extractRefLevelDT.Rd | 2 ++ man/isCharacterDT.Rd | 1 + man/isFactorDT.Rd | 1 + man/isIntegerDT.Rd | 1 + man/isLogicalDT.Rd | 1 + man/isNumericDT.Rd | 1 + man/lowFreqLevel2MissingDT.Rd | 2 ++ man/rbindDT.Rd | 8 -------- man/removeEmptyLevelsDT.Rd | 1 + man/setRefLevelDT.Rd | 2 ++ man/sortByRowIndexDT.Rd | 1 + 21 files changed, 69 insertions(+), 31 deletions(-)
Title: Thresholds and Invariant Intervals for Network Meta-Analysis
Description: Calculation and presentation of decision-invariant bias adjustment
thresholds and intervals for Network Meta-Analysis, as described by
Phillippo et al. (2018) <doi:10.1111/rssa.12341>. These describe the
smallest changes to the data that would result in a change of decision.
Author: David Phillippo [aut, cre]
Maintainer: David Phillippo <david.phillippo@bristol.ac.uk>
Diff between nmathresh versions 0.1.4 dated 2019-01-07 and 0.1.5 dated 2020-03-19
nmathresh-0.1.4/nmathresh/vignettes/Thumbs.db |only nmathresh-0.1.5/nmathresh/DESCRIPTION | 9 nmathresh-0.1.5/nmathresh/MD5 | 37 - nmathresh-0.1.5/nmathresh/NAMESPACE | 2 nmathresh-0.1.5/nmathresh/NEWS.md | 5 nmathresh-0.1.5/nmathresh/R/nma_thresh.R | 12 nmathresh-0.1.5/nmathresh/R/recon_vcov.R | 30 - nmathresh-0.1.5/nmathresh/build/vignette.rds |binary nmathresh-0.1.5/nmathresh/inst/doc/Examples.html | 27 - nmathresh-0.1.5/nmathresh/man/SocAnx.post.cov.Rd | 62 +-- nmathresh-0.1.5/nmathresh/man/SocAnx.post.summary.Rd | 78 +-- nmathresh-0.1.5/nmathresh/man/Thrombo.post.cov.Rd | 52 +- nmathresh-0.1.5/nmathresh/man/Thrombo.post.summary.Rd | 66 +-- nmathresh-0.1.5/nmathresh/man/d_ab2i.Rd | 92 ++-- nmathresh-0.1.5/nmathresh/man/get.int.Rd | 92 ++-- nmathresh-0.1.5/nmathresh/man/nma_thresh.Rd | 341 ++++++++-------- nmathresh-0.1.5/nmathresh/man/recon_vcov.Rd | 185 ++++---- nmathresh-0.1.5/nmathresh/man/thresh-class.Rd | 88 ++-- nmathresh-0.1.5/nmathresh/man/thresh_2d.Rd | 202 +++++---- nmathresh-0.1.5/nmathresh/man/thresh_forest.Rd | 372 +++++++++--------- 20 files changed, 915 insertions(+), 837 deletions(-)
Title: The Complete R6 Probability Distributions Interface
Description: An R6 object oriented distributions package. Unified interface for 42 probability distributions and 11 kernels including functionality for multiple scientific types. Additionally functionality for composite distributions and numerical imputation. Design patterns including wrappers and decorators are described in Gamma et al. (1994, ISBN:0-201-63361-2). For quick reference of probability distributions including d/p/q/r functions and results we refer to McLaughlin, M. P. (2001). Additionally Devroye (1986, ISBN:0-387-96305-7) for sampling the Dirichlet distribution, Gentle (2009) <doi:10.1007/978-0-387-98144-4> for sampling the Multivariate Normal distribution and Michael et al. (1976) <doi:10.2307/2683801> for sampling the Wald distribution.
Author: Raphael Sonabend [aut, cre] (<https://orcid.org/0000-0001-9225-4654>),
Franz Kiraly [aut],
Peter Ruckdeschel [ctb] (Author of distr),
Matthias Kohl [ctb] (Author of distr),
Shen Chen [ctb],
Jordan Deenichin [ctb],
Chengyang Gao [ctb],
Chloe Zhaoyuan Gu [ctb],
Yunjie He [ctb],
Xiaowen Huang [ctb],
Shuhan Liu [ctb],
Runlong Yu [ctb],
Chijing Zeng [ctb],
Qian Zhou [ctb]
Maintainer: Raphael Sonabend <raphael.sonabend.15@ucl.ac.uk>
Diff between distr6 versions 1.3.4 dated 2020-02-19 and 1.3.5 dated 2020-03-19
DESCRIPTION | 9 MD5 | 353 ++++++++------- NAMESPACE | 1 NEWS.md | 7 R/Distribution.R | 491 ++++++++++------------ R/DistributionDecorator.R | 1 R/DistributionDecorator_CoreStatistics.R | 16 R/DistributionDecorator_ExoticStatistics.R | 22 R/DistributionDecorator_FunctionImputation.R | 22 R/Distribution_Kernel.R | 30 - R/Distribution_SDistribution.R | 28 - R/SDistribution_Categorical.R | 14 R/SDistribution_DiscreteUniform.R | 4 R/SDistribution_Empirical.R | 14 R/SDistribution_Erlang.R |only R/SDistribution_NegBinomal.R | 8 R/SDistribution_Weibull.R | 2 R/Wrapper.R | 28 - R/Wrapper_Convolution.R | 10 R/Wrapper_HuberizedDistribution.R | 50 +- R/Wrapper_ProductDistribution.R | 4 R/Wrapper_TruncatedDistribution.R | 26 - R/Wrapper_VectorDistribution.R | 26 - R/assertions.R | 26 - R/c.Distribution.R | 4 R/decorate.R | 2 R/getParameterSet.R | 22 R/lines.R | 4 R/plot.R | 10 R/simulateEmpiricalDistribution.R | 6 R/zzz.R | 2 inst/doc/distr6.R | 8 inst/doc/distr6.html | 22 inst/doc/distr6.rmd | 8 man/Arcsine.Rd | 28 - man/ArrayDistribution-deprecated.Rd | 28 - man/Bernoulli.Rd | 28 - man/Beta.Rd | 28 - man/BetaNoncentral.Rd | 28 - man/Binomial.Rd | 28 - man/Categorical.Rd | 28 - man/Cauchy.Rd | 28 - man/ChiSquared.Rd | 28 - man/ChiSquaredNoncentral.Rd | 28 - man/Cosine.Rd | 28 - man/Degenerate.Rd | 28 - man/Dirichlet.Rd | 28 - man/DiscreteUniform.Rd | 28 - man/Distribution.Rd | 28 - man/DistributionWrapper.Rd | 28 - man/Empirical.Rd | 28 - man/Epanechnikov.Rd | 28 - man/Erlang.Rd |only man/Exponential.Rd | 28 - man/FDistribution.Rd | 28 - man/FDistributionNoncentral.Rd | 28 - man/Frechet.Rd | 28 - man/Gamma.Rd | 28 - man/Geometric.Rd | 28 - man/Gompertz.Rd | 28 - man/Gumbel.Rd | 28 - man/HuberizedDistribution.Rd | 30 - man/Hypergeometric.Rd | 28 - man/InverseGamma.Rd | 28 - man/Kernel.Rd | 28 - man/Laplace.Rd | 28 - man/Logarithmic.Rd | 28 - man/Logistic.Rd | 28 - man/LogisticKernel.Rd | 28 - man/Loglogistic.Rd | 28 - man/Lognormal.Rd | 28 - man/MixtureDistribution.Rd | 28 - man/Multinomial.Rd | 28 - man/MultivariateNormal.Rd | 28 - man/NegativeBinomial.Rd | 28 - man/Normal.Rd | 28 - man/NormalKernel.Rd | 28 - man/Pareto.Rd | 28 - man/Poisson.Rd | 28 - man/ProductDistribution.Rd | 28 - man/Quartic.Rd | 28 - man/Rayleigh.Rd | 28 - man/SDistribution.Rd | 28 - man/Sigmoid.Rd | 28 - man/Silverman.Rd | 28 - man/StudentT.Rd | 28 - man/StudentTNoncentral.Rd | 28 - man/Triangular.Rd | 28 - man/TriangularKernel.Rd | 28 - man/Tricube.Rd | 28 - man/Triweight.Rd | 28 - man/TruncatedDistribution.Rd | 30 - man/Uniform.Rd | 28 - man/UniformKernel.Rd | 28 - man/VectorDistribution.Rd | 28 - man/Wald.Rd | 28 - man/Weibull.Rd | 30 - man/WeightedDiscrete.Rd | 28 - man/decorators.Rd | 2 man/dmax.Rd | 2 man/dmin.Rd | 2 man/inf.Rd | 2 man/kurtosisType.Rd | 2 man/properties.Rd | 2 man/skewnessType.Rd | 2 man/sup.Rd | 2 man/support.Rd | 2 man/symmetry.Rd | 2 man/traits.Rd | 2 man/type.Rd | 2 man/valueSupport.Rd | 2 man/variateForm.Rd | 2 tests/testthat/Rplots.pdf |only tests/testthat/test-DistArcsine.R | 14 tests/testthat/test-DistBernoulli.R | 14 tests/testthat/test-DistBeta.R | 16 tests/testthat/test-DistBetaNoncentral.R | 16 tests/testthat/test-DistBinomial.R | 16 tests/testthat/test-DistCategorical.R | 8 tests/testthat/test-DistCauchy.R | 14 tests/testthat/test-DistChiSquared.R | 20 tests/testthat/test-DistChiSquaredNoncentral.R | 18 tests/testthat/test-DistDegenerate.R | 14 tests/testthat/test-DistDirichlet.R | 14 tests/testthat/test-DistDiscreteUniform.R | 16 tests/testthat/test-DistEmpirical.R | 6 tests/testthat/test-DistErlang.R |only tests/testthat/test-DistExponential.R | 14 tests/testthat/test-DistFDistribution.R | 18 tests/testthat/test-DistFDistributionNoncentral.R | 18 tests/testthat/test-DistFrechet.R | 14 tests/testthat/test-DistGamma.R | 14 tests/testthat/test-DistGeometric.R | 14 tests/testthat/test-DistGompertz.R | 14 tests/testthat/test-DistGumbel.R | 14 tests/testthat/test-DistHypergeometric.R | 14 tests/testthat/test-DistInverseGamma.R | 14 tests/testthat/test-DistLaplace.R | 14 tests/testthat/test-DistLogLogistic.R | 16 tests/testthat/test-DistLogarithmic.R | 14 tests/testthat/test-DistLogistic.R | 14 tests/testthat/test-DistLognormal.R | 14 tests/testthat/test-DistMultinomial.R | 14 tests/testthat/test-DistMultivariateNormal.R | 18 tests/testthat/test-DistNegativeBinomial.R | 20 tests/testthat/test-DistNormal.R | 14 tests/testthat/test-DistPareto.R | 14 tests/testthat/test-DistPoisson.R | 14 tests/testthat/test-DistRayleigh.R | 14 tests/testthat/test-DistStudentT.R | 14 tests/testthat/test-DistStudentTNoncentral.R | 14 tests/testthat/test-DistTriangular.R | 18 tests/testthat/test-DistUniform.R | 14 tests/testthat/test-DistWald.R | 14 tests/testthat/test-DistWeibull.R | 14 tests/testthat/test-DistWeightedDiscrete.R | 6 tests/testthat/test-Distributions.R | 20 tests/testthat/test-KernelCosine.R | 2 tests/testthat/test-KernelEpanechnikov.R | 2 tests/testthat/test-KernelLogistic.R | 2 tests/testthat/test-KernelLogistic.R-e |only tests/testthat/test-KernelNormal.R | 2 tests/testthat/test-KernelNormal.R-e |only tests/testthat/test-KernelQuartic.R | 2 tests/testthat/test-KernelQuartic.R-e |only tests/testthat/test-KernelSigmoid.R | 2 tests/testthat/test-KernelSilverman.R | 2 tests/testthat/test-KernelTriangular.R | 2 tests/testthat/test-KernelTriangular.R-e |only tests/testthat/test-KernelTricube.R | 2 tests/testthat/test-KernelTricube.R-e |only tests/testthat/test-KernelTriweight.R | 2 tests/testthat/test-KernelUniform.R | 2 tests/testthat/test-ProductDistribution.R | 8 tests/testthat/test-VectorDistribution.R | 14 tests/testthat/test-cDistribution.R | 6 tests/testthat/test-continuousDistribution.R | 8 tests/testthat/test-decorator.R | 2 tests/testthat/test-discreteDistribution.R | 12 tests/testthat/test-huberization.R | 16 tests/testthat/test-truncation.R | 26 - vignettes/distr6.rmd | 8 182 files changed, 1935 insertions(+), 1893 deletions(-)
Title: Sparse Multi-Type Regularized Feature Modeling
Description: Implementation of the SMuRF algorithm of Devriendt et al. (2018) <arXiv:1810.03136> to fit generalized linear models (GLMs) with multiple types of predictors via regularized maximum likelihood.
Author: Tom Reynkens [aut, cre] (<https://orcid.org/0000-0002-5516-5107>),
Sander Devriendt [aut],
Katrien Antonio [aut]
Maintainer: Tom Reynkens <tomreynkens@hotmail.com>
Diff between smurf versions 1.0.4 dated 2020-02-12 and 1.0.5 dated 2020-03-19
smurf-1.0.4/smurf/R/rent.R |only smurf-1.0.4/smurf/data |only smurf-1.0.4/smurf/man/rent.Rd |only smurf-1.0.5/smurf/DESCRIPTION | 14 +++--- smurf-1.0.5/smurf/MD5 | 51 +++++++++++------------- smurf-1.0.5/smurf/NAMESPACE | 3 - smurf-1.0.5/smurf/R/Lambda_select.R | 2 smurf-1.0.5/smurf/R/PO.R | 2 smurf-1.0.5/smurf/R/glmsmurf_fit.R | 2 smurf-1.0.5/smurf/R/residuals.R | 2 smurf-1.0.5/smurf/R/smurf.R | 6 ++ smurf-1.0.5/smurf/R/stand.R | 2 smurf-1.0.5/smurf/build/vignette.rds |binary smurf-1.0.5/smurf/inst/NEWS.Rd | 18 ++++++++ smurf-1.0.5/smurf/inst/doc/smurf.R | 2 smurf-1.0.5/smurf/inst/doc/smurf.Rmd | 6 +- smurf-1.0.5/smurf/inst/doc/smurf.html | 7 +-- smurf-1.0.5/smurf/inst/examples/Rent_example1.R | 4 - smurf-1.0.5/smurf/inst/examples/Rent_example2.R | 4 - smurf-1.0.5/smurf/inst/examples/Rent_example3.R | 4 - smurf-1.0.5/smurf/man/glmsmurf.Rd | 4 - smurf-1.0.5/smurf/man/p.Rd | 4 - smurf-1.0.5/smurf/man/plot_lambda.Rd | 4 - smurf-1.0.5/smurf/tests/testthat/helper_fit.R | 8 +-- smurf-1.0.5/smurf/tests/testthat/test_PO.R | 6 +- smurf-1.0.5/smurf/tests/testthat/test_input.R | 5 ++ smurf-1.0.5/smurf/tests/testthat/test_output.R | 8 +-- smurf-1.0.5/smurf/vignettes/smurf.Rmd | 6 +- 28 files changed, 101 insertions(+), 73 deletions(-)
Title: Phylogenetic Tools for Comparative Biology (and Other Things)
Description: A wide range of functions for phylogenetic analysis. Functionality is concentrated in phylogenetic comparative biology, but also includes a diverse array of methods for visualizing, manipulating, reading or writing, and even inferring phylogenetic trees and data. Included among the functions in phylogenetic comparative biology are various for ancestral state reconstruction, model-fitting, simulation of phylogenies and data, and multivariate analysis. There are a broad range of plotting methods for phylogenies and comparative data which include, but are not restricted to, methods for mapping trait evolution on trees, for projecting trees into phenotypic space or a geographic map, and for visualizing correlated speciation between trees. Finally, there are a number of functions for reading, writing, analyzing, inferring, simulating, and manipulating phylogenetic trees and comparative data not covered by other packages. For instance, there are functions for randomly or non-randomly attaching species or clades to a phylogeny, for estimating supertrees or consensus phylogenies from a set, for simulating trees and phylogenetic data under a range of models, and for a wide variety of other manipulations and analyses that phylogenetic biologists might find useful in their research.
Author: Liam J. Revell
Maintainer: Liam J. Revell <liam.revell@umb.edu>
Diff between phytools versions 0.6-99 dated 2019-06-18 and 0.7-20 dated 2020-03-19
DESCRIPTION | 8 - MD5 | 96 ++++++++-------- NAMESPACE | 22 ++- R/backbonePhylo.R | 10 + R/bd.R | 21 ++- R/brownie.lite.R | 9 + R/densityMap.R | 6 - R/densityTree.R | 19 ++- R/fitMk.R | 17 ++ R/fitpolyMk.R | 3 R/ltt.R | 35 +++-- R/map.to.singleton.R | 30 +++-- R/mcmcMk.R | 27 ++-- R/phyl.pca.R | 39 ++++++ R/phylosig.R | 234 +++++++++++++++++++++++++++++++-------- R/plotBranchbyTrait.R | 22 ++- R/plotSimmap.R | 81 ++++++++++--- R/read.simmap.R | 3 R/simBMphylo.R |only R/threshBayes.R | 8 + R/tree.grow.R |only R/utilities.R | 91 +++++++++------ R/write.simmap.R | 275 ++++++++++++++++++++++++++++++++++++---------- man/ancThresh.Rd | 4 man/bd.Rd | 2 man/bind.tip.Rd | 32 +++++ man/densityMap.Rd | 2 man/densityTree.Rd | 2 man/fit.bd.Rd | 4 man/fitMk.Rd | 3 man/genSeq.Rd | 2 man/likMlambda.Rd | 2 man/map.to.singleton.Rd | 2 man/phyl.RMA.Rd | 4 man/phyl.cca.Rd | 4 man/phyl.pca.Rd | 13 +- man/phyl.resid.Rd | 2 man/phyl.vcv.Rd | 4 man/phylosig.Rd | 17 +- man/plotBranchbyTrait.Rd | 2 man/plotSimmap.Rd | 5 man/plotTree.wBars.Rd | 3 man/posterior.evolrate.Rd | 4 man/ratebytree.Rd | 14 +- man/sim.ratebystate.Rd | 8 - man/simBMphylo.Rd |only man/threshBayes.Rd | 2 man/threshDIC.Rd | 2 man/threshState.Rd | 2 man/tree.grow.Rd |only man/write.simmap.Rd | 9 + 51 files changed, 886 insertions(+), 320 deletions(-)
Title: A Collection of Contrast Methods
Description: One degree of freedom contrasts for 'lm', 'glm', 'gls', and 'geese' objects.
Author: Alan O'Callaghan [aut, cre],
Max Kuhn [aut],
Steve Weston [aut],
Jed Wing [aut],
James Forester [aut],
Thorn Thaler [aut]
Maintainer: Alan O'Callaghan <alan.ocallaghan@outlook.com>
Diff between contrast versions 0.21 dated 2016-09-22 and 0.22 dated 2020-03-19
contrast-0.21/contrast/inst/NEWS.Rd |only contrast-0.21/contrast/inst/doc/contrast.Rnw |only contrast-0.21/contrast/inst/doc/contrast.pdf |only contrast-0.21/contrast/man/contrast.Rd |only contrast-0.21/contrast/vignettes/contrast.Rnw |only contrast-0.22/contrast/DESCRIPTION | 38 + contrast-0.22/contrast/MD5 | 44 +- contrast-0.22/contrast/NAMESPACE | 76 ++- contrast-0.22/contrast/NEWS.md |only contrast-0.22/contrast/R/0_imports.R |only contrast-0.22/contrast/R/contrast.lm.R | 300 ++++++++++----- contrast-0.22/contrast/R/data.R |only contrast-0.22/contrast/R/gets.R | 19 contrast-0.22/contrast/R/misc.R | 21 - contrast-0.22/contrast/R/model.frames.R | 330 +++++++++++------ contrast-0.22/contrast/R/print.contrast.R | 67 ++- contrast-0.22/contrast/R/testStatistic.R | 33 + contrast-0.22/contrast/README.md |only contrast-0.22/contrast/build/vignette.rds |binary contrast-0.22/contrast/data |only contrast-0.22/contrast/inst/doc/contrast.R | 446 +++++++---------------- contrast-0.22/contrast/inst/doc/contrast.Rmd |only contrast-0.22/contrast/inst/doc/contrast.html |only contrast-0.22/contrast/man/contrast.lm.Rd |only contrast-0.22/contrast/man/print.contrast.Rd |only contrast-0.22/contrast/man/reexports.Rd |only contrast-0.22/contrast/man/two_factor_crossed.Rd |only contrast-0.22/contrast/man/two_factor_incompl.Rd |only contrast-0.22/contrast/tests |only contrast-0.22/contrast/vignettes/contrast.Rmd |only 30 files changed, 755 insertions(+), 619 deletions(-)
Title: Bias Reduction in Generalized Linear Models
Description: Estimation and inference from generalized linear models based on various methods for bias reduction and maximum penalized likelihood with powers of the Jeffreys prior as penalty. The 'brglmFit' fitting method can achieve reduction of estimation bias by solving either the mean bias-reducing adjusted score equations in Firth (1993) <doi:10.1093/biomet/80.1.27> and Kosmidis and Firth (2009) <doi:10.1093/biomet/asp055>, or the median bias-reduction adjusted score equations in Kenne et al. (2016) <arXiv:1604.04768>, or through the direct subtraction of an estimate of the bias of the maximum likelihood estimator from the maximum likelihood estimates as in Cordeiro and McCullagh (1991) <http://www.jstor.org/stable/2345592>. See Kosmidis et al (2019) <doi:10.1007/s11222-019-09860-6> for more details. Estimation in all cases takes place via a quasi Fisher scoring algorithm, and S3 methods for the construction of of confidence intervals for the reduced-bias estimates are provided. In the special case of generalized linear models for binomial and multinomial responses (both ordinal and nominal), the adjusted score approaches return estimates with improved frequentist properties, that are also always finite, even in cases where the maximum likelihood estimates are infinite (e.g. complete and quasi-complete separation). 'brglm2' also provides pre-fit and post-fit methods for detecting separation and infinite maximum likelihood estimates in binomial response generalized linear models.
Author: Ioannis Kosmidis [aut, cre] (<https://orcid.org/0000-0003-1556-0302>),
Kjell Konis [ctb],
Euloge Clovis Kenne Pagui [ctb],
Nicola Sartori [ctb]
Maintainer: Ioannis Kosmidis <ioannis.kosmidis@warwick.ac.uk>
Diff between brglm2 versions 0.6.1 dated 2020-02-06 and 0.6.2 dated 2020-03-19
DESCRIPTION | 6 - MD5 | 60 ++++++------ NEWS.md | 167 ++++++++++++++++++++++-------------- R/brglm2-package.R | 17 +++ R/brglmControl.R | 1 R/brglmFit.R | 17 ++- R/brmultinom.R | 6 - R/check_infinite_estimates.R | 14 ++- R/data.R | 8 - R/detect_separation.R | 28 ++++-- R/warnings.R |only README.md | 5 - build/vignette.rds |binary inst/WORDLIST |only inst/doc/adjacent.Rmd | 2 inst/doc/adjacent.html | 17 +++ inst/doc/iteration.html | 15 +++ inst/doc/multinomial.html | 20 +++- inst/doc/separation.Rmd | 2 inst/doc/separation.html | 77 ++++++++++------ man/alligators.Rd | 2 man/brmultinom.Rd | 2 man/check_infinite_estimates.Rd | 10 ++ man/check_infinite_estimates.glm.Rd | 11 ++ man/detect_separation.Rd | 13 ++ man/endometrial.Rd | 4 man/predict.brmultinom.Rd | 2 man/residuals.brmultinom.Rd | 2 man/stemcell.Rd | 2 man/vcov.brglmFit.Rd | 17 +++ vignettes/adjacent.Rmd | 2 vignettes/separation.Rmd | 2 32 files changed, 365 insertions(+), 166 deletions(-)
Title: Statistical Hypothesis Testing Toolbox
Description: We provide a collection of statistical hypothesis testing procedures ranging from classical to modern methods for non-trivial settings such as high-dimensional scenario. For the general treatment of statistical hypothesis testing, see the book by Lehmann and Romano (2005) <doi:10.1007/0-387-27605-X>.
Author: Kyoungjae Lee [aut],
Lizhen Lin [aut],
Hyungmin Park [aut],
Kisung You [aut, cre] (<https://orcid.org/0000-0002-8584-459X>)
Maintainer: Kisung You <kyoustat@gmail.com>
Diff between SHT versions 0.1.2 dated 2019-12-04 and 0.1.3 dated 2020-03-19
DESCRIPTION | 8 MD5 | 72 ++- NAMESPACE | 9 NEWS.md | 3 R/aux_etc.R | 74 +++ R/cov2.2013CLX.R | 2 R/mean1.ttest.R | 2 R/mean2.1980Johansen.R | 2 R/mean2.2014CLX.R | 2 R/mean2.2014Thulin.R | 2 R/mean2.ttest.R | 2 R/meank.2007Schott.R | 2 R/meank.2009ZX.R | 2 R/mvar1.1998AS.R |only R/mvar1.LRT.R |only R/mvar2.1930PN.R |only R/mvar2.1976PL.R |only R/mvar2.1982Muirhead.R |only R/mvar2.2012ZXC.R |only R/mvar2.LRT.R |only R/package-SHT.R | 2 R/silent_sim1.2020YLL.R |only R/silent_sim2.2020YLL.R |only build/partial.rdb |binary inst/REFERENCES.bib | 919 +++++++++++++++++++++++----------------------- man/cov2.2013CLX.Rd | 2 man/mean1.ttest.Rd | 10 man/mean2.1980Johansen.Rd | 2 man/mean2.2014CLX.Rd | 2 man/mean2.2014Thulin.Rd | 2 man/mean2.ttest.Rd | 2 man/meank.2007Schott.Rd | 2 man/meank.2009ZX.Rd | 2 man/mvar1.1998AS.Rd |only man/mvar1.LRT.Rd |only man/mvar2.1930PN.Rd |only man/mvar2.1976PL.Rd |only man/mvar2.1982Muirhead.Rd |only man/mvar2.2012ZXC.Rd |only man/mvar2.LRT.Rd |only src/cpp_cov1_mxPBF.cpp | 33 + src/cpp_cov2_mxPBF.cpp | 47 +- src/cpp_energy.cpp | 36 + src/cpp_extras.cpp |only src/cpp_extras.h |only src/cpp_mean2_mxPBF.cpp | 27 - 46 files changed, 734 insertions(+), 536 deletions(-)
Title: R Interface to the 'Protocol Buffers' 'API' (Version 2 or 3)
Description: Protocol Buffers are a way of encoding structured data in an
efficient yet extensible format. Google uses Protocol Buffers for almost all
of its internal 'RPC' protocols and file formats. Additional documentation
is available in two included vignettes one of which corresponds to our 'JSS'
paper (2016, <doi:10.18637/jss.v071.i02>. Either version 2 or 3 of the
'Protocol Buffers' 'API' is supported.
Author: Romain Francois, Dirk Eddelbuettel, Murray Stokely and Jeroen Ooms
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RProtoBuf versions 0.4.15 dated 2020-02-08 and 0.4.16 dated 2020-03-19
ChangeLog | 30 ++++++++++++++++++++++ DESCRIPTION | 8 +++--- MD5 | 39 +++++++++++++++-------------- NAMESPACE | 6 ++-- R/00classes.R | 2 + R/completion.R | 4 +-- R/debug_string.R | 24 ++++++++++++------ R/read.R | 27 ++++++++++++++++++++ build/vignette.rds |binary inst/NEWS.Rd | 9 ++++++ inst/doc/RProtoBuf-intro.pdf |binary inst/doc/RProtoBuf-paper.pdf |binary inst/doc/RProtoBuf-quickref.pdf |binary inst/tinytest/test_addressbook.R | 28 +++++++++++++++++++++ man/Message-class.Rd | 6 +++- man/bytesize.Rd | 2 - man/readJSON.Rd |only src/init.c | 6 ++++ src/rprotobuf.h | 6 ++++ src/wrapper_Descriptor.cpp | 52 +++++++++++++++++++++++++++++++++++++++ src/wrapper_Message.cpp | 31 +++++++++++++++++++++-- 21 files changed, 240 insertions(+), 40 deletions(-)
Title: Visualizing and Analyzing Animal Track Data
Description: Contains functions to access movement data stored in 'movebank.org'
as well as tools to visualize and statistically analyze animal movement data,
among others functions to calculate dynamic Brownian Bridge Movement Models.
Move helps addressing movement ecology questions.
Author: Bart Kranstauber [aut, cre],
Marco Smolla [aut],
Anne K Scharf [aut]
Maintainer: Bart Kranstauber <b.kranstauber@uva.nl>
Diff between move versions 3.2.2 dated 2019-09-07 and 3.3.0 dated 2020-03-19
move-3.2.2/move/data/datalist |only move-3.2.2/move/data/ricky.RData |only move-3.2.2/move/data/ricky.csv.gz |only move-3.2.2/move/inst/doc/browseMovebank.Rnw |only move-3.2.2/move/inst/doc/browseMovebank.pdf |only move-3.2.2/move/inst/doc/move.Rnw |only move-3.2.2/move/inst/doc/move.pdf |only move-3.2.2/move/man/ricky.Rd |only move-3.2.2/move/vignettes/browseMovebank.Rnw |only move-3.2.2/move/vignettes/move.Rnw |only move-3.3.0/move/ChangeLog | 5 move-3.3.0/move/DESCRIPTION | 14 move-3.3.0/move/MD5 | 113 +- move-3.3.0/move/NAMESPACE | 4 move-3.3.0/move/R/WebImport.R | 131 ++ move-3.3.0/move/R/getDataRepositoryData.R | 20 move-3.3.0/move/R/move.R | 49 + move-3.3.0/move/R/move2ade.R | 137 +++ move-3.3.0/move/build/vignette.rds |binary move-3.3.0/move/data/dbbmmstack.RData |binary move-3.3.0/move/data/fishers.RData |binary move-3.3.0/move/inst/doc/browseMovebank.R | 255 ++--- move-3.3.0/move/inst/doc/browseMovebank.Rmd |only move-3.3.0/move/inst/doc/browseMovebank.html |only move-3.3.0/move/inst/doc/move.R | 619 +++++++++----- move-3.3.0/move/inst/doc/move.Rmd |only move-3.3.0/move/inst/doc/move.html |only move-3.3.0/move/inst/extdata/createsRDataFile.R | 6 move-3.3.0/move/inst/extdata/ricky.csv.gz |only move-3.3.0/move/man/MovebankLogin-class.Rd | 6 move-3.3.0/move/man/brownian.bridge.dyn.Rd | 8 move-3.3.0/move/man/brownian.motion.variance.dyn.Rd | 6 move-3.3.0/move/man/dynBGB-methods.Rd | 4 move-3.3.0/move/man/dynBGBvariance-methods.Rd | 6 move-3.3.0/move/man/equalProj.Rd | 3 move-3.3.0/move/man/getDuplicatedTimestamps.Rd | 2 move-3.3.0/move/man/getMovebank.Rd | 19 move-3.3.0/move/man/getMovebankAnimals.Rd | 4 move-3.3.0/move/man/getMovebankData.Rd | 8 move-3.3.0/move/man/getMovebankLocationData.Rd |only move-3.3.0/move/man/getMovebankNonLocationData.Rd | 2 move-3.3.0/move/man/getMovebankReferenceTable.Rd | 1 move-3.3.0/move/man/getVolumeUD.Rd | 6 move-3.3.0/move/man/move-package.Rd | 24 move-3.3.0/move/man/move.Rd | 31 move-3.3.0/move/man/move2ade.Rd | 2 move-3.3.0/move/man/moveStack.Rd | 2 move-3.3.0/move/man/movebankLogin.Rd | 2 move-3.3.0/move/man/n.indiv.Rd | 2 move-3.3.0/move/man/n.locs.Rd | 2 move-3.3.0/move/man/namesIndiv.Rd | 2 move-3.3.0/move/man/plotBursts.Rd | 4 move-3.3.0/move/man/points.Rd | 2 move-3.3.0/move/man/split.Rd | 2 move-3.3.0/move/man/subset.Rd | 3 move-3.3.0/move/man/thinTrack.Rd | 2 move-3.3.0/move/man/timestamps.Rd | 2 move-3.3.0/move/tests/testthat/test.brownian.bridge.dyn.R | 2 move-3.3.0/move/tests/testthat/test.move.R | 3 move-3.3.0/move/tests/testthat/test.moveAde.R | 36 move-3.3.0/move/tests/testthat/test.smallFunctions.R | 2 move-3.3.0/move/tests/testthat/test.storedData.R | 2 move-3.3.0/move/tests/testthat/test.udFunctions.R | 4 move-3.3.0/move/tests/testthat/test.web.R | 2 move-3.3.0/move/vignettes/base_map.RData |only move-3.3.0/move/vignettes/browseMovebank.Rmd |only move-3.3.0/move/vignettes/move.Rmd |only 67 files changed, 1076 insertions(+), 485 deletions(-)
Title: Easy Access to 'ggplot2' Commands
Description: Provides a series of aliases to commonly used but difficult
to remember 'ggplot2' sequences.
Author: Jonathan Carroll [aut, cre] (<https://orcid.org/0000-0002-1404-5264>),
Alicia Schep [aut] (<https://orcid.org/0000-0002-3915-0618>),
Jonathan Sidi [aut] (<https://orcid.org/0000-0002-4222-1819>),
Bob Rudis [ctb] (<https://orcid.org/0000-0001-5670-2640>),
Mohamed El Fodil Ihaddaden [ctb]
Maintainer: Jonathan Carroll <rpkg@jcarroll.com.au>
Diff between ggeasy versions 0.1.1 dated 2020-01-31 and 0.1.2 dated 2020-03-19
ggeasy-0.1.1/ggeasy/tests/README_files |only ggeasy-0.1.1/ggeasy/tools/readme/README-example-1.png |only ggeasy-0.1.1/ggeasy/tools/readme/README-example-10.png |only ggeasy-0.1.1/ggeasy/tools/readme/README-example-11.png |only ggeasy-0.1.1/ggeasy/tools/readme/README-example-2.png |only ggeasy-0.1.1/ggeasy/tools/readme/README-example-3.png |only ggeasy-0.1.1/ggeasy/tools/readme/README-example-4.png |only ggeasy-0.1.1/ggeasy/tools/readme/README-example-5.png |only ggeasy-0.1.1/ggeasy/tools/readme/README-example-6.png |only ggeasy-0.1.1/ggeasy/tools/readme/README-example-7.png |only ggeasy-0.1.1/ggeasy/tools/readme/README-example-8.png |only ggeasy-0.1.1/ggeasy/tools/readme/README-example-9.png |only ggeasy-0.1.1/ggeasy/tools/readme/README-teach-1.png |only ggeasy-0.1.1/ggeasy/tools/readme/README-teach-2.png |only ggeasy-0.1.2/ggeasy/DESCRIPTION | 14 + ggeasy-0.1.2/ggeasy/MD5 | 70 ++++----- ggeasy-0.1.2/ggeasy/NAMESPACE | 1 ggeasy-0.1.2/ggeasy/NEWS.md | 9 + ggeasy-0.1.2/ggeasy/R/labs2.R | 2 ggeasy-0.1.2/ggeasy/R/legend.R | 31 ++++ ggeasy-0.1.2/ggeasy/R/text.R | 6 ggeasy-0.1.2/ggeasy/README.md | 28 +-- ggeasy-0.1.2/ggeasy/build/vignette.rds |binary ggeasy-0.1.2/ggeasy/inst/doc/shortcuts.R | 16 +- ggeasy-0.1.2/ggeasy/inst/doc/shortcuts.html | 23 +-- ggeasy-0.1.2/ggeasy/inst/doc/tests_and_coverage.R | 2 ggeasy-0.1.2/ggeasy/inst/doc/tests_and_coverage.html | 13 - ggeasy-0.1.2/ggeasy/man/easy_change_legend.Rd | 16 +- ggeasy-0.1.2/ggeasy/man/easy_change_text.Rd | 11 - ggeasy-0.1.2/ggeasy/man/easy_remove_axes.Rd | 13 - ggeasy-0.1.2/ggeasy/man/easy_remove_legend_title.Rd |only ggeasy-0.1.2/ggeasy/man/easy_rotate_labels.Rd | 22 ++ ggeasy-0.1.2/ggeasy/man/figures/example-1.png |only ggeasy-0.1.2/ggeasy/man/figures/example-10.png |only ggeasy-0.1.2/ggeasy/man/figures/example-11.png |only ggeasy-0.1.2/ggeasy/man/figures/example-2.png |only ggeasy-0.1.2/ggeasy/man/figures/example-3.png |only ggeasy-0.1.2/ggeasy/man/figures/example-4.png |only ggeasy-0.1.2/ggeasy/man/figures/example-5.png |only ggeasy-0.1.2/ggeasy/man/figures/example-6.png |only ggeasy-0.1.2/ggeasy/man/figures/example-7.png |only ggeasy-0.1.2/ggeasy/man/figures/example-8.png |only ggeasy-0.1.2/ggeasy/man/figures/example-9.png |only ggeasy-0.1.2/ggeasy/man/figures/teach-1.png |only ggeasy-0.1.2/ggeasy/man/figures/teach-2.png |only ggeasy-0.1.2/ggeasy/man/ggeasy.Rd | 1 ggeasy-0.1.2/ggeasy/tests/README.md | 127 ++++++++--------- ggeasy-0.1.2/ggeasy/tests/testthat/test-labs.R | 36 ++-- ggeasy-0.1.2/ggeasy/tests/testthat/test-legend.R | 8 + ggeasy-0.1.2/ggeasy/tests/testthat/test-text.R | 69 +++++---- 50 files changed, 295 insertions(+), 223 deletions(-)
Title: Dendrochronology Program Library in R
Description: Perform tree-ring analyses such as detrending, chronology
building, and cross dating. Read and write standard file formats
used in dendrochronology.
Author: Andy Bunn [aut, cph, cre, trl],
Mikko Korpela [aut, cph, trl],
Franco Biondi [aut, cph],
Filipe Campelo [aut, cph],
Pierre Mérian [aut, cph],
Fares Qeadan [aut, cph],
Christian Zang [aut, cph],
Allan Buras [ctb],
Jacob Cecile [ctb],
Manfred Mudelsee [ctb],
Michael Schulz [ctb]
Maintainer: Andy Bunn <andy.bunn@wwu.edu>
Diff between dplR versions 1.7.0 dated 2019-07-18 and 1.7.1 dated 2020-03-19
ChangeLog | 15 ++++++++++++--- DESCRIPTION | 8 ++++---- MD5 | 20 +++++++++++--------- NAMESPACE | 3 ++- R/ccf.series.rwl.R | 20 ++++++++------------ R/xdate.floater.R |only build/vignette.rds |binary inst/doc/chron-dplR.pdf |binary inst/doc/intro-dplR.pdf |binary inst/doc/timeseries-dplR.pdf |binary inst/doc/xdate-dplR.pdf |binary man/xdate.floater.Rd |only 12 files changed, 37 insertions(+), 29 deletions(-)
Title: Discriminant Analysis Incorporating Individual Uncertainties
Description: The qda() function from package 'MASS' is extended to calculate a weighted linear (LDA) and quadratic discriminant analysis (QDA) by changing the group variances and group means based on cell-wise uncertainties.
The uncertainties can be derived e.g. through relative errors for each individual measurement (cell), not only row-wise or column-wise uncertainties.
The method can be applied compositional data (e.g. portions of substances, concentrations) and non-compositional data.
Author: Solveig Pospiech [aut, cre],
K. Gerald van den Boogaart [ctb]
Maintainer: Solveig Pospiech <s.pospiech@hzdr.de>
Diff between vdar versions 0.1.1 dated 2020-03-10 and 0.1.2-1 dated 2020-03-19
DESCRIPTION | 8 +++---- MD5 | 8 +++---- R/weighted_DA.R | 62 ++++++++++++++++++++++++++++++++++++-------------------- man/vlda.Rd | 31 ++++++++++++++++++---------- man/vqda.Rd | 31 ++++++++++++++++++---------- 5 files changed, 88 insertions(+), 52 deletions(-)
Title: Non-Interactive Spatial Tools for Raster Processing and
Visualization
Description: S3 classes and methods for manipulation with georeferenced raster data: reading/writing, processing, multi-panel visualization.
Author: Nikita Platonov [aut, cre] (<https://orcid.org/0000-0001-7196-7882>)
Maintainer: Nikita Platonov <platonov@sevin.ru>
Diff between ursa versions 3.8.16 dated 2020-02-28 and 3.8.17 dated 2020-03-19
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- NEWS.md | 11 ++++++++++- R/classRaster.R | 11 ++++++++++- R/compose_open.R | 8 ++++++-- R/panel_graticule.R | 2 +- R/panel_plot.R | 2 ++ R/xxx.browse.R | 2 +- R/xxx.geomap.R | 2 +- R/yyy.project.R | 18 ++++++++++++++++-- man/classRaster.Rd | 5 ++++- 11 files changed, 64 insertions(+), 23 deletions(-)
Title: Operationalizing Social Determinants of Health Data for
Researchers
Description: Accesses raw data via API and calculates social
determinants of health measures for user-specified locations in the
US, returning them in tidyverse- and sf-compatible data frames.
Author: Nik Krieger [aut, cre],
Jarrod Dalton [aut],
Cindy Wang [aut],
Adam Perzynski [aut],
National Institutes of Health/National Institute on Aging [fnd] (The
development of this software package was supported by a research
grant from the National Institutes of Health/National Institute on
Aging, (Principal Investigators: Jarrod E. Dalton, PhD and Adam T.
Perzynski, PhD; Grant Number: 5R01AG055480-02). All of its contents
are solely the responsibility of the authors and do not necessarily
represent the official views of the NIH.)
Maintainer: Nik Krieger <nk@case.edu>
Diff between sociome versions 1.3.2 dated 2020-01-27 and 1.4.0 dated 2020-03-19
sociome-1.3.2/sociome/tests/testthat/test_arg_tibble_acs.R |only sociome-1.3.2/sociome/tests/testthat/test_arg_tibble_decennial1990.R |only sociome-1.3.2/sociome/tests/testthat/test_arg_tibble_decennial2000.R |only sociome-1.3.2/sociome/tests/testthat/test_arg_tibble_decennial2010.R |only sociome-1.3.2/sociome/tests/testthat/test_calculate_adi.R |only sociome-1.4.0/sociome/DESCRIPTION | 8 sociome-1.4.0/sociome/MD5 | 26 sociome-1.4.0/sociome/NEWS.md | 10 sociome-1.4.0/sociome/R/calculate_adi.R | 6 sociome-1.4.0/sociome/R/get_adi.R | 307 +++++++--- sociome-1.4.0/sociome/R/get_geoids.R | 47 - sociome-1.4.0/sociome/R/validation.R | 85 +- sociome-1.4.0/sociome/man/acs_vars.Rd | 6 sociome-1.4.0/sociome/man/calculate_adi.Rd | 4 sociome-1.4.0/sociome/man/decennial_vars.Rd | 6 sociome-1.4.0/sociome/man/get_adi.Rd | 4 sociome-1.4.0/sociome/tests/testthat/test_tidycensus_related.R |only 17 files changed, 332 insertions(+), 177 deletions(-)
Title: Project Multidimensional Data in 2D Space
Description: An implementation of the radviz projection in R. It enables the visualization of
multidimensional data while maintaining the relation to the original dimensions.
This package provides functions to create and plot radviz projections, and a number of summary
plots that enable comparison and analysis. For reference see Ankerst *et al.* (1996)
(<http://citeseer.ist.psu.edu/viewdoc/summary?doi=10.1.1.68.1811>) for original implementation,
see Di Caro *et al* (2012) (<http://link.springer.com/chapter/10.1007/978-3-642-13672-6_13>)
for the original method for dimensional anchor arrangements, see Demsar *et al.* (2007)
(<doi:10.1016/j.jbi.2007.03.010>) for the original Freeviz implementation.
Author: Yann Abraham [aut, cre],
Nicolas Sauwen [aut]
Maintainer: Yann Abraham <yann.abraham@gmail.com>
Diff between Radviz versions 0.8.2 dated 2020-02-04 and 0.9.0 dated 2020-03-19
Radviz-0.8.2/Radviz/R/do.optim.R |only Radviz-0.8.2/Radviz/man/do.optim.Rd |only Radviz-0.9.0/Radviz/DESCRIPTION | 29 - Radviz-0.9.0/Radviz/MD5 | 53 +- Radviz-0.9.0/Radviz/NAMESPACE | 18 Radviz-0.9.0/Radviz/NEWS.md | 6 Radviz-0.9.0/Radviz/R/DB_weightedIdx.R |only Radviz-0.9.0/Radviz/R/RcppExports.R |only Radviz-0.9.0/Radviz/R/do.optimFreeviz.R |only Radviz-0.9.0/Radviz/R/do.optimGraphviz.R |only Radviz-0.9.0/Radviz/R/do.optimRadviz.R |only Radviz-0.9.0/Radviz/R/do.radviz.R | 53 +- Radviz-0.9.0/Radviz/R/forceTuning.R |only Radviz-0.9.0/Radviz/R/get.optim.R | 8 Radviz-0.9.0/Radviz/R/identify.radviz.R | 4 Radviz-0.9.0/Radviz/R/rescalePlot.R |only Radviz-0.9.0/Radviz/R/subset.radviz.R | 15 Radviz-0.9.0/Radviz/build/vignette.rds |binary Radviz-0.9.0/Radviz/inst/doc/multivariate_analysis.R |only Radviz-0.9.0/Radviz/inst/doc/multivariate_analysis.Rmd |only Radviz-0.9.0/Radviz/inst/doc/multivariate_analysis.html |only Radviz-0.9.0/Radviz/inst/doc/single_cell_projections.R | 10 Radviz-0.9.0/Radviz/inst/doc/single_cell_projections.Rmd | 35 - Radviz-0.9.0/Radviz/inst/doc/single_cell_projections.html | 341 +++++++------- Radviz-0.9.0/Radviz/man/DB_weightedIdx.Rd |only Radviz-0.9.0/Radviz/man/do.optimFreeviz.Rd |only Radviz-0.9.0/Radviz/man/do.optimGraphviz.Rd |only Radviz-0.9.0/Radviz/man/do.optimRadviz.Rd |only Radviz-0.9.0/Radviz/man/do.radviz.Rd | 30 - Radviz-0.9.0/Radviz/man/get.optim.Rd | 6 Radviz-0.9.0/Radviz/man/rescalePlot.Rd |only Radviz-0.9.0/Radviz/man/subset.radviz.Rd | 8 Radviz-0.9.0/Radviz/man/tuneForceRatio.Rd |only Radviz-0.9.0/Radviz/src |only Radviz-0.9.0/Radviz/vignettes/multivariate_analysis.Rmd |only Radviz-0.9.0/Radviz/vignettes/single_cell_projections.Rmd | 35 - 36 files changed, 366 insertions(+), 285 deletions(-)
Title: Development Utilities for R Packages
Description: Provides some low-level utilities to use for package
development. It currently provides managers for multiple package specific
options and registries, vignette, unit test and bibtex related utilities.
It serves as a base package for packages like NMF, RcppOctave, doRNG, and
as an incubator package for other general purposes utilities, that will
eventually be packaged separately.
It is still under heavy development and changes in the interface(s) are
more than likely to happen.
Author: Renaud Gaujoux [aut, cre]
Maintainer: Renaud Gaujoux <renozao@protonmail.com>
Diff between pkgmaker versions 0.31 dated 2020-01-22 and 0.31.1 dated 2020-03-19
DESCRIPTION | 8 MD5 | 12 NAMESPACE | 2 R/devutils.R | 1447 ++++++++++++++++++++++---------------------- R/is.R | 4 man/packageData.Rd | 13 tests/testthat/test-utils.r | 5 7 files changed, 752 insertions(+), 739 deletions(-)
Title: Bayesian Calibrations of p-Values
Description: Implements transformations of p-values to the smallest possible Bayes factor within the specified class of alternative hypotheses, as described in Held & Ott (2018, <doi:10.1146/annurev-statistics-031017-100307>). Covers several common testing scenarios such as z-tests, t-tests, likelihood ratio tests and the F-test.
Author: Manuela Ott [aut, cre] (<https://orcid.org/0000-0002-8050-7279>),
Leonhard Held [aut] (<https://orcid.org/0000-0002-8686-5325>)
Maintainer: Manuela Ott <manuela.c.ott@gmail.com>
Diff between pCalibrate versions 0.1-1 dated 2017-11-06 and 0.2-1 dated 2020-03-19
pCalibrate-0.1-1/pCalibrate/tests/Test_pCalibrate.Rout.save |only pCalibrate-0.2-1/pCalibrate/DESCRIPTION | 23 pCalibrate-0.2-1/pCalibrate/MD5 | 40 - pCalibrate-0.2-1/pCalibrate/NAMESPACE | 7 pCalibrate-0.2-1/pCalibrate/R/BF2pp.R |only pCalibrate-0.2-1/pCalibrate/R/FCalibrate.R |only pCalibrate-0.2-1/pCalibrate/R/LRCalibrate.R |only pCalibrate-0.2-1/pCalibrate/R/formatBF.R |only pCalibrate-0.2-1/pCalibrate/R/p2z.R |only pCalibrate-0.2-1/pCalibrate/R/pCalibrate.R | 425 ------------ pCalibrate-0.2-1/pCalibrate/R/tCalibrate.R |only pCalibrate-0.2-1/pCalibrate/R/twoby2Calibrate.R |only pCalibrate-0.2-1/pCalibrate/R/z2p.R |only pCalibrate-0.2-1/pCalibrate/R/zCalibrate.R |only pCalibrate-0.2-1/pCalibrate/build/partial.rdb |binary pCalibrate-0.2-1/pCalibrate/inst/CITATION | 8 pCalibrate-0.2-1/pCalibrate/man/FCalibrate.Rd | 65 + pCalibrate-0.2-1/pCalibrate/man/LRCalibrate.Rd | 45 - pCalibrate-0.2-1/pCalibrate/man/formatBF.Rd | 6 pCalibrate-0.2-1/pCalibrate/man/p2z.Rd |only pCalibrate-0.2-1/pCalibrate/man/pCalibrate-package.Rd | 61 - pCalibrate-0.2-1/pCalibrate/man/pCalibrate.Rd | 67 + pCalibrate-0.2-1/pCalibrate/man/tCalibrate.Rd | 79 +- pCalibrate-0.2-1/pCalibrate/man/twoby2Calibrate.Rd | 119 +-- pCalibrate-0.2-1/pCalibrate/man/z2p.Rd |only pCalibrate-0.2-1/pCalibrate/man/zCalibrate.Rd | 54 - pCalibrate-0.2-1/pCalibrate/tests/Test_pCalibrate.R | 18 27 files changed, 333 insertions(+), 684 deletions(-)
Title: 'Opencast' External API Package
Description: Query the external API of a 'Opencast' video management server for information related to the recorded videos. For more information about 'Opencast' see: <https://opencast.org>.
Author: Daniel Ebbert [cre, aut] (<https://orcid.org/0000-0003-3666-7205>)
Maintainer: Daniel Ebbert <daniel@ebbert.nrw>
Diff between opencastR versions 0.1.2 dated 2019-11-04 and 0.1.3 dated 2020-03-19
DESCRIPTION | 12 ++-- MD5 | 26 ++++----- NEWS.md | 4 + R/oc_group.R | 4 + build/vignette.rds |binary inst/doc/getting_started.R | 10 +-- inst/doc/getting_started.html | 102 +++++++++++++++++++----------------- man/oc_event.Rd | 11 ++- man/oc_group.Rd | 2 man/oc_list_events.Rd | 14 +++- man/oc_list_workflow_definitions.Rd | 11 ++- man/oc_list_workflow_instances.Rd | 11 ++- man/oc_package_query.Rd | 3 - man/print.oc_group.Rd | 2 14 files changed, 128 insertions(+), 84 deletions(-)
Title: Classification, Regression, Clustering with K Nearest Neighbors
Description: Classification, regression, and clustering with k nearest neighbors
algorithm. Implements several distance and similarity measures, covering
continuous and logical features. Outputs ranked neighbors. Most features of
this package are directly based on the PMML specification for KNN.
Author: Dmitriy Bolotov [aut, cre],
Software AG [cph]
Maintainer: Dmitriy Bolotov <dmitriy.bolotov@softwareag.com>
Diff between neighbr versions 1.0.2 dated 2019-03-15 and 1.0.3 dated 2020-03-19
DESCRIPTION | 12 +- MD5 | 32 ++--- NEWS.md | 4 R/distance.R | 10 + R/knn.R | 44 ++++---- R/neighbr.R | 8 - R/similarity.R | 14 +- R/utility_functions.R | 28 ++--- build/vignette.rds |binary inst/doc/neighbr-help.R | 14 +- inst/doc/neighbr-help.Rmd | 4 inst/doc/neighbr-help.html | 242 +++++++++++++++++++++++++++++++++++++++------ man/knn.Rd | 15 ++ man/neighbr.Rd | 1 man/similarity.Rd | 4 tests/testthat/test_knn.R | 33 +++--- vignettes/neighbr-help.Rmd | 4 17 files changed, 336 insertions(+), 133 deletions(-)
Title: Download and Process GIMMS NDVI3g Data
Description: This is a set of functions to retrieve information about GIMMS
NDVI3g files currently available online; download (and re-arrange, in the
case of NDVI3g.v0) the half-monthly data sets from NASA Ames Ecological
Forecasting Lab (ECOCAST); import downloaded files from ENVI binary
(NDVI3g.v0) or NetCDF format (NDVI3g.v1) directly into R based on the
widespread 'raster' package; conduct quality control; and generate monthly
composites (e.g., maximum values) from the half-monthly input data. As a
special gimmick, a method is included to conveniently apply the Mann-Kendall
trend test upon 'Raster*' images, optionally featuring trend-free
pre-whitening to account for lag-1 autocorrelation.
Author: Florian Detsch [cre, aut]
Maintainer: Florian Detsch <fdetsch@web.de>
Diff between gimms versions 1.1.1 dated 2018-12-07 and 1.1.3 dated 2020-03-19
DESCRIPTION | 28 ++-- MD5 | 44 +++--- NAMESPACE | 4 NEWS | 15 ++ NEWS.md | 15 ++ R/gimms-package.R | 111 ++++++++--------- R/oldNaming.R | 156 ++++++++++++------------ R/updateInventory.R | 304 ++++++++++++++++++++++++------------------------ README.md | 202 +++++++++++++++++-------------- build/partial.rdb |binary data/bale3g.v1.rda |binary data/kili3g.v0.rda |binary man/bale3g.v1.Rd | 4 man/downloadGimms.Rd | 49 ++++++- man/kili3g.v0.Rd | 4 man/monthlyComposite.Rd | 17 +- man/monthlyIndices.Rd | 10 + man/oldNaming.Rd | 4 man/qualityControl.Rd | 4 man/rasterizeGimms.Rd | 12 + man/rearrangeFiles.Rd | 9 + man/significantTau.Rd | 21 ++- man/updateInventory.Rd | 3 23 files changed, 569 insertions(+), 447 deletions(-)
Title: Fast Estimators for Design-Based Inference
Description: Fast procedures for small set of commonly-used, design-appropriate estimators with robust standard errors and confidence intervals. Includes estimators for linear regression, instrumental variables regression, difference-in-means, Horvitz-Thompson estimation, and regression improving precision of experimental estimates by interacting treatment with centered pre-treatment covariates introduced by Lin (2013) <doi:10.1214/12-AOAS583>.
Author: Graeme Blair [aut, cre],
Jasper Cooper [aut],
Alexander Coppock [aut],
Macartan Humphreys [aut],
Luke Sonnet [aut],
Neal Fultz [ctb],
Lily Medina [ctb],
Russell Lenth [ctb]
Maintainer: Graeme Blair <graeme.blair@ucla.edu>
Diff between estimatr versions 0.20.0 dated 2019-09-09 and 0.22.0 dated 2020-03-19
DESCRIPTION | 8 ++--- MD5 | 50 ++++++++++++++++----------------- NEWS.md | 8 +++-- R/estimatr.R | 2 + R/estimatr_lh_robust.R | 1 R/helper_extract.R | 8 +++++ R/helper_lm_robust_fit.R | 2 - R/helper_na_omit_detailed.R | 1 R/helper_starprep.R | 20 +++++++++++-- man/alo_star_men.Rd | 6 ++- man/commarobust.Rd | 3 - man/declaration_to_condition_pr_mat.Rd | 8 +++-- man/difference_in_means.Rd | 16 ++++++++-- man/estimatr.Rd | 3 - man/extract.lm_robust.Rd | 48 ++++++++++++++++++++++++------- man/horvitz_thompson.Rd | 22 +++++++++++--- man/iv_robust.Rd | 17 +++++++++-- man/lh_robust.Rd | 3 - man/lm_lin.Rd | 16 ++++++++-- man/lm_robust.Rd | 16 ++++++++-- man/lm_robust_fit.Rd | 21 +++++++++++-- man/na.omit_detailed.data.frame.Rd | 2 - man/predict.lm_robust.Rd | 14 +++++++-- man/starprep.Rd | 9 ++++- tests/testthat/test-lm-robust-fes.R | 6 +++ tests/testthat/test-starprep.R | 45 +++++++++++++++++++++++++++++ 26 files changed, 269 insertions(+), 86 deletions(-)
Title: Creating Contact and Social Networks
Description: Process spatially- and temporally-discrete data into contact and
social networks, and facilitate network analysis by randomizing
individuals' movement paths and/or related categorical variables. To use
this package, users need only have a dataset containing spatial data
(i.e., latitude/longitude, or planar x & y coordinates), individual IDs
relating spatial data to specific individuals, and date/time information
relating spatial locations to temporal locations. The functionality of this
package ranges from data "cleaning" via multiple filtration functions, to
spatial and temporal data interpolation, and network creation and analysis.
Functions within this package are not limited to describing interpersonal
contacts. Package functions can also identify and quantify "contacts"
between individuals and fixed areas (e.g., home ranges, water bodies,
buildings, etc.). As such, this package is an incredibly useful resource
for facilitating epidemiological, ecological, ethological and sociological
research.
Author: Trevor Farthing [aut, cre],
Daniel Dawson [aut],
Cristina Lanzas [ctb]
Maintainer: Trevor Farthing <tsfarthi@ncsu.edu>
Diff between contact versions 1.2.0 dated 2020-03-16 and 1.2.1 dated 2020-03-19
contact-1.2.0/contact/inst/doc/Using_the_contact_package_v1.2.0.R |only contact-1.2.0/contact/inst/doc/Using_the_contact_package_v1.2.0.Rmd |only contact-1.2.0/contact/inst/doc/Using_the_contact_package_v1.2.0.html |only contact-1.2.0/contact/vignettes/Using_the_contact_package_v1.2.0.Rmd |only contact-1.2.1/contact/DESCRIPTION | 6 - contact-1.2.1/contact/MD5 | 42 +++---- contact-1.2.1/contact/R/calves2018.R | 3 contact-1.2.1/contact/R/contactCompare_chisq.R | 20 ++- contact-1.2.1/contact/R/contactTest.R | 38 ------ contact-1.2.1/contact/R/findDistThresh.R | 2 contact-1.2.1/contact/R/mps.R | 2 contact-1.2.1/contact/R/ntwrkEdges.R | 56 ++++------ contact-1.2.1/contact/R/randomizeFeature.R | 7 - contact-1.2.1/contact/R/randomizePaths.R | 2 contact-1.2.1/contact/R/summarizeContacts.R | 2 contact-1.2.1/contact/build/vignette.rds |binary contact-1.2.1/contact/inst/doc/Using_the_contact_package_v1_2_1.R |only contact-1.2.1/contact/inst/doc/Using_the_contact_package_v1_2_1.Rmd |only contact-1.2.1/contact/inst/doc/Using_the_contact_package_v1_2_1.html |only contact-1.2.1/contact/man/calves2018.Rd | 5 contact-1.2.1/contact/man/contactTest.Rd | 39 ------ contact-1.2.1/contact/man/findDistThresh.Rd | 2 contact-1.2.1/contact/man/mps.Rd | 2 contact-1.2.1/contact/man/randomizeFeature.Rd | 7 - contact-1.2.1/contact/man/randomizePaths.Rd | 2 contact-1.2.1/contact/vignettes/Using_the_contact_package_v1_2_1.Rmd |only 26 files changed, 78 insertions(+), 159 deletions(-)
Title: Best Subset Selection in Linear, Logistic and CoxPH Models
Description: An implementation of best subset selection in generalized linear model and Cox proportional hazard model via the primal dual active set algorithm proposed by Wen, C., Zhang, A., Quan, S. and Wang, X. (2017) <arXiv:1709.06254>. The algorithm formulates coefficient parameters and residuals as primal and dual variables and utilizes efficient active set selection strategies based on the complementarity of the primal and dual variables.
Author: Canhong Wen [aut, cre],
Aijun Zhang [aut],
Shijie Quan [aut],
Xueqin Wang [aut]
Maintainer: Canhong Wen <wencanhong@gmail.com>
Diff between BeSS versions 1.0.7 dated 2020-03-18 and 1.0.8 dated 2020-03-19
BeSS-1.0.7/BeSS/src/Makevars |only BeSS-1.0.7/BeSS/src/Makevars.win |only BeSS-1.0.7/BeSS/src/registerDynamicSymbol.c |only BeSS-1.0.8/BeSS/DESCRIPTION | 15 BeSS-1.0.8/BeSS/MD5 | 78 ++- BeSS-1.0.8/BeSS/NAMESPACE | 7 BeSS-1.0.8/BeSS/R/RcppExports.R | 32 + BeSS-1.0.8/BeSS/R/bess.R | 631 ++++++++++++++-------------- BeSS-1.0.8/BeSS/R/bess.cox.R | 186 ++++---- BeSS-1.0.8/BeSS/R/bess.glm.R | 168 +++---- BeSS-1.0.8/BeSS/R/bess.lm.R | 114 ++--- BeSS-1.0.8/BeSS/R/bess.one.R | 29 - BeSS-1.0.8/BeSS/R/coef.bess.R | 10 BeSS-1.0.8/BeSS/R/gbess.cox.R |only BeSS-1.0.8/BeSS/R/gbess.glm.R |only BeSS-1.0.8/BeSS/R/gbess.lm.R |only BeSS-1.0.8/BeSS/R/gen.data.R | 134 ++--- BeSS-1.0.8/BeSS/R/plot.bess.R | 3 BeSS-1.0.8/BeSS/R/predict.bess.R | 59 ++ BeSS-1.0.8/BeSS/R/print.bess.R | 4 BeSS-1.0.8/BeSS/R/print.bess.one.R |only BeSS-1.0.8/BeSS/R/summary.bess.R | 48 +- BeSS-1.0.8/BeSS/R/summary.bess.one.R |only BeSS-1.0.8/BeSS/data/SAheart.RData |only BeSS-1.0.8/BeSS/data/prostate.RData |only BeSS-1.0.8/BeSS/inst |only BeSS-1.0.8/BeSS/man/SAheart.Rd |only BeSS-1.0.8/BeSS/man/aic.Rd | 2 BeSS-1.0.8/BeSS/man/bess-internal.Rd | 26 + BeSS-1.0.8/BeSS/man/bess.Rd | 59 +- BeSS-1.0.8/BeSS/man/bess.one.Rd | 47 +- BeSS-1.0.8/BeSS/man/coef.bess.Rd | 6 BeSS-1.0.8/BeSS/man/coef.bess.one.Rd |only BeSS-1.0.8/BeSS/man/deviance.bess.Rd | 6 BeSS-1.0.8/BeSS/man/deviance.bess.one.Rd |only BeSS-1.0.8/BeSS/man/gen.data.Rd | 2 BeSS-1.0.8/BeSS/man/gravier.Rd | 6 BeSS-1.0.8/BeSS/man/logLik.bess.Rd | 8 BeSS-1.0.8/BeSS/man/logLik.bess.one.Rd |only BeSS-1.0.8/BeSS/man/plot.bess.Rd | 2 BeSS-1.0.8/BeSS/man/predict.bess.Rd | 11 BeSS-1.0.8/BeSS/man/predict.bess.one.Rd |only BeSS-1.0.8/BeSS/man/print.bess.Rd | 4 BeSS-1.0.8/BeSS/man/print.bess.one.Rd |only BeSS-1.0.8/BeSS/man/prostate.Rd |only BeSS-1.0.8/BeSS/man/summary.bess.Rd |only BeSS-1.0.8/BeSS/man/summary.bess.one.Rd |only BeSS-1.0.8/BeSS/src/RcppExports.cpp | 296 ++++++++++++- BeSS-1.0.8/BeSS/src/bess.cpp | 192 ++++---- BeSS-1.0.8/BeSS/src/group.cpp |only 50 files changed, 1354 insertions(+), 831 deletions(-)
Title: Analysis, Seriation and Visualization of Archaeological Count
Data
Description: An easy way to examine archaeological count data. This package
provides a convenient and reproducible toolkit for relative and absolute
dating and analysis of (chronological) patterns. It includes functions for
matrix seriation (reciprocal ranking, CA-based seriation), chronological
modeling and dating of archaeological assemblages and/or objects.
Beyond these, the package provides several tests and measures of diversity:
heterogeneity and evenness (Brillouin, Shannon, Simpson, etc.),
richness and rarefaction (Chao1, Chao2, ACE, ICE, etc.),
turnover and similarity (Brainerd-Robinson, etc.).
The package make it easy to visualize count data and statistical thresholds:
rank vs. abundance plots, heatmaps, Ford (1962) and Bertin (1977) diagrams.
Author: Nicolas Frerebeau [aut, cre] (<https://orcid.org/0000-0001-5759-4944>),
Brice Lebrun [ctb] (<https://orcid.org/0000-0001-7503-8685>),
Matthew Peeples [ctb] (<https://orcid.org/0000-0003-4496-623X>),
Ben Marwick [ctb] (<https://orcid.org/0000-0001-7879-4531>),
Anne Philippe [ctb],
Jean-Baptiste Fourvel [ctb] (<https://orcid.org/0000-0002-1061-4642>)
Maintainer: Nicolas Frerebeau
<nicolas.frerebeau@u-bordeaux-montaigne.fr>
Diff between tabula versions 1.5.0 dated 2020-01-16 and 1.5.1 dated 2020-03-19
DESCRIPTION | 8 MD5 | 120 - NEWS.md | 8 R/AllClasses.R | 4 R/refine.R | 5 R/tabula-package.R | 2 R/validate.R | 4 README.md | 8 build/vignette.rds |binary inst/doc/bibliography.R | 2 inst/doc/bibliography.html | 15 inst/doc/dating.R | 12 inst/doc/dating.html | 29 inst/doc/diversity.R | 18 inst/doc/diversity.html | 27 inst/doc/seriation.R | 16 inst/doc/seriation.html | 29 man/BootCA-class.Rd | 7 man/DateModel-class.Rd | 7 man/DiversityIndex.Rd | 7 man/PermutationOrder-class.Rd | 7 man/access.Rd | 3 man/boves.Rd | 14 man/compiegne.Rd | 14 man/date.Rd | 9 man/deprecated.Rd | 92 - man/heterogeneity-index.Rd | 34 man/merzbach.Rd | 14 man/mississippi.Rd | 14 man/plot_bar.Rd | 12 man/plot_date.Rd | 31 man/plot_diversity.Rd | 9 man/plot_line.Rd | 9 man/plot_matrix.Rd | 12 man/plot_spot.Rd | 9 man/richness-index.Rd | 40 man/seriation.Rd | 18 man/similarity-method.Rd | 17 man/subset.Rd | 3 man/tabula-package.Rd | 4 man/test.Rd | 1 man/turnover-index.Rd | 26 man/zuni.Rd | 14 tests/figs/date-time/date-activity-event-false.svg | 6 tests/figs/date-time/date-activity-event-true.svg | 6 tests/figs/date-time/date.svg | 4 tests/figs/plots/bertin-threshold.svg | 4 tests/figs/plots/ford-count-eppm-false.svg | 746 ++++++------ tests/figs/plots/ford-count-eppm-true.svg | 1222 +++++++++---------- tests/figs/plots/gg-old-bar1.svg | 154 +- tests/figs/plots/gg-old-bar2.svg | 154 +- tests/figs/plots/gg-old-bar3.svg | 1296 ++++++++++----------- tests/figs/plots/gg-old-bar4.svg | 624 +++++----- tests/figs/plots/mtx-count-pvi-false.svg | 32 tests/figs/plots/mtx-count-pvi-true.svg | 32 tests/figs/plots/mtx-freq.svg | 32 tests/figs/plots/mtx-incid.svg | 4 tests/figs/plots/spot-count.svg | 10 tests/figs/plots/spot-freq.svg | 14 tests/figs/plots/spot-occ.svg | 40 tests/figs/plots/spot-sim.svg | 28 61 files changed, 2625 insertions(+), 2517 deletions(-)
Title: Latent Dirichlet Allocation Coupled with Time Series Analyses
Description: Combines Latent Dirichlet Allocation (LDA) and Bayesian multinomial
time series methods in a two-stage analysis to quantify dynamics in
high-dimensional temporal data. LDA decomposes multivariate data into
lower-dimension latent groupings, whose relative proportions are modeled
using generalized Bayesian time series models that include abrupt
changepoints and smooth dynamics. The methods are described in Blei
et al. (2003) <doi:10.1162/jmlr.2003.3.4-5.993>, Western and Kleykamp
(2004) <doi:10.1093/pan/mph023>, Venables and Ripley
(2002, ISBN-13:978-0387954578), and Christensen et al.
(2018) <doi:10.1002/ecy.2373>.
Author: Juniper L. Simonis [aut, cre] (<https://orcid.org/0000-0001-9798-0460>),
Erica M. Christensen [aut] (<https://orcid.org/0000-0002-5635-2502>),
David J. Harris [aut] (<https://orcid.org/0000-0003-3332-9307>),
Renata M. Diaz [aut] (<https://orcid.org/0000-0003-0803-4734>),
Hao Ye [aut] (<https://orcid.org/0000-0002-8630-1458>),
Ethan P. White [aut] (<https://orcid.org/0000-0001-6728-7745>),
S.K. Morgan Ernest [aut] (<https://orcid.org/0000-0002-6026-8530>),
Weecology [cph]
Maintainer: Juniper L. Simonis <juniper.simonis@weecology.org>
Diff between LDATS versions 0.2.6 dated 2020-03-03 and 0.2.7 dated 2020-03-19
DESCRIPTION | 9 MD5 | 26 - NEWS.md | 9 README.md | 2 inst/WORDLIST | 1 inst/doc/LDATS_codebase.html | 2 inst/doc/paper-comparison.R | 537 ++++++++++++++++------------ inst/doc/paper-comparison.Rmd | 294 +++++++++++---- inst/doc/paper-comparison.html | 761 ++++++++++++++++++++--------------------- inst/doc/rodents-example.R | 6 inst/doc/rodents-example.Rmd | 6 inst/doc/rodents-example.html | 2 vignettes/paper-comparison.Rmd | 294 +++++++++++---- vignettes/rodents-example.Rmd | 6 14 files changed, 1150 insertions(+), 805 deletions(-)
Title: Hierarchical Model of Species Communities
Description: Hierarchical Modelling of Species Communities (HMSC) is
a model-based approach for analyzing community ecological data.
This package implements it in the Bayesian framework with Gibbs
Markov chain Monte Carlo (MCMC) sampling.
Author: Gleb Tikhonov [aut],
Otso Ovaskainen [aut, cre] (<https://orcid.org/0000-0001-9750-4421>),
Jari Oksanen [aut],
Melinda de Jonge [aut],
Oystein Opedal [aut],
Tad Dallas [aut]
Maintainer: Otso Ovaskainen <otso.ovaskainen@helsinki.fi>
Diff between Hmsc versions 3.0-4 dated 2019-12-16 and 3.0-6 dated 2020-03-19
DESCRIPTION | 10 +- MD5 | 58 +++++++------ NAMESPACE | 1 R/Hmsc.R | 18 ++-- R/computeInitialParameters.R | 2 R/computePredictedValues.R | 52 ++++++++---- R/constructGradient.R | 17 ++- R/plotGradient.R | 16 ++- R/predict.R | 10 ++ R/predictLatentFactor.R | 6 - R/prepareGradient.R | 8 - R/print.Hmsc.R | 15 +++ R/sampleMcmc.R | 45 ++++++---- R/samplePrior.R | 2 R/setPriors.Hmsc.R | 13 ++- R/updateEta.R | 129 +++++++++++++++++++----------- R/updateZ.R | 2 R/updatewRRR.R | 4 build/vignette.rds |binary data/TD.rda |binary inst/NEWS.md | 55 ++++++++++++ inst/doc/vignette_5_performance.pdf |only inst/doc/vignette_5_performance.pdf.asis |only man/computePredictedValues.Rd | 9 +- man/plotGradient.Rd | 1 man/prepareGradient.Rd | 7 - man/sampleMcmc.Rd | 10 +- tests/Examples/Hmsc-Ex.Rout.save | 69 ++++------------ tests/testthat/test-sampling.R | 4 vignettes/load_libraries.R |only vignettes/makedata.R |only vignettes/vignette_5_performance.Rmd |only vignettes/vignette_5_performance.pdf.asis |only 33 files changed, 344 insertions(+), 219 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-04-15 0.1.1
2019-04-08 0.1.0
Title: Retrieving Information of Proteins from Uniprot
Description: Connect to Uniprot <https://www.uniprot.org/> to retrieve information about proteins using their accession number such information could be name or taxonomy information, For detailed information kindly read the publication <https://www.sciencedirect.com/science/article/pii/S1874391919303859>.
Author: Mohamed Soudy [aut, cre],
Ali Mostafa [aut]
Maintainer: Mohamed Soudy <MohmedSoudy2009@gmail.com>
Diff between UniprotR versions 1.2.3 dated 2020-01-21 and 1.2.4 dated 2020-03-19
UniprotR-1.2.3/UniprotR/man/UniprotR.Rd |only UniprotR-1.2.4/UniprotR/DESCRIPTION | 10 +-- UniprotR-1.2.4/UniprotR/MD5 | 11 +-- UniprotR-1.2.4/UniprotR/R/GetSeqLength.R |only UniprotR-1.2.4/UniprotR/R/UniprotR.r | 76 ------------------------- UniprotR-1.2.4/UniprotR/R/plotGoannotation.R | 1 UniprotR-1.2.4/UniprotR/inst/doc/UniprotR.html | 14 +--- UniprotR-1.2.4/UniprotR/man/GetSeqLength.Rd |only 8 files changed, 19 insertions(+), 93 deletions(-)
Title: Using KEEL in R Code
Description: 'KEEL' is a popular Java software for a large number of different knowledge data discovery tasks.
This package takes the advantages of 'KEEL' and R, allowing to use 'KEEL' algorithms in simple R code.
The implemented R code layer between R and 'KEEL' makes easy both using 'KEEL' algorithms in R as implementing new algorithms for 'RKEEL' in a very simple way.
It includes more than 100 algorithms for classification, regression, preprocess, association rules and imbalance learning, which allows a more complete experimentation process.
For more information about KEEL, see <http://www.keel.es/>.
Author: Jose M. Moyano [aut, cre],
Luciano Sanchez [aut],
Oliver Sanchez [ctb],
Jesus Alcala-Fernandez [ctb]
Maintainer: Jose M. Moyano <jmoyano@uco.es>
Diff between RKEEL versions 1.3.1 dated 2019-07-18 and 1.3.2 dated 2020-03-19
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- man/CART-C.Rd | 10 +++++----- man/CART-R.Rd | 10 +++++----- man/FPgrowth-A.Rd | 10 +++++----- man/writeDatFromDataframe.Rd | 40 ++++++++++++++++++++-------------------- 6 files changed, 44 insertions(+), 44 deletions(-)
Title: Network Analysis and Visualization
Description: Routines for simple graphs and network analysis. It can
handle large graphs very well and provides functions for generating random
and regular graphs, graph visualization, centrality methods and much more.
Author: See AUTHORS file.
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between igraph versions 1.2.4.2 dated 2019-11-27 and 1.2.5 dated 2020-03-19
igraph-1.2.4.2/igraph/man/printr.Rd |only igraph-1.2.5/igraph/DESCRIPTION | 10 igraph-1.2.5/igraph/MD5 | 618 +- igraph-1.2.5/igraph/R/adjacency.R | 23 igraph-1.2.5/igraph/R/community.R | 5 igraph-1.2.5/igraph/R/degseq.R | 4 igraph-1.2.5/igraph/R/games.R | 7 igraph-1.2.5/igraph/R/incidence.R | 2 igraph-1.2.5/igraph/R/make.R | 3 igraph-1.2.5/igraph/R/printr.R | 6 igraph-1.2.5/igraph/cleanup |only igraph-1.2.5/igraph/configure | 18 igraph-1.2.5/igraph/configure.ac | 2 igraph-1.2.5/igraph/inst/NEWS.md | 6 igraph-1.2.5/igraph/man/E.Rd | 19 igraph-1.2.5/igraph/man/V.Rd | 19 igraph-1.2.5/igraph/man/add_edges.Rd | 14 igraph-1.2.5/igraph/man/add_layout_.Rd | 41 igraph-1.2.5/igraph/man/add_vertices.Rd | 14 igraph-1.2.5/igraph/man/adjacent_vertices.Rd | 21 igraph-1.2.5/igraph/man/all_simple_paths.Rd | 8 igraph-1.2.5/igraph/man/alpha_centrality.Rd | 12 igraph-1.2.5/igraph/man/are_adjacent.Rd | 21 igraph-1.2.5/igraph/man/arpack.Rd | 14 igraph-1.2.5/igraph/man/as.directed.Rd | 7 igraph-1.2.5/igraph/man/as_adjacency_matrix.Rd | 21 igraph-1.2.5/igraph/man/as_incidence_matrix.Rd | 9 igraph-1.2.5/igraph/man/authority_score.Rd | 3 igraph-1.2.5/igraph/man/betweenness.Rd | 23 igraph-1.2.5/igraph/man/bfs.Rd | 21 igraph-1.2.5/igraph/man/bipartite_projection.Rd | 11 igraph-1.2.5/igraph/man/c.igraph.es.Rd | 30 igraph-1.2.5/igraph/man/c.igraph.vs.Rd | 30 igraph-1.2.5/igraph/man/categorical_pal.Rd | 6 igraph-1.2.5/igraph/man/centr_betw.Rd | 18 igraph-1.2.5/igraph/man/centr_betw_tmax.Rd | 15 igraph-1.2.5/igraph/man/centr_clo.Rd | 18 igraph-1.2.5/igraph/man/centr_clo_tmax.Rd | 18 igraph-1.2.5/igraph/man/centr_degree.Rd | 22 igraph-1.2.5/igraph/man/centr_degree_tmax.Rd | 22 igraph-1.2.5/igraph/man/centr_eigen.Rd | 23 igraph-1.2.5/igraph/man/centr_eigen_tmax.Rd | 17 igraph-1.2.5/igraph/man/centralize.Rd | 14 igraph-1.2.5/igraph/man/cliques.Rd | 3 igraph-1.2.5/igraph/man/closeness.Rd | 19 igraph-1.2.5/igraph/man/cluster_edge_betweenness.Rd | 13 igraph-1.2.5/igraph/man/cluster_fast_greedy.Rd | 9 igraph-1.2.5/igraph/man/cluster_infomap.Rd | 14 igraph-1.2.5/igraph/man/cluster_label_prop.Rd | 3 igraph-1.2.5/igraph/man/cluster_leading_eigen.Rd | 13 igraph-1.2.5/igraph/man/cluster_spinglass.Rd | 18 igraph-1.2.5/igraph/man/cluster_walktrap.Rd | 10 igraph-1.2.5/igraph/man/cohesive_blocks.Rd | 18 igraph-1.2.5/igraph/man/communities.Rd | 17 igraph-1.2.5/igraph/man/compare.Rd | 7 igraph-1.2.5/igraph/man/component_wise.Rd | 44 igraph-1.2.5/igraph/man/components.Rd | 3 igraph-1.2.5/igraph/man/consensus_tree.Rd | 14 igraph-1.2.5/igraph/man/contract.Rd | 3 igraph-1.2.5/igraph/man/count_isomorphisms.Rd | 15 igraph-1.2.5/igraph/man/count_motifs.Rd | 5 igraph-1.2.5/igraph/man/count_subgraph_isomorphisms.Rd | 18 igraph-1.2.5/igraph/man/decompose.Rd | 3 igraph-1.2.5/igraph/man/degree.Rd | 9 igraph-1.2.5/igraph/man/delete_edge_attr.Rd | 30 igraph-1.2.5/igraph/man/delete_edges.Rd | 14 igraph-1.2.5/igraph/man/delete_graph_attr.Rd | 30 igraph-1.2.5/igraph/man/delete_vertex_attr.Rd | 30 igraph-1.2.5/igraph/man/delete_vertices.Rd | 14 igraph-1.2.5/igraph/man/dfs.Rd | 22 igraph-1.2.5/igraph/man/difference.igraph.es.Rd | 30 igraph-1.2.5/igraph/man/difference.igraph.vs.Rd | 30 igraph-1.2.5/igraph/man/distances.Rd | 33 igraph-1.2.5/igraph/man/diverging_pal.Rd | 6 igraph-1.2.5/igraph/man/each_edge.Rd | 5 igraph-1.2.5/igraph/man/eccentricity.Rd | 3 igraph-1.2.5/igraph/man/edge.Rd | 15 igraph-1.2.5/igraph/man/edge_attr-set.Rd | 31 igraph-1.2.5/igraph/man/edge_attr.Rd | 31 igraph-1.2.5/igraph/man/edge_attr_names.Rd | 31 igraph-1.2.5/igraph/man/ego.Rd | 27 igraph-1.2.5/igraph/man/eigen_centrality.Rd | 9 igraph-1.2.5/igraph/man/embed_adjacency_matrix.Rd | 12 igraph-1.2.5/igraph/man/embed_laplacian_matrix.Rd | 14 igraph-1.2.5/igraph/man/ends.Rd | 21 igraph-1.2.5/igraph/man/erdos.renyi.game.Rd | 10 igraph-1.2.5/igraph/man/fit_hrg.Rd | 14 igraph-1.2.5/igraph/man/fit_power_law.Rd | 10 igraph-1.2.5/igraph/man/get.edge.ids.Rd | 24 igraph-1.2.5/igraph/man/gorder.Rd | 21 igraph-1.2.5/igraph/man/graph_attr-set.Rd | 30 igraph-1.2.5/igraph/man/graph_attr.Rd | 31 igraph-1.2.5/igraph/man/graph_attr_names.Rd | 30 igraph-1.2.5/igraph/man/graph_from_adj_list.Rd | 7 igraph-1.2.5/igraph/man/graph_from_adjacency_matrix.Rd | 11 igraph-1.2.5/igraph/man/graph_from_atlas.Rd | 20 igraph-1.2.5/igraph/man/graph_from_edgelist.Rd | 20 igraph-1.2.5/igraph/man/graph_from_graphdb.Rd | 13 igraph-1.2.5/igraph/man/graph_from_graphnel.Rd | 3 igraph-1.2.5/igraph/man/graph_from_incidence_matrix.Rd | 11 igraph-1.2.5/igraph/man/graph_from_isomorphism_class.Rd | 15 igraph-1.2.5/igraph/man/graph_from_literal.Rd | 20 igraph-1.2.5/igraph/man/graphlet_basis.Rd | 9 igraph-1.2.5/igraph/man/gsize.Rd | 21 igraph-1.2.5/igraph/man/head_of.Rd | 21 igraph-1.2.5/igraph/man/head_print.Rd | 10 igraph-1.2.5/igraph/man/hrg-methods.Rd | 14 igraph-1.2.5/igraph/man/hrg.Rd | 14 igraph-1.2.5/igraph/man/hrg_tree.Rd | 14 igraph-1.2.5/igraph/man/hub_score.Rd | 3 igraph-1.2.5/igraph/man/igraph-dollar.Rd | 30 igraph-1.2.5/igraph/man/igraph-es-attributes.Rd | 36 igraph-1.2.5/igraph/man/igraph-es-indexing.Rd | 48 igraph-1.2.5/igraph/man/igraph-es-indexing2.Rd | 48 igraph-1.2.5/igraph/man/igraph-minus.Rd | 14 igraph-1.2.5/igraph/man/igraph-vs-attributes.Rd | 47 igraph-1.2.5/igraph/man/igraph-vs-indexing.Rd | 48 igraph-1.2.5/igraph/man/igraph-vs-indexing2.Rd | 48 igraph-1.2.5/igraph/man/igraph_options.Rd | 3 igraph-1.2.5/igraph/man/incident.Rd | 21 igraph-1.2.5/igraph/man/incident_edges.Rd | 21 igraph-1.2.5/igraph/man/intersection.igraph.Rd | 3 igraph-1.2.5/igraph/man/intersection.igraph.es.Rd | 30 igraph-1.2.5/igraph/man/intersection.igraph.vs.Rd | 30 igraph-1.2.5/igraph/man/is_chordal.Rd | 9 igraph-1.2.5/igraph/man/is_degseq.Rd | 18 igraph-1.2.5/igraph/man/is_directed.Rd | 21 igraph-1.2.5/igraph/man/is_graphical.Rd | 18 igraph-1.2.5/igraph/man/is_printer_callback.Rd | 3 igraph-1.2.5/igraph/man/isomorphic.Rd | 26 igraph-1.2.5/igraph/man/isomorphism_class.Rd | 14 igraph-1.2.5/igraph/man/isomorphisms.Rd | 15 igraph-1.2.5/igraph/man/keeping_degseq.Rd | 5 igraph-1.2.5/igraph/man/laplacian_matrix.Rd | 8 igraph-1.2.5/igraph/man/layout_.Rd | 42 igraph-1.2.5/igraph/man/layout_as_bipartite.Rd | 44 igraph-1.2.5/igraph/man/layout_as_star.Rd | 41 igraph-1.2.5/igraph/man/layout_as_tree.Rd | 51 igraph-1.2.5/igraph/man/layout_in_circle.Rd | 41 igraph-1.2.5/igraph/man/layout_nicely.Rd | 41 igraph-1.2.5/igraph/man/layout_on_grid.Rd | 41 igraph-1.2.5/igraph/man/layout_on_sphere.Rd | 41 igraph-1.2.5/igraph/man/layout_randomly.Rd | 41 igraph-1.2.5/igraph/man/layout_with_dh.Rd | 56 igraph-1.2.5/igraph/man/layout_with_drl.Rd | 11 igraph-1.2.5/igraph/man/layout_with_fr.Rd | 66 igraph-1.2.5/igraph/man/layout_with_gem.Rd | 52 igraph-1.2.5/igraph/man/layout_with_graphopt.Rd | 54 igraph-1.2.5/igraph/man/layout_with_kk.Rd | 66 igraph-1.2.5/igraph/man/layout_with_lgl.Rd | 54 igraph-1.2.5/igraph/man/layout_with_mds.Rd | 44 igraph-1.2.5/igraph/man/layout_with_sugiyama.Rd | 55 igraph-1.2.5/igraph/man/local_scan.Rd | 16 igraph-1.2.5/igraph/man/make_chordal_ring.Rd | 20 igraph-1.2.5/igraph/man/make_clusters.Rd | 9 igraph-1.2.5/igraph/man/make_empty_graph.Rd | 20 igraph-1.2.5/igraph/man/make_full_bipartite_graph.Rd | 8 igraph-1.2.5/igraph/man/make_full_citation_graph.Rd | 20 igraph-1.2.5/igraph/man/make_full_graph.Rd | 21 igraph-1.2.5/igraph/man/make_graph.Rd | 32 igraph-1.2.5/igraph/man/make_lattice.Rd | 32 igraph-1.2.5/igraph/man/make_ring.Rd | 21 igraph-1.2.5/igraph/man/make_star.Rd | 21 igraph-1.2.5/igraph/man/make_tree.Rd | 21 igraph-1.2.5/igraph/man/matching.Rd | 8 igraph-1.2.5/igraph/man/merge_coords.Rd | 42 igraph-1.2.5/igraph/man/min_cut.Rd | 9 igraph-1.2.5/igraph/man/motifs.Rd | 5 igraph-1.2.5/igraph/man/neighbors.Rd | 21 igraph-1.2.5/igraph/man/nexus.Rd | 32 igraph-1.2.5/igraph/man/norm_coords.Rd | 53 igraph-1.2.5/igraph/man/normalize.Rd | 55 igraph-1.2.5/igraph/man/page_rank.Rd | 24 igraph-1.2.5/igraph/man/path.Rd | 14 igraph-1.2.5/igraph/man/plot.igraph.Rd | 14 igraph-1.2.5/igraph/man/plot.sir.Rd | 22 igraph-1.2.5/igraph/man/plot_dendrogram.communities.Rd | 10 igraph-1.2.5/igraph/man/plot_dendrogram.igraphHRG.Rd | 3 igraph-1.2.5/igraph/man/plus-.igraph.Rd | 14 igraph-1.2.5/igraph/man/power_centrality.Rd | 11 igraph-1.2.5/igraph/man/predict_edges.Rd | 23 igraph-1.2.5/igraph/man/print.igraph.Rd | 11 igraph-1.2.5/igraph/man/print.igraph.es.Rd | 18 igraph-1.2.5/igraph/man/print.igraph.vs.Rd | 18 igraph-1.2.5/igraph/man/print.igraphHRG.Rd | 18 igraph-1.2.5/igraph/man/print.igraphHRGConsensus.Rd | 14 igraph-1.2.5/igraph/man/printer_callback.Rd | 3 igraph-1.2.5/igraph/man/r_pal.Rd | 6 igraph-1.2.5/igraph/man/random_walk.Rd | 9 igraph-1.2.5/igraph/man/read_graph.Rd | 8 igraph-1.2.5/igraph/man/rev.igraph.es.Rd | 31 igraph-1.2.5/igraph/man/rev.igraph.vs.Rd | 31 igraph-1.2.5/igraph/man/rewire.Rd | 5 igraph-1.2.5/igraph/man/sample_bipartite.Rd | 11 igraph-1.2.5/igraph/man/sample_correlated_gnp.Rd | 3 igraph-1.2.5/igraph/man/sample_correlated_gnp_pair.Rd | 4 igraph-1.2.5/igraph/man/sample_degseq.Rd | 7 igraph-1.2.5/igraph/man/sample_dirichlet.Rd | 5 igraph-1.2.5/igraph/man/sample_dot_product.Rd | 2 igraph-1.2.5/igraph/man/sample_fitness.Rd | 9 igraph-1.2.5/igraph/man/sample_fitness_pl.Rd | 12 igraph-1.2.5/igraph/man/sample_forestfire.Rd | 3 igraph-1.2.5/igraph/man/sample_hierarchical_sbm.Rd | 4 igraph-1.2.5/igraph/man/sample_hrg.Rd | 15 igraph-1.2.5/igraph/man/sample_last_cit.Rd | 28 igraph-1.2.5/igraph/man/sample_motifs.Rd | 14 igraph-1.2.5/igraph/man/sample_pa.Rd | 14 igraph-1.2.5/igraph/man/sample_pa_age.Rd | 20 igraph-1.2.5/igraph/man/sample_pref.Rd | 21 igraph-1.2.5/igraph/man/sample_sbm.Rd | 5 igraph-1.2.5/igraph/man/sample_sphere_surface.Rd | 5 igraph-1.2.5/igraph/man/sample_sphere_volume.Rd | 5 igraph-1.2.5/igraph/man/sample_traits_callaway.Rd | 21 igraph-1.2.5/igraph/man/scan_stat.Rd | 3 igraph-1.2.5/igraph/man/scg.Rd | 26 igraph-1.2.5/igraph/man/scg_eps.Rd | 9 igraph-1.2.5/igraph/man/scg_group.Rd | 11 igraph-1.2.5/igraph/man/scg_semi_proj.Rd | 10 igraph-1.2.5/igraph/man/sequential_pal.Rd | 6 igraph-1.2.5/igraph/man/set_edge_attr.Rd | 30 igraph-1.2.5/igraph/man/set_graph_attr.Rd | 30 igraph-1.2.5/igraph/man/set_vertex_attr.Rd | 30 igraph-1.2.5/igraph/man/shapes.Rd | 3 igraph-1.2.5/igraph/man/similarity.Rd | 10 igraph-1.2.5/igraph/man/simplified.Rd | 11 igraph-1.2.5/igraph/man/simplify.Rd | 8 igraph-1.2.5/igraph/man/spectrum.Rd | 9 igraph-1.2.5/igraph/man/stochastic_matrix.Rd | 7 igraph-1.2.5/igraph/man/strength.Rd | 9 igraph-1.2.5/igraph/man/sub-.igraph.Rd | 37 igraph-1.2.5/igraph/man/sub-sub-.igraph.Rd | 25 igraph-1.2.5/igraph/man/subgraph.Rd | 7 igraph-1.2.5/igraph/man/subgraph_isomorphic.Rd | 26 igraph-1.2.5/igraph/man/subgraph_isomorphisms.Rd | 15 igraph-1.2.5/igraph/man/tail_of.Rd | 21 igraph-1.2.5/igraph/man/transitivity.Rd | 12 igraph-1.2.5/igraph/man/union.igraph.es.Rd | 30 igraph-1.2.5/igraph/man/union.igraph.vs.Rd | 30 igraph-1.2.5/igraph/man/unique.igraph.es.Rd | 30 igraph-1.2.5/igraph/man/unique.igraph.vs.Rd | 30 igraph-1.2.5/igraph/man/vertex.Rd | 14 igraph-1.2.5/igraph/man/vertex_attr-set.Rd | 30 igraph-1.2.5/igraph/man/vertex_attr.Rd | 30 igraph-1.2.5/igraph/man/vertex_attr_names.Rd | 29 igraph-1.2.5/igraph/man/vertex_connectivity.Rd | 3 igraph-1.2.5/igraph/man/with_edge_.Rd | 11 igraph-1.2.5/igraph/man/with_graph_.Rd | 11 igraph-1.2.5/igraph/man/with_igraph_opt.Rd | 3 igraph-1.2.5/igraph/man/with_vertex_.Rd | 11 igraph-1.2.5/igraph/man/without_attr.Rd | 11 igraph-1.2.5/igraph/man/without_loops.Rd | 11 igraph-1.2.5/igraph/man/without_multiples.Rd | 11 igraph-1.2.5/igraph/man/write_graph.Rd | 9 igraph-1.2.5/igraph/src/CHOLMOD/Include/cholmod_blas.h | 6 igraph-1.2.5/igraph/src/Makevars.in | 2 igraph-1.2.5/igraph/src/Makevars.win | 4 igraph-1.2.5/igraph/src/arpack.c | 10 igraph-1.2.5/igraph/src/blas.c | 22 igraph-1.2.5/igraph/src/cliquer/cliquer_graph.c | 6 igraph-1.2.5/igraph/src/cliquer/set.h | 2 igraph-1.2.5/igraph/src/config.h |only igraph-1.2.5/igraph/src/dgetv0.f | 6 igraph-1.2.5/igraph/src/dnaitr.f | 8 igraph-1.2.5/igraph/src/dnapps.f | 16 igraph-1.2.5/igraph/src/dnaup2.f | 14 igraph-1.2.5/igraph/src/dnaupd.f | 4 igraph-1.2.5/igraph/src/dneupd.f | 6 igraph-1.2.5/igraph/src/dngets.f | 4 igraph-1.2.5/igraph/src/dsaitr.f | 8 igraph-1.2.5/igraph/src/dsaup2.f | 14 igraph-1.2.5/igraph/src/dseupd.f | 6 igraph-1.2.5/igraph/src/foreign-dl-lexer.c | 943 ++- igraph-1.2.5/igraph/src/foreign-dl-lexer.l | 11 igraph-1.2.5/igraph/src/foreign-dl-parser.c | 2030 ++++---- igraph-1.2.5/igraph/src/foreign-dl-parser.h | 117 igraph-1.2.5/igraph/src/foreign-gml-lexer.c | 889 ++- igraph-1.2.5/igraph/src/foreign-gml-lexer.l | 10 igraph-1.2.5/igraph/src/foreign-gml-parser.c | 1803 +++---- igraph-1.2.5/igraph/src/foreign-gml-parser.h | 94 igraph-1.2.5/igraph/src/foreign-lgl-lexer.c | 908 ++- igraph-1.2.5/igraph/src/foreign-lgl-lexer.l | 10 igraph-1.2.5/igraph/src/foreign-lgl-parser.c | 1747 +++--- igraph-1.2.5/igraph/src/foreign-lgl-parser.h | 87 igraph-1.2.5/igraph/src/foreign-ncol-lexer.c | 906 ++- igraph-1.2.5/igraph/src/foreign-ncol-lexer.l | 10 igraph-1.2.5/igraph/src/foreign-ncol-parser.c | 1739 +++--- igraph-1.2.5/igraph/src/foreign-ncol-parser.h | 84 igraph-1.2.5/igraph/src/foreign-pajek-lexer.c | 919 ++- igraph-1.2.5/igraph/src/foreign-pajek-lexer.l | 10 igraph-1.2.5/igraph/src/foreign-pajek-parser.c | 2523 +++++----- igraph-1.2.5/igraph/src/foreign-pajek-parser.h | 222 igraph-1.2.5/igraph/src/igraph_arpack_internal.h | 36 igraph-1.2.5/igraph/src/igraph_blas_internal.h | 28 igraph-1.2.5/igraph/src/igraph_version.h | 2 igraph-1.2.5/igraph/src/lsap.c | 4 igraph-1.2.5/igraph/src/plfit/plfit.c | 2 igraph-1.2.5/igraph/src/sparsemat.c | 2 igraph-1.2.5/igraph/src/uuid/gen_uuid.c | 6 igraph-1.2.5/igraph/src/wrap.f |only igraph-1.2.5/igraph/tests/testthat.R | 1 igraph-1.2.5/igraph/tests/testthat/helper.R | 20 igraph-1.2.5/igraph/tests/testthat/test-vs-es-printing.R | 4 igraph-1.2.5/igraph/tests/testthat/test_bipartite.projection.R | 1 igraph-1.2.5/igraph/tests/testthat/test_contract.vertices.R | 1 igraph-1.2.5/igraph/tests/testthat/test_graph.adjacency.R | 5 igraph-1.2.5/igraph/tests/testthat/test_graph.subisomorphic.lad.R | 1 igraph-1.2.5/igraph/tests/testthat/test_igraph.options.R | 2 igraph-1.2.5/igraph/tests/testthat/test_layout.fr.R | 18 igraph-1.2.5/igraph/tests/testthat/test_optimal.community.R | 1 igraph-1.2.5/igraph/tests/testthat/test_scan.R | 1 igraph-1.2.5/igraph/tests/testthat/test_sgm.R | 3 igraph-1.2.5/igraph/tests/testthat/test_sir.R | 10 312 files changed, 11754 insertions(+), 8946 deletions(-)
Title: Statistical Toolbox for Radiometric Geochronology
Description: Plots U-Pb data on Wetherill and Tera-Wasserburg concordia diagrams. Calculates concordia and discordia ages. Performs linear regression of measurements with correlated errors using 'York', 'Titterington' and 'Ludwig' approaches. Generates Kernel Density Estimates (KDEs) and Cumulative Age Distributions (CADs). Produces Multidimensional Scaling (MDS) configurations and Shepard plots of multi-sample detrital datasets using the Kolmogorov-Smirnov distance as a dissimilarity measure. Calculates 40Ar/39Ar ages, isochrons, and age spectra. Computes weighted means accounting for overdispersion. Calculates U-Th-He (single grain and central) ages, logratio plots and ternary diagrams. Processes fission track data using the external detector method and LA-ICP-MS, calculates central ages and plots fission track and other data on radial (a.k.a. 'Galbraith') plots. Constructs total Pb-U, Pb-Pb, Th-Pb, K-Ca, Re-Os, Sm-Nd, Lu-Hf, Rb-Sr and 230Th-U isochrons as well as 230Th-U evolution plots.
Author: Pieter Vermeesch [aut, cre]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>
Diff between IsoplotR versions 3.2 dated 2020-01-23 and 3.3 dated 2020-03-19
IsoplotR-3.2/IsoplotR/inst/UPb8.csv |only IsoplotR-3.3/IsoplotR/DESCRIPTION | 10 - IsoplotR-3.3/IsoplotR/MD5 | 87 +++++---- IsoplotR-3.3/IsoplotR/NAMESPACE | 12 + IsoplotR-3.3/IsoplotR/R/ArAr.R | 77 -------- IsoplotR-3.3/IsoplotR/R/IsoplotR.R | 2 IsoplotR-3.3/IsoplotR/R/PbPb.R | 108 ------------ IsoplotR-3.3/IsoplotR/R/ThPb.R |only IsoplotR-3.3/IsoplotR/R/UPb.R | 102 +++-------- IsoplotR-3.3/IsoplotR/R/UThPb.R |only IsoplotR-3.3/IsoplotR/R/age.R | 59 +++--- IsoplotR-3.3/IsoplotR/R/cad.R | 34 ++- IsoplotR-3.3/IsoplotR/R/commonPb.R | 268 +++++++++++------------------- IsoplotR-3.3/IsoplotR/R/concordia.R | 26 +- IsoplotR-3.3/IsoplotR/R/constants.R | 6 IsoplotR-3.3/IsoplotR/R/discordia.R | 76 ++++---- IsoplotR-3.3/IsoplotR/R/documentation.R | 7 IsoplotR-3.3/IsoplotR/R/io.R | 157 ++++++++++------- IsoplotR-3.3/IsoplotR/R/isochron.R | 197 ++++++++++++++-------- IsoplotR-3.3/IsoplotR/R/kde.R | 33 ++- IsoplotR-3.3/IsoplotR/R/ludwig.R | 120 +++++++------ IsoplotR-3.3/IsoplotR/R/peakfit.R | 35 ++- IsoplotR-3.3/IsoplotR/R/radialplot.R | 32 ++- IsoplotR-3.3/IsoplotR/R/tests.R |only IsoplotR-3.3/IsoplotR/R/toolbox.R | 4 IsoplotR-3.3/IsoplotR/R/weightedmean.R | 29 ++- IsoplotR-3.3/IsoplotR/R/york.R | 167 ++++++++++-------- IsoplotR-3.3/IsoplotR/data/examples.rda |binary IsoplotR-3.3/IsoplotR/inst/PbPb2.csv | 28 +-- IsoplotR-3.3/IsoplotR/inst/PbPb3.csv | 38 ++-- IsoplotR-3.3/IsoplotR/inst/ThPb1.csv |only IsoplotR-3.3/IsoplotR/inst/ThPb2.csv |only IsoplotR-3.3/IsoplotR/inst/ThPb3.csv |only IsoplotR-3.3/IsoplotR/inst/UPb7.csv | 32 ++- IsoplotR-3.3/IsoplotR/man/IsoplotR.Rd | 2 IsoplotR-3.3/IsoplotR/man/age.Rd | 41 ++-- IsoplotR-3.3/IsoplotR/man/cad.Rd | 23 +- IsoplotR-3.3/IsoplotR/man/concordia.Rd | 9 - IsoplotR-3.3/IsoplotR/man/data2york.Rd | 134 +++++++-------- IsoplotR-3.3/IsoplotR/man/examples.Rd | 7 IsoplotR-3.3/IsoplotR/man/isochron.Rd | 127 +++++++------- IsoplotR-3.3/IsoplotR/man/kde.Rd | 26 +- IsoplotR-3.3/IsoplotR/man/ludwig.Rd | 14 - IsoplotR-3.3/IsoplotR/man/peakfit.Rd | 29 +-- IsoplotR-3.3/IsoplotR/man/radialplot.Rd | 24 +- IsoplotR-3.3/IsoplotR/man/read.data.Rd | 44 ++-- IsoplotR-3.3/IsoplotR/man/settings.Rd | 6 IsoplotR-3.3/IsoplotR/man/weightedmean.Rd | 19 +- 48 files changed, 1142 insertions(+), 1109 deletions(-)
Title: Build Graphs for Landscape Genetics Analysis
Description: Build graphs for landscape genetics analysis. This set of
functions can be used to import and convert spatial and genetic data
initially in different formats, import landscape graphs created with
'GRAPHAB' software (Foltete et al., 2012) <doi:10.1016/j.envsoft.2012.07.002>,
make diagnosis plots of isolation by distance relationships in order to
choose how to build genetic graphs, create graphs with a large range of
pruning methods, weight their links with several genetic distances, plot
and analyse graphs, compare them with other graphs. It uses functions from
other packages such as 'adegenet'
(Jombart, 2008) <doi:10.1093/bioinformatics/btn129> and 'igraph' (Csardi
et Nepusz, 2006) <https://bit.ly/35a3V3H>. It also implements methods
commonly used in landscape genetics to create graphs, described by Dyer et
Nason (2004) <doi:10.1111/j.1365-294X.2004.02177.x> and Greenbaum et
Fefferman (2017) <doi:10.1111/mec.14059>, and to analyse distance data
(van Strien et al., 2015) <doi:10.1038/hdy.2014.62>.
Author: Paul Savary
Maintainer: Paul Savary <savarypaul660@gmail.com>
Diff between graph4lg versions 0.2.0 dated 2019-12-12 and 0.3.0 dated 2020-03-19
DESCRIPTION | 6 MD5 | 34 NEWS.md | 5 R/aux_25_09.R | 3 R/genind_to_genepop.R | 10 R/graph_plan.R | 21 R/mat_gen_dist.R | 16 R/mat_pw_d_jost.R | 2 R/mat_pw_fst.R | 2 R/mat_pw_gst.R | 2 R/plot_graph_lg.R | 2 build/partial.rdb |binary inst/doc/vignette_graph4lg.R | 64 - inst/doc/vignette_graph4lg.Rmd | 126 +- inst/doc/vignette_graph4lg.html | 2516 ++++++++++++++++++++++++++++++---------- man/graph_plan.Rd | 5 man/plot_graph_lg.Rd | 2 vignettes/vignette_graph4lg.Rmd | 126 +- 18 files changed, 2196 insertions(+), 746 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-07-21 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-02-19 0.5.0
2018-12-14 0.4.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-02-17 0.1.14
2020-02-17 0.1.15
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-01-25 1.0.1
Title: Pedigree and Genetic Groups
Description: Calculates additive and dominance genetic relationship matrices and their inverses, in matrix and tabular-sparse formats. It includes functions for checking and processing pedigree, as well as functions to calculate the matrix of genetic group contributions (Q), and adding those contributions to the genetic merit of animals (Quaas (1988) <doi:10.3168/jds.S0022-0302(88)79691-5>). Calculation of Q is computationally extensive. There are computationally optimized functions to calculate Q.
Author: Mohammad Ali Nilforooshan [aut, cre]
(<https://orcid.org/0000-0003-0339-5442>)
Maintainer: Mohammad Ali Nilforooshan <m.a.nilforooshan@gmail.com>
Diff between ggroups versions 2.0.2 dated 2020-02-28 and 2.0.3 dated 2020-03-19
DESCRIPTION | 7 +++---- MD5 | 6 +++--- NEWS.md | 4 ++++ R/tabAinv.R | 2 +- 4 files changed, 11 insertions(+), 8 deletions(-)
Title: Use 'Python' from Within 'R'
Description: Interact with 'Python' <https://www.python.org/> from within 'R'.
Author: Florian Schwendinger [aut, cre],
Kimyen Truong [ctb]
Maintainer: Florian Schwendinger <FlorianSchwendinger@gmx.at>
Diff between PythonInR versions 0.1-9 dated 2020-03-10 and 0.1-11 dated 2020-03-19
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- configure | 9 +++++++++ src/Makevars.in | 2 +- src/PythonInR.c | 6 +++++- src/PythonInRMacros.h | 6 +----- 6 files changed, 24 insertions(+), 15 deletions(-)
Title: Port of the 'Scilab' 'n1qn1' and 'qnbd' Modules for
(Un)constrained BFGS Optimization
Description: Provides 'Scilab' 'n1qn1', or Quasi-Newton BFGS
"qn" without constraints and 'qnbd' or Quasi-Newton BFGS with constraints.
This takes more memory than traditional L-BFGS. The n1qn1 routine is useful since it allows prespecification of a Hessian.
If the Hessian is near enough the truth in optimization it can speed up the optimization problem. Both algorithms are described in the
'Scilab' optimization documentation located at
<https://www.scilab.org/sites/default/files/optimization_in_scilab.pdf>.
Author: Matthew Fidler [aut, cre],
Wenping Wang [aut],
Claude Lemarechal [aut, ctb],
Joseph Bonnans [ctb],
Jean-Charles Gilbert [ctb],
Claudia Sagastizabal [ctb],
Stephen L. Campbell, [ctb],
Jean-Philippe Chancelier [ctb],
Ramine Nikoukhah [ctb],
Dirk Eddelbuettel [ctb],
Bruno Jofret [ctb],
INRIA [cph]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between n1qn1 versions 6.0.1-6 dated 2020-03-02 and 6.0.1-7 dated 2020-03-19
n1qn1-6.0.1-6/n1qn1/src/vfinite.c |only n1qn1-6.0.1-7/n1qn1/DESCRIPTION | 6 +++--- n1qn1-6.0.1-7/n1qn1/MD5 | 13 ++++++------- n1qn1-6.0.1-7/n1qn1/R/n1qn1.R | 2 +- n1qn1-6.0.1-7/n1qn1/man/n1qn1.Rd | 20 ++++---------------- n1qn1-6.0.1-7/n1qn1/man/qnbd.Rd | 19 +++++-------------- n1qn1-6.0.1-7/n1qn1/src/Makevars | 2 +- n1qn1-6.0.1-7/n1qn1/src/n1qn1_all.f | 27 +++++++++++++++++---------- 8 files changed, 37 insertions(+), 52 deletions(-)
Title: Decomposition of Bulk Expression with Single-Cell Sequencing
Description: Provides tools to accurately estimate cell type abundances
from heterogeneous bulk expression. A reference-based method utilizes
single-cell information to generate a signature matrix and transformation
of bulk expression for accurate regression based estimates. A marker-based
method utilizes known cell-specific marker genes to measure relative
abundances across samples.
For more details, see Jew and Alvarez et al (2019) <doi:10.1101/669911>.
Author: Brandon Jew [aut, cre],
Marcus Alvarez [aut]
Maintainer: Brandon Jew <brandon.jew@ucla.edu>
Diff between BisqueRNA versions 1.0.1 dated 2019-12-15 and 1.0.2 dated 2020-03-19
DESCRIPTION | 8 MD5 | 12 R/reference_based.R | 2 build/vignette.rds |binary inst/doc/bisque.R | 32 +- inst/doc/bisque.html | 633 ++++++++++++++++++++++++++++++---------------- tests/testthat/test_sim.R | 1 7 files changed, 453 insertions(+), 235 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-03-04 0.9
2014-09-11 0.6
2014-08-06 0.5