Title: Stemming Algorithms for the Portuguese Language
Description: Wraps a collection of stemming algorithms for the Portuguese
Language.
Author: Daniel Falbel [aut, cre]
Maintainer: Daniel Falbel <dfalbel@gmail.com>
Diff between ptstem versions 0.0.6 dated 2020-05-11 and 0.0.7 dated 2020-05-12
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- R/ptstem.R | 6 +++--- R/stem_modified_hunspell.R | 2 +- R/stem_porter.R | 2 +- R/stem_rslp.R | 2 +- inst/doc/ptstem.html | 4 ++-- man/ptstem.Rd | 6 +++--- man/stem_modified_hunspell.Rd | 2 +- man/stem_porter.Rd | 2 +- man/stem_rslp.Rd | 2 +- 11 files changed, 27 insertions(+), 27 deletions(-)
Title: Distributions for Ecological Models in 'nimble'
Description: Common ecological distributions for 'nimble' models in the form of nimbleFunction objects.
Includes Cormack-Jolly-Seber, occupancy, dynamic occupancy, hidden Markov, dynamic hidden Markov, and N-mixture models.
(Jolly (1965) <DOI: 10.2307/2333826>, Seber (1965) <DOI: 10.2307/2333827>, Turek et al. (2016) <doi:10.1007/s10651-016-0353-z>).
Author: Benjamin R. Goldstein [aut, cre],
Daniel Turek [aut],
Lauren Ponisio [aut],
Perry de Valpine [aut]
Maintainer: Benjamin R. Goldstein <ben.goldstein@berkeley.edu>
Diff between nimbleEcology versions 0.2.1 dated 2020-04-07 and 0.2.2 dated 2020-05-12
DESCRIPTION | 12 +++++----- MD5 | 16 +++++++------- R/dNmixture.R | 62 ++++++++++++++++++++++++++++++++++++++++--------------- README.md | 2 - man/dCJS.Rd | 4 +-- man/dDHMM.Rd | 6 ++--- man/dDynOcc.Rd | 20 +++++++++-------- man/dHMM.Rd | 6 +---- man/dNmixture.Rd | 2 - 9 files changed, 80 insertions(+), 50 deletions(-)
Title: Mixed-Frequency GARCH Models
Description: Estimating GARCH-MIDAS (MIxed-DAta-Sampling) models (Engle, Ghysels, Sohn, 2013, <doi:10.1162/REST_a_00300>) and related statistical inference, accompanying the paper "Two are better than one: Volatility forecasting using multiplicative component GARCH models" by Conrad and Kleen (2020, <doi:10.1002/jae.2742>). The GARCH-MIDAS model decomposes the conditional variance of (daily) stock returns into a short- and long-term component, where the latter may depend on an exogenous covariate sampled at a lower frequency.
Author: Onno Kleen [aut, cre] (<https://orcid.org/0000-0003-4731-4640>)
Maintainer: Onno Kleen <r@onnokleen.de>
Diff between mfGARCH versions 0.1.9 dated 2019-12-04 and 0.2.0 dated 2020-05-12
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- NEWS.md | 3 +++ R/fit_mfgarch.R | 6 +++--- man/df_financial.Rd | 6 ++++-- man/df_mfgarch.Rd | 6 ++++-- man/fit_mfgarch.Rd | 21 ++++++++++++++++----- man/simulate_mfgarch.Rd | 21 ++++++++++++++++++--- man/simulate_mfgarch_diffusion.Rd | 17 +++++++++++++++-- man/simulate_mfgarch_rv_dependent.Rd | 17 +++++++++++++++-- 10 files changed, 92 insertions(+), 33 deletions(-)
Title: Modular Approach to Dose Finding Clinical Trials
Description: Methods for working with dose-finding clinical trials. We start by
providing a common interface to various dose-finding methodologies like the
continual reassessment method (CRM) by O'Quigley et al. (1990)
<doi:10.2307/2531628>, the Bayesian optimal interval design (BOIN) by Liu &
Yuan (2015) <doi:10.1111/rssc.12089>, and the 3+3 described by Korn et al.
(1994) <doi:10.1002/sim.4780131802>. We then add optional embellishments to
provide extra desirable behaviour, like avoiding skipping doses, stopping
after n patients have been treated at the recommended dose, or demanding
that n patients are treated before stopping is allowed. By daisy-chaining
together these embellishments using the pipe operator from 'magrittr', it is
simple to tailor the behaviour of dose-finding designs so that they do what
you want. Furthermore, using this flexible interface for creating
dose-finding designs, it is simple to run simulations or calculate
dose-pathways for future cohorts of patients.
Author: Kristian Brock [aut, cre] (<https://orcid.org/0000-0002-3921-0166>)
Maintainer: Kristian Brock <kristian.brock@gmail.com>
Diff between escalation versions 0.1.2 dated 2020-04-14 and 0.1.3 dated 2020-05-12
DESCRIPTION | 12 MD5 | 38 NAMESPACE | 2 NEWS.md | 7 R/crystallised_dose_paths.R | 44 R/graph_paths.R | 3 R/selector.R | 15 R/simulations.R | 24 build/vignette.rds |binary inst/doc/DosePaths.Rmd | 9 inst/doc/DosePaths.html | 1754 ++++++++++++++++++++++++++++-------- inst/doc/DoseSelectorInterface.Rmd | 9 inst/doc/DoseSelectorInterface.html | 30 inst/doc/Simulation.Rmd | 9 inst/doc/Simulation.html | 124 +- man/graph_paths.Rd | 3 tests/testthat/test_dose_paths.R | 16 vignettes/DosePaths.Rmd | 9 vignettes/DoseSelectorInterface.Rmd | 9 vignettes/Simulation.Rmd | 9 20 files changed, 1583 insertions(+), 543 deletions(-)
Title: Read and Write Rectangular Text Data Quickly
Description: The goal of 'vroom' is to read and write data (like
'csv', 'tsv' and 'fwf') quickly. When reading it uses a quick initial
indexing step, then reads the values lazily , so only the data you
actually use needs to be read. The writer formats the data in
parallel and writes to disk asynchronously from formatting.
Author: Jim Hester [aut, cre] (<https://orcid.org/0000-0002-2739-7082>),
Hadley Wickham [aut] (<https://orcid.org/0000-0003-4757-117X>),
https://github.com/mandreyel/ [cph] (mio library),
R Core Team [ctb] (localtime.c code adapted from R),
Jukka Jylänki [cph] (grisu3 implementation),
Mikkel Jørgensen [cph] (grisu3 implementation),
RStudio [cph, fnd]
Maintainer: Jim Hester <james.f.hester@gmail.com>
Diff between vroom versions 1.2.0 dated 2020-01-13 and 1.2.1 dated 2020-05-12
DESCRIPTION | 15 MD5 | 73 ++-- NEWS.md | 16 R/RcppExports.R | 4 R/vroom.R | 6 R/vroom_fwf.R | 10 R/vroom_lines.R | 6 R/vroom_write.R | 8 README.md | 30 - build/vignette.rds |binary build/vroom.pdf |binary inst/doc/benchmarks.html | 37 +- inst/doc/vroom.html | 632 ++++++++++++++++++------------------ man/vroom-package.Rd | 1 man/vroom.Rd | 4 man/vroom_format.Rd | 16 man/vroom_lines.Rd | 7 man/vroom_write.Rd | 16 src/RcppExports.cpp | 9 src/delimited_index.cc | 4 src/delimited_index_connection.cc | 12 src/fixed_width_index.h | 4 src/fixed_width_index_connection.cc | 6 src/unicode_fopen.h |only src/utils.h | 2 src/vroom.cc | 4 src/vroom_big_int.cc | 3 src/vroom_chr.h | 2 src/vroom_fwf.cc | 4 src/vroom_vec.h | 11 src/vroom_write.cc | 14 tests/testthat.R | 6 tests/testthat/test-datetime.R | 2 tests/testthat/test-int.R | 2 tests/testthat/test-multi-file.R | 2 tests/testthat/test-vroom.R | 16 tests/testthat/test-vroom_fwf.R | 13 tests/testthat/test-vroom_write.R | 26 + 38 files changed, 570 insertions(+), 453 deletions(-)
Title: Genotype Calling with Uncertainty from Sequencing Data in
Polyploids and Diploids
Description: Read depth data from genotyping-by-sequencing (GBS) or restriction
site-associated DNA sequencing (RAD-seq) are imported and used to make Bayesian
probability estimates of genotypes in polyploids or diploids. The genotype
probabilities, posterior mean genotypes, or most probable genotypes can then
be exported for downstream analysis. 'polyRAD' is described by Clark et al.
(2019) <doi:10.1534/g3.118.200913>. A variant calling pipeline for highly
duplicated genomes is also included and is described by Clark et al. (2020)
<doi:10.1101/2020.01.11.902890>.
Author: Lindsay V. Clark [aut, cre] (<https://orcid.org/0000-0002-3881-9252>),
U.S. National Science Foundation [fnd]
Maintainer: Lindsay V. Clark <lvclark@illinois.edu>
Diff between polyRAD versions 1.1 dated 2019-06-04 and 1.2 dated 2020-05-12
polyRAD-1.1/polyRAD/R/sort_isoloci.R |only polyRAD-1.2/polyRAD/DESCRIPTION | 19 polyRAD-1.2/polyRAD/MD5 | 74 polyRAD-1.2/polyRAD/NAMESPACE | 29 polyRAD-1.2/polyRAD/NEWS | 51 polyRAD-1.2/polyRAD/R/RcppExports.R | 40 polyRAD-1.2/polyRAD/R/calculations.R | 226 ++ polyRAD-1.2/polyRAD/R/classes_methods.R | 374 ++-- polyRAD-1.2/polyRAD/R/data_export.R | 104 + polyRAD-1.2/polyRAD/R/data_import.R | 267 ++ polyRAD-1.2/polyRAD/R/hindhe.R |only polyRAD-1.2/polyRAD/build/vignette.rds |binary polyRAD-1.2/polyRAD/data/exampleRAD.RData |binary polyRAD-1.2/polyRAD/data/exampleRAD_mapping.RData |binary polyRAD-1.2/polyRAD/inst/CITATION | 8 polyRAD-1.2/polyRAD/inst/doc/isolocus_sorting.R |only polyRAD-1.2/polyRAD/inst/doc/isolocus_sorting.Rmd |only polyRAD-1.2/polyRAD/inst/doc/isolocus_sorting.html |only polyRAD-1.2/polyRAD/inst/doc/polyRADtutorial.R | 152 + polyRAD-1.2/polyRAD/inst/doc/polyRADtutorial.Rmd | 186 ++ polyRAD-1.2/polyRAD/inst/doc/polyRADtutorial.html | 896 ++++++---- polyRAD-1.2/polyRAD/inst/extdata/MsaHindHe.RData |only polyRAD-1.2/polyRAD/inst/extdata/MsaHindHe2.RData |only polyRAD-1.2/polyRAD/inst/python |only polyRAD-1.2/polyRAD/man/AddGenotypeLikelihood.Rd | 10 polyRAD-1.2/polyRAD/man/AddGenotypePriorProb_Mapping2Parents.Rd | 27 polyRAD-1.2/polyRAD/man/ExportGAPIT.Rd | 2 polyRAD-1.2/polyRAD/man/GetWeightedMeanGenotypes.Rd | 12 polyRAD-1.2/polyRAD/man/HindHe.Rd |only polyRAD-1.2/polyRAD/man/InbreedingFromHindHe.Rd |only polyRAD-1.2/polyRAD/man/MakeTasselVcfFilter.Rd | 6 polyRAD-1.2/polyRAD/man/MergeIdenticalHaplotypes.Rd |only polyRAD-1.2/polyRAD/man/RADdata.Rd | 25 polyRAD-1.2/polyRAD/man/RADdata2VCF.Rd |only polyRAD-1.2/polyRAD/man/VCF2RADdata.Rd | 12 polyRAD-1.2/polyRAD/man/readProcessIsoloci.Rd |only polyRAD-1.2/polyRAD/man/readProcessSamMulti.Rd |only polyRAD-1.2/polyRAD/src/BestGenos.cpp | 119 + polyRAD-1.2/polyRAD/src/GiniSimpson.cpp |only polyRAD-1.2/polyRAD/src/InitHapAssign.cpp |only polyRAD-1.2/polyRAD/src/PrepVCFexport.cpp |only polyRAD-1.2/polyRAD/src/RcppExports.cpp | 149 + polyRAD-1.2/polyRAD/vignettes/isolocus_sorting.Rmd |only polyRAD-1.2/polyRAD/vignettes/isolocus_sorting.md |only polyRAD-1.2/polyRAD/vignettes/polyRADtutorial.Rmd | 186 ++ polyRAD-1.2/polyRAD/vignettes/polyRADtutorial.md |only 46 files changed, 2414 insertions(+), 560 deletions(-)
Title: A Forward Agent-Based Transmission Chain Simulator
Description: The aim of 'nosoi' (pronounced no.si) is to provide a flexible agent-based stochastic transmission chain/epidemic simulator (Lequime et al. bioRxiv 2020.03.03.973107). It is named after the daimones of plague, sickness and disease that escaped Pandora's jar in the Greek mythology. 'nosoi' is able to take into account the influence of multiple variable on the transmission process (e.g. dual-host systems (such as arboviruses), within-host viral dynamics, transportation, population structure), alone or taken together, to create complex but relatively intuitive epidemiological simulations.
Author: Sebastian Lequime [aut, cre] (<https://orcid.org/0000-0002-3140-0651>),
Paul Bastide [aut] (<https://orcid.org/0000-0002-8084-9893>),
Simon Dellicour [aut] (<https://orcid.org/0000-0001-9558-1052>),
Philippe Lemey [aut] (<https://orcid.org/0000-0003-2826-5353>),
Guy Baele [aut] (<https://orcid.org/0000-0002-1915-7732>)
Maintainer: Sebastian Lequime <sebastian.lequime@gmail.com>
Diff between nosoi versions 1.0.2 dated 2020-04-03 and 1.0.3 dated 2020-05-12
DESCRIPTION | 14 - MD5 | 65 +++--- NAMESPACE | 12 - R/nosoiSim.R | 4 R/nosoi_sanityChecks-Messages.R | 3 R/nosoi_step1-makeMoves.R | 13 - R/output_nosoiSummary.R | 269 ++++++++++++++++++++++--- R/output_treeGenerator.r | 22 +- inst/doc/continuous.Rmd | 1 inst/doc/continuous.html | 4 inst/doc/discrete.R | 26 +- inst/doc/discrete.Rmd | 27 +- inst/doc/discrete.html | 4 inst/doc/none.Rmd | 1 inst/doc/none.html | 4 inst/doc/nosoi.R | 6 inst/doc/nosoi.Rmd | 6 inst/doc/nosoi.html | 4 inst/doc/output.Rmd | 1 inst/doc/output.html | 14 - man/numberInfected.Rd | 4 man/numberInfectedStates.Rd |only tests/testthat/testDualContinuous.R | 76 +++++-- tests/testthat/testDualDiscrete.R | 111 ++++++++-- tests/testthat/testDualNone.R | 62 ++++- tests/testthat/testSingleContinuous.R | 25 ++ tests/testthat/testSingleDiscrete.R | 146 +++++++++++++ tests/testthat/testSingleNone.R | 62 +++++ tests/testthat/testTransmissionTree.R | 361 +++++++++++++++++++++++++++------- vignettes/continuous.Rmd | 1 vignettes/discrete.Rmd | 27 +- vignettes/none.Rmd | 1 vignettes/nosoi.Rmd | 6 vignettes/output.Rmd | 1 34 files changed, 1108 insertions(+), 275 deletions(-)
Title: Visible Vowels: Visualization of Vowel Variation
Description: Visualizes vowel variation in f0, F1, F2, F3 and duration.
Author: Wilbert Heeringa, Hans Van de Velde
Maintainer: Wilbert Heeringa <wjheeringa@gmail.com>
Diff between visvow versions 0.8.0 dated 2019-09-23 and 0.9.0 dated 2020-05-12
visvow-0.8.0/visvow/inst/FA.jpg |only visvow-0.8.0/visvow/tests/testthat/data/ERB_Glasberg_Moore_1990.csv |only visvow-0.8.0/visvow/tests/testthat/data/ERB_Greenwood_1961.csv |only visvow-0.8.0/visvow/tests/testthat/data/ERB_Moore_Glasberg_1983.csv |only visvow-0.8.0/visvow/tests/testthat/data/bark_Schroeder_et_al._1979.csv |only visvow-0.8.0/visvow/tests/testthat/data/bark_Traunmueller_1990.csv |only visvow-0.8.0/visvow/tests/testthat/data/bark_Zwicker_Terhardt_1980.csv |only visvow-0.8.0/visvow/tests/testthat/data/mel_Fant_1968.csv |only visvow-0.8.0/visvow/tests/testthat/data/mel_OShaughnessy_1987.csv |only visvow-0.9.0/visvow/DESCRIPTION | 15 visvow-0.9.0/visvow/MD5 | 33 visvow-0.9.0/visvow/NAMESPACE | 8 visvow-0.9.0/visvow/R/visvow.R | 1570 ++++++---- visvow-0.9.0/visvow/build/partial.rdb |binary visvow-0.9.0/visvow/build/vignette.rds |binary visvow-0.9.0/visvow/inst/FA1.jpg |only visvow-0.9.0/visvow/inst/FA2.png |only visvow-0.9.0/visvow/inst/email.png |binary visvow-0.9.0/visvow/tests/testthat/data/ERB_I.csv |only visvow-0.9.0/visvow/tests/testthat/data/ERB_II.csv |only visvow-0.9.0/visvow/tests/testthat/data/ERB_III.csv |only visvow-0.9.0/visvow/tests/testthat/data/bark_I.csv |only visvow-0.9.0/visvow/tests/testthat/data/bark_II.csv |only visvow-0.9.0/visvow/tests/testthat/data/bark_III.csv |only visvow-0.9.0/visvow/tests/testthat/data/mel_I.csv |only visvow-0.9.0/visvow/tests/testthat/data/mel_II.csv |only visvow-0.9.0/visvow/tests/testthat/test.R | 27 27 files changed, 1109 insertions(+), 544 deletions(-)
Title: Mixtures of Exponential-Distance Models with Covariates
Description: Implements a model-based clustering method for categorical life-course sequences relying on mixtures of exponential-distance models introduced by Murphy et al. (2019) <arXiv:1908.07963>. A range of flexible precision parameter settings corresponding to weighted generalisations of the Hamming distance metric are considered, along with the potential inclusion of a noise component. Gating covariates can be supplied in order to relate sequences to baseline characteristics. Sampling weights are also accommodated. The models are fitted using the EM algorithm and tools for visualising the results are also provided.
Author: Keefe Murphy [aut, cre] (<https://orcid.org/0000-0002-7709-3159>),
Thomas Brendan Murphy [ctb] (<https://orcid.org/0000-0002-5668-7046>),
Raffaella Piccarreta [ctb],
Isobel Claire Gormley [ctb]
Maintainer: Keefe Murphy <keefe.murphy@ucd.ie>
Diff between MEDseq versions 1.1.0 dated 2020-03-31 and 1.1.1 dated 2020-05-12
DESCRIPTION | 12 ++-- MD5 | 32 +++++----- NAMESPACE | 1 R/Functions.R | 149 +++++++++++++++++++++++++++++++++++--------------- R/Hidden_Functions.R | 2 R/MEDseq.R | 10 +-- build/vignette.rds |binary inst/NEWS.md | 13 ++++ inst/doc/MEDseq.R | 6 +- inst/doc/MEDseq.Rmd | 10 ++- inst/doc/MEDseq.html | 37 ++++-------- man/MEDseq-package.Rd | 6 +- man/MEDseq_compare.Rd | 4 - man/MEDseq_fit.Rd | 9 ++- man/MEDseq_stderr.Rd | 2 man/plot.MEDseq.Rd | 4 + vignettes/MEDseq.Rmd | 10 ++- 17 files changed, 193 insertions(+), 114 deletions(-)
Title: R Templates for Reproducible Data Analyses
Description: A collection of R Markdown templates for nicely structured, reproducible
data analyses in R. The templates have embedded examples on how to write
citations, footnotes, equations and use colored message/info boxes, how to
cross-reference different parts/sections in the report, provide a nice
table of contents (toc) with a References section and proper R session
information as well as examples using DT tables and ggplot2 graphs.
The bookdown Lite template theme supports code folding.
Author: John Zobolas [aut, cph, cre] (<https://orcid.org/0000-0002-3609-8674>)
Maintainer: John Zobolas <bblodfon@gmail.com>
Diff between rtemps versions 0.5.0 dated 2020-05-02 and 0.6.0 dated 2020-05-12
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ R/create_temp.R | 9 ++++----- 4 files changed, 14 insertions(+), 11 deletions(-)
Title: R Wrapper for the Energy Information Administration (EIA) API
Description: An R wrapper to allow the user to query categories and Series IDs, and import data, from the EIA's API <https://www.eia.gov/opendata/>.
Author: Matthew Brigida and others (see GitHub)
Maintainer: Matthew Brigida <mdbrigida@gmail.com>
Diff between EIAdata versions 0.0.5 dated 2019-08-23 and 0.1.1 dated 2020-05-12
DESCRIPTION | 8 +- MD5 | 6 - R/source.R | 158 ++++++++++++++++++++++++++++++++++++++----------- man/EIAdata-package.Rd | 6 - 4 files changed, 135 insertions(+), 43 deletions(-)
Title: Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests
Description: Comprehensive open-source toolbox for analysing Spatial Point Patterns. Focused mainly on two-dimensional point patterns, including multitype/marked points, in any spatial region. Also supports three-dimensional point patterns, space-time point patterns in any number of dimensions, point patterns on a linear network, and patterns of other geometrical objects. Supports spatial covariate data such as pixel images.
Contains over 2000 functions for plotting spatial data, exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference.
Data types include point patterns, line segment patterns, spatial windows, pixel images, tessellations, and linear networks.
Exploratory methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Monte Carlo, Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Monte Carlo) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov, ANOVA) are also supported.
Parametric models can be fitted to point pattern data using the functions ppm(), kppm(), slrm(), dppm() similar to glm(). Types of models include Poisson, Gibbs and Cox point processes, Neyman-Scott cluster processes, and determinantal point processes. Models may involve dependence on covariates, inter-point interaction, cluster formation and dependence on marks. Models are fitted by maximum likelihood, logistic regression, minimum contrast, and composite likelihood methods.
A model can be fitted to a list of point patterns (replicated point pattern data) using the function mppm(). The model can include random effects and fixed effects depending on the experimental design, in addition to all the features listed above.
Fitted point process models can be simulated, automatically. Formal hypothesis tests of a fitted model are supported (likelihood ratio test, analysis of deviance, Monte Carlo tests) along with basic tools for model selection (stepwise(), AIC()) and variable selection (sdr). Tools for validating the fitted model include simulation envelopes, residuals, residual plots and Q-Q plots, leverage and influence diagnostics, partial residuals, and added variable plots.
Author: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>,
Rolf Turner <r.turner@auckland.ac.nz>
and Ege Rubak <rubak@math.aau.dk>,
with substantial contributions of code by
Kasper Klitgaard Berthelsen;
Ottmar Cronie;
Tilman Davies;
Yongtao Guan;
Ute Hahn;
Abdollah Jalilian;
Marie-Colette van Lieshout;
Greg McSwiggan;
Tuomas Rajala;
Suman Rakshit;
Dominic Schuhmacher;
Rasmus Waagepetersen;
and Hangsheng Wang.
Additional contributions
by M. Adepeju;
C. Anderson;
Q.W. Ang;
R. Arellano;
J. Astrom;
R. Aue;
M. Austenfeld;
S. Azaele;
M. Baddeley;
C. Beale;
M. Bell;
R. Bernhardt;
T. Bendtsen;
A. Bevan;
B. Biggerstaff;
A. Bilgrau;
L. Bischof;
C. Biscio;
R. Bivand;
J.M. Blanco Moreno;
F. Bonneu;
J. Brown;
J. Burgos;
S. Byers;
Y.M. Chang;
J.B. Chen;
I. Chernayavsky;
Y.C. Chin;
B. Christensen;
L. Cobo Sanchez;
J.-F. Coeurjolly;
K. Colyvas;
H. Commenges;
R. Constantine;
R. Corria Ainslie;
R. Cotton;
M. de la Cruz;
P. Dalgaard;
M. D'Antuono;
S. Das;
P.J. Diggle;
P. Donnelly;
I. Dryden;
S. Eglen;
A. El-Gabbas;
B. Fandohan;
O. Flores;
E.D. Ford;
P. Forbes;
S. Frank;
J. Franklin;
N. Funwi-Gabga;
O. Garcia;
A. Gault;
J. Geldmann;
M. Genton;
S. Ghalandarayeshi;
J. Gilbey;
J. Goldstick;
P. Grabarnik;
C. Graf;
U. Hahn;
A. Hardegen;
M.B. Hansen;
M. Hazelton;
J. Heikkinen;
M. Hering;
M. Herrmann;
M. Hesselbarth;
P. Hewson;
H. Heydarian;
K. Hingee;
K. Hornik;
P. Hunziker;
J. Hywood;
R. Ihaka;
C. Icos;
A. Jammalamadaka;
R. John-Chandran;
D. Johnson;
M. Khanmohammadi;
R. Klaver;
P. Kovesi;
L. Kozmian-Ledward;
M. Kuhn;
J. Laake;
R.A. Lamb;
F. Lavancier;
T. Lawrence;
T. Lazauskas;
J. Lee;
G.P. Leser;
A. Li;
H.T. Li;
G. Limitsios;
A. Lister;
N. Luambua;
B. Madin;
M. Maechler;
J. Marcus;
K. Marchikanti;
R. Mark;
J. Mateu;
P. McCullagh;
U. Mehlig;
F. Mestre;
S. Meyer;
X.C. Mi;
L. De Middeleer;
R.K. Milne;
E. Miranda;
J. Moller;
A. Mollie;
I. Moncada;
M. Moradi;
V. Morera Pujol;
E. Mudrak;
G.M. Nair;
N. Najari;
N. Nava;
L.S. Nielsen;
F. Nunes;
J.R. Nyengaard;
J. Oehlschlaegel;
T. Onkelinx;
S. O'Riordan;
E. Parilov;
J. Picka;
N. Picard;
T. Pollington;
M. Porter;
S. Protsiv;
A. Raftery;
S. Rakshit;
B. Ramage;
P. Ramon;
X. Raynaud;
N. Read;
M. Reiter;
I. Renner;
T.O. Richardson;
B.D. Ripley;
E. Rosenbaum;
B. Rowlingson;
J. Rudokas;
T. Rudolph;
J. Rudge;
C. Ryan;
F. Safavimanesh;
A. Sarkka;
C. Schank;
K. Schladitz;
S. Schutte;
B.T. Scott;
O. Semboli;
F. Semecurbe;
V. Shcherbakov;
G.C. Shen;
P. Shi;
H.-J. Ship;
T.L. Silva;
I.-M. Sintorn;
Y. Song;
M. Spiess;
M. Stevenson;
K. Stucki;
J. Sulavik;
M. Sumner;
P. Surovy;
B. Taylor;
T. Thorarinsdottir;
L. Torres;
B. Turlach;
T. Tvedebrink;
K. Ummer;
M. Uppala;
A. van Burgel;
T. Verbeke;
M. Vihtakari;
A. Villers;
F. Vinatier;
M. Vogtland;
S. Voss;
S. Wagner;
H. Wang;
H. Wendrock;
J. Wild;
C. Witthoft;
S. Wong;
M. Woringer;
L. Yates;
M.E. Zamboni
and
A. Zeileis.
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat versions 1.63-3 dated 2020-03-01 and 1.64-1 dated 2020-05-12
spatstat-1.63-3/spatstat/R/iplot.R |only spatstat-1.63-3/spatstat/R/iplotlayered.R |only spatstat-1.63-3/spatstat/R/istat.R |only spatstat-1.63-3/spatstat/man/iplot.Rd |only spatstat-1.63-3/spatstat/man/istat.Rd |only spatstat-1.63-3/spatstat/man/lengths.psp.Rd |only spatstat-1.64-1/spatstat/DESCRIPTION | 17 spatstat-1.64-1/spatstat/MD5 | 329 +-- spatstat-1.64-1/spatstat/NAMESPACE | 37 spatstat-1.64-1/spatstat/NEWS | 219 ++ spatstat-1.64-1/spatstat/R/Kmeasure.R | 4 spatstat-1.64-1/spatstat/R/Math.im.R | 34 spatstat-1.64-1/spatstat/R/Math.imlist.R | 48 spatstat-1.64-1/spatstat/R/Math.linim.R | 8 spatstat-1.64-1/spatstat/R/breakpts.R | 21 spatstat-1.64-1/spatstat/R/bw.lppl.R |only spatstat-1.64-1/spatstat/R/bw.optim.R | 34 spatstat-1.64-1/spatstat/R/bw.ppl.R | 67 spatstat-1.64-1/spatstat/R/convexify.R | 4 spatstat-1.64-1/spatstat/R/crossdistlpp.R | 205 +- spatstat-1.64-1/spatstat/R/density.loo.R |only spatstat-1.64-1/spatstat/R/density.lpp.R | 678 +++++-- spatstat-1.64-1/spatstat/R/density.ppp.R | 13 spatstat-1.64-1/spatstat/R/density.psp.R | 4 spatstat-1.64-1/spatstat/R/densityfun.R | 10 spatstat-1.64-1/spatstat/R/densityfunlpp.R |only spatstat-1.64-1/spatstat/R/densitylppVoronoi.R | 4 spatstat-1.64-1/spatstat/R/distan3D.R | 5 spatstat-1.64-1/spatstat/R/distanxD.R | 40 spatstat-1.64-1/spatstat/R/fii.R | 32 spatstat-1.64-1/spatstat/R/fv.R | 89 spatstat-1.64-1/spatstat/R/heatapprox.R |only spatstat-1.64-1/spatstat/R/hotrod.R |only spatstat-1.64-1/spatstat/R/hyperframe.R | 15 spatstat-1.64-1/spatstat/R/indices.R | 43 spatstat-1.64-1/spatstat/R/laslett.R | 10 spatstat-1.64-1/spatstat/R/leverage.R | 22 spatstat-1.64-1/spatstat/R/linalg.R | 174 + spatstat-1.64-1/spatstat/R/lindirichlet.R | 4 spatstat-1.64-1/spatstat/R/lineardisc.R | 8 spatstat-1.64-1/spatstat/R/linequad.R | 4 spatstat-1.64-1/spatstat/R/linim.R | 22 spatstat-1.64-1/spatstat/R/linnet.R | 49 spatstat-1.64-1/spatstat/R/linnetsurgery.R | 183 + spatstat-1.64-1/spatstat/R/lintess.R | 6 spatstat-1.64-1/spatstat/R/lixellate.R | 8 spatstat-1.64-1/spatstat/R/lpp.R | 29 spatstat-1.64-1/spatstat/R/marks.R | 28 spatstat-1.64-1/spatstat/R/morphology.R | 4 spatstat-1.64-1/spatstat/R/mpl.R | 9 spatstat-1.64-1/spatstat/R/mppm.R | 7 spatstat-1.64-1/spatstat/R/nncross3D.R | 7 spatstat-1.64-1/spatstat/R/nndistlpp.R | 17 spatstat-1.64-1/spatstat/R/nnfromvertex.R | 4 spatstat-1.64-1/spatstat/R/options.R | 2 spatstat-1.64-1/spatstat/R/pairdistlpp.R | 188 + spatstat-1.64-1/spatstat/R/pairs.im.R | 16 spatstat-1.64-1/spatstat/R/pointsonlines.R | 4 spatstat-1.64-1/spatstat/R/ppmclass.R | 5 spatstat-1.64-1/spatstat/R/ppp.R | 43 spatstat-1.64-1/spatstat/R/psp.R | 73 spatstat-1.64-1/spatstat/R/pspcross.R | 7 spatstat-1.64-1/spatstat/R/quickndirty.R | 18 spatstat-1.64-1/spatstat/R/randomlpp.R | 4 spatstat-1.64-1/spatstat/R/randomonlines.R | 6 spatstat-1.64-1/spatstat/R/rcelllpp.R | 4 spatstat-1.64-1/spatstat/R/relrisk.R | 65 spatstat-1.64-1/spatstat/R/relrisk.lpp.R |only spatstat-1.64-1/spatstat/R/rhohat.R | 4 spatstat-1.64-1/spatstat/R/rshift.R | 107 - spatstat-1.64-1/spatstat/R/solist.R | 12 spatstat-1.64-1/spatstat/R/sparse3Darray.R | 18 spatstat-1.64-1/spatstat/R/sparsecommon.R | 12 spatstat-1.64-1/spatstat/R/sparselinalg.R | 142 + spatstat-1.64-1/spatstat/R/split.ppp.R | 18 spatstat-1.64-1/spatstat/R/subfits.R | 18 spatstat-1.64-1/spatstat/R/summary.mppm.R | 15 spatstat-1.64-1/spatstat/R/sysdata.rda |binary spatstat-1.64-1/spatstat/R/transect.R | 7 spatstat-1.64-1/spatstat/R/util.R | 12 spatstat-1.64-1/spatstat/R/vcov.mppm.R | 74 spatstat-1.64-1/spatstat/R/wingeom.R | 6 spatstat-1.64-1/spatstat/build/vignette.rds |binary spatstat-1.64-1/spatstat/demo/spatstat.R | 10 spatstat-1.64-1/spatstat/inst/doc/Nickname.txt | 3 spatstat-1.64-1/spatstat/inst/doc/bugfixes.Rnw | 27 spatstat-1.64-1/spatstat/inst/doc/bugfixes.pdf |binary spatstat-1.64-1/spatstat/inst/doc/datasets.pdf |binary spatstat-1.64-1/spatstat/inst/doc/getstart.pdf |binary spatstat-1.64-1/spatstat/inst/doc/packagesizes.txt | 2 spatstat-1.64-1/spatstat/inst/doc/replicated.pdf |binary spatstat-1.64-1/spatstat/inst/doc/shapefiles.pdf |binary spatstat-1.64-1/spatstat/inst/doc/spatstatguisize.txt |only spatstat-1.64-1/spatstat/inst/doc/spatstatlocalsize.txt | 1 spatstat-1.64-1/spatstat/inst/doc/updates.R | 8 spatstat-1.64-1/spatstat/inst/doc/updates.Rnw | 186 + spatstat-1.64-1/spatstat/inst/doc/updates.pdf |binary spatstat-1.64-1/spatstat/man/F3est.Rd | 9 spatstat-1.64-1/spatstat/man/G3est.Rd | 11 spatstat-1.64-1/spatstat/man/K3est.Rd | 14 spatstat-1.64-1/spatstat/man/Kest.Rd | 13 spatstat-1.64-1/spatstat/man/Math.im.Rd | 3 spatstat-1.64-1/spatstat/man/Math.imlist.Rd | 27 spatstat-1.64-1/spatstat/man/addVertices.Rd |only spatstat-1.64-1/spatstat/man/angles.psp.Rd | 2 spatstat-1.64-1/spatstat/man/as.linfun.Rd | 2 spatstat-1.64-1/spatstat/man/as.linnet.psp.Rd | 27 spatstat-1.64-1/spatstat/man/as.lpp.Rd | 11 spatstat-1.64-1/spatstat/man/bw.lppl.Rd | 9 spatstat-1.64-1/spatstat/man/bw.relrisklpp.Rd |only spatstat-1.64-1/spatstat/man/bw.scott.Rd | 4 spatstat-1.64-1/spatstat/man/cbind.hyperframe.Rd | 2 spatstat-1.64-1/spatstat/man/collapse.fv.Rd | 5 spatstat-1.64-1/spatstat/man/crossdist.lpp.Rd | 45 spatstat-1.64-1/spatstat/man/density.lpp.Rd | 55 spatstat-1.64-1/spatstat/man/density.splitppp.Rd | 29 spatstat-1.64-1/spatstat/man/densityEqualSplit.Rd |only spatstat-1.64-1/spatstat/man/densityHeat.Rd |only spatstat-1.64-1/spatstat/man/densityQuick.lpp.Rd | 10 spatstat-1.64-1/spatstat/man/densityfun.lpp.Rd |only spatstat-1.64-1/spatstat/man/domain.Rd | 2 spatstat-1.64-1/spatstat/man/endpoints.psp.Rd | 2 spatstat-1.64-1/spatstat/man/extrapolate.psp.Rd | 2 spatstat-1.64-1/spatstat/man/heatkernelapprox.Rd |only spatstat-1.64-1/spatstat/man/hotrod.Rd |only spatstat-1.64-1/spatstat/man/insertVertices.Rd | 3 spatstat-1.64-1/spatstat/man/joinVertices.Rd | 5 spatstat-1.64-1/spatstat/man/lengths_psp.Rd |only spatstat-1.64-1/spatstat/man/lintess.Rd | 2 spatstat-1.64-1/spatstat/man/methods.linnet.Rd | 11 spatstat-1.64-1/spatstat/man/midpoints.psp.Rd | 2 spatstat-1.64-1/spatstat/man/nndist.lpp.Rd | 25 spatstat-1.64-1/spatstat/man/nndist.pp3.Rd | 18 spatstat-1.64-1/spatstat/man/nndist.ppx.Rd | 21 spatstat-1.64-1/spatstat/man/pairdist.lpp.Rd | 26 spatstat-1.64-1/spatstat/man/pcf3est.Rd | 19 spatstat-1.64-1/spatstat/man/pixellate.psp.Rd | 2 spatstat-1.64-1/spatstat/man/plot.ppp.Rd | 5 spatstat-1.64-1/spatstat/man/psp.Rd | 2 spatstat-1.64-1/spatstat/man/psp.object.Rd | 2 spatstat-1.64-1/spatstat/man/relrisk.lpp.Rd |only spatstat-1.64-1/spatstat/man/relrisk.ppp.Rd | 29 spatstat-1.64-1/spatstat/man/repairNetwork.Rd | 2 spatstat-1.64-1/spatstat/man/rshift.ppp.Rd | 25 spatstat-1.64-1/spatstat/man/rshift.splitppp.Rd | 18 spatstat-1.64-1/spatstat/man/spatstat-internal.Rd | 116 - spatstat-1.64-1/spatstat/man/spatstat-package.Rd | 25 spatstat-1.64-1/spatstat/man/spatstat.options.Rd | 19 spatstat-1.64-1/spatstat/man/sumouter.Rd | 13 spatstat-1.64-1/spatstat/man/transect.im.Rd | 5 spatstat-1.64-1/spatstat/src/heatapprox.c |only spatstat-1.64-1/spatstat/src/hotrod.c |only spatstat-1.64-1/spatstat/src/init.c | 10 spatstat-1.64-1/spatstat/src/linScrossdist.c |only spatstat-1.64-1/spatstat/src/linSpairdist.c |only spatstat-1.64-1/spatstat/src/linSpairdist.h |only spatstat-1.64-1/spatstat/src/linalg.c | 31 spatstat-1.64-1/spatstat/src/proto.h | 16 spatstat-1.64-1/spatstat/src/sparselinalg.c | 12 spatstat-1.64-1/spatstat/src/spasumsymout.h | 4 spatstat-1.64-1/spatstat/src/sumsymouter.h | 28 spatstat-1.64-1/spatstat/tests/testsAtoC.R | 516 +++-- spatstat-1.64-1/spatstat/tests/testsD.R | 636 ++++-- spatstat-1.64-1/spatstat/tests/testsEtoF.R | 235 +- spatstat-1.64-1/spatstat/tests/testsGtoJ.R | 129 - spatstat-1.64-1/spatstat/tests/testsK.R | 688 +++---- spatstat-1.64-1/spatstat/tests/testsL.R | 1540 ++++++++-------- spatstat-1.64-1/spatstat/tests/testsM.R | 536 +++-- spatstat-1.64-1/spatstat/tests/testsNtoO.R | 681 +++---- spatstat-1.64-1/spatstat/tests/testsP1.R | 44 spatstat-1.64-1/spatstat/tests/testsP2.R | 1062 +++++------ spatstat-1.64-1/spatstat/tests/testsQ.R | 19 spatstat-1.64-1/spatstat/tests/testsR1.R | 369 ++- spatstat-1.64-1/spatstat/tests/testsR2.R | 1380 +++++++------- spatstat-1.64-1/spatstat/tests/testsS.R | 931 +++------ spatstat-1.64-1/spatstat/tests/testsT.R | 125 - spatstat-1.64-1/spatstat/tests/testsUtoZ.R | 823 ++++---- spatstat-1.64-1/spatstat/vignettes/bugfixes.Rnw | 27 spatstat-1.64-1/spatstat/vignettes/updates.Rnw | 186 + 179 files changed, 8454 insertions(+), 5925 deletions(-)
Title: Model Based Treatment of Missing Data
Description: Contains model-based treatment of missing data for regression
models with missing values in covariates or the dependent
variable using maximum likelihood or Bayesian estimation
(Ibrahim et al., 2005; <doi:10.1198/016214504000001844>;
Luedtke, Robitzsch, & West, 2019a, 2019b, <doi:10.1037/met0000233>;
<doi:10.1080/00273171.2019.1640104>).
The regression model can be nonlinear (e.g., interaction
effects, quadratic effects or B-spline functions).
Multilevel models with missing data in predictors are
available for Bayesian estimation. Substantive-model compatible
multiple imputation can be also conducted.
Author: Alexander Robitzsch [aut, cre], Oliver Luedtke [aut]
Maintainer: Alexander Robitzsch <robitzsch@leibniz-ipn.de>
Diff between mdmb versions 1.3-18 dated 2019-04-16 and 1.4-12 dated 2020-05-12
DESCRIPTION | 14 +++++++----- MD5 | 45 ++++++++++++++++++++-------------------- R/RcppExports.R | 2 - R/frm_check_predictor_matrix.R |only R/frm_define_model_R_function.R | 13 +++++++++-- R/frm_em.R | 2 - R/frm_fb.R | 2 - R/frm_fb_sample_parameters.R | 2 - R/frm_linreg_density.R | 2 - R/frm_prepare_models.R | 10 ++++++-- README.md | 6 ++++- build/partial.rdb |binary data/data.mb01.rda |binary data/data.mb02.rda |binary data/data.mb03.rda |binary data/data.mb04.rda |binary data/data.mb05.rda |binary inst/NEWS | 12 +++++++++- man/data.mb.Rd | 3 +- man/frm.Rd | 30 +++++++++++++++++++++----- man/mdmb-package.Rd | 12 +++++++++- man/mdmb_regression.Rd | 8 ++++--- man/yjt_dist.Rd | 8 ++++--- src/RcppExports.cpp | 2 - 24 files changed, 118 insertions(+), 55 deletions(-)
Title: Tidy IP Addresses
Description: Classes and functions for working with IP (Internet
Protocol) addresses and networks, inspired by the Python 'ipaddress'
module. Offers full support for both IPv4 and IPv6 (Internet Protocol
versions 4 and 6) address spaces. It is specifically designed to work
well with the 'tidyverse'.
Author: David Hall [aut, cre] (<https://orcid.org/0000-0002-2193-0480>)
Maintainer: David Hall <david.hall.physics@gmail.com>
Diff between ipaddress versions 0.2.0 dated 2020-03-25 and 0.3.0 dated 2020-05-12
ipaddress-0.2.0/ipaddress/R/binary.R |only ipaddress-0.2.0/ipaddress/R/vctrs-cast.R |only ipaddress-0.2.0/ipaddress/R/vctrs-coerce.R |only ipaddress-0.2.0/ipaddress/man/binary.Rd |only ipaddress-0.2.0/ipaddress/man/hostname.Rd |only ipaddress-0.2.0/ipaddress/man/packed.Rd |only ipaddress-0.2.0/ipaddress/tests/testthat/test-binary.R |only ipaddress-0.3.0/ipaddress/DESCRIPTION | 15 + ipaddress-0.3.0/ipaddress/MD5 | 70 ++++----- ipaddress-0.3.0/ipaddress/NAMESPACE | 63 +------- ipaddress-0.3.0/ipaddress/NEWS.md | 24 +++ ipaddress-0.3.0/ipaddress/R/RcppExports.R | 16 +- ipaddress-0.3.0/ipaddress/R/hostname.R | 62 +++----- ipaddress-0.3.0/ipaddress/R/ip_address.R | 73 +++++---- ipaddress-0.3.0/ipaddress/R/ip_interface.R | 55 +++---- ipaddress-0.3.0/ipaddress/R/ip_network.R | 69 +++++---- ipaddress-0.3.0/ipaddress/R/other_repr.R |only ipaddress-0.3.0/ipaddress/R/pillar.R |only ipaddress-0.3.0/ipaddress/R/zzz.R |only ipaddress-0.3.0/ipaddress/README.md | 19 ++ ipaddress-0.3.0/ipaddress/inst/doc/ipaddress.Rmd | 6 ipaddress-0.3.0/ipaddress/inst/doc/ipaddress.html | 2 ipaddress-0.3.0/ipaddress/man/figures |only ipaddress-0.3.0/ipaddress/man/ip_address.Rd | 33 ++-- ipaddress-0.3.0/ipaddress/man/ip_interface.Rd | 33 ++-- ipaddress-0.3.0/ipaddress/man/ip_network.Rd | 34 ++-- ipaddress-0.3.0/ipaddress/man/ip_to_binary.Rd |only ipaddress-0.3.0/ipaddress/man/ip_to_bytes.Rd |only ipaddress-0.3.0/ipaddress/man/ip_to_hostname.Rd |only ipaddress-0.3.0/ipaddress/man/ip_to_integer.Rd |only ipaddress-0.3.0/ipaddress/man/ipaddress-package.Rd | 2 ipaddress-0.3.0/ipaddress/man/ipaddress-vctrs.Rd | 21 -- ipaddress-0.3.0/ipaddress/src/IpAddressVector.cpp | 76 +++++++++- ipaddress-0.3.0/ipaddress/src/IpAddressVector.h | 10 + ipaddress-0.3.0/ipaddress/src/RcppExports.cpp | 45 ++++- ipaddress-0.3.0/ipaddress/src/encoding.h | 39 +++++ ipaddress-0.3.0/ipaddress/src/wrapper.cpp | 18 +- ipaddress-0.3.0/ipaddress/tests/testthat/test-hostname.R | 66 ++++---- ipaddress-0.3.0/ipaddress/tests/testthat/test-ip_address_v4.R | 18 -- ipaddress-0.3.0/ipaddress/tests/testthat/test-ip_interface.R | 25 --- ipaddress-0.3.0/ipaddress/tests/testthat/test-ip_network_v4.R | 15 - ipaddress-0.3.0/ipaddress/tests/testthat/test-other_repr.R |only ipaddress-0.3.0/ipaddress/tests/testthat/test-pillar.R |only ipaddress-0.3.0/ipaddress/tests/testthat/test-pillar.txt |only ipaddress-0.3.0/ipaddress/vignettes/ipaddress.Rmd | 6 45 files changed, 538 insertions(+), 377 deletions(-)
Title: Interactive R Unit Tests
Description: Simplifies regression tests by comparing objects produced by test
code with earlier versions of those same objects. If objects are unchanged
the tests pass, otherwise execution stops with error details. If in
interactive mode, tests can be reviewed through the provided interactive
environment.
Author: Brodie Gaslam [aut, cre]
Maintainer: Brodie Gaslam <brodie.gaslam@yahoo.com>
Diff between unitizer versions 1.4.9 dated 2020-03-02 and 1.4.10 dated 2020-05-12
DESCRIPTION | 6 +- MD5 | 28 +++++----- NEWS.md | 4 + build/vignette.rds |binary inst/doc/u0_unitizer_index.html | 9 ++- inst/doc/u1_intro.R | 4 - inst/doc/u1_intro.html | 11 ++-- inst/doc/u2_tests.html | 9 ++- inst/doc/u3_interactive-env.html | 9 ++- inst/doc/u4_reproducible-tests.html | 9 ++- inst/doc/u5_miscellaneous.html | 9 ++- tests/testthat/helper/runtt.R | 2 tests/testthat/testthat.parse.R | 82 +++++++++++++++++++++++++------- tests/unitizer/tests2.R | 3 - tests/unitizer/tests2.unitizer/data.rds |binary 15 files changed, 129 insertions(+), 56 deletions(-)
Title: Parametric Survival Simulation with Parameter Uncertainty
Description: Perform survival simulation with parametric survival model generated from 'survreg' function in 'survival' package.
In each simulation coefficients are resampled from variance-covariance matrix of parameter estimates to
capture uncertainty in model parameters.
Prediction intervals of Kaplan-Meier estimates and hazard ratio of treatment effect can be further calculated using simulated survival data.
Author: Kenta Yoshida [aut, cre] (<https://orcid.org/0000-0003-4967-3831>),
Laurent Claret [aut]
Maintainer: Kenta Yoshida <6.kurabupasu@gmail.com>
Diff between survParamSim versions 0.1.0 dated 2020-01-13 and 0.1.1 dated 2020-05-12
DESCRIPTION | 6 MD5 | 71 NAMESPACE | 40 NEWS.md |only R/calc_hr_pi.R | 562 ++--- R/calc_km_pi.R | 632 +++--- R/extract_pi.R | 278 +- R/extract_raw_sim.R | 88 R/surv_param_sim.R | 394 ++-- R/surv_param_sim_resample.R | 184 - R/survparamsim-methods.R | 50 R/utils.R | 28 R/yyy.R | 46 README.md | 297 +-- build/vignette.rds |binary inst/doc/survParamSim.R | 154 - inst/doc/survParamSim.Rmd | 284 +- inst/doc/survParamSim.html | 972 +++++----- man/figures/README-hr_pi-1.png |binary man/figures/README-km_pi_group-1.png |binary man/pipe.Rd | 2 man/plot_hr_pi.Rd | 2 man/survparamsim.Rd | 212 +- tests/figs/deps.txt | 6 tests/figs/test-calc-km-pi/km-plot-with-sex-and-ph-ecog-as-group.svg | 28 tests/figs/test-calc-km-pi/km-plot-with-sex-as-trt.svg | 8 tests/figs/test-calc-km-pi/long-sim-time-not-truncating-with-censor.svg | 8 tests/figs/test-calc-km-pi/long-sim-time-truncating-with-censor.svg | 8 tests/figs/test-calc-km-pi/no-observed-km-curves.svg | 8 tests/testthat.R | 8 tests/testthat/test-calc_hr_pi.R | 234 +- tests/testthat/test-calc_km_pi.R | 189 - tests/testthat/test-extract_raw_sim.R | 50 tests/testthat/test-surv_param_sim.R | 48 tests/testthat/test-surv_param_sim_resample.R | 50 tests/testthat/test-survparamsim-methods.R | 10 vignettes/survParamSim.Rmd | 284 +- 37 files changed, 2684 insertions(+), 2557 deletions(-)
Title: Optimal Channel Networks
Description: Generate and analyze Optimal Channel Networks (OCNs):
oriented spanning trees reproducing all scaling features characteristic
of real, natural river networks. As such, they can be used in a variety
of numerical experiments in the fields of hydrology, ecology and
epidemiology. See Carraro et al. (2020) <doi:10.1101/2020.02.17.948851>
for a presentation of the package; Rinaldo et al. (2014)
<doi:10.1073/pnas.1322700111> for a theoretical overview on the OCN
concept; Furrer and Sain (2010) <doi:10.18637/jss.v036.i10> for the
construct used.
Author: Luca Carraro [aut, cre],
Florian Altermatt [ctb],
Emanuel A. Fronhofer [ctb],
Reinhard Furrer [ctb],
Isabelle Gounand [ctb],
Andrea Rinaldo [ctb],
Enrico Bertuzzo [aut]
Maintainer: Luca Carraro <luca.carraro@hotmail.it>
Diff between OCNet versions 0.2.0 dated 2020-02-19 and 0.3.0 dated 2020-05-12
DESCRIPTION | 6 MD5 | 26 +- NEWS.md | 13 + R/aggregate_OCN.R | 40 +++- R/draw_elev2D_OCN.R | 9 R/draw_thematic_OCN.R | 38 ++-- R/find_area_threshold_OCN.R | 41 +++- R/landscape_OCN.R | 6 inst/doc/OCNet.html | 415 ++++++++++++++++++++++---------------------- man/draw_contour_OCN.Rd | 4 man/draw_elev2D_OCN.Rd | 6 man/draw_elev3D_OCN.Rd | 2 man/draw_elev3Drgl_OCN.Rd | 4 man/draw_thematic_OCN.Rd | 12 - 14 files changed, 350 insertions(+), 272 deletions(-)
Title: Gaussian Parsimonious Clustering Models with Covariates and a
Noise Component
Description: Clustering via parsimonious Gaussian Mixtures of Experts using the MoEClust models introduced by Murphy and Murphy (2019) <doi:10.1007/s11634-019-00373-8>. This package fits finite Gaussian mixture models with a formula interface for supplying gating and/or expert network covariates using a range of parsimonious covariance parameterisations from the GPCM family via the EM/CEM algorithm. Visualisation of the results of such models using generalised pairs plots and the inclusion of an additional noise component is also facilitated. A greedy forward stepwise search algorithm is provided for identifying the optimal model in terms of the number of components, the GPCM covariance parameterisation, and the subsets of gating/expert network covariates.
Author: Keefe Murphy [aut, cre] (<https://orcid.org/0000-0002-7709-3159>),
Thomas Brendan Murphy [ctb] (<https://orcid.org/0000-0002-5668-7046>)
Maintainer: Keefe Murphy <keefe.murphy@ucd.ie>
Diff between MoEClust versions 1.3.0 dated 2020-03-30 and 1.3.1 dated 2020-05-12
DESCRIPTION | 10 +- MD5 | 36 +++++----- R/Functions.R | 164 +++++++++++++++++++++++++++++++++--------------- R/MoEClust.R | 7 +- R/Plotting_Functions.R | 49 ++++++++------ build/vignette.rds |binary inst/NEWS.md | 11 +++ inst/doc/MoEClust.R | 9 -- inst/doc/MoEClust.Rmd | 15 ++-- inst/doc/MoEClust.html | 53 +++++++-------- man/MoEClust-package.Rd | 7 +- man/MoE_clust.Rd | 11 ++- man/MoE_compare.Rd | 2 man/MoE_crit.Rd | 2 man/MoE_gpairs.Rd | 3 man/MoE_plotGate.Rd | 13 ++- man/as.Mclust.Rd | 4 - man/plot.MoEClust.Rd | 2 vignettes/MoEClust.Rmd | 15 ++-- 19 files changed, 253 insertions(+), 160 deletions(-)
Title: Infinite Mixtures of Infinite Factor Analysers and Related
Models
Description: Provides flexible Bayesian estimation of Infinite Mixtures of Infinite Factor Analysers and related models, for nonparametrically clustering high-dimensional data, introduced by Murphy et al. (2019) <doi:10.1214/19-BA1179>. The IMIFA model conducts Bayesian nonparametric model-based clustering with factor analytic covariance structures without recourse to model selection criteria to choose the number of clusters or cluster-specific latent factors, mostly via efficient Gibbs updates. Model-specific diagnostic tools are also provided, as well as many options for plotting results, conducting posterior inference on parameters of interest, posterior predictive checking, and quantifying uncertainty.
Author: Keefe Murphy [aut, cre] (<https://orcid.org/0000-0002-7709-3159>),
Cinzia Viroli [ctb],
Isobel Claire Gormley [ctb]
Maintainer: Keefe Murphy <keefe.murphy@ucd.ie>
Diff between IMIFA versions 2.1.2 dated 2020-03-30 and 2.1.3 dated 2020-05-12
IMIFA-2.1.2/IMIFA/data/datalist |only IMIFA-2.1.3/IMIFA/DESCRIPTION | 10 - IMIFA-2.1.3/IMIFA/MD5 | 37 +-- IMIFA-2.1.3/IMIFA/NAMESPACE | 1 IMIFA-2.1.3/IMIFA/R/Diagnostics.R | 2 IMIFA-2.1.3/IMIFA/R/FullConditionals.R | 96 ++++++---- IMIFA-2.1.3/IMIFA/R/Gibbs_IMFA.R | 25 +- IMIFA-2.1.3/IMIFA/R/Gibbs_IMIFA.R | 28 +- IMIFA-2.1.3/IMIFA/R/IMIFA.R | 4 IMIFA-2.1.3/IMIFA/R/PlottingFunctions.R | 79 ++++---- IMIFA-2.1.3/IMIFA/build/vignette.rds |binary IMIFA-2.1.3/IMIFA/inst/NEWS.md | 13 + IMIFA-2.1.3/IMIFA/inst/doc/IMIFA.R | 6 IMIFA-2.1.3/IMIFA/inst/doc/IMIFA.Rmd | 12 - IMIFA-2.1.3/IMIFA/inst/doc/IMIFA.html | 52 ++--- IMIFA-2.1.3/IMIFA/man/IMIFA-package.Rd | 4 IMIFA-2.1.3/IMIFA/man/bnpControl.Rd | 10 - IMIFA-2.1.3/IMIFA/man/get_IMIFA_results.Rd | 3 IMIFA-2.1.3/IMIFA/vignettes/IMIFA.Rmd | 12 - IMIFA-2.1.3/IMIFA/vignettes/res_olive_IMIFA__Edited-Vignette-only-Version.rda |binary 20 files changed, 225 insertions(+), 169 deletions(-)
Title: Econometric Analysis of Explosive Time Series
Description: Testing for and dating periods of explosive
dynamics (exuberance) in time series using the univariate and panel
recursive unit root tests proposed by Phillips et al. (2015)
<doi:10.1111/iere.12132> and Pavlidis et al. (2016)
<doi:10.1007/s11146-015-9531-2>. The recursive least-squares
algorithm utilizes the matrix inversion lemma to avoid matrix
inversion which results in significant speed improvements. Simulation
of a variety of periodically-collapsing bubble processes.
Author: Kostas Vasilopoulos [cre, aut],
Efthymios Pavlidis [aut],
Simon Spavound [aut],
Enrique Martínez-García [aut]
Maintainer: Kostas Vasilopoulos <k.vasilopoulo@gmail.com>
Diff between exuber versions 0.4.0 dated 2020-05-04 and 0.4.1 dated 2020-05-12
exuber-0.4.0/exuber/inst/doc/Tidy.R |only exuber-0.4.0/exuber/inst/doc/Tidy.Rmd |only exuber-0.4.0/exuber/inst/doc/Tidy.html |only exuber-0.4.0/exuber/vignettes/Tidy.Rmd |only exuber-0.4.1/exuber/DESCRIPTION | 20 ++++++++++---------- exuber-0.4.1/exuber/MD5 | 27 ++++++++++++--------------- exuber-0.4.1/exuber/NAMESPACE | 2 ++ exuber-0.4.1/exuber/NEWS.md | 4 ++++ exuber-0.4.1/exuber/R/datestamp.R | 4 +++- exuber-0.4.1/exuber/R/distr-pvalues.R | 2 +- exuber-0.4.1/exuber/R/radf_mc.R | 2 +- exuber-0.4.1/exuber/R/tidiers-radf_cv.R | 6 ++++++ exuber-0.4.1/exuber/R/utils.R | 6 +++--- exuber-0.4.1/exuber/R/zzz.R | 4 ++++ exuber-0.4.1/exuber/build/vignette.rds |binary exuber-0.4.1/exuber/inst/WORDLIST | 1 + exuber-0.4.1/exuber/vignettes/tidy |only 17 files changed, 47 insertions(+), 31 deletions(-)
Title: S<e9>ries Temporelles Avec R
Description: Functions, data sets and exercises solutions for the book 'S<e9>ries Temporelles Avec R' (Yves Aragon, edp sciences, 2016). For all chapters, a vignette is available with some additional material and exercises solutions.
Author: Yves Aragon
Maintainer: Thibault Laurent <Thibault.Laurent@univ-tlse1.fr>
Diff between caschrono versions 2.1 dated 2019-01-28 and 2.2 dated 2020-05-12
DESCRIPTION | 10 +++---- MD5 | 60 ++++++++++++++++++++++----------------------- build/vignette.rds |binary inst/doc/Anx1.R | 1 inst/doc/Anx1.pdf |binary inst/doc/Anx10.R | 1 inst/doc/Anx10.pdf |binary inst/doc/Anx12.R | 1 inst/doc/Anx12.pdf |binary inst/doc/Anx2.R | 1 inst/doc/Anx2.pdf |binary inst/doc/Anx3.R | 3 -- inst/doc/Anx3.Rnw | 2 - inst/doc/Anx3.pdf |binary inst/doc/Anx4.R | 29 --------------------- inst/doc/Anx4.Rnw | 29 ++------------------- inst/doc/Anx4.pdf |binary inst/doc/Anx5.R | 1 inst/doc/Anx5.pdf |binary inst/doc/Anx6.R | 1 inst/doc/Anx6.pdf |binary inst/doc/Anx7.R | 1 inst/doc/Anx7.Rnw | 5 --- inst/doc/Anx7.pdf |binary inst/doc/Anx9.R | 1 inst/doc/Anx9.pdf |binary man/caschrono-package.Rd | 62 +++++++++++++++++++++++------------------------ man/t_stat.rd | 56 +++++++++++++++++++++--------------------- vignettes/Anx3.Rnw | 2 - vignettes/Anx4.Rnw | 29 ++------------------- vignettes/Anx7.Rnw | 5 --- 31 files changed, 103 insertions(+), 197 deletions(-)
Title: D-Score for Child Development
Description: The D-score is a quantitative measure of child development.
The D-score follows the Rasch model. See Jacobusse, van Buuren and
Verkerk (2006) <doi:10.1002/sim.2351>. The user can convert
milestone scores from 19 assessment instruments into the D-score
and the DAZ (D-score adjusted for age). Several tools assist in
mapping milestone names into the 9-position Global Scale of Early
Development (GSED) convention. Supports calculation of the D-score
using 'dutch' <doi:10.1177/0962280212473300>,
'gcdg' <doi:10.1136/bmjgh-2019-001724> and 'gsed' conversion keys.
The user can calculate DAZ using 'dutch' and 'gcdg' age-conditional
references.
Author: Stef van Buuren [cre, aut],
Iris Eekhout [aut],
Arjan Huizing [aut]
Maintainer: Stef van Buuren <stef.vanbuuren@tno.nl>
Diff between dscore versions 1.2.0 dated 2020-04-02 and 1.3.0 dated 2020-05-12
DESCRIPTION | 9 +- MD5 | 30 +++---- NAMESPACE | 2 NEWS.md | 9 ++ R/builtin_itembank.R | 10 +- R/builtin_itemtable.R | 10 -- R/get_itemtable.R | 43 +++++++--- R/import.R | 14 +-- README.md | 2 build/vignette.rds |binary data/builtin_itembank.rda |binary data/builtin_itemtable.rda |binary inst/doc/start.html | 184 ++++++++++++++++++++++++++++++++------------- man/builtin_itembank.Rd | 10 +- man/builtin_itemtable.Rd | 10 -- man/get_itemtable.Rd | 7 + 16 files changed, 224 insertions(+), 116 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-05-11 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-02-09 0.99.2
Title: Analysis of Evolutionary Rates in an OU Framework
Description: Estimates rates for continuous character evolution under Brownian motion and a new set of Ornstein-Uhlenbeck based Hansen models that allow both the strength of the pull and stochastic motion to vary across selective regimes. Beaulieu et al (2012) <doi:10.1111/j.1558-5646.2012.01619.x>.
Author: Jeremy M. Beaulieu <jbeaulieu@nimbios.org>, Brian O'Meara <bomeara@utk.edu>
Maintainer: Jeremy Beaulieu <jbeaulieu@nimbios.org>
Diff between OUwie versions 1.57 dated 2019-12-06 and 2.1 dated 2020-05-12
OUwie-1.57/OUwie/R/OUwie.joint.R |only OUwie-1.57/OUwie/R/OUwie.slice.R |only OUwie-1.57/OUwie/R/hOUwie.R |only OUwie-1.57/OUwie/R/pathLike.R |only OUwie-1.57/OUwie/man/OUwie.joint.Rd |only OUwie-1.57/OUwie/man/OUwie.slice.Rd |only OUwie-2.1/OUwie/DESCRIPTION | 17 OUwie-2.1/OUwie/MD5 | 57 + OUwie-2.1/OUwie/NAMESPACE | 24 OUwie-2.1/OUwie/R/OUwie.R | 567 ++++++++++-------- OUwie-2.1/OUwie/R/OUwie.anc.R | 8 OUwie-2.1/OUwie/R/OUwie.boot.R | 8 OUwie-2.1/OUwie/R/OUwie.contour.r |only OUwie-2.1/OUwie/R/OUwie.dredge.R |only OUwie-2.1/OUwie/R/OUwie.fixed.R | 691 +++++++++++------------ OUwie-2.1/OUwie/R/OUwie.sim.R | 167 ++--- OUwie-2.1/OUwie/R/check.identify.R |only OUwie-2.1/OUwie/R/expect.trendy.R | 78 +- OUwie-2.1/OUwie/R/varcov.ou.R | 235 ++++--- OUwie-2.1/OUwie/R/weight.mat.R | 272 +++------ OUwie-2.1/OUwie/build |only OUwie-2.1/OUwie/inst |only OUwie-2.1/OUwie/man/OUwie.Rd | 24 OUwie-2.1/OUwie/man/OUwie.anc.Rd | 12 OUwie-2.1/OUwie/man/OUwie.boot.Rd | 5 OUwie-2.1/OUwie/man/OUwie.contour.Rd |only OUwie-2.1/OUwie/man/OUwie.dredge.Rd |only OUwie-2.1/OUwie/man/OUwie.fixed.Rd | 18 OUwie-2.1/OUwie/man/OUwie.sim.Rd | 4 OUwie-2.1/OUwie/man/check.identify.Rd |only OUwie-2.1/OUwie/man/plot.OUwie.contour.Rd |only OUwie-2.1/OUwie/tests/testthat/test-likelihood.R |only OUwie-2.1/OUwie/vignettes |only 33 files changed, 1121 insertions(+), 1066 deletions(-)
Title: Straightforward 'NetCDF' Metadata
Description: Extract metadata from 'NetCDF' data sources, these can be files, file handles or
servers. This package leverages and extends the lower level functions of the 'RNetCDF' package
providing a consistent set of functions that all return data frames. We introduce named concepts
of 'grid', 'axis' and 'source' which are all meaningful entities without formal definition in the
'NetCDF' library <https://www.unidata.ucar.edu/software/netcdf/>. 'RNetCDF' matches the library
itself with only the named concepts of 'variables', 'dimensions' and 'attributes'. 'ncmeta'
provides a required framework for the in-development 'tidync' project <https://github.com/hypertidy/tidync>.
Author: Michael Sumner [aut, cre],
Tomas Remenyi [ctb],
Ben Raymond [ctb],
David Blodgett [ctb]
Maintainer: Michael Sumner <mdsumner@gmail.com>
Diff between ncmeta versions 0.2.0 dated 2019-10-22 and 0.2.5 dated 2020-05-12
ncmeta-0.2.0/ncmeta/inst/eke-speed |only ncmeta-0.2.0/ncmeta/inst/flowchart |only ncmeta-0.2.0/ncmeta/inst/test-RNetCDF |only ncmeta-0.2.5/ncmeta/DESCRIPTION | 8 - ncmeta-0.2.5/ncmeta/MD5 | 21 -- ncmeta-0.2.5/ncmeta/NEWS.md | 4 ncmeta-0.2.5/ncmeta/R/nc_sources.R | 2 ncmeta-0.2.5/ncmeta/README.md | 185 ++++++++++++------------ ncmeta-0.2.5/ncmeta/man/ncmeta.Rd | 1 ncmeta-0.2.5/ncmeta/tests/testthat.R | 11 - ncmeta-0.2.5/ncmeta/tests/testthat/test-coord.R | 6 11 files changed, 119 insertions(+), 119 deletions(-)
Title: Most Likely Transformations
Description: Likelihood-based estimation of conditional transformation
models via the most likely transformation approach described in
Hothorn et al. (2018) <DOI:10.1111/sjos.12291>.
Author: Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>)
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mlt versions 1.1-2 dated 2020-02-14 and 1.2-0 dated 2020-05-12
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- NAMESPACE | 2 +- R/ctm.R | 2 +- R/distr.R | 9 ++++++++- R/dpq_etc.R | 32 ++++++++++++++++++++++++++++++-- R/plot.R | 3 ++- R/predict.R | 6 +++++- build/partial.rdb |binary inst/NEWS.Rd | 8 ++++++++ man/ctm.Rd | 5 +++-- man/predict.Rd | 6 ++++-- 12 files changed, 77 insertions(+), 26 deletions(-)
Title: Kinetic Evaluation of Chemical Degradation Data
Description: Calculation routines based on the FOCUS Kinetics Report (2006,
2014). Includes a function for conveniently defining differential equation
models, model solution based on eigenvalues if possible or using numerical
solvers. If a C compiler (on windows: 'Rtools') is installed, differential
equation models are solved using automatically generated C functions. Please
note that no warranty is implied for correctness of results or fitness for a
particular purpose.
Author: Johannes Ranke [aut, cre, cph]
(<https://orcid.org/0000-0003-4371-6538>),
Katrin Lindenberger [ctb],
René Lehmann [ctb],
Eurofins Regulatory AG [cph]
Maintainer: Johannes Ranke <jranke@uni-bremen.de>
Diff between mkin versions 0.9.50.1 dated 2020-05-11 and 0.9.50.2 dated 2020-05-12
DESCRIPTION | 9 +- MD5 | 101 +++++++++++++++-------------- NEWS.md | 14 ++-- R/add_err.R | 2 R/endpoints.R | 2 R/mkinfit.R | 12 ++- R/mkinmod.R | 7 +- R/mkinpredict.R | 2 R/parent_solutions.R | 2 R/transform_odeparms.R | 2 README.md | 4 - inst/WORDLIST |only inst/doc/FOCUS_D.html | 10 +- inst/doc/FOCUS_L.html | 52 +++++++-------- inst/doc/mkin.Rmd | 4 - inst/doc/mkin.html | 8 +- inst/doc/twa.html | 4 - man/AIC.mmkin.Rd | 2 man/DFOP.solution.Rd | 16 ++-- man/FOMC.solution.Rd | 26 +++---- man/HS.solution.Rd | 16 ++-- man/IORE.solution.Rd | 8 +- man/SFO.solution.Rd | 16 ++-- man/SFORB.solution.Rd | 18 ++--- man/add_err.Rd | 4 - man/confint.mkinfit.Rd | 14 ++-- man/endpoints.Rd | 8 +- man/get_deg_func.Rd | 2 man/ilr.Rd | 8 +- man/logLik.mkinfit.Rd | 6 - man/logistic.solution.Rd | 20 ++--- man/max_twa_parent.Rd | 12 +-- man/mccall81_245T.Rd | 2 man/mkinerrplot.Rd | 4 - man/mkinfit.Rd | 132 ++++++++++++++++++++------------------- man/mkinmod.Rd | 59 +++++++++-------- man/mkinparplot.Rd | 2 man/mkinpredict.Rd | 2 man/mkinresplot.Rd | 6 - man/mmkin.Rd | 6 - man/nafta.Rd | 24 +++---- man/nlme.Rd | 6 - man/nlme.mmkin.Rd | 2 man/plot.mkinfit.Rd | 2 man/plot.mmkin.Rd | 2 man/plot.nlme.mmkin.Rd | 2 man/sigma_twocomp.Rd | 8 +- man/summary.mkinfit.Rd | 50 +++++++------- man/transform_odeparms.Rd | 4 - tests/testthat/FOCUS_2006_D.csf | 2 tests/testthat/test_analytical.R | 3 vignettes/mkin.Rmd | 4 - 52 files changed, 381 insertions(+), 352 deletions(-)
Title: Areal Weighted Interpolation
Description: A pipeable, transparent implementation of areal weighted interpolation
with support for interpolating multiple variables in a single function call.
These tools provide a full-featured workflow for validation and estimation
that fits into both modern data management (e.g. tidyverse) and spatial
data (e.g. sf) frameworks.
Author: Christopher Prener [aut, cre] (<https://orcid.org/0000-0002-4310-9888>),
Charlie Revord [aut],
Branson Fox [aut] (<https://orcid.org/0000-0002-4361-2811>)
Maintainer: Christopher Prener <chris.prener@slu.edu>
Diff between areal versions 0.1.5 dated 2019-05-21 and 0.1.6 dated 2020-05-12
DESCRIPTION | 17 MD5 | 56 + NAMESPACE | 4 NEWS.md | 8 R/ar_tessellate.R |only R/aw_aggregate.R | 2 R/aw_calculate.R | 4 R/aw_interpolate.R | 21 R/aw_intersect.R | 7 R/aw_preview_weights.R | 4 R/aw_total.R | 4 R/aw_weight.R | 4 README.md | 50 - build/vignette.rds |binary inst/doc/areal-weighted-interpolation.R | 58 - inst/doc/areal-weighted-interpolation.html | 859 ++++++++++++++--------------- inst/doc/areal.R | 6 inst/doc/areal.Rmd | 2 inst/doc/areal.html | 110 ++- inst/doc/data-preparation.R | 34 - inst/doc/data-preparation.html | 356 ++++++------ inst/extdata/sandbox.R |only man/ar_stl_asthma.Rd | 6 man/ar_stl_race.Rd | 6 man/ar_stl_wards.Rd | 6 man/ar_stl_wardsClipped.Rd | 6 man/ar_tessellate.Rd |only tests/testthat/test_ar_tessellate.R |only tests/testthat/test_aw_interpolate.R | 8 tests/testthat/test_aw_intersect.R | 2 vignettes/areal.Rmd | 2 31 files changed, 873 insertions(+), 769 deletions(-)
Title: Adherence to Medications
Description: Computation of adherence to medications from Electronic Health care
Data and visualization of individual medication histories and adherence
patterns. The package implements a set of S3 classes and
functions consistent with current adherence guidelines and definitions.
It allows the computation of different measures of
adherence (as defined in the literature, but also several original ones),
their publication-quality plotting,
the estimation of event duration and time to initiation,
the interactive exploration of patient medication history and
the real-time estimation of adherence given various parameter settings.
It scales from very small datasets stored in flat CSV files to very large
databases and from single-thread processing on mid-range consumer
laptops to parallel processing on large heterogeneous computing clusters.
It exposes a standardized interface allowing it to be used from other
programming languages and platforms, such as Python.
Author: Dan Dediu [aut, cre],
Alexandra Dima [aut],
Samuel Allemann [aut]
Maintainer: Dan Dediu <ddediu@gmail.com>
Diff between AdhereR versions 0.6.0 dated 2020-05-07 and 0.6.1 dated 2020-05-12
DESCRIPTION | 12 - MD5 | 10 - NEWS.md | 5 R/plotting.R | 272 ++++++++++++++++++++++++----- inst/doc/AdhereR-overview.html | 4 inst/doc/calling-AdhereR-from-python3.html | 4 6 files changed, 253 insertions(+), 54 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-06-30 2.0
2013-10-15 1.8
2013-08-27 1.6
2013-04-25 1.5
2013-04-04 1.4
2012-07-16 1.2
2012-07-10 1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-06-05 1.0
Title: Data Manipulation Verbs for the Spatial Classes
Description: Methods for 'dplyr' verbs for 'sp' 'Spatial' classes. The basic
verbs that modify data attributes, remove or re-arrange rows are supported
and provide complete 'Spatial' analogues of the input data. The group by
and summarize work flow returns a non-topological spatial union. There is
limited support for joins, with left and inner to copy attributes from
another table.
Author: Michael D. Sumner [aut, cre],
Joscha Legewie [ctb],
Jussi Jousimo [ctb]
Maintainer: Michael D. Sumner <mdsumner@gmail.com>
Diff between spdplyr versions 0.3.0 dated 2019-05-13 and 0.4.0 dated 2020-05-12
spdplyr-0.3.0/spdplyr/tests/testthat/test-dplyr-0.6.0.R |only spdplyr-0.4.0/spdplyr/DESCRIPTION | 10 spdplyr-0.4.0/spdplyr/MD5 | 33 spdplyr-0.4.0/spdplyr/NAMESPACE | 21 spdplyr-0.4.0/spdplyr/NEWS.md | 7 spdplyr-0.4.0/spdplyr/R/sdplyr-Spatial.r | 671 +++++-------- spdplyr-0.4.0/spdplyr/R/sdplyr-package.r | 21 spdplyr-0.4.0/spdplyr/README.md | 76 - spdplyr-0.4.0/spdplyr/build/vignette.rds |binary spdplyr-0.4.0/spdplyr/inst/WORDLIST | 2 spdplyr-0.4.0/spdplyr/inst/doc/spdplyr.R | 68 - spdplyr-0.4.0/spdplyr/inst/doc/spdplyr.html | 775 ++++++++-------- spdplyr-0.4.0/spdplyr/man/dplyr-Spatial.Rd | 80 - spdplyr-0.4.0/spdplyr/man/sp-methods.Rd | 1 spdplyr-0.4.0/spdplyr/man/spdplyr-package.Rd | 4 spdplyr-0.4.0/spdplyr/tests/testthat/test-adv-dplyr.R | 150 +-- spdplyr-0.4.0/spdplyr/tests/testthat/test-basic-dplyr.R | 344 +++---- spdplyr-0.4.0/spdplyr/tests/testthat/test-various.R | 40 18 files changed, 1106 insertions(+), 1197 deletions(-)
Title: 3D Brain Visualization
Description: In neuroscience, 'AFNI/SUMA' is a great tool to visualize 3D brain.
However, it takes efforts to interact and share the viewer to others. In
addition, 'AFNI/SUMA' doesn't support Windows platform. In the 'EEG/iEEG'
field, it's hard to have multiple cortical electrodes mapped to a template
brain for group analysis. Therefore this package is written aimed at
providing a fast, stable, interactive and easy to share tool based on 'Three.js',
a 'WebGL' engine to render 3D objects in the web browser such that we can
display brain surfaces on webpage interactively. This package translates R
objects to JavaScript objects via 'JSON' format, and provides 'R-Shiny' interface
to manipulate geometries interactively. The visualizations can also serve as
standalone widgets that can be easily shared across different platforms.
Along with 'rave', another package developed by Beauchamp's lab at Baylor
College Medicine, this package provides solutions to easily map surface
electrodes from multiple subjects to one template 141 brain.
Author: Zhengjia Wang [aut, cre, cph],
John Magnotti [aut],
Brian Metzger [aut],
Elizabeth Nesbitt [res],
Michael Beauchamp [aut, dtc, fnd]
Maintainer: Zhengjia Wang <zhengjia.wang@rice.edu>
Diff between threeBrain versions 0.1.5 dated 2020-01-20 and 0.1.7 dated 2020-05-12
threeBrain-0.1.5/threeBrain/R/py_installer.R |only threeBrain-0.1.5/threeBrain/man/ravepy.Rd |only threeBrain-0.1.7/threeBrain/DESCRIPTION | 13 threeBrain-0.1.7/threeBrain/MD5 | 46 threeBrain-0.1.7/threeBrain/NAMESPACE | 1 threeBrain-0.1.7/threeBrain/NEWS.md | 29 threeBrain-0.1.7/threeBrain/R/aaa.R | 105 threeBrain-0.1.7/threeBrain/R/class_animations.R | 13 threeBrain-0.1.7/threeBrain/R/class_brain.R | 10 threeBrain-0.1.7/threeBrain/R/class_multibrain.R | 36 threeBrain-0.1.7/threeBrain/R/fs_brain.R | 2 threeBrain-0.1.7/threeBrain/R/fs_brain2.R | 64 threeBrain-0.1.7/threeBrain/R/s3_geom.R | 7 threeBrain-0.1.7/threeBrain/R/threejs_brain.R | 20 threeBrain-0.1.7/threeBrain/R/viewer_ctint1.R |only threeBrain-0.1.7/threeBrain/R/zzz.R | 27 threeBrain-0.1.7/threeBrain/inst/WORDLIST | 46 threeBrain-0.1.7/threeBrain/inst/htmlwidgets/lib/dipterixThreeBrain-1.0.1/main.js | 3297 +++------- threeBrain-0.1.7/threeBrain/man/create_group.Rd | 5 threeBrain-0.1.7/threeBrain/man/freesurfer_brain.Rd | 5 threeBrain-0.1.7/threeBrain/man/geom_freemesh.Rd | 2 threeBrain-0.1.7/threeBrain/man/merge_brain.Rd | 5 threeBrain-0.1.7/threeBrain/man/read_gii2.Rd | 4 threeBrain-0.1.7/threeBrain/man/read_mgz.Rd | 4 threeBrain-0.1.7/threeBrain/man/threejs_brain.Rd | 7 threeBrain-0.1.7/threeBrain/man/view_ct_t1.Rd |only 26 files changed, 1356 insertions(+), 2392 deletions(-)
Title: Stable Isotope Bayesian Ellipses in R
Description: Fits bi-variate ellipses to stable isotope data using Bayesian
inference with the aim being to describe and compare their isotopic
niche.
Author: Andrew Jackson and Andrew Parnell
Maintainer: Andrew Jackson <jacksoan@tcd.ie>
Diff between SIBER versions 2.1.4 dated 2019-02-24 and 2.1.5 dated 2020-05-12
SIBER-2.1.4/SIBER/R/ellipsoidTranform.R |only SIBER-2.1.4/SIBER/R/siberDensityPlot.R |only SIBER-2.1.5/SIBER/DESCRIPTION | 17 SIBER-2.1.5/SIBER/MD5 | 80 SIBER-2.1.5/SIBER/NEWS.md | 9 SIBER-2.1.5/SIBER/R/createSiberObject.R | 69 SIBER-2.1.5/SIBER/R/ellipsoidTransform.R |only SIBER-2.1.5/SIBER/R/generateSiberCommunity.R | 2 SIBER-2.1.5/SIBER/R/generateSiberData.R | 2 SIBER-2.1.5/SIBER/R/generateSiberGroup.R | 2 SIBER-2.1.5/SIBER/R/plotSiberObject.R | 71 SIBER-2.1.5/SIBER/R/siberDensityplot.R |only SIBER-2.1.5/SIBER/build/vignette.rds |binary SIBER-2.1.5/SIBER/inst/doc/Centroid-Vectors.R | 12 SIBER-2.1.5/SIBER/inst/doc/Centroid-Vectors.html | 760 +++++--- SIBER-2.1.5/SIBER/inst/doc/Customising-Plots-Manually.R | 6 SIBER-2.1.5/SIBER/inst/doc/Customising-Plots-Manually.html | 438 +++-- SIBER-2.1.5/SIBER/inst/doc/Ellipse-Overlap.R | 8 SIBER-2.1.5/SIBER/inst/doc/Ellipse-Overlap.html | 688 +++++-- SIBER-2.1.5/SIBER/inst/doc/Introduction-to-SIBER.R | 16 SIBER-2.1.5/SIBER/inst/doc/Introduction-to-SIBER.html | 874 ++++++---- SIBER-2.1.5/SIBER/inst/doc/Plot-posterior-ellipses.R | 10 SIBER-2.1.5/SIBER/inst/doc/Plot-posterior-ellipses.html | 546 ++++-- SIBER-2.1.5/SIBER/inst/doc/Points-Inside-Outside-Ellipse.R | 8 SIBER-2.1.5/SIBER/inst/doc/Points-Inside-Outside-Ellipse.html | 508 ++++- SIBER-2.1.5/SIBER/inst/doc/Test-convergence.R | 6 SIBER-2.1.5/SIBER/inst/doc/Test-convergence.html | 414 +++- SIBER-2.1.5/SIBER/man/SIBER.Rd | 1 SIBER-2.1.5/SIBER/man/addEllipse.Rd | 13 SIBER-2.1.5/SIBER/man/bayesianOverlap.Rd | 11 SIBER-2.1.5/SIBER/man/createSiberObject.Rd | 21 SIBER-2.1.5/SIBER/man/demo.siber.data.2.Rd | 6 SIBER-2.1.5/SIBER/man/demo.siber.data.Rd | 6 SIBER-2.1.5/SIBER/man/ellipsoidTransform.Rd | 2 SIBER-2.1.5/SIBER/man/generateSiberCommunity.Rd | 11 SIBER-2.1.5/SIBER/man/generateSiberData.Rd | 11 SIBER-2.1.5/SIBER/man/generateSiberGroup.Rd | 5 SIBER-2.1.5/SIBER/man/maxLikOverlap.Rd | 10 SIBER-2.1.5/SIBER/man/plotCommunityHulls.Rd | 8 SIBER-2.1.5/SIBER/man/plotSiberObject.Rd | 25 SIBER-2.1.5/SIBER/man/siberDensityPlot.Rd | 44 SIBER-2.1.5/SIBER/man/siberKapow.Rd | 8 SIBER-2.1.5/SIBER/man/specificCentroidVectors.Rd | 3 43 files changed, 3177 insertions(+), 1554 deletions(-)
Title: Mark-Recapture Distance Sampling
Description: Animal abundance estimation via conventional, multiple covariate
and mark-recapture distance sampling (CDS/MCDS/MRDS). Detection function
fitting is performed via maximum likelihood. Also included are diagnostics
and plotting for fitted detection functions. Abundance estimation is via a
Horvitz-Thompson-like estimator.
Author: Jeff Laake <jeff.laake@noaa.gov>, David Borchers
<dlb@st-and.ac.uk>, Len Thomas <len.thomas@st-and.ac.uk>, David
Miller <dave@ninepointeightone.net> and Jon Bishop
Maintainer: Laura Marshall <lhm@st-andrews.ac.uk>
Diff between mrds versions 2.2.1 dated 2020-01-22 and 2.2.2 dated 2020-05-12
DESCRIPTION | 8 ++-- MD5 | 91 +++++++++++++++++++++++++--------------------- NAMESPACE | 6 +++ NEWS | 8 ++++ R/AIC.R |only R/add_df_covar_line.R |only R/check.bounds.R | 2 - R/ddf.rem.R | 2 - R/ddf.trial.R | 2 - R/dht.R | 8 ++-- R/histline.R | 2 - R/logLik.R |only R/p_dist_table.R |only R/plot.det.tables.R | 75 +++++++++++++++++++++++-------------- R/plot.ds.R | 67 ++++++++++++++------------------- R/plot.io.R | 18 ++++----- R/plot.io.fi.R | 13 +++--- R/plot.layout.R | 4 +- R/plot.rem.R | 66 +++++++++++++++++---------------- R/plot.rem.fi.R | 59 +++++++++++++++-------------- R/plot.trial.R | 25 ++++++------ R/plot.trial.fi.R | 22 +++++------ R/predict.ds.R | 2 - man/AIC.ds.Rd |only man/add_df_covar_line.Rd |only man/book.tee.data.Rd | 6 ++- man/check.bounds.Rd | 2 - man/ddf.rem.Rd | 2 - man/ddf.trial.Rd | 2 - man/dht.Rd | 2 - man/lfbcvi.Rd | 6 ++- man/lfgcwa.Rd | 6 ++- man/logLik.ds.Rd |only man/p_dist_table.Rd |only man/plot.det.tables.Rd | 28 +++++++++----- man/plot.ds.Rd | 34 ++++++++--------- man/plot.io.Rd | 16 ++++---- man/plot.io.fi.Rd | 14 +++---- man/plot.layout.Rd | 4 +- man/plot.rem.Rd | 20 +++++----- man/plot.rem.fi.Rd | 20 +++++----- man/plot.trial.Rd | 22 +++++------ man/plot.trial.fi.Rd | 20 +++++----- man/print.p_dist_table.Rd |only man/pronghorn.Rd | 6 ++- man/ptdata.distance.Rd | 6 ++- man/ptdata.dual.Rd | 6 ++- man/ptdata.removal.Rd | 6 ++- man/ptdata.single.Rd | 6 ++- man/stake77.Rd | 6 ++- man/stake78.Rd | 6 ++- 51 files changed, 396 insertions(+), 330 deletions(-)
More information about RobustBayesianCopas at CRAN
Permanent link
More information about extendedFamily at CRAN
Permanent link
Title: A Dipping Sauce for Data Analysis and Visualizations
Description: Works as an "add-on" to packages like 'shiny', 'future', as well as
'rlang', and provides utility functions. Just like dipping sauce adding
flavors to potato chips or pita bread, 'dipsaus' for data analysis and
visualizations adds handy functions and enhancements to popular packages.
The goal is to provide simple solutions that are frequently asked for
online, such as how to synchronize 'shiny' inputs without freezing the app,
or how to get memory size on 'Linux' or 'MacOS' system. The enhancements
roughly fall into these four categories: 1. 'shiny' input widgets; 2.
high-performance computing using 'RcppParallel' and 'future' package; 3.
modify R calls and convert among numbers, strings, and other objects. 4.
utility functions to get system information such like CPU chip-set, memory
limit, etc.
Author: Zhengjia Wang [aut, cre]
Maintainer: Zhengjia Wang <zhengjia.wang@rice.edu>
Diff between dipsaus versions 0.0.6 dated 2020-04-05 and 0.0.7 dated 2020-05-12
dipsaus-0.0.6/dipsaus/R/queue-s3.R |only dipsaus-0.0.7/dipsaus/DESCRIPTION | 18 - dipsaus-0.0.7/dipsaus/MD5 | 45 ++-- dipsaus-0.0.7/dipsaus/NAMESPACE | 5 dipsaus-0.0.7/dipsaus/NEWS.md | 20 + dipsaus-0.0.7/dipsaus/R/aaa.R | 1 dipsaus-0.0.7/dipsaus/R/fastmap2.R | 35 ++- dipsaus-0.0.7/dipsaus/R/language.R | 131 +++++++++++ dipsaus-0.0.7/dipsaus/R/queue-txtq.R | 197 +++++++++--------- dipsaus-0.0.7/dipsaus/R/shiny-compoundInput2.R | 17 + dipsaus-0.0.7/dipsaus/R/strings.R | 1 dipsaus-0.0.7/dipsaus/R/utils-package.R | 4 dipsaus-0.0.7/dipsaus/build/vignette.rds |binary dipsaus-0.0.7/dipsaus/inst/WORDLIST | 2 dipsaus-0.0.7/dipsaus/inst/doc/r_expr_addons.Rmd | 2 dipsaus-0.0.7/dipsaus/inst/doc/r_expr_addons.html | 14 - dipsaus-0.0.7/dipsaus/inst/doc/utility_functions.Rmd | 2 dipsaus-0.0.7/dipsaus/inst/doc/utility_functions.html | 4 dipsaus-0.0.7/dipsaus/man/compoundInput2.Rd | 3 dipsaus-0.0.7/dipsaus/man/list_to_fastmap2.Rd |only dipsaus-0.0.7/dipsaus/man/mask_function2.Rd |only dipsaus-0.0.7/dipsaus/man/new_function2.Rd |only dipsaus-0.0.7/dipsaus/tests/testthat/test.fastmap2.R |only dipsaus-0.0.7/dipsaus/tests/testthat/test.queues.R | 2 dipsaus-0.0.7/dipsaus/vignettes/r_expr_addons.Rmd | 2 dipsaus-0.0.7/dipsaus/vignettes/utility_functions.Rmd | 2 26 files changed, 352 insertions(+), 155 deletions(-)
Title: Gaussian Mixture Models, K-Means, Mini-Batch-Kmeans, K-Medoids
and Affinity Propagation Clustering
Description: Gaussian mixture models, k-means, mini-batch-kmeans, k-medoids and affinity propagation clustering with the option to plot, validate, predict (new data) and estimate the optimal number of clusters. The package takes advantage of 'RcppArmadillo' to speed up the computationally intensive parts of the functions. For more information, see (i) "Clustering in an Object-Oriented Environment" by Anja Struyf, Mia Hubert, Peter Rousseeuw (1997), Journal of Statistical Software, <doi:10.18637/jss.v001.i04>; (ii) "Web-scale k-means clustering" by D. Sculley (2010), ACM Digital Library, <doi:10.1145/1772690.1772862>; (iii) "Armadillo: a template-based C++ library for linear algebra" by Sanderson et al (2016), The Journal of Open Source Software, <doi:10.21105/joss.00026>; (iv) "Clustering by Passing Messages Between Data Points" by Brendan J. Frey and Delbert Dueck, Science 16 Feb 2007: Vol. 315, Issue 5814, pp. 972-976, <doi:10.1126/science.1136800>.
Author: Lampros Mouselimis [aut, cre],
Conrad Sanderson [cph] (Author of the C++ Armadillo library),
Ryan Curtin [cph] (Author of the C++ Armadillo library),
Siddharth Agrawal [cph] (Author of the C code of the Mini-Batch-Kmeans
algorithm
(https://github.com/siddharth-agrawal/Mini-Batch-K-Means)),
Brendan Frey [cph] (Author of the matlab code of the Affinity
propagation algorithm (for commercial use please contact the author
of the matlab code)),
Delbert Dueck [cph] (Author of the matlab code of the Affinity
propagation algorithm)
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>
Diff between ClusterR versions 1.2.1 dated 2019-11-29 and 1.2.2 dated 2020-05-12
DESCRIPTION | 10 MD5 | 62 ++--- NEWS.md | 8 R/RcppExports.R | 4 R/clustering_functions.R | 29 +- README.md | 1 build/vignette.rds |binary inst/doc/the_clusterR_package.R | 46 +-- inst/doc/the_clusterR_package.html | 453 ++++++++++++++++++------------------- inst/include/ClusterRHeader.h | 21 + man/AP_affinity_propagation.Rd | 14 - man/Clara_Medoids.Rd | 16 + man/Cluster_Medoids.Rd | 14 - man/GMM.Rd | 14 - man/KMeans_arma.Rd | 11 man/KMeans_rcpp.Rd | 16 + man/MiniBatchKmeans.Rd | 19 + man/Optimal_Clusters_GMM.Rd | 17 + man/Optimal_Clusters_KMeans.Rd | 20 + man/Optimal_Clusters_Medoids.Rd | 18 + man/distance_matrix.Rd | 10 man/external_validation.Rd | 8 man/function_interactive.Rd | 3 man/predict_KMeans.Rd | 6 man/predict_Medoids.Rd | 10 man/tryCatch_GMM.Rd | 13 - man/tryCatch_KMEANS_arma.Rd | 11 man/tryCatch_optimal_clust_GMM.Rd | 14 - src/RcppExports.cpp | 7 src/export_inst_folder_headers.cpp | 4 src/init.c | 4 tests/testthat/test-AP.R | 2 32 files changed, 530 insertions(+), 355 deletions(-)
Title: Quickly Get Datetime Data Ready for Analysis
Description: Transforms datetime data into a format ready for analysis.
It offers two core functionalities; aggregating data to a higher level interval
(thicken) and imputing records where observations were absent (pad).
Author: Edwin Thoen
Maintainer: Edwin Thoen <edwinthoen@gmail.com>
Diff between padr versions 0.5.1 dated 2020-04-03 and 0.5.2 dated 2020-05-12
padr-0.5.1/padr/data/datalist |only padr-0.5.2/padr/DESCRIPTION | 6 - padr-0.5.2/padr/MD5 | 23 ++--- padr-0.5.2/padr/NEWS.md | 4 + padr-0.5.2/padr/R/pad.R | 2 padr-0.5.2/padr/build/vignette.rds |binary padr-0.5.2/padr/inst/doc/padr.R | 28 +++---- padr-0.5.2/padr/inst/doc/padr.html | 88 ++++++++++------------ padr-0.5.2/padr/inst/doc/padr_custom.R | 8 +- padr-0.5.2/padr/inst/doc/padr_custom.html | 21 ++--- padr-0.5.2/padr/inst/doc/padr_implementation.R | 8 +- padr-0.5.2/padr/inst/doc/padr_implementation.html | 21 ++--- padr-0.5.2/padr/tests/testthat/test_pad_cust.R | 20 ++--- 13 files changed, 116 insertions(+), 113 deletions(-)
Title: A Tidy Approach to 'NetCDF' Data Exploration and Extraction
Description: Tidy tools for 'NetCDF' data sources. Explore the contents of a
'NetCDF' source (file or URL) presented as variables organized by grid with a
database-like interface. The hyper_filter() interactive function translates the
filter value or index expressions to array-slicing form. No data is read until
explicitly requested, as a data frame or list of arrays via hyper_tibble() or
hyper_array().
Author: Michael Sumner [aut, cre],
Simon Wotherspoon [ctb],
Tomas Remenyi [ctb],
Ben Raymond [ctb],
Jakub Nowosad [ctb],
Tim Lucas [ctb],
Hadley Wickham [ctb]
Maintainer: Michael Sumner <mdsumner@gmail.com>
Diff between tidync versions 0.2.3 dated 2019-11-06 and 0.2.4 dated 2020-05-12
tidync-0.2.3/tidync/inst/blog-01/tidync.html |only tidync-0.2.4/tidync/DESCRIPTION | 16 tidync-0.2.4/tidync/MD5 | 21 tidync-0.2.4/tidync/NEWS.md | 4 tidync-0.2.4/tidync/R/hyper_tbl_cube.R | 4 tidync-0.2.4/tidync/README.md | 129 +-- tidync-0.2.4/tidync/build/vignette.rds |binary tidync-0.2.4/tidync/inst/doc/netcdf-with-tidync.R | 28 tidync-0.2.4/tidync/inst/doc/netcdf-with-tidync.html | 780 +++++++++---------- tidync-0.2.4/tidync/man/hyper_array.Rd | 33 tidync-0.2.4/tidync/man/hyper_tbl_cube.Rd | 4 tidync-0.2.4/tidync/man/tidync.Rd | 2 12 files changed, 527 insertions(+), 494 deletions(-)
Title: A Tidy API for Graph Manipulation
Description: A graph, while not "tidy" in itself, can be thought of as two tidy
data frames describing node and edge data respectively. 'tidygraph'
provides an approach to manipulate these two virtual data frames using the
API defined in the 'dplyr' package, as well as provides tidy interfaces to
a lot of common graph algorithms.
Author: Thomas Lin Pedersen [cre, aut]
(<https://orcid.org/0000-0002-5147-4711>)
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>
Diff between tidygraph versions 1.1.2 dated 2019-02-18 and 1.2.0 dated 2020-05-12
tidygraph-1.1.2/tidygraph/R/dplyr.R |only tidygraph-1.2.0/tidygraph/DESCRIPTION | 18 - tidygraph-1.2.0/tidygraph/MD5 | 99 ++--- tidygraph-1.2.0/tidygraph/NAMESPACE | 25 + tidygraph-1.2.0/tidygraph/NEWS.md | 18 + tidygraph-1.2.0/tidygraph/R/bind.R | 39 +- tidygraph-1.2.0/tidygraph/R/centrality.R | 27 + tidygraph-1.2.0/tidygraph/R/data_tree.R | 2 tidygraph-1.2.0/tidygraph/R/graph_measures.R | 15 tidygraph-1.2.0/tidygraph/R/group.R | 23 + tidygraph-1.2.0/tidygraph/R/group_by.R | 32 + tidygraph-1.2.0/tidygraph/R/list.R | 16 tidygraph-1.2.0/tidygraph/R/local.R | 3 tidygraph-1.2.0/tidygraph/R/map.R | 8 tidygraph-1.2.0/tidygraph/R/morph.R | 4 tidygraph-1.2.0/tidygraph/R/morphers.R | 28 + tidygraph-1.2.0/tidygraph/R/node.R | 8 tidygraph-1.2.0/tidygraph/R/node_rank.R | 70 +++- tidygraph-1.2.0/tidygraph/R/pair_measures.R | 10 tidygraph-1.2.0/tidygraph/R/pull.R | 10 tidygraph-1.2.0/tidygraph/R/tbl_graph.R | 30 + tidygraph-1.2.0/tidygraph/R/tidygraph-package.R | 1 tidygraph-1.2.0/tidygraph/README.md | 133 +++++-- tidygraph-1.2.0/tidygraph/man/activate.Rd | 4 tidygraph-1.2.0/tidygraph/man/bind_graphs.Rd | 10 tidygraph-1.2.0/tidygraph/man/centrality.Rd | 80 +++- tidygraph-1.2.0/tidygraph/man/component_games.Rd | 16 tidygraph-1.2.0/tidygraph/man/create_graphs.Rd | 5 tidygraph-1.2.0/tidygraph/man/evolution_games.Rd | 60 ++- tidygraph-1.2.0/tidygraph/man/figures/logo.png |binary tidygraph-1.2.0/tidygraph/man/graph_join.Rd | 32 + tidygraph-1.2.0/tidygraph/man/graph_measures.Rd | 7 tidygraph-1.2.0/tidygraph/man/group_graph.Rd | 8 tidygraph-1.2.0/tidygraph/man/local_graph.Rd | 4 tidygraph-1.2.0/tidygraph/man/map_bfs.Rd | 8 tidygraph-1.2.0/tidygraph/man/map_bfs_back.Rd | 8 tidygraph-1.2.0/tidygraph/man/map_dfs.Rd | 10 tidygraph-1.2.0/tidygraph/man/map_dfs_back.Rd | 10 tidygraph-1.2.0/tidygraph/man/map_local.Rd | 6 tidygraph-1.2.0/tidygraph/man/morphers.Rd | 9 tidygraph-1.2.0/tidygraph/man/node_measures.Rd | 4 tidygraph-1.2.0/tidygraph/man/node_rank.Rd | 168 +++++++--- tidygraph-1.2.0/tidygraph/man/node_types.Rd | 3 tidygraph-1.2.0/tidygraph/man/pair_measures.Rd | 18 - tidygraph-1.2.0/tidygraph/man/reexports.Rd | 9 tidygraph-1.2.0/tidygraph/man/sampling_games.Rd | 20 - tidygraph-1.2.0/tidygraph/man/tbl_graph.Rd | 18 - tidygraph-1.2.0/tidygraph/man/tidygraph-package.Rd | 6 tidygraph-1.2.0/tidygraph/man/type_games.Rd | 53 ++- tidygraph-1.2.0/tidygraph/tests/testthat/test-bind.R | 2 tidygraph-1.2.0/tidygraph/tests/testthat/test-graph_measures.R | 1 51 files changed, 855 insertions(+), 343 deletions(-)
Title: Mediation Analysis for Complex Surveys
Description: It is a computer tool to conduct mediation analysis for complex surveys using multi-stage sampling. Specifically, the mediation analysis method using balanced repeated replication was proposed by Mai, Ha, and Soulakova (2019) <DOI:10.1080/10705511.2018.1559065>. The development of 'MedSurvey' was sponsored by American Lebanese Syrian Associated Charities (ALSAC). However, the contents of MedSurvey do not necessarily represent the policy of the ALSAC.
Author: Yujiao Mai [aut, cre],
Deo Kumar Srivastava [aut],
Hui Zhang [aut]
Maintainer: Hui Zhang <hzhang@northwestern.edu>
Diff between MedSurvey versions 1.1.1.1.0 dated 2019-07-23 and 1.1.1.2.0 dated 2020-05-12
MedSurvey-1.1.1.1.0/MedSurvey/data/datalist |only MedSurvey-1.1.1.2.0/MedSurvey/DESCRIPTION | 16 +++++++--------- MedSurvey-1.1.1.2.0/MedSurvey/MD5 | 13 ++++++------- MedSurvey-1.1.1.2.0/MedSurvey/man/MedData.Rd | 6 ++++-- MedSurvey-1.1.1.2.0/MedSurvey/man/chisq.BRR.Rd | 13 ++++++++++--- MedSurvey-1.1.1.2.0/MedSurvey/man/med.fit.BRR.Rd | 17 +++++++++++++---- MedSurvey-1.1.1.2.0/MedSurvey/man/med.p.adjust.Rd | 7 +++++-- MedSurvey-1.1.1.2.0/MedSurvey/man/med.summary.Rd | 7 +++++-- 8 files changed, 50 insertions(+), 29 deletions(-)
Title: Common Forms for Complex Hierarchical and Relational Data
Structures
Description: Generate common data forms for complex data suitable for conversions and
transmission by decomposition as paths or primitives. Paths are sequentially-linked records,
primitives are basic atomic elements and both can model many forms and be grouped into hierarchical
structures. The universal models 'SC0' (structural) and 'SC' (labelled, relational) are composed of
edges and can represent any hierarchical form. Specialist models 'PATH', 'ARC' and 'TRI' provide the
most common intermediate forms used for converting from one form to another. The methods are
inspired by the simplicial complex <https://en.wikipedia.org/wiki/Simplicial_complex> and
provide intermediate forms that relate spatial data structures to this mathematical construct.
Author: Michael D. Sumner [aut, cre],
John Corbett [ctb] (the original inspiration),
Simon Wotherspoon [ctb],
Kent Johnson [dtc],
Mark Padgham [aut]
Maintainer: Michael D. Sumner <mdsumner@gmail.com>
Diff between silicate versions 0.4.0 dated 2020-04-15 and 0.6.1 dated 2020-05-12
DESCRIPTION | 10 MD5 | 48 +- NAMESPACE | 11 NEWS.md | 270 ++++++++------- R/00_arc.R | 4 R/00_coord.R | 640 +++++++++++++++++++------------------ R/00_path.R | 508 +++++++++++++++-------------- R/PATH-model.R | 3 R/SC-model.R | 2 R/SC0-model.R | 390 ++++++++++------------ R/TIN.R | 61 +-- R/TRI-model.R | 254 ++++++++------ R/TRI0-model.R | 395 ++++++++++++---------- R/silicate-package.R | 294 ++++++++-------- R/utils.R | 31 + data/ear_gc.rda |only inst/doc/silicate_topology_01.html | 80 ++-- inst/misc/ARC-data.R | 2 man/TRI.Rd | 67 ++- man/TRI0.Rd | 29 + man/ear_gc.Rd |only man/sc_coord.Rd | 194 +++++------ man/sc_path.Rd | 195 +++++------ tests/testthat/Rplots.pdf |binary tests/testthat/test-generic-data.R | 2 tests/testthat/test-plot.R | 58 +-- 26 files changed, 1870 insertions(+), 1678 deletions(-)
Title: Residual Diagnostics for Hierarchical (Multi-Level / Mixed)
Regression Models
Description: The 'DHARMa' package uses a simulation-based approach to create
readily interpretable scaled (quantile) residuals for fitted (generalized) linear mixed
models. Currently supported are linear and generalized linear (mixed) models from 'lme4'
(classes 'lmerMod', 'glmerMod'), 'glmmTMB' and 'spaMM', generalized additive models ('gam' from
'mgcv'), 'glm' (including 'negbin' from 'MASS', but excluding quasi-distributions) and 'lm' model
classes. Moreover, externally created simulations, e.g. posterior predictive simulations
from Bayesian software such as 'JAGS', 'STAN', or 'BUGS' can be processed as well.
The resulting residuals are standardized to values between 0 and 1 and can be interpreted
as intuitively as residuals from a linear regression. The package also provides a number of
plot and test functions for typical model misspecification problems, such as
over/underdispersion, zero-inflation, and residual spatial and temporal autocorrelation.
Author: Florian Hartig [aut, cre] (<https://orcid.org/0000-0002-6255-9059>)
Maintainer: Florian Hartig <florian.hartig@biologie.uni-regensburg.de>
Diff between DHARMa versions 0.3.0 dated 2020-04-20 and 0.3.1 dated 2020-05-12
DHARMa-0.3.0/DHARMa/man/hasWeigths.Rd |only DHARMa-0.3.0/DHARMa/tests/testthat/Rplots.pdf |only DHARMa-0.3.1/DHARMa/DESCRIPTION | 14 DHARMa-0.3.1/DHARMa/MD5 | 68 - DHARMa-0.3.1/DHARMa/NAMESPACE | 9 DHARMa-0.3.1/DHARMa/NEWS | 39 - DHARMa-0.3.1/DHARMa/R/DHARMa.R | 38 + DHARMa-0.3.1/DHARMa/R/compatibility.R | 243 +++--- DHARMa-0.3.1/DHARMa/R/createData.R | 8 DHARMa-0.3.1/DHARMa/R/helper.R | 132 ++- DHARMa-0.3.1/DHARMa/R/plots.R | 263 +++---- DHARMa-0.3.1/DHARMa/R/simulateResiduals.R | 234 +++--- DHARMa-0.3.1/DHARMa/R/tests.R | 401 +++++------ DHARMa-0.3.1/DHARMa/inst/doc/DHARMa.R | 72 -- DHARMa-0.3.1/DHARMa/inst/doc/DHARMa.Rmd | 133 +-- DHARMa-0.3.1/DHARMa/inst/doc/DHARMa.html | 603 ++++++----------- DHARMa-0.3.1/DHARMa/inst/examples/checkModelHelp.R |only DHARMa-0.3.1/DHARMa/man/checkDots.Rd | 7 DHARMa-0.3.1/DHARMa/man/checkModel.Rd | 8 DHARMa-0.3.1/DHARMa/man/createDHARMa.Rd | 5 DHARMa-0.3.1/DHARMa/man/createData.Rd | 4 DHARMa-0.3.1/DHARMa/man/getQuantile.Rd | 33 DHARMa-0.3.1/DHARMa/man/getRefit.Rd | 4 DHARMa-0.3.1/DHARMa/man/getSimulations.Rd | 12 DHARMa-0.3.1/DHARMa/man/outliers.Rd |only DHARMa-0.3.1/DHARMa/man/plot.DHARMa.Rd | 4 DHARMa-0.3.1/DHARMa/man/plotResiduals.Rd | 8 DHARMa-0.3.1/DHARMa/man/recalculateResiduals.Rd | 4 DHARMa-0.3.1/DHARMa/man/simulateResiduals.Rd | 23 DHARMa-0.3.1/DHARMa/man/testDispersion.Rd | 6 DHARMa-0.3.1/DHARMa/man/testOutliers.Rd | 6 DHARMa-0.3.1/DHARMa/man/testQuantiles.Rd | 2 DHARMa-0.3.1/DHARMa/man/testSpatialAutocorrelation.Rd | 6 DHARMa-0.3.1/DHARMa/man/testTemporalAutocorrelation.Rd | 4 DHARMa-0.3.1/DHARMa/man/testZeroInflation.Rd | 2 DHARMa-0.3.1/DHARMa/tests/testthat/testModelTypes.R | 318 +++++--- DHARMa-0.3.1/DHARMa/vignettes/DHARMa.Rmd | 133 +-- 37 files changed, 1454 insertions(+), 1392 deletions(-)
Title: Local Randomization Methods for RD Designs
Description: The regression discontinuity (RD) design is a popular quasi-experimental design for causal inference and policy evaluation. Under the local randomization approach, RD designs can be interpreted as randomized experiments inside a window around the cutoff. This package provides tools to perform randomization inference for RD designs under local randomization: rdrandinf() to perform hypothesis testing using randomization inference, rdwinselect() to select a window around the cutoff in which randomization is likely to hold, rdsensitivity() to assess the sensitivity of the results to different window lengths and null hypotheses and rdrbounds() to construct Rosenbaum bounds for sensitivity to unobserved confounders. See Cattaneo, Titiunik and Vazquez-Bare (2016) <https://sites.google.com/site/rdpackages/rdlocrand/Cattaneo-Titiunik-VazquezBare_2016_Stata.pdf> for further methodological details.
Author: Matias D. Cattaneo, Rocio Titiunik, Gonzalo Vazquez-Bare
Maintainer: Gonzalo Vazquez-Bare <gvazquez@econ.ucsb.edu>
Diff between rdlocrand versions 0.5 dated 2019-08-21 and 0.6 dated 2020-05-12
DESCRIPTION | 8 MD5 | 24 - R/rdlocrand_fun.R | 298 ++++++++++----------- R/rdlocrand_package.R | 3 R/rdrandinf.R | 573 +++++++++++++++++++++------------------- R/rdrbounds.R | 327 +++++++++++------------ R/rdsensitivity.R | 157 +++++------ R/rdwinselect.R | 660 +++++++++++++++++++++++++++++------------------ man/rdlocrand-package.Rd | 74 ++--- man/rdrandinf.Rd | 279 ++++++++++--------- man/rdrbounds.Rd | 187 +++++++------ man/rdsensitivity.Rd | 167 ++++++----- man/rdwinselect.Rd | 210 ++++++++------ 13 files changed, 1625 insertions(+), 1342 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-05-08 1.3.0
2020-04-25 1.2.1
2020-04-14 1.2.0
2020-03-13 1.1.0
2020-02-21 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-05-08 2.1.2
2020-04-14 2.1.1
2020-04-08 2.1.0
2019-12-18 2.0.1
2019-03-03 2.0.0
Title: Time Series Regression Models with Distributed Lag Models
Description: Provides time series regression models with one predictor using finite distributed lag models, polynomial (Almon) distributed lag models, geometric distributed lag models with Koyck transformation, and autoregressive distributed lag models. It also consists of functions for computation of h-step ahead forecasts from these models. See Demirhan (2020)(<doi:10.1371/journal.pone.0228812>) and Baltagi (2011)(<doi:10.1007/978-3-642-20059-5>) for more information.
Author: Haydar Demirhan [aut, cre, cph] (<https://orcid.org/0000-0002-8565-4710>)
Maintainer: Haydar Demirhan <haydar.demirhan@rmit.edu.au>
Diff between dLagM versions 1.1.2 dated 2020-02-29 and 1.1.3 dated 2020-05-12
DESCRIPTION | 12 ++++++------ MD5 | 8 ++++---- NEWS.md | 3 +++ R/ardlBound.R | 12 +++++++++--- man/dLagM-package.Rd | 4 ++-- 5 files changed, 24 insertions(+), 15 deletions(-)
Title: Quantitative Support of Decision Making under Uncertainty
Description: Supporting the quantitative analysis of binary welfare based
decision making processes using Monte Carlo simulations. Decision support
is given on two levels: (i) The actual decision level is to choose between
two alternatives under probabilistic uncertainty. This package calculates
the optimal decision based on maximizing expected welfare. (ii) The meta
decision level is to allocate resources to reduce the uncertainty in the
underlying decision problem, i.e to increase the current information to
improve the actual decision making process. This problem is dealt with
using the Value of Information Analysis. The Expected Value of
Information for arbitrary prospective estimates can be calculated as
well as Individual Expected Value of Perfect Information.
The probabilistic calculations are done via Monte Carlo
simulations. This Monte Carlo functionality can be used on its own.
Author: Eike Luedeling [cre, aut] (University of Bonn),
Lutz Goehring [aut] (ICRAF and Lutz Goehring Consulting),
Katja Schiffers [aut] (University of Bonn)
Maintainer: Eike Luedeling <eike@eikeluedeling.com>
Diff between decisionSupport versions 1.105.2 dated 2019-10-16 and 1.105.3 dated 2020-05-12
DESCRIPTION | 10 +- MD5 | 68 +++++++-------- R/mcSimulation.R | 8 + build/vignette.rds |binary inst/doc/wildfire_example.R | 38 ++++---- inst/doc/wildfire_example.html | 143 +++++++++++++++------------------ man/as.data.frame.mcSimulation.Rd | 13 ++- man/chance_event.Rd | 11 ++ man/decisionSupport.Rd | 22 +++-- man/estimate_write_csv.Rd | 9 +- man/eviSimulation.Rd | 14 ++- man/gompertz_yield.Rd | 14 ++- man/hist.eviSimulation.Rd | 16 ++- man/hist.mcSimulation.Rd | 15 ++- man/hist.welfareDecisionAnalysis.Rd | 17 ++- man/individualEvpiSimulation.Rd | 19 ++-- man/make_CPT.Rd | 13 ++- man/mcSimulation.Rd | 13 ++- man/multi_EVPI.Rd | 13 ++- man/paramtnormci_fit.Rd | 13 ++- man/paramtnormci_numeric.Rd | 11 ++ man/plsr.mcSimulation.Rd | 12 ++ man/random.Rd | 23 +++-- man/random.estimate.Rd | 3 man/random.estimate1d.Rd | 3 man/rdistq_fit.Rd | 13 ++- man/rtnorm90ci.Rd | 35 ++++++-- man/sample_simple_CPT.Rd | 9 +- man/sort.summary.eviSimulation.Rd | 3 man/summary.eviSimulation.Rd | 7 - man/summary.mcSimulation.Rd | 17 ++- man/summary.welfareDecisionAnalysis.Rd | 12 +- man/temp_situations.Rd | 11 ++ man/vv.Rd | 12 ++ man/welfareDecisionAnalysis.Rd | 12 ++ 35 files changed, 412 insertions(+), 240 deletions(-)
More information about decisionSupport at CRAN
Permanent link
Title: CRISPR Pooled Screen Analysis using Beta-Binomial Test
Description: Provides functions for hit gene identification and quantification of sgRNA (single-guided RNA) abundances for CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) pooled screen data analysis.
Details are in Jeong et al. (2019) <doi:10.1101/gr.245571.118> and Baggerly et al. (2003) <doi:10.1093/bioinformatics/btg173>.
Author: Hyun-Hwan Jeong [aut, cre]
Maintainer: Hyun-Hwan Jeong <hyun-hwan.jeong@bcm.edu>
Diff between CB2 versions 1.3.1 dated 2020-04-15 and 1.3.2 dated 2020-05-12
CB2-1.3.1/CB2/data/datalist |only CB2-1.3.2/CB2/DESCRIPTION | 10 ++--- CB2-1.3.2/CB2/MD5 | 17 ++++----- CB2-1.3.2/CB2/build/vignette.rds |binary CB2-1.3.2/CB2/inst/doc/cb2-input-handling.html | 25 ++++++++++--- CB2-1.3.2/CB2/inst/doc/cb2-tutorial.Rmd | 4 +- CB2-1.3.2/CB2/inst/doc/cb2-tutorial.html | 45 +++++++++++++++---------- CB2-1.3.2/CB2/man/Evers_CRISPRn_RT112.Rd | 6 ++- CB2-1.3.2/CB2/man/Sanson_CRISPRn_A375.Rd | 6 ++- CB2-1.3.2/CB2/vignettes/cb2-tutorial.Rmd | 4 +- 10 files changed, 71 insertions(+), 46 deletions(-)
Title: Access, Retrieve, and Work with Canadian Census Data and
Geography
Description: Integrated, convenient, and uniform access to Canadian
Census data and geography retrieved using the 'CensusMapper' API. This package produces analysis-ready
tidy data frames and spatial data in multiple formats, as well as convenience functions
for working with Census variables, variable hierarchies, and region selection. API
keys are freely available with free registration at <https://censusmapper.ca/api>.
Census data and boundary geometries are reproduced and distributed on an "as
is" basis with the permission of Statistics Canada (Statistics Canada 2001; 2006;
2011; 2016).
Author: Jens von Bergmann [aut] (API creator and maintainer),
Dmitry Shkolnik [aut, cre] (Package maintainer, responsible for
correspondence),
Aaron Jacobs [aut]
Maintainer: Dmitry Shkolnik <shkolnikd@gmail.com>
Diff between cancensus versions 0.2.1 dated 2020-03-05 and 0.2.2 dated 2020-05-12
DESCRIPTION | 12 LICENSE | 2 MD5 | 34 - NAMESPACE | 1 NEWS.md | 56 + R/cancensus.R | 55 - R/census_regions.R | 8 R/census_vectors.R | 15 R/helpers.R | 3 README.md | 8 build/vignette.rds |binary inst/CITATION | 4 inst/doc/Making_maps_with_cancensus.R | 4 inst/doc/Making_maps_with_cancensus.Rmd | 7 inst/doc/Making_maps_with_cancensus.html | 899 +++++++++++++++---------------- inst/doc/cancensus.html | 36 - man/get_census.Rd | 4 vignettes/Making_maps_with_cancensus.Rmd | 7 18 files changed, 577 insertions(+), 578 deletions(-)