Title: A Framework for Clustering Longitudinal Data
Description: A framework for clustering longitudinal datasets in a standardized way.
The package provides an interface to existing R packages for clustering longitudinal univariate trajectories, facilitating reproducible and transparent analyses.
Additionally, standard tools are provided to support cluster analyses, including repeated estimation, model validation, and model assessment.
The interface enables users to compare results between methods, and to implement and evaluate new methods with ease.
Author: Niek Den Teuling [aut, cre] ,
Steffen Pauws [ctb],
Edwin van den Heuvel [ctb],
Koninklijke Philips N.V. [cph]
Maintainer: Niek Den Teuling <niek.den.teuling@philips.com>
Diff between latrend versions 1.4.3 dated 2022-10-26 and 1.5.0 dated 2022-11-10
DESCRIPTION | 21 MD5 | 129 +-- NAMESPACE | 544 ++++++------- NEWS.md | 16 R/generics.R | 1475 ++++++++++++++++++------------------ R/matrix.R | 2 R/meta-fit-converged.R |only R/meta-fit-rep.R |only R/meta-fit.R |only R/meta-method.R |only R/method.R | 42 - R/methodAKMedoids.R | 10 R/methodCrimCV.R | 12 R/methodDtwclust.R | 12 R/methodFeature.R | 10 R/methodFlexmix.R | 12 R/methodFlexmixGBTM.R | 10 R/methodFunFEM.R | 12 R/methodFunction.R | 10 R/methodGCKM.R | 10 R/methodKML.R | 12 R/methodLMKM.R | 21 R/methodLcmmGBTM.R | 14 R/methodLcmmGMM.R | 14 R/methodMatrix.R | 6 R/methodMclustLLPA.R | 14 R/methodMixAK_GLMM.R | 14 R/methodMixTVEM.R | 12 R/methodMixtoolsGMM.R | 12 R/methodMixtoolsNPRM.R | 10 R/methodRandom.R | 8 R/methodStratify.R | 10 R/model-transform.R | 16 R/model.R | 58 - R/modelApprox.R | 2 R/modelCrimCV.R | 190 ++-- R/modelDtwclust.R | 92 +- R/modelFlexmix.R | 6 R/modelFunFEM.R | 124 +-- R/modelKML.R | 8 R/modelLMKM.R | 7 R/modelLcmmGMM.R | 6 R/modelMclustLLPA.R | 8 R/modelMixAK_GLMM.R | 150 +-- R/modelMixAK_GLMMlist.R | 74 - R/modelMixTVEM.R | 198 ++-- R/modelMixtoolsGMM.R | 4 R/modelMixtoolsRM.R | 6 R/modelPartition.R | 562 ++++++------- R/models.R | 28 R/trajectories.R | 648 +++++++-------- R/zzz.R | 435 +++++----- build/partial.rdb |binary build/vignette.rds |binary inst/doc/demo.html | 54 + inst/doc/implement.html | 2 inst/doc/simulation.html | 6 man/getLcMethod.Rd | 3 man/interface-featureBased.Rd | 3 man/interface-metaMethods.Rd |only man/latrend-generics.Rd | 2 man/lcFitMethods.Rd |only man/lcModelPartition.Rd | 3 tests/testthat/test-fit-converged.R |only tests/testthat/test-fit-rep.R |only tests/testthat/test-meta-method.R |only tests/testthat/test-model-err.R | 8 tests/testthat/test-model-ext.R | 4 tests/testthat/test-parallel.R | 324 +++---- tests/testthat/test-partition.R | 308 ++++--- 70 files changed, 2992 insertions(+), 2821 deletions(-)
Title: Variable Selection under Ranked Sparsity Principles for
Interactions and Polynomials
Description: An implementation of ranked sparsity methods, including
penalized regression methods such as the sparsity-ranked lasso, its
non-convex alternatives, and elastic net, as well as the sparsity-ranked
Bayesian Information Criterion. As described in Peterson and
Cavanaugh (2022) <doi:10.1007/s10182-021-00431-7>, ranked
sparsity is a philosophy with methods primarily useful for
variable selection in the presence of prior informational
asymmetry, which occurs in the context of trying to perform variable
selection in the presence of interactions and/or polynomials. Ultimately,
this package attempts to facilitate dealing with cumbersome interactions
and polynomials while not avoiding them entirely. Typically, models
selected under ranked sparsity principles will also be more transparent,
having fewer falsely selected interactions and polynomials than other
methods.
Author: Ryan Andrew Peterson [aut, cre]
Maintainer: Ryan Andrew Peterson <ryan.a.peterson@cuanschutz.edu>
Diff between sparseR versions 0.2.0 dated 2022-08-17 and 0.2.1 dated 2022-11-10
DESCRIPTION | 10 MD5 | 29 NEWS.md | 4 R/sparseRBIC_bootstrap.R | 3 R/sparseRBIC_sampsplit.R | 3 R/sparseR_prep.R | 11 README.md | 45 build/vignette.rds |binary inst/doc/sparseR.R | 74 - inst/doc/sparseR.Rmd | 57 - inst/doc/sparseR.html | 1923 ++++++++++++++++++------------------ tests/testthat/Rplots.pdf |only tests/testthat/test_preprocessing.R | 6 tests/testthat/test_sparseR.R | 35 tests/testthat/test_sparseRBIC.R | 2 vignettes/sparseR.Rmd | 57 - 16 files changed, 1140 insertions(+), 1119 deletions(-)
Title: Random Effects Meta-Analysis for Correlated Test Statistics
Description: Meta-analysis is widely used to summarize estimated effects sizes across multiple statistical tests. Standard fixed and random effect meta-analysis methods assume that the estimated of the effect sizes are statistically independent. Here we relax this assumption and enable meta-analysis when the correlation matrix between effect size estimates is known. Fixed effect meta-analysis uses the method of Lin and Sullivan (2009) <doi:10.1016/j.ajhg.2009.11.001>, and random effects meta-analysis uses the method of Han, et al. <doi:10.1093/hmg/ddw049>.
Author: Gabriel Hoffman [aut, cre]
Maintainer: Gabriel Hoffman <gabriel.hoffman@mssm.edu>
Diff between remaCor versions 0.0.9 dated 2022-09-07 and 0.0.11 dated 2022-11-10
remaCor-0.0.11/remaCor/DESCRIPTION | 12 remaCor-0.0.11/remaCor/MD5 | 39 - remaCor-0.0.11/remaCor/NEWS.md | 9 remaCor-0.0.11/remaCor/R/LS.R | 4 remaCor-0.0.11/remaCor/R/RE2C.R | 64 + remaCor-0.0.11/remaCor/R/plots.R | 19 remaCor-0.0.11/remaCor/README.md | 4 remaCor-0.0.11/remaCor/TODO |only remaCor-0.0.11/remaCor/build/partial.rdb |binary remaCor-0.0.11/remaCor/inst/doc/remaCor.Rmd | 18 remaCor-0.0.11/remaCor/inst/doc/remaCor.html | 325 ++++------ remaCor-0.0.11/remaCor/vignettes/remaCor.Rmd | 18 remaCor-0.0.11/remaCor/vignettes/remaCor_cache/html/out_e501ac499f4c5fd162d3f0ebc7bf33a0.RData |only remaCor-0.0.11/remaCor/vignettes/remaCor_cache/html/out_e501ac499f4c5fd162d3f0ebc7bf33a0.rdb |only remaCor-0.0.11/remaCor/vignettes/remaCor_cache/html/out_e501ac499f4c5fd162d3f0ebc7bf33a0.rdx |only remaCor-0.0.11/remaCor/vignettes/remaCor_cache/html/rema_0c2f05a04310f95de4b68795f0b19a72.RData |only remaCor-0.0.11/remaCor/vignettes/remaCor_cache/html/rema_0c2f05a04310f95de4b68795f0b19a72.rdb |only remaCor-0.0.11/remaCor/vignettes/remaCor_cache/html/rema_0c2f05a04310f95de4b68795f0b19a72.rdx |only remaCor-0.0.11/remaCor/vignettes/remaCor_cache/html/sessionInfo_5fb8a7d9d1692a6a0373a37502dc5213.RData |only remaCor-0.0.11/remaCor/vignettes/remaCor_cache/html/sessionInfo_5fb8a7d9d1692a6a0373a37502dc5213.rdb |only remaCor-0.0.11/remaCor/vignettes/remaCor_cache/html/sessionInfo_5fb8a7d9d1692a6a0373a37502dc5213.rdx |only remaCor-0.0.9/remaCor/vignettes/remaCor_cache/html/out_a15af3ba37016f4bb758f87af2abe199.RData |only remaCor-0.0.9/remaCor/vignettes/remaCor_cache/html/out_a15af3ba37016f4bb758f87af2abe199.rdb |only remaCor-0.0.9/remaCor/vignettes/remaCor_cache/html/out_a15af3ba37016f4bb758f87af2abe199.rdx |only remaCor-0.0.9/remaCor/vignettes/remaCor_cache/html/rema_f901a1cec04ad9c311d2b79dad18c8aa.RData |only remaCor-0.0.9/remaCor/vignettes/remaCor_cache/html/rema_f901a1cec04ad9c311d2b79dad18c8aa.rdb |only remaCor-0.0.9/remaCor/vignettes/remaCor_cache/html/rema_f901a1cec04ad9c311d2b79dad18c8aa.rdx |only remaCor-0.0.9/remaCor/vignettes/remaCor_cache/html/sessionInfo_7db25a96354f0e5bb2139d00a36c177a.RData |only remaCor-0.0.9/remaCor/vignettes/remaCor_cache/html/sessionInfo_7db25a96354f0e5bb2139d00a36c177a.rdb |only remaCor-0.0.9/remaCor/vignettes/remaCor_cache/html/sessionInfo_7db25a96354f0e5bb2139d00a36c177a.rdx |only 30 files changed, 271 insertions(+), 241 deletions(-)
Title: Bootstrapped Differences of Time Series
Description: Analyze differences among time series curves with p-value
adjustment for multiple comparisons introduced in Oleson et al
(2015) <DOI:10.1177/0962280215607411>.
Author: Collin Nolte, Michael Seedorff, Jacob Oleson, Grant Brown,
Joseph Cavanaugh, and Bob McMurray
Maintainer: Collin Nolte <collin-nolte@uiowa.edu>
Diff between bdots versions 1.1.0 dated 2022-05-31 and 1.2.0 dated 2022-11-10
bdots-1.1.0/bdots/R/curveBooter.R |only bdots-1.2.0/bdots/DESCRIPTION | 10 bdots-1.2.0/bdots/MD5 | 69 +-- bdots-1.2.0/bdots/NAMESPACE | 1 bdots-1.2.0/bdots/NEWS.md | 40 +- bdots-1.2.0/bdots/R/bdotsBoot.R | 49 +- bdots-1.2.0/bdots/R/bdotsCorr.R | 5 bdots-1.2.0/bdots/R/bdotsFit.R | 46 +- bdots-1.2.0/bdots/R/bootHelper.R | 215 ++++++++--- bdots-1.2.0/bdots/R/curveFunctions.R | 2 bdots-1.2.0/bdots/R/helper.R | 46 ++ bdots-1.2.0/bdots/R/methods.R | 14 bdots-1.2.0/bdots/R/modifiedAlphaFunctions.R | 1 bdots-1.2.0/bdots/R/plotFunctions.R | 112 +++++ bdots-1.2.0/bdots/R/writeCSV.R | 12 bdots-1.2.0/bdots/build/vignette.rds |binary bdots-1.2.0/bdots/inst/doc/bdots.R | 6 bdots-1.2.0/bdots/inst/doc/bdots.Rmd | 7 bdots-1.2.0/bdots/inst/doc/bdots.html | 496 +++++++------------------ bdots-1.2.0/bdots/inst/doc/correlations.R | 7 bdots-1.2.0/bdots/inst/doc/correlations.Rmd | 10 bdots-1.2.0/bdots/inst/doc/correlations.html | 403 +++++--------------- bdots-1.2.0/bdots/inst/doc/customCurves.R | 6 bdots-1.2.0/bdots/inst/doc/customCurves.Rmd | 6 bdots-1.2.0/bdots/inst/doc/customCurves.html | 519 ++++++++------------------- bdots-1.2.0/bdots/inst/doc/refitCoef.R | 8 bdots-1.2.0/bdots/inst/doc/refitCoef.Rmd | 8 bdots-1.2.0/bdots/inst/doc/refitCoef.html | 402 +++++--------------- bdots-1.2.0/bdots/man/bdotsBoot.Rd | 4 bdots-1.2.0/bdots/man/createCurveList.Rd |only bdots-1.2.0/bdots/man/expCurve.Rd | 2 bdots-1.2.0/bdots/man/getBootDist.Rd |only bdots-1.2.0/bdots/man/getSubCurveValues.Rd |only bdots-1.2.0/bdots/man/print.bdotsBootObj.Rd |only bdots-1.2.0/bdots/vignettes/bdots.Rmd | 7 bdots-1.2.0/bdots/vignettes/correlations.Rmd | 10 bdots-1.2.0/bdots/vignettes/customCurves.Rmd | 6 bdots-1.2.0/bdots/vignettes/refitCoef.Rmd | 8 38 files changed, 1064 insertions(+), 1473 deletions(-)
Title: Bayesian Models for Data from Unmarked Animals using 'Stan'
Description: Fit Bayesian hierarchical models of animal abundance and occurrence
via the 'rstan' package, the R interface to the 'Stan' C++ library.
Supported models include single-season occupancy, dynamic occupancy, and
N-mixture abundance models. Covariates on model parameters are specified
using a formula-based interface similar to package 'unmarked', while also
allowing for estimation of random slope and intercept terms. References:
Carpenter et al. (2017) <doi:10.18637/jss.v076.i01>;
Fiske and Chandler (2011) <doi:10.18637/jss.v043.i10>.
Author: Ken Kellner [cre, aut]
Maintainer: Ken Kellner <contact@kenkellner.com>
Diff between ubms versions 1.1.0 dated 2021-11-30 and 1.2.2 dated 2022-11-10
DESCRIPTION | 20 - MD5 | 133 ++++----- NAMESPACE | 4 NEWS.md | 18 + R/RcppExports.R | 24 + R/colext.R | 6 R/fit.R | 50 ++- R/fitlist.R | 19 - R/inputs.R | 15 - R/kfold.R |only R/loglik.R |only R/mb_chisq.R | 8 R/missing.R | 5 R/multinomPois.R | 6 R/occu.R | 6 R/occuRN.R | 6 R/occuTTD.R | 6 R/pcount.R | 6 R/priors.R | 10 R/spatial.R | 4 R/stanmodels.R | 2 R/submodel.R | 11 R/ubmsFit-methods.R | 12 build/vignette.rds |binary inst/CITATION | 9 inst/doc/JAGS-comparison.Rmd | 3 inst/doc/JAGS-comparison.html | 364 ++++++++++++++----------- inst/doc/random-effects.html | 213 +++++++++----- inst/doc/spatial-models.Rmd | 51 +-- inst/doc/spatial-models.html | 369 ++++++++++++++----------- inst/doc/ubms.R | 8 inst/doc/ubms.Rmd | 8 inst/doc/ubms.html | 458 ++++++++++++++++++-------------- inst/stan/colext.stan | 10 inst/stan/include/functions_priors.stan | 2 man/extract_log_lik.Rd |only man/fitList-ubmsFit-method.Rd | 4 man/kfold-ubmsFit-method.Rd |only man/priors.Rd | 3 man/stan_colext.Rd | 5 man/stan_multinomPois.Rd | 5 man/stan_occu.Rd | 5 man/stan_occuRN.Rd | 5 man/stan_occuTTD.Rd | 5 man/stan_pcount.Rd | 5 src/Makevars | 9 src/Makevars.win | 2 src/exp_counts_occu.cpp | 2 src/loglik.cpp |only src/simz.cpp | 2 tests/testthat/test_colext.R | 7 tests/testthat/test_distsamp.R | 14 tests/testthat/test_fit.R | 19 - tests/testthat/test_fitlist.R | 22 + tests/testthat/test_inputs.R | 11 tests/testthat/test_multinomPois.R | 7 tests/testthat/test_occu.R | 47 +++ tests/testthat/test_occuRN.R | 7 tests/testthat/test_occuTTD.R | 7 tests/testthat/test_pcount.R | 7 tests/testthat/test_priors.R | 12 tests/testthat/test_spatial.R | 23 + tests/testthat/test_submodel.R | 35 ++ tests/testthat/test_ubmsFit_methods.R | 25 + vignettes/JAGS-comparison.Rmd | 3 vignettes/JAGS-comparison.Rmd.orig | 5 vignettes/references.bib | 18 + vignettes/spatial-models.Rmd | 51 +-- vignettes/spatial-models.Rmd.orig | 15 - vignettes/ubms.Rmd | 8 70 files changed, 1461 insertions(+), 800 deletions(-)
Title: Assessing Skill of Climate Forecasts on Seasonal-to-Decadal
Timescales
Description: Exploits dynamical seasonal forecasts in order to provide
information relevant to stakeholders at the seasonal timescale. The package
contains process-based methods for forecast calibration, bias correction,
statistical and stochastic downscaling, optimal forecast combination and
multivariate verification, as well as basic and advanced tools to obtain
tailored products. This package was developed in the context of the
ERA4CS project MEDSCOPE and the H2020 S2S4E project.
Pérez-Zanón et al. (2022) <doi:10.5194/gmd-15-6115-2022>.
Doblas-Reyes et al. (2005) <doi:10.1111/j.1600-0870.2005.00104.x>.
Mishra et al. (2018) <doi:10.1007/s00382-018-4404-z>.
Sanchez-Garcia et al. (2019) <doi:10.5194/asr-16-165-2019>.
Straus et al. (2007) <doi:10.1175/JCLI4070.1>.
Terzago et al. (2018) <doi:10.5194/nhess-18-2825-2018>.
Torralba et al. (2017) <doi:10.1175/JAMC-D-16-0204.1>.
D'Onofrio et al. (2014) <doi:10.1175/JHM-D-13-096.1>.
Verfaillie et al. (2017) & [...truncated...]
Author: Nuria Perez-Zanon [aut] ,
Louis-Philippe Caron [aut] ,
Carmen Alvarez-Castro [aut] ,
Lauriane Batte [aut],
Carlos Delgado [aut],
Jost von Hardenberg [aut] ,
Llorenc LLedo [aut],
Nicolau Manubens [aut],
Lluis Palma [aut],
Eroteida Sanchez-Garcia [aut] [...truncated...]
Maintainer: Eva Rifa <eva.rifarovira@bsc.es>
Diff between CSTools versions 4.1.0 dated 2022-10-26 and 4.1.1 dated 2022-11-10
DESCRIPTION | 6 MD5 | 24 - NEWS.md | 7 R/CST_Analogs.R | 410 +++++++++++++++++----------------- R/CST_Anomaly.R | 250 +++++++++++--------- R/PlotCombinedMap.R | 101 +++++--- inst/doc/WeatherRegimes_vignette.Rmd | 4 inst/doc/WeatherRegimes_vignette.html | 2 man/Analogs.Rd | 70 ++--- man/CST_Analogs.Rd | 53 ++-- man/CST_Anomaly.Rd | 66 +++-- man/PlotCombinedMap.Rd | 106 +++++--- vignettes/WeatherRegimes_vignette.Rmd | 4 13 files changed, 621 insertions(+), 482 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-10-30 0.1.0
Title: Exploratory Data Analysis for the 'spatstat' Family
Description: Functionality for exploratory data analysis and nonparametric analysis of
spatial data, mainly spatial point patterns,
in the 'spatstat' family of packages.
(Excludes analysis of spatial data on a linear network,
which is covered by the separate package 'spatstat.linnet'.)
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.
Author: Adrian Baddeley [aut, cre, cph]
,
Rolf Turner [aut, cph] ,
Ege Rubak [aut, cph] ,
Kasper Klitgaard Berthelsen [ctb],
Warick Brown [cph],
Achmad Choiruddin [ctb],
Jean-Francois Coeurjolly [ctb],
Ottmar Cronie [ctb],
Tilman Davies [ctb, cph],
Julian Gi [...truncated...]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.explore versions 3.0-3 dated 2022-11-04 and 3.0-5 dated 2022-11-10
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 33 +++++++++++++++++++++++++++++++++ R/pcf.R | 4 ++-- inst/doc/packagesizes.txt | 3 ++- src/KrectIncrem.h | 6 +++--- src/ripleybox.h | 4 ++-- 7 files changed, 52 insertions(+), 18 deletions(-)
More information about spatstat.explore at CRAN
Permanent link
Title: General Purpose 'Oai-PMH' Services Client
Description: A general purpose client to work with any 'OAI-PMH'
(Open Archives Initiative Protocol for 'Metadata' Harvesting) service.
The 'OAI-PMH' protocol is described at
<http://www.openarchives.org/OAI/openarchivesprotocol.html>.
Functions are provided to work with the 'OAI-PMH' verbs: 'GetRecord',
'Identify', 'ListIdentifiers', 'ListMetadataFormats', 'ListRecords', and
'ListSets'.
Author: Scott Chamberlain [aut],
Michal Bojanowski [aut, cre] ,
National Science Centre [fnd]
Maintainer: Michal Bojanowski <michal2992@gmail.com>
Diff between oai versions 0.3.2 dated 2021-05-13 and 0.4.0 dated 2022-11-10
DESCRIPTION | 27 ++- MD5 | 23 +-- NAMESPACE | 1 NEWS.md | 16 ++ R/oai-package.R | 8 - R/while_oai.R | 3 README.md | 231 +++++++++++++++++---------------- build/vignette.rds |binary inst/doc/oai.html | 59 ++------ man/figures |only man/oai-package.Rd | 14 +- tests/testthat/test-handle_errors.R | 19 +- tests/testthat/test-list_identifiers.R | 8 - 13 files changed, 217 insertions(+), 192 deletions(-)
Title: Nonlinear Mixed Effects Models in Population PK/PD, Estimation
Routines
Description: Fit and compare nonlinear mixed-effects models in
differential equations with flexible dosing information commonly seen
in pharmacokinetics and pharmacodynamics (Almquist, Leander, and
Jirstrand 2015 <doi:10.1007/s10928-015-9409-1>). Differential equation
solving is by compiled C code provided in the 'rxode2' package (Wang,
Hallow, and James 2015 <doi:10.1002/psp4.12052>).
Author: Matthew Fidler [aut, cre] ,
Yuan Xiong [aut],
Rik Schoemaker [aut] ,
Justin Wilkins [aut] ,
Wenping Wang [aut],
Robert Leary [ctb],
Mason McComb [ctb] ,
Vipul Mann [aut],
Mirjam Trame [ctb],
Mahmoud Abdelwahab [ctb],
Teun Post [ctb],
Richard Hooijmai [...truncated...]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between nlmixr2est versions 2.1.2 dated 2022-11-02 and 2.1.3 dated 2022-11-10
DESCRIPTION | 20 +- MD5 | 40 ++--- NEWS.md | 16 +- R/addCwres.R | 17 ++ R/nlmixr2_md5.R | 2 R/nmObjGet.R | 39 ++++- R/ofv.R | 1 R/resid.R | 3 R/utils.R | 6 src/inner.cpp | 14 + tests/testthat/test-cwres.R | 13 + tests/testthat/test-lag.R | 76 +++++---- tests/testthat/test-nonmu.R | 62 ++++++++ tests/testthat/test-restart.R | 58 +++---- tests/testthat/test-rxsolve.R | 112 +++++++------- tests/testthat/test-saem-aic.R | 64 ++++---- tests/testthat/test-saem-drop.R | 83 +++++----- tests/testthat/test-table-cmt.R | 274 ++++++++++++++++++------------------ tests/testthat/test-timing.R | 2 tests/testthat/test-ui-est-change.R | 58 +++---- tests/testthat/test-unary-mu.R | 88 +++++------ 21 files changed, 597 insertions(+), 451 deletions(-)
Title: The Time Series Modeling Companion to 'healthyR'
Description: Hospital time series data analysis workflow tools, modeling, and automations.
This library provides many useful tools to review common administrative time
series hospital data. Some of these include average length of stay, and
readmission rates. The aim is to provide a simple and consistent verb
framework that takes the guesswork out of everything.
Author: Steven Sanderson [aut, cre],
Steven Sanderson [cph]
Maintainer: Steven Sanderson <spsanderson@gmail.com>
Diff between healthyR.ts versions 0.2.3 dated 2022-10-03 and 0.2.4 dated 2022-11-10
DESCRIPTION | 6 - MD5 | 20 ++-- NEWS.md | 15 +++ R/step-ts-acceleration.R | 9 -- R/step-ts-velocity.R | 9 -- R/ts-tune-spec-template.R | 2 README.md | 16 +-- inst/doc/getting-started.html | 30 +++---- inst/doc/using-tidy-fft.html | 75 +++++++++--------- man/figures/README-ts_random_walk_ggplot_layers-1.png |binary man/figures/README-unnamed-chunk-2-1.png |binary 11 files changed, 96 insertions(+), 86 deletions(-)
Title: R Interface to C API of GLPK
Description: R Interface to C API of GLPK, depends on GLPK Version >= 4.42.
Author: Mihail Anton [cre],
Mayo Roettger [ctb],
Gabriel Gelius-Dietrich [aut],
Louis Luangkesorn [ctb]
Maintainer: Mihail Anton <mihail.anton@chalmers.se>
Diff between glpkAPI versions 1.3.3 dated 2021-10-28 and 1.3.4 dated 2022-11-10
DESCRIPTION | 22 ++++++++++++---------- LICENSE |only MD5 | 17 +++++++++-------- README.md | 9 +++++++-- build/vignette.rds |binary inst/NEWS.Rd | 10 ++++++++++ inst/doc/glpk-gmpl-intro.pdf |binary inst/doc/glpkAPI.pdf |binary src/glpkAPI.c | 14 +++++++------- src/glpkAPI.h | 16 ++++++++-------- 10 files changed, 53 insertions(+), 35 deletions(-)
Title: Miscellaneous Functions for the Analysis of Educational
Assessments
Description: Miscellaneous functions for data cleaning and data analysis of educational assessments. Includes functions for descriptive
analyses, character vector manipulations and weighted statistics. Mainly a lightweight dependency for the packages 'eatRep',
'eatGADS', 'eatPrep' and 'eatModel' (which will be subsequently submitted to 'CRAN').
The function for defining (weighted) contrasts in weighted effect coding refers to
te Grotenhuis et al. (2017) <doi:10.1007/s00038-016-0901-1>.
Functions for weighted statistics refer to
Wolter (2007) <doi:10.1007/978-0-387-35099-8>.
Author: Sebastian Weirich [aut, cre],
Martin Hecht [aut],
Karoline Sachse [aut],
Benjamin Becker [aut],
Nicole Mahler [aut]
Maintainer: Sebastian Weirich <sebastian.weirich@iqb.hu-berlin.de>
Diff between eatTools versions 0.7.3 dated 2022-06-28 and 0.7.4 dated 2022-11-10
DESCRIPTION | 8 ++++---- MD5 | 17 ++++++++++------- NAMESPACE | 1 + NEWS.md | 7 +++++++ R/descr.r | 6 ++++++ R/mergeAttr.r | 9 ++++++--- R/rbind_common.r |only R/remove_funs.R | 5 +++-- man/halveString.rd | 8 ++++---- man/rbind_common.rd |only tests/testthat/test_rbindCommon.R |only 11 files changed, 41 insertions(+), 20 deletions(-)
Title: Tokenization, Parts of Speech Tagging, Lemmatization and
Dependency Parsing with the 'UDPipe' 'NLP' Toolkit
Description: This natural language processing toolkit provides language-agnostic
'tokenization', 'parts of speech tagging', 'lemmatization' and 'dependency
parsing' of raw text. Next to text parsing, the package also allows you to train
annotation models based on data of 'treebanks' in 'CoNLL-U' format as provided
at <https://universaldependencies.org/format.html>. The techniques are explained
in detail in the paper: 'Tokenizing, POS Tagging, Lemmatizing and Parsing UD 2.0
with UDPipe', available at <doi:10.18653/v1/K17-3009>.
The toolkit also contains functionalities for commonly used data manipulations on texts
which are enriched with the output of the parser. Namely functionalities and algorithms
for collocations, token co-occurrence, document term matrix handling,
term frequency inverse document frequency calculations,
information retrieval metrics (Okapi BM25), handling of multi-word expressions,
keyword detection (Rapid Automatic Keyword Extraction, noun phrase extraction, syntact [...truncated...]
Author: Jan Wijffels [aut, cre, cph],
BNOSAC [cph],
Institute of Formal and Applied Linguistics, Faculty of Mathematics and
Physics, Charles University in Prague, Czech Republic [cph],
Milan Straka [ctb, cph],
Jana Strakova [ctb, cph]
Maintainer: Jan Wijffels <jwijffels@bnosac.be>
Diff between udpipe versions 0.8.9 dated 2022-03-25 and 0.8.10 dated 2022-11-10
DESCRIPTION | 8 +- MD5 | 38 ++++++------ NEWS.md | 5 + R/nlp_collocation.R | 9 +- R/nlp_cooccurrence.R | 3 R/nlp_flow.R | 56 ++++++++++++++---- inst/doc/udpipe-annotation.html | 6 - inst/doc/udpipe-parallel.html | 6 - inst/doc/udpipe-train.html | 6 - inst/doc/udpipe-tryitout.html | 4 - inst/doc/udpipe-universe.html | 4 - inst/doc/udpipe-usecase-postagging-lemmatisation.html | 4 - inst/doc/udpipe-usecase-topicmodelling.html | 4 - man/cooccurrence.Rd | 3 man/document_term_frequencies.Rd | 8 ++ man/document_term_frequencies_statistics.Rd | 4 + man/document_term_matrix.Rd | 28 ++++++--- man/dtm_bind.Rd | 6 + man/keywords_collocation.Rd | 9 +- src/udpipe.cpp | 2 20 files changed, 146 insertions(+), 67 deletions(-)
Title: Parsing and Code Generation Functions for 'rxode2'
Description: Provides the parsing needed for 'rxode2' (Wang, Hallow and
James (2016) <doi:10.1002/psp4.12052>). It also provides the 'stan'
based advan linear compartment model solutions with gradients
(Carpenter et al (2015), <arXiv:1509.07164>) needed in 'nlmixr2'
(Fidler et al (2019) <doi:10.1002/psp4.12445>).
This split will reduce computational burden of recompiling 'rxode2'.
Author: Matthew L. Fidler [aut, cre] ,
Wenping Wang [aut],
Richard Upton [ctb]
Maintainer: Matthew L. Fidler <matthew.fidler@gmail.com>
Diff between rxode2parse versions 2.0.12 dated 2022-10-29 and 2.0.13 dated 2022-11-10
DESCRIPTION | 6 +++--- MD5 | 4 ++-- NEWS.md | 4 ++++ 3 files changed, 9 insertions(+), 5 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 correlatio [...truncated...]
Author: Adrian Baddeley [aut, cre] ,
Rolf Turner [aut] ,
Ege Rubak [aut]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat versions 2.3-4 dated 2022-04-01 and 3.0-2 dated 2022-11-10
DESCRIPTION | 31 +- MD5 | 62 ++-- NAMESPACE | 3 NEWS | 40 +++ R/First.R | 15 - R/news.R | 7 build/vignette.rds |binary demo/data.R | 9 demo/spatstat.R | 36 ++ demo/sumfun.R | 13 inst/doc/bugfixes.R | 23 - inst/doc/bugfixes.Rnw | 56 +++- inst/doc/bugfixes.pdf |binary inst/doc/datasets.pdf |binary inst/doc/getstart.pdf |binary inst/doc/packagesizes.txt | 2 inst/doc/replicated.pdf |binary inst/doc/shapefiles.pdf |binary inst/doc/spatstatKnetsize.txt | 3 inst/doc/spatstatcoreNEWS |only inst/doc/spatstatcoresize.txt |only inst/doc/spatstatguisize.txt | 4 inst/doc/spatstatlocalsize.txt | 20 - inst/doc/updates.R | 69 ++--- inst/doc/updates.Rnw | 333 +++++++++++++++++++------ inst/doc/updates.pdf |binary man/bugfixes.Rd | 9 man/macros/defns.Rd | 25 + man/spatstat-internal.Rd | 2 man/spatstat-package.Rd | 544 ++++++++++++++++++++--------------------- man/spatstat.family.Rd | 3 vignettes/bugfixes.Rnw | 56 +++- vignettes/updates.Rnw | 333 +++++++++++++++++++------ 33 files changed, 1139 insertions(+), 559 deletions(-)
Title: Nonparametric Circular Methods
Description: Nonparametric smoothing methods for density and regression estimation involving circular data,
including the estimation of the mean regression function and other conditional characteristics.
Author: Maria Alonso-Pena [aut, cre],
Maria Oliveira [aut],
Jose Ameijeiras-Alonso [aut],
Rosa M. Crujeiras [aut],
Irene Gijbels [aut],
Alberto Rodriguez-Casal [aut],
Felicita Scapini [dtc]
Maintainer: Maria Alonso-Pena <maria.alonsopena@kuleuven.be>
Diff between NPCirc versions 3.0.1 dated 2021-07-22 and 3.1.1 dated 2022-11-10
NPCirc-3.0.1/NPCirc/NEWS |only NPCirc-3.1.1/NPCirc/DESCRIPTION | 32 +- NPCirc-3.1.1/NPCirc/MD5 | 106 ++++++--- NPCirc-3.1.1/NPCirc/NAMESPACE | 14 - NPCirc-3.1.1/NPCirc/R/CRSC.R |only NPCirc-3.1.1/NPCirc/R/RcppExports.R |only NPCirc-3.1.1/NPCirc/R/bw.AA.R |only NPCirc-3.1.1/NPCirc/R/bw.circ.local.lik.R |only NPCirc-3.1.1/NPCirc/R/bw.joint.dpcirc.R |only NPCirc-3.1.1/NPCirc/R/bw.modalreg.circ.circ.R |only NPCirc-3.1.1/NPCirc/R/bw.modalreg.circ.lin.R |only NPCirc-3.1.1/NPCirc/R/bw.modalreg.lin.circ.R |only NPCirc-3.1.1/NPCirc/R/bw.pi.R | 12 - NPCirc-3.1.1/NPCirc/R/bw.reg.circ.lin.R | 5 NPCirc-3.1.1/NPCirc/R/circ.local.lik.R |only NPCirc-3.1.1/NPCirc/R/circsizer.map.R | 28 +- NPCirc-3.1.1/NPCirc/R/cross_validation.R |only NPCirc-3.1.1/NPCirc/R/dpreg.circ.R |only NPCirc-3.1.1/NPCirc/R/est_bias.R |only NPCirc-3.1.1/NPCirc/R/est_variance.R |only NPCirc-3.1.1/NPCirc/R/interna_cvDP.R |only NPCirc-3.1.1/NPCirc/R/internas_PDP.R |only NPCirc-3.1.1/NPCirc/R/internas_kern.dens.R |only NPCirc-3.1.1/NPCirc/R/internas_multimodal.R |only NPCirc-3.1.1/NPCirc/R/kern.den.circ.R | 213 +++++++++++++------ NPCirc-3.1.1/NPCirc/R/kern.dpreg.circ.R |only NPCirc-3.1.1/NPCirc/R/kern.reg.circ.lin.R | 14 - NPCirc-3.1.1/NPCirc/R/loc_loglik.R |only NPCirc-3.1.1/NPCirc/R/modalreg.circ.circ.R |only NPCirc-3.1.1/NPCirc/R/modalreg.circ.lin.R |only NPCirc-3.1.1/NPCirc/R/modalreg.lin.circ.R |only NPCirc-3.1.1/NPCirc/R/refined_rule.R |only NPCirc-3.1.1/NPCirc/build |only NPCirc-3.1.1/NPCirc/data/HumanMotorResonance.txt |only NPCirc-3.1.1/NPCirc/data/flywheels.txt |only NPCirc-3.1.1/NPCirc/data/pm10.txt |only NPCirc-3.1.1/NPCirc/data/sandhoppers.rda |only NPCirc-3.1.1/NPCirc/data/spikes.txt |only NPCirc-3.1.1/NPCirc/data/zebrafish.txt |only NPCirc-3.1.1/NPCirc/man/HumanMotorResonance.Rd |only NPCirc-3.1.1/NPCirc/man/NPCirc-internal.Rd |only NPCirc-3.1.1/NPCirc/man/NPCirc-package.Rd | 45 ++-- NPCirc-3.1.1/NPCirc/man/ancova.circ.lin.Rd | 71 ++---- NPCirc-3.1.1/NPCirc/man/bw.AA.Rd |only NPCirc-3.1.1/NPCirc/man/bw.CV.Rd | 17 - NPCirc-3.1.1/NPCirc/man/bw.boot.Rd | 6 NPCirc-3.1.1/NPCirc/man/bw.circ.local.lik.Rd |only NPCirc-3.1.1/NPCirc/man/bw.joint.dpcirc.Rd |only NPCirc-3.1.1/NPCirc/man/bw.modalreg.circ.lin.Rd |only NPCirc-3.1.1/NPCirc/man/bw.pi.Rd | 6 NPCirc-3.1.1/NPCirc/man/bw.reg.circ.lin.Rd | 6 NPCirc-3.1.1/NPCirc/man/bw.rt.Rd | 8 NPCirc-3.1.1/NPCirc/man/circ.local.lik.Rd |only NPCirc-3.1.1/NPCirc/man/circsizer.density.Rd | 4 NPCirc-3.1.1/NPCirc/man/circsizer.map.Rd | 4 NPCirc-3.1.1/NPCirc/man/circsizer.regression.Rd | 6 NPCirc-3.1.1/NPCirc/man/cycle.changes.Rd | 4 NPCirc-3.1.1/NPCirc/man/dcircmix.Rd | 6 NPCirc-3.1.1/NPCirc/man/dpreg.circ.Rd |only NPCirc-3.1.1/NPCirc/man/dwsn.Rd | 2 NPCirc-3.1.1/NPCirc/man/flywheels.Rd |only NPCirc-3.1.1/NPCirc/man/kern.den.circ.Rd | 101 +++++---- NPCirc-3.1.1/NPCirc/man/kern.dpreg.circ.Rd |only NPCirc-3.1.1/NPCirc/man/kern.reg.circ.lin.Rd | 12 - NPCirc-3.1.1/NPCirc/man/lines.regression.circular.Rd | 4 NPCirc-3.1.1/NPCirc/man/modalreg.circ.lin.Rd |only NPCirc-3.1.1/NPCirc/man/noeffect.circ.lin.Rd | 2 NPCirc-3.1.1/NPCirc/man/plot.regression.circular.Rd | 4 NPCirc-3.1.1/NPCirc/man/pm10.Rd |only NPCirc-3.1.1/NPCirc/man/sandhoppers.Rd |only NPCirc-3.1.1/NPCirc/man/speed.wind.Rd | 4 NPCirc-3.1.1/NPCirc/man/spikes.Rd |only NPCirc-3.1.1/NPCirc/man/temp.wind.Rd | 4 NPCirc-3.1.1/NPCirc/man/zebrafish.Rd |only NPCirc-3.1.1/NPCirc/src |only 75 files changed, 439 insertions(+), 301 deletions(-)
Title: Linguistic Typology and Mapping
Description: Provides R with the Glottolog database <https://glottolog.org/> and some more abilities for purposes of linguistic mapping. The Glottolog database contains the catalogue of languages of the world. This package helps researchers to make a linguistic maps, using philosophy of the Cross-Linguistic Linked Data project <https://clld.org/>, which allows for while at the same time facilitating uniform access to the data across publications. A tutorial for this package is available on GitHub pages <https://docs.ropensci.org/lingtypology/> and package vignette. Maps created by this package can be used both for the investigation and linguistic teaching. In addition, package provides an ability to download data from typological databases such as WALS, AUTOTYP and some others and to create your own database website.
Author: George Moroz [aut, cre] ,
Kirill Koncha [ctb] ,
Mikhail Leonov [ctb],
Anna Smirnova [ctb],
Ekaterina Zalivina [ctb]
Maintainer: George Moroz <agricolamz@gmail.com>
Diff between lingtypology versions 1.1.9 dated 2022-06-24 and 1.1.10 dated 2022-11-10
lingtypology-1.1.10/lingtypology/DESCRIPTION | 15 +-- lingtypology-1.1.10/lingtypology/MD5 | 49 +++++----- lingtypology-1.1.10/lingtypology/NAMESPACE | 4 lingtypology-1.1.10/lingtypology/NEWS | 7 + lingtypology-1.1.10/lingtypology/R/autotyp.R | 2 lingtypology-1.1.10/lingtypology/R/autotyp.feature.R | 10 +- lingtypology-1.1.10/lingtypology/R/frequency_list.feature.R |only lingtypology-1.1.10/lingtypology/R/iso.R |only lingtypology-1.1.10/lingtypology/R/iso3.iso1.R |only lingtypology-1.1.10/lingtypology/R/map.feature.R | 15 +-- lingtypology-1.1.10/lingtypology/R/soundcomparisons.R | 24 ++-- lingtypology-1.1.10/lingtypology/R/soundcomparisons.feature.R | 2 lingtypology-1.1.10/lingtypology/R/zzz.r |only lingtypology-1.1.10/lingtypology/build/vignette.rds |binary lingtypology-1.1.10/lingtypology/data/autotyp.RData |binary lingtypology-1.1.10/lingtypology/data/iso_639.RData |only lingtypology-1.1.10/lingtypology/inst/doc/lingtypology_creating_maps.html | 17 ++- lingtypology-1.1.10/lingtypology/inst/doc/lingtypology_db_API.html | 17 ++- lingtypology-1.1.10/lingtypology/inst/doc/lingtypology_dplyr.html | 17 ++- lingtypology-1.1.10/lingtypology/inst/doc/lingtypology_glottolog_functions.html | 17 ++- lingtypology-1.1.10/lingtypology/inst/doc/lingtypology_intro.html | 17 ++- lingtypology-1.1.10/lingtypology/man/autotyp.Rd | 4 lingtypology-1.1.10/lingtypology/man/frequency_list.feature.Rd |only lingtypology-1.1.10/lingtypology/man/iso3.iso1.Rd |only lingtypology-1.1.10/lingtypology/man/iso_639.Rd |only lingtypology-1.1.10/lingtypology/man/soundcomparisons.Rd | 2 lingtypology-1.1.10/lingtypology/man/soundcomparisons.feature.Rd | 2 lingtypology-1.1.9/lingtypology/R/amap.R |only lingtypology-1.1.9/lingtypology/R/ggmap.feature.R |only lingtypology-1.1.9/lingtypology/data/amap.RData |only lingtypology-1.1.9/lingtypology/man/amap.Rd |only lingtypology-1.1.9/lingtypology/man/ggmap.feature.Rd |only 32 files changed, 132 insertions(+), 89 deletions(-)
Title: Port of 'Dparser' Package
Description: A Scannerless GLR parser/parser generator. Note that GLR standing for "generalized LR", where L stands for "left-to-right" and
R stands for "rightmost (derivation)". For more information see <https://en.wikipedia.org/wiki/GLR_parser>. This parser is based on the Tomita
(1987) algorithm. (Paper can be found at <https://aclanthology.org/P84-1073.pdf>).
The original 'dparser' package documentation can be found at <https://dparser.sourceforge.net/>. This allows you to add mini-languages to R (like
RxODE's ODE mini-language Wang, Hallow, and James 2015 <DOI:10.1002/psp4.12052>) or to parse other languages like 'NONMEM' to automatically translate
them to R code. To use this in your code, add a LinkingTo dparser in your DESCRIPTION file and instead of using #include <dparse.h> use
#include <dparser.h>. This also provides a R-based port of the make_dparser <https://dparser.sourceforge.net/d/make_dparser.cat> command called
mkdparser(). Additiona [...truncated...]
Author: Matthew Fidler [aut, cre],
John Plevyak [aut, cph]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between dparser versions 1.3.1-8 dated 2022-10-29 and 1.3.1-9 dated 2022-11-10
dparser-1.3.1-8/dparser/tests/testthat/g32.test.g |only dparser-1.3.1-8/dparser/tests/testthat/g33.test.g |only dparser-1.3.1-8/dparser/tests/testthat/g47.test.g |only dparser-1.3.1-8/dparser/tests/testthat/g48.test.g |only dparser-1.3.1-8/dparser/tests/testthat/python.test.g |only dparser-1.3.1-9/dparser/DESCRIPTION | 6 +++--- dparser-1.3.1-9/dparser/MD5 | 13 ++++--------- dparser-1.3.1-9/dparser/NEWS.md | 6 ++++++ dparser-1.3.1-9/dparser/src/Makevars | 2 +- dparser-1.3.1-9/dparser/src/write_tables.c | 2 ++ 10 files changed, 16 insertions(+), 13 deletions(-)
Title: Complex Network Generation
Description: Providing a set of functions to easily generate and iterate complex networks.
The functions can be used to generate realistic networks with a wide range of different clustering, density, and average path length.
For more information consult research articles by Amiyaal Ilany and Erol Akcay (2016) <doi:10.1093/icb/icw068> and Ilany and Erol Akcay (2016) <doi:10.1101/026120>, which have inspired many methods in this package.
Author: Marco Smolla [aut, cre]
Maintainer: Marco Smolla <drsmolla@icloud.com>
Diff between complexNet versions 0.1.0 dated 2021-03-31 and 0.2.0 dated 2022-11-10
complexNet-0.1.0/complexNet/R/avg_degree_brn.R |only complexNet-0.1.0/complexNet/man/avg_degree_brn.Rd |only complexNet-0.2.0/complexNet/DESCRIPTION | 11 complexNet-0.2.0/complexNet/MD5 | 37 - complexNet-0.2.0/complexNet/NAMESPACE | 6 complexNet-0.2.0/complexNet/NEWS.md |only complexNet-0.2.0/complexNet/R/avg_degree_bnr.R |only complexNet-0.2.0/complexNet/R/init_graph.R | 1 complexNet-0.2.0/complexNet/R/iterate_bnr.R | 4 complexNet-0.2.0/complexNet/R/iterate_kp.R |only complexNet-0.2.0/complexNet/R/make_bnr.R | 6 complexNet-0.2.0/complexNet/R/make_kp.R |only complexNet-0.2.0/complexNet/README.md | 99 ++- complexNet-0.2.0/complexNet/build/partial.rdb |binary complexNet-0.2.0/complexNet/build/vignette.rds |binary complexNet-0.2.0/complexNet/inst/doc/complexNet-vignette.R | 1 complexNet-0.2.0/complexNet/inst/doc/complexNet-vignette.Rmd | 3 complexNet-0.2.0/complexNet/inst/doc/complexNet-vignette.html | 321 ++++++++-- complexNet-0.2.0/complexNet/man/avg_degree_bnr.Rd |only complexNet-0.2.0/complexNet/man/iterate_bnr.Rd | 3 complexNet-0.2.0/complexNet/man/iterate_kp.Rd |only complexNet-0.2.0/complexNet/man/make_bnr.Rd | 5 complexNet-0.2.0/complexNet/man/make_kp.Rd |only complexNet-0.2.0/complexNet/vignettes/complexNet-vignette.Rmd | 3 24 files changed, 395 insertions(+), 105 deletions(-)
Title: Antarctic Spatial Data Manipulation
Description: Loads and creates spatial data, including layers and tools that are relevant
to the activities of the Commission for the Conservation of Antarctic Marine Living
Resources. Provides two categories of functions: load functions and create functions.
Load functions are used to import existing spatial layers from the online CCAMLR GIS
such as the ASD boundaries. Create functions are used to create layers from user data
such as polygons and grids.
Author: Stephane Thanassekos [aut, cre],
Keith Reid [aut],
Lucy Robinson [aut],
Michael D. Sumner [ctb],
Roger Bivand [ctb]
Maintainer: Stephane Thanassekos <stephane.thanassekos@ccamlr.org>
Diff between CCAMLRGIS versions 4.0.1 dated 2022-08-22 and 4.0.2 dated 2022-11-10
DESCRIPTION | 13 +- MD5 | 78 +++++++------- NAMESPACE | 3 NEWS.md | 4 R/CCAMLRGIS.R | 3 R/CCAMLRGIS_DataDescription.R | 7 - R/Clip2Coast.R | 8 - R/Pies.R | 227 ++---------------------------------------- R/add_Cscale.R | 22 ---- R/add_col.R | 31 ----- R/add_labels.R | 6 - R/create.R | 173 +++----------------------------- R/get_depths.R | 2 R/get_iso_polys.R |only R/load.R | 83 +++------------ README.md | 73 +++++++++++++ build/vignette.rds |binary inst/doc/CCAMLRGIS.html | 4 man/Clip2Coast.Rd | 8 - man/Labels.Rd | 7 - man/add_Cscale.Rd | 22 ---- man/add_PieLegend.Rd | 114 +-------------------- man/add_col.Rd | 31 ----- man/add_labels.Rd | 6 - man/create_Lines.Rd | 44 -------- man/create_Pies.Rd | 113 -------------------- man/create_Points.Rd | 24 ---- man/create_PolyGrids.Rd | 37 ------ man/create_Polys.Rd | 24 ---- man/create_Stations.Rd | 44 -------- man/get_depths.Rd | 2 man/get_iso_polys.Rd |only man/load_ASDs.Rd | 11 -- man/load_Bathy.Rd | 2 man/load_Coastline.Rd | 10 - man/load_EEZs.Rd | 10 - man/load_MAs.Rd | 10 - man/load_MPAs.Rd | 10 - man/load_RBs.Rd | 10 - man/load_SSMUs.Rd | 10 - man/load_SSRUs.Rd | 10 - 41 files changed, 254 insertions(+), 1042 deletions(-)
Title: Grouped Date Classes
Description: Provides a coherent interface and implementation for creating
grouped date classes. This package is part of the RECON
(<https://www.repidemicsconsortium.org/>) toolkit for outbreak analysis.
Author: Tim Taylor [aut, cre]
Maintainer: Tim Taylor <tim.taylor@hiddenelephants.co.uk>
Diff between grates versions 0.3.0 dated 2021-10-21 and 0.3.1 dated 2022-11-10
grates-0.3.0/grates/tests/testthat/test-accessors.R |only grates-0.3.1/grates/DESCRIPTION | 10 grates-0.3.1/grates/MD5 | 69 +-- grates-0.3.1/grates/NEWS.md | 8 grates-0.3.1/grates/R/int_period.R | 2 grates-0.3.1/grates/R/month.R | 2 grates-0.3.1/grates/R/period.R | 2 grates-0.3.1/grates/R/quarter.R | 2 grates-0.3.1/grates/R/year.R | 2 grates-0.3.1/grates/R/yearweek.R | 4 grates-0.3.1/grates/README.md | 16 grates-0.3.1/grates/build/vignette.rds |binary grates-0.3.1/grates/inst/doc/introduction.html | 201 +++++----- grates-0.3.1/grates/man/as_yearweek.Rd | 6 grates-0.3.1/grates/man/grates-package.Rd | 4 grates-0.3.1/grates/man/yearweek.Rd | 6 grates-0.3.1/grates/tests/testthat/_snaps/int_period.md | 19 grates-0.3.1/grates/tests/testthat/_snaps/month.md | 66 +-- grates-0.3.1/grates/tests/testthat/_snaps/period.md | 119 +++-- grates-0.3.1/grates/tests/testthat/_snaps/plots/month.png |binary grates-0.3.1/grates/tests/testthat/_snaps/plots/month2.png |binary grates-0.3.1/grates/tests/testthat/_snaps/plots/quarter.png |binary grates-0.3.1/grates/tests/testthat/_snaps/plots/twentyeight_days.png |binary grates-0.3.1/grates/tests/testthat/_snaps/plots/two_weeks.png |binary grates-0.3.1/grates/tests/testthat/_snaps/plots/year.png |binary grates-0.3.1/grates/tests/testthat/_snaps/plots/yearweek_monday.png |binary grates-0.3.1/grates/tests/testthat/_snaps/plots/yearweek_thursday.png |binary grates-0.3.1/grates/tests/testthat/_snaps/quarter.md | 20 grates-0.3.1/grates/tests/testthat/_snaps/year.md | 25 - grates-0.3.1/grates/tests/testthat/_snaps/yearweek.md | 111 ++--- grates-0.3.1/grates/tests/testthat/test-int_period.R | 6 grates-0.3.1/grates/tests/testthat/test-month.R | 16 grates-0.3.1/grates/tests/testthat/test-period.R | 6 grates-0.3.1/grates/tests/testthat/test-quarter.R | 12 grates-0.3.1/grates/tests/testthat/test-year.R | 6 grates-0.3.1/grates/tests/testthat/test-yearweek.R | 6 36 files changed, 420 insertions(+), 326 deletions(-)
Title: Privacy Preserving Record Linkage
Description: A toolbox for deterministic, probabilistic and privacy-preserving record linkage techniques. Combines the functionality of the 'Merge ToolBox' (<https://www.record-linkage.de>) with current privacy-preserving techniques.
Author: Rainer Schnell [aut, cph],
Dorothea Rukasz [aut, cre],
Christian Borgs [ctb],
Stefan Brumme [ctb] ,
William B. Brogden [ctb] ,
Tim O'Brien [ctb] ,
Stephen Lacy [ctb] ,
Apache Software Foundation [cph]
Maintainer: Dorothea Rukasz <mitarbeiter.schnell@uni-due.de>
Diff between PPRL versions 0.3.7 dated 2022-09-05 and 0.3.8 dated 2022-11-10
DESCRIPTION | 8 +- MD5 | 4 - src/Standardisation.cpp | 151 +++++++++++++++++++++++++++--------------------- 3 files changed, 92 insertions(+), 71 deletions(-)
Title: Quantitative Analysis of Mass Spectrometry Data
Description: A complete analysis pipeline for matrix-assisted laser
desorption/ionization-time-of-flight (MALDI-TOF) and other
two-dimensional mass spectrometry data. In addition to commonly
used plotting and processing methods it includes distinctive
features, namely baseline subtraction methods such as
morphological filters (TopHat) or the statistics-sensitive
non-linear iterative peak-clipping algorithm (SNIP), peak
alignment using warping functions, handling of replicated
measurements as well as allowing spectra with different
resolutions.
Author: Sebastian Gibb [aut, cre] ,
Korbinian Strimmer [ths] ,
Sigurdur Smarason [ctb],
Laurent Gatto [ctb] ,
Paolo Inglese [ctb]
Maintainer: Sebastian Gibb <mail@sebastiangibb.de>
Diff between MALDIquant versions 1.21 dated 2021-12-23 and 1.22 dated 2022-11-10
DESCRIPTION | 14 ++++++------- MD5 | 17 ++++++++-------- NEWS | 19 ++++++++++++++++-- R/merge-functions.R | 16 ++++++++------- build/partial.rdb |only build/vignette.rds |binary inst/doc/MALDIquant-intro.pdf |binary man/fiedler2009subset.Rd | 4 +-- man/msiSlices-functions.Rd | 2 - tests/testthat/test_averageMassSpectra-functions.R | 22 +++++++++++++++++++++ 10 files changed, 67 insertions(+), 27 deletions(-)
Title: A Package for Graphical Modelling in R
Description: The 'gRbase' package provides graphical modelling features
used by e.g. the packages 'gRain', 'gRim' and 'gRc'. 'gRbase' implements
graph algorithms including (i) maximum cardinality search (for marked
and unmarked graphs).
(ii) moralization, (iii) triangulation, (iv) creation of junction tree.
'gRbase' facilitates array operations,
'gRbase' implements functions for testing for conditional independence.
'gRbase' illustrates how hierarchical log-linear models may be
implemented and describes concept of graphical meta
data.
The facilities of the package are documented in the book by Højsgaard,
Edwards and Lauritzen (2012,
<doi:10.1007/978-1-4614-2299-0>) and in the paper by
Dethlefsen and Højsgaard, (2005, <doi:10.18637/jss.v014.i17>).
Please see 'citation("gRbase")' for citation details.
NOTICE 'gRbase' requires that the packages graph,
'Rgraphviz' and 'RBGL' are installed from 'bioconductor'. For
installation instructions please refer to the web page given below.
Author: Soeren Hoejsgaard <sorenh@math.aau.dk>
Maintainer: Soeren Hoejsgaard <sorenh@math.aau.dk>
Diff between gRbase versions 1.8.8 dated 2022-10-18 and 1.8.9 dated 2022-11-10
DESCRIPTION | 9 +-- MD5 | 22 +++---- NEWS | 11 +++ R/api_array_tab-create.R | 140 ++++++++++++++++++++++++++++++++--------------- R/api_array_tabX.R | 8 ++ README.md | 8 +- build/vignette.rds |binary inst/doc/arrays.pdf |binary inst/doc/graphs.pdf |binary man/api-tabNew.Rd | 35 +++++------ src/_u_rowsums_etc.c | 2 src/api_array_tab_X.cpp | 10 +-- 12 files changed, 158 insertions(+), 87 deletions(-)
Title: The Full Bayesian Evidence Test, Full Bayesian Significance Test
and the e-Value
Description: Provides access to a range of functions for computing and visualizing the Full Bayesian Significance Test (FBST) and the e-value for testing a sharp hypothesis against its alternative, and the Full Bayesian Evidence Test (FBET) and the (generalized) Bayesian evidence value for testing a composite (or interval) hypothesis against its alternative. The methods are widely applicable as long as a posterior MCMC sample is available.
Author: Riko Kelter
Maintainer: Riko Kelter <riko.kelter@uni-siegen.de>
Diff between fbst versions 1.9 dated 2022-09-23 and 2.1 dated 2022-11-10
fbst-1.9/fbst/vignettes/twodimfbst_files |only fbst-2.1/fbst/DESCRIPTION | 8 fbst-2.1/fbst/MD5 | 26 fbst-2.1/fbst/R/fbst.R | 255 ++++---- fbst-2.1/fbst/build/partial.rdb |binary fbst-2.1/fbst/build/vignette.rds |binary fbst-2.1/fbst/inst/doc/fbet.R | 20 fbst-2.1/fbst/inst/doc/fbet.Rmd | 49 - fbst-2.1/fbst/inst/doc/fbet.html | 908 ++++++++++++++++--------------- fbst-2.1/fbst/inst/doc/fbst.html | 735 ++++++++++++++----------- fbst-2.1/fbst/inst/doc/twodimfbst.html | 866 ++++++++++++++++------------- fbst-2.1/fbst/man/fbet.Rd | 19 fbst-2.1/fbst/man/plot.fbst.Rd | 16 fbst-2.1/fbst/vignettes/fbet.Rmd | 49 - 14 files changed, 1661 insertions(+), 1290 deletions(-)
Title: Efficient Phylogenetics on Large Trees
Description: Efficient phylogenetic analyses on massive phylogenies comprising up to millions of tips. Functions include pruning, rerooting, calculation of most-recent common ancestors, calculating distances from the tree root and calculating pairwise distances. Calculation of phylogenetic signal and mean trait depth (trait conservatism), ancestral state reconstruction and hidden character prediction of discrete characters, simulating and fitting models of trait evolution, fitting and simulating diversification models, dating trees, comparing trees, and reading/writing trees in Newick format. Citation: Louca, Stilianos and Doebeli, Michael (2017) <doi:10.1093/bioinformatics/btx701>.
Author: Stilianos Louca
Maintainer: Stilianos Louca <louca@zoology.ubc.ca>
Diff between castor versions 1.7.4 dated 2022-10-22 and 1.7.5 dated 2022-11-10
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/get_trait_acf.R | 2 +- R/pick_random_tips.R | 5 +++-- R/simulate_mk_model.R | 10 ++++++++-- man/geographic_acf.Rd | 6 +++++- man/get_trait_acf.Rd | 11 +++++++---- src/phylogenetics_cpp_routines.cpp | 11 ++++++----- 8 files changed, 41 insertions(+), 26 deletions(-)
Title: Query the 'UniProtKB' REST API
Description: Retrieve protein information from
the 'UniProtKB' REST API (see <https://www.uniprot.org/help/api_queries>).
Author: Guillaume Voisinne [aut, cre]
Maintainer: Guillaume Voisinne <voisinne@gmail.com>
Diff between queryup versions 1.0.0 dated 2022-09-12 and 1.0.1 dated 2022-11-10
DESCRIPTION | 6 ++-- MD5 | 16 ++++++------ NEWS.md | 5 +++ R/query_uniprot.R | 5 ++- README.md | 44 ++++++++++++++++++++++++--------- inst/doc/queryup.html | 25 +++++++++++------- man/query_uniprot.Rd | 2 - tests/testthat/test-get_uniprot_data.R | 6 +++- tests/testthat/test-query_uniprot.R | 4 +-- 9 files changed, 73 insertions(+), 40 deletions(-)
Title: Retrieve and Plot Google n-Gram Data
Description: Retrieve and plot word frequencies through time from the "Google
Ngram Viewer" <https://books.google.com/ngrams>.
Author: Sean Carmody [aut, cre, cph]
Maintainer: Sean Carmody <seancarmody@gmail.com>
Diff between ngramr versions 1.9.0 dated 2022-10-07 and 1.9.1 dated 2022-11-10
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 4 ++++ R/ngram.R | 12 +++++------- 4 files changed, 16 insertions(+), 14 deletions(-)
Title: Statistical Analysis of Contingency Tables
Description: Provides functions to perform statistical inference of data organized in contingency tables. This package is a companion to the "Statistical Analysis of Contingency Tables" book by Fagerland et al. <ISBN 9781466588172>.
Author: Morten Wang Fagerland [aut],
Stian Lydersen [ctb],
Petter Laake [ctb],
Waldir Leoncio [cre],
Ole Christian Lingjærde [trl]
Maintainer: Waldir Leoncio <w.l.netto@medisin.uio.no>
Diff between contingencytables versions 1.0.2 dated 2022-06-07 and 1.0.3 dated 2022-11-10
DESCRIPTION | 10 +++--- MD5 | 11 +++---- NAMESPACE | 1 R/Chacko_test_1xc.R | 66 +++++++++++++++++++++++++----------------- man/Chacko_test_1xc.Rd | 18 ++++++++--- tests/testthat/test-ch3.R | 2 - tests/testthat/test-issue36.R |only 7 files changed, 67 insertions(+), 41 deletions(-)
More information about contingencytables at CRAN
Permanent link
Title: Graphical Elements of the University of Konstanz's Corporate
Design
Description: Define and use graphical elements of corporate design manuals in R. The 'unikn' package provides color functions (by defining dedicated colors and color palettes, and commands for finding, changing, viewing, and using them) and styled text elements (e.g., for marking, underlining, or plotting colored titles). The pre-defined range of colors and text decoration functions is based on the corporate design of the University of Konstanz <https://www.uni-konstanz.de/>, but can be adapted and extended for other purposes or institutions.
Author: Hansjoerg Neth [aut, cre] ,
Nico Gradwohl [aut]
Maintainer: Hansjoerg Neth <h.neth@uni.kn>
Diff between unikn versions 0.6.0 dated 2022-09-20 and 0.7.0 dated 2022-11-10
unikn-0.6.0/unikn/R/color_util.R |only unikn-0.6.0/unikn/R/plot_util.R |only unikn-0.6.0/unikn/inst/pix/README-col-scale-1-1.png |only unikn-0.6.0/unikn/inst/pix/README-col-scale-2-1.png |only unikn-0.6.0/unikn/inst/pix/README-col-scale-3-1.png |only unikn-0.6.0/unikn/inst/pix/README-compare-custom-pals-1.png |only unikn-0.6.0/unikn/inst/pix/README-heading-demo-2-1.png |only unikn-0.6.0/unikn/inst/pix/README-mpg-use-pal-1.png |only unikn-0.6.0/unikn/inst/pix/README-pal_all-1.png |only unikn-0.6.0/unikn/inst/pix/README-pal_unikn-1.png |only unikn-0.6.0/unikn/inst/pix/README-uni-freiburg-seecol-1.png |only unikn-0.6.0/unikn/inst/pix/README-uni-princeton-demopal-1.png |only unikn-0.6.0/unikn/inst/pix/README-use-pal-demo-image-1.png |only unikn-0.6.0/unikn/inst/pix/README-use-pal-ggplot2-1.png |only unikn-0.6.0/unikn/inst/pix/README-use_ggplot2_princeton-1.png |only unikn-0.6.0/unikn/inst/pix/README-use_pal_ggplot2-1.png |only unikn-0.6.0/unikn/inst/pix/README-usepal-demo-barplot-1-1.png |only unikn-0.6.0/unikn/inst/pix/README-usepal-demo-barplot-2-1.png |only unikn-0.6.0/unikn/inst/pix/README-usepal-demo-scatter-1.png |only unikn-0.7.0/unikn/DESCRIPTION | 21 unikn-0.7.0/unikn/MD5 | 185 +- unikn-0.7.0/unikn/NAMESPACE | 14 unikn-0.7.0/unikn/NEWS.md | 134 + unikn-0.7.0/unikn/R/add_pals.R |only unikn-0.7.0/unikn/R/color_def_1.R | 147 + unikn-0.7.0/unikn/R/color_def_2.R | 42 unikn-0.7.0/unikn/R/color_fun_1.R | 575 ++++--- unikn-0.7.0/unikn/R/color_fun_2.R | 183 +- unikn-0.7.0/unikn/R/plot_demo.R | 364 +++- unikn-0.7.0/unikn/R/start_unikn.R | 4 unikn-0.7.0/unikn/R/util.R |only unikn-0.7.0/unikn/R/util_color.R |only unikn-0.7.0/unikn/R/util_plot.R |only unikn-0.7.0/unikn/README.md | 804 ++++------ unikn-0.7.0/unikn/build/partial.rdb |only unikn-0.7.0/unikn/inst/CITATION | 10 unikn-0.7.0/unikn/inst/doc/color_inst.R | 115 - unikn-0.7.0/unikn/inst/doc/color_inst.Rmd | 212 +- unikn-0.7.0/unikn/inst/doc/color_inst.html | 234 +- unikn-0.7.0/unikn/inst/doc/color_recipes.R | 39 unikn-0.7.0/unikn/inst/doc/color_recipes.Rmd | 64 unikn-0.7.0/unikn/inst/doc/color_recipes.html | 137 - unikn-0.7.0/unikn/inst/doc/colors.R | 79 unikn-0.7.0/unikn/inst/doc/colors.Rmd | 215 +- unikn-0.7.0/unikn/inst/doc/colors.html | 333 ++-- unikn-0.7.0/unikn/inst/doc/text.R | 135 - unikn-0.7.0/unikn/inst/doc/text.Rmd | 59 unikn-0.7.0/unikn/inst/doc/text.html | 69 unikn-0.7.0/unikn/inst/pix/README-demopal-1.png |only unikn-0.7.0/unikn/inst/pix/README-grepal-example-1-1.png |binary unikn-0.7.0/unikn/inst/pix/README-grepal-example-2-1.png |binary unikn-0.7.0/unikn/inst/pix/README-newpal-google-1.png |binary unikn-0.7.0/unikn/inst/pix/README-others-google-1.png |binary unikn-0.7.0/unikn/inst/pix/README-pal-all-1.png |binary unikn-0.7.0/unikn/inst/pix/README-pal-n-1.png |binary unikn-0.7.0/unikn/inst/pix/README-pal-unikn-1.png |binary unikn-0.7.0/unikn/inst/pix/README-pal-unikn-pref-1.png |only unikn-0.7.0/unikn/inst/pix/README-seecol-add-pals-1.png |only unikn-0.7.0/unikn/inst/pix/README-seecol-pref-1.png |binary unikn-0.7.0/unikn/inst/pix/README-simcol-example-1.png |only unikn-0.7.0/unikn/inst/pix/README-uline-demo-1.png |binary unikn-0.7.0/unikn/inst/pix/README-usecol-1-1.png |only unikn-0.7.0/unikn/inst/pix/README-usecol-2-1.png |only unikn-0.7.0/unikn/inst/pix/README-usecol-ggplot2-1.png |only unikn-0.7.0/unikn/inst/pix/logo_freiburg_2023.png |only unikn-0.7.0/unikn/man/Bordeaux.Rd | 4 unikn-0.7.0/unikn/man/Grau.Rd | 4 unikn-0.7.0/unikn/man/Karpfenblau.Rd | 4 unikn-0.7.0/unikn/man/Peach.Rd | 3 unikn-0.7.0/unikn/man/Petrol.Rd | 4 unikn-0.7.0/unikn/man/Pinky.Rd | 4 unikn-0.7.0/unikn/man/Seeblau.Rd | 4 unikn-0.7.0/unikn/man/Seegruen.Rd | 4 unikn-0.7.0/unikn/man/Signal.Rd | 4 unikn-0.7.0/unikn/man/all_colors.Rd | 6 unikn-0.7.0/unikn/man/demopal.Rd | 15 unikn-0.7.0/unikn/man/eth_pal.Rd |only unikn-0.7.0/unikn/man/eth_pal_grey.Rd |only unikn-0.7.0/unikn/man/eth_pal_light.Rd |only unikn-0.7.0/unikn/man/grepal.Rd | 2 unikn-0.7.0/unikn/man/mpg_pal.Rd |only unikn-0.7.0/unikn/man/newpal.Rd | 32 unikn-0.7.0/unikn/man/pal_bordeaux.Rd | 3 unikn-0.7.0/unikn/man/pal_grau.Rd | 4 unikn-0.7.0/unikn/man/pal_karpfenblau.Rd | 3 unikn-0.7.0/unikn/man/pal_peach.Rd | 4 unikn-0.7.0/unikn/man/pal_petrol.Rd | 4 unikn-0.7.0/unikn/man/pal_pinky.Rd | 4 unikn-0.7.0/unikn/man/pal_seeblau.Rd | 4 unikn-0.7.0/unikn/man/pal_seegruen.Rd | 4 unikn-0.7.0/unikn/man/pal_signal.Rd | 3 unikn-0.7.0/unikn/man/pal_unikn.Rd | 7 unikn-0.7.0/unikn/man/pal_unikn_dark.Rd | 7 unikn-0.7.0/unikn/man/pal_unikn_light.Rd | 7 unikn-0.7.0/unikn/man/pal_unikn_pair.Rd | 7 unikn-0.7.0/unikn/man/pal_unikn_ppt.Rd | 4 unikn-0.7.0/unikn/man/pal_unikn_pref.Rd | 7 unikn-0.7.0/unikn/man/pal_unikn_web.Rd | 4 unikn-0.7.0/unikn/man/seecol.Rd | 16 unikn-0.7.0/unikn/man/shades_of.Rd | 2 unikn-0.7.0/unikn/man/simcol.Rd | 11 unikn-0.7.0/unikn/man/uni_freiburg_blue.Rd |only unikn-0.7.0/unikn/man/uni_freiburg_br.Rd |only unikn-0.7.0/unikn/man/uni_freiburg_grey.Rd |only unikn-0.7.0/unikn/man/uni_freiburg_info.Rd |only unikn-0.7.0/unikn/man/uni_konstanz.Rd |only unikn-0.7.0/unikn/man/uni_konstanz_pref.Rd |only unikn-0.7.0/unikn/man/uni_princeton_0.Rd |only unikn-0.7.0/unikn/man/uni_princeton_1.Rd |only unikn-0.7.0/unikn/man/uni_princeton_2.Rd |only unikn-0.7.0/unikn/man/url_unikn.Rd | 2 unikn-0.7.0/unikn/man/usecol.Rd | 2 unikn-0.7.0/unikn/vignettes/color_inst.Rmd | 212 +- unikn-0.7.0/unikn/vignettes/color_recipes.Rmd | 64 unikn-0.7.0/unikn/vignettes/colors.Rmd | 215 +- unikn-0.7.0/unikn/vignettes/text.Rmd | 59 116 files changed, 2862 insertions(+), 2061 deletions(-)