Title: Tidy Messy Data
Description: Tools to help to create tidy data, where each column is a
variable, each row is an observation, and each cell contains a single value.
'tidyr' contains tools for changing the shape (pivoting) and hierarchy
(nesting and 'unnesting') of a dataset, turning deeply nested lists
into rectangular data frames ('rectangling'), and extracting values out
of string columns. It also includes tools for working with missing values
(both implicit and explicit).
Author: Hadley Wickham [aut, cre],
Lionel Henry [aut],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between tidyr versions 0.8.3 dated 2019-03-01 and 1.0.0 dated 2019-09-11
tidyr-0.8.3/tidyr/R/unnest.R |only tidyr-0.8.3/tidyr/demo |only tidyr-0.8.3/tidyr/man/unnest.Rd |only tidyr-0.8.3/tidyr/tests/testthat/test-underscored.R |only tidyr-0.8.3/tidyr/tests/testthat/test-unnest.R |only tidyr-0.8.3/tidyr/vignettes/billboard.csv |only tidyr-0.8.3/tidyr/vignettes/pew.csv |only tidyr-1.0.0/tidyr/DESCRIPTION | 28 tidyr-1.0.0/tidyr/MD5 | 186 ++- tidyr-1.0.0/tidyr/NAMESPACE | 50 tidyr-1.0.0/tidyr/NEWS.md | 150 ++ tidyr-1.0.0/tidyr/R/chop.R |only tidyr-1.0.0/tidyr/R/complete.R | 4 tidyr-1.0.0/tidyr/R/data.R | 101 + tidyr-1.0.0/tidyr/R/dep-lazyeval.R | 46 tidyr-1.0.0/tidyr/R/drop-na.R | 3 tidyr-1.0.0/tidyr/R/expand.R | 185 ++- tidyr-1.0.0/tidyr/R/extract.R | 45 tidyr-1.0.0/tidyr/R/fill.R | 42 tidyr-1.0.0/tidyr/R/gather.R | 20 tidyr-1.0.0/tidyr/R/nest-legacy.R |only tidyr-1.0.0/tidyr/R/nest.R | 379 +++++- tidyr-1.0.0/tidyr/R/pack.R |only tidyr-1.0.0/tidyr/R/pivot-long.R |only tidyr-1.0.0/tidyr/R/pivot-wide.R |only tidyr-1.0.0/tidyr/R/pivot.R |only tidyr-1.0.0/tidyr/R/rectangle.R |only tidyr-1.0.0/tidyr/R/replace_na.R | 1 tidyr-1.0.0/tidyr/R/separate-rows.R | 31 tidyr-1.0.0/tidyr/R/separate.R | 41 tidyr-1.0.0/tidyr/R/seq.R | 11 tidyr-1.0.0/tidyr/R/spread.R | 16 tidyr-1.0.0/tidyr/R/tidyr.R | 43 tidyr-1.0.0/tidyr/R/uncount.R | 2 tidyr-1.0.0/tidyr/R/unite.R | 39 tidyr-1.0.0/tidyr/R/utils.R | 89 + tidyr-1.0.0/tidyr/README.md | 65 - tidyr-1.0.0/tidyr/build/tidyr.pdf |only tidyr-1.0.0/tidyr/build/vignette.rds |binary tidyr-1.0.0/tidyr/data/billboard.rda |only tidyr-1.0.0/tidyr/data/construction.rda |only tidyr-1.0.0/tidyr/data/fish_encounters.rda |only tidyr-1.0.0/tidyr/data/relig_income.rda |only tidyr-1.0.0/tidyr/data/us_rent_income.rda |only tidyr-1.0.0/tidyr/data/world_bank_pop.rda |only tidyr-1.0.0/tidyr/inst/doc/in-packages.R |only tidyr-1.0.0/tidyr/inst/doc/in-packages.Rmd |only tidyr-1.0.0/tidyr/inst/doc/in-packages.html |only tidyr-1.0.0/tidyr/inst/doc/nest.R |only tidyr-1.0.0/tidyr/inst/doc/nest.Rmd |only tidyr-1.0.0/tidyr/inst/doc/nest.html |only tidyr-1.0.0/tidyr/inst/doc/pivot.R |only tidyr-1.0.0/tidyr/inst/doc/pivot.Rmd |only tidyr-1.0.0/tidyr/inst/doc/pivot.html |only tidyr-1.0.0/tidyr/inst/doc/rectangle.R |only tidyr-1.0.0/tidyr/inst/doc/rectangle.Rmd |only tidyr-1.0.0/tidyr/inst/doc/rectangle.html |only tidyr-1.0.0/tidyr/inst/doc/tidy-data.R | 11 tidyr-1.0.0/tidyr/inst/doc/tidy-data.Rmd | 21 tidyr-1.0.0/tidyr/inst/doc/tidy-data.html | 684 +++++------- tidyr-1.0.0/tidyr/man/billboard.Rd |only tidyr-1.0.0/tidyr/man/chop.Rd |only tidyr-1.0.0/tidyr/man/complete.Rd | 2 tidyr-1.0.0/tidyr/man/construction.Rd |only tidyr-1.0.0/tidyr/man/deprecated-se.Rd | 45 tidyr-1.0.0/tidyr/man/expand.Rd | 17 tidyr-1.0.0/tidyr/man/expand_grid.Rd |only tidyr-1.0.0/tidyr/man/extract.Rd | 19 tidyr-1.0.0/tidyr/man/figures/lifecycle-archived.svg |only tidyr-1.0.0/tidyr/man/figures/lifecycle-defunct.svg |only tidyr-1.0.0/tidyr/man/figures/lifecycle-deprecated.svg |only tidyr-1.0.0/tidyr/man/figures/lifecycle-experimental.svg |only tidyr-1.0.0/tidyr/man/figures/lifecycle-maturing.svg |only tidyr-1.0.0/tidyr/man/figures/lifecycle-questioning.svg |only tidyr-1.0.0/tidyr/man/figures/lifecycle-retired.svg |only tidyr-1.0.0/tidyr/man/figures/lifecycle-soft-deprecated.svg |only tidyr-1.0.0/tidyr/man/figures/lifecycle-stable.svg |only tidyr-1.0.0/tidyr/man/fill.Rd | 16 tidyr-1.0.0/tidyr/man/fish_encounters.Rd |only tidyr-1.0.0/tidyr/man/full_seq.Rd | 2 tidyr-1.0.0/tidyr/man/gather.Rd | 16 tidyr-1.0.0/tidyr/man/hoist.Rd |only tidyr-1.0.0/tidyr/man/nest.Rd | 213 ++- tidyr-1.0.0/tidyr/man/nest_legacy.Rd |only tidyr-1.0.0/tidyr/man/pack.Rd |only tidyr-1.0.0/tidyr/man/pivot_longer.Rd |only tidyr-1.0.0/tidyr/man/pivot_longer_spec.Rd |only tidyr-1.0.0/tidyr/man/pivot_wider.Rd |only tidyr-1.0.0/tidyr/man/pivot_wider_spec.Rd |only tidyr-1.0.0/tidyr/man/reexports.Rd |only tidyr-1.0.0/tidyr/man/relig_income.Rd |only tidyr-1.0.0/tidyr/man/separate.Rd | 7 tidyr-1.0.0/tidyr/man/separate_rows.Rd | 3 tidyr-1.0.0/tidyr/man/smiths.Rd | 2 tidyr-1.0.0/tidyr/man/spread.Rd | 12 tidyr-1.0.0/tidyr/man/table1.Rd | 2 tidyr-1.0.0/tidyr/man/tidyr-package.Rd | 14 tidyr-1.0.0/tidyr/man/tidyr_legacy.Rd |only tidyr-1.0.0/tidyr/man/uncount.Rd | 2 tidyr-1.0.0/tidyr/man/unite.Rd | 24 tidyr-1.0.0/tidyr/man/us_rent_income.Rd |only tidyr-1.0.0/tidyr/man/who.Rd | 2 tidyr-1.0.0/tidyr/man/world_bank_pop.Rd |only tidyr-1.0.0/tidyr/src/melt.cpp | 22 tidyr-1.0.0/tidyr/tests/testthat/test-chop.R |only tidyr-1.0.0/tidyr/tests/testthat/test-complete.R | 10 tidyr-1.0.0/tidyr/tests/testthat/test-drop-na.R | 2 tidyr-1.0.0/tidyr/tests/testthat/test-expand.R | 56 tidyr-1.0.0/tidyr/tests/testthat/test-extract.R | 6 tidyr-1.0.0/tidyr/tests/testthat/test-fill.R | 19 tidyr-1.0.0/tidyr/tests/testthat/test-full_seq.R | 9 tidyr-1.0.0/tidyr/tests/testthat/test-gather.R | 11 tidyr-1.0.0/tidyr/tests/testthat/test-nest-legacy.R |only tidyr-1.0.0/tidyr/tests/testthat/test-nest.R | 276 ++++ tidyr-1.0.0/tidyr/tests/testthat/test-pack.R |only tidyr-1.0.0/tidyr/tests/testthat/test-pivot-long.R |only tidyr-1.0.0/tidyr/tests/testthat/test-pivot-wide.R |only tidyr-1.0.0/tidyr/tests/testthat/test-pivot.R |only tidyr-1.0.0/tidyr/tests/testthat/test-rectangle.R |only tidyr-1.0.0/tidyr/tests/testthat/test-separate-rows.R | 2 tidyr-1.0.0/tidyr/tests/testthat/test-unite.R | 8 tidyr-1.0.0/tidyr/tests/testthat/test-utils.R |only tidyr-1.0.0/tidyr/vignettes/in-packages.Rmd |only tidyr-1.0.0/tidyr/vignettes/nest.Rmd |only tidyr-1.0.0/tidyr/vignettes/pivot.Rmd |only tidyr-1.0.0/tidyr/vignettes/rectangle.Rmd |only tidyr-1.0.0/tidyr/vignettes/tidy-data.Rmd | 21 127 files changed, 2182 insertions(+), 951 deletions(-)
Title: A Set of Tools that Enhance Reproducibility Beyond Package
Management
Description: Collection of high-level, robust, machine- and OS-independent tools
for making deeply reproducible and reusable content in R.
This includes light weight package management (similar to 'packrat' and
'checkpoint', but more flexible, lightweight, simpler yet less tested than both),
tools for caching, downloading and verifying or writing checksums, post-processing
of common spatial datasets, and accessing GitHub repositories.
Some features are still under active development.
Author: Eliot J B McIntire [aut, cre] (<https://orcid.org/0000-0002-6914-8316>),
Alex M Chubaty [aut] (<https://orcid.org/0000-0001-7146-8135>),
Tati Micheletti [ctb] (<https://orcid.org/0000-0003-4838-8342>),
Ceres Barros [ctb] (<https://orcid.org/0000-0003-4036-977X>),
Ian Eddy [ctb] (<https://orcid.org/0000-0001-7397-2116>),
Her Majesty the Queen in Right of Canada, as represented by the
Minister of Natural Resources Canada [cph]
Maintainer: Eliot J B McIntire <eliot.mcintire@canada.ca>
Diff between reproducible versions 0.2.9 dated 2019-07-09 and 0.2.10 dated 2019-09-11
DESCRIPTION | 14 MD5 | 103 - NAMESPACE | 4 NEWS.md | 49 R/cache-helpers.R | 23 R/cache-tools.R | 57 R/cache.R | 88 - R/checksums.R | 1 R/cloud.R | 45 R/convertPaths.R | 27 R/download.R | 22 R/helpers.R | 53 R/objectSize.R | 164 ++ R/packages.R | 230 ++- R/postProcess.R | 82 - R/preProcess.R | 63 R/prepInputs.R | 22 R/robustDigest.R | 4 R/zzz.R | 12 build/vignette.rds |binary inst/WORDLIST | 9 inst/doc/Intro-to-Cache.html | 2484 +++++++++++++++++++----------------- inst/examples/example_postProcess.R | 2 man/Filenames.Rd | 11 man/cache-helpers.Rd | 7 man/cache.Rd | 23 man/checkAndMakeCloudFolderID.Rd | 2 man/cloudDownload.Rd | 9 man/cloudSyncCacheOld.Rd | 9 man/cloudUpload.Rd | 9 man/cloudUploadFromCache.Rd | 21 man/cropInputs.Rd | 2 man/determineFilename.Rd | 2 man/dot-removeCacheAtts.Rd | 4 man/fastMask.Rd | 2 man/fixErrors.Rd | 2 man/grepSysCalls.Rd | 4 man/listFilesInArchive.Rd | 4 man/maskInputs.Rd | 2 man/objSize.Rd | 86 + man/pkgDep.Rd | 24 man/pkgEnv.Rd |only man/postProcess.Rd | 7 man/preProcess.Rd | 3 man/prepInputs.Rd | 3 man/prepareFileBackedRaster.Rd | 1 man/projectInputs.Rd | 4 man/retry.Rd | 16 man/viewCache.Rd | 11 man/writeOutputs.Rd | 2 tests/testthat/helper-allEqual.R | 55 tests/testthat/test-packages.R | 108 + tests/testthat/test-prepInputs.R | 1027 +++++++++----- 53 files changed, 3028 insertions(+), 1990 deletions(-)
Title: Fine-Gray Regression via Forward-Backward Scan
Description: In competing risks regression, the proportional subdistribution hazards (PSH) model is popular for its direct assessment of covariate effects on the cumulative incidence function. This package allows for both penalized and unpenalized PSH regression in linear time using a novel forward-backward scan. Penalties include Ridge, Lease Absolute Shrinkage and Selection Operator (LASSO), Smoothly Clipped Absolute Deviation (SCAD), Minimax Concave Plus (MCP), and elastic net.
Author: Eric S. Kawaguchi
Maintainer: Eric S. Kawaguchi <ekawaguc@usc.edu>
Diff between fastcmprsk versions 1.1.0 dated 2019-09-07 and 1.1.1 dated 2019-09-11
DESCRIPTION | 6 MD5 | 22 - src/denseElastic.c | 129 ++++------- src/denseFit.c | 507 ++++++++++++++++++++------------------------ src/densePen.c | 118 +++------- src/package_internal.c | 8 src/penalty.c | 9 src/sexp.c | 47 +++- src/utils.c | 58 ++--- src/utils.h | 1 tests/runs/test-ENET.R | 4 tests/runs/test-modelFits.R | 12 - 12 files changed, 434 insertions(+), 487 deletions(-)
Title: The Gaussian Covariate Method for Variable Selection
Description: Given the standard linear model the traditional way of deciding whether to include the jth covariate is to apply the F-test to decide whether the corresponding beta coefficient is zero. The Gaussian covariate method is completely different. The question as to whether the beta coefficient is or is not zero is replaced by the question as to whether the covariate is better or worse than i.i.d. Gaussian noise. The P-value for the covariate is the probability that Gaussian noise is better. Surprisingly this can be given exactly and it is the same a the P-value for the classical model based on the F-distribution. The Gaussian covariate P-value is model free, it is the same for any data set. Using the idea it is possible to do covariate selection for a small number of covariates 25 by considering all subsets. Post selection inference causes no problems as the P-values hold whatever the data. The idea extends to stepwise regression again with exact probabilities. In the simplest version the only parameter is a specified cut-off P-value which can be interpreted as the probability of a false positive being included in the final selection. For more information see the website below and the accompanying papers: L. Davies and L. Duembgen, "A Model-free Approach to Linear Least Squares Regression with Exact Probabilities and Applications to Covariate Selection", 2019, <arXiv:1906.01990>. L. Davies, "Lasso, Knockoff and Gaussian covariates: A comparison", 2018, <arXiv:1807.09633v4>.
Author: Laurie Davies [aut, cre]
Maintainer: Laurie Davies <laurie.davies@uni-due.de>
Diff between gausscov versions 0.0.1 dated 2019-06-18 and 0.0.2 dated 2019-09-11
gausscov-0.0.1/gausscov/data/gausscov.rda |only gausscov-0.0.2/gausscov/DESCRIPTION | 7 ++- gausscov-0.0.2/gausscov/MD5 | 50 +++++++++++++++------------ gausscov-0.0.2/gausscov/R/fgeninter.R | 2 - gausscov-0.0.2/gausscov/R/fgraphst.R | 1 gausscov-0.0.2/gausscov/R/fgraphstst.R | 1 gausscov-0.0.2/gausscov/R/flmmdch.R | 1 gausscov-0.0.2/gausscov/R/frobreg.R | 1 gausscov-0.0.2/gausscov/R/frobstepwise.R | 1 gausscov-0.0.2/gausscov/R/fstepstepwise.R | 2 + gausscov-0.0.2/gausscov/R/fstepwise.R | 2 + gausscov-0.0.2/gausscov/data/boston.rda |only gausscov-0.0.2/gausscov/data/colonx.rda |only gausscov-0.0.2/gausscov/data/colony.rda |only gausscov-0.0.2/gausscov/data/datalist | 10 ++++- gausscov-0.0.2/gausscov/data/leukemiax.rda |only gausscov-0.0.2/gausscov/data/leukemiay.rda |only gausscov-0.0.2/gausscov/data/prostatex.rda |only gausscov-0.0.2/gausscov/data/prostatey.rda |only gausscov-0.0.2/gausscov/data/redwine.rda |only gausscov-0.0.2/gausscov/data/stackloss.rda |only gausscov-0.0.2/gausscov/man/fgeninter.Rd | 2 - gausscov-0.0.2/gausscov/man/fgraphst.Rd | 2 - gausscov-0.0.2/gausscov/man/fgraphstst.Rd | 2 - gausscov-0.0.2/gausscov/man/flmmdch.Rd | 2 - gausscov-0.0.2/gausscov/man/frobreg.Rd | 2 - gausscov-0.0.2/gausscov/man/frobstepwise.Rd | 2 - gausscov-0.0.2/gausscov/man/fselect.Rd | 2 - gausscov-0.0.2/gausscov/man/fstepstepwise.Rd | 3 + gausscov-0.0.2/gausscov/man/fstepwise.Rd | 3 + gausscov-0.0.2/gausscov/src/gaucov.f | 20 +++++----- 31 files changed, 73 insertions(+), 45 deletions(-)
Title: Get Data Frame Representations of 'Elasticsearch' Results
Description: 'Elasticsearch' is an open-source, distributed, document-based datastore
(<https://www.elastic.co/products/elasticsearch>).
It provides an 'HTTP' 'API' for querying the database and extracting datasets, but that
'API' was not designed for common data science workflows like pulling large batches of
records and normalizing those documents into a data frame that can be used as a training
dataset for statistical models. 'uptasticsearch' provides an interface for 'Elasticsearch'
that is explicitly designed to make these data science workflows easy and fun.
Author: James Lamb [aut, cre],
Nick Paras [aut],
Austin Dickey [aut],
Michael Frasco [ctb],
Weiwen Gu [ctb],
Will Dearden [ctb],
Uptake Technologies Inc. [cph]
Maintainer: James Lamb <jaylamb20@gmail.com>
Diff between uptasticsearch versions 0.3.1 dated 2019-01-30 and 0.4.0 dated 2019-09-11
DESCRIPTION | 18 +-- MD5 | 22 ++- NEWS.md | 29 +++-- R/es_search.R | 8 + R/get_fields.R | 70 +++++++++++- README.md | 35 +++--- build/vignette.rds |binary inst/doc/FAQ.html | 9 + inst/testdata/es7_shakespeare_mapping.json |only inst/testdata/sample_es7.json |only man/es_search.Rd | 2 tests/testthat/test-get_fields.R | 17 +-- tests/testthat/test-integration.R | 160 +++++++++++++++-------------- 13 files changed, 232 insertions(+), 138 deletions(-)
More information about uptasticsearch at CRAN
Permanent link
Title: Simulation and Likelihood Calculation of Phylogenetic
Comparative Models
Description: Phylogenetic comparative methods represent models of continuous trait
data associated with the tips of a phylogenetic tree. Examples of such models
are Gaussian continuous time branching stochastic processes such as Brownian
motion (BM) and Ornstein-Uhlenbeck (OU) processes, which regard the data at the
tips of the tree as an observed (final) state of a Markov process starting from
an initial state at the root and evolving along the branches of the tree. The
PCMBase R package provides a general framework for manipulating such models.
This framework consists of an application programming interface for specifying
data and model parameters, and efficient algorithms for simulating trait evolution
under a model and calculating the likelihood of model parameters for an assumed
model and trait data. The package implements a growing collection of models,
which currently includes BM, OU, BM/OU with jumps, two-speed OU as well as mixed
Gaussian models, in which different types of the above models can be associated
with different branches of the tree. The PCMBase package is limited to
trait-simulation and likelihood calculation of (mixed) Gaussian phylogenetic
models. The PCMFit package provides functionality for ML and Bayesian fit of
these models to tree and trait data. The package web-site
<https://venelin.github.io/PCMBase/>
provides access to the documentation and other resources.
Author: Venelin Mitov [aut, cre, cph],
Krzysztof Bartoszek [ctb],
Georgios Asimomitis [ctb],
Tanja Stadler [ths]
Maintainer: Venelin Mitov <vmitov@gmail.com>
Diff between PCMBase versions 1.2.9 dated 2019-03-15 and 1.2.10 dated 2019-09-11
PCMBase-1.2.10/PCMBase/DESCRIPTION | 17 PCMBase-1.2.10/PCMBase/MD5 | 196 PCMBase-1.2.10/PCMBase/NAMESPACE | 698 PCMBase-1.2.10/PCMBase/NEWS.md | 16 PCMBase-1.2.10/PCMBase/R/AutoGeneratedModelTypes.R | 7908 +++++++++- PCMBase-1.2.10/PCMBase/R/BM.R | 16 PCMBase-1.2.10/PCMBase/R/BMdrift.R |only PCMBase-1.2.10/PCMBase/R/DOU.R | 14 PCMBase-1.2.10/PCMBase/R/DefaultModelTypes.R | 52 PCMBase-1.2.10/PCMBase/R/GaussianPCM.R | 478 PCMBase-1.2.10/PCMBase/R/JOU.R | 20 PCMBase-1.2.10/PCMBase/R/LatexTools.R |only PCMBase-1.2.10/PCMBase/R/MixedGaussian.R | 36 PCMBase-1.2.10/PCMBase/R/OU.R | 22 PCMBase-1.2.10/PCMBase/R/PCM.R | 381 PCMBase-1.2.10/PCMBase/R/PCMBaseTestObjects.R | 29 PCMBase-1.2.10/PCMBase/R/PCMParam.R | 304 PCMBase-1.2.10/PCMBase/R/PCMTable.R |only PCMBase-1.2.10/PCMBase/R/PCMTree.R | 193 PCMBase-1.2.10/PCMBase/R/Utilities.R | 110 PCMBase-1.2.10/PCMBase/R/White.R | 8 PCMBase-1.2.10/PCMBase/R/matrixparametrizations.R | 40 PCMBase-1.2.10/PCMBase/R/zzz.R | 17 PCMBase-1.2.10/PCMBase/README.md | 227 PCMBase-1.2.10/PCMBase/build/vignette.rds |binary PCMBase-1.2.10/PCMBase/data/PCMBaseTestObjects.rda |binary PCMBase-1.2.10/PCMBase/data/dataFig3.rda |only PCMBase-1.2.10/PCMBase/inst/CITATION | 20 PCMBase-1.2.10/PCMBase/inst/doc/PCMBase.R | 81 PCMBase-1.2.10/PCMBase/inst/doc/PCMBase.Rmd | 195 PCMBase-1.2.10/PCMBase/inst/doc/PCMBase.html | 812 - 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Title: A Statistically Sound 'data.frame' Processor/Conditioner
Description: A 'data.frame' processor/conditioner that prepares real-world data for predictive modeling in a statistically sound manner.
'vtreat' prepares variables so that data has fewer exceptional cases, making
it easier to safely use models in production. Common problems 'vtreat' defends
against: 'Inf', 'NA', too many categorical levels, rare categorical levels, and new
categorical levels (levels seen during application, but not during training). Reference:
"'vtreat': a data.frame Processor for Predictive Modeling", Zumel, Mount, 2016, <DOI:10.5281/zenodo.1173313>.
Author: John Mount [aut, cre],
Nina Zumel [aut],
Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>
Diff between vtreat versions 1.4.4 dated 2019-07-27 and 1.4.5 dated 2019-09-11
DESCRIPTION | 8 MD5 | 38 +- NEWS.md | 4 README.md | 109 +++++--- inst/doc/MultiClassVtreat.html | 10 inst/doc/SavingTreamentPlans.html | 10 inst/doc/VariableImportance.html | 16 - inst/doc/vtreat.R | 100 +++---- inst/doc/vtreat.Rmd | 450 +++++++++++++++++++++++++--------- inst/doc/vtreat.html | 493 ++++++++++++++++++++++---------------- inst/doc/vtreatCrossFrames.html | 44 +-- inst/doc/vtreatGrouping.html | 10 inst/doc/vtreatOverfit.html | 44 +-- inst/doc/vtreatRareLevels.html | 10 inst/doc/vtreatScaleMode.html | 22 + inst/doc/vtreatSignificance.html | 24 + inst/doc/vtreatSplitting.html | 10 inst/doc/vtreatVariableTypes.html | 48 ++- inst/doc/vtreat_article.pdf |binary vignettes/vtreat.Rmd | 450 +++++++++++++++++++++++++--------- 20 files changed, 1232 insertions(+), 668 deletions(-)
Title: Bootstrap Test for the Similarity of Dose Response Curves
Concerning the Maximum Absolute Deviation
Description: Provides a bootstrap test which decides whether two dose response curves can be assumed as equal concerning their maximum absolute deviation. A plenty of choices for the model types are available, which can be found in the 'DoseFinding' package, which is used for the fitting of the models. See <doi:10.1080/01621459.2017.1281813> for details.
Author: Kathrin Moellenhoff
Maintainer: Kathrin Moellenhoff <kathrin.moellenhoff@rub.de>
Diff between TestingSimilarity versions 1.0 dated 2015-09-16 and 1.1 dated 2019-09-11
DESCRIPTION | 19 +- MD5 | 30 +-- NAMESPACE | 22 +- R/DoseResponseModels.R | 202 +++++++++++------------ R/bootstrap_test.R | 413 ++++++++++++++++++++++++------------------------- R/dff.R | 26 +-- man/betaMod.Rd | 47 ++--- man/bootstrap_test.Rd | 84 +++++---- man/dff.Rd | 43 ++--- man/emax.Rd | 39 ++-- man/exponential.Rd | 39 ++-- man/linear.Rd | 39 ++-- man/linlog.Rd | 45 ++--- man/logistic.Rd | 39 ++-- man/quadratic.Rd | 39 ++-- man/sigEmax.Rd | 39 ++-- 16 files changed, 578 insertions(+), 587 deletions(-)
More information about TestingSimilarity at CRAN
Permanent link
Title: Fit Univariate Mixed and Usual Distributions
Description: Extends the fitdist() (from 'fitdistrplus') adding the Anderson-Darling ad.test() (from 'ADGofTest') and Kolmogorov Smirnov Test ks.test() inside, trying the distributions from 'stats' package by default and offering a second function which uses mixed distributions to fit, this distributions are split with unsupervised learning, with Mclust() function (from 'mclust').
Author: José Carlos Del Valle <jcval94@gmail.com>
Maintainer: José Carlos Del Valle <jcval94@gmail.com>
Diff between FitUltD versions 3.0.0 dated 2019-05-15 and 3.1.0 dated 2019-09-11
DESCRIPTION | 8 +- MD5 | 16 ++--- NEWS.md |only R/FDist.R | 113 +++++++++++++++++++++++------------- R/FDistUlt.R | 69 ++++++++++++++++----- README.md | 41 +++++-------- man/FDist.Rd | 29 +++++++-- man/FDistUlt.Rd | 35 +++++++---- man/figures/README-plots-mult-1.png |only man/figures/README-pressure-1.png |binary 10 files changed, 202 insertions(+), 109 deletions(-)
Title: Continuous Time Structural Equation Modelling
Description: Hierarchical continuous time state space modelling, for linear
and nonlinear systems measured by continuous variables, with limited support for
binary data. The subject specific dynamic system is modelled as a stochastic
differential equation (SDE), measurement models are typically multivariate normal factor models.
Using the original ctsem formulation based on OpenMx, described in the JSS paper
"Continuous Time Structural Equation Modeling with R Package ctsem", with updated version
as CRAN vignette <https://cran.r-project.org/web/packages/ctsem/vignettes/ctsem.pdf> ,
linear mixed effects SDE's estimated via maximum likelihood and optimization are possible.
Using the Stan based formulation, described in <https://github.com/cdriveraus/ctsem/raw/master/vignettes/hierarchicalmanual.pdf> ,
nonlinearity (state dependent parameters) and random effects on all parameters
are possible, using either optimization (with optional importance sampling) or
Stan's Hamiltonian Monte Carlo sampling. Priors may be used. For the conceptual
overview of the hierarchical Bayesian linear SDE approach, see <https://www.researchgate.net/publication/324093594_Hierarchical_Bayesian_Continuous_Time_Dynamic_Modeling>.
Exogenous inputs may also be included, for an overview of such possibilities see <https://www.researchgate.net/publication/328221807_Understanding_the_Time_Course_of_Interventions_with_Continuous_Time_Dynamic_Models> .
Stan based functions are not available on 32 bit Windows systems at present.
Author: Charles Driver [aut, cre, cph],
Manuel Voelkle [aut, cph],
Han Oud [aut, cph],
Trustees of Columbia University [cph]
Maintainer: Charles Driver <driver@mpib-berlin.mpg.de>
Diff between ctsem versions 3.0.1 dated 2019-08-23 and 3.0.3 dated 2019-09-11
ctsem-3.0.1/ctsem/man/ctKalmanPlot.Rd |only ctsem-3.0.3/ctsem/DESCRIPTION | 8 ctsem-3.0.3/ctsem/MD5 | 56 ctsem-3.0.3/ctsem/NAMESPACE | 4 ctsem-3.0.3/ctsem/NEWS | 7 ctsem-3.0.3/ctsem/R/ctDiscretePars.R | 8 ctsem-3.0.3/ctsem/R/ctKalman.R | 86 - ctsem-3.0.3/ctsem/R/ctStanFit.R | 304 ++--- ctsem-3.0.3/ctsem/R/ctStanGenerateFromFit.R | 6 ctsem-3.0.3/ctsem/R/ctStanKalman.R | 19 ctsem-3.0.3/ctsem/R/ctStanModelWriter.R | 218 ++- ctsem-3.0.3/ctsem/R/ctStanParMatrices.R | 2 ctsem-3.0.3/ctsem/R/ctStanProfileCI.R | 4 ctsem-3.0.3/ctsem/R/ctStanTIpredeffects.R | 22 ctsem-3.0.3/ctsem/R/ctsem.R | 4 ctsem-3.0.3/ctsem/R/ctsemUtils.R | 9 ctsem-3.0.3/ctsem/R/plot.ctStanFit.R | 3 ctsem-3.0.3/ctsem/R/stanoptimis.R | 1103 ++++++++++--------- ctsem-3.0.3/ctsem/data/ctstantestfit.rda |binary ctsem-3.0.3/ctsem/inst/CITATION | 25 ctsem-3.0.3/ctsem/inst/doc/ctsem.pdf |binary ctsem-3.0.3/ctsem/man/ctCollapse.Rd | 4 ctsem-3.0.3/ctsem/man/ctKalman.Rd | 9 ctsem-3.0.3/ctsem/man/ctStanFit.Rd | 299 ++--- ctsem-3.0.3/ctsem/man/ctStanGenerateFromFit.Rd | 2 ctsem-3.0.3/ctsem/man/plot.ctKalman.Rd |only ctsem-3.0.3/ctsem/man/stan_reinitsf.Rd |only ctsem-3.0.3/ctsem/man/standatact_specificsubjects.Rd |only ctsem-3.0.3/ctsem/man/stanoptimis.Rd | 2 ctsem-3.0.3/ctsem/src/stan_files/ctsm.stan | 164 +- ctsem-3.0.3/ctsem/src/stan_files/ctsmgen.stan | 211 ++- 31 files changed, 1446 insertions(+), 1133 deletions(-)
Title: Common Public Health Statistics and their Confidence Intervals
Description: Functions to calculate commonly used public health statistics and
their confidence intervals using methods approved for use in the production
of Public Health England indicators such as those presented via Fingertips
(<http://fingertips.phe.org.uk/>). It provides functions for the generation
of proportions, crude rates, means, directly standardised rates, indirectly
standardised rates, standardised mortality ratios, slope and relative index
of inequality and life expectancy.
Statistical methods are referenced in the following publications.
Breslow NE, Day NE (1987) <doi:10.1002/sim.4780080614>.
Dobson et al (1991) <doi:10.1002/sim.4780100317>.
Armitage P, Berry G (2002) <doi:10.1002/9780470773666>.
Wilson EB. (1927) <doi:10.1080/01621459.1927.10502953>.
Altman DG et al (2000, ISBN: 978-0-727-91375-3).
Chiang CL. (1968, ISBN: 978-0-882-75200-6).
Newell C. (1994, ISBN: 978-0-898-62451-9).
Eayres DP, Williams ES (2004) <doi:10.1136/jech.2003.009654>.
Silcocks PBS et al (2001) <doi:10.1136/jech.55.1.38>.
Low and Low (2004) <doi:10.1093/pubmed/fdh175>.
Author: Anderson Georgina [aut, cre],
Fox Sebastian [ctb],
Francis Matthew [ctb],
Fryers Paul [ctb],
Clegg Emma [ctb]
Maintainer: Anderson Georgina <georgina.anderson@phe.gov.uk>
Diff between PHEindicatormethods versions 1.1.3 dated 2019-05-15 and 1.1.5 dated 2019-09-11
DESCRIPTION | 8 MD5 | 24 NEWS.md | 8 R/LifeExpectancy.R | 3 R/SII_function.R | 259 ++--- README.md | 94 + build/vignette.rds |binary inst/doc/DSR-vignette.html | 456 ++++----- inst/doc/Introduction_to_PHEindicatormethods.Rmd | 2 inst/doc/Introduction_to_PHEindicatormethods.html | 1114 +++++++++++----------- inst/doc/WorkedExamples_phe_sii.html | 362 +++---- man/phe_sii.Rd | 4 vignettes/Introduction_to_PHEindicatormethods.Rmd | 2 13 files changed, 1227 insertions(+), 1109 deletions(-)
More information about PHEindicatormethods at CRAN
Permanent link
Title: Statistical Modelling with Applications in Forestry
Description: Developed for the following tasks. I) Computing the probability density function, cumulative distribution function, random generation, and estimating the parameters of the eleven mixture models including mixture of Birnbaum-Saunders, BurrXII, Chen, F, Frechet, gamma, Gompertz, log-logistic, log-normal, Lomax, and Weibull. II) Point estimation of the parameters of two- and three-parameter Weibull distributions. In the case of two-parameter, twelve methods consist of generalized least square type 1, generalized least square type 2, L-moment, maximum likelihood, logarithmic moment, moment, percentile, rank correlation, least square, weighted maximum likelihood, U-statistic, weighted least square are used and investigated methods for the three-parameter case are: maximum likelihood, modified moment type 1, modified moment type 2, modified moment type 3, modified maximum likelihood type 1, modified maximum likelihood type 2, modified maximum likelihood type 3, modified maximum likelihood type 4, moment, maximum product spacing, T-L moment, and weighted maximum likelihood. III) The Bayesian estimators of the three-parameter Weibull distribution. IV) Estimating parameters of the three-parameter Weibull distribution fitted to grouped data using three methods including approximated maximum likelihood, expectation maximization, and maximum likelihood. V) Estimating the parameters of the gamma, log-normal, and Weibull mixture models fitted to the grouped data through the EM algorithm. VI) Estimating parameters of the non-linear growth curve fitted to the height-diameter observations.
Author: Mahdi Teimouri
Maintainer: Mahdi Teimouri <teimouri@aut.ac.ir>
Diff between ForestFit versions 0.3 dated 2019-07-18 and 0.4 dated 2019-09-11
ForestFit-0.3/ForestFit/man/fitbayes.Rd |only ForestFit-0.3/ForestFit/man/fitungrouped.Rd |only ForestFit-0.4/ForestFit/DESCRIPTION | 29 ForestFit-0.4/ForestFit/MD5 | 23 ForestFit-0.4/ForestFit/NAMESPACE | 6 ForestFit-0.4/ForestFit/R/ForestFit.R | 1836 +++++++++++++++++------ ForestFit-0.4/ForestFit/man/dmixture.Rd | 28 ForestFit-0.4/ForestFit/man/fitWeibull.Rd |only ForestFit-0.4/ForestFit/man/fitbayesJSB.Rd |only ForestFit-0.4/ForestFit/man/fitbayesWeibull.Rd |only ForestFit-0.4/ForestFit/man/fitgrouped.Rd | 41 ForestFit-0.4/ForestFit/man/fitgrowth.Rd |only ForestFit-0.4/ForestFit/man/fitmixture.Rd | 33 ForestFit-0.4/ForestFit/man/fitmixturegrouped.Rd |only ForestFit-0.4/ForestFit/man/pmixture.Rd | 24 ForestFit-0.4/ForestFit/man/rmixture.Rd | 32 16 files changed, 1460 insertions(+), 592 deletions(-)
Title: Ferguson-Klass Type Algorithm for Posterior Normalized Random
Measures
Description: Bayesian nonparametric density estimation modeling mixtures by a Ferguson-Klass type algorithm for posterior normalized random measures.
Author: Julyan Arbel [ctb],
Ernesto Barrios [aut],
Guillaume Kon Kam King [aut, cre],
Antonio Lijoi [aut],
Luis E. Nieto-Barajas [aut],
Igor Prünster [aut]
Maintainer: Guillaume Kon Kam King <guillaume.konkamking.work@gmail.com>
Diff between BNPdensity versions 2019.7.9 dated 2019-07-11 and 2019.9.11 dated 2019-09-11
BNPdensity-2019.7.9/BNPdensity/R/GOF_plots.R |only BNPdensity-2019.7.9/BNPdensity/man/plotGOF.Rd |only BNPdensity-2019.7.9/BNPdensity/man/plotGOF_censored.Rd |only BNPdensity-2019.7.9/BNPdensity/man/plotGOF_noncensored.Rd |only BNPdensity-2019.9.11/BNPdensity/CHANGES | 18 BNPdensity-2019.9.11/BNPdensity/DESCRIPTION | 6 BNPdensity-2019.9.11/BNPdensity/MD5 | 350 +++++----- BNPdensity-2019.9.11/BNPdensity/NAMESPACE | 21 BNPdensity-2019.9.11/BNPdensity/R/BNPdensity-package.R |only BNPdensity-2019.9.11/BNPdensity/R/GOFplots.R |only BNPdensity-2019.9.11/BNPdensity/R/MixNRMI1.R | 280 +++++++- BNPdensity-2019.9.11/BNPdensity/R/MixNRMI1cens.R | 214 ++++++ BNPdensity-2019.9.11/BNPdensity/R/MixNRMI2.R | 274 +++++++ BNPdensity-2019.9.11/BNPdensity/R/MixNRMI2cens.R | 229 ++++++ BNPdensity-2019.9.11/BNPdensity/R/Mv.R | 22 BNPdensity-2019.9.11/BNPdensity/R/MvInv.R | 24 BNPdensity-2019.9.11/BNPdensity/R/cens_data_check.R | 20 BNPdensity-2019.9.11/BNPdensity/R/censor_code_rl.R | 26 BNPdensity-2019.9.11/BNPdensity/R/comment_on_NRMI_type.R |only BNPdensity-2019.9.11/BNPdensity/R/comp1.R | 35 + BNPdensity-2019.9.11/BNPdensity/R/comp2.R | 44 + BNPdensity-2019.9.11/BNPdensity/R/convert_fit_to_MCMC_chain.R | 7 BNPdensity-2019.9.11/BNPdensity/R/cpo.R | 15 BNPdensity-2019.9.11/BNPdensity/R/dhalfcauchy.R | 16 BNPdensity-2019.9.11/BNPdensity/R/dhalfnorm.R | 16 BNPdensity-2019.9.11/BNPdensity/R/dhalft.R | 16 BNPdensity-2019.9.11/BNPdensity/R/dk.R | 56 + BNPdensity-2019.9.11/BNPdensity/R/dkcens2.R | 34 BNPdensity-2019.9.11/BNPdensity/R/dkcens2_1val.R | 24 BNPdensity-2019.9.11/BNPdensity/R/dt_.R | 13 BNPdensity-2019.9.11/BNPdensity/R/dtnorm.R | 37 + BNPdensity-2019.9.11/BNPdensity/R/expected_number_of_clusters_stable_process.R | 115 ++- BNPdensity-2019.9.11/BNPdensity/R/fcondXA.R | 20 BNPdensity-2019.9.11/BNPdensity/R/fcondXA2.R | 20 BNPdensity-2019.9.11/BNPdensity/R/fcondXA2cens2.R | 25 BNPdensity-2019.9.11/BNPdensity/R/fcondYXA.R | 21 BNPdensity-2019.9.11/BNPdensity/R/fcondYXAcens2.R | 24 BNPdensity-2019.9.11/BNPdensity/R/fcondYZXA.R | 30 BNPdensity-2019.9.11/BNPdensity/R/fcondYZXAcens2.R | 34 BNPdensity-2019.9.11/BNPdensity/R/give_kernel_name.R |only BNPdensity-2019.9.11/BNPdensity/R/gs3.R | 30 BNPdensity-2019.9.11/BNPdensity/R/gs4.R | 33 BNPdensity-2019.9.11/BNPdensity/R/gs4cens2.R | 37 + BNPdensity-2019.9.11/BNPdensity/R/gs5.R | 30 BNPdensity-2019.9.11/BNPdensity/R/gs5cens2.R | 37 + BNPdensity-2019.9.11/BNPdensity/R/gsHP.R | 44 + BNPdensity-2019.9.11/BNPdensity/R/gsYZstar.R | 58 + BNPdensity-2019.9.11/BNPdensity/R/gsYZstarcens2.R | 67 + BNPdensity-2019.9.11/BNPdensity/R/helper_functions.R | 60 + BNPdensity-2019.9.11/BNPdensity/R/multMixNRMI.R | 336 +++++++-- BNPdensity-2019.9.11/BNPdensity/R/noncentral_generalised_factorial_coefficient.R |only BNPdensity-2019.9.11/BNPdensity/R/p0.R | 43 + BNPdensity-2019.9.11/BNPdensity/R/phalfcauchy.R | 16 BNPdensity-2019.9.11/BNPdensity/R/phalfnorm.R | 16 BNPdensity-2019.9.11/BNPdensity/R/phalft.R | 16 BNPdensity-2019.9.11/BNPdensity/R/pk.R | 80 ++ BNPdensity-2019.9.11/BNPdensity/R/plotfit.R |only BNPdensity-2019.9.11/BNPdensity/R/posterior_clustering_analysis.R | 41 - BNPdensity-2019.9.11/BNPdensity/R/prepare_independent_rng.R |only BNPdensity-2019.9.11/BNPdensity/R/pt_.R | 13 BNPdensity-2019.9.11/BNPdensity/R/ptnorm.R | 48 + BNPdensity-2019.9.11/BNPdensity/R/qgeneric.R | 69 + BNPdensity-2019.9.11/BNPdensity/R/qhalfcauchy.R | 16 BNPdensity-2019.9.11/BNPdensity/R/qhalfnorm.R | 16 BNPdensity-2019.9.11/BNPdensity/R/qhalft.R | 16 BNPdensity-2019.9.11/BNPdensity/R/qt_.R | 13 BNPdensity-2019.9.11/BNPdensity/R/qtnorm.R | 21 BNPdensity-2019.9.11/BNPdensity/R/rfystar.R | 23 BNPdensity-2019.9.11/BNPdensity/R/rfystarcens2.R | 33 BNPdensity-2019.9.11/BNPdensity/R/rfyzstar.R | 26 BNPdensity-2019.9.11/BNPdensity/R/rfyzstarcens2.R | 36 + BNPdensity-2019.9.11/BNPdensity/R/rhalfcauchy.R | 13 BNPdensity-2019.9.11/BNPdensity/R/rhalfnorm.R | 13 BNPdensity-2019.9.11/BNPdensity/R/rhalft.R | 13 BNPdensity-2019.9.11/BNPdensity/R/rk.R | 56 + BNPdensity-2019.9.11/BNPdensity/R/rt_.R | 13 BNPdensity-2019.9.11/BNPdensity/R/rtnorm.R | 78 ++ BNPdensity-2019.9.11/BNPdensity/R/summarytext.R |only BNPdensity-2019.9.11/BNPdensity/R/traceplot.R | 5 BNPdensity-2019.9.11/BNPdensity/README.md | 102 ++ BNPdensity-2019.9.11/BNPdensity/man/BNPdensity-package.Rd | 113 +-- BNPdensity-2019.9.11/BNPdensity/man/Enzyme1.out.Rd | 16 BNPdensity-2019.9.11/BNPdensity/man/Enzyme2.out.Rd | 18 BNPdensity-2019.9.11/BNPdensity/man/GOFplots.Rd |only BNPdensity-2019.9.11/BNPdensity/man/GOFplots_censored.Rd |only BNPdensity-2019.9.11/BNPdensity/man/GOFplots_noncensored.Rd |only BNPdensity-2019.9.11/BNPdensity/man/Galaxy1.out.Rd | 16 BNPdensity-2019.9.11/BNPdensity/man/Galaxy2.out.Rd | 18 BNPdensity-2019.9.11/BNPdensity/man/MixNRMI1.Rd | 330 +++++---- BNPdensity-2019.9.11/BNPdensity/man/MixNRMI1cens.Rd | 274 ++++--- BNPdensity-2019.9.11/BNPdensity/man/MixNRMI2.Rd | 319 +++++---- BNPdensity-2019.9.11/BNPdensity/man/MixNRMI2cens.Rd | 288 ++++---- BNPdensity-2019.9.11/BNPdensity/man/Mv.Rd | 36 - BNPdensity-2019.9.11/BNPdensity/man/MvInv.Rd | 44 - BNPdensity-2019.9.11/BNPdensity/man/acidity.Rd | 27 BNPdensity-2019.9.11/BNPdensity/man/add.Rd |only BNPdensity-2019.9.11/BNPdensity/man/as.mcmc.multNRMI.Rd |only BNPdensity-2019.9.11/BNPdensity/man/asNumeric_no_warning.Rd |only BNPdensity-2019.9.11/BNPdensity/man/cens_data_check.Rd | 56 - BNPdensity-2019.9.11/BNPdensity/man/censor_code_rl.Rd | 68 + BNPdensity-2019.9.11/BNPdensity/man/comment_on_NRMI_type.Rd |only BNPdensity-2019.9.11/BNPdensity/man/comp1.Rd | 58 - BNPdensity-2019.9.11/BNPdensity/man/comp2.Rd | 72 +- BNPdensity-2019.9.11/BNPdensity/man/compute_optimal_clustering.Rd | 15 BNPdensity-2019.9.11/BNPdensity/man/compute_thinning_grid.Rd | 6 BNPdensity-2019.9.11/BNPdensity/man/cpo.Rd | 47 - BNPdensity-2019.9.11/BNPdensity/man/dhalfcauchy.Rd | 48 - BNPdensity-2019.9.11/BNPdensity/man/dhalfnorm.Rd | 48 - BNPdensity-2019.9.11/BNPdensity/man/dhalft.Rd | 48 - BNPdensity-2019.9.11/BNPdensity/man/dk.Rd | 127 +-- BNPdensity-2019.9.11/BNPdensity/man/dkcens2.Rd | 77 +- BNPdensity-2019.9.11/BNPdensity/man/dkcens2_1val.Rd | 64 - BNPdensity-2019.9.11/BNPdensity/man/dt_.Rd | 44 - BNPdensity-2019.9.11/BNPdensity/man/dtnorm.Rd | 99 +- BNPdensity-2019.9.11/BNPdensity/man/enzyme.Rd | 31 BNPdensity-2019.9.11/BNPdensity/man/expected_number_of_components_Dirichlet.Rd | 14 BNPdensity-2019.9.11/BNPdensity/man/expected_number_of_components_stable.Rd | 17 BNPdensity-2019.9.11/BNPdensity/man/fcondXA.Rd | 59 - BNPdensity-2019.9.11/BNPdensity/man/fcondXA2.Rd | 58 - BNPdensity-2019.9.11/BNPdensity/man/fcondXA2cens2.Rd | 62 - BNPdensity-2019.9.11/BNPdensity/man/fcondYXA.Rd | 59 - BNPdensity-2019.9.11/BNPdensity/man/fcondYXAcens2.Rd | 62 - BNPdensity-2019.9.11/BNPdensity/man/fcondYZXA.Rd | 72 +- BNPdensity-2019.9.11/BNPdensity/man/fcondYZXAcens2.Rd | 77 +- BNPdensity-2019.9.11/BNPdensity/man/figures/README-unnamed-chunk-4-1.png |binary BNPdensity-2019.9.11/BNPdensity/man/fill_sigmas.Rd | 9 BNPdensity-2019.9.11/BNPdensity/man/galaxy.Rd | 24 BNPdensity-2019.9.11/BNPdensity/man/give_kernel_name.Rd |only BNPdensity-2019.9.11/BNPdensity/man/gs3.Rd | 77 +- BNPdensity-2019.9.11/BNPdensity/man/gs4.Rd | 51 - BNPdensity-2019.9.11/BNPdensity/man/gs4cens2.Rd | 64 - BNPdensity-2019.9.11/BNPdensity/man/gs5.Rd | 76 +- BNPdensity-2019.9.11/BNPdensity/man/gs5cens2.Rd | 88 +- BNPdensity-2019.9.11/BNPdensity/man/gsHP.Rd | 105 +-- BNPdensity-2019.9.11/BNPdensity/man/gsYZstar.Rd | 124 +-- BNPdensity-2019.9.11/BNPdensity/man/gsYZstarcens2.Rd | 141 ++-- BNPdensity-2019.9.11/BNPdensity/man/is_censored.Rd | 1 BNPdensity-2019.9.11/BNPdensity/man/is_semiparametric.Rd | 4 BNPdensity-2019.9.11/BNPdensity/man/multMixNRMI1.Rd | 43 - BNPdensity-2019.9.11/BNPdensity/man/multMixNRMI1cens.Rd | 56 + BNPdensity-2019.9.11/BNPdensity/man/multMixNRMI2.Rd | 49 - BNPdensity-2019.9.11/BNPdensity/man/multMixNRMI2cens.Rd | 66 + BNPdensity-2019.9.11/BNPdensity/man/p0.Rd | 100 +- BNPdensity-2019.9.11/BNPdensity/man/phalfcauchy.Rd | 47 - BNPdensity-2019.9.11/BNPdensity/man/phalfnorm.Rd | 48 - BNPdensity-2019.9.11/BNPdensity/man/phalft.Rd | 48 - BNPdensity-2019.9.11/BNPdensity/man/pk.Rd | 168 ++-- BNPdensity-2019.9.11/BNPdensity/man/plot.NRMI1.Rd |only BNPdensity-2019.9.11/BNPdensity/man/plot.NRMI1cens.Rd |only BNPdensity-2019.9.11/BNPdensity/man/plot.NRMI2.Rd |only BNPdensity-2019.9.11/BNPdensity/man/plot.NRMI2cens.Rd |only BNPdensity-2019.9.11/BNPdensity/man/plot.multNRMI.Rd |only BNPdensity-2019.9.11/BNPdensity/man/plotCDF_censored.Rd | 6 BNPdensity-2019.9.11/BNPdensity/man/plotCDF_noncensored.Rd | 6 BNPdensity-2019.9.11/BNPdensity/man/plotPDF_censored.Rd | 6 BNPdensity-2019.9.11/BNPdensity/man/plotPDF_noncensored.Rd | 6 BNPdensity-2019.9.11/BNPdensity/man/plot_clustering_and_CDF.Rd | 15 BNPdensity-2019.9.11/BNPdensity/man/plot_prior_number_of_components.Rd | 18 BNPdensity-2019.9.11/BNPdensity/man/plotfit_censored.Rd |only BNPdensity-2019.9.11/BNPdensity/man/plotfit_noncensored.Rd |only BNPdensity-2019.9.11/BNPdensity/man/pp_plot_censored.Rd | 12 BNPdensity-2019.9.11/BNPdensity/man/pp_plot_noncensored.Rd | 6 BNPdensity-2019.9.11/BNPdensity/man/print.NRMI1.Rd |only BNPdensity-2019.9.11/BNPdensity/man/print.NRMI1cens.Rd |only BNPdensity-2019.9.11/BNPdensity/man/print.NRMI2.Rd |only BNPdensity-2019.9.11/BNPdensity/man/print.NRMI2cens.Rd |only BNPdensity-2019.9.11/BNPdensity/man/print.multNRMI.Rd |only BNPdensity-2019.9.11/BNPdensity/man/pt_.Rd | 44 - BNPdensity-2019.9.11/BNPdensity/man/ptnorm.Rd | 119 +-- BNPdensity-2019.9.11/BNPdensity/man/qgeneric.Rd | 154 ++-- BNPdensity-2019.9.11/BNPdensity/man/qhalfcauchy.Rd | 47 - BNPdensity-2019.9.11/BNPdensity/man/qhalfnorm.Rd | 48 - BNPdensity-2019.9.11/BNPdensity/man/qhalft.Rd | 48 - BNPdensity-2019.9.11/BNPdensity/man/qq_plot_censored.Rd | 19 BNPdensity-2019.9.11/BNPdensity/man/qq_plot_noncensored.Rd | 16 BNPdensity-2019.9.11/BNPdensity/man/qt_.Rd | 43 - BNPdensity-2019.9.11/BNPdensity/man/qtnorm.Rd | 71 +- BNPdensity-2019.9.11/BNPdensity/man/rfystar.Rd | 64 - BNPdensity-2019.9.11/BNPdensity/man/rfystarcens2.Rd | 80 +- BNPdensity-2019.9.11/BNPdensity/man/rfyzstar.Rd | 71 +- BNPdensity-2019.9.11/BNPdensity/man/rfyzstarcens2.Rd | 85 +- BNPdensity-2019.9.11/BNPdensity/man/rhalfcauchy.Rd | 42 - BNPdensity-2019.9.11/BNPdensity/man/rhalfnorm.Rd | 43 - BNPdensity-2019.9.11/BNPdensity/man/rhalft.Rd | 43 - BNPdensity-2019.9.11/BNPdensity/man/rk.Rd | 128 +-- BNPdensity-2019.9.11/BNPdensity/man/rt_.Rd | 43 - BNPdensity-2019.9.11/BNPdensity/man/rtnorm.Rd | 183 ++--- BNPdensity-2019.9.11/BNPdensity/man/salinity.Rd | 34 BNPdensity-2019.9.11/BNPdensity/man/summary.NRMI1.Rd |only BNPdensity-2019.9.11/BNPdensity/man/summary.NRMI1cens.Rd |only BNPdensity-2019.9.11/BNPdensity/man/summary.NRMI2.Rd |only BNPdensity-2019.9.11/BNPdensity/man/summary.NRMI2cens.Rd |only BNPdensity-2019.9.11/BNPdensity/man/summary.multNRMI.Rd |only BNPdensity-2019.9.11/BNPdensity/man/summarytext.Rd |only BNPdensity-2019.9.11/BNPdensity/man/traceplot.Rd | 3 195 files changed, 6464 insertions(+), 2968 deletions(-)
Title: Parametric Voice Synthesis
Description: Tools for sound synthesis and acoustic analysis.
Performs parametric synthesis of sounds with harmonic and noise components
such as animal vocalizations or human voice. Also includes tools for
spectral analysis, pitch tracking, audio segmentation, self-similarity
matrices, morphing, etc.
Author: Andrey Anikin [aut, cre]
Maintainer: Andrey Anikin <rty.anik@rambler.ru>
Diff between soundgen versions 1.4.1 dated 2019-07-05 and 1.5.0 dated 2019-09-11
soundgen-1.4.1/soundgen/inst/shiny/soundgen_main/www/cecg7xgy.wav |only soundgen-1.4.1/soundgen/inst/shiny/soundgen_main/www/n0h2ayvu.wav |only soundgen-1.5.0/soundgen/DESCRIPTION | 8 soundgen-1.5.0/soundgen/MD5 | 87 - soundgen-1.5.0/soundgen/NAMESPACE | 1 soundgen-1.5.0/soundgen/NEWS | 16 soundgen-1.5.0/soundgen/R/SSM.R | 2 soundgen-1.5.0/soundgen/R/analyze.R | 559 ++++------ soundgen-1.5.0/soundgen/R/postprocessing.R | 37 soundgen-1.5.0/soundgen/R/presets.R | 75 + soundgen-1.5.0/soundgen/R/soundgen.R | 2 soundgen-1.5.0/soundgen/R/soundgenShiny.R | 70 + soundgen-1.5.0/soundgen/R/spectrogram.R | 83 + soundgen-1.5.0/soundgen/R/utilities_analyze.R | 152 +- soundgen-1.5.0/soundgen/R/utilities_pitch_postprocessing.R | 504 ++++++--- soundgen-1.5.0/soundgen/README.md | 1 soundgen-1.5.0/soundgen/build/vignette.rds |binary soundgen-1.5.0/soundgen/data/defaults_analyze.rda |only soundgen-1.5.0/soundgen/inst/doc/acoustic_analysis.R | 34 soundgen-1.5.0/soundgen/inst/doc/acoustic_analysis.Rmd | 47 soundgen-1.5.0/soundgen/inst/doc/acoustic_analysis.html | 139 +- soundgen-1.5.0/soundgen/inst/doc/sound_generation.html | 100 - soundgen-1.5.0/soundgen/inst/shiny/pitch_app |only soundgen-1.5.0/soundgen/man/addPitchCands.Rd |only soundgen-1.5.0/soundgen/man/analyze.Rd | 75 - soundgen-1.5.0/soundgen/man/analyzeFolder.Rd | 83 - soundgen-1.5.0/soundgen/man/analyzeFrame.Rd | 10 soundgen-1.5.0/soundgen/man/costPerPath.Rd | 8 soundgen-1.5.0/soundgen/man/defaults_analyze.Rd |only soundgen-1.5.0/soundgen/man/filled.contour.mod.Rd |only soundgen-1.5.0/soundgen/man/findVoicedSegments.Rd | 7 soundgen-1.5.0/soundgen/man/forcePerPath.Rd | 3 soundgen-1.5.0/soundgen/man/generatePath.Rd | 3 soundgen-1.5.0/soundgen/man/getPitchAutocor.Rd | 4 soundgen-1.5.0/soundgen/man/getPitchCep.Rd | 7 soundgen-1.5.0/soundgen/man/getPrior.Rd |only soundgen-1.5.0/soundgen/man/interpolate.Rd | 14 soundgen-1.5.0/soundgen/man/medianSmoother.Rd | 13 soundgen-1.5.0/soundgen/man/pathfinder.Rd | 20 soundgen-1.5.0/soundgen/man/pathfinding_fast.Rd | 10 soundgen-1.5.0/soundgen/man/pathfinding_slow.Rd | 7 soundgen-1.5.0/soundgen/man/permittedValues.Rd | 7 soundgen-1.5.0/soundgen/man/pitch_app.Rd |only soundgen-1.5.0/soundgen/man/playme.Rd | 15 soundgen-1.5.0/soundgen/man/snake.Rd | 5 soundgen-1.5.0/soundgen/man/soundgen_app.Rd | 6 soundgen-1.5.0/soundgen/man/spectrogram.Rd | 35 soundgen-1.5.0/soundgen/vignettes/acoustic_analysis.Rmd | 47 48 files changed, 1431 insertions(+), 865 deletions(-)
Title: Detecting Anomalies in Data
Description: Implements Collective And Point Anomaly (CAPA) <arXiv:1806.01947>, Multi-Variate Collective And Point Anomaly (MVCAPA) <arXiv:1909.01691>, and Proportion Adaptive Segment Selection (PASS) <doi:10.1093/biomet/ass059> methods for the detection of anomalies in time series data.
Author: Alex Fisch [aut],
Daniel Grose [aut, cre],
Lawrence Bardwell [ctb],
Idris Eckley [ths],
Paul Fearnhead [ths]
Maintainer: Daniel Grose <dan.grose@lancaster.ac.uk>
Diff between anomaly versions 1.1.0 dated 2018-09-21 and 2.0.1 dated 2019-09-11
anomaly-1.1.0/anomaly/R/plot.anomaly_series.R |only anomaly-1.1.0/anomaly/R/print.anomaly_series.R |only anomaly-1.1.0/anomaly/R/summary.anomaly_series.R |only anomaly-1.1.0/anomaly/man/Lightcurves.Rd |only anomaly-1.1.0/anomaly/man/plot.anomaly_series.Rd |only anomaly-1.1.0/anomaly/man/print.anomaly_series.Rd |only anomaly-1.1.0/anomaly/man/summary.anomaly_series.Rd |only anomaly-1.1.0/anomaly/src/check_user_interrupt.c |only anomaly-1.1.0/anomaly/src/init.c |only anomaly-1.1.0/anomaly/src/meanvarwithanomaly.c |only anomaly-1.1.0/anomaly/src/meanvarwithanomaly_mean.c |only anomaly-1.1.0/anomaly/src/meanvarwithanomalysupport.c |only anomaly-1.1.0/anomaly/src/meanvarwithanomalysupport_mean.c |only anomaly-2.0.1/anomaly/DESCRIPTION | 25 anomaly-2.0.1/anomaly/MD5 | 103 +- anomaly-2.0.1/anomaly/NAMESPACE | 18 anomaly-2.0.1/anomaly/R/RcppExports.R |only anomaly-2.0.1/anomaly/R/ac_corrected.R |only anomaly-2.0.1/anomaly/R/anomaly_series.R | 424 ++++------ anomaly-2.0.1/anomaly/R/capa.R |only anomaly-2.0.1/anomaly/R/data.R |only anomaly-2.0.1/anomaly/R/pass.R |only anomaly-2.0.1/anomaly/R/pass.class.R |only anomaly-2.0.1/anomaly/R/period_average.R | 26 anomaly-2.0.1/anomaly/R/robustscale.R |only anomaly-2.0.1/anomaly/R/simulate.R |only anomaly-2.0.1/anomaly/build/partial.rdb |binary anomaly-2.0.1/anomaly/data/datalist | 1 anomaly-2.0.1/anomaly/data/machinetemp.RData |only anomaly-2.0.1/anomaly/inst/REFERENCES.bib | 79 + anomaly-2.0.1/anomaly/man/ac_corrected.Rd |only anomaly-2.0.1/anomaly/man/anomaly_series.Rd | 17 anomaly-2.0.1/anomaly/man/capa.Rd |only anomaly-2.0.1/anomaly/man/capa.mv.Rd |only anomaly-2.0.1/anomaly/man/capa.uv.Rd |only anomaly-2.0.1/anomaly/man/collective_anomalies-methods.Rd |only anomaly-2.0.1/anomaly/man/lightcurves-data.Rd |only anomaly-2.0.1/anomaly/man/machine-temperature-data.Rd |only anomaly-2.0.1/anomaly/man/pass.Rd |only anomaly-2.0.1/anomaly/man/period_average.Rd | 19 anomaly-2.0.1/anomaly/man/plot-methods.Rd |only anomaly-2.0.1/anomaly/man/point_anomaly-methods.Rd |only anomaly-2.0.1/anomaly/man/robustscale.Rd |only anomaly-2.0.1/anomaly/man/show-methods.Rd |only anomaly-2.0.1/anomaly/man/simulate.Rd |only anomaly-2.0.1/anomaly/man/summary-methods.Rd |only anomaly-2.0.1/anomaly/src/Functions.h | 100 ++ anomaly-2.0.1/anomaly/src/Functions_mean.h |only anomaly-2.0.1/anomaly/src/Makevars |only anomaly-2.0.1/anomaly/src/MeanAnomaly.h |only anomaly-2.0.1/anomaly/src/MeanAnomalyMV.cpp |only anomaly-2.0.1/anomaly/src/MeanAnomalyMV.h |only anomaly-2.0.1/anomaly/src/MeanVarAnomaly.h |only anomaly-2.0.1/anomaly/src/MultivariateCOD.cpp |only anomaly-2.0.1/anomaly/src/MultivariateCOD.h |only anomaly-2.0.1/anomaly/src/RcppExports.cpp |only anomaly-2.0.1/anomaly/src/changepointreturn.cpp |only anomaly-2.0.1/anomaly/src/changepointreturn_mean.cpp |only anomaly-2.0.1/anomaly/src/changepointreturn_mean_online.cpp |only anomaly-2.0.1/anomaly/src/changepointreturn_online.cpp |only anomaly-2.0.1/anomaly/src/check_user_interrupt.cpp |only anomaly-2.0.1/anomaly/src/check_user_interrupt.h |only anomaly-2.0.1/anomaly/src/cmpfunc_nosorting.cpp |only anomaly-2.0.1/anomaly/src/cmpfunc_sorting.cpp |only anomaly-2.0.1/anomaly/src/collective_anom_parameters.cpp |only anomaly-2.0.1/anomaly/src/collective_anom_parameters_mean.cpp |only anomaly-2.0.1/anomaly/src/compute_cost_of_starting_anomalies.cpp |only anomaly-2.0.1/anomaly/src/compute_cost_of_starting_anomalies_mean.cpp |only anomaly-2.0.1/anomaly/src/find_best_option.cpp |only anomaly-2.0.1/anomaly/src/find_best_option_mean.cpp |only anomaly-2.0.1/anomaly/src/find_lowest_end_cost.cpp |only anomaly-2.0.1/anomaly/src/marshalling.cpp |only anomaly-2.0.1/anomaly/src/meanvarwithanomaly.cpp |only anomaly-2.0.1/anomaly/src/meanvarwithanomaly_mean.cpp |only anomaly-2.0.1/anomaly/src/meanvarwithanomalysupport.cpp |only anomaly-2.0.1/anomaly/src/meanvarwithanomalysupport_mean.cpp |only anomaly-2.0.1/anomaly/src/pass.cpp |only anomaly-2.0.1/anomaly/src/pass.h |only anomaly-2.0.1/anomaly/src/point_anom_parameters.cpp |only anomaly-2.0.1/anomaly/src/point_anom_parameters_mean.cpp |only anomaly-2.0.1/anomaly/src/populate.cpp |only anomaly-2.0.1/anomaly/src/populate_mean.cpp |only anomaly-2.0.1/anomaly/src/pruner.cpp |only anomaly-2.0.1/anomaly/src/pruner_mean.cpp |only anomaly-2.0.1/anomaly/src/recursive_anomalies.cpp |only anomaly-2.0.1/anomaly/src/recursive_anomalies.h |only anomaly-2.0.1/anomaly/src/recursive_mvanomalies.cpp |only anomaly-2.0.1/anomaly/src/recursive_mvanomalies.h |only anomaly-2.0.1/anomaly/src/sequential_quantiles.cpp |only anomaly-2.0.1/anomaly/src/sequential_quantiles.h |only anomaly-2.0.1/anomaly/src/solveorderedobservationlist.cpp |only anomaly-2.0.1/anomaly/src/solveorderedobservationlist_mean.cpp |only anomaly-2.0.1/anomaly/src/update_cumsums_and_segmentcosts.cpp |only anomaly-2.0.1/anomaly/src/update_cumsums_and_segmentcosts_mean.cpp |only 94 files changed, 528 insertions(+), 284 deletions(-)
Title: Modelling Microbial Populations
Description: Modelling interacting microbial populations - example applications
include human gut microbiota, rumen microbiota and phytoplankton. Solves a
system of ordinary differential equations to simulate microbial growth and
resource uptake over time.
Author: Helen Kettle [aut, cre]
Maintainer: Helen Kettle <Helen.Kettle@bioss.ac.uk>
Diff between microPop versions 1.4.1 dated 2019-04-26 and 1.5 dated 2019-09-11
microPop-1.4.1/microPop/R/microPop-internal.R |only microPop-1.5/microPop/DESCRIPTION | 16 +- microPop-1.5/microPop/MD5 | 76 ++++++------- microPop-1.5/microPop/R/getAllResources.R | 13 +- microPop-1.5/microPop/R/getStrainPHcorners.R | 23 ++- microPop-1.5/microPop/R/microPopModel.R | 6 - microPop-1.5/microPop/data/Acetogens.RData |binary microPop-1.5/microPop/data/Bacteroides.RData |binary microPop-1.5/microPop/data/ButyrateProducers1.RData |binary microPop-1.5/microPop/data/ButyrateProducers2.RData |binary microPop-1.5/microPop/data/ButyrateProducers3.RData |binary microPop-1.5/microPop/data/LactateProducers.RData |binary microPop-1.5/microPop/data/MFG.RData |binary microPop-1.5/microPop/data/Methanogens.RData |binary microPop-1.5/microPop/data/NoButyFibreDeg.RData |binary microPop-1.5/microPop/data/NoButyStarchDeg.RData |binary microPop-1.5/microPop/data/PropionateProducers.RData |binary microPop-1.5/microPop/data/Xaa.RData |binary microPop-1.5/microPop/data/Xh2.RData |binary microPop-1.5/microPop/data/Xsu.RData |binary microPop-1.5/microPop/data/microbeSysInfo.RData |only microPop-1.5/microPop/data/microbeSysInfoHuman.RData |binary microPop-1.5/microPop/data/microbeSysInfoRumen.RData |binary microPop-1.5/microPop/data/resourceSysInfo.RData |only microPop-1.5/microPop/data/resourceSysInfoHuman.RData |binary microPop-1.5/microPop/data/resourceSysInfoRumen.RData |binary microPop-1.5/microPop/data/strainParams.RData |binary microPop-1.5/microPop/data/systemInfoMicrobesPhyto.RData |binary microPop-1.5/microPop/data/systemInfoMicrobesVirus.RData |binary microPop-1.5/microPop/data/systemInfoResourcesPhyto.RData |binary microPop-1.5/microPop/data/systemInfoResourcesVirus.RData |binary microPop-1.5/microPop/inst/DemoFiles/rumen.R | 6 - microPop-1.5/microPop/inst/extdata/Xaa.csv | 2 microPop-1.5/microPop/inst/extdata/Xh2.csv | 1 microPop-1.5/microPop/inst/extdata/Xsu.csv | 1 microPop-1.5/microPop/inst/extdata/microbeSysInfo.csv |only microPop-1.5/microPop/inst/extdata/resourceSysInfo.csv |only microPop-1.5/microPop/inst/testdata |only microPop-1.5/microPop/man/getStrainPHcorners.Rd | 6 - microPop-1.5/microPop/man/microPopModel.Rd | 2 microPop-1.5/microPop/tests/testthat/testsForModelRun1.R | 20 +-- microPop-1.5/microPop/tests/testthat/testsForStrainFuncs.R | 28 ++++ 42 files changed, 116 insertions(+), 84 deletions(-)
Title: Bayesian Estimation for Finite Mixture of Distributions
Description: Provides statistical tools for Bayesian estimation for finite mixture of distributions, mainly mixture of Gamma, Normal and t-distributions. The package is implemented the recent improvements in Bayesian literature for the finite mixture of distributions, including Mohammadi and et al. (2013) <doi:10.1007/s00180-012-0323-3> and Mohammadi and Salehi-Rad (2012) <doi:10.1080/03610918.2011.588358>.
Author: Reza Mohammadi <https://orcid.org/0000-0001-9538-0648>
Maintainer: Reza Mohammadi <a.mohammadi@uva.nl>
Diff between bmixture versions 1.3 dated 2019-04-23 and 1.4 dated 2019-09-11
DESCRIPTION | 8 ++++---- MD5 | 30 +++++++++++++++--------------- NEWS | 6 +++--- man/bmixgamma.Rd | 4 ++++ man/bmixnorm.Rd | 4 ++++ man/bmixt.Rd | 4 ++++ man/bmixture-package.Rd | 2 +- man/mixgamma.Rd | 3 +++ man/mixnorm.Rd | 2 ++ man/mixt.Rd | 3 +++ man/plot.bmixgamma.Rd | 3 +++ man/plot.bmixnorm.Rd | 2 ++ man/plot.bmixt.Rd | 3 +++ man/print.bmixgamma.Rd | 2 ++ man/print.bmixnorm.Rd | 2 ++ man/print.bmixt.Rd | 2 ++ 16 files changed, 57 insertions(+), 23 deletions(-)
Title: Image Registration Using the 'NiftyReg' Library
Description: Provides an 'R' interface to the 'NiftyReg' image registration tools
<http://sourceforge.net/projects/niftyreg/>. Linear and nonlinear registration
are supported, in two and three dimensions.
Author: Jon Clayden [cre, aut],
Marc Modat [aut],
Benoit Presles [aut],
Thanasis Anthopoulos [aut],
Pankaj Daga [aut]
Maintainer: Jon Clayden <code@clayden.org>
Diff between RNiftyReg versions 2.6.6 dated 2019-03-20 and 2.6.7 dated 2019-09-11
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS | 11 +++++++++++ src/main.cpp | 24 +++++++++++++++--------- src/reg-lib/_reg_aladin.cpp | 3 +++ 5 files changed, 37 insertions(+), 17 deletions(-)
Title: Photobiological Calculations
Description: Definitions of classes, methods, operators and functions for use in
photobiology and radiation meteorology and climatology. Calculation of
effective (weighted) and not-weighted irradiances/doses, fluence rates,
transmittance, reflectance, absorptance, absorbance and diverse
ratios and other derived quantities from spectral data. Local maxima and
minima. Conversion between energy- and photon-based units. Wavelength
interpolation. Astronomical calculations related solar angles and day
length. Colours and vision. This package is part of the
'r4photobiology' suite, Aphalo P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.
Author: Pedro J. Aphalo [aut, cre] (<https://orcid.org/0000-0003-3385-972X>),
Titta K. Kotilainen [ctb] (<https://orcid.org/0000-0002-2822-9734>),
Glenn Davis [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between photobiology versions 0.9.28 dated 2019-06-08 and 0.9.29 dated 2019-09-11
DESCRIPTION | 8 +-- MD5 | 76 ++++++++++++++++++------------------- NAMESPACE | 3 + NEWS | 7 +++ R/na.rm.R | 22 ++++++++++ R/spct.clean.r | 40 +++++++++++++++++++ build/vignette.rds |binary data/A.illuminant.spct.rda |binary data/D2-FEL-constants.rda |binary data/D65.illuminant.spct.rda |binary data/Ler-leaf-spct.rda |binary data/beesxyz.spct.rda |binary data/black_body.spct.rda |binary data/ccd.spct.rda |binary data/ciev10.spct.rda |binary data/ciev2.spct.rda |binary data/ciexyzCC10.spct.rda |binary data/ciexyzCC2.spct.rda |binary data/ciexyzCMF10.spct.rda |binary data/ciexyzCMF2.spct.rda |binary data/clear.spct.rda |binary data/clear_body.spct.rda |binary data/filter-cps-mspct.rda |binary data/green_leaf.spct.rda |binary data/opaque.spct.rda |binary data/photodiode.spct.rda |binary data/polyester.spct.rda |binary data/sun.daily.data.rda |binary data/sun.daily.spct.rda |binary data/sun.data.rda |binary data/sun.spct.rda |binary data/white-led-spct.rda |binary data/white_body.spct.rda |binary data/yellow.gel.rda |binary inst/doc/userguide1-intro.html | 10 +++- inst/doc/userguide2-radiation.html | 12 +++-- inst/doc/userguide3-astronomy.html | 34 +++++++++------- man/clean.Rd | 6 ++ man/na.omit.Rd | 8 +++ 39 files changed, 163 insertions(+), 63 deletions(-)
Title: HTTP and WebSocket Server Library
Description: Provides low-level socket and protocol support for handling
HTTP and WebSocket requests directly from within R. It is primarily
intended as a building block for other packages, rather than making it
particularly easy to create complete web applications using httpuv alone.
httpuv is built on top of the libuv and http-parser C libraries, both of
which were developed by Joyent, Inc. (See LICENSE file for libuv and
http-parser license information.)
Author: Joe Cheng, Hector Corrada Bravo [ctb], Jeroen Ooms [ctb],
Winston Chang [ctb]
Maintainer: Joe Cheng <joe@rstudio.com>
Diff between httpuv versions 1.5.1 dated 2019-04-05 and 1.5.2 dated 2019-09-11
DESCRIPTION | 22 ++++-- MD5 | 75 ++++++++++++----------- NAMESPACE | 1 NEWS.md | 21 ++++++ R/RcppExports.R | 12 ++- R/httpuv.R | 30 ++++++--- R/random_port.R |only R/server.R | 10 +-- R/static_paths.R | 3 R/utils.R | 29 +++++++++ man/logLevel.Rd |only man/randomPort.Rd |only man/runServer.Rd | 6 + man/startDaemonizedServer.Rd | 4 - man/startServer.Rd | 6 + src/Makevars | 2 src/Makevars.win | 2 src/RcppExports.cpp | 32 +++++++-- src/auto_deleter.h | 4 - src/filedatasource-win.cpp | 6 + src/fs.cpp |only src/fs.h | 60 ------------------ src/http.cpp | 72 ++++++++++++++-------- src/http.h | 6 + src/httprequest.cpp | 74 ++++++++++++----------- src/httprequest.h | 7 -- src/httpresponse.cpp | 8 +- src/httpuv.cpp | 18 +++-- src/socket.cpp | 4 - src/staticpath.cpp | 4 + src/utils.cpp | 44 ++++++++++++- src/utils.h | 18 ++++- src/webapplication.cpp | 21 +++--- src/websockets.cpp | 14 +++- src/websockets.h | 2 src/winutils.cpp |only src/winutils.h |only tests/testthat/helper-app.R | 23 ------- tests/testthat/test-app.R | 10 +-- tests/testthat/test-frame-completion.R |only tests/testthat/test-static-paths.R | 106 +++++++++++++++++++++++++++++---- tests/testthat/test-traffic.R | 16 ++-- 42 files changed, 486 insertions(+), 286 deletions(-)
Title: Disk-Based Constrained Change-Point Detection
Description: Disk-based implementation of
Functional Pruning Optimal Partitioning with up-down constraints
<arXiv:1810.00117> for single-sample peak calling
(independently for each sample and genomic problem),
can handle huge data sets (10^7 or more).
Author: Toby Dylan Hocking
Maintainer: Toby Dylan Hocking <toby.hocking@r-project.org>
Diff between PeakSegDisk versions 2019.7.29 dated 2019-07-31 and 2019.9.10 dated 2019-09-11
DESCRIPTION | 8 +++---- MD5 | 28 ++++++++++++++------------ NAMESPACE | 1 NEWS | 10 +++++++++ R/fread.R | 34 ++++++++++++++++++++++++++++---- inst/doc/Examples.pdf |binary inst/doc/Worst_case.html | 40 +++++++++++++++++++------------------- man/PeakSegFPOP_dir.Rd | 2 - man/PeakSegFPOP_file.Rd | 2 - man/col.name.list.Rd | 2 - man/fread.first.Rd | 4 +-- man/fread.last.Rd | 4 +-- man/sequentialSearch_dir.Rd | 2 - man/wc2int.Rd |only src/PeakSegFPOPLog.cpp | 1 tests/testthat/test-CRAN-wc2int.R |only 16 files changed, 89 insertions(+), 49 deletions(-)
Title: Quadratic Programming Solver using the 'OSQP' Library
Description: Provides bindings to the 'OSQP' solver. The 'OSQP' solver is a numerical optimization package or solving convex quadratic programs written in 'C' and based on the alternating direction method of multipliers. See <arXiv:1711.08013> for details.
Author: Bartolomeo Stellato [aut, ctb, cph],
Goran Banjac [aut, ctb, cph],
Paul Goulart [cre, aut, ctb, cph],
Stephen Boyd [aut, ctb, cph],
Eric Anderson [ctb]
Maintainer: Paul Goulart <paul.goulart@eng.ox.ac.uk>
Diff between osqp versions 0.6.0.1 dated 2019-09-07 and 0.6.0.2 dated 2019-09-11
DESCRIPTION | 20 ++++++++++---------- MD5 | 10 +++++----- NEWS.md | 4 ++-- configure | 14 ++------------ src/Makevars | 31 +++++++++++++++---------------- src/osqp/Makefile | 6 +++--- 6 files changed, 37 insertions(+), 48 deletions(-)