Title: Modeling Workflows
Description: Managing both a 'parsnip' model and a preprocessor, such as a
model formula or recipe from 'recipes', can often be challenging. The goal
of 'workflows' is to streamline this process by bundling the model alongside
the preprocessor, all within the same object.
Author: Davis Vaughan [aut, cre],
RStudio [cph]
Maintainer: Davis Vaughan <davis@rstudio.com>
Diff between workflows versions 0.2.2 dated 2021-03-10 and 0.2.3 dated 2021-07-15
DESCRIPTION | 14 ++--- MD5 | 51 ++++++++++-------- NAMESPACE | 19 ++++++ NEWS.md | 12 ++++ R/broom.R | 10 +-- R/butcher.R | 20 +++---- R/extract.R |only R/fit.R | 8 +- R/pre-action-variables.R | 2 R/predict.R | 4 - R/pull.R | 15 +++++ R/reexports.R |only R/tune.R | 4 - R/workflow.R | 84 ++++++++++++++++++++++-------- R/workflows-package.R | 10 +-- README.md | 3 - build/vignette.rds |binary man/add_formula.Rd | 20 ++++--- man/add_variables.Rd | 2 man/extract-workflow.Rd |only man/figures/lifecycle-deprecated.svg |only man/figures/lifecycle-soft-deprecated.svg |only man/predict-workflow.Rd | 9 +-- man/reexports.Rd |only man/tidy.workflow.Rd | 2 man/workflow-extractors.Rd | 4 + man/workflow.Rd | 46 +++++++++++----- tests/testthat/_snaps/workflow.md | 14 +++++ tests/testthat/test-extract.R |only tests/testthat/test-workflow.R | 29 ++++++++++ 30 files changed, 271 insertions(+), 111 deletions(-)
Title: Simple R Cache
Description: Simple result caching in R based on R.cache. The global environment is not
considered when caching results simplifying moving files between multiple instances
of R. Relies on more base functions than R.cache (e.g. cached results are saved using
saveRDS() and readRDS()).
Author: Augustin Luna, Vinodh Rajapakse
Maintainer: Augustin Luna <lunaa@cbio.mskcc.org>
Diff between simpleRCache versions 0.3.2 dated 2017-04-09 and 0.3.3 dated 2021-07-15
simpleRCache-0.3.2/simpleRCache/inst/doc/usingSimpleRCache.md |only simpleRCache-0.3.3/simpleRCache/DESCRIPTION | 12 simpleRCache-0.3.3/simpleRCache/MD5 | 13 simpleRCache-0.3.3/simpleRCache/R/memoizedCall.R | 18 simpleRCache-0.3.3/simpleRCache/build/vignette.rds |binary simpleRCache-0.3.3/simpleRCache/inst/doc/usingSimpleRCache.R | 6 simpleRCache-0.3.3/simpleRCache/inst/doc/usingSimpleRCache.Rmd | 15 simpleRCache-0.3.3/simpleRCache/inst/doc/usingSimpleRCache.html | 396 ++++++++-- 8 files changed, 388 insertions(+), 72 deletions(-)
Title: Compare Provenance Collections to Explain Changed Script Outputs
Description: Inspects provenance collected by the 'rdt' or 'rdtLite' packages,
or other tools providing compatible PROV JSON output created by
the execution of a script, and find differences between two provenance
collections. Factors under examination included the hardware and
software used to execute the script, versions of attached libraries,
use of global variables, modified inputs and outputs, and changes
in main and sourced scripts. Based on detected changes, 'provExplainR'
can be used to study how these factors affect the behavior of
the script and generate a promising diagnosis of the causes of different
script results. More information about 'rdtLite' and associated tools is available
at <https://github.com/End-to-end-provenance/> and Barbara Lerner,
Emery Boose, and Luis Perez (2018), Using Introspection to Collect
Provenance in R, Informatics, <doi:10.3390/informatics5010012>.
Author: Barbara Lerner [cre],
Emery Boose [aut],
Khanh Ngo [aut]
Maintainer: Barbara Lerner <blerner@mtholyoke.edu>
Diff between provExplainR versions 1.0 dated 2020-10-17 and 1.1 dated 2021-07-15
DESCRIPTION | 11 MD5 | 11 R/provExplainR.R | 256 +++++++++----------- inst/testdata/prov_factorial_2021-03-31T12.01.36EDT |only inst/testdata/prov_factorial_2021-04-26T16.34.16EDT |only tests/testthat/testScriptChange.R | 4 6 files changed, 141 insertions(+), 141 deletions(-)
Title: Multi Environment Trials Analysis
Description: Performs stability analysis of multi-environment
trial data using parametric and non-parametric methods. Parametric
methods includes Additive Main Effects and Multiplicative Interaction
(AMMI) analysis by Gauch (2013) <doi:10.2135/cropsci2013.04.0241>,
Ecovalence by Wricke (1965), Genotype plus Genotype-Environment (GGE)
biplot analysis by Yan & Kang (2003) <doi:10.1201/9781420040371>,
geometric adaptability index by Mohammadi & Amri (2008)
<doi:10.1007/s10681-007-9600-6>, joint regression analysis by Eberhart
& Russel (1966) <doi:10.2135/cropsci1966.0011183X000600010011x>,
genotypic confidence index by Annicchiarico (1992), Murakami & Cruz's
(2004) method, power law residuals
(POLAR) statistics by Doring et al. (2015)
<doi:10.1016/j.fcr.2015.08.005>, scale-adjusted coefficient of
variation by Doring & Reckling (2018) <doi:10.1016/j.eja.2018.06.007>,
stability variance by Shukla (1972) <doi:10.1038/hdy.1972.87>,
weighted average of absolute scores by Olivoto et al. (2019a)
<doi:10.2134/agronj2019.03.0220>, and multi-trait stability index by
Olivoto et al. (2019b) <doi:10.2134/agronj2019.03.0221>.
Non-parametric methods includes superiority index by Lin & Binns
(1988) <doi:10.4141/cjps88-018>, nonparametric measures of phenotypic
stability by Huehn (1990)
<https://link.springer.com/article/10.1007/BF00024241>, TOP third
statistic by Fox et al. (1990) <doi:10.1007/BF00040364>. Functions for
computing biometrical analysis such as path analysis, canonical
correlation, partial correlation, clustering analysis, and tools for
inspecting, manipulating, summarizing and plotting typical
multi-environment trial data are also provided.
Author: Tiago Olivoto [aut, cre, cph] (<https://orcid.org/0000-0002-0241-9636>)
Maintainer: Tiago Olivoto <tiagoolivoto@gmail.com>
Diff between metan versions 1.14.0 dated 2021-06-07 and 1.15.0 dated 2021-07-15
DESCRIPTION | 6 MD5 | 32 NEWS.md | 6 R/Smith_Hazel.R | 7 R/fai_blup.R | 2 R/get_model_data.R | 14 R/inspect.R | 6 R/mps.R | 4 R/utilities.R | 56 R/utils-tidy-eval.R | 32 R/zzz.R | 16 build/metan.pdf |14527 ++++++++++++++++++++++------------------------ build/partial.rdb |binary build/vignette.rds |binary inst/doc/metan_start.html | 41 man/Smith_Hazel.Rd | 3 man/tidyeval.Rd | 19 17 files changed, 7386 insertions(+), 7385 deletions(-)
Title: Geostatistics for Compositional Analysis
Description: Support for geostatistical analysis of multivariate data,
in particular data with restrictions, e.g. positive amounts data,
compositional data, distributional data, microstructural data, etc.
It includes descriptive analysis and modelling for such data, both
from a two-point Gaussian perspective and multipoint perspective.
The methods mainly follow Tolosana-Delgado, Mueller and van den
Boogaart (2018) <doi:10.1007/s11004-018-9769-3>.
Author: Raimon Tolosana-Delgado [aut] (<https://orcid.org/0000-0001-9847-0462>),
Ute Mueller [aut],
K. Gerald van den Boogaart [ctb, cre],
Hassan Talebi [ctb, cph],
Helmholtz-Zentrum Dresden-Rossendorf [cph],
Edith Cowan University [cph]
Maintainer: K. Gerald van den Boogaart <support@boogaart.de>
Diff between gmGeostats versions 0.10-7 dated 2020-10-03 and 0.10-8 dated 2021-07-15
gmGeostats-0.10-7/gmGeostats/man/predict.gmSpatialModel.Rd |only gmGeostats-0.10-8/gmGeostats/DESCRIPTION | 22 gmGeostats-0.10-8/gmGeostats/MD5 | 103 gmGeostats-0.10-8/gmGeostats/NAMESPACE | 6 gmGeostats-0.10-8/gmGeostats/NEWS.md | 26 gmGeostats-0.10-8/gmGeostats/R/Anamorphosis.R | 6 gmGeostats-0.10-8/gmGeostats/R/abstractClasses.R | 20 gmGeostats-0.10-8/gmGeostats/R/accuracy.R | 86 gmGeostats-0.10-8/gmGeostats/R/closeup.R |only gmGeostats-0.10-8/gmGeostats/R/compositionsCompatibility.R | 60 gmGeostats-0.10-8/gmGeostats/R/genDiag.R | 3 gmGeostats-0.10-8/gmGeostats/R/geostats.R | 13 gmGeostats-0.10-8/gmGeostats/R/gmSimulation.R | 18 gmGeostats-0.10-8/gmGeostats/R/gmSpatialMethodParameters.R | 10 gmGeostats-0.10-8/gmGeostats/R/gmSpatialModel.R | 297 - gmGeostats-0.10-8/gmGeostats/R/gmValidationStrategy.R | 21 gmGeostats-0.10-8/gmGeostats/R/grids.R | 6 gmGeostats-0.10-8/gmGeostats/R/gstatCompatibility.R | 41 gmGeostats-0.10-8/gmGeostats/R/preparations.R |only gmGeostats-0.10-8/gmGeostats/R/uncorrelationTest.R | 8 gmGeostats-0.10-8/gmGeostats/R/variograms.R | 2309 ++++------ gmGeostats-0.10-8/gmGeostats/R/zzz.R | 4 gmGeostats-0.10-8/gmGeostats/README.md | 50 gmGeostats-0.10-8/gmGeostats/build/vignette.rds |binary gmGeostats-0.10-8/gmGeostats/inst/doc/gmGeostats.Rmd | 20 gmGeostats-0.10-8/gmGeostats/inst/doc/gmGeostats.html | 78 gmGeostats-0.10-8/gmGeostats/inst/doc/register_new_layer_datatype.R |only gmGeostats-0.10-8/gmGeostats/inst/doc/register_new_layer_datatype.Rmd |only gmGeostats-0.10-8/gmGeostats/inst/doc/register_new_layer_datatype.html |only gmGeostats-0.10-8/gmGeostats/man/CholeskyDecomposition.Rd | 2 gmGeostats-0.10-8/gmGeostats/man/DSpars.Rd | 2 gmGeostats-0.10-8/gmGeostats/man/KrigingNeighbourhood.Rd | 2 gmGeostats-0.10-8/gmGeostats/man/SequentialSimulation.Rd | 2 gmGeostats-0.10-8/gmGeostats/man/TurningBands.Rd | 2 gmGeostats-0.10-8/gmGeostats/man/accuracy.Rd | 13 gmGeostats-0.10-8/gmGeostats/man/as.LMCAnisCompo.Rd | 26 gmGeostats-0.10-8/gmGeostats/man/as.gmSpatialModel.Rd | 4 gmGeostats-0.10-8/gmGeostats/man/figures/README-structural-1.png |binary gmGeostats-0.10-8/gmGeostats/man/fit_lmc.Rd | 20 gmGeostats-0.10-8/gmGeostats/man/gmSpatialModel-class.Rd | 4 gmGeostats-0.10-8/gmGeostats/man/gsi.DS.Rd | 16 gmGeostats-0.10-8/gmGeostats/man/image_cokriged.Rd | 2 gmGeostats-0.10-8/gmGeostats/man/logratioVariogram-acomp-method.Rd | 2 gmGeostats-0.10-8/gmGeostats/man/make.gmCompositionalGaussianSpatialModel.Rd | 6 gmGeostats-0.10-8/gmGeostats/man/make.gmCompositionalMPSSpatialModel.Rd | 6 gmGeostats-0.10-8/gmGeostats/man/make.gmMultivariateGaussianSpatialModel.Rd | 6 gmGeostats-0.10-8/gmGeostats/man/mean.accuracy.Rd | 1 gmGeostats-0.10-8/gmGeostats/man/noSpatCorr.test.Rd | 8 gmGeostats-0.10-8/gmGeostats/man/plot.accuracy.Rd | 1 gmGeostats-0.10-8/gmGeostats/man/precision.Rd | 1 gmGeostats-0.10-8/gmGeostats/man/predict_gmSpatialModel.Rd |only gmGeostats-0.10-8/gmGeostats/man/validate.Rd | 1 gmGeostats-0.10-8/gmGeostats/man/xvErrorMeasures.data.frame.Rd | 3 gmGeostats-0.10-8/gmGeostats/man/xvErrorMeasures.default.Rd |only gmGeostats-0.10-8/gmGeostats/src/gmGeostats.c | 21 gmGeostats-0.10-8/gmGeostats/vignettes/gmGeostats.Rmd | 20 gmGeostats-0.10-8/gmGeostats/vignettes/register_new_layer_datatype.Rmd |only 57 files changed, 1837 insertions(+), 1541 deletions(-)
Title: Handling Taxonomic Lists
Description: Handling taxonomic lists through objects of class 'taxlist'.
This package provides functions to import species lists from 'Turboveg'
(<https://www.synbiosys.alterra.nl/turboveg/>) and the possibility to create
backups from resulting R-objects.
Also quick displays are implemented as summary-methods.
Author: Miguel Alvarez [aut, cre] (<https://orcid.org/0000-0003-1500-1834>),
Zachary Foster [ctb] (<https://orcid.org/0000-0002-5075-0948>),
Sam Levin [rev],
Margaret Siple [rev]
Maintainer: Miguel Alvarez <kamapu78@gmail.com>
Diff between taxlist versions 0.2.1 dated 2021-03-29 and 0.2.2 dated 2021-07-15
taxlist-0.2.1/taxlist/R/taxlist2taxmap.R |only taxlist-0.2.1/taxlist/man/taxlist2taxmap.Rd |only taxlist-0.2.1/taxlist/tests/testthat/temp.rda |only taxlist-0.2.1/taxlist/tests/testthat/temp_2020-07-05.rda |only taxlist-0.2.1/taxlist/tests/testthat/temp_2020-07-08.rda |only taxlist-0.2.1/taxlist/tests/testthat/temp_2020-09-16.rda |only taxlist-0.2.1/taxlist/tests/testthat/temp_2020-10-02.rda |only taxlist-0.2.1/taxlist/tests/testthat/temp_2020-10-04.rda |only taxlist-0.2.1/taxlist/tests/testthat/temp_2020-10-07.rda |only taxlist-0.2.1/taxlist/tests/testthat/temp_2020-10-18.rda |only taxlist-0.2.1/taxlist/tests/testthat/temp_2021-03-27.rda |only taxlist-0.2.1/taxlist/tests/testthat/test-taxlist2taxmap.R |only taxlist-0.2.2/taxlist/DESCRIPTION | 8 - taxlist-0.2.2/taxlist/MD5 | 34 ++----- taxlist-0.2.2/taxlist/NAMESPACE | 4 taxlist-0.2.2/taxlist/NEWS.md | 8 + taxlist-0.2.2/taxlist/R/deprecated-functions.R | 36 ++++++- taxlist-0.2.2/taxlist/R/imports.R | 3 taxlist-0.2.2/taxlist/R/merge_taxa.R | 6 - taxlist-0.2.2/taxlist/R/taxlist-class.R | 63 +++++++------ taxlist-0.2.2/taxlist/build/partial.rdb |binary taxlist-0.2.2/taxlist/build/vignette.rds |binary taxlist-0.2.2/taxlist/inst/doc/taxlist-intro.html | 4 taxlist-0.2.2/taxlist/man/Deprecated-functions.Rd | 6 + 24 files changed, 104 insertions(+), 68 deletions(-)
Title: Mixtures of Exponential-Distance Models with Covariates
Description: Implements a model-based clustering method for categorical life-course sequences relying on mixtures of exponential-distance models introduced by Murphy et al. (2021) <doi:10.1111/rssa.12712>. A range of flexible precision parameter settings corresponding to weighted generalisations of the Hamming distance metric are considered, along with the potential inclusion of a noise component. Gating covariates can be supplied in order to relate sequences to baseline characteristics. Sampling weights are also accommodated. The models are fitted using the EM algorithm and tools for visualising the results are also provided.
Author: Keefe Murphy [aut, cre] (<https://orcid.org/0000-0002-7709-3159>),
Thomas Brendan Murphy [ctb] (<https://orcid.org/0000-0002-5668-7046>),
Raffaella Piccarreta [ctb],
Isobel Claire Gormley [ctb] (<https://orcid.org/0000-0001-7713-681X>)
Maintainer: Keefe Murphy <keefe.murphy@mu.ie>
Diff between MEDseq versions 1.2.1 dated 2021-01-06 and 1.3.0 dated 2021-07-15
MEDseq-1.2.1/MEDseq/vignettes/MVAD_Mean.png |only MEDseq-1.3.0/MEDseq/DESCRIPTION | 16 MEDseq-1.3.0/MEDseq/MD5 | 62 - MEDseq-1.3.0/MEDseq/NAMESPACE | 17 MEDseq-1.3.0/MEDseq/R/Functions.R | 1010 ++++++++++++++++++------- MEDseq-1.3.0/MEDseq/R/Hidden_Functions.R | 84 +- MEDseq-1.3.0/MEDseq/R/MEDseq.R | 12 MEDseq-1.3.0/MEDseq/R/data.R | 10 MEDseq-1.3.0/MEDseq/README.md | 6 MEDseq-1.3.0/MEDseq/build/partial.rdb |only MEDseq-1.3.0/MEDseq/build/vignette.rds |binary MEDseq-1.3.0/MEDseq/inst/CITATION | 39 MEDseq-1.3.0/MEDseq/inst/NEWS.md | 51 + MEDseq-1.3.0/MEDseq/inst/doc/MEDseq.R | 48 - MEDseq-1.3.0/MEDseq/inst/doc/MEDseq.Rmd | 81 -- MEDseq-1.3.0/MEDseq/inst/doc/MEDseq.html | 520 ++++-------- MEDseq-1.3.0/MEDseq/man/MEDseq-package.Rd | 10 MEDseq-1.3.0/MEDseq/man/MEDseq_clustnames.Rd |only MEDseq-1.3.0/MEDseq/man/MEDseq_compare.Rd | 14 MEDseq-1.3.0/MEDseq/man/MEDseq_control.Rd | 13 MEDseq-1.3.0/MEDseq/man/MEDseq_fit.Rd | 305 +++---- MEDseq-1.3.0/MEDseq/man/MEDseq_meantime.Rd | 19 MEDseq-1.3.0/MEDseq/man/MEDseq_stderr.Rd | 11 MEDseq-1.3.0/MEDseq/man/biofam.Rd | 7 MEDseq-1.3.0/MEDseq/man/get_MEDseq_results.Rd | 6 MEDseq-1.3.0/MEDseq/man/mvad.Rd | 3 MEDseq-1.3.0/MEDseq/man/plot.MEDseq.Rd | 327 ++++---- MEDseq-1.3.0/MEDseq/man/predict.MEDgating.Rd |only MEDseq-1.3.0/MEDseq/vignettes/BIO_Clusters.png |binary MEDseq-1.3.0/MEDseq/vignettes/MEDseq.Rmd | 81 -- MEDseq-1.3.0/MEDseq/vignettes/MVAD_Central.png |only MEDseq-1.3.0/MEDseq/vignettes/bio_mod.rda |only MEDseq-1.3.0/MEDseq/vignettes/mvad_mod1.rda |binary MEDseq-1.3.0/MEDseq/vignettes/mvad_mod2.rda |binary MEDseq-1.3.0/MEDseq/vignettes/mvad_mod3.rda |binary 35 files changed, 1604 insertions(+), 1148 deletions(-)
Title: Rendering Math to HTML, 'MathML', or R-Documentation Format
Description: Convert latex math expressions to HTML and 'MathML' for use in
markdown documents or package manual pages. The rendering is done in
R using the V8 engine (i.e. server-side), which eliminates the need
for embedding the 'MathJax' library into your web pages. In addition
a 'math-to-rd' wrapper is provided to automatically render beautiful
math in R documentation files.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between katex versions 1.0.0 dated 2021-07-07 and 1.1.0 dated 2021-07-15
DESCRIPTION | 8 +++++--- MD5 | 18 ++++++++++++------ NEWS |only R/katex.R | 9 ++++++--- R/rd.R | 17 ++++++++++++++++- build/partial.rdb |binary build/vignette.rds |only inst/doc |only man/katex.Rd | 3 +++ man/math_to_rd.Rd | 10 ++++++++++ vignettes |only 11 files changed, 52 insertions(+), 13 deletions(-)
Title: A Fast Clustering Algorithm for High Dimensional Data Based on
the Gram Matrix Decomposition
Description: Clustering algorithm for high dimensional data. Assuming that P feature measurements on N objects are arranged in an N×P matrix X, this package provides clustering based on the left Gram matrix XX^T. To simulate test data, type "help('simulate_HD_data')" and to learn how to use the clustering algorithm, type "help('RJclust')". To cite this package, type 'citation("RJcluster")'.
Author: Shahina Rahman [aut],
Valen E. Johnson [aut],
Suhasini Subba Rao [aut],
Rachael Shudde [aut, cre, trl]
Maintainer: Rachael Shudde <rachael.shudde@gmail.com>
Diff between RJcluster versions 3.0.0 dated 2021-07-07 and 3.0.1 dated 2021-07-15
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ R/AlgorithmImplementation.R | 2 +- R/FUNC_RJ_calls.R | 5 +++-- build/partial.rdb |binary inst/doc/RJclust_Vignette.pdf |binary src/RcppExports.cpp | 5 +++++ 7 files changed, 18 insertions(+), 12 deletions(-)
Title: Genotype Quality Control with 'PLINK'
Description: Genotyping arrays enable the direct measurement of an individuals
genotype at thousands of markers. 'plinkQC' facilitates genotype quality
control for genetic association studies as described by Anderson and
colleagues (2010) <doi:10.1038/nprot.2010.116>. It makes 'PLINK' basic
statistics (e.g. missing genotyping rates per individual, allele frequencies
per genetic marker) and relationship functions accessible from 'R' and
generates a per-individual and per-marker quality control report.
Individuals and markers that fail the quality control can subsequently be
removed to generate a new, clean dataset. Removal of individuals based on
relationship status is optimised to retain as many individuals as possible
in the study.
Author: Hannah Meyer [aut, cre] (<https://orcid.org/0000-0003-4564-0899>)
Maintainer: Hannah Meyer <hannah.v.meyer@gmail.com>
Diff between plinkQC versions 0.3.3 dated 2021-02-08 and 0.3.4 dated 2021-07-15
DESCRIPTION | 9 +-- MD5 | 28 +++++------ NEWS.md | 11 ++++ R/individualQC.R | 106 +++++++++++++++++++++++++++++++++---------- R/markerQC.R | 14 +++-- R/utils.R | 4 - README.md | 4 - build/vignette.rds |binary inst/doc/AncestryCheck.pdf |binary inst/doc/Genomes1000.pdf |binary inst/doc/HapMap.pdf |binary inst/doc/plinkQC.pdf |binary man/check_relatedness.Rd | 18 +++++++ man/perIndividualQC.Rd | 18 +++++++ man/run_check_relatedness.Rd | 18 +++++++ 15 files changed, 178 insertions(+), 52 deletions(-)
Title: Sequential Design for Deep Gaussian Processes using MCMC
Description: Performs model fitting and sequential design for deep Gaussian
processes following Sauer, Gramacy, and Higdon (2020) <arXiv:2012.08015>.
Models extend up to three layers deep; a one layer model is equivalent to
typical Gaussian process regression. Sequential design criteria include
integrated mean-squared error (IMSE), active learning Cohn (ALC), and
expected improvement (EI). Covariance structure is based on inverse
exponentiated squared euclidean distance. Applicable to noisy and
deterministic functions. Incorporates SNOW parallelization and utilizes
C under the hood.
Author: Annie Sauer <anniees@vt.edu>
Maintainer: Annie Sauer <anniees@vt.edu>
Diff between deepgp versions 0.2.0 dated 2020-12-16 and 0.2.1 dated 2021-07-15
deepgp-0.2.0/deepgp/R/fit_models.R |only deepgp-0.2.1/deepgp/DESCRIPTION | 23 ++--- deepgp-0.2.1/deepgp/MD5 | 45 ++++++----- deepgp-0.2.1/deepgp/R/continue.R |only deepgp-0.2.1/deepgp/R/deepgp-package.R | 31 +++---- deepgp-0.2.1/deepgp/R/fit.R |only deepgp-0.2.1/deepgp/R/general.R | 41 +++++----- deepgp-0.2.1/deepgp/R/mcmc.R |only deepgp-0.2.1/deepgp/R/plot.R |only deepgp-0.2.1/deepgp/R/predict.R |only deepgp-0.2.1/deepgp/R/seq_design.R | 117 ++++++++++++++++------------- deepgp-0.2.1/deepgp/R/trim.R |only deepgp-0.2.1/deepgp/README.md | 12 ++ deepgp-0.2.1/deepgp/man/ALC.Rd | 39 +++++---- deepgp-0.2.1/deepgp/man/EI.Rd | 16 ++- deepgp-0.2.1/deepgp/man/IMSE.Rd | 24 +++-- deepgp-0.2.1/deepgp/man/continue.Rd | 2 deepgp-0.2.1/deepgp/man/deepgp-package.Rd | 31 +++---- deepgp-0.2.1/deepgp/man/fit_one_layer.Rd | 36 ++++---- deepgp-0.2.1/deepgp/man/fit_three_layer.Rd | 86 +++++++++++---------- deepgp-0.2.1/deepgp/man/fit_two_layer.Rd | 53 +++++++------ deepgp-0.2.1/deepgp/man/plot.Rd | 9 +- deepgp-0.2.1/deepgp/man/predict.Rd | 78 ++++++++++--------- deepgp-0.2.1/deepgp/man/rmse.Rd | 7 - deepgp-0.2.1/deepgp/man/score.Rd | 10 +- deepgp-0.2.1/deepgp/man/sq_dist.Rd | 11 +- deepgp-0.2.1/deepgp/man/trim.Rd | 10 +- 27 files changed, 375 insertions(+), 306 deletions(-)
Title: Discrete Event Simulation in R and C++, with Tools for
Cost-Effectiveness Analysis
Description: Discrete event simulation using both R and C++ (Karlsson et al 2016; <doi:10.1109/eScience.2016.7870915>). The C++ code is adapted from the SSIM library <https://www.inf.usi.ch/carzaniga/ssim/>, allowing for both event-oriented and process-oriented simulation. The code includes a SummaryReport class for reporting events and costs by age and other covariates. The C++ code is available as a static library for linking to other packages. A priority queue implementation is given in C++ together with an S3 closure and a reference class implementation. Finally, some tools are provided for cost-effectiveness analysis.
Author: Mark Clements [aut, cre, cph],
Alexandra Jauhiainen [aut],
Andreas Karlsson [aut],
Antonio Carzaniga [cph],
University of Colorado [cph],
Pierre L'Ecuyer [cph]
Maintainer: Mark Clements <mark.clements@ki.se>
Diff between microsimulation versions 1.3.3 dated 2021-03-20 and 1.3.5 dated 2021-07-15
DESCRIPTION | 10 +++++--- MD5 | 29 ++++++++++++++----------- R/rcpp_hello_world.R | 46 +++++++++++++++++++++------------------- configure.ac | 14 ++++++++++++ inst/doc/index.html |only inst/include/RngStream.cpp |only inst/include/microsimulation.cc |only inst/include/microsimulation.h | 6 ++--- inst/include/siena/tprocess.h | 2 - inst/include/ssim.cc |only inst/include/tprocess.cc |only man/Classes.Rd | 28 ++++++++++++------------ man/Internal.Rd | 15 +++++++++++++ man/Utilities.Rd | 24 ++++++++++++++++++++ man/discountedInterval.Rd | 3 ++ man/microsimulation-package.Rd | 6 +---- src/Makevars | 2 - src/Makevars.win | 2 - 18 files changed, 126 insertions(+), 61 deletions(-)
More information about microsimulation at CRAN
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Title: Flexible and Robust GARCH-X Modelling
Description: Flexible and robust estimation and inference of generalised autoregressive conditional heteroscedasticity (GARCH) models with covariates ('X') based on the results by Francq and Thieu (2018) <doi:10.1017/S0266466617000512>. Coefficients can straightforwardly be set to zero by omission, and quasi maximum likelihood methods ensure estimates are generally consistent and inference valid, even when the standardised innovations are non-normal and/or dependent over time.
Author: Genaro Sucarrat [aut, cre]
Maintainer: Genaro Sucarrat <gsucarrat@gmail.com>
Diff between garchx versions 1.2 dated 2021-01-23 and 1.3 dated 2021-07-15
DESCRIPTION | 8 +- MD5 | 18 +++-- NAMESPACE | 5 - NEWS | 21 ++++++ R/garchx-internal.R | 2 R/garchx-source-code.R | 161 ++++++++++++++++++++++++++++++++++++++++++------- man/coef.garchx.Rd | 4 - man/garchx-package.Rd | 4 - man/garchx.Rd | 14 ++-- man/gdiff.Rd |only man/glag.Rd |only 11 files changed, 191 insertions(+), 46 deletions(-)
Title: Visible Vowels: Visualization of Vowel Variation
Description: Visualizes vowel variation in f0, F1, F2, F3 and duration.
Author: Wilbert Heeringa, Hans Van de Velde
Maintainer: Wilbert Heeringa <wjheeringa@gmail.com>
Diff between visvow versions 1.3.2 dated 2021-06-24 and 1.3.3 dated 2021-07-15
DESCRIPTION | 6 ++-- MD5 | 8 +++--- R/visvow.R | 4 +-- build/partial.rdb |binary tests/testthat/data/SussmanF.csv | 52 +++++++++++++++++++-------------------- 5 files changed, 35 insertions(+), 35 deletions(-)
Title: Innovative and/or Additive Outlier Robust Kalman Filtering
Description: Implements a series of robust Kalman filtering approaches. It implements the additive outlier robust filters of Ruckdeschel et al. (2014) <arXiv:1204.3358> and Agamennoni et al. (2018) <doi:10.1109/ICRA.2011.5979605>, the innovative outlier robust filter of Ruckdeschel et al. (2014) <arXiv:1204.3358>, as well as the innovative and additive outlier robust filter of Fisch et al. (2020) <arXiv:2007.03238>.
Author: Alex TM Fisch [aut],
Daniel Grose [aut, cre],
Idris A Eckley [aut, ths],
Paul Fearnhead [aut, ths],
Lawrence Bardwell [aut, ctb]
Maintainer: Daniel Grose <dan.grose@lancaster.ac.uk>
Diff between RobKF versions 1.0.1 dated 2021-02-10 and 1.0.2 dated 2021-07-15
DESCRIPTION | 26 +++++++++++++------------- MD5 | 6 +++--- build/partial.rdb |binary src/RcppExports.cpp | 5 +++++ 4 files changed, 21 insertions(+), 16 deletions(-)
Title: TERN AusPlots Analysis Package
Description: Extraction, preparation, visualisation and analysis of TERN AusPlots ecosystem monitoring data. Direct access to plot-based data on vegetation and soils across Australia, including physical sample barcode numbers. Simple function calls extract the data and merge them into species occurrence matrices for downstream analysis, or calculate things like basal area and fractional cover. TERN AusPlots is a national field plot-based ecosystem surveillance monitoring method and dataset for Australia. The data have been collected across a national network of plots and transects by the Terrestrial Ecosystem Research Network (TERN - <https://www.tern.org.au>), an Australian Government NCRIS-enabled project, and its Ecosystem Surveillance platform (<https://www.tern.org.au/tern-observatory/tern-ecosystem-surveillance/>).
Author: Greg Guerin [aut, cre],
Tom Saleeba [aut],
Samantha Munroe [aut],
Bernardo Blanco-Martin [aut],
Irene Martín-Forés [aut],
Andrew Tokmakoff [aut]
Maintainer: Greg Guerin <ggueri01@gmail.com>
Diff between ausplotsR versions 1.2.4 dated 2021-04-18 and 1.2.5 dated 2021-07-15
DESCRIPTION | 10 - MD5 | 18 +- NAMESPACE | 1 R/ausplots_queries.r | 20 ++- R/get_ausplots.R | 20 +-- inst/doc/start_guide.R | 88 -------------- inst/doc/start_guide.Rmd | 2 inst/doc/start_guide.html | 282 ---------------------------------------------- man/ausplotsR-package.Rd | 4 vignettes/start_guide.Rmd | 2 10 files changed, 51 insertions(+), 396 deletions(-)
Title: Multi-Reader, Multi-Case Analysis Methods (ROC, Agreement, and
Other Metrics)
Description: Do Multi-Reader, Multi-Case (MRMC) analyses of data from imaging studies where clinicians (readers)
evaluate patient images (cases). What does this mean? ... Many imaging studies are designed
so that every reader reads every case in all modalities, a fully-crossed study. In this case, the
data is cross-correlated, and we consider the readers and cases to be cross-correlated random effects.
An MRMC analysis accounts for the variability and correlations from the readers and cases when
estimating variances, confidence intervals, and p-values. The functions in this package can treat
arbitrary study designs and studies with missing data, not just fully-crossed study designs.
The initial package analyzes the reader-average area under the receiver operating characteristic (ROC)
curve with U-statistics according to Gallas, Bandos, Samuelson,
and Wagner 2009 <doi:10.1080/03610920802610084>.
Additional functions analyze other endpoints with U-statistics (binary performance
and score differences) following the work by Gallas, Pennello, and Myers 2007
<doi:10.1364/JOSAA.24.000B70>.
Package development and documentation is at <https://github.com/DIDSR/iMRMC/tree/master>.
Author: Brandon Gallas
Maintainer: Brandon Gallas <Brandon.Gallas@fda.hhs.gov>
Diff between iMRMC versions 1.2.2 dated 2020-03-24 and 1.2.3 dated 2021-07-15
DESCRIPTION | 8 - MD5 | 44 ++++++---- NAMESPACE | 2 R/iMRMC.R | 120 ++++++++++++++++++----------- R/limitsOfAgreement.R | 5 - R/simMRMC.R | 4 R/uStats.R | 14 +++ R/utils.R | 27 ++---- inst/data-raw/simulationData |only man/createIMRMCdf.Rd | 4 man/doIMRMC.Rd | 18 ++-- man/extractPairedComparisonsBRBM.Rd | 4 man/extractPairedComparisonsWRBM.Rd | 4 man/getBRBM.Rd | 5 - man/sim.gRoeMetz.Rd | 2 tests/testthat/Rplots.pdf |binary tests/testthat/test_createANDundoIMRMCdf.R | 2 tests/testthat/test_doIMRMCfromFile.R | 2 tests/testthat/test_simRoeMetz.Rdata |binary 19 files changed, 161 insertions(+), 104 deletions(-)
Title: Noncompartmental Analysis for Pharmacokinetic Data
Description: Conduct a noncompartmental analysis with industrial strength.
Some features are
1) Use of CDISC SDTM terms
2) Automatic or manual slope selection
3) Supporting both 'linear-up linear-down' and 'linear-up log-down' method
4) Interval(partial) AUCs with 'linear' or 'log' interpolation method
* Reference: Gabrielsson J, Weiner D. Pharmacokinetic and Pharmacodynamic Data Analysis - Concepts and Applications. 5th ed. 2016. (ISBN:9198299107).
Author: Kyun-Seop Bae [aut]
Maintainer: Kyun-Seop Bae <k@acr.kr>
Diff between NonCompart versions 0.4.8 dated 2021-06-16 and 0.4.9 dated 2021-07-15
DESCRIPTION | 8 +-- MD5 | 30 ++++++------ R/BestSlope.R | 98 ++++++++++++++++++++++++++++++----------- R/DetSlope.R | 5 +- R/IntAUC.R | 11 ++-- R/Slope.R | 6 +- R/sNCA.R | 72 +++++++++++++++--------------- R/tblNCA.R | 34 ++++---------- inst/NEWS.Rd | 6 ++ inst/doc/NonCompart-manual.pdf |binary man/BestSlope.Rd | 7 ++ man/DetSlope.Rd | 3 - man/IntAUC.Rd | 2 man/Slope.Rd | 1 man/sNCA.Rd | 9 ++- man/tblNCA.Rd | 7 ++ 16 files changed, 176 insertions(+), 123 deletions(-)
Title: Convert Country Names and Country Codes
Description: Standardize country names, convert them into one of 40
different coding schemes, convert between coding schemes, and assign
region descriptors.
Author: Vincent Arel-Bundock [aut, cre]
(<https://orcid.org/0000-0003-2042-7063>),
CJ Yetman [ctb] (<https://orcid.org/0000-0001-5099-9500>),
Nils Enevoldsen [ctb] (<https://orcid.org/0000-0001-7195-4117>)
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Diff between countrycode versions 1.2.0 dated 2020-05-22 and 1.3.0 dated 2021-07-15
countrycode-1.2.0/countrycode/NEWS |only countrycode-1.3.0/countrycode/DESCRIPTION | 50 +- countrycode-1.3.0/countrycode/MD5 | 37 - countrycode-1.3.0/countrycode/NEWS.md |only countrycode-1.3.0/countrycode/R/codelist.R | 137 ++--- countrycode-1.3.0/countrycode/R/countrycode.R | 231 ++++++---- countrycode-1.3.0/countrycode/R/countryname.R | 16 countrycode-1.3.0/countrycode/data/codelist.rda |binary countrycode-1.3.0/countrycode/data/codelist_panel.rda |binary countrycode-1.3.0/countrycode/man/cldr_examples.Rd | 4 countrycode-1.3.0/countrycode/man/codelist.Rd | 142 +++--- countrycode-1.3.0/countrycode/man/countrycode-package.Rd | 5 countrycode-1.3.0/countrycode/man/countrycode.Rd | 81 ++- countrycode-1.3.0/countrycode/man/countryname.Rd | 19 countrycode-1.3.0/countrycode/man/countryname_dict.Rd | 4 countrycode-1.3.0/countrycode/man/guess_field.Rd | 6 countrycode-1.3.0/countrycode/tests/testthat/data-known-name-variations.R | 17 countrycode-1.3.0/countrycode/tests/testthat/test-corner-cases.R | 21 countrycode-1.3.0/countrycode/tests/testthat/test-countryname.R | 5 countrycode-1.3.0/countrycode/tests/testthat/test-destination.R |only countrycode-1.3.0/countrycode/tests/testthat/test-regex-special.R | 5 21 files changed, 466 insertions(+), 314 deletions(-)
Title: Calculating Likelihoods by Pedigree Paring
Description: A fast and general implementation of the Elston-Stewart algorithm
that can calculate the likelihoods of large and complex pedigrees.
References for the Elston-Stewart algorithm are
Elston & Stewart (1971) <doi:10.1159/000152448>,
Lange & Elston (1975) <doi:10.1159/000152714> and
Cannings et al. (1978) <doi:10.2307/1426718>.
Author: James Dowty [aut, cre],
Kevin Wong [aut]
Maintainer: James Dowty <jgdowty@gmail.com>
Diff between clipp versions 1.0.0 dated 2021-05-05 and 1.0.1 dated 2021-07-15
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/pedigree_loglikelihood.R | 1 + R/pedigree_loglikelihood_g.R | 11 +++++++---- 4 files changed, 14 insertions(+), 10 deletions(-)
Title: The Bayes Factor Playground
Description: A lightweight modelling syntax for defining likelihoods and priors
and for computing Bayes factors for simple one parameter models. It includes
functionality for computing and plotting priors, likelihoods, and model
predictions. Additional functionality is included for computing and plotting
posteriors.
Author: Lincoln J Colling [aut, cre] (<https://orcid.org/0000-0002-3572-7758>)
Maintainer: Lincoln J Colling <lincoln@colling.net.nz>
Diff between bayesplay versions 0.9.0 dated 2021-06-17 and 0.9.1 dated 2021-07-15
DESCRIPTION | 16 +- MD5 | 51 ++++--- R/classes.r | 6 R/likelihoods.R | 9 - R/plots.R | 113 +++++++++++------ R/priors.r | 84 ++++++++---- README.md | 10 + inst/doc/advanced.html | 2 inst/doc/basic.R | 4 inst/doc/basic.Rmd | 6 inst/doc/basic.html | 14 +- inst/doc/default_ttests.Rmd | 2 inst/doc/default_ttests.html | 3 inst/doc/plots.R | 45 ++++++ inst/doc/plots.Rmd | 70 ++++++++++ inst/doc/plots.html | 63 +++++++++ man/likelihood.Rd | 4 man/prior.Rd | 2 man/visual_compare.Rd | 4 tests/figs/plots/point-posterior.svg |only tests/testthat/test-family.R |only tests/testthat/test-function_text.R |only tests/testthat/test-plots.R | 230 +++++++++++++++++------------------ tests/testthat/test-posterior.R | 2 tests/testthat/test-priors.R | 2 vignettes/basic.Rmd | 6 vignettes/default_ttests.Rmd | 2 vignettes/plots.Rmd | 70 ++++++++++ 28 files changed, 572 insertions(+), 248 deletions(-)