Title: Subsampling Ranking Forward Selection (SuRF)
Description: Performs variable selection based on subsampling, ranking forward selection. Details of the method are published in Lihui Liu, Hong Gu, Johan Van Limbergen, Toby Kenney (2020) SuRF: A new method for sparse variable selection, with application in microbiome data analysis Statistics in Medicine 40 897-919 <doi:10.1002/sim.8809>. Xo is the matrix of predictor variables. y is the response variable. Currently only binary responses using logistic regression are supported. X is a matrix of additional predictors which should be scaled to have sum 1 prior to analysis. fold is the number of folds for cross-validation. Alpha is the parameter for the elastic net method used in the subsampling procedure: the default value of 1 corresponds to LASSO. prop is the proportion of variables to remove in the each subsample. weights indicates whether observations should be weighted by class size. When the class sizes are unbalanced, weighting observations can improve results. B is the number of subsamples to use for ranking the variables. C is the number of permutations to use for estimating the critical value of the null distribution. If the 'doParallel' package is installed, the function can be run in parallel by setting ncores to the number of threads to use. If the default value of 1 is used, or if the 'doParallel' package is not installed, the function does not run in parallel. display.progress indicates whether the function should display messages indicating its progress. family is a family variable for the glm() fitting. Note that the 'glmnet' package does not permit the use of nonstandard link functions, so will always use the default link function. However, the glm() fitting will use the specified link. The default is binomial with logistic regression, because this is a common use case. pval is the p-value for inclusion of a variable in the model. Under the null case, the number of false positives will be geometrically distributed with this as probability of success, so if this parameter is set to p, the expected number of false positives should be p/(1-p).
Author: Lihui Liu [aut],
Toby Kenney [aut, cre]
Maintainer: Toby Kenney <tkenney@mathstat.dal.ca>
Diff between SuRF.vs versions 1.1.0 dated 2022-01-05 and 1.1.0.1 dated 2022-01-07
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ inst/doc/SURF.R | 3 +++ inst/doc/SURF.Rmd | 3 +++ inst/doc/SURF.html | 17 ++++++++++++++--- man/SURF.Rd | 30 +++++++++++++++++++++++++++--- vignettes/SURF.Rmd | 3 +++ 7 files changed, 60 insertions(+), 16 deletions(-)
Title: R Interface for the RAPIDS cuML Suite of Libraries
Description: R interface for RAPIDS cuML (<https://github.com/rapidsai/cuml>),
a suite of GPU-accelerated machine learning libraries powered by CUDA
(<https://en.wikipedia.org/wiki/CUDA>).
Author: Yitao Li [aut, cph] (<https://orcid.org/0000-0002-1261-905X>),
Tomasz Kalinowski [cph, ctb],
Daniel Falbel [aut, cre, cph],
RStudio [cph, fnd]
Maintainer: Daniel Falbel <daniel@rstudio.com>
Diff between cuda.ml versions 0.3.1 dated 2021-11-09 and 0.3.2 dated 2022-01-07
cuda.ml-0.3.1/cuda.ml/src/glm.cpp |only cuda.ml-0.3.1/cuda.ml/src/glm.cu |only cuda.ml-0.3.1/cuda.ml/src/glm.h |only cuda.ml-0.3.2/cuda.ml/DESCRIPTION | 16 cuda.ml-0.3.2/cuda.ml/MD5 | 80 +++- cuda.ml-0.3.2/cuda.ml/NAMESPACE | 19 + cuda.ml-0.3.2/cuda.ml/R/RcppExports.R | 20 - cuda.ml-0.3.2/cuda.ml/R/elastic_net.R |only cuda.ml-0.3.2/cuda.ml/R/kmeans.R | 3 cuda.ml-0.3.2/cuda.ml/R/knn.R | 2 cuda.ml-0.3.2/cuda.ml/R/lasso.R | 36 +- cuda.ml-0.3.2/cuda.ml/R/lm.R | 2 cuda.ml-0.3.2/cuda.ml/R/logistic_reg.R |only cuda.ml-0.3.2/cuda.ml/R/ols.R | 12 cuda.ml-0.3.2/cuda.ml/R/rand_forest.R | 2 cuda.ml-0.3.2/cuda.ml/R/ridge.R | 20 - cuda.ml-0.3.2/cuda.ml/R/sgd.R |only cuda.ml-0.3.2/cuda.ml/R/svm.R | 2 cuda.ml-0.3.2/cuda.ml/man/cuda_ml_elastic_net.Rd |only cuda.ml-0.3.2/cuda.ml/man/cuda_ml_kmeans.Rd | 3 cuda.ml-0.3.2/cuda.ml/man/cuda_ml_lasso.Rd | 13 cuda.ml-0.3.2/cuda.ml/man/cuda_ml_logistic_reg.Rd |only cuda.ml-0.3.2/cuda.ml/man/cuda_ml_ridge.Rd | 8 cuda.ml-0.3.2/cuda.ml/man/cuda_ml_sgd.Rd |only cuda.ml-0.3.2/cuda.ml/man/predict.cuda_ml_logistic_reg.Rd |only cuda.ml-0.3.2/cuda.ml/src/CMakeLists.txt.in | 33 +- cuda.ml-0.3.2/cuda.ml/src/Makevars.in | 3 cuda.ml-0.3.2/cuda.ml/src/RcppExports.cpp | 94 ++++- cuda.ml-0.3.2/cuda.ml/src/lm_predict.cpp |only cuda.ml-0.3.2/cuda.ml/src/lm_predict.cu |only cuda.ml-0.3.2/cuda.ml/src/lm_predict.h |only cuda.ml-0.3.2/cuda.ml/src/qn.cpp |only cuda.ml-0.3.2/cuda.ml/src/qn.cu |only cuda.ml-0.3.2/cuda.ml/src/qn.h |only cuda.ml-0.3.2/cuda.ml/src/qn_constants.h |only cuda.ml-0.3.2/cuda.ml/src/sgd.cpp |only cuda.ml-0.3.2/cuda.ml/src/sgd.cu |only cuda.ml-0.3.2/cuda.ml/src/sgd.h |only cuda.ml-0.3.2/cuda.ml/src/sgd_fit_impl.cu |only cuda.ml-0.3.2/cuda.ml/src/sgd_fit_impl.h |only cuda.ml-0.3.2/cuda.ml/src/stubs/treelite/c_api.h | 4 cuda.ml-0.3.2/cuda.ml/src/warn_cuml_missing.h | 16 cuda.ml-0.3.2/cuda.ml/tests/testthat/helper-initialize.R | 2 cuda.ml-0.3.2/cuda.ml/tests/testthat/test-elastic-net.R |only cuda.ml-0.3.2/cuda.ml/tests/testthat/test-lasso.R | 3 cuda.ml-0.3.2/cuda.ml/tests/testthat/test-logistic-reg.R |only cuda.ml-0.3.2/cuda.ml/tests/testthat/test-ols.R | 3 cuda.ml-0.3.2/cuda.ml/tests/testthat/test-ridge.R | 3 cuda.ml-0.3.2/cuda.ml/tests/testthat/test-sgd.R |only cuda.ml-0.3.2/cuda.ml/tools/config/configure.R | 227 ++------------ cuda.ml-0.3.2/cuda.ml/tools/config/libcuml_versions.R |only cuda.ml-0.3.2/cuda.ml/tools/config/utils |only cuda.ml-0.3.2/cuda.ml/tools/launch-rstudio |only 53 files changed, 329 insertions(+), 297 deletions(-)
Title: Install Packages from Snapshots on the Checkpoint Server for
Reproducibility
Description: The goal of checkpoint is to solve the problem of package
reproducibility in R. Specifically, checkpoint allows you to install packages
as they existed on CRAN on a specific snapshot date as if you had a CRAN time
machine. To achieve reproducibility, the checkpoint() function installs the
packages required or called by your project and scripts to a local library
exactly as they existed at the specified point in time. Only those packages
are available to your project, thereby avoiding any package updates that came
later and may have altered your results. In this way, anyone using checkpoint's
checkpoint() can ensure the reproducibility of your scripts or projects at any
time. To create the snapshot archives, once a day (at midnight UTC) Microsoft
refreshes the Austria CRAN mirror on the "Microsoft R Archived Network"
server (<https://mran.microsoft.com/>). Immediately after completion
of the rsync mirror process, the process takes a snapshot, thus creating the
archive. Snapshot archives exist starting from 2014-09-17.
Author: Folashade Daniel [cre],
Hong Ooi [aut],
Andrie de Vries [aut],
Gábor Csárdi [ctb] (Assistance with pkgdepends),
Microsoft [aut, cph]
Maintainer: Folashade Daniel <fdaniel@microsoft.com>
Diff between checkpoint versions 1.0.0 dated 2021-06-14 and 1.0.1 dated 2022-01-07
DESCRIPTION | 12 - MD5 | 8 - NEWS.md | 4 build/vignette.rds |binary inst/doc/checkpoint.html | 296 ++++++++++------------------------------------- 5 files changed, 82 insertions(+), 238 deletions(-)
Title: Model-Based Response Dimension Reduction
Description: Functions for model-based response dimension reduction. Usual dimension reduction methods in multivariate regression focus on the reduction of predictors, not responses. The response dimension reduction is theoretically founded in Yoo and Cook (2008) <doi:10.1016/j.csda.2008.07.029>. Later, three model-based response dimension reduction approaches are proposed in Yoo (2016) <doi:10.1080/02331888.2017.1410152> and Yoo (2019) <doi:10.1016/j.jkss.2019.02.001>. The method by Yoo and Cook (2008) is based on non-parametric ordinary least squares, but the model-based approaches are done through maximum likelihood estimation. For two model-based response dimension reduction methods called principal fitted response reduction and unstructured principal fitted response reduction, chi-squared tests are provided for determining the dimension of the response subspace.
Author: Jae Keun Yoo
Maintainer: Jae Keun Yoo <peter.yoo@ewha.ac.kr>
Diff between mbrdr versions 1.0.8 dated 2021-08-17 and 1.1.0 dated 2022-01-07
DESCRIPTION | 8 ++-- MD5 | 4 +- R/mbrdr.R | 116 ++++++++++++++++++++++++++++++++---------------------------- 3 files changed, 68 insertions(+), 60 deletions(-)
Title: Dynamic Function-Oriented 'Make'-Like Declarative Workflows
Description: As a pipeline toolkit for Statistics and data science in R,
the 'targets' package brings together function-oriented programming and
'Make'-like declarative workflows.
It analyzes the dependency relationships among the tasks of a workflow,
skips steps that are already up to date, runs the necessary
computation with optional parallel workers, abstracts files as
R objects, and provides tangible evidence that the results match
the underlying code and data. The methodology in this package
borrows from GNU 'Make' (2015, ISBN:978-9881443519)
and 'drake' (2018, <doi:10.21105/joss.00550>).
Author: William Michael Landau [aut, cre]
(<https://orcid.org/0000-0003-1878-3253>),
Matthew T. Warkentin [ctb],
Samantha Oliver [rev] (<https://orcid.org/0000-0001-5668-1165>),
Tristan Mahr [rev] (<https://orcid.org/0000-0002-8890-5116>),
Eli Lilly and Company [cph]
Maintainer: William Michael Landau <will.landau@gmail.com>
Diff between targets versions 0.9.0 dated 2021-12-04 and 0.10.0 dated 2022-01-07
targets-0.10.0/targets/DESCRIPTION | 17 targets-0.10.0/targets/MD5 | 224 +++++----- targets-0.10.0/targets/NAMESPACE | 50 +- targets-0.10.0/targets/NEWS.md | 30 + targets-0.10.0/targets/R/class_active.R | 8 targets-0.10.0/targets/R/class_aws.R | 41 - targets-0.10.0/targets/R/class_aws_feather.R | 4 targets-0.10.0/targets/R/class_aws_file.R | 6 targets-0.10.0/targets/R/class_aws_fst.R | 4 targets-0.10.0/targets/R/class_aws_fst_dt.R | 4 targets-0.10.0/targets/R/class_aws_fst_tbl.R | 4 targets-0.10.0/targets/R/class_aws_keras.R | 5 targets-0.10.0/targets/R/class_aws_parquet.R | 4 targets-0.10.0/targets/R/class_aws_qs.R | 4 targets-0.10.0/targets/R/class_aws_rds.R | 4 targets-0.10.0/targets/R/class_aws_torch.R | 5 targets-0.10.0/targets/R/class_builder.R | 40 + targets-0.10.0/targets/R/class_cloud.R | 2 targets-0.10.0/targets/R/class_clustermq.R | 6 targets-0.10.0/targets/R/class_feather.R | 9 targets-0.10.0/targets/R/class_file.R | 1 targets-0.10.0/targets/R/class_fst.R | 6 targets-0.10.0/targets/R/class_fst_dt.R | 6 targets-0.10.0/targets/R/class_fst_tbl.R | 8 targets-0.10.0/targets/R/class_future.R | 6 targets-0.10.0/targets/R/class_keras.R | 10 targets-0.10.0/targets/R/class_nonexportable.R |only targets-0.10.0/targets/R/class_parquet.R | 9 targets-0.10.0/targets/R/class_pipeline.R | 12 targets-0.10.0/targets/R/class_qs.R | 4 targets-0.10.0/targets/R/class_rds.R | 4 targets-0.10.0/targets/R/class_runtime.R | 49 +- targets-0.10.0/targets/R/class_store.R | 62 +- targets-0.10.0/targets/R/class_store_custom.R |only targets-0.10.0/targets/R/class_store_file.R | 8 targets-0.10.0/targets/R/class_target.R | 25 - targets-0.10.0/targets/R/class_torch.R | 10 targets-0.10.0/targets/R/class_url.R | 6 targets-0.10.0/targets/R/tar_active.R |only targets-0.10.0/targets/R/tar_call.R |only targets-0.10.0/targets/R/tar_envvars.R | 18 targets-0.10.0/targets/R/tar_format.R |only targets-0.10.0/targets/R/tar_glimpse.R | 4 targets-0.10.0/targets/R/tar_make.R | 4 targets-0.10.0/targets/R/tar_make_clustermq.R | 4 targets-0.10.0/targets/R/tar_make_future.R | 4 targets-0.10.0/targets/R/tar_make_interactive.R | 2 targets-0.10.0/targets/R/tar_manifest.R | 4 targets-0.10.0/targets/R/tar_network.R | 4 targets-0.10.0/targets/R/tar_outdated.R | 4 targets-0.10.0/targets/R/tar_package.R | 3 targets-0.10.0/targets/R/tar_prune.R | 4 targets-0.10.0/targets/R/tar_renv.R | 4 targets-0.10.0/targets/R/tar_sitrep.R | 4 targets-0.10.0/targets/R/tar_target.R | 11 targets-0.10.0/targets/R/tar_validate.R | 4 targets-0.10.0/targets/R/tar_visnetwork.R | 4 targets-0.10.0/targets/R/utils_assert.R | 32 + targets-0.10.0/targets/R/utils_callr.R | 28 - targets-0.10.0/targets/R/utils_data.R | 10 targets-0.10.0/targets/R/utils_envvars.R |only targets-0.10.0/targets/R/utils_imports.R | 2 targets-0.10.0/targets/build/partial.rdb |binary targets-0.10.0/targets/inst/WORDLIST | 10 targets-0.10.0/targets/inst/doc/overview.Rmd | 2 targets-0.10.0/targets/inst/doc/overview.html | 2 targets-0.10.0/targets/man/tar_active.Rd |only targets-0.10.0/targets/man/tar_assert.Rd | 6 targets-0.10.0/targets/man/tar_call.Rd |only targets-0.10.0/targets/man/tar_cancel.Rd | 2 targets-0.10.0/targets/man/tar_cue.Rd | 1 targets-0.10.0/targets/man/tar_definition.Rd | 2 targets-0.10.0/targets/man/tar_envir.Rd | 2 targets-0.10.0/targets/man/tar_envvars.Rd | 17 targets-0.10.0/targets/man/tar_format.Rd |only targets-0.10.0/targets/man/tar_group.Rd | 2 targets-0.10.0/targets/man/tar_name.Rd | 2 targets-0.10.0/targets/man/tar_path.Rd | 2 targets-0.10.0/targets/man/tar_runtime_object.Rd |only targets-0.10.0/targets/man/tar_seed.Rd | 2 targets-0.10.0/targets/man/tar_store.Rd | 2 targets-0.10.0/targets/man/tar_target.Rd | 12 targets-0.10.0/targets/man/tar_target_raw.Rd | 1 targets-0.10.0/targets/man/target_run_worker.Rd | 8 targets-0.10.0/targets/man/targets-package.Rd | 2 targets-0.10.0/targets/tests/aws/test-aws_custom.R |only targets-0.10.0/targets/tests/aws/test-aws_hpc.R |only targets-0.10.0/targets/tests/aws/test-class_aws_qs.R | 2 targets-0.10.0/targets/tests/hpc/sge_batchtools.tmpl | 2 targets-0.10.0/targets/tests/hpc/sge_clustermq.tmpl | 2 targets-0.10.0/targets/tests/hpc/test-clustermq_keras.R | 4 targets-0.10.0/targets/tests/hpc/test-clustermq_local.R | 18 targets-0.10.0/targets/tests/hpc/test-clustermq_sge.R | 61 +- targets-0.10.0/targets/tests/hpc/test-exports.R |only targets-0.10.0/targets/tests/hpc/test-future_keras.R | 4 targets-0.10.0/targets/tests/hpc/test-future_local.R | 4 targets-0.10.0/targets/tests/hpc/test-future_sge.R | 76 ++- targets-0.10.0/targets/tests/interactive/test-tar_watch.R | 2 targets-0.10.0/targets/tests/performance/test-stems.R | 2 targets-0.10.0/targets/tests/testthat/test-class_active.R | 12 targets-0.10.0/targets/tests/testthat/test-class_aws.R | 16 targets-0.10.0/targets/tests/testthat/test-class_builder.R | 10 targets-0.10.0/targets/tests/testthat/test-class_clustermq.R | 16 targets-0.10.0/targets/tests/testthat/test-class_future.R | 16 targets-0.10.0/targets/tests/testthat/test-class_pipeline.R | 7 targets-0.10.0/targets/tests/testthat/test-class_runtime.R | 31 + targets-0.10.0/targets/tests/testthat/test-class_store.R | 4 targets-0.10.0/targets/tests/testthat/test-class_store_custom.R |only targets-0.10.0/targets/tests/testthat/test-class_store_file.R | 24 + targets-0.10.0/targets/tests/testthat/test-set_envvars.R |only targets-0.10.0/targets/tests/testthat/test-tar_active.R |only targets-0.10.0/targets/tests/testthat/test-tar_call.R |only targets-0.10.0/targets/tests/testthat/test-tar_envvars.R | 6 targets-0.10.0/targets/tests/testthat/test-tar_format.R |only targets-0.10.0/targets/tests/testthat/test-tar_make.R | 24 + targets-0.10.0/targets/tests/testthat/test-tar_path.R | 2 targets-0.10.0/targets/tests/testthat/test-tar_workspace.R | 2 targets-0.10.0/targets/tests/testthat/test-utils_assert.R | 16 targets-0.10.0/targets/tests/testthat/test-utils_data.R | 16 targets-0.10.0/targets/vignettes/overview.Rmd | 2 targets-0.9.0/targets/R/class_unexportable.R |only targets-0.9.0/targets/R/utils_oop.R |only targets-0.9.0/targets/tests/aws/test-aws-hpc.R |only targets-0.9.0/targets/tests/hpc/test-options.R |only 124 files changed, 875 insertions(+), 434 deletions(-)
Title: Archetypes for Targets
Description: Function-oriented Make-like declarative workflows for
Statistics and data science are supported in the 'targets' R package.
As an extension to 'targets', the 'tarchetypes' package provides
convenient user-side functions to make 'targets' easier to use.
By establishing reusable archetypes for common kinds of
targets and pipelines, these functions help express complicated
reproducible workflows concisely and compactly.
The methods in this package were influenced by the 'drake' R package
by Will Landau (2018) <doi:10.21105/joss.00550>.
Author: William Michael Landau [aut, cre]
(<https://orcid.org/0000-0003-1878-3253>),
Samantha Oliver [rev] (<https://orcid.org/0000-0001-5668-1165>),
Tristan Mahr [rev] (<https://orcid.org/0000-0002-8890-5116>),
Eli Lilly and Company [cph]
Maintainer: William Michael Landau <will.landau@gmail.com>
Diff between tarchetypes versions 0.4.0 dated 2021-12-10 and 0.4.1 dated 2022-01-07
DESCRIPTION | 6 ++-- MD5 | 8 ++--- NEWS.md | 4 ++ R/tar_map2_raw.R | 7 ++++- tests/testthat/test-tar_map2.R | 55 +++++++++++++++++++++++++++++++++++++++++ 5 files changed, 72 insertions(+), 8 deletions(-)
Title: Interactive Graphics for QTL Experiments
Description: Web-based interactive charts (using D3.js) for the analysis of
experimental crosses to identify genetic loci (quantitative trait
loci, QTL) contributing to variation in quantitative traits.
Broman (2015) <doi:10.1534/genetics.114.172742>.
Author: Karl W Broman [aut, cre] (<https://orcid.org/0000-0002-4914-6671>),
Michael Bostock [ctb, cph] (d3.js library in htmlwidgets/lib,
https://d3js.org),
jQuery Foundation [cph] (jQuery library in htmlwidgets/lib,
https://jquery.com),
jQuery contributors [ctb] (jQuery library in htmlwidgets/lib; see
https://github.com/jquery/jquery/blob/master/AUTHORS.txt),
jQuery UI contributors [ctb] (jQuery UI library in htmlwidgets/lib; see
https://jqueryui.com/about/)
Maintainer: Karl W Broman <broman@wisc.edu>
Diff between qtlcharts versions 0.14 dated 2021-08-06 and 0.16 dated 2022-01-07
DESCRIPTION | 10 ++-- LICENSE | 46 +++++++-------------- MD5 | 56 +++++++++++++------------- NEWS.md | 10 ++++ R/qtlchartsversion.R | 8 ++- README.md | 8 +-- data/geneExpr.rda |binary data/grav.rda |binary inst/LICENSE | 46 +++++++-------------- inst/htmlwidgets/iboxplot.yaml | 6 +- inst/htmlwidgets/idotplot.yaml | 6 +- inst/htmlwidgets/iheatmap.yaml | 6 +- inst/htmlwidgets/ipleiotropy.yaml | 6 +- inst/htmlwidgets/iplot.yaml | 6 +- inst/htmlwidgets/iplotCorr.yaml | 6 +- inst/htmlwidgets/iplotCurves.yaml | 6 +- inst/htmlwidgets/iplotMScanone.yaml | 6 +- inst/htmlwidgets/iplotMap.yaml | 6 +- inst/htmlwidgets/iplotRF.yaml | 6 +- inst/htmlwidgets/iplotScanone.yaml | 6 +- inst/htmlwidgets/iplotScantwo.yaml | 6 +- inst/htmlwidgets/itriplot.yaml | 6 +- inst/htmlwidgets/lib/d3/d3.min.js | 4 - inst/htmlwidgets/lib/d3/package.json | 4 - inst/htmlwidgets/lib/d3panels/LICENSE.md | 2 inst/htmlwidgets/lib/d3panels/README.md | 10 ++-- inst/htmlwidgets/lib/d3panels/d3panels.min.js | 2 inst/htmlwidgets/lib/d3panels/package.json | 4 - inst/htmlwidgets/scat2scat.yaml | 6 +- 29 files changed, 139 insertions(+), 155 deletions(-)
Title: Access Elevation Data from Various APIs
Description: Several web services are available that provide access to elevation
data. This package provides access to several of those services and
returns elevation data either as a SpatialPointsDataFrame from
point elevation services or as a raster object from raster
elevation services. Currently, the package supports access to the
Amazon Web Services Terrain Tiles <https://registry.opendata.aws/terrain-tiles/>,
the Open Topography Global Datasets API <https://opentopography.org/developers/>,
and the USGS Elevation Point Query Service <https://nationalmap.gov/epqs/>.
Author: Jeffrey Hollister [aut, cre] (<https://orcid.org/0000-0002-9254-9740>),
Tarak Shah [ctb],
Alec L. Robitaille [ctb] (<https://orcid.org/0000-0002-4706-1762>),
Marcus W. Beck [rev] (<https://orcid.org/0000-0002-4996-0059>),
Mike Johnson [ctb] (<https://orcid.org/0000-0002-5288-8350>)
Maintainer: Jeffrey Hollister <hollister.jeff@epa.gov>
Diff between elevatr versions 0.4.1 dated 2021-07-22 and 0.4.2 dated 2022-01-07
DESCRIPTION | 12 - MD5 | 31 +- NAMESPACE | 33 +-- R/get_elev_point.R | 41 ++- R/get_elev_raster.R | 55 ++++- R/internal.R | 85 +++++++- README.md | 26 ++ inst/CITATION | 4 inst/doc/introduction_to_elevatr.R | 87 ++++++++ inst/doc/introduction_to_elevatr.Rmd | 57 +++++ inst/doc/introduction_to_elevatr.html | 352 +++++++++++++++++++++++++++++++--- man/get_opentopo_key.Rd |only man/get_tilexy_coords.Rd |only man/set_opentopo_key.Rd |only tests/testthat/test-get_elev_point.R | 4 tests/testthat/test-get_elev_raster.R | 9 tests/testthat/test-internal.R | 7 vignettes/introduction_to_elevatr.Rmd | 57 +++++ 18 files changed, 736 insertions(+), 124 deletions(-)
Title: Online Bayesian Methods for Change Point Analysis
Description: It implements the online Bayesian methods for change point analysis. It can
also perform missing data imputation with methods from 'VIM'. The reference
is Yigiter A, Chen J, An L, Danacioglu N (2015) <doi:10.1080/02664763.2014.1001330>.
Author: Hongyan Xu [cre, aut],
Ayten Yigiter [aut],
Jie Chen [aut]
Maintainer: Hongyan Xu <hxu@augusta.edu>
Diff between onlineBcp versions 0.1.3 dated 2021-11-22 and 0.1.4 dated 2022-01-07
DESCRIPTION | 6 +++--- MD5 | 11 ++++++----- NAMESPACE | 1 + NEWS | 8 ++++++++ R/online_cp.R | 17 +++++++++++++++-- man/addDatapoint.Rd |only man/online_cp.Rd | 4 +++- 7 files changed, 36 insertions(+), 11 deletions(-)
Title: Multivariate Hypothesis Tests
Description: Multivariate hypothesis tests and the confidence intervals. It can be used to test the hypothesizes about mean vector or vectors (one-sample, two independent samples, paired samples), covariance matrix (one or more matrices), and the correlation matrix. Moreover, it can be used for robust Hotelling T^2 test at one sample case in high dimensional data. For this package, we have benefited from the studies Rencher (2003), Nel and Merwe (1986) <DOI: 10.1080/03610928608829342>, Tatlidil (1996), Tsagris (2014), Villasenor Alva and Estrada (2009) <DOI: 10.1080/03610920802474465>.
Author: Hasan BULUT [aut,cre]
Maintainer: Hasan BULUT <hasan.bulut@omu.edu.tr>
Diff between MVTests versions 2.0.8 dated 2021-07-08 and 2.1.1 dated 2022-01-07
DESCRIPTION | 12 ++++++------ MD5 | 6 ++++-- NAMESPACE | 2 ++ R/RobCat.R |only man/RobCat.Rd |only 5 files changed, 12 insertions(+), 8 deletions(-)
Title: Waveband Definitions for UV, VIS, and IR Radiation
Description: Constructors of waveband objects for commonly used biological
spectral weighting functions (BSWFs) and for different wavebands describing
named ranges of wavelengths in the ultraviolet (UV), visible (VIS)
and infrared (IR) regions of the electromagnetic spectrum. 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>)
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between photobiologyWavebands versions 0.4.4 dated 2020-04-28 and 0.4.5 dated 2022-01-07
photobiologyWavebands-0.4.4/photobiologyWavebands/NEWS |only photobiologyWavebands-0.4.5/photobiologyWavebands/DESCRIPTION | 14 photobiologyWavebands-0.4.5/photobiologyWavebands/MD5 | 107 +-- photobiologyWavebands-0.4.5/photobiologyWavebands/NEWS.md |only photobiologyWavebands-0.4.5/photobiologyWavebands/R/blue.r | 32 - photobiologyWavebands-0.4.5/photobiologyWavebands/R/cie.e.fun.r | 27 photobiologyWavebands-0.4.5/photobiologyWavebands/R/cie.q.fun.r | 5 photobiologyWavebands-0.4.5/photobiologyWavebands/R/cie.r | 19 photobiologyWavebands-0.4.5/photobiologyWavebands/R/dna.gm.q.fun.r | 7 photobiologyWavebands-0.4.5/photobiologyWavebands/R/dna.gm.r | 17 photobiologyWavebands-0.4.5/photobiologyWavebands/R/dna.n.q.fun.r | 28 photobiologyWavebands-0.4.5/photobiologyWavebands/R/dna.n.r | 17 photobiologyWavebands-0.4.5/photobiologyWavebands/R/dna.p.q.fun.r | 14 photobiologyWavebands-0.4.5/photobiologyWavebands/R/dna.p.r | 17 photobiologyWavebands-0.4.5/photobiologyWavebands/R/flav.q.fun.r | 21 photobiologyWavebands-0.4.5/photobiologyWavebands/R/flav.r | 19 photobiologyWavebands-0.4.5/photobiologyWavebands/R/gen.g.q.fun.r | 11 photobiologyWavebands-0.4.5/photobiologyWavebands/R/gen.g.r | 16 photobiologyWavebands-0.4.5/photobiologyWavebands/R/gen.m.q.fun.r | 12 photobiologyWavebands-0.4.5/photobiologyWavebands/R/gen.m.r | 16 photobiologyWavebands-0.4.5/photobiologyWavebands/R/gen.t.q.fun.r | 22 photobiologyWavebands-0.4.5/photobiologyWavebands/R/gen.t.r | 16 photobiologyWavebands-0.4.5/photobiologyWavebands/R/green.r | 46 + photobiologyWavebands-0.4.5/photobiologyWavebands/R/icnirp.e.fun.r | 24 photobiologyWavebands-0.4.5/photobiologyWavebands/R/ir.bands.r | 6 photobiologyWavebands-0.4.5/photobiologyWavebands/R/ir.r | 205 +++++- photobiologyWavebands-0.4.5/photobiologyWavebands/R/meth.e.fun.r | 5 photobiologyWavebands-0.4.5/photobiologyWavebands/R/meth.q.fun.r | 3 photobiologyWavebands-0.4.5/photobiologyWavebands/R/meth.r | 18 photobiologyWavebands-0.4.5/photobiologyWavebands/R/orange.r | 11 photobiologyWavebands-0.4.5/photobiologyWavebands/R/par.r | 2 photobiologyWavebands-0.4.5/photobiologyWavebands/R/pg.q.fun.r | 9 photobiologyWavebands-0.4.5/photobiologyWavebands/R/pg.r | 18 photobiologyWavebands-0.4.5/photobiologyWavebands/R/photobiologyWavebands.R | 4 photobiologyWavebands-0.4.5/photobiologyWavebands/R/plant.bands.r | 4 photobiologyWavebands-0.4.5/photobiologyWavebands/R/purple.r | 16 photobiologyWavebands-0.4.5/photobiologyWavebands/R/red.r | 80 +- photobiologyWavebands-0.4.5/photobiologyWavebands/R/uv.bands.r | 8 photobiologyWavebands-0.4.5/photobiologyWavebands/R/uv.r | 9 photobiologyWavebands-0.4.5/photobiologyWavebands/R/uva.r | 83 ++ photobiologyWavebands-0.4.5/photobiologyWavebands/R/uvb.r | 38 - photobiologyWavebands-0.4.5/photobiologyWavebands/R/uvc.r | 29 photobiologyWavebands-0.4.5/photobiologyWavebands/R/uvi.r | 4 photobiologyWavebands-0.4.5/photobiologyWavebands/R/uvi.wb.r | 29 photobiologyWavebands-0.4.5/photobiologyWavebands/R/vis.bands.r | 2 photobiologyWavebands-0.4.5/photobiologyWavebands/R/vis.r | 22 photobiologyWavebands-0.4.5/photobiologyWavebands/R/yellow.r | 6 photobiologyWavebands-0.4.5/photobiologyWavebands/README.md | 81 +- photobiologyWavebands-0.4.5/photobiologyWavebands/build/partial.rdb |only photobiologyWavebands-0.4.5/photobiologyWavebands/build/vignette.rds |binary photobiologyWavebands-0.4.5/photobiologyWavebands/inst/doc/r4p-introduction.Rmd |only photobiologyWavebands-0.4.5/photobiologyWavebands/inst/doc/r4p-introduction.html |only photobiologyWavebands-0.4.5/photobiologyWavebands/inst/doc/user-guide.html | 307 ++-------- photobiologyWavebands-0.4.5/photobiologyWavebands/man/UVA.Rd | 13 photobiologyWavebands-0.4.5/photobiologyWavebands/man/UVB.Rd | 7 photobiologyWavebands-0.4.5/photobiologyWavebands/man/figures |only photobiologyWavebands-0.4.5/photobiologyWavebands/man/photobiologyWavebands-package.Rd | 12 photobiologyWavebands-0.4.5/photobiologyWavebands/vignettes/r4p-introduction.Rmd |only 58 files changed, 905 insertions(+), 633 deletions(-)
More information about photobiologyWavebands at CRAN
Permanent link
Title: Version, Share, Deploy, and Monitor Models
Description: The goal of 'vetiver' is to provide fluent tooling to version,
share, deploy, and monitor a trained model. Functions handle both
recording and checking the model's input data prototype, and
predicting from a remote API endpoint. The 'vetiver' package is
extensible, with generics that can support many kinds of models.
Author: Julia Silge [cre, aut] (<https://orcid.org/0000-0002-3671-836X>),
RStudio [cph, fnd]
Maintainer: Julia Silge <julia.silge@rstudio.com>
Diff between vetiver versions 0.1.0 dated 2021-11-02 and 0.1.1 dated 2022-01-07
DESCRIPTION | 21 ++--- MD5 | 84 ++++++++++++++------ NAMESPACE | 28 ++++++ NEWS.md | 16 +++ R/caret.R |only R/deploy-rsconnect.R |only R/handlers.R | 27 ++++-- R/mlr3.R |only R/open-api-spec.R | 60 +++++++++----- R/pin-read-write.R | 8 + R/pr-predict.R | 77 ++++++++++++++++-- R/tidymodels.R |only R/vetiver-model.R | 7 + R/vetiver-package.R | 11 ++ R/write-plumber.R | 5 - README.md | 80 +++++++++++++++---- build |only inst/biv_tidymodels.R |only inst/chicago_rpart.R |only inst/doc |only inst/netflix_tidymodels.R |only inst/pima_Learner.R |only inst/plumber/biv-svm |only inst/plumber/chicago-rpart |only inst/plumber/netflix-descriptions |only inst/rmarkdown |only man/api_spec.Rd | 22 +++-- man/handler_startup.Rd | 27 +++++- man/reexports.Rd |only man/vetiver-package.Rd | 2 man/vetiver_create_description.Rd | 23 +++++ man/vetiver_create_meta.Rd | 28 ++++-- man/vetiver_create_ptype.Rd | 14 ++- man/vetiver_deploy_rsconnect.Rd |only man/vetiver_pin_write.Rd | 2 man/vetiver_pr_predict.Rd | 37 ++++++++- man/vetiver_type_convert.Rd | 2 man/vetiver_write_plumber.Rd | 2 tests/testthat/_snaps/caret.md |only tests/testthat/_snaps/mlr3.md |only tests/testthat/_snaps/tidymodels.md |only tests/testthat/_snaps/write-plumber.md | 2 tests/testthat/test-caret.R |only tests/testthat/test-mlr3.R |only tests/testthat/test-pr-predict.R | 135 ++++++++++++++++++++++----------- tests/testthat/test-tidymodels.R |only tests/testthat/test-type-convert.R | 15 +++ tests/testthat/test-write-plumber.R | 4 tests/testthat/test-xgboost.R | 14 ++- vignettes |only 50 files changed, 580 insertions(+), 173 deletions(-)
Title: Proportional Odds Model with Censored, Time-Lagged Categorical
Outcome
Description: Implements a semiparametric estimator for the odds ratio model with
censored, time-lagged, ordered categorical outcome in a randomized clinical
trial that incorporates baseline and time-dependent information.
Tsiatis, A. A. and Davidian, M. (2021) <arXiv:2106.15559>.
Author: Marie Davidian [aut],
A. A. Tsiatis [aut],
Shannon T. Holloway [aut, cre]
Maintainer: Shannon T. Holloway <sthollow@ncsu.edu>
Diff between tLagPropOdds versions 1.5 dated 2021-12-03 and 1.6 dated 2022-01-07
DESCRIPTION | 13 +++++++------ MD5 | 11 ++++++++--- NAMESPACE | 2 ++ R/catProbs.R |only R/print.catProbsObj.R |only R/prob_aipw.R |only R/prob_ipw.R |only man/catProbs.Rd |only man/print.Rd | 16 +++++++++++++++- 9 files changed, 32 insertions(+), 10 deletions(-)
Title: PS-Integrated Methods for Incorporating RWE in Clinical Studies
Description: High-quality real-world data can be transformed into scientific
real-world evidence (RWE) for regulatory and healthcare decision-making
using proven analytical methods and techniques. For example, propensity
score (PS) methodology can be applied to pre-select a subset of real-world
data containing patients that are similar to those in the current clinical
study in terms of covariates, and to stratify the selected patients together
with those in the current study into more homogeneous strata. Then, methods
such as the power prior approach or composite likelihood approach can be
applied in each stratum to draw inference for the parameters of interest.
This package provides functions that implement the PS-integrated RWE
analysis methods proposed in Wang et al. (2019)
<doi:10.1080/10543406.2019.1657133>, Wang et al. (2020)
<doi:10.1080/10543406.2019.1684309> and Chen et al. (2020)
<doi:10.1080/10543406.2020.1730877>.
Author: Chenguang Wang [aut, cre],
Trustees of Columbia University [cph] (tools/make_cpp.R,
R/stanmodels.R),
Wei-Chen Chen [aut]
Maintainer: Chenguang Wang <chenguang.wang.0517@gmail.com>
Diff between psrwe versions 1.3 dated 2021-04-16 and 3.0 dated 2022-01-07
psrwe-1.3/psrwe/R/psrwe_balance.R |only psrwe-1.3/psrwe/R/psrwe_ps.R |only psrwe-1.3/psrwe/man/plot.RWE_DWITHPS.Rd |only psrwe-1.3/psrwe/man/rwe_ps.Rd |only psrwe-1.3/psrwe/man/rwe_ps_borrow.Rd |only psrwe-1.3/psrwe/man/rwe_ps_cl.Rd |only psrwe-1.3/psrwe/man/rwe_ps_cl2arm.Rd |only psrwe-1.3/psrwe/man/rwe_ps_dist.Rd |only psrwe-1.3/psrwe/man/rwe_ps_match.Rd |only psrwe-1.3/psrwe/man/rwe_ps_powerp.Rd |only psrwe-1.3/psrwe/man/summary.RWE_CLRST.Rd |only psrwe-1.3/psrwe/man/summary.RWE_POWERPRST.Rd |only psrwe-1.3/psrwe/man/tkCallFun.Rd |only psrwe-1.3/psrwe/man/tkExpRst.Rd |only psrwe-1.3/psrwe/man/tkMakeLocal.Rd |only psrwe-3.0/psrwe/DESCRIPTION | 48 psrwe-3.0/psrwe/MD5 | 115 +- psrwe-3.0/psrwe/NAMESPACE | 44 psrwe-3.0/psrwe/NEWS.md |only psrwe-3.0/psrwe/R/000_globalVariables.r |only psrwe-3.0/psrwe/R/psrwe_borrow.R |only psrwe-3.0/psrwe/R/psrwe_complikel.R | 287 +---- psrwe-3.0/psrwe/R/psrwe_confintv.R |only psrwe-3.0/psrwe/R/psrwe_distance.R |only psrwe-3.0/psrwe/R/psrwe_infer.R |only psrwe-3.0/psrwe/R/psrwe_outana.R |only psrwe-3.0/psrwe/R/psrwe_package.R | 93 - psrwe-3.0/psrwe/R/psrwe_powerprior.R | 540 +++++++--- psrwe-3.0/psrwe/R/psrwe_ps_est.R |only psrwe-3.0/psrwe/R/psrwe_ps_match.R |only psrwe-3.0/psrwe/R/psrwe_survkm.R |only psrwe-3.0/psrwe/R/psrwe_tools.R | 1151 +++++++++++++++++----- psrwe-3.0/psrwe/R/stanmodels.R | 5 psrwe-3.0/psrwe/R/toolkit.R | 59 - psrwe-3.0/psrwe/R/zzz.R | 3 psrwe-3.0/psrwe/README.md |only psrwe-3.0/psrwe/build/vignette.rds |binary psrwe-3.0/psrwe/configure |only psrwe-3.0/psrwe/configure.win |only psrwe-3.0/psrwe/data/ex_dta.rda |binary psrwe-3.0/psrwe/data/ex_dta_rct.rda |binary psrwe-3.0/psrwe/demo |only psrwe-3.0/psrwe/inst/doc/index.html |only psrwe-3.0/psrwe/inst/doc/vignette.R | 61 - psrwe-3.0/psrwe/inst/doc/vignette.Rmd | 72 - psrwe-3.0/psrwe/inst/doc/vignette.html | 526 ++-------- psrwe-3.0/psrwe/man/ex_dta.Rd | 20 psrwe-3.0/psrwe/man/ex_dta_rct.Rd | 21 psrwe-3.0/psrwe/man/get_distance.Rd | 35 psrwe-3.0/psrwe/man/plot.PSRWE_DTA.Rd |only psrwe-3.0/psrwe/man/plot.PSRWE_DTA_MAT.Rd |only psrwe-3.0/psrwe/man/plot.PSRWE_RST.Rd |only psrwe-3.0/psrwe/man/print.PSRWE_BOR.Rd |only psrwe-3.0/psrwe/man/print.PSRWE_DTA.Rd |only psrwe-3.0/psrwe/man/print.PSRWE_DTA_MAT.Rd |only psrwe-3.0/psrwe/man/print.PSRWE_RST.Rd |only psrwe-3.0/psrwe/man/print.PSRWE_RST_OUTANA.Rd |only psrwe-3.0/psrwe/man/psrwe-package.Rd | 47 psrwe-3.0/psrwe/man/psrwe_borrow.Rd |only psrwe-3.0/psrwe/man/psrwe_ci.Rd |only psrwe-3.0/psrwe/man/psrwe_compl.Rd |only psrwe-3.0/psrwe/man/psrwe_est.Rd |only psrwe-3.0/psrwe/man/psrwe_infer.Rd |only psrwe-3.0/psrwe/man/psrwe_match.Rd |only psrwe-3.0/psrwe/man/psrwe_outana.Rd |only psrwe-3.0/psrwe/man/psrwe_powerp.Rd |only psrwe-3.0/psrwe/man/psrwe_survkm.Rd |only psrwe-3.0/psrwe/man/rwe_cl.Rd | 2 psrwe-3.0/psrwe/man/rwe_cut.Rd | 7 psrwe-3.0/psrwe/man/rwe_km.Rd |only psrwe-3.0/psrwe/man/rwe_stan.Rd | 2 psrwe-3.0/psrwe/man/summary.PSRWE_DTA.Rd |only psrwe-3.0/psrwe/man/summary.PSRWE_DTA_MAT.Rd |only psrwe-3.0/psrwe/man/summary.PSRWE_RST.Rd |only psrwe-3.0/psrwe/src/Makevars | 5 psrwe-3.0/psrwe/src/Makevars.win | 8 psrwe-3.0/psrwe/src/RcppExports.cpp | 5 psrwe-3.0/psrwe/src/psrwe_cpp_tools.cpp | 2 psrwe-3.0/psrwe/src/stan_files/powerp.stan | 11 psrwe-3.0/psrwe/src/stan_files/powerps.stan | 15 psrwe-3.0/psrwe/src/stan_files/powerpsbinary.stan | 17 psrwe-3.0/psrwe/vignettes/vignette.Rmd | 72 - 82 files changed, 1972 insertions(+), 1301 deletions(-)
Title: Easy Access to Model Information for Various Model Objects
Description: A tool to provide an easy, intuitive and consistent
access to information contained in various R models, like model
formulas, model terms, information about random effects, data that was
used to fit the model or data from response variables. 'insight'
mainly revolves around two types of functions: Functions that find
(the names of) information, starting with 'find_', and functions that
get the underlying data, starting with 'get_'. The package has a
consistent syntax and works with many different model objects, where
otherwise functions to access these information are missing.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>,
@strengejacke),
Dominique Makowski [aut, ctb] (<https://orcid.org/0000-0001-5375-9967>,
@Dom_Makowski),
Indrajeet Patil [aut, ctb] (<https://orcid.org/0000-0003-1995-6531>,
@patilindrajeets),
Philip Waggoner [aut, ctb] (<https://orcid.org/0000-0002-7825-7573>),
Mattan S. Ben-Shachar [aut, ctb]
(<https://orcid.org/0000-0002-4287-4801>),
Brenton M. Wiernik [aut] (<https://orcid.org/0000-0001-9560-6336>,
@bmwiernik),
Vincent Arel-Bundock [ctb] (<https://orcid.org/0000-0003-2042-7063>),
Alex Hayes [rev] (<https://orcid.org/0000-0002-4985-5160>)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between insight versions 0.14.5 dated 2021-10-16 and 0.15.0 dated 2022-01-07
insight-0.14.5/insight/R/data_match.R |only insight-0.14.5/insight/R/data_relocate.R |only insight-0.14.5/insight/R/data_reshape.R |only insight-0.14.5/insight/R/data_restoretype.R |only insight-0.14.5/insight/R/reshape_ci.R |only insight-0.14.5/insight/man/reshape_ci.Rd |only insight-0.14.5/insight/tests/testthat/_snaps |only insight-0.15.0/insight/DESCRIPTION | 25 insight-0.15.0/insight/MD5 | 183 +++---- insight-0.15.0/insight/NAMESPACE | 25 insight-0.15.0/insight/NEWS.md | 146 +++-- insight-0.15.0/insight/R/check_if_installed.R | 4 insight-0.15.0/insight/R/clean_names.R | 3 insight-0.15.0/insight/R/clean_parameters.R | 2 insight-0.15.0/insight/R/compute_variances.R | 225 +++++++- insight-0.15.0/insight/R/datawizard.R |only insight-0.15.0/insight/R/export_table.R | 236 ++++++++- insight-0.15.0/insight/R/find_formula.R | 51 +- insight-0.15.0/insight/R/find_parameters_bayesian.R | 14 insight-0.15.0/insight/R/find_parameters_other.R | 14 insight-0.15.0/insight/R/find_predictors.R | 12 insight-0.15.0/insight/R/find_response.R | 28 + insight-0.15.0/insight/R/find_smooth.R | 2 insight-0.15.0/insight/R/find_statistic.R | 22 insight-0.15.0/insight/R/find_terms.R | 28 + insight-0.15.0/insight/R/find_transformation.R | 1 insight-0.15.0/insight/R/format_p.R | 30 + insight-0.15.0/insight/R/format_table.R | 3 insight-0.15.0/insight/R/format_value.R | 4 insight-0.15.0/insight/R/get_auxiliary.R | 12 insight-0.15.0/insight/R/get_data.R | 154 +++--- insight-0.15.0/insight/R/get_df.R | 51 +- insight-0.15.0/insight/R/get_family.R | 2 insight-0.15.0/insight/R/get_loglikelihood.R | 2 insight-0.15.0/insight/R/get_parameters.R | 17 insight-0.15.0/insight/R/get_parameters_bayesian.R | 6 insight-0.15.0/insight/R/get_predicted.R | 202 +++++-- insight-0.15.0/insight/R/get_predicted_ci.R | 34 + insight-0.15.0/insight/R/get_predicted_ci_zeroinflated.R |only insight-0.15.0/insight/R/get_predicted_methods.R | 10 insight-0.15.0/insight/R/get_response.R | 2 insight-0.15.0/insight/R/get_sigma.R | 37 - insight-0.15.0/insight/R/get_statistic.R | 17 insight-0.15.0/insight/R/get_transformation.R | 9 insight-0.15.0/insight/R/get_varcov.R | 60 +- insight-0.15.0/insight/R/get_weights.R | 2 insight-0.15.0/insight/R/helper_functions.R | 4 insight-0.15.0/insight/R/is_model.R | 6 insight-0.15.0/insight/R/is_model_supported.R | 4 insight-0.15.0/insight/R/model_info.R | 27 - insight-0.15.0/insight/R/n_obs.R | 22 insight-0.15.0/insight/R/standardize_column_order.R |only insight-0.15.0/insight/R/standardize_names.R | 90 +-- insight-0.15.0/insight/R/utils_get_data.R | 142 ++++- insight-0.15.0/insight/R/utils_model_info.R | 7 insight-0.15.0/insight/README.md | 166 +++--- insight-0.15.0/insight/build/partial.rdb |binary insight-0.15.0/insight/build/vignette.rds |binary insight-0.15.0/insight/inst/WORDLIST | 10 insight-0.15.0/insight/inst/doc/display.R | 8 insight-0.15.0/insight/inst/doc/display.Rmd | 8 insight-0.15.0/insight/inst/doc/display.html | 179 +++---- insight-0.15.0/insight/inst/doc/export.R |only insight-0.15.0/insight/inst/doc/export.Rmd |only insight-0.15.0/insight/inst/doc/export.html |only insight-0.15.0/insight/man/check_if_installed.Rd | 4 insight-0.15.0/insight/man/data_match.Rd | 51 +- insight-0.15.0/insight/man/data_relocate.Rd | 64 +- insight-0.15.0/insight/man/data_restoretype.Rd | 60 +- insight-0.15.0/insight/man/data_to_long.Rd | 253 ++++------ insight-0.15.0/insight/man/export_table.Rd | 52 +- insight-0.15.0/insight/man/find_formula.Rd | 55 -- insight-0.15.0/insight/man/format_p.Rd | 8 insight-0.15.0/insight/man/format_table.Rd | 3 insight-0.15.0/insight/man/format_value.Rd | 2 insight-0.15.0/insight/man/get_data.Rd | 2 insight-0.15.0/insight/man/get_predicted_ci.Rd | 4 insight-0.15.0/insight/man/get_varcov.Rd | 22 insight-0.15.0/insight/man/n_obs.Rd | 21 insight-0.15.0/insight/man/standardize_column_order.Rd |only insight-0.15.0/insight/man/to_numeric.Rd | 43 - insight-0.15.0/insight/tests/testthat/test-BayesFactorBF.R | 4 insight-0.15.0/insight/tests/testthat/test-brms.R | 29 + insight-0.15.0/insight/tests/testthat/test-clm.R | 2 insight-0.15.0/insight/tests/testthat/test-clmm.R | 2 insight-0.15.0/insight/tests/testthat/test-cpglmm.R | 2 insight-0.15.0/insight/tests/testthat/test-find_response.R |only insight-0.15.0/insight/tests/testthat/test-find_smooth.R | 2 insight-0.15.0/insight/tests/testthat/test-formatting.R | 9 insight-0.15.0/insight/tests/testthat/test-gam.R | 15 insight-0.15.0/insight/tests/testthat/test-get_predicted.R | 22 insight-0.15.0/insight/tests/testthat/test-glmmTMB.R | 11 insight-0.15.0/insight/tests/testthat/test-glmrob_base.R | 3 insight-0.15.0/insight/tests/testthat/test-panelr.R | 7 insight-0.15.0/insight/tests/testthat/test-polr.R | 1 insight-0.15.0/insight/tests/testthat/test-proportion_response.R | 8 insight-0.15.0/insight/tests/testthat/test-rstanarm.R | 114 +++- insight-0.15.0/insight/tests/testthat/test-standardize_column_order.R |only insight-0.15.0/insight/vignettes/display.Rmd | 8 insight-0.15.0/insight/vignettes/export.Rmd |only insight-0.15.0/insight/vignettes/export_table.png |only 101 files changed, 2172 insertions(+), 1059 deletions(-)
Title: Explore and Visualize Your Data Interactively
Description: A 'shiny' gadget to create 'ggplot2' figures interactively with drag-and-drop to map your variables to different aesthetics.
You can quickly visualize your data accordingly to their type, export in various formats,
and retrieve the code to reproduce the plot.
Author: Fanny Meyer [aut],
Victor Perrier [aut, cre],
Ian Carroll [ctb] (Faceting support),
Xiangnan Dang [ctb] (Facets rows and cols, X/Y limits),
Nicolas Bevacqua [cph] (author of dragula JavaScript library),
Daybrush (Younkue Choi) [cph] (author of moveable JavaScript library),
Zeno Rocha [cph] (author of clipboard JavaScript library)
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>
Diff between esquisse versions 1.0.2 dated 2021-07-05 and 1.1.0 dated 2022-01-07
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Title: Microbial Community Ecology Data Analysis
Description: A series of statistical and plotting approaches in microbial community ecology based on the R6 class. The classes are designed for data preprocessing, taxa abundance plotting, alpha diversity statistics, beta diversity statistics, differential abundance test and indicator taxon analysis, environmental data analysis, null model analysis, network analysis and functional analysis.
Author: Chi Liu [aut, cre],
Felipe R. P. Mansoldo [ctb],
Umer Zeeshan Ijaz [ctb],
Chenhao Li [ctb],
Yang Cao [ctb],
Minjie Yao [ctb],
Xiangzhen Li [ctb]
Maintainer: Chi Liu <liuchi0426@126.com>
Diff between microeco versions 0.6.0 dated 2021-11-16 and 0.6.5 dated 2022-01-07
microeco-0.6.0/microeco/data/datalist |only microeco-0.6.5/microeco/DESCRIPTION | 8 microeco-0.6.5/microeco/MD5 | 89 microeco-0.6.5/microeco/NAMESPACE | 60 microeco-0.6.5/microeco/R/data.R | 350 +- microeco-0.6.5/microeco/R/import.R | 32 microeco-0.6.5/microeco/R/microtable.R | 1409 ++++---- microeco-0.6.5/microeco/R/trans_abund.R | 1130 +++---- microeco-0.6.5/microeco/R/trans_alpha.R | 550 +-- microeco-0.6.5/microeco/R/trans_beta.R | 1080 +++--- microeco-0.6.5/microeco/R/trans_diff.R | 2740 ++++++++--------- microeco-0.6.5/microeco/R/trans_env.R | 1690 +++++----- microeco-0.6.5/microeco/R/trans_func.R | 1871 +++++------ microeco-0.6.5/microeco/R/trans_network.R | 1756 +++++----- microeco-0.6.5/microeco/R/trans_venn.R | 834 ++--- microeco-0.6.5/microeco/R/utility.R | 190 - microeco-0.6.5/microeco/inst/CITATION | 36 microeco-0.6.5/microeco/man/Tax4Fun2_KEGG.Rd | 26 microeco-0.6.5/microeco/man/clone.Rd | 46 microeco-0.6.5/microeco/man/dataset.Rd | 56 microeco-0.6.5/microeco/man/dropallfactors.Rd | 54 microeco-0.6.5/microeco/man/env_data_16S.Rd | 26 microeco-0.6.5/microeco/man/fungi_func_FUNGuild.Rd | 26 microeco-0.6.5/microeco/man/fungi_func_FungalTraits.Rd | 26 microeco-0.6.5/microeco/man/ko_map.Rd | 26 microeco-0.6.5/microeco/man/microtable.Rd | 1497 ++++----- microeco-0.6.5/microeco/man/otu_table_16S.Rd | 26 microeco-0.6.5/microeco/man/otu_table_ITS.Rd | 26 microeco-0.6.5/microeco/man/phylo_tree_16S.Rd | 26 microeco-0.6.5/microeco/man/prok_func_FAPROTAX.Rd | 26 microeco-0.6.5/microeco/man/prok_func_NJC19_list.Rd | 26 microeco-0.6.5/microeco/man/rep_fasta_16S.Rd | 26 microeco-0.6.5/microeco/man/sample_info_16S.Rd | 26 microeco-0.6.5/microeco/man/sample_info_ITS.Rd | 26 microeco-0.6.5/microeco/man/taxonomy_table_16S.Rd | 26 microeco-0.6.5/microeco/man/taxonomy_table_ITS.Rd | 26 microeco-0.6.5/microeco/man/tidy_taxonomy.Rd | 48 microeco-0.6.5/microeco/man/trans_abund.Rd | 926 ++--- microeco-0.6.5/microeco/man/trans_alpha.Rd | 454 +- microeco-0.6.5/microeco/man/trans_beta.Rd | 901 ++--- microeco-0.6.5/microeco/man/trans_diff.Rd | 834 ++--- microeco-0.6.5/microeco/man/trans_env.Rd | 1212 +++---- microeco-0.6.5/microeco/man/trans_func.Rd | 846 ++--- microeco-0.6.5/microeco/man/trans_network.Rd | 1212 +++---- microeco-0.6.5/microeco/man/trans_nullmodel.Rd | 972 +++--- microeco-0.6.5/microeco/man/trans_venn.Rd | 448 +- 46 files changed, 11916 insertions(+), 11805 deletions(-)
Title: Optimal Stratification of Sampling Frames for Multipurpose
Sampling Surveys
Description: In the field of stratified sampling design, this package offers an approach for the determination of the best stratification of a sampling frame, the one that ensures the minimum sample cost under the condition to satisfy precision constraints in a multivariate and multidomain case. This approach is based on the use of the genetic algorithm: each solution (i.e. a particular partition in strata of the sampling frame) is considered as an individual in a population; the fitness of all individuals is evaluated applying the Bethel-Chromy algorithm to calculate the sampling size satisfying precision constraints on the target estimates. Functions in the package allows to: (a) analyse the obtained results of the optimisation step; (b) assign the new strata labels to the sampling frame; (c) select a sample from the new frame accordingly to the best allocation. Functions for the execution of the genetic algorithm are a modified version of the functions in the 'genalg' package. M.Ballin, G.Barcaroli (2020) <arXiv:2004.09366> "R package SamplingStrata: new developments and extension to Spatial Sampling".
Author: Giulio Barcaroli, Marco Ballin, Hanjo Odendaal, Daniela Pagliuca, Egon Willighagen,
Diego Zardetto
Maintainer: Giulio Barcaroli <gbarcaroli@gmail.com>
Diff between SamplingStrata versions 1.5-1 dated 2020-03-02 and 1.5-2 dated 2022-01-07
SamplingStrata-1.5-1/SamplingStrata/vignettes/spatial_figures/mapped_strata.png |only SamplingStrata-1.5-1/SamplingStrata/vignettes/spatial_figures/optimization.png |only SamplingStrata-1.5-1/SamplingStrata/vignettes/spatial_figures/optimized_strata.png |only SamplingStrata-1.5-1/SamplingStrata/vignettes/spatial_figures/selected_sample.png |only SamplingStrata-1.5-1/SamplingStrata/vignettes/spatial_figures/strata.png |only SamplingStrata-1.5-2/SamplingStrata/DESCRIPTION | 20 SamplingStrata-1.5-2/SamplingStrata/MD5 | 97 - SamplingStrata-1.5-2/SamplingStrata/NAMESPACE | 12 SamplingStrata-1.5-2/SamplingStrata/NEWS | 146 - SamplingStrata-1.5-2/SamplingStrata/R/KmeansSolution.R | 21 SamplingStrata-1.5-2/SamplingStrata/R/adjustSize.R | 7 SamplingStrata-1.5-2/SamplingStrata/R/buildStrataDFSpatial_4.R | 1 SamplingStrata-1.5-2/SamplingStrata/R/buildStrataDF_models_4.R | 9 SamplingStrata-1.5-2/SamplingStrata/R/evalSolution.r | 8 SamplingStrata-1.5-2/SamplingStrata/R/expected_CV.R | 6 SamplingStrata-1.5-2/SamplingStrata/R/optimStrata.R | 8 SamplingStrata-1.5-2/SamplingStrata/R/optimizeStrata.R | 6 SamplingStrata-1.5-2/SamplingStrata/R/optimizeStrata2.R | 14 SamplingStrata-1.5-2/SamplingStrata/R/optimizeStrataSpatial.R | 8 SamplingStrata-1.5-2/SamplingStrata/R/plotSamprate.R | 10 SamplingStrata-1.5-2/SamplingStrata/R/plotStrata2d_new.R | 16 SamplingStrata-1.5-2/SamplingStrata/R/procBethel.R |only SamplingStrata-1.5-2/SamplingStrata/R/selectSampleSpatial.R |only SamplingStrata-1.5-2/SamplingStrata/build/vignette.rds |binary SamplingStrata-1.5-2/SamplingStrata/data/errors.rda |binary SamplingStrata-1.5-2/SamplingStrata/data/nations.rda |binary SamplingStrata-1.5-2/SamplingStrata/data/strata.rda |binary SamplingStrata-1.5-2/SamplingStrata/data/swisserrors.rda |binary SamplingStrata-1.5-2/SamplingStrata/data/swissframe.rda |binary SamplingStrata-1.5-2/SamplingStrata/data/swissmunicipalities.rda |binary SamplingStrata-1.5-2/SamplingStrata/data/swissstrata.rda |binary SamplingStrata-1.5-2/SamplingStrata/inst/CITATION | 20 SamplingStrata-1.5-2/SamplingStrata/inst/doc/SamplingStrata.R | 16 SamplingStrata-1.5-2/SamplingStrata/inst/doc/SamplingStrata.Rmd | 16 SamplingStrata-1.5-2/SamplingStrata/inst/doc/SamplingStrata.html | 922 ++++------ SamplingStrata-1.5-2/SamplingStrata/inst/doc/models.html | 484 +---- SamplingStrata-1.5-2/SamplingStrata/inst/doc/spatial.R | 129 - SamplingStrata-1.5-2/SamplingStrata/inst/doc/spatial.Rmd | 163 - SamplingStrata-1.5-2/SamplingStrata/inst/doc/spatial.html | 764 ++++---- SamplingStrata-1.5-2/SamplingStrata/man/adjustSize.Rd | 8 SamplingStrata-1.5-2/SamplingStrata/man/procBethel.Rd |only SamplingStrata-1.5-2/SamplingStrata/man/selectSample.Rd | 4 SamplingStrata-1.5-2/SamplingStrata/man/selectSampleSpatial.Rd |only SamplingStrata-1.5-2/SamplingStrata/man/selectSampleSystematic.Rd | 4 SamplingStrata-1.5-2/SamplingStrata/man/swissmunicipalities.Rd | 3 SamplingStrata-1.5-2/SamplingStrata/vignettes/SamplingStrata.Rmd | 16 SamplingStrata-1.5-2/SamplingStrata/vignettes/SamplingStrata.bib | 37 SamplingStrata-1.5-2/SamplingStrata/vignettes/spatial.Rmd | 163 - SamplingStrata-1.5-2/SamplingStrata/vignettes/spatial_figures/unnamed-chunk-10-1.jpg |only SamplingStrata-1.5-2/SamplingStrata/vignettes/spatial_figures/unnamed-chunk-2-1.png |binary SamplingStrata-1.5-2/SamplingStrata/vignettes/spatial_figures/unnamed-chunk-3-1.png |binary SamplingStrata-1.5-2/SamplingStrata/vignettes/spatial_figures/unnamed-chunk-3-2.png |binary SamplingStrata-1.5-2/SamplingStrata/vignettes/spatial_figures/unnamed-chunk-7-1.png |only SamplingStrata-1.5-2/SamplingStrata/vignettes/spatial_figures/unnamed-chunk-8-1.png |only SamplingStrata-1.5-2/SamplingStrata/vignettes/spatial_figures/unnamed-chunk-9-1.png |only SamplingStrata-1.5-2/SamplingStrata/vignettes/spatial_vignette.RData |binary 56 files changed, 1499 insertions(+), 1639 deletions(-)
More information about SamplingStrata at CRAN
Permanent link
Title: Response Time Distributions
Description: Provides response time distributions (density/PDF,
distribution function/CDF, quantile function, and random
generation): (a) Ratcliff diffusion model (Ratcliff &
McKoon, 2008, <doi:10.1162/neco.2008.12-06-420>) based on C
code by Andreas and Jochen Voss and (b) linear ballistic
accumulator (LBA; Brown & Heathcote, 2008,
<doi:10.1016/j.cogpsych.2007.12.002>) with different
distributions underlying the drift rate.
Author: Henrik Singmann [aut, cre] (<https://orcid.org/0000-0002-4842-3657>),
Scott Brown [aut],
Matthew Gretton [aut],
Andrew Heathcote [aut],
Andreas Voss [ctb],
Jochen Voss [ctb],
Andrew Terry [ctb]
Maintainer: Henrik Singmann <singmann@gmail.com>
Diff between rtdists versions 0.11-4 dated 2021-12-14 and 0.11-5 dated 2022-01-07
DESCRIPTION | 6 +++--- MD5 | 6 +++--- inst/doc/reanalysis_rr98.html | 4 ++-- src/Density.h | 8 ++++++-- 4 files changed, 14 insertions(+), 10 deletions(-)
Title: Spatial Ecology Miscellaneous Methods
Description: Collection of R functions and data sets for the support of spatial ecology analyses with a focus on pre, core and post modelling analyses of species distribution, niche quantification and community assembly. Written by current and former members and collaborators of the ecospat group of Antoine Guisan, Department of Ecology and Evolution (DEE) and Institute of Earth Surface Dynamics (IDYST), University of Lausanne, Switzerland. Read Di Cola et al. (2016) <doi:10.1111/ecog.02671> for details.
Author: Olivier Broennimann [cre, aut, ctb],
Valeria Di Cola [aut, ctb],
Blaise Petitpierre [ctb],
Frank Breiner [ctb],
Daniel Scherrer [ctb],
Manuela D`Amen [ctb],
Christophe Randin [ctb],
Robin Engler [ctb],
Wim Hordijk [ctb],
Heidi Mod [ctb],
Julien Pottier [ctb],
Mirko Di Febbraro [ctb],
Loic Pellissier [ctb],
Dorothea Pio [ctb],
Ruben Garcia Mateo [ctb],
Anne Dubuis [ctb],
Luigi Maiorano [ctb],
Achilleas Psomas [ctb],
Charlotte Ndiribe [ctb],
Nicolas Salamin [ctb],
Niklaus Zimmermann [ctb],
Antoine Guisan [aut]
Maintainer: Olivier Broennimann <olivier.broennimann@unil.ch>
Diff between ecospat versions 3.2 dated 2021-02-19 and 3.2.1 dated 2022-01-07
ecospat-3.2.1/ecospat/DESCRIPTION | 11 ecospat-3.2.1/ecospat/MD5 | 59 ++- ecospat-3.2.1/ecospat/NAMESPACE | 6 ecospat-3.2.1/ecospat/NEWS | 16 + ecospat-3.2.1/ecospat/R/ecospat.ESM.R | 8 ecospat-3.2.1/ecospat/R/ecospat.boyce.R | 87 ++--- ecospat-3.2.1/ecospat/R/ecospat.modelingtools.R | 6 ecospat-3.2.1/ecospat/R/ecospat.nichePOSNB.R |only ecospat-3.2.1/ecospat/R/ecospat.nichedynamic.R | 169 ++++++----- ecospat-3.2.1/ecospat/R/ecospat.nicheoverlap.R | 162 +++++++--- ecospat-3.2.1/ecospat/build/partial.rdb |binary ecospat-3.2.1/ecospat/build/vignette.rds |binary ecospat-3.2.1/ecospat/data/datalist | 1 ecospat-3.2.1/ecospat/data/ecospat.testNichePOSNB.txt |only ecospat-3.2.1/ecospat/inst/doc/vignette_ecospat_package.R | 23 + ecospat-3.2.1/ecospat/inst/doc/vignette_ecospat_package.Rmd | 29 + ecospat-3.2.1/ecospat/inst/doc/vignette_ecospat_package.pdf |binary ecospat-3.2.1/ecospat/man/ecospat.ESM.VarContrib.Rd | 2 ecospat-3.2.1/ecospat/man/ecospat.binary.model.Rd | 10 ecospat-3.2.1/ecospat/man/ecospat.boyce.Rd | 16 - ecospat-3.2.1/ecospat/man/ecospat.cv.me.Rd | 10 ecospat-3.2.1/ecospat/man/ecospat.maxentvarimport.Rd | 12 ecospat-3.2.1/ecospat/man/ecospat.niche.dyn.index.Rd | 6 ecospat-3.2.1/ecospat/man/ecospat.niche.equivalency.test.Rd | 20 - ecospat-3.2.1/ecospat/man/ecospat.niche.similarity.test.Rd | 28 + ecospat-3.2.1/ecospat/man/ecospat.nichePOSNB.Rd |only ecospat-3.2.1/ecospat/man/ecospat.occupied.patch.Rd | 10 ecospat-3.2.1/ecospat/man/ecospat.plot.niche.dyn.Rd | 21 + ecospat-3.2.1/ecospat/man/ecospat.plot.overlap.test.Rd | 2 ecospat-3.2.1/ecospat/man/ecospat.rangesize.Rd | 10 ecospat-3.2.1/ecospat/man/ecospat.testNichePOSNB.Rd |only ecospat-3.2.1/ecospat/vignettes/vignette_ecospat_package.Rmd | 29 + ecospat-3.2/ecospat/inst/extdata/maxent.txt |only 33 files changed, 461 insertions(+), 292 deletions(-)
Title: Analyses of Phylogenetics and Evolution
Description: Functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from DNA sequences, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood, dating trees with non-contemporaneous sequences, translating DNA into AA sequences, and assessing sequence alignments. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle) whose results are returned into R.
Author: Emmanuel Paradis [aut, cre, cph]
(<https://orcid.org/0000-0003-3092-2199>),
Simon Blomberg [aut, cph] (<https://orcid.org/0000-0003-1062-0839>),
Ben Bolker [aut, cph] (<https://orcid.org/0000-0002-2127-0443>),
Joseph Brown [aut, cph] (<https://orcid.org/0000-0002-3835-8062>),
Santiago Claramunt [aut, cph] (<https://orcid.org/0000-0002-8926-5974>),
Julien Claude [aut, cph] (<https://orcid.org/0000-0002-9267-1228>),
Hoa Sien Cuong [aut, cph],
Richard Desper [aut, cph],
Gilles Didier [aut, cph] (<https://orcid.org/0000-0003-0596-9112>),
Benoit Durand [aut, cph],
Julien Dutheil [aut, cph] (<https://orcid.org/0000-0001-7753-4121>),
RJ Ewing [aut, cph],
Olivier Gascuel [aut, cph],
Thomas Guillerme [aut, cph] (<https://orcid.org/0000-0003-4325-1275>),
Christoph Heibl [aut, cph] (<https://orcid.org/0000-0002-7655-3299>),
Anthony Ives [aut, cph] (<https://orcid.org/0000-0001-9375-9523>),
Bradley Jones [aut, cph] (<https://orcid.org/0000-0003-4498-1069>),
Franz Krah [aut, cph] (<https://orcid.org/0000-0001-7866-7508>),
Daniel Lawson [aut, cph] (<https://orcid.org/0000-0002-5311-6213>),
Vincent Lefort [aut, cph],
Pierre Legendre [aut, cph] (<https://orcid.org/0000-0002-3838-3305>),
Jim Lemon [aut, cph],
Guillaume Louvel [aut, cph] (<https://orcid.org/0000-0002-7745-0785>),
Eric Marcon [aut, cph] (<https://orcid.org/0000-0002-5249-321X>),
Rosemary McCloskey [aut, cph] (<https://orcid.org/0000-0002-9772-8553>),
Johan Nylander [aut, cph],
Rainer Opgen-Rhein [aut, cph],
Andrei-Alin Popescu [aut, cph],
Manuela Royer-Carenzi [aut, cph],
Klaus Schliep [aut, cph] (<https://orcid.org/0000-0003-2941-0161>),
Korbinian Strimmer [aut, cph] (<https://orcid.org/0000-0001-7917-2056>),
Damien de Vienne [aut, cph] (<https://orcid.org/0000-0001-9532-5251>)
Maintainer: Emmanuel Paradis <Emmanuel.Paradis@ird.fr>
Diff between ape versions 5.6 dated 2021-12-21 and 5.6-1 dated 2022-01-07
DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++-------------- R/as.bitsplits.R | 20 ++++++++++++++------ R/scales.R | 13 ++++++++++--- R/summary.phylo.R | 6 +++--- build/partial.rdb |binary inst/doc/DrawingPhylogenies.pdf |binary inst/doc/MoranI.pdf |binary inst/doc/RandomTopologies.pdf |binary man/bird.families.Rd | 3 +-- man/chiroptera.Rd | 5 ++--- man/getAnnotationsGenBank.Rd | 3 ++- man/hivtree.Rd | 36 ++++-------------------------------- man/mst.Rd | 3 +-- src/bitsplits.c | 31 ++++++++++++++++++++++++------- 15 files changed, 79 insertions(+), 77 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-03-24 1.0
Title: Single-Species, Multi-Species, and Integrated Spatial Occupancy
Models
Description: Fits single-species, multi-species, and integrated non-spatial and spatial occupancy models using Markov Chain Monte Carlo (MCMC). Models are fit using Polya-Gamma data augmentation detailed in Polson, Scott, and Windle (2013) <doi:10.1080/01621459.2013.829001>. Spatial models are fit using either Gaussian processes or Nearest Neighbor Gaussian Processes (NNGP) for large spatial datasets. Details on NNGP models are given in Datta, Banerjee, Finley, and Gelfand (2016) <doi:10.1080/01621459.2015.1044091> and Finley, Datta, and Banerjee (2020) <arXiv:2001.09111>. Provides functionality for data integration of multiple single-species occupancy data sets using a joint likelihood framework. Details on data integration are given in Miller, Pacifici, Sanderlin, and Reich (2019) <doi:10.1111/2041-210X.13110>. Details on single-species and multi-species models are found in MacKenzie, Nichols, Lachman, Droege, Royle, and Langtimm (2002) <doi:10.1890/0012-9658(2002)083[2248:ESORWD]2.0.CO;2> and Dorazio and Royle <doi:10.1198/016214505000000015>, respectively.
Author: Jeffrey Doser [aut, cre],
Andrew Finley [aut]
Maintainer: Jeffrey Doser <doserjef@msu.edu>
Diff between spOccupancy versions 0.2.0 dated 2021-12-19 and 0.2.1 dated 2022-01-07
DESCRIPTION | 6 ++-- MD5 | 64 ++++++++++++++++++++++--------------------- NEWS.md |only README.md | 30 ++++++++++---------- build/partial.rdb |binary inst |only man/figures/logo.png |binary src/PGOcc.cpp | 7 ---- src/PGOccREBoth.cpp | 40 +++++++++++++------------- src/PGOccREDet.cpp | 9 ------ src/PGOccREOcc.cpp | 11 ------- src/init.cpp | 36 ++++++++++++------------ src/intPGOcc.cpp | 10 ------ src/msPGOcc.cpp | 8 ----- src/msPGOccREBoth.cpp | 7 ---- src/msPGOccREDet.cpp | 8 ----- src/msPGOccREOcc.cpp | 8 ----- src/nn.cpp | 3 -- src/spIntPGOcc.cpp | 10 ------ src/spIntPGOccNNGP.cpp | 12 -------- src/spMsPGOcc.cpp | 7 ---- src/spMsPGOccNNGP.cpp | 12 -------- src/spMsPGOccNNGPPredict.cpp | 8 ----- src/spMsPGOccNNGPRE.cpp | 11 ------- src/spMsPGOccPredict.cpp | 5 --- src/spMsPGOccRE.cpp | 6 ---- src/spOccupancy.h | 47 +++++++++++++++++++------------ src/spPGOcc.cpp | 8 ----- src/spPGOccNNGP.cpp | 9 ------ src/spPGOccNNGPPredict.cpp | 8 ----- src/spPGOccNNGPRE.cpp | 8 ----- src/spPGOccPredict.cpp | 5 --- src/spPGOccRE.cpp | 6 ---- src/util.cpp | 3 -- 34 files changed, 137 insertions(+), 275 deletions(-)
Title: Modelling of Soil Water Retention and Hydraulic Conductivity
Data
Description: Provides functions for efficiently estimating properties of the Van Genuchten-Mualem model for soil hydraulic parameters from possibly sparse soil water retention and hydraulic conductivity data by multi-response parameter estimation methods (Stewart, W.E., Caracotsios, M. Soerensen, J.P. (1992) "Parameter estimation from multi-response data" <doi:10.1002/aic.690380502>). Parameter estimation is simplified by exploiting the fact that residual and saturated water contents and saturated conductivity are conditionally linear parameters (Bates, D. M. and Watts, D. G. (1988) "Nonlinear Regression Analysis and Its Applications" <doi:10.1002/9780470316757>). Estimated parameters are optionally constrained by the evaporation characteristic length (Lehmann, P., Bickel, S., Wei, Z. and Or, D. (2020) "Physical Constraints for Improved Soil Hydraulic Parameter Estimation by Pedotransfer Functions" <doi:10.1029/2019WR025963>) to ensure that the estimated parameters are physically valid. Common S3 methods and further utility functions allow to process, explore and visualise estimation results.
Author: Andreas Papritz [aut, cre]
Maintainer: Andreas Papritz <andreas.papritz@env.ethz.ch>
Diff between soilhypfit versions 0.1-4 dated 2021-12-08 and 0.1-5 dated 2022-01-07
ChangeLog | 58 ++ DESCRIPTION | 10 MD5 | 41 - NAMESPACE | 5 NEWS | 1 R/soilhypfit_S3methods.R | 298 ++++++++++- R/soilhypfit_exported_functions.R | 914 ++++++++++++++++++++++++++++++---- R/soilhypfit_private_functions.R | 435 +--------------- build/partial.rdb |binary man/soilhypfit_S3methods.Rd | 53 + man/soilhypfit_control_fit_wrc_hcc.Rd | 23 man/soilhypfit_evaporative_length.Rd | 7 man/soilhypfit_fit_wrc_hcc.Rd | 133 +++- man/soilhypfit_hcc_model.Rd | 4 man/soilhypfit_internal_functions.Rd | 5 man/soilhypfit_package.Rd | 52 + man/soilhypfit_prfloglik.Rd |only man/soilhypfit_sim_wrc_hcc.Rd | 4 man/soilhypfit_swissforestsoils.Rd | 4 man/soilhypfit_utility_functions.Rd | 16 man/soilhypfit_vcov.Rd | 7 man/soilhypfit_wrc_model.Rd | 7 22 files changed, 1431 insertions(+), 646 deletions(-)
Title: The Truncated Elliptical Family of Distributions
Description: It offers random numbers generation from members of the truncated multivariate elliptical family of distribution such as the truncated versions of the Normal, Student-t, Pearson VII, Slash, Logistic, among others. Particular distributions can be provided by specifying the density generating function. It also computes the first two moments (covariance matrix as well) for some particular distributions.
Author: Katherine A. L. Valeriano [aut, cre]
(<https://orcid.org/0000-0001-6388-4753>),
Larissa Avila Matos [ctb] (<https://orcid.org/0000-0002-2635-0901>),
Christian Galarza Morales [ctb]
(<https://orcid.org/0000-0002-4818-6006>)
Maintainer: Katherine A. L. Valeriano <katandreina@gmail.com>
Diff between relliptical versions 0.9.0 dated 2021-11-26 and 1.1.0 dated 2022-01-07
DESCRIPTION | 11 MD5 | 12 NAMESPACE | 1 R/Compute_Moments.R | 1 build/partial.rdb |binary src/Functions.cpp | 988 ++++++++++++++++++++++++---------------------------- src/RcppExports.cpp | 175 ++++----- 7 files changed, 565 insertions(+), 623 deletions(-)
Title: Automatic Time Series Forecasting and Missing Value Imputation
Description: Machine learning algorithm for predicting and imputing time series. It can automatically set all the parameters needed, thus in the minimal configuration it only requires the target variable and the dependent variables if present. It can address large problems with hundreds or thousands of dependent variables and problems in which the number of dependent variables is greater than the number of observations. Moreover it can be used not only for time series but also for any other real valued target variable. The algorithm implemented includes a Bayesian stochastic search methodology for model selection and a robust estimation based on bootstrapping. 'rego' is fast because all the code is C++.
Author: Davide Altomare [cre, aut],
David Loris [aut]
Maintainer: Davide Altomare <info@channelattribution.net>
Diff between rego versions 1.2.2 dated 2022-01-05 and 1.2.3 dated 2022-01-07
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- man/rego-package.Rd | 4 ++-- src/rego.cpp | 13 ++++++------- 4 files changed, 15 insertions(+), 16 deletions(-)
Title: Genome-Wide Association Study with SNP-Set Methods
Description: By using 'RAINBOWR' (Reliable Association INference By Optimizing Weights with R), users can test multiple SNPs (Single Nucleotide Polymorphisms) simultaneously by kernel-based (SNP-set) methods. This package can also be applied to haplotype-based GWAS (Genome-Wide Association Study). Users can test not only additive effects but also dominance and epistatic effects. In detail, please check our paper on PLOS Computational Biology: Kosuke Hamazaki and Hiroyoshi Iwata (2020) <doi:10.1371/journal.pcbi.1007663>.
Author: Kosuke Hamazaki [aut, cre],
Hiroyoshi Iwata [aut, ctb]
Maintainer: Kosuke Hamazaki <hamazaki@ut-biomet.org>
Diff between RAINBOWR versions 0.1.26 dated 2021-02-08 and 0.1.29 dated 2022-01-07
DESCRIPTION | 16 MD5 | 95 NAMESPACE | 22 NEWS.md |only R/EMM_functions_cpp.R | 883 +++- R/RGWAS.epistasis.R | 366 + R/RGWAS.multisnp.R | 461 +- R/RGWAS.normal.R | 327 + R/RGWAS.normal.interaction.R |only R/RGWAS.twostep.R | 355 + R/RGWAS.twostep.epi.R | 180 R/examples/EM3.cpp_example.R | 12 R/examples/EM3.general_example.R |only R/examples/EM3.linker.cpp_example.R | 6 R/examples/RGWAS.epistasis_example.R | 38 R/examples/RGWAS.multisnp_example.R | 64 R/examples/RGWAS.normal.interaction_example.R |only R/examples/RGWAS.normal_example.R | 54 R/examples/RGWAS.twostep.epi_example.R | 62 R/examples/RGWAS.twostep_example.R | 55 R/functions_for_RGWAS.R | 4953 +++++++++++++++++++++----- R/genetrait.R | 2 R/other_useful_functions.R | 190 README.md | 30 build/vignette.rds |binary inst/doc/RAINBOWR.Rmd | 28 inst/doc/RAINBOWR.html | 456 +- man/EM3.cpp.Rd | 29 man/EM3.general.Rd |only man/EM3.linker.cpp.Rd | 25 man/EM3.op.Rd |only man/RGWAS.epistasis.Rd | 39 man/RGWAS.multisnp.Rd | 35 man/RGWAS.normal.Rd | 39 man/RGWAS.normal.interaction.Rd |only man/RGWAS.twostep.Rd | 35 man/RGWAS.twostep.epi.Rd | 39 man/genetrait.Rd | 2 man/is.diag.Rd |only man/parallel.compute.Rd |only man/score.calc.LR.MC.Rd | 32 man/score.calc.LR.Rd | 9 man/score.calc.MC.Rd | 40 man/score.calc.Rd | 17 man/score.calc.epistasis.LR.MC.Rd |only man/score.calc.epistasis.LR.Rd | 13 man/score.calc.epistasis.score.MC.Rd |only man/score.calc.epistasis.score.Rd | 6 man/score.calc.int.MC.Rd |only man/score.calc.int.Rd |only man/score.calc.score.MC.Rd | 27 man/score.calc.score.Rd | 2 src/EMM_functions.cpp | 21 src/RcppExports.cpp | 9 vignettes/RAINBOWR.Rmd | 28 55 files changed, 6837 insertions(+), 2265 deletions(-)
Title: Easy Installation of the 'ped suite' Packages for Pedigree
Analysis
Description: The 'ped suite' is a collection of packages for pedigree
analysis, covering applications in forensic genetics, medical genetics
and more. A detailed presentation of the 'ped suite' is given in the
book 'Pedigree Analysis in R' (Vigeland, 2021, ISBN: 9780128244302).
Author: Magnus Dehli Vigeland [aut, cre]
(<https://orcid.org/0000-0002-9134-4962>),
Thore Egeland [aut] (<https://orcid.org/0000-0002-3465-8885>)
Maintainer: Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>
Diff between pedsuite versions 1.0.4 dated 2021-06-21 and 1.1.0 dated 2022-01-07
pedsuite-1.0.4/pedsuite/R/pedsuite-package.R |only pedsuite-1.0.4/pedsuite/vignettes/web_only |only pedsuite-1.1.0/pedsuite/DESCRIPTION | 29 +++++-------- pedsuite-1.1.0/pedsuite/MD5 | 23 ++++------- pedsuite-1.1.0/pedsuite/NAMESPACE | 8 +++ pedsuite-1.1.0/pedsuite/NEWS.md | 7 +++ pedsuite-1.1.0/pedsuite/R/pedsuite.R |only pedsuite-1.1.0/pedsuite/README.md | 47 ++++++++++++---------- pedsuite-1.1.0/pedsuite/build/vignette.rds |binary pedsuite-1.1.0/pedsuite/inst/doc/pedsuite.Rmd | 6 +- pedsuite-1.1.0/pedsuite/inst/doc/pedsuite.html | 20 ++++----- pedsuite-1.1.0/pedsuite/man/pedsuite.Rd | 52 ++++++++++++++++++++++--- pedsuite-1.1.0/pedsuite/vignettes/pedsuite.Rmd | 6 +- 13 files changed, 125 insertions(+), 73 deletions(-)
Title: An R Wrapper for the 'OpenTripPlanner' REST API
Description: A wrapper for the 'OpenTripPlanner' <http://www.opentripplanner.org/>
REST API. Queries are submitted to the relevant 'OpenTripPlanner' API resource, the response
is parsed and useful R objects are returned.
Author: Marcus Young [aut, cre] (<https://orcid.org/0000-0003-4627-1116>)
Maintainer: Marcus Young <M.A.Young@soton.ac.uk>
Diff between otpr versions 0.5.0 dated 2021-01-04 and 0.5.1 dated 2022-01-07
DESCRIPTION | 9 +- LICENSE | 2 MD5 | 16 ++-- NEWS.md | 8 ++ R/otp_evaluate_surface.R | 11 ++ README.md | 147 ++++++++++++++++++-------------------- inst/CITATION | 6 - man/figures/unnamed-chunk-9-1.png |binary tests/launch-otp.R | 4 - 9 files changed, 107 insertions(+), 96 deletions(-)
Title: Umbrella Review Package for R
Description: A comprehensive range of facilities to perform umbrella reviews with stratification of the evidence in R. The package accomplishes this aim by building on three core functions that: (i) automatically perform all required calculations in an umbrella review (including but not limited to meta-analyses), (ii) stratify evidence according to various classification criteria, and (iii) generate a visual representation of the results. Note that if you are not familiar with R, the core features of this package are available from a web browser (<https://www.metaumbrella.org/>).
Author: Corentin J Gosling [aut, cre],
Aleix Solanes [aut],
Paolo Fusar-Poli [aut],
Joaquim Radua [aut]
Maintainer: Corentin J Gosling <cgosling@parisnanterre.fr>
Diff between metaumbrella versions 1.0.0 dated 2021-12-20 and 1.0.1 dated 2022-01-07
DESCRIPTION | 10 MD5 | 124 - NEWS.md | 4 R/add_evidence.R | 84 R/check_data.R | 6 R/data.R | 116 R/esb_test.R | 99 R/estimate_or.R | 4 R/estimate_smd.R | 31 R/functions_forest_plot.R | 42 R/functions_format_dataset.R | 31 R/functions_meta.R | 7 R/functions_other.R | 36 R/functions_publication_bias.R | 12 R/functions_summary.R | 105 R/metaumbrella.R | 143 - R/subset.R | 2 R/umbrella.R | 100 R/umbrella_GUI.R | 19 R/umbrella_XLS.R | 29 R/union.R | 14 R/view_errors_umbrella.R | 33 build/vignette.rds |binary inst/CITATION | 6 inst/WORDLIST | 2 inst/doc/forest_plot.html | 201 + inst/doc/stratification_evidence.Rmd | 32 inst/doc/stratification_evidence.html | 2851 ++++++++++++++++++++++- inst/doc/train_well_formatted_dataset.html | 2795 ++++++++++++++++++++++ man/add.evidence.Rd | 82 man/df.HR.Rd | 7 man/df.IRR.Rd | 12 man/df.OR.Rd | 13 man/df.OR.multi.Rd | 13 man/df.RR.Rd | 9 man/df.SMD.Rd | 15 man/df.radua2019.Rd | 19 man/df.train.Rd | 23 man/drop.evidence.Rd | 8 man/esb.test.Rd | 60 man/forest.Rd | 8 man/forest.umbrella.Rd | 36 man/metaumbrella-package.Rd | 143 - man/subset.umbrella.Rd | 2 man/summary.umbrella.Rd | 70 man/umbrella.Rd | 41 man/umbrella.gui.Rd | 19 man/umbrella.xls.Rd | 27 man/union.umbrella.Rd | 14 man/view.errors.umbrella.Rd | 33 tests/testthat/test-esb_test.R | 183 - tests/testthat/test-estimate_n_from_es.R | 8 tests/testthat/test-estimate_or.R | 1 tests/testthat/test-estimate_rr_irr.R | 1 tests/testthat/test-estimate_smd.R | 3 tests/testthat/test-format_dataset.R | 179 - tests/testthat/test-functions_meta.R | 60 tests/testthat/test-functions_multilevel.R | 51 tests/testthat/test-functions_other.R | 16 tests/testthat/test-functions_power.R | 65 tests/testthat/test-functions_publication_bias.R | 25 tests/testthat/test-umbrella.R | 32 vignettes/stratification_evidence.Rmd | 32 63 files changed, 7020 insertions(+), 1228 deletions(-)
Title: Financial and Actuarial Mathematics for Life Contingencies
Description: Classes and methods that allow the user to manage life table,
actuarial tables (also multiple decrements tables). Moreover, functions to easily
perform demographic, financial and actuarial mathematics on life contingencies
insurances calculations are contained therein. See Spedicato (2013) <doi:10.18637/jss.v055.i10>.
Author: Giorgio Alfredo Spedicato [aut, cre]
(<https://orcid.org/0000-0002-0315-8888>),
Christophe Dutang [ctb] (<https://orcid.org/0000-0001-6732-1501>),
Reinhold Kainhofer [ctb] (<https://orcid.org/0000-0002-7895-1311>),
Kevin J Owens [ctb],
Ernesto Schirmacher [ctb],
Gian Paolo Clemente [ctb] (<https://orcid.org/0000-0001-6795-4595>),
Ivan Williams [ctb]
Maintainer: Giorgio Alfredo Spedicato <spedicato_giorgio@yahoo.it>
Diff between lifecontingencies versions 1.3.7 dated 2021-03-21 and 1.3.8 dated 2022-01-07
lifecontingencies-1.3.7/lifecontingencies/inst/doc/introToLifecontingencies.R |only lifecontingencies-1.3.7/lifecontingencies/inst/doc/introToLifecontingencies.Rmd |only lifecontingencies-1.3.7/lifecontingencies/inst/doc/introToLifecontingencies.pdf |only lifecontingencies-1.3.7/lifecontingencies/vignettes/introToLifecontingencies.Rmd |only lifecontingencies-1.3.8/lifecontingencies/ChangeLog | 3 lifecontingencies-1.3.8/lifecontingencies/DESCRIPTION | 8 lifecontingencies-1.3.8/lifecontingencies/MD5 | 60 +-- lifecontingencies-1.3.8/lifecontingencies/NEWS | 8 lifecontingencies-1.3.8/lifecontingencies/R/data.R | 5 lifecontingencies-1.3.8/lifecontingencies/build/vignette.rds |binary lifecontingencies-1.3.8/lifecontingencies/data/AF92Lt.rda |binary lifecontingencies-1.3.8/lifecontingencies/data/AM92Lt.rda |binary lifecontingencies-1.3.8/lifecontingencies/data/SoAISTdata.rda |binary lifecontingencies-1.3.8/lifecontingencies/data/de_angelis_di_falco.rda |binary lifecontingencies-1.3.8/lifecontingencies/data/demoCanada.rda |binary lifecontingencies-1.3.8/lifecontingencies/data/demoChina.rda |binary lifecontingencies-1.3.8/lifecontingencies/data/demoFrance.rda |binary lifecontingencies-1.3.8/lifecontingencies/data/demoGermany.rda |binary lifecontingencies-1.3.8/lifecontingencies/data/demoIta.rda |binary lifecontingencies-1.3.8/lifecontingencies/data/demoJapan.rda |binary lifecontingencies-1.3.8/lifecontingencies/data/demoUk.rda |binary lifecontingencies-1.3.8/lifecontingencies/data/demoUsa.rda |binary lifecontingencies-1.3.8/lifecontingencies/data/soa08.rda |binary lifecontingencies-1.3.8/lifecontingencies/data/soa08Act.rda |binary lifecontingencies-1.3.8/lifecontingencies/data/soaLt.rda |binary lifecontingencies-1.3.8/lifecontingencies/inst/doc/PensionPlanVal.html | 65 +-- lifecontingencies-1.3.8/lifecontingencies/inst/doc/an_introduction_to_lifecontingencies_package.pdf |binary lifecontingencies-1.3.8/lifecontingencies/inst/doc/compute-detail.pdf |binary lifecontingencies-1.3.8/lifecontingencies/inst/doc/mortality_projection.pdf |binary lifecontingencies-1.3.8/lifecontingencies/inst/doc/pensionfunding.html | 189 +++++----- lifecontingencies-1.3.8/lifecontingencies/man/demoJapan.Rd | 7 lifecontingencies-1.3.8/lifecontingencies/src/RcppExports.cpp | 5 lifecontingencies-1.3.8/lifecontingencies/vignettes/lifecontingenciesBiblio.bib | 6 33 files changed, 178 insertions(+), 178 deletions(-)
More information about lifecontingencies at CRAN
Permanent link
Title: The Machine Learning and AI Modeling Companion to 'healthyR'
Description: Hospital machine learning and ai data analysis workflow tools, modeling, and automations.
This library provides many useful tools to review common administrative
hospital data. Some of these include predicting length of stay, and readmits.
The aim is to provide a simple and consistent verb framework that takes the
guesswork out of everything.
Author: Steven Sanderson [aut, cre, cph]
Maintainer: Steven Sanderson <spsanderson@gmail.com>
Diff between healthyR.ai versions 0.0.4 dated 2021-12-08 and 0.0.5 dated 2022-01-07
DESCRIPTION | 9 - MD5 | 54 ++++++---- NAMESPACE | 8 + NEWS.md | 15 +++ R/augment-hai-scale-zero-one.R |only R/hai-range-statistic.R |only R/step-hai-scale-zero-one.R |only R/vec-hai-scale-zero-one.R |only inst/doc/getting-started.html | 165 ++++++++++++++++----------------- man/figures/README-example-1.png |binary man/figures/README-example-2.png |binary man/hai_fourier_augment.Rd | 1 man/hai_fourier_discrete_augment.Rd | 1 man/hai_fourier_discrete_vec.Rd | 1 man/hai_fourier_vec.Rd | 1 man/hai_hyperbolic_augment.Rd | 1 man/hai_hyperbolic_vec.Rd | 1 man/hai_polynomial_augment.Rd | 1 man/hai_range_statistic.Rd |only man/hai_scale_zero_one_augment.Rd |only man/hai_scale_zero_one_vec.Rd |only man/hai_winsorized_move_augment.Rd | 1 man/hai_winsorized_move_vec.Rd | 1 man/hai_winsorized_truncate_augment.Rd | 1 man/hai_winsorized_truncate_vec.Rd | 1 man/required_pkgs.healthyR.ai.Rd | 11 +- man/step_hai_fourier.Rd | 1 man/step_hai_fourier_discrete.Rd | 1 man/step_hai_hyperbolic.Rd | 1 man/step_hai_scale_zero_one.Rd |only man/step_hai_winsorized_move.Rd | 1 man/step_hai_winsorized_truncate.Rd | 1 32 files changed, 166 insertions(+), 112 deletions(-)
Title: Phylogenetic Comparative Methods with Uncertainty Estimates
Description: A framework for analytically computing the asymptotic confidence intervals and maximum-likelihood estimates of a class of continuous-time Gaussian branching processes defined by Mitov V, Bartoszek K, Asimomitis G, Stadler T (2019) <doi:10.1016/j.tpb.2019.11.005>. The class of model includes the widely used Ornstein-Uhlenbeck and Brownian motion branching processes. The framework is designed to be flexible enough so that the users can easily specify their own sub-models, or re-parameterizations, and obtain the maximum-likelihood estimates and confidence intervals of their own custom models.
Author: Hao Chi Kiang [cre, aut]
Maintainer: Hao Chi Kiang <hello@hckiang.com>
Diff between glinvci versions 1.1.16 dated 2021-12-21 and 1.1.17 dated 2022-01-07
DESCRIPTION | 6 +- MD5 | 8 +- inst/doc/Getting_Started.pdf |binary src/Makevars.in | 20 ++++++- src/phytr.c | 121 +++++++++++++++++++++++++------------------ 5 files changed, 97 insertions(+), 58 deletions(-)
Title: Feldman-Cousins Confidence Intervals
Description: Provides support for building Feldman-Cousins confidence intervals
[G. J. Feldman and R. D. Cousins (1998) <doi:10.1103/PhysRevD.57.3873>].
Author: Valerio Gherardi [aut, cre] (<https://orcid.org/0000-0002-8215-3013>)
Maintainer: Valerio Gherardi <vgherard840@gmail.com>
Diff between fcci versions 1.0.0 dated 2021-04-06 and 1.0.1 dated 2022-01-07
DESCRIPTION | 12 ++++++------ MD5 | 9 +++++---- NEWS.md |only README.md | 27 +++++++++++++++++++++------ src/RcppExports.cpp | 5 +++++ tests/testthat/test-algorithm_pois.R | 4 ++-- 6 files changed, 39 insertions(+), 18 deletions(-)
Title: Plot Positive and Negative Predictive Values for Medical Tests
Description: Functions to plot and help understand positive and negative
predictive values (PPV and NPV), and their relationship with
sensitivity, specificity, and prevalence. See Akobeng, A.K. (2007)
<doi:10.1111/j.1651-2227.2006.00180.x> for a theoretical overview of
the technical concepts and Navarrete et al. (2015) for a practical
explanation about the importance of their understanding
<doi:10.3389/fpsyg.2015.01327>.
Author: Gorka Navarrete [aut, cre] (<https://orcid.org/0000-0001-7678-8656>)
Maintainer: Gorka Navarrete <gorkang@gmail.com>
Diff between BayesianReasoning versions 0.4.0 dated 2021-12-21 and 0.4.1 dated 2022-01-07
BayesianReasoning-0.4.0/BayesianReasoning/man/dot-createPPVmatrix.Rd |only BayesianReasoning-0.4.0/BayesianReasoning/man/dot-get_point_ppv_npv.Rd |only BayesianReasoning-0.4.0/BayesianReasoning/man/dot-number_decimals_plot_axis.Rd |only BayesianReasoning-0.4.0/BayesianReasoning/man/dot-plot_creation.Rd |only BayesianReasoning-0.4.0/BayesianReasoning/man/dot-plot_overlay_area.Rd |only BayesianReasoning-0.4.0/BayesianReasoning/man/dot-plot_overlay_line.Rd |only BayesianReasoning-0.4.0/BayesianReasoning/man/dot-translate_labels.Rd |only BayesianReasoning-0.4.0/BayesianReasoning/man/process_variables.Rd |only BayesianReasoning-0.4.1/BayesianReasoning/DESCRIPTION | 34 - BayesianReasoning-0.4.1/BayesianReasoning/MD5 | 32 - BayesianReasoning-0.4.1/BayesianReasoning/NEWS.md | 9 BayesianReasoning-0.4.1/BayesianReasoning/R/PPV_heatmap.R | 19 BayesianReasoning-0.4.1/BayesianReasoning/R/helper_functions.R | 288 +++++----- BayesianReasoning-0.4.1/BayesianReasoning/README.md | 12 BayesianReasoning-0.4.1/BayesianReasoning/inst/doc/PPV_NPV.html | 14 BayesianReasoning-0.4.1/BayesianReasoning/inst/doc/introduction.R | 51 + BayesianReasoning-0.4.1/BayesianReasoning/inst/doc/introduction.Rmd | 57 + BayesianReasoning-0.4.1/BayesianReasoning/inst/doc/introduction.html | 6 BayesianReasoning-0.4.1/BayesianReasoning/man/PPV_heatmap.Rd | 12 BayesianReasoning-0.4.1/BayesianReasoning/tests/testthat/test-PPV_heatmap.R | 80 ++ BayesianReasoning-0.4.1/BayesianReasoning/vignettes/introduction.Rmd | 57 + 21 files changed, 458 insertions(+), 213 deletions(-)
More information about BayesianReasoning at CRAN
Permanent link
Title: Antimicrobial Resistance Data Analysis
Description: Functions to simplify and standardise antimicrobial resistance (AMR)
data analysis and to work with microbial and antimicrobial properties by
using evidence-based methods and reliable reference data such as LPSN
<doi:10.1099/ijsem.0.004332>.
Author: Matthijs S. Berends [aut, cre]
(<https://orcid.org/0000-0001-7620-1800>),
Christian F. Luz [aut, ctb] (<https://orcid.org/0000-0001-5809-5995>),
Dennis Souverein [aut, ctb] (<https://orcid.org/0000-0003-0455-0336>),
Erwin E. A. Hassing [aut, ctb],
Casper J. Albers [ths] (<https://orcid.org/0000-0002-9213-6743>),
Judith M. Fonville [ctb],
Alex W. Friedrich [ths] (<https://orcid.org/0000-0003-4881-038X>),
Corinna Glasner [ths] (<https://orcid.org/0000-0003-1241-1328>),
Eric H. L. C. M. Hazenberg [ctb],
Gwen Knight [ctb] (<https://orcid.org/0000-0002-7263-9896>),
Annick Lenglet [ctb] (<https://orcid.org/0000-0003-2013-8405>),
Bart C. Meijer [ctb],
Sofia Ny [ctb] (<https://orcid.org/0000-0002-2017-1363>),
Rogier P. Schade [ctb],
Bhanu N. M. Sinha [ths] (<https://orcid.org/0000-0003-1634-0010>),
Anthony Underwood [ctb] (<https://orcid.org/0000-0002-8547-4277>)
Maintainer: Matthijs S. Berends <m.s.berends@umcg.nl>
Diff between AMR versions 1.7.1 dated 2021-06-03 and 1.8.0 dated 2022-01-07
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AMR-1.8.0/AMR/inst/tinytest/test-pca.R | 4 AMR-1.8.0/AMR/inst/tinytest/test-proportion.R | 4 AMR-1.8.0/AMR/inst/tinytest/test-random.R | 2 AMR-1.8.0/AMR/inst/tinytest/test-resistance_predict.R | 6 AMR-1.8.0/AMR/inst/tinytest/test-rsi.R | 14 AMR-1.8.0/AMR/inst/tinytest/test-skewness.R | 2 AMR-1.8.0/AMR/inst/tinytest/test-zzz.R | 70 +- AMR-1.8.0/AMR/man/AMR-deprecated.Rd | 199 ------ AMR-1.8.0/AMR/man/AMR.Rd | 4 AMR-1.8.0/AMR/man/ab_from_text.Rd | 2 AMR-1.8.0/AMR/man/ab_property.Rd | 94 ++ AMR-1.8.0/AMR/man/age.Rd | 2 AMR-1.8.0/AMR/man/age_groups.Rd | 2 AMR-1.8.0/AMR/man/antibiotic_class_selectors.Rd | 185 ++++- AMR-1.8.0/AMR/man/antibiotics.Rd | 26 AMR-1.8.0/AMR/man/as.ab.Rd | 6 AMR-1.8.0/AMR/man/as.disk.Rd | 12 AMR-1.8.0/AMR/man/as.mic.Rd | 14 AMR-1.8.0/AMR/man/as.mo.Rd | 16 AMR-1.8.0/AMR/man/as.rsi.Rd | 26 AMR-1.8.0/AMR/man/atc_online.Rd | 10 AMR-1.8.0/AMR/man/availability.Rd | 2 AMR-1.8.0/AMR/man/bug_drug_combinations.Rd | 8 AMR-1.8.0/AMR/man/catalogue_of_life.Rd | 6 AMR-1.8.0/AMR/man/catalogue_of_life_version.Rd | 2 AMR-1.8.0/AMR/man/count.Rd | 14 AMR-1.8.0/AMR/man/custom_eucast_rules.Rd | 60 + AMR-1.8.0/AMR/man/eucast_rules.Rd | 13 AMR-1.8.0/AMR/man/first_isolate.Rd | 19 AMR-1.8.0/AMR/man/get_episode.Rd | 4 AMR-1.8.0/AMR/man/ggplot_pca.Rd | 2 AMR-1.8.0/AMR/man/ggplot_rsi.Rd | 15 AMR-1.8.0/AMR/man/guess_ab_col.Rd | 2 AMR-1.8.0/AMR/man/intrinsic_resistant.Rd | 18 AMR-1.8.0/AMR/man/italicise_taxonomy.Rd | 14 AMR-1.8.0/AMR/man/join.Rd | 4 AMR-1.8.0/AMR/man/key_antimicrobials.Rd | 2 AMR-1.8.0/AMR/man/kurtosis.Rd | 2 AMR-1.8.0/AMR/man/lifecycle.Rd | 2 AMR-1.8.0/AMR/man/like.Rd | 4 AMR-1.8.0/AMR/man/mdro.Rd | 11 AMR-1.8.0/AMR/man/microorganisms.Rd | 25 AMR-1.8.0/AMR/man/microorganisms.codes.Rd | 6 AMR-1.8.0/AMR/man/microorganisms.old.Rd | 6 AMR-1.8.0/AMR/man/mo_matching_score.Rd | 6 AMR-1.8.0/AMR/man/mo_property.Rd | 82 +- AMR-1.8.0/AMR/man/mo_source.Rd | 2 AMR-1.8.0/AMR/man/pca.Rd | 2 AMR-1.8.0/AMR/man/plot.Rd | 92 +- AMR-1.8.0/AMR/man/proportion.Rd | 10 AMR-1.8.0/AMR/man/random.Rd | 14 AMR-1.8.0/AMR/man/resistance_predict.Rd | 23 AMR-1.8.0/AMR/man/rsi_translation.Rd | 7 AMR-1.8.0/AMR/man/skewness.Rd | 2 AMR-1.8.0/AMR/man/translate.Rd | 30 AMR-1.8.0/AMR/tests/tinytest.R | 10 AMR-1.8.0/AMR/vignettes/welcome_to_AMR.Rmd | 22 170 files changed, 3109 insertions(+), 2666 deletions(-)
Title: Diverse Datasets for 'tsibble'
Description: Provides diverse datasets in the 'tsibble' data structure. These datasets are useful for learning and demonstrating how tidy temporal data can tidied, visualised, and forecasted.
Author: Mitchell O'Hara-Wild [aut, cre],
Rob Hyndman [aut],
Earo Wang [aut],
Rakshitha Godahewa [aut],
Christoph Bergmeir [ctb]
Maintainer: Mitchell O'Hara-Wild <mail@mitchelloharawild.com>
Diff between tsibbledata versions 0.3.0 dated 2021-03-16 and 0.4.0 dated 2022-01-07
DESCRIPTION | 18 +++++++++++------- MD5 | 23 +++++++++++++---------- NAMESPACE | 4 ++++ NEWS.md | 8 +++++++- R/data.R | 13 +++++++------ R/forecastingdata_org.R |only R/utils.R |only README.md | 8 ++++++-- man/aus_livestock.Rd | 9 +++++---- man/figures/README-elecdemand-1.png |binary man/gafa_stock.Rd | 2 +- man/monash_forecasting_repository.Rd |only man/olympic_running.Rd | 2 +- man/tsibbledata-package.Rd | 6 ++++++ 14 files changed, 61 insertions(+), 32 deletions(-)
Title: Design Shaded Contour Lines (or Tanaka) Maps
Description: The Tanaka method enhances the representation of topography on
a map using shaded contour lines. In this simplified implementation of
the method, north-west white contours represent illuminated topography
and south-east black contours represent shaded topography. See Tanaka
(1950) <doi:10.2307/211219>.
Author: Timothée Giraud [cre, aut] (<https://orcid.org/0000-0002-1932-3323>)
Maintainer: Timothée Giraud <timothee.giraud@cnrs.fr>
Diff between tanaka versions 0.1.3 dated 2020-04-14 and 0.2.0 dated 2022-01-07
tanaka-0.1.3/tanaka/inst/grd |only tanaka-0.1.3/tanaka/tests/testthat |only tanaka-0.1.3/tanaka/tests/testthat.R |only tanaka-0.2.0/tanaka/DESCRIPTION | 23 ++++--- tanaka-0.2.0/tanaka/MD5 | 25 +++----- tanaka-0.2.0/tanaka/NAMESPACE | 13 +--- tanaka-0.2.0/tanaka/NEWS.md | 8 ++ tanaka-0.2.0/tanaka/R/legend.R | 11 ++- tanaka-0.2.0/tanaka/R/tanaka.R | 41 +++++++------ tanaka-0.2.0/tanaka/R/tanaka_contour.R | 42 +++++++------ tanaka-0.2.0/tanaka/README.md | 91 +++++++++++++++++------------- tanaka-0.2.0/tanaka/inst/tif |only tanaka-0.2.0/tanaka/inst/tinytest |only tanaka-0.2.0/tanaka/man/tanaka.Rd | 4 - tanaka-0.2.0/tanaka/man/tanaka_contour.Rd | 4 - tanaka-0.2.0/tanaka/tests/tinytest.R |only 16 files changed, 150 insertions(+), 112 deletions(-)
Title: Predictive Evaluation Metrics in Survival Analysis
Description: An implementation of popular evaluation metrics that are commonly used in survival prediction
including Concordance Index, Brier Score, Integrated Brier Score,
Integrated Square Error, Integrated Absolute Error and Mean Absolute Error.
For a detailed information, see (Ishwaran H, Kogalur UB, Blackstone EH and Lauer MS (2008) <doi:10.1214/08-AOAS169>) and
(Moradian H, Larocque D and Bellavance F (2017) <doi:10.1007/s10985-016-9372-1>) for different evaluation metrics.
Author: Hanpu Zhou [aut, cre],
Xuewei Cheng [aut],
Sizheng Wang [aut],
Yi Zou [aut],
Hong Wang [aut]
Maintainer: Hanpu Zhou <zhouhanpu@csu.edu.cn>
Diff between SurvMetrics versions 0.3.5 dated 2021-08-10 and 0.4.0 dated 2022-01-07
DESCRIPTION | 8 ++++---- MD5 | 12 +++++++----- NAMESPACE | 1 + NEWS.md | 11 ++++++++++- R/CindexCR.R |only R/IBS.R | 1 + inst/doc/SurvMetrics-vignette.html | 2 +- man/CindexCR.Rd |only 8 files changed, 24 insertions(+), 11 deletions(-)
Title: Risk Tool Library - Trading, Risk, 'Analytics' for Commodities
Description: A toolkit for Commodities 'analytics', risk management and trading professionals. Includes functions for API calls to 'Morningstar Commodities' and 'Genscape'.
Author: Philippe Cote [aut, cre],
Nima Safaian [aut]
Maintainer: Philippe Cote <pcote@ualberta.ca>
Diff between RTL versions 0.1.9 dated 2022-01-04 and 0.1.91 dated 2022-01-07
DESCRIPTION | 12 ++++++------ MD5 | 14 +++++++------- NEWS.md | 9 +++++++++ data/dflong.rda |binary data/dfwide.rda |binary data/eiaStocks.rda |binary data/fxfwd.rda |binary data/tradeCycle.rda |binary 8 files changed, 22 insertions(+), 13 deletions(-)
Title: Tables, Labels and Some Useful Functions from Spreadsheets and
'SPSS' Statistics
Description: Package computes and displays tables with support for 'SPSS'-style
labels, multiple and nested banners, weights, multiple-response variables
and significance testing. There are facilities for nice output of tables
in 'knitr', 'Shiny', '*.xlsx' files, R and 'Jupyter' notebooks. Methods
for labelled variables add value labels support to base R functions and to
some functions from other packages. Additionally, the package brings
popular data transformation functions from 'SPSS' Statistics and 'Excel':
'RECODE', 'COUNT', 'COUNTIF', 'VLOOKUP' and etc.
These functions are very useful for data processing in marketing research
surveys. Package intended to help people to move data
processing from 'Excel' and 'SPSS' to R.
Author: Gregory Demin [aut, cre],
Sebastian Jeworutzki [ctb] (<https://orcid.org/0000-0002-2671-5253>)
Maintainer: Gregory Demin <gdemin@gmail.com>
Diff between expss versions 0.10.7 dated 2020-11-15 and 0.11.1 dated 2022-01-07
expss-0.10.7/expss/R/cro.R |only expss-0.10.7/expss/R/cro_fun.R |only expss-0.10.7/expss/R/default_dataset.R |only expss-0.10.7/expss/R/ref.R |only expss-0.10.7/expss/R/vlookup.R |only expss-0.10.7/expss/R/zzz_experimental.R |only expss-0.10.7/expss/man/cro.Rd |only expss-0.10.7/expss/man/cro_fun.Rd |only expss-0.10.7/expss/man/default_dataset.Rd |only expss-0.10.7/expss/man/experimental.Rd |only expss-0.10.7/expss/man/ref.Rd |only expss-0.10.7/expss/man/vlookup.Rd |only expss-0.10.7/expss/tests/testthat/test_compute.R |only expss-0.10.7/expss/tests/testthat/test_do_repeat.R |only expss-0.10.7/expss/tests/testthat/test_into.R |only expss-0.10.7/expss/tests/testthat/test_keep.R |only expss-0.10.7/expss/tests/testthat/test_parameter.R |only expss-0.10.7/expss/tests/testthat/test_ref.R |only expss-0.10.7/expss/tests/testthat/test_selectors.R |only expss-0.10.7/expss/tests/testthat/test_vlookup.R |only expss-0.10.7/expss/tests/testthat/test_where.R |only expss-0.11.1/expss/DESCRIPTION | 20 expss-0.11.1/expss/MD5 | 258 +- expss-0.11.1/expss/NAMESPACE | 124 - expss-0.11.1/expss/NEWS | 9 expss-0.11.1/expss/R/aaa_utils.R | 7 expss-0.11.1/expss/R/add_columns.R |only expss-0.11.1/expss/R/add_rows.R | 47 expss-0.11.1/expss/R/apply_labels.R | 42 expss-0.11.1/expss/R/caption.R | 4 expss-0.11.1/expss/R/common_table_utils.R | 1 expss-0.11.1/expss/R/compute.R | 121 - expss-0.11.1/expss/R/count_if.R | 61 expss-0.11.1/expss/R/cross.R |only expss-0.11.1/expss/R/cross_fun.R |only expss-0.11.1/expss/R/custom_tables.R | 37 expss-0.11.1/expss/R/deprecated_cro.R |only expss-0.11.1/expss/R/do_repeat.R | 15 expss-0.11.1/expss/R/drop_empty.R | 6 expss-0.11.1/expss/R/expss.R | 190 - expss-0.11.1/expss/R/fre.R | 388 +-- expss-0.11.1/expss/R/html_table.R | 11 expss-0.11.1/expss/R/keep.R | 62 expss-0.11.1/expss/R/labels.R | 31 expss-0.11.1/expss/R/merge.R | 45 expss-0.11.1/expss/R/mrset.R | 10 expss-0.11.1/expss/R/names2labels.R | 31 expss-0.11.1/expss/R/nest.R | 12 expss-0.11.1/expss/R/prepend_names.R | 6 expss-0.11.1/expss/R/qc.R | 63 expss-0.11.1/expss/R/read_spss.R | 31 expss-0.11.1/expss/R/recode.R | 12 expss-0.11.1/expss/R/selectors.R | 94 expss-0.11.1/expss/R/sheet.R | 25 expss-0.11.1/expss/R/significance_cpct.R | 42 expss-0.11.1/expss/R/significance_pvalue.R | 2 expss-0.11.1/expss/R/sort.R | 32 expss-0.11.1/expss/R/split_by.R | 19 expss-0.11.1/expss/R/split_labels.R | 2 expss-0.11.1/expss/R/sum.R | 34 expss-0.11.1/expss/R/tab_sort.R | 6 expss-0.11.1/expss/R/values2labels.R | 6 expss-0.11.1/expss/R/weight_by.R |only expss-0.11.1/expss/R/weighted_stats.R | 106 expss-0.11.1/expss/R/where.R | 28 expss-0.11.1/expss/R/write_labelled.R | 35 expss-0.11.1/expss/R/xl_write.R | 4 expss-0.11.1/expss/build/vignette.rds |binary expss-0.11.1/expss/inst/doc/examples.R | 30 expss-0.11.1/expss/inst/doc/examples.Rmd | 31 expss-0.11.1/expss/inst/doc/examples.html | 326 -- expss-0.11.1/expss/inst/doc/labels-support.html | 296 -- expss-0.11.1/expss/inst/doc/tables-with-labels.R | 273 -- expss-0.11.1/expss/inst/doc/tables-with-labels.Rmd | 511 ---- expss-0.11.1/expss/inst/doc/tables-with-labels.html | 1202 ---------- expss-0.11.1/expss/inst/doc/xlsx-export.R | 4 expss-0.11.1/expss/inst/doc/xlsx-export.Rmd | 6 expss-0.11.1/expss/inst/doc/xlsx-export.html | 302 -- expss-0.11.1/expss/man/add_columns.Rd |only expss-0.11.1/expss/man/add_rows.Rd | 40 expss-0.11.1/expss/man/apply_labels.Rd | 32 expss-0.11.1/expss/man/compare_proportions.Rd | 2 expss-0.11.1/expss/man/compute.Rd | 78 expss-0.11.1/expss/man/count_if.Rd | 55 expss-0.11.1/expss/man/cross_cases.Rd |only expss-0.11.1/expss/man/cross_fun.Rd |only expss-0.11.1/expss/man/do_repeat.Rd | 6 expss-0.11.1/expss/man/drop_empty_rows.Rd | 6 expss-0.11.1/expss/man/expss.Rd | 7 expss-0.11.1/expss/man/fre.Rd | 26 expss-0.11.1/expss/man/htmlTable.etable.Rd | 11 expss-0.11.1/expss/man/keep.Rd | 44 expss-0.11.1/expss/man/merge.etable.Rd | 56 expss-0.11.1/expss/man/mrset.Rd | 10 expss-0.11.1/expss/man/names2labels.Rd | 31 expss-0.11.1/expss/man/nest.Rd | 12 expss-0.11.1/expss/man/prepend_values.Rd | 6 expss-0.11.1/expss/man/qc.Rd | 30 expss-0.11.1/expss/man/read_spss.Rd | 14 expss-0.11.1/expss/man/reexports.Rd | 55 expss-0.11.1/expss/man/set_caption.Rd | 4 expss-0.11.1/expss/man/sheet.Rd | 12 expss-0.11.1/expss/man/significance.Rd | 42 expss-0.11.1/expss/man/sort_asc.Rd | 9 expss-0.11.1/expss/man/split_by.Rd | 17 expss-0.11.1/expss/man/split_labels.Rd | 2 expss-0.11.1/expss/man/sum_row.Rd | 31 expss-0.11.1/expss/man/tab_sort_asc.Rd | 6 expss-0.11.1/expss/man/tables.Rd | 37 expss-0.11.1/expss/man/values2labels.Rd | 6 expss-0.11.1/expss/man/var_lab.Rd | 31 expss-0.11.1/expss/man/vars.Rd | 97 expss-0.11.1/expss/man/w_mean.Rd | 36 expss-0.11.1/expss/man/weight_by.Rd |only expss-0.11.1/expss/man/where.Rd | 21 expss-0.11.1/expss/man/write_labelled_csv.Rd | 35 expss-0.11.1/expss/man/xl_write.Rd | 4 expss-0.11.1/expss/tests/testthat/test_add_columns.R |only expss-0.11.1/expss/tests/testthat/test_add_rows.R | 35 expss-0.11.1/expss/tests/testthat/test_apply_labels.R | 168 + expss-0.11.1/expss/tests/testthat/test_count_if.R | 7 expss-0.11.1/expss/tests/testthat/test_cro_extended.R | 73 expss-0.11.1/expss/tests/testthat/test_cro_fun_df_extended.R | 90 expss-0.11.1/expss/tests/testthat/test_cro_fun_extended.R | 218 - expss-0.11.1/expss/tests/testthat/test_custom_tables.R | 74 expss-0.11.1/expss/tests/testthat/test_custom_tables_sig.R | 4 expss-0.11.1/expss/tests/testthat/test_drop_empty.R | 3 expss-0.11.1/expss/tests/testthat/test_fre.R | 120 expss-0.11.1/expss/tests/testthat/test_htmlTable.R | 18 expss-0.11.1/expss/tests/testthat/test_huxtable.R | 24 expss-0.11.1/expss/tests/testthat/test_merge.R | 112 expss-0.11.1/expss/tests/testthat/test_methods.R | 73 expss-0.11.1/expss/tests/testthat/test_recode.R | 62 expss-0.11.1/expss/tests/testthat/test_recode_with_na.R | 6 expss-0.11.1/expss/tests/testthat/test_siginificance_cases.R | 2 expss-0.11.1/expss/tests/testthat/test_significance_cell_chisq.R | 2 expss-0.11.1/expss/tests/testthat/test_significance_cpct.R | 2 expss-0.11.1/expss/tests/testthat/test_split_by.R | 78 expss-0.11.1/expss/tests/testthat/test_split_labels.R | 2 expss-0.11.1/expss/tests/testthat/test_weight_by.R |only expss-0.11.1/expss/tests/testthat/test_weighted_stats.R | 15 expss-0.11.1/expss/tests/testthat/test_with_data.table.R | 130 - expss-0.11.1/expss/tests/testthat/test_xl_write.R | 18 expss-0.11.1/expss/vignettes/examples.Rmd | 31 expss-0.11.1/expss/vignettes/tables-with-labels.Rmd | 511 ---- expss-0.11.1/expss/vignettes/xlsx-export.Rmd | 6 146 files changed, 1882 insertions(+), 5973 deletions(-)
Title: Tools for the Analysis of Epidemiological Data
Description: Tools for the analysis of epidemiological and surveillance data. Contains functions for directly and indirectly adjusting measures of disease frequency, quantifying measures of association on the basis of single or multiple strata of count data presented in a contingency table, computation of confidence intervals around incidence risk and incidence rate estimates and sample size calculations for cross-sectional, case-control and cohort studies. Surveillance tools include functions to calculate an appropriate sample size for 1- and 2-stage representative freedom surveys, functions to estimate surveillance system sensitivity and functions to support scenario tree modelling analyses.
Author: Mark Stevenson <mark.stevenson1@unimelb.edu.au> and Evan Sergeant <evansergeant@gmail.com> with contributions from Telmo Nunes, Cord Heuer, Jonathon Marshall, Javier Sanchez, Ron Thornton, Jeno Reiczigel, Jim Robison-Cox, Paola Sebastiani, Peter Solymos, Kazuki Yoshida, Geoff Jones, Sarah Pirikahu, Simon Firestone, Ryan Kyle, Johann Popp, Mathew Jay, Charles Reynard, Allison Cheung, Nagendra Singanallur and Aniko Szabo.
Maintainer: Mark Stevenson <mark.stevenson1@unimelb.edu.au>
Diff between epiR versions 2.0.40 dated 2021-12-15 and 2.0.41 dated 2022-01-07
DESCRIPTION | 8 MD5 | 100 ++++---- NAMESPACE | 2 NEWS | 10 R/epi.interaction.R | 349 ++++++++++++++--------------- build/vignette.rds |binary inst/doc/epiR_RSurveillance.html | 4 inst/doc/epiR_descriptive.html | 60 ++-- inst/doc/epiR_measures_of_association.html | 8 inst/doc/epiR_sample_size.html | 4 inst/doc/epiR_surveillance.html | 4 man/epi.2by2.Rd | 4 man/epi.about.Rd | 2 man/epi.ccc.Rd | 2 man/epi.conf.Rd | 6 man/epi.cpresids.Rd | 4 man/epi.directadj.Rd | 8 man/epi.indirectadj.Rd | 4 man/epi.interaction.Rd | 25 +- man/epi.kappa.Rd | 2 man/epi.nomogram.Rd | 4 man/epi.pooled.Rd | 2 man/epi.prcc.Rd | 2 man/epi.smr.Rd | 2 man/epi.sscc.Rd | 4 man/epi.ssclus1estb.Rd | 8 man/epi.ssclus1estc.Rd | 2 man/epi.ssclus2estb.Rd | 16 - man/epi.ssclus2estc.Rd | 2 man/epi.sscohortc.Rd | 4 man/epi.sscohortt.Rd | 4 man/epi.sscompb.Rd | 4 man/epi.sscompc.Rd | 6 man/epi.sscomps.Rd | 2 man/epi.ssdetect.Rd | 4 man/epi.ssdxtest.Rd | 4 man/epi.ssequb.Rd | 10 man/epi.ssequc.Rd | 6 man/epi.ssninfb.Rd | 8 man/epi.ssninfc.Rd | 10 man/epi.sssimpleestb.Rd | 2 man/epi.sssupc.Rd | 4 man/epi.ssxsectn.Rd | 4 man/epi.tests.Rd | 2 man/rsu.dxtest.Rd | 6 man/rsu.pfree.rs.Rd | 2 man/rsu.pstar.Rd | 2 man/rsu.sep.Rd | 2 man/rsu.sep.cens.Rd | 4 man/rsu.sep.rspool.Rd | 2 man/rsu.spp.rs.Rd | 6 51 files changed, 388 insertions(+), 358 deletions(-)
Title: Joint Dimension Reduction and Spatial Clustering
Description: Joint dimension reduction and spatial clustering is conducted for
Single-cell RNA sequencing and spatial transcriptomics data, and more details can be referred to
Wei Liu, Xu Liao, Xiang Zhou, Shijie Shi and Jin Liu. (2021) <doi:10.1101/2021.12.25.474153>. It is not only computationally efficient and scalable to the sample size increment, but also is capable of choosing the smoothness parameter and the number of clusters as well.
Author: Wei Liu [aut, cre],
Xingjie Shi [aut],
Jin Liu [aut]
Maintainer: Wei Liu <wei.liu@duke-nus.edu.sg>
Diff between DR.SC versions 2.3 dated 2021-11-21 and 2.4 dated 2022-01-07
DR.SC-2.3/DR.SC/man/getneighborhood_fast.Rd |only DR.SC-2.4/DR.SC/DESCRIPTION | 13 +- DR.SC-2.4/DR.SC/MD5 | 28 ++--- DR.SC-2.4/DR.SC/NAMESPACE | 9 - DR.SC-2.4/DR.SC/R/main.R | 156 ++++++++++++++++++++++++---- DR.SC-2.4/DR.SC/R/visualizationR.R | 2 DR.SC-2.4/DR.SC/inst/doc/DR.SC.HCC1.R | 9 + DR.SC-2.4/DR.SC/inst/doc/DR.SC.HCC1.Rmd | 12 +- DR.SC-2.4/DR.SC/inst/doc/DR.SC.HCC1.html | 35 +++--- DR.SC-2.4/DR.SC/inst/doc/DR.SC.Simu.html | 4 DR.SC-2.4/DR.SC/man/DR.SC.Rd | 4 DR.SC-2.4/DR.SC/man/DR.SC.fit.Rd | 2 DR.SC-2.4/DR.SC/man/getAdj.Rd | 32 +---- DR.SC-2.4/DR.SC/man/getAdj_auto.Rd |only DR.SC-2.4/DR.SC/man/getAdj_manual.Rd |only DR.SC-2.4/DR.SC/man/getAdj_reg.Rd |only DR.SC-2.4/DR.SC/vignettes/DR.SC.HCC1.Rmd | 12 +- 17 files changed, 223 insertions(+), 95 deletions(-)
Title: Automatic Structural Time Series Models
Description: Automatic model selection for structural time series decomposition into trend, cycle, and seasonal components, plus optionality for structural interpolation, using the Kalman filter.
Koopman, Siem Jan and Marius Ooms (2012) "Forecasting Economic Time Series Using Unobserved Components Time Series Models" <doi:10.1093/oxfordhb/9780195398649.013.0006>.
Kim, Chang-Jin and Charles R. Nelson (1999) "State-Space Models with Regime Switching: Classical and Gibbs-Sampling Approaches with Applications" <doi:10.7551/mitpress/6444.001.0001><http://econ.korea.ac.kr/~cjkim/>.
Author: Alex Hubbard
Maintainer: Alex Hubbard <hubbard.alex@gmail.com>
Diff between autostsm versions 2.1 dated 2021-12-02 and 2.1.1 dated 2022-01-07
DESCRIPTION | 8 - MD5 | 18 +-- R/stsm_constraints.R | 6 - R/stsm_estimate.R | 2 R/zzz.R | 20 ++-- inst/doc/autostsm_vignette.R | 65 +++++++------ inst/doc/autostsm_vignette.Rmd | 65 +++++++------ inst/doc/autostsm_vignette.html | 199 ++++++++++++++++++++-------------------- man/autostsm.Rd | 2 vignettes/autostsm_vignette.Rmd | 65 +++++++------ 10 files changed, 239 insertions(+), 211 deletions(-)
Title: Seeded-LDA for Topic Modeling
Description: Implements the seeded-LDA model (Lu, Ott, Cardie & Tsou 2010) <doi:10.1109/ICDMW.2011.125> using the quanteda package and the GibbsLDA++ library for semisupervised topic modeling.
Seeded-LDA allows users to pre-define topics with keywords to perform theory-driven analysis of textual data in social sciences and humanities (Watanabe & Zhou 2020) <doi:10.1177/0894439320907027>.
Author: Kohei Watanabe [aut, cre, cph],
Phan Xuan-Hieu [aut, cph] (GibbsLDA++)
Maintainer: Kohei Watanabe <watanabe.kohei@gmail.com>
Diff between seededlda versions 0.6.0 dated 2021-04-08 and 0.8.0 dated 2022-01-07
DESCRIPTION | 8 +-- MD5 | 26 +++++------ NEWS.md | 14 ++++-- R/lda.R | 51 ++++++++++++++++++--- R/predict.R | 2 R/seededlda.R | 41 ++++++++++++----- man/predict.textmodel_lda.Rd | 32 ++++++++++--- man/print.textmodel_lda.Rd | 1 man/terms.Rd | 7 ++- man/textmodel_seededlda.Rd | 44 ++++++++++++++---- man/topics.Rd | 8 ++- src/RcppExports.cpp | 5 ++ tests/testthat/test-textmodel_lda.R | 60 ++++++++++++++++++++++++- tests/testthat/test-textmodel_seededlda.R | 70 +++++++++++++++++++++++++++--- 14 files changed, 296 insertions(+), 73 deletions(-)
Title: Density Goodness-of-Fit Test
Description: Provides functions for the implementation of a density goodness-of-fit test, based on piecewise approximation of the L2 distance.
Author: Dimitrios Bagkavos [aut, cre]
Maintainer: Dimitrios Bagkavos <dimitrios.bagkavos@gmail.com>
Diff between L2DensityGoFtest versions 0.3.0 dated 2021-12-18 and 0.4.0 dated 2022-01-07
DESCRIPTION | 8 ++++---- MD5 | 24 ++++++++++++++---------- NAMESPACE | 3 ++- R/Kernels.R | 2 +- R/S.n.Boot.R |only R/S.n.R | 4 ++-- R/cutoff.bootstrap.R |only man/Kernels.Rd | 4 +++- man/S.n.Boot.Rd |only man/S.n.Rd | 36 ++++++++++++++++++++++-------------- man/cutoff.asymptotic.Rd | 19 +++++++++---------- man/cutoff.bootstrap.Rd |only man/cutoff.edgeworth.Rd | 30 ++++++++++++------------------ man/hopt.be.Rd | 17 ++++++++--------- man/hopt.edgeworth.Rd | 23 +++++++++++------------ 15 files changed, 88 insertions(+), 82 deletions(-)
More information about L2DensityGoFtest at CRAN
Permanent link
Title: Toolkit for Credit Modeling, Analysis and Visualization
Description: Provides a highly efficient R tool suite for Credit Modeling, Analysis and Visualization.Contains infrastructure functionalities such as data exploration and preparation, missing values treatment, outliers treatment, variable derivation, variable selection, dimensionality reduction, grid search for hyper parameters, data mining and visualization, model evaluation, strategy analysis etc. This package is designed to make the development of binary classification models (machine learning based models as well as credit scorecard) simpler and faster. The references including: 1 Refaat, M. (2011, ISBN: 9781447511199). Credit Risk Scorecard: Development and Implementation Using SAS; 2 Bezdek, James C.FCM: The fuzzy c-means clustering algorithm. Computers & Geosciences (0098-3004),<DOI:10.1016/0098-3004(84)90020-7>.
Author: Dongping Fan [aut, cre]
Maintainer: Dongping Fan <fdp@pku.edu.cn>
Diff between creditmodel versions 1.3.0 dated 2021-01-25 and 1.3.1 dated 2022-01-07
creditmodel-1.3.0/creditmodel/man/check_rules.Rd |only creditmodel-1.3.0/creditmodel/man/cohort_analysis.Rd |only creditmodel-1.3.0/creditmodel/man/cross_table.Rd |only creditmodel-1.3.0/creditmodel/man/get_ctree_rules.Rd |only creditmodel-1.3.0/creditmodel/man/get_plots.Rd |only creditmodel-1.3.0/creditmodel/man/plot_bar.Rd |only creditmodel-1.3.0/creditmodel/man/plot_box.Rd |only creditmodel-1.3.0/creditmodel/man/plot_density.Rd |only creditmodel-1.3.0/creditmodel/man/plot_distribution.Rd |only creditmodel-1.3.0/creditmodel/man/plot_line.Rd |only creditmodel-1.3.0/creditmodel/man/plot_relative_freq_histogram.Rd |only creditmodel-1.3.0/creditmodel/man/pred_xgb.Rd |only creditmodel-1.3.0/creditmodel/man/rule_value_replace.Rd |only creditmodel-1.3.0/creditmodel/man/rules_filter.Rd |only creditmodel-1.3.0/creditmodel/man/rules_result.Rd |only creditmodel-1.3.0/creditmodel/man/swap_analysis.Rd |only creditmodel-1.3.1/creditmodel/DESCRIPTION | 10 creditmodel-1.3.1/creditmodel/MD5 | 60 creditmodel-1.3.1/creditmodel/NAMESPACE | 21 creditmodel-1.3.1/creditmodel/NEWS.md | 6 creditmodel-1.3.1/creditmodel/R/data_anaylsis.R | 1265 ----- creditmodel-1.3.1/creditmodel/R/data_visualization.R | 2275 +++------- creditmodel-1.3.1/creditmodel/R/model_training.R | 48 creditmodel-1.3.1/creditmodel/R/variable_binning.R | 163 creditmodel-1.3.1/creditmodel/build/partial.rdb |binary creditmodel-1.3.1/creditmodel/build/vignette.rds |binary creditmodel-1.3.1/creditmodel/inst/doc/introduction.html | 407 - creditmodel-1.3.1/creditmodel/man/customer_segmentation.Rd | 2 creditmodel-1.3.1/creditmodel/man/fuzzy_cluster_means.Rd | 11 creditmodel-1.3.1/creditmodel/man/get_breaks_all.Rd | 2 creditmodel-1.3.1/creditmodel/man/get_tree_breaks.Rd | 2 creditmodel-1.3.1/creditmodel/man/love_color.Rd | 11 creditmodel-1.3.1/creditmodel/man/lr_params.Rd | 2 creditmodel-1.3.1/creditmodel/man/plot_colors.Rd | 3 creditmodel-1.3.1/creditmodel/man/psi_iv_filter.Rd | 2 creditmodel-1.3.1/creditmodel/man/split_bins.Rd | 5 creditmodel-1.3.1/creditmodel/man/split_bins_all.Rd | 6 creditmodel-1.3.1/creditmodel/man/train_lr.Rd | 2 creditmodel-1.3.1/creditmodel/man/training_model.Rd | 2 39 files changed, 1079 insertions(+), 3226 deletions(-)
Title: Rendering Parameterized SQL and Translation to Dialects
Description: A rendering tool for parameterized SQL that also translates into
different SQL dialects. These dialects include 'Microsoft Sql Server', 'Oracle',
'PostgreSql', 'Amazon RedShift', 'Apache Impala', 'IBM Netezza', 'Google BigQuery', 'Microsoft PDW', 'Apache Spark', and 'SQLite'.
Author: Martijn Schuemie [aut, cre],
Marc Suchard [aut]
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>
Diff between SqlRender versions 1.8.1 dated 2021-09-15 and 1.8.3 dated 2022-01-07
DESCRIPTION | 11 MD5 | 64 ++-- NAMESPACE | 3 NEWS.md | 24 + R/HelperFunctions.R | 20 + R/RenderSql.R | 24 + R/ShinyApps.R | 2 R/SqlRender.R | 4 build/vignette.rds |binary inst/csv/jarChecksum.txt | 2 inst/csv/replacementPatterns.csv | 14 - inst/csv/supportedDialects.csv |only inst/doc/UsingSqlRender.R | 2 inst/doc/UsingSqlRender.Rmd | 5 inst/doc/UsingSqlRender.pdf |binary inst/java/SqlRender.jar |binary java/org/ohdsi/sql/BigQuerySparkTranslate.java | 2 java/org/ohdsi/sql/JarChecksum.java | 2 java/org/ohdsi/sql/MainClass.java | 2 java/org/ohdsi/sql/SqlRender.java | 2 java/org/ohdsi/sql/SqlSplit.java | 2 java/org/ohdsi/sql/SqlTranslate.java | 118 +++++--- java/org/ohdsi/sql/StringUtils.java | 2 java/org/ohdsi/sql/TestSqlRender.java | 15 - man/SqlRender-package.Rd | 4 man/getTempTablePrefix.Rd |only man/launchSqlRenderDeveloper.Rd | 38 +- man/listSupportedDialects.Rd |only man/supportsJava8.Rd | 36 +- man/translate.Rd | 3 tests/testthat/test-helperFunctions.R | 8 tests/testthat/test-translate-bigquery.R |only tests/testthat/test-translate-spark.R | 2 tests/testthat/test-translateSql.R | 348 ------------------------- vignettes/UsingSqlRender.Rmd | 5 35 files changed, 276 insertions(+), 488 deletions(-)
Title: List Comprehensions
Description: An implementation of list comprehensions as purely syntactic
sugar with a minor runtime overhead. It constructs nested for-loops and
executes the byte-compiled loops to collect the results.
Author: Dirk Schumacher [aut, cre, cph]
Maintainer: Dirk Schumacher <mail@dirk-schumacher.net>
Diff between listcomp versions 0.3.0 dated 2020-05-24 and 0.4.0 dated 2022-01-07
DESCRIPTION | 11 ++--- LICENSE | 2 MD5 | 16 +++---- NAMESPACE | 2 NEWS.md | 8 +++ R/lst.R | 13 +++--- README.md | 95 +++++++++++++++++++++----------------------- man/gen_list.Rd | 5 +- tests/testthat/test-lists.R | 12 +++++ 9 files changed, 94 insertions(+), 70 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-01-04 0.9.0.3
Title: MR Spectroscopy Analysis Tools
Description: Tools for reading, visualising and processing Magnetic Resonance
Spectroscopy data. The package includes methods for spectral fitting: Wilson
(2021) <DOI:10.1002/mrm.28385> and spectral alignment: Wilson (2018)
<DOI:10.1002/mrm.27605>.
Author: Martin Wilson [cre, aut] (<https://orcid.org/0000-0002-2089-3956>),
Yong Wang [ctb],
John Muschelli [ctb]
Maintainer: Martin Wilson <martin@pipegrep.co.uk>
Diff between spant versions 1.16.0 dated 2021-11-18 and 1.17.0 dated 2022-01-07
DESCRIPTION | 8 - MD5 | 170 +++++++++++++++---------------- NAMESPACE | 2 NEWS.md | 11 ++ R/dicom_reader.R | 2 R/fit_display.R | 22 +++- R/image_reg.R | 42 ++++++- R/interactive_plotting.R | 9 + R/mrs_data_display.R | 5 R/mrs_data_io.R | 16 ++ R/mrs_data_proc.R | 201 +++++++++++++++++++++++++------------ R/mrs_read_pfile.R | 83 ++++++++------- R/mrs_read_twix.R | 9 + R/utils.R | 12 ++ inst/doc/spant-intro.html | 124 +++++++++++----------- inst/doc/spant-preprocessing.html | 4 man/acquire.Rd | 46 ++++---- man/append_coils.Rd | 38 +++--- man/append_dyns.Rd | 38 +++--- man/apply_axes.Rd | 60 +++++------ man/apply_mrs.Rd | 44 ++++---- man/auto_phase.Rd | 50 ++++----- man/bbase.Rd | 46 ++++---- man/bc_constant.Rd | 40 +++---- man/calc_ed_from_lambda.Rd | 42 +++---- man/calc_peak_info_vec.Rd | 40 +++---- man/calc_spec_diff.Rd | 42 +++---- man/calc_spec_snr.Rd | 88 ++++++++-------- man/comb_coils.Rd | 6 - man/crop_td_pts.Rd | 42 +++---- man/ecc.Rd | 52 ++++----- man/est_noise_sd.Rd | 12 +- man/fit_amps.Rd | 58 +++++----- man/fp_phase_correct.Rd | 44 ++++---- man/get_1h_brain_basis_paras.Rd | 48 ++++---- man/get_1h_brain_basis_paras_v1.Rd | 48 ++++---- man/get_1h_brain_basis_paras_v2.Rd | 48 ++++---- man/get_2d_psf.Rd | 46 ++++---- man/get_mrsi2d_seg.Rd | 3 man/get_mrsi_voi.Rd | 46 ++++---- man/get_mrsi_voxel.Rd | 50 ++++----- man/get_mrsi_voxel_xy_psf.Rd | 50 ++++----- man/get_seg_ind.Rd | 42 +++---- man/get_voi_seg.Rd | 38 +++--- man/get_voi_seg_psf.Rd | 38 +++--- man/get_voxel.Rd | 54 ++++----- man/grid_shift_xy.Rd | 42 +++---- man/l2_reg.Rd | 14 ++ man/lb.Rd | 54 ++++----- man/mrs_data2basis.Rd | 42 +++---- man/mrs_data2vec.Rd | 54 ++++----- man/nifti_flip_lr.Rd | 42 +++---- man/peak_info.Rd | 72 ++++++------- man/plot_bc.Rd | 36 +++--- man/plot_slice_map.Rd | 94 ++++++++--------- man/re_weighting.Rd | 42 +++---- man/read_lcm_coord.Rd | 36 +++--- man/read_mrs_tqn.Rd | 64 +++++------ man/read_tqn_result.Rd | 48 ++++---- man/recon_twix_2d_mrsi.Rd |only man/rep_mrs.Rd | 12 ++ man/resample_img.Rd | 42 +++---- man/seq_cpmg_ideal.Rd | 50 ++++----- man/seq_mega_press_ideal.Rd | 84 +++++++-------- man/seq_press_ideal.Rd | 50 ++++----- man/seq_pulse_acquire.Rd | 42 +++---- man/seq_pulse_acquire_31p.Rd | 42 +++---- man/seq_slaser_ideal.Rd | 54 ++++----- man/seq_spin_echo_ideal.Rd | 46 ++++---- man/seq_spin_echo_ideal_31p.Rd | 46 ++++---- man/seq_steam_ideal.Rd | 50 ++++----- man/set_lw.Rd | 42 +++---- man/sim_basis.Rd | 64 +++++------ man/sim_basis_1h_brain.Rd | 70 ++++++------ man/sim_basis_1h_brain_press.Rd | 70 ++++++------ man/sim_basis_tqn.Rd | 66 ++++++------ man/sim_brain_1h.Rd | 82 +++++++-------- man/sim_mol.Rd | 80 +++++++------- man/sim_resonances.Rd | 6 - man/spin_sys.Rd | 42 +++---- man/spm_pve2categorical.Rd | 38 +++--- man/td_conv_filt.Rd | 42 +++---- man/varpro_3_para_opts.Rd | 100 +++++++++--------- man/varpro_opts.Rd | 96 ++++++++--------- man/write_basis_tqn.Rd | 46 ++++---- man/zero_fade_spec.Rd |only man/zf.Rd | 52 ++++----- 87 files changed, 2151 insertions(+), 1922 deletions(-)
Title: Gradient-Free Gradient Boosting
Description: Implementation of routines of the author's PhD thesis on gradient-free Gradient Boosting (Werner, Tino (2020) "Gradient-Free Gradient Boosting", URL '<https://oops.uni-oldenburg.de/id/eprint/4290>').
Author: Tino Werner [aut, cre, cph]
Maintainer: Tino Werner <tino.werner1@uni-oldenburg.de>
Diff between gfboost versions 0.1.0 dated 2020-11-03 and 0.1.1 dated 2022-01-07
DESCRIPTION | 7 +++---- MD5 | 6 +++--- R/CMB_Stabsel.R | 2 +- inst/NEWS | 25 ++++++++++++++++--------- 4 files changed, 23 insertions(+), 17 deletions(-)