Title: Mappable Vector Library for Handling Large Datasets
Description: Mappable vector library provides convenient way to access large datasets on solid state drives. This bypasses limitation of physical memory size as well as limited bandwidth of database interfaces. Memory mapped data can be shared between multiple R processes. Access speed depends on storage medium, so solid state drive is recommended, preferably with PCI Express (or M.2 nvme) interface. The data is memory mapped into R and then accessed using usual R list and array subscription operators. Convenience functions are provided for merging, grouping and indexing large vectors and data.frames. The layout of underlying MVL files is optimized for large datasets. The vectors are stored to guarantee alignment for vector intrinsics after memory map. The package is built on top of libMVL, which can be used as standalone C library. libMVL has simple C API making it easy to interchange of datasets with outside programs.
Author: Vladimir Dergachev [aut, cre] (<https://orcid.org/0000-0003-4708-6625>)
Maintainer: Vladimir Dergachev <support@altumrete.com>
Diff between RMVL versions 0.0.2.1 dated 2021-08-15 and 0.0.3.0 dated 2021-09-20
DESCRIPTION | 8 MD5 | 51 NAMESPACE | 16 R/RMVL.R | 780 +++++++++- man/mvl_class.Rd | 4 man/mvl_close.Rd | 8 man/mvl_find_matches.Rd |only man/mvl_fused_write_objects.Rd | 12 man/mvl_get_groups.Rd |only man/mvl_get_neighbors.Rd |only man/mvl_group.Rd |only man/mvl_group_lapply.Rd |only man/mvl_hash_vectors.Rd |only man/mvl_indexed_copy.Rd |only man/mvl_inherits.Rd |only man/mvl_merge.Rd |only man/mvl_neighbors_lapply.Rd |only man/mvl_object_stats.Rd | 2 man/mvl_open.Rd | 3 man/mvl_order_vectors.Rd |only man/mvl_remap.Rd |only man/mvl_write_groups.Rd |only man/mvl_write_hash_vectors.Rd |only man/mvl_write_object.Rd | 18 man/mvl_write_spatial_groups.Rd |only man/mvl_xlength.Rd |only src/RlibMVL.c | 3015 +++++++++++++++++++++++++++++++++++++++- src/libMVL.c | 1086 ++++++++++++++ src/libMVL.h | 284 +++ src/libMVL_sort.cc |only src/pdqidxsort.h |only src/pdqsort.h |only tests |only 33 files changed, 5168 insertions(+), 119 deletions(-)
Title: Extended Multiplicative Signal Correction
Description: Background correction of spectral like data. Handles variations in
scaling, polynomial baselines, interferents, constituents and replicate variation.
Parameters for corrections are stored for further analysis, and spectra are corrected
accordingly.
Author: Kristian Hovde Liland [aut, cre]
(<https://orcid.org/0000-0001-6468-9423>),
Ulf Geir Indahl [ctb]
Maintainer: Kristian Hovde Liland <kristian.liland@nmbu.no>
Diff between EMSC versions 0.9.2 dated 2020-06-19 and 0.9.3 dated 2021-09-20
DESCRIPTION | 27 ++++++++++++++++++++------- MD5 | 9 +++++---- NEWS | 4 ++++ R/EMSC.R | 8 ++++---- README.md |only man/EMSC.Rd | 2 -- 6 files changed, 33 insertions(+), 17 deletions(-)
Title: Import Data in the JCAMP-DX Format
Description: Import data written in the JCAMP-DX format. This is an instrument-independent format used in the field of spectroscopy. Examples include IR, NMR, and Raman spectroscopy. See the vignette for background and supported formats. The official JCAMP-DX site is <http://www.jcamp-dx.org/>.
Author: Bryan A. Hanson [aut, cre] (<https://orcid.org/0000-0003-3536-8246>)
Maintainer: Bryan A. Hanson <hanson@depauw.edu>
Diff between readJDX versions 0.5.61 dated 2021-08-08 and 0.6.1 dated 2021-09-20
readJDX-0.5.61/readJDX/R/processDT.R |only readJDX-0.5.61/readJDX/R/processPT.R |only readJDX-0.5.61/readJDX/R/processVariableList.R |only readJDX-0.5.61/readJDX/inst/doc/ProgramFlow.R |only readJDX-0.5.61/readJDX/inst/doc/ProgramFlow.Rmd |only readJDX-0.5.61/readJDX/inst/doc/ProgramFlow.pdf |only readJDX-0.5.61/readJDX/vignettes/ProgramFlow.Rmd |only readJDX-0.6.1/readJDX/DESCRIPTION | 12 +- readJDX-0.6.1/readJDX/MD5 | 76 ++++++------- readJDX-0.6.1/readJDX/NEWS.md | 13 ++ readJDX-0.6.1/readJDX/R/charXYnumXY.R |only readJDX-0.6.1/readJDX/R/decompLines.R | 7 - readJDX-0.6.1/readJDX/R/extractParams.R | 19 +-- readJDX-0.6.1/readJDX/R/findVariableLists.R | 23 +++- readJDX-0.6.1/readJDX/R/getComp.R | 5 readJDX-0.6.1/readJDX/R/insertDUPs.R | 2 readJDX-0.6.1/readJDX/R/onAttach.R | 2 readJDX-0.6.1/readJDX/R/process2DNMR.R |only readJDX-0.6.1/readJDX/R/processLCMS.R |only readJDX-0.6.1/readJDX/R/processVariableLIst.R |only readJDX-0.6.1/readJDX/R/processXYXY.R |only readJDX-0.6.1/readJDX/R/processXYY.R | 27 +--- readJDX-0.6.1/readJDX/R/readJDX.R | 35 +++--- readJDX-0.6.1/readJDX/R/sinkall.R | 2 readJDX-0.6.1/readJDX/R/splitMultiblockDX.R | 6 - readJDX-0.6.1/readJDX/R/yValueCheck.R | 2 readJDX-0.6.1/readJDX/build/vignette.rds |binary readJDX-0.6.1/readJDX/inst/doc/GuideToVignettes.R | 3 readJDX-0.6.1/readJDX/inst/doc/GuideToVignettes.Rmd | 74 +++++------- readJDX-0.6.1/readJDX/inst/doc/GuideToVignettes.pdf |binary readJDX-0.6.1/readJDX/inst/doc/MiniDIFDUP_1.Rnw | 2 readJDX-0.6.1/readJDX/inst/doc/MiniDIFDUP_1.pdf |binary readJDX-0.6.1/readJDX/inst/doc/MiniDIFDUP_2.pdf |binary readJDX-0.6.1/readJDX/inst/doc/Taxonomy.R |only readJDX-0.6.1/readJDX/inst/doc/Taxonomy.Rmd |only readJDX-0.6.1/readJDX/inst/doc/Taxonomy.pdf |only readJDX-0.6.1/readJDX/inst/doc/readJDX.Rmd | 109 +++++++------------ readJDX-0.6.1/readJDX/inst/doc/readJDX.pdf |binary readJDX-0.6.1/readJDX/man/decompLines.Rd | 10 + readJDX-0.6.1/readJDX/man/readJDX.Rd | 1 readJDX-0.6.1/readJDX/man/sinkall.Rd | 2 readJDX-0.6.1/readJDX/man/splitMultiblockDX.Rd | 6 - readJDX-0.6.1/readJDX/vignettes/GuideToVignettes.Rmd | 74 +++++------- readJDX-0.6.1/readJDX/vignettes/JCAMP-DX.bib | 16 +- readJDX-0.6.1/readJDX/vignettes/MiniDIFDUP_1.Rnw | 2 readJDX-0.6.1/readJDX/vignettes/Taxonomy.Rmd |only readJDX-0.6.1/readJDX/vignettes/readJDX.Rmd | 109 +++++++------------ 47 files changed, 300 insertions(+), 339 deletions(-)
Title: Tools to Accompany the 'psych' Package for Psychological
Research
Description: Support functions, data sets, and vignettes for the 'psych' package. Contains several of the biggest data sets for the 'psych' package as well as one vignette. A few helper functions for file manipulation are included as well. For more information, see the <https://personality-project.org/r/> web page.
Author: William Revelle [aut, cre] (<https://orcid.org/0000-0003-4880-9610>)
Maintainer: William Revelle <revelle@northwestern.edu>
Diff between psychTools versions 2.1.6 dated 2021-06-18 and 2.1.8 dated 2021-09-20
DESCRIPTION | 8 ++++---- MD5 | 25 ++++++++++++++----------- NAMESPACE | 2 +- R/df2latex.R | 8 ++++++-- build/partial.rdb |only build/vignette.rds |binary data/GERAS.rda |only inst/NEWS.Rd | 1 + inst/doc/factor.pdf |binary inst/doc/mediation.pdf |binary inst/doc/omega.pdf |binary inst/doc/overview.pdf |binary man/GERAS.Rd |only man/ability.Rd | 9 +++++++-- man/iqitems.Rd | 6 ++++++ 15 files changed, 39 insertions(+), 20 deletions(-)
Title: Deduplication Across Multiple Columns
Description: Duplicated data can exist in different rows and columns and user may need to
treat observations (rows) connected by duplicated data as one observation,
e.g. companies can belong to one family (and thus: be one company) by sharing
some telephone numbers. This package provides a function to find connected rows
based on data on chosen columns and collapse it into one row.
Author: Grzegorz Smoliński [aut, cre]
Maintainer: Grzegorz Smoliński <g.smolinski1@gmail.com>
Diff between dedupewider versions 0.0.1 dated 2021-07-09 and 0.0.2 dated 2021-09-20
DESCRIPTION | 8 ++++---- MD5 | 15 ++++++++------- NEWS.md | 12 +++++++++--- R/dedupe_wide.R | 2 +- README.md | 22 +++++++++++++++++++++- build/vignette.rds |binary inst/doc/usage-and-algorithm-explained.html | 1 + man/dedupe_wide.Rd | 2 +- man/figures |only 9 files changed, 45 insertions(+), 17 deletions(-)
Title: Random Forests for Dependent Data
Description: Fits non-linear regression models on dependant data with Generalised Least Square (GLS) based Random Forest (RF-GLS) detailed in Saha, Basu and Datta (2020) <arXiv:2007.15421>.
Author: Arkajyoti Saha [aut, cre],
Sumanta Basu [aut],
Abhirup Datta [aut]
Maintainer: Arkajyoti Saha <arkajyotisaha93@gmail.com>
Diff between RandomForestsGLS versions 0.1.2 dated 2021-01-30 and 0.1.3 dated 2021-09-20
DESCRIPTION | 6 +++--- MD5 | 11 ++++++----- build/vignette.rds |binary inst/doc/RandomForestsGLS_user_guide.R |only inst/doc/RandomForestsGLS_user_guide.pdf |binary src/RFGLS.cpp | 14 ++++++++------ src/util.cpp | 12 ++++++++---- 7 files changed, 25 insertions(+), 18 deletions(-)
More information about RandomForestsGLS at CRAN
Permanent link
Title: Simulate Data from R or 'JAGS' Code
Description: Generates data from R or 'JAGS' code for use in simulation
studies. The data are returned as an 'nlist::nlists' object and/or
saved to file as individual '.rds' files. Parallelization is
implemented using the 'future' package. Progress is reported using
the 'progressr' package.
Author: Audrey Beliveau [aut],
Joe Thorley [aut, cre] (<https://orcid.org/0000-0002-7683-4592>)
Maintainer: Joe Thorley <joe@poissonconsulting.ca>
Diff between sims versions 0.0.2 dated 2021-01-18 and 0.0.3 dated 2021-09-20
sims-0.0.2/sims/man/figures |only sims-0.0.2/sims/tests/testthat/test-variable-nodes.R |only sims-0.0.3/sims/DESCRIPTION | 21 - sims-0.0.3/sims/MD5 | 63 +-- sims-0.0.3/sims/NEWS.md | 8 sims-0.0.3/sims/R/check.R | 5 sims-0.0.3/sims/R/copy.R | 8 sims-0.0.3/sims/R/data-files.R | 5 sims-0.0.3/sims/R/data.R | 6 sims-0.0.3/sims/R/info.R | 5 sims-0.0.3/sims/R/params.R |only sims-0.0.3/sims/R/simulate.R | 33 - sims-0.0.3/sims/R/testthat-helpers.R |only sims-0.0.3/sims/R/utils.R | 1 sims-0.0.3/sims/README.md | 26 - sims-0.0.3/sims/build/vignette.rds |binary sims-0.0.3/sims/inst/WORDLIST | 6 sims-0.0.3/sims/inst/doc/sims.R | 8 sims-0.0.3/sims/inst/doc/sims.Rmd | 10 sims-0.0.3/sims/inst/doc/sims.html | 343 ++++--------------- sims-0.0.3/sims/man/params.Rd |only sims-0.0.3/sims/man/sims_check.Rd | 2 sims-0.0.3/sims/man/sims_data.Rd | 5 sims-0.0.3/sims/man/sims_data_files.Rd | 2 sims-0.0.3/sims/man/sims_info.Rd | 2 sims-0.0.3/sims/man/sims_simulate.Rd | 2 sims-0.0.3/sims/tests/testthat/test-add.R | 24 - sims-0.0.3/sims/tests/testthat/test-check.R | 6 sims-0.0.3/sims/tests/testthat/test-copy.R | 14 sims-0.0.3/sims/tests/testthat/test-data.R | 8 sims-0.0.3/sims/tests/testthat/test-internal.R | 2 sims-0.0.3/sims/tests/testthat/test-rdists.R | 2 sims-0.0.3/sims/tests/testthat/test-rjags.R | 11 sims-0.0.3/sims/tests/testthat/test-simulate.R | 245 +++++++------ sims-0.0.3/sims/vignettes/sims.Rmd | 10 35 files changed, 360 insertions(+), 523 deletions(-)
Title: Set 'RStudio' Preferences
Description: As of 'RStudio' v1.3, the preferences in the Global Options
dialog (and a number of other preferences that aren’t) are now saved
in simple, plain-text JSON files. This package provides an interface
for working with these 'RStudio' JSON preference files to easily make
modifications without using the point-and-click option menus. This is
particularly helpful when working on teams to ensure a unified
experience across machines and utilizing settings for best practices.
Author: Daniel D. Sjoberg [aut, cre, cph]
(<https://orcid.org/0000-0003-0862-2018>)
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>
Diff between rstudio.prefs versions 0.1.5 dated 2021-07-22 and 0.1.6 dated 2021-09-20
DESCRIPTION | 6 MD5 | 36 +-- NAMESPACE | 2 NEWS.md | 8 R/fetch_rstudio_prefs.R | 110 +++++----- R/pretty.R | 51 +++- R/rstudio.prefs-package.R | 28 +- R/use_rstudio_keyboard_shortcut.R | 220 ++++++++++---------- R/use_rstudio_prefs.R | 166 +++++++-------- R/use_rstudio_secondary_repo.R | 19 + R/utils.R | 23 +- README.md | 172 +++++++-------- inst/WORDLIST | 2 man/check_min_rstudio_version.Rd |only man/rstudio_config_path.Rd |only man/use_rstudio_secondary_repo.Rd | 6 tests/testthat.R | 8 tests/testthat/test-pretty_print_updates.R | 12 - tests/testthat/test-repo_string_as_named_list.R | 24 +- tests/testthat/test-use_rstudio_keyboard_shortcut.R | 36 +-- 20 files changed, 495 insertions(+), 434 deletions(-)
Title: Nonlinear Nonparametric Statistics
Description: Nonlinear nonparametric statistics using partial moments. Partial moments are the elements of variance and asymptotically approximate the area of f(x). These robust statistics provide the basis for nonlinear analysis while retaining linear equivalences. NNS offers: Numerical integration, Numerical differentiation, Clustering, Correlation, Dependence, Causal analysis, ANOVA, Regression, Classification, Seasonality, Autoregressive modeling, Normalization and Stochastic dominance. All routines based on: Viole, F. and Nawrocki, D. (2013), Nonlinear Nonparametric Statistics: Using Partial Moments (ISBN: 1490523995).
Author: Fred Viole
Maintainer: Fred Viole <ovvo.financial.systems@gmail.com>
Diff between NNS versions 0.8.0 dated 2021-09-13 and 0.8.1 dated 2021-09-20
DESCRIPTION | 8 +- MD5 | 20 ++--- R/Boost.R | 20 ++--- R/Dependence.R | 15 ++- R/Multivariate_Regression.R | 21 +++-- R/Regression.R | 5 - R/dy_d_wrt.R | 6 - README.md | 4 - inst/doc/NNSvignette_Classification.html | 79 ++++++++++++-------- inst/doc/NNSvignette_Clustering_and_Regression.html | 10 +- inst/doc/NNSvignette_Forecasting.html | 12 +-- 11 files changed, 113 insertions(+), 87 deletions(-)
Title: A 'HTTP' Server Graphics Device
Description: A graphics device for R that is accessible via network protocols.
This package was created to make it easier to embed live R graphics in
integrated development environments and other applications.
The included 'HTML/JavaScript' client (plot viewer) aims to provide a better overall user experience when dealing with R graphics.
The device asynchronously serves graphics via 'HTTP' and 'WebSockets'.
Author: Florian Rupprecht [aut, cre] (<https://orcid.org/0000-0002-1795-8624>),
Kun Ren [ctb],
Jeroen Ooms [ctb] (<https://orcid.org/0000-0002-4035-0289>),
Hadley Wickham [cph] (Author of included svglite code),
Lionel Henry [cph] (Author of included svglite code),
Thomas Lin Pedersen [cph] (Author and creator of included svglite code),
T Jake Luciani [cph] (Author of included svglite code),
Matthieu Decorde [cph] (Author of included svglite code),
Vaudor Lise [cph] (Author of included svglite code),
Tony Plate [cph] (Contributor to included svglite code),
David Gohel [cph] (Contributor to included svglite code),
Yixuan Qiu [cph] (Contributor to included svglite code),
Håkon Malmedal [cph] (Contributor to included svglite code),
RStudio [cph] (Copyright holder of included svglite code),
Brett Robinson [cph] (Author of included belle library),
Google [cph] (Copyright holder of included material design icons),
Victor Zverovich [cph] (Author of included fmt library)
Maintainer: Florian Rupprecht <floruppr@gmail.com>
Diff between httpgd versions 1.2.0 dated 2021-09-18 and 1.2.1 dated 2021-09-20
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- NEWS.md | 5 +++++ README.md | 6 ++++-- inst/doc/api-documentation.Rmd | 2 +- inst/doc/api-documentation.html | 2 +- src/HttpgdDev.cpp | 4 ++-- src/HttpgdGeom.h | 13 +++++++------ src/RendererSvg.cpp | 4 ++-- src/RendererTikZ.cpp | 4 +++- vignettes/api-documentation.Rmd | 2 +- 11 files changed, 39 insertions(+), 29 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, cre] (<https://orcid.org/0000-0002-1261-905X>)
Maintainer: Yitao Li <yitao@rstudio.com>
Diff between cuml versions 0.2.0 dated 2021-09-16 and 0.2.1 dated 2021-09-20
DESCRIPTION | 8 ++--- MD5 | 49 +++++++++++++++++-------------- NAMESPACE | 2 + R/RcppExports.R | 20 +++++++++++-- R/fil.R | 2 - R/model.R | 65 ++++++++++++++++++++++++++---------------- R/package.R | 11 +++++-- R/svm.R | 48 ++++++++++++++++++++++++++++--- R/umap.R | 14 +++++++++ man/cuml_fil_load_model.Rd | 2 - man/cuml_serialize.Rd | 7 +++- man/cuml_unserialize.Rd | 3 + src/CMakeLists.txt.in | 3 + src/RcppExports.cpp | 48 +++++++++++++++++++++++++++++++ src/pinned_host_vector.h | 2 + src/svm_classifier.cpp | 30 +++++++++++++++++++ src/svm_classifier.cu | 50 ++++++++++++++++++++++++++++++-- src/svm_classifier.h | 4 ++ src/svm_regressor.cpp | 30 +++++++++++++++++++ src/svm_regressor.cu | 69 ++++++++++++++++++++++++++++++++++++++------- src/svm_regressor.h | 4 ++ src/svm_serde.cu |only src/svm_serde.h |only src/umap.cpp | 4 +- src/umap.cu | 32 ++++++++++++-------- tests |only 26 files changed, 415 insertions(+), 92 deletions(-)
Title: Fast Inference for Large Spatial Datasets using BRISC
Description: Fits bootstrap with univariate spatial regression models using Bootstrap for Rapid Inference on Spatial Covariances (BRISC) for large datasets using nearest neighbor Gaussian processes detailed in Saha and Datta (2018) <doi:10.1002/sta4.184>.
Author: Arkajyoti Saha [aut, cre],
Abhirup Datta [aut],
Jorge Nocedal [ctb],
Naoaki Okazaki [ctb]
Maintainer: Arkajyoti Saha <arkajyotisaha93@gmail.com>
Diff between BRISC versions 1.0.1 dated 2021-03-09 and 1.0.2 dated 2021-09-20
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- src/BRISC.cpp | 16 ++++++++++------ src/BRISC_Predict.cpp | 10 ++++++---- src/util.cpp | 10 ++++++---- 5 files changed, 29 insertions(+), 21 deletions(-)
Title: Statistical Inference and Sure Independence Screening via Ball
Statistics
Description: Hypothesis tests and sure independence screening (SIS) procedure based on ball statistics, including ball divergence <doi:10.1214/17-AOS1579>, ball covariance <doi:10.1080/01621459.2018.1543600>, and ball correlation <doi:10.1080/01621459.2018.1462709>, are developed to analyze complex data in metric spaces, e.g, shape, directional, compositional and symmetric positive definite matrix data. The ball divergence and ball covariance based distribution-free tests are implemented to detecting distribution difference and association in metric spaces <doi:10.18637/jss.v097.i06>. Furthermore, several generic non-parametric feature selection procedures based on ball correlation, BCor-SIS and all of its variants, are implemented to tackle the challenge in the context of ultra high dimensional data. A fast implementation for large-scale multiple K-sample testing with ball divergence <doi: 10.1002/gepi.22423> is supported, which is particularly helpful for genome-wide association study.
Author: Jin Zhu [aut, cre] (<https://orcid.org/0000-0001-8550-5822>),
Wenliang Pan [aut],
Yuan Tian [aut],
Weinan Xiao [aut],
Chengfeng Liu [aut],
Ruihuang Liu [aut],
Yue Hu [aut],
Hongtu Zhu [aut],
Heping Zhang [aut],
Xueqin Wang [aut] (<https://orcid.org/0000-0001-5205-9950>)
Maintainer: Jin Zhu <zhuj37@mail2.sysu.edu.cn>
Diff between Ball versions 1.3.11 dated 2021-03-17 and 1.3.12 dated 2021-09-20
Ball-1.3.11/Ball/data/datalist |only Ball-1.3.12/Ball/DESCRIPTION | 35 Ball-1.3.12/Ball/MD5 | 72 - Ball-1.3.12/Ball/NAMESPACE | 68 - Ball-1.3.12/Ball/NEWS.md | 107 +- Ball-1.3.12/Ball/R/Ball.R | 15 Ball-1.3.12/Ball/R/bcorsis.R | 826 +++++++-------- Ball-1.3.12/Ball/R/bcov.R | 1240 +++++++++++------------ Ball-1.3.12/Ball/R/bd.R | 864 ++++++++-------- Ball-1.3.12/Ball/R/bd.gaws.R |only Ball-1.3.12/Ball/R/data.R | 460 ++++---- Ball-1.3.12/Ball/R/nhdist.R | 658 ++++++------ Ball-1.3.12/Ball/R/utilize.R | 796 +++++++------- Ball-1.3.12/Ball/R/wrap_c.R | 680 ++++++------ Ball-1.3.12/Ball/README.md | 313 +++-- Ball-1.3.12/Ball/build/vignette.rds |binary Ball-1.3.12/Ball/inst/CITATION | 46 Ball-1.3.12/Ball/inst/doc/Ball.R | 270 ++--- Ball-1.3.12/Ball/inst/doc/Ball.Rmd | 968 +++++++++--------- Ball-1.3.12/Ball/inst/doc/Ball.html | 1327 ++++++++++--------------- Ball-1.3.12/Ball/inst/doc/bd_gwas.R |only Ball-1.3.12/Ball/inst/doc/bd_gwas.Rmd |only Ball-1.3.12/Ball/inst/doc/bd_gwas.html |only Ball-1.3.12/Ball/man/bcorsis.Rd | 4 Ball-1.3.12/Ball/man/bd.gwas.test.Rd |only Ball-1.3.12/Ball/man/bd.test.Rd | 2 Ball-1.3.12/Ball/src/Ball_omp.h | 16 Ball-1.3.12/Ball/src/Makevars | 4 Ball-1.3.12/Ball/src/Makevars.win | 4 Ball-1.3.12/Ball/src/ball_init.c | 4 Ball-1.3.12/Ball/src/bcor.c | 4 Ball-1.3.12/Ball/src/bd_gwas.c |only Ball-1.3.12/Ball/src/bd_gwas.h |only Ball-1.3.12/Ball/src/tmp |only Ball-1.3.12/Ball/tests/testthat.R | 8 Ball-1.3.12/Ball/tests/testthat/test_bcorsis.R | 290 ++--- Ball-1.3.12/Ball/tests/testthat/test_bcov.R | 150 +- Ball-1.3.12/Ball/tests/testthat/test_bd.R | 262 ++-- Ball-1.3.12/Ball/tests/testthat/test_bd_gwas.R |only Ball-1.3.12/Ball/vignettes/Ball.Rmd | 968 +++++++++--------- Ball-1.3.12/Ball/vignettes/bd_gwas.Rmd |only Ball-1.3.12/Ball/vignettes/kbd_gwas.png |only 42 files changed, 5153 insertions(+), 5308 deletions(-)
Title: Export Domain Logic from Shiny using Meta-Programming
Description: Provides tools for capturing logic in a Shiny app and exposing it as code that can be run outside of Shiny (e.g., from an R console). It also provides tools for bundling both the code and results to the end user.
Author: Joe Cheng [aut],
Carson Sievert [cre, aut] (<https://orcid.org/0000-0002-4958-2844>),
RStudio [cph]
Maintainer: Carson Sievert <carson@rstudio.com>
Diff between shinymeta versions 0.2.0 dated 2021-06-15 and 0.2.0.2 dated 2021-09-20
DESCRIPTION | 12 ++++++------ MD5 | 10 +++++----- NEWS.md | 8 ++++++++ README.md | 14 ++++++++++---- tests/testthat/test-comments.R | 16 ++++++++-------- tests/testthat/test-report.R | 5 +++++ 6 files changed, 42 insertions(+), 23 deletions(-)
Title: Manage R Environments Better
Description: Provides a small set of functions for managing R environments, with defaults designed to encourage usage patterns that scale well to larger code bases. It provides: import_from(), a flexible way to assign bindings that defaults to the current environment; include(), a vectorized alternative to base::source() that also default to the current environment; and attach_eval() and attach_source(), a way to evaluate expressions in attached environments. Together, these (and other) functions pair to provide a robust alternative to base::library() and base::source().
Author: Tomasz Kalinowski [aut, cre]
Maintainer: Tomasz Kalinowski <kalinowskit@gmail.com>
Diff between envir versions 0.2.0 dated 2021-02-27 and 0.2.1 dated 2021-09-20
DESCRIPTION | 9 +--- MD5 | 13 +++-- NEWS.md |only R/attach_source.R | 42 +++++++++--------- R/import_from.R | 91 +++++++++++++++++++++++++++-------------- README.md | 2 man/attach_source.Rd | 20 +++------ man/set_library_default_pos.Rd | 2 8 files changed, 102 insertions(+), 77 deletions(-)
Title: Blood Pressure Analysis in R
Description: A comprehensive package to aid in the analysis of blood pressure data of all forms by providing both descriptive and visualization tools for researchers.
Author: John Schwenck [aut, cre],
Irina Gaynanova [aut] (<https://orcid.org/0000-0002-4116-0268>)
Maintainer: John Schwenck <jschwenck12@gmail.com>
Diff between bp versions 1.0.1 dated 2021-03-05 and 2.0.0 dated 2021-09-20
bp-1.0.1/bp/data/hypnos_data.rda |only bp-1.0.1/bp/man/hypnos_data.Rd |only bp-2.0.0/bp/DESCRIPTION | 18 bp-2.0.0/bp/MD5 | 116 +- bp-2.0.0/bp/NAMESPACE | 7 bp-2.0.0/bp/NEWS.md | 36 bp-2.0.0/bp/R/arv.R | 30 bp-2.0.0/bp/R/bp_arv.R |only bp-2.0.0/bp/R/bp_center.R | 19 bp-2.0.0/bp/R/bp_cv.R |only bp-2.0.0/bp/R/bp_mag.R | 20 bp-2.0.0/bp/R/bp_range.R | 22 bp-2.0.0/bp/R/bp_report.R | 574 +++++------- bp-2.0.0/bp/R/bp_sleep_metrics.R |only bp-2.0.0/bp/R/bp_stages.R |only bp-2.0.0/bp/R/bp_stats.R | 40 bp-2.0.0/bp/R/bp_sv.R |only bp-2.0.0/bp/R/bp_tables.R | 106 +- bp-2.0.0/bp/R/bp_visuals_hist.R | 103 +- bp-2.0.0/bp/R/bp_visuals_scatter.R | 731 +++++++++++---- bp-2.0.0/bp/R/bp_visuals_tables.R | 574 ++++++++---- bp-2.0.0/bp/R/bp_visuals_ts_plot.R |only bp-2.0.0/bp/R/cv.R | 35 bp-2.0.0/bp/R/data.R | 285 ++++++ bp-2.0.0/bp/R/data_process.R | 872 ++++++------------- bp-2.0.0/bp/R/data_process_helpers.R |only bp-2.0.0/bp/R/dip_calc.R | 260 +---- bp-2.0.0/bp/R/dip_class_plot.R |only bp-2.0.0/bp/R/helper_functions.R | 285 ++++++ bp-2.0.0/bp/R/sv.R | 31 bp-2.0.0/bp/README.md | 280 +++--- bp-2.0.0/bp/build/partial.rdb |binary bp-2.0.0/bp/data/bp_children.rda |only bp-2.0.0/bp/data/bp_ghana.rda |only bp-2.0.0/bp/data/bp_hypnos.rda |only bp-2.0.0/bp/data/bp_jhs.rda |binary bp-2.0.0/bp/data/bp_preg.rda |only bp-2.0.0/bp/data/bp_rats.rda |only bp-2.0.0/bp/inst/doc/bp.R | 44 bp-2.0.0/bp/inst/doc/bp.Rmd | 134 +- bp-2.0.0/bp/inst/doc/bp.html | 478 +++++++--- bp-2.0.0/bp/man/arv.Rd | 183 ++- bp-2.0.0/bp/man/bp_arv.Rd |only bp-2.0.0/bp/man/bp_center.Rd | 22 bp-2.0.0/bp/man/bp_children.Rd |only bp-2.0.0/bp/man/bp_cv.Rd |only bp-2.0.0/bp/man/bp_ghana.Rd |only bp-2.0.0/bp/man/bp_hist.Rd | 16 bp-2.0.0/bp/man/bp_hypnos.Rd |only bp-2.0.0/bp/man/bp_jhs.Rd | 1 bp-2.0.0/bp/man/bp_mag.Rd | 22 bp-2.0.0/bp/man/bp_preg.Rd |only bp-2.0.0/bp/man/bp_range.Rd | 23 bp-2.0.0/bp/man/bp_rats.Rd |only bp-2.0.0/bp/man/bp_report.Rd | 58 - bp-2.0.0/bp/man/bp_scatter.Rd | 279 +++--- bp-2.0.0/bp/man/bp_sleep_metrics.Rd |only bp-2.0.0/bp/man/bp_stages.Rd |only bp-2.0.0/bp/man/bp_stats.Rd | 27 bp-2.0.0/bp/man/bp_sv.Rd |only bp-2.0.0/bp/man/bp_tables.Rd | 15 bp-2.0.0/bp/man/bp_ts_plots.Rd |only bp-2.0.0/bp/man/create_grps.Rd | 7 bp-2.0.0/bp/man/cv.Rd | 173 ++- bp-2.0.0/bp/man/dip_calc.Rd | 31 bp-2.0.0/bp/man/dip_class_plot.Rd |only bp-2.0.0/bp/man/dow_tod_plots.Rd | 18 bp-2.0.0/bp/man/figures/README-unnamed-chunk-5-1.png |binary bp-2.0.0/bp/man/process_data.Rd | 387 +++++--- bp-2.0.0/bp/man/sleep_int.Rd |only bp-2.0.0/bp/man/stage_check.Rd | 2 bp-2.0.0/bp/man/sv.Rd | 186 ++-- bp-2.0.0/bp/vignettes/bp.Rmd | 134 +- 73 files changed, 3984 insertions(+), 2700 deletions(-)
Title: 'ggplot2' Based Tool to Facilitate Diagnostic Plots for NLME
Models
Description: At Novartis, we aimed at standardizing the set of diagnostic plots used for modeling
activities in order to reduce the overall effort required for generating such plots.
For this, we developed a guidance that proposes an adequate set of diagnostics and a toolbox,
called 'ggPMX' to execute them. 'ggPMX' is a toolbox that can generate all diagnostic plots at a quality sufficient
for publication and submissions using few lines of code.
Author: Amine Gassem [aut],
Bruno Bieth [aut],
Irina Baltcheva [aut],
Thomas Dumortier [aut],
Christian Bartels [aut],
Souvik Bhattacharya [aut],
Inga Ludwig [aut],
Ines Paule [aut],
Didier Renard [aut],
Matthew Fidler [aut, cre] (<https://orcid.org/0000-0001-8538-6691>),
Seid Hamzic [aut],
Benjamin Guiastrennec [ctb],
Kyle T Baron [ctb] (<https://orcid.org/0000-0001-7252-5656>),
Qing Xi Ooi [ctb],
Novartis Pharma AG [cph]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between ggPMX versions 1.2.3 dated 2021-05-29 and 1.2.4 dated 2021-09-20
DESCRIPTION | 8 - MD5 | 22 +-- R/param_table.R | 219 +++++++++++++++++--------------------- R/plot-eta-pairs.R | 12 +- R/pmx-plots-eta-cov.R | 2 R/pmx-reader.R | 30 +++-- R/pmx-report.R | 27 +++- R/pmxClass.R | 53 +++++---- inst/doc/ggPMX-guide.pdf |binary man/param_table.Rd | 6 - tests/testthat/test-param_table.R | 46 +++++-- tests/testthat/test-pmx-report.R | 63 +++++++++- 12 files changed, 292 insertions(+), 196 deletions(-)
Title: Formatting and Harmonizing Ecological Trait-Data
Description: Assistance for handling ecological trait data and applying the
Ecological Trait-Data Standard terminology (Schneider et al. 2019
<doi:10.1111/2041-210X.13288>). There are two major use cases: (1) preparation of
own trait datasets for publication, and (2) harmonizing
trait datasets from different sources by re-formatting them into a unified
format. See 'traitdataform' website for full documentation.
Author: Florian D. Schneider [aut, cre]
(<https://orcid.org/0000-0002-1494-5684>),
Caterina Penone [ctb] (<https://orcid.org/0000-0002-8170-6659>),
Andreas Ostrowski [ctb] (<https://orcid.org/0000-0002-2033-779X>),
Dennis Heimann [ctb],
Felix Neff [ctb],
Markus J. Ankenbrand [ctb],
Jessica Burnett [ctb],
Iñaki Ucar [ctb],
Matthias Grenié [ctb]
Maintainer: Florian D. Schneider <florian.dirk.schneider@gmail.com>
Diff between traitdataform versions 0.6.6 dated 2021-09-02 and 0.6.7 dated 2021-09-20
DESCRIPTION | 15 MD5 | 52 +- NAMESPACE | 1 NEWS.md | 7 R/data.R | 93 +++- R/get_gbif_taxonomy.R | 45 +- R/standardize.R | 2 build/partial.rdb |binary data |only inst/doc/traitdataform.R | 63 +- inst/doc/traitdataform.Rmd | 15 inst/doc/traitdataform.html | 712 ++++++++++++++++---------------- inst/extdata/arthropodtraits.R | 28 - inst/extdata/carabids.R | 5 inst/extdata/heteroptera.R | 15 inst/extdata/heteroptera_raw.R | 15 man/amniota.Rd | 2 man/arthropodtraits.Rd | 72 +++ man/as.traitdata.Rd | 2 man/heteroptera_raw.Rd | 11 man/pantheria.Rd | 2 man/standardize_taxa.Rd | 2 tests/testthat/test.columns_to_ETS.R | 5 tests/testthat/test.map_gbif_taxonomy.R | 29 - tests/testthat/test.standardize.R | 16 vignettes/traitdataform.Rmd | 15 26 files changed, 701 insertions(+), 523 deletions(-)
Title: Send Messages, Images, R Objects and Files to 'Slack'
Channels/Users
Description: 'Slack' <https://slack.com/> provides a service for teams to
collaborate by sharing messages, images, links, files and more.
Functions are provided that make it possible to interact with the
'Slack' platform 'API'. When you need to share information or data
from R, rather than resort to copy/ paste in e-mails or other services
like 'Skype' <https://www.skype.com/en/>, you can use this package to
send well-formatted output from multiple R objects and expressions to
all teammates at the same time with little effort. You can also send
images from the current graphics device, R objects, and upload files.
Author: Bob Rudis [aut, cre], Jay Jacobs [ctb], David Severski [ctb],
Quinn Weber [ctb], Konrad Karczewski [ctb], Shinya Uryu [ctb], Gregory
Jefferis [ctb], Ed Niles [ctb], Rick Saporta [ctb], Jonathan Sidi
[aut, ctb], Matt Kaye [aut, ctb], Xinye Li [ctb], Andrie de Vries
[aut, ctb]
Maintainer: Matt Kaye <mrkaye97@gmail.com>
Diff between slackr versions 3.0.1 dated 2021-08-20 and 3.2.0 dated 2021-09-20
DESCRIPTION | 11 ++- MD5 | 26 +++++---- NAMESPACE | 2 NEWS.md | 14 +++++ R/call_slack_api.R | 2 R/gg_slackr.R | 7 ++ R/globals.R | 2 R/slackr.R | 113 +++++++++++++++++++++++----------------- R/slackr_bot.r | 117 +++++++++++++++++++++++++----------------- R/slackr_tex.R | 12 +++- R/slackr_utils.R | 9 +-- R/utils-pipe.R |only man/ggslackr.Rd | 3 + man/pipe.Rd |only tests/testthat/test-posting.R | 86 ++++++++++++++++++++++++++++-- 15 files changed, 273 insertions(+), 131 deletions(-)
Title: Utility Functions for Working with Random Number Generators
Description: Provides a set of functions for working with
Random Number Generators (RNGs). In particular, a generic
S4 framework is defined for getting/setting the current RNG, or RNG data
that are embedded into objects for reproducibility.
Notably, convenient default methods greatly facilitate the way current
RNG settings can be changed.
Author: Renaud Gaujoux [aut, cre],
Max Kuhn [ctb]
Maintainer: Renaud Gaujoux <renozao@protonmail.com>
Diff between rngtools versions 1.5 dated 2020-01-23 and 1.5.2 dated 2021-09-20
DESCRIPTION | 10 +++---- MD5 | 6 ++-- R/RNG.R | 61 ++++++++++++++++++++++++++++++---------------- tests/testthat/test-RNG.r | 11 ++++---- 4 files changed, 55 insertions(+), 33 deletions(-)
Title: Mail Merge Using R Markdown Documents and 'gmailr'
Description: Perform a mail merge (mass email) using the message defined in
markdown, the recipients in a csv, and gmail as the mailing engine. With
this package you can parse markdown documents as the body of email, and the
'yaml' header to specify the subject line of the email. Any '{}' braces in
the email will be encoded with 'glue::glue()'. You can preview the email in
the RStudio viewer pane, and send (draft) email using 'gmailr'.
Author: Andrie de Vries [aut, cre]
Maintainer: Andrie de Vries <apdevries@gmail.com>
Diff between mailmerge versions 0.2.1 dated 2021-05-11 and 0.2.2 dated 2021-09-20
DESCRIPTION | 20 ++++++++++---------- MD5 | 16 ++++++++-------- NEWS.md | 10 +++++++++- R/mail_merge.R | 4 ++-- build/vignette.rds |binary inst/WORDLIST | 5 ++--- inst/doc/introduction.html | 28 +++++++++++++--------------- man/mailmerge-package.Rd | 12 ++++++------ tests/testthat/test-mail_merge.R | 3 ++- 9 files changed, 52 insertions(+), 46 deletions(-)
Title: Companion to "Learning Statistics with R"
Description: A collection of tools intended to make introductory
statistics easier to teach, including wrappers for common
hypothesis tests and basic data manipulation. It accompanies
Navarro, D. J. (2015). Learning Statistics with R: A Tutorial
for Psychology Students and Other Beginners, Version 0.6.
Author: Danielle Navarro [aut, cre] (<https://orcid.org/0000-0001-7648-6578>)
Maintainer: Danielle Navarro <d.navarro@unsw.edu.au>
Diff between lsr versions 0.5 dated 2015-03-02 and 0.5.1 dated 2021-09-20
lsr-0.5.1/lsr/DESCRIPTION | 30 + lsr-0.5.1/lsr/LICENSE |only lsr-0.5.1/lsr/MD5 | 130 ++++---- lsr-0.5.1/lsr/NAMESPACE | 71 ++-- lsr-0.5.1/lsr/NEWS | 10 lsr-0.5.1/lsr/R/aad.R | 39 +- lsr-0.5.1/lsr/R/associationTest.R | 180 ++++++----- lsr-0.5.1/lsr/R/bars.R | 282 ++++++++++-------- lsr-0.5.1/lsr/R/ciMean.R | 108 ++++-- lsr-0.5.1/lsr/R/cohensD.R | 344 +++++++++++++--------- lsr-0.5.1/lsr/R/colCopy.R | 43 ++ lsr-0.5.1/lsr/R/correlate.R | 270 +++++++++++------ lsr-0.5.1/lsr/R/cramersV.R | 61 +++ lsr-0.5.1/lsr/R/etaSquared.R | 142 ++++++--- lsr-0.5.1/lsr/R/expandFactors.R | 42 ++ lsr-0.5.1/lsr/R/goodnessOfFitTest.R | 130 +++++--- lsr-0.5.1/lsr/R/importList.R | 90 ++++- lsr-0.5.1/lsr/R/independentSamplesTTest.R | 227 +++++++++----- lsr-0.5.1/lsr/R/longToWide.R | 82 ++++- lsr-0.5.1/lsr/R/maxFreq.R | 23 - lsr-0.5.1/lsr/R/modeOf.R | 81 ++++- lsr-0.5.1/lsr/R/oneSampleTTest.R | 119 +++++-- lsr-0.5.1/lsr/R/pairedSamplesTTest.R | 418 ++++++++++++++++----------- lsr-0.5.1/lsr/R/permuteLevels.R | 78 ++++- lsr-0.5.1/lsr/R/posthocPairwiseT.R | 63 +++- lsr-0.5.1/lsr/R/printTTest.R | 77 ++-- lsr-0.5.1/lsr/R/quantileCut.R | 63 +++- lsr-0.5.1/lsr/R/rmAll.R | 56 ++- lsr-0.5.1/lsr/R/rowCopy.R | 12 lsr-0.5.1/lsr/R/sortFrame.R | 89 ++++- lsr-0.5.1/lsr/R/standardCoefs.R | 86 ++++- lsr-0.5.1/lsr/R/tFrame.R | 56 +++ lsr-0.5.1/lsr/R/unlibrary.R | 38 +- lsr-0.5.1/lsr/R/who.R | 116 +++++-- lsr-0.5.1/lsr/R/wideToLong.R | 127 ++++++-- lsr-0.5.1/lsr/README.md |only lsr-0.5.1/lsr/inst/CITATION | 20 - lsr-0.5.1/lsr/man/aad.Rd | 62 +--- lsr-0.5.1/lsr/man/associationTest.Rd | 72 +--- lsr-0.5.1/lsr/man/bars.Rd | 103 +++--- lsr-0.5.1/lsr/man/ciMean.Rd | 56 +-- lsr-0.5.1/lsr/man/cohensD.Rd | 178 ++++------- lsr-0.5.1/lsr/man/copy.Rd |only lsr-0.5.1/lsr/man/correlate.Rd | 119 ++++--- lsr-0.5.1/lsr/man/cramersV.Rd | 53 +-- lsr-0.5.1/lsr/man/etaSquared.Rd | 74 +--- lsr-0.5.1/lsr/man/expandFactors.Rd | 55 +-- lsr-0.5.1/lsr/man/goodnessOfFitTest.Rd | 81 ++--- lsr-0.5.1/lsr/man/importList.Rd | 65 +--- lsr-0.5.1/lsr/man/independentSamplesTTest.Rd | 105 +++--- lsr-0.5.1/lsr/man/longToWide.Rd | 106 +++--- lsr-0.5.1/lsr/man/mode.Rd |only lsr-0.5.1/lsr/man/oneSampleTTest.Rd | 94 ++---- lsr-0.5.1/lsr/man/pairedSamplesTTest.Rd | 144 +++++---- lsr-0.5.1/lsr/man/permuteLevels.Rd | 77 ++-- lsr-0.5.1/lsr/man/posthocPairwiseT.Rd | 84 ++--- lsr-0.5.1/lsr/man/print.TTest.Rd |only lsr-0.5.1/lsr/man/print.assocTest.Rd |only lsr-0.5.1/lsr/man/print.correlate.Rd |only lsr-0.5.1/lsr/man/print.gofTest.Rd |only lsr-0.5.1/lsr/man/print.whoList.Rd |only lsr-0.5.1/lsr/man/quantileCut.Rd | 75 ++-- lsr-0.5.1/lsr/man/rmAll.Rd | 54 +-- lsr-0.5.1/lsr/man/sortFrame.Rd | 249 +++------------- lsr-0.5.1/lsr/man/standardCoefs.Rd | 75 +--- lsr-0.5.1/lsr/man/tFrame.Rd | 75 ++-- lsr-0.5.1/lsr/man/unlibrary.Rd | 91 ++--- lsr-0.5.1/lsr/man/who.Rd | 123 ++----- lsr-0.5.1/lsr/man/wideToLong.Rd | 105 +++--- lsr-0.5/lsr/man/lsr-package.Rd |only lsr-0.5/lsr/man/modeOf.Rd |only lsr-0.5/lsr/man/rowCopy.Rd |only 72 files changed, 3555 insertions(+), 2623 deletions(-)
Title: 'hms' Based Timer
Description: Tracks elapsed clock time using a `hms::hms()` scalar, which
if running has an attribute named start that specifies the system time
when the timer was started. The elapsed time is the value of the
scalar plus the difference between the current system time and the
system time when the timer was started.
Author: Joe Thorley [aut, cre] (<https://orcid.org/0000-0002-7683-4592>),
Poisson Consulting [cph, fnd]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>
Diff between hmstimer versions 0.1.0 dated 2020-07-09 and 0.1.1 dated 2021-09-20
DESCRIPTION | 41 ++++++++++++++++++++++------------------- MD5 | 31 ++++++++++++++++--------------- NAMESPACE | 1 - NEWS.md | 10 ++++++++-- R/hmstimer-package.R | 1 - R/reset.R | 7 +------ README.md | 21 ++++++++------------- inst/WORDLIST | 6 +++--- man/figures/logo.png |only man/hmstimer-package.Rd | 13 +++++++------ man/tmr_reset.Rd | 4 +--- tests/testthat/test-ceiling.R | 2 -- tests/testthat/test-floor.R | 2 -- tests/testthat/test-format.R | 2 -- tests/testthat/test-reset.R | 3 --- tests/testthat/test-round.R | 2 -- tests/testthat/test-timer.R | 6 ++---- 17 files changed, 68 insertions(+), 84 deletions(-)
Title: An Easy Text and Sentiment Analysis Library
Description: Implement text and sentiment analysis with 'texter'.
Generate sentiment scores on text data and also visualize sentiments.
'texter' allows you to quickly generate insights on your data.
It includes support for lexicons such as 'NRC' and 'Bing'.
Author: Simi Kafaru [aut, cre]
Maintainer: Simi Kafaru <kafarusimileoluwa@gmail.com>
Diff between texter versions 0.0.0.9 dated 2021-08-17 and 0.1.9 dated 2021-09-20
DESCRIPTION | 10 +- MD5 | 25 +++-- NAMESPACE | 5 + R/counter.R | 81 +++++++++--------- R/globals.R | 11 +- R/nrc.R | 91 ++++++++++---------- R/sentimentAnalyzer.R | 121 ++++++++++++++------------- R/stop_words.R |only R/top_Sentiments.R | 156 ++++++++++++++++++----------------- R/top_bigrams.R |only R/top_words.R | 152 +++++++++++++++++----------------- R/top_words_Retriever.R | 185 +++++++++++++++++++++--------------------- README.md | 210 ++++++++++++++++++++++++++++-------------------- data/stop_words.rda |only man/stop_words.Rd |only man/top_bigrams.Rd |only 16 files changed, 556 insertions(+), 491 deletions(-)
Title: Spatial Regression Models for Large Datasets using Nearest
Neighbor Gaussian Processes
Description: Fits univariate Bayesian spatial regression models for large datasets using Nearest Neighbor Gaussian Processes (NNGP) detailed in Finley, Datta, Banerjee (2020) <arXiv:2001.09111>, and Finley, Datta, Cook, Morton, Andersen, and Banerjee (2019) <doi:10.1080/10618600.2018.1537924> and Datta, Banerjee, Finley, and Gelfand (2016) <doi:10.1080/01621459.2015.1044091>.
Author: Andrew Finley [aut, cre],
Abhirup Datta [aut],
Sudipto Banerjee [aut]
Maintainer: Andrew Finley <finleya@msu.edu>
Diff between spNNGP versions 0.1.5 dated 2021-02-17 and 0.1.6 dated 2021-09-20
DESCRIPTION | 8 ++++---- MD5 | 26 +++++++++++++------------- build/partial.rdb |binary src/PGLogit.cpp | 13 +++++++------ src/cNNGP.cpp | 11 ++++++----- src/cSLGP.cpp | 11 ++++++----- src/nn.cpp | 10 +++++----- src/rNNGP.cpp | 11 ++++++----- src/rNNGPPredict.cpp | 11 ++++++----- src/rNNGPReplicated.cpp | 11 ++++++----- src/sNNGP.cpp | 11 ++++++----- src/sNNGPLogit.cpp | 13 +++++++------ src/sNNGPPredict.cpp | 11 ++++++----- src/util.cpp | 11 ++++++----- 14 files changed, 84 insertions(+), 74 deletions(-)
Title: Univariate and Multivariate Spatial-Temporal Modeling
Description: Fits univariate and multivariate spatio-temporal
random effects models for point-referenced data using Markov chain Monte Carlo (MCMC). Details are given in Finley, Banerjee, and Gelfand (2015) <doi:10.18637/jss.v063.i13> and Finley, Banerjee, and Cook (2014) <doi:10.1111/2041-210X.12189>.
Author: Andrew Finley [aut, cre],
Sudipto Banerjee [aut]
Maintainer: Andrew Finley <finleya@msu.edu>
Diff between spBayes versions 0.4-3 dated 2020-02-06 and 0.4-4 dated 2021-09-20
DESCRIPTION | 8 ++++---- MD5 | 32 ++++++++++++++++---------------- R/spPredict.R | 8 +++++--- inst/CITATION | 8 ++++---- inst/ChangeLog | 5 +++++ man/spDynLM.Rd | 2 +- man/spGLM.Rd | 2 +- man/spLM.Rd | 2 +- man/spMvGLM.Rd | 2 +- man/spMvLM.Rd | 2 +- man/spPredict.Rd | 4 ++-- man/spRecover.Rd | 4 ++-- man/spSVC.Rd | 4 ++-- src/spSVC.cpp | 11 ++++++----- src/spSVCPredictJoint.cpp | 11 ++++++----- src/spSVCPredictMarg.cpp | 11 ++++++----- src/spSVCRecover.cpp | 11 ++++++----- 17 files changed, 69 insertions(+), 58 deletions(-)
More information about robCompositions at CRAN
Permanent link
Title: Repeatable Analysis in R
Description: Set of utilities to facilitate the reproduction of analysis in R.
It allow to make_structure(), clean_structure(), and run and log programs in a
predefined order to allow secondary files, analysis and reports be constructed in
an ordered form.
Author: John J. Aponte [aut, cre] (<https://orcid.org/0000-0002-3014-3673>)
Maintainer: John J. Aponte <john.j.aponte@gmail.com>
Diff between repana versions 1.23.1 dated 2021-05-18 and 1.23.2 dated 2021-09-20
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NEWS.md | 2 ++ R/render_report.R | 8 +++++++- build/vignette.rds |binary inst/WORDLIST | 1 + inst/doc/using_repana.html | 4 ++-- tests/testthat/test_render_report.R | 21 +++++++++++++++++++++ 8 files changed, 44 insertions(+), 14 deletions(-)
Title: Tools for Easier Analysis of Meteorological Fields
Description: Many useful functions and extensions for dealing
with meteorological data in the tidy data framework. Extends 'ggplot2'
for better plotting of scalar and vector fields and provides commonly
used analysis methods in the atmospheric sciences.
Author: Elio Campitelli [cre, aut] (<https://orcid.org/0000-0002-7742-9230>)
Maintainer: Elio Campitelli <elio.campitelli@cima.fcen.uba.ar>
Diff between metR versions 0.10.0 dated 2021-08-07 and 0.11.0 dated 2021-09-20
DESCRIPTION | 6 MD5 | 70 +++-- NAMESPACE | 9 NEWS.md | 11 R/geom_contour2.r | 161 ++++++++++++- R/geom_label_contour.R | 13 - R/geom_text_contour.R | 27 +- R/helpfunctions.R | 4 R/label-placement.R | 169 ++++++++++++-- R/label-scales.R |only R/textContourGrob.R | 19 - README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/Visualization-tools.html | 24 + inst/doc/Working-with-data.Rmd | 2 inst/doc/Working-with-data.html | 12 man/contour_placement.Rd | 74 +++++- man/discretised_scale.Rd | 33 +- man/geom_contour2.Rd | 53 ++++ man/geom_text_contour.Rd | 18 - man/label_scales.Rd |only man/scale_divergent.Rd | 18 - man/scale_longitude.Rd | 6 man/scale_mag.Rd | 3 tests/figs/stat-contour2/aesthetics-in-contour-labels.svg |only tests/figs/stat-contour2/contour2-base-geom.svg | 38 +-- tests/figs/stat-contour2/contour2-base-stat.svg | 38 +-- tests/figs/stat-contour2/contour2-fun.svg | 38 +-- tests/figs/stat-contour2/contour2-global-breaks.svg | 60 ++-- tests/figs/stat-contour2/contour2-labels.svg |only tests/figs/text-contour/placement-minmax-horizontal.svg | 4 tests/figs/text-contour/placement-minmax-vertical.svg | 8 tests/testthat/Rplots.pdf |binary tests/testthat/test-GetSMNData.R | 2 tests/testthat/test-vis-contour2.R | 22 + tests/testthat/test-vis-text-contour.R | 8 vignettes/Working-with-data.Rmd | 2 38 files changed, 701 insertions(+), 253 deletions(-)
Title: Generalized Linear Mixed Models using Template Model Builder
Description: Fit linear and generalized linear mixed models with various
extensions, including zero-inflation. The models are fitted using maximum
likelihood estimation via 'TMB' (Template Model Builder). Random effects are
assumed to be Gaussian on the scale of the linear predictor and are integrated
out using the Laplace approximation. Gradients are calculated using automatic
differentiation.
Author: Arni Magnusson [aut] (<https://orcid.org/0000-0003-2769-6741>),
Hans Skaug [aut],
Anders Nielsen [aut] (<https://orcid.org/0000-0001-9683-9262>),
Casper Berg [aut] (<https://orcid.org/0000-0002-3812-5269>),
Kasper Kristensen [aut],
Martin Maechler [aut] (<https://orcid.org/0000-0002-8685-9910>),
Koen van Bentham [aut],
Ben Bolker [aut] (<https://orcid.org/0000-0002-2127-0443>),
Nafis Sadat [ctb] (<https://orcid.org/0000-0001-5715-616X>),
Daniel Lüdecke [ctb] (<https://orcid.org/0000-0002-8895-3206>),
Russ Lenth [ctb],
Joseph O'Brien [ctb] (<https://orcid.org/0000-0001-9851-5077>),
Charles J. Geyer [ctb],
Maeve McGillycuddy [ctb],
Mollie Brooks [aut, cre] (<https://orcid.org/0000-0001-6963-8326>)
Maintainer: Mollie Brooks <mollieebrooks@gmail.com>
Diff between glmmTMB versions 1.1.2.2 dated 2021-09-01 and 1.1.2.3 dated 2021-09-20
glmmTMB-1.1.2.2/glmmTMB/man/expandAllGrpVar.Rd |only glmmTMB-1.1.2.2/glmmTMB/man/fbx.Rd |only glmmTMB-1.1.2.2/glmmTMB/man/formFuns.Rd |only glmmTMB-1.1.2.3/glmmTMB/DESCRIPTION | 23 glmmTMB-1.1.2.3/glmmTMB/MD5 | 94 - glmmTMB-1.1.2.3/glmmTMB/NAMESPACE | 17 glmmTMB-1.1.2.3/glmmTMB/R/emmeans.R | 2 glmmTMB-1.1.2.3/glmmTMB/R/glmmTMB.R | 42 glmmTMB-1.1.2.3/glmmTMB/R/methods.R | 5 glmmTMB-1.1.2.3/glmmTMB/R/reformulas.R |only glmmTMB-1.1.2.3/glmmTMB/R/utils.R | 700 ++------- glmmTMB-1.1.2.3/glmmTMB/R/zzz.R | 1 glmmTMB-1.1.2.3/glmmTMB/build/partial.rdb |binary glmmTMB-1.1.2.3/glmmTMB/build/vignette.rds |binary glmmTMB-1.1.2.3/glmmTMB/inst/Matrix-version |only glmmTMB-1.1.2.3/glmmTMB/inst/NEWS.Rd | 30 glmmTMB-1.1.2.3/glmmTMB/inst/TMB-version |only glmmTMB-1.1.2.3/glmmTMB/inst/doc/covstruct.html | 739 +++------- glmmTMB-1.1.2.3/glmmTMB/inst/doc/glmmTMB.pdf |binary glmmTMB-1.1.2.3/glmmTMB/inst/doc/mcmc.html | 450 +----- glmmTMB-1.1.2.3/glmmTMB/inst/doc/miscEx.html | 310 ---- glmmTMB-1.1.2.3/glmmTMB/inst/doc/model_evaluation.R | 19 glmmTMB-1.1.2.3/glmmTMB/inst/doc/model_evaluation.Rnw | 5 glmmTMB-1.1.2.3/glmmTMB/inst/doc/model_evaluation.pdf |binary glmmTMB-1.1.2.3/glmmTMB/inst/doc/parallel.html | 354 ---- glmmTMB-1.1.2.3/glmmTMB/inst/doc/sim.html | 312 ---- glmmTMB-1.1.2.3/glmmTMB/inst/doc/troubleshooting.R | 4 glmmTMB-1.1.2.3/glmmTMB/inst/doc/troubleshooting.html | 439 +---- glmmTMB-1.1.2.3/glmmTMB/inst/doc/troubleshooting.rmd | 4 glmmTMB-1.1.2.3/glmmTMB/inst/test_data/make_ex.R | 5 glmmTMB-1.1.2.3/glmmTMB/inst/test_data/models.rda |binary glmmTMB-1.1.2.3/glmmTMB/inst/vignette_data/model_evaluation.rda |binary glmmTMB-1.1.2.3/glmmTMB/man/RHSForm.Rd |only glmmTMB-1.1.2.3/glmmTMB/man/downstream_methods.Rd | 2 glmmTMB-1.1.2.3/glmmTMB/man/dtruncated_nbinom2.Rd |only glmmTMB-1.1.2.3/glmmTMB/man/expandGrpVar.Rd |only glmmTMB-1.1.2.3/glmmTMB/man/findReTrmClasses.Rd | 2 glmmTMB-1.1.2.3/glmmTMB/man/formfuns.Rd |only glmmTMB-1.1.2.3/glmmTMB/man/glmmTMB.Rd | 16 glmmTMB-1.1.2.3/glmmTMB/man/gt_load.Rd |only glmmTMB-1.1.2.3/glmmTMB/man/reinstalling.Rd |only glmmTMB-1.1.2.3/glmmTMB/man/splitForm.Rd | 11 glmmTMB-1.1.2.3/glmmTMB/src/Makevars | 6 glmmTMB-1.1.2.3/glmmTMB/src/utils.cpp | 5 glmmTMB-1.1.2.3/glmmTMB/tests/testthat/setup_makeex.R | 12 glmmTMB-1.1.2.3/glmmTMB/tests/testthat/test-basics.R | 42 glmmTMB-1.1.2.3/glmmTMB/tests/testthat/test-families.R | 12 glmmTMB-1.1.2.3/glmmTMB/tests/testthat/test-formulas.R | 4 glmmTMB-1.1.2.3/glmmTMB/tests/testthat/test-methods.R | 49 glmmTMB-1.1.2.3/glmmTMB/tests/testthat/test-offset.R | 14 glmmTMB-1.1.2.3/glmmTMB/tests/testthat/test-predict.R | 2 glmmTMB-1.1.2.3/glmmTMB/tests/testthat/test-sparseX.R | 14 glmmTMB-1.1.2.3/glmmTMB/vignettes/model_evaluation.Rnw | 5 glmmTMB-1.1.2.3/glmmTMB/vignettes/troubleshooting.rmd | 4 54 files changed, 1041 insertions(+), 2714 deletions(-)
Title: Diffusion Model of Conflict (DMC) in Reaction Time Tasks
Description: DMC model simulation detailed in Ulrich, R., Schroeter, H., Leuthold, H., & Birngruber, T. (2015).
Automatic and controlled stimulus processing in conflict tasks: Superimposed diffusion processes and delta functions.
Cognitive Psychology, 78, 148-174. Ulrich et al. (2015) <doi:10.1016/j.cogpsych.2015.02.005>.
Decision processes within choice reaction-time (CRT) tasks are often modelled using evidence accumulation models (EAMs),
a variation of which is the Diffusion Decision Model (DDM, for a review, see Ratcliff & McKoon, 2008).
Ulrich et al. (2015) introduced a Diffusion Model for Conflict tasks (DMC). The DMC model combines common
features from within standard diffusion models with the addition of superimposed controlled and automatic activation.
The DMC model is used to explain distributional reaction time (and error rate) patterns in common behavioural
conflict-like tasks (e.g., Flanker task, Simon task). This R-package implements the DMC model and provides functionality
to fit the model to observed data.
Author: Ian G. Mackenzie [cre, aut],
Carolin Dudschig [aut]
Maintainer: Ian G. Mackenzie <ian.mackenzie@uni-tuebingen.de>
Diff between DMCfun versions 1.3.0 dated 2021-01-10 and 2.0.0 dated 2021-09-20
DMCfun-1.3.0/DMCfun/data/flankerDataRaw.rda |only DMCfun-1.3.0/DMCfun/data/simonDataRaw.rda |only DMCfun-1.3.0/DMCfun/man/calculateCostValue.Rd |only DMCfun-1.3.0/DMCfun/man/flankerDataRaw.Rd |only DMCfun-1.3.0/DMCfun/man/simonDataRaw.Rd |only DMCfun-1.3.0/DMCfun/tests/testthat/test-addDataDF.R |only DMCfun-1.3.0/DMCfun/tests/testthat/test-calculateCAF.R |only DMCfun-1.3.0/DMCfun/tests/testthat/test-calculateCostValue.R |only DMCfun-1.3.0/DMCfun/tests/testthat/test-createDF.R |only DMCfun-1.3.0/DMCfun/tests/testthat/test-dmcFitSubject.R |only DMCfun-1.3.0/DMCfun/tests/testthat/test-dmcObservedData.R |only DMCfun-1.3.0/DMCfun/tests/testthat/test-errDist.R |only DMCfun-1.3.0/DMCfun/tests/testthat/test-plot.dmcfit.R |only DMCfun-1.3.0/DMCfun/tests/testthat/test-plot.dmcob.R |only DMCfun-1.3.0/DMCfun/tests/testthat/test-plot.dmcsim.R |only DMCfun-1.3.0/DMCfun/tests/testthat/test-rtDist.R |only DMCfun-2.0.0/DMCfun/DESCRIPTION | 14 DMCfun-2.0.0/DMCfun/LICENSE | 2 DMCfun-2.0.0/DMCfun/MD5 | 111 - DMCfun-2.0.0/DMCfun/NAMESPACE | 23 DMCfun-2.0.0/DMCfun/R/dmcData.R | 326 +- DMCfun-2.0.0/DMCfun/R/dmcFit.R | 1184 ++++++---- DMCfun-2.0.0/DMCfun/R/dmcSim.R | 165 - DMCfun-2.0.0/DMCfun/R/methods.R | 4 DMCfun-2.0.0/DMCfun/R/plot.R | 1219 +++++------ DMCfun-2.0.0/DMCfun/R/summary.R | 16 DMCfun-2.0.0/DMCfun/R/zzz.R | 17 DMCfun-2.0.0/DMCfun/README.md | 2 DMCfun-2.0.0/DMCfun/data/flankerData.rda |binary DMCfun-2.0.0/DMCfun/data/simonData.rda |binary DMCfun-2.0.0/DMCfun/inst |only DMCfun-2.0.0/DMCfun/man/addErrorBars.Rd | 2 DMCfun-2.0.0/DMCfun/man/calculateBinProbabilities.Rd |only DMCfun-2.0.0/DMCfun/man/calculateCAF.Rd | 8 DMCfun-2.0.0/DMCfun/man/calculateCostValueCS.Rd |only DMCfun-2.0.0/DMCfun/man/calculateCostValueGS.Rd |only DMCfun-2.0.0/DMCfun/man/calculateCostValueRMSE.Rd |only DMCfun-2.0.0/DMCfun/man/calculateCostValueSPE.Rd |only DMCfun-2.0.0/DMCfun/man/calculateDelta.Rd | 11 DMCfun-2.0.0/DMCfun/man/createDF.Rd | 2 DMCfun-2.0.0/DMCfun/man/dmcCombineObservedData.Rd | 10 DMCfun-2.0.0/DMCfun/man/dmcFit.Rd | 108 DMCfun-2.0.0/DMCfun/man/dmcFitDE.Rd | 68 DMCfun-2.0.0/DMCfun/man/dmcFitSubject.Rd | 69 DMCfun-2.0.0/DMCfun/man/dmcFitSubjectDE.Rd | 53 DMCfun-2.0.0/DMCfun/man/dmcObservedData.Rd | 32 DMCfun-2.0.0/DMCfun/man/dmcSim.Rd | 51 DMCfun-2.0.0/DMCfun/man/dmcSimApp.Rd |only DMCfun-2.0.0/DMCfun/man/flankerData.Rd | 15 DMCfun-2.0.0/DMCfun/man/mean.dmcfit.Rd | 6 DMCfun-2.0.0/DMCfun/man/plot.dmcfit.Rd | 17 DMCfun-2.0.0/DMCfun/man/plot.dmclist.Rd | 18 DMCfun-2.0.0/DMCfun/man/plot.dmcob.Rd | 22 DMCfun-2.0.0/DMCfun/man/plot.dmcobs.Rd | 32 DMCfun-2.0.0/DMCfun/man/plot.dmcsim.Rd | 29 DMCfun-2.0.0/DMCfun/man/rtDist.Rd | 4 DMCfun-2.0.0/DMCfun/man/simonData.Rd | 15 DMCfun-2.0.0/DMCfun/man/summary.dmcfit.Rd | 2 DMCfun-2.0.0/DMCfun/src/RcppExports.cpp | 5 DMCfun-2.0.0/DMCfun/src/dmcCppR.cpp | 47 DMCfun-2.0.0/DMCfun/src/inDMC.cpp | 12 DMCfun-2.0.0/DMCfun/src/inDMC.h | 10 DMCfun-2.0.0/DMCfun/src/outDMC.cpp | 96 DMCfun-2.0.0/DMCfun/src/runDMC.cpp | 311 +- DMCfun-2.0.0/DMCfun/src/runDMC.h | 113 - DMCfun-2.0.0/DMCfun/tests/testthat/test-dmcData.R |only DMCfun-2.0.0/DMCfun/tests/testthat/test-dmcFit.R | 62 DMCfun-2.0.0/DMCfun/tests/testthat/test-dmcSim.R | 43 DMCfun-2.0.0/DMCfun/tests/testthat/test-plot.R |only 69 files changed, 2516 insertions(+), 1840 deletions(-)
Title: Analyze Cricket Performances Based on Data from Cricsheet
Description: Analyzing performances of cricketers and cricket teams
based on 'yaml' match data from Cricsheet <https://cricsheet.org/>.
Author: Tinniam V Ganesh
Maintainer: Tinniam V Ganesh <tvganesh.85@gmail.com>
Diff between yorkr versions 0.0.25 dated 2021-07-10 and 0.0.26 dated 2021-09-20
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/convertAllYaml2RDataframesT20.R | 6 ++++++ R/convertYaml2RDataframeT20.R | 5 +++++ 4 files changed, 18 insertions(+), 7 deletions(-)
Title: Robust Change-Point Tests
Description: Provides robust methods to detect change-points in uni- or multivariate time series. They can cope with corrupted data and heavy tails. Focus is on the detection of abrupt changes in location, but changes scale or dependence structure can be detected as well. This package provides tests for change detection in uni- and multivariate time series based on Huberized versions of CUSUM tests proposed in Duerre and Fried (2019) <arXiv:1905.06201>. Furthermore, robcp provides tests for change detection in univariate time series based on 2-sample U-statistics or 2-sample U-quantiles as proposed by Dehling et al. (2015) <DOI:10.1007/978-1-4939-3076-0_12> and Dehling, Fried and Wendler (2020) <DOI:10.1093/biomet/asaa004>.
Author: Sheila Goerz [aut, cre],
Alexander Duerre [aut]
Maintainer: Sheila Goerz <sheila.goerz@tu-dortmund.de>
Diff between robcp versions 0.3.1 dated 2021-09-11 and 0.3.2 dated 2021-09-20
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- R/Hodges_Lehmann.R | 8 ++++++-- R/hl_test.R | 2 +- R/lrv.R | 10 +++++++++- man/huber_cusum.Rd | 4 +++- src/kthPair.cpp | 2 +- src/lrv.c | 2 +- tests/testthat/test-Hodges_Lehmann.R | 4 ++-- tests/testthat/test-Wilcox.R | 7 +++++-- tests/testthat/test-lrv.R | 2 +- 11 files changed, 42 insertions(+), 25 deletions(-)
Title: Efficient Simulation-Based Power and Sample Size Calculations
for a Broad Class of Late-Stage Clinical Trials
Description: The following modules are included in the package:
Adaptive designs with data-driven sample size or event count re-estimation,
Adaptive designs with data-driven treatment selection,
Adaptive designs with data-driven population selection,
Optimal selection of a futility stopping rule,
Event prediction in event-driven trials.
Adaptive trials with response-adaptive randomization (experimental module).
Traditional trials with multiple objectives (experimental module).
Author: Alex Dmitrienko [aut, cre]
Maintainer: Alex Dmitrienko <admitrienko@mediana.us>
Diff between MedianaDesigner versions 0.2.3 dated 2021-08-16 and 0.3 dated 2021-09-20
CHANGELOG | 10 DESCRIPTION | 14 - MD5 | 54 +++-- NAMESPACE | 6 R/ADRand.r | 11 - R/MultAdj.r |only R/RcppExports.R | 12 + R/ShinyApps.r | 7 R/common.r | 26 +- inst/MultAdjApp |only man/ADRand.Rd | 1 man/ADRandExample.Rd | 4 man/GenerateReport.Rd | 2 man/MedianaDesigner-package.Rd | 22 +- man/MultAdj.Rd |only man/MultAdjApp.Rd |only man/MultAdjExample1.Rd |only man/MultAdjExample2.Rd |only man/MultAdjExample3.Rd |only src/RcppExports.cpp | 36 +++ src/md.cpp | 432 ++++++++++++++++++++++++++++++++++++++++- src/meddist.h | 60 +++-- src/medmult.h |only src/medstattest.h | 35 +-- src/medstruct.h | 142 ------------- src/medsupport.h | 9 src/varcuboid.h |only tests/testthat/test-ADRand.r | 49 ++++ tests/testthat/test-FutRule.r | 5 tests/testthat/test-MultAdj.r |only tests/testthat/test-common.R | 14 + 31 files changed, 722 insertions(+), 229 deletions(-)
More information about MedianaDesigner at CRAN
Permanent link
Title: Generative Neural Networks
Description: Tools to set up, train, store, load, investigate and analyze
generative neural networks. In particular, functionality for
generative moment matching networks is provided.
Author: Marius Hofert [aut, cre] (<https://orcid.org/0000-0001-8009-4665>),
Avinash Prasad [aut]
Maintainer: Marius Hofert <marius.hofert@uwaterloo.ca>
Diff between gnn versions 0.0-2 dated 2020-03-03 and 0.0-3 dated 2021-09-20
gnn-0.0-2/gnn/R/GMMN.R |only gnn-0.0-2/gnn/R/VAE.R |only gnn-0.0-2/gnn/R/rda.R |only gnn-0.0-2/gnn/R/saving.R |only gnn-0.0-2/gnn/R/serialization.R |only gnn-0.0-2/gnn/R/train.R |only gnn-0.0-2/gnn/data |only gnn-0.0-2/gnn/demo |only gnn-0.0-2/gnn/man/GMMN_model.Rd |only gnn-0.0-2/gnn/man/GMMN_trained.Rd |only gnn-0.0-2/gnn/man/VAE_model.Rd |only gnn-0.0-2/gnn/man/human_time.Rd |only gnn-0.0-2/gnn/man/rda.Rd |only gnn-0.0-2/gnn/man/to_savable_callable.Rd |only gnn-0.0-2/gnn/man/trafos_componentwise.Rd |only gnn-0.0-2/gnn/man/train.Rd |only gnn-0.0-2/gnn/tests |only gnn-0.0-3/gnn/DESCRIPTION | 15 - gnn-0.0-3/gnn/MD5 | 91 ++++------ gnn-0.0-3/gnn/NAMESPACE | 87 ++++++++-- gnn-0.0-3/gnn/R/FNN.R |only gnn-0.0-3/gnn/R/GNN_class.R |only gnn-0.0-3/gnn/R/auxiliaries.R | 67 +++++--- gnn-0.0-3/gnn/R/ffGNN.R |only gnn-0.0-3/gnn/R/fitGNN.R |only gnn-0.0-3/gnn/R/gof.R |only gnn-0.0-3/gnn/R/loss.R | 250 ++++++++++++++++++++++++------ gnn-0.0-3/gnn/R/model.R |only gnn-0.0-3/gnn/R/plot.R |only gnn-0.0-3/gnn/R/rGNN.R |only gnn-0.0-3/gnn/R/rPrior.R |only gnn-0.0-3/gnn/R/raw_keras.R |only gnn-0.0-3/gnn/R/save_load.R |only gnn-0.0-3/gnn/R/time.R |only gnn-0.0-3/gnn/R/trafos.R | 5 gnn-0.0-3/gnn/R/zzz.R |only gnn-0.0-3/gnn/TODO | 17 +- gnn-0.0-3/gnn/build |only gnn-0.0-3/gnn/man/FNN.Rd |only gnn-0.0-3/gnn/man/GNN_basics.Rd |only gnn-0.0-3/gnn/man/Tensorflow_available.Rd |only gnn-0.0-3/gnn/man/catch.Rd |only gnn-0.0-3/gnn/man/ffGNN.Rd |only gnn-0.0-3/gnn/man/fitGNN.Rd |only gnn-0.0-3/gnn/man/loss.Rd | 43 +++-- gnn-0.0-3/gnn/man/plot.Rd |only gnn-0.0-3/gnn/man/rGNN.Rd |only gnn-0.0-3/gnn/man/rPrior.Rd |only gnn-0.0-3/gnn/man/raw_keras.Rd |only gnn-0.0-3/gnn/man/rm_ext.Rd | 2 gnn-0.0-3/gnn/man/save_load.Rd |only gnn-0.0-3/gnn/man/time.Rd |only gnn-0.0-3/gnn/man/trafos_dimreduction.Rd | 2 gnn-0.0-3/gnn/man/trafos_margins.Rd |only 54 files changed, 412 insertions(+), 167 deletions(-)
Title: Species Distribution Modelling Predictor Datasets
Description: Terrestrial and marine predictors for species distribution modelling
from multiple sources, including WorldClim <https://www.worldclim.org/>,,
ENVIREM <https://envirem.github.io/>, Bio-ORACLE <https://bio-oracle.org/>
and MARSPEC <http://www.marspec.org/>.
Author: Samuel Bosch [aut],
Lennert Tyberghein [ctb],
Olivier De Clerck [ctb],
Salvador Fernandez [aut, cre],
Lennert Schepers [ctb]
Maintainer: Salvador Fernandez <salvador.fernandez@vliz.be>
Diff between sdmpredictors versions 0.2.9 dated 2020-10-13 and 0.2.10 dated 2021-09-20
DESCRIPTION | 15 - MD5 | 44 ++-- NAMESPACE | 1 NEWS.md | 6 R/get_sysdata.R | 2 R/list.R | 2 R/load.R | 85 ++++++-- R/sdmpredictors.R | 21 + R/sysdata.rda |binary R/translator.R |only README.md | 7 build/partial.rdb |only inst/doc/quickstart.R | 26 +- inst/doc/quickstart.Rmd | 2 inst/doc/quickstart.html | 403 ++++++++++---------------------------- man/equalarea_project.Rd |only man/sdm_to_bo.Rd |only man/sdmpredictors.Rd | 21 + tests/testthat.R | 4 tests/testthat/test_citations.R | 26 +- tests/testthat/test_get_sysdata.R | 4 tests/testthat/test_load.R | 155 ++++++++++---- tests/testthat/test_stats.R | 22 +- tests/testthat/test_zzzfinal.R | 4 vignettes/quickstart.Rmd | 2 25 files changed, 405 insertions(+), 447 deletions(-)
Title: 32-Bit Floats
Description: R comes with a suite of utilities for linear algebra with "numeric"
(double precision) vectors/matrices. However, sometimes single precision (or
less!) is more than enough for a particular task. This package extends R's
linear algebra facilities to include 32-bit float (single precision) data.
Float vectors/matrices have half the precision of their "numeric"-type
counterparts but are generally faster to numerically operate on, for a
performance vs accuracy trade-off. The internal representation is an S4
class, which allows us to keep the syntax identical to that of base R's.
Interaction between floats and base types for binary operators is generally
possible; in these cases, type promotion always defaults to the higher
precision. The package ships with copies of the single precision 'BLAS' and
'LAPACK', which are automatically built in the event they are not available
on the system.
Author: Drew Schmidt [aut, cre, cph],
Wei-Chen Chen [aut],
Dmitriy Selivanov [ctb] (improvements in external package linking),
ORNL [cph]
Maintainer: Drew Schmidt <wrathematics@gmail.com>
Diff between float versions 0.2-4 dated 2020-04-22 and 0.2-6 dated 2021-09-20
ChangeLog | 6 DESCRIPTION | 10 MD5 | 34 NAMESPACE | 1 R/converters.r | 15 README.md | 4 configure | 1811 ++++----------------------------------------------- configure.ac | 13 man/Machine_float.Rd | 6 man/NA_float_.Rd | 4 man/NaNf.Rd | 4 man/converters.Rd | 3 src/NA.c | 3 src/Rfloat.h | 5 src/config.h |only src/config.h.in |only src/eigen.c | 3 src/norm.h | 5 src/scale.c | 3 19 files changed, 222 insertions(+), 1708 deletions(-)
Title: Meta-Analysis of Diagnosis and Prognosis Research Studies
Description: Facilitate frequentist and Bayesian meta-analysis of diagnosis and prognosis research studies. It includes functions to summarize multiple estimates of prediction model discrimination and calibration performance (Debray et al., 2019) <doi:10.1177/0962280218785504>. It also includes functions to evaluate funnel plot asymmetry (Debray et al., 2018) <doi:10.1002/jrsm.1266>. Finally, the package provides functions for developing multivariable prediction models from datasets with clustering (de Jong et al., 2021) <doi:10.1002/sim.8981>.
Author: Thomas Debray [aut, cre] (<https://orcid.org/0000-0002-1790-2719>),
Valentijn de Jong [aut] (<https://orcid.org/0000-0001-9921-3468>)
Maintainer: Thomas Debray <thomas.debray@gmail.com>
Diff between metamisc versions 0.2.4 dated 2021-09-02 and 0.2.5 dated 2021-09-20
metamisc-0.2.4/metamisc/tests/testthat/test_valmeta_2.R |only metamisc-0.2.4/metamisc/tests/testthat/test_valmeta_3.R |only metamisc-0.2.5/metamisc/DESCRIPTION | 16 metamisc-0.2.5/metamisc/MD5 | 59 +- metamisc-0.2.5/metamisc/NAMESPACE | 19 metamisc-0.2.5/metamisc/R/basics.r | 20 metamisc-0.2.5/metamisc/R/bugs_utils.r | 177 ++++++++ metamisc-0.2.5/metamisc/R/bugsmodels.r | 46 +- metamisc-0.2.5/metamisc/R/fat.r | 1 metamisc-0.2.5/metamisc/R/oecalc.R | 1 metamisc-0.2.5/metamisc/R/plot_utils.r | 207 +++++++++- metamisc-0.2.5/metamisc/R/uvmeta.r | 138 +++++- metamisc-0.2.5/metamisc/R/valmeta.r | 202 ++++++--- metamisc-0.2.5/metamisc/R/valmeta_utils.r | 115 ----- metamisc-0.2.5/metamisc/man/acplot.Rd |only metamisc-0.2.5/metamisc/man/acplot.mcmc.list.Rd |only metamisc-0.2.5/metamisc/man/acplot.uvmeta.Rd |only metamisc-0.2.5/metamisc/man/acplot.valmeta.Rd | 4 metamisc-0.2.5/metamisc/man/dplot.Rd | 3 metamisc-0.2.5/metamisc/man/dplot.mcmc.list.Rd | 3 metamisc-0.2.5/metamisc/man/dplot.valmeta.Rd | 2 metamisc-0.2.5/metamisc/man/gelmanplot.Rd |only metamisc-0.2.5/metamisc/man/gelmanplot.mcmc.list.Rd |only metamisc-0.2.5/metamisc/man/gelmanplot.uvmeta.Rd |only metamisc-0.2.5/metamisc/man/gelmanplot.valmeta.Rd |only metamisc-0.2.5/metamisc/man/metamisc-package.Rd | 4 metamisc-0.2.5/metamisc/man/plot.fat.Rd | 1 metamisc-0.2.5/metamisc/man/rmplot.Rd |only metamisc-0.2.5/metamisc/man/rmplot.mcmc.list.Rd |only metamisc-0.2.5/metamisc/man/rmplot.uvmeta.Rd |only metamisc-0.2.5/metamisc/man/rmplot.valmeta.Rd | 4 metamisc-0.2.5/metamisc/man/valmeta.Rd | 16 metamisc-0.2.5/metamisc/tests/testthat/Rplots.pdf |only metamisc-0.2.5/metamisc/tests/testthat/test_valmeta_2_cstat_freq.R |only metamisc-0.2.5/metamisc/tests/testthat/test_valmeta_3_cstat_bayes.R |only metamisc-0.2.5/metamisc/tests/testthat/test_valmeta_4_oe_freq.R | 78 +++ metamisc-0.2.5/metamisc/tests/testthat/test_valmeta_5_oe_bayes.R | 37 + metamisc-0.2.5/metamisc/tests/testthat/test_valmeta_6_plots.R | 73 ++- 38 files changed, 881 insertions(+), 345 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-09-02 0.1.3
2020-05-26 0.1.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-01-14 1.2.5
Title: Functions for Working with Two- And Four-Parameter Beta
Probability Distributions
Description: Package providing a number of functions for working with Two- and
Four-parameter Beta and closely related distributions (i.e., the Gamma and
Binomial distributions), including parameterization in terms of moments,
and fitting of Beta distributions to vectors of values. Also includes
functions for estimating classification accuracy, diagnostic performance,
and consistency, making use of what is generally known as the 'Livingston
and Lewis approach' in the psychometric literature as the foundational
method, which makes extensive use of the Beta distribution. A shiny app is
available, providing a GUI for the Livingston and Lewis approach for binary
classifications. For link, see documentation for the LL.CA() function.
Livingston and Lewis (1995) <doi:10.1111/j.1745-3984.1995.tb00462.x>.
Lord (1965) <doi:10.1007/BF02289490>.
Hanson (1991) <https://files.eric.ed.gov/fulltext/ED344945.pdf>.
Tharwat (2020) <doi:10.1016/j.aci.2018.08.003>.
Author: Haakon Eidem Haakstad
Maintainer: Haakon Eidem Haakstad <h.t.haakstad@cemo.uio.no>
Diff between betafunctions versions 1.6.0 dated 2021-08-19 and 1.6.1 dated 2021-09-20
DESCRIPTION | 11 ++-- MD5 | 20 ++++----- NAMESPACE | 2 NEWS.md | 14 +++++- R/betafunctions.R | 50 ++++++++++++++++++++-- R/classification.R | 117 ++++++++++++++++++++++++++++++++--------------------- README.md | 14 +++--- man/LL.CA.MC.Rd | 7 ++- man/LL.CA.Rd | 7 ++- man/betamedian.Rd |only man/betamode.Rd |only man/betamoments.Rd | 8 +-- 12 files changed, 171 insertions(+), 79 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-08-10 0.2.0
Title: Data Fusion using Optimal Transportation Theory
Description: In the context of data fusion, the package provides a set of functions dedicated to the solving of 'recoding problems' using optimal transportation theory (Gares, Guernec, Savy (2019) <doi:10.1515/ijb-2018-0106> and Gares, Omer (2020) <doi:10.1080/01621459.2020.1775615>). From two databases with no overlapping part except a subset of shared variables, the functions of the package assist users until obtaining a unique synthetic database, where the missing information is fully completed.
Author: Gregory Guernec [aut, cre],
Valerie Gares [aut],
Pierre Navaro [ctb],
Jeremy Omer [ctb],
Philippe Saint-Pierre [ctb],
Nicolas Savy [ctb]
Maintainer: Gregory Guernec <otrecod.pkg@gmail.com>
Diff between OTrecod versions 0.1.0 dated 2021-01-29 and 0.1.1 dated 2021-09-20
OTrecod-0.1.0/OTrecod/R/OT_joint.r |only OTrecod-0.1.1/OTrecod/DESCRIPTION | 8 OTrecod-0.1.1/OTrecod/MD5 | 88 OTrecod-0.1.1/OTrecod/NAMESPACE | 96 OTrecod-0.1.1/OTrecod/R/OT_outcome.r | 1424 ++++---- OTrecod-0.1.1/OTrecod/R/api29.r | 60 OTrecod-0.1.1/OTrecod/R/api35.r | 60 OTrecod-0.1.1/OTrecod/R/imput_cov.r | 2 OTrecod-0.1.1/OTrecod/R/indiv_grp_optimal.r | 608 +-- OTrecod-0.1.1/OTrecod/R/merge_dbs.r | 30 OTrecod-0.1.1/OTrecod/R/ot_joint.r |only OTrecod-0.1.1/OTrecod/R/select_pred.r | 30 OTrecod-0.1.1/OTrecod/R/transfo_target.r | 8 OTrecod-0.1.1/OTrecod/R/verif_OT.r | 1105 +++--- OTrecod-0.1.1/OTrecod/README.md | 634 +-- OTrecod-0.1.1/OTrecod/build/partial.rdb |binary OTrecod-0.1.1/OTrecod/build/vignette.rds |binary OTrecod-0.1.1/OTrecod/inst/doc/an-application-of-the-OTrecod-package.R | 312 - OTrecod-0.1.1/OTrecod/inst/doc/an-application-of-the-OTrecod-package.Rmd | 822 ++-- OTrecod-0.1.1/OTrecod/inst/doc/an-application-of-the-OTrecod-package.html | 1729 ++++------ OTrecod-0.1.1/OTrecod/man/OT_joint.Rd | 502 +- OTrecod-0.1.1/OTrecod/man/OT_outcome.Rd | 604 +-- OTrecod-0.1.1/OTrecod/man/compare_lists.Rd | 88 OTrecod-0.1.1/OTrecod/man/error_group.Rd | 200 - OTrecod-0.1.1/OTrecod/man/ham.Rd | 156 OTrecod-0.1.1/OTrecod/man/imput_cov.Rd | 166 OTrecod-0.1.1/OTrecod/man/indiv_grp_optimal.Rd | 322 - OTrecod-0.1.1/OTrecod/man/merge_dbs.Rd | 370 +- OTrecod-0.1.1/OTrecod/man/select_pred.Rd | 8 OTrecod-0.1.1/OTrecod/man/verif_OT.Rd | 324 - OTrecod-0.1.1/OTrecod/tests/testthat.R | 8 OTrecod-0.1.1/OTrecod/tests/testthat/test-OT-joint.R | 100 OTrecod-0.1.1/OTrecod/tests/testthat/test-OT-outcome.R | 132 OTrecod-0.1.1/OTrecod/tests/testthat/test-compare-lists.R | 70 OTrecod-0.1.1/OTrecod/tests/testthat/test-error-group.R | 32 OTrecod-0.1.1/OTrecod/tests/testthat/test-ham.R | 52 OTrecod-0.1.1/OTrecod/tests/testthat/test-imput-cov.R | 154 OTrecod-0.1.1/OTrecod/tests/testthat/test-merge_dbs.R | 202 - OTrecod-0.1.1/OTrecod/tests/testthat/test-power-set.R | 18 OTrecod-0.1.1/OTrecod/tests/testthat/test-proxim-dist.R | 224 - OTrecod-0.1.1/OTrecod/tests/testthat/test-select-pred.R | 194 - OTrecod-0.1.1/OTrecod/tests/testthat/test-transfo-dist.R | 134 OTrecod-0.1.1/OTrecod/tests/testthat/test-transfo-quali.R | 62 OTrecod-0.1.1/OTrecod/tests/testthat/test-transfo-target.R | 130 OTrecod-0.1.1/OTrecod/tests/testthat/test-verif-OT.R | 139 OTrecod-0.1.1/OTrecod/vignettes/an-application-of-the-OTrecod-package.Rmd | 822 ++-- 46 files changed, 5966 insertions(+), 6263 deletions(-)
Title: Automated Data Preparation
Description: Do most of the painful data preparation for a data science project with a minimum amount of code; Take advantages of 'data.table' efficiency and use some algorithmic trick in order to perform data preparation in a time and RAM efficient way.
Author: Emmanuel-Lin Toulemonde [aut, cre]
Maintainer: Emmanuel-Lin Toulemonde <el.toulemonde@protonmail.com>
Diff between dataPreparation versions 1.0.1 dated 2020-12-15 and 1.0.2 dated 2021-09-20
DESCRIPTION | 8 MD5 | 170 +-- NAMESPACE | 114 +- NEWS | 456 ++++---- NEWS.md | 456 ++++---- R/aggregate.R | 374 +++---- R/data_set.R | 90 - R/dates_manipulations.R | 968 +++++++++--------- R/discretization.R | 474 ++++----- R/factor_manipulation.R | 158 +-- R/fast_functions.r | 810 +++++++-------- R/generate_from_character.R | 152 +- R/generate_from_date.R | 470 ++++----- R/generate_from_factor.R | 760 +++++++------- R/generic_functions.R | 864 ++++++++-------- R/numeric_manipulations.R | 310 ++--- R/on_load.R | 36 R/prepare_set.R | 356 +++--- R/row_filtering.R | 400 +++---- R/same_shape.R | 394 +++---- R/set_col_as.R | 790 +++++++-------- R/shape_set.R | 264 ++--- R/which_functions.R | 688 ++++++------- man/adult.Rd | 50 man/aggregate_by_key.Rd | 118 +- man/as.POSIXct_fast.Rd | 56 - man/build_bins.Rd | 90 - man/build_date_factor.Rd | 54 - man/build_encoding.Rd | 94 - man/build_scales.Rd | 58 - man/build_target_encoding.Rd | 86 - man/data_preparation_news.Rd | 22 man/date_format_unifier.Rd | 70 - man/description.Rd | 56 - man/fast_discretization.Rd | 94 - man/fast_filter_variables.Rd | 98 - man/fast_handle_na.Rd | 122 +- man/fast_is_equal.Rd | 70 - man/fast_round.Rd | 84 - man/fast_scale.Rd | 106 +- man/find_and_transform_dates.Rd | 166 +-- man/find_and_transform_numerics.Rd | 100 - man/generate_date_diffs.Rd | 116 +- man/generate_factor_from_date.Rd | 104 +- man/generate_from_character.Rd | 100 - man/generate_from_factor.Rd | 98 - man/identify_dates.Rd | 138 +- man/messy_adult.Rd | 52 - man/one_hot_encoder.Rd | 114 +- man/prepare_set.Rd | 162 +-- man/remove_percentile_outlier.Rd | 98 - man/remove_rare_categorical.Rd | 96 - man/remove_sd_outlier.Rd | 94 - man/same_shape.Rd | 108 +- man/set_as_numeric_matrix.Rd | 60 - man/set_col_as_character.Rd | 58 - man/set_col_as_date.Rd | 106 +- man/set_col_as_factor.Rd | 78 - man/set_col_as_numeric.Rd | 84 - man/shape_set.Rd | 72 - man/target_encode.Rd | 78 - man/un_factor.Rd | 92 - man/which_are_bijection.Rd | 88 - man/which_are_constant.Rd | 70 - man/which_are_in_double.Rd | 104 +- man/which_are_included.Rd | 116 +- tests/testthat/test_aggregate.R | 298 ++--- tests/testthat/test_dates_manipulation.R | 576 +++++------ tests/testthat/test_description.R | 56 - tests/testthat/test_discretization.R | 478 ++++----- tests/testthat/test_factor_manipulation.R | 98 - tests/testthat/test_fast_functions.R | 652 ++++++------ tests/testthat/test_fast_posixct.R | 30 tests/testthat/test_generate_from_character.R | 60 - tests/testthat/test_generate_from_date.R | 412 +++---- tests/testthat/test_generate_from_factor.R | 340 +++--- tests/testthat/test_generic_functions.R | 1348 +++++++++++++------------- tests/testthat/test_numerics_manipulations.R | 238 ++-- tests/testthat/test_on_load.R | 22 tests/testthat/test_prepare_set.R | 36 tests/testthat/test_row_filtering.R | 148 +- tests/testthat/test_same_shape.R | 394 +++---- tests/testthat/test_scale.R | 298 ++--- tests/testthat/test_set_col_as.R | 508 ++++----- tests/testthat/test_shape_set.R | 218 ++-- tests/testthat/test_which_functions.R | 396 +++---- 86 files changed, 10030 insertions(+), 10018 deletions(-)
More information about dataPreparation at CRAN
Permanent link
Title: Download and Visualize Essential Climate Change Data
Description: Provides easy access to essential climate change datasets to non-climate experts. Users can download the latest raw data from authoritative sources and view it via pre-defined 'ggplot2' charts. Datasets include atmospheric CO2, emissions, instrumental and proxy temperature records, sea levels, Arctic/Antarctic sea-ice, Hurricanes, and Paleoclimate data. Sources include: NOAA Mauna Loa Laboratory <https://gml.noaa.gov/ccgg/trends/data.html>, Global Carbon Project <https://www.globalcarbonproject.org/carbonbudget/20/data.htm>, NASA GISTEMP <https://data.giss.nasa.gov/gistemp/>, National Snow and Sea Ice Data Center <https://nsidc.org/data/seaice_index/archives>, CSIRO <https://research.csiro.au/slrwavescoast/sea-level/measurements-and-data/sea-level-data/>, NOAA Laboratory for Satellite Altimetry <https://www.star.nesdis.noaa.gov/socd/lsa/SeaLevelRise/> and HURDAT Atlantic Hurricane Database <https://www.aoml.noaa.gov/hrd/hurdat/Data_Storm.html>, Vostok Paleo carbon dioxide and temperature data: <https://cdiac.ess-dive.lbl.gov/trends/co2/vostok.html>.
Author: Hernando Cortina [aut, cre] (<https://orcid.org/0000-0001-6790-4870>)
Maintainer: Hernando Cortina <hch@alum.mit.edu>
Diff between hockeystick versions 0.5.1 dated 2021-05-18 and 0.6.1 dated 2021-09-20
hockeystick-0.5.1/hockeystick/R/isconnecting.R |only hockeystick-0.6.1/hockeystick/DESCRIPTION | 10 hockeystick-0.6.1/hockeystick/MD5 | 79 +- hockeystick-0.6.1/hockeystick/NAMESPACE | 6 hockeystick-0.6.1/hockeystick/NEWS.md | 12 hockeystick-0.6.1/hockeystick/R/2kyears_temp.R | 250 +++---- hockeystick-0.6.1/hockeystick/R/carbon.R | 21 hockeystick-0.6.1/hockeystick/R/data_cache.R | 13 hockeystick-0.6.1/hockeystick/R/emissions.R |only hockeystick-0.6.1/hockeystick/R/extra_viz.R | 250 +++---- hockeystick-0.6.1/hockeystick/R/globalvars.R | 2 hockeystick-0.6.1/hockeystick/R/hurricanes.R | 324 +++++----- hockeystick-0.6.1/hockeystick/R/instrumental_temp.R | 236 +++---- hockeystick-0.6.1/hockeystick/R/paleo.R | 260 ++++---- hockeystick-0.6.1/hockeystick/R/zzz.R | 5 hockeystick-0.6.1/hockeystick/README.md | 61 + hockeystick-0.6.1/hockeystick/build/partial.rdb |binary hockeystick-0.6.1/hockeystick/inst/WORDLIST | 12 hockeystick-0.6.1/hockeystick/man/figures/README-carbon-1.png |binary hockeystick-0.6.1/hockeystick/man/figures/README-emissions-1.png |only hockeystick-0.6.1/hockeystick/man/figures/README-grid-1.png |binary hockeystick-0.6.1/hockeystick/man/figures/README-icecurves-1.png |binary hockeystick-0.6.1/hockeystick/man/figures/README-si-1.png |binary hockeystick-0.6.1/hockeystick/man/figures/README-sl-1.png |binary hockeystick-0.6.1/hockeystick/man/figures/README-stripes-1.png |binary hockeystick-0.6.1/hockeystick/man/figures/README-stripes2-1.png |binary hockeystick-0.6.1/hockeystick/man/figures/README-temp-1.png |binary hockeystick-0.6.1/hockeystick/man/get_carbon.Rd | 4 hockeystick-0.6.1/hockeystick/man/get_emissions.Rd |only hockeystick-0.6.1/hockeystick/man/get_hurricanes.Rd | 104 +-- hockeystick-0.6.1/hockeystick/man/get_icecurves.Rd | 124 +-- hockeystick-0.6.1/hockeystick/man/get_paleo.Rd | 102 +-- hockeystick-0.6.1/hockeystick/man/get_seaice.Rd | 130 ++-- hockeystick-0.6.1/hockeystick/man/get_temp.Rd | 110 +-- hockeystick-0.6.1/hockeystick/man/get_temp2k.Rd | 104 +-- hockeystick-0.6.1/hockeystick/man/hockeystick-package.Rd | 2 hockeystick-0.6.1/hockeystick/man/hockeystick_cache.Rd | 170 ++--- hockeystick-0.6.1/hockeystick/man/plot_carbon.Rd | 84 +- hockeystick-0.6.1/hockeystick/man/plot_emissions.Rd |only hockeystick-0.6.1/hockeystick/man/plot_hurricane_nrg.Rd | 86 +- hockeystick-0.6.1/hockeystick/man/plot_hurricanes.Rd | 82 +- hockeystick-0.6.1/hockeystick/man/plot_temp.Rd | 82 +- hockeystick-0.6.1/hockeystick/man/plot_temp2k.Rd | 100 +-- 43 files changed, 1446 insertions(+), 1379 deletions(-)
Title: Visualization and Tools for Ichimoku Kinko Hyo Strategies
Description: An implementation of 'Ichimoku Kinko Hyo', also commonly known as
'cloud charts'. Static and interactive visualizations with tools for
creating, backtesting and development of quantitative 'ichimoku' strategies.
As described in Sasaki (1996, ISBN:4925152009), the technique is a refinement
on candlestick charting originating from Japan, now in widespread use in
technical analysis worldwide. Translating as 'one-glance equilibrium chart',
it allows the price action and market structure of financial securities to
be determined 'at-a-glance'. Incorporates an interface with the OANDA
fxTrade API <https://developer.oanda.com/> for retrieving historical and
live streaming price data for major currencies, metals, commodities,
government bonds and stock indices.
Author: Charlie Gao [aut, cre] (<https://orcid.org/0000-0002-0750-061X>)
Maintainer: Charlie Gao <charlie.gao@shikokuchuo.net>
Diff between ichimoku versions 1.1.0 dated 2021-08-23 and 1.2.0 dated 2021-09-20
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Title: Toolbox for Error-Driven Learning Simulations with Two-Layer
Networks
Description: Error-driven learning (based on the Widrow & Hoff (1960)<https://isl.stanford.edu/~widrow/papers/c1960adaptiveswitching.pdf> learning rule, and essentially the same as Rescorla-Wagner's learning equations (Rescorla & Wagner, 1972, ISBN: 0390718017), which are also at the core of Naive Discrimination Learning, (Baayen et al, 2011, <doi:10.1037/a0023851>) can be used to explain bottom-up human learning (Hoppe et al, <doi:10.31234/osf.io/py5kd>), but is also at the core of artificial neural networks applications in the form of the Delta rule. This package provides a set of functions for building small-scale simulations to investigate the dynamics of error-driven learning and it's interaction with the structure of the input. For modeling error-driven learning using the Rescorla-Wagner equations the package 'ndl' (Baayen et al, 2011, <doi:10.1037/a0023851>) is available on CRAN at <https://cran.r-project.org/package=ndl>. However, the package currently only allows tracing of a cue-outcome combination, rather than returning the learned networks. To fill this gap, we implemented a new package with a few functions that facilitate inspection of the networks for small error driven learning simulations. Note that our functions are not optimized for training large data sets (no parallel processing), as they are intended for small scale simulations and course examples. (Consider the python implementation 'pyndl' <https://pyndl.readthedocs.io/en/latest/> for that purpose.)
Author: Jacolien van Rij [aut, cre] (<https://orcid.org/0000-0001-7445-5647>),
Dorothée Hoppe [aut]
Maintainer: Jacolien van Rij <j.c.van.rij@rug.nl>
Diff between edl versions 1.0 dated 2021-04-12 and 1.1 dated 2021-09-20
DESCRIPTION | 8 MD5 | 14 - R/RWlearningNoCueCompetition.R | 12 - R/edl.R | 4 R/updateWeightsNoCueCompetition.R | 12 - inst/CITATION |only inst/NEWS |only inst/doc/edl.html | 313 +++++++++++++++++++------------------- man/edl.Rd | 4 9 files changed, 189 insertions(+), 178 deletions(-)
Title: Count Transformation Models
Description: Count transformation models featuring
parameters interpretable as discrete hazard ratios, odds ratios,
reverse-time discrete hazard ratios, or transformed expectations.
An appropriate data transformation for a count outcome and
regression coefficients are simultaneously estimated by maximising
the exact discrete log-likelihood using the computational framework
provided in package 'mlt', technical details are given in
Siegfried & Hothorn (2020) <DOI:10.1111/2041-210X.13383>.
The package also contains an experimental implementation of
multivariate count transformation models with an application
to multi-species distribution models.
Author: Sandra Siegfried [aut] (<https://orcid.org/0000-0002-7312-1001>),
Luisa Barbanti [aut] (<https://orcid.org/0000-0001-5352-5802>),
Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>)
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between cotram versions 0.2-1 dated 2021-02-24 and 0.3-0 dated 2021-09-20
DESCRIPTION | 25 ++- MD5 | 34 +++-- NAMESPACE | 9 - R/mcotram.R |only build/partial.rdb |binary build/vignette.rds |binary data |only demo |only inst/NEWS.Rd | 8 + inst/doc/cotram.Rnw | 298 +++++++++++++++++++++++--------------------- inst/doc/cotram.pdf |binary man/confband.Rd | 4 man/cotram.Rd | 9 + man/mcotram.Rd |only man/spiders.Rd |only tests/Examples |only tests/confband-Ex.R | 1 tests/confband-Ex.Rout.save |only tests/mcotram-Ex.R |only tests/mcotram-Ex.Rout.save |only vignettes/cotram.Rnw | 298 +++++++++++++++++++++++--------------------- vignettes/count_mlt.bib | 6 22 files changed, 386 insertions(+), 306 deletions(-)
Title: A Bayesian No-Effect- Concentration (NEC) Algorithm
Description: Implementation of No-Effect-Concentration estimation that uses 'brms' (see Burkner (2017)<doi:10.18637/jss.v080.i01>; Burkner (2018)<doi:10.32614/RJ-2018-017>; Carpenter 'et al.' (2017)<doi:10.18637/jss.v076.i01> to fit concentration(dose)-response data using Bayesian methods for the purpose of estimating 'ECX' values, but more particularly 'NEC' (see Fox (2010)<doi:10.1016/j.ecoenv.2009.09.012>. This package expands and supersedes an original version implemented in R2jags, see Fisher, Ricardo and Fox (2020)<doi:10.5281/ZENODO.3966864>.
Author: Rebecca Fisher [aut, cre],
Diego Barneche [aut],
Gerard Ricardo [aut],
David Fox [aut]
Maintainer: Rebecca Fisher <r.fisher@aims.gov.au>
Diff between bayesnec versions 2.0 dated 2021-09-16 and 2.0.1 dated 2021-09-20
DESCRIPTION | 6 MD5 | 336 +++--- NAMESPACE | 346 +++---- NEWS.md | 104 +- R/add_criteria.R | 48 R/amend.R | 330 +++--- R/autoplot.R | 822 ++++++++--------- R/average_endpoints.R | 178 +-- R/bayesmanecfit-class.R | 102 +- R/bayesmanecfit-methods.R | 772 ++++++++-------- R/bayesnec-package.R | 39 R/bayesnecfit-class.R | 122 +- R/bayesnecfit-methods.R | 626 ++++++------- R/bayesnecformula.R | 1348 ++++++++++++++-------------- R/beta_binomial2.R | 190 +-- R/bnec.R | 504 +++++----- R/bnecfit-class.R | 60 - R/bnecfit-methods.R | 292 +++--- R/check_chains.R | 236 ++-- R/check_data.R | 177 +-- R/check_models.R | 213 ++-- R/check_priors.R | 216 ++-- R/compare_endpoints.R | 158 +-- R/compare_fitted.R | 140 +- R/compare_posterior.R | 122 +- R/data.R | 113 +- R/define_prior.R | 278 ++--- R/dispersion.R | 168 +-- R/ecx.R | 492 +++++----- R/expand_classes.R | 338 +++---- R/extract_simdat.R | 38 R/fit_bayesnec.R | 150 +-- R/helpers.R | 1066 +++++++++++----------- R/inits_functions.R | 244 ++--- R/manecsummary-class.R | 114 +- R/models.R | 172 +-- R/nec.R | 230 ++-- R/necsummary-class.R | 86 - R/nsec.R | 372 +++---- R/prebayesnecfit-class.R | 132 +- R/pred_equations.R | 260 ++--- R/pull_out.R | 204 ++-- R/pull_prior.R | 60 - R/sample_priors.R | 164 +-- R/set_distribution.R | 102 +- R/show_params.R | 76 - R/validate_family.R | 64 - R/validate_loo_controls.R | 80 - R/validate_priors.R | 70 - README.md | 140 +- data/herbicide.rda |only inst/doc/example1.Rmd | 841 ++++++++--------- inst/doc/example1.html | 34 inst/doc/example2.Rmd | 555 +++++------ inst/doc/example2.html | 28 inst/doc/example2b.Rmd | 1015 ++++++++++----------- inst/doc/example2b.html | 66 - inst/doc/example3.Rmd | 351 +++---- inst/doc/example3.html | 78 - inst/doc/example4.Rmd | 391 ++++---- inst/doc/example4.html | 3 man/amend.Rd | 142 +- man/autoplot.bayesmanecfit.Rd | 178 +-- man/autoplot.bayesnecfit.Rd | 122 +- man/average_endpoints.Rd | 186 +-- man/bayesmanecfit-class.Rd | 112 +- man/bayesnec-package.Rd | 37 man/bayesnecfit-class.Rd | 148 +-- man/bayesnecformula.Rd | 266 ++--- man/beta_binomial2.Rd | 24 man/beta_binomial2_lpmf.Rd | 46 man/beta_binomial2_rng.Rd | 42 man/bnec.Rd | 452 ++++----- man/bnecfit-class.Rd | 46 man/c.bnecfit.Rd | 46 man/check_chains.Rd | 58 - man/check_chains.bayesmanecfit.Rd | 66 - man/check_chains.bayesnecfit.Rd | 58 - man/check_chains.default.Rd | 58 - man/check_formula.Rd | 166 +-- man/check_priors.Rd | 66 - man/compare_endpoints.Rd | 134 +- man/compare_fitted.Rd | 82 - man/compare_posterior.Rd | 134 +- man/dispersion.Rd | 94 - man/ecx.Rd | 166 +-- man/expand_manec.Rd | 114 +- man/expand_nec.Rd | 110 +- man/formula.bayesmanecfit.Rd | 46 man/formula.bayesnecfit.Rd | 40 man/ggbnec_data.Rd | 102 +- man/herbicide.Rd |only man/is_manecsummary.Rd | 34 man/is_necsummary.Rd | 28 man/log_lik_beta_binomial2.Rd | 38 man/make_brmsformula.Rd | 100 +- man/manec_example.Rd | 42 man/manecsummary-class.Rd | 120 +- man/model.frame.bayesmanecfit.Rd | 48 man/model.frame.bayesnecfit.Rd | 42 man/model.frame.bayesnecformula.Rd | 114 +- man/models.Rd | 132 +- man/nec.Rd | 84 - man/nec_data.Rd | 36 man/necsummary-class.Rd | 88 - man/nsec.Rd | 144 +- man/plot.bayesmanecfit.Rd | 158 +-- man/plot.bayesnecfit.Rd | 148 +-- man/plus-.bnecfit.Rd | 46 man/posterior_epred_beta_binomial2.Rd | 34 man/posterior_predict_beta_binomial2.Rd | 42 man/prebayesnecfit-class.Rd | 82 - man/predict.bayesmanecfit.Rd | 60 - man/predict.bayesnecfit.Rd | 60 - man/print.bayesmanecfit.Rd | 42 man/print.bayesnecfit.Rd | 42 man/print.manecsummary.Rd | 40 man/print.necsummary.Rd | 42 man/pull_out.Rd | 102 +- man/pull_prior.Rd | 50 - man/rhat.bayesmanecfit.Rd | 50 - man/rhat.bayesnecfit.Rd | 44 man/sample_priors.Rd | 54 - man/show_params.Rd | 58 - man/summary.bayesmanecfit.Rd | 54 - man/summary.bayesnecfit.Rd | 54 - man/update.bnecfit.Rd | 174 +-- tests/testthat.R | 8 tests/testthat/setup.R | 60 - tests/testthat/test-amend.R | 80 - tests/testthat/test-average_endpoints.R | 62 - tests/testthat/test-bayesmanec_methods.R | 108 +- tests/testthat/test-bayesnec_methods.R | 64 - tests/testthat/test-bayesnecformula.R | 46 tests/testthat/test-beta_binomial2.R | 40 tests/testthat/test-bnec.R | 24 tests/testthat/test-check_chains.R | 32 tests/testthat/test-check_formula.R | 184 +-- tests/testthat/test-check_models.R | 112 +- tests/testthat/test-check_priors.R | 34 tests/testthat/test-compare_endpoints.R | 28 tests/testthat/test-compare_fitted.R | 30 tests/testthat/test-compare_posterior.R | 36 tests/testthat/test-data.R | 26 tests/testthat/test-define_prior.R | 182 +-- tests/testthat/test-dispersion.R | 14 tests/testthat/test-ecx.R | 182 +-- tests/testthat/test-expand_classes.R | 262 ++--- tests/testthat/test-helpers.R | 42 tests/testthat/test-make_brmsformula.R | 80 - tests/testthat/test-model.frame.R | 102 +- tests/testthat/test-nec.R | 88 - tests/testthat/test-nsec.R | 166 +-- tests/testthat/test-pull_out.R | 36 tests/testthat/test-set_distribution.R | 56 - tests/testthat/test-validate_loo_controls.R | 200 ++-- tests/testthat/test-wrangle_model_formula.R | 28 vignettes/bayesnec.bib | 360 +++---- vignettes/example1.Rmd | 841 ++++++++--------- vignettes/example1.Rmd.orig | 557 +++++------ vignettes/example2.Rmd | 555 +++++------ vignettes/example2.Rmd.orig | 423 ++++---- vignettes/example2b.Rmd | 1015 ++++++++++----------- vignettes/example2b.Rmd.orig | 729 +++++++-------- vignettes/example3.Rmd | 351 +++---- vignettes/example3.Rmd.orig | 331 +++--- vignettes/example4.Rmd | 391 ++++---- vignettes/example4.Rmd.orig | 343 +++---- vignettes/exmp2b_theoretical_curves.R | 142 +- vignettes/precompile.R | 66 - 170 files changed, 15172 insertions(+), 15233 deletions(-)
Title: R Client for the eBird Database of Bird Observations
Description: A programmatic client for the eBird database
(<https://ebird.org/home>), including functions for searching for bird
observations by geographic location (latitude, longitude), eBird
hotspots, location identifiers, by notable sightings, by region, and by
taxonomic name.
Author: Rafael Maia [aut],
Scott Chamberlain [aut] (<https://orcid.org/0000-0003-1444-9135>),
Andy Teucher [aut],
Guy Babineau [ctb],
Marianna Foos [ctb],
David Bradnum [ctb],
Sebastian Pardo [aut, cre] (<https://orcid.org/0000-0002-4147-5796>)
Maintainer: Sebastian Pardo <sebpardo@gmail.com>
Diff between rebird versions 1.2.0 dated 2021-01-27 and 1.3.0 dated 2021-09-20
DESCRIPTION | 6 ++-- MD5 | 14 ++++----- NEWS.md | 6 ++++ R/sysdata.rda |binary build/vignette.rds |binary inst/doc/rebird_vignette.html | 10 ++++++ tests/testthat/test-ebirdhistorical.R | 51 ++++++++++++++++------------------ tests/testthat/test-ebirdtaxonomy.R | 3 +- 8 files changed, 52 insertions(+), 38 deletions(-)
Title: Owen Q-Function
Description: Evaluates the Owen Q-function for an integer value of the degrees of freedom, by applying Owen's algorithm (1965) <doi:10.1093/biomet/52.3-4.437>.
It is useful for the calculation of the power of equivalence tests.
Author: Stéphane Laurent
Maintainer: Stéphane Laurent <laurent_step@outlook.fr>
Diff between OwenQ versions 1.0.3 dated 2020-01-08 and 1.0.4 dated 2021-09-20
DESCRIPTION | 8 MD5 | 28 NEWS.md | 4 build/vignette.rds |binary inst/doc/OwenQ.html | 391 ++------- inst/doc/Validation.Rmd | 1458 ++++++++++++++++++------------------- inst/doc/Validation.html | 960 ++++++++++-------------- src/RcppExports.cpp | 5 tests/testthat/test-OwenQ2_algo1.R | 153 +-- tests/testthat/test-OwenQ2_algo2.R | 153 +-- tests/testthat/test-OwenT.R | 186 ++-- tests/testthat/test-pOwen_algo1.R | 818 ++++++++++---------- tests/testthat/test-pOwen_algo2.R | 818 ++++++++++---------- tests/testthat/test-ptOwen.R | 51 - vignettes/Validation.Rmd | 1458 ++++++++++++++++++------------------- 15 files changed, 3090 insertions(+), 3401 deletions(-)
Title: Compute the Coefficient of Determination for Vector or Matrix
Outcomes
Description: Compute the coefficient of determination for outcomes in n-dimensions.
May be useful for multidimensional predictions (such as a multinomial model) or
calculating goodness of fit from latent variable models such as probabilistic
topic models like latent Dirichlet allocation or deterministic topic models
like latent semantic analysis. Based on Jones (2019) <arXiv:1911.11061>.
Author: Tommy Jones [aut, cre]
Maintainer: Tommy Jones <jones.thos.w@gmail.com>
Diff between mvrsquared versions 0.1.1 dated 2020-10-21 and 0.1.2 dated 2021-09-20
DESCRIPTION | 7 MD5 | 20 NEWS.md | 3 README.md | 3 build/vignette.rds |binary inst/WORDLIST | 14 inst/doc/getting_started_with_mvrsquared.html | 668 ++++++++------------------ src/Makevars | 3 src/Makevars.win | 3 src/RcppExports.cpp | 5 src/calc_sum_squares_latent.cpp | 9 11 files changed, 257 insertions(+), 478 deletions(-)
Title: Bayesian Inference of Non-Linear and Non-Gaussian State Space
Models
Description: Efficient methods for Bayesian inference of state space models
via particle Markov chain Monte Carlo (MCMC) and MCMC based on parallel
importance sampling type weighted estimators
(Vihola, Helske, and Franks, 2020, <doi:10.1111/sjos.12492>).
Gaussian, Poisson, binomial, negative binomial, and Gamma
observation densities and basic stochastic volatility models
with linear-Gaussian state dynamics,
as well as general non-linear Gaussian models and discretised
diffusion models are supported.
Author: Jouni Helske [aut, cre] (<https://orcid.org/0000-0001-7130-793X>),
Matti Vihola [aut] (<https://orcid.org/0000-0002-8041-7222>)
Maintainer: Jouni Helske <jouni.helske@iki.fi>
Diff between bssm versions 1.1.6 dated 2021-09-06 and 1.1.7 dated 2021-09-20
bssm-1.1.6/bssm/R/nlg_example_models.R |only bssm-1.1.6/bssm/man/asymptotic_var.Rd |only bssm-1.1.6/bssm/man/logLik.Rd |only bssm-1.1.6/bssm/man/logLik.nongaussian.Rd |only bssm-1.1.6/bssm/man/logLik.ssm_nlg.Rd |only bssm-1.1.6/bssm/man/logLik.ssm_sde.Rd |only bssm-1.1.6/bssm/man/nlg_example_models.Rd |only bssm-1.1.6/bssm/man/priors.Rd |only bssm-1.1.6/bssm/man/run_mcmc.ssm_nlg.Rd |only bssm-1.1.6/bssm/man/run_mcmc.ssm_sde.Rd |only bssm-1.1.6/bssm/man/run_mcmc_g.Rd |only bssm-1.1.6/bssm/man/run_mcmc_ng.Rd |only bssm-1.1.7/bssm/DESCRIPTION | 12 bssm-1.1.7/bssm/MD5 | 164 +++--- bssm-1.1.7/bssm/NAMESPACE | 17 bssm-1.1.7/bssm/NEWS | 13 bssm-1.1.7/bssm/R/approx.R | 41 + bssm-1.1.7/bssm/R/as_bssm.R | 11 bssm-1.1.7/bssm/R/as_draws.R |only bssm-1.1.7/bssm/R/bootstrap_filter.R | 60 +- bssm-1.1.7/bssm/R/bssm-package.R | 20 bssm-1.1.7/bssm/R/check_arguments.R | 64 ++ bssm-1.1.7/bssm/R/cpp_example_models.R |only bssm-1.1.7/bssm/R/ekpf_filter.R | 24 bssm-1.1.7/bssm/R/importance_sample.R | 25 bssm-1.1.7/bssm/R/kfilter.R | 83 ++- bssm-1.1.7/bssm/R/loglik.R | 113 +--- bssm-1.1.7/bssm/R/models.R | 513 ++++++++++---------- bssm-1.1.7/bssm/R/particle_smoother.R | 86 ++- bssm-1.1.7/bssm/R/post_correction.R | 106 ++-- bssm-1.1.7/bssm/R/predict.R | 67 +- bssm-1.1.7/bssm/R/print_mcmc.R | 37 - bssm-1.1.7/bssm/R/priors.R | 132 +++-- bssm-1.1.7/bssm/R/run_mcmc.R | 496 +++++++++---------- bssm-1.1.7/bssm/R/sim_smoother.R | 37 - bssm-1.1.7/bssm/R/smoother.R | 56 ++ bssm-1.1.7/bssm/inst/doc/bssm.Rmd | 396 +++++++-------- bssm-1.1.7/bssm/inst/doc/bssm.html | 4 bssm-1.1.7/bssm/inst/doc/growth_model.html | 4 bssm-1.1.7/bssm/inst/doc/sde_model.html | 2 bssm-1.1.7/bssm/man/ar1_lg.Rd | 98 ++- bssm-1.1.7/bssm/man/ar1_ng.Rd | 132 +++-- bssm-1.1.7/bssm/man/as.data.frame.mcmc_output.Rd | 124 ++-- bssm-1.1.7/bssm/man/as_bssm.Rd | 70 +- bssm-1.1.7/bssm/man/as_draws.Rd |only bssm-1.1.7/bssm/man/bootstrap_filter.Rd | 170 +++--- bssm-1.1.7/bssm/man/bsm_lg.Rd | 169 +++--- bssm-1.1.7/bssm/man/bsm_ng.Rd | 247 +++++---- bssm-1.1.7/bssm/man/bssm.Rd | 64 +- bssm-1.1.7/bssm/man/bssm_prior.Rd |only bssm-1.1.7/bssm/man/cpp_example_model.Rd |only bssm-1.1.7/bssm/man/drownings.Rd | 66 +- bssm-1.1.7/bssm/man/ekf.Rd | 82 ++- bssm-1.1.7/bssm/man/ekf_smoother.Rd | 88 ++- bssm-1.1.7/bssm/man/ekpf_filter.Rd | 124 ++-- bssm-1.1.7/bssm/man/exchange.Rd | 56 +- bssm-1.1.7/bssm/man/expand_sample.Rd | 62 +- bssm-1.1.7/bssm/man/gaussian_approx.Rd | 108 ++-- bssm-1.1.7/bssm/man/importance_sample.Rd | 123 ++-- bssm-1.1.7/bssm/man/kfilter.Rd | 87 +-- bssm-1.1.7/bssm/man/logLik_bssm.Rd |only bssm-1.1.7/bssm/man/particle_smoother.Rd | 257 +++++----- bssm-1.1.7/bssm/man/poisson_series.Rd | 38 - bssm-1.1.7/bssm/man/post_correct.Rd | 20 bssm-1.1.7/bssm/man/predict.mcmc_output.Rd | 33 - bssm-1.1.7/bssm/man/print.mcmc_output.Rd | 32 - bssm-1.1.7/bssm/man/run_mcmc.Rd | 376 +++++++++++++- bssm-1.1.7/bssm/man/sim_smoother.Rd | 119 ++-- bssm-1.1.7/bssm/man/smoother.Rd | 82 ++- bssm-1.1.7/bssm/man/ssm_mlg.Rd | 208 ++++---- bssm-1.1.7/bssm/man/ssm_mng.Rd | 272 +++++----- bssm-1.1.7/bssm/man/ssm_nlg.Rd | 225 ++++---- bssm-1.1.7/bssm/man/ssm_sde.Rd | 179 +++--- bssm-1.1.7/bssm/man/ssm_ulg.Rd | 432 ++++++++-------- bssm-1.1.7/bssm/man/ssm_ung.Rd | 239 ++++----- bssm-1.1.7/bssm/man/suggest_N.Rd | 48 + bssm-1.1.7/bssm/man/summary.mcmc_output.Rd | 76 +- bssm-1.1.7/bssm/man/svm.Rd | 133 +++-- bssm-1.1.7/bssm/man/ukf.Rd | 86 ++- bssm-1.1.7/bssm/src/R_predict.cpp | 12 bssm-1.1.7/bssm/src/R_predict_past.cpp | 11 bssm-1.1.7/bssm/src/model_ar1_lg.cpp | 65 +- bssm-1.1.7/bssm/src/model_ar1_ng.cpp | 60 +- bssm-1.1.7/bssm/src/model_ssm_nlg.cpp | 13 bssm-1.1.7/bssm/tests/testthat/test_approx.R | 4 bssm-1.1.7/bssm/tests/testthat/test_as_data_frame.R | 2 bssm-1.1.7/bssm/tests/testthat/test_ekpf.R | 4 bssm-1.1.7/bssm/tests/testthat/test_mcmc.R | 6 bssm-1.1.7/bssm/tests/testthat/test_post_correct.R | 44 + bssm-1.1.7/bssm/tests/testthat/test_predict.R | 39 - bssm-1.1.7/bssm/tests/testthat/test_sde.R | 164 +++--- bssm-1.1.7/bssm/vignettes/bssm.Rmd | 396 +++++++-------- 92 files changed, 4629 insertions(+), 3499 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-09-06 0.0.1
Title: Estimating Abundance of Clones from DNA Fragmentation Data
Description: Estimate the abundance of cell clones from the
distribution of lengths of DNA fragments (as created by
sonication, whence `sonicLength'). The algorithm in
"Estimating abundances of retroviral insertion sites from
DNA fragment length data" by Berry CC, Gillet NA, Melamed
A, Gormley N, Bangham CR, Bushman FD. Bioinformatics;
2012 Mar 15;28(6):755-62 is implemented. The
experimental setting and estimation details are described
in detail there. Briefly, integration of new DNA in a
host genome (due to retroviral infection or gene therapy)
can be tracked using DNA sequencing, potentially allowing
characterization of the abundance of individual cell
clones bearing distinct integration sites. The locations
of integration sites can be determined by fragmenting the
host DNA (via sonication or fragmentase), breaking the
newly integrated DNA at a known sequence, amplifying the
fragments containing both host and integrated DNA,
sequencing those amplicons, then mapping the host
sequences to positions on the reference genome. The
relative number of fragments containing a given position
in the host genome estimates the relative abundance of
cells hosting the corresponding integration site, but
that number is not available and the count of amplicons
per fragment varies widely. However, the expected number
of distinct fragment lengths is a function of the
abundance of cells hosting an integration site at a given
position and a certain nuisance parameter. The algorithm
implicitly estimates that function to estimate the
relative abundance.
Author: Charles Berry <ccberry@ucsd.edu>
Maintainer: Charles Berry <ccberry@ucsd.edu>
Diff between sonicLength versions 1.4.6 dated 2019-03-05 and 1.4.7 dated 2021-09-20
DESCRIPTION | 12 ++++++------ MD5 | 10 +++++----- R/maxEM.R | 3 ++- build/vignette.rds |binary data/A1.RData |binary inst/doc/EstAbund.pdf |binary 6 files changed, 13 insertions(+), 12 deletions(-)
Title: Common Functionality for the 'dynverse' Packages
Description: Provides common functionality for the 'dynverse' packages.
'dynverse' is created to support the development, execution, and benchmarking of trajectory inference methods.
For more information, check out <https://dynverse.org>.
Author: Robrecht Cannoodt [aut, cre] (<https://orcid.org/0000-0003-3641-729X>,
rcannood),
Wouter Saelens [aut] (<https://orcid.org/0000-0002-7114-6248>, zouter)
Maintainer: Robrecht Cannoodt <rcannood@gmail.com>
Diff between dynutils versions 1.0.7 dated 2021-09-04 and 1.0.8 dated 2021-09-20
DESCRIPTION | 6 ++-- MD5 | 10 +++---- NEWS.md | 4 ++ R/h5.R | 2 + inst/doc/functionality.html | 8 ++--- tests/testthat/test-h5.R | 62 ++++++++++++++++++++++---------------------- 6 files changed, 50 insertions(+), 42 deletions(-)
Title: A Multi-Modal Simulator for Spearheading Single-Cell Omics
Analyses
Description: A novel, multi-modal simulation engine for
studying dynamic cellular processes at single-cell resolution. 'dyngen'
is more flexible than current single-cell simulation engines. It
allows better method development and benchmarking, thereby stimulating
development and testing of novel computational methods. Cannoodt et
al. (2021) <doi:10.1038/s41467-021-24152-2>.
Author: Robrecht Cannoodt [aut, cre, cph]
(<https://orcid.org/0000-0003-3641-729X>),
Wouter Saelens [aut] (<https://orcid.org/0000-0002-7114-6248>)
Maintainer: Robrecht Cannoodt <rcannood@gmail.com>
Diff between dyngen versions 1.0.2 dated 2021-06-24 and 1.0.3 dated 2021-09-20
DESCRIPTION | 8 ++-- MD5 | 16 ++++---- NEWS.md | 6 +++ R/7_experiment.R | 54 ++++++++++++++++-------------- R/package.R | 1 README.md | 14 +++---- man/dyngen.Rd | 1 man/generate_experiment.Rd | 16 ++++++-- tests/testthat/test-generate_partitions.R | 9 +++-- 9 files changed, 73 insertions(+), 52 deletions(-)