Title: High-Dimensional Undirected Graph Estimation
Description: Provides a general framework for
high-dimensional undirected graph estimation. It integrates
data preprocessing, neighborhood screening, graph estimation,
and model selection techniques into a pipeline. In
preprocessing stage, the nonparanormal(npn) transformation is
applied to help relax the normality assumption. In the graph
estimation stage, the graph structure is estimated by
Meinshausen-Buhlmann graph estimation or the graphical lasso,
and both methods can be further accelerated by the lossy
screening rule preselecting the neighborhood of each variable
by correlation thresholding. We target on high-dimensional data
analysis usually d >> n, and the computation is
memory-optimized using the sparse matrix output. We also
provide a computationally efficient approach, correlation
thresholding graph estimation. Three
regularization/thresholding parameter selection methods are
included in this package: (1)stability approach for
regularization selection (2) rotation information criterion (3)
extended Bayesian information criterion which is only available
for the graphical lasso.
Author: Haoming Jiang, Xinyu Fei, Han Liu, Kathryn Roeder, John Lafferty, Larry
Wasserman, Xingguo Li, and Tuo Zhao
Maintainer: Haoming Jiang <jianghm.ustc@gmail.com>
Diff between huge versions 1.3.4.1 dated 2020-04-01 and 1.3.5 dated 2021-06-30
DESCRIPTION | 8 +-- MD5 | 48 +++++++++---------- R/RcppExports.R | 1 R/huge.plot.R | 3 - R/huge.select.R | 123 +++++++++++++++++++++++++------------------------- build/vignette.rds |binary configure | 18 +++---- configure.ac | 2 data/stockdata.rda |binary inst/doc/vignette.pdf |binary man/huge.Rd | 15 ++++-- man/huge.ct.Rd | 9 ++- man/huge.generator.Rd | 13 ++++- man/huge.glasso.Rd | 11 +++- man/huge.inference.Rd | 3 - man/huge.mb.Rd | 14 ++++- man/huge.npn.Rd | 3 - man/huge.plot.Rd | 15 +++--- man/huge.select.Rd | 12 +++- man/huge.tiger.Rd | 10 +++- man/stockdata.Rd | 6 +- src/Makevars.in | 2 src/Makevars.win | 2 src/SFGen.cpp | 4 - src/SPMBgraph.cpp | 92 ++++++++++++++++++------------------- 25 files changed, 234 insertions(+), 180 deletions(-)
Title: Consistent Significance Controlled Variable Selection in
Generalized Linear Regression
Description: Provides significance controlled variable selection algorithms with different directions (forward, backward, stepwise) based on diverse criteria (AIC, BIC, adjusted r-square, PRESS, or p-value). The algorithm selects a final model with only significant variables defined as those with significant p-values after multiple testing correction such as Bonferroni, False Discovery Rate, etc.
Author: Jongwook Kim, Adriano Zanin Zambom
Maintainer: Jongwook Kim <jongwook226@gmail.com>
Diff between SignifReg versions 4.0 dated 2021-06-16 and 4.1 dated 2021-06-30
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/SignifReg.R | 5 ++++- R/add1SignifReg.R | 5 ++++- R/add1summary.R | 12 +++++++----- R/drop1SignifReg.R | 5 ++++- R/drop1summary.R | 8 +++++--- build/partial.rdb |binary 8 files changed, 35 insertions(+), 22 deletions(-)
Title: Infrastructure for Ordering Objects Using Seriation
Description: Infrastructure for ordering objects with an implementation of several
seriation/sequencing/ordination techniques to reorder matrices, dissimilarity
matrices, and dendrograms. Also provides (optimally) reordered heatmaps,
color images and clustering visualizations like dissimilarity plots, and
visual assessment of cluster tendency plots (VAT and iVAT). Hahsler et al (2008) <doi:10.18637/jss.v025.i03>.
Author: Michael Hahsler [aut, cre, cph],
Christian Buchta [aut, cph],
Kurt Hornik [aut, cph],
Fionn Murtagh [ctb, cph],
Michael Brusco [ctb, cph],
Stephanie Stahl [ctb, cph],
Hans-Friedrich Koehn [ctb, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between seriation versions 1.2-9 dated 2020-10-01 and 1.3.0 dated 2021-06-30
seriation-1.2-9/seriation/R/AAAcolors.R |only seriation-1.2-9/seriation/R/AAAgrid.R |only seriation-1.2-9/seriation/R/AAAinstalled.R |only seriation-1.2-9/seriation/R/AAAmap.R |only seriation-1.2-9/seriation/R/AAAparameter.R |only seriation-1.2-9/seriation/man/col.Rd |only seriation-1.3.0/seriation/DESCRIPTION | 14 seriation-1.3.0/seriation/MD5 | 154 - seriation-1.3.0/seriation/NAMESPACE | 35 seriation-1.3.0/seriation/NEWS.md | 35 seriation-1.3.0/seriation/R/AAAregistry.R | 61 seriation-1.3.0/seriation/R/VAT.R | 18 seriation-1.3.0/seriation/R/bea.R | 121 - seriation-1.3.0/seriation/R/bertinplot.R | 372 +-- seriation-1.3.0/seriation/R/check_installed.R |only seriation-1.3.0/seriation/R/colors.R |only seriation-1.3.0/seriation/R/criterion.R | 76 seriation-1.3.0/seriation/R/criterion.array.R | 46 seriation-1.3.0/seriation/R/criterion.dist.R | 347 ++- seriation-1.3.0/seriation/R/criterion.matrix.R | 149 - seriation-1.3.0/seriation/R/data.R | 85 seriation-1.3.0/seriation/R/dissimilartiy.R | 272 +- seriation-1.3.0/seriation/R/dissplot.R | 1062 +++++----- seriation-1.3.0/seriation/R/ggVAT.R |only seriation-1.3.0/seriation/R/ggbertinplot.R |only seriation-1.3.0/seriation/R/ggdissplot.R |only seriation-1.3.0/seriation/R/gghmap.R |only seriation-1.3.0/seriation/R/ggpimage.R |only seriation-1.3.0/seriation/R/grid_helpers.R |only seriation-1.3.0/seriation/R/hclust_greedy.R | 8 seriation-1.3.0/seriation/R/hmap.R | 514 ++-- seriation-1.3.0/seriation/R/map.R |only seriation-1.3.0/seriation/R/parameters.R |only seriation-1.3.0/seriation/R/permutation.R | 50 seriation-1.3.0/seriation/R/permutation_vector.R | 110 - seriation-1.3.0/seriation/R/permute.R | 184 + seriation-1.3.0/seriation/R/pimage.R | 378 ++- seriation-1.3.0/seriation/R/register_DendSer.R | 61 seriation-1.3.0/seriation/R/register_GA.R | 56 seriation-1.3.0/seriation/R/reorder.hclust.R | 52 seriation-1.3.0/seriation/R/robinson.R | 42 seriation-1.3.0/seriation/R/seriate.R | 91 seriation-1.3.0/seriation/R/seriate.array.R | 75 seriation-1.3.0/seriation/R/seriate.data.frame.R |only seriation-1.3.0/seriation/R/seriate.dist.R | 29 seriation-1.3.0/seriation/R/seriate.matrix.R | 63 seriation-1.3.0/seriation/R/seriate_ARSA_Branch-Bound.R | 96 seriation-1.3.0/seriation/R/seriate_BEA.R | 44 seriation-1.3.0/seriation/R/seriate_HC.R | 122 - seriation-1.3.0/seriation/R/seriate_MDS.R | 73 seriation-1.3.0/seriation/R/seriate_PCA.R | 86 seriation-1.3.0/seriation/R/seriate_QAP.R | 83 seriation-1.3.0/seriation/R/seriate_R2E.R | 19 seriation-1.3.0/seriation/R/seriate_SA.R | 88 seriation-1.3.0/seriation/R/seriate_SPIN.R | 122 - seriation-1.3.0/seriation/R/seriate_TSP.R | 23 seriation-1.3.0/seriation/R/seriate_VAT.R | 18 seriation-1.3.0/seriation/R/seriate_heatmap.R |only seriation-1.3.0/seriation/R/seriate_spectral.R | 28 seriation-1.3.0/seriation/R/uniscale.R | 79 seriation-1.3.0/seriation/build/partial.rdb |binary seriation-1.3.0/seriation/build/vignette.rds |binary seriation-1.3.0/seriation/inst/doc/seriation.R | 138 - seriation-1.3.0/seriation/inst/doc/seriation.Rnw | 87 seriation-1.3.0/seriation/inst/doc/seriation.pdf |binary seriation-1.3.0/seriation/man/Chameleon.Rd | 4 seriation-1.3.0/seriation/man/VAT.Rd | 53 seriation-1.3.0/seriation/man/bertinplot.Rd | 124 - seriation-1.3.0/seriation/man/colors.Rd |only seriation-1.3.0/seriation/man/criterion.Rd | 2 seriation-1.3.0/seriation/man/criterion_methods.Rd | 44 seriation-1.3.0/seriation/man/dissimilarity.Rd | 29 seriation-1.3.0/seriation/man/dissplot.Rd | 191 + seriation-1.3.0/seriation/man/get_order.Rd | 2 seriation-1.3.0/seriation/man/hmap.Rd | 186 + seriation-1.3.0/seriation/man/permute.Rd | 58 seriation-1.3.0/seriation/man/pimage.Rd | 196 + seriation-1.3.0/seriation/man/register_DendSer.Rd | 2 seriation-1.3.0/seriation/man/register_GA.Rd | 4 seriation-1.3.0/seriation/man/reorder_hclust.Rd | 28 seriation-1.3.0/seriation/man/robinson.Rd | 2 seriation-1.3.0/seriation/man/seriate.Rd | 83 seriation-1.3.0/seriation/man/seriation_methods.Rd | 43 seriation-1.3.0/seriation/man/uniscale.Rd | 4 seriation-1.3.0/seriation/tests/testthat/test-map.R |only seriation-1.3.0/seriation/tests/testthat/test-permuation_vector.R | 40 seriation-1.3.0/seriation/tests/testthat/test-seriate.R | 55 seriation-1.3.0/seriation/vignettes/seriation.Rnw | 87 88 files changed, 4315 insertions(+), 2588 deletions(-)
Title: Radiomics Image Analysis Toolbox for Medial Images
Description: Radiomics image analysis toolbox for 2D and 3D radiological images. RIA supports DICOM, NIfTI and
nrrd file formats. RIA calculates first-order, gray level co-occurrence matrix,
gray level run length matrix and geometry-based statistics. Almost all calculations are done
using vectorized formulas to optimize run speeds. Calculation of several thousands of parameters
only takes minutes on a single core of a conventional PC.
Author: Marton Kolossvary [aut, cre]
Maintainer: Marton Kolossvary <marton.kolossvary@gmail.com>
Diff between RIA versions 1.5.0 dated 2021-01-29 and 1.5.1 dated 2021-06-30
DESCRIPTION | 8 ++-- MD5 | 12 +++--- R/load_nifti.R | 2 - README.md | 95 +++++++++++++++++++++++++++--------------------------- inst/doc/RIA.Rmd | 5 ++ inst/doc/RIA.html | 14 ++++++- vignettes/RIA.Rmd | 5 ++ 7 files changed, 81 insertions(+), 60 deletions(-)
Title: Helpers for Developing Command Line Interfaces
Description: A suite of tools to build attractive command line interfaces
('CLIs'), from semantic elements: headings, lists, alerts, paragraphs,
etc. Supports custom themes via a 'CSS'-like language. It also contains a
number of lower level 'CLI' elements: rules, boxes, trees, and
'Unicode' symbols with 'ASCII' alternatives. It support ANSI colors and
text styles as well.
Author: Gábor Csárdi [aut, cre],
Hadley Wickham [ctb],
Kirill Müller [ctb],
RStudio [cph]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between cli versions 2.5.0 dated 2021-04-26 and 3.0.0 dated 2021-06-30
DESCRIPTION | 14 - MD5 | 179 ++++++++++++++++------- NAMESPACE | 45 +++++ NEWS.md | 11 + R/aaa-utils.R | 12 + R/ansiex.R | 15 + R/cli.R | 21 ++ R/cliapp-docs.R | 13 + R/cliapp.R | 4 R/containers.R | 4 R/debug.R | 2 R/docs.R | 45 +++++ R/format-conditions.R | 17 +- R/format.R | 2 R/inline.R | 23 ++ R/internals.R | 29 ++- R/num-ansi-colors.R | 6 R/onload.R | 92 +++++++++++ R/progress-along.R |only R/progress-bar.R |only R/progress-c.R |only R/progress-client.R |only R/progress-server.R |only R/progress-ticking.R |only R/progress-utils.R |only R/progress-variables.R |only R/rlang.R |only R/rstudio-detect.R | 6 R/sizes.R |only R/spinner.R | 43 ++++- R/status-bar.R | 47 ++++-- R/themes.R | 51 ++++-- R/time-ago.R |only R/time.R |only R/timer.R |only R/tty.R | 84 ++++++++++ R/utils.R | 4 R/width.R | 26 ++- README.md | 24 +-- inst/include |only inst/shiny |only man/chunks/pluralization.Rmd | 2 man/cli-config.Rd |only man/cli_abort.Rd |only man/cli_debug_doc.Rd | 2 man/cli_process_start.Rd | 2 man/cli_progress_along.Rd |only man/cli_progress_bar.Rd |only man/cli_progress_builtin_handlers.Rd |only man/cli_progress_demo.Rd |only man/cli_progress_message.Rd |only man/cli_progress_output.Rd |only man/cli_progress_step.Rd |only man/cli_progress_styles.Rd |only man/cli_status.Rd | 2 man/console_width.Rd | 6 man/format_inline.Rd |only man/get_spinner.Rd | 8 - man/inline-markup.Rd | 15 + man/make_spinner.Rd | 8 - man/pluralization.Rd | 30 +-- man/progress-c.Rd |only man/progress-utils.Rd |only man/progress-variables.Rd |only src |only tests/testthat/_snaps/deep-lists.md | 36 ++-- tests/testthat/_snaps/format-conditions.md | 14 + tests/testthat/_snaps/inline-2.md | 36 ++++ tests/testthat/_snaps/lists.md | 11 + tests/testthat/_snaps/progress-along.md |only tests/testthat/_snaps/progress-bar.md |only tests/testthat/_snaps/progress-c.md |only tests/testthat/_snaps/progress-client.md |only tests/testthat/_snaps/progress-handler-logger.md |only tests/testthat/_snaps/progress-message.md |only tests/testthat/_snaps/progress-ticking.md |only tests/testthat/_snaps/progress-types.md |only tests/testthat/_snaps/progress-variables.md |only tests/testthat/_snaps/rlang-errors.md |only tests/testthat/_snaps/text.md | 19 +- tests/testthat/_snaps/themes.md | 8 - tests/testthat/_snaps/utf8 |only tests/testthat/helper.R | 96 ++++++++++++ tests/testthat/progress-1.c |only tests/testthat/progress-2.c |only tests/testthat/progresstest |only tests/testthat/progresstestcpp |only tests/testthat/setup.R |only tests/testthat/test-format-conditions.R | 11 + tests/testthat/test-inline-2.R | 27 +++ tests/testthat/test-lists.R | 12 + tests/testthat/test-num-ansi-colors.R |only tests/testthat/test-progress-along.R |only tests/testthat/test-progress-bar.R |only tests/testthat/test-progress-c.R |only tests/testthat/test-progress-client.R |only tests/testthat/test-progress-handler-logger.R |only tests/testthat/test-progress-handler-say.R |only tests/testthat/test-progress-handlers.R |only tests/testthat/test-progress-message.R |only tests/testthat/test-progress-ticking.R |only tests/testthat/test-progress-types.R |only tests/testthat/test-progress-utils.R |only tests/testthat/test-progress-variables.R |only tests/testthat/test-rlang-errors.R |only tests/testthat/test-status-bar.R | 106 +++++++++---- tests/testthat/test-text.R | 2 tests/testthat/test-themes.R | 2 tests/testthat/test-timer.R |only tests/testthat/test-utf8.R |only 110 files changed, 1044 insertions(+), 230 deletions(-)
Title: Zero-Variance Control Variates
Description: Stein control variates can be used to improve Monte Carlo estimates of expectations when the derivatives of the log target are available. This package implements a variety of such methods, including zero-variance control variates (ZV-CV, Mira et al. (2013) <doi:10.1007/s11222-012-9344-6>), regularised ZV-CV (South et al., 2018 <arXiv:1811.05073>), control functionals (CF, Oates et al. (2017) <doi:10.1111/rssb.12185>) and semi-exact control functionals (SECF, South et al., 2020 <arXiv:2002.00033>). ZV-CV is a parametric approach that is exact for (low order) polynomial integrands with Gaussian targets. CF is a non-parametric alternative that offers better than the standard Monte Carlo convergence rates. SECF has both a parametric and a non-parametric component and it offers the advantages of both for an additional computational cost. Functions for applying ZV-CV and CF to two estimators for the normalising constant of the posterior distribution in Bayesian statistics are also supplied in this package. The basic requirements for using the package are a set of samples, derivatives and function evaluations.
Author: Leah F. South [aut, cre] (<https://orcid.org/0000-0002-5646-2963>)
Maintainer: Leah F. South <leah.south@hdr.qut.edu.au>
Diff between ZVCV versions 2.1.0 dated 2020-06-17 and 2.1.1 dated 2021-06-30
DESCRIPTION | 10 MD5 | 10 NEWS.md | 10 R/kernel_methods.R | 1022 ++++++++++++++++++++++++++-------------------------- src/RcppExports.cpp | 5 src/fnToExport.cpp | 14 6 files changed, 552 insertions(+), 519 deletions(-)
Title: Robust Preprocessing of Time Series Data
Description: Methods for handling the missing values outliers are introduced in
this package. The recognized missing values and outliers are replaced
using a model-based approach. The model may consist of both autoregressive
components and external regressors. The methods work robust and efficient,
and they are fully tunable. The primary motivation for writing the package
was preprocessing of the energy systems data, e.g. power plant production
time series, but the package could be used with any time series data.
Author: Michał Narajewski [aut, cre] (<https://orcid.org/0000-0002-3115-0162>),
Jens Kley-Holsteg [aut],
Florian Ziel [aut] (<https://orcid.org/0000-0002-2974-2660>)
Maintainer: Michał Narajewski <michal.narajewski@uni-due.de>
Diff between tsrobprep versions 0.1.0 dated 2021-04-11 and 0.3.0 dated 2021-06-30
DESCRIPTION | 25 - LICENSE | 2 MD5 | 24 - NAMESPACE | 1 R/auto_data_cleaning.R | 106 +++++-- R/detect_outliers.R | 571 ++++++++++++++++++++++++++---------------- R/impute_modelled_data.R | 36 +- R/model_missing_data.R | 596 +++++++++++++++++++++++++++++++++----------- R/robust_decompose.R |only man/auto_data_cleaning.Rd | 48 +-- man/detect_outliers.Rd | 200 +++++++------- man/impute_modelled_data.Rd | 20 - man/model_missing_data.Rd | 94 ++++-- man/robust_decompose.Rd |only 14 files changed, 1131 insertions(+), 592 deletions(-)
Title: Causes of Outcome Learning
Description: Implementing the computational phase of the Causes of Outcome Learning approach as described in Rieckmann, Dworzynski, Arras, Lapuschkin, Samek, Arah, Rod, Ekstrom. Causes of outcome learning: A causal inference-inspired machine learning approach to disentangling common combinations of potential causes of a health outcome. medRxiv (2020) <doi:10.1101/2020.12.10.20225243>. The optional 'ggtree' package can be obtained through Bioconductor.
Author: Andreas Rieckmann [aut, cre],
Piotr Dworzynski [aut],
Leila Arras [ctb],
Claus Thorn Ekstrom [aut]
Maintainer: Andreas Rieckmann <aric@sund.ku.dk>
Diff between CoOL versions 1.0.1 dated 2021-02-23 and 1.0.2 dated 2021-06-30
DESCRIPTION | 9 +- MD5 | 22 ++--- R/CoOL_functions.R | 80 ++++++++++++++++----- R/RcppExports.R | 9 +- man/CoOL_2_train_neural_network.Rd | 14 +++ man/CoOL_6_dendrogram.Rd | 5 + man/CoOL_6_sub_groups.Rd | 4 - man/CoOL_7_prevalence_and_mean_risk_plot.Rd | 5 + man/CoOL_8_mean_risk_contributions_by_sub_group.Rd | 5 + man/cpp_train_network_relu.Rd | 17 ++++ src/RcppExports.cpp | 13 ++- src/train_relu.cpp | 38 +++++++-- 12 files changed, 167 insertions(+), 54 deletions(-)
Title: Package Dependency Resolution and Downloads
Description: Find recursive dependencies of 'R' packages from various
sources. Solve the dependencies to obtain a consistent set of
packages to install. Download packages, and install them. It
supports packages on 'CRAN', 'Bioconductor' and other 'CRAN-like'
repositories, 'GitHub', package 'URLs', and local package trees
and files. It caches metadata and package files via the 'pkgcache'
package, and performs all 'HTTP' requests, downloads, builds and
installations in parallel. 'pkgdepends' is the workhorse of the
'pak' package.
Author: Gábor Csárdi
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between pkgdepends versions 0.1.1 dated 2021-05-16 and 0.1.2 dated 2021-06-30
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/resolution.R | 2 +- R/type-installed.R | 2 +- man/pkg_download_proposal.Rd | 2 +- man/pkgdepends-package.Rd | 10 +++++----- 6 files changed, 16 insertions(+), 16 deletions(-)
Title: Visualization of a Correlation Matrix
Description: Provides a visual exploratory tool on correlation matrix that supports automatic variable reordering to help detect hidden patterns among variables.
Author: Taiyun Wei [cre, aut],
Viliam Simko [aut],
Michael Levy [ctb],
Yihui Xie [ctb],
Yan Jin [ctb],
Jeff Zemla [ctb],
Moritz Freidank [ctb],
Jun Cai [ctb],
Tomas Protivinsky [ctb]
Maintainer: Taiyun Wei <weitaiyun@gmail.com>
Diff between corrplot versions 0.89 dated 2021-06-07 and 0.90 dated 2021-06-30
DESCRIPTION | 34 LICENSE | 4 MD5 | 75 - NAMESPACE | 24 NEWS.md |only R/colorlegend.R | 210 +-- R/cor-mtest.R | 100 - R/corrMatOrder.R | 158 +- R/corrRect.R | 169 ++ R/corrRect.hclust.R | 90 - R/corrplot-package.R | 86 - R/corrplot.R | 2109 ++++++++++++++++++------------------ R/corrplot.mixed.R | 172 +- README.md |only build/vignette.rds |binary inst/CITATION | 48 inst/NEWS | 124 -- inst/doc/corrplot-intro.R | 363 +++--- inst/doc/corrplot-intro.Rmd | 751 +++++++----- inst/doc/corrplot-intro.html | 868 +++++++------- man/colorlegend.Rd | 162 +- man/cor.mtest.Rd | 70 - man/corrMatOrder.Rd | 160 +- man/corrRect.Rd | 191 ++- man/corrRect.hclust.Rd | 150 +- man/corrplot-package.Rd | 80 - man/corrplot.Rd | 1080 +++++++++--------- man/corrplot.mixed.Rd | 150 +- tests/testthat.R | 8 tests/testthat/test-colorlegend.R | 112 - tests/testthat/test-cor-mtest.R | 50 tests/testthat/test-corrRect.R |only tests/testthat/test-corrplot.R | 465 +++---- vignettes/corrplot-intro.Rmd | 751 +++++++----- vignettes/example-colorlegend.R | 48 vignettes/example-corrMatOrder.R | 56 vignettes/example-corrRect.R | 104 + vignettes/example-corrRect.hclust.R | 66 - vignettes/example-corrplot.R | 446 +++---- vignettes/example-corrplot.mixed.R | 26 40 files changed, 4950 insertions(+), 4610 deletions(-)
More information about clinDataReview at CRAN
Permanent link
Title: Alternating Optimization
Description: Alternating optimization of high-dimensional functions is an iterative procedure for minimizing (or maximizing) jointly over all parameters by alternately optimizing for parameter subsets. For a reference, see Bezdek and Hathaway (2002) "Some Notes on Alternating Optimization" <doi:10.1007/3-540-45631-7_39>.
Author: Lennart Oelschläger [aut, cre]
(<https://orcid.org/0000-0001-5421-9313>)
Maintainer: Lennart Oelschläger <lennart.oelschlaeger@uni-bielefeld.de>
Diff between ao versions 0.1.0 dated 2021-06-21 and 0.1.1 dated 2021-06-30
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NEWS.md | 3 +++ R/ao.R | 55 +++++++++++++++++++++---------------------------------- README.md | 10 ++++------ man/ao.Rd | 30 +++++++++--------------------- 6 files changed, 47 insertions(+), 71 deletions(-)
More information about flipdownWidgets at CRAN
Permanent link
Title: Simple Neural Application
Description: A simple wrapper to easily design vanilla deep neural networks using 'Tensorflow'/'Keras' backend for regression, classification and multi-label tasks, with some tweaks and tricks (skip shortcuts, embedding, feature selection and anomaly detection).
Author: Giancarlo Vercellino
Maintainer: Giancarlo Vercellino <giancarlo.vercellino@gmail.com>
Diff between snap versions 1.0.0 dated 2021-05-11 and 1.1.0 dated 2021-06-30
DESCRIPTION | 16 ++++++++-------- MD5 | 10 +++++----- NEWS.md | 7 +++++-- R/main.R | 32 +++++++++++++++----------------- R/support.R | 2 +- man/snap.Rd | 10 ++++------ 6 files changed, 38 insertions(+), 39 deletions(-)
Title: Tools to Measure Climate Scenario Alignment of Corporate Lending
Portfolios
Description: These tools help you to assess if a corporate lending
portfolio aligns with climate goals. They summarize key climate
indicators attributed to the portfolio (e.g. production, emission
factors), and calculate alignment targets based on climate scenarios.
They implement in R the last step of the free software 'PACTA' (Paris
Agreement Capital Transition Assessment;
<https://2degrees-investing.org/>). Financial institutions use 'PACTA'
to study how their capital allocation decisions align with climate
change mitigation goals.
Author: Jackson Hoffart [aut, cre] (<https://orcid.org/0000-0002-8600-5042>),
Mauro Lepore [aut, ctr] (<https://orcid.org/0000-0002-1986-7988>),
Klaus Hogedorn [aut],
2 Degrees Investing Initiative [cph, fnd]
Maintainer: Jackson Hoffart <jackson.hoffart@gmail.com>
Diff between r2dii.analysis versions 0.1.8 dated 2021-05-22 and 0.1.9 dated 2021-06-30
DESCRIPTION | 6 +-- MD5 | 20 ++++++------ NAMESPACE | 1 NEWS.md | 10 ++++-- R/imports.R | 4 +- R/summarize_weighted_production.R | 1 R/target_market_share.R | 2 - R/target_sda.R | 8 ++++ README.md | 36 +++++++++++----------- tests/testthat/test-target_market_share.R | 31 ++++++++++++++++++ tests/testthat/test-target_sda.R | 49 ++++++++++++++++++++++++++++++ 11 files changed, 130 insertions(+), 38 deletions(-)
More information about r2dii.analysis at CRAN
Permanent link
Title: Multivariate Normality Tests
Description: Performs multivariate normality tests and graphical approaches and
implements multivariate outlier detection and univariate normality of marginal
distributions through plots and tests, and performs multivariate Box-Cox transformation
(Korkmaz et al, (2014), <https://journal.r-project.org/archive/2014-2/korkmaz-goksuluk-zararsiz.pdf>).
Author: Selcuk Korkmaz [aut, cre] (<https://orcid.org/0000-0003-4632-6850>),
Dincer Goksuluk [aut],
Gokmen Zararsiz [aut]
Maintainer: Selcuk Korkmaz <selcukorkmaz@gmail.com>
Diff between MVN versions 5.8 dated 2019-09-27 and 5.9 dated 2021-06-30
MVN-5.8/MVN/R/hzTest.R |only MVN-5.8/MVN/R/mardiaTest.R |only MVN-5.8/MVN/R/roystonTest.R |only MVN-5.8/MVN/inst/doc/MVN.Rnw |only MVN-5.8/MVN/inst/doc/MVN.pdf |only MVN-5.8/MVN/man/hzTest.Rd |only MVN-5.8/MVN/man/mardiaTest.Rd |only MVN-5.8/MVN/man/roystonTest.Rd |only MVN-5.8/MVN/vignettes/MVN.Rnw |only MVN-5.8/MVN/vignettes/MVN.bib |only MVN-5.9/MVN/DESCRIPTION | 33 +++--- MVN-5.9/MVN/MD5 | 26 ++--- MVN-5.9/MVN/NAMESPACE | 8 - MVN-5.9/MVN/R/mvn.R | 102 ++++++++++++++------- MVN-5.9/MVN/README.md |only MVN-5.9/MVN/build/vignette.rds |binary MVN-5.9/MVN/inst/doc/MVN.R | 194 ++++++++++++++++++----------------------- MVN-5.9/MVN/inst/doc/MVN.Rmd |only MVN-5.9/MVN/inst/doc/MVN.html |only MVN-5.9/MVN/man/mvn.Rd | 71 ++++++++------- MVN-5.9/MVN/vignettes/MVN.Rmd |only 21 files changed, 223 insertions(+), 211 deletions(-)
Title: Intraclass Correlation Coefficient for Count Data
Description: Estimates the intraclass correlation coefficient (ICC) for count data to assess repeatability (intra-methods concordance) and concordance (between-method concordance). In the concordance setting, the ICC is equivalent to the concordance correlation coefficient estimated by variance components. The ICC is estimated using the estimates from generalized linear mixed models. The within-subjects distributions considered are: Poisson; Negative Binomial with additive and proportional extradispersion; Zero-Inflated Poisson; and Zero-Inflated Negative Binomial with additive and proportional extradispersion. The statistical methodology used to estimate the ICC with count data can be found in Carrasco (2010) <doi:10.1111/j.1541-0420.2009.01335.x>.
Author: Josep L. Carrasco <jlcarrasco@ub.edu>
Maintainer: Josep L. Carrasco <jlcarrasco@ub.edu>
Diff between iccCounts versions 1.0.1 dated 2021-06-01 and 1.0.2 dated 2021-06-30
DESCRIPTION | 6 MD5 | 10 R/gof_functions.R | 2 build/vignette.rds |binary inst/doc/iccCounts_examples.html | 500 ++++++++++----------------------------- vignettes/examples_1_0_1.R.RData |binary 6 files changed, 146 insertions(+), 372 deletions(-)
Title: 'Fitbit' Visualizations
Description: Connection to the 'Fitbit' Web API <https://dev.fitbit.com/build/reference/web-api/> by including 'ggplot2' Visualizations, 'Leaflet' and 3-dimensional 'Rayshader' Maps. The 3-dimensional 'Rayshader' Map requires the installation of the 'CopernicusDEM' R package which includes the 30- and 90-meter elevation data.
Author: Lampros Mouselimis [aut, cre] (<https://orcid.org/0000-0002-8024-1546>)
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>
Diff between fitbitViz versions 1.0.1 dated 2021-05-20 and 1.0.2 dated 2021-06-30
DESCRIPTION | 10 +-- MD5 | 21 +++--- NEWS.md | 8 ++ R/fitbit_utils.R | 38 +++++++++-- README.md | 106 ++++++++++++++++++++++++++++++--- inst/doc/fitbit_viz.R | 38 ++++++----- inst/doc/fitbit_viz.Rmd | 10 ++- inst/doc/fitbit_viz.html | 73 +++++++++------------- man/figures/fitbit_parameters.png |binary man/rayshader_3d_DEM.Rd | 11 +++ vignettes/data_plots/rayshader_map.png |only vignettes/fitbit_viz.Rmd | 10 ++- 12 files changed, 225 insertions(+), 100 deletions(-)
Title: Bayesian "Now-Cast" Estimation of Event Probabilities in
Multi-Party Democracies
Description: An implementation of a Bayesian framework for the opinion poll
based estimation of event probabilities in multi-party electoral systems
(Bender and Bauer (2018) <doi:10.21105/joss.00606>).
Author: Andreas Bender [aut, cre] (<https://orcid.org/0000-0001-5628-8611>),
Alexander Bauer [aut] (<https://orcid.org/0000-0003-3495-5131>)
Maintainer: Andreas Bender <bender.at.R@gmail.com>
Diff between coalitions versions 0.6.18 dated 2021-03-18 and 0.6.20 dated 2021-06-30
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 3 +++ R/scrapers.R | 11 ++++++++++- tests/testthat/test-scrapers.R | 6 +++--- 5 files changed, 24 insertions(+), 12 deletions(-)
Title: Tools for Clinical Research
Description: Every research team have their own script for data management, statistics and
most importantly hemodynamic indices. The purpose is to standardize scripts
utilized in clinical research. The hemodynamic indices can be used in a long-format dataframe,
and add both periods of interest (trigger-periods), and delete artifacts with deleter-files.
Transfer function analysis (Claassen et al. (2016) <doi:10.1177/0271678X15626425>) and
Mx (Czosnyka et al. (1996) <doi:10.1161/01.str.27.10.1829>) can be calculated using this package.
Author: Markus Harboe Olsen [cre, aut],
Christian Riberholt [aut],
Ronan Berg [aut],
Kirsten Moeller [aut]
Maintainer: Markus Harboe Olsen <oel@oelfam.com>
Diff between clintools versions 0.8.1 dated 2021-06-01 and 0.8.2 dated 2021-06-30
DESCRIPTION | 6 +++--- LICENSE | 2 +- MD5 | 12 ++++++------ NEWS.md | 7 +++++++ R/clinmon_helper.R | 19 +++++++++++++++---- R/tfa.R | 12 +++++++----- man/TFA.Rd | 2 +- 7 files changed, 40 insertions(+), 20 deletions(-)
Title: Contextual Importance and Utility
Description: Implementation of the Contextual Importance and Utility
(CIU) concepts for Explainable AI (XAI). A recent description of CIU
can be found in e.g. Främling (2020) <arXiv:2009.13996>.
Author: Kary Främling
Maintainer: Kary Främling <Kary.Framling@umu.se>
Diff between ciu versions 0.1.0 dated 2020-11-20 and 0.5.0 dated 2021-06-30
DESCRIPTION | 9 MD5 | 35 +- NAMESPACE | 13 R/ContextualImportanceUtility.R | 561 ++++++++++++++++------------------------ R/MetaExplain.R |only R/TextualCIU.R |only R/ciu-package.r | 21 + R/ciu.R |only R/ciu.ggplot.col.R |only R/ciu.relative.R | 1 inst |only man/barplot.ciu.Rd | 2 man/ciu-package.Rd | 21 + man/ciu.Rd |only man/ciu.barplot.Rd |only man/ciu.explain.Rd |only man/ciu.ggplot.col.Rd |only man/ciu.list.to.frame.Rd |only man/ciu.meta.explain.Rd |only man/ciu.meta.result.new.Rd |only man/ciu.new.Rd | 12 man/ciu.pie.Rd |only man/ciu.plot.3D.Rd |only man/ciu.plot.Rd |only man/ciu.relative.Rd | 3 man/ciu.textual.Rd |only man/ciu.to.CIU.Rd |only 27 files changed, 322 insertions(+), 356 deletions(-)
Title: Diagnostics for Pharmacometric Models
Description: Diagnostics for non-linear mixed-effects (population)
models from 'NONMEM' <https://www.iconplc.com/innovation/nonmem/>.
'xpose' facilitates data import, creation of numerical run summary
and provide 'ggplot2'-based graphics for data exploration and model
diagnostics.
Author: Benjamin Guiastrennec [aut, cre, cph],
Andrew C. Hooker [aut, cph],
Sebastian Ueckert [aut, cph],
Mike K. Smith [ctb],
Mats O. Karlsson [aut, cph]
Maintainer: Benjamin Guiastrennec <guiastrennec@gmail.com>
Diff between xpose versions 0.4.12 dated 2021-01-12 and 0.4.13 dated 2021-06-30
DESCRIPTION | 12 MD5 | 38 +-- NEWS.md | 4 R/read_nm_tables.R | 10 R/xpose_save.R | 67 +++-- README.md | 89 +++---- build/vignette.rds |binary data/xpdb_ex_pk.rda |binary inst/doc/access_xpdb_data.html | 256 ++------------------ inst/doc/customize_plots.html | 366 +++++++----------------------- inst/doc/import_model_outputs.html | 240 ++----------------- inst/doc/introduction.html | 284 +++-------------------- inst/doc/multiple_pages.html | 274 +++------------------- inst/doc/vpc.html | 278 +++------------------- man/figures/readme_example_figure_1-1.png |binary man/read_nm_tables.Rd | 2 man/xpose-package.Rd | 6 man/xpose_save.Rd | 47 ++- tests/testthat/test-read_nm_tables.R | 18 - tests/testthat/test-xpose_data.R | 4 20 files changed, 453 insertions(+), 1542 deletions(-)
Title: Simple 'ggplot2' Visualisation with Less Brainpower
Description: Wrapper functions to make 'ggplot2' visualisation easier with less brainpower required.
Author: David Hodge [aut, cre] (<https://orcid.org/0000-0002-3868-7501>),
Statistics New Zealand [cph]
Maintainer: David Hodge <davidhodge931@gmail.com>
Diff between simplevis versions 4.2.0 dated 2021-06-24 and 4.3.0 dated 2021-06-30
simplevis-4.2.0/simplevis/R/gg_point_col_dev.R |only simplevis-4.2.0/simplevis/man/theme_bar.Rd |only simplevis-4.2.0/simplevis/man/theme_boxplot.Rd |only simplevis-4.2.0/simplevis/man/theme_hbar.Rd |only simplevis-4.2.0/simplevis/man/theme_line.Rd |only simplevis-4.2.0/simplevis/man/theme_mobile_graph.Rd |only simplevis-4.2.0/simplevis/man/theme_mobile_map.Rd |only simplevis-4.2.0/simplevis/man/theme_point.Rd |only simplevis-4.2.0/simplevis/man/theme_sf.Rd |only simplevis-4.3.0/simplevis/DESCRIPTION | 16 simplevis-4.3.0/simplevis/MD5 | 134 +++--- simplevis-4.3.0/simplevis/NAMESPACE | 14 simplevis-4.3.0/simplevis/NEWS.md | 46 ++ simplevis-4.3.0/simplevis/R/gg_bar.R | 145 ++++-- simplevis-4.3.0/simplevis/R/gg_boxplot.R | 80 ++- simplevis-4.3.0/simplevis/R/gg_density.R |only simplevis-4.3.0/simplevis/R/gg_hbar.R | 149 ++++-- simplevis-4.3.0/simplevis/R/gg_line.R | 61 ++ simplevis-4.3.0/simplevis/R/gg_point.R | 108 ++++ simplevis-4.3.0/simplevis/R/gg_sf.R | 45 +- simplevis-4.3.0/simplevis/R/ggplotly.R | 11 simplevis-4.3.0/simplevis/R/internal.R | 204 +++++++++ simplevis-4.3.0/simplevis/R/leaflet_basemap.R | 1 simplevis-4.3.0/simplevis/R/leaflet_sf.R | 18 simplevis-4.3.0/simplevis/R/mutate_text.R | 13 simplevis-4.3.0/simplevis/R/theme.R | 274 +----------- simplevis-4.3.0/simplevis/README.md | 2 simplevis-4.3.0/simplevis/inst/doc/simplevis.R | 171 +++++-- simplevis-4.3.0/simplevis/inst/doc/simplevis.Rmd | 223 +++++++--- simplevis-4.3.0/simplevis/inst/doc/simplevis.html | 306 ++++++++------ simplevis-4.3.0/simplevis/man/example_sf_point.Rd | 4 simplevis-4.3.0/simplevis/man/example_sf_polygon.Rd | 4 simplevis-4.3.0/simplevis/man/gg_bar.Rd | 59 -- simplevis-4.3.0/simplevis/man/gg_bar_col.Rd | 80 +-- simplevis-4.3.0/simplevis/man/gg_bar_col_facet.Rd | 80 +-- simplevis-4.3.0/simplevis/man/gg_bar_facet.Rd | 66 --- simplevis-4.3.0/simplevis/man/gg_boxplot.Rd | 64 -- simplevis-4.3.0/simplevis/man/gg_boxplot_col.Rd | 77 +-- simplevis-4.3.0/simplevis/man/gg_boxplot_col_facet.Rd | 86 +-- simplevis-4.3.0/simplevis/man/gg_boxplot_facet.Rd | 67 --- simplevis-4.3.0/simplevis/man/gg_density.Rd |only simplevis-4.3.0/simplevis/man/gg_density_col.Rd |only simplevis-4.3.0/simplevis/man/gg_density_col_facet.Rd |only simplevis-4.3.0/simplevis/man/gg_density_facet.Rd |only simplevis-4.3.0/simplevis/man/gg_hbar.Rd | 59 -- simplevis-4.3.0/simplevis/man/gg_hbar_col.Rd | 83 +-- simplevis-4.3.0/simplevis/man/gg_hbar_col_facet.Rd | 80 +-- simplevis-4.3.0/simplevis/man/gg_hbar_facet.Rd | 65 -- simplevis-4.3.0/simplevis/man/gg_line.Rd | 56 -- simplevis-4.3.0/simplevis/man/gg_line_col.Rd | 67 --- simplevis-4.3.0/simplevis/man/gg_line_col_facet.Rd | 76 +-- simplevis-4.3.0/simplevis/man/gg_line_facet.Rd | 64 -- simplevis-4.3.0/simplevis/man/gg_point.Rd | 63 +- simplevis-4.3.0/simplevis/man/gg_point_col.Rd | 80 +-- simplevis-4.3.0/simplevis/man/gg_point_col_facet.Rd | 87 +-- simplevis-4.3.0/simplevis/man/gg_point_facet.Rd | 71 +-- simplevis-4.3.0/simplevis/man/gg_sf.Rd | 32 - simplevis-4.3.0/simplevis/man/gg_sf_col.Rd | 63 +- simplevis-4.3.0/simplevis/man/gg_sf_col_facet.Rd | 54 -- simplevis-4.3.0/simplevis/man/gg_sf_facet.Rd | 39 - simplevis-4.3.0/simplevis/man/leaflet_basemap.Rd | 1 simplevis-4.3.0/simplevis/man/leaflet_sf.Rd | 16 simplevis-4.3.0/simplevis/man/leaflet_sf_col.Rd | 42 - simplevis-4.3.0/simplevis/man/mutate_text.Rd | 13 simplevis-4.3.0/simplevis/man/nz.Rd | 4 simplevis-4.3.0/simplevis/man/plotly_camera.Rd | 5 simplevis-4.3.0/simplevis/man/plotly_col_legend.Rd | 6 simplevis-4.3.0/simplevis/man/sv_density_max.Rd |only simplevis-4.3.0/simplevis/man/sv_density_max_col.Rd |only simplevis-4.3.0/simplevis/man/sv_density_max_col_facet.Rd |only simplevis-4.3.0/simplevis/man/sv_density_max_facet.Rd |only simplevis-4.3.0/simplevis/man/sv_numeric_breaks_h.Rd | 10 simplevis-4.3.0/simplevis/man/sv_numeric_breaks_v.Rd | 9 simplevis-4.3.0/simplevis/man/theme_map.Rd |only simplevis-4.3.0/simplevis/man/theme_mobile_extra.Rd |only simplevis-4.3.0/simplevis/man/theme_mobile_extra_map.Rd |only simplevis-4.3.0/simplevis/man/theme_x_gridlines.Rd |only simplevis-4.3.0/simplevis/man/theme_xy_gridlines.Rd |only simplevis-4.3.0/simplevis/man/theme_y_gridlines.Rd |only simplevis-4.3.0/simplevis/vignettes/simplevis.Rmd | 223 +++++++--- 80 files changed, 2016 insertions(+), 1960 deletions(-)
Title: A Framework for Data-Driven Stochastic Disease Spread
Simulations
Description: Provides an efficient and very flexible framework to
conduct data-driven epidemiological modeling in realistic large
scale disease spread simulations. The framework integrates
infection dynamics in subpopulations as continuous-time Markov
chains using the Gillespie stochastic simulation algorithm and
incorporates available data such as births, deaths and movements
as scheduled events at predefined time-points. Using C code for
the numerical solvers and 'OpenMP' (if available) to divide work
over multiple processors ensures high performance when simulating
a sample outcome. One of our design goals was to make the package
extendable and enable usage of the numerical solvers from other R
extension packages in order to facilitate complex epidemiological
research. The package contains template models and can be extended
with user-defined models. For more details see the paper by
Widgren, Bauer, Eriksson and Engblom (2019)
<doi:10.18637/jss.v091.i12>. The package also provides
functionality to fit models to time series data using the
Approximate Bayesian Computation Sequential Monte Carlo
('ABC-SMC') algorithm of Toni and others (2009)
<doi:10.1098/rsif.2008.0172>.
Author: Stefan Widgren [aut, cre] (<https://orcid.org/0000-0001-5745-2284>),
Robin Eriksson [aut] (<https://orcid.org/0000-0002-4291-712X>),
Stefan Engblom [aut] (<https://orcid.org/0000-0002-3614-1732>),
Pavol Bauer [aut] (<https://orcid.org/0000-0003-4328-7171>),
Thomas Rosendal [ctb] (<https://orcid.org/0000-0002-6576-9668>),
Attractive Chaos [cph] (Author of 'kvec.h'.)
Maintainer: Stefan Widgren <stefan.widgren@gmail.com>
Diff between SimInf versions 8.3.0 dated 2021-06-25 and 8.3.2 dated 2021-06-30
SimInf-8.3.0/SimInf/cleanup.win |only SimInf-8.3.2/SimInf/DESCRIPTION | 6 - SimInf-8.3.2/SimInf/MD5 | 35 +++--- SimInf-8.3.2/SimInf/NEWS.md | 14 ++ SimInf-8.3.2/SimInf/README.md | 7 - SimInf-8.3.2/SimInf/build/partial.rdb |binary SimInf-8.3.2/SimInf/build/vignette.rds |binary SimInf-8.3.2/SimInf/cleanup | 2 SimInf-8.3.2/SimInf/inst/doc/SimInf.pdf |binary SimInf-8.3.2/SimInf/inst/doc/scheduled-events.html | 110 +++++++-------------- SimInf-8.3.2/SimInf/src/Makevars.ucrt | 31 +++++ SimInf-8.3.2/SimInf/src/Makevars.win | 2 SimInf-8.3.2/SimInf/tests/SimInf.R | 22 ++-- SimInf-8.3.2/SimInf/tests/abc/abc-gdata.R | 3 SimInf-8.3.2/SimInf/tests/measures.R | 12 +- SimInf-8.3.2/SimInf/tests/phi.R | 8 - SimInf-8.3.2/SimInf/tests/punchcard.R | 6 - SimInf-8.3.2/SimInf/tests/sample_select.R | 30 ++--- SimInf-8.3.2/SimInf/tests/solver_aem.R | 6 - 19 files changed, 150 insertions(+), 144 deletions(-)
Title: Process Analysis for Exponential Random Graph Models
Description: Calculates marginal effects and conducts process analysis in exponential family random graph models (ERGM).
Includes functions to conduct mediation and moderation analyses and to diagnose
multicollinearity.
URL: <https://github.com/sduxbury/ergMargins>.
BugReports: <https://github.com/sduxbury/ergMargins/issues>.
Duxbury, Scott W (2021) <doi:10.1177/0049124120986178>.
Long, J. Scott, and Sarah Mustillo (2018) <doi:10.1177/0049124118799374>.
Mize, Trenton D. (2019) <doi:10.15195/v6.a4>.
Karlson, Kristian Bernt, Anders Holm, and Richard Breen (2012) <doi:10.1177/0081175012444861>.
Duxbury, Scott W (2018) <doi:10.1177/0049124118782543>.
Author: Scott Duxbury [aut, cre, cph]
Maintainer: Scott Duxbury <duxbury@email.unc.edu>
Diff between ergMargins versions 0.1.2 dated 2021-02-23 and 0.1.3 dated 2021-06-30
DESCRIPTION | 11 ++++----- MD5 | 12 +++++----- R/edgeprob2.R.R | 38 +++++++++++++++++++------------ R/ergmAME.R.R | 42 +++++++++++++++++++---------------- R/ergmMEM.R.R | 44 ++++++++++++++++++++----------------- R/tergmprepare.R.R | 63 ++++++++++++++++++++++++++++++++++++++++++++++------- man/ergm.mma.Rd | 3 -- 7 files changed, 137 insertions(+), 76 deletions(-)
Title: Clustering on the Torus by Conformal Prediction
Description: Provides various tools of for clustering multivariate angular
data on the torus. The package provides angular
adaptations of usual clustering methods such as the k-means
clustering, pairwise angular distances, which can be used as an
input for distance-based clustering algorithms, and implements
clustering based on the conformal prediction framework. Options
for the conformal scores include scores based on a kernel density
estimate, multivariate von Mises mixtures, and naive k-means clusters.
Moreover, the package provides some basic data handling tools for
angular data.
Author: Sungkyu Jung [aut, cph],
Seungki Hong [aut, cre],
Kiho Park [ctb],
Byungwon Kim [ctb]
Maintainer: Seungki Hong <skgaboja@snu.ac.kr>
Diff between ClusTorus versions 0.0.1 dated 2021-02-10 and 0.1.1 dated 2021-06-30
ClusTorus-0.0.1/ClusTorus/R/cluster.assign.number.R |only ClusTorus-0.0.1/ClusTorus/man/cluster.assign.number.Rd |only ClusTorus-0.1.1/ClusTorus/DESCRIPTION | 8 ClusTorus-0.1.1/ClusTorus/MD5 | 54 +- ClusTorus-0.1.1/ClusTorus/NAMESPACE | 4 ClusTorus-0.1.1/ClusTorus/R/cluster.assign.torus.R | 12 ClusTorus-0.1.1/ClusTorus/R/conn.comp.ellipse.R | 4 ClusTorus-0.1.1/ClusTorus/R/data.R | 48 + ClusTorus-0.1.1/ClusTorus/R/hyperparam.J.R |only ClusTorus-0.1.1/ClusTorus/R/hyperparam.alpha.R |only ClusTorus-0.1.1/ClusTorus/R/hyperparam.torus.R |only ClusTorus-0.1.1/ClusTorus/R/icp.torus.R | 14 ClusTorus-0.1.1/ClusTorus/R/kmeans.kspheres.R | 34 - ClusTorus-0.1.1/ClusTorus/R/norm.appr.param.R | 2 ClusTorus-0.1.1/ClusTorus/R/plot.ellipsoids.R | 60 +- ClusTorus-0.1.1/ClusTorus/build/partial.rdb |binary ClusTorus-0.1.1/ClusTorus/build/vignette.rds |binary ClusTorus-0.1.1/ClusTorus/data/toydata1.rda |only ClusTorus-0.1.1/ClusTorus/data/toydata2.rda |only ClusTorus-0.1.1/ClusTorus/inst/doc/ClusTorus.R | 7 ClusTorus-0.1.1/ClusTorus/inst/doc/ClusTorus.Rmd | 9 ClusTorus-0.1.1/ClusTorus/inst/doc/ClusTorus.html | 432 +++++------------ ClusTorus-0.1.1/ClusTorus/man/ILE.Rd | 4 ClusTorus-0.1.1/ClusTorus/man/SARS_CoV_2.Rd | 4 ClusTorus-0.1.1/ClusTorus/man/cluster.assign.torus.Rd | 9 ClusTorus-0.1.1/ClusTorus/man/hyperparam.J.Rd |only ClusTorus-0.1.1/ClusTorus/man/hyperparam.alpha.Rd |only ClusTorus-0.1.1/ClusTorus/man/hyperparam.torus.Rd |only ClusTorus-0.1.1/ClusTorus/man/icp.torus.eval.Rd | 2 ClusTorus-0.1.1/ClusTorus/man/icp.torus.score.Rd | 6 ClusTorus-0.1.1/ClusTorus/man/kmeans.kspheres.Rd | 14 ClusTorus-0.1.1/ClusTorus/man/toydata1.Rd |only ClusTorus-0.1.1/ClusTorus/man/toydata2.Rd |only ClusTorus-0.1.1/ClusTorus/vignettes/ClusTorus.Rmd | 9 34 files changed, 319 insertions(+), 417 deletions(-)
Title: Intrinsic Peak Analysis for LC-MS Data
Description: A sophisticated pipeline for processing
high-resolution LC/MS data to extract signals of organic compounds. The
package performs isotope pairing, peak detection, alignment, RT correction,
gap filling, peak annotation and visualization of extracted ion chromatograms and total ion chromatograms.
Author: Sadjad Fakouri-Baygi [cre, aut]
(<https://orcid.org/0000-0002-6864-6911>),
Dinesh Barupal [aut] (<https://orcid.org/0000-0002-9954-8628>)
Maintainer: Sadjad Fakouri-Baygi <sadjad.fakouri-baygi@mssm.edu>
Diff between IDSL.IPA versions 1.1 dated 2021-05-28 and 1.2 dated 2021-06-30
DESCRIPTION | 8 MD5 | 26 +- R/EIC_plotter.R | 266 ++++++++++----------- R/IPA_GapFiller.R | 34 -- R/IPA_PeakAlignment.R | 1 R/IPA_PeakAnalyzer.R | 17 - R/IPA_PeaklistAnnotation.R | 27 -- R/IPA_TargetedAnalysis.R | 535 +++++++++++++++++++++----------------------- R/MS_deconvoluter.R |only R/XIC.R | 34 +- R/chromatography_analysis.R | 441 ++++++++++++++++++------------------ R/primary_peak_analyzer.R | 2 man/MS_deconvoluter.Rd |only man/XIC.Rd | 56 ++-- man/der_5points_stencil.Rd | 2 15 files changed, 709 insertions(+), 740 deletions(-)
Title: Functions for 'Ecdat'
Description: Functions and vignettes to update
data sets in 'Ecdat' and to create, manipulate,
plot, and analyze those and similar data sets.
Author: Spencer Graves <spencer.graves@effectivedefense.org>
Maintainer: Spencer Graves <spencer.graves@effectivedefense.org>
Diff between Ecfun versions 0.2-4 dated 2020-10-27 and 0.2-5 dated 2021-06-30
Ecfun-0.2-4/Ecfun/R/UShouse.senate.R |only Ecfun-0.2-4/Ecfun/R/USsenateClass.R |only Ecfun-0.2-4/Ecfun/R/mergeUShouse.senate.R |only Ecfun-0.2-4/Ecfun/R/readCookPVI.R |only Ecfun-0.2-4/Ecfun/R/readCookPVI0.R |only Ecfun-0.2-4/Ecfun/R/readFinancialCrisisFiles.R |only Ecfun-0.2-4/Ecfun/R/readUShouse.R |only Ecfun-0.2-4/Ecfun/R/readUSsenate.R |only Ecfun-0.2-4/Ecfun/R/readUSstateAbbreviations.R |only Ecfun-0.2-4/Ecfun/man/UShouse.senate.Rd |only Ecfun-0.2-4/Ecfun/man/USsenateClass.Rd |only Ecfun-0.2-4/Ecfun/man/mergeUShouse.senate.Rd |only Ecfun-0.2-4/Ecfun/man/readCookPVI.Rd |only Ecfun-0.2-4/Ecfun/man/readFinancialCrisisFiles.Rd |only Ecfun-0.2-4/Ecfun/man/readUShouse.Rd |only Ecfun-0.2-4/Ecfun/man/readUSsenate.Rd |only Ecfun-0.2-4/Ecfun/man/readUSstateAbbreviations.Rd |only Ecfun-0.2-5/Ecfun/DESCRIPTION | 13 Ecfun-0.2-5/Ecfun/MD5 | 43 - Ecfun-0.2-5/Ecfun/NAMESPACE | 7 Ecfun-0.2-5/Ecfun/NEWS.md | 5 Ecfun-0.2-5/Ecfun/R/compareOverlap.R |only Ecfun-0.2-5/Ecfun/R/deletedFunctions.R |only Ecfun-0.2-5/Ecfun/R/pmatchIC.R |only Ecfun-0.2-5/Ecfun/README.md | 11 Ecfun-0.2-5/Ecfun/build/vignette.rds |binary Ecfun-0.2-5/Ecfun/inst/WORDLIST | 1 Ecfun-0.2-5/Ecfun/inst/doc/UpdatingUSGDPpresidents.html | 259 --------- Ecfun-0.2-5/Ecfun/inst/doc/nuclearArmageddon.html | 355 ++----------- Ecfun-0.2-5/Ecfun/inst/doc/update_nuclearWeaponStates.html | 261 --------- Ecfun-0.2-5/Ecfun/man/compareOverlap.Rd |only Ecfun-0.2-5/Ecfun/man/deletedFunctions.Rd |only Ecfun-0.2-5/Ecfun/man/pmatch2.Rd | 9 Ecfun-0.2-5/Ecfun/man/pmatchIC.Rd |only 34 files changed, 176 insertions(+), 788 deletions(-)
Title: Enhancing the 'parallel' Package
Description: Utility functions that enhance the 'parallel' package and support the built-in parallel backends of the 'future' package. For example, availableCores() gives the number of CPU cores available to your R process as given by the operating system, 'cgroups' and Linux containers, R options, and environment variables, including those set by job schedulers on high-performance compute clusters. If none is set, it will fall back to parallel::detectCores(). Another example is makeClusterPSOCK(), which is backward compatible with parallel::makePSOCKcluster() while doing a better job in setting up remote cluster workers without the need for configuring the firewall to do port-forwarding to your local computer.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between parallelly versions 1.26.0 dated 2021-06-09 and 1.26.1 dated 2021-06-30
DESCRIPTION | 6 ++-- MD5 | 21 +++++++------- NEWS | 35 +++++++++++++++++++++++- R/availableCores.R | 15 +++++++++- R/makeClusterPSOCK.R | 6 ++++ R/options.R | 2 - R/parallelly_disable_parallel_setup_if_needed.R |only R/zzz.R | 4 ++ README.md | 10 ++++-- inst/WORDLIST | 5 ++- man/parallelly.options.Rd | 2 - tests/as.cluster.R | 4 +- 12 files changed, 86 insertions(+), 24 deletions(-)
Title: Tools for 'iNZight'
Description: Provides a collection of wrapper functions for common variable and dataset manipulation workflows primarily used by 'iNZight', a graphical user interface providing easy exploration and visualisation of data for students of statistics, available in both desktop and online versions. Additionally, many of the functions return the 'tidyverse' code used to obtain the result in an effort to bridge the gap between GUI and coding.
Author: Tom Elliott [aut, cre] (<https://orcid.org/0000-0002-7815-6318>),
Christoph Knopf [ctb],
Akshay Gupta [ctb],
Owen Jin [aut] (Tidyverse variable/data manipulation functions),
Lushi Cai [ctb],
Yiwen He [aut] (Dates/times and dataset manipulation),
Daniel Barnett [aut] (Data validation)
Maintainer: Tom Elliott <tom.elliott@auckland.ac.nz>
Diff between iNZightTools versions 1.11.0 dated 2021-04-23 and 1.11.1 dated 2021-06-30
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/aggregate_data.R | 7 ++++++- tests/testthat/test_aggregateData.R | 8 +++++++- 4 files changed, 19 insertions(+), 8 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-06-02 0.2.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-05-19 1.6.3
Title: Vehicular Emissions Inventories
Description: Elaboration of vehicular emissions inventories,
consisting in four stages, pre-processing activity data, preparing
emissions factors, estimating the emissions and post-processing of emissions
in maps and databases. More details in Ibarra-Espinosa et al (2018) <doi:10.5194/gmd-11-2209-2018>.
Before using VEIN you need to know the vehicular composition of your study area, in other words,
the combination of of type of vehicles, size and fuel of the fleet. Then, it is recommended to
start with the project to download a template to create a structure of directories and scripts.
Author: Sergio Ibarra-Espinosa [aut, cre, wdc]
(<https://orcid.org/0000-0002-3162-1905>)
Maintainer: Sergio Ibarra-Espinosa <sergio.ibarra@usp.br>
Diff between vein versions 0.9.2 dated 2021-06-22 and 0.9.3 dated 2021-06-30
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- NEWS.md | 3 +++ R/emis_chem2.R | 21 +++------------------ R/get_project.R | 2 +- R/sysdata.rda |binary inst/doc/basics.html | 4 ++-- man/emis_chem2.Rd | 2 +- tests/testthat/test-split_emis.R | 4 ++-- 9 files changed, 25 insertions(+), 37 deletions(-)
Title: Pedigree, Genetic Merit and Phenotype Simulation
Description: Simulate pedigree, genetic merits and phenotypes with random/non-random matings followed by random/non-random selection with different intensities and patterns in males and females.
Bijma, P. & Rutten, M. (2002) <https://www.wur.nl/en/Research-Results/Chair-groups/Animal-Sciences/Animal-Breeding-and-Genomics-Group/Research/Software.htm>.
Author: Mohammad Ali Nilforooshan [aut, cre]
(<https://orcid.org/0000-0003-0339-5442>)
Maintainer: Mohammad Ali Nilforooshan <m.a.nilforooshan@gmail.com>
Diff between pedSimulate versions 1.0.0 dated 2021-06-17 and 1.0.1 dated 2021-06-30
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ R/simulatePed.R | 2 +- 4 files changed, 11 insertions(+), 7 deletions(-)