Title: Power in a Group Sequential Design
Description: Tools for the evaluation of interim analysis plans for sequentially
monitored trials on a survival endpoint; tools to construct efficacy and
futility boundaries, for deriving power of a sequential design at a specified
alternative, template for evaluating the performance of candidate plans at a
set of time varying alternatives. See Izmirlian, G. (2014) <doi:10.4310/SII.2014.v7.n1.a4>.
Author: Grant Izmirlian [aut, cre]
Maintainer: Grant Izmirlian <izmirlig@mail.nih.gov>
Diff between PwrGSD versions 2.3.7 dated 2024-07-26 and 2.3.8 dated 2024-10-10
PwrGSD-2.3.7/PwrGSD/inst/doc/PwrGSD-manual.pdf |only PwrGSD-2.3.7/PwrGSD/inst/log |only PwrGSD-2.3.8/PwrGSD/DESCRIPTION | 12 - PwrGSD-2.3.8/PwrGSD/MD5 | 37 ++-- PwrGSD-2.3.8/PwrGSD/inst/doc/GrpSeqBnds-vignette.pdf |binary PwrGSD-2.3.8/PwrGSD/inst/doc/PwrGSD-vignette.pdf |binary PwrGSD-2.3.8/PwrGSD/inst/doc/cpd-PwrGSD-vignette.pdf |binary PwrGSD-2.3.8/PwrGSD/src/AsyPwrGSD.c | 57 +++--- PwrGSD-2.3.8/PwrGSD/src/PwrGSD_mem.h |only PwrGSD-2.3.8/PwrGSD/src/SimPwrGSD.c | 155 +++++++++---------- PwrGSD-2.3.8/PwrGSD/src/WtdLogRank.c | 7 PwrGSD-2.3.8/PwrGSD/src/agghaz.c | 3 PwrGSD-2.3.8/PwrGSD/src/cpblocked.c | 8 PwrGSD-2.3.8/PwrGSD/src/drift.c | 49 +++--- PwrGSD-2.3.8/PwrGSD/src/driftfu.c | 25 +-- PwrGSD-2.3.8/PwrGSD/src/grpseqbnds.c | 7 PwrGSD-2.3.8/PwrGSD/src/htilde.c | 12 - PwrGSD-2.3.8/PwrGSD/src/intsurvdiff.c | 12 - PwrGSD-2.3.8/PwrGSD/src/mysurvfit.c | 4 PwrGSD-2.3.8/PwrGSD/src/projectend.c | 30 +-- PwrGSD-2.3.8/PwrGSD/src/rao-blackwell.c | 13 - 21 files changed, 226 insertions(+), 205 deletions(-)
Title: High-Dimensional Aggregate Density Forecasts
Description: Provides a forecasting method that efficiently maps vast
numbers of (scalar-valued) signals into an aggregate density forecast
in a time-varying and computationally fast manner. The method proceeds
in two steps: First, it transforms a predictive signal into a density
forecast and, second, it combines the resulting candidate density
forecasts into an ultimate aggregate density forecast. For a detailed
explanation of the method, please refer to Adaemmer et al. (2023)
<doi:10.2139/ssrn.4342487>.
Author: Sven Lehmann [aut, cre, cph],
Philipp Adaemmer [aut],
Rainer Schuessler [aut]
Maintainer: Sven Lehmann <sven.lehmann@uni-rostock.de>
Diff between hdflex versions 0.2.1 dated 2024-02-29 and 0.3.0 dated 2024-10-10
hdflex-0.2.1/hdflex/R/summary_stsc.R |only hdflex-0.2.1/hdflex/data/benchmark_ar2.rda |only hdflex-0.2.1/hdflex/man/benchmark_ar2.Rd |only hdflex-0.2.1/hdflex/man/summary_stsc.Rd |only hdflex-0.2.1/hdflex/tests/testthat/test-summary_stsc.R |only hdflex-0.3.0/hdflex/DESCRIPTION | 30 hdflex-0.3.0/hdflex/MD5 | 62 hdflex-0.3.0/hdflex/NAMESPACE | 13 hdflex-0.3.0/hdflex/NEWS.md | 10 hdflex-0.3.0/hdflex/R/ClassMethods.R |only hdflex-0.3.0/hdflex/R/RcppExports.R | 88 hdflex-0.3.0/hdflex/R/data-documentation.R | 122 - hdflex-0.3.0/hdflex/R/dsc.R | 511 ++--- hdflex-0.3.0/hdflex/R/stsc.R | 939 +++++---- hdflex-0.3.0/hdflex/R/tvc.R | 792 +++----- hdflex-0.3.0/hdflex/R/zzz.R |only hdflex-0.3.0/hdflex/README.md | 611 +++--- hdflex-0.3.0/hdflex/build |only hdflex-0.3.0/hdflex/data/inflation_data.rda |binary hdflex-0.3.0/hdflex/man/dsc.Rd | 207 +- hdflex-0.3.0/hdflex/man/hdflex.Rd | 2 hdflex-0.3.0/hdflex/man/inflation_data.Rd | 97 - hdflex-0.3.0/hdflex/man/stsc.Rd | 494 +++-- hdflex-0.3.0/hdflex/man/summary.dsc_obj.Rd |only hdflex-0.3.0/hdflex/man/summary.stsc_obj.Rd |only hdflex-0.3.0/hdflex/man/tvc.Rd | 394 ++-- hdflex-0.3.0/hdflex/src/Makevars | 16 hdflex-0.3.0/hdflex/src/Makevars.win | 14 hdflex-0.3.0/hdflex/src/RcppExports.cpp | 386 ---- hdflex-0.3.0/hdflex/src/dsc.cpp | 746 +++++-- hdflex-0.3.0/hdflex/src/init.c | 53 hdflex-0.3.0/hdflex/src/stsc.cpp | 1324 +++++++------ hdflex-0.3.0/hdflex/src/stsc_parallel.cpp |only hdflex-0.3.0/hdflex/src/tvc.cpp | 469 +++- hdflex-0.3.0/hdflex/tests/testthat/test-dsc.R | 481 +++-- hdflex-0.3.0/hdflex/tests/testthat/test-stsc.R | 1623 ++++++++++------- hdflex-0.3.0/hdflex/tests/testthat/test-summary.R |only hdflex-0.3.0/hdflex/tests/testthat/test-tvc.R | 484 ++--- 38 files changed, 5537 insertions(+), 4431 deletions(-)
Title: Cross-Entropy Clustering
Description: Splits data into Gaussian type clusters using the Cross-Entropy
Clustering ('CEC') method. This method allows for the simultaneous use of
various types of Gaussian mixture models, for performing the reduction of
unnecessary clusters, and for discovering new clusters by splitting them.
'CEC' is based on the work of Spurek, P. and Tabor, J. (2014)
<doi:10.1016/j.patcog.2014.03.006>.
Author: Kamieniecki Konrad [aut],
Spurek Przemyslaw [ctb],
Simon Garnier [cre, ctb]
Maintainer: Simon Garnier <garnier@njit.edu>
Diff between CEC versions 0.11.1 dated 2024-01-08 and 0.11.2 dated 2024-10-10
DESCRIPTION | 10 +++--- MD5 | 30 ++++++++++---------- NEWS.md | 12 ++++++++ R/CEC-package.R | 73 ++------------------------------------------------ R/cec.R | 14 ++++----- R/utils.R | 69 +++++++++++++++++++++++++++++++++++++++++++++++ man/CEC-package.Rd | 2 + man/Tset.Rd | 2 - man/cec.Rd | 8 ++--- man/fourGaussians.Rd | 2 - man/mixShapes.Rd | 2 - man/threeGaussians.Rd | 2 - src/cec_r.cpp | 12 ++++---- src/cov.h | 2 - src/r_result.cpp | 16 +++++----- src/r_utils.h | 16 +++++----- 16 files changed, 145 insertions(+), 127 deletions(-)
Title: Visualization of Clonal Expansion for Single Cell Immune
Profiles
Description: Visualize clonal expansion via circle-packing. 'APackOfTheClones' extends 'scRepertoire' to produce a publication-ready visualization of clonal expansion at a single cell resolution, by representing expanded clones as differently sized circles. The method was originally implemented by Murray Christian and Ben Murrell in the following immunology study: Ma et al. (2021) <doi:10.1126/sciimmunol.abg6356>.
Author: Qile Yang [cre, aut, cph]
Maintainer: Qile Yang <qile.yang@berkeley.edu>
Diff between APackOfTheClones versions 1.2.0 dated 2024-04-16 and 1.2.1 dated 2024-10-10
DESCRIPTION | 23 MD5 | 163 +- NAMESPACE | 4 R/APOTCPlot.R | 6 R/APackOfTheClones-package.R | 3 R/AdjustAPOTC.R | 4 R/ApotcClonalNetwork.R | 22 R/ApotcData.R | 12 R/ApotcIndexing.R | 15 R/Main_algo.R | 68 R/Repulsion.R | 3 R/RunAPOTC.R | 23 R/clusters.R | 97 + R/colors.R | 4 R/get_clone_sizes.R | 14 R/insert_legend.R | 22 R/plot_API.R | 4 R/seurat_command.R | 2 R/showCloneHighlight.R | 18 R/utils.R | 39 R/vizAPOTC.R | 17 R/zzz.R | 7 build/partial.rdb |binary build/vignette.rds |binary data/combined_pbmc.rda |binary inst/CITATION | 5 inst/WORDLIST | 11 inst/doc/APackOfTheClones-install.Rmd | 2 inst/doc/APackOfTheClones-install.html | 157 +- inst/doc/APackOfTheClones-runs.R | 4 inst/doc/APackOfTheClones-runs.Rmd | 22 inst/doc/APackOfTheClones-runs.html | 427 ++--- inst/doc/APackOfTheClones-shared.R | 2 inst/doc/APackOfTheClones-shared.Rmd | 4 inst/doc/APackOfTheClones-shared.html | 297 +-- inst/doc/APackOfTheClones-utils.R | 2 inst/doc/APackOfTheClones-utils.Rmd | 6 inst/doc/APackOfTheClones-utils.html | 257 +-- inst/doc/APackOfTheClones.Rmd | 10 inst/doc/APackOfTheClones.html | 333 ++-- man/APOTCPlot.Rd | 8 man/APackOfTheClones-package.Rd | 2 man/AdjustAPOTC.Rd | 6 man/RunAPOTC.Rd | 11 man/countCloneSizes.Rd | 2 man/getLastApotcDataId.Rd | 4 man/getSharedClones.Rd | 4 man/overlayLegend.Rd | 10 man/removeLegend.Rd | 4 man/renameApotcRun.Rd | 2 man/showCloneHighlight.Rd | 12 man/vizAPOTC.Rd | 10 src/APOTCPlotHelpers.cpp | 2 src/Circle.h | 2 src/CirclePacker.h | 14 src/CloneLinkHelpers.cpp | 2 src/ClusterList.h | 2 src/dataConversion.h | 2 src/math.h | 11 src/reduction_coords.cpp | 2 tests/testthat/_snaps/ApotcClonalNetwork/default-shared-clone-line-link-plot.svg | 164 +- tests/testthat/_snaps/noscript-defaultApotcPlot/default-apotcplot.svg | 766 +++++----- tests/testthat/_snaps/showCloneHighlight |only tests/testthat/_snaps/vizAPOTC/sample19.svg | 140 - tests/testthat/helper-vdiffr.R | 14 tests/testthat/test-ApotcClonalNetwork.R | 2 tests/testthat/test-ApotcData.R | 6 tests/testthat/test-Main_algo.R | 4 tests/testthat/test-Repulsion.R | 30 tests/testthat/test-clusters.R | 10 tests/testthat/test-colors.R | 16 tests/testthat/test-noscript-defaultApotcPlot.R | 102 - tests/testthat/test-showCloneHighlight.R | 77 - tests/testthat/test-vizAPOTC.R | 7 tests/testthat/testdata/combined_pbmc/expected_clusterlists.rds |binary tests/testthat/testdata/showCloneHighlight/cl_5_9_highlighted_data.rds |binary tests/testthat/testdata/v0/cluster_lists.R | 45 vignettes/APackOfTheClones-install.Rmd | 2 vignettes/APackOfTheClones-runs.Rmd | 22 vignettes/APackOfTheClones-shared.Rmd | 4 vignettes/APackOfTheClones-utils.Rmd | 6 vignettes/APackOfTheClones.Rmd | 10 vignettes/archive/v0-main.Rmd | 12 83 files changed, 1880 insertions(+), 1780 deletions(-)
More information about APackOfTheClones at CRAN
Permanent link
Title: Operations to Ease Data Analyses Specific to Nigeria
Description: A set of convenience functions as well as geographical/political
data about Nigeria, aimed at simplifying work with data and information that
are specific to the country.
Author: Victor Ordu [aut, cre] ,
Laura DeCicco [ctb],
Emily Riederer [rev],
Margaret Siple [rev],
Cagri Alican [rev]
Maintainer: Victor Ordu <victorordu@outlook.com>
Diff between naijR versions 0.6.0 dated 2023-08-08 and 0.6.1 dated 2024-10-10
naijR-0.6.0/naijR/R/asreg.R |only naijR-0.6.0/naijR/R/isreg.R |only naijR-0.6.0/naijR/man/coerce.Rd |only naijR-0.6.0/naijR/man/fix_region_manual.Rd |only naijR-0.6.0/naijR/man/is_lga.Rd |only naijR-0.6.0/naijR/man/is_state.Rd |only naijR-0.6.1/naijR/DESCRIPTION | 50 naijR-0.6.1/naijR/MD5 | 73 - naijR-0.6.1/naijR/NAMESPACE | 29 naijR-0.6.1/naijR/NEWS.md | 5 naijR-0.6.1/naijR/R/disambi.R |only naijR-0.6.1/naijR/R/fct.R | 6 naijR-0.6.1/naijR/R/fixmob.R | 20 naijR-0.6.1/naijR/R/fixreg.R | 339 ------ naijR-0.6.1/naijR/R/fixregint.R |only naijR-0.6.1/naijR/R/helpers.R | 40 naijR-0.6.1/naijR/R/map.R | 808 +-------------- naijR-0.6.1/naijR/R/mapint.R |only naijR-0.6.1/naijR/R/naijR-package.R | 11 naijR-0.6.1/naijR/R/regions.R | 586 +++++----- naijR-0.6.1/naijR/R/regionsint.R |only naijR-0.6.1/naijR/R/zzz.R | 8 naijR-0.6.1/naijR/README.md | 82 - naijR-0.6.1/naijR/build/vignette.rds |binary naijR-0.6.1/naijR/inst/doc/interactive.R | 8 naijR-0.6.1/naijR/inst/doc/interactive.html | 4 naijR-0.6.1/naijR/inst/doc/nigeria-maps.R | 14 naijR-0.6.1/naijR/inst/doc/nigeria-maps.Rmd | 14 naijR-0.6.1/naijR/inst/doc/nigeria-maps.html | 68 - naijR-0.6.1/naijR/man/disambiguate_lga.Rd | 78 - naijR-0.6.1/naijR/man/fix_mobile.Rd | 4 naijR-0.6.1/naijR/man/fix_region.Rd | 30 naijR-0.6.1/naijR/man/lgas.Rd | 73 + naijR-0.6.1/naijR/man/map_ng.Rd | 25 naijR-0.6.1/naijR/man/naijR.Rd | 7 naijR-0.6.1/naijR/man/states.Rd | 95 + naijR-0.6.1/naijR/tests/testthat/data/state-capitals.rds |only naijR-0.6.1/naijR/tests/testthat/test-asreg.R | 23 naijR-0.6.1/naijR/tests/testthat/test-fixreg.R | 74 - naijR-0.6.1/naijR/tests/testthat/test-isreg.R | 1 naijR-0.6.1/naijR/tests/testthat/test-map.R | 244 ++-- naijR-0.6.1/naijR/tests/testthat/test-regions.R | 123 +- naijR-0.6.1/naijR/vignettes/nigeria-maps.Rmd | 14 43 files changed, 1162 insertions(+), 1794 deletions(-)
Title: A Collection of Tools for Network Analysis
Description: Provides a collection of network analytic (convenience) functions which are missing in other standard packages. This includes triad census with attributes <doi:10.1016/j.socnet.2019.04.003>, core-periphery models <doi:10.1016/S0378-8733(99)00019-2>, and several graph generators. Most functions are build upon 'igraph'.
Author: David Schoch [aut, cre]
Maintainer: David Schoch <david@schochastics.net>
Diff between netUtils versions 0.8.2 dated 2023-06-29 and 0.8.3 dated 2024-10-10
netUtils-0.8.2/netUtils/man/figures/netUtils.xcf |only netUtils-0.8.2/netUtils/man/graph_to_sage.Rd |only netUtils-0.8.2/netUtils/tests/testthat/test-lfr.R |only netUtils-0.8.3/netUtils/DESCRIPTION | 13 netUtils-0.8.3/netUtils/MD5 | 89 +-- netUtils-0.8.3/netUtils/NAMESPACE | 1 netUtils-0.8.3/netUtils/NEWS.md | 5 netUtils-0.8.3/netUtils/R/core_periphery.R | 283 ++-------- netUtils-0.8.3/netUtils/R/dyad_census_attr.R | 110 +-- netUtils-0.8.3/netUtils/R/fast_cliques.R | 89 +-- netUtils-0.8.3/netUtils/R/graph_products.R | 58 +- netUtils-0.8.3/netUtils/R/graph_structures.R | 64 +- netUtils-0.8.3/netUtils/R/graphs.R | 208 +++---- netUtils-0.8.3/netUtils/R/lfr_benchmark.R | 141 ++-- netUtils-0.8.3/netUtils/R/print_igraph.R | 184 +++--- netUtils-0.8.3/netUtils/R/qap.R | 22 netUtils-0.8.3/netUtils/R/reciprocity.R | 30 - netUtils-0.8.3/netUtils/R/sample_kcores.R | 159 ++--- netUtils-0.8.3/netUtils/R/sample_pa_homophilic.R | 81 +- netUtils-0.8.3/netUtils/R/structural_equivalence.R | 38 - netUtils-0.8.3/netUtils/R/triad_census_attr.R | 116 ++-- netUtils-0.8.3/netUtils/R/utils.R | 7 netUtils-0.8.3/netUtils/README.md | 2 netUtils-0.8.3/netUtils/man/as_adj_weighted.Rd | 2 netUtils-0.8.3/netUtils/man/bipartite_from_data_frame.Rd | 4 netUtils-0.8.3/netUtils/man/clique_vertex_mat.Rd | 2 netUtils-0.8.3/netUtils/man/core_periphery.Rd | 4 netUtils-0.8.3/netUtils/man/dyad_census_attr.Rd | 6 netUtils-0.8.3/netUtils/man/graph_cartesian.Rd | 2 netUtils-0.8.3/netUtils/man/graph_direct.Rd | 2 netUtils-0.8.3/netUtils/man/graph_from_multi_edgelist.Rd | 8 netUtils-0.8.3/netUtils/man/graph_kpartite.Rd | 4 netUtils-0.8.3/netUtils/man/reciprocity_cor.Rd | 2 netUtils-0.8.3/netUtils/man/sample_coreseq.Rd | 4 netUtils-0.8.3/netUtils/man/sample_lfr.Rd | 18 netUtils-0.8.3/netUtils/man/split_graph.Rd | 2 netUtils-0.8.3/netUtils/man/triad_census_attr.Rd | 6 netUtils-0.8.3/netUtils/tests/testthat/test-core_periphery.R | 16 netUtils-0.8.3/netUtils/tests/testthat/test-dyad_census_attr.R | 22 netUtils-0.8.3/netUtils/tests/testthat/test-graph_products.R | 14 netUtils-0.8.3/netUtils/tests/testthat/test-graph_structures.R | 26 netUtils-0.8.3/netUtils/tests/testthat/test-graphs.R | 40 - netUtils-0.8.3/netUtils/tests/testthat/test-lfr_benchmark.R |only netUtils-0.8.3/netUtils/tests/testthat/test-reciprocity.R | 16 netUtils-0.8.3/netUtils/tests/testthat/test-sample_kcores.R | 22 netUtils-0.8.3/netUtils/tests/testthat/test-sample_pa_homophilic.R |only netUtils-0.8.3/netUtils/tests/testthat/test-structural_equivalence.R | 10 netUtils-0.8.3/netUtils/tests/testthat/test-triad_census_attr.R | 22 48 files changed, 913 insertions(+), 1041 deletions(-)
Title: Linear and Non-Linear AUC for Discounting Data
Description: Area under the curve (AUC; Myerson et al., 2001) <doi:10.1901/jeab.2001.76-235>
is a popular measure used in discounting research. Although the calculation of
AUC is standardized, there are differences in AUC based on some assumptions.
For example, Myerson et al. (2001) <doi:10.1901/jeab.2001.76-235>
assumed that (with delay discounting data) a researcher would impute an
indifference point at zero delay equal to the value of the larger, later outcome.
However, this practice is not clearly followed. This imputed zero-delay indifference
point plays an important role in log and ordinal versions of AUC.
Ordinal and log versions of AUC are described by Borges et al. (2016)<doi:10.1002/jeab.219>.
The package can calculate all three versions of AUC [and includes a new version: IHS(AUC)],
impute indifference points when x = 0, calculate ordinal AUC in the case of Halton
sampling of x-values, and account for probability discounting AUC.
Author: Jonathan E. Friedel [aut, cre]
Maintainer: Jonathan E. Friedel <jfriedel@georgiasouthern.edu>
Diff between discAUC versions 1.0.0 dated 2023-03-17 and 1.0.3 dated 2024-10-10
DESCRIPTION | 10 MD5 | 18 R/log_AUC.R | 13 README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/discAUC_vignette.R | 2 inst/doc/discAUC_vignette.html | 1162 ++++++++++++++++++++--------------------- man/prep_log_AUC.Rd | 4 tests/testthat/test-log_AUC.R | 210 ++++--- 10 files changed, 744 insertions(+), 677 deletions(-)
More information about Certara.VPCResults at CRAN
Permanent link
Title: Cite 'R' Packages on the Fly in 'R Markdown' and 'Quarto'
Description: References and cites 'R' and 'R' packages on the fly in 'R
Markdown' and 'Quarto'. 'pakret' provides a minimalistic API that
generates preformatted citations of 'R' and 'R' packages, and adds
their reference to a '.bib' file directly from within your document.
Author: Arnaud Gallou [aut, cre, cph]
Maintainer: Arnaud Gallou <arangacas@gmail.com>
Diff between pakret versions 0.2.0 dated 2024-10-03 and 0.2.1 dated 2024-10-10
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 6 ++++++ R/pakret.R | 2 +- R/pkrt-list.R | 2 +- R/utils-local.R | 23 +++++++++++++---------- tests/testthat/test-pkrt-list.R | 9 +++++---- tests/testthat/test-pkrt.R | 22 ++++++++++++++++++++++ 8 files changed, 58 insertions(+), 26 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-07-03 0.2.3
2024-04-15 0.2.2
2023-11-30 0.2.1
2023-11-21 0.1.2
Title: Quantum Walk-Based Data Analysis and Prediction
Description: The modeling and prediction of graph-associated time series(GATS) based on continuous time quantum walk. This software is mainly used for feature extraction, modeling, prediction and result evaluation of GATS, including continuous time quantum walk simulation, feature selection, regression analysis, time series prediction, and series fit calculation. A paper is attached to the package for reference.
Author: Binghuang Pan [aut, cre],
Zhaoyuan Yu [aut],
Xu Hu [ctb],
Yuhao Teng [ctb]
Maintainer: Binghuang Pan <bright1up@163.com>
Diff between QWDAP versions 1.1.18 dated 2024-04-19 and 1.1.20 dated 2024-10-10
DESCRIPTION | 10 +++++----- MD5 | 3 ++- inst |only 3 files changed, 7 insertions(+), 6 deletions(-)
Title: Graphical Independence Networks
Description: Probability propagation in Bayesian networks, also known as graphical independence networks. Documentation
of the package is provided in vignettes included in the package and in
the paper by Højsgaard (2012, <doi:10.18637/jss.v046.i10>).
See 'citation("gRain")' for details.
Author: Soeren Hoejsgaard [aut, cre]
Maintainer: Soeren Hoejsgaard <sorenh@math.aau.dk>
Diff between gRain versions 1.4.3 dated 2024-10-08 and 1.4.4 dated 2024-10-10
DESCRIPTION | 6 - MD5 | 26 +++---- R/evidence.R | 84 +++++++++---------------- inst/doc/grain.pdf |binary man/grain_evidence.Rd | 6 - man/old_grain_evidence.Rd | 6 - vignettes/figures/grain-bn1-1.png |binary vignettes/figures/grain-bn2-1.png |binary vignettes/figures/grain-chest-LS-1.png |binary vignettes/figures/grain-unnamed-chunk-35-1.png |binary vignettes/figures/grain-unnamed-chunk-36-1.png |binary vignettes/figures/grain-unnamed-chunk-39-1.png |binary vignettes/figures/grain-unnamed-chunk-53-1.png |binary vignettes/grain.html | 18 ++--- 14 files changed, 58 insertions(+), 88 deletions(-)
More information about genetic.algo.optimizeR at CRAN
Permanent link
Title: Differentially Private Statistical Analysis and Machine Learning
Description: An implementation of common statistical analysis and models with
differential privacy (Dwork et al., 2006a) <doi:10.1007/11681878_14>
guarantees. The package contains, for example, functions providing
differentially private computations of mean, variance, median, histograms,
and contingency tables. It also implements some statistical models and
machine learning algorithms such as linear regression (Kifer et al., 2012)
<https://proceedings.mlr.press/v23/kifer12.html>
and SVM (Chaudhuri et al., 2011)
<https://jmlr.org/papers/v12/chaudhuri11a.html>. In addition, it implements
some popular randomization mechanisms, including
the Laplace mechanism (Dwork et al., 2006a)
<doi:10.1007/11681878_14>, Gaussian mechanism (Dwork et al., 2006b)
<doi:10.1007/11761679_29>, analytic Gaussian mechanism (Balle & Wang, 2018)
<https://proceedings.mlr.press/v80/balle18a.html>, and exponential mechanism
(McSherry & Talwar, 2007) <doi:10.1109/FOCS.2007.66>.
Author: Spencer Giddens [aut, cre],
Fang Liu [ctb]
Maintainer: Spencer Giddens <giddens2spencer@gmail.com>
Diff between DPpack versions 0.2.0 dated 2024-09-19 and 0.2.1 dated 2024-10-10
DPpack-0.2.0/DPpack/man/AnalyticGaussianMechanism.Rd |only DPpack-0.2.1/DPpack/DESCRIPTION | 6 DPpack-0.2.1/DPpack/MD5 | 31 +- DPpack-0.2.1/DPpack/NAMESPACE | 1 DPpack-0.2.1/DPpack/R/Mechanisms.R | 178 ++------------- DPpack-0.2.1/DPpack/R/Mechanisms_test.R | 220 +------------------ DPpack-0.2.1/DPpack/R/StatFunctions.R | 90 +++---- DPpack-0.2.1/DPpack/build/partial.rdb |binary DPpack-0.2.1/DPpack/man/GaussianMechanism.Rd | 19 + DPpack-0.2.1/DPpack/man/covDP.Rd | 5 DPpack-0.2.1/DPpack/man/histogramDP.Rd | 5 DPpack-0.2.1/DPpack/man/meanDP.Rd | 5 DPpack-0.2.1/DPpack/man/pooledCovDP.Rd | 5 DPpack-0.2.1/DPpack/man/pooledVarDP.Rd | 5 DPpack-0.2.1/DPpack/man/sdDP.Rd | 5 DPpack-0.2.1/DPpack/man/tableDP.Rd | 5 DPpack-0.2.1/DPpack/man/varDP.Rd | 5 17 files changed, 149 insertions(+), 436 deletions(-)
Title: Extension of `data.frame`
Description: Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group using no copies at all, list columns, friendly and fast character-separated-value read/write. Offers a natural and flexible syntax, for faster development.
Author: Tyson Barrett [aut, cre] ,
Matt Dowle [aut],
Arun Srinivasan [aut],
Jan Gorecki [aut],
Michael Chirico [aut] ,
Toby Hocking [aut] ,
Benjamin Schwendinger [aut] ,
Pasha Stetsenko [ctb],
Tom Short [ctb],
Steve Lianoglou [ctb],
Eduard Antonyan [ctb],
Ma [...truncated...]
Maintainer: Tyson Barrett <t.barrett88@gmail.com>
Diff between data.table versions 1.16.0 dated 2024-08-27 and 1.16.2 dated 2024-10-10
DESCRIPTION | 12 +- MD5 | 56 +++++---- NEWS.md | 26 ++++ R/data.table.R | 2 R/print.data.table.R | 12 +- configure | 11 + inst/doc/datatable-benchmarking.html | 2 inst/doc/datatable-faq.html | 2 inst/doc/datatable-importing.html | 2 inst/doc/datatable-intro.html | 2 inst/doc/datatable-keys-fast-subset.html | 8 - inst/doc/datatable-programming.html | 4 inst/doc/datatable-reference-semantics.html | 2 inst/doc/datatable-reshape.html | 2 inst/doc/datatable-sd-usage.html | 2 inst/doc/datatable-secondary-indices-and-auto-indexing.html | 12 +- inst/po/es |only inst/po/pt_BR |only inst/po/zh_CN/LC_MESSAGES/R-data.table.mo |binary inst/po/zh_CN/LC_MESSAGES/data.table.mo |binary inst/tests/tests.Rraw.bz2 |binary src/assign.c | 6 - src/bmerge.c | 6 - src/data.table.h | 21 +-- src/fifelse.c | 68 ++++++------ src/fread.c | 11 + src/fread.h | 2 src/init.c | 2 src/snprintf.c | 1 29 files changed, 163 insertions(+), 111 deletions(-)
Title: Choice Modeling in R
Description: Implements an MCMC algorithm to estimate a hierarchical multinomial logit model with a normal heterogeneity distribution. The algorithm uses a hybrid Gibbs Sampler with a random walk metropolis step for the MNL coefficients for each unit. Dependent variable may be discrete or continuous. Independent variables may be discrete or continuous with optional order constraints. Means of the distribution of heterogeneity can optionally be modeled as a linear function of unit characteristics variables.
Author: Ryan Sermas [aut],
John V Colias [ctb, cre],
Decision Analyst, Inc. [cph]
Maintainer: John V Colias <jcolias@decisionanalyst.com>
Diff between ChoiceModelR versions 1.3.0 dated 2022-05-30 and 1.3.1 dated 2024-10-10
DESCRIPTION | 6 +++--- INDEX |only MD5 | 21 +++++++++++---------- NEWS.md | 10 +++++++--- R/ChoiceModelR.R | 15 ++++++++++----- README.md | 2 +- data/datar.rda |binary data/sharedatar.rda |binary data/truebetas.rda |binary man/ChoiceModelR-package.Rd | 9 ++++----- man/choicemodelr.Rd | 7 +++---- tests/testthat/Rplots.pdf |binary 12 files changed, 39 insertions(+), 31 deletions(-)
Title: Functions to Set and Get the IEEE Rounding Mode
Description: A pair of functions for getting and setting the IEEE rounding
mode for floating point computations.
Author: Gianluca Amato [aut, cre]
Maintainer: Gianluca Amato <gianluca.amato@unich.it>
Diff between ieeeround versions 0.2-0 dated 2011-08-18 and 0.2-2 dated 2024-10-10
ChangeLog | 7 ++++++- DESCRIPTION | 25 +++++++++++++++---------- MD5 | 16 +++++++++------- NAMESPACE | 7 +++---- NEWS | 5 ++++- R/ieeeround.R | 4 ++-- README.md |only src/ieeeround.h | 2 +- src/init.c |only tests/Examples/ieeeround-Ex.Rout.save | 15 +++++++++------ 10 files changed, 49 insertions(+), 32 deletions(-)
Title: Single-Sample Mutation-Based Pathway Analysis
Description: A systematic bioinformatics tool to perform single-sample mutation-based pathway analysis by integrating somatic mutation data with the Protein-Protein Interaction (PPI) network. In this method, we use local and global weighted strategies to evaluate the effects of network genes from mutations according to the network topology and then calculate the mutation-based pathway enrichment score (ssMutPES) to reflect the accumulated effect of mutations of each pathway. Subsequently, the ssMutPES profiles are used for unsupervised spectral clustering to identify cancer subtypes.
Author: Junwei Han [aut, cre, cph],
Yalan He [aut],
Qian Wang [aut]
Maintainer: Junwei Han <hanjunwei1981@163.com>
Diff between ssMutPA versions 0.1.0 dated 2024-04-16 and 0.1.1 dated 2024-10-10
DESCRIPTION | 8 ++++---- MD5 | 26 +++++++++++++------------- R/plot.R | 2 +- inst/doc/ssMutPA.R | 2 +- inst/doc/ssMutPA.Rmd | 2 +- inst/doc/ssMutPA.html | 21 ++++++++------------- man/MRWR.Rd | 4 +--- man/Oncoplot.Rd | 4 ++-- man/dotplot.Rd | 4 ++-- man/get_RWR_ES.Rd | 4 +--- man/get_heatmap.Rd | 2 +- man/get_samp_class.Rd | 4 +--- man/mountain_plot.Rd | 2 +- vignettes/ssMutPA.Rmd | 2 +- 14 files changed, 38 insertions(+), 49 deletions(-)
Title: Utilities and Kinship Information for Research with the NLSY
Description: Utilities and kinship information for behavior genetics and
developmental research using the National Longitudinal Survey of Youth
(NLSY; <https://www.nlsinfo.org/>).
Author: William Howard Beasley [aut] ,
Joseph Lee Rodgers [ctb] ,
David Bard [ctb],
Michael D. Hunter [ctb] ,
Patrick O'Keefe [ctb] ,
Kelly Meredith Williams [ctb],
S. Mason Garrison [aut, cre]
Maintainer: S. Mason Garrison <garrissm@wfu.edu>
Diff between NlsyLinks versions 2.2.1 dated 2023-09-22 and 2.2.2 dated 2024-10-10
NlsyLinks-2.2.1/NlsyLinks/tests/spelling.R |only NlsyLinks-2.2.1/NlsyLinks/tests/spelling.Rout.save |only NlsyLinks-2.2.2/NlsyLinks/DESCRIPTION | 8 NlsyLinks-2.2.2/NlsyLinks/MD5 | 47 - NlsyLinks-2.2.2/NlsyLinks/NEWS.md | 6 NlsyLinks-2.2.2/NlsyLinks/R/NlsyLinks-package.R |only NlsyLinks-2.2.2/NlsyLinks/R/ace-estimate.R | 2 NlsyLinks-2.2.2/NlsyLinks/R/ace-lavaan-group.R | 7 NlsyLinks-2.2.2/NlsyLinks/R/create-pair-links-double-entered.R | 4 NlsyLinks-2.2.2/NlsyLinks/R/nlsy-links.R | 6 NlsyLinks-2.2.2/NlsyLinks/R/read-csv-nlsy-79.R | 22 NlsyLinks-2.2.2/NlsyLinks/R/subject-details-79-doc.R | 1 NlsyLinks-2.2.2/NlsyLinks/R/validate-pair-links-are-symmetric.R | 40 - NlsyLinks-2.2.2/NlsyLinks/README.md | 6 NlsyLinks-2.2.2/NlsyLinks/build/vignette.rds |binary NlsyLinks-2.2.2/NlsyLinks/inst/doc/about.html | 4 NlsyLinks-2.2.2/NlsyLinks/inst/doc/faq.R | 4 NlsyLinks-2.2.2/NlsyLinks/inst/doc/faq.html | 8 NlsyLinks-2.2.2/NlsyLinks/inst/doc/nls-investigator.html | 22 NlsyLinks-2.2.2/NlsyLinks/inst/doc/nlsy-ace.R | 2 NlsyLinks-2.2.2/NlsyLinks/inst/doc/nlsy-ace.html | 243 +++------- NlsyLinks-2.2.2/NlsyLinks/inst/doc/software-and-support.html | 6 NlsyLinks-2.2.2/NlsyLinks/man/AceEstimate-class.Rd | 2 NlsyLinks-2.2.2/NlsyLinks/man/NlsyLinks-package.Rd | 34 + NlsyLinks-2.2.2/NlsyLinks/man/ReadCsvNlsy79.Rd | 2 NlsyLinks-2.2.2/NlsyLinks/man/ValidatePairLinksAreSymmetric.Rd | 18 26 files changed, 236 insertions(+), 258 deletions(-)
Title: Neo-Normal Distributions Family for Markov Chain Monte Carlo
(MCMC) Models in 'JAGS'
Description: A 'JAGS' extension module provides neo-normal distributions
family including MSNBurr, MSNBurr-IIa, GMSNBurr, Lunetta Exponential Power,
Fernandez-Steel Skew t, Fernandez-Steel Skew Normal, Fernandez-Osiewalski-Steel
Skew Exponential Power, Jones Skew Exponential Power.
References:
Choir, A. S. (2020). "The New Neo-Normal Distributions and Their Properties".Unpublished Dissertation.
Denwood, M.J. (2016) <doi:10.18637/jss.v071.i09>.
Fernandez, C., Osiewalski, J., & Steel, M. F. (1995) <doi:10.1080/01621459.1995.10476637>.
Fernandez, C., & Steel, M. F. (1998) <doi:10.1080/01621459.1998.10474117>.
Iriawan, N. (2000). "Computationally Intensive Approaches to Inference in NeoNormal Linear Models".Unpublished Dissertation.
Mineo, A., & Ruggieri, M. (2005) <doi:10.18637/jss.v012.i04>.
Rigby, R. A., & Stasinopoulos, D. M. (2005) <doi:10.1111/j.1467-9876.2005.00510.x>.
Lunetta, G. (1963). "Di una Generalizzazione dello Schema della Curva Normale".
Ri [...truncated...]
Author: Achmad Syahrul Choir [aut, cre],
Resi Ramadani [aut],
Nur Iriawan [aut],
S Sifa'ul Khusna Malikhatul Mutmainah [ctb],
Matthew Denwood [cph],
Martyn Plummer [cph]
Maintainer: Achmad Syahrul Choir <madsyair@stis.ac.id>
Diff between neojags versions 0.1.4 dated 2023-08-08 and 0.1.5 dated 2024-10-10
neojags-0.1.4/neojags/tests/moduletargets.Rsave |only neojags-0.1.4/neojags/tests/spelling.Rout.save |only neojags-0.1.5/neojags/CHANGELOG | 32 neojags-0.1.5/neojags/DESCRIPTION | 10 neojags-0.1.5/neojags/MD5 | 39 neojags-0.1.5/neojags/R/example.R | 106 - neojags-0.1.5/neojags/R/load.module.neojags.R | 770 ++++------ neojags-0.1.5/neojags/R/utilities.R | 24 neojags-0.1.5/neojags/R/utilities.invisible.R | 740 ++++----- neojags-0.1.5/neojags/R/zzz.R | 24 neojags-0.1.5/neojags/README.md | 6 neojags-0.1.5/neojags/build/vignette.rds |binary neojags-0.1.5/neojags/inst/WORDLIST |only neojags-0.1.5/neojags/inst/doc/vignettes.R | 156 +- neojags-0.1.5/neojags/inst/doc/vignettes.Rmd | 242 +-- neojags-0.1.5/neojags/inst/doc/vignettes.html | 1048 +++++++------- neojags-0.1.5/neojags/man/load.neojagsmodule.Rd | 429 ++--- neojags-0.1.5/neojags/tests/checkmodule.R | 367 ++-- neojags-0.1.5/neojags/tests/spelling.R | 25 neojags-0.1.5/neojags/tests/testthat.R | 25 neojags-0.1.5/neojags/tests/testthat/test-basic_example.R | 25 neojags-0.1.5/neojags/vignettes/vignettes.Rmd | 242 +-- 22 files changed, 2055 insertions(+), 2255 deletions(-)
Title: Introductory Statistics with R
Description: Data sets and scripts for text examples and exercises in
P. Dalgaard (2008), `Introductory Statistics with R', 2nd ed., Springer Verlag, ISBN 978-0387790534.
Author: Peter Dalgaard [aut, cre]
Maintainer: Peter Dalgaard <pd.mes@cbs.dk>
Diff between ISwR versions 2.0-8 dated 2020-01-20 and 2.0-9 dated 2024-10-10
ISwR-2.0-8/ISwR/data/IgM.R |only ISwR-2.0-8/ISwR/data/alkfos.R |only ISwR-2.0-8/ISwR/data/alkfos.csv |only ISwR-2.0-8/ISwR/data/ashina.txt |only ISwR-2.0-8/ISwR/data/bcmort.R |only ISwR-2.0-8/ISwR/data/bp.obese.txt |only ISwR-2.0-8/ISwR/data/caesarean.R |only ISwR-2.0-8/ISwR/data/coking.R |only ISwR-2.0-8/ISwR/data/coking.txt |only ISwR-2.0-8/ISwR/data/cystfibr.txt |only ISwR-2.0-8/ISwR/data/eba1977.txt |only ISwR-2.0-8/ISwR/data/energy.txt |only ISwR-2.0-8/ISwR/data/ewrates.R |only ISwR-2.0-8/ISwR/data/fake.trypsin.R |only ISwR-2.0-8/ISwR/data/graft.vs.host.txt |only ISwR-2.0-8/ISwR/data/heart.rate.R |only ISwR-2.0-8/ISwR/data/hellung.txt |only ISwR-2.0-8/ISwR/data/intake.R |only ISwR-2.0-8/ISwR/data/juul.txt |only ISwR-2.0-8/ISwR/data/juul2.txt |only ISwR-2.0-8/ISwR/data/kfm.txt |only ISwR-2.0-8/ISwR/data/lung.R |only ISwR-2.0-8/ISwR/data/malaria.txt |only ISwR-2.0-8/ISwR/data/melanom.txt |only ISwR-2.0-8/ISwR/data/nickel.R |only ISwR-2.0-8/ISwR/data/nickel.expand.R |only ISwR-2.0-8/ISwR/data/philion.txt |only ISwR-2.0-8/ISwR/data/react.R |only ISwR-2.0-8/ISwR/data/red.cell.folate.R |only ISwR-2.0-8/ISwR/data/rmr.txt |only ISwR-2.0-8/ISwR/data/secher.txt |only ISwR-2.0-8/ISwR/data/secretin.txt |only ISwR-2.0-8/ISwR/data/stroke.R |only ISwR-2.0-8/ISwR/data/stroke.csv |only ISwR-2.0-8/ISwR/data/tb.dilute.R |only ISwR-2.0-8/ISwR/data/thuesen.txt |only ISwR-2.0-8/ISwR/data/tlc.txt |only ISwR-2.0-8/ISwR/data/vitcap.txt |only ISwR-2.0-8/ISwR/data/vitcap2.txt |only ISwR-2.0-8/ISwR/data/wright.txt |only ISwR-2.0-8/ISwR/data/zelazo.R |only ISwR-2.0-9/ISwR/DESCRIPTION | 16 +-- ISwR-2.0-9/ISwR/MD5 | 98 +++++++++---------- ISwR-2.0-9/ISwR/NAMESPACE | 2 ISwR-2.0-9/ISwR/data/IgM.rda |only ISwR-2.0-9/ISwR/data/alkfos.csv.gz |only ISwR-2.0-9/ISwR/data/alkfos.rda |only ISwR-2.0-9/ISwR/data/ashina.txt.gz |only ISwR-2.0-9/ISwR/data/bcmort.rda |only ISwR-2.0-9/ISwR/data/bp.obese.txt.gz |only ISwR-2.0-9/ISwR/data/caesarean.rda |only ISwR-2.0-9/ISwR/data/coking.rda |only ISwR-2.0-9/ISwR/data/coking.txt.gz |only ISwR-2.0-9/ISwR/data/cystfibr.txt.gz |only ISwR-2.0-9/ISwR/data/eba1977.txt.gz |only ISwR-2.0-9/ISwR/data/energy.txt.gz |only ISwR-2.0-9/ISwR/data/ewrates.rda |only ISwR-2.0-9/ISwR/data/fake.trypsin.rda |only ISwR-2.0-9/ISwR/data/graft.vs.host.txt.gz |only ISwR-2.0-9/ISwR/data/heart.rate.rda |only ISwR-2.0-9/ISwR/data/hellung.txt.gz |only ISwR-2.0-9/ISwR/data/intake.rda |only ISwR-2.0-9/ISwR/data/juul.txt.gz |only ISwR-2.0-9/ISwR/data/juul2.txt.gz |only ISwR-2.0-9/ISwR/data/kfm.txt.gz |only ISwR-2.0-9/ISwR/data/lung.rda |only ISwR-2.0-9/ISwR/data/malaria.txt.gz |only ISwR-2.0-9/ISwR/data/melanom.txt.gz |only ISwR-2.0-9/ISwR/data/nickel.expand.rda |only ISwR-2.0-9/ISwR/data/nickel.rda |only ISwR-2.0-9/ISwR/data/philion.txt.gz |only ISwR-2.0-9/ISwR/data/react.rda |only ISwR-2.0-9/ISwR/data/red.cell.folate.rda |only ISwR-2.0-9/ISwR/data/rmr.txt.gz |only ISwR-2.0-9/ISwR/data/secher.txt.gz |only ISwR-2.0-9/ISwR/data/secretin.txt.gz |only ISwR-2.0-9/ISwR/data/stroke.csv.gz |only ISwR-2.0-9/ISwR/data/stroke.rda |only ISwR-2.0-9/ISwR/data/tb.dilute.rda |only ISwR-2.0-9/ISwR/data/thuesen.txt.gz |only ISwR-2.0-9/ISwR/data/tlc.txt.gz |only ISwR-2.0-9/ISwR/data/vitcap.txt.gz |only ISwR-2.0-9/ISwR/data/vitcap2.txt.gz |only ISwR-2.0-9/ISwR/data/wright.txt.gz |only ISwR-2.0-9/ISwR/data/zelazo.rda |only ISwR-2.0-9/ISwR/man/philion.Rd | 2 ISwR-2.0-9/ISwR/man/secretin.Rd | 14 +- ISwR-2.0-9/ISwR/tests/allexercises.R | 10 + ISwR-2.0-9/ISwR/tests/allexercises.Rout.save | 76 ++++---------- ISwR-2.0-9/ISwR/tests/allscripts.R | 3 ISwR-2.0-9/ISwR/tests/allscripts.Rout.save | 138 ++++++++------------------- 91 files changed, 146 insertions(+), 213 deletions(-)
Title: Fast Kernel Density Estimation with Hexagonal Grid
Description: Kernel density estimation with hexagonal grid for bivariate data.
Hexagonal grid has many beneficial properties like equidistant neighbours
and less edge bias, making it better for spatial analyses than the more
commonly used rectangular grid.
Carr, D. B. et al. (1987) <doi:10.2307/2289444>.
Diggle, P. J. (2010) <doi:10.1201/9781420072884>.
Hill, B. (2017) <https://blog.bruce-hill.com/meandering-triangles>.
Jones, M. C. (1993) <doi:10.1007/BF00147776>.
Author: Quoc Hoang Nguyen [aut, cre] ,
Yunshun Chen [aut] ,
Dan Carr [ctb],
binning routine ported by Nicholas Lewin-Koh [ctb],
Martin Maechler [ctb]
Maintainer: Quoc Hoang Nguyen <nguyen.q@wehi.edu.au>
Diff between hexDensity versions 1.4.4 dated 2024-09-23 and 1.4.5 dated 2024-10-10
DESCRIPTION | 12 +++++++++--- MD5 | 4 ++-- src/meanderingTriangleC.cpp | 2 ++ 3 files changed, 13 insertions(+), 5 deletions(-)
Title: Modeling Over Dispersed Binomial Outcome Data Using BMD and ABD
Description: Contains Probability Mass Functions, Cumulative Mass
Functions, Negative Log Likelihood value, parameter estimation and
modeling data using Binomial Mixture Distributions (BMD) (Manoj et al
(2013) <doi:10.5539/ijsp.v2n2p24>) and Alternate Binomial
Distributions (ABD) (Paul (1985) <doi:10.1080/03610928508828990>),
also Journal article to use the package(<doi:10.21105/joss.01505>).
Author: Amalan Mahendran [aut, cre] ,
Pushpakanthie Wijekoon [aut, ctb]
Maintainer: Amalan Mahendran <amalan0595@gmail.com>
Diff between fitODBOD versions 1.5.2 dated 2024-06-28 and 1.5.3 dated 2024-10-10
DESCRIPTION | 6 +++--- MD5 | 6 +++--- build/partial.rdb |binary tests/spelling.Rout.save | 2 +- 4 files changed, 7 insertions(+), 7 deletions(-)
Title: Swarm Space Creation
Description: Provides a pipeline for the comparative analysis of
collective movement data (e.g. fish schools, bird flocks, baboon troops) by
processing 2-dimensional positional data (x,y,t) from GPS trackers or computer
vision tracking systems, discretizing events of collective motion, calculating
a set of established metrics that characterize each event, and placing the
events in a multi-dimensional swarm space constructed from these metrics.
The swarm space concept, the metrics and data sets included are described in:
Papadopoulou Marina, Furtbauer Ines, O'Bryan Lisa R., Garnier Simon,
Georgopoulou Dimitra G., Bracken Anna M., Christensen Charlotte and King
Andrew J. (2023) <doi:10.1098/rstb.2022.0068>.
Author: Marina Papadopoulou [aut, cre]
,
Simon Garnier [ctb, cph]
Maintainer: Marina Papadopoulou <m.papadopoulou.rug@gmail.com>
Diff between swaRmverse versions 0.1.0 dated 2024-03-26 and 0.1.1 dated 2024-10-10
DESCRIPTION | 8 ++++---- MD5 | 26 +++++++++++++------------- NEWS.md | 12 ++++++++++++ R/events_metrics.R | 4 ++-- R/swaRm_bearing_angle.R | 2 -- README.md | 2 +- data/multi_species_metrics.rda |binary data/multi_species_pca.rda |binary data/new_species_metrics.rda |binary inst/doc/step2_data_analysis.Rmd | 2 +- inst/doc/step2_data_analysis.html | 18 +++++++++--------- inst/doc/step3_swarm_space.html | 2 +- man/nnba.Rd | 3 --- vignettes/step2_data_analysis.Rmd | 2 +- 14 files changed, 44 insertions(+), 37 deletions(-)
Title: Efficient Monitoring of Global Biodiversity Portfolios
Description: Biodiversity areas, especially primary forest, serve a
multitude of functions for local economy, regional functionality of
the ecosystems as well as the global health of our planet. Recently,
adverse changes in human land use practices and climatic responses to
increased greenhouse gas emissions, put these biodiversity areas under
a variety of different threats. The present package helps to analyse a
number of biodiversity indicators based on freely available
geographical datasets. It supports computational efficient routines
that allow the analysis of potentially global biodiversity portfolios.
The primary use case of the package is to support evidence based
reporting of an organization's effort to protect biodiversity areas
under threat and to identify regions were intervention is most duly
needed.
Author: Darius A. Goergen [aut, cre] ,
Om Prakash Bhandari [aut],
Andreas Petutschnig [ctb]
Maintainer: Darius A. Goergen <info@dariusgoergen.com>
Diff between mapme.biodiversity versions 0.9.1 dated 2024-09-02 and 0.9.2 dated 2024-10-10
mapme.biodiversity-0.9.1/mapme.biodiversity/R/calc_exposed_population.R |only mapme.biodiversity-0.9.1/mapme.biodiversity/R/calc_fatalities.R |only mapme.biodiversity-0.9.1/mapme.biodiversity/man/exposed_population.Rd |only mapme.biodiversity-0.9.1/mapme.biodiversity/man/fatalities.Rd |only mapme.biodiversity-0.9.1/mapme.biodiversity/tests/testthat/test-calc_exposed_population.R |only mapme.biodiversity-0.9.1/mapme.biodiversity/tests/testthat/test-calc_fatalities.R |only mapme.biodiversity-0.9.2/mapme.biodiversity/DESCRIPTION | 45 +++++----- mapme.biodiversity-0.9.2/mapme.biodiversity/MD5 | 44 ++++++--- mapme.biodiversity-0.9.2/mapme.biodiversity/NAMESPACE | 8 + mapme.biodiversity-0.9.2/mapme.biodiversity/NEWS.md | 26 +++++ mapme.biodiversity-0.9.2/mapme.biodiversity/R/calc_exposed_population_acled.R |only mapme.biodiversity-0.9.2/mapme.biodiversity/R/calc_exposed_population_ucdp.R |only mapme.biodiversity-0.9.2/mapme.biodiversity/R/calc_fatalities_acled.R |only mapme.biodiversity-0.9.2/mapme.biodiversity/R/calc_fatalities_ucdp.R |only mapme.biodiversity-0.9.2/mapme.biodiversity/R/calc_mangroves_area.R | 5 - mapme.biodiversity-0.9.2/mapme.biodiversity/R/get_acled.R |only mapme.biodiversity-0.9.2/mapme.biodiversity/R/get_gfw_emissions.R | 2 mapme.biodiversity-0.9.2/mapme.biodiversity/R/portfolio.R | 19 ++-- mapme.biodiversity-0.9.2/mapme.biodiversity/R/spatial-utils.R | 14 ++- mapme.biodiversity-0.9.2/mapme.biodiversity/README.md | 9 +- mapme.biodiversity-0.9.2/mapme.biodiversity/inst/doc/quickstart.html | 32 +++---- mapme.biodiversity-0.9.2/mapme.biodiversity/inst/res/acled |only mapme.biodiversity-0.9.2/mapme.biodiversity/man/acled.Rd |only mapme.biodiversity-0.9.2/mapme.biodiversity/man/calc_exposed_population_acled.Rd |only mapme.biodiversity-0.9.2/mapme.biodiversity/man/exposed_population_ucdp.Rd |only mapme.biodiversity-0.9.2/mapme.biodiversity/man/fatalities_acled.Rd |only mapme.biodiversity-0.9.2/mapme.biodiversity/man/fatalities_ucpd.Rd |only mapme.biodiversity-0.9.2/mapme.biodiversity/tests/testthat/test-calc_exposed_population_acled.R |only mapme.biodiversity-0.9.2/mapme.biodiversity/tests/testthat/test-calc_exposed_population_ucdp.R |only mapme.biodiversity-0.9.2/mapme.biodiversity/tests/testthat/test-calc_fatalities_acled.R |only mapme.biodiversity-0.9.2/mapme.biodiversity/tests/testthat/test-calc_fatalities_ucpd.R |only mapme.biodiversity-0.9.2/mapme.biodiversity/tests/testthat/test-calc_indicator.R | 23 ++--- mapme.biodiversity-0.9.2/mapme.biodiversity/tests/testthat/test-get_acled.R |only mapme.biodiversity-0.9.2/mapme.biodiversity/tests/testthat/test-portfolio.R | 11 ++ 34 files changed, 153 insertions(+), 85 deletions(-)
More information about mapme.biodiversity at CRAN
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Title: Quality Control for Label-Free Proteomics Expression Data
Description: Label-free bottom-up proteomics expression data is often affected by data heterogeneity and missing values. Normalization and missing value imputation are commonly used techniques to address these issues and make the dataset suitable for further downstream analysis. This package provides an optimal combination of normalization and imputation methods for the dataset. The package utilizes three normalization methods and three imputation methods.The statistical evaluation measures named pooled co-efficient of variance, pooled estimate of variance and pooled median absolute deviation are used for selecting the best combination of normalization and imputation method for the given dataset. The user can also visualize the results by using various plots available in this package. The user can also perform the differential expression analysis between two sample groups with the function included in this package. The chosen three normalization methods, three imputation methods and three evaluati [...truncated...]
Author: Kabilan S [aut, cre],
Dr Shashi Bhushan Lal [aut, ths],
Dr Sudhir Srivastava [aut, ths],
Dr Krishna Kumar Chaturvedi [ths],
Dr Yasin Jeshima K [ths],
Dr Ramasubramanian V [ths],
Dr Girish Kumar Jha [ctb]
Maintainer: Kabilan S <kabilan151414@gmail.com>
Diff between lfproQC versions 1.3.0 dated 2024-09-30 and 1.4.0 dated 2024-10-10
DESCRIPTION | 10 ++++++---- MD5 | 12 ++++++------ NEWS | 32 ++++++++++++++------------------ R/MAplot_DE_fn.R | 4 ++-- R/volcanoplot_DE_fn.R | 8 +++----- inst/doc/user_guide.html | 2 +- man/lfproQC-package.Rd | 2 ++ 7 files changed, 34 insertions(+), 36 deletions(-)
Title: Parsing and Evaluation Tools that Provide More Details than the
Default
Description: Parsing and evaluation tools that make it easy to recreate
the command line behaviour of R.
Author: Hadley Wickham [aut, cre],
Yihui Xie [aut] ,
Michael Lawrence [ctb],
Thomas Kluyver [ctb],
Jeroen Ooms [ctb],
Barret Schloerke [ctb],
Adam Ryczkowski [ctb],
Hiroaki Yutani [ctb],
Michel Lang [ctb],
Karolis Koncevicius [ctb],
Posit Software, PBC [cph, [...truncated...]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between evaluate versions 1.0.0 dated 2024-09-17 and 1.0.1 dated 2024-10-10
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ R/evaluate.R | 2 +- 4 files changed, 11 insertions(+), 7 deletions(-)
Title: Useful Wrappers Around Commonly Used Functions
Description: The main functionalities of 'wrappedtools' are:
adding backticks to variable names; rounding to desired precision
with special case for p-values;
selecting columns based on pattern and storing their position, name,
and backticked name; computing and formatting of descriptive statistics
(e.g. mean±SD), comparing groups and creating publication-ready tables with
descriptive statistics and p-values; creating specialized plots for
correlation matrices. Functions were mainly written for my own daily work or
teaching, but may be of use to others as well.
Author: Andreas Busjahn [cre, aut] ,
Bilal Asser [aut]
Maintainer: Andreas Busjahn <andreas@busjahn.net>
Diff between wrappedtools versions 0.9.5 dated 2024-03-16 and 0.9.6 dated 2024-10-10
DESCRIPTION | 12 ++-- MD5 | 36 ++++++------- NEWS.md | 8 ++- R/basefunctions.R | 48 ++++++++++++------ R/tests.R | 99 +++++++++++++++++++++----------------- build/vignette.rds |binary inst/doc/wrappedtools.html | 11 ++-- man/ColSeeker.Rd | 9 ++- man/compare_n_numvars.Rd | 4 - man/ksnormal.Rd | 6 +- man/pairwise_ordcat_test.Rd | 4 - man/pairwise_wilcox_test.Rd | 4 - man/pdf_kable.Rd | 4 - man/print_kable.Rd | 4 - tests/testthat.R | 8 +-- tests/testthat/ksnormal_out.rda |binary tests/testthat/n_numvars_out1.rda |binary tests/testthat/n_numvars_out2.rda |binary tests/testthat/test-ksnormal.R | 9 +-- 19 files changed, 155 insertions(+), 111 deletions(-)
Title: Multidimensional Scaling
Description: Implements the following approaches for multidimensional scaling (MDS) based on stress minimization using majorization (smacof): ratio/interval/ordinal/spline MDS on symmetric dissimilarity matrices, MDS with external constraints on the configuration, individual differences scaling (idioscal, indscal), MDS with spherical restrictions, and ratio/interval/ordinal/spline unfolding (circular restrictions, row-conditional). Various tools and extensions like jackknife MDS, bootstrap MDS, permutation tests, MDS biplots, gravity models, unidimensional scaling, drift vectors (asymmetric MDS), classical scaling, and Procrustes are implemented as well.
Author: Patrick Mair [aut, cre],
Jan De Leeuw [aut],
Patrick J. F. Groenen [aut],
Ingwer Borg [ctb]
Maintainer: Patrick Mair <mair@fas.harvard.edu>
Diff between smacof versions 2.1-6 dated 2024-03-01 and 2.1-7 dated 2024-10-10
DESCRIPTION | 11 +++++------ MD5 | 16 ++++++++-------- NAMESPACE | 1 - R/plot.mdsbi.R | 46 ++++++++++++++++++++++++++++++++++++++++++++++ build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 6 ++++++ inst/doc/smacof.pdf |binary man/jackknife.smacofB.Rd | 2 +- 9 files changed, 66 insertions(+), 16 deletions(-)
Title: Create Random ADaM Datasets
Description: A set of functions to create random Analysis Data Model
(ADaM) datasets and cached dataset. ADaM dataset specifications are
described by the Clinical Data Interchange Standards Consortium
(CDISC) Analysis Data Model Team.
Author: Pawel Rucki [aut],
Nick Paszty [aut],
Jana Stoilova [aut],
Joe Zhu [aut, cre],
Davide Garolini [aut],
Emily de la Rua [aut],
Christopher DiPietrantonio [aut],
Adrian Waddell [aut],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Joe Zhu <joe.zhu@roche.com>
Diff between random.cdisc.data versions 0.3.15 dated 2024-03-27 and 0.3.16 dated 2024-10-10
random.cdisc.data-0.3.15/random.cdisc.data/man/var_relabel.Rd |only random.cdisc.data-0.3.16/random.cdisc.data/DESCRIPTION | 24 ++-- random.cdisc.data-0.3.16/random.cdisc.data/MD5 | 56 +++++----- random.cdisc.data-0.3.16/random.cdisc.data/NAMESPACE | 1 random.cdisc.data-0.3.16/random.cdisc.data/NEWS.md | 7 + random.cdisc.data-0.3.16/random.cdisc.data/R/radab.R | 8 + random.cdisc.data-0.3.16/random.cdisc.data/R/radae.R | 2 random.cdisc.data-0.3.16/random.cdisc.data/R/radaette.R | 4 random.cdisc.data-0.3.16/random.cdisc.data/R/radcm.R | 2 random.cdisc.data-0.3.16/random.cdisc.data/R/raddv.R | 2 random.cdisc.data-0.3.16/random.cdisc.data/R/radeg.R | 8 - random.cdisc.data-0.3.16/random.cdisc.data/R/radex.R | 2 random.cdisc.data-0.3.16/random.cdisc.data/R/radhy.R | 2 random.cdisc.data-0.3.16/random.cdisc.data/R/radlb.R | 4 random.cdisc.data-0.3.16/random.cdisc.data/R/radmh.R | 2 random.cdisc.data-0.3.16/random.cdisc.data/R/radqlqc.R | 4 random.cdisc.data-0.3.16/random.cdisc.data/R/radqs.R | 4 random.cdisc.data-0.3.16/random.cdisc.data/R/radrs.R | 4 random.cdisc.data-0.3.16/random.cdisc.data/R/radsub.R | 2 random.cdisc.data-0.3.16/random.cdisc.data/R/radtte.R | 4 random.cdisc.data-0.3.16/random.cdisc.data/R/radvs.R | 4 random.cdisc.data-0.3.16/random.cdisc.data/R/utils.R | 28 ++--- random.cdisc.data-0.3.16/random.cdisc.data/README.md | 13 +- random.cdisc.data-0.3.16/random.cdisc.data/data/cadab.RData |binary random.cdisc.data-0.3.16/random.cdisc.data/inst/WORDLIST | 1 random.cdisc.data-0.3.16/random.cdisc.data/inst/doc/rebuild_cached_data.html | 2 random.cdisc.data-0.3.16/random.cdisc.data/man/random.cdisc.data-package.Rd | 9 + random.cdisc.data-0.3.16/random.cdisc.data/man/rcd_var_relabel.Rd |only random.cdisc.data-0.3.16/random.cdisc.data/tests/testthat/_snaps/row_values.md | 50 ++++---- random.cdisc.data-0.3.16/random.cdisc.data/tests/testthat/test-utils.R | 8 - 30 files changed, 143 insertions(+), 114 deletions(-)
More information about random.cdisc.data at CRAN
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Title: A Tool for Creating Custom Neural Networks in C++ and using Them
in R
Description: Contains a module to define neural networks from custom components and versions of Autoencoder, BP, LVQ, MAM NN.
Author: Vasilis Nikolaidis [aut, cph, cre]
Maintainer: Vasilis Nikolaidis <v.nikolaidis@uop.gr>
Diff between nnlib2Rcpp versions 0.2.8 dated 2024-06-10 and 0.2.9 dated 2024-10-10
nnlib2Rcpp-0.2.8/nnlib2Rcpp/R/LVQs_wrapper_functions.R |only nnlib2Rcpp-0.2.9/nnlib2Rcpp/DESCRIPTION | 6 +-- nnlib2Rcpp-0.2.9/nnlib2Rcpp/MD5 | 14 ++++----- nnlib2Rcpp-0.2.9/nnlib2Rcpp/R/LVQs_helper_functions.R |only nnlib2Rcpp-0.2.9/nnlib2Rcpp/build/partial.rdb |binary nnlib2Rcpp-0.2.9/nnlib2Rcpp/build/vignette.rds |binary nnlib2Rcpp-0.2.9/nnlib2Rcpp/inst/doc/intro.pdf |binary nnlib2Rcpp-0.2.9/nnlib2Rcpp/man/LVQs_recall.Rd | 6 +-- nnlib2Rcpp-0.2.9/nnlib2Rcpp/man/LVQs_train.Rd | 26 +++++++++++------ 9 files changed, 30 insertions(+), 22 deletions(-)
Title: Analysis of Spatial Stratified Heterogeneity
Description: Analyzing spatial factors and exploring spatial associations based on the concept of spatial
stratified heterogeneity, and also takes into account local spatial dependencies, spatial
interpretability, potential spatial interactions, and robust spatial stratification. Additionally,
it supports geographical detector models established in academic literature.
Author: Wenbo Lv [aut, cre, cph] ,
Yangyang Lei [aut] ,
Yongze Song [aut] ,
Wufan Zhao [aut] ,
Jianwu Yan [aut]
Maintainer: Wenbo Lv <lyu.geosocial@gmail.com>
Diff between gdverse versions 1.0-3 dated 2024-09-29 and 1.1.0 dated 2024-10-10
gdverse-1.0-3/gdverse/R/discretization.R |only gdverse-1.0-3/gdverse/R/esp_old.R |only gdverse-1.0-3/gdverse/R/fuzzyoverlay.R |only gdverse-1.0-3/gdverse/R/loess.R |only gdverse-1.0-3/gdverse/R/spvar.R |only gdverse-1.0-3/gdverse/man/loess_optdiscnum.Rd |only gdverse-1.0-3/gdverse/man/spvar.Rd |only gdverse-1.0-3/gdverse/man/st_fuzzyoverlay.Rd |only gdverse-1.0-3/gdverse/man/st_unidisc.Rd |only gdverse-1.0-3/gdverse/man/unidisc_methods.Rd |only gdverse-1.0-3/gdverse/tests/testthat/test-spvar.R |only gdverse-1.1.0/gdverse/DESCRIPTION | 12 gdverse-1.1.0/gdverse/MD5 | 149 gdverse-1.1.0/gdverse/NAMESPACE | 5 gdverse-1.1.0/gdverse/NEWS.md | 6 gdverse-1.1.0/gdverse/R/gd_bestunidisc.R |only gdverse-1.1.0/gdverse/R/geodetector.R | 1156 ++--- gdverse-1.1.0/gdverse/R/globals.R | 30 gdverse-1.1.0/gdverse/R/idsa.R | 14 gdverse-1.1.0/gdverse/R/loess_optscale.R |only gdverse-1.1.0/gdverse/R/opgd.R | 11 gdverse-1.1.0/gdverse/R/pid_idsa.R | 32 gdverse-1.1.0/gdverse/R/psd_pseudop.R | 14 gdverse-1.1.0/gdverse/R/psd_spade.R | 18 gdverse-1.1.0/gdverse/R/r_interact_py.R | 72 gdverse-1.1.0/gdverse/R/rid.R | 6 gdverse-1.1.0/gdverse/R/robustdisc.R | 108 gdverse-1.1.0/gdverse/R/sesu_gozh.R | 388 - gdverse-1.1.0/gdverse/R/sesu_opgd.R | 372 - gdverse-1.1.0/gdverse/R/spade.R | 7 gdverse-1.1.0/gdverse/R/spd_lesh.R | 366 - gdverse-1.1.0/gdverse/R/srs_geodetecor.R | 750 +-- gdverse-1.1.0/gdverse/R/utils_helper.R | 341 - gdverse-1.1.0/gdverse/R/zzz.R | 8 gdverse-1.1.0/gdverse/README.md | 18 gdverse-1.1.0/gdverse/inst/doc/gd.Rmd | 860 ++-- gdverse-1.1.0/gdverse/inst/doc/idsa.Rmd | 34 gdverse-1.1.0/gdverse/inst/doc/idsa.html | 38 gdverse-1.1.0/gdverse/inst/doc/opgd.Rmd | 400 - gdverse-1.1.0/gdverse/inst/doc/opgd.html | 76 gdverse-1.1.0/gdverse/inst/doc/sesu.Rmd | 200 gdverse-1.1.0/gdverse/inst/doc/sesu.html | 678 +-- gdverse-1.1.0/gdverse/inst/doc/shegd.Rmd | 380 - gdverse-1.1.0/gdverse/inst/doc/spade.Rmd | 76 gdverse-1.1.0/gdverse/inst/doc/spade.html | 78 gdverse-1.1.0/gdverse/inst/extdata/Depression.csv | 2146 +++++----- gdverse-1.1.0/gdverse/inst/python/__pycache__/cpd_disc.cpython-39.pyc |binary gdverse-1.1.0/gdverse/man/cpsd_disc.Rd | 2 gdverse-1.1.0/gdverse/man/cpsd_spade.Rd | 2 gdverse-1.1.0/gdverse/man/figures/idsa/idsa_map-1.png |binary gdverse-1.1.0/gdverse/man/figures/idsa/idsa_modeling-1.png |binary gdverse-1.1.0/gdverse/man/figures/logo.png |binary gdverse-1.1.0/gdverse/man/figures/opgd/opgd_plot-1.png |binary gdverse-1.1.0/gdverse/man/figures/sesu/opgd-1.png |binary gdverse-1.1.0/gdverse/man/figures/spade/spade-1.png |binary gdverse-1.1.0/gdverse/man/gd_bestunidisc.Rd | 24 gdverse-1.1.0/gdverse/man/idsa.Rd | 2 gdverse-1.1.0/gdverse/man/loess_optscale.Rd | 6 gdverse-1.1.0/gdverse/man/opgd.Rd | 7 gdverse-1.1.0/gdverse/man/pid_idsa.Rd | 2 gdverse-1.1.0/gdverse/man/plot.srsgd_result.Rd | 44 gdverse-1.1.0/gdverse/man/print.srsgd_result.Rd | 44 gdverse-1.1.0/gdverse/man/psd_iev.Rd | 4 gdverse-1.1.0/gdverse/man/psd_pseudop.Rd | 2 gdverse-1.1.0/gdverse/man/psd_spade.Rd | 2 gdverse-1.1.0/gdverse/man/psmd_pseudop.Rd | 4 gdverse-1.1.0/gdverse/man/psmd_spade.Rd | 5 gdverse-1.1.0/gdverse/man/sesu_opgd.Rd | 7 gdverse-1.1.0/gdverse/man/spade.Rd | 5 gdverse-1.1.0/gdverse/man/srs_geodetector.Rd | 92 gdverse-1.1.0/gdverse/vignettes/gd.Rmd | 860 ++-- gdverse-1.1.0/gdverse/vignettes/gd.Rmd.orig | 416 - gdverse-1.1.0/gdverse/vignettes/idsa.Rmd | 34 gdverse-1.1.0/gdverse/vignettes/idsa.Rmd.orig | 136 gdverse-1.1.0/gdverse/vignettes/opgd.Rmd | 400 - gdverse-1.1.0/gdverse/vignettes/precompile.R | 44 gdverse-1.1.0/gdverse/vignettes/rgdrid.Rmd.orig | 162 gdverse-1.1.0/gdverse/vignettes/sesu.Rmd | 200 gdverse-1.1.0/gdverse/vignettes/sesu.Rmd.orig | 6 gdverse-1.1.0/gdverse/vignettes/shegd.Rmd | 380 - gdverse-1.1.0/gdverse/vignettes/spade.Rmd | 76 gdverse-1.1.0/gdverse/vignettes/spade.Rmd.orig | 226 - 82 files changed, 6007 insertions(+), 6036 deletions(-)