Title: Intrinsic Peak Analysis (IPA) for HRMS Data
Description: A multi-layered untargeted pipeline for high-throughput LC/HRMS data processing to extract signals of organic small molecules. The package performs ion pairing, peak detection, peak table alignment, retention time correction, aligned peak table gap filling, peak annotation and visualization of extracted ion chromatograms (EICs) and total ion chromatograms (TICs). The 'IDSL.IPA' package was introduced in <doi:10.1021/acs.jproteome.2c00120> .
Author: Sadjad Fakouri-Baygi [aut] ,
Dinesh Barupal [cre, aut]
Maintainer: Dinesh Barupal <dinesh.barupal@mssm.edu>
Diff between IDSL.IPA versions 2.8 dated 2023-05-18 and 2.9 dated 2023-05-31
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- build/partial.rdb |binary data/peak_spline.rda |binary data/segment.rda |binary man/IPA_targeted_xlsxAnalyzer.Rd | 28 ++++++++++++++++++---------- man/IPA_workflow.Rd | 23 ++++++++++++++--------- man/IPA_xlsxAnalyzer.Rd | 20 +++++++++++++------- 8 files changed, 55 insertions(+), 36 deletions(-)
Title: Compute and Plot Zonohedra from Vector Generators
Description: Computes a zonohedron from real vector generators. The package also computes zonogons (2D zonotopes) and zonosegs (1D zonotopes). An elementary S3 class for matroids is included, which supports matroids with rank 3, 2, and 1. Optimization methods are taken from Heckbert (1985) <https://www.cs.cmu.edu/~ph/zono.ps.gz>.
Author: Glenn Davis [aut, cre]
Maintainer: Glenn Davis <gdavis@gluonics.com>
Diff between zonohedra versions 0.2-1 dated 2023-05-29 and 0.2-2 dated 2023-05-31
DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++-------------- NEWS.md | 5 +++++ R/zonohedron.R | 21 ++++++++++++++++++--- inst/doc/matroids.html | 6 +++--- inst/doc/raytrace.html | 14 +++++++------- inst/doc/transitions.Rmd | 11 +++++++---- inst/doc/transitions.html | 18 +++++++++--------- inst/doc/zonohedra-guide.R | 4 ++-- inst/doc/zonohedra-guide.Rmd | 12 +++++++++--- inst/doc/zonohedra-guide.html | 23 ++++++++++++----------- inst/doc/zonotopes.html | 8 ++++---- src/matroid.c | 6 ++++-- vignettes/transitions.Rmd | 11 +++++++---- vignettes/zonohedra-guide.Rmd | 12 +++++++++--- 15 files changed, 114 insertions(+), 73 deletions(-)
Title: Statistical Pattern Recognition and daTing using Archaeological
Artefacts assemblageS
Description: Statistical pattern recognition and dating using archaeological artefacts assemblages.
Package of statistical tools for archaeology.
hclustcompro(perioclust): Bellanger Lise, Coulon Arthur, Husi Philippe (2021, ISBN:978-3-030-60103-4).
mapclust: Bellanger Lise, Coulon Arthur, Husi Philippe (2021) <doi:10.1016/j.jas.2021.105431>.
seriograph: Desachy Bruno (2004) <doi:10.3406/pica.2004.2396>.
cerardat: Bellanger Lise, Husi Philippe (2012) <doi:10.1016/j.jas.2011.06.031>.
Author: Arthur Coulon [aut, cre],
Lise Bellanger [aut],
Philippe Husi [aut],
Bruno Desachy [ctb],
Benjamin Martineau [ctb]
Maintainer: Arthur Coulon <arthur-coulon@outlook.fr>
Diff between SPARTAAS versions 1.1.0 dated 2021-10-22 and 1.2.0 dated 2023-05-31
SPARTAAS-1.1.0/SPARTAAS/inst/shiny-examples/hclustcompro.app/www/icon.ico |only SPARTAAS-1.2.0/SPARTAAS/DESCRIPTION | 30 + SPARTAAS-1.2.0/SPARTAAS/MD5 | 78 ++-- SPARTAAS-1.2.0/SPARTAAS/NAMESPACE | 42 +- SPARTAAS-1.2.0/SPARTAAS/R/cerardat.R |only SPARTAAS-1.2.0/SPARTAAS/R/cerardat.app.R |only SPARTAAS-1.2.0/SPARTAAS/R/mapclust.R | 65 +--- SPARTAAS-1.2.0/SPARTAAS/R/perioclust.R | 132 ++++---- SPARTAAS-1.2.0/SPARTAAS/R/util.R | 135 +------- SPARTAAS-1.2.0/SPARTAAS/README.md |only SPARTAAS-1.2.0/SPARTAAS/build/partial.rdb |binary SPARTAAS-1.2.0/SPARTAAS/data/datacerardat.RData |only SPARTAAS-1.2.0/SPARTAAS/inst/shiny-examples/cerardat.app |only SPARTAAS-1.2.0/SPARTAAS/inst/shiny-examples/hclustcompro.app/server.R | 24 - SPARTAAS-1.2.0/SPARTAAS/inst/shiny-examples/hclustcompro.app/ui.R | 31 + SPARTAAS-1.2.0/SPARTAAS/inst/shiny-examples/map.app/ui.R | 7 SPARTAAS-1.2.0/SPARTAAS/inst/shiny-examples/serio.app/server.R | 142 ++++++++ SPARTAAS-1.2.0/SPARTAAS/inst/shiny-examples/serio.app/ui.R | 15 SPARTAAS-1.2.0/SPARTAAS/man/CAdist.Rd | 6 SPARTAAS-1.2.0/SPARTAAS/man/SPARTAAS-package.Rd | 49 +-- SPARTAAS-1.2.0/SPARTAAS/man/adjacency.Rd | 10 SPARTAAS-1.2.0/SPARTAAS/man/arrondi.Rd | 115 +++---- SPARTAAS-1.2.0/SPARTAAS/man/cerardat.Rd |only SPARTAAS-1.2.0/SPARTAAS/man/cerardat_app.Rd |only SPARTAAS-1.2.0/SPARTAAS/man/cerardat_estim_nf.Rd |only SPARTAAS-1.2.0/SPARTAAS/man/datacancer.Rd | 2 SPARTAAS-1.2.0/SPARTAAS/man/dataceram.Rd | 6 SPARTAAS-1.2.0/SPARTAAS/man/datacerardat.Rd |only SPARTAAS-1.2.0/SPARTAAS/man/datangkor.Rd | 6 SPARTAAS-1.2.0/SPARTAAS/man/datarcheo.Rd | 68 ++-- SPARTAAS-1.2.0/SPARTAAS/man/extract_results.Rd |only SPARTAAS-1.2.0/SPARTAAS/man/hclust.Rd | 158 +++++----- SPARTAAS-1.2.0/SPARTAAS/man/hclustcompro.Rd | 24 - SPARTAAS-1.2.0/SPARTAAS/man/hclustcompro_detail_resampling.Rd | 12 SPARTAAS-1.2.0/SPARTAAS/man/hclustcompro_select_alpha.Rd | 88 +---- SPARTAAS-1.2.0/SPARTAAS/man/hclustcompro_subdivide.Rd | 4 SPARTAAS-1.2.0/SPARTAAS/man/mapclust.Rd | 49 +-- SPARTAAS-1.2.0/SPARTAAS/man/mapclust_app.Rd | 16 - SPARTAAS-1.2.0/SPARTAAS/man/mapclust_cut_tree.Rd | 30 - SPARTAAS-1.2.0/SPARTAAS/man/overlap.Rd | 8 SPARTAAS-1.2.0/SPARTAAS/man/plot.cerardat_obj.Rd |only SPARTAAS-1.2.0/SPARTAAS/man/seriograph.Rd | 8 SPARTAAS-1.2.0/SPARTAAS/man/timerange.Rd | 14 43 files changed, 716 insertions(+), 658 deletions(-)
Title: Bindings for the 'Geospatial' Data Abstraction Library
Description: Provides bindings to the 'Geospatial' Data Abstraction Library ('GDAL') (>= 1.11.4) and access to projection/transformation operations from the 'PROJ' library. Please note that 'rgdal' will be retired during October 2023, plan transition to sf/stars/'terra' functions using 'GDAL' and 'PROJ' at your earliest convenience (see <https://r-spatial.org/r/2023/05/15/evolution4.html> and earlier blogs for guidance). Use is made of classes defined in the 'sp' package. Raster and vector map data can be imported into R, and raster and vector 'sp' objects exported. The 'GDAL' and 'PROJ' libraries are external to the package, and, when installing the package from source, must be correctly installed first; it is important that 'GDAL' < 3 be matched with 'PROJ' < 6. From 'rgdal' 1.5-8, installed with to 'GDAL' >=3, 'PROJ' >=6 and 'sp' >= 1.4, coordinate reference systems use 'WKT2_2019' strings, not 'PROJ' strings. 'Windows' and 'macOS' binaries (including 'GDAL', 'PROJ' and t [...truncated...]
Author: Roger Bivand [cre, aut] ,
Tim Keitt [aut],
Barry Rowlingson [aut, ctb],
Edzer Pebesma [ctb],
Michael Sumner [ctb],
Robert Hijmans [ctb],
Daniel Baston [ctb],
Even Rouault [cph, ctb],
Frank Warmerdam [cph, ctb],
Jeroen Ooms [ctb],
Colin Rundel [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between rgdal versions 1.6-6 dated 2023-04-18 and 1.6-7 dated 2023-05-31
DESCRIPTION | 10 MD5 | 24 NEWS.md | 8 R/AAA.R | 14 build/vignette.rds |binary configure | 18 inst/SVN_VERSION | 2 inst/doc/CRS_projections_transformations.R | 4 inst/doc/CRS_projections_transformations.html | 2275 +++++++++++++++++++++----- inst/doc/OGR_shape_encoding.pdf |binary inst/doc/PROJ6_GDAL3.html | 1961 +++++++++++++++++++--- tests/tripup.R | 12 tests/tripup.Rout.save | 18 13 files changed, 3637 insertions(+), 709 deletions(-)
Title: Open Source Geometry Engine ('GEOS') R API
Description: Provides an R API to the Open Source Geometry Engine
('GEOS') library (<https://libgeos.org/>) and a vector format
with which to efficiently store 'GEOS' geometries. High-performance functions
to extract information from, calculate relationships between, and
transform geometries are provided. Finally, facilities to import
and export geometry vectors to other spatial formats are provided.
Author: Dewey Dunnington [aut, cre] ,
Edzer Pebesma [aut]
Maintainer: Dewey Dunnington <dewey@fishandwhistle.net>
Diff between geos versions 0.2.2 dated 2022-10-22 and 0.2.3 dated 2023-05-31
DESCRIPTION | 9 ++++----- MD5 | 10 +++++----- NEWS.md | 5 +++++ tests/testthat/Rplots.pdf |binary tests/testthat/test-compat-wk.R | 2 +- tests/testthat/test-geos-unary-geometry.R | 8 +++++--- 6 files changed, 20 insertions(+), 14 deletions(-)
Title: Downscaling Species Occupancy
Description: Uses species occupancy at coarse grain sizes to predict species occupancy at fine grain sizes. Ten models are provided to fit and extrapolate the occupancy-area relationship, as well as methods for preparing atlas data for modelling. See Marsh et. al. (2018) <doi:10.18637/jss.v086.c03>.
Author: Charles Marsh [aut, cre, cph]
Maintainer: Charles Marsh <charlie.marsh@mailbox.org>
Diff between downscale versions 4.2-0 dated 2021-11-24 and 5.0.0 dated 2023-05-31
downscale-4.2-0/downscale/NEWS |only downscale-4.2-0/downscale/R/OptimiseParameters.R |only downscale-4.2-0/downscale/R/OptimiseParametersFNB.R |only downscale-4.2-0/downscale/R/OptimiseParametersGNB.R |only downscale-4.2-0/downscale/R/OptimiseParametersLogis.R |only downscale-4.2-0/downscale/R/OptimiseParametersThomas.R |only downscale-4.2-0/downscale/inst/extdata/Polyommatus_coridon_gbif_records.csv |only downscale-5.0.0/downscale/DESCRIPTION | 36 downscale-5.0.0/downscale/MD5 | 86 downscale-5.0.0/downscale/NAMESPACE | 22 downscale-5.0.0/downscale/NEWS.md |only downscale-5.0.0/downscale/R/DataInput.R | 119 downscale-5.0.0/downscale/R/OptimisePars.R |only downscale-5.0.0/downscale/R/OptimiseParsFNB.R |only downscale-5.0.0/downscale/R/OptimiseParsGNB.R |only downscale-5.0.0/downscale/R/OptimiseParsLogis.R |only downscale-5.0.0/downscale/R/OptimiseParsThomas.R |only downscale-5.0.0/downscale/R/PredictFunctions.R | 46 downscale-5.0.0/downscale/R/ResidFunctions.R | 50 downscale-5.0.0/downscale/R/StartingParams.R | 112 downscale-5.0.0/downscale/R/ThomasFunctions.R | 35 downscale-5.0.0/downscale/R/checkInputs.R |only downscale-5.0.0/downscale/R/downscale.R | 125 downscale-5.0.0/downscale/R/ensemble.downscale.R | 156 - downscale-5.0.0/downscale/R/hui.downscale.R | 148 - downscale-5.0.0/downscale/R/plot.predict.downscale.R | 40 downscale-5.0.0/downscale/R/predict.downscale.R | 86 downscale-5.0.0/downscale/R/upgrain.R | 538 +--- downscale-5.0.0/downscale/R/upgrain.threshold.R | 351 +- downscale-5.0.0/downscale/R/zzz.R |only downscale-5.0.0/downscale/README.md |only downscale-5.0.0/downscale/build/vignette.rds |binary downscale-5.0.0/downscale/inst/CITATION | 25 downscale-5.0.0/downscale/inst/doc/Downscaling.R | 60 downscale-5.0.0/downscale/inst/doc/Downscaling.Rmd | 77 downscale-5.0.0/downscale/inst/doc/Downscaling.html | 1286 +++++----- downscale-5.0.0/downscale/inst/doc/Upgraining.R | 2 downscale-5.0.0/downscale/inst/doc/Upgraining.Rmd | 2 downscale-5.0.0/downscale/inst/doc/Upgraining.html | 314 +- downscale-5.0.0/downscale/man/Downscale-package.Rd | 13 downscale-5.0.0/downscale/man/downscale.Rd | 32 downscale-5.0.0/downscale/man/ensemble.downscale.Rd | 29 downscale-5.0.0/downscale/man/figures/Flow.png |binary downscale-5.0.0/downscale/man/hui.downscale.Rd | 19 downscale-5.0.0/downscale/man/plot.predict.downscale.Rd | 2 downscale-5.0.0/downscale/man/predict.downscale.Rd | 37 downscale-5.0.0/downscale/man/upgrain.Rd | 20 downscale-5.0.0/downscale/man/upgrain.threshold.Rd | 12 downscale-5.0.0/downscale/vignettes/Downscaling.Rmd | 77 downscale-5.0.0/downscale/vignettes/Upgraining.Rmd | 2 downscale-5.0.0/downscale/vignettes/figures/Flow.png |binary downscale-5.0.0/downscale/vignettes/figures/Saturation.png |binary 52 files changed, 2123 insertions(+), 1836 deletions(-)
Title: Tools for Causal Inference with Possibly Invalid Instrumental
Variables
Description: Two stage curvature identification with machine learning for causal
inference in settings when instrumental variable regression is not suitable
because of potentially invalid instrumental variables. Based on Guo and
Buehlmann (2022) "Two Stage Curvature Identification with Machine Learning:
Causal Inference with Possibly Invalid Instrumental Variables"
<arXiv:2203.12808>. The vignette is available in Carl, Emmenegger, Bühlmann and Guo (2023)
"TSCI: two stage curvature identification for causal inference with
invalid instruments" <arXiv:2304.00513>.
Author: David Carl [aut, cre] ,
Corinne Emmenegger [aut] ,
Wei Yuan [aut],
Mengchu Zheng [aut],
Zijian Guo [aut]
Maintainer: David Carl <david.carl@phd.unibocconi.it>
Diff between TSCI versions 2.0.0 dated 2023-04-04 and 3.0.0 dated 2023-05-31
DESCRIPTION | 8 ++++---- MD5 | 44 +++++++++++++++++++++++--------------------- NAMESPACE | 1 + R/aggregate_output.R | 12 ++++++------ R/backfitting.R | 2 +- R/coef-method.R | 33 ++++++++++++++++++++++++--------- R/confint-method.R | 5 ++--- R/create_interactions.R | 2 +- R/create_monomials.R | 10 +++++----- R/cross_validate.R | 2 +- R/print-method.R | 21 ++++++++++++++++----- R/print-summary-method.R | 20 +++++++++++++++----- R/summary-method.R | 10 ++++------ R/tsci_fit_NA_return.R | 14 +++++++------- R/tsci_selection.R | 12 ++++++------ R/tsci_selection_stats.R | 12 +++++------- README.md | 4 ++-- man/coef.tsci.Rd | 15 ++++++++------- man/confint.tsci.Rd | 2 +- man/create_interactions.Rd | 2 +- man/create_monomials.Rd | 2 +- man/print.summary.tsci.Rd |only man/print.tsci.Rd |only man/summary.tsci.Rd | 4 ++-- 24 files changed, 136 insertions(+), 101 deletions(-)
More information about rgoogleclassroom at CRAN
Permanent link
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-05-20 0.0.2
2020-03-14 0.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-04-01 1.2.0
2020-07-10 1.1.0
2019-07-18 1.0.0
Title: VA CVD Risk Score
Description: Estimates the predicted 10-year cardiovascular (CVD) risk score (in probability) for women military service
members and veterans by inputting patient profiles. The proposed women CVD risk score improves the accuracy of the
existing American College of Cardiology/American Heart Association CVD risk assessment
tool in predicting long‐term CVD risk for VA women, particularly in young and racial/ethnic
minority women. See the reference: Jeon‐Slaughter, H., Chen, X., Tsai, S., Ramanan, B., & Ebrahimi, R.
(2021) <doi:10.1161/JAHA.120.019217>.
Author: Xiaofei Chen [aut, cre],
Haekyung Jeon-Slaughter [aut]
Maintainer: Xiaofei Chen <bill.nj08873@gmail.com>
Diff between vaRiskScore versions 1.0.0 dated 2023-02-16 and 1.1.0 dated 2023-05-31
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/vaScore.R | 9 +++------ 3 files changed, 8 insertions(+), 11 deletions(-)
Title: Large-Scale Bayesian Variable Selection Using Variational
Methods
Description: Fast algorithms for fitting Bayesian variable selection
models and computing Bayes factors, in which the outcome (or
response variable) is modeled using a linear regression or a
logistic regression. The algorithms are based on the variational
approximations described in "Scalable variational inference for
Bayesian variable selection in regression, and its accuracy in
genetic association studies" (P. Carbonetto & M. Stephens, 2012,
<DOI:10.1214/12-BA703>). This software has been applied to large
data sets with over a million variables and thousands of samples.
Author: Peter Carbonetto [aut, cre],
Matthew Stephens [aut],
David Gerard [ctb]
Maintainer: Peter Carbonetto <peter.carbonetto@gmail.com>
Diff between varbvs versions 2.6-8 dated 2023-03-22 and 2.6-10 dated 2023-05-31
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- R/misc.R | 12 +++++++----- R/varbvs.R | 18 +++++++++--------- R/varbvsmix.R | 2 +- inst/doc/cd.html | 18 +++++++++++++----- inst/doc/cfw.html | 18 +++++++++++++----- inst/doc/cytokine.html | 18 +++++++++++++----- inst/doc/leukemia.html | 32 ++++++++++++++++++++------------ tests/testthat/test_varbvs.R | 22 +++++++++++----------- 10 files changed, 100 insertions(+), 66 deletions(-)
Title: Calculating Linkage Disequilibrium (LD) in Human Population
Groups of Interest
Description: Provides access to the 'LDlink' API (<https://ldlink.nih.gov/?tab=apiaccess>)
using the R console. This programmatic access facilitates researchers who are
interested in performing batch queries in 1000 Genomes Project (2015) <doi:10.1038/nature15393>
data using 'LDlink'. 'LDlink' is an interactive and powerful suite of web-based tools for querying
germline variants in human population groups of interest. For more details, please see
Machiela et al. (2015) <doi:10.1093/bioinformatics/btv402>.
Author: Timothy A. Myers [aut, cre] ,
Stephen J. Chanock [aut],
Mitchell J. Machiela [aut]
Maintainer: Timothy A. Myers <myersta@mail.nih.gov>
Diff between LDlinkR versions 1.2.3 dated 2022-12-15 and 1.3.0 dated 2023-05-31
DESCRIPTION | 12 ++--- MD5 | 82 ++++++++++++++++++------------------ NEWS.md | 7 ++- R/LDexpress.R | 6 +- R/LDhap.R | 6 +- R/LDmatrix.R | 6 +- R/LDpair.R | 6 +- R/LDpop.R | 6 +- R/LDproxy.R | 6 +- R/LDproxy_batch.R | 4 - R/LDtrait.R | 6 +- R/SNPchip.R | 6 +- R/SNPclip.R | 6 +- README.md | 14 +++--- build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 27 ++++++----- inst/WORDLIST | 8 +-- inst/doc/LDlinkR.Rmd | 26 +++++------ inst/doc/LDlinkR.html | 57 ++++++++++--------------- man/LDexpress.Rd | 4 - man/LDhap.Rd | 4 - man/LDlinkR-package.Rd | 4 - man/LDmatrix.Rd | 4 - man/LDpair.Rd | 4 - man/LDpop.Rd | 4 - man/LDproxy.Rd | 4 - man/LDproxy_batch.Rd | 4 - man/LDtrait.Rd | 4 - man/SNPchip.Rd | 4 - man/SNPclip.Rd | 4 - tests/testthat/test-ldexpress.R | 2 tests/testthat/test-ldhap.R | 8 +++ tests/testthat/test-ldmatrix.R | 2 tests/testthat/test-ldpair.R | 2 tests/testthat/test-ldpop.R | 5 ++ tests/testthat/test-ldproxy.R | 5 ++ tests/testthat/test-ldproxy_batch.R | 3 + tests/testthat/test-ldtrait.R | 2 tests/testthat/test-snpchip.R | 5 ++ tests/testthat/test-snpclip.R | 5 ++ vignettes/LDlinkR.Rmd | 26 +++++------ 42 files changed, 218 insertions(+), 182 deletions(-)
Title: Entropy Partitioning to Measure Diversity
Description: Measurement and partitioning of diversity, based on Tsallis entropy, following Marcon and Herault (2015) <doi:10.18637/jss.v067.i08>.
'entropart' provides functions to calculate alpha, beta and gamma diversity of communities, including phylogenetic and functional diversity.
Estimation-bias corrections are available.
Author: Eric Marcon [aut, cre] ,
Bruno Herault [aut]
Maintainer: Eric Marcon <eric.marcon@agroparistech.fr>
Diff between entropart versions 1.6-11 dated 2022-07-11 and 1.6-12 dated 2023-05-31
DESCRIPTION | 6 - MD5 | 28 ++++---- NEWS.md | 10 +++ R/Preprocess.Tree.R | 4 + R/Shannon.R | 4 - R/SpeciesDistribution.R | 4 - README.md | 2 build/vignette.rds |binary inst/doc/entropart.Rmd | 2 inst/doc/entropart.html | 148 +++++++++++++++++++++++---------------------- man/Coverage.Rd | 2 man/Richness.Rd | 2 man/SpeciesDistribution.Rd | 4 - man/rCommunity.Rd | 2 vignettes/entropart.Rmd | 2 15 files changed, 121 insertions(+), 99 deletions(-)
Title: Deal with Dependencies
Description: Manage dependencies during package development. This can
retrieve all dependencies that are used in ".R" files in the "R/"
directory, in ".Rmd" files in "vignettes/" directory and in 'roxygen2'
documentation of functions. There is a function to update the
"DESCRIPTION" file of your package with 'CRAN' packages or any other
remote package. All functions to retrieve dependencies of ".R"
scripts and ".Rmd" or ".qmd" files can be used independently of a
package development.
Author: Sebastien Rochette [cre, aut] ,
Vincent Guyader [aut] ,
Murielle Delmotte [aut] ,
Swann Floc'hlay [aut] ,
ThinkR [cph, fnd]
Maintainer: Sebastien Rochette <sebastien@thinkr.fr>
Diff between attachment versions 0.3.1 dated 2023-01-27 and 0.4.0 dated 2023-05-31
DESCRIPTION | 55 +++--- MD5 | 66 ++++--- NAMESPACE | 2 NEWS.md | 22 ++ R/amend_with_config.R |only R/att_from_rmds.R | 11 - R/att_to_description.R | 73 +++++++- R/create_dependencies_file.R | 125 ++++++-------- R/create_renv.R | 17 + R/dependencies_file_text.R |only R/install_from_description.R | 6 R/set_remotes.R | 2 README.md | 86 ++++++--- build/vignette.rds |binary inst/doc/a-fill-pkg-description.R | 24 ++ inst/doc/a-fill-pkg-description.Rmd | 79 ++++++++ inst/doc/a-fill-pkg-description.html | 221 ++++++++++++++++--------- inst/doc/b-bookdown-and-scripts.Rmd | 2 inst/doc/b-bookdown-and-scripts.html | 6 inst/doc/create-dependencies-file.R |only inst/doc/create-dependencies-file.Rmd |only inst/doc/create-dependencies-file.html |only man/att_amend_desc.Rd | 46 ++++- man/attachment-package.Rd | 2 man/create_dependencies_file.Rd | 36 ++-- man/create_renv_for_dev.Rd | 1 man/find_remotes.Rd | 2 man/install_from_description.Rd | 3 man/install_if_missing.Rd | 3 tests/testthat/test-amend-description.R | 40 +++- tests/testthat/test-amend_with_config.R |only tests/testthat/test-create_dependencies_file.R | 85 +++++++++ tests/testthat/test-dependencies_file_text.R |only tests/testthat/test-renv_create.R | 51 ++--- tests/testthat/test-rmd.R | 21 ++ vignettes/a-fill-pkg-description.Rmd | 79 ++++++++ vignettes/b-bookdown-and-scripts.Rmd | 2 vignettes/create-dependencies-file.Rmd |only 38 files changed, 856 insertions(+), 312 deletions(-)
Title: Enhance Reproducibility of R Code
Description: A collection of high-level, machine- and OS-independent tools
for making reproducible and reusable content in R.
The two workhorse functions are Cache() and prepInputs(). Cache()
allows for nested caching, is robust to environments and objects with
environments (like functions), and has deals with some classes of
file-backed R objects e.g., from terra and raster packages.
Both functions have been developed to
be foundational components of data retrieval
and processing in continuous workflow situations. In both functions,
efforts are made to make the first and subsequent calls of functions have
the same result, but faster at subsequent times by way of checksums
and digesting. Several features are still under development, including
cloud storage of cached objects, allowing for sharing between users. Several
advanced options are available, see ?reproducibleOptions().
Author: Eliot J B McIntire [aut, cre] ,
Alex M Chubaty [aut] ,
Tati Micheletti [ctb] ,
Ceres Barros [ctb] ,
Ian Eddy [ctb] ,
His Majesty the King in Right of Canada, as represented by the Minister
of Natural Resources Canada [cph]
Maintainer: Eliot J B McIntire <eliot.mcintire@canada.ca>
Diff between reproducible versions 2.0.2 dated 2023-05-07 and 2.0.4 dated 2023-05-31
DESCRIPTION | 12 MD5 | 138 +- NAMESPACE | 2 NEWS.md | 114 + R/DBI.R | 6 R/cache-helpers.R | 5 R/cache-internals.R | 2 R/cache.R | 71 - R/cacheGeo.R | 3 R/checksums.R | 29 R/cloud.R | 32 R/download.R | 66 - R/exportedMethods.R | 52 R/helpers.R | 95 + R/options.R | 42 R/packages.R | 43 R/paths.R | 82 - R/postProcess.R | 54 R/postProcessTo.R | 185 ++- R/preProcess.R | 214 ++- R/prepInputs.R | 70 - R/robustDigest.R | 40 R/showCacheEtc.R | 11 R/terra-migration.R | 2 R/zzz.R | 1 inst/WORDLIST | 2 inst/doc/Intro-to-Cache.html | 1334 +++++++++++------------ inst/examples/example_assessDataType.R | 219 +-- inst/examples/example_postProcess.R | 2 man/Cache.Rd | 12 man/CacheGeo.Rd | 3 man/Checksums.Rd | 6 man/assessDataType.Rd | 221 +-- man/checkRelative.Rd | 13 man/deprecated.Rd | 2 man/dlGeneric.Rd | 11 man/dot-removeCacheAtts.Rd | 6 man/downloadFile.Rd | 2 man/exportedMethods.Rd | 2 man/linkOrCopy.Rd | 2 man/postProcess.Rd | 55 man/postProcessTo.Rd | 69 - man/prepInputs.Rd | 20 man/reproducibleOptions.Rd | 18 man/robustDigest.Rd | 2 man/setSubAttrInList.Rd | 3 man/terra-migration.Rd | 2 tests/test-all.R | 25 tests/testthat/helper-allEqual.R | 98 + tests/testthat/setup.R | 20 tests/testthat/test-cache.R | 149 +- tests/testthat/test-cacheGeo.R | 1 tests/testthat/test-cacheHelpers.R | 1 tests/testthat/test-checkPath.R | 37 tests/testthat/test-checksums.R | 14 tests/testthat/test-cloud.R | 14 tests/testthat/test-cluster.R | 9 tests/testthat/test-copy.R | 1 tests/testthat/test-devMode.R | 2 tests/testthat/test-download.R | 6 tests/testthat/test-filesMissingExtension.R | 5 tests/testthat/test-gis.R | 40 tests/testthat/test-misc.R | 24 tests/testthat/test-postProcess.R | 10 tests/testthat/test-postProcessTerra.R | 547 ++++----- tests/testthat/test-preProcessDoesntWork.R | 25 tests/testthat/test-preProcessWorks.R | 153 ++ tests/testthat/test-prepInputs-large-files.R | 1 tests/testthat/test-prepInputs.R | 77 - tests/testthat/test-prepInputsInNestedArchives.R | 23 70 files changed, 2687 insertions(+), 1972 deletions(-)
Title: Permutation Tests for Randomization Model
Description: Perform permutation-based hypothesis testing for randomized
experiments as suggested in Ludbrook & Dudley (1998) <doi:10.2307/2685470>
and Ernst (2004) <doi:10.1214/088342304000000396>, introduced in Pham et al.
(2022) <doi:10.1016/j.chemosphere.2022.136736>.
Author: Duy Nghia Pham [aut, cre] ,
Inna M. Sokolova [ths]
Maintainer: Duy Nghia Pham <nghiapham@yandex.com>
Diff between peramo versions 0.1.2 dated 2023-03-29 and 0.1.3 dated 2023-05-31
peramo-0.1.2/peramo/R/copper_temp-data.R |only peramo-0.1.2/peramo/data/copper_temp.RData |only peramo-0.1.2/peramo/man/copper_temp.Rd |only peramo-0.1.3/peramo/DESCRIPTION | 14 ++++----- peramo-0.1.3/peramo/MD5 | 28 +++++++++---------- peramo-0.1.3/peramo/NAMESPACE | 4 ++ peramo-0.1.3/peramo/R/XY.R | 2 - peramo-0.1.3/peramo/R/ctm-data.R |only peramo-0.1.3/peramo/R/ensulizole-data.R | 6 ++-- peramo-0.1.3/peramo/R/peramo-package.R | 4 ++ peramo-0.1.3/peramo/R/tw_complex.R | 42 ++++++++++++++++++++++++++--- peramo-0.1.3/peramo/build/partial.rdb |binary peramo-0.1.3/peramo/data/ctm.RData |only peramo-0.1.3/peramo/data/ensulizole.RData |binary peramo-0.1.3/peramo/man/XY.Rd | 2 - peramo-0.1.3/peramo/man/ctm.Rd |only peramo-0.1.3/peramo/man/ensulizole.Rd | 12 ++++---- peramo-0.1.3/peramo/man/tw_complex.Rd | 6 ++-- 18 files changed, 82 insertions(+), 38 deletions(-)
Title: Data on Asylum and Resettlement for the UK
Description: Data on Asylum and Resettlement for the UK,
provided by the Home Office <https://www.gov.uk/government/statistical-data-sets/immigration-system-statistics-data-tables-year-ending-march-2023>.
Author: Matthew Gwynfryn Thomas [cre, aut],
Mike Page [aut],
British Red Cross [cph]
Maintainer: Matthew Gwynfryn Thomas <matthewgthomas@gmail.com>
Diff between asylum versions 1.0.3 dated 2023-03-11 and 1.1.0 dated 2023-05-31
DESCRIPTION | 8 MD5 | 162 +++++++------ NEWS.md | 5 R/data.R | 303 +++++++++++++++++++++---- R/sysdata.rda |binary README.md | 6 data/age_disputes.rda |binary data/age_of_asylum_operations.rda |binary data/appeal_representation_rate.rda |binary data/appeals_determined.rda |binary data/appeals_lodged.rda |binary data/applications.rda |binary data/applications_processed_in_6_months.rda |binary data/awaiting_decision.rda |binary data/children_entering_detention.rda |binary data/claims_certified_section_94.rda |binary data/decisions_resettlement.rda |binary data/detention_cost_per_day.rda |only data/detention_pregnant_women.rda |only data/family_reunion.rda |binary data/grant_rates_initial_annual.rda |only data/grant_rates_initial_quarterly.rda |only data/inadmissibility_cases_considered.rda |only data/irregular_migration.rda |binary data/local_authority_resettlement.rda |binary data/local_authority_support.rda |binary data/notices_of_intent.rda |only data/nrpf_change_of_conditions_age.rda |binary data/nrpf_change_of_conditions_decisions.rda |binary data/nrpf_change_of_conditions_gender.rda |binary data/nrpf_change_of_conditions_nationality.rda |binary data/nts.rda |binary data/oral_hearings_volume.rda |binary data/people_entering_detention.rda |binary data/people_in_detention.rda |binary data/people_leaving_detention.rda |binary data/returns.rda |binary data/returns_by_destination.rda |binary data/returns_offenders_by_destination.rda |binary data/returns_offenders_by_nationality.rda |binary data/small_boat_NRM_outcomes.rda |only data/small_boat_NRM_referrals.rda |only data/small_boat_asylum_applications.rda |only data/small_boat_initial_decisions.rda |only data/support_applications_rasi.rda |binary data/support_received.rda |binary data/travel_documents.rda |binary man/age_disputes.Rd | 2 man/age_of_asylum_operations.Rd | 2 man/appeal_representation_rate.Rd | 2 man/appeals_determined.Rd | 2 man/appeals_lodged.Rd | 2 man/applications.Rd | 2 man/applications_processed_in_6_months.Rd | 76 +++--- man/awaiting_decision.Rd | 2 man/children_entering_detention.Rd | 58 ++-- man/claims_certified_section_94.Rd | 66 ++--- man/decisions_resettlement.Rd | 2 man/detention_cost_per_day.Rd |only man/detention_pregnant_women.Rd |only man/detention_summary_flow.Rd | 64 ++--- man/detentions_deaths_and_absconds.Rd | 56 ++-- man/detentions_deaths_details.Rd | 60 ++-- man/family_reunion.Rd | 2 man/figures |only man/grant_rates_initial_annual.Rd |only man/grant_rates_initial_quarterly.Rd |only man/inadmissibility_cases_considered.Rd |only man/irregular_migration.Rd | 64 ++--- man/local_authority_resettlement.Rd | 2 man/local_authority_support.Rd | 4 man/notices_of_intent.Rd |only man/nrpf_change_of_conditions_age.Rd | 2 man/nrpf_change_of_conditions_decisions.Rd | 2 man/nrpf_change_of_conditions_gender.Rd | 2 man/nrpf_change_of_conditions_nationality.Rd | 3 man/nts.Rd | 2 man/oral_hearings_volume.Rd | 2 man/people_entering_detention.Rd | 64 ++--- man/people_in_detention.Rd | 66 ++--- man/people_leaving_detention.Rd | 66 ++--- man/returns.Rd | 68 ++--- man/returns_by_destination.Rd | 60 ++-- man/returns_offenders_by_destination.Rd | 56 ++-- man/returns_offenders_by_nationality.Rd | 60 ++-- man/small_boat_NRM_outcomes.Rd |only man/small_boat_NRM_referrals.Rd |only man/small_boat_asylum_applications.Rd |only man/small_boat_initial_decisions.Rd |only man/support_applications_rasi.Rd | 2 man/support_received.Rd | 4 man/travel_documents.Rd | 2 92 files changed, 832 insertions(+), 581 deletions(-)
Title: Applies Multiclass AdaBoost.M1, SAMME and Bagging
Description: It implements Freund and Schapire's Adaboost.M1 algorithm and Breiman's Bagging
algorithm using classification trees as individual classifiers. Once these classifiers have been
trained, they can be used to predict on new data. Also, cross validation estimation of the error can
be done. Since version 2.0 the function margins() is available to calculate the margins for these
classifiers. Also a higher flexibility is achieved giving access to the rpart.control() argument
of 'rpart'. Four important new features were introduced on version 3.0, AdaBoost-SAMME (Zhu
et al., 2009) is implemented and a new function errorevol() shows the error of the ensembles as
a function of the number of iterations. In addition, the ensembles can be pruned using the option
'newmfinal' in the predict.bagging() and predict.boosting() functions and the posterior probability of
each class for observations can be obtained. Version 3.1 modifies the relative importance measure
to take into account the gain of the Gin [...truncated...]
Author: Alfaro, Esteban; Gamez, Matias and Garcia, Noelia; with contributions from L. Guo, A. Albano, M. Sciandra and A. Plaia
Maintainer: Esteban Alfaro <Esteban.Alfaro@uclm.es>
Diff between adabag versions 4.3 dated 2023-05-01 and 5.0 dated 2023-05-31
DESCRIPTION | 18 ++++++---- MD5 | 17 +++++++-- NAMESPACE | 23 ++++++++----- R/Ensemble_ranking_IW.R |only R/errorevol_ranking_vector_IW.R |only R/internal_functions.R |only R/prep_data.R |only data |only man/Ensemble_ranking_IW.Rd |only man/adabag-internal.Rd | 23 +++++++++++-- man/adabag-package.Rd | 63 +++++++++++++++++-------------------- man/errorevol_ranking_vector_IW.Rd |only man/prep_data.Rd |only man/simulatedRankingData.Rd |only 14 files changed, 88 insertions(+), 56 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-04-10 1.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-08-23 1.9.3
2021-06-03 1.8.0
2020-10-01 1.6.2
2020-02-19 1.5.2
2019-05-22 1.3.9
2019-05-07 1.3.8
2019-03-18 1.3.3
2019-01-02 1.2.3
2018-10-22 1.2.0
2018-03-03 1.1.2
2017-12-05 1.0.6
2017-09-08 0.9.2
2017-06-08 0.8.1
2017-03-02 0.7.0
2016-12-22 0.5.0
2016-12-07 0.4.5
2016-11-15 0.4.3
2016-09-19 0.4.0
2016-08-11 0.2.0
2016-06-13 0.1.3
2016-04-18 0.1.2
2016-04-15 0.1.1
2016-04-04 0.1.0
Title: Discrete Nonlinear Filtering for Stochastic Volatility Models
Description: Generates simulated paths from various financial stochastic volatility models
with jumps and applies the discrete nonlinear filter (DNF) of Kitagawa (1987) <doi:10.1080/01621459.1987.10478534> to
compute likelihood evaluations, filtering distribution estimates, and maximum likelihood parameter estimates.
The algorithm is implemented following the work of Bégin and Boudreault (2021) <doi:10.1080/10618600.2020.1840995>.
Author: Louis Arsenault-Mahjoubi [aut, cre],
Jean-Francois Begin [aut],
Mathieu Boudreault [aut]
Maintainer: Louis Arsenault-Mahjoubi <larsenau@sfu.ca>
Diff between SVDNF versions 0.1.4 dated 2023-03-01 and 0.1.5 dated 2023-05-31
SVDNF-0.1.4/SVDNF/R/plot.SVDNF.R |only SVDNF-0.1.5/SVDNF/DESCRIPTION | 7 SVDNF-0.1.5/SVDNF/MD5 | 26 - SVDNF-0.1.5/SVDNF/NAMESPACE | 37 +- SVDNF-0.1.5/SVDNF/R/DNF.R | 21 + SVDNF-0.1.5/SVDNF/R/DNFOptim.R | 421 ++++++++++++++++--------- SVDNF-0.1.5/SVDNF/R/Methods.R |only SVDNF-0.1.5/SVDNF/R/dynamicsSVM.R | 69 +++- SVDNF-0.1.5/SVDNF/R/gridMaker.R | 21 - SVDNF-0.1.5/SVDNF/R/modelSim.R | 1 SVDNF-0.1.5/SVDNF/man/DNF.dynamicsSVM.Rd | 3 SVDNF-0.1.5/SVDNF/man/DNFOptim.Rd | 17 - SVDNF-0.1.5/SVDNF/man/logLik.SVDNF.Rd |only SVDNF-0.1.5/SVDNF/man/plot.SVDNF.Rd | 10 SVDNF-0.1.5/SVDNF/man/plot.predict.DNFOptim.Rd |only SVDNF-0.1.5/SVDNF/man/predict.DNFOptim.Rd |only SVDNF-0.1.5/SVDNF/man/summary.DNFOptim.Rd |only 17 files changed, 421 insertions(+), 212 deletions(-)
Title: R Programming: Zero to Pro
Description: This is a companion package of the book "R Programming: Zero to Pro" <https://r02pro.github.io/>. It contains the datasets used in the book and provides interactive exercises corresponding to the book. It covers a wide range of topics including visualization, data transformation, tidying data, data input and output.
Author: Yang Feng [aut, cre],
Jianan Zhu [aut]
Maintainer: Yang Feng <yangfengstat@gmail.com>
Diff between r02pro versions 0.1 dated 2021-07-05 and 0.2 dated 2023-05-31
r02pro-0.1/r02pro/inst/tutorials/1.1 |only r02pro-0.1/r02pro/inst/tutorials/1.2 |only r02pro-0.2/r02pro/DESCRIPTION | 8 ++++---- r02pro-0.2/r02pro/MD5 | 21 ++++++++++++++------- r02pro-0.2/r02pro/R/gm.R |only r02pro-0.2/r02pro/R/gm2004.R |only r02pro-0.2/r02pro/data/ahp.RData |binary r02pro-0.2/r02pro/data/gm.RData |only r02pro-0.2/r02pro/data/gm2004.RData |only r02pro-0.2/r02pro/data/sahp.RData |binary r02pro-0.2/r02pro/inst/tutorials/1 |only r02pro-0.2/r02pro/inst/tutorials/2 |only r02pro-0.2/r02pro/inst/tutorials/4 |only r02pro-0.2/r02pro/man/gm.Rd |only r02pro-0.2/r02pro/man/gm2004.Rd |only 15 files changed, 18 insertions(+), 11 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-06-17 1.2.8
2022-06-09 1.2.7
2022-02-01 1.2.6
2022-01-15 1.2.5
2021-09-20 1.2.4
2021-05-29 1.2.3
2021-05-28 1.2.2
2021-05-25 1.2.1
2020-06-25 1.1.2
2020-05-14 1.1.1
2020-04-09 1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-02-09 0.7.7
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-04-05 2.5.0
2023-02-12 2.4.0
2023-01-10 2.3.0
2022-11-09 2.2.2
2022-09-20 2.2.1
2022-08-19 2.2.0
2022-05-13 2.1.2
2022-04-03 2.1.1
2022-04-01 2.1.0
2020-10-28 2.0.2
2020-10-26 2.0.0
2020-04-01 1.1.6
2020-01-30 1.1.5
Title: Get Data from the French National Database on Water 'Hub'Eau'
Description: Collection of functions to help retrieving data from
'Hub'Eau' the free and public French National APIs on water
<https://hubeau.eaufrance.fr/>.
Author: David Dorchies [aut, cre] ,
Pascal Irz [ctb],
Sebastien Grall [ctb]
Maintainer: David Dorchies <david.dorchies@inrae.fr>
Diff between hubeau versions 0.4.0 dated 2023-03-15 and 0.4.1 dated 2023-05-31
DESCRIPTION | 12 +++++----- MD5 | 12 +++++----- NAMESPACE | 1 NEWS.md | 7 ++++++ R/hubeau.R | 1 R/sysdata.rda |binary inst/doc/example_ecoulement_api.html | 39 ++++++++++++++++++----------------- 7 files changed, 42 insertions(+), 30 deletions(-)
Title: Calculate Earth’s Obliquity and Precession in the Past
Description: Easily calculate precession and obliquity from an orbital solution (defaults to ZB18a from Zeebe and Lourens (2019) <doi:10.1126/science.aax0612>) and assumed or reconstructed values for tidal dissipation (Td) and dynamical ellipticity (Ed). This is a translation and adaptation of the C-code in the supplementary material to Zeebe and Lourens (2022) <doi:10.1029/2021PA004349>, with further details on the methodology described in Zeebe (2022) <doi:10.3847/1538-3881/ac80f8>. The name of the C-routine is snvec, which refers to the key units of computation: spin vector s and orbit normal vector n.
Author: Ilja Kocken [aut, cre, trl, cph]
,
Richard Zeebe [aut]
Maintainer: Ilja Kocken <ikocken@hawaii.edu>
Diff between snvecR versions 3.7.5 dated 2023-05-19 and 3.7.6 dated 2023-05-31
DESCRIPTION | 6 - MD5 | 14 ++-- NEWS.md | 3 R/snvec.R | 2 inst/doc/analyze_grid_td-ed.html | 119 +++++++++++++++++----------------- man/snvec.Rd | 2 tests/testthat/_snaps/get_solution.md | 20 ++--- tests/testthat/test-get_solution.R | 3 8 files changed, 88 insertions(+), 81 deletions(-)
Title: Customizing Structural Equation Modelling Plots
Description: Most function focus on specific ways to customize a graph.
They use a 'qgraph' output as the first argument, and return a
modified 'qgraph' object. This allows the functions to be chained
by a pipe operator.
Author: Shu Fai Cheung [aut, cre] ,
Mark Hok Chio Lai [aut]
Maintainer: Shu Fai Cheung <shufai.cheung@gmail.com>
Diff between semptools versions 0.2.9.6 dated 2022-08-25 and 0.2.9.11 dated 2023-05-31
DESCRIPTION | 12 MD5 | 42 - NEWS.md | 21 R/data2.R |only R/nodes_keep_drop.R | 10 R/set_curve.R | 10 R/set_sem_layout.R | 98 +-- README.md | 18 build/vignette.rds |binary data/sem_2nd_order_example.rda |only inst/doc/keep_or_drop_nodes.html | 318 +++++----- inst/doc/layout_matrix.html | 537 +++++++++-------- inst/doc/quick_start_cfa.html | 383 ++++++------ inst/doc/quick_start_sem.html | 550 ++++++++++------- inst/doc/second_order.R |only inst/doc/second_order.Rmd |only inst/doc/second_order.html |only inst/doc/semptools.html | 768 ++++++++++++++----------- man/figures |only man/sem_2nd_order_example.Rd |only man/semptools-package.Rd | 2 man/set_sem_layout.Rd | 10 tests/testthat/test-change-node.R | 36 - tests/testthat/test-keep_drop_nodes.R | 17 tests/testthat/test-set_curve_bidirectional.R |only tests/testthat/test-set_sem_layout_2nd_order.R |only vignettes/second_order.Rmd |only 27 files changed, 1628 insertions(+), 1204 deletions(-)
Title: History Matching and Emulation Package
Description: A set of objects and functions for Bayes Linear emulation and history matching.
Core functionality includes automated training of emulators to data, diagnostic functions
to ensure suitability, and a variety of proposal methods for generating 'waves' of points.
For details on the mathematical background, there are many papers available on the topic
(see references attached to function help files); for details of the functions in this package,
consult the manual or help files.
Author: Andrew Iskauskas [aut, cre] ,
TJ McKinley [aut]
Maintainer: Andrew Iskauskas <andrew.iskauskas@durham.ac.uk>
Diff between hmer versions 1.4.0 dated 2023-03-29 and 1.5.0 dated 2023-05-31
DESCRIPTION | 6 MD5 | 199 +- NAMESPACE | 7 NEWS.md | 24 R/HierarchicalEmulatorDocumentation.R | 6 R/ProtoEmulatorDocumentation.R | 2 R/covariancehelpers.R |only R/diagnostics.R | 5 R/fullwave.R | 8 R/genpoints.R | 199 ++ R/idemc.R | 4 R/implausibility.R | 6 R/modelbuilding.R | 1560 ++++++++++++++-------- R/utils.R | 22 README.md | 30 build/vignette.rds |binary data/BirthDeath.rda |binary data/SIREmulators.rda |binary data/SIRImplausibility.rda |binary data/SIRMultiWaveData.rda |binary data/SIRMultiWaveEmulators.rda |binary data/SIRSample.rda |binary data/bimodalData.rda |binary data/problemData.rda |binary inst/doc/demonstrating-the-hmer-package.Rmd | 27 inst/doc/demonstrating-the-hmer-package.html | 176 +- inst/doc/emulationhandbook.Rmd | 102 - inst/doc/emulationhandbook.html | 359 ++--- inst/doc/low-dimensional-examples.Rmd | 19 inst/doc/low-dimensional-examples.html | 134 - inst/doc/stochasticandbimodalemulation.Rmd | 79 - inst/doc/stochasticandbimodalemulation.html | 337 ++-- man/HierarchicalEmulator.Rd | 6 man/Proto_emulator.Rd | 2 man/bimodal_emulator_from_data.Rd | 3 man/collect_emulators.Rd | 2 man/emulator_from_data.Rd | 251 +-- man/full_wave.Rd | 6 man/generate_new_design.Rd |only man/generate_new_runs.Rd | 27 man/idemc.Rd | 4 man/nth_implausible.Rd | 4 man/subset_emulators.Rd | 4 man/variance_emulator_from_data.Rd | 7 tests/testthat/Rplots.pdf |binary tests/testthat/test-cluster.R | 162 +- tests/testthat/test-custom_functionality.R | 8 tests/testthat/test-derivative_functions.R | 3 tests/testthat/test-em_building.R | 29 tests/testthat/test-emulator.R | 8 tests/testthat/test-implausibility.R | 10 tests/testthat/test-plotting.R | 5 tests/testthat/test-point_gen.R | 24 tests/testthat/test-proto_em.R | 6 tests/testthat/test-validation_diag.R | 14 tests/testthat/test-variance_ems.R | 47 vignettes/demo-em-plot-1.png |binary vignettes/demo-em-plot-2.png |binary vignettes/demo-em-plot-augment-1.png |binary vignettes/demo-em-plot-imp-1.png |binary vignettes/demo-em-plot-imp-2.png |binary vignettes/demo-gen-new-runs-1.png |binary vignettes/demo-lattice-plot-1.png |binary vignettes/demo-plot-waves-1.png |binary vignettes/demo-space-removed-1.png |binary vignettes/demo-validate-1.png |binary vignettes/demonstrating-the-hmer-package.Rmd | 27 vignettes/demonstrating-the-hmer-package.Rmd.orig | 7 vignettes/emulationhandbook.Rmd | 102 - vignettes/emulationhandbook.Rmd.orig | 48 vignettes/handbook-bad-design-diagnostic-1.png |binary vignettes/handbook-bad_design_generation-1.png |binary vignettes/handbook-behaviour-plot-1.png |binary vignettes/handbook-behaviour-plot-2.png |binary vignettes/handbook-dirac-delta-1.png |binary vignettes/handbook-output-active-1-1.png |binary vignettes/handbook-output-active-1-2.png |binary vignettes/handbook-output-active-2-1.png |binary vignettes/handbook-output-active-2-2.png |binary vignettes/handbook-plot-active-1.png |binary vignettes/handbook-problem-imp-1.png |binary vignettes/handbook-transformed-imp-1.png |binary vignettes/low-dimensional-examples.Rmd | 19 vignettes/low-dimensional-examples.Rmd.orig | 18 vignettes/stoch-multistate-demo-1.png |only vignettes/stoch-multistate-imp-1.png |only vignettes/stoch-multistate-indiv-imp-1.png |only vignettes/stoch-multistate-indiv-imp-2.png |only vignettes/stoch-plot-modes-1.png |binary vignettes/stoch-plot-modes-2.png |binary vignettes/stoch-plot-multistate-1.png |only vignettes/stoch-plot-multistate-2.png |only vignettes/stoch-plot-stoch-ems-1.png |binary vignettes/stoch-plot-stoch-ems-2.png |binary vignettes/stoch-plot-stoch-imp-1.png |binary vignettes/stoch-plot-stoch-var-1.png |binary vignettes/stoch-propose-multistate-1.png |only vignettes/stoch-propose-var-em-1.png |binary vignettes/stoch-validate-multistate-1.png |only vignettes/stoch-validate-multistate-2.png |only vignettes/stoch-validate-stoch-em-1.png |binary vignettes/stoch-validate-stoch-em-2.png |binary vignettes/stoch-validate-stoch-em-3.png |binary vignettes/stoch-validate-var-em-1.png |binary vignettes/stochasticandbimodalemulation.Rmd | 79 - vignettes/stochasticandbimodalemulation.Rmd.orig | 48 106 files changed, 2595 insertions(+), 1696 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-08-26 2.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-05-17 0.9.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-11-05 2.4
2018-06-13 2.3
2018-04-25 2.2
2017-05-07 2.1
2017-04-23 2.0
2016-11-14 1.7.1
2016-10-17 1.7
2016-07-29 1.6
2016-07-06 1.5
2016-05-04 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-11-09 3.5.1
2018-07-29 3.5.0
2018-03-28 3.4.1
2017-10-24 3.4.0
2017-09-28 3.3.2
2017-06-30 3.3.1
2017-06-29 3.3.0
2017-06-07 3.2.0
2017-05-14 3.0.1
2017-05-13 3.0.0
2017-03-12 2.1.0
2016-12-15 2.0.0
2016-08-10 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-01-27 5.1
Title: Symbolic Computation for Structural Equation Models
Description: A collection of functions for symbolic computation using the
'caracas' package for structural equation models and other
statistical analyses. Among its features is the ability
to calculate the model-implied covariance (and correlation)
matrix and the sampling covariance matrix of variable functions
using the delta method.
Author: Mike Cheung [aut, cre]
Maintainer: Mike Cheung <mikewlcheung@nus.edu.sg>
Diff between symSEM versions 0.1 dated 2020-07-16 and 0.2 dated 2023-05-31
symSEM-0.1/symSEM/R/helper.R |only symSEM-0.1/symSEM/build |only symSEM-0.1/symSEM/man/as.Matrix.Rd |only symSEM-0.1/symSEM/man/sym.Rd |only symSEM-0.2/symSEM/DESCRIPTION | 29 ++- symSEM-0.2/symSEM/MD5 | 24 +-- symSEM-0.2/symSEM/NAMESPACE | 68 +------- symSEM-0.2/symSEM/NEWS |only symSEM-0.2/symSEM/R/deltamethod.R | 176 ++++++++++++++++------ symSEM-0.2/symSEM/R/impliedS.R | 119 ++++++++++---- symSEM-0.2/symSEM/R/symsem-package.R |only symSEM-0.2/symSEM/README.md | 48 +++++- symSEM-0.2/symSEM/man/deltamethod.Rd | 77 +++++---- symSEM-0.2/symSEM/man/impliedS.Rd | 46 +++-- symSEM-0.2/symSEM/man/symSEM-package.Rd | 37 +--- symSEM-0.2/symSEM/tests/testthat/test_utilities.R | 61 +------ 16 files changed, 394 insertions(+), 291 deletions(-)
Title: Categorical Data Analysis Program Package
Description: Categorical data analysis by AIC. The methodology is described in
Sakamoto (1992) <ISBN 978-0-7923-1429-5>.
Author: The Institute of Statistical Mathematics
Maintainer: Masami Saga <msaga@mtb.biglobe.ne.jp>
Diff between catdap versions 1.3.5 dated 2020-03-12 and 1.3.7 dated 2023-05-31
catdap-1.3.5/catdap/R/catdap.R |only catdap-1.3.5/catdap/src/catdap1m.c |only catdap-1.3.5/catdap/src/catdap2m.c |only catdap-1.3.5/catdap/src/catdap_f.h |only catdap-1.3.7/catdap/DESCRIPTION | 14 - catdap-1.3.7/catdap/MD5 | 36 +- catdap-1.3.7/catdap/NAMESPACE | 6 catdap-1.3.7/catdap/NEWS.md |only catdap-1.3.7/catdap/R/catdap1.R |only catdap-1.3.7/catdap/R/catdap2.R |only catdap-1.3.7/catdap/R/util.R |only catdap-1.3.7/catdap/data/HealthData.rda |binary catdap-1.3.7/catdap/data/HelloGoodbye.rda |binary catdap-1.3.7/catdap/data/JNcharacter.rda |binary catdap-1.3.7/catdap/data/MissingHealthData.rda |binary catdap-1.3.7/catdap/man/Barplot2WayTable.Rd | 16 - catdap-1.3.7/catdap/man/catdap1.Rd | 8 catdap-1.3.7/catdap/man/catdap2.Rd | 41 +-- catdap-1.3.7/catdap/src/catdap-win.def |only catdap-1.3.7/catdap/src/catdap.h | 42 +-- catdap-1.3.7/catdap/src/catdap1f.f | 28 +- catdap-1.3.7/catdap/src/catdap2mf.f | 315 ++++++++++++++----------- catdap-1.3.7/catdap/src/init.c | 46 ++- catdap-1.3.7/catdap/src/regF77.h |only 24 files changed, 312 insertions(+), 240 deletions(-)
Title: Get Data from the Swiss Statistical Office
Description: Search and download data from the Swiss Federal Statistical Office (BFS) <https://www.bfs.admin.ch/>.
Author: Felix Luginbuhl [aut, cre]
Maintainer: Felix Luginbuhl <felix.luginbuhl@protonmail.ch>
Diff between BFS versions 0.4.7 dated 2023-05-19 and 0.4.8 dated 2023-05-31
DESCRIPTION | 10 - LICENSE | 2 MD5 | 30 ++-- NAMESPACE | 3 NEWS.md | 7 + R/bfs_get_catalog_data.R | 154 ++++++++++++++++++++----- R/bfs_get_catalog_tables.R | 159 +++++++++++++++++++++----- R/bfs_get_data.R | 26 ++-- R/bfs_get_data_comments.R | 16 +- R/bfs_get_metadata.R | 16 +- README.md | 253 +++++++++++++++++++----------------------- man/bfs_get_catalog_data.Rd | 42 +++++- man/bfs_get_catalog_tables.Rd | 48 ++++++- man/bfs_get_data.Rd | 18 +- man/bfs_get_data_comments.Rd | 12 - man/figures/logo.png |binary 16 files changed, 532 insertions(+), 264 deletions(-)
More information about WeibullR.plotly at CRAN
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More information about mirai.promises at CRAN
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Title: Classes and Methods for Spatial Data
Description: Classes and methods for spatial
data; the classes document where the spatial location information
resides, for 2D or 3D data. Utility functions are provided, e.g. for
plotting data as maps, spatial selection, as well as methods for
retrieving coordinates, for subsetting, print, summary, etc.
Author: Edzer Pebesma [aut, cre],
Roger Bivand [aut],
Barry Rowlingson [ctb],
Virgilio Gomez-Rubio [ctb],
Robert Hijmans [ctb],
Michael Sumner [ctb],
Don MacQueen [ctb],
Jim Lemon [ctb],
Finn Lindgren [ctb],
Josh O'Brien [ctb],
Joseph O'Rourke [ctb]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between sp versions 1.6-0 dated 2023-01-19 and 1.6-1 dated 2023-05-31
sp-1.6-0/sp/inst/doc/over.R |only sp-1.6-0/sp/inst/doc/over.Rnw |only sp-1.6-0/sp/inst/doc/over.pdf |only sp-1.6-0/sp/vignettes/over.Rnw |only sp-1.6-1/sp/DESCRIPTION | 10 +- sp-1.6-1/sp/MD5 | 64 +++++++++--------- sp-1.6-1/sp/NAMESPACE | 4 + sp-1.6-1/sp/R/AAA.R | 2 sp-1.6-1/sp/R/CRS-methods.R | 13 ++- sp-1.6-1/sp/R/SpatialGridDataFrame-methods.R | 8 +- sp-1.6-1/sp/R/SpatialMultiPoints-methods.R | 2 sp-1.6-1/sp/R/elide.R |only sp-1.6-1/sp/R/spplot.R | 4 - sp-1.6-1/sp/build/vignette.rds |binary sp-1.6-1/sp/inst/CITATION | 21 ++---- sp-1.6-1/sp/inst/NEWS.Rd | 10 ++ sp-1.6-1/sp/inst/doc/CRS_warnings.html | 82 ++++++------------------ sp-1.6-1/sp/inst/doc/csdacm.pdf |binary sp-1.6-1/sp/inst/doc/intro_sp.pdf |binary sp-1.6-1/sp/inst/doc/retiring_rgdal_geos_1.R |only sp-1.6-1/sp/inst/doc/retiring_rgdal_geos_1.Rmd |only sp-1.6-1/sp/inst/doc/retiring_rgdal_geos_1.html |only sp-1.6-1/sp/inst/include/sp.h | 2 sp-1.6-1/sp/man/elide-methods.Rd |only sp-1.6-1/sp/src/sp.h | 2 sp-1.6-1/sp/tests/agg.Rout.save | 19 +++-- sp-1.6-1/sp/tests/base.Rout.save | 10 ++ sp-1.6-1/sp/tests/fail1.Rout.save | 12 ++- sp-1.6-1/sp/tests/grid.Rout.save | 10 ++ sp-1.6-1/sp/tests/over2.Rout.save | 19 +++-- sp-1.6-1/sp/tests/pass1.Rout.save | 10 ++ sp-1.6-1/sp/tests/point.in.polygon.Rout.save | 10 ++ sp-1.6-1/sp/tests/sel.Rout.save | 10 ++ sp-1.6-1/sp/tests/sp1.Rout.save | 10 ++ sp-1.6-1/sp/tests/spDists.Rout.save | 10 ++ sp-1.6-1/sp/tests/spplot.Rout.save | 10 ++ sp-1.6-1/sp/tests/zerodist.Rout.save | 10 ++ sp-1.6-1/sp/vignettes/retiring_rgdal_geos_1.Rmd |only 38 files changed, 197 insertions(+), 167 deletions(-)
Title: Stability-enHanced Approaches using Resampling Procedures
Description: In stability selection (N Meinshausen, P Bühlmann (2010) <doi:10.1111/j.1467-9868.2010.00740.x>) and consensus clustering (S Monti et al (2003) <doi:10.1023/A:1023949509487>), resampling techniques are used to enhance the reliability of the results. In this package, hyper-parameters are calibrated by maximising model stability, which is measured under the null hypothesis that all selection (or co-membership) probabilities are identical (B Bodinier et al (2021) <arXiv:2106.02521>). Functions are readily implemented for the use of LASSO regression, sparse PCA, sparse (group) PLS or graphical LASSO in stability selection, and hierarchical clustering, partitioning around medoids, K means or Gaussian mixture models in consensus clustering.
Author: Barbara Bodinier [aut, cre]
Maintainer: Barbara Bodinier <barbara.bodinier@gmail.com>
Diff between sharp versions 1.4.0 dated 2023-04-18 and 1.4.1 dated 2023-05-31
DESCRIPTION | 15 - MD5 | 81 +++++---- NAMESPACE | 4 NEWS.md | 9 + R/algorithms.R | 11 + R/calibration.R | 5 R/clustering.R | 20 +- R/clustering_models.R | 51 +----- R/explanatory_performance.R | 323 +++++++++++++++++++------------------- R/parallelisation.R | 10 - R/s3_coef.R | 27 +++ R/s3_plot.R | 23 +- R/s3_predict.R | 7 R/s3_print.R | 13 + R/s3_summary.R | 24 ++ R/selection_performance.R | 16 + R/sharp-package.R | 8 R/stability_output.R | 31 +++ R/stability_score.R | 4 R/structural_equation_modelling.R | 10 - build/partial.rdb |binary build/vignette.rds |only inst/REFERENCES.bib | 14 + inst/doc |only man/AggregatedEffects.Rd | 2 man/ArgmaxId.Rd | 3 man/BiSelection.Rd | 1 man/Clustering.Rd | 3 man/ConsensusScore.Rd | 4 man/DBSCANClustering.Rd | 4 man/ExplanatoryPerformance.Rd | 21 -- man/GMMClustering.Rd | 5 man/GraphicalModel.Rd | 1 man/HierarchicalClustering.Rd | 8 man/Incremental.Rd | 32 --- man/KMeansClustering.Rd | 5 man/PAMClustering.Rd | 12 - man/Refit.Rd | 20 +- man/StructuralModel.Rd | 8 man/VariableSelection.Rd | 3 man/sharp-package.Rd | 6 vignettes |only 42 files changed, 473 insertions(+), 371 deletions(-)
Title: Multi-Scale Geomorphometric Terrain Attributes
Description: Calculates multi-scale geomorphometric terrain attributes from regularly gridded digital terrain models using a variable focal windows size (Ilich et al. (2023) <doi:10.1111/tgis.13067>).
Author: Alexander Ilich [aut, cre] ,
Vincent Lecours [aut],
Benjamin Misiuk [aut],
Steven Murawski [aut]
Maintainer: Alexander Ilich <ailich@usf.edu>
Diff between MultiscaleDTM versions 0.8 dated 2023-04-25 and 0.8.1 dated 2023-05-31
DESCRIPTION | 10 +++++----- MD5 | 34 +++++++++++++++++----------------- NAMESPACE | 1 + R/AdjSD.R | 4 +++- R/SAPA.R | 4 +++- R/VRM.R | 3 ++- README.md | 33 ++++++++++++++++++++------------- build/vignette.rds |binary inst/CITATION | 16 ++++++++++++++++ inst/doc/README.html | 32 +++++++++++++++++++------------- man/AdjSD.Rd | 5 ++++- man/SAPA.Rd | 4 +++- man/figures/qmetrics.jpg |binary man/figures/sub_qfit03.png |binary man/figures/sub_qfit04.png |binary man/figures/sub_qfit05.png |binary man/figures/sub_qfit12.png |binary man/fragments/README_Frag.Rmd | 10 ++++++---- 18 files changed, 99 insertions(+), 57 deletions(-)
Title: Fits Multivariate Spatio-Temporal Occupancy Model
Description: Spatio-temporal multivariate occupancy models can handle multiple species in occupancy models. This method for fitting such models is described in Hepler and Erhardt (2021) "A spatiotemporal model for multivariate occupancy data" <https://onlinelibrary.wiley.com/doi/abs/10.1002/env.2657>.
Author: Staci Hepler [aut, cre],
Rob Erhardt [aut]
Maintainer: Staci Hepler <heplersa@wfu.edu>
Diff between multiocc versions 0.2.0 dated 2023-05-25 and 0.2.1 dated 2023-05-31
DESCRIPTION | 6 MD5 | 10 - R/multioccbuild.R | 50 ++++---- inst/doc/Intro_multiocc.html | 221 +++++++++++++++++------------------- man/multioccbuild.Rd | 2 tests/testthat/test-multioccbuild.R | 5 6 files changed, 151 insertions(+), 143 deletions(-)
Title: Make 'PICRUSt2' Output Analysis and Visualization Easier
Description: Provides a convenient way to analyze and visualize 'PICRUSt2' output with pre-defined plots and functions. Allows for generating statistical plots about microbiome functional predictions and offers customization options. Features a one-click option for creating publication-level plots, saving time and effort in producing professional-grade figures. Streamlines the 'PICRUSt2' analysis and visualization process. For more details, see Yang et al. (2023) <arXiv:2303.10388>.
Author: Chen Yang [aut, cre],
Liangliang Zhang [aut]
Maintainer: Chen Yang <cafferychen7850@gmail.com>
Diff between ggpicrust2 versions 1.6.5 dated 2023-05-13 and 1.7.0 dated 2023-05-31
DESCRIPTION | 14 MD5 | 59 ++ NAMESPACE | 1 NEWS.md | 4 R/compare_daa_results.R |only R/compare_metagenome_results.R |only R/daa_annotated_results_df.R |only R/daa_results_df.R |only R/ggpicrust2.R | 296 +++++++++----- R/import_MicrobiomeAnalyst_daa_results.R |only R/kegg_abundance.R |only R/ko2kegg_abundance.R | 111 +++-- R/ko_abundance.R |only R/metacyc_abundance.R |only R/metadata.R |only R/pathway_annotation.R | 2 R/pathway_daa.R | 44 +- R/pathway_errorbar.R | 44 +- R/pathway_heatmap.R | 53 ++ R/pathway_pca.R | 20 README.md | 629 +++++++++++++++++-------------- build |only data |only inst/doc |only man/daa_annotated_results_df.Rd |only man/daa_results_df.Rd |only man/ggpicrust2.Rd | 86 +++- man/kegg_abundance.Rd |only man/ko2kegg_abundance.Rd | 18 man/ko_abundance.Rd |only man/metacyc_abundance.Rd |only man/metadata.Rd |only man/pathway_daa.Rd | 28 + man/pathway_heatmap.Rd | 22 - man/pathway_pca.Rd | 18 vignettes |only 36 files changed, 946 insertions(+), 503 deletions(-)
Title: Doubly Robust Inference for Cox Marginal Structural Model with
Informative Censoring
Description: Doubly robust estimation and inference of log hazard ratio under the Cox marginal structural model with informative censoring. An augmented inverse probability weighted estimator that involves 3 working models, one for conditional failure time T, one for conditional censoring time C and one for propensity score. Both models for T and C can depend on both a binary treatment A and additional baseline covariates Z, while the propensity score model only depends on Z. With the help of cross-fitting techniques, achieves the rate-doubly robust property that allows the use of most machine learning or non-parametric methods for all 3 working models, which are not permitted in classic inverse probability weighting or doubly robust estimators. Reference: Luo & Xu (2022) <doi:10.48550/arXiv.2206.02296>; Rava (2021) <https://escholarship.org/uc/item/8h1846gs>.
Author: Jiyu Luo [cre, aut],
Dennis Rava [aut],
Ronghui Xu [aut]
Maintainer: Jiyu Luo <charlesluo1002@gmail.com>
Diff between CoxAIPW versions 0.0.1 dated 2023-02-08 and 0.0.2 dated 2023-05-31
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 13 +++++++++++++ R/CoxAIPW.R | 53 +++++++++++++++++++++++++++++++++++++++++++---------- man/CoxAIPW.Rd | 16 +++++++++++++--- 5 files changed, 77 insertions(+), 21 deletions(-)
Title: Bayesian Spectral Inference for Time Series
Description: Implementations of Bayesian parametric, nonparametric and semiparametric procedures for univariate and multivariate time series. The package is based on the methods presented in C. Kirch et al (2018) <doi:10.1214/18-BA1126>, A. Meier (2018) <https://opendata.uni-halle.de//handle/1981185920/13470> and Y. Tang et al (2023) <arXiv:2303.11561>. It was supported by DFG grants KI 1443/3-1 and KI 1443/3-2.
Author: Alexander Meier [aut],
Claudia Kirch [aut],
Matthew C. Edwards [aut],
Renate Meyer [aut, cre],
Yifu Tang [aut]
Maintainer: Renate Meyer <renate.meyer@auckland.ac.nz>
Diff between beyondWhittle versions 1.1.3 dated 2022-04-04 and 1.2.0 dated 2023-05-31
DESCRIPTION | 27 +- MD5 | 81 ++++-- NAMESPACE | 129 +++++---- R/RcppExports.R | 404 +++++++++++++++--------------- R/dynamicWhittle_MCMC_zigzag.R |only R/dynamicWhittle_S3method.R |only R/dynamicWhittle_miscellanea_zigzag.R |only R/dynamicWhittle_prior_and_mcmc_params.R |only man/PSIwgt.Rd |only man/VARMAcov_muted.Rd | 3 man/bayes_factor.Rd |only man/bayes_factor.bdp_dw_result.Rd |only man/bdp_dw_bayes_factor_k1.Rd |only man/bdp_dw_est_post_stats.Rd |only man/bdp_dw_mcmc.Rd |only man/bdp_dw_mcmc_params_gen.Rd |only man/bdp_dw_prior_params_gen.Rd |only man/betaBasis_k_dw.Rd |only man/beyondWhittle-package.Rd | 106 ++++--- man/dbList.Rd | 3 man/dbList_dw_Bern.Rd |only man/dbList_dw_Bern_for_lambda.Rd |only man/gibbs_AR_nuisance_intern.Rd | 9 man/gibbs_VAR_nuisance_intern.Rd | 9 man/gibbs_ar.Rd | 22 + man/gibbs_bdp_dw.Rd |only man/gibbs_multivariate_nuisance.Rd | 9 man/gibbs_multivariate_nuisance_cpp.Rd | 26 + man/gibbs_np.Rd | 234 +++++++++-------- man/gibbs_npc.Rd | 297 +++++++++++----------- man/gibbs_nuisance.Rd | 10 man/gibbs_var.Rd | 17 - man/gibbs_vnp.Rd | 26 + man/llike.Rd | 20 + man/llike_dw.Rd |only man/local_moving_FT_zigzag.Rd |only man/lpost.Rd | 30 ++ man/lpost_AR.Rd | 12 man/lprior.Rd | 19 + man/lprior_dw.Rd |only man/plot.bdp_dw_result.Rd |only man/plot.bdp_dw_tv_psd.Rd |only man/plotMPsd.Rd | 24 + man/print.bdp_dw_result.Rd |only man/psd_tvarma12.Rd |only man/psd_varma.Rd | 8 man/psd_varma_help.Rd | 8 man/qpsd_dw.Rd |only man/qpsd_dw.tilde_zigzag_cpp_expedited.Rd |only man/sim_tvarma12.Rd |only man/summary.bdp_dw_result.Rd |only src/Makevars | 1 src/Makevars.win | 1 src/RcppExports.cpp | 17 + src/qpsd_cal_cpp_expedited.cpp |only tests/testthat/testGibbsBDPDW.R |only 56 files changed, 915 insertions(+), 637 deletions(-)
More information about PortalHacienda at CRAN
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Title: Threshold Indicator Taxa Analysis
Description: Uses indicator species scores across binary partitions of
a sample set to detect congruence in taxon-specific changes of abundance
and occurrence frequency along an environmental gradient as evidence of
an ecological community threshold. Relevant references include: Baker,
ME and RS King. 2010. A new method for detecting and interpreting
biodiversity and ecological community thresholds. Methods in Ecology and
Evolution 1(1): 25:37. King, RS and ME Baker. 2010. Considerations for
identifying and interpreting ecological community thresholds. Journal
of the North American Benthological Association 29(3):998-1008. Baker ME
and RS King. 2013. Of TITAN and straw men: an appeal for greater
understanding of community data. Freshwater Science 32(2):489-506.
Author: Matthew E. Baker [aut, cph] ,
Ryan S. King [aut, cph] ,
David Kahle [aut, cph, cre]
Maintainer: David Kahle <david@kahle.io>
Diff between TITAN2 versions 2.4.1 dated 2020-12-07 and 2.4.2 dated 2023-05-31
DESCRIPTION | 10 MD5 | 16 NEWS.md | 16 R/boot.functions.R | 3 R/plot_taxa_ridges.R | 3 README.md | 16 build/vignette.rds |binary man/plot_sumz_density.Rd | 14 vignettes/titan2-intro.html | 1359 ++++++++++++++++++++++++++++++++------------ 9 files changed, 1057 insertions(+), 380 deletions(-)
Title: Seeded Sequential LDA for Topic Modeling
Description: Seeded Sequential LDA can classify sentences of texts into pre-define topics with a small number of seed words (Watanabe & Baturo, 2023) <doi:10.1177/08944393231178605>.
Implements Seeded LDA (Lu et al., 2010) <doi:10.1109/ICDMW.2011.125> and Sequential LDA (Du et al., 2012) <doi:10.1007/s10115-011-0425-1> with the distributed LDA algorithm (Newman, et al., 2009) for parallel computing.
Author: Kohei Watanabe [aut, cre, cph],
Phan Xuan-Hieu [aut, cph]
Maintainer: Kohei Watanabe <watanabe.kohei@gmail.com>
Diff between seededlda versions 0.9.1 dated 2023-05-01 and 1.0.0 dated 2023-05-31
DESCRIPTION | 15 - MD5 | 45 ++- NEWS.md | 7 R/RcppExports.R | 4 R/catch-routine-registration.R |only R/lda.R | 65 ++++- R/seededlda.R | 30 +- R/seqlda.R | 18 - R/utils.R | 4 man/divergence.Rd | 4 man/textmodel_lda.Rd | 33 ++ man/textmodel_seededlda.Rd | 21 + man/textmodel_seqlda.Rd | 15 + src/RcppExports.cpp | 14 - src/array.h |only src/lda.cpp | 30 +- src/lda.h | 360 +++++++++++++++++------------- src/test-array.cpp |only src/test-runner.cpp |only tests/benchmark |only tests/testthat/test-cpp.R |only tests/testthat/test-internal.R | 4 tests/testthat/test-textmodel_lda.R | 132 +++++++++-- tests/testthat/test-textmodel_seededlda.R | 101 +++++++- tests/testthat/test-utils.R | 2 25 files changed, 627 insertions(+), 277 deletions(-)
Title: Batch Correction of Single Cell Transcriptome Data
Description: Non-linear/linear hybrid method for batch-effect correction
that uses Mutual Nearest Neighbors (MNNs) to identify similar cells between
datasets. Reference: Loza M. et al. (NAR Genomics and Bioinformatics, 2020) <doi:10.1093/nargab/lqac022>.
Author: Martin Loza [aut, cre] ,
Diego Diez [aut]
Maintainer: Martin Loza <martin.loza.lopez@gmail.com>
Diff between Canek versions 0.2.1 dated 2022-05-10 and 0.2.2 dated 2023-05-31
Canek-0.2.1/Canek/man/figures |only Canek-0.2.2/Canek/DESCRIPTION | 15 Canek-0.2.2/Canek/MD5 | 29 - Canek-0.2.2/Canek/NEWS.md | 19 + Canek-0.2.2/Canek/R/RunCanek.R | 80 ++-- Canek-0.2.2/Canek/README.md | 100 ++++- Canek-0.2.2/Canek/build/partial.rdb |only Canek-0.2.2/Canek/data/SimBatches.rda |binary Canek-0.2.2/Canek/inst/CITATION | 32 + Canek-0.2.2/Canek/inst/doc/toy_example.html | 167 +++++----- Canek-0.2.2/Canek/man/Canek-package.Rd | 10 Canek-0.2.2/Canek/man/RunCanek.Rd | 21 + Canek-0.2.2/Canek/tests/testthat/test-Estimation.R | 2 Canek-0.2.2/Canek/tests/testthat/test_RunCanek.R | 7 Canek-0.2.2/Canek/vignettes/articles/Best_practices_thymus.Rmd |only Canek-0.2.2/Canek/vignettes/articles/SingleCellExperiment.Rmd |only Canek-0.2.2/Canek/vignettes/articles/seurat.Rmd | 18 - Canek-0.2.2/Canek/vignettes/articles/seurat_pca.Rmd |only 18 files changed, 294 insertions(+), 206 deletions(-)