Title: Spatial Data Analysis
Description: Methods for spatial data analysis with raster and vector data. Raster methods allow for low-level data manipulation as well as high-level global, local, zonal, and focal computation. The predict and interpolate methods facilitate the use of regression type (interpolation, machine learning) models for spatial prediction, including with satellite remote sensing data. Processing of very large files is supported. See the manual and tutorials on <https://rspatial.org/terra/> to get started. 'terra' is a replacement for the 'raster' package ('terra' can do more, and it is faster and easier to use).
Author: Robert J. Hijmans [cre, aut] ,
Roger Bivand [ctb] ,
Karl Forner [ctb],
Jeroen Ooms [ctb] ,
Edzer Pebesma [ctb] ,
Michael D. Sumner [ctb]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between terra versions 1.6-7 dated 2022-08-07 and 1.6-17 dated 2022-09-10
DESCRIPTION | 10 MD5 | 216 +++++----- NAMESPACE | 2 NEWS.md | 179 +++++--- R/Agenerics.R | 7 R/Arith_generics.R | 70 ++- R/aggregate.R | 8 R/app.R | 4 R/approximate.R | 2 R/arith.R | 2 R/coerce.R | 23 - R/connect.R | 2 R/crs.R | 1 R/deprecated.R | 14 R/distance.R | 50 +- R/extent.R | 10 R/extract.R | 98 +++- R/focal.R | 26 - R/generics.R | 130 ++++-- R/geom.R | 14 R/init.R | 2 R/interpolate.R | 2 R/lapp.R | 30 - R/levels.R | 13 R/lines.R | 92 ++-- R/match.R | 2 R/names.R | 12 R/options.R | 13 R/plotRGB.R | 11 R/plot_raster.R | 15 R/plot_vector.R | 129 +++--- R/predict.R | 4 R/rapp.R | 2 R/rast.R | 2 R/rasterize.R | 2 R/relate.R | 189 ++++++++- R/sample.R | 367 +++++++++++------- R/select.R | 4 R/show.R | 19 R/spatvec.R | 22 + R/subset.R | 7 R/tapp.R | 2 R/values.R | 59 ++ R/vect.R | 18 R/write.R | 4 R/zonal.R | 4 inst/tinytest/test_cats.R | 19 man/arith-generic.Rd | 4 man/as.data.frame.Rd | 4 man/classify.Rd | 7 man/click.Rd | 5 man/compareGeom.Rd | 15 man/crop.Rd | 4 man/distance.Rd | 25 - man/extract.Rd | 7 man/factors.Rd | 24 - man/inplace.Rd | 1 man/is.bool.Rd | 24 - man/lapp.Rd | 5 man/lines.Rd | 4 man/mask.Rd | 8 man/merge.Rd | 4 man/normalize.longitude.Rd |only man/plot.Rd | 8 man/plotRGB.Rd | 5 man/project.Rd | 17 man/readwrite.Rd | 8 man/relate.Rd | 27 - man/resample.Rd | 6 man/sample.Rd | 42 -- man/scoff.Rd |only man/setValues.Rd | 5 man/sources.Rd | 1 man/subset.Rd | 1 man/subst.Rd | 3 man/vect.Rd | 4 man/vrt.Rd | 10 man/where.Rd | 8 man/writeRaster.Rd | 2 src/RcppModule.cpp | 71 ++- src/arith.cpp | 151 +++++-- src/distRaster.cpp | 370 ++++++++++-------- src/distance.cpp | 11 src/distance.h | 2 src/file_utils.cpp | 99 +++- src/file_utils.h | 2 src/focal.cpp | 341 ---------------- src/gdal_algs.cpp | 67 ++- src/gdalio.cpp | 16 src/geos_methods.cpp | 905 +++++++++++++++++++++++++++++++++++++++------ src/geos_spat.h | 4 src/geosphere.cpp | 2 src/raster_methods.cpp | 77 ++- src/raster_stats.cpp | 2 src/rasterize.cpp | 10 src/read_gdal.cpp | 29 + src/read_ogr.cpp | 28 - src/recycle.h | 6 src/sample.cpp | 58 +- src/spatBase.cpp | 7 src/spatBase.h | 8 src/spatRaster.cpp | 156 +++++++ src/spatRaster.h | 29 - src/spatRasterMultiple.h | 27 + src/spatSources.cpp | 36 + src/spatVector.cpp | 130 ++++++ src/spatVector.h | 39 + src/vector_methods.cpp | 2 src/write.cpp | 86 ---- src/write_gdal.cpp | 81 ++-- 110 files changed, 3326 insertions(+), 1727 deletions(-)
Title: Solving Mixed Model Equations in R
Description: Structural multivariate-univariate linear mixed model solver for estimation of multiple random effects with unknown variance-covariance structures (e.g., heterogeneous and unstructured) and known covariance among levels of random effects (e.g., pedigree and genomic relationship matrices) (Covarrubias-Pazaran, 2016 <doi:10.1371/journal.pone.0156744>; Maier et al., 2015 <doi:10.1016/j.ajhg.2014.12.006>). REML estimates can be obtained using the Direct-Inversion Newton-Raphson and Direct-Inversion Average Information algorithms for the problems r x r (r being the number of records) or using the mixed-model-equations-based average information algorithm for the problem c x c (c being the number of coefficients to estimate). Spatial models can also be fitted using the two-dimensional spline functionality available in sommer.
Author: Giovanny Covarrubias-Pazaran
Maintainer: Giovanny Covarrubias-Pazaran <cova_ruber@live.com.mx>
Diff between sommer versions 4.1.9 dated 2022-09-09 and 4.2.0 dated 2022-09-10
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- man/bivariateRun.Rd | 16 ++++++++-------- man/vpredict.Rd | 10 +++++----- man/vsc.Rd | 2 +- vignettes/v1.sommer.quick.start.html | 12 ++++++------ vignettes/v2.sommer.changes.and.faqs.html | 4 ++-- vignettes/v3.sommer.qg.html | 4 ++-- vignettes/v4.sommer.gxe.html | 4 ++-- vignettes/v5.sommer.vs.lme4.html | 4 ++-- vignettes/v6.sommer.spatial.html | 4 ++-- 11 files changed, 44 insertions(+), 44 deletions(-)
Title: Sparse and Dense Matrix Classes and Methods
Description: A rich hierarchy of matrix classes, including triangular,
symmetric, and diagonal matrices, both dense and sparse and with
pattern, logical and numeric entries. Numerous methods for and
operations on these matrices, using 'LAPACK' and 'SuiteSparse' libraries.
Author: Douglas Bates [aut],
Martin Maechler [aut, cre] ,
Mikael Jagan [aut] ,
Timothy A. Davis [ctb] )),
Jens Oehlschlaegel [ctb] ),
Jason Riedy [ctb] and onenormest for octave, Copyright:
Regents of the University of California),
R Core Team [ctb]
Maintainer: Martin Maechler <mmaechler+Matrix@gmail.com>
Diff between Matrix versions 1.4-1 dated 2022-03-25 and 1.5-0 dated 2022-09-10
DESCRIPTION | 49 MD5 | 563 ++--- NAMESPACE | 6 R/AllClass.R | 813 +++----- R/Auxiliaries.R | 1071 +++++++--- R/BunchKaufman.R |only R/CHMfactor.R | 222 -- R/Csparse.R | 334 ++- R/HBMM.R | 15 R/KhatriRao.R | 52 R/LU.R | 192 + R/Math.R | 416 ++-- R/Matrix.R | 364 ++- R/MatrixFactorization.R | 13 R/Ops.R | 429 ++-- R/Rsparse.R | 143 - R/SparseM-conv.R | 135 - R/Summary.R | 18 R/Tsparse.R | 121 - R/bandSparse.R | 19 R/bind2.R | 67 R/chol.R |only R/colSums.R | 175 - R/corMatrix.R | 48 R/dMatrix.R | 6 R/ddenseMatrix.R | 139 - R/denseMatrix.R | 628 +++++- R/determinant.R |only R/dgCMatrix.R | 133 - R/dgTMatrix.R | 132 - R/dgeMatrix.R | 87 R/diagMatrix.R | 913 +++++---- R/dpoMatrix.R | 109 - R/dppMatrix.R | 120 - R/dsCMatrix.R | 169 - R/dsTMatrix.R | 21 R/dspMatrix.R | 68 R/dsparseMatrix.R | 75 R/dsyMatrix.R | 120 - R/dtCMatrix.R | 91 R/dtTMatrix.R | 19 R/dtpMatrix.R | 80 R/dtrMatrix.R | 104 - R/eigen.R | 195 - R/expm.R | 84 R/graph-conv.R |only R/image.R |only R/indMatrix.R | 373 ++- R/is.na.R |only R/kronecker.R | 81 R/lMatrix.R | 83 R/ldenseMatrix.R | 59 R/lgCMatrix.R | 17 R/lgTMatrix.R | 37 R/lsCMatrix.R | 29 R/lsTMatrix.R | 9 R/lsparseMatrix.R | 23 R/ltCMatrix.R | 21 R/ltTMatrix.R | 11 R/ndenseMatrix.R | 32 R/ngCMatrix.R | 6 R/ngTMatrix.R | 46 R/nnzero.R | 165 - R/norm.R |only R/not.R | 150 - R/nsCMatrix.R | 24 R/nsTMatrix.R | 7 R/nsparseMatrix.R | 22 R/ntCMatrix.R | 26 R/ntTMatrix.R | 11 R/pMatrix.R | 97 R/packedMatrix.R | 112 + R/products.R | 260 +- R/qr.R |only R/rcond.R |only R/solve.R |only R/spModels.R | 476 ++-- R/sparseMatrix.R | 774 ++++--- R/sparseQR.R | 85 R/sparseVector.R | 210 -- R/symmetricMatrix.R | 207 -- R/triangularMatrix.R | 87 R/unpackedMatrix.R |only R/which.R |only R/zzz.R | 316 ++- TODO | 10 build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 541 +++++ inst/doc/Comparisons.R | 2 inst/doc/Comparisons.Rnw | 2 inst/doc/Comparisons.pdf |binary inst/doc/Design-issues.R | 24 inst/doc/Design-issues.Rnw | 73 inst/doc/Design-issues.pdf |binary inst/doc/Intro2Matrix.pdf |binary inst/doc/Introduction.pdf |binary inst/doc/sparseModels.pdf |binary inst/test-tools-1.R | 23 inst/test-tools-Matrix.R | 116 - inst/test-tools.R | 12 man/BunchKaufman-methods.Rd | 13 man/CAex.Rd | 7 man/CHMfactor-class.Rd | 22 man/Cholesky-class.Rd | 11 man/Cholesky.Rd | 25 man/CsparseMatrix-class.Rd | 32 man/Diagonal.Rd | 2 man/Hilbert.Rd | 2 man/KNex.Rd | 4 man/KhatriRao.Rd | 39 man/LU-class.Rd | 4 man/Matrix-class.Rd | 122 - man/Matrix.Rd | 10 man/MatrixFactorization-class.Rd | 9 man/RsparseMatrix-class.Rd | 21 man/Schur-class.Rd | 3 man/Schur.Rd | 24 man/SparseM-conv.Rd | 40 man/Subassign-methods.Rd | 115 - man/TsparseMatrix-class.Rd | 23 man/USCounties.Rd | 6 man/Xtrct-methods.Rd | 86 man/abIndex-class.Rd | 42 man/all-methods.Rd | 18 man/all.equal-methods.Rd | 17 man/atomicVector-class.Rd | 14 man/band.Rd | 141 - man/bandSparse.Rd | 2 man/bdiag.Rd | 2 man/boolean-matprod.Rd | 82 man/cBind.Rd | 9 man/chol.Rd | 83 man/chol2inv-methods.Rd | 10 man/colSums.Rd | 80 man/compMatrix-class.Rd | 7 man/condest.Rd | 4 man/dMatrix-class.Rd | 69 man/ddenseMatrix-class.Rd | 38 man/ddiMatrix-class.Rd | 60 man/denseMatrix-class.Rd | 61 man/dgCMatrix-class.Rd | 44 man/dgRMatrix-class.Rd | 19 man/dgTMatrix-class.Rd | 24 man/dgeMatrix-class.Rd | 47 man/diagU2N.Rd | 21 man/diagonalMatrix-class.Rd | 219 -- man/dmperm.Rd | 6 man/dpoMatrix-class.Rd | 74 man/drop0.Rd | 2 man/dsCMatrix-class.Rd | 51 man/dsRMatrix-class.Rd | 13 man/dsparseMatrix-class.Rd | 18 man/dsyMatrix-class.Rd | 51 man/dtCMatrix-class.Rd | 42 man/dtRMatrix-class-def.Rd | 13 man/dtpMatrix-class.Rd | 23 man/dtrMatrix-class.Rd | 33 man/expand.Rd | 13 man/expm.Rd | 18 man/externalFormats.Rd | 7 man/facmul.Rd | 6 man/forceSymmetric.Rd | 63 man/formatSparseM.Rd | 2 man/generalMatrix-class.Rd | 7 man/graph2T.Rd | 18 man/image-methods.Rd | 17 man/indMatrix-class.Rd | 52 man/index-class.Rd | 2 man/invPerm.Rd | 2 man/is.na-methods.Rd | 107 - man/is.null.DN.Rd | 13 man/isSymmetric-methods.Rd | 116 - man/isTriangular.Rd | 126 - man/kronecker-methods.Rd | 16 man/ldenseMatrix-class.Rd | 22 man/ldiMatrix-class.Rd | 64 man/lgeMatrix-class.Rd | 18 man/lsparseMatrix-classes.Rd | 169 + man/lsyMatrix-class.Rd | 30 man/ltrMatrix-class.Rd | 32 man/lu.Rd | 60 man/mat2triplet.Rd | 2 man/matrix-products.Rd | 447 ++-- man/nMatrix-class.Rd | 24 man/ndenseMatrix-class.Rd | 28 man/nearPD.Rd | 2 man/ngeMatrix-class.Rd | 14 man/nnzero.Rd | 9 man/norm.Rd | 19 man/nsparseMatrix-classes.Rd | 187 + man/nsyMatrix-class.Rd | 35 man/ntrMatrix-class.Rd | 33 man/number-class.Rd | 2 man/pMatrix-class.Rd | 22 man/packedMatrix-class.Rd | 86 man/printSpMatrix.Rd | 2 man/qr-methods.Rd | 11 man/rankMatrix.Rd | 8 man/rcond.Rd | 14 man/rep2abI.Rd | 2 man/replValue-class.Rd | 4 man/rleDiff-class.Rd | 2 man/rsparsematrix.Rd | 2 man/solve-methods.Rd | 170 - man/spMatrix.Rd | 2 man/sparse.model.matrix.Rd | 8 man/sparseLU-class.Rd | 3 man/sparseMatrix-class.Rd | 68 man/sparseMatrix.Rd | 2 man/sparseQR-class.Rd | 22 man/sparseVector-class.Rd | 118 - man/symmetricMatrix-class.Rd | 6 man/symmpart.Rd | 28 man/triangularMatrix-class.Rd | 13 man/uniqTsparse.Rd | 16 man/unpack.Rd | 120 - man/unpackedMatrix-class.Rd |only man/unused-classes.Rd | 5 man/updown.Rd | 5 man/wrld_1deg.Rd | 5 src/CHMfactor.c | 2 src/CHMfactor.h | 2 src/CHOLMOD/MatrixOps/t_cholmod_sdmult.c | 6 src/Csparse.c | 150 - src/Csparse.h | 86 src/Mutils.c | 3100 +++++++++++++++++++++++-------- src/Mutils.h | 662 ++++-- src/Syms.h | 16 src/TMatrix_as.c | 25 src/Tsparse.c | 17 src/Tsparse.h | 8 src/cs.c | 39 src/cs_utils.c | 11 src/dense.c | 1202 ++++++++++-- src/dense.h | 44 src/dgCMatrix.c | 41 src/dgCMatrix.h | 17 src/dgTMatrix.c | 12 src/dgTMatrix.h | 5 src/dgeMatrix.c | 78 src/dgeMatrix.h | 10 src/dpoMatrix.c | 72 src/dpoMatrix.h | 5 src/dppMatrix.c | 31 src/dppMatrix.h | 3 src/dsCMatrix.c | 8 src/dspMatrix.c | 128 - src/dspMatrix.h | 12 src/dsyMatrix.c | 96 src/dsyMatrix.h | 12 src/dtpMatrix.c | 125 - src/dtpMatrix.h | 17 src/dtrMatrix.c | 84 src/dtrMatrix.h | 17 src/factorizations.c | 57 src/init.c | 321 ++- src/ldense.c | 50 src/ldense.h | 9 src/packedMatrix.c | 1324 +++++++++---- src/packedMatrix.h | 14 src/scripts/0get-SuiteSparse.sh | 8 src/scripts/DEPS.mkf | 2 src/scripts/SOURCES_C.mkf | 4 src/sparse.c |only src/sparse.h |only src/sparseQR.c | 12 src/t_gCMatrix_colSums.c | 6 src/t_matrix_to_Csp.c | 2 src/unpackedMatrix.c |only src/unpackedMatrix.h |only tests/Class+Meth.R | 65 tests/Simple.R | 303 ++- tests/bind.R | 18 tests/bind.Rout.save | 41 tests/dg_Matrix.R | 20 tests/dpo-test.R | 16 tests/dtpMatrix.R | 19 tests/factorizing.R | 67 tests/group-methods.R | 104 - tests/indexing.R | 104 - tests/indexing.Rout.save | 388 +-- tests/matprod.R | 133 - tests/matr-exp.R | 10 tests/other-pkgs.R | 18 tests/packed-unpacked.R |only tests/spModel.matrix.R | 33 tests/symmDN.R |only tests/validObj.R | 21 tests/write-read.R | 6 vignettes/Comparisons.Rnw | 2 vignettes/Design-issues.Rnw | 73 292 files changed, 16648 insertions(+), 10547 deletions(-)
Title: 'Rcpp' Integration for the 'Armadillo' Templated Linear Algebra
Library
Description: 'Armadillo' is a templated C++ linear algebra library (by Conrad
Sanderson) that aims towards a good balance between speed and ease of
use. Integer, floating point and complex numbers are supported, as
well as a subset of trigonometric and statistics functions. Various
matrix decompositions are provided through optional integration with
LAPACK and ATLAS libraries. The 'RcppArmadillo' package includes the
header files from the templated 'Armadillo' library. Thus users do
not need to install 'Armadillo' itself in order to use
'RcppArmadillo'. From release 7.800.0 on, 'Armadillo' is licensed
under Apache License 2; previous releases were under licensed as MPL
2.0 from version 3.800.0 onwards and LGPL-3 prior to that;
'RcppArmadillo' (the 'Rcpp' bindings/bridge to Armadillo) is licensed
under the GNU GPL version 2 or later, as is the rest of 'Rcpp'.
Author: Dirk Eddelbuettel, Romain Francois, Doug Bates, Binxiang Ni, and Conrad Sanderson
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppArmadillo versions 0.11.2.3.1 dated 2022-08-18 and 0.11.2.4.0 dated 2022-09-10
ChangeLog | 33 +++++ DESCRIPTION | 8 - MD5 | 38 +++--- README.md | 11 - configure | 18 +-- configure.ac | 2 inst/NEWS.Rd | 26 ++++ inst/doc/RcppArmadillo-intro.pdf |binary inst/doc/RcppArmadillo-sparseMatrix.pdf |binary inst/include/RcppArmadilloForward.h | 16 ++ inst/include/armadillo_bits/Col_meat.hpp | 2 inst/include/armadillo_bits/Cube_bones.hpp | 3 inst/include/armadillo_bits/Cube_meat.hpp | 18 ++- inst/include/armadillo_bits/Mat_bones.hpp | 3 inst/include/armadillo_bits/Mat_meat.hpp | 16 ++ inst/include/armadillo_bits/Row_meat.hpp | 10 - inst/include/armadillo_bits/arma_version.hpp | 2 inst/include/armadillo_bits/compiler_setup.hpp | 140 +++++++++++++------------ inst/include/armadillo_bits/injector_meat.hpp | 4 src/fastLm.cpp | 23 +--- 20 files changed, 234 insertions(+), 139 deletions(-)
Title: Nested Cross-Validation with 'glmnet' and 'caret'
Description: Implements nested k*l-fold cross-validation for lasso and elastic-net regularised linear models via the 'glmnet' package and other machine learning models via the 'caret' package. Cross-validation of 'glmnet' alpha mixing parameter and embedded fast filter functions for feature selection are provided. Described as double cross-validation by Stone (1977) <doi:10.1111/j.2517-6161.1977.tb01603.x>. Also implemented is a method using outer CV to measure unbiased model performance metrics when fitting Bayesian linear and logistic regression shrinkage models using the horseshoe prior over parameters to encourage a sparse model as described by Piironen & Vehtari (2017) <doi:10.1214/17-EJS1337SI>.
Author: Myles Lewis [aut, cre] ,
Athina Spiliopoulou [aut] ,
Katriona Goldmann [aut]
Maintainer: Myles Lewis <myles.lewis@qmul.ac.uk>
Diff between nestedcv versions 0.2.3 dated 2022-07-07 and 0.3.0 dated 2022-09-10
DESCRIPTION | 14 +-- MD5 | 45 ++++++---- NAMESPACE | 34 +++++++ NEWS.md | 20 ++++ R/boot_filter.R |only R/checkxy.R |only R/class_balance.R |only R/nest_filter_balance.R |only R/nestcv.train.R | 86 ++++++++++++++++--- R/nestedcv.R | 137 +++++++++++++++++-------------- R/outercv.R | 63 ++++++++++---- R/plots.R | 116 ++++++++++++++++++++------ R/randomsample.R |only R/smote.R |only README.md | 4 inst/doc/nestedcv.R | 9 +- inst/doc/nestedcv.Rmd | 95 ++++++++++++++++++--- inst/doc/nestedcv.html | 210 ++++++++++++++++++++++++++++++++---------------- man/boot_filter.Rd |only man/boot_ttest.Rd |only man/class_balance.Rd |only man/nestcv.glmnet.Rd | 14 +++ man/nestcv.train.Rd | 12 ++ man/outercv.Rd | 10 ++ man/plot.cva.glmnet.Rd | 10 +- man/plot_varImp.Rd |only man/randomsample.Rd |only man/smote.Rd |only man/summary_vars.Rd |only vignettes/nestedcv.Rmd | 95 ++++++++++++++++++--- 30 files changed, 720 insertions(+), 254 deletions(-)
Title: Read Non-Rectangular Text Data
Description: The goal of 'meltr' is to provide a fast and friendly way to
read non-rectangular data, such as ragged forms of csv (comma-separated
values), tsv (tab-separated values), and fwf (fixed-width format) files.
Author: Hadley Wickham [aut],
Duncan Garmonsway [aut, cre] ,
Jim Hester [aut] ,
RStudio [cph, fnd],
https://github.com/mandreyel/ [cph]
Maintainer: Duncan Garmonsway <nacnudus@gmail.com>
Diff between meltr versions 1.0.0 dated 2021-08-23 and 1.0.1 dated 2022-09-10
DESCRIPTION | 10 +- MD5 | 25 ++--- NEWS.md |only R/date-symbols.R | 2 R/utils.R | 8 + README.md | 29 +++--- man/callback.Rd | 220 +++++++++++++++++++++++----------------------- man/date_names.Rd | 2 man/melt_delim.Rd | 26 ++--- man/melt_delim_chunked.Rd | 24 ++--- man/melt_fwf.Rd | 18 +-- man/melt_table.Rd | 19 ++- src/QiParsers.h | 7 + src/cpp11.cpp | 12 -- 14 files changed, 210 insertions(+), 192 deletions(-)
Title: An R Implementation of the 'Align-GVGD' Method
Description: 'Align-GVGD' ('A-GVGD') is a method to predict the impact of
'missense' substitutions based on the properties of amino acid side
chains and protein multiple sequence alignments
<doi:10.1136/jmg.2005.033878>. 'A-GVGD' is an extension of the original
'Grantham' distance to multiple sequence alignments. This package
provides an alternative R implementation to the web version found on
<http://agvgd.hci.utah.edu/>.
Author: Ramiro Magno [aut, cre] ,
Isabel Duarte [aut] ,
Ana-Teresa Maia [aut] ,
CINTESIS [cph, fnd]
Maintainer: Ramiro Magno <ramiro.magno@gmail.com>
Diff between agvgd versions 0.1.1 dated 2022-02-02 and 0.1.2 dated 2022-09-10
DESCRIPTION | 12 ++--- MD5 | 50 ++++++++++++++++-------- NAMESPACE | 4 + NEWS.md | 6 ++ R/agvgd.R | 24 ++++++++++- R/get_orthologs.R |only R/import_agvgdweb.R | 63 +++++++++++++++++++++++++++---- R/is_poi_a_gap.R |only R/line_annotation.R | 2 R/profile_to_alignment.R |only R/read_substitutions.R | 40 +++++++++++++------ R/safe_rownames.R |only R/str_chop.R |only R/sysdata.rda |binary R/write_alignment.R |only R/write_substitutions.R |only README.md | 19 +++++++-- build/partial.rdb |binary inst/extdata/lee2010_sub.txt |only inst/nature.csl |only inst/references.bib |only man/agvgd-package.Rd | 2 man/agvgd.Rd | 22 +++++++++- man/dev.Rd | 4 + man/figures/dev-plot-1.png |binary man/figures/lee2010_fig03.png |only man/profile_to_alignment.Rd |only man/read_agvgdweb_results.Rd |only man/read_substitutions.Rd | 6 ++ man/str_chop.Rd |only man/write_alignment.Rd |only man/write_substitutions.Rd |only tests/testthat/test-agvgd.R | 36 ++++++++--------- tests/testthat/test-read_substitutions.R | 6 +- 34 files changed, 222 insertions(+), 74 deletions(-)
Title: Missing Data Imputation Using Gaussian Copulas
Description: Provides functions to impute missing values using Gaussian
copulas for mixed data types as described by Christoffersen et al.
(2021) <arXiv:2102.02642>. The method is related to Hoff (2007)
<doi:10.1214/07-AOAS107> and Zhao and Udell (2019) <arXiv:1910.12845>
but differs by making a direct approximation of the log marginal likelihood
using an extended version of the Fortran code created by Genz and Bretz
(2002) <doi:10.1198/106186002394> in addition to also support multinomial
variables.
Author: Benjamin Christoffersen [cre, aut]
,
Alan Genz [cph],
Frank Bretz [cph],
Torsten Hothorn [cph],
R-core [cph],
Ross Ihaka [cph]
Maintainer: Benjamin Christoffersen <boennecd@gmail.com>
Diff between mdgc versions 0.1.5 dated 2021-06-14 and 0.1.6 dated 2022-09-10
DESCRIPTION | 6 +- MD5 | 28 ++++++------ src/RcppExports.cpp | 5 ++ src/arma-wrap.h | 5 +- src/cpp-to-R.cpp | 2 src/logLik.h | 8 +-- src/mdgc-mem.h | 8 +-- src/multinomial-probit.cpp | 6 +- src/new-mvt.h | 8 +-- src/norm-cdf-approx.h | 12 ++--- src/openmp-exception_ptr.h | 2 src/qnorm.h | 2 src/restrict-cdf.h | 54 ++++++++++++------------ src/test-pmvnorm.cpp | 15 ++---- src/test-restrict-cdf.cpp | 98 ++++++++++++++++++--------------------------- 15 files changed, 122 insertions(+), 137 deletions(-)
Title: R Implementation of Leiden Clustering Algorithm
Description: Implements the 'Python leidenalg' module to be called in R.
Enables clustering using the leiden algorithm for partition a graph into communities.
See the 'Python' repository for more details: <https://github.com/vtraag/leidenalg>
Traag et al (2018) From Louvain to Leiden: guaranteeing well-connected communities. <arXiv:1810.08473>.
Author: S. Thomas Kelly [aut, cre, trl],
Vincent A. Traag [com]
Maintainer: S. Thomas Kelly <tomkellygenetics@gmail.com>
Diff between leiden versions 0.4.2 dated 2022-05-10 and 0.4.3 dated 2022-09-10
DESCRIPTION | 12 MD5 | 46 - NAMESPACE | 3 NEWS.md | 13 R/find_partition.R | 2 R/leiden.R | 6 build/vignette.rds |binary inst/CITATION | 6 inst/doc/benchmarking.R | 2 inst/doc/benchmarking.Rmd | 2 inst/doc/benchmarking.html | 1091 ++++++++++++++++++++++++++++++++++++---- inst/doc/run_bipartite.html | 22 inst/doc/run_igraph.html | 30 - inst/doc/run_leiden.R | 2 inst/doc/run_leiden.Rmd | 2 inst/doc/run_leiden.html | 34 - inst/doc/run_multiplex.R | 6 inst/doc/run_multiplex.Rmd | 6 inst/doc/run_multiplex.html | 36 - tests/testthat/test_multiplex.R | 25 tests/testthat/test_weighted.R | 43 - vignettes/benchmarking.Rmd | 2 vignettes/run_leiden.Rmd | 2 vignettes/run_multiplex.Rmd | 6 24 files changed, 1156 insertions(+), 243 deletions(-)
Title: Fair Models in Machine Learning
Description: Fair machine learning regression models which take sensitive attributes into account in
model estimation. Currently implementing Komiyama et al. (2018)
<http://proceedings.mlr.press/v80/komiyama18a/komiyama18a.pdf>, Zafar et al.
(2019) <https://www.jmlr.org/papers/volume20/18-262/18-262.pdf> and my own
approach that uses ridge regression to enforce fairness.
Author: Marco Scutari [aut, cre]
Maintainer: Marco Scutari <scutari@bnlearn.com>
Diff between fairml versions 0.6.3 dated 2022-05-10 and 0.7 dated 2022-09-10
Changelog | 8 ++++++++ DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/crossvalidation.R | 10 ++++++---- R/sanitization-data.R | 2 +- 5 files changed, 23 insertions(+), 13 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-03-05 1.0.5
2021-02-09 1.0.4
2021-01-07 1.0.3
2021-01-06 1.0.2
2021-01-05 1.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-01-17 1.0.2
2021-03-29 1.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-10-14 2.1.2
2021-04-23 2.1.1
2021-04-22 2.1.0
Title: Plot Heatmap
Description: The flexibility and excellence of 'ggplot2' is unquestionable,
so many drawing tools basically need 'ggplot2' as the operating object.
In order to develop a heatmap drawing system based on ggplot2, we developed
this tool, mainly to solve the heatmap puzzle problem and the flexible
connection between the heatmap and the 'ggplot2' object.
The advantages of this tool are as follows:
1. More flexible label settings;
2. Realize the linkage of heatmap and 'ggplot2' drawing system,
which is helpful for operations such as puzzles;
3. Simple and easy to operate;
4. Optimization of clustering tree visualization.
Author: Baiwei Luo [aut, cre]
Maintainer: Baiwei Luo <2734782653@qq.com>
Diff between ggheatmap versions 2.1 dated 2021-07-25 and 2.2 dated 2022-09-10
DESCRIPTION | 6 - MD5 | 12 ++- R/ggheatmap.R | 92 ------------------------------ R/ggheatmap_test.R |only R/ggheatmap_theme.R | 4 - man/ggheatmap.Rd | 152 +++++++++----------------------------------------- man/ggheatmap_test.Rd |only tests |only 8 files changed, 45 insertions(+), 221 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/statistics/immigration-statistics-year-ending-june-2022>.
Author: Matthew Gwynfryn Thomas [cre, aut],
Mike Page [aut],
British Red Cross [cph]
Maintainer: Matthew Gwynfryn Thomas <matthewgthomas@gmail.com>
Diff between asylum versions 1.0.1 dated 2021-09-06 and 1.0.2 dated 2022-09-10
asylum-1.0.1/asylum/data/applications_proccessed_in_6_months.rda |only asylum-1.0.1/asylum/man/applications_proccessed_in_6_months.Rd |only asylum-1.0.2/asylum/DESCRIPTION | 10 asylum-1.0.2/asylum/MD5 | 124 +++++----- asylum-1.0.2/asylum/NAMESPACE | 4 asylum-1.0.2/asylum/NEWS.md | 4 asylum-1.0.2/asylum/R/data.R | 63 ++--- asylum-1.0.2/asylum/R/sysdata.rda |binary asylum-1.0.2/asylum/data/age_disputes.rda |binary asylum-1.0.2/asylum/data/age_of_asylum_operations.rda |binary asylum-1.0.2/asylum/data/appeal_representation_rate.rda |binary asylum-1.0.2/asylum/data/appeals_determined.rda |binary asylum-1.0.2/asylum/data/appeals_lodged.rda |binary asylum-1.0.2/asylum/data/appeals_non_suspensive.rda |binary asylum-1.0.2/asylum/data/applications.rda |binary asylum-1.0.2/asylum/data/applications_processed_in_6_months.rda |only asylum-1.0.2/asylum/data/asylum_costs_and_productivity.rda |binary asylum-1.0.2/asylum/data/asylum_work_in_progress.rda |binary asylum-1.0.2/asylum/data/awaiting_decision.rda |binary asylum-1.0.2/asylum/data/decision_quality.rda |binary asylum-1.0.2/asylum/data/decisions_resettlement.rda |binary asylum-1.0.2/asylum/data/family_reunion.rda |binary asylum-1.0.2/asylum/data/local_authority_resettlement.rda |binary asylum-1.0.2/asylum/data/local_authority_support.rda |binary asylum-1.0.2/asylum/data/nrpf_change_of_conditions_age.rda |binary asylum-1.0.2/asylum/data/nrpf_change_of_conditions_decisions.rda |binary asylum-1.0.2/asylum/data/nrpf_change_of_conditions_gender.rda |binary asylum-1.0.2/asylum/data/nrpf_change_of_conditions_nationality.rda |binary asylum-1.0.2/asylum/data/nts.rda |binary asylum-1.0.2/asylum/data/oral_hearings_volume.rda |binary asylum-1.0.2/asylum/data/outcomes.rda |binary asylum-1.0.2/asylum/data/support_applications.rda |binary asylum-1.0.2/asylum/data/support_applications_rasi.rda |binary asylum-1.0.2/asylum/data/support_received.rda |binary asylum-1.0.2/asylum/data/travel_documents.rda |binary asylum-1.0.2/asylum/man/age_disputes.Rd | 60 ++-- asylum-1.0.2/asylum/man/age_of_asylum_operations.Rd | 62 ++--- asylum-1.0.2/asylum/man/appeal_representation_rate.Rd | 58 ++-- asylum-1.0.2/asylum/man/appeals_determined.Rd | 62 ++--- asylum-1.0.2/asylum/man/appeals_lodged.Rd | 58 ++-- asylum-1.0.2/asylum/man/appeals_non_suspensive.Rd | 64 ++--- asylum-1.0.2/asylum/man/applications.Rd | 68 ++--- asylum-1.0.2/asylum/man/applications_processed_in_6_months.Rd |only asylum-1.0.2/asylum/man/aspen.Rd | 52 ++-- asylum-1.0.2/asylum/man/aspen_support.Rd | 58 ++-- asylum-1.0.2/asylum/man/asylum_costs_and_productivity.Rd | 68 ++--- asylum-1.0.2/asylum/man/asylum_work_in_progress.Rd | 78 +++--- asylum-1.0.2/asylum/man/awaiting_decision.Rd | 60 ++-- asylum-1.0.2/asylum/man/decision_quality.Rd | 54 ++-- asylum-1.0.2/asylum/man/decisions_resettlement.Rd | 76 +++--- asylum-1.0.2/asylum/man/dublin_regulation.Rd | 62 ++--- asylum-1.0.2/asylum/man/family_reunion.Rd | 62 ++--- asylum-1.0.2/asylum/man/local_authority_resettlement.Rd | 60 ++-- asylum-1.0.2/asylum/man/local_authority_support.Rd | 61 ++-- asylum-1.0.2/asylum/man/nrpf_change_of_conditions_age.Rd | 76 +++--- asylum-1.0.2/asylum/man/nrpf_change_of_conditions_decisions.Rd | 72 ++--- asylum-1.0.2/asylum/man/nrpf_change_of_conditions_gender.Rd | 64 ++--- asylum-1.0.2/asylum/man/nrpf_change_of_conditions_nationality.Rd | 90 +++---- asylum-1.0.2/asylum/man/nts.Rd | 64 ++--- asylum-1.0.2/asylum/man/oral_hearings_volume.Rd | 54 ++-- asylum-1.0.2/asylum/man/outcomes.Rd | 98 +++---- asylum-1.0.2/asylum/man/support_applications.Rd | 58 ++-- asylum-1.0.2/asylum/man/support_applications_rasi.Rd | 54 ++-- asylum-1.0.2/asylum/man/support_received.Rd | 60 ++-- asylum-1.0.2/asylum/man/travel_documents.Rd | 54 ++-- 65 files changed, 1043 insertions(+), 1029 deletions(-)
Title: SQLite Interface for R
Description: Embeds the SQLite database engine in R and
provides an interface compliant with the DBI package. The source for
the SQLite engine and for various extensions in a recent version is
included. System libraries will never be consulted because
this package relies on static linking for the plugins it includes;
this also ensures a consistent experience across all installations.
Author: Kirill Mueller [aut, cre] ,
Hadley Wickham [aut],
David A. James [aut],
Seth Falcon [aut],
D. Richard Hipp [ctb] ,
Dan Kennedy [ctb] ,
Joe Mistachkin [ctb] ,
SQLite Authors [ctb] ,
Liam Healy [ctb] ,
R Consortium [fnd],
RStudio [cph]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between RSQLite versions 2.2.16 dated 2022-08-17 and 2.2.17 dated 2022-09-10
DESCRIPTION | 8 +- MD5 | 10 +-- NEWS.md | 5 + inst/doc/RSQLite.html | 14 +++- src/vendor/sqlite3/sqlite3.c | 126 +++++++++++++++++++++++++++++++++---------- src/vendor/sqlite3/sqlite3.h | 6 +- 6 files changed, 125 insertions(+), 44 deletions(-)
Title: Retrieve and Plot Google n-Gram Data
Description: Retrieve and plot word frequencies through time from the "Google
Ngram Viewer" <https://books.google.com/ngrams>.
Author: Sean Carmody [aut, cre, cph]
Maintainer: Sean Carmody <seancarmody@gmail.com>
Diff between ngramr versions 1.7.5 dated 2022-01-08 and 1.7.7 dated 2022-09-10
ngramr-1.7.5/ngramr/NEWS |only ngramr-1.7.5/ngramr/man/figures/lifecycle-archived.svg |only ngramr-1.7.5/ngramr/man/figures/lifecycle-defunct.svg |only ngramr-1.7.5/ngramr/man/figures/lifecycle-deprecated.svg |only ngramr-1.7.5/ngramr/man/figures/lifecycle-experimental.svg |only ngramr-1.7.5/ngramr/man/figures/lifecycle-maturing.svg |only ngramr-1.7.5/ngramr/man/figures/lifecycle-questioning.svg |only ngramr-1.7.5/ngramr/man/figures/lifecycle-soft-deprecated.svg |only ngramr-1.7.5/ngramr/man/figures/lifecycle-stable.svg |only ngramr-1.7.5/ngramr/man/figures/lifecycle-superseded.svg |only ngramr-1.7.7/ngramr/DESCRIPTION | 13 - ngramr-1.7.7/ngramr/MD5 | 33 +- ngramr-1.7.7/ngramr/NEWS.md |only ngramr-1.7.7/ngramr/R/ggram.R | 2 ngramr-1.7.7/ngramr/R/ngram.R | 122 ++++------ ngramr-1.7.7/ngramr/R/ngrami.R | 1 ngramr-1.7.7/ngramr/R/sysdata.rda |binary ngramr-1.7.7/ngramr/R/utilities.R | 5 ngramr-1.7.7/ngramr/man/chunk.Rd | 2 ngramr-1.7.7/ngramr/man/figures/archy.png |only ngramr-1.7.7/ngramr/man/figures/hacker.png |only ngramr-1.7.7/ngramr/man/ngram.Rd | 76 +++--- ngramr-1.7.7/ngramr/man/ngrami.Rd | 1 ngramr-1.7.7/ngramr/tests/testthat/test-ngramr.R | 8 24 files changed, 121 insertions(+), 142 deletions(-)
Title: Hierarchical Bayesian Modeling of Decision-Making Tasks
Description: Fit an array of decision-making tasks with computational models in
a hierarchical Bayesian framework. Can perform hierarchical Bayesian analysis of
various computational models with a single line of coding
(Ahn et al., 2017) <doi:10.1162/CPSY_a_00002>.
Author: Woo-Young Ahn [aut, cre],
Nate Haines [aut],
Lei Zhang [aut],
Harhim Park [ctb],
Jaeyeong Yang [ctb],
Jethro Lee [ctb]
Maintainer: Woo-Young Ahn <wooyoung.ahn@gmail.com>
Diff between hBayesDM versions 1.1.1 dated 2021-05-03 and 1.2.0 dated 2022-09-10
DESCRIPTION | 47 ++++++----- MD5 | 70 +++++++++++++--- NAMESPACE | 10 ++ NEWS.md | 6 + R/bandit4arm2_kalman_filter.R | 6 - R/banditNarm_2par_lapse.R |only R/banditNarm_4par.R |only R/banditNarm_delta.R |only R/banditNarm_kalman_filter.R |only R/banditNarm_lapse.R |only R/banditNarm_lapse_decay.R |only R/banditNarm_singleA_lapse.R |only R/hBayesDM_model.R | 2 R/plotInd.R | 2 R/preprocess_funcs.R | 103 +++++++++++++++++++++++++ R/pstRT_ddm.R |only R/pstRT_rlddm1.R |only R/pstRT_rlddm6.R |only R/pst_Q.R | 2 R/rhat.R | 2 inst/extdata/banditNarm_exampleData.txt |only inst/extdata/pstRT_exampleData.txt |only inst/plotting/plot_functions.R | 37 ++++++++ inst/stan_files/bandit4arm2_kalman_filter.stan | 40 ++++----- inst/stan_files/banditNarm_2par_lapse.stan |only inst/stan_files/banditNarm_4par.stan |only inst/stan_files/banditNarm_delta.stan |only inst/stan_files/banditNarm_kalman_filter.stan |only inst/stan_files/banditNarm_lapse.stan |only inst/stan_files/banditNarm_lapse_decay.stan |only inst/stan_files/banditNarm_singleA_lapse.stan |only inst/stan_files/bart_ewmv.stan | 52 ++++++------ inst/stan_files/pstRT_ddm.stan |only inst/stan_files/pstRT_rlddm1.stan |only inst/stan_files/pstRT_rlddm6.stan |only man/bandit4arm2_kalman_filter.Rd | 2 man/banditNarm_2par_lapse.Rd |only man/banditNarm_4par.Rd |only man/banditNarm_delta.Rd |only man/banditNarm_kalman_filter.Rd |only man/banditNarm_lapse.Rd |only man/banditNarm_lapse_decay.Rd |only man/banditNarm_singleA_lapse.Rd |only man/pstRT_ddm.Rd |only man/pstRT_rlddm1.Rd |only man/pstRT_rlddm6.Rd |only man/pst_Q.Rd | 2 tests/testthat/test_banditNarm_2par_lapse.R |only tests/testthat/test_banditNarm_4par.R |only tests/testthat/test_banditNarm_delta.R |only tests/testthat/test_banditNarm_kalman_filter.R |only tests/testthat/test_banditNarm_lapse.R |only tests/testthat/test_banditNarm_lapse_decay.R |only tests/testthat/test_banditNarm_singleA_lapse.R |only tests/testthat/test_pstRT_ddm.R |only tests/testthat/test_pstRT_rlddm1.R |only tests/testthat/test_pstRT_rlddm6.R |only 57 files changed, 293 insertions(+), 90 deletions(-)