Title: Read Spectral and Logged Data from Foreign Files
Description: Functions for reading, and in some cases writing, foreign files
containing spectral data from spectrometers and their associated software,
output from daylight simulation models in common use, and some spectral
data repositories. As well as functions for exchange of spectral data with
other R packages. Part of the 'r4photobiology' suite,
Aphalo P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.
Author: Pedro J. Aphalo [aut, cre] (<https://orcid.org/0000-0003-3385-972X>),
Titta K. Kotilainen [ctb] (<https://orcid.org/0000-0002-2822-9734>),
Glenn Davis [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between photobiologyInOut versions 0.4.17-1 dated 2018-09-27 and 0.4.18 dated 2018-11-24
DESCRIPTION | 22 ++++----- MD5 | 18 +++---- NEWS | 11 ++++ R/read-oojaz-file.r | 31 ++++++++----- R/read-oopi-file.r | 75 ++++++++++++++++++++++++++++---- R/read-tuv-file.r | 5 +- inst/doc/user-guide.html | 62 ++++++++++++-------------- inst/extdata/tuv-azimuth-00-O3-300.html | 2 man/read_oo_pidata.Rd | 18 +++++-- tests/testthat/test-oo.R | 32 ++++++++++--- 10 files changed, 189 insertions(+), 87 deletions(-)
More information about photobiologyInOut at CRAN
Permanent link
Title: Routines for Performing Empirical Calibration of Observational
Study Estimates
Description: Routines for performing empirical calibration of observational
study estimates. By using a set of negative control hypotheses we can
estimate the empirical null distribution of a particular observational
study setup. This empirical null distribution can be used to compute a
calibrated p-value, which reflects the probability of observing an
estimated effect size when the null hypothesis is true taking both random
and systematic error into account. A similar approach can be used to
calibrate confidence intervals, using both negative and positive controls.
Author: Martijn Schuemie [aut, cre],
Marc Suchard [aut]
Maintainer: Martijn Schuemie <schuemie@ohdsi.org>
Diff between EmpiricalCalibration versions 1.3.6 dated 2017-11-07 and 1.4.0 dated 2018-11-24
EmpiricalCalibration-1.3.6/EmpiricalCalibration/NEWS |only EmpiricalCalibration-1.4.0/EmpiricalCalibration/DESCRIPTION | 23 - EmpiricalCalibration-1.4.0/EmpiricalCalibration/MD5 | 37 +- EmpiricalCalibration-1.4.0/EmpiricalCalibration/NAMESPACE | 1 EmpiricalCalibration-1.4.0/EmpiricalCalibration/NEWS.md |only EmpiricalCalibration-1.4.0/EmpiricalCalibration/R/Evaluation.R | 3 EmpiricalCalibration-1.4.0/EmpiricalCalibration/R/Plots.R | 160 ++++++++-- EmpiricalCalibration-1.4.0/EmpiricalCalibration/README.md | 44 +- EmpiricalCalibration-1.4.0/EmpiricalCalibration/build/vignette.rds |binary EmpiricalCalibration-1.4.0/EmpiricalCalibration/inst/CITATION | 26 + EmpiricalCalibration-1.4.0/EmpiricalCalibration/inst/doc/EmpiricalCiCalibrationVignette.R | 3 EmpiricalCalibration-1.4.0/EmpiricalCalibration/inst/doc/EmpiricalCiCalibrationVignette.Rmd | 6 EmpiricalCalibration-1.4.0/EmpiricalCalibration/inst/doc/EmpiricalCiCalibrationVignette.pdf |binary EmpiricalCalibration-1.4.0/EmpiricalCalibration/inst/doc/EmpiricalPCalibrationVignette.pdf |binary EmpiricalCalibration-1.4.0/EmpiricalCalibration/man/evaluateCiCalibration.Rd | 3 EmpiricalCalibration-1.4.0/EmpiricalCalibration/man/plotCalibration.Rd | 4 EmpiricalCalibration-1.4.0/EmpiricalCalibration/man/plotCalibrationEffect.Rd | 11 EmpiricalCalibration-1.4.0/EmpiricalCalibration/man/plotCiCalibration.Rd | 3 EmpiricalCalibration-1.4.0/EmpiricalCalibration/man/plotCiCalibrationEffect.Rd |only EmpiricalCalibration-1.4.0/EmpiricalCalibration/man/simulateControls.Rd | 4 EmpiricalCalibration-1.4.0/EmpiricalCalibration/vignettes/EmpiricalCiCalibrationVignette.Rmd | 6 21 files changed, 259 insertions(+), 75 deletions(-)
More information about EmpiricalCalibration at CRAN
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Title: MAGIC - Markov Affinity-Based Graph Imputation of Cells
Description: MAGIC (Markov affinity-based graph imputation of cells) is a method for addressing technical noise in single-cell data, including under-sampling of mRNA molecules, often termed "dropout" which can severely obscure important gene-gene relationships. MAGIC shares information across similar cells, via data diffusion, to denoise the cell count matrix and fill in missing transcripts. Read more: van Dijk et al. (2018) <DOI:10.1016/j.cell.2018.05.061>.
Author: David van Dijk [aut],
Scott Gigante [cre] (<https://orcid.org/0000-0002-4544-2764>)
Maintainer: Scott Gigante <scott.gigante@yale.edu>
Diff between Rmagic versions 1.3.0 dated 2018-09-21 and 1.4.0 dated 2018-11-24
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/magic.R | 29 ++++++++++++++++++++++------- R/utils.R | 19 +++++++++++++++++++ README.md | 2 +- 5 files changed, 49 insertions(+), 15 deletions(-)
Title: 'Rcpp' Integration for the 'Eigen' Templated Linear Algebra
Library
Description: R and 'Eigen' integration using 'Rcpp'.
'Eigen' is a C++ template library for linear algebra: matrices, vectors,
numerical solvers and related algorithms. It supports dense and sparse
matrices on integer, floating point and complex numbers, decompositions of
such matrices, and solutions of linear systems. Its performance on many
algorithms is comparable with some of the best implementations based on
'Lapack' and level-3 'BLAS'. The 'RcppEigen' package includes the header
files from the 'Eigen' C++ template library (currently version 3.3.4). Thus
users do not need to install 'Eigen' itself in order to use 'RcppEigen'.
Since version 3.1.1, 'Eigen' is licensed under the Mozilla Public License
(version 2); earlier version were licensed under the GNU LGPL version 3 or
later. 'RcppEigen' (the 'Rcpp' bindings/bridge to 'Eigen') is licensed under
the GNU GPL version 2 or later, as is the rest of 'Rcpp'.
Author: Douglas Bates, Dirk Eddelbuettel, Romain Francois, and Yixuan Qiu;
the authors of Eigen for the included version of Eigen
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppEigen versions 0.3.3.4.0 dated 2018-02-07 and 0.3.3.5.0 dated 2018-11-24
ChangeLog | 30 ++ DESCRIPTION | 10 MD5 | 106 ++++----- README.md | 6 build/vignette.rds |binary inst/NEWS.Rd | 10 inst/doc/RcppEigen-Introduction.pdf |binary inst/examples/lmBenchmark.R | 117 +++++----- inst/include/Eigen/Core | 4 inst/include/Eigen/src/Cholesky/LDLT.h | 7 inst/include/Eigen/src/Core/Assign_MKL.h | 6 inst/include/Eigen/src/Core/CoreEvaluators.h | 33 ++ inst/include/Eigen/src/Core/Diagonal.h | 5 inst/include/Eigen/src/Core/Dot.h | 17 - inst/include/Eigen/src/Core/MathFunctions.h | 28 -- inst/include/Eigen/src/Core/MathFunctionsImpl.h | 23 + inst/include/Eigen/src/Core/Product.h | 10 inst/include/Eigen/src/Core/ProductEvaluators.h | 31 +- inst/include/Eigen/src/Core/Redux.h | 2 inst/include/Eigen/src/Core/Ref.h | 2 inst/include/Eigen/src/Core/SelfAdjointView.h | 6 inst/include/Eigen/src/Core/SelfCwiseBinaryOp.h | 4 inst/include/Eigen/src/Core/Transpositions.h | 2 inst/include/Eigen/src/Core/arch/AVX/PacketMath.h | 11 inst/include/Eigen/src/Core/arch/AVX512/MathFunctions.h | 33 +- inst/include/Eigen/src/Core/arch/AVX512/PacketMath.h | 6 inst/include/Eigen/src/Core/arch/AltiVec/PacketMath.h | 46 +++ inst/include/Eigen/src/Core/arch/CUDA/Half.h | 4 inst/include/Eigen/src/Core/arch/NEON/Complex.h | 8 inst/include/Eigen/src/Core/arch/NEON/PacketMath.h | 31 ++ inst/include/Eigen/src/Core/arch/SSE/Complex.h | 10 inst/include/Eigen/src/Core/arch/SSE/PacketMath.h | 22 + inst/include/Eigen/src/Core/arch/SSE/TypeCasting.h | 28 +- inst/include/Eigen/src/Core/functors/BinaryFunctors.h | 25 -- inst/include/Eigen/src/Core/functors/StlFunctors.h | 4 inst/include/Eigen/src/Core/products/TriangularMatrixMatrix.h | 24 +- inst/include/Eigen/src/Core/products/TriangularMatrixVector.h | 22 + inst/include/Eigen/src/Core/util/DisableStupidWarnings.h | 19 - inst/include/Eigen/src/Core/util/Macros.h | 10 inst/include/Eigen/src/Core/util/Memory.h | 2 inst/include/Eigen/src/Core/util/Meta.h | 20 + inst/include/Eigen/src/Core/util/StaticAssert.h | 6 inst/include/Eigen/src/Eigenvalues/GeneralizedEigenSolver.h | 5 inst/include/Eigen/src/Eigenvalues/RealSchur.h | 4 inst/include/Eigen/src/Eigenvalues/SelfAdjointEigenSolver_LAPACKE.h | 25 -- inst/include/Eigen/src/LU/InverseImpl.h | 2 inst/include/Eigen/src/SVD/BDCSVD.h | 4 inst/include/Eigen/src/SparseCore/SparseSelfAdjointView.h | 8 inst/include/Eigen/src/SparseQR/SparseQR.h | 26 +- inst/include/RcppEigenWrap.h | 9 inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorDeviceThreadPool.h | 11 inst/include/unsupported/Eigen/CXX11/src/Tensor/TensorStorage.h | 8 inst/include/unsupported/Eigen/src/IterativeSolvers/DGMRES.h | 60 ++--- inst/include/unsupported/Eigen/src/SparseExtra/MarketIO.h | 1 54 files changed, 588 insertions(+), 365 deletions(-)
Title: Programming with Big Data -- Base Wrappers for Distributed
Matrices
Description: An interface to and extensions for the 'PBLAS' and
'ScaLAPACK' numerical libraries. This enables R to utilize
distributed linear algebra for codes written in the 'SPMD' fashion.
This interface is deliberately low-level and mimics the style of
the native libraries it wraps. For a much higher level way of
managing distributed matrices, see the 'pbdDMAT' package.
Author: Drew Schmidt [aut, cre],
Wei-Chen Chen [aut],
George Ostrouchov [aut],
Pragneshkumar Patel [aut],
Ewan Higgs [ctb]
Maintainer: ORPHANED
Diff between pbdBASE versions 0.4-5.1 dated 2018-02-05 and 0.4-5.2 dated 2018-11-24
DESCRIPTION | 6 +++--- MD5 | 6 +++--- src/Makevars.in | 10 +++++----- src/Makevars.win | 8 ++++---- 4 files changed, 15 insertions(+), 15 deletions(-)
Title: Automatic Codebooks from Survey Metadata Encoded in Attributes
Description: Easily automate the following tasks to describe data frames:
summarise the distributions of scales and items graphically and using descriptive statistics,
compute reliabilities (internal consistencies, retest, multilevel) for psychological scales,
combine this information with metadata (such as item labels and labelled values) that is derived from R attributes.
To do so, the package relies on 'rmarkdown' partials, so you can generate HTML, PDF, and Word documents. Codebooks
are also available as tables (CSV, Excel, etc.).
The metadata and codebooks are also available at your fingertips via RStudio Addins.
Author: Ruben Arslan [aut, cre]
Maintainer: Ruben Arslan <ruben.arslan@gmail.com>
Diff between codebook versions 0.6.3 dated 2018-08-01 and 0.7.4 dated 2018-11-24
codebook-0.6.3/codebook/man/detect_missings.Rd |only codebook-0.6.3/codebook/man/zap_label.Rd |only codebook-0.7.4/codebook/DESCRIPTION | 15 codebook-0.7.4/codebook/MD5 | 110 codebook-0.7.4/codebook/NAMESPACE | 27 codebook-0.7.4/codebook/NEWS.md | 24 codebook-0.7.4/codebook/R/codebook.R | 214 - codebook-0.7.4/codebook/R/correct_attributes.R | 172 codebook-0.7.4/codebook/R/create_metadata.R | 155 codebook-0.7.4/codebook/R/label_browser.R | 26 codebook-0.7.4/codebook/R/misc.R | 66 codebook-0.7.4/codebook/R/plot_helpers.R | 26 codebook-0.7.4/codebook/R/reliability.R | 11 codebook-0.7.4/codebook/R/rmarkdown_helpers.R | 30 codebook-0.7.4/codebook/README.md | 29 codebook-0.7.4/codebook/build/vignette.rds |binary codebook-0.7.4/codebook/data/bfi.rda |binary codebook-0.7.4/codebook/inst/CITATION | 14 codebook-0.7.4/codebook/inst/_codebook.Rmd | 9 codebook-0.7.4/codebook/inst/_codebook_data_info.Rmd |only codebook-0.7.4/codebook/inst/_codebook_item.Rmd | 31 codebook-0.7.4/codebook/inst/_codebook_missingness.Rmd | 15 codebook-0.7.4/codebook/inst/_codebook_scale.Rmd | 4 codebook-0.7.4/codebook/inst/_metadata_jsonld.Rmd | 2 codebook-0.7.4/codebook/inst/_template_codebook.Rmd |only codebook-0.7.4/codebook/inst/doc/codebook.R | 166 codebook-0.7.4/codebook/inst/doc/codebook.Rmd | 38 codebook-0.7.4/codebook/inst/doc/codebook.html | 2127 ++++++++-- codebook-0.7.4/codebook/inst/doc/codebook_labelled_manual.R | 253 - codebook-0.7.4/codebook/inst/doc/codebook_labelled_manual.Rmd | 97 codebook-0.7.4/codebook/inst/doc/codebook_labelled_manual.html | 1854 +++++++- codebook-0.7.4/codebook/inst/doc/codebook_nested_scale.R | 124 codebook-0.7.4/codebook/inst/doc/codebook_nested_scale.Rmd | 22 codebook-0.7.4/codebook/inst/doc/codebook_nested_scale.html | 335 - codebook-0.7.4/codebook/inst/doc/codebook_qualtrics.R | 198 codebook-0.7.4/codebook/inst/doc/codebook_qualtrics.Rmd | 23 codebook-0.7.4/codebook/inst/doc/codebook_qualtrics.html | 261 - codebook-0.7.4/codebook/inst/doc/codebook_sav.R | 307 + codebook-0.7.4/codebook/inst/doc/codebook_sav.Rmd | 80 codebook-0.7.4/codebook/inst/doc/codebook_sav.html | 1545 ++++++- codebook-0.7.4/codebook/inst/doc/codebook_tutorial.R |only codebook-0.7.4/codebook/inst/doc/codebook_tutorial.Rmd |only codebook-0.7.4/codebook/inst/doc/codebook_tutorial.pdf |only codebook-0.7.4/codebook/inst/www/codebook.js | 2 codebook-0.7.4/codebook/inst/www/index.html | 16 codebook-0.7.4/codebook/man/add_R.Rd |only codebook-0.7.4/codebook/man/codebook_data_info.Rd |only codebook-0.7.4/codebook/man/data_description_default.Rd |only codebook-0.7.4/codebook/man/detect_missing.Rd |only codebook-0.7.4/codebook/man/list_to_dict.Rd |only codebook-0.7.4/codebook/man/md_pattern.Rd | 10 codebook-0.7.4/codebook/man/metadata.Rd |only codebook-0.7.4/codebook/man/metadata_list.Rd | 5 codebook-0.7.4/codebook/man/new_codebook_rmd.Rd |only codebook-0.7.4/codebook/man/plot_labelled.Rd | 2 codebook-0.7.4/codebook/man/reexports.Rd | 12 codebook-0.7.4/codebook/man/reverse_labelled_values.Rd | 4 codebook-0.7.4/codebook/vignettes/codebook.Rmd | 38 codebook-0.7.4/codebook/vignettes/codebook_labelled_manual.Rmd | 97 codebook-0.7.4/codebook/vignettes/codebook_nested_scale.Rmd | 22 codebook-0.7.4/codebook/vignettes/codebook_qualtrics.Rmd | 23 codebook-0.7.4/codebook/vignettes/codebook_sav.Rmd | 80 codebook-0.7.4/codebook/vignettes/codebook_tutorial.Rmd |only codebook-0.7.4/codebook/vignettes/codebook_tutorial.html |only 64 files changed, 7187 insertions(+), 1534 deletions(-)
Title: Functional Data Clustering
Description: This package proposes a model-based clustering algorithm for
multivariate functional data. The parametric mixture model, based on the
assumption of normality of the principal components resulting from a
multivariate functional PCA, is estimated by an EM-like algorithm. The main
advantage of the proposed algorithm is its ability to take into account the
dependence among curves.
Author: Mohamed Soueidatt <mohamed.soueidatt@inria.fr>, <msoueidatt@gmail.com>*.
Maintainer: ORPHANED
Diff between Funclustering versions 1.0.1 dated 2014-01-15 and 1.0.2 dated 2018-11-24
DESCRIPTION | 19 ++++++++++--------- MD5 | 8 ++++---- NAMESPACE | 5 ++++- src/Makevars | 6 +++--- src/Makevars.win | 6 +++--- 5 files changed, 24 insertions(+), 20 deletions(-)
Title: Selection of Training Populations by Genetic Algorithm
Description: Combining Predictive Analytics and Experimental Design to Optimize Results. To be utilized to select a test data calibrated training population in high dimensional prediction problems and assumes that the explanatory variables are observed for all of the individuals. Once a "good" training set is identified, the response variable can be obtained only for this set to build a model for predicting the response in the test set. The algorithms in the package can be tweaked to solve some other subset selection problems.
Author: Deniz Akdemir
Maintainer: Deniz Akdemir <deniz.akdemir.work@gmail.com>
Diff between STPGA versions 5.2 dated 2018-09-21 and 5.2.1 dated 2018-11-24
DESCRIPTION | 11 +++++------ MD5 | 4 ++-- R/GenAlgForSubsetSelectionMONoTest.R | 6 +++++- 3 files changed, 12 insertions(+), 9 deletions(-)
Title: Statistical Framework to Define Subgroups in Complex Datasets
Description: High-dimensional datasets that do not exhibit a clear intrinsic clustered structure pose a challenge to conventional clustering algorithms. For this reason, we developed an unsupervised framework that helps scientists to better subgroup their datasets based on visual cues, please see Gao S, Mutter S, Casey A, Makinen V-P (2018) Numero: a statistical framework to define multivariable subgroups in complex population-based datasets, Int J Epidemiology, dyy113, <doi:10.1093/ije/dyy113>. The framework includes the necessary functions to construct a self-organizing map of the data, to evaluate the statistical significance of the observed data patterns, and to visualize the results.
Author: Song Gao [aut],
Stefan Mutter [aut],
Aaron E. Casey [aut],
Ville-Petteri Makinen [aut, cre]
Maintainer: Ville-Petteri Makinen <vpmakine@gmail.com>
Diff between Numero versions 1.0.3 dated 2017-12-01 and 1.1.1 dated 2018-11-24
Numero-1.0.3/Numero/R/nroCircus.R |only Numero-1.0.3/Numero/R/nroFigure.R |only Numero-1.0.3/Numero/R/nroKoho.R |only Numero-1.0.3/Numero/R/nroMatrix.R |only Numero-1.0.3/Numero/man/nroCircus.Rd |only Numero-1.0.3/Numero/man/nroFigure.Rd |only Numero-1.0.3/Numero/man/nroKoho.Rd |only Numero-1.0.3/Numero/man/nroMatrix.Rd |only Numero-1.0.3/Numero/src/abacus.matrixbuffer.key.cpp |only Numero-1.0.3/Numero/src/abacus.shuffle.cpp |only Numero-1.0.3/Numero/src/koho.buffer.insert.cpp |only Numero-1.0.3/Numero/src/koho.engine.count.cpp |only Numero-1.0.3/Numero/src/koho.engine.put.cpp |only Numero-1.0.3/Numero/src/koho.enginebuffer.organize.cpp |only Numero-1.0.3/Numero/src/koho.kmeans.cpp |only Numero-1.0.3/Numero/src/koho.model.distance.cpp |only Numero-1.0.3/Numero/src/koho.model.location.cpp |only Numero-1.0.3/Numero/src/koho.model.size.cpp |only Numero-1.0.3/Numero/src/koho.modelbuffer.calcdist.cpp |only Numero-1.0.3/Numero/src/koho.modelbuffer.match.cpp |only Numero-1.0.3/Numero/src/koho.modelbuffer.update.cpp |only Numero-1.0.3/Numero/src/koho.operate.cpp |only Numero-1.0.3/Numero/src/koho.variable.cpp |only Numero-1.0.3/Numero/src/medusa.panic.cpp |only Numero-1.0.3/Numero/src/medusa.worry.cpp |only Numero-1.0.3/Numero/src/nro.engine.cpp |only Numero-1.0.3/Numero/src/nro.model.cpp |only Numero-1.0.3/Numero/src/nro_aggregate.cpp |only Numero-1.0.3/Numero/src/nro_kmeans.cpp |only Numero-1.0.3/Numero/src/nro_koho.cpp |only Numero-1.0.3/Numero/src/nro_matrix.cpp |only Numero-1.0.3/Numero/src/scriptum.artist.close.cpp |only Numero-1.0.3/Numero/vignettes/biochemistry.svg |only Numero-1.0.3/Numero/vignettes/endpoints.svg |only Numero-1.0.3/Numero/vignettes/qualityOverview.svg |only Numero-1.0.3/Numero/vignettes/styles.css |only Numero-1.1.1/Numero/DESCRIPTION | 30 Numero-1.1.1/Numero/MD5 | 310 Numero-1.1.1/Numero/NAMESPACE | 11 Numero-1.1.1/Numero/R/nroAggregate.R | 98 Numero-1.1.1/Numero/R/nroColorize.R | 94 Numero-1.1.1/Numero/R/nroKmeans.R | 84 Numero-1.1.1/Numero/R/nroKohonen.R |only Numero-1.1.1/Numero/R/nroLabel.R | 42 Numero-1.1.1/Numero/R/nroMatch.R | 123 Numero-1.1.1/Numero/R/nroPermute.R | 117 Numero-1.1.1/Numero/R/nroPlot.R |only Numero-1.1.1/Numero/R/nroPreprocess.R |only Numero-1.1.1/Numero/R/nroSummary.R |only Numero-1.1.1/Numero/R/nroTrain.R | 97 Numero-1.1.1/Numero/inst/CITATION |only Numero-1.1.1/Numero/inst/doc/NumeroGuide.R | 407 Numero-1.1.1/Numero/inst/doc/NumeroGuide.html | 1204 - Numero-1.1.1/Numero/inst/doc/NumeroGuide.rmd | 677 Numero-1.1.1/Numero/man/nroAggregate.Rd | 47 Numero-1.1.1/Numero/man/nroColorize.Rd | 31 Numero-1.1.1/Numero/man/nroKmeans.Rd | 34 Numero-1.1.1/Numero/man/nroKohonen.Rd |only Numero-1.1.1/Numero/man/nroLabel.Rd | 40 Numero-1.1.1/Numero/man/nroMatch.Rd | 52 Numero-1.1.1/Numero/man/nroPermute.Rd | 66 Numero-1.1.1/Numero/man/nroPlot.Rd |only Numero-1.1.1/Numero/man/nroPreprocess.Rd |only Numero-1.1.1/Numero/man/nroSummary.Rd |only Numero-1.1.1/Numero/man/nroTrain.Rd | 23 Numero-1.1.1/Numero/src/Numero_init.c | 38 Numero-1.1.1/Numero/src/abacus.array.cpp |only Numero-1.1.1/Numero/src/abacus.convergence.cpp | 72 Numero-1.1.1/Numero/src/abacus.destratify.cpp | 4 Numero-1.1.1/Numero/src/abacus.empirical.add.cpp | 2 Numero-1.1.1/Numero/src/abacus.empirical.p.cpp | 4 Numero-1.1.1/Numero/src/abacus.h | 13 Numero-1.1.1/Numero/src/abacus.local.h | 50 Numero-1.1.1/Numero/src/abacus.matrix.add.cpp | 23 Numero-1.1.1/Numero/src/abacus.matrix.column.cpp | 17 Numero-1.1.1/Numero/src/abacus.matrix.count.cpp | 7 Numero-1.1.1/Numero/src/abacus.matrix.elements.cpp | 22 Numero-1.1.1/Numero/src/abacus.matrix.insert.cpp | 15 Numero-1.1.1/Numero/src/abacus.matrix.kruskal.cpp | 4 Numero-1.1.1/Numero/src/abacus.matrix.remove.cpp | 47 Numero-1.1.1/Numero/src/abacus.matrix.row.cpp | 13 Numero-1.1.1/Numero/src/abacus.matrix.symmetric.cpp | 2 Numero-1.1.1/Numero/src/abacus.matrix.value.cpp | 25 Numero-1.1.1/Numero/src/abacus.matrix.values.cpp | 28 Numero-1.1.1/Numero/src/abacus.statistic.cpp | 2 Numero-1.1.1/Numero/src/abacus.version.cpp | 2 Numero-1.1.1/Numero/src/akkad.fieldset.cpp |only Numero-1.1.1/Numero/src/akkad.h |only Numero-1.1.1/Numero/src/akkad.local.h |only Numero-1.1.1/Numero/src/akkad.messenger.null.cpp |only Numero-1.1.1/Numero/src/akkad.scribe.accessible.cpp |only Numero-1.1.1/Numero/src/akkad.scribe.add.cpp |only Numero-1.1.1/Numero/src/akkad.scribe.assign.cpp |only Numero-1.1.1/Numero/src/akkad.scribe.contents.cpp |only Numero-1.1.1/Numero/src/akkad.scribe.cpp |only Numero-1.1.1/Numero/src/akkad.scribe.find.cpp |only Numero-1.1.1/Numero/src/akkad.scribe.get.cpp |only Numero-1.1.1/Numero/src/akkad.scribe.keys.cpp |only Numero-1.1.1/Numero/src/akkad.scribe.operator[].cpp |only Numero-1.1.1/Numero/src/akkad.scribe.remove.cpp |only Numero-1.1.1/Numero/src/akkad.scribe.save.cpp |only Numero-1.1.1/Numero/src/akkad.scribe.size.cpp |only Numero-1.1.1/Numero/src/akkad.version.cpp |only Numero-1.1.1/Numero/src/koho.engine.average.cpp | 43 Numero-1.1.1/Numero/src/koho.engine.cpp | 2 Numero-1.1.1/Numero/src/koho.engine.histogram.cpp |only Numero-1.1.1/Numero/src/koho.engine.insert.cpp | 45 Numero-1.1.1/Numero/src/koho.engine.shuffle.cpp | 56 Numero-1.1.1/Numero/src/koho.enginebuffer.diffuse.cpp |only Numero-1.1.1/Numero/src/koho.enginebuffer.prepare.cpp |only Numero-1.1.1/Numero/src/koho.h | 105 Numero-1.1.1/Numero/src/koho.local.h | 190 Numero-1.1.1/Numero/src/koho.model.configure.cpp | 32 Numero-1.1.1/Numero/src/koho.model.connect.cpp |only Numero-1.1.1/Numero/src/koho.model.cpp | 26 Numero-1.1.1/Numero/src/koho.model.distances.cpp |only Numero-1.1.1/Numero/src/koho.model.identities.cpp | 8 Numero-1.1.1/Numero/src/koho.model.insert.cpp | 32 Numero-1.1.1/Numero/src/koho.model.prototype.cpp | 6 Numero-1.1.1/Numero/src/koho.model.topology.cpp | 2 Numero-1.1.1/Numero/src/koho.model.train.cpp | 86 Numero-1.1.1/Numero/src/koho.point.cpp |only Numero-1.1.1/Numero/src/koho.subset.cpp |only Numero-1.1.1/Numero/src/koho.subset.join.cpp |only Numero-1.1.1/Numero/src/koho.subset.match.cpp |only Numero-1.1.1/Numero/src/koho.subset.moments.cpp |only Numero-1.1.1/Numero/src/koho.trainer.codebook.cpp |only Numero-1.1.1/Numero/src/koho.trainer.cpp |only Numero-1.1.1/Numero/src/koho.trainer.cycle.cpp |only Numero-1.1.1/Numero/src/koho.trainer.distance.cpp |only Numero-1.1.1/Numero/src/koho.trainer.distances.cpp |only Numero-1.1.1/Numero/src/koho.trainer.euclidean.cpp |only Numero-1.1.1/Numero/src/koho.trainer.match.cpp |only Numero-1.1.1/Numero/src/koho.trainer.update.cpp |only Numero-1.1.1/Numero/src/koho.transformation.cpp |only Numero-1.1.1/Numero/src/koho.version.cpp | 2 Numero-1.1.1/Numero/src/medusa.combine.cpp | 4 Numero-1.1.1/Numero/src/medusa.currtime.cpp |only Numero-1.1.1/Numero/src/medusa.file.cpp | 61 Numero-1.1.1/Numero/src/medusa.h | 21 Numero-1.1.1/Numero/src/medusa.lnan.cpp |only Numero-1.1.1/Numero/src/medusa.local.h | 12 Numero-1.1.1/Numero/src/medusa.long2text.cpp | 14 Numero-1.1.1/Numero/src/medusa.match.cpp | 2 Numero-1.1.1/Numero/src/medusa.openfile.cpp | 2 Numero-1.1.1/Numero/src/medusa.string2long.cpp |only Numero-1.1.1/Numero/src/medusa.string2size.cpp | 4 Numero-1.1.1/Numero/src/medusa.table.cpp | 38 Numero-1.1.1/Numero/src/medusa.uniqreal.cpp | 2 Numero-1.1.1/Numero/src/medusa.uniqsize.cpp | 4 Numero-1.1.1/Numero/src/medusa.uniqstr.cpp | 2 Numero-1.1.1/Numero/src/medusa.version.cpp | 2 Numero-1.1.1/Numero/src/nro.akkadmessengerstandard.cpp |only Numero-1.1.1/Numero/src/nro.h | 26 Numero-1.1.1/Numero/src/nro.matrix2reals.cpp | 49 Numero-1.1.1/Numero/src/nro.medusapanic.cpp |only Numero-1.1.1/Numero/src/nro.medusaworry.cpp |only Numero-1.1.1/Numero/src/nro.reals2matrix.cpp | 23 Numero-1.1.1/Numero/src/nro.reals2topology.cpp | 25 Numero-1.1.1/Numero/src/nro.reals2vector.cpp | 15 Numero-1.1.1/Numero/src/nro.scriptumartistclose.cpp |only Numero-1.1.1/Numero/src/nro.vector2reals.cpp | 13 Numero-1.1.1/Numero/src/nro.vector2sizes.cpp | 3 Numero-1.1.1/Numero/src/nro_circus.cpp | 102 Numero-1.1.1/Numero/src/nro_colorize.cpp | 12 Numero-1.1.1/Numero/src/nro_diffuse.cpp |only Numero-1.1.1/Numero/src/nro_figure.cpp | 18 Numero-1.1.1/Numero/src/nro_kohonen.cpp |only Numero-1.1.1/Numero/src/nro_label.cpp | 138 Numero-1.1.1/Numero/src/nro_match.cpp | 76 Numero-1.1.1/Numero/src/nro_permute.cpp | 148 Numero-1.1.1/Numero/src/nro_train.cpp | 91 Numero-1.1.1/Numero/src/punos.h | 29 Numero-1.1.1/Numero/src/punos.local.h | 8 Numero-1.1.1/Numero/src/punos.smoothen.cpp | 7 Numero-1.1.1/Numero/src/punos.topology.cpp | 25 Numero-1.1.1/Numero/src/punos.topology.diffuse.cpp | 41 Numero-1.1.1/Numero/src/punos.topology.highlight.cpp |only Numero-1.1.1/Numero/src/punos.topology.interpolate.cpp | 3 Numero-1.1.1/Numero/src/punos.topology.paint.cpp | 59 Numero-1.1.1/Numero/src/punos.topology.rewire.cpp | 23 Numero-1.1.1/Numero/src/punos.topology.stratify.cpp | 2 Numero-1.1.1/Numero/src/punos.topology.weight.cpp | 3 Numero-1.1.1/Numero/src/punos.version.cpp | 2 Numero-1.1.1/Numero/src/scriptum.artist.paint.cpp | 8 Numero-1.1.1/Numero/src/scriptum.colormap.cpp | 3 Numero-1.1.1/Numero/src/scriptum.frame.horizontal.cpp | 5 Numero-1.1.1/Numero/src/scriptum.frame.style.cpp |only Numero-1.1.1/Numero/src/scriptum.frame.stylize.cpp | 3 Numero-1.1.1/Numero/src/scriptum.frame.text.cpp | 58 Numero-1.1.1/Numero/src/scriptum.frame.vertical.cpp | 5 Numero-1.1.1/Numero/src/scriptum.h | 10 Numero-1.1.1/Numero/src/scriptum.local.h | 13 Numero-1.1.1/Numero/src/scriptum.style.cpp | 33 Numero-1.1.1/Numero/src/scriptum.style2code.cpp | 9 Numero-1.1.1/Numero/src/scriptum.version.cpp | 2 Numero-1.1.1/Numero/vignettes/NumeroGuide.rmd | 677 Numero-1.1.1/Numero/vignettes/legumes.jpg |binary Numero-1.1.1/Numero/vignettes/split.jpg |binary Numero-1.1.1/Numero/vignettes/step1.jpg |only Numero-1.1.1/Numero/vignettes/step2.jpg |only Numero-1.1.1/Numero/vignettes/step3.jpg |only Numero-1.1.1/Numero/vignettes/step4.jpg |only Numero-1.1.1/Numero/vignettes/subgroups.svg |19995 +++++++++++++++-- Numero-1.1.1/Numero/vignettes/trainingColorings.svg |only 205 files changed, 21247 insertions(+), 5295 deletions(-)
Title: Isotonic Proportional Hazards Model
Description: Nonparametric estimation of an isotonic covariate effect for proportional hazards model.
Author: Yunro Chung [cre]
Maintainer: Yunro Chung <yunro.chung@asu.edu>
Diff between isoph versions 1.1.2 dated 2017-12-11 and 1.1.3 dated 2018-11-24
DESCRIPTION | 14 +++---- MD5 | 6 +-- R/isoph.R | 94 ++------------------------------------------------- man/isoph-package.Rd | 10 ++--- 4 files changed, 19 insertions(+), 105 deletions(-)
Title: Tools for Eurostat Open Data
Description: Tools to download data from the Eurostat database
<http://ec.europa.eu/eurostat> together with search and
manipulation utilities.
Author: Leo Lahti [aut, cre],
Janne Huovari [aut],
Markus Kainu [aut],
Przemyslaw Biecek [aut],
Joona Lehtomaki [ctb],
Francois Briatte [ctb],
Oliver Reiter [ctb]
Maintainer: Leo Lahti <leo.lahti@iki.fi>
Diff between eurostat versions 3.2.9 dated 2018-09-20 and 3.3.1 dated 2018-11-24
DESCRIPTION | 12 MD5 | 50 NEWS |only R/data_spatial.R | 10 R/get_eurostat_geospatial.R | 25 R/label_eurostat.R | 68 - README.md | 2 data/eurostat_geodata_60_2016.rda |binary inst/doc/blogposts.html | 4 inst/doc/cheatsheet.html | 4 inst/doc/eurostat_tutorial.R | 9 inst/doc/eurostat_tutorial.Rmd | 9 inst/doc/eurostat_tutorial.pdf | 2405 +++++++++++++++++--------------------- inst/doc/publications.html | 4 man/get_eurostat_geospatial.Rd | 9 man/label_eurostat.Rd | 30 tests/testthat/test-all.R | 26 vignettes/eurostat_tutorial.Rmd | 9 vignettes/eurostat_tutorial.html | 151 +- vignettes/eurostat_tutorial.md | 152 +- vignettes/fig/map1ex-1.pdf |binary vignettes/fig/maps2-1.pdf |binary vignettes/fig/maps3-1.png |binary vignettes/fig/maps4-1.png |binary vignettes/fig/plotGallery-1.pdf |binary vignettes/fig/trains_plot-1.pdf |binary vignettes/tmp.R |only 27 files changed, 1491 insertions(+), 1488 deletions(-)
Title: A 'Shiny' Application for Inspecting Structural Topic Models
Description: This app enables interactive validation, interpretation and visualization of structural topic models from the 'stm' package by Roberts and others (2014) <doi:10.1111/ajps.12103>. It also includes helper functions for model diagnostics and extracting data from effect estimates.
Author: Carsten Schwemmer [aut, cre] (<https://orcid.org/0000-0001-9084-946X>),
Jonne Guyt [ctb]
Maintainer: Carsten Schwemmer <c.schwem2er@gmail.com>
Diff between stminsights versions 0.2.2 dated 2018-08-30 and 0.3.0 dated 2018-11-24
DESCRIPTION | 22 MD5 | 16 NEWS.md | 107 - README.md | 15 inst/app/app.R | 3934 +++++++++++++++++++++++++++------------------------ inst/doc/intro.Rmd | 258 +-- inst/doc/intro.html | 34 man/figures/logo.png |binary vignettes/intro.Rmd | 258 +-- 9 files changed, 2495 insertions(+), 2149 deletions(-)
Title: Plot 'rpart' Models: An Enhanced Version of 'plot.rpart'
Description: Plot 'rpart' models. Extends plot.rpart() and text.rpart()
in the 'rpart' package.
Author: Stephen Milborrow
Maintainer: Stephen Milborrow <milbo@sonic.net>
Diff between rpart.plot versions 3.0.5 dated 2018-11-03 and 3.0.6 dated 2018-11-24
DESCRIPTION | 7 +- MD5 | 42 ++++++------- NEWS | 7 ++ R/lib.R | 6 + R/node.labs.R | 2 R/palette.R | 2 R/prp.R | 8 ++ R/rpart.predict.R | 2 R/rpart.rules.R | 9 ++ inst/doc/prp.pdf |binary inst/slowtests/test.na.R | 6 + inst/slowtests/test.na.Rout.save | 6 + inst/slowtests/test.palette.R | 6 - inst/slowtests/test.palette.Rout.save | 6 - inst/slowtests/test.prolog.R | 8 ++ inst/slowtests/test.prp.Rout.save | 4 - inst/slowtests/test.rpart.plot.R | 89 +++++++++++++--------------- inst/slowtests/test.rpart.plot.Rout.save | 95 ++++++++++++++---------------- inst/slowtests/test.rpart.rules.R | 6 + inst/slowtests/test.rpart.rules.Rout.save | 6 + inst/slowtests/vignette.R | 22 +++--- inst/slowtests/vignette.Rout.save | 22 +++--- 22 files changed, 205 insertions(+), 156 deletions(-)
Title: Lookup Tables to Generate Poverty Likelihoods and Rates using
the Poverty Probability Index (PPI)
Description: The Poverty Probability Index (PPI) is a poverty measurement tool
for organizations and businesses with a mission to serve the poor. The PPI
is statistically-sound, yet simple to use: the answers to 10 questions about
a household’s characteristics and asset ownership are scored to compute the
likelihood that the household is living below the poverty line – or above by
only a narrow margin. This package contains country-specific lookup data tables
used as reference to determine the poverty likelihood of a household based
on their score from the country-specific PPI questionnaire. These lookup
tables have been extracted from documentation of the PPI found at
<https://www.povertyindex.org> and managed by Innovations for Poverty Action
<https://www.poverty-action.org>.
Author: Ernest Guevarra [aut, cre] (<https://orcid.org/0000-0002-4887-4415>)
Maintainer: Ernest Guevarra <ernestgmd@gmail.com>
Diff between ppitables versions 0.2.0 dated 2018-05-25 and 0.3.0 dated 2018-11-24
DESCRIPTION | 15 ++--- LICENSE |only MD5 | 17 ++++-- NEWS.md | 27 ++++++++-- R/data.R | 89 ++++++++++++++++++++++++--------- R/sysdata.rda |binary README.md | 134 +++++++++++++++++++++++++++----------------------- data/ppiKEN2018.rda |only data/ppiSEN2018.rda |only man/ppiKEN2018.Rd |only man/ppiSEN2018.Rd |only man/ppiZMB2013_cso.Rd | 7 -- 12 files changed, 180 insertions(+), 109 deletions(-)
Title: Plot a Model's Residuals, Response, and Partial Dependence Plots
Description: Plot model surfaces for a wide variety of models
using partial dependence plots and other techniques.
Also plot model residuals and other information on the model.
Author: Stephen Milborrow
Maintainer: Stephen Milborrow <milbo@sonic.net>
Diff between plotmo versions 3.5.0 dated 2018-08-20 and 3.5.1 dated 2018-11-24
DESCRIPTION | 7 MD5 | 66 +- NEWS | 12 R/grid.R | 15 R/plot_glmnet.R | 2 R/plotresids.R | 4 R/pre.R | 7 R/rpart.R | 6 R/xy.R | 9 inst/doc/modguide.pdf |binary inst/doc/plotmo-notes.pdf |binary inst/doc/plotres-notes.pdf |binary inst/slowtests/linmod.R | 44 - inst/slowtests/test.caret.Rout.save | 434 ++++++++-------- inst/slowtests/test.fac.R | 12 inst/slowtests/test.fac.Rout.save | 32 - inst/slowtests/test.gbm.Rout.save | 13 inst/slowtests/test.linmod.R | 129 +++- inst/slowtests/test.linmod.Rout.save | 862 +++++++++++++++++++++++++++----- inst/slowtests/test.mlr.Rout.save | 15 inst/slowtests/test.non.earth.Rout.save | 124 ++-- inst/slowtests/test.partdep.Rout.save | 6 inst/slowtests/test.partykit.Rout.save | 2 inst/slowtests/test.plotmo.R | 72 +- inst/slowtests/test.plotmo.Rout.save | 204 ++++--- inst/slowtests/test.plotmo.x.Rout.save | 10 inst/slowtests/test.plotmo3.Rout.save | 29 - inst/slowtests/test.plotres.Rout.save | 2 inst/slowtests/test.pre.R | 2 inst/slowtests/test.pre.Rout.save | 17 inst/slowtests/test.printcall.R | 1 inst/slowtests/test.printcall.Rout.save | 1 inst/slowtests/test.prolog.R | 6 man/plotmo.Rd | 2 34 files changed, 1419 insertions(+), 728 deletions(-)
Title: Manipulate MCMC Samples
Description: Functions and classes to store, manipulate and summarise
Monte Carlo Markov Chain (MCMC) samples.
Author: Joe Thorley [aut, cre] (<https://orcid.org/0000-0002-7683-4592>)
Maintainer: Joe Thorley <joe@poissonconsulting.ca>
Diff between mcmcr versions 0.0.2 dated 2018-10-30 and 0.0.3 dated 2018-11-24
DESCRIPTION | 17 ++++++++------- MD5 | 55 ++++++++++++++++++++++++------------------------- NAMESPACE | 6 ++++- NEWS.md | 5 ++++ R/as.R | 26 +++++++++++------------ R/bind-chains.R | 37 ++++++++++++++++---------------- R/bind-dimensions-n.R | 8 +++---- R/bind-dimensions.R | 14 ++++++------ R/bind-iterations.R | 37 ++++++++++++++++---------------- R/bind-parameters.R | 22 +++++++++---------- R/coef.R | 6 ++--- R/combine-dimensions.R | 2 - R/combine-samples.R | 10 ++++---- R/esr.R | 8 +++---- R/estimates.R | 6 ++--- R/internal.R | 10 ++++++-- R/mcmc-map.R | 2 - R/namespace.R | 3 +- R/rhat.R | 10 ++++---- R/split-chains.R | 2 - R/utils.R | 2 - R/zzz.R |only README.md | 26 ++--------------------- man/as.mcarray.Rd | 2 - man/coef.Rd | 2 - man/esr.Rd | 4 +-- man/ess.Rd | 2 - man/estimates.Rd | 4 +-- man/rhat.Rd | 2 - 29 files changed, 165 insertions(+), 165 deletions(-)
Title: Generalized Random Forests (Beta)
Description: A pluggable package for forest-based statistical estimation and inference.
GRF currently provides methods for non-parametric least-squares regression,
quantile regression, and treatment effect estimation (optionally using instrumental
variables). This package is currently in beta, and we expect to make continual
improvements to its performance and usability.
Author: Julie Tibshirani [aut, cre],
Susan Athey [aut],
Stefan Wager [aut],
Rina Friedberg [ctb],
Luke Miner [ctb],
Marvin Wright [ctb]
Maintainer: Julie Tibshirani <jtibs@cs.stanford.edu>
Diff between grf versions 0.10.1 dated 2018-09-24 and 0.10.2 dated 2018-11-24
DESCRIPTION | 8 MD5 | 96 +++---- NAMESPACE | 2 R/RcppExports.R | 8 R/average_partial_effect.R | 48 ++- R/average_treatment_effect.R | 52 ++-- R/causal_forest.R | 9 R/custom_forest.R | 13 - R/forest_summary.R | 70 +++-- R/input_utilities.R | 10 R/instrumental_forest.R | 9 R/local_linear_forest.R | 46 ++- R/local_linear_tuning.R | 11 R/quantile_forest.R | 9 R/regression_forest.R | 40 +-- man/average_partial_effect.Rd | 11 man/average_treatment_effect.Rd | 6 man/causal_forest.Rd | 22 + man/custom_forest.Rd | 18 - man/instrumental_forest.Rd | 23 + man/local_linear_forest.Rd | 20 + man/predict.causal_forest.Rd | 4 man/predict.custom_forest.Rd | 4 man/predict.local_linear_forest.Rd | 10 man/predict.quantile_forest.Rd | 4 man/predict.regression_forest.Rd | 14 - man/quantile_forest.Rd | 9 man/regression_forest.Rd | 17 - man/tune_causal_forest.Rd | 10 man/tune_local_linear_forest.Rd | 5 man/tune_regression_forest.Rd | 9 src/InstrumentalForestBindings.cpp | 2 src/RcppExports.cpp | 26 +- src/RegressionForestBindings.cpp | 35 ++ src/src/forest/ForestPredictor.cpp | 3 src/src/forest/ForestPredictor.h | 1 src/src/forest/ForestPredictors.cpp | 15 - src/src/forest/ForestPredictors.h | 7 src/src/prediction/CustomPredictionStrategy.cpp | 9 src/src/prediction/CustomPredictionStrategy.h | 10 src/src/prediction/DefaultPredictionStrategy.h | 58 +++- src/src/prediction/InstrumentalPredictionStrategy.cpp | 4 src/src/prediction/LocalLinearPredictionStrategy.cpp | 149 +++++++++++- src/src/prediction/LocalLinearPredictionStrategy.h | 16 + src/src/prediction/QuantilePredictionStrategy.cpp | 10 src/src/prediction/QuantilePredictionStrategy.h | 9 src/src/prediction/collector/DefaultPredictionCollector.cpp | 36 ++ src/src/prediction/collector/DefaultPredictionCollector.h | 6 src/src/sampling/RandomSampler.cpp | 12 49 files changed, 708 insertions(+), 317 deletions(-)