Title: R Interface to Geochemical Modeling Software
Description: A geochemical modeling program developed by the US Geological
Survey that is designed to perform a wide variety of aqueous geochemical
calculations, including speciation, batch-reaction, one-dimensional
reactive-transport, and inverse geochemical calculations.
Author: S.R. Charlton [aut, cre], D.L. Parkhurst [aut], and C.A.J. Appelo [aut], with contributions
from D. Gillespie [ctb] for Chipmunk BASIC and S.D. Cohen [ctb], A.C. Hindmarsh [ctb],
R. Serban [ctb], D. Shumaker [ctb], and A.G. Taylor [ctb] for CVODE/SUN [...truncated...]
Maintainer: S.R. Charlton <charlton@usgs.gov>
Diff between phreeqc versions 3.7.5 dated 2023-01-23 and 3.7.6 dated 2023-12-06
DESCRIPTION | 6 +- MD5 | 86 ++++++++++++++++++------------------ R/phreeqc.R | 70 ++++++++++++++--------------- build/partial.rdb |binary data/databases.rda |binary data/examples.rda |binary man/Amm.dat.Rd | 2 man/ex1.Rd | 2 man/ex10.Rd | 2 man/ex11.Rd | 2 man/ex12.Rd | 2 man/ex13.Rd | 2 man/ex14.Rd | 2 man/ex15.Rd | 2 man/ex15.dat.Rd | 2 man/ex16.Rd | 2 man/ex17.Rd | 2 man/ex18.Rd | 2 man/ex19.Rd | 2 man/ex2.Rd | 2 man/ex20.Rd | 2 man/ex21.Rd | 2 man/ex22.Rd | 2 man/ex3.Rd | 2 man/ex4.Rd | 2 man/ex5.Rd | 2 man/ex6.Rd | 2 man/ex7.Rd | 2 man/ex8.Rd | 2 man/ex9.Rd | 2 man/iso.dat.Rd | 2 man/llnl.dat.Rd | 2 man/minteq.dat.Rd | 2 man/minteq.v4.dat.Rd | 2 man/phrGetSelectedOutputFileName.Rd | 2 man/phrSetSelectedOutputFileName.Rd | 2 man/phreeqc-package.Rd | 2 man/phreeqc.dat.Rd | 2 man/pitzer.dat.Rd | 2 man/sit.dat.Rd | 2 man/wateq4f.dat.Rd | 2 src/IPhreeqc.h | 2 src/R.cpp | 18 +++---- src/Version.h | 8 +-- 44 files changed, 130 insertions(+), 130 deletions(-)
Title: 'RStudio' Addins and 'Shiny' Modules for Medical Research
Description: 'RStudio' addins and 'Shiny' modules for descriptive statistics, regression and survival analysis.
Author: Jinseob Kim [aut, cre] ,
Zarathu [cph, fnd],
Hyunki Lee [aut],
Changwoo Lim [aut],
Jinhwan Kim [aut]
Maintainer: Jinseob Kim <jinseob2kim@gmail.com>
Diff between jsmodule versions 1.4.3 dated 2023-10-18 and 1.4.4 dated 2023-12-06
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NAMESPACE | 1 + NEWS.md | 4 ++++ R/line.R | 12 ++++++++++-- R/roc.R | 24 ++++++++++++++++-------- inst/doc/jsmodule.html | 4 ++-- 7 files changed, 43 insertions(+), 22 deletions(-)
Title: Fractional Weighted Bootstrap
Description: An implementation of the fractional weighted bootstrap to be used as a drop-in for functions in
the 'boot' package. The fractional weighted bootstrap (also known as the Bayesian bootstrap) involves drawing
weights randomly that are applied to the data rather than resampling units from the data. See Xu et al. (2020)
<doi:10.1080/00031305.2020.1731599> for details.
Author: Noah Greifer [aut, cre]
Maintainer: Noah Greifer <noah.greifer@gmail.com>
Diff between fwb versions 0.1.2 dated 2023-10-02 and 0.2.0 dated 2023-12-06
DESCRIPTION | 6 +- MD5 | 30 ++++++------ NAMESPACE | 2 NEWS.md | 6 ++ R/fwb.R | 74 +++++++++++++++++++++++-------- R/fwb.ci.R | 35 ++++++++------ R/set_fwb_wtype.R |only R/summary.fwb.R | 6 +- R/utils.R | 34 +++++++++++++- R/vcovFWB.R | 32 ++++++++----- README.md | 18 ++++--- build/fwb.pdf |binary build/stage23.rdb |binary man/figures/README-unnamed-chunk-9-1.png |binary man/fwb.Rd | 43 +++++++++++++++++- man/set_fwb_wtype.Rd |only man/vcovFWB.Rd | 12 +++++ 17 files changed, 224 insertions(+), 74 deletions(-)
Title: Model Diagnostics for Accelerated Failure Time Models
Description: A collection of model checking methods for semiparametric accelerated
failure time (AFT) models under the rank-based approach. For the (computational)
efficiency, Gehan's weight is used. It provides functions to verify whether the
observed data fit the specific model assumptions such as a functional form of
each covariate, a link function, and an omnibus test. The p-value offered in this
package is based on the Kolmogorov-type supremum test and the variance of the
proposed test statistics is estimated through the re-sampling method. Furthermore,
a graphical technique to compare the shape of the observed residual to a number of
the approximated realizations is provided.
Author: WooJung Bae [aut, cre] ,
Dongrak Choi [aut] ,
Jun Yan [aut] ,
Sangwook Kang [aut]
Maintainer: WooJung Bae <matt.woojung@gmail.com>
Diff between afttest versions 4.3.1.1 dated 2023-07-09 and 4.3.2 dated 2023-12-06
afttest-4.3.1.1/afttest/R/export.R |only afttest-4.3.1.1/afttest/man/export_Surv.Rd |only afttest-4.3.1.1/afttest/man/export_aes.Rd |only afttest-4.3.1.1/afttest/man/export_aftsrr.Rd |only afttest-4.3.1.1/afttest/man/export_as.formula.Rd |only afttest-4.3.1.1/afttest/man/export_element_text.Rd |only afttest-4.3.1.1/afttest/man/export_geom_step.Rd |only afttest-4.3.1.1/afttest/man/export_get_all_vars.Rd |only afttest-4.3.1.1/afttest/man/export_ggplot.Rd |only afttest-4.3.1.1/afttest/man/export_ggtitle.Rd |only afttest-4.3.1.1/afttest/man/export_grid.arrange.Rd |only afttest-4.3.1.1/afttest/man/export_is.Surv.Rd |only afttest-4.3.1.1/afttest/man/export_labs.Rd |only afttest-4.3.1.1/afttest/man/export_optim.Rd |only afttest-4.3.1.1/afttest/man/export_quantile.Rd |only afttest-4.3.1.1/afttest/man/export_scale_y_continuous.Rd |only afttest-4.3.1.1/afttest/man/export_theme.Rd |only afttest-4.3.1.1/afttest/man/export_theme_minimal.Rd |only afttest-4.3.1.1/afttest/man/export_xlab.Rd |only afttest-4.3.1.1/afttest/man/export_ylab.Rd |only afttest-4.3.1.1/afttest/src/source_cpp.cpp |only afttest-4.3.2/afttest/DESCRIPTION | 50 +- afttest-4.3.2/afttest/MD5 | 50 -- afttest-4.3.2/afttest/NAMESPACE | 23 - afttest-4.3.2/afttest/R/afttest.R | 143 +++--- afttest-4.3.2/afttest/R/afttestplot.R | 322 +++++++-------- afttest-4.3.2/afttest/R/generic.R | 86 +--- afttest-4.3.2/afttest/README.md |only afttest-4.3.2/afttest/inst/CITATION |only afttest-4.3.2/afttest/inst/bib/afttest.bib | 4 afttest-4.3.2/afttest/inst/examples/ex_afttest.R | 13 afttest-4.3.2/afttest/inst/examples/ex_afttestplot.R | 14 afttest-4.3.2/afttest/man/afttest.Rd | 13 afttest-4.3.2/afttest/man/afttestplot.Rd | 35 - afttest-4.3.2/afttest/man/print.afttest.Rd |only afttest-4.3.2/afttest/man/summary.afttest.Rd | 13 afttest-4.3.2/afttest/src/afttest.cpp |only afttest-4.3.2/afttest/tests |only 38 files changed, 364 insertions(+), 402 deletions(-)
Title: Efficient Branch and Bound Variable Selection for GLMs using
'RcppArmadillo'
Description: Performs efficient and scalable glm best
subset selection using a novel implementation of a branch and bound algorithm.
To speed up the model fitting process, a range of optimization
methods are implemented in 'RcppArmadillo'. Parallel computation
is available using 'OpenMP'.
Author: Jacob Seedorff [aut, cre]
Maintainer: Jacob Seedorff <jwseedorff@uiowa.edu>
Diff between BranchGLM versions 2.1.2 dated 2023-08-31 and 2.1.3 dated 2023-12-06
DESCRIPTION | 8 MD5 | 66 ++--- NAMESPACE | 2 R/BranchGLM.R | 88 +++++-- R/BranchGLMCIs.R | 8 R/RcppExports.R | 4 R/VariableSelection.R | 220 ++++++++++++------- R/summaryBranchGLMVS.R | 97 +++++--- build/vignette.rds |binary inst/doc/BranchGLM-Vignette.Rmd | 12 - inst/doc/BranchGLM-Vignette.html | 14 - inst/doc/VariableSelection-Vignette.R | 24 +- inst/doc/VariableSelection-Vignette.Rmd | 24 +- inst/doc/VariableSelection-Vignette.html | 306 ++++++++++++++------------- man/BranchGLM.Rd | 19 - man/VariableSelection.Rd | 57 ++--- man/coef.BranchGLMVS.Rd | 25 +- man/fit.Rd | 27 -- man/plot.BranchGLMCIs.Rd | 2 man/plot.summary.BranchGLMVS.Rd | 26 ++ man/predict.BranchGLM.Rd | 16 + man/predict.BranchGLMVS.Rd | 35 ++- man/summary.BranchGLMVS.Rd | 6 src/BranchAndBound.cpp | 223 +++++++++---------- src/BranchGLMHelpers.cpp | 4 src/MetricRegion.cpp | 347 ++++++++++++++++++++++--------- src/ParBranchGLMHelpers.cpp | 35 +-- src/RcppExports.cpp | 10 src/StepwiseMethods.cpp | 67 ++--- src/VariableSelection.cpp | 52 +--- src/VariableSelection.h | 10 tests/testthat/test-BranchGLM.R | 69 ++---- vignettes/BranchGLM-Vignette.Rmd | 12 - vignettes/VariableSelection-Vignette.Rmd | 24 +- 34 files changed, 1123 insertions(+), 816 deletions(-)
Title: Random Forest with Canonical Correlation Analysis
Description: Random Forest with Canonical Correlation Analysis (RFCCA) is a
random forest method for estimating the canonical correlations between two
sets of variables depending on the subject-related covariates. The trees are
built with a splitting rule specifically designed to partition the data to
maximize the canonical correlation heterogeneity between child nodes. The
method is described in Alakus et al. (2021) <doi:10.1093/bioinformatics/btab158>.
RFCCA uses 'randomForestSRC' package (Ishwaran and Kogalur, 2020) by freezing
at the version 2.9.3. The custom splitting rule feature is utilised to apply
the proposed splitting rule. LAPACK and BLAS libraries are used for matrix
decompositions. The ‘RFCCA’ package includes the header files ‘lapacke.h’ and
‘cblas.h’ from the LAPACK and BLAS libraries. The LAPACK library is licensed
under modified BSD license.
Author: Cansu Alakus [aut, cre],
Denis Larocque [aut],
Aurelie Labbe [aut],
Hemant Ishwaran [ctb] ,
Udaya B. Kogalur [ctb] ,
Intel Corporation [cph] ,
Keita Teranishi [ctb]
Maintainer: Cansu Alakus <cansu.alakus@hec.ca>
Diff between RFCCA versions 1.0.11 dated 2023-09-19 and 1.0.12 dated 2023-12-06
DESCRIPTION | 14 +++++++------- MD5 | 10 +++++----- NEWS.md | 3 +++ configure | 18 +++++++++--------- configure.ac | 6 +++--- src/randomForestSRC.c | 2 +- 6 files changed, 28 insertions(+), 25 deletions(-)
Title: Covariance Regression with Random Forests
Description: Covariance Regression with Random Forests ('CovRegRF') is a
random forest method for estimating the covariance matrix of a
multivariate response given a set of covariates. Random forest trees
are built with a new splitting rule which is designed to maximize the
distance between the sample covariance matrix estimates of the child
nodes. The method is described in Alakus et al. (2023)
<doi:10.1186/s12859-023-05377-y>. 'CovRegRF' uses 'randomForestSRC' package
(Ishwaran and Kogalur, 2022)
<https://cran.r-project.org/package=randomForestSRC> by freezing at the
version 3.1.0. The custom splitting rule feature is utilised to apply the
proposed splitting rule. 'LAPACK' and 'BLAS' libraries are used for matrix
decompositions. The 'CovRegRF' package includes the header files 'lapacke.h'
and 'cblas.h' from the 'LAPACK' and 'BLAS' libraries. The 'LAPACK' library
is licensed under modified BSD license.
Author: Cansu Alakus [aut, cre],
Denis Larocque [aut],
Aurelie Labbe [aut],
Hemant Ishwaran [ctb] ,
Udaya B. Kogalur [ctb] ,
Intel Corporation [cph] ,
Keita Teranishi [ctb]
Maintainer: Cansu Alakus <cansu.alakus@hec.ca>
Diff between CovRegRF versions 1.0.4 dated 2023-09-22 and 1.0.5 dated 2023-12-06
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 3 +++ configure | 18 +++++++++--------- configure.ac | 6 +++--- src/randomForestSRC.c | 2 +- 6 files changed, 24 insertions(+), 21 deletions(-)
Title: Inference of Gene Regulatory Networks
Description: We present 'corto' (Correlation Tool), a simple package to infer
gene regulatory networks and visualize master regulators from gene expression
data using DPI (Data Processing Inequality) and bootstrapping to recover edges.
An initial step is performed to calculate all significant
edges between a list of source nodes (centroids) and target genes.
Then all triplets containing two centroids and one target are tested
in a DPI step which removes edges. A bootstrapping process then calculates
the robustness of the network, eventually re-adding edges previously removed by DPI.
The algorithm has been optimized to run outside a computing cluster, using a fast correlation
implementation. The package finally provides functions to calculate network enrichment
analysis from RNA-Seq and ATAC-Seq signatures as described in the article by
Giorgi lab (2020) <doi:10.1093/bioinformatics/btaa223>.
Author: Federico M. Giorgi [aut, cre],
Daniele Mercatelli [ctb],
Gonzalo Lopez-Garcia [ctb]
Maintainer: Federico M. Giorgi <federico.giorgi@gmail.com>
Diff between corto versions 1.2.2 dated 2023-03-28 and 1.2.4 dated 2023-12-06
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- R/functions.R | 25 ++++++++++++++++++++----- R/gsea.R | 23 ++++++++++++++++++----- build/vignette.rds |binary inst/doc/corto_vignette.R | 2 +- inst/doc/corto_vignette.html | 2 +- man/barplot2.Rd | 6 +++++- man/plot_gsea2.Rd | 12 +++++++++++- 9 files changed, 69 insertions(+), 27 deletions(-)
Title: Bayesian Fractional Polynomials
Description: Implements the Bayesian paradigm for fractional
polynomial models under the assumption of normally distributed error terms, see
Sabanes Bove, D. and Held, L. (2011) <doi:10.1007/s11222-010-9170-7>.
Author: Daniel Sabanes Bove [aut, cre],
Isaac Gravestock [aut],
Robert Davies [cph],
Stephen Moshier [cph],
Gareth Ambler [cph],
Axel Benner [cph]
Maintainer: Daniel Sabanes Bove <daniel.sabanesbove@gmx.net>
Diff between bfp versions 0.0-46 dated 2022-10-31 and 0.0-47 dated 2023-12-06
ChangeLog | 5 ++ DESCRIPTION | 12 +++--- MD5 | 14 +++---- inst/CITATION | 4 +- man/getFpTransforms.Rd | 70 ++++++++++++++++++------------------ man/posteriors.Rd | 94 +++++++++++++++++++++++-------------------------- src/Makevars | 1 src/bayesMfp.cpp | 10 ++--- 8 files changed, 106 insertions(+), 104 deletions(-)
Title: Standard Young Tableaux
Description: Deals with standard Young tableaux (field of combinatorics).
Performs enumeration, counting, random generation, the
Robinson-Schensted correspondence, and conversion to and from paths on
the Young lattice. Also performs enumeration and counting of
semistandard Young tableaux.
Author: Stephane Laurent
Maintainer: Stephane Laurent <laurent_step@outlook.fr>
Diff between syt versions 0.2.0 dated 2021-01-16 and 0.3.0 dated 2023-12-06
DESCRIPTION | 27 +- MD5 | 76 +++---- NAMESPACE | 44 ++-- NEWS.md | 28 +- R/RSK.R | 72 +++--- R/ballot.R | 150 +++++++------- R/dualsyt.R | 38 +-- R/enumeration.R | 400 +++++++++++++++++++------------------- R/hooks.R | 146 ++++++------- R/internal.R | 86 ++++---- R/plancherel.R | 78 +++---- R/randomsyt.R | 106 +++++----- R/ssyt.R |only R/syt2matrix.R | 100 ++++----- R/syt2path.R | 180 ++++++++--------- man/RS.Rd | 42 +-- man/all_ssytx.Rd |only man/all_sytx.Rd | 40 +-- man/ballot2syt.Rd | 50 ++-- man/count_ssytx.Rd |only man/count_sytx.Rd | 48 ++-- man/dualsyt.Rd | 42 +-- man/firstsyt.Rd | 40 +-- man/gprocess2syt.Rd | 52 ++-- man/hooklengths.Rd | 46 ++-- man/hooks.Rd | 46 ++-- man/matrix2syt.Rd | 48 ++-- man/nextsyt.Rd | 46 ++-- man/rgprocess.Rd | 50 ++-- man/rsyt.Rd | 40 +-- man/syt2ballot.Rd | 50 ++-- man/syt2gprocess.Rd | 52 ++-- man/syt2matrix.Rd | 48 ++-- tests/testthat.R | 8 tests/testthat/test-RS.R | 18 - tests/testthat/test-dual.R | 14 - tests/testthat/test-enumeration.R | 20 - tests/testthat/test-gprocess.R | 14 - tests/testthat/test-random.R | 12 - tests/testthat/test-ssyt.R |only tests/testthat/test-syt2ballot.R | 18 - 41 files changed, 1195 insertions(+), 1180 deletions(-)
Title: Owen's T Function and Bivariate Normal Integral
Description: Computes the Owen's T function or the bivariate
normal integral using one of the following:
modified Euler's arctangent series, tetrachoric
series, or Vasicek's series. For the methods,
see Komelj, J. (2023) <doi:10.4236/ajcm.2023.134026>
(or reprint <arXiv:2312.00011> with better typography)
and Vasicek, O. A. (1998) <doi:10.21314/JCF.1998.015>.
Author: Janez Komelj [aut, cre]
Maintainer: Janez Komelj <jkomelj@siol.net>
Diff between Phi2rho versions 1.0 dated 2023-07-20 and 1.0.1 dated 2023-12-06
CHANGES |only DESCRIPTION | 15 +++++++++------ MD5 | 25 +++++++++++++------------ R/OwenT.R | 19 +++++++++---------- R/Phi2xy.R | 6 +++--- R/chkArgs1.R | 3 +-- R/chkArgs2.R | 3 +-- R/mOwenT.R | 17 ++++++++--------- R/tOwenT.R | 31 +++++++++++++++++-------------- R/vOwenT.R | 16 +++++++--------- build/partial.rdb |binary man/OwenT.Rd | 4 ++-- man/Phi2rho-package.Rd | 13 ++++++++----- man/Phi2xy.Rd | 4 ++-- 14 files changed, 80 insertions(+), 76 deletions(-)
Title: Protein Quantification in Mass Spectrometry-Based Proteomics
Description: An implementation of the MaxLFQ algorithm by
Cox et al. (2014) <doi:10.1074/mcp.M113.031591> in a comprehensive
pipeline for processing proteomics data in data-independent acquisition mode
(Pham et al. 2020 <doi:10.1093/bioinformatics/btz961>).
It offers additional options for protein quantification using
the N most intense fragment ions, using all fragment ions, and
a wrapper for the median polish algorithm by Tukey (1977, ISBN:0201076160).
In general, the tool can be used to integrate multiple
proportional observations into a single quantitative value.
Author: Thang Pham [aut, cre, cph, ctb]
,
Alex Henneman [ctb]
Maintainer: Thang Pham <t.pham@amsterdamumc.nl>
Diff between iq versions 1.9.10 dated 2023-03-29 and 1.9.12 dated 2023-12-06
DESCRIPTION | 6 +- MD5 | 14 ++--- build/vignette.rds |binary inst/doc/iq-fast.R | 4 - inst/doc/iq-fast.html | 123 ++++++++++++++++++++++++-------------------------- inst/doc/iq.R | 46 +++++++++--------- inst/doc/iq.html | 18 +++---- src/iq.cpp | 16 +++--- 8 files changed, 113 insertions(+), 114 deletions(-)
Title: Interpretable Discovery and Inference of Heterogeneous Treatment
Effects
Description: Provides a new method for interpretable heterogeneous
treatment effects characterization in terms of decision rules
via an extensive exploration of heterogeneity patterns by an
ensemble-of-trees approach, enforcing high stability in the
discovery. It relies on a two-stage pseudo-outcome regression, and
it is supported by theoretical convergence guarantees. Bargagli-Stoffi,
F. J., Cadei, R., Lee, K., & Dominici, F. (2023) Causal rule ensemble:
Interpretable Discovery and Inference of Heterogeneous Treatment Effects.
arXiv preprint <arXiv:2009.09036>.
Author: Naeem Khoshnevis [aut, cre] ,
Daniela Maria Garcia [aut] ,
Riccardo Cadei [aut] ,
Kwonsang Lee [aut] ,
Falco Joannes Bargagli Stoffi [aut]
Maintainer: Naeem Khoshnevis <nkhoshnevis@g.harvard.edu>
Diff between CRE versions 0.2.4 dated 2023-06-14 and 0.2.5 dated 2023-12-06
CRE-0.2.4/CRE/tests/testthat/test-check_input_data.R |only CRE-0.2.4/CRE/tests/testthat/test-cre.R |only CRE-0.2.4/CRE/tests/testthat/test-discover_rules.R |only CRE-0.2.4/CRE/tests/testthat/test-estimate_cate.R |only CRE-0.2.4/CRE/tests/testthat/test-estimate_ite.R |only CRE-0.2.4/CRE/tests/testthat/test-estimate_ite_aipw.R |only CRE-0.2.4/CRE/tests/testthat/test-estimate_ite_bart.R |only CRE-0.2.4/CRE/tests/testthat/test-estimate_ite_cf.R |only CRE-0.2.4/CRE/tests/testthat/test-estimate_ite_poisson.R |only CRE-0.2.4/CRE/tests/testthat/test-estimate_ite_slearner.R |only CRE-0.2.4/CRE/tests/testthat/test-estimate_ite_tlearner.R |only CRE-0.2.4/CRE/tests/testthat/test-estimate_ite_xlearner.R |only CRE-0.2.4/CRE/tests/testthat/test-estimate_ps.R |only CRE-0.2.4/CRE/tests/testthat/test-evaluate.R |only CRE-0.2.4/CRE/tests/testthat/test-extract_effect_modifiers.R |only CRE-0.2.4/CRE/tests/testthat/test-extract_rules.R |only CRE-0.2.4/CRE/tests/testthat/test-filter_correlated_rules.R |only CRE-0.2.4/CRE/tests/testthat/test-filter_extreme_rules.R |only CRE-0.2.4/CRE/tests/testthat/test-filter_irrelevant_rules.R |only CRE-0.2.4/CRE/tests/testthat/test-generate_cre_dataset.R |only CRE-0.2.4/CRE/tests/testthat/test-generate_rules.R |only CRE-0.2.4/CRE/tests/testthat/test-generate_rules_matrix.R |only CRE-0.2.4/CRE/tests/testthat/test-honest_splitting.R |only CRE-0.2.4/CRE/tests/testthat/test-interpret_rules.R |only CRE-0.2.5/CRE/DESCRIPTION | 6 CRE-0.2.5/CRE/MD5 | 146 +++---- CRE-0.2.5/CRE/NAMESPACE | 1 CRE-0.2.5/CRE/NEWS.md | 35 + CRE-0.2.5/CRE/R/CRE_package.R | 40 +- CRE-0.2.5/CRE/R/check_hyper_params.R | 118 ++---- CRE-0.2.5/CRE/R/check_input_data.R | 2 CRE-0.2.5/CRE/R/check_method_params.R | 103 +---- CRE-0.2.5/CRE/R/cre.R | 211 +++++------ CRE-0.2.5/CRE/R/discover_rules.R | 46 +- CRE-0.2.5/CRE/R/estimate_cate.R | 141 ++++--- CRE-0.2.5/CRE/R/estimate_ite.R | 62 +-- CRE-0.2.5/CRE/R/estimate_ite_aipw.R | 16 CRE-0.2.5/CRE/R/estimate_ite_bart.R | 10 CRE-0.2.5/CRE/R/estimate_ite_cf.R | 10 CRE-0.2.5/CRE/R/estimate_ite_slearner.R | 12 CRE-0.2.5/CRE/R/estimate_ite_tlearner.R | 14 CRE-0.2.5/CRE/R/estimate_ite_tpoisson.R | 6 CRE-0.2.5/CRE/R/estimate_ite_xlearner.R | 14 CRE-0.2.5/CRE/R/extract_effect_modifiers.R | 2 CRE-0.2.5/CRE/R/extract_rules.R | 22 - CRE-0.2.5/CRE/R/filter_correlated_rules.R | 2 CRE-0.2.5/CRE/R/filter_irrelevant_rules.R | 12 CRE-0.2.5/CRE/R/generate_cre_dataset.R | 87 +++- CRE-0.2.5/CRE/R/generate_rules.R | 58 --- CRE-0.2.5/CRE/R/logger_utils.R | 37 + CRE-0.2.5/CRE/R/plot.R | 12 CRE-0.2.5/CRE/R/predict.R |only CRE-0.2.5/CRE/R/print.R | 81 +--- CRE-0.2.5/CRE/R/select_rules.R | 97 ++--- CRE-0.2.5/CRE/README.md | 115 ++--- CRE-0.2.5/CRE/inst/doc/CRE.Rmd | 92 ++-- CRE-0.2.5/CRE/inst/doc/CRE.html | 180 ++++----- CRE-0.2.5/CRE/inst/doc/Testing-the-Package.R | 30 - CRE-0.2.5/CRE/inst/doc/Testing-the-Package.Rmd | 30 - CRE-0.2.5/CRE/inst/doc/Testing-the-Package.html | 58 +-- CRE-0.2.5/CRE/man/CRE-package.Rd | 2 CRE-0.2.5/CRE/man/autoplot.cre.Rd | 6 CRE-0.2.5/CRE/man/check_hyper_params.Rd | 2 CRE-0.2.5/CRE/man/check_input_data.Rd | 2 CRE-0.2.5/CRE/man/cre.Rd | 137 +++---- CRE-0.2.5/CRE/man/estimate_cate.Rd | 21 - CRE-0.2.5/CRE/man/estimate_ite.Rd | 36 - CRE-0.2.5/CRE/man/estimate_ite_aipw.Rd | 14 CRE-0.2.5/CRE/man/estimate_ite_bart.Rd | 4 CRE-0.2.5/CRE/man/estimate_ite_cf.Rd | 4 CRE-0.2.5/CRE/man/estimate_ite_slearner.Rd | 8 CRE-0.2.5/CRE/man/estimate_ite_tlearner.Rd | 8 CRE-0.2.5/CRE/man/estimate_ite_tpoisson.Rd | 6 CRE-0.2.5/CRE/man/estimate_ite_xlearner.Rd | 8 CRE-0.2.5/CRE/man/extract_effect_modifiers.Rd | 2 CRE-0.2.5/CRE/man/filter_correlated_rules.Rd | 2 CRE-0.2.5/CRE/man/filter_irrelevant_rules.Rd | 7 CRE-0.2.5/CRE/man/generate_cre_dataset.Rd | 87 +++- CRE-0.2.5/CRE/man/generate_rules.Rd | 23 - CRE-0.2.5/CRE/man/get_logger.Rd | 3 CRE-0.2.5/CRE/man/plot.cre.Rd | 6 CRE-0.2.5/CRE/man/predict.cre.Rd |only CRE-0.2.5/CRE/man/print.cre.Rd | 6 CRE-0.2.5/CRE/man/select_rules.Rd | 17 CRE-0.2.5/CRE/man/set_logger.Rd | 35 + CRE-0.2.5/CRE/vignettes/CRE.Rmd | 92 ++-- CRE-0.2.5/CRE/vignettes/Testing-the-Package.Rmd | 30 - 87 files changed, 1253 insertions(+), 1223 deletions(-)
Title: Variable Selection under Ranked Sparsity Principles for
Interactions and Polynomials
Description: An implementation of ranked sparsity methods, including
penalized regression methods such as the sparsity-ranked lasso, its
non-convex alternatives, and elastic net, as well as the sparsity-ranked
Bayesian Information Criterion. As described in Peterson and
Cavanaugh (2022) <doi:10.1007/s10182-021-00431-7>, ranked
sparsity is a philosophy with methods primarily useful for
variable selection in the presence of prior informational
asymmetry, which occurs in the context of trying to perform variable
selection in the presence of interactions and/or polynomials. Ultimately,
this package attempts to facilitate dealing with cumbersome interactions
and polynomials while not avoiding them entirely. Typically, models
selected under ranked sparsity principles will also be more transparent,
having fewer falsely selected interactions and polynomials than other
methods.
Author: Ryan Andrew Peterson [aut, cre]
Maintainer: Ryan Andrew Peterson <ryan.a.peterson@cuanschutz.edu>
Diff between sparseR versions 0.2.2 dated 2023-03-28 and 0.2.3 dated 2023-12-06
DESCRIPTION | 8 +++--- MD5 | 18 ++++++------- NAMESPACE | 2 + NEWS.md | 7 +++++ R/custom_ICs.R | 4 +++ R/sparseR.R | 8 ++++++ R/sparseR_prep.R | 5 +-- inst/doc/sparseR.R | 54 ++++++++++++++++++++--------------------- inst/doc/sparseR.html | 65 ++++++++++++++++++++++++++------------------------ man/custom_ics.Rd | 6 ++++ 10 files changed, 103 insertions(+), 74 deletions(-)
Title: Data Exchange Between R and 'LabKey' Server
Description: The 'LabKey' client library for R makes it easy for R users to
load live data from a 'LabKey' Server, <https://www.labkey.com/>,
into the R environment for analysis, provided users have permissions
to read the data. It also enables R users to insert, update, and
delete records stored on a 'LabKey' Server, provided they have appropriate
permissions to do so.
Author: Peter Hussey
Maintainer: Cory Nathe <cnathe@labkey.com>
Diff between Rlabkey versions 3.0.0 dated 2023-11-07 and 3.1.0 dated 2023-12-06
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- NEWS | 4 ++++ R/labkey.deleteRows.R | 6 +++++- R/labkey.insertRows.R | 6 +++++- R/labkey.query.import.R | 2 +- R/labkey.updateRows.R | 6 +++++- man/Rlabkey-package.Rd | 4 ++-- man/labkey.deleteRows.Rd | 12 +++++++++++- man/labkey.insertRows.Rd | 20 ++++++++++++++++---- man/labkey.updateRows.Rd | 19 +++++++++++++++---- 11 files changed, 78 insertions(+), 29 deletions(-)
Title: Calculations and Visualisations Related to Geometric
Morphometrics
Description: A toolset for Geometric Morphometrics and mesh processing. This
includes (among other stuff) mesh deformations based on reference points,
permutation tests, detection of outliers, processing of sliding
semi-landmarks and semi-automated surface landmark placement.
Author: Stefan Schlager [aut, cre, cph],
Gregory Jefferis [ctb],
Dryden Ian [cph]
Maintainer: Stefan Schlager <zarquon42@gmail.com>
Diff between Morpho versions 2.11 dated 2023-01-27 and 2.12 dated 2023-12-06
DESCRIPTION | 10 +++--- MD5 | 70 +++++++++++++++++++++++----------------------- R/Morpho-package.R | 4 +- R/bindArr.r | 4 +- R/equidistantCurve.r | 3 + R/mergeMeshes.r | 4 +- R/meshDist.r | 2 - R/regdist.raw.r | 12 ++++--- R/restoreShapes.r | 2 + R/virtualMeshScan.r | 7 ++-- inst/NEWS.Rd | 9 +++++ man/Morpho-deprecated.Rd | 3 + man/Morpho-package.Rd | 4 +- man/equidistantCurve.Rd | 3 + man/getOuterViewpoints.Rd | 7 ++-- man/getPCscores.Rd | 2 + man/mergeMeshes.Rd | 2 - man/regdist.Rd | 12 +++++++ src/CVAdists.cpp | 4 +- src/CubeStuff.cpp | 12 +++---- src/ang_calc.cpp | 8 ++--- src/armaGinvCpp.cpp | 4 +- src/asymPerm.cpp | 8 ++--- src/barycenter.cpp | 4 +- src/covPCA.cpp | 4 +- src/createL.cpp | 4 +- src/doozers.cpp | 8 ++--- src/edgePlane.cpp | 4 +- src/face_zero.cpp | 4 +- src/fastSubsetMeans.cpp | 4 +- src/meshres.cpp | 4 +- src/permudistArma.cpp | 4 +- src/points2mesh.cpp | 4 +- src/tpsfx.cpp | 4 +- src/tweakU.cpp | 4 +- src/updateNormals.cpp | 8 ++--- 36 files changed, 144 insertions(+), 112 deletions(-)
Title: A Functionally Oriented Interface for Integrating 'Julia' with R
Description: Allows to import functions and whole packages from 'Julia' in R.
Imported 'Julia' functions can directly be called as R functions.
Data structures can be translated between 'Julia' and R.
More details can also be found in the corresponding article
<doi:10.18637/jss.v101.i06>.
Author: Stefan Lenz [aut, cre] ,
Harald Binder [aut, ths] ,
Angelo D'Ambrosio [ctb]
Maintainer: Stefan Lenz <stefan-m-lenz@web.de>
Diff between JuliaConnectoR versions 1.1.2 dated 2023-11-28 and 1.1.3 dated 2023-12-06
DESCRIPTION | 8 +-- MD5 | 25 +++++---- R/accessing_mutating.R | 88 +++++++++++++++------------------- R/connecting.R | 11 ++-- R/handling_dataframes.R | 2 R/importing.R | 4 - R/main.R | 8 +-- inst/Julia/reading.jl | 4 - man/AccessMutate.JuliaProxy.Rd | 88 +++++++++++++++------------------- man/as.data.frame.JuliaProxy.Rd | 2 man/juliaEval.Rd | 8 +-- man/juliaImport.Rd | 4 - tests/testthat/test.R | 15 +++++ tests/testthat/test_examples_notrun.R |only 14 files changed, 132 insertions(+), 135 deletions(-)
More information about JuliaConnectoR at CRAN
Permanent link
Title: Generation of Different Animated Christmas Cards
Description: Generation of different Christmas cards, most of them being
animated. Most of the cards can be generated in three languages (English,
Catalan and Spanish). The collection started in 2009.
Author: Jose Barrera-Gomez [aut, cre]
Maintainer: Jose Barrera-Gomez <jose.barrera@isglobal.org>
Diff between christmas versions 1.2.0 dated 2022-12-18 and 1.3.0 dated 2023-12-06
christmas-1.2.0/christmas/R/christmas.R |only christmas-1.2.0/christmas/man/christmas.Rd |only christmas-1.3.0/christmas/DESCRIPTION | 6 +++--- christmas-1.3.0/christmas/MD5 | 14 ++++++++------ christmas-1.3.0/christmas/NAMESPACE | 1 + christmas-1.3.0/christmas/NEWS | 5 +++++ christmas-1.3.0/christmas/R/christmas-package.R |only christmas-1.3.0/christmas/R/xmasflag.R | 1 - christmas-1.3.0/christmas/R/xmashelix.R |only christmas-1.3.0/christmas/man/christmas-package.Rd |only christmas-1.3.0/christmas/man/xmashelix.Rd |only 11 files changed, 17 insertions(+), 10 deletions(-)
Title: Simulation and Estimation for Branching Processes
Description: Simulation and parameter estimation of multitype Bienayme - Galton - Watson processes.
Author: Camilo Jose Torres-Jimenez <cjtorresj@unal.edu.co>
Maintainer: Camilo Jose Torres-Jimenez <cjtorresj@unal.edu.co>
Diff between Branching versions 0.9.4 dated 2016-12-06 and 0.9.6 dated 2023-12-06
DESCRIPTION | 10 +++++----- MD5 | 28 ++++++++++++++-------------- R/BGWM.covar.R | 4 ++-- R/BGWM.covar.estim.R | 4 ++-- R/BGWM.mean.R | 4 ++-- R/BGWM.mean.estim.R | 4 ++-- R/rBGWM.R | 4 ++-- inst/CITATION | 15 +++++++++------ man/BGWM.covar.Rd | 4 ++-- man/BGWM.covar.estim.Rd | 4 ++-- man/BGWM.mean.Rd | 4 ++-- man/BGWM.mean.estim.Rd | 4 ++-- man/rBGWM.Rd | 4 ++-- src/rBGWM.cc | 2 +- src/util.cc | 18 +++++++++--------- 15 files changed, 58 insertions(+), 55 deletions(-)
Title: Clustering Method Based on Boxplot Statistics
Description: Following Arroyo-Maté-Roque (2006), the function calculates the distance between rows or columns of the dataset using the generalized Minkowski metric as described by Ichino-Yaguchi (1994). The distance measure gives more weight to differences between quartiles than to differences between extremes, making it less sensitive to outliers. Further,the function calculates the silhouette width (Rousseeuw 1987) for different numbers of clusters and selects the number of clusters that maximizes the average silhouette width, unless a specific number of clusters is provided by the user. The approach implemented in this package is based on the following publications: Rousseeuw (1987) <doi:10.1016/0377-0427(87)90125-7>; Ichino-Yaguchi (1994) <doi:10.1109/21.286391>; Arroyo-Maté-Roque (2006) <doi:10.1007/3-540-34416-0_7>.
Author: Gianmarco Alberti [aut, cre]
Maintainer: Gianmarco Alberti <gianmarcoalberti@gmail.com>
Diff between boxplotcluster versions 0.2 dated 2023-06-06 and 0.3 dated 2023-12-06
DESCRIPTION | 6 - MD5 | 10 +- NEWS.md | 16 +-- R/boxplotcluster.R | 215 +++++++++++++++++++++++++++++++------------------- README.md | 13 ++- man/boxplotcluster.Rd | 107 +++++++++++++++++------- 6 files changed, 241 insertions(+), 126 deletions(-)
More information about boxplotcluster at CRAN
Permanent link
Title: Manipulations of Triangular Meshes Based on the 'VCGLIB' API
Description: Operations on triangular meshes based on 'VCGLIB'. This package
integrates nicely with the R-package 'rgl' to render the meshes processed by
'Rvcg'. The Visualization and Computer Graphics Library (VCG for short) is
an open source portable C++ templated library for manipulation, processing
and displaying with OpenGL of triangle and tetrahedral meshes. The library,
composed by more than 100k lines of code, is released under the GPL license,
and it is the base of most of the software tools of the Visual Computing Lab of
the Italian National Research Council Institute ISTI <https://vcg.isti.cnr.it/>,
like 'metro' and 'MeshLab'. The 'VCGLIB' source is pulled from trunk
<https://github.com/cnr-isti-vclab/vcglib> and patched to work with options
determined by the configure script as well as to work with the header files
included by 'RcppEigen'.
Author: Stefan Schlager [aut, cre, cph],
Girinon Francois [ctb],
Tim Schaefer [ctb]
Maintainer: Stefan Schlager <zarquon42@gmail.com>
Diff between Rvcg versions 0.22.1 dated 2023-01-26 and 0.22.2 dated 2023-12-06
DESCRIPTION | 12 +++---- MD5 | 76 +++++++++++++++++++++++----------------------- R/Rvcg-package.R | 4 +- R/vcgMetro.r | 2 - inst/NEWS.Rd | 8 ++++ man/Rvcg-package.Rd | 4 +- man/vcgMetro.Rd | 2 - src/Makevars | 1 src/ROneRing.cpp | 2 - src/RQEdecim.cpp | 4 +- src/RallRead.cpp | 2 - src/Rarea.cpp | 4 +- src/Rballpivot.cpp | 4 +- src/Rclean.cpp | 4 +- src/Rclost.cpp | 4 +- src/Rcurvature.cpp | 4 +- src/Rdijkstra.cpp | 8 ++-- src/Rexport.cpp | 6 +-- src/RgetEdge.cpp | 2 - src/Rintersect.cpp | 4 +- src/Risolated.cpp | 4 +- src/Risoremesh.cpp | 2 - src/Rkdtree.cpp | 12 +++---- src/RkdtreeXptr.cpp | 12 +++---- src/Rkmeans.cpp | 8 ++-- src/Rmarch.cpp | 4 +- src/Rmeshres.cpp | 2 - src/Rmeshvol.cpp | 13 +------ src/Rmetro.cpp | 7 ++-- src/Rplatonic.cpp | 36 ++++++++++----------- src/Rsample.cpp | 2 - src/Rsmooth.cpp | 2 - src/Rsubdivision.cpp | 4 +- src/Runiform_resample.cpp | 2 - src/RupdateNormals.cpp | 4 +- src/RvcgIO.h | 8 ++-- src/RvcgKD.h | 21 ++++-------- src/checkListNames.cpp | 5 +-- src/metroSampling.h | 6 +-- 39 files changed, 153 insertions(+), 158 deletions(-)
Title: Fast Unified Random Forests for Survival, Regression, and
Classification (RF-SRC)
Description: Fast OpenMP parallel computing of Breiman's random forests for univariate, multivariate, unsupervised, survival, competing risks, class imbalanced classification and quantile regression. New Mahalanobis splitting for correlated outcomes. Extreme random forests and randomized splitting. Suite of imputation methods for missing data. Fast random forests using subsampling. Confidence regions and standard errors for variable importance. New improved holdout importance. Case-specific importance. Minimal depth variable importance. Visualize trees on your Safari or Google Chrome browser. Anonymous random forests for data privacy.
Author: Hemant Ishwaran <hemant.ishwaran@gmail.com>, Udaya B. Kogalur <ubk@kogalur.com>
Maintainer: Udaya B. Kogalur <ubk@kogalur.com>
Diff between randomForestSRC versions 3.2.2 dated 2023-05-23 and 3.2.3 dated 2023-12-06
DESCRIPTION | 8 ++++---- MD5 | 42 +++++++++++++++++++++--------------------- R/generic.predict.rfsrc.R | 2 +- R/rfsrc.R | 4 ++-- configure | 18 +++++++++--------- configure.ac | 2 +- data/breast.rda |binary data/follic.rda |binary data/hd.rda |binary data/housing.rda |binary data/nutrigenomic.rda |binary data/pbc.rda |binary data/peakVO2.rda |binary data/vdv.rda |binary data/veteran.rda |binary data/wihs.rda |binary data/wine.rda |binary inst/NEWS | 11 ++++++++--- man/predict.rfsrc.Rd | 3 ++- man/print.rfsrc.Rd | 3 ++- man/rfsrc.Rd | 13 +++++++------ src/randomForestSRC.c | 19 +++++++++++++++---- 22 files changed, 72 insertions(+), 53 deletions(-)
More information about randomForestSRC at CRAN
Permanent link
Title: Uncertainty Propagation for R Vectors
Description: Support for measurement errors in R vectors, matrices and arrays:
automatic uncertainty propagation and reporting.
Documentation about 'errors' is provided in the paper by Ucar, Pebesma &
Azcorra (2018, <doi:10.32614/RJ-2018-075>), included in this package as a
vignette; see 'citation("errors")' for details.
Author: Inaki Ucar [aut, cph, cre] ,
Lionel Henry [ctb],
RStudio [cph]
Maintainer: Inaki Ucar <iucar@fedoraproject.org>
Diff between errors versions 0.4.0 dated 2022-12-04 and 0.4.1 dated 2023-12-06
errors-0.4.0/errors/vignettes/includes |only errors-0.4.1/errors/DESCRIPTION | 15 - errors-0.4.1/errors/MD5 | 48 ++-- errors-0.4.1/errors/NAMESPACE | 3 errors-0.4.1/errors/NEWS.md | 50 ++-- errors-0.4.1/errors/R/errors.R | 6 errors-0.4.1/errors/R/geom_errors.R | 16 + errors-0.4.1/errors/R/misc.R | 17 + errors-0.4.1/errors/R/summary.R | 17 + errors-0.4.1/errors/R/utils.R | 14 + errors-0.4.1/errors/README.md | 6 errors-0.4.1/errors/build/partial.rdb |binary errors-0.4.1/errors/build/vignette.rds |binary errors-0.4.1/errors/inst/doc/rjournal.R | 99 +++++++-- errors-0.4.1/errors/inst/doc/rjournal.Rmd | 219 +++++++++++++------- errors-0.4.1/errors/inst/doc/rjournal.pdf |binary errors-0.4.1/errors/man/cbind.errors.Rd | 5 errors-0.4.1/errors/man/geom_errors.Rd | 16 + errors-0.4.1/errors/man/mean.errors.Rd | 15 + errors-0.4.1/errors/tests/testthat/test-misc.R | 25 ++ errors-0.4.1/errors/tests/testthat/test-summary.R | 11 - errors-0.4.1/errors/tests/testthat/test-tidyverse.R | 4 errors-0.4.1/errors/vignettes/rjournal-preamble.tex |only errors-0.4.1/errors/vignettes/rjournal.Rmd | 219 +++++++++++++------- errors-0.4.1/errors/vignettes/rjournal.bib | 12 - 25 files changed, 574 insertions(+), 243 deletions(-)
Title: Operationalizing Social Determinants of Health Data for
Researchers
Description: Accesses raw data via API and calculates social
determinants of health measures for user-specified locations in the
US, returning them in tidyverse- and sf-compatible data frames.
Author: Nik Krieger [aut, cre],
Jarrod Dalton [aut],
Cindy Wang [aut],
Adam Perzynski [aut],
National Institutes of Health/National Institute on Aging [fnd] . All of its contents
are solely the responsibility of the authors and do not necessarily
represent t [...truncated...]
Maintainer: Nik Krieger <nikkrieger@gmail.com>
Diff between sociome versions 2.2.1 dated 2023-04-25 and 2.2.5 dated 2023-12-06
DESCRIPTION | 12 LICENSE | 2 MD5 | 52 - NEWS.md | 331 ++++----- R/census_api_key.R | 14 R/centers.R | 955 +++++++++++++-------------- R/data_documentation.R | 184 ++--- R/dissimilarity.R | 284 ++++---- R/get_adi.R | 812 +++++++++++----------- R/get_tidycensus.R | 534 +++++++-------- R/setup.R | 2 R/synthetic_population.R | 670 +++++++++--------- R/utils-pipe.R | 24 man/acs_age_sex_race_ethnicity_vars.Rd | 58 - man/acs_vars.Rd | 82 +- man/append_dissimilarities.Rd | 170 ++-- man/calculate_adi.Rd | 150 ++-- man/census_api_key.Rd | 16 man/decennial_age_sex_race_ethnicity_vars.Rd | 58 - man/decennial_vars.Rd | 48 - man/get_areas_near_coordinates.Rd | 317 ++++---- man/get_geoids.Rd | 124 +-- man/lon_lat_from_area.Rd | 120 +-- man/pipe.Rd | 24 man/synthetic_population.Rd | 348 ++++----- tests/testthat.R | 8 tests/testthat/test_tidycensus_related.R | 286 ++++---- 27 files changed, 2854 insertions(+), 2831 deletions(-)
Title: Clinical Trial Style Data Readout Listings
Description: Listings are often part of the submission of clinical trial
data in regulatory settings. We provide a framework for the specific
formatting features often used when displaying large datasets in that
context.
Author: Gabriel Becker [aut] ,
Adrian Waddell [aut],
Joe Zhu [aut, cre],
Davide Garolini [ctb],
Emily de la Rua [ctb],
Abinaya Yogasekaram [ctb],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Joe Zhu <joe.zhu@roche.com>
Diff between rlistings versions 0.2.4 dated 2023-08-26 and 0.2.7 dated 2023-12-06
rlistings-0.2.4/rlistings/man/figures/rlistings.png |only rlistings-0.2.7/rlistings/DESCRIPTION | 18 rlistings-0.2.7/rlistings/MD5 | 58 rlistings-0.2.7/rlistings/NEWS.md | 20 rlistings-0.2.7/rlistings/R/paginate_listing.R | 69 rlistings-0.2.7/rlistings/R/rlistings.R | 44 rlistings-0.2.7/rlistings/R/rlistings_methods.R | 11 rlistings-0.2.7/rlistings/build/vignette.rds |binary rlistings-0.2.7/rlistings/inst/WORDLIST | 1 rlistings-0.2.7/rlistings/inst/doc/col_formatting.R |only rlistings-0.2.7/rlistings/inst/doc/col_formatting.Rmd |only rlistings-0.2.7/rlistings/inst/doc/col_formatting.html |only rlistings-0.2.7/rlistings/inst/doc/pagination.R |only rlistings-0.2.7/rlistings/inst/doc/pagination.Rmd |only rlistings-0.2.7/rlistings/inst/doc/pagination.html |only rlistings-0.2.7/rlistings/inst/doc/ref_footnotes.R |only rlistings-0.2.7/rlistings/inst/doc/ref_footnotes.Rmd |only rlistings-0.2.7/rlistings/inst/doc/ref_footnotes.html |only rlistings-0.2.7/rlistings/inst/doc/rlistings.R | 5 rlistings-0.2.7/rlistings/inst/doc/rlistings.Rmd | 17 rlistings-0.2.7/rlistings/inst/doc/rlistings.html | 1749 +--------- rlistings-0.2.7/rlistings/man/defunct.Rd | 4 rlistings-0.2.7/rlistings/man/figures/logo.png |only rlistings-0.2.7/rlistings/man/listing_methods.Rd | 6 rlistings-0.2.7/rlistings/man/matrix_form-listing_df-method.Rd | 4 rlistings-0.2.7/rlistings/man/paginate.Rd | 4 rlistings-0.2.7/rlistings/man/rlistings-package.Rd | 2 rlistings-0.2.7/rlistings/tests/testthat/_snaps/export.md | 57 rlistings-0.2.7/rlistings/tests/testthat/_snaps/print.md | 117 rlistings-0.2.7/rlistings/tests/testthat/test-export.R | 40 rlistings-0.2.7/rlistings/tests/testthat/test-listings.R | 75 rlistings-0.2.7/rlistings/tests/testthat/test-paginate_listing.R | 17 rlistings-0.2.7/rlistings/tests/testthat/test-print.R | 57 rlistings-0.2.7/rlistings/vignettes/col_formatting.Rmd |only rlistings-0.2.7/rlistings/vignettes/pagination.Rmd |only rlistings-0.2.7/rlistings/vignettes/ref_footnotes.Rmd |only rlistings-0.2.7/rlistings/vignettes/rlistings.Rmd | 17 37 files changed, 699 insertions(+), 1693 deletions(-)
Title: Numeric Routines for Optically Stimulated Luminescence Dating
Description: Optimizing regular numeric problems in optically stimulated luminescence dating,
such as: equivalent dose calculation, dose rate determination, growth curve fitting, decay
curve decomposition, statistical age model optimization, and statistical plot visualization.
Author: Jun Peng [aut, cre],
Bo Li [aut],
Chunxin Wang [aut],
Jorge More [ctb],
Burton Garbow [ctb],
Kenneth Hillstrom [ctb],
John Burkardt [ctb],
Paul Gilbert [ctb],
Ravi Varadhan [ctb]
Maintainer: Jun Peng <pengjun10@mails.ucas.ac.cn>
Diff between numOSL versions 2.7 dated 2023-09-18 and 2.8 dated 2023-12-06
DESCRIPTION | 8 MD5 | 17 - NAMESPACE | 5 R/analyseBINdata0.R |only R/calDA.R | 525 ++++++++++++++++++++++++-------------------------- R/calDAbatch.R | 213 +++++++++++++------- R/dbED.R | 4 man/analyseBINdata.Rd | 14 + man/calDA.Rd | 84 +++++--- man/numOSL-package.Rd | 4 10 files changed, 494 insertions(+), 380 deletions(-)
Title: Bayesian Exponential Random Graph Models
Description: Bayesian analysis for exponential random graph models using
advanced computational algorithms. More information can be found at:
<https://acaimo.github.io/Bergm/>.
Author: Alberto Caimo [aut, cre], Lampros Bouranis [aut], Robert Krause
[aut] Nial Friel [ctb]
Maintainer: Alberto Caimo <alberto.caimo1@ucd.ie>
Diff between Bergm versions 5.0.6 dated 2023-09-13 and 5.0.7 dated 2023-12-06
DESCRIPTION | 8 MD5 | 20 - R/bergm.R | 15 - R/bergmC.R | 5 R/bergmM.R | 10 R/evidence.R | 19 - R/evidenceCJ.R | 9 R/evidencePP.R | 646 +++++++++++++++++++++++++++--------------------------- README.md | 13 - man/bergm.Rd | 2 man/evidencePP.Rd | 1 11 files changed, 372 insertions(+), 376 deletions(-)
Title: Bayesian Vector Heterogeneous Autoregressive Modeling
Description: Tools to research Bayesian Vector heterogeneous autoregressive (VHAR) model,
referring to Kim & Baek (2023+) (<doi:10.1080/00949655.2023.2281644>).
'bvhar' can model Vector Autoregressive (VAR), VHAR, Bayesian VAR (BVAR), and Bayesian VHAR (BVHAR) models.
Author: Young Geun Kim [aut, cre, cph]
,
Changryong Baek [ctb]
Maintainer: Young Geun Kim <dudrms33@g.skku.edu>
Diff between bvhar versions 1.0.1 dated 2023-11-10 and 1.0.2 dated 2023-12-06
bvhar-1.0.1/bvhar/LICENSE |only bvhar-1.0.2/bvhar/DESCRIPTION | 8 +-- bvhar-1.0.2/bvhar/MD5 | 53 +++++++++++------------- bvhar-1.0.2/bvhar/NEWS.md | 6 ++ bvhar-1.0.2/bvhar/build/partial.rdb |binary bvhar-1.0.2/bvhar/build/vignette.rds |binary bvhar-1.0.2/bvhar/inst/doc/bvhar.html | 42 +++++++++---------- bvhar-1.0.2/bvhar/inst/doc/empirical-bayes.html | 12 ++--- bvhar-1.0.2/bvhar/inst/doc/forecasting.html | 2 bvhar-1.0.2/bvhar/src/design.cpp | 2 bvhar-1.0.2/bvhar/src/estimate-bvar.cpp | 2 bvhar-1.0.2/bvhar/src/estimate-hierarchical.cpp | 3 - bvhar-1.0.2/bvhar/src/estimate-ssvs.cpp | 3 - bvhar-1.0.2/bvhar/src/estimate-sv.cpp | 3 - bvhar-1.0.2/bvhar/src/estimate-var.cpp | 2 bvhar-1.0.2/bvhar/src/estimate-vhar.cpp | 2 bvhar-1.0.2/bvhar/src/forecast-bvar.cpp | 2 bvhar-1.0.2/bvhar/src/forecast-bvhar.cpp | 2 bvhar-1.0.2/bvhar/src/forecast-expand.cpp | 6 -- bvhar-1.0.2/bvhar/src/forecast-roll.cpp | 2 bvhar-1.0.2/bvhar/src/forecast-var.cpp | 2 bvhar-1.0.2/bvhar/src/forecast-vhar.cpp | 2 bvhar-1.0.2/bvhar/src/generate-distn.cpp | 2 bvhar-1.0.2/bvhar/src/is-stable.cpp | 2 bvhar-1.0.2/bvhar/src/mcmc-draw.cpp | 2 bvhar-1.0.2/bvhar/src/misc-eigen.cpp | 2 bvhar-1.0.2/bvhar/src/simulate-data.cpp | 2 bvhar-1.0.2/bvhar/src/tuning-models.cpp | 2 28 files changed, 64 insertions(+), 104 deletions(-)
Title: Terminal Progress Bars
Description: Configurable Progress bars, they may include percentage,
elapsed time, and/or the estimated completion time. They work in
terminals, in 'Emacs' 'ESS', 'RStudio', 'Windows' 'Rgui' and the
'macOS' 'R.app'. The package also provides a 'C++' 'API', that works
with or without 'Rcpp'.
Author: Gabor Csardi [aut, cre],
Rich FitzJohn [aut],
Posit Software, PBC [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between progress versions 1.2.2 dated 2019-05-16 and 1.2.3 dated 2023-12-06
DESCRIPTION | 30 +++++++++---- LICENSE | 4 - MD5 | 22 +++++----- NEWS.md | 4 + R/progress-package.R |only R/progress.R | 36 ++++++++-------- README.md | 50 ++++++++++++++++++++-- inst/include/RProgress.h | 8 +-- man/progress-package.Rd |only man/progress_bar.Rd | 90 ++++++++++++++++++++--------------------- tests/testthat.R | 16 +++++-- tests/testthat/test-cpp.R | 6 +- tests/testthat/test-progress.R | 3 - 13 files changed, 165 insertions(+), 104 deletions(-)
Title: Bayesian Variable Selection and Model Averaging using Bayesian
Adaptive Sampling
Description: Package for Bayesian Variable Selection and Model Averaging
in linear models and generalized linear models using stochastic or
deterministic sampling without replacement from posterior
distributions. Prior distributions on coefficients are
from Zellner's g-prior or mixtures of g-priors
corresponding to the Zellner-Siow Cauchy Priors or the
mixture of g-priors from Liang et al (2008)
<DOI:10.1198/016214507000001337>
for linear models or mixtures of g-priors from Li and Clyde
(2019) <DOI:10.1080/01621459.2018.1469992> in generalized linear models.
Other model selection criteria include AIC, BIC and Empirical Bayes
estimates of g. Sampling probabilities may be updated based on the sampled
models using sampling w/out replacement or an efficient MCMC algorithm which
samples models using a tree structure of the model space
as an efficient hash table. See Clyde, Ghosh and Littman (2010)
<DOI:10.1198/jcgs.2010.09049> for details on the sampling algorithms.
Uniform prior [...truncated...]
Author: Merlise Clyde [aut, cre, cph] ,
Michael Littman [ctb],
Joyee Ghosh [ctb],
Yingbo Li [ctb],
Betsy Bersson [ctb],
Don van de Bergh [ctb],
Quanli Wang [ctb]
Maintainer: Merlise Clyde <clyde@duke.edu>
Diff between BAS versions 1.6.6 dated 2023-11-28 and 1.7.1 dated 2023-12-06
DESCRIPTION | 8 +- MD5 | 28 ++++---- NEWS.md | 36 +++++++---- R/bas_glm.R | 23 +++++++ R/bas_lm.R | 21 ++++++ R/glm_fit.R | 7 +- inst/doc/BAS-vignette.html | 118 ++++++++++++++++++------------------- src/family.c | 12 +-- src/glm_fit.c | 9 +- src/hyp1F1.c | 3 src/hypergeometric1F1.c | 2 tests/testthat/Rplots.pdf |binary tests/testthat/test-glm-fit.R | 76 ++++++++++++++++++++--- tests/testthat/test-model-priors.R | 2 tests/testthat/test-predict.R | 55 +++++++++++++++++ 15 files changed, 288 insertions(+), 112 deletions(-)
Title: Time Series Analysis and Computational Finance
Description: Time series analysis and computational finance.
Author: Adrian Trapletti [aut],
Kurt Hornik [aut, cre] ,
Blake LeBaron [ctb]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between tseries versions 0.10-54 dated 2023-05-02 and 0.10-55 dated 2023-12-06
ChangeLog | 6 ++++++ DESCRIPTION | 6 +++--- MD5 | 24 ++++++++++++------------ R/test.R | 14 ++++++++++++-- build/partial.rdb |binary data/NelPlo.rda |binary data/USeconomic.rda |binary data/bev.rda |binary data/camp.rda |binary data/ice.river.rda |binary data/nino.rda |binary data/tcm.rda |binary data/tcmd.rda |binary 13 files changed, 33 insertions(+), 17 deletions(-)
Title: Deconvolution of Spatial Transcriptomics Data Based on Neural
Networks
Description: Deconvolution of spatial transcriptomics data using deconvolution models based on deep neural networks and single-cell RNA-seq data. These models are able to make accurate estimates of the cell composition of spots in spatial transcriptomics datasets from the same context using the advances provided by deep learning and the meaningful information provided by single-cell RNA-Seq data. See Torroja and Sanchez-Cabo (2019) <doi:10.3389/fgene.2019.00978> and Mañanes et al. (2023) <doi:10.1101/2023.08.31.555677> to get an overview of the method and see some examples of its performance.
Author: Diego Mananes [aut, cre] ,
Carlos Torroja [aut] ,
Fatima Sanchez-Cabo [aut]
Maintainer: Diego Mananes <dmananesc@cnic.es>
Diff between SpatialDDLS versions 0.1.0 dated 2023-05-07 and 1.0.0 dated 2023-12-06
SpatialDDLS-0.1.0/SpatialDDLS/vignettes/abserr-celltype-2-1.png |only SpatialDDLS-0.1.0/SpatialDDLS/vignettes/pred-spatial-sep-10.png |only SpatialDDLS-0.1.0/SpatialDDLS/vignettes/pred-spatial-sep-11.png |only SpatialDDLS-0.1.0/SpatialDDLS/vignettes/pred-spatial-sep-12.png |only SpatialDDLS-0.1.0/SpatialDDLS/vignettes/pred-spatial-sep-4.png |only SpatialDDLS-0.1.0/SpatialDDLS/vignettes/pred-spatial-sep-5.png |only SpatialDDLS-0.1.0/SpatialDDLS/vignettes/pred-spatial-sep-6.png |only SpatialDDLS-0.1.0/SpatialDDLS/vignettes/pred-spatial-sep-7.png |only SpatialDDLS-0.1.0/SpatialDDLS/vignettes/pred-spatial-sep-8.png |only SpatialDDLS-0.1.0/SpatialDDLS/vignettes/pred-spatial-sep-9.png |only SpatialDDLS-1.0.0/SpatialDDLS/DESCRIPTION | 24 SpatialDDLS-1.0.0/SpatialDDLS/MD5 | 148 +- SpatialDDLS-1.0.0/SpatialDDLS/NAMESPACE | 19 SpatialDDLS-1.0.0/SpatialDDLS/NEWS.md | 16 SpatialDDLS-1.0.0/SpatialDDLS/R/AllClasses.R | 82 - SpatialDDLS-1.0.0/SpatialDDLS/R/AllGenerics.R | 12 SpatialDDLS-1.0.0/SpatialDDLS/R/SpatialDDLS.R | 15 SpatialDDLS-1.0.0/SpatialDDLS/R/dnnModel.R | 505 +++++++- SpatialDDLS-1.0.0/SpatialDDLS/R/evalMetrics.R | 104 + SpatialDDLS-1.0.0/SpatialDDLS/R/interGradientsDL.R |only SpatialDDLS-1.0.0/SpatialDDLS/R/loadData.R | 362 ++++-- SpatialDDLS-1.0.0/SpatialDDLS/R/plotSpatialCoor.R | 350 +++++- SpatialDDLS-1.0.0/SpatialDDLS/R/simMixedSpots.R | 77 - SpatialDDLS-1.0.0/SpatialDDLS/R/simSingleCell.R | 4 SpatialDDLS-1.0.0/SpatialDDLS/R/spatialClustering.R |only SpatialDDLS-1.0.0/SpatialDDLS/R/utils.R | 54 SpatialDDLS-1.0.0/SpatialDDLS/README.md | 13 SpatialDDLS-1.0.0/SpatialDDLS/build/partial.rdb |binary SpatialDDLS-1.0.0/SpatialDDLS/build/vignette.rds |binary SpatialDDLS-1.0.0/SpatialDDLS/inst/doc/realModelExample.Rmd | 480 +++++--- SpatialDDLS-1.0.0/SpatialDDLS/inst/doc/realModelExample.html | 573 ++++++---- SpatialDDLS-1.0.0/SpatialDDLS/man/DeconvDLModel-class.Rd | 13 SpatialDDLS-1.0.0/SpatialDDLS/man/PropCellTypes-class.Rd | 23 SpatialDDLS-1.0.0/SpatialDDLS/man/SpatialDDLS-Rpackage.Rd | 15 SpatialDDLS-1.0.0/SpatialDDLS/man/SpatialDDLS-class.Rd | 12 SpatialDDLS-1.0.0/SpatialDDLS/man/barErrorPlot.Rd | 7 SpatialDDLS-1.0.0/SpatialDDLS/man/barPlotCellTypes.Rd | 8 SpatialDDLS-1.0.0/SpatialDDLS/man/blandAltmanLehPlot.Rd | 9 SpatialDDLS-1.0.0/SpatialDDLS/man/calculateEvalMetrics.Rd | 4 SpatialDDLS-1.0.0/SpatialDDLS/man/corrExpPredPlot.Rd | 10 SpatialDDLS-1.0.0/SpatialDDLS/man/createSpatialDDLSobject.Rd | 73 - SpatialDDLS-1.0.0/SpatialDDLS/man/deconv.spots.Rd | 4 SpatialDDLS-1.0.0/SpatialDDLS/man/deconvSpatialDDLS.Rd | 123 +- SpatialDDLS-1.0.0/SpatialDDLS/man/distErrorPlot.Rd | 15 SpatialDDLS-1.0.0/SpatialDDLS/man/estimateZinbwaveParams.Rd | 3 SpatialDDLS-1.0.0/SpatialDDLS/man/genMixedCellProp.Rd | 30 SpatialDDLS-1.0.0/SpatialDDLS/man/installTFpython.Rd | 2 SpatialDDLS-1.0.0/SpatialDDLS/man/interGradientsDL.Rd |only SpatialDDLS-1.0.0/SpatialDDLS/man/loadSTProfiles.Rd | 5 SpatialDDLS-1.0.0/SpatialDDLS/man/plotDistances.Rd |only SpatialDDLS-1.0.0/SpatialDDLS/man/plotHeatmapGradsAgg.Rd |only SpatialDDLS-1.0.0/SpatialDDLS/man/plotSpatialClustering.Rd |only SpatialDDLS-1.0.0/SpatialDDLS/man/plotSpatialGeneExpr.Rd |only SpatialDDLS-1.0.0/SpatialDDLS/man/plotSpatialProp.Rd | 7 SpatialDDLS-1.0.0/SpatialDDLS/man/plotSpatialPropAll.Rd | 9 SpatialDDLS-1.0.0/SpatialDDLS/man/saveRDS.Rd | 8 SpatialDDLS-1.0.0/SpatialDDLS/man/showProbPlot.Rd | 7 SpatialDDLS-1.0.0/SpatialDDLS/man/simMixedProfiles.Rd | 5 SpatialDDLS-1.0.0/SpatialDDLS/man/simSCProfiles.Rd | 1 SpatialDDLS-1.0.0/SpatialDDLS/man/spatialPropClustering.Rd |only SpatialDDLS-1.0.0/SpatialDDLS/man/topGradientsCellType.Rd |only SpatialDDLS-1.0.0/SpatialDDLS/man/trainDeconvModel.Rd | 82 - SpatialDDLS-1.0.0/SpatialDDLS/tests/testthat/test_dnnModel.R | 137 +- SpatialDDLS-1.0.0/SpatialDDLS/tests/testthat/test_evalMetrics.R | 13 SpatialDDLS-1.0.0/SpatialDDLS/tests/testthat/test_loadData.R | 139 +- SpatialDDLS-1.0.0/SpatialDDLS/tests/testthat/test_plotSpatialCoor.R | 9 SpatialDDLS-1.0.0/SpatialDDLS/tests/testthat/test_simMixedSpots.R | 5 SpatialDDLS-1.0.0/SpatialDDLS/tests/testthat/test_simSingleCell.R | 3 SpatialDDLS-1.0.0/SpatialDDLS/tests/testthat/test_utils.R | 11 SpatialDDLS-1.0.0/SpatialDDLS/vignettes/abserr-celltype-1.png |binary SpatialDDLS-1.0.0/SpatialDDLS/vignettes/abserr-celltype-sep-1.png |binary SpatialDDLS-1.0.0/SpatialDDLS/vignettes/clustering-1.png |only SpatialDDLS-1.0.0/SpatialDDLS/vignettes/corr-pred-1.png |binary SpatialDDLS-1.0.0/SpatialDDLS/vignettes/distances-1.png |only SpatialDDLS-1.0.0/SpatialDDLS/vignettes/negative-grad-1.png |only SpatialDDLS-1.0.0/SpatialDDLS/vignettes/positive-grad-1.png |only SpatialDDLS-1.0.0/SpatialDDLS/vignettes/pred-spatial-1.png |binary SpatialDDLS-1.0.0/SpatialDDLS/vignettes/pred-spatial-sep-1.png |binary SpatialDDLS-1.0.0/SpatialDDLS/vignettes/pred-spatial-sep-2.png |binary SpatialDDLS-1.0.0/SpatialDDLS/vignettes/pred-spatial-sep-3.png |binary SpatialDDLS-1.0.0/SpatialDDLS/vignettes/pred-spatial-sep-extrinsic-1.png |only SpatialDDLS-1.0.0/SpatialDDLS/vignettes/pred-spatial-sep-extrinsic-2.png |only SpatialDDLS-1.0.0/SpatialDDLS/vignettes/pred-spatial-sep-extrinsic-3.png |only SpatialDDLS-1.0.0/SpatialDDLS/vignettes/realModelExample.Rmd | 480 +++++--- SpatialDDLS-1.0.0/SpatialDDLS/vignettes/realModelExample.Rmd.orig | 212 ++- SpatialDDLS-1.0.0/SpatialDDLS/vignettes/references.bib | 22 SpatialDDLS-1.0.0/SpatialDDLS/vignettes/spatialdata-cond-1.png |binary SpatialDDLS-1.0.0/SpatialDDLS/vignettes/zscores-1.png |binary 88 files changed, 3098 insertions(+), 1246 deletions(-)
Title: Simplicial Generalized Beta Regression
Description: Main properties and regression procedures using a generalization of the Dirichlet distribution called Simplicial Generalized Beta distribution. It is a new distribution on the simplex (i.e. on the space of compositions or positive vectors with sum of components equal to 1). The Dirichlet distribution can be constructed from a random vector of independent Gamma variables divided by their sum. The SGB follows the same construction with generalized Gamma instead of Gamma variables. The Dirichlet exponents are supplemented by an overall shape parameter and a vector of scales. The scale vector is itself a composition and can be modeled with auxiliary variables through a log-ratio transformation. Graf, M. (2017, ISBN: 978-84-947240-0-8). See also the vignette enclosed in the package.
Author: Monique Graf
Maintainer: Monique Graf <monique.p.n.graf@bluewin.ch>
Diff between SGB versions 1.0.1 dated 2020-02-05 and 1.0.1.1 dated 2023-12-06
DESCRIPTION | 7 +++---- MD5 | 20 ++++++++++---------- build/partial.rdb |binary build/vignette.rds |binary data/arc.RData |binary data/carseg.RData |binary data/ocar.RData |binary data/oilr.RData |binary inst/doc/SGB-manual.pdf |binary inst/doc/vignette.R | 30 +++++++++++++++--------------- inst/doc/vignette.pdf |binary 11 files changed, 28 insertions(+), 29 deletions(-)
Title: Sets, Generalized Sets, Customizable Sets and Intervals
Description: Data structures and basic operations for ordinary sets,
generalizations such as fuzzy sets, multisets, and
fuzzy multisets, customizable sets, and intervals.
Author: David Meyer [aut, cre] ,
Kurt Hornik [aut] ,
Christian Buchta [ctb]
Maintainer: David Meyer <David.Meyer@R-project.org>
Diff between sets versions 1.0-24 dated 2023-03-07 and 1.0-25 dated 2023-12-06
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ build/partial.rdb |binary build/vignette.rds |binary inst/NEWS.Rd | 6 ++++++ inst/doc/sets.pdf |binary src/closure.c | 2 +- 7 files changed, 16 insertions(+), 10 deletions(-)
Title: Quick Serialization of R Objects
Description: Provides functions for quickly writing and reading any R object to and from disk.
Author: Travers Ching [aut, cre, cph],
Yann Collet [ctb, cph] ,
Facebook, Inc. [cph] ,
Reichardt Tino [ctb, cph] ,
Skibinski Przemyslaw [ctb, cph] ,
Mori Yuta [ctb, cph] ,
Romain Francois [ctb, cph] ,
Francesc Alted [ctb, cph] ,
Bryce Chamberlain [ctb] ,
Sal [...truncated...]
Maintainer: Travers Ching <traversc@gmail.com>
Diff between qs versions 0.25.6 dated 2023-11-28 and 0.25.7 dated 2023-12-06
ChangeLog | 3 + DESCRIPTION | 8 ++--- MD5 | 6 +-- src/RcppExports.cpp | 80 ++++++++++++++++++++++++++-------------------------- 4 files changed, 50 insertions(+), 47 deletions(-)
Title: Translate Text
Description: The goal of the this package is to provide easy methods to
translate pieces of text. Functions send requests to translation services online.
Author: Tomer Iwan [aut, cre, cph]
Maintainer: Tomer Iwan <t.iwan@vu.nl>
Diff between polyglotr versions 1.2.2 dated 2023-10-30 and 1.3.0 dated 2023-12-06
DESCRIPTION | 12 + LICENSE | 4 MD5 | 49 ++++--- NAMESPACE | 2 NEWS.md | 6 R/create_translation_table.R | 62 ++++----- R/google_get_supported_languages.R |only R/google_is_valid_language_code.R |only R/google_supported_languages.R |only R/google_translate.R | 11 + R/utils-pipe.R | 28 ++-- README.md | 116 ++++++++--------- data |only inst/doc/Linguee.R | 2 inst/doc/Linguee.Rmd | 124 +++++++++--------- inst/doc/Linguee.html | 175 +++++++++++++------------- inst/doc/Movie_Reviews.R | 2 inst/doc/Movie_Reviews.html | 220 ++++++++++++++++----------------- inst/doc/polyglotr.R | 2 inst/doc/polyglotr.html | 141 ++++++++++----------- man/google_get_supported_languages.Rd |only man/google_is_valid_language_code.Rd |only man/google_supported_languages.Rd |only man/language_detect.Rd | 34 ++--- man/pipe.Rd | 40 +++--- man/translate_file.Rd | 60 ++++----- tests/testthat/helpers.R | 30 ++-- tests/testthat/test-google_translate.R | 31 ++++ vignettes/Linguee.Rmd | 124 +++++++++--------- 29 files changed, 668 insertions(+), 607 deletions(-)
Title: Sample Size for Development of a Prediction Model
Description: Computes the minimum sample size required for the development of a new multivariable prediction model using the criteria proposed by Riley et al. (2018) <doi: 10.1002/sim.7992>. pmsampsize can be used to calculate the minimum sample size for the development of models with continuous, binary or survival (time-to-event) outcomes. Riley et al. (2018) <doi: 10.1002/sim.7992> lay out a series of criteria the sample size should meet. These aim to minimise the overfitting and to ensure precise estimation of key parameters in the prediction model.
Author: Joie Ensor [aut, cre]
Maintainer: Joie Ensor <j.ensor@bham.ac.uk>
Diff between pmsampsize versions 1.1.2 dated 2022-02-12 and 1.1.3 dated 2023-12-06
DESCRIPTION | 23 ++----- MD5 | 18 ++--- NEWS.md | 5 + R/pmsampsize.R | 138 ++++++++++++++++++++++++++++++------------- R/pmsampsize_cont.R | 33 +--------- R/pmsampsize_errorcheck.R | 21 ++++-- man/pmsampsize.Rd | 86 ++++++++++++++------------ tests/testthat/test_bin.R | 8 +- tests/testthat/test_surv.R | 18 ++--- tests/testthat/test_syntax.R | 32 ++++----- 10 files changed, 218 insertions(+), 164 deletions(-)
Title: Utilities for Scheduling Functions to Execute Later with Event
Loops
Description: Executes arbitrary R or C functions some time after the current
time, after the R execution stack has emptied. The functions are scheduled
in an event loop.
Author: Winston Chang [aut, cre],
Joe Cheng [aut],
Posit Software, PBC [cph],
Marcus Geelnard [ctb, cph] ,
Evan Nemerson [ctb, cph]
Maintainer: Winston Chang <winston@posit.co>
Diff between later versions 1.3.1 dated 2023-05-02 and 1.3.2 dated 2023-12-06
DESCRIPTION | 16 ++++++++-------- MD5 | 12 ++++++------ NEWS.md | 8 ++++++++ build/vignette.rds |binary inst/doc/later-cpp.html | 4 ++-- inst/include/later.h | 14 ++++++++------ src/later_posix.cpp | 3 ++- 7 files changed, 34 insertions(+), 23 deletions(-)
Title: HTTP and WebSocket Server Library
Description: Provides low-level socket and protocol support for handling
HTTP and WebSocket requests directly from within R. It is primarily
intended as a building block for other packages, rather than making it
particularly easy to create complete web applications using httpuv
alone. httpuv is built on top of the libuv and http-parser C
libraries, both of which were developed by Joyent, Inc. (See LICENSE
file for libuv and http-parser license information.)
Author: Joe Cheng [aut],
Winston Chang [aut, cre],
Posit, PBC fnd [cph],
Hector Corrada Bravo [ctb],
Jeroen Ooms [ctb],
Andrzej Krzemienski [cph] ,
libuv project contributors [cph] ,
Joyent, Inc. and other Node contributors [cph] ,
Niels Provos [cph] ,
Inter [...truncated...]
Maintainer: Winston Chang <winston@posit.co>
Diff between httpuv versions 1.6.12 dated 2023-10-23 and 1.6.13 dated 2023-12-06
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ src/webapplication.cpp | 2 +- 4 files changed, 11 insertions(+), 7 deletions(-)
Title: Geometrically Designed Spline Regression
Description: Geometrically Designed Spline ('GeDS') Regression is a non-parametric geometrically
motivated method for fitting variable knots spline predictor models in one or two independent
variables, in the context of generalized (non-)linear models. 'GeDS' estimates the number and
position of the knots and the order of the spline, assuming the response variable has a
distribution from the exponential family. A description of the method can be found in
Kaishev et al. (2016) <doi:10.1007/s00180-015-0621-7> and Dimitrova et al. (2017) <https://openaccess.city.ac.uk/id/eprint/18460/>.
Author: Dimitrina S. Dimitrova <D.Dimitrova@city.ac.uk>,
Emilio S. Guillen <emilio.saenz-guillen@bayes.city.ac.uk>,
Vladimir K. Kaishev <V.Kaishev@city.ac.uk>,
Andrea Lattuada <andrea.lattuada@hotmail.com> and
Richard J. Verrall <R.J.Verrall@city.ac.uk>
Maintainer: Emilio S. Guillen <emilio.saenz-guillen@bayes.city.ac.uk>
Diff between GeDS versions 0.1.3 dated 2017-12-19 and 0.1.4 dated 2023-12-06
DESCRIPTION | 22 +++++++------- MD5 | 72 ++++++++++++++++++++++++----------------------- R/GEDSClass.R | 2 - R/GGeDS.R | 4 +- R/GeDS-package.R | 4 +- R/IntegrateDerive.R | 4 +- R/NGeDS.R | 2 - R/SplineReg.R | 6 +-- R/UnivariateFitter.R | 4 +- R/dynlib.R | 10 +++--- R/pprep.R | 2 - R/unexported.R | 5 +-- README.md |only build |only inst/CITATION | 40 ++++++++++++++------------ man/BaFe2As2.Rd | 11 +++---- man/Derive.Rd | 1 man/EWmortality.Rd | 7 ++-- man/Fitters.Rd | 51 ++++++++++++++++++++++++--------- man/GGeDS.Rd | 22 ++++++++++---- man/GeDS-class.Rd | 6 +-- man/GeDS-package.Rd | 19 +++++------- man/IRLSfit.Rd | 12 +++++-- man/Integrate.Rd | 9 ++--- man/NGeDS.Rd | 20 +++++++++---- man/PPolyRep.Rd | 1 man/SplineReg.Rd | 41 +++++++++++++++++++------- man/coalMining.Rd | 7 ++-- man/coef.Rd | 1 man/deviance.GeDS.Rd | 1 man/f.Rd | 1 man/formula.GeDS.Rd | 1 man/knots.Rd | 1 man/lines-GeDS-method.Rd | 12 +++++-- man/plot-GeDS-method.Rd | 18 ++++++++--- man/predict.GeDS.Rd | 4 -- man/print.GeDS.Rd | 1 src/RcppExports.cpp | 5 +++ 38 files changed, 257 insertions(+), 172 deletions(-)
Title: ASCII Formatting for Values and Tables
Description: We provide a framework for rendering complex tables to ASCII,
and a set of formatters for transforming values or sets of values into
ASCII-ready display strings.
Author: Gabriel Becker [aut] ,
Adrian Waddell [aut],
Davide Garolini [ctb],
Emily de la Rua [ctb],
Abinaya Yogasekaram [ctb],
Joe Zhu [ctb, cre],
F. Hoffmann-La Roche AG [cph, fnd]
Maintainer: Joe Zhu <joe.zhu@roche.com>
Diff between formatters versions 0.5.2 dated 2023-08-25 and 0.5.5 dated 2023-12-06
formatters-0.5.2/formatters/man/default_hsep.Rd |only formatters-0.5.2/formatters/man/figures/formatters_hexSticker.pdf |only formatters-0.5.2/formatters/man/figures/formatters_hexSticker.png |only formatters-0.5.5/formatters/DESCRIPTION | 25 formatters-0.5.5/formatters/MD5 | 72 formatters-0.5.5/formatters/NAMESPACE | 18 formatters-0.5.5/formatters/NEWS.md | 22 formatters-0.5.5/formatters/R/format_value.R | 29 formatters-0.5.5/formatters/R/generics.R | 81 formatters-0.5.5/formatters/R/labels.R | 4 formatters-0.5.5/formatters/R/matrix_form.R | 850 ++++--- formatters-0.5.5/formatters/R/mpf_exporters.R | 368 ++- formatters-0.5.5/formatters/R/package.R |only formatters-0.5.5/formatters/R/page_size.R | 64 formatters-0.5.5/formatters/R/pagination.R | 1100 +++++---- formatters-0.5.5/formatters/R/tostring.R | 1102 ++++++---- formatters-0.5.5/formatters/R/utils.R | 10 formatters-0.5.5/formatters/README.md | 2 formatters-0.5.5/formatters/inst/WORDLIST | 4 formatters-0.5.5/formatters/inst/doc/formatters.R | 3 formatters-0.5.5/formatters/inst/doc/formatters.Rmd | 3 formatters-0.5.5/formatters/inst/doc/formatters.html | 6 formatters-0.5.5/formatters/man/MatrixPrintForm.Rd | 14 formatters-0.5.5/formatters/man/decimal_align.Rd | 2 formatters-0.5.5/formatters/man/default_horizontal_sep.Rd |only formatters-0.5.5/formatters/man/export_as_pdf.Rd |only formatters-0.5.5/formatters/man/export_as_txt.Rd | 10 formatters-0.5.5/formatters/man/figures/logo.png |only formatters-0.5.5/formatters/man/font_lcpi.Rd | 4 formatters-0.5.5/formatters/man/formatters-package.Rd |only formatters-0.5.5/formatters/man/make_row_df.Rd | 24 formatters-0.5.5/formatters/man/matrix_form.Rd | 4 formatters-0.5.5/formatters/man/paginate_indices.Rd | 14 formatters-0.5.5/formatters/man/tostring.Rd | 20 formatters-0.5.5/formatters/man/wrap_string.Rd | 49 formatters-0.5.5/formatters/tests/testthat/setup.R | 36 formatters-0.5.5/formatters/tests/testthat/test-exporters.R | 259 +- formatters-0.5.5/formatters/tests/testthat/test-formatters.R | 912 ++++---- formatters-0.5.5/formatters/tests/testthat/test-pagination.R | 583 ++--- formatters-0.5.5/formatters/tests/testthat/test-txt_wrap.R | 155 + formatters-0.5.5/formatters/vignettes/formatters.Rmd | 3 41 files changed, 3458 insertions(+), 2394 deletions(-)
Title: Misc Functions of the Department of Statistics, Probability
Theory Group (Formerly: E1071), TU Wien
Description: Functions for latent class analysis, short time Fourier
transform, fuzzy clustering, support vector machines,
shortest path computation, bagged clustering, naive Bayes
classifier, generalized k-nearest neighbour ...
Author: David Meyer [aut, cre] ,
Evgenia Dimitriadou [aut, cph],
Kurt Hornik [aut] ,
Andreas Weingessel [aut],
Friedrich Leisch [aut],
Chih-Chung Chang [ctb, cph] ,
Chih-Chen Lin [ctb, cph]
Maintainer: David Meyer <David.Meyer@R-project.org>
Diff between e1071 versions 1.7-13 dated 2023-02-01 and 1.7-14 dated 2023-12-06
DESCRIPTION | 6 ++-- MD5 | 22 +++++++-------- NAMESPACE | 3 +- R/fclustIndex.R | 64 +++++++++++++++++++++++----------------------- R/gknn.R | 4 ++ R/lca.R | 6 ++-- R/svm.R | 11 +++++-- build/vignette.rds |binary inst/NEWS.Rd | 12 +++++++- inst/doc/svmdoc.pdf |binary inst/doc/svminternals.pdf |binary src/svm.cpp | 2 - 12 files changed, 74 insertions(+), 56 deletions(-)
Title: Estimate and Manipulate Age-Depth Models
Description: Estimate age-depth models from stratigraphic and sedimentological data,
and transform data
between the time and stratigraphic domain.
Author: Niklas Hohmann [aut, cre]
Maintainer: Niklas Hohmann <N.H.Hohmann@uu.nl>
Diff between admtools versions 0.0.1 dated 2023-11-29 and 0.1.0 dated 2023-12-06
admtools-0.0.1/admtools/R/CarboCatLite_data.R |only admtools-0.0.1/admtools/R/merge_adm_2_multiadm.R |only admtools-0.0.1/admtools/R/tp_2_adm.R |only admtools-0.0.1/admtools/data/CarboCatLite_data.rda |only admtools-0.0.1/admtools/man/merge_adm_2_multiadm.Rd |only admtools-0.0.1/admtools/man/tp_2_adm.Rd |only admtools-0.0.1/admtools/tests/testthat/test_merge_adm_2_multiadm.R |only admtools-0.0.1/admtools/tests/testthat/test_tp_2_adm.R |only admtools-0.1.0/admtools/DESCRIPTION | 9 admtools-0.1.0/admtools/MD5 | 129 ++-- admtools-0.1.0/admtools/NAMESPACE | 12 admtools-0.1.0/admtools/NEWS.md |only admtools-0.1.0/admtools/R/CarboCATLite_data.R |only admtools-0.1.0/admtools/R/add_adm_to_multiadm.R |only admtools-0.1.0/admtools/R/admtools-package.R |only admtools-0.1.0/admtools/R/get_completeness.R | 2 admtools-0.1.0/admtools/R/get_hiat_no.R | 4 admtools-0.1.0/admtools/R/get_hiat_pos.R | 2 admtools-0.1.0/admtools/R/is_adm.R | 48 + admtools-0.1.0/admtools/R/is_multiadm.R | 15 admtools-0.1.0/admtools/R/merge_adm_to_multiadm.R |only admtools-0.1.0/admtools/R/merge_multiadm.R |only admtools-0.1.0/admtools/R/plot.adm.R | 12 admtools-0.1.0/admtools/R/plot.multiadm.R | 7 admtools-0.1.0/admtools/R/print.adm.R |only admtools-0.1.0/admtools/R/print.multiadm.R |only admtools-0.1.0/admtools/R/sedrate_to_multiadm.R | 6 admtools-0.1.0/admtools/R/split_multiadm.R | 13 admtools-0.1.0/admtools/R/strat_cont_to_multiadm.R | 6 admtools-0.1.0/admtools/R/strat_to_time.R |only admtools-0.1.0/admtools/R/strat_to_time.phylo.R |only admtools-0.1.0/admtools/R/summary.adm.R | 2 admtools-0.1.0/admtools/R/time_to_strat.R |only admtools-0.1.0/admtools/R/time_to_strat.phylo.R |only admtools-0.1.0/admtools/R/tp_to_adm.R |only admtools-0.1.0/admtools/README.md | 63 +- admtools-0.1.0/admtools/build/partial.rdb |binary admtools-0.1.0/admtools/build/vignette.rds |binary admtools-0.1.0/admtools/data/CarboCATLite_data.rda |only admtools-0.1.0/admtools/inst/doc/adm_from_sedrate.R | 38 - admtools-0.1.0/admtools/inst/doc/adm_from_sedrate.Rmd | 88 +-- admtools-0.1.0/admtools/inst/doc/adm_from_sedrate.html | 145 ++--- admtools-0.1.0/admtools/inst/doc/adm_from_trace_cont.html | 6 admtools-0.1.0/admtools/inst/doc/admtools.R | 76 ++ admtools-0.1.0/admtools/inst/doc/admtools.Rmd | 184 +++++- admtools-0.1.0/admtools/inst/doc/admtools.html | 290 +++++++--- admtools-0.1.0/admtools/man/CarboCATLite_data.Rd | 2 admtools-0.1.0/admtools/man/add_adm_to_multiadm.Rd |only admtools-0.1.0/admtools/man/admtools-package.Rd |only admtools-0.1.0/admtools/man/get_completeness.Rd | 2 admtools-0.1.0/admtools/man/get_hiat_no.Rd | 2 admtools-0.1.0/admtools/man/get_hiat_pos.Rd | 2 admtools-0.1.0/admtools/man/is_adm.Rd | 10 admtools-0.1.0/admtools/man/is_multiadm.Rd | 36 - admtools-0.1.0/admtools/man/merge_adm_to_multiadm.Rd |only admtools-0.1.0/admtools/man/merge_multiadm.Rd |only admtools-0.1.0/admtools/man/plot.adm.Rd |only admtools-0.1.0/admtools/man/plot.multiadm.Rd |only admtools-0.1.0/admtools/man/sedrate_to_multiadm.Rd | 7 admtools-0.1.0/admtools/man/split_multiadm.Rd | 34 - admtools-0.1.0/admtools/man/strat_cont_to_multiadm.Rd | 7 admtools-0.1.0/admtools/man/strat_to_time.Rd |only admtools-0.1.0/admtools/man/summary.adm.Rd | 2 admtools-0.1.0/admtools/man/time_to_strat.Rd |only admtools-0.1.0/admtools/man/tp_to_adm.Rd |only admtools-0.1.0/admtools/tests/testthat.R |only admtools-0.1.0/admtools/tests/testthat/test_get_completeness.R | 6 admtools-0.1.0/admtools/tests/testthat/test_get_height.R | 4 admtools-0.1.0/admtools/tests/testthat/test_get_hiat_duration.R | 12 admtools-0.1.0/admtools/tests/testthat/test_get_hiat_list.R | 12 admtools-0.1.0/admtools/tests/testthat/test_get_hiat_no.R | 12 admtools-0.1.0/admtools/tests/testthat/test_get_hiat_pos.R | 12 admtools-0.1.0/admtools/tests/testthat/test_get_time.R | 14 admtools-0.1.0/admtools/tests/testthat/test_get_total_thickness.R | 4 admtools-0.1.0/admtools/tests/testthat/test_is_adm.R | 64 ++ admtools-0.1.0/admtools/tests/testthat/test_is_destructive.R | 12 admtools-0.1.0/admtools/tests/testthat/test_is_multiadm.R | 30 - admtools-0.1.0/admtools/tests/testthat/test_merge_adm_to_multiadm.R |only admtools-0.1.0/admtools/tests/testthat/test_phylo_helpers.R |only admtools-0.1.0/admtools/tests/testthat/test_strat_to_time.R |only admtools-0.1.0/admtools/tests/testthat/test_time_to_strat.R |only admtools-0.1.0/admtools/tests/testthat/test_tp_to_adm.R |only admtools-0.1.0/admtools/vignettes/adm_from_sedrate.Rmd | 88 +-- admtools-0.1.0/admtools/vignettes/admtools.Rmd | 184 +++++- 84 files changed, 1243 insertions(+), 472 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-11-22 0.3.3
2023-09-11 0.3.2
2023-08-18 0.3.1
2023-07-04 0.2.5
2023-04-20 0.2.4
2023-02-24 0.2.3
2023-01-20 0.2.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2023-05-08 2.0.7
2023-01-27 2.0.6
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2022-12-07 2.17.2
2021-04-06 2.17.1
2021-01-14 2.17.0
2019-10-20 2.16.2.0
2018-05-10 2.16.0.0
2016-09-22 2.14.3.1
2016-04-19 2.14.3
2016-02-05 2.14.2
2015-07-22 2.14.1
2015-07-03 2.14.0
2015-06-03 2.13.3
2014-06-20 2.13.2
2014-06-16 2.13
2013-07-17 2.12
2013-02-26 2.11
2012-10-17 2.10
2012-03-28 2.9
2012-02-07 2.8
2011-12-18 2.7
Title: Extreme Gradient Boosting
Description: Extreme Gradient Boosting, which is an efficient implementation
of the gradient boosting framework from Chen & Guestrin (2016) <doi:10.1145/2939672.2939785>.
This package is its R interface. The package includes efficient linear
model solver and tree learning algorithms. The package can automatically
do parallel computation on a single machine which could be more than 10
times faster than existing gradient boosting packages. It supports
various objective functions, including regression, classification and ranking.
The package is made to be extensible, so that users are also allowed to define
their own objectives easily.
Author: Tianqi Chen [aut],
Tong He [aut],
Michael Benesty [aut],
Vadim Khotilovich [aut],
Yuan Tang [aut] ,
Hyunsu Cho [aut],
Kailong Chen [aut],
Rory Mitchell [aut],
Ignacio Cano [aut],
Tianyi Zhou [aut],
Mu Li [aut],
Junyuan Xie [aut],
Min Lin [aut],
Yifen [...truncated...]
Maintainer: Jiaming Yuan <jm.yuan@outlook.com>
Diff between xgboost versions 1.7.5.1 dated 2023-03-30 and 1.7.6.1 dated 2023-12-06
DESCRIPTION | 8 MD5 | 147 ++++++------ R/callbacks.R | 22 + R/xgb.Booster.R | 26 +- R/xgb.DMatrix.R | 7 R/xgb.load.R | 15 + R/xgb.model.dt.tree.R | 5 R/xgb.plot.deepness.R | 7 R/xgb.plot.importance.R | 9 R/xgb.plot.multi.trees.R | 11 R/xgb.plot.shap.R | 16 - R/xgb.save.R | 14 - R/xgb.save.raw.R | 9 R/xgb.train.R | 29 +- build/vignette.rds |binary configure | 18 - configure.ac | 2 inst/doc/discoverYourData.R | 43 ++- inst/doc/discoverYourData.Rmd | 27 ++ inst/doc/discoverYourData.html | 105 +++++---- inst/doc/xgboost.R | 9 inst/doc/xgboost.Rnw | 9 inst/doc/xgboost.pdf |binary inst/doc/xgboostPresentation.R | 29 ++ inst/doc/xgboostPresentation.Rmd | 27 +- inst/doc/xgboostPresentation.html | 163 +++++++------- inst/doc/xgboostfromJSON.Rmd | 2 inst/doc/xgboostfromJSON.html | 160 ++++++------- man/cb.gblinear.history.Rd | 14 - man/predict.xgb.Booster.Rd | 7 man/xgb.DMatrix.Rd | 7 man/xgb.config.Rd | 9 man/xgb.load.Rd | 15 + man/xgb.model.dt.tree.Rd | 5 man/xgb.plot.deepness.Rd | 7 man/xgb.plot.importance.Rd | 9 man/xgb.plot.multi.trees.Rd | 11 man/xgb.plot.shap.Rd | 12 - man/xgb.plot.shap.summary.Rd | 4 man/xgb.save.Rd | 14 - man/xgb.save.raw.Rd | 9 man/xgb.train.Rd | 29 +- src/include/xgboost/tree_model.h | 13 - src/include/xgboost/version_config.h | 2 src/src/common/common.h | 7 src/src/data/gradient_index.cc | 49 +++- src/src/data/gradient_index.h | 5 src/src/gbm/gbtree_model.cc | 29 +- src/src/predictor/cpu_predictor.cc | 32 +- src/src/tree/hist/evaluate_splits.h | 1 src/src/tree/split_evaluator.h | 2 src/src/tree/updater_gpu_hist.cu | 12 - src/src/tree/updater_quantile_hist.cc | 2 src/src/tree/updater_refresh.cc | 2 src/xgboost_R.cc | 45 ++- tests/testthat/test_basic.R | 298 ++++++++++++++++---------- tests/testthat/test_callbacks.R | 19 + tests/testthat/test_custom_objective.R | 22 + tests/testthat/test_dmatrix.R | 73 +++++- tests/testthat/test_feature_weights.R | 10 tests/testthat/test_glm.R | 22 + tests/testthat/test_helpers.R | 6 tests/testthat/test_interaction_constraints.R | 17 + tests/testthat/test_interactions.R | 24 +- tests/testthat/test_io.R | 3 tests/testthat/test_model_compatibility.R | 2 tests/testthat/test_parameter_exposure.R | 8 tests/testthat/test_poisson_regression.R | 6 tests/testthat/test_ranking.R | 16 - tests/testthat/test_unicode.R |only tests/testthat/test_update.R | 22 + vignettes/discoverYourData.Rmd | 27 ++ vignettes/xgboost.Rnw | 9 vignettes/xgboostPresentation.Rmd | 27 +- vignettes/xgboostfromJSON.Rmd | 2 75 files changed, 1226 insertions(+), 659 deletions(-)
Title: Processing and Transforming Relational Event History Data
Description: Efficiently processes relational event history data and transforms them into formats suitable for other packages. The primary objective of this package is to convert event history data into a format that integrates with the packages in 'remverse' and is compatible with various analytical tools (e.g., computing network statistics, estimating tie-oriented or actor-oriented social network models). Second, it can also transform the data into formats compatible with other packages out of 'remverse'. The package processes the data for two types of temporal social network models: tie-oriented modeling framework (Butts, C., 2008, <doi:10.1111/j.1467-9531.2008.00203.x>) and actor-oriented modeling framework (Stadtfeld, C., & Block, P., 2017, <doi:10.15195/v4.a14>).
Author: Giuseppe Arena [aut, cre],
Rumana Lakdawala [ctb],
Marlyne Meijerink-Bosman [ctb],
Diana Karimova [ctb],
Fabio Generoso Vieira [ctb],
Mahdi Shafiee Kamalabad [ctb],
Roger Leenders [ctb],
Joris Mulder [ctb]
Maintainer: Giuseppe Arena <g.arena@tilburguniversity.edu>
Diff between remify versions 3.2.3 dated 2023-12-05 and 3.2.4 dated 2023-12-06
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- inst/doc/remify.html | 2 +- src/remify.cpp | 6 +++--- 4 files changed, 11 insertions(+), 11 deletions(-)
Title: Interaction Statistics
Description: Fast, model-agnostic implementation of different H-statistics
introduced by Jerome H. Friedman and Bogdan E. Popescu (2008)
<doi:10.1214/07-AOAS148>. These statistics quantify interaction
strength per feature, feature pair, and feature triple. The package
supports multi-output predictions and can account for case weights.
In addition, several variants of the original statistics are provided.
The shape of the interactions can be explored through partial
dependence plots or individual conditional expectation plots. 'DALEX'
explainers, meta learners ('mlr3', 'tidymodels', 'caret') and most
other models work out-of-the-box.
Author: Michael Mayer [aut, cre]
Maintainer: Michael Mayer <mayermichael79@gmail.com>
Diff between hstats versions 1.1.0 dated 2023-11-13 and 1.1.1 dated 2023-12-06
DESCRIPTION | 6 ++-- MD5 | 20 ++++++++-------- NEWS.md | 12 +++++++++ R/pd_raw.R | 10 ++++---- R/perm_importance.R | 16 +++++++++---- R/utils_calculate.R | 40 ++++++++++++++++++++++++++++----- R/utils_statistics.R | 1 README.md | 2 - tests/testthat/test_calculate.R | 20 ++++++++++++++++ tests/testthat/test_hstats.R | 41 ++++++++++++++++++++++++++++++++++ tests/testthat/test_perm_importance.R | 18 ++++++++++---- 11 files changed, 151 insertions(+), 35 deletions(-)
Title: R Commander Plug-in for Dichotomous Choice Contingent Valuation
Description: Adds menu items to the R Commander for parametric analysis of dichotomous choice contingent valuation (DCCV) data. CV is a question-based survey method to elicit individuals' preferences for goods and services. This package depends on functions regarding parametric DCCV analysis in the package DCchoice. See Carson and Hanemann (2005) <doi:10.1016/S1574-0099(05)02017-6> for DCCV.
Author: Hideo Aizaki
Maintainer: Hideo Aizaki <azk-r@spa.nifty.com>
Diff between RcmdrPlugin.DCCV versions 0.1-2 dated 2023-03-11 and 0.1-3 dated 2023-12-06
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS | 7 ++++++- R/RcmdrPlugin.DCCV.R | 8 ++++---- man/RcmdrPlugin.DCCV-package.Rd | 6 ++++++ 5 files changed, 24 insertions(+), 13 deletions(-)
More information about RcmdrPlugin.DCCV at CRAN
Permanent link
Title: Supplemental S-PLUS Functionality in R
Description: Currently there are many functions in S-PLUS that are
missing in R. To facilitate the conversion of S-PLUS packages to R packages,
this package provides some missing S-PLUS functionality in R.
Author: William Constantine [aut],
Tim Hesterberg [aut],
Knut Wittkowski [ctb],
Tingting Song [ctb],
Bill Dunlap [ctb],
Stephen Kaluzny [ctb, cre]
Maintainer: Stephen Kaluzny <spkaluzny@gmail.com>
Diff between splus2R versions 1.3-3 dated 2021-01-30 and 1.3-4 dated 2023-12-06
splus2R-1.3-3/splus2R/tests/showStructure.R |only splus2R-1.3-3/splus2R/tests/showStructure.Rout |only splus2R-1.3-4/splus2R/DESCRIPTION | 6 +++--- splus2R-1.3-4/splus2R/MD5 | 8 +++----- splus2R-1.3-4/splus2R/NEWS | 6 ++++++ splus2R-1.3-4/splus2R/man/nDotArgs.Rd | 3 +-- 6 files changed, 13 insertions(+), 10 deletions(-)
Title: Tools for Social Network Analysis
Description: A range of tools for social network analysis, including node and graph-level indices, structural distance and covariance methods, structural equivalence detection, network regression, random graph generation, and 2D/3D network visualization.
Author: Carter T. Butts [aut, cre, cph]
Maintainer: Carter T. Butts <buttsc@uci.edu>
Diff between sna versions 2.7-1 dated 2023-01-24 and 2.7-2 dated 2023-12-06
ChangeLog | 3 ++ DESCRIPTION | 8 ++--- MD5 | 74 +++++++++++++++++++++++++++--------------------------- R/connectivity.R | 1 R/dataprep.R | 1 R/fileio.R | 1 R/gli.R | 1 R/gmultiv.R | 1 R/gtest.R | 1 R/models.R | 1 R/nli.R | 1 R/permutation.R | 1 R/randomgraph.R | 1 R/roles.R | 1 R/sna-operators.R | 1 R/visualization.R | 1 R/zzz.R | 1 src/cohesion.c | 2 - src/cohesion.h | 2 - src/components.c | 1 src/components.h | 1 src/geodist.c | 1 src/geodist.h | 1 src/gli.c | 1 src/gli.h | 1 src/layout.c | 1 src/layout.h | 1 src/likelihood.c | 1 src/likelihood.h | 1 src/nli.c | 1 src/nli.h | 1 src/paths.c | 15 +++++----- src/paths.h | 1 src/randomgraph.c | 1 src/randomgraph.h | 1 src/triads.c | 1 src/triads.h | 1 src/utils.c | 3 +- 38 files changed, 87 insertions(+), 51 deletions(-)
Title: R Commander Plug-in for Discrete Choice Experiments
Description: Adds menu items for discrete choice experiments (DCEs) to the R Commander. DCE is a question-based survey method that designs various combinations (profiles) of attribute levels using the experimental designs, asks respondents to select the most preferred profile in each choice set, and then measures preferences for the attribute levels by analyzing the responses. For details on DCEs, refer to Louviere et al. (2000) <doi:10.1017/CBO9780511753831>.
Author: Hideo Aizaki
Maintainer: Hideo Aizaki <azk-r@spa.nifty.com>
Diff between RcmdrPlugin.DCE versions 0.2-0 dated 2023-11-07 and 0.2-1 dated 2023-12-06
DESCRIPTION | 8 +-- MD5 | 10 +-- NEWS | 3 + R/RcmdrPlugin.DCE.R | 109 ++++++++++++++++++++++------------------- inst/CITATION | 15 +++++ man/RcmdrPlugin.DCE-package.Rd | 1 6 files changed, 87 insertions(+), 59 deletions(-)
More information about RcmdrPlugin.DCE at CRAN
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Title: R Commander Plug-in for Case 3 Best-Worst Scaling
Description: Adds menu items for case 3 (multi-profile) best-worst scaling (BWS3) to the R Commander. BWS3 is a question-based survey method that designs various combinations of attribute levels (profiles), asks respondents to select the best and worst profiles in each choice set, and then measures preferences for the attribute levels by analyzing the responses. For details on BWS3, refer to Louviere et al. (2015) <doi:10.1017/CBO9781107337855>.
Author: Hideo Aizaki
Maintainer: Hideo Aizaki <azk-r@spa.nifty.com>
Diff between RcmdrPlugin.BWS3 versions 0.2-0 dated 2023-11-23 and 0.2-1 dated 2023-12-06
DESCRIPTION | 8 ++-- MD5 | 6 +-- NEWS | 5 ++ R/RcmdrPlugin.BWS3.R | 99 +++++++++++++++++++++++++++------------------------ 4 files changed, 65 insertions(+), 53 deletions(-)
More information about RcmdrPlugin.BWS3 at CRAN
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Title: HTML Widgets for R
Description: A framework for creating HTML widgets that render in various
contexts including the R console, 'R Markdown' documents, and 'Shiny'
web applications.
Author: Ramnath Vaidyanathan [aut, cph],
Yihui Xie [aut],
JJ Allaire [aut],
Joe Cheng [aut],
Carson Sievert [aut, cre] ,
Kenton Russell [aut, cph],
Ellis Hughes [ctb],
Posit Software, PBC [cph, fnd]
Maintainer: Carson Sievert <carson@posit.co>
Diff between htmlwidgets versions 1.6.3 dated 2023-11-22 and 1.6.4 dated 2023-12-06
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 4 ++++ R/utils.R | 3 ++- inst/doc/develop_advanced.R | 2 +- inst/doc/develop_advanced.html | 6 +++--- inst/doc/develop_intro.html | 4 ++-- inst/doc/develop_sizing.html | 4 ++-- 8 files changed, 24 insertions(+), 19 deletions(-)
Title: Creation and Evaluation of Acceptance Sampling Plans
Description: Provides functionality for creating and
evaluating acceptance sampling plans. Sampling plans can be single,
double or multiple.
Author: Andreas Kiermeier [aut, cre],
Peter Bloomfield [ctb]
Maintainer: Andreas Kiermeier <Andreas.Kiermeier@gmail.com>
Diff between AcceptanceSampling versions 1.0-8 dated 2022-04-06 and 1.0-10 dated 2023-12-06
DESCRIPTION | 10 ++++++---- MD5 | 13 +++++++------ NEWS.md |only R/code_generic.R | 4 +++- R/code_twoclass.R | 18 +++++++++++++++--- build/vignette.rds |binary inst/CITATION | 29 +++++++++++------------------ inst/doc/acceptance_sampling_manual.pdf |binary 8 files changed, 42 insertions(+), 32 deletions(-)
More information about AcceptanceSampling at CRAN
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