Title: Create and Format Correlation Matrices
Description: Create correlation (or partial correlation) matrices. Correlation matrices are formatted with significance stars based on user preferences. Matrices of coefficients, p-values, and number of pairwise observations are returned. Send resultant formatted matrices to the clipboard to be pasted into excel and other programs. A plot method allows users to visualize correlation matrices created with 'corx'.
Author: James Conigrave [aut, cre]
Maintainer: James Conigrave <james.conigrave@gmail.com>
Diff between corx versions 1.0.6.1 dated 2020-06-30 and 1.0.7.0 dated 2022-08-25
corx-1.0.6.1/corx/R/partial_matrix.R |only corx-1.0.6.1/corx/R/utils-pipe.R |only corx-1.0.6.1/corx/man/get_cor.Rd |only corx-1.0.6.1/corx/man/par_matrix.Rd |only corx-1.0.6.1/corx/man/partial_matrix.Rd |only corx-1.0.6.1/corx/man/pipe.Rd |only corx-1.0.7.0/corx/DESCRIPTION | 18 corx-1.0.7.0/corx/MD5 | 42 corx-1.0.7.0/corx/NAMESPACE | 3 corx-1.0.7.0/corx/NEWS.md |only corx-1.0.7.0/corx/R/adjust_p.R |only corx-1.0.7.0/corx/R/cormat_list.R |only corx-1.0.7.0/corx/R/corx.R | 517 ++++++------ corx-1.0.7.0/corx/R/methods.R |only corx-1.0.7.0/corx/R/plot_mds.R | 15 corx-1.0.7.0/corx/R/to_table.R |only corx-1.0.7.0/corx/README.md | 251 ++--- corx-1.0.7.0/corx/man/adjust_pmat.Rd |only corx-1.0.7.0/corx/man/apa_table.corx.Rd |only corx-1.0.7.0/corx/man/check_for_vec.Rd |only corx-1.0.7.0/corx/man/cormat_list.Rd |only corx-1.0.7.0/corx/man/corx.Rd | 53 - corx-1.0.7.0/corx/man/figures/README-unnamed-chunk-10-1.png |binary corx-1.0.7.0/corx/man/figures/README-unnamed-chunk-11-1.png |binary corx-1.0.7.0/corx/man/figures/README-unnamed-chunk-13-1.png |binary corx-1.0.7.0/corx/man/figures/README-unnamed-chunk-9-1.png |binary corx-1.0.7.0/corx/man/partial_n_matrix.Rd |only corx-1.0.7.0/corx/man/plot_mds.Rd | 10 corx-1.0.7.0/corx/man/to_table.Rd |only corx-1.0.7.0/corx/tests/testthat/test_classes.R |only corx-1.0.7.0/corx/tests/testthat/test_matrix.R | 122 ++ 31 files changed, 578 insertions(+), 453 deletions(-)
Title: Article Formats for R Markdown
Description: A suite of custom R Markdown formats and templates for
authoring journal articles and conference submissions.
Author: JJ Allaire [aut],
Yihui Xie [aut] ,
Christophe Dervieux [aut, cre]
,
RStudio [cph, fnd],
R Foundation [aut, cph],
Hadley Wickham [aut],
Journal of Statistical Software [aut, cph],
Ramnath Vaidyanathan [aut, cph],
Association for Computing Machinery [ [...truncated...]
Maintainer: Christophe Dervieux <cderv@rstudio.com>
Diff between rticles versions 0.23 dated 2022-03-04 and 0.24 dated 2022-08-25
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Title: Nonparametric Failure Time Bayesian Additive Regression Trees
Description: Nonparametric Failure Time (NFT) Bayesian Additive Regression Trees (BART): Time-to-event Machine Learning with Heteroskedastic Bayesian Additive Regression Trees (HBART) and Low Information Omnibus (LIO) Dirichlet Process Mixtures (DPM). An NFT BART model is of the form Y = mu + f(x) + sd(x) E where functions f and sd have BART and HBART priors, respectively, while E is a nonparametric error distribution due to a DPM LIO prior hierarchy. See the following for a technical description of the model <https://www.mcw.edu/-/media/MCW/Departments/Biostatistics/tr72.pdf?la=en>.
Author: Rodney Sparapani [aut, cre],
Robert McCulloch [aut],
Matthew Pratola [ctb],
Hugh Chipman [ctb]
Maintainer: Rodney Sparapani <rsparapa@mcw.edu>
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Title: Event Prediction for Time-to-Event Endpoints
Description: Implements the hybrid framework for event prediction described in Fang & Zheng (2011, <doi:10.1016/j.cct.2011.05.013>). To estimate the survival function the event prediction is based on, a piecewise exponential hazard function is fit to the time-to-event data to infer the potential change points. Prior to the last identified change point, the survival function is estimated using Kaplan-Meier, and the tail after the change point is fit using piecewise exponential.
Author: Kaspar Rufibach
Maintainer: Kaspar Rufibach <kaspar.rufibach@roche.com>
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Title: Dimension Reduction for Outlier Detection
Description: A dimension reduction technique for outlier detection. DOBIN: a Distance
based Outlier BasIs using Neighbours, constructs a set of basis vectors for outlier
detection. This is not an outlier detection method; rather it is a pre-processing
method for outlier detection. It brings outliers to the fore-front using fewer basis
vectors (Kandanaarachchi, Hyndman 2020) <doi:10.1080/10618600.2020.1807353>.
Author: Sevvandi Kandanaarachchi [aut, cre]
Maintainer: Sevvandi Kandanaarachchi <sevvandik@gmail.com>
Diff between dobin versions 1.0.3 dated 2022-05-18 and 1.0.4 dated 2022-08-25
DESCRIPTION | 8 LICENSE | 4 MD5 | 41 - NAMESPACE | 34 - R/autoplot_dobin.R | 58 +- R/dobin-package.R | 20 R/dobin.R | 282 +++++------ R/print.R | 26 - R/utils.R | 58 +- R/y_space.R | 98 ++-- build/partial.rdb |only build/vignette.rds |binary inst/doc/dobin.R | 402 ++++++++-------- inst/doc/dobin.Rmd | 504 ++++++++++----------- inst/doc/dobin.html | 1006 +++++++++++++++++++++--------------------- man/dobin-package.Rd | 4 man/dobin.Rd | 98 ++-- man/figures/bimodal-1.png |binary man/figures/bimodal_pca-1.png |binary man/figures/plotting-1.png |binary vignettes/bibliography.bib | 74 +-- vignettes/dobin.Rmd | 504 ++++++++++----------- 22 files changed, 1611 insertions(+), 1610 deletions(-)
Title: Matched Samples that are Balanced and Representative by Design
Description: Includes functions for the construction of matched samples that are balanced and representative by design. Among others, these functions can be used for matching in observational studies with treated and control units, with cases and controls, in related settings with instrumental variables, and in discontinuity designs. Also, they can be used for the design of randomized experiments, for example, for matching before randomization. By default, 'designmatch' uses the 'GLPK' optimization solver, but its performance is greatly enhanced by the 'Gurobi' optimization solver and its associated R interface. For their installation, please follow the instructions at <https://www.gurobi.com/documentation/quickstart.html> and <https://www.gurobi.com/documentation/7.0/refman/r_api_overview.html>. We have also included directions in the gurobi_installation file in the inst folder.
Author: Jose R. Zubizarreta <zubizarreta@hcp.med.harvard.edu>, Cinar Kilcioglu <ckilcioglu16@gsb.columbia.edu>, Juan P. Vielma <jvielma@mit.edu>, Eric R. Cohn <ericcohn@g.harvard.edu>
Maintainer: Jose R. Zubizarreta <zubizarreta@hcp.med.harvard.edu>
Diff between designmatch versions 0.3.1 dated 2018-06-18 and 0.4.1 dated 2022-08-25
DESCRIPTION | 12 +-- MD5 | 18 +++-- R/oneprob_profmatch.r |only R/problemparameters_profmatch.R |only R/profmatch.r |only man/bmatch.Rd | 135 +++++++++++++++++++--------------------- man/cardmatch.Rd | 4 - man/distmatch.Rd | 2 man/germancities.Rd | 2 man/lalonde.Rd | 6 - man/nmatch.Rd | 103 +++++++++++++++--------------- man/profmatch.Rd |only 12 files changed, 143 insertions(+), 139 deletions(-)
Title: A Collection of Statistical Tools for Biologists
Description: Contains functions from: Aho, K. (2014) Foundational and Applied Statistics for Biologists using R. CRC/Taylor and Francis, Boca Raton, FL, ISBN: 978-1-4398-7338-0.
Author: Ken Aho
Maintainer: Ken Aho <kenaho1@gmail.com>
Diff between asbio versions 1.8-1 dated 2022-07-11 and 1.8-2 dated 2022-08-25
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/print.ci.R | 6 +++--- inst/doc/ranef.cov.pdf |binary inst/doc/simpson.pdf |binary man/chi.plot.Rd | 5 ++--- man/ci.prat.rd | 6 +++--- man/starkey.Rd | 6 +++--- 8 files changed, 22 insertions(+), 23 deletions(-)
Title: Read and Write MAT Files and Call MATLAB from Within R
Description: Methods readMat() and writeMat() for reading and writing MAT files. For user with MATLAB v6 or newer installed (either locally or on a remote host), the package also provides methods for controlling MATLAB (trademark) via R and sending and retrieving data between R and MATLAB.
Author: Henrik Bengtsson [aut, cre, cph],
Andy Jacobson [ctb] ,
Jason Riedy [ctb]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between R.matlab versions 3.6.2 dated 2018-09-27 and 3.7.0 dated 2022-08-25
R.matlab-3.6.2/R.matlab/NEWS |only R.matlab-3.7.0/R.matlab/DESCRIPTION | 9 +- R.matlab-3.7.0/R.matlab/MD5 | 34 +++++----- R.matlab-3.7.0/R.matlab/NAMESPACE | 2 R.matlab-3.7.0/R.matlab/NEWS.md |only R.matlab-3.7.0/R.matlab/R/901.MatlabServer.R | 6 - R.matlab-3.7.0/R.matlab/R/999.package.R | 10 +- R.matlab-3.7.0/R.matlab/R/Matlab.R | 10 +- R.matlab-3.7.0/R.matlab/R/readMat.R | 33 +++++++-- R.matlab-3.7.0/R.matlab/R/writeMat.R | 6 - R.matlab-3.7.0/R.matlab/inst/mat-files/2by3cellarray.mat |only R.matlab-3.7.0/R.matlab/inst/mat-files/ADI_LabChart_Export.mat |only R.matlab-3.7.0/R.matlab/man/1._The_MATLAB_server_running_in_MATLAB.Rd | 6 - R.matlab-3.7.0/R.matlab/man/Matlab.Rd | 6 - R.matlab-3.7.0/R.matlab/man/R.matlab-package.Rd | 14 +--- R.matlab-3.7.0/R.matlab/man/readMat.Rd | 6 - R.matlab-3.7.0/R.matlab/man/setFunction.Matlab.Rd | 2 R.matlab-3.7.0/R.matlab/man/startServer.Matlab.Rd | 2 R.matlab-3.7.0/R.matlab/man/writeMat.Rd | 6 - R.matlab-3.7.0/R.matlab/tests/readMat.R | 33 +++++++++ 20 files changed, 117 insertions(+), 68 deletions(-)
Title: Splitting Conic Solver
Description: Solves convex cone programs via operator splitting. Can solve:
linear programs ('LPs'), second-order cone programs ('SOCPs'), semidefinite programs
('SDPs'), exponential cone programs ('ECPs'), and power cone programs ('PCPs'), or
problems with any combination of those cones. 'SCS' uses 'AMD' (a set of routines for permuting sparse matrices prior to factorization) and 'LDL' (a sparse 'LDL' factorization and solve package) from 'SuiteSparse' (<https://people.engr.tamu.edu/davis/suitesparse.html>).
Author: Florian Schwendinger [aut, cre],
Brendan O'Donoghue [aut, cph],
Balasubramanian Narasimhan [aut],
Timothy A. Davis [cph],
Patrick R. Amestory [cph],
Iain S. Duff [cph]
Maintainer: Florian Schwendinger <FlorianSchwendinger@gmx.at>
Diff between scs versions 3.0-0 dated 2021-11-07 and 3.0-1 dated 2022-08-25
scs-3.0-0/scs/tests/testthat/test_problems.R |only scs-3.0-0/scs/tests/testthat/test_sparse_utils.R |only scs-3.0-1/scs/DESCRIPTION | 10 +++++----- scs-3.0-1/scs/MD5 | 6 ++---- scs-3.0-1/scs/tests/testthat.R | 1 - 5 files changed, 7 insertions(+), 10 deletions(-)
Title: Imputation Estimator from Borusyak, Jaravel, and Spiess (2021)
Description: Estimates Two-way Fixed Effects difference-in-differences/event-study models using the imputation-based approach proposed by Borusyak, Jaravel, and Spiess (2021).
Author: Kyle Butts [aut, cre]
Maintainer: Kyle Butts <kyle.butts@colorado.edu>
Diff between didimputation versions 0.1.0 dated 2021-08-02 and 0.3.0 dated 2022-08-25
DESCRIPTION | 14 MD5 | 26 - NAMESPACE | 1 R/data.R | 4 R/did_imputation.R | 491 +++++++++++++++++++---------------- R/utils.R | 52 ++- man/df_het.Rd | 10 man/df_hom.Rd | 10 man/did_imputation.Rd | 86 +++--- src/Makevars | 1 src/Makevars.win | 1 src/RcppExports.cpp | 2 src/code.cpp | 5 tests/testthat/test-did_imputation.R | 2 14 files changed, 395 insertions(+), 310 deletions(-)
Title: Automated Grading of R Scripts
Description: Tools for grading the coding style and documentation of R
scripts. This is the R component of Roger the Omni Grader, an
automated grading system for computer programming projects based on
Unix shell scripts; see <https://gitlab.com/roger-project>. The
package also provides an R interface to the shell scripts. Inspired by
the lintr package.
Author: Vincent Goulet [aut, cre],
Samuel Frechette [aut],
Jean-Christophe Langlois [aut],
Jim Hester [ctb]
Maintainer: Vincent Goulet <vincent.goulet@act.ulaval.ca>
Diff between roger versions 0.99-2 dated 2022-01-13 and 1.0-0 dated 2022-08-25
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/documentation.R | 5 +++-- R/nomagic_style.R | 5 +++-- R/roger_interface.R | 13 +++---------- inst/NEWS.Rd | 23 +++++++++++++++++++++++ man/roger-interface.Rd | 5 ++--- tests/interface-tests.R | 11 ++++++----- 8 files changed, 51 insertions(+), 33 deletions(-)
Title: Rasch Model Parameters by Pairwise Algorithm
Description: Performs the explicit calculation
-- not estimation! -- of the Rasch item parameters for dichotomous and
polytomous item responses, using a pairwise comparison approach. Person
parameters (WLE) are calculated according to Warm's weighted likelihood
approach.
Author: Joerg-Henrik Heine <jhheine@googlemail.com>
Maintainer: Joerg-Henrik Heine <jhheine@googlemail.com>
Diff between pairwise versions 0.5.0-2 dated 2021-01-06 and 0.6.0-0 dated 2022-08-25
pairwise-0.5.0-2/pairwise/inst/doc/vignettes |only pairwise-0.6.0-0/pairwise/DESCRIPTION | 11 pairwise-0.6.0-0/pairwise/MD5 | 140 +- pairwise-0.6.0-0/pairwise/NAMESPACE | 10 pairwise-0.6.0-0/pairwise/NEWS | 6 pairwise-0.6.0-0/pairwise/R/andersentest.pers.R | 7 pairwise-0.6.0-0/pairwise/R/deltapar.R | 1 pairwise-0.6.0-0/pairwise/R/esc.R | 2 pairwise-0.6.0-0/pairwise/R/gif.R | 6 pairwise-0.6.0-0/pairwise/R/grm.R | 276 ++-- pairwise-0.6.0-0/pairwise/R/logLik.pers.R | 134 +- pairwise-0.6.0-0/pairwise/R/pair.R | 644 +++++++--- pairwise-0.6.0-0/pairwise/R/pairSE.R | 217 +-- pairwise-0.6.0-0/pairwise/R/pairwise-package.R | 118 - pairwise-0.6.0-0/pairwise/R/pairwise.S.R | 7 pairwise-0.6.0-0/pairwise/R/pairwise.item.fit.R | 1 pairwise-0.6.0-0/pairwise/R/pairwise.person.fit.R | 1 pairwise-0.6.0-0/pairwise/R/pers.R | 1 pairwise-0.6.0-0/pairwise/R/plot.grm.R | 142 +- pairwise-0.6.0-0/pairwise/R/plot.pair.R | 146 +- pairwise-0.6.0-0/pairwise/R/plot.pairSE.R | 182 +- pairwise-0.6.0-0/pairwise/R/plot.pers.R | 170 +- pairwise-0.6.0-0/pairwise/R/plot.rfa.R | 94 - pairwise-0.6.0-0/pairwise/R/ptbis.R | 5 pairwise-0.6.0-0/pairwise/R/q3.R | 1 pairwise-0.6.0-0/pairwise/R/residuals.pers.R | 4 pairwise-0.6.0-0/pairwise/R/rfa.R | 5 pairwise-0.6.0-0/pairwise/R/summary.grm.R | 54 pairwise-0.6.0-0/pairwise/R/summary.pair.R | 8 pairwise-0.6.0-0/pairwise/R/summary.pairS.R | 70 - pairwise-0.6.0-0/pairwise/R/summary.pairSE.R | 64 pairwise-0.6.0-0/pairwise/R/summary.pers.R | 68 - pairwise-0.6.0-0/pairwise/R/summary.pifit.R | 62 pairwise-0.6.0-0/pairwise/R/summary.ppfit.R | 60 pairwise-0.6.0-0/pairwise/R/summary.q3.R | 4 pairwise-0.6.0-0/pairwise/R/summary.rfa.R | 76 - pairwise-0.6.0-0/pairwise/build |only pairwise-0.6.0-0/pairwise/data/DEU_PISA2012.RData |binary pairwise-0.6.0-0/pairwise/data/KCT.RData |only pairwise-0.6.0-0/pairwise/data/Neoffi5.RData |binary pairwise-0.6.0-0/pairwise/data/bfiN.RData |binary pairwise-0.6.0-0/pairwise/data/bfiN_miss.RData |binary pairwise-0.6.0-0/pairwise/data/bfi_cov.RData |binary pairwise-0.6.0-0/pairwise/data/cog.RData |binary pairwise-0.6.0-0/pairwise/data/cogBOOKLET.RData |binary pairwise-0.6.0-0/pairwise/data/kft5.RData |binary pairwise-0.6.0-0/pairwise/data/sim200x3.RData |binary pairwise-0.6.0-0/pairwise/inst/doc/DEU_PISA2012_description.R |only pairwise-0.6.0-0/pairwise/inst/doc/DEU_PISA2012_description.Rnw |only pairwise-0.6.0-0/pairwise/inst/doc/DEU_PISA2012_description.pdf |only pairwise-0.6.0-0/pairwise/man/DEU_PISA2012.Rd | 5 pairwise-0.6.0-0/pairwise/man/KCT.Rd |only pairwise-0.6.0-0/pairwise/man/cog.Rd | 7 pairwise-0.6.0-0/pairwise/man/cogBOOKLET.Rd | 7 pairwise-0.6.0-0/pairwise/man/grm.Rd | 12 pairwise-0.6.0-0/pairwise/man/logLik.pers.Rd | 1 pairwise-0.6.0-0/pairwise/man/pair.Rd | 57 pairwise-0.6.0-0/pairwise/man/pairSE.Rd | 48 pairwise-0.6.0-0/pairwise/man/pairwise-package.Rd | 4 pairwise-0.6.0-0/pairwise/man/plot.grm.Rd | 3 pairwise-0.6.0-0/pairwise/man/plot.pair.Rd | 3 pairwise-0.6.0-0/pairwise/man/plot.pairSE.Rd | 1 pairwise-0.6.0-0/pairwise/man/plot.pers.Rd | 1 pairwise-0.6.0-0/pairwise/man/plot.rfa.Rd | 1 pairwise-0.6.0-0/pairwise/man/residuals.pers.Rd | 5 pairwise-0.6.0-0/pairwise/man/summary.grm.Rd | 1 pairwise-0.6.0-0/pairwise/man/summary.pair.Rd | 5 pairwise-0.6.0-0/pairwise/man/summary.pairS.Rd | 37 pairwise-0.6.0-0/pairwise/man/summary.pairSE.Rd | 3 pairwise-0.6.0-0/pairwise/man/summary.pers.Rd | 1 pairwise-0.6.0-0/pairwise/man/summary.pifit.Rd | 73 - pairwise-0.6.0-0/pairwise/man/summary.ppfit.Rd | 73 - pairwise-0.6.0-0/pairwise/man/summary.q3.Rd |only pairwise-0.6.0-0/pairwise/man/summary.rfa.Rd | 3 pairwise-0.6.0-0/pairwise/vignettes |only 75 files changed, 1793 insertions(+), 1355 deletions(-)
Title: Differentially Private Statistical Analysis and Machine Learning
Description: An implementation of common statistical analysis and models with
differential privacy (Dwork et al., 2006a) <doi:10.1007/11681878_14>
guarantees. The package contains, for example, functions providing
differentially private computations of mean, variance, median, histograms,
and contingency tables. It also implements some statistical models and
machine learning algorithms such as linear regression (Kifer et al., 2012)
<https://proceedings.mlr.press/v23/kifer12.html>
and SVM (Chaudhuri et al., 2011)
<https://jmlr.org/papers/v12/chaudhuri11a.html>. In addition, it implements
some popular randomization mechanisms
such as the Laplace mechanism (Dwork et al., 2006a)
<doi:10.1007/11681878_14>, Gaussian mechanism (Dwork et al., 2006b)
<doi:10.1007/11761679_29>, and exponential mechanism
(McSherry & Talwar, 2007) <doi:10.1109/FOCS.2007.66>.
Author: Spencer Giddens <giddens2spencer@gmail.com> with contributions from Fang
Liu <fliu2@nd.edu>
Maintainer: Spencer Giddens <giddens2spencer@gmail.com>
Diff between DPpack versions 0.0.1 dated 2022-04-28 and 0.0.11 dated 2022-08-25
DESCRIPTION | 8 +++---- MD5 | 14 ++++++------ build/partial.rdb |binary man/EmpiricalRiskMinimizationDP.CMS.Rd | 24 +++++++++++----------- man/EmpiricalRiskMinimizationDP.KST.Rd | 24 +++++++++++----------- man/LinearRegressionDP.Rd | 32 ++++++++++++++--------------- man/LogisticRegressionDP.Rd | 30 +++++++++++---------------- man/svmDP.Rd | 36 +++++++++++++-------------------- 8 files changed, 78 insertions(+), 90 deletions(-)
Title: Common Network Asset Indices Methodology (CNAIM)
Description: Implementation of the CNAIM standard in R. Contains a series of
algorithms which determine the probability of failure, consequences of
failure and monetary risk associated with electricity distribution
companies' assets such as transformers and cables. Results are visualized
in an easy-to-understand risk matrix.
Author: Emil Larsen [aut],
Kalle Hansen [aut, cph],
Kenneth Rosenorn [aut],
Peter Larsen [aut],
Mohsin Vindhani [aut, cre]
Maintainer: Mohsin Vindhani <mohsin@utiligize.com>
Diff between CNAIM versions 2.1.2 dated 2022-08-06 and 2.1.3 dated 2022-08-25
DESCRIPTION | 14 +++--- MD5 | 14 +++--- R/risk_calculation.R | 68 ++++++++++++++++++++++----------- R/zzz.R | 2 man/predict_weibull_model.Rd | 28 ++++++------- man/risk_calculation.Rd | 42 +++++++++++++++----- tests/testthat/test-matrix_functions.R | 12 ++--- tests/testthat/test-risk_calculation.R | 12 ++--- 8 files changed, 120 insertions(+), 72 deletions(-)
Title: Core Functionality for Environmental Time Series
Description: Utility functions for working with environmental time series data from known
locations. The compact data model is structured as a list with two dataframes. A
'meta' dataframe contains spatial and measuring device metadata associated with
deployments at known locations. A 'data' dataframe contains a 'datetime' column
followed by columns of measurements associated with each "device-deployment".
Ephemerides calculations are based on code originally found in NOAA's
"Solar Calculator" <https://gml.noaa.gov/grad/solcalc/>.
Author: Jonathan Callahan [aut, cre],
Hans Martin [ctb],
Eli Grosman [ctb],
Roger Bivand [ctb],
Sebastian Luque [ctb]
Maintainer: Jonathan Callahan <jonathan.s.callahan@gmail.com>
Diff between MazamaTimeSeries versions 0.2.5 dated 2022-04-05 and 0.2.7 dated 2022-08-25
DESCRIPTION | 8 +-- MD5 | 31 +++++++----- NAMESPACE | 1 NEWS.md | 14 +++++ R/mts_combine.R | 2 R/mts_filterMeta.R | 6 +- R/mts_sample.R |only R/sts_filter.R | 6 +- R/utils-sampling.R |only inst/doc/Developer_Style_Guide.html | 86 +++++++++++++++++++++++++--------- inst/doc/MazamaTimeSeries.html | 88 +++++++++++++++++++++++++++-------- man/dot-flagOutliers.Rd |only man/dot-sample.Rd |only man/mts_combine.Rd | 2 man/mts_filterMeta.Rd | 4 + man/mts_sample.Rd |only man/sts_filter.Rd | 4 + tests/testthat/test-mts_filterMeta.R | 11 ++++ tests/testthat/test-sts_filter.R | 23 ++++++--- 19 files changed, 220 insertions(+), 66 deletions(-)
More information about MazamaTimeSeries at CRAN
Permanent link
Title: Quickly Find, Extract, and Marginalize U.S. Census Tables
Description: Extracting desired data using the proper Census variable names can
be time-consuming. This package takes the pain out of that process by
providing functions to quickly locate variables and download labeled tables
from the Census APIs (<https://www.census.gov/data/developers/data-sets.html>).
Author: Cory McCartan [aut, cre]
Maintainer: Cory McCartan <cmccartan@g.harvard.edu>
Diff between easycensus versions 0.2.1 dated 2022-02-28 and 1.0.0 dated 2022-08-25
easycensus-0.2.1/easycensus/R/find_table.R |only easycensus-0.2.1/easycensus/R/get_table.R |only easycensus-0.2.1/easycensus/man/find_table.Rd |only easycensus-0.2.1/easycensus/man/get_table.Rd |only easycensus-0.2.1/easycensus/man/marginalize.Rd |only easycensus-0.2.1/easycensus/man/reexports.Rd |only easycensus-1.0.0/easycensus/DESCRIPTION | 19 - easycensus-1.0.0/easycensus/MD5 | 55 ++-- easycensus-1.0.0/easycensus/NAMESPACE | 58 +++- easycensus-1.0.0/easycensus/NEWS.md | 13 + easycensus-1.0.0/easycensus/R/cens_find.R |only easycensus-1.0.0/easycensus/R/cens_geo.R |only easycensus-1.0.0/easycensus/R/cens_get.R |only easycensus-1.0.0/easycensus/R/easycensus-package.R | 13 - easycensus-1.0.0/easycensus/R/estimate.R |only easycensus-1.0.0/easycensus/R/parse_table.R |only easycensus-1.0.0/easycensus/R/sysdata.rda |binary easycensus-1.0.0/easycensus/R/table.R |only easycensus-1.0.0/easycensus/R/tidy_labels.R | 78 ++++++ easycensus-1.0.0/easycensus/R/utils.R | 93 +++---- easycensus-1.0.0/easycensus/README.md | 133 +++++------ easycensus-1.0.0/easycensus/data |only easycensus-1.0.0/easycensus/man/cens_auth.Rd |only easycensus-1.0.0/easycensus/man/cens_find.Rd |only easycensus-1.0.0/easycensus/man/cens_geo.Rd |only easycensus-1.0.0/easycensus/man/cens_get.Rd |only easycensus-1.0.0/easycensus/man/cens_margin_to.Rd |only easycensus-1.0.0/easycensus/man/cens_parse_tables.Rd |only easycensus-1.0.0/easycensus/man/easycensus-package.Rd | 9 easycensus-1.0.0/easycensus/man/est_extract.Rd |only easycensus-1.0.0/easycensus/man/est_special.Rd |only easycensus-1.0.0/easycensus/man/estimate-vctrs.Rd |only easycensus-1.0.0/easycensus/man/estimate.Rd |only easycensus-1.0.0/easycensus/man/format.estimate.Rd |only easycensus-1.0.0/easycensus/man/tables.Rd |only easycensus-1.0.0/easycensus/man/tidiers.Rd | 16 + easycensus-1.0.0/easycensus/tests/testthat.R | 5 easycensus-1.0.0/easycensus/tests/testthat/test-estimate.R |only easycensus-1.0.0/easycensus/tests/testthat/test-find_table.R | 4 easycensus-1.0.0/easycensus/tests/testthat/test-get_table.R | 17 + easycensus-1.0.0/easycensus/tests/testthat/test-tidiers.R | 10 41 files changed, 347 insertions(+), 176 deletions(-)
Title: Tabulate P.L. 94-171 Redistricting Data Summary Files
Description: Tools to process legacy format summary redistricting data files
produced by the United States Census Bureau pursuant to P.L. 94-171. These
files are generally available earlier but are difficult to work with as-is.
Author: Cory McCartan [aut, cre],
Christopher T. Kenny [aut]
Maintainer: Cory McCartan <cmccartan@g.harvard.edu>
Diff between PL94171 versions 1.0.2 dated 2022-05-10 and 1.1.1 dated 2022-08-25
DESCRIPTION | 13 +++---- MD5 | 34 +++++++++--------- NEWS.md | 4 ++ R/pl_crosswalk.R | 8 ++-- R/pl_get_baf.R | 3 - R/pl_get_prototype.R | 86 +++++++++++++++++++++--------------------------- R/pl_get_vtd.R | 3 - R/pl_read.R | 2 - R/pl_tidy_shp.R | 12 +++--- R/utils.R | 70 +++++++++++++++++++++++++++++++++++++++ README.md | 51 ++++++++++++++-------------- inst/doc/PL94171.R | 5 +- inst/doc/PL94171.Rmd | 5 +- inst/doc/PL94171.html | 59 +++++++++++++++++--------------- man/PL94171-package.Rd | 4 +- man/pl_get_prototype.Rd | 2 - man/pl_retally.Rd | 2 - vignettes/PL94171.Rmd | 5 +- 18 files changed, 221 insertions(+), 147 deletions(-)
Title: Convert Files to and from Binary Objects (BLOBs)
Description: Converts files to and from flobs. A flob is a file that was
read into binary in integer-mode as little endian, saved as the single
element of a named list (where the name is the name of the original
file) and then serialized before being coerced into a blob. Flobs are
useful for writing and reading files to and from databases.
Author: Joe Thorley [aut, cre] ,
Evan Amies-Galonski [aut] ,
Poisson Consulting [cph, fnd]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>
Diff between flobr versions 0.2.2 dated 2021-10-27 and 0.2.3 dated 2022-08-25
DESCRIPTION | 11 ++++++----- MD5 | 18 +++++++++--------- NEWS.md | 11 ++++------- R/chk.R | 1 + R/flob.R | 4 +++- build/flobr.pdf |binary man/flobr-package.Rd | 2 +- man/pkgtemplate_deprecated.Rd | 4 ++-- tests/testthat/test-aaa-deprecated.R | 4 ++-- tests/testthat/test-flobr.R | 2 +- 10 files changed, 29 insertions(+), 28 deletions(-)
Title: Customizing Structural Equation Modelling Plots
Description: Most function focus on specific ways to customize a graph.
They use a 'qgraph' output as the first argument, and return a
modified 'qgraph' object. This allows the functions to be chained
by a pipe operator.
Author: Shu Fai Cheung [aut, cre] ,
Mark Hok Chio Lai [aut]
Maintainer: Shu Fai Cheung <shufai.cheung@gmail.com>
Diff between semptools versions 0.2.9.3 dated 2021-10-11 and 0.2.9.6 dated 2022-08-25
DESCRIPTION | 10 +-- MD5 | 67 ++++++++++---------- NEWS.md | 27 ++++++-- R/nodes_keep_drop.R | 16 +++- R/set_sem_layout.R | 49 +++++++++------ README.md | 30 +++++++-- build/vignette.rds |binary inst/doc/keep_or_drop_nodes.R | 4 - inst/doc/keep_or_drop_nodes.Rmd | 12 +-- inst/doc/keep_or_drop_nodes.html | 11 +-- inst/doc/layout_matrix.R | 26 ++++---- inst/doc/layout_matrix.Rmd | 46 +++++++------- inst/doc/layout_matrix.html | 35 +++++----- inst/doc/quick_start_cfa.R | 14 ++-- inst/doc/quick_start_cfa.Rmd | 48 +++++++------- inst/doc/quick_start_cfa.html | 19 +++-- inst/doc/quick_start_sem.R | 26 ++++---- inst/doc/quick_start_sem.Rmd | 84 +++++++++++++------------- inst/doc/quick_start_sem.html | 27 ++++---- inst/doc/semptools.R | 28 ++++---- inst/doc/semptools.Rmd | 90 ++++++++++++++-------------- inst/doc/semptools.html | 33 +++++----- man/cfa_example.Rd | 6 + man/pa_example.Rd | 6 + man/pa_example_3covs.Rd | 6 + man/sem_example.Rd | 6 + man/semptools-package.Rd | 5 - man/set_sem_layout.Rd | 15 +++- tests/testthat/test-keep_drop_nodes.R | 23 +++++++ tests/testthat/test-set_sem_layout_single.R |only vignettes/keep_or_drop_nodes.Rmd | 12 +-- vignettes/layout_matrix.Rmd | 46 +++++++------- vignettes/quick_start_cfa.Rmd | 48 +++++++------- vignettes/quick_start_sem.Rmd | 84 +++++++++++++------------- vignettes/semptools.Rmd | 90 ++++++++++++++-------------- 35 files changed, 570 insertions(+), 479 deletions(-)
Title: Concentration-Response Data Analysis using Curvep
Description: Provide an R interface for processing concentration-response datasets using Curvep, a response noise filtering algorithm. The algorithm was described in the publications (Sedykh A et al. (2011) <doi:10.1289/ehp.1002476> and Sedykh A (2016) <doi:10.1007/978-1-4939-6346-1_14>). Other parametric fitting approaches (e.g., Hill equation) are also adopted for ease of comparison. Also, methods for calculating the confidence interval around the activity metrics are also provided. The methods are based on the bootstrap approach to simulate the datasets (Hsieh J-H et al. <doi:10.1093/toxsci/kfy258>). The simulated datasets can be used to derive the baseline noise threshold in an assay endpoint. This threshold is critical in the toxicological studies to derive the point-of-departure (POD).
Author: Jui-Hua Hsieh [aut, cre],
Alexander Sedykh [aut]
Maintainer: Jui-Hua Hsieh <juihua.hsieh@gmail.com>
Diff between Rcurvep versions 1.2.0 dated 2021-01-07 and 1.2.1 dated 2022-08-25
DESCRIPTION | 8 +-- MD5 | 18 +++---- NEWS.md | 6 +- R/rcurvep_bmr.R | 8 +-- R/rcurvep_summary.R | 3 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/practical_rcurvep.html | 100 +++++++++++----------------------------- man/cal_knee_point.Rd | 8 +-- man/estimate_dataset_bmr.Rd | 8 +-- 10 files changed, 58 insertions(+), 101 deletions(-)
Title: Cognitive Diagnosis Modeling
Description: Functions for cognitive diagnosis modeling and multidimensional item response modeling
for dichotomous and polytomous item responses. This package enables the estimation of
the DINA and DINO model (Junker & Sijtsma, 2001, <doi:10.1177/01466210122032064>),
the multiple group (polytomous) GDINA model (de la Torre, 2011,
<doi:10.1007/s11336-011-9207-7>), the multiple choice DINA model (de la Torre, 2009,
<doi:10.1177/0146621608320523>), the general diagnostic model (GDM; von Davier, 2008,
<doi:10.1348/000711007X193957>), the structured latent class model (SLCA; Formann, 1992,
<doi:10.1080/01621459.1992.10475229>) and regularized latent class analysis
(Chen, Li, Liu, & Ying, 2017, <doi:10.1007/s11336-016-9545-6>).
See George, Robitzsch, Kiefer, Gross, and Uenlue (2017) <doi:10.18637/jss.v074.i02>
or Robitzsch and George (2019, <doi:10.1007/978-3-030-05584-4_26>)
for further details on estimation and the package structure.
For tutorial [...truncated...]
Author: Alexander Robitzsch [aut, cre], Thomas Kiefer [aut],
Ann Cathrice George [aut], Ali Uenlue [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between CDM versions 8.1-12 dated 2022-05-13 and 8.2-6 dated 2022-08-25
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- R/RcppExports.R | 2 +- README.md | 3 +++ build/partial.rdb |binary inst/NEWS | 10 ++++++++++ man/discrim.index.Rd | 14 +++++++------- man/gdina.Rd | 12 ++++++------ src/RcppExports.cpp | 2 +- src/init.c | 2 +- 10 files changed, 42 insertions(+), 29 deletions(-)
Title: bartMachine JARs
Description: These are bartMachine's Java dependency libraries. Note: this package has no functionality of its own and should not be installed as a standalone package without bartMachine.
Author: Adam Kapelner and Justin Bleich , see COPYRIGHTS file for the authors of the java libraries
Maintainer: Adam Kapelner <kapelner@qc.cuny.edu>
Diff between bartMachineJARs versions 1.1 dated 2018-03-02 and 1.2 dated 2022-08-25
bartMachineJARs-1.1/bartMachineJARs/inst/java/trove-3.0.3.jar |only bartMachineJARs-1.2/bartMachineJARs/DESCRIPTION | 10 +++++----- bartMachineJARs-1.2/bartMachineJARs/MD5 | 4 ++-- bartMachineJARs-1.2/bartMachineJARs/inst/java/fastutil-core-8.5.8.jar |only 4 files changed, 7 insertions(+), 7 deletions(-)
More information about bartMachineJARs at CRAN
Permanent link
Title: Tidy RSS for R
Description: With the objective of including data from RSS feeds into your analysis,
'tidyRSS' parses RSS, Atom and JSON feeds and returns a tidy data frame.
Author: Robert Myles McDonnell [aut, cre],
Jonathan Carroll [ctb],
Mike Smith [ctb],
Joseph Stachelek [ctb],
Chung-hong Chan [ctb]
Maintainer: Robert Myles McDonnell <robertmylesmcdonnell@gmail.com>
Diff between tidyRSS versions 2.0.5 dated 2022-05-29 and 2.0.6 dated 2022-08-25
DESCRIPTION | 12 +++++++----- MD5 | 11 ++++++----- NEWS.md | 6 ++++++ R/rss_parse.R | 2 +- R/utils.R | 7 +++++++ tests/testthat/test_general.R | 4 ++++ tests/testthat/ws_catalog.rss.xml |only 7 files changed, 31 insertions(+), 11 deletions(-)
Title: Repeated Measures Correlation
Description: Compute the repeated measures correlation, a statistical technique
for determining the overall within-individual relationship among paired measures
assessed on two or more occasions, first introduced by Bland and Altman (1995).
Includes functions for diagnostics, p-value, effect size with confidence
interval including optional bootstrapping, as well as graphing. Also includes
several example datasets. For more details, see the web documentation
<https://lmarusich.github.io/rmcorr/index.html> and the
original paper: Bakdash and Marusich (2017) <doi:10.3389/fpsyg.2017.00456>.
Author: Jonathan Z. Bakdash [aut] ,
Laura R. Marusich [aut, cre]
Maintainer: Laura R. Marusich <lmarusich@gmail.com>
Diff between rmcorr versions 0.5.0 dated 2022-08-08 and 0.5.2 dated 2022-08-25
DESCRIPTION | 10 - MD5 | 48 +++-- NEWS.md | 8 R/data.R | 91 ++-------- README.md | 2 build/partial.rdb |binary build/vignette.rds |binary inst/doc/FAQ_and_limitations.R | 3 inst/doc/FAQ_and_limitations.Rmd | 111 ++++++++++-- inst/doc/FAQ_and_limitations.html | 213 +++++++++++++++++------- inst/doc/New_rmcorr_paper_analyses_figures.Rmd | 2 inst/doc/New_rmcorr_paper_analyses_figures.html | 6 inst/doc/compcor.R |only inst/doc/compcor.Rmd |only inst/doc/compcor.html |only inst/doc/rmcorr_mat.R |only inst/doc/rmcorr_mat.Rmd |only inst/doc/rmcorr_mat.html |only man/bland1995.Rd | 6 man/figures/Gpower_approx_df.jpg |only man/figures/Gpower_exact_df.jpg |only man/gilden2010.Rd | 8 man/marusich2016_exp2.Rd | 8 man/raz2005.Rd | 8 man/twedt_dist_measures.Rd | 70 +------ vignettes/FAQ_and_limitations.Rmd | 111 ++++++++++-- vignettes/Gpower_approx_df.jpg |only vignettes/Gpower_exact_df.jpg |only vignettes/New_rmcorr_paper_analyses_figures.Rmd | 2 vignettes/compcor.Rmd |only vignettes/rmcorr_mat.Rmd |only 31 files changed, 444 insertions(+), 263 deletions(-)
Title: Access, Retrieve, and Work with Canadian Census Data and
Geography
Description: Integrated, convenient, and uniform access to Canadian
Census data and geography retrieved using the 'CensusMapper' API. This package produces analysis-ready
tidy data frames and spatial data in multiple formats, as well as convenience functions
for working with Census variables, variable hierarchies, and region selection. API
keys are freely available with free registration at <https://censusmapper.ca/api>.
Census data and boundary geometries are reproduced and distributed on an "as
is" basis with the permission of Statistics Canada (Statistics Canada 2001; 2006;
2011; 2016; 2021).
Author: Jens von Bergmann [aut] ,
Dmitry Shkolnik [aut, cre] ,
Aaron Jacobs [aut]
Maintainer: Dmitry Shkolnik <shkolnikd@gmail.com>
Diff between cancensus versions 0.5.2 dated 2022-08-19 and 0.5.3 dated 2022-08-25
DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- NEWS.md | 11 +++++++---- R/cancensus.R | 25 ++++++++++++++++++++----- R/helpers.R | 1 + R/recalled_data.R | 4 ++-- R/vector_discovery.R | 3 +-- README.md | 6 +++--- man/find_census_vectors.Rd | 2 +- man/get_census.Rd | 2 +- 10 files changed, 48 insertions(+), 30 deletions(-)
Title: Breeding Program Simulations
Description: The successor to the 'AlphaSim' software for breeding program
simulation [Faux et al. (2016) <doi:10.3835/plantgenome2016.02.0013>].
Used for stochastic simulations of breeding programs to the level of DNA
sequence for every individual. Contained is a wide range of functions for
modeling common tasks in a breeding program, such as selection and crossing.
These functions allow for constructing simulations of highly complex plant and
animal breeding programs via scripting in the R software environment. Such
simulations can be used to evaluate overall breeding program performance and
conduct research into breeding program design, such as implementation of
genomic selection. Included is the 'Markovian Coalescent Simulator' ('MaCS')
for fast simulation of biallelic sequences according to a population
demographic history [Chen et al. (2009) <doi:10.1101/gr.083634.108>].
Author: Chris Gaynor [aut, cre] ,
Gregor Gorjanc [ctb] ,
John Hickey [ctb] ,
Daniel Money [ctb] ,
David Wilson [ctb],
Thiago Oliveira [ctb]
Maintainer: Chris Gaynor <gaynor.robert@hotmail.com>
Diff between AlphaSimR versions 1.2.1 dated 2022-07-05 and 1.3.1 dated 2022-08-25
AlphaSimR-1.2.1/AlphaSimR/NEWS |only AlphaSimR-1.3.1/AlphaSimR/DESCRIPTION | 17 AlphaSimR-1.3.1/AlphaSimR/MD5 | 140 +-- AlphaSimR-1.3.1/AlphaSimR/NAMESPACE | 12 AlphaSimR-1.3.1/AlphaSimR/NEWS.md |only AlphaSimR-1.3.1/AlphaSimR/R/AlphaSimR.R | 1 AlphaSimR-1.3.1/AlphaSimR/R/Class-HybridPop.R | 13 AlphaSimR-1.3.1/AlphaSimR/R/Class-LociMap.R | 72 - AlphaSimR-1.3.1/AlphaSimR/R/Class-Pop.R | 343 +++++--- AlphaSimR-1.3.1/AlphaSimR/R/Class-SimParam.R | 891 +++++++++++---------- AlphaSimR-1.3.1/AlphaSimR/R/GS.R | 86 -- AlphaSimR-1.3.1/AlphaSimR/R/RcppExports.R | 40 AlphaSimR-1.3.1/AlphaSimR/R/founderPop.R | 157 +++ AlphaSimR-1.3.1/AlphaSimR/R/hybrids.R | 119 -- AlphaSimR-1.3.1/AlphaSimR/R/mergePops.R | 5 AlphaSimR-1.3.1/AlphaSimR/R/misc.R | 40 AlphaSimR-1.3.1/AlphaSimR/R/phenotypes.R | 178 ++-- AlphaSimR-1.3.1/AlphaSimR/R/pullGeno.R | 303 +++++-- AlphaSimR-1.3.1/AlphaSimR/README.md | 1 AlphaSimR-1.3.1/AlphaSimR/build/partial.rdb |only AlphaSimR-1.3.1/AlphaSimR/build/vignette.rds |binary AlphaSimR-1.3.1/AlphaSimR/inst/REFERENCES.bib |only AlphaSimR-1.3.1/AlphaSimR/inst/doc/intro.html | 6 AlphaSimR-1.3.1/AlphaSimR/inst/doc/traits.pdf |binary AlphaSimR-1.3.1/AlphaSimR/man/AlphaSimR-package.Rd | 2 AlphaSimR-1.3.1/AlphaSimR/man/HybridPop-class.Rd | 10 AlphaSimR-1.3.1/AlphaSimR/man/MapPop-class.Rd | 14 AlphaSimR-1.3.1/AlphaSimR/man/MegaPop-class.Rd | 14 AlphaSimR-1.3.1/AlphaSimR/man/NamedMapPop-class.Rd | 10 AlphaSimR-1.3.1/AlphaSimR/man/Pop-class.Rd | 21 AlphaSimR-1.3.1/AlphaSimR/man/RRBLUP.Rd | 4 AlphaSimR-1.3.1/AlphaSimR/man/RRBLUP2.Rd | 8 AlphaSimR-1.3.1/AlphaSimR/man/RRBLUP_D.Rd | 4 AlphaSimR-1.3.1/AlphaSimR/man/RRBLUP_D2.Rd | 4 AlphaSimR-1.3.1/AlphaSimR/man/RRBLUP_GCA.Rd | 4 AlphaSimR-1.3.1/AlphaSimR/man/RRBLUP_GCA2.Rd | 4 AlphaSimR-1.3.1/AlphaSimR/man/RRBLUP_SCA.Rd | 4 AlphaSimR-1.3.1/AlphaSimR/man/RRBLUP_SCA2.Rd | 4 AlphaSimR-1.3.1/AlphaSimR/man/RawPop-class.Rd | 14 AlphaSimR-1.3.1/AlphaSimR/man/SimParam.Rd | 260 +++--- AlphaSimR-1.3.1/AlphaSimR/man/TraitA-class.Rd | 2 AlphaSimR-1.3.1/AlphaSimR/man/TraitA2-class.Rd | 4 AlphaSimR-1.3.1/AlphaSimR/man/TraitA2D-class.Rd | 2 AlphaSimR-1.3.1/AlphaSimR/man/TraitAD-class.Rd | 2 AlphaSimR-1.3.1/AlphaSimR/man/TraitADE-class.Rd | 2 AlphaSimR-1.3.1/AlphaSimR/man/TraitADEG-class.Rd | 2 AlphaSimR-1.3.1/AlphaSimR/man/TraitADG-class.Rd | 2 AlphaSimR-1.3.1/AlphaSimR/man/TraitAE-class.Rd | 2 AlphaSimR-1.3.1/AlphaSimR/man/TraitAEG-class.Rd | 2 AlphaSimR-1.3.1/AlphaSimR/man/TraitAG-class.Rd | 2 AlphaSimR-1.3.1/AlphaSimR/man/addSegSite.Rd |only AlphaSimR-1.3.1/AlphaSimR/man/cChr.Rd | 6 AlphaSimR-1.3.1/AlphaSimR/man/dot-newPop.Rd | 4 AlphaSimR-1.3.1/AlphaSimR/man/getGenMap.Rd |only AlphaSimR-1.3.1/AlphaSimR/man/getPed.Rd |only AlphaSimR-1.3.1/AlphaSimR/man/isFemale.Rd | 4 AlphaSimR-1.3.1/AlphaSimR/man/isPop.Rd |only AlphaSimR-1.3.1/AlphaSimR/man/newEmptyPop.Rd |only AlphaSimR-1.3.1/AlphaSimR/man/newMegaPop.Rd | 5 AlphaSimR-1.3.1/AlphaSimR/man/newPop.Rd | 11 AlphaSimR-1.3.1/AlphaSimR/man/pullMarkerGeno.Rd | 6 AlphaSimR-1.3.1/AlphaSimR/man/pullMarkerHaplo.Rd | 6 AlphaSimR-1.3.1/AlphaSimR/man/pullSegSiteGeno.Rd | 7 AlphaSimR-1.3.1/AlphaSimR/man/pullSegSiteHaplo.Rd | 7 AlphaSimR-1.3.1/AlphaSimR/man/resetPop.Rd | 2 AlphaSimR-1.3.1/AlphaSimR/man/runMacs.Rd | 23 AlphaSimR-1.3.1/AlphaSimR/man/runMacs2.Rd | 12 AlphaSimR-1.3.1/AlphaSimR/man/setMarkerHaplo.Rd |only AlphaSimR-1.3.1/AlphaSimR/man/setPheno.Rd | 15 AlphaSimR-1.3.1/AlphaSimR/man/setPhenoGCA.Rd | 42 AlphaSimR-1.3.1/AlphaSimR/man/setPhenoProgTest.Rd | 20 AlphaSimR-1.3.1/AlphaSimR/src/MME.cpp | 163 +-- AlphaSimR-1.3.1/AlphaSimR/src/RcppExports.cpp | 106 +- AlphaSimR-1.3.1/AlphaSimR/src/datastructures.cpp | 5 AlphaSimR-1.3.1/AlphaSimR/src/getGeno.cpp | 49 + AlphaSimR-1.3.1/AlphaSimR/vignettes/AlphaSimR.bib | 2 76 files changed, 1995 insertions(+), 1327 deletions(-)
Title: R Interface to Global Biotic Interactions
Description: A programmatic interface to the web service methods
provided by Global Biotic Interactions (GloBI)
(<https://www.globalbioticinteractions.org/>). GloBI provides
access to spatial-temporal species interaction records from
sources all over the world. rglobi provides methods to search
species interactions by location, interaction type, and
taxonomic name. In addition, it supports Cypher, a graph query
language, to allow for executing custom queries on the GloBI
aggregate species interaction data set.
Author: Jorrit Poelen [aut, cre],
Stephen Gosnell [aut],
Sergey Slyusarev [aut],
Helen Waters [aut]
Maintainer: Jorrit Poelen <jhpoelen@xs4all.nl>
Diff between rglobi versions 0.2.27 dated 2021-10-18 and 0.2.28 dated 2022-08-25
DESCRIPTION | 15 +-- MD5 | 10 +- NEWS | 202 ++++++++++---------------------------------- R/rglobi.R | 9 + build/vignette.rds |binary tests/testthat/test-globi.R | 12 +- 6 files changed, 80 insertions(+), 168 deletions(-)
Title: Network-Based Genome Wide Association Studies
Description: A multi-core R package that contains a set of tools based on copula graphical
models for accomplishing the three interrelated goals in genetics and genomics in an
unified way: (1) linkage map construction, (2) constructing linkage disequilibrium
networks, and (3) exploring high-dimensional genotype-phenotype network and genotype-
phenotype-environment interactions networks.
The 'netgwas' package can deal with biparental inbreeding and outbreeding species with
any ploidy level, namely diploid (2 sets of chromosomes), triploid (3 sets of chromosomes),
tetraploid (4 sets of chromosomes) and so on. We target on high-dimensional data where
number of variables p is considerably larger than number of sample sizes (p >> n).
The computations is memory-optimized using the sparse matrix output. The 'netgwas'
implements the methodological developments in Behrouzi and Wit (2017)
<doi:10.1111/rssc.12287> and Behrouzi and Wit (2017) <doi:10.1093/bioinformatics/bty777>.
Author: Pariya Behrouzi [aut, cre] ,
Ernst C. Wit [ctb]
Maintainer: Pariya Behrouzi <pariya.behrouzi@gmail.com>
Diff between netgwas versions 1.14 dated 2022-08-17 and 1.14.1 dated 2022-08-25
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/buildMap.R | 6 +++--- man/buildMap.Rd | 2 +- man/netmap.Rd | 4 ++-- man/tetraPotato.Rd | 2 +- 6 files changed, 16 insertions(+), 16 deletions(-)
Title: Fuzzy and Non-Fuzzy Classifiers
Description: It provides classifiers which can be used for discrete variables and for continuous variables based on the Naive Bayes and Fuzzy Naive Bayes hypothesis. Those methods were developed by researchers belong to the 'Laboratory of Technologies for Virtual Teaching and Statistics (LabTEVE)' (<http://www.de.ufpb.br/~labteve/>) and 'Laboratory of Applied Statistics to Image Processing and Geoprocessing (LEAPIG)' (<http://www.de.ufpb.br/~leapig/>) at 'Federal University of Paraiba, Brazil'. They considered some statistical distributions and their papers were published in the scientific literature, as for instance, the Gaussian classifier using fuzzy parameters, proposed by 'Moraes, Ferreira and Machado' (2021) <doi:10.1007/s40815-020-00936-4>.
Author: Jodavid Ferreira [aut, cre] ,
Ronei Moraes [ctb] ,
Arthur Ricardo [ctb]
Maintainer: Jodavid Ferreira <jodavid@protonmail.com>
Diff between FuzzyClass versions 0.1.1 dated 2022-05-27 and 0.1.2 dated 2022-08-25
DESCRIPTION | 17 - MD5 | 46 ++-- NAMESPACE | 5 NEWS.md | 8 R/FuzzyBetaNaiveBayes.R | 2 R/FuzzyBinomialNaiveBayes.R | 2 R/FuzzyGammaNaiveBayes.R | 2 R/FuzzyGaussianNaiveBayes.R | 4 R/FuzzyNaiveBayes.R | 4 R/FuzzyTrapeNaiveBayes.R |only R/FuzzyTriangNaiveBayes.R | 8 R/getMembershipsTrapezoidal.R | 13 - README.md | 399 ++++++++++++++------------------------ build/partial.rdb |binary data/HouseVotes84.rda |only inst/REFERENCES.bib | 9 inst/WORDLIST |only man/FuzzyBetaNaiveBayes.Rd | 2 man/FuzzyBinomialNaiveBayes.Rd | 2 man/FuzzyClass-package.Rd | 4 man/FuzzyGammaNaiveBayes.Rd | 2 man/FuzzyGaussianNaiveBayes.Rd | 4 man/FuzzyNaiveBayes.Rd | 2 man/FuzzyTrapezoidalNaiveBayes.Rd |only man/FuzzyTriangularNaiveBayes.Rd | 5 man/HouseVotes84.Rd |only tests |only 27 files changed, 237 insertions(+), 303 deletions(-)
Title: Visualization and Imputation of Missing Values
Description: New tools for the visualization of missing and/or imputed values
are introduced, which can be used for exploring the data and the structure of
the missing and/or imputed values. Depending on this structure of the missing
values, the corresponding methods may help to identify the mechanism generating
the missing values and allows to explore the data including missing values.
In addition, the quality of imputation can be visually explored using various
univariate, bivariate, multiple and multivariate plot methods. A graphical user
interface available in the separate package VIMGUI allows an easy handling of
the implemented plot methods.
Author: Matthias Templ [aut, cre],
Alexander Kowarik [aut] ,
Andreas Alfons [aut],
Gregor de Cillia [aut],
Bernd Prantner [ctb],
Wolfgang Rannetbauer [aut]
Maintainer: Matthias Templ <matthias.templ@gmail.com>
Diff between VIM versions 6.1.1 dated 2021-07-22 and 6.2.2 dated 2022-08-25
VIM-6.1.1/VIM/tests/testthat |only VIM-6.1.1/VIM/tests/testthat.R |only VIM-6.2.2/VIM/DESCRIPTION | 10 VIM-6.2.2/VIM/MD5 | 123 - VIM-6.2.2/VIM/NAMESPACE | 1 VIM-6.2.2/VIM/R/VIM-package.R | 27 VIM-6.2.2/VIM/R/colSequence.R | 216 +-- VIM-6.2.2/VIM/R/impPCA.R |only VIM-6.2.2/VIM/R/irmi.R | 8 VIM-6.2.2/VIM/R/kNN.R | 3 VIM-6.2.2/VIM/R/matrixplot.R | 2 VIM-6.2.2/VIM/R/medianSamp.R | 1 VIM-6.2.2/VIM/R/parcoordMiss.R | 2 VIM-6.2.2/VIM/R/sampleCat.R | 1 VIM-6.2.2/VIM/R/scattmatrixMiss.R | 2 VIM-6.2.2/VIM/R/utils.R | 2 VIM-6.2.2/VIM/build/vignette.rds |binary VIM-6.2.2/VIM/data/Animals_na.rda |only VIM-6.2.2/VIM/data/SBS5242.rda |binary VIM-6.2.2/VIM/data/bcancer.rda |binary VIM-6.2.2/VIM/data/brittleness.rda |binary VIM-6.2.2/VIM/data/chorizonDL.rda |binary VIM-6.2.2/VIM/data/colic.rda |binary VIM-6.2.2/VIM/data/collisions.rda |binary VIM-6.2.2/VIM/data/diabetes.rda |binary VIM-6.2.2/VIM/data/food.rda |binary VIM-6.2.2/VIM/data/kola.background.rda |binary VIM-6.2.2/VIM/data/sleep.rda |binary VIM-6.2.2/VIM/data/tao.rda |binary VIM-6.2.2/VIM/data/testdata.RData |binary VIM-6.2.2/VIM/data/toydataMiss.rda |binary VIM-6.2.2/VIM/data/wine.rda |binary VIM-6.2.2/VIM/inst/doc/VIM.html | 374 ++++- VIM-6.2.2/VIM/inst/doc/VisualImp.html | 441 +++++- VIM-6.2.2/VIM/inst/doc/donorImp.html | 2125 +++++++++++++++++++++++++++++++-- VIM-6.2.2/VIM/inst/doc/irmi.html | 2124 +++++++++++++++++++++++++++++++- VIM-6.2.2/VIM/inst/doc/modelImp.html | 2122 +++++++++++++++++++++++++++++++- VIM-6.2.2/VIM/inst/tinytest |only VIM-6.2.2/VIM/man/Animals_na.Rd |only VIM-6.2.2/VIM/man/colSequence.Rd | 2 VIM-6.2.2/VIM/man/hotdeck.Rd | 5 VIM-6.2.2/VIM/man/impPCA.Rd |only VIM-6.2.2/VIM/man/irmi.Rd | 5 VIM-6.2.2/VIM/man/kNN.Rd | 5 VIM-6.2.2/VIM/man/matchImpute.Rd | 5 VIM-6.2.2/VIM/man/matrixplot.Rd | 2 VIM-6.2.2/VIM/man/medianSamp.Rd | 12 VIM-6.2.2/VIM/man/rangerImpute.Rd | 5 VIM-6.2.2/VIM/man/regressionImp.Rd | 5 VIM-6.2.2/VIM/man/sampleCat.Rd | 12 VIM-6.2.2/VIM/man/tao.Rd | 3 VIM-6.2.2/VIM/src/RcppExports.cpp | 5 VIM-6.2.2/VIM/tests/tinytest.R |only 53 files changed, 7036 insertions(+), 614 deletions(-)
Title: Read and Write ESRI Shapefiles
Description: Functions to read and write ESRI shapefiles.
Author: Ben Stabler <benstabler@yahoo.com>
Maintainer: Ben Stabler <benstabler@yahoo.com>
Diff between shapefiles versions 0.7.1 dated 2022-08-24 and 0.7.2 dated 2022-08-25
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/shapefiles.R | 4 ++-- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Representing Graphs as 'graph6', 'digraph6' or 'sparse6' Strings
Description: Encode network data as strings of printable ASCII characters. Implemented
functions include encoding and decoding adjacency matrices, edgelists, igraph, and
network objects to/from formats 'graph6', 'sparse6', and 'digraph6'. The formats and
methods are described in McKay, B.D. and Piperno, A (2014)
<doi:10.1016/j.jsc.2013.09.003>.
Author: Michal Bojanowski [aut, cre] ,
David Schoch [aut]
Maintainer: Michal Bojanowski <michal2992@gmail.com>
Diff between rgraph6 versions 2.0-1 dated 2022-03-09 and 2.0-2 dated 2022-08-25
DESCRIPTION | 8 ++--- MD5 | 20 ++++++------ NEWS.md | 10 ++++++ build/partial.rdb |binary build/vignette.rds |binary inst/doc/rgraph6.html | 78 +++++++++++++++++++++++++++++++------------------ man/as_digraph6.Rd | 12 +++---- man/as_graph6.Rd | 12 +++---- man/as_sparse6.Rd | 12 +++---- man/graph_as_text.Rd | 6 +-- man/rgraph6-package.Rd | 16 +++++++--- 11 files changed, 107 insertions(+), 67 deletions(-)
Title: Enrichment Analysis Utilizing Active Subnetworks
Description: Enrichment analysis enables researchers to uncover mechanisms
underlying a phenotype. However, conventional methods for enrichment
analysis do not take into account protein-protein interaction information,
resulting in incomplete conclusions. pathfindR is a tool for enrichment
analysis utilizing active subnetworks. The main function identifies active
subnetworks in a protein-protein interaction network using a user-provided
list of genes and associated p values. It then performs enrichment analyses
on the identified subnetworks, identifying enriched terms (i.e. pathways or,
more broadly, gene sets) that possibly underlie the phenotype of interest.
pathfindR also offers functionalities to cluster the enriched terms and
identify representative terms in each cluster, to score the enriched terms
per sample and to visualize analysis results. The enrichment, clustering and
other methods implemented in pathfindR are described in detail in
Ulgen E, Ozisik O, Sezerman OU. 2019. pathfindR: An R [...truncated...]
Author: Ege Ulgen [cre, cph] ,
Ozan Ozisik [aut]
Maintainer: Ege Ulgen <egeulgen@gmail.com>
Diff between pathfindR versions 1.6.3 dated 2021-11-15 and 1.6.4 dated 2022-08-25
DESCRIPTION | 8 MD5 | 66 +- NEWS.md | 13 R/clustering_functions.R | 13 R/core_functions.R | 17 R/data_generation.R | 4 R/visualization_functions.R | 126 +++-- build/vignette.rds |binary inst/doc/comparing_results.html | 233 +++++++++ inst/doc/intro_vignette.html | 618 ++++++++++++++++++++++---- inst/doc/manual_execution.html | 298 +++++++++++- inst/doc/non_hs_analysis.R | 4 inst/doc/non_hs_analysis.Rmd | 4 inst/doc/non_hs_analysis.html | 330 ++++++++++++- inst/doc/obtain_data.html | 251 +++++++++- inst/doc/visualization_vignette.html | 293 +++++++++++- man/UpSet_plot.Rd | 4 man/active_snw_search.Rd | 2 man/cluster_graph_vis.Rd | 8 man/color_kegg_pathway.Rd | 4 man/enrichment_analyses.Rd | 2 man/fetch_gene_set.Rd | 2 man/get_biogrid_pin.Rd | 4 man/input_processing.Rd | 2 man/return_pin_path.Rd | 2 man/run_pathfindR.Rd | 4 man/term_gene_heatmap.Rd | 11 man/visualize_active_subnetworks.Rd | 2 man/visualize_hsa_KEGG.Rd | 4 man/visualize_term_interactions.Rd | 7 man/visualize_terms.Rd | 5 tests/testthat/test-data_generation.R | 7 tests/testthat/test-visualization_functions.R | 33 - vignettes/non_hs_analysis.Rmd | 4 34 files changed, 2054 insertions(+), 331 deletions(-)
Title: Bayesian Logistic Regression for Oncology Dose-Escalation Trials
Description: Bayesian logistic regression model with optional
EXchangeability-NonEXchangeability parameter modelling for flexible
borrowing from historical or concurrent data-sources. The safety model
can guide dose-escalation decisions for adaptive oncology Phase I
dose-escalation trials which involve an arbitrary number of
drugs. Please refer to Neuenschwander et al. (2008)
<doi:10.1002/sim.3230> and Neuenschwander et al. (2016)
<doi:10.1080/19466315.2016.1174149> for details on the methodology.
Author: Novartis Pharma AG [cph],
Sebastian Weber [aut, cre],
Lukas A. Widmer [aut],
Andrew Bean [aut],
Trustees of Columbia University [cph]
Maintainer: Sebastian Weber <sebastian.weber@novartis.com>
Diff between OncoBayes2 versions 0.8-6 dated 2022-05-02 and 0.8-7 dated 2022-08-25
OncoBayes2-0.8-6/OncoBayes2/R/stan_tools.R |only OncoBayes2-0.8-6/OncoBayes2/inst/NEWS |only OncoBayes2-0.8-6/OncoBayes2/man/dot-marginSums.Rd |only OncoBayes2-0.8-6/OncoBayes2/man/dot-proportions.Rd |only OncoBayes2-0.8-6/OncoBayes2/man/log_sum_exp.Rd |only OncoBayes2-0.8-6/OncoBayes2/tools |only OncoBayes2-0.8-7/OncoBayes2/DESCRIPTION | 18 OncoBayes2-0.8-7/OncoBayes2/MD5 | 75 OncoBayes2-0.8-7/OncoBayes2/NAMESPACE | 35 OncoBayes2-0.8-7/OncoBayes2/NEWS.md |only OncoBayes2-0.8-7/OncoBayes2/R/OncoBayes2-package.R | 6 OncoBayes2-0.8-7/OncoBayes2/R/RcppExports.R |only OncoBayes2-0.8-7/OncoBayes2/R/blrm_exnex.R | 56 OncoBayes2-0.8-7/OncoBayes2/R/blrm_trial.R | 177 +- OncoBayes2-0.8-7/OncoBayes2/R/diagnostics.R |only OncoBayes2-0.8-7/OncoBayes2/R/log_sum_exp.R | 15 OncoBayes2-0.8-7/OncoBayes2/R/pp_data.R | 96 - OncoBayes2-0.8-7/OncoBayes2/R/summary.R | 126 - OncoBayes2-0.8-7/OncoBayes2/R/sysdata.rda |binary OncoBayes2-0.8-7/OncoBayes2/R/update.R | 9 OncoBayes2-0.8-7/OncoBayes2/inst/doc/OncoBayes2.pdf |binary OncoBayes2-0.8-7/OncoBayes2/inst/doc/introduction.R | 14 OncoBayes2-0.8-7/OncoBayes2/inst/doc/introduction.Rmd | 64 OncoBayes2-0.8-7/OncoBayes2/inst/doc/introduction.html | 868 ++++++---- OncoBayes2-0.8-7/OncoBayes2/inst/sbc/calibration.md5 | 6 OncoBayes2-0.8-7/OncoBayes2/inst/sbc/make_reference_rankhist.R | 64 OncoBayes2-0.8-7/OncoBayes2/inst/sbc/sbc_example_models.R | 12 OncoBayes2-0.8-7/OncoBayes2/inst/sbc/sbc_report.R | 72 OncoBayes2-0.8-7/OncoBayes2/inst/sbc/sbc_report.html | 797 ++++++--- OncoBayes2-0.8-7/OncoBayes2/inst/sbc/sbc_tools.R | 164 + OncoBayes2-0.8-7/OncoBayes2/man/diagnostic-quantities.Rd |only OncoBayes2-0.8-7/OncoBayes2/man/summary.blrm_trial.Rd | 53 OncoBayes2-0.8-7/OncoBayes2/src/RcppExports.cpp | 24 OncoBayes2-0.8-7/OncoBayes2/src/numeric_utils.cpp |only OncoBayes2-0.8-7/OncoBayes2/tests/testthat/helper-sampling.R | 39 OncoBayes2-0.8-7/OncoBayes2/tests/testthat/test-blrm_exnex.R | 106 + OncoBayes2-0.8-7/OncoBayes2/tests/testthat/test-blrm_trial.R | 328 ++- OncoBayes2-0.8-7/OncoBayes2/tests/testthat/test-numeric_utils.R |only OncoBayes2-0.8-7/OncoBayes2/vignettes/introduction.Rmd | 64 39 files changed, 2267 insertions(+), 1021 deletions(-)
Title: Measures of Network Segregation and Homophily
Description: Segregation is a network-level property such that edges between
predefined groups of vertices are relatively less likely. Network homophily
is a individual-level tendency to form relations with people who are similar
on some attribute (e.g. gender, music taste, social status, etc.). In general
homophily leads to segregation, but segregation might arise without
homophily. This package implements descriptive indices measuring
homophily/segregation. It is a computational companion
to Bojanowski & Corten (2014) <doi:10.1016/j.socnet.2014.04.001>.
Author: Michal Bojanowski [aut, cre]
Maintainer: Michal Bojanowski <michal2992@gmail.com>
Diff between netseg versions 1.0-0 dated 2021-02-17 and 1.0-1 dated 2022-08-25
DESCRIPTION | 11 ++++++----- MD5 | 24 ++++++++++++++++-------- NEWS.md |only R/freeman.R | 2 +- R/ssi.R | 4 ++-- README.md | 7 +++---- build/partial.rdb |binary build/vignette.rds |only inst |only man/Catania.Rd | 16 +++++++++------- man/freeman.Rd | 2 +- man/netseg-package.Rd | 11 ++--------- vignettes |only 13 files changed, 40 insertions(+), 37 deletions(-)
Title: Combining Tree-Boosting with Gaussian Process and Mixed Effects
Models
Description: An R package that allows for combining tree-boosting with Gaussian process and mixed effects models. It also allows for independently doing tree-boosting as well as inference and prediction for Gaussian process and mixed effects models. See <https://github.com/fabsig/GPBoost> for more information on the software and Sigrist (2020) <arXiv:2004.02653> and Sigrist (2021) <arXiv:2105.08966> for more information on the methodology.
Author: Fabio Sigrist [aut, cre],
Benoit Jacob [cph],
Gael Guennebaud [cph],
Nicolas Carre [cph],
Pierre Zoppitelli [cph],
Gauthier Brun [cph],
Jean Ceccato [cph],
Jitse Niesen [cph],
Other authors of Eigen for the included version of Eigen [ctb, cph],
Timot [...truncated...]
Maintainer: Fabio Sigrist <fabiosigrist@gmail.com>
Diff between gpboost versions 0.7.8 dated 2022-07-08 and 0.7.9 dated 2022-08-25
DESCRIPTION | 8 MD5 | 67 ++-- NAMESPACE | 1 R/GPModel.R | 74 +++- R/gpb.Booster.R | 4 configure.ac | 2 demo/GPBoost_algorithm.R | 40 +- demo/Grabit.R | 2 demo/generalized_linear_Gaussian_process_mixed_effects_models.R | 6 man/GPModel_shared_params.Rd | 6 man/get_nested_categories.Rd |only man/predict.GPModel.Rd | 20 - man/predict.gpb.Booster.Rd | 10 src/boosting/gbdt.cpp | 25 + src/boosting/gbdt.h | 9 src/c_api.cpp | 8 src/gpboost_R.cpp | 10 src/gpboost_R.h | 6 src/include/GPBoost/re_model.h | 11 src/include/GPBoost/re_model_template.h | 19 - src/include/LightGBM/c_api.h | 8 src/include/LightGBM/config.h | 4 src/include/LightGBM/metric.h | 4 src/include/unconstrained/gd.hpp | 3 src/metric/binary_metric.hpp | 52 --- src/metric/map_metric.hpp | 2 src/metric/metric.cpp | 2 src/metric/multiclass_metric.hpp | 4 src/metric/random_effects_metric.hpp | 4 src/metric/rank_metric.hpp | 2 src/metric/regression_metric.hpp | 158 +++++++--- src/metric/xentropy_metric.hpp | 6 src/re_model.cpp | 50 +-- tests/testthat/test_GPBoost_algorithm.R | 43 ++ tests/testthat/test_GPModel_grouped_random_effects.R | 2 35 files changed, 447 insertions(+), 225 deletions(-)
Title: R API Serialization
Description: Access to the internal R serialization code is provided for
use by other packages at the C function level by using the registration of
native function mechanism. Client packages simply include a single header
file RApiSerializeAPI.h provided by this package. This packages builds on
the Rhpc package by Ei-ji Nakama and Junji Nakano which also includes a
(partial) copy of the file src/main/serialize.c from R itself. The R Core
group is the original author of the serialization code made available by
this package.
Author: Dirk Eddelbuettel, Ei-ji Nakama, Junji Nakano, and R Core
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RApiSerialize versions 0.1.1 dated 2022-08-07 and 0.1.2 dated 2022-08-25
ChangeLog | 7 +++++++ DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- inst/NEWS.Rd | 7 +++++++ src/serialize.cpp | 2 +- 5 files changed, 23 insertions(+), 9 deletions(-)
Title: Authentication, User Administration, and Hosting for 'shiny'
Apps
Description: Authentication, user administration, hosting, and additional infrastructure for 'shiny' apps.
Author: Andy Merlino [aut, cre],
Patrick Howard [aut]
Maintainer: Andy Merlino <andy.merlino@tychobra.com>
Diff between polished versions 0.6.1 dated 2022-02-24 and 0.7.0 dated 2022-08-25
polished-0.6.1/polished/R/admin_module.R |only polished-0.6.1/polished/R/sentry_ui.R |only polished-0.6.1/polished/R/two_fa_module.R |only polished-0.6.1/polished/R/verify_email_module.R |only polished-0.6.1/polished/inst/examples |only polished-0.6.1/polished/man/secure_static.Rd |only polished-0.7.0/polished/DESCRIPTION | 24 polished-0.7.0/polished/LICENSE | 2 polished-0.7.0/polished/MD5 | 132 +- polished-0.7.0/polished/NAMESPACE | 13 polished-0.7.0/polished/NEWS.md | 74 - polished-0.7.0/polished/R/admin_app.R |only polished-0.7.0/polished/R/admin_button.R | 2 polished-0.7.0/polished/R/api_02_users.R | 40 polished-0.7.0/polished/R/api_05_user_roles.R | 18 polished-0.7.0/polished/R/api_06_sessions.R | 8 polished-0.7.0/polished/R/auth_email.R | 4 polished-0.7.0/polished/R/auth_social.R | 61 - polished-0.7.0/polished/R/auth_utils.R | 4 polished-0.7.0/polished/R/deploy_app.R | 21 polished-0.7.0/polished/R/polished_config.R | 24 polished-0.7.0/polished/R/secure_rmd.R | 2 polished-0.7.0/polished/R/secure_server.R | 283 ++---- polished-0.7.0/polished/R/secure_static.R | 4 polished-0.7.0/polished/R/secure_ui.R | 191 ++-- polished-0.7.0/polished/R/send_password_reset_email_module.R | 15 polished-0.7.0/polished/R/sign_in_components.R | 2 polished-0.7.0/polished/R/sign_in_module.R | 23 polished-0.7.0/polished/R/sign_in_module_2.R | 8 polished-0.7.0/polished/R/sign_in_ui_default.R | 6 polished-0.7.0/polished/R/two_fa_app.R |only polished-0.7.0/polished/R/user_access_module.R | 30 polished-0.7.0/polished/R/user_edit_module.R | 13 polished-0.7.0/polished/R/utils.R | 23 polished-0.7.0/polished/R/verify_email_app.R |only polished-0.7.0/polished/build/vignette.rds |binary polished-0.7.0/polished/inst/assets/js/two_fa.js |only polished-0.7.0/polished/inst/assets/js/two_fa_module.js |only polished-0.7.0/polished/inst/doc/api_wrappers.Rmd | 1 polished-0.7.0/polished/inst/doc/api_wrappers.html | 207 ++++ polished-0.7.0/polished/inst/doc/create_custom_sign_in_pages.R | 80 - polished-0.7.0/polished/inst/doc/create_custom_sign_in_pages.Rmd | 82 - polished-0.7.0/polished/inst/doc/create_custom_sign_in_pages.html | 458 +++++++--- polished-0.7.0/polished/man/add_user.Rd | 2 polished-0.7.0/polished/man/add_user_role.Rd | 15 polished-0.7.0/polished/man/admin_server.Rd |only polished-0.7.0/polished/man/admin_ui.Rd |only polished-0.7.0/polished/man/delete_user.Rd | 2 polished-0.7.0/polished/man/deploy_app.Rd | 2 polished-0.7.0/polished/man/get_users.Rd | 11 polished-0.7.0/polished/man/normalize_ui.Rd |only polished-0.7.0/polished/man/polished_config.Rd | 14 polished-0.7.0/polished/man/secure_server.Rd | 21 polished-0.7.0/polished/man/secure_ui.Rd | 21 polished-0.7.0/polished/man/send_password_reset_email_module_ui.Rd | 4 polished-0.7.0/polished/man/sign_in_js.Rd | 2 polished-0.7.0/polished/man/sign_in_module_ui.Rd | 10 polished-0.7.0/polished/man/sign_in_ui_default.Rd | 5 polished-0.7.0/polished/man/update_user.Rd |only polished-0.7.0/polished/man/user_access_module.Rd |only polished-0.7.0/polished/man/user_access_module_ui.Rd |only polished-0.7.0/polished/tests/testthat/setup-api-options.R | 8 polished-0.7.0/polished/tests/testthat/test-api-02-users.R | 29 polished-0.7.0/polished/vignettes/api_wrappers.Rmd | 1 polished-0.7.0/polished/vignettes/create_custom_sign_in_pages.Rmd | 82 - 65 files changed, 1278 insertions(+), 806 deletions(-)
Title: Tuning for 'mlr3'
Description: Implements methods for hyperparameter tuning with 'mlr3',
e.g. grid search, random search, generalized simulated annealing and
iterated racing. Various termination criteria can be set and
combined. The class 'AutoTuner' provides a convenient way to perform
nested resampling in combination with 'mlr3'.
Author: Marc Becker [cre, aut] ,
Michel Lang [aut] ,
Jakob Richter [aut] ,
Bernd Bischl [aut] ,
Daniel Schalk [aut]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3tuning versions 0.13.1 dated 2022-05-03 and 0.14.0 dated 2022-08-25
DESCRIPTION | 12 +-- MD5 | 52 +++++++-------- NEWS.md | 5 + R/Tuner.R | 5 + R/TunerFromOptimizer.R | 7 +- R/TunerGenSA.R | 7 +- R/TuningInstanceMulticrit.R | 13 ++- R/TuningInstanceSingleCrit.R | 16 ++-- R/helper.R | 28 +++++++- R/tune.R | 15 +--- build/partial.rdb |binary man/ArchiveTuning.Rd | 74 +++++++++++----------- man/AutoTuner.Rd | 52 +++++++-------- man/ObjectiveTuning.Rd | 34 +++++----- man/Tuner.Rd | 36 +++++----- man/TunerFromOptimizer.Rd | 36 +++++----- man/TuningInstanceMultiCrit.Rd | 51 ++++++++------- man/TuningInstanceSingleCrit.Rd | 51 ++++++++------- man/mlr_tuners_cmaes.Rd | 38 +++++------ man/mlr_tuners_design_points.Rd | 38 +++++------ man/mlr_tuners_gensa.Rd | 41 ++++++------ man/mlr_tuners_grid_search.Rd | 38 +++++------ man/mlr_tuners_irace.Rd | 42 ++++++------ man/mlr_tuners_nloptr.Rd | 38 +++++------ man/mlr_tuners_random_search.Rd | 38 +++++------ man/tune.Rd | 5 + tests/testthat/test_tune.R | 134 ++++++++++++++++++++++++++++++++++++++++ 27 files changed, 554 insertions(+), 352 deletions(-)
Title: Hyperband for 'mlr3'
Description: Implements hyperband method for hyperparameter
tuning. Various termination criteria can be set and combined. The
class 'AutoTuner' provides a convenient way to perform nested
resampling in combination with 'mlr3'. The hyperband algorithm was
proposed by Lisha Li, Kevin Jamieson, Giulia DeSalvo, Afshin
Rostamizadeh and Ameet Talwalkar (2018) <arXiv:1603.06560>.
Author: Marc Becker [aut, cre] ,
Sebastian Gruber [aut] ,
Jakob Richter [aut] ,
Julia Moosbauer [aut] ,
Bernd Bischl [aut]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3hyperband versions 0.4.1 dated 2022-05-04 and 0.4.2 dated 2022-08-25
DESCRIPTION | 8 ++--- MD5 | 14 +++++----- NEWS.md | 4 ++ man/mlr3hyperband-package.Rd | 2 - man/mlr_optimizers_hyperband.Rd | 43 +++++++++++++++++-------------- man/mlr_optimizers_successive_halving.Rd | 37 ++++++++++++++------------ man/mlr_tuners_hyperband.Rd | 43 +++++++++++++++++-------------- man/mlr_tuners_successive_halving.Rd | 37 ++++++++++++++------------ 8 files changed, 104 insertions(+), 84 deletions(-)
Title: Poisson Lognormal Models
Description: The Poisson-lognormal model and variants (Chiquet, Mariadassou and Robin,
2021 <doi:10.3389/fevo.2021.588292>) can be used for
a variety of multivariate problems when count data are at play, including
principal component analysis for count data, discriminant analysis, model-based clustering and
network inference. Implements variational algorithms to fit such models accompanied with a set of
functions for visualization and diagnostic.
Author: Julien Chiquet [aut, cre] ,
Mahendra Mariadassou [aut] ,
Stephane Robin [ctb],
Giovanni Poggiato [ctb],
Francois Gindraud [aut]
Maintainer: Julien Chiquet <julien.chiquet@inrae.fr>
Diff between PLNmodels versions 0.11.6 dated 2022-02-01 and 0.11.7 dated 2022-08-25
DESCRIPTION | 12 MD5 | 95 ++-- NAMESPACE | 2 NEWS.md | 7 R/PLN.R | 7 R/PLNLDA.R | 12 R/PLNLDAfit-class.R | 4 R/PLNfamily-class.R | 2 R/PLNfit-S3methods.R | 36 + R/PLNfit-class.R | 126 ++++- R/RcppExports.R | 4 R/utils.R | 15 build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 12 inst/doc/Import_data.html | 601 +++++++++++++++++++++----- inst/doc/PLN.html | 443 ++++++++++++++++--- inst/doc/PLNLDA.html | 801 +++++++++++++++++++++++++---------- inst/doc/PLNPCA.html | 675 ++++++++++++++++++++++------- inst/doc/PLNmixture.html | 557 +++++++++++++++++++----- inst/doc/PLNnetwork.html | 511 +++++++++++++++++++--- inst/doc/Trichoptera.html | 360 ++++++++++++++- man/PLN.Rd | 7 man/PLNLDAfit.Rd | 89 +-- man/PLNPCAfamily.Rd | 62 +- man/PLNPCAfit.Rd | 103 ++-- man/PLNfamily.Rd | 51 +- man/PLNfit.Rd | 130 +++-- man/PLNmixturefamily.Rd | 74 +-- man/PLNmixturefit.Rd | 54 +- man/PLNnetworkfamily.Rd | 82 +-- man/PLNnetworkfit.Rd | 77 +-- man/fisher.Rd | 4 man/getBestModel.Rd | 8 man/getModel.Rd | 8 man/predict_cond.Rd |only man/standard_error.Rd | 4 src/RcppExports.cpp | 10 src/nlopt_wrapper.cpp | 1 src/optim_full_cov.cpp | 2 src/optim_genet_cov.cpp | 33 - src/utils.h | 5 tests/testthat/Rplots.pdf |binary tests/testthat/test-plnfit.R | 37 + tests/testthat/test-plnlda-fit.R | 47 +- tests/testthat/test-plnlda.R | 6 tests/testthat/test-plnpcafit.R | 3 tests/testthat/test-standard-error.R | 6 vignettes/article/PLNreferences.bib | 1 49 files changed, 3923 insertions(+), 1263 deletions(-)
Title: Feature Selection for 'mlr3'
Description: Implements methods for feature selection with
'mlr3', e.g. random search and sequential selection. Various
termination criteria can be set and combined. The class
'AutoFSelector' provides a convenient way to perform nested resampling
in combination with 'mlr3'.
Author: Marc Becker [aut, cre] ,
Patrick Schratz [aut] ,
Michel Lang [aut] ,
Bernd Bischl [aut]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3fselect versions 0.7.1 dated 2022-05-03 and 0.7.2 dated 2022-08-25
DESCRIPTION | 8 +-- MD5 | 36 +++++++-------- NEWS.md | 4 + build/partial.rdb |binary man/ArchiveFSelect.Rd | 64 +++++++++++++-------------- man/AutoFSelector.Rd | 48 ++++++++++---------- man/FSelectInstanceMultiCrit.Rd | 44 +++++++++--------- man/FSelectInstanceSingleCrit.Rd | 44 +++++++++--------- man/FSelector.Rd | 38 ++++++++-------- man/FSelectorFromOptimizer.Rd | 36 +++++++-------- man/ObjectiveFSelect.Rd | 34 +++++++------- man/mlr_fselectors_design_points.Rd | 38 ++++++++-------- man/mlr_fselectors_exhaustive_search.Rd | 38 ++++++++-------- man/mlr_fselectors_genetic_search.Rd | 38 ++++++++-------- man/mlr_fselectors_random_search.Rd | 38 ++++++++-------- man/mlr_fselectors_rfe.Rd | 38 ++++++++-------- man/mlr_fselectors_sequential.Rd | 44 +++++++++--------- man/mlr_fselectors_shadow_variable_search.Rd | 44 +++++++++--------- tests/testthat/test_FSelectorGeneticSearch.R | 2 19 files changed, 328 insertions(+), 308 deletions(-)
Title: Easy Computation of Alpha Functional Diversity Indices
Description: Computes 5 alpha-functional diversity indices: Functional
Divergence (FDiv), Function Evenness (FEve), Functional Richness (FRic),
Functional Dispersion (FDis) and Rao's entropy (Q) (reviewed in Villéger
et al. 2008 <doi:10.1890/07-1206.1>). Provides efficient, modular, and
parallel functions to compute functional diversity indices.
Author: Matthias Grenie [aut, cre] ,
Hugo Gruson [aut]
Maintainer: Matthias Grenie <matthias.grenie@gmail.com>
Diff between fundiversity versions 0.2.1 dated 2021-09-21 and 1.0.0 dated 2022-08-25
DESCRIPTION | 14 - MD5 | 82 ++++++----- NEWS.md | 25 +++ R/fd_chull_intersect.R | 4 R/fd_fdis.R | 11 + R/fd_fdiv.R | 14 + R/fd_feve.R | 14 + R/fd_fric.R | 16 +- R/fd_fric_intersect.R | 13 + R/fd_raoq.R | 11 + R/fundiversity-package.R |only R/species_in_common.R | 8 - R/zzz.R | 2 README.md | 44 +++--- build/partial.rdb |binary build/vignette.rds |binary inst/doc/correctness.R |only inst/doc/correctness.Rmd |only inst/doc/correctness.html |only inst/doc/design-principles.Rmd | 4 inst/doc/design-principles.html | 3 inst/doc/fundiversity.Rmd | 3 inst/doc/fundiversity.html | 216 ++++++++++++++++-------------- inst/doc/parallel.html | 14 + inst/doc/performance.Rmd | 8 - inst/doc/performance.html | 28 ++- inst/hexlogo |only man/fd_fdis.Rd | 5 man/fd_fdiv.Rd | 5 man/fd_feve.Rd | 5 man/fd_fric.Rd | 5 man/fd_fric_intersect.Rd | 5 man/fd_raoq.Rd | 5 man/figures |only man/fundiversity-package.Rd |only man/rmdchunks/_fundiversity_functions.Rmd | 4 tests/testthat/test-fdis.R | 22 ++- tests/testthat/test-fdiv.R | 32 ++++ tests/testthat/test-feve.R | 21 ++ tests/testthat/test-fric.R | 21 ++ tests/testthat/test-fric_intersect.R | 21 ++ tests/testthat/test-raoq.R | 21 ++ vignettes/correctness.Rmd |only vignettes/design-principles.Rmd | 4 vignettes/fundiversity.Rmd | 3 vignettes/performance.Rmd | 8 - 46 files changed, 480 insertions(+), 241 deletions(-)
Title: Comparison of Survival Curves Between Two Groups
Description: Various statistical methods for survival analysis in comparing survival curves between two groups, including overall hypothesis tests described in Li et al. (2015) <doi:10.1371/journal.pone.0116774> and Huang et al. (2020) <doi:10.1080/03610918.2020.1753075>, fixed-point tests in Klein et al. (2007) <doi:10.1002/sim.2864>, short-term tests, and long-term tests in Logan et al. (2008) <doi:10.1111/j.1541-0420.2007.00975.x>. Some commonly used descriptive statistics and plots are also included.
Author: Jingjing Lyu [aut],
Zheng Chen [cre],
Huimin Li [ctb],
Jinbao Chen [ctb],
Xinghui Huang [ctb]
Maintainer: Zheng Chen <zheng-chen@hotmail.com>
Diff between ComparisonSurv versions 1.1.0 dated 2022-06-17 and 1.1.1 dated 2022-08-25
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/ComparisonSurv.R | 4 ++-- 3 files changed, 8 insertions(+), 8 deletions(-)
More information about ComparisonSurv at CRAN
Permanent link
Title: Black-Box Optimization Toolkit
Description: Provides a common framework for optimization of black-box
functions for other packages, e.g. 'mlr3tuning' or 'mlr3fselect'. It
offers various optimization methods e.g. grid search, random search,
generalized simulated annealing and iterated racing.
Author: Marc Becker [cre, aut] ,
Jakob Richter [aut] ,
Michel Lang [aut] ,
Bernd Bischl [aut] ,
Martin Binder [aut],
Olaf Mersmann [ctb]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between bbotk versions 0.5.3 dated 2022-05-04 and 0.5.4 dated 2022-08-25
DESCRIPTION | 18 +- MD5 | 72 ++++---- NAMESPACE | 2 NEWS.md | 4 R/OptimizerFocusSearch.R |only R/OptimizerGenSA.R | 20 +- build/partial.rdb |binary inst/WORDLIST | 2 inst/doc/bbotk.html | 259 ++++++++++++++--------------- man/Archive.Rd | 48 ++--- man/ArchiveBest.Rd | 48 ++--- man/Codomain.Rd | 53 +++-- man/Objective.Rd | 42 ++-- man/ObjectiveRFun.Rd | 38 ++-- man/ObjectiveRFunDt.Rd | 42 ++-- man/OptimInstance.Rd | 48 ++--- man/OptimInstanceMultiCrit.Rd | 44 ++-- man/OptimInstanceSingleCrit.Rd | 44 ++-- man/Optimizer.Rd | 36 ++-- man/Progressor.Rd | 18 +- man/Terminator.Rd | 36 ++-- man/mlr_optimizers_cmaes.Rd | 38 ++-- man/mlr_optimizers_design_points.Rd | 38 ++-- man/mlr_optimizers_focus_search.Rd |only man/mlr_optimizers_gensa.Rd | 45 ++--- man/mlr_optimizers_grid_search.Rd | 38 ++-- man/mlr_optimizers_irace.Rd | 44 ++-- man/mlr_optimizers_nloptr.Rd | 32 +-- man/mlr_optimizers_random_search.Rd | 38 ++-- man/mlr_terminators_clock_time.Rd | 44 ++-- man/mlr_terminators_combo.Rd | 62 +++--- man/mlr_terminators_evals.Rd | 44 ++-- man/mlr_terminators_none.Rd | 44 ++-- man/mlr_terminators_perf_reached.Rd | 44 ++-- man/mlr_terminators_run_time.Rd | 44 ++-- man/mlr_terminators_stagnation.Rd | 44 ++-- man/mlr_terminators_stagnation_batch.Rd | 44 ++-- man/shrink_ps.Rd |only tests/testthat/test_OptimizerFocusSearch.R |only 39 files changed, 793 insertions(+), 724 deletions(-)
Title: Interface to the Numerai Machine Learning Tournament API
Description: Routines to interact with the Numerai Machine Learning Tournament
API <https://numer.ai>. The functionality includes the ability to automatically download the
current tournament data, submit predictions, and to get information for your
user.
Author: Omni Analytics Group [aut],
Eric Hare [cre],
Yogesh Bansal [ctb]
Maintainer: Eric Hare <eric@omnianalytics.org>
Diff between Rnumerai versions 2.1.4 dated 2021-10-08 and 3.0.0 dated 2022-08-25
Rnumerai-2.1.4/Rnumerai/R/source.R |only Rnumerai-2.1.4/Rnumerai/man/account_info.Rd |only Rnumerai-2.1.4/Rnumerai/man/current_round.Rd |only Rnumerai-2.1.4/Rnumerai/man/download_data.Rd |only Rnumerai-2.1.4/Rnumerai/man/get_password.Rd |only Rnumerai-2.1.4/Rnumerai/man/get_valid_data.Rd |only Rnumerai-2.1.4/Rnumerai/man/leaderboard.Rd |only Rnumerai-2.1.4/Rnumerai/man/performance_distribution.Rd |only Rnumerai-2.1.4/Rnumerai/man/performance_over_time.Rd |only Rnumerai-2.1.4/Rnumerai/man/release_nmr.Rd |only Rnumerai-2.1.4/Rnumerai/man/round_stats.Rd |only Rnumerai-2.1.4/Rnumerai/man/run_query.Rd |only Rnumerai-2.1.4/Rnumerai/man/set_password.Rd |only Rnumerai-2.1.4/Rnumerai/man/stake_nmr.Rd |only Rnumerai-2.1.4/Rnumerai/man/status_submission_by_id.Rd |only Rnumerai-2.1.4/Rnumerai/man/submit_predictions.Rd |only Rnumerai-2.1.4/Rnumerai/man/summary_statistics.Rd |only Rnumerai-2.1.4/Rnumerai/man/user_info.Rd |only Rnumerai-2.1.4/Rnumerai/man/user_performance.Rd |only Rnumerai-2.1.4/Rnumerai/man/user_performance_data.Rd |only Rnumerai-3.0.0/Rnumerai/DESCRIPTION | 25 - Rnumerai-3.0.0/Rnumerai/MD5 | 59 +- Rnumerai-3.0.0/Rnumerai/NAMESPACE | 56 -- Rnumerai-3.0.0/Rnumerai/R/baseapi.R |only Rnumerai-3.0.0/Rnumerai/R/numerapi.R |only Rnumerai-3.0.0/Rnumerai/R/queries.R |only Rnumerai-3.0.0/Rnumerai/R/signalsapi.R |only Rnumerai-3.0.0/Rnumerai/README.md | 400 ++++++++++------ Rnumerai-3.0.0/Rnumerai/man/diagnostics.Rd |only Rnumerai-3.0.0/Rnumerai/man/download_dataset.Rd |only Rnumerai-3.0.0/Rnumerai/man/download_validation_data.Rd |only Rnumerai-3.0.0/Rnumerai/man/get_account.Rd |only Rnumerai-3.0.0/Rnumerai/man/get_api_key.Rd | 2 Rnumerai-3.0.0/Rnumerai/man/get_competitions.Rd |only Rnumerai-3.0.0/Rnumerai/man/get_current_round.Rd |only Rnumerai-3.0.0/Rnumerai/man/get_leaderboard.Rd |only Rnumerai-3.0.0/Rnumerai/man/get_models.Rd | 15 Rnumerai-3.0.0/Rnumerai/man/get_public_id.Rd | 2 Rnumerai-3.0.0/Rnumerai/man/list_datasets.Rd |only Rnumerai-3.0.0/Rnumerai/man/round_model_performances.Rd |only Rnumerai-3.0.0/Rnumerai/man/set_api_key.Rd | 2 Rnumerai-3.0.0/Rnumerai/man/set_bio.Rd |only Rnumerai-3.0.0/Rnumerai/man/set_link.Rd |only Rnumerai-3.0.0/Rnumerai/man/set_public_id.Rd | 2 Rnumerai-3.0.0/Rnumerai/man/set_stake_type.Rd |only Rnumerai-3.0.0/Rnumerai/man/set_submission_webhook.Rd |only Rnumerai-3.0.0/Rnumerai/man/stake_change.Rd |only Rnumerai-3.0.0/Rnumerai/man/submission_status.Rd |only Rnumerai-3.0.0/Rnumerai/man/ticker_universe.Rd |only Rnumerai-3.0.0/Rnumerai/man/upload_diagnostics.Rd |only Rnumerai-3.0.0/Rnumerai/man/upload_predictions.Rd |only Rnumerai-3.0.0/Rnumerai/man/wallet_transactions.Rd |only 52 files changed, 352 insertions(+), 211 deletions(-)
Title: Sparsity by Worst-Case Quadratic Penalties
Description: Fits classical sparse regression models with
efficient active set algorithms by solving quadratic problems as described by
Grandvalet, Chiquet and Ambroise (2017) <arXiv:1210.2077>. Also provides a few
methods for model selection purpose (cross-validation, stability selection).
Author: Julien Chiquet [aut, cre]
Maintainer: Julien Chiquet <julien.chiquet@inrae.fr>
Diff between quadrupen versions 0.2-8 dated 2020-11-18 and 0.2-9 dated 2022-08-25
DESCRIPTION | 10 ++++----- MD5 | 40 ++++++++++++++++++------------------ NEWS.md | 5 ++++ R/init.R | 2 - R/quadrupen-package.R | 8 ++++--- R/quadrupen.R | 22 ++++++++++++------- README.md | 1 inst/examples/bounded.reg.R | 2 - inst/examples/crossval.R | 2 - inst/examples/elastic.net.R | 2 - inst/examples/minimal.R | 2 - inst/examples/plot.quadrupen.R | 2 - inst/examples/plot.stability.R | 2 - inst/examples/stability.R | 2 - inst/tests/check_breg_bulletproof.R | 2 - inst/tests/check_cv_bulletproof.R | 1 inst/tests/check_monitor.R | 2 - man/bounded.reg.Rd | 11 ++++++--- man/elastic.net.Rd | 11 ++++++--- man/quadrupen-package.Rd | 8 ++++--- tests/testthat/test-sparse.R | 8 +++---- 21 files changed, 74 insertions(+), 71 deletions(-)
Title: Some Additional Multiple Imputation Functions, Especially for
'mice'
Description: Contains functions for multiple imputation which
complements existing functionality in R.
In particular, several imputation methods for the
mice package (van Buuren & Groothuis-Oudshoorn, 2011,
<doi:10.18637/jss.v045.i03>) are included.
Main features of the miceadds package include
plausible value imputation (Mislevy, 1991,
<doi:10.1007/BF02294457>), multilevel imputation for
variables at any level or with any number of hierarchical
and non-hierarchical levels (Grund, Luedtke & Robitzsch,
2018, <doi:10.1177/1094428117703686>; van Buuren, 2018,
Ch.7, <doi:10.1201/9780429492259>), imputation using
partial least squares (PLS) for high dimensional
predictors (Robitzsch, Pham & Yanagida, 2016),
nested multiple imputation (Rubin, 2003,
<doi:10.1111/1467-9574.00217>), substantive model
compatible imputation (Bartlett et al., 2015,
<doi:10.1177/0962280214521348>), and features
for the generation of synthetic datasets
(Reiter, 2005, <doi:10.111 [...truncated...]
Author: Alexander Robitzsch [aut,cre] ,
Simon Grund [aut] ,
Thorsten Henke [ctb]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between miceadds versions 3.13-12 dated 2022-06-01 and 3.14-3 dated 2022-08-25
DESCRIPTION | 8 - MD5 | 116 +++++++++++----------- R/GroupMean.R | 5 R/RcppExports.R | 2 R/Rcppfunction_remove_classes.R | 6 - R/Rhat1.R | 8 - R/datlist_create.R | 11 -- R/draw.pv.ctt.R | 5 R/filename_split_vec.R | 6 - R/fleishman_coef.R | 7 - R/kernelpls.fit2.R | 40 +++---- R/latent.regression.em.R | 8 - R/latent_regression_em_sampling.R | 8 - R/lmer_vcov.R | 6 - R/ma_lme4_formula_design_matrices.R | 11 +- R/ma_lme4_formula_terms.R | 12 +- R/mice.1chain.R | 11 +- R/mice.impute.2l.latentgroupmean.mcmc.R | 16 +-- R/mice.impute.2l.latentgroupmean.ml.R | 5 R/mice.impute.2l.pls2.R | 48 +++++---- R/mice.impute.2l.pmm.R | 7 - R/mice.impute.pmm4.R | 7 - R/mice.impute.simputation.R | 4 R/mice.impute.smcfcs.R | 6 - R/mice.impute.tricube.pmm.R | 11 +- R/mice_imputation_2l_lmer.R | 11 +- R/mice_imputation_smcfcs_evaluate_loglikelihood.R | 8 - R/mice_imputation_tricube_pmm_match.R | 5 R/mice_imputation_weighted_norm_prepare.R | 10 + R/mice_ml_lmer_aggregate_data_higher_level.R | 5 R/mice_ml_lmer_collect_lme4_input.R | 5 R/mice_ml_lmer_construct_lme4_formula.R | 8 - R/mice_ml_lmer_extract_input.R | 15 +- R/mice_ml_lmer_include_cluster_means.R | 6 - R/mice_ml_lmer_interactions_pls.R | 6 - R/mice_multilevel_add_groupmeans.R | 3 R/mice_multilevel_imputation_pmm5.R | 5 R/micombine.cor.R | 12 +- R/ml_mcmc.R | 9 - R/ml_mcmc_fit.R | 9 - R/ml_mcmc_initial_values.R | 12 +- R/ml_mcmc_summary_print_descriptives.R | 5 R/plausible.value.draw.R | 5 R/plausible.value.imputation.R | 8 - R/save.Rdata.R | 12 +- R/save.data.R | 11 +- R/subset_datlist.R | 11 +- R/subset_nested.datlist.R | 5 README.md | 6 - build/partial.rdb |binary inst/NEWS | 11 ++ man/ml_mcmc.Rd | 6 - man/with.miceadds.Rd | 4 src/RcppExports.cpp | 2 src/miceadds_rcpp_create_interactions.cpp | 5 src/miceadds_rcpp_kernelpls_1dim.cpp | 8 - src/miceadds_rcpp_ml_mcmc_sampler.cpp | 13 +- src/miceadds_rcpp_pmm6.cpp | 8 - src/miceadds_rcpp_weighted_pmm.cpp | 5 59 files changed, 354 insertions(+), 274 deletions(-)
Title: Fuzzy Clustering of Vegetation Data
Description: A set of functions to: (1) perform fuzzy clustering of vegetation data (De Caceres et al, 2010) <doi:10.1111/j.1654-1103.2010.01211.x>; (2) to assess ecological community similarity on the basis of structure and composition (De Caceres et al, 2013) <doi:10.1111/2041-210X.12116>.
Author: Miquel De Caceres [aut, cre]
Maintainer: Miquel De Caceres <miquelcaceres@gmail.com>
Diff between vegclust versions 2.0.0 dated 2021-06-01 and 2.0.2 dated 2022-08-25
vegclust-2.0.0/vegclust/R/RcppExports.R |only vegclust-2.0.0/vegclust/inst/doc/VegetationClassification.Rnw |only vegclust-2.0.0/vegclust/inst/doc/VegetationClassification.pdf |only vegclust-2.0.0/vegclust/vignettes/VegetationClassification.Rnw |only vegclust-2.0.2/vegclust/DESCRIPTION | 14 vegclust-2.0.2/vegclust/MD5 | 77 - vegclust-2.0.2/vegclust/NAMESPACE | 6 vegclust-2.0.2/vegclust/NEWS.md | 9 vegclust-2.0.2/vegclust/R/crossmemb.R | 4 vegclust-2.0.2/vegclust/R/vegclustdist.R | 19 vegclust-2.0.2/vegclust/build/partial.rdb |binary vegclust-2.0.2/vegclust/build/vignette.rds |binary vegclust-2.0.2/vegclust/inst/doc/MedRegExample.R | 64 - vegclust-2.0.2/vegclust/inst/doc/MedRegExample.html | 477 ++++++++-- vegclust-2.0.2/vegclust/inst/doc/VegetationClassification.R | 287 +----- vegclust-2.0.2/vegclust/inst/doc/VegetationClassification.Rmd |only vegclust-2.0.2/vegclust/inst/doc/VegetationClassification.html |only vegclust-2.0.2/vegclust/man/CAP.Rd | 2 vegclust-2.0.2/vegclust/man/CAS.Rd | 2 vegclust-2.0.2/vegclust/man/as.memb.Rd | 2 vegclust-2.0.2/vegclust/man/as.vegclust.Rd | 2 vegclust-2.0.2/vegclust/man/clustcentroid.Rd | 2 vegclust-2.0.2/vegclust/man/clustconst.Rd | 2 vegclust-2.0.2/vegclust/man/clustvar.Rd | 2 vegclust-2.0.2/vegclust/man/concordance.Rd | 6 vegclust-2.0.2/vegclust/man/crossmemb.Rd | 2 vegclust-2.0.2/vegclust/man/defuzzify.Rd | 4 vegclust-2.0.2/vegclust/man/hcr.Rd | 2 vegclust-2.0.2/vegclust/man/hier.vegclust.Rd | 2 vegclust-2.0.2/vegclust/man/incr.vegclust.Rd | 2 vegclust-2.0.2/vegclust/man/interclustdist.Rd | 2 vegclust-2.0.2/vegclust/man/plot.CAP.Rd | 2 vegclust-2.0.2/vegclust/man/plot.CAS.Rd | 2 vegclust-2.0.2/vegclust/man/plot.mvegclust.Rd | 2 vegclust-2.0.2/vegclust/man/relate.levels.Rd | 2 vegclust-2.0.2/vegclust/man/stratifyvegdata.Rd | 4 vegclust-2.0.2/vegclust/man/vegclass.Rd | 4 vegclust-2.0.2/vegclust/man/vegclust.Rd | 4 vegclust-2.0.2/vegclust/man/vegclust2kmeans.Rd | 2 vegclust-2.0.2/vegclust/man/vegclustIndex.Rd | 4 vegclust-2.0.2/vegclust/man/vegdiststruct.Rd | 2 vegclust-2.0.2/vegclust/vignettes/VegetationClassification.Rmd |only vegclust-2.0.2/vegclust/vignettes/vegclust.bib | 82 - 43 files changed, 625 insertions(+), 476 deletions(-)
Title: 3D Brain Visualization
Description: A fast, interactive cross-platform, and easy to share
'WebGL'-based 3D brain viewer that visualizes 'FreeSurfer' and/or
'AFNI/SUMA' surfaces. The viewer widget can be either standalone or
embedded into 'R-shiny' applications. The standalone version only require
a web browser with 'WebGL2' support (for example, 'Chrome', 'Firefox',
'Safari'), and can be inserted into any websites. The 'R-shiny'
support allows the 3D viewer to be dynamically generated from reactive user
inputs. This feature has been fully adopted by 'RAVE'
<https://openwetware.org/wiki/RAVE>, an interactive toolbox to
analyze 'iEEG' data. Documentation about 'threeBrain' is provided
by <https://dipterix.org/threeBrain/> and several vignettes included
in this package. To cite the package, please check our 'NeuroImage' paper
by Magnotti, Wang, and Beauchamp (2020, <doi:10.1016/j.neuroimage.2020.117341>),
or see 'citation("threeBrain")' for details.
Author: Zhengjia Wang [aut, cre, cph],
John Magnotti [aut],
Xiang Zhang [ctb, res],
Brian Metzger [res],
Elizabeth Nesbitt [res],
Meng Li [ths],
Michael Beauchamp [aut, dtc]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Diff between threeBrain versions 0.2.5 dated 2022-05-30 and 0.2.6 dated 2022-08-25
DESCRIPTION | 11 LICENSE | 5 MD5 | 44 NAMESPACE | 1 NEWS.md | 16 R/aaa.R | 17 R/class_brain.R | 43 R/class_brainelectrodes.R | 1 R/class_multibrain.R | 7 R/geom_electrode.R | 4 R/geom_linesegments.R |only R/loaders.R | 8 R/shiny-localization.R | 13 R/zzz.R | 117 build/vignette.rds |binary inst/doc/A-getting-started.html | 22 inst/doc/B-electrode-localization.html | 31 inst/doc/C-data-visualization.html | 26 inst/htmlwidgets/lib/dipterixThreeBrain-1.0.1/main.js |74461 ---------- inst/htmlwidgets/lib/dipterixThreeBrain-1.0.1/main.js.LICENSE.txt | 606 inst/htmlwidgets/threejs_brain.yaml | 2 man/LineSegmentsGeom.Rd |only man/template_subject.Rd | 2 man/threejs_brain.Rd | 4 24 files changed, 735 insertions(+), 74706 deletions(-)
Title: Spatial Network Autocorrelation for Flow Data
Description: Identify statistically significant flow clusters using the local spatial network autocorrelation statistic G_ij*
proposed by 'Berglund' and 'Karlström' (1999) <doi:10.1007/s101090050013>.
The metric, an extended statistic of 'Getis/Ord' G ('Getis' and 'Ord' 1992) <doi:10.1111/j.1538-4632.1992.tb00261.x>,
detects a group of flows having similar traits in terms of directionality.
You provide OD data and the associated polygon to get results
with several parameters, some of which are defined by spdep package.
Author: Youngbin Lee [aut, cre] ,
Hui Jeong Ha [aut] ,
Sohyun Park [aut] ,
Kyusik Kim [aut] ,
Jinhyung Lee [aut]
Maintainer: Youngbin Lee <youngbin@snu.ac.kr>
Diff between spnaf versions 0.2.0 dated 2022-08-07 and 0.2.1 dated 2022-08-25
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- R/Boot.R | 2 +- R/Gstat.R | 2 +- inst/doc/Introduction_to_spnaf.html | 28 ++++++++++++++-------------- 5 files changed, 25 insertions(+), 25 deletions(-)
Title: Species Distribution Model Selection
Description: User-friendly framework that enables the training and the
evaluation of species distribution models (SDMs). The package implements
functions for data driven variable selection and model tuning and includes
numerous utilities to display the results. All the functions used to select
variables or to tune model hyperparameters have an interactive real-time
chart displayed in the 'RStudio' viewer pane during their execution.
Author: Sergio Vignali [aut, cre] ,
Arnaud Barras [aut] ,
Veronika Braunisch [aut] ,
Conservation Biology - University of Bern [fnd]
Maintainer: Sergio Vignali <sergio.vignali@iee.unibe.ch>
Diff between SDMtune versions 1.1.5 dated 2021-07-17 and 1.1.6 dated 2022-08-25
SDMtune-1.1.5/SDMtune/man/plot-methods.Rd |only SDMtune-1.1.6/SDMtune/DESCRIPTION | 8 SDMtune-1.1.6/SDMtune/MD5 | 119 +- SDMtune-1.1.6/SDMtune/NAMESPACE | 9 SDMtune-1.1.6/SDMtune/NEWS.md | 17 SDMtune-1.1.6/SDMtune/R/ANN-class.R | 6 SDMtune-1.1.6/SDMtune/R/BRT-class.R | 4 SDMtune-1.1.6/SDMtune/R/Maxent-class.R | 4 SDMtune-1.1.6/SDMtune/R/Maxnet-class.R | 4 SDMtune-1.1.6/SDMtune/R/RF-class.R | 4 SDMtune-1.1.6/SDMtune/R/SDMmodel-class.R | 4 SDMtune-1.1.6/SDMtune/R/SDMmodel2MaxEnt.R | 2 SDMtune-1.1.6/SDMtune/R/SDMmodelCV-class.R | 4 SDMtune-1.1.6/SDMtune/R/SDMtune-class.R | 10 SDMtune-1.1.6/SDMtune/R/SWD-class.R | 4 SDMtune-1.1.6/SDMtune/R/addSamplesToBg.R | 2 SDMtune-1.1.6/SDMtune/R/aicc.R | 4 SDMtune-1.1.6/SDMtune/R/auc.R | 6 SDMtune-1.1.6/SDMtune/R/confMatrix.R | 4 SDMtune-1.1.6/SDMtune/R/corVar.R | 2 SDMtune-1.1.6/SDMtune/R/doJk.R | 6 SDMtune-1.1.6/SDMtune/R/getTunableArgs.R | 2 SDMtune-1.1.6/SDMtune/R/gridSearch.R | 2 SDMtune-1.1.6/SDMtune/R/maxentTh.R | 2 SDMtune-1.1.6/SDMtune/R/maxentVarImp.R | 2 SDMtune-1.1.6/SDMtune/R/mergeSWD.R | 4 SDMtune-1.1.6/SDMtune/R/optimizeModel.R | 4 SDMtune-1.1.6/SDMtune/R/plotPA.R | 2 SDMtune-1.1.6/SDMtune/R/plotPred.R | 2 SDMtune-1.1.6/SDMtune/R/plotROC.R | 2 SDMtune-1.1.6/SDMtune/R/plotResponse.R | 2 SDMtune-1.1.6/SDMtune/R/predict-SDMmodel.R | 2 SDMtune-1.1.6/SDMtune/R/predict-SDMmodelCV.R | 2 SDMtune-1.1.6/SDMtune/R/randomFolds.R | 2 SDMtune-1.1.6/SDMtune/R/reduceVar.R | 2 SDMtune-1.1.6/SDMtune/R/trainValTest.R | 2 SDMtune-1.1.6/SDMtune/R/tss.R | 4 SDMtune-1.1.6/SDMtune/R/utils.R | 18 SDMtune-1.1.6/SDMtune/R/varImp.R | 4 SDMtune-1.1.6/SDMtune/R/varSel.R | 2 SDMtune-1.1.6/SDMtune/README.md | 14 SDMtune-1.1.6/SDMtune/build/vignette.rds |binary SDMtune-1.1.6/SDMtune/inst/doc/basic-use.html | 600 +++++++++--- SDMtune-1.1.6/SDMtune/inst/doc/hyper-tuning.html | 363 ++++++- SDMtune-1.1.6/SDMtune/inst/doc/presence-absence.html | 248 ++++ SDMtune-1.1.6/SDMtune/inst/doc/var-selection.html | 413 +++++++- SDMtune-1.1.6/SDMtune/man/ANN-class.Rd | 10 SDMtune-1.1.6/SDMtune/man/BRT-class.Rd | 8 SDMtune-1.1.6/SDMtune/man/Maxent-class.Rd | 8 SDMtune-1.1.6/SDMtune/man/Maxnet-class.Rd | 8 SDMtune-1.1.6/SDMtune/man/RF-class.Rd | 8 SDMtune-1.1.6/SDMtune/man/SDMmodel-class.Rd | 8 SDMtune-1.1.6/SDMtune/man/SDMmodelCV-class.Rd | 8 SDMtune-1.1.6/SDMtune/man/SDMtune-class.Rd | 66 + SDMtune-1.1.6/SDMtune/man/SDMtune-package.Rd | 9 SDMtune-1.1.6/SDMtune/man/SWD-class.Rd | 8 SDMtune-1.1.6/SDMtune/src/RcppExports.cpp | 5 SDMtune-1.1.6/SDMtune/tests/testthat/test-SDMmodel2MaxEnt.R | 3 SDMtune-1.1.6/SDMtune/tests/testthat/test-mergeSWD.R | 6 SDMtune-1.1.6/SDMtune/tests/testthat/test-randomFolds.R | 4 SDMtune-1.1.6/SDMtune/vignettes/SDMtune.bib | 87 - 61 files changed, 1757 insertions(+), 412 deletions(-)
Title: 'SaTScan' (TM) Results Mapper
Description: Supports the generation of maps based on the results from
'SaTScan' (TM) cluster analysis.
The package handles mapping of Spatial and Spatial-Time analysis using
the discrete Poisson, Bernoulli, and exponential models of case data generating
cluster and location ('GIS') records containing observed, expected and observed/expected
ratio for U. S. states (and DC), counties or census tracts of individual
states based on the U. S. 'FIPS' codes for state, county and census tracts
(locations) using 2000 or 2010 Census areas, 'FIPS' codes, and boundary data.
'satscanMapper' uses the 'SeerMapper' package for the boundary data and
mapping of locations. Not all of the 'SaTScan' (TM) analysis and models generate
the observed, expected and observed/expected ratio values for the clusters and
locations.
The user can map the observed/expected ratios for locations
(states, counties, or census tracts) for each cluster with a p-value less than 0.05
or a user specified p-value.
The locations are categori [...truncated...]
Author: Jim Pearson [aut, cre, cph]
Maintainer: Jim Pearson <jbpearson353@gmail.com>
Diff between satscanMapper versions 1.0.1 dated 2018-07-05 and 1.0.2 dated 2022-08-25
satscanMapper-1.0.1/satscanMapper/NEWS |only satscanMapper-1.0.2/satscanMapper/DESCRIPTION | 15 satscanMapper-1.0.2/satscanMapper/MD5 | 32 satscanMapper-1.0.2/satscanMapper/NAMESPACE | 2 satscanMapper-1.0.2/satscanMapper/R/CreateGeo4SS.r | 15 satscanMapper-1.0.2/satscanMapper/R/satscanMapper.r | 2830 ++++------ satscanMapper-1.0.2/satscanMapper/data/co99_M_data.rda |binary satscanMapper-1.0.2/satscanMapper/data/co99_data.rda |binary satscanMapper-1.0.2/satscanMapper/data/pl99_data.rda |binary satscanMapper-1.0.2/satscanMapper/data/sa99_data.rda |binary satscanMapper-1.0.2/satscanMapper/data/st99_M_data.rda |binary satscanMapper-1.0.2/satscanMapper/data/st99_data.rda |binary satscanMapper-1.0.2/satscanMapper/data/tr99_M_data.rda |binary satscanMapper-1.0.2/satscanMapper/data/tr99_data.rda |binary satscanMapper-1.0.2/satscanMapper/inst/doc |only satscanMapper-1.0.2/satscanMapper/man/satscanMapper-package.Rd | 10 satscanMapper-1.0.2/satscanMapper/man/satscanMapper.Rd | 21 satscanMapper-1.0.2/satscanMapper/man/satscanMapper.Version.Rd | 2 18 files changed, 1272 insertions(+), 1655 deletions(-)
Title: Signal Processing Toolbox for Analyzing 'Electrophysiology' Data
Description: Implemented fast and memory-efficient 'Notch'-filter,
'Welch-periodogram', and discrete wavelet transform algorithm for hours of
high-resolution signals; providing fundamental toolbox
for 'iEEG' preprocess pipelines.
Documentation and examples about 'RAVE' project are provided at
<https://openwetware.org/wiki/RAVE>, and the paper by John F. Magnotti,
Zhengjia Wang, Michael S. Beauchamp (2020)
<doi:10.1016/j.neuroimage.2020.117341>; see 'citation("ravetools")' for
details.
Author: Zhengjia Wang [aut, cre, cph],
Beauchamp lab [cph],
Karim Rahim [cph] ,
Prerau Lab [cph] ,
RcppParallel Authors [cph] ,
Marcus Geelnard [cph]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Diff between ravetools versions 0.0.5 dated 2022-08-06 and 0.0.6 dated 2022-08-25
DESCRIPTION | 6 - MD5 | 18 ++--- NAMESPACE | 1 NEWS.md | 7 ++ R/plot-signals.R |only R/pwelch-diagnosis.R | 94 ++++++++++++++++++++------- R/pwelch.R | 162 +++++++++++++++++++++++++++++++++++++++--------- README.md | 4 - man/diagnose_channel.Rd | 37 ++++++---- man/plot_signals.Rd |only man/pwelch.Rd | 36 ++++++++-- 11 files changed, 278 insertions(+), 87 deletions(-)
Title: File-System Toolbox for RAVE Project
Description: Includes multiple cross-platform read/write interfaces for
'RAVE' project. 'RAVE' stands for "R analysis and visualization of human
intracranial electroencephalography data". The whole project aims at
providing powerful free-source package that analyze brain recordings from
patients with electrodes placed on the cortical surface or inserted into
the brain. 'raveio' as part of this project provides tools to read/write
neurophysiology data from/to 'RAVE' file structure, as well as several
popular formats including 'EDF(+)', 'Matlab', 'BIDS-iEEG', and 'HDF5',
etc. Documentation and examples about 'RAVE' project are provided at
<https://openwetware.org/wiki/RAVE>, and the paper by John F. Magnotti,
Zhengjia Wang, Michael S. Beauchamp (2020)
<doi:10.1016/j.neuroimage.2020.117341>; see 'citation("raveio")' for
details.
Author: Zhengjia Wang [aut, cre],
Beauchamp lab [cph, fnd]
Maintainer: Zhengjia Wang <dipterix.wang@gmail.com>
Diff between raveio versions 0.0.7 dated 2022-06-20 and 0.0.8 dated 2022-08-25
DESCRIPTION | 8 - MD5 | 92 +++++++++----- NAMESPACE | 22 +++ NEWS.md | 25 +++ R/aaa.R | 8 + R/backward-compatibility.R |only R/blackrock-parser.R |only R/class-BlackrockFile.R |only R/class-pipeline_tools.R | 29 ++++ R/class-subject.R | 30 +++- R/class-watch-dog.R |only R/cmd-3dAlineate.R |only R/cmd-aaa.R |only R/cmd-dcm2niix.R |only R/cmd-flirt.R |only R/cmd-recon-all.R |only R/cmd.R | 160 +++++++++++++++++------- R/hdf5r.R | 15 -- R/module-pipeline-registry.R |only R/pipeline-install.R | 20 +++ R/pipeline-tools.R | 71 ++++++++++ R/rave-import.R | 171 ++++++++++++++++++++++++++ R/rave-merge-subjects.R |only R/rave-prepare-subjectbare.R | 91 ++++++++------ R/rave-prepare-subjectblock.R |only R/rave-prepare.R | 11 + R/rave-raw.R | 62 +++++++++ R/rave-reference.R | 8 + R/rave2-experimental.R | 220 ++++++++++++++++++---------------- R/tensor.R | 11 - R/validate-subject.R |only R/zzz.R | 39 +++++- build/partial.rdb |binary inst/WORDLIST | 7 + inst/module-registry.yaml |only inst/shell-templates |only inst/specifications |only man/BlackrockFile.Rd |only man/ECoGTensor.Rd | 20 +-- man/LFP_electrode.Rd | 2 man/LFP_reference.Rd | 2 man/PipelineTools.Rd | 25 +++ man/auto_process_blackrock.Rd |only man/cmd-external.Rd |only man/install_modules.Rd |only man/module_registry.Rd |only man/power_baseline.Rd | 5 man/rave-pipeline.Rd | 9 + man/rave-prepare.Rd | 42 +++++- man/rave-raw-validation.Rd | 2 man/rave_command_line_path.Rd | 5 man/rave_subject_format_conversion.Rd |only man/read_nsx_nev.Rd |only man/validate_subject.Rd |only tests/testthat/test-preprocess-v2.R | 106 ++++++++++------ 55 files changed, 1002 insertions(+), 316 deletions(-)
Title: 'Amazon Web Services' Compute Services
Description: Interface to 'Amazon Web Services' compute services,
including 'Elastic Compute Cloud' ('EC2'), 'Lambda'
functions-as-a-service, containers, batch processing, and more
<https://aws.amazon.com/>.
Author: David Kretch [aut],
Adam Banker [aut],
Dyfan Jones [cre],
Amazon.com, Inc. [cph]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>
Diff between paws.compute versions 0.1.12 dated 2021-08-23 and 0.1.13 dated 2022-08-25
DESCRIPTION | 28 MD5 | 682 R/batch_interfaces.R | 464 R/batch_operations.R | 5340 R/batch_service.R | 226 R/ec2_interfaces.R |10264 - R/ec2_operations.R |92576 +++++++------- R/ec2_service.R | 1070 R/ec2instanceconnect_interfaces.R | 32 R/ec2instanceconnect_operations.R | 146 R/ec2instanceconnect_service.R | 170 R/ecr_interfaces.R | 824 R/ecr_operations.R | 4888 R/ecr_service.R | 250 R/ecs_interfaces.R | 1208 R/ecs_operations.R |18040 +- R/ecs_service.R | 296 R/eks_interfaces.R | 656 R/eks_operations.R | 5552 R/eks_service.R | 256 R/elasticbeanstalk_interfaces.R | 1076 R/elasticbeanstalk_operations.R | 8800 - R/elasticbeanstalk_service.R | 286 R/lambda_interfaces.R | 1356 R/lambda_operations.R |11772 - R/lambda_service.R | 294 R/lightsail_interfaces.R | 3392 R/lightsail_operations.R |26682 ++-- R/lightsail_service.R | 472 R/serverlessapplicationrepository_interfaces.R | 336 R/serverlessapplicationrepository_operations.R | 2340 R/serverlessapplicationrepository_service.R | 244 man/batch.Rd | 180 man/batch_cancel_job.Rd | 90 man/batch_create_compute_environment.Rd | 484 man/batch_create_job_queue.Rd | 236 man/batch_delete_compute_environment.Rd | 90 man/batch_describe_job_definitions.Rd | 616 man/batch_describe_job_queues.Rd | 172 man/batch_describe_jobs.Rd | 658 man/batch_list_jobs.Rd | 232 man/batch_register_job_definition.Rd | 716 man/batch_submit_job.Rd | 406 man/batch_update_compute_environment.Rd | 184 man/batch_update_job_queue.Rd | 148 man/ec2.Rd | 1014 man/ec2_allocate_hosts.Rd | 182 man/ec2_assign_ipv_6_addresses.Rd | 108 man/ec2_associate_address.Rd | 250 man/ec2_associate_enclave_certificate_iam_role.Rd | 118 man/ec2_associate_subnet_cidr_block.Rd | 84 man/ec2_cancel_reserved_instances_listing.Rd | 134 man/ec2_copy_image.Rd | 214 man/ec2_copy_snapshot.Rd | 294 man/ec2_create_capacity_reservation.Rd | 374 man/ec2_create_dhcp_options.Rd | 260 man/ec2_create_fleet.Rd | 452 man/ec2_create_image.Rd | 272 man/ec2_create_instance_export_task.Rd | 166 man/ec2_create_key_pair.Rd | 2 man/ec2_create_launch_template.Rd | 534 man/ec2_create_launch_template_version.Rd | 782 man/ec2_create_local_gateway_route.Rd | 100 man/ec2_create_nat_gateway.Rd | 232 man/ec2_create_placement_group.Rd | 184 man/ec2_create_reserved_instances_listing.Rd | 224 man/ec2_create_security_group.Rd | 222 man/ec2_create_snapshot.Rd | 228 man/ec2_create_snapshots.Rd | 166 man/ec2_create_subnet.Rd | 292 man/ec2_create_traffic_mirror_session.Rd | 234 man/ec2_delete_fleets.Rd | 174 man/ec2_delete_placement_group.Rd | 88 man/ec2_delete_vpc_endpoints.Rd | 98 man/ec2_describe_addresses.Rd | 276 man/ec2_describe_capacity_reservations.Rd | 310 man/ec2_describe_carrier_gateways.Rd | 168 man/ec2_describe_classic_link_instances.Rd | 192 man/ec2_describe_coip_pools.Rd | 152 man/ec2_describe_customer_gateways.Rd | 194 man/ec2_describe_dhcp_options.Rd | 216 man/ec2_describe_egress_only_internet_gateways.Rd | 164 man/ec2_describe_fleet_history.Rd | 160 man/ec2_describe_fleet_instances.Rd | 132 man/ec2_describe_fleets.Rd | 404 man/ec2_describe_flow_logs.Rd | 206 man/ec2_describe_fpga_images.Rd | 248 man/ec2_describe_host_reservation_offerings.Rd | 176 man/ec2_describe_host_reservations.Rd | 192 man/ec2_describe_image_attribute.Rd | 188 man/ec2_describe_images.Rd | 406 man/ec2_describe_instance_credit_specifications.Rd | 190 man/ec2_describe_instance_status.Rd | 366 man/ec2_describe_instance_type_offerings.Rd | 138 man/ec2_describe_instance_types.Rd | 550 man/ec2_describe_instances.Rd | 1014 man/ec2_describe_internet_gateways.Rd | 216 man/ec2_describe_ipv_6_pools.Rd | 164 man/ec2_describe_key_pairs.Rd | 184 man/ec2_describe_launch_template_versions.Rd | 540 man/ec2_describe_launch_templates.Rd | 202 man/ec2_describe_nat_gateways.Rd | 254 man/ec2_describe_network_acls.Rd | 290 man/ec2_describe_network_interfaces.Rd | 434 man/ec2_describe_placement_groups.Rd | 170 man/ec2_describe_public_ipv_4_pools.Rd | 162 man/ec2_describe_reserved_instances.Rd | 276 man/ec2_describe_reserved_instances_listings.Rd | 214 man/ec2_describe_reserved_instances_modifications.Rd | 218 man/ec2_describe_reserved_instances_offerings.Rd | 370 man/ec2_describe_route_tables.Rd | 352 man/ec2_describe_security_groups.Rd | 478 man/ec2_describe_snapshots.Rd | 432 man/ec2_describe_spot_fleet_requests.Rd | 486 man/ec2_describe_spot_instance_requests.Rd | 566 man/ec2_describe_spot_price_history.Rd | 260 man/ec2_describe_subnets.Rd | 288 man/ec2_describe_tags.Rd | 186 man/ec2_describe_transit_gateway_peering_attachments.Rd | 208 man/ec2_describe_volumes.Rd | 362 man/ec2_describe_vpc_classic_link.Rd | 138 man/ec2_describe_vpc_endpoint_service_configurations.Rd | 224 man/ec2_describe_vpc_endpoint_services.Rd | 230 man/ec2_describe_vpc_endpoints.Rd | 248 man/ec2_describe_vpc_peering_connections.Rd | 290 man/ec2_describe_vpcs.Rd | 278 man/ec2_describe_vpn_connections.Rd | 354 man/ec2_describe_vpn_gateways.Rd | 188 man/ec2_enable_ebs_encryption_by_default.Rd | 98 man/ec2_export_image.Rd | 180 man/ec2_get_coip_pool_usage.Rd | 136 man/ec2_get_console_output.Rd | 138 man/ec2_get_default_credit_specification.Rd | 84 man/ec2_get_launch_template_data.Rd | 392 man/ec2_get_password_data.Rd | 122 man/ec2_import_image.Rd | 402 man/ec2_import_instance.Rd | 280 man/ec2_import_snapshot.Rd | 282 man/ec2_import_volume.Rd | 208 man/ec2_modify_availability_zone_group.Rd | 92 man/ec2_modify_capacity_reservation.Rd | 144 man/ec2_modify_default_credit_specification.Rd | 122 man/ec2_modify_fleet.Rd | 218 man/ec2_modify_hosts.Rd | 160 man/ec2_modify_instance_attribute.Rd | 378 man/ec2_modify_instance_credit_specification.Rd | 126 man/ec2_modify_instance_metadata_options.Rd | 158 man/ec2_modify_network_interface_attribute.Rd | 212 man/ec2_modify_reserved_instances.Rd | 106 man/ec2_modify_spot_fleet_request.Rd | 232 man/ec2_modify_volume.Rd | 274 man/ec2_monitor_instances.Rd | 94 man/ec2_purchase_host_reservation.Rd | 174 man/ec2_purchase_reserved_instances_offering.Rd | 136 man/ec2_reboot_instances.Rd | 106 man/ec2_register_image.Rd | 314 man/ec2_request_spot_fleet.Rd | 712 man/ec2_request_spot_instances.Rd | 794 man/ec2_reset_instance_attribute.Rd | 114 man/ec2_run_instances.Rd | 1416 man/ec2_run_scheduled_instances.Rd | 348 man/ec2_send_diagnostic_interrupt.Rd | 100 man/ec2_start_instances.Rd | 170 man/ec2_stop_instances.Rd | 240 man/ec2_terminate_instances.Rd | 174 man/ec2_unassign_ipv_6_addresses.Rd | 72 man/ec2_unmonitor_instances.Rd | 90 man/ec2instanceconnect.Rd | 124 man/ec2instanceconnect_send_ssh_public_key.Rd | 112 man/ecr.Rd | 204 man/ecr_get_lifecycle_policy_preview.Rd | 22 man/ecr_put_lifecycle_policy.Rd | 2 man/ecs.Rd | 248 man/ecs_create_cluster.Rd | 404 man/ecs_create_service.Rd | 1390 man/ecs_create_task_set.Rd | 490 man/ecs_delete_cluster.Rd | 196 man/ecs_delete_service.Rd | 538 man/ecs_deregister_task_definition.Rd | 606 man/ecs_describe_clusters.Rd | 262 man/ecs_describe_services.Rd | 536 man/ecs_describe_task_definition.Rd | 628 man/ecs_describe_tasks.Rd | 436 man/ecs_list_account_settings.Rd | 184 man/ecs_put_account_setting.Rd | 214 man/ecs_put_cluster_capacity_providers.Rd | 298 man/ecs_register_container_instance.Rd | 386 man/ecs_register_task_definition.Rd | 1590 man/ecs_run_task.Rd | 900 man/ecs_start_task.Rd | 678 man/ecs_stop_task.Rd | 410 man/ecs_submit_task_state_change.Rd | 172 man/ecs_update_capacity_provider.Rd | 128 man/ecs_update_cluster_settings.Rd | 180 man/ecs_update_container_agent.Rd | 230 man/ecs_update_service.Rd | 1008 man/ecs_update_task_set.Rd | 226 man/eks.Rd | 210 man/eks_create_addon.Rd | 204 man/eks_create_cluster.Rd | 460 man/eks_create_nodegroup.Rd | 484 man/eks_delete_addon.Rd | 128 man/eks_delete_nodegroup.Rd | 192 man/eks_describe_addon.Rd | 120 man/eks_describe_nodegroup.Rd | 190 man/eks_describe_update.Rd | 134 man/eks_tag_resource.Rd | 80 man/eks_update_addon.Rd | 166 man/eks_update_cluster_config.Rd | 228 man/eks_update_cluster_version.Rd | 140 man/eks_update_nodegroup_config.Rd | 166 man/eks_update_nodegroup_version.Rd | 242 man/elasticbeanstalk.Rd | 234 man/elasticbeanstalk_create_configuration_template.Rd | 310 man/lambda.Rd | 244 man/lambda_create_event_source_mapping.Rd | 486 man/lambda_create_function.Rd | 646 man/lambda_get_function.Rd | 300 man/lambda_get_function_configuration.Rd | 276 man/lambda_get_layer_version.Rd | 118 man/lambda_get_layer_version_by_arn.Rd | 110 man/lambda_get_provisioned_concurrency_config.Rd | 134 man/lambda_list_code_signing_configs.Rd | 100 man/lambda_list_functions.Rd | 272 man/lambda_list_layer_versions.Rd | 126 man/lambda_list_layers.Rd | 130 man/lambda_list_versions_by_function.Rd | 282 man/lambda_publish_layer_version.Rd | 200 man/lambda_publish_version.Rd | 312 man/lambda_update_event_source_mapping.Rd | 388 man/lambda_update_function_code.Rd | 340 man/lambda_update_function_configuration.Rd | 486 man/lightsail.Rd | 424 man/lightsail_allocate_static_ip.Rd | 100 man/lightsail_attach_certificate_to_distribution.Rd | 162 man/lightsail_attach_disk.Rd | 126 man/lightsail_attach_instances_to_load_balancer.Rd | 142 man/lightsail_attach_load_balancer_tls_certificate.Rd | 142 man/lightsail_attach_static_ip.Rd | 106 man/lightsail_close_instance_public_ports.Rd | 134 man/lightsail_copy_snapshot.Rd | 234 man/lightsail_create_certificate.Rd | 332 man/lightsail_create_cloud_formation_stack.Rd | 142 man/lightsail_create_contact_method.Rd | 176 man/lightsail_create_container_service.Rd | 486 man/lightsail_create_container_service_deployment.Rd | 338 man/lightsail_create_container_service_registry_login.Rd | 106 man/lightsail_create_disk.Rd | 178 man/lightsail_create_disk_from_snapshot.Rd | 298 man/lightsail_create_disk_snapshot.Rd | 210 man/lightsail_create_distribution.Rd | 396 man/lightsail_create_domain.Rd | 134 man/lightsail_create_domain_entry.Rd | 144 man/lightsail_create_instance_snapshot.Rd | 142 man/lightsail_create_instances.Rd | 242 man/lightsail_create_instances_from_snapshot.Rd | 348 man/lightsail_create_key_pair.Rd | 168 man/lightsail_create_load_balancer.Rd | 212 man/lightsail_create_load_balancer_tls_certificate.Rd | 186 man/lightsail_create_relational_database.Rd | 348 man/lightsail_create_relational_database_from_snapshot.Rd | 282 man/lightsail_create_relational_database_snapshot.Rd | 154 man/lightsail_delete_alarm.Rd | 110 man/lightsail_delete_auto_snapshot.Rd | 114 man/lightsail_delete_certificate.Rd | 120 man/lightsail_delete_contact_method.Rd | 126 man/lightsail_delete_disk.Rd | 122 man/lightsail_delete_disk_snapshot.Rd | 126 man/lightsail_delete_distribution.Rd | 106 man/lightsail_delete_domain.Rd | 104 man/lightsail_delete_domain_entry.Rd | 130 man/lightsail_delete_instance.Rd | 116 man/lightsail_delete_instance_snapshot.Rd | 110 man/lightsail_delete_key_pair.Rd | 104 man/lightsail_delete_known_host_keys.Rd | 122 man/lightsail_delete_load_balancer.Rd | 116 man/lightsail_delete_load_balancer_tls_certificate.Rd | 138 man/lightsail_delete_relational_database.Rd | 160 man/lightsail_delete_relational_database_snapshot.Rd | 112 man/lightsail_detach_certificate_from_distribution.Rd | 112 man/lightsail_detach_disk.Rd | 114 man/lightsail_detach_instances_from_load_balancer.Rd | 128 man/lightsail_detach_static_ip.Rd | 104 man/lightsail_disable_add_on.Rd | 108 man/lightsail_enable_add_on.Rd | 120 man/lightsail_export_snapshot.Rd | 140 man/lightsail_get_alarms.Rd | 178 man/lightsail_get_auto_snapshots.Rd | 92 man/lightsail_get_blueprints.Rd | 126 man/lightsail_get_contact_methods.Rd | 120 man/lightsail_get_container_services.Rd | 262 man/lightsail_get_distributions.Rd | 230 man/lightsail_get_export_snapshot_records.Rd | 168 man/lightsail_get_instance.Rd | 266 man/lightsail_get_instance_access_details.Rd | 138 man/lightsail_get_instance_metric_data.Rd | 378 man/lightsail_get_instance_port_states.Rd | 90 man/lightsail_get_instances.Rd | 282 man/lightsail_get_load_balancer.Rd | 140 man/lightsail_get_load_balancers.Rd | 156 man/lightsail_get_operation.Rd | 100 man/lightsail_get_operations.Rd | 122 man/lightsail_get_operations_for_resource.Rd | 124 man/lightsail_import_key_pair.Rd | 102 man/lightsail_open_instance_public_ports.Rd | 140 man/lightsail_peer_vpc.Rd | 86 man/lightsail_put_alarm.Rd | 402 man/lightsail_put_instance_public_ports.Rd | 158 man/lightsail_reboot_instance.Rd | 108 man/lightsail_reboot_relational_database.Rd | 110 man/lightsail_register_container_image.Rd | 142 man/lightsail_release_static_ip.Rd | 100 man/lightsail_reset_distribution_cache.Rd | 120 man/lightsail_send_contact_method_verification.Rd | 132 man/lightsail_start_instance.Rd | 120 man/lightsail_start_relational_database.Rd | 112 man/lightsail_stop_instance.Rd | 134 man/lightsail_stop_relational_database.Rd | 120 man/lightsail_tag_resource.Rd | 138 man/lightsail_test_alarm.Rd | 140 man/lightsail_unpeer_vpc.Rd | 86 man/lightsail_untag_resource.Rd | 130 man/lightsail_update_container_service.Rd | 354 man/lightsail_update_distribution.Rd | 234 man/lightsail_update_distribution_bundle.Rd | 144 man/lightsail_update_domain_entry.Rd | 134 man/lightsail_update_load_balancer_attribute.Rd | 126 man/lightsail_update_relational_database.Rd | 284 man/lightsail_update_relational_database_parameters.Rd | 160 man/serverlessapplicationrepository.Rd | 200 man/serverlessapplicationrepository_create_application.Rd | 356 man/serverlessapplicationrepository_update_application.Rd | 224 tests/testthat/test_batch.R | 26 tests/testthat/test_ec2.R | 1346 tests/testthat/test_ec2instanceconnect.R | 6 tests/testthat/test_ecr.R | 18 tests/testthat/test_ecs.R | 50 tests/testthat/test_eks.R | 18 tests/testthat/test_elasticbeanstalk.R | 66 tests/testthat/test_lambda.R | 34 tests/testthat/test_lightsail.R | 6 tests/testthat/test_serverlessapplicationrepository.R | 10 342 files changed, 138426 insertions(+), 138430 deletions(-)
Title: Feature Selection (Including Multiple Solutions) and Bayesian
Networks
Description: Many feature selection methods for a wide range of response variables, including minimal, statistically-equivalent and equally-predictive feature subsets. Bayesian network algorithms and related functions are also included. The package name 'MXM' stands for "Mens eX Machina", meaning "Mind from the Machine" in Latin. References: a) Lagani, V. and Athineou, G. and Farcomeni, A. and Tsagris, M. and Tsamardinos, I. (2017). Feature Selection with the R Package MXM: Discovering Statistically Equivalent Feature Subsets. Journal of Statistical Software, 80(7). <doi:10.18637/jss.v080.i07>. b) Tsagris, M., Lagani, V. and Tsamardinos, I. (2018). Feature selection for high-dimensional temporal data. BMC Bioinformatics, 19:17. <doi:10.1186/s12859-018-2023-7>. c) Tsagris, M., Borboudakis, G., Lagani, V. and Tsamardinos, I. (2018). Constraint-based causal discovery with mixed data. International Journal of Data Science and Analytics, 6(1): 19-30. <doi:10.1007/s41060-018-0097-y>. d) [...truncated...]
Author: Konstantina Biza [aut, cre],
Ioannis Tsamardinos [aut, cph],
Vincenzo Lagani [aut, cph],
Giorgos Athineou [aut],
Michail Tsagris [aut],
Giorgos Borboudakis [ctb],
Anna Roumpelaki [ctb]
Maintainer: Konstantina Biza <kbiza@csd.uoc.gr>
Diff between MXM versions 1.5.4 dated 2022-06-06 and 1.5.5 dated 2022-08-25
DESCRIPTION | 16 ++++++---- MD5 | 58 +++++++++++++++++++-------------------- R/bbc.R | 7 ++-- inst/doc/FS_guide.pdf |binary inst/doc/MMPC_tutorial.html | 12 ++++---- inst/doc/SES_KMVerrou_11_12.html | 36 ++++++++++++------------ inst/doc/article.pdf |binary inst/doc/guide.pdf |binary man/MXM-package.Rd | 21 ++++++-------- man/MXMCondIndTests.Rd | 10 +++--- man/SES.glmm.Rd | 4 +- man/big.gomp.Rd | 7 ++-- man/cond.regs.Rd | 2 - man/cv.fbed.lmm.reg.Rd | 2 - man/cv.gomp.Rd | 7 ++-- man/cv.ses.Rd | 2 - man/ebic.glmm.bsreg.Rd | 2 - man/ebic.regs.Rd | 2 - man/fbed.gee.reg.Rd | 4 +- man/fbed.glmm.reg.Rd | 2 - man/glmm.bsreg.Rd | 2 - man/glmm.ci.mm.Rd | 2 - man/gomp.Rd | 7 ++-- man/mmhc.skel.Rd | 2 - man/mmpc.glmm.model.Rd | 4 +- man/mmpc.glmm2.Rd | 4 +- man/pc.skel.Rd | 2 - man/testIndGEEReg.Rd | 2 - man/testIndGLMMReg.Rd | 4 +- man/univregs.Rd | 2 - 30 files changed, 111 insertions(+), 114 deletions(-)
Title: Computation of the Double-Entry Intraclass Correlation
Description: The function computes the double-entry intraclass correlation, which is an index of profile similarity (Furr, 2010; McCrae, 2008). The double-entry intraclass correlation is a more precise index of the agreement of two empirically observed profiles than the often-used intraclass correlation (McCrae, 2008). The function transforms profiles comprising correlations according to the Fisher z-transformation before the double-entry intraclass correlation is calculated. If the profiles comprise scores such as sum scores from various personality scales, it is recommended to standardize each individual score before entering into the function (McCrae, 2008). See Furr (2010) <doi:10.1080/00223890903379134> or McCrae (2008) <doi:10.1080/00223890701845104> for details.
Author: Christian Bloetner, Michael Paul Grosz
Maintainer: Christian Bloetner <c.bloetner@gmail.com>
Diff between iccde versions 0.3.3 dated 2022-04-22 and 0.3.4 dated 2022-08-25
DESCRIPTION | 8 ++-- MD5 | 6 +-- R/iccde.R | 15 ++++--- man/iccde.Rd | 115 +++++++++++++++++++++++++++++------------------------------ 4 files changed, 73 insertions(+), 71 deletions(-)
Title: A Small Collection of Geometries, and Stats for 'ggplot2'
Description: A collection of geometries and stats for
'ggplot2'. Currently it supports geom_pointless() which adds
minimal emphasis to your plots. Or just some visual sugar.
geom_lexis() draws a 45° lifeline of an event that mimics
lexis diagrams. geom_chaikin() applies Chaikin's corner
cutting algorithm to a path.
Author: Markus Doering [aut, cre]
Maintainer: Markus Doering <m4rkus.doering@gmail.com>
Diff between ggpointless versions 0.0.2 dated 2022-06-08 and 0.0.3 dated 2022-08-25
DESCRIPTION | 28 +- MD5 | 54 +++-- NAMESPACE | 3 NEWS.md | 6 R/geom-chaikin.R |only R/geom-lexis.R | 19 + R/geom-pointless.R | 10 - R/legend-draw.R | 16 - R/stat-lexis.R | 44 ++-- R/utils.R | 7 README.md | 97 ++++++--- build/vignette.rds |binary inst/doc/examples.html | 243 +++++++++++++++++++++++-- inst/doc/ggpointless.R | 32 ++- inst/doc/ggpointless.Rmd | 44 +++- inst/doc/ggpointless.html | 330 ++++++++++++++++++++++++++++++---- man/figures/README-geom-chaikin-1.png |only man/geom_chaikin.Rd |only man/geom_lexis.Rd | 25 +- man/geom_pointless.Rd | 10 - man/ggpointless-ggproto.Rd | 5 man/ggpointless-package.Rd | 6 tests/testthat/Rplots.pdf |binary tests/testthat/_snaps/geom-chaikin |only tests/testthat/_snaps/stat-chaikin |only tests/testthat/test-cut_corners.R |only tests/testthat/test-geom-chaikin.R |only tests/testthat/test-is_integer.R |only tests/testthat/test-lerp.R |only tests/testthat/test-lerp_neighbors.R |only tests/testthat/test-neighbors.R |only tests/testthat/test-stat-chaikin.R |only tests/testthat/test-stat-lexis.R | 6 vignettes/ggpointless.Rmd | 44 +++- 34 files changed, 809 insertions(+), 220 deletions(-)
Title: Excursion Sets and Contour Credibility Regions for Random Fields
Description: Functions that compute probabilistic excursion sets, contour credibility regions, contour avoiding regions, and simultaneous confidence bands for latent Gaussian random processes and fields. The package also contains functions that calculate these quantities for models estimated with the INLA package. The main references for excursions are Bolin and Lindgren (2015) <doi:10.1111/rssb.12055>, Bolin and Lindgren (2017) <doi:10.1080/10618600.2016.1228537>, and Bolin and Lindgren (2018) <doi:10.18637/jss.v086.i05>. These can be generated by the citation function in R.
Author: David Bolin [cre, aut],
Finn Lindgren [aut]
Maintainer: David Bolin <davidbolin@gmail.com>
Diff between excursions versions 2.5.2 dated 2021-09-17 and 2.5.3 dated 2022-08-25
DESCRIPTION | 11 ++++----- MD5 | 31 +++++++++++++------------ NEWS.md | 5 ++++ R/inlautils.R | 41 +++++++++++++++++++++++++++++----- R/utils.R | 19 +++++++++++++-- man/local_exc_testthat.Rd | 4 +-- tests/testthat.R | 10 ++++++++ tests/testthat/_snaps |only tests/testthat/helper-data.R | 18 ++++++++------ tests/testthat/test.continuous.R | 2 - tests/testthat/test.contourmap.R | 2 - tests/testthat/test.contourmap.inla.R | 26 +++++---------------- tests/testthat/test.excursions.R | 3 -- tests/testthat/test.excursions.inla.R | 19 ++++++++++++++- tests/testthat/test.integration.R | 1 tests/testthat/test.simconf.R | 2 - tests/testthat/test.variances.R | 1 17 files changed, 125 insertions(+), 70 deletions(-)
Title: Fisher's z-Tests Concerning Difference of Correlations
Description: Computations of Fisher's z-tests concerning differences between correlations. diffcor.one() tests whether an expected value differs from an observed value, for example, in construct validation. diffcor.two() tests whether the correlation between two constructs differed across two studies/samples. diffcor.dep() checks whether the correlation between two constructs (r12) is significantly different from the correlation between the first construct with a third one (r13), given the intercorrelation of the compared constructs (r23). All outputs provide the compared correlations, test statistic in z-units, and p-values. For diffcor.one() and diffcor.two(), the output further provides confidence intervals of the empirical correlations and the effect size Cohens q. According to Cohen (1988), q = |.10|, |.30| and |.50| are considered small, moderate, and large differences, respectively.
Author: Christian Bloetner
Maintainer: Christian Bloetner <c.bloetner@gmail.com>
Diff between diffcor versions 0.7.1 dated 2022-05-05 and 0.7.2 dated 2022-08-25
diffcor-0.7.1/diffcor/R/source_code_diffcor.R |only diffcor-0.7.1/diffcor/man/diffcor.Rd |only diffcor-0.7.2/diffcor/DESCRIPTION | 10 +++++----- diffcor-0.7.2/diffcor/MD5 | 10 +++++++--- diffcor-0.7.2/diffcor/R/diffcor.dep.R |only diffcor-0.7.2/diffcor/R/diffcor.one.R |only diffcor-0.7.2/diffcor/R/diffcor.two.R |only diffcor-0.7.2/diffcor/man/diffcor.dep.Rd |only diffcor-0.7.2/diffcor/man/diffcor.one.Rd |only diffcor-0.7.2/diffcor/man/diffcor.two.Rd |only 10 files changed, 12 insertions(+), 8 deletions(-)
Title: A Graphical User Interface for Antitrust and Trade Practitioners
Description: A graphical user interface for simulating the effects of mergers, tariffs, and quotas under an
assortment of different economic models. The interface is powered by the 'Shiny' web application framework from
'RStudio'.
Author: Charles Taragin [aut, cre],
Kenneth Rios [aut],
Paulette Wolak [aut]
Maintainer: Charles Taragin <ctaragin+competitiontoolbox@gmail.com>
Diff between competitiontoolbox versions 0.7.0 dated 2021-05-21 and 0.7.1 dated 2022-08-25
competitiontoolbox-0.7.0/competitiontoolbox/README.md |only competitiontoolbox-0.7.1/competitiontoolbox/DESCRIPTION | 12 - competitiontoolbox-0.7.1/competitiontoolbox/MD5 | 22 +-- competitiontoolbox-0.7.1/competitiontoolbox/R/ct_shiny.R | 1 competitiontoolbox-0.7.1/competitiontoolbox/R/data.R | 17 +- competitiontoolbox-0.7.1/competitiontoolbox/build |only competitiontoolbox-0.7.1/competitiontoolbox/inst/ct_shiny/rsconnect/shinyapps.io/daag/ct_shiny.dcf | 5 competitiontoolbox-0.7.1/competitiontoolbox/man/indicboxdata.Rd | 66 +++++----- competitiontoolbox-0.7.1/competitiontoolbox/man/indicboxmktCnt.Rd | 2 competitiontoolbox-0.7.1/competitiontoolbox/man/sumboxdata.Rd | 4 competitiontoolbox-0.7.1/competitiontoolbox/man/sumboxdata_trade.Rd | 66 +++++----- competitiontoolbox-0.7.1/competitiontoolbox/man/sumboxmktCnt.Rd | 4 competitiontoolbox-0.7.1/competitiontoolbox/man/sumboxmktCnt_trade.Rd | 50 +++---- 13 files changed, 125 insertions(+), 124 deletions(-)
More information about competitiontoolbox at CRAN
Permanent link
Title: Model Butcher
Description: Provides a set of S3 generics to axe components of fitted
model objects and help reduce the size of model objects saved to disk.
Author: Joyce Cahoon [aut] ,
Davis Vaughan [aut],
Max Kuhn [aut],
Alex Hayes [aut],
Julia Silge [cre, aut] ,
RStudio [cph, fnd]
Maintainer: Julia Silge <julia.silge@rstudio.com>
Diff between butcher versions 0.2.0 dated 2022-06-14 and 0.3.0 dated 2022-08-25
DESCRIPTION | 28 ++++++----- MD5 | 23 +++++---- NAMESPACE | 5 ++ NEWS.md | 8 +++ R/gam.R |only R/ui.R | 2 build/butcher.pdf |binary build/vignette.rds |binary inst/doc/adding-models-to-butcher.html | 13 ++++- inst/doc/available-axe-methods.html | 80 ++++++++++++++++++--------------- inst/doc/butcher.html | 19 +++++-- man/axe-gam.Rd |only man/butcher-package.Rd | 3 - tests/testthat/test-gam.R |only 14 files changed, 112 insertions(+), 69 deletions(-)
Title: Interface to the Algorithm Selection Benchmark Library
Description: Provides an interface to the algorithm selection benchmark library
at <http://www.aslib.net> and the 'LLAMA' package
(<https://cran.r-project.org/package=llama>) for building
algorithm selection models; see Bischl et al. (2016)
<doi:10.1016/j.artint.2016.04.003>.
Author: Bernd Bischl <bernd_bischl@gmx.net>, Lars Kotthoff <larsko@uwyo.edu>,
Pascal Kerschke <kerschke@uni-muenster.de> [ctb],
Damir Pulatov <damirpolat@protonmail.com> [ctb]
Maintainer: Lars Kotthoff <larsko@uwyo.edu>
Diff between aslib versions 0.1.1 dated 2020-05-24 and 0.1.2 dated 2022-08-25
aslib-0.1.1/aslib/R/convertToMlr.R |only aslib-0.1.2/aslib/DESCRIPTION | 19 - aslib-0.1.2/aslib/MD5 | 127 +++--- aslib-0.1.2/aslib/NAMESPACE | 4 aslib-0.1.2/aslib/NEWS | 5 aslib-0.1.2/aslib/R/convertFeats.R | 49 +- aslib-0.1.2/aslib/R/convertPerf.R | 6 aslib-0.1.2/aslib/R/convertToCheck.R | 5 aslib-0.1.2/aslib/R/convertToLlama.R | 127 ++++-- aslib-0.1.2/aslib/R/convertToLlamaCVFolds.R | 16 aslib-0.1.2/aslib/R/getCostsAndPresolvedStatus.R | 45 +- aslib-0.1.2/aslib/R/getFeatureNames.R | 16 aslib-0.1.2/aslib/R/getFeatureStepNames.R | 14 aslib-0.1.2/aslib/R/getProvidedFeatures.R | 20 - aslib-0.1.2/aslib/R/parseASScenario.R | 185 +++++++--- aslib-0.1.2/aslib/R/parseDescription.R | 15 aslib-0.1.2/aslib/R/runLlamaModels.R | 87 ++-- aslib-0.1.2/aslib/R/summarizeFeatureSteps.R | 29 + aslib-0.1.2/aslib/R/summarizeFeatureValues.R | 13 aslib-0.1.2/aslib/R/summarizeLlamaExps.R |only aslib-0.1.2/aslib/R/utils.R | 10 aslib-0.1.2/aslib/R/writeASScenario.R | 13 aslib-0.1.2/aslib/R/zzz.R | 3 aslib-0.1.2/aslib/man/ASScenarioDesc.Rd | 7 aslib-0.1.2/aslib/man/checkDuplicatedInstances.Rd | 1 aslib-0.1.2/aslib/man/convertAlgoPerfToWideFormat.Rd | 1 aslib-0.1.2/aslib/man/convertToLlama.Rd | 1 aslib-0.1.2/aslib/man/convertToLlamaCVFolds.Rd | 18 aslib-0.1.2/aslib/man/createCVSplits.Rd | 1 aslib-0.1.2/aslib/man/findDominatedAlgos.Rd | 1 aslib-0.1.2/aslib/man/fixFeckingPresolve.Rd | 1 aslib-0.1.2/aslib/man/getAlgorithmNames.Rd | 1 aslib-0.1.2/aslib/man/getCosealASScenario.Rd | 1 aslib-0.1.2/aslib/man/getCostsAndPresolvedStatus.Rd | 18 aslib-0.1.2/aslib/man/getDefaultFeatureStepNames.Rd | 1 aslib-0.1.2/aslib/man/getFeatureNames.Rd | 6 aslib-0.1.2/aslib/man/getFeatureStepNames.Rd | 6 aslib-0.1.2/aslib/man/getInstanceNames.Rd | 1 aslib-0.1.2/aslib/man/getNumberOfCVFolds.Rd | 1 aslib-0.1.2/aslib/man/getNumberOfCVReps.Rd | 1 aslib-0.1.2/aslib/man/getProvidedFeatures.Rd | 6 aslib-0.1.2/aslib/man/getSummedFeatureCosts.Rd | 1 aslib-0.1.2/aslib/man/imputeAlgoPerf.Rd | 11 aslib-0.1.2/aslib/man/parseASScenario.Rd | 31 + aslib-0.1.2/aslib/man/plotAlgoCorMatrix.Rd | 10 aslib-0.1.2/aslib/man/plotAlgoPerf.Rd | 49 +- aslib-0.1.2/aslib/man/runLlamaModels.Rd | 15 aslib-0.1.2/aslib/man/summarizeAlgoPerf.Rd | 1 aslib-0.1.2/aslib/man/summarizeAlgoRunstatus.Rd | 1 aslib-0.1.2/aslib/man/summarizeFeatureSteps.Rd | 1 aslib-0.1.2/aslib/man/summarizeFeatureValues.Rd | 6 aslib-0.1.2/aslib/man/summarizeLlamaExps.Rd |only aslib-0.1.2/aslib/man/writeASScenario.Rd | 1 aslib-0.1.2/aslib/tests/testthat/gluhack18-algo |only aslib-0.1.2/aslib/tests/testthat/helper.R | 3 aslib-0.1.2/aslib/tests/testthat/test_convertToLlama.R | 18 aslib-0.1.2/aslib/tests/testthat/test_convertToLlamaCVFolds.R | 8 aslib-0.1.2/aslib/tests/testthat/test_getCostsAndPresolvedStatus.R | 22 - aslib-0.1.2/aslib/tests/testthat/test_getFeatureNames.R | 2 aslib-0.1.2/aslib/tests/testthat/test_getProvidedFeatures.R | 21 - aslib-0.1.2/aslib/tests/testthat/test_parseScenario.R | 40 ++ aslib-0.1.2/aslib/tests/testthat/test_runLlamaModels.R | 24 - aslib-0.1.2/aslib/tests/testthat/test_summarizeFeatureValues.R | 2 63 files changed, 793 insertions(+), 355 deletions(-)
Title: Support for Spatial Objects Within the 'mlr3' Ecosystem
Description: Extends the 'mlr3' ML framework with methods for spatial
objects. Data storage and prediction are supported for packages
'terra', 'raster' and 'stars'.
Author: Marc Becker [aut, cre] ,
Patrick Schratz [aut]
Maintainer: Marc Becker <marcbecker@posteo.de>
Diff between mlr3spatial versions 0.2.0 dated 2022-08-18 and 0.2.1 dated 2022-08-25
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 6 +++++- R/zzz.R | 6 +++--- data/leipzig.rda |binary tests/testthat/test_predict_spatial.R | 1 + 6 files changed, 18 insertions(+), 13 deletions(-)
Title: Uniform Manifold Approximation and Projection
Description: Uniform manifold approximation and projection is a technique
for dimension reduction. The algorithm was described by McInnes and
Healy (2018) in <arXiv:1802.03426>. This package provides an interface
for two implementations. One is written from scratch, including components
for nearest-neighbor search and for embedding. The second implementation
is a wrapper for 'python' package 'umap-learn' (requires separate
installation, see vignette for more details).
Author: Tomasz Konopka [aut, cre]
Maintainer: Tomasz Konopka <tokonopka@gmail.com>
Diff between umap versions 0.2.8.0 dated 2022-03-25 and 0.2.9.0 dated 2022-08-25
DESCRIPTION | 8 - MD5 | 82 ++++++------ R/coo.R | 108 +++++++--------- R/coo_spectral.R | 110 +++++++--------- R/embedding.R | 122 ++++++++---------- R/knn.R | 256 ++++++++++++++++++-------------------- R/umap.R | 52 +++---- R/umap_checks.R | 62 ++++----- R/umap_learn.R | 66 ++++----- R/umap_naive.R | 268 ++++++++++++++++++---------------------- R/umap_print.R | 36 ++--- R/umap_small.R | 15 -- R/umap_universal.R | 107 +++++++-------- R/utils.R | 20 -- inst/doc/umap.R | 54 ++++---- inst/doc/umap.Rmd | 56 ++++---- inst/doc/umap.html | 72 +++++----- inst/doc/umap_learn.R | 24 +-- inst/doc/umap_learn.Rmd | 24 +-- inst/doc/umap_learn.html | 28 ++-- man/umap.defaults.Rd | 1 src/RcppExports.cpp | 5 tests/testthat/synthetic.R | 79 +++++------ tests/testthat/test_checks.R | 188 +++++++++++----------------- tests/testthat/test_config.R | 6 tests/testthat/test_coo.R | 192 ++++++++++++---------------- tests/testthat/test_embedding.R | 135 +++++++++----------- tests/testthat/test_knn.R | 166 ++++++++++-------------- tests/testthat/test_methods.R | 129 ++++++++----------- tests/testthat/test_naive.R | 224 +++++++++++++++------------------ tests/testthat/test_predict.R | 39 ++--- tests/testthat/test_print.R | 33 +--- tests/testthat/test_python.R | 89 +++++-------- tests/testthat/test_rcpp.R | 96 +++++--------- tests/testthat/test_small.R | 35 ++--- tests/testthat/test_spectral.R | 147 +++++++++------------ tests/testthat/test_synthetic.R | 31 ++-- tests/testthat/test_universal.R | 142 ++++++++------------- tests/testthat/test_utils.R | 3 tests/testthat/train_test.R | 26 +-- vignettes/umap.Rmd | 56 ++++---- vignettes/umap_learn.Rmd | 24 +-- 42 files changed, 1529 insertions(+), 1887 deletions(-)
Title: Tour Methods for Multivariate Data Visualisation
Description: Implements geodesic interpolation and basis
generation functions that allow you to create new tour
methods from R.
Author: Hadley Wickham [aut, ctb] ,
Di Cook [aut, cre] ,
Nick Spyrison [ctb],
Ursula Laa [ctb] ,
H. Sherry Zhang [ctb],
Stuart Lee [ctb]
Maintainer: Di Cook <dicook@monash.edu>
Diff between tourr versions 0.6.0 dated 2020-12-11 and 0.6.1 dated 2022-08-25
tourr-0.6.0/tourr/NEWS |only tourr-0.6.1/tourr/DESCRIPTION | 8 tourr-0.6.1/tourr/LICENSE | 2 tourr-0.6.1/tourr/MD5 | 90 ++++---- tourr-0.6.1/tourr/NAMESPACE | 1 tourr-0.6.1/tourr/NEWS.md | 6 tourr-0.6.1/tourr/R/animate.r | 6 tourr-0.6.1/tourr/R/data.r | 13 - tourr-0.6.1/tourr/R/display-xy.r | 9 tourr-0.6.1/tourr/R/geodesic-path.r | 4 tourr-0.6.1/tourr/R/history.r | 11 tourr-0.6.1/tourr/R/interpolate.r | 2 tourr-0.6.1/tourr/R/render.r | 12 - tourr-0.6.1/tourr/R/search-better.r | 27 ++ tourr-0.6.1/tourr/R/search-frozen-geodesic.r | 3 tourr-0.6.1/tourr/R/search-geodesic.r | 9 tourr-0.6.1/tourr/R/search_polish.r | 5 tourr-0.6.1/tourr/R/tour-frozen.r | 40 ++- tourr-0.6.1/tourr/R/tour-grand.r | 3 tourr-0.6.1/tourr/R/tour-guided.r | 44 ++- tourr-0.6.1/tourr/R/tour-radial.r |only tourr-0.6.1/tourr/R/tour.r | 24 +- tourr-0.6.1/tourr/build/vignette.rds |binary tourr-0.6.1/tourr/inst/CITATION | 2 tourr-0.6.1/tourr/inst/doc/edges.R | 3 tourr-0.6.1/tourr/inst/doc/edges.Rmd | 5 tourr-0.6.1/tourr/inst/doc/edges.html | 190 +++++++++------- tourr-0.6.1/tourr/inst/doc/tourr.R | 3 tourr-0.6.1/tourr/inst/doc/tourr.Rmd | 3 tourr-0.6.1/tourr/inst/doc/tourr.html | 302 +++++++++++++++------------ tourr-0.6.1/tourr/man/Ozone-measurements.Rd | 14 - tourr-0.6.1/tourr/man/animate.Rd | 6 tourr-0.6.1/tourr/man/correct_orientation.Rd |only tourr-0.6.1/tourr/man/draw_tour_axes.Rd | 2 tourr-0.6.1/tourr/man/frozen_tour.Rd | 25 -- tourr-0.6.1/tourr/man/grand_tour.Rd | 4 tourr-0.6.1/tourr/man/guided_tour.Rd | 2 tourr-0.6.1/tourr/man/new_tour.Rd | 3 tourr-0.6.1/tourr/man/radial_tour.Rd |only tourr-0.6.1/tourr/man/render.Rd | 10 tourr-0.6.1/tourr/man/render_gif.Rd | 2 tourr-0.6.1/tourr/man/save_history.Rd | 6 tourr-0.6.1/tourr/man/search_better.Rd | 8 tourr-0.6.1/tourr/man/search_geodesic.Rd | 8 tourr-0.6.1/tourr/man/search_polish.Rd | 2 tourr-0.6.1/tourr/man/tourr-package.Rd | 6 tourr-0.6.1/tourr/vignettes/edges.Rmd | 5 tourr-0.6.1/tourr/vignettes/tourr.Rmd | 3 48 files changed, 531 insertions(+), 402 deletions(-)
Title: Easily Create Presentation-Ready Display Tables
Description: Build display tables from tabular data with an easy-to-use set of
functions. With its progressive approach, we can construct display tables
with a cohesive set of table parts. Table values can be formatted using any
of the included formatting functions. Footnotes and cell styles can be
precisely added through a location targeting system. The way in which 'gt'
handles things for you means that you don't often have to worry about the
fine details.
Author: Richard Iannone [aut, cre] ,
Joe Cheng [aut],
Barret Schloerke [aut] ,
Ellis Hughes [aut] ,
RStudio [cph, fnd]
Maintainer: Richard Iannone <rich@rstudio.com>
Diff between gt versions 0.6.0 dated 2022-05-24 and 0.7.0 dated 2022-08-25
gt-0.6.0/gt/R/utils_render_footnotes.R |only gt-0.6.0/gt/tests/testthat/test-gtsave.R |only gt-0.7.0/gt/DESCRIPTION | 42 gt-0.7.0/gt/MD5 | 448 +++--- gt-0.7.0/gt/NAMESPACE | 19 gt-0.7.0/gt/NEWS.md | 40 gt-0.7.0/gt/R/as_data_frame.R | 23 gt-0.7.0/gt/R/build_data.R | 3 gt-0.7.0/gt/R/compile_scss.R | 19 gt-0.7.0/gt/R/data_color.R | 102 - gt-0.7.0/gt/R/datasets.R | 12 gt-0.7.0/gt/R/dt__.R | 3 gt-0.7.0/gt/R/dt_body.R | 7 gt-0.7.0/gt/R/dt_boxhead.R | 124 - gt-0.7.0/gt/R/dt_cols_merge.R | 17 gt-0.7.0/gt/R/dt_data.R | 11 gt-0.7.0/gt/R/dt_footnotes.R | 71 - gt-0.7.0/gt/R/dt_formats.R | 10 gt-0.7.0/gt/R/dt_groups_rows.R | 32 gt-0.7.0/gt/R/dt_has_built.R | 9 gt-0.7.0/gt/R/dt_heading.R | 16 gt-0.7.0/gt/R/dt_locale.R | 10 gt-0.7.0/gt/R/dt_options.R | 16 gt-0.7.0/gt/R/dt_row_groups.R | 8 gt-0.7.0/gt/R/dt_source_notes.R | 25 gt-0.7.0/gt/R/dt_spanners.R | 83 - gt-0.7.0/gt/R/dt_stub_df.R | 95 - gt-0.7.0/gt/R/dt_stubhead.R | 8 gt-0.7.0/gt/R/dt_styles.R | 87 - gt-0.7.0/gt/R/dt_summary.R | 82 - gt-0.7.0/gt/R/dt_transforms.R | 12 gt-0.7.0/gt/R/export.R | 408 ++++-- gt-0.7.0/gt/R/format_data.R | 997 +++++++++++++-- gt-0.7.0/gt/R/format_vec.R |only gt-0.7.0/gt/R/gt.R | 46 gt-0.7.0/gt/R/gt_preview.R | 2 gt-0.7.0/gt/R/helpers.R | 194 +- gt-0.7.0/gt/R/image.R | 8 gt-0.7.0/gt/R/info_tables.R | 12 gt-0.7.0/gt/R/location_methods.R | 103 - gt-0.7.0/gt/R/modify_columns.R | 183 +- gt-0.7.0/gt/R/modify_rows.R | 19 gt-0.7.0/gt/R/opts.R | 226 ++- gt-0.7.0/gt/R/print.R | 16 gt-0.7.0/gt/R/resolver.R | 122 - gt-0.7.0/gt/R/shiny.R | 11 gt-0.7.0/gt/R/substitution.R | 29 gt-0.7.0/gt/R/summary_rows.R | 4 gt-0.7.0/gt/R/sysdata.rda |binary gt-0.7.0/gt/R/tab_create_modify.R | 385 ++++- gt-0.7.0/gt/R/text_transform.R | 11 gt-0.7.0/gt/R/utils.R | 848 ++++++++---- gt-0.7.0/gt/R/utils_formatters.R | 386 ++--- gt-0.7.0/gt/R/utils_general_str_formatting.R | 231 +-- gt-0.7.0/gt/R/utils_render_common.R | 127 - gt-0.7.0/gt/R/utils_render_html.R | 164 +- gt-0.7.0/gt/R/utils_render_latex.R | 134 +- gt-0.7.0/gt/R/utils_render_rtf.R | 74 - gt-0.7.0/gt/R/utils_render_xml.R |only gt-0.7.0/gt/R/z_utils_render_footnotes.R |only gt-0.7.0/gt/R/zzz.R | 11 gt-0.7.0/gt/inst/css/gt_styles_default.scss | 43 gt-0.7.0/gt/man/adjust_luminance.Rd | 6 gt-0.7.0/gt/man/as_latex.Rd | 27 gt-0.7.0/gt/man/as_raw_html.Rd | 5 gt-0.7.0/gt/man/as_rtf.Rd | 5 gt-0.7.0/gt/man/as_word.Rd |only gt-0.7.0/gt/man/cell_borders.Rd | 18 gt-0.7.0/gt/man/cell_fill.Rd | 6 gt-0.7.0/gt/man/cell_text.Rd | 6 gt-0.7.0/gt/man/cells_body.Rd | 6 gt-0.7.0/gt/man/cells_column_labels.Rd | 6 gt-0.7.0/gt/man/cells_column_spanners.Rd | 6 gt-0.7.0/gt/man/cells_footnotes.Rd | 6 gt-0.7.0/gt/man/cells_grand_summary.Rd | 6 gt-0.7.0/gt/man/cells_row_groups.Rd | 6 gt-0.7.0/gt/man/cells_source_notes.Rd | 6 gt-0.7.0/gt/man/cells_stub.Rd | 6 gt-0.7.0/gt/man/cells_stub_grand_summary.Rd | 6 gt-0.7.0/gt/man/cells_stub_summary.Rd | 6 gt-0.7.0/gt/man/cells_stubhead.Rd | 6 gt-0.7.0/gt/man/cells_summary.Rd | 6 gt-0.7.0/gt/man/cells_title.Rd | 6 gt-0.7.0/gt/man/cols_align.Rd | 6 gt-0.7.0/gt/man/cols_hide.Rd | 8 gt-0.7.0/gt/man/cols_label.Rd | 8 gt-0.7.0/gt/man/cols_merge.Rd | 6 gt-0.7.0/gt/man/cols_merge_n_pct.Rd | 6 gt-0.7.0/gt/man/cols_merge_range.Rd | 6 gt-0.7.0/gt/man/cols_merge_uncert.Rd | 6 gt-0.7.0/gt/man/cols_move.Rd | 6 gt-0.7.0/gt/man/cols_move_to_end.Rd | 8 gt-0.7.0/gt/man/cols_move_to_start.Rd | 8 gt-0.7.0/gt/man/cols_unhide.Rd | 8 gt-0.7.0/gt/man/cols_width.Rd | 6 gt-0.7.0/gt/man/countrypops.Rd | 20 gt-0.7.0/gt/man/currency.Rd | 6 gt-0.7.0/gt/man/data_color.Rd | 9 gt-0.7.0/gt/man/default_fonts.Rd | 6 gt-0.7.0/gt/man/escape_latex.Rd | 4 gt-0.7.0/gt/man/exibble.Rd | 28 gt-0.7.0/gt/man/extract_summary.Rd | 75 - gt-0.7.0/gt/man/fmt.Rd | 9 gt-0.7.0/gt/man/fmt_bytes.Rd | 9 gt-0.7.0/gt/man/fmt_currency.Rd | 9 gt-0.7.0/gt/man/fmt_date.Rd | 9 gt-0.7.0/gt/man/fmt_datetime.Rd | 7 gt-0.7.0/gt/man/fmt_duration.Rd |only gt-0.7.0/gt/man/fmt_engineering.Rd | 7 gt-0.7.0/gt/man/fmt_fraction.Rd | 20 gt-0.7.0/gt/man/fmt_integer.Rd | 7 gt-0.7.0/gt/man/fmt_markdown.Rd | 9 gt-0.7.0/gt/man/fmt_number.Rd | 9 gt-0.7.0/gt/man/fmt_partsper.Rd | 7 gt-0.7.0/gt/man/fmt_passthrough.Rd | 9 gt-0.7.0/gt/man/fmt_percent.Rd | 7 gt-0.7.0/gt/man/fmt_scientific.Rd | 7 gt-0.7.0/gt/man/fmt_time.Rd | 9 gt-0.7.0/gt/man/ggplot_image.Rd | 6 gt-0.7.0/gt/man/google_font.Rd | 8 gt-0.7.0/gt/man/grand_summary_rows.Rd | 6 gt-0.7.0/gt/man/gt-options.Rd | 4 gt-0.7.0/gt/man/gt-package.Rd | 1 gt-0.7.0/gt/man/gt.Rd | 8 gt-0.7.0/gt/man/gt_latex_dependencies.Rd | 4 gt-0.7.0/gt/man/gt_preview.Rd | 6 gt-0.7.0/gt/man/gtcars.Rd | 40 gt-0.7.0/gt/man/gtsave.Rd | 33 gt-0.7.0/gt/man/html.Rd | 6 gt-0.7.0/gt/man/info_currencies.Rd | 8 gt-0.7.0/gt/man/info_date_style.Rd | 6 gt-0.7.0/gt/man/info_google_fonts.Rd | 6 gt-0.7.0/gt/man/info_locales.Rd | 6 gt-0.7.0/gt/man/info_paletteer.Rd | 6 gt-0.7.0/gt/man/info_time_style.Rd | 6 gt-0.7.0/gt/man/local_image.Rd | 6 gt-0.7.0/gt/man/md.Rd | 6 gt-0.7.0/gt/man/opt_align_table_header.Rd | 7 gt-0.7.0/gt/man/opt_all_caps.Rd | 7 gt-0.7.0/gt/man/opt_css.Rd | 9 gt-0.7.0/gt/man/opt_footnote_marks.Rd | 7 gt-0.7.0/gt/man/opt_horizontal_padding.Rd | 7 gt-0.7.0/gt/man/opt_row_striping.Rd | 7 gt-0.7.0/gt/man/opt_stylize.Rd |only gt-0.7.0/gt/man/opt_table_font.Rd | 9 gt-0.7.0/gt/man/opt_table_lines.Rd | 7 gt-0.7.0/gt/man/opt_table_outline.Rd | 9 gt-0.7.0/gt/man/opt_vertical_padding.Rd | 7 gt-0.7.0/gt/man/pct.Rd | 6 gt-0.7.0/gt/man/pizzaplace.Rd | 24 gt-0.7.0/gt/man/px.Rd | 6 gt-0.7.0/gt/man/random_id.Rd | 4 gt-0.7.0/gt/man/row_group_order.Rd | 4 gt-0.7.0/gt/man/sp500.Rd | 24 gt-0.7.0/gt/man/sub_large_vals.Rd | 37 gt-0.7.0/gt/man/sub_missing.Rd | 7 gt-0.7.0/gt/man/sub_small_vals.Rd | 37 gt-0.7.0/gt/man/sub_zero.Rd | 33 gt-0.7.0/gt/man/summary_rows.Rd | 6 gt-0.7.0/gt/man/sza.Rd | 18 gt-0.7.0/gt/man/tab_footnote.Rd | 9 gt-0.7.0/gt/man/tab_header.Rd | 7 gt-0.7.0/gt/man/tab_options.Rd | 23 gt-0.7.0/gt/man/tab_row_group.Rd | 9 gt-0.7.0/gt/man/tab_source_note.Rd | 9 gt-0.7.0/gt/man/tab_spanner.Rd | 7 gt-0.7.0/gt/man/tab_spanner_delim.Rd | 7 gt-0.7.0/gt/man/tab_stub_indent.Rd |only gt-0.7.0/gt/man/tab_stubhead.Rd | 7 gt-0.7.0/gt/man/tab_style.Rd | 13 gt-0.7.0/gt/man/test_image.Rd | 4 gt-0.7.0/gt/man/text_transform.Rd | 7 gt-0.7.0/gt/man/vec_fmt_bytes.Rd |only gt-0.7.0/gt/man/vec_fmt_currency.Rd |only gt-0.7.0/gt/man/vec_fmt_date.Rd |only gt-0.7.0/gt/man/vec_fmt_datetime.Rd |only gt-0.7.0/gt/man/vec_fmt_duration.Rd |only gt-0.7.0/gt/man/vec_fmt_engineering.Rd |only gt-0.7.0/gt/man/vec_fmt_fraction.Rd |only gt-0.7.0/gt/man/vec_fmt_integer.Rd |only gt-0.7.0/gt/man/vec_fmt_markdown.Rd |only gt-0.7.0/gt/man/vec_fmt_number.Rd |only gt-0.7.0/gt/man/vec_fmt_partsper.Rd |only gt-0.7.0/gt/man/vec_fmt_percent.Rd |only gt-0.7.0/gt/man/vec_fmt_scientific.Rd |only gt-0.7.0/gt/man/vec_fmt_time.Rd |only gt-0.7.0/gt/man/web_image.Rd | 8 gt-0.7.0/gt/tests/performance-monitoring |only gt-0.7.0/gt/tests/testthat.R | 1 gt-0.7.0/gt/tests/testthat/helper-gt_attr_expectations.R | 15 gt-0.7.0/gt/tests/testthat/test-color_handling.R | 17 gt-0.7.0/gt/tests/testthat/test-cols_align.R | 9 gt-0.7.0/gt/tests/testthat/test-cols_label.R | 29 gt-0.7.0/gt/tests/testthat/test-cols_merge.R | 21 gt-0.7.0/gt/tests/testthat/test-cols_move.R | 115 + gt-0.7.0/gt/tests/testthat/test-cols_width.R | 13 gt-0.7.0/gt/tests/testthat/test-conditional_fmt.R | 45 gt-0.7.0/gt/tests/testthat/test-fmt_bytes.R | 97 - gt-0.7.0/gt/tests/testthat/test-fmt_currency.R | 435 ++++-- gt-0.7.0/gt/tests/testthat/test-fmt_date_time.R | 8 gt-0.7.0/gt/tests/testthat/test-fmt_engineering.R | 514 ++++--- gt-0.7.0/gt/tests/testthat/test-fmt_integer.R | 125 + gt-0.7.0/gt/tests/testthat/test-fmt_markdown.R | 4 gt-0.7.0/gt/tests/testthat/test-fmt_number.R | 347 +++-- gt-0.7.0/gt/tests/testthat/test-fmt_partsper.R | 15 gt-0.7.0/gt/tests/testthat/test-fmt_passthrough.R | 4 gt-0.7.0/gt/tests/testthat/test-fmt_percent.R | 64 gt-0.7.0/gt/tests/testthat/test-fmt_scientific.R | 209 +-- gt-0.7.0/gt/tests/testthat/test-gt_object.R | 134 +- gt-0.7.0/gt/tests/testthat/test-gt_preview.R | 2 gt-0.7.0/gt/tests/testthat/test-h_md_html.R | 2 gt-0.7.0/gt/tests/testthat/test-helper_functions.R | 2 gt-0.7.0/gt/tests/testthat/test-info_tables.R | 23 gt-0.7.0/gt/tests/testthat/test-input_data_validation.R | 32 gt-0.7.0/gt/tests/testthat/test-l_cols_align.R | 4 gt-0.7.0/gt/tests/testthat/test-l_cols_merge.R | 2 gt-0.7.0/gt/tests/testthat/test-l_cols_move.R | 2 gt-0.7.0/gt/tests/testthat/test-l_fmt_currency.R | 2 gt-0.7.0/gt/tests/testthat/test-l_fmt_date_time.R | 2 gt-0.7.0/gt/tests/testthat/test-l_fmt_engineering.R | 2 gt-0.7.0/gt/tests/testthat/test-l_fmt_integer.R | 2 gt-0.7.0/gt/tests/testthat/test-l_fmt_markdown.R | 4 gt-0.7.0/gt/tests/testthat/test-l_fmt_passthrough.R | 2 gt-0.7.0/gt/tests/testthat/test-l_fmt_scientific.R | 2 gt-0.7.0/gt/tests/testthat/test-l_row_group_order.R | 10 gt-0.7.0/gt/tests/testthat/test-l_tab_spanner_delim.R | 2 gt-0.7.0/gt/tests/testthat/test-opt_functions.R | 17 gt-0.7.0/gt/tests/testthat/test-resolver.R | 4 gt-0.7.0/gt/tests/testthat/test-row_group_order.R | 6 gt-0.7.0/gt/tests/testthat/test-rtf_column_widths.R | 2 gt-0.7.0/gt/tests/testthat/test-rtf_page_options.R | 1 gt-0.7.0/gt/tests/testthat/test-tab_style.R | 24 gt-0.7.0/gt/tests/testthat/test-text_transform.R | 33 gt-0.7.0/gt/tests/testthat/test-util_functions.R | 68 - gt-0.7.0/gt/tests/testthat/test-utils_formatters.R | 22 235 files changed, 6127 insertions(+), 3675 deletions(-)