Title: Running Operations for Vectors
Description: Calculates running functions with varying window size and missing handling options.
Package brings also running streak and running which, what extends beyond range of functions
already implemented in R packages. Calculating on windows depending on date also available.
Author: Dawid Kałędkowski [aut, cre]
Maintainer: Dawid Kałędkowski <dawid.kaledkowski@gmail.com>
Diff between runner versions 0.2.3 dated 2019-10-27 and 0.3.0 dated 2019-12-09
runner-0.2.3/runner/man/figures/custom_idx_k_lag.png |only runner-0.2.3/runner/src/aggr_run.cpp |only runner-0.2.3/runner/vignettes/images/custom_idx_k_lag.png |only runner-0.3.0/runner/DESCRIPTION | 13 runner-0.3.0/runner/MD5 | 98 runner-0.3.0/runner/NEWS.md | 25 runner-0.3.0/runner/R/RcppExports.R | 171 - runner-0.3.0/runner/README.md | 23 runner-0.3.0/runner/build/vignette.rds |binary runner-0.3.0/runner/inst/WORDLIST |only runner-0.3.0/runner/inst/doc/built-in_functions.R | 18 runner-0.3.0/runner/inst/doc/built-in_functions.Rmd | 55 runner-0.3.0/runner/inst/doc/built-in_functions.html | 10 runner-0.3.0/runner/inst/doc/runner_examples.R | 11 runner-0.3.0/runner/inst/doc/runner_examples.Rmd | 7 runner-0.3.0/runner/inst/doc/runner_examples.html | 50 runner-0.3.0/runner/inst/doc/the_runner_package.R | 4 runner-0.3.0/runner/inst/doc/the_runner_package.Rmd | 12 runner-0.3.0/runner/inst/doc/the_runner_package.html | 51 runner-0.3.0/runner/man/figures/running_date_windows_explain.png |only runner-0.3.0/runner/man/figures/running_windows_explain.png |binary runner-0.3.0/runner/man/fill_run.Rd | 10 runner-0.3.0/runner/man/lag_run.Rd | 19 runner-0.3.0/runner/man/length_run.Rd | 11 runner-0.3.0/runner/man/max_run.Rd | 13 runner-0.3.0/runner/man/mean_run.Rd | 10 runner-0.3.0/runner/man/min_run.Rd | 10 runner-0.3.0/runner/man/minmax_run.Rd | 6 runner-0.3.0/runner/man/runner.Rd | 16 runner-0.3.0/runner/man/streak_run.Rd | 13 runner-0.3.0/runner/man/sum_run.Rd | 10 runner-0.3.0/runner/man/which_run.Rd | 10 runner-0.3.0/runner/man/window_run.Rd | 7 runner-0.3.0/runner/src/Makevars |only runner-0.3.0/runner/src/Makevars.win |only runner-0.3.0/runner/src/RcppExports.cpp | 121 - runner-0.3.0/runner/src/aggregations.h | 2 runner-0.3.0/runner/src/checks.h |only runner-0.3.0/runner/src/fill_run.cpp | 10 runner-0.3.0/runner/src/lag_run.cpp | 78 runner-0.3.0/runner/src/lag_run.h | 170 + runner-0.3.0/runner/src/length_run.cpp | 19 runner-0.3.0/runner/src/runner.cpp | 1180 +++++++--- runner-0.3.0/runner/src/runner.h | 146 - runner-0.3.0/runner/src/utils.h | 38 runner-0.3.0/runner/src/window.cpp |only runner-0.3.0/runner/src/window.h |only runner-0.3.0/runner/tests/spelling.R |only runner-0.3.0/runner/tests/testthat/test_lag_run.R | 118 - runner-0.3.0/runner/tests/testthat/test_mean_run.R | 4 runner-0.3.0/runner/tests/testthat/test_runner.R | 101 runner-0.3.0/runner/vignettes/built-in_functions.Rmd | 55 runner-0.3.0/runner/vignettes/images/running_date_windows_explain.png |only runner-0.3.0/runner/vignettes/images/running_windows_explain.png |binary runner-0.3.0/runner/vignettes/runner_examples.Rmd | 7 runner-0.3.0/runner/vignettes/the_runner_package.Rmd | 12 56 files changed, 1836 insertions(+), 908 deletions(-)
Title: Download, Compile and Link 'OpenBLAS' Library with R
Description: The 'ropenblas' package (<https://prdm0.github.io/ropenblas/>) is useful for users of any 'GNU/Linux' distribution. It will be possible to download, compile and link the 'OpenBLAS' library (<https://www.openblas.net/>) with the R language, always by the same procedure, regardless of the 'GNU/Linux' distribution used. With the 'ropenblas' package it is possible to download, compile and link the latest version of the 'OpenBLAS' library even the repositories of the 'GNU/Linux' distribution used do not include the latest versions of 'OpenBLAS'. If of interest, older versions of the 'OpenBLAS' library may be considered. Linking R with an optimized version of 'BLAS' (<http://www.netlib.org/blas/>) may improve the computational performance of R code. The 'OpenBLAS' library is an optimized implementation of 'BLAS' that can be easily linked to R with the 'ropenblas' package.
Author: Pedro Rafael D. Marinho [aut, cre]
Maintainer: Pedro Rafael D. Marinho <pedro.rafael.marinho@gmail.com>
Diff between ropenblas versions 0.1.0 dated 2019-12-02 and 0.2.0 dated 2019-12-09
DESCRIPTION | 19 + MD5 | 14 - NAMESPACE | 12 + NEWS.md | 14 + R/ropenblas.R | 539 ++++++++++++++++++++++++++++++++++++++++++-------- README.md | 94 +++++++- man/last_version_r.Rd |only man/rcompiler.Rd |only man/ropenblas.Rd | 16 + 9 files changed, 593 insertions(+), 115 deletions(-)
Title: Joint Sentiment Topic Modelling
Description: Estimates the Joint Sentiment Topic model and its reversed variety,
as described by Lin and He, 2009 <DOI:10.1145/1645953.1646003> and Lin, He, Everson and Ruger
(2012) <DOI:10.1109/TKDE.2011.48>.
Author: Max Boiten [cre, aut],
Chenghua Lin [cph],
Yulan He [cph]
Maintainer: Max Boiten <max_boiten@live.nl>
Diff between rJST versions 1.0 dated 2018-11-14 and 1.1 dated 2019-12-09
DESCRIPTION | 15 - MD5 | 43 ++--- NAMESPACE | 2 R/get_parameter.R | 91 +++++----- R/jst.R | 215 ++++++++++++++----------- R/jst_reversed.R | 227 +++++++++++++++----------- README.md | 2 build/vignette.rds |binary inst/doc/rJST.html | 331 +++++++++++++++++++++++++++++++++------ man/JST.result-class.Rd | 56 +++--- man/JST_reversed.result-class.Rd | 56 +++--- man/dictionary_wordstem.Rd | 34 ++-- man/get_parameter.Rd | 56 +++--- man/is.JST.result.Rd | 32 +-- man/is.JST_reversed.result.Rd | 32 +-- man/jst.Rd | 129 ++++++++------- man/jst_reversed.Rd | 121 +++++++------- man/paradigm.Rd | 44 ++--- man/rJST-package.Rd | 50 ++--- man/top20words-method.Rd | 94 +++++------ man/topNwords-method.Rd | 96 +++++------ tests |only 22 files changed, 1020 insertions(+), 706 deletions(-)
Title: Restricted Statistical Estimation and Inference for Linear
Models
Description: Allow for easy-to-use testing or evaluating of linear equality and inequality
restrictions about parameters and effects in (generalized) linear statistical models.
Author: Leonard Vanbrabant [aut, cre],
Yves Rosseel [ctb]
Maintainer: Leonard Vanbrabant <info@restriktor.org>
Diff between restriktor versions 0.2-250 dated 2019-12-02 and 0.2-500 dated 2019-12-09
DESCRIPTION | 10 +++--- MD5 | 16 +++++----- R/conGLM.R | 4 ++ R/conLM.R | 37 ++++------------------- R/conMLM.R | 14 ++------ R/conRLM.R | 4 ++ R/con_constraints.R | 72 +++++++++++++++++++++++++++++----------------- R/con_gorica_est.R | 4 ++ man/restriktor-package.rd | 4 +- 9 files changed, 84 insertions(+), 81 deletions(-)
Title: Project Environments
Description: A dependency management toolkit for R. Using 'renv', you can create
and manage project-local R libraries, save the state of these libraries to
a 'lockfile', and later restore your library as required. Together, these
tools can help make your projects more isolated, portable, and reproducible.
Author: Kevin Ushey [aut, cre],
RStudio [cph]
Maintainer: Kevin Ushey <kevin@rstudio.com>
Diff between renv versions 0.9.1 dated 2019-12-09 and 0.9.2 dated 2019-12-09
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 4 ++++ R/cache.R | 4 ++++ inst/doc/docker.html | 2 +- inst/doc/lockfile.html | 2 +- inst/doc/renv.html | 6 +++--- 7 files changed, 22 insertions(+), 14 deletions(-)
Title: Solver for Delay Differential Equations
Description: Functions for solving systems of delay differential equations by
interfacing with numerical routines written by Simon N. Wood, including
contributions from Benjamin J. Cairns. These numerical routines first
appeared in Simon Wood's 'solv95' program. This package includes a vignette
and a complete user's guide. 'PBSddesolve' originally appeared on CRAN under
the name 'ddesolve'. That version is no longer supported. The current name
emphasizes a close association with other 'PBS' packages, particularly
'PBSmodelling'.
Author: Alex Couture-Beil [aut],
Jon T. Schnute [aut],
Rowan Haigh [aut, cre],
Simon N. Wood [aut],
Benjamin J. Cairns [aut],
Nicholas Boers [ctb]
Maintainer: Rowan Haigh <rowan.haigh@dfo-mpo.gc.ca>
Diff between PBSddesolve versions 1.12.5 dated 2019-12-06 and 1.12.6 dated 2019-12-09
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- inst/doc/ChangeLog.txt | 22 +++++++++++++++++----- src/PBSddesolve.c | 1 - src/r_model.c | 3 --- 5 files changed, 25 insertions(+), 17 deletions(-)
Title: Disaggregation Modelling
Description: Fits disaggregation regression models using 'TMB' ('Template Model
Builder'). When the response data are aggregated to polygon level but
the predictor variables are at a higher resolution, these models can be
useful. Regression models with spatial random fields. A useful reference for disaggregation modelling is
Lucas et al. (2019) <doi:10.1101/548719>.
Author: Anita Nandi [aut, cre] (<https://orcid.org/0000-0002-5087-2494>),
Tim Lucas [aut] (<https://orcid.org/0000-0003-4694-8107>),
Rohan Arambepola [aut],
Andre Python [aut] (<https://orcid.org/0000-0001-8094-7226>)
Maintainer: Anita Nandi <anita.k.nandi@gmail.com>
Diff between disaggregation versions 0.1.0 dated 2019-12-06 and 0.1.1 dated 2019-12-09
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- inst/doc/disaggregation.html | 4 ++-- man/prepare_data.Rd | 2 +- src/disaggregation.cpp | 5 ++--- 5 files changed, 12 insertions(+), 13 deletions(-)
More information about disaggregation at CRAN
Permanent link
Title: Client for the Open Citations Corpus
Description: Client for the Open Citations Corpus (<http://opencitations.net/>).
Includes a set of functions for getting one identifier type from another,
as well as getting references and citations for a given identifier.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between citecorp versions 0.2.0 dated 2019-11-07 and 0.2.2 dated 2019-12-09
DESCRIPTION | 8 MD5 | 39 +-- NAMESPACE | 1 NEWS.md | 8 R/citecorp-package.R | 2 R/http.R | 13 + R/oc_coci.R | 40 ++- R/oc_lookup.R | 19 + README.md | 66 +++--- man/citecorp-package.Rd | 4 man/oc_coci.Rd | 32 +- man/oc_lookup.Rd | 11 - man/oc_lookup_check.Rd |only tests/fixtures/oc_coci_citation.yml | 22 +- tests/fixtures/oc_coci_cites.yml | 118 +++++----- tests/fixtures/oc_coci_meta.yml | 34 +-- tests/fixtures/oc_coci_refs.yml | 302 ++++++++++++++-------------- tests/fixtures/oc_doi2ids.yml | 13 - tests/fixtures/oc_doi2ids_fewer_columns.yml | 26 +- tests/fixtures/oc_pmcid2ids.yml | 13 - tests/fixtures/oc_pmid2ids.yml | 13 - 21 files changed, 425 insertions(+), 359 deletions(-)
Title: Manipulating External Pointer
Description: There is limited native support for external pointers in the R interface.
This package provides some basic tools to verify, create and modify 'externalptr' objects.
Author: Randy Lai [aut, cre]
Maintainer: Randy Lai <randy.cs.lai@gmail.com>
Diff between xptr versions 1.1.1 dated 2019-01-13 and 1.1.2 dated 2019-12-09
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- R/xptr.R | 15 +++++---------- src/xptr.c | 15 ++++++++++----- 4 files changed, 23 insertions(+), 23 deletions(-)
Title: Friendly R Startup Configuration
Description: Adds support for R startup configuration via '.Renviron.d' and '.Rprofile.d' directories in addition to '.Renviron' and '.Rprofile' files. This makes it possible to keep private / secret environment variables separate from other environment variables. It also makes it easier to share specific startup settings by simply copying a file to a directory.
Author: Henrik Bengtsson [aut, cre, cph]
Maintainer: Henrik Bengtsson <henrikb@braju.com>
Diff between startup versions 0.13.0 dated 2019-10-27 and 0.14.0 dated 2019-12-09
DESCRIPTION | 10 ++-- MD5 | 22 +++++----- NEWS | 40 +++++++++++++++++++ R/check.R | 9 +++- R/find_files.R | 4 - R/rprofile_d.R | 3 - R/startup.R | 101 ++++++++++++++++++++++++++++++++++++++++++++---- R/utils.R | 56 ++++++++++++++++++++++++++ man/install.Rd | 3 - man/reset_when_cache.Rd | 5 +- man/restart.Rd | 19 ++++++--- man/startup.Rd | 52 ++++++++++++++++++------ 12 files changed, 272 insertions(+), 52 deletions(-)
Title: Computerized Adaptive Testing for Survey Research
Description: Provides methods of computerized adaptive testing for survey researchers. See Montgomery and Rossiter (2019) <doi:10.1093/jssam/smz027>. Includes functionality for data fit with the classic item response methods including the latent trait model, Birnbaum`s three parameter model, the graded response, and the generalized partial credit model. Additionally, includes several ability parameter estimation and item selection routines. During item selection, all calculations are done in compiled C++ code.
Author: Jacob Montgomery [aut],
Erin Rossiter [aut, cre]
Maintainer: Erin Rossiter <erinrossiter@wustl.edu>
Diff between catSurv versions 1.1.3 dated 2019-11-19 and 1.2.0 dated 2019-12-09
DESCRIPTION | 6 +- MD5 | 26 +++++++----- NEWS.md | 16 +++++++ R/data.R | 70 +++++++++++++++++++++++++++++++++ R/plot.Cat.R | 11 ++--- R/readQualtrics.R | 34 ++++++++-------- R/simulateThetas.R | 1 data/ex_qualtrics_results.rda |only data/ex_qualtrics_results_multiple.rda |only data/nte.rda |only man/ex_qualtrics_results.Rd |only man/ex_qualtrics_results_multiple.Rd |only man/nte.Rd |only man/plot.Cat.Rd | 11 ++--- man/readQualtrics.Rd | 15 ++++--- src/RANDOMSelector.cpp | 2 tests/testthat/test-d1LL.R | 1 17 files changed, 146 insertions(+), 47 deletions(-)
Title: Statistical Process Control for Stochastic Textured Surfaces
Description: Provides statistical process control tools for stochastic
textured surfaces. The current version supports the following tools:
(1) generic modeling of stochastic textured surfaces.
(2) local defect monitoring and diagnostics in stochastic
textured surfaces, which was proposed by Bui and Apley (2018a)
<doi:10.1080/00401706.2017.1302362>.
(3) global change monitoring in the nature of stochastic
textured surfaces, which was proposed by Bui and Apley (2018b)
<doi:10.1080/00224065.2018.1507559>.
(4) computation of dissimilarity matrix of stochastic textured
surface images, which was proposed by Bui and Apley (2019b)
<doi:10.1016/j.csda.2019.01.019>.
Author: Anh Tuan Bui [aut, cre] and Daniel W. Apley [ths]
Maintainer: Anh Bui <atbui@u.northwestern.edu>
Diff between spc4sts versions 0.5.1 dated 2019-09-04 and 0.5.2 dated 2019-12-09
DESCRIPTION | 8 +-- MD5 | 16 +++--- NAMESPACE | 1 R/climit.R | 129 +++++++++++++++++++++++++++++------------------------ R/disMat.R | 10 ++-- R/monitoringStat.R | 6 +- R/surfacemodel.R | 6 +- man/climit.Rd | 6 ++ man/dataPrep.Rd | 2 9 files changed, 102 insertions(+), 82 deletions(-)
Title: 'Lua' filters for R Markdown
Description: A collection of 'Lua' filters that extend the functionality
of R Markdown templates (e.g., count words or post-process 'pandoc-citeproc'-
citations).
Author: Frederik Aust [aut, cre] (<https://orcid.org/0000-0003-4900-788X>)
Maintainer: Frederik Aust <frederik.aust@uni-koeln.de>
Diff between rmdfiltr versions 0.1.0 dated 2019-05-05 and 0.1.1 dated 2019-12-09
DESCRIPTION | 8 ++--- MD5 | 34 +++++++++++------------ NEWS.md | 5 +++ R/add_lua_filter.R | 40 ++++++++++++++++------------ R/utils.R | 2 - README.md | 11 ++++--- inst/doc/replace_ampersands.R | 2 - inst/doc/replace_ampersands.Rmd | 2 - inst/doc/replace_ampersands.html | 14 ++++++--- inst/doc/wordcount.R | 2 - inst/doc/wordcount.Rmd | 2 - inst/doc/wordcount.html | 18 +++++++----- inst/replace_ampersands.lua | 7 ++-- man/add_lua_filter.Rd | 24 ++++++++-------- tests/testthat/test_convenience_functions.R | 10 +++---- tests/testthat/test_vectorization.R | 10 +++---- vignettes/replace_ampersands.Rmd | 2 - vignettes/wordcount.Rmd | 2 - 18 files changed, 109 insertions(+), 86 deletions(-)
Title: Generate Codes to Uniquely and Robustly Identify Individuals for
Animal Behavior Studies
Description: Facilitates the design and generation of optimal color (or symbol) codes that can be used to mark and identify individual animals. These codes are made such that the IDs are robust to partial erasure: even if sections of the code are lost, the entire identity of the animal can be reconstructed. Thus, animal subjects are not confused and no ambiguity is introduced.
Author: Andrew Taylor Burchill [aut, cre]
(<https://orcid.org/0000-0002-4197-6689>),
Theodore P. Pavlic [ctb] (<https://orcid.org/0000-0002-7073-6932>)
Maintainer: Andrew Taylor Burchill <andrew.burchill@asu.edu>
Diff between rabi versions 1.0.0 dated 2019-01-24 and 1.0.2 dated 2019-12-09
DESCRIPTION | 17 - MD5 | 49 ++-- NAMESPACE | 3 NEWS.md | 10 R/brutegenerator.R | 4 R/codestocolors.R | 7 R/exampleGUI.R | 1 R/howmany.R | 4 R/howrobust.R | 11 - R/pkgname.R | 1 R/poversample.R | 3 R/simplecodes.R | 4 R/tweaker.R | 14 - README.md | 104 ++++++--- build/vignette.rds |binary inst/CITATION |only inst/doc/loosebirdtag.html | 469 +++++++++++++++++++++++++++++++-------------- man/brute_IDs.Rd | 134 ++++++------ man/codes_to_colors.Rd | 81 ++++--- man/exampleGUI.Rd | 47 ++-- man/how_many.Rd | 75 +++---- man/how_robust.Rd | 84 ++++---- man/rabi.Rd | 61 +++-- man/rs_IDs.Rd | 110 +++++----- man/simple_IDs.Rd | 85 ++++---- man/tweaked_IDs.Rd | 126 ++++++------ 26 files changed, 892 insertions(+), 612 deletions(-)
Title: Multivariate Generalized Kernel Smoothing and Related
Statistical Methods
Description: Constructs, plots and evaluates probability distributions (probability mass/density functions, cumulative distribution functions and quantile functions) with continuous kernel smoothing, and to a lesser extent, discrete kernel smoothing. Supports univariate, multivariate and conditional distributions, including multivariate-conditional distributions. Also, supports other probability distributions (categorical, frequency and empirical-like) and weighted data, which is possibly useful mixed with fuzzy clustering. Furthermore, there are extensions for computing multivariate probabilities and multivariate random numbers, and for parameter and mode estimation.
Author: Abby Spurdle
Maintainer: Abby Spurdle <spurdle.a@gmail.com>
Diff between probhat versions 0.1.1 dated 2019-03-05 and 0.2.0 dated 2019-12-09
probhat-0.1.1/probhat/R/conditional.r |only probhat-0.1.1/probhat/R/eccdf.r |only probhat-0.1.1/probhat/R/marginal.r |only probhat-0.1.1/probhat/R/multivariate.r |only probhat-0.1.1/probhat/R/plots_conditional.r |only probhat-0.1.1/probhat/R/plots_eccdf.r |only probhat-0.1.1/probhat/R/reglike.r |only probhat-0.1.1/probhat/R/sbc.r |only probhat-0.1.1/probhat/R/spline.r |only probhat-0.1.1/probhat/R/univariate.r |only probhat-0.1.1/probhat/man/rd_1_sbc.Rd |only probhat-0.1.1/probhat/man/rd_2_nonparametric.Rd |only probhat-0.1.1/probhat/man/rd_3_marginal.Rd |only probhat-0.1.1/probhat/man/rd_4_most_plots.Rd |only probhat-0.1.1/probhat/man/rd_5_plots_bivariate.Rd |only probhat-0.1.1/probhat/man/rd_6_plots_marginal.Rd |only probhat-0.1.1/probhat/man/rd_7_combinatoric_probability.Rd |only probhat-0.1.1/probhat/man/rd_8_stats.Rd |only probhat-0.2.0/probhat/DESCRIPTION | 20 probhat-0.2.0/probhat/MD5 | 82 probhat-0.2.0/probhat/NAMESPACE | 67 probhat-0.2.0/probhat/R/categorical.r |only probhat-0.2.0/probhat/R/cks_constructors.r |only probhat-0.2.0/probhat/R/cks_eval.r |only probhat-0.2.0/probhat/R/cks_init.r |only probhat-0.2.0/probhat/R/combinatoric.r | 29 probhat-0.2.0/probhat/R/cplots.r |only probhat-0.2.0/probhat/R/dataprep.r |only probhat-0.2.0/probhat/R/distribution_set.r |only probhat-0.2.0/probhat/R/dks.r |only probhat-0.2.0/probhat/R/dplots.r |only probhat-0.2.0/probhat/R/empirical.r |only probhat-0.2.0/probhat/R/init.r |only probhat-0.2.0/probhat/R/kernel.r |only probhat-0.2.0/probhat/R/kubik_ext.r |only probhat-0.2.0/probhat/R/math_other.r |only probhat-0.2.0/probhat/R/phmodel.r |only probhat-0.2.0/probhat/R/plots_bivariate.r | 122 - probhat-0.2.0/probhat/R/plots_other.r |only probhat-0.2.0/probhat/R/plots_univariate.r | 198 + probhat-0.2.0/probhat/R/stats.r | 158 - probhat-0.2.0/probhat/R/theme.r |only probhat-0.2.0/probhat/R/utility_other.r |only probhat-0.2.0/probhat/build/vignette.rds |binary probhat-0.2.0/probhat/inst/doc/probhat.R | 450 ++- probhat-0.2.0/probhat/inst/doc/probhat.Rnw | 1178 ++++++---- probhat-0.2.0/probhat/inst/doc/probhat.pdf |binary probhat-0.2.0/probhat/inst/doc/probhatx_ckernels.R |only probhat-0.2.0/probhat/inst/doc/probhatx_ckernels.Rnw |only probhat-0.2.0/probhat/inst/doc/probhatx_ckernels.pdf |only probhat-0.2.0/probhat/man/01_unstandardized_discrete_kernels.Rd |only probhat-0.2.0/probhat/man/02_standardized_continuous_kernels.Rd |only probhat-0.2.0/probhat/man/03_discrete_kernel_smoothing.Rd |only probhat-0.2.0/probhat/man/04_continuous_kernel_smoothing.Rd |only probhat-0.2.0/probhat/man/05_categorical_distributions.Rd |only probhat-0.2.0/probhat/man/06_empirical_like_distributions.Rd |only probhat-0.2.0/probhat/man/07_distribution_sets.Rd |only probhat-0.2.0/probhat/man/08_is_functions.Rd |only probhat-0.2.0/probhat/man/09_print_methods.Rd |only probhat-0.2.0/probhat/man/10_most_plot_methods.Rd |only probhat-0.2.0/probhat/man/11_bivariate_plot_methods.Rd |only probhat-0.2.0/probhat/man/12_pairwise_kernel_arrays.Rd |only probhat-0.2.0/probhat/man/13_themes.Rd |only probhat-0.2.0/probhat/man/14_range_and_sequence_functions.Rd |only probhat-0.2.0/probhat/man/15_multivariate_probabilities.Rd |only probhat-0.2.0/probhat/man/16_random_numbers.Rd |only probhat-0.2.0/probhat/man/17_parameter_estimates.Rd |only probhat-0.2.0/probhat/man/18_other_functions.Rd |only probhat-0.2.0/probhat/vignettes/Makefile | 8 probhat-0.2.0/probhat/vignettes/probhat.Rnw | 1178 ++++++---- probhat-0.2.0/probhat/vignettes/probhatx_ckernels.Rnw |only 71 files changed, 2240 insertions(+), 1250 deletions(-)
Title: Wrap Vectors in Markdown Formatting
Description: Ease the transition between R vectors and markdown
text. With 'gluedown' and 'rmarkdown', users can create traditional
vectors in R, glue those strings together with the markdown syntax,
and print those formatted vectors directly to the document. This
package primarily uses GitHub Flavored Markdown (GFM), an offshoot of
the unambiguous CommonMark specification by John MacFarlane (2019)
<https://spec.commonmark.org/>.
Author: Kiernan Nicholls [aut, cre]
Maintainer: Kiernan Nicholls <kiernann@protonmail.com>
Diff between gluedown versions 1.0.0 dated 2019-11-28 and 1.0.1 dated 2019-12-09
gluedown-1.0.0/gluedown/R/map_md.R |only gluedown-1.0.0/gluedown/R/md-define.R |only gluedown-1.0.0/gluedown/man/map_md.Rd |only gluedown-1.0.0/gluedown/man/md_define.Rd |only gluedown-1.0.0/gluedown/tests/testthat/test-definition-lists.R |only gluedown-1.0.0/gluedown/tests/testthat/test-targeted-markdown.R |only gluedown-1.0.1/gluedown/DESCRIPTION | 33 gluedown-1.0.1/gluedown/MD5 | 112 - gluedown-1.0.1/gluedown/NAMESPACE | 9 gluedown-1.0.1/gluedown/NEWS.md | 10 gluedown-1.0.1/gluedown/R/md-chunk.R | 6 gluedown-1.0.1/gluedown/R/md-convert.R | 57 gluedown-1.0.1/gluedown/R/md-escape.R | 12 gluedown-1.0.1/gluedown/R/md-heading.R | 6 gluedown-1.0.1/gluedown/R/md-list.R | 13 gluedown-1.0.1/gluedown/R/md-rule.R | 1 gluedown-1.0.1/gluedown/README.md | 85 - gluedown-1.0.1/gluedown/build/vignette.rds |binary gluedown-1.0.1/gluedown/inst/WORDLIST | 21 gluedown-1.0.1/gluedown/inst/doc/github-spec.R | 143 +- gluedown-1.0.1/gluedown/inst/doc/github-spec.Rmd | 9 gluedown-1.0.1/gluedown/inst/doc/github-spec.html | 625 +++++----- gluedown-1.0.1/gluedown/inst/doc/literal-programming.R | 75 - gluedown-1.0.1/gluedown/inst/doc/literal-programming.Rmd | 94 - gluedown-1.0.1/gluedown/inst/doc/literal-programming.html | 381 +++--- gluedown-1.0.1/gluedown/man/gluedown.Rd | 5 gluedown-1.0.1/gluedown/man/md_autolink.Rd | 25 gluedown-1.0.1/gluedown/man/md_blank.Rd | 15 gluedown-1.0.1/gluedown/man/md_bold.Rd | 27 gluedown-1.0.1/gluedown/man/md_bullet.Rd | 12 gluedown-1.0.1/gluedown/man/md_chunk.Rd | 17 gluedown-1.0.1/gluedown/man/md_code.Rd | 23 gluedown-1.0.1/gluedown/man/md_convert.Rd | 23 gluedown-1.0.1/gluedown/man/md_disallow.Rd | 43 gluedown-1.0.1/gluedown/man/md_escape.Rd | 26 gluedown-1.0.1/gluedown/man/md_fence.Rd | 17 gluedown-1.0.1/gluedown/man/md_hardline.Rd | 25 gluedown-1.0.1/gluedown/man/md_heading.Rd | 29 gluedown-1.0.1/gluedown/man/md_image.Rd | 25 gluedown-1.0.1/gluedown/man/md_indent.Rd | 17 gluedown-1.0.1/gluedown/man/md_issue.Rd | 26 gluedown-1.0.1/gluedown/man/md_italic.Rd | 27 gluedown-1.0.1/gluedown/man/md_link.Rd | 29 gluedown-1.0.1/gluedown/man/md_list.Rd | 8 gluedown-1.0.1/gluedown/man/md_order.Rd | 16 gluedown-1.0.1/gluedown/man/md_paragraph.Rd | 17 gluedown-1.0.1/gluedown/man/md_quote.Rd | 10 gluedown-1.0.1/gluedown/man/md_reference.Rd | 17 gluedown-1.0.1/gluedown/man/md_rule.Rd | 21 gluedown-1.0.1/gluedown/man/md_setext.Rd | 19 gluedown-1.0.1/gluedown/man/md_softline.Rd | 23 gluedown-1.0.1/gluedown/man/md_strike.Rd | 28 gluedown-1.0.1/gluedown/man/md_table.Rd | 20 gluedown-1.0.1/gluedown/man/md_task.Rd | 22 gluedown-1.0.1/gluedown/man/md_text.Rd | 21 gluedown-1.0.1/gluedown/tests/testthat/test-4.3-setext-headings.R | 2 gluedown-1.0.1/gluedown/tests/testthat/test-6.5-strikethrough.R | 9 gluedown-1.0.1/gluedown/tests/testthat/test-github-issue.R | 8 gluedown-1.0.1/gluedown/vignettes/github-spec.Rmd | 9 gluedown-1.0.1/gluedown/vignettes/literal-programming.Rmd | 94 - 60 files changed, 1272 insertions(+), 1175 deletions(-)
Title: Stochastic Frontier Analysis
Description: Maximum Likelihood Estimation of
Stochastic Frontier Production and Cost Functions.
Two specifications are available:
the error components specification with time-varying efficiencies
(Battese and Coelli, 1992, <doi:10.1007/BF00158774>)
and a model specification in which the firm effects are directly
influenced by a number of variables (Battese and Coelli, 1995,
<doi:10.1007/BF01205442>).
Author: Tim Coelli, Arne Henningsen
Maintainer: Arne Henningsen <arne.henningsen@gmail.com>
Diff between frontier versions 1.1-2 dated 2017-03-17 and 1.1-6 dated 2019-12-09
DESCRIPTION | 13 ++++--- MD5 | 20 ++++++------ NEWS | 6 +++ R/front41WriteInput.R | 78 ++++++++++++++++++++++++----------------------- R/frontierDataTable.R | 2 - R/logLik.frontier.R | 2 - R/lrtest.frontier.R | 4 +- R/sfa.R | 4 +- man/front41ReadOutput.Rd | 9 +++-- man/front41WriteInput.Rd | 14 +++++--- tests/frontier41.R | 27 +++++++--------- 11 files changed, 97 insertions(+), 82 deletions(-)
Title: Discrete-Event Simulation for R
Description: A process-oriented and trajectory-based Discrete-Event Simulation
(DES) package for R. It is designed as a generic yet powerful framework. The
architecture encloses a robust and fast simulation core written in 'C++' with
automatic monitoring capabilities. It provides a rich and flexible R API that
revolves around the concept of trajectory, a common path in the simulation
model for entities of the same type. Documentation about 'simmer' is provided
by several vignettes included in this package, via the paper by Ucar, Smeets
& Azcorra (2019, <doi:10.18637/jss.v090.i02>), and the paper by Ucar,
Hernández, Serrano & Azcorra (2018, <doi:10.1109/MCOM.2018.1700960>);
see 'citation("simmer")' for details.
Author: Iñaki Ucar [aut, cph, cre] (<https://orcid.org/0000-0001-6403-5550>),
Bart Smeets [aut, cph]
Maintainer: Iñaki Ucar <iucar@fedoraproject.org>
Diff between simmer versions 4.3.0 dated 2019-07-30 and 4.4.0 dated 2019-12-09
simmer-4.3.0/simmer/inst/include/simmer/activity/leave.h |only simmer-4.3.0/simmer/man/leave.Rd |only simmer-4.3.0/simmer/man/renege_in.Rd |only simmer-4.3.0/simmer/tests/testthat/test-trajectory-leave.R |only simmer-4.4.0/simmer/DESCRIPTION | 8 simmer-4.4.0/simmer/MD5 | 125 +-- simmer-4.4.0/simmer/NEWS.md | 24 simmer-4.4.0/simmer/R/RcppExports.R | 48 - simmer-4.4.0/simmer/R/generators.R | 55 - simmer-4.4.0/simmer/R/monitor-methods.R | 21 simmer-4.4.0/simmer/R/simmer-methods.R | 184 ++-- simmer-4.4.0/simmer/R/trajectory-activities.R | 376 +++++----- simmer-4.4.0/simmer/R/trajectory-methods.R | 9 simmer-4.4.0/simmer/R/utils.R | 60 - simmer-4.4.0/simmer/R/wrap-methods.R | 5 simmer-4.4.0/simmer/build/partial.rdb |binary simmer-4.4.0/simmer/build/vignette.rds |binary simmer-4.4.0/simmer/inst/doc/simmer-01-introduction.R | 22 simmer-4.4.0/simmer/inst/doc/simmer-01-introduction.html | 50 - simmer-4.4.0/simmer/inst/doc/simmer-02-jss.R | 100 +- simmer-4.4.0/simmer/inst/doc/simmer-02-jss.pdf |binary simmer-4.4.0/simmer/inst/doc/simmer-03-trajectories.R | 38 - simmer-4.4.0/simmer/inst/doc/simmer-03-trajectories.html | 49 - simmer-4.4.0/simmer/inst/doc/simmer-04-bank-1.R | 30 simmer-4.4.0/simmer/inst/doc/simmer-04-bank-1.html | 58 - simmer-4.4.0/simmer/inst/doc/simmer-04-bank-2.R | 26 simmer-4.4.0/simmer/inst/doc/simmer-04-bank-2.html | 108 -- simmer-4.4.0/simmer/inst/doc/simmer-05-simpy.R | 46 - simmer-4.4.0/simmer/inst/doc/simmer-05-simpy.html | 142 +-- simmer-4.4.0/simmer/inst/doc/simmer-06-queueing.R | 24 simmer-4.4.0/simmer/inst/doc/simmer-06-queueing.html | 37 simmer-4.4.0/simmer/inst/doc/simmer-07-ctmc.R | 34 simmer-4.4.0/simmer/inst/doc/simmer-07-ctmc.html | 9 simmer-4.4.0/simmer/inst/doc/simmer-08-philosophers.R | 10 simmer-4.4.0/simmer/inst/doc/simmer-08-philosophers.html | 11 simmer-4.4.0/simmer/inst/doc/simmer-aa-5G.R | 22 simmer-4.4.0/simmer/inst/doc/simmer-aa-5G.html | 7 simmer-4.4.0/simmer/inst/include/simmer.h | 3 simmer-4.4.0/simmer/inst/include/simmer/activity/renege.h | 60 + simmer-4.4.0/simmer/inst/include/simmer/activity/resource_internal.h | 1 simmer-4.4.0/simmer/inst/include/simmer/activity/source.h | 61 - simmer-4.4.0/simmer/inst/include/simmer/process/arrival.h | 16 simmer-4.4.0/simmer/inst/include/simmer/process/arrival_impl.h | 22 simmer-4.4.0/simmer/inst/include/simmer/process/batched.h | 8 simmer-4.4.0/simmer/inst/include/simmer/resource.h | 39 - simmer-4.4.0/simmer/inst/include/simmer/resource/preemptive.h | 7 simmer-4.4.0/simmer/inst/include/simmer/resource/priority.h | 7 simmer-4.4.0/simmer/man/activate.Rd | 6 simmer-4.4.0/simmer/man/add_generator.Rd | 3 simmer-4.4.0/simmer/man/add_resource.Rd | 57 - simmer-4.4.0/simmer/man/batch.Rd | 3 simmer-4.4.0/simmer/man/generators.Rd | 7 simmer-4.4.0/simmer/man/monitor.Rd | 5 simmer-4.4.0/simmer/man/renege.Rd |only simmer-4.4.0/simmer/man/run.Rd | 19 simmer-4.4.0/simmer/man/seize.Rd | 17 simmer-4.4.0/simmer/man/set_trajectory.Rd | 6 simmer-4.4.0/simmer/man/simmer.Rd | 3 simmer-4.4.0/simmer/src/RcppExports.cpp | 100 +- simmer-4.4.0/simmer/src/activity.cpp | 55 - simmer-4.4.0/simmer/tests/testthat/test-convenience-funcs.R | 27 simmer-4.4.0/simmer/tests/testthat/test-simmer-generator.R | 9 simmer-4.4.0/simmer/tests/testthat/test-simmer-resource-preemption.R | 57 + simmer-4.4.0/simmer/tests/testthat/test-simmer-resource.R | 9 simmer-4.4.0/simmer/tests/testthat/test-trajectory-renege.R | 144 +++ simmer-4.4.0/simmer/tests/testthat/test-utils.R | 32 66 files changed, 1403 insertions(+), 1118 deletions(-)
Title: Include Tables, Images and Graphs in Leaflet Pop-Ups
Description: Creates 'HTML' strings to embed tables, images or graphs in pop-ups
of interactive maps created with packages like 'leaflet' or 'mapview'. Handles
local images located on the file system or via remote URL. Handles graphs created
with 'lattice' or 'ggplot2' as well as interactive plots created with 'htmlwidgets'.
Author: Tim Appelhans [cre, aut],
Florian Detsch [aut]
Maintainer: Tim Appelhans <tim.appelhans@gmail.com>
Diff between leafpop versions 0.0.1 dated 2019-04-07 and 0.0.5 dated 2019-12-09
leafpop-0.0.1/leafpop/R/RcppExports.R |only leafpop-0.0.1/leafpop/R/popup.R |only leafpop-0.0.1/leafpop/inst/templates/popup.brew |only leafpop-0.0.1/leafpop/src |only leafpop-0.0.5/leafpop/DESCRIPTION | 19 -- leafpop-0.0.5/leafpop/LICENSE | 2 leafpop-0.0.5/leafpop/MD5 | 34 ++- leafpop-0.0.5/leafpop/NAMESPACE | 11 - leafpop-0.0.5/leafpop/NEWS |only leafpop-0.0.5/leafpop/NEWS.md |only leafpop-0.0.5/leafpop/R/addPopupGraphs.R |only leafpop-0.0.5/leafpop/R/addPopupIframes.R |only leafpop-0.0.5/leafpop/R/addPopupImages.R |only leafpop-0.0.5/leafpop/R/addPopupVideos.R |only leafpop-0.0.5/leafpop/R/addPopupWidgets.R |only leafpop-0.0.5/leafpop/R/brewRy.R |only leafpop-0.0.5/leafpop/R/graph.R |only leafpop-0.0.5/leafpop/R/image.R |only leafpop-0.0.5/leafpop/R/leafpop-package.R | 2 leafpop-0.0.5/leafpop/R/table.R |only leafpop-0.0.5/leafpop/R/utils.R |only leafpop-0.0.5/leafpop/README.md | 44 ++++ leafpop-0.0.5/leafpop/inst/htmlwidgets |only leafpop-0.0.5/leafpop/inst/templates/popup-graph.brew | 4 leafpop-0.0.5/leafpop/man/addPopupGraphs.Rd |only leafpop-0.0.5/leafpop/man/addPopupImages.Rd |only leafpop-0.0.5/leafpop/man/popup.Rd | 163 +++++++++--------- 27 files changed, 167 insertions(+), 112 deletions(-)
Title: Semiparametric Competing Risks Regression under Left Truncation
and Interval Censoring with Missing Cause of Failure
Description: Semiparametric regression models on the cumulative incidence function for interval-censored competing risks data as described in Bakoyannis, Yu, & Yiannoutsos (2017) <doi:10.1002/sim.7350>, left-truncated and interval-censored competing risks data, and interval-censored compering risks data and missing cause of failure. We provide the proportional subdistribution hazards model (Fine-Gray model), the proportional odds model, and other models that belong to the class of semiparametric generalized odds rate transformation models.
Author: Giorgos Bakoyannis <gbakogia@iu.edu>, Jun Park <jp84@iu.edu>
Maintainer: Jun Park <jp84@iu.edu>
Diff between intccr versions 2.0.0 dated 2019-11-04 and 3.0.0 dated 2019-12-09
intccr-2.0.0/intccr/data/output.RData |only intccr-3.0.0/intccr/DESCRIPTION | 12 +- intccr-3.0.0/intccr/MD5 | 98 +++++++++++-------- intccr-3.0.0/intccr/NAMESPACE | 8 + intccr-3.0.0/intccr/R/Surv2.R | 25 +++- intccr-3.0.0/intccr/R/bsderivs.R | 10 - intccr-3.0.0/intccr/R/bssmle.R | 12 ++ intccr-3.0.0/intccr/R/bssmle_aipw.R |only intccr-3.0.0/intccr/R/bssmle_lse.R | 14 +- intccr-3.0.0/intccr/R/bssmle_lse_lt.R | 22 ++-- intccr-3.0.0/intccr/R/bssmle_lt.R | 26 +---- intccr-3.0.0/intccr/R/bssmle_se.R | 8 - intccr-3.0.0/intccr/R/bssmle_se_aipw.R |only intccr-3.0.0/intccr/R/ciregic.R | 22 +++- intccr-3.0.0/intccr/R/ciregic_aipw.R |only intccr-3.0.0/intccr/R/ciregic_lt.R | 13 +- intccr-3.0.0/intccr/R/dataprep.R | 24 +++- intccr-3.0.0/intccr/R/dataprep_lt.R | 16 ++- intccr-3.0.0/intccr/R/longdata.R | 7 - intccr-3.0.0/intccr/R/longdata_lt.R | 2 intccr-3.0.0/intccr/R/output.R | 4 intccr-3.0.0/intccr/R/output_aipw.R |only intccr-3.0.0/intccr/R/output_lt.R | 4 intccr-3.0.0/intccr/R/simdata.R | 17 ++- intccr-3.0.0/intccr/R/simdata_aipw.R |only intccr-3.0.0/intccr/R/simdata_lt.R | 15 ++ intccr-3.0.0/intccr/R/waldtest.R | 8 - intccr-3.0.0/intccr/data/fit.RData |only intccr-3.0.0/intccr/data/fit_aipw.RData |only intccr-3.0.0/intccr/data/simdata_aipw.rda |only intccr-3.0.0/intccr/man/Surv2.Rd | 8 + intccr-3.0.0/intccr/man/bs.derivs.Rd | 6 - intccr-3.0.0/intccr/man/bssmle.Rd | 9 + intccr-3.0.0/intccr/man/bssmle_aipw.Rd |only intccr-3.0.0/intccr/man/bssmle_lse.Rd | 8 - intccr-3.0.0/intccr/man/bssmle_lse_lt.Rd | 8 - intccr-3.0.0/intccr/man/bssmle_lt.Rd | 14 +- intccr-3.0.0/intccr/man/bssmle_se.Rd | 1 intccr-3.0.0/intccr/man/bssmle_se_aipw.Rd |only intccr-3.0.0/intccr/man/ciregic.Rd | 5 intccr-3.0.0/intccr/man/ciregic_aipw.Rd |only intccr-3.0.0/intccr/man/ciregic_lt.Rd | 9 - intccr-3.0.0/intccr/man/dataprep.Rd | 6 - intccr-3.0.0/intccr/man/dataprep_lt.Rd | 2 intccr-3.0.0/intccr/man/dbs.Rd | 6 - intccr-3.0.0/intccr/man/fit.Rd | 2 intccr-3.0.0/intccr/man/fit_aipw.Rd |only intccr-3.0.0/intccr/man/fit_lt.Rd | 4 intccr-3.0.0/intccr/man/longdata.Rd | 7 - intccr-3.0.0/intccr/man/longdata_lt.Rd | 2 intccr-3.0.0/intccr/man/predict.ciregic_aipw.Rd |only intccr-3.0.0/intccr/man/predict.dbs.Rd | 2 intccr-3.0.0/intccr/man/simdata.Rd | 17 ++- intccr-3.0.0/intccr/man/simdata_aipw.Rd |only intccr-3.0.0/intccr/man/simdata_lt.Rd | 17 ++- intccr-3.0.0/intccr/man/summary.ciregic_aipw.Rd |only intccr-3.0.0/intccr/man/vcov.ciregic_aipw.Rd |only intccr-3.0.0/intccr/man/vcov.summary.ciregic_aipw.Rd |only intccr-3.0.0/intccr/man/waldtest.Rd | 6 - 59 files changed, 319 insertions(+), 187 deletions(-)
Title: Regression with Functional Data
Description: Methods for regression for functional
data, including function-on-scalar, scalar-on-function, and
function-on-function regression. Some of the functions are applicable to
image data.
Author: Jeff Goldsmith [aut],
Fabian Scheipl [aut],
Lei Huang [aut],
Julia Wrobel [aut, cre],
Chongzhi Di [aut],
Jonathan Gellar [aut],
Jaroslaw Harezlak [aut],
Mathew W. McLean [aut],
Bruce Swihart [aut],
Luo Xiao [aut],
Ciprian Crainiceanu [aut],
Philip T. Reiss [aut],
Yakuan Chen [ctb],
Sonja Greven [ctb],
Lan Huo [ctb],
Madan Gopal Kundu [ctb],
So Young Park [ctb],
David L. Miller [ctb],
Ana-Maria Staicu [ctb]
Maintainer: Julia Wrobel <julia.wrobel@cuanschutz.edu>
Diff between refund versions 0.1-17 dated 2018-05-15 and 0.1-21 dated 2019-12-09
DESCRIPTION | 24 MD5 | 288 ++-- NAMESPACE | 3 R/DTI-data.R | 96 - R/DTI2-data.R | 92 - R/GLS_CS.R | 342 ++--- R/Gibbs_CS_FPCA.R | 556 ++++----- R/Gibbs_CS_Wish.R | 444 +++---- R/Gibbs_Mult_FPCA.R | 657 +++++------ R/Gibbs_Mult_Wish.R | 585 +++++----- R/OLS_CS.R | 264 ++-- R/Omegas.R | 46 R/VB_CS_FPCA.R | 574 ++++----- R/VB_CS_Wish.R | 440 +++---- R/VB_Mult_FPCA.R | 614 +++++----- R/VB_Mult_Wish.R | 554 ++++----- R/XtSiginvX.R | 70 - R/af.R | 522 ++++----- R/af_old.R | 316 ++--- R/amc.R | 153 +- R/bayes_fosr.R | 256 ++-- R/ccb.fpc.R | 318 ++--- R/coefficients.pfr.R | 496 ++++---- R/create.prep.func.R | 150 +- R/dt_basis.R | 768 ++++++------- R/f_sum.R | 44 R/f_sum2.R | 44 R/f_sum4.R | 64 - R/f_trace.R | 46 R/fbps.R | 684 +++++------ R/fgam.R | 546 ++++----- R/fosr.R | 785 ++++++------- R/fosr.perm.R | 206 +-- R/fosr.perm.fit.R | 244 ++-- R/fosr.perm.test.R | 32 R/fosr.vs.R | 272 ++-- R/fosr2s.R | 218 +-- R/fpc.R | 530 ++++----- R/fpca.face.R | 766 ++++++------- R/fpca.lfda.R | 958 ++++++++-------- R/fpca.sc.R | 670 +++++------ R/fpca.ssvd.R | 616 +++++----- R/fpca2s.R | 394 +++--- R/fpcr.R | 614 +++++----- R/fpcr.setup.R | 166 +- R/lf.R | 351 +++--- R/lf.vd.R | 704 ++++++------ R/lf_old.R | 232 ++-- R/lofocv.R | 194 +-- R/lpeer.R | 1112 +++++++++---------- R/lpfr.R | 440 +++---- R/lw.test.R | 22 R/mfpca.sc.R | 738 ++++++------ R/parse.predict.pfr.R | 108 - R/peer.R | 556 ++++----- R/peer_old.R | 612 +++++----- R/pffr-ff.R | 566 ++++----- R/pffr-ffpc.R | 450 +++---- R/pffr-methods.R | 1590 +++++++++++++-------------- R/pffr-pcre.R | 312 ++--- R/pffr-robust.R | 1835 +++++++++++++++---------------- R/pffr-sff.R | 318 ++--- R/pffr-utilities.R | 763 ++++++------- R/pffr.R | 1853 ++++++++++++++++---------------- R/pfr.R | 651 +++++------ R/pfr_old.R | 524 ++++----- R/pi_basis.R | 460 +++---- R/plot.fosr.R | 88 - R/plot.fosr.perm.R | 40 R/plot.fosr.vs.R | 116 +- R/plot.fpcr.R | 68 - R/plot.lpeer.R | 116 +- R/plot.peer.R | 94 - R/plot.pfr.R | 1476 ++++++++++++------------- R/poridge.R | 830 +++++++------- R/postprocess.pfr.R | 60 - R/predict.fbps.R | 236 ++-- R/predict.fosr.vs.R | 112 - R/predict.pfr.R | 502 ++++---- R/predict.pfr_old.R | 94 - R/pspline.setting.R | 186 +-- R/pwcv.R | 220 +-- R/quadWeights.R | 44 R/re.R | 42 R/select_knots.R | 34 R/summary.pfr.R | 58 - R/vis.fgam.R | 492 ++++---- R/vis.pfr.R | 494 ++++---- data/datalist | 14 man/af.Rd | 4 man/af_old.Rd | 9 man/bayes_fosr.Rd | 4 man/cmdscale_lanczos.Rd | 19 man/coef.pffr.Rd | 4 man/coefboot.pffr.Rd | 4 man/coefficients.pfr.Rd | 4 man/create.prep.func.Rd | 4 man/fbps.Rd | 12 man/ff.Rd | 6 man/ffpc.Rd | 4 man/fosr.Rd | 6 man/fosr.perm.Rd | 6 man/fosr.vs.Rd | 4 man/fpc.Rd | 10 man/fpca.face.Rd | 5 man/fpca.lfda.Rd | 9 man/fpca.ssvd.Rd | 2 man/fpca2s.Rd | 2 man/gibbs_mult_fpca.Rd | 6 man/gibbs_mult_wish.Rd | 4 man/lf.Rd | 4 man/lf.vd.Rd | 8 man/lofocv.Rd | 3 man/mfpca.sc.Rd | 5 man/pco_predict_preprocess.Rd | 42 man/peer.Rd | 2 man/peer_old.Rd | 2 man/pffr.Rd | 5 man/pffrGLS.Rd | 6 man/pffrSim.Rd | 10 man/pfr_old.Rd | 2 man/pfr_plot.gam.Rd | 34 man/plot.fpcr.Rd | 4 man/plot.peer.Rd | 5 man/predict.fbps.Rd | 4 man/predict.fgam.Rd | 4 man/predict.pfr.Rd | 4 man/refund-internal.Rd | 56 man/refund-package.Rd | 48 man/residuals.pffr.Rd | 1 man/sff.Rd | 6 man/smooth.construct.dt.smooth.spec.Rd | 6 man/smooth.construct.pco.smooth.spec.Rd | 57 man/smooth.construct.pss.smooth.spec.Rd | 2 man/sofa.Rd | 4 man/vb_cs_wish.Rd | 9 man/vb_mult_wish.Rd | 10 man/vis.fgam.Rd | 2 man/vis.pfr.Rd | 7 tests |only 140 files changed, 18503 insertions(+), 18311 deletions(-)
Title: An Extended Mixed-Effects Framework for Meta-Analysis
Description: A collection of functions to perform various meta-analytical models
through a unified mixed-effects framework, including standard univariate
fixed and random-effects meta-analysis and meta-regression, and non-standard
extensions such as multivariate, multilevel, longitudinal, and dose-response
models.
Author: Antonio Gasparrini [aut, cre],
Francesco Sera [aut]
Maintainer: Antonio Gasparrini <antonio.gasparrini@lshtm.ac.uk>
Diff between mixmeta versions 1.0.5 dated 2019-11-11 and 1.0.7 dated 2019-12-09
DESCRIPTION | 8 - MD5 | 12 +- NEWS.md | 25 +++++ R/mixmeta.R | 258 ++++++++++++++++++++++++++++----------------------------- inst/NEWS | 25 +++++ man/dbs.Rd | 7 - man/gliomas.Rd | 3 7 files changed, 195 insertions(+), 143 deletions(-)
Title: General-Purpose MCMC and SMC Samplers and Tools for Bayesian
Statistics
Description: General-purpose MCMC and SMC samplers, as well as plot and
diagnostic functions for Bayesian statistics, with a particular focus on
calibrating complex system models. Implemented samplers include various
Metropolis MCMC variants (including adaptive and/or delayed rejection MH), the
T-walk, two differential evolution MCMCs, two DREAM MCMCs, and a sequential
Monte Carlo (SMC) particle filter.
Author: Florian Hartig [aut, cre] (<https://orcid.org/0000-0002-6255-9059>),
Francesco Minunno [aut],
Stefan Paul [aut],
David Cameron [ctb],
Tankred Ott [ctb],
Maximilian Pichler [ctb]
Maintainer: Florian Hartig <florian.hartig@biologie.uni-regensburg.de>
Diff between BayesianTools versions 0.1.6 dated 2019-01-21 and 0.1.7 dated 2019-12-09
DESCRIPTION | 25 ++-- MD5 | 91 +++++++++-------- NEWS | 9 + R/BayesianTools.R | 2 R/GOF.R | 27 +++-- R/SMC.R | 2 R/classBayesianOutput.R | 17 ++- R/classBayesianSetup.R | 11 +- R/classMcmcSampler.R | 8 - R/classMcmcSamplerList.R | 5 R/classPrior.R | 12 ++ R/diagnosticsGelman.R | 14 ++ R/marginalLikelihood.R | 17 +-- R/mcmcDE.R | 2 R/mcmcDEzs.R | 4 R/mcmcDREAM.R | 2 R/mcmcDREAMzs.R | 4 R/mcmcRun.R | 10 + R/plotMarginals.R | 41 ++++++- R/plotSensitivityOAT.R | 51 +++++++-- R/plotTimeSeries.R | 9 - R/utils-Numerics.R | 7 - R/utils.R | 2 build/vignette.rds |binary inst/doc/BayesianTools.Rmd | 2 inst/doc/BayesianTools.html | 155 +++++++++++++++++------------- inst/doc/InterfacingAModel.R |only inst/doc/InterfacingAModel.Rmd |only inst/doc/InterfacingAModel.html |only inst/examples/marginalLikelihoodHelp.R | 118 ++++++++++++++++++++-- inst/examples/plotSensitivityHelp.R |only inst/examples/plotTimeSeriesResultsHelp.R | 3 man/BayesianTools.Rd | 2 man/GOF.Rd | 11 +- man/createBayesianSetup.Rd | 10 + man/createPriorDensity.Rd | 11 ++ man/getSample.Rd | 72 +++++++++++++ man/logSumExp.Rd | 2 man/marginalLikelihood.Rd | 124 ++++++++++++++++++++---- man/marginalPlot.Rd | 6 - man/plotSensitivity.Rd | 11 +- man/plotTimeSeries.Rd | 8 - man/plotTimeSeriesResults.Rd | 3 man/runMCMC.Rd | 2 tests/testthat/test-getSample.R |only tests/testthat/test-marginalLikelihood.R | 11 +- tests/testthat/test-marginalPlot.R | 40 +++---- tests/testthat/test-runMCMC.R |only vignettes/BayesianTools.Rmd | 2 vignettes/InterfacingAModel.Rmd |only 50 files changed, 696 insertions(+), 269 deletions(-)
Title: Exploratory Graphics for Pharmacometrics
Description: Supports a structured approach
for exploring PKPD data <https://opensource.nibr.com/xgx>. It also
contains helper functions for enabling the modeler to follow best R
practices (by appending the program name, figure name location, and
draft status to each plot). In addition, it enables the modeler to
follow best graphical practices (by providing a theme that
reduces chart ink, and by providing time-scale, log-scale, and
reverse-log-transform-scale functions for more readable axes).
Finally, it provides some data checking and summarizing functions for
rapidly exploring pharmacokinetics and pharmacodynamics (PKPD) datasets.
Author: Andrew Stein [aut, cre],
Alison Margolskee [aut],
Fariba Khanshan [aut],
Konstantin Krismer [aut] (<https://orcid.org/0000-0001-8994-3416>),
Matthew Fidler [ctb] (<https://orcid.org/0000-0001-8538-6691>),
Novartis Pharma AG [cph, fnd]
Maintainer: Andrew Stein <andy.stein@gmail.com>
Diff between xgxr versions 1.0.5 dated 2019-10-17 and 1.0.6 dated 2019-12-09
DESCRIPTION | 6 - MD5 | 30 +++---- NEWS | 7 + R/xgx_breaks_time.R | 9 +- R/xgx_check_data.R | 2 R/xgx_scale_x_reverselog10.R | 13 ++- R/xgx_scale_y_reverselog10.R | 13 ++- inst/doc/sad_pkpd.R | 12 ++- inst/doc/sad_pkpd.Rmd | 12 ++- inst/doc/sad_pkpd.html | 157 ++++++++++++++++++++-------------------- inst/doc/theoph.html | 6 - inst/doc/xgxr_overview.html | 38 ++++----- man/xgx_breaks_time.Rd | 4 - man/xgx_scale_x_reverselog10.Rd | 7 + man/xgx_scale_y_reverselog10.Rd | 7 + vignettes/sad_pkpd.Rmd | 12 ++- 16 files changed, 193 insertions(+), 142 deletions(-)
Title: Maximum Likelihood Shrinkage using Generalized Ridge or Least
Angle Regression Methods
Description: Functions are provided to calculate and display ridge TRACEs for various
shrinkage PATHS. They determine the m-Extent of shrinkage most likely, under
Normal-distribution theory, to produce biased estimates of regression (beta) coefficients
with minimum MSE Risk. An alternative function, correct.signs(), provides beta coefficient
estimates when an ill-conditioned (nearly multicollinear) model yields OLS estimates with
("wrong") numerical signs that disagree with the signs of the observed correlations between
the Y-outcome and the selected X-predictor variables.
Author: Bob Obenchain
Maintainer: Bob Obenchain <wizbob@att.net>
Diff between RXshrink versions 1.1 dated 2018-11-06 and 1.3 dated 2019-12-09
RXshrink-1.1/RXshrink/R/RXsigns.R |only RXshrink-1.1/RXshrink/man/RXlarlso.Rd |only RXshrink-1.1/RXshrink/man/RXridge.Rd |only RXshrink-1.1/RXshrink/man/RXsigns.Rd |only RXshrink-1.1/RXshrink/man/RXtrisk.Rd |only RXshrink-1.1/RXshrink/man/RXtsimu.Rd |only RXshrink-1.1/RXshrink/man/RXuclars.Rd |only RXshrink-1.1/RXshrink/man/plot.RXlarlso.Rd |only RXshrink-1.1/RXshrink/man/plot.RXridge.Rd |only RXshrink-1.1/RXshrink/man/plot.RXtrisk.Rd |only RXshrink-1.1/RXshrink/man/plot.RXtsimu.Rd |only RXshrink-1.1/RXshrink/man/plot.RXuclars.Rd |only RXshrink-1.3/RXshrink/DESCRIPTION | 26 - RXshrink-1.3/RXshrink/MD5 | 50 +- RXshrink-1.3/RXshrink/NAMESPACE | 46 +- RXshrink-1.3/RXshrink/R/RXshrink.R | 480 ++++---------------------- RXshrink-1.3/RXshrink/R/correct.signs.R |only RXshrink-1.3/RXshrink/R/qm.ridge.R |only RXshrink-1.3/RXshrink/R/unr.ridge.R |only RXshrink-1.3/RXshrink/data/haldport.rda |binary RXshrink-1.3/RXshrink/data/longley2.rda |binary RXshrink-1.3/RXshrink/data/mpg.rda |binary RXshrink-1.3/RXshrink/demo/haldport.R | 10 RXshrink-1.3/RXshrink/demo/longley2.R | 29 - RXshrink-1.3/RXshrink/demo/mpg.R | 10 RXshrink-1.3/RXshrink/man/RXshrink-package.Rd | 63 +-- RXshrink-1.3/RXshrink/man/aug.lars.Rd |only RXshrink-1.3/RXshrink/man/correct.signs.Rd |only RXshrink-1.3/RXshrink/man/internal.Rd | 32 + RXshrink-1.3/RXshrink/man/plot.aug.lars.Rd |only RXshrink-1.3/RXshrink/man/plot.qm.ridge.Rd |only RXshrink-1.3/RXshrink/man/plot.true.risk.Rd |only RXshrink-1.3/RXshrink/man/plot.true.simu.Rd |only RXshrink-1.3/RXshrink/man/plot.uc.lars.Rd |only RXshrink-1.3/RXshrink/man/plot.unr.ridge.Rd |only RXshrink-1.3/RXshrink/man/qm.ridge.Rd |only RXshrink-1.3/RXshrink/man/true.risk.Rd |only RXshrink-1.3/RXshrink/man/true.simu.Rd |only RXshrink-1.3/RXshrink/man/uc.lars.Rd |only RXshrink-1.3/RXshrink/man/unr.ridge.Rd |only 40 files changed, 222 insertions(+), 524 deletions(-)
Title: Estimate Percentiles from an Ordered Categorical Variable
Description: An implementation of two functions that estimate values for percentiles from an ordered categorical variable as described by Reardon (2011, isbn:978-0-87154-372-1). One function estimates percentile differences from two percentiles while the other returns the values for every percentile from 1 to 100.
Author: Jorge Cimentada [aut, cre] (<https://orcid.org/0000-0001-5594-1156>)
Maintainer: Jorge Cimentada <cimentadaj@gmail.com>
Diff between perccalc versions 1.0.3 dated 2018-08-24 and 1.0.4 dated 2019-12-09
DESCRIPTION | 19 LICENSE | 3 MD5 | 49 + NAMESPACE | 10 NEWS.md | 39 - R/data.R |only R/perc_diff.R | 405 +++++++------ R/perc_dist.R | 246 +++----- R/utils.R |only build/vignette.rds |binary data |only inst/CITATION |only inst/doc/perc_calculator_example.R | 308 +++++----- inst/doc/perc_calculator_example.Rmd | 8 inst/doc/perc_calculator_example.html | 1002 +++++++++++++++++----------------- inst/doc/perc_warning_example.R | 68 +- inst/doc/perc_warning_example.html | 750 +++++++++++++------------ inst/doc/pisa_example.R |only inst/doc/pisa_example.Rmd |only inst/doc/pisa_example.html |only inst/figures |only man/figures |only man/perc_diff.Rd | 140 ++-- man/perc_dist.Rd | 105 +-- man/pisa_2006.Rd |only man/pisa_2012.Rd |only tests/spelling.R | 2 tests/testthat/test-perc_funs.R | 178 +++--- vignettes/perc_calculator_example.Rmd | 8 vignettes/pisa_example.Rmd |only 30 files changed, 1742 insertions(+), 1598 deletions(-)
Title: Length-Based Multispecies Analysis by Numerical Simulation
Description: Set up, run and explore the outputs of the Length-based Multi-species model (LeMans; Hall et al. 2006 <doi:10.1139/f06-039>), focused on the marine environment.
Author: Michael A. Spence [aut, cre] (<https://orcid.org/0000-0002-3445-7979>),
Hayley J. Bannister [aut] (<https://orcid.org/0000-0002-2546-5168>),
Johnathan E. Ball [aut],
Paul J. Dolder [aut] (<https://orcid.org/0000-0002-4179-712X>),
Robert B. Thorpe [aut] (<https://orcid.org/0000-0001-8193-6932>),
Christopher A. Griffiths [ctb]
Maintainer: Michael A. Spence <michael.spence@cefas.co.uk>
Diff between LeMaRns versions 0.1.1 dated 2019-10-08 and 0.1.2 dated 2019-12-09
DESCRIPTION | 10 MD5 | 90 +- NAMESPACE | 3 R/calc_Q.R | 2 R/calc_phi.R | 4 R/other.R | 1 R/param_setup.R | 5 R/run_LeMans.R | 2 build/vignette.rds |binary inst/doc/lemarns.html | 1359 +++++++++++++++++++++++-------------------- man/LeMansParam.Rd | 365 ++++++----- man/LeMans_outputs-class.Rd | 40 - man/LeMans_param-class.Rd | 126 +-- man/NS_L50.Rd | 32 - man/NS_eta.Rd | 32 - man/NS_mixed_fish.Rd | 44 - man/NS_other.Rd | 26 man/NS_par.Rd | 52 - man/NS_tau.Rd | 38 - man/calc_LFI.Rd | 118 +-- man/calc_M1.Rd | 207 +++--- man/calc_M2.Rd | 168 ++--- man/calc_Q.Rd | 268 ++++---- man/calc_SSB.Rd | 86 +- man/calc_growth.Rd | 110 +-- man/calc_mature.Rd | 131 ++-- man/calc_phi.Rd | 140 ++-- man/calc_prefs.Rd | 122 +-- man/calc_ration_growthfac.Rd | 204 +++--- man/calc_recruits.Rd | 156 ++-- man/calc_suit_vect.Rd | 130 ++-- man/comb_LeMans_run.Rd | 86 +- man/get_N0.Rd | 132 ++-- man/get_SSB.Rd | 212 +++--- man/get_annual_catch.Rd | 251 ++++--- man/get_indicators.Rd | 472 ++++++++------ man/get_rec_fun.Rd | 78 +- man/make_rec_fun.Rd | 78 +- man/plot_SSB.Rd | 211 +++--- man/plot_indicators.Rd | 453 ++++++++------ man/rec_BH.Rd | 138 ++-- man/rec_Ricker.Rd | 140 ++-- man/rec_const.Rd | 130 ++-- man/rec_hockey.Rd | 140 ++-- man/rec_linear.Rd | 136 ++-- man/run_LeMans.Rd | 340 +++++----- 46 files changed, 3790 insertions(+), 3278 deletions(-)
Title: Parametric Voice Synthesis
Description: Tools for sound synthesis and acoustic analysis.
Performs parametric synthesis of sounds with harmonic and noise components
such as animal vocalizations or human voice. Also includes tools for
spectral analysis, pitch tracking, audio segmentation, self-similarity
matrices, morphing, etc.
Author: Andrey Anikin [aut, cre]
Maintainer: Andrey Anikin <rty.anik@rambler.ru>
Diff between soundgen versions 1.5.1 dated 2019-10-12 and 1.6.0 dated 2019-12-09
soundgen-1.5.1/soundgen/R/utilities_postprocessing.R |only soundgen-1.6.0/soundgen/DESCRIPTION | 10 soundgen-1.6.0/soundgen/MD5 | 252 +-- soundgen-1.6.0/soundgen/NAMESPACE | 6 soundgen-1.6.0/soundgen/NEWS | 21 soundgen-1.6.0/soundgen/R/SSM.R | 4 soundgen-1.6.0/soundgen/R/amplitude.R | 315 ++++ soundgen-1.6.0/soundgen/R/analyze.R | 102 + soundgen-1.6.0/soundgen/R/data.R | 14 soundgen-1.6.0/soundgen/R/formants.R | 342 ++-- soundgen-1.6.0/soundgen/R/invertModulSpec.R |only soundgen-1.6.0/soundgen/R/invertSpectrogram.R |only soundgen-1.6.0/soundgen/R/loudness.R | 4 soundgen-1.6.0/soundgen/R/matchPars.R | 10 soundgen-1.6.0/soundgen/R/modulationSpectrum.R | 197 +- soundgen-1.6.0/soundgen/R/morph.R | 2 soundgen-1.6.0/soundgen/R/optimize.R | 2 soundgen-1.6.0/soundgen/R/postprocessing.R | 118 - soundgen-1.6.0/soundgen/R/presets.R | 3 soundgen-1.6.0/soundgen/R/segment.R | 50 soundgen-1.6.0/soundgen/R/smoothContours.R | 9 soundgen-1.6.0/soundgen/R/soundgen.R | 44 soundgen-1.6.0/soundgen/R/source.R | 47 soundgen-1.6.0/soundgen/R/spectrogram.R | 34 soundgen-1.6.0/soundgen/R/utilities_analyze.R | 75 soundgen-1.6.0/soundgen/R/utilities_math.R | 25 soundgen-1.6.0/soundgen/R/utilities_morph.R | 4 soundgen-1.6.0/soundgen/R/utilities_pitch_postprocessing.R | 2 soundgen-1.6.0/soundgen/R/utilities_segment.R | 31 soundgen-1.6.0/soundgen/R/utilities_soundgen.R | 6 soundgen-1.6.0/soundgen/R/vtl.R | 4 soundgen-1.6.0/soundgen/data/permittedValues.rda |binary soundgen-1.6.0/soundgen/data/pitchContour.rda |only soundgen-1.6.0/soundgen/data/pitchManual.rda |binary soundgen-1.6.0/soundgen/inst/doc/acoustic_analysis.R | 84 - soundgen-1.6.0/soundgen/inst/doc/acoustic_analysis.Rmd | 14 soundgen-1.6.0/soundgen/inst/doc/acoustic_analysis.html | 139 - soundgen-1.6.0/soundgen/inst/doc/sound_generation.R | 212 +- soundgen-1.6.0/soundgen/inst/doc/sound_generation.Rmd | 97 - soundgen-1.6.0/soundgen/inst/doc/sound_generation.html | 997 ++++++------- soundgen-1.6.0/soundgen/inst/shiny/pitch_app/server.R | 51 soundgen-1.6.0/soundgen/inst/shiny/pitch_app/ui.R | 6 soundgen-1.6.0/soundgen/man/addFormants.Rd | 38 soundgen-1.6.0/soundgen/man/addPitchCands.Rd | 14 soundgen-1.6.0/soundgen/man/analyze.Rd | 95 - soundgen-1.6.0/soundgen/man/analyzeFolder.Rd | 136 + soundgen-1.6.0/soundgen/man/analyzeFrame.Rd | 33 soundgen-1.6.0/soundgen/man/beat.Rd | 11 soundgen-1.6.0/soundgen/man/compareSounds.Rd | 20 soundgen-1.6.0/soundgen/man/costPerPath.Rd | 10 soundgen-1.6.0/soundgen/man/crossFade.Rd | 12 soundgen-1.6.0/soundgen/man/divideIntoSyllables.Rd | 14 soundgen-1.6.0/soundgen/man/drawContour.Rd | 10 soundgen-1.6.0/soundgen/man/estimateVTL.Rd | 8 soundgen-1.6.0/soundgen/man/evaluatePars.Rd | 16 soundgen-1.6.0/soundgen/man/fade.Rd | 12 soundgen-1.6.0/soundgen/man/fart.Rd | 13 soundgen-1.6.0/soundgen/man/filled.contour.mod.Rd | 26 soundgen-1.6.0/soundgen/man/filterMS.Rd |only soundgen-1.6.0/soundgen/man/filterSoundByMS.Rd |only soundgen-1.6.0/soundgen/man/findBursts.Rd | 11 soundgen-1.6.0/soundgen/man/findSyllables.Rd | 10 soundgen-1.6.0/soundgen/man/findVoicedSegments.Rd | 14 soundgen-1.6.0/soundgen/man/flatEnv.Rd | 16 soundgen-1.6.0/soundgen/man/flatSpectrum.Rd | 14 soundgen-1.6.0/soundgen/man/gaussianSmooth2D.Rd | 3 soundgen-1.6.0/soundgen/man/generateGC.Rd | 9 soundgen-1.6.0/soundgen/man/generateHarmonics.Rd | 54 soundgen-1.6.0/soundgen/man/generateNoise.Rd | 18 soundgen-1.6.0/soundgen/man/getCheckerboardKernel.Rd | 9 soundgen-1.6.0/soundgen/man/getDiscreteContour.Rd | 13 soundgen-1.6.0/soundgen/man/getDom.Rd | 3 soundgen-1.6.0/soundgen/man/getEntropy.Rd | 8 soundgen-1.6.0/soundgen/man/getEnv.Rd | 20 soundgen-1.6.0/soundgen/man/getFormantDispersion.Rd | 7 soundgen-1.6.0/soundgen/man/getFrameBank.Rd | 13 soundgen-1.6.0/soundgen/man/getIntegerRandomWalk.Rd | 10 soundgen-1.6.0/soundgen/man/getLoudness.Rd | 18 soundgen-1.6.0/soundgen/man/getLoudnessFolder.Rd | 16 soundgen-1.6.0/soundgen/man/getMelSpec.Rd | 12 soundgen-1.6.0/soundgen/man/getPitchAutocor.Rd | 14 soundgen-1.6.0/soundgen/man/getPitchCep.Rd | 12 soundgen-1.6.0/soundgen/man/getPitchSpec.Rd | 17 soundgen-1.6.0/soundgen/man/getPrior.Rd | 12 soundgen-1.6.0/soundgen/man/getRMS.Rd | 22 soundgen-1.6.0/soundgen/man/getRMSFolder.Rd | 15 soundgen-1.6.0/soundgen/man/getRandomWalk.Rd | 9 soundgen-1.6.0/soundgen/man/getRolloff.Rd | 18 soundgen-1.6.0/soundgen/man/getRough.Rd | 7 soundgen-1.6.0/soundgen/man/getSigmoid.Rd | 3 soundgen-1.6.0/soundgen/man/getSmoothContour.Rd | 28 soundgen-1.6.0/soundgen/man/getSpectralEnvelope.Rd | 69 soundgen-1.6.0/soundgen/man/getVocalFry.Rd | 10 soundgen-1.6.0/soundgen/man/getVocalFry_per_epoch.Rd | 9 soundgen-1.6.0/soundgen/man/guessPhase_GL.Rd |only soundgen-1.6.0/soundgen/man/guessPhase_spsi.Rd |only soundgen-1.6.0/soundgen/man/interpolMatrix.Rd | 3 soundgen-1.6.0/soundgen/man/interpolate.Rd | 11 soundgen-1.6.0/soundgen/man/invertSpectrogram.Rd |only soundgen-1.6.0/soundgen/man/killDC.Rd | 11 soundgen-1.6.0/soundgen/man/matchLengths.Rd | 8 soundgen-1.6.0/soundgen/man/matchPars.Rd | 25 soundgen-1.6.0/soundgen/man/modulationSpectrum.Rd | 80 - soundgen-1.6.0/soundgen/man/modulationSpectrumFolder.Rd | 37 soundgen-1.6.0/soundgen/man/morph.Rd | 10 soundgen-1.6.0/soundgen/man/morphDF.Rd | 12 soundgen-1.6.0/soundgen/man/msToSpec.Rd |only soundgen-1.6.0/soundgen/man/normalizeFolder.Rd | 17 soundgen-1.6.0/soundgen/man/optimizePars.Rd | 20 soundgen-1.6.0/soundgen/man/osc_dB.Rd | 16 soundgen-1.6.0/soundgen/man/pathfinder.Rd | 20 soundgen-1.6.0/soundgen/man/pathfinding_fast.Rd | 10 soundgen-1.6.0/soundgen/man/pathfinding_slow.Rd | 11 soundgen-1.6.0/soundgen/man/pitchContour.Rd |only soundgen-1.6.0/soundgen/man/pitchManual.Rd | 4 soundgen-1.6.0/soundgen/man/playme.Rd | 8 soundgen-1.6.0/soundgen/man/rnorm_truncated.Rd | 12 soundgen-1.6.0/soundgen/man/schwa.Rd | 9 soundgen-1.6.0/soundgen/man/segment.Rd | 44 soundgen-1.6.0/soundgen/man/segmentFolder.Rd | 42 soundgen-1.6.0/soundgen/man/segmentManual.Rd | 4 soundgen-1.6.0/soundgen/man/snake.Rd | 11 soundgen-1.6.0/soundgen/man/soundgen.Rd | 98 - soundgen-1.6.0/soundgen/man/specToMS.Rd |only soundgen-1.6.0/soundgen/man/spectrogram.Rd | 58 soundgen-1.6.0/soundgen/man/spectrogramFolder.Rd | 24 soundgen-1.6.0/soundgen/man/ssm.Rd | 38 soundgen-1.6.0/soundgen/man/summarizeAnalyze.Rd | 7 soundgen-1.6.0/soundgen/man/transplantEnv.Rd |only soundgen-1.6.0/soundgen/man/transplantFormants.Rd | 69 soundgen-1.6.0/soundgen/man/upsamplePitchContour.Rd |only soundgen-1.6.0/soundgen/man/wiggleAnchors.Rd | 13 soundgen-1.6.0/soundgen/vignettes/acoustic_analysis.Rmd | 14 soundgen-1.6.0/soundgen/vignettes/sound_generation.Rmd | 97 - 134 files changed, 3413 insertions(+), 1754 deletions(-)
Title: Extended Structural Equation Modelling
Description: Create structural equation models that can be manipulated programmatically.
Models may be specified with matrices or paths (LISREL or RAM)
Example models include confirmatory factor, multiple group, mixture
distribution, categorical threshold, modern test theory, differential
Fit functions include full information maximum likelihood, maximum likelihood, and weighted least squares.
equations, state space, and many others.
Support and advanced package binaries available at <http://openmx.ssri.psu.edu>.
The software is described in Neale, Hunter, Pritikin, Zahery, Brick,
Kirkpatrick, Estabrook, Bates, Maes, & Boker (2016) <doi:10.1007/s11336-014-9435-8>.
Author: Steven M. Boker [aut],
Michael C. Neale [aut],
Hermine H. Maes [aut],
Michael J. Wilde [ctb],
Michael Spiegel [aut],
Timothy R. Brick [aut],
Ryne Estabrook [aut],
Timothy C. Bates [aut],
Paras Mehta [ctb],
Timo von Oertzen [ctb],
Ross J. Gore [aut],
Michael D. Hunter [aut],
Daniel C. Hackett [ctb],
Julian Karch [ctb],
Andreas M. Brandmaier [ctb],
Joshua N. Pritikin [aut, cre],
Mahsa Zahery [aut],
Robert M. Kirkpatrick [aut],
Yang Wang [ctb],
Ben Goodrich [ctb],
Charles Driver [ctb],
Massachusetts Institute of Technology [cph],
S. G. Johnson [cph],
Association for Computing Machinery [cph],
Dieter Kraft [cph],
Stefan Wilhelm [cph],
Sarah Medland [cph],
Carl F. Falk [cph],
Matt Keller [cph],
Manjunath B G [cph],
The Regents of the University of California [cph],
Lester Ingber [cph],
Wong Shao Voon [cph],
Juan Palacios [cph],
Jiang Yang [cph],
Gael Guennebaud [cph],
Jitse Niesen [cph]
Maintainer: Joshua N. Pritikin <jpritikin@pobox.com>
Diff between OpenMx versions 2.15.4 dated 2019-11-21 and 2.15.5 dated 2019-12-09
OpenMx-2.15.4/OpenMx/inst/models/passing/check_1_var_RAM_works.R |only OpenMx-2.15.4/OpenMx/inst/models/passing/check_mxSE_works.R |only OpenMx-2.15.5/OpenMx/DESCRIPTION | 8 - OpenMx-2.15.5/OpenMx/MD5 | 43 ++--- OpenMx-2.15.5/OpenMx/R/MxSE.R | 2 OpenMx-2.15.5/OpenMx/R/MxVersion.R | 2 OpenMx-2.15.5/OpenMx/inst/CITATION | 2 OpenMx-2.15.5/OpenMx/inst/models/passing/AnalyticConstraintJacobians--Eq_and_Ineq.R | 2 OpenMx-2.15.5/OpenMx/inst/models/passing/multinomSE.R | 1 OpenMx-2.15.5/OpenMx/src/Compute.cpp | 2 OpenMx-2.15.5/OpenMx/src/RAMInternal.h | 17 ++ OpenMx-2.15.5/OpenMx/src/omxAlgebra.cpp | 32 +--- OpenMx-2.15.5/OpenMx/src/omxData.cpp | 3 OpenMx-2.15.5/OpenMx/src/omxFIMLFitFunction.cpp | 2 OpenMx-2.15.5/OpenMx/src/omxHessianCalculation.cpp | 5 OpenMx-2.15.5/OpenMx/src/omxMatrix.cpp | 4 OpenMx-2.15.5/OpenMx/src/omxMatrix.h | 2 OpenMx-2.15.5/OpenMx/src/omxRAMExpectation.cpp | 77 +++++++++- OpenMx-2.15.5/OpenMx/src/omxState.cpp | 9 - OpenMx-2.15.5/OpenMx/src/omxState.h | 1 OpenMx-2.15.5/OpenMx/src/path.h | 1 OpenMx-2.15.5/OpenMx/src/povRAM.cpp | 3 OpenMx-2.15.5/OpenMx/tests/testthat/test-AlgebraComputePassing.R | 2 OpenMx-2.15.5/OpenMx/tests/testthat/test-mxSE.R |only 24 files changed, 155 insertions(+), 65 deletions(-)
Title: Fractionally Differenced ARIMA aka ARFIMA(P,d,q) Models
Description: Maximum likelihood estimation of the parameters of a fractionally
differenced ARIMA(p,d,q) model (Haslett and Raftery, Appl.Statistics, 1989);
including inference and basic methods. Some alternative algorithms to estimate "H".
Author: Martin Maechler [aut, cre] (<https://orcid.org/0000-0002-8685-9910>),
Chris Fraley [ctb, cph] (S original; Fortran code),
Friedrich Leisch [ctb] (R port,
<https://orcid.org/0000-0001-7278-1983>),
Valderio Reisen [ctb] (fdGPH() & fdSperio()),
Artur Lemonte [ctb] (fdGPH() & fdSperio()),
Rob Hyndman [ctb] (residuals() & fitted(),
<https://orcid.org/0000-0002-2140-5352>)
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between fracdiff versions 1.4-2 dated 2012-12-02 and 1.5-0 dated 2019-12-09
fracdiff-1.4-2/fracdiff/Calling |only fracdiff-1.4-2/fracdiff/Done |only fracdiff-1.4-2/fracdiff/filters.R |only fracdiff-1.5-0/fracdiff/ChangeLog | 21 ++++++++ fracdiff-1.5-0/fracdiff/DESCRIPTION | 47 +++++++++++++----- fracdiff-1.5-0/fracdiff/MD5 | 44 ++++++++-------- fracdiff-1.5-0/fracdiff/NAMESPACE | 12 ++++ fracdiff-1.5-0/fracdiff/R/diffseries.R | 52 +++++++++++++++++++- fracdiff-1.5-0/fracdiff/R/fd-methods.R | 9 ++- fracdiff-1.5-0/fracdiff/R/fdGPH.R | 20 +++---- fracdiff-1.5-0/fracdiff/R/fdSperio.R | 16 +++--- fracdiff-1.5-0/fracdiff/R/fracdiff.R | 15 +++++ fracdiff-1.5-0/fracdiff/TODO | 2 fracdiff-1.5-0/fracdiff/build |only fracdiff-1.5-0/fracdiff/man/confint.fracdiff.Rd | 13 +++-- fracdiff-1.5-0/fracdiff/man/diffseries.Rd | 23 ++++++-- fracdiff-1.5-0/fracdiff/man/fd-methods.Rd | 13 ++--- fracdiff-1.5-0/fracdiff/man/fracdiff.Rd | 12 +++- fracdiff-1.5-0/fracdiff/man/fracdiff.sim.Rd | 2 fracdiff-1.5-0/fracdiff/man/fracdiff.var.Rd | 6 ++ fracdiff-1.5-0/fracdiff/src/fdgam.c | 3 - fracdiff-1.5-0/fracdiff/tests/Valderio-ex.R | 22 ++++++-- fracdiff-1.5-0/fracdiff/tests/Valderio-ex.Rout.save | 37 ++++++++++---- fracdiff-1.5-0/fracdiff/tests/ex.Rout-64b | 16 +++--- fracdiff-1.5-0/fracdiff/tests/ex.Rout.save | 16 +++--- 25 files changed, 290 insertions(+), 111 deletions(-)
Title: Call R from R
Description: It is sometimes useful to perform a computation in a
separate R process, without affecting the current R process at all.
This packages does exactly that.
Author: Gábor Csárdi [aut, cre, cph] (<https://orcid.org/0000-0001-7098-9676>),
Winston Chang [aut],
RStudio [cph, fnd],
Mango Solutions [cph, fnd]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between callr versions 3.3.2 dated 2019-09-22 and 3.4.0 dated 2019-12-09
DESCRIPTION | 8 MD5 | 103 +++-- NAMESPACE | 1 NEWS.md | 19 + R/check.R | 2 R/error.R | 7 R/errors.R | 149 +++++++- R/eval-bg.R | 3 R/eval.R | 32 + R/hook.R | 20 + R/options.R | 6 R/package.R | 8 R/presets.R | 4 R/r-process.R | 6 R/r-session.R | 11 R/rcmd-bg.R | 3 R/rcmd-process.R | 6 R/rcmd.R | 7 R/result.R | 29 - R/rscript.R | 12 R/script.R | 54 ++- R/setup.R | 34 + R/utils.R | 2 inst/WORDLIST | 3 inst/client.R | 158 ++++++++- inst/doc/Task-queue-with-callr.html | 620 ++++++++++++++++++------------------ man/callr.Rd | 1 man/r.Rd | 95 ++++- man/r_bg.Rd | 40 +- man/r_copycat.Rd | 37 +- man/r_session.Rd | 2 man/r_session_debug.Rd | 10 man/r_vanilla.Rd | 37 +- man/rcmd.Rd | 93 ++++- man/rcmd_bg.Rd | 45 ++ man/rcmd_copycat.Rd | 29 + man/rcmd_process.Rd | 4 man/rcmd_process_options.Rd | 4 man/rcmd_safe.Rd | 4 man/reexports.Rd | 2 man/rscript.Rd | 47 ++ man/rscript_process.Rd | 2 tests/testthat/fixtures/csomag |only tests/testthat/helper.R | 73 +++- tests/testthat/test-error.R | 29 + tests/testthat/test-eval.R | 56 +++ tests/testthat/test-libpath.R | 67 +++ tests/testthat/test-r-bg.R | 26 + tests/testthat/test-r-session.R | 18 - tests/testthat/test-rcmd-process.R | 29 + tests/testthat/test-rcmd.R | 21 + tests/testthat/test-rscript.R | 54 +++ 52 files changed, 1517 insertions(+), 615 deletions(-)
Title: Analyze Experimental High-Throughput (Omics) Data
Description: The efficient treatment and convenient analysis of experimental high-throughput (omics) data gets facilitated through this collection of diverse functions. Several functions address advanced object-conversions, like manipulating lists of lists or lists of arrays, reorganizing lists to arrays or into separate vectors, merging of multiple entries, etc. Another set of functions provides speed-optimized calculation of standard deviation (sd), coefficient of variance (CV) or standard error of the mean (SEM) for data in matrixes or means per line with respect to additional grouping (eg n groups of replicates). Other functions facilitate dealing with non-redundant information, by indexing unique, adding counters to redundant or eliminating lines with respect redundancy in a given reference-column, etc. Help is provided to identify very closely matching numeric values to generate (partial) distance matrixes for very big data in a memory efficient manner or to reduce the complexity of large data-sets by combining very close values. Many times large experimental datasets need some additional filtering, adequate functions are provided. Batch reading (or writing) of sets of files and combining data to arrays is supported, too. Convenient data normalization is supported in various different modes, parameter estimation via permutations or boot-strap as well as flexible testing of multiple pair-wise combinations using the framework of 'limma' is provided, too.
Author: Wolfgang Raffelsberger [aut, cre]
Maintainer: Wolfgang Raffelsberger <w.raffelsberger@unistra.fr>
Diff between wrMisc versions 1.0.4 dated 2019-11-04 and 1.1.0 dated 2019-12-09
DESCRIPTION | 6 +-- MD5 | 50 +++++++++++++++-------------- NAMESPACE | 2 + R/asSepList.R | 1 R/buildTree.R | 4 +- R/convMatr2df.R | 2 - R/filtSizeUniq.R | 75 +++++++++++++++++++++++++++++--------------- R/getValuesByUnique.R |only R/listBatchReplace.R | 2 - R/lrbind.R | 15 ++++---- R/mergeW2.R | 28 ++++++++++------ R/moderTestXgrp.R | 2 - R/pVal2lfdr.R | 2 - R/partUnlist.R | 42 +++++++++--------------- R/randIndFx.R | 5 +- R/readCsvBatch.R | 4 +- R/readXlsxBatch.R | 2 - R/rowMedSds.R | 2 - R/searchLinesAtGivenSlope.R | 2 - R/stdErrMedBoot.R | 2 - R/tableToPlot.R | 5 ++ R/test2factLimma.R | 4 +- man/filtSizeUniq.Rd | 20 +++++++---- man/getValuesByUnique.Rd |only man/lrbind.Rd | 4 +- man/partUnlist.Rd | 5 +- man/tableToPlot.Rd | 4 +- 27 files changed, 165 insertions(+), 125 deletions(-)
Title: Robust Methods for High-Dimensional Data
Description: Robust methods for high-dimensional data, in particular linear
model selection techniques based on least angle regression and sparse
regression.
Author: Andreas Alfons [aut, cre]
Maintainer: Andreas Alfons <alfons@ese.eur.nl>
Diff between robustHD versions 0.5.1 dated 2016-01-08 and 0.6.0 dated 2019-12-09
robustHD-0.5.1/robustHD/inst/doc/examples/example-wt.R |only robustHD-0.5.1/robustHD/man/wt.Rd |only robustHD-0.6.0/robustHD/DESCRIPTION | 12 robustHD-0.6.0/robustHD/MD5 | 151 +-- robustHD-0.6.0/robustHD/NAMESPACE | 6 robustHD-0.6.0/robustHD/NEWS | 12 robustHD-0.6.0/robustHD/R/AIC.R | 90 +- robustHD-0.6.0/robustHD/R/accessors.R | 6 robustHD-0.6.0/robustHD/R/coef.R | 78 - robustHD-0.6.0/robustHD/R/corHuber.R | 114 +- robustHD-0.6.0/robustHD/R/fastLasso.R | 30 robustHD-0.6.0/robustHD/R/fitted.R | 74 - robustHD-0.6.0/robustHD/R/fortify.R | 156 +-- robustHD-0.6.0/robustHD/R/grouplars.R | 74 - robustHD-0.6.0/robustHD/R/grplars.R | 329 ++++--- robustHD-0.6.0/robustHD/R/initialSubsets.R | 19 robustHD-0.6.0/robustHD/R/lambda0.R | 92 +- robustHD-0.6.0/robustHD/R/perry.R | 150 +-- robustHD-0.6.0/robustHD/R/plot.R | 21 robustHD-0.6.0/robustHD/R/predict.R | 118 +- robustHD-0.6.0/robustHD/R/print.R | 6 robustHD-0.6.0/robustHD/R/regFun.R | 8 robustHD-0.6.0/robustHD/R/residuals.R | 80 - robustHD-0.6.0/robustHD/R/rlars.R | 285 +++--- robustHD-0.6.0/robustHD/R/robustHD-deprecated.R | 76 + robustHD-0.6.0/robustHD/R/seqModel.R | 22 robustHD-0.6.0/robustHD/R/sparseLTS.R | 496 ++++++------ robustHD-0.6.0/robustHD/R/standardize.R | 70 - robustHD-0.6.0/robustHD/R/test.R | 27 robustHD-0.6.0/robustHD/R/tsBlocks.R | 180 ++-- robustHD-0.6.0/robustHD/R/tslars.R | 230 ++--- robustHD-0.6.0/robustHD/R/tslarsP.R | 282 +++--- robustHD-0.6.0/robustHD/R/utils.R | 48 - robustHD-0.6.0/robustHD/R/weights.R | 70 - robustHD-0.6.0/robustHD/R/winsorize.R | 124 +-- robustHD-0.6.0/robustHD/build/partial.rdb |binary robustHD-0.6.0/robustHD/data/TopGear.RData |binary robustHD-0.6.0/robustHD/inst/doc/examples/example-weights.R |only robustHD-0.6.0/robustHD/man/AIC.seqModel.Rd | 22 robustHD-0.6.0/robustHD/man/coef.seqModel.Rd | 30 robustHD-0.6.0/robustHD/man/coefPlot.Rd | 36 robustHD-0.6.0/robustHD/man/corHuber.Rd | 17 robustHD-0.6.0/robustHD/man/critPlot.Rd | 44 - robustHD-0.6.0/robustHD/man/diagnosticPlot.Rd | 61 - robustHD-0.6.0/robustHD/man/fitted.seqModel.Rd | 26 robustHD-0.6.0/robustHD/man/fortify.seqModel.Rd | 81 - robustHD-0.6.0/robustHD/man/getScale.Rd | 15 robustHD-0.6.0/robustHD/man/grplars.Rd | 133 +-- robustHD-0.6.0/robustHD/man/lambda0.Rd | 14 robustHD-0.6.0/robustHD/man/perry.seqModel.Rd | 59 - robustHD-0.6.0/robustHD/man/plot.seqModel.Rd | 36 robustHD-0.6.0/robustHD/man/predict.seqModel.Rd | 32 robustHD-0.6.0/robustHD/man/residuals.seqModel.Rd | 30 robustHD-0.6.0/robustHD/man/rlars.Rd | 111 +- robustHD-0.6.0/robustHD/man/robustHD-deprecated.Rd | 31 robustHD-0.6.0/robustHD/man/sparseLTS.Rd | 180 +--- robustHD-0.6.0/robustHD/man/standardize.Rd | 17 robustHD-0.6.0/robustHD/man/tsBlocks.Rd | 10 robustHD-0.6.0/robustHD/man/tslars.Rd | 61 - robustHD-0.6.0/robustHD/man/tslarsP.Rd | 99 -- robustHD-0.6.0/robustHD/man/weights.sparseLTS.Rd |only robustHD-0.6.0/robustHD/man/winsorize.Rd | 36 robustHD-0.6.0/robustHD/src/corHuber.cpp | 2 robustHD-0.6.0/robustHD/src/corHuber.h | 2 robustHD-0.6.0/robustHD/src/fastGrplars.cpp | 4 robustHD-0.6.0/robustHD/src/fastGrplars.h | 2 robustHD-0.6.0/robustHD/src/fastLars.cpp | 2 robustHD-0.6.0/robustHD/src/fastLars.h | 2 robustHD-0.6.0/robustHD/src/fastLasso.cpp | 22 robustHD-0.6.0/robustHD/src/fastLasso.h | 10 robustHD-0.6.0/robustHD/src/fastRlars.cpp | 2 robustHD-0.6.0/robustHD/src/fastRlars.h | 2 robustHD-0.6.0/robustHD/src/fastSparseLTS.cpp | 16 robustHD-0.6.0/robustHD/src/fastSparseLTS.h | 6 robustHD-0.6.0/robustHD/src/initialSubsets.cpp | 20 robustHD-0.6.0/robustHD/src/initialSubsets.h | 6 robustHD-0.6.0/robustHD/src/robustHD_init.c |only robustHD-0.6.0/robustHD/src/utils.cpp | 2 robustHD-0.6.0/robustHD/src/utils.h | 2 79 files changed, 2413 insertions(+), 2406 deletions(-)
Title: Polygonal Symbolic Data Analysis
Description: A toolbox in symbolic data framework as a statistical learning and data mining solution for symbolic polygonal data analysis. This study is a new approach in data analysis and it was proposed by
Silva et al. (2019) <doi:10.1016/j.knosys.2018.08.009>. The package presents the estimation of main descriptive statistical measures, e.g, mean, covariance, variance, correlation and coefficient of variation.
In addition, a method to obtain polygonal data from classical data is presented. Empirical probability distribution function based on symbolic polygonal histogram and a regression model with its main measures are presented.
Author: Wagner Silva [aut, cre, ths],
Renata Souza [aut],
Francisco Cysneiros [aut]
Maintainer: Wagner Silva <wjfs@cin.ufpe.br>
Diff between psda versions 1.3.2 dated 2019-06-24 and 1.3.3 dated 2019-12-09
DESCRIPTION | 13 ++++++++----- MD5 | 20 +++++++++++++------- R/pfreq.R | 2 +- R/plr.R | 10 ++++++++++ R/pplot.R | 21 +++++++++++++++++---- README.md |only build |only inst/CITATION | 2 +- inst/doc |only man/plr.Rd | 12 ++++++++++++ man/pplot.Rd | 8 ++++++-- vignettes |only 12 files changed, 68 insertions(+), 20 deletions(-)
Title: Tools to create, modify and manage 'CWB' Corpora
Description: The 'Corpus Workbench' ('CWB', <http://cwb.sourceforge.net/>) offers a classic and mature
approach for working with large, linguistically and structurally annotated corpora. The 'CWB'
is memory efficient and its design makes running queries fast (Evert and Hardie 2011,
<http://www.stefan-evert.de/PUB/EvertHardie2011.pdf>). The 'cwbtools' package offers
pure R tools to create indexed corpus files as well as high-level wrappers for the original C
implementation of CWB as exposed by the 'RcppCWB' package
<https://CRAN.R-project.org/package=RcppCWB>. Additional functionality to add and
modify annotations of corpora from within R makes working with CWB indexed corpora
much more flexible and convenient. The 'cwbtools' package in combination with the R packages
'RcppCWB' (<https://CRAN.R-project.org/package=RcppCWB>) and 'polmineR'
(<https://CRAN.R-project.org/package=polmineR>) offers a lightweight infrastructure
to support the combination of quantitative and qualitative approaches for working
with textual data.
Author: Andreas Blaette [aut, cre],
Christoph Leonhardt [ctb]
Maintainer: Andreas Blaette <andreas.blaette@uni-due.de>
Diff between cwbtools versions 0.1.0 dated 2019-10-21 and 0.1.1 dated 2019-12-09
DESCRIPTION | 10 +++---- MD5 | 24 +++++++++--------- NEWS.md | 63 +++++++++++++++++++++++++++++++++++++++---------- R/CorpusData.R | 2 - R/corpus.R | 4 +-- R/pkg.R | 17 ++++++------- R/s_attribute.R | 4 +-- inst/doc/europarl.Rmd | 2 - inst/doc/europarl.html | 6 ++-- inst/doc/vignette.Rmd | 4 +-- inst/doc/vignette.html | 14 +++++----- vignettes/europarl.Rmd | 2 - vignettes/vignette.Rmd | 4 +-- 13 files changed, 97 insertions(+), 59 deletions(-)
Title: (Robust) Canonical Correlation Analysis via Projection Pursuit
Description: Canonical correlation analysis and maximum correlation via
projection pursuit, as well as fast implementations of correlation
estimators, with a focus on robust and nonparametric methods.
Author: Andreas Alfons [aut, cre],
David Simcha [ctb]
Maintainer: Andreas Alfons <alfons@ese.eur.nl>
Diff between ccaPP versions 0.3.2 dated 2016-03-07 and 0.3.3 dated 2019-12-09
DESCRIPTION | 14 - MD5 | 45 ++--- NAMESPACE | 4 NEWS | 80 +++++---- R/cca.R | 377 +++++++++++++++++++++++------------------------ R/cor.R | 117 +++++++------- R/fastMAD.R | 34 ++-- R/fastMedian.R | 24 +- R/maxCor.R | 318 +++++++++++++++++++-------------------- R/permTest.R | 92 +++++------ build/partial.rdb |binary build/vignette.rds |binary data/diabetes.RData |binary inst/doc/ccaPP-intro.pdf |binary man/ccaGrid.Rd | 46 ++--- man/ccaProj.Rd | 39 +--- man/corFunctions.Rd | 21 +- man/fastMAD.Rd | 13 - man/fastMedian.Rd | 11 - man/maxCorGrid.Rd | 21 -- man/maxCorProj.Rd | 25 +-- man/permTest.Rd | 23 +- src/ccaPP_init.c |only vignettes/maxCor.bib | 21 +- 24 files changed, 650 insertions(+), 675 deletions(-)
Title: Multi-Site Stochastic Models for Daily Precipitation and
Temperature
Description: Application of multi-site models for daily precipitation and temperature data.
This package is designed for an application to 105 precipitation and 26 temperature gauges located in Switzerland.
It applies fitting procedures and provides weather generators described in the following references:
- Evin, G., A.-C. Favre, and B. Hingray. (2018) <doi:10.5194/hess-22-655-2018>.
- Evin, G., A.-C. Favre, and B. Hingray. (2018) <doi:10.1007/s00704-018-2404-x>.
Author: Guillaume Evin [aut, cre]
Maintainer: Guillaume Evin <guillaume.evin@irstea.fr>
Diff between GWEX versions 1.0.1 dated 2019-02-25 and 1.0.2 dated 2019-12-09
DESCRIPTION | 10 +++++----- MD5 | 5 +++-- R/GWex_lib.r | 4 ++-- README.md |only 4 files changed, 10 insertions(+), 9 deletions(-)
Title: Dynamic Programming Domain-Specific Language
Description: A domain-specific language for specifying translating recursions
into dynamic-programming algorithms. See
<https://en.wikipedia.org/wiki/Dynamic_programming> for a description
of dynamic programming.
Author: Thomas Mailund [aut, cre]
Maintainer: Thomas Mailund <mailund@birc.au.dk>
Diff between dynprog versions 0.1.0 dated 2018-03-27 and 0.1.1 dated 2019-12-09
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/evaluate.R | 2 +- README.md | 8 ++++---- man/make_update_expr.Rd | 2 +- 5 files changed, 14 insertions(+), 14 deletions(-)
Title: Multivariate Interpolation
Description: Contains methods for creating multivariate/multidimensional
interpolations of functions on a hypercube. If available through fftw3, the DCT-II/FFT
is used to compute coefficients for a Chebyshev interpolation.
Other interpolation methods for arbitrary Cartesian grids are also provided, a piecewise multilinear,
and the Floater-Hormann barycenter method. For scattered data polyharmonic splines with a linear term
is provided. The time-critical parts are written in C for speed. All interpolants are parallelized if
used to evaluate more than one point.
Author: Simen Gaure [aut, cre] (<https://orcid.org/0000-0001-7251-8747>)
Maintainer: Simen Gaure <Simen.Gaure@frisch.uio.no>
Diff between chebpol versions 2.1-1 dated 2019-09-07 and 2.1-2 dated 2019-12-09
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- build/vignette.rds |binary cleanup | 2 +- inst/doc/chebpol.pdf |binary inst/doc/chebusage.pdf |binary inst/doc/stalker.pdf |binary tests/all.R | 2 +- tests/all.Rout.save | 8 ++++---- 9 files changed, 18 insertions(+), 18 deletions(-)
Title: Group Sequential Bayes Design
Description: Group Sequential Operating Characteristics for Clinical,
Bayesian two-arm Trials with known Sigma and Normal Endpoints.
Author: Florian Gerber, Thomas Gsponer
Maintainer: Bjoern Bornkamp <bbnkmp@mail.de>
Diff between gsbDesign versions 1.00 dated 2016-03-29 and 1.0-1 dated 2019-12-09
ChangeLog | 2 ++ DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- R/package.r | 14 +++++++------- build/vignette.rds |binary inst/doc/JSS-gsbDesign.pdf |binary 6 files changed, 19 insertions(+), 17 deletions(-)
Title: Functional Rarity Indices Computation
Description: Computes functional rarity indices as proposed by Violle et al.
(2017) <doi:10.1016/j.tree.2017.02.002>. Various indices can be computed
using both regional and local information. Functional Rarity combines both
the functional aspect of rarity as well as the extent aspect of rarity.
'funrar' is presented in Grenié et al. (2017) <doi:10.1111/ddi.12629>.
Author: Matthias Grenié [aut, cre] (<https://orcid.org/0000-0002-4659-7522>),
Pierre Denelle [aut] (<https://orcid.org/0000-0001-5037-2281>),
Caroline Tucker [aut] (<https://orcid.org/0000-0002-4871-2010>),
François Munoz [ths] (<https://orcid.org/0000-0001-8776-4705>),
Cyrille Violle [ths] (<https://orcid.org/0000-0002-2471-9226>)
Maintainer: Matthias Grenié <matthias.grenie@gmail.com>
Diff between funrar versions 1.3.0 dated 2019-05-18 and 1.3.1 dated 2019-12-09
DESCRIPTION | 8 MD5 | 130 +- NAMESPACE | 60 - NEWS.md | 118 +- R/check_functions.R | 498 ++++---- R/compute_dist_matrix.R | 198 +-- R/distinctiveness.R | 676 +++++------ R/distinctiveness_alt.R | 230 +-- R/distinctiveness_range.R | 366 +++--- R/funrar.R | 226 +-- R/make_relative.R | 180 +-- R/rarity_dimensions.R | 272 ++-- R/restrictedness.R | 366 +++--- R/scarcity.R | 350 +++--- R/stack_matrix.R | 364 +++--- R/uniqueness.R | 302 ++--- README.md | 110 - build/vignette.rds |binary inst/CITATION | 46 inst/doc/new_distinctiveness.R | 338 ++--- inst/doc/new_distinctiveness.Rmd | 822 +++++++------- inst/doc/new_distinctiveness.pdf |binary inst/doc/rarity_indices.R | 324 ++--- inst/doc/rarity_indices.Rmd | 704 ++++++------ inst/doc/rarity_indices.html | 1613 ++++++++++++++-------------- inst/doc/sparse_matrices.R | 186 +-- inst/doc/sparse_matrices.Rmd | 320 ++--- inst/doc/sparse_matrices.html | 933 ++++++++-------- man/combination_trait_dist.Rd | 2 man/compute_dist_matrix.Rd | 10 man/distinctiveness.Rd | 2 man/distinctiveness_alt.Rd | 2 man/distinctiveness_com.Rd | 11 man/distinctiveness_dimensions.Rd | 2 man/distinctiveness_range.Rd | 5 man/distinctiveness_stack.Rd | 26 man/funrar.Rd | 2 man/funrar_stack.Rd | 2 man/is_relative.Rd | 2 man/make_relative.Rd | 2 man/matrix_to_stack.Rd | 9 man/restrictedness.Rd | 2 man/restrictedness_stack.Rd | 4 man/scarcity.Rd | 2 man/scarcity_com.Rd | 2 man/scarcity_stack.Rd | 4 man/stack_to_matrix.Rd | 13 man/uniqueness.Rd | 2 man/uniqueness_dimensions.Rd | 2 man/uniqueness_stack.Rd | 4 tests/testthat.R | 8 tests/testthat/test-check_functions.R | 350 +++--- tests/testthat/test-dist_matrix.R | 290 ++--- tests/testthat/test-distinctiveness.R | 678 +++++------ tests/testthat/test-distinctiveness_alt.R | 304 ++--- tests/testthat/test-distinctiveness_range.R | 428 +++---- tests/testthat/test-funrar.R | 300 ++--- tests/testthat/test-rarity_dimensions.R | 276 ++-- tests/testthat/test-rel_abund.R | 166 +- tests/testthat/test-restrictedness.R | 82 - tests/testthat/test-scarcity.R | 308 ++--- tests/testthat/test-tidy_matrix.R | 386 +++--- tests/testthat/test-uniqueness.R | 160 +- vignettes/new_distinctiveness.Rmd | 822 +++++++------- vignettes/rarity_indices.Rmd | 704 ++++++------ vignettes/sparse_matrices.Rmd | 320 ++--- 66 files changed, 7735 insertions(+), 7699 deletions(-)
Title: Read and Write Ecological Metadata Language Files
Description: Work with Ecological Metadata Language ('EML') files.
'EML' is a widely used metadata standard in the ecological and
environmental sciences, described in Jones et al. (2006),
<doi:10.1146/annurev.ecolsys.37.091305.110031>.
Author: Carl Boettiger [aut, cre, cph]
(<https://orcid.org/0000-0002-1642-628X>),
Matthew B. Jones [aut] (<https://orcid.org/0000-0003-0077-4738>),
Mitchell Maier [ctb] (<https://orcid.org/0000-0001-6955-0535>),
Bryce Mecum [ctb] (<https://orcid.org/0000-0002-0381-3766>),
Maëlle Salmon [ctb] (<https://orcid.org/0000-0002-2815-0399>),
Jeanette Clark [ctb] (<https://orcid.org/0000-0003-4703-1974>)
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between EML versions 2.0.0 dated 2019-04-23 and 2.0.1 dated 2019-12-09
DESCRIPTION | 6 +-- MD5 | 30 +++++++-------- NEWS.md | 8 ++++ R/get_attributes.R | 12 +++++- R/set_TextType.R | 23 ++++++++---- R/set_attributes.R | 62 ++++++++++++++++++++------------- R/set_coverage.R | 1 README.md | 17 ++++----- build/vignette.rds |binary inst/doc/creating-EML.html | 10 +++-- inst/doc/working-with-units.html | 10 +++-- man/set_attributes.Rd | 53 +++++++++++++++++----------- tests/testthat/test-additional-tests.R | 6 +-- tests/testthat/test-eml2.R | 2 + tests/testthat/test-get_attributes.R | 14 +++++++ tests/testthat/test-set_attributes.R | 19 +++++++++- 16 files changed, 181 insertions(+), 92 deletions(-)
Title: Generate Alluvial Plots with a Single Line of Code
Description: Alluvial plots are similar to sankey diagrams and visualise categorical data
over multiple dimensions as flows. (Rosvall M, Bergstrom CT (2010) Mapping Change in
Large Networks. PLoS ONE 5(1): e8694. <doi:10.1371/journal.pone.0008694>
Their graphical grammar however is a bit more complex then that of a regular x/y
plots. The 'ggalluvial' package made a great job of translating that grammar into
'ggplot2' syntax and gives you many options to tweak the appearance of an alluvial
plot, however there still remains a multi-layered complexity that makes it difficult
to use 'ggalluvial' for explorative data analysis. 'easyalluvial' provides a simple
interface to this package that allows you to produce a decent alluvial plot from any
dataframe in either long or wide format from a single line of code while also handling
continuous data. It is meant to allow a quick visualisation of entire dataframes
with a focus on different colouring options that can make alluvial plots a great
tool for data exploration.
Author: Bjoern Koneswarakantha [aut, cre]
(<https://orcid.org/0000-0003-4585-7799>)
Maintainer: Bjoern Koneswarakantha <datistics@gmail.com>
Diff between easyalluvial versions 0.2.1 dated 2019-09-17 and 0.2.2 dated 2019-12-09
DESCRIPTION | 14 - MD5 | 68 +++---- NAMESPACE | 2 README.md | 148 ++++++++++------ inst/logo/logo.R | 2 man/add_imp_plot.Rd | 94 +++++----- man/add_marginal_histograms.Rd | 90 +++++---- man/alluvial_long.Rd | 283 ++++++++++++++++--------------- man/alluvial_model_response.Rd | 214 ++++++++++++----------- man/alluvial_model_response_caret.Rd | 180 ++++++++++--------- man/alluvial_wide.Rd | 225 ++++++++++++------------ man/figures/README-plot_long-1.png |binary man/figures/README-unnamed-chunk-3-1.png |binary man/figures/README-unnamed-chunk-4-1.png |binary man/figures/README-wide_plot-1.png |binary man/get_data_space.Rd | 128 +++++++------- man/get_pdp_predictions.Rd | 131 +++++++------- man/manip_bin_numerics.Rd | 100 +++++----- man/manip_factor_2_numeric.Rd | 60 +++--- man/mtcars2.Rd | 66 +++---- man/palette_filter.Rd | 133 +++++++------- man/palette_increase_length.Rd | 56 +++--- man/palette_plot_intensity.Rd | 56 +++--- man/palette_plot_rgp.Rd | 56 +++--- man/palette_qualitative.Rd | 40 ++-- man/plot_all_hists.Rd | 72 +++---- man/plot_condensation.Rd | 82 ++++---- man/plot_hist.Rd | 46 ++--- man/plot_imp.Rd | 80 ++++---- man/quarterly_flights.Rd | 48 ++--- man/quarterly_sunspots.Rd | 44 ++-- man/tidy_imp.Rd | 64 +++---- man/titanic.Rd | 58 +++--- man/use_e1071.Rd | 44 ++-- tests/testthat/Rplots.pdf |binary 35 files changed, 1395 insertions(+), 1289 deletions(-)
Title: Differential Gene Correlation Analysis
Description: Performs differential correlation analysis on input
matrices, with multiple conditions specified by a design matrix. Contains
functions to filter, process, save, visualize, and interpret differential
correlations of identifier-pairs across the entire identifier space, or with
respect to a particular set of identifiers (e.g., one). Also contains several
functions to perform differential correlation analysis on clusters (i.e., modules)
or genes. Finally, it contains functions to generate empirical p-values for the
hypothesis tests and adjust them for multiple comparisons. Although the package
was built with gene expression data in mind, it is applicable to other types of
genomics data as well, in addition to being potentially applicable to data from
other fields entirely. It is described more fully in the manuscript
introducing it, freely available at <doi:10.1186/s12918-016-0349-1>.
Author: Bin Zhang [aut],
Andrew McKenzie [aut, cre]
Maintainer: Andrew McKenzie <amckenz@gmail.com>
Diff between DGCA versions 1.0.1 dated 2016-11-17 and 1.0.2 dated 2019-12-09
DGCA-1.0.1/DGCA/inst/doc/DGCA.Rmd |only DGCA-1.0.1/DGCA/inst/doc/DGCA.html |only DGCA-1.0.1/DGCA/inst/doc/DGCA_modules.Rmd |only DGCA-1.0.1/DGCA/inst/doc/DGCA_modules.pdf |only DGCA-1.0.2/DGCA/DESCRIPTION | 6 DGCA-1.0.2/DGCA/MD5 | 28 -- DGCA-1.0.2/DGCA/NAMESPACE | 1 DGCA-1.0.2/DGCA/R/ddMEGENA.R | 4 DGCA-1.0.2/DGCA/R/ddcorAll.R | 2 DGCA-1.0.2/DGCA/R/getCors.R | 3 DGCA-1.0.2/DGCA/R/moduleDC.R | 2 DGCA-1.0.2/DGCA/R/plotCors.R | 2 DGCA-1.0.2/DGCA/R/plotVals.R | 2 DGCA-1.0.2/DGCA/README.md | 17 + DGCA-1.0.2/DGCA/build/vignette.rds |binary DGCA-1.0.2/DGCA/inst/doc/DGCA_basic.html | 319 ++++++++++++++++++++++---- DGCA-1.0.2/DGCA/tests/testthat/test-dCorAvg.R | 1 17 files changed, 308 insertions(+), 79 deletions(-)
Title: Extension of `data.frame`
Description: Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group using no copies at all, list columns, friendly and fast character-separated-value read/write. Offers a natural and flexible syntax, for faster development.
Author: Matt Dowle [aut, cre],
Arun Srinivasan [aut],
Jan Gorecki [ctb],
Michael Chirico [ctb],
Pasha Stetsenko [ctb],
Tom Short [ctb],
Steve Lianoglou [ctb],
Eduard Antonyan [ctb],
Markus Bonsch [ctb],
Hugh Parsonage [ctb],
Scott Ritchie [ctb],
Kun Ren [ctb],
Xianying Tan [ctb],
Rick Saporta [ctb],
Otto Seiskari [ctb],
Xianghui Dong [ctb],
Michel Lang [ctb],
Watal Iwasaki [ctb],
Seth Wenchel [ctb],
Karl Broman [ctb],
Tobias Schmidt [ctb],
David Arenburg [ctb],
Ethan Smith [ctb],
Francois Cocquemas [ctb],
Matthieu Gomez [ctb],
Philippe Chataignon [ctb],
Declan Groves [ctb],
Daniel Possenriede [ctb],
Felipe Parages [ctb],
Denes Toth [ctb],
Mus Yaramaz-David [ctb],
Ayappan Perumal [ctb],
James Sams [ctb],
Martin Morgan [ctb],
Michael Quinn [ctb],
@javrucebo [ctb],
@marc-outins [ctb],
Roy Storey [ctb],
Manish Saraswat [ctb],
Morgan Jacob [ctb],
Michael Schubmehl [ctb],
Davis Vaughan [ctb]
Maintainer: Matt Dowle <mattjdowle@gmail.com>
Diff between data.table versions 1.12.6 dated 2019-10-18 and 1.12.8 dated 2019-12-09
DESCRIPTION | 12 MD5 | 110 +-- NEWS.md | 25 R/data.table.R | 81 +- R/devel.R |only R/fread.R | 4 R/groupingsets.R | 2 R/onAttach.R | 42 - R/print.data.table.R | 2 R/setops.R | 5 R/test.data.table.R | 48 - inst/doc/datatable-benchmarking.html | 7 inst/doc/datatable-faq.R | 42 - inst/doc/datatable-faq.html | 7 inst/doc/datatable-importing.html | 7 inst/doc/datatable-intro.R | 2 inst/doc/datatable-intro.html | 7 inst/doc/datatable-keys-fast-subset.R | 2 inst/doc/datatable-keys-fast-subset.html | 11 inst/doc/datatable-reference-semantics.R | 2 inst/doc/datatable-reference-semantics.html | 7 inst/doc/datatable-reshape.R | 2 inst/doc/datatable-reshape.html | 7 inst/doc/datatable-sd-usage.R | 32 inst/doc/datatable-sd-usage.html | 429 +++++------- inst/doc/datatable-secondary-indices-and-auto-indexing.R | 2 inst/doc/datatable-secondary-indices-and-auto-indexing.html | 19 inst/tests/froll.Rraw.bz2 |binary inst/tests/tests.Rraw.bz2 |binary man/assign.Rd | 6 man/data.table.Rd | 2 man/fread.Rd | 8 man/like.Rd | 4 man/openmp-utils.Rd | 2 man/rbindlist.Rd | 2 man/setkey.Rd | 2 man/test.data.table.Rd | 15 man/update.dev.pkg.Rd | 5 src/assign.c | 99 +- src/between.c | 2 src/chmatch.c | 2 src/data.table.h | 64 - src/dt_stdio.h |only src/fifelse.c | 6 src/forder.c | 10 src/fread.c | 88 +- src/fread.h | 7 src/freadR.c | 2 src/froll.c | 12 src/frollR.c | 27 src/frolladaptive.c | 12 src/fsort.c | 11 src/fwrite.c | 44 - src/init.c | 37 - src/rbindlist.c | 4 src/uniqlist.c | 2 src/wrappers.c | 11 57 files changed, 708 insertions(+), 694 deletions(-)
Title: Helpers for Developing Command Line Interfaces
Description: A suite of tools to build attractive command line interfaces
('CLIs'), from semantic elements: headings, lists, alerts, paragraphs,
etc. Supports custom themes via a 'CSS'-like language. It also contains a
number of lower level 'CLI' elements: rules, boxes, trees, and
'Unicode' symbols with 'ASCII' alternatives. It integrates with the
'crayon' package to support 'ANSI' terminal colors.
Author: Gábor Csárdi [aut, cre],
Hadley Wickham [ctb],
Kirill Müller [ctb]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between cli versions 1.1.0 dated 2019-03-19 and 2.0.0 dated 2019-12-09
cli-1.1.0/cli/R/html-readme.R |only cli-1.1.0/cli/inst/demo.R |only cli-2.0.0/cli/DESCRIPTION | 23 cli-2.0.0/cli/MD5 | 154 ++++- cli-2.0.0/cli/NAMESPACE | 56 ++ cli-2.0.0/cli/NEWS.md | 15 cli-2.0.0/cli/R/app.R |only cli-2.0.0/cli/R/cli.R |only cli-2.0.0/cli/R/cliapp-docs.R |only cli-2.0.0/cli/R/cliapp.R |only cli-2.0.0/cli/R/containers.R |only cli-2.0.0/cli/R/defer.R |only cli-2.0.0/cli/R/format.R |only cli-2.0.0/cli/R/inline.R |only cli-2.0.0/cli/R/internals.R |only cli-2.0.0/cli/R/lazyrmd.R |only cli-2.0.0/cli/R/lorem.R |only cli-2.0.0/cli/R/onload.R | 28 + cli-2.0.0/cli/R/pluralize.R |only cli-2.0.0/cli/R/print.R |only cli-2.0.0/cli/R/rstudio-detect.R |only cli-2.0.0/cli/R/rules.R | 9 cli-2.0.0/cli/R/server.R |only cli-2.0.0/cli/R/simple-theme.R |only cli-2.0.0/cli/R/sitrep.R | 2 cli-2.0.0/cli/R/status-bar.R |only cli-2.0.0/cli/R/symbol.R | 59 ++ cli-2.0.0/cli/R/themes.R |only cli-2.0.0/cli/R/tree.R | 67 ++ cli-2.0.0/cli/R/tty.R | 59 +- cli-2.0.0/cli/R/utils.R | 37 + cli-2.0.0/cli/README.md | 442 ++++------------- cli-2.0.0/cli/build |only cli-2.0.0/cli/inst/doc |only cli-2.0.0/cli/inst/examples |only cli-2.0.0/cli/inst/logo.txt |only cli-2.0.0/cli/inst/scripts |only cli-2.0.0/cli/man/ansi-styles.Rd | 19 cli-2.0.0/cli/man/boxx.Rd | 20 cli-2.0.0/cli/man/builtin_theme.Rd |only cli-2.0.0/cli/man/cat_line.Rd | 12 cli-2.0.0/cli/man/chunks |only cli-2.0.0/cli/man/cli_alert.Rd |only cli-2.0.0/cli/man/cli_blockquote.Rd |only cli-2.0.0/cli/man/cli_code.Rd |only cli-2.0.0/cli/man/cli_div.Rd |only cli-2.0.0/cli/man/cli_dl.Rd |only cli-2.0.0/cli/man/cli_end.Rd |only cli-2.0.0/cli/man/cli_format.Rd |only cli-2.0.0/cli/man/cli_format_method.Rd |only cli-2.0.0/cli/man/cli_h1.Rd |only cli-2.0.0/cli/man/cli_li.Rd |only cli-2.0.0/cli/man/cli_list_themes.Rd |only cli-2.0.0/cli/man/cli_ol.Rd |only cli-2.0.0/cli/man/cli_output_connection.Rd |only cli-2.0.0/cli/man/cli_par.Rd |only cli-2.0.0/cli/man/cli_process_start.Rd |only cli-2.0.0/cli/man/cli_rule.Rd |only cli-2.0.0/cli/man/cli_status.Rd |only cli-2.0.0/cli/man/cli_status_clear.Rd |only cli-2.0.0/cli/man/cli_status_update.Rd |only cli-2.0.0/cli/man/cli_text.Rd |only cli-2.0.0/cli/man/cli_ul.Rd |only cli-2.0.0/cli/man/cli_verbatim.Rd |only cli-2.0.0/cli/man/combine_ansi_styles.Rd | 11 cli-2.0.0/cli/man/containers.Rd |only cli-2.0.0/cli/man/demo_spinners.Rd | 6 cli-2.0.0/cli/man/figures |only cli-2.0.0/cli/man/get_spinner.Rd | 6 cli-2.0.0/cli/man/inline-markup.Rd |only cli-2.0.0/cli/man/is_ansi_tty.Rd | 3 cli-2.0.0/cli/man/is_dynamic_tty.Rd | 17 cli-2.0.0/cli/man/list_spinners.Rd | 6 cli-2.0.0/cli/man/make_ansi_style.Rd | 10 cli-2.0.0/cli/man/make_spinner.Rd | 44 - cli-2.0.0/cli/man/match_selector.Rd |only cli-2.0.0/cli/man/match_selector_node.Rd |only cli-2.0.0/cli/man/parse_selector.Rd |only cli-2.0.0/cli/man/pluralization-helpers.Rd |only cli-2.0.0/cli/man/pluralization.Rd |only cli-2.0.0/cli/man/rule.Rd | 16 cli-2.0.0/cli/man/simple_theme.Rd |only cli-2.0.0/cli/man/start_app.Rd |only cli-2.0.0/cli/man/symbol.Rd | 9 cli-2.0.0/cli/man/themes.Rd |only cli-2.0.0/cli/man/tree.Rd | 61 ++ cli-2.0.0/cli/tests/testthat/helper-app.R |only cli-2.0.0/cli/tests/testthat/helper.R | 5 cli-2.0.0/cli/tests/testthat/test-alerts.R |only cli-2.0.0/cli/tests/testthat/test-cliapp-output.R |only cli-2.0.0/cli/tests/testthat/test-collapsing.R |only cli-2.0.0/cli/tests/testthat/test-containers.R |only cli-2.0.0/cli/tests/testthat/test-css.R |only cli-2.0.0/cli/tests/testthat/test-custom-handler.R |only cli-2.0.0/cli/tests/testthat/test-headers.R |only cli-2.0.0/cli/tests/testthat/test-inline.R |only cli-2.0.0/cli/tests/testthat/test-lists.R |only cli-2.0.0/cli/tests/testthat/test-non-breaking-space.R |only cli-2.0.0/cli/tests/testthat/test-pluralization.R |only cli-2.0.0/cli/tests/testthat/test-sitrep.R | 2 cli-2.0.0/cli/tests/testthat/test-status-bar.R |only cli-2.0.0/cli/tests/testthat/test-subprocess.R |only cli-2.0.0/cli/tests/testthat/test-substitution.R |only cli-2.0.0/cli/tests/testthat/test-text.R |only cli-2.0.0/cli/tests/testthat/test-themes.R |only cli-2.0.0/cli/tests/testthat/test-tree.R | 82 +++ cli-2.0.0/cli/vignettes |only 107 files changed, 814 insertions(+), 466 deletions(-)
Title: Simple Definition Of Time Intervals
Description: Simple definition of time intervals for the current, previous, and next week, month, quarter and year.
Author: Alexey Seleznev [aut, cre]
Maintainer: Alexey Seleznev <selesnow@gmail.com>
Diff between timeperiodsR versions 0.2.0 dated 2019-11-14 and 0.3.0 dated 2019-12-09
DESCRIPTION | 10 ++--- MD5 | 17 ++++----- NAMESPACE | 7 ++- R/methods.R | 25 ++++++++++++- build/partial.rdb |binary inst/doc/tpr_intro.R | 5 ++ inst/doc/tpr_intro.Rmd | 45 ++++++++++++++++++------ inst/doc/tpr_intro.html | 88 ++++++++++++++++++++++++++++++------------------ man/as_timeperiod.Rd |only vignettes/tpr_intro.Rmd | 45 ++++++++++++++++++------ 10 files changed, 167 insertions(+), 75 deletions(-)
Title: Handling and Manipulating Remote Sensing Data
Description: Herein, we provide a broad variety of functions which are useful
for handling, manipulating, and visualizing satellite-based remote sensing
data. These operations range from mere data import and layer handling (eg
subsetting), over Raster* typical data wrangling (eg crop, extend), to more
sophisticated (pre-)processing tasks typically applied to satellite imagery
(eg atmospheric and topographic correction). This functionality is
complemented by a full access to the satellite layers' metadata at any
stage and the documentation of performed actions in a separate log file.
Currently available sensors include Landsat 4-5 (TM), 7 (ETM+), and 8
(OLI/TIRS Combined), and additional compatibility is ensured for the Landsat
Global Land Survey data set.
Author: Thomas Nauss, Hanna Meyer, Tim Appelhans, Florian Detsch
Maintainer: Florian Detsch <fdetsch@web.de>
Diff between satellite versions 1.0.1 dated 2017-10-18 and 1.0.2 dated 2019-12-09
DESCRIPTION | 16 LICENSE | 677 ---------------------------------- MD5 | 128 +++--- NAMESPACE | 4 NEWS | 9 NEWS.md | 102 ++--- R/alignGeometry.R | 2 R/calcAtmosCorr.R | 442 +++++++++++----------- R/calcDODN.R | 2 R/calcPathRadDOS.R | 476 +++++++++++------------ R/calcTOAIrradModel.R | 302 +++++++-------- R/calcTOAIrradTable.R | 256 ++++++------ R/convRad2BT.R | 4 R/convRad2Ref.R | 4 R/convRef2RadLinear.R | 6 R/convSC2Rad.R | 4 R/convSC2Ref.R | 4 R/lutInfo.R | 324 +++++++--------- R/satInfo.R | 2 R/satellite.R | 238 +++++------ R/sysdata.rda |binary build/vignette.rds |binary data/l7.rda |binary data/l8.rda |binary inst/CITATION | 40 +- inst/doc/landsat-calibration.R | 4 inst/doc/landsat-calibration.html | 336 ++++++++++++++-- inst/doc/satellite.R | 14 inst/doc/satellite.html | 468 +++++++++++++++++------ man/Satellite-class.Rd | 16 man/SatelliteInfo-class.Rd | 46 +- man/SatelliteLayers-class.Rd | 28 - man/SatelliteLog-class.Rd | 28 - man/SatelliteMetaData-class.Rd | 28 - man/alignGeometry.Rd | 113 ++--- man/brick.Rd | 60 +-- man/calcAtmosCorr.Rd | 300 +++++++-------- man/calcDODN.Rd | 103 ++--- man/calcEarthSunDist.Rd | 114 ++--- man/calcPathRadDOS.Rd | 315 ++++++++------- man/calcTOAIrradModel.Rd | 181 ++++----- man/calcTOAIrradRadRef.Rd | 147 +++---- man/calcTOAIrradTable.Rd | 149 +++---- man/calcTopoCorr.Rd | 143 +++---- man/compFilePathLandsat.Rd | 88 ++-- man/compMetaLandsat.Rd | 116 ++--- man/convRad2BT.Rd | 95 ++-- man/convRad2Ref.Rd | 133 +++--- man/convRef2RadLinear.Rd | 68 +-- man/convSC2Rad.Rd | 130 +++--- man/convSC2Ref.Rd | 142 +++---- man/crop.Rd | 115 ++--- man/demTools.Rd | 99 ++-- man/extend.Rd | 99 ++-- man/l7.Rd | 44 +- man/l8.Rd | 46 +- man/lutInfo.Rd | 222 +++++------ man/maskInvarFeatures.Rd | 150 +++---- man/names.Rd | 64 +-- man/plot.Rd | 86 ++-- man/satInfo.Rd | 756 +++++++++++++++++++------------------- man/satellite-package.Rd | 52 +- man/satellite.Rd | 125 +++--- man/stack.Rd | 60 +-- man/subset.Rd | 86 ++-- 65 files changed, 4099 insertions(+), 4312 deletions(-)
Title: Litter Analysis
Description: Data sets on various litter types like beach litter, riverain
litter, floating litter, and seafloor litter are rapidly growing. This
package offers a simple user interface to analyse these litter data in
a consistent and reproducible way. It also provides functions to
facilitate several kinds of litter analysis, e.g., trend analysis,
power analysis, and baseline analysis. Under the hood, these functions
are also used by the user interface. See Schulz et al. (2019)
<doi:10.1016/j.envpol.2019.02.030> for details. MS-Windows users are
advised to run 'litteR' in 'RStudio'. See our vignette: Installation manual
for 'RStudio' and 'litteR'.
Author: Dennis Walvoort [aut, cre, cph],
Willem van Loon [aut, cph],
Rijkswaterstaat - The Netherlands [cph, fnd, dtc]
Maintainer: Dennis Walvoort <dennis.Walvoort@wur.nl>
Diff between litteR versions 0.6.6 dated 2019-11-25 and 0.7.0 dated 2019-12-09
DESCRIPTION | 10 MD5 | 32 NAMESPACE | 1 NEWS.md | 137 ++-- R/gui.R | 377 +++++------ R/io.R | 1213 ++++++++++++++++++------------------ R/utils.R | 582 ++++++++--------- build/partial.rdb |binary inst/app/litter-main.Rmd | 1279 +++++++++++++++++++------------------- inst/doc/litter-installation.html | 7 inst/doc/litter-manual.Rmd | 786 +++++++++++------------ inst/doc/litter-manual.html | 32 inst/extdata/ospar-groups.csv | 264 ++++--- inst/extdata/settings.yaml | 92 +- tests/testthat/test-io.R | 272 ++++---- vignettes/litter-manual.Rmd | 786 +++++++++++------------ vignettes/tbl/settings.csv | 34 - 17 files changed, 2976 insertions(+), 2928 deletions(-)
Title: Optimizing Consistency and Coverage in Configurational Causal
Modeling
Description: This is an add-on to the 'cna' package <https://CRAN.R-project.org/package=cna> comprising various functions for optimizing consistency and coverage scores of models of configurational comparative methods as Coincidence Analysis (CNA) and Qualitative Comparative Analysis (QCA). The function conCovOpt() calculates con-cov optima, selectMax() selects con-cov maxima among the con-cov optima, DNFbuild() can be used to build models actually reaching those optima, and findOutcomes() identifies those factor values in analyzed data that can be modeled as outcomes. For a theoretical introduction to these functions see <https://people.uib.no/mba110/docs/ConCovOpt.pdf>.
Author: Mathias Ambuehl [aut, cre, cph],
Michael Baumgartner [aut, cph]
Maintainer: Mathias Ambuehl <mathias.ambuehl@consultag.ch>
Diff between cnaOpt versions 0.1.0 dated 2019-10-21 and 0.1.1 dated 2019-12-09
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- R/conCovOpt_utils.R | 2 +- man/rreduce_ereduce.Rd | 3 ++- 4 files changed, 11 insertions(+), 10 deletions(-)
Title: Visualizes a Matrix as Heatmap
Description: Visualizes a matrix object plainly as heatmap. It provides S3 functions to plot simple matrices and loading matrices.
Author: Sigbert Klinke [aut, cre],
Frédéric Chevalier [ctb]
Maintainer: Sigbert Klinke <sigbert@hu-berlin.de>
Diff between plot.matrix versions 1.2 dated 2019-07-03 and 1.4 dated 2019-12-09
plot.matrix-1.2/plot.matrix/R/bfi.2.R |only plot.matrix-1.4/plot.matrix/DESCRIPTION | 17 - plot.matrix-1.4/plot.matrix/MD5 | 45 +- plot.matrix-1.4/plot.matrix/NAMESPACE | 8 plot.matrix-1.4/plot.matrix/R/air.pvalue.R |only plot.matrix-1.4/plot.matrix/R/as.cor.R |only plot.matrix-1.4/plot.matrix/R/data.R |only plot.matrix-1.4/plot.matrix/R/plot.assoc.R |only plot.matrix-1.4/plot.matrix/R/plot.cor.R |only plot.matrix-1.4/plot.matrix/R/plot.loadings.R | 31 + plot.matrix-1.4/plot.matrix/R/plot.matrix.R | 166 ++++++++-- plot.matrix-1.4/plot.matrix/R/plot.pvalue.R |only plot.matrix-1.4/plot.matrix/README.md | 20 + plot.matrix-1.4/plot.matrix/build/vignette.rds |binary plot.matrix-1.4/plot.matrix/data/Titanic.cramer.rda |only plot.matrix-1.4/plot.matrix/data/air.pvalue.rda |only plot.matrix-1.4/plot.matrix/inst/data-raw |only plot.matrix-1.4/plot.matrix/inst/doc/plot.matrix.R | 98 ++++++ plot.matrix-1.4/plot.matrix/inst/doc/plot.matrix.Rmd | 211 ++++++++++++ plot.matrix-1.4/plot.matrix/inst/doc/plot.matrix.html | 293 +++++++++++++++--- plot.matrix-1.4/plot.matrix/man/Titanic.cramer.Rd |only plot.matrix-1.4/plot.matrix/man/air.pvalue.Rd |only plot.matrix-1.4/plot.matrix/man/as.cor.Rd |only plot.matrix-1.4/plot.matrix/man/bfi.2.Rd | 4 plot.matrix-1.4/plot.matrix/man/ind.Rd |only plot.matrix-1.4/plot.matrix/man/plot.assoc.Rd |only plot.matrix-1.4/plot.matrix/man/plot.cor.Rd |only plot.matrix-1.4/plot.matrix/man/plot.loadings.Rd | 19 - plot.matrix-1.4/plot.matrix/man/plot.matrix.Rd | 28 + plot.matrix-1.4/plot.matrix/man/plot.pvalue.Rd |only plot.matrix-1.4/plot.matrix/vignettes/plot.matrix.Rmd | 211 ++++++++++++ 31 files changed, 1037 insertions(+), 114 deletions(-)
Title: Multinomial Logit Models
Description: Maximum Likelihood estimation of random utility discrete
choice models, as described in Kenneth Train (2009) Discrete Choice
Methods with Simulations <doi:10.1017/CBO9780511805271>.
Author: Yves Croissant [aut, cre]
Maintainer: Yves Croissant <yves.croissant@univ-reunion.fr>
Diff between mlogit versions 1.0-1 dated 2019-07-22 and 1.0-2 dated 2019-12-09
DESCRIPTION | 13 ++- MD5 | 66 ++++++++-------- NEWS.md | 5 + R/formula.data.R | 4 - R/lnl.rlogit.R | 1 R/mlogit.R | 1 build/partial.rdb |binary build/vignette.rds |binary data/Car.rda |binary data/Catsup.rda |binary data/Cracker.rda |binary data/Electricity.rda |binary data/Fishing.rda |binary data/Game.rda |binary data/Game2.rda |binary data/HC.rda |binary data/Heating.rda |binary data/JapaneseFDI.rda |binary data/Mode.rda |binary data/ModeCanada.rda |binary data/NOx.rda |binary data/RiskyTransport.rda |binary data/Train.rda |binary inst/doc/c2.formula.data.html | 93 ++++++++++++----------- inst/doc/c3.rum.html | 117 +++++++++++++++-------------- inst/doc/c4.relaxiid.html | 149 +++++++++++++++++++------------------ inst/doc/c5.mxl.html | 165 +++++++++++++++++++++--------------------- inst/doc/c6.mprobit.html | 23 +++-- inst/doc/c7.miscmodels.html | 55 +++++++------- inst/doc/e1mlogit.html | 121 +++++++++++++++--------------- inst/doc/e2nlogit.html | 87 +++++++++++----------- inst/doc/e3mxlogit.html | 97 ++++++++++++------------ inst/doc/e4mprobit.html | 61 ++++++++------- inst/doc/mlogit.html | 9 +- 34 files changed, 554 insertions(+), 513 deletions(-)
Title: Measure of Agreement Between Two Raters
Description: Measure of agreement delta was originally by Martín & Femia (2004) <DOI:10.1348/000711004849268>.
Since then has been considered as agreement measure for different
fields, since their behavior is usually better than the usual kappa index
by Cohen (1960) <DOI:10.1177/001316446002000104>. The main issue with delta
is that can not be computed by hand contrary to kappa. The current algorithm
is based on the Version 5 of the delta windows program that can be found on
<https://www.ugr.es/~bioest/software/delta/cmd.php?seccion=downloads>.
Author: Antonio Rodriguez [aut, cre],
Pedro Femia [cph, ctb],
Antonio Martin [cph, ctb]
Maintainer: Antonio Rodriguez <tonirodriguezcontesti@gmail.com>
Diff between Delta versions 0.2.0.2 dated 2018-10-04 and 0.2.0.3 dated 2019-12-09
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/GetM1.R | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-09-19 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-08-30 0.9.9
2016-07-16 0.9.8
2016-05-11 0.9.7
2016-05-09 0.9.6
2016-03-05 0.9.5
2015-10-12 0.9.4
2015-08-11 0.9.3
2015-08-01 0.9.2
2015-05-10 0.9.1
2015-04-26 0.9
Title: Estimating Systems of Simultaneous Equations
Description: Econometric estimation of simultaneous
systems of linear and nonlinear equations using Ordinary Least
Squares (OLS), Weighted Least Squares (WLS), Seemingly Unrelated
Regressions (SUR), Two-Stage Least Squares (2SLS), Weighted
Two-Stage Least Squares (W2SLS), and Three-Stage Least Squares (3SLS)
as suggested, e.g., by Zellner (1962) <doi:10.2307/2281644>,
Zellner and Theil (1962) <doi:10.2307/1911287>, and
Schmidt (1990) <doi:10.1016/0304-4076(90)90127-F>.
Author: Arne Henningsen and Jeff D. Hamann
Maintainer: Arne Henningsen <arne.henningsen@gmail.com>
Diff between systemfit versions 1.1-22 dated 2018-04-04 and 1.1-24 dated 2019-12-09
DESCRIPTION | 13 MD5 | 24 NEWS | 10 R/calcGLS.R | 25 R/calcResidCov.R | 2 R/lrtest.R | 4 R/systemfit.R | 21 R/systemfitPanel.R | 28 build/vignette.rds |binary inst/doc/systemfit.pdf |binary man/GrunfeldGreene.Rd | 2 tests/test_panel.R | 77 ++ tests/test_panel.Rout.save | 1454 +++++++++++++++++++++++++++++++++++++++++---- 13 files changed, 1514 insertions(+), 146 deletions(-)
Title: Retinal Reconstruction Program
Description: Reconstructs retinae by morphing a flat surface with cuts (a
dissected flat-mount retina) onto a curvilinear surface (the standard retinal
shape). It can estimate the position of a point on the intact adult retina
to within 8 degrees of arc (3.6% of nasotemporal axis). The coordinates in
reconstructed retinae can be transformed to visuotopic coordinates.
Author: David C. Sterratt [aut, cre, cph],
Daniel Lyngholm [aut, cph]
Maintainer: David C. Sterratt <david.c.sterratt@ed.ac.uk>
Diff between retistruct versions 0.6.0 dated 2019-07-10 and 0.6.1 dated 2019-12-09
retistruct-0.6.0/retistruct/man/sphericalplot.reconstructedOutline.Rd |only retistruct-0.6.1/retistruct/DESCRIPTION | 10 retistruct-0.6.1/retistruct/MD5 | 137 ++- retistruct-0.6.1/retistruct/NAMESPACE | 4 retistruct-0.6.1/retistruct/NEWS | 33 retistruct-0.6.1/retistruct/R/AnnotatedOutline.R | 10 retistruct-0.6.1/retistruct/R/CountSet.R | 13 retistruct-0.6.1/retistruct/R/FeatureSet.R | 45 - retistruct-0.6.1/retistruct/R/LandmarkSet.R | 2 retistruct-0.6.1/retistruct/R/Outline.R | 16 retistruct-0.6.1/retistruct/R/PathOutline.R | 18 retistruct-0.6.1/retistruct/R/PointSet.R | 9 retistruct-0.6.1/retistruct/R/ReconstructedCountSet.R | 12 retistruct-0.6.1/retistruct/R/ReconstructedFeatureSet.R | 33 retistruct-0.6.1/retistruct/R/ReconstructedOutline.R | 348 +++++----- retistruct-0.6.1/retistruct/R/ReconstructedPointSet.R | 50 + retistruct-0.6.1/retistruct/R/RetinalReconstructedOutline.R | 52 + retistruct-0.6.1/retistruct/R/StitchedOutline.R | 24 retistruct-0.6.1/retistruct/R/TriangulatedOutline.R | 2 retistruct-0.6.1/retistruct/R/format-common.R | 45 + retistruct-0.6.1/retistruct/R/format-csv.R | 6 retistruct-0.6.1/retistruct/R/format-idt.R | 2 retistruct-0.6.1/retistruct/R/format-ijroi.R | 13 retistruct-0.6.1/retistruct/R/geometry.R | 20 retistruct-0.6.1/retistruct/R/kernel-density.R | 12 retistruct-0.6.1/retistruct/R/misc.R | 11 retistruct-0.6.1/retistruct/R/r6-serialize.R |only retistruct-0.6.1/retistruct/R/retistruct-batch.R | 52 - retistruct-0.6.1/retistruct/R/retistruct-gui.R | 50 - retistruct-0.6.1/retistruct/R/retistruct.R | 42 - retistruct-0.6.1/retistruct/R/spheristruct.R | 13 retistruct-0.6.1/retistruct/R/zzz.R | 1 retistruct-0.6.1/retistruct/inst/extdata/GM509/R-CONTRA/markup.csv | 2 retistruct-0.6.1/retistruct/inst/extdata/ijroi1/P.csv | 124 +-- retistruct-0.6.1/retistruct/inst/extdata/ijroi1/T.csv | 4 retistruct-0.6.1/retistruct/inst/extdata/ijroi1/datacounts.csv |only retistruct-0.6.1/retistruct/inst/extdata/ijroi1/markup.csv | 2 retistruct-0.6.1/retistruct/inst/extdata/smi32/T.csv | 2 retistruct-0.6.1/retistruct/inst/extdata/smi32/markup.csv | 2 retistruct-0.6.1/retistruct/man/AnnotatedOutline.Rd | 2 retistruct-0.6.1/retistruct/man/CountSet.Rd | 2 retistruct-0.6.1/retistruct/man/FeatureSet.Rd | 2 retistruct-0.6.1/retistruct/man/Fragment.Rd | 2 retistruct-0.6.1/retistruct/man/LandmarkSet.Rd | 2 retistruct-0.6.1/retistruct/man/Outline.Rd | 2 retistruct-0.6.1/retistruct/man/PathOutline.Rd | 2 retistruct-0.6.1/retistruct/man/PointSet.Rd | 2 retistruct-0.6.1/retistruct/man/R6_to_list.Rd |only retistruct-0.6.1/retistruct/man/ReconstructedCountSet.Rd | 2 retistruct-0.6.1/retistruct/man/ReconstructedFeatureSet.Rd | 2 retistruct-0.6.1/retistruct/man/ReconstructedLandmarkSet.Rd | 2 retistruct-0.6.1/retistruct/man/ReconstructedOutline.Rd | 12 retistruct-0.6.1/retistruct/man/ReconstructedPointSet.Rd | 2 retistruct-0.6.1/retistruct/man/RetinalOutline.Rd | 2 retistruct-0.6.1/retistruct/man/RetinalReconstructedOutline.Rd | 2 retistruct-0.6.1/retistruct/man/StitchedOutline.Rd | 2 retistruct-0.6.1/retistruct/man/TriangulatedFragment.Rd | 2 retistruct-0.6.1/retistruct/man/TriangulatedOutline.Rd | 2 retistruct-0.6.1/retistruct/man/flipped.triangles.Rd | 7 retistruct-0.6.1/retistruct/man/list_to_R6.Rd |only retistruct-0.6.1/retistruct/man/report.Rd |only retistruct-0.6.1/retistruct/man/retistruct.read.dataset.Rd | 2 retistruct-0.6.1/retistruct/man/retistruct.read.markup.Rd | 8 retistruct-0.6.1/retistruct/man/retistruct.read.recdata.Rd | 2 retistruct-0.6.1/retistruct/man/retistruct.reconstruct.Rd | 4 retistruct-0.6.1/retistruct/man/sphere.spherical.to.sphere.cart.Rd | 9 retistruct-0.6.1/retistruct/man/sphericalplot.ReconstructedOutline.Rd |only retistruct-0.6.1/retistruct/tests/testthat/test-count-set.R |only retistruct-0.6.1/retistruct/tests/testthat/test-format-idt.R | 10 retistruct-0.6.1/retistruct/tests/testthat/test-format-ijroi.R | 44 - retistruct-0.6.1/retistruct/tests/testthat/test-r6-serialize.R |only retistruct-0.6.1/retistruct/tests/testthat/test-reconstruct.R | 96 ++ retistruct-0.6.1/retistruct/tests/testthat/test-reconstructed-outline.R | 6 retistruct-0.6.1/retistruct/tests/testthat/test-regressions.R | 4 74 files changed, 899 insertions(+), 560 deletions(-)
Title: Project Environments
Description: A dependency management toolkit for R. Using 'renv', you can create
and manage project-local R libraries, save the state of these libraries to
a 'lockfile', and later restore your library as required. Together, these
tools can help make your projects more isolated, portable, and reproducible.
Author: Kevin Ushey [aut, cre],
RStudio [cph]
Maintainer: Kevin Ushey <kevin@rstudio.com>
Diff between renv versions 0.9.0 dated 2019-12-05 and 0.9.1 dated 2019-12-09
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 4 ++++ R/files.R | 3 +-- R/platform.R | 2 +- inst/doc/docker.html | 2 +- inst/doc/lockfile.html | 2 +- inst/doc/renv.html | 6 +++--- 8 files changed, 21 insertions(+), 18 deletions(-)
Title: Deprecated 'classic' 'Rcpp' 'API'
Description: The 'RcppClassic' package provides a deprecated C++ library which
facilitates the integration of R and C++. New projects should use the new 'Rcpp'
'API' in the 'Rcpp' package.
Author: Dirk Eddelbuettel and Romain Francois, with contributions by David Reiss,
and based on code written during 2005 and 2006 by Dominick Samperi
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppClassic versions 0.9.11 dated 2018-07-15 and 0.9.12 dated 2019-12-09
RcppClassic-0.9.11/RcppClassic/inst/doc/RcppClassic-intro.R |only RcppClassic-0.9.11/RcppClassic/inst/doc/RcppClassic-intro.Rmd |only RcppClassic-0.9.11/RcppClassic/inst/doc/RcppClassic-unitTests.R |only RcppClassic-0.9.11/RcppClassic/inst/doc/RcppClassic-unitTests.Rnw |only RcppClassic-0.9.11/RcppClassic/inst/doc/RcppClassic-unitTests.pdf |only RcppClassic-0.9.11/RcppClassic/inst/unitTests |only RcppClassic-0.9.11/RcppClassic/tests/doRUnit.R |only RcppClassic-0.9.11/RcppClassic/vignettes/RcppClassic-intro.Rmd |only RcppClassic-0.9.11/RcppClassic/vignettes/RcppClassic-unitTests.Rnw |only RcppClassic-0.9.11/RcppClassic/vignettes/bib.tex |only RcppClassic-0.9.11/RcppClassic/vignettes/header.tex |only RcppClassic-0.9.11/RcppClassic/vignettes/unitTests |only RcppClassic-0.9.12/RcppClassic/ChangeLog | 59 ++++++++++ RcppClassic-0.9.12/RcppClassic/DESCRIPTION | 12 +- RcppClassic-0.9.12/RcppClassic/MD5 | 45 +++---- RcppClassic-0.9.12/RcppClassic/README.md | 7 + RcppClassic-0.9.12/RcppClassic/build/vignette.rds |binary RcppClassic-0.9.12/RcppClassic/cleanup | 12 +- RcppClassic-0.9.12/RcppClassic/inst/doc/RcppClassic-intro.Rnw |only RcppClassic-0.9.12/RcppClassic/inst/doc/RcppClassic-intro.pdf |binary RcppClassic-0.9.12/RcppClassic/inst/tinytest |only RcppClassic-0.9.12/RcppClassic/src/Makevars | 21 +-- RcppClassic-0.9.12/RcppClassic/tests/tinytest.R |only RcppClassic-0.9.12/RcppClassic/vignettes/RcppClassic-intro.Rnw |only RcppClassic-0.9.12/RcppClassic/vignettes/pdf |only RcppClassic-0.9.12/RcppClassic/vignettes/rmd |only 26 files changed, 112 insertions(+), 44 deletions(-)
Title: Mark-Recapture Analysis for Survival and Abundance Estimation
Description: Functions for fitting various models to capture-recapture data
including mixed-effects Cormack-Jolly-Seber(CJS) and multistate models and
the multi-variate state model structure for survival
estimation and POPAN structured Jolly-Seber models for abundance estimation.
There are also Hidden Markov model (HMM) implementations of CJS and multistate
models with and without state uncertainty and a simulation capability for HMM
models.
Author: Jeff Laake <jefflaake@gmail.com>, Devin Johnson
<devin.johnson@noaa.gov>, Paul Conn <paul.conn@noaa.gov>, example for simHMM
from Jay Rotella
Maintainer: Jeff Laake <jefflaake@gmail.com>
Diff between marked versions 1.2.1 dated 2018-03-30 and 1.2.6 dated 2019-12-09
marked-1.2.1/marked/inst/doc/markedVignette.Rnw |only marked-1.2.1/marked/inst/doc/markedVignette.pdf |only marked-1.2.1/marked/man/compute.real.Rd |only marked-1.2.1/marked/vignettes/markedVignette.Rnw |only marked-1.2.6/marked/DESCRIPTION | 17 marked-1.2.6/marked/MD5 | 260 +++---- marked-1.2.6/marked/NAMESPACE | 7 marked-1.2.6/marked/NEWS | 65 + marked-1.2.6/marked/R/HMMutilities.r | 21 marked-1.2.6/marked/R/admbutils.R | 43 - marked-1.2.6/marked/R/cjs.R | 18 marked-1.2.6/marked/R/cjs.hessian.r | 2 marked-1.2.6/marked/R/cjs.lnl.r | 49 - marked-1.2.6/marked/R/cjs_tmb.R | 57 - marked-1.2.6/marked/R/coef.r | 4 marked-1.2.6/marked/R/compute.real.R | 79 +- marked-1.2.6/marked/R/convert.link.to.real.r | 2 marked-1.2.6/marked/R/create.dmdf.R | 7 marked-1.2.6/marked/R/crm.R | 140 ++- marked-1.2.6/marked/R/crm.wrapper.R | 13 marked-1.2.6/marked/R/deriv.inverse.link.R | 2 marked-1.2.6/marked/R/inverse.link.R | 4 marked-1.2.6/marked/R/js.hessian.R | 2 marked-1.2.6/marked/R/make.design.data.R | 30 marked-1.2.6/marked/R/marked-package.R | 115 ++- marked-1.2.6/marked/R/mscjs.r | 34 marked-1.2.6/marked/R/mscjs_tmb.r | 74 +- marked-1.2.6/marked/R/msld_tmb.r |only marked-1.2.6/marked/R/mvmscjs.R | 14 marked-1.2.6/marked/R/mvmscjs_tmb.R |only marked-1.2.6/marked/R/predict.crm.r | 80 +- marked-1.2.6/marked/R/print.crm.r | 6 marked-1.2.6/marked/R/probitCJS.R | 2 marked-1.2.6/marked/R/process.data.R | 59 + marked-1.2.6/marked/R/scale.r | 13 marked-1.2.6/marked/R/set.initial.r | 4 marked-1.2.6/marked/R/setup.model.R | 2 marked-1.2.6/marked/R/simplify.r | 41 - marked-1.2.6/marked/build/vignette.rds |binary marked-1.2.6/marked/data/Paradise_shelduck.rda |only marked-1.2.6/marked/inst/cjs_tmb.cpp | 78 +- marked-1.2.6/marked/inst/cjsre_tmb.cpp | 119 +-- marked-1.2.6/marked/inst/doc/markedVignette.R | 158 +--- marked-1.2.6/marked/inst/doc/markedVignette.Rmd |only marked-1.2.6/marked/inst/doc/markedVignette.html |only marked-1.2.6/marked/inst/models.txt | 37 - marked-1.2.6/marked/inst/msld_tmb.cpp |only marked-1.2.6/marked/inst/multistate_tmb.cpp | 522 +++++++------- marked-1.2.6/marked/inst/mvms.tpl | 88 +- marked-1.2.6/marked/inst/mvms_tmb.cpp |only marked-1.2.6/marked/inst/parameters.txt | 17 marked-1.2.6/marked/man/HMMLikelihood.Rd | 170 ++-- marked-1.2.6/marked/man/Paradise_shelduck.Rd |only marked-1.2.6/marked/man/Phi.mean.Rd | 82 +- marked-1.2.6/marked/man/R_HMMLikelihood.Rd | 86 +- marked-1.2.6/marked/man/backward_prob.Rd | 72 - marked-1.2.6/marked/man/cjs.accumulate.Rd | 68 - marked-1.2.6/marked/man/cjs.hessian.Rd | 44 - marked-1.2.6/marked/man/cjs.initial.Rd | 56 - marked-1.2.6/marked/man/cjs.lnl.Rd | 255 +++--- marked-1.2.6/marked/man/cjs_admb.Rd | 223 +++--- marked-1.2.6/marked/man/cjs_delta.Rd | 68 - marked-1.2.6/marked/man/cjs_gamma.Rd | 64 - marked-1.2.6/marked/man/cjs_tmb.Rd | 246 +++--- marked-1.2.6/marked/man/coef.crm.Rd | 54 - marked-1.2.6/marked/man/compute_matrices.Rd | 46 - marked-1.2.6/marked/man/compute_real.Rd |only marked-1.2.6/marked/man/convert.link.to.real.Rd | 84 +- marked-1.2.6/marked/man/create.dm.Rd | 122 +-- marked-1.2.6/marked/man/create.dmdf.Rd | 486 ++++++------- marked-1.2.6/marked/man/create.fixed.matrix.Rd | 44 - marked-1.2.6/marked/man/create.links.Rd | 48 - marked-1.2.6/marked/man/crm.Rd | 667 +++++++++--------- marked-1.2.6/marked/man/crm.wrapper.Rd | 176 ++-- marked-1.2.6/marked/man/deriv_inverse.link.Rd | 82 +- marked-1.2.6/marked/man/dipper.Rd | 112 +-- marked-1.2.6/marked/man/dmat_hsmm2hmm.Rd | 48 - marked-1.2.6/marked/man/fix.parameters.Rd | 58 - marked-1.2.6/marked/man/function.wrapper.Rd | 74 +- marked-1.2.6/marked/man/global_decode.Rd | 76 +- marked-1.2.6/marked/man/hmmDemo.Rd | 104 +- marked-1.2.6/marked/man/hsmm2hmm.Rd | 52 - marked-1.2.6/marked/man/initiate_pi.Rd | 94 +- marked-1.2.6/marked/man/inverse.link.Rd | 102 +- marked-1.2.6/marked/man/js.Rd | 197 ++--- marked-1.2.6/marked/man/js.accumulate.Rd | 68 - marked-1.2.6/marked/man/js.hessian.Rd | 44 - marked-1.2.6/marked/man/js.lnl.Rd | 102 +- marked-1.2.6/marked/man/local_decode.Rd | 76 +- marked-1.2.6/marked/man/make.design.data.Rd | 146 +-- marked-1.2.6/marked/man/merge_design.covariates.Rd | 194 ++--- marked-1.2.6/marked/man/mixed.model.admb.Rd | 126 +-- marked-1.2.6/marked/man/mscjs.Rd | 348 ++++----- marked-1.2.6/marked/man/mscjs_tmb.Rd | 208 +++-- marked-1.2.6/marked/man/msld_tmb.Rd |only marked-1.2.6/marked/man/mstrata.Rd | 109 +- marked-1.2.6/marked/man/mvms_design_data.Rd | 60 - marked-1.2.6/marked/man/mvms_dmat.Rd | 72 - marked-1.2.6/marked/man/mvmscjs.Rd | 770 ++++++++++----------- marked-1.2.6/marked/man/mvmscjs_tmb.Rd |only marked-1.2.6/marked/man/omega.Rd | 44 - marked-1.2.6/marked/man/predict.crm.Rd | 126 +-- marked-1.2.6/marked/man/print.crm.Rd | 52 - marked-1.2.6/marked/man/print.crmlist.Rd | 50 - marked-1.2.6/marked/man/probitCJS.Rd | 216 +++-- marked-1.2.6/marked/man/proc.form.Rd | 52 - marked-1.2.6/marked/man/process.ch.Rd | 76 +- marked-1.2.6/marked/man/process.data.Rd | 350 ++++----- marked-1.2.6/marked/man/resight.matrix.Rd | 70 - marked-1.2.6/marked/man/sealions.Rd | 141 +-- marked-1.2.6/marked/man/set.fixed.Rd | 48 - marked-1.2.6/marked/man/set.initial.Rd | 50 - marked-1.2.6/marked/man/set.scale.Rd | 72 - marked-1.2.6/marked/man/set_mvms.Rd | 80 +- marked-1.2.6/marked/man/setup.model.Rd | 102 +- marked-1.2.6/marked/man/setup.parameters.Rd | 141 +-- marked-1.2.6/marked/man/setup_admb.Rd | 50 - marked-1.2.6/marked/man/setup_tmb.Rd | 36 marked-1.2.6/marked/man/simHMM.Rd | 314 ++++---- marked-1.2.6/marked/man/skagit.Rd | 94 +- marked-1.2.6/marked/man/splitCH.Rd | 94 +- marked-1.2.6/marked/man/tagloss.Rd | 262 +++---- marked-1.2.6/marked/man/valid.parameters.Rd | 56 - marked-1.2.6/marked/src/cjs.f | 50 - marked-1.2.6/marked/src/cjs1tldmat.f | 14 marked-1.2.6/marked/src/cjs1tlgam.f | 16 marked-1.2.6/marked/src/cjs2tldmat.f | 14 marked-1.2.6/marked/src/cjs2tlgam.f | 14 marked-1.2.6/marked/src/cjsdmat.f | 3 marked-1.2.6/marked/src/cjsgamma.f | 3 marked-1.2.6/marked/src/hmm_like.f | 27 marked-1.2.6/marked/src/ms2gamma.f | 9 marked-1.2.6/marked/src/msdmat.f | 12 marked-1.2.6/marked/src/msgamma.f | 22 marked-1.2.6/marked/src/mvmsdmat.f | 59 - marked-1.2.6/marked/src/ums2dmat.f | 27 marked-1.2.6/marked/src/umsdmat.f | 14 marked-1.2.6/marked/vignettes/markedVignette.Rmd |only marked-1.2.6/marked/vignettes/markedWriteUpBib.bib | 345 +++------ 139 files changed, 6262 insertions(+), 5711 deletions(-)