Title: Group Animal Relocation Data by Spatial and Temporal
Relationship
Description: Detects spatial and temporal groups in GPS relocations
(Robitaille et al. (2020) <doi:10.1111/2041-210X.13215>).
It can be used to convert GPS relocations to
gambit-of-the-group format to build proximity-based social networks
In addition, the randomizations function provides data-stream
randomization methods suitable for GPS data.
Author: Alec L. Robitaille [aut, cre] (<https://orcid.org/0000-0002-4706-1762>),
Quinn Webber [aut] (<https://orcid.org/0000-0002-0434-9360>),
Eric Vander Wal [aut] (<https://orcid.org/0000-0002-8534-4317>)
Maintainer: Alec L. Robitaille <robit.alec@gmail.com>
Diff between spatsoc versions 0.1.14 dated 2020-07-05 and 0.1.15 dated 2020-10-21
DESCRIPTION | 10 ++--- MD5 | 22 +++++------ NEWS.md | 13 ++++-- R/group_lines.R | 2 - R/randomizations.R | 2 - build/vignette.rds |binary inst/doc/intro-spatsoc.html | 66 +++++++++++++++++------------------ inst/doc/using-edge-and-dyad.html | 71 ++++++++++++++++++++++++++++++++++++++ man/group_lines.Rd | 2 - man/randomizations.Rd | 2 - man/spatsoc.Rd | 2 - tests/testthat/test-time.R | 4 +- 12 files changed, 135 insertions(+), 61 deletions(-)
Title: Methods to Analyse Signed Networks
Description: Methods for the analysis of signed networks. This includes several measures for structural balance as introduced by Cartwright and Harary (1956) <doi:10.1037/h0046049>, blockmodeling algorithms from Doreian (2008) <doi:10.1016/j.socnet.2008.03.005>, various centrality indices, and projections of signed two-mode networks introduced by Schoch (2020) <doi:10.1080/0022250X.2019.1711376>.
Author: David Schoch [aut, cre]
Maintainer: David Schoch <david.schoch@manchester.ac.uk>
Diff between signnet versions 0.6.0 dated 2020-08-13 and 0.7.0 dated 2020-10-21
DESCRIPTION | 6 MD5 | 27 +- NAMESPACE | 1 NEWS.md | 4 R/RcppExports.R | 8 R/complex_matrices.R | 6 R/signed_triangles.R | 433 +++++++++++++++++++++++++++++++++ README.md | 14 - inst/doc/signed_2mode.html | 8 inst/doc/signed_networks.html | 4 man/figures/README-block_example-1.png |binary man/figures/signed_triads.png |only man/triad_census_signed.Rd |only src/RcppExports.cpp | 27 ++ src/triadCensus.cpp |only tests/testthat/test-signed_triangles.R | 13 16 files changed, 524 insertions(+), 27 deletions(-)
Title: Spatio-Temporal Estimation and Prediction for Censored/Missing
Responses
Description: It estimates the parameters of a censored or missing data in spatio-temporal models using the SAEM algorithm (Delyon et al., 1999). This algorithm is a stochastic approximation of the widely used EM algorithm and an important tool for models in which the E-step does not have an analytic form. Besides the expressions obtained to estimate the parameters to the proposed model, we include the calculations for the observed information matrix using the method developed by Louis (1982). To examine the performance of the fitted model, case-deletion measure are provided.
Author: Larissa A. Matos [aut, cre] (<https://orcid.org/0000-0002-2635-0901>),
Katherine L. Valeriano [aut] (<https://orcid.org/0000-0001-6388-4753>),
Victor H. Lachos [ctb] (<https://orcid.org/0000-0002-7239-2459>)
Maintainer: Larissa A. Matos <larissa.amatos@gmail.com>
Diff between StempCens versions 0.1.0 dated 2019-02-08 and 1.1.0 dated 2020-10-21
StempCens-0.1.0/StempCens/R/utils_SpatioTemporal.R |only StempCens-0.1.0/StempCens/inst/cran-comments.Rmd |only StempCens-0.1.0/StempCens/inst/cran-comments.md |only StempCens-0.1.0/StempCens/tests/testthat/test_CovarianceM.R |only StempCens-0.1.0/StempCens/tests/testthat/test_CrossStempCens.R |only StempCens-0.1.0/StempCens/tests/testthat/test_DiagStempCens.R |only StempCens-0.1.0/StempCens/tests/testthat/test_EstStempCens.R |only StempCens-0.1.0/StempCens/tests/testthat/test_PredStempCens.R |only StempCens-0.1.0/StempCens/tests/testthat/test_utils_SpatioTemporal.R |only StempCens-1.1.0/StempCens/DESCRIPTION | 39 StempCens-1.1.0/StempCens/MD5 | 59 - StempCens-1.1.0/StempCens/NAMESPACE | 28 StempCens-1.1.0/StempCens/NEWS.md | 15 StempCens-1.1.0/StempCens/R/CovarianceM.R | 131 +-- StempCens-1.1.0/StempCens/R/CrossStempCens.R | 194 ++-- StempCens-1.1.0/StempCens/R/DiagStempCens.R | 90 +- StempCens-1.1.0/StempCens/R/EffectiveRange.R |only StempCens-1.1.0/StempCens/R/EstStempCens.R | 310 ++++--- StempCens-1.1.0/StempCens/R/PredStempCens.R | 232 +++-- StempCens-1.1.0/StempCens/R/RcppExports.R |only StempCens-1.1.0/StempCens/R/StempCens-package.R |only StempCens-1.1.0/StempCens/R/utils_SpatioTemporal_Rcpp.R |only StempCens-1.1.0/StempCens/README.md | 226 ++++- StempCens-1.1.0/StempCens/build |only StempCens-1.1.0/StempCens/inst/CITATION |only StempCens-1.1.0/StempCens/inst/REFERENCES.bib |only StempCens-1.1.0/StempCens/man/CovarianceM.Rd | 110 +- StempCens-1.1.0/StempCens/man/CrossStempCens.Rd | 186 ++-- StempCens-1.1.0/StempCens/man/DiagStempCens.Rd | 203 ++--- StempCens-1.1.0/StempCens/man/EffectiveRange.Rd |only StempCens-1.1.0/StempCens/man/EstStempCens.Rd | 399 ++++------ StempCens-1.1.0/StempCens/man/PredStempCens.Rd | 206 ++--- StempCens-1.1.0/StempCens/man/StempCens-package.Rd |only StempCens-1.1.0/StempCens/src |only StempCens-1.1.0/StempCens/tests/testthat.R | 8 StempCens-1.1.0/StempCens/tests/testthat/test-CovarianceM.R |only StempCens-1.1.0/StempCens/tests/testthat/test-CrossStempCens.R |only StempCens-1.1.0/StempCens/tests/testthat/test-DiagStempCens.R |only StempCens-1.1.0/StempCens/tests/testthat/test-EffectiveRange.R |only StempCens-1.1.0/StempCens/tests/testthat/test-EstStempCens.R |only StempCens-1.1.0/StempCens/tests/testthat/test-PredStempCens.R |only StempCens-1.1.0/StempCens/tests/testthat/test-utils_SpatioTemporal_Rcpp.R |only 42 files changed, 1321 insertions(+), 1115 deletions(-)
Title: Squared Extrapolation Methods for Accelerating EM-Like Monotone
Algorithms
Description: Algorithms for accelerating the convergence of slow,
monotone sequences from smooth, contraction mapping such as the
EM algorithm. It can be used to accelerate any smooth, linearly
convergent acceleration scheme. A tutorial style introduction
to this package is available in a vignette on the CRAN download
page or, when the package is loaded in an R session, with
vignette("SQUAREM"). Refer to the J Stat Software article: <doi:10.18637/jss.v092.i07>.
Author: Ravi Varadhan
Maintainer: Ravi Varadhan <ravi.varadhan@jhu.edu>
Diff between SQUAREM versions 2020.4 dated 2020-08-26 and 2020.5 dated 2020-10-21
DESCRIPTION | 8 - MD5 | 20 +- NEWS | 5 R/squarem.R | 22 +- demo/factoranalysis.R | 369 ++++++++++++++++++++++++++------------------------ demo/intcensoring.R | 216 ++++++++++++++--------------- demo/mmlogistic.R | 234 +++++++++++++++---------------- demo/poissonmix.R | 160 +++++++++++---------- inst/doc/SQUAREM.pdf |binary man/internal.Rd | 42 ++--- man/squarem.Rd | 40 +++-- 11 files changed, 586 insertions(+), 530 deletions(-)
Title: Stratigraphic Data Analysis
Description: A fast, consistent tool for plotting and facilitating the analysis of stratigraphic
and sedimentological data. Taking advantage of the flexible plotting tools available in R,
'SDAR' uses stratigraphic and sedimentological data to produce detailed graphic logs for
outcrop sections and borehole logs. These logs can include multiple features (e.g., bed thickness,
lithology, samples, sedimentary structures, colors, fossil content, bioturbation index,
gamma ray logs) (Johnson, 1992, <ISSN 0037-0738>).
Author: John R. Ortiz [aut, cre],
Carlos Jaramillo [aut],
Carlos Moreno [ctb]
Maintainer: John R. Ortiz <jrortizt@unal.edu.co>
Diff between SDAR versions 0.9-5 dated 2020-10-20 and 0.9-55 dated 2020-10-21
DESCRIPTION | 10 +++++----- MD5 | 24 ++++++++++++------------ inst/doc/SDAR_data_model.Rmd | 2 +- inst/doc/SDAR_data_model.html | 2 +- inst/doc/introduction_to_SDAR.Rmd | 4 ++-- inst/doc/introduction_to_SDAR.html | 12 ++++++------ man/plot.Rd | 2 +- vignettes/SDAR_data_model.Rmd | 2 +- vignettes/SDAR_output_fig_1.png |binary vignettes/SDAR_output_fig_2.png |binary vignettes/SDAR_output_fig_3.png |binary vignettes/SDAR_output_fig_4.png |binary vignettes/introduction_to_SDAR.Rmd | 4 ++-- 13 files changed, 31 insertions(+), 31 deletions(-)
Title: Comparison of Phylogenetic Trees Using Quartet and Split
Measures
Description: Calculates the number of four-taxon subtrees consistent with a pair
of cladograms, calculating the symmetric quartet distance of Bandelt & Dress (1986),
Reconstructing the shape of a tree from observed dissimilarity data,
Advances in Applied Mathematics, 7, 309-343 <doi:10.1016/0196-8858(86)90038-2>,
and using the tqDist algorithm of Sand et al. (2014), tqDist: a library for
computing the quartet and triplet distances between binary or general trees,
Bioinformatics, 30, 2079–2080 <doi:10.1093/bioinformatics/btu157>
for pairs of binary trees.
Author: Martin R. Smith [aut, cre, cph]
(<https://orcid.org/0000-0001-5660-1727>),
Andreas Sand [ant],
Gerth Stølting Brodal [ant],
Rolf Fagerberg [ant],
Thomas Mailund [ant],
Christian N. S. Pedersen [ant],
Jens Johansen [ant],
Morten K. Holt [ant]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between Quartet versions 1.1.0 dated 2020-01-28 and 1.2.0 dated 2020-10-21
Quartet-1.1.0/Quartet/inst/doc/Critical-distances.R |only Quartet-1.1.0/Quartet/inst/doc/Critical-distances.Rmd |only Quartet-1.1.0/Quartet/inst/doc/Critical-distances.pdf |only Quartet-1.1.0/Quartet/inst/doc/Tree-distance-metrics.R |only Quartet-1.1.0/Quartet/inst/doc/Tree-distance-metrics.Rmd |only Quartet-1.1.0/Quartet/inst/doc/Tree-distance-metrics.pdf |only Quartet-1.1.0/Quartet/vignettes/Critical-distances.Rmd |only Quartet-1.1.0/Quartet/vignettes/Tree-distance-metrics.Rmd |only Quartet-1.2.0/Quartet/DESCRIPTION | 16 Quartet-1.2.0/Quartet/MD5 | 135 ++- Quartet-1.2.0/Quartet/NAMESPACE | 29 Quartet-1.2.0/Quartet/NEWS.md | 27 Quartet-1.2.0/Quartet/R/CompareQuartets.R |only Quartet-1.2.0/Quartet/R/Metrics.R | 257 ++++--- Quartet-1.2.0/Quartet/R/PartitionDistance.R | 84 +- Quartet-1.2.0/Quartet/R/Quartet-package.R |only Quartet-1.2.0/Quartet/R/QuartetDistance.R | 236 ------ Quartet-1.2.0/Quartet/R/RcppExports.R | 254 +++---- Quartet-1.2.0/Quartet/R/ResolvedQuartets.R | 45 - Quartet-1.2.0/Quartet/R/TernaryPoints.R | 34 Quartet-1.2.0/Quartet/R/VisualizeQuartets.R |only Quartet-1.2.0/Quartet/R/data.R | 2 Quartet-1.2.0/Quartet/R/tqDist.r | 357 ++++++---- Quartet-1.2.0/Quartet/R/zzz.R | 4 Quartet-1.2.0/Quartet/README.md | 65 + Quartet-1.2.0/Quartet/build/partial.rdb |binary Quartet-1.2.0/Quartet/build/vignette.rds |binary Quartet-1.2.0/Quartet/inst/CITATION | 2 Quartet-1.2.0/Quartet/inst/REFERENCES.bib | 17 Quartet-1.2.0/Quartet/inst/WORDLIST | 18 Quartet-1.2.0/Quartet/inst/doc/Quartet-Distance.R |only Quartet-1.2.0/Quartet/inst/doc/Quartet-Distance.Rmd |only Quartet-1.2.0/Quartet/inst/doc/Quartet-Distance.pdf |only Quartet-1.2.0/Quartet/inst/doc/Using-Quartet.R |only Quartet-1.2.0/Quartet/inst/doc/Using-Quartet.Rmd |only Quartet-1.2.0/Quartet/inst/doc/Using-Quartet.pdf |only Quartet-1.2.0/Quartet/man/AllQuartets.Rd | 36 - Quartet-1.2.0/Quartet/man/CompareQuartets.Rd | 121 +-- Quartet-1.2.0/Quartet/man/CompareQuartetsMulti.Rd |only Quartet-1.2.0/Quartet/man/CompareSplits.Rd | 137 +-- Quartet-1.2.0/Quartet/man/Distances.Rd | 21 Quartet-1.2.0/Quartet/man/PairSharedQuartetStatus.Rd | 85 +- Quartet-1.2.0/Quartet/man/PairSharedSplitStatus.Rd | 64 - Quartet-1.2.0/Quartet/man/PlotQuartet.Rd | 31 Quartet-1.2.0/Quartet/man/Quartet-package.Rd |only Quartet-1.2.0/Quartet/man/QuartetPoints.Rd | 146 +--- Quartet-1.2.0/Quartet/man/QuartetState.Rd | 103 +- Quartet-1.2.0/Quartet/man/QuartetStatus.Rd | 111 +-- Quartet-1.2.0/Quartet/man/ResolvedQuartets.Rd | 119 +-- Quartet-1.2.0/Quartet/man/SimilarityMetrics.Rd | 155 ++-- Quartet-1.2.0/Quartet/man/SplitStatus.Rd | 61 - Quartet-1.2.0/Quartet/man/SymmetricDifferenceLineEnds.Rd | 70 - Quartet-1.2.0/Quartet/man/TQDist.Rd | 41 - Quartet-1.2.0/Quartet/man/TQFile.Rd | 2 Quartet-1.2.0/Quartet/man/ValidateQuartetFile.Rd | 46 - Quartet-1.2.0/Quartet/man/VisualizeQuartets.Rd |only Quartet-1.2.0/Quartet/man/dot-AddSlice.Rd | 54 - Quartet-1.2.0/Quartet/man/dot-CheckSize.Rd |only Quartet-1.2.0/Quartet/man/dot-NormalizeStatus.Rd | 6 Quartet-1.2.0/Quartet/man/dot-StatusToMatrix.Rd | 15 Quartet-1.2.0/Quartet/man/sq_trees.Rd | 74 +- Quartet-1.2.0/Quartet/man/tqdist_QuartetDistance.Rd | 2 Quartet-1.2.0/Quartet/src/AllQuartets.cpp |only Quartet-1.2.0/Quartet/src/RcppExports.cpp | 37 + Quartet-1.2.0/Quartet/src/int_stuff.h | 5 Quartet-1.2.0/Quartet/src/rQuartetDist.cpp | 2 Quartet-1.2.0/Quartet/tests/figs/deps.txt | 2 Quartet-1.2.0/Quartet/tests/figs/quartetdistance-r/plotquartet-gain.svg |only Quartet-1.2.0/Quartet/tests/figs/quartetdistance-r/plotquartet-one-star.svg |only Quartet-1.2.0/Quartet/tests/figs/quartetdistance-r/plotquartet.svg | 2 Quartet-1.2.0/Quartet/tests/figs/vq-label.svg |only Quartet-1.2.0/Quartet/tests/figs/vq-size.svg |only Quartet-1.2.0/Quartet/tests/figs/vq-tworow.svg |only Quartet-1.2.0/Quartet/tests/testthat.R | 4 Quartet-1.2.0/Quartet/tests/testthat/test-1-tqdist.R | 71 + Quartet-1.2.0/Quartet/tests/testthat/test-AllQuartets.R |only Quartet-1.2.0/Quartet/tests/testthat/test-CompareQuartets.R |only Quartet-1.2.0/Quartet/tests/testthat/test-PartitionDistance.R | 23 Quartet-1.2.0/Quartet/tests/testthat/test-QuartetDistance.R | 39 - Quartet-1.2.0/Quartet/tests/testthat/test-QuartetStates.R |only Quartet-1.2.0/Quartet/tests/testthat/test-ResolvedQuartets.R | 13 Quartet-1.2.0/Quartet/tests/testthat/test-VisualizeQuartet.R |only Quartet-1.2.0/Quartet/tests/testthat/test-ZZZ-Metrics.R | 62 + Quartet-1.2.0/Quartet/vignettes/Quartet-Distance.Rmd |only Quartet-1.2.0/Quartet/vignettes/Using-Quartet.Rmd |only 85 files changed, 1891 insertions(+), 1451 deletions(-)
Title: Qualitative Comparative Analysis
Description: An extensive set of functions to perform Qualitative Comparative Analysis:
crisp sets ('csQCA'), temporal ('tQCA'), multi-value ('mvQCA')
and fuzzy sets ('fsQCA'), using a GUI - graphical user interface.
'QCA' is a methodology that bridges the qualitative and quantitative divide
in social science research. It uses a Boolean algorithm that results in a
minimal causal combination that explains a given phenomenon.
Author: Adrian Dusa [aut, cre, cph] (<https://orcid.org/0000-0002-3525-9253>),
Ciprian Paduraru [ctb] (<https://orcid.org/0000-0002-4518-374X>),
jQuery Foundation [cph] (jQuery library and jQuery UI library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/gui/www/lib/jquery-AUTHORS.txt),
lp_solve [cph] (http://lpsolve.sourceforge.net),
Vasil Dinkov [ctb, cph] (jquery.smartmenus.js library),
Dmitry Baranovskiy [ctb, cph] (raphael.js library),
Emmanuel Quentin [ctb, cph] (raphael.inline_text_editing.js library),
Jimmy Breck-McKye [ctb, cph] (raphael-paragraph.js library),
Alrik Thiem [aut] (from version 1.0-0 up to version 1.1-3)
Maintainer: Adrian Dusa <dusa.adrian@unibuc.ro>
Diff between QCA versions 3.9 dated 2020-09-01 and 3.10 dated 2020-10-21
QCA-3.10/QCA/DESCRIPTION | 10 QCA-3.10/QCA/MD5 | 306 - QCA-3.10/QCA/R/findmin.R | 7 QCA-3.10/QCA/R/getSolution.R | 26 QCA-3.10/QCA/R/minimize.R | 24 QCA-3.10/QCA/R/onAttach.R | 5 QCA-3.10/QCA/R/print.R | 3 QCA-3.10/QCA/R/solveChart.R | 17 QCA-3.10/QCA/inst/ChangeLog | 17 QCA-3.10/QCA/inst/gui/www/js/maincode.js | 2 QCA-3.10/QCA/inst/staticdocs/CV.html | 4 QCA-3.10/QCA/inst/staticdocs/LegacyDatasets.html | 4 QCA-3.10/QCA/inst/staticdocs/Lipset.html | 4 QCA-3.10/QCA/inst/staticdocs/QCA.package.html | 8 QCA-3.10/QCA/inst/staticdocs/RS.html | 4 QCA-3.10/QCA/inst/staticdocs/SOPexpressions.html | 4 QCA-3.10/QCA/inst/staticdocs/XYplot.html | 4 QCA-3.10/QCA/inst/staticdocs/Xplot.html | 4 QCA-3.10/QCA/inst/staticdocs/calibrate.html | 4 QCA-3.10/QCA/inst/staticdocs/causalChain.html | 4 QCA-3.10/QCA/inst/staticdocs/chartFunctions.html | 4 QCA-3.10/QCA/inst/staticdocs/export.html | 4 QCA-3.10/QCA/inst/staticdocs/factorize.html | 4 QCA-3.10/QCA/inst/staticdocs/findRows.html | 4 QCA-3.10/QCA/inst/staticdocs/findTh.html | 4 QCA-3.10/QCA/inst/staticdocs/fuzzyops.html | 4 QCA-3.10/QCA/inst/staticdocs/generate.html | 4 QCA-3.10/QCA/inst/staticdocs/implicantMatrixFunctions.html | 4 QCA-3.10/QCA/inst/staticdocs/index.html | 4 QCA-3.10/QCA/inst/staticdocs/intersection.html | 4 QCA-3.10/QCA/inst/staticdocs/minimize.html | 4 QCA-3.10/QCA/inst/staticdocs/modelFit.html | 4 QCA-3.10/QCA/inst/staticdocs/negate.html | 4 QCA-3.10/QCA/inst/staticdocs/pof.html | 4 QCA-3.10/QCA/inst/staticdocs/recode.html | 4 QCA-3.10/QCA/inst/staticdocs/retention.html | 4 QCA-3.10/QCA/inst/staticdocs/runGUI.html | 4 QCA-3.10/QCA/inst/staticdocs/subsetsAndSupersets.html | 4 QCA-3.10/QCA/inst/staticdocs/truthTable.html | 4 QCA-3.10/QCA/man/QCA.package.Rd | 4 QCA-3.10/QCA/man/chartFunctions.Rd | 14 QCA-3.10/QCA/man/minimize.Rd | 100 QCA-3.10/QCA/src/CCubes |only QCA-3.10/QCA/src/Makevars | 12 QCA-3.10/QCA/src/QCA.c | 2229 ++----------- QCA-3.10/QCA/src/lpSolve |only QCA-3.10/QCA/src/registerDynamicSymbol.c | 1 QCA-3.9/QCA/src/lpsolve |only QCA-3.9/QCA/src/unateCovering_lpSolve.c |only QCA-3.9/QCA/src/unateCovering_lpSolve.h |only 50 files changed, 748 insertions(+), 2149 deletions(-)
Title: Define and Work with Parameter Spaces for Complex Algorithms
Description: Define parameter spaces, constraints and
dependencies for arbitrary algorithms, to program on such spaces. Also
includes statistical designs and random samplers. Objects are
implemented as 'R6' classes.
Author: Michel Lang [cre, aut] (<https://orcid.org/0000-0001-9754-0393>),
Bernd Bischl [aut] (<https://orcid.org/0000-0001-6002-6980>),
Jakob Richter [aut] (<https://orcid.org/0000-0003-4481-5554>),
Xudong Sun [aut] (<https://orcid.org/0000-0003-3269-2307>),
Martin Binder [aut],
Marc Becker [ctb] (<https://orcid.org/0000-0002-8115-0400>)
Maintainer: Michel Lang <michellang@gmail.com>
Diff between paradox versions 0.4.0 dated 2020-07-21 and 0.5.0 dated 2020-10-21
DESCRIPTION | 8 MD5 | 60 +++---- NAMESPACE | 1 NEWS.md | 6 R/Condition.R | 2 R/Design.R | 14 - R/NoDefault.R | 2 R/Param.R | 6 R/ParamDbl.R | 14 + R/ParamFct.R | 2 R/ParamSet.R | 111 ++++++++----- R/ParamSetCollection.R | 8 R/Sampler1D.R | 8 R/SamplerJointIndep.R | 6 R/generate_design_grid.R | 3 R/helper.R | 12 + R/zzz.R | 6 README.md | 256 ++++++++++++++----------------- man/Param.Rd | 2 man/ParamDbl.Rd | 5 man/ParamFct.Rd | 14 - man/ParamSet.Rd | 15 + man/Sampler1D.Rd | 3 tests/testthat/helper_01_params.R | 3 tests/testthat/test_ParamDbl.R | 6 tests/testthat/test_ParamSet.R | 8 tests/testthat/test_ParamSetCollection.R | 8 tests/testthat/test_ParamUty.R | 2 tests/testthat/test_deps.R | 6 tests/testthat/test_generate_design.R | 1 tests/testthat/test_param_vals.R | 7 31 files changed, 351 insertions(+), 254 deletions(-)
Title: Create and Evaluate NONMEM Models in a Project Context
Description: Systematically creates and modifies NONMEM(R) control streams. Harvests
NONMEM output, builds run logs, creates derivative data, generates diagnostics.
NONMEM (ICON Development Solutions <http://www.iconplc.com/>) is software for
nonlinear mixed effects modeling. See 'package?nonmemica'.
Author: Tim Bergsma
Maintainer: Tim Bergsma <bergsmat@gmail.com>
Diff between nonmemica versions 0.9.4 dated 2020-10-02 and 0.9.6 dated 2020-10-21
DESCRIPTION | 8 +- MD5 | 155 +++++++++++++++++++++--------------------- NAMESPACE | 5 + R/init.R | 1 R/safejoin.R |only inst/doc/parameter-table.html | 4 - man/absolute.Rd | 32 ++++---- man/as.bootstrap.numeric.Rd | 48 ++++++------- man/as.inits.numeric.Rd | 56 +++++++-------- man/as.items.Rd | 34 ++++----- man/as.items.character.Rd | 40 +++++----- man/as.list.model.Rd | 40 +++++----- man/as.matrices.Rd | 44 +++++------ man/as.matrices.records.Rd | 44 +++++------ man/as.omega.Rd | 42 +++++------ man/as.omega.model.Rd | 48 ++++++------- man/as.sigma.Rd | 32 ++++---- man/as.sigma.model.Rd | 40 +++++----- man/as.tab.Rd | 42 +++++------ man/as.tab.model.Rd | 48 ++++++------- man/as.theta.Rd | 42 +++++------ man/as.theta.model.Rd | 48 ++++++------- man/but.Rd | 42 +++++------ man/cash-.init.Rd | 48 ++++++------- man/cash-set-.init.Rd | 52 +++++++------- man/comwidth.inits.Rd | 46 ++++++------ man/comwidth.items.Rd | 46 ++++++------ man/comwidthOne.Rd | 42 +++++------ man/contains.Rd | 46 ++++++------ man/depends.Rd | 42 +++++------ man/depends.default.Rd | 46 ++++++------ man/errors.Rd | 44 +++++------ man/errors.numeric.Rd | 44 +++++------ man/estimates.Rd | 44 +++++------ man/estimates.numeric.Rd | 44 +++++------ man/fixed-set.Rd | 50 ++++++------- man/format.init.Rd | 52 +++++++------- man/format.inits.Rd | 52 +++++++------- man/format.items.Rd | 52 +++++++------- man/format.model.Rd | 58 +++++++-------- man/initDex.Rd | 42 +++++------ man/initSubscripts.Rd | 42 +++++------ man/initial-set-.model.Rd | 44 +++++------ man/initial-set.Rd | 46 ++++++------ man/initial.Rd | 46 ++++++------ man/is.defined.Rd | 40 +++++----- man/like.Rd | 42 +++++------ man/like.default.Rd | 48 ++++++------- man/lower-set-.model.Rd | 44 +++++------ man/lower-set.Rd | 46 ++++++------ man/lower.Rd | 46 ++++++------ man/maxWidths.Rd | 42 +++++------ man/maxWidths.list.Rd | 42 +++++------ man/nms_canonical.Rd | 32 ++++---- man/nms_canonical.numeric.Rd | 32 ++++---- man/nms_nonmem.Rd | 46 ++++++------ man/nms_psn.Rd | 32 ++++---- man/nms_psn.numeric.Rd | 32 ++++---- man/num_parameters.Rd | 32 ++++---- man/ord.items.Rd | 54 +++++++------- man/parameters.Rd | 44 +++++------ man/parameters.numeric.Rd | 44 +++++------ man/prettycom.Rd | 42 +++++------ man/print.init.Rd | 52 +++++++------- man/print.inits.Rd | 52 +++++++------- man/print.items.Rd | 52 +++++++------- man/print.model.Rd | 58 +++++++-------- man/problem.Rd | 48 ++++++------- man/resolve.Rd | 38 +++++----- man/runlog.Rd | 48 ++++++------- man/runlog.numeric.Rd | 44 +++++------ man/safe_join.Rd |only man/safe_join.data.frame.Rd |only man/sub-.inits.Rd | 44 +++++------ man/tweak.Rd | 48 ++++++------- man/updated.Rd | 44 +++++------ man/updated.numeric.Rd | 44 +++++------ man/upper-set-.model.Rd | 44 +++++------ man/upper-set.Rd | 46 ++++++------ man/upper.Rd | 46 ++++++------ 80 files changed, 1689 insertions(+), 1682 deletions(-)
Title: Historical and Ahistorical Population Projection Matrix Analysis
Description: Creates matrix population models for use in population ecological
analyses. Specializes on the construction of historical matrices,
which are 2d matrices comprising 3 time intervals of demographic
information. Estimates both raw and function-based forms of
historical and standard ahistorical matrices. Methodology based on
Ehrlen (2000) <doi:10.1890/0012-9658(2000)081[1675:TDOPPD]2.0.CO;2>.
Author: Richard P. Shefferson [aut, cre]
(<https://orcid.org/0000-0002-5234-3131>),
Johan Ehrlen [aut] (<https://orcid.org/0000-0001-8539-8967>)
Maintainer: Richard P. Shefferson <cdorm@g.ecc.u-tokyo.ac.jp>
Diff between lefko3 versions 2.4.2 dated 2020-09-17 and 3.0.0 dated 2020-10-21
lefko3-2.4.2/lefko3/R/lefko3.R |only lefko3-2.4.2/lefko3/src/PopDynamics.cpp |only lefko3-2.4.2/lefko3/vignettes/Ch2an2st1ln333-1.png |only lefko3-2.4.2/lefko3/vignettes/Ch2an2st1ln339-1.png |only lefko3-2.4.2/lefko3/vignettes/Ch3an1st1aln79pl-1.png |only lefko3-2.4.2/lefko3/vignettes/Ch3an2st5ln703-1.png |only lefko3-3.0.0/lefko3/DESCRIPTION | 11 lefko3-3.0.0/lefko3/MD5 | 137 lefko3-3.0.0/lefko3/NAMESPACE | 8 lefko3-3.0.0/lefko3/R/RcppExports.R | 391 + lefko3-3.0.0/lefko3/R/datamanag.R | 585 +- lefko3-3.0.0/lefko3/R/lefko3-package.R | 1 lefko3-3.0.0/lefko3/R/matrixcreation.R | 1083 ++- lefko3-3.0.0/lefko3/R/modelselection.R | 779 +- lefko3-3.0.0/lefko3/R/popchar.R | 200 lefko3-3.0.0/lefko3/R/popdyn.R | 1035 ++- lefko3-3.0.0/lefko3/build/vignette.rds |binary lefko3-3.0.0/lefko3/inst/doc/Chapter1.Rmd | 323 - lefko3-3.0.0/lefko3/inst/doc/Chapter1.html | 386 + lefko3-3.0.0/lefko3/inst/doc/Chapter2.Rmd | 3375 +++++------- lefko3-3.0.0/lefko3/inst/doc/Chapter2.html | 5336 ++++++++----------- lefko3-3.0.0/lefko3/inst/doc/Chapter3.Rmd | 2382 +++----- lefko3-3.0.0/lefko3/inst/doc/Chapter3.html | 3568 +++++------- lefko3-3.0.0/lefko3/man/aflefko2.Rd |only lefko3-3.0.0/lefko3/man/elasticity3.Rd |only lefko3-3.0.0/lefko3/man/elasticity3.lefkoMat.Rd |only lefko3-3.0.0/lefko3/man/elasticity3.matrix.Rd |only lefko3-3.0.0/lefko3/man/flefko2.Rd | 156 lefko3-3.0.0/lefko3/man/flefko3.Rd | 113 lefko3-3.0.0/lefko3/man/historicalize3.Rd | 375 - lefko3-3.0.0/lefko3/man/lambda3.Rd | 18 lefko3-3.0.0/lefko3/man/lambda3.lefkoMat.Rd | 23 lefko3-3.0.0/lefko3/man/lambda3.matrix.Rd | 19 lefko3-3.0.0/lefko3/man/lefko3.Rd | 26 lefko3-3.0.0/lefko3/man/lmean.Rd | 58 lefko3-3.0.0/lefko3/man/modelsearch.Rd | 283 - lefko3-3.0.0/lefko3/man/overwrite.Rd | 43 lefko3-3.0.0/lefko3/man/repvalue3.Rd | 19 lefko3-3.0.0/lefko3/man/repvalue3.lefkoMat.Rd | 46 lefko3-3.0.0/lefko3/man/repvalue3.matrix.Rd | 27 lefko3-3.0.0/lefko3/man/rlefko2.Rd | 95 lefko3-3.0.0/lefko3/man/rlefko3.Rd | 112 lefko3-3.0.0/lefko3/man/sensitivity3.Rd |only lefko3-3.0.0/lefko3/man/sensitivity3.lefkoMat.Rd |only lefko3-3.0.0/lefko3/man/sensitivity3.matrix.Rd |only lefko3-3.0.0/lefko3/man/sf_create.Rd | 65 lefko3-3.0.0/lefko3/man/stablestage3.Rd | 18 lefko3-3.0.0/lefko3/man/stablestage3.lefkoMat.Rd | 59 lefko3-3.0.0/lefko3/man/stablestage3.matrix.Rd | 15 lefko3-3.0.0/lefko3/man/summary.lefkoMat.Rd | 1 lefko3-3.0.0/lefko3/man/summary.lefkoMod.Rd | 27 lefko3-3.0.0/lefko3/man/verticalize3.Rd | 250 lefko3-3.0.0/lefko3/src/DataManagement.cpp | 509 + lefko3-3.0.0/lefko3/src/Makevars |only lefko3-3.0.0/lefko3/src/Makevars.win |only lefko3-3.0.0/lefko3/src/MatrixEstimators.cpp | 169 lefko3-3.0.0/lefko3/src/RcppExports.cpp | 254 lefko3-3.0.0/lefko3/src/popdynamics.cpp |only lefko3-3.0.0/lefko3/vignettes/Ch2an1.28-1.png |only lefko3-3.0.0/lefko3/vignettes/Ch2an1.30-1.png |only lefko3-3.0.0/lefko3/vignettes/Ch2an1.31-1.png |only lefko3-3.0.0/lefko3/vignettes/Ch2an1.40-1.png |only lefko3-3.0.0/lefko3/vignettes/Ch2an2.1-1.png |only lefko3-3.0.0/lefko3/vignettes/Ch2an2.2-1.png |only lefko3-3.0.0/lefko3/vignettes/Ch2an2.20-1.png |only lefko3-3.0.0/lefko3/vignettes/Ch2an2.21-1.png |only lefko3-3.0.0/lefko3/vignettes/Ch2an2.22-1.png |only lefko3-3.0.0/lefko3/vignettes/Ch2an2.23-1.png |only lefko3-3.0.0/lefko3/vignettes/Ch2an2.27-1.png |only lefko3-3.0.0/lefko3/vignettes/Ch2an3.17-1.png |only lefko3-3.0.0/lefko3/vignettes/Ch2an3.18-1.png |only lefko3-3.0.0/lefko3/vignettes/Ch2an3.19-1.png |only lefko3-3.0.0/lefko3/vignettes/Ch2an3.21-1.png |only lefko3-3.0.0/lefko3/vignettes/Ch3an1.2-1.png |only lefko3-3.0.0/lefko3/vignettes/Ch3an1.24-1.png |only lefko3-3.0.0/lefko3/vignettes/Ch3an1.26-1.png |only lefko3-3.0.0/lefko3/vignettes/Ch3an1.27-1.png |only lefko3-3.0.0/lefko3/vignettes/Ch3an1.30-1.png |only lefko3-3.0.0/lefko3/vignettes/Ch3an2.17-1.png |only lefko3-3.0.0/lefko3/vignettes/Ch3an2.18-1.png |only lefko3-3.0.0/lefko3/vignettes/Ch3an2.19-1.png |only lefko3-3.0.0/lefko3/vignettes/Ch3an2.23-1.png |only lefko3-3.0.0/lefko3/vignettes/Chapter1.Rmd | 323 - lefko3-3.0.0/lefko3/vignettes/Chapter2.Rmd | 3375 +++++------- lefko3-3.0.0/lefko3/vignettes/Chapter2.Rmd.orig | 885 ++- lefko3-3.0.0/lefko3/vignettes/Chapter3.Rmd | 2382 +++----- lefko3-3.0.0/lefko3/vignettes/Chapter3.Rmd.orig | 582 +- lefko3-3.0.0/lefko3/vignettes/Lefko3Tutorial.bib | 194 lefko3-3.0.0/lefko3/vignettes/cypscreen2.png |only lefko3-3.0.0/lefko3/vignettes/matrix2.png |binary 90 files changed, 15019 insertions(+), 15102 deletions(-)
Title: Fit and Simulate Generalised Hypergeometric Ensembles of Graphs
Description: Provides functions for model fitting and selection of generalised hypergeometric ensembles of random graphs (gHypEG).
To learn how to use it, check the vignettes for a quick tutorial.
Please reference its use as Casiraghi, G., Nanumyan, V. (2019) <doi:10.5281/zenodo.2555300>
together with those relevant references from the one listed below.
The package is based on the research developed at the Chair of Systems Design, ETH Zurich.
Casiraghi, G., Nanumyan, V., Scholtes, I., Schweitzer, F. (2016) <arXiv:1607.02441>.
Casiraghi, G., Nanumyan, V., Scholtes, I., Schweitzer, F. (2017) <doi:10.1007/978-3-319-67256-4_11>.
Casiraghi, G., (2017) <arxiv:1702.02048>
Casiraghi, G., Nanumyan, V. (2018) <arXiv:1810.06495>.
Brandenberger, L., Casiraghi, G., Nanumyan, V., Schweitzer, F. (2019) <doi:10.1145/3341161.3342926>
Casiraghi, G. (2019) <doi:10.1007/s41109-019-0241-1>.
Author: Giona Casiraghi [aut, cre] (<https://orcid.org/0000-0003-0233-5747>),
Vahan Nanumyan [aut] (<https://orcid.org/0000-0001-9054-3217>),
Laurence Brandenberger [aut],
Giacomo Vaccario [ctb]
Maintainer: Giona Casiraghi <giona@ethz.ch>
Diff between ghypernet versions 1.0.0 dated 2020-05-20 and 1.0.1 dated 2020-10-21
ghypernet-1.0.0/ghypernet/man/createPredictors.Rd |only ghypernet-1.0.0/ghypernet/man/createPredictors.list.Rd |only ghypernet-1.0.0/ghypernet/man/nrmChoose.Rd |only ghypernet-1.0.1/ghypernet/DESCRIPTION | 18 ghypernet-1.0.1/ghypernet/MD5 | 53 ghypernet-1.0.1/ghypernet/NAMESPACE | 10 ghypernet-1.0.1/ghypernet/NEWS.md |only ghypernet-1.0.1/ghypernet/R/auxilliary.R | 20 ghypernet-1.0.1/ghypernet/R/blockmodel.R | 28 ghypernet-1.0.1/ghypernet/R/createPredictors.R | 14 ghypernet-1.0.1/ghypernet/R/deprecated.R |only ghypernet-1.0.1/ghypernet/R/igraphintegration.R | 8 ghypernet-1.0.1/ghypernet/R/logl.R | 11 ghypernet-1.0.1/ghypernet/R/nr.ci.R | 2 ghypernet-1.0.1/ghypernet/R/nrm.R | 2 ghypernet-1.0.1/ghypernet/R/nrmSelection.R | 52 ghypernet-1.0.1/ghypernet/R/print.R | 34 ghypernet-1.0.1/ghypernet/R/tests.R | 2 ghypernet-1.0.1/ghypernet/README.md | 47 ghypernet-1.0.1/ghypernet/build/vignette.rds |binary ghypernet-1.0.1/ghypernet/inst/doc/Significantlinks.html | 112 ghypernet-1.0.1/ghypernet/inst/doc/Tutorial_NRM.R | 25 ghypernet-1.0.1/ghypernet/inst/doc/Tutorial_NRM.Rmd | 29 ghypernet-1.0.1/ghypernet/inst/doc/Tutorial_NRM.html | 2778 +++++++-------- ghypernet-1.0.1/ghypernet/inst/doc/tutorial.html | 368 - ghypernet-1.0.1/ghypernet/man/bccm.Rd | 7 ghypernet-1.0.1/ghypernet/man/create_predictors.Rd |only ghypernet-1.0.1/ghypernet/man/create_predictors.list.Rd |only ghypernet-1.0.1/ghypernet/man/extract.nrm.cluster.Rd |only ghypernet-1.0.1/ghypernet/man/nrm_choose.Rd |only ghypernet-1.0.1/ghypernet/man/nrm_selection.Rd | 20 ghypernet-1.0.1/ghypernet/vignettes/Tutorial_NRM.Rmd | 29 32 files changed, 1836 insertions(+), 1833 deletions(-)
Title: Tools for Behavior Change Researchers and Professionals
Description: Contains specialised analyses and
visualisation tools for behavior change science.
These facilitate conducting determinant studies
(for example, using confidence interval-based
estimation of relevance, CIBER, or CIBERlite
plots, see Crutzen, Noijen & Peters (2017)
<doi:10.3389/fpubh.2017.00165>),
systematically developing, reporting,
and analysing interventions (for example, using
Acyclic Behavior Change Diagrams), and reporting
about intervention effectiveness (for example, using
the Numbers Needed for Change, see Gruijters & Peters
(2017) <doi:10.31234/osf.io/2bau7>), and computing the
required sample size (using the Meaningful Change
Definition, see Gruijters & Peters (2019)
<doi:10.31234/osf.io/jc295>).
This package is especially useful for
researchers in the field of behavior change or
health psychology and to behavior change
professionals such as intervention developers and
prevention workers.
Author: Gjalt-Jorn Peters [aut, cre] (<https://orcid.org/0000-0002-0336-9589>),
Rik Crutzen [ctb] (<https://orcid.org/0000-0002-3731-6610>),
Stefan Gruijters [ctb] (<https://orcid.org/0000-0003-0141-0071>)
Maintainer: Gjalt-Jorn Peters <gjalt-jorn@a-bc.eu>
Diff between behaviorchange versions 0.2.2 dated 2020-03-01 and 0.2.4 dated 2020-10-21
behaviorchange-0.2.2/behaviorchange/data/datalist |only behaviorchange-0.2.4/behaviorchange/DESCRIPTION | 28 + behaviorchange-0.2.4/behaviorchange/MD5 | 59 ++- behaviorchange-0.2.4/behaviorchange/NAMESPACE | 4 behaviorchange-0.2.4/behaviorchange/R/CIBER.R | 139 ++++++--- behaviorchange-0.2.4/behaviorchange/R/complecs.R | 148 ++++++---- behaviorchange-0.2.4/behaviorchange/R/compute.es_des.R |only behaviorchange-0.2.4/behaviorchange/R/dMCD.R | 56 +++ behaviorchange-0.2.4/behaviorchange/R/pies.R |only behaviorchange-0.2.4/behaviorchange/README.md | 14 behaviorchange-0.2.4/behaviorchange/build/partial.rdb |binary behaviorchange-0.2.4/behaviorchange/build/vignette.rds |binary behaviorchange-0.2.4/behaviorchange/inst/doc/abcd-laagdrempelige_nederlandse_uitleg.Rmd | 12 behaviorchange-0.2.4/behaviorchange/inst/doc/abcd-laagdrempelige_nederlandse_uitleg.html | 35 +- behaviorchange-0.2.4/behaviorchange/inst/doc/abcd.R | 2 behaviorchange-0.2.4/behaviorchange/inst/doc/abcd.Rmd | 22 - behaviorchange-0.2.4/behaviorchange/inst/doc/abcd.html | 85 +++-- behaviorchange-0.2.4/behaviorchange/inst/doc/complecs.R | 17 - behaviorchange-0.2.4/behaviorchange/inst/doc/complecs.Rmd | 19 + behaviorchange-0.2.4/behaviorchange/inst/doc/complecs.html | 56 ++- behaviorchange-0.2.4/behaviorchange/inst/doc/matrix-van-aspecten-van-de-psychologie.html | 17 + behaviorchange-0.2.4/behaviorchange/inst/extdata |only behaviorchange-0.2.4/behaviorchange/man/CIBER.Rd | 3 behaviorchange-0.2.4/behaviorchange/man/abcd_specs_examples.Rd | 6 behaviorchange-0.2.4/behaviorchange/man/behaviorchange-package.Rd | 129 ++++---- behaviorchange-0.2.4/behaviorchange/man/complecs.Rd | 17 + behaviorchange-0.2.4/behaviorchange/man/dMCD.Rd | 21 + behaviorchange-0.2.4/behaviorchange/man/opts.Rd | 4 behaviorchange-0.2.4/behaviorchange/man/partypanelData.Rd | 6 behaviorchange-0.2.4/behaviorchange/man/pies.Rd |only behaviorchange-0.2.4/behaviorchange/vignettes/abcd-laagdrempelige_nederlandse_uitleg.Rmd | 12 behaviorchange-0.2.4/behaviorchange/vignettes/abcd.Rmd | 22 - behaviorchange-0.2.4/behaviorchange/vignettes/complecs.Rmd | 19 + 33 files changed, 618 insertions(+), 334 deletions(-)
More information about behaviorchange at CRAN
Permanent link
Title: Tools for Computation on Batch Systems
Description: As a successor of the packages 'BatchJobs' and 'BatchExperiments',
this package provides a parallel implementation of the Map function for high
performance computing systems managed by schedulers 'IBM Spectrum LSF'
(<https://www.ibm.com/products/hpc-workload-management>),
'OpenLava' (<https://www.openlava.org/>), 'Univa Grid Engine'/'Oracle Grid
Engine' (<https://www.univa.com/>), 'Slurm' (<https://slurm.schedmd.com/>),
'TORQUE/PBS'
(<https://adaptivecomputing.com/cherry-services/torque-resource-manager/>),
or 'Docker Swarm' (<https://docs.docker.com/engine/swarm/>).
A multicore and socket mode allow the parallelization on a local machines,
and multiple machines can be hooked up via SSH to create a makeshift
cluster. Moreover, the package provides an abstraction mechanism to define
large-scale computer experiments in a well-organized and reproducible way.
Author: Michel Lang [cre, aut] (<https://orcid.org/0000-0001-9754-0393>),
Bernd Bischl [aut],
Dirk Surmann [ctb] (<https://orcid.org/0000-0003-0873-137X>)
Maintainer: Michel Lang <michellang@gmail.com>
Diff between batchtools versions 0.9.13 dated 2020-03-19 and 0.9.14 dated 2020-10-21
batchtools-0.9.13/batchtools/inst/doc/batchtools.pdf |only batchtools-0.9.14/batchtools/DESCRIPTION | 20 +-- batchtools-0.9.14/batchtools/MD5 | 54 +++++----- batchtools-0.9.14/batchtools/NAMESPACE | 2 batchtools-0.9.14/batchtools/NEWS.md | 8 + batchtools-0.9.14/batchtools/R/Job.R | 2 batchtools-0.9.14/batchtools/R/Joins.R | 2 batchtools-0.9.14/batchtools/R/Registry.R | 2 batchtools-0.9.14/batchtools/R/batchMap.R | 2 batchtools-0.9.14/batchtools/R/btlapply.R | 2 batchtools-0.9.14/batchtools/R/clusterFunctionsDocker.R | 2 batchtools-0.9.14/batchtools/R/clusterFunctionsLSF.R | 2 batchtools-0.9.14/batchtools/R/clusterFunctionsSGE.R | 2 batchtools-0.9.14/batchtools/R/clusterFunctionsSlurm.R | 2 batchtools-0.9.14/batchtools/README.md | 9 - batchtools-0.9.14/batchtools/build/vignette.rds |binary batchtools-0.9.14/batchtools/inst/CITATION | 4 batchtools-0.9.14/batchtools/inst/doc/batchtools.Rmd | 6 - batchtools-0.9.14/batchtools/inst/doc/batchtools.html |only batchtools-0.9.14/batchtools/inst/templates/lsf-simple.tmpl | 10 - batchtools-0.9.14/batchtools/man/JoinTables.Rd | 2 batchtools-0.9.14/batchtools/man/Worker.Rd | 4 batchtools-0.9.14/batchtools/man/btlapply.Rd | 2 batchtools-0.9.14/batchtools/man/makeClusterFunctionsDocker.Rd | 2 batchtools-0.9.14/batchtools/man/makeClusterFunctionsLSF.Rd | 2 batchtools-0.9.14/batchtools/man/makeClusterFunctionsSGE.Rd | 2 batchtools-0.9.14/batchtools/man/makeClusterFunctionsSlurm.Rd | 2 batchtools-0.9.14/batchtools/tests/testthat/test_batchMap.R | 9 + batchtools-0.9.14/batchtools/vignettes/batchtools.Rmd | 6 - 29 files changed, 91 insertions(+), 71 deletions(-)
Title: Geometric Morphometric Methods and Virtual Anthropology Tools
Description: Tools for geometric morphometric analysis. The package includes tools of virtual anthropology to align two not articulated parts belonging to the same specimen, to build virtual cavities as endocast (Profico et al, 2018 <doi:10.1002/ajpa.23493>).
Author: Antonio Profico, Costantino Buzi, Silvia Castiglione, Marina Melchionna, Paolo Piras, Pasquale Raia, Alessio Veneziano
Maintainer: Antonio Profico <antonio.profico@york.ac.uk>
Diff between Arothron versions 1.1.1 dated 2019-12-05 and 2.0.1 dated 2020-10-21
DESCRIPTION | 18 ++-- MD5 | 126 ++++++++++++++++-------------- NAMESPACE | 124 +++++++++++++++-------------- R/Arothron.R | 9 +- R/CScorreffect.R |only R/MLECScorrection.R |only R/PCscoresCorr.R |only R/dta.R | 2 R/endomaker.R | 2 R/endomaker_dir.R | 2 R/ext.int.mesh.R | 3 R/femsets.R |only R/localmeshdiff.R |only R/primendoR.R |only R/spherical.flipping.R | 4 R/twodvarshape.R | 38 +++++---- R/twodviews.R | 44 +++++++--- data/datalist | 2 data/femsets.rda |only data/primendoR.rda |only man/Arothron-package.Rd | 26 +++--- man/CScorreffect.Rd |only man/DM_base_sur.Rd | 32 +++---- man/DM_face_sur.Rd | 32 +++---- man/DM_set.Rd | 32 +++---- man/Lset2D_list.Rd | 32 +++---- man/Lset3D_array.Rd | 32 +++---- man/MAs_sets.Rd | 32 +++---- man/MLECScorrection.Rd |only man/PCscoresCorr.Rd |only man/RMs_sets.Rd | 32 +++---- man/SCP1.mesh.Rd | 32 +++---- man/SM_set.Rd | 32 +++---- man/aro.clo.points.Rd | 64 +++++++-------- man/arraytolist.Rd | 40 ++++----- man/bary.mesh.Rd | 52 ++++++------ man/compare_check.set.Rd | 113 +++++++++++++-------------- man/dec.curve.Rd | 68 ++++++++-------- man/dta.Rd | 192 ++++++++++++++++++++++++---------------------- man/endo_set.Rd | 32 +++---- man/endomaker.Rd | 181 ++++++++++++++++++++++++------------------- man/endomaker_dir.Rd | 156 +++++++++++++++++++++---------------- man/export_amira.Rd | 54 ++++++------ man/export_amira.path.Rd | 66 ++++++++------- man/ext.int.mesh.Rd | 109 ++++++++++++++------------ man/ext.mesh.rai.Rd | 38 ++++----- man/femsets.Rd |only man/grid_pov.Rd | 44 +++++----- man/human_skull.Rd | 32 +++---- man/krd1_tooth.Rd | 32 +++---- man/landmark_frm2amira.Rd | 38 ++++----- man/listtoarray.Rd | 44 +++++----- man/localmeshdiff.Rd |only man/malleus_bone.Rd | 32 +++---- man/noise.mesh.Rd | 74 ++++++++--------- man/out.inn.mesh.Rd | 120 ++++++++++++++-------------- man/patches_frm2amira.Rd | 38 ++++----- man/pov_selecter.Rd | 52 ++++++------ man/primendoR.Rd |only man/read.amira.dir.Rd | 44 +++++----- man/read.amira.set.Rd | 44 +++++----- man/read.path.amira.Rd | 40 ++++----- man/repmat.Rd | 48 +++++------ man/sinus_set.Rd | 32 +++---- man/spherical.flipping.Rd | 52 ++++++------ man/trasf.mesh.Rd | 44 +++++----- man/twodvarshape.Rd | 85 ++++++++++---------- man/twodviews.Rd | 118 +++++++++++++++------------- man/volendo.Rd | 66 +++++++-------- man/yoda_set.Rd | 32 +++---- man/yoda_sur.Rd | 32 +++---- 71 files changed, 1572 insertions(+), 1424 deletions(-)
Title: Estimation of Dynamic Heritability and Comparison of Twin Models
Description: Estimate the dynamic behaviour of the variance components in the classical twin models with respect to age using B-splines and P-splines.
Author: Liang He [aut, cre]
Maintainer: Liang He <liang.he@duke.edu>
Diff between ACEt versions 1.8.0 dated 2017-05-07 and 1.8.1 dated 2020-10-21
DESCRIPTION | 21 +++++++++++---------- MD5 | 22 +++++++++++----------- data/data_ace.rda |binary man/ACEt-package.Rd | 4 +++- man/AtCtEt.Rd | 5 +++-- man/AtCtEtp.Rd | 5 +++-- man/acetp_mcmc.Rd | 3 +-- man/plot_acet.Rd | 3 +-- man/test_acetp.Rd | 5 +++-- src/AtCtEt.cpp | 15 ++++++++++++--- src/AtCtEtp.cpp | 20 ++++++++++++++++---- src/AtEtp.cpp | 20 ++++++++++++++++---- 12 files changed, 80 insertions(+), 43 deletions(-)
Title: RDF Library Bindings in R
Description: Provides methods to parse, query and serialize information
stored in the Resource Description Framework (RDF). RDF is described at <https://www.w3.org/TR/rdf-primer/>.
This package supports RDF by implementing an R interface to the Redland RDF C library,
described at <http://librdf.org/docs/api/index.html>. In brief, RDF provides a structured graph
consisting of Statements composed of Subject, Predicate, and Object Nodes.
Author: Matthew B. Jones [aut, cre],
Peter Slaughter [aut],
Jeroen Ooms [aut],
Carl Boettiger [aut],
Scott Chamberlain [aut],
David Beckett [cph],
University of Bristol [cph],
Regents of the University of California [cph]
Maintainer: Matthew B. Jones <jones@nceas.ucsb.edu>
Diff between redland versions 1.0.17-13 dated 2020-10-09 and 1.0.17-14 dated 2020-10-21
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS | 8 +++++++- configure | 11 +++++++---- inst/doc/redland_overview.html | 4 ++-- 5 files changed, 24 insertions(+), 15 deletions(-)
Title: Satellite Derived Water Quality Detection Algorithms
Description: The main purpose of waterquality is to quickly and easily convert
satellite-based reflectance imagery into one or many well-known water quality
algorithms designed for the detection of harmful algal blooms or the following
pigment proxies: chlorophyll-a, blue-green algae (phycocyanin), and turbidity.
Johansen et al. (2019) <doi:10.21079/11681/35053>.
Author: Richard Johansen [aut, cre] (<https://orcid.org/0000-0003-4287-9677>),
Jakub Nowosad [aut] (<https://orcid.org/0000-0002-1057-3721>),
Molly Reif [aut] (<https://orcid.org/0000-0003-4207-1459>),
Erich Emery [aut],
U.S. Army Corps of Engineers [fnd]
Maintainer: Richard Johansen <richard.a.johansen@erdc.dren.mil>
Diff between waterquality versions 0.2.5 dated 2020-10-02 and 0.2.6 dated 2020-10-21
DESCRIPTION | 9 +++++---- MD5 | 12 ++++++------ R/map_wq.R | 31 ++++++++++++++++--------------- inst/doc/waterquality_vignette.R | 16 ++++++++-------- inst/doc/waterquality_vignette.Rmd | 2 +- inst/doc/waterquality_vignette.html | 31 +++++++++++++++---------------- vignettes/waterquality_vignette.Rmd | 2 +- 7 files changed, 52 insertions(+), 51 deletions(-)
Title: Group Dates
Description: Tooling to group dates by a variety of periods
including: yearly, monthly, by second, by week of the month, and more.
The groups are defined in such a way that they also represent the
distance between dates in terms of the period. This extracts valuable
information that can be used in further calculations that rely on a
specific temporal spacing between observations.
Author: Davis Vaughan [aut, cre],
RStudio [cph]
Maintainer: Davis Vaughan <davis@rstudio.com>
Diff between warp versions 0.1.0 dated 2020-01-14 and 0.2.0 dated 2020-10-21
warp-0.1.0/warp/tests/testthat/test-changes.R |only warp-0.2.0/warp/DESCRIPTION | 8 warp-0.2.0/warp/MD5 | 42 +- warp-0.2.0/warp/NEWS.md |only warp-0.2.0/warp/R/boundary.R | 7 warp-0.2.0/warp/R/change.R | 57 ++- warp-0.2.0/warp/R/distance.R | 11 warp-0.2.0/warp/R/dots.R |only warp-0.2.0/warp/README.md | 2 warp-0.2.0/warp/build/vignette.rds |binary warp-0.2.0/warp/inst/doc/hour.html | 382 +++++++++++++---------- warp-0.2.0/warp/man/warp_boundary.Rd | 6 warp-0.2.0/warp/man/warp_change.Rd | 59 +++ warp-0.2.0/warp/man/warp_distance.Rd | 6 warp-0.2.0/warp/src/boundary.c | 6 warp-0.2.0/warp/src/change.c | 72 +++- warp-0.2.0/warp/src/distance.c | 2 warp-0.2.0/warp/src/init.c | 4 warp-0.2.0/warp/src/utils.c | 36 ++ warp-0.2.0/warp/src/utils.h | 2 warp-0.2.0/warp/src/warp.h | 9 warp-0.2.0/warp/tests/testthat/test-boundaries.R | 7 warp-0.2.0/warp/tests/testthat/test-change.R |only warp-0.2.0/warp/tests/testthat/test-distance.R | 6 24 files changed, 492 insertions(+), 232 deletions(-)
Title: Interface to 'Python'
Description: Interface to 'Python' modules, classes, and functions. When calling
into 'Python', R data types are automatically converted to their equivalent 'Python'
types. When values are returned from 'Python' to R they are converted back to R
types. Compatible with all versions of 'Python' >= 2.7.
Author: Kevin Ushey [aut, cre],
JJ Allaire [aut],
RStudio [cph, fnd],
Yuan Tang [aut, cph] (<https://orcid.org/0000-0001-5243-233X>),
Dirk Eddelbuettel [ctb, cph],
Bryan Lewis [ctb, cph],
Sigrid Keydana [ctb],
Ryan Hafen [ctb, cph],
Marcus Geelnard [ctb, cph] (TinyThread library,
http://tinythreadpp.bitsnbites.eu/)
Maintainer: Kevin Ushey <kevin@rstudio.com>
Diff between reticulate versions 1.16 dated 2020-05-27 and 1.17 dated 2020-10-21
reticulate-1.16/reticulate/tests/testthat/test-aaa.R |only reticulate-1.17/reticulate/DESCRIPTION | 8 reticulate-1.17/reticulate/MD5 | 123 - reticulate-1.17/reticulate/NAMESPACE | 3 reticulate-1.17/reticulate/NEWS.md | 90 + reticulate-1.17/reticulate/R/RcppExports.R | 8 reticulate-1.17/reticulate/R/conda.R | 84 - reticulate-1.17/reticulate/R/config.R | 170 +- reticulate-1.17/reticulate/R/conversion.R | 53 reticulate-1.17/reticulate/R/help.R | 25 reticulate-1.17/reticulate/R/import.R |only reticulate-1.17/reticulate/R/install.R | 20 reticulate-1.17/reticulate/R/knitr-engine.R | 11 reticulate-1.17/reticulate/R/miniconda.R | 54 reticulate-1.17/reticulate/R/package.R | 54 reticulate-1.17/reticulate/R/pip.R | 23 reticulate-1.17/reticulate/R/python-packages.R | 4 reticulate-1.17/reticulate/R/python-tools.R | 78 - reticulate-1.17/reticulate/R/python.R | 209 -- reticulate-1.17/reticulate/R/repl.R | 31 reticulate-1.17/reticulate/R/source.R | 2 reticulate-1.17/reticulate/R/utils-format.R | 26 reticulate-1.17/reticulate/R/utils.R | 58 reticulate-1.17/reticulate/R/virtualenv.R | 64 reticulate-1.17/reticulate/build/vignette.rds |binary reticulate-1.17/reticulate/inst/config/config.py | 58 reticulate-1.17/reticulate/inst/doc/arrays.Rmd | 10 reticulate-1.17/reticulate/inst/doc/arrays.html | 740 +++++----- reticulate-1.17/reticulate/inst/doc/calling_python.Rmd | 2 reticulate-1.17/reticulate/inst/doc/calling_python.html | 248 ++- reticulate-1.17/reticulate/inst/doc/package.html | 174 +- reticulate-1.17/reticulate/inst/doc/python_dependencies.html | 64 reticulate-1.17/reticulate/inst/doc/python_packages.html | 130 + reticulate-1.17/reticulate/inst/doc/r_markdown.Rmd | 4 reticulate-1.17/reticulate/inst/doc/r_markdown.html | 52 reticulate-1.17/reticulate/inst/doc/versions.html | 70 reticulate-1.17/reticulate/inst/python/rpytools/__pycache__/__init__.cpython-38.pyc |only reticulate-1.17/reticulate/inst/python/rpytools/__pycache__/call.cpython-38.pyc |only reticulate-1.17/reticulate/inst/python/rpytools/__pycache__/generator.cpython-38.pyc |only reticulate-1.17/reticulate/inst/python/rpytools/__pycache__/help.cpython-38.pyc |only reticulate-1.17/reticulate/inst/python/rpytools/__pycache__/loader.cpython-37.pyc |only reticulate-1.17/reticulate/inst/python/rpytools/__pycache__/loader.cpython-38.pyc |only reticulate-1.17/reticulate/inst/python/rpytools/__pycache__/output.cpython-38.pyc |only reticulate-1.17/reticulate/inst/python/rpytools/__pycache__/test.cpython-38.pyc |only reticulate-1.17/reticulate/inst/python/rpytools/__pycache__/thread.cpython-38.pyc |only reticulate-1.17/reticulate/inst/python/rpytools/loader.py |only reticulate-1.17/reticulate/inst/python/rpytools/output.py | 39 reticulate-1.17/reticulate/man/conda-tools.Rd | 3 reticulate-1.17/reticulate/man/import.Rd | 88 - reticulate-1.17/reticulate/man/py_del_attr.Rd |only reticulate-1.17/reticulate/man/py_help_handler.Rd |only reticulate-1.17/reticulate/man/py_module_available.Rd | 5 reticulate-1.17/reticulate/man/py_none.Rd |only reticulate-1.17/reticulate/man/py_run.Rd | 6 reticulate-1.17/reticulate/man/r-py-conversion.Rd | 6 reticulate-1.17/reticulate/man/source_python.Rd | 6 reticulate-1.17/reticulate/man/virtualenv-tools.Rd | 18 reticulate-1.17/reticulate/src/RcppExports.cpp | 23 reticulate-1.17/reticulate/src/event_loop.cpp | 12 reticulate-1.17/reticulate/src/output.cpp | 4 reticulate-1.17/reticulate/src/python.cpp | 34 reticulate-1.17/reticulate/tests/testthat/helper-init.R | 31 reticulate-1.17/reticulate/tests/testthat/resources/eng-reticulate-example.html | 6 reticulate-1.17/reticulate/tests/testthat/resources/eng-reticulate-example_files |only reticulate-1.17/reticulate/tests/testthat/test-delay-load.R | 2 reticulate-1.17/reticulate/tests/testthat/test-python-datetime.R | 18 reticulate-1.17/reticulate/tests/testthat/test-python-knitr-engine.R | 2 reticulate-1.17/reticulate/vignettes/arrays.Rmd | 10 reticulate-1.17/reticulate/vignettes/calling_python.Rmd | 2 reticulate-1.17/reticulate/vignettes/r_markdown.Rmd | 4 70 files changed, 2007 insertions(+), 1062 deletions(-)
Title: Calculate Pairwise Multiple Comparisons of Mean Rank Sums
Extended
Description: For one-way layout experiments the one-way ANOVA can
be performed as an omnibus test. All-pairs multiple comparisons
tests (Tukey-Kramer test, Scheffe test, LSD-test)
and many-to-one tests (Dunnett test) for normally distributed
residuals and equal within variance are available. Furthermore,
all-pairs tests (Games-Howell test, Tamhane's T2 test,
Dunnett T3 test, Ury-Wiggins-Hochberg test) and many-to-one
(Tamhane-Dunnett Test) for normally distributed residuals
and heterogeneous variances are provided. Van der Waerden's normal
scores test for omnibus, all-pairs and many-to-one tests is
provided for non-normally distributed residuals and homogeneous
variances. The Kruskal-Wallis, BWS and Anderson-Darling
omnibus test and all-pairs tests
(Nemenyi test, Dunn test, Conover test, Dwass-Steele-Critchlow-
Fligner test) as well as many-to-one (Nemenyi test, Dunn test,
U-test) are given for the analysis of variance by ranks.
Non-parametric trend tests (Jonckheere test, Cuzick test,
Johnson-Mehrotra test, Spearman test) are included.
In addition, a Friedman-test for one-way ANOVA with repeated
measures on ranks (CRBD) and Skillings-Mack test for unbalanced
CRBD is provided with consequent all-pairs tests (Nemenyi test,
Siegel test, Miller test, Conover test, Exact test)
and many-to-one tests (Nemenyi test, Demsar test, Exact test).
A trend can be tested with Pages's test. Durbin's test
for a two-way balanced incomplete block design (BIBD) is given
in this package as well as Gore's test for CRBD with multiple
observations per cell is given. Outlier tests, Mandel's k- and
h statistic as well as functions for Type I error and Power
analysis as well as generic summary, print and plot methods
are provided.
Author: Thorsten Pohlert [aut, cre] (<https://orcid.org/0000-0003-3855-3025>)
Maintainer: Thorsten Pohlert <thorsten.pohlert@gmx.de>
Diff between PMCMRplus versions 1.6.0 dated 2020-10-14 and 1.6.1 dated 2020-10-21
PMCMRplus-1.6.0/PMCMRplus/R/print.steelTest.R |only PMCMRplus-1.6.0/PMCMRplus/R/print.williamsTest.R |only PMCMRplus-1.6.0/PMCMRplus/man/print.steel.Rd |only PMCMRplus-1.6.0/PMCMRplus/man/print.williams.Rd |only PMCMRplus-1.6.0/PMCMRplus/man/summary.steel.Rd |only PMCMRplus-1.6.0/PMCMRplus/man/summary.williams.Rd |only PMCMRplus-1.6.1/PMCMRplus/DESCRIPTION | 10 PMCMRplus-1.6.1/PMCMRplus/MD5 | 48 ++-- PMCMRplus-1.6.1/PMCMRplus/NAMESPACE | 6 PMCMRplus-1.6.1/PMCMRplus/R/MTest.R | 76 ++++-- PMCMRplus-1.6.1/PMCMRplus/R/approxHayter.R |only PMCMRplus-1.6.1/PMCMRplus/R/chaAllPairsNashimotoTest.R | 73 +++--- PMCMRplus-1.6.1/PMCMRplus/R/osrtTest.R | 131 ++++++++---- PMCMRplus-1.6.1/PMCMRplus/R/powerOneWayTests.R | 6 PMCMRplus-1.6.1/PMCMRplus/R/print.osrt.R |only PMCMRplus-1.6.1/PMCMRplus/R/shirleyWilliamsTest.R | 33 +-- PMCMRplus-1.6.1/PMCMRplus/R/steelTest.R | 32 +- PMCMRplus-1.6.1/PMCMRplus/R/sysdata.rda |binary PMCMRplus-1.6.1/PMCMRplus/R/williamsTest.R | 47 +--- PMCMRplus-1.6.1/PMCMRplus/inst/NEWS.Rd | 30 ++ PMCMRplus-1.6.1/PMCMRplus/inst/doc/QuickReferenceGuide.html | 4 PMCMRplus-1.6.1/PMCMRplus/man/MTest.Rd | 26 ++ PMCMRplus-1.6.1/PMCMRplus/man/chaAllPairsNashimotoTest.Rd | 34 +-- PMCMRplus-1.6.1/PMCMRplus/man/osrtTest.Rd | 68 +++++- PMCMRplus-1.6.1/PMCMRplus/man/powerOneWayTests.Rd | 3 PMCMRplus-1.6.1/PMCMRplus/man/print.osrt.Rd |only PMCMRplus-1.6.1/PMCMRplus/man/shirleyWilliamsTest.Rd | 12 - PMCMRplus-1.6.1/PMCMRplus/man/steelTest.Rd | 13 - PMCMRplus-1.6.1/PMCMRplus/man/summary.osrt.Rd |only PMCMRplus-1.6.1/PMCMRplus/man/williamsTest.Rd | 15 - 30 files changed, 408 insertions(+), 259 deletions(-)
Title: Apply Mapping Functions in Parallel using Futures
Description: Implementations of the family of map() functions
from 'purrr' that can be resolved using any 'future'-supported
backend, e.g. parallel on the local machine or distributed on a
compute cluster.
Author: Davis Vaughan [aut, cre],
Matt Dancho [aut],
RStudio [cph]
Maintainer: Davis Vaughan <davis@rstudio.com>
Diff between furrr versions 0.2.0 dated 2020-10-12 and 0.2.1 dated 2020-10-21
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 8 ++++++++ R/future-invoke-map.R | 2 +- R/future-map.R | 2 +- man/future_invoke_map.Rd | 2 +- man/future_map.Rd | 2 +- tests/testthat/helper-furrr-test-that.R | 4 +--- 8 files changed, 23 insertions(+), 17 deletions(-)
Title: The Gaussian Covariate Method for Variable Selection
Description: Given the standard linear model the traditional way of deciding whether to include the jth covariate is to apply the F-test to decide whether the corresponding beta coefficient is zero. The Gaussian covariate method is completely different. The question as to whether the beta coefficient is or is not zero is replaced by the question as to whether the covariate is better or worse than i.i.d. Gaussian noise. The P-value for the covariate is the probability that Gaussian noise is better. Surprisingly this can be given exactly and it is the same a the P-value for the classical model based on the F-distribution. The Gaussian covariate P-value is model free, it is the same for any data set. Using the idea it is possible to do covariate selection for a small number of covariates 25 by considering all subsets. Post selection inference causes no problems as the P-values hold whatever the data. The idea extends to stepwise regression again with exact probabilities. In the simplest version the only parameter is a specified cut-off P-value which can be interpreted as the probability of a false positive being included in the final selection. For more information see the website below and the accompanying papers: L. Davies and L. Duembgen, "Covariate Selection Based on a Model-free Approach to Linear Regression with Exact Probabilities", 2020, <arXiv:1906.01990>. L. Davies, "Lasso, Knockoff and Gaussian covariates: A comparison", 2018, <arXiv:1807.09633>.
Author: Laurie Davies [aut, cre]
Maintainer: Laurie Davies <laurie.davies@uni-due.de>
Diff between gausscov versions 0.0.7 dated 2020-09-14 and 0.0.8 dated 2020-10-21
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/frmch.R | 11 ++++++++--- R/frobreg.R | 12 +++++++++--- R/frobregp.R | 15 +++++++++------ src/gaucov.f | 9 +++++---- 6 files changed, 40 insertions(+), 25 deletions(-)
Title: Tidy Quantitative Financial Analysis
Description: Bringing business and financial analysis to the 'tidyverse'. The 'tidyquant'
package provides a convenient wrapper to various 'xts', 'zoo', 'quantmod', 'TTR'
and 'PerformanceAnalytics' package
functions and returns the objects in the tidy 'tibble' format. The main
advantage is being able to use quantitative functions with the 'tidyverse'
functions including 'purrr', 'dplyr', 'tidyr', 'ggplot2', 'lubridate', etc. See
the 'tidyquant' website for more information, documentation and examples.
Author: Matt Dancho [aut, cre],
Davis Vaughan [aut]
Maintainer: Matt Dancho <mdancho@business-science.io>
Diff between tidyquant versions 1.0.1 dated 2020-07-02 and 1.0.2 dated 2020-10-21
DESCRIPTION | 22 - MD5 | 71 ++-- NAMESPACE | 1 NEWS.md | 17 R/data.R | 2 R/ggplot-geom_bbands.R | 12 R/ggplot-geom_chart.R | 4 R/ggplot-geom_ma.R | 12 R/ggplot-theme_tq.R | 31 - R/tq_get.R | 2 R/tq_stock_list.R | 84 ++-- R/utils-downloaders.R |only README.md | 12 build/vignette.rds |binary inst/doc/TQ00-introduction-to-tidyquant.Rmd | 2 inst/doc/TQ00-introduction-to-tidyquant.html | 15 inst/doc/TQ01-core-functions-in-tidyquant.Rmd | 2 inst/doc/TQ01-core-functions-in-tidyquant.html | 113 +++++- inst/doc/TQ02-quant-integrations-in-tidyquant.html | 127 +++++-- inst/doc/TQ03-scaling-and-modeling-with-tidyquant.Rmd | 6 inst/doc/TQ03-scaling-and-modeling-with-tidyquant.html | 291 ++++++++++------- inst/doc/TQ04-charting-with-tidyquant.Rmd | 18 - inst/doc/TQ04-charting-with-tidyquant.html | 115 +++++- inst/doc/TQ05-performance-analysis-with-tidyquant.Rmd | 4 inst/doc/TQ05-performance-analysis-with-tidyquant.html | 105 +++++- inst/doc/TQ06-excel-in-r.html | 9 man/FANG.Rd | 2 man/geom_bbands.Rd | 12 man/geom_chart.Rd | 4 man/geom_ma.Rd | 12 man/tq_get.Rd | 2 man/tq_index.Rd | 2 vignettes/TQ00-introduction-to-tidyquant.Rmd | 2 vignettes/TQ01-core-functions-in-tidyquant.Rmd | 2 vignettes/TQ03-scaling-and-modeling-with-tidyquant.Rmd | 6 vignettes/TQ04-charting-with-tidyquant.Rmd | 18 - vignettes/TQ05-performance-analysis-with-tidyquant.Rmd | 4 37 files changed, 759 insertions(+), 384 deletions(-)
Title: Querying and Managing Large Biodiversity Occurrence Datasets
Description: Facilitates the gathering of biodiversity occurrence data
from disparate sources. Metadata is managed throughout the process to facilitate
reporting and enhanced ability to repeat analyses.
Author: Hannah L. Owens [aut, cre] (<https://orcid.org/0000-0003-0071-1745>),
Cory Merow [aut] (<https://orcid.org/0000-0003-0561-053X>),
Brian Maitner [aut] (<https://orcid.org/0000-0002-2118-9880>),
Jamie M. Kass [aut] (<https://orcid.org/0000-0002-9432-895X>),
Vijay Barve [aut] (<https://orcid.org/0000-0002-4852-2567>),
Robert P. Guralnick [aut] (<https://orcid.org/0000-0001-6682-1504>)
Maintainer: Hannah L. Owens <hannah.owens@gmail.com>
Diff between occCite versions 0.3.0 dated 2020-10-06 and 0.4.0 dated 2020-10-21
DESCRIPTION | 15 - MD5 | 31 +- NAMESPACE | 4 NEWS.md | 9 R/BIENtableCleanup.R | 2 R/GBIFtableCleanup.R | 33 +- R/gbifRetriever.R | 17 + R/occCitation.R | 41 ++- R/occCitePrint.R | 31 +- R/occCite_plotting.R | 27 ++ R/occSum.R | 21 - build/vignette.rds |binary inst/doc/occCite_Vignette.html | 506 ++++++++++++++++++++++++++++------------- inst/extdata/sampleScript.R | 4 man/BIENtableCleanup.Rd | 2 man/figures |only man/summary.occCiteData.Rd | 2 17 files changed, 508 insertions(+), 237 deletions(-)
Title: Network-Based Genome Wide Association Studies
Description: A multi-core R package that contains a set of tools based on copula graphical
models for accomplishing the three interrelated goals in genetics and genomics in an
unified way: (1) linkage map construction, (2) constructing linkage disequilibrium
networks, and (3) exploring high-dimensional genotype-phenotype network and genotype-
phenotype-environment interactions networks.
The netgwas package can deal with biparental inbreeding and outbreeding species with
any ploidy level, namely diploid (2 sets of chromosomes), triploid (3 sets of chromosomes),
tetraploid (4 sets of chromosomes) and so on. We target on high-dimensional data where
number of variables p is considerably larger than number of sample sizes (p >> n).
The computations is memory-optimized using the sparse matrix output. The package is
implemented the recent methodological developments in Behrouzi and Wit (2017) <doi:10.1111/rssc.12287>
and Behrouzi and Wit (2017) <doi:10.1093/bioinformatics/bty777>.
NOTICE proper functionality of 'netgwas' requires that the 'RBGL' package is installed from 'bioconductor'; for installation instruction please refer to the 'RBGL' web page given below.
Author: Pariya Behrouzi <https://orcid.org/0000-0001-6762-5433> and Ernst C. Wit
Maintainer: Pariya Behrouzi <pariya.behrouzi@gmail.com>
Diff between netgwas versions 1.11 dated 2019-10-15 and 1.12 dated 2020-10-21
netgwas-1.11/netgwas/data/bp.RData |only netgwas-1.11/netgwas/data/hdl.RData |only netgwas-1.11/netgwas/man/bp.Rd |only netgwas-1.11/netgwas/man/hdl.Rd |only netgwas-1.12/netgwas/DESCRIPTION | 8 netgwas-1.12/netgwas/MD5 | 22 - netgwas-1.12/netgwas/R/buildMap.R | 438 ++++++++++++++++---------------- netgwas-1.12/netgwas/R/netmap.R | 10 netgwas-1.12/netgwas/R/netphenogeno.R | 3 netgwas-1.12/netgwas/R/netsnp.R | 6 netgwas-1.12/netgwas/R/selectnet.R | 18 + netgwas-1.12/netgwas/R/simgeno.R | 310 +++++++++++----------- netgwas-1.12/netgwas/man/plot.select.Rd | 5 netgwas-1.12/netgwas/man/selectnet.Rd | 7 14 files changed, 422 insertions(+), 405 deletions(-)
Title: Machine Learning in R - Next Generation
Description: Efficient, object-oriented programming on the
building blocks of machine learning. Provides 'R6' objects for tasks,
learners, resamplings, and measures. The package is geared towards
scalability and larger datasets by supporting parallelization and
out-of-memory data-backends like databases. While 'mlr3' focuses on
the core computational operations, add-on packages provide additional
functionality.
Author: Michel Lang [cre, aut] (<https://orcid.org/0000-0001-9754-0393>),
Bernd Bischl [aut] (<https://orcid.org/0000-0001-6002-6980>),
Jakob Richter [aut] (<https://orcid.org/0000-0003-4481-5554>),
Patrick Schratz [aut] (<https://orcid.org/0000-0003-0748-6624>),
Giuseppe Casalicchio [ctb] (<https://orcid.org/0000-0001-5324-5966>),
Stefan Coors [ctb] (<https://orcid.org/0000-0002-7465-2146>),
Quay Au [ctb] (<https://orcid.org/0000-0002-5252-8902>),
Martin Binder [aut],
Marc Becker [ctb] (<https://orcid.org/0000-0002-8115-0400>)
Maintainer: Michel Lang <michellang@gmail.com>
Diff between mlr3 versions 0.7.0 dated 2020-10-07 and 0.8.0 dated 2020-10-21
DESCRIPTION | 6 MD5 | 126 ++++++++--------- NEWS.md | 9 + R/LearnerClassifFeatureless.R | 2 R/LearnerRegrFeatureless.R | 2 R/MeasureOOBError.R | 2 R/ResultData.R | 2 R/mlr_reflections.R | 2 R/worker.R | 69 ++++----- build/partial.rdb |binary man/figures/mlr3verse.svg | 2 tests/testthat/test_DataBackend.R | 2 tests/testthat/test_DataBackendCbind.R | 2 tests/testthat/test_DataBackendDataTable.R | 2 tests/testthat/test_DataBackendMatrix.R | 4 tests/testthat/test_DataBackendRbind.R | 2 tests/testthat/test_DataBackendRename.R | 2 tests/testthat/test_Dictionary.R | 2 tests/testthat/test_Learner.R | 2 tests/testthat/test_Measure.R | 2 tests/testthat/test_MeasureClassif.R | 2 tests/testthat/test_MeasureRegr.R | 2 tests/testthat/test_PredictionClassif.R | 2 tests/testthat/test_PredictionDataClassif.R | 7 tests/testthat/test_PredictionDataRegr.R | 7 tests/testthat/test_PredictionRegr.R | 2 tests/testthat/test_Resampling.R | 6 tests/testthat/test_Task.R | 7 tests/testthat/test_TaskClassif.R | 2 tests/testthat/test_TaskRegr.R | 2 tests/testthat/test_TaskSupervised.R | 2 tests/testthat/test_auto_convert.R | 2 tests/testthat/test_benchmark.R | 6 tests/testthat/test_convert_task.R | 2 tests/testthat/test_encapsulate.R | 2 tests/testthat/test_errorhandling.R | 2 tests/testthat/test_fallback.R | 8 - tests/testthat/test_hashes.R | 2 tests/testthat/test_lgr.R | 10 - tests/testthat/test_mlr_learners.R | 2 tests/testthat/test_mlr_learners_classif_debug.R | 2 tests/testthat/test_mlr_learners_classif_featureless.R | 2 tests/testthat/test_mlr_learners_classif_rpart.R | 2 tests/testthat/test_mlr_learners_regr_featureless.R | 2 tests/testthat/test_mlr_learners_regr_rpart.R | 2 tests/testthat/test_mlr_measures.R | 2 tests/testthat/test_mlr_measures_classif.costs.R | 2 tests/testthat/test_mlr_measures_selected_features.R | 2 tests/testthat/test_mlr_resampling_bootstrap.R | 2 tests/testthat/test_mlr_resampling_custom.R | 2 tests/testthat/test_mlr_resampling_cv.R | 2 tests/testthat/test_mlr_resampling_holdout.R | 2 tests/testthat/test_mlr_resampling_loo.R | 2 tests/testthat/test_mlr_resampling_repeated_cv.R | 2 tests/testthat/test_mlr_resampling_subsampling.R | 2 tests/testthat/test_mlr_resamplings.R | 4 tests/testthat/test_mlr_sugar.R | 2 tests/testthat/test_mlr_task_generators.R | 2 tests/testthat/test_mlr_tasks.R | 2 tests/testthat/test_parallel.R | 2 tests/testthat/test_predict.R | 2 tests/testthat/test_resample.R | 18 ++ tests/testthat/test_resampling_insample.R | 2 tests/testthat/test_resultdata.R | 21 ++ 64 files changed, 169 insertions(+), 235 deletions(-)
Title: Formatting and Harmonizing Ecological Trait-Data
Description: Assistance for handling ecological trait data and applying the
Ecological Trait-Data Standard terminology (Schneider et al. 2019
<doi:10.1111/2041-210X.13288>). There are two major use cases: (1) preparation of
own trait datasets for upload into public data bases, and (2) harmonizing
trait datasets from different sources by re-formatting them into a unified
format. See 'traitdataform' website for full documentation.
Author: Florian D. Schneider [aut, cre]
(<https://orcid.org/0000-0002-1494-5684>),
Caterina Penone [ctb] (<https://orcid.org/0000-0002-8170-6659>),
Andreas Ostrowski [ctb] (<https://orcid.org/0000-0002-2033-779X>),
Dennis Heimann [ctb],
Felix Neff [ctb],
Markus J. Ankenbrand [ctb],
Jessica Burnett [ctb]
Maintainer: Florian D. Schneider <florian.dirk.schneider@gmail.com>
Diff between traitdataform versions 0.5.7 dated 2020-04-05 and 0.6.0 dated 2020-10-21
DESCRIPTION | 25 - MD5 | 64 +- NAMESPACE | 1 NEWS.md | 12 R/as.metadata.R | 9 R/as.traitdata.R | 75 +-- R/cast.traitdata.R | 20 R/get_gbif_taxonomy.R | 21 R/glossary.R | 2 R/mutate.traitdata.R | 44 - R/standardize.R | 62 +- R/thesaurus.R | 2 R/utils.R | 21 README.md | 10 build/vignette.rds |binary inst/doc/traitdataform.R | 4 inst/doc/traitdataform.Rmd | 28 - inst/doc/traitdataform.html | 790 ++++++++++++++++++-------------- man/as.metadata.Rd | 2 man/as.trait.Rd | 2 man/as.traitdata.Rd | 6 man/cast.traitdata.Rd | 20 man/get_gbif_taxonomy.Rd | 7 man/glossary.Rd | 2 man/mutate.traitdata.Rd | 26 - man/standardize.Rd | 2 man/standardize_taxa.Rd | 4 man/standardize_traits.Rd | 6 tests/testthat/test.columns_to_ETS.R | 20 tests/testthat/test.map_gbif_taxonomy.R | 41 - tests/testthat/test.standardize.R | 20 vignettes/div05.bib | 12 vignettes/traitdataform.Rmd | 28 - 33 files changed, 801 insertions(+), 587 deletions(-)
Title: Simulated Maximum Likelihood Estimation of Mixed Logit Models
for Large Datasets
Description: Specification and estimation of multinomial logit
models. Large datasets and complex models are supported, with an
intuitive syntax. Multinomial Logit Models, Mixed models, random
coefficients and Hybrid Choice are all supported. For more
information, see Molloy et al. (2019) <doi:10.3929/ethz-b-000334289>.
Author: Joseph Molloy [aut, cre]
Maintainer: Joseph Molloy <joseph.molloy@ivt.baug.ethz.ch>
Diff between mixl versions 1.2.2 dated 2020-07-13 and 1.2.3 dated 2020-10-21
DESCRIPTION | 8 MD5 | 36 +- R/compiler.R | 20 - R/mle.R | 5 R/model_stats.R | 6 build/vignette.rds |binary inst/doc/user-guide.Rmd | 12 inst/doc/user-guide.html | 62 ++++- inst/include/mixl/cpp_mixed_prediction_template.h | 2 inst/include/mixl/cpp_mnl_posteriors.cpp | 2 inst/include/mixl/cpp_mnl_prediction_template.h | 2 inst/include/mixl/cpp_mnl_template.h | 2 inst/include/mixl/cpp_posteriors.cpp | 2 inst/include/mixl/cpp_utility_template.h | 2 man/specify_model.Rd | 5 src/Makefile | 1 tests/testthat/test_maxlikelihood.R | 6 vignettes/user-guide.Rmd | 12 vignettes/user-guide.md | 272 +++++++++++----------- 19 files changed, 244 insertions(+), 213 deletions(-)
Title: Compound Poisson Linear Models
Description: Likelihood-based and Bayesian methods for various compound Poisson linear models based on Zhang, Yanwei (2013) <https://link.springer.com/article/10.1007/s11222-012-9343-7>.
Author: Yanwei (Wayne) Zhang
Maintainer: Yanwei (Wayne) Zhang <actuary_zhang@hotmail.com>
Diff between cplm versions 0.7-8 dated 2019-03-05 and 0.7-9 dated 2020-10-21
cplm-0.7-8/cplm/R/zcpglm.R |only cplm-0.7-8/cplm/man/zcpglm.Rd |only cplm-0.7-9/cplm/DESCRIPTION | 6 cplm-0.7-9/cplm/MD5 | 28 cplm-0.7-9/cplm/NAMESPACE | 4 cplm-0.7-9/cplm/NEWS | 8 cplm-0.7-9/cplm/R/classMethods.R | 141 --- cplm-0.7-9/cplm/R/utilities.R | 2 cplm-0.7-9/cplm/data/AutoClaim.RData |binary cplm-0.7-9/cplm/data/ClaimTriangle.RData |binary cplm-0.7-9/cplm/data/FineRoot.RData |binary cplm-0.7-9/cplm/inst/doc/cplm.Rnw | 1320 ++++++++++++++----------------- cplm-0.7-9/cplm/inst/doc/cplm.pdf |binary cplm-0.7-9/cplm/man/class-methods.Rd | 43 - cplm-0.7-9/cplm/man/cplm-package.Rd | 2 cplm-0.7-9/cplm/vignettes/cplm.Rnw | 126 -- 16 files changed, 629 insertions(+), 1051 deletions(-)
Title: Soil Database Interface
Description: A collection of functions for reading data from USDA-NCSS soil databases.
Author: Dylan Beaudette [aut],
Jay Skovlin [aut],
Stephen Roecker [aut],
Andrew Brown [aut, cre]
Maintainer: Andrew Brown <andrew.g.brown@usda.gov>
Diff between soilDB versions 2.5 dated 2020-01-28 and 2.5.8 dated 2020-10-21
soilDB-2.5.8/soilDB/.Rinstignore | 8 soilDB-2.5.8/soilDB/DESCRIPTION | 31 soilDB-2.5.8/soilDB/MD5 | 255 - soilDB-2.5.8/soilDB/NAMESPACE | 196 - soilDB-2.5.8/soilDB/NEWS.md | 733 ++-- soilDB-2.5.8/soilDB/R/AAAA.R | 48 soilDB-2.5.8/soilDB/R/KSSL_VG_model.R | 91 soilDB-2.5.8/soilDB/R/OSDquery.R | 102 soilDB-2.5.8/soilDB/R/SDA-spatial.R | 684 +++- soilDB-2.5.8/soilDB/R/SDA_query.R | 396 +- soilDB-2.5.8/soilDB/R/STR.R | 646 ++-- soilDB-2.5.8/soilDB/R/estimateColorMixture.R |only soilDB-2.5.8/soilDB/R/fetchHenry.R | 726 ++-- soilDB-2.5.8/soilDB/R/fetchKSSL.R | 449 ++ soilDB-2.5.8/soilDB/R/fetchNASIS_components.R | 41 soilDB-2.5.8/soilDB/R/fetchNASIS_pedons.R | 12 soilDB-2.5.8/soilDB/R/fetchNASIS_report.R | 695 ++-- soilDB-2.5.8/soilDB/R/fetchNOAA.R |only soilDB-2.5.8/soilDB/R/fetchOSD.R | 487 ++- soilDB-2.5.8/soilDB/R/fetchRaCA.R | 365 +- soilDB-2.5.8/soilDB/R/fetchSCAN.R | 694 ++-- soilDB-2.5.8/soilDB/R/fetchSDA_spatial.R | 328 +- soilDB-2.5.8/soilDB/R/fetchSoilGrids.R |only soilDB-2.5.8/soilDB/R/fetchVegdata.R | 72 soilDB-2.5.8/soilDB/R/filter_KSSL.R |only soilDB-2.5.8/soilDB/R/get_RMF_from_NASIS_db.R | 106 soilDB-2.5.8/soilDB/R/get_colors_from_NASIS_db.R | 110 soilDB-2.5.8/soilDB/R/get_component_data_from_NASIS_db.R | 1559 +++++----- soilDB-2.5.8/soilDB/R/get_component_from_GDB.R |only soilDB-2.5.8/soilDB/R/get_component_from_LIMS.R | 27 soilDB-2.5.8/soilDB/R/get_component_from_SDA.R | 1373 +++++--- soilDB-2.5.8/soilDB/R/get_concentrations_from_NASIS_db.R |only soilDB-2.5.8/soilDB/R/get_cosoilmoist_from_LIMS.R | 10 soilDB-2.5.8/soilDB/R/get_cosoilmoist_from_NASIS.R | 62 soilDB-2.5.8/soilDB/R/get_extended_data_from_NASIS_db.R | 1058 +++--- soilDB-2.5.8/soilDB/R/get_hz_data_from_NASIS_db.R | 128 soilDB-2.5.8/soilDB/R/get_lablayer_data_from_NASIS_db.R | 100 soilDB-2.5.8/soilDB/R/get_labpedon_data_from_NASIS_db.R | 48 soilDB-2.5.8/soilDB/R/get_phfmp_from_NASIS_db.R |only soilDB-2.5.8/soilDB/R/get_phlabresults_data_from_NASIS_db.R | 276 - soilDB-2.5.8/soilDB/R/get_projectmapunit_from_NASIS.R | 98 soilDB-2.5.8/soilDB/R/get_site_data_from_NASIS_db.R | 233 - soilDB-2.5.8/soilDB/R/get_soilseries_from_NASIS.R | 118 soilDB-2.5.8/soilDB/R/get_text_notes_from_NASIS_db.R | 120 soilDB-2.5.8/soilDB/R/get_veg_data_from_NASIS_db.R | 142 soilDB-2.5.8/soilDB/R/get_vegplot_data_from_NASIS_db.R | 848 ++--- soilDB-2.5.8/soilDB/R/mapunit_geom_by_ll_bbox.R | 208 - soilDB-2.5.8/soilDB/R/mix_and_clean_colors.R | 141 soilDB-2.5.8/soilDB/R/openNASISchannel.R | 78 soilDB-2.5.8/soilDB/R/seriesExtent.R | 237 + soilDB-2.5.8/soilDB/R/siblings.R | 174 - soilDB-2.5.8/soilDB/R/simplfyFragmentData.R | 482 +-- soilDB-2.5.8/soilDB/R/simplifyArtifactData.R | 370 +- soilDB-2.5.8/soilDB/R/simplifyColorData.R | 258 - soilDB-2.5.8/soilDB/R/taxaExtent.R |only soilDB-2.5.8/soilDB/R/utils.R | 94 soilDB-2.5.8/soilDB/R/waterDayYear.R | 60 soilDB-2.5.8/soilDB/data/gopheridge.rda |binary soilDB-2.5.8/soilDB/data/loafercreek.rda |binary soilDB-2.5.8/soilDB/data/mineralKing.rda |binary soilDB-2.5.8/soilDB/inst |only soilDB-2.5.8/soilDB/man/KSSL_VG_model.Rd | 109 soilDB-2.5.8/soilDB/man/OSDquery.Rd | 165 - soilDB-2.5.8/soilDB/man/SCAN_SNOTEL_metadata.Rd | 68 soilDB-2.5.8/soilDB/man/SDA_query.Rd | 190 - soilDB-2.5.8/soilDB/man/SDA_spatialQuery.Rd |only soilDB-2.5.8/soilDB/man/SSURGO_spatial_query.Rd | 82 soilDB-2.5.8/soilDB/man/STRplot.Rd | 82 soilDB-2.5.8/soilDB/man/estimateColorMixture.Rd |only soilDB-2.5.8/soilDB/man/estimateSTR.Rd | 89 soilDB-2.5.8/soilDB/man/fetchGDB.Rd |only soilDB-2.5.8/soilDB/man/fetchHenry.Rd | 128 soilDB-2.5.8/soilDB/man/fetchKSSL.Rd | 204 - soilDB-2.5.8/soilDB/man/fetchNASIS.Rd | 202 - soilDB-2.5.8/soilDB/man/fetchNASISLabData.Rd | 70 soilDB-2.5.8/soilDB/man/fetchNASISWebReport.Rd | 312 +- soilDB-2.5.8/soilDB/man/fetchOSD.Rd | 194 - soilDB-2.5.8/soilDB/man/fetchPedonPC.Rd | 73 soilDB-2.5.8/soilDB/man/fetchRaCA.Rd | 150 soilDB-2.5.8/soilDB/man/fetchSCAN.Rd | 108 soilDB-2.5.8/soilDB/man/fetchSDA_component.Rd | 377 +- soilDB-2.5.8/soilDB/man/fetchSDA_spatial.Rd | 120 soilDB-2.5.8/soilDB/man/fetchSoilGrids.Rd |only soilDB-2.5.8/soilDB/man/filter_geochem.Rd |only soilDB-2.5.8/soilDB/man/format_SQL_in_statement.Rd |only soilDB-2.5.8/soilDB/man/get_NOAA_GHCND.Rd |only soilDB-2.5.8/soilDB/man/get_NOAA_stations_nearXY.Rd |only soilDB-2.5.8/soilDB/man/get_colors_from_NASIS_db.Rd | 48 soilDB-2.5.8/soilDB/man/get_colors_from_pedon_db.Rd | 52 soilDB-2.5.8/soilDB/man/get_comonth_from_NASIS_db.Rd | 82 soilDB-2.5.8/soilDB/man/get_component_data_from_NASIS_db.Rd | 82 soilDB-2.5.8/soilDB/man/get_cosoilmoist_from_NASIS.Rd | 72 soilDB-2.5.8/soilDB/man/get_extended_data_from_NASIS.Rd | 80 soilDB-2.5.8/soilDB/man/get_hz_data_from_NASIS_db.Rd | 54 soilDB-2.5.8/soilDB/man/get_hz_data_from_pedon_db.Rd | 54 soilDB-2.5.8/soilDB/man/get_lablayer_data_from_NASIS_db.Rd | 46 soilDB-2.5.8/soilDB/man/get_labpedon_data_from_NASIS_db.Rd | 46 soilDB-2.5.8/soilDB/man/get_site_data_from_NASIS_db.Rd | 104 soilDB-2.5.8/soilDB/man/get_site_data_from_pedon_db.Rd | 56 soilDB-2.5.8/soilDB/man/get_soilseries_from_NASIS.Rd | 52 soilDB-2.5.8/soilDB/man/get_text_notes_from_NASIS_db.Rd | 81 soilDB-2.5.8/soilDB/man/get_veg_data_from_NASIS_db.Rd | 61 soilDB-2.5.8/soilDB/man/get_veg_from_AK_Site.Rd | 52 soilDB-2.5.8/soilDB/man/get_veg_from_MT_veg_db.Rd | 50 soilDB-2.5.8/soilDB/man/get_veg_from_NPS_PLOTS_db.Rd | 40 soilDB-2.5.8/soilDB/man/get_veg_other_from_MT_veg_db.Rd | 50 soilDB-2.5.8/soilDB/man/get_veg_species_from_MT_veg_db.Rd | 50 soilDB-2.5.8/soilDB/man/local_NASIS_defined.Rd |only soilDB-2.5.8/soilDB/man/makeChunks.Rd |only soilDB-2.5.8/soilDB/man/mapunit_geom_by_ll_bbox.Rd | 130 soilDB-2.5.8/soilDB/man/parseWebReport.Rd | 60 soilDB-2.5.8/soilDB/man/processSDA_WKT.Rd |only soilDB-2.5.8/soilDB/man/seriesExtent.Rd | 99 soilDB-2.5.8/soilDB/man/siblings.Rd | 120 soilDB-2.5.8/soilDB/man/simplfyFragmentData.Rd | 56 soilDB-2.5.8/soilDB/man/simplifyColorData.Rd | 76 soilDB-2.5.8/soilDB/man/taxaExtent.Rd |only soilDB-2.5.8/soilDB/man/uncode.Rd | 106 soilDB-2.5.8/soilDB/man/us_ss_timeline.Rd | 117 soilDB-2.5.8/soilDB/man/waterDayYear.Rd | 76 soilDB-2.5.8/soilDB/tests/testthat.R | 10 soilDB-2.5.8/soilDB/tests/testthat/test-OSDquery.R | 76 soilDB-2.5.8/soilDB/tests/testthat/test-SDA_query.R | 371 +- soilDB-2.5.8/soilDB/tests/testthat/test-estimateColorMixture.R |only soilDB-2.5.8/soilDB/tests/testthat/test-estimateSTR.R | 86 soilDB-2.5.8/soilDB/tests/testthat/test-fetchKSSL.R | 283 + soilDB-2.5.8/soilDB/tests/testthat/test-fetchNASIS.R | 238 - soilDB-2.5.8/soilDB/tests/testthat/test-fetchNASISLabData.R | 88 soilDB-2.5.8/soilDB/tests/testthat/test-fetchNASISWebReport.R | 184 - soilDB-2.5.8/soilDB/tests/testthat/test-fetchOSD.R | 251 - soilDB-2.5.8/soilDB/tests/testthat/test-fetchSCAN.R | 4 soilDB-2.5.8/soilDB/tests/testthat/test-fetchSDA_component.R | 122 soilDB-2.5.8/soilDB/tests/testthat/test-fetchSDA_spatial.R | 58 soilDB-2.5.8/soilDB/tests/testthat/test-fetchSoilGrids.R |only soilDB-2.5.8/soilDB/tests/testthat/test-multi-row-simplification.R | 108 soilDB-2.5.8/soilDB/tests/testthat/test-siblings.R | 92 soilDB-2.5.8/soilDB/tests/testthat/test-simplifyArtifactData.R | 388 +- soilDB-2.5.8/soilDB/tests/testthat/test-simplifyColorData.R | 202 - soilDB-2.5.8/soilDB/tests/testthat/test-simplifyFragmentData.R | 983 +++--- soilDB-2.5.8/soilDB/tests/testthat/test-waterDayYear.R | 66 soilDB-2.5/soilDB/man/SDA_query_features.Rd |only soilDB-2.5/soilDB/tests/testthat/test-mix_and_clean_colors.R |only 142 files changed, 12752 insertions(+), 11210 deletions(-)
Title: Package for Environmental Statistics, Including US EPA Guidance
Description: Graphical and statistical analyses of environmental data, with
focus on analyzing chemical concentrations and physical parameters, usually in
the context of mandated environmental monitoring. Major environmental
statistical methods found in the literature and regulatory guidance documents,
with extensive help that explains what these methods do, how to use them,
and where to find them in the literature. Numerous built-in data sets from
regulatory guidance documents and environmental statistics literature. Includes
scripts reproducing analyses presented in the book "EnvStats: An R Package for
Environmental Statistics" (Millard, 2013, Springer, ISBN 978-1-4614-8455-4,
<https://www.springer.com/book/9781461484554>).
Author: Steven P. Millard [aut],
Alexander Kowarik [ctb, cre] (<https://orcid.org/0000-0001-8598-4130>)
Maintainer: Alexander Kowarik <alexander.kowarik@statistik.gv.at>
Diff between EnvStats versions 2.3.1 dated 2018-07-15 and 2.4.0 dated 2020-10-21
EnvStats-2.3.1/EnvStats/inst/doc |only EnvStats-2.4.0/EnvStats/DESCRIPTION | 23 EnvStats-2.4.0/EnvStats/MD5 | 64 EnvStats-2.4.0/EnvStats/NEWS | 1223 ++-- EnvStats-2.4.0/EnvStats/R/EnvStats-internal.R | 1791 +++---- EnvStats-2.4.0/EnvStats/R/pred.int.norm.CA.on.r.K.R | 83 EnvStats-2.4.0/EnvStats/R/pred.int.norm.Modified.CA.on.r.K.R | 75 EnvStats-2.4.0/EnvStats/R/pred.int.norm.k.of.m.on.r.K.R | 111 EnvStats-2.4.0/EnvStats/R/predIntLnormAltSimultaneous.R | 2 EnvStats-2.4.0/EnvStats/R/predIntLnormSimultaneous.R | 2 EnvStats-2.4.0/EnvStats/R/predIntNormSimultaneous.R | 213 EnvStats-2.4.0/EnvStats/R/predIntNormSimultaneousK.R | 165 EnvStats-2.4.0/EnvStats/R/qnormMix.R | 59 EnvStats-2.4.0/EnvStats/R/rosnerTestLambda.R | 46 EnvStats-2.4.0/EnvStats/README.md |only EnvStats-2.4.0/EnvStats/inst/CITATION | 24 EnvStats-2.4.0/EnvStats/man/ACE.13.TCE.df.Rd | 52 EnvStats-2.4.0/EnvStats/man/Distribution.df.Rd | 864 +-- EnvStats-2.4.0/EnvStats/man/EnvStats-package.Rd | 684 +- EnvStats-2.4.0/EnvStats/man/Olympic.NH4.df.Rd | 33 EnvStats-2.4.0/EnvStats/man/Skagit.NH3_N.df.Rd | 23 EnvStats-2.4.0/EnvStats/man/distChoose.Rd | 1400 ++--- EnvStats-2.4.0/EnvStats/man/distChooseCensored.Rd | 1622 +++--- EnvStats-2.4.0/EnvStats/man/eqnpar.Rd | 1752 +++--- EnvStats-2.4.0/EnvStats/man/gofTest.Rd | 2786 +++++------ EnvStats-2.4.0/EnvStats/man/kendallSeasonalTrendTest.Rd | 1540 +++--- EnvStats-2.4.0/EnvStats/man/kendallTrendTest.Rd | 958 +-- EnvStats-2.4.0/EnvStats/man/predIntLnormSimultaneous.Rd | 898 +-- EnvStats-2.4.0/EnvStats/man/predIntNormSimultaneous.Rd | 1126 +--- EnvStats-2.4.0/EnvStats/man/predIntNormSimultaneousK.Rd | 1030 ++-- EnvStats-2.4.0/EnvStats/man/simulateMvMatrix.Rd | 1006 +-- EnvStats-2.4.0/EnvStats/man/simulateVector.Rd | 422 - EnvStats-2.4.0/EnvStats/tests |only 33 files changed, 9824 insertions(+), 10253 deletions(-)
Title: Plotting Field Plans for Agricultural Experiments
Description: A function for plotting maps of agricultural field experiments that
are laid out in grids.
Author: Kevin Wright [aut, cre] (<https://orcid.org/0000-0002-0617-8673>)
Maintainer: Kevin Wright <kw.stat@gmail.com>
Diff between desplot versions 1.7 dated 2020-07-20 and 1.8 dated 2020-10-21
DESCRIPTION | 6 MD5 | 16 - NEWS.md | 12 R/desplot.R | 16 - R/geom_tileborder.R | 1 R/ggdesplot.R | 6 build/vignette.rds |binary inst/doc/desplot_examples.html | 627 +++++++++++++++++++++++++++-------------- tests/testthat/test_desplot.R | 6 9 files changed, 463 insertions(+), 227 deletions(-)
Title: Presentation Ninja
Description: Create HTML5 slides with R Markdown and the JavaScript library
'remark.js' (<https://remarkjs.com>).
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>),
Alessandro Gasparini [ctb] (<https://orcid.org/0000-0002-8319-7624>),
Benjie Gillam [ctb],
Claus Thorn Ekstrøm [ctb],
Daniel Anderson [ctb],
Dawei Lang [ctb],
Emi Tanaka [ctb],
Garrick Aden-Buie [ctb] (<https://orcid.org/0000-0002-7111-0077>),
Iñaki Ucar [ctb] (<https://orcid.org/0000-0001-6403-5550>),
John Little [ctb],
Joselyn Chávez [ctb] (<https://orcid.org/0000-0002-4974-4591>),
Joseph Casillas [ctb],
Lucy D'Agostino McGowan [ctb] (<https://orcid.org/0000-0001-7297-9359>),
Malcolm Barrett [ctb] (<https://orcid.org/0000-0003-0299-5825>),
Matthew Mark Strasiotto [ctb] (mstr3336),
Michael Wayne Kearney [ctb],
Nan-Hung Hsieh [ctb],
Ole Petter Bang [ctb] (CSS in
rmarkdown/templates/xaringan/resources/default.css),
Patrick Schratz [ctb],
Paul Klemm [ctb] (<https://orcid.org/0000-0002-5985-1737>),
Paul Lemmens [ctb],
Sean Lopp [ctb],
Susan VanderPlas [ctb] (<https://orcid.org/0000-0002-3803-0972>),
Waldir Leoncio [ctb],
Yongfu Liao [ctb],
Yue Jiang [ctb] (<https://orcid.org/0000-0002-9798-5517>)
Maintainer: Yihui Xie <xie@yihui.name>
Diff between xaringan versions 0.17 dated 2020-09-24 and 0.18 dated 2020-10-21
DESCRIPTION | 12 + MD5 | 16 +- NAMESPACE | 2 R/render.R | 79 +++++++++---- R/utils.R | 68 ++++++++++- inst/rmarkdown/templates/xaringan/resources/js/data-uri.js |only inst/rmarkdown/templates/xaringan/resources/uio-fonts.css |only inst/rmarkdown/templates/xaringan/resources/uio.css |only man/moon_reader.Rd | 38 ++++-- tests/testit/1x1.gif |only tests/testit/test-utils.R | 39 ++++++ 11 files changed, 207 insertions(+), 47 deletions(-)
Title: Suess and Laws Corrections for Marine Stable Carbon Isotope Data
Description: Generates region-specific Suess and Laws corrections for
stable carbon isotope data from marine organisms collected between 1850 and 2019. Version
0.1.1 of 'SuessR' contains four built-in regions: the Bering Sea ('Bering Sea'), the
Aleutian archipelago ('Aleutians Islands'), the Gulf of Alaska ('Gulf of Alaska'), and the
subpolar North Atlantic ('Subpolar North Atlantic'). Users can supply their own environmental
data for regions currently not built into the package to generate corrections for those regions.
Author: Casey Clark [cre, aut],
Mattias Cape [aut],
Mark Shapley [aut],
Franz Mueter [aut],
Bruce Finney [aut],
Nicole Misarti [aut]
Maintainer: Casey Clark <casey.t.clark@gmail.com>
Diff between SuessR versions 0.1.0 dated 2020-09-09 and 0.1.1 dated 2020-10-21
DESCRIPTION | 8 +++--- MD5 | 11 ++++---- NEWS.md |only R/SuessR_Package.R | 51 +++++++++++++++++++++++---------------- data/SuessR_Reference_Data.RData |binary man/SuessR.Rd | 2 - man/SuessR.custom.Rd | 4 +-- 7 files changed, 44 insertions(+), 32 deletions(-)
Title: Dynamic Documents for R
Description: Convert R Markdown documents into a variety of formats.
Author: JJ Allaire [aut],
Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>),
Jonathan McPherson [aut],
Javier Luraschi [aut],
Kevin Ushey [aut],
Aron Atkins [aut],
Hadley Wickham [aut],
Joe Cheng [aut],
Winston Chang [aut],
Richard Iannone [aut] (<https://orcid.org/0000-0003-3925-190X>),
Andrew Dunning [ctb] (<https://orcid.org/0000-0003-0464-5036>),
Atsushi Yasumoto [ctb, cph] (<https://orcid.org/0000-0002-8335-495X>,
Number sections Lua filter),
Barret Schloerke [ctb],
Christophe Dervieux [ctb],
Frederik Aust [ctb] (<https://orcid.org/0000-0003-4900-788X>),
Jeff Allen [ctb],
JooYoung Seo [ctb] (<https://orcid.org/0000-0002-4064-6012>),
Malcolm Barrett [ctb],
Rob Hyndman [ctb],
Romain Lesur [ctb],
Roy Storey [ctb],
Ruben Arslan [ctb],
Sergio Oller [ctb],
RStudio, PBC [cph],
jQuery Foundation [cph] (jQuery library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/rmd/h/jquery-AUTHORS.txt),
jQuery UI contributors [ctb, cph] (jQuery UI library; authors listed in
inst/rmd/h/jqueryui-AUTHORS.txt),
Mark Otto [ctb] (Bootstrap library),
Jacob Thornton [ctb] (Bootstrap library),
Bootstrap contributors [ctb] (Bootstrap library),
Twitter, Inc [cph] (Bootstrap library),
Alexander Farkas [ctb, cph] (html5shiv library),
Scott Jehl [ctb, cph] (Respond.js library),
Ivan Sagalaev [ctb, cph] (highlight.js library),
Greg Franko [ctb, cph] (tocify library),
John MacFarlane [ctb, cph] (Pandoc templates),
Google, Inc. [ctb, cph] (ioslides library),
Dave Raggett [ctb] (slidy library),
W3C [cph] (slidy library),
Dave Gandy [ctb, cph] (Font-Awesome),
Ben Sperry [ctb] (Ionicons),
Drifty [cph] (Ionicons),
Aidan Lister [ctb, cph] (jQuery StickyTabs),
Benct Philip Jonsson [ctb, cph] (pagebreak Lua filter),
Albert Krewinkel [ctb, cph] (pagebreak Lua filter)
Maintainer: Yihui Xie <xie@yihui.name>
Diff between rmarkdown versions 2.4 dated 2020-09-30 and 2.5 dated 2020-10-21
DESCRIPTION | 14 - MD5 | 54 ++-- NAMESPACE | 1 NEWS.md | 22 + R/draft.R | 4 R/github_document.R | 34 ++- R/html_dependencies.R | 13 - R/html_document.R | 8 R/html_paged.R | 2 R/html_resource_copy.R | 2 R/html_resources.R | 10 R/ioslides_presentation.R | 2 R/jupyter.R | 5 R/output_format.R | 2 R/pandoc.R | 42 +++ R/render.R | 33 +- R/render_site.R | 6 R/shiny.R | 6 R/shiny_prerendered.R | 8 R/util.R | 27 +- inst/doc/lua-filters.html | 313 ++++++++++++---------------- inst/doc/rmarkdown.html | 49 +++- inst/rmd/h/anchor-sections |only inst/rmd/h/default.html | 5 inst/rmd/ioslides/ioslides_presentation.lua | 4 man/html_document.Rd | 3 man/pandoc_args.Rd | 11 man/render.Rd | 2 28 files changed, 392 insertions(+), 290 deletions(-)
Title: Random Subspace Ensemble Classification
Description: We propose a flexible ensemble classification framework, RaSE algorithm, for the sparse classification problem. In RaSE algorithm, for each weak learner, some random subspaces are generated and the optimal one is chosen to train the model on the basis of some criterion. To be adapted to the problem, a novel criterion, ratio information criterion (RIC) is put up with based on Kullback-Leibler divergence. Besides minimizing RIC, multiple criteria can be applied, for instance, minimizing extended Bayesian information criterion (eBIC), minimizing training error, minimizing the validation error, minimizing the cross-validation error, minimizing leave-one-out error. And the choices of base classifiers are also various, for instance, linear discriminant analysis, quadratic discriminant analysis, k-nearest neighbor, logistic regression, decision trees, random forest, support vector machines. RaSE algorithm can also be applied to do feature ranking, providing us the importance of each feature based on the selected percentage in multiple subspaces. In addition, to relax the requirement of the number of random subspaces to be generated, we propose an iterative version of RaSE, which is shown to be effective under many sparse binary classification settings.
Author: Ye Tian [aut, cre] and Yang Feng [aut]
Maintainer: Ye Tian <ye.t@columbia.edu>
Diff between RaSEn versions 1.0.0 dated 2020-06-12 and 1.1.0 dated 2020-10-21
RaSEn-1.0.0/RaSEn/vignettes/RaSEn-demo.html |only RaSEn-1.0.0/RaSEn/vignettes/RaSEn-demo.md |only RaSEn-1.1.0/RaSEn/DESCRIPTION | 10 +- RaSEn-1.1.0/RaSEn/MD5 | 28 +++---- RaSEn-1.1.0/RaSEn/NAMESPACE | 1 RaSEn-1.1.0/RaSEn/R/RaModel.R | 35 ++++++--- RaSEn-1.1.0/RaSEn/R/RaSubset.R | 87 ++++++++++++++++------ RaSEn-1.1.0/RaSEn/R/Rase.R | 108 +++++++++++++++++----------- RaSEn-1.1.0/RaSEn/R/funcs.R | 3 RaSEn-1.1.0/RaSEn/inst/doc/RaSEn-demo.R | 8 +- RaSEn-1.1.0/RaSEn/inst/doc/RaSEn-demo.Rmd | 18 +++- RaSEn-1.1.0/RaSEn/inst/doc/RaSEn-demo.pdf |binary RaSEn-1.1.0/RaSEn/man/RaModel.Rd | 13 ++- RaSEn-1.1.0/RaSEn/man/Rase.Rd | 24 ++++-- RaSEn-1.1.0/RaSEn/vignettes/RaSEn-demo.Rmd | 18 +++- RaSEn-1.1.0/RaSEn/vignettes/reference.bib | 5 - 16 files changed, 239 insertions(+), 119 deletions(-)
Title: Penalized Regression with Inferred Seasonality Module -
Forecasting Unemployment Initial Claims using 'Google Trends'
Data
Description: Implements Penalized Regression with Inferred Seasonality Module (PRISM) to generate forecast estimation of weekly unemployment initial claims using 'Google Trends' data. It includes required data and tools for backtesting the performance in 2007-2020.
Author: Dingdong Yi [aut, cre],
Samuel Kou [aut],
Shaoyang Ning [aut]
Maintainer: Dingdong Yi <ryan.ddyi@gmail.com>
Diff between PRISM.forecast versions 0.2.0 dated 2020-04-22 and 0.2.1 dated 2020-10-21
DESCRIPTION | 8 +- MD5 | 43 ++++++++++-- R/back_test.R | 2 R/prism.R | 4 - R/prism_batch.R | 4 - inst/extdata/ICNSA.csv | 121 +++++++++++++++++++++++------------- inst/extdata/search_data_5year/1721 |only man/back_test.Rd | 15 +++- man/prism.Rd | 18 ++++- man/prism_batch.Rd | 18 ++++- man/var_generator.Rd | 10 ++ 11 files changed, 171 insertions(+), 72 deletions(-)
More information about PRISM.forecast at CRAN
Permanent link
Title: Compute the Coefficient of Determination for Vector or Matrix
Outcomes
Description: Compute the coefficient of determination for outcomes in n-dimensions.
May be useful for multidimensional predictions (such as a multinomial model) or
calculating goodness of fit from latent variable models such as probabilistic
topic models like latent Dirichlet allocation or deterministic topic models
like latent semantic analysis. Based on Jones (2019) <arXiv:1911.11061>.
Author: Tommy Jones [aut, cre]
Maintainer: Tommy Jones <jones.thos.w@gmail.com>
Diff between mvrsquared versions 0.1.0 dated 2020-06-25 and 0.1.1 dated 2020-10-21
DESCRIPTION | 8 +- MD5 | 14 ++-- NEWS.md | 5 + R/calc_rsquared.R | 5 + build/vignette.rds |binary inst/doc/getting_started_with_mvrsquared.html | 78 ++++++++++++++++++++++++-- man/calc_rsquared.Rd | 7 ++ tests/testthat/test-mvrsquared.R | 6 +- 8 files changed, 105 insertions(+), 18 deletions(-)
Title: Multivariate Autoregressive State-Space Modeling
Description: The MARSS package provides maximum-likelihood parameter estimation for constrained and unconstrained linear multivariate autoregressive state-space (MARSS) models fit to multivariate time-series data. Fitting is primarily via an Expectation-Maximization (EM) algorithm, although fitting via the BFGS algorithm (using the optim function) is also provided. MARSS models are a class of dynamic linear model (DLM) and vector autoregressive model (VAR) model. Functions are provided for parametric and innovations bootstrapping, Kalman filtering and smoothing, bootstrap model selection criteria (AICb), confidences intervals via the Hessian approximation and via bootstrapping and calculation of auxiliary residuals for detecting outliers and shocks. The user guide shows examples of using MARSS for parameter estimation for a variety of applications, model selection, dynamic factor analysis, outlier and shock detection, and addition of covariates. Type RShowDoc("UserGuide", package="MARSS") at the R command line to open the MARSS user guide. Online workshops (lectures and computer labs) at <https://nwfsc-timeseries.github.io/> See the NEWS file for update information.
Author: Eli Holmes, Eric Ward, Mark Scheuerell, and Kellie Wills, NOAA, Seattle, USA
Maintainer: Elizabeth Holmes - NOAA Federal <eli.holmes@noaa.gov>
Diff between MARSS versions 3.11.1 dated 2020-08-27 and 3.11.3 dated 2020-10-21
MARSS-3.11.1/MARSS/R/plot.marssMLE.R |only MARSS-3.11.1/MARSS/inst/WORDLIST |only MARSS-3.11.3/MARSS/DESCRIPTION | 12 MARSS-3.11.3/MARSS/MD5 | 252 ++--- MARSS-3.11.3/MARSS/NEWS.md | 94 + MARSS-3.11.3/MARSS/R/MARSS.R | 194 ++- MARSS-3.11.3/MARSS/R/MARSS_dfa.r | 5 MARSS-3.11.3/MARSS/R/MARSS_marss.R | 10 MARSS-3.11.3/MARSS/R/MARSS_marxss.R | 25 MARSS-3.11.3/MARSS/R/MARSSharveyobsFI.R | 3 MARSS-3.11.3/MARSS/R/MARSShatyt.r | 36 MARSS-3.11.3/MARSS/R/MARSShessian.R | 13 MARSS-3.11.3/MARSS/R/MARSSinfo.R | 28 MARSS-3.11.3/MARSS/R/MARSSinits.R | 2 MARSS-3.11.3/MARSS/R/MARSSkf.r | 17 MARSS-3.11.3/MARSS/R/MARSSkfas.r | 88 + MARSS-3.11.3/MARSS/R/MARSSkfss.R | 298 +++--- MARSS-3.11.3/MARSS/R/MARSSoptim.r | 13 MARSS-3.11.3/MARSS/R/MARSSparamCIs.R | 12 MARSS-3.11.3/MARSS/R/MARSSresiduals.R | 15 MARSS-3.11.3/MARSS/R/MARSSresiduals.tT.R | 73 - MARSS-3.11.3/MARSS/R/MARSSresiduals_tt.R | 100 +- MARSS-3.11.3/MARSS/R/MARSSresiduals_tt1.R | 132 +- MARSS-3.11.3/MARSS/R/MARSSsimulate.R | 2 MARSS-3.11.3/MARSS/R/accuracy_marssMLE.R | 102 +- MARSS-3.11.3/MARSS/R/autoplot_marssMLE.R | 57 - MARSS-3.11.3/MARSS/R/autoplot_marssPredict.R | 142 +- MARSS-3.11.3/MARSS/R/checkMARSSInputs.r | 4 MARSS-3.11.3/MARSS/R/coef_marssMLE.r | 23 MARSS-3.11.3/MARSS/R/fitted_marssMLE.r | 151 +-- MARSS-3.11.3/MARSS/R/forecast_marssMLE.R | 197 ++- MARSS-3.11.3/MARSS/R/glance_marssMLE.R | 4 MARSS-3.11.3/MARSS/R/is_marssMODEL.R | 10 MARSS-3.11.3/MARSS/R/logLik_marssMLE.R | 2 MARSS-3.11.3/MARSS/R/plot_marssMLE.R | 67 - MARSS-3.11.3/MARSS/R/plot_marssPredict.R | 147 +- MARSS-3.11.3/MARSS/R/predict_marssMLE.R | 74 - MARSS-3.11.3/MARSS/R/print_marssMLE.r | 678 +++++++------ MARSS-3.11.3/MARSS/R/print_marssPredict.R | 8 MARSS-3.11.3/MARSS/R/residuals_marssMLE.R | 66 - MARSS-3.11.3/MARSS/R/summary_marssMLE.R | 20 MARSS-3.11.3/MARSS/R/tidy_marssMLE.R | 50 - MARSS-3.11.3/MARSS/R/toLatex_marssMODEL.R | 2 MARSS-3.11.3/MARSS/R/tsSmooth_marssMLE.R | 91 + MARSS-3.11.3/MARSS/R/utility_functions.R | 72 - MARSS-3.11.3/MARSS/build/vignette.rds |binary MARSS-3.11.3/MARSS/inst/doc/Chapter_AnimalTracking.R | 20 MARSS-3.11.3/MARSS/inst/doc/Chapter_CombiningTrendData.R | 8 MARSS-3.11.3/MARSS/inst/doc/Chapter_Covariates.R | 41 MARSS-3.11.3/MARSS/inst/doc/Chapter_DFA.R | 61 - MARSS-3.11.3/MARSS/inst/doc/Chapter_KFAS.R | 692 ++++++++------ MARSS-3.11.3/MARSS/inst/doc/Chapter_MARp.R | 54 - MARSS-3.11.3/MARSS/inst/doc/Chapter_MLR.R | 6 MARSS-3.11.3/MARSS/inst/doc/Chapter_PVA.R | 6 MARSS-3.11.3/MARSS/inst/doc/Chapter_SealPopStructure.R | 2 MARSS-3.11.3/MARSS/inst/doc/Chapter_SealTrend.R | 6 MARSS-3.11.3/MARSS/inst/doc/Chapter_SpeciesInteractions.R | 10 MARSS-3.11.3/MARSS/inst/doc/Chapter_StructuralBreaks.R | 10 MARSS-3.11.3/MARSS/inst/doc/Chapter_Structural_TS.R | 268 +++-- MARSS-3.11.3/MARSS/inst/doc/Chapter_inits.R | 6 MARSS-3.11.3/MARSS/inst/doc/EMDerivation.Rnw | 98 + MARSS-3.11.3/MARSS/inst/doc/EMDerivation.pdf |binary MARSS-3.11.3/MARSS/inst/doc/Quick_Examples.R | 52 - MARSS-3.11.3/MARSS/inst/doc/Quick_Start.Rnw | 6 MARSS-3.11.3/MARSS/inst/doc/Quick_Start.pdf |binary MARSS-3.11.3/MARSS/inst/doc/Residuals.Rnw | 11 MARSS-3.11.3/MARSS/inst/doc/Residuals.pdf |binary MARSS-3.11.3/MARSS/inst/doc/UserGuide.pdf |binary MARSS-3.11.3/MARSS/man/CSEGriskfigure.Rd | 4 MARSS-3.11.3/MARSS/man/CSEGtmufigure.Rd | 2 MARSS-3.11.3/MARSS/man/MARSS-package.Rd | 17 MARSS-3.11.3/MARSS/man/MARSS.Rd | 45 MARSS-3.11.3/MARSS/man/MARSSFisherI.Rd | 10 MARSS-3.11.3/MARSS/man/MARSS_dfa.Rd | 4 MARSS-3.11.3/MARSS/man/MARSS_marss.Rd | 8 MARSS-3.11.3/MARSS/man/MARSS_marxss.Rd | 10 MARSS-3.11.3/MARSS/man/MARSSaic.Rd | 4 MARSS-3.11.3/MARSS/man/MARSSapplynames.Rd | 2 MARSS-3.11.3/MARSS/man/MARSSboot.Rd | 4 MARSS-3.11.3/MARSS/man/MARSSharveyobsFI.Rd | 4 MARSS-3.11.3/MARSS/man/MARSShatyt.Rd | 4 MARSS-3.11.3/MARSS/man/MARSShessian.Rd | 2 MARSS-3.11.3/MARSS/man/MARSShessian_numerical.Rd | 2 MARSS-3.11.3/MARSS/man/MARSSinfo.Rd | 2 MARSS-3.11.3/MARSS/man/MARSSinits.Rd | 2 MARSS-3.11.3/MARSS/man/MARSSinnovationsboot.Rd | 4 MARSS-3.11.3/MARSS/man/MARSSkem.Rd | 6 MARSS-3.11.3/MARSS/man/MARSSkemcheck.Rd | 2 MARSS-3.11.3/MARSS/man/MARSSkf.Rd | 68 - MARSS-3.11.3/MARSS/man/MARSSoptim.Rd | 11 MARSS-3.11.3/MARSS/man/MARSSparamCIs.Rd | 4 MARSS-3.11.3/MARSS/man/MARSSresiduals.Rd | 38 MARSS-3.11.3/MARSS/man/MARSSresiduals_tT.Rd | 50 - MARSS-3.11.3/MARSS/man/MARSSresiduals_tt1.Rd | 54 - MARSS-3.11.3/MARSS/man/MARSSresiduals_ttt.Rd | 28 MARSS-3.11.3/MARSS/man/MARSSsimulate.Rd | 2 MARSS-3.11.3/MARSS/man/MARSSvectorizeparam.Rd | 4 MARSS-3.11.3/MARSS/man/accuracy_marssMLE.Rd | 2 MARSS-3.11.3/MARSS/man/as_marssMODEL.Rd | 2 MARSS-3.11.3/MARSS/man/checkModelList.Rd | 2 MARSS-3.11.3/MARSS/man/coef_marssMLE.Rd | 6 MARSS-3.11.3/MARSS/man/describe_marssMODEL.Rd | 4 MARSS-3.11.3/MARSS/man/fitted_marssMLE.Rd | 37 MARSS-3.11.3/MARSS/man/forecast_marssMLE.Rd | 28 MARSS-3.11.3/MARSS/man/is_marssMLE.Rd | 2 MARSS-3.11.3/MARSS/man/is_marssMODEL.Rd | 2 MARSS-3.11.3/MARSS/man/ldiag.Rd | 2 MARSS-3.11.3/MARSS/man/logLik_marssMLE.Rd | 2 MARSS-3.11.3/MARSS/man/marssMLE-class.Rd | 2 MARSS-3.11.3/MARSS/man/marssMODEL-class.Rd | 2 MARSS-3.11.3/MARSS/man/marssPredict-class.Rd | 4 MARSS-3.11.3/MARSS/man/marssResiduals-class.Rd | 6 MARSS-3.11.3/MARSS/man/model_frame_marssMODEL.Rd | 2 MARSS-3.11.3/MARSS/man/plot_marssMLE.Rd | 16 MARSS-3.11.3/MARSS/man/predict_marssMLE.Rd | 36 MARSS-3.11.3/MARSS/man/print_marssMLE.Rd | 32 MARSS-3.11.3/MARSS/man/print_marssMODEL.Rd | 2 MARSS-3.11.3/MARSS/man/print_marssPredict.Rd | 2 MARSS-3.11.3/MARSS/man/residuals_marssMLE.Rd | 10 MARSS-3.11.3/MARSS/man/stdInnov.Rd | 8 MARSS-3.11.3/MARSS/man/tidy_marssMLE.Rd | 2 MARSS-3.11.3/MARSS/man/toLatex_marssMLE.Rd | 2 MARSS-3.11.3/MARSS/man/tsSmooth_marssMLE.Rd | 22 MARSS-3.11.3/MARSS/man/utility_functions.Rd | 4 MARSS-3.11.3/MARSS/man/zscore.Rd | 5 MARSS-3.11.3/MARSS/vignettes/EMDerivation.Rnw | 98 + MARSS-3.11.3/MARSS/vignettes/Quick_Start.Rnw | 6 MARSS-3.11.3/MARSS/vignettes/Residuals.Rnw | 11 128 files changed, 3057 insertions(+), 2449 deletions(-)