Title: Create Ternary Plots
Description: Plots ternary diagrams (simplex plots / Gibbs triangles) using the
standard graphics functions.
An alternative to 'ggtern', which uses the 'ggplot2' family of plotting
functions.
Includes a 'Shiny' user interface for point-and-click plotting.
Author: Martin R. Smith [aut, cre, cph]
(<https://orcid.org/0000-0001-5660-1727>),
Lilian Sanselme [ctb]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between Ternary versions 1.1.4 dated 2020-02-27 and 1.2.0 dated 2020-10-16
DESCRIPTION | 30 ++- MD5 | 85 ++++++---- NAMESPACE | 2 NEWS.md | 7 R/Contours.R | 13 + R/Coordinates.R | 6 R/Ternary-package.R | 15 + R/TernaryPlot.R | 142 ++++++++++------- R/shiny.R |only R/zzz.R | 3 README.md | 15 + build/partial.rdb |binary build/vignette.rds |binary inst/TernaryApp |only inst/WORDLIST | 8 inst/doc/Ternary.R | 157 ++++++++++--------- inst/doc/Ternary.Rmd | 165 +++++++++++--------- inst/doc/Ternary.html | 149 ++++++++++-------- man/AddToTernary.Rd | 166 ++++++++++---------- man/ColourTernary.Rd | 143 +++++++++-------- man/CoordinatesToXY.Rd | 52 +++--- man/OutsidePlot.Rd | 91 +++++------ man/ReflectedEquivalents.Rd | 96 ++++++----- man/Ternary-package.Rd | 20 +- man/TernaryApp.Rd |only man/TernaryContour.Rd | 99 ++++++------ man/TernaryCoords.Rd | 120 +++++++------- man/TernaryDensityContour.Rd | 179 +++++++++++----------- man/TernaryPlot.Rd | 95 ++++++++--- man/TernaryPointValues.Rd | 160 ++++++++++--------- man/TernaryTiles.Rd | 115 +++++++------- man/TernaryXRange.Rd | 79 ++++----- man/TriangleCentres.Rd | 89 +++++----- man/XYToTernary.Rd | 71 ++++---- man/cbPalettes.Rd | 10 + tests/figs/axis-rotate |only tests/figs/deps.txt | 2 tests/figs/ternary-plotting/axisstyle.svg | 20 +- tests/figs/ternary-plotting/colours-and-water.svg | 4 tests/testthat/Rplots.pdf |only tests/testthat/test-axis.rotate.R |only tests/testthat/test-ternary.R | 3 vignettes/Ternary.Rmd | 165 +++++++++++--------- 43 files changed, 1428 insertions(+), 1148 deletions(-)
Title: Estimate the Shattering Coefficient for a Particular Dataset
Description: The Statistical Learning Theory (SLT) provides the theoretical background to ensure that a supervised algorithm generalizes the mapping f:X -> Y given f is selected from its search space bias F. This formal result depends on the Shattering coefficient function N(F,2n) to upper bound the empirical risk minimization principle, from which one can estimate the necessary training sample size to ensure the probabilistic learning convergence and, most importantly, the characterization of the capacity of F, including its under and overfitting abilities while addressing specific target problems. In this context, we propose a new approach to estimate the maximal number of hyperplanes required to shatter a given sample, i.e., to separate every pair of points from one another, based on the recent contributions by Har-Peled and Jones in the dataset partitioning scenario, and use such foundation to analytically compute the Shattering coefficient function for both binary and multi-class problems. As main contributions, one can use our approach to study the complexity of the search space bias F, estimate training sample sizes, and parametrize the number of hyperplanes a learning algorithm needs to address some supervised task, what is specially appealing to deep neural networks. Reference: de Mello, R.F. (2019) "On the Shattering Coefficient of Supervised Learning Algorithms" <arXiv:1911.05461>; de Mello, R.F., Ponti, M.A. (2018, ISBN: 978-3319949888) "Machine Learning: A Practical Approach on the Statistical Learning Theory".
Author: Rodrigo F. de Mello [aut, cre]
(<https://orcid.org/0000-0002-0435-3992>)
Maintainer: Rodrigo F. de Mello <mello@icmc.usp.br>
Diff between shattering versions 1.0.2 dated 2020-10-10 and 1.0.3 dated 2020-10-16
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/complexity_analysis.R | 9 ++++++--- 3 files changed, 12 insertions(+), 9 deletions(-)
Title: Randomization Tests
Description: A collection of randomization tests, data sets and examples. The current version focuses on four testing problems and their implementation in empirical work. First, it facilitates the empirical researcher to test for particular hypotheses, such as comparisons of means, medians, and variances from k populations using robust permutation tests, which asymptotic validity holds under very weak assumptions, while retaining the exact rejection probability in finite samples when the underlying distributions are identical. Second, the description and implementation of a permutation test for testing the continuity assumption of the baseline covariates in the sharp regression discontinuity design (RDD) as in Canay and Kamat (2018) <https://goo.gl/UZFqt7>. More specifically, it allows the user to select a set of covariates and test the aforementioned hypothesis using a permutation test based on the Cramer-von Miss test statistic. Graphical inspection of the empirical CDF and histograms for the variables of interest is also supported in the package. Third, it provides the practitioner with an effortless implementation of a permutation test based on the martingale decomposition of the empirical process for testing for heterogeneous treatment effects in the presence of an estimated nuisance parameter as in Chung and Olivares (2020) <https://rb.gy/dwbbyx>. Lastly, this version considers the two-sample goodness-of-fit testing problem under covariate adaptive randomization and implements a permutation test based on a prepivoted Kolmogorov-Smirnov test statistic.
Author: Mauricio Olivares [aut, cre],
Ignacio Sarmiento-Barbieri [aut]
Maintainer: Mauricio Olivares <maurice.olivares@gmail.com>
Diff between RATest versions 0.1.7 dated 2020-01-24 and 0.1.8 dated 2020-10-16
DESCRIPTION | 13 ++++--- MD5 | 60 ++++++++++++++++++----------------- NAMESPACE | 4 ++ R/CvM.stat.R | 4 +- R/H.cdf.R | 4 +- R/PT.Khmaladze.MultTest.R | 2 - R/PT.Khmaladze.fit.R | 39 ++-------------------- R/RDperm.R | 10 ++--- R/RPT.R | 2 - R/group.action.R | 2 - R/plot.RDperm.R | 4 +- R/prepivot.ks.permtest.R |only R/randomization.test.R | 12 ++++--- R/summary.prepivot.ks.permtest.R |only build/vignette.rds |binary inst/doc/RDperm.R | 10 ++--- inst/doc/RDperm.pdf |binary man/CvM.stat.Rd | 4 +- man/H.cdf.Rd | 4 +- man/PT.Khmaladze.MultTest.Rd | 12 +++++-- man/PT.Khmaladze.fit.Rd | 10 ++--- man/RDperm.Rd | 21 ++++++++---- man/RPT.Rd | 12 +++++-- man/group.action.Rd | 2 - man/lee2008.Rd | 6 ++- man/plot.RDperm.Rd | 4 +- man/prepivot.ks.permtest.Rd |only man/randomization.test.Rd | 10 ++++- man/summary.PT.Khmaladze.MultTest.Rd | 3 - man/summary.PT.Khmaladze.fit.Rd | 3 - man/summary.RDperm.Rd | 3 - man/summary.RPT.Rd | 3 - man/summary.prepivot.ks.permtest.Rd |only 33 files changed, 133 insertions(+), 130 deletions(-)
Title: Fisher's z-Tests Concerning Difference of Correlations
Description: Computations of Fisher's z-tests concerning differences between correlations. diffcor.one() could be used to test for differences regarding an expected value, e.g., in construct validation. diffcor.two() may be useful in replication studies, to test if the original study and the replication study differed in terms of effects. diffcor.dep() can be applied to check if the correlation between one construct with another one (r12) is significantly different/higher/smaller than the correlation of one of the constructs with a third construct (r13), given the correlation of the constructs that are compared (r23). The outputs for all the three functions provide the test statistic in z-units, p-values, and alpha levels that were corrected in terms of multiple testing according to Bonferroni (if you did not set bonferroni = FALSE). To help interpret the output, the procedure prompts if a single p value is smaller than the corrected alpha. For diffcor.one() and diffcor.two(), the effect size Cohens q is additionally provided. It is a descriptive index to evaluate differences of independent correlations. Cohen (1988) suggested q = |.10|, |.30| and |.50| as small, moderate, and large differences.
Author: Christian Blötner
Maintainer: Christian Blötner <c.bloetner@gmail.com>
Diff between diffcor versions 0.4.0 dated 2020-09-19 and 0.6.2 dated 2020-10-16
DESCRIPTION | 9 +++---- MD5 | 6 ++-- R/source_code_diffcor.R | 61 +++++++++++++++++++++++++++++++++--------------- man/diffcor.Rd | 49 +++++++++++++++++++++++++------------- 4 files changed, 82 insertions(+), 43 deletions(-)
Title: Produce Descriptive and Comparative Tables Easily
Description: Easily create descriptive and comparative tables.
It makes use and integrates directly with the tidyverse family of packages, and pipes.
Tables are produced as data frames/lists of data frames for easy manipulation after creation,
and ready to be saved as csv, or piped to DT::datatable() or pander::pander() to integrate into reports.
Author: Maxime Wack [aut, cre],
Adrien Boukobza [aut],
Yihui Xie [ctb]
Maintainer: Maxime Wack <maximewack@free.fr>
Diff between desctable versions 0.1.7 dated 2020-02-03 and 0.1.9 dated 2020-10-16
DESCRIPTION | 20 MD5 | 45 - NAMESPACE | 3 NEWS | 11 R/build.R | 170 ++--- R/convenience_functions.R | 81 +- R/imports.R | 2 R/output.R | 53 - R/stats.R | 123 +-- R/tests.R | 79 +- R/utils.R | 200 +++-- README.md | 823 +++++++++++------------- build/vignette.rds |binary inst/doc/desctable.R | 2 inst/doc/desctable.Rmd | 6 inst/doc/desctable.html | 1528 ++++++++++++++++++++++++++------------------- man/datatable.Rd | 17 man/insert.Rd | 7 man/pander.desctable.Rd | 2 man/reexports.Rd | 5 man/set_desctable_class.Rd |only man/statColumn.Rd | 7 man/statTable.Rd | 4 vignettes/desctable.Rmd | 6 24 files changed, 1716 insertions(+), 1478 deletions(-)
Title: Inspect, Read, Edit and Run 'APSIM' "Next Generation" and
'APSIM' Classic
Description: The functions in this package inspect, read, edit and run files for 'APSIM' "Next Generation" ('JSON')
and 'APSIM' "Classic" ('XML'). The files with an 'apsim' extension correspond to
'APSIM' Classic (7.x) - Windows only - and the ones with an 'apsimx' extension correspond to 'APSIM' "Next Generation".
For more information about 'APSIM' see (<https://www.apsim.info/>) and for 'APSIM'
next generation (<https://apsimnextgeneration.netlify.app/>).
Author: Fernando Miguez [aut, cre] (<https://orcid.org/0000-0002-4627-8329>)
Maintainer: Fernando Miguez <femiguez@iastate.edu>
Diff between apsimx versions 1.946 dated 2020-07-09 and 1.964 dated 2020-10-16
apsimx-1.946/apsimx/inst/extdata/MaizeSoybean.db |only apsimx-1.946/apsimx/inst/extdata/ames-10-19.met |only apsimx-1.964/apsimx/DESCRIPTION | 15 apsimx-1.964/apsimx/MD5 | 102 ++++-- apsimx-1.964/apsimx/NAMESPACE | 20 + apsimx-1.964/apsimx/R/apsim_classic.R | 59 ++- apsimx-1.964/apsimx/R/apsimx.R | 5 apsimx-1.964/apsimx/R/apsimx_soil_profile.R | 2 apsimx-1.964/apsimx/R/compare_apsim_met.R |only apsimx-1.964/apsimx/R/data-doc.R |only apsimx-1.964/apsimx/R/edit_apsim.R | 21 + apsimx-1.964/apsimx/R/edit_apsim_xml.R | 18 - apsimx-1.964/apsimx/R/edit_apsimx_json.R | 136 +++++++- apsimx-1.964/apsimx/R/edit_apsimx_replacement.R | 4 apsimx-1.964/apsimx/R/get_gsod_apsim_met.R |only apsimx-1.964/apsimx/R/get_iemre_apsim_met.R | 7 apsimx-1.964/apsimx/R/get_power_apsim_met.R | 4 apsimx-1.964/apsimx/R/inspect_apsim_xml.R | 160 +++++++++ apsimx-1.964/apsimx/R/inspect_apsimx_json.R | 60 +++ apsimx-1.964/apsimx/R/inspect_apsimx_replacement.R | 26 - apsimx-1.964/apsimx/R/optim_apsim.R |only apsimx-1.964/apsimx/R/optim_apsimx.R |only apsimx-1.964/apsimx/README.md | 7 apsimx-1.964/apsimx/build/vignette.rds |binary apsimx-1.964/apsimx/data |only apsimx-1.964/apsimx/inst/doc/apsimx-scripts.Rmd | 2 apsimx-1.964/apsimx/inst/doc/apsimx-scripts.html | 8 apsimx-1.964/apsimx/inst/doc/apsimx.R | 8 apsimx-1.964/apsimx/inst/doc/apsimx.Rmd | 52 +-- apsimx-1.964/apsimx/inst/doc/apsimx.html | 241 +++++++-------- apsimx-1.964/apsimx/inst/doc/optim-apsim.R |only apsimx-1.964/apsimx/inst/doc/optim-apsim.Rmd |only apsimx-1.964/apsimx/inst/doc/optim-apsim.html |only apsimx-1.964/apsimx/inst/extdata/MaizeSoybean.apsimx | 172 ++++++++-- apsimx-1.964/apsimx/inst/extdata/Wheat-opt-ex.apsimx |only apsimx-1.964/apsimx/inst/extdata/maize-manager-folder.db |only apsimx-1.964/apsimx/inst/extdata/wheat-sim-b4-opt.csv |only apsimx-1.964/apsimx/inst/extdata/wheat-sim-opt.csv |only apsimx-1.964/apsimx/man/apsim.Rd | 8 apsimx-1.964/apsimx/man/compare_apsim_met.Rd |only apsimx-1.964/apsimx/man/edit_apsim.Rd | 3 apsimx-1.964/apsimx/man/edit_apsim_xml.Rd | 18 - apsimx-1.964/apsimx/man/edit_apsimx.Rd | 2 apsimx-1.964/apsimx/man/extract_values_apsimx.Rd |only apsimx-1.964/apsimx/man/get_gsod_apsim_met.Rd |only apsimx-1.964/apsimx/man/get_power_apsim_met.Rd | 2 apsimx-1.964/apsimx/man/inspect_apsim.Rd | 21 + apsimx-1.964/apsimx/man/inspect_apsim_xml.Rd |only apsimx-1.964/apsimx/man/inspect_apsimx.Rd | 6 apsimx-1.964/apsimx/man/inspect_apsimx_replacement.Rd | 2 apsimx-1.964/apsimx/man/mcmc.apsim.env.Rd |only apsimx-1.964/apsimx/man/mcmc.apsimx.env.Rd |only apsimx-1.964/apsimx/man/obsWheat.Rd |only apsimx-1.964/apsimx/man/optim_apsim.Rd |only apsimx-1.964/apsimx/man/optim_apsimx.Rd |only apsimx-1.964/apsimx/man/read_apsim_all.Rd | 5 apsimx-1.964/apsimx/man/view_apsim_xml.Rd |only apsimx-1.964/apsimx/man/wop.Rd |only apsimx-1.964/apsimx/man/wop.h.Rd |only apsimx-1.964/apsimx/tests/test_edit.R | 6 apsimx-1.964/apsimx/tests/test_extract_values_apsimx.R |only apsimx-1.964/apsimx/tests/test_inspect.R | 21 + apsimx-1.964/apsimx/tests/test_inspect_apsim_factorial.R |only apsimx-1.964/apsimx/tests/test_optim_apsimx.R |only apsimx-1.964/apsimx/vignettes/apsimx-scripts.Rmd | 2 apsimx-1.964/apsimx/vignettes/apsimx.Rmd | 52 +-- apsimx-1.964/apsimx/vignettes/optim-apsim.Rmd |only 67 files changed, 927 insertions(+), 350 deletions(-)
Title: Succinct and Correct Statistical Summaries for Reports
Description: Succinctly and correctly format statistical summaries of
various models and tests (F-test, Chi-Sq-test, Fisher-test, T-test, and rank-significance).
This package also includes empirical tests, such as Monte Carlo and bootstrap distribution estimates.
Author: John Mount [aut, cre],
Nina Zumel [aut],
Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>
Diff between sigr versions 1.1.2 dated 2020-10-01 and 1.1.3 dated 2020-10-16
sigr-1.1.2/sigr/R/run_sigr_tests.R |only sigr-1.1.2/sigr/inst/unit_tests |only sigr-1.1.2/sigr/man/find_ROC_matching_ab.Rd |only sigr-1.1.2/sigr/man/find_ROC_matching_ab1.Rd |only sigr-1.1.2/sigr/man/run_sigr_tests.Rd |only sigr-1.1.2/sigr/tests/package_test_runner.R |only sigr-1.1.3/sigr/DESCRIPTION | 16 +-- sigr-1.1.3/sigr/MD5 | 30 +++--- sigr-1.1.3/sigr/NAMESPACE | 3 sigr-1.1.3/sigr/NEWS.md | 6 + sigr-1.1.3/sigr/R/ROC.R | 44 +++++++-- sigr-1.1.3/sigr/inst/doc/lmExample.html | 76 ++++++++++++++++- sigr-1.1.3/sigr/inst/doc/sigrFormatting.html | 76 ++++++++++++++++- sigr-1.1.3/sigr/inst/tinytest |only sigr-1.1.3/sigr/man/find_AUC_q.Rd | 11 ++ sigr-1.1.3/sigr/man/find_area_q.Rd | 6 + sigr-1.1.3/sigr/man/find_matching_a1_1b.Rd |only sigr-1.1.3/sigr/man/find_matching_conditional_betas.Rd |only sigr-1.1.3/sigr/tests/tinytest.R |only 19 files changed, 224 insertions(+), 44 deletions(-)
Title: Sparse and Dense Multidimensional Array Storage Engine for Data
Science
Description: The data science storage engine 'TileDB' introduces a
powerful on-disk format for multi-dimensional arrays. It supports
dense and sparse arrays, dataframes and key-values stores, cloud
storage ('S3', 'GCS', 'Azure'), chunked arrays, multiple compression,
encryption and checksum filters, uses a fully multi-threaded
implementation, supports parallel I/O, data versioning ('time
travel'), metadata and groups. It is implemented as an embeddable
cross-platform C++ library with APIs from several languages, and
integrations.
Author: TileDB, Inc.
Maintainer: Dirk Eddelbuettel <dirk@tiledb.com>
Diff between tiledb versions 0.8.1 dated 2020-10-08 and 0.8.2 dated 2020-10-16
DESCRIPTION | 6 +- MD5 | 35 ++++++++--------- NAMESPACE | 2 R/Config.R | 91 +++++++++++++++++++++++++-------------------- R/RcppExports.R | 4 + R/Stats.R | 17 +++++++- build/vignette.rds |binary inst/NEWS.md | 17 ++++++++ inst/doc/introduction.html | 5 +- man/limitTileDBCores.Rd | 9 +++- man/tiledb_config.Rd | 7 ++- man/tiledb_stats_dump.Rd | 3 + man/tiledb_stats_reset.Rd |only src/Makevars.win | 2 src/RcppExports.cpp | 10 ++++ src/libtiledb.cpp | 5 ++ tools/fetchTileDBLib.R | 8 ++- tools/fetchTileDBSrc.R | 5 +- tools/winlibs.R | 3 + 19 files changed, 157 insertions(+), 72 deletions(-)
Title: Create Interactive Graphs with 'Echarts JavaScript' Version 4
Description: Easily create interactive charts by leveraging the 'Echarts Javascript' library which includes
36 chart types, themes, 'Shiny' proxies and animations.
Author: John Coene [aut, cre, cph],
Wei Su [ctb]
Maintainer: John Coene <jcoenep@gmail.com>
Diff between echarts4r versions 0.3.2 dated 2020-06-18 and 0.3.3 dated 2020-10-16
echarts4r-0.3.2/echarts4r/man/e_facet.Rd |only echarts4r-0.3.3/echarts4r/DESCRIPTION | 26 echarts4r-0.3.3/echarts4r/MD5 | 298 echarts4r-0.3.3/echarts4r/NAMESPACE | 4 echarts4r-0.3.3/echarts4r/NEWS.md | 26 echarts4r-0.3.3/echarts4r/R/actions.R | 471 - echarts4r-0.3.3/echarts4r/R/add.R | 3662 +++++----- echarts4r-0.3.3/echarts4r/R/add_.R | 2006 ++--- echarts4r-0.3.3/echarts4r/R/append.R | 245 echarts4r-0.3.3/echarts4r/R/boxes.R |only echarts4r-0.3.3/echarts4r/R/button.R | 40 echarts4r-0.3.3/echarts4r/R/calendar.R | 49 echarts4r-0.3.3/echarts4r/R/callbacks.R | 53 echarts4r-0.3.3/echarts4r/R/color.R | 40 echarts4r-0.3.3/echarts4r/R/echarts4r.R | 300 echarts4r-0.3.3/echarts4r/R/facets.R | 60 echarts4r-0.3.3/echarts4r/R/general.R | 10 echarts4r-0.3.3/echarts4r/R/geo.R | 133 echarts4r-0.3.3/echarts4r/R/globe.R | 56 echarts4r-0.3.3/echarts4r/R/graphic.R | 147 echarts4r-0.3.3/echarts4r/R/grid.R | 688 + echarts4r-0.3.3/echarts4r/R/grid3d.R | 168 echarts4r-0.3.3/echarts4r/R/group2series.R | 48 echarts4r-0.3.3/echarts4r/R/helpers.R | 323 echarts4r-0.3.3/echarts4r/R/leaflet.R | 55 echarts4r-0.3.3/echarts4r/R/loading.R | 58 echarts4r-0.3.3/echarts4r/R/map.R | 357 echarts4r-0.3.3/echarts4r/R/mark.R | 213 echarts4r-0.3.3/echarts4r/R/nesting.R | 85 echarts4r-0.3.3/echarts4r/R/opts.R | 900 +- echarts4r-0.3.3/echarts4r/R/plugins.R | 165 echarts4r-0.3.3/echarts4r/R/proxies.R | 657 - echarts4r-0.3.3/echarts4r/R/themes.R | 55 echarts4r-0.3.3/echarts4r/R/timeline.R | 112 echarts4r-0.3.3/echarts4r/R/utils.R | 636 - echarts4r-0.3.3/echarts4r/R/zzz.R | 7 echarts4r-0.3.3/echarts4r/README.md | 27 echarts4r-0.3.3/echarts4r/inst/box |only echarts4r-0.3.3/echarts4r/inst/htmlwidgets/echarts4r.js | 20 echarts4r-0.3.3/echarts4r/inst/htmlwidgets/lib/echarts-4.8.0/echarts-en.min.js | 2 echarts4r-0.3.3/echarts4r/inst/htmlwidgets/lib/mapbox/mapbox-gl.css | 330 echarts4r-0.3.3/echarts4r/inst/htmlwidgets/lib/mapbox/mapbox-gl.js | 490 - echarts4r-0.3.3/echarts4r/man/angle_axis.Rd | 27 echarts4r-0.3.3/echarts4r/man/append.Rd | 91 echarts4r-0.3.3/echarts4r/man/axis.Rd | 42 echarts4r-0.3.3/echarts4r/man/axis3d.Rd | 31 echarts4r-0.3.3/echarts4r/man/band.Rd | 13 echarts4r-0.3.3/echarts4r/man/callbacks.Rd | 9 echarts4r-0.3.3/echarts4r/man/connections.Rd | 30 echarts4r-0.3.3/echarts4r/man/e-tooltip.Rd | 31 echarts4r-0.3.3/echarts4r/man/e_add.Rd | 41 echarts4r-0.3.3/echarts4r/man/e_animation.Rd | 11 echarts4r-0.3.3/echarts4r/man/e_area.Rd | 21 echarts4r-0.3.3/echarts4r/man/e_aria.Rd | 10 echarts4r-0.3.3/echarts4r/man/e_axis_labels.Rd | 17 echarts4r-0.3.3/echarts4r/man/e_axis_pointer.Rd | 2 echarts4r-0.3.3/echarts4r/man/e_axis_stagger.Rd | 15 echarts4r-0.3.3/echarts4r/man/e_bar.Rd | 13 echarts4r-0.3.3/echarts4r/man/e_bar_3d.Rd | 70 echarts4r-0.3.3/echarts4r/man/e_boxplot.Rd | 9 echarts4r-0.3.3/echarts4r/man/e_brush.Rd | 25 echarts4r-0.3.3/echarts4r/man/e_button.Rd | 15 echarts4r-0.3.3/echarts4r/man/e_calendar.Rd | 19 echarts4r-0.3.3/echarts4r/man/e_candle.Rd | 17 echarts4r-0.3.3/echarts4r/man/e_capture.Rd | 19 echarts4r-0.3.3/echarts4r/man/e_cloud.Rd | 15 echarts4r-0.3.3/echarts4r/man/e_color.Rd | 15 echarts4r-0.3.3/echarts4r/man/e_color_range.Rd | 1 echarts4r-0.3.3/echarts4r/man/e_correlations.Rd | 13 echarts4r-0.3.3/echarts4r/man/e_country_names.Rd | 6 echarts4r-0.3.3/echarts4r/man/e_datazoom.Rd | 19 echarts4r-0.3.3/echarts4r/man/e_dispatch_action_p.Rd | 54 echarts4r-0.3.3/echarts4r/man/e_draft.Rd | 7 echarts4r-0.3.3/echarts4r/man/e_draw_p.Rd | 19 echarts4r-0.3.3/echarts4r/man/e_flip_coords.Rd | 11 echarts4r-0.3.3/echarts4r/man/e_flow_gl.Rd | 45 echarts4r-0.3.3/echarts4r/man/e_funnel.Rd | 7 echarts4r-0.3.3/echarts4r/man/e_gauge.Rd | 5 echarts4r-0.3.3/echarts4r/man/e_geo.Rd | 27 echarts4r-0.3.3/echarts4r/man/e_geo_3d.Rd | 23 echarts4r-0.3.3/echarts4r/man/e_get_data.Rd | 13 echarts4r-0.3.3/echarts4r/man/e_globe.Rd | 18 echarts4r-0.3.3/echarts4r/man/e_grid.Rd | 15 echarts4r-0.3.3/echarts4r/man/e_grid_3d.Rd | 27 echarts4r-0.3.3/echarts4r/man/e_heatmap.Rd | 77 echarts4r-0.3.3/echarts4r/man/e_hide_grid_lines.Rd | 9 echarts4r-0.3.3/echarts4r/man/e_labels.Rd | 33 echarts4r-0.3.3/echarts4r/man/e_legend.Rd | 15 echarts4r-0.3.3/echarts4r/man/e_line.Rd | 23 echarts4r-0.3.3/echarts4r/man/e_lines.Rd | 46 echarts4r-0.3.3/echarts4r/man/e_lines_gl.Rd | 2 echarts4r-0.3.3/echarts4r/man/e_liquid.Rd | 9 echarts4r-0.3.3/echarts4r/man/e_list.Rd | 5 echarts4r-0.3.3/echarts4r/man/e_map_register.Rd | 8 echarts4r-0.3.3/echarts4r/man/e_modularity.Rd | 13 echarts4r-0.3.3/echarts4r/man/e_parallel.Rd | 9 echarts4r-0.3.3/echarts4r/man/e_pictorial.Rd | 62 echarts4r-0.3.3/echarts4r/man/e_pie.Rd | 19 echarts4r-0.3.3/echarts4r/man/e_polar.Rd | 15 echarts4r-0.3.3/echarts4r/man/e_radar.Rd | 13 echarts4r-0.3.3/echarts4r/man/e_radar_opts.Rd | 5 echarts4r-0.3.3/echarts4r/man/e_remove.Rd | 23 echarts4r-0.3.3/echarts4r/man/e_restore.Rd | 13 echarts4r-0.3.3/echarts4r/man/e_river.Rd | 11 echarts4r-0.3.3/echarts4r/man/e_sankey.Rd | 9 echarts4r-0.3.3/echarts4r/man/e_scatter_3d.Rd | 57 echarts4r-0.3.3/echarts4r/man/e_scatter_gl.Rd | 27 echarts4r-0.3.3/echarts4r/man/e_single_axis.Rd | 11 echarts4r-0.3.3/echarts4r/man/e_step.Rd | 25 echarts4r-0.3.3/echarts4r/man/e_sunburst.Rd | 122 echarts4r-0.3.3/echarts4r/man/e_surface.Rd | 9 echarts4r-0.3.3/echarts4r/man/e_text_style.Rd | 11 echarts4r-0.3.3/echarts4r/man/e_title.Rd | 13 echarts4r-0.3.3/echarts4r/man/e_tree.Rd | 38 echarts4r-0.3.3/echarts4r/man/e_treemap.Rd | 57 echarts4r-0.3.3/echarts4r/man/e_utc.Rd | 2 echarts4r-0.3.3/echarts4r/man/e_visual_map.Rd | 47 echarts4r-0.3.3/echarts4r/man/e_visual_map_range.Rd | 13 echarts4r-0.3.3/echarts4r/man/e_zoom.Rd | 13 echarts4r-0.3.3/echarts4r/man/echarts4r-shiny.Rd | 2 echarts4r-0.3.3/echarts4r/man/echarts4rBox.Rd |only echarts4r-0.3.3/echarts4r/man/echarts4rBoxOutput.Rd |only echarts4r-0.3.3/echarts4r/man/echartsNJSON.Rd | 23 echarts4r-0.3.3/echarts4r/man/errorbar.Rd | 19 echarts4r-0.3.3/echarts4r/man/formatters.Rd | 13 echarts4r-0.3.3/echarts4r/man/graph.Rd | 15 echarts4r-0.3.3/echarts4r/man/graph_action.Rd | 11 echarts4r-0.3.3/echarts4r/man/graphic.Rd | 7 echarts4r-0.3.3/echarts4r/man/highlight_action.Rd | 13 echarts4r-0.3.3/echarts4r/man/highlight_proxy.Rd | 116 echarts4r-0.3.3/echarts4r/man/histogram.Rd | 25 echarts4r-0.3.3/echarts4r/man/init.Rd | 8 echarts4r-0.3.3/echarts4r/man/leaflet.Rd | 16 echarts4r-0.3.3/echarts4r/man/legend_action.Rd | 21 echarts4r-0.3.3/echarts4r/man/line3D.Rd | 81 echarts4r-0.3.3/echarts4r/man/loading.Rd | 30 echarts4r-0.3.3/echarts4r/man/map.Rd | 78 echarts4r-0.3.3/echarts4r/man/map_actions.Rd | 13 echarts4r-0.3.3/echarts4r/man/mapbox.Rd | 20 echarts4r-0.3.3/echarts4r/man/mark.Rd | 49 echarts4r-0.3.3/echarts4r/man/node_adjacency.Rd | 87 echarts4r-0.3.3/echarts4r/man/pie_action.Rd | 13 echarts4r-0.3.3/echarts4r/man/radius_axis.Rd | 15 echarts4r-0.3.3/echarts4r/man/renderEcharts4rBox.Rd |only echarts4r-0.3.3/echarts4r/man/scatter.Rd | 81 echarts4r-0.3.3/echarts4r/man/smooth.Rd | 40 echarts4r-0.3.3/echarts4r/man/theme.Rd | 17 echarts4r-0.3.3/echarts4r/man/timeline-opts.Rd | 33 echarts4r-0.3.3/echarts4r/man/toolbox.Rd | 29 echarts4r-0.3.3/echarts4r/man/tooltip_action.Rd | 13 echarts4r-0.3.3/echarts4r/man/tooltip_proxy.Rd | 118 echarts4r-0.3.3/echarts4r/tests |only 152 files changed, 7859 insertions(+), 7951 deletions(-)
Title: Compute, Handle and Plot Incidence of Dated Events
Description: Provides functions and classes to compute, handle and visualise
incidence from dated events for a defined time interval. Dates can be
provided in various standard formats. The class 'incidence2' is used to store
computed incidence and can be easily manipulated, subsetted, and plotted.
This package is part of the RECON (<https://www.repidemicsconsortium.org/>)
toolkit for outbreak analysis.
Author: Tim Taylor [aut, cre] (<https://orcid.org/0000-0002-8587-7113>),
Thibaut Jombart [aut],
Zhian N. Kamvar [aut] (<https://orcid.org/0000-0003-1458-7108>),
Rich FitzJohn [aut],
Jun Cai [ctb] (<https://orcid.org/0000-0001-9495-1226>),
Sangeeta Bhatia [ctb],
Jakob Schumacher [ctb],
Juliet R.C. Pulliam [ctb] (<https://orcid.org/0000-0003-3314-8223>)
Maintainer: Tim Taylor <tim.taylor@hiddenelephants.co.uk>
Diff between incidence2 versions 0.2.0 dated 2020-09-22 and 0.2.1 dated 2020-10-16
DESCRIPTION | 6 MD5 | 38 - NAMESPACE | 10 NEWS.md | 4 R/conversion.R | 1 R/cumulate.R | 2 R/incidence.R | 26 - R/make_incidence.R | 14 R/plot.R | 4 R/regroup.R | 5 R/trim_observations.R | 8 inst/doc/Introduction.R | 10 inst/doc/Introduction.Rmd | 17 inst/doc/Introduction.html | 301 +++++++++----- inst/doc/customizing_incidence_plots.html | 228 +++++++--- inst/doc/handling_incidence_objects.html | 622 +++++++++++++++++------------- man/plot.incidence2.Rd | 3 tests/testthat/rds/incidence.res1.rds |binary tests/testthat/rds/incidence.res2.rds |binary vignettes/Introduction.Rmd | 17 20 files changed, 800 insertions(+), 516 deletions(-)
Title: Log Rotation and Conditional Backups
Description: Conditionally rotate or back-up files based on
their size or the date of the last backup; inspired by the 'Linux'
utility 'logrotate'.
Author: Stefan Fleck [aut, cre] (<https://orcid.org/0000-0003-3344-9851>)
Maintainer: Stefan Fleck <stefan.b.fleck@gmail.com>
Diff between rotor versions 0.2.4 dated 2020-01-07 and 0.3.0 dated 2020-10-16
DESCRIPTION | 11 MD5 | 54 ++- NAMESPACE | 6 NEWS.md | 17 + R/BackupQueue.R | 516 ++++++++++++++++++++++--------------- R/Cache.R |only R/DirectoryQueue.R |only R/conditions.R |only R/list_backups.R | 54 +-- R/rotate.R | 63 +++- R/rotate_date.R | 16 - R/rotate_rds.R |only R/rotate_time.R | 16 - R/utils-predicates.R | 26 - R/utils-sfmisc.R | 156 +++++------ README.md | 109 +++++-- inst/WORDLIST | 7 inst/benchmarks/benchmarks.R | 8 man/BackupQueue.Rd | 259 +++++++++++------- man/BackupQueueDate.Rd |only man/BackupQueueDateTime.Rd |only man/BackupQueueIndex.Rd |only man/Cache.Rd |only man/DirectoryQueue.Rd |only man/backup_info.Rd | 12 man/rotate.Rd | 36 +- man/rotate_rds.Rd |only tests/testthat/test_BackupQueue.R | 254 ++++++++++-------- tests/testthat/test_Cache.R |only tests/testthat/test_list_backups.R | 22 - tests/testthat/test_rotate.R | 59 +++- tests/testthat/test_rotate_date.R | 46 +-- tests/testthat/test_rotate_rds.R |only tests/testthat/test_rotate_time.R | 30 +- 34 files changed, 1081 insertions(+), 696 deletions(-)
Title: Extended Model Formulas
Description: Infrastructure for extended formulas with multiple parts on the
right-hand side and/or multiple responses on the left-hand side
(see <doi:10.18637/jss.v034.i01>).
Author: Achim Zeileis [aut, cre] (<https://orcid.org/0000-0003-0918-3766>),
Yves Croissant [aut]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between Formula versions 1.2-3 dated 2018-05-03 and 1.2-4 dated 2020-10-16
Formula-1.2-3/Formula/NEWS |only Formula-1.2-4/Formula/DESCRIPTION | 10 +++++----- Formula-1.2-4/Formula/MD5 | 17 +++++++++-------- Formula-1.2-4/Formula/NEWS.md |only Formula-1.2-4/Formula/R/Formula.R | 4 ++-- Formula-1.2-4/Formula/build/partial.rdb |only Formula-1.2-4/Formula/build/vignette.rds |binary Formula-1.2-4/Formula/inst/CITATION | 7 +------ Formula-1.2-4/Formula/inst/doc/Formula.pdf |binary Formula-1.2-4/Formula/man/Formula.Rd | 2 +- Formula-1.2-4/Formula/man/model.frame.Formula.Rd | 2 +- 11 files changed, 19 insertions(+), 23 deletions(-)
Title: Call 'BEAST2'
Description: 'BEAST2' (<https://www.beast2.org>) is a widely used
Bayesian phylogenetic tool, that uses DNA/RNA/protein data
and many model priors to create a posterior of jointly estimated
phylogenies and parameters.
'BEAST2' is a command-line tool.
This package provides a way to call 'BEAST2'
from an 'R' function call.
Author: Richèl J.C. Bilderbeek [aut, cre]
(<https://orcid.org/0000-0003-1107-7049>),
Joëlle Barido-Sottani [rev] (Joëlle reviewed the package for rOpenSci,
see https://github.com/ropensci/onboarding/issues/209),
David Winter [rev] (David reviewed the package for rOpenSci, see
https://github.com/ropensci/onboarding/issues/209),
Thijs Janzen [ctb]
Maintainer: Richèl J.C. Bilderbeek <richel@richelbilderbeek.nl>
Diff between beastier versions 2.1.3 dated 2020-08-07 and 2.2 dated 2020-10-16
DESCRIPTION | 10 - MD5 | 156 +++++++++++++-------------- NAMESPACE | 1 R/are_beast2_input_lines.R | 15 +- R/beastier.R | 22 +-- R/check_beast2.R | 6 - R/check_beast2_internal_filenames.R | 16 -- R/check_beast2_options.R | 9 - R/check_beast2_optionses.R | 9 - R/check_beast2_path.R | 10 - R/check_input_filename.R | 27 +--- R/check_n_threads.R | 16 -- R/check_os.R | 19 --- R/check_rng_seed.R | 17 -- R/create_beast2_internal_filenames.R | 9 - R/create_beast2_options.R | 14 -- R/create_mcbette_beast2_options.R |only R/create_random_fasta.R | 18 --- R/create_random_phylogeny.R | 8 - R/do_minimal_run.R | 8 - R/get_alignment_ids.R | 16 -- R/get_beast2_example_filename.R | 9 - R/get_beast2_options_filenames.R | 5 R/get_beast2_version.R | 4 R/get_default_beast2_download_url.R | 18 --- R/get_default_beast2_jar_path.R | 11 - R/get_default_beast2_path.R | 11 - R/get_java_version.R | 3 R/get_path.R | 12 -- R/get_paths.R | 19 +-- R/get_trees_filenames.R | 13 -- R/gives_beast2_warning.R | 28 +--- R/has_unique_ids.R | 12 +- R/is_beast2_input_file.R | 10 - R/is_bin_path.R | 28 ++-- R/is_jar_path.R | 14 +- R/run_beast2.R | 13 -- R/run_beast2_from_options.R | 11 - R/save_lines.R | 11 - R/uninstall_beast2.R | 15 -- R/upgrade_beast2.R | 6 - inst/WORDLIST | 1 inst/doc/demo.html | 167 ++++++++++++----------------- man/are_beast2_input_lines.Rd | 10 - man/are_beast2_input_lines_fast.Rd | 5 man/beastier.Rd | 20 +-- man/check_beast2.Rd | 6 - man/check_beast2_internal_filenames.Rd | 16 -- man/check_beast2_options.Rd | 9 - man/check_beast2_optionses.Rd | 9 - man/check_beast2_path.Rd | 10 - man/check_input_filename.Rd | 11 - man/check_n_threads.Rd | 16 -- man/check_os.Rd | 19 --- man/check_rng_seed.Rd | 17 -- man/create_beast2_internal_filenames.Rd | 9 - man/create_beast2_options.Rd | 14 -- man/create_mcbette_beast2_options.Rd |only man/do_minimal_run.Rd | 8 - man/get_alignment_ids_from_xml_filename.Rd | 16 -- man/get_beast2_example_filename.Rd | 9 - man/get_beast2_options_filenames.Rd | 5 man/get_beast2_version.Rd | 4 man/get_beastier_path.Rd | 12 -- man/get_beastier_paths.Rd | 19 +-- man/get_default_beast2_download_url.Rd | 18 --- man/get_default_beast2_jar_path.Rd | 11 - man/get_default_beast2_path.Rd | 11 - man/get_java_version.Rd | 3 man/get_trees_filenames.Rd | 13 -- man/gives_beast2_warning.Rd | 28 +--- man/has_unique_ids.Rd | 12 +- man/is_beast2_input_file.Rd | 10 - man/is_bin_path.Rd | 18 +-- man/is_jar_path.Rd | 14 +- man/run_beast2.Rd | 13 -- man/run_beast2_from_options.Rd | 11 - man/save_lines.Rd | 11 - man/uninstall_beast2.Rd | 15 -- man/upgrade_beast2.Rd | 7 - 80 files changed, 406 insertions(+), 860 deletions(-)
Title: Biodiversity Assessment Tools
Description: Includes algorithms to assess alpha and beta
diversity in all their dimensions (taxon, phylogenetic and functional
diversity), whether communities are completely sampled or not. It allows
performing a number of analyses based on either species identities or
phylogenetic/functional trees or functional kernel n-dimensional hypervolumes
depicting species relationships.
Author: Pedro Cardoso, Stefano Mammola, Francois Rigal, Jose Carlos Carvalho
Maintainer: Pedro Cardoso <pedro.cardoso@helsinki.fi>
Diff between BAT versions 2.2.0 dated 2020-09-30 and 2.2.1 dated 2020-10-16
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/BAT.R | 30 ++++++++++++++++++++++-------- 3 files changed, 28 insertions(+), 14 deletions(-)
Title: Create Interactive Chart with the JavaScript 'ApexCharts'
Library
Description: Provides an 'htmlwidgets' interface to 'apexcharts.js'.
'Apexcharts' is a modern JavaScript charting library to build interactive charts and visualizations with simple API.
'Apexcharts' examples and documentation are available here: <https://apexcharts.com/>.
Author: Victor Perrier [aut, cre],
Fanny Meyer [aut],
Juned Chhipa [cph] (apexcharts.js library),
Mike Bostock [cph] (d3.format library)
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>
Diff between apexcharter versions 0.1.6 dated 2020-09-09 and 0.1.7 dated 2020-10-16
apexcharter-0.1.6/apexcharter/inst/htmlwidgets/lib/apexcharts-3.19 |only apexcharter-0.1.6/apexcharter/inst/htmlwidgets/lib/apexcharts-3.20 |only apexcharter-0.1.7/apexcharter/DESCRIPTION | 6 apexcharter-0.1.7/apexcharter/MD5 | 45 - apexcharter-0.1.7/apexcharter/NAMESPACE | 2 apexcharter-0.1.7/apexcharter/NEWS.md | 10 apexcharter-0.1.7/apexcharter/R/apex.R | 9 apexcharter-0.1.7/apexcharter/R/apexcharter.R | 2 apexcharter-0.1.7/apexcharter/R/colors.R |only apexcharter-0.1.7/apexcharter/R/mixed-charts.R | 3 apexcharter-0.1.7/apexcharter/R/proxy.R | 24 apexcharter-0.1.7/apexcharter/inst/doc/apexcharter.R | 15 apexcharter-0.1.7/apexcharter/inst/doc/apexcharter.Rmd | 29 + apexcharter-0.1.7/apexcharter/inst/doc/apexcharter.html | 248 +++++++--- apexcharter-0.1.7/apexcharter/inst/doc/chart-options.html | 191 +++++-- apexcharter-0.1.7/apexcharter/inst/doc/shiny-integration.html | 143 ++++- apexcharter-0.1.7/apexcharter/inst/doc/spark-box.html | 127 ++++- apexcharter-0.1.7/apexcharter/inst/doc/sync-charts.html | 131 ++++- apexcharter-0.1.7/apexcharter/inst/htmlwidgets/apexcharter.js | 41 + apexcharter-0.1.7/apexcharter/inst/htmlwidgets/apexcharter.yaml | 4 apexcharter-0.1.7/apexcharter/inst/htmlwidgets/lib/apexcharts-3.22 |only apexcharter-0.1.7/apexcharter/man/add-line.Rd | 3 apexcharter-0.1.7/apexcharter/man/apex.Rd | 5 apexcharter-0.1.7/apexcharter/man/apexcharter-shiny.Rd | 2 apexcharter-0.1.7/apexcharter/man/ax_colors_manual.Rd |only apexcharter-0.1.7/apexcharter/vignettes/apexcharter.Rmd | 29 + 26 files changed, 815 insertions(+), 254 deletions(-)
Title: Configural Frequencies Analysis Using Log-Linear Modeling
Description: Offers several functions for Configural Frequencies
Analysis (CFA), which is a useful statistical tool for the analysis of
multiway contingency tables. CFA was introduced by G. A. Lienert as
'Konfigurations Frequenz Analyse - KFA'. Lienert, G. A. (1971).
Die Konfigurationsfrequenzanalyse: I. Ein neuer Weg zu Typen und Syndromen.
Zeitschrift für Klinische Psychologie und Psychotherapie, 19(2), 99–115.
Author: Joerg-Henrik Heine, R.W. Alexandrowicz (function stirling_cfa() )
and some package testing by Mark Stemmler
Maintainer: Joerg-Henrik Heine <jhheine@googlemail.com>
Diff between confreq versions 1.5.5-1 dated 2020-06-05 and 1.5.5-2 dated 2020-10-16
DESCRIPTION | 8 - MD5 | 6 - NEWS | 196 ++++++++++++++++---------------- R/CFA.R | 358 ++++++++++++++++++++++++++++++------------------------------ 4 files changed, 287 insertions(+), 281 deletions(-)
Title: Create and Manipulate BioCompute Objects
Description: Tools to create, validate, and export BioCompute Objects
described in King et al. (2019) <doi:10.17605/osf.io/h59uh>.
Users can encode information in data frames, and compose
BioCompute Objects from the domains defined by the standard.
A checksum validator and a JSON schema validator are provided.
This package also supports exporting BioCompute Objects as JSON,
PDF, HTML, or 'Word' documents, and exporting to cloud-based platforms.
Author: Soner Koc [aut, cre],
Nan Xiao [aut],
Dennis Dean [aut] (<https://orcid.org/0000-0002-7621-9717>),
Seven Bridges Genomics [cph, fnd]
Maintainer: Soner Koc <soner.koc@sevenbridges.com>
Diff between biocompute versions 1.0.3 dated 2019-11-28 and 1.0.4 dated 2020-10-16
DESCRIPTION | 19 MD5 | 54 NEWS.md | 6 R/compose-error.R | 2 R/compose-parametric.R | 2 R/compose-top-level-fields.R | 2 R/compose-usability.R | 2 R/export-docs.R | 12 R/export-sevenbridges.R | 16 R/validate-checksum.R | 2 R/validate-schema.R | 2 README.md | 6 build/vignette.rds |binary inst/doc/case-study.Rmd | 1 inst/doc/case-study.html | 2462 ++++++++----------------------------------- inst/doc/intro.Rmd | 1 inst/doc/intro.html | 856 ++++---------- man/biocompute-package.Rd | 4 man/compose_error.Rd | 2 man/compose_parametric.Rd | 2 man/compose_tlf.Rd | 2 man/compose_usability.Rd | 2 man/export_json.Rd | 2 man/export_sevenbridges.Rd | 12 man/validate_checksum.Rd | 2 man/validate_schema.Rd | 2 vignettes/case-study.Rmd | 1 vignettes/intro.Rmd | 1 28 files changed, 847 insertions(+), 2630 deletions(-)
Title: Tensor Regression with Envelope Structure and Three Generic
Envelope Estimation Approaches
Description: Provides three estimators for tensor response regression (TRR) and tensor predictor regression (TPR) models with tensor envelope structure. The three types of estimation approaches are generic and can be applied to any envelope estimation problems. The full Grassmannian (FG) optimization is often associated with likelihood-based estimation but requires heavy computation and good initialization; the one-directional optimization approaches (1D and ECD algorithms) are faster, stable and does not require carefully chosen initial values; the SIMPLS-type is motivated by the partial least squares regression and is computationally the least expensive. For details of TRR, see Li L, Zhang X (2017) <doi:10.1080/01621459.2016.1193022>. For details of TPR, see Zhang X, Li L (2017) <doi:10.1080/00401706.2016.1272495>. For details of 1D algorithm, see Cook RD, Zhang X (2016) <doi:10.1080/10618600.2015.1029577>. For details of ECD algorithm, see Cook RD, Zhang X (2018) <doi:10.5705/ss.202016.0037>.
Author: Wenjing Wang [aut],
Jing Zeng [aut, cre],
Xin Zhang [aut]
Maintainer: Jing Zeng <jing.zeng@stat.fsu.edu>
Diff between TRES versions 1.1.2 dated 2020-07-23 and 1.1.3 dated 2020-10-16
TRES-1.1.2/TRES/data/datalist |only TRES-1.1.3/TRES/DESCRIPTION | 8 - TRES-1.1.3/TRES/MD5 | 53 +++++----- TRES-1.1.3/TRES/NAMESPACE | 1 TRES-1.1.3/TRES/NEWS.md | 11 ++ TRES-1.1.3/TRES/R/1Dfunctions.R | 124 +++++++++++++----------- TRES-1.1.3/TRES/R/ECD.R | 2 TRES-1.1.3/TRES/R/FG_TPR.R | 1 TRES-1.1.3/TRES/R/OptM1D.R | 2 TRES-1.1.3/TRES/R/OptStiefelGBB.R | 10 - TRES-1.1.3/TRES/R/TPR.fit.R | 1 TRES-1.1.3/TRES/R/TPRsim.R | 4 TRES-1.1.3/TRES/R/TRR.fit.R | 5 TRES-1.1.3/TRES/R/TRRsim.R | 7 - TRES-1.1.3/TRES/R/TensPLS_fit.R | 3 TRES-1.1.3/TRES/R/Tenv_Pval.R | 2 TRES-1.1.3/TRES/R/kroncov.R | 6 - TRES-1.1.3/TRES/R/manifold1D.R | 3 TRES-1.1.3/TRES/R/manifoldFG.R | 3 TRES-1.1.3/TRES/R/oneD_bic.R | 2 TRES-1.1.3/TRES/R/predict.Tenv.R | 3 TRES-1.1.3/TRES/R/print.Tenv.R | 2 TRES-1.1.3/TRES/R/show.R | 3 TRES-1.1.3/TRES/R/subspace.R | 2 TRES-1.1.3/TRES/README.md | 4 TRES-1.1.3/TRES/tests/testthat/test-TRR_TPR.R | 1 TRES-1.1.3/TRES/tests/testthat/test-auxiliary.R | 1 TRES-1.1.3/TRES/tests/testthat/test-examples.R | 57 ++++++++--- 28 files changed, 184 insertions(+), 137 deletions(-)
Title: Create Full Text Browsers from Annotated Token Lists
Description: Create browsers for reading full texts from a token list format.
Information obtained from text analyses (e.g., topic modeling, word scaling)
can be used to annotate the texts.
Author: Kasper Welbers and Wouter van Atteveldt
Maintainer: Kasper Welbers <kasperwelbers@gmail.com>
Diff between tokenbrowser versions 0.1.4 dated 2020-03-19 and 0.1.5 dated 2020-10-16
DESCRIPTION | 8 +-- MD5 | 44 +++++++++--------- R/attributes.r | 1 R/html_misc.r | 20 +++++++- R/quick_view.r | 2 R/tag_tokens.r | 93 +++++++++++++++++++++++++++++++-------- R/tokenvis.r | 41 +++++++++++------ R/wrap_documents.r | 19 +++++-- inst/template/browser.html | 18 +++++++ man/add_tag.Rd | 11 ++++ man/categorical_browser.Rd | 8 ++- man/category_highlight_tokens.Rd | 17 +++++-- man/colorscale_tokens.Rd | 13 +++++ man/colorscaled_browser.Rd | 8 ++- man/create_browser.Rd | 7 ++ man/highlight_tokens.Rd | 18 +++++++ man/highlighted_browser.Rd | 8 ++- man/sotu_data.Rd | 4 + man/sotu_lda.Rd | 4 + man/tag_tokens.Rd | 19 +++++++ man/view_browser.Rd | 1 man/wrap_documents.Rd | 3 + tests/testthat/test_tokenvis.r | 4 - 23 files changed, 289 insertions(+), 82 deletions(-)
Title: 'RStudio' Addins to Prettify 'HTML', 'CSS', 'JavaScript', and
More
Description: Provides 'RStudio' addins to prettify 'HTML', 'CSS', 'SCSS', 'JavaScript', 'JSX', 'Markdown', and to format 'C', 'C++', 'Julia', 'Python', 'Shell' and 'SQL'. Two addins are provided: 'Prettify' and 'Indent'. The 'Indent' addin only reindents the code, while the 'Prettify' addin also modifies the code, e.g. it adds trailing semi-colons to 'JavaScript' code when they are missing.
Author: Stéphane Laurent [aut, cre],
James Long and contributors [ctb, cph] ('Prettier' library),
Zeb Zhao [ctb, cph] ('indent.js' library),
Marijn Haverbeke [ctb, cph] ('CodeMirror' library)
Maintainer: Stéphane Laurent <laurent_step@outlook.fr>
Diff between prettifyAddins versions 0.1.0 dated 2020-09-29 and 1.0.0 dated 2020-10-16
DESCRIPTION | 9 +++++---- MD5 | 23 ++++++++++++++--------- NAMESPACE | 4 ++++ NEWS.md | 8 ++++++++ R/internal.R |only R/prettify.R | 2 ++ R/prettifyCLANG.R |only R/prettifyV8.R |only R/prettifyXML.R |only README.md | 14 +++++++++++++- inst/clang-format.txt |only inst/rstudio/addins.dcf | 26 +++++++++++++++++++++++--- inst/shinyApp/server.R | 4 +++- inst/shinyApp/ui.R | 6 +++++- inst/shinyApp/www/prettify.js | 23 ++++++++++++++--------- 15 files changed, 91 insertions(+), 28 deletions(-)
More information about prettifyAddins at CRAN
Permanent link
Title: Reading Portable Encapsulated Projects
Description: A PEP, or Portable Encapsulated Project, is a dataset that
subscribes to the PEP structure for organizing metadata. It is written using
a simple YAML + CSV format, it is your one-stop solution to metadata
management across data analysis environments. This package reads this
standardized project configuration structure into R.
Author: Nathan Sheffield [aut, cph],
Michal Stolarczyk [aut, cre]
Maintainer: Michal Stolarczyk <michal@virginia.edu>
Diff between pepr versions 0.3.2 dated 2020-06-04 and 0.4.0 dated 2020-10-16
pepr-0.3.2/pepr/inst/extdata/example_peps-master/data |only pepr-0.4.0/pepr/DESCRIPTION | 8 pepr-0.4.0/pepr/MD5 | 65 -- pepr-0.4.0/pepr/NEWS.md | 10 pepr-0.4.0/pepr/R/config.R | 6 pepr-0.4.0/pepr/R/pepr.R | 2 pepr-0.4.0/pepr/R/project.R | 38 - pepr-0.4.0/pepr/R/utils.R | 24 pepr-0.4.0/pepr/README.md | 21 pepr-0.4.0/pepr/inst/doc/feature1_constantAttributes.html | 80 +- pepr-0.4.0/pepr/inst/doc/feature2_impliedAttributes.html | 130 ++-- pepr-0.4.0/pepr/inst/doc/feature3_derivedAttributes.html | 100 +-- pepr-0.4.0/pepr/inst/doc/feature4_derivedImpliedAttributes.html | 70 +- pepr-0.4.0/pepr/inst/doc/feature5_sampleSubtable.html | 308 +++++----- pepr-0.4.0/pepr/inst/doc/feature6_amendments.html | 132 ++-- pepr-0.4.0/pepr/inst/doc/gettingStarted.Rmd | 2 pepr-0.4.0/pepr/inst/doc/gettingStarted.html | 72 +- pepr-0.4.0/pepr/inst/extdata/example_peps-master/example_subtable1/project_config.yaml | 3 pepr-0.4.0/pepr/inst/extdata/example_peps-master/example_subtable2/project_config.yaml | 5 pepr-0.4.0/pepr/inst/extdata/example_peps-master/example_subtable3/project_config.yaml | 5 pepr-0.4.0/pepr/inst/extdata/example_peps-master/example_subtable4/project_config.yaml | 5 pepr-0.4.0/pepr/inst/extdata/example_peps-master/example_subtable5/project_config.yaml | 5 pepr-0.4.0/pepr/inst/extdata/example_peps-master/example_subtables |only pepr-0.4.0/pepr/man/dot-loadSubsampleAnnotation.Rd |only pepr-0.4.0/pepr/man/dot-mergeAttrs.Rd | 4 pepr-0.4.0/pepr/man/pepr.Rd | 2 pepr-0.4.0/pepr/tests/testthat/test_project.R | 22 pepr-0.4.0/pepr/vignettes/gettingStarted.Rmd | 2 28 files changed, 595 insertions(+), 526 deletions(-)
Title: Advanced Graphics and Image-Processing in R
Description: Bindings to 'ImageMagick': the most comprehensive open-source image
processing library available. Supports many common formats (png, jpeg, tiff,
pdf, etc) and manipulations (rotate, scale, crop, trim, flip, blur, etc).
All operations are vectorized via the Magick++ STL meaning they operate either
on a single frame or a series of frames for working with layers, collages,
or animation. In RStudio images are automatically previewed when printed to
the console, resulting in an interactive editing environment. The latest
version of the package includes a native graphics device for creating
in-memory graphics or drawing onto images using pixel coordinates.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between magick versions 2.4.0 dated 2020-06-23 and 2.5.0 dated 2020-10-16
DESCRIPTION | 10 - MD5 | 91 +++++++------- NAMESPACE | 3 NEWS | 9 + R/EBImage.R | 2 R/RcppExports.R | 16 +- R/animation.R | 35 ++++- R/color.R | 6 R/defines.R |only R/edit.R | 32 ++--- R/ggplot2.R | 3 R/index.R | 2 R/options.R | 6 R/transform.R | 15 ++ build/vignette.rds |binary inst/doc/intro.Rmd | 6 inst/doc/intro.html | 291 ++++++++++++++++++++++++----------------------- inst/images/building.jpg |only man/analysis.Rd | 1 man/animation.Rd | 34 +++++ man/as_EBImage.Rd | 2 man/attributes.Rd | 1 man/color.Rd | 7 - man/composite.Rd | 1 man/defines.Rd |only man/device.Rd | 1 man/edges.Rd | 1 man/editing.Rd | 15 +- man/effects.Rd | 1 man/fx.Rd | 1 man/geometry.Rd | 1 man/magick.Rd | 3 man/morphology.Rd | 1 man/ocr.Rd | 1 man/options.Rd | 4 man/painting.Rd | 1 man/segmentation.Rd | 1 man/transform.Rd | 12 + man/video.Rd | 1 src/Makevars.win | 5 src/RcppExports.cpp | 52 +++++++- src/composite.cpp | 4 src/config.cc | 4 src/convolve.cpp | 2 src/edit.cpp | 36 +++++ src/magick_types.h | 2 src/transformations.cpp | 26 ++++ vignettes/intro.Rmd | 6 48 files changed, 494 insertions(+), 260 deletions(-)
Title: Methods for Estimating Optimal Dynamic Treatment Regimes
Description: Methods to estimate dynamic treatment regimes using Interactive
Q-Learning, Q-Learning, weighted learning, and value-search methods based on
Augmented Inverse Probability Weighted Estimators and Inverse Probability
Weighted Estimators. Dynamic Treatment Regimes: Statistical Methods for
Precision Medicine, Tsiatis, A. A., Davidian, M. D., Holloway, S. T., and Laber, E. B.,
Chapman & Hall/CRC Press, 2020, ISBN:978-1-4987-6977-8.
Author: S. T. Holloway, E. B. Laber, K. A. Linn, B. Zhang, M. Davidian, and A. A. Tsiatis
Maintainer: Shannon T. Holloway <sthollow@ncsu.edu>
Diff between DynTxRegime versions 4.7 dated 2020-07-22 and 4.8 dated 2020-10-16
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS | 7 +++++++ R/H_class_OptimalSeqMissing.R | 1 + R/O_LearningMulti.R | 22 +++++++++++++++++++++- 5 files changed, 37 insertions(+), 9 deletions(-)
Title: Foreach Parallel Adaptor for the 'snow' Package
Description: Provides a parallel backend for the %dopar% function using
the snow package of Tierney, Rossini, Li, and Sevcikova.
Author: Michelle Wallig [cre],
Microsoft Corporation [aut, cph],
Stephen Weston [aut]
Maintainer: Michelle Wallig <Michelle.Wallig@microsoft.com>
Diff between doSNOW versions 1.0.18 dated 2019-07-27 and 1.0.19 dated 2020-10-16
DESCRIPTION | 15 +++++++-------- MD5 | 4 ++-- NEWS | 6 ++++++ 3 files changed, 15 insertions(+), 10 deletions(-)
Title: Foreach Parallel Adaptor for the 'parallel' Package
Description: Provides a parallel backend for the %dopar% function using
the parallel package.
Author: Michelle Wallig [cre],
Microsoft Corporation [aut, cph],
Steve Weston [aut],
Dan Tenenbaum [ctb]
Maintainer: Michelle Wallig <Michelle.Wallig@microsoft.com>
Diff between doParallel versions 1.0.15 dated 2019-08-02 and 1.0.16 dated 2020-10-16
DESCRIPTION | 16 ++++++++-------- MD5 | 8 ++++---- NEWS | 6 ++++++ build/vignette.rds |binary inst/doc/gettingstartedParallel.pdf |binary 5 files changed, 18 insertions(+), 12 deletions(-)
Title: Depth Tools Package
Description: Implementation of different statistical tools for the
description and analysis of gene expression data based on the
concept of data depth, namely, the scale curves for
visualizing the dispersion of one or various groups of samples
(e.g. types of tumors), a rank test to decide whether two groups
of samples come from a single distribution and two methods of
supervised classification techniques, the DS and TAD methods.
All these techniques are based on the Modified Band Depth, which
is a recent notion of depth with a low computational cost, what
renders it very appropriate for high dimensional data such as
gene expression data.
Author: Sara Lopez-Pintado <sl2929@columbia.edu> and Aurora Torrente
<etorrent@est-econ.uc3m.es>.
Maintainer: Aurora Torrente <etorrent@est-econ.uc3m.es>
Diff between depthTools versions 0.4 dated 2013-06-13 and 0.5 dated 2020-10-16
DESCRIPTION | 30 +++++++++++++++--------------- MD5 | 4 ++-- NAMESPACE | 5 +++++ 3 files changed, 22 insertions(+), 17 deletions(-)
Title: Cohort Data Analyses
Description: Functions to make lifetables and to calculate hazard function estimate using Poisson regression model with splines. Includes function to draw simple flowchart of cohort study. Function boxesLx() makes boxes of transition rates between states. It utilizes 'Epi' package 'Lexis' data.
Author: Jari Haukka [aut, cre]
Maintainer: Jari Haukka <jari.haukka@helsinki.fi>
Diff between cohorttools versions 0.1.2 dated 2020-03-13 and 0.1.3 dated 2020-10-16
DESCRIPTION | 6 ++--- MD5 | 7 +++-- NAMESPACE | 1 R/cohorttools.R | 60 +++++++++++++++++++++++++++++++++++++++++++++++++-- man/plotratetable.Rd |only 5 files changed, 66 insertions(+), 8 deletions(-)
Title: 'BEAUti' from R
Description: 'BEAST2' (<https://www.beast2.org>) is a widely used
Bayesian phylogenetic tool, that uses DNA/RNA/protein data
and many model priors to create a posterior of jointly estimated
phylogenies and parameters.
'BEAUti 2' (which is part of 'BEAST2') is a GUI tool
that allows users to specify the many possible setups
and generates the XML file 'BEAST2' needs to run.
This package provides a way to create 'BEAST2' input
files without active user input, but using
R function calls instead.
Author: Richèl J.C. Bilderbeek [aut, cre]
(<https://orcid.org/0000-0003-1107-7049>),
Joëlle Barido-Sottani [rev] (Joëlle reviewed the package for rOpenSci,
see https://github.com/ropensci/onboarding/issues/209),
David Winter [rev] (David reviewed the package for rOpenSci, see
https://github.com/ropensci/onboarding/issues/209),
Paul Van Els [ctb],
Raphael Scherrer [ctb],
Yacine B. Chehida [ctb],
Katharine S. Walter [ctb] (<https://orcid.org/0000-0003-0065-2204>),
Jana Riederer [ctb]
Maintainer: Richèl J.C. Bilderbeek <richel@richelbilderbeek.nl>
Diff between beautier versions 2.3.7 dated 2020-08-05 and 2.4 dated 2020-10-16
DESCRIPTION | 6 MD5 | 538 +++++++-------- NAMESPACE | 1 R/are_clock_models.R | 17 R/are_equal_mcmcs.R | 8 R/are_equal_screenlogs.R | 8 R/are_equal_tracelogs.R | 7 R/are_equal_treelogs.R | 7 R/are_fasta_filenames.R | 29 R/are_tree_priors.R | 10 R/beautier.R | 21 R/check_alignment_id.R | 8 R/check_beauti_options.R | 7 R/check_clock_model.R | 23 R/check_clock_models.R | 20 R/check_file_exists.R | 21 R/check_gamma_site_model.R | 13 R/check_gtr_site_model.R | 10 R/check_inference_model.R | 7 R/check_inference_models.R | 12 R/check_mcmc.R | 9 R/check_mrca_prior.R | 27 R/check_param.R | 20 R/check_phylogeny.R | 10 R/check_site_model.R | 25 R/check_site_models.R | 18 R/check_tn93_site_model.R | 10 R/check_tree_prior.R | 26 R/check_tree_priors.R | 16 R/count_trailing_spaces.R | 20 R/create_beast2_beast_xml.R | 19 R/create_beast2_input_file.R | 2 R/create_beast2_input_file_from_model.R | 16 R/create_beast2_input_from_model.R | 4 R/create_beast2_input_xml.R | 6 R/create_beauti_options.R | 21 R/create_beauti_options_v2_4.R | 4 R/create_beauti_options_v2_6.R | 4 R/create_clock_model_from_name.R | 6 R/create_clock_models.R | 6 R/create_clock_models_from_names.R | 7 R/create_inference_model.R | 27 R/create_mcmc.R | 4 R/create_ns_inference_model.R |only R/create_site_model.R | 6 R/create_site_model_from_name.R | 6 R/create_site_models.R | 15 R/create_site_models_from_names.R | 7 R/create_test_inference_model.R | 16 R/create_test_mcmc.R | 13 R/create_test_ns_inference_model.R | 9 R/create_test_ns_mcmc.R | 3 R/create_tree_prior.R | 15 R/create_tree_priors.R | 13 R/distr_to_xml.R | 7 R/get_alignment_id.R | 7 R/get_beautier_path.R | 8 R/get_clock_model_name.R | 14 R/get_clock_model_names.R | 4 R/get_distr_n_params.R | 21 R/get_distr_names.R | 15 R/get_file_base_sans_ext.R | 8 R/get_freq_equilibrium_names.R | 7 R/get_inference_model_filenames.R | 20 R/get_mcmc_filenames.R | 9 R/get_n_taxa.R | 5 R/get_operator_id_pre.R | 6 R/get_param_names.R | 20 R/get_remove_hex_fun.R | 18 R/get_site_model_n_distrs.R | 30 R/get_site_models_n_distrs.R | 14 R/get_tree_prior_n_distrs.R | 22 R/get_tree_prior_names.R | 9 R/get_tree_priors_n_distrs.R | 16 R/get_tree_priors_n_params.R | 16 R/get_xml_closing_tag.R | 17 R/get_xml_opening_tag.R | 10 R/has_mrca_prior.R | 20 R/has_xml_short_closing_tag.R | 8 R/init_clock_models.R | 14 R/init_gamma_site_model.R | 8 R/init_site_models.R | 25 R/is_beauti_options.R | 16 R/is_clock_model.R | 50 - R/is_clock_model_name.R | 7 R/is_default_mcmc.R | 9 R/is_distr.R | 181 ++--- R/is_distr_name.R | 25 R/is_freq_equilibrium_name.R | 11 R/is_gamma_site_model.R | 16 R/is_id.R | 14 R/is_init_site_model.R | 28 R/is_mcmc.R | 28 R/is_mrca_prior.R | 12 R/is_one_bool.R | 20 R/is_one_double.R | 25 R/is_one_int.R | 24 R/is_param.R | 1010 ++++++++++++++--------------- R/is_param_name.R | 50 - R/is_site_model.R | 116 +-- R/is_site_model_name.R | 14 R/is_tree_prior_name.R | 15 R/mcmc_to_xml_run.R | 33 R/mrca_prior_to_xml_state.R | 5 R/mrca_prior_to_xml_taxonset.R | 21 R/mrca_prior_to_xml_tracelog.R | 12 R/mrca_priors_to_xml_distr.R | 18 R/mrca_priors_to_xml_tracelog.R | 12 R/parameter_to_xml.R | 6 R/rename_inference_model_filenames.R | 20 R/rename_mcmc_filenames.R | 13 build/vignette.rds |binary inst/WORDLIST | 9 inst/doc/demo.html | 6 inst/doc/examples.html | 4 inst/doc/inference_models.R |only inst/doc/inference_models.Rmd |only inst/doc/inference_models.html |only man/are_clock_models.Rd | 17 man/are_equal_mcmcs.Rd | 8 man/are_equal_screenlogs.Rd | 8 man/are_equal_tracelogs.Rd | 7 man/are_equal_treelogs.Rd | 7 man/are_fasta_filenames.Rd | 29 man/are_tree_priors.Rd | 10 man/beautier.Rd | 21 man/check_alignment_id.Rd | 8 man/check_beauti_options.Rd | 7 man/check_clock_model.Rd | 9 man/check_clock_models.Rd | 20 man/check_file_exists.Rd | 21 man/check_gamma_site_model.Rd | 13 man/check_gtr_site_model.Rd | 10 man/check_inference_model.Rd | 7 man/check_inference_models.Rd | 12 man/check_mcmc.Rd | 9 man/check_mrca_prior.Rd | 27 man/check_param.Rd | 20 man/check_phylogeny.Rd | 10 man/check_rln_clock_model.Rd | 7 man/check_site_model.Rd | 25 man/check_site_models.Rd | 18 man/check_strict_clock_model.Rd | 7 man/check_tn93_site_model.Rd | 10 man/check_tree_prior.Rd | 26 man/check_tree_priors.Rd | 16 man/count_trailing_spaces.Rd | 20 man/create_beast2_beast_xml.Rd | 19 man/create_beast2_input_file.Rd | 2 man/create_beast2_input_file_from_model.Rd | 16 man/create_beast2_input_from_model.Rd | 4 man/create_beauti_options.Rd | 22 man/create_beauti_options_v2_4.Rd | 4 man/create_beauti_options_v2_6.Rd | 4 man/create_clock_model_from_name.Rd | 6 man/create_clock_models.Rd | 6 man/create_clock_models_from_names.Rd | 7 man/create_inference_model.Rd | 26 man/create_mcmc.Rd | 4 man/create_ns_inference_model.Rd |only man/create_site_model.Rd | 6 man/create_site_model_from_name.Rd | 6 man/create_site_models.Rd | 15 man/create_site_models_from_names.Rd | 7 man/create_test_inference_model.Rd | 15 man/create_test_mcmc.Rd | 13 man/create_test_ns_inference_model.Rd | 15 man/create_test_ns_mcmc.Rd | 3 man/create_tree_priors.Rd | 13 man/create_xml_declaration.Rd | 6 man/create_yule_tree_prior.Rd | 15 man/distr_to_xml.Rd | 7 man/get_alignment_id.Rd | 7 man/get_beautier_path.Rd | 8 man/get_clock_model_name.Rd | 14 man/get_clock_model_names.Rd | 4 man/get_distr_n_params.Rd | 21 man/get_distr_names.Rd | 15 man/get_file_base_sans_ext.Rd | 8 man/get_freq_equilibrium_names.Rd | 7 man/get_inference_model_filenames.Rd | 20 man/get_mcmc_filenames.Rd | 9 man/get_n_taxa.Rd | 5 man/get_operator_id_pre.Rd | 6 man/get_param_names.Rd | 20 man/get_remove_hex_fun.Rd | 18 man/get_site_model_n_distrs.Rd | 30 man/get_site_models_n_distrs.Rd | 14 man/get_tree_prior_n_distrs.Rd | 22 man/get_tree_prior_names.Rd | 9 man/get_tree_priors_n_distrs.Rd | 16 man/get_tree_priors_n_params.Rd | 16 man/get_xml_closing_tag.Rd | 17 man/get_xml_opening_tag.Rd | 10 man/has_mrca_prior.Rd | 20 man/has_xml_short_closing_tag.Rd | 8 man/init_gamma_site_model.Rd | 8 man/init_gtr_site_model.Rd | 10 man/init_hky_site_model.Rd | 5 man/init_jc69_site_model.Rd | 5 man/init_rln_clock_model.Rd | 7 man/init_strict_clock_model.Rd | 7 man/init_tn93_site_model.Rd | 5 man/is_alpha_param.Rd | 51 - man/is_beauti_options.Rd | 16 man/is_beta_distr.Rd | 15 man/is_beta_param.Rd | 51 - man/is_clock_model.Rd | 18 man/is_clock_model_name.Rd | 7 man/is_clock_rate_param.Rd | 51 - man/is_default_mcmc.Rd | 9 man/is_distr.Rd | 30 man/is_distr_name.Rd | 25 man/is_exp_distr.Rd | 14 man/is_freq_equilibrium_name.Rd | 11 man/is_gamma_distr.Rd | 15 man/is_gamma_site_model.Rd | 16 man/is_gtr_site_model.Rd | 21 man/is_hky_site_model.Rd | 21 man/is_id.Rd | 14 man/is_init_gtr_site_model.Rd | 7 man/is_init_hky_site_model.Rd | 7 man/is_init_jc69_site_model.Rd | 7 man/is_init_tn93_site_model.Rd | 7 man/is_inv_gamma_distr.Rd | 15 man/is_jc69_site_model.Rd | 21 man/is_kappa_1_param.Rd | 51 - man/is_kappa_2_param.Rd | 51 - man/is_lambda_param.Rd | 51 - man/is_laplace_distr.Rd | 15 man/is_log_normal_distr.Rd | 15 man/is_m_param.Rd | 51 - man/is_mcmc.Rd | 18 man/is_mcmc_nested_sampling.Rd | 10 man/is_mean_param.Rd | 51 - man/is_mrca_prior.Rd | 12 man/is_mu_param.Rd | 51 - man/is_normal_distr.Rd | 15 man/is_one_bool.Rd | 20 man/is_one_div_x_distr.Rd | 15 man/is_one_double.Rd | 25 man/is_one_int.Rd | 24 man/is_param.Rd | 54 - man/is_param_name.Rd | 50 - man/is_poisson_distr.Rd | 15 man/is_rate_ac_param.Rd | 51 - man/is_rate_ag_param.Rd | 51 - man/is_rate_at_param.Rd | 51 - man/is_rate_cg_param.Rd | 51 - man/is_rate_ct_param.Rd | 51 - man/is_rate_gt_param.Rd | 51 - man/is_rln_clock_model.Rd | 15 man/is_s_param.Rd | 51 - man/is_scale_param.Rd | 51 - man/is_sigma_param.Rd | 51 - man/is_site_model.Rd | 26 man/is_site_model_name.Rd | 14 man/is_strict_clock_model.Rd | 15 man/is_tn93_site_model.Rd | 25 man/is_tree_prior_name.Rd | 15 man/is_uniform_distr.Rd | 15 man/mcmc_to_xml_run.Rd | 9 man/mcmc_to_xml_run_default.Rd | 8 man/mcmc_to_xml_run_nested_sampling.Rd | 16 man/mrca_prior_to_xml_state.Rd | 5 man/mrca_prior_to_xml_taxonset.Rd | 18 man/mrca_prior_to_xml_tracelog.Rd | 12 man/mrca_priors_to_xml_prior_distr.Rd | 18 man/mrca_priors_to_xml_tracelog.Rd | 12 man/parameter_to_xml.Rd | 6 man/rename_inference_model_filenames.Rd | 20 man/rename_mcmc_filenames.Rd | 13 vignettes/inference_models.Rmd |only 273 files changed, 2663 insertions(+), 3513 deletions(-)
Title: Check-Fields and Check-Boxes for 'rmarkdown'
Description: Creates auto checking check-fields and check-boxes for 'rmarkdown' html. It could be used in class, when teacher share materials and tasks, so student can solve some problems and check themselves. In contrast with the 'learnr' package the 'checkdown' package works without 'shiny'.
Author: George Moroz [aut, cre] (<https://orcid.org/0000-0003-1990-6083>)
Maintainer: George Moroz <agricolamz@gmail.com>
Diff between checkdown versions 0.0.5 dated 2020-05-16 and 0.0.6 dated 2020-10-16
DESCRIPTION | 16 ++-- MD5 | 18 ++--- NEWS | 3 R/check_hint.R | 6 + R/check_hints.R | 18 ++--- build/vignette.rds |binary inst/doc/start_checkdown.Rmd | 2 inst/doc/start_checkdown.html | 143 +++++++++++++++++++++++------------------- man/check_hint.Rd | 2 vignettes/start_checkdown.Rmd | 2 10 files changed, 121 insertions(+), 89 deletions(-)
Title: R Commander Depth Tools Plug-in
Description: We provide an Rcmdr plug-in based on the depthTools
package, which implements different robust statistical tools
for the description and analysis of gene expression data based
on the Modified Band Depth, namely, the scale curves for
visualizing the dispersion of one or various groups of samples
(e.g. types of tumors), a rank test to decide whether two
groups of samples come from a single distribution and two
methods of supervised classification techniques, the DS and
TAD methods.
Author: Sara Lopez-Pintado <sl2929@columbia.edu> and Aurora Torrente
<etorrent@est-econ.uc3m.es>.
Maintainer: Aurora Torrente <etorrent@est-econ.uc3m.es>
Diff between RcmdrPlugin.depthTools versions 1.3 dated 2013-06-13 and 1.4 dated 2020-10-16
DESCRIPTION | 28 ++++++++++++++-------------- MD5 | 8 ++++---- NAMESPACE | 4 +++- R/RcmdrPlugin.depthTools.R | 11 +++-------- man/plotCentralCurves.Rd | 14 +++++++++++--- 5 files changed, 35 insertions(+), 30 deletions(-)
More information about RcmdrPlugin.depthTools at CRAN
Permanent link