Title: Manipulations of Triangular Meshes Based on the 'VCGLIB' API
Description: Operations on triangular meshes based on 'VCGLIB'. This package
integrates nicely with the R-package 'rgl' to render the meshes processed by
'Rvcg'. The Visualization and Computer Graphics Library (VCG for short) is
an open source portable C++ templated library for manipulation, processing
and displaying with OpenGL of triangle and tetrahedral meshes. The library,
composed by more than 100k lines of code, is released under the GPL license,
and it is the base of most of the software tools of the Visual Computing Lab of
the Italian National Research Council Institute ISTI <http://vcg.isti.cnr.it>,
like 'metro' and 'MeshLab'. The 'VCGLIB' source is pulled from trunk
<https://github.com/cnr-isti-vclab/vcglib> and patched to work with options
determined by the configure script as well as to work with the header files
included by 'RcppEigen'.
Author: Stefan Schlager [aut, cre, cph],
Girinon Francois [ctb]
Maintainer: Stefan Schlager <zarquon42@gmail.com>
Diff between Rvcg versions 0.19 dated 2020-02-06 and 0.19.1 dated 2020-02-07
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- R/Rvcg-package.R | 4 ++-- man/Rvcg-package.Rd | 4 ++-- src/vcglib/vcg/space/tetra3.h | 4 ++-- src/vcglib/wrap/ply/plylib.cpp | 3 +-- 6 files changed, 17 insertions(+), 18 deletions(-)
Title: Safely Access the RStudio API
Description: Access the RStudio API (if available) and provide informative error
messages when it's not.
Author: Kevin Ushey [aut, cre],
JJ Allaire [aut],
Hadley Wickham [aut],
Gary Ritchie [aut],
RStudio [cph]
Maintainer: Kevin Ushey <kevin@rstudio.com>
Diff between rstudioapi versions 0.10 dated 2019-03-19 and 0.11 dated 2020-02-07
DESCRIPTION | 10 MD5 | 135 ++++---- NAMESPACE | 7 NEWS.md | 24 + R/bug-report.R |only R/code.R | 23 + R/commands.R | 9 R/dependencies.R |only R/dialogs.R | 32 - R/highlight-ui.R |only R/jobs.R | 1 R/launcher-functions.R | 4 R/prefs.R |only R/remote.R |only R/stubs.R | 4 R/tutorial.R |only R/user.R |only R/utils.R | 19 + build/vignette.rds |binary inst/doc/dialogs.R | 8 inst/doc/dialogs.html | 505 +++++++++++++++++++------------ inst/doc/document-manipulation.R | 8 inst/doc/document-manipulation.html | 521 +++++++++++++++++++------------- inst/doc/introduction.html | 347 +++++++++++++-------- inst/doc/projects.R | 4 inst/doc/projects.html | 472 ++++++++++++++++++----------- inst/doc/r-session.R | 10 inst/doc/r-session.Rmd | 15 inst/doc/r-session.html | 480 +++++++++++++++++++---------- inst/doc/terminal.R | 6 inst/doc/terminal.html | 567 +++++++++++++++++++++-------------- inst/resources |only man/askForSecret.Rd | 7 man/bugReport.Rd |only man/build-tools.Rd | 16 man/convertTheme.Rd | 10 man/createProjectTemplate.Rd | 15 man/executeCommand.Rd | 5 man/figures |only man/file-dialogs.Rd | 17 - man/getRStudioPackageDependencies.Rd |only man/highlightUi.Rd |only man/isAvailable.Rd | 7 man/jobAdd.Rd | 23 + man/jobAddOutput.Rd | 12 man/jobAddProgress.Rd | 12 man/jobRemove.Rd | 12 man/jobRunScript.Rd | 22 - man/jobSetProgress.Rd | 12 man/jobSetState.Rd | 18 - man/jobSetStatus.Rd | 12 man/launcher.Rd | 8 man/launcherConfig.Rd | 15 man/launcherContainer.Rd | 15 man/launcherControlJob.Rd | 6 man/launcherHostMount.Rd | 15 man/launcherNfsMount.Rd | 15 man/launcherPlacementConstraint.Rd | 15 man/launcherResourceLimit.Rd | 15 man/launcherSubmitJob.Rd | 45 +- man/launcherSubmitR.Rd | 15 man/readPreference.Rd | 18 - man/readRStudioPreference.Rd |only man/rstudio-documents.Rd | 8 man/savePlotAsImage.Rd | 8 man/systemUsername.Rd |only man/terminalActivate.Rd | 2 man/terminalBusy.Rd | 2 man/terminalClear.Rd | 2 man/terminalExecute.Rd | 3 man/terminalRunning.Rd | 2 man/terminalSend.Rd | 2 man/userIdentity.Rd |only man/writePreference.Rd | 13 man/writeRStudioPreference.Rd |only vignettes/r-session.Rmd | 15 76 files changed, 2284 insertions(+), 1366 deletions(-)
Title: Local Individual Conditional Expectation
Description: Local Individual Conditional Expectation ('localICE') is a local explanation approach from the field of eXplainable Artificial Intelligence (XAI). localICE is a model-agnostic XAI approach which provides three-dimensional local explanations for particular data instances. The approach is proposed in the master thesis of Martin Walter as an extension to ICE (see Reference). The three dimensions are the two features at the horizontal and vertical axes as well as the target represented by different colors. The approach is applicable for classification and regression problems to explain interactions of two features towards the target. For classification models, the number of classes can be more than two and each class is added as a different color to the plot. The given instance is added to the plot as two dotted lines according to the feature values. The localICE-package can explain features of type factor and numeric of any machine learning model. Automatically supported machine learning packages are 'mlr', 'randomForest', 'caret' or all other with an S3 predict function. For further model types from other libraries, a predict function has to be provided as an argument in order to get access to the model. Reference to the ICE approach: Alex Goldstein, Adam Kapelner, Justin Bleich, Emil Pitkin (2013) <arXiv:1309.6392>.
Author: Martin Walter [aut, cre]
Maintainer: Martin Walter <mf-walter@web.de>
Diff between localICE versions 0.1.0 dated 2019-02-01 and 0.1.1 dated 2020-02-07
DESCRIPTION | 10 LICENSE | 6 MD5 | 24 - NAMESPACE | 12 R/localICE.R | 454 ++++++++++++++++---------------- README.md | 166 +++++------ man/documentation.Rd | 183 ++++++------ tests/testthat.R | 12 tests/testthat/test-arguments-missing.R | 228 ++++++++-------- tests/testthat/test-arguments-wrong.R | 416 ++++++++++++++--------------- tests/testthat/test-classification.R | 114 ++++---- tests/testthat/test-regression.R | 114 ++++---- tests/testthat/test-return.R | 62 ++-- 13 files changed, 903 insertions(+), 898 deletions(-)
Title: A Numerical Implementation of Interval-Valued Kriging
Description: An interval-valued extension of ordinary and simple kriging.
Optimization of the function is based on a generalized interval distance.
This creates a non-differentiable cost function that requires a
differentiable approximation to the absolute value function. This
differentiable approximation is optimized using a Newton-Raphson algorithm
with a penalty function to impose the constraints. Analyses in the package
are driven by the 'intsp' and 'intgrd'
classes,
which are interval-valued extensions of
'SpatialPointsDataFrame' and 'SpatialPixelsDataFrame' respectively.
The package includes several wrappers to functions in the
'gstat' and 'sp' packages.
Author: Brennan Bean [aut, cre]
Maintainer: Brennan Bean <brennan.bean@usu.edu>
Diff between intkrige versions 1.0.0 dated 2019-07-07 and 1.0.1 dated 2020-02-07
intkrige-1.0.0/intkrige/man/assign-methods.Rd |only intkrige-1.0.1/intkrige/DESCRIPTION | 14 intkrige-1.0.1/intkrige/MD5 | 91 - intkrige-1.0.1/intkrige/NAMESPACE | 2 intkrige-1.0.1/intkrige/NEWS.md | 6 intkrige-1.0.1/intkrige/R/data.R | 70 + intkrige-1.0.1/intkrige/R/generics.R | 41 intkrige-1.0.1/intkrige/R/intKrigeDriver.R | 32 intkrige-1.0.1/intkrige/R/intgrd-class.R | 38 intkrige-1.0.1/intkrige/R/intsp-class.R | 72 + intkrige-1.0.1/intkrige/build/partial.rdb |binary intkrige-1.0.1/intkrige/build/vignette.rds |binary intkrige-1.0.1/intkrige/data/utsnow_dtl.rda |only intkrige-1.0.1/intkrige/data/utsnow_dtl2.rda |only intkrige-1.0.1/intkrige/inst/doc/intkriging-workflow.R | 18 intkrige-1.0.1/intkrige/inst/doc/intkriging-workflow.html | 537 ++++++---- intkrige-1.0.1/intkrige/man/dist_cpp.Rd | 78 - intkrige-1.0.1/intkrige/man/extract-methods.Rd | 76 - intkrige-1.0.1/intkrige/man/fit.intvariogram.Rd | 48 intkrige-1.0.1/intkrige/man/head.intgrd.Rd | 54 - intkrige-1.0.1/intkrige/man/head.intsp.Rd | 56 - intkrige-1.0.1/intkrige/man/interval-methods-assign.Rd | 61 - intkrige-1.0.1/intkrige/man/interval-methods.Rd | 47 intkrige-1.0.1/intkrige/man/interval.as.data.frame-methods.Rd | 43 intkrige-1.0.1/intkrige/man/intgrd-class.Rd | 32 intkrige-1.0.1/intkrige/man/intkrige-package.Rd | 118 +- intkrige-1.0.1/intkrige/man/intkrige.Rd | 297 ++--- intkrige-1.0.1/intkrige/man/intsp-class.Rd | 32 intkrige-1.0.1/intkrige/man/intvCheck.Rd | 44 intkrige-1.0.1/intkrige/man/intvariogram-methods.Rd | 61 - intkrige-1.0.1/intkrige/man/ohMap.Rd | 30 intkrige-1.0.1/intkrige/man/ohtemp.Rd | 66 - intkrige-1.0.1/intkrige/man/plot-intgrd-missing-method.Rd | 64 - intkrige-1.0.1/intkrige/man/plot-intsp-missing-method.Rd | 80 - intkrige-1.0.1/intkrige/man/print.intgrd.Rd | 50 intkrige-1.0.1/intkrige/man/print.intsp.Rd | 52 intkrige-1.0.1/intkrige/man/print.summary.intgrd.Rd | 42 intkrige-1.0.1/intkrige/man/print.summary.intsp.Rd | 42 intkrige-1.0.1/intkrige/man/show-intgrd-method.Rd | 27 intkrige-1.0.1/intkrige/man/show-intsp-method.Rd | 27 intkrige-1.0.1/intkrige/man/summary.intgrd.Rd | 46 intkrige-1.0.1/intkrige/man/summary.intsp.Rd | 46 intkrige-1.0.1/intkrige/man/tail.intgrd.Rd | 54 - intkrige-1.0.1/intkrige/man/tail.intsp.Rd | 54 - intkrige-1.0.1/intkrige/man/utsnow.Rd | 78 - intkrige-1.0.1/intkrige/man/utsnow_dtl.Rd |only intkrige-1.0.1/intkrige/man/utsnow_dtl2.Rd |only intkrige-1.0.1/intkrige/src/nrShell.cpp | 15 intkrige-1.0.1/intkrige/tests/testthat/test_intkrige.R | 7 49 files changed, 1571 insertions(+), 1177 deletions(-)
Title: An Individual-Based Population Genetic Simulation Environment
Description: An interface between R and the metasim simulation engine.
The simulation environment is documented in: "Strand, A.(2002) <DOI:10.1046/j.1471-8286.2002.00208.x> Metasim 1.0: an individual-based environment for simulating population genetics of
complex population dynamics. Mol. Ecol. Notes.
Please see the vignettes CreatingLandscapes and Simulating to get some ideas on how to use the packages.
See the rmetasim vignette to get an overview and to see important changes to the
code in the most recent version.
Author: Allan Strand <stranda@cofc.edu>,
James Niehaus
Maintainer: Allan Strand <stranda@cofc.edu>
Diff between rmetasim versions 3.1.13 dated 2020-01-29 and 3.1.14 dated 2020-02-07
CHANGELOG | 3 +++ DESCRIPTION | 6 +++--- MD5 | 18 +++++++++--------- inst/doc/ApplyCarryToStage.R | 12 ++++++------ inst/doc/ApplyCarryToStage.html | 4 ++-- inst/doc/CreatingLandscapes.R | 20 ++++++++++---------- inst/doc/CreatingLandscapes.html | 12 ++++++------ inst/doc/Sexuality-and-mating.R | 6 +++--- inst/doc/Simulating.R | 12 ++++++------ inst/doc/Simulating.html | 8 ++++---- 10 files changed, 52 insertions(+), 49 deletions(-)
Title: R Front End for 'Apache Spark'
Description: Provides an R Front end for 'Apache Spark' <https://spark.apache.org>.
Author: Shivaram Venkataraman [aut, cre],
Xiangrui Meng [aut],
Felix Cheung [aut],
The Apache Software Foundation [aut, cph]
Maintainer: Shivaram Venkataraman <shivaram@cs.berkeley.edu>
Diff between SparkR versions 2.4.4 dated 2019-09-02 and 2.4.5 dated 2020-02-07
DESCRIPTION | 8 MD5 | 332 +++++++++++++++++----------------- R/DataFrame.R | 8 R/SQLContext.R | 7 R/context.R | 6 R/functions.R | 6 R/group.R | 2 R/utils.R | 6 inst/doc/sparkr-vignettes.R | 190 +++++++++---------- inst/doc/sparkr-vignettes.html | 95 ++++----- inst/worker/worker.R | 2 man/SparkDataFrame.Rd | 127 ++++++++----- man/alias.Rd | 142 +++++++++----- man/approxQuantile.Rd | 13 - man/arrange.Rd | 134 ++++++++----- man/as.data.frame.Rd | 131 ++++++++----- man/attach.Rd | 134 +++++++++---- man/avg.Rd | 12 - man/awaitTermination.Rd | 12 - man/between.Rd | 13 - man/broadcast.Rd | 127 ++++++++----- man/cache.Rd | 127 ++++++++----- man/cast.Rd | 13 - man/checkpoint.Rd | 127 ++++++++----- man/coalesce.Rd | 127 ++++++++----- man/collect.Rd | 127 ++++++++----- man/coltypes.Rd | 127 ++++++++----- man/column.Rd | 5 man/column_aggregate_functions.Rd | 12 - man/column_collection_functions.Rd | 13 - man/column_datetime_diff_functions.Rd | 4 man/column_datetime_functions.Rd | 10 - man/column_math_functions.Rd | 1 man/column_misc_functions.Rd | 1 man/column_nonaggregate_functions.Rd | 6 man/column_string_functions.Rd | 7 man/column_window_functions.Rd | 4 man/columns.Rd | 127 ++++++++----- man/corr.Rd | 26 +- man/count.Rd | 12 - man/cov.Rd | 23 +- man/createDataFrame.Rd | 6 man/createExternalTable-deprecated.Rd | 3 man/createOrReplaceTempView.Rd | 126 ++++++++---- man/createTable.Rd | 3 man/crossJoin.Rd | 127 ++++++++----- man/crosstab.Rd | 10 - man/cube.Rd | 127 ++++++++----- man/dapply.Rd | 130 ++++++++----- man/dapplyCollect.Rd | 127 ++++++++----- man/describe.Rd | 127 ++++++++----- man/dim.Rd | 127 ++++++++----- man/distinct.Rd | 127 ++++++++----- man/drop.Rd | 127 ++++++++----- man/dropDuplicates.Rd | 127 ++++++++----- man/dtypes.Rd | 127 ++++++++----- man/endsWith.Rd | 13 - man/eq_null_safe.Rd | 1 man/except.Rd | 127 ++++++++----- man/exceptAll.Rd | 127 ++++++++----- man/explain.Rd | 140 +++++++++----- man/filter.Rd | 134 ++++++++----- man/first.Rd | 140 +++++++++----- man/fitted.Rd | 1 man/freqItems.Rd | 10 - man/gapply.Rd | 128 ++++++++----- man/gapplyCollect.Rd | 127 ++++++++----- man/getNumPartitions.Rd | 127 ++++++++----- man/glm.Rd | 19 + man/groupBy.Rd | 127 ++++++++----- man/head.Rd | 127 ++++++++----- man/hint.Rd | 127 ++++++++----- man/histogram.Rd | 130 ++++++++----- man/insertInto.Rd | 130 ++++++++----- man/install.spark.Rd | 8 man/intersect.Rd | 127 ++++++++----- man/intersectAll.Rd | 127 ++++++++----- man/isActive.Rd | 12 - man/isLocal.Rd | 127 ++++++++----- man/isStreaming.Rd | 127 ++++++++----- man/join.Rd | 130 ++++++++----- man/last.Rd | 12 - man/lastProgress.Rd | 12 - man/limit.Rd | 127 ++++++++----- man/localCheckpoint.Rd | 127 ++++++++----- man/match.Rd | 1 man/merge.Rd | 144 +++++++++----- man/mutate.Rd | 127 ++++++++----- man/nafunctions.Rd | 133 ++++++++----- man/ncol.Rd | 127 ++++++++----- man/not.Rd | 6 man/nrow.Rd | 127 ++++++++----- man/orderBy.Rd | 7 man/otherwise.Rd | 13 - man/over.Rd | 13 - man/partitionBy.Rd | 7 man/persist.Rd | 127 ++++++++----- man/pivot.Rd | 1 man/printSchema.Rd | 127 ++++++++----- man/queryName.Rd | 12 - man/randomSplit.Rd | 127 ++++++++----- man/rangeBetween.Rd | 7 man/rbind.Rd | 127 ++++++++----- man/read.df.Rd | 6 man/read.jdbc.Rd | 15 + man/registerTempTable-deprecated.Rd | 1 man/rename.Rd | 130 ++++++++----- man/repartition.Rd | 130 ++++++++----- man/repartitionByRange.Rd | 130 ++++++++----- man/rollup.Rd | 128 ++++++++----- man/rowsBetween.Rd | 7 man/sample.Rd | 134 ++++++++----- man/sampleBy.Rd | 13 - man/saveAsTable.Rd | 131 ++++++++----- man/schema.Rd | 128 ++++++++----- man/select.Rd | 135 ++++++++----- man/selectExpr.Rd | 128 ++++++++----- man/setCheckpointDir.Rd | 2 man/show.Rd | 128 ++++++++----- man/showDF.Rd | 131 ++++++++----- man/spark.als.Rd | 22 +- man/spark.bisectingKmeans.Rd | 17 + man/spark.decisionTree.Rd | 28 +- man/spark.fpGrowth.Rd | 13 - man/spark.gaussianMixture.Rd | 7 man/spark.gbt.Rd | 31 ++- man/spark.glm.Rd | 23 +- man/spark.isoreg.Rd | 13 - man/spark.kmeans.Rd | 17 + man/spark.kstest.Rd | 9 man/spark.lapply.Rd | 4 man/spark.lda.Rd | 18 + man/spark.logit.Rd | 29 +- man/spark.mlp.Rd | 25 +- man/spark.naiveBayes.Rd | 12 - man/spark.randomForest.Rd | 32 ++- man/spark.survreg.Rd | 14 - man/spark.svmLinear.Rd | 20 +- man/sparkR.init-deprecated.Rd | 12 - man/sparkR.session.Rd | 13 + man/startsWith.Rd | 13 - man/status.Rd | 12 - man/stopQuery.Rd | 12 - man/storageLevel.Rd | 128 ++++++++----- man/str.Rd | 128 ++++++++----- man/subset.Rd | 135 ++++++++----- man/substr.Rd | 13 - man/summarize.Rd | 128 ++++++++----- man/summary.Rd | 128 ++++++++----- man/take.Rd | 128 ++++++++----- man/toJSON.Rd | 128 ++++++++----- man/union.Rd | 128 ++++++++----- man/unionByName.Rd | 128 ++++++++----- man/unpersist.Rd | 128 ++++++++----- man/windowOrderBy.Rd | 1 man/windowPartitionBy.Rd | 1 man/with.Rd | 128 ++++++++----- man/withColumn.Rd | 128 ++++++++----- man/withWatermark.Rd | 131 ++++++++----- man/write.df.Rd | 134 ++++++++----- man/write.jdbc.Rd | 131 ++++++++----- man/write.json.Rd | 131 ++++++++----- man/write.orc.Rd | 131 ++++++++----- man/write.parquet.Rd | 131 ++++++++----- man/write.stream.Rd | 140 +++++++++----- man/write.text.Rd | 131 ++++++++----- tests/run-all.R | 23 +- 167 files changed, 7807 insertions(+), 4438 deletions(-)
Title: Sequentially-Allocated Latent Structure Optimization
Description: Point estimation for partition distributions using the sequentially-allocated latent structure optimization (SALSO) method to minimize the expectation of the Binder loss or the lower bound of the expectation of the variation of information loss. The SALSO method was presented at the workshop "Bayesian Nonparametric Inference: Dependence Structures and their Applications" in Oaxaca, Mexico on December 6, 2017. See <https://www.birs.ca/events/2017/5-day-workshops/17w5060/schedule>.
Author: David B. Dahl
Maintainer: David B. Dahl <dahl@stat.byu.edu>
Diff between salso versions 0.1.11 dated 2020-01-07 and 0.1.16 dated 2020-02-07
DESCRIPTION | 9 - INSTALL | 25 +++- MD5 | 34 +++--- NEWS | 14 ++ R/confidence.R | 3 R/dlso.R | 7 - R/plot.salso.confidence.R | 5 R/psm.R | 1 R/salso.R | 74 +++++++++----- man/confidence.Rd | 3 man/dlso.Rd | 7 - man/plot.salso.confidence.Rd | 5 man/psm.Rd | 1 man/salso.Rd | 65 +++++++----- src/rustlib/Cargo.lock | 224 +++++++++++++++++++++---------------------- src/rustlib/Cargo.toml | 2 src/rustlib/dahl-salso.h | 10 + src/wrapper.c | 28 +++-- 18 files changed, 300 insertions(+), 217 deletions(-)
Title: An 'SVG' Graphics Device
Description: A graphics device for R that produces 'Scalable Vector Graphics'.
'svglite' is a fork of the older 'RSvgDevice' package.
Author: Hadley Wickham [aut],
Lionel Henry [aut],
Thomas Lin Pedersen [cre, aut]
(<https://orcid.org/0000-0002-5147-4711>),
T Jake Luciani [aut],
Matthieu Decorde [aut],
Vaudor Lise [aut],
Tony Plate [ctb] (Early line dashing code),
David Gohel [ctb] (Line dashing code and raster code),
Yixuan Qiu [ctb] (Improved styles; polypath implementation),
Håkon Malmedal [ctb] (Opacity code),
RStudio [cph]
Maintainer: Thomas Lin Pedersen <thomas.pedersen@rstudio.com>
Diff between svglite versions 1.2.2 dated 2019-05-17 and 1.2.3 dated 2020-02-07
DESCRIPTION | 17 ++--- MD5 | 30 ++++---- NEWS.md | 10 ++ R/SVG.R | 5 - R/inlineSVG.R | 1 build/vignette.rds |binary inst/doc/fonts.R | 16 ++-- inst/doc/fonts.html | 125 ++++++++++++++++++------------------- inst/doc/scaling.html | 25 ++++--- man/svglite.Rd | 17 +++-- man/svgstring.Rd | 13 ++- src/SvgStream.h | 16 ++++ src/devSVG.cpp | 2 src/utils.h | 3 tests/testthat/test-points.R | 4 - tests/testthat/test-scale-text.svg | 2 16 files changed, 164 insertions(+), 122 deletions(-)
Title: Random Partition Distribution Indexed by Pairwise Information
Description: Implementations are provided for the models described in the paper D. B. Dahl, R. Day, J. Tsai (2017) <DOI:10.1080/01621459.2016.1165103>. The Ewens, Ewens-Pitman, Ewens attraction, Ewens-Pitman attraction, and ddCRP distributions are available for prior and posterior simulation. Posterior simulation is based on a user-supplied likelihood. Supporting functions for partition estimation and plotting are also provided.
Author: David B. Dahl [aut, cre]
Maintainer: David B. Dahl <dahl@stat.byu.edu>
Diff between shallot versions 0.4.7 dated 2019-10-02 and 0.4.8 dated 2020-02-07
shallot-0.4.7/shallot/man/sample.partitions.posterior.Rd |only shallot-0.4.8/shallot/DESCRIPTION | 10 ++-- shallot-0.4.8/shallot/MD5 | 31 +++++++-------- shallot-0.4.8/shallot/NEWS | 3 + shallot-0.4.8/shallot/R/shallot.R | 10 +--- shallot-0.4.8/shallot/inst/java/scala-2.11/shallot.jar |binary shallot-0.4.8/shallot/inst/java/scala-2.12/shallot.jar |binary shallot-0.4.8/shallot/inst/java/scala-2.13/shallot.jar |binary shallot-0.4.8/shallot/java/shallot-source.jar |binary shallot-0.4.8/shallot/man/default.mass.Rd | 23 ++++++++--- shallot-0.4.8/shallot/man/estimate.partition.Rd | 9 +++- shallot-0.4.8/shallot/man/mass.algorithm.Rd | 7 +-- shallot-0.4.8/shallot/man/nsubsets.random.Rd | 2 shallot-0.4.8/shallot/man/pairwise.probabilities.Rd | 2 shallot-0.4.8/shallot/man/partition.confidence.Rd | 7 +-- shallot-0.4.8/shallot/man/sample.partitions.Rd | 4 - shallot-0.4.8/shallot/man/variance.ratio.Rd | 7 +-- 17 files changed, 64 insertions(+), 51 deletions(-)
Title: Bayesian Reconstruction of Disease Outbreaks by Combining
Epidemiologic and Genomic Data
Description: Bayesian reconstruction of disease outbreaks using epidemiological
and genetic information. Jombart T, Cori A, Didelot X, Cauchemez S, Fraser
C and Ferguson N. 2014. <doi:10.1371/journal.pcbi.1003457>. Campbell, F,
Cori A, Ferguson N, Jombart T. 2019. <doi:10.1371/journal.pcbi.1006930>.
Author: Thibaut Jombart [aut],
Finlay Campbell [aut, cre],
Rich Fitzjohn [aut],
Gerry Tonkin-Hill [ctb],
Alexis Robert [ctb]
Maintainer: Finlay Campbell <finlaycampbell93@gmail.com>
Diff between outbreaker2 versions 1.1.0 dated 2019-06-13 and 1.1.1 dated 2020-02-07
DESCRIPTION | 14 +- MD5 | 107 +++++++++------- NEWS.md | 13 + R/bind_to_function.R | 2 R/custom_likelihoods.R | 2 R/sim_ctd.R | 2 README.md | 2 inst/doc/Rcpp_API.html | 40 ++--- inst/doc/customisation.html | 64 ++++----- inst/doc/introduction.html | 28 ++-- inst/doc/overview.html | 4 man/bind_to_function.Rd | 2 man/sim_ctd.Rd | 2 src/likelihoods.cpp | 2 src/moves.cpp | 4 vignettes/customisation_cache |only vignettes/figs-customisation/null_trees-1.png |binary vignettes/figs-customisation/res_new_move-1.png |binary vignettes/figs-customisation/res_new_move-2.png |binary vignettes/figs-customisation/res_null_diag-1.png |binary vignettes/figs-customisation/res_null_diag-2.png |binary vignettes/figs-customisation/res_null_model-1.png |binary vignettes/figs-customisation/res_null_model-2.png |binary vignettes/figs-customisation/res_null_model-3.png |binary vignettes/figs-customisation/res_wt-1.png |binary vignettes/figs-customisation/res_wt-2.png |binary vignettes/figs-customisation/res_wt-3.png |binary vignettes/figs-customisation/run_custom_move_mu-1.png |binary vignettes/figs-customisation/run_custom_move_mu-2.png |binary vignettes/figs-customisation/run_custom_move_mu-3.png |binary vignettes/figs-customisation/traces_custom_priors-1.png |binary vignettes/figs-customisation/traces_custom_priors-2.png |binary vignettes/figs-customisation/traces_custom_priors-3.png |binary vignettes/figs-customisation/traces_custom_priors-4.png |binary vignettes/figs-customisation/traces_custom_priors-5.png |binary vignettes/figs-introduction/basic_trace-1.png |binary vignettes/figs-introduction/basic_trace_burn-1.png |binary vignettes/figs-introduction/config2-1.png |binary vignettes/figs-introduction/config2-2.png |binary vignettes/figs-introduction/many_plots-1.png |binary vignettes/figs-introduction/many_plots-2.png |binary vignettes/figs-introduction/many_plots-3.png |binary vignettes/figs-introduction/many_plots-4.png |binary vignettes/figs-introduction/many_plots-5.png |binary vignettes/figs-introduction/traces-1.png |binary vignettes/figs-introduction/traces-2.png |binary vignettes/figs-introduction/traces-3.png |binary vignettes/introduction_cache |only 48 files changed, 151 insertions(+), 137 deletions(-)
Title: Expanded Replacement and Extension of the 'optim' Function
Description: Provides a replacement and extension of the optim()
function to call to several function minimization codes in R in a single
statement. These methods handle smooth, possibly box constrained functions
of several or many parameters. Note that function 'optimr()' was prepared to
simplify the incorporation of minimization codes going forward. Also implements some
utility codes and some extra solvers, including safeguarded Newton methods.
Many methods previously separate are now included here.
This is the version for CRAN.
Author: John C Nash [aut, cre],
Ravi Varadhan [aut],
Gabor Grothendieck [ctb]
Maintainer: John C Nash <nashjc@uottawa.ca>
Diff between optimx versions 2020-1.31 dated 2020-02-01 and 2020-2.2 dated 2020-02-07
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/optimr.R | 6 +++--- tests/hobbs.R | 21 ++++++++++++++++++--- 4 files changed, 28 insertions(+), 13 deletions(-)
Title: Animal Sounds for Bioacustic Analysis
Description: Collection of example animal sounds for bioacoustic analysis.
Author: Marcelo Araya-Salas [aut, cre]
Maintainer: Marcelo Araya-Salas <marceloa27@gmail.com>
Diff between NatureSounds versions 1.0.1 dated 2019-01-07 and 1.0.2 dated 2020-02-07
DESCRIPTION | 18 +++++++------- MD5 | 56 +++++++++++++++++++++++++++++++-------------- NAMESPACE | 1 NEWS.md | 8 ++++++ R/NatureSounds-package.R | 14 +++++------ R/Phae.long.est-data.R | 5 +++- R/Phae.long1-data.R | 6 ---- R/lbh.est-data.R |only R/monk.parakeet.est-data.R |only R/thyroptera.est-data.R |only README.md | 11 ++++---- build |only data/Cryp.soui.rda |binary data/Phae.long.est.rda |binary data/Phae.long1.rda |binary data/Phae.long2.rda |binary data/Phae.long3.rda |binary data/Phae.long4.rda |binary data/datalist | 3 ++ data/lbh.est.rda |only data/monk.parakeet.est.rda |only data/thyroptera.est.rda |only inst/doc |only man/NatureSounds.Rd | 13 ++++------ man/Phae.long.est.Rd | 5 +++- man/Phae.long1.Rd | 9 ------- man/lbh.est.Rd |only man/monk.parakeet.est.Rd |only man/thyroptera.est.Rd |only vignettes |only 30 files changed, 86 insertions(+), 63 deletions(-)
Title: Movement Data Visualization
Description: Tools to visualize movement data (e.g. from GPS tracking) and temporal changes of environmental data (e.g. from remote sensing) by creating video animations.
Author: Jakob Schwalb-Willmann [aut, cre]
Maintainer: Jakob Schwalb-Willmann <movevis@schwalb-willmann.de>
Diff between moveVis versions 0.10.3 dated 2019-10-06 and 0.10.4 dated 2020-02-07
moveVis-0.10.3/moveVis/R/basemap_data.R |only moveVis-0.10.3/moveVis/R/move_data.R |only moveVis-0.10.4/moveVis/DESCRIPTION | 12 moveVis-0.10.4/moveVis/MD5 | 96 +- moveVis-0.10.4/moveVis/NAMESPACE | 15 moveVis-0.10.4/moveVis/NEWS.md | 28 moveVis-0.10.4/moveVis/R/add_colourscale.R | 1 moveVis-0.10.4/moveVis/R/align_move.R | 8 moveVis-0.10.4/moveVis/R/animate_frames.R | 6 moveVis-0.10.4/moveVis/R/data.R |only moveVis-0.10.4/moveVis/R/df2move.R | 2 moveVis-0.10.4/moveVis/R/frames_graph.R | 42 - moveVis-0.10.4/moveVis/R/frames_spatial.R | 38 - moveVis-0.10.4/moveVis/R/get_frametimes.R | 2 moveVis-0.10.4/moveVis/R/moveVis-internal.R | 390 +++++++----- moveVis-0.10.4/moveVis/R/pkgname.R | 2 moveVis-0.10.4/moveVis/R/settings.R |only moveVis-0.10.4/moveVis/R/subset_move.R | 4 moveVis-0.10.4/moveVis/README.md | 24 moveVis-0.10.4/moveVis/data/datalist | 1 moveVis-0.10.4/moveVis/data/whitestork_data.rda |only moveVis-0.10.4/moveVis/inst |only moveVis-0.10.4/moveVis/man/add_colourscale.Rd | 15 moveVis-0.10.4/moveVis/man/add_gg.Rd | 2 moveVis-0.10.4/moveVis/man/add_labels.Rd | 15 moveVis-0.10.4/moveVis/man/add_northarrow.Rd | 19 moveVis-0.10.4/moveVis/man/add_progress.Rd | 2 moveVis-0.10.4/moveVis/man/add_scalebar.Rd | 17 moveVis-0.10.4/moveVis/man/add_text.Rd | 14 moveVis-0.10.4/moveVis/man/add_timestamps.Rd | 5 moveVis-0.10.4/moveVis/man/align_move.Rd | 9 moveVis-0.10.4/moveVis/man/animate_frames.Rd | 18 moveVis-0.10.4/moveVis/man/basemap_data.Rd | 4 moveVis-0.10.4/moveVis/man/frames_graph.Rd | 25 moveVis-0.10.4/moveVis/man/frames_spatial.Rd | 47 + moveVis-0.10.4/moveVis/man/join_frames.Rd | 2 moveVis-0.10.4/moveVis/man/moveVis-package.Rd | 2 moveVis-0.10.4/moveVis/man/move_data.Rd | 6 moveVis-0.10.4/moveVis/man/settings.Rd |only moveVis-0.10.4/moveVis/man/suggest_formats.Rd | 5 moveVis-0.10.4/moveVis/man/view_spatial.Rd | 15 moveVis-0.10.4/moveVis/man/whitestork_data.Rd |only moveVis-0.10.4/moveVis/tests/testthat/helper-vars.R | 18 moveVis-0.10.4/moveVis/tests/testthat/test-add_.R | 113 +++ moveVis-0.10.4/moveVis/tests/testthat/test-align_move.R | 23 moveVis-0.10.4/moveVis/tests/testthat/test-animate_frames.R | 17 moveVis-0.10.4/moveVis/tests/testthat/test-df2move.R | 31 moveVis-0.10.4/moveVis/tests/testthat/test-frames_graph.R | 54 + moveVis-0.10.4/moveVis/tests/testthat/test-frames_spatial.R | 86 +- moveVis-0.10.4/moveVis/tests/testthat/test-get_frametimes.R |only moveVis-0.10.4/moveVis/tests/testthat/test-join_frames.R | 5 moveVis-0.10.4/moveVis/tests/testthat/test-settings.R |only moveVis-0.10.4/moveVis/tests/testthat/test-subset_move.R | 8 moveVis-0.10.4/moveVis/tests/testthat/test-view_spatial.R | 11 54 files changed, 868 insertions(+), 391 deletions(-)
Title: The Kernel Method of Test Equating
Description: Implements the kernel method of test equating as defined in von Davier, A. A., Holland, P. W. and Thayer, D. T. (2004) <doi: 10.1007/b97446> and Andersson, B. and Wiberg, M. (2017) <doi: 10.1007/s11336-016-9528-7> using the CB, EG, SG, NEAT CE/PSE and NEC designs, supporting Gaussian, logistic and uniform kernels and unsmoothed and pre-smoothed input data.
Author: Björn Andersson [aut, cre],
Kenny Bränberg [aut],
Marie Wiberg [aut]
Maintainer: Björn Andersson <bjoern.h.andersson@gmail.com>
Diff between kequate versions 1.6.2 dated 2019-05-31 and 1.6.3 dated 2020-02-07
DESCRIPTION | 8 MD5 | 16 - NEWS | 6 R/kernel.R | 611 ++++++++++++++++++++++++++----------------------- build/vignette.rds |binary inst/doc/irtguide.pdf |binary inst/doc/kequate.pdf |binary man/irtose.Rd | 2 man/kequate-package.Rd | 4 9 files changed, 353 insertions(+), 294 deletions(-)
Title: A 'Shiny' App for Exploration of Text Collections
Description: Facilitates dynamic exploration of text collections through an
intuitive graphical user interface and the power of regular expressions.
The package contains 1) a helper function to convert a data frame to a
'corporaexplorerobject', 2) a 'Shiny' app for fast and flexible exploration
of a 'corporaexplorerobject', and 3) a 'Shiny' app for simple
retrieval/extraction of documents from a 'corporaexplorerobject' in a
reading-friendly format. The package also includes demo apps with which
one can explore Jane Austen's novels and the State of the Union Addresses
(data from the 'janeaustenr' and 'sotu' packages respectively).
Author: Kristian Lundby Gjerde [aut, cre]
Maintainer: Kristian Lundby Gjerde <kristian.gjerde@gmail.com>
Diff between corporaexplorer versions 0.8.1 dated 2020-02-06 and 0.8.1.1 dated 2020-02-07
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 2 +- data/test_data.rda |binary 4 files changed, 8 insertions(+), 8 deletions(-)
More information about corporaexplorer at CRAN
Permanent link
Title: Graph-Based Permutation Tests for Microbiome Data
Description: Provides functions for graph-based multiple-sample
testing and visualization of microbiome data, in particular data
stored in 'phyloseq' objects. The tests are based on those
described in Friedman and Rafsky (1979)
<http://www.jstor.org/stable/2958919>, and the tests are described
in more detail in Callahan et al. (2016)
<doi:10.12688/f1000research.8986.1>.
Author: Julia Fukuyama [aut, cre]
Maintainer: Julia Fukuyama <julia.fukuyama@gmail.com>
Diff between phyloseqGraphTest versions 0.0.2 dated 2018-06-27 and 0.1.0 dated 2020-02-07
DESCRIPTION | 6 MD5 | 10 R/graphtest-functions.R | 10 build/vignette.rds |binary inst/doc/gt_vignette.R | 12 inst/doc/gt_vignette.html | 1518 +++++++++++++++++++++++++++++++++++++++++++--- 6 files changed, 1456 insertions(+), 100 deletions(-)
More information about phyloseqGraphTest at CRAN
Permanent link
Title: Fits Models Inside the Database
Description: Uses 'dplyr' and 'tidyeval' to fit statistical models inside the database. It currently supports KMeans and linear regression models.
Author: Edgar Ruiz [aut, cre]
Maintainer: Edgar Ruiz <edgararuiz@gmail.com>
Diff between modeldb versions 0.2.0 dated 2019-07-20 and 0.2.1 dated 2020-02-07
DESCRIPTION | 12 ++++++------ MD5 | 32 ++++++++++++++++---------------- NAMESPACE | 1 + NEWS.md | 4 ++++ R/kmeans-viz.R | 4 ++-- R/lm.R | 12 ++++++------ R/model_prep.R | 2 +- R/modeldb.R | 1 + build/vignette.rds |binary inst/doc/kmeans.R | 14 +++++++------- inst/doc/kmeans.html | 13 ++++++++----- inst/doc/linear-regression.R | 22 +++++++++++----------- inst/doc/linear-regression.html | 15 +++++++++------ man/add_dummy_variables.Rd | 9 +++++++-- man/linear_regression_db.Rd | 3 +-- man/modeldb-package.Rd | 4 ++-- man/simple_kmeans_db.Rd | 12 +++++++++--- 17 files changed, 91 insertions(+), 69 deletions(-)
Title: Required 'libphonenumber' jars for the 'dialr' Package
Description: Collects 'libphonenumber' jars required for the
'dialr' package.
Author: Danny Smith [aut, cre],
Google Inc. [ctb, cph] (libphonenumber),
Vonage Holdings Corp. [ctb, cph] (libphonenumber),
Ian Galpin [ctb, cph] (libphonenumber),
Ben Gertzfield [ctb, cph] (libphonenumber)
Maintainer: Danny Smith <danny@gorcha.org>
Diff between dialrjars versions 8.10.14 dated 2019-06-26 and 8.11.3 dated 2020-02-07
dialrjars-8.10.14/dialrjars/inst/java/carrier-1.110.jar |only dialrjars-8.10.14/dialrjars/inst/java/geocoder-2.120.jar |only dialrjars-8.10.14/dialrjars/inst/java/libphonenumber-8.10.14.jar |only dialrjars-8.10.14/dialrjars/inst/java/prefixmapper-2.120.jar |only dialrjars-8.11.3/dialrjars/DESCRIPTION | 6 dialrjars-8.11.3/dialrjars/MD5 | 28 - dialrjars-8.11.3/dialrjars/NAMESPACE | 6 dialrjars-8.11.3/dialrjars/NEWS.md | 202 ++++++---- dialrjars-8.11.3/dialrjars/R/dialrjars.R | 6 dialrjars-8.11.3/dialrjars/README.md | 58 +- dialrjars-8.11.3/dialrjars/inst/COPYRIGHTS | 18 dialrjars-8.11.3/dialrjars/inst/java/carrier-1.123.jar |only dialrjars-8.11.3/dialrjars/inst/java/geocoder-2.133.jar |only dialrjars-8.11.3/dialrjars/inst/java/libphonenumber-8.11.3.jar |only dialrjars-8.11.3/dialrjars/inst/java/prefixmapper-2.133.jar |only dialrjars-8.11.3/dialrjars/java/README | 14 dialrjars-8.11.3/dialrjars/man/dialrjars-package.Rd | 66 +-- dialrjars-8.11.3/dialrjars/tests/testthat.R | 8 dialrjars-8.11.3/dialrjars/tests/testthat/test-dialrjars.R | 76 +-- 19 files changed, 279 insertions(+), 209 deletions(-)
Title: Integrates with the 'RStudio' Connections Pane and 'pins'
Description: Enables 'DBI' compliant packages to integrate with the 'RStudio' connections
pane, and the 'pins' package. It automates the display of schemata, tables, views, as well
as the preview of the table's top 1000 records.
Author: Javier Luraschi [aut, cre],
Edgar Ruiz [aut]
Maintainer: Javier Luraschi <javier@rstudio.com>
Diff between connections versions 0.1.0 dated 2019-10-28 and 0.1.1 dated 2020-02-07
DESCRIPTION | 18 +++++++++++------- MD5 | 7 ++++--- NEWS.md |only man/DBI.Rd | 4 ++-- man/connection_view.Rd | 9 +++++++-- 5 files changed, 24 insertions(+), 14 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 1.5.4-6 dated 2020-02-02 and 1.5.4-7 dated 2020-02-07
DESCRIPTION | 9 ++++----- MD5 | 6 +++--- NAMESPACE | 2 ++ NEWS | 4 ++++ 4 files changed, 13 insertions(+), 8 deletions(-)
Title: Limit of Detection Imputation for Single-Pollutant Models
Description: Impute observed values below the limit of detection (LOD) via
censored likelihood multiple imputation (CLMI) in single-pollutant
models, developed by Boss et al (2019) <doi:10.1097/EDE.0000000000001052>.
CLMI handles exposure detection limits that may change throughout the course
of exposure assessment. 'lodi' provides functions for imputing and
pooling for this method.
Author: Jonathan Boss [aut],
Alexander Rix [aut, cre]
Maintainer: Alexander Rix <alexrix@umich.edu>
Diff between lodi versions 0.9.1 dated 2019-08-28 and 0.9.2 dated 2020-02-07
DESCRIPTION | 12 - MD5 | 20 +- NEWS.md | 13 + R/cca-r2.R | 109 ++++++----- R/clmi.R | 486 +++++++++++++++++++++++++++-------------------------- README.md | 97 ++++++---- inst/doc/lodi.R | 14 - inst/doc/lodi.html | 34 +-- man/clmi.Rd | 8 man/lod_root2.Rd | 12 - tests |only 11 files changed, 432 insertions(+), 373 deletions(-)
Title: Harrell Miscellaneous
Description: Contains many functions useful for data
analysis, high-level graphics, utility operations, functions for
computing sample size and power, importing and annotating datasets,
imputing missing values, advanced table making, variable clustering,
character string manipulation, conversion of R objects to LaTeX and html code,
and recoding variables.
Author: Frank E Harrell Jr <f.harrell@vanderbilt.edu>, with
contributions from Charles Dupont and many others.
Maintainer: Frank E Harrell Jr <f.harrell@vanderbilt.edu>
Diff between Hmisc versions 4.3-0 dated 2019-11-07 and 4.3-1 dated 2020-02-07
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NEWS | 6 ++++++ R/html.s | 19 ++++++++++++++++++- R/popower.s | 1 + man/mChoice.Rd | 5 ----- 6 files changed, 35 insertions(+), 16 deletions(-)
Title: Methods for Temporal Disaggregation and Interpolation of Time
Series
Description: Temporal disaggregation methods are used to disaggregate and
interpolate a low frequency time series to a higher frequency series, where
either the sum, the mean, the first or the last value of the resulting
high frequency series is consistent with the low frequency series. Temporal
disaggregation can be performed with or without one or more high frequency
indicator series. Contains the methods of Chow-Lin, Santos-Silva-Cardoso,
Fernandez, Litterman, Denton and Denton-Cholette, summarized in Sax and
Steiner (2013) <doi:10.32614/RJ-2013-028>. Supports most R time series
classes.
Author: Christoph Sax [aut, cre] (<https://orcid.org/0000-0002-7192-7044>),
Peter Steiner [aut],
Tommaso Di Fonzo [ctb]
Maintainer: Christoph Sax <christoph.sax@gmail.com>
Diff between tempdisagg versions 0.25.0 dated 2016-07-10 and 1.0 dated 2020-02-07
tempdisagg-0.25.0/tempdisagg/NEWS |only tempdisagg-1.0/tempdisagg/DESCRIPTION | 27 tempdisagg-1.0/tempdisagg/MD5 | 56 - tempdisagg-1.0/tempdisagg/NEWS.md |only tempdisagg-1.0/tempdisagg/R/irregular.R |only tempdisagg-1.0/tempdisagg/R/ta.R | 155 ++-- tempdisagg-1.0/tempdisagg/R/td.R | 767 ++++++++++++-------- tempdisagg-1.0/tempdisagg/R/td.calc.R | 162 ++-- tempdisagg-1.0/tempdisagg/R/td.output.R | 230 +++-- tempdisagg-1.0/tempdisagg/R/td.sub.R | 316 +++++--- tempdisagg-1.0/tempdisagg/R/tempdisagg-package.R | 99 +- tempdisagg-1.0/tempdisagg/R/utils.R |only tempdisagg-1.0/tempdisagg/README.md | 18 tempdisagg-1.0/tempdisagg/build |only tempdisagg-1.0/tempdisagg/data/tempdisagg.RData |only tempdisagg-1.0/tempdisagg/demo/tempdisagg.R | 22 tempdisagg-1.0/tempdisagg/inst |only tempdisagg-1.0/tempdisagg/man/exports.m.Rd | 7 tempdisagg-1.0/tempdisagg/man/gdp.q.Rd |only tempdisagg-1.0/tempdisagg/man/plot.td.Rd | 16 tempdisagg-1.0/tempdisagg/man/predict.td.Rd | 16 tempdisagg-1.0/tempdisagg/man/spi.d.Rd |only tempdisagg-1.0/tempdisagg/man/summary.td.Rd | 56 - tempdisagg-1.0/tempdisagg/man/ta.Rd | 24 tempdisagg-1.0/tempdisagg/man/td.Rd | 360 +++++---- tempdisagg-1.0/tempdisagg/man/tempdisagg-package.Rd | 37 tempdisagg-1.0/tempdisagg/tests/test-all.R | 67 + tempdisagg-1.0/tempdisagg/tests/testthat |only tempdisagg-1.0/tempdisagg/vignettes |only 29 files changed, 1420 insertions(+), 1015 deletions(-)
Title: Access to the 'Google Cloud Vision' API for Image Recognition,
OCR and Labeling
Description: Interact with the 'Google Cloud Vision' <https://cloud.google.com/vision/>
API in R. Part of the 'cloudyr' <https://cloudyr.github.io/> project.
Author: Jeno Pal [cre],
Tamas Koncz [aut],
Balazs Varkoly [aut],
Peter Lukacs [aut],
Eszter Kocsis [aut],
Florian Teschner [ctb]
Maintainer: Jeno Pal <paljenczy@gmail.com>
Diff between googleCloudVisionR versions 0.1.0 dated 2019-06-28 and 0.2.0 dated 2020-02-07
googleCloudVisionR-0.1.0/googleCloudVisionR/man/getBoundingBoxes.Rd |only googleCloudVisionR-0.1.0/googleCloudVisionR/man/get_feature_types.Rd |only googleCloudVisionR-0.1.0/googleCloudVisionR/tests/testthat/annotated_images.csv |only googleCloudVisionR-0.2.0/googleCloudVisionR/DESCRIPTION | 19 googleCloudVisionR-0.2.0/googleCloudVisionR/MD5 | 53 - googleCloudVisionR-0.2.0/googleCloudVisionR/NAMESPACE | 2 googleCloudVisionR-0.2.0/googleCloudVisionR/NEWS.md | 13 googleCloudVisionR-0.2.0/googleCloudVisionR/R/get_available_feature_types.R |only googleCloudVisionR-0.2.0/googleCloudVisionR/R/get_google_vision_response.R | 357 +++++----- googleCloudVisionR-0.2.0/googleCloudVisionR/R/googleCloudVisionR-package.R | 2 googleCloudVisionR-0.2.0/googleCloudVisionR/R/input_validations.R |only googleCloudVisionR-0.2.0/googleCloudVisionR/R/zzz.R | 95 +- googleCloudVisionR-0.2.0/googleCloudVisionR/README.md | 12 googleCloudVisionR-0.2.0/googleCloudVisionR/man/call_vision_api.Rd | 7 googleCloudVisionR-0.2.0/googleCloudVisionR/man/extract_annotations.Rd | 4 googleCloudVisionR-0.2.0/googleCloudVisionR/man/extractor.Rd | 4 googleCloudVisionR-0.2.0/googleCloudVisionR/man/figures |only googleCloudVisionR-0.2.0/googleCloudVisionR/man/gcv_get_available_feature_types.Rd |only googleCloudVisionR-0.2.0/googleCloudVisionR/man/gcv_get_image_annotations.Rd | 4 googleCloudVisionR-0.2.0/googleCloudVisionR/man/gcv_get_raw_response.Rd |only googleCloudVisionR-0.2.0/googleCloudVisionR/man/get_bounding_boxes.Rd |only googleCloudVisionR-0.2.0/googleCloudVisionR/man/get_invalid_image_paths.Rd | 2 googleCloudVisionR-0.2.0/googleCloudVisionR/man/googleCloudVisionR-package.Rd | 12 googleCloudVisionR-0.2.0/googleCloudVisionR/tests/testthat/test-get_google_vision_response.R | 254 ++++--- googleCloudVisionR-0.2.0/googleCloudVisionR/tests/testthat/test-integration-tests.R | 62 - googleCloudVisionR-0.2.0/googleCloudVisionR/tests/testthat/test-utils.R | 45 - googleCloudVisionR-0.2.0/googleCloudVisionR/tests/testthat/test_data/document_text_detection.csv | 5 googleCloudVisionR-0.2.0/googleCloudVisionR/tests/testthat/test_data/face_detection.csv | 6 googleCloudVisionR-0.2.0/googleCloudVisionR/tests/testthat/test_data/label_detection.csv | 22 googleCloudVisionR-0.2.0/googleCloudVisionR/tests/testthat/test_data/landmark_detection.csv | 6 googleCloudVisionR-0.2.0/googleCloudVisionR/tests/testthat/test_data/logo_detection.csv | 10 googleCloudVisionR-0.2.0/googleCloudVisionR/tests/testthat/test_data/text_detection.csv | 5 32 files changed, 564 insertions(+), 437 deletions(-)
More information about googleCloudVisionR at CRAN
Permanent link
Title: Find, Download and Process Sentinel-2 Data
Description: Functions to download Sentinel-2 optical images
and perform preliminary processing operations.
'sen2r' provides the instruments required to easily perform
(and eventually automate) the steps necessary to build a complete
Sentinel-2 processing chain.
A Graphical User Interface to facilitate data processing is also provided.
Author: Luigi Ranghetti [aut, cre] (<https://orcid.org/0000-0001-6207-5188>),
Lorenzo Busetto [aut] (<https://orcid.org/0000-0001-9634-6038>)
Maintainer: Luigi Ranghetti <luigi@ranghetti.info>
Diff between sen2r versions 1.3.0 dated 2020-02-04 and 1.3.1 dated 2020-02-07
DESCRIPTION | 8 MD5 | 137 +++++----- NAMESPACE | 2 NEWS.md | 21 + R/build_example_param_file.R | 4 R/check_gdal.R | 3 R/check_param_list.R | 28 +- R/gdal_abs2rel.R | 2 R/gdal_warp.R | 8 R/gdalwarp_grid.R | 4 R/init_python.R | 39 ++ R/load_binpaths.R | 6 R/print_message.R | 10 R/raster_metadata.R | 2 R/s2_calcindices.R | 26 + R/s2_download.R | 12 R/s2_gui.R | 13 R/s2_mask.R | 46 ++- R/s2_rgb.R | 8 R/s2_thumbnails.R | 1 R/s2_translate.R | 16 - R/safe_getMetadata.R | 44 +-- R/sen2r.R | 60 ++-- R/sen2r_process_report.R | 7 R/smooth_mask.R | 2 R/st_crs2.R | 2 build/vignette.rds |binary inst/CITATION | 4 inst/WORDLIST | 12 inst/doc/installation.Rmd | 13 inst/doc/installation.html | 15 - inst/doc/outstructure.R |only inst/doc/outstructure.Rmd |only inst/doc/outstructure.html |only inst/doc/sen2r_cmd.R |only inst/doc/sen2r_cmd.Rmd |only inst/doc/sen2r_cmd.html |only inst/doc/sen2r_gui.R |only inst/doc/sen2r_gui.Rmd |only inst/doc/sen2r_gui.html |only inst/extdata/out/S2A1C_20190723_022_Barbellino_RGB432T_10.tif |only inst/extdata/out/S2A1C_20190723_022_Barbellino_TOA_10.tif |only inst/extdata/out/S2A2A_20190723_022_Barbellino_BOA_10.tif |only inst/extdata/out/S2A2A_20190723_022_Barbellino_MSAVI2_10.tif |only inst/extdata/out/S2A2A_20190723_022_Barbellino_NDVI_10.tif |only inst/extdata/out/S2A2A_20190723_022_Barbellino_RGB432B_10.tif |only inst/extdata/out/S2A2A_20190723_022_Barbellino_RGB432B_10.vrt |only inst/extdata/out/S2A2A_20190723_022_Barbellino_RGB843B_10.tif |only inst/extdata/out/S2A2A_20190723_022_Barbellino_SCL_10.tif |only man/figures/sen2r_gui_sheet1.png |binary man/figures/sen2r_gui_sheet1_small.png |binary man/figures/sen2r_gui_sheet2.png |binary man/figures/sen2r_gui_sheet3.png |binary man/figures/sen2r_gui_sheet4.png |binary man/figures/sen2r_gui_sheet5.png |binary man/gdal_abs2rel_rel2abs.Rd | 2 man/gdal_warp.Rd | 4 man/gdalwarp_grid.Rd | 4 man/init_python.Rd | 9 man/raster_metadata.Rd | 2 man/s2_calcindices.Rd | 2 man/s2_mask.Rd | 6 man/s2_rgb.Rd | 2 man/s2_translate.Rd | 16 - man/safe_getMetadata.Rd | 12 man/sen2r.Rd | 22 - man/st_crs2.Rd | 2 tests/testthat/test-t06_scihub_login.R | 6 tests/testthat/test-t12_s2_download.R | 32 +- tests/testthat/test-t14_sen2cor.R | 58 ++-- tests/testthat/test-t20_s2_merge.R | 21 - tests/testthat/test-t21_s2_warp.R | 56 ++-- tests/testthat/test-t22_s2_mask.R | 37 +- tests/testthat/test-t23_s2_indices.R | 36 +- tests/testthat/test-t24_s2_rgb.R | 24 - tests/testthat/test-t34_st_crs2.R | 2 vignettes/installation.Rmd | 13 vignettes/outstructure.Rmd |only vignettes/sen2r_cmd.Rmd |only vignettes/sen2r_gui.Rmd |only 80 files changed, 566 insertions(+), 357 deletions(-)
Title: Optimal Project Prioritization
Description: A decision support tool for prioritizing conservation projects.
Prioritizations can be developed by maximizing expected feature richness,
expected phylogenetic diversity, the number of features that meet
persistence targets, or identifying a set of projects that meet persistence
targets for minimal cost. Constraints (e.g. lock in specific actions) and
feature weights can also be specified to further customize prioritizations.
After defining a project prioritization problem, solutions can be obtained
using exact algorithms, heuristic algorithms, or random processes. In
particular, it is recommended to install the 'Gurobi' optimizer (available
from <https://www.gurobi.com>) because it can identify optimal solutions
very quickly. Finally, methods are provided for comparing different
prioritizations and evaluating their benefits. For more information, see
Hanson et al. (2019) <doi:10.1111/2041-210X.13264>.
Author: Jeffrey O Hanson [aut, cre],
Richard Schuster [aut],
Matthew Strimas-Mackey [aut],
Joseph Bennett [aut]
Maintainer: Jeffrey O Hanson <jeffrey.hanson@uqconnect.edu.au>
Diff between oppr versions 0.0.4 dated 2019-08-10 and 1.0.0 dated 2020-02-07
DESCRIPTION | 11 ++- MD5 | 14 ++-- NEWS.md | 9 +++ R/show.R | 2 README.md | 20 +++---- inst/CITATION | 17 +++++ inst/doc/oppr.html | 151 ++++++++++++++++++++++++++++------------------------- man/show.Rd | 2 8 files changed, 128 insertions(+), 98 deletions(-)
Title: Create Beautiful, Customizable, Publication-Ready Summary Tables
for Statistical Models
Description: Create beautiful, customizable, publication-ready summary tables
for statistical models. 'modelsummary' leverages the power of the 'gt' and
'broom' packages. It can produce tables in HTML, RTF, JPG, and LaTeX formats
(text/markdown/ascii tables coming soon). The 'gt' package is hosted on
'Github' by the 'RStudio' organization: <http://github.com/rstudio/gt>.
Author: Vincent Arel-Bundock [aut, cre]
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Diff between modelsummary versions 0.1.0 dated 2019-07-15 and 0.1.1 dated 2020-02-07
modelsummary-0.1.0/modelsummary/R/knit_latex.R |only modelsummary-0.1.1/modelsummary/DESCRIPTION | 8 modelsummary-0.1.1/modelsummary/MD5 | 79 +- modelsummary-0.1.1/modelsummary/NAMESPACE | 2 modelsummary-0.1.1/modelsummary/NEWS.md | 12 modelsummary-0.1.1/modelsummary/R/clean_latex.R |only modelsummary-0.1.1/modelsummary/R/extract.R | 50 + modelsummary-0.1.1/modelsummary/R/extract_estimates.R | 100 +-- modelsummary-0.1.1/modelsummary/R/extract_gof.R | 2 modelsummary-0.1.1/modelsummary/R/modelsummary.R | 30 modelsummary-0.1.1/modelsummary/R/sanity_checks.R | 12 modelsummary-0.1.1/modelsummary/README.md | 122 ++-- modelsummary-0.1.1/modelsummary/man/clean_latex.Rd |only modelsummary-0.1.1/modelsummary/man/extract.Rd | 29 modelsummary-0.1.1/modelsummary/man/extract_estimates.Rd | 18 modelsummary-0.1.1/modelsummary/man/extract_statistic_override.Rd | 6 modelsummary-0.1.1/modelsummary/man/glance.mira.Rd | 3 modelsummary-0.1.1/modelsummary/man/knit_latex.Rd | 9 modelsummary-0.1.1/modelsummary/man/modelsummary.Rd | 35 - modelsummary-0.1.1/modelsummary/man/msummary.Rd | 35 - modelsummary-0.1.1/modelsummary/man/reexports.Rd | 2 modelsummary-0.1.1/modelsummary/man/sanity_checks.Rd | 30 modelsummary-0.1.1/modelsummary/man/statistic_override_vector.Rd | 3 modelsummary-0.1.1/modelsummary/man/tidy.mira.Rd | 3 modelsummary-0.1.1/modelsummary/tests/testthat/known_output/background_color.html | 274 ++++---- modelsummary-0.1.1/modelsummary/tests/testthat/known_output/coef_map_collapse_coefficients.html | 109 +-- modelsummary-0.1.1/modelsummary/tests/testthat/known_output/coef_omit.html | 178 ++--- modelsummary-0.1.1/modelsummary/tests/testthat/known_output/complex_table.html | 305 ++++------ modelsummary-0.1.1/modelsummary/tests/testthat/known_output/conf.int.html | 274 ++++---- modelsummary-0.1.1/modelsummary/tests/testthat/known_output/p.value.html | 274 ++++---- modelsummary-0.1.1/modelsummary/tests/testthat/known_output/rounding.html | 274 ++++---- modelsummary-0.1.1/modelsummary/tests/testthat/known_output/stars_custom.html | 268 ++++---- modelsummary-0.1.1/modelsummary/tests/testthat/known_output/stars_default.html | 268 ++++---- modelsummary-0.1.1/modelsummary/tests/testthat/known_output/statistic.html | 274 ++++---- modelsummary-0.1.1/modelsummary/tests/testthat/known_output/statistic_override_1.html | 274 ++++---- modelsummary-0.1.1/modelsummary/tests/testthat/known_output/statistic_override_2.html | 274 ++++---- modelsummary-0.1.1/modelsummary/tests/testthat/known_output/statistic_override_3.html | 274 ++++---- modelsummary-0.1.1/modelsummary/tests/testthat/known_output/statistic_override_4.html | 274 ++++---- modelsummary-0.1.1/modelsummary/tests/testthat/known_output/std.error.html | 274 ++++---- modelsummary-0.1.1/modelsummary/tests/testthat/known_output/title.html | 274 ++++---- modelsummary-0.1.1/modelsummary/tests/testthat/known_output/title_subtitle.html | 274 ++++---- modelsummary-0.1.1/modelsummary/tests/testthat/test-known-output.R | 11 42 files changed, 2582 insertions(+), 2435 deletions(-)
Title: Tools for Analyzing Finite Mixture Models
Description: Analyzes finite mixture models for various parametric and semiparametric settings. This includes mixtures of parametric distributions (normal, multivariate normal, multinomial, gamma), various Reliability Mixture Models (RMMs), mixtures-of-regressions settings (linear regression, logistic regression, Poisson regression, linear regression with changepoints, predictor-dependent mixing proportions, random effects regressions, hierarchical mixtures-of-experts), and tools for selecting the number of components (bootstrapping the likelihood ratio test statistic, mixturegrams, and model selection criteria). Bayesian estimation of mixtures-of-linear-regressions models is available as well as a novel data depth method for obtaining credible bands. This package is based upon work supported by the National Science Foundation under Grant No. SES-0518772.
Author: Derek Young [aut, cre] (<https://orcid.org/0000-0002-3048-3803>),
Tatiana Benaglia [aut],
Didier Chauveau [aut],
David Hunter [aut],
Ryan Elmore [ctb],
Thomas Hettmansperger [ctb],
Hoben Thomas [ctb],
Fengjuan Xuan [ctb]
Maintainer: Derek Young <derek.young@uky.edu>
Diff between mixtools versions 1.1.0 dated 2017-03-12 and 1.2.0 dated 2020-02-07
DESCRIPTION | 18 +- MD5 | 53 ++++--- NAMESPACE | 6 NEWS | 15 ++ R/flaremixEM.R | 38 ++--- R/gammamixEM.R | 281 ++++++++++++++++++++++++++++++----------- R/gammamixinit.R | 72 +++++----- R/lambda.R | 60 ++++---- R/ldc.R |only R/logisregmixinit.R | 68 ++++------ R/mixturegram.R |only R/multmixEM.R | 2 R/multmixmodelsel.R | 116 ++++++++--------- R/normalmixinit.R | 113 ++++++++-------- R/poisregmixinit.R | 67 ++++----- R/tryflare.R | 318 +++++++++++++++++++++++------------------------ build/vignette.rds |binary inst/doc/mixtools.pdf |binary man/CO2data.Rd | 46 +++--- man/NOdata.Rd | 48 +++---- man/RTdata.Rd | 52 +++---- man/RTdata2.Rd | 58 ++++---- man/RanEffdata.Rd | 34 ++--- man/RodFramedata.Rd | 44 +++--- man/Waterdata.Rd | 142 ++++++++++---------- man/flaremixEM.Rd | 168 ++++++++++++------------ man/gammamixEM.Rd | 125 +++++++++--------- man/mixtools-internal.Rd | 11 + man/mixturegram.Rd |only 29 files changed, 1060 insertions(+), 895 deletions(-)
Title: An Implementation of Grammar of Graphics for Graphs and Networks
Description: The grammar of graphics as implemented in ggplot2 is a poor fit for
graph and network visualizations due to its reliance on tabular data input.
ggraph is an extension of the ggplot2 API tailored to graph visualizations
and provides the same flexible approach to building up plots layer by layer.
Author: Thomas Lin Pedersen [cre, aut]
(<https://orcid.org/0000-0002-5147-4711>),
RStudio [cph]
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>
Diff between ggraph versions 2.0.0 dated 2019-09-02 and 2.0.1 dated 2020-02-07
ggraph-2.0.0/ggraph/R/qgraph.R |only ggraph-2.0.1/ggraph/DESCRIPTION | 11 ggraph-2.0.1/ggraph/MD5 | 167 ++++++------ ggraph-2.0.1/ggraph/NAMESPACE | 2 ggraph-2.0.1/ggraph/NEWS.md | 10 ggraph-2.0.1/ggraph/R/autograph.R |only ggraph-2.0.1/ggraph/R/connections.R | 2 ggraph-2.0.1/ggraph/R/geom_edge_span.R | 2 ggraph-2.0.1/ggraph/R/layout_stress.R | 2 ggraph-2.0.1/ggraph/R/layout_unrooted.R | 4 ggraph-2.0.1/ggraph/R/parallelPath.R | 4 ggraph-2.0.1/ggraph/README.md | 2 ggraph-2.0.1/ggraph/inst/doc/Edges.R | 54 +-- ggraph-2.0.1/ggraph/inst/doc/Edges.Rmd | 16 - ggraph-2.0.1/ggraph/inst/doc/Edges.html | 71 ++--- ggraph-2.0.1/ggraph/inst/doc/Layouts.R | 50 +-- ggraph-2.0.1/ggraph/inst/doc/Layouts.Rmd | 2 ggraph-2.0.1/ggraph/inst/doc/Layouts.html | 62 ++-- ggraph-2.0.1/ggraph/inst/doc/Nodes.R | 18 - ggraph-2.0.1/ggraph/inst/doc/Nodes.html | 23 - ggraph-2.0.1/ggraph/inst/doc/tidygraph.R | 16 - ggraph-2.0.1/ggraph/inst/doc/tidygraph.html | 17 - ggraph-2.0.1/ggraph/man/autograph.Rd |only ggraph-2.0.1/ggraph/man/facet_edges.Rd | 27 + ggraph-2.0.1/ggraph/man/facet_graph.Rd | 26 + ggraph-2.0.1/ggraph/man/facet_nodes.Rd | 27 + ggraph-2.0.1/ggraph/man/geom_axis_hive.Rd | 21 + ggraph-2.0.1/ggraph/man/geom_conn_bundle.Rd | 47 ++- ggraph-2.0.1/ggraph/man/geom_edge_arc.Rd | 108 +++++-- ggraph-2.0.1/ggraph/man/geom_edge_bend.Rd | 105 +++++-- ggraph-2.0.1/ggraph/man/geom_edge_density.Rd | 37 +- ggraph-2.0.1/ggraph/man/geom_edge_diagonal.Rd | 105 +++++-- ggraph-2.0.1/ggraph/man/geom_edge_elbow.Rd | 104 +++++-- ggraph-2.0.1/ggraph/man/geom_edge_fan.Rd | 105 +++++-- ggraph-2.0.1/ggraph/man/geom_edge_hive.Rd | 105 +++++-- ggraph-2.0.1/ggraph/man/geom_edge_link.Rd | 97 ++++--- ggraph-2.0.1/ggraph/man/geom_edge_loop.Rd | 69 +++- ggraph-2.0.1/ggraph/man/geom_edge_parallel.Rd | 100 ++++--- ggraph-2.0.1/ggraph/man/geom_edge_point.Rd | 37 +- ggraph-2.0.1/ggraph/man/geom_edge_span.Rd | 102 +++++-- ggraph-2.0.1/ggraph/man/geom_edge_tile.Rd | 37 +- ggraph-2.0.1/ggraph/man/geom_node_arc_bar.Rd | 22 + ggraph-2.0.1/ggraph/man/geom_node_circle.Rd | 22 + ggraph-2.0.1/ggraph/man/geom_node_point.Rd | 28 +- ggraph-2.0.1/ggraph/man/geom_node_range.Rd | 28 +- ggraph-2.0.1/ggraph/man/geom_node_text.Rd | 54 ++- ggraph-2.0.1/ggraph/man/geom_node_tile.Rd | 28 +- ggraph-2.0.1/ggraph/man/geom_node_voronoi.Rd | 30 +- ggraph-2.0.1/ggraph/man/geometry.Rd | 12 ggraph-2.0.1/ggraph/man/get_con.Rd | 19 - ggraph-2.0.1/ggraph/man/get_edges.Rd | 11 ggraph-2.0.1/ggraph/man/get_nodes.Rd | 5 ggraph-2.0.1/ggraph/man/ggraph-extensions.Rd | 6 ggraph-2.0.1/ggraph/man/ggraph-package.Rd | 5 ggraph-2.0.1/ggraph/man/guide_edge_colourbar.Rd | 80 ++++- ggraph-2.0.1/ggraph/man/guide_edge_direction.Rd | 36 +- ggraph-2.0.1/ggraph/man/layout_tbl_graph_auto.Rd | 35 +- ggraph-2.0.1/ggraph/man/layout_tbl_graph_backbone.Rd | 35 +- ggraph-2.0.1/ggraph/man/layout_tbl_graph_centrality.Rd | 49 ++- ggraph-2.0.1/ggraph/man/layout_tbl_graph_circlepack.Rd | 44 +-- ggraph-2.0.1/ggraph/man/layout_tbl_graph_dendrogram.Rd | 48 ++- ggraph-2.0.1/ggraph/man/layout_tbl_graph_eigen.Rd | 43 +-- ggraph-2.0.1/ggraph/man/layout_tbl_graph_fabric.Rd | 43 +-- ggraph-2.0.1/ggraph/man/layout_tbl_graph_focus.Rd | 45 +-- ggraph-2.0.1/ggraph/man/layout_tbl_graph_hive.Rd | 56 ++-- ggraph-2.0.1/ggraph/man/layout_tbl_graph_igraph.Rd | 45 +-- ggraph-2.0.1/ggraph/man/layout_tbl_graph_linear.Rd | 44 +-- ggraph-2.0.1/ggraph/man/layout_tbl_graph_manual.Rd | 35 +- ggraph-2.0.1/ggraph/man/layout_tbl_graph_matrix.Rd | 35 +- ggraph-2.0.1/ggraph/man/layout_tbl_graph_partition.Rd | 48 ++- ggraph-2.0.1/ggraph/man/layout_tbl_graph_pmds.Rd | 35 +- ggraph-2.0.1/ggraph/man/layout_tbl_graph_stress.Rd | 59 ++-- ggraph-2.0.1/ggraph/man/layout_tbl_graph_treemap.Rd | 48 ++- ggraph-2.0.1/ggraph/man/layout_tbl_graph_unrooted.Rd | 51 ++- ggraph-2.0.1/ggraph/man/qgraph.Rd | 47 --- ggraph-2.0.1/ggraph/man/scale_edge_alpha.Rd | 19 - ggraph-2.0.1/ggraph/man/scale_edge_colour.Rd | 235 ++++++++++++----- ggraph-2.0.1/ggraph/man/scale_edge_fill.Rd | 119 ++++++-- ggraph-2.0.1/ggraph/man/scale_edge_linetype.Rd | 17 - ggraph-2.0.1/ggraph/man/scale_edge_shape.Rd | 17 - ggraph-2.0.1/ggraph/man/scale_edge_size.Rd | 21 - ggraph-2.0.1/ggraph/man/scale_edge_width.Rd | 21 - ggraph-2.0.1/ggraph/man/scale_label_size.Rd | 21 - ggraph-2.0.1/ggraph/man/theme_graph.Rd | 56 ++-- ggraph-2.0.1/ggraph/vignettes/Edges.Rmd | 16 - ggraph-2.0.1/ggraph/vignettes/Layouts.Rmd | 2 86 files changed, 2204 insertions(+), 1365 deletions(-)
Title: Categorical Data
Description: This R-package contains examples from the book "Regression for Categorical Data", Tutz 2012, Cambridge University Press. The names of the examples refer to the chapter and the data set that is used.
Author: Gunther Schauberger, Gerhard Tutz
Maintainer: Gunther Schauberger <gunther.schauberger@tum.de>
Diff between catdata versions 1.2.1 dated 2014-11-11 and 1.2.2 dated 2020-02-07
catdata-1.2.1/catdata/build |only catdata-1.2.1/catdata/inst/doc/altbin-teratology.R |only catdata-1.2.1/catdata/inst/doc/altbin-teratology.Rnw |only catdata-1.2.1/catdata/inst/doc/binary-unemployment.R |only catdata-1.2.1/catdata/inst/doc/binary-unemployment.Rnw |only catdata-1.2.1/catdata/inst/doc/binary-vaso.R |only catdata-1.2.1/catdata/inst/doc/binary-vaso.Rnw |only catdata-1.2.1/catdata/inst/doc/count-children.R |only catdata-1.2.1/catdata/inst/doc/count-children.Rnw |only catdata-1.2.1/catdata/inst/doc/count-encephalitis.R |only catdata-1.2.1/catdata/inst/doc/count-encephalitis.Rnw |only catdata-1.2.1/catdata/inst/doc/count-insolvency.R |only catdata-1.2.1/catdata/inst/doc/count-insolvency.Rnw |only catdata-1.2.1/catdata/inst/doc/count-medcare.R |only catdata-1.2.1/catdata/inst/doc/count-medcare.Rnw |only catdata-1.2.1/catdata/inst/doc/loglinear-birth.R |only catdata-1.2.1/catdata/inst/doc/loglinear-birth.Rnw |only catdata-1.2.1/catdata/inst/doc/loglinear-leukoplakia.R |only catdata-1.2.1/catdata/inst/doc/loglinear-leukoplakia.Rnw |only catdata-1.2.1/catdata/inst/doc/modbin-dust.R |only catdata-1.2.1/catdata/inst/doc/modbin-dust.Rnw |only catdata-1.2.1/catdata/inst/doc/modbin-foodstamp.R |only catdata-1.2.1/catdata/inst/doc/modbin-foodstamp.Rnw |only catdata-1.2.1/catdata/inst/doc/modbin-unemployment1.R |only catdata-1.2.1/catdata/inst/doc/modbin-unemployment1.Rnw |only catdata-1.2.1/catdata/inst/doc/modbin-unemployment2.R |only catdata-1.2.1/catdata/inst/doc/modbin-unemployment2.Rnw |only catdata-1.2.1/catdata/inst/doc/multinomial-addiction1.R |only catdata-1.2.1/catdata/inst/doc/multinomial-addiction1.Rnw |only catdata-1.2.1/catdata/inst/doc/multinomial-addiction2.R |only catdata-1.2.1/catdata/inst/doc/multinomial-addiction2.Rnw |only catdata-1.2.1/catdata/inst/doc/multinomial-party1.R |only catdata-1.2.1/catdata/inst/doc/multinomial-party1.Rnw |only catdata-1.2.1/catdata/inst/doc/multinomial-party2.R |only catdata-1.2.1/catdata/inst/doc/multinomial-party2.Rnw |only catdata-1.2.1/catdata/inst/doc/multinomial-travel.R |only catdata-1.2.1/catdata/inst/doc/multinomial-travel.Rnw |only catdata-1.2.1/catdata/inst/doc/multivariate-birth1.R |only catdata-1.2.1/catdata/inst/doc/multivariate-birth1.Rnw |only catdata-1.2.1/catdata/inst/doc/multivariate-birth2.R |only catdata-1.2.1/catdata/inst/doc/multivariate-birth2.Rnw |only catdata-1.2.1/catdata/inst/doc/multivariate-knee.R |only catdata-1.2.1/catdata/inst/doc/multivariate-knee.Rnw |only catdata-1.2.1/catdata/inst/doc/ordinal-arthritis.R |only catdata-1.2.1/catdata/inst/doc/ordinal-arthritis.Rnw |only catdata-1.2.1/catdata/inst/doc/ordinal-knee1.R |only catdata-1.2.1/catdata/inst/doc/ordinal-knee1.Rnw |only catdata-1.2.1/catdata/inst/doc/ordinal-knee2.R |only catdata-1.2.1/catdata/inst/doc/ordinal-knee2.Rnw |only catdata-1.2.1/catdata/inst/doc/ordinal-retinopathy1.R |only catdata-1.2.1/catdata/inst/doc/ordinal-retinopathy1.Rnw |only catdata-1.2.1/catdata/inst/doc/ordinal-retinopathy2.R |only catdata-1.2.1/catdata/inst/doc/ordinal-retinopathy2.Rnw |only catdata-1.2.1/catdata/inst/doc/prediction-glass.R |only catdata-1.2.1/catdata/inst/doc/prediction-glass.Rnw |only catdata-1.2.1/catdata/inst/doc/prediction-glass.pdf |only catdata-1.2.1/catdata/inst/doc/prediction-medcare.R |only catdata-1.2.1/catdata/inst/doc/prediction-medcare.Rnw |only catdata-1.2.1/catdata/inst/doc/random-aids.R |only catdata-1.2.1/catdata/inst/doc/random-aids.Rnw |only catdata-1.2.1/catdata/inst/doc/random-betablocker.R |only catdata-1.2.1/catdata/inst/doc/random-betablocker.Rnw |only catdata-1.2.1/catdata/inst/doc/random-knee1.R |only catdata-1.2.1/catdata/inst/doc/random-knee1.Rnw |only catdata-1.2.1/catdata/inst/doc/random-knee2.R |only catdata-1.2.1/catdata/inst/doc/random-knee2.Rnw |only catdata-1.2.1/catdata/inst/doc/random-knee3.R |only catdata-1.2.1/catdata/inst/doc/random-knee3.Rnw |only catdata-1.2.1/catdata/inst/doc/regsel-heartdisease1.R |only catdata-1.2.1/catdata/inst/doc/regsel-heartdisease1.Rnw |only catdata-1.2.1/catdata/inst/doc/regsel-heartdisease1.pdf |only catdata-1.2.1/catdata/inst/doc/regsel-heartdisease2.R |only catdata-1.2.1/catdata/inst/doc/regsel-heartdisease2.Rnw |only catdata-1.2.1/catdata/inst/doc/regsel-heartdisease2.pdf |only catdata-1.2.1/catdata/inst/doc/regsel-heartdisease3.R |only catdata-1.2.1/catdata/inst/doc/regsel-heartdisease3.Rnw |only catdata-1.2.1/catdata/inst/doc/regsel-heartdisease3.pdf |only catdata-1.2.1/catdata/inst/doc/regsel-heartdisease4.R |only catdata-1.2.1/catdata/inst/doc/regsel-heartdisease4.Rnw |only catdata-1.2.1/catdata/inst/doc/regsel-heartdisease4.pdf |only catdata-1.2.1/catdata/inst/doc/regsel-heartdisease5.R |only catdata-1.2.1/catdata/inst/doc/regsel-heartdisease5.Rnw |only catdata-1.2.1/catdata/inst/doc/regsel-heartdisease5.pdf |only catdata-1.2.1/catdata/inst/doc/regsel-heartdisease6.R |only catdata-1.2.1/catdata/inst/doc/regsel-heartdisease6.Rnw |only catdata-1.2.1/catdata/inst/doc/regsel-heartdisease6.pdf |only catdata-1.2.1/catdata/inst/doc/semiparametric-addiction.R |only catdata-1.2.1/catdata/inst/doc/semiparametric-addiction.Rnw |only catdata-1.2.1/catdata/inst/doc/semiparametric-children.R |only catdata-1.2.1/catdata/inst/doc/semiparametric-children.Rnw |only catdata-1.2.1/catdata/inst/doc/semiparametric-dust.R |only catdata-1.2.1/catdata/inst/doc/semiparametric-dust.Rnw |only catdata-1.2.1/catdata/inst/doc/semiparametric-unemployment.R |only catdata-1.2.1/catdata/inst/doc/semiparametric-unemployment.Rnw |only catdata-1.2.1/catdata/inst/doc/tree-dust.R |only catdata-1.2.1/catdata/inst/doc/tree-dust.Rnw |only catdata-1.2.1/catdata/inst/doc/tree-unemployment.R |only catdata-1.2.1/catdata/inst/doc/tree-unemployment.Rnw |only catdata-1.2.1/catdata/vignettes/disc_comp_roc.r |only catdata-1.2.1/catdata/vignettes/gdscode.txt |only catdata-1.2.1/catdata/vignettes/glmOSCAR_101028.r |only catdata-1.2.1/catdata/vignettes/prediction-glass.Rnw |only catdata-1.2.1/catdata/vignettes/regsel-heartdisease1.Rnw |only catdata-1.2.1/catdata/vignettes/regsel-heartdisease2.Rnw |only catdata-1.2.1/catdata/vignettes/regsel-heartdisease3.Rnw |only catdata-1.2.1/catdata/vignettes/regsel-heartdisease4.Rnw |only catdata-1.2.1/catdata/vignettes/regsel-heartdisease5.Rnw |only catdata-1.2.1/catdata/vignettes/regsel-heartdisease6.Rnw |only catdata-1.2.2/catdata/DESCRIPTION | 16 catdata-1.2.2/catdata/MD5 | 238 +++------- catdata-1.2.2/catdata/data/birth.rda |binary catdata-1.2.2/catdata/inst/doc/altbin-teratology.pdf |binary catdata-1.2.2/catdata/inst/doc/binary-unemployment.pdf |binary catdata-1.2.2/catdata/inst/doc/binary-vaso.pdf |binary catdata-1.2.2/catdata/inst/doc/count-children.pdf |binary catdata-1.2.2/catdata/inst/doc/count-encephalitis.pdf |binary catdata-1.2.2/catdata/inst/doc/count-insolvency.pdf |binary catdata-1.2.2/catdata/inst/doc/count-medcare.pdf |binary catdata-1.2.2/catdata/inst/doc/loglinear-birth.pdf |binary catdata-1.2.2/catdata/inst/doc/loglinear-leukoplakia.pdf |binary catdata-1.2.2/catdata/inst/doc/modbin-dust.pdf |binary catdata-1.2.2/catdata/inst/doc/modbin-foodstamp.pdf |binary catdata-1.2.2/catdata/inst/doc/modbin-unemployment1.pdf |binary catdata-1.2.2/catdata/inst/doc/modbin-unemployment2.pdf |binary catdata-1.2.2/catdata/inst/doc/multinomial-addiction1.pdf |binary catdata-1.2.2/catdata/inst/doc/multinomial-addiction2.pdf |binary catdata-1.2.2/catdata/inst/doc/multinomial-party1.pdf |binary catdata-1.2.2/catdata/inst/doc/multinomial-party2.pdf |binary catdata-1.2.2/catdata/inst/doc/multinomial-travel.pdf |binary catdata-1.2.2/catdata/inst/doc/multivariate-birth1.pdf |binary catdata-1.2.2/catdata/inst/doc/multivariate-birth2.pdf |binary catdata-1.2.2/catdata/inst/doc/multivariate-knee.pdf |binary catdata-1.2.2/catdata/inst/doc/ordinal-arthritis.pdf |binary catdata-1.2.2/catdata/inst/doc/ordinal-knee1.pdf |binary catdata-1.2.2/catdata/inst/doc/ordinal-knee2.pdf |binary catdata-1.2.2/catdata/inst/doc/prediction-medcare.pdf |binary catdata-1.2.2/catdata/inst/doc/random-aids.pdf |binary catdata-1.2.2/catdata/inst/doc/random-betablocker.pdf |binary catdata-1.2.2/catdata/inst/doc/random-knee1.pdf |binary catdata-1.2.2/catdata/inst/doc/random-knee2.pdf |binary catdata-1.2.2/catdata/inst/doc/random-knee3.pdf |binary catdata-1.2.2/catdata/inst/doc/semiparametric-addiction.pdf |binary catdata-1.2.2/catdata/inst/doc/semiparametric-children.pdf |binary catdata-1.2.2/catdata/inst/doc/semiparametric-dust.pdf |binary catdata-1.2.2/catdata/inst/doc/semiparametric-unemployment.pdf |binary catdata-1.2.2/catdata/inst/doc/tree-dust.pdf |binary catdata-1.2.2/catdata/inst/doc/tree-unemployment.pdf |binary catdata-1.2.2/catdata/man/addiction.Rd | 3 catdata-1.2.2/catdata/man/catdata-package.Rd | 21 catdata-1.2.2/catdata/man/dust.Rd | 2 catdata-1.2.2/catdata/man/medcare.Rd | 2 catdata-1.2.2/catdata/man/rent.Rd | 2 catdata-1.2.2/catdata/man/vaso.Rd | 2 catdata-1.2.2/catdata/vignettes/altbin-teratology.pdf |only catdata-1.2.2/catdata/vignettes/binary-unemployment.pdf |only catdata-1.2.2/catdata/vignettes/binary-vaso.pdf |only catdata-1.2.2/catdata/vignettes/count-children.pdf |only catdata-1.2.2/catdata/vignettes/count-encephalitis.pdf |only catdata-1.2.2/catdata/vignettes/count-insolvency.pdf |only catdata-1.2.2/catdata/vignettes/count-medcare.pdf |only catdata-1.2.2/catdata/vignettes/loglinear-birth.pdf |only catdata-1.2.2/catdata/vignettes/loglinear-leukoplakia.pdf |only catdata-1.2.2/catdata/vignettes/modbin-dust.pdf |only catdata-1.2.2/catdata/vignettes/modbin-foodstamp.pdf |only catdata-1.2.2/catdata/vignettes/modbin-unemployment1.pdf |only catdata-1.2.2/catdata/vignettes/modbin-unemployment2.pdf |only catdata-1.2.2/catdata/vignettes/multinomial-addiction1.pdf |only catdata-1.2.2/catdata/vignettes/multinomial-addiction2.pdf |only catdata-1.2.2/catdata/vignettes/multinomial-party1.pdf |only catdata-1.2.2/catdata/vignettes/multinomial-party2.pdf |only catdata-1.2.2/catdata/vignettes/multinomial-travel.pdf |only catdata-1.2.2/catdata/vignettes/multivariate-birth1.pdf |only catdata-1.2.2/catdata/vignettes/multivariate-birth2.pdf |only catdata-1.2.2/catdata/vignettes/multivariate-knee.pdf |only catdata-1.2.2/catdata/vignettes/ordinal-arthritis.pdf |only catdata-1.2.2/catdata/vignettes/ordinal-knee1.pdf |only catdata-1.2.2/catdata/vignettes/ordinal-knee2.pdf |only catdata-1.2.2/catdata/vignettes/ordinal-retinopathy1.Rnw | 60 +- catdata-1.2.2/catdata/vignettes/ordinal-retinopathy1.pdf |only catdata-1.2.2/catdata/vignettes/ordinal-retinopathy2.Rnw | 61 +- catdata-1.2.2/catdata/vignettes/ordinal-retinopathy2.pdf |only catdata-1.2.2/catdata/vignettes/prediction-medcare.pdf |only catdata-1.2.2/catdata/vignettes/random-aids.pdf |only catdata-1.2.2/catdata/vignettes/random-betablocker.pdf |only catdata-1.2.2/catdata/vignettes/random-knee1.pdf |only catdata-1.2.2/catdata/vignettes/random-knee2.pdf |only catdata-1.2.2/catdata/vignettes/random-knee3.pdf |only catdata-1.2.2/catdata/vignettes/semiparametric-addiction.pdf |only catdata-1.2.2/catdata/vignettes/semiparametric-children.pdf |only catdata-1.2.2/catdata/vignettes/semiparametric-dust.pdf |only catdata-1.2.2/catdata/vignettes/semiparametric-unemployment.pdf |only catdata-1.2.2/catdata/vignettes/tree-dust.pdf |only catdata-1.2.2/catdata/vignettes/tree-unemployment.pdf |only 193 files changed, 161 insertions(+), 246 deletions(-)
Title: Analysis of Massive SNP Arrays
Description: Easy-to-use, efficient, flexible and scalable tools
for analyzing massive SNP arrays <doi:10.1093/bioinformatics/bty185>.
Author: Florian Privé [aut, cre],
Michael Blum [ths],
Hugues Aschard [ths]
Maintainer: Florian Privé <florian.prive.21@gmail.com>
Diff between bigsnpr versions 1.2.1 dated 2020-02-03 and 1.2.2 dated 2020-02-07
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- tests/testthat/test-1-attach.R | 8 +++++++- 3 files changed, 13 insertions(+), 7 deletions(-)
Title: Exchange Commands Between R and 'JavaScript'
Description: An 'httpuv' based bridge between R and 'JavaScript'. Provides an easy way to exchange commands and data between a web page and a currently running R session.
Author: Svetlana Ovchinnikova [aut, cre],
Simon Anders [aut]
Maintainer: Svetlana Ovchinnikova <s.ovchinnikova@zmbh.uni-heidelberg.de>
Diff between jrc versions 0.3.0 dated 2020-01-14 and 0.3.1 dated 2020-02-07
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 6 ++++++ R/jrc.R | 7 +++---- 4 files changed, 16 insertions(+), 11 deletions(-)
Title: Generalised Joint Regression Modelling
Description: Routines for fitting various joint (and univariate) regression models, with several types of covariate effects, in the presence of equations' errors association, endogeneity, non-random sample selection or partial observability.
Author: Giampiero Marra <giampiero.marra@ucl.ac.uk> and Rosalba Radice <rosalba.radice@city.ac.uk>
Maintainer: Giampiero Marra <giampiero.marra@ucl.ac.uk>
Diff between GJRM versions 0.2-1 dated 2019-10-02 and 0.2-2 dated 2020-02-07
ChangeLog | 4 ++++ DESCRIPTION | 6 +++--- MD5 | 30 ++++++++++++++++-------------- NAMESPACE | 4 ++-- R/gamlss.r | 8 +++++--- R/hazsurv.plot.r | 27 ++++++++++++++++++++------- R/jc.probs.r | 5 +++-- R/jc.probs1.r | 14 +++++++------- R/lmc.R |only R/plot.SemiParBIV.r | 16 ++++++++-------- R/pream.wm.r | 11 +++-------- R/r.resp.R | 14 ++++++++++++-- man/gamlss.Rd | 4 ++-- man/hazsurv.plot.Rd | 12 +++++++++--- man/jc.probs.Rd | 5 ++++- man/lmc.Rd |only man/summary.gamlss.Rd | 4 ++-- 17 files changed, 100 insertions(+), 64 deletions(-)
Title: Utility Functions for 'spatstat'
Description: Contains utility functions for the 'spatstat' package
which may also be useful for other purposes.
Author: Adrian Baddeley [aut, cre] (<https://orcid.org/0000-0001-9499-8382>),
Rolf Turner [aut] (<https://orcid.org/0000-0001-5521-5218>),
Ege Rubak [aut] (<https://orcid.org/0000-0002-6675-533X>)
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.utils versions 1.15-0 dated 2019-12-02 and 1.17-0 dated 2020-02-07
DESCRIPTION | 8 ++++---- MD5 | 9 +++++---- R/utilmatrix.R | 6 +++--- R/utiltext.R | 8 +++++--- inst/doc/packagesizes.txt | 2 +- tests/tekst.R |only 6 files changed, 18 insertions(+), 15 deletions(-)
More information about spatstat.utils at CRAN
Permanent link
Title: Sparse Multi-Type Regularized Feature Modeling
Description: Implementation of the SMuRF algorithm of Devriendt et al. (2018) <arXiv:1810.03136> to fit generalized linear models (GLMs) with multiple types of predictors via regularized maximum likelihood.
Author: Tom Reynkens [aut, cre] (<https://orcid.org/0000-0002-5516-5107>),
Sander Devriendt [aut],
Katrien Antonio [aut]
Maintainer: Tom Reynkens <tomreynkens@hotmail.com>
Diff between smurf versions 1.0.2 dated 2019-11-25 and 1.0.3 dated 2020-02-07
DESCRIPTION | 14 ++++++------- MD5 | 43 ++++++++++++++++++++++-------------------- NAMESPACE | 1 R/rent.R |only R/smurf.R | 2 - build/vignette.rds |binary data |only inst/NEWS.Rd | 18 +++++++++++++++++ inst/doc/smurf.R | 4 +-- inst/doc/smurf.Rmd | 6 ++--- inst/doc/smurf.html | 13 +++++------- inst/examples/Rent_example1.R | 6 ++--- inst/examples/Rent_example2.R | 6 ++--- inst/examples/Rent_example3.R | 6 ++--- man/glmsmurf.Rd | 6 ++--- man/p.Rd | 6 ++--- man/plot_lambda.Rd | 6 ++--- man/rent.Rd |only tests/testthat/helper_fit.R | 6 ++--- tests/testthat/test_PO.R | 12 +++++++++++ tests/testthat/test_control.R | 8 +++++++ tests/testthat/test_general.R | 16 +++++++++++++++ tests/testthat/test_input.R | 6 +++++ vignettes/smurf.Rmd | 6 ++--- 24 files changed, 125 insertions(+), 66 deletions(-)
Title: Quick Serialization of R Objects
Description: Provides functions for quickly writing and reading any R object to and from disk.
Author: Travers Ching [aut, cre, cph],
Yann Collet [ctb, cph] (Yann Collet is the author of the bundled zstd
and lz4 code),
Facebook, Inc. [cph] (Facebook is the copyright holder of the bundled
zstd code),
Reichardt Tino [ctb, cph] (Contributor/copyright holder of zstd bundled
code),
Skibinski Przemyslaw [ctb, cph] (Contributor/copyright holder of zstd
bundled code),
Mori Yuta [ctb, cph] (Contributor/copyright holder of zstd bundled
code),
Romain Francois [ctb, cph] (Derived example/tutorials for Alt-Rep
structures),
Francesc Alted [ctb, cph] (Shuffling routines derived from Blosc
library)
Maintainer: Travers Ching <traversc@gmail.com>
Diff between qs versions 0.20.2 dated 2019-12-02 and 0.21.1 dated 2020-02-07
ChangeLog | 5 + DESCRIPTION | 8 +- MD5 | 36 +++++----- R/help_files.R | 8 +- R/zzz.R | 2 inst/doc/vignette.html | 2 man/qsave.Rd | 2 man/qsave_fd.Rd | 2 man/qsave_handle.Rd | 2 man/qserialize.Rd | 2 src/qs_common.h | 80 +++++++++++++++++++++- src/qs_deserialization.h | 5 + src/qs_deserialization_stream.h | 4 + src/qs_deserialize_common.h | 109 +++++++++++++++++++++++++++++- src/qs_mt_deserialization.h | 5 + src/qs_mt_serialization.h | 14 +-- src/qs_serialization.h | 14 +-- src/qs_serialization_stream.h | 10 +- src/qs_serialize_common.h | 141 ++++++++++++++++++++++++++++++++-------- 19 files changed, 366 insertions(+), 85 deletions(-)
Title: Load Data from Facebook API Marketing
Description: Load data by campaigns, ads, ad sets and insights, ad account and business manager
from Facebook Marketing API into R. For more details see official documents by Facebook
Marketing API <https://developers.facebook.com/docs/marketing-apis/>.
Author: Alexey Seleznev <selesnow@gmail.com>
Maintainer: Alexey Seleznev <selesnow@gmail.com>
Diff between rfacebookstat versions 2.0.0 dated 2019-12-17 and 2.0.1 dated 2020-02-07
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NEWS.md | 7 +++++++ R/zzz.R | 12 ++++++------ build/partial.rdb |binary inst/doc/rfacebookstat-get-statistics.html | 4 ++-- 6 files changed, 25 insertions(+), 18 deletions(-)
Title: Setup, Run and Analyze 'NetLogo' Model Simulations from 'R' via
'XML'
Description: Setup, run and analyze 'NetLogo' (<https://ccl.northwestern.edu/netlogo/>) model simulations in 'R'.
'nlrx' experiments use a similar structure as 'NetLogos' Behavior Space experiments.
However, 'nlrx' offers more flexibility and additional tools for running and analyzing complex simulation designs and sensitivity analyses.
The user defines all information that is needed in an intuitive framework, using class objects.
Experiments are submitted from 'R' to 'NetLogo' via 'XML' files that are dynamically written, based on specifications defined by the user.
By nesting model calls in future environments, large simulation design with many runs can be executed in parallel.
This also enables simulating 'NetLogo' experiments on remote high performance computing machines.
In order to use this package, 'Java' and 'NetLogo' (>= 5.3.1) need to be available on the executing system.
Author: Jan Salecker [aut, cre] (<https://orcid.org/0000-0002-9000-4229>),
Marco Sciaini [aut] (<https://orcid.org/0000-0002-3042-5435>),
Marina Papadopoulou [rev] (Marina reviewed the package for ropensci,
see <https://github.com/ropensci/software-review/issues/262>)
Maintainer: Jan Salecker <jsaleck@gwdg.de>
Diff between nlrx versions 0.4.0 dated 2019-12-03 and 0.4.1 dated 2020-02-07
DESCRIPTION | 8 MD5 | 22 - NEWS.md | 5 inst/doc/abc.html | 386 ++++++++++++++-------------- inst/doc/furthernotes.html | 220 ++++++++-------- inst/doc/getstarted.html | 124 ++++----- inst/doc/optimization.html | 200 +++++++-------- inst/doc/sensitivity.html | 268 ++++++++++---------- inst/doc/simdesign-examples.html | 520 +++++++++++++++++++-------------------- man/nlrx-package.Rd | 1 tests/testthat/WSP.nlogo |only tests/testthat/WSP.nls |only tests/testthat/test-nldoc.R | 4 13 files changed, 889 insertions(+), 869 deletions(-)
Title: High Performance Container Data Types
Description: Provides high performance container data types such
as Queue, Stack, Deque, Dict and OrderedDict. Benchmarks
<https://randy3k.github.io/collections/articles/benchmark.html> have
shown that these containers are asymptotically more efficient than
those offered by other packages.
Author: Randy Lai [aut, cre],
Andrea Mazzoleni [cph] (tommy hash table library)
Maintainer: Randy Lai <randy.cs.lai@gmail.com>
Diff between collections versions 0.2.3 dated 2019-11-02 and 0.2.4 dated 2020-02-07
DESCRIPTION | 18 +++++++++--------- MD5 | 10 +++++----- README.md | 1 + man/collections-package.Rd | 4 ++-- src/dict.c | 20 +++++++++----------- tests/testthat/test-dict.R | 14 ++++++++++++++ 6 files changed, 40 insertions(+), 27 deletions(-)
Title: An R Front End for 'ACER ConQuest'
Description: Extends 'ACER ConQuest' by allowing R users to call 'ACER ConQuest' from within R.
Users can also read 'ACER ConQuest' System Files (generated by the command 'put').
This is of particular use to those who are parsing text file output (e.g., 'show' files) as this is not consistent across releases of 'ACER ConQuest'.
Requires 'ACER ConQuest' version 4.34.0 or later. A demonstration version can be downloaded from <https://shop.acer.edu.au/acer-conquest-4>.
Author: Dan Cloney [cre, aut],
Ray Adams [aut]
Maintainer: Dan Cloney <dan.cloney@acer.org>
Diff between conquestr versions 0.3.7 dated 2019-03-08 and 0.5.1 dated 2020-02-07
conquestr-0.3.7/conquestr/inst/extdata/myPutFile.cqs |only conquestr-0.3.7/conquestr/inst/extdata/test.dat |only conquestr-0.5.1/conquestr/DESCRIPTION | 25 - conquestr-0.5.1/conquestr/MD5 | 50 +- conquestr-0.5.1/conquestr/NAMESPACE | 3 conquestr-0.5.1/conquestr/NEWS.md |only conquestr-0.5.1/conquestr/R/RcppExports.R |only conquestr-0.5.1/conquestr/R/ReadConQuestLibrary.R | 42 +- conquestr-0.5.1/conquestr/R/ReadConQuestState.R | 31 + conquestr-0.5.1/conquestr/R/ReadConQuestState_createDF.R |only conquestr-0.5.1/conquestr/R/conquestr.R | 69 ++- conquestr-0.5.1/conquestr/R/conquestrFunc.R | 93 ++++ conquestr-0.5.1/conquestr/README.md | 9 conquestr-0.5.1/conquestr/build/vignette.rds |binary conquestr-0.5.1/conquestr/inst/doc/intro-to-conquestr.R | 2 conquestr-0.5.1/conquestr/inst/doc/intro-to-conquestr.Rmd | 48 +- conquestr-0.5.1/conquestr/inst/doc/intro-to-conquestr.html | 247 +++++++++++-- conquestr-0.5.1/conquestr/inst/extdata/ConQuestAbout.cqc | 1 conquestr-0.5.1/conquestr/inst/extdata/ConQuestTest.cqc | 19 - conquestr-0.5.1/conquestr/inst/extdata/Ex1.cqs |binary conquestr-0.5.1/conquestr/inst/extdata/ex1.cqc | 2 conquestr-0.5.1/conquestr/inst/extdata/myIcc.rout |only conquestr-0.5.1/conquestr/inst/extdata/mySysFile.cqs |only conquestr-0.5.1/conquestr/inst/extdata/x.dat |only conquestr-0.5.1/conquestr/man/ConQuestRout.Rd |only conquestr-0.5.1/conquestr/man/ReadRandomStructure.Rd |only conquestr-0.5.1/conquestr/man/createDfFromSys.Rd |only conquestr-0.5.1/conquestr/man/replaceInDataFrame.Rd |only conquestr-0.5.1/conquestr/man/replaceInVector.Rd |only conquestr-0.5.1/conquestr/man/searchConQuestSys.Rd |only conquestr-0.5.1/conquestr/man/timesTwo.Rd |only conquestr-0.5.1/conquestr/man/transformPvs.Rd |only conquestr-0.5.1/conquestr/src |only conquestr-0.5.1/conquestr/vignettes/intro-to-conquestr.Rmd | 48 +- 34 files changed, 555 insertions(+), 134 deletions(-)
Title: Utilities for Multi-Label Learning
Description: Multi-label learning strategies and others procedures to support multi-
label classification in R. The package provides a set of multi-label procedures such as
sampling methods, transformation strategies, threshold functions, pre-processing
techniques and evaluation metrics. A complete overview of the matter can be seen in
Zhang, M. and Zhou, Z. (2014) <doi:10.1109/TKDE.2013.39> and Gibaja, E. and
Ventura, S. (2015) A Tutorial on Multi-label Learning.
Author: Adriano Rivolli [aut, cre]
Maintainer: Adriano Rivolli <rivolli@utfpr.edu.br>
Diff between utiml versions 0.1.5 dated 2019-03-16 and 0.1.6 dated 2020-02-07
DESCRIPTION | 12 MD5 | 210 ++++----- NAMESPACE | 1 NEWS.md | 5 R/evaluation.R | 6 R/method_baseline.R | 4 R/method_br.R | 4 R/method_brplus.R | 4 R/method_cc.R | 4 R/method_clr.R | 4 R/method_ctrl.R | 4 R/method_dbr.R | 6 R/method_ebr.R | 4 R/method_ecc.R | 4 R/method_eps.R | 4 R/method_esl.R | 4 R/method_homer.R | 4 R/method_lift.R | 4 R/method_lp.R | 4 R/method_mbr.R | 4 R/method_mlknn.R | 2 R/method_ns.R | 4 R/method_ppt.R | 4 R/method_prudent.R | 4 R/method_ps.R | 4 R/method_rakel.R | 4 R/method_rdbr.R | 4 R/method_rpc.R | 4 R/sampling.R | 6 R/threshold.R | 4 R/utiml.R | 1 build/vignette.rds |binary inst/doc/utiml-overview.html | 718 +++++++++++++++++++++------------- man/as.mlresult.Rd | 3 man/baseline.Rd | 7 man/br.Rd | 40 + man/brplus.Rd | 43 +- man/cc.Rd | 41 + man/clr.Rd | 43 +- man/compute_multilabel_predictions.Rd | 7 man/create_holdout_partition.Rd | 14 man/create_kfold_partition.Rd | 14 man/create_random_subset.Rd | 15 man/create_subset.Rd | 7 man/ctrl.Rd | 45 +- man/cv.Rd | 22 - man/dbr.Rd | 41 + man/ebr.Rd | 52 +- man/ecc.Rd | 52 +- man/eps.Rd | 62 ++ man/esl.Rd | 42 + man/fill_sparse_mldata.Rd | 15 man/fixed_threshold.Rd | 19 man/homer.Rd | 44 +- man/lcard_threshold.Rd | 19 man/lift.Rd | 41 + man/lp.Rd | 47 +- man/mbr.Rd | 47 +- man/mcut_threshold.Rd | 13 man/mlknn.Rd | 12 man/multilabel_confusion_matrix.Rd | 7 man/multilabel_evaluate.Rd | 13 man/multilabel_measures.Rd | 7 man/multilabel_prediction.Rd | 7 man/normalize_mldata.Rd | 15 man/ns.Rd | 42 + man/pcut_threshold.Rd | 13 man/ppt.Rd | 51 +- man/predict.BASELINEmodel.Rd | 3 man/predict.BRPmodel.Rd | 15 man/predict.BRmodel.Rd | 12 man/predict.CCmodel.Rd | 11 man/predict.CLRmodel.Rd | 12 man/predict.CTRLmodel.Rd | 13 man/predict.DBRmodel.Rd | 13 man/predict.EBRmodel.Rd | 13 man/predict.ECCmodel.Rd | 13 man/predict.EPSmodel.Rd | 13 man/predict.ESLmodel.Rd | 12 man/predict.HOMERmodel.Rd | 12 man/predict.LIFTmodel.Rd | 12 man/predict.LPmodel.Rd | 12 man/predict.MBRmodel.Rd | 12 man/predict.MLKNNmodel.Rd | 12 man/predict.NSmodel.Rd | 11 man/predict.PPTmodel.Rd | 12 man/predict.PSmodel.Rd | 12 man/predict.PruDentmodel.Rd | 12 man/predict.RAkELmodel.Rd | 12 man/predict.RDBRmodel.Rd | 16 man/predict.RPCmodel.Rd | 12 man/prudent.Rd | 40 + man/ps.Rd | 53 +- man/rakel.Rd | 52 +- man/rcut_threshold.Rd | 13 man/rdbr.Rd | 40 + man/remove_attributes.Rd | 15 man/remove_labels.Rd | 15 man/remove_skewness_labels.Rd | 15 man/remove_unique_attributes.Rd | 15 man/remove_unlabeled_instances.Rd | 15 man/replace_nominal_attributes.Rd | 15 man/rpc.Rd | 42 + man/scut_threshold.Rd | 41 + man/subset_correction.Rd | 13 man/utiml.Rd | 1 106 files changed, 1721 insertions(+), 958 deletions(-)
Title: Solving Mixed Model Equations in R
Description: Structural multivariate-univariate linear mixed model solver for estimation of multiple random effects and unknown variance-covariance structures (i.e. heterogeneous and unstructured variance models) (Covarrubias-Pazaran, 2016 <doi:10.1371/journal.pone.0156744>; Maier et al., 2015 <doi:10.1016/j.ajhg.2014.12.006>). ML/REML estimates can be obtained using the Direct-Inversion Newton-Raphson and Direct-Inversion Average Information algorithms. Designed for genomic prediction and genome wide association studies (GWAS), particularly focused in the p > n problem (more coefficients than observations) and dense known covariance structures for levels of random effects. Spatial models can also be fitted using i.e. the two-dimensional spline functionality available in sommer.
Author: Giovanny Covarrubias-Pazaran
Maintainer: Giovanny Covarrubias-Pazaran <cova_ruber@live.com.mx>
Diff between sommer versions 4.0.8 dated 2019-11-01 and 4.0.9 dated 2020-02-07
DESCRIPTION | 8 - MD5 | 10 +- R/FUN_utils.R | 2 R/mmer.R | 2 vignettes/sommer.html | 154 +++++++++++++++++++------------------- vignettes/sommer.start.html | 178 ++++++++++++++++++++++---------------------- 6 files changed, 177 insertions(+), 177 deletions(-)
Title: Bridge Between 'R' and 'Scala' with Callbacks
Description: 'Scala' <http://www.scala-lang.org/> is embedded in 'R' and callbacks from 'Scala' to 'R' are available. Support is provided to write 'R' packages that access 'Scala'. After installation, please run 'rscala::scalaConfig()'.
Author: David B. Dahl [aut, cre]
Maintainer: David B. Dahl <dahl@stat.byu.edu>
Diff between rscala versions 3.2.16 dated 2019-10-03 and 3.2.17 dated 2020-02-07
DESCRIPTION | 13 +- MD5 | 43 +++--- NEWS | 3 R/INTERNAL-io.R | 1 R/scala.R | 4 R/scalaConfig.R | 80 +++++++----- R/sysdata.rda |binary README.md | 2 build/vignette.rds |binary inst/doc/rscala.R | 249 +++++++++++---------------------------- inst/doc/rscala.Rnw | 66 +++++----- inst/doc/rscala.pdf |binary inst/java/scala-2.11/rscala.jar |binary inst/java/scala-2.12/rscala.jar |binary inst/java/scala-2.13/rscala.jar |binary java/rscala-source.jar |binary man/scala.Rd | 14 +- man/scalaConfig.Rd | 10 + man/scalaDevelDownloadJARs.Rd | 7 - man/scalaSBT.Rd | 7 - tests/testthat.R | 8 - vignettes/rscala-concordance.tex |only vignettes/rscala.Rnw | 66 +++++----- 23 files changed, 261 insertions(+), 312 deletions(-)
Title: The Symmetric Group: Permutations of a Finite Set
Description: Manipulates invertible functions from a finite set to itself. Can transform from word form to cycle form and back.
Author: Robin K. S. Hankin [aut, cre] (<https://orcid.org/0000-0001-5982-0415>)
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between permutations versions 1.0-5 dated 2019-10-17 and 1.0-6 dated 2020-02-07
DESCRIPTION | 6 +++--- MD5 | 21 ++++++++++++--------- build/partial.rdb |binary build/vignette.rds |binary data/megaminx.rda |binary inst/doc/permutations.pdf |binary inst/megaminx.py |only inst/read.me | 27 +++++++++++++++++++++++++-- inst/starminx.py |only inst/starminx_III.py |only man/fixed.Rd | 3 +-- man/megaminx_plotter.Rd | 2 +- man/perm_matrix.Rd | 14 +++++++------- 13 files changed, 49 insertions(+), 24 deletions(-)
Title: Generative Mechanism Estimation in Temporal Complex Networks
Description: Statistical methods for estimating preferential attachment and node fitness generative mechanisms in temporal complex networks are provided. Thong Pham et al. (2015) <doi:10.1371/journal.pone.0137796>. Thong Pham et al. (2016) <doi:10.1038/srep32558>.
Author: Thong Pham, Paul Sheridan, Hidetoshi Shimodaira
Maintainer: Thong Pham <thongphamthe@gmail.com>
Diff between PAFit versions 1.0.1.6 dated 2020-01-09 and 1.0.1.7 dated 2020-02-07
DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++-------------- build/vignette.rds |binary man/PAFit-package.Rd | 4 ++-- man/graph_from_file.rd | 4 ---- man/joint_estimate.rd | 4 +++- man/only_A_estimate.rd | 5 +++-- man/only_F_estimate.rd | 4 +++- man/plot.Full_PAFit_result.Rd | 5 ++--- man/plot.PAFit_net.Rd | 5 ++--- man/plot.PAFit_result.rd | 3 +-- man/plot.PA_result.rd | 4 ++-- man/print.CV_Result.rd | 3 +-- man/print.CV_data.rd | 3 +-- man/print.Full_PAFit_result.Rd | 3 +-- 15 files changed, 39 insertions(+), 44 deletions(-)
Title: NeuroAnatomy Toolbox for Analysis of 3D Image Data
Description: NeuroAnatomy Toolbox (nat) enables analysis and visualisation of 3D
biological image data, especially traced neurons. Reads and writes 3D images
in NRRD and 'Amira' AmiraMesh formats and reads surfaces in 'Amira' hxsurf
format. Traced neurons can be imported from and written to SWC and 'Amira'
LineSet and SkeletonGraph formats. These data can then be visualised in 3D
via 'rgl', manipulated including applying calculated registrations, e.g.
using the 'CMTK' registration suite, and analysed. There is also a simple
representation for neurons that have been subjected to 3D skeletonisation
but not formally traced; this allows morphological comparison between
neurons including searches and clustering (via the 'nat.nblast' extension
package).
Author: Gregory Jefferis [aut, cre] (<https://orcid.org/0000-0002-0587-9355>),
James Manton [aut] (<https://orcid.org/0000-0001-9260-3156>)
Maintainer: Gregory Jefferis <jefferis@gmail.com>
Diff between nat versions 1.8.13 dated 2019-08-22 and 1.8.14 dated 2020-02-07
DESCRIPTION | 8 - MD5 | 214 +++++++++++++++++------------------ NEWS | 6 R/hxsurf.R | 3 build/vignette.rds |binary inst/doc/Installation.html | 15 -- inst/doc/neurons-intro.R | 76 ++++++------ inst/doc/neurons-intro.html | 66 ++++------ man/Cell07PNs.Rd | 4 man/MBL.surf.Rd | 5 man/affmat2cmtkparams.Rd | 7 - man/all.equal.dotprops.Rd | 9 + man/all.equal.im3d.Rd | 12 + man/all.equal.neuron.Rd | 17 +- man/amiramesh-io.Rd | 20 ++- man/amiratype.Rd | 8 - man/as.hxsurf.Rd | 11 + man/as.im3d.Rd | 24 ++- man/as.mesh3d.Rd | 14 +- man/as.neuronlist.Rd | 3 man/boundingbox.Rd | 24 ++- man/cmtk.bindir.Rd | 17 +- man/cmtk.call.Rd | 9 + man/cmtk.dof2mat.Rd | 10 - man/cmtk.extract_affine.Rd | 8 - man/cmtk.mat2dof.Rd | 13 +- man/cmtk.reformatx.Rd | 20 ++- man/cmtk.statistics.Rd | 10 + man/cmtkparams2affmat.Rd | 28 +++- man/cmtkreglist.Rd | 3 man/coord2ind.Rd | 12 + man/dotprops.Rd | 3 man/fileformats.Rd | 24 ++- man/find.neuron.Rd | 11 + man/find.soma.Rd | 10 + man/get-set-neuronlist-data.frame.Rd | 3 man/graph.nodes.Rd | 8 - man/im3d-coords.Rd | 21 ++- man/im3d-io.Rd | 30 +++- man/im3d.Rd | 32 +++-- man/image.im3d.Rd | 21 ++- man/imexpand.grid.Rd | 21 ++- man/imscalebar.Rd | 14 +- man/imslice.Rd | 21 ++- man/is.amiramesh.Rd | 8 - man/is.im3d.Rd | 21 ++- man/is.neuronlist.Rd | 13 +- man/is.nrrd.Rd | 3 man/kcs20.Rd | 5 man/mask.Rd | 24 ++- man/materials.Rd | 11 + man/mirror.Rd | 13 +- man/ndigest.Rd | 8 - man/neuron.Rd | 33 +++-- man/neuronlist-arithmetic.Rd | 13 +- man/neuronlist-dataframe-methods.Rd | 12 + man/neuronlist.Rd | 13 +- man/neuronlistfh.Rd | 36 +++-- man/ngraph.Rd | 29 +++- man/nlapply.Rd | 39 ++++-- man/nlscan.Rd | 16 ++ man/normalise_swc.Rd | 13 +- man/nview3d.Rd | 10 + man/origin.Rd | 21 ++- man/plot.neuron.Rd | 44 +++++-- man/plot.neuronlist.Rd | 13 +- man/plot3d.dotprops.Rd | 13 +- man/plot3d.hxsurf.Rd | 11 + man/plot3d.neuron.Rd | 16 ++ man/plot3d.neuronlist.Rd | 14 +- man/pointsinside.Rd | 6 man/potential_synapses.Rd | 38 ++++-- man/projection.Rd | 31 +++-- man/prune.Rd | 17 +- man/read.cmtk.Rd | 8 - man/read.cmtkreg.Rd | 8 - man/read.hxsurf.Rd | 30 +++- man/read.landmarks.Rd | 11 + man/read.neuronlistfh.Rd | 8 - man/read.neurons.Rd | 27 +++- man/read.nrrd.Rd | 11 + man/read.vaa3draw.Rd | 3 man/remotesync.Rd | 32 +++-- man/resample.Rd | 14 +- man/rootpoints.Rd | 14 +- man/segmentgraph.Rd | 11 + man/spine.Rd | 23 ++- man/sub-.neuronlistfh.Rd | 9 - man/subset.hxsurf.Rd | 14 +- man/subset.neuron.Rd | 14 +- man/subset.neuronlist.Rd | 9 + man/summary.neuron.Rd | 3 man/threshold.Rd | 29 +++- man/unmask.Rd | 30 +++- man/voxdims.Rd | 21 ++- man/write.amiramesh.Rd | 9 + man/write.cmtk.Rd | 8 - man/write.cmtkreg.Rd | 8 - man/write.hxsurf.Rd | 19 +-- man/write.neuron.Rd | 12 + man/write.neuronlistfh.Rd | 8 - man/write.neurons.Rd | 25 ++-- man/write.nrrd.Rd | 12 + man/write.vtk.Rd | 10 + man/xform.Rd | 24 ++- man/xformimage.Rd | 9 + man/xformpoints.Rd | 10 + tests/testthat/test-ndigest.R | 2 108 files changed, 1247 insertions(+), 677 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-12-12 3.1.2
2019-10-03 3.1.1
2019-08-20 3.1.0
2019-06-14 3.0.2
2019-05-16 3.0.1
2019-04-15 3.0.0
2018-07-17 2.3.4
2018-07-02 2.3.3
2018-06-12 2.3.2
2018-05-06 2.3.1
2018-03-23 2.3.0
2018-02-14 2.2.1
2018-01-10 2.2.0
2017-10-12 2.1.0
2017-08-22 2.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-01-23 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-02-05 1.0.1
2014-01-28 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-05-03 1.1.0
2016-05-02 1.0.0
Title: Methods and Measures for Semantic Network Analysis
Description: Implements several functions for the analysis of semantic networks including partial node bootstrapping (Kenett, Anaki, & Faust, 2014 <doi:10.3389/fnhum.2014.00407>), random walk simulation (Kenett & Austerweil, 2016 <http://alab.psych.wisc.edu/papers/files/Kenett16CreativityRW.pdf>), and a function to compute global network measures. Significance tests and plotting features are also implemented.
Author: Alexander P. Christensen [aut, cre]
(<https://orcid.org/0000-0002-9798-7037>),
Yoed N. Kenett [aut, ctb] (<https://orcid.org/0000-0003-3872-7689>)
Maintainer: Alexander P. Christensen <alexpaulchristensen@gmail.com>
Diff between SemNeT versions 1.1.2 dated 2019-10-28 and 1.1.3 dated 2020-02-07
DESCRIPTION | 10 - MD5 | 61 ++++--- NAMESPACE | 5 NEWS | 5 R/animals.freq.R |only R/partboot.R | 6 R/partboot.one.test.R | 235 +++++++++++++++++++++++------- R/partboot.test.R | 133 ++++++++++++---- R/sim.fluency.R | 60 +++++-- build/vignette.rds |binary data/animals.freq.RData |only inst/doc/Analyzing.R | 8 - inst/doc/Analyzing.html | 8 - man/SemNeT-package.Rd | 82 +++++----- man/animals.freq.Rd |only man/compare.nets.Rd | 212 +++++++++++++-------------- man/convert2cytoscape.Rd | 98 ++++++------ man/net.high.Rd | 46 ++--- man/net.low.Rd | 46 ++--- man/one.result.Rd | 32 ++-- man/org.plot.Rd | 116 +++++++------- man/partboot.Rd | 156 +++++++++---------- man/partboot.one.test.Rd | 199 +++++++++++++++---------- man/partboot.test.Rd | 200 +++++++++++++++---------- man/plot.partboot.Rd | 79 ++++------ man/randnet.test.Rd | 104 ++++++------- man/randwalk.Rd | 143 +++++++++--------- man/semnetmeas.Rd | 92 +++++------ man/sim.fluency.Rd | 76 +++++---- man/similarity.Rd | 148 +++++++++--------- man/two.result.Rd | 32 ++-- man/vignette.plots.Rd | 46 ++--- vignettes/Christensen_General_Library.bib | 1 33 files changed, 1384 insertions(+), 1055 deletions(-)
Title: Age-Depth Modelling using Bayesian Statistics
Description: An approach to age-depth modelling that uses Bayesian statistics to reconstruct accumulation histories for deposits, through combining radiocarbon and other dates with prior information. See Blaauw & Christen (2011) <doi:10.1214/11-BA618>.
Author: Maarten Blaauw [aut, cre],
J. Andres Christen [aut, ctb, cph],
Marco A. Aquino L. [aut],
Judith Esquivel Vazquez [ctb],
Oscar M. Gonzalez V. [ctb],
Ted Belding [cph],
James Theiler [cph],
Brian Gough [cph],
Charles Karney [cph]
Maintainer: Maarten Blaauw <maarten.blaauw@qub.ac.uk>
Diff between rbacon versions 2.3.9.1 dated 2019-07-03 and 2.4.0 dated 2020-02-07
rbacon-2.3.9.1/rbacon/inst/extdata/default_settings.txt |only rbacon-2.3.9.1/rbacon/man/Bacon_runs.Rd |only rbacon-2.4.0/rbacon/DESCRIPTION | 22 rbacon-2.4.0/rbacon/MD5 | 99 +- rbacon-2.4.0/rbacon/NAMESPACE | 6 rbacon-2.4.0/rbacon/NEWS.md | 8 rbacon-2.4.0/rbacon/R/Bacon.R | 243 +++-- rbacon-2.4.0/rbacon/R/MCMC.R | 83 + rbacon-2.4.0/rbacon/R/accrate.R | 160 +-- rbacon-2.4.0/rbacon/R/agedepth.R | 163 ++- rbacon-2.4.0/rbacon/R/calc.R | 154 +-- rbacon-2.4.0/rbacon/R/calibrate.R | 391 +++++++-- rbacon-2.4.0/rbacon/R/internal_plots.R | 139 ++- rbacon-2.4.0/rbacon/R/plots.R | 70 - rbacon-2.4.0/rbacon/R/read_write.R | 160 +-- rbacon-2.4.0/rbacon/R/read_write_plum.R |only rbacon-2.4.0/rbacon/inst/extdata/defaultBacon_settings.txt |only rbacon-2.4.0/rbacon/man/A.modelled.Rd |only rbacon-2.4.0/rbacon/man/AgesOfEvents.Rd | 41 rbacon-2.4.0/rbacon/man/Bacon.Age.d.Rd | 15 rbacon-2.4.0/rbacon/man/Bacon.Rd | 155 ++- rbacon-2.4.0/rbacon/man/Bacon.hist.Rd | 33 rbacon-2.4.0/rbacon/man/Baconvergence.Rd | 20 rbacon-2.4.0/rbacon/man/accrate.age.Rd | 12 rbacon-2.4.0/rbacon/man/accrate.age.ghost.Rd | 48 - rbacon-2.4.0/rbacon/man/accrate.depth.Rd | 10 rbacon-2.4.0/rbacon/man/accrate.depth.ghost.Rd | 33 rbacon-2.4.0/rbacon/man/add.dates.Rd | 44 - rbacon-2.4.0/rbacon/man/age.pMC.Rd | 6 rbacon-2.4.0/rbacon/man/agedepth.Rd | 133 ++- rbacon-2.4.0/rbacon/man/agemodel.it.Rd | 6 rbacon-2.4.0/rbacon/man/bacon2clam.Rd | 9 rbacon-2.4.0/rbacon/man/calib.plot.Rd | 46 - rbacon-2.4.0/rbacon/man/calib.plumbacon.plot.Rd |only rbacon-2.4.0/rbacon/man/clam2bacon.Rd | 11 rbacon-2.4.0/rbacon/man/copyCalibrationCurve.Rd | 2 rbacon-2.4.0/rbacon/man/draw.pbmodelled.Rd |only rbacon-2.4.0/rbacon/man/flux.age.ghost.Rd | 51 - rbacon-2.4.0/rbacon/man/mix.curves.Rd | 18 rbacon-2.4.0/rbacon/man/pMC.age.Rd | 6 rbacon-2.4.0/rbacon/man/proxy.ghost.Rd | 46 - rbacon-2.4.0/rbacon/man/rbacon.Rd | 1 rbacon-2.4.0/rbacon/man/scissors.Rd | 12 rbacon-2.4.0/rbacon/man/thinner.Rd | 4 rbacon-2.4.0/rbacon/src/Matrix.cpp | 3 rbacon-2.4.0/rbacon/src/Matrix.h | 33 rbacon-2.4.0/rbacon/src/bacon.cpp | 5 rbacon-2.4.0/rbacon/src/bacon.h | 546 +++++++++---- rbacon-2.4.0/rbacon/src/cal.h | 151 +++ rbacon-2.4.0/rbacon/src/input.cpp | 152 +++ rbacon-2.4.0/rbacon/src/input.h | 51 - rbacon-2.4.0/rbacon/src/kernel.cpp | 30 rbacon-2.4.0/rbacon/src/twalk.h | 149 +-- rbacon-2.4.0/rbacon/src/vector.cpp | 29 54 files changed, 2404 insertions(+), 1205 deletions(-)
Title: Network Reverse Engineering with Approximate Bayesian
Computation
Description: We developed an inference tool based on approximate Bayesian computation to decipher network data and assess the strength of the inferred links between network's actors. It is a new multi-level approximate Bayesian computation (ABC) approach. At the first level, the method captures the global properties of the network, such as scale-freeness and clustering coefficients, whereas the second level is targeted to capture local properties, including the probability of each couple of genes being linked. Up to now, Approximate Bayesian Computation (ABC) algorithms have been scarcely used in that setting and, due to the computational overhead, their application was limited to a small number of genes. On the contrary, our algorithm was made to cope with that issue and has low computational cost. It can be used, for instance, for elucidating gene regulatory network, which is an important step towards understanding the normal cell physiology and complex pathological phenotype. Reverse-engineering consists in using gene expressions over time or over different experimental conditions to discover the structure of the gene network in a targeted cellular process. The fact that gene expression data are usually noisy, highly correlated, and have high dimensionality explains the need for specific statistical methods to reverse engineer the underlying network.
Author: Frederic Bertrand [cre, aut] (<https://orcid.org/0000-0002-0837-8281>),
Myriam Maumy-Bertrand [aut] (<https://orcid.org/0000-0002-4615-1512>),
Khadija Musayeva [ctb],
Nicolas Jung [ctb],
Université de Strasbourg [cph],
CNRS [cph]
Maintainer: Frederic Bertrand <frederic.bertrand@math.unistra.fr>
Diff between networkABC versions 0.5-3 dated 2019-03-06 and 0.6-0 dated 2020-02-07
DESCRIPTION | 11 MD5 | 27 NEWS.md | 9 R/datasets.R | 6 build/vignette.rds |binary data/datalist |only inst/doc/vignette.R | 30 inst/doc/vignette.html | 501 ++++++++---- man/abc.Rd | 14 man/networkABC.Rd | 1 src/abc_R.c | 4 vignettes/vignette_files/figure-html/unnamed-chunk-12-1.png |binary vignettes/vignette_files/figure-html/unnamed-chunk-13-1.png |binary vignettes/vignette_files/figure-html/unnamed-chunk-3-1.png |binary vignettes/vignette_files/figure-html/unnamed-chunk-8-1.png |binary 15 files changed, 419 insertions(+), 184 deletions(-)