Title: Tracking the Progress of Mc*pply with Progress Bar
Description: A light-weight package helps you track and visualize
the progress of parallel version of vectorized R functions (mc*apply).
Parallelization (mc.core > 1) works only on *nix (Linux, Unix such as macOS) system due to
the lack of fork() functionality, which is essential for mc*apply, on Windows.
Author: Kevin Kuang (aut), Quyu Kong (ctb), Francesco Napolitano (ctb)
Maintainer: Kevin kuang <kvn.kuang@mail.utoronto.ca>
Diff between pbmcapply versions 1.4.1 dated 2019-04-01 and 1.5.0 dated 2019-07-10
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/pbmclapply.R | 51 ++++++++++++++++++++++++++++++++++++--------------- R/pbmcmapply.R | 50 +++++++++++++++++++++++++++++++++++--------------- R/utils.R | 32 ++++++++++---------------------- src/process.c | 1 + 6 files changed, 90 insertions(+), 60 deletions(-)
Title: Descriptive Statistics
Description: Performs various analyzes of descriptive statistics, including correlations, graphics and tables.
Author: Emmanuel Arnhold
Maintainer: Emmanuel Arnhold <emmanuelarnhold@yahoo.com.br>
Diff between ds versions 3.0 dated 2014-09-02 and 4.0 dated 2019-07-10
DESCRIPTION | 11 ++++++----- MD5 | 8 ++++---- NAMESPACE | 5 +++++ R/tables.R | 2 +- man/ds-package.Rd | 4 ++-- 5 files changed, 18 insertions(+), 12 deletions(-)
Title: Multidimensional Scaling of Asymmetric Data
Description: Multidimensional scaling models and methods for the visualization for asymmetric data <doi:10.1111/j.2044-8317.1996.tb01078.x>. An asymmetric matrix has the same number of rows and columns, and these rows and columns refer to the same set of objects. At least some elements in the upper-triangle are different from the corresponding elements in the lower triangle. An example is a student migration table, where the rows correspond to the countries of origin of the students and the columns to the destination countries. This package provides the slide-vector model <doi:10.1007/BF02294474>, a scaling model with unique dimensions and the asymscal model for asymmetric multidimensional scaling. Furthermore, a heat map for skew-symmetric data, and the decomposition of asymmetry are provided for the analysis of asymmetric tables.
Author: Berrie Zielman
Maintainer: Berrie Zielman <berrie.zielman@gmail.com>
Diff between asymmetry versions 2.0 dated 2018-10-15 and 2.0.2 dated 2019-07-10
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- NAMESPACE | 2 +- R/asymscal.R | 3 --- R/mdsunique.R | 12 ++---------- R/slidevector.R | 3 +-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/asymmetry.html | 12 ++++++------ man/hmap.Rd | 4 ++-- man/slidevector.Rd | 2 +- man/studentmigration.Rd | 2 +- 12 files changed, 29 insertions(+), 41 deletions(-)
Title: Retinal Reconstruction Program
Description: Reconstructs retinae by morphing a flat surface with cuts (a
dissected flat-mount retina) onto a curvilinear surface (the standard retinal
shape). It can estimate the position of a point on the intact adult retina
to within 8 degrees of arc (3.6% of nasotemporal axis). The coordinates in
reconstructed retinae can be transformed to visuotopic coordinates.
Author: David C. Sterratt [aut, cre, cph],
Daniel Lyngholm [aut, cph]
Maintainer: David C. Sterratt <david.c.sterratt@ed.ac.uk>
Diff between retistruct versions 0.5.12 dated 2017-08-09 and 0.6.0 dated 2019-07-10
retistruct-0.5.12/retistruct/R/Dataset.R |only retistruct-0.5.12/retistruct/R/ReconstructedDataset.R |only retistruct-0.5.12/retistruct/R/RetinalDataset.R |only retistruct-0.5.12/retistruct/R/RetinalReconstructedDataset.R |only retistruct-0.5.12/retistruct/man/Dataset.Rd |only retistruct-0.5.12/retistruct/man/ReconstructedDataset.Rd |only retistruct-0.5.12/retistruct/man/RetinalDataset.Rd |only retistruct-0.5.12/retistruct/man/RetinalReconstructedDataset.Rd |only retistruct-0.5.12/retistruct/man/addClass.Rd |only retistruct-0.5.12/retistruct/man/addTear.Rd |only retistruct-0.5.12/retistruct/man/azel.to.sphere.colattitude.Rd |only retistruct-0.5.12/retistruct/man/checkTears.Rd |only retistruct-0.5.12/retistruct/man/computeTearRelationships.Rd |only retistruct-0.5.12/retistruct/man/ensureFixedPointInRim.Rd |only retistruct-0.5.12/retistruct/man/flatplot.annotatedOutline.Rd |only retistruct-0.5.12/retistruct/man/flatplot.dataset.Rd |only retistruct-0.5.12/retistruct/man/flatplot.outline.Rd |only retistruct-0.5.12/retistruct/man/flatplot.reconstructedOutline.Rd |only retistruct-0.5.12/retistruct/man/flatplot.retinalDataset.Rd |only retistruct-0.5.12/retistruct/man/flatplot.stitchedOutline.Rd |only retistruct-0.5.12/retistruct/man/flatplot.triangulatedOutline.Rd |only retistruct-0.5.12/retistruct/man/getDss.Rd |only retistruct-0.5.12/retistruct/man/getDss.reconstructedDataset.Rd |only retistruct-0.5.12/retistruct/man/getDss.retinalReconstructedDataset.Rd |only retistruct-0.5.12/retistruct/man/getDssHullarea.Rd |only retistruct-0.5.12/retistruct/man/getDssMean.Rd |only retistruct-0.5.12/retistruct/man/getDssMean.reconstructedDataset.Rd |only retistruct-0.5.12/retistruct/man/getDssMean.retinalReconstructedDataset.Rd |only retistruct-0.5.12/retistruct/man/getFlatRimLength.Rd |only retistruct-0.5.12/retistruct/man/getGss.Rd |only retistruct-0.5.12/retistruct/man/getGss.reconstructedDataset.Rd |only retistruct-0.5.12/retistruct/man/getGss.retinalReconstructedDataset.Rd |only retistruct-0.5.12/retistruct/man/getIDs.Rd |only retistruct-0.5.12/retistruct/man/getIDs.dataset.Rd |only retistruct-0.5.12/retistruct/man/getIDs.reconstructedDataset.Rd |only retistruct-0.5.12/retistruct/man/getIms.Rd |only retistruct-0.5.12/retistruct/man/getIms.reconstructedOutline.Rd |only retistruct-0.5.12/retistruct/man/getKDE.Rd |only retistruct-0.5.12/retistruct/man/getKR.Rd |only retistruct-0.5.12/retistruct/man/getSss.Rd |only retistruct-0.5.12/retistruct/man/getSss.reconstructedDataset.Rd |only retistruct-0.5.12/retistruct/man/getSss.retinalReconstructedDataset.Rd |only retistruct-0.5.12/retistruct/man/getSssMean.Rd |only retistruct-0.5.12/retistruct/man/getStrains.Rd |only retistruct-0.5.12/retistruct/man/getTear.Rd |only retistruct-0.5.12/retistruct/man/getTss.Rd |only retistruct-0.5.12/retistruct/man/labelTearPoints.Rd |only retistruct-0.5.12/retistruct/man/mergePointsEdges.Rd |only retistruct-0.5.12/retistruct/man/nameLandmark.Rd |only retistruct-0.5.12/retistruct/man/nameLandmark.retinalDataset.Rd |only retistruct-0.5.12/retistruct/man/optimiseMapping.Rd |only retistruct-0.5.12/retistruct/man/projectToSphere.Rd |only retistruct-0.5.12/retistruct/man/projection.reconstructedDataset.Rd |only retistruct-0.5.12/retistruct/man/projection.reconstructedOutline.Rd |only retistruct-0.5.12/retistruct/man/recfile.version.Rd |only retistruct-0.5.12/retistruct/man/removeTear.Rd |only retistruct-0.5.12/retistruct/man/retistruct.batch.plot.ods.Rd |only retistruct-0.5.12/retistruct/man/retistruct.potential.od.Rd |only retistruct-0.5.12/retistruct/man/setFixedPoint.Rd |only retistruct-0.5.12/retistruct/man/simplify.outline.Rd |only retistruct-0.5.12/retistruct/man/solveMappingCart.Rd |only retistruct-0.5.12/retistruct/man/sphericalplot.reconstructedDataset.Rd |only retistruct-0.5.12/retistruct/man/titrate.reconstructedOutline.Rd |only retistruct-0.5.12/retistruct/man/transform.image.reconstructedOutline.Rd |only retistruct-0.5.12/retistruct/man/whichTear.Rd |only retistruct-0.5.12/retistruct/tests/getFuns.R |only retistruct-0.5.12/retistruct/tests/getFuns.Rout.save |only retistruct-0.5.12/retistruct/tests/ijroi-format.R |only retistruct-0.5.12/retistruct/tests/ijroi-format.Rout.save |only retistruct-0.6.0/retistruct/DESCRIPTION | 17 retistruct-0.6.0/retistruct/MD5 | 289 -- retistruct-0.6.0/retistruct/NAMESPACE | 105 retistruct-0.6.0/retistruct/NEWS | 27 retistruct-0.6.0/retistruct/R/AnnotatedOutline.R | 586 ++-- retistruct-0.6.0/retistruct/R/CountSet.R |only retistruct-0.6.0/retistruct/R/FeatureSet.R |only retistruct-0.6.0/retistruct/R/Fragment.R |only retistruct-0.6.0/retistruct/R/LandmarkSet.R |only retistruct-0.6.0/retistruct/R/Outline.R | 260 + retistruct-0.6.0/retistruct/R/OutlineCommon.R |only retistruct-0.6.0/retistruct/R/PathOutline.R |only retistruct-0.6.0/retistruct/R/PointSet.R |only retistruct-0.6.0/retistruct/R/ReconstructedCountSet.R |only retistruct-0.6.0/retistruct/R/ReconstructedFeatureSet.R |only retistruct-0.6.0/retistruct/R/ReconstructedLandmarkSet.R |only retistruct-0.6.0/retistruct/R/ReconstructedOutline.R | 1392 ++++++---- retistruct-0.6.0/retistruct/R/ReconstructedPointSet.R |only retistruct-0.6.0/retistruct/R/RetinalOutline.R |only retistruct-0.6.0/retistruct/R/RetinalReconstructedOutline.R | 289 +- retistruct-0.6.0/retistruct/R/StitchedOutline.R | 240 - retistruct-0.6.0/retistruct/R/TriangulatedFragment.R |only retistruct-0.6.0/retistruct/R/TriangulatedOutline.R | 279 -- retistruct-0.6.0/retistruct/R/bary2sph.R |only retistruct-0.6.0/retistruct/R/fire.R | 7 retistruct-0.6.0/retistruct/R/format-common.R | 44 retistruct-0.6.0/retistruct/R/format-csv.R | 31 retistruct-0.6.0/retistruct/R/format-idt.R | 33 retistruct-0.6.0/retistruct/R/format-ijroi.R | 31 retistruct-0.6.0/retistruct/R/generics.R | 221 - retistruct-0.6.0/retistruct/R/geometry.R | 102 retistruct-0.6.0/retistruct/R/misc.R | 54 retistruct-0.6.0/retistruct/R/paths.R |only retistruct-0.6.0/retistruct/R/plots.R | 1 retistruct-0.6.0/retistruct/R/projections.R | 4 retistruct-0.6.0/retistruct/R/retistruct-batch.R | 169 - retistruct-0.6.0/retistruct/R/retistruct-cli.R | 16 retistruct-0.6.0/retistruct/R/retistruct-gui.R | 252 + retistruct-0.6.0/retistruct/R/retistruct.R | 251 - retistruct-0.6.0/retistruct/R/spheristruct.R | 469 --- retistruct-0.6.0/retistruct/R/zzz.R | 2 retistruct-0.6.0/retistruct/README.md |only retistruct-0.6.0/retistruct/inst/WORDLIST |only retistruct-0.6.0/retistruct/inst/extdata/GM509/R-CONTRA/P.csv | 326 ++ retistruct-0.6.0/retistruct/inst/extdata/GM509/R-CONTRA/markup.csv | 2 retistruct-0.6.0/retistruct/inst/extdata/issue21 |only retistruct-0.6.0/retistruct/inst/extdata/smi32/P.csv | 2 retistruct-0.6.0/retistruct/man/AnnotatedOutline.Rd | 25 retistruct-0.6.0/retistruct/man/CountSet.Rd |only retistruct-0.6.0/retistruct/man/E.Rd | 6 retistruct-0.6.0/retistruct/man/Ecart.Rd | 2 retistruct-0.6.0/retistruct/man/Fcart.Rd | 2 retistruct-0.6.0/retistruct/man/FeatureSet.Rd |only retistruct-0.6.0/retistruct/man/Fragment.Rd |only retistruct-0.6.0/retistruct/man/LandmarkSet.Rd |only retistruct-0.6.0/retistruct/man/Outline.Rd | 19 retistruct-0.6.0/retistruct/man/PathOutline.Rd |only retistruct-0.6.0/retistruct/man/PointSet.Rd |only retistruct-0.6.0/retistruct/man/Rcart.Rd | 2 retistruct-0.6.0/retistruct/man/ReconstructedCountSet.Rd |only retistruct-0.6.0/retistruct/man/ReconstructedFeatureSet.Rd |only retistruct-0.6.0/retistruct/man/ReconstructedLandmarkSet.Rd |only retistruct-0.6.0/retistruct/man/ReconstructedOutline.Rd | 43 retistruct-0.6.0/retistruct/man/ReconstructedPointSet.Rd |only retistruct-0.6.0/retistruct/man/RetinalOutline.Rd |only retistruct-0.6.0/retistruct/man/RetinalReconstructedOutline.Rd | 12 retistruct-0.6.0/retistruct/man/StitchedOutline.Rd | 10 retistruct-0.6.0/retistruct/man/TriangulatedFragment.Rd |only retistruct-0.6.0/retistruct/man/TriangulatedOutline.Rd | 52 retistruct-0.6.0/retistruct/man/azel.to.sphere.colatitude.Rd |only retistruct-0.6.0/retistruct/man/bary.to.sphere.cart.Rd | 2 retistruct-0.6.0/retistruct/man/compute.kernel.estimate.Rd | 2 retistruct-0.6.0/retistruct/man/csv.read.dataset.Rd | 6 retistruct-0.6.0/retistruct/man/dE.Rd | 6 retistruct-0.6.0/retistruct/man/depthplot3D.Rd |only retistruct-0.6.0/retistruct/man/f.Rd | 4 retistruct-0.6.0/retistruct/man/fire.Rd | 9 retistruct-0.6.0/retistruct/man/flatplot.AnnotatedOutline.Rd |only retistruct-0.6.0/retistruct/man/flatplot.Outline.Rd |only retistruct-0.6.0/retistruct/man/flatplot.Rd | 12 retistruct-0.6.0/retistruct/man/flatplot.ReconstructedOutline.Rd |only retistruct-0.6.0/retistruct/man/flatplot.StitchedOutline.Rd |only retistruct-0.6.0/retistruct/man/flatplot.TriangulatedOutline.Rd |only retistruct-0.6.0/retistruct/man/flipped.triangles.cart.Rd | 2 retistruct-0.6.0/retistruct/man/fp.Rd | 2 retistruct-0.6.0/retistruct/man/idt.read.dataset.Rd | 4 retistruct-0.6.0/retistruct/man/ijroi.read.dataset.Rd | 6 retistruct-0.6.0/retistruct/man/interpolate.image.Rd |only retistruct-0.6.0/retistruct/man/karcher.mean.sphere.Rd | 2 retistruct-0.6.0/retistruct/man/lvsLplot.Rd | 4 retistruct-0.6.0/retistruct/man/name.list.Rd | 6 retistruct-0.6.0/retistruct/man/orthographic.Rd | 2 retistruct-0.6.0/retistruct/man/parabola.arclength.Rd |only retistruct-0.6.0/retistruct/man/parabola.invarclength.Rd |only retistruct-0.6.0/retistruct/man/parse.dependencies.Rd | 2 retistruct-0.6.0/retistruct/man/polar.cart.to.sphere.spherical.Rd | 2 retistruct-0.6.0/retistruct/man/projection.Rd | 8 retistruct-0.6.0/retistruct/man/projection.ReconstructedOutline.Rd |only retistruct-0.6.0/retistruct/man/projection.RetinalReconstructedOutline.Rd |only retistruct-0.6.0/retistruct/man/read.datacounts.Rd | 14 retistruct-0.6.0/retistruct/man/remove.intersections.Rd | 3 retistruct-0.6.0/retistruct/man/retistruct.batch.Rd | 14 retistruct-0.6.0/retistruct/man/retistruct.batch.export.matlab.Rd | 6 retistruct-0.6.0/retistruct/man/retistruct.cli.process.Rd | 8 retistruct-0.6.0/retistruct/man/retistruct.export.matlab.Rd | 14 retistruct-0.6.0/retistruct/man/retistruct.read.dataset.Rd | 9 retistruct-0.6.0/retistruct/man/retistruct.read.markup.Rd | 2 retistruct-0.6.0/retistruct/man/retistruct.reconstruct.Rd | 20 retistruct-0.6.0/retistruct/man/retistruct.save.markup.Rd | 4 retistruct-0.6.0/retistruct/man/retistruct.save.recdata.Rd | 7 retistruct-0.6.0/retistruct/man/simplifyFragment.Rd |only retistruct-0.6.0/retistruct/man/simplifyOutline.Rd |only retistruct-0.6.0/retistruct/man/sinusoidal.Rd | 6 retistruct-0.6.0/retistruct/man/sphere.cart.to.sphere.dualwedge.Rd | 8 retistruct-0.6.0/retistruct/man/sphere.spherical.to.polar.cart.Rd | 2 retistruct-0.6.0/retistruct/man/sphere.tri.area.Rd | 2 retistruct-0.6.0/retistruct/man/sphericalplot.Rd | 5 retistruct-0.6.0/retistruct/man/sphericalplot.reconstructedOutline.Rd | 4 retistruct-0.6.0/retistruct/man/tri.area.Rd | 2 retistruct-0.6.0/retistruct/man/tri.area.signed.Rd | 2 retistruct-0.6.0/retistruct/src/bary2sph.c |only retistruct-0.6.0/retistruct/src/retistruct_init.c | 2 retistruct-0.6.0/retistruct/tests/testthat/test-annotated-outline.R |only retistruct-0.6.0/retistruct/tests/testthat/test-bary2sph.R |only retistruct-0.6.0/retistruct/tests/testthat/test-feature-set.R |only retistruct-0.6.0/retistruct/tests/testthat/test-format-csv.R | 16 retistruct-0.6.0/retistruct/tests/testthat/test-format-idt.R | 30 retistruct-0.6.0/retistruct/tests/testthat/test-format-ijroi.R | 11 retistruct-0.6.0/retistruct/tests/testthat/test-karcher.R | 2 retistruct-0.6.0/retistruct/tests/testthat/test-outline.R |only retistruct-0.6.0/retistruct/tests/testthat/test-path-outline.R |only retistruct-0.6.0/retistruct/tests/testthat/test-reconstruct.R | 43 retistruct-0.6.0/retistruct/tests/testthat/test-reconstructed-outline.R |only retistruct-0.6.0/retistruct/tests/testthat/test-regressions.R |only retistruct-0.6.0/retistruct/tests/testthat/test-stitched-outline.R |only retistruct-0.6.0/retistruct/tests/testthat/test-triangulated-outline.R |only retistruct-0.6.0/retistruct/tests/testthat/test-wedge.R | 4 206 files changed, 3218 insertions(+), 2777 deletions(-)
Title: Variance Component Analysis
Description: ANOVA and REML estimation of linear mixed models is implemented, once following
Searle et al. (1991, ANOVA for unbalanced data), once making use of the 'lme4' package.
The primary objective of this package is to perform a variance component analysis (VCA)
according to CLSI EP05-A3 guideline "Evaluation of Precision of Quantitative Measurement
Procedures" (2014). There are plotting methods for visualization of an experimental design,
plotting random effects and residuals. For ANOVA type estimation two methods for computing
ANOVA mean squares are implemented (SWEEP and quadratic forms). The covariance matrix of
variance components can be derived, which is used in estimating confidence intervals. Linear
hypotheses of fixed effects and LS means can be computed. LS means can be computed at specific
values of covariables and with custom weighting schemes for factor variables. See ?VCA for a
more comprehensive description of the features.
Author: Andre Schuetzenmeister [aut, cre], Florian Dufey [aut]
Maintainer: Andre Schuetzenmeister <andre.schuetzenmeister@roche.com>
Diff between VCA versions 1.3.4 dated 2018-07-18 and 1.4.0 dated 2019-07-10
VCA-1.3.4/VCA/man/Csweep.Rd |only VCA-1.3.4/VCA/man/Sinv.Rd |only VCA-1.3.4/VCA/man/anovaDF.Rd |only VCA-1.3.4/VCA/man/getAmatrix.Rd |only VCA-1.3.4/VCA/man/getBasis.Rd |only VCA-1.3.4/VCA/man/getCmatrix.Rd |only VCA-1.3.4/VCA/man/getSSQqf.Rd |only VCA-1.3.4/VCA/man/getVCvar.Rd |only VCA-1.3.4/VCA/src/vca.c |only VCA-1.4.0/VCA/DESCRIPTION | 14 VCA-1.4.0/VCA/MD5 | 193 VCA-1.4.0/VCA/NAMESPACE | 3 VCA-1.4.0/VCA/R/anova.R |only VCA-1.4.0/VCA/R/plot.R | 19 VCA-1.4.0/VCA/R/reml.R |only VCA-1.4.0/VCA/R/utils.R |only VCA-1.4.0/VCA/R/vca.R | 7253 ++---------------------- VCA-1.4.0/VCA/inst/ChangeLog.txt | 12 VCA-1.4.0/VCA/inst/UnitTests/LSMeans_Data.RData |only VCA-1.4.0/VCA/inst/UnitTests/RunAllTests.R | 5 VCA-1.4.0/VCA/inst/UnitTests/runit.anovaVCA.R | 69 VCA-1.4.0/VCA/inst/UnitTests/runit.misc.R | 27 VCA-1.4.0/VCA/man/CA19_9.Rd | 4 VCA-1.4.0/VCA/man/DfSattHelper.Rd | 5 VCA-1.4.0/VCA/man/Fsweep.Rd |only VCA-1.4.0/VCA/man/Glucose.Rd | 4 VCA-1.4.0/VCA/man/HugeData.Rd | 2 VCA-1.4.0/VCA/man/MLrepro.Rd | 2 VCA-1.4.0/VCA/man/MPinv.Rd | 5 VCA-1.4.0/VCA/man/Orthodont.Rd | 2 VCA-1.4.0/VCA/man/ReproData1.Rd | 4 VCA-1.4.0/VCA/man/SattDF.Rd | 7 VCA-1.4.0/VCA/man/Scale.Rd | 11 VCA-1.4.0/VCA/man/Solve.Rd | 3 VCA-1.4.0/VCA/man/Trace.Rd | 5 VCA-1.4.0/VCA/man/VCA-Package.Rd | 16 VCA-1.4.0/VCA/man/VCAdata1.Rd | 2 VCA-1.4.0/VCA/man/VCAinference.Rd | 41 VCA-1.4.0/VCA/man/anovaMM.Rd | 78 VCA-1.4.0/VCA/man/anovaVCA.Rd | 113 VCA-1.4.0/VCA/man/as.matrix.VCA.Rd | 13 VCA-1.4.0/VCA/man/as.matrix.VCAinference.Rd | 13 VCA-1.4.0/VCA/man/buildList.Rd | 3 VCA-1.4.0/VCA/man/check4MKL.Rd | 7 VCA-1.4.0/VCA/man/chol2invData.Rd | 2 VCA-1.4.0/VCA/man/coef.VCA.Rd | 3 VCA-1.4.0/VCA/man/dataEP05A2_1.Rd | 4 VCA-1.4.0/VCA/man/dataEP05A2_2.Rd | 4 VCA-1.4.0/VCA/man/dataEP05A2_3.Rd | 4 VCA-1.4.0/VCA/man/dataEP05A3_MS_1.Rd | 4 VCA-1.4.0/VCA/man/dataEP05A3_MS_2.Rd | 4 VCA-1.4.0/VCA/man/dataEP05A3_MS_3.Rd | 4 VCA-1.4.0/VCA/man/dataRS0003_1.Rd | 2 VCA-1.4.0/VCA/man/dataRS0003_2.Rd | 2 VCA-1.4.0/VCA/man/dataRS0003_3.Rd | 2 VCA-1.4.0/VCA/man/dataRS0005_1.Rd | 2 VCA-1.4.0/VCA/man/dataRS0005_2.Rd | 2 VCA-1.4.0/VCA/man/dataRS0005_3.Rd | 2 VCA-1.4.0/VCA/man/fitLMM.Rd | 17 VCA-1.4.0/VCA/man/fitVCA.Rd | 9 VCA-1.4.0/VCA/man/fixef.Rd | 7 VCA-1.4.0/VCA/man/fixef.VCA.Rd | 7 VCA-1.4.0/VCA/man/getDDFM.Rd | 11 VCA-1.4.0/VCA/man/getDF.Rd | 5 VCA-1.4.0/VCA/man/getGB.Rd | 15 VCA-1.4.0/VCA/man/getL.Rd | 7 VCA-1.4.0/VCA/man/getMM.Rd | 8 VCA-1.4.0/VCA/man/getMat.Rd | 5 VCA-1.4.0/VCA/man/getSSQsweep.Rd | 21 VCA-1.4.0/VCA/man/getV.Rd | 5 VCA-1.4.0/VCA/man/isBalanced.Rd | 7 VCA-1.4.0/VCA/man/legend.m.Rd | 9 VCA-1.4.0/VCA/man/lmerG.Rd | 6 VCA-1.4.0/VCA/man/lmerMatrices.Rd | 11 VCA-1.4.0/VCA/man/lmerSummary.Rd | 13 VCA-1.4.0/VCA/man/load_if_installed.Rd | 5 VCA-1.4.0/VCA/man/lsmMat.Rd | 9 VCA-1.4.0/VCA/man/lsmeans.Rd | 13 VCA-1.4.0/VCA/man/model.frame.VCA.Rd | 5 VCA-1.4.0/VCA/man/model.matrix.VCA.Rd | 5 VCA-1.4.0/VCA/man/orderData.Rd | 5 VCA-1.4.0/VCA/man/plot.VCA.Rd | 8 VCA-1.4.0/VCA/man/plotRandVar.Rd | 1 VCA-1.4.0/VCA/man/predict.VCA.Rd | 3 VCA-1.4.0/VCA/man/print.VCA.Rd | 3 VCA-1.4.0/VCA/man/print.VCAinference.Rd | 9 VCA-1.4.0/VCA/man/ranef.Rd | 7 VCA-1.4.0/VCA/man/ranef.VCA.Rd | 5 VCA-1.4.0/VCA/man/reScale.Rd | 12 VCA-1.4.0/VCA/man/realData.Rd | 2 VCA-1.4.0/VCA/man/remlMM.Rd | 19 VCA-1.4.0/VCA/man/remlVCA.Rd | 76 VCA-1.4.0/VCA/man/residuals.VCA.Rd | 11 VCA-1.4.0/VCA/man/scaleData.Rd | 7 VCA-1.4.0/VCA/man/sleepstudy.Rd | 2 VCA-1.4.0/VCA/man/solveMME.Rd | 9 VCA-1.4.0/VCA/man/stepwiseVCA.Rd | 15 VCA-1.4.0/VCA/man/test.fixef.Rd | 15 VCA-1.4.0/VCA/man/test.lsmeans.Rd | 15 VCA-1.4.0/VCA/man/varPlot.Rd | 7 VCA-1.4.0/VCA/man/vcov.VCA.Rd | 5 VCA-1.4.0/VCA/man/vcovFixed.Rd | 5 VCA-1.4.0/VCA/man/vcovVC.Rd | 21 VCA-1.4.0/VCA/src/Makevars |only VCA-1.4.0/VCA/src/init.c |only VCA-1.4.0/VCA/src/vca.f95 |only 106 files changed, 1438 insertions(+), 7000 deletions(-)
Title: Create Useful Summaries of the Portal Data
Description: Download and generate summaries for the rodent, plant, ant, and
weather data from the Portal Project. Portal is a long-term (and ongoing)
experimental monitoring site in the Chihuahua desert. The raw data files
can be found at <https://github.com/weecology/portaldata>.
Author: Glenda M. Yenni [aut, cre] (<https://orcid.org/0000-0001-6969-1848>),
Hao Ye [aut] (<https://orcid.org/0000-0002-8630-1458>),
Erica M. Christensen [aut] (<https://orcid.org/0000-0002-5635-2502>),
Juniper L. Simonis [aut] (<https://orcid.org/0000-0001-9798-0460>),
Ellen K. Bledsoe [aut] (<https://orcid.org/0000-0002-3629-7235>),
Renata M. Diaz [aut] (<https://orcid.org/0000-0003-0803-4734>),
Shawn D. Taylor [aut] (<https://orcid.org/0000-0002-6178-6903>),
Ethan P, White [aut] (<https://orcid.org/0000-0001-6728-7745>),
S.K. Morgan Ernest [aut] (<https://orcid.org/0000-0002-6026-8530>)
Maintainer: Glenda M. Yenni <glenda@weecology.org>
Diff between portalr versions 0.2.5 dated 2019-06-22 and 0.2.6 dated 2019-07-10
DESCRIPTION | 6 - MD5 | 44 +++++------ NAMESPACE | 1 R/NDVI.R | 17 ++-- R/Weather.R | 100 +++++++++++++++---------- R/get_future_moons.R | 11 +- R/load_data.R | 32 ++++---- R/make_monthly_timeseries.R | 120 ++++++++++++++++--------------- R/portalr-package.R | 15 --- R/process_data_utils.R | 30 +++---- R/process_plant_data.R | 79 ++++++++++---------- R/process_rodent_data.R | 101 ++++++++++++++------------ R/season_function.R | 44 +++++------ R/summarize_ants.R | 26 ++---- R/summarize_individual_rodents.R | 5 - R/summarize_plants.R | 28 ++++--- R/summarize_rodents.R | 7 + README.md | 2 inst/doc/portal_researcher_examples.html | 4 - inst/doc/rodent-abundance-demo.html | 12 +-- man/add_seasons.Rd | 4 - tests/testthat/test-07-seasons.R | 4 - tests/testthat/test-99-regression.R | 7 + 23 files changed, 371 insertions(+), 328 deletions(-)
Title: Simulation-Based Maximum Likelihood Parameter Estimation
Description: An estimation method that can use computer simulations to
approximate maximum-likelihood estimates even when the likelihood function can not
be evaluated directly. It can be applied whenever it is feasible to conduct many
simulations, but works best when the data is approximately Poisson distributed.
It was originally designed for demographic inference in evolutionary
biology. It has optional support for conducting coalescent simulation using
the 'coala' package.
Author: Paul Staab [aut, cre],
Lisha Mathew [aut],
Dirk Metzler [aut, ths]
Maintainer: Paul Staab <develop@paulstaab.de>
Diff between jaatha versions 3.2.0 dated 2016-05-13 and 3.2.1 dated 2019-07-10
DESCRIPTION | 8 MD5 | 38 +-- NAMESPACE | 1 NEWS.md | 9 R/coala_interface.R | 1 R/likelihood.R | 4 README.md | 9 build/vignette.rds |binary inst/doc/jaatha-evolution.html | 333 ++++++++++++++++++++++++++++----- inst/doc/jaatha-intro.html | 351 +++++++++++++++++++++++++++++------ man/boot_jaatha.Rd | 1 man/coarsen_jsfs.Rd | 7 man/create_jaatha_data.Rd | 1 man/create_jaatha_model.Rd | 1 man/create_jaatha_model.coalmodel.Rd | 5 man/create_jaatha_model.function.Rd | 1 man/create_jaatha_stat.Rd | 4 man/estimate_llh.Rd | 1 man/get_start_pos.Rd | 1 man/jaatha.Rd | 9 20 files changed, 627 insertions(+), 158 deletions(-)
Title: Group Sequential Enrichment Design
Description: Provides function to apply "Group sequential enrichment design incorporating subgroup selection" (GSED) method proposed by Magnusson and Turnbull (2013) <doi:10.1002/sim.5738>.
Author: Marie-Karelle Riviere
Maintainer: Marie-Karelle Riviere <eldamjh@gmail.com>
Diff between GSED versions 2.1 dated 2019-06-14 and 2.3 dated 2019-07-10
DESCRIPTION | 8 +-- MD5 | 6 +- R/GSED.R | 120 ++++++++++++++++++++-------------------------------- man/GSED-package.Rd | 4 - 4 files changed, 56 insertions(+), 82 deletions(-)
Title: General-to-Specific (GETS) Modelling and Indicator Saturation
Methods
Description: Automated General-to-Specific (GETS) modelling of the mean and variance of a regression, and indicator saturation methods for detecting and testing for structural breaks in the mean.
Author: Genaro Sucarrat [aut, cre], Felix Pretis [aut], James Reade [aut]
Maintainer: Genaro Sucarrat <genaro.sucarrat@bi.no>
Diff between gets versions 0.18 dated 2019-02-25 and 0.19 dated 2019-07-10
gets-0.18/gets/R/gets.default.R |only gets-0.19/gets/DESCRIPTION | 10 - gets-0.19/gets/MD5 | 55 +++++--- gets-0.19/gets/NAMESPACE | 50 ++++++- gets-0.19/gets/NEWS | 29 ++++ gets-0.19/gets/R/gets-internal.R | 8 - gets-0.19/gets/R/getsm.R | 2 gets-0.19/gets/R/isatdates.R |only gets-0.19/gets/R/isatloop.R |only gets-0.19/gets/R/isatvar.R | 222 ++++++++++++++++----------------- gets-0.19/gets/R/isatvarcorrect.R |only gets-0.19/gets/R/isvarcor.R | 16 +- gets-0.19/gets/R/isvareffcor.R | 14 +- gets-0.19/gets/R/mvrnormsim.R |only gets-0.19/gets/R/ols.R | 18 +- gets-0.19/gets/R/outlierscaletest.R |only gets-0.19/gets/R/outliertest.R |only gets-0.19/gets/R/predict.arx.R | 4 gets-0.19/gets/R/predict.isat.R | 18 +- gets-0.19/gets/R/print.isat.R | 68 ++++++---- gets-0.19/gets/R/printtex.R | 17 +- gets-0.19/gets/R/vargaugeiis.R |only gets-0.19/gets/data/hpdata.rda |binary gets-0.19/gets/data/infldata.rda |binary gets-0.19/gets/data/so2data.rda |binary gets-0.19/gets/data/sp500data.rda |binary gets-0.19/gets/man/gets-package.Rd | 4 gets-0.19/gets/man/gets.Rd | 6 gets-0.19/gets/man/isatdates.Rd |only gets-0.19/gets/man/isatloop.Rd |only gets-0.19/gets/man/isatvarcorrect.Rd |only gets-0.19/gets/man/mvrnormsim.Rd |only gets-0.19/gets/man/outlierscaletest.Rd |only gets-0.19/gets/man/outliertest.Rd |only gets-0.19/gets/man/printtex.Rd | 2 gets-0.19/gets/man/vargaugeiis.Rd |only 36 files changed, 315 insertions(+), 228 deletions(-)
Title: Create and Visualize Hillshaded Maps from Elevation Matrices
Description: Uses a combination of raytracing, spherical texture mapping, lambertian reflectance, and ambient occlusion to produce 2D and 3D data visualizations and maps. Includes water detection and layering functions, programmable color palette generation, several built-in textures for hillshading, 2D and 3D plotting options, and the ability to export 3D visualizations to a 3D printable format.
Author: Tyler Morgan-Wall
Maintainer: Tyler Morgan-Wall <tylermw@gmail.com>
Diff between rayshader versions 0.10.1 dated 2019-02-20 and 0.11.4 dated 2019-07-10
DESCRIPTION | 12 ++++----- MD5 | 52 ++++++++++++++++++++++++------------------ NAMESPACE | 3 ++ R/add_overlay.R | 9 +++++++ R/ambient_shade.R | 30 ++++++++++++++++++++---- R/gg_internal_functions.R |only R/make_water.R | 1 R/plot_3d.R | 14 ++++------- R/plot_gg.R |only R/render_camera.R | 24 ++++++++++++------- R/render_depth.R | 10 +++++--- R/render_label.R | 3 -- R/render_movie.R |only R/render_snapshot.R | 13 ++++++---- R/render_water.R | 3 -- R/save_3dprint.R | 23 +++++++++++------- R/save_png.R | 7 +++-- man/drawkeyfunction_lines.Rd |only man/drawkeyfunction_points.Rd |only man/plot_3d.Rd | 14 ++++------- man/plot_gg.Rd |only man/render_camera.Rd | 16 ++++++------ man/render_depth.Rd | 7 +++-- man/render_label.Rd | 3 -- man/render_movie.Rd |only man/render_snapshot.Rd | 7 +++-- man/render_water.Rd | 3 -- man/save_3dprint.Rd | 20 ++++++++-------- man/save_png.Rd | 4 ++- man/translate_shape_string.Rd |only src/make_base_cpp.cpp | 36 ++++++++++++----------------- 31 files changed, 182 insertions(+), 132 deletions(-)
Title: Geographic Data Analysis and Modeling
Description: Reading, writing, manipulating, analyzing and modeling of gridded spatial data. The package implements basic and high-level functions. Processing of very large files is supported. There is a also support for vector data operations such as intersections. See the manual and tutorials on <https://rspatial.org/> to get started.
Author: Robert J. Hijmans [cre, aut] (<https://orcid.org/0000-0001-5872-2872>),
Jacob van Etten [ctb],
Michael Sumner [ctb],
Joe Cheng [ctb],
Andrew Bevan [ctb],
Roger Bivand [ctb],
Lorenzo Busetto [ctb],
Mort Canty [ctb],
David Forrest [ctb],
Aniruddha Ghosh [ctb],
Duncan Golicher [ctb],
Josh Gray [ctb],
Jonathan A. Greenberg [ctb],
Paul Hiemstra [ctb],
Institute for Mathematics Applied Geosciences [cph],
Charles Karney [ctb],
Matteo Mattiuzzi [ctb],
Steven Mosher [ctb],
Jakub Nowosad [ctb],
Edzer Pebesma [ctb],
Oscar Perpinan Lamigueiro [ctb],
Etienne B. Racine [ctb],
Barry Rowlingson [ctb],
Ashton Shortridge [ctb],
Bill Venables [ctb],
Rafael Wueest [ctb]
Maintainer: Robert J. Hijmans <r.hijmans@gmail.com>
Diff between raster versions 2.9-5 dated 2019-05-14 and 2.9-22 dated 2019-07-10
raster-2.9-22/raster/ChangeLog | 18 raster-2.9-22/raster/DESCRIPTION | 12 raster-2.9-22/raster/MD5 | 227 +++++----- raster-2.9-22/raster/NAMESPACE | 3 raster-2.9-22/raster/R/AAgeneric_functions.R | 40 + raster-2.9-22/raster/R/RcppExports.R | 36 + raster-2.9-22/raster/R/approxNA.R | 7 raster-2.9-22/raster/R/boundaries.R | 30 - raster-2.9-22/raster/R/brick.R | 9 raster-2.9-22/raster/R/cellRowCol.R | 24 - raster-2.9-22/raster/R/clamp.R | 4 raster-2.9-22/raster/R/contour.R | 2 raster-2.9-22/raster/R/dataProperties.R | 23 - raster-2.9-22/raster/R/extend.R | 5 raster-2.9-22/raster/R/factor.R | 14 raster-2.9-22/raster/R/flip.R | 5 raster-2.9-22/raster/R/focal.R | 33 - raster-2.9-22/raster/R/geom.R | 23 + raster-2.9-22/raster/R/getValuesFocal.R | 2 raster-2.9-22/raster/R/gridDistance2.R | 16 raster-2.9-22/raster/R/ifelse.R |only raster-2.9-22/raster/R/init.R | 8 raster-2.9-22/raster/R/interpolate.R | 4 raster-2.9-22/raster/R/isLonLat.R | 26 - raster-2.9-22/raster/R/layerize.R | 6 raster-2.9-22/raster/R/netCDFtoRasterCD.R | 68 ++- raster-2.9-22/raster/R/netCDFutil.R | 12 raster-2.9-22/raster/R/netCDFwriteCD.R | 5 raster-2.9-22/raster/R/plot.R | 6 raster-2.9-22/raster/R/plotCT.R | 10 raster-2.9-22/raster/R/plotRGB.R | 5 raster-2.9-22/raster/R/pointdistance.R | 5 raster-2.9-22/raster/R/predict.R | 50 -- raster-2.9-22/raster/R/raster.R | 5 raster-2.9-22/raster/R/rasterFromRasterFile.R | 158 +++++-- raster-2.9-22/raster/R/ratify.R | 39 + raster-2.9-22/raster/R/reclassify.R | 4 raster-2.9-22/raster/R/sampleAlong.R | 4 raster-2.9-22/raster/R/setMinMax.R | 11 raster-2.9-22/raster/R/shift.R | 80 +-- raster-2.9-22/raster/R/spplot.R | 21 - raster-2.9-22/raster/R/stack.R | 7 raster-2.9-22/raster/R/stretch.R | 7 raster-2.9-22/raster/R/terrain.R | 8 raster-2.9-22/raster/R/unique.R | 6 raster-2.9-22/raster/R/writeRaster.R | 4 raster-2.9-22/raster/R/xyResolution.R | 36 + raster-2.9-22/raster/build/vignette.rds |binary raster-2.9-22/raster/inst/doc/Raster.R | 357 ----------------- raster-2.9-22/raster/inst/doc/Raster.Rnw | 543 -------------------------- raster-2.9-22/raster/inst/doc/Raster.pdf |binary raster-2.9-22/raster/inst/doc/functions.pdf |binary raster-2.9-22/raster/inst/doc/rasterfile.pdf |binary raster-2.9-22/raster/man/Summary-methods.Rd | 4 raster-2.9-22/raster/man/boundaries.Rd | 1 raster-2.9-22/raster/man/brick.Rd | 1 raster-2.9-22/raster/man/cellFrom.Rd | 3 raster-2.9-22/raster/man/cellStats.Rd | 2 raster-2.9-22/raster/man/clearValues.Rd | 2 raster-2.9-22/raster/man/cluster.Rd | 4 raster-2.9-22/raster/man/dataType.Rd | 2 raster-2.9-22/raster/man/datasource.Rd | 15 raster-2.9-22/raster/man/erase.Rd | 2 raster-2.9-22/raster/man/extract.Rd | 2 raster-2.9-22/raster/man/factor.Rd | 9 raster-2.9-22/raster/man/geom.Rd | 11 raster-2.9-22/raster/man/gridDistance.Rd | 2 raster-2.9-22/raster/man/hdrFiles.Rd | 4 raster-2.9-22/raster/man/init.Rd | 12 raster-2.9-22/raster/man/interpolate.Rd | 2 raster-2.9-22/raster/man/intersect.Rd | 2 raster-2.9-22/raster/man/isLonLat.Rd | 13 raster-2.9-22/raster/man/layerize.Rd | 7 raster-2.9-22/raster/man/metadata.Rd | 8 raster-2.9-22/raster/man/persp.Rd | 2 raster-2.9-22/raster/man/pointDistance.Rd |only raster-2.9-22/raster/man/predict.Rd | 2 raster-2.9-22/raster/man/projectRaster.Rd | 2 raster-2.9-22/raster/man/raster-package.Rd | 10 raster-2.9-22/raster/man/raster.Rd | 3 raster-2.9-22/raster/man/rasterOptions.Rd | 2 raster-2.9-22/raster/man/resolution.Rd | 2 raster-2.9-22/raster/man/saveStack.Rd | 3 raster-2.9-22/raster/man/setMinMax.Rd | 9 raster-2.9-22/raster/man/shift.Rd | 18 raster-2.9-22/raster/man/spplot.Rd | 27 - raster-2.9-22/raster/man/stack.Rd | 3 raster-2.9-22/raster/man/strech.Rd | 9 raster-2.9-22/raster/man/subs.Rd |only raster-2.9-22/raster/man/subset.Rd | 2 raster-2.9-22/raster/man/symdif.Rd | 2 raster-2.9-22/raster/man/union.Rd | 2 raster-2.9-22/raster/man/update.Rd | 6 raster-2.9-22/raster/man/writeRaster.Rd | 15 raster-2.9-22/raster/man/writeValues.Rd | 3 raster-2.9-22/raster/man/xyFromCell.Rd | 8 raster-2.9-22/raster/src/RcppExports.cpp | 160 ++++++- raster-2.9-22/raster/src/broom.cpp |only raster-2.9-22/raster/src/clamp.cpp |only raster-2.9-22/raster/src/distance.cpp | 14 raster-2.9-22/raster/src/edge.cpp |only raster-2.9-22/raster/src/focal_fun.cpp |only raster-2.9-22/raster/src/focal_get.cpp |only raster-2.9-22/raster/src/focal_sum.cpp |only raster-2.9-22/raster/src/layerize.cpp |only raster-2.9-22/raster/src/raster_aggregate.cpp |only raster-2.9-22/raster/src/raster_distance.cpp |only raster-2.9-22/raster/src/rasterize.cpp | 3 raster-2.9-22/raster/src/reclass.cpp |only raster-2.9-22/raster/src/terrain.cpp |only raster-2.9-22/raster/src/util.cpp |only raster-2.9-22/raster/src/xyCell.cpp |only raster-2.9-22/raster/vignettes/Raster.Rnw | 543 -------------------------- raster-2.9-5/raster/R/resolution.R |only raster-2.9-5/raster/man/pointdistance.Rd |only raster-2.9-5/raster/man/substitute.Rd |only raster-2.9-5/raster/src/broom.c |only raster-2.9-5/raster/src/clamp.c |only raster-2.9-5/raster/src/edge.c |only raster-2.9-5/raster/src/focal_fun.c |only raster-2.9-5/raster/src/focal_get.c |only raster-2.9-5/raster/src/focal_sum.c |only raster-2.9-5/raster/src/intersect.c |only raster-2.9-5/raster/src/intersect.h |only raster-2.9-5/raster/src/layerize.c |only raster-2.9-5/raster/src/r_terrain.c |only raster-2.9-5/raster/src/rcpp_aggregate.cpp |only raster-2.9-5/raster/src/rcpp_distance.cpp |only raster-2.9-5/raster/src/rcpp_xyCell.cpp |only raster-2.9-5/raster/src/reclass.c |only raster-2.9-5/raster/src/util.c |only raster-2.9-5/raster/src/wirth.c |only 132 files changed, 942 insertions(+), 2044 deletions(-)
Title: Case-Wise and Cluster-Wise Derivatives for Mixed Effects Models
Description: Compute case-wise and cluster-wise derivative for
mixed effects models with respect to fixed effects parameter, random effect (co)variances,
and residual variance.
Author: Ting Wang [aut, cre],
Edgar Merkle [aut] (<https://orcid.org/0000-0001-7158-0653>),
Yves Rosseel [ctb]
Maintainer: Ting Wang <twb8d@mail.missouri.edu>
Diff between merDeriv versions 0.1-6 dated 2018-11-30 and 0.1-7 dated 2019-07-10
DESCRIPTION | 22 ++++++----- MD5 | 32 +++++++++------- NAMESPACE | 21 +++++++--- R/bread.glmerMod.R |only R/estfun.glmerMod.R |only R/estfun.lmerMod.R | 2 + R/llcont.glmerMod.R |only R/llcont.lmerMod.R | 2 + R/vcov.glmerMod.R | 2 - R/vcov.lmerMod.R | 95 ++++++++++++++++++++++--------------------------- README.md | 6 ++- build/partial.rdb |binary man/bread.glmerMod.Rd |only man/bread.lmerMod.Rd | 8 ++-- man/estfun.glmerMod.Rd |only man/estfun.lmerMod.Rd | 12 +++--- man/llcont.glmerMod.Rd |only man/llcont.lmerMod.Rd | 8 ++-- man/vcov.glmerMod.Rd | 12 +++--- man/vcov.lmerMod.Rd | 8 ++-- 20 files changed, 124 insertions(+), 106 deletions(-)
Title: Visualise Twitter Interactions
Description: Allows building an edge table from data frame of tweets,
also provides function to build nodes and another create a temporal graph.
Author: John Coene [aut, cre]
Maintainer: John Coene <jcoenep@gmail.com>
Diff between graphTweets versions 0.5.1 dated 2019-02-14 and 0.5.2 dated 2019-07-10
graphTweets-0.5.1/graphTweets/man/edges_deprecated.Rd |only graphTweets-0.5.2/graphTweets/DESCRIPTION | 9 graphTweets-0.5.2/graphTweets/MD5 | 21 - graphTweets-0.5.2/graphTweets/NAMESPACE | 6 graphTweets-0.5.2/graphTweets/NEWS.md | 5 graphTweets-0.5.2/graphTweets/R/graphTweets.R | 3 graphTweets-0.5.2/graphTweets/R/overhaul.R | 181 +++-------- graphTweets-0.5.2/graphTweets/man/edges.Rd | 17 - graphTweets-0.5.2/graphTweets/man/figures/logo.png |binary graphTweets-0.5.2/graphTweets/man/graphTweets.Rd | 2 graphTweets-0.5.2/graphTweets/man/gt_nodes.Rd | 17 - graphTweets-0.5.2/graphTweets/tests/testthat/test_overhaul.R | 18 - 12 files changed, 126 insertions(+), 153 deletions(-)
Title: Simulation and Parameter Estimation of Randomized Sierpinski
Carpets using the p-p-p-q-Model
Description: The parameters p and q are estimated with the aid of a randomized Sierpinski Carpet which is built on a [p-p-p-q]-model. Thereby, for three times a simulation with a p-value and once with a q-value is assumed. Hence, these parameters are estimated and displayed. Moreover, functions for simulating random Sierpinski-Carpets with constant and variable probabilities are included. For more details on the method please see Hermann et al. (2015) <doi:10.1002/sim.6497>.
Author: Philipp Hermann, Jozef Kiselak, Milan Stehlik
Maintainer: Philipp Hermann <philipp.hermann@jku.at>
Diff between FractalParameterEstimation versions 1.1.1 dated 2017-09-12 and 1.1.2 dated 2019-07-10
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- R/GSC_seq.R | 2 +- 3 files changed, 8 insertions(+), 8 deletions(-)
More information about FractalParameterEstimation at CRAN
Permanent link
Title: Analysis of Diffusion Weighted Imaging (DWI) Data
Description: Diffusion Weighted Imaging (DWI) is a Magnetic Resonance Imaging
modality, that measures diffusion of water in tissues like the human
brain. The package contains R-functions to process diffusion-weighted
data. The functionality includes diffusion tensor imaging (DTI),
diffusion kurtosis imaging (DKI), modeling for high angular resolution
diffusion weighted imaging (HARDI) using Q-ball-reconstruction and
tensor mixture models, several methods for structural adaptive
smoothing including POAS and msPOAS, and a streamline fiber tracking
for tensor and tensor mixture models.
The package provides functionality to manipulate and visualize results
in 2D and 3D.
Author: Karsten Tabelow [aut, cre],
Joerg Polzehl [aut],
Felix Anker [ctb]
Maintainer: Karsten Tabelow <karsten.tabelow@wias-berlin.de>
Diff between dti versions 1.4 dated 2019-05-09 and 1.4.1 dated 2019-07-10
DESCRIPTION | 11 ++--- MD5 | 60 +++++++++++++++--------------- R/aws.r | 2 - R/aws2.r | 6 +-- R/awsse3.r | 6 +-- R/awsse3ms.r | 4 +- R/fibers.r | 9 ++-- R/misc.r | 11 +++-- R/mixtensorpl.r | 17 ++++---- R/plot.r | 4 +- R/tracking.r | 6 +-- R/utilities.r | 6 ++- R/varest.r | 20 +++++----- build/partial.rdb |binary demo/dti_art.r | 19 ++++----- demo/mixtens_art.r | 31 +++++++-------- man/polyeder.Rd | 8 ++-- man/readDWIdata.Rd | 24 ++++++------ src/Makevars | 2 - src/aniso.f | 8 ++-- src/awsvar.f | 12 +++--- src/dtifull.f | 6 +-- src/dtinraw2.f | 16 ++++---- src/fibers.f | 42 ++++++++++----------- src/init.c | 105 +++++++++++++++++++++++++---------------------------- src/misc.f | 41 ++++++++++---------- src/mixtenbv.f | 10 ++--- src/mixtens.f | 33 ++++++++-------- src/rice.f | 5 +- src/smse3.f | 44 +++++++++++----------- src/varest.f | 38 +++++++++---------- 31 files changed, 302 insertions(+), 304 deletions(-)
Title: Dependent Mixture Models - Hidden Markov Models of GLMs and
Other Distributions in S4
Description: Fits latent (hidden) Markov models on mixed categorical and continuous (time series) data, otherwise known as dependent mixture models, see Visser & Speekenbrink (2010, <DOI:10.18637/jss.v036.i07>).
Author: Ingmar Visser <i.visser@uva.nl>, Maarten Speekenbrink <m.speekenbrink@ucl.ac.uk>
Maintainer: Ingmar Visser <i.visser@uva.nl>
Diff between depmixS4 versions 1.3-5 dated 2018-08-24 and 1.4-0 dated 2019-07-10
depmixS4-1.3-5/depmixS4/R/hess2cov.R |only depmixS4-1.4-0/depmixS4/DESCRIPTION | 12 - depmixS4-1.4-0/depmixS4/MD5 | 40 +++-- depmixS4-1.4-0/depmixS4/NAMESPACE | 18 +- depmixS4-1.4-0/depmixS4/NEWS | 19 ++ depmixS4-1.4-0/depmixS4/R/EM.R | 4 depmixS4-1.4-0/depmixS4/R/allGenerics.R | 4 depmixS4-1.4-0/depmixS4/R/confint.R |only depmixS4-1.4-0/depmixS4/R/depmix-class.R | 2 depmixS4-1.4-0/depmixS4/R/depmixfit.R | 11 - depmixS4-1.4-0/depmixS4/R/depmixsim-class.R | 4 depmixS4-1.4-0/depmixS4/R/format.perc.R |only depmixS4-1.4-0/depmixS4/R/hessian.R |only depmixS4-1.4-0/depmixS4/R/hessian2vcov.R |only depmixS4-1.4-0/depmixS4/R/responseMVN.R | 206 +++++++++++++++++++------- depmixS4-1.4-0/depmixS4/R/responseNORM.R | 2 depmixS4-1.4-0/depmixS4/R/standardError.R |only depmixS4-1.4-0/depmixS4/R/stationary.R | 4 depmixS4-1.4-0/depmixS4/R/vcov.R |only depmixS4-1.4-0/depmixS4/build/vignette.rds |binary depmixS4-1.4-0/depmixS4/inst/doc/depmixS4.pdf |binary depmixS4-1.4-0/depmixS4/man/depmix.Rd | 2 depmixS4-1.4-0/depmixS4/man/depmix.fit.Rd | 4 depmixS4-1.4-0/depmixS4/man/formatperc.Rd |only depmixS4-1.4-0/depmixS4/man/stationary.Rd |only depmixS4-1.4-0/depmixS4/man/vcov.Rd |only 26 files changed, 239 insertions(+), 93 deletions(-)
Title: A Suite of Checks for Identification of Potential Errors in a
Data Frame as Part of the Data Screening Process
Description: Data screening is an important first step of any statistical
analysis. dataMaid auto generates a customizable data report with a thorough
summary of the checks and the results that a human can use to identify possible
errors. It provides an extendable suite of test for common potential
errors in a dataset.
Author: Anne Helby Petersen [aut],
Claus Thorn Ekstrøm [aut, cre]
Maintainer: Claus Thorn Ekstrøm <ekstrom@sund.ku.dk>
Diff between dataMaid versions 1.3.0 dated 2019-06-07 and 1.3.1 dated 2019-07-10
DESCRIPTION | 12 ++++++------ MD5 | 6 +++--- R/makeDataReport.R | 2 ++ inst/doc/extending_dataMaid.html | 30 +++++++++++++++--------------- 4 files changed, 26 insertions(+), 24 deletions(-)
Title: Wrapper of Python Library 'shap'
Description: Provides SHAP explanations of machine learning models. In applied machine learning, there is a strong belief that we need to strike a balance between interpretability and accuracy. However, in field of the Interpretable Machine Learning, there are more and more new ideas for explaining black-box models. One of the best known method for local explanations is SHapley Additive exPlanations (SHAP) introduced by Lundberg, S., et al., (2016) <arXiv:1705.07874> The SHAP method is used to calculate influences of variables on the particular observation. This method is based on Shapley values, a technique used in game theory. The R package 'shapper' is a port of the Python library 'shap'.
Author: Szymon Maksymiuk [aut, cre],
Alicja Gosiewska [aut],
Przemyslaw Biecek [aut],
Mateusz Staniak [ctb],
Michal Burdukiewicz [ctb]
Maintainer: Szymon Maksymiuk <sz.maksymiuk@gmail.com>
Diff between shapper versions 0.1.0 dated 2019-03-02 and 0.1.1 dated 2019-07-10
DESCRIPTION | 19 MD5 | 55 +- NAMESPACE | 39 +- NEWS.md |only R/individual_variable_effect.R | 391 ++++++++++---------- R/install_shap.R | 61 ++- R/onLoad.R | 12 R/plot_individual_variable_effect.R | 291 ++++++++------ R/print_individual_variable_effect.R | 64 +-- R/theme_drwhy.R |only build/vignette.rds |binary inst/doc/shapper_classification.R | 103 ++--- inst/doc/shapper_classification.Rmd | 235 +++++------- inst/doc/shapper_classification.html | 583 ++++++++++++++--------------- inst/doc/shapper_regression.R | 99 ++--- inst/doc/shapper_regression.Rmd | 274 ++++++-------- inst/doc/shapper_regression.html | 623 +++++++++++++++----------------- man/individual_variable_effect.Rd | 175 ++++---- man/install_shap.Rd | 53 +- man/plot.individual_variable_effect.Rd | 127 +++--- man/print.individual_variable_effect.Rd | 74 +-- man/theme_drwhy.Rd |only tests/testthat.R | 8 tests/testthat/objects_for_tests.R | 62 +-- tests/testthat/test_ive.R | 42 +- tests/testthat/test_onLoad.R | 6 tests/testthat/test_plot.R | 16 tests/testthat/test_print.R | 2 vignettes/shapper_classification.Rmd | 235 +++++------- vignettes/shapper_regression.Rmd | 274 ++++++-------- 30 files changed, 1945 insertions(+), 1978 deletions(-)
Title: 'RBi' Helper Functions
Description: Contains a collection of helper functions to use with 'RBi', the R interface to 'LibBi', described in Murray et al. (2015) <doi:10.18637/jss.v067.i10>. It contains functions to adapt the proposal distribution and number of particles in particle Markov-Chain Monte Carlo, as well as calculating the Deviance Information Criterion (DIC) and converting between times in 'LibBi' results and R time/dates.
Author: Sebastian Funk <sebastian.funk@lshtm.ac.uk>
Maintainer: Sebastian Funk <sebastian.funk@lshtm.ac.uk>
Diff between rbi.helpers versions 0.3.0 dated 2019-02-22 and 0.3.1 dated 2019-07-10
DESCRIPTION | 10 +-- MD5 | 14 ++-- NEWS.md | 4 + R/adapt_particles.R | 3 - build/vignette.rds |binary inst/doc/introduction.Rmd.rsp | 16 ++++- inst/doc/introduction.html | 120 ++++++++++++++++++++--------------------- vignettes/introduction.Rmd.rsp | 16 ++++- 8 files changed, 104 insertions(+), 79 deletions(-)
Title: R Interface to LibBi
Description: Provides a complete R interface to LibBi, a library for Bayesian inference (see <http://libbi.org> and <doi:10.18637/jss.v067.i10> for more information). This includes functions for manipulating LibBi models, for reading and writing LibBi input/output files, for converting LibBi output to provide traces for use with the coda package, and for running LibBi from R.
Author: Pierre E. Jacob [aut],
Anthony Lee [ctb],
Lawrence M. Murray [ctb],
Sebastian Funk [aut, cre],
Sam Abbott [ctb]
Maintainer: Sebastian Funk <sebastian.funk@lshtm.ac.uk>
Diff between rbi versions 0.10.1 dated 2019-01-08 and 0.10.2 dated 2019-07-10
DESCRIPTION | 10 ++-- MD5 | 28 ++++++------ NEWS.md | 8 +++ R/get_traces.R | 6 ++ R/libbi.R | 69 +++++++++++++++++++++++-------- build/vignette.rds |binary demo/PZ_PMMH.R | 2 demo/PZ_SMC2.R | 5 -- demo/PZ_filtering.R | 2 inst/doc/introduction.Rmd.rsp | 8 +-- inst/doc/introduction.html | 90 ++++++++++++++++++++--------------------- man/attach_data.Rd | 2 man/sample_obs.Rd | 4 + man/summary.Rd | 6 ++ vignettes/introduction.Rmd.rsp | 8 +-- 15 files changed, 148 insertions(+), 100 deletions(-)
Title: Randomization Inference Tools
Description: Tools for randomization-based inference. Current focus is on the d^2 omnibus test of differences of means following Hansen and Bowers (2008) useful for assessing balance in matched observational studies or for analysis of outcomes in block-randomized experiments.
Author: Jake Bowers <jwbowers@illinois.edu>, Mark Fredrickson
<mark.m.fredrickson@gmail.com>, and Ben Hansen <ben.hansen@umich.edu>
Maintainer: Jake Bowers <jwbowers@illinois.edu>
Diff between RItools versions 0.1-16.1 dated 2019-05-26 and 0.1-17 dated 2019-07-10
RItools-0.1-16.1/RItools/inst/doc |only RItools-0.1-16.1/RItools/tests/naImputeTests.R |only RItools-0.1-16.1/RItools/tests/naImputeTests.Rout.save |only RItools-0.1-16.1/RItools/tests/xBalanceTests.R |only RItools-0.1-16.1/RItools/tests/xBalanceTests.Rout.save |only RItools-0.1-17/RItools/DESCRIPTION | 17 +++++++---------- RItools-0.1-17/RItools/MD5 | 17 +++++------------ RItools-0.1-17/RItools/NEWS.md | 5 +++++ RItools-0.1-17/RItools/man/balanceplot.Rd | 8 ++++---- RItools-0.1-17/RItools/man/xBalance.Rd | 11 ++++++----- RItools-0.1-17/RItools/man/xtable.xbal.Rd | 4 ++-- 11 files changed, 29 insertions(+), 33 deletions(-)
Title: Mining Rigs for Specialized Subset Sum, Multi-Subset Sum,
Multidimensional Subset Sum, Multidimensional Knapsack,
Generalized Assignment Problems
Description: Specialized solvers for combinatorial optimization problems in the Subset Sum family. These solvers differ from the mainstream in the options of (i) restricting subset size, (ii) bounding subset elements, (iii) mining real-value sets with predefined subset sum errors, and (iv) finding one or more subsets in limited time. A novel algorithm for mining the one-dimensional Subset Sum induced algorithms for the multi-Subset Sum and the multidimensional Subset Sum. The latter decomposes the problem in a novel approach, and the multi-threaded framework offers exact algorithms to the multidimensional Knapsack and the Generalized Assignment problems. Package updates include (a) renewed implementation of the multi-Subset Sum, multidimensional Knapsack and Generalized Assignment solvers; (b) availability of bounding solution space in the multidimensional Subset Sum; (c) fundamental data structure and architectural changes for enhanced cache locality and better chance of SIMD vectorization; (d) an option of mapping real-domain problems to the integer domain with user-controlled precision loss, and those integers are further zipped non-uniformly in 64-bit buffers. Arithmetic on compressed integers is done by bit-manipulation and the design has virtually zero speed lag relative to normal integers arithmetic. The consequent reduction in dimensionality may yield substantial acceleration. Compilation with g++ '-Ofast' is recommended. See package vignette (<arXiv:1612.04484v3>) for details. Functions prefixed with 'aux' (auxiliary) are or will be implementations of existing foundational or cutting-edge algorithms for solving optimization problems of interest.
Author: Charlie Wusuo Liu
Maintainer: Charlie Wusuo Liu <liuwusuo@gmail.com>
Diff between FLSSS versions 8.5.2 dated 2019-01-11 and 8.5.5 dated 2019-07-10
DESCRIPTION | 6 MD5 | 35 R/RcppExports.R | 36 R/rinterface.r | 1828 +++++++++++++-------------- inst/NEWS.Rd | 8 src/RcppExports.cpp | 186 +- src/findBoundInterface.cpp | 2 src/flsss.cpp | 12 src/flsssVariableTree.cpp | 19 src/header/PATclass.hpp | 63 src/header/oneDfindBound.hpp | 49 src/header/oneDoperation.hpp | 2 src/header/singleDstack.hpp | 23 src/legacy/PATclass.hpp | 40 src/legacy/oneDfindBound.hpp | 12 src/legacy/raiseSupressBound.hpp | 6 src/legacy/singleDstack.hpp | 3 src/legacy/triMatOneD.hpp | 4 tests/debugTests/FLSSSnumericIssue20190708.r |only 19 files changed, 1258 insertions(+), 1076 deletions(-)
Title: Compare Detrital Zircon Suites
Description: Compare detrital zircon suites by uploading univariate,
U-Pb age, or bivariate, U-Pb age and Lu-Hf data, in a 'shiny'-based
user-interface. Outputs publication quality figures using 'ggplot2', and
tables of statistics currently in use in the detrital zircon geochronology
community.
Author: Magnus Kristoffersen [aut, cre]
Maintainer: Magnus Kristoffersen <magnus.kristoffersen@geo.uio.no>
Diff between detzrcr versions 0.2.5 dated 2019-03-27 and 0.2.6 dated 2019-07-10
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- NEWS.md | 8 ++++++++ R/calculations.R | 26 ++++++++++++++------------ R/plotting.R | 21 +++++++++------------ build/vignette.rds |binary inst/doc/detzrcr-vignette.html | 14 +++++++------- inst/shiny-apps/detzrcr_app/app.R | 6 +++++- 8 files changed, 53 insertions(+), 42 deletions(-)
Title: Creates and Plots P-Value Functions, S-Value Functions,
Confidence Distributions and Confidence Densities
Description: Contains functions to compute and plot confidence distributions, confidence densities, p-value functions and s-value (surprisal) functions for several commonly used estimates. Instead of just calculating one p-value and one confidence interval, p-value functions display p-values and confidence intervals for many levels thereby allowing to gauge the compatibility of several parameter values with the data. These methods are discussed by Infanger D, Schmidt-Trucksäss A. (2019) <doi:10.1002/sim.8293>; Poole C. (1987) <doi:10.2105/AJPH.77.2.195>; Schweder T, Hjort NL. (2002) <doi:10.1111/1467-9469.00285>; Bender R, Berg G, Zeeb H. (2005) <doi:10.1002/bimj.200410104> ; Singh K, Xie M, Strawderman WE. (2007) <doi:10.1214/074921707000000102>; Rothman KJ, Greenland S, Lash TL. (2008, ISBN:9781451190052); Amrhein V, Trafimow D, Greenland S. (2019) <doi:10.1080/00031305.2018.1543137>; and Greenland S. (2019) <doi:10.1080/00031305.2018.1529625>.
Author: Denis Infanger [aut, cre] (<https://orcid.org/0000-0001-9028-7110>)
Maintainer: Denis Infanger <denis.infanger@unibas.ch>
Diff between pvaluefunctions versions 1.2.0 dated 2019-06-13 and 1.3.0 dated 2019-07-10
pvaluefunctions-1.2.0/pvaluefunctions/NEWS |only pvaluefunctions-1.3.0/pvaluefunctions/DESCRIPTION | 8 pvaluefunctions-1.3.0/pvaluefunctions/MD5 | 47 pvaluefunctions-1.3.0/pvaluefunctions/NEWS.md |only pvaluefunctions-1.3.0/pvaluefunctions/R/confidence_distributions.R | 206 - pvaluefunctions-1.3.0/pvaluefunctions/README.md | 106 pvaluefunctions-1.3.0/pvaluefunctions/build/vignette.rds |binary pvaluefunctions-1.3.0/pvaluefunctions/inst/doc/pvaluefun.R | 59 pvaluefunctions-1.3.0/pvaluefunctions/inst/doc/pvaluefun.Rmd | 103 pvaluefunctions-1.3.0/pvaluefunctions/inst/doc/pvaluefun.html | 1412 +++++----- pvaluefunctions-1.3.0/pvaluefunctions/man/conf_dist.Rd | 44 pvaluefunctions-1.3.0/pvaluefunctions/man/figures/README-corr_pearson-1.png |binary pvaluefunctions-1.3.0/pvaluefunctions/man/figures/README-linreg_multiple_pval-1.png |binary pvaluefunctions-1.3.0/pvaluefunctions/man/figures/README-linreg_multiple_sval-1.png |binary pvaluefunctions-1.3.0/pvaluefunctions/man/figures/README-linreg_single_cdf-1.png |binary pvaluefunctions-1.3.0/pvaluefunctions/man/figures/README-linreg_single_pval-1.png |binary pvaluefunctions-1.3.0/pvaluefunctions/man/figures/README-logreg-1.png |binary pvaluefunctions-1.3.0/pvaluefunctions/man/figures/README-prop-1.png |binary pvaluefunctions-1.3.0/pvaluefunctions/man/figures/README-propdiff_Wilson-1.png |binary pvaluefunctions-1.3.0/pvaluefunctions/man/figures/README-propdiff_agresticaffo-1.png |binary pvaluefunctions-1.3.0/pvaluefunctions/man/figures/README-ttest-1.png |binary pvaluefunctions-1.3.0/pvaluefunctions/man/figures/README-variance_calcs-1.png |binary pvaluefunctions-1.3.0/pvaluefunctions/man/figures/README-variance_plot-1.png |binary pvaluefunctions-1.3.0/pvaluefunctions/man/figures/logo2.svg | 78 pvaluefunctions-1.3.0/pvaluefunctions/vignettes/pvaluefun.Rmd | 103 pvaluefunctions-1.3.0/pvaluefunctions/vignettes/pvaluefun.md |only 26 files changed, 1212 insertions(+), 954 deletions(-)
More information about pvaluefunctions at CRAN
Permanent link
Title: Multivariate Imputation by Chained Equations
Description: Multiple imputation using Fully Conditional Specification (FCS)
implemented by the MICE algorithm as described in Van Buuren and
Groothuis-Oudshoorn (2011) <doi:10.18637/jss.v045.i03>. Each variable has
its own imputation model. Built-in imputation models are provided for
continuous data (predictive mean matching, normal), binary data (logistic
regression), unordered categorical data (polytomous logistic regression)
and ordered categorical data (proportional odds). MICE can also impute
continuous two-level data (normal model, pan, second-level variables).
Passive imputation can be used to maintain consistency between variables.
Various diagnostic plots are available to inspect the quality of the
imputations.
Author: Stef van Buuren [aut, cre],
Karin Groothuis-Oudshoorn [aut],
Alexander Robitzsch [ctb],
Gerko Vink [ctb],
Lisa Doove [ctb],
Shahab Jolani [ctb],
Rianne Schouten [ctb],
Philipp Gaffert [ctb],
Florian Meinfelder [ctb],
Bernie Gray [ctb]
Maintainer: Stef van Buuren <stef.vanbuuren@tno.nl>
Diff between mice versions 3.5.0 dated 2019-05-13 and 3.6.0 dated 2019-07-10
DESCRIPTION | 14 ++++----- MD5 | 47 ++++++++++++++++--------------- NEWS.md | 8 ++++- R/md.pattern.R | 19 ++++++++---- R/mice.impute.2l.bin.R | 2 - R/mice.impute.2l.lmer.R | 2 - R/mice.impute.2l.norm.R | 2 - R/mice.impute.2l.pan.R | 2 - R/mice.impute.2lonly.mean.R | 2 - R/mice.impute.2lonly.norm.R | 2 - R/mice.impute.2lonly.pmm.R | 2 - R/mice.impute.jomoImpute.R | 2 - R/mice.impute.panImpute.R | 2 - R/toenail.R |only data/toenail.rda |only man/mice.impute.2l.bin.Rd | 4 +- man/mice.impute.2l.lmer.Rd | 4 +- man/mice.impute.2l.norm.Rd | 4 +- man/mice.impute.2l.pan.Rd | 4 +- man/mice.impute.2lonly.mean.Rd | 4 +- man/mice.impute.2lonly.norm.Rd | 4 +- man/mice.impute.2lonly.pmm.Rd | 4 +- man/mice.impute.jomoImpute.Rd | 4 +- man/mice.impute.panImpute.Rd | 4 +- man/toenail.Rd |only tests/testthat/test-mice.impute.2l.bin.R | 2 - 26 files changed, 80 insertions(+), 64 deletions(-)
Title: Bayesian Model Averaging for Random and Fixed Effects
Meta-Analysis
Description: Computes the posterior model probabilities for standard meta-analysis models
(null model vs. alternative model assuming either fixed- or random-effects, respectively).
These posterior probabilities are used to estimate the overall mean effect size
as the weighted average of the mean effect size estimates of the random- and
fixed-effect model as proposed by Gronau, Van Erp, Heck, Cesario, Jonas, &
Wagenmakers (2017, <doi:10.1080/23743603.2017.1326760>). The user can define
a wide range of non-informative or informative priors for the mean effect size
and the heterogeneity coefficient. Moreover, using pre-compiled Stan models,
meta-analysis with continuous and discrete moderators with Jeffreys-Zellner-Siow (JZS)
priors can be fitted and tested. This allows to compute Bayes factors and
perform Bayesian model averaging across random- and fixed-effects meta-analysis
with and without moderators.
Author: Daniel W. Heck [aut, cre],
Quentin F. Gronau [ctb]
Maintainer: Daniel W. Heck <heck@uni-mannheim.de>
Diff between metaBMA versions 0.3.9 dated 2017-08-04 and 0.6.1 dated 2019-07-10
metaBMA-0.3.9/metaBMA/R/auxiliary.R |only metaBMA-0.3.9/metaBMA/R/dtriangular.R |only metaBMA-0.3.9/metaBMA/R/dtruncnorm.R |only metaBMA-0.3.9/metaBMA/R/get_samples.R |only metaBMA-0.3.9/metaBMA/R/jags_modelfile.R |only metaBMA-0.3.9/metaBMA/R/metaBMA-package.R |only metaBMA-0.3.9/metaBMA/R/predictive.R |only metaBMA-0.3.9/metaBMA/R/stats_density.R |only metaBMA-0.3.9/metaBMA/R/stats_samples.R |only metaBMA-0.3.9/metaBMA/man/dtriangular.Rd |only metaBMA-0.3.9/metaBMA/man/dtruncnorm.Rd |only metaBMA-0.3.9/metaBMA/man/predictive.Rd |only metaBMA-0.6.1/metaBMA/DESCRIPTION | 44 metaBMA-0.6.1/metaBMA/MD5 | 157 +-- metaBMA-0.6.1/metaBMA/NAMESPACE | 28 metaBMA-0.6.1/metaBMA/NEWS | 20 metaBMA-0.6.1/metaBMA/R/bma.R | 84 - metaBMA-0.6.1/metaBMA/R/bounds.R | 90 - metaBMA-0.6.1/metaBMA/R/check_input.R |only metaBMA-0.6.1/metaBMA/R/check_posterior.R | 57 - metaBMA-0.6.1/metaBMA/R/data_facial_feedback.R | 20 metaBMA-0.6.1/metaBMA/R/data_list.R | 57 - metaBMA-0.6.1/metaBMA/R/data_power_pose.R | 4 metaBMA-0.6.1/metaBMA/R/deprecated.R |only metaBMA-0.6.1/metaBMA/R/inclusion.R | 70 - metaBMA-0.6.1/metaBMA/R/integrate_wrapper.R | 91 - metaBMA-0.6.1/metaBMA/R/metaBMA.R |only metaBMA-0.6.1/metaBMA/R/meta_bma.R | 171 ++- metaBMA-0.6.1/metaBMA/R/meta_bridge_sampling.R |only metaBMA-0.6.1/metaBMA/R/meta_default.R | 143 +- metaBMA-0.6.1/metaBMA/R/meta_fixed.R | 110 +- metaBMA-0.6.1/metaBMA/R/meta_ordered.R |only metaBMA-0.6.1/metaBMA/R/meta_random.R | 149 +- metaBMA-0.6.1/metaBMA/R/meta_stan.R |only metaBMA-0.6.1/metaBMA/R/ml_estimates.R |only metaBMA-0.6.1/metaBMA/R/plot_forest.R | 110 -- metaBMA-0.6.1/metaBMA/R/plot_posterior.R | 108 -- metaBMA-0.6.1/metaBMA/R/plot_prediction.R | 12 metaBMA-0.6.1/metaBMA/R/plot_prior.R | 32 metaBMA-0.6.1/metaBMA/R/posterior.R | 114 +- metaBMA-0.6.1/metaBMA/R/posterior_fixed.R | 39 metaBMA-0.6.1/metaBMA/R/posterior_logspline.R |only metaBMA-0.6.1/metaBMA/R/posterior_random.R | 84 - metaBMA-0.6.1/metaBMA/R/predicted_bf.R |only metaBMA-0.6.1/metaBMA/R/print.R | 107 +- metaBMA-0.6.1/metaBMA/R/prior.R | 307 ++++- metaBMA-0.6.1/metaBMA/R/prior_functions.R | 219 ++-- metaBMA-0.6.1/metaBMA/R/rstudy.R | 16 metaBMA-0.6.1/metaBMA/R/stanmodels.R |only metaBMA-0.6.1/metaBMA/R/stanpackage-internal.R |only metaBMA-0.6.1/metaBMA/R/summary_parameters.R |only metaBMA-0.6.1/metaBMA/R/zzz.R |only metaBMA-0.6.1/metaBMA/build/vignette.rds |binary metaBMA-0.6.1/metaBMA/inst/doc/metaBMA.R | 42 metaBMA-0.6.1/metaBMA/inst/doc/metaBMA.Rmd | 85 - metaBMA-0.6.1/metaBMA/inst/doc/metaBMA.html | 523 +++++++--- metaBMA-0.6.1/metaBMA/inst/include |only metaBMA-0.6.1/metaBMA/man/bma.Rd | 36 metaBMA-0.6.1/metaBMA/man/facial_feedback.Rd | 20 metaBMA-0.6.1/metaBMA/man/inclusion.Rd | 21 metaBMA-0.6.1/metaBMA/man/metaBMA-package.Rd | 49 metaBMA-0.6.1/metaBMA/man/meta_bma.Rd | 102 + metaBMA-0.6.1/metaBMA/man/meta_default.Rd | 57 - metaBMA-0.6.1/metaBMA/man/meta_fixed.Rd | 60 - metaBMA-0.6.1/metaBMA/man/meta_ordered.Rd |only metaBMA-0.6.1/metaBMA/man/meta_random.Rd | 84 + metaBMA-0.6.1/metaBMA/man/plot.meta_pred.Rd | 11 metaBMA-0.6.1/metaBMA/man/plot.prior.Rd |only metaBMA-0.6.1/metaBMA/man/plot_default.Rd | 10 metaBMA-0.6.1/metaBMA/man/plot_forest.Rd | 21 metaBMA-0.6.1/metaBMA/man/plot_posterior.Rd | 10 metaBMA-0.6.1/metaBMA/man/power_pose.Rd | 4 metaBMA-0.6.1/metaBMA/man/predicted_bf.Rd |only metaBMA-0.6.1/metaBMA/man/prior.Rd | 57 - metaBMA-0.6.1/metaBMA/src |only metaBMA-0.6.1/metaBMA/tests/testthat.R | 6 metaBMA-0.6.1/metaBMA/tests/testthat/test_H0_logml.R |only metaBMA-0.6.1/metaBMA/tests/testthat/test_bma.R |only metaBMA-0.6.1/metaBMA/tests/testthat/test_data_frame_evaluation.R |only metaBMA-0.6.1/metaBMA/tests/testthat/test_gronau2017powerpose.R |only metaBMA-0.6.1/metaBMA/tests/testthat/test_integrate.R |only metaBMA-0.6.1/metaBMA/tests/testthat/test_jzs.R |only metaBMA-0.6.1/metaBMA/tests/testthat/test_ordered.R |only metaBMA-0.6.1/metaBMA/tests/testthat/test_prior.R | 66 - metaBMA-0.6.1/metaBMA/tests/testthat/test_stan.R |only metaBMA-0.6.1/metaBMA/tools |only metaBMA-0.6.1/metaBMA/vignettes/metaBMA.Rmd | 85 - 87 files changed, 2383 insertions(+), 1409 deletions(-)
Title: Index Number Calculation
Description: Computes bilateral and multilateral index numbers.
It has support for several standard bilateral indices as well as
the GEKS multilateral index number methods
(see Ivancic, Diewert and Fox (2011) <doi:10.1016/j.jeconom.2010.09.003>) .
It also supports updating of GEKS indexes using several splicing methods.
Author: Graham White
Maintainer: Graham White <g.white@unswalumni.com>
Diff between IndexNumR versions 0.1.1 dated 2019-01-22 and 0.1.2 dated 2019-07-10
DESCRIPTION | 6 MD5 | 22 - R/bilateral.R | 68 +++--- R/multilateral.R | 81 ++++--- R/unitValues.R | 162 +++++++------- R/utils.R | 7 README.md | 3 build/vignette.rds |binary inst/doc/indexnumr.html | 534 ++++++++++++++++++++++++++++++++---------------- man/GEKSIndex.Rd | 10 man/geomean.Rd | 2 man/priceIndex.Rd | 5 12 files changed, 571 insertions(+), 329 deletions(-)
Title: Computes and Plots Consonance (Confidence) Intervals, P-Values,
and S-Values to Form Consonance and Surprisal Functions
Description: Allows one to compute consonance (confidence) intervals for various statistical tests along with their corresponding P-values and S-values. The intervals can be plotted to create consonance and surprisal functions allowing one to see what effect sizes are compatible with the test model at various consonance levels rather than being limited to one interval estimate such as 95%. These methods are discussed by Poole C. (1987) <doi:10.2105/AJPH.77.2.195>, Schweder T, Hjort NL. (2002) <doi:10.1111/1467-9469.00285>, Singh K, Xie M, Strawderman WE. (2007) <arXiv:0708.0976>, Rothman KJ, Greenland S, Lash TL. (2008, ISBN:9781451190052), Amrhein V, Trafimow D, Greenland S. (2019) <doi:10.1080/00031305.2018.1543137>, and Greenland S. (2019) <doi:10.1080/00031305.2018.1529625>.
Author: Zad R. Chow [aut, cre] (<https://orcid.org/0000-0003-1545-8199>),
Andrew D. Vigotsky [aut] (<https://orcid.org/0000-0003-3166-0688>)
Maintainer: Zad R. Chow <zad@lesslikely.com>
Diff between concurve versions 1.0.6 dated 2019-05-14 and 2.0 dated 2019-07-10
concurve-1.0.6/concurve/R/genintervals.R |only concurve-1.0.6/concurve/R/meanintervals.R |only concurve-1.0.6/concurve/R/metaintervals.R |only concurve-1.0.6/concurve/R/plotpint.R |only concurve-1.0.6/concurve/R/plotsint.R |only concurve-1.0.6/concurve/man/figures/function1.png |only concurve-1.0.6/concurve/man/figures/function2.png |only concurve-1.0.6/concurve/man/figures/function3.png |only concurve-1.0.6/concurve/man/figures/function4.png |only concurve-1.0.6/concurve/man/figures/function5.png |only concurve-1.0.6/concurve/man/figures/function6.png |only concurve-1.0.6/concurve/man/genintervals.Rd |only concurve-1.0.6/concurve/man/meanintervals.Rd |only concurve-1.0.6/concurve/man/metaintervals.Rd |only concurve-1.0.6/concurve/man/plotpint.Rd |only concurve-1.0.6/concurve/man/plotsint.Rd |only concurve-2.0/concurve/DESCRIPTION | 11 - concurve-2.0/concurve/MD5 | 67 +++--- concurve-2.0/concurve/NAMESPACE | 13 + concurve-2.0/concurve/NEWS.md | 27 ++ concurve-2.0/concurve/R/curve_corr.R |only concurve-2.0/concurve/R/curve_gen.R |only concurve-2.0/concurve/R/curve_mean.R |only concurve-2.0/concurve/R/curve_meta.R |only concurve-2.0/concurve/R/curve_rev.R |only concurve-2.0/concurve/R/curve_surv.R |only concurve-2.0/concurve/R/defunct.R |only concurve-2.0/concurve/R/ggconcurve.R |only concurve-2.0/concurve/R/plot_concurve.R |only concurve-2.0/concurve/README.md | 84 ++++--- concurve-2.0/concurve/build/vignette.rds |binary concurve-2.0/concurve/inst/CITATION | 3 concurve-2.0/concurve/inst/doc/examples.Rmd | 172 ++++++++------- concurve-2.0/concurve/inst/doc/examples.html | 186 +++++++++-------- concurve-2.0/concurve/man/curve_corr.Rd |only concurve-2.0/concurve/man/curve_gen.Rd |only concurve-2.0/concurve/man/curve_mean.Rd |only concurve-2.0/concurve/man/curve_meta.Rd |only concurve-2.0/concurve/man/curve_rev.Rd |only concurve-2.0/concurve/man/curve_surv.Rd |only concurve-2.0/concurve/man/defunct.Rd |only concurve-2.0/concurve/man/ggconcurve.Rd |only concurve-2.0/concurve/man/plot_concurve.Rd |only concurve-2.0/concurve/tests/testthat/testdfstructure.R | 162 +++++++------- concurve-2.0/concurve/vignettes/examples.Rmd | 172 ++++++++------- concurve-2.0/concurve/vignettes/figures/function1.png |binary concurve-2.0/concurve/vignettes/figures/function2.png |binary concurve-2.0/concurve/vignettes/figures/function3.png |binary concurve-2.0/concurve/vignettes/figures/function4.png |binary concurve-2.0/concurve/vignettes/figures/function5.png |binary concurve-2.0/concurve/vignettes/figures/function6.png |binary concurve-2.0/concurve/vignettes/figures/likelihood.png |only 52 files changed, 490 insertions(+), 407 deletions(-)
Title: Bayesian Synthetic Likelihood
Description: Bayesian synthetic likelihood (BSL, Price et al. (2018) <doi:10.1080/10618600.2017.1302882>)
is an alternative to standard, non-parametric approximate Bayesian
computation (ABC). BSL assumes a multivariate normal distribution
for the summary statistic likelihood and it is suitable when the
distribution of the model summary statistics is sufficiently regular.
This package provides a Metropolis Hastings Markov chain Monte Carlo
implementation of three methods (BSL, uBSL and semiBSL) and two
shrinkage estimations (graphical lasso and Warton's estimation).
uBSL (Price et al. (2018) <doi:10.1080/10618600.2017.1302882>) uses
an unbiased estimator to the normal density. A semi-parametric version
of BSL (semiBSL, An et al. (2018) <arXiv:1809.05800>) is more robust
to non-normal summary statistics. Shrinkage estimations can help to
bring down the number of simulations when the dimension of the summary
statistic is high (e.g., BSLasso, An et al. (2019)
<doi:10.1080/10618600.2018.1537928>). Extensions to this package are
planned.
Author: Ziwen An [aut, cre] (<https://orcid.org/0000-0002-9947-5182>),
Leah F. South [aut] (<https://orcid.org/0000-0002-5646-2963>),
Christopher C. Drovandi [aut] (<https://orcid.org/0000-0001-9222-8763>)
Maintainer: Ziwen An <ziwen.an@hdr.qut.edu.au>
Diff between BSL versions 2.0.0 dated 2019-01-16 and 3.0.0 dated 2019-07-10
BSL-2.0.0/BSL/R/glasso_cv.R |only BSL-3.0.0/BSL/DESCRIPTION | 35 +- BSL-3.0.0/BSL/MD5 | 74 +++-- BSL-3.0.0/BSL/NAMESPACE | 17 - BSL-3.0.0/BSL/NEWS.md | 20 + BSL-3.0.0/BSL/R/BSL_model.R |only BSL-3.0.0/BSL/R/BSL_package.R | 45 ++- BSL-3.0.0/BSL/R/S3_penbsl.R | 8 BSL-3.0.0/BSL/R/S4.R | 101 +++---- BSL-3.0.0/BSL/R/S4Functions.R | 63 +--- BSL-3.0.0/BSL/R/bsl.R | 322 ++++++++++++------------ BSL-3.0.0/BSL/R/cell.R | 94 +++---- BSL-3.0.0/BSL/R/combinePlotsBSL.R | 12 BSL-3.0.0/BSL/R/gaussianRankCorr.R |only BSL-3.0.0/BSL/R/gaussianSynLike.R | 64 +++- BSL-3.0.0/BSL/R/gaussianSynLikeGhuryeOlkin.R |only BSL-3.0.0/BSL/R/imports.R | 5 BSL-3.0.0/BSL/R/kernelCDF.R | 1 BSL-3.0.0/BSL/R/logitTransform.R | 7 BSL-3.0.0/BSL/R/ma2.R | 149 ++++++++--- BSL-3.0.0/BSL/R/multignk.R | 99 ++++--- BSL-3.0.0/BSL/R/selectPenalty.R | 131 ++++----- BSL-3.0.0/BSL/R/semiparaKernelEstimate.R | 30 -- BSL-3.0.0/BSL/man/BSL-package.Rd | 45 ++- BSL-3.0.0/BSL/man/BSLMODEL-class.Rd |only BSL-3.0.0/BSL/man/bsl-class.Rd | 76 ++--- BSL-3.0.0/BSL/man/bsl.Rd | 133 +++++---- BSL-3.0.0/BSL/man/cell.Rd | 78 +++-- BSL-3.0.0/BSL/man/combinePlotsBSL.Rd | 12 BSL-3.0.0/BSL/man/cor2cov.Rd |only BSL-3.0.0/BSL/man/fn.Rd |only BSL-3.0.0/BSL/man/gaussianRankCorr.Rd |only BSL-3.0.0/BSL/man/gaussianSynLike.Rd | 38 +- BSL-3.0.0/BSL/man/gaussianSynLikeGhuryeOlkin.Rd |only BSL-3.0.0/BSL/man/ma2.Rd | 133 +++++++-- BSL-3.0.0/BSL/man/mgnk.Rd | 81 +++--- BSL-3.0.0/BSL/man/penbsl.Rd | 4 BSL-3.0.0/BSL/man/plot.bsl.Rd | 6 BSL-3.0.0/BSL/man/selectPenalty.Rd | 62 +++- BSL-3.0.0/BSL/man/semiparaKernelEstimate.Rd | 25 - BSL-3.0.0/BSL/man/setns.Rd |only BSL-3.0.0/BSL/man/show.bsl.Rd | 4 BSL-3.0.0/BSL/man/summary.bsl.Rd | 6 43 files changed, 1137 insertions(+), 843 deletions(-)
Title: A Shiny App for UCSC Xena Database
Description: Provides a web app for downloading, analyzing and visualizing datasets
from UCSC Xena, which is a collection of
UCSC-hosted public databases such as TCGA, ICGC, TARGET, GTEx, CCLE, and others.
Author: Shixiang Wang [aut, cre] (<https://orcid.org/0000-0001-9855-7357>),
Yi Xiong [aut] (<https://orcid.org/0000-0002-4370-9824>),
Longfei Zhao [aut] (<https://orcid.org/0000-0002-6277-0137>),
Kai Gu [aut] (<https://orcid.org/0000-0002-0177-0774>),
Yin Li [aut],
Fei Zhao [aut]
Maintainer: Shixiang Wang <w_shixiang@163.com>
Diff between UCSCXenaShiny versions 0.1.1 dated 2019-05-19 and 0.2.0 dated 2019-07-10
DESCRIPTION | 13 +++++---- MD5 | 42 ++++++++++++++++++++++---------- NAMESPACE | 10 +++++++ NEWS.md | 5 +++ R/GeomSplitViolin.R |only R/data.R | 36 +++++++++++++++++++++++++-- R/get_pancan_value.R |only R/ope_pancan_value.R |only R/run.R | 13 +++++---- R/utils-pipe.R | 5 +++ R/vis_pancan_value.R |only R/xenashiny.R | 2 - data/tcga_gtex_sampleinfo.rda |only data/toil_info.rda |only data/toil_surv.rda |only inst/shinyapp/App.R | 43 +++++++++++++++++++++++++++++---- man/XenaInfo.Rd | 2 - man/app_run.Rd | 4 ++- man/available_hosts.Rd |only man/dat_datasets.Rd | 2 - man/dat_samples.Rd | 2 - man/get_pancan_value.Rd |only man/ope_toil_gene.Rd |only man/tcga_gtex.Rd |only man/toil_info.Rd |only man/toil_surv.Rd |only man/vis_toil_TvsN.Rd |only man/vis_toil_gene.Rd |only tests/testthat/test-run_app.R | 1 tests/testthat/test-vis_pancan_value.R |only 30 files changed, 143 insertions(+), 37 deletions(-)
Title: Calculating Proportionality Between Vectors of Compositional
Data
Description: The bioinformatic evaluation of gene co-expression often begins with
correlation-based analyses. However, correlation lacks validity when
applied to relative data, including count data generated by next-generation
sequencing. This package implements several metrics for proportionality, including
phi [Lovell et al (2015) <DOI:10.1371/journal.pcbi.1004075>] and
rho [Erb and Notredame (2016) <DOI:10.1007/s12064-015-0220-8>]. This package also
implements several metrics for differential proportionality. Unlike correlation,
these measures give the same result for both relative and absolute data.
Author: Thomas Quinn [aut, cre],
David Lovell [aut],
Ionas Erb [aut],
Anders Bilgrau [ctb],
Greg Gloor [ctb]
Maintainer: Thomas Quinn <contacttomquinn@gmail.com>
Diff between propr versions 4.1.1 dated 2018-11-19 and 4.1.6 dated 2019-07-10
DESCRIPTION | 6 - MD5 | 50 ++++++------ NAMESPACE | 2 NEWS.md | 41 ++++++++++ R/1-propr.R | 2 R/4-propd.R | 19 ++-- R/5-propdCall.R | 81 +++++++++----------- R/8-get.R | 31 +++++++ R/RcppExports.R | 8 + build/vignette.rds |binary inst/doc/a_introduction.html | 52 ++++++++++-- inst/doc/b_visualization.html | 61 ++++++++++----- inst/doc/d_advanced.html | 161 +++++++++++++++++++++++----------------- inst/doc/e_differential.html | 89 ++++++++++++++-------- inst/doc/f_moderation.html | 45 ++++++++--- inst/doc/g_questions.html | 45 ++++++++--- man/calculateTheta.Rd | 2 man/getAdj.Rd |only man/getAdjacency.Rd | 2 man/getMatrix.Rd | 1 man/propr.Rd | 3 man/qtheta.Rd | 13 ++- src/RcppExports.cpp | 21 +++-- src/omega.cpp | 26 +++++- tests/testthat/test-Fstat.R | 36 ++++---- tests/testthat/test-getMatrix.R |only tests/testthat/test-propd.R | 8 - 27 files changed, 536 insertions(+), 269 deletions(-)
Title: Streamline Physical Activity Research
Description: A collection of utilities that are useful for a broad range of
tasks that are common in physical activity research, including the
following: creation of Bland-Altman plots, formatted descriptive
statistics, metabolic calculations (e.g. basal metabolic rate predictions)
and conversions, demographic calculations (age and age-for-body-mass-index
percentile), bout analysis of moderate-to-vigorous intensity physical
activity, and analysis of bout detection algorithm performance.
Author: Paul R. Hibbing [aut, cre],
Centers for Disease Control and Prevention [ctb]
Maintainer: Paul R. Hibbing <paulhibbing@gmail.com>
Diff between PAutilities versions 0.1.2 dated 2019-03-06 and 0.2.0 dated 2019-07-10
DESCRIPTION | 10 +-- MD5 | 40 +++++++----- NAMESPACE | 4 + NEWS.md | 13 ++++ R/ba_plot.R | 20 +++--- R/get_matchings.R | 106 ++++++++++++++++++++++++++++++++-- R/get_transition_info.R | 20 ++++-- R/manage_procedure.R |only R/plot_transition.R | 12 ++- R/rmr_sliding.R |only R/summary_transition.R | 68 ++++++++++----------- R/test_errors.R |only inst/CITATION | 4 - man/ba_plot.Rd | 4 - man/get_transition_info.Rd | 8 +- man/manage_procedure.Rd |only man/n_crossings.Rd |only man/plot.transition.Rd | 7 +- man/rmr_sliding.Rd |only man/sequence_check.Rd |only man/summary.transition.Rd | 7 +- man/test_errors.Rd |only tests/testthat/test_transitions.R | 9 ++ tests/testthat/transition_info.rds |binary tests/testthat/transition_summary.rds |binary 25 files changed, 241 insertions(+), 91 deletions(-)
Title: Visualize Balances of Compositional Data
Description: Balances have become a cornerstone of compositional data analysis. However,
conceptualizing balances is difficult, especially for high-dimensional data. Most often,
investigators visualize balances with "balance dendrograms". However, this visualization
tool does not scale well for large data. This package provides an alternative scheme for
visualizing balances, described in [Quinn (2018) <DOI:10.12688/f1000research.15858.1>].
This package also provides a method for principal balance analysis.
Author: Thomas Quinn [aut, cre]
Maintainer: Thomas Quinn <contacttomquinn@gmail.com>
Diff between balance versions 0.1.9 dated 2018-12-10 and 0.2.4 dated 2019-07-10
DESCRIPTION | 8 +-- MD5 | 33 +++++++++------ NAMESPACE | 4 + NEWS.md | 37 +++++++++++++++++ R/balance.plot.R | 22 ++++++++-- R/global.R | 2 R/pba.R | 14 +++++- R/sbp.R | 95 +++++++++++++++++++++++++++++++++++++--------- R/vlr.R | 92 ++++++++++++++++++++++++++++++++++++++++++++ build/vignette.rds |binary inst/doc/balance.html | 62 ++++++++++++++++++++++-------- man/pba.Rd | 9 ++-- man/sbp.fromABA.Rd | 12 ++--- man/sbp.fromADBA.Rd |only man/sbp.fromPDBA.Rd |only man/sbp.fromPropd.Rd | 15 ++----- man/ssBetween.Rd |only man/ssWithin.Rd |only tests/testthat/test-pba.R | 18 +++++++- tests/testthat/test-ss.R |only 20 files changed, 342 insertions(+), 81 deletions(-)