Title: Structural Equation Models
Description: Functions for fitting general linear structural
equation models (with observed and latent variables) using the RAM approach,
and for fitting structural equations in observed-variable models by two-stage least squares.
Author: John Fox [aut, cre],
Zhenghua Nie [aut],
Jarrett Byrnes [aut],
Michael Culbertson [ctb],
Saikat DebRoy [ctb],
Michael Friendly [ctb],
Benjamin Goodrich [ctb],
Richard H. Jones [ctb],
Adam Kramer [ctb],
Georges Monette [ctb],
R-Core [ctb]
Maintainer: John Fox <jfox@mcmaster.ca>
Diff between sem versions 3.1-8 dated 2016-08-16 and 3.1-9 dated 2017-04-24
DESCRIPTION | 14 +++++++------- MD5 | 15 ++++++++------- NEWS | 4 ++++ data/Bollen.rda |binary data/CNES.rda |binary data/Tests.rda |binary src/Makevars | 2 +- src/csem.cpp | 17 ++++++++++++----- src/init.c |only 9 files changed, 32 insertions(+), 20 deletions(-)
Title: Importing Real-Time Thermo Cycler (qPCR) Data from RDML Format
Files
Description: Imports real-time thermo cycler (qPCR) data from Real-time PCR
Data Markup Language (RDML) and transforms to the appropriate formats of
the 'qpcR' and 'chipPCR' packages. Contains a dendrogram visualization
for the structure of RDML object and GUI for RDML editing.
Author: Konstantin A. Blagodatskikh [cre, aut],
Stefan Roediger [aut],
Michal Burdukiewicz [aut]
Maintainer: Konstantin A. Blagodatskikh <k.blag@yandex.ru>
Diff between RDML versions 0.9-5 dated 2016-12-13 and 0.9-6 dated 2017-04-24
RDML-0.9-5/RDML/inst/RDMLedit/md/help.html |only RDML-0.9-6/RDML/CHANGELOG | 4 RDML-0.9-6/RDML/DESCRIPTION | 20 RDML-0.9-6/RDML/MD5 | 158 +- RDML-0.9-6/RDML/R/RDML.R | 13 RDML-0.9-6/RDML/R/RDML.SetFData.R | 20 RDML-0.9-6/RDML/R/RDML.init.R | 35 RDML-0.9-6/RDML/R/RDML.types.R | 474 ++------ RDML-0.9-6/RDML/README.md | 28 RDML-0.9-6/RDML/build/vignette.rds |binary RDML-0.9-6/RDML/inst/RDMLedit/md/help.md | 11 RDML-0.9-6/RDML/inst/RDMLedit/rdml.extensions.R |only RDML-0.9-6/RDML/inst/RDMLedit/server.R | 713 ++++++++++-- RDML-0.9-6/RDML/inst/RDMLedit/ui.R | 1160 +++++++++++--------- RDML-0.9-6/RDML/inst/RDMLedit/www |only RDML-0.9-6/RDML/inst/doc/CreateRDML.R | 14 RDML-0.9-6/RDML/inst/doc/CreateRDML.Rmd | 58 - RDML-0.9-6/RDML/inst/doc/CreateRDML.html | 90 - RDML-0.9-6/RDML/inst/doc/RDML.R | 14 RDML-0.9-6/RDML/inst/doc/RDML.Rmd | 35 RDML-0.9-6/RDML/inst/doc/RDML.html | 247 ++-- RDML-0.9-6/RDML/man/AsDendrogram-function.Rd | 1 RDML-0.9-6/RDML/man/GetFData-function.Rd | 1 RDML-0.9-6/RDML/man/MergeRDMLs.Rd | 1 RDML-0.9-6/RDML/man/RDML.Rd | 12 RDML-0.9-6/RDML/man/adpsType.Rd | 2 RDML-0.9-6/RDML/man/annotationType.Rd | 2 RDML-0.9-6/RDML/man/asdendrogram-method.Rd | 1 RDML-0.9-6/RDML/man/astable-function.Rd | 1 RDML-0.9-6/RDML/man/astable-method.Rd | 1 RDML-0.9-6/RDML/man/baseTemperatureType.Rd | 2 RDML-0.9-6/RDML/man/cdnaSynthesisMethodType.Rd | 2 RDML-0.9-6/RDML/man/commercialAssayType.Rd | 2 RDML-0.9-6/RDML/man/cqDetectionMethodType.Rd | 2 RDML-0.9-6/RDML/man/dataCollectionSoftwareType.Rd | 2 RDML-0.9-6/RDML/man/dataType.Rd | 2 RDML-0.9-6/RDML/man/documentationType.Rd | 2 RDML-0.9-6/RDML/man/dyeType.Rd | 2 RDML-0.9-6/RDML/man/enumType.Rd | 2 RDML-0.9-6/RDML/man/experimentType.Rd | 2 RDML-0.9-6/RDML/man/experimenterType.Rd | 2 RDML-0.9-6/RDML/man/getfdata-method.Rd | 1 RDML-0.9-6/RDML/man/gradientType.Rd | 2 RDML-0.9-6/RDML/man/idReferencesType.Rd | 2 RDML-0.9-6/RDML/man/idType.Rd | 2 RDML-0.9-6/RDML/man/labelFormatType.Rd | 2 RDML-0.9-6/RDML/man/lidOpenType.Rd | 2 RDML-0.9-6/RDML/man/loopType.Rd | 2 RDML-0.9-6/RDML/man/mdpsType.Rd | 2 RDML-0.9-6/RDML/man/measureType.Rd | 2 RDML-0.9-6/RDML/man/new-method.Rd | 4 RDML-0.9-6/RDML/man/nucleotideType.Rd | 2 RDML-0.9-6/RDML/man/oligoType.Rd | 2 RDML-0.9-6/RDML/man/pauseType.Rd | 2 RDML-0.9-6/RDML/man/pcrFormatType.Rd | 2 RDML-0.9-6/RDML/man/primingMethodType.Rd | 2 RDML-0.9-6/RDML/man/quantityType.Rd | 2 RDML-0.9-6/RDML/man/quantityUnitType.Rd | 2 RDML-0.9-6/RDML/man/rdmlBaseType.Rd | 2 RDML-0.9-6/RDML/man/rdmlEdit.Rd | 1 RDML-0.9-6/RDML/man/rdmlIdType.Rd | 2 RDML-0.9-6/RDML/man/reactIdType.Rd | 2 RDML-0.9-6/RDML/man/reactType.Rd | 2 RDML-0.9-6/RDML/man/runType.Rd | 2 RDML-0.9-6/RDML/man/sampleType.Rd | 2 RDML-0.9-6/RDML/man/sampleTypeType.Rd | 2 RDML-0.9-6/RDML/man/sequencesType.Rd | 2 RDML-0.9-6/RDML/man/setfdata-function.Rd | 1 RDML-0.9-6/RDML/man/setfdata-method.Rd | 1 RDML-0.9-6/RDML/man/stepType.Rd | 2 RDML-0.9-6/RDML/man/targetType.Rd | 2 RDML-0.9-6/RDML/man/targetTypeType.Rd | 2 RDML-0.9-6/RDML/man/temperatureType.Rd | 2 RDML-0.9-6/RDML/man/templateQuantityType.Rd | 2 RDML-0.9-6/RDML/man/thermalCyclingConditionsType.Rd | 2 RDML-0.9-6/RDML/man/xRefType.Rd | 2 RDML-0.9-6/RDML/vignettes/CreateRDML.Rmd | 58 - RDML-0.9-6/RDML/vignettes/File_import.png |only RDML-0.9-6/RDML/vignettes/RDML.Rmd | 35 RDML-0.9-6/RDML/vignettes/RDML.bib | 97 + RDML-0.9-6/RDML/vignettes/data_view.png |only 81 files changed, 2093 insertions(+), 1303 deletions(-)
Title: Read Data Stored by Minitab, S, SAS, SPSS, Stata, Systat, Weka,
dBase, ...
Description: Functions for reading and writing data stored by some versions of
Epi Info, Minitab, S, SAS, SPSS, Stata, Systat and Weka
and for reading and writing some dBase files.
Author: R Core Team [aut, cph, cre],
Roger Bivand [ctb, cph],
Vincent J. Carey [ctb, cph],
Saikat DebRoy [ctb, cph],
Stephen Eglen [ctb, cph],
Rajarshi Guha [ctb, cph],
Nicholas Lewin-Koh [ctb, cph],
Mark Myatt [ctb, cph],
Ben Pfaff [ctb],
Brian Quistorff [ctb],
Frank Warmerdam [ctb, cph],
Stephen Weigand [ctb, cph],
Free Software Foundation, Inc. [cph]
Maintainer: R Core Team <R-core@R-project.org>
Diff between foreign versions 0.8-67 dated 2016-09-13 and 0.8-68 dated 2017-04-24
ChangeLog | 10 ++++++++++ DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ man/read.dta.Rd | 2 +- man/write.dbf.Rd | 2 +- src/init.c | 2 -- src/sfm-read.c | 15 +++++++++------ 7 files changed, 31 insertions(+), 20 deletions(-)
Title: Static and Dynamic 3D Plots for the 'vegan' Package
Description: Static and dynamic 3D plots to be used with ordination
results and in diversity analysis, especially with the vegan package.
Author: Jari Oksanen [aut, cre],
Roeland Kindt [aut],
Gavin L. Simpson [aut]
Maintainer: Jari Oksanen <jari.oksanen@oulu.fi>
Diff between vegan3d versions 1.0-1 dated 2016-06-15 and 1.1-0 dated 2017-04-24
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ R/ordiplot3d.R | 22 ++++++++-------------- build/partial.rdb |binary inst/NEWS.md | 7 +++++++ man/ordiplot3d.Rd | 8 -------- man/vegan3d-package.Rd | 9 --------- 7 files changed, 26 insertions(+), 42 deletions(-)
Title: Various Functions to Facilitate Visualization of Data and
Analysis
Description: When analyzing data, plots are a helpful tool for visualizing data and interpreting statistical models. This package provides a set of simple tools for building plots incrementally, starting with an empty plot region, and adding bars, data points, regression lines, error bars, gradient legends, density distributions in the margins, and even pictures. The package builds further on R graphics by simply combining functions and settings in order to reduce the amount of code to produce for the user. As a result, the package does not use formula input or special syntax, but can be used in combination with default R plot functions. Note: Most of the functions were part of the package 'itsadug', which is now split in two packages: 1. the package 'itsadug', which contains the core functions for visualizing and evaluating nonlinear regression models, and 2. the package 'plotfunctions', which contains more general plot functions.
Author: Jacolien van Rij [aut, cre]
Maintainer: Jacolien van Rij <vanrij.jacolien@gmail.com>
Diff between plotfunctions versions 1.0 dated 2016-05-27 and 1.2 dated 2017-04-24
plotfunctions-1.0/plotfunctions/man/drawArrows.Rd |only plotfunctions-1.2/plotfunctions/DESCRIPTION | 9 plotfunctions-1.2/plotfunctions/MD5 | 85 - plotfunctions-1.2/plotfunctions/NAMESPACE | 7 plotfunctions-1.2/plotfunctions/R/data.R |only plotfunctions-1.2/plotfunctions/R/plot.R | 837 ++++++++------- plotfunctions-1.2/plotfunctions/R/plotfunctions.R | 6 plotfunctions-1.2/plotfunctions/R/util.R | 398 +++++++ plotfunctions-1.2/plotfunctions/build |only plotfunctions-1.2/plotfunctions/data |only plotfunctions-1.2/plotfunctions/inst |only plotfunctions-1.2/plotfunctions/man/addInterval.Rd | 2 plotfunctions-1.2/plotfunctions/man/add_bars.Rd | 2 plotfunctions-1.2/plotfunctions/man/add_n_points.Rd | 6 plotfunctions-1.2/plotfunctions/man/alpha.Rd | 2 plotfunctions-1.2/plotfunctions/man/alphaPalette.Rd | 2 plotfunctions-1.2/plotfunctions/man/check_normaldist.Rd | 2 plotfunctions-1.2/plotfunctions/man/color_contour.Rd | 2 plotfunctions-1.2/plotfunctions/man/dotplot_error.Rd | 2 plotfunctions-1.2/plotfunctions/man/drawDevArrows.Rd |only plotfunctions-1.2/plotfunctions/man/emptyPlot.Rd | 2 plotfunctions-1.2/plotfunctions/man/errorBars.Rd | 2 plotfunctions-1.2/plotfunctions/man/fill_area.Rd | 2 plotfunctions-1.2/plotfunctions/man/findAbsMin.Rd | 6 plotfunctions-1.2/plotfunctions/man/find_n_neighbors.Rd | 6 plotfunctions-1.2/plotfunctions/man/getArrowPos.Rd |only plotfunctions-1.2/plotfunctions/man/getCoords.Rd | 2 plotfunctions-1.2/plotfunctions/man/getDec.Rd | 9 plotfunctions-1.2/plotfunctions/man/getFigCoords.Rd | 2 plotfunctions-1.2/plotfunctions/man/getProps.Rd | 2 plotfunctions-1.2/plotfunctions/man/getRange.Rd | 9 plotfunctions-1.2/plotfunctions/man/getRatioCoords.Rd |only plotfunctions-1.2/plotfunctions/man/gradientLegend.Rd | 2 plotfunctions-1.2/plotfunctions/man/group_sort.Rd | 9 plotfunctions-1.2/plotfunctions/man/img.Rd |only plotfunctions-1.2/plotfunctions/man/inch2coords.Rd |only plotfunctions-1.2/plotfunctions/man/isColor.Rd |only plotfunctions-1.2/plotfunctions/man/legend_margin.Rd | 2 plotfunctions-1.2/plotfunctions/man/list2str.Rd | 9 plotfunctions-1.2/plotfunctions/man/marginDensityPlot.Rd | 25 plotfunctions-1.2/plotfunctions/man/move_n_point.Rd | 9 plotfunctions-1.2/plotfunctions/man/plot_error.Rd | 2 plotfunctions-1.2/plotfunctions/man/plot_image.Rd | 7 plotfunctions-1.2/plotfunctions/man/plot_signifArea.Rd |only plotfunctions-1.2/plotfunctions/man/plotfunctions.Rd | 5 plotfunctions-1.2/plotfunctions/man/plotsurface.Rd | 14 plotfunctions-1.2/plotfunctions/man/se.Rd | 31 plotfunctions-1.2/plotfunctions/vignettes |only 48 files changed, 1073 insertions(+), 446 deletions(-)
Title: Optimum Contribution Selection and Population Genetics
Description: A framework for the optimization of breeding programs via optimum contribution selection. An easy to use set of function for computation of optimum contributions of selection candidates, and of the population genetic parameters to be optimized. These parameters can be estimated using pedigree or genotype information, and include kinships, kinships at native haplotype segments, and breed composition of crossbred individuals. They are suitable for managing genetic diversity, removing introgressed genetic material, and accelerating genetic gain. Additionally, functions are provided for computing genetic contributions from ancestors, inbreeding coefficients, the native effective size, the native genome equivalent, pedigree completeness, and for preparing and plotting pedigrees.
Author: Robin Wellmann
Maintainer: Robin Wellmann <r.wellmann@uni-hohenheim.de>
Diff between optiSel versions 0.7.1 dated 2017-04-15 and 0.8 dated 2017-04-24
DESCRIPTION | 11 MD5 | 124 ++-- NAMESPACE | 10 R/RcppExports.R | 102 +-- R/completeness.R | 15 R/haplofreq.R | 83 ++ R/opticont.R | 31 - R/opticont4mb.R | 418 ++++++------- R/pedplot.R | 2 R/plot.HaploFreq.R | 4 R/prePed.R | 12 R/segBreedComp.R | 174 ++--- R/segIBD.R | 243 ++++---- R/segIBDandN.R | 284 +++++---- R/segIBDatN.R | 132 ++-- R/segInbreeding.R | 2 R/segN.R | 198 +++--- R/summary.opticont.R | 273 ++++----- build/partial.rdb |binary build/vignette.rds |binary data/Cattle.rda |binary data/PedigWithErrors.rda |binary data/Phen.rda |binary data/map.rda |binary inst/doc/ocs-vignette.R | 519 ++++++++--------- inst/doc/ocs-vignette.Rmd | 1213 ++++++++++++++++++++-------------------- inst/doc/ocs-vignette.html | 1200 +++++++++++++++++++-------------------- inst/doc/ped-vignette.R | 248 ++++---- inst/doc/ped-vignette.Rmd | 728 ++++++++++++------------ inst/doc/ped-vignette.html | 858 ++++++++++++++-------------- inst/doc/seg-vignette.R | 238 +++---- inst/doc/seg-vignette.Rmd | 788 ++++++++++++------------- inst/doc/seg-vignette.html | 840 +++++++++++++-------------- man/PedigWithErrors.Rd | 18 man/freqlist.Rd | 6 man/haplofreq.Rd | 30 man/makeA.Rd | 2 man/map.Rd | 2 man/noffspring.Rd | 6 man/opticomp.Rd | 2 man/opticont.Rd | 422 ++++++------- man/opticont4mb.Rd | 580 +++++++++---------- man/pedInbreeding.Rd | 76 +- man/prePed.Rd | 2 man/segBreedComp.Rd | 158 ++--- man/segIBD.Rd | 146 ++-- man/segIBDandN.Rd | 175 ++--- man/segIBDatN.Rd | 163 ++--- man/segInbreeding.Rd | 138 ++-- man/segN.Rd | 147 ++-- man/sim2dis.Rd | 2 src/RcppExports.cpp | 141 ++-- src/init.c | 20 src/rcpp_haplofreq.cpp | 3 src/rcpp_nativecont.cpp | 12 src/rcpp_segBreedComp.cpp | 13 src/rcpp_segIBD.cpp | 5 src/rcpp_segIBDandN.cpp | 5 src/rcpp_segIBDandNVersion2.cpp | 5 src/rcpp_segN.cpp | 13 vignettes/ocs-vignette.Rmd | 1213 ++++++++++++++++++++-------------------- vignettes/ped-vignette.Rmd | 728 ++++++++++++------------ vignettes/seg-vignette.Rmd | 788 ++++++++++++------------- 63 files changed, 7036 insertions(+), 6735 deletions(-)
Title: Image Processing Library Based on 'CImg'
Description: Fast image processing for images in up to 4 dimensions (two spatial
dimensions, one time/depth dimension, one colour dimension). Provides most
traditional image processing tools (filtering, morphology, transformations,
etc.) as well as various functions for easily analysing image data using R. The
package wraps CImg, <http://cimg.eu>, a simple, modern C++ library for image
processing.
Author: Simon Barthelme [aut, cre]
Maintainer: Simon Barthelme <simon.barthelme@gipsa-lab.fr>
Diff between imager versions 0.40.1 dated 2017-03-13 and 0.40.2 dated 2017-04-24
DESCRIPTION | 10 - MD5 | 298 +++++++++++++++++++++---------------------- NAMESPACE | 1 NEWS | 17 ++ NEWS.md | 5 R/canny.R | 1 R/drawing.R | 2 R/loading.R | 7 + R/pixset.R | 53 +++++++ R/splitcombine.R | 19 ++ R/utils.R | 9 + build/vignette.rds |binary inst/doc/gettingstarted.Rmd | 2 inst/doc/gettingstarted.html | 105 +++++++-------- inst/doc/pixsets.html | 71 ++++------ inst/include/CImg.h | 103 ++++++++------ man/FFT.Rd | 1 man/RasterPackage.Rd | 1 man/add.colour.Rd | 4 man/as.cimg.Rd | 16 +- man/as.cimg.array.Rd | 1 man/as.cimg.data.frame.Rd | 1 man/as.cimg.function.Rd | 1 man/as.cimg.raster.Rd | 1 man/as.data.frame.cimg.Rd | 1 man/as.data.frame.imlist.Rd | 1 man/as.data.frame.pixset.Rd | 1 man/as.imlist.Rd | 6 man/as.pixset.Rd | 4 man/as.raster.cimg.Rd | 7 - man/at.Rd | 2 man/autocrop.Rd | 1 man/bbox.Rd | 13 + man/blur_anisotropic.Rd | 1 man/boats.Rd | 1 man/boundary.Rd | 1 man/boxblur.Rd | 1 man/boxblur_xy.Rd | 1 man/bucketfill.Rd | 3 man/cannyEdges.Rd | 1 man/capture.plot.Rd | 1 man/center.stencil.Rd | 1 man/channels.Rd | 1 man/ci.Rd | 1 man/cimg.Rd | 1 man/cimg.dimensions.Rd | 6 man/cimg.extract.Rd | 10 - man/cimg.use.openmp.Rd | 1 man/cimg2im.Rd | 7 - man/clean.Rd | 29 ++-- man/common_pixsets.Rd | 14 +- man/contours.Rd | 7 - man/convolve.Rd | 1 man/coord.index.Rd | 7 - man/correlate.Rd | 1 man/crop.borders.Rd | 1 man/deriche.Rd | 1 man/diffusion_tensors.Rd | 1 man/displacement.Rd | 1 man/display.Rd | 1 man/display.cimg.Rd | 1 man/display.list.Rd | 1 man/distance_transform.Rd | 1 man/erode.Rd | 12 - man/extract_patches.Rd | 2 man/flatten.alpha.Rd | 7 - man/frames.Rd | 1 man/get.locations.Rd | 1 man/get.stencil.Rd | 1 man/get_gradient.Rd | 1 man/get_hessian.Rd | 1 man/grab.Rd | 9 - man/grapes-inr-grapes.Rd | 1 man/grayscale.Rd | 1 man/grow.Rd | 2 man/haar.Rd | 1 man/highlight.Rd | 1 man/idply.Rd | 1 man/iiply.Rd | 1 man/ilply.Rd | 1 man/im2cimg.Rd | 1 man/im_split.Rd | 1 man/imager.Rd | 1 man/imager.colourspaces.Rd | 28 ++-- man/imager.combine.Rd | 36 ++--- man/imager.replace.Rd | 10 - man/imager.subset.Rd | 1 man/imappend.Rd | 1 man/imcoord.Rd | 6 man/imdirac.Rd | 1 man/imdraw.Rd | 7 - man/imeval.Rd | 1 man/imfill.Rd | 1 man/imgradient.Rd | 1 man/imhessian.Rd | 1 man/iminfo.Rd | 1 man/imlap.Rd | 1 man/imlist.Rd | 1 man/imnoise.Rd | 1 man/implot.Rd | 7 - man/imrep.Rd | 1 man/imrotate.Rd | 1 man/imsharpen.Rd | 1 man/imshift.Rd | 1 man/imsplit.Rd | 1 man/imsub.Rd | 2 man/imwarp.Rd | 7 - man/index.coord.Rd | 7 - man/interp.Rd | 1 man/is.cimg.Rd | 1 man/is.imlist.Rd | 1 man/is.pixset.Rd | 1 man/isoblur.Rd | 1 man/label.Rd | 1 man/liply.Rd | 1 man/load.example.Rd | 1 man/load.image.Rd | 1 man/load.video.Rd | 7 - man/magick.Rd | 9 - man/make.video.Rd | 8 - man/map_il.Rd | 1 man/medianblur.Rd | 1 man/mirror.Rd | 1 man/pad.Rd | 1 man/patch_summary_cimg.Rd | 1 man/patchstat.Rd | 1 man/periodic.part.Rd | 7 - man/permute_axes.Rd | 1 man/pixel.grid.Rd | 1 man/pixset.Rd | 1 man/play.Rd | 1 man/plot.cimg.Rd | 1 man/plot.imlist.Rd | 1 man/px.flood.Rd | 1 man/px.na.Rd | 1 man/renorm.Rd | 1 man/resize.Rd | 1 man/resize_uniform.Rd | 10 - man/rm.alpha.Rd | 7 - man/rotate_xy.Rd | 1 man/save.image.Rd | 1 man/split_connected.Rd | 7 - man/squeeze.Rd | 1 man/stencil.cross.Rd | 7 - man/threshold.Rd | 9 + man/vanvliet.Rd | 1 man/warp.Rd | 1 man/watershed.Rd | 1 man/where.Rd | 1 vignettes/gettingstarted.Rmd | 2 150 files changed, 575 insertions(+), 573 deletions(-)
Title: Simply Create LaTeX and HTML Tables
Description: Creates HTML and LaTeX tables. Provides similar
functionality to 'xtable', but does more, with a simpler interface.
Author: David Hugh-Jones
Maintainer: David Hugh-Jones <davidhughjones@gmail.com>
Diff between huxtable versions 0.2.0 dated 2017-04-21 and 0.2.1 dated 2017-04-24
DESCRIPTION | 6 - MD5 | 44 ++++++------ NAMESPACE | 19 ++++- NEWS.md | 5 + R/HTML.R | 6 - R/LaTeX.R | 15 +--- R/dplyr.R |only R/huxreg.R | 1 R/huxtable.R | 138 ++++------------------------------------ R/themes.R | 2 R/utils.R | 6 + README.md | 2 inst/doc/design-principles.html | 11 ++- inst/doc/huxreg.html | 14 ++-- inst/doc/huxtable.R | 2 inst/doc/huxtable.Rmd | 2 inst/doc/huxtable.html | 62 ++++++++--------- man/add_colnames.Rd | 1 man/dplyr-verbs.Rd | 15 ++-- man/filter.Rd |only man/themes.Rd | 2 tests/testthat/test-huxreg.R | 17 ++++ tests/testthat/test-output.R | 1 vignettes/huxtable.Rmd | 2 24 files changed, 157 insertions(+), 216 deletions(-)
More information about BarBorGradient at CRAN
Permanent link
Title: Simulation of Meiosis in Plant Breeding Research
Description: Tools for simulation of meiosis in plant breeding research.
Author: Dominik Mueller [aut, cre],
Karl W. Broman [aut]
Maintainer: Dominik Mueller <dominikmueller64@yahoo.de>
Diff between Meiosis versions 1.0.0 dated 2017-04-04 and 1.0.1 dated 2017-04-24
Meiosis-1.0.0/Meiosis/R/RcppExports.R |only Meiosis-1.0.0/Meiosis/R/create_xodat_founders.R |only Meiosis-1.0.0/Meiosis/R/create_xodat_param.R |only Meiosis-1.0.0/Meiosis/R/functions.R |only Meiosis-1.0.0/Meiosis/inst/doc/Meiosis.R |only Meiosis-1.0.0/Meiosis/inst/doc/Meiosis.Rmd |only Meiosis-1.0.0/Meiosis/inst/doc/Meiosis.html |only Meiosis-1.0.0/Meiosis/src/RcppExports.cpp |only Meiosis-1.0.0/Meiosis/src/bcgv.cpp |only Meiosis-1.0.0/Meiosis/tests/testthat/test_check_xo_individual.R |only Meiosis-1.0.0/Meiosis/vignettes/Meiosis.Rmd |only Meiosis-1.0.1/Meiosis/DESCRIPTION | 10 Meiosis-1.0.1/Meiosis/MD5 | 81 ++--- Meiosis-1.0.1/Meiosis/NAMESPACE | 1 Meiosis-1.0.1/Meiosis/NEWS.md |only Meiosis-1.0.1/Meiosis/R/Meiosis.R | 14 Meiosis-1.0.1/Meiosis/R/check_functions.R |only Meiosis-1.0.1/Meiosis/R/create_xo_founder.R |only Meiosis-1.0.1/Meiosis/R/create_xoparam.R |only Meiosis-1.0.1/Meiosis/R/exports.R |only Meiosis-1.0.1/Meiosis/README.md | 2 Meiosis-1.0.1/Meiosis/build/vignette.rds |binary Meiosis-1.0.1/Meiosis/data/exdat.rda |binary Meiosis-1.0.1/Meiosis/inst/doc/Introduction.R |only Meiosis-1.0.1/Meiosis/inst/doc/Introduction.Rmd |only Meiosis-1.0.1/Meiosis/inst/doc/Introduction.html |only Meiosis-1.0.1/Meiosis/inst/include/hinterface/realized_ibd.hpp | 3 Meiosis-1.0.1/Meiosis/man/calc_Lstar.Rd | 2 Meiosis-1.0.1/Meiosis/man/check_geno_individual.Rd | 2 Meiosis-1.0.1/Meiosis/man/check_positions.Rd | 2 Meiosis-1.0.1/Meiosis/man/check_xo_individual.Rd | 2 Meiosis-1.0.1/Meiosis/man/check_xoparam.Rd |only Meiosis-1.0.1/Meiosis/man/create_xo_founder.Rd | 2 Meiosis-1.0.1/Meiosis/man/create_xoparam.Rd | 2 Meiosis-1.0.1/Meiosis/man/cross_geno.Rd | 8 Meiosis-1.0.1/Meiosis/man/cross_xo.Rd | 8 Meiosis-1.0.1/Meiosis/man/crossover.Rd | 2 Meiosis-1.0.1/Meiosis/man/dh_geno.Rd | 6 Meiosis-1.0.1/Meiosis/man/dh_xo.Rd | 6 Meiosis-1.0.1/Meiosis/man/meiosis_geno.Rd | 6 Meiosis-1.0.1/Meiosis/man/meiosis_xo.Rd | 6 Meiosis-1.0.1/Meiosis/man/realized_coancestry.Rd | 6 Meiosis-1.0.1/Meiosis/man/realized_heter.Rd | 6 Meiosis-1.0.1/Meiosis/man/seed_rng.Rd | 2 Meiosis-1.0.1/Meiosis/man/self_geno.Rd | 6 Meiosis-1.0.1/Meiosis/man/self_xo.Rd | 6 Meiosis-1.0.1/Meiosis/src/R_interface.cpp | 162 ++-------- Meiosis-1.0.1/Meiosis/src/exports.cpp |only Meiosis-1.0.1/Meiosis/src/helper.cpp | 58 +-- Meiosis-1.0.1/Meiosis/src/init.c | 6 Meiosis-1.0.1/Meiosis/tests/testthat/test_checks.R |only Meiosis-1.0.1/Meiosis/tests/testthat/test_meiosis.R | 86 ++--- Meiosis-1.0.1/Meiosis/vignettes/Introduction.Rmd |only 53 files changed, 225 insertions(+), 278 deletions(-)
Title: Seasonal Adjustment by Frequency Analysis
Description: Decompose a time series into seasonal, trend and irregular components using transformations to amplitude-frequency domain.
Author: Francisco Parra <parra_fj@cantabria.es>
Maintainer: Francisco Parra <parra_fj@cantabria.es>
Diff between descomponer versions 1.2 dated 2015-03-26 and 1.3 dated 2017-04-24
descomponer-1.2/descomponer/vignettes/figure |only descomponer-1.3/descomponer/DESCRIPTION | 8 - descomponer-1.3/descomponer/MD5 | 40 +++++---- descomponer-1.3/descomponer/NAMESPACE | 3 descomponer-1.3/descomponer/R/MW.R | 2 descomponer-1.3/descomponer/R/cdf.R | 2 descomponer-1.3/descomponer/R/descomponer.R | 41 +++++----- descomponer-1.3/descomponer/R/gdt.R | 2 descomponer-1.3/descomponer/R/gtd.R |only descomponer-1.3/descomponer/R/periodograma.R | 2 descomponer-1.3/descomponer/R/rdf.R |only descomponer-1.3/descomponer/R/td.R |only descomponer-1.3/descomponer/build/vignette.rds |binary descomponer-1.3/descomponer/data/PIB.rda |only descomponer-1.3/descomponer/data/celec.rda |only descomponer-1.3/descomponer/inst/doc/descomponer_texto.R | 11 ++ descomponer-1.3/descomponer/inst/doc/descomponer_texto.Rnw | 18 +++- descomponer-1.3/descomponer/inst/doc/descomponer_texto.pdf |binary descomponer-1.3/descomponer/man/PIB.rd |only descomponer-1.3/descomponer/man/celec.rd |only descomponer-1.3/descomponer/man/gtd.rd |only descomponer-1.3/descomponer/man/rdf.rd |only descomponer-1.3/descomponer/man/td.rd |only descomponer-1.3/descomponer/vignettes/descomponer_texto-concordance.tex | 2 descomponer-1.3/descomponer/vignettes/descomponer_texto.Rnw | 18 +++- 25 files changed, 100 insertions(+), 49 deletions(-)
Title: Data Menu for Radiant: Business Analytics using R and Shiny
Description: The Radiant Data menu includes interfaces for loading, saving,
viewing, visualizing, summarizing, transforming, and combining data. It also
contains functionality to generate reproducible reports of the analyses
conducted in the application.
Author: Vincent Nijs [aut, cre]
Maintainer: Vincent Nijs <radiant@rady.ucsd.edu>
Diff between radiant.data versions 0.6.0 dated 2016-09-11 and 0.8.0 dated 2017-04-24
radiant.data-0.6.0/radiant.data/inst/app/tools/data/generate.R |only radiant.data-0.6.0/radiant.data/man/mutate_each.Rd |only radiant.data-0.6.0/radiant.data/man/sdp_rm.Rd |only radiant.data-0.6.0/radiant.data/man/varp_rm.Rd |only radiant.data-0.8.0/radiant.data/DESCRIPTION | 34 radiant.data-0.8.0/radiant.data/LICENSE | 4 radiant.data-0.8.0/radiant.data/MD5 | 345 ++-- radiant.data-0.8.0/radiant.data/NAMESPACE | 27 radiant.data-0.8.0/radiant.data/NEWS.md |only radiant.data-0.8.0/radiant.data/R/aaa.R | 13 radiant.data-0.8.0/radiant.data/R/deprecated.R | 26 radiant.data-0.8.0/radiant.data/R/explore.R | 116 + radiant.data-0.8.0/radiant.data/R/pivotr.R | 94 - radiant.data-0.8.0/radiant.data/R/radiant.R | 115 + radiant.data-0.8.0/radiant.data/R/transform.R | 266 +-- radiant.data-0.8.0/radiant.data/R/view.R | 35 radiant.data-0.8.0/radiant.data/R/visualize.R | 83 radiant.data-0.8.0/radiant.data/README.md | 63 radiant.data-0.8.0/radiant.data/inst/app/global.R | 22 radiant.data-0.8.0/radiant.data/inst/app/init.R | 1 radiant.data-0.8.0/radiant.data/inst/app/radiant.R | 84 radiant.data-0.8.0/radiant.data/inst/app/tools/app/about.md | 63 radiant.data-0.8.0/radiant.data/inst/app/tools/app/code.R | 46 radiant.data-0.8.0/radiant.data/inst/app/tools/app/help.R | 2 radiant.data-0.8.0/radiant.data/inst/app/tools/app/report.R | 848 +++++----- radiant.data-0.8.0/radiant.data/inst/app/tools/app/state.R | 12 radiant.data-0.8.0/radiant.data/inst/app/tools/app/stop.R | 3 radiant.data-0.8.0/radiant.data/inst/app/tools/app/tutorials.md | 15 radiant.data-0.8.0/radiant.data/inst/app/tools/data/combine_ui.R | 25 radiant.data-0.8.0/radiant.data/inst/app/tools/data/explore_ui.R | 12 radiant.data-0.8.0/radiant.data/inst/app/tools/data/manage.R | 23 radiant.data-0.8.0/radiant.data/inst/app/tools/data/manage_ui.R | 84 radiant.data-0.8.0/radiant.data/inst/app/tools/data/pivotr_ui.R | 40 radiant.data-0.8.0/radiant.data/inst/app/tools/data/transform_ui.R | 564 +++--- radiant.data-0.8.0/radiant.data/inst/app/tools/data/view.R | 16 radiant.data-0.8.0/radiant.data/inst/app/tools/data/visualize_ui.R | 210 -- radiant.data-0.8.0/radiant.data/inst/app/tools/help/code.md | 4 radiant.data-0.8.0/radiant.data/inst/app/tools/help/combine.Rmd | 4 radiant.data-0.8.0/radiant.data/inst/app/tools/help/combine.md | 2 radiant.data-0.8.0/radiant.data/inst/app/tools/help/explore.md | 10 radiant.data-0.8.0/radiant.data/inst/app/tools/help/pivotr.md | 8 radiant.data-0.8.0/radiant.data/inst/app/tools/help/report.md | 8 radiant.data-0.8.0/radiant.data/inst/app/tools/help/state.md | 2 radiant.data-0.8.0/radiant.data/inst/app/tools/help/transform.Rmd | 23 radiant.data-0.8.0/radiant.data/inst/app/tools/help/transform.md | 23 radiant.data-0.8.0/radiant.data/inst/app/tools/help/view.Rmd | 2 radiant.data-0.8.0/radiant.data/inst/app/tools/help/view.md | 2 radiant.data-0.8.0/radiant.data/inst/app/tools/help/visualize.md | 53 radiant.data-0.8.0/radiant.data/inst/app/www/js/run_return.js |only radiant.data-0.8.0/radiant.data/inst/app/www/style.css | 4 radiant.data-0.8.0/radiant.data/man/Search.Rd | 1 radiant.data-0.8.0/radiant.data/man/add_class.Rd | 1 radiant.data-0.8.0/radiant.data/man/as_character.Rd | 1 radiant.data-0.8.0/radiant.data/man/as_data_frame.Rd | 1 radiant.data-0.8.0/radiant.data/man/as_distance.Rd | 1 radiant.data-0.8.0/radiant.data/man/as_dmy.Rd | 1 radiant.data-0.8.0/radiant.data/man/as_dmy_hm.Rd | 1 radiant.data-0.8.0/radiant.data/man/as_dmy_hms.Rd | 1 radiant.data-0.8.0/radiant.data/man/as_duration.Rd | 1 radiant.data-0.8.0/radiant.data/man/as_factor.Rd | 9 radiant.data-0.8.0/radiant.data/man/as_hm.Rd | 1 radiant.data-0.8.0/radiant.data/man/as_hms.Rd | 1 radiant.data-0.8.0/radiant.data/man/as_integer.Rd | 6 radiant.data-0.8.0/radiant.data/man/as_mdy.Rd | 1 radiant.data-0.8.0/radiant.data/man/as_mdy_hm.Rd | 1 radiant.data-0.8.0/radiant.data/man/as_mdy_hms.Rd | 1 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radiant.data-0.8.0/radiant.data/man/wday.Rd |only radiant.data-0.8.0/radiant.data/man/weighted.sd.Rd | 1 radiant.data-0.8.0/radiant.data/man/which.pmax.Rd | 1 radiant.data-0.8.0/radiant.data/man/which.pmin.Rd | 1 radiant.data-0.8.0/radiant.data/man/xtile.Rd | 1 184 files changed, 2007 insertions(+), 1629 deletions(-)
Title: Generate Chemical Strings (SMILES) with the Inverse QSPR Model
Description: Generate chemical structures possibly satisfying desired properties
using the inverse QSPR model. It has three reference classes. ENgram is a class for learning the grammar
structure of existing chemical strings using an extended N-gram model. QSPRpred contains
a simple Bayes regression model to predict properties from structures. SmcChem is a class of the generator of
chemical strings from the Inverse-QSPR model. This class has ENgram and QSPRpred class objects inside.
The generator is implemented by the Sequential Monte Carlo sampler.
Author: Hisaki Ikebata
Maintainer: Ryo Yoshida <yoshidar@ism.ac.jp>
Diff between iqspr versions 1.0 dated 2016-05-21 and 1.1 dated 2017-04-24
DESCRIPTION | 12 +-- MD5 | 30 ++++----- NAMESPACE | 46 ++++++------- data/datalist | 8 +- man/ENgram-class.Rd | 54 ++++++++-------- man/Esmi-class.Rd | 22 +++--- man/QSPRpred-class.Rd | 143 +++++++++++++++++++++---------------------- man/SmcChem-class.Rd | 165 +++++++++++++++++++++++++------------------------- man/genENgram.Rd | 57 ++++++++--------- man/get_hiscores.Rd | 57 ++++++++--------- man/get_score.Rd | 55 ++++++++-------- man/get_smiles.Rd | 47 ++++++-------- man/iqspr.Rd | 83 ++++++++++++------------- man/predict.Rd | 43 ++++++------- man/smcexec.Rd | 65 +++++++++---------- man/viewstr.Rd | 39 +++++------ 16 files changed, 460 insertions(+), 466 deletions(-)
Title: Tidy Quantitative Financial Analysis
Description: Bringing financial analysis to the 'tidyverse'. The 'tidyquant'
package provides a convenient wrapper to various 'xts', 'zoo', 'quantmod', 'TTR'
and 'PerformanceAnalytics' package
functions and returns the objects in the tidy 'tibble' format. The main
advantage is being able to use quantitative functions with the 'tidyverse'
functions including 'purrr', 'dplyr', 'tidyr', 'ggplot2', 'lubridate', etc. See
the 'tidyquant' website for more information, documentation and examples.
Author: Matt Dancho [aut, cre],
Davis Vaughan [aut]
Maintainer: Matt Dancho <mdancho@business-science.io>
Diff between tidyquant versions 0.5.0 dated 2017-04-03 and 0.5.1 dated 2017-04-24
DESCRIPTION | 10 LICENSE | 4 MD5 | 179 - NAMESPACE | 174 - NEWS.md | 170 - R/as_tibble.R | 244 - R/as_xts.R | 190 - R/coord_date.R | 156 - R/data.R | 38 R/deprecated.R | 72 R/geom_bbands.R | 658 ++--- R/geom_chart.R | 466 +-- R/geom_ma.R | 488 +-- R/global_vars.R | 252 - R/quandl.R | 124 R/scale_manual.R | 288 +- R/theme_tq.R | 286 +- R/tidyquant.R | 90 R/tq_get.R | 1783 +++++++------ R/tq_mutate.R | 810 +++--- R/tq_performance.R | 630 ++-- R/tq_portfolio.R | 875 +++--- R/tq_stock_list.R | 666 ++--- R/tq_transmute.R | 776 +++--- R/utils-dates.R | 254 - R/utils-formatting.R | 86 README.md | 171 - build/vignette.rds |binary inst/doc/TQ00-introduction-to-tidyquant.R | 56 inst/doc/TQ00-introduction-to-tidyquant.Rmd | 246 - inst/doc/TQ00-introduction-to-tidyquant.html | 272 +- inst/doc/TQ01-core-functions-in-tidyquant.R | 429 +-- inst/doc/TQ01-core-functions-in-tidyquant.Rmd | 1010 +++---- inst/doc/TQ01-core-functions-in-tidyquant.html | 1579 ++++++------ inst/doc/TQ02-quant-integrations-in-tidyquant.R | 589 ++-- inst/doc/TQ02-quant-integrations-in-tidyquant.Rmd | 1075 ++++---- inst/doc/TQ02-quant-integrations-in-tidyquant.html | 1520 ++++++----- inst/doc/TQ03-scaling-and-modeling-with-tidyquant.R | 276 +- inst/doc/TQ03-scaling-and-modeling-with-tidyquant.Rmd | 648 ++--- inst/doc/TQ03-scaling-and-modeling-with-tidyquant.html | 971 +++---- inst/doc/TQ04-charting-with-tidyquant.R | 667 ++--- inst/doc/TQ04-charting-with-tidyquant.Rmd | 1099 ++++---- inst/doc/TQ04-charting-with-tidyquant.html | 1124 ++++---- inst/doc/TQ05-performance-analysis-with-tidyquant.R | 697 ++--- inst/doc/TQ05-performance-analysis-with-tidyquant.Rmd | 1385 +++++----- inst/doc/TQ05-performance-analysis-with-tidyquant.html | 2196 ++++++++--------- man/FANG.Rd | 58 man/as_tibble.Rd | 106 man/as_xts.Rd | 112 man/coord_x_date.Rd | 136 - man/deprecated.Rd | 84 man/geom_bbands.Rd | 340 +- man/geom_chart.Rd | 248 - man/geom_ma.Rd | 288 +- man/palette_tq.Rd | 46 man/quandl_api_key.Rd | 60 man/quandl_search.Rd | 72 man/scale_manual.Rd | 114 man/theme_tq.Rd | 98 man/tidyquant.Rd | 68 man/tq_get.Rd | 254 - man/tq_mutate.Rd | 314 +- man/tq_performance.Rd | 206 - man/tq_portfolio.Rd | 276 +- man/tq_stock_list.Rd | 134 - tests/testthat.R | 8 tests/testthat/test_as_tibble.R | 62 tests/testthat/test_as_xts.R | 86 tests/testthat/test_tq_exchange.R | 68 tests/testthat/test_tq_get_compound_getters.R | 152 - tests/testthat/test_tq_get_dividends.R | 56 tests/testthat/test_tq_get_economic_data.R | 72 tests/testthat/test_tq_get_exchange_rates.R | 72 tests/testthat/test_tq_get_financials.R | 72 tests/testthat/test_tq_get_key_ratios.R | 72 tests/testthat/test_tq_get_key_stats.R | 58 tests/testthat/test_tq_get_metal_prices.R | 73 tests/testthat/test_tq_get_splits.R | 56 tests/testthat/test_tq_get_stock_prices.R | 78 tests/testthat/test_tq_index.R | 98 tests/testthat/test_tq_mutate.R | 396 +-- tests/testthat/test_tq_performance.R | 114 tests/testthat/test_tq_portfolio.R | 129 tests/testthat/test_tq_transmute.R | 346 +- tools |only vignettes/TQ00-introduction-to-tidyquant.Rmd | 246 - vignettes/TQ01-core-functions-in-tidyquant.Rmd | 1010 +++---- vignettes/TQ02-quant-integrations-in-tidyquant.Rmd | 1104 ++++---- vignettes/TQ03-scaling-and-modeling-with-tidyquant.Rmd | 648 ++--- vignettes/TQ04-charting-with-tidyquant.Rmd | 1099 ++++---- vignettes/TQ05-performance-analysis-with-tidyquant.Rmd | 1385 +++++----- 91 files changed, 18314 insertions(+), 18039 deletions(-)
Title: Phylogenies with Annotations
Description: Functions to read and write APE-compatible phylogenetic
trees in NEXUS and Newick formats, while preserving annotations.
Author: Daniel Beer
Maintainer: Daniel Beer <dlbeer@gmail.com>
Diff between phylotate versions 1.0 dated 2017-01-03 and 1.1 dated 2017-04-24
DESCRIPTION | 8 ++++---- MD5 | 9 +++++---- NEWS |only R/newick.R | 15 +++++++++------ R/tokenize.R | 1 + tests/round_trip.R | 2 +- 6 files changed, 20 insertions(+), 15 deletions(-)
Title: Multi-Step Adaptive Estimation Methods for Sparse Regressions
Description: Multi-step adaptive elastic-net (MSAENet) algorithm for
feature selection in high-dimensional regressions proposed in
Xiao and Xu (2015) <DOI:10.1080/00949655.2015.1016944>,
with additional support for multi-step adaptive MCP-net
(MSAMNet) and multi-step adaptive SCAD-net (MSASNet) methods.
Author: Nan Xiao [aut, cre]
Maintainer: Nan Xiao <me@nanx.me>
Diff between msaenet versions 2.5 dated 2017-03-25 and 2.6 dated 2017-04-24
DESCRIPTION | 8 ++-- MD5 | 74 +++++++++++++++++++------------------- NEWS.md | 6 +++ R/aenet.R | 17 ++++++++ R/msaenet-tune-glmnet.R | 17 ++++++-- R/msaenet.R | 20 ++++++++-- R/msamnet.R | 3 - R/msasnet.R | 3 - build/vignette.rds |binary inst/doc/msaenet.html | 20 +++++----- man/aenet.Rd | 16 ++++++-- man/amnet.Rd | 1 man/asnet.Rd | 1 man/coef.msaenet.Rd | 1 man/msaenet-package.Rd | 7 ++- man/msaenet.Rd | 19 ++++++--- man/msaenet.fn.Rd | 1 man/msaenet.fp.Rd | 1 man/msaenet.mae.Rd | 1 man/msaenet.mse.Rd | 1 man/msaenet.nzv.Rd | 1 man/msaenet.nzv.all.Rd | 1 man/msaenet.rmse.Rd | 1 man/msaenet.rmsle.Rd | 1 man/msaenet.sim.binomial.Rd | 1 man/msaenet.sim.cox.Rd | 7 ++- man/msaenet.sim.gaussian.Rd | 7 ++- man/msaenet.sim.poisson.Rd | 1 man/msaenet.tp.Rd | 1 man/msaenet.tune.glmnet.Rd | 11 +++-- man/msaenet.tune.ncvreg.Rd | 7 ++- man/msaenet.tune.nsteps.glmnet.Rd | 1 man/msaenet.tune.nsteps.ncvreg.Rd | 1 man/msamnet.Rd | 4 +- man/msasnet.Rd | 4 +- man/plot.msaenet.Rd | 1 man/predict.msaenet.Rd | 1 man/print.msaenet.Rd | 1 38 files changed, 175 insertions(+), 94 deletions(-)
Title: Generalized Joint Attribute Modeling
Description: Analyzes joint attribute data (e.g., species abundance) that are combinations of continuous and discrete data with Gibbs sampling.
Author: James S. Clark, Daniel Taylor-Rodriquez
Maintainer: James S. Clark <jimclark@duke.edu>
Diff between gjam versions 2.1.1 dated 2016-12-14 and 2.1.3 dated 2017-04-24
DESCRIPTION | 8 MD5 | 65 NAMESPACE | 15 R/RcppExports.R | 50 R/gjamCensorY.r | 4 R/gjamHfunctions.R | 6202 ++++++++++++++++++++++++++++----------------- R/gjamIIE.r | 20 R/gjamPlot.r | 22 R/gjamPriorTemplate.r |only R/gjamSpec2Trait.r | 2 R/gjamTrimY.r | 6 build/vignette.rds |binary inst/CITATION | 11 inst/doc/gjamVignette.R | 245 + inst/doc/gjamVignette.Rmd | 453 +-- inst/doc/gjamVignette.html | 569 ++-- man/gjam-package.Rd | 15 man/gjam.Rd | 130 man/gjamCensorY.Rd | 63 man/gjamDeZero.Rd | 6 man/gjamIIE.Rd | 4 man/gjamIIEplot.Rd | 4 man/gjamOrdination.Rd | 2 man/gjamPlot.Rd | 19 man/gjamPoints2Grid.Rd | 4 man/gjamPredict.Rd | 10 man/gjamPriorTemplate.Rd |only man/gjamReZero.Rd | 6 man/gjamSimData.Rd | 13 man/gjamSpec2Trait.Rd | 4 man/gjamTrimY.Rd | 4 src/RcppExports.cpp | 94 src/cppFns.cpp | 106 src/init.c |only vignettes/gjamVignette.Rmd | 453 +-- 35 files changed, 5354 insertions(+), 3255 deletions(-)
Title: Chi-Square and Exact Tests for Non-Parametric Functional
Dependencies
Description: Statistical hypothesis testing methods for
non-parametric functional dependencies using asymptotic
chi-square or exact statistics. Functional chi-squares are
asymmetric and functional optimal, unique from other related
statistics. These tests reveal evidence for causality based on
the causality-by-functionality principle. They include
asymptotic functional chi-square tests, an exact functional
test, a comparative functional chi-square test, and also a
comparative chi-square test. The normalized non-constant
functional chi-square test was used by Best Performer
NMSUSongLab in HPN-DREAM (DREAM8) Breast Cancer Network
Inference Challenges. For continuous data, these tests offer an
advantage over regression analysis when a parametric functional
form cannot be assumed; for categorical data, they provide a
novel means to assess directional dependencies not possible with
symmetrical Pearson's chi-square or Fisher's exact tests.
Author: Yang Zhang [aut], Hua Zhong [aut], Ruby Sharma [aut], Sajal Kumar [aut], Joe Song [aut, cre]
Maintainer: Joe Song <joemsong@cs.nmsu.edu>
Diff between FunChisq versions 2.4.0 dated 2017-02-28 and 2.4.2 dated 2017-04-24
FunChisq-2.4.0/FunChisq/R/house_noise_model.R |only FunChisq-2.4.0/FunChisq/man/house_noise_model.Rd |only FunChisq-2.4.0/FunChisq/tests/testthat/test_HouseNoiseModel.R |only FunChisq-2.4.2/FunChisq/DESCRIPTION | 36 FunChisq-2.4.2/FunChisq/MD5 | 36 FunChisq-2.4.2/FunChisq/NAMESPACE | 2 FunChisq-2.4.2/FunChisq/NEWS | 18 FunChisq-2.4.2/FunChisq/R/noise_model.R |only FunChisq-2.4.2/FunChisq/R/simulate_tables.R | 251 ++ FunChisq-2.4.2/FunChisq/build/vignette.rds |binary FunChisq-2.4.2/FunChisq/inst/CITATION | 4 FunChisq-2.4.2/FunChisq/inst/doc/exact.fun.test.html | 6 FunChisq-2.4.2/FunChisq/inst/doc/fun.chisq.test.html | 6 FunChisq-2.4.2/FunChisq/man/FunChisq-package.Rd | 14 FunChisq-2.4.2/FunChisq/man/cp.chisq.test.Rd | 2 FunChisq-2.4.2/FunChisq/man/fun.chisq.test.Rd | 4 FunChisq-2.4.2/FunChisq/man/noise_model.Rd |only FunChisq-2.4.2/FunChisq/man/simulate_tables.Rd | 107 - FunChisq-2.4.2/FunChisq/src/ExactFunctionalTest.cpp | 10 FunChisq-2.4.2/FunChisq/tests/testthat.R | 1 FunChisq-2.4.2/FunChisq/tests/testthat/test_NoiseModel.R |only FunChisq-2.4.2/FunChisq/tests/testthat/test_simulate.R | 981 +++++----- 22 files changed, 877 insertions(+), 601 deletions(-)
Title: Discrete Global Grids for R
Description: Spatial analyses involving binning require that every bin have the same area, but this is impossible using a rectangular grid laid over the Earth or over any projection of the Earth. Discrete global grids use hexagons, triangles, and diamonds to overcome this issue, overlaying the Earth with equally-sized bins. This package provides utilities for working with discrete global grids, along with utilities to aid in plotting such data.
Author: Richard Barnes [aut, cre], Kevin Sahr [ctb], Gerald Evenden [ctb], Angus Johnson [ctb], Frank Warmerdam [ctb]
Maintainer: Richard Barnes <rbarnes@umn.edu>
Diff between dggridR versions 0.1.11 dated 2016-09-18 and 1.0.1 dated 2017-04-24
DESCRIPTION | 12 ++--- MD5 | 75 ++++++++++++++++++------------------ NAMESPACE | 13 +++--- NEWS | 25 ++++++++++++ R/dggridR.R | 77 ++++++++++++++++++++++++++++++++++--- build/vignette.rds |binary inst/doc/dggridR.R | 25 ++++++++++-- inst/doc/dggridR.Rmd | 35 +++++++++++++++- inst/doc/dggridR.html | 33 +++++++++------ man/dg_closest_res.Rd | 1 man/dg_closest_res_to_area.Rd | 1 man/dg_closest_res_to_cls.Rd | 1 man/dg_closest_res_to_spacing.Rd | 1 man/dg_env.Rd | 1 man/dg_exe_path.Rd | 1 man/dg_process_kml.Rd | 1 man/dg_shpfname_south_africa.Rd | 1 man/dg_transform_for_output.Rd |only man/dgcellstogrid.Rd | 1 man/dgconstruct.Rd | 13 +++++- man/dgearthgrid.Rd | 1 man/dggetres.Rd | 1 man/dginfo.Rd | 1 man/dgmaxcell.Rd | 1 man/dgrectgrid.Rd | 1 man/dgrun.Rd | 1 man/dgsetres.Rd | 1 man/dgshptogrid.Rd | 1 man/dgtransform.Rd | 1 man/dgverify.Rd | 1 src/Makevars | 12 ++--- src/Makevars.win | 12 ++--- src/apps/appex/Makefile | 6 +- src/apps/dggrid/Makefile | 6 +- src/lib/clipper/Makefile | 2 src/lib/dglib/lib/DgOutKMLfile.cpp | 12 ++--- src/lib/dglib/lib/Makefile | 2 src/lib/proj4lib/lib/Makefile | 2 vignettes/dggridR.Rmd | 35 +++++++++++++++- 39 files changed, 290 insertions(+), 126 deletions(-)
Title: Continuous-Time Movement Modeling
Description: Functions for identifying, fitting, and applying continuous-space, continuous-time stochastic movement models to animal tracking data.
Author: Christen H. Fleming [aut, cre],
Justin M. Calabrese [aut],
Xianghui Dong [ctb],
Kevin Winner [ctb],
Guillaume Péron [ctb],
Bart Kranstauber [ctb],
Eliezer Gurarie [ctb],
Kamran Safi [ctb],
Paul C. Cross [dtc],
Thomas Mueller [dtc]
Maintainer: Christen H. Fleming <flemingc@si.edu>
Diff between ctmm versions 0.3.5 dated 2017-02-03 and 0.3.6 dated 2017-04-24
ctmm-0.3.5/ctmm/NEWS |only ctmm-0.3.6/ctmm/DESCRIPTION | 21 ctmm-0.3.6/ctmm/MD5 | 111 - ctmm-0.3.6/ctmm/NAMESPACE | 162 +- ctmm-0.3.6/ctmm/NEWS.md |only ctmm-0.3.6/ctmm/R/1.R |only ctmm-0.3.6/ctmm/R/QP.R |only ctmm-0.3.6/ctmm/R/acf.R |only ctmm-0.3.6/ctmm/R/color.R |only ctmm-0.3.6/ctmm/R/ctmm.R | 799 +++++------ ctmm-0.3.6/ctmm/R/export.R |only ctmm-0.3.6/ctmm/R/extent.R |only ctmm-0.3.6/ctmm/R/filter.R |only ctmm-0.3.6/ctmm/R/generic.R | 889 ++++-------- ctmm-0.3.6/ctmm/R/kde.R | 1899 ++++++++++++-------------- ctmm-0.3.6/ctmm/R/krige.R | 953 ++++++------- ctmm-0.3.6/ctmm/R/likelihood.R | 2271 +++++++++++++++----------------- ctmm-0.3.6/ctmm/R/matrix.R |only ctmm-0.3.6/ctmm/R/mean.R | 962 ++++++------- ctmm-0.3.6/ctmm/R/numDeriv.R |only ctmm-0.3.6/ctmm/R/optim.R | 1454 +++++++++++++------- ctmm-0.3.6/ctmm/R/overlap.R | 629 +++++--- ctmm-0.3.6/ctmm/R/periodogram.R | 651 ++++----- ctmm-0.3.6/ctmm/R/select.R | 790 +++++------ ctmm-0.3.6/ctmm/R/telemetry.R | 1623 +++++++++++----------- ctmm-0.3.6/ctmm/R/temp_unzip.R |only ctmm-0.3.6/ctmm/R/uere.R | 84 - ctmm-0.3.6/ctmm/R/units.R |only ctmm-0.3.6/ctmm/R/variogram.R | 1961 ++++++++++++++------------- ctmm-0.3.6/ctmm/README.md | 11 ctmm-0.3.6/ctmm/TODO | 265 +-- ctmm-0.3.6/ctmm/build/vignette.rds |binary ctmm-0.3.6/ctmm/data/buffalo.rda |binary ctmm-0.3.6/ctmm/inst/doc/akde.R | 10 ctmm-0.3.6/ctmm/inst/doc/akde.Rmd | 114 - ctmm-0.3.6/ctmm/inst/doc/akde.html | 26 ctmm-0.3.6/ctmm/inst/doc/variogram.Rmd | 566 +++---- ctmm-0.3.6/ctmm/inst/doc/variogram.html | 38 ctmm-0.3.6/ctmm/man/akde.Rd | 184 +- ctmm-0.3.6/ctmm/man/as.telemetry.Rd | 144 +- ctmm-0.3.6/ctmm/man/bandwidth.Rd | 158 +- ctmm-0.3.6/ctmm/man/buffalo.Rd | 90 - ctmm-0.3.6/ctmm/man/ctmm-FAQ.Rd | 89 - ctmm-0.3.6/ctmm/man/ctmm-package.Rd | 145 +- ctmm-0.3.6/ctmm/man/ctmm.fit.Rd | 243 +-- ctmm-0.3.6/ctmm/man/export.Rd | 153 +- ctmm-0.3.6/ctmm/man/extent.Rd |only ctmm-0.3.6/ctmm/man/gazelle.Rd | 76 - ctmm-0.3.6/ctmm/man/homerange.Rd | 122 - ctmm-0.3.6/ctmm/man/mean.variogram.Rd | 110 - ctmm-0.3.6/ctmm/man/occurrence.Rd | 128 - ctmm-0.3.6/ctmm/man/overlap.Rd | 106 - ctmm-0.3.6/ctmm/man/periodogram.Rd | 164 +- ctmm-0.3.6/ctmm/man/plot.telemetry.Rd | 178 +- ctmm-0.3.6/ctmm/man/plot.variogram.Rd | 129 - ctmm-0.3.6/ctmm/man/residuals.Rd |only ctmm-0.3.6/ctmm/man/simulate.ctmm.Rd | 172 +- ctmm-0.3.6/ctmm/man/summary.UD.Rd | 132 - ctmm-0.3.6/ctmm/man/summary.ctmm.Rd | 131 - ctmm-0.3.6/ctmm/man/uere.Rd | 98 - ctmm-0.3.6/ctmm/man/variogram.Rd | 135 - ctmm-0.3.6/ctmm/man/variogram.fit.Rd | 124 - ctmm-0.3.6/ctmm/vignettes/akde.Rmd | 114 - ctmm-0.3.6/ctmm/vignettes/variogram.Rmd | 566 +++---- 64 files changed, 10151 insertions(+), 9829 deletions(-)