Title: Fast R and C++ Access to NIfTI Images
Description: Provides very fast access to images stored in the NIfTI-1 file
format <http://nifti.nimh.nih.gov/nifti-1>, with seamless synchronisation
between compiled C and interpreted R code. Not to be confused with
'RNiftyReg', which provides tools for image registration.
Author: Jon Clayden [cre, aut],
Bob Cox [aut],
Mark Jenkinson [aut],
Rick Reynolds [ctb],
Kate Fissell [ctb],
Jean-loup Gailly [cph],
Mark Adler [cph]
Maintainer: Jon Clayden <code@clayden.org>
Diff between RNifti versions 0.4.0 dated 2017-02-03 and 0.5.0 dated 2017-03-08
DESCRIPTION | 8 MD5 | 187 ++-- NEWS | 13 README.md | 10 inst/doxygen/html/_nifti_image_8h_source.html | 81 + inst/doxygen/html/annotated.html | 6 inst/doxygen/html/class_r_nifti_1_1_nifti_image-members.html | 89 + inst/doxygen/html/class_r_nifti_1_1_nifti_image.html | 453 ++++++++-- inst/doxygen/html/classes.html | 6 inst/doxygen/html/dir_2b5d1a398a9eec011391d543f21db223.html | 6 inst/doxygen/html/dir_920884c6b3b2f0be94e27d51660adee5.html | 6 inst/doxygen/html/dir_98a44f28b9ced65c076c4e168f5923c6.html | 6 inst/doxygen/html/doxygen.css | 90 + inst/doxygen/html/files.html | 6 inst/doxygen/html/functions.html | 50 - inst/doxygen/html/functions_func.html | 52 - inst/doxygen/html/functions_vars.html | 6 inst/doxygen/html/index.html | 6 inst/doxygen/html/menudata.js | 81 - inst/doxygen/html/search/all_0.html | 2 inst/doxygen/html/search/all_0.js | 3 inst/doxygen/html/search/all_1.html | 2 inst/doxygen/html/search/all_1.js | 3 inst/doxygen/html/search/all_2.html | 2 inst/doxygen/html/search/all_2.js | 4 inst/doxygen/html/search/all_3.html | 2 inst/doxygen/html/search/all_3.js | 2 inst/doxygen/html/search/all_4.html | 2 inst/doxygen/html/search/all_4.js | 9 inst/doxygen/html/search/all_5.html | 2 inst/doxygen/html/search/all_5.js | 11 inst/doxygen/html/search/all_6.html | 2 inst/doxygen/html/search/all_6.js | 6 inst/doxygen/html/search/all_7.html | 2 inst/doxygen/html/search/all_7.js | 5 inst/doxygen/html/search/all_8.html | 2 inst/doxygen/html/search/all_8.js | 4 inst/doxygen/html/search/all_9.html | 2 inst/doxygen/html/search/all_9.js | 7 inst/doxygen/html/search/all_a.html | 2 inst/doxygen/html/search/all_a.js | 8 inst/doxygen/html/search/all_b.html | 2 inst/doxygen/html/search/all_b.js | 6 inst/doxygen/html/search/all_c.html | 2 inst/doxygen/html/search/all_c.js | 3 inst/doxygen/html/search/all_d.html | 2 inst/doxygen/html/search/all_d.js | 2 inst/doxygen/html/search/all_e.html | 2 inst/doxygen/html/search/all_e.js | 2 inst/doxygen/html/search/all_f.html |only inst/doxygen/html/search/all_f.js |only inst/doxygen/html/search/classes_0.html | 2 inst/doxygen/html/search/classes_1.html | 2 inst/doxygen/html/search/functions_0.html | 2 inst/doxygen/html/search/functions_0.js | 2 inst/doxygen/html/search/functions_1.html | 2 inst/doxygen/html/search/functions_1.js | 3 inst/doxygen/html/search/functions_2.html | 2 inst/doxygen/html/search/functions_2.js | 4 inst/doxygen/html/search/functions_3.html | 2 inst/doxygen/html/search/functions_3.js | 2 inst/doxygen/html/search/functions_4.html | 2 inst/doxygen/html/search/functions_4.js | 7 inst/doxygen/html/search/functions_5.html | 2 inst/doxygen/html/search/functions_5.js | 8 inst/doxygen/html/search/functions_6.html | 2 inst/doxygen/html/search/functions_6.js | 6 inst/doxygen/html/search/functions_7.html | 2 inst/doxygen/html/search/functions_7.js | 5 inst/doxygen/html/search/functions_8.html | 2 inst/doxygen/html/search/functions_8.js | 5 inst/doxygen/html/search/functions_9.html | 2 inst/doxygen/html/search/functions_9.js | 6 inst/doxygen/html/search/functions_a.html | 2 inst/doxygen/html/search/functions_a.js | 6 inst/doxygen/html/search/functions_b.html | 2 inst/doxygen/html/search/functions_b.js | 5 inst/doxygen/html/search/functions_c.html | 2 inst/doxygen/html/search/functions_c.js | 3 inst/doxygen/html/search/functions_d.html | 2 inst/doxygen/html/search/functions_d.js | 2 inst/doxygen/html/search/functions_e.html |only inst/doxygen/html/search/functions_e.js |only inst/doxygen/html/search/functions_f.html |only inst/doxygen/html/search/functions_f.js |only inst/doxygen/html/search/pages_0.html | 2 inst/doxygen/html/search/searchdata.js | 4 inst/doxygen/html/search/variables_0.html | 2 inst/doxygen/html/search/variables_1.html | 2 inst/doxygen/html/search/variables_2.html | 2 inst/doxygen/html/struct_r_nifti_1_1_nifti_image_1_1_block-members.html | 13 inst/doxygen/html/struct_r_nifti_1_1_nifti_image_1_1_block.html | 15 inst/include/RNiftiAPI.h | 18 inst/include/lib/NiftiImage.h | 412 +++------ inst/include/lib/NiftiImage_internal.h | 231 +++-- src/main.cpp | 2 tests/testthat/test-05-nifti.R | 9 tests/testthat/test-15-foreign.R |only 98 files changed, 1343 insertions(+), 732 deletions(-)
Title: Moment and Inverse Moment Bayes Factors
Description: Model selection and parameter estimation based on non-local and Zellner priors. Bayes factors, marginal densities and variable selection in regression setups. Routines to sample, evaluate prior densities, distribution functions and quantiles are included.
Author: David Rossell, John D. Cook, Donatello Telesca, P. Roebuck
Maintainer: David Rossell <rosselldavid@gmail.com>
Diff between mombf versions 1.9.3 dated 2017-03-07 and 1.9.4 dated 2017-03-08
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- inst/doc/mombf.pdf |binary src/modelSel.cpp | 46 ++++++++++++++++++++++++++-------------------- 4 files changed, 33 insertions(+), 27 deletions(-)
Title: Time Series Missing Value Imputation
Description: Imputation (replacement) of missing values in univariate time
series.
Author: Steffen Moritz
Maintainer: Steffen Moritz <steffen.moritz10@gmail.com>
Diff between imputeTS versions 1.8 dated 2017-01-25 and 1.9 dated 2017-03-08
DESCRIPTION | 13 ++++---- MD5 | 66 +++++++++++++++++++++++++----------------- NEWS | 5 +++ R/plotNA.imputations.R | 10 +++--- README.md | 2 - build |only inst/doc |only man/imputeTS-package.Rd | 1 man/na.interpolation.Rd | 7 +--- man/na.kalman.Rd | 7 +--- man/na.locf.Rd | 7 +--- man/na.ma.Rd | 7 +--- man/na.mean.Rd | 7 +--- man/na.random.Rd | 7 +--- man/na.remove.Rd | 7 +--- man/na.replace.Rd | 7 +--- man/na.seadec.Rd | 7 +--- man/na.seasplit.Rd | 7 +--- man/plotNA.distribution.Rd | 7 +--- man/plotNA.distributionBar.Rd | 7 +--- man/plotNA.gapsize.Rd | 7 +--- man/plotNA.imputations.Rd | 7 +--- man/statsNA.Rd | 7 +--- man/tsAirgap.Rd | 1 man/tsAirgapComplete.Rd | 1 man/tsHeating.Rd | 1 man/tsHeatingComplete.Rd | 1 man/tsNH4.Rd | 1 man/tsNH4Complete.Rd | 1 vignettes |only 30 files changed, 103 insertions(+), 105 deletions(-)
Title: Colour Vision Models
Description: Colour vision models, colour spaces and colour thresholds. Includes Vorobyev & Osorio Receptor Noise Limited models, Chittka colour hexagon, and Endler & Mielke model. Models have been extended to accept any number of photoreceptor types.
Author: Felipe M. Gawryszewski
Maintainer: Felipe Malheiros Gawrysewski <f.gawry@gmail.com>
Diff between colourvision versions 0.1 dated 2016-11-10 and 1.0 dated 2017-03-08
DESCRIPTION | 13 MD5 | 43 - NAMESPACE | 7 NEWS |only R/colourvision_package.R | 1300 ++++++++++++++++++++++++++++--------------- build/partial.rdb |binary inst/CITATION | 6 man/CTTKhexagon.Rd | 24 man/CTTKhexagon3D.Rd | 50 - man/CTTKmodel.Rd | 55 + man/EMmodel.Rd | 58 - man/EMtetrahedron.Rd | 52 - man/EMtriangle.Rd | 30 man/Q.Rd | 2 man/Qr.Rd | 2 man/RNLmodel.Rd | 106 ++- man/RNLthres.Rd |only man/colour_space.Rd |only man/colourvision-package.Rd | 5 man/noise_e.Rd | 12 man/photor.Rd | 5 man/plot.colourvision.Rd |only man/plot3d.colourvision.Rd |only man/spec.denoise.Rd | 4 tests/testthat/test.models.R | 245 +++++--- 25 files changed, 1281 insertions(+), 738 deletions(-)
Title: Biodiversity Data Visualizations
Description: Provides a set of functions to create basic visualizations to quickly
preview different aspects of biodiversity information such as inventory
completeness, extent of coverage (taxonomic, temporal and geographic), gaps
and biases.
Author: Vijay Barve <vijay.barve@gmail.com>, Javier Otegui
<javier.otegui@gmail.com>
Maintainer: Vijay Barve <vijay.barve@gmail.com>
Diff between bdvis versions 0.2.9 dated 2016-11-20 and 0.2.15 dated 2017-03-08
DESCRIPTION | 10 +++---- MD5 | 36 ++++++++++++------------- NEWS | 10 +++++++ R/bdcomplete.R | 28 ++++++++++++++++--- R/mapgrid.R | 71 +++++++++++++++++++++++++++++++++++--------------- README.md | 1 man/bdcalendarheat.Rd | 1 man/bdcomplete.Rd | 16 +++++++---- man/bdsummary.Rd | 1 man/bdwebmap.Rd | 1 man/chronohorogram.Rd | 1 man/distrigraph.Rd | 1 man/fixstr.Rd | 1 man/format_bdvis.Rd | 1 man/getcellid.Rd | 1 man/gettaxo.Rd | 1 man/mapgrid.Rd | 6 ++-- man/taxotree.Rd | 1 man/tempolar.Rd | 1 19 files changed, 122 insertions(+), 67 deletions(-)
Title: Bayesian Analysis of Location-Scale Mixture Models using a
Weakly Informative Prior
Description: A generic reference Bayesian analysis of unidimensional mixture distributions obtained by a location-scale parameterisation of the model is implemented. The including functions simulate and summarize posterior samples for location-scale mixture models using a weakly informative prior. There is no need to define priors for scale-location parameters except two hyperparameters in which are associated with a Dirichlet prior for weights and a simplex.
Author: Kaniav Kamary, Kate Lee
Maintainer: Kaniav Kamary <kamary@ceremade.dauphine.fr>
Diff between Ultimixt versions 2.0 dated 2015-12-18 and 2.1 dated 2017-03-08
DESCRIPTION | 14 +++++----- MD5 | 24 ++++++++++------- NAMESPACE | 3 +- R/K.MixPois.R |only R/K.MixReparametrized.R | 2 - R/Plot.MixReparametrized.R | 4 +- R/SM.MixPois.R |only R/SM.MixReparametrized.R | 55 ++++++++++++++++------------------------ man/K.MixPois.Rd |only man/K.MixReparametrized.Rd | 10 +++---- man/Plot.MixReparametrized.Rd | 8 ++--- man/SM.MAP.MixReparametrized.Rd | 4 +- man/SM.MixPois.Rd |only man/SM.MixReparametrized.Rd | 11 +++----- man/Ultimixt-package.Rd | 23 ++++++++++------ 15 files changed, 80 insertions(+), 78 deletions(-)
Title: A Plotting Toolbox for 2D Oceanographic Data
Description: Plotting toolbox for 2D oceanographic data (satellite data, sst, chla, ocean fronts & bathymetry). Recognized classes and formats include ncdf4, Raster, '.nc' and '.gz' files.
Author: Robert K. Bauer
Maintainer: Robert K. Bauer <robert.bauer@ird.fr>
Diff between oceanmap versions 0.0.2 dated 2016-09-16 and 0.0.3 dated 2017-03-08
ChangeLog | 4 +++ DESCRIPTION | 8 +++---- MD5 | 41 ++++++++++++++++++------------------ R/figure.r | 6 ++--- R/get.bathy.r | 14 +++++++----- R/get.worldmap.r | 2 - R/hidden.r |only R/plotmap.r | 3 ++ R/regions.r | 2 - R/set.colorbar.r | 20 ++++++++++++++++- R/set.colorbarp.r | 1 R/sysdata.rda |binary data/cmap.rda |binary data/cmap_topo.rda |binary data/parameter_definitions.rda |binary data/region_definitions.bkp.rda |binary data/region_definitions.bkp_old.rda |binary data/region_definitions.rda |binary inst/doc/oceanmap.pdf |binary man/get.bathy.Rd | 2 - man/set.colorbar.Rd | 7 +++++- man/v.Rd | 2 - 22 files changed, 74 insertions(+), 38 deletions(-)
Title: Multivariate Variance Components Tests for Multilevel Data
Description: Permutation tests for variance components for 2-level, 3-level and 4-level data with univariate or multivariate responses.
Author: Denis Larocque
Maintainer: Denis Larocque <denis.larocque@hec.ca>
Diff between mvctm versions 1.0 dated 2014-05-16 and 1.1 dated 2017-03-08
DESCRIPTION | 14 ++++++++------ MD5 | 24 +++++++++++++----------- NAMESPACE | 9 +++++++++ R/mvctm.R | 13 +++++++------ R/permcluster.R |only R/testvc2level.R | 4 ++-- R/testvc3levelt1.R | 4 ++-- R/testvc3levelt2.R | 4 ++-- R/testvc4levelt1.R | 4 ++-- R/testvc4levelt2.R | 4 ++-- R/testvc4levelt3.R | 4 ++-- man/mvctm-package.Rd | 6 +++--- man/mvctm.Rd | 10 ++++------ man/permcluster.Rd |only 14 files changed, 56 insertions(+), 44 deletions(-)
Title: Germination Indexes for Seed Germination Variables for
Ecophysiological Studies
Description: Different types of seed indexes, rates and visualization techniques
are used to provide a robust approach for germination data analysis. The package
aims to make available germination seed indexes and graphical functions to
analyze germination seed data.
Author: Flavio Lozano Isla [aut, cre],
Omar Benites Alfaro [aut],
Denise Garcia de Santana [ctb],
Marli A. Ranal [ctb],
Marcelo F. Pompelli [aut, ths],
Federal University of Pernambuco [cph] (Register of application),
Federal Rural University of Pernambuco [cph] (Post Graduate Program)
Maintainer: Flavio Lozano Isla <flavjack@gmail.com>
Diff between GerminaR versions 1.0 dated 2016-12-24 and 1.1 dated 2017-03-08
GerminaR-1.0/GerminaR/R/germ_datasets.R |only GerminaR-1.0/GerminaR/data/GerminaR.rda |only GerminaR-1.0/GerminaR/inst/GerminaQuant/myapp |only GerminaR-1.0/GerminaR/man/GerminaR.Rd |only GerminaR-1.0/GerminaR/man/runGerminaQuant.Rd |only GerminaR-1.1/GerminaR/DESCRIPTION | 46 - GerminaR-1.1/GerminaR/MD5 | 97 +-- GerminaR-1.1/GerminaR/NAMESPACE | 23 GerminaR-1.1/GerminaR/R/datasets.R |only GerminaR-1.1/GerminaR/R/indexes.R | 47 - GerminaR-1.1/GerminaR/R/plot.R | 545 ++++++++++++++--- GerminaR-1.1/GerminaR/R/processing.R | 27 GerminaR-1.1/GerminaR/R/runApp.R | 4 GerminaR-1.1/GerminaR/R/utils.R | 116 ++- GerminaR-1.1/GerminaR/README.md | 2 GerminaR-1.1/GerminaR/data/prosopis.rda |only GerminaR-1.1/GerminaR/inst/GerminaQuant/gb.html |only GerminaR-1.1/GerminaR/inst/GerminaQuant/rsconnect |only GerminaR-1.1/GerminaR/inst/GerminaQuant/server.R |only GerminaR-1.1/GerminaR/inst/GerminaQuant/ui.R |only GerminaR-1.1/GerminaR/inst/GerminaQuant/www |only GerminaR-1.1/GerminaR/inst/doc/GerminaR.R | 72 +- GerminaR-1.1/GerminaR/inst/doc/GerminaR.Rmd | 98 +-- GerminaR-1.1/GerminaR/inst/doc/GerminaR.html | 705 +++++++++++----------- GerminaR-1.1/GerminaR/man/GerminaQuant.Rd |only GerminaR-1.1/GerminaR/man/evalDays.Rd | 4 GerminaR-1.1/GerminaR/man/evalFactor.Rd | 4 GerminaR-1.1/GerminaR/man/fplot.Rd | 14 GerminaR-1.1/GerminaR/man/ger_ASG.Rd | 6 GerminaR-1.1/GerminaR/man/ger_CVG.Rd | 4 GerminaR-1.1/GerminaR/man/ger_GRP.Rd | 4 GerminaR-1.1/GerminaR/man/ger_GRS.Rd | 4 GerminaR-1.1/GerminaR/man/ger_GSP.Rd | 4 GerminaR-1.1/GerminaR/man/ger_MGR.Rd | 4 GerminaR-1.1/GerminaR/man/ger_MGT.Rd | 4 GerminaR-1.1/GerminaR/man/ger_SDG.Rd | 4 GerminaR-1.1/GerminaR/man/ger_SYN.Rd | 4 GerminaR-1.1/GerminaR/man/ger_UNC.Rd | 4 GerminaR-1.1/GerminaR/man/ger_VGT.Rd | 4 GerminaR-1.1/GerminaR/man/ger_boxp.Rd |only GerminaR-1.1/GerminaR/man/ger_cumsum.Rd | 6 GerminaR-1.1/GerminaR/man/ger_getdata.Rd |only GerminaR-1.1/GerminaR/man/ger_intime.Rd | 8 GerminaR-1.1/GerminaR/man/ger_leq.Rd |only GerminaR-1.1/GerminaR/man/ger_linereg.Rd |only GerminaR-1.1/GerminaR/man/ger_summary.Rd | 4 GerminaR-1.1/GerminaR/man/ger_testcomp.Rd |only GerminaR-1.1/GerminaR/man/prosopis.Rd |only GerminaR-1.1/GerminaR/vignettes/GerminaR.Rmd | 98 +-- GerminaR-1.1/GerminaR/vignettes/GerminaR_files |only 50 files changed, 1283 insertions(+), 683 deletions(-)
Title: White Matter Normalization for Magnetic Resonance Images using
Whitestripe
Description: Shinohara et. al (2014) <DOI:10.1016/j.nicl.2014.08.008>
introduced Whitestripe, an intensity-based normalization of T1
and T2 images, where normal
appearing white matter performs well, but requires segmentation.
This method performs white matter mean and standard deviation
estimates on data that has been rigidly-registered to the MNI
template and uses histogram-based methods.
Author: R. Taki Shinohara, John Muschelli
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between WhiteStripe versions 1.1.1 dated 2015-05-21 and 2.2.2 dated 2017-03-08
WhiteStripe-1.1.1/WhiteStripe/README.md |only WhiteStripe-2.2.2/WhiteStripe/DESCRIPTION | 29 - WhiteStripe-2.2.2/WhiteStripe/MD5 | 49 +- WhiteStripe-2.2.2/WhiteStripe/NAMESPACE | 7 WhiteStripe-2.2.2/WhiteStripe/R/download_img_data.R | 47 +- WhiteStripe-2.2.2/WhiteStripe/R/get.largest.mode.R | 12 WhiteStripe-2.2.2/WhiteStripe/R/whitestripe_ind.R | 230 +++++------ WhiteStripe-2.2.2/WhiteStripe/build |only WhiteStripe-2.2.2/WhiteStripe/inst/CITATION | 48 +- WhiteStripe-2.2.2/WhiteStripe/inst/doc |only WhiteStripe-2.2.2/WhiteStripe/man/download_img_data.Rd | 9 WhiteStripe-2.2.2/WhiteStripe/man/get.deriv.smooth.hist.Rd | 5 WhiteStripe-2.2.2/WhiteStripe/man/get.first.mode.Rd | 4 WhiteStripe-2.2.2/WhiteStripe/man/get.largest.mode.Rd | 3 WhiteStripe-2.2.2/WhiteStripe/man/get.last.mode.Rd | 4 WhiteStripe-2.2.2/WhiteStripe/man/make_img_voi.Rd | 3 WhiteStripe-2.2.2/WhiteStripe/man/s.hist.Rd | 5 WhiteStripe-2.2.2/WhiteStripe/man/smooth_hist.Rd | 7 WhiteStripe-2.2.2/WhiteStripe/man/t1.voi.hist.Rd | 11 WhiteStripe-2.2.2/WhiteStripe/man/t2.voi.hist.Rd | 15 WhiteStripe-2.2.2/WhiteStripe/man/whitestripe.Rd | 18 WhiteStripe-2.2.2/WhiteStripe/man/whitestripe_hybrid.Rd | 5 WhiteStripe-2.2.2/WhiteStripe/man/whitestripe_ind_to_mask.Rd | 5 WhiteStripe-2.2.2/WhiteStripe/man/whitestripe_norm.Rd | 3 WhiteStripe-2.2.2/WhiteStripe/man/ws_img_data.Rd |only WhiteStripe-2.2.2/WhiteStripe/man/xvals.Rd | 3 WhiteStripe-2.2.2/WhiteStripe/vignettes |only 27 files changed, 296 insertions(+), 226 deletions(-)
Title: 3D Visualization Using OpenGL
Description: Provides medium to high level functions for 3D interactive graphics, including
functions modelled on base graphics (plot3d(), etc.) as well as functions for
constructing representations of geometric objects (cube3d(), etc.). Output
may be on screen using OpenGL, or to various standard 3D file formats including
WebGL, PLY, OBJ, STL as well as 2D image formats, including PNG, Postscript, SVG, PGF.
Author: Daniel Adler <dadler@uni-goettingen.de>, Duncan Murdoch <murdoch@stats.uwo.ca>, and others (see README)
Maintainer: Duncan Murdoch <murdoch@stats.uwo.ca>
Diff between rgl versions 0.97.0 dated 2017-01-10 and 0.98.1 dated 2017-03-08
DESCRIPTION | 9 MD5 | 75 NAMESPACE | 9 R/Sweave_knitr.R | 9 R/persp3d.R | 16 R/playwidget.R | 87 R/rglcontroller.R | 46 R/rglwidget.R | 2 R/subscenes.R | 2 README | 3 build/vignette.rds |binary configure | 167 configure.ac | 11 configure.win | 13 inst/NEWS | 19 inst/doc/WebGL.R | 204 inst/doc/WebGL.Rmd | 506 - inst/doc/WebGL.html | 4215 ----------- inst/doc/legacyWebGL.R |only inst/doc/legacyWebGL.Rmd |only inst/doc/legacyWebGL.html |only inst/doc/rgl.R | 156 inst/doc/rgl.Rmd | 1 inst/doc/rgl.html | 9494 +++++++++++++------------- inst/htmlwidgets/lib/rglClass/rglClass.src.js | 118 inst/htmlwidgets/rglPlayer.js | 4 inst/htmlwidgets/rglWebGL.js | 15 inst/initNotes.txt |only man/figWidth.Rd |only man/par3dinterpControl.Rd |only man/persp3d.deldir.Rd | 13 man/persp3d.function.Rd | 8 man/playwidget.Rd | 13 man/rglwidget.Rd | 6 man/toggleWidget.Rd |only man/webGLcontrols.Rd | 6 po |only src/Makevars.in | 7 src/init.cpp | 2 vignettes/WebGL.Rmd | 506 - vignettes/legacyWebGL.Rmd |only vignettes/rgl.Rmd | 1 vignettes/setup.R | 2 43 files changed, 6065 insertions(+), 9680 deletions(-)
Title: Robust Data-Driven Statistical Inference in
Regression-Discontinuity Designs
Description: Regression-discontinuity (RD) designs are quasi-experimental research designs popular in social, behavioral and natural sciences. The RD design is usually employed to study the (local) causal effect of a treatment, intervention or policy. This package provides tools for data-driven graphical and analytical statistical inference in RD designs: rdrobust() to construct local-polynomial point estimators and robust confidence intervals for average treatment effects at the cutoff in Sharp, Fuzzy and Kink RD settings, rdbwselect() to perform bandwidth selection for the different procedures implemented, and rdplot() to conduct exploratory data analysis (RD plots).
Author: Sebastian Calonico <scalonico@bus.miami.edu>, Matias D. Cattaneo <cattaneo@umich.edu>, Max H. Farrell <max.farrell@chicagobooth.edu>, Rocio Titiunik <titiunik@umich.edu>
Maintainer: Sebastian Calonico <scalonico@bus.miami.edu>
Diff between rdrobust versions 0.95 dated 2016-12-13 and 0.96 dated 2017-03-08
DESCRIPTION | 10 +-- MD5 | 18 +++--- R/functions.R | 1 R/rdbwselect.R | 82 ++++++++++++++----------------- R/rdplot.R | 126 ++++++++++++++++++++++++++---------------------- R/rdrobust.R | 28 ++++++++-- man/rdbwselect.Rd | 57 ++++++++++----------- man/rdplot.Rd | 46 +++++++++-------- man/rdrobust-package.Rd | 4 - man/rdrobust.Rd | 80 +++++++++++++++++------------- 10 files changed, 245 insertions(+), 207 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2013-09-10 0.8-10
2013-03-21 0.8-8
Title: Sequential Parameter Optimization Toolbox
Description: A set of tools for model based optimization and tuning of
algorithms. It includes surrogate models, optimizers and design of experiment
approaches. The main interface is spot, which uses sequentially updated
surrogate models for the purpose of efficient optimization. The main goal is
to ease the burden of objective function evaluations, when a single evaluation
requires a significant amount of resources.
Author: Thomas Bartz-Beielstein [aut],
Joerg Stork [aut],
Martin Zaefferer [aut, cre],
Margarita Rebolledo [ctb],
Christian Lasarczyk [ctb],
Joerg Ziegenhirt [ctb],
Wolfgang Konen [ctb],
Oliver Flasch [ctb],
Patrick Koch [ctb],
Martina Friese [ctb]
Maintainer: Martin Zaefferer <martin.zaefferer@gmx.de>
Diff between SPOT versions 1.1.0 dated 2016-06-13 and 2.0.1 dated 2017-03-08
SPOT-1.1.0/SPOT/R/sms_emoa.r |only SPOT-1.1.0/SPOT/R/spotAlgStartEs.R |only SPOT-1.1.0/SPOT/R/spotAlgStartEsGlg.R |only SPOT-1.1.0/SPOT/R/spotAlgStartRgp.R |only SPOT-1.1.0/SPOT/R/spotAlgStartSann.R |only SPOT-1.1.0/SPOT/R/spotAlgStartSmsEmoaGlg.R |only SPOT-1.1.0/SPOT/R/spotCreateDesignBasicDoe.R |only SPOT-1.1.0/SPOT/R/spotCreateDesignFactors.R |only SPOT-1.1.0/SPOT/R/spotCreateDesignFrF2.R |only SPOT-1.1.0/SPOT/R/spotCreateDesignLhd.R |only SPOT-1.1.0/SPOT/R/spotCreateDesignLhs.R |only SPOT-1.1.0/SPOT/R/spotCreateDesignLhsOpt.R |only SPOT-1.1.0/SPOT/R/spotEnsembleFunctions.R |only SPOT-1.1.0/SPOT/R/spotEnsembleSingleBLAbern.R |only SPOT-1.1.0/SPOT/R/spotEnsembleSingleBLAnorm.R |only SPOT-1.1.0/SPOT/R/spotEnsembleSingleEpsGreedy.R |only SPOT-1.1.0/SPOT/R/spotEnsembleSinglePOKER.R |only SPOT-1.1.0/SPOT/R/spotEnsembleSingleRoundSearch.R |only SPOT-1.1.0/SPOT/R/spotEnsembleSingleSoftMax.R |only SPOT-1.1.0/SPOT/R/spotEnsembleSingleUCB1.R |only SPOT-1.1.0/SPOT/R/spotExpectedImprovement.R |only SPOT-1.1.0/SPOT/R/spotFuncStartBranin.R |only SPOT-1.1.0/SPOT/R/spotFuncStartMexicanHat.R |only SPOT-1.1.0/SPOT/R/spotFuncStartRastrigin.R |only SPOT-1.1.0/SPOT/R/spotFuncStartRosenbrock.R |only SPOT-1.1.0/SPOT/R/spotFuncStartSixHump.R |only SPOT-1.1.0/SPOT/R/spotFuncStartSphere.R |only SPOT-1.1.0/SPOT/R/spotFuncTools.R |only SPOT-1.1.0/SPOT/R/spotGaussianLandscapeGenerator.R |only SPOT-1.1.0/SPOT/R/spotGenerateSequentialDesign.R |only SPOT-1.1.0/SPOT/R/spotGetOptions.R |only SPOT-1.1.0/SPOT/R/spotGui.R |only SPOT-1.1.0/SPOT/R/spotHelpFunctions.R |only SPOT-1.1.0/SPOT/R/spotMcoSort.R |only SPOT-1.1.0/SPOT/R/spotMeta.R |only SPOT-1.1.0/SPOT/R/spotModelOptim.R |only SPOT-1.1.0/SPOT/R/spotModelParetoOptim.R |only SPOT-1.1.0/SPOT/R/spotModelSelection.R |only SPOT-1.1.0/SPOT/R/spotOcba.R |only SPOT-1.1.0/SPOT/R/spotOptim.R |only SPOT-1.1.0/SPOT/R/spotOptimEs.R |only SPOT-1.1.0/SPOT/R/spotOptimizationFunctions.R |only SPOT-1.1.0/SPOT/R/spotPlot.R |only SPOT-1.1.0/SPOT/R/spotPredictCoForrester.R |only SPOT-1.1.0/SPOT/R/spotPredictDace.R |only SPOT-1.1.0/SPOT/R/spotPredictDice.R |only SPOT-1.1.0/SPOT/R/spotPredictEarth.R |only SPOT-1.1.0/SPOT/R/spotPredictEnsembleMultiAlternate.R |only SPOT-1.1.0/SPOT/R/spotPredictEnsembleMultiAverage.R |only SPOT-1.1.0/SPOT/R/spotPredictEnsembleMultiChoose.R |only SPOT-1.1.0/SPOT/R/spotPredictEnsembleMultiRank.R |only SPOT-1.1.0/SPOT/R/spotPredictEnsembleMultiRankWeighted.R |only SPOT-1.1.0/SPOT/R/spotPredictEsvm.R |only SPOT-1.1.0/SPOT/R/spotPredictForrester.R |only SPOT-1.1.0/SPOT/R/spotPredictGausspr.R |only SPOT-1.1.0/SPOT/R/spotPredictHelpFunctions.R |only SPOT-1.1.0/SPOT/R/spotPredictKrig.R |only SPOT-1.1.0/SPOT/R/spotPredictKsvm.R |only SPOT-1.1.0/SPOT/R/spotPredictLm.R |only SPOT-1.1.0/SPOT/R/spotPredictLmFactor.R |only SPOT-1.1.0/SPOT/R/spotPredictMCO.R |only SPOT-1.1.0/SPOT/R/spotPredictMLP.R |only SPOT-1.1.0/SPOT/R/spotPredictMlegp.R |only SPOT-1.1.0/SPOT/R/spotPredictNeuralnet.R |only SPOT-1.1.0/SPOT/R/spotPredictQrnn.R |only SPOT-1.1.0/SPOT/R/spotPredictRandomForest.R |only SPOT-1.1.0/SPOT/R/spotPredictRandomForestMlegp.R |only SPOT-1.1.0/SPOT/R/spotPredictTest.R |only SPOT-1.1.0/SPOT/R/spotPredictTgp.R |only SPOT-1.1.0/SPOT/R/spotPredictTree.R |only SPOT-1.1.0/SPOT/R/spotPrepareData.R |only SPOT-1.1.0/SPOT/R/spotRepairMissingValues.R |only SPOT-1.1.0/SPOT/R/spotRepeats.R |only SPOT-1.1.0/SPOT/R/spotReport3d.R |only SPOT-1.1.0/SPOT/R/spotReportContour.R |only SPOT-1.1.0/SPOT/R/spotReportDefault.R |only SPOT-1.1.0/SPOT/R/spotReportEarth.R |only SPOT-1.1.0/SPOT/R/spotReportMAMP.R |only SPOT-1.1.0/SPOT/R/spotReportMetaDefault.R |only SPOT-1.1.0/SPOT/R/spotReportSAMP.R |only SPOT-1.1.0/SPOT/R/spotReportSens.R |only SPOT-1.1.0/SPOT/R/spotSeqDesignIncreaseFunctions.R |only SPOT-1.1.0/SPOT/R/spotStatistics.R |only SPOT-1.1.0/SPOT/R/spotSurf.R |only SPOT-1.1.0/SPOT/R/spotTargetFunctions.R |only SPOT-1.1.0/SPOT/demo |only SPOT-1.1.0/SPOT/inst/GUI |only SPOT-1.1.0/SPOT/inst/demo01TreeBranin |only SPOT-1.1.0/SPOT/inst/demo02RandomForestBranin |only SPOT-1.1.0/SPOT/inst/demo03LmBranin |only SPOT-1.1.0/SPOT/inst/demo04MlegpBranin |only SPOT-1.1.0/SPOT/inst/demo05TgpBranin |only SPOT-1.1.0/SPOT/inst/demo06TreeSann |only SPOT-1.1.0/SPOT/inst/demo07RandomForestSann |only SPOT-1.1.0/SPOT/inst/demo08LmSann |only SPOT-1.1.0/SPOT/inst/demo09MlegpSann |only SPOT-1.1.0/SPOT/inst/demo10TgpSann |only SPOT-1.1.0/SPOT/inst/demo11Java |only SPOT-1.1.0/SPOT/inst/demo12Sann |only SPOT-1.1.0/SPOT/inst/demo13RandomForestMlegpSann |only SPOT-1.1.0/SPOT/inst/demo14LmOptimSann |only SPOT-1.1.0/SPOT/inst/demo16EsBranin |only SPOT-1.1.0/SPOT/inst/demo17Rgp |only SPOT-1.1.0/SPOT/inst/demo23RgpKtfg |only SPOT-1.1.0/SPOT/inst/demoMixedModelAnalysis |only SPOT-1.1.0/SPOT/inst/doc |only SPOT-1.1.0/SPOT/java |only SPOT-1.1.0/SPOT/man/Testfunctions.Rd |only SPOT-1.1.0/SPOT/man/daceBuilder.Rd |only SPOT-1.1.0/SPOT/man/dacePredictor.Rd |only SPOT-1.1.0/SPOT/man/forrBuilder.Rd |only SPOT-1.1.0/SPOT/man/forrCoBuilder.Rd |only SPOT-1.1.0/SPOT/man/forrCoLikelihood.Rd |only SPOT-1.1.0/SPOT/man/forrCoModel.Rd |only SPOT-1.1.0/SPOT/man/forrCoRegPredictor.Rd |only SPOT-1.1.0/SPOT/man/forrIF.Rd |only SPOT-1.1.0/SPOT/man/forrRegLikelihood.Rd |only SPOT-1.1.0/SPOT/man/forrRegPredictor.Rd |only SPOT-1.1.0/SPOT/man/forrReintPredictor.Rd |only SPOT-1.1.0/SPOT/man/predict.forr.Rd |only SPOT-1.1.0/SPOT/man/spotAlgEs.Rd |only SPOT-1.1.0/SPOT/man/spotAlgEsDominantReco.Rd |only SPOT-1.1.0/SPOT/man/spotAlgEsGetSuccessRate.Rd |only SPOT-1.1.0/SPOT/man/spotAlgEsHps.Rd |only SPOT-1.1.0/SPOT/man/spotAlgEsIndividualInitial.Rd |only SPOT-1.1.0/SPOT/man/spotAlgEsInitParentPop.Rd |only SPOT-1.1.0/SPOT/man/spotAlgEsInterReco.Rd |only SPOT-1.1.0/SPOT/man/spotAlgEsInterRecoBeSw02.Rd |only SPOT-1.1.0/SPOT/man/spotAlgEsMarriage.Rd |only SPOT-1.1.0/SPOT/man/spotAlgEsMarriageWithReplace.Rd |only SPOT-1.1.0/SPOT/man/spotAlgEsObjMutation.Rd |only SPOT-1.1.0/SPOT/man/spotAlgEsQuickTest.Rd |only SPOT-1.1.0/SPOT/man/spotAlgEsSelection.Rd |only SPOT-1.1.0/SPOT/man/spotAlgEsStratMutation.Rd |only SPOT-1.1.0/SPOT/man/spotAlgEsTermination.Rd |only SPOT-1.1.0/SPOT/man/spotAlgStartEs.Rd |only SPOT-1.1.0/SPOT/man/spotAlgStartEsGlg.Rd |only SPOT-1.1.0/SPOT/man/spotAlgStartEsVar.Rd |only SPOT-1.1.0/SPOT/man/spotAlgStartRgp.Rd |only SPOT-1.1.0/SPOT/man/spotAlgStartSann.Rd |only SPOT-1.1.0/SPOT/man/spotAlgStartSannVar.Rd |only SPOT-1.1.0/SPOT/man/spotAlgStartSmsEmoaGlg.Rd |only SPOT-1.1.0/SPOT/man/spotCalcNoise.Rd |only SPOT-1.1.0/SPOT/man/spotCallCoFunction.Rd |only SPOT-1.1.0/SPOT/man/spotCodeFormulas.Rd |only SPOT-1.1.0/SPOT/man/spotCreateDesignBasicDoe.Rd |only SPOT-1.1.0/SPOT/man/spotCreateDesignFactors.Rd |only SPOT-1.1.0/SPOT/man/spotCreateDesignFrF2.Rd |only SPOT-1.1.0/SPOT/man/spotCreateDesignLhd.Rd |only SPOT-1.1.0/SPOT/man/spotCreateDesignLhs.Rd |only SPOT-1.1.0/SPOT/man/spotCreateDesignLhsOpt.Rd |only SPOT-1.1.0/SPOT/man/spotEnsembleMinimum.Rd |only SPOT-1.1.0/SPOT/man/spotEnsembleModelBuilding.Rd |only SPOT-1.1.0/SPOT/man/spotEnsembleModelEvaluate.Rd |only SPOT-1.1.0/SPOT/man/spotEnsembleMultiAlternate.Rd |only SPOT-1.1.0/SPOT/man/spotEnsembleMultiAverage.Rd |only SPOT-1.1.0/SPOT/man/spotEnsembleMultiChoose.Rd |only SPOT-1.1.0/SPOT/man/spotEnsembleMultiRank.Rd |only SPOT-1.1.0/SPOT/man/spotEnsembleMultiRankWeighted.Rd |only SPOT-1.1.0/SPOT/man/spotEnsembleSingleBLAbern.Rd |only SPOT-1.1.0/SPOT/man/spotEnsembleSingleBLAnorm.Rd |only SPOT-1.1.0/SPOT/man/spotEnsembleSingleEpsGreedy.Rd |only SPOT-1.1.0/SPOT/man/spotEnsembleSinglePOKER.Rd |only SPOT-1.1.0/SPOT/man/spotEnsembleSingleRoundSearch.Rd |only SPOT-1.1.0/SPOT/man/spotEnsembleSingleSoftMax.Rd |only SPOT-1.1.0/SPOT/man/spotEnsembleSingleUCB1.Rd |only SPOT-1.1.0/SPOT/man/spotEnsembleStatsMin.Rd |only SPOT-1.1.0/SPOT/man/spotEnsembleStatsSd.Rd |only SPOT-1.1.0/SPOT/man/spotEnsembleSubdesigns.Rd |only SPOT-1.1.0/SPOT/man/spotEnsembleSummedRank.Rd |only SPOT-1.1.0/SPOT/man/spotEnsembleSummedRankWeighted.Rd |only SPOT-1.1.0/SPOT/man/spotExiPsi.Rd |only SPOT-1.1.0/SPOT/man/spotFeedback.Rd |only SPOT-1.1.0/SPOT/man/spotForceFactorDesign.Rd |only SPOT-1.1.0/SPOT/man/spotForceFactorX.Rd |only SPOT-1.1.0/SPOT/man/spotFuncStartBranin.Rd |only SPOT-1.1.0/SPOT/man/spotFuncStartDisBranin.Rd |only SPOT-1.1.0/SPOT/man/spotFuncStartMexicanHat.Rd |only SPOT-1.1.0/SPOT/man/spotFuncStartRastrigin.Rd |only SPOT-1.1.0/SPOT/man/spotFuncStartRosenbrock.Rd |only SPOT-1.1.0/SPOT/man/spotFuncStartSixHump.Rd |only SPOT-1.1.0/SPOT/man/spotFuncStartSphere.Rd |only SPOT-1.1.0/SPOT/man/spotGenerateSequentialDesign.Rd |only SPOT-1.1.0/SPOT/man/spotGetAllRepeats.Rd |only SPOT-1.1.0/SPOT/man/spotGetMergedDataMatrixB.Rd |only SPOT-1.1.0/SPOT/man/spotGetOptions.Rd |only SPOT-1.1.0/SPOT/man/spotGetRawDataMatrixB.Rd |only SPOT-1.1.0/SPOT/man/spotGetRawResData.Rd |only SPOT-1.1.0/SPOT/man/spotGetRepeats.Rd |only SPOT-1.1.0/SPOT/man/spotGlgCore.Rd |only SPOT-1.1.0/SPOT/man/spotGlgCreate.Rd |only SPOT-1.1.0/SPOT/man/spotGlgCreateN.Rd |only SPOT-1.1.0/SPOT/man/spotGlgCreateRot.Rd |only SPOT-1.1.0/SPOT/man/spotGlgCreateRotSearched.Rd |only SPOT-1.1.0/SPOT/man/spotGlgEval.Rd |only SPOT-1.1.0/SPOT/man/spotGlgEvalN.Rd |only SPOT-1.1.0/SPOT/man/spotGlgEvalRot.Rd |only SPOT-1.1.0/SPOT/man/spotGlgInit.Rd |only SPOT-1.1.0/SPOT/man/spotGlgInitN.Rd |only SPOT-1.1.0/SPOT/man/spotGui.Rd |only SPOT-1.1.0/SPOT/man/spotHlpF.norm.Rd |only SPOT-1.1.0/SPOT/man/spotHlpF.norminv.Rd |only SPOT-1.1.0/SPOT/man/spotInfillExpImp.Rd |only SPOT-1.1.0/SPOT/man/spotInfillHyperVolume.Rd |only SPOT-1.1.0/SPOT/man/spotInfillLcbHyperVolume.Rd |only SPOT-1.1.0/SPOT/man/spotInfillLcbMulti.Rd |only SPOT-1.1.0/SPOT/man/spotInfillLcbSingle.Rd |only SPOT-1.1.0/SPOT/man/spotInfillProbImp.Rd |only SPOT-1.1.0/SPOT/man/spotInfillSD.Rd |only SPOT-1.1.0/SPOT/man/spotInfillSExI2d.Rd |only SPOT-1.1.0/SPOT/man/spotInitializePredictor.Rd |only SPOT-1.1.0/SPOT/man/spotInstAndLoadPackages.Rd |only SPOT-1.1.0/SPOT/man/spotInvChisq.Rd |only SPOT-1.1.0/SPOT/man/spotMcoCrowdTournament.Rd |only SPOT-1.1.0/SPOT/man/spotMcoSelectionHypervol.Rd |only SPOT-1.1.0/SPOT/man/spotMcoSort.Rd |only SPOT-1.1.0/SPOT/man/spotMcoTournament.Rd |only SPOT-1.1.0/SPOT/man/spotMetaFlattenFbsRow.Rd |only SPOT-1.1.0/SPOT/man/spotModel.func.Rd |only SPOT-1.1.0/SPOT/man/spotModel.predict.Rd |only SPOT-1.1.0/SPOT/man/spotModel.train.Rd |only SPOT-1.1.0/SPOT/man/spotModelDescentLm.Rd |only SPOT-1.1.0/SPOT/man/spotModelOptim.Rd |only SPOT-1.1.0/SPOT/man/spotModelParetoOptim.Rd |only SPOT-1.1.0/SPOT/man/spotNormDesign.Rd |only SPOT-1.1.0/SPOT/man/spotNormalizeMatrix.Rd |only SPOT-1.1.0/SPOT/man/spotNormalizeMatrix2.Rd |only SPOT-1.1.0/SPOT/man/spotOcba.Rd |only SPOT-1.1.0/SPOT/man/spotOptim.Rd |only SPOT-1.1.0/SPOT/man/spotOptimEs.Rd |only SPOT-1.1.0/SPOT/man/spotOptimInterface.Rd |only SPOT-1.1.0/SPOT/man/spotOptimLHS.Rd |only SPOT-1.1.0/SPOT/man/spotOptimizationInterface.Rd |only SPOT-1.1.0/SPOT/man/spotOptimizationInterfaceMco.Rd |only SPOT-1.1.0/SPOT/man/spotParetoOptMulti.Rd |only SPOT-1.1.0/SPOT/man/spotPenalizeMissingValues.Rd |only SPOT-1.1.0/SPOT/man/spotPlotBst.Rd |only SPOT-1.1.0/SPOT/man/spotPredictCoForrester.Rd |only SPOT-1.1.0/SPOT/man/spotPredictDace.Rd |only SPOT-1.1.0/SPOT/man/spotPredictDice.Rd |only SPOT-1.1.0/SPOT/man/spotPredictEarth.Rd |only SPOT-1.1.0/SPOT/man/spotPredictEsvm.Rd |only SPOT-1.1.0/SPOT/man/spotPredictForrester.Rd |only SPOT-1.1.0/SPOT/man/spotPredictGausspr.Rd |only SPOT-1.1.0/SPOT/man/spotPredictKrig.Rd |only SPOT-1.1.0/SPOT/man/spotPredictKsvm.Rd |only SPOT-1.1.0/SPOT/man/spotPredictLm.Rd |only SPOT-1.1.0/SPOT/man/spotPredictLmFactor.Rd |only SPOT-1.1.0/SPOT/man/spotPredictMCO.Rd |only SPOT-1.1.0/SPOT/man/spotPredictMLP.Rd |only SPOT-1.1.0/SPOT/man/spotPredictMlegp.Rd |only SPOT-1.1.0/SPOT/man/spotPredictNeuralnet.Rd |only SPOT-1.1.0/SPOT/man/spotPredictOptMulti.Rd |only SPOT-1.1.0/SPOT/man/spotPredictQrnn.Rd |only SPOT-1.1.0/SPOT/man/spotPredictRandomForest.Rd |only SPOT-1.1.0/SPOT/man/spotPredictRandomForestMlegp.Rd |only SPOT-1.1.0/SPOT/man/spotPredictTest.Rd |only SPOT-1.1.0/SPOT/man/spotPredictTgp.Rd |only SPOT-1.1.0/SPOT/man/spotPredictTree.Rd |only SPOT-1.1.0/SPOT/man/spotPrepare.Rd |only SPOT-1.1.0/SPOT/man/spotPrepareData.Rd |only SPOT-1.1.0/SPOT/man/spotPrepareDataAsMatrixC.Rd |only SPOT-1.1.0/SPOT/man/spotPrepareResult.Rd |only SPOT-1.1.0/SPOT/man/spotPrint.Rd |only SPOT-1.1.0/SPOT/man/spotROI.Rd |only SPOT-1.1.0/SPOT/man/spotReadBstFile.Rd |only SPOT-1.1.0/SPOT/man/spotReadRoi.Rd |only SPOT-1.1.0/SPOT/man/spotRepairMissingValues.Rd |only SPOT-1.1.0/SPOT/man/spotRepairMissingValuesCoKriging.Rd |only SPOT-1.1.0/SPOT/man/spotRepeats.Rd |only SPOT-1.1.0/SPOT/man/spotRepeatsOcba.Rd |only SPOT-1.1.0/SPOT/man/spotReport3d.Rd |only SPOT-1.1.0/SPOT/man/spotReport3dMulti.Rd |only SPOT-1.1.0/SPOT/man/spotReportContour.Rd |only SPOT-1.1.0/SPOT/man/spotReportContourMulti.Rd |only SPOT-1.1.0/SPOT/man/spotReportDefault.Rd |only SPOT-1.1.0/SPOT/man/spotReportEarth.Rd |only SPOT-1.1.0/SPOT/man/spotReportMAMP.Rd |only SPOT-1.1.0/SPOT/man/spotReportMetaDefault.Rd |only SPOT-1.1.0/SPOT/man/spotReportSAMP.Rd |only SPOT-1.1.0/SPOT/man/spotReportSens.Rd |only SPOT-1.1.0/SPOT/man/spotReportSensY.Rd |only SPOT-1.1.0/SPOT/man/spotReverseNormalizeMatrix.Rd |only SPOT-1.1.0/SPOT/man/spotRgpTargetFunction.Rd |only SPOT-1.1.0/SPOT/man/spotSExI2d.Rd |only SPOT-1.1.0/SPOT/man/spotSelectionCriteria.Rd |only SPOT-1.1.0/SPOT/man/spotSeqDesignIncreaseMultTwo.Rd |only SPOT-1.1.0/SPOT/man/spotSeqDesignIncreasePlusOne.Rd |only SPOT-1.1.0/SPOT/man/spotSmsEmoa.Rd |only SPOT-1.1.0/SPOT/man/spotSmsEmoaKriging.Rd |only SPOT-1.1.0/SPOT/man/spotStepAutoOpt.Rd |only SPOT-1.1.0/SPOT/man/spotStepInitial.Rd |only SPOT-1.1.0/SPOT/man/spotStepMetaOpt.Rd |only SPOT-1.1.0/SPOT/man/spotStepReport.Rd |only SPOT-1.1.0/SPOT/man/spotStepRunAlg.Rd |only SPOT-1.1.0/SPOT/man/spotStepSequential.Rd |only SPOT-1.1.0/SPOT/man/spotSurf3d.Rd |only SPOT-1.1.0/SPOT/man/spotSurfContour.Rd |only SPOT-1.1.0/SPOT/man/spotVersion.Rd |only SPOT-1.1.0/SPOT/man/spotWriteAroi.Rd |only SPOT-1.1.0/SPOT/man/spotWriteBest.Rd |only SPOT-1.1.0/SPOT/man/spotWriteDes.Rd |only SPOT-1.1.0/SPOT/man/spotWriteLines.Rd |only SPOT-1.1.0/SPOT/man/spotWriteRes.Rd |only SPOT-1.1.0/SPOT/man/spotWriteRoiFileForRepeats.Rd |only SPOT-1.1.0/SPOT/vignettes |only SPOT-2.0.1/SPOT/.Rinstignore | 1 SPOT-2.0.1/SPOT/DESCRIPTION | 56 SPOT-2.0.1/SPOT/MD5 | 522 +------- SPOT-2.0.1/SPOT/NAMESPACE | 220 --- SPOT-2.0.1/SPOT/NEWS | 17 SPOT-2.0.1/SPOT/R/buildEnsembleStack.R |only SPOT-2.0.1/SPOT/R/buildKrigingDACE.R |only SPOT-2.0.1/SPOT/R/buildKrigingForrester.R |only SPOT-2.0.1/SPOT/R/buildLM.R |only SPOT-2.0.1/SPOT/R/buildRandomForest.R |only SPOT-2.0.1/SPOT/R/buildSO.R |only SPOT-2.0.1/SPOT/R/cyclone.R |only SPOT-2.0.1/SPOT/R/dataGasSensor.R |only SPOT-2.0.1/SPOT/R/designLHD.R |only SPOT-2.0.1/SPOT/R/designUniformRandom.R |only SPOT-2.0.1/SPOT/R/duplicateHandling.R |only SPOT-2.0.1/SPOT/R/evaluate.R |only SPOT-2.0.1/SPOT/R/infill.R |only SPOT-2.0.1/SPOT/R/objectiveFunctionEvaluation.R |only SPOT-2.0.1/SPOT/R/optimLBFGSB.R |only SPOT-2.0.1/SPOT/R/optimLHD.R |only SPOT-2.0.1/SPOT/R/package.R |only SPOT-2.0.1/SPOT/R/repair.R |only SPOT-2.0.1/SPOT/R/repeatsOCBA.R |only SPOT-2.0.1/SPOT/R/sphere.R |only SPOT-2.0.1/SPOT/R/spot.R | 933 +++------------ SPOT-2.0.1/SPOT/data |only SPOT-2.0.1/SPOT/inst/CITATION | 30 SPOT-2.0.1/SPOT/man/OCBA.Rd |only SPOT-2.0.1/SPOT/man/SPOT-package.Rd | 55 SPOT-2.0.1/SPOT/man/buildEnsembleStack.Rd |only SPOT-2.0.1/SPOT/man/buildKriging.Rd |only SPOT-2.0.1/SPOT/man/buildKrigingDACE.Rd |only SPOT-2.0.1/SPOT/man/buildLM.Rd |only SPOT-2.0.1/SPOT/man/buildRandomForest.Rd |only SPOT-2.0.1/SPOT/man/buildSO.Rd |only SPOT-2.0.1/SPOT/man/calculationBarthMuschelknautz.Rd |only SPOT-2.0.1/SPOT/man/corrcubic.Rd | 9 SPOT-2.0.1/SPOT/man/correxp.Rd | 9 SPOT-2.0.1/SPOT/man/correxpg.Rd | 9 SPOT-2.0.1/SPOT/man/corrgauss.Rd | 9 SPOT-2.0.1/SPOT/man/corrkriging.Rd | 9 SPOT-2.0.1/SPOT/man/corrlin.Rd | 9 SPOT-2.0.1/SPOT/man/corrnoisygauss.Rd | 9 SPOT-2.0.1/SPOT/man/corrnoisykriging.Rd | 9 SPOT-2.0.1/SPOT/man/corrspherical.Rd | 9 SPOT-2.0.1/SPOT/man/corrspline.Rd | 9 SPOT-2.0.1/SPOT/man/daceEvalFit.Rd | 5 SPOT-2.0.1/SPOT/man/daceFixTheta.Rd | 7 SPOT-2.0.1/SPOT/man/daceGetFit.Rd | 9 SPOT-2.0.1/SPOT/man/daceLikelihood.Rd | 5 SPOT-2.0.1/SPOT/man/daceObjfunc.Rd | 9 SPOT-2.0.1/SPOT/man/dacePrepareFit.Rd | 9 SPOT-2.0.1/SPOT/man/daceStartParameters.Rd | 7 SPOT-2.0.1/SPOT/man/dataGasSensor.Rd |only SPOT-2.0.1/SPOT/man/designLHD.Rd |only SPOT-2.0.1/SPOT/man/designLHDNorm.Rd |only SPOT-2.0.1/SPOT/man/designUniformRandom.Rd |only SPOT-2.0.1/SPOT/man/duplicateAndReplicateHandling.Rd |only SPOT-2.0.1/SPOT/man/evaluateModel.Rd |only SPOT-2.0.1/SPOT/man/expectedImprovement.Rd |only SPOT-2.0.1/SPOT/man/funCyclone.Rd |only SPOT-2.0.1/SPOT/man/funSphere.Rd |only SPOT-2.0.1/SPOT/man/krigingLikelihood.Rd |only SPOT-2.0.1/SPOT/man/normalizeMatrix.Rd |only SPOT-2.0.1/SPOT/man/normalizeMatrix2.Rd |only SPOT-2.0.1/SPOT/man/objectiveFunctionEvaluation.Rd |only SPOT-2.0.1/SPOT/man/optimLBFGSB.Rd |only SPOT-2.0.1/SPOT/man/optimLHD.Rd |only SPOT-2.0.1/SPOT/man/predict.dace.Rd |only SPOT-2.0.1/SPOT/man/predict.ensembleStack.Rd |only SPOT-2.0.1/SPOT/man/predict.kriging.Rd |only SPOT-2.0.1/SPOT/man/predict.spotLinearModel.Rd |only SPOT-2.0.1/SPOT/man/predict.spotRandomForest.Rd |only SPOT-2.0.1/SPOT/man/predict.spotSecondOrderModel.Rd |only SPOT-2.0.1/SPOT/man/predictKrigingReinterpolation.Rd |only SPOT-2.0.1/SPOT/man/print.Rd | 28 SPOT-2.0.1/SPOT/man/print.spotLinearModel.Rd |only SPOT-2.0.1/SPOT/man/print.spotRandomForest.Rd |only SPOT-2.0.1/SPOT/man/print.spotSecondOrderModel.Rd |only SPOT-2.0.1/SPOT/man/regpoly0.Rd | 9 SPOT-2.0.1/SPOT/man/regpoly1.Rd | 9 SPOT-2.0.1/SPOT/man/regpoly2.Rd | 9 SPOT-2.0.1/SPOT/man/repairNonNumeric.Rd |only SPOT-2.0.1/SPOT/man/repeatsOCBA.Rd |only SPOT-2.0.1/SPOT/man/repmat.Rd | 3 SPOT-2.0.1/SPOT/man/spot.Rd | 178 ++ SPOT-2.0.1/SPOT/man/spotHelpBslash.Rd | 3 SPOT-2.0.1/SPOT/tests |only 395 files changed, 678 insertions(+), 1536 deletions(-)
Title: Perform Spatial Error Estimation and Variable Importance in
Parallel
Description: Implements spatial error estimation and
permutation-based variable importance measures for predictive models using
spatial cross-validation and spatial block bootstrap.
Author: Alexander Brenning [aut, cre],
Patrick Schratz [aut],
Tobias Herrmann [aut]
Maintainer: Alexander Brenning <alexander.brenning@uni-jena.de>
Diff between sperrorest versions 0.2-1 dated 2012-06-20 and 1.0.0 dated 2017-03-08
sperrorest-0.2-1/sperrorest/data/ecuador.RData |only sperrorest-1.0.0/sperrorest/DESCRIPTION | 52 sperrorest-1.0.0/sperrorest/MD5 | 105 sperrorest-1.0.0/sperrorest/NAMESPACE | 130 sperrorest-1.0.0/sperrorest/NEWS |only sperrorest-1.0.0/sperrorest/NEWS.md |only sperrorest-1.0.0/sperrorest/R/parsperrorest.R |only sperrorest-1.0.0/sperrorest/R/resample.R |only sperrorest-1.0.0/sperrorest/R/sperrorest-package.R | 52 sperrorest-1.0.0/sperrorest/R/sperrorest.R | 1623 ++++---- sperrorest-1.0.0/sperrorest/R/sperrorest_data.R | 80 sperrorest-1.0.0/sperrorest/R/sperrorest_error.R | 276 - sperrorest-1.0.0/sperrorest/R/sperrorest_misc.R | 1149 +++-- sperrorest-1.0.0/sperrorest/R/sperrorest_resampling.R | 1989 ++++++---- sperrorest-1.0.0/sperrorest/README.md |only sperrorest-1.0.0/sperrorest/build |only sperrorest-1.0.0/sperrorest/data/ecuador.rda |only sperrorest-1.0.0/sperrorest/data/maipo.rda |only sperrorest-1.0.0/sperrorest/inst/doc |only sperrorest-1.0.0/sperrorest/inst/figure |only sperrorest-1.0.0/sperrorest/inst/testfiles |only sperrorest-1.0.0/sperrorest/man/add.distance.Rd | 122 sperrorest-1.0.0/sperrorest/man/as.represampling.Rd | 132 sperrorest-1.0.0/sperrorest/man/as.resampling.Rd | 210 - sperrorest-1.0.0/sperrorest/man/as.tilename.Rd | 97 sperrorest-1.0.0/sperrorest/man/dataset.distance.Rd | 102 sperrorest-1.0.0/sperrorest/man/ecuador.Rd | 77 sperrorest-1.0.0/sperrorest/man/err.default.Rd | 106 sperrorest-1.0.0/sperrorest/man/figures |only sperrorest-1.0.0/sperrorest/man/get.small.tiles.Rd | 95 sperrorest-1.0.0/sperrorest/man/maipo.Rd |only sperrorest-1.0.0/sperrorest/man/parsperrorest.Rd |only sperrorest-1.0.0/sperrorest/man/partition.cv.Rd | 146 sperrorest-1.0.0/sperrorest/man/partition.cv.strat.Rd | 139 sperrorest-1.0.0/sperrorest/man/partition.disc.Rd | 190 sperrorest-1.0.0/sperrorest/man/partition.factor.Rd | 121 sperrorest-1.0.0/sperrorest/man/partition.factor.cv.Rd |only sperrorest-1.0.0/sperrorest/man/partition.kmeans.Rd | 172 sperrorest-1.0.0/sperrorest/man/partition.tiles.Rd | 271 - sperrorest-1.0.0/sperrorest/man/plot.represampling.Rd | 107 sperrorest-1.0.0/sperrorest/man/represampling.bootstrap.Rd | 109 sperrorest-1.0.0/sperrorest/man/represampling.disc.bootstrap.Rd | 137 sperrorest-1.0.0/sperrorest/man/represampling.factor.bootstrap.Rd | 159 sperrorest-1.0.0/sperrorest/man/represampling.kmeans.bootstrap.Rd | 86 sperrorest-1.0.0/sperrorest/man/represampling.tile.bootstrap.Rd | 82 sperrorest-1.0.0/sperrorest/man/resample.factor.Rd |only sperrorest-1.0.0/sperrorest/man/resample.strat.uniform.Rd | 88 sperrorest-1.0.0/sperrorest/man/resample.uniform.Rd | 77 sperrorest-1.0.0/sperrorest/man/sperrorest-package.Rd | 69 sperrorest-1.0.0/sperrorest/man/sperrorest.Rd | 461 +- sperrorest-1.0.0/sperrorest/man/summary.represampling.Rd | 49 sperrorest-1.0.0/sperrorest/man/summary.sperrorest.Rd | 103 sperrorest-1.0.0/sperrorest/man/summary.sperrorestbenchmarks.Rd |only sperrorest-1.0.0/sperrorest/man/summary.sperroresterror.Rd | 120 sperrorest-1.0.0/sperrorest/man/summary.sperrorestimportance.Rd | 66 sperrorest-1.0.0/sperrorest/man/summary.sperrorestpackageversion.Rd |only sperrorest-1.0.0/sperrorest/man/tile.neighbors.Rd | 55 sperrorest-1.0.0/sperrorest/tests |only sperrorest-1.0.0/sperrorest/vignettes |only 59 files changed, 4979 insertions(+), 4225 deletions(-)
Title: Clustering Mutations using High Throughput Sequencing (HTS) Data
Description: Using HTS data, clusters mutations in order to recreate putative
clones from the data provided. It requires genotype at the location of the
variant as well as the depth of coverage and number of reads supporting the
mutation. Additional information may be provided, such as the contamination
in the tumor sample. This package also provides a function QuantumCat() which
simulates data obtained from tumor sequencing.
Author: Paul Deveau [aut, cre]
Maintainer: Paul Deveau <paul.deveau@curie.fr>
Diff between QuantumClone versions 1.0.0.3 dated 2017-03-02 and 1.0.0.4 dated 2017-03-08
DESCRIPTION | 8 - MD5 | 126 +++++++++++++++---------------- inst/doc/Release.Rmd | 19 +++- inst/doc/Release.html | 15 ++- inst/doc/Use_case.R | 4 inst/doc/Use_case.Rmd | 10 +- inst/doc/Use_case.html | 16 +-- man/BIC_criterion.Rd | 1 man/BIC_criterion_FLASH.Rd | 1 man/Cellular_preclustering.Rd | 1 man/CellularitiesFromFreq.Rd | 1 man/Cluster_plot_from_cell.Rd | 1 man/Compute_NMI.Rd | 1 man/Compute_objective.Rd | 1 man/Create_prior_cutTree.Rd | 1 man/EM.algo.Rd | 1 man/EM_clustering.Rd | 1 man/FLASH_main.Rd | 1 man/FlashQC.Rd | 1 man/From_freq_to_cell.Rd | 1 man/FullEM.Rd | 1 man/Input_Example.Rd | 1 man/MajorityVote.Rd | 1 man/NMI_cutree.Rd | 1 man/One_D_plot.Rd | 1 man/One_step_clustering.Rd | 1 man/Patient_schrodinger_cellularities.Rd | 1 man/Precision_Recall.Rd | 1 man/ProbDistMatrix.Rd | 1 man/Probability.to.belong.to.clone.Rd | 1 man/QC_output.Rd | 1 man/QuantumCat.Rd | 1 man/QuantumClone.Rd | 1 man/Tidy_output.Rd | 1 man/Tree.Rd | 1 man/Tree_generation.Rd | 1 man/add_leaf_list.Rd | 1 man/check_leaf.Rd | 1 man/check_split.Rd | 1 man/create_priors.Rd | 1 man/e.step.Rd | 1 man/eval.fik.m.Rd | 1 man/evolution_plot.Rd | 1 man/filter_on_fik.Rd | 1 man/find_x_position.Rd | 1 man/grbase.Rd | 1 man/grzero.Rd | 1 man/hard.clustering.Rd | 1 man/is_included.Rd | 1 man/list_prod.Rd | 1 man/longueur.Rd | 1 man/m.step.Rd | 1 man/manual_plot_trees.Rd | 1 man/multiplot_trees.Rd | 1 man/parallelEM.Rd | 1 man/phylo_tree_generation.Rd | 1 man/plot_QC_out.Rd | 1 man/plot_cell_from_Return_out.Rd | 1 man/plot_with_margins_densities.Rd | 1 man/strcount.Rd | 1 man/update_probs.Rd | 1 man/zscore.Rd | 1 vignettes/Release.Rmd | 19 +++- vignettes/Use_case.Rmd | 10 +- 64 files changed, 132 insertions(+), 150 deletions(-)
Title: Analyzing Combination of Proportions and Relative Risk
Description: Carrying out inferences about any linear combination of proportions and the ratio of two proportions.
Author: Maria Alvarez and Javier Roca-Pardinas
Maintainer: Maria Alvarez <maria.alvarez@uvigo.es>
Diff between prop.comb.RR versions 1.1 dated 2015-09-18 and 1.2 dated 2017-03-08
DESCRIPTION | 10 +- MD5 | 28 +++---- R/FindLambda.MA.R | 5 - R/FindZ.MA.R | 12 +-- R/coverageRR.R |only R/coveragecomb.R |only R/prop.RR.R | 95 ++++++++++++++---------- R/prop.comb.R | 171 ++++++++++++++++++++++++++------------------ R/score.MA.R | 8 +- R/summary.prop.RR.R | 14 ++- R/summary.prop.comb.R | 28 +++---- man/prop.RR.Rd | 11 +- man/prop.comb.RR-package.Rd | 2 man/prop.comb.Rd | 11 ++ man/summary.prop.RR.Rd | 2 man/summary.prop.comb.Rd | 2 16 files changed, 234 insertions(+), 165 deletions(-)
Title: Client for the 'Pangaea' Database
Description: Tools to interact with the 'Pangaea' Database
(<https://www.pangaea.de>), including functions for searching for data,
fetching 'datasets' by 'dataset' 'ID', and working with the 'Pangaea'
'OAI-PMH' service.
Author: Scott Chamberlain [aut, cre],
Kara Woo [aut],
Andrew MacDonald [aut],
Naupaka Zimmerman [aut],
Gavin Simpson [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between pangaear versions 0.2.4 dated 2016-10-07 and 0.3.0 dated 2017-03-08
DESCRIPTION | 21 +-- LICENSE | 2 MD5 | 58 ++++---- NAMESPACE | 4 NEWS.md | 23 +++ R/pangaear-package.R | 12 + R/pg_cache.R | 7 - R/pg_data.R | 26 ++- R/pg_get_record.R | 24 ++- R/pg_identify.R | 8 - R/pg_list_identifiers.R | 28 ++-- R/pg_list_metadata_formats.R | 5 R/pg_list_records.R | 15 +- R/pg_list_sets.R | 16 +- R/pg_search.R | 33 +++- R/pg_search_es.R |only R/zzz.R | 42 +++--- README.md | 245 ++++++++++++++++++++++-------------- man/pangaear-package.Rd | 11 + man/pg_data.Rd | 14 -- man/pg_get_record.Rd | 28 ++-- man/pg_identify.Rd | 12 + man/pg_list_identifiers.Rd | 39 ++++- man/pg_list_metadata_formats.Rd | 12 + man/pg_list_records.Rd | 21 ++- man/pg_list_sets.Rd | 24 ++- man/pg_search.Rd | 41 ++++-- man/pg_search_es.Rd |only tests/testthat/test-oai_functions.R | 18 +- tests/testthat/test-pg_identify.R |only tests/testthat/test-pg_search.r | 26 +++ tests/testthat/test-pg_search_es.R |only 32 files changed, 540 insertions(+), 275 deletions(-)
Title: L-Moments, Censored L-Moments, Trimmed L-Moments, L-Comoments,
and Many Distributions
Description: Extensive functions for L-moments (LMs) and probability-weighted moments
(PWMs), parameter estimation for distributions, LM computation for distributions, and
L-moment ratio diagrams. Maximum likelihood and maximum product of spacings estimation
are also available. LMs for right-tail and left-tail censoring by known or unknown
threshold and by indicator variable are available. Asymmetric (asy) trimmed LMs
(TL-moments, TLMs) are supported. LMs of residual (resid) and reversed (rev) resid life
are implemented along with 13 quantile function operators for reliability and survival
analyses. Exact analytical bootstrap estimates of order statistics, LMs, and variances-
covariances of LMs are provided. The Harri-Coble Tau34-squared Normality Test is available.
Distribution support with "L" (LMs), "TL" (TLMs) and added (+) support for right-tail
censoring (RC) encompasses: Asy Exponential (Exp) Power [L], Asy Triangular [L],
Cauchy [TL], Eta-Mu [L], Exp. [L], Gamma [L], Generalized (Gen) Exp Poisson [L],
Gen Extreme Value [L], Gen Lambda [L,TL], Gen Logistic [L), Gen Normal [L],
Gen Pareto [L+RC, TL], Govindarajulu [L], Gumbel [L], Kappa [L], Kappa-Mu [L],
Kumaraswamy [L], Laplace [L], Linear Mean Resid. Quantile Function [L], Normal [L],
3-p log-Normal [L], Pearson Type III [L], Rayleigh [L], Rev-Gumbel [L+RC], Rice/Rician [L],
Slash [TL], 3-p Student t [L], Truncated Exponential [L], Wakeby [L], and Weibull [L].
Multivariate sample L-comoments (LCMs) are implemented to measure asymmetric associations.
Author: William Asquith
Maintainer: William Asquith <william.asquith@ttu.edu>
Diff between lmomco versions 2.2.6 dated 2017-03-06 and 2.2.7 dated 2017-03-08
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS | 7 +++++++ R/are.lmom.valid.R | 6 +++--- 4 files changed, 16 insertions(+), 9 deletions(-)
Title: Process Control and Internal Validation of Forensic STR Kits
Description: An open source platform for validation and process control.
Tools to analyse data from internal validation of forensic short tandem
repeat (STR) kits are provided. The tools are developed to provide
the necessary data to conform with guidelines for internal validation
issued by the European Network of Forensic Science Institutes (ENFSI)
DNA Working Group, and the Scientific Working Group on DNA Analysis Methods
(SWGDAM). A front-end graphical user interface is provided.
More information about each function can be found in the
respective help documentation.
Author: Oskar Hansson
Maintainer: Oskar Hansson <oskhan@ous-hf.no>
Diff between strvalidator versions 1.8.0 dated 2016-10-03 and 1.9.0 dated 2017-03-08
DESCRIPTION | 12 - MD5 | 304 ++++++++++++++++++++-------------------- NAMESPACE | 1 NEWS | 28 +++ R/addColor.r | 4 R/addData.r | 6 R/addDye_gui.r | 106 ++++++++++++- R/addOrder.r |only R/calculateAT6.r | 7 R/calculateDropout.r | 4 R/calculateLb_gui.r | 2 R/columns_gui.r | 2 R/combine_gui.r | 17 +- R/cropData_gui.r | 62 ++++++-- R/modelDropout_gui.r | 34 ++-- R/plotDistribution_gui.r | 127 ++++++++++++---- R/plotDropout_gui.r | 4 R/plotPrecision_gui.r | 5 R/plotStutter_gui.r | 34 +++- R/strvalidator-package.r | 6 R/strvalidator.r | 10 + man/addColor.Rd | 3 man/addData.Rd | 1 man/addData_gui.Rd | 1 man/addDye_gui.Rd | 12 + man/addMarker.Rd | 1 man/addMarker_gui.Rd | 1 man/addOrder.Rd |only man/addSize.Rd | 1 man/addSize_gui.Rd | 1 man/calculateAT.Rd | 1 man/calculateAT6.Rd | 2 man/calculateAT6_gui.Rd | 1 man/calculateAT_gui.Rd | 1 man/calculateAllele.Rd | 1 man/calculateAllele_gui.Rd | 1 man/calculateCapillary.Rd | 1 man/calculateCapillary_gui.Rd | 1 man/calculateConcordance.Rd | 1 man/calculateConcordance_gui.Rd | 1 man/calculateCopies.Rd | 1 man/calculateCopies_gui.Rd | 1 man/calculateDropout.Rd | 3 man/calculateDropout_gui.Rd | 1 man/calculateHb.Rd | 1 man/calculateHb_gui.Rd | 1 man/calculateHeight.Rd | 1 man/calculateHeight_gui.Rd | 1 man/calculateLb.Rd | 1 man/calculateLb_gui.Rd | 1 man/calculateMixture.Rd | 1 man/calculateMixture_gui.Rd | 1 man/calculateOL.Rd | 1 man/calculateOL_gui.Rd | 1 man/calculateOverlap.Rd | 1 man/calculateOverlap_gui.Rd | 1 man/calculatePeaks.Rd | 1 man/calculatePeaks_gui.Rd | 1 man/calculatePullup.Rd | 1 man/calculatePullup_gui.Rd | 1 man/calculateRatio.Rd | 1 man/calculateRatio_gui.Rd | 1 man/calculateResultType.Rd | 1 man/calculateResultType_gui.Rd | 1 man/calculateSlope.Rd | 1 man/calculateSlope_gui.Rd | 1 man/calculateSpike.Rd | 1 man/calculateSpike_gui.Rd | 1 man/calculateStutter.Rd | 1 man/calculateStutter_gui.Rd | 1 man/checkDataset.Rd | 1 man/checkSubset.Rd | 1 man/checkSubset_gui.Rd | 1 man/colConvert.Rd | 1 man/colNames.Rd | 1 man/columns.Rd | 1 man/columns_gui.Rd | 1 man/combineBinsAndPanels.Rd | 1 man/combine_gui.Rd | 7 man/cropData_gui.Rd | 1 man/detectKit.Rd | 1 man/editData_gui.Rd | 1 man/export.Rd | 1 man/export_gui.Rd | 1 man/filterProfile.Rd | 1 man/filterProfile_gui.Rd | 1 man/generateEPG.Rd | 1 man/generateEPG_gui.Rd | 1 man/getDb.Rd | 1 man/getKit.Rd | 1 man/ggsave_gui.Rd | 1 man/guessProfile.Rd | 1 man/guessProfile_gui.Rd | 1 man/heightToPeak.Rd | 1 man/import.Rd | 1 man/import_gui.Rd | 1 man/listObjects.Rd | 1 man/makeKit_gui.Rd | 1 man/maskAT.Rd | 1 man/modelDropout_gui.Rd | 30 ++- man/plotAT_gui.Rd | 1 man/plotBalance_gui.Rd | 1 man/plotCapillary_gui.Rd | 1 man/plotContamination_gui.Rd | 1 man/plotDistribution_gui.Rd | 4 man/plotDropout_gui.Rd | 1 man/plotKit_gui.Rd | 1 man/plotPeaks_gui.Rd | 1 man/plotPrecision_gui.Rd | 1 man/plotPullup_gui.Rd | 1 man/plotRatio_gui.Rd | 1 man/plotResultType_gui.Rd | 1 man/plotSlope_gui.Rd | 1 man/plotStutter_gui.Rd | 1 man/readBinsFile.Rd | 1 man/readPanelsFile.Rd | 1 man/ref1.Rd | 1 man/ref11.Rd | 1 man/ref2.Rd | 1 man/ref3.Rd | 1 man/ref4.Rd | 1 man/ref51.Rd | 1 man/ref52.Rd | 1 man/ref61.Rd | 1 man/ref62.Rd | 1 man/ref7.Rd | 1 man/removeArtefact.Rd | 1 man/removeArtefact_gui.Rd | 1 man/removeSpike.Rd | 1 man/removeSpike_gui.Rd | 1 man/saveObject.Rd | 1 man/scrambleAlleles.Rd | 1 man/set1.Rd | 1 man/set2.Rd | 1 man/set3.Rd | 1 man/set4.Rd | 1 man/set5.Rd | 1 man/set6.Rd | 1 man/set7.Rd | 1 man/slim.Rd | 1 man/slim_gui.Rd | 1 man/sortMarker.Rd | 1 man/strvalidator-package.Rd | 9 - man/strvalidator.Rd | 1 man/tableBalance.Rd | 1 man/tableBalance_gui.Rd | 1 man/tableCapillary.Rd | 1 man/tableCapillary_gui.Rd | 1 man/tablePrecision.Rd | 1 man/tablePrecision_gui.Rd | 1 man/tableStutter.Rd | 1 man/tableStutter_gui.Rd | 1 man/trim.Rd | 1 man/trim_gui.Rd | 1 154 files changed, 548 insertions(+), 421 deletions(-)
Title: R/Package Version Check
Description: Check latest release version of R and R package (both in 'CRAN', 'Bioconductor' or 'Github').
Author: Guangchuang Yu [aut, cre]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between rvcheck versions 0.0.5 dated 2016-09-20 and 0.0.8 dated 2017-03-08
DESCRIPTION | 10 +++++----- MD5 | 10 ++++++---- NAMESPACE | 2 +- NEWS | 6 +++++- R/update_all.R | 6 ++++-- R/utilities.R |only man/get_fun_from_pkg.Rd |only 7 files changed, 21 insertions(+), 13 deletions(-)
Title: Multivariate Multinomial Distribution Approximation and
Imputation for Incomplete Data
Description: Fit incomplete categorical data with infinite mixture of multinomial distribution
(Dunson and Xing (2009) <DOI:10.1198/jasa.2009.tm08439>). Perform efficient missing data imputation and
other statistical inference based on joint distribution estimation.
Author: Chaojie Wang
Maintainer: Chaojie Wang <wang910930@163.com>
Diff between MMDai versions 1.0.1 dated 2017-02-24 and 1.1.0 dated 2017-03-08
MMDai-1.0.1/MMDai/R/Example.R |only MMDai-1.0.1/MMDai/data/Example.rda |only MMDai-1.0.1/MMDai/man/Example.Rd |only MMDai-1.1.0/MMDai/DESCRIPTION | 6 +++--- MMDai-1.1.0/MMDai/MD5 | 20 +++++++++++++------- MMDai-1.1.0/MMDai/NAMESPACE | 3 +++ MMDai-1.1.0/MMDai/R/DBhattacharyya.R |only MMDai-1.1.0/MMDai/R/FisherTest.R |only MMDai-1.1.0/MMDai/R/JointTable.R | 6 +++--- MMDai-1.1.0/MMDai/R/MovieRate.R |only MMDai-1.1.0/MMDai/R/SampleJointTable.R |only MMDai-1.1.0/MMDai/data/MovieRate.rda |only MMDai-1.1.0/MMDai/man/DBhattacharyya.Rd |only MMDai-1.1.0/MMDai/man/FisherTest.Rd |only MMDai-1.1.0/MMDai/man/JointTable.Rd | 4 ++-- MMDai-1.1.0/MMDai/man/MovieRate.Rd |only MMDai-1.1.0/MMDai/man/SampleJointTable.Rd |only 17 files changed, 24 insertions(+), 15 deletions(-)
Title: B Cell Receptor Somatic Hyper Mutation Analysis
Description: Includes a set of functions to analyze for instance nucleotide frequencies as well as transition and transversion. Can reconstruct germline sequences based on the international ImMunoGeneTics information system (IMGT/HighV-QUEST) outputs, calculate and plot the difference (%) of nucleotides at 6 positions around a mutation to identify and characterize hotspot motifs as well as calculate and plot average mutation frequencies of nucleotide mutations resulting in amino acid substitution.
Author: Olena Ohlei <olena.ohlei@student.uni-luebeck.de>
Maintainer: Olena Ohlei <olena.ohlei@student.uni-luebeck.de>
Diff between BCellMA versions 0.3.2 dated 2016-11-29 and 0.3.4 dated 2017-03-08
DESCRIPTION | 8 ++--- MD5 | 62 ++++++++++++++++++++++++------------------- NAMESPACE | 3 ++ R/aa_plot.R | 9 +++--- R/data.R | 21 ++++++++++++++ R/gene_comb_funk.R |only R/gene_comb_plot.R |only R/germlineReconstr.R | 2 - R/lengthCDR3.R |only R/targetingMatrix.R | 4 +- R/targeting_motiv.R | 16 +++++------ R/targeting_motive_plot.R | 2 - build/vignette.rds |binary data/IMGTtab1.rda |only data/datalist | 1 inst/doc/vignette.R | 21 +++++++++++++- inst/doc/vignette.Rmd | 28 ++++++++++++++++++- inst/doc/vignette.html | 57 ++++++++++++++++++++++++++++++--------- man/IMGTtab1.Rd |only man/IMGTtab2.Rd | 1 man/IMGTtab7.Rd | 1 man/IMGTtab8.Rd | 1 man/Klassen.Rd | 1 man/aa_cdr3_dist.Rd | 1 man/aa_dist.Rd | 1 man/aa_plot.Rd | 1 man/gene_comb_funk.Rd |only man/gene_comb_plot.Rd |only man/germlineReconstr.Rd | 1 man/lengthCDR3.Rd |only man/na_funktion.Rd | 1 man/nucleotide_mutation.Rd | 1 man/targetingMatrix.Rd | 1 man/targeting_motiv.Rd | 1 man/targeting_motive_plot.Rd | 1 vignettes/vignette.Rmd | 28 ++++++++++++++++++- 36 files changed, 196 insertions(+), 79 deletions(-)
Title: Compiling the NHL Real Time Scoring System Database for easy use
in R
Description: Compiling the NHL Real Time Scoring System Database for easy use in R.
Author: A.C. Thomas, Samuel L. Ventura
Maintainer: ORPHANED
Diff between nhlscrapr versions 1.8 dated 2014-10-21 and 1.8.1 dated 2017-03-08
DESCRIPTION | 13 ++++++++----- MD5 | 4 ++-- R/integrate.R | 1 + 3 files changed, 11 insertions(+), 7 deletions(-)
Title: Temporal Sensory Data Analysis
Description: Analysis and visualization of data from temporal sensory methods, including for temporal check-all-that-apply (TCATA) and temporal dominance of sensations (TDS).
Author: J. C. Castura [aut, cre]
Maintainer: J. C. Castura <jcastura@compusense.com>
Diff between tempR versions 0.9.9.9 dated 2016-12-21 and 0.9.9.10 dated 2017-03-08
DESCRIPTION | 8 +- MD5 | 36 ++++++------- R/tcata.R | 91 ++++++++++++++++++++++++++-------- R/tds.R | 14 ++--- man/get.chance.Rd | 2 man/get.decluttered.Rd | 2 man/get.differences.Rd | 2 man/get.dominance.rates.Rd | 2 man/get.mat.diff.sign.Rd | 2 man/get.significance.Rd | 2 man/get.significance.diff.Rd | 2 man/get.smooth.Rd | 2 man/plot_pca.trajectories.Rd | 2 man/similarity.tcata.repeatability.Rd | 2 man/similarity.tcata.replication.Rd | 2 man/tcata.diff.plot.Rd | 16 ++++- man/tcata.line.plot.Rd | 2 man/tds.diff.plot.Rd | 2 man/tds.plot.Rd | 2 19 files changed, 126 insertions(+), 67 deletions(-)
Title: Spatio-Temporal Median Polish
Description: Analyses spatio-temporal data, decomposing data in n-dimensional arrays and using the median polish technique.
Author: William MartÃnez [aut, cre], Melo Carlos [aut], Melo Oscar [aut].
Maintainer: William MartÃnez <willimarti2008@gmail.com>
Diff between STMedianPolish versions 0.1 dated 2015-06-21 and 0.2 dated 2017-03-08
DESCRIPTION | 21 +++--- MD5 | 52 ++++++++------- NAMESPACE | 22 ++++++ R/ConstructMPst.R | 89 ++++++++++++++------------- R/MedianPolishM.ConstructMPst.R | 5 - R/MedianPolishM.R | 8 +- R/MedianPolishM.default.R | 41 ++++++------ R/Mpplot.R | 25 ++++--- R/krige0STlocalMP.R |only R/plot.MedianPolishM.R | 4 - R/print.plot.MedianPolishM.R | 10 +-- R/removetrendMPst.R | 121 ++++++++++++++++++++++--------------- R/splineMPST.R | 44 +++++++------ data/HZRMeta.rda |binary data/Metadb.rda |binary data/VRes.rda |only man/ConstructMPst.Rd | 29 ++++---- man/DemMeta.Rd | 6 - man/HZRMeta.Rd | 1 man/MedianPolishM.ConstructMPst.Rd | 9 +- man/MedianPolishM.Rd | 11 +-- man/MedianPolishM.default.Rd | 9 +- man/Metabd.Rd | 2 man/Mpplot.Rd | 11 ++- man/VRes.Rd |only man/krige0STlocalMP.Rd |only man/plot.MedianPolishM.Rd | 7 +- man/removetrendMPst.Rd | 37 ++++++----- man/splineMPST.Rd | 29 ++++---- 29 files changed, 343 insertions(+), 250 deletions(-)
More information about STMedianPolish at CRAN
Permanent link
Title: Software for Analyzing Limiting Dilution Assays
Description: Calculates maximum likelihood estimate, exact and asymptotic confidence intervals, and exact and asymptotic goodness of fit p-values for infectious units per million (IUPM) from serial limiting dilution assays. This package uses the likelihood equation, exact PGOF, and exact confidence intervals described in Meyers et al. (1994) <http://jcm.asm.org/content/32/3/732.full.pdf>. This software is also implemented as a web application through the Shiny R package <https://iupm.shinyapps.io/sldassay/>.
Author: Michael Hudgens, Ilana Trumble, Andrew Allmon
Maintainer: Ilana Trumble <itrumble@unc.edu>
Diff between SLDAssay versions 1.5 dated 2016-07-19 and 1.6 dated 2017-03-08
DESCRIPTION | 12 ++++++------ MD5 | 6 +++--- R/IUPM.R | 19 ++++++++++--------- man/get.iupm.Rd | 14 +++++++------- 4 files changed, 26 insertions(+), 25 deletions(-)
Title: Correlation and Regression Analyses for Randomized Response Data
Description: Univariate and multivariate methods to analyze randomized response (RR) survey designs (e.g., Warner, S. L. (1965). Randomized response: A survey technique for eliminating evasive answer bias. Journal of the American Statistical Association, 60, 63–69). <doi:10.2307/2283137> Besides univariate estimates of true proportions, RR variables can be used for correlations, as dependent variable in a logistic regression (with or without random effects), as predictors in a linear regression, or as dependent variable in a beta-binomial ANOVA. For simulation and bootstrap purposes, RR data can be generated according to several models.
Author: Daniel W. Heck [aut, cre], Morten Moshagen [aut]
Maintainer: Daniel W. Heck <heck@uni-mannheim.de>
Diff between RRreg versions 0.6.1 dated 2016-01-12 and 0.6.2 dated 2017-03-08
RRreg-0.6.1/RRreg/vignettes/markdown10.css |only RRreg-0.6.2/RRreg/DESCRIPTION | 26 - RRreg-0.6.2/RRreg/MD5 | 76 +-- RRreg-0.6.2/RRreg/NAMESPACE | 10 RRreg-0.6.2/RRreg/NEWS | 9 RRreg-0.6.2/RRreg/R/RRcheck.R | 5 RRreg-0.6.2/RRreg/R/RRcor.R | 9 RRreg-0.6.2/RRreg/R/RRcor.models.R | 2 RRreg-0.6.2/RRreg/R/RRgen.R | 9 RRreg-0.6.2/RRreg/R/RRlin.R | 8 RRreg-0.6.2/RRreg/R/RRlin.getPW.R | 8 RRreg-0.6.2/RRreg/R/RRlog.R | 28 - RRreg-0.6.2/RRreg/R/RRlog_check.R |only RRreg-0.6.2/RRreg/R/RRlog_fit.R | 2 RRreg-0.6.2/RRreg/R/RRmixed.R | 3 RRreg-0.6.2/RRreg/R/RRreg-package.R | 21 RRreg-0.6.2/RRreg/R/RRsimu.R | 5 RRreg-0.6.2/RRreg/R/RRuni.R | 6 RRreg-0.6.2/RRreg/R/RRuni.models.R | 13 RRreg-0.6.2/RRreg/R/helper_functions.R | 2 RRreg-0.6.2/RRreg/build/vignette.rds |binary RRreg-0.6.2/RRreg/inst/CITATION | 6 RRreg-0.6.2/RRreg/inst/doc/RRreg.Rmd | 81 ++- RRreg-0.6.2/RRreg/inst/doc/RRreg.html | 497 +++++++++++----------- RRreg-0.6.2/RRreg/man/RRcor.Rd | 3 RRreg-0.6.2/RRreg/man/RRgen.Rd | 3 RRreg-0.6.2/RRreg/man/RRlin.Rd | 9 RRreg-0.6.2/RRreg/man/RRlog.Rd | 9 RRreg-0.6.2/RRreg/man/RRmixed.Rd | 3 RRreg-0.6.2/RRreg/man/RRreg-package.Rd | 21 RRreg-0.6.2/RRreg/man/RRsimu.Rd | 1 RRreg-0.6.2/RRreg/man/RRuni.Rd | 6 RRreg-0.6.2/RRreg/man/getPW.Rd | 1 RRreg-0.6.2/RRreg/man/minarets.Rd | 2 RRreg-0.6.2/RRreg/man/plot.RRlog.Rd | 1 RRreg-0.6.2/RRreg/man/plot.powerplot.Rd | 1 RRreg-0.6.2/RRreg/man/powerplot.Rd | 1 RRreg-0.6.2/RRreg/man/predict.RRlog.Rd | 1 RRreg-0.6.2/RRreg/vignettes/RRreg.Rmd | 81 ++- RRreg-0.6.2/RRreg/vignettes/figures/Crosswise.jpg |binary 40 files changed, 530 insertions(+), 439 deletions(-)
Title: Wrapper for MUMPS Library
Description: Some basic features of MUMPS (Multifrontal Massively Parallel
sparse direct Solver) are wrapped in a class whose methods can be used
for sequentially solving a sparse linear system (symmetric or not)
with one or many right hand sides (dense or sparse).
There is a possibility to do separately symbolic analysis, LU factorization
and system solving.
Author: Serguei Sokol
Maintainer: Serguei Sokol <sokol@insa-toulouse.fr>
Diff between rmumps versions 5.0.1.12 dated 2017-03-06 and 5.0.1.12-1 dated 2017-03-08
DESCRIPTION | 6 ++--- MD5 | 24 +++++++++++------------ src/Makevars | 4 +-- src/Makevars.win | 4 +-- src/lib/Makefile | 2 - src/lib/scotch_6.0.4/src/Makefile.inc | 4 +-- src/lib/scotch_6.0.4/src/Makefile.inc.rmumps | 4 +-- src/lib/scotch_6.0.4/src/Makefile.inc.win | 2 - src/lib/scotch_6.0.4/src/esmumps/Makefile | 2 - src/lib/scotch_6.0.4/src/libscotch/Makefile | 6 ++--- src/lib/scotch_6.0.4/src/libscotchmetis/Makefile | 2 - src/lib/scotch_6.0.4/src/scotch/Makefile | 10 ++++----- src/rmumps_module.cpp | 4 +-- 13 files changed, 37 insertions(+), 37 deletions(-)
Title: A Semi-Parametric Test for Specifying Functional Form
Description: A central decision in a parametric regression is how to specify the relation between an dependent variable and each explanatory variable. This package provides a semi-parametric tool for comparing different transformations of an explanatory variables in a parametric regression. The functions is relevant in a situation, where you would use a box-cox or Box-Tidwell transformations. In contrast to the classic power-transformations, the methods in this package allows for theoretical driven user input and the possibility to compare with a non-parametric transformation.
Author: Toke Emil Panduro <tepp@ifro.ku.dk>, Cathrine Ulla Jensen <cuj@ifro.ku.dk>
Maintainer: Cathrine Ulla Jensen <cuj@ifro.ku.dk>
Diff between PanJen versions 1.1 dated 2017-02-27 and 1.3 dated 2017-03-08
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/PanJen.R | 40 ++++++++++++++++------------------------ man/choose.fform.Rd | 3 ++- man/fform.Rd | 5 +++-- 5 files changed, 29 insertions(+), 35 deletions(-)
Title: Multilevel B-Spline Approximation
Description: Functions to interpolate irregularly and regularly spaced data using Multilevel B-spline Approximation (MBA). Functions call portions of the SINTEF Multilevel B-spline Library written by Øyvind Hjelle which implements methods developed by Lee, Wolberg and Shin (1997; <doi:10.1109/2945.620490>).
Author: Andrew Finley [aut, cre],
Sudipto Banerjee [aut],
Øyvind Hjelle [aut],
Roger Bivand [ctb]
Maintainer: Andrew Finley <finleya@msu.edu>
Diff between MBA versions 0.0-8 dated 2014-04-29 and 0.0-9 dated 2017-03-08
DESCRIPTION | 27 ++++++++++++++++----------- MD5 | 18 ++++++++++-------- NAMESPACE | 6 ++++-- R/mba.points.R | 2 +- R/mba.surf.R | 8 ++++---- man/mba.points.Rd | 10 ++++------ man/mba.surf.Rd | 11 ++++------- src/MBAPoints.cpp | 3 +-- src/MBASurf.cpp | 2 +- src/include/RMBA.h |only src/init.cpp |only 11 files changed, 45 insertions(+), 42 deletions(-)
Title: High-Quality Visualizations of Large, High-Dimensional Datasets
Description: Implements the largeVis algorithm (see Tang, et al. (2016) <https://arxiv.org/abs/1602.00370>) for visualizing very large high-dimensional datasets. Also very fast search for approximate nearest neighbors; outlier detection; and optimized implementations of the HDBSCAN*, DBSCAN and OPTICS clustering algorithms; plotting functions for visualizing the above.
Author: Amos B. Elberg
Maintainer: Amos Elberg <amos.elberg@gmail.com>
Diff between largeVis versions 0.1.10.2 dated 2016-11-26 and 0.2 dated 2017-03-08
largeVis-0.1.10.2/largeVis/man/as_dendrogram_hdbscan.Rd |only largeVis-0.1.10.2/largeVis/src/pq.h |only largeVis-0.2/largeVis/DESCRIPTION | 17 - largeVis-0.2/largeVis/MD5 | 129 ++++++------ largeVis-0.2/largeVis/NAMESPACE | 8 largeVis-0.2/largeVis/NEWS.md | 16 + largeVis-0.2/largeVis/R/buildEdgeMatrix.R | 59 +++-- largeVis-0.2/largeVis/R/dbscan.R | 10 largeVis-0.2/largeVis/R/dendrogram.R | 111 +++++++--- largeVis-0.2/largeVis/R/distance.R | 1 largeVis-0.2/largeVis/R/hdbscan.R | 102 +++++---- largeVis-0.2/largeVis/R/largeVis-package.r | 32 ++ largeVis-0.2/largeVis/R/largeVis.R | 9 largeVis-0.2/largeVis/R/optics.R | 14 - largeVis-0.2/largeVis/inst/doc/largeVis.R | 33 --- largeVis-0.2/largeVis/inst/doc/largeVis.Rmd | 33 --- largeVis-0.2/largeVis/inst/doc/largeVis.html | 41 +-- largeVis-0.2/largeVis/inst/doc/momentumandusedata.R | 55 ++--- largeVis-0.2/largeVis/inst/doc/momentumandusedata.Rmd | 59 ++--- largeVis-0.2/largeVis/inst/doc/momentumandusedata.html | 6 largeVis-0.2/largeVis/inst/testdata/glassEdges.Rda |binary largeVis-0.2/largeVis/inst/testdata/spiral.Rda |binary largeVis-0.2/largeVis/man/as.dendrogram.hdbscan.Rd |only largeVis-0.2/largeVis/man/buildEdgeMatrix.Rd | 13 - largeVis-0.2/largeVis/man/buildWijMatrix.Rd | 8 largeVis-0.2/largeVis/man/distance.Rd | 3 largeVis-0.2/largeVis/man/ggManifoldMap.Rd | 1 largeVis-0.2/largeVis/man/gplot.Rd | 8 largeVis-0.2/largeVis/man/hdbscan.Rd | 23 +- largeVis-0.2/largeVis/man/largeVis-package.Rd | 41 +++ largeVis-0.2/largeVis/man/largeVis.Rd | 3 largeVis-0.2/largeVis/man/lof.Rd | 3 largeVis-0.2/largeVis/man/lv_dbscan.Rd | 3 largeVis-0.2/largeVis/man/lv_optics.Rd | 1 largeVis-0.2/largeVis/man/manifoldMap.Rd | 1 largeVis-0.2/largeVis/man/manifoldMapStretch.Rd | 1 largeVis-0.2/largeVis/man/neighborsToVectors.Rd | 1 largeVis-0.2/largeVis/man/projectKNNs.Rd | 1 largeVis-0.2/largeVis/man/randomProjectionTreeSearch.Rd | 3 largeVis-0.2/largeVis/man/sgdBatches.Rd | 1 largeVis-0.2/largeVis/src/Makevars | 2 largeVis-0.2/largeVis/src/RcppExports.cpp | 6 largeVis-0.2/largeVis/src/alias.h | 14 - largeVis-0.2/largeVis/src/dbscan.cpp | 3 largeVis-0.2/largeVis/src/distance.cpp | 4 largeVis-0.2/largeVis/src/edgeweights.cpp | 20 - largeVis-0.2/largeVis/src/gradients.cpp | 49 ++-- largeVis-0.2/largeVis/src/gradients.h | 38 +-- largeVis-0.2/largeVis/src/hdbscan.cpp | 109 +--------- largeVis-0.2/largeVis/src/hdbscan.h |only largeVis-0.2/largeVis/src/hdbscanobj.cpp |only largeVis-0.2/largeVis/src/hdcluster.cpp |only largeVis-0.2/largeVis/src/largeVis.cpp | 108 +++++----- largeVis-0.2/largeVis/src/minindexedpq.h | 8 largeVis-0.2/largeVis/src/minpq.cpp |only largeVis-0.2/largeVis/src/minpq.h | 86 +------- largeVis-0.2/largeVis/src/neighbors.cpp | 97 ++++----- largeVis-0.2/largeVis/src/neighbors.h | 24 +- largeVis-0.2/largeVis/src/optics.cpp | 4 largeVis-0.2/largeVis/src/primsalgorithm.h |only largeVis-0.2/largeVis/src/registration.cpp |only largeVis-0.2/largeVis/src/sparse.cpp | 31 +- largeVis-0.2/largeVis/tests/testthat/test_b_neighbors.R | 1 largeVis-0.2/largeVis/tests/testthat/test_c_sparse.R | 4 largeVis-0.2/largeVis/tests/testthat/test_d_edgematrixwij.R | 13 - largeVis-0.2/largeVis/tests/testthat/test_e_vis.R | 24 +- largeVis-0.2/largeVis/tests/testthat/test_g_dbandoptics.R | 14 + largeVis-0.2/largeVis/tests/testthat/test_h_hdbscan.R | 88 +++++--- largeVis-0.2/largeVis/vignettes/largeVis.Rmd | 33 --- largeVis-0.2/largeVis/vignettes/momentumandusedata.Rmd | 59 ++--- 70 files changed, 837 insertions(+), 852 deletions(-)
Title: Scientific Journal and Sci-Fi Themed Color Palettes for
'ggplot2'
Description: A collection of 'ggplot2' color palettes inspired by
plots in scientific journals, data visualization libraries,
science fiction movies, and TV shows.
Author: Nan Xiao <me@nanx.me>, Miaozhu Li <miaozhu.li@duke.edu>
Maintainer: Nan Xiao <me@nanx.me>
Diff between ggsci versions 2.0 dated 2016-11-21 and 2.4 dated 2017-03-08
ggsci-2.0/ggsci/R/continuous.01.gsea.R |only ggsci-2.0/ggsci/R/discrete.01.npg.R |only ggsci-2.0/ggsci/R/discrete.02.aaas.R |only ggsci-2.0/ggsci/R/discrete.03.lancet.R |only ggsci-2.0/ggsci/R/discrete.04.jco.R |only ggsci-2.0/ggsci/R/discrete.05.ucscgb.R |only ggsci-2.0/ggsci/R/discrete.06.d3.R |only ggsci-2.0/ggsci/R/discrete.07.uchicago.R |only ggsci-2.0/ggsci/R/discrete.08.simpsons.R |only ggsci-2.0/ggsci/R/discrete.09.futurama.R |only ggsci-2.0/ggsci/R/discrete.10.rickandmorty.R |only ggsci-2.4/ggsci/DESCRIPTION | 14 +- ggsci-2.4/ggsci/LICENSE |only ggsci-2.4/ggsci/MD5 | 107 +++++++++------- ggsci-2.4/ggsci/NAMESPACE | 16 ++ ggsci-2.4/ggsci/NEWS.md | 58 +++++--- ggsci-2.4/ggsci/R/continuous-gsea.R |only ggsci-2.4/ggsci/R/discrete-aaas.R |only ggsci-2.4/ggsci/R/discrete-d3.R |only ggsci-2.4/ggsci/R/discrete-futurama.R |only ggsci-2.4/ggsci/R/discrete-igv.R |only ggsci-2.4/ggsci/R/discrete-jco.R |only ggsci-2.4/ggsci/R/discrete-lancet.R |only ggsci-2.4/ggsci/R/discrete-locuszoom.R |only ggsci-2.4/ggsci/R/discrete-nejm.R |only ggsci-2.4/ggsci/R/discrete-npg.R |only ggsci-2.4/ggsci/R/discrete-rickandmorty.R |only ggsci-2.4/ggsci/R/discrete-simpsons.R |only ggsci-2.4/ggsci/R/discrete-startrek.R |only ggsci-2.4/ggsci/R/discrete-uchicago.R |only ggsci-2.4/ggsci/R/discrete-ucscgb.R |only ggsci-2.4/ggsci/R/ggsci-package.R | 2 ggsci-2.4/ggsci/R/sysdata.rda |binary ggsci-2.4/ggsci/README.md | 77 ++++++++++- ggsci-2.4/ggsci/TODO | 10 + ggsci-2.4/ggsci/build/vignette.rds |binary ggsci-2.4/ggsci/inst/doc/ggsci.R | 59 ++++----- ggsci-2.4/ggsci/inst/doc/ggsci.Rmd | 132 +++++++++++++------- ggsci-2.4/ggsci/inst/doc/ggsci.html | 175 ++++++++++++++++----------- ggsci-2.4/ggsci/man/ggsci-package.Rd | 2 ggsci-2.4/ggsci/man/pal_aaas.Rd | 6 ggsci-2.4/ggsci/man/pal_d3.Rd | 4 ggsci-2.4/ggsci/man/pal_futurama.Rd | 4 ggsci-2.4/ggsci/man/pal_gsea.Rd | 4 ggsci-2.4/ggsci/man/pal_igv.Rd |only ggsci-2.4/ggsci/man/pal_jco.Rd | 6 ggsci-2.4/ggsci/man/pal_lancet.Rd | 6 ggsci-2.4/ggsci/man/pal_locuszoom.Rd |only ggsci-2.4/ggsci/man/pal_nejm.Rd |only ggsci-2.4/ggsci/man/pal_npg.Rd | 8 - ggsci-2.4/ggsci/man/pal_rickandmorty.Rd | 4 ggsci-2.4/ggsci/man/pal_simpsons.Rd | 4 ggsci-2.4/ggsci/man/pal_startrek.Rd |only ggsci-2.4/ggsci/man/pal_uchicago.Rd | 4 ggsci-2.4/ggsci/man/pal_ucscgb.Rd | 4 ggsci-2.4/ggsci/man/rgb_gsea.Rd | 4 ggsci-2.4/ggsci/man/scale_aaas.Rd | 4 ggsci-2.4/ggsci/man/scale_d3.Rd | 4 ggsci-2.4/ggsci/man/scale_futurama.Rd | 4 ggsci-2.4/ggsci/man/scale_gsea.Rd | 4 ggsci-2.4/ggsci/man/scale_igv.Rd |only ggsci-2.4/ggsci/man/scale_jco.Rd | 4 ggsci-2.4/ggsci/man/scale_lancet.Rd | 4 ggsci-2.4/ggsci/man/scale_locuszoom.Rd |only ggsci-2.4/ggsci/man/scale_nejm.Rd |only ggsci-2.4/ggsci/man/scale_npg.Rd | 4 ggsci-2.4/ggsci/man/scale_rickandmorty.Rd | 4 ggsci-2.4/ggsci/man/scale_simpsons.Rd | 4 ggsci-2.4/ggsci/man/scale_startrek.Rd |only ggsci-2.4/ggsci/man/scale_uchicago.Rd | 4 ggsci-2.4/ggsci/man/scale_ucscgb.Rd | 4 ggsci-2.4/ggsci/vignettes/ggsci.Rmd | 132 +++++++++++++------- 72 files changed, 560 insertions(+), 326 deletions(-)
Title: Build Error Correction Models
Description: Functions for easy building of error correction models (ECM) for time series regression.
Author: Gaurav Bansal
Maintainer: Gaurav Bansal <gaurbans@gmail.com>
Diff between ecm versions 0.8.0 dated 2017-03-01 and 0.9.0 dated 2017-03-08
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/ecmback.r | 20 +++++++++----------- 3 files changed, 14 insertions(+), 16 deletions(-)
Title: Encoders for Categorical Variables
Description: Contains some commonly used categorical variable encoders, such as 'LabelEncoder' and 'OneHotEncoder'. Inspired by the encoders implemented in Python 'sklearn.preprocessing' package (see <http://scikit-learn.org/stable/modules/preprocessing.html>).
Author: nl zhang
Maintainer: nl zhang <setseed2016@gmail.com>
Diff between CatEncoders versions 0.1.0 dated 2016-09-13 and 0.1.1 dated 2017-03-08
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/basic.R | 3 +-- 3 files changed, 7 insertions(+), 8 deletions(-)
Title: Confidence Intervals and Sample Size Determination for a
Binomial Proportion under Simple Random Sampling and Pooled
Sampling
Description:
A suite of functions to compute confidence intervals and necessary
sample sizes for the parameter p of the Bernoulli B(p)
distribution under simple random sampling or under pooled
sampling. Such computations are e.g. of interest when investigating
the incidence or prevalence in populations.
The package contains functions to compute coverage probabilities and
coverage coefficients of the provided confidence intervals
procedures. Sample size calculations are based on expected length.
Author: Michael Höhle [aut, cre], Wei Liu [ctb]
Maintainer: Michael Höhle <hoehle@math.su.se>
Diff between binomSamSize versions 0.1-4 dated 2016-12-05 and 0.1-5 dated 2017-03-08
DESCRIPTION | 9 +++++---- MD5 | 9 +++++---- NAMESPACE | 2 +- R/ciss.liubailey.R | 4 ++-- src/register.c |only src/wei_helper.c | 10 +++++----- 6 files changed, 18 insertions(+), 16 deletions(-)
Title: Tools for Accessing the Botanical Information and Ecology
Network Database
Description: Provides Tools for Accessing the Botanical Information and Ecology Network Database. The BIEN database contains cleaned and standardized botanical data including occurrence, trait, plot and taxonomic data (See <http://Bien.nceas.ucsb.edu/bien/> for more Information). This package provides functions that query the BIEN database by constructing and executing optimized SQL queries.
Author: Brian Maitner [aut, cre]
Maintainer: Brian Maitner <bmaitner@gmail.com>
Diff between BIEN versions 1.0.0 dated 2017-01-12 and 1.1.0 dated 2017-03-08
BIEN-1.0.0/BIEN/man/BIEN_sql.Rd |only BIEN-1.1.0/BIEN/DESCRIPTION | 16 BIEN-1.1.0/BIEN/MD5 | 123 BIEN-1.1.0/BIEN/NEWS | 18 BIEN-1.1.0/BIEN/R/BIEN.R | 1605 ++++++++----- BIEN-1.1.0/BIEN/build/vignette.rds |binary BIEN-1.1.0/BIEN/inst/doc/BIEN.Rmd | 14 BIEN-1.1.0/BIEN/inst/doc/BIEN.html | 19 BIEN-1.1.0/BIEN/man/BIEN.Rd | 3 BIEN-1.1.0/BIEN/man/BIEN_list_all.Rd | 7 BIEN-1.1.0/BIEN/man/BIEN_list_country.Rd | 8 BIEN-1.1.0/BIEN/man/BIEN_list_county.Rd | 7 BIEN-1.1.0/BIEN/man/BIEN_list_shapefile.Rd | 7 BIEN-1.1.0/BIEN/man/BIEN_list_state.Rd | 7 BIEN-1.1.0/BIEN/man/BIEN_metadata_citation.Rd |only BIEN-1.1.0/BIEN/man/BIEN_metadata_database_version.Rd | 9 BIEN-1.1.0/BIEN/man/BIEN_metadata_match_data.Rd | 9 BIEN-1.1.0/BIEN/man/BIEN_occurrence_box.Rd | 8 BIEN-1.1.0/BIEN/man/BIEN_occurrence_country.Rd | 9 BIEN-1.1.0/BIEN/man/BIEN_occurrence_county.Rd | 10 BIEN-1.1.0/BIEN/man/BIEN_occurrence_family.Rd | 9 BIEN-1.1.0/BIEN/man/BIEN_occurrence_genus.Rd | 9 BIEN-1.1.0/BIEN/man/BIEN_occurrence_records_per_species.Rd | 7 BIEN-1.1.0/BIEN/man/BIEN_occurrence_shapefile.Rd | 10 BIEN-1.1.0/BIEN/man/BIEN_occurrence_species.Rd | 9 BIEN-1.1.0/BIEN/man/BIEN_occurrence_state.Rd | 10 BIEN-1.1.0/BIEN/man/BIEN_phylogeny_complete.Rd | 3 BIEN-1.1.0/BIEN/man/BIEN_phylogeny_conservative.Rd | 3 BIEN-1.1.0/BIEN/man/BIEN_plot_country.Rd | 7 BIEN-1.1.0/BIEN/man/BIEN_plot_dataset.Rd | 7 BIEN-1.1.0/BIEN/man/BIEN_plot_datasource.Rd | 7 BIEN-1.1.0/BIEN/man/BIEN_plot_list_datasource.Rd | 3 BIEN-1.1.0/BIEN/man/BIEN_plot_list_sampling_protocols.Rd | 3 BIEN-1.1.0/BIEN/man/BIEN_plot_metadata.Rd | 15 BIEN-1.1.0/BIEN/man/BIEN_plot_name.Rd | 9 BIEN-1.1.0/BIEN/man/BIEN_plot_sampling_protocol.Rd | 10 BIEN-1.1.0/BIEN/man/BIEN_plot_state.Rd | 7 BIEN-1.1.0/BIEN/man/BIEN_ranges_box.Rd | 8 BIEN-1.1.0/BIEN/man/BIEN_ranges_genus.Rd | 8 BIEN-1.1.0/BIEN/man/BIEN_ranges_intersect_species.Rd | 15 BIEN-1.1.0/BIEN/man/BIEN_ranges_list.Rd |only BIEN-1.1.0/BIEN/man/BIEN_ranges_load_species.Rd | 8 BIEN-1.1.0/BIEN/man/BIEN_ranges_shapefile.Rd | 8 BIEN-1.1.0/BIEN/man/BIEN_ranges_species.Rd | 8 BIEN-1.1.0/BIEN/man/BIEN_stem_datasource.Rd |only BIEN-1.1.0/BIEN/man/BIEN_stem_family.Rd |only BIEN-1.1.0/BIEN/man/BIEN_stem_genus.Rd |only BIEN-1.1.0/BIEN/man/BIEN_stem_species.Rd | 14 BIEN-1.1.0/BIEN/man/BIEN_taxonomy_family.Rd | 7 BIEN-1.1.0/BIEN/man/BIEN_taxonomy_genus.Rd | 7 BIEN-1.1.0/BIEN/man/BIEN_taxonomy_species.Rd | 7 BIEN-1.1.0/BIEN/man/BIEN_trait_family.Rd | 10 BIEN-1.1.0/BIEN/man/BIEN_trait_genus.Rd | 10 BIEN-1.1.0/BIEN/man/BIEN_trait_list.Rd | 7 BIEN-1.1.0/BIEN/man/BIEN_trait_mean.Rd | 5 BIEN-1.1.0/BIEN/man/BIEN_trait_species.Rd | 10 BIEN-1.1.0/BIEN/man/BIEN_trait_trait.Rd | 14 BIEN-1.1.0/BIEN/man/BIEN_trait_traitbyfamily.Rd | 16 BIEN-1.1.0/BIEN/man/BIEN_trait_traitbygenus.Rd | 16 BIEN-1.1.0/BIEN/man/BIEN_trait_traitbyspecies.Rd | 16 BIEN-1.1.0/BIEN/man/BIEN_trait_traits_per_species.Rd | 7 BIEN-1.1.0/BIEN/man/is_char.Rd | 1 BIEN-1.1.0/BIEN/man/is_log.Rd | 1 BIEN-1.1.0/BIEN/man/is_num.Rd | 1 BIEN-1.1.0/BIEN/tests |only BIEN-1.1.0/BIEN/vignettes/BIEN.Rmd | 15 66 files changed, 1298 insertions(+), 928 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-03-13 0.4.0
2014-10-29 0.3.1
2014-10-15 0.3.0
2014-06-18 0.1.9
2014-06-11 0.1.8
2014-04-22 0.1.6
2014-04-04 0.1.4
2013-11-01 0.1.1
2013-10-05 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-10-31 3.0.6