Title: Bayesian Nonparametric Modeling in R
Description: Functions to perform inference via
simulation from the posterior distributions for Bayesian
nonparametric and semiparametric models. Although the name of
the package was motivated by the Dirichlet Process prior, the
package considers and will consider other priors on functional
spaces. So far, DPpackage includes models considering Dirichlet
Processes, Dependent Dirichlet Processes, Dependent Poisson-
Dirichlet Processes, Hierarchical Dirichlet Processes, Polya
Trees, Linear Dependent Tailfree Processes, Mixtures of
Triangular distributions, Random Bernstein polynomials priors
and Dependent Bernstein Polynomials. The package also includes
models considering Penalized B-Splines.
Includes semiparametric models for marginal and conditional
density estimation, ROC curve analysis, interval censored data,
binary regression models, generalized linear mixed models, IRT
type models, and generalized additive models. Also
contains functions to compute Pseudo-Bayes factors for model
comparison, and to elicitate the precision parameter of the
Dirichlet Process. To maximize computational efficiency, the
actual sampling for each model is done in compiled FORTRAN. The
functions return objects which can be subsequently analyzed
with functions provided in the 'coda' package.
Author: Alejandro Jara [aut, cre], Timothy Hanson [ctb], Fernando
Quintana [ctb], Peter Mueller [ctb], Gary Rosner [ctb]
Maintainer: ORPHANED
Diff between DPpackage versions 1.1-6 dated 2012-09-14 and 1.1-7 dated 2017-09-14
DPpackage-1.1-6/DPpackage/LICENSE |only DPpackage-1.1-7/DPpackage/DESCRIPTION | 29 DPpackage-1.1-7/DPpackage/MD5 | 182 DPpackage-1.1-7/DPpackage/NAMESPACE | 129 DPpackage-1.1-7/DPpackage/R/BDPdensity.R | 1144 ++--- DPpackage-1.1-7/DPpackage/R/CSDPbinary.R | 2420 ++++++------ DPpackage-1.1-7/DPpackage/R/DPMdencens.R | 1640 ++++---- DPpackage-1.1-7/DPpackage/R/DPMglmm.R | 3520 +++++++++--------- DPpackage-1.1-7/DPpackage/R/DPMlmm.R | 2670 ++++++------- DPpackage-1.1-7/DPpackage/R/DPMmeta.R | 2444 ++++++------ DPpackage-1.1-7/DPpackage/R/DPMolmm.R | 2832 +++++++------- DPpackage-1.1-7/DPpackage/R/DPMrandom.R | 1272 +++--- DPpackage-1.1-7/DPpackage/R/DPMrasch.R | 2074 +++++----- DPpackage-1.1-7/DPpackage/R/DPMraschpoisson.R | 2196 +++++------ DPpackage-1.1-7/DPpackage/R/DPbetabinom.R | 1078 ++--- DPpackage-1.1-7/DPpackage/R/DPbinary.R | 2928 +++++++-------- DPpackage-1.1-7/DPpackage/R/DPcaterpillar.R | 358 - DPpackage-1.1-7/DPpackage/R/DPcdensity.R | 1748 ++++----- DPpackage-1.1-7/DPpackage/R/DPdensity.R | 2442 ++++++------ DPpackage-1.1-7/DPpackage/R/DPelicit.R | 440 +- DPpackage-1.1-7/DPpackage/R/DPglmm.R | 3334 ++++++++--------- DPpackage-1.1-7/DPpackage/R/DPlmm.R | 2608 ++++++------- DPpackage-1.1-7/DPpackage/R/DPmeta.R | 2318 ++++++------ DPpackage-1.1-7/DPpackage/R/DPmultmeta.R | 1632 ++++---- DPpackage-1.1-7/DPpackage/R/DPolmm.R | 2802 +++++++------- DPpackage-1.1-7/DPpackage/R/DPpsBF.R | 198 - DPpackage-1.1-7/DPpackage/R/DPrandom.R | 2882 +++++++------- DPpackage-1.1-7/DPpackage/R/DPrasch.R | 1878 ++++----- DPpackage-1.1-7/DPpackage/R/DPraschpoisson.R | 1878 ++++----- DPpackage-1.1-7/DPpackage/R/DProc.R | 582 +-- DPpackage-1.1-7/DPpackage/R/DPsurvint.R | 2444 ++++++------ DPpackage-1.1-7/DPpackage/R/FPTbinary.R | 2502 ++++++------ DPpackage-1.1-7/DPpackage/R/FPTrasch.R | 1910 ++++----- DPpackage-1.1-7/DPpackage/R/FPTraschpoisson.R | 1908 ++++----- DPpackage-1.1-7/DPpackage/R/HDPMcdensity.R | 2180 +++++------ DPpackage-1.1-7/DPpackage/R/HDPMdensity.R | 2002 +++++----- DPpackage-1.1-7/DPpackage/R/LDBDPdensity.R | 1816 ++++----- DPpackage-1.1-7/DPpackage/R/LDDPdensity.R | 1654 ++++---- DPpackage-1.1-7/DPpackage/R/LDDPrasch.R | 1946 +++++----- DPpackage-1.1-7/DPpackage/R/LDDPraschpoisson.R | 1058 ++--- DPpackage-1.1-7/DPpackage/R/LDDProc.R | 1630 ++++---- DPpackage-1.1-7/DPpackage/R/LDDPsurvival.R | 1634 ++++---- DPpackage-1.1-7/DPpackage/R/LDDPtwopl.R | 1848 ++++----- DPpackage-1.1-7/DPpackage/R/LDPDdoublyint.R | 2402 ++++++------ DPpackage-1.1-7/DPpackage/R/LDTFPdensity.R | 1630 ++++---- DPpackage-1.1-7/DPpackage/R/LDTFPglmm.R | 1840 ++++----- DPpackage-1.1-7/DPpackage/R/LDTFPsurvival.R | 1648 ++++---- DPpackage-1.1-7/DPpackage/R/PSgam.R | 4052 ++++++++++----------- DPpackage-1.1-7/DPpackage/R/PTdensity.R | 2144 +++++------ DPpackage-1.1-7/DPpackage/R/PTglmm.R | 3932 ++++++++++---------- DPpackage-1.1-7/DPpackage/R/PTlm.R | 2264 +++++------ DPpackage-1.1-7/DPpackage/R/PTlmm.R | 3064 +++++++-------- DPpackage-1.1-7/DPpackage/R/PTmeta.R | 2472 ++++++------ DPpackage-1.1-7/DPpackage/R/PTolmm.R | 3302 ++++++++--------- DPpackage-1.1-7/DPpackage/R/PTrandom.R | 1650 ++++---- DPpackage-1.1-7/DPpackage/R/PTsampler.R | 1776 ++++----- DPpackage-1.1-7/DPpackage/R/Pbinary.R | 2008 +++++----- DPpackage-1.1-7/DPpackage/R/Plm.R | 1482 +++---- DPpackage-1.1-7/DPpackage/R/TDPdensity.R | 1264 +++--- DPpackage-1.1-7/DPpackage/R/hidden.R | 82 DPpackage-1.1-7/DPpackage/R/ps.R | 132 DPpackage-1.1-7/DPpackage/inst/CITATION | 4 DPpackage-1.1-7/DPpackage/src/BDPdensity.f | 6 DPpackage-1.1-7/DPpackage/src/DPMglmmpois.f | 4 DPpackage-1.1-7/DPpackage/src/DPMglmmprob.f | 4 DPpackage-1.1-7/DPpackage/src/DPMlm.f | 4 DPpackage-1.1-7/DPpackage/src/DPMlmm.f | 4 DPpackage-1.1-7/DPpackage/src/DPMmeta.f | 4 DPpackage-1.1-7/DPpackage/src/DPMolmmp.f | 4 DPpackage-1.1-7/DPpackage/src/DPbivdensityg.f | 2 DPpackage-1.1-7/DPpackage/src/DPglmmgam.f | 4 DPpackage-1.1-7/DPpackage/src/DPglmmlogit.f | 4 DPpackage-1.1-7/DPpackage/src/DPglmmlogita.f | 4 DPpackage-1.1-7/DPpackage/src/DPglmmpois.f | 4 DPpackage-1.1-7/DPpackage/src/DPglmmprob.f | 4 DPpackage-1.1-7/DPpackage/src/DPlmm.f | 4 DPpackage-1.1-7/DPpackage/src/DPmeta.f | 4 DPpackage-1.1-7/DPpackage/src/DPolmmp.f | 4 DPpackage-1.1-7/DPpackage/src/LDPDdoublyintsba.f | 2 DPpackage-1.1-7/DPpackage/src/PSgamgam.f | 2 DPpackage-1.1-7/DPpackage/src/PSgamgauss.f | 2 DPpackage-1.1-7/DPpackage/src/PSgamlogit.f | 2 DPpackage-1.1-7/DPpackage/src/PSgampois.f | 2 DPpackage-1.1-7/DPpackage/src/PSgamprob.f | 2 DPpackage-1.1-7/DPpackage/src/PTmeta.f | 4 DPpackage-1.1-7/DPpackage/src/TDPdensity.f | 6 DPpackage-1.1-7/DPpackage/src/TDPdensitypl.f | 6 DPpackage-1.1-7/DPpackage/src/ToolsDistributions.f | 2 DPpackage-1.1-7/DPpackage/src/ToolsPT.f | 10 DPpackage-1.1-7/DPpackage/src/ToolsRnumbers.f | 4 DPpackage-1.1-7/DPpackage/src/ToolsSparseMatrix.f | 32 DPpackage-1.1-7/DPpackage/src/ToolsTDP.f | 26 DPpackage-1.1-7/DPpackage/src/init.c |only 93 files changed, 56763 insertions(+), 56741 deletions(-)
Title: Calculate and Analyze Blau Status for (Covert) Organizations
Description: An integrated set of tools to calculate and analyze Blau statuses quantifying social distance between individuals belonging to (covert) organizations. Relational (network) data may be incorporated for additional analyses. This project is supported by Defense Threat Reduction Agency (DTRA) Grant HDTRA-10-1-0043.
Author: Cheng Wang*, Michael Genkin*, George Berry, Liyuan Chen, Matthew Brashears *Both authors contributed equally to this work and their names are randomly ordered
Maintainer: Cheng Wang <cwang3@nd.edu>
Diff between Blaunet versions 2.0.4 dated 2016-04-13 and 2.0.5 dated 2017-09-14
DESCRIPTION | 15 +++++++++------ MD5 | 19 +++++++++++-------- NAMESPACE | 2 +- R/blaunetgui.r |only R/zzz.R |only inst/scripts/analysis.R | 2 +- inst/scripts/blaunetgui.R | 27 +++++++++++++++------------ inst/scripts/command.pdf |binary inst/scripts/graphic.pdf |binary inst/scripts/open.R | 4 ++-- man/blaunet-package.Rd | 4 ++-- man/blaunetgui.Rd |only 12 files changed, 41 insertions(+), 32 deletions(-)
Title: Wavelet Analysis of Genomic Data from Admixed Populations
Description: Implements wavelet-based approaches for describing population admixture. Principal Components Analysis (PCA) is used to define the population structure and produce a localized admixture signal for each individual. Wavelet summaries of the PCA output describe variation present in the data and can be related to population-level demographic processes. For more details, see Sanderson et al. (2015).
Author: Jean Sanderson
Maintainer: Murray Cox <murray.p.cox@gmail.com>
Diff between adwave versions 1.1 dated 2015-06-25 and 1.2 dated 2017-09-14
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- NAMESPACE | 2 ++ 3 files changed, 9 insertions(+), 7 deletions(-)
Title: Random Forests Model Selection and Performance Evaluation
Description: Utilities for Random Forest model selection, class balance
correction, significance test, cross validation and partial dependency
plots.
Author: Jeffrey S. Evans [cre, aut],
Melanie A. Murphy [ctb]
Maintainer: Jeffrey S. Evans <jeffrey_evans@tnc.org>
Diff between rfUtilities versions 2.1-0 dated 2017-06-12 and 2.1-1 dated 2017-09-14
DESCRIPTION | 8 ++--- MD5 | 30 ++++++++++---------- R/multi.collinear.R | 13 +++++--- R/plot.rf.cv.R | 14 ++++++--- R/print.rf.cv.R | 9 ++++-- R/rf.classBalance.R | 6 +--- R/rf.crossValidation.R | 67 ++++++++++++++++++++++++++++++++++---------- R/rf.modelSel.R | 16 ++++++---- R/rf.partial.prob.R | 6 +--- R/rf.significance.R | 6 +--- R/summary.rf.cv.R | 69 ++++++++++++++++++++++++++++------------------ inst/NEWS | 11 +++++++ man/multi.collinear.Rd | 7 +++- man/plot.rf.cv.Rd | 2 - man/rf.crossValidation.Rd | 16 +++++++--- man/rf.modelSel.Rd | 11 +++++-- 16 files changed, 188 insertions(+), 103 deletions(-)
Title: Nonparametric Robust Estimation and Inference Methods using
Local Polynomial Regression and Kernel Density Estimation
Description: Tools for data-driven statistical analysis using local polynomial regression and kernel density estimation methods as described in Calonico, Cattaneo and Farrell (2017a): lprobust() for local polynomial point estimation and robust bias-corrected inference and kdrobust() for kernel density point estimation and robust bias-corrected inference. Several optimal bandwidth selection procedures are computed by lpbwselect() and kdbwselect() for local polynomial and kernel density estimation, respectively. Finally, nprobust.plot() for density and regression plots with robust confidence interval.
Author: Sebastian Calonico <scalonico@bus.miami.edu>, Matias D. Cattaneo <cattaneo@umich.edu>, Max H. Farrell <max.farrell@chicagobooth.edu>
Maintainer: Sebastian Calonico <scalonico@bus.miami.edu>
Diff between nprobust versions 0.1.0 dated 2017-09-01 and 0.1.1 dated 2017-09-14
DESCRIPTION | 10 +++++----- MD5 | 28 ++++++++++++++-------------- R/kdbwselect.R | 10 ++++++---- R/kdrobust.R | 10 ++++++---- R/lpbwselect.R | 10 ++++++---- R/lprobust.R | 13 ++++++------- R/npfunctions.R | 3 ++- R/nprobust.plot.R | 2 +- man/kdbwselect.Rd | 18 +++++++++--------- man/kdrobust.Rd | 24 ++++++++++++------------ man/lpbwselect.Rd | 23 ++++++++++++----------- man/lprobust.Rd | 30 +++++++++++++++--------------- man/nprobust-package.Rd | 6 +++--- man/nprobust.plot.Rd | 8 ++++---- src/lpbwce.cpp | 2 +- 15 files changed, 102 insertions(+), 95 deletions(-)
Title: Mathematical Morphology in Any Number of Dimensions
Description: Provides tools for performing mathematical morphology operations,
such as erosion and dilation, on data of arbitrary dimensionality. Can also
be used for finding connected components, resampling, filtering, smoothing
and other image processing-style operations.
Author: Jon Clayden
Maintainer: Jon Clayden <code@clayden.org>
Diff between mmand versions 1.5.2 dated 2017-08-22 and 1.5.3 dated 2017-09-14
mmand-1.5.2/mmand/src/Makevars |only mmand-1.5.3/mmand/DESCRIPTION | 8 ++++---- mmand-1.5.3/mmand/MD5 | 10 +++++++--- mmand-1.5.3/mmand/NEWS | 7 +++++++ mmand-1.5.3/mmand/cleanup |only mmand-1.5.3/mmand/configure |only mmand-1.5.3/mmand/configure.ac |only mmand-1.5.3/mmand/src/Makevars.in |only mmand-1.5.3/mmand/src/Makevars.win |only 9 files changed, 18 insertions(+), 7 deletions(-)
Title: Simple Peak Alignment for Gas-Chromatography Data
Description: Aligns peak based on peak retention times and matches homologous peaks
across samples. The underlying alignment procedure comprises three sequential steps.
(1) Full alignment of samples by linear transformation of retention times to
maximise similarity among homologous peaks (2) Partial alignment of peaks within
a user-defined retention time window to cluster homologous peaks (3) Merging rows
that are likely representing homologous substances (i.e. no sample shows peaks in
both rows and the rows have similar retention time means). The algorithm is described in detail
in Ottensmann et al. submitted <doi:10.1101/110494>.
Author: Meinolf Ottensmann [aut, cre],
Martin Stoffel [aut],
Hazel J. Nichols [aut],
Joseph I. Hoffman [aut]
Maintainer: Meinolf Ottensmann <meinolf.ottensmann@web.de>
Diff between GCalignR versions 0.1.0 dated 2017-02-06 and 1.0.0 dated 2017-09-14
GCalignR-0.1.0/GCalignR/R/bfla.R |only GCalignR-0.1.0/GCalignR/R/bfla_ms.R |only GCalignR-0.1.0/GCalignR/inst/extdata/bfla.txt |only GCalignR-0.1.0/GCalignR/inst/extdata/bfla_ms.txt |only GCalignR-0.1.0/GCalignR/man/bfla.Rd |only GCalignR-0.1.0/GCalignR/man/bfla_ms.Rd |only GCalignR-0.1.0/GCalignR/man/delete_empty_rows.Rd |only GCalignR-1.0.0/GCalignR/DESCRIPTION | 41 - GCalignR-1.0.0/GCalignR/MD5 | 124 +-- GCalignR-1.0.0/GCalignR/NAMESPACE | 10 GCalignR-1.0.0/GCalignR/NEWS.md |only GCalignR-1.0.0/GCalignR/R/GC_Heatmap.R | 131 +-- GCalignR-1.0.0/GCalignR/R/GCalignR.R | 38 GCalignR-1.0.0/GCalignR/R/align_chromatograms.R | 235 ++--- GCalignR-1.0.0/GCalignR/R/align_peaks.R | 170 ---- GCalignR-1.0.0/GCalignR/R/as.data.frame.GCalign.R |only GCalignR-1.0.0/GCalignR/R/check_input.R | 79 + GCalignR-1.0.0/GCalignR/R/choose_optimal_reference.R | 107 +- GCalignR-1.0.0/GCalignR/R/draw_chromatogram.R |only GCalignR-1.0.0/GCalignR/R/find_peaks.R |only GCalignR-1.0.0/GCalignR/R/formatting_filtering_gc_data.R | 399 +++++++--- GCalignR-1.0.0/GCalignR/R/linear_transformation.R | 211 ++--- GCalignR-1.0.0/GCalignR/R/merge_redundant_rows.R |only GCalignR-1.0.0/GCalignR/R/norm_peaks.R | 40 - GCalignR-1.0.0/GCalignR/R/peak_interspace.R | 42 - GCalignR-1.0.0/GCalignR/R/plot.GCalign.R | 163 ++-- GCalignR-1.0.0/GCalignR/R/print.GCalign.R | 9 GCalignR-1.0.0/GCalignR/R/read_peak_list.R |only GCalignR-1.0.0/GCalignR/R/remove_blanks.R |only GCalignR-1.0.0/GCalignR/R/remove_singletons.R |only GCalignR-1.0.0/GCalignR/R/simple_chroma.R |only GCalignR-1.0.0/GCalignR/README.md | 32 GCalignR-1.0.0/GCalignR/build/vignette.rds |binary GCalignR-1.0.0/GCalignR/data/aligned_peak_data.RData |binary GCalignR-1.0.0/GCalignR/inst/CITATION |only GCalignR-1.0.0/GCalignR/inst/doc/GCalignR_How_does_the_Algorithm_works.R |only GCalignR-1.0.0/GCalignR/inst/doc/GCalignR_How_does_the_Algorithm_works.Rmd |only GCalignR-1.0.0/GCalignR/inst/doc/GCalignR_How_does_the_Algorithm_works.html |only GCalignR-1.0.0/GCalignR/inst/doc/GCalignR_step_by_step.R | 27 GCalignR-1.0.0/GCalignR/inst/doc/GCalignR_step_by_step.Rmd | 123 +-- GCalignR-1.0.0/GCalignR/inst/doc/GCalignR_step_by_step.html | 284 +++---- GCalignR-1.0.0/GCalignR/inst/extdata/simulated_peak_data.txt |only GCalignR-1.0.0/GCalignR/man/GCalignR.Rd | 38 GCalignR-1.0.0/GCalignR/man/align_chromatograms.Rd | 107 -- GCalignR-1.0.0/GCalignR/man/align_peaks.Rd | 15 GCalignR-1.0.0/GCalignR/man/aligned_peak_data.Rd | 1 GCalignR-1.0.0/GCalignR/man/as.data.frame.GCalign.Rd |only GCalignR-1.0.0/GCalignR/man/check_input.Rd | 22 GCalignR-1.0.0/GCalignR/man/choose_optimal_reference.Rd | 28 GCalignR-1.0.0/GCalignR/man/draw_chromatogram.Rd |only GCalignR-1.0.0/GCalignR/man/find_peaks.Rd |only GCalignR-1.0.0/GCalignR/man/gc_heatmap.Rd | 49 - GCalignR-1.0.0/GCalignR/man/linear_transformation.Rd | 38 GCalignR-1.0.0/GCalignR/man/merge_redundant_rows.Rd |only GCalignR-1.0.0/GCalignR/man/norm_peaks.Rd | 22 GCalignR-1.0.0/GCalignR/man/peak_data.Rd | 1 GCalignR-1.0.0/GCalignR/man/peak_factors.Rd | 1 GCalignR-1.0.0/GCalignR/man/peak_interspace.Rd | 15 GCalignR-1.0.0/GCalignR/man/plot.GCalign.Rd | 26 GCalignR-1.0.0/GCalignR/man/print.GCalign.Rd | 8 GCalignR-1.0.0/GCalignR/man/read_peak_list.Rd |only GCalignR-1.0.0/GCalignR/man/remove_blanks.Rd |only GCalignR-1.0.0/GCalignR/man/remove_singletons.Rd |only GCalignR-1.0.0/GCalignR/man/simple_chroma.Rd |only GCalignR-1.0.0/GCalignR/tests/testthat/test-align_chromatograms.R | 7 GCalignR-1.0.0/GCalignR/tests/testthat/test-align_peaks.R |only GCalignR-1.0.0/GCalignR/tests/testthat/test-choose_optimal_reference.R | 7 GCalignR-1.0.0/GCalignR/tests/testthat/test-draw_chromatograms.R |only GCalignR-1.0.0/GCalignR/tests/testthat/test-gc_heatmap.R | 2 GCalignR-1.0.0/GCalignR/tests/testthat/test-linear_transformation.R |only GCalignR-1.0.0/GCalignR/tests/testthat/test-norm_peaks.R | 14 GCalignR-1.0.0/GCalignR/tests/testthat/test-plot.GCalign.R | 2 GCalignR-1.0.0/GCalignR/tests/testthat/test-remove_blanks.R |only GCalignR-1.0.0/GCalignR/tests/testthat/test-simple_chroma.R |only GCalignR-1.0.0/GCalignR/vignettes/Algorithm_Figure.png |only GCalignR-1.0.0/GCalignR/vignettes/GCalignR_How_does_the_Algorithm_works.Rmd |only GCalignR-1.0.0/GCalignR/vignettes/GCalignR_step_by_step.Rmd | 123 +-- GCalignR-1.0.0/GCalignR/vignettes/Lin_Shift.png |only GCalignR-1.0.0/GCalignR/vignettes/Two_Chromas_Peak_List.png |only GCalignR-1.0.0/GCalignR/vignettes/align_peaks.png |only GCalignR-1.0.0/GCalignR/vignettes/bibliography.bib | 155 --- GCalignR-1.0.0/GCalignR/vignettes/chroma_not_aligned.png |only GCalignR-1.0.0/GCalignR/vignettes/lin_shift.tiff |only GCalignR-1.0.0/GCalignR/vignettes/merge_row.png |only 84 files changed, 1528 insertions(+), 1418 deletions(-)
Title: E-Statistics: Multivariate Inference via the Energy of Data
Description: E-statistics (energy) tests and statistics for multivariate and univariate inference,
including distance correlation, one-sample, two-sample, and multi-sample tests for
comparing multivariate distributions, are implemented. Measuring and testing
multivariate independence based on distance correlation, partial distance correlation,
multivariate goodness-of-fit tests, clustering based on energy distance, testing for
multivariate normality, distance components (disco) for non-parametric analysis of
structured data, and other energy statistics/methods are implemented.
Author: Maria L. Rizzo and Gabor J. Szekely
Maintainer: Maria Rizzo <mrizzo@bgsu.edu>
Diff between energy versions 1.7-0 dated 2016-08-26 and 1.7-2 dated 2017-09-14
DESCRIPTION | 9 ++--- MD5 | 41 ++++++++++++----------- NAMESPACE | 3 + NEWS | 11 ++++++ R/Eeqdist.R | 2 - R/Eindep.R | 14 +++++--- R/Emvnorm.R | 5 +- R/Epoisson.R | 5 +- R/RcppExports.R | 18 +++++----- R/dcov.R | 58 +++++++++++++++++++++++++++++++-- R/disco.R | 4 +- man/dcov.test.Rd | 29 ++++++++++------ man/disco.Rd | 8 ++-- man/energy-deprecated.Rd | 2 - man/energy-package.Rd | 4 ++ man/eqdist.etest.Rd | 2 - man/indep.test.Rd | 2 - man/mvI.test.Rd | 2 - man/mvnorm-etest.Rd | 4 +- man/poisson.mtest.Rd | 2 - src/RcppExports.cpp | 82 +++++++++++++++++++++++------------------------ src/energy_init.c |only 22 files changed, 197 insertions(+), 110 deletions(-)
Title: Inferring Causal Effects using Bayesian Structural Time-Series
Models
Description: Implements a Bayesian approach to causal impact estimation in time
series, as described in Brodersen et al. (2015) <DOI:10.1214/14-AOAS788>.
See the package documentation on GitHub
<https://google.github.io/CausalImpact/> to get started.
Author: Kay H. Brodersen <kbrodersen@google.com>,
Alain Hauser <alhauser@google.com>
Maintainer: Alain Hauser <alhauser@google.com>
Diff between CausalImpact versions 1.2.2 dated 2017-09-14 and 1.2.3 dated 2017-09-14
DESCRIPTION | 6 +++--- MD5 | 6 +++--- inst/doc/CausalImpact.html | 10 +++++----- tests/testthat/test-impact-misc.R | 9 ++++++--- 4 files changed, 17 insertions(+), 14 deletions(-)
Title: Alignment of Phonetic Sequences Using the 'ALINE' Algorithm
Description: Functions are provided to calculate the 'ALINE' Distance between words as per
(Kondrak 2000) and (Downey, Hallmark, Cox, Norquest, & Lansing, 2008,
<doi:10.1080/09296170802326681>). The score is based on phonetic features represented
using the Unicode-compliant International Phonetic Alphabet (IPA). Parameterized
features weights are used to determine the optimal alignment and functions are
provided to estimate optimum values using a genetic algorithm and supervised
learning. See (Downey, Sun, and Norquest 2017,
<https://journal.r-project.org/archive/2017/RJ-2017-005/index.html>.
Author: Sean Downey [aut, cre],
Guowei Sun [aut],
Greg Kondrak [cph] (Copyright holder of original ALINE algorithm C++
source code included in package.)
Maintainer: Sean Downey <sean@codexdata.com>
Diff between alineR versions 1.1.3 dated 2016-04-01 and 1.1.4 dated 2017-09-14
DESCRIPTION | 30 ++++++++++++++++++++---------- MD5 | 9 +++++---- NAMESPACE | 2 +- inst/CITATION | 21 ++++++++++++--------- man/aline-package.Rd | 16 ++++++++++------ src/registerDynamicsSymbol.c |only 6 files changed, 48 insertions(+), 30 deletions(-)
Title: Markov-Switching GARCH Models
Description: The MSGARCH package offers methods to fit (by Maximum Likelihood or MCMC/Bayesian), simulate, and forecast various
Markov-Switching GARCH models as described in Ardia et al. (2017) <https://ssrn.com/abstract=2845809>.
Author: David Ardia [aut],
Keven Bluteau [aut, cre],
Kris Boudt [ctb],
Leopoldo Catania [aut],
Brian Peterson [ctb],
Denis-Alexandre Trottier [aut]
Maintainer: Keven Bluteau <Keven.Bluteau@unine.ch>
Diff between MSGARCH versions 0.17.7 dated 2017-01-09 and 1.1 dated 2017-09-14
MSGARCH-0.17.7/MSGARCH/R/Pstate.R |only MSGARCH-0.17.7/MSGARCH/R/bayes.R |only MSGARCH-0.17.7/MSGARCH/R/cdf.R |only MSGARCH-0.17.7/MSGARCH/R/create.spec.R |only MSGARCH-0.17.7/MSGARCH/R/crps.R |only MSGARCH-0.17.7/MSGARCH/R/f.theta.IndDist.R |only MSGARCH-0.17.7/MSGARCH/R/f.theta.mixture.R |only MSGARCH-0.17.7/MSGARCH/R/findParameters.R |only MSGARCH-0.17.7/MSGARCH/R/ht.R |only MSGARCH-0.17.7/MSGARCH/R/kernel.R |only MSGARCH-0.17.7/MSGARCH/R/mle.R |only MSGARCH-0.17.7/MSGARCH/R/pdf.R |only MSGARCH-0.17.7/MSGARCH/R/pit.R |only MSGARCH-0.17.7/MSGARCH/R/pred.R |only MSGARCH-0.17.7/MSGARCH/R/risk.R |only MSGARCH-0.17.7/MSGARCH/R/sim.R |only MSGARCH-0.17.7/MSGARCH/R/simahead.R |only MSGARCH-0.17.7/MSGARCH/R/spec.R |only MSGARCH-0.17.7/MSGARCH/R/transmat.R |only MSGARCH-0.17.7/MSGARCH/R/unc.vol.R |only MSGARCH-0.17.7/MSGARCH/R/utils.R |only MSGARCH-0.17.7/MSGARCH/data/AMZN.rda |only MSGARCH-0.17.7/MSGARCH/data/sp500.rda |only MSGARCH-0.17.7/MSGARCH/man/AMZN.Rd |only MSGARCH-0.17.7/MSGARCH/man/Pstate.Rd |only MSGARCH-0.17.7/MSGARCH/man/cdf.Rd |only MSGARCH-0.17.7/MSGARCH/man/create.spec.Rd |only MSGARCH-0.17.7/MSGARCH/man/crps.Rd |only MSGARCH-0.17.7/MSGARCH/man/fit.bayes.Rd |only MSGARCH-0.17.7/MSGARCH/man/fit.mle.Rd |only MSGARCH-0.17.7/MSGARCH/man/ht.Rd |only MSGARCH-0.17.7/MSGARCH/man/kernel.Rd |only MSGARCH-0.17.7/MSGARCH/man/pdf.Rd |only MSGARCH-0.17.7/MSGARCH/man/pit.Rd |only MSGARCH-0.17.7/MSGARCH/man/pred.Rd |only MSGARCH-0.17.7/MSGARCH/man/risk.Rd |only MSGARCH-0.17.7/MSGARCH/man/sim.Rd |only MSGARCH-0.17.7/MSGARCH/man/simahead.Rd |only MSGARCH-0.17.7/MSGARCH/man/sp500.Rd |only MSGARCH-0.17.7/MSGARCH/man/transmat.Rd |only MSGARCH-0.17.7/MSGARCH/man/unc.vol.Rd |only MSGARCH-0.17.7/MSGARCH/src/Gas.cpp |only MSGARCH-0.17.7/MSGARCH/src/spec.h |only MSGARCH-1.1/MSGARCH/DESCRIPTION | 23 MSGARCH-1.1/MSGARCH/MD5 | 173 +++-- MSGARCH-1.1/MSGARCH/NAMESPACE | 203 +++--- MSGARCH-1.1/MSGARCH/NEWS | 103 ++- MSGARCH-1.1/MSGARCH/R/AIC.R | 102 +-- MSGARCH-1.1/MSGARCH/R/BIC.R | 104 +-- MSGARCH-1.1/MSGARCH/R/CondVol.R |only MSGARCH-1.1/MSGARCH/R/CreateSpec.R |only MSGARCH-1.1/MSGARCH/R/DIC.R | 113 +-- MSGARCH-1.1/MSGARCH/R/Distributions.R |only MSGARCH-1.1/MSGARCH/R/ExtractStateFit.R |only MSGARCH-1.1/MSGARCH/R/FitMCMC.R |only MSGARCH-1.1/MSGARCH/R/FitML.R |only MSGARCH-1.1/MSGARCH/R/Forecast.R |only MSGARCH-1.1/MSGARCH/R/Inference.R |only MSGARCH-1.1/MSGARCH/R/Kernel.R |only MSGARCH-1.1/MSGARCH/R/Likelihood.R |only MSGARCH-1.1/MSGARCH/R/MSGARCH.R | 109 ++- MSGARCH-1.1/MSGARCH/R/Optimizers.R |only MSGARCH-1.1/MSGARCH/R/PIT.R |only MSGARCH-1.1/MSGARCH/R/ParameterConstraints.R |only MSGARCH-1.1/MSGARCH/R/ParameterTransformation.R |only MSGARCH-1.1/MSGARCH/R/Plot.R |only MSGARCH-1.1/MSGARCH/R/Posterior.R |only MSGARCH-1.1/MSGARCH/R/Pred.R |only MSGARCH-1.1/MSGARCH/R/RcppExports.R |only MSGARCH-1.1/MSGARCH/R/Risk.R |only MSGARCH-1.1/MSGARCH/R/Samplers.R |only MSGARCH-1.1/MSGARCH/R/Sim.R |only MSGARCH-1.1/MSGARCH/R/StartingValues.R |only MSGARCH-1.1/MSGARCH/R/State.R |only MSGARCH-1.1/MSGARCH/R/TransMat.R |only MSGARCH-1.1/MSGARCH/R/UncVol.R |only MSGARCH-1.1/MSGARCH/R/Utils.R |only MSGARCH-1.1/MSGARCH/R/Volatility.R |only MSGARCH-1.1/MSGARCH/R/print.R | 607 +++++++----------- MSGARCH-1.1/MSGARCH/R/zzz.R | 29 MSGARCH-1.1/MSGARCH/THANKS | 5 MSGARCH-1.1/MSGARCH/data/SMI.rda |only MSGARCH-1.1/MSGARCH/data/dem2gbp.rda |only MSGARCH-1.1/MSGARCH/inst/CITATION | 63 - MSGARCH-1.1/MSGARCH/inst/COPYRIGHTS | 20 MSGARCH-1.1/MSGARCH/inst/test |only MSGARCH-1.1/MSGARCH/man/AIC.Rd | 87 +- MSGARCH-1.1/MSGARCH/man/BIC.Rd | 87 +- MSGARCH-1.1/MSGARCH/man/CreateSpec.Rd |only MSGARCH-1.1/MSGARCH/man/DIC.Rd | 102 +-- MSGARCH-1.1/MSGARCH/man/ExtractStateFit.Rd |only MSGARCH-1.1/MSGARCH/man/FitMCMC.Rd |only MSGARCH-1.1/MSGARCH/man/FitML.Rd |only MSGARCH-1.1/MSGARCH/man/Forecast.Rd |only MSGARCH-1.1/MSGARCH/man/MSGARCH-package.Rd |only MSGARCH-1.1/MSGARCH/man/PIT.Rd |only MSGARCH-1.1/MSGARCH/man/Pred.Rd |only MSGARCH-1.1/MSGARCH/man/Risk.Rd |only MSGARCH-1.1/MSGARCH/man/SMI.Rd |only MSGARCH-1.1/MSGARCH/man/Sim.Rd |only MSGARCH-1.1/MSGARCH/man/State.Rd |only MSGARCH-1.1/MSGARCH/man/TransMat.Rd |only MSGARCH-1.1/MSGARCH/man/UncVol.Rd |only MSGARCH-1.1/MSGARCH/man/Volatility.Rd |only MSGARCH-1.1/MSGARCH/man/dem2gbp.Rd |only MSGARCH-1.1/MSGARCH/src/Decoding.cpp |only MSGARCH-1.1/MSGARCH/src/Decoding.h |only MSGARCH-1.1/MSGARCH/src/EM.cpp |only MSGARCH-1.1/MSGARCH/src/EM.h |only MSGARCH-1.1/MSGARCH/src/Egarch.cpp | 325 +++++---- MSGARCH-1.1/MSGARCH/src/Ged.cpp |only MSGARCH-1.1/MSGARCH/src/Ged.h |only MSGARCH-1.1/MSGARCH/src/MSgarch.cpp | 56 - MSGARCH-1.1/MSGARCH/src/MSgarch.h | 800 +++++++++++++----------- MSGARCH-1.1/MSGARCH/src/Makevars |only MSGARCH-1.1/MSGARCH/src/Makevars.win |only MSGARCH-1.1/MSGARCH/src/Mapping.cpp |only MSGARCH-1.1/MSGARCH/src/Normal.cpp |only MSGARCH-1.1/MSGARCH/src/Normal.h |only MSGARCH-1.1/MSGARCH/src/RcppExports.cpp |only MSGARCH-1.1/MSGARCH/src/SingleRegime.h | 686 ++++++++++---------- MSGARCH-1.1/MSGARCH/src/Skewed.h |only MSGARCH-1.1/MSGARCH/src/Student.cpp |only MSGARCH-1.1/MSGARCH/src/Student.h |only MSGARCH-1.1/MSGARCH/src/Symmetric.h |only MSGARCH-1.1/MSGARCH/src/Tgarch.cpp | 329 +++++---- MSGARCH-1.1/MSGARCH/src/Utils.h |only MSGARCH-1.1/MSGARCH/src/eGARCH.h |only MSGARCH-1.1/MSGARCH/src/gjrGARCH.cpp | 327 +++++---- MSGARCH-1.1/MSGARCH/src/gjrGARCH.h |only MSGARCH-1.1/MSGARCH/src/pdf_c.cpp |only MSGARCH-1.1/MSGARCH/src/sARCH.cpp |only MSGARCH-1.1/MSGARCH/src/sARCH.h |only MSGARCH-1.1/MSGARCH/src/sGARCH.cpp | 325 +++++---- MSGARCH-1.1/MSGARCH/src/sGARCH.h |only MSGARCH-1.1/MSGARCH/src/tGARCH.h |only MSGARCH-1.1/MSGARCH/tests |only 137 files changed, 2573 insertions(+), 2205 deletions(-)
Title: Joint Modelling of Repeated Measurements and Time-to-Event Data
Description: Analysis of repeated measurements and time-to-event data via random
effects joint models. Fits the joint models proposed by Henderson and colleagues
<doi:10.1093/biostatistics/1.4.465> (single event time) and by Williamson and
colleagues (2008) <doi:10.1002/sim.3451> (competing risks events time) to a
single continuous repeated measure. The time-to-event data is modelled using a
(cause-specific) Cox proportional hazards regression model with time-varying
covariates. The longitudinal outcome is modelled using a linear mixed effects
model. The association is captured by a latent Gaussian process. The model is
estimated using am Expectation Maximization algorithm. Some plotting functions
and the variogram are also included. This project is funded by the Medical
Research Council (Grant numbers G0400615 and MR/M013227/1).
Author: Pete Philipson [aut],
Ines Sousa [aut],
Peter J. Diggle [aut],
Paula Williamson [aut],
Ruwanthi Kolamunnage-Dona [aut],
Robin Henderson [aut],
Graeme L. Hickey [aut, cre],
Maria Sudell [ctb]
Maintainer: Graeme L. Hickey <graeme.hickey@liverpool.ac.uk>
Diff between joineR versions 1.2.1 dated 2017-07-24 and 1.2.2 dated 2017-09-14
DESCRIPTION | 6 +-- MD5 | 15 ++++---- NEWS.md | 15 ++++++++ R/longst.R | 8 ++-- README.md | 20 +++++------ inst/doc/competing-risks.html | 12 +++---- inst/doc/joineR.html | 70 ++++++++++++++++++++--------------------- man/figures |only tests/testthat/test-comprisk.R | 2 - 9 files changed, 82 insertions(+), 66 deletions(-)
Title: Linkage Map Construction using the MSTmap Algorithm
Description: Functions for Accurate and Speedy linkage map construction, manipulation and diagnosis of Doubled Haploid, Backcross and Recombinant Inbred 'R/qtl' objects. This includes extremely fast linkage map clustering and optimal marker ordering using 'MSTmap' (see Wu et al.,2008).
Author: Julian Taylor <julian.taylor@adelaide.edu.au>, David Butler
<dbutler@uow.edu.au>.
Maintainer: Julian Taylor <julian.taylor@adelaide.edu.au>
Diff between ASMap versions 1.0-1 dated 2017-07-26 and 1.0-2 dated 2017-09-14
DESCRIPTION | 8 MD5 | 20 - build/vignette.rds |binary data/mapBC.RData |binary data/mapBCu.RData |binary data/mapDH.RData |binary data/mapDHf.RData |binary data/mapF2.RData |binary inst/doc/asmapvignette.R | 766 ++++++++++++++++++++++----------------------- inst/doc/asmapvignette.pdf |binary man/heatMap.Rd | 6 11 files changed, 400 insertions(+), 400 deletions(-)
Title: Fast R and C++ Access to NIfTI Images
Description: Provides very fast access to images stored in the NIfTI-1 file
format <http://www.nitrc.org/docman/view.php/26/64/nifti1.h>, 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],
Matt Hall [ctb],
Rick Reynolds [ctb],
Kate Fissell [ctb],
Jean-loup Gailly [cph],
Mark Adler [cph]
Maintainer: Jon Clayden <code@clayden.org>
Diff between RNifti versions 0.7.0 dated 2017-06-12 and 0.7.1 dated 2017-09-14
RNifti-0.7.0/RNifti/inst/doxygen |only RNifti-0.7.1/RNifti/DESCRIPTION | 8 RNifti-0.7.1/RNifti/MD5 | 138 ------------- RNifti-0.7.1/RNifti/NEWS | 8 RNifti-0.7.1/RNifti/inst/include/lib/NiftiImage.h | 5 RNifti-0.7.1/RNifti/inst/include/lib/NiftiImage_internal.h | 13 - RNifti-0.7.1/RNifti/src/main.cpp | 9 7 files changed, 37 insertions(+), 144 deletions(-)
Title: Get Data for Brazilian Bonds (Tesouro Direto)
Description: Downloads and aggregates data for Brazilian government issued bonds directly from the website of Tesouro Direto <http://www.tesouro.fazenda.gov.br/tesouro-direto-balanco-e-estatisticas>.
Author: Marcelo Perlin [aut, cre]
Maintainer: Marcelo Perlin <marceloperlin@gmail.com>
Diff between GetTDData versions 1.2.5 dated 2016-11-07 and 1.3 dated 2017-09-14
GetTDData-1.2.5/GetTDData/inst/doc/gtdd-vignette.R |only GetTDData-1.2.5/GetTDData/inst/doc/gtdd-vignette.Rmd |only GetTDData-1.2.5/GetTDData/inst/doc/gtdd-vignette.html |only GetTDData-1.2.5/GetTDData/vignettes/gtdd-vignette.Rmd |only GetTDData-1.3/GetTDData/DESCRIPTION | 13 GetTDData-1.3/GetTDData/MD5 | 29 GetTDData-1.3/GetTDData/NAMESPACE | 1 GetTDData-1.3/GetTDData/NEWS.md | 60 - GetTDData-1.3/GetTDData/R/gtdd_get_yield_curve.R |only GetTDData-1.3/GetTDData/R/gtdd_read_TD_files.R | 419 +++++----- GetTDData-1.3/GetTDData/README.md |only GetTDData-1.3/GetTDData/build/vignette.rds |binary GetTDData-1.3/GetTDData/inst/doc/gtdd-vignette_GetTDData.R |only GetTDData-1.3/GetTDData/inst/doc/gtdd-vignette_GetTDData.Rmd |only GetTDData-1.3/GetTDData/inst/doc/gtdd-vignette_GetTDData.html |only GetTDData-1.3/GetTDData/inst/doc/gtdd-vignette_YieldCurve.R |only GetTDData-1.3/GetTDData/inst/doc/gtdd-vignette_YieldCurve.Rmd |only GetTDData-1.3/GetTDData/inst/doc/gtdd-vignette_YieldCurve.html |only GetTDData-1.3/GetTDData/man/download.TD.data.Rd | 1 GetTDData-1.3/GetTDData/man/get.yield.curve.Rd |only GetTDData-1.3/GetTDData/man/read.TD.files.Rd | 1 GetTDData-1.3/GetTDData/vignettes/gtdd-vignette_GetTDData.Rmd |only GetTDData-1.3/GetTDData/vignettes/gtdd-vignette_YieldCurve.Rmd |only 23 files changed, 271 insertions(+), 253 deletions(-)
Title: Causal Learning of Mixed Graphical Models
Description: Allows users to learn undirected and directed (causal) graphs over mixed data types (i.e., continuous and discrete variables). To learn a directed graph over mixed data, it first calculates the undirected graph (Sedgewick et al, 2016) and then it uses local search strategies to prune-and-orient this graph (Sedgewick et al, 2017). AJ Sedgewick, I Shi, RM Donovan, PV Benos (2016) <doi:10.1186/s12859-016-1039-0>. AJ Sedgewick, JD Ramsey, P Spirtes, C Glymour, PV Benos (2017) <arXiv:1704.02621>.
Author: Andrew J Sedgewick, Neha Abraham <neha.abraham@pitt.edu>, Vineet Raghu <vineetraghu@gmail.com>, Panagiotis Benos <benos@pitt.edu>
Maintainer: Neha Abraham <mgmquery@pitt.edu>
Diff between causalMGM versions 0.1.0 dated 2017-08-30 and 0.1.1 dated 2017-09-14
causalMGM-0.1.0/causalMGM/R/steps.R |only causalMGM-0.1.0/causalMGM/man/steps.Rd |only causalMGM-0.1.1/causalMGM/DESCRIPTION | 6 +++--- causalMGM-0.1.1/causalMGM/MD5 | 6 ++---- causalMGM-0.1.1/causalMGM/README.md | 7 ------- 5 files changed, 5 insertions(+), 14 deletions(-)
Title: Computation of v Values for U and Copula C(U, v)
Description: Computation the value of one of two uniformly
distributed marginals if the copula probability value is known
and the value of the second marginal is also known.
Computation and plotting corresponding cumulative
distribution function or survival function.
The numerical definition of a common area limited by lines
of the cumulative distribution function and survival function.
Approximate quantification of the probability of this area.
Author: Josef Brejcha
Maintainer: Josef Brejcha <brchjo@gmail.com>
Diff between vfcp versions 1.2.0 dated 2017-09-01 and 1.3.0 dated 2017-09-14
DESCRIPTION | 10 +++++----- MD5 | 40 +++++++++++++++++++++++----------------- NAMESPACE | 6 +++++- NEWS | 11 +++++++++++ R/CSmeze.R | 4 ++-- R/CSmezesi.R |only R/fxa.R | 7 +++---- R/vfcfaj.R | 6 ++++-- R/vfcfg.R | 10 +++++++--- R/vfex.R | 4 +++- R/vffgm.R | 3 ++- R/vfpripo.R | 2 ++ R/vfpsae.R |only R/vfpsimsi.R |only man/CSmeze.Rd | 35 ++--------------------------------- man/CSmezesi.Rd |only man/fxa.Rd | 2 +- man/vfclayton.Rd | 4 ++-- man/vfcp-package.Rd | 4 ++-- man/vffrank.Rd | 4 ++-- man/vfgumbel.Rd | 4 ++-- man/vfjoe.Rd | 4 ++-- man/vfpsae.Rd |only man/vfpsimsi.Rd |only 24 files changed, 80 insertions(+), 80 deletions(-)
Title: PLS Analyses for Genomics
Description: Routines for PLS-based genomic analyses,
implementing PLS methods for classification with
microarray data and prediction of transcription factor
activities from combined ChIP-chip analysis. The >=1.2-1
versions include two new classification methods for microarray
data: GSIM and Ridge PLS. The >=1.3 versions includes a
new classification method combining variable selection and
compression in logistic regression context: logit-SPLS; and
an adaptive version of the sparse PLS.
Author: Anne-Laure Boulesteix <boulesteix@ibe.med.uni-muenchen.de>,
Ghislain Durif <gd.dev@libertymail.net>,
Sophie Lambert-Lacroix
<sophie.lambert-lacroix@univ-grenoble-alpes.fr>, Julie Peyre
<Julie.Peyre@univ-grenoble-alpes.fr>, and Korbinian Strimmer
<k.strimmer@imperial.ac.uk>.
Maintainer: Ghislain Durif <gd.dev@libertymail.net>
Diff between plsgenomics versions 1.5 dated 2017-08-30 and 1.5-1 dated 2017-09-14
DESCRIPTION | 8 +++--- MD5 | 10 +++---- R/logit.spls.cv.R | 2 - R/multinom.spls.cv.R | 2 - R/spls.cv.R | 68 ++++++++++++++++++++++++++++++++++++++++----------- R/zzz.R | 1 6 files changed, 66 insertions(+), 25 deletions(-)
Title: Pakistan Population Census 2017
Description: Provides data sets and functions for exploration of Pakistan Population Census 2017 (<http://www.pbscensus.gov.pk/>).
Author: Muhammad Yaseen [aut, cre]
Maintainer: Muhammad Yaseen <myaseen208@gmail.com>
Diff between PakPC2017 versions 0.1.0 dated 2017-09-05 and 0.2.0 dated 2017-09-14
DESCRIPTION | 8 ++++---- MD5 | 42 +++++++++++++++++++++--------------------- NEWS.md | 7 +++++++ R/PakPC2017Balochistan.R | 38 +++++++++++++++++++------------------- R/PakPC2017City10.R | 21 ++++++++++++++++----- R/PakPC2017FATA.R | 38 +++++++++++++++++++------------------- R/PakPC2017Islamabad.R | 37 +++++++++++++++++++------------------ R/PakPC2017KPK.R | 37 +++++++++++++++++++------------------ R/PakPC2017Pak.R | 34 +++++++++++++++++----------------- R/PakPC2017Pakistan.R | 39 ++++++++++++++++++++------------------- R/PakPC2017Punjab.R | 36 +++++++++++++++++------------------- R/PakPC2017Sindh.R | 38 +++++++++++++++++++------------------- inst/doc/PakPC2017-Intro.pdf |binary man/PakPC2017Balochistan.Rd | 38 ++++++++++++++++---------------------- man/PakPC2017City10.Rd | 23 +++++++++++++++-------- man/PakPC2017FATA.Rd | 38 ++++++++++++++++---------------------- man/PakPC2017Islamabad.Rd | 37 ++++++++++++++++--------------------- man/PakPC2017KPK.Rd | 37 ++++++++++++++++--------------------- man/PakPC2017Pak.Rd | 36 ++++++++++++++++-------------------- man/PakPC2017Pakistan.Rd | 38 ++++++++++++++++---------------------- man/PakPC2017Punjab.Rd | 38 ++++++++++++++++---------------------- man/PakPC2017Sindh.Rd | 38 ++++++++++++++++---------------------- 22 files changed, 340 insertions(+), 358 deletions(-)
Title: A Powerful Tool to Quickly Compare Huge Lists and Draw Venn
Diagrams
Description: Compare lists (from 2 to infinite) and plot the results in a Venn diagram if (N<=4) with regulation details. It allows to produce a complete annotated file, merging the annotations of the compared lists. It is also possible to compute an overlaps table to show the overlaps proportions of all the couples of lists and draw proportional Venn diagrams.
Author: Nicolas Cagnard
Maintainer: Nicolas Cagnard <nicolas.cagnard@gmail.com>
Diff between eVenn versions 2.3.6 dated 2017-08-22 and 2.4 dated 2017-09-14
DESCRIPTION | 8 MD5 | 8 R/evenn.R | 733 ++++++++++++++++++++++++++++++++------------------- R/man.evenn.R | 18 - man/eVenn-package.Rd | 4 5 files changed, 482 insertions(+), 289 deletions(-)
Title: Business Days Calculations and Utilities
Description: Business days calculations based on a list of holidays and
nonworking weekdays. Quite useful for fixed income and derivatives pricing.
Author: Wilson Freitas <wilson.freitas@gmail.com>
Maintainer: Wilson Freitas <wilson.freitas@gmail.com>
Diff between bizdays versions 1.0.3 dated 2017-05-03 and 1.0.4 dated 2017-09-14
DESCRIPTION | 10 +-- MD5 | 31 +++++---- NAMESPACE | 12 +++ NEWS | 8 ++ R/R-bizdays-package.r | 1 R/bizdiff.R |only R/calendar.R | 68 ++++++++++++++++++++- R/create-calendars.R | 20 ++++-- README.md | 2 build/vignette.rds |binary inst/doc/Creating_Calendars.R | 2 inst/doc/Creating_Calendars.Rmd | 2 inst/doc/Creating_Calendars.html | 11 --- inst/doc/Setting_default_calendar_in_Rprofile.html | 6 - man/bizdiff.Rd |only man/calendar-holidays-weekdays.Rd |only tests/testthat/test-calendar.R | 24 +++++++ vignettes/Creating_Calendars.Rmd | 2 18 files changed, 159 insertions(+), 40 deletions(-)
Title: Fast Simulation of Normal/Exponential Random Variables and
Stochastic Differential Equations / Poisson Processes
Description: Fast simulation of some random variables than the usual native functions, including rnorm() and rexp(), using Ziggurat method, reference: MARSAGLIA, George, TSANG, Wai Wan, and al. (2000) <doi:10.18637/jss.v005.i08>, and fast simulation of stochastic differential equations / Poisson processes.
Author: Nicolas Baradel
Maintainer: Nicolas Baradel - PGM Solutions <nicolas.baradel@pgm-solutions.com>
Diff between rpgm versions 1.0.1 dated 2017-07-08 and 1.0.2 dated 2017-09-14
rpgm-1.0.1/rpgm/src/jarquebera.c |only rpgm-1.0.1/rpgm/src/rbernou_rpgm.c |only rpgm-1.0.1/rpgm/src/rbrownian.c |only rpgm-1.0.1/rpgm/src/rcantor_rpgm.c |only rpgm-1.0.1/rpgm/src/rexp_rpgm.c |only rpgm-1.0.1/rpgm/src/rgpd.c |only rpgm-1.0.1/rpgm/src/rnorm_rpgm.c |only rpgm-1.0.1/rpgm/src/rpoisson.c |only rpgm-1.0.1/rpgm/src/vasicek.c |only rpgm-1.0.2/rpgm/DESCRIPTION | 9 ++++--- rpgm-1.0.2/rpgm/MD5 | 43 +++++++++++++++++++---------------- rpgm-1.0.2/rpgm/R/rpgm.set.seed.R |only rpgm-1.0.2/rpgm/man/colMaxs.Rd | 2 - rpgm-1.0.2/rpgm/man/rbernou.Rd | 2 - rpgm-1.0.2/rpgm/man/rpgm.rgeom.Rd | 2 - rpgm-1.0.2/rpgm/man/rpgm.rlnorm.Rd | 2 - rpgm-1.0.2/rpgm/man/rpgm.rnorm.Rd | 2 - rpgm-1.0.2/rpgm/man/rpgm.rt.Rd | 2 - rpgm-1.0.2/rpgm/man/rpgm.set.seed.Rd |only rpgm-1.0.2/rpgm/src/Makevars |only rpgm-1.0.2/rpgm/src/jarquebera.cpp |only rpgm-1.0.2/rpgm/src/mt19337.cpp |only rpgm-1.0.2/rpgm/src/mt19337.h |only rpgm-1.0.2/rpgm/src/rbernou_rpgm.cpp |only rpgm-1.0.2/rpgm/src/rbrownian.cpp |only rpgm-1.0.2/rpgm/src/rcantor_rpgm.cpp |only rpgm-1.0.2/rpgm/src/rexp_rpgm.cpp |only rpgm-1.0.2/rpgm/src/rexp_rpgm.h | 11 +++++++- rpgm-1.0.2/rpgm/src/rgpd.cpp |only rpgm-1.0.2/rpgm/src/rnorm_rpgm.cpp |only rpgm-1.0.2/rpgm/src/rnorm_rpgm.h | 7 ++++- rpgm-1.0.2/rpgm/src/rpgm_init.c | 4 +++ rpgm-1.0.2/rpgm/src/rpoisson.cpp |only rpgm-1.0.2/rpgm/src/vasicek.cpp |only 34 files changed, 54 insertions(+), 32 deletions(-)
Title: Kinetic Evaluation of Chemical Degradation Data
Description: Calculation routines based on the FOCUS Kinetics Report (2006,
2014). Includes a function for conveniently defining differential equation
models, model solution based on eigenvalues if possible or using numerical
solvers and a choice of the optimisation methods made available by the 'FME'
package. If a C compiler (on windows: 'Rtools') is installed, differential
equation models are solved using compiled C functions. Please note that no
warranty is implied for correctness of results or fitness for a particular
purpose.
Author: Johannes Ranke [aut, cre, cph],
Katrin Lindenberger [ctb],
René Lehmann [ctb],
Eurofins Regulatory AG [cph]
Maintainer: Johannes Ranke <jranke@uni-bremen.de>
Diff between mkin versions 0.9.46 dated 2017-07-29 and 0.9.46.1 dated 2017-09-14
DESCRIPTION | 8 ++--- MD5 | 22 +++++++------- NEWS.md | 8 +++++ R/mkinfit.R | 2 - R/plot.mkinfit.R | 11 ++++--- README.md | 2 - inst/doc/FOCUS_D.html | 14 ++++---- inst/doc/FOCUS_L.html | 66 +++++++++++++++++++++--------------------- inst/doc/FOCUS_Z.pdf |binary inst/doc/compiled_models.html | 18 +++++------ inst/doc/mkin.html | 6 +-- inst/doc/twa.html | 4 +- 12 files changed, 86 insertions(+), 75 deletions(-)
Title: Inferring Causal Effects using Bayesian Structural Time-Series
Models
Description: Implements a Bayesian approach to causal impact estimation in time
series, as described in Brodersen et al. (2015) <DOI:10.1214/14-AOAS788>.
See the package documentation on GitHub
<https://google.github.io/CausalImpact/> to get started.
Author: Kay H. Brodersen <kbrodersen@google.com>,
Alain Hauser <alhauser@google.com>
Maintainer: Alain Hauser <alhauser@google.com>
Diff between CausalImpact versions 1.2.1 dated 2017-05-31 and 1.2.2 dated 2017-09-14
DESCRIPTION | 10 +++--- MD5 | 26 +++++++-------- R/impact_analysis.R | 41 ++++++++++++------------ R/impact_inference.R | 46 +++++++++++++++------------ R/impact_misc.R | 63 +++----------------------------------- R/impact_model.R | 12 ++++--- R/impact_plot.R | 4 +- README.md | 16 ++++++--- build/vignette.rds |binary inst/doc/CausalImpact.Rmd | 9 +++-- inst/doc/CausalImpact.html | 19 ++++++----- man/CausalImpact.Rd | 10 +++--- tests/testthat/test-impact-misc.R | 52 +++---------------------------- vignettes/CausalImpact.Rmd | 9 +++-- 14 files changed, 121 insertions(+), 196 deletions(-)
Title: Smoothing of Two-Dimensional Demographic Data, Optionally Taking
into Account Period and Cohort Effects
Description: The implemented method uses for smoothing bivariate thin plate
splines, bivariate lasso-type regularization, and allows for both period
and cohort effects. Thus the mortality rates are modelled as the sum of four
components: a smooth bivariate function of age and time, smooth one-dimensional
cohort effects, smooth one-dimensional period effects and random errors.
Author: Alexander Dokumentov, Rob J Hyndman
Maintainer: Alexander Dokumentov <alexander.dokumentov@gmail.com>
Diff between smoothAPC versions 0.1 dated 2016-09-18 and 0.2 dated 2017-09-14
DESCRIPTION | 16 +- MD5 | 26 +-- R/auto.l1tp.smooth.R | 203 +++++++++++++++++-------------- R/l1tp.smooth.R | 34 +++-- man/autoSmoothAPC.Rd | 24 ++- man/plot.matrix.Rd | 1 man/plot.smAPC.Rd | 1 man/plot3d.Rd | 1 man/plot3d.matrix.Rd | 1 man/plot3d.smAPC.Rd | 1 man/signifAutoSmoothAPC.Rd | 18 +- man/smoothAPC.Rd | 16 +- tests/testthat/test_demogSmooth.R | 19 ++ tests/testthat/test_twoStepDemogSmooth.R | 15 ++ 14 files changed, 230 insertions(+), 146 deletions(-)
Title: A Data-Centered Data Flow Manager
Description: A data manager meant to avoid manual storage/retrieval of
data to/from the file system. It builds one (or more) centralized
repository where R objects are stored with rich annotations,
including corresponding code chunks, and easily searched and
retrieved.
Author: Francesco Napolitano <franapoli@gmail.com>
Maintainer: Francesco Napolitano <franapoli@gmail.com>
Diff between repo versions 2.0.2 dated 2016-05-03 and 2.1.1 dated 2017-09-14
repo-2.0.2/repo/R/repoS3.R |only repo-2.0.2/repo/man/print.repo.Rd |only repo-2.0.2/repo/man/repo_append.Rd |only repo-2.1.1/repo/DESCRIPTION | 18 repo-2.1.1/repo/MD5 | 92 +- repo-2.1.1/repo/NAMESPACE | 18 repo-2.1.1/repo/NEWS.md | 172 +++ repo-2.1.1/repo/R/repo.R | 1277 ++--------------------------- repo-2.1.1/repo/R/repo_private.R |only repo-2.1.1/repo/R/repo_public.R |only repo-2.1.1/repo/README.md | 158 +++ repo-2.1.1/repo/build/vignette.rds |binary repo-2.1.1/repo/inst/CITATION |only repo-2.1.1/repo/inst/README-depgraph-1.png |only repo-2.1.1/repo/inst/doc/index.R | 103 -- repo-2.1.1/repo/inst/doc/index.Rmd | 327 ++----- repo-2.1.1/repo/inst/doc/index.html | 1136 ++++++++++++++++--------- repo-2.1.1/repo/man/repo-package.Rd | 12 repo-2.1.1/repo/man/repo_attach.Rd | 26 repo-2.1.1/repo/man/repo_attr.Rd |only repo-2.1.1/repo/man/repo_build.Rd |only repo-2.1.1/repo/man/repo_bulkedit.Rd | 7 repo-2.1.1/repo/man/repo_check.Rd | 8 repo-2.1.1/repo/man/repo_chunk.Rd |only repo-2.1.1/repo/man/repo_copy.Rd | 16 repo-2.1.1/repo/man/repo_cpanel.Rd | 1 repo-2.1.1/repo/man/repo_dependencies.Rd | 24 repo-2.1.1/repo/man/repo_depends.Rd |only repo-2.1.1/repo/man/repo_entries.Rd | 8 repo-2.1.1/repo/man/repo_export.Rd | 10 repo-2.1.1/repo/man/repo_find.Rd | 10 repo-2.1.1/repo/man/repo_get.Rd | 10 repo-2.1.1/repo/man/repo_handlers.Rd | 12 repo-2.1.1/repo/man/repo_has.Rd |only repo-2.1.1/repo/man/repo_info.Rd | 7 repo-2.1.1/repo/man/repo_lazydo.Rd | 9 repo-2.1.1/repo/man/repo_load.Rd |only repo-2.1.1/repo/man/repo_open.Rd | 3 repo-2.1.1/repo/man/repo_options.Rd |only repo-2.1.1/repo/man/repo_pies.Rd |only repo-2.1.1/repo/man/repo_print.Rd |only repo-2.1.1/repo/man/repo_project.Rd |only repo-2.1.1/repo/man/repo_pull.Rd | 7 repo-2.1.1/repo/man/repo_put.Rd | 55 - repo-2.1.1/repo/man/repo_related.Rd |only repo-2.1.1/repo/man/repo_rm.Rd | 7 repo-2.1.1/repo/man/repo_root.Rd | 10 repo-2.1.1/repo/man/repo_set.Rd | 29 repo-2.1.1/repo/man/repo_stash.Rd | 31 repo-2.1.1/repo/man/repo_stashclear.Rd | 12 repo-2.1.1/repo/man/repo_sys.Rd | 7 repo-2.1.1/repo/man/repo_tag.Rd | 7 repo-2.1.1/repo/man/repo_tags.Rd | 7 repo-2.1.1/repo/man/repo_untag.Rd | 7 repo-2.1.1/repo/tests |only repo-2.1.1/repo/vignettes/index.Rmd | 327 ++----- 56 files changed, 1680 insertions(+), 2290 deletions(-)
Title: Designing Multi-Arm Multi-Stage Studies
Description: Designing multi-arm multi-stage studies with (asymptotically) normal endpoints and known variance.
Author: Thomas Jaki <jaki.thomas@gmail.com>, Dominic Magirr <d.magirr@gmail.com>, Philip Pallmann <p.pallmann@lancaster.ac.uk>
Maintainer: Thomas Jaki <jaki.thomas@gmail.com>
Diff between MAMS versions 1.01 dated 2017-02-23 and 1.2 dated 2017-09-14
MAMS-1.01/MAMS/R/step_down_mams.R |only MAMS-1.01/MAMS/R/update_mams.R |only MAMS-1.01/MAMS/man/step_down_mams.Rd |only MAMS-1.01/MAMS/man/update_mams.Rd |only MAMS-1.2/MAMS/DESCRIPTION | 11 MAMS-1.2/MAMS/MD5 | 38 - MAMS-1.2/MAMS/NAMESPACE | 53 +- MAMS-1.2/MAMS/R/generics.R | 468 +++++++++++---------- MAMS-1.2/MAMS/R/internal.R | 24 - MAMS-1.2/MAMS/R/mams.R | 753 ++++++++++++++++++----------------- MAMS-1.2/MAMS/R/mams.sim.R | 269 ++++++------ MAMS-1.2/MAMS/R/new.bounds.R | 528 ++++++++++++------------ MAMS-1.2/MAMS/R/ordinal.mams.R |only MAMS-1.2/MAMS/R/stepdown.mams.R |only MAMS-1.2/MAMS/R/stepdown.update.R |only MAMS-1.2/MAMS/R/tite.mams.R |only MAMS-1.2/MAMS/inst/CITATION | 30 - MAMS-1.2/MAMS/inst/NEWS | 182 ++++---- MAMS-1.2/MAMS/man/generic.Rd | 47 -- MAMS-1.2/MAMS/man/mams.Rd | 214 +++++---- MAMS-1.2/MAMS/man/mams.sim.Rd | 177 ++++---- MAMS-1.2/MAMS/man/new.bounds.Rd | 177 +++----- MAMS-1.2/MAMS/man/ordinal.mams.Rd |only MAMS-1.2/MAMS/man/stepdown.mams.Rd |only MAMS-1.2/MAMS/man/stepdown.update.Rd |only MAMS-1.2/MAMS/man/tite.mams.Rd |only 26 files changed, 1534 insertions(+), 1437 deletions(-)
Title: Implementation of Augmented Network Log Anomaly Detection
Procedures
Description: Implements procedures to aid in detecting network log anomalies. By
combining various multivariate analytic approaches relevant to network anomaly
detection, it provides cyber analysts efficient means to detect suspected
anomalies requiring further evaluation.
Author: Andrew McCarthy [aut, cre],
Brandon Greenwell [aut],
Bradley Boehmke [aut],
Robert Gutierrez [aut],
Kenneth Bauer [ctb],
Trevor Bihl [ctb],
Cade Saie [ctb]
Maintainer: Andrew McCarthy <andrew.mccarthy@theperducogroup.com>
Diff between anomalyDetection versions 0.2.2 dated 2017-09-01 and 0.2.3 dated 2017-09-14
DESCRIPTION | 8 - MD5 | 16 +- R/hmat.R | 18 ++- R/tabulate_state_vector.R | 66 +++++------ README.md | 4 inst/doc/Introduction.html | 164 ++++++++++++++-------------- man/hmat.Rd | 11 + tests/testthat/test_hmat.R | 8 + tests/testthat/test_tabulate_state_vector.R | 6 - 9 files changed, 165 insertions(+), 136 deletions(-)
More information about anomalyDetection at CRAN
Permanent link
Title: General Purpose Interface to 'Elasticsearch'
Description: Connect to 'Elasticsearch', a 'NoSQL' database built on the 'Java'
Virtual Machine. Interacts with the 'Elasticsearch' 'HTTP' 'API'
(<https://www.elastic.co/products/elasticsearch>), including functions for
setting connection details to 'Elasticsearch' instances, loading bulk data,
searching for documents with both 'HTTP' query variables and 'JSON' based body
requests. In addition, 'elastic' provides functions for interacting with 'APIs'
for 'indices', documents, nodes, clusters, an interface to the cat 'API', and
more.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between elastic versions 0.7.8 dated 2016-11-09 and 0.8.0 dated 2017-09-14
elastic-0.7.8/elastic/build |only elastic-0.7.8/elastic/inst/doc |only elastic-0.7.8/elastic/vignettes |only elastic-0.8.0/elastic/DESCRIPTION | 11 elastic-0.8.0/elastic/LICENSE | 2 elastic-0.8.0/elastic/MD5 | 210 +- elastic-0.8.0/elastic/NAMESPACE | 13 elastic-0.8.0/elastic/NEWS.md | 72 elastic-0.8.0/elastic/R/Search_uri.R | 45 elastic-0.8.0/elastic/R/cluster.R | 2 elastic-0.8.0/elastic/R/connect.R | 92 elastic-0.8.0/elastic/R/docs_bulk.r | 93 elastic-0.8.0/elastic/R/docs_bulk_utils.R | 16 elastic-0.8.0/elastic/R/docs_create.R | 3 elastic-0.8.0/elastic/R/docs_delete.R | 8 elastic-0.8.0/elastic/R/docs_get.r | 6 elastic-0.8.0/elastic/R/docs_mget.r | 13 elastic-0.8.0/elastic/R/docs_update.R | 2 elastic-0.8.0/elastic/R/elastic-package.r | 2 elastic-0.8.0/elastic/R/explain.R | 13 elastic-0.8.0/elastic/R/field_caps.R |only elastic-0.8.0/elastic/R/field_stats.R | 86 elastic-0.8.0/elastic/R/fielddata.R |only elastic-0.8.0/elastic/R/httr-verbs.R | 45 elastic-0.8.0/elastic/R/index.R | 185 + elastic-0.8.0/elastic/R/index_templates.R |only elastic-0.8.0/elastic/R/mapping.R | 45 elastic-0.8.0/elastic/R/msearch.R | 13 elastic-0.8.0/elastic/R/mtermvectors.R | 41 elastic-0.8.0/elastic/R/parsers.r | 7 elastic-0.8.0/elastic/R/percolater.R | 125 + elastic-0.8.0/elastic/R/reindex.R |only elastic-0.8.0/elastic/R/scroll.R | 261 +- elastic-0.8.0/elastic/R/search.r | 64 elastic-0.8.0/elastic/R/search_shards.R | 25 elastic-0.8.0/elastic/R/search_template.R | 24 elastic-0.8.0/elastic/R/tasks.R |only elastic-0.8.0/elastic/R/termvectors.R | 11 elastic-0.8.0/elastic/R/tokenizer_set.R | 7 elastic-0.8.0/elastic/R/zzz.r | 72 elastic-0.8.0/elastic/README.md | 52 elastic-0.8.0/elastic/inst/examples/gbif_data.json | 1198 ------------ elastic-0.8.0/elastic/inst/examples/gbif_geo.json | 598 ----- elastic-0.8.0/elastic/inst/examples/gbif_geopoint.json | 598 ----- elastic-0.8.0/elastic/inst/examples/gbif_geosmall.json | 2 elastic-0.8.0/elastic/inst/examples/shakespeare_data.json | 6 elastic-0.8.0/elastic/inst/vign/elastic_intro.Rmd | 4 elastic-0.8.0/elastic/inst/vign/elastic_intro.md | 35 elastic-0.8.0/elastic/inst/vign/search.Rmd | 44 elastic-0.8.0/elastic/inst/vign/search.md | 334 +-- elastic-0.8.0/elastic/man/Search.Rd | 451 ++-- elastic-0.8.0/elastic/man/Search_template.Rd | 9 elastic-0.8.0/elastic/man/Search_uri.Rd | 149 - elastic-0.8.0/elastic/man/alias.Rd | 13 elastic-0.8.0/elastic/man/cat.Rd | 9 elastic-0.8.0/elastic/man/cluster.Rd | 7 elastic-0.8.0/elastic/man/connect.Rd | 47 elastic-0.8.0/elastic/man/count.Rd | 1 elastic-0.8.0/elastic/man/docs_bulk.Rd | 81 elastic-0.8.0/elastic/man/docs_bulk_prep.Rd | 17 elastic-0.8.0/elastic/man/docs_create.Rd | 1 elastic-0.8.0/elastic/man/docs_delete.Rd | 6 elastic-0.8.0/elastic/man/docs_get.Rd | 1 elastic-0.8.0/elastic/man/docs_mget.Rd | 1 elastic-0.8.0/elastic/man/docs_update.Rd | 1 elastic-0.8.0/elastic/man/documents.Rd | 1 elastic-0.8.0/elastic/man/elastic-defunct.Rd | 1 elastic-0.8.0/elastic/man/elastic.Rd | 3 elastic-0.8.0/elastic/man/es_auth.Rd | 1 elastic-0.8.0/elastic/man/es_parse.Rd | 20 elastic-0.8.0/elastic/man/explain.Rd | 1 elastic-0.8.0/elastic/man/field_caps.Rd |only elastic-0.8.0/elastic/man/field_stats.Rd | 72 elastic-0.8.0/elastic/man/fielddata.Rd |only elastic-0.8.0/elastic/man/index.Rd | 80 elastic-0.8.0/elastic/man/index_status-defunct.Rd | 1 elastic-0.8.0/elastic/man/index_template.Rd |only elastic-0.8.0/elastic/man/info.Rd | 1 elastic-0.8.0/elastic/man/mapping.Rd | 32 elastic-0.8.0/elastic/man/mapping_delete-defunct.Rd | 1 elastic-0.8.0/elastic/man/mlt-defunct.Rd | 1 elastic-0.8.0/elastic/man/msearch.Rd | 10 elastic-0.8.0/elastic/man/mtermvectors.Rd | 24 elastic-0.8.0/elastic/man/nodes-defunct.Rd | 1 elastic-0.8.0/elastic/man/nodes.Rd | 5 elastic-0.8.0/elastic/man/percolate.Rd | 95 elastic-0.8.0/elastic/man/ping.Rd | 1 elastic-0.8.0/elastic/man/preference.Rd | 1 elastic-0.8.0/elastic/man/reindex.Rd |only elastic-0.8.0/elastic/man/scroll.Rd | 178 + elastic-0.8.0/elastic/man/search_body.Rd | 1 elastic-0.8.0/elastic/man/search_shards.Rd | 22 elastic-0.8.0/elastic/man/searchapis.Rd | 1 elastic-0.8.0/elastic/man/tasks.Rd |only elastic-0.8.0/elastic/man/termvectors.Rd | 1 elastic-0.8.0/elastic/man/tokenizer_set.Rd | 4 elastic-0.8.0/elastic/man/units-distance.Rd | 1 elastic-0.8.0/elastic/man/units-time.Rd | 1 elastic-0.8.0/elastic/man/validate.Rd | 1 elastic-0.8.0/elastic/tests/testthat/helper-elastic.R | 4 elastic-0.8.0/elastic/tests/testthat/test-alias.R | 19 elastic-0.8.0/elastic/tests/testthat/test-cat.R | 3 elastic-0.8.0/elastic/tests/testthat/test-docs.R | 52 elastic-0.8.0/elastic/tests/testthat/test-docs_bulk.R | 74 elastic-0.8.0/elastic/tests/testthat/test-docs_bulk_prep.R | 42 elastic-0.8.0/elastic/tests/testthat/test-indices.R | 6 elastic-0.8.0/elastic/tests/testthat/test-mappings.R | 88 elastic-0.8.0/elastic/tests/testthat/test-nodes.R | 2 elastic-0.8.0/elastic/tests/testthat/test-scroll.R |only elastic-0.8.0/elastic/tests/testthat/test-search.r | 19 elastic-0.8.0/elastic/tests/testthat/test-search_template.R | 66 111 files changed, 2414 insertions(+), 3802 deletions(-)
Title: Analysis of Diversity
Description: Includes functions, data sets and examples for the calculation of various indices of biodiversity including species, functional and phylogenetic diversity. Part of the indices are expressed in terms of equivalent numbers of species. It also provides ways to partition biodiversity across spatial or temporal scales (alpha, beta, gamma diversities). In addition to the quantification of biodiversity, ordination approaches are available which rely on diversity indices and allow the detailed identification of species, functional or phylogenetic differences between communities.
Author: Sandrine Pavoine
Maintainer: Sandrine Pavoine <sandrine.pavoine@mnhn.fr>
Diff between adiv versions 1.0 dated 2017-07-19 and 1.1 dated 2017-09-14
DESCRIPTION | 13 +++++++------ MD5 | 20 ++++++++++---------- NAMESPACE | 5 +++-- R/evodiss_ternaryplot.R | 4 ++-- R/plot.rlqESLTP.R | 18 +++++++----------- build/partial.rdb |binary man/evoCA.Rd | 5 ++--- man/evoNSCA.Rd | 5 ++--- man/evodiss_family.Rd | 8 +++----- man/evopca.Rd | 10 ++++------ man/rlqESLTP.Rd | 15 +++++++++------ 11 files changed, 49 insertions(+), 54 deletions(-)
Title: A Tool for Downloading Functional Traits Data for Plant Species
Description: Plant ecologists often need to collect "traits" data
about plant species which are often scattered among various
databases: TR8 contains a set of tools which take care of
automatically retrieving some of those functional traits data
for plant species from publicly available databases (Biolflor,
The Ecological Flora of the British Isles, LEDA traitbase, Ellenberg
values for Italian Flora, Mycorrhizal intensity databases, Catminat, BROT,
PLANTS, Jepson Flora Project).
The TR8 name, inspired by "car plates" jokes, was chosen since
it both reminds of the main object of the package and is
extremely short to type.
Author: Gionata Bocci <boccigionata@gmail.com>
Maintainer: Gionata Bocci <boccigionata@gmail.com>
Diff between TR8 versions 0.9.16 dated 2017-03-16 and 0.9.18 dated 2017-09-14
DESCRIPTION | 9 +++++---- MD5 | 40 ++++++++++++++++++++-------------------- R/catminat_download.R | 2 +- R/ecoflora.R | 8 +++++--- R/leda_general.R | 9 ++++----- R/tr8.R | 4 +++- build/vignette.rds |binary data/available_tr8.rda |binary data/biolflor_lookup.rda |binary data/column_list.rda |binary data/imkerbond_data.rda |binary data/leda_lookup.rda |binary data/pignatti.rda |binary data/ref_PLANTS.rda |binary data/traits_Biolflor.rda |binary data/traits_eco.rda |binary inst/doc/Expanding_TR8.pdf |binary inst/doc/TR8.pdf |binary inst/doc/TR8_workflow.pdf |binary man/TR8-package.Rd | 2 +- man/column_list.Rd | 4 ---- 21 files changed, 39 insertions(+), 39 deletions(-)
Title: Response Surface Analysis
Description: Advanced response surface analysis. The main function RSA computes
and compares several nested polynomial regression models (full polynomial,
shifted and rotated squared differences, rising ridge surfaces, basic
squared differences). The package provides plotting functions for 3d
wireframe surfaces, interactive 3d plots, and contour plots. Calculates
many surface parameters (a1 to a4, principal axes, stationary point,
eigenvalues) and provides standard, robust, or bootstrapped standard errors
and confidence intervals for them.
Author: Felix Schönbrodt [aut, cre],
Sarah Humberg [ctb]
Maintainer: Felix Schönbrodt <felix@nicebread.de>
Diff between RSA versions 0.9.10 dated 2016-02-22 and 0.9.11 dated 2017-09-14
RSA-0.9.10/RSA/inst/NEWS.Rd |only RSA-0.9.11/RSA/DESCRIPTION | 17 - RSA-0.9.11/RSA/MD5 | 44 +-- RSA-0.9.11/RSA/R/RSA.R | 68 +++-- RSA-0.9.11/RSA/R/RSA.ST.R | 418 ++++++++++++++++++------------------ RSA-0.9.11/RSA/R/confint.R | 2 RSA-0.9.11/RSA/R/plot.RSA.R | 61 +++-- RSA-0.9.11/RSA/R/print.RSA.R | 8 RSA-0.9.11/RSA/inst/News.Rd |only RSA-0.9.11/RSA/man/RSA.Rd | 1 RSA-0.9.11/RSA/man/RSA.ST.Rd | 4 RSA-0.9.11/RSA/man/aictab.Rd | 1 RSA-0.9.11/RSA/man/compare.Rd | 1 RSA-0.9.11/RSA/man/compare2.Rd | 1 RSA-0.9.11/RSA/man/confint.RSA.Rd | 5 RSA-0.9.11/RSA/man/demoRSA.Rd | 1 RSA-0.9.11/RSA/man/fitted.RSA.Rd | 1 RSA-0.9.11/RSA/man/getPar.Rd | 1 RSA-0.9.11/RSA/man/modeltree.Rd | 1 RSA-0.9.11/RSA/man/motcon.Rd | 1 RSA-0.9.11/RSA/man/motcon2.Rd | 1 RSA-0.9.11/RSA/man/movieRSA.Rd | 1 RSA-0.9.11/RSA/man/plotRSA.Rd | 35 +-- RSA-0.9.11/RSA/man/residuals.RSA.Rd | 3 24 files changed, 360 insertions(+), 316 deletions(-)
Title: Modelling and Analysis of Leaf Gas Exchange Data
Description: Coupled leaf gas exchange model, A-Ci curve simulation and
fitting, Ball-Berry stomatal conductance models,
leaf energy balance using Penman-Monteith, Cowan-Farquhar
optimization, humidity unit conversions.
See Duursma (2015) <doi:10.1371/journal.pone.0143346>.
Author: Remko Duursma [aut, cre]
Maintainer: Remko Duursma <remkoduursma@gmail.com>
Diff between plantecophys versions 1.2-9 dated 2017-08-08 and 1.3 dated 2017-09-14
DESCRIPTION | 9 MD5 | 58 ++-- NAMESPACE | 6 R/AciC4.R | 12 R/FARAO.R | 47 ++- R/RHtoVPD.R | 21 + R/fitBB.R | 41 +- R/fitBBs.R |only R/fitaci.R | 470 ++++++++++++++++++++++----------- R/fitacis.R | 11 R/photosyn.R | 192 ++++++++++--- R/tuzet.R |only build/partial.rdb |binary build/vignette.rds |binary inst/doc/Introduction_to_fitaci.Rmd | 2 inst/doc/Introduction_to_fitaci.html | 4 inst/doc/fitaci-FAQ.html | 6 man/AciC4.Rd | 6 man/Conversions.Rd | 19 - man/FARAO.Rd | 36 +- man/Photosyn.Rd | 188 +++++++++---- man/PhotosynTuzet.Rd |only man/fitBB.Rd | 10 man/fitBBs.Rd |only man/fitaci.Rd | 188 +++++++++---- man/fitacis.Rd | 9 tests/testthat/Rplots.pdf |only tests/testthat/testacic4.R |only tests/testthat/testbb.R |only tests/testthat/testconversions.R |only tests/testthat/testfarao.R |only tests/testthat/testfitaci.R | 56 +++ tests/testthat/testleafenergybalance.R |only tests/testthat/testphotosyn.R |only tests/testthat/testtuzet.R |only vignettes/Introduction_to_fitaci.Rmd | 2 36 files changed, 988 insertions(+), 405 deletions(-)
Title: An R-Tool for Comprehensive Science Mapping Analysis
Description: Tool for quantitative research in scientometrics and bibliometrics.
It provides various routines for importing bibliographic data from SCOPUS (<http://scopus.com>) and
Clarivate Analytics Web of Science (<http://www.webofknowledge.com/>) databases, performing bibliometric analysis
and building data matrices for co-citation, coupling, scientific collaboration and co-word analysis.
Author: Massimo Aria [cre, aut],
Corrado Cuccurullo [aut]
Maintainer: Massimo Aria <aria@unina.it>
Diff between bibliometrix versions 1.7 dated 2017-07-08 and 1.8 dated 2017-09-14
DESCRIPTION | 10 - MD5 | 64 +++---- NAMESPACE | 2 NEWS | 10 + R/cocMatrix.R | 2 R/conceptualStructure.R | 4 R/convert2df.R | 45 +++-- R/histNetwork.R | 101 +++++------ R/histPlot.R | 69 +++++--- R/isi2df.R | 51 +++-- R/isibib2df.R | 118 ++++++++----- R/networkPlot.R | 11 + R/scopus2df.R | 84 +++++---- build/vignette.rds |binary data/biblio.rda |binary data/biblio_df.rda |binary data/countries.rda |binary data/garfield.rda |binary data/isiCollection.rda |binary data/scientometrics.rda |binary data/scientometrics_text.rda |binary data/scopusCollection.rda |binary data/stopwords.rda |binary inst/CITATION | 22 +- inst/doc/bibliometrix-vignette.R | 6 inst/doc/bibliometrix-vignette.Rmd | 19 +- inst/doc/bibliometrix-vignette.html | 308 +++++++++++++++++++----------------- man/histNetwork.Rd | 5 man/histPlot.Rd | 19 +- man/isibib2df.Rd | 16 - man/networkPlot.Rd | 10 - man/scopus2df.Rd | 10 - vignettes/bibliometrix-vignette.Rmd | 19 +- 33 files changed, 571 insertions(+), 434 deletions(-)