Title: k-Nearest Neighbor Join for Spatial Data
Description: K-nearest neighbor search for projected and non-projected 'sf' spatial layers. Nearest neighbor search uses (1) C implementation of the Vincenty Formula for lon-lat point layers, (2) function nn2() from package 'RANN' for projected point layers, or (3) function st_distance() from package 'sf' for line or polygon layers.
Author: Michael Dorman [aut, cre],
Johnathan Rush [ctb],
Ian Hough [ctb],
Jan Antala [ctb, cph] (Author of C code for Vincenty distance)
Maintainer: Michael Dorman <dorman@post.bgu.ac.il>
Diff between nngeo versions 0.2.1 dated 2018-07-21 and 0.2.2 dated 2018-09-29
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NEWS.md | 12 +++++++++++- build/vignette.rds |binary inst/doc/intro.R | 5 ++++- inst/doc/intro.Rmd | 8 +++++++- inst/doc/intro.pdf |binary man/st_nn.Rd | 4 ++-- src/distance.cpp | 3 ++- vignettes/intro.Rmd | 8 +++++++- 10 files changed, 46 insertions(+), 20 deletions(-)
Title: Nested Association Mapping
Description: Designed for association studies in nested association mapping (NAM) panels, experimental and random panels. The method is described by Xavier et al. (2015) <doi:10.1093/bioinformatics/btv448>. It includes tools for genome-wide associations of multiple populations, marker quality control, population genetics analysis, genome-wide prediction, solving mixed models and finding variance components through likelihood and Bayesian methods.
Author: Alencar Xavier, William Muir, Katy Rainey, Shizhong Xu.
Maintainer: Alencar Xavier <alenxav@gmail.com>
Diff between NAM versions 1.6.3 dated 2018-09-12 and 1.6.4 dated 2018-09-29
NAM-1.6.3/NAM/README.md |only NAM-1.6.4/NAM/DESCRIPTION | 8 NAM-1.6.4/NAM/MD5 | 43 NAM-1.6.4/NAM/R/RcppExports.R | 242 ++--- NAM-1.6.4/NAM/R/gmm.R | 14 NAM-1.6.4/NAM/R/reml.R | 74 + NAM-1.6.4/NAM/R/snp.R | 2 NAM-1.6.4/NAM/build/vignette.rds |binary NAM-1.6.4/NAM/inst/add/cvNAM.R | 10 NAM-1.6.4/NAM/inst/add/sparseGMM.R | 32 NAM-1.6.4/NAM/inst/add/wgrMIXED.R | 14 NAM-1.6.4/NAM/inst/doc/gwa_description.pdf |binary NAM-1.6.4/NAM/inst/doc/vignette1.Rmd | 9 NAM-1.6.4/NAM/inst/doc/vignette1.html | 1293 +++++++++++------------------ NAM-1.6.4/NAM/inst/doc/vignette2.R | 38 NAM-1.6.4/NAM/inst/doc/vignette2.Rmd | 2 NAM-1.6.4/NAM/inst/doc/vignette2.html | 463 +++------- NAM-1.6.4/NAM/man/Internals.Rd | 10 NAM-1.6.4/NAM/man/NAM-package.Rd | 4 NAM-1.6.4/NAM/src/Functions.cpp | 120 ++ NAM-1.6.4/NAM/src/RcppExports.cpp | 31 NAM-1.6.4/NAM/vignettes/vignette1.Rmd | 9 NAM-1.6.4/NAM/vignettes/vignette2.Rmd | 2 23 files changed, 1116 insertions(+), 1304 deletions(-)
Title: Dynamic Model Averaging and Dynamic Model Selection for
Continuous Outcomes
Description: Allows to estimate dynamic model averaging, dynamic model selection and median probability model. The original methods are implemented, as well as, selected further modifications of these methods. In particular the user might choose between recursive moment estimation and exponentially moving average for variance updating. Inclusion probabilities might be modified in a way using 'Google Trends'. The code is written in a way which minimises the computational burden (which is quite an obstacle for dynamic model averaging if many variables are used). For example, this package allows for parallel computations and Occam's window approach. The package is designed in a way that is hoped to be especially useful in economics and finance. Main reference: Raftery, A.E., Karny, M., Ettler, P. (2010) <doi:10.1198/TECH.2009.08104>.
Author: Krzysztof Drachal [aut, cre] (Faculty of Economic Sciences, University
of Warsaw, Poland)
Maintainer: Krzysztof Drachal <kdrachal@wne.uw.edu.pl>
Diff between fDMA versions 2.2.3.1 dated 2018-06-29 and 2.2.4 dated 2018-09-29
DESCRIPTION | 12 MD5 | 220 ++++++++-------- NAMESPACE | 15 - NEWS | 97 ++++--- R/altf.R | 6 R/altf2.R | 276 ++++++++++---------- R/altf3.R | 16 - R/altf4.R | 83 ++---- R/archtest.R | 8 R/dmtest.R | 7 R/fDMA.R | 580 +++++++++++++++++++++++++++---------------- R/grid.DMA.R | 61 +--- R/grid.roll.reg.R | 11 R/grid.tvp.R | 11 R/hit.ratio.R | 4 R/hmdmtest.R | 7 R/mdmtest.R | 7 R/other.methods.dma.R |only R/plot.altf.R | 67 +--- R/plot.altf2.R | 133 ++------- R/plot.altf3.R | 78 +---- R/plot.altf4.R | 67 +--- R/plot.dma.R | 137 +++++----- R/plot.grid.dma.R | 87 ++---- R/plot.grid.roll.reg.R | 73 +---- R/plot.grid.tvp.R | 51 +-- R/plot.reg.R | 72 +---- R/plot.tvp.R | 50 +-- R/print.altf.R | 3 R/print.altf2.R | 3 R/print.altf3.R | 3 R/print.altf4.R | 3 R/print.dma.R | 5 R/print.grid.dma.R | 5 R/print.grid.roll.reg.R | 3 R/print.grid.tvp.R | 3 R/print.reg.R | 3 R/print.tvp.R | 3 R/rec.reg.R | 3 R/reduce.size.R |only R/roll.reg.R | 3 R/stest.R | 8 R/summary.altf.R | 23 - R/summary.altf2.R | 13 R/summary.altf3.R | 7 R/summary.altf4.R | 3 R/summary.dma.R | 8 R/summary.grid.dma.R | 7 R/summary.grid.roll.reg.R | 7 R/summary.grid.tvp.R | 7 R/summary.reg.R | 5 R/summary.tvp.R | 2 R/tvp.R | 34 +- inst/doc/fDMA_vignette.pdf |binary man/altf.Rd | 1 man/altf2.Rd | 1 man/altf3.Rd | 1 man/altf4.Rd | 10 man/archtest.Rd | 1 man/coef.dma.Rd |only man/descstat.Rd | 2 man/dmtest.Rd | 1 man/fDMA.Rd | 46 ++- man/fitted.dma.Rd |only man/gNormalize.Rd | 1 man/grid.DMA.Rd | 16 - man/grid.roll.reg.Rd | 1 man/grid.tvp.Rd | 1 man/hit.ratio.Rd | 1 man/hmdmtest.Rd | 1 man/mdmtest.Rd | 1 man/normalize.Rd | 1 man/onevar.Rd | 1 man/plot.altf.Rd | 6 man/plot.altf2.Rd | 7 man/plot.altf3.Rd | 6 man/plot.altf4.Rd | 6 man/plot.dma.Rd | 6 man/plot.grid.dma.Rd | 6 man/plot.grid.roll.reg.Rd | 6 man/plot.grid.tvp.Rd | 6 man/plot.reg.Rd | 6 man/plot.tvp.Rd | 6 man/predict.dma.Rd |only man/print.altf.Rd | 1 man/print.altf2.Rd | 1 man/print.altf3.Rd | 1 man/print.altf4.Rd | 1 man/print.dma.Rd | 1 man/print.grid.dma.Rd | 1 man/print.grid.roll.reg.Rd | 1 man/print.grid.tvp.Rd | 1 man/print.reg.Rd | 1 man/print.tvp.Rd | 1 man/rec.reg.Rd | 1 man/reduce.size.Rd |only man/residuals.dma.Rd |only man/roll.reg.Rd | 1 man/rvi.Rd |only man/standardize.Rd | 2 man/stest.Rd | 1 man/summary.altf.Rd | 1 man/summary.altf2.Rd | 1 man/summary.altf3.Rd | 1 man/summary.altf4.Rd | 1 man/summary.dma.Rd | 1 man/summary.grid.dma.Rd | 1 man/summary.grid.roll.reg.Rd | 1 man/summary.grid.tvp.Rd | 1 man/summary.reg.Rd | 1 man/summary.tvp.Rd | 1 man/tvp.Rd | 1 src/Makevars | 7 src/Makevars.win | 7 src/tvpcpp.cpp | 22 - 115 files changed, 1241 insertions(+), 1369 deletions(-)
Title: Geometric Shadow Calculations
Description: Functions for calculating: (1) shadow height, (2) logical shadow flag, (3) shadow footprint, (4) Sky View Factor and (5) radiation load. Basic required inputs include a polygonal layer of obstacle outlines along with their heights (i.e. "extruded polygons"), sun azimuth and sun elevation. The package also provides functions for related preliminary calculations: breaking polygons into line segments, determining azimuth of line segments, shifting segments by azimuth and distance, constructing the footprint of a line-of-sight between an observer and the sun, and creating a 3D grid covering the surface area of extruded polygons.
Author: Michael Dorman [aut, cre],
Evyatar Erell [ctb],
Itai Kloog [ctb],
Adi Vulkan [ctb]
Maintainer: Michael Dorman <dorman@post.bgu.ac.il>
Diff between shadow versions 0.5.5 dated 2018-07-19 and 0.5.7 dated 2018-09-29
DESCRIPTION | 9 +++++---- MD5 | 28 +++++++++++++++++----------- NEWS.md | 10 +++++++++- R/coefDirect.R | 3 +++ R/data.R | 49 +++++++++++++++++++++++++++++++++++++++++++++++-- R/surfaceGrid.R | 2 +- build/vignette.rds |binary data/beersheva.RData |only data/elev.RData |only data/tmy.RData |binary data/tmy2.RData |only man/beersheva.Rd |only man/build.Rd | 4 ++-- man/elev.Rd |only man/inShadow.Rd | 3 ++- man/plotGrid.Rd | 4 ++-- man/shadowHeight.Rd | 6 +++--- man/tmy2.Rd |only 18 files changed, 91 insertions(+), 27 deletions(-)
Title: Utility Functions for Building Web Databrowsers
Description: A suite of utility functions providing standardized functionality
often needed in web services including: logging, cache management
and parsing of http request headers.
Author: Jonathan Callahan [aut, cre]
Maintainer: Jonathan Callahan <jonathan.s.callahan@gmail.com>
Diff between MazamaWebUtils versions 0.1.5 dated 2017-12-06 and 0.1.7 dated 2018-09-29
MazamaWebUtils-0.1.5/MazamaWebUtils/man/mimeType.Rd |only MazamaWebUtils-0.1.7/MazamaWebUtils/DESCRIPTION | 18 + MazamaWebUtils-0.1.7/MazamaWebUtils/MD5 | 30 ++- MazamaWebUtils-0.1.7/MazamaWebUtils/NAMESPACE | 15 + MazamaWebUtils-0.1.7/MazamaWebUtils/R/cacheManagement.R | 16 + MazamaWebUtils-0.1.7/MazamaWebUtils/R/errorHandling.R |only MazamaWebUtils-0.1.7/MazamaWebUtils/R/httpResponse.R | 64 ------ MazamaWebUtils-0.1.7/MazamaWebUtils/R/initializeLogging.R |only MazamaWebUtils-0.1.7/MazamaWebUtils/R/pylogger.R | 96 +++++----- MazamaWebUtils-0.1.7/MazamaWebUtils/README.md | 17 - MazamaWebUtils-0.1.7/MazamaWebUtils/man/httpResponse.header.Rd | 4 MazamaWebUtils-0.1.7/MazamaWebUtils/man/initializeLogging.Rd |only MazamaWebUtils-0.1.7/MazamaWebUtils/man/logger.setLevel.Rd | 7 MazamaWebUtils-0.1.7/MazamaWebUtils/man/manageCache.Rd | 6 MazamaWebUtils-0.1.7/MazamaWebUtils/man/stopOnError.Rd |only MazamaWebUtils-0.1.7/MazamaWebUtils/tests |only 16 files changed, 130 insertions(+), 143 deletions(-)
More information about MazamaWebUtils at CRAN
Permanent link
Title: A Companion to the Multi-CAST Collection
Description: Provides a basic interface for accessing annotation data from
the Multi-CAST collection, a database of spoken natural language texts
edited by Geoffrey Haig and Stefan Schnell. The collection draws from a
diverse set of languages and has been annotated across multiple levels.
Annotation data is downloaded on request from the servers of the
Language Archive Cologne. See the Multi-CAST website
<https://lac.uni-koeln.de/multicast/> for more information and a list of
related publications.
Author: Nils Norman Schiborr [aut, cre]
Maintainer: Nils Norman Schiborr <nils-norman.schiborr@uni-bamberg.de>
Diff between multicastR versions 1.0.0 dated 2018-06-15 and 1.0.1 dated 2018-09-29
multicastR-1.0.0/multicastR/R/mctable.R |only multicastR-1.0.0/multicastR/man/mcmissarg.Rd |only multicastR-1.0.1/multicastR/DESCRIPTION | 11 +- multicastR-1.0.1/multicastR/MD5 | 26 ++++- multicastR-1.0.1/multicastR/NAMESPACE | 3 multicastR-1.0.1/multicastR/R/mc_eaf_to_mcr.R |only multicastR-1.0.1/multicastR/R/mc_miscellanea.R |only multicastR-1.0.1/multicastR/R/mc_read_eaf.R |only multicastR-1.0.1/multicastR/R/mc_subfunc.R |only multicastR-1.0.1/multicastR/R/mc_table.R |only multicastR-1.0.1/multicastR/R/mc_utilities.R |only multicastR-1.0.1/multicastR/R/multicast.R | 88 +++++++------------- multicastR-1.0.1/multicastR/man/mc_convert_mcr.Rd |only multicastR-1.0.1/multicastR/man/mc_count_clauses.Rd |only multicastR-1.0.1/multicastR/man/mc_eaf_to_mcr.Rd |only multicastR-1.0.1/multicastR/man/mc_meta_eaf.Rd |only multicastR-1.0.1/multicastR/man/mc_missarg.Rd |only multicastR-1.0.1/multicastR/man/mc_read_eaf.Rd |only multicastR-1.0.1/multicastR/man/mc_subfunc.Rd |only multicastR-1.0.1/multicastR/man/mc_write_mcr.Rd |only multicastR-1.0.1/multicastR/man/mcindex.Rd | 18 ++-- multicastR-1.0.1/multicastR/man/multicast.Rd | 25 ++--- 22 files changed, 80 insertions(+), 91 deletions(-)
Title: Connecting R and 'Raven' Sound Analysis Software
Description: A tool to exchange data between R and 'Raven' sound analysis software <http://www.birds.cornell.edu/brp/raven/RavenOverview.html> (Cornell Lab of Ornithology). Functions work on data formats compatible with the R package 'warbleR'.
Author: Marcelo Araya-Salas [aut, cre]
Maintainer: Marcelo Araya-Salas <araya-salas@cornell.edu>
Diff between Rraven versions 1.0.3 dated 2018-05-22 and 1.0.4 dated 2018-09-29
DESCRIPTION | 17 ++-- MD5 | 48 ++++++------- NAMESPACE | 2 NEWS.md | 13 +-- R/Rraven-package.R | 3 R/exp_raven.R | 92 ++++++++++++++----------- R/extract_ts.R | 12 +-- R/fix_path.R |only R/imp_corr_mat.R | 2 R/imp_raven.R | 168 +++++++++++++++++++++------------------------- R/imp_syrinx.R | 28 +++---- R/match_wav_case.R | 13 +-- R/raven_batch_detec.R | 69 ++++++++++++------ R/relabel_colms.R | 22 +++--- R/run_raven.R | 42 +++++------ R/sort_colms.R | 4 - R/to_sound_selection.R | 22 +++--- README.md | 5 - inst/doc/Rraven.html | 101 ++++++--------------------- man/Rraven.Rd | 2 man/exp_raven.Rd | 9 +- man/fix_path.Rd |only man/imp_raven.Rd | 8 +- man/raven_batch_detec.Rd | 13 ++- man/relabel_colms.Rd | 4 - man/to_sound_selection.Rd | 4 - 26 files changed, 343 insertions(+), 360 deletions(-)
Title: 'Rcpp' Interface to the APT Package Manager
Description: The 'APT Package Management System' provides Debian and
Debian-derived Linux systems with a powerful system to resolve package
dependencies. This package offers access directly from R. This can
only work on a system with a suitable 'libapt-pkg-dev' installation
so functionality is curtailed if such a library is not found.
Author: Dirk Eddelbuettel
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppAPT versions 0.0.4 dated 2017-07-18 and 0.0.5 dated 2018-09-29
RcppAPT-0.0.4/RcppAPT/src/Makevars |only RcppAPT-0.0.5/RcppAPT/ChangeLog | 68 RcppAPT-0.0.5/RcppAPT/DESCRIPTION | 17 RcppAPT-0.0.5/RcppAPT/MD5 | 53 RcppAPT-0.0.5/RcppAPT/NAMESPACE | 2 RcppAPT-0.0.5/RcppAPT/R/RcppExports.R | 32 RcppAPT-0.0.5/RcppAPT/R/init.R |only RcppAPT-0.0.5/RcppAPT/build/vignette.rds |binary RcppAPT-0.0.5/RcppAPT/cleanup | 2 RcppAPT-0.0.5/RcppAPT/configure | 7 RcppAPT-0.0.5/RcppAPT/inst/NEWS.Rd | 16 RcppAPT-0.0.5/RcppAPT/inst/doc/binnmuAfterR340.R | 565 ++--- RcppAPT-0.0.5/RcppAPT/inst/doc/binnmuAfterR340.Rmd | 631 ++--- RcppAPT-0.0.5/RcppAPT/inst/doc/binnmuAfterR340.html | 1087 ++++------ RcppAPT-0.0.5/RcppAPT/inst/scripts/debian-packages/01data.r | 18 RcppAPT-0.0.5/RcppAPT/inst/scripts/debian-packages/02bioc_other.r |only RcppAPT-0.0.5/RcppAPT/inst/scripts/debian-packages/03finalize.r |only RcppAPT-0.0.5/RcppAPT/inst/scripts/debian-packages/debpackages.rds |binary RcppAPT-0.0.5/RcppAPT/inst/scripts/debian-packages/debpackagesout.rds |binary RcppAPT-0.0.5/RcppAPT/inst/scripts/debian-packages/nmuList.txt |only RcppAPT-0.0.5/RcppAPT/inst/scripts/debian-packages/pkg.txt | 109 - RcppAPT-0.0.5/RcppAPT/man/suitable.Rd |only RcppAPT-0.0.5/RcppAPT/src/Makevars.in |only RcppAPT-0.0.5/RcppAPT/src/Makevars.win |only RcppAPT-0.0.5/RcppAPT/src/RcppExports.cpp | 11 RcppAPT-0.0.5/RcppAPT/src/buildDepends.cpp | 57 RcppAPT-0.0.5/RcppAPT/src/getPackages.cpp | 17 RcppAPT-0.0.5/RcppAPT/src/hasPackage.cpp | 14 RcppAPT-0.0.5/RcppAPT/src/reverseDepends.cpp | 37 RcppAPT-0.0.5/RcppAPT/src/utils.cpp |only RcppAPT-0.0.5/RcppAPT/tests/simpleTests.R | 60 RcppAPT-0.0.5/RcppAPT/vignettes/binnmuAfterR340.Rmd | 631 ++--- 32 files changed, 1689 insertions(+), 1745 deletions(-)
Title: Multiple-Direction Logrank Test
Description: Implemented are the one-sided and two-sided
multiple-direction logrank test for two-sample right
censored data. In addition to the statistics p-values are calculated:
1. For the one-sided testing problem one p-value based on a
wild bootstrap approach is determined. 2. In the two-sided case
one p-value based on a chi-squared approximation and
a second p-values based on a permutation approach are calculated.
Ditzhaus, M. and Friedrich, S. (2018) <arXiv:1807.05504>.
Ditzhaus, M. and Pauly, M. (2018) <arXiv:1808.05627>.
Author: Marc Ditzhaus and Sarah Friedrich
Maintainer: Sarah Friedrich <sarah.friedrich@alumni.uni-ulm.de>
Diff between mdir.logrank versions 0.0.2 dated 2018-07-27 and 0.0.4 dated 2018-09-29
DESCRIPTION | 31 +- MD5 | 18 - NAMESPACE | 3 R/GUI.R | 565 +++++++++++++++++++++++++++++++++++++++++++++++++- R/mdir.logrank.R | 2 R/mdir.onesided.R |only R/teststatistic.R | 104 ++++++++- R/utility_functions.R | 55 ++++ man/calculateGUI.Rd | 4 man/mdir.logrank.Rd | 3 man/mdir.onesided.Rd |only 11 files changed, 746 insertions(+), 39 deletions(-)
Title: Learning Plane Geometry
Description: Contains some functions to learn and teach basic plane Geometry at undergraduate level with the aim of being helpful to young students with little programming skills.
Author: Alvaro Briz-Redon, Angel Serrano-Aroca
Maintainer: Alvaro Briz-Redon <albrizre@gmail.com>
Diff between LearnGeom versions 1.3 dated 2018-01-05 and 1.4 dated 2018-09-29
LearnGeom-1.3/LearnGeom/R/CoordinateImage.R |only LearnGeom-1.3/LearnGeom/build |only LearnGeom-1.3/LearnGeom/inst/doc |only LearnGeom-1.3/LearnGeom/man/CoordinateImage.Rd |only LearnGeom-1.3/LearnGeom/vignettes |only LearnGeom-1.4/LearnGeom/DESCRIPTION | 8 +++----- LearnGeom-1.4/LearnGeom/MD5 | 14 ++++---------- LearnGeom-1.4/LearnGeom/NAMESPACE | 2 -- LearnGeom-1.4/LearnGeom/R/ImportPackages.R | 1 - LearnGeom-1.4/LearnGeom/inst/CITATION |only 10 files changed, 7 insertions(+), 18 deletions(-)
Title: Tests for General Factorial Designs
Description: Implemented are the Wald-type statistic,
a permuted version thereof as well as the ANOVA-type statistic
for general factorial designs, even with non-normal error terms
and/or heteroscedastic variances, for crossed designs with an
arbitrary number of factors and nested designs with up to three factors.
Author: Sarah Friedrich, Frank Konietschke, Markus Pauly
Maintainer: Sarah Friedrich <sarah.friedrich@alumni.uni-ulm.de>
Diff between GFD versions 0.2.5 dated 2018-01-04 and 0.2.6 dated 2018-09-29
DESCRIPTION | 12 - MD5 | 7 build/vignette.rds |binary inst/doc/IntroductionToGFD.html | 398 +++++++++++++--------------------------- vignettes/IntroductionToGFD.md |only 5 files changed, 143 insertions(+), 274 deletions(-)
Title: A Toolkit for Year-Quarter, Year-Month and Year-Isoweek Dates
Description: S3 classes and methods to create and work with year-quarter, year-month and
year-isoweek vectors. Basic arithmetic operations (such as adding and
subtracting) are supported, as well as formatting and converting to and from
standard R date types.
Author: Stefan Fleck [aut, cre]
Maintainer: Stefan Fleck <stefan.b.fleck@gmail.com>
Diff between dint versions 1.0.0 dated 2018-08-13 and 2.0.0 dated 2018-09-29
dint-1.0.0/dint/R/first_day_of_month.R |only dint-1.0.0/dint/R/first_day_of_quarter.R |only dint-1.0.0/dint/R/first_day_of_year.R |only dint-1.0.0/dint/R/get_month.R |only dint-1.0.0/dint/R/get_quarter.R |only dint-1.0.0/dint/R/get_year.R |only dint-1.0.0/dint/man/first_day_ym.Rd |only dint-1.0.0/dint/man/first_day_yq.Rd |only dint-1.0.0/dint/man/format.date_ym.Rd |only dint-1.0.0/dint/man/format.date_yq.Rd |only dint-1.0.0/dint/tests/testthat/test_first_day_of_month.R |only dint-1.0.0/dint/tests/testthat/test_first_day_of_quarter.R |only dint-1.0.0/dint/tests/testthat/test_first_day_of_year.R |only dint-2.0.0/dint/DESCRIPTION | 20 - dint-2.0.0/dint/MD5 | 108 +++--- dint-2.0.0/dint/NAMESPACE | 124 +++++-- dint-2.0.0/dint/NEWS.md |only dint-2.0.0/dint/R/accessors.R |only dint-2.0.0/dint/R/arithmetic.R |only dint-2.0.0/dint/R/date_xx.R | 93 +++++ dint-2.0.0/dint/R/date_y.R | 2 dint-2.0.0/dint/R/date_ym.R | 190 ----------- dint-2.0.0/dint/R/date_yq.R | 217 ------------- dint-2.0.0/dint/R/date_yw.R |only dint-2.0.0/dint/R/extract.r |only dint-2.0.0/dint/R/first_of.R |only dint-2.0.0/dint/R/format.R |only dint-2.0.0/dint/R/increment.R | 17 - dint-2.0.0/dint/R/predicates.R |only dint-2.0.0/dint/R/seq.R |only dint-2.0.0/dint/R/utils.R | 98 +++++ dint-2.0.0/dint/R/zzz_deprecated.R |only dint-2.0.0/dint/README.md | 48 +- dint-2.0.0/dint/build/vignette.rds |binary dint-2.0.0/dint/inst/doc/dint.R | 57 +-- dint-2.0.0/dint/inst/doc/dint.Rmd | 83 +++- dint-2.0.0/dint/inst/doc/dint.html | 118 ++++--- dint-2.0.0/dint/man/Ops.date_xx.Rd |only dint-2.0.0/dint/man/Summary.date_xx.Rd |only dint-2.0.0/dint/man/as.Date.date_xx.Rd | 10 dint-2.0.0/dint/man/c.date_xx.Rd |only dint-2.0.0/dint/man/date_xx.Rd | 2 dint-2.0.0/dint/man/date_xx_arithmetic.Rd | 56 +-- dint-2.0.0/dint/man/date_xx_arithmetic_disabled.Rd |only dint-2.0.0/dint/man/date_xx_sequences.Rd |only dint-2.0.0/dint/man/date_y.Rd | 6 dint-2.0.0/dint/man/date_ym.Rd | 10 dint-2.0.0/dint/man/date_yq.Rd | 14 dint-2.0.0/dint/man/date_yw.Rd |only dint-2.0.0/dint/man/day_of_isoweek.Rd |only dint-2.0.0/dint/man/day_of_isoyear.Rd |only dint-2.0.0/dint/man/day_of_month.Rd | 52 ++- dint-2.0.0/dint/man/day_of_quarter.Rd | 28 - dint-2.0.0/dint/man/day_of_year.Rd | 52 +-- dint-2.0.0/dint/man/deprecated.Rd |only dint-2.0.0/dint/man/dint-package.Rd | 10 dint-2.0.0/dint/man/extract_date_xx.Rd |only dint-2.0.0/dint/man/first_of_yq.Rd |only dint-2.0.0/dint/man/format_date_xx.Rd |only dint-2.0.0/dint/man/format_ym.Rd | 38 +- dint-2.0.0/dint/man/format_yq.Rd | 37 +- dint-2.0.0/dint/man/format_yw.Rd |only dint-2.0.0/dint/man/getters.Rd | 35 +- dint-2.0.0/dint/man/is_quarter_bounds.Rd |only dint-2.0.0/dint/man/y-plus.Rd |only dint-2.0.0/dint/man/year.Rd | 18 - dint-2.0.0/dint/tests/testthat/test_accessors.R |only dint-2.0.0/dint/tests/testthat/test_arithmetic.R |only dint-2.0.0/dint/tests/testthat/test_date_xx.R |only dint-2.0.0/dint/tests/testthat/test_date_yq.R | 31 - dint-2.0.0/dint/tests/testthat/test_date_yw.R |only dint-2.0.0/dint/tests/testthat/test_extract.r |only dint-2.0.0/dint/tests/testthat/test_first_of.R |only dint-2.0.0/dint/tests/testthat/test_format.R |only dint-2.0.0/dint/tests/testthat/test_increment.R | 81 ++-- dint-2.0.0/dint/tests/testthat/test_predicates.R |only dint-2.0.0/dint/tests/testthat/test_seq.R |only dint-2.0.0/dint/tests/testthat/test_utils.R |only dint-2.0.0/dint/vignettes/dint.Rmd | 83 +++- 79 files changed, 896 insertions(+), 842 deletions(-)
Title: Interface to the 'Open Tree of Life' API
Description: An interface to the 'Open Tree of Life' API to retrieve
phylogenetic trees, information about studies used to assemble the synthetic
tree, and utilities to match taxonomic names to 'Open Tree identifiers'. The
'Open Tree of Life' aims at assembling a comprehensive phylogenetic tree for all
named species.
Author: Francois Michonneau [aut, cre]
(<https://orcid.org/0000-0002-9092-966X>),
Joseph Brown [aut] (<https://orcid.org/0000-0002-3835-8062>),
David Winter [aut] (<https://orcid.org/0000-0002-6165-0029>),
Scott Chamberlain [rev] (<https://orcid.org/0000-0003-1444-9135>)
Maintainer: Francois Michonneau <francois.michonneau@gmail.com>
Diff between rotl versions 3.0.4 dated 2018-04-03 and 3.0.5 dated 2018-09-29
DESCRIPTION | 9 MD5 | 58 +-- NEWS.md | 12 R/is_in_tree.R | 28 - R/match_names.R | 4 R/tnrs.R | 64 ++-- R/tol.R | 78 ++--- build/vignette.rds |binary inst/doc/data_mashups.R | 14 inst/doc/data_mashups.Rmd | 16 - inst/doc/data_mashups.html | 82 +++-- inst/doc/how-to-use-rotl.html | 146 +++++++-- inst/doc/meta-analysis.Rmd | 2 inst/doc/meta-analysis.html | 153 +++++++++- man/get_study.Rd | 4 man/get_study_subtree.Rd | 6 man/match_names.Rd | 3 man/taxonomy_subtree.Rd | 4 man/tnrs_match_names.Rd | 4 man/tol_induced_subtree.Rd | 4 man/tol_node_info.Rd | 3 man/tol_subtree.Rd | 3 tests/testthat/test-match_names.R | 4 tests/testthat/test-studies.R | 24 - tests/testthat/test-taxonomy.R | 6 tests/testthat/test-tnrs.R | 2 tests/testthat/test-tol.R | 9 vignettes/data_mashups.Rmd | 16 - vignettes/meta-analysis.Rmd | 2 vignettes/meta-analysis_files/figure-html/birds_in_a_tree-1.png |binary 30 files changed, 517 insertions(+), 243 deletions(-)
Title: Evaluate Function Calls on HPC Schedulers (LSF, SGE, SLURM,
PBS/Torque)
Description: Evaluate arbitrary function calls using workers on HPC schedulers
in single line of code. All processing is done on the network without
accessing the file system. Remote schedulers are supported via SSH.
Author: Michael Schubert <mschu.dev@gmail.com>
Maintainer: Michael Schubert <mschu.dev@gmail.com>
Diff between clustermq versions 0.8.4.1 dated 2018-06-29 and 0.8.5 dated 2018-09-29
clustermq-0.8.4.1/clustermq/R/bind_avail.r |only clustermq-0.8.4.1/clustermq/R/purrr_rettype.r |only clustermq-0.8.4.1/clustermq/R/qsys_pbs.r |only clustermq-0.8.4.1/clustermq/man/PBS.Rd |only clustermq-0.8.5/clustermq/DESCRIPTION | 13 clustermq-0.8.5/clustermq/MD5 | 97 - clustermq-0.8.5/clustermq/NAMESPACE | 1 clustermq-0.8.5/clustermq/R/Q.r | 5 clustermq-0.8.5/clustermq/R/Q_rows.r | 27 clustermq-0.8.5/clustermq/R/foreach.r |only clustermq-0.8.5/clustermq/R/master.r | 121 - clustermq-0.8.5/clustermq/R/qsys.r | 173 +- clustermq-0.8.5/clustermq/R/qsys_local.r | 5 clustermq-0.8.5/clustermq/R/qsys_lsf.r | 58 clustermq-0.8.5/clustermq/R/qsys_multicore.r | 32 clustermq-0.8.5/clustermq/R/qsys_sge.r | 78 - clustermq-0.8.5/clustermq/R/qsys_slurm.r | 60 clustermq-0.8.5/clustermq/R/qsys_ssh.r | 47 clustermq-0.8.5/clustermq/R/ssh_proxy.r | 11 clustermq-0.8.5/clustermq/R/util.r |only clustermq-0.8.5/clustermq/R/worker.r | 12 clustermq-0.8.5/clustermq/R/workers.r | 21 clustermq-0.8.5/clustermq/R/zzz.r | 8 clustermq-0.8.5/clustermq/build/vignette.rds |binary clustermq-0.8.5/clustermq/inst/LSF.tmpl |only clustermq-0.8.5/clustermq/inst/PBS.tmpl |only clustermq-0.8.5/clustermq/inst/SGE.tmpl |only clustermq-0.8.5/clustermq/inst/SLURM.tmpl |only clustermq-0.8.5/clustermq/inst/TORQUE.tmpl |only clustermq-0.8.5/clustermq/inst/doc/clustermq.R | 33 clustermq-0.8.5/clustermq/inst/doc/clustermq.Rmd | 38 clustermq-0.8.5/clustermq/inst/doc/clustermq.html | 775 +++++------ clustermq-0.8.5/clustermq/man/LSF.Rd | 2 clustermq-0.8.5/clustermq/man/Q.Rd | 5 clustermq-0.8.5/clustermq/man/Q_rows.Rd | 5 clustermq-0.8.5/clustermq/man/SGE.Rd | 2 clustermq-0.8.5/clustermq/man/SLURM.Rd | 2 clustermq-0.8.5/clustermq/man/SSH.Rd | 2 clustermq-0.8.5/clustermq/man/bind_avail.Rd | 2 clustermq-0.8.5/clustermq/man/cmq_foreach.Rd |only clustermq-0.8.5/clustermq/man/dot-onAttach.Rd |only clustermq-0.8.5/clustermq/man/dot-onLoad.Rd |only clustermq-0.8.5/clustermq/man/host.Rd |only clustermq-0.8.5/clustermq/man/master.Rd | 5 clustermq-0.8.5/clustermq/man/purrr_lookup.Rd | 2 clustermq-0.8.5/clustermq/man/register_dopar_cmq.Rd |only clustermq-0.8.5/clustermq/man/summarize_result.Rd | 4 clustermq-0.8.5/clustermq/man/vec_lookup.Rd | 2 clustermq-0.8.5/clustermq/man/workers.Rd | 3 clustermq-0.8.5/clustermq/tests/bin/bkill |only clustermq-0.8.5/clustermq/tests/bin/qdel |only clustermq-0.8.5/clustermq/tests/bin/scancel |only clustermq-0.8.5/clustermq/tests/testthat/helper-util.r | 20 clustermq-0.8.5/clustermq/tests/testthat/test-2-work_chunk.r | 2 clustermq-0.8.5/clustermq/tests/testthat/test-3-worker.r | 37 clustermq-0.8.5/clustermq/tests/testthat/test-4-qsys.r | 6 clustermq-0.8.5/clustermq/tests/testthat/test-5-qsys_impl.r | 45 clustermq-0.8.5/clustermq/tests/testthat/test-6-ssh_proxy.r | 6 clustermq-0.8.5/clustermq/vignettes/clustermq.Rmd | 38 59 files changed, 897 insertions(+), 908 deletions(-)
Title: Local Projections Impulse Response Functions
Description: Provides functions to estimate and plot linear as well as nonlinear impulse
responses based on local projections by Jordà (2005) <doi:10.1257/0002828053828518>.
Author: Philipp Adämmer [aut, cre] (<https://orcid.org/0000-0003-3770-0097>),
James P. LeSage [ctb],
Mehmet Balcilar [ctb]
Maintainer: Philipp Adämmer <adaemmer@hsu-hh.de>
Diff between lpirfs versions 0.1.2 dated 2018-08-17 and 0.1.3 dated 2018-09-29
lpirfs-0.1.2/lpirfs/R/plot_lin_irfs.R |only lpirfs-0.1.2/lpirfs/R/plot_nl_irfs.R |only lpirfs-0.1.2/lpirfs/man/plot_lin_irfs.Rd |only lpirfs-0.1.2/lpirfs/man/plot_nl_irfs.Rd |only lpirfs-0.1.3/lpirfs/DESCRIPTION | 14 - lpirfs-0.1.3/lpirfs/MD5 | 74 +++--- lpirfs-0.1.3/lpirfs/NAMESPACE | 1 lpirfs-0.1.3/lpirfs/NEWS.md | 16 + lpirfs-0.1.3/lpirfs/R/RcppExports.R | 25 +- lpirfs-0.1.3/lpirfs/R/create_lin_data.R | 72 ++++-- lpirfs-0.1.3/lpirfs/R/create_nl_data.R | 29 -- lpirfs-0.1.3/lpirfs/R/data-documentation.R | 20 - lpirfs-0.1.3/lpirfs/R/lp_lin.R | 15 - lpirfs-0.1.3/lpirfs/R/lp_lin_iv.R | 239 +++++++++++++++----- lpirfs-0.1.3/lpirfs/R/lp_nl.R | 11 lpirfs-0.1.3/lpirfs/R/lp_nl_iv.R | 64 +++-- lpirfs-0.1.3/lpirfs/R/package.R | 2 lpirfs-0.1.3/lpirfs/R/plot_lin.R | 2 lpirfs-0.1.3/lpirfs/R/plot_nl.R | 2 lpirfs-0.1.3/lpirfs/README.md | 64 +---- lpirfs-0.1.3/lpirfs/inst/CITATION | 2 lpirfs-0.1.3/lpirfs/man/ag_data.Rd | 7 lpirfs-0.1.3/lpirfs/man/hp_filter.Rd | 6 lpirfs-0.1.3/lpirfs/man/interest_rules_var_data.Rd | 6 lpirfs-0.1.3/lpirfs/man/lp_lin.Rd | 12 - lpirfs-0.1.3/lpirfs/man/lp_lin_iv.Rd | 145 +++++++++--- lpirfs-0.1.3/lpirfs/man/lp_nl.Rd | 8 lpirfs-0.1.3/lpirfs/man/lp_nl_iv.Rd | 59 ++-- lpirfs-0.1.3/lpirfs/man/lpirfs-package.Rd | 2 lpirfs-0.1.3/lpirfs/man/monetary_var_data.Rd | 4 lpirfs-0.1.3/lpirfs/man/newey_west_tsls.Rd |only lpirfs-0.1.3/lpirfs/man/plot_lin.Rd | 2 lpirfs-0.1.3/lpirfs/man/plot_nl.Rd | 2 lpirfs-0.1.3/lpirfs/src/RcppExports.cpp | 15 + lpirfs-0.1.3/lpirfs/src/hp_filter.cpp | 6 lpirfs-0.1.3/lpirfs/src/newey_west.cpp | 8 lpirfs-0.1.3/lpirfs/src/newey_west_tsls.cpp |only lpirfs-0.1.3/lpirfs/tests/testthat/test-lp_lin_iv.R | 36 +-- lpirfs-0.1.3/lpirfs/tests/testthat/test-lp_nl_iv.R | 32 +- lpirfs-0.1.3/lpirfs/tests/testthat/test-plot_lin.R | 2 lpirfs-0.1.3/lpirfs/tests/testthat/test-plot_nl.R | 2 41 files changed, 649 insertions(+), 357 deletions(-)
Title: Classification, Regression and Feature Evaluation
Description: A suite of machine learning algorithms written in C++ with the R
interface contains several learning techniques for classification and regression.
Predictive models include e.g., classification and regression trees with
optional constructive induction and models in the leaves, random forests, kNN,
naive Bayes, and locally weighted regression. All predictions obtained with these
models can be explained and visualized with the 'ExplainPrediction' package.
This package is especially strong in feature evaluation where it contains several variants of
Relief algorithm and many impurity based attribute evaluation functions, e.g., Gini,
information gain, MDL, and DKM. These methods can be used for feature selection
or discretization of numeric attributes.
The OrdEval algorithm and its visualization is used for evaluation
of data sets with ordinal features and class, enabling analysis according to the
Kano model of customer satisfaction.
Several algorithms support parallel multithreaded execution via OpenMP.
The top-level documentation is reachable through ?CORElearn.
Author: Marko Robnik-Sikonja and Petr Savicky
Maintainer: "Marko Robnik-Sikonja" <marko.robnik@fri.uni-lj.si>
Diff between CORElearn versions 1.52.1 dated 2018-04-02 and 1.53.1 dated 2018-09-29
CORElearn-1.52.1/CORElearn/src/platform.h |only CORElearn-1.53.1/CORElearn/ChangeLog | 2 CORElearn-1.53.1/CORElearn/DESCRIPTION | 8 +- CORElearn-1.53.1/CORElearn/MD5 | 31 ++++------ CORElearn-1.53.1/CORElearn/man/CORElearn-package.Rd | 11 ++- CORElearn-1.53.1/CORElearn/src/Makevars.in | 2 CORElearn-1.53.1/CORElearn/src/Rfront.cpp | 6 - CORElearn-1.53.1/CORElearn/src/binarize.cpp | 44 +++++++++----- CORElearn-1.53.1/CORElearn/src/binarizeReg.cpp | 61 +++++++++++--------- CORElearn-1.53.1/CORElearn/src/c45read.h | 2 CORElearn-1.53.1/CORElearn/src/error.cpp | 1 CORElearn-1.53.1/CORElearn/src/frontend.cpp | 2 CORElearn-1.53.1/CORElearn/src/general.h | 2 CORElearn-1.53.1/CORElearn/src/options.cpp | 3 CORElearn-1.53.1/CORElearn/src/options.h | 2 CORElearn-1.53.1/CORElearn/src/treenode.cpp | 3 CORElearn-1.53.1/CORElearn/src/utils.h | 1 17 files changed, 107 insertions(+), 74 deletions(-)
Title: Cluster Evaluation
Description: CLUster Evaluation (CLUE) is a computational method for identifying
optimal number of clusters in a given time-course dataset clustered by
cmeans or kmeans algorithms and subsequently identify key kinases or
pathways from each cluster. Its implementation in R is called ClueR.
See README on <https://github.com/PengyiYang/ClueR> for more details.
P Yang et al. (2015) <doi:10.1371/journal.pcbi.1004403>.
Author: Pengyi Yang
Maintainer: Pengyi Yang <yangpy7@gmail.com>
Diff between ClueR versions 1.3 dated 2018-06-11 and 1.4 dated 2018-09-29
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- NAMESPACE | 2 +- R/runClue.R | 32 +++++++++++++++++--------------- README.md | 18 +++++++++--------- data/adipocyte.rda |binary man/ClueR-package.Rd | 4 ++-- man/runClue.Rd | 26 ++++++++++++++------------ 8 files changed, 55 insertions(+), 51 deletions(-)
Title: Shadow Text Grob and Layer
Description: Implement shadowtextGrob() for 'grid' and geom_shadowtext() layer for 'ggplot2'.
These functions create/draw text grob with background shadow.
Author: Guangchuang Yu [aut, cre]
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between shadowtext versions 0.0.2 dated 2017-10-30 and 0.0.3 dated 2018-09-29
DESCRIPTION | 10 +- MD5 | 20 ++--- R/geom-shadowtext.R | 4 - R/shadowtext-grob.R | 12 +-- build/vignette.rds |binary inst/doc/shadowtext.R | 4 - inst/doc/shadowtext.Rmd | 4 - inst/doc/shadowtext.html | 170 ++++++++++++++++++++++++++++------------------- man/geom_shadowtext.Rd | 6 - man/shadowtextGrob.Rd | 9 +- vignettes/shadowtext.Rmd | 4 - 11 files changed, 140 insertions(+), 103 deletions(-)
Title: CRISPR-Based Salmonella Enterica Serotype Analyzer
Description: Salmonella enterica is a major cause of bacterial food-borne disease worldwide. Serotype identification is the most commonly used typing method to characterize Salmonella isolates. However, experimental serotyping needs great cost on manpower and resources. Recently, we found that the newly incorporated spacer in the clustered regularly interspaced short palindromic repeat (CRISPR) could serve as an effective marker for typing of Salmonella. It was further revealed by Li et. al (2014) <doi:10.1128/JCM.00696-14> that recognized types based on the combination of two newly incorporated spacer in both CRISPR loci showed high accordance with serotypes. Here, we developed an R package 'CSESA' to predict the serotype based on this finding. Considering it’s time saving and of high accuracy, we recommend to predict the serotypes of unknown Salmonella isolates using 'CSESA' before doing the traditional serotyping.
Author: Xia Zhang [aut, cre],
Lang Yang [aut]
Maintainer: Xia Zhang <zhangxia9403@gmail.com>
Diff between CSESA versions 1.1.0 dated 2018-09-24 and 1.1.1 dated 2018-09-29
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/CSESA.R | 8 ++++---- tests/testthat/test-CSESA.R | 2 +- 4 files changed, 11 insertions(+), 11 deletions(-)
Title: Reversible-Jump MCMC Using Post-Processing
Description: Performs reversible-jump Markov chain Monte Carlo (Green, 1995)
<doi:10.2307/2337340>, specifically the restriction introduced by
Barker & Link (2013) <doi:10.1080/00031305.2013.791644>. By utilising
a 'universal parameter' space, RJMCMC is treated as a Gibbs sampling
problem. Previously-calculated posterior distributions are used to
quickly estimate posterior model probabilities. Jacobian matrices are
found using automatic differentiation.
Author: Nick Gelling [aut, cre],
Matthew R. Schofield [aut],
Richard J. Barker [aut]
Maintainer: Nick Gelling <nick_gelling@hotmail.com>
Diff between rjmcmc versions 0.4.1 dated 2018-06-27 and 0.4.2 dated 2018-09-29
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ R/getsampler.R | 15 +++++++++------ inst/doc/rjmcmcVig.pdf |binary man/defaultpost.Rd | 5 +++-- man/getsampler.Rd | 2 +- man/rjmethods.Rd | 4 ++-- 7 files changed, 26 insertions(+), 22 deletions(-)