Title: Adaptive Shrinkage of Correlation and Covariance Matrices
Description: Performs adaptive shrinkage of correlation and covariance
matrices using a mixture model prior over the Fisher z-transformation of the
correlations. It allows separate shrinkage intensity for each cell of the
correlation matrix. Can also we flexibly extended to shrinking correlation like
quantities such as cosine similarities in word2vec models and to partial
correlations in conditional graph estimation. For details on methods, refer
to Stephens (2017) "False discovery rates: a new deal",
<DOI:10.1093/biostatistics/kxw041>.
Author: c(person("Kushal","Dey",role=c("aut","cre"), email="kkdey@uchicago.edu"),
person("Matthew","Stephens",role="aut"),
person("Peter","Carbonetto",role="ctb"))
Maintainer: Kushal Dey <kkdey@uchicago.edu>
Diff between CorShrink versions 0.1-5 dated 2018-04-10 and 0.1-6 dated 2018-07-12
DESCRIPTION | 36 +++++----- MD5 | 36 ++++++---- NAMESPACE | 8 ++ R/CorShrinkData.R | 11 ++- R/CorShrinkMatrix.R | 5 + R/CorShrinkVector.R | 7 +- R/pCorShrinkData.R |only R/pCorShrinkData2.R |only README.md | 16 +++- build/vignette.rds |binary inst/doc/corshrink.R | 58 +++++++++++++---- inst/doc/corshrink.Rmd | 81 +++++++++++++++++++----- inst/doc/corshrink.html | 159 ++++++++++++++++++++++++++++++------------------ inst/doc/plot1.png |binary inst/doc/plot2.png |binary man/CorShrinkData.Rd | 10 ++- man/CorShrinkMatrix.Rd | 5 + man/CorShrinkVector.Rd | 6 + man/pCorShrinkData.Rd |only man/pCorShrinkData2.Rd |only vignettes/corshrink.Rmd | 81 +++++++++++++++++++----- 21 files changed, 367 insertions(+), 152 deletions(-)
Title: Power Calculations for RD Designs
Description: The regression discontinuity (RD) design is a popular quasi-experimental design for causal inference and policy evaluation. The 'rdpower' package provides tools to perform power and sample size calculations in RD designs: rdpower() calculates the power of an RD design and rdsampsi() calculates the required sample size to achieve a desired power. See Cattaneo, Titiunik and Vazquez-Bare (2018) <https://sites.google.com/site/rdpackages/rdpower/Cattaneo-Titiunik-VazquezBare_2018_Stata.pdf> for further methodological details.
Author: Matias D. Cattaneo, Rocio Titiunik, Gonzalo Vazquez-Bare
Maintainer: Gonzalo Vazquez-Bare <gvazquez@umich.edu>
Diff between rdpower versions 0.1 dated 2018-03-23 and 0.2 dated 2018-07-12
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/rdpower.R | 6 +++--- R/rdpower_fun.R | 32 ++++++++++++++++---------------- R/rdpower_package.R | 2 +- R/rdsampsi.R | 6 +++--- 6 files changed, 31 insertions(+), 31 deletions(-)
Title: Data Exchange Between R and 'LabKey' Server
Description: The 'LabKey' client library for R makes it easy for R users to
load live data from a 'LabKey' Server, <http://www.labkey.com/>,
into the R environment for analysis, provided users have permissions
to read the data. It also enables R users to insert, update, and
delete records stored on a 'LabKey' Server, provided they have appropriate
permissions to do so.
Author: Peter Hussey
Maintainer: Cory Nathe <cnathe@labkey.com>
Diff between Rlabkey versions 2.2.1 dated 2018-03-13 and 2.2.2 dated 2018-07-12
DESCRIPTION | 10 - MD5 | 57 ++++++----- NAMESPACE | 8 - NEWS | 7 + R/labkey.defaults.R | 81 +++++++++++++--- R/labkey.deleteRows.R | 71 ++++++-------- R/labkey.domain.R |only R/labkey.executeSql.R | 53 ++++------ R/labkey.getFolders.R | 70 ++++++------- R/labkey.getQueryInfo.R | 171 ++++++++++++++++----------------- R/labkey.getQueryLists.R | 18 +-- R/labkey.getSchemas.R | 53 ++++------ R/labkey.importRows.R | 73 ++++++-------- R/labkey.insertRows.R | 73 ++++++-------- R/labkey.makeRemotePath.R | 86 ++++++++--------- R/labkey.rstudio.R |only R/labkey.saveBatch.R | 130 ++++++++++++------------- R/labkey.selectRows.R | 182 +++++++++++++++++------------------- R/labkey.updateRows.R | 71 ++++++-------- R/makeDF.R | 6 - build/vignette.rds |binary inst/doc/RlabkeyExample.pdf |binary man/Rlabkey-package.Rd | 4 man/getFolderPath.Rd | 2 man/getSession.Rd | 2 man/labkey.domain.create.Rd |only man/labkey.domain.createAndLoad.Rd |only man/labkey.domain.createDesign.Rd |only man/labkey.domain.drop.Rd |only man/labkey.domain.get.Rd |only man/labkey.domain.inferFields.Rd |only man/labkey.domain.save.Rd |only man/labkey.rstudio.initReport.Rd |only man/labkey.rstudio.isInitialized.Rd |only man/labkey.rstudio.saveReport.Rd |only man/labkey.setDebugMode.Rd |only 36 files changed, 621 insertions(+), 607 deletions(-)
Title: The q-Gaussian Distribution
Description: Density, distribution function, quantile function and
random generation for the q-gaussian distribution with parameters mu and sig.
Author: Emerson Luis de Santa Helena <elsh@ufs.br>
Wagner Santos de Lima <wagnersantos.ufs@hotmail.com>
Maintainer: Wagner Santos de Lima <wagnersantos.ufs@hotmail.com>
Diff between qGaussian versions 0.1.6 dated 2017-09-28 and 0.1.8 dated 2018-07-12
qGaussian-0.1.6/qGaussian/R/cqgauss_0.1.5.R |only qGaussian-0.1.6/qGaussian/R/dqgauss_0.1.5.R |only qGaussian-0.1.6/qGaussian/R/pqgauss_0.1.5.R |only qGaussian-0.1.6/qGaussian/R/qbymc_0.1.5.R |only qGaussian-0.1.6/qGaussian/R/rqgauss_0.1.5.R |only qGaussian-0.1.8/qGaussian/DESCRIPTION | 9 ++++----- qGaussian-0.1.8/qGaussian/MD5 | 27 ++++++++++++++------------- qGaussian-0.1.8/qGaussian/NAMESPACE | 8 ++++---- qGaussian-0.1.8/qGaussian/R/Chaotic_0.1.8.R |only qGaussian-0.1.8/qGaussian/R/cqgauss_0.1.8.R |only qGaussian-0.1.8/qGaussian/R/dqgauss_0.1.8.R |only qGaussian-0.1.8/qGaussian/R/pqgauss_0.1.8.R |only qGaussian-0.1.8/qGaussian/R/qbymc_0.1.8.R |only qGaussian-0.1.8/qGaussian/R/rqgauss_0.1.8.R |only qGaussian-0.1.8/qGaussian/man/chaotic.Rd | 2 +- qGaussian-0.1.8/qGaussian/man/cqgauss.Rd | 2 +- qGaussian-0.1.8/qGaussian/man/dqgauss.Rd | 2 +- qGaussian-0.1.8/qGaussian/man/pqgauss.Rd | 2 +- qGaussian-0.1.8/qGaussian/man/qbymc.Rd | 2 +- qGaussian-0.1.8/qGaussian/man/rqgauss.Rd | 2 +- 20 files changed, 28 insertions(+), 28 deletions(-)
Title: Robust Data-Driven Statistical Inference in
Regression-Discontinuity Designs
Description: Regression-discontinuity (RD) designs are quasi-experimental research designs popular in social, behavioral and natural sciences. The RD design is usually employed to study the (local) causal effect of a treatment, intervention or policy. This package provides tools for data-driven graphical and analytical statistical inference in RD designs: rdrobust() to construct local-polynomial point estimators and robust confidence intervals for average treatment effects at the cutoff in Sharp, Fuzzy and Kink RD settings, rdbwselect() to perform bandwidth selection for the different procedures implemented, and rdplot() to conduct exploratory data analysis (RD plots).
Author: Sebastian Calonico <scalonico@bus.miami.edu>, Matias D. Cattaneo <cattaneo@umich.edu>, Max H. Farrell <max.farrell@chicagobooth.edu>, Rocio Titiunik <titiunik@umich.edu>
Maintainer: Sebastian Calonico <scalonico@bus.miami.edu>
Diff between rdrobust versions 0.99.2 dated 2018-07-09 and 0.99.3 dated 2018-07-12
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/rdrobust.R | 18 +++++++++++------- man/rdrobust-package.Rd | 4 ++-- 4 files changed, 20 insertions(+), 16 deletions(-)
Title: Time Series Outlier Detection
Description: Time series outlier detection by mean of non parametric test. Outlier detection regarding two methodologies: single time series variability (a vector) and grouped similar time series (a data frame). Andrea Venturini(2011) Statistica-Universita' Bologna, Vol.71, pp.329-344.
Author: Andrea Venturini
Maintainer: Andrea Venturini <andrea.venturini@bancaditalia.it>
Diff between washeR versions 0.1.0 dated 2018-07-11 and 0.1.2 dated 2018-07-12
DESCRIPTION | 10 MD5 | 14 R/dati.R | 30 - R/ts.R | 22 - R/wash.out.R | 890 ++++++++++++++++++++++++++--------------------------- R/washeR-package.r | 30 - man/wash.out.Rd | 4 man/washeR.Rd | 2 8 files changed, 501 insertions(+), 501 deletions(-)
Title: Iterated Racing for Automatic Algorithm Configuration
Description: Iterated race is an extension of the Iterated F-race method for
the automatic configuration of optimization algorithms, that is,
(offline) tuning their parameters by finding the most appropriate
settings given a set of instances of an optimization problem.
Author: Manuel López-Ibáñez [aut, cre]
(<https://orcid.org/0000-0001-9974-1295>),
Jérémie Dubois-Lacoste [aut],
Leslie Pérez Cáceres [aut],
Thomas Stützle [aut],
Mauro Birattari [aut],
Eric Yuan [ctb],
Prasanna Balaprakash [ctb]
Maintainer: Manuel López-Ibáñez <manuel.lopez-ibanez@manchester.ac.uk>
Diff between irace versions 3.0 dated 2018-07-05 and 3.1 dated 2018-07-12
BUGS | 5 DESCRIPTION | 8 MD5 | 38 +-- NEWS | 7 R/parameterExploration.R | 44 +-- R/race.R | 12 - R/readConfiguration.R | 29 +- R/version.R | 2 README.md | 10 build/partial.rdb |binary inst/doc/irace-package.R | 5 inst/doc/irace-package.Rnw | 35 +- inst/doc/irace-package.pdf |binary inst/examples/acotsp/parameters-acotsp.txt | 4 man/psRace.Rd | 2 tests/test-targetRunnerParallel.R |only tests/testmisc.R |only tests/testthat |only tests/testthat.R | 340 ----------------------------- vignettes/NEWS.txt | 7 vignettes/irace-package.Rnw | 35 +- 21 files changed, 140 insertions(+), 443 deletions(-)
Title: Fit the Gambin Model to Species Abundance Distributions
Description: Fits unimodal and multimodal gambin distributions to species-abundance distributions
from ecological data, as in in Matthews et al. (2014) <DOI:10.1111/ecog.00861>.
'gambin' is short for 'gamma-binomial'. The main function is fit_abundances(), which estimates
the 'alpha' parameter(s) of the gambin distribution using maximum likelihood. Functions are
also provided to generate the gambin distribution and for calculating likelihood statistics.
Author: Thomas Matthews [aut, cre],
Michael Krabbe Borregaard [aut],
Karl Ugland [aut],
Colin Gillespie [aut]
Maintainer: Thomas Matthews <txm676@gmail.com>
Diff between gambin versions 2.3.0 dated 2018-02-18 and 2.4.0 dated 2018-07-12
DESCRIPTION | 6 MD5 | 54 +++-- NAMESPACE | 4 NEWS.md | 8 R/confint.R | 63 +++++- R/create_octaves.R | 3 R/data_docs.R | 17 + R/deconstruct_gambin.R |only R/dgambin.R | 17 + R/fit_gambin.R | 30 ++- R/gambin-package.R | 4 R/logLik_gambin.R | 8 R/plot_gambin.R | 2 R/print_gambin.R | 2 R/print_summary_gambin.R | 16 + R/summary_gambin.R | 55 +++++ build/vignette.rds |binary data/categ.rda |only inst/doc/overview.R | 8 inst/doc/overview.Rmd | 17 + inst/doc/overview.html | 386 ++++++++++++++++++++++++++++++--------- man/categ.Rd |only man/create_octaves.Rd | 3 man/deconstruct_modes.Rd |only man/dgambin.Rd | 10 + man/fit_abundances.Rd | 14 - man/gambin-package.Rd | 4 man/summary.gambin.Rd |only tests/testthat/testing_dgambin.R | 2 tests/testthat/testing_rgambin.R |only vignettes/overview.Rmd | 17 + 31 files changed, 592 insertions(+), 158 deletions(-)
Title: Client for the 'DKAN' API
Description: Provides functions to facilitate access to the 'DKAN' API (<https://dkan.readthedocs.io/en/latest/apis/index.html>), including the 'DKAN' REST API (metadata), and the 'DKAN' datastore API (data). Includes functions to list, create, retrieve, update, and delete datasets and resources nodes. It also includes functions to search and retrieve data from the 'DKAN' datastore.
Author: Tony Fujs [aut, cre],
Meera Desai [aut],
Karthik Ramanathan [aut]
Maintainer: Tony Fujs <tonyfujs@gmail.com>
Diff between dkanr versions 0.1.1 dated 2018-04-30 and 0.1.2 dated 2018-07-12
dkanr-0.1.1/dkanr/tests/testthat/datacatalog.worldbank.org/api/dataset/system/connect-c34ae0-POST.R |only dkanr-0.1.2/dkanr/DESCRIPTION | 6 dkanr-0.1.2/dkanr/MD5 | 17 dkanr-0.1.2/dkanr/NEWS.md | 5 dkanr-0.1.2/dkanr/R/utils.R | 6 dkanr-0.1.2/dkanr/README.md | 1 dkanr-0.1.2/dkanr/build/vignette.rds |binary dkanr-0.1.2/dkanr/inst/doc/getting_started_with_dkanr.html | 350 ++++++++-- dkanr-0.1.2/dkanr/tests/testthat/datacatalog.worldbank.org/api/dataset/system/connect-c34ae0-POST.json | 14 dkanr-0.1.2/dkanr/tests/testthat/test-fix_download_url.R | 9 10 files changed, 323 insertions(+), 85 deletions(-)
Title: Study Planning and Adaptation of Sample Size
Description: Sample size estimation and blinded sample size reestimation in Adaptive Study Design.
Author: T. Asendorf, R. Gera, S. Islam, M. Harden and M. Placzek
Maintainer: Marius Placzek <marius.placzek@med.uni-goettingen.de>
Diff between spass versions 1.1 dated 2017-11-02 and 1.2 dated 2018-07-12
DESCRIPTION | 8 +++---- MD5 | 12 +++++------ R/RcppExports.r | 28 +++++++++++++------------- R/bssr.nb.gf.r | 8 ++++--- R/fit.nb.gf.r | 16 +++++++------- R/n.nb.gf.r | 6 ++--- src/RcppExports.cpp | 56 ++++++++++++++++++++++++++-------------------------- 7 files changed, 68 insertions(+), 66 deletions(-)
Title: L1 (Lasso and Fused Lasso) and L2 (Ridge) Penalized Estimation
in GLMs and in the Cox Model
Description: Fitting possibly high dimensional penalized
regression models. The penalty structure can be any combination
of an L1 penalty (lasso and fused lasso), an L2 penalty (ridge) and a
positivity constraint on the regression coefficients. The
supported regression models are linear, logistic and Poisson
regression and the Cox Proportional Hazards model.
Cross-validation routines allow optimization of the tuning
parameters.
Author: Jelle Goeman, Rosa Meijer, Nimisha Chaturvedi, Matthew Lueder
Maintainer: ORPHANED
Diff between penalized versions 0.9-50.1 dated 2018-06-30 and 0.9-51 dated 2018-07-12
ChangeLog | 9 DESCRIPTION | 14 MD5 | 21 - R/checkinput.R | 646 ++++++++++++++++++++++---------------------- build/vignette.rds |binary data/nki70.RData |binary inst/doc/penalized.R | 700 ++++++++++++++++++++++++------------------------ inst/doc/penalized.Rnw | 4 inst/doc/penalized.pdf |binary src/init.c |only src/lasso.cpp | 8 vignettes/penalized.Rnw | 4 12 files changed, 705 insertions(+), 701 deletions(-)
Title: Simulation and Prediction with Seasonal ARIMA Models
Description: Functions, classes and methods for time series modelling with ARIMA
and related models. The aim of the package is to provide consistent
interface for the user. For example, a single function autocorrelations()
computes various kinds of theoretical and sample autocorrelations. This is
work in progress, see the documentation and vignettes for the current
functionality. Function sarima() fits extended multiplicative seasonal
ARIMA models with trends, exogenous variables and arbitrary roots on the
unit circle, which can be fixed or estimated.
Author: Georgi N. Boshnakov [aut, cre],
Jamie Halliday [ctb]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>
Diff between sarima versions 0.7.2 dated 2018-07-09 and 0.7.3 dated 2018-07-12
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 6 ++++++ build/partial.rdb |binary inst/doc/garch_tests_example.pdf |binary inst/doc/white_noise_tests.pdf |binary src/arimaQ0.cpp | 2 +- 7 files changed, 17 insertions(+), 11 deletions(-)
Title: Functions for Optimal Matching
Description: Distance based bipartite matching using the RELAX-IV minimum cost flow solver,
oriented to matching of treatment and control groups in observational
studies. Routines are provided to generate distances from generalised linear models (propensity
score matching), formulas giving variables on which to limit matched distances, stratified or
exact matching directives, or calipers, alone or in combination.
Author: Ben B. Hansen <ben.hansen@umich.edu>, Mark Fredrickson
<mark.m.fredrickson@gmail.com>, Josh Buckner, Josh Errickson, and Peter
Solenberger, with embedded Fortran code due to Dimitri P. Bertsekas
<dimitrib@mit.edu> and Paul Tseng
Maintainer: Mark M. Fredrickson <mark.m.fredrickson@gmail.com>
Diff between optmatch versions 0.9-9 dated 2018-05-14 and 0.9-10 dated 2018-07-12
optmatch-0.9-10/optmatch/DESCRIPTION | 6 +- optmatch-0.9-10/optmatch/MD5 | 14 ++--- optmatch-0.9-10/optmatch/NEWS | 3 + optmatch-0.9-10/optmatch/build/vignette.rds |binary optmatch-0.9-10/optmatch/inst/doc/fullmatch-vignette.html |only optmatch-0.9-10/optmatch/inst/doc/matching-from-foreign-software.html |only optmatch-0.9-10/optmatch/tests/testthat/test.compute_mahal.R | 23 +++++++- optmatch-0.9-10/optmatch/tests/testthat/test.rank.mahal.R | 28 +++++++--- optmatch-0.9-9/optmatch/inst/doc/fullmatch-vignette.pdf |only optmatch-0.9-9/optmatch/inst/doc/matching-from-foreign-software.pdf |only 10 files changed, 56 insertions(+), 18 deletions(-)
Title: Dealing with Several Images of a Same Object Constituted of
Different Zones
Description: Deals with several images of a same object, constituted of different zones. Each image constitutes a variable for a given pixel. The user can interactively select different zones of an image. Then, multivariate analysis (PCA) can be run in order to characterize the different selected zones, according to the different images. Hotelling (Hotelling, 1931, <doi:10.1214/aoms/1177732979>) and Srivastava (Srivastava, 2009, <doi:10.1016/j.jmva.2006.11.002>) tests can be run to detect multivariate differences between the zones.
Author: Caroline Peltier
Maintainer: Caroline Peltier <caroline.peltier@agrosupdijon.fr>
Diff between multifluo versions 1.0 dated 2018-01-24 and 1.1 dated 2018-07-12
DESCRIPTION | 10 +++--- MD5 | 46 +++++++++++++++++----------- NAMESPACE | 4 +- R/binning.R |only R/generic.plot.R | 5 +-- R/intpca.R | 16 ++++----- R/pcapic.R |only R/plotimage.R | 85 ++++++++++++++++++++++++++++------------------------ R/plotpca.R | 12 +++---- R/plotzone.R | 24 ++++++++++++++ R/summaryrshp.R |only R/translation.R | 44 ++++++++++++++++++++++++-- build/partial.rdb |binary data/df.scaled.rda |binary data/dfTest.rda |only data/dfboolTest.rda |only data/zone.img.rda |binary man/binning.Rd |only man/create.zones.Rd | 2 - man/dfTest.Rd |only man/dfboolTest.Rd |only man/erase.Rd | 4 +- man/img.zone.Rd | 2 - man/pcapic.Rd |only man/plotimage.Rd | 15 +++++---- man/plotpca.Rd | 2 - man/reshapimg.Rd | 4 +- man/summaryrshp.Rd |only man/translation.Rd | 14 +++----- 29 files changed, 184 insertions(+), 105 deletions(-)
Title: Spatial Data Framework for ggplot2
Description: Spatial data plus the power of the ggplot2 framework means easier mapping when input
data are already in the form of spatial objects.
Author: Dewey Dunnington [aut, cre],
Brent Thorne [ctb]
Maintainer: Dewey Dunnington <dewey@fishandwhistle.net>
Diff between ggspatial versions 0.2.1 dated 2017-04-02 and 1.0.1 dated 2018-07-12
ggspatial-0.2.1/ggspatial/R/data.R |only ggspatial-0.2.1/ggspatial/R/extract-projection.R |only ggspatial-0.2.1/ggspatial/R/fortify-sp.R |only ggspatial-0.2.1/ggspatial/R/geom-osm.R |only ggspatial-0.2.1/ggspatial/R/geom-spraster.R |only ggspatial-0.2.1/ggspatial/R/stat-project.R |only ggspatial-0.2.1/ggspatial/data |only ggspatial-0.2.1/ggspatial/man/annotation_spraster.Rd |only ggspatial-0.2.1/ggspatial/man/as.CRS.Rd |only ggspatial-0.2.1/ggspatial/man/fortify.Raster.Rd |only ggspatial-0.2.1/ggspatial/man/geom_osm.Rd |only ggspatial-0.2.1/ggspatial/man/geom_spatial.Raster.Rd |only ggspatial-0.2.1/ggspatial/man/geom_spatial.Rd |only ggspatial-0.2.1/ggspatial/man/longlake.Rd |only ggspatial-0.2.1/ggspatial/man/stat_project.Rd |only ggspatial-0.2.1/ggspatial/man/stat_rgba.Rd |only ggspatial-0.2.1/ggspatial/man/xyTransform.Rd |only ggspatial-0.2.1/ggspatial/tests/test-all.R |only ggspatial-1.0.1/ggspatial/DESCRIPTION | 28 - ggspatial-1.0.1/ggspatial/MD5 | 251 ++++++++- ggspatial-1.0.1/ggspatial/NAMESPACE | 81 ++- ggspatial-1.0.1/ggspatial/R/annotation-map-tile.R |only ggspatial-1.0.1/ggspatial/R/annotation-north-arrow.R |only ggspatial-1.0.1/ggspatial/R/annotation-scale.R |only ggspatial-1.0.1/ggspatial/R/deprecated-functions.R |only ggspatial-1.0.1/ggspatial/R/df-spatial.R |only ggspatial-1.0.1/ggspatial/R/geom-polypath.R | 50 + ggspatial-1.0.1/ggspatial/R/geom-spatial.R | 368 +++++--------- ggspatial-1.0.1/ggspatial/R/layer-spatial-raster.R |only ggspatial-1.0.1/ggspatial/R/layer-spatial.R |only ggspatial-1.0.1/ggspatial/R/longlake-data.R |only ggspatial-1.0.1/ggspatial/build |only ggspatial-1.0.1/ggspatial/inst |only ggspatial-1.0.1/ggspatial/man/annotation_map_tile.Rd |only ggspatial-1.0.1/ggspatial/man/annotation_north_arrow.Rd |only ggspatial-1.0.1/ggspatial/man/annotation_scale.Rd |only ggspatial-1.0.1/ggspatial/man/deprecated.Rd |only ggspatial-1.0.1/ggspatial/man/df_spatial.Rd |only ggspatial-1.0.1/ggspatial/man/geom_polypath.Rd |only ggspatial-1.0.1/ggspatial/man/layer_spatial.Raster.Rd |only ggspatial-1.0.1/ggspatial/man/layer_spatial.Rd |only ggspatial-1.0.1/ggspatial/man/load_longlake_data.Rd |only ggspatial-1.0.1/ggspatial/man/north_arrow_orienteering.Rd |only ggspatial-1.0.1/ggspatial/man/stat_spatial_identity.Rd |only ggspatial-1.0.1/ggspatial/man/xy_transform.Rd |only ggspatial-1.0.1/ggspatial/tests/testthat |only ggspatial-1.0.1/ggspatial/tests/testthat.R |only ggspatial-1.0.1/ggspatial/vignettes |only 48 files changed, 489 insertions(+), 289 deletions(-)
Title: Modelling Spatial Variation in Disease Risk for Areal Data
Description: Formatting of population and case data, calculation of Standardized
Incidence Ratios, and fitting the BYM model using INLA.
Author: Patrick Brown <patrick.brown@utoronto.ca>, Lutong Zhou
Maintainer: Patrick Brown <patrick.brown@utoronto.ca>
Diff between diseasemapping versions 1.4.2 dated 2016-09-20 and 1.4.6 dated 2018-07-12
DESCRIPTION | 14 ++++----- MD5 | 37 +++++++++++++------------ NAMESPACE | 1 R/bym.R | 11 ++++--- R/formatCases.R | 9 +++--- R/getExpected.R | 22 +++++++++++++++ R/getRates.R | 49 +++++++++++++++++++++++++--------- R/getSMR.R | 67 ++++++++++++++++++++++++++++++----------------- build/diseasemapping.pdf |only build/vignette.rds |binary data/casedata.RData |binary data/kentucky.RData |binary data/kentuckyTract.RData |binary data/popdata.RData |binary data/referencepop.RData |binary inst/CITATION | 2 - inst/doc/bym.Rnw | 46 ++++++++++++++++++++++---------- inst/doc/bym.pdf |binary man/bym.Rd | 36 ++++++++++++++++++++++--- vignettes/bym.Rnw | 46 ++++++++++++++++++++++---------- 20 files changed, 237 insertions(+), 103 deletions(-)
More information about diseasemapping at CRAN
Permanent link
Title: Data Visualization for Statistics in Social Science
Description: Collection of plotting and table output functions for data
visualization. Results of various statistical analyses (that are commonly used
in social sciences) can be visualized using this package, including simple and
cross tabulated frequencies, histograms, box plots, (generalized) linear models,
mixed effects models, principal component analysis and correlation matrices,
cluster analyses, scatter plots, stacked scales, effects plots of regression
models (including interaction terms) and much more. This package supports
labelled data.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>),
Carsten Schwemmer [ctb]
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjPlot versions 2.4.1 dated 2018-02-05 and 2.5.0 dated 2018-07-12
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Title: 'caret' Applications for Spatial-Temporal Models
Description: Supporting functionality to run 'caret' with spatial or spatial-temporal data. 'caret' is a frequently used package for model training and prediction using machine learning. This package includes functions to improve spatial-temporal modelling tasks using 'caret'. It prepares data for Leave-Location-Out and Leave-Time-Out cross-validation which are target-oriented validation strategies for spatial-temporal models. To decrease overfitting and improve model performances, the package implements a forward feature selection that selects suitable predictor variables in view to their contribution to the target-oriented performance.
Author: Hanna Meyer [cre, aut],
Chris Reudenbach [ctb],
Marvin Ludwig [ctb],
Thomas Nauss [ctb]
Maintainer: Hanna Meyer <hanna.meyer@geo.uni-marburg.de>
Diff between CAST versions 0.2.0 dated 2018-05-06 and 0.2.1 dated 2018-07-12
DESCRIPTION | 10 ++- MD5 | 15 ++++- NEWS.md | 6 ++ R/ffs.R | 83 +++++++++++++++++++++++---------- build |only inst/doc |only inst/extdata/predictors_2012-03-25.grd |only inst/extdata/predictors_2012-03-25.gri |only man/ffs.Rd | 40 ++++++++++++--- vignettes |only 10 files changed, 114 insertions(+), 40 deletions(-)
Title: Implementations of Semi-Supervised Learning Approaches for
Classification
Description: A collection of implementations of semi-supervised classifiers
and methods to evaluate their performance. The package includes implementations
of, among others, Implicitly Constrained Learning, Moment Constrained Learning,
the Transductive SVM, Manifold regularization, Maximum Contrastive Pessimistic
Likelihood estimation, S4VM and WellSVM.
Author: Jesse Krijthe [aut, cre]
Maintainer: Jesse Krijthe <jkrijthe@gmail.com>
Diff between RSSL versions 0.6.1 dated 2016-10-06 and 0.7 dated 2018-07-12
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Title: Datasets and Functions Featured in Pollock and Edwards, An R
Companion to Essentials of Political Analysis, Second Edition
Description: Bundles the datasets and functions used in the book by Philip
Pollock and Barry Edwards, An R Companion to Essentials of Political Analysis,
Second Edition.
Author: Barry Edwards and Philip Pollock
Maintainer: Barry Edwards <barry.edwards@ucf.edu>
Diff between poliscidata versions 1.2.0 dated 2016-10-24 and 2.2.0 dated 2018-07-12
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Title: Generalized Correlations and Initial Causal Path
Description: Since causal paths from data are important for all sciences, the
package provides sophisticated functions. The idea is simply
that if X causes Y (path: X to Y) then non-deterministic variation in X
is more "original or independent" than similar variation in Y. Since causal variables are
also exogenous in a model, we provide new exogeneity tests. We compare
two flipped kernel regressions: X=f(Y, Z) and Y=g(X,Z), where Z are control
variables. Our first two criteria compare absolute cross products
of regressor values and residuals (Cr1) and
absolute residuals (Cr2), are both quantified by stochastic dominance of four
orders (SD1 to SD4). Our third criterion (Cr3) expects X to be better able
to predict Y than the other way around using generalized partial correlation
If |r*(x|y,z)|> |r*(y|x,z)| it suggests that y is more likely
the "kernel cause" of x. The usual partial correlations are generalized with
a new non-symmetric matrix developed here.
Partial correlations help asses effect of x on y after removing the effect of a
set of variables.
The package provides additional tools for causal assessment,
for printing the causal directions in a clear, comprehensive compact summary form,
for matrix algebra, for "outlier detection", and for numerical integration by the
trapezoidal rule, stochastic dominance, etc.
The package has functions for bootstrap-based statistical inference.
Author: Prof. H. D. Vinod, Fordham University, NY.
Maintainer: H. D. Vinod <vinod@fordham.edu>
Diff between generalCorr versions 1.1.1 dated 2018-01-24 and 1.1.2 dated 2018-07-12
DESCRIPTION | 16 +++++++------- MD5 | 40 +++++++++++++++++++++++-------------- NAMESPACE | 5 ++++ NEWS | 5 ++++ R/bootQuantile.R | 8 +++---- R/bootSign.R | 13 +++++++----- R/bootSignPcent.R |only R/parcorMany.R | 15 ++++++------- R/parcorMtx.R |only R/parcorSilent.R |only R/parcor_ijk.R | 7 +++--- R/parcor_ijkOLD.R |only R/parcor_ridg.R |only build/vignette.rds |binary inst/doc/generalCorr-vignette.pdf |binary inst/doc/generalCorr-vignette2.pdf |binary inst/doc/generalCorr-vignette3.pdf |binary man/bootQuantile.Rd | 8 +++---- man/bootSign.Rd | 13 +++++++----- man/bootSignPcent.Rd |only man/parcorMany.Rd | 13 +++++------- man/parcorMtx.Rd |only man/parcorSilent.Rd |only man/parcor_ijk.Rd | 5 ++-- man/parcor_ijkOLD.Rd |only man/parcor_ridg.Rd |only 26 files changed, 87 insertions(+), 61 deletions(-)
Title: Fast Estimators for Design-Based Inference
Description: Fast procedures for small set of commonly-used, design-appropriate estimators with robust standard errors and confidence intervals. Includes estimators for linear regression, instrumental variables regression, difference-in-means, Horvitz-Thompson estimation, and regression improving precision of experimental estimates by interacting treatment with centered pre-treatment covariates introduced by Lin (2013) <doi:10.1214/12-AOAS583>.
Author: Graeme Blair [aut, cre],
Jasper Cooper [aut],
Alexander Coppock [aut],
Macartan Humphreys [aut],
Luke Sonnet [aut],
Neal Fultz [ctb]
Maintainer: Graeme Blair <graeme.blair@ucla.edu>
Diff between estimatr versions 0.8.0 dated 2018-06-02 and 0.10.0 dated 2018-07-12
DESCRIPTION | 10 +- MD5 | 66 ++++++------- NEWS.md | 10 +- R/S3_confint.R | 10 +- R/S3_summary.R | 10 +- R/S3_tidy.R | 36 ++----- R/estimatr_difference_in_means.R | 20 ++-- R/estimatr_horvitz_thompson.R | 43 +++++--- R/estimatr_iv_robust.R | 5 - R/estimatr_lm_lin.R | 5 - R/estimatr_lm_robust.R | 7 - R/helper_cis_pvals.R | 15 +-- R/helper_clean_model_data.R | 22 ++++ R/helper_condition_pr_matrix.R | 7 + R/helper_extract.R | 24 ++--- R/helper_lm_robust_fit.R | 30 +++++- R/helper_return.R | 2 R/helper_starprep.R | 6 - man/difference_in_means.Rd | 5 - man/horvitz_thompson.Rd | 8 + man/iv_robust.Rd | 5 - man/lm_lin.Rd | 5 - man/lm_robust.Rd | 7 - man/starprep.Rd | 6 - tests/sleep.Rout.save | 12 +- tests/testthat/test-difference-in-means.R | 20 ++-- tests/testthat/test-horvitz-thompson.R | 39 ++++++-- tests/testthat/test-iv-robust.R | 48 +++++----- tests/testthat/test-lm-cluster.R | 8 - tests/testthat/test-lm-robust-fes.R | 144 +++++++++++++++++++++++++++++- tests/testthat/test-lm-robust.R | 4 tests/testthat/test-replicate-lin2013.R | 8 - tests/testthat/test-return.R | 4 tests/testthat/test-s3-methods.R | 35 +++++-- 34 files changed, 464 insertions(+), 222 deletions(-)
Title: Seasonal Adjustment by Frequency Analysis
Description: Decompose a time series into seasonal, trend and irregular components using transformations to amplitude-frequency domain.
Author: Francisco Parra <parra_fj@cantabria.es>
Maintainer: Francisco Parra <parra_fj@cantabria.es>
Diff between descomponer versions 1.4 dated 2017-08-21 and 1.5 dated 2018-07-12
DESCRIPTION | 10 - MD5 | 28 ++-- NAMESPACE | 3 R/descomponer.R | 40 ++---- R/predecirdf.R |only R/rdf.R | 186 +++++++++++++++------------- build/vignette.rds |binary data/PIB.rda |binary inst/doc/descomponer_texto.R | 10 + inst/doc/descomponer_texto.Rnw | 16 ++ inst/doc/descomponer_texto.pdf |binary man/descomponer.rd | 2 man/predecirdf.Rd |only man/rdf.rd | 14 +- vignettes/descomponer_texto-concordance.tex | 3 vignettes/descomponer_texto.Rnw | 16 ++ 16 files changed, 191 insertions(+), 137 deletions(-)
Title: Extrema-Weighted Feature Extraction
Description: Extrema-weighted feature extraction for varying length functional data. Functional data analysis method that performs dimensionality reduction based on predefined features and allows for quantile weighting. Method implemented as presented in Van den Boom et al. (2018) <doi:10.1093/bioinformatics/bty120>.
Author: Willem van den Boom [aut, cre]
Maintainer: Willem van den Boom <willem@wvdboom.nl>
Diff between xwf versions 0.2-1 dated 2018-01-31 and 0.2-2 dated 2018-07-12
DESCRIPTION | 10 +++++----- MD5 | 3 ++- README |only 3 files changed, 7 insertions(+), 6 deletions(-)
Title: Java GUI for R
Description: Java GUI for R - cross-platform, universal and unified Graphical User Interface for R. For full functionality on Windows and Mac OS X JGR requires a start application which depends on your OS.
Author: Markus Helbig <info@markushelbig.de>, Simon Urbanek, Ian Fellows
Maintainer: Markus Helbig <info@markushelbig.de>
Diff between JGR versions 1.8-4 dated 2017-09-24 and 1.8-6 dated 2018-07-12
DESCRIPTION | 8 - MD5 | 46 +++---- NEWS | 8 + R/JGR.R | 6 - inst/java/JGR.jar |binary java/jedit/syntax/InputHandler.java | 8 - java/jedit/syntax/JEditTextArea.java | 32 ++--- java/jedit/syntax/SyntaxDocument.java | 2 java/jedit/syntax/TextAreaPainter.java | 2 java/org/rosuda/JGR/JGRConsole.java | 6 - java/org/rosuda/JGR/JGRDataFileOpenDialog.java | 2 java/org/rosuda/JGR/JGRHelp.java | 4 java/org/rosuda/JGR/RController.java | 118 +++++++------------- java/org/rosuda/JGR/TxtTableLoader.java | 6 - java/org/rosuda/JGR/browser/DefaultBrowserNode.java | 6 - java/org/rosuda/JGR/browser/EnvironmentNode.java | 2 java/org/rosuda/JGR/browser/HeadNode.java | 2 java/org/rosuda/JGR/editor/RInputHandler.java | 2 java/org/rosuda/JGR/toolkit/ConsoleOutput.java | 18 ++- java/org/rosuda/JGR/toolkit/JGRListener.java | 2 java/org/rosuda/JGR/toolkit/JavaGD.java | 12 +- java/org/rosuda/JGR/toolkit/PrefDialog.java | 2 java/org/rosuda/JGR/util/ErrorMsg.java | 4 man/supplements.Rd | 4 24 files changed, 147 insertions(+), 155 deletions(-)
Title: Plot 'rpart' Models: An Enhanced Version of 'plot.rpart'
Description: Plot 'rpart' models. Extends plot.rpart() and text.rpart()
in the 'rpart' package.
Author: Stephen Milborrow
Maintainer: Stephen Milborrow <milbo@sonic.net>
Diff between rpart.plot versions 2.2.0 dated 2018-05-19 and 3.0.0 dated 2018-07-12
rpart.plot-2.2.0/rpart.plot/inst/slowtests/code.in.rpart.report.with.prp.R |only rpart.plot-2.2.0/rpart.plot/inst/slowtests/test.prp.R |only rpart.plot-2.2.0/rpart.plot/inst/slowtests/user-manual-figs.R |only rpart.plot-2.2.0/rpart.plot/inst/slowtests/webpage-figs.R |only rpart.plot-3.0.0/rpart.plot/DESCRIPTION | 6 rpart.plot-3.0.0/rpart.plot/MD5 | 105 rpart.plot-3.0.0/rpart.plot/NAMESPACE | 8 rpart.plot-3.0.0/rpart.plot/NEWS | 33 rpart.plot-3.0.0/rpart.plot/R/as.char.R | 20 rpart.plot-3.0.0/rpart.plot/R/branches.R | 22 rpart.plot-3.0.0/rpart.plot/R/check.index.R | 19 rpart.plot-3.0.0/rpart.plot/R/describe.col.R | 85 rpart.plot-3.0.0/rpart.plot/R/dotlib.R |only rpart.plot-3.0.0/rpart.plot/R/layout.R | 48 rpart.plot-3.0.0/rpart.plot/R/lib.R | 105 rpart.plot-3.0.0/rpart.plot/R/lib.rpart.plot.R | 20 rpart.plot-3.0.0/rpart.plot/R/mvpart.labs.R | 4 rpart.plot-3.0.0/rpart.plot/R/my.snip.rpart.R | 2 rpart.plot-3.0.0/rpart.plot/R/node.labs.R | 71 rpart.plot-3.0.0/rpart.plot/R/node.numbers.R | 10 rpart.plot-3.0.0/rpart.plot/R/palette.R | 44 rpart.plot-3.0.0/rpart.plot/R/printcall.R |only rpart.plot-3.0.0/rpart.plot/R/prp.R | 194 - rpart.plot-3.0.0/rpart.plot/R/rpart.rules.R |only rpart.plot-3.0.0/rpart.plot/R/rpart.terms.R |only rpart.plot-3.0.0/rpart.plot/R/snip.R | 2 rpart.plot-3.0.0/rpart.plot/R/split.labs.R | 124 rpart.plot-3.0.0/rpart.plot/R/yes.no.R | 2 rpart.plot-3.0.0/rpart.plot/inst/doc/prp.pdf |binary rpart.plot-3.0.0/rpart.plot/inst/slowtests/README.txt | 27 rpart.plot-3.0.0/rpart.plot/inst/slowtests/header.R |only rpart.plot-3.0.0/rpart.plot/inst/slowtests/make.bat | 57 rpart.plot-3.0.0/rpart.plot/inst/slowtests/rpart.report.R |only rpart.plot-3.0.0/rpart.plot/inst/slowtests/rpart.report.Rout.save |only rpart.plot-3.0.0/rpart.plot/inst/slowtests/rpart.report.bat |only rpart.plot-3.0.0/rpart.plot/inst/slowtests/test.describe.col.R |only rpart.plot-3.0.0/rpart.plot/inst/slowtests/test.describe.col.Rout.save |only rpart.plot-3.0.0/rpart.plot/inst/slowtests/test.describe.col.bat |only rpart.plot-3.0.0/rpart.plot/inst/slowtests/test.epilog.R |only rpart.plot-3.0.0/rpart.plot/inst/slowtests/test.imports.R | 16 rpart.plot-3.0.0/rpart.plot/inst/slowtests/test.imports.Rout.save |only rpart.plot-3.0.0/rpart.plot/inst/slowtests/test.imports.bat |only rpart.plot-3.0.0/rpart.plot/inst/slowtests/test.na.R | 65 rpart.plot-3.0.0/rpart.plot/inst/slowtests/test.na.Rout.save |only rpart.plot-3.0.0/rpart.plot/inst/slowtests/test.na.bat |only rpart.plot-3.0.0/rpart.plot/inst/slowtests/test.palette.R | 87 rpart.plot-3.0.0/rpart.plot/inst/slowtests/test.palette.Rout.save |only rpart.plot-3.0.0/rpart.plot/inst/slowtests/test.palette.bat |only rpart.plot-3.0.0/rpart.plot/inst/slowtests/test.prolog.R |only rpart.plot-3.0.0/rpart.plot/inst/slowtests/test.prp.Rout.save | 1290 +++++++++- rpart.plot-3.0.0/rpart.plot/inst/slowtests/test.rpart.plot.R |only rpart.plot-3.0.0/rpart.plot/inst/slowtests/test.rpart.plot.Rout.save |only rpart.plot-3.0.0/rpart.plot/inst/slowtests/test.rpart.plot.bat |only rpart.plot-3.0.0/rpart.plot/inst/slowtests/test.rpart.rules.R |only rpart.plot-3.0.0/rpart.plot/inst/slowtests/test.rpart.rules.Rout.save |only rpart.plot-3.0.0/rpart.plot/inst/slowtests/test.rpart.rules.bat |only rpart.plot-3.0.0/rpart.plot/inst/slowtests/test.type5.R | 55 rpart.plot-3.0.0/rpart.plot/inst/slowtests/test.type5.Rout.save |only rpart.plot-3.0.0/rpart.plot/inst/slowtests/test.type5.bat |only rpart.plot-3.0.0/rpart.plot/inst/slowtests/vignette.R |only rpart.plot-3.0.0/rpart.plot/inst/slowtests/vignette.Rout.save |only rpart.plot-3.0.0/rpart.plot/inst/slowtests/vignette.bat |only rpart.plot-3.0.0/rpart.plot/inst/slowtests/webpage.figs.R |only rpart.plot-3.0.0/rpart.plot/inst/slowtests/webpage.figs.Rout.save |only rpart.plot-3.0.0/rpart.plot/inst/slowtests/webpage.figs.bat |only rpart.plot-3.0.0/rpart.plot/man/prp.Rd | 183 - rpart.plot-3.0.0/rpart.plot/man/ptitanic.Rd | 18 rpart.plot-3.0.0/rpart.plot/man/rpart.plot.Rd | 92 rpart.plot-3.0.0/rpart.plot/man/rpart.plot.version1.Rd | 39 rpart.plot-3.0.0/rpart.plot/man/rpart.rules.Rd |only rpart.plot-3.0.0/rpart.plot/man/show.prp.palettes.Rd | 3 rpart.plot-3.0.0/rpart.plot/tests |only 72 files changed, 2105 insertions(+), 751 deletions(-)
Title: File Conversion for 'Gem Infrasound Logger'
Description: Reads data files from the 'Gem infrasound logger' for analysis and converts to segy format (which is convenient for reading with traditional seismic analysis software). The Gem infrasound logger is an in-development low-cost, lightweight, low-power instrument for recording infrasound in field campaigns; email the maintainer for more information.
Author: Jake Anderson
Maintainer: Jake Anderson <ajakef@gmail.com>
Diff between gemlog versions 0.26 dated 2017-10-05 and 0.30 dated 2018-07-12
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/ReadGem_v0.8.R | 3 ++- R/ReadGem_v0.85.R | 1 + build/partial.rdb |binary data/gem_metadata.RData |binary man/gemlog-package.Rd | 4 +++- 7 files changed, 16 insertions(+), 12 deletions(-)
Title: Univariate Feature Selection and Compound Covariate for
Predicting Survival
Description: Univariate feature selection and compound covariate methods under the Cox model with high-dimensional features (e.g., gene expressions).
Available are survival data for non-small-cell lung cancer patients with gene expressions (Chen et al 2007 New Engl J Med) <DOI:10.1056/NEJMoa060096>,
statistical methods in Emura et al (2012 PLoS ONE) <DOI:10.1371/journal.pone.0047627>,
Emura & Chen (2016 Stat Methods Med Res) <DOI:10.1177/0962280214533378>, and Emura et al. (2018-)<submitted>.
Algorithms for generating correlated gene expressions are also available.
Author: Takeshi Emura, Hsuan-Yu Chen, Shigeyuki Matsui, Yi-Hau Chen
Maintainer: Takeshi Emura <takeshiemura@gmail.com>
Diff between compound.Cox versions 3.12 dated 2018-07-02 and 3.13 dated 2018-07-12
DESCRIPTION | 8 ++++---- MD5 | 30 ++++++++++++++++-------------- R/CG.Clayton.R | 2 +- R/CG.Gumbel.R |only man/CG.Clayton.Rd | 2 +- man/CG.Gumbel.Rd |only man/Lung.Rd | 3 ++- man/PBC.Rd | 1 + man/X.pathway.Rd | 2 +- man/X.tag.Rd | 2 +- man/cindex.CV.Rd | 2 +- man/compound.Cox-package.Rd | 6 +++--- man/dependCox.reg.CV.Rd | 1 + man/dependCox.reg.Rd | 1 + man/uni.Wald.Rd | 8 ++++++-- man/uni.score.Rd | 8 ++++++-- man/uni.selection.Rd | 9 +++++---- 17 files changed, 50 insertions(+), 35 deletions(-)