Title: Geographically Weighted Regression
Description: Functions for computing geographically weighted
regressions are provided, based on work by Chris
Brunsdon, Martin Charlton and Stewart Fotheringham.
Author: Roger Bivand [cre, aut],
Danlin Yu [aut],
Tomoki Nakaya [ctb],
Miquel-Angel Garcia-Lopez [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between spgwr versions 0.6-26 dated 2014-12-09 and 0.6-28 dated 2015-09-28
ChangeLog | 440 +++++++++++++++++++++-------------------------------- DESCRIPTION | 18 +- MD5 | 18 +- NAMESPACE | 3 R/gwe.R | 6 build/vignette.rds |binary inst/ChangeLog | 440 +++++++++++++++++++++-------------------------------- inst/doc/GWR.pdf |binary man/georgia.Rd | 2 man/gw.cov.Rd | 12 + 10 files changed, 386 insertions(+), 553 deletions(-)
Title: Convolution-Based Nonstationary Spatial Modeling
Description: Fits convolution-based nonstationary
Gaussian process models to point-referenced spatial data. The nonstationary
covariance function allows the user to specify the underlying correlation
structure and which spatial dependence parameters should be allowed to
vary over space: the anisotropy, nugget variance, and process variance.
The parameters are estimated via maximum likelihood, using a local
likelihood approach. Also provided are functions to fit stationary spatial
models for comparison, calculate the kriging predictor and standard errors,
and create various plots to visualize nonstationarity.
Author: Mark D. Risser [aut, cre]
Maintainer: Mark D. Risser <markdrisser@gmail.com>
Diff between convoSPAT versions 0.1 dated 2015-07-21 and 1.0 dated 2015-09-28
convoSPAT-0.1/convoSPAT/data/USprecip.RData |only convoSPAT-0.1/convoSPAT/man/Aniso_pred.Rd |only convoSPAT-0.1/convoSPAT/man/NSconvo_pred.Rd |only convoSPAT-0.1/convoSPAT/man/USprecip.Rd |only convoSPAT-0.1/convoSPAT/man/plot_correlation.Rd |only convoSPAT-0.1/convoSPAT/man/plot_ellipses.Rd |only convoSPAT-0.1/convoSPAT/man/plot_mc.Rd |only convoSPAT-0.1/convoSPAT/man/plot_preds.Rd |only convoSPAT-0.1/convoSPAT/man/summary_NS.Rd |only convoSPAT-0.1/convoSPAT/vignettes/MDR_package.pdf |only convoSPAT-1.0/convoSPAT/DESCRIPTION | 8 convoSPAT-1.0/convoSPAT/MD5 | 35 convoSPAT-1.0/convoSPAT/NAMESPACE | 15 convoSPAT-1.0/convoSPAT/R/DataDocumentation.R | 30 convoSPAT-1.0/convoSPAT/R/convoSPAT_fitpred.R | 381 +++---- convoSPAT-1.0/convoSPAT/R/convoSPAT_summplot.R | 585 +++++------- convoSPAT-1.0/convoSPAT/data/USmcgrids.RData |only convoSPAT-1.0/convoSPAT/data/USprecip97.RData |only convoSPAT-1.0/convoSPAT/data/USpredictionlocs.RData |only convoSPAT-1.0/convoSPAT/man/NSconvo_fit.Rd | 2 convoSPAT-1.0/convoSPAT/man/US.mc.grids.Rd |only convoSPAT-1.0/convoSPAT/man/US.prediction.locs.Rd |only convoSPAT-1.0/convoSPAT/man/USprecip97.Rd |only convoSPAT-1.0/convoSPAT/man/plot.Aniso.Rd |only convoSPAT-1.0/convoSPAT/man/plot.NSconvo.Rd |only convoSPAT-1.0/convoSPAT/man/predict.Aniso.Rd |only convoSPAT-1.0/convoSPAT/man/predict.NSconvo.Rd |only convoSPAT-1.0/convoSPAT/man/summary.Aniso.Rd |only convoSPAT-1.0/convoSPAT/man/summary.NSconvo.Rd |only convoSPAT-1.0/convoSPAT/vignettes/RisserCalder_LLEpaper.pdf |only 30 files changed, 505 insertions(+), 551 deletions(-)
Title: Choose Univariate Class Intervals
Description: Selected commonly used methods for choosing univariate class intervals for mapping or other graphics purposes.
Author: Roger Bivand [aut, cre],
Hisaji Ono [ctb],
Richard Dunlap [ctb],
Matthieu Stigler [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between classInt versions 0.1-22 dated 2015-01-06 and 0.1-23 dated 2015-09-28
ChangeLog | 34 ++++++++++++++++++++++++++++++++++ DESCRIPTION | 16 ++++++++-------- MD5 | 10 +++++----- NAMESPACE | 3 ++- data/jenks71.rda |binary inst/ChangeLog | 34 ++++++++++++++++++++++++++++++++++ 6 files changed, 83 insertions(+), 14 deletions(-)
Title: Simplify the Creation of Choropleth Maps in R
Description: Choropleths are thematic maps where geographic regions, such as
states, are colored according to some metric, such as the number of people
who live in that state. This package simplifies this process by 1.
Providing ready-made functions for creating choropleths of common maps. 2.
Providing data and API connections to interesting data sources for making
choropleths. 3. Providing a framework for creating choropleths from
arbitrary shapefiles. 4. Overlaying those maps over reference maps from
Google Maps. Please see the vignettes for more details.
Author: Ari Lamstein <arilamstein@gmail.com>[cre, aut],
Brian P Johnson <brian@pjohnson.info> [ctb, frontend animation code]
Maintainer: Ari Lamstein <arilamstein@gmail.com>
Diff between choroplethr versions 3.2.0 dated 2015-08-26 and 3.3.0 dated 2015-09-28
DESCRIPTION | 12 ++-- MD5 | 38 +++++++------- NAMESPACE | 6 ++ R/choropleth.R | 88 +++++++++++++++++++++++++++++++-- R/country.R | 1 R/county.R | 52 +++++++++++++------ R/state.R | 37 ++++++++++--- inst/doc/f-world-bank-data.html | 4 - inst/doc/h-creating-your-own-maps.html | 2 inst/tests/test-county.R | 7 ++ inst/tests/test-state.R | 8 +++ man/Admin1Choropleth.Rd | 2 man/Choropleth.Rd | 2 man/CountryChoropleth.Rd | 2 man/CountyChoropleth.Rd | 2 man/CountyZoomChoropleth.Rd | 2 man/StateChoropleth.Rd | 2 man/USAChoropleth.Rd | 2 man/county_choropleth.Rd | 37 +++++++++---- man/state_choropleth.Rd | 27 +++++++--- 20 files changed, 251 insertions(+), 82 deletions(-)
Title: Modelling Heterogeneity in Paired Comparison Data
Description: Performs 'BTLLasso', a method to model heterogeneity in paired comparison data. Subject-specific covariates are allowed to have an influence on the attractivity/strength of the objects. An L1 penalty on the pairwise differences between the object-specific parameters allows for both clustering of objects with regard to covariates and elimination of irrelevant covariates.
Author: Gunther Schauberger
Maintainer: Gunther Schauberger <gunther@stat.uni-muenchen.de>
Diff between BTLLasso versions 0.1-1 dated 2015-09-07 and 0.1-2 dated 2015-09-28
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/cppfunctions.cpp | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
Title: Spatial and Space-Time Point Pattern Analysis
Description: The Splancs package was written as an enhancement to S-Plus for display and analysis of spatial point pattern data; it has been ported to R and is in "maintenance mode".
Author: Roger Bivand [cre],
Barry Rowlingson [aut],
Peter Diggle [aut],
Giovanni Petris [ctb],
Stephen Eglen [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between splancs versions 2.01-37 dated 2015-03-18 and 2.01-38 dated 2015-09-28
ChangeLog | 299 +++++++++++++++++++++------------------------------------ DESCRIPTION | 11 +- MD5 | 8 - NAMESPACE | 8 - inst/ChangeLog | 299 +++++++++++++++++++++------------------------------------ 5 files changed, 239 insertions(+), 386 deletions(-)
Title: Interface Between GRASS 6+ Geographical Information System and R
Description: Interpreted interface between GRASS 6+ geographical
information system and R, based on starting R from within the GRASS
environment, or running free-standing R in a temporary GRASS location;
the package provides facilities for using all GRASS commands from the
R command line. This package may not be used for GRASS 7, for which
spgrass7 should be used.
Author: Roger Bivand [cre, aut],
Rainer Krug [ctb],
Markus Neteler [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between spgrass6 versions 0.8-6 dated 2014-10-14 and 0.8-8 dated 2015-09-28
ChangeLog | 1161 +++------------------------------------------- DESCRIPTION | 20 MD5 | 34 - NAMESPACE | 11 R/AAA.R | 7 R/bin_link.R | 111 ++-- R/initGRASS.R | 8 R/options.R | 10 R/spgrass6.R | 31 + R/vect_link.R | 87 +-- R/xml1.R | 12 inst/ChangeLog | 1161 +++------------------------------------------- inst/doc/spgrass6_0.3.pdf |binary man/gmeta6.Rd | 20 man/initGRASS.Rd | 6 man/readRAST6.Rd | 42 + man/readVECT6.Rd | 30 - man/spgrass6.Rd | 20 18 files changed, 458 insertions(+), 2313 deletions(-)
Title: Analyse Citation Data from Google Scholar
Description: Provides functions to extract citation data from Google
Scholar. Convenience functions are also provided for comparing
multiple scholars and predicting future h-index values.
Author: James Keirstead <j.keirstead@imperial.ac.uk>
Maintainer: James Keirstead <j.keirstead@imperial.ac.uk>
Diff between scholar versions 0.1.2 dated 2014-08-22 and 0.1.3 dated 2015-09-28
DESCRIPTION | 17 ++-- LICENSE | 4 - MD5 | 29 +++---- NAMESPACE | 1 NEWS | 16 ++++ R/compare.r | 158 ++++++++++++++++++++-------------------- R/predict.r | 18 ++++ R/publications.r | 66 +++++++++++++--- R/scholar.r | 12 +-- README.md | 104 +++++++++++++------------- inst/CITATION | 20 ++--- man/compare_scholars.Rd | 5 + man/get_article_cite_history.Rd |only man/get_citation_history.Rd | 10 +- man/get_publications.Rd | 10 ++ man/predict_h_index.Rd | 8 ++ 16 files changed, 289 insertions(+), 189 deletions(-)
Title: Entropy Partitioning to Measure Diversity
Description: Measurement and partitioning of diversity, based on Tsallis entropy.
Author: Eric Marcon, Bruno Herault
Maintainer: Eric Marcon <Eric.Marcon@ecofog.gf>
Diff between entropart versions 1.3.3 dated 2015-09-08 and 1.4.1 dated 2015-09-28
DESCRIPTION | 10 MD5 | 50 +- NAMESPACE | 6 NEWS | 17 R/AllenH.R | 52 +- R/ChaoPD.R | 55 +- R/CheckentropartArguments.R | 14 R/Hqz.R | 8 R/PhyloApply.R | 16 R/Preprocess.Tree.R | 39 + R/Rao.R | 8 R/Richness.R | 49 + R/Shannon.R | 8 R/Simpson.R | 8 R/Tsallis.R | 26 - inst/CITATION | 33 - inst/doc/entropart.Rnw | 10 inst/doc/entropart.pdf |binary man/AllenH.Rd | 6 man/ChaoPD.Rd | 4 man/PPtree.Rd | 5 man/SpeciesDistribution.Rd | 7 man/Tsallis.Rd | 2 man/entropart-package.Rd | 4 vignettes/entropart.Rnw | 10 vignettes/entropart.bib | 1082 +++++++++++++++++++++----------------------- 26 files changed, 795 insertions(+), 734 deletions(-)
Title: Interface to the Agave API
Description: Provides an interface to the the many computational resources iPlant offers through their RESTful application programming interface, see <http://www.iplantcollaborative.org/> for more information about iPlant, and <http://www.iplantcollaborative.org/ci/iplant-science-apis> for its APIs. Currently, 'rPlant' functions interact with the iPlant Agave API, the Taxonomic Name Resolution Service API, and the Phylotastic Taxosaurus API. Before using 'rPlant', users will have to register with the iPlant Collaborative. See <http://agaveapi.co/> for more information on the Agave API and <http://user.iplantcollaborative.org/> to register with iPlant.
Author: Barb Banbury <darwinthesun@gmail.com> and Kurt Michels <kamichels@math.arizona.edu>, Jeremy M. Beaulieu <jeremy.beaulieu@yale.edu>, Brian O'Meara <bomeara@utk.edu>
Maintainer: Kurt Michels <kamichels@math.arizona.edu>
Diff between rPlant versions 2.7 dated 2013-05-21 and 2.11 dated 2015-09-28
rPlant-2.11/rPlant/DESCRIPTION | 35 rPlant-2.11/rPlant/MD5 | 82 rPlant-2.11/rPlant/NAMESPACE | 7 rPlant-2.11/rPlant/R/ClustalW.R |only rPlant-2.11/rPlant/R/FaST_LMM.R |only rPlant-2.11/rPlant/R/Fasttree.R |only rPlant-2.11/rPlant/R/Mafft.R |only rPlant-2.11/rPlant/R/Muscle.R |only rPlant-2.11/rPlant/R/PLINK.R |only rPlant-2.11/rPlant/R/PLINKConversion.R |only rPlant-2.11/rPlant/R/RAxML.R |only rPlant-2.11/rPlant/R/TNRS.R | 12 rPlant-2.11/rPlant/R/find.input.R |only rPlant-2.11/rPlant/R/help.R |only rPlant-2.11/rPlant/R/rPlant.R | 3187 ++++++++++++++--- rPlant-2.11/rPlant/data/DNA.fasta.rda |only rPlant-2.11/rPlant/data/PROTEIN.fasta.rda |only rPlant-2.11/rPlant/data/fasta_aa.aln.rda |only rPlant-2.11/rPlant/data/fasta_dna.aln.rda |only rPlant-2.11/rPlant/data/geno_test.tfam.rda |only rPlant-2.11/rPlant/data/geno_test.tped.rda |only rPlant-2.11/rPlant/data/phylip_interleaved_aa.aln.rda |only rPlant-2.11/rPlant/data/phylip_interleaved_dna.aln.rda |only rPlant-2.11/rPlant/data/simulation1.map.rda |only rPlant-2.11/rPlant/data/simulation1.ped.rda |only rPlant-2.11/rPlant/inst/extdata/DNA.fasta |only rPlant-2.11/rPlant/inst/extdata/PROTEIN.fasta |only rPlant-2.11/rPlant/inst/extdata/geno_test.tfam |only rPlant-2.11/rPlant/inst/extdata/geno_test.tped |only rPlant-2.11/rPlant/inst/tests |only rPlant-2.11/rPlant/man/ClustalW.Rd |only rPlant-2.11/rPlant/man/FaST_LMM.Rd |only rPlant-2.11/rPlant/man/Fasttree.Rd |only rPlant-2.11/rPlant/man/GetAppList.Rd | 26 rPlant-2.11/rPlant/man/ListDir.Rd | 67 rPlant-2.11/rPlant/man/Mafft.Rd |only rPlant-2.11/rPlant/man/Muscle.Rd |only rPlant-2.11/rPlant/man/PLINK.Rd |only rPlant-2.11/rPlant/man/PLINKConversion.Rd |only rPlant-2.11/rPlant/man/RAxML.Rd |only rPlant-2.11/rPlant/man/SubmitJob.Rd | 121 rPlant-2.11/rPlant/man/TNRS.Rd | 23 rPlant-2.11/rPlant/man/UploadFile.Rd | 99 rPlant-2.11/rPlant/man/Validate.Rd |only rPlant-2.11/rPlant/man/rPlant-data.Rd |only rPlant-2.11/rPlant/man/rPlant-internal.Rd |only rPlant-2.11/rPlant/man/rplant-package.Rd | 24 rPlant-2.11/rPlant/vignettes |only rPlant-2.7/rPlant/R/GetCitations.R |only rPlant-2.7/rPlant/R/RunClustal.R |only rPlant-2.7/rPlant/R/RunMafft.R |only rPlant-2.7/rPlant/R/RunMuscle.R |only rPlant-2.7/rPlant/R/RunParsdna.R |only rPlant-2.7/rPlant/R/RunParsprotein.R |only rPlant-2.7/rPlant/R/RunQuicktree.R |only rPlant-2.7/rPlant/R/RunRAxMLdna.R |only rPlant-2.7/rPlant/R/RunRAxMLprotein.R |only rPlant-2.7/rPlant/data/ex.lp.fasta.rda |only rPlant-2.7/rPlant/inst/extdata/ex.lp.fasta |only rPlant-2.7/rPlant/inst/extdata/short.landplants.phy |only rPlant-2.7/rPlant/man/GetCitations.Rd |only rPlant-2.7/rPlant/man/GetToken.Rd |only rPlant-2.7/rPlant/man/RunClustal.Rd |only rPlant-2.7/rPlant/man/RunMafft.Rd |only rPlant-2.7/rPlant/man/RunMuscle.Rd |only rPlant-2.7/rPlant/man/RunParsdna.Rd |only rPlant-2.7/rPlant/man/RunParsprotein.Rd |only rPlant-2.7/rPlant/man/RunQuicktree.Rd |only rPlant-2.7/rPlant/man/RunRAxMLdna.Rd |only rPlant-2.7/rPlant/man/RunRAxMLprotein.Rd |only rPlant-2.7/rPlant/man/landplants.Rd |only 71 files changed, 3042 insertions(+), 641 deletions(-)
Title: An API Client for the Internet Archive
Description: Search the Internet Archive, retrieve metadata, and download
files.
Author: Lincoln Mullen [aut, cre]
Maintainer: Lincoln Mullen <lincoln@lincolnmullen.com>
Diff between internetarchive versions 0.1.2 dated 2015-03-24 and 0.1.4 dated 2015-09-28
DESCRIPTION | 11 ++++++----- MD5 | 34 +++++++++++++++++----------------- NAMESPACE | 2 +- NEWS | 4 ++++ R/ia_browse.R | 2 +- README.md | 14 ++++++++++---- build/vignette.rds |binary man/ia_browse.Rd | 2 +- man/ia_download.Rd | 2 +- man/ia_files.Rd | 2 +- man/ia_get_items.Rd | 2 +- man/ia_item_id.Rd | 2 +- man/ia_keyword_search.Rd | 2 +- man/ia_list_fields.Rd | 2 +- man/ia_metadata.Rd | 2 +- man/ia_search.Rd | 2 +- man/internetarchive.Rd | 2 +- vignettes/internet-archive.Rmd | 2 +- 18 files changed, 50 insertions(+), 39 deletions(-)
More information about internetarchive at CRAN
Permanent link
Title: Convert Between Spatial Objects and Well-Known Binary Geometry
Description: Utility functions to convert between the 'Spatial' classes
specified by the package 'sp', and the well-known binary '(WKB)'
representation for geometry specified by the Open Geospatial Consortium.
Supports 'Spatial' objects of class 'SpatialPoints',
'SpatialPointsDataFrame', 'SpatialLines', 'SpatialLinesDataFrame',
'SpatialPolygons', and 'SpatialPolygonsDataFrame'. Supports 'WKB' geometry
types 'Point', 'LineString', 'Polygon', 'MultiPoint', 'MultiLineString', and
'MultiPolygon'. Includes extensions to enable creation of maps with
'TIBCO Spotfire'.
Author: TIBCO Software Inc.
Maintainer: Ian Cook <icook@tibco.com>
Diff between wkb versions 0.1-0 dated 2015-02-28 and 0.2-0 dated 2015-09-28
DESCRIPTION | 29 - LICENSE | 6 MD5 | 34 +- NAMESPACE | 29 - R/SpatialLinesToWKBLineString.R | 439 +++++++++++++++------------- R/SpatialPointsToWKBPoint.R | 501 +++++++++++++++++--------------- R/SpatialPolygonsToWKBPolygon.R | 255 ++++++++-------- R/hex2raw.R |only R/readWKB.R | 608 ++++++++++++++++++++-------------------- R/writeEnvelope.R | 134 ++++---- R/writeWKB.R | 282 +++++++++--------- man/hex2raw.Rd |only man/readWKB.Rd | 268 ++++++++--------- man/writeEnvelope.Rd | 96 +++--- man/writeWKB.Rd | 240 ++++++++------- tests |only 16 files changed, 1506 insertions(+), 1415 deletions(-)
Title: Interface to Geometry Engine - Open Source (GEOS)
Description: Interface to Geometry Engine - Open Source (GEOS) using the C API for topology operations on geometries. The GEOS library is external to the package, and, when installing the package from source, must be correctly installed first. Windows and Mac Intel OS X binaries are provided on CRAN.
Author: Roger Bivand [cre, aut],
Colin Rundel [aut],
Edzer Pebesma [ctb],
Karl Ove Hufthammer [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between rgeos versions 0.3-12 dated 2015-09-01 and 0.3-13 dated 2015-09-28
ChangeLog | 67 +++++++++++ DESCRIPTION | 8 - MD5 | 54 ++++----- R/over.R | 4 R/rgeos_predicate_binary.R | 130 +++++++++++++++++++--- R/rgeos_topology_binary.R | 55 +++++++-- configure | 18 +-- inst/ChangeLog | 67 +++++++++++ inst/SVN_VERSION | 2 inst/tests/testxml/general/TestFunctionLLPrec.xml | 3 inst/tests/testxml/validate/TestRelateLL.xml | 3 inst/tests/testxml/validate/TestRelatePA.xml | 3 inst/tests/testxml/validate/TestRelatePL.xml | 3 inst/tests/testxml/validate/TestRelatePP.xml | 3 man/labelpt.Rd | 3 man/misc-over.Rd | 2 man/pred-binary-gContains.Rd | 14 +- man/pred-binary-gCrosses.Rd | 9 + man/pred-binary-gEquals.Rd | 9 + man/pred-binary-gIntersects.Rd | 9 + man/pred-binary-gRelate.Rd | 6 - man/pred-binary-gTouches.Rd | 6 - man/topo-bin-gDifference.Rd | 6 - man/topo-bin-gIntersection.Rd | 30 ++++- man/topo-bin-gSymdifference.Rd | 7 + man/topo-bin-gUnion.Rd | 7 + src/rgeos_geos2R.c | 21 ++- src/rgeos_topology_binary.c | 12 ++ 28 files changed, 462 insertions(+), 99 deletions(-)
Title: Meta-Analysis Package for R
Description: A comprehensive collection of functions for conducting meta-analyses in R. The package includes functions to calculate various effect sizes or outcome measures, fit fixed-, random-, and mixed-effects models to such data, carry out moderator and meta-regression analyses, and create various types of meta-analytical plots (e.g., forest, funnel, radial, L'Abbe, Baujat plots). For meta-analyses of binomial and person-time data, the package also provides functions that implement specialized methods, including the Mantel-Haenszel method, Peto's method, and a variety of suitable generalized linear (mixed-effects) models (i.e., mixed-effects logistic and Poisson regression models). Finally, the package provides functionality for fitting meta-analytic multivariate/multilevel models that account for non-independent sampling errors and/or true effects (e.g., due to the inclusion of multiple treatment studies, multiple endpoints, or other forms of clustering). Network meta-analyses and meta-analyses accounting for known correlation structures (e.g., due to phylogenetic relatedness) can also be conducted.
Author: Wolfgang Viechtbauer [aut, cre]
Maintainer: Wolfgang Viechtbauer <wvb@metafor-project.org>
Diff between metafor versions 1.9-7 dated 2015-05-22 and 1.9-8 dated 2015-09-28
DESCRIPTION | 16 MD5 | 179 +++-- NAMESPACE | 6 NEWS | 71 ++ R/AIC.rma.r | 27 R/BIC.rma.r | 21 R/addpoly.default.r | 4 R/anova.rma.r | 18 R/baujat.rma.mh.r | 16 R/baujat.rma.peto.r | 6 R/baujat.rma.uni.r | 7 R/blup.rma.uni.r | 4 R/coef.permutest.rma.uni.r | 2 R/coef.summary.rma.r | 4 R/confint.rma.mv.r | 406 ++++++++++++- R/confint.rma.uni.r | 249 +++++-- R/cooks.distance.rma.uni.r | 7 R/cumul.rma.mh.r | 18 R/cumul.rma.peto.r | 6 R/cumul.rma.uni.r | 7 R/dfbetas.rma.uni.r | 7 R/escalc.default.r | 30 R/fitstats.rma.r | 32 - R/forest.cumul.rma.r | 4 R/forest.default.r | 4 R/forest.rma.r | 4 R/fsn.r | 4 R/funnel.rma.r | 2 R/influence.rma.uni.r | 7 R/labbe.rma.r | 7 R/leave1out.rma.mh.r | 16 R/leave1out.rma.peto.r | 6 R/leave1out.rma.uni.r | 7 R/llplot.r | 4 R/misc.func.hidden.r | 171 ++++- R/permutest.rma.uni.r | 10 R/predict.rma.r | 4 R/print.anova.rma.r | 16 R/print.confint.rma.r | 6 R/print.infl.rma.uni.r | 3 R/print.permutest.rma.uni.r | 10 R/print.rma.glmm.r | 14 R/print.rma.mv.r | 30 R/print.rma.uni.r | 14 R/print.robust.rma.r |only R/profile.rma.mv.r | 115 +++ R/profile.rma.uni.r | 12 R/radial.rma.r | 2 R/ranktest.rma.r | 2 R/regtest.rma.r | 4 R/rma.glmm.r | 245 ++++--- R/rma.mh.r | 33 - R/rma.mv.r | 208 +++++- R/rma.peto.r | 20 R/rma.uni.r | 148 ++-- R/robust.r |only R/robust.rma.mv.r |only R/robust.rma.uni.r |only R/rstudent.rma.mh.r | 16 R/rstudent.rma.peto.r | 6 R/rstudent.rma.uni.r | 7 R/to.long.r | 49 - R/to.table.r | 49 - R/update.rma.r | 2 R/zzz.R | 2 README.md |only data/dat.konstantopoulos2011.rda |binary inst/CITATION | 4 inst/doc/metafor_diagram.pdf |binary man/anova.rma.Rd | 2 man/confint.rma.Rd | 79 ++ man/dat.fine1993.Rd | 7 man/dat.konstantopoulos2011.Rd | 7 man/dat.nielweise2007.Rd | 3 man/dat.nielweise2008.Rd | 3 man/escalc.Rd | 4 man/fitstats.Rd | 24 man/forest.rma.Rd | 2 man/hc.Rd | 2 man/influence.rma.mv.Rd | 4 man/influence.rma.uni.Rd | 4 man/permutest.Rd | 6 man/predict.rma.Rd | 2 man/print.confint.rma.Rd | 2 man/print.rma.uni.Rd | 2 man/print.robust.rma.Rd |only man/profile.rma.Rd | 15 man/rma.glmm.Rd | 14 man/rma.mv.Rd | 12 man/rma.uni.Rd | 2 man/robust.Rd |only man/weights.rma.Rd | 2 tests/testthat/Rplots.pdf |only tests/testthat/test_analysis_example_konstantopoulos2011.r | 10 tests/testthat/test_rma_handling_nas.r |only 95 files changed, 1827 insertions(+), 791 deletions(-)
Title: Cardiovascular Safety Exposure-Response Modeling in Early-Phase
Clinical Studies
Description: Includes 100 mixed-effects model structures describing the relationship between drug concentration and QT interval, heart rate/pulse rate or blood pressure. Given an exposure-response dataset, the tool fits each model structure to the observed data.
Author: Daniela J Conrado [aut, cre], William S Denney [aut], Gregory J Hather [aut], Danny Chen [ctb]
Maintainer: Daniela J Conrado <danielac@metrumrg.com>
Diff between cardioModel versions 1.1 dated 2015-09-25 and 1.2 dated 2015-09-28
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/21_cardioModel.R | 48 ++++++++++++++++++++++++++---------------------- 3 files changed, 32 insertions(+), 28 deletions(-)
Title: Computed ABC Analysis
Description: For a given data set, the package provides a novel method of computing precise limits to acquire subsets which are easily interpreted. Closely related to the Lorenz curve, the ABC curve visualizes the data by graphically representing the cumulative distribution function. Based on an ABC analysis the algorithm calculates, with the help of the ABC curve, the optimal limits by exploiting the mathematical properties pertaining to distribution of analyzed items. The data containing positive values is divided into three disjoint subsets A, B and C, with subset A comprising very profitable values, i.e. largest data values ("the important few"), subset B comprising values where the yield equals to the effort required to obtain it, and the subset C comprising of non-profitable values, i.e., the smallest data sets ("the trivial many"). Package is based on Ultsch. A ., Lotsch J.: Computed ABC Analysis for rational Selection of most informative Variables in multivariate Data, PLoS One, 2015.
Author: Michael Thrun, Jorn Lotsch, Alfred Ultsch
Maintainer: Michael Thrun <mthrun@mathematik.uni-marburg.de>
Diff between ABCanalysis versions 1.0.2 dated 2015-06-15 and 1.1.0 dated 2015-09-28
DESCRIPTION | 8 ++++---- MD5 | 26 +++++++++++++++----------- NAMESPACE | 4 ++++ R/ABCRemoveSmallYields.R |only R/ABCanalysis.R | 1 - R/ABCanalysisPlot.R | 20 ++++++++++++++++++-- R/ABCcleanData.R | 29 ++++------------------------- R/ABCcurve.R | 8 +++----- R/ABCplot.R | 20 ++++++++++++-------- R/calculatedABCanalysis.R |only man/ABCRemoveSmallYields.Rd |only man/ABCanalysisPlot.Rd | 18 +++++++++++++++++- man/ABCcleanData.Rd | 9 ++------- man/ABCcurve.Rd | 7 ++----- man/ABCplot.Rd | 7 ++----- man/calculatedABCanalysis.Rd |only 16 files changed, 83 insertions(+), 74 deletions(-)
Title: Regression Modeling Strategies
Description: Regression modeling, testing, estimation, validation,
graphics, prediction, and typesetting by storing enhanced model design
attributes in the fit. 'rms' is a collection of functions that
assist with and streamline modeling. It also contains functions for
binary and ordinal logistic regression models, ordinal models for
continuous Y with a variety of distribution families, and the Buckley-James
multiple regression model for right-censored responses, and implements
penalized maximum likelihood estimation for logistic and ordinary
linear models. 'rms' works with almost any regression model, but it
was especially written to work with binary or ordinal regression
models, Cox regression, accelerated failure time models,
ordinary linear models, the Buckley-James model, generalized least
squares for serially or spatially correlated observations, generalized
linear models, and quantile regression.
Author: Frank E Harrell Jr <f.harrell@vanderbilt.edu>
Maintainer: Frank E Harrell Jr <f.harrell@vanderbilt.edu>
Diff between rms versions 4.3-1 dated 2015-04-30 and 4.4-0 dated 2015-09-28
DESCRIPTION | 14 - MD5 | 74 +++-- NAMESPACE | 24 + NEWS | 22 + R/Glm.s | 18 - R/Gls.s | 4 R/Predict.s | 19 + R/Rq.s | 4 R/bj.s | 5 R/calibrate.cph.s | 229 ++++++++--------- R/contrast.s | 16 - R/cph.s | 170 +++++++------ R/ggplot.Predict.s | 29 +- R/lrm.s | 12 R/ols.s | 8 R/orm.s | 7 R/plot.Predict.s | 29 +- R/predab.resample.s | 72 ++--- R/predictrms.s | 40 +-- R/print.psm.s | 1 R/psm.s | 4 R/rms.s | 314 ++++++++++++++---------- R/rms.trans.s | 117 ++++----- R/rmsMisc.s | 497 +++++++++++++++++++++------------------ R/summary.rms.s | 2 R/validate.Rq.s | 9 demo/all.R | 79 +++--- man/Predict.Rd | 14 - man/calibrate.Rd | 30 +- man/cph.Rd | 6 man/ggplot.Predict.Rd | 4 man/rmsMisc.Rd | 32 ++ man/survplot.Rd | 30 +- tests/Glm.s | 3 tests/Predict.s | 2 tests/contrast.r |only tests/cph4.r |only tests/ggplot.Predict.Rd.timing.r |only tests/offset.r |only tests/rcs.r |only tests/strat.model.matrix.r |only 41 files changed, 1084 insertions(+), 856 deletions(-)
Title: Permutation Distribution Clustering
Description: Permutation Distribution Clustering is a clustering method for time series. Dissimilarity of time series is formalized as the divergence between their permutation distributions. The permutation distribution was proposed as measure of the complexity of a time series.
Author: Andreas M. Brandmaier
Maintainer: Andreas M. Brandmaier <brandmaier@mpib-berlin.mpg.de>
Diff between pdc versions 1.0.2 dated 2014-11-21 and 1.0.3 dated 2015-09-28
DESCRIPTION | 9 +++++---- MD5 | 32 ++++++++++++++++---------------- NAMESPACE | 24 +++++++++++++++++++++++- NEWS | 4 ++++ inst/CITATION | 34 +++++++++++++++++++--------------- man/codebook.Rd | 7 +++++-- man/complex.shapes.Rd | 6 ++++-- man/distance.Rd | 3 +-- man/entropy.heuristic.Rd | 9 +++++---- man/loo1nn.Rd | 8 +++++--- man/mds.plot.Rd | 10 ++++------ man/pdc-package.Rd | 10 +++++----- man/pdc.dist.Rd | 7 +++++-- man/pdclust.Rd | 10 +++++----- man/rasterPlot.Rd | 9 ++++----- man/star.shapes.Rd | 6 ++++-- man/trace.image.Rd | 7 +++++-- 17 files changed, 119 insertions(+), 76 deletions(-)
Title: Nonparametric Interaction Tests for Factorial Designs with
Repeated Measures
Description: Nonparametric aligned rank tests for interaction in two-way factorial designs, on data set with repeated measures in 'wide' format. There is a choice between 0) CHECK for alignment 1) Aligned REGULAR 2) FRIEDMAN 3) KOCH ranks.
Author: Jos Feys
Maintainer: Jos Feys <jos.feys@faber.kuleuven.be>
Diff between npIntFactRep versions 1.2 dated 2015-02-19 and 1.3 dated 2015-09-28
DESCRIPTION | 14 ++-- MD5 | 8 +- NAMESPACE | 3 R/npIntFactRep.R | 178 ++++++++++++++++++++++++++++++++++------------------ man/npIntFactRep.Rd | 51 +++++++++----- 5 files changed, 163 insertions(+), 91 deletions(-)
Title: Functions for a Variety of Stylometric Analyses
Description: A number of functions, supplemented by GUI, to perform various analyses in the field of computational stylistics, authorship attribution, etc.
Author: Maciej Eder, Jan Rybicki, Mike Kestemont
Maintainer: Maciej Eder <maciejeder@gmail.com>
Diff between stylo versions 0.6.0 dated 2015-08-18 and 0.6.1 dated 2015-09-28
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/txt.to.words.ext.R | 5 ++++- man/make.frequency.list.Rd | 2 +- 4 files changed, 12 insertions(+), 9 deletions(-)
Title: Non-Parametric Estimation of the Off-Pulse Interval of a Pulsar
Description: Provides functions to non-parametrically estimate the off-pulse interval of a source
function originating from a pulsar. The technique is based on a sequential application of P-values
obtained from goodness-of-fit tests for the uniform distribution, such as the Kolmogorov-Smirnov,
Cramer-von Mises, Anderson-Darling and Rayleigh goodness-of-fit tests.
Author: Willem Daniel Schutte
Maintainer: Willem Daniel Schutte <wd.schutte@nwu.ac.za>
Diff between SOPIE versions 1.4 dated 2015-06-05 and 1.5 dated 2015-09-28
SOPIE-1.4/SOPIE/R/adgoftestpval.R |only SOPIE-1.4/SOPIE/R/adgofteststat.R |only SOPIE-1.4/SOPIE/R/ppvonmises.R |only SOPIE-1.4/SOPIE/R/r.test.R |only SOPIE-1.5/SOPIE/DESCRIPTION | 11 SOPIE-1.5/SOPIE/MD5 | 48 +-- SOPIE-1.5/SOPIE/NAMESPACE | 6 SOPIE-1.5/SOPIE/NEWS |only SOPIE-1.5/SOPIE/R/CVM_pvall.R | 55 ++-- SOPIE-1.5/SOPIE/R/SOPIE.R | 129 ++------- SOPIE-1.5/SOPIE/R/a.estimate.R | 465 +++++++++++++--------------------- SOPIE-1.5/SOPIE/R/b.estimate.R | 464 +++++++++++++-------------------- SOPIE-1.5/SOPIE/R/circ.kernel.R | 47 +-- SOPIE-1.5/SOPIE/R/findh.R | 179 +++++-------- SOPIE-1.5/SOPIE/R/von_mises_density.R | 8 SOPIE-1.5/SOPIE/R/von_mises_sim.R | 34 +- SOPIE-1.5/SOPIE/data/J1709.rda |binary SOPIE-1.5/SOPIE/data/crab.rda |binary SOPIE-1.5/SOPIE/data/simdata.rda |binary SOPIE-1.5/SOPIE/inst |only SOPIE-1.5/SOPIE/man/SOPIE-package.Rd | 8 SOPIE-1.5/SOPIE/man/SOPIE.Rd | 2 SOPIE-1.5/SOPIE/man/a.estimate.Rd | 12 SOPIE-1.5/SOPIE/man/b.estimate.Rd | 16 - SOPIE-1.5/SOPIE/man/circ.kernel.Rd | 16 - SOPIE-1.5/SOPIE/man/crab.Rd | 4 SOPIE-1.5/SOPIE/man/findh.Rd | 14 - SOPIE-1.5/SOPIE/man/von_mises_sim.Rd | 4 28 files changed, 659 insertions(+), 863 deletions(-)
Title: A Collection of Methods for Singular Spectrum Analysis
Description: Methods and tools for Singular Spectrum Analysis including decomposition, forecasting and gap-filling for univariate and multivariate time series.
Author: Anton Korobeynikov, Alex Shlemov, Konstantin Usevich, Nina Golyandina
Maintainer: Anton Korobeynikov <anton@korobeynikov.info>
Diff between Rssa versions 0.13 dated 2015-03-03 and 0.13-1 dated 2015-09-28
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NAMESPACE | 9 +++++++++ inst/CITATION | 40 ++++++++++++++++++++++++++++++++-------- 4 files changed, 47 insertions(+), 14 deletions(-)
Title: Draw Geographical Maps
Description: Display of maps. Projection code and larger maps are in
separate packages ('mapproj' and 'mapdata').
Author: Original S code by Richard A. Becker and Allan R. Wilks.
R version by Ray Brownrigg.
Enhancements by Thomas P Minka and Alex Deckmyn.
Maintainer: Alex Deckmyn <alex.deckmyn@meteo.be>
Diff between maps versions 3.0.0 dated 2015-09-27 and 3.0.0-1 dated 2015-09-28
DESCRIPTION | 10 +++++----- MD5 | 6 +++--- src/Makefile | 1 + src/world.name | 2 +- 4 files changed, 10 insertions(+), 9 deletions(-)
Title: Conditional Maximum Likelihood for Quadratic Exponential Models
for Binary Panel Data
Description: Estimation, based on conditional maximum likelihood, of the quadratic exponential model proposed by Bartolucci, F. & Nigro, V. (2010, Econometrica) and of a simplified and a modified version of this model. The quadratic exponential model is suitable for the analysis of binary longitudinal data when state dependence (further to the effect of the covariates and a time-fixed individual intercept) has to be taken into account. Therefore, this is an alternative to the dynamic logit model having the advantage of easily allowing conditional inference in order to eliminate the individual intercepts and then getting consistent estimates of the parameters of main interest (for the covariates and the lagged response). The simplified version of this model does not distinguish, as the original model does, between the last time occasion and the previous occasions. The modified version formulates in a different way the interaction terms and it may be used to test in a easy way state dependence as shown in Bartolucci, F., Nigro, V. & Pigini, C. (2013, Econometric Reviews). The package also includes estimation of the dynamic logit model by a pseudo conditional estimator based on the quadratic exponential model, as proposed by Bartolucci, F. & Nigro, V. (2012, Journal of Econometrics).
Author: Francesco Bartolucci (University of Perugia), Claudia Pigini (University of Ancona "Politecnica delle Marche")
Maintainer: Francesco Bartolucci <francesco.bartolucci@unipg.it>
Diff between cquad versions 1.2 dated 2015-07-22 and 1.3 dated 2015-09-28
DESCRIPTION | 10 +++++----- MD5 | 26 ++++++++++++++------------ NAMESPACE | 1 + R/cquad.R |only R/cquad_basic.R | 7 ++++--- R/cquad_equ.R | 7 ++++--- R/cquad_ext.R | 5 +++-- R/cquad_pseudo.R | 9 +++++---- R/summary.cquad.R | 4 ++-- man/cquad-package.Rd | 11 ++++------- man/cquad.Rd |only man/cquad_basic.Rd | 4 +++- man/cquad_equ.Rd | 4 +++- man/cquad_ext.Rd | 4 +++- man/cquad_pseudo.Rd | 4 +++- 15 files changed, 54 insertions(+), 42 deletions(-)
Title: General Utility Functions for the 'Agricultural Production
Systems Simulator'
Description: Contains functions designed to facilitate the loading
and transformation of 'Agricultural Production Systems Simulator'
output files <https://www.apsim.info>. Input meteorological data
(also known as "weather" or "met") files can also be generated
from user supplied data.
Author: Justin Fainges
Maintainer: Justin Fainges <Justin.Fainges@csiro.au>
Diff between APSIM versions 0.8.1 dated 2015-07-13 and 0.8.2 dated 2015-09-28
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/LoadAPSIMouts.R | 2 +- R/MetFunctions.R | 18 +++++++++++++++--- README.md | 17 +++++++++++++++++ data/met.rda |binary man/checkCont.Rd | 2 +- man/metFile-class.Rd | 2 ++ 8 files changed, 47 insertions(+), 16 deletions(-)