Title: Convert Country Names and Country Codes
Description: Standardize country names, convert them into one of
eleven coding schemes, convert between coding schemes, and
assign region descriptors.
Author: Vincent Arel-Bundock [aut, cre]
(<https://orcid.org/0000-0003-2042-7063>),
CJ Yetman [ctb] (<https://orcid.org/0000-0001-5099-9500>),
Nils Enevoldsen [ctb] (<https://orcid.org/0000-0001-7195-4117>)
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Diff between countrycode versions 1.00.0 dated 2018-02-11 and 1.1.0 dated 2018-10-27
DESCRIPTION | 21 ++++++++++++--------- MD5 | 15 ++++++++------- NEWS | 14 ++++++++++++-- R/codelist.R | 5 ++++- R/countrycode.R | 16 +++++++++------- data/codelist.rda |binary data/codelist_panel.rda |binary inst |only man/codelist.Rd | 5 ++++- 9 files changed, 49 insertions(+), 27 deletions(-)
Title: MHC Allele-Based Differencing Between Populations
Description: Tools for the analysis of population differences
using the Major Histocompatibility Complex (MHC) genotypes of samples
having a variable number of alleles (1-4) recorded for each
individual. A hierarchical Dirichlet-Multinomial model on the
genotype counts is used to pool small samples from multiple
populations for pairwise tests of equality. Bayesian inference is
implemented via the 'rstan' package. Bootstrapped and posterior
p-values are provided for chi-squared and likelihood ratio tests of
equal genotype probabilities.
Author: Martin Lysy [cre, aut],
Peter W.J. Kim [aut],
Terin Robinson [ctb]
Maintainer: Martin Lysy <mlysy@uwaterloo.ca>
Diff between MADPop versions 1.1 dated 2017-01-18 and 1.1.1 dated 2018-10-27
MADPop-1.1.1/MADPop/DESCRIPTION | 50 MADPop-1.1.1/MADPop/MD5 | 78 MADPop-1.1.1/MADPop/NAMESPACE | 26 MADPop-1.1.1/MADPop/R/LRT.stat.R | 60 MADPop-1.1.1/MADPop/R/MADPop-package.R |only MADPop-1.1.1/MADPop/R/UM.eqtest.R | 130 - MADPop-1.1.1/MADPop/R/UM.suff.R | 92 - MADPop-1.1.1/MADPop/R/chi2.stat.R | 64 MADPop-1.1.1/MADPop/R/colSort.R | 22 MADPop-1.1.1/MADPop/R/fish215.R | 18 MADPop-1.1.1/MADPop/R/geno.format.R | 86 - MADPop-1.1.1/MADPop/R/hUM.post.R | 166 +- MADPop-1.1.1/MADPop/R/stanmodels.R | 65 MADPop-1.1.1/MADPop/build/vignette.rds |binary MADPop-1.1.1/MADPop/inst/doc/MADPop-quicktut.R | 312 +-- MADPop-1.1.1/MADPop/inst/doc/MADPop-quicktut.Rmd | 638 ++++---- MADPop-1.1.1/MADPop/inst/doc/MADPop-quicktut.html | 943 +++++++----- MADPop-1.1.1/MADPop/inst/extdata/fish_study_215.csv | 432 ++--- MADPop-1.1.1/MADPop/inst/include |only MADPop-1.1.1/MADPop/inst/stan |only MADPop-1.1.1/MADPop/man/LRT.stat.Rd | 69 MADPop-1.1.1/MADPop/man/MADPop.Rd | 101 - MADPop-1.1.1/MADPop/man/UM.eqtest.Rd | 115 - MADPop-1.1.1/MADPop/man/UM.suff.Rd | 69 MADPop-1.1.1/MADPop/man/chi2.stat.Rd | 81 - MADPop-1.1.1/MADPop/man/colSort.Rd | 37 MADPop-1.1.1/MADPop/man/fish215.Rd | 37 MADPop-1.1.1/MADPop/man/geno.format.Rd | 51 MADPop-1.1.1/MADPop/man/hUM.post.Rd | 127 - MADPop-1.1.1/MADPop/src/Makevars | 13 MADPop-1.1.1/MADPop/src/Makevars.win | 14 MADPop-1.1.1/MADPop/src/RcppExports.cpp |only MADPop-1.1.1/MADPop/src/stanExports_DirichletMultinomial.cc |only MADPop-1.1.1/MADPop/src/stanExports_DirichletMultinomial.h |only MADPop-1.1.1/MADPop/tests |only MADPop-1.1.1/MADPop/vignettes/MADPop-quicktut.Rmd | 638 ++++---- MADPop-1.1/MADPop/R/MADPop.R |only MADPop-1.1/MADPop/R/zzz.R |only MADPop-1.1/MADPop/exec |only MADPop-1.1/MADPop/inst/staninclude |only MADPop-1.1/MADPop/src/Modules.cpp |only MADPop-1.1/MADPop/src/include |only MADPop-1.1/MADPop/tools |only 43 files changed, 2387 insertions(+), 2147 deletions(-)
Title: 'Rcpp' Bindings for 'Redis' using the 'hiredis' Library
Description: Connection to the 'Redis' key/value store using the
C-language client library 'hiredis' (included as a fallback) with
'MsgPack' encoding provided via 'RcppMsgPack' headers.
Author: Dirk Eddelbuettel <edd@debian.org>
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppRedis versions 0.1.8 dated 2017-09-09 and 0.1.9 dated 2018-10-27
ChangeLog | 70 ++++++++++++++++++++++++++++++ DESCRIPTION | 25 +++++----- MD5 | 41 ++++++++++++----- NAMESPACE | 4 - README.md | 54 ++++++++++++----------- cleanup | 1 configure | 78 ++++++++++++++++++++------------- configure.ac | 61 +++++++++++++++----------- inst/NEWS.Rd | 15 ++++++ inst/tests/runit.basicRtests.R | 14 +++--- inst/tests/runit.hashTests.R |only src/Makevars.in | 15 +++++- src/Redis.cpp | 95 +++++++++++++++++++++++++++++++++++++---- src/hiredis |only tests/runUnitTests.R | 95 +++++++++++++++++++++++------------------ 15 files changed, 403 insertions(+), 165 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 1.0.1 dated 2018-07-12 and 1.0.2 dated 2018-10-27
ggspatial-1.0.1/ggspatial/R/deprecated-functions.R |only ggspatial-1.0.1/ggspatial/man/deprecated.Rd |only ggspatial-1.0.1/ggspatial/tests/testthat/test-deprecated.R |only ggspatial-1.0.2/ggspatial/DESCRIPTION | 6 - ggspatial-1.0.2/ggspatial/MD5 | 31 ++++------ ggspatial-1.0.2/ggspatial/NAMESPACE | 31 ---------- ggspatial-1.0.2/ggspatial/R/layer-spatial-raster.R | 16 +++++ ggspatial-1.0.2/ggspatial/R/layer-spatial.R | 2 ggspatial-1.0.2/ggspatial/inst/doc/ggspatial.R | 6 - ggspatial-1.0.2/ggspatial/inst/doc/ggspatial.Rmd | 6 - ggspatial-1.0.2/ggspatial/inst/doc/ggspatial.html | 18 ++--- ggspatial-1.0.2/ggspatial/inst/longlake/LongLakeDepthSurvey.dbf |binary ggspatial-1.0.2/ggspatial/inst/longlake/LongLakeDepthSurvey.prj | 2 ggspatial-1.0.2/ggspatial/man/layer_spatial.Rd | 2 ggspatial-1.0.2/ggspatial/tests/testthat/test-df_spatial.R | 2 ggspatial-1.0.2/ggspatial/tests/testthat/test-geom_spatial.R | 18 ++--- ggspatial-1.0.2/ggspatial/tests/testthat/test-layer-spatial.R | 8 +- ggspatial-1.0.2/ggspatial/vignettes/ggspatial.Rmd | 6 - 18 files changed, 68 insertions(+), 86 deletions(-)
Title: Unpacking Assignment for Lists via Pattern Matching
Description: Provides an operator for assigning nested components of a list to
names via a concise pattern matching syntax. This is especially convenient for
assigning individual names to the multiple values that a function may return
in the form of a list, and for extracting deeply nested list components.
Author: Eugene Ha [aut, cre]
Maintainer: Eugene Ha <eha@posteo.de>
Diff between dub versions 0.1.0 dated 2018-02-16 and 0.2.0 dated 2018-10-27
DESCRIPTION | 15 ++---- MD5 | 22 ++++---- NAMESPACE | 4 - NEWS | 7 ++ R/assert.R | 13 ++--- R/assign.R | 94 +++++++++++++++++++------------------- R/names.R | 28 ++++++----- R/tree.R | 3 - R/util.R | 14 +++-- man/assign.Rd | 95 +++++++++++++++++++------------------- tests/testthat/test-assign.R | 106 +++++++++++++++++++++---------------------- tests/testthat/test-errors.R | 54 ++++++++++----------- 12 files changed, 235 insertions(+), 220 deletions(-)
Title: WHOIS Server Querying
Description: Queries data from WHOIS servers.
Author: Brad Cable
Maintainer: Brad Cable <brad@bcable.net>
Diff between Rwhois versions 1.0.2 dated 2018-10-19 and 1.0.3 dated 2018-10-27
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/functions.R | 2 +- README.md | 20 +++++++++++++++----- 4 files changed, 22 insertions(+), 12 deletions(-)
Title: Paired Lasso Regression
Description: Implements sparse regression with paired covariates (Rauschenberger et al.).
Author: Armin Rauschenberger [aut, cre]
Maintainer: Armin Rauschenberger <a.rauschenberger@vumc.nl>
Diff between palasso versions 0.0.1 dated 2018-05-31 and 0.0.2 dated 2018-10-27
DESCRIPTION | 15 - MD5 | 48 +-- NEWS.md | 6 R/function.R | 728 ++++++++++++++++++++++++++++++++++++------------- R/hidden.R | 184 +++++++----- R/methods.R | 32 +- README.md | 48 +-- build/vignette.rds |binary data/toydata.rda |binary inst/CITATION | 18 - inst/doc/article.Rmd | 8 inst/doc/article.html | 190 ------------ inst/doc/vignette.Rmd | 9 inst/doc/vignette.html | 318 +++------------------ man/arguments.Rd |only man/dot-args.Rd |only man/dot-cor.Rd |only man/dot-cv.Rd |only man/dot-dims.Rd |only man/dot-extract.Rd |only man/dot-fit.Rd |only man/dot-folds.Rd |only man/dot-loss.Rd |only man/dot-weight.Rd |only man/other.Rd | 57 +-- man/palasso.Rd | 22 - man/plots.Rd | 12 tests/testthat/test.R | 14 vignettes/article.Rmd | 8 vignettes/vignette.Rmd | 9 30 files changed, 886 insertions(+), 840 deletions(-)
Title: Treatment of Zeros, Left-Censored and Missing Values in
Compositional Data Sets
Description: Principled methods for the imputation of zeros, left-censored and missing data in
compositional data sets.
Author: Javier Palarea-Albaladejo and Josep Antoni Martin-Fernandez
Maintainer: Javier Palarea-Albaladejo <javier.palarea@bioss.ac.uk>
Diff between zCompositions versions 1.1.1 dated 2017-08-09 and 1.1.1-1 dated 2018-10-27
DESCRIPTION | 13 +++++++------ MD5 | 6 +++--- NEWS | 7 +++++++ man/zCompositions-package.Rd | 6 +++--- 4 files changed, 20 insertions(+), 12 deletions(-)
Title: Operations Research LOCational Analysis Models
Description: Objects and methods to handle and solve the min-sum location problem, also known as Fermat-Weber problem. The min-sum location problem search for a point such that the weighted sum of the distances to the demand points are minimized. See "The Fermat-Weber location problem revisited" by Brimberg, Mathematical Programming, 1, pg. 71-76, 1995. <DOI:10.1007/BF01592245>.
General global optimization algorithms are used to solve the problem, along with the adhoc Weiszfeld method, see "Sur le point pour lequel la Somme des distances de n points donnes est minimum", by Weiszfeld, Tohoku Mathematical Journal, First Series, 43, pg. 355-386, 1937 or "On the point for which the sum of the distances to n given points is minimum", by E. Weiszfeld and F. Plastria, Annals of Operations Research, 167, pg. 7-41, 2009. <DOI:10.1007/s10479-008-0352-z>.
Author: Manuel Munoz-Marquez <manuel.munoz@uca.es>
Maintainer: Manuel Munoz-Marquez <manuel.munoz@uca.es>
Diff between orloca versions 4.5 dated 2018-04-21 and 4.6 dated 2018-10-27
orloca-4.5/orloca/R/zsum.R |only orloca-4.5/orloca/R/zsumgra.R |only orloca-4.5/orloca/R/zsuml2.R |only orloca-4.5/orloca/R/zsuml2min.R |only orloca-4.5/orloca/R/zsumlp.R |only orloca-4.5/orloca/R/zsumlpmin.R |only orloca-4.5/orloca/R/zsummin.R |only orloca-4.5/orloca/man/andalusia-data.Rd |only orloca-4.5/orloca/man/zsum.Rd |only orloca-4.5/orloca/man/zsumgra.Rd |only orloca-4.5/orloca/man/zsuml2.Rd |only orloca-4.5/orloca/man/zsuml2min.Rd |only orloca-4.5/orloca/man/zsumlp.Rd |only orloca-4.5/orloca/man/zsumlpmin.Rd |only orloca-4.5/orloca/man/zsummin.Rd |only orloca-4.6/orloca/ChangeLog | 6 - orloca-4.6/orloca/DESCRIPTION | 20 +-- orloca-4.6/orloca/MD5 | 93 +++++++++--------- orloca-4.6/orloca/NAMESPACE | 24 ++-- orloca-4.6/orloca/R/andalusia.R | 3 orloca-4.6/orloca/R/as.R | 41 ++++++-- orloca-4.6/orloca/R/contour.loca.p.R | 13 +- orloca-4.6/orloca/R/distsum.R |only orloca-4.6/orloca/R/distsumgra.R |only orloca-4.6/orloca/R/distsuml2.R |only orloca-4.6/orloca/R/distsuml2min.R |only orloca-4.6/orloca/R/distsumlp.R |only orloca-4.6/orloca/R/distsumlpmin.R |only orloca-4.6/orloca/R/distsummin.R |only orloca-4.6/orloca/R/loca.p.R | 6 - orloca-4.6/orloca/R/orloca-package.R | 29 +++-- orloca-4.6/orloca/R/persp.loca.p.R | 7 - orloca-4.6/orloca/R/plot.loca.p.R | 1 orloca-4.6/orloca/build/vignette.rds |binary orloca-4.6/orloca/demo/orloca.R | 10 - orloca-4.6/orloca/demo/orloca_andalusia.R | 2 orloca-4.6/orloca/inst/doc/localizacionplana.Rmd | 18 +-- orloca-4.6/orloca/inst/doc/localizacionplana.html | 22 ++-- orloca-4.6/orloca/inst/doc/planarlocation.Rmd | 94 +++++++++--------- orloca-4.6/orloca/inst/doc/planarlocation.html | 96 +++++++++---------- orloca-4.6/orloca/inst/po/es/LC_MESSAGES/R-orloca.mo |binary orloca-4.6/orloca/man/andalusia.Rd |only orloca-4.6/orloca/man/as-methods.Rd | 11 -- orloca-4.6/orloca/man/as.data.frame.loca.p.Rd |only orloca-4.6/orloca/man/as.loca.p.Rd |only orloca-4.6/orloca/man/as.loca.p.data.frame.Rd |only orloca-4.6/orloca/man/as.loca.p.matrix.Rd |only orloca-4.6/orloca/man/as.matrix.loca.p.Rd |only orloca-4.6/orloca/man/contour.loca.p.Rd | 14 +- orloca-4.6/orloca/man/distsum.Rd |only orloca-4.6/orloca/man/distsumgra.Rd |only orloca-4.6/orloca/man/distsuml2.Rd |only orloca-4.6/orloca/man/distsuml2min.Rd |only orloca-4.6/orloca/man/distsumlp.Rd |only orloca-4.6/orloca/man/distsumlpmin.Rd |only orloca-4.6/orloca/man/distsummin.Rd |only orloca-4.6/orloca/man/loca.p.Rd | 9 - orloca-4.6/orloca/man/orloca-package.Rd | 22 ++-- orloca-4.6/orloca/man/persp.loca.p.Rd | 3 orloca-4.6/orloca/man/plot.Rd | 13 +- orloca-4.6/orloca/man/rloca.p.Rd | 3 orloca-4.6/orloca/po/R-orloca-es.po | 64 ++++++++++-- orloca-4.6/orloca/po/R-orloca.pot | 52 +++++++++- orloca-4.6/orloca/vignettes/localizacionplana.Rmd | 18 +-- orloca-4.6/orloca/vignettes/planarlocation.Rmd | 94 +++++++++--------- 65 files changed, 449 insertions(+), 339 deletions(-)
Title: Camera Trap Data Management and Preparation of Occupancy and
Spatial Capture-Recapture Analyses
Description: Management of and data extraction from camera trap photographs in wildlife studies. The package provides a workflow for storing and sorting camera trap photographs, computes record databases and detection/non-detection matrices for occupancy and spatial capture-recapture analyses with great flexibility. In addition, it provides simple mapping functions (number of species, number of independent species detections by station) and can visualise activity data.
Author: Juergen Niedballa [aut, cre],
Alexandre Courtiol [aut],
Rahel Sollmann [aut],
John Mathai [ctb],
Seth Timothy Wong [ctb],
An The Truong Nguyen [ctb],
Azlan bin Mohamed [ctb],
Andrew Tilker [ctb],
Andreas Wilting [ctb, ths]
Maintainer: Juergen Niedballa <camtrapr@gmail.com>
Diff between camtrapR versions 0.99.9 dated 2017-10-25 and 1.0 dated 2018-10-27
DESCRIPTION | 12 - MD5 | 80 +++++----- NAMESPACE | 10 - NEWS | 25 ++- R/activityDensity.R | 39 ----- R/activityOverlap.R | 64 ++++---- R/appendSpeciesNames.R | 10 + R/checkSpeciesIdentification.R | 10 + R/detectionHistory.R | 10 - R/detectionMaps.R | 31 +++- R/imageRename.R | 19 +- R/recordTable.R | 29 ++- R/recordTableIndividual.R | 56 ++++--- R/spatialDetectionHistory.R | 13 + R/surveyReport.R | 10 - R/variousOtherHelperFunctions.R | 45 +++--- R/variousPlottingHelperFunctions.R | 194 -------------------------- build/vignette.rds |binary inst/doc/DataExploration.R | 20 ++ inst/doc/DataExploration.Rmd | 28 ++- inst/doc/DataExploration.html | 69 +++++---- inst/doc/DataExtraction.Rmd | 4 inst/doc/DataExtraction.html | 174 +++++++++++------------ inst/doc/ImageOrganisation.R | 4 inst/doc/ImageOrganisation.Rmd | 8 - inst/doc/ImageOrganisation.html | 78 +++++----- inst/doc/SpeciesIndividualIdentification.Rmd | 4 inst/doc/SpeciesIndividualIdentification.html | 124 ++++++++-------- man/activityDensity.Rd | 2 man/activityOverlap.Rd | 32 +++- man/camtrapR-package.Rd | 5 man/checkSpeciesIdentification.Rd | 3 man/detectionMaps.Rd | 2 man/recordTable.Rd | 30 ++-- man/recordTableIndividual.Rd | 8 - man/spatialDetectionHistory.Rd | 2 man/timeShiftImages.Rd | 4 vignettes/DataExploration.Rmd | 28 ++- vignettes/DataExtraction.Rmd | 4 vignettes/ImageOrganisation.Rmd | 8 - vignettes/SpeciesIndividualIdentification.Rmd | 4 41 files changed, 645 insertions(+), 657 deletions(-)
Title: Linkage Map Construction using the MSTmap Algorithm
Description: Functions for Accurate and Speedy linkage map construction, manipulation and diagnosis of Doubled Haploid, Backcross and Recombinant Inbred 'R/qtl' objects. This includes extremely fast linkage map clustering and optimal marker ordering using 'MSTmap' (see Wu et al.,2008).
Author: Julian Taylor <julian.taylor@adelaide.edu.au>, David Butler
<dbutler@uow.edu.au>.
Maintainer: Julian Taylor <julian.taylor@adelaide.edu.au>
Diff between ASMap versions 1.0-2 dated 2017-09-14 and 1.0-4 dated 2018-10-27
ASMap-1.0-2/ASMap/R/mstmap13.R |only ASMap-1.0-4/ASMap/DESCRIPTION | 10 ASMap-1.0-4/ASMap/MD5 | 75 +- ASMap-1.0-4/ASMap/R/mstmap14.R |only ASMap-1.0-4/ASMap/build/vignette.rds |binary ASMap-1.0-4/ASMap/data/mapBC.RData |binary ASMap-1.0-4/ASMap/data/mapBCu.RData |binary ASMap-1.0-4/ASMap/data/mapDH.RData |binary ASMap-1.0-4/ASMap/data/mapDHf.RData |binary ASMap-1.0-4/ASMap/data/mapF2.RData |binary ASMap-1.0-4/ASMap/inst/NEWS.Rd | 17 ASMap-1.0-4/ASMap/inst/doc/asmapvignette.R | 767 +++++++++++++------------- ASMap-1.0-4/ASMap/inst/doc/asmapvignette.Rnw | 1 ASMap-1.0-4/ASMap/inst/doc/asmapvignette.pdf |binary ASMap-1.0-4/ASMap/man/ASMap-package.Rd | 10 ASMap-1.0-4/ASMap/man/alignCross.Rd | 2 ASMap-1.0-4/ASMap/man/breakCross.Rd | 9 ASMap-1.0-4/ASMap/man/combineMap.Rd | 10 ASMap-1.0-4/ASMap/man/fixClones.Rd | 2 ASMap-1.0-4/ASMap/man/genClones.Rd | 4 ASMap-1.0-4/ASMap/man/heatMap.Rd | 13 ASMap-1.0-4/ASMap/man/mapBC.Rd | 4 ASMap-1.0-4/ASMap/man/mapBCu.Rd | 4 ASMap-1.0-4/ASMap/man/mapDH.Rd | 4 ASMap-1.0-4/ASMap/man/mapDHf.Rd | 4 ASMap-1.0-4/ASMap/man/mapF2.Rd | 8 ASMap-1.0-4/ASMap/man/mergeCross.Rd | 6 ASMap-1.0-4/ASMap/man/mstmap.cross.Rd | 28 ASMap-1.0-4/ASMap/man/mstmap.data.frame.Rd | 9 ASMap-1.0-4/ASMap/man/pValue.Rd | 4 ASMap-1.0-4/ASMap/man/pp.init.Rd | 4 ASMap-1.0-4/ASMap/man/profileGen.Rd | 8 ASMap-1.0-4/ASMap/man/profileMark.Rd | 8 ASMap-1.0-4/ASMap/man/pullCross.Rd | 8 ASMap-1.0-4/ASMap/man/pushCross.Rd | 11 ASMap-1.0-4/ASMap/man/statGen.Rd | 7 ASMap-1.0-4/ASMap/man/statMark.Rd | 7 ASMap-1.0-4/ASMap/man/subsetCross.Rd | 2 ASMap-1.0-4/ASMap/vignettes/asmapvignette.Rnw | 1 ASMap-1.0-4/ASMap/vignettes/titlesec.sty |only 40 files changed, 532 insertions(+), 515 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-08-02 0.3.0
2017-06-27 0.2.0
2016-06-14 0.1.2
2016-04-14 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-08-29 1.5-3
2015-04-01 1.5-2