Title: Spatial Dependence: Weighting Schemes, Statistics and Models
Description: A collection of functions to create spatial weights matrix
objects from polygon contiguities, from point patterns by distance and
tessellations, for summarizing these objects, and for permitting their
use in spatial data analysis, including regional aggregation by minimum
spanning tree; a collection of tests for spatial autocorrelation,
including global Moran's I, APLE, Geary's C, Hubert/Mantel general cross
product statistic, Empirical Bayes estimates and Assunção/Reis Index,
Getis/Ord G and multicoloured join count statistics, local Moran's I
and Getis/Ord G, saddlepoint approximations and exact tests for global
and local Moran's I; and functions for estimating spatial simultaneous
autoregressive (SAR) lag and error models, impact measures for lag
models, weighted and unweighted SAR and CAR spatial regression models,
semi-parametric and Moran eigenvector spatial filtering, GM SAR error
models, and generalized spatial two stage least squares models.
Author: Roger Bivand [cre, aut],
Micah Altman [ctb],
Luc Anselin [ctb],
Renato Assunção [ctb],
Olaf Berke [ctb],
Andrew Bernat [ctb],
Guillaume Blanchet [ctb],
Eric Blankmeyer [ctb],
Marilia Carvalho [ctb],
Bjarke Christensen [ctb],
Yongwan Chun [ctb],
Carsten Dormann [ctb],
Stéphane Dray [ctb],
Virgilio Gómez-Rubio [ctb],
Rein Halbersma [ctb],
Elias Krainski [ctb],
Pierre Legendre [ctb],
Nicholas Lewin-Koh [ctb],
Hongfei Li [ctb],
Jielai Ma [ctb],
Giovanni Millo [ctb],
Werner Mueller [ctb],
Hisaji Ono [ctb],
Pedro Peres-Neto [ctb],
Gianfranco Piras [ctb],
Markus Reder [ctb],
Michael Tiefelsdorf [ctb],
Danlin Yu [ctb]
Maintainer: Roger Bivand
Diff between spdep versions 0.5-83 dated 2015-01-16 and 0.5-86 dated 2015-03-15
ChangeLog | 118 ++++++++++++++++++++++++++++++++++++++++++ DESCRIPTION | 8 +- MD5 | 84 +++++++++++++++-------------- NAMESPACE | 5 + R/autocov.R | 3 - R/error.spsarlm.R | 49 +++++++++++------ R/jacobian_setup.R | 7 +- R/lag.spsarlm.R | 110 ++++++++++++++++++++++----------------- R/lextrB.R |only R/lextrW.R |only R/localmoran.exact.R | 2 R/moran.exact.R | 2 R/sacsarlm.R | 31 +++++++---- R/utils.R | 20 +++++-- build/vignette.rds |binary data/oldcol.rda |binary inst/ChangeLog | 118 ++++++++++++++++++++++++++++++++++++++++++ inst/doc/CO69.R | 2 inst/doc/CO69.Rnw | 2 inst/doc/CO69.pdf |binary inst/doc/SpatialFiltering.pdf |binary inst/doc/nb.pdf |binary inst/doc/nb_igraph.Rmd | 13 ++-- inst/doc/nb_igraph.html | 16 ++--- inst/doc/sids.R | 1 inst/doc/sids.pdf |binary man/COL.OLD.Rd | 6 +- man/NY_data.Rd | 2 man/autocov_dist.Rd | 21 ++++--- man/baltimore.Rd | 2 man/boston.Rd | 2 man/columbus.Rd | 2 man/eire.Rd | 2 man/graphneigh.Rd | 11 +++ man/lextrB.Rd |only man/lm.morantest.Rd | 2 man/nc.sids.Rd | 2 man/read.gal.Rd | 4 - man/read.gwt2nb.Rd | 2 man/wheat.Rd | 2 src/eminmaxC.c |only src/init.c | 5 + src/spdep.h | 5 + vignettes/CO69.Rnw | 2 vignettes/nb_igraph.Rmd | 13 ++-- 45 files changed, 500 insertions(+), 176 deletions(-)
Title: Penalized Quantile Regression
Description: Performs penalized quantile regression for LASSO, SCAD and MCP functions. Provides a function that automatically generates lambdas and evaluates different models with cross validation or BIC, including a large p version of BIC.
Author: Ben Sherwood
Maintainer: Ben Sherwood
Diff between rqPen versions 1.0 dated 2014-10-29 and 1.1 dated 2015-03-15
rqPen-1.0/rqPen/man/scad_1_deriv.Rd |only rqPen-1.0/rqPen/man/scad_2_deriv.Rd |only rqPen-1.1/rqPen/DESCRIPTION | 10 ++-- rqPen-1.1/rqPen/LICENSE | 2 rqPen-1.1/rqPen/MD5 | 19 +++----- rqPen-1.1/rqPen/NAMESPACE | 2 rqPen-1.1/rqPen/NEWS |only rqPen-1.1/rqPen/R/rqPen.R | 82 +++++++++++++++++++++++------------- rqPen-1.1/rqPen/man/beta_plots.Rd | 2 rqPen-1.1/rqPen/man/cv.rq.pen.Rd | 6 +- rqPen-1.1/rqPen/man/rq.lasso.fit.Rd | 4 - rqPen-1.1/rqPen/man/rq.nc.fit.Rd | 4 - 12 files changed, 76 insertions(+), 55 deletions(-)
Title: R Code for Mark Analysis
Description: An interface to the software package MARK that constructs input
files for MARK and extracts the output. MARK was developed by Gary White
and is freely available at (http://www.phidot.org/software/mark/downloads/)
but is not open source.
Author: Jeff Laake
Maintainer: Jeff Laake
Diff between RMark versions 2.1.9 dated 2014-10-06 and 2.1.12 dated 2015-03-15
RMark-2.1.12/RMark/DESCRIPTION | 23 - RMark-2.1.12/RMark/MD5 | 311 ++++++++-------- RMark-2.1.12/RMark/NAMESPACE | 14 RMark-2.1.12/RMark/NEWS | 36 + RMark-2.1.12/RMark/R/PIMS.R | 1 RMark-2.1.12/RMark/R/RMark-package.R | 64 ++- RMark-2.1.12/RMark/R/TransitionMatrix.R | 7 RMark-2.1.12/RMark/R/add.design.data.R | 1 RMark-2.1.12/RMark/R/adjust.chat.R | 11 RMark-2.1.12/RMark/R/adjust.parameter.count.R | 1 RMark-2.1.12/RMark/R/convert.inp.r | 17 RMark-2.1.12/RMark/R/covariate.predictions.r | 37 + RMark-2.1.12/RMark/R/create.mark.mcmc.R | 6 RMark-2.1.12/RMark/R/create.model.list.R | 1 RMark-2.1.12/RMark/R/deltamethod.r | 1 RMark-2.1.12/RMark/R/export.MARK.r | 62 --- RMark-2.1.12/RMark/R/export.model.r | 2 RMark-2.1.12/RMark/R/extract.mark.output.R | 55 ++ RMark-2.1.12/RMark/R/fill.covariates.R | 4 RMark-2.1.12/RMark/R/get.real.R | 2 RMark-2.1.12/RMark/R/import.chdata.R | 3 RMark-2.1.12/RMark/R/make.design.data.R | 36 + RMark-2.1.12/RMark/R/make.mark.model.R | 35 + RMark-2.1.12/RMark/R/mark.R | 17 RMark-2.1.12/RMark/R/mark.wrapper.R | 7 RMark-2.1.12/RMark/R/mark.wrapper.parallel.r | 10 RMark-2.1.12/RMark/R/merge.design.covariates.r | 1 RMark-2.1.12/RMark/R/merge.mark.r | 4 RMark-2.1.12/RMark/R/model.average.list.r | 3 RMark-2.1.12/RMark/R/model.average.marklist.R | 3 RMark-2.1.12/RMark/R/model.table.R | 3 RMark-2.1.12/RMark/R/popan.r | 87 +++- RMark-2.1.12/RMark/R/print.mark.R | 48 +- RMark-2.1.12/RMark/R/print.summary.mark.R | 23 - RMark-2.1.12/RMark/R/process.data.R | 5 RMark-2.1.12/RMark/R/read.mark.binary.R | 63 +-- RMark-2.1.12/RMark/R/read.mark.binary.linux.R | 73 +-- RMark-2.1.12/RMark/R/release.gof.R | 6 RMark-2.1.12/RMark/R/rerun.mark.R | 1 RMark-2.1.12/RMark/R/run.mark.model.R | 22 - RMark-2.1.12/RMark/R/setup.model.R | 9 RMark-2.1.12/RMark/R/splitCH.r | 1 RMark-2.1.12/RMark/R/summary.mark.R | 19 RMark-2.1.12/RMark/R/utility.r | 82 ++++ RMark-2.1.12/RMark/R/var.components.R | 1 RMark-2.1.12/RMark/R/var.components.reml.r | 1 RMark-2.1.12/RMark/inst/DerivedPar.txt |only RMark-2.1.12/RMark/inst/extdata/blackduck.txt |only RMark-2.1.12/RMark/inst/extdata/blckduck.inp |only RMark-2.1.12/RMark/inst/extdata/brownadt.inp |only RMark-2.1.12/RMark/inst/extdata/brownie.inp |only RMark-2.1.12/RMark/inst/extdata/donovan.7.inp |only RMark-2.1.12/RMark/inst/extdata/donovan.8.inp |only RMark-2.1.12/RMark/inst/extdata/edwardsandeberhardt.inp |only RMark-2.1.12/RMark/inst/extdata/f_age.inp |only RMark-2.1.12/RMark/inst/extdata/ld1.inp |only RMark-2.1.12/RMark/inst/extdata/linear.inp |only RMark-2.1.12/RMark/inst/extdata/m_age.inp |only RMark-2.1.12/RMark/inst/extdata/mallardnestexample.inp |only RMark-2.1.12/RMark/inst/extdata/ms_rdsimple1.inp |only RMark-2.1.12/RMark/inst/extdata/mssurv.inp |only RMark-2.1.12/RMark/inst/extdata/nicholsmsoccupancy.inp |only RMark-2.1.12/RMark/inst/extdata/pass3mstrata5.inp |only RMark-2.1.12/RMark/inst/extdata/rdsalamander.inp |only RMark-2.1.12/RMark/inst/extdata/robust.inp |only RMark-2.1.12/RMark/inst/models.txt | 196 +++++----- RMark-2.1.12/RMark/man/ABeginnersGuide.Rd | 3 RMark-2.1.12/RMark/man/Blackduck.Rd | 5 RMark-2.1.12/RMark/man/Donovan.7.Rd | 9 RMark-2.1.12/RMark/man/Donovan.8.Rd | 6 RMark-2.1.12/RMark/man/IELogitNormalMR.Rd | 10 RMark-2.1.12/RMark/man/LogitNormalMR.Rd | 5 RMark-2.1.12/RMark/man/MS_popan.Rd |only RMark-2.1.12/RMark/man/NicholsMSOccupancy.Rd | 4 RMark-2.1.12/RMark/man/PIMS.Rd | 4 RMark-2.1.12/RMark/man/PoissonMR.Rd | 4 RMark-2.1.12/RMark/man/Poisson_twoMR.Rd | 4 RMark-2.1.12/RMark/man/RDOccupancy.Rd | 6 RMark-2.1.12/RMark/man/RDSalamander.Rd | 4 RMark-2.1.12/RMark/man/TransitionMatrix.Rd | 10 RMark-2.1.12/RMark/man/Whatsnew.Rd | 3 RMark-2.1.12/RMark/man/add.design.data.Rd | 4 RMark-2.1.12/RMark/man/adjust.parameter.count.Rd | 4 RMark-2.1.12/RMark/man/adjust.value.Rd | 14 RMark-2.1.12/RMark/man/brownie.Rd | 4 RMark-2.1.12/RMark/man/cleanup.Rd | 3 RMark-2.1.12/RMark/man/coef.mark.Rd |only RMark-2.1.12/RMark/man/collect.model.names.Rd | 3 RMark-2.1.12/RMark/man/collect.models.Rd | 3 RMark-2.1.12/RMark/man/compute.design.data.Rd | 3 RMark-2.1.12/RMark/man/compute.link.Rd | 3 RMark-2.1.12/RMark/man/compute.links.from.reals.Rd | 3 RMark-2.1.12/RMark/man/compute.real.Rd | 3 RMark-2.1.12/RMark/man/convert.inp.Rd | 8 RMark-2.1.12/RMark/man/convert.link.to.real.Rd | 3 RMark-2.1.12/RMark/man/covariate.predictions.Rd | 4 RMark-2.1.12/RMark/man/crdms.Rd | 19 RMark-2.1.12/RMark/man/create.mark.mcmc.Rd | 3 RMark-2.1.12/RMark/man/create.model.list.Rd | 4 RMark-2.1.12/RMark/man/deer.Rd | 4 RMark-2.1.12/RMark/man/deltamethod.special.Rd | 4 RMark-2.1.12/RMark/man/deriv_inverse.link.Rd | 3 RMark-2.1.12/RMark/man/dipper.Rd | 4 RMark-2.1.12/RMark/man/edwards.eberhardt.Rd | 4 RMark-2.1.12/RMark/man/example.data.Rd | 4 RMark-2.1.12/RMark/man/export.MARK.Rd | 65 --- RMark-2.1.12/RMark/man/export.chdata.Rd | 3 RMark-2.1.12/RMark/man/export.model.Rd | 5 RMark-2.1.12/RMark/man/extract.indices.Rd | 4 RMark-2.1.12/RMark/man/extract.mark.output.Rd | 3 RMark-2.1.12/RMark/man/fill.covariates.Rd | 5 RMark-2.1.12/RMark/man/find.covariates.Rd | 3 RMark-2.1.12/RMark/man/get.link.Rd | 3 RMark-2.1.12/RMark/man/get.real.Rd | 5 RMark-2.1.12/RMark/man/import.chdata.Rd | 6 RMark-2.1.12/RMark/man/inverse.link.Rd | 3 RMark-2.1.12/RMark/man/killdeer.Rd | 4 RMark-2.1.12/RMark/man/larksparrow.Rd | 4 RMark-2.1.12/RMark/man/load.model.Rd | 3 RMark-2.1.12/RMark/man/make.design.data.Rd | 36 + RMark-2.1.12/RMark/man/make.mark.model.Rd | 8 RMark-2.1.12/RMark/man/make.time.factor.Rd | 3 RMark-2.1.12/RMark/man/mallard.Rd | 6 RMark-2.1.12/RMark/man/mark.Rd | 9 RMark-2.1.12/RMark/man/mark.wrapper.Rd | 3 RMark-2.1.12/RMark/man/mark.wrapper.parallel.Rd | 6 RMark-2.1.12/RMark/man/mata.wald.Rd | 3 RMark-2.1.12/RMark/man/merge.mark.Rd | 6 RMark-2.1.12/RMark/man/merge_design.covariates.Rd | 4 RMark-2.1.12/RMark/man/model.average.Rd | 3 RMark-2.1.12/RMark/man/model.average.list.Rd | 4 RMark-2.1.12/RMark/man/model.average.marklist.Rd | 4 RMark-2.1.12/RMark/man/model.table.Rd | 4 RMark-2.1.12/RMark/man/mstrata.Rd | 10 RMark-2.1.12/RMark/man/popan.derived.Rd | 4 RMark-2.1.12/RMark/man/print.mark.Rd | 14 RMark-2.1.12/RMark/man/print.marklist.Rd |only RMark-2.1.12/RMark/man/print.summary.mark.Rd |only RMark-2.1.12/RMark/man/process.data.Rd | 3 RMark-2.1.12/RMark/man/read.mark.binary.Rd | 7 RMark-2.1.12/RMark/man/release.gof.Rd | 4 RMark-2.1.12/RMark/man/remove.mark.Rd | 3 RMark-2.1.12/RMark/man/rerun.mark.Rd | 4 RMark-2.1.12/RMark/man/robust.Rd | 4 RMark-2.1.12/RMark/man/run.mark.model.Rd | 4 RMark-2.1.12/RMark/man/run.models.Rd | 3 RMark-2.1.12/RMark/man/salamander.Rd | 4 RMark-2.1.12/RMark/man/setup.model.Rd | 3 RMark-2.1.12/RMark/man/setup.parameters.Rd | 3 RMark-2.1.12/RMark/man/splitCH.Rd | 4 RMark-2.1.12/RMark/man/store.Rd | 3 RMark-2.1.12/RMark/man/strip.comments.Rd | 3 RMark-2.1.12/RMark/man/summary.mark.Rd | 9 RMark-2.1.12/RMark/man/summary_ch.Rd | 3 RMark-2.1.12/RMark/man/valid.parameters.Rd | 3 RMark-2.1.12/RMark/man/var.components.Rd | 4 RMark-2.1.12/RMark/man/var.components.reml.Rd | 4 RMark-2.1.12/RMark/man/weta.Rd | 4 RMark-2.1.12/RMark/man/wwdo.popan.Rd | 4 RMark-2.1.9/RMark/inst/extdata/BLCKDUCK.INP |only RMark-2.1.9/RMark/inst/extdata/BROWNADT.INP |only RMark-2.1.9/RMark/inst/extdata/Blackduck.txt |only RMark-2.1.9/RMark/inst/extdata/Brownie.inp |only RMark-2.1.9/RMark/inst/extdata/Donovan.7.inp |only RMark-2.1.9/RMark/inst/extdata/Donovan.8.inp |only RMark-2.1.9/RMark/inst/extdata/EDWARDSANDEBERHARDT.INP |only RMark-2.1.9/RMark/inst/extdata/F_AGE.INP |only RMark-2.1.9/RMark/inst/extdata/LD1.inp |only RMark-2.1.9/RMark/inst/extdata/LINEAR.INP |only RMark-2.1.9/RMark/inst/extdata/MSSURV.INP |only RMark-2.1.9/RMark/inst/extdata/MS_rdsimple1.inp |only RMark-2.1.9/RMark/inst/extdata/M_AGE.INP |only RMark-2.1.9/RMark/inst/extdata/MallardNestExample.inp |only RMark-2.1.9/RMark/inst/extdata/NicholsMSOccupancy.inp |only RMark-2.1.9/RMark/inst/extdata/Pass3MStrata5.inp |only RMark-2.1.9/RMark/inst/extdata/RDSalamander.inp |only RMark-2.1.9/RMark/inst/extdata/ROBUST.INP |only 177 files changed, 1186 insertions(+), 743 deletions(-)
Title: Bindings for the Geospatial Data Abstraction Library
Description: Provides bindings to Frank Warmerdam's Geospatial Data Abstraction Library (GDAL) (>= 1.6.3, < 2) and access to projection/transformation operations from the PROJ.4 library. The GDAL and PROJ.4 libraries are external to the package, and, when installing the package from source, must be correctly installed first. Both GDAL raster and OGR vector map data can be imported into R, and GDAL raster data and OGR vector data exported. Use is made of classes defined in the sp package. Windows and Mac Intel OS X binaries (including GDAL, PROJ.4 and Expat) are provided on CRAN.
Author: Roger Bivand [cre, aut],
Tim Keitt [aut],
Barry Rowlingson [aut],
Edzer Pebesma [ctb],
Michael Sumner [ctb],
Robert Hijmans [ctb],
Even Rouault [ctb]
Maintainer: Roger Bivand
Diff between rgdal versions 0.9-1 dated 2014-09-18 and 0.9-2 dated 2015-03-15
ChangeLog | 44 +++++++++++++++++ DESCRIPTION | 8 +-- MD5 | 42 +++++++++------- NAMESPACE | 1 R/ogr.R | 101 ++++++++++++++++++++++++++-------------- R/ogr_sp.R | 78 ++++++++++++++++++++++-------- build/vignette.rds |binary configure | 95 +++++++++++++++++++++++++++++++++---- configure.ac | 28 ++++++++++- inst/ChangeLog | 44 +++++++++++++++++ inst/README | 16 ++++++ inst/SVN_VERSION | 2 inst/doc/OGR_shape_encoding.pdf |binary inst/vectors/PacoursIKA2.DAT |only inst/vectors/PacoursIKA2.ID |only inst/vectors/PacoursIKA2.MAP |only inst/vectors/PacoursIKA2.TAB |only inst/vectors/SOURCES | 2 man/make_EPSG.Rd | 2 man/project.Rd | 5 + man/readOGR.Rd | 10 +++ man/spTransform-methods.Rd | 6 +- tests/test_proj.R | 5 + tests/test_proj.Rout.save | 12 ++-- 24 files changed, 393 insertions(+), 108 deletions(-)
Title: Bayesian Mixture Analysis for Metagenomic Community Profiling
Description: Resolves complex metagenomic mixtures by analysing
deep sequencing data, using a mixture model based approach.
The use of parallel Monte Carlo Markov chains for the exploration
of the species space enables the identification of the set
of species more likely to contribute to the mixture.
Author: Sofia Morfopoulou
Maintainer: Sofia Morfopoulou
Diff between metaMix versions 0.1 dated 2014-10-15 and 0.2 dated 2015-03-15
DESCRIPTION | 10 +++---- MD5 | 30 ++++++++++++----------- R/Gibbs.R | 6 ++-- R/logmean.R |only R/step1_preprocess.R | 12 ++++----- R/step2_allInclusive_MM.R | 13 ++++++---- R/step3_parallelTemper.R | 8 +++--- R/step3_parallelTemper_nucl.R | 10 +++---- R/step4_bayesModelAver.R | 53 ++++++++++++++++++++++++++++++++++++------ data/step3.RData |binary inst/doc/guide.Rnw | 2 + inst/doc/guide.pdf |binary man/generative.prob.Rd | 4 +-- man/parallel.temper.nucl.Rd | 6 ++-- man/reduce.space.Rd | 6 +++- vignettes/guide.Rnw | 2 + vignettes/guide.Rnw.bck |only 17 files changed, 106 insertions(+), 56 deletions(-)
Title: Modelling and Validation of Non Homogeneous Poisson Processes
Description: Tools for modelling, ML estimation, validation analysis and simulation of non homogeneous Poisson processes in time.
Author: Ana C. Cebrian
Maintainer: Ana C. Cebrian
Diff between NHPoisson versions 3.0 dated 2014-05-26 and 3.1 dated 2015-03-15
DESCRIPTION | 10 ++-- MD5 | 71 +++++++++++++++++----------------- R/GenEnv.fun.r | 11 ++--- R/emplambda.fun.r | 1 R/emplambdaD.fun.r | 1 R/fitPP.fun.r | 4 - R/funSim.fun.r | 4 - R/globalval.fun.r | 25 +++++++----- R/graphResCov.fun.r | 35 +++-------------- R/graphrate.fun.r | 8 ++- R/graphres.fun.r | 98 ++++-------------------------------------------- R/graphresU.fun.r | 90 ++++++++------------------------------------ R/resQQplot.fun.r | 100 ++++++++++++++++++++++++++----------------------- R/resSim.fun.r | 4 - R/simNHP.fun.r | 34 +++++++++------- inst |only man/BarTxTn.Rd | 8 +++ man/CIdelta.fun.Rd | 5 ++ man/CItran.fun.Rd | 5 ++ man/CalcRes.fun.Rd | 5 ++ man/CalcResD.fun.Rd | 5 ++ man/GenEnv.fun.Rd | 26 ++++++++---- man/VARbeta.fun.Rd | 4 + man/confintAsin.fun.Rd | 5 ++ man/dropAIC.fun.Rd | 5 ++ man/fitPP.fun.Rd | 5 ++ man/globalval.fun.Rd | 71 +++++++++++++++++++++++----------- man/graphResCov.fun.Rd | 29 ++++++++++---- man/graphResX.fun.Rd | 5 ++ man/graphrate.fun.Rd | 6 ++ man/graphres.fun.Rd | 44 ++++++++++++++------- man/graphresU.fun.Rd | 27 +++++++++++-- man/resQQplot.fun.Rd | 30 +++++++++++--- man/simNHP.fun.Rd | 31 ++++++++++----- man/stepAICmle.fun.Rd | 4 + man/transfH.fun.Rd | 8 +++ man/unifres.fun.Rd | 3 + 37 files changed, 440 insertions(+), 387 deletions(-)
Title: Traveling Salesperson Problem (TSP)
Description: Basic infrastructure and some algorithms for the traveling
salesperson problem (also traveling salesman problem; TSP).
The package provides some simple algorithms and
an interface to the Concorde TSP solver and its implementation of the
Chained-Lin-Kernighan heuristic. Concorde
itself is not included in the package and has to be obtained separately
from http://www.math.uwaterloo.ca/tsp/concorde.html.
Author: Michael Hahsler [aut, cre, cph],
Kurt Hornik [aut, cph]
Maintainer: Michael Hahsler
Diff between TSP versions 1.0-10 dated 2015-02-03 and 1.1-0 dated 2015-03-15
DESCRIPTION | 20 +- MD5 | 72 ++++---- NAMESPACE | 30 +++ R/ATSP.R | 36 ++-- R/ETSP.R |only R/TOUR.R | 62 +++---- R/TSP.R | 44 ++--- R/insert_dummy.R | 15 - R/read_TSPLIB.R | 181 +++++++++++---------- R/solve_TSP.R | 147 ++++++++++------- R/tour_length.R | 52 ++++-- R/tsp_concorde.R | 343 +++++++++++++++++++---------------------- R/tsp_insertion.R | 202 +++++++++++++----------- R/tsp_nn.R | 36 ++-- R/tsp_two_opt.R | 2 R/write_TSPLIB.R | 171 +++++++++++--------- build/vignette.rds |binary data/USCA312.rda |binary data/USCA312_map.rda |binary data/USCA50.rda |binary inst/NEWS | 15 + inst/doc/TSP.R | 6 inst/doc/TSP.Rnw | 8 inst/doc/TSP.pdf |binary inst/examples |only inst/tests |only man/ATSP.Rd | 10 - man/ETSP.Rd |only man/TOUR.Rd | 3 man/TSP.Rd | 2 man/TSPLIB.Rd | 52 +++++- man/USCA312.Rd | 4 man/insert_dummy.Rd | 3 man/reformulate_ATSP_as_TSP.Rd | 10 - man/solve_TSP.Rd | 107 +++++++++--- man/tour_length.Rd | 32 ++- src/two_opt.c | 9 - tests |only vignettes/TSP.Rnw | 8 39 files changed, 967 insertions(+), 715 deletions(-)
Title: A Boosted Tweedie Compound Poisson Model
Description: A boosted Tweedie compound Poisson model using the gradient boosting. It is capable of fitting a flexible nonlinear Tweedie compound Poisson model (or a gamma model) and capturing interactions among predictors.
Author: Yi Yang
Maintainer: Yi Yang
Diff between TDboost versions 1.0 dated 2014-10-22 and 1.1 dated 2015-03-15
DESCRIPTION | 12 +++--- MD5 | 20 +++++------ NAMESPACE | 6 ++- R/TDboost.R | 6 +-- man/FHT.Rd | 2 - man/TDboost.Rd | 17 ++++++++- man/TDboost.perf.Rd | 2 - man/plot.TDboost.Rd | 2 - man/relative.influence.Rd | 4 -- man/summary.TDboost.Rd | 7 +-- src/EDM.cpp | 82 +++++++++++++++++++++++++++++----------------- 11 files changed, 98 insertions(+), 62 deletions(-)
Title: Functions for Creating Summary Tables for Statistical Reports
Description: Contains functions for generating tables for statistical reports written in Microsoft Word or LaTeX. There are functions for I-by-J frequency tables, comparison of means or medians across levels of a categorical variable, and summarizing fitted generalized linear models, generalized estimating equations, and Cox proportional hazards regression. Functions are available to handle data simple random samples or survey data. The package is intended to make it easier for researchers to translate results from statistical analyses in R to their reports or manuscripts.
Author: Dane R. Van Domelen
Maintainer: Dane R. Van Domelen
Diff between tab versions 2.1.3 dated 2014-09-16 and 3.1.1 dated 2015-03-15
DESCRIPTION | 12 - MD5 | 52 +++---- R/tabcox.R | 132 ++++++++++++++---- R/tabfreq.R | 359 ++++++++++++++++++++++++++++++++++++++++++++------ R/tabfreq_svy.R | 73 +++++++--- R/tabgee.R | 67 ++++++++- R/tabglm.R | 70 ++++++++- R/tabglm_svy.R | 70 ++++++++- R/tabmeans.R | 352 ++++++++++++++++++++++++++++++++++++++++--------- R/tabmeans_svy.R | 38 ++++- R/tabmedians.R | 212 +++++++++++++++++++++-------- R/tabmedians_svy.R |only R/tabmulti.R | 153 ++++++++++++++++----- R/tabmulti_svy.R |only data/d.rda |binary man/d.Rd | 12 - man/tab-package.Rd | 37 ++--- man/tabcox.Rd | 64 ++++++-- man/tabfreq.Rd | 114 ++++++++++----- man/tabfreq_svy.Rd | 45 ++++-- man/tabgee.Rd | 34 +++- man/tabglm.Rd | 36 ++++- man/tabglm_svy.Rd | 26 +++ man/tabmeans.Rd | 118 +++++++++++----- man/tabmeans_svy.Rd | 36 +++-- man/tabmedians.Rd | 97 ++++++++----- man/tabmedians_svy.Rd |only man/tabmulti.Rd | 138 ++++++++++++------- man/tabmulti_svy.Rd |only 29 files changed, 1816 insertions(+), 531 deletions(-)
Title: Species Distribution Modeling
Description: Functions for species distribution modeling, that is, predicting entire geographic distributions form occurrences at a number of sites.
Author: Robert J. Hijmans, Steven Phillips, John Leathwick and Jane Elith
Maintainer: Robert J. Hijmans
Diff between dismo versions 1.0-5 dated 2014-09-10 and 1.0-12 dated 2015-03-15
dismo-1.0-12/dismo/ChangeLog | 3 dismo-1.0-12/dismo/DESCRIPTION | 14 - dismo-1.0-12/dismo/MD5 | 71 +++--- dismo-1.0-12/dismo/R/biogeomancer.R | 2 dismo-1.0-12/dismo/R/biovars.R | 2 dismo-1.0-12/dismo/R/check.R | 10 dismo-1.0-12/dismo/R/circles.R | 20 + dismo-1.0-12/dismo/R/circularArea.R | 2 dismo-1.0-12/dismo/R/domain.predict.R | 7 dismo-1.0-12/dismo/R/evaluate.R | 2 dismo-1.0-12/dismo/R/gbif.R | 331 ++++++++++---------------------- dismo-1.0-12/dismo/R/gbif_old.R |only dismo-1.0-12/dismo/R/gbm.fixed.R | 7 dismo-1.0-12/dismo/R/gbm.holdout.R | 8 dismo-1.0-12/dismo/R/gbm.interactions.R | 5 dismo-1.0-12/dismo/R/gbm.perspec.R | 5 dismo-1.0-12/dismo/R/gbm.plot.R | 6 dismo-1.0-12/dismo/R/gbm.simplify.R | 6 dismo-1.0-12/dismo/R/gbm.step.R | 13 - dismo-1.0-12/dismo/R/geoIDW.R | 2 dismo-1.0-12/dismo/R/geocode.R | 3 dismo-1.0-12/dismo/R/gmap.R | 8 dismo-1.0-12/dismo/R/gorilla.R | 2 dismo-1.0-12/dismo/R/maxent.R | 2 dismo-1.0-12/dismo/R/mess.R | 10 dismo-1.0-12/dismo/R/voronoi.R | 2 dismo-1.0-12/dismo/R/voronoiHull.R | 4 dismo-1.0-12/dismo/build/vignette.rds |binary dismo-1.0-12/dismo/inst/doc/brt.R | 1 dismo-1.0-12/dismo/inst/doc/brt.Rnw | 1 dismo-1.0-12/dismo/inst/doc/brt.pdf |binary dismo-1.0-12/dismo/inst/doc/sdm.pdf |binary dismo-1.0-12/dismo/man/gbif.Rd | 52 +---- dismo-1.0-12/dismo/man/gmap.Rd | 3 dismo-1.0-12/dismo/man/randomPoints.Rd | 2 dismo-1.0-12/dismo/vignettes/brt.Rnw | 1 dismo-1.0-5/dismo/R/rowMinMax.R |only dismo-1.0-5/dismo/man/lookUp.Rd |only 38 files changed, 243 insertions(+), 364 deletions(-)