More information about TrackReconstruction at CRAN
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Title: Programmatic interface to the API serving UC Berkeley's Natural
History Data
Diff between ecoengine versions 1.2 dated 2014-03-04 and 1.2.2 dated 2014-03-14
Description: The ecoengine (http://ecoengine.berkeley.edu/) provides access to
more than 2 million georeferenced specimen records from the Berkeley
Natural History Museums. http://bnhm.berkeley.edu/
Author: Karthik Ram [aut, cre]
Maintainer: Karthik Ram
DESCRIPTION | 6 +++---
MD5 | 14 +++++++-------
NEWS | 4 ++++
R/ee_observations.R | 6 ++++--
R/ee_utils.R | 2 +-
README.md | 1 +
man/ee_cbind.Rd | 3 ++-
man/ee_observations.Rd | 5 ++++-
8 files changed, 26 insertions(+), 15 deletions(-)
Title: dplyr: a grammar of data manipulation
Diff between dplyr versions 0.1.2 dated 2014-02-24 and 0.1.3 dated 2014-03-14
Description: A fast, consistent tool for working with data frame like objects,
both in memory and out of memory.
Author: Hadley Wickham
Maintainer: Hadley Wickham
DESCRIPTION | 8 ++--
MD5 | 56 ++++++++++++++++-----------------
NAMESPACE | 1
R/dbi-s3.r | 7 +++-
R/join-sql.r | 23 +++++++------
R/manip-dt.r | 5 ++
R/manip-grouped-dt.r | 1
R/utils-format.r | 16 +++++----
inst/doc/databases.R | 10 ++---
inst/doc/databases.Rmd | 32 +++++++++---------
inst/doc/databases.html | 49 ++++++++++++++--------------
inst/doc/introduction.Rmd | 6 +--
inst/doc/introduction.html | 22 ++++++------
inst/doc/window-functions.R | 4 +-
inst/doc/window-functions.Rmd | 4 +-
inst/doc/window-functions.html | 16 ++++-----
inst/include/dplyr/Collecter.h | 10 ++++-
inst/include/dplyr/GroupedDataFrame.h | 2 -
inst/include/dplyr/JoinVisitorImpl.h | 6 ++-
inst/include/dplyr/VectorVisitorImpl.h | 23 +++++++++++--
inst/tests/test-arrange.r | 7 ++++
inst/tests/test-joins.r | 8 ++++
inst/tests/test-rbind.r | 10 +++++
inst/tests/test-select.r | 23 +++++++++++++
man/join.tbl_sql.Rd | 2 -
src/dplyr.cpp | 9 ++---
vignettes/databases.Rmd | 32 +++++++++---------
vignettes/introduction.Rmd | 6 +--
vignettes/window-functions.Rmd | 4 +-
29 files changed, 245 insertions(+), 157 deletions(-)
Title: The Clustering of Regression Models Method
Diff between CORM versions 1.0.0 dated 2013-12-09 and 1.0.1 dated 2014-03-14
Description: We proposed a new model-based clustering method, called the clustering of
regression models method(CORM), which groups genes that share a similar
relationship to the covariate(s). This method provides a unified approach
for a family of clustering procedures and can be applied to data collected
with various experimental designs. This package includes the implementation
for two such clustering procedures: (1) the Clustering of Linear Models
(CLM) method, and (2) the Clustering of Linear Mixed Models (CLMM) method.
Author: Li-Xuan Qin [aut],
Jiejun Shi [cre]
Maintainer: Jiejun Shi
DESCRIPTION | 18 +
MD5 | 24 +-
NAMESPACE | 20 -
R/function_fit_clmm_simple_v4_sigmaK_NA.R |only
R/function_fit_clmm_simple_v4_sigmaK_twoData.R |only
R/function_fit_clmm_simple_v4_sigmaK_twoData_NA.R |only
data/YeastCellCycle2.RData |only
data/miRTargetGenes.RData |only
man/BreastCancer.Rd | 58 ++---
man/CORM-package.Rd | 101 ++++-----
man/YeastCellCycle.Rd | 66 +++---
man/YeastCellCycle2.Rd |only
man/fit.CLM.Rd | 233 ++++++++++++---------
man/fit.CLMM.2.Rd |only
man/fit.CLMM.NA.2.Rd |only
man/fit.CLMM.NA.Rd |only
man/fit.CLMM.Rd | 239 +++++++++++-----------
man/miRTargetGenes.Rd |only
18 files changed, 410 insertions(+), 349 deletions(-)
Title: General purpose R interface to Solr
Diff between solr versions 0.1.0 dated 2013-12-31 and 0.1.4 dated 2014-03-14
Description: This package provides a set of functions for querying and parsing
data from Solr endpoints (local and remote), including search, faceting,
highlighting, stats, and 'more like this'.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain
DESCRIPTION | 11 -
LICENSE | 2
MD5 | 76 ++++----
NAMESPACE | 7
NEWS | 20 ++
R/parsers.r | 179 ++++++++++++++++----
R/solr_all.r |only
R/solr_facet.r | 73 +++-----
R/solr_group.r |only
R/solr_highlight.r | 31 ++-
R/solr_mlt.r | 37 ++--
R/solr_search.r | 62 ++++---
R/solr_stats.r | 50 ++---
R/zzz.r |only
README.md | 92 +++++++++-
build/vignette.rds |binary
inst/doc/solr_localsetup.Rmd | 23 ++
inst/doc/solr_localsetup.pdf |binary
inst/doc/solr_vignette.Rmd | 271 ++++++++++++++++++-------------
inst/doc/solr_vignette.pdf |binary
man/collectargs.Rd |only
man/is-sr.Rd | 1
man/makemultiargs.Rd |only
man/solr-package.Rd | 22 +-
man/solr_all.Rd |only
man/solr_facet.Rd | 286 ++++++++++++++++-----------------
man/solr_group.Rd |only
man/solr_highlight.Rd | 29 +--
man/solr_mlt.Rd | 30 ++-
man/solr_parse.Rd | 15 +
man/solr_search.Rd | 57 +++---
man/solr_stats.Rd | 34 ++-
tests/testthat/test-solr_facet.r | 5
tests/testthat/test-solr_group.r |only
tests/testthat/test-solr_highlight.r | 5
tests/testthat/test-solr_mlt.r | 21 +-
tests/testthat/test-solr_search.r | 5
tests/testthat/test-solr_stats.r | 9 -
vignettes/solr_localsetup.Rmd | 23 ++
vignettes/solr_localsetup.html | 48 ++++-
vignettes/solr_localsetup.md |only
vignettes/solr_vignette.Rmd | 271 ++++++++++++++++++-------------
vignettes/solr_vignette.html | 303 +++++++++++++++++++----------------
vignettes/solr_vignette.md |only
44 files changed, 1253 insertions(+), 845 deletions(-)
Title: Diverse basic statistical and graphical functions
Diff between RVAideMemoire versions 0.9-32 dated 2014-03-04 and 0.9-35 dated 2014-03-14
Description: This package contains diverse more or less complicated functions, written to simplify user's life: simplifications of existing functions, basic but not implemented tests, easy-to-use tools, bridges between functions of different packages... All functions are presented in the French book 'Aide-memoire de statistique appliquee a la biologie', written by the same author and available on CRAN.
Author: Maxime Hervé
Maintainer: Maxime Hervé
RVAideMemoire-0.9-32/RVAideMemoire/man/predict.least.rect.Rd |only
RVAideMemoire-0.9-32/RVAideMemoire/man/print.RV.multcomp.Rd |only
RVAideMemoire-0.9-32/RVAideMemoire/man/print.RVtest.Rd |only
RVAideMemoire-0.9-32/RVAideMemoire/man/print.byf.test.Rd |only
RVAideMemoire-0.9-32/RVAideMemoire/man/summary.least.rect.Rd |only
RVAideMemoire-0.9-35/RVAideMemoire/DESCRIPTION | 14 -
RVAideMemoire-0.9-35/RVAideMemoire/MD5 | 79 +++++---
RVAideMemoire-0.9-35/RVAideMemoire/NAMESPACE | 88 ++++++++--
RVAideMemoire-0.9-35/RVAideMemoire/R/Anova.clm.R |only
RVAideMemoire-0.9-35/RVAideMemoire/R/Anova.clmm.R |only
RVAideMemoire-0.9-35/RVAideMemoire/R/DA.confusion.R | 8
RVAideMemoire-0.9-35/RVAideMemoire/R/DA.valid.R | 8
RVAideMemoire-0.9-35/RVAideMemoire/R/DA.var.R | 2
RVAideMemoire-0.9-35/RVAideMemoire/R/PLSDA.VIP.R | 2
RVAideMemoire-0.9-35/RVAideMemoire/R/PLSDA.ncomp.R | 6
RVAideMemoire-0.9-35/RVAideMemoire/R/PLSDA.test.R | 8
RVAideMemoire-0.9-35/RVAideMemoire/R/bootstrap.R | 2
RVAideMemoire-0.9-35/RVAideMemoire/R/cramer.test.R | 2
RVAideMemoire-0.9-35/RVAideMemoire/R/fc.multcomp.R | 7
RVAideMemoire-0.9-35/RVAideMemoire/R/friedman.rating.test.R |only
RVAideMemoire-0.9-35/RVAideMemoire/R/kruskal.rating.test.R |only
RVAideMemoire-0.9-35/RVAideMemoire/R/lsm.basis.clm.R |only
RVAideMemoire-0.9-35/RVAideMemoire/R/lsm.basis.clmm.R |only
RVAideMemoire-0.9-35/RVAideMemoire/R/median.factor.R |only
RVAideMemoire-0.9-35/RVAideMemoire/R/mod.R | 30 ++-
RVAideMemoire-0.9-35/RVAideMemoire/R/overdisp.glmer.R | 4
RVAideMemoire-0.9-35/RVAideMemoire/R/pairwise.wilcox.rating.test.R |only
RVAideMemoire-0.9-35/RVAideMemoire/R/plotresid.R | 13 -
RVAideMemoire-0.9-35/RVAideMemoire/R/rating.lsmeans.R |only
RVAideMemoire-0.9-35/RVAideMemoire/R/rating.prob.R |only
RVAideMemoire-0.9-35/RVAideMemoire/R/scat.mix.categorical.R | 2
RVAideMemoire-0.9-35/RVAideMemoire/R/scat.mix.numeric.R | 2
RVAideMemoire-0.9-35/RVAideMemoire/R/spearman.ci.R | 2
RVAideMemoire-0.9-35/RVAideMemoire/R/wilcox.paired.rating.multcomp.R |only
RVAideMemoire-0.9-35/RVAideMemoire/R/wilcox.rating.signtest.R |only
RVAideMemoire-0.9-35/RVAideMemoire/R/wilcox.rating.test.R |only
RVAideMemoire-0.9-35/RVAideMemoire/R/zzz.R | 2
RVAideMemoire-0.9-35/RVAideMemoire/man/Anova.clm.Rd |only
RVAideMemoire-0.9-35/RVAideMemoire/man/DA.confusion.Rd | 1
RVAideMemoire-0.9-35/RVAideMemoire/man/DA.valid.Rd | 1
RVAideMemoire-0.9-35/RVAideMemoire/man/PLSDA.VIP.Rd | 1
RVAideMemoire-0.9-35/RVAideMemoire/man/RVAideMemoire-package.Rd | 4
RVAideMemoire-0.9-35/RVAideMemoire/man/chisq.exp.Rd | 1
RVAideMemoire-0.9-35/RVAideMemoire/man/friedman.rating.test.Rd |only
RVAideMemoire-0.9-35/RVAideMemoire/man/kruskal.rating.test.Rd |only
RVAideMemoire-0.9-35/RVAideMemoire/man/least.rect.Rd | 4
RVAideMemoire-0.9-35/RVAideMemoire/man/mod.Rd | 6
RVAideMemoire-0.9-35/RVAideMemoire/man/pairwise.G.test.Rd | 2
RVAideMemoire-0.9-35/RVAideMemoire/man/pairwise.wilcox.rating.test.Rd |only
RVAideMemoire-0.9-35/RVAideMemoire/man/rating.lsmeans.Rd |only
RVAideMemoire-0.9-35/RVAideMemoire/man/rating.prob.Rd |only
RVAideMemoire-0.9-35/RVAideMemoire/man/wilcox.paired.rating.multcomp.Rd |only
RVAideMemoire-0.9-35/RVAideMemoire/man/wilcox.rating.signtest.Rd |only
RVAideMemoire-0.9-35/RVAideMemoire/man/wilcox.rating.test.Rd |only
54 files changed, 198 insertions(+), 103 deletions(-)
Title: paleofire: an R package to analyse sedimentary charcoal records
from the Global Charcoal Database to reconstruct past biomass
burning
Diff between paleofire versions 1.0 dated 2014-01-08 and 1.1 dated 2014-03-14
Description: The paleofire package provides tools to extract and analyse charcoal sedimentary data stored in the Global Charcoal Database. Main functionalities includes data extraction and sites selection, transformation and interpolation of the charcoal records as well as compositing.
Author: Global Paleofire Working Group
Maintainer: Olivier Blarquez
DESCRIPTION | 14 +-
MD5 | 84 +++++++-----
NAMESPACE | 6
NEWS |only
R/pfAddData.R | 81 ++++++-----
R/pfBoxCox.R | 96 ++++++-------
R/pfCircular.R | 3
R/pfComposite.R | 14 +-
R/pfCompositeLF.R | 114 +++++++++-------
R/pfDiagnostic.R | 50 +++----
R/pfDotMap.R |only
R/pfExtract.R | 4
R/pfGridding.R |only
R/pfInteractive.R | 12 -
R/pfKruskal.R |only
R/pfResolution.R | 22 +--
R/pfSiteSel.R | 178 ++++++++++---------------
R/pfTransform.R | 222 ++++++++++++++++++++------------
R/pretreatment.R | 316 +++++++++++++++++++++++-----------------------
R/zzz.R | 7 -
README.md | 9 +
data/datalist |only
data/dem.rda |only
demo |only
man/1paleofiRe-package.Rd | 46 ++----
man/checkGCDversion.Rd | 4
man/paleofire-internal.Rd |only
man/pfAddData.Rd | 24 +--
man/pfBoxCox.Rd | 6
man/pfCircular.Rd | 6
man/pfComposite.Rd | 10 -
man/pfCompositeLF.Rd | 24 +--
man/pfDiagnostic.Rd | 8 -
man/pfDotMap.Rd |only
man/pfExtract.Rd | 12 -
man/pfGridding.Rd |only
man/pfKruskal.Rd |only
man/pfMinMax.Rd | 11 -
man/pfResolution.Rd | 6
man/pfSiteSel.Rd | 79 +++++------
man/pfTransform.Rd | 18 +-
man/plot.pfCircular.Rd | 8 -
man/plot.pfComposite.Rd | 18 +-
man/plot.pfCompositeLF.Rd | 30 +++-
man/plot.pfGridding.Rd |only
man/plot.pfKruskal.Rd |only
man/plot.pfSiteSel.Rd | 19 ++
man/pretreatment.Rd | 12 +
man/summary.pfSiteSel.Rd | 6
49 files changed, 843 insertions(+), 736 deletions(-)
Title: L-moments, Censored L-moments, Trimmed L-moments, L-comoments,
and Many Distributions
Diff between lmomco versions 1.8.1 dated 2014-01-27 and 2.0.1 dated 2014-03-14
Description: The package is a comparatively comprehensive implementation of the theory of L-moments. L-moment, probability-weighted moment (PWM), and parameter estimation for numerous familiar and not-so-familiar distributions are provided. L-moment estimate for the same distributions are provided. L-moments are analogous to product moments; however, L-moments have many advantages including unbiasedness, robustness, and consistency. L-moments can outperform maximum likelihood for small to moderate samples. The package originally was originally oriented around circa 1996-FORTRAN algorithms by Hosking, and the nomenclature parallels that of Hosking. The Hosking algorithms later became available in the lmom package. However, vast extensions, components, concepts, more distributions, L-moment curiosities, and research topics are added. Such extensions the Sen weighted mean, Gini mean difference, plotting positions, and conditional probability adjustments. L-moment ratio diagrams are supported. L-moment support for right-tail and left-tail censoring by known or unknown censoring threshold and also by indicator variable. Asymmetric trimmed L-moments are supported as are numerical integration to dynamically compute trajectories of select TL-moment ratios for the construction of TL-moment ratio diagrams. L-moments have multi-variate analogs; the sample L-comoments are implemented and might have considerable application with copulas because L-comoments measure asymmetric association and higher comoments or comovements of variables. Support exists for exact analytical boot-strap estimates of order statistics, L-moments, and variances-covariances of L-moments. The Harri-Coble Tau34-squared Test for Normality using sample L-skew and L-kurtosis is available. Support for the following distributions, with moment type shown as "L" (L-moments) or "TL" (trimmed L-moments) and additional support for right-tail censoring ([RC]) include, is available: Asymmetric Exponential Power (L), Cauchy (TL), Eta-Mu (L), Exponential (L), Gamma (L), Generalized Extreme Value (L), Generalized Lambda (L & TL), Generalized Logistic (L), Generalized Normal (L), Generalized Pareto (L[RC] & TL), Govindarajulu (L), Gumbel (L), Kappa (L), Kappa-Mu (L), Kumaraswamy (L), Laplace (L), Normal (L), 3-parameter log-Normal (L), Pearson Type III (L), Rayleigh (L), Reverse Gumbel (L[RC]), Rice/Rician (L), Slash (TL), 3-parameter Student T (L), Truncated Exponential (L), Wakeby (L), and Weibull (L).
Author: William Asquith
Maintainer: William Asquith
DESCRIPTION | 10 +--
MD5 | 122 +++++++++++++++++++++++++++++++----------------
NAMESPACE | 21 ++++++++
NEWS | 59 ++++++++++++++++++++++
R/are.par.valid.R | 23 ++++++--
R/are.pargov.valid.R |only
R/are.parsla.valid.R |only
R/are.parst3.valid.R |only
R/cdfgov.R |only
R/cdfsla.R |only
R/cdfst3.R |only
R/check.pdf.R | 4 +
R/dist.list.R | 4 -
R/is.gov.R |only
R/is.sla.R |only
R/is.st3.R |only
R/lmomgov.R |only
R/lmoms.bootbarvar.R | 33 ++++++++++++
R/lmomsla.R |only
R/lmomst3.R |only
R/lmrdia.R | 11 +++-
R/par2cdf.R | 9 +++
R/par2lmom.R | 3 +
R/par2pdf.R | 9 +++
R/par2qua.R | 9 +++
R/pargov.R |only
R/parsla.R |only
R/parst3.R |only
R/pdfgov.R |only
R/pdfsla.R |only
R/pdfst3.R |only
R/plotlmrdia.R | 11 ++++
R/prettydist.R | 3 +
R/quagov.R |only
R/quakap.R | 4 -
R/quasla.R |only
R/quast3.R |only
R/theoTLmoms.R | 5 -
R/vec2par.R | 12 ++++
R/x2xlo.R | 41 +++++++++++++--
README | 5 +
man/are.par.valid.Rd | 12 +---
man/are.paraep4.valid.Rd | 2
man/are.pargov.valid.Rd |only
man/are.parsla.valid.Rd |only
man/are.parst3.valid.Rd |only
man/cdfaep4.Rd | 2
man/cdfglo.Rd | 2
man/cdfgov.Rd |only
man/cdfsla.Rd |only
man/cdfst3.Rd |only
man/dist.list.Rd | 9 +--
man/is.gov.Rd |only
man/is.sla.Rd |only
man/is.st3.Rd |only
man/lmomaep4.Rd | 2
man/lmomgld.Rd | 10 +--
man/lmomglo.Rd | 2
man/lmomgov.Rd |only
man/lmoms.bootbarvar.Rd | 5 +
man/lmomsla.Rd |only
man/lmomst3.Rd |only
man/lmrdia.Rd | 6 ++
man/par2lmom.Rd | 2
man/paraep4.Rd | 2
man/parcau.Rd | 18 ------
man/parglo.Rd | 4 -
man/pargov.Rd |only
man/parsla.Rd |only
man/parst3.Rd |only
man/pdfglo.Rd | 2
man/pdfgov.Rd |only
man/pdfsla.Rd |only
man/pdfst3.Rd |only
man/plotlmrdia.Rd | 12 +++-
man/quaaep4.Rd | 2
man/quaaep4kapmix.Rd | 2
man/quaglo.Rd | 2
man/quagov.Rd |only
man/quasla.Rd |only
man/quast3.Rd |only
man/vec2par.Rd | 6 +-
man/x2xlo.Rd | 6 +-
83 files changed, 378 insertions(+), 130 deletions(-)
Title: R wrapper to Gaug.es API
Diff between rgauges versions 0.1.5 dated 2013-11-13 and 0.2.0 dated 2014-03-14
Description: This package provides functions to interact with the
Gaug.es API. Gaug.es is a web analytics service, like Google
analytics. You have to have a Gaug.es account to use this package.
Author: Scott Chamberlain [aut, cre],
Karthik Ram [aut]
Maintainer: Scott Chamberlain
rgauges-0.1.5/rgauges/R/clients.R |only
rgauges-0.1.5/rgauges/R/content.R |only
rgauges-0.1.5/rgauges/R/engines.R |only
rgauges-0.1.5/rgauges/R/locations.R |only
rgauges-0.1.5/rgauges/R/me.R |only
rgauges-0.1.5/rgauges/R/pageviews.R |only
rgauges-0.1.5/rgauges/R/referrers.R |only
rgauges-0.1.5/rgauges/R/resolution.R |only
rgauges-0.1.5/rgauges/R/sharing.R |only
rgauges-0.1.5/rgauges/R/technology.R |only
rgauges-0.1.5/rgauges/R/terms.R |only
rgauges-0.1.5/rgauges/R/traffic.R |only
rgauges-0.2.0/rgauges/DESCRIPTION | 20 +--
rgauges-0.2.0/rgauges/LICENSE |only
rgauges-0.2.0/rgauges/MD5 | 91 ++++++++------
rgauges-0.2.0/rgauges/NAMESPACE | 2
rgauges-0.2.0/rgauges/NEWS | 13 ++
rgauges-0.2.0/rgauges/R/gauges.R | 45 ++++--
rgauges-0.2.0/rgauges/R/gs_clients.R |only
rgauges-0.2.0/rgauges/R/gs_content.R |only
rgauges-0.2.0/rgauges/R/gs_engines.R |only
rgauges-0.2.0/rgauges/R/gs_locations.R |only
rgauges-0.2.0/rgauges/R/gs_me.R |only
rgauges-0.2.0/rgauges/R/gs_pageviews.R |only
rgauges-0.2.0/rgauges/R/gs_referrers.R |only
rgauges-0.2.0/rgauges/R/gs_reso.R |only
rgauges-0.2.0/rgauges/R/gs_shares.R |only
rgauges-0.2.0/rgauges/R/gs_tech.R |only
rgauges-0.2.0/rgauges/R/gs_terms.R |only
rgauges-0.2.0/rgauges/R/gs_traffic.R |only
rgauges-0.2.0/rgauges/R/vis_gauge.R | 1
rgauges-0.2.0/rgauges/README.md | 156 +++++++++++++++---------
rgauges-0.2.0/rgauges/build |only
rgauges-0.2.0/rgauges/inst |only
rgauges-0.2.0/rgauges/man/gs_clients.Rd | 20 ++-
rgauges-0.2.0/rgauges/man/gs_content.Rd | 24 ++-
rgauges-0.2.0/rgauges/man/gs_engines.Rd | 28 ++--
rgauges-0.2.0/rgauges/man/gs_gauge_create.Rd | 27 ++--
rgauges-0.2.0/rgauges/man/gs_gauge_delete.Rd | 17 +-
rgauges-0.2.0/rgauges/man/gs_gauge_detail.Rd | 23 ++-
rgauges-0.2.0/rgauges/man/gs_gauge_list.Rd | 21 ++-
rgauges-0.2.0/rgauges/man/gs_gauge_update.Rd | 27 ++--
rgauges-0.2.0/rgauges/man/gs_locations.Rd | 26 ++--
rgauges-0.2.0/rgauges/man/gs_me.Rd | 22 ++-
rgauges-0.2.0/rgauges/man/gs_me_update.Rd | 6
rgauges-0.2.0/rgauges/man/gs_pageviews.Rd | 15 +-
rgauges-0.2.0/rgauges/man/gs_ref.Rd | 24 ++-
rgauges-0.2.0/rgauges/man/gs_reso.Rd | 23 ++-
rgauges-0.2.0/rgauges/man/gs_shares.Rd | 22 ++-
rgauges-0.2.0/rgauges/man/gs_tech.Rd | 26 ++--
rgauges-0.2.0/rgauges/man/gs_terms.Rd | 24 ++-
rgauges-0.2.0/rgauges/man/gs_traffic.Rd | 21 ++-
rgauges-0.2.0/rgauges/man/is.gauge.Rd | 5
rgauges-0.2.0/rgauges/man/parse_gauge_detail.Rd | 5
rgauges-0.2.0/rgauges/man/vis_gauge.Rd | 16 +-
rgauges-0.2.0/rgauges/vignettes |only
56 files changed, 484 insertions(+), 266 deletions(-)
Title: Cubature over Polygonal Domains
Diff between polyCub versions 0.4-2 dated 2014-02-12 and 0.4-3 dated 2014-03-14
Description: A package providing methods for cubature (numerical integration)
over polygonal domains.
Currently, four cubature methods are implemented:
the two-dimensional midpoint rule as a simple wrapper around
as.im.function() from package spatstat (Baddeley and Turner, 2005),
the product Gauss cubature by Sommariva and Vianello (2007),
an adaptive cubature for isotropic functions via line integrate()
along the boundary (Meyer and Held, 2014),
and quasi-exact methods specific to the integration of the
bivariate Gaussian density over polygonal and circular domains
(based on formulae from the Abramowitz and Stegun (1972) handbook).
For cubature over simple hypercubes, the packages cubature and
R2Cuba are more appropriate.
Author: Sebastian Meyer [aut, cre, trl],
Michael Hoehle [ths]
Maintainer: Sebastian Meyer
DESCRIPTION | 24 ++++++++-------
MD5 | 43 ++++++++++++++-------------
NAMESPACE | 1
R/circleCub.R | 10 +++---
R/polyCub.SV.R | 12 +++----
R/polyCub.exact.Gauss.R | 13 ++++----
R/polyCub.iso.R | 60 ++++++++++++++++++++++++++++-----------
R/polyCub.midpoint.R | 14 +++++----
R/tools.R | 5 +--
R/xylist.R | 16 +++-------
R/zzz.R | 28 +++++++++---------
inst/CITATION |only
inst/NEWS.Rd | 21 +++++++++++++
man/checkintrfr.Rd |only
man/circleCub.Gauss.Rd | 7 +---
man/polyCub-package.Rd | 39 +++++++++++++------------
man/polyCub.SV.Rd | 7 ++--
man/polyCub.exact.Gauss.Rd | 19 +++++-------
man/polyCub.iso.Rd | 21 +++++++------
man/polyCub.midpoint.Rd | 12 +++----
man/polygauss.Rd | 7 ++--
man/xylist.Rd | 2 -
tests/testthat/test-polyCub.R | 2 -
tests/testthat/test-regression.R |only
24 files changed, 212 insertions(+), 151 deletions(-)
Title: GGIR
Diff between GGIR versions 1.0-1 dated 2014-01-29 and 1.0-2 dated 2014-03-14
Description: GGIR is a tool to process multi-day raw acceleration data
Author: Vincent T van Hees [aut, cre], Zhou Fang [ctb], Jing Hua Zhao [ctb]
Maintainer: Vincent T van Hees
DESCRIPTION | 8
MD5 | 10
R/g.analyse.R | 1607 ++++++++++++++++++++++++++--------------------------
inst/NEWS.Rd | 17
man/GGIR-package.Rd | 4
man/g.analyse.Rd | 141 ++--
6 files changed, 930 insertions(+), 857 deletions(-)
Title: adegenet: an R package for the exploratory analysis of genetic
and genomic data.
Diff between adegenet versions 1.3-9.2 dated 2013-08-09 and 1.4-0 dated 2014-03-14
Description: Classes and functions for genetic data analysis within the multivariate framework.
Author: Thibaut Jombart, Caitlin Collins, Peter Solymos, Ismail Ahmed, Federico Calboli, Anne Cori
Maintainer: Thibaut Jombart
adegenet-1.3-9.2/adegenet/README |only
adegenet-1.3-9.2/adegenet/inst/doc |only
adegenet-1.3-9.2/adegenet/vignettes |only
adegenet-1.4-0/adegenet/ChangeLog | 21 +
adegenet-1.4-0/adegenet/DESCRIPTION | 16 -
adegenet-1.4-0/adegenet/MD5 | 142 ++++------
adegenet-1.4-0/adegenet/NAMESPACE | 8
adegenet-1.4-0/adegenet/R/SNPbin.R | 2
adegenet-1.4-0/adegenet/R/auxil.R | 60 ++--
adegenet-1.4-0/adegenet/R/chooseCN.R | 1
adegenet-1.4-0/adegenet/R/dapc.R | 12
adegenet-1.4-0/adegenet/R/find.clust.R | 10
adegenet-1.4-0/adegenet/R/glFunctions.R | 6
adegenet-1.4-0/adegenet/R/glHandle.R | 2
adegenet-1.4-0/adegenet/R/glSim.R | 334 +++++++++++++++---------
adegenet-1.4-0/adegenet/R/import.R | 6
adegenet-1.4-0/adegenet/R/inbreeding.R | 7
adegenet-1.4-0/adegenet/R/servers.R |only
adegenet-1.4-0/adegenet/R/setAs.R | 2
adegenet-1.4-0/adegenet/R/snpposi.R |only
adegenet-1.4-0/adegenet/R/snpzip.R |only
adegenet-1.4-0/adegenet/R/spca.R | 7
adegenet-1.4-0/adegenet/R/spca.rtests.R | 20 -
adegenet-1.4-0/adegenet/R/xvalDapc.R | 305 +++++++++------------
adegenet-1.4-0/adegenet/data/H3N2.RData |binary
adegenet-1.4-0/adegenet/data/dapcIllus.RData |binary
adegenet-1.4-0/adegenet/data/datalist | 2
adegenet-1.4-0/adegenet/data/eHGDP.RData |binary
adegenet-1.4-0/adegenet/data/microbov.RData |binary
adegenet-1.4-0/adegenet/data/nancycats.RData |binary
adegenet-1.4-0/adegenet/data/rupica.RData |binary
adegenet-1.4-0/adegenet/data/sim2pop.RData |binary
adegenet-1.4-0/adegenet/data/spcaIllus.RData |binary
adegenet-1.4-0/adegenet/inst/dapcServer |only
adegenet-1.4-0/adegenet/man/adegenet.package.Rd | 27 +
adegenet-1.4-0/adegenet/man/as-methods.Rd | 3
adegenet-1.4-0/adegenet/man/auxil.Rd | 12
adegenet-1.4-0/adegenet/man/chooseCN.Rd | 2
adegenet-1.4-0/adegenet/man/colorplot.Rd | 2
adegenet-1.4-0/adegenet/man/coords.monmonier.Rd | 2
adegenet-1.4-0/adegenet/man/dist.genpop.Rd | 3
adegenet-1.4-0/adegenet/man/genind.Rd | 3
adegenet-1.4-0/adegenet/man/genlight.Rd | 4
adegenet-1.4-0/adegenet/man/genpop.Rd | 3
adegenet-1.4-0/adegenet/man/glSim.Rd | 62 ++--
adegenet-1.4-0/adegenet/man/hybridize.Rd | 3
adegenet-1.4-0/adegenet/man/makefreq.Rd | 2
adegenet-1.4-0/adegenet/man/microbov.Rd | 3
adegenet-1.4-0/adegenet/man/propShared.Rd | 3
adegenet-1.4-0/adegenet/man/rupica.Rd | 2
adegenet-1.4-0/adegenet/man/scale.Rd | 3
adegenet-1.4-0/adegenet/man/sequences.Rd | 5
adegenet-1.4-0/adegenet/man/servers.Rd |only
adegenet-1.4-0/adegenet/man/snpposi.Rd |only
adegenet-1.4-0/adegenet/man/snpzip.rd |only
adegenet-1.4-0/adegenet/man/spcaIllus.Rd | 2
adegenet-1.4-0/adegenet/man/web.Rd |only
adegenet-1.4-0/adegenet/man/xvalDapc.Rd | 73 +++--
adegenet-1.4-0/adegenet/src/GLfunctions.c | 4
59 files changed, 638 insertions(+), 548 deletions(-)
Title: Methods for statistical disclosure control in tabular data
Diff between sdcTable versions 0.12.0 dated 2014-03-10 and 0.13.0 dated 2014-03-14
Description: Implementation of methods for statistical disclosure control in
tabular data
Author: Bernhard Meindl
Maintainer: Bernhard Meindl
DESCRIPTION | 17 +++++++++--------
MD5 | 4 ++--
src/csp.cpp | 4 +++-
3 files changed, 14 insertions(+), 11 deletions(-)
Title: Power in a Group Sequential Design
Diff between PwrGSD versions 1.171 dated 2012-10-13 and 1.172 dated 2014-03-14
Description: Tools the evaluation of interim analysis plans for sequentially
monitored trials on a survival endpoint; tools to construct efficacy and
futility boundaries, for deriving power of a sequential design at a specified
alternative, template for evaluating the performance of candidate plans at a
set of time varying alternatives.
Author: Grant Izmirlian
Maintainer: Grant Izmirlian
PwrGSD-1.171/PwrGSD/INDEX |only
PwrGSD-1.171/PwrGSD/inst/doc/GrpSeqBnds-vignette-1.Rnw |only
PwrGSD-1.171/PwrGSD/inst/doc/GrpSeqBnds-vignette-1.pdf |only
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PwrGSD-1.171/PwrGSD/src/Dnsty.c |only
PwrGSD-1.172/PwrGSD/DESCRIPTION | 18
PwrGSD-1.172/PwrGSD/MD5 | 108 +--
PwrGSD-1.172/PwrGSD/NAMESPACE | 9
PwrGSD-1.172/PwrGSD/R/PwrGSD.R | 522 ++++++-----------
PwrGSD-1.172/PwrGSD/R/mysurvfit.R | 3
PwrGSD-1.172/PwrGSD/build |only
PwrGSD-1.172/PwrGSD/inst/doc/GrpSeqBnds-vignette.R |only
PwrGSD-1.172/PwrGSD/inst/doc/GrpSeqBnds-vignette.Rnw |only
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PwrGSD-1.172/PwrGSD/src/AsyPwrGSD.c | 21
PwrGSD-1.172/PwrGSD/src/SimPwrGSD.c | 151 ++--
PwrGSD-1.172/PwrGSD/src/WtdLogRank.c | 12
PwrGSD-1.172/PwrGSD/src/drift.c | 6
PwrGSD-1.172/PwrGSD/src/grpseqbnds.c | 16
PwrGSD-1.172/PwrGSD/src/myapprox.c |only
PwrGSD-1.172/PwrGSD/src/projectend.c |only
PwrGSD-1.172/PwrGSD/src/rao-blackwell.c |only
PwrGSD-1.172/PwrGSD/vignettes |only
97 files changed, 393 insertions(+), 473 deletions(-)
Title: Seamless R and C++ Integration
Diff between Rcpp versions 0.11.0 dated 2014-02-03 and 0.11.1 dated 2014-03-14
Description: The Rcpp package provides R functions as well as a C++ library
which facilitate the integration of R and C++.
R data types (SEXP) are matched to C++ objects in a class hierarchy. All R
types are supported (vectors, functions, environment, etc ...) and each
type is mapped to a dedicated class. For example, numeric vectors are
represented as instances of the Rcpp::NumericVector class, environments are
represented as instances of Rcpp::Environment, functions are represented as
Rcpp::Function, etc ... The "Rcpp-introduction" vignette provides a good
entry point to Rcpp.
Conversion from C++ to R and back is driven by the templates Rcpp::wrap
and Rcpp::as which are highly flexible and extensible, as documented
in the "Rcpp-extending" vignette.
Rcpp also provides Rcpp modules, a framework that allows exposing
C++ functions and classes to the R level. The "Rcpp-modules" vignette
details the current set of features of Rcpp-modules.
Rcpp includes a concept called Rcpp sugar that brings many R functions
into C++. Sugar takes advantage of lazy evaluation and expression templates
to achieve great performance while exposing a syntax that is much nicer
to use than the equivalent low-level loop code. The "Rcpp-sugar" vignette
gives an overview of the feature.
Rcpp attributes provide a high-level syntax for declaring C++
functions as callable from R and automatically generating the code
required to invoke them. Attributes are intended to facilitate both
interactive use of C++ within R sessions as well as to support R
package development. Attributes are built on top of Rcpp modules and
their implementation is based on previous work in the inline package.
Many examples are included, and around 891 unit tests in 430 unit
test functions provide additional usage examples.
An earlier version of Rcpp, containing what we now call the 'classic Rcpp
API' was written during 2005 and 2006 by Dominick Samperi. This code has
been factored out of Rcpp into the package RcppClassic, and it is still
available for code relying on the older interface. New development should
always use this Rcpp package instead.
Additional documentation is available via the paper by Eddelbuettel and
Francois (2011, JSS) paper and the book by Eddelbuettel (2013, Springer);
see 'citation("Rcpp")' for details.
Author: Dirk Eddelbuettel [aut, cre],
Romain Francois [aut],
JJ Allaire [ctb],
John Chambers [ctb],
Douglas Bates [ctb],
Kevin Ushey [ctb]
Maintainer: Dirk Eddelbuettel
Rcpp-0.11.0/inst/include/Rcpp/api/meat/AttributeProxy.h |only
Rcpp-0.11.0/inst/include/Rcpp/api/meat/DottedPairProxy.h |only
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Rcpp-0.11.0/inst/include/Rcpp/traits/comparator_type.h |only
Rcpp-0.11.1/ChangeLog | 71 +
Rcpp-0.11.1/DESCRIPTION | 8
Rcpp-0.11.1/MD5 | 140 +-
Rcpp-0.11.1/R/Rcpp.package.skeleton.R | 2
Rcpp-0.11.1/R/unit.tests.R | 96 +
Rcpp-0.11.1/README.md | 6
Rcpp-0.11.1/build/vignette.rds |binary
Rcpp-0.11.1/inst/NEWS.Rd | 51
Rcpp-0.11.1/inst/doc/Rcpp-FAQ.pdf |binary
Rcpp-0.11.1/inst/doc/Rcpp-attributes.pdf |binary
Rcpp-0.11.1/inst/doc/Rcpp-extending.pdf |binary
Rcpp-0.11.1/inst/doc/Rcpp-introduction.pdf |binary
Rcpp-0.11.1/inst/doc/Rcpp-modules.pdf |binary
Rcpp-0.11.1/inst/doc/Rcpp-package.pdf |binary
Rcpp-0.11.1/inst/doc/Rcpp-quickref.pdf |binary
Rcpp-0.11.1/inst/doc/Rcpp-sugar.pdf |binary
Rcpp-0.11.1/inst/doc/Rcpp-unitTests.pdf |binary
Rcpp-0.11.1/inst/examples/Attributes/Export.cpp | 2
Rcpp-0.11.1/inst/examples/ConvolveBenchmarks/Makefile | 2
Rcpp-0.11.1/inst/include/Rcpp.h | 4
Rcpp-0.11.1/inst/include/Rcpp/DataFrame.h | 7
Rcpp-0.11.1/inst/include/Rcpp/Environment.h | 3
Rcpp-0.11.1/inst/include/Rcpp/Module.h | 4
Rcpp-0.11.1/inst/include/Rcpp/Reference.h | 3
Rcpp-0.11.1/inst/include/Rcpp/api/meat/Vector.h | 654 ------------
Rcpp-0.11.1/inst/include/Rcpp/api/meat/meat.h | 10
Rcpp-0.11.1/inst/include/Rcpp/config.h | 2
Rcpp-0.11.1/inst/include/Rcpp/hash/IndexHash.h | 22
Rcpp-0.11.1/inst/include/Rcpp/hash/SelfHash.h | 4
Rcpp-0.11.1/inst/include/Rcpp/internal/NAComparator.h |only
Rcpp-0.11.1/inst/include/Rcpp/internal/NAEquals.h |only
Rcpp-0.11.1/inst/include/Rcpp/internal/na.h |only
Rcpp-0.11.1/inst/include/Rcpp/internal/r_coerce.h | 16
Rcpp-0.11.1/inst/include/Rcpp/internal/wrap.h | 14
Rcpp-0.11.1/inst/include/Rcpp/internal/wrap_end.h | 6
Rcpp-0.11.1/inst/include/Rcpp/longlong.h | 33
Rcpp-0.11.1/inst/include/Rcpp/module/Module.h | 10
Rcpp-0.11.1/inst/include/Rcpp/platform/solaris.h |only
Rcpp-0.11.1/inst/include/Rcpp/proxy/AttributeProxy.h | 13
Rcpp-0.11.1/inst/include/Rcpp/proxy/Binding.h | 13
Rcpp-0.11.1/inst/include/Rcpp/proxy/DottedPairProxy.h | 16
Rcpp-0.11.1/inst/include/Rcpp/proxy/FieldProxy.h | 15
Rcpp-0.11.1/inst/include/Rcpp/proxy/NamesProxy.h | 13
Rcpp-0.11.1/inst/include/Rcpp/proxy/ProtectedProxy.h | 15
Rcpp-0.11.1/inst/include/Rcpp/proxy/SlotProxy.h | 24
Rcpp-0.11.1/inst/include/Rcpp/proxy/TagProxy.h | 15
Rcpp-0.11.1/inst/include/Rcpp/proxy/proxy.h | 8
Rcpp-0.11.1/inst/include/Rcpp/r_cast.h | 1
Rcpp-0.11.1/inst/include/Rcpp/sugar/functions/table.h | 6
Rcpp-0.11.1/inst/include/Rcpp/traits/get_na.h | 4
Rcpp-0.11.1/inst/include/Rcpp/traits/is_na.h | 5
Rcpp-0.11.1/inst/include/Rcpp/traits/is_nan.h | 4
Rcpp-0.11.1/inst/include/Rcpp/traits/longlong.h |only
Rcpp-0.11.1/inst/include/Rcpp/traits/num2type.h |only
Rcpp-0.11.1/inst/include/Rcpp/traits/traits.h | 14
Rcpp-0.11.1/inst/include/Rcpp/traits/un_pointer.h | 4
Rcpp-0.11.1/inst/include/Rcpp/traits/wrap_type_traits.h | 7
Rcpp-0.11.1/inst/include/Rcpp/vector/Matrix.h | 122 +-
Rcpp-0.11.1/inst/include/Rcpp/vector/Subsetter.h |only
Rcpp-0.11.1/inst/include/Rcpp/vector/Vector.h | 610 ++++++++++-
Rcpp-0.11.1/inst/include/Rcpp/vector/const_string_proxy.h | 5
Rcpp-0.11.1/inst/include/RcppCommon.h | 13
Rcpp-0.11.1/inst/unitTests/cpp/Subset.cpp |only
Rcpp-0.11.1/inst/unitTests/cpp/Vector.cpp | 41
Rcpp-0.11.1/inst/unitTests/cpp/VectorOld.cpp |only
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Rcpp-0.11.1/inst/unitTests/runit.Vector.R | 28
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Rcpp-0.11.1/inst/unitTests/runit.na.R |only
Rcpp-0.11.1/inst/unitTests/runit.subset.R |only
Rcpp-0.11.1/src/attributes.cpp | 66 -
Rcpp-0.11.1/src/barrier.cpp | 11
83 files changed, 1284 insertions(+), 959 deletions(-)
Title: Simulation of high-dimensional data and parallelized repeated
penalized regression
Diff between pensim versions 1.2.6 dated 2013-01-15 and 1.2.9 dated 2014-03-14
Description: Simulation of continuous, correlated high-dimensional data with time to event or binary response, and parallelized functions for Lasso, Ridge, and Elastic Net penalized regression with repeated starts and two-dimensional tuning of the Elastic Net.
Author: L. Waldron, M. Pintilie, M.-S. Tsao, F. A. Shepherd, C. Huttenhower*, I. Jurisica* (*equal contribution)
Maintainer: Levi Waldron
pensim-1.2.6/pensim/inst/doc/pensim.bib |only
pensim-1.2.9/pensim/Changelog | 4
pensim-1.2.9/pensim/DESCRIPTION | 22 -
pensim-1.2.9/pensim/MD5 | 45 +-
pensim-1.2.9/pensim/NAMESPACE | 2
pensim-1.2.9/pensim/R/opt.nested.crossval.R | 97 ++--
pensim-1.2.9/pensim/R/opt.splitval.R | 106 ++---
pensim-1.2.9/pensim/R/opt1D.R | 73 +--
pensim-1.2.9/pensim/R/opt2D.R | 331 ++++++++---------
pensim-1.2.9/pensim/R/scan.l1l2.R | 117 ++----
pensim-1.2.9/pensim/build |only
pensim-1.2.9/pensim/inst/doc/pensim.R |only
pensim-1.2.9/pensim/inst/doc/pensim.Rnw | 93 ++--
pensim-1.2.9/pensim/inst/doc/pensim.pdf |binary
pensim-1.2.9/pensim/man/beer.exprs.Rd | 4
pensim-1.2.9/pensim/man/beer.survival.Rd | 9
pensim-1.2.9/pensim/man/create.data.Rd | 26 -
pensim-1.2.9/pensim/man/opt.nested.crossval.Rd | 65 +--
pensim-1.2.9/pensim/man/opt.splitval.Rd | 8
pensim-1.2.9/pensim/man/opt1D.Rd | 107 ++---
pensim-1.2.9/pensim/man/opt2D.Rd | 96 ++--
pensim-1.2.9/pensim/man/pensim-package.Rd | 16
pensim-1.2.9/pensim/man/scan.l1l2.Rd | 42 +-
pensim-1.2.9/pensim/tests/opt.nested.crossval.checks.R | 2
pensim-1.2.9/pensim/vignettes |only
25 files changed, 642 insertions(+), 623 deletions(-)
Title: Multivariate Normality Tests
Diff between MVN versions 2.0 dated 2014-03-02 and 3.0 dated 2014-03-14
Description: Assessing the assumption of multivariate normality is required by many parametric multivariate statistical methods, such as discriminant analysis, principal component analysis, MANOVA, etc. Here, we present an R package to asses multivariate normality. The MVN package contains three most widely used multivariate normality tests, including Mardia's, Henze-Zirkler's and Royston's multivariate normality tests.
Author: Selcuk Korkmaz and Dincer Goksuluk
Maintainer: Selcuk Korkmaz
MVN-2.0/MVN/R/HZ.test.R |only
MVN-2.0/MVN/R/mardia.test.R |only
MVN-2.0/MVN/R/mvn.plot.R |only
MVN-2.0/MVN/R/royston.test.R |only
MVN-2.0/MVN/man/HZ.test.Rd |only
MVN-2.0/MVN/man/mardia.test.Rd |only
MVN-2.0/MVN/man/mvn.plot.Rd |only
MVN-2.0/MVN/man/royston.test.Rd |only
MVN-3.0/MVN/DESCRIPTION | 16 +
MVN-3.0/MVN/MD5 | 36 ++--
MVN-3.0/MVN/NAMESPACE | 26 +-
MVN-3.0/MVN/R/classes.R |only
MVN-3.0/MVN/R/hzTest.R |only
MVN-3.0/MVN/R/mardiaTest.R |only
MVN-3.0/MVN/R/mvnPlot.R |only
MVN-3.0/MVN/R/roystonTest.R |only
MVN-3.0/MVN/build/vignette.rds |binary
MVN-3.0/MVN/inst/doc/MVN.R | 120 ++++++-------
MVN-3.0/MVN/inst/doc/MVN.Rnw | 345 +++++++++++++++++++--------------------
MVN-3.0/MVN/inst/doc/MVN.pdf |binary
MVN-3.0/MVN/man/MVN-package.Rd | 47 ++---
MVN-3.0/MVN/man/hz-class.Rd |only
MVN-3.0/MVN/man/hzTest.Rd |only
MVN-3.0/MVN/man/mardia-class.Rd |only
MVN-3.0/MVN/man/mardiaTest.Rd |only
MVN-3.0/MVN/man/mvnPlot.Rd |only
MVN-3.0/MVN/man/royston-class.Rd |only
MVN-3.0/MVN/man/roystonTest.Rd |only
MVN-3.0/MVN/vignettes/MVN.Rnw | 345 +++++++++++++++++++--------------------
29 files changed, 465 insertions(+), 470 deletions(-)
Title: Sorting and reordering dendrogram nodes.
Diff between dendsort versions 0.1.1 dated 2014-03-01 and 0.2.0 dated 2014-03-14
Description: This package includes functions to optimize ordering of nodes in a dendrogram,
without affecting the meaning of the dendrogram. A dendrogram can be sorted based
on the average distance of subtrees, or based on the smallest distance value.
These sorting methods improve readability and interpretability of tree structure,
especially for tasks such as comparison of different distance measures or linkage
types and identification of tight clusters and outliers. As a result, it also
introduces more meaningful reordering for a coupled heatmap visualization.
Author: Ryo Sakai
Maintainer: Ryo Sakai
DESCRIPTION | 14 +++++++-------
MD5 | 28 +++++++++++++++++-----------
R/cal_length.R |only
R/cal_node_limit.R |only
R/cal_total_length.R |only
R/dendsort.R | 17 +++++++++++------
R/sort_average.R | 4 ++--
R/sort_average_r.R | 4 ++--
R/sort_smallest.R | 4 ++--
R/sort_smallest_r.R | 4 ++--
man/cal_length.Rd |only
man/cal_node_limit.Rd |only
man/cal_total_length.Rd |only
man/dendsort.Rd | 11 +++++------
man/sort_average.Rd | 4 ++--
man/sort_average_r.Rd | 4 ++--
man/sort_smallest.Rd | 4 ++--
man/sort_smallest_r.Rd | 4 ++--
18 files changed, 56 insertions(+), 46 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2014-03-02 0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-09-29 0.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2012-08-23 1.0-5
Title: Analysis of evolutionary rates in an OU framework
Diff between OUwie versions 1.40 dated 2014-02-18 and 1.41 dated 2014-03-14
Description: Calculates and compares rate differences of continuous character evolution under Brownian motion and a new set of Ornstein-Uhlenbeck-based Hansen models that allow the strength of selection and stochastic motion to vary across selective regimes.
Author: Jeremy M. Beaulieu
Maintainer: Jeremy Beaulieu
DESCRIPTION | 8 ++++----
MD5 | 4 ++--
NAMESPACE | 3 ++-
3 files changed, 8 insertions(+), 7 deletions(-)
Title: Linear mixed-effects models using Eigen and S4
Diff between lme4 versions 1.0-6 dated 2014-02-02 and 1.1-5 dated 2014-03-14
Description: Fit linear and generalized linear mixed-effects models.
The models and their components are represented using S4 classes and
methods. The core computational algorithms are implemented using the
Eigen C++ library for numerical linear algebra and RcppEigen "glue".
Author: Douglas Bates [aut], Martin Maechler [aut],
Ben Bolker [aut, cre], Steven Walker [aut],
Rune Haubo Bojesen Christensen [ctb],
Henrik Singmann [ctb]
Maintainer: Ben Bolker
lme4-1.0-6/lme4/R/hooks.r |only
lme4-1.0-6/lme4/man/NelderMead.Rd |only
lme4-1.0-6/lme4/man/densityplot.thpr.Rd |only
lme4-1.0-6/lme4/man/splom.thpr.Rd |only
lme4-1.0-6/lme4/tests/HSAURtrees.Rout |only
lme4-1.0-6/lme4/tests/bootMer.Rout |only
lme4-1.0-6/lme4/tests/coefs.R |only
lme4-1.0-6/lme4/tests/doubleVertNotation.Rout |only
lme4-1.0-6/lme4/tests/dynload.R.orig |only
lme4-1.0-6/lme4/tests/glmer-1.Rout |only
lme4-1.0-6/lme4/tests/glmmExt.Rout |only
lme4-1.0-6/lme4/tests/lmer.R |only
lme4-1.0-6/lme4/tests/nadrop.R |only
lme4-1.0-6/lme4/tests/napredict.R |only
lme4-1.0-6/lme4/tests/optimizer.Rout |only
lme4-1.0-6/lme4/tests/prLogistic.Rout |only
lme4-1.0-6/lme4/tests/profile.R |only
lme4-1.0-6/lme4/tests/profile_plots.R |only
lme4-1.0-6/lme4/tests/test-all.R |only
lme4-1.0-6/lme4/tests/test-all.Rout |only
lme4-1.0-6/lme4/tests/testOptControl.Rout |only
lme4-1.1-5/lme4/DESCRIPTION | 25
lme4-1.1-5/lme4/MD5 | 261 +--
lme4-1.1-5/lme4/NAMESPACE | 46
lme4-1.1-5/lme4/R/AllClass.R | 104 -
lme4-1.1-5/lme4/R/bootMer.R | 91 -
lme4-1.1-5/lme4/R/checkConv.R |only
lme4-1.1-5/lme4/R/deriv.R |only
lme4-1.1-5/lme4/R/hooks.R |only
lme4-1.1-5/lme4/R/lmList.R | 3
lme4-1.1-5/lme4/R/lmer.R | 1253 ++++++++---------
lme4-1.1-5/lme4/R/lmerControl.R | 250 ++-
lme4-1.1-5/lme4/R/mcmcsamp.R | 2
lme4-1.1-5/lme4/R/modular.R | 421 ++++-
lme4-1.1-5/lme4/R/optimizer.R | 86 -
lme4-1.1-5/lme4/R/plot.R | 47
lme4-1.1-5/lme4/R/predict.R | 710 ++++++++-
lme4-1.1-5/lme4/R/profile.R | 449 +++---
lme4-1.1-5/lme4/R/utilities.R | 632 ++++----
lme4-1.1-5/lme4/R/vcconv.R | 37
lme4-1.1-5/lme4/README.md | 24
lme4-1.1-5/lme4/inst/NEWS.Rd | 177 ++
lme4-1.1-5/lme4/inst/doc/PB_mcmcsamp.pdf |only
lme4-1.1-5/lme4/inst/testdata/Johnson.rda |only
lme4-1.1-5/lme4/inst/testdata/hotpower.csv |only
lme4-1.1-5/lme4/inst/testdata/koller-data.R | 35
lme4-1.1-5/lme4/inst/testdata/lme-tst-fits.R | 9
lme4-1.1-5/lme4/inst/testdata/lme-tst-fits.Rout |only
lme4-1.1-5/lme4/inst/testdata/lme-tst-funs.R | 47
lme4-1.1-5/lme4/inst/testdata/polytom2.RData |only
lme4-1.1-5/lme4/inst/testdata/polytom3.RData |only
lme4-1.1-5/lme4/inst/testdata/polytomous_vcov_ex.RData |only
lme4-1.1-5/lme4/inst/testdata/rankMatrix.rda |only
lme4-1.1-5/lme4/inst/tests/napredict2.R |only
lme4-1.1-5/lme4/inst/tests/test-NAhandling.R |only
lme4-1.1-5/lme4/inst/tests/test-doubleVertNotation.R |only
lme4-1.1-5/lme4/inst/tests/test-glmer.R | 118 +
lme4-1.1-5/lme4/inst/tests/test-glmer.Rout | 71
lme4-1.1-5/lme4/inst/tests/test-glmmFail.R | 18
lme4-1.1-5/lme4/inst/tests/test-lmer.R | 188 +-
lme4-1.1-5/lme4/inst/tests/test-methods.R | 112 +
lme4-1.1-5/lme4/inst/tests/test-rank.R | 57
lme4-1.1-5/lme4/inst/tests/test-resids.R | 34
lme4-1.1-5/lme4/inst/tests/test-start.R | 18
lme4-1.1-5/lme4/inst/tests/test-summary.R | 2
lme4-1.1-5/lme4/inst/tests/test-utils.R |only
lme4-1.1-5/lme4/inst/tests/wenseleers.rda |only
lme4-1.1-5/lme4/inst/vignettedata |only
lme4-1.1-5/lme4/man/Dyestuff.Rd | 2
lme4-1.1-5/lme4/man/NelderMead-class.Rd | 39
lme4-1.1-5/lme4/man/Nelder_Mead.Rd |only
lme4-1.1-5/lme4/man/Pastes.Rd | 1
lme4-1.1-5/lme4/man/Penicillin.Rd | 3
lme4-1.1-5/lme4/man/VarCorr.Rd | 47
lme4-1.1-5/lme4/man/VerbAgg.Rd | 13
lme4-1.1-5/lme4/man/bootMer.Rd | 175 +-
lme4-1.1-5/lme4/man/cake.Rd | 27
lme4-1.1-5/lme4/man/cbpp.Rd | 4
lme4-1.1-5/lme4/man/confint.merMod.Rd | 2
lme4-1.1-5/lme4/man/drop1.merMod.Rd |only
lme4-1.1-5/lme4/man/dummy.Rd |only
lme4-1.1-5/lme4/man/expandDoubleVerts.Rd |only
lme4-1.1-5/lme4/man/findbars.Rd | 13
lme4-1.1-5/lme4/man/fortify.Rd | 19
lme4-1.1-5/lme4/man/getME.Rd | 40
lme4-1.1-5/lme4/man/lmList.Rd | 36
lme4-1.1-5/lme4/man/lme4-package.Rd | 47
lme4-1.1-5/lme4/man/lmer.Rd | 36
lme4-1.1-5/lme4/man/lmerControl.Rd | 252 ++-
lme4-1.1-5/lme4/man/merMod-class.Rd | 95 +
lme4-1.1-5/lme4/man/mkMerMod.Rd | 4
lme4-1.1-5/lme4/man/modular.Rd | 357 ++--
lme4-1.1-5/lme4/man/ngrps.Rd |only
lme4-1.1-5/lme4/man/nlmer.Rd | 58
lme4-1.1-5/lme4/man/plot.merMod.Rd | 3
lme4-1.1-5/lme4/man/plots.thpr.Rd |only
lme4-1.1-5/lme4/man/predict.merMod.Rd | 64
lme4-1.1-5/lme4/man/profile-methods.Rd | 102 -
lme4-1.1-5/lme4/man/pvalues.Rd | 65
lme4-1.1-5/lme4/man/ranef.Rd | 58
lme4-1.1-5/lme4/man/refit.Rd | 6
lme4-1.1-5/lme4/man/simulate.merMod.Rd | 98 +
lme4-1.1-5/lme4/man/sleepstudy.Rd | 1
lme4-1.1-5/lme4/src/external.cpp | 114 -
lme4-1.1-5/lme4/src/glmFamily.cpp | 19
lme4-1.1-5/lme4/src/optimizer.cpp | 48
lme4-1.1-5/lme4/src/optimizer.h | 19
lme4-1.1-5/lme4/src/predModule.cpp | 63
lme4-1.1-5/lme4/src/respModule.cpp | 42
lme4-1.1-5/lme4/src/respModule.h | 4
lme4-1.1-5/lme4/tests/AAAtest-all.R |only
lme4-1.1-5/lme4/tests/HSAURtrees.R | 5
lme4-1.1-5/lme4/tests/README | 4
lme4-1.1-5/lme4/tests/README.md | 8
lme4-1.1-5/lme4/tests/Rplots.pdf |binary
lme4-1.1-5/lme4/tests/ST.R |only
lme4-1.1-5/lme4/tests/agridat_gotway.R | 14
lme4-1.1-5/lme4/tests/bootMer.R | 22
lme4-1.1-5/lme4/tests/boundary.R | 203 ++
lme4-1.1-5/lme4/tests/condVar.R |only
lme4-1.1-5/lme4/tests/confint.R | 22
lme4-1.1-5/lme4/tests/elston.R | 5
lme4-1.1-5/lme4/tests/extras.R | 30
lme4-1.1-5/lme4/tests/falsezero_dorie.R | 2
lme4-1.1-5/lme4/tests/fewlevels.R | 44
lme4-1.1-5/lme4/tests/glmer-1.R | 19
lme4-1.1-5/lme4/tests/glmmExt.R | 9
lme4-1.1-5/lme4/tests/glmmWeights.R | 57
lme4-1.1-5/lme4/tests/lme4_nlme.R | 4
lme4-1.1-5/lme4/tests/lmer-0.R |only
lme4-1.1-5/lme4/tests/lmer-1.R | 65
lme4-1.1-5/lme4/tests/lmer-1.Rout.save | 243 +--
lme4-1.1-5/lme4/tests/lmer2_ex.R | 2
lme4-1.1-5/lme4/tests/minval.R | 5
lme4-1.1-5/lme4/tests/modFormula.R | 24
lme4-1.1-5/lme4/tests/nbinom.R | 17
lme4-1.1-5/lme4/tests/nlmer-conv.R | 3
lme4-1.1-5/lme4/tests/nlmer.R | 3
lme4-1.1-5/lme4/tests/nlmer.Rout.save | 19
lme4-1.1-5/lme4/tests/offset.R | 12
lme4-1.1-5/lme4/tests/optimizer.R | 31
lme4-1.1-5/lme4/tests/polytomous.R | 2
lme4-1.1-5/lme4/tests/prLogistic.R | 28
lme4-1.1-5/lme4/tests/predict.R | 60
lme4-1.1-5/lme4/tests/predict.Rout |only
lme4-1.1-5/lme4/tests/predict_basis.R | 12
lme4-1.1-5/lme4/tests/predict_basis.Rout |only
lme4-1.1-5/lme4/tests/predsim.R | 41
lme4-1.1-5/lme4/tests/predsim.Rout | 17
lme4-1.1-5/lme4/tests/priorWeights.R | 151 +-
lme4-1.1-5/lme4/tests/priorWeightsModComp.R |only
lme4-1.1-5/lme4/tests/profile-tst.R |only
lme4-1.1-5/lme4/tests/refit.R | 61
lme4-1.1-5/lme4/tests/simulate.R | 113 +
lme4-1.1-5/lme4/tests/testcolonizer.R | 8
lme4-1.1-5/lme4/tests/testcrab.R | 6
lme4-1.1-5/lme4/tests/vcov-etc.R | 114 +
157 files changed, 5765 insertions(+), 3023 deletions(-)
Title: Model-diagnostics based on cumulative residuals
Diff between gof versions 0.9.0 dated 2013-04-25 and 0.9.1 dated 2014-03-14
Description: Implementation of model-checking techniques for generalized linear
models and linear structural equation models based on cumulative residuals
Author: Klaus K. Holst
Maintainer: Klaus. K. Holst
gof-0.9.0/gof/src/Makevars.in |only
gof-0.9.1/gof/DESCRIPTION | 17 ++++-----
gof-0.9.1/gof/MD5 | 18 ++++-----
gof-0.9.1/gof/NAMESPACE | 1
gof-0.9.1/gof/NEWS | 39 +++++++++++----------
gof-0.9.1/gof/R/cumres.coxph.R | 5 +-
gof-0.9.1/gof/R/cumres.lvmfit.R | 11 +++--
gof-0.9.1/gof/R/gof-package.R | 70 +++++++++++++++++---------------------
gof-0.9.1/gof/man/cumres.coxph.Rd | 4 +-
gof-0.9.1/gof/man/gof-package.Rd | 10 +----
gof-0.9.1/gof/src/Makevars.win |only
11 files changed, 83 insertions(+), 92 deletions(-)
Title: A complementary package to the FAOSTAT database and the
Statistical Yearbook of the Food and Agricultural Organization
of the United Nations.
Diff between FAOSTAT versions 1.4 dated 2013-05-30 and 1.6 dated 2014-03-14
Description: The package hosts a list of functions to download, manipulate,
construct and aggregate agricultural statistics provided by the FAOSTAT
database of the Food and Agricultural Organization of the United Nations.
Author: Michael C. J. Kao
Maintainer: Michael C. J. Kao
FAOSTAT-1.4/FAOSTAT/inst |only
FAOSTAT-1.6/FAOSTAT/DESCRIPTION | 28 ++++-------
FAOSTAT-1.6/FAOSTAT/MD5 | 35 +++++++-------
FAOSTAT-1.6/FAOSTAT/NAMESPACE | 8 +++
FAOSTAT-1.6/FAOSTAT/R/CHMT.R | 55 +++++++++++-----------
FAOSTAT-1.6/FAOSTAT/R/FAOSTAT-package.R | 8 +++
FAOSTAT-1.6/FAOSTAT/R/FAOsearch.R | 7 --
FAOSTAT-1.6/FAOSTAT/R/aggCountry.R | 1
FAOSTAT-1.6/FAOSTAT/R/geogr.R | 13 +----
FAOSTAT-1.6/FAOSTAT/R/getFAO.R | 57 +++++++++++++++--------
FAOSTAT-1.6/FAOSTAT/R/getFAOtoSYB.R | 19 ++++---
FAOSTAT-1.6/FAOSTAT/R/lsgr.R | 5 +-
FAOSTAT-1.6/FAOSTAT/data/FAOcountryProfile.RData |binary
FAOSTAT-1.6/FAOSTAT/data/FAOmetaTable.RData |binary
FAOSTAT-1.6/FAOSTAT/data/FAOregionProfile.RData |binary
FAOSTAT-1.6/FAOSTAT/demo |only
FAOSTAT-1.6/FAOSTAT/man/getFAO.Rd | 9 +++
FAOSTAT-1.6/FAOSTAT/man/getFAOtoSYB.Rd | 5 +-
FAOSTAT-1.6/FAOSTAT/vignettes |only
19 files changed, 145 insertions(+), 105 deletions(-)