Title: Functions to Explore L-Systems (Lindenmayer Systems)
Diff between LindenmayeR versions 0.1-0 dated 2014-08-12 and 0.1.4 dated 2015-04-16
Description: L-systems or Lindenmayer systems are parallel rewriting systems which can
be used to simulate biological forms and certain kinds of fractals.
Briefly, in an L-system a series of symbols in a string are replaced
iteratively according to rules to give a more complex string. Eventually,
the symbols are translated into turtle graphics for plotting. Wikipedia has
a very good introduction: en.wikipedia.org/wiki/L-system This package
provides basic functions for exploring L-systems.
Author: Bryan Hanson [aut, cre]
Maintainer: Bryan Hanson
DESCRIPTION | 12 ++++++------
MD5 | 18 +++++++++---------
NAMESPACE | 3 ++-
NEWS | 23 +++++++++++++++++++----
R/LindenmayeR-package.R | 2 ++
R/Lsys.R | 12 ++++++++++--
R/drawLsys.R | 24 +++++++++++++++++++++---
man/LindenmayeR-package.Rd | 4 +++-
man/Lsys.Rd | 3 ++-
man/drawLsys.Rd | 13 ++++++++++++-
10 files changed, 86 insertions(+), 28 deletions(-)
Title: Crunch.io Data Tools
Diff between crunch versions 1.0.2 dated 2015-04-04 and 1.1.0 dated 2015-04-16
Description: The Crunch.io service (http://crunch.io/) provides a cloud-based
data store and analytic engine, as well as an intuitive web interface.
Using this package, analysts can interact with and manipulate Crunch
datasets from within R. Importantly, this allows technical researchers to
collaborate naturally with team members, managers, and clients who prefer a
point-and-click interface.
Author: Neal Richardson [aut, cre]
Maintainer: Neal Richardson
DESCRIPTION | 10 ++--
MD5 | 73 +++++++++++++++++++-----------------
NAMESPACE | 15 ++++++-
R/AllClasses.R | 2
R/AllGenerics.R | 25 ++++++++++++
R/api.R | 15 +------
R/append-dataset.R | 9 ++--
R/as-data-frame.R |only
R/auth.R | 2
R/categories.R | 21 ----------
R/crest.R |only
R/crunch.R | 3 +
R/dataset.R | 7 +--
R/get-datasets.R | 1
R/json.R |only
R/log.R |only
R/misc.R | 14 ++----
R/new-dataset.R | 9 +---
R/share.R | 2
R/shoji-catalog.R | 2
R/shoji.R | 1
R/tuple.R | 5 +-
R/variable-catalog.R | 4 -
R/variable-order.R | 25 ------------
R/variable-to-R.R | 24 -----------
R/variable-update.R | 8 ++-
R/variable.R | 25 +++++++++---
inst/doc/variables.html | 3 -
man/dataset-to-R.Rd | 25 ++++++++++--
man/tojson-crunch.Rd | 69 ++++++++++++++++------------------
tests/testthat/helper.R | 4 +
tests/testthat/test-api.R | 26 ++++++------
tests/testthat/test-as-data-frame.R | 33 +++++++++++++---
tests/testthat/test-encoding.R | 35 +----------------
tests/testthat/utftesting.R |only
vignettes/array-variables.RData |binary
vignettes/economist.RData |binary
vignettes/getting-started.RData |binary
vignettes/variable-order.RData |binary
vignettes/variables.RData |binary
40 files changed, 246 insertions(+), 251 deletions(-)
Title: Analysis of Heavy Tailed Distributions
Diff between poweRlaw versions 0.30.1 dated 2015-03-13 and 0.30.2 dated 2015-04-16
Description: An implementation of maximum likelihood estimators for a variety
of heavy tailed distributions, including both the discrete and continuous
power law distributions. Additionally, a goodness-of-fit based approach is
used to estimate the lower cut-off for the scaling region.
Author: Colin Gillespie [aut, cre]
Maintainer: Colin Gillespie
poweRlaw-0.30.1/poweRlaw/inst/doc/compare_distributions.R |only
poweRlaw-0.30.1/poweRlaw/inst/doc/compare_distributions.Rnw |only
poweRlaw-0.30.1/poweRlaw/inst/doc/compare_distributions.pdf |only
poweRlaw-0.30.1/poweRlaw/inst/doc/examples.R |only
poweRlaw-0.30.1/poweRlaw/inst/doc/examples.Rnw |only
poweRlaw-0.30.1/poweRlaw/inst/doc/examples.pdf |only
poweRlaw-0.30.1/poweRlaw/inst/doc/poweRlaw.R |only
poweRlaw-0.30.1/poweRlaw/inst/doc/poweRlaw.Rnw |only
poweRlaw-0.30.1/poweRlaw/inst/doc/poweRlaw.pdf |only
poweRlaw-0.30.1/poweRlaw/inst/doc/v64i02.Rnw |only
poweRlaw-0.30.1/poweRlaw/inst/doc/v64i02.pdf |only
poweRlaw-0.30.1/poweRlaw/vignettes/compare_distributions.Rnw |only
poweRlaw-0.30.1/poweRlaw/vignettes/examples.Rnw |only
poweRlaw-0.30.1/poweRlaw/vignettes/poweRlaw.Rnw |only
poweRlaw-0.30.1/poweRlaw/vignettes/v64i02.Rnw |only
poweRlaw-0.30.2/poweRlaw/DESCRIPTION | 8 +-
poweRlaw-0.30.2/poweRlaw/MD5 | 39 +++++-----
poweRlaw-0.30.2/poweRlaw/NEWS | 6 +
poweRlaw-0.30.2/poweRlaw/R/plot_methods.R | 2
poweRlaw-0.30.2/poweRlaw/build/vignette.rds |binary
poweRlaw-0.30.2/poweRlaw/inst/doc/a_introduction.R |only
poweRlaw-0.30.2/poweRlaw/inst/doc/a_introduction.Rnw |only
poweRlaw-0.30.2/poweRlaw/inst/doc/a_introduction.pdf |only
poweRlaw-0.30.2/poweRlaw/inst/doc/b_powerlaw_examples.R |only
poweRlaw-0.30.2/poweRlaw/inst/doc/b_powerlaw_examples.Rnw |only
poweRlaw-0.30.2/poweRlaw/inst/doc/b_powerlaw_examples.pdf |only
poweRlaw-0.30.2/poweRlaw/inst/doc/c_comparing_distributions.R |only
poweRlaw-0.30.2/poweRlaw/inst/doc/c_comparing_distributions.Rnw |only
poweRlaw-0.30.2/poweRlaw/inst/doc/c_comparing_distributions.pdf |only
poweRlaw-0.30.2/poweRlaw/inst/doc/d_jss_paper.Rnw |only
poweRlaw-0.30.2/poweRlaw/inst/doc/d_jss_paper.pdf |only
poweRlaw-0.30.2/poweRlaw/vignettes/a_introduction.Rnw |only
poweRlaw-0.30.2/poweRlaw/vignettes/b_powerlaw_examples.Rnw |only
poweRlaw-0.30.2/poweRlaw/vignettes/blackouts.txt |only
poweRlaw-0.30.2/poweRlaw/vignettes/c_comparing_distributions.Rnw |only
poweRlaw-0.30.2/poweRlaw/vignettes/d_jss_paper.Rnw |only
36 files changed, 31 insertions(+), 24 deletions(-)
Title: Missing Data Imputation and Model Checking
Diff between mi versions 0.10-2 dated 2015-04-07 and 1.0 dated 2015-04-16
Description: The mi package provides functions for data manipulation, imputing missing values in an approximate Bayesian framework, diagnostics of the models used to generate the imputations, confidence-building mechanisms to validate some of the assumptions of the imputation algorithm, and functions to analyze multiply imputed data sets with the appropriate degree of sampling uncertainty.
Author: Andrew Gelman [ctb],
Jennifer Hill [ctb],
Yu-Sung Su [aut],
Masanao Yajima [ctb],
Maria Pittau [ctb],
Ben Goodrich [cre, aut],
Yajuan Si [ctb],
Jon Kropko [aut]
Maintainer: Ben Goodrich
mi-0.10-2/mi/CHANGELOG |only
mi-0.10-2/mi/R/AllInternal.R |only
mi-0.10-2/mi/R/bayesglm.mi.R |only
mi-0.10-2/mi/R/bayespolr.mi.R |only
mi-0.10-2/mi/R/coef.R |only
mi-0.10-2/mi/R/convergence.plot.R |only
mi-0.10-2/mi/R/display.R |only
mi-0.10-2/mi/R/fitted.R |only
mi-0.10-2/mi/R/glm.mi.R |only
mi-0.10-2/mi/R/imputation.models.R |only
mi-0.10-2/mi/R/imputed.R |only
mi-0.10-2/mi/R/lm.mi.R |only
mi-0.10-2/mi/R/lmer.mi.R |only
mi-0.10-2/mi/R/load.first.R |only
mi-0.10-2/mi/R/mi.binary.R |only
mi-0.10-2/mi/R/mi.categorical.R |only
mi-0.10-2/mi/R/mi.completed.R |only
mi-0.10-2/mi/R/mi.continuous.R |only
mi-0.10-2/mi/R/mi.count.R |only
mi-0.10-2/mi/R/mi.fixed.R |only
mi-0.10-2/mi/R/mi.hist.R |only
mi-0.10-2/mi/R/mi.info.R |only
mi-0.10-2/mi/R/mi.mean.R |only
mi-0.10-2/mi/R/mi.median.R |only
mi-0.10-2/mi/R/mi.misc.R |only
mi-0.10-2/mi/R/mi.pmm.R |only
mi-0.10-2/mi/R/mi.polr.R |only
mi-0.10-2/mi/R/mi.pooled.R |only
mi-0.10-2/mi/R/mi.preprocess.R |only
mi-0.10-2/mi/R/mi.scatterplot.R |only
mi-0.10-2/mi/R/missing.pattern.plot.R |only
mi-0.10-2/mi/R/plot.R |only
mi-0.10-2/mi/R/polr.mi.R |only
mi-0.10-2/mi/R/print.R |only
mi-0.10-2/mi/R/random.imp.R |only
mi-0.10-2/mi/R/resid.R |only
mi-0.10-2/mi/R/residual.plot.R |only
mi-0.10-2/mi/R/se.coef.R |only
mi-0.10-2/mi/R/show.R |only
mi-0.10-2/mi/R/sigma.hat.R |only
mi-0.10-2/mi/R/typecast.R |only
mi-0.10-2/mi/R/write.mi.R |only
mi-0.10-2/mi/TODO |only
mi-0.10-2/mi/data/CHAIN.rda |only
mi-0.10-2/mi/man/convergence.plot.Rd |only
mi-0.10-2/mi/man/mi.Rd |only
mi-0.10-2/mi/man/mi.binary.Rd |only
mi-0.10-2/mi/man/mi.categorical.Rd |only
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mi-0.10-2/mi/man/mi.count.Rd |only
mi-0.10-2/mi/man/mi.fixed.Rd |only
mi-0.10-2/mi/man/mi.hist.Rd |only
mi-0.10-2/mi/man/mi.info.Rd |only
mi-0.10-2/mi/man/mi.info.update.Rd |only
mi-0.10-2/mi/man/mi.method.Rd |only
mi-0.10-2/mi/man/mi.pmm.Rd |only
mi-0.10-2/mi/man/mi.polr.Rd |only
mi-0.10-2/mi/man/mi.pooled.Rd |only
mi-0.10-2/mi/man/mi.preprocess.Rd |only
mi-0.10-2/mi/man/mi.scatterplot.Rd |only
mi-0.10-2/mi/man/missing.pattern.plot.Rd |only
mi-0.10-2/mi/man/noise.control.Rd |only
mi-0.10-2/mi/man/plot.mi.Rd |only
mi-0.10-2/mi/man/random.imp.Rd |only
mi-0.10-2/mi/man/type.models.Rd |only
mi-0.10-2/mi/man/typecast.Rd |only
mi-0.10-2/mi/man/write.mi.Rd |only
mi-1.0/mi/DESCRIPTION | 44
mi-1.0/mi/MD5 | 143 -
mi-1.0/mi/NAMESPACE | 213 --
mi-1.0/mi/R/AllClass.R | 1380 ++++++++++++++--
mi-1.0/mi/R/AllGeneric.R | 244 --
mi-1.0/mi/R/change.R |only
mi-1.0/mi/R/change_family.R |only
mi-1.0/mi/R/change_imputation_method.R |only
mi-1.0/mi/R/change_link.R |only
mi-1.0/mi/R/change_model.R |only
mi-1.0/mi/R/change_size.R |only
mi-1.0/mi/R/change_transformation.R |only
mi-1.0/mi/R/change_type.R |only
mi-1.0/mi/R/complete.R |only
mi-1.0/mi/R/convenience.R |only
mi-1.0/mi/R/debug.R |only
mi-1.0/mi/R/fit_model.R |only
mi-1.0/mi/R/get_parameters.R |only
mi-1.0/mi/R/hist_methods.R |only
mi-1.0/mi/R/mi.R | 1783 ++++++++++++---------
mi-1.0/mi/R/misc.R |only
mi-1.0/mi/R/missing_data.frame.R |only
mi-1.0/mi/R/missing_variable.R |only
mi-1.0/mi/R/plot_methods.R |only
mi-1.0/mi/R/pool.R |only
mi-1.0/mi/R/random_df.R |only
mi-1.0/mi/R/sysdata.rda |only
mi-1.0/mi/R/tobin5.R |only
mi-1.0/mi/R/zzz.R |only
mi-1.0/mi/build |only
mi-1.0/mi/data/CHAIN.RData |only
mi-1.0/mi/data/nlsyV.RData |only
mi-1.0/mi/inst/CITATION | 30
mi-1.0/mi/inst/doc |only
mi-1.0/mi/man/00mi-package.Rd |only
mi-1.0/mi/man/01missing_variable.Rd |only
mi-1.0/mi/man/02missing_data.frame.Rd |only
mi-1.0/mi/man/03change.Rd |only
mi-1.0/mi/man/04mi.Rd |only
mi-1.0/mi/man/05Rhats.Rd |only
mi-1.0/mi/man/06pool.Rd |only
mi-1.0/mi/man/07complete.Rd |only
mi-1.0/mi/man/CHAIN.Rd | 63
mi-1.0/mi/man/allcategorical_missing_data.frame.Rd |only
mi-1.0/mi/man/bounded.Rd |only
mi-1.0/mi/man/categorical.Rd |only
mi-1.0/mi/man/censored-continuous.Rd |only
mi-1.0/mi/man/continuous.Rd |only
mi-1.0/mi/man/count.Rd |only
mi-1.0/mi/man/experiment_missing_data.frame.Rd |only
mi-1.0/mi/man/fit_model.Rd |only
mi-1.0/mi/man/get_parameters.Rd |only
mi-1.0/mi/man/hist.Rd |only
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mi-1.0/mi/man/mi2stata.Rd |only
mi-1.0/mi/man/mipply.Rd |only
mi-1.0/mi/man/multilevel_missing_data.frame.Rd |only
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mi-1.0/mi/man/nlsyV.Rd |only
mi-1.0/mi/man/positive.Rd |only
mi-1.0/mi/man/rdata.frame.Rd |only
mi-1.0/mi/man/semi-continuous.Rd |only
mi-1.0/mi/tests |only
mi-1.0/mi/vignettes |only
133 files changed, 2503 insertions(+), 1397 deletions(-)
Title: Least-Squares Means
Diff between lsmeans versions 2.16 dated 2015-03-14 and 2.17 dated 2015-04-16
Description: Obtain least-squares means for many linear, generalized linear, and mixed models. Compute contrasts or linear functions of least-squares means, and comparisons of slopes. Plots and compact letter displays.
Author: Russell V. Lenth [aut], Maxime Hervé [ctb]
Maintainer: Russ Lenth
DESCRIPTION | 18 ++++++++---------
MD5 | 45 ++++++++++++++++++++++----------------------
NAMESPACE | 34 ++++++++++++++++++++++++++-------
R/MCMC-support.R |only
R/S4-classes.R | 4 ++-
R/helpers.R | 9 +++++++-
R/lsmeans.R | 11 ++++++----
R/nonlin-support.R | 2 +
R/ref.grid.R | 25 +++++++++++++++---------
R/summary.R | 1
inst/NEWS | 16 +++++++++++++++
inst/doc/extending.pdf |binary
inst/doc/extending.rnw | 3 ++
inst/doc/using-lsmeans.R | 23 ++++++++++++++++++++++
inst/doc/using-lsmeans.pdf |binary
inst/doc/using-lsmeans.rnw | 19 ++++++++++++++++++
man/extending.Rd | 4 +--
man/lsmeans.Rd | 3 +-
man/models.Rd | 10 +++++++++
man/ref.grid.Rd | 2 -
man/ref.grid.class.Rd | 1
man/summary.Rd | 12 +++++++++--
vignettes/extending.rnw | 3 ++
vignettes/using-lsmeans.rnw | 19 ++++++++++++++++++
24 files changed, 205 insertions(+), 59 deletions(-)
Title: Tools for Retrieval and Storage of Functional Genomics Data
Diff between compendiumdb versions 0.1.0 dated 2014-08-29 and 1.0.0 dated 2015-04-16
Description: Package for the systematic retrieval and storage of
functional genomics data via a MySQL database.
Author: Umesh K. Nandal
Maintainer: Umesh Nandal
compendiumdb-0.1.0/compendiumdb/inst/scripts/README.txt |only
compendiumdb-0.1.0/compendiumdb/inst/tests |only
compendiumdb-1.0.0/compendiumdb/DESCRIPTION | 25
compendiumdb-1.0.0/compendiumdb/INSTALL |only
compendiumdb-1.0.0/compendiumdb/MD5 | 93
compendiumdb-1.0.0/compendiumdb/NAMESPACE | 2
compendiumdb-1.0.0/compendiumdb/R/GDSforGSE.R | 20
compendiumdb-1.0.0/compendiumdb/R/GSEforGPL.R | 10
compendiumdb-1.0.0/compendiumdb/R/GSEinDB.R | 55
compendiumdb-1.0.0/compendiumdb/R/GSMdescriptions.R | 19
compendiumdb-1.0.0/compendiumdb/R/connectDatabase.R | 20
compendiumdb-1.0.0/compendiumdb/R/createESET.R | 225 -
compendiumdb-1.0.0/compendiumdb/R/downloadGEOdata.R | 12
compendiumdb-1.0.0/compendiumdb/R/loadDataToCompendium.R | 8
compendiumdb-1.0.0/compendiumdb/R/loadDatabaseSchema.R | 6
compendiumdb-1.0.0/compendiumdb/R/parseSampleAnnot.R | 96
compendiumdb-1.0.0/compendiumdb/R/removeGSE.R | 19
compendiumdb-1.0.0/compendiumdb/R/tagExperiment.R | 4
compendiumdb-1.0.0/compendiumdb/R/updatePhenoData.R | 99
compendiumdb-1.0.0/compendiumdb/inst/doc/compendiumdb.pdf |binary
compendiumdb-1.0.0/compendiumdb/inst/extdata/compendiumSchema.sql | 1174 +++++-----
compendiumdb-1.0.0/compendiumdb/inst/scripts/BigMac/COMPENDIUM/compendiumSUB.pm | 2
compendiumdb-1.0.0/compendiumdb/inst/scripts/Perl/deleteAllforGPL.pl | 4
compendiumdb-1.0.0/compendiumdb/inst/scripts/Perl/deleteAllforGSE.pl | 4
compendiumdb-1.0.0/compendiumdb/inst/scripts/Perl/expDesign.pl | 236 +-
compendiumdb-1.0.0/compendiumdb/inst/scripts/Perl/fetchESET.pl | 4
compendiumdb-1.0.0/compendiumdb/inst/scripts/Perl/getAllForGSE.pl | 34
compendiumdb-1.0.0/compendiumdb/inst/scripts/Perl/loadAllforGSEeset.pl | 38
compendiumdb-1.0.0/compendiumdb/inst/scripts/Perl/loadGDS.pl | 4
compendiumdb-1.0.0/compendiumdb/inst/scripts/Perl/loadGPL.pl | 23
compendiumdb-1.0.0/compendiumdb/inst/scripts/Perl/loadGSMeset.pl | 6
compendiumdb-1.0.0/compendiumdb/inst/scripts/Perl/load_notGDS.pl | 4
compendiumdb-1.0.0/compendiumdb/inst/scripts/Perl/parsingSoftFile_forESET.pl | 36
compendiumdb-1.0.0/compendiumdb/inst/scripts/R/downloadSoftFile.R | 20
compendiumdb-1.0.0/compendiumdb/inst/scripts/R/esetGeneration.R | 2
compendiumdb-1.0.0/compendiumdb/inst/scripts/README |only
compendiumdb-1.0.0/compendiumdb/man/GDSforGSE.Rd | 84
compendiumdb-1.0.0/compendiumdb/man/GSEforGPL.Rd | 73
compendiumdb-1.0.0/compendiumdb/man/GSEinDB.Rd | 108
compendiumdb-1.0.0/compendiumdb/man/GSMdescriptions.Rd | 92
compendiumdb-1.0.0/compendiumdb/man/compendiumdb-package.Rd | 62
compendiumdb-1.0.0/compendiumdb/man/connectDatabase.Rd | 117
compendiumdb-1.0.0/compendiumdb/man/createESET.Rd | 147 -
compendiumdb-1.0.0/compendiumdb/man/downloadGEOdata.Rd | 122 -
compendiumdb-1.0.0/compendiumdb/man/loadDataToCompendium.Rd | 129 -
compendiumdb-1.0.0/compendiumdb/man/loadDatabaseSchema.Rd | 98
compendiumdb-1.0.0/compendiumdb/man/removeGSE.Rd | 68
compendiumdb-1.0.0/compendiumdb/man/tagExperiment.Rd | 88
compendiumdb-1.0.0/compendiumdb/man/updatePhenoData.Rd | 83
compendiumdb-1.0.0/compendiumdb/tests |only
50 files changed, 1825 insertions(+), 1750 deletions(-)
Title: Soft Classification Performance Measures
Diff between softclassval versions 1.0-20130317 dated 2013-04-03 and 1.0-20150416 dated 2015-04-16
Description: An extension of sensitivity, specificity, positive and negative
predictive value to continuous predicted and reference memberships in
[0, 1].
Author: C. Beleites
Maintainer: C. Beleites
softclassval-1.0-20130317/softclassval/inst/NEWS.Rd |only
softclassval-1.0-20150416/softclassval/DESCRIPTION | 30 +-
softclassval-1.0-20150416/softclassval/MD5 | 37 +--
softclassval-1.0-20150416/softclassval/NAMESPACE | 12 -
softclassval-1.0-20150416/softclassval/R/make01.R | 1
softclassval-1.0-20150416/softclassval/R/operators.R | 24 +-
softclassval-1.0-20150416/softclassval/R/softclassval.R | 4
softclassval-1.0-20150416/softclassval/R/unittests.R | 3
softclassval-1.0-20150416/softclassval/inst/CITATION | 9
softclassval-1.0-20150416/softclassval/man/checkrp.Rd | 36 +--
softclassval-1.0-20150416/softclassval/man/dev.Rd | 23 +-
softclassval-1.0-20150416/softclassval/man/factor2matrix.Rd | 15 -
softclassval-1.0-20150416/softclassval/man/hard.Rd | 23 +-
softclassval-1.0-20150416/softclassval/man/hardclasses.Rd | 39 +--
softclassval-1.0-20150416/softclassval/man/nsamples.Rd | 32 +--
softclassval-1.0-20150416/softclassval/man/operators.Rd | 79 +++----
softclassval-1.0-20150416/softclassval/man/performance.Rd | 106 ++++------
softclassval-1.0-20150416/softclassval/man/postproc.Rd | 29 +-
softclassval-1.0-20150416/softclassval/man/softclassval-package.Rd | 9
softclassval-1.0-20150416/softclassval/man/softclassval.unittest.Rd | 16 -
20 files changed, 248 insertions(+), 279 deletions(-)
Title: Loading Google Adwords Data into R
Diff between RAdwords versions 0.1.3 dated 2015-04-07 and 0.1.4 dated 2015-04-16
Description: Aims at loading Google Adwords data into R. Adwords is an online
advertising service that enables advertisers to display advertising copy to web users.
Therefore the package implements three main features. First, the package provides an
authentication process for R with the Google Adwords API via OAUTH2. Second, the
package offers an interface to apply the Adwords query language in R and
query the Adwords API with ad-hoc reports. Third, the received data are
transformed into suitable data formats for further data processing and data
analysis.
Author: Johannes Burkhardt
Maintainer: Johannes Burkhardt
DESCRIPTION | 17 ++++++++++-------
MD5 | 6 +++---
NEWS | 7 +++++++
R/transformData.R | 18 +++++++++++++-----
4 files changed, 33 insertions(+), 15 deletions(-)
Title: Tools for Data Handling and Analysis in Macroecology
Diff between letsR versions 2.0 dated 2015-02-09 and 2.1 dated 2015-04-16
Description: R functions for handling, processing, and analyzing geographic data on
species' distributions and environmental variables as well as species' description
and conservation information.
Author: Bruno Vilela & Fabricio Villalobos
Maintainer: Bruno Vilela
letsR-2.0/letsR/R/Data_iucn.R |only
letsR-2.0/letsR/data/iucn.rda |only
letsR-2.0/letsR/man/iucn.Rd |only
letsR-2.1/letsR/DESCRIPTION | 25 -
letsR-2.1/letsR/MD5 | 205 +++++++----
letsR-2.1/letsR/R/Data_helps.R |only
letsR-2.1/letsR/R/PresenceAbsence-class.R |only
letsR-2.1/letsR/R/getcode.R |only
letsR-2.1/letsR/R/getnames.R |only
letsR-2.1/letsR/R/letsR-package.R | 43 +-
letsR-2.1/letsR/R/lets_addpoly.R | 84 +++-
letsR-2.1/letsR/R/lets_addvar.R | 90 +++-
letsR-2.1/letsR/R/lets_classvar.R | 60 +--
letsR-2.1/letsR/R/lets_correl.R | 334 +++++++++++-------
letsR-2.1/letsR/R/lets_distmat.R | 68 +--
letsR-2.1/letsR/R/lets_field.R | 194 ++++++----
letsR-2.1/letsR/R/lets_gridirizer.R | 23 -
letsR-2.1/letsR/R/lets_iucn.R | 306 ++++++++--------
letsR-2.1/letsR/R/lets_iucn_habitats.R | 152 ++++----
letsR-2.1/letsR/R/lets_iucn_historic.R | 282 +++++++++------
letsR-2.1/letsR/R/lets_iucncont.R | 47 +-
letsR-2.1/letsR/R/lets_maplizer.R | 103 +++--
letsR-2.1/letsR/R/lets_midpoint.R | 102 +++--
letsR-2.1/letsR/R/lets_overlap.R | 118 +++---
letsR-2.1/letsR/R/lets_pamcrop.R | 60 ++-
letsR-2.1/letsR/R/lets_presab.R | 287 +++++++++------
letsR-2.1/letsR/R/lets_presab_birds.R | 344 +++++++++++--------
letsR-2.1/letsR/R/lets_presab_points.R | 128 ++++---
letsR-2.1/letsR/R/lets_rangesize.R | 146 +++++---
letsR-2.1/letsR/R/lets_shpfilter.R | 85 ++--
letsR-2.1/letsR/R/lets_summaryze.R | 58 ++-
letsR-2.1/letsR/R/lets_transf.R | 24 -
letsR-2.1/letsR/R/plot_PresenceAbsence.R | 67 ++-
letsR-2.1/letsR/R/print_PresenceAbsence.R | 10
letsR-2.1/letsR/R/print_summary_PresenceAbsence.R | 9
letsR-2.1/letsR/R/removecells.R | 14
letsR-2.1/letsR/R/removesp.R | 25 -
letsR-2.1/letsR/R/summary_PresenceAbsence.R | 45 +-
letsR-2.1/letsR/R/unicas.R | 27 -
letsR-2.1/letsR/README.md | 22 -
letsR-2.1/letsR/data/IUCN.rda |only
letsR-2.1/letsR/data/PAM.rda |binary
letsR-2.1/letsR/data/temp.rda |binary
letsR-2.1/letsR/inst |only
letsR-2.1/letsR/man/IUCN.Rd |only
letsR-2.1/letsR/man/PAM.Rd | 5
letsR-2.1/letsR/man/Phyllomedusa.Rd | 6
letsR-2.1/letsR/man/PresenceAbsence.Rd |only
letsR-2.1/letsR/man/lets.addpoly.Rd | 10
letsR-2.1/letsR/man/lets.addvar.Rd | 26 +
letsR-2.1/letsR/man/lets.classvar.Rd | 27 -
letsR-2.1/letsR/man/lets.correl.Rd | 40 +-
letsR-2.1/letsR/man/lets.distmat.Rd | 26 +
letsR-2.1/letsR/man/lets.field.Rd | 32 +
letsR-2.1/letsR/man/lets.gridirizer.Rd | 13
letsR-2.1/letsR/man/lets.iucn.Rd | 16
letsR-2.1/letsR/man/lets.iucn.ha.Rd | 14
letsR-2.1/letsR/man/lets.iucn.his.Rd | 44 ++
letsR-2.1/letsR/man/lets.iucncont.Rd | 20 -
letsR-2.1/letsR/man/lets.maplizer.Rd | 34 +
letsR-2.1/letsR/man/lets.midpoint.Rd | 16
letsR-2.1/letsR/man/lets.overlap.Rd | 32 +
letsR-2.1/letsR/man/lets.pamcrop.Rd | 23 +
letsR-2.1/letsR/man/lets.presab.Rd | 33 +
letsR-2.1/letsR/man/lets.presab.birds.Rd | 84 +++-
letsR-2.1/letsR/man/lets.presab.points.Rd | 28 -
letsR-2.1/letsR/man/lets.rangesize.Rd | 38 +-
letsR-2.1/letsR/man/lets.shFilter.Rd | 7
letsR-2.1/letsR/man/lets.summarizer.Rd | 23 +
letsR-2.1/letsR/man/lets.transf.Rd | 2
letsR-2.1/letsR/man/letsR.Rd |only
letsR-2.1/letsR/man/plot.PresenceAbsence.Rd | 16
letsR-2.1/letsR/man/print.PresenceAbsence.Rd | 2
letsR-2.1/letsR/man/print.summary.PresenceAbsence.Rd | 2
letsR-2.1/letsR/man/summary.PresenceAbsence.Rd | 2
letsR-2.1/letsR/man/temp.Rd | 12
letsR-2.1/letsR/tests |only
77 files changed, 2543 insertions(+), 1677 deletions(-)
Title: Efficient Iterator for Permutations and Combinations
Diff between iterpc versions 0.2.6 dated 2014-11-14 and 0.2.7 dated 2015-04-16
Description: It helps in 1) generating permutations and combinations with or without replacement; 2) with distinct items or non-distinct items (multiset); 3) calculating number of combinations or permutations in various situations. All generated sequences are in lexicographical order (AKA, dictionary order). The algorithms to generate permutations and combinations are memory efficient. These iterative algorithms enable users to process all sequences without putting all results in the memory at the same time. The algorithms are written in C/C++ for faster performances.
Author: Randy Lai [aut, cre], Martin Broadhurst [aut]
Maintainer: Randy Lai
DESCRIPTION | 10 +--
MD5 | 28 +++++-----
NAMESPACE | 2
README.md | 2
man/getall.Rd | 3 -
man/getcurrent.Rd | 3 -
man/getlength.Rd | 3 -
man/getnext.Rd | 3 -
man/iterpc.Rd | 3 -
man/multichoose.Rd | 3 -
man/nc_multiset.Rd | 3 -
man/np_multiset.Rd | 3 -
src/RcppExports.cpp | 118 ++++++++++++++++++----------------------------
src/utils/k-permutation.c | 11 +---
src/utils/k-permutation.h | 2
15 files changed, 90 insertions(+), 107 deletions(-)
Title: Mixed FLP and ML Estimation of ETAS Space-Time Point Processes
Diff between etasFLP versions 1.2.0 dated 2014-12-22 and 1.2.1 dated 2015-04-16
Description: Estimation of the components of an ETAS model for earthquake description. Non-parametric background seismicity can be estimated through FLP (Forward Likelihood Predictive), while parametric components are estimated through maximum likelihood. The two estimation steps are alternated until convergence is obtained. For each event the probability of being a background event is estimated and used as a weight for declustering steps. Many options to control the estimation process are present, together with some diagnostic tools. Some descriptive functions for earthquakes catalogs are present; also plot, print, summary, profile methods are defined for main output (objects of class 'etasclass').
Author: Marcello Chiodi [aut, cre],
Giada Adelfio [aut]
Maintainer: Marcello Chiodi
ChangeLog | 8 ++++++++
DESCRIPTION | 13 +++++--------
MD5 | 32 ++++++++++++++++----------------
R/eqcat.R | 2 +-
R/etasclass.R | 1 +
R/kde2dnew.fortran.R | 3 +++
R/plot.etasclass.R | 2 +-
R/plot.profile.etasclass.R | 4 ++--
R/summary.etasclass.R | 6 ++++--
data/californiacatalog.RData |binary
data/italycatalog.RData |binary
man/etasFLP-package.Rd | 17 ++++++++++-------
man/etasclass.Rd | 37 ++++++++++++++++++++-----------------
man/plot.etasclass.Rd | 14 +++++++-------
man/plot.profile.etasclass.Rd | 4 ++--
man/profile.etasclass.Rd | 15 +++++++--------
man/summary.etasclass.Rd | 3 +--
17 files changed, 88 insertions(+), 73 deletions(-)
Title: Biodiversity Assessment Tools
Diff between BAT versions 1.2.1 dated 2015-03-05 and 1.3.0 dated 2015-04-16
Description: Includes algorithms to assess alpha and beta
diversity in all their dimensions (taxon, phylogenetic and functional
diversity), whether communities are completely sampled or not. It allows
performing a number of analyses based on either species identities or
phylogenetic/functional trees depicting species relationships.
Author: Pedro Cardoso, Francois Rigal, Jose Carlos Carvalho
Maintainer: Pedro Cardoso
DESCRIPTION | 10 -
MD5 | 35 ++-
NAMESPACE | 3
R/BAT.R | 428 +++++++++++++++++++++++++++++++++--------------
man/accuracy.Rd | 3
man/alpha.Rd | 2
man/alpha.accum.Rd | 8
man/alpha.estimate.Rd | 2
man/beta.Rd | 10 -
man/beta.accum.Rd | 9
man/beta.multi.Rd | 8
man/contribution.Rd |only
man/dispersion.Rd |only
man/optim.alpha.Rd | 8
man/optim.alpha.stats.Rd | 2
man/optim.beta.Rd | 10 -
man/optim.beta.stats.Rd | 2
man/sim.sample.Rd | 2
man/sim.tree.Rd | 2
man/uniqueness.Rd |only
20 files changed, 370 insertions(+), 174 deletions(-)
Title: 'vcd' Extensions and Additions
Diff between vcdExtra versions 0.6-5 dated 2015-01-02 and 0.6-8 dated 2015-04-16
Description: Provides additional data sets, methods and documentation to complement the 'vcd' package for Visualizing Categorical Data
and the 'gnm' package for Generalized Nonlinear Models.
In particular, 'vcdExtra' extends mosaic, assoc and sieve plots from 'vcd' to handle 'glm()' and 'gnm()' models and
adds a 3D version in 'mosaic3d'. Additionally, methods are provided for comparing and visualizing lists of
'glm' and 'loglm' objects. This package is now a support package for the book, "Discrete Data Analysis with R" by
Michael Friendly and David Meyer.
Author: Michael Friendly [aut, cre], Heather Turner [ctb], Achim Zeileis [ctb], Duncan Murdoch [ctb], David Firth [ctb]
Maintainer: Michael Friendly
vcdExtra-0.6-5/vcdExtra/R/loddsratio.R |only
vcdExtra-0.6-5/vcdExtra/man/loddsratio.Rd |only
vcdExtra-0.6-8/vcdExtra/DESCRIPTION | 25 +-
vcdExtra-0.6-8/vcdExtra/MD5 | 110 +++++-----
vcdExtra-0.6-8/vcdExtra/NAMESPACE | 216 ++++++++++----------
vcdExtra-0.6-8/vcdExtra/NEWS | 17 +
vcdExtra-0.6-8/vcdExtra/R/CMHtest.R | 9
vcdExtra-0.6-8/vcdExtra/R/mosaic3d.R | 2
vcdExtra-0.6-8/vcdExtra/build/vignette.rds |binary
vcdExtra-0.6-8/vcdExtra/data/Abortion.rda |binary
vcdExtra-0.6-8/vcdExtra/data/Accident.RData |binary
vcdExtra-0.6-8/vcdExtra/data/AirCrash.RData |only
vcdExtra-0.6-8/vcdExtra/data/Alligator.RData |binary
vcdExtra-0.6-8/vcdExtra/data/Bartlett.rda |binary
vcdExtra-0.6-8/vcdExtra/data/Caesar.rda |binary
vcdExtra-0.6-8/vcdExtra/data/Cancer.rda |binary
vcdExtra-0.6-8/vcdExtra/data/Cormorants.RData |binary
vcdExtra-0.6-8/vcdExtra/data/CyclingDeaths.RData |binary
vcdExtra-0.6-8/vcdExtra/data/DaytonSurvey.RData |binary
vcdExtra-0.6-8/vcdExtra/data/Depends.RData |binary
vcdExtra-0.6-8/vcdExtra/data/Detergent.rda |binary
vcdExtra-0.6-8/vcdExtra/data/Donner.RData |binary
vcdExtra-0.6-8/vcdExtra/data/Draft1970.RData |binary
vcdExtra-0.6-8/vcdExtra/data/Draft1970table.RData |binary
vcdExtra-0.6-8/vcdExtra/data/Dyke.rda |binary
vcdExtra-0.6-8/vcdExtra/data/Fungicide.rda |binary
vcdExtra-0.6-8/vcdExtra/data/GSS.rda |binary
vcdExtra-0.6-8/vcdExtra/data/Geissler.RData |binary
vcdExtra-0.6-8/vcdExtra/data/Gilby.rda |binary
vcdExtra-0.6-8/vcdExtra/data/HairEyePlace.RData |binary
vcdExtra-0.6-8/vcdExtra/data/Hauser79.RData |binary
vcdExtra-0.6-8/vcdExtra/data/Heart.rda |binary
vcdExtra-0.6-8/vcdExtra/data/Heckman.rda |binary
vcdExtra-0.6-8/vcdExtra/data/Hoyt.rda |binary
vcdExtra-0.6-8/vcdExtra/data/ICU.RData |binary
vcdExtra-0.6-8/vcdExtra/data/JobSat.rda |binary
vcdExtra-0.6-8/vcdExtra/data/Mammograms.RData |binary
vcdExtra-0.6-8/vcdExtra/data/Mental.rda |binary
vcdExtra-0.6-8/vcdExtra/data/Mobility.rda |binary
vcdExtra-0.6-8/vcdExtra/data/PhdPubs.RData |binary
vcdExtra-0.6-8/vcdExtra/data/ShakeWords.RData |binary
vcdExtra-0.6-8/vcdExtra/data/TV.rda |binary
vcdExtra-0.6-8/vcdExtra/data/Titanicp.rda |binary
vcdExtra-0.6-8/vcdExtra/data/Toxaemia.RData |binary
vcdExtra-0.6-8/vcdExtra/data/Vietnam.RData |binary
vcdExtra-0.6-8/vcdExtra/data/Vietnam.rda |binary
vcdExtra-0.6-8/vcdExtra/data/Vote1980.RData |binary
vcdExtra-0.6-8/vcdExtra/data/WorkerSat.RData |only
vcdExtra-0.6-8/vcdExtra/data/Yamaguchi87.RData |binary
vcdExtra-0.6-8/vcdExtra/man/AirCrash.Rd |only
vcdExtra-0.6-8/vcdExtra/man/CMHtest.Rd | 2
vcdExtra-0.6-8/vcdExtra/man/Caesar.Rd | 168 +++++++--------
vcdExtra-0.6-8/vcdExtra/man/Fungicide.Rd | 8
vcdExtra-0.6-8/vcdExtra/man/HairEyePlace.Rd | 2
vcdExtra-0.6-8/vcdExtra/man/Toxaemia.Rd | 2
vcdExtra-0.6-8/vcdExtra/man/Vietnam.Rd | 8
vcdExtra-0.6-8/vcdExtra/man/WorkerSat.Rd |only
vcdExtra-0.6-8/vcdExtra/man/expand.dft.Rd | 2
vcdExtra-0.6-8/vcdExtra/man/vcdExtra-package.Rd | 232 +++++++++++-----------
59 files changed, 416 insertions(+), 387 deletions(-)
Title: Functions Relating to the Smoothing of Numerical Data
Diff between smoother versions 1.0.0.0 dated 2014-09-16 and 1.1 dated 2015-04-16
Description: A collection of methods for smoothing numerical data, commencing with a port of the Matlab gaussian window smoothing function. In addition, several functions typically used in smoothing of financial data are included.
Author: Nicholas Hamilton
Maintainer: Nicholas Hamilton
DESCRIPTION | 16 ++++----
MD5 | 21 ++++++----
NAMESPACE | 7 +++
NEWS | 20 +++++++++-
R/functions.R | 44 ++++++++++++++++++++--
R/onLoad.R |only
R/smoother-package.R | 17 +++++---
R/smth-gaussian.R | 100 +++++++++++++++++++++++++++++++--------------------
R/smth.R | 71 +++++++++++++++---------------------
man/smoother.Rd | 18 +++++----
man/smth.Rd | 59 ++++++++++++++----------------
man/smth.gaussian.Rd |only
man/smth.options.Rd |only
13 files changed, 226 insertions(+), 147 deletions(-)
Title: Simulate Bipartite Graphs with Fixed Marginals Through
Sequential Importance Sampling
Diff between networksis versions 2.1-2 dated 2013-05-01 and 2.1-3 dated 2015-04-16
Description: Tools to simulate bipartite networks/graphs with the
degrees of the nodes fixed and specified. 'networksis' is part
of the 'statnet' suite of packages for network analysis.
Author: Ryan Admiraal
Maintainer: Ryan Admiraal
networksis-2.1-2/networksis/R/simulate.network.R |only
networksis-2.1-2/networksis/man/networksis-internal.Rd |only
networksis-2.1-3/networksis/DESCRIPTION | 17 ++++----
networksis-2.1-3/networksis/MD5 | 16 +++-----
networksis-2.1-3/networksis/NAMESPACE | 11 +++--
networksis-2.1-3/networksis/R/simulate.sisnetwork.R | 11 ++++-
networksis-2.1-3/networksis/R/zzz.R | 34 +++++++----------
networksis-2.1-3/networksis/inst/CITATION | 30 ++++++++-------
networksis-2.1-3/networksis/man/networksis-package.Rd | 8 ++--
networksis-2.1-3/networksis/man/simulate.sisnetwork.Rd | 10 ++---
10 files changed, 72 insertions(+), 65 deletions(-)
Title: Fitting the copCAR Regression Model for Discrete Areal Data
Diff between copCAR versions 1.0 dated 2014-09-07 and 1.0-1 dated 2015-04-16
Description: Provides tools for fitting the copCAR regression model for discrete areal data. Three types of estimation are supported: continuous extension, composite marginal likelihood, and distributional transform.
Author: Emily Goren
Maintainer: John Hughes
DESCRIPTION | 12 ++++++------
MD5 | 8 ++++----
R/zzz.R | 2 +-
inst/CITATION | 5 ++---
man/rcopCAR.Rd | 4 ++--
5 files changed, 15 insertions(+), 16 deletions(-)
Title: Package for Community Ecology and Suitability Analysis
Diff between BiodiversityR versions 2.5-1 dated 2014-11-23 and 2.5-2 dated 2015-04-16
Description: Graphical User Interface (via the R-Commander) and utility functions (often based on the vegan package) for statistical analysis of biodiversity and ecological communities, including species accumulation curves, diversity indices, Renyi profiles, GLMs for analysis of species abundance and presence-absence, distance matrices, Mantel tests, and cluster, constrained and unconstrained ordination analysis. A book on biodiversity and community ecology analysis is available for free download from the website. In 2012, methods for (ensemble) suitability modelling and mapping were expanded in the package.
Author: Roeland Kindt
Maintainer: Roeland Kindt
BiodiversityR-2.5-1/BiodiversityR/R/bioenv.numeric.R |only
BiodiversityR-2.5-1/BiodiversityR/R/bioenv.test.R |only
BiodiversityR-2.5-1/BiodiversityR/R/ensemble.category.simplify.R |only
BiodiversityR-2.5-2/BiodiversityR/DESCRIPTION | 12
BiodiversityR-2.5-2/BiodiversityR/MD5 | 78 ++--
BiodiversityR-2.5-2/BiodiversityR/NAMESPACE | 6
BiodiversityR-2.5-2/BiodiversityR/R/CAPdiscrim.R | 2
BiodiversityR-2.5-2/BiodiversityR/R/NMSrandom.R | 2
BiodiversityR-2.5-2/BiodiversityR/R/balanced.specaccum.R | 4
BiodiversityR-2.5-2/BiodiversityR/R/distdisplayed.R | 2
BiodiversityR-2.5-2/BiodiversityR/R/diversityresult.R | 2
BiodiversityR-2.5-2/BiodiversityR/R/ensemble.accepted.categories.R | 4
BiodiversityR-2.5-2/BiodiversityR/R/ensemble.analogue.R | 4
BiodiversityR-2.5-2/BiodiversityR/R/ensemble.batch.R | 4
BiodiversityR-2.5-2/BiodiversityR/R/ensemble.drop1.R | 2
BiodiversityR-2.5-2/BiodiversityR/R/ensemble.dummy.variables.R | 4
BiodiversityR-2.5-2/BiodiversityR/R/ensemble.formulae.R | 4
BiodiversityR-2.5-2/BiodiversityR/R/ensemble.mean.R | 25 +
BiodiversityR-2.5-2/BiodiversityR/R/ensemble.raster.R | 75 ++--
BiodiversityR-2.5-2/BiodiversityR/R/ensemble.simplified.categories.R | 6
BiodiversityR-2.5-2/BiodiversityR/R/ensemble.strategy.R | 2
BiodiversityR-2.5-2/BiodiversityR/R/ensemble.test.R | 169 +++++-----
BiodiversityR-2.5-2/BiodiversityR/R/ensemble.test.gbm.R | 4
BiodiversityR-2.5-2/BiodiversityR/R/ensemble.test.nnet.R | 4
BiodiversityR-2.5-2/BiodiversityR/R/ensemble.test.splits.R | 2
BiodiversityR-2.5-2/BiodiversityR/R/evaluation.strip.data.R | 59 +--
BiodiversityR-2.5-2/BiodiversityR/R/import.from.Access.R | 4
BiodiversityR-2.5-2/BiodiversityR/R/import.from.Excel.R | 4
BiodiversityR-2.5-2/BiodiversityR/R/importancevalue.R | 4
BiodiversityR-2.5-2/BiodiversityR/R/nested.anova.dbrda.R | 4
BiodiversityR-2.5-2/BiodiversityR/R/nested.npmanova.R | 4
BiodiversityR-2.5-2/BiodiversityR/R/ordicoeno.R | 2
BiodiversityR-2.5-2/BiodiversityR/R/prepare.bioenv.R |only
BiodiversityR-2.5-2/BiodiversityR/R/removeNAcomm.R | 7
BiodiversityR-2.5-2/BiodiversityR/R/residualssurface.R | 6
BiodiversityR-2.5-2/BiodiversityR/R/spatialsample.R | 2
BiodiversityR-2.5-2/BiodiversityR/data/BCI.env.txt.gz |binary
BiodiversityR-2.5-2/BiodiversityR/inst/etc/BiodiversityGUI.R | 16
BiodiversityR-2.5-2/BiodiversityR/man/BCI.env.Rd | 35 --
BiodiversityR-2.5-2/BiodiversityR/man/dist.eval.Rd | 38 +-
BiodiversityR-2.5-2/BiodiversityR/man/diversityresult.Rd | 2
BiodiversityR-2.5-2/BiodiversityR/man/ensemble.raster.Rd | 2
42 files changed, 311 insertions(+), 295 deletions(-)