Title: Structural Equation Modelling in R with 'OpenMx'
Description: Create, run, and report structural equation and twin models
quickly. If you're just starting out, try typing '?umx'.
Author: Timothy C Bates [aut, cre]
Maintainer: Timothy C Bates <timothy.c.bates@gmail.com>
Diff between umx versions 1.4.9 dated 2016-12-05 and 1.5.0 dated 2017-01-12
umx-1.4.9/umx/R/mxSE.R |only umx-1.4.9/umx/man/mxSE.Rd |only umx-1.5.0/umx/DESCRIPTION | 12 +- umx-1.5.0/umx/MD5 | 90 +++++++-------- umx-1.5.0/umx/NAMESPACE | 1 umx-1.5.0/umx/NEWS | 10 + umx-1.5.0/umx/R/build_run_modify.r | 117 +++++++++----------- umx-1.5.0/umx/R/deprecated.r | 2 umx-1.5.0/umx/R/fit_and_reporting.r | 132 ++++++++++++----------- umx-1.5.0/umx/R/misc_and_utility.r | 39 +++--- umx-1.5.0/umx/R/model_builders.r | 48 ++++++-- umx-1.5.0/umx/R/xmu.r | 8 - umx-1.5.0/umx/README.md | 28 ++-- umx-1.5.0/umx/man/RMSEA.Rd | 2 umx-1.5.0/umx/man/extractAIC.MxModel.Rd | 2 umx-1.5.0/umx/man/loadings.MxModel.Rd | 11 - umx-1.5.0/umx/man/logLik.Rd | 2 umx-1.5.0/umx/man/plot.MxModel.Rd | 8 - umx-1.5.0/umx/man/umx-deprecated.Rd | 2 umx-1.5.0/umx/man/umx.Rd | 9 - umx-1.5.0/umx/man/umxACE.Rd | 22 --- umx-1.5.0/umx/man/umxAPA.Rd | 19 ++- umx-1.5.0/umx/man/umxCI_boot.Rd | 4 umx-1.5.0/umx/man/umxEFA.Rd | 21 ++- umx-1.5.0/umx/man/umxExpCov.Rd | 4 umx-1.5.0/umx/man/umxExpMeans.Rd | 2 umx-1.5.0/umx/man/umxFitIndices.Rd | 9 + umx-1.5.0/umx/man/umxGetParameters.Rd | 9 - umx-1.5.0/umx/man/umxPlotACEcov.Rd | 2 umx-1.5.0/umx/man/umxPlotCP.Rd | 2 umx-1.5.0/umx/man/umxPlotIP.Rd | 2 umx-1.5.0/umx/man/umxSummary.Rd | 3 umx-1.5.0/umx/man/umx_APA_pval.Rd | 9 - umx-1.5.0/umx/man/umx_add_variances.Rd | 2 umx-1.5.0/umx/man/umx_aggregate.Rd | 21 ++- umx-1.5.0/umx/man/umx_fix_first_loadings.Rd | 2 umx-1.5.0/umx/man/umx_fix_latents.Rd | 2 umx-1.5.0/umx/man/umx_is_endogenous.Rd | 6 - umx-1.5.0/umx/man/umx_is_exogenous.Rd | 6 - umx-1.5.0/umx/man/umx_make_bin_cont_pair_data.Rd | 2 umx-1.5.0/umx/man/umx_msg.Rd | 2 umx-1.5.0/umx/man/umx_print.Rd | 9 - umx-1.5.0/umx/man/umx_reorder.Rd | 5 umx-1.5.0/umx/man/umx_set_checkpoint.Rd | 2 umx-1.5.0/umx/man/umx_show.Rd | 9 - umx-1.5.0/umx/man/umx_time.Rd | 9 - umx-1.5.0/umx/man/umx_trim.Rd | 2 47 files changed, 372 insertions(+), 338 deletions(-)
Title: Installing, Managing, and Switching Between Distinct Sets of
Installed Packages
Description: Provides an abstraction for managing, installing,
and switching between sets of installed R packages. This allows users to
maintain multiple package libraries simultaneously, e.g. to maintain
strict, package-version-specific reproducibility of many analyses, or
work within a development/production release paradigm. Introduces a
generalized package installation process which supports multiple repository
and non-repository sources and tracks package provenance.
Author: Gabriel Becker[aut, cre]
Maintainer: Gabriel Becker <becker.gabriel@gene.com>
Diff between switchr versions 0.11.0 dated 2016-10-24 and 0.11.2 dated 2017-01-12
DESCRIPTION | 10 +-- MD5 | 107 +++++++++++++++++----------------- NAMESPACE | 2 R/AllClasses.R | 8 ++ R/Install.R | 19 +++--- R/SwitchrParam.R | 2 R/Utilities.R | 22 +++---- R/accessors.R | 56 ++++++++--------- R/allGenerics.R | 2 R/biocversion.R | 13 ++++ R/cmethods.R | 12 +-- R/conditionalCode.R | 7 -- R/crandbtmp.R | 2 R/findCtx.R | 12 ++- R/flushSession.R | 15 +++- R/makeBiocVersions.R | 30 ++++----- R/manifest.R | 1 R/manifestFromLib.R | 40 ++++++------ R/methods.R | 138 ++++++++++++++++++++++++++------------------ R/removeLibrary.R | 1 R/retrievePkgVersion.R | 5 + R/zzz.R |only build/vignette.rds |binary inst/doc/switchrvign.pdf |binary inst/testlimma.R |only inst/xtable.R |only man/BiocDevel.Rd | 2 man/BiocRelease.Rd | 2 man/BiocVers.Rd | 10 --- man/LibraryProfile-class.Rd | 6 + man/PkgSource-class.Rd | 6 - man/SwitchrParam.Rd | 10 +-- man/addPkg.Rd | 2 man/branch.Rd | 2 man/cmethods.Rd | 10 +-- man/cranPkgVersManifest.Rd | 7 -- man/dl_method.Rd | 2 man/flushSession.Rd | 4 - man/gotoVersCommit.Rd | 4 - man/libManifest.Rd | 5 - man/location-methods.Rd | 6 - man/logfun.Rd | 2 man/makeBiocSVNURL.Rd | 3 man/makeManifest.Rd | 4 - man/makePkgDir.Rd | 6 + man/packages.Rd | 2 man/pkgname.Rd | 2 man/rVersionManifest.Rd | 5 - man/removeLib.Rd | 4 - man/sh_init.Rd | 2 man/subdir.Rd | 2 man/switchDeps.Rd | 4 - man/switchTo.Rd | 24 ++++--- man/switchrDontUnload.Rd | 5 - man/switchrNoUnload.Rd | 2 tests/winpath.R | 15 +++- 56 files changed, 360 insertions(+), 304 deletions(-)
Title: Prepare Reproducible Example Code for Sharing
Description: Convenience wrapper that uses the 'rmarkdown' package to render
small snippets of code to target formats that include both code and output.
The goal is to encourage the sharing of small, reproducible, and runnable
examples on code-oriented websites, such as <http://stackoverflow.com> and
<https://github.com>, or in email. 'reprex' also extracts clean, runnable R
code from various common formats, such as copy/paste from an R session.
Author: Jennifer Bryan [aut, cre],
David Robinson [aut]
Maintainer: Jennifer Bryan <jenny.f.bryan@gmail.com>
Diff between reprex versions 0.1.0 dated 2017-01-10 and 0.1.1 dated 2017-01-12
DESCRIPTION | 7 ++++--- MD5 | 14 +++++++------- NEWS.md | 8 ++++++-- R/reprex-addin.R | 4 ++-- R/reprex.R | 2 +- README.md | 10 +++++++++- tests/testthat/test-input.R | 2 +- tests/testthat/test-outfiles.R | 2 +- 8 files changed, 31 insertions(+), 18 deletions(-)
Title: PC-Axis with R
Description: Provides a set of functions for reading and writing PC-Axis files, used by different statistical organizations around the globe for data dissemination.
Author: Carlos J. Gil Bellosta [cre, aut],
Francisco J. Viciana [aut],
Oscar Perpinan Lamigueiro [aut],
Emilio Torres Manzanera [ctb]
Maintainer: Carlos J. Gil Bellosta <cgb@datanalytics.com>
Diff between pxR versions 0.40.0 dated 2014-04-28 and 0.42.2 dated 2017-01-12
pxR-0.40.0/pxR/man/as.px.array.Rd |only pxR-0.42.2/pxR/DESCRIPTION | 29 +++--- pxR-0.42.2/pxR/MD5 | 26 +++-- pxR-0.42.2/pxR/NAMESPACE | 31 +++--- pxR-0.42.2/pxR/R/as.array.px.R | 57 ++++++------ pxR-0.42.2/pxR/R/as.data.frame.px.R | 13 -- pxR-0.42.2/pxR/R/as.px.array.R | 71 +++++---------- pxR-0.42.2/pxR/R/as.px.data.frame.R |only pxR-0.42.2/pxR/R/read.px.R | 71 ++++++++++++--- pxR-0.42.2/pxR/R/write.px.R | 161 ++++++++++++++++++++++++++++++------ pxR-0.42.2/pxR/README.md |only pxR-0.42.2/pxR/man/as.px.Rd |only pxR-0.42.2/pxR/man/read.px.Rd | 2 pxR-0.42.2/pxR/man/write.px.Rd | 31 ++++-- pxR-0.42.2/pxR/tests/example6.px |only pxR-0.42.2/pxR/tests/example7.px |only pxR-0.42.2/pxR/tests/test.R | 60 +++++++++---- 17 files changed, 355 insertions(+), 197 deletions(-)
Title: The IsoSpec Algorithm
Description: IsoSpec is a fine structure calculator used for obtaining the most
probable masses of a chemical compound given the frequencies of the composing
isotopes and their masses. It finds the smallest set of isotopologues with
a given probability. The probability is assumed to be that of the product of
multinomial distributions, each corresponding to one particular element and
parametrized by the frequencies of finding these elements in nature. These
numbers are supplied by IUPAC - the International Union of Pure and Applied
Chemistry.
Author: Mateusz Krzysztof Łącki and Michał Startek
Maintainer: Matteo Lacki <matteo.lacki@gmail.com>
Diff between IsoSpecR versions 1.0.1 dated 2016-09-01 and 1.0.3 dated 2017-01-12
DESCRIPTION | 10 +-- MD5 | 20 +++---- R/IsoSpecR.R | 85 +++++++++++--------------------- R/RcppExports.R | 22 +------- man/IsoSpecify.Rd | 21 ++++---- src/RcppExports.cpp | 22 ++++---- src/Rinterface.cpp | 131 ++++++++++++++++++++++++++++---------------------- src/cwrapper.cpp | 76 ++++------------------------- src/cwrapper.h | 30 +---------- src/isoSpec++.cpp | 136 +++++++++++++++++++++++----------------------------- src/isoSpec++.h | 25 ++++++--- 11 files changed, 240 insertions(+), 338 deletions(-)
Title: Learn Data Science Through the "Data Science Live Book"
Description: Around 10% of almost any predictive modeling project is spent in predictive modeling, 'funModeling' and the book <http://livebook.datascienceheroes.com/> are intended to cover remaining 90%: data preparation, profiling, selecting best variables 'dataViz', assessing model performance and other functions.
Author: Pablo Casas
Maintainer: Pablo Casas <pabloc@datascienceheroes.com>
Diff between funModeling versions 1.5 dated 2016-11-12 and 1.6 dated 2017-01-12
DESCRIPTION | 8 ++-- MD5 | 23 ++++++++----- NAMESPACE | 7 ++++ R/bayesian_plot.R |only R/common_lib.R | 11 ++++++ R/cross_plot.R | 8 ++-- R/data.R | 12 +++++++ R/data_preparation.R |only R/numbers.R | 63 +++++++++++++++++++++++++++---------- R/target_profiling.R | 84 ++++++++++++++++++++++++++++++++++++++++++++++++-- data/data_country.rda |only man/auto_grouping.Rd |only man/bayesian_plot.Rd |only man/categ_analysis.Rd |only man/data_country.Rd |only man/plotar.Rd | 3 + 16 files changed, 183 insertions(+), 36 deletions(-)
Title: Fit Hydraulic Vulnerability Curves
Description: Fits the Weibull equation to percent loss conductivity (plc) curves as a function of plant water potential, computes SE of parameter estimates and location of curve with bootstrap or parametric methods, and provides convenient plotting methods.
Author: Remko Duursma
Maintainer: Remko Duursma <remkoduursma@gmail.com>
Diff between fitplc versions 1.0 dated 2016-10-19 and 1.1-3 dated 2017-01-12
fitplc-1.0/fitplc/R/fweibull.R |only fitplc-1.0/fitplc/README.md |only fitplc-1.1-3/fitplc/DESCRIPTION | 8 fitplc-1.1-3/fitplc/MD5 | 37 +- fitplc-1.1-3/fitplc/NAMESPACE | 8 fitplc-1.1-3/fitplc/R/bootfit.R | 2 fitplc-1.1-3/fitplc/R/coef.manyplcfit.R | 10 fitplc-1.1-3/fitplc/R/coef.plcfit.R | 20 - fitplc-1.1-3/fitplc/R/fitcond.R | 6 fitplc-1.1-3/fitplc/R/fitplc.R | 487 +++++++++++++++++++++--------- fitplc-1.1-3/fitplc/R/getPx.R | 83 +++-- fitplc-1.1-3/fitplc/R/plot.plcfit.R | 163 ++++++---- fitplc-1.1-3/fitplc/R/predict_nls.R | 7 fitplc-1.1-3/fitplc/R/print.manyplcfit.R | 2 fitplc-1.1-3/fitplc/R/print.plcfit.R | 2 fitplc-1.1-3/fitplc/R/utils.R |only fitplc-1.1-3/fitplc/R/weibull_sigmoidal.R |only fitplc-1.1-3/fitplc/man/fitplc.Rd | 67 ++-- fitplc-1.1-3/fitplc/man/fsigmoidal.Rd |only fitplc-1.1-3/fitplc/man/fweibull.Rd | 10 fitplc-1.1-3/fitplc/man/getPx.Rd | 29 - fitplc-1.1-3/fitplc/man/plot.plcfit.Rd | 32 + 22 files changed, 643 insertions(+), 330 deletions(-)
Title: Bayesian Estimation of the GARCH(1,1) Model with Student-t
Innovations
Description: Provides the bayesGARCH() function which performs the
Bayesian estimation of the GARCH(1,1) model with Student's t innovations.
Author: David Ardia [aut, cre]
Maintainer: David Ardia <david.ardia.ch@gmail.com>
Diff between bayesGARCH versions 2.0.2 dated 2015-12-15 and 2.1.2 dated 2017-01-12
COPYING | 680 +++++++++++++++++++++++++++--------------------------- DESCRIPTION | 15 - MD5 | 18 - NAMESPACE | 3 NEWS | 116 ++++----- README.md |only THANKS | 10 build |only inst/CITATION | 2 inst/COPYRIGHTS | 20 - man/bayesGARCH.Rd | 8 11 files changed, 441 insertions(+), 431 deletions(-)
Title: Exploring Genomic Relations for Enhanced Interpretation Through
Enrichment, Similarity, Network and Annotation Analysis
Description: The central goal of XGR is to provide a data interpretation system. It is designed to make a user-defined gene or SNP list (or genomic regions) more interpretable by comprehensively utilising ontology annotations and interaction networks to reveal relationships and enhance opportunities for biological discovery. XGR is unique in supporting a broad range of ontologies (including knowledge of biological and molecular functions, pathways, diseases and phenotypes - in both human and mouse) and different types of networks (including functional, physical and pathway interactions). There are two core functionalities of XGR. The first is to provide basic infrastructures for easy access to built-in ontologies and networks. The second is to support data interpretations via 1) enrichment analysis using either built-in or custom ontologies, 2) similarity analysis for calculating semantic similarity between genes (or SNPs) based on their ontology annotation profiles, 3) network analysis for identification of gene networks given a query list of (significant) genes, SNPs or genomic regions, and 4) annotation analysis for interpreting genomic regions using co-localised functional genomic annotations (such as open chromatin, epigenetic marks, TF binding sites and genomic segments) and using nearby gene annotations (by ontologies). Together with its web app, XGR aims to provide a user-friendly tool for exploring genomic relations at the gene, SNP and genomic region level.
Author: Hai Fang, Bogdan Knezevic, Katie L Burnham, Julian C Knight
Maintainer: Hai Fang <hfang@well.ox.ac.uk>
Diff between XGR versions 1.0.6 dated 2016-12-13 and 1.0.7 dated 2017-01-12
DESCRIPTION | 15 +++--- MD5 | 39 +++++++++-------- NAMESPACE | 1 R/xCheckParallel.r |only R/xDAGsim.r | 2 R/xGR2GeneScores.r | 90 +++++++++++++++++++++++++---------------- R/xGR2nGenes.r | 46 +++++++++++++++----- R/xGRviaGenomicAnno.r | 10 +++- R/xGRviaGenomicAnnoAdv.r | 4 - R/xSM2DF.r | 47 +++++++++++++++------ R/xSNP2GeneScores.r | 28 ++++-------- R/xSNP2nGenes.r | 2 R/xSocialiser.r | 2 R/xVisNet.r | 8 +++ inst/CITATION | 2 inst/NEWS | 10 ++++ inst/xCheckParallel.html |only inst/xGRviaGenomicAnno.html | 2 inst/xGRviaGenomicAnnoAdv.html | 2 man/xCheckParallel.Rd |only man/xGRviaGenomicAnno.Rd | 2 man/xGRviaGenomicAnnoAdv.Rd | 2 22 files changed, 197 insertions(+), 117 deletions(-)
Title: Infrastructure for Running and Cycling Data from GPS-Enabled
Tracking Devices
Description: The aim of this package is to provide infrastructure for handling running and cycling
data from GPS-enabled tracking devices. After extraction and appropriate
manipulation of the training or competition attributes, the data are placed
into session-based and unit-aware data objects of class trackeRdata (S3 class). The
information in the resulting data objects can then be visualised, summarised,
and analysed through corresponding flexible and extensible methods.
Author: Hannah Frick [aut, cre],
Ioannis Kosmidis [aut]
Maintainer: Hannah Frick <h.frick@ucl.ac.uk>
Diff between trackeR versions 0.0.4 dated 2016-10-20 and 0.0.5 dated 2017-01-12
DESCRIPTION | 8 ++++---- MD5 | 33 +++++++++++++++++---------------- NEWS | 9 +++++++++ R/trackeRdata_plot.R | 6 +++--- R/trackeRdata_zones.R | 20 +++++++++++--------- build/vignette.rds |binary data/run.rda |binary data/runs.rda |binary inst/doc/TourDetrackeR.Rmd | 8 ++++---- inst/doc/TourDetrackeR.html | 18 +++++++++--------- inst/doc/trackeR.R | 12 ++++++------ inst/doc/trackeR.Rnw | 31 ++++++++++++++++--------------- inst/doc/trackeR.pdf |binary man/plotRoute.Rd | 6 +++--- vignettes/TourDetrackeR.Rmd | 8 ++++---- vignettes/TourDetrackeR.md |only vignettes/trackeR.Rnw | 31 ++++++++++++++++--------------- vignettes/trackeR.bib | 10 +++++----- 18 files changed, 107 insertions(+), 93 deletions(-)
Title: SBML Integration in Package 'Sybil'
Description: 'SBML' (Systems Biology Markup Language) with FBC (Flux Balance Constraints) integration in 'sybil'. Many constraint based metabolic models are published in 'SBML' format ('*.xml'). Herewith is the ability to read, write, and check 'SBML' files in 'sybil' provided.
Author: C. Jonathan Fritzemeier [cre, ctb],
Gabriel Gelius-Dietrich [aut, ctb],
Deya Alzoubi [ctb],
Ardalan Habil [ctb]
Maintainer: C. Jonathan Fritzemeier <clausjonathan.fritzemeier@uni-duesseldorf.de>
Diff between sybilSBML versions 2.0.11 dated 2016-06-06 and 3.0.1 dated 2017-01-12
DESCRIPTION | 16 MD5 | 28 NAMESPACE | 6 R/readSBMLmod.R | 202 ++- R/sybilSBML.R | 855 ++++++++---- build/vignette.rds |binary configure | 198 ++ configure.ac | 34 inst/NEWS.Rd | 19 inst/doc/sybilSBML.pdf |binary man/getSBMLFbcversion.Rd |only man/getSBMLmodAnnotation.Rd |only man/getSBMLmodNotes.Rd |only man/writeSBML.Rd |only src/init.c | 6 src/sybilSBML.c | 2943 +++++++++++++++++++++++++++++++------------- src/sybilSBML.h | 12 17 files changed, 3131 insertions(+), 1188 deletions(-)
Title: Visual Exploration of Protein Alignments Resulting from Multiple
Substitution Matrices
Description: Substitution matrices are important parameters in protein alignment algorithms. These matrices represent the likelihood that an amino acid will be substituted for another during mutation. This tool allows users to apply predefined and custom matrices and then explore the resulting alignments with interactive visualizations. 'SubVis' requires the availability of a web browser.
Author: Scott Barlowe <sabarlowe@email.wcu.edu>
Maintainer: Scott Barlowe <sabarlowe@email.wcu.edu>
Diff between SubVis versions 2.0.0 dated 2017-01-06 and 2.0.1 dated 2017-01-12
SubVis-2.0.0/SubVis/inst/extdata/Example_FASTA_files/tempPatt.fasta |only SubVis-2.0.0/SubVis/inst/extdata/Example_FASTA_files/tempSubj.fasta |only SubVis-2.0.0/SubVis/inst/extdata/Example_custom_matrix/disorder.txt |only SubVis-2.0.0/SubVis/inst/extdata/Example_custom_matrix/falcNuc.txt |only SubVis-2.0.1/SubVis/DESCRIPTION | 8 SubVis-2.0.1/SubVis/MD5 | 16 SubVis-2.0.1/SubVis/inst/SubVisApp/ui.R | 2 SubVis-2.0.1/SubVis/inst/doc/SubVis.Rmd | 228 ++++----- SubVis-2.0.1/SubVis/inst/doc/SubVis.html | 241 +++++----- SubVis-2.0.1/SubVis/inst/extdata/Example_custom_matrix/disorder_mat.txt |only SubVis-2.0.1/SubVis/inst/extdata/Example_custom_matrix/masterFile_disorder.txt |only SubVis-2.0.1/SubVis/vignettes/SubVis.Rmd | 228 ++++----- 12 files changed, 369 insertions(+), 354 deletions(-)
Title: Access NBN Data
Description: Access to data held by the National Biodiversity Network (NBN,
www.nbn.org.uk). The NBN acts as a data warehouse for biological records data in
the UK and is the UK node of GBIF (Global Biodiversity Information Facility). In
this package NBN data is accessed via its web-services.
Author: Tom August [aut, cre],
Stuart Ball [aut]
Maintainer: Tom August <tomaug@ceh.ac.uk>
Diff between rnbn versions 1.0.3 dated 2014-12-12 and 1.1.2 dated 2017-01-12
rnbn-1.0.3/rnbn/R/dataProviders.r |only rnbn-1.0.3/rnbn/R/datasetTaxa.r |only rnbn-1.0.3/rnbn/R/getTVKQuery.r |only rnbn-1.0.3/rnbn/R/getVCid.r |only rnbn-1.0.3/rnbn/R/gr2gps_latlon.r |only rnbn-1.0.3/rnbn/R/nbnlogin.r |only rnbn-1.0.3/rnbn/inst/tests |only rnbn-1.1.2/rnbn/DESCRIPTION | 22 rnbn-1.1.2/rnbn/MD5 | 121 ++-- rnbn-1.1.2/rnbn/NAMESPACE | 7 rnbn-1.1.2/rnbn/R/createWKT.R |only rnbn-1.1.2/rnbn/R/dataProviders.R |only rnbn-1.1.2/rnbn/R/datasetTaxa.R |only rnbn-1.1.2/rnbn/R/getFeature.R | 5 rnbn-1.1.2/rnbn/R/getGroupSpeciesTVKs.R | 7 rnbn-1.1.2/rnbn/R/getOccurrences.R | 36 + rnbn-1.1.2/rnbn/R/getTVKQuery.R |only rnbn-1.1.2/rnbn/R/getTaxonomy.R | 7 rnbn-1.1.2/rnbn/R/getVCid.R |only rnbn-1.1.2/rnbn/R/gr2gps_latlon.R |only rnbn-1.1.2/rnbn/R/listDatasets.R | 60 +- rnbn-1.1.2/rnbn/R/listGroups.R | 7 rnbn-1.1.2/rnbn/R/listOrganisations.R | 7 rnbn-1.1.2/rnbn/R/listVCs.R | 7 rnbn-1.1.2/rnbn/R/makenbnurl.R | 13 rnbn-1.1.2/rnbn/R/nbnlogin.R |only rnbn-1.1.2/rnbn/R/onAttach_information.R |only rnbn-1.1.2/rnbn/R/runnbnurl.R | 15 rnbn-1.1.2/rnbn/build/vignette.rds |binary rnbn-1.1.2/rnbn/inst/doc/rnbn_vignette.Rmd | 168 ++++-- rnbn-1.1.2/rnbn/inst/doc/rnbn_vignette.html | 782 ++++++++++++---------------- rnbn-1.1.2/rnbn/man/createWKT.Rd |only rnbn-1.1.2/rnbn/man/dataProviders.Rd | 10 rnbn-1.1.2/rnbn/man/datasetTaxa.Rd | 10 rnbn-1.1.2/rnbn/man/datePart.Rd | 20 rnbn-1.1.2/rnbn/man/getFeature.Rd | 10 rnbn-1.1.2/rnbn/man/getGroupSpeciesTVKs.Rd | 12 rnbn-1.1.2/rnbn/man/getOccurrences.Rd | 38 - rnbn-1.1.2/rnbn/man/getTVKQuery.Rd | 14 rnbn-1.1.2/rnbn/man/getTaxonomy.Rd | 11 rnbn-1.1.2/rnbn/man/gr2gps_latlon.Rd | 4 rnbn-1.1.2/rnbn/man/gridCoords.Rd | 4 rnbn-1.1.2/rnbn/man/gridRef.Rd | 8 rnbn-1.1.2/rnbn/man/listDatasets.Rd | 13 rnbn-1.1.2/rnbn/man/listGroups.Rd | 10 rnbn-1.1.2/rnbn/man/listOrganisations.Rd | 12 rnbn-1.1.2/rnbn/man/listVCs.Rd | 10 rnbn-1.1.2/rnbn/man/makenbnurl.Rd | 26 rnbn-1.1.2/rnbn/man/nbnLogin.Rd | 3 rnbn-1.1.2/rnbn/man/rnbn.Rd | 2 rnbn-1.1.2/rnbn/man/runnbnurl.Rd | 24 rnbn-1.1.2/rnbn/tests |only rnbn-1.1.2/rnbn/vignettes/rnbn_vignette.Rmd | 168 ++++-- rnbn-1.1.2/rnbn/vignettes/rnbn_vignette.md |only 54 files changed, 952 insertions(+), 721 deletions(-)
Title: Post-Processing of the Markov Chain Simulated by ChronoModel or
Oxcal
Description: Provides a list of functions for the statistical analysis and the post-processing of the Markov Chains simulated by ChronoModel (see <http://www.chronomodel.fr> for more information). ChronoModel is a friendly software to construct a chronological model in a Bayesian framework. Its output is a sampled Markov chain from the posterior distribution of dates component the chronology. The functions can also be applied to the analyse of mcmc output generated by Oxcal software.
Author: Anne Philippe and Marie-Anne Vibet
Maintainer: Anne Philippe <anne.philippe@univ-nantes.fr>
Diff between RChronoModel versions 0.3 dated 2016-10-04 and 0.4 dated 2017-01-12
DESCRIPTION | 13 - MD5 | 31 +-- NAMESPACE | 1 R/prog.R | 394 ++++++++++++++++++++++++------------------- man/CreateMinMaxGroup.Rd |only man/MultiPhasePlot.Rd | 13 - man/MultiPhaseTimeRange.Rd | 14 - man/MultiPhasesGap.Rd | 15 - man/MultiPhasesTransition.Rd | 15 - man/MultiSuccessionPlot.Rd | 14 - man/PhaseDurationPlot.Rd | 10 - man/PhasePlot.Rd | 13 - man/PhaseStatistics.Rd | 17 - man/PhaseTimeRange.Rd | 12 - man/PhasesGap.Rd | 15 - man/PhasesTransition.Rd | 9 man/SuccessionPlot.Rd | 25 +- 17 files changed, 333 insertions(+), 278 deletions(-)
Title: Fast and Exact Algorithms for Computing Phylogenetic
Biodiversity Measures
Description: Given a phylogenetic tree T and an assemblage S of species represented as
a subset of tips in T, we want to compute a measure of the diversity
of the species in S with respect to T. The current package offers
efficient algorithms that can process large phylogenetic data for several such measures.
Most importantly, the package includes algorithms for computing
efficiently the standardized versions of phylogenetic measures and their p-values, which are
essential for null model comparisons. Among other functions,
the package provides efficient computation of richness-standardized versions
for indices such as the net relatedness index (NRI),
nearest taxon index (NTI), phylogenetic
diversity index (PDI), and the corresponding indices of two-sample measures.
The package also introduces a new
single-sample measure, the Core Ancestor Cost (CAC); the package provides
functions for computing the value and the standardised index of the CAC and,
more than that, there is an extra function available that can compute exactly
any statistical moment of the measure. The package supports computations
under different null models, including abundance-weighted models.
Author: Constantinos Tsirogiannis [aut, cre], Brody Sandel [aut]
Maintainer: Constantinos Tsirogiannis <tsirogiannis.c@gmail.com>
Diff between PhyloMeasures versions 1.1 dated 2015-04-07 and 2.0 dated 2017-01-12
DESCRIPTION | 39 MD5 | 143 NAMESPACE | 9 R/PhyloMeasures.R | 1193 ++++ man/PhyloMeasures-package.Rd | 50 man/cac.moments.Rd | 43 man/cac.pvalues.Rd |only man/cac.query.Rd | 45 man/cbl.moments.Rd | 5 man/cbl.query.Rd | 16 man/cd.moments.Rd | 5 man/cd.query.Rd | 16 man/cdnt.averaged.query.Rd | 2 man/cdnt.directed.query.Rd | 2 man/cdnt.query.Rd | 2 man/mntd.moments.Rd | 47 man/mntd.pvalues.Rd |only man/mntd.query.Rd | 58 man/mpd.moments.Rd | 42 man/mpd.pvalues.Rd |only man/mpd.query.Rd | 57 man/pd.moments.Rd | 37 man/pd.pvalues.Rd |only man/pd.query.Rd | 51 man/phylosor.query.Rd | 2 man/unifrac.query.Rd | 2 src/Exception_related_types.h | 2 src/Exception_related_types/Exception_functor.h | 2 src/Exception_related_types/Exception_type.h | 2 src/Incremental_Monte_Carlo_types |only src/Measures/Common_branch_length.h | 39 src/Measures/Common_branch_length_impl.h | 2 src/Measures/Community_distance.h | 10 src/Measures/Community_distance_impl.h | 2 src/Measures/Community_distance_nearest_taxon.h | 12 src/Measures/Community_distance_nearest_taxon_impl.h | 2 src/Measures/Core_ancestor_cost.h | 304 + src/Measures/Core_ancestor_cost_impl.h | 452 + src/Measures/Mean_nearest_taxon_distance.h | 241 src/Measures/Mean_nearest_taxon_distance_impl.h | 847 +++ src/Measures/Mean_pairwise_distance.h | 333 + src/Measures/Mean_pairwise_distance_impl.h | 368 + src/Measures/Measure_base.h | 2 src/Measures/Measure_base/Mean_pairwise_distance_base.h | 59 src/Measures/Measure_base/Mean_pairwise_distance_base_impl.h | 2 src/Measures/Measure_base/Measure_base_bimodal.h | 87 src/Measures/Measure_base/Measure_base_bimodal_impl.h | 460 + src/Measures/Measure_base/Measure_base_unimodal.h | 126 src/Measures/Measure_base/Measure_base_unimodal_impl.h | 609 +- src/Measures/Phylogenetic_Sorensens_similarity.h | 10 src/Measures/Phylogenetic_Sorensens_similarity_impl.h | 2 src/Measures/Phylogenetic_diversity.h | 344 + src/Measures/Phylogenetic_diversity_impl.h | 146 src/Measures/Poisson_binomial_moments_Mean_nearest_taxon_distance.h |only src/Measures/Poisson_binomial_moments_Mean_pairwise_distance.h |only src/Measures/Poisson_binomial_moments_Phylogenetic_diversity.h |only src/Measures/Poisson_binomial_types.h |only src/Measures/Polynomial_related_types |only src/Measures/Polynomial_related_types.h |only src/Measures/Unique_fraction.h | 11 src/Measures/Unique_fraction_impl.h | 2 src/Numeric_traits_double.h | 39 src/Numeric_traits_types |only src/PhyloMeasures.cpp | 2605 +++++++--- src/Phylogenetic_measures.h | 2 src/Phylogenetic_measures_kernel.h | 59 src/Phylogenetic_tree_base.h | 185 src/Phylogenetic_tree_base_impl.h | 639 ++ src/Phylogenetic_tree_bimodal.h | 39 src/Phylogenetic_tree_bimodal_impl.h | 2 src/Random_samplers |only src/Random_samplers.h |only src/Tree_node.h | 2 src/Tree_node_types/Community_distance_nearest_taxon_node_type.h | 33 src/Tree_node_types/Mean_nearest_taxon_distance_node_type.h | 33 src/Tree_node_types/Tree_node_bimodal.h | 42 src/Tree_node_types/Tree_node_unimodal.h | 74 tests/tests.R | 25 78 files changed, 8812 insertions(+), 1311 deletions(-)
Title: A GraphQL Query Parser
Description: Bindings to the 'libgraphqlparser' C++ library. Currently parses
GraphQL and exports the AST in JSON format.
Author: Jeroen Ooms [cre, aut],
Barret Schloerke [ctb],
Scott Wolchok [ctb],
Facebook, Inc [aut, cph] (libgraphqlparser C++ library)
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between graphql versions 1.1 dated 2016-12-17 and 1.2 dated 2017-01-12
DESCRIPTION | 13 MD5 | 61 NEWS | 4 R/RcppExports.R | 4 R/graphql2json.R | 13 man/graphql.Rd | 9 src/RcppExports.cpp | 7 src/dump_json_ast.cpp | 6 src/libgraphqlparser/Ast.cpp | 128 src/libgraphqlparser/Ast.h | 452 +++ src/libgraphqlparser/AstVisitor.h | 41 src/libgraphqlparser/GraphQLParser.cpp | 32 src/libgraphqlparser/GraphQLParser.h | 14 src/libgraphqlparser/JsonVisitor.cpp | 516 --- src/libgraphqlparser/JsonVisitor.cpp.inc |only src/libgraphqlparser/JsonVisitor.h | 157 - src/libgraphqlparser/JsonVisitor.h.inc |only src/libgraphqlparser/c/GraphQLAst.cpp | 146 + src/libgraphqlparser/c/GraphQLAst.h | 64 src/libgraphqlparser/c/GraphQLAstForEachConcreteType.h | 17 src/libgraphqlparser/c/GraphQLParser.cpp | 11 src/libgraphqlparser/c/GraphQLParser.h | 10 src/libgraphqlparser/lexer.cpp | 656 ++-- src/libgraphqlparser/lexer.h | 90 src/libgraphqlparser/lexer.lpp | 10 src/libgraphqlparser/location.hh | 12 src/libgraphqlparser/parser.tab.cpp | 2369 +++++++++++------ src/libgraphqlparser/parser.tab.hpp | 137 src/libgraphqlparser/position.hh | 12 src/libgraphqlparser/stack.hh | 12 tests |only 31 files changed, 3267 insertions(+), 1736 deletions(-)
Title: Tools for Interacting with the Brazilian Flora 2020
Description: Tools to quickly compile taxonomic and distribution data from
the Brazilian Flora 2020 at http://floradobrasil.jbrj.gov.br/.
Author: Gustavo Carvalho
Maintainer: Gustavo Carvalho <gustavo.bio@gmail.com>
Diff between flora versions 0.2.7 dated 2016-02-26 and 0.2.8 dated 2017-01-12
DESCRIPTION | 10 +++++----- MD5 | 28 +++++++++++++++++----------- NAMESPACE | 7 +++++-- NEWS | 14 ++++++++++++++ R/df2phytaxa.R | 4 ++++ R/get.synonyms.R |only R/get.taxa.R | 10 +++++----- R/get_domains.R |only R/get_vegtype.R |only R/help.R | 5 +++-- R/occurrence.R | 5 ++++- R/sysdata.rda |binary R/vernacular.R | 4 ++-- R/web.flora.R | 10 ++++++++-- data/plants.rda |binary man/get.synonyms.Rd |only man/get_domains.Rd |only man/get_vegtype.Rd |only 18 files changed, 67 insertions(+), 30 deletions(-)
Title: Translate Integers into English
Description: Allow numbers to be presented in an English language
version, one, two, three, ...
Author: John Fox and Bill Venables.
Maintainer: Bill Venables <Bill.Venables@gmail.com>
Diff between english versions 1.0-1 dated 2011-01-03 and 1.0-2 dated 2017-01-12
DESCRIPTION | 12 ++-- MD5 |only NAMESPACE | 1 R/english.R | 118 +++++++++++++++++++++++--------------------- man/Ops.english.Rd | 2 man/as.character.english.Rd | 7 +- man/as.english.Rd | 17 ++++-- man/as.numeric.english.Rd | 2 man/english-package.Rd | 4 - man/print.english.Rd | 2 man/sort.english.Rd | 8 +- 11 files changed, 100 insertions(+), 73 deletions(-)
Title: Functions to Import Data from 'z-Tree' into R
Description: Read '.xls' and '.sbj' files which are written by the
Microsoft Windows program 'z-Tree'. The latter is a software for
developing and carrying out economic experiments
(see <http://www.ztree.uzh.ch/> for more information).
Author: Oliver Kirchkamp
Maintainer: Oliver Kirchkamp <oliver@kirchkamp.de>
Diff between zTree versions 1.0.3 dated 2016-12-19 and 1.0.4 dated 2017-01-12
DESCRIPTION | 13 ++++++++----- MD5 | 11 ++++++----- NEWS.md | 4 ++++ R/zTreeSbj.R | 2 -- R/zTreeTables.R | 2 -- R/zzz.R |only build/partial.rdb |binary 7 files changed, 18 insertions(+), 14 deletions(-)
Title: Reproducible, Accessible & Shareable Species Distribution
Modelling
Description: Reproducible and remixable species distribution modelling. The
package reads user submitted modules from an online repository, runs full
SDM workflows and returns output that is fully reproducible.
Author: Tom August [aut, cre], Tim Lucas [aut], Nick Golding [aut], Emiel van Loon [ctb], Greg McInerny [aut]
Maintainer: Tom August <tomaug@ceh.ac.uk>
Diff between zoon versions 0.5 dated 2016-06-13 and 0.6 dated 2017-01-12
zoon-0.5/zoon/R/print.zoonSummary.R |only zoon-0.5/zoon/man/print.Summary.Rd |only zoon-0.5/zoon/tests/testthat/testprint.zoonSummary.R |only zoon-0.6/zoon/DESCRIPTION | 19 zoon-0.6/zoon/MD5 | 149 +-- zoon-0.6/zoon/NAMESPACE | 12 zoon-0.6/zoon/R/BuildModule.R | 25 zoon-0.6/zoon/R/CombineRasters.R |only zoon-0.6/zoon/R/GetPackage.R | 2 zoon-0.6/zoon/R/Replicate.R | 4 zoon-0.6/zoon/R/SearchFunctions.R | 5 zoon-0.6/zoon/R/TransformCRS.R |only zoon-0.6/zoon/R/ZoonModuleParse.R | 34 zoon-0.6/zoon/R/attributeFunctions.R |only zoon-0.6/zoon/R/summary.zoonWorkflow.R | 495 +++++++++++- zoon-0.6/zoon/R/test_module.R | 7 zoon-0.6/zoon/R/test_outputs.R | 608 +++++++++------ zoon-0.6/zoon/R/test_parameters.R | 14 zoon-0.6/zoon/R/workflow.R | 81 + zoon-0.6/zoon/R/zoonHelpers.R | 140 ++- zoon-0.6/zoon/R/zoonPredict.R | 10 zoon-0.6/zoon/build/vignette.rds |binary zoon-0.6/zoon/inst/doc/Building_a_module.Rmd | 38 zoon-0.6/zoon/inst/doc/Building_a_module.html | 60 + zoon-0.6/zoon/inst/doc/basic-zoon-usage.Rmd | 186 +--- zoon-0.6/zoon/inst/doc/basic-zoon-usage.html | 152 +-- zoon-0.6/zoon/inst/doc/interactive_zoon_usage.Rmd | 16 zoon-0.6/zoon/inst/doc/interactive_zoon_usage.html | 22 zoon-0.6/zoon/man/BuildModule.Rd | 13 zoon-0.6/zoon/man/CombineRasters.Rd |only zoon-0.6/zoon/man/Replicate.Rd | 2 zoon-0.6/zoon/man/TransformCRS.Rd |only zoon-0.6/zoon/man/ZoonPredict.Rd | 3 zoon-0.6/zoon/man/cbindZoon.Rd |only zoon-0.6/zoon/man/subsetColumnsZoon.Rd |only zoon-0.6/zoon/man/summary.zoonWorkflow.Rd | 7 zoon-0.6/zoon/man/workflow.Rd | 22 zoon-0.6/zoon/tests/testthat/Rplots.pdf |binary zoon-0.6/zoon/tests/testthat/testChangeWorkflow.R | 4 zoon-0.6/zoon/tests/testthat/testCombineRasters.R |only zoon-0.6/zoon/tests/testthat/testExtractAndCombData.R | 7 zoon-0.6/zoon/tests/testthat/testGetPackage.R | 3 zoon-0.6/zoon/tests/testthat/testTransformCRS.R |only zoon-0.6/zoon/tests/testthat/testWholeWorkflows.R | 9 zoon-0.6/zoon/tests/testthat/testWriteWorkflowMetadata.R |only zoon-0.6/zoon/tests/testthat/testaccessors.R | 2 zoon-0.6/zoon/tests/testthat/testcall_path.R | 70 - zoon-0.6/zoon/tests/testthat/testcbindZoon.R |only zoon-0.6/zoon/tests/testthat/testplot.zoonWorkflow.r | 8 zoon-0.6/zoon/tests/testthat/testsubsetColumnsZoon.R |only zoon-0.6/zoon/tests/testthat/testsummary.zoonWorkflow.R | 62 + zoon-0.6/zoon/tests/testthat/testtestModule.R | 17 zoon-0.6/zoon/vignettes/Building_a_module.Rmd | 38 zoon-0.6/zoon/vignettes/basic-zoon-usage.Rmd | 186 +--- zoon-0.6/zoon/vignettes/basic_11-2.png |binary zoon-0.6/zoon/vignettes/basic_12-1.png |binary zoon-0.6/zoon/vignettes/basic_12-2.png |binary zoon-0.6/zoon/vignettes/basic_12-3.png |binary zoon-0.6/zoon/vignettes/basic_15-1.png |binary zoon-0.6/zoon/vignettes/basic_5-1.png |binary zoon-0.6/zoon/vignettes/building_cov4-1.png |binary zoon-0.6/zoon/vignettes/building_cov5-1.png |binary zoon-0.6/zoon/vignettes/building_cov5-2.png |binary zoon-0.6/zoon/vignettes/building_cov5-3.png |binary zoon-0.6/zoon/vignettes/building_cov5-4.png |binary zoon-0.6/zoon/vignettes/building_mod6-1.png |binary zoon-0.6/zoon/vignettes/building_mod6-2.png |binary zoon-0.6/zoon/vignettes/building_mod6-3.png |binary zoon-0.6/zoon/vignettes/building_mod6-4.png |binary zoon-0.6/zoon/vignettes/building_occ6-1.png |binary zoon-0.6/zoon/vignettes/building_out7-1.png |binary zoon-0.6/zoon/vignettes/building_out7-2.png |binary zoon-0.6/zoon/vignettes/building_out8-1.png |binary zoon-0.6/zoon/vignettes/building_out8-2.png |binary zoon-0.6/zoon/vignettes/building_out8-3.png |binary zoon-0.6/zoon/vignettes/building_out9-1.png |binary zoon-0.6/zoon/vignettes/building_out9-2.png |binary zoon-0.6/zoon/vignettes/building_pro6-1.png |binary zoon-0.6/zoon/vignettes/building_pro6-2.png |binary zoon-0.6/zoon/vignettes/building_pro6-3.png |binary zoon-0.6/zoon/vignettes/building_pro6-4.png |binary zoon-0.6/zoon/vignettes/building_pro7-1.png |binary zoon-0.6/zoon/vignettes/interactive_zoon_usage.Rmd | 16 83 files changed, 1678 insertions(+), 870 deletions(-)
Title: Tools for Detecting Predatory Publishers and Journals
Description: Allows the user to check and find (allegedly) predatory journals based on Beall's list available at <https://scholarlyoa.com/>.
As part of a research project, the data from the website has been scraped with web scraping algorithms and manual work.
The package includes a search function and direct access to this database of predatory journals. The use of this tool
should facilitate the detection of predatory publications by researchers and librarians.
Author: Marcelo Perlin [aut, cre]
Maintainer: Marcelo Perlin <marceloperlin@gmail.com>
Diff between predatory versions 1.0 dated 2016-12-09 and 1.1 dated 2017-01-12
DESCRIPTION | 10 MD5 | 12 NEWS.md | 5 inst/doc/predatory-vignette.Rmd | 2 inst/doc/predatory-vignette.html | 42 inst/extdata/predpub.csv |20371 ++++++++++++++++++++------------------- vignettes/predatory-vignette.Rmd | 2 7 files changed, 10625 insertions(+), 9819 deletions(-)
More information about classifierplots at CRAN
Permanent link
Title: Interface for the 'Box.com API'
Description: An R interface for the remote file hosting service 'Box'
(<https://www.box.com/>). In addition to uploading and downloading files,
this package includes functions which mirror base R operations for local
files, (e.g. box_load(), box_save(), box_read(), box_setwd(), etc.), as well
as 'git' style functions for entire directories (e.g. box_fetch(),
box_push()).
Author: Brendan Rocks [aut, cre],
Ian Lyttle [ctb]
Maintainer: Brendan Rocks <foss@brendanrocks.com>
Diff between boxr versions 0.3.3 dated 2016-08-16 and 0.3.4 dated 2017-01-12
DESCRIPTION | 12 +- MD5 | 18 ++-- NEWS.md | 222 ++++++++++++++++++++++++++++++++++++++++++++--------- R/boxr_auth.R | 2 R/boxr_misc.R | 5 - R/boxr_search.R | 15 +-- build/vignette.rds |binary inst/doc/boxr.html | 4 man/box_ls.Rd | 3 man/box_search.Rd | 7 - 10 files changed, 216 insertions(+), 72 deletions(-)