Title: Fitting the Centered Autologistic and Sparse Spatial Generalized
Linear Mixed Models for Areal Data
Description: Provides tools for analyzing spatial data, especially
non-Gaussian areal data. The current version supports the sparse spatial
generalized linear mixed model of Hughes and Haran (2013) and the centered
autologistic model of Caragea and Kaiser (2009).
Author: John Hughes <jphughesjr@gmail.com> and Xiaohui Cui
Maintainer: John Hughes <jphughesjr@gmail.com>
Diff between ngspatial versions 1.0-5 dated 2015-01-16 and 1.1-1 dated 2016-08-15
COPYING | 2 +- DESCRIPTION | 22 +++++++++++----------- MD5 | 40 ++++++++++++++++++++-------------------- NAMESPACE | 10 +++++++--- R/autologistic.R | 22 +++++++++++----------- R/zzz.R | 12 +++++------- inst/CITATION | 4 ++-- man/adjacency.matrix.Rd | 3 ++- man/autologistic.Rd | 35 ++++++++++++++++++----------------- man/rautologistic.Rd | 9 +++++---- man/residuals.autologistic.Rd | 3 ++- man/residuals.sparse.sglmm.Rd | 3 ++- man/sparse.sglmm.Rd | 5 +++-- man/summary.autologistic.Rd | 3 ++- man/summary.sparse.sglmm.Rd | 3 ++- man/vcov.autologistic.Rd | 3 ++- man/vcov.sparse.sglmm.Rd | 3 ++- src/Makevars | 6 ++---- src/moller.cpp | 8 ++++---- src/perfsampler.cpp | 4 ++-- src/perfsampler.h | 2 +- 21 files changed, 106 insertions(+), 96 deletions(-)
Title: Bayesian Non-Parametric Dependent Models for Time-Indexed
Functional Data
Description: Estimates a collection of time-indexed functions under
either of Gaussian process (GP) or intrinsic Gaussian Markov
random field (iGMRF) prior formulations where a Dirichlet process
mixture allows sub-groupings of the functions to share the same
covariance or precision parameters. The GP and iGMRF formulations
both support any number of additive covariance or precision terms,
respectively, expressing either or both of multiple trend and
seasonality.
Author: Terrance Savitsky
Maintainer: Terrance Savitsky <tds151@gmail.com>
Diff between growfunctions versions 0.12 dated 2015-11-13 and 0.13 dated 2016-08-15
DESCRIPTION | 10 +- MD5 | 26 +++-- NAMESPACE | 66 +++++++------- NEWS | 9 + R/gen_informative_sample.R | 3 R/gp_car_fit_compare_facet.R | 2 R/gp_cluster_plot.R | 2 R/help.R | 24 ++--- R/plot_cluster.R | 2 R/predict_plot.R | 2 build |only inst |only man/growfunctions-package.Rd | 22 ++-- src/gpdpbmix.cpp | 15 +-- src/gpdpmix_moves.cpp | 194 +++++++++++++++++++++++++++++++++++++++++-- 15 files changed, 285 insertions(+), 92 deletions(-)
Title: Get Data for Brazilian Bonds (Tesouro Direto)
Description: Downloads and aggregates data for Brazilian government issued bonds directly from the website of Tesouro Direto <http://www.tesouro.fazenda.gov.br/tesouro-direto-balanco-e-estatisticas>.
Author: Marcelo Perlin [aut, cre]
Maintainer: Marcelo Perlin <marceloperlin@gmail.com>
Diff between GetTDData versions 1.2.3 dated 2016-05-24 and 1.2.4 dated 2016-08-15
DESCRIPTION | 6 - MD5 | 26 ++--- NEWS.md | 3 R/gtdd_download_TD_data.R | 5 - R/gtdd_read_TD_files.R | 6 - build/vignette.rds |binary inst/doc/gtdd-vignette.R | 58 +++++++----- inst/doc/gtdd-vignette.Rmd | 21 ++++ inst/doc/gtdd-vignette.html | 209 ++------------------------------------------ inst/extdata |only man/download.TD.data.Rd | 87 +++++++++--------- man/read.TD.files.Rd | 88 +++++++++--------- tests/testthat/test_gtdd.R | 30 +++--- vignettes/gtdd-vignette.Rmd | 21 ++++ 14 files changed, 217 insertions(+), 343 deletions(-)
Title: Download and Aggregate High Frequency Trading Data from Bovespa
Description: Downloads and aggregates high frequency trading data for Brazilian instruments directly from Bovespa ftp site <ftp://ftp.bmf.com.br/MarketData/>.
Author: Marcelo Perlin [aut, cre]
Maintainer: Marcelo Perlin <marceloperlin@gmail.com>
Diff between GetHFData versions 1.0.0 dated 2016-07-21 and 1.1.0 dated 2016-08-15
DESCRIPTION | 6 +- MD5 | 26 +++++----- NEWS.md | 12 ++++ R/ghfd_get_HF_data.R | 13 ++++- R/ghfd_get_available_tickers_from_file.R | 18 +++++-- R/ghfd_get_available_tickers_from_ftp.R | 31 ++++++++++-- R/ghfd_read_file.R | 70 ++++++++++++++++++++++++---- inst/doc/ghfd-vignette.R | 9 +-- inst/doc/ghfd-vignette.Rmd | 15 ++---- inst/doc/ghfd-vignette.html | 50 ++++++++++++-------- man/ghfd_get_available_tickers_from_file.Rd | 6 +- man/ghfd_get_available_tickers_from_ftp.Rd | 6 +- man/ghfd_read_file.Rd | 2 vignettes/ghfd-vignette.Rmd | 15 ++---- 14 files changed, 191 insertions(+), 88 deletions(-)
Title: Request Data from the U.S. Bureau of Labor Statistics API
Description: Allows users to request data for one or multiple series through the
U.S. Bureau of Labor Statistics API. Users provide parameters as specified in
http://www.bls.gov/developers/api_signature.htm and the function returns a JSON
string.
Author: Michael Silva <mike.a.silva@gmail.com>
Maintainer: Michael Silva <mike.a.silva@gmail.com>
Diff between blsAPI versions 0.1.4 dated 2016-05-08 and 0.1.5 dated 2016-08-15
DESCRIPTION | 6 - MD5 | 12 +- NAMESPACE | 14 +-- R/blsAPI.R | 240 ++++++++++++++++++++++++++++----------------------------- R/blsQCEW.R | 214 +++++++++++++++++++++++++------------------------- man/blsAPI.Rd | 146 +++++++++++++++++----------------- man/blsQCEW.Rd | 128 +++++++++++++++--------------- 7 files changed, 380 insertions(+), 380 deletions(-)
Title: Interface to PHAST Software for Comparative Genomics
Description: Provides an R interface to the PHAST software
(Phylogenetic Analysis with Space/Time Models). It can be used for
many types of analysis in comparative and evolutionary genomics,
such as estimating models of evolution from sequence data, scoring
alignments for conservation or acceleration, and predicting
elements based on conservation or custom phylogenetic hidden Markov
models. It can also perform many basic operations on multiple
sequence alignments and phylogenetic trees.
Author: Melissa Hubisz, Katherine Pollard, and Adam Siepel
Maintainer: Melissa Hubisz <mjhubisz@cornell.edu>
Diff between rphast versions 1.6.4 dated 2016-06-02 and 1.6.5 dated 2016-08-15
ChangeLog | 3 ++- DESCRIPTION | 8 ++++---- LICENSE | 4 ++-- MD5 | 20 ++++++++++---------- configure | 5 ++++- configure.ac | 5 ++++- inst/doc/vignette1.pdf |binary inst/doc/vignette3.pdf |binary inst/doc/vignette4.pdf |binary man/rphast-package.Rd | 6 +++--- src/Makevars.win | 2 +- 11 files changed, 30 insertions(+), 23 deletions(-)
Title: Automatic Marking of R Assignments
Description: Automatic marking of R assignments for students and teachers based
on 'testthat' test suites.
Author: Mans Magnusson, Oscar Pettersson
Maintainer: Mans Magnusson <mons.magnusson@gmail.com>
Diff between markmyassignment versions 0.6.0 dated 2016-04-15 and 0.6.1 dated 2016-08-15
DESCRIPTION | 8 +- MD5 | 8 +- R/expectations.R | 26 +------ build/vignette.rds |binary inst/doc/markmyassignment.html | 137 ++++++++++++++++++++++------------------- 5 files changed, 89 insertions(+), 90 deletions(-)
More information about markmyassignment at CRAN
Permanent link
Title: Sequence Analysis
Description: Provides: 1) By Giving UniProtKB, the Protein Sequence will be returned from UniProt database. 2)By Giving UniProtKB, the Nucleotide Sequence will be returned from EBI database. 3) Amino acid Composition is calculated by four different methods: a) Twenty-two independent categories are considered, with one amino acid for each category. B) Five categories (Nonpolar Aliphatic, Nonpolar Aromatic, Polar Uncharged, Polar Positively Charged, Polar Negatively Charged) are considered according to the standard chemical structures of amino acids. c) Six categories (Nonpolar Aliphatic, Nonpolar Aromatic, Polar Uncharged, Polar Positively Charged, Polar Negatively Charged, Special cases) are considered which Cysteine, Selenocysteine, Glycine and Proline are placed in Special cases group. d)Eight categories are clustered via k-means algorithm on Physicochemical index of amino acids. 4) GC Content: Percentage of nucleotide g and c in sequence. 5) Codon usage: Frequency of occurrence of synonymous codons. 6) Stacking Energy: The NN model for nucleic acids assumes that the stability of a given base pair depends on the identity and orientation of neighboring base pairs. Stacking Energy = DeltaG(total) = Sigma (n(i)*DeltaG(i)) + DeltaG(init) + DeltaG(end) + DeltaG(sym), which DeltaG for i, init and end is obtained by Unified NN free energy parameter. Symmetry of self-complementary duplexes is also included by DeltaG(sym) equals to +0.43 (kcal/mol) if the duplex is self-complementary and zero if it is non-self-complementary. 7) Complement of desired nucleotide sequence. 8) Reverse of desired nucleotide sequence. 9) Reverse-Complement of desired nucleotide sequence. 10) Protein, Gene and Organism of desired UniProt ID. 11) Converting nucleotide sequence to protein sequence. 12) Getting Localization From Gene Ontology Cellular Component inside Uniprot. 13) All related codons of desired amino acid.
Author: Babak Khorsand [aut, cre],
Javad Zahiri [ths],
Abdorreza Savadi [ths]
Maintainer: Babak Khorsand <khorsand@yahoo.com>
Diff between SequenceAnalysis versions 1.2 dated 2016-08-10 and 1.3 dated 2016-08-15
DESCRIPTION | 10 +- MD5 | 35 ++++--- NAMESPACE | 3 R/AAC.R | 4 R/AminoAcidToCodon.R |only R/CodonToAminoAcid.R |only R/CodonUsage.R | 9 - R/Complement.R | 15 +-- R/GC.R | 15 +-- R/GetLocalization.R |only R/GetNuclotideSequence.R | 129 ++++++-------------------- R/GetProteinOrganism.R | 9 - R/GetProteinSequence.R | 12 +- R/Reverse.R | 13 +- R/ReverseComplement.R | 13 +- R/StackingEnergy.R | 20 ++-- R/sysdata.rda |only man/SequenceAnalysis.AminoAcidToCodon.Rd |only man/SequenceAnalysis.CodonToAminoAcid.Rd |only man/SequenceAnalysis.GetLocalization.Rd |only man/SequenceAnalysis.GetNucleotideSequence.Rd | 2 man/SequenceAnalysis.StackingEnergy.Rd | 4 22 files changed, 126 insertions(+), 167 deletions(-)
More information about SequenceAnalysis at CRAN
Permanent link
Title: Robust Data-Driven Statistical Inference in
Regression-Discontinuity Designs
Description: Regression-discontinuity (RD) designs are quasi-experimental research designs popular in social, behavioral and natural sciences. The RD design is usually employed to study the (local) causal effect of a treatment, intervention or policy. This package provides tools for data-driven graphical and analytical statistical inference in RD designs: rdrobust() to construct local-polynomial point estimators and robust confidence intervals for average treatment effects at the cutoff in Sharp, Fuzzy and Kink RD settings, rdbwselect() to perform bandwidth selection for the different procedures implemented, and rdplot() to conduct exploratory data analysis (RD plots).
Author: Sebastian Calonico <scalonico@bus.miami.edu>, Matias D. Cattaneo <cattaneo@umich.edu>, Max H. Farrell, <max.farrell@chicagobooth.edu>, Rocio Titiunik <titiunik@umich.edu>
Maintainer: Sebastian Calonico <scalonico@bus.miami.edu>
Diff between rdrobust versions 0.92 dated 2016-08-09 and 0.93 dated 2016-08-15
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/rdrobust.R | 16 ++++++++-------- man/rdrobust-package.Rd | 4 ++-- 4 files changed, 17 insertions(+), 17 deletions(-)
Title: Perform Pharmacokinetic Non-Compartmental Analysis
Description: Compute standard Non-Compartmental Analysis (NCA)
parameters and summarize them. In addition to this core work, it
also provides standardized plotting routines, basic assessments
for biocomparison or drug interaction, and model-based estimation
routines for calculating doses to reach specific values of AUC or
Cmax.
Author: Bill Denney [aut, cre],
Clare Buckeridge [aut],
Sridhar Duvvuri [ctb]
Maintainer: Bill Denney <wdenney@humanpredictions.com>
Diff between PKNCA versions 0.7 dated 2016-04-01 and 0.7.1 dated 2016-08-15
DESCRIPTION | 24 MD5 | 207 +- NAMESPACE | 283 +- NEWS.md | 8 R/002-pk.business.rules.R | 21 R/check.intervals.R | 304 +-- R/data.classes.R | 48 R/general.functions.R | 107 - R/pk.calc.simple.R | 105 - README.md | 6 build/vignette.rds |binary inst/doc/Example-theophylline.R | 114 - inst/doc/Example-theophylline.Rmd | 18 inst/doc/Example-theophylline.html | 2189 ++++++++++++++++++----- inst/doc/Introduction-and-Usage.R | 206 +- inst/doc/Introduction-and-Usage.Rmd | 2 inst/doc/Introduction-and-Usage.html | 1113 ++++++----- inst/doc/Superposition.R |only inst/doc/Superposition.Rmd |only inst/doc/Superposition.html |only man/AIC.list.Rd | 60 man/PKNCA.Rd | 34 man/PKNCA.choose.option.Rd | 52 man/PKNCA.options.Rd | 114 - man/PKNCA.set.summary.Rd | 84 man/PKNCAconc.Rd | 93 man/PKNCAdata.Rd | 116 - man/PKNCAdose.Rd | 77 man/PKNCAresults.Rd | 50 man/add.interval.col.Rd | 56 man/adj.r.squared.Rd | 40 man/as.data.frame.PKNCAresults.Rd | 48 man/business.mean.Rd | 96 - man/check.conc.time.Rd | 72 man/check.conversion.Rd | 48 man/check.interval.deps.Rd | 52 man/check.interval.specification.Rd | 152 - man/choose.auc.intervals.Rd | 92 man/clean.conc.blq.Rd | 136 - man/clean.conc.na.Rd | 66 man/count.non.missing.Rd | 36 man/find.tau.Rd | 78 man/findOperator.Rd | 56 man/formula.PKNCAconc.Rd | 46 man/formula.parseFormula.Rd | 54 man/geomean.Rd | 57 man/get.best.model.Rd | 48 man/get.first.model.Rd | 40 man/get.interval.cols.Rd | 24 man/getData.PKNCAconc.Rd | 36 man/getDepVar.Rd | 44 man/getGroups.PKNCAconc.Rd | 86 man/getIndepVar.Rd | 44 man/interp.extrap.conc.Rd | 202 +- man/merge.splitByData.Rd | 54 man/model.frame.PKNCAconc.Rd | 54 man/parseFormula.Rd | 92 man/pk.business.Rd | 62 man/pk.calc.aucpext.Rd | 42 man/pk.calc.auxc.Rd | 288 +-- man/pk.calc.c0.Rd | 138 - man/pk.calc.cav.Rd | 44 man/pk.calc.cl.Rd | 70 man/pk.calc.clast.obs.Rd | 48 man/pk.calc.cmax.Rd | 58 man/pk.calc.ctrough.Rd | 46 man/pk.calc.f.Rd | 46 man/pk.calc.half.life.Rd | 170 - man/pk.calc.kel.Rd | 36 man/pk.calc.mrt.Rd | 52 man/pk.calc.ptr.Rd | 40 man/pk.calc.thalf.eff.Rd | 36 man/pk.calc.tlag.Rd | 48 man/pk.calc.tlast.Rd | 62 man/pk.calc.tmax.Rd | 78 man/pk.calc.vd.Rd | 58 man/pk.calc.vss.Rd | 40 man/pk.calc.vz.Rd | 40 man/pk.nca.Rd | 46 man/pk.nca.interval.Rd | 80 man/pk.tss.Rd | 58 man/pk.tss.data.prep.Rd | 94 man/pk.tss.monoexponential.Rd | 98 - man/pk.tss.monoexponential.individual.Rd | 74 man/pk.tss.monoexponential.population.Rd | 78 man/pk.tss.stepwise.linear.Rd | 98 - man/plot.PKNCAconc.Rd | 66 man/print.PKNCAconc.Rd | 68 man/print.PKNCAdata.Rd | 36 man/roundString.Rd | 54 man/roundingSummarize.Rd | 46 man/sapplyBy.Rd | 50 man/signifString.Rd | 54 man/sort.interval.cols.Rd | 24 man/summary.PKNCAdata.Rd | 38 man/summary.PKNCAresults.Rd | 74 man/superposition.Rd | 178 - man/tss.monoexponential.generate.formula.Rd | 40 tests/testthat/test-check.intervals.R | 568 +++-- tests/testthat/test-data.classes.R | 596 +++--- tests/testthat/test-general.functions.R | 16 tests/testthat/test-pk.calc.all.R | 4 tests/testthat/test-pk.calc.simple.R | 120 - vignettes/Example-theophylline.Rmd | 18 vignettes/Introduction-and-Usage.Rmd | 2 vignettes/PKNCA-ISoP_Study_Group-2016-05-25.pptx |only vignettes/Superposition.Rmd |only 107 files changed, 6694 insertions(+), 4830 deletions(-)
Title: The Observatory of Economic Complexity
Description: Use The Observatory of Economic Complexity's API from R console to obtain international trade data to create spreadsheets (csv format) and D3plus visualizations.
Author: Mauricio Vargas S.
Maintainer: Mauricio Vargas S. <mauriciovargas@ug.uchile.cl>
Diff between oec versions 1.0.3 dated 2016-07-30 and 2.0 dated 2016-08-15
oec-1.0.3/oec/R/d3plus.R |only oec-1.0.3/oec/R/network.compare.R |only oec-1.0.3/oec/man/d3plus.Rd |only oec-1.0.3/oec/man/network.compare.Rd |only oec-2.0/oec/DESCRIPTION | 12 oec-2.0/oec/MD5 | 37 - oec-2.0/oec/NAMESPACE | 5 oec-2.0/oec/R/getdata.R | 554 ++++++++-------- oec-2.0/oec/R/install_d3plus.R |only oec-2.0/oec/R/network.R | 159 ++-- oec-2.0/oec/R/network_comparison.R |only oec-2.0/oec/R/oec.r | 30 oec-2.0/oec/R/treemap.R | 108 +-- oec-2.0/oec/inst/extdata/barchart_compare_template.html |only oec-2.0/oec/inst/extdata/demo_examples.R | 22 oec-2.0/oec/inst/extdata/network_compare_template.html | 35 - oec-2.0/oec/inst/extdata/network_template.html | 34 oec-2.0/oec/inst/extdata/treemap_template.html | 34 oec-2.0/oec/man/getdata.Rd | 13 oec-2.0/oec/man/install_d3plus.Rd |only oec-2.0/oec/man/network.Rd | 12 oec-2.0/oec/man/network_comparison.Rd |only oec-2.0/oec/man/oec-package.Rd | 30 oec-2.0/oec/man/treemap.Rd | 16 24 files changed, 568 insertions(+), 533 deletions(-)
Title: Multidimensional Projection Techniques
Description: Multidimensional projection techniques are used to create two
dimensional representations of multidimensional data sets.
Author: Francisco M. Fatore,
Samuel G. Fadel
Maintainer: Francisco M. Fatore <fmfatore@gmail.com>
Diff between mp versions 0.3.1 dated 2015-09-01 and 0.4.1 dated 2016-08-15
DESCRIPTION | 12 +++++++----- MD5 | 38 ++++++++++++++++++++------------------ NAMESPACE | 3 ++- R/RcppExports.R | 8 ++++---- R/lamp.R | 3 ++- R/lsp.R | 10 +++------- R/pekalska.R |only R/plmp.R | 9 ++++----- R/tSNE.R | 43 +++++++++++++++++++++++++++++++++++++++++-- man/forceScheme.Rd | 2 +- man/is.symmetric.Rd | 2 +- man/lamp.Rd | 6 ++++-- man/lsp.Rd | 3 ++- man/mp.Rd | 2 +- man/pekalska.Rd |only man/plmp.Rd | 4 +++- man/tSNE.Rd | 27 +++++++++++++++++++++++++-- src/RcppExports.cpp | 22 +++++++++++++++------- src/forceScheme.cpp | 6 +++--- src/lamp.cpp | 30 +++++++++++++++++++++--------- src/tSNE.cpp | 42 +++++++++++++++++++++++------------------- 21 files changed, 182 insertions(+), 90 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-07-28 1.1.4
2015-06-11 1.1.1
2015-04-22 1.0
2015-03-18 0.13
2015-02-04 0.12.1
2015-01-27 0.12
2014-12-16 0.11
2014-10-20 0.10.0.1
2014-10-16 0.10
2014-09-11 0.9.1
2014-08-26 0.9
2014-08-06 0.8
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2011-12-15 1.1
2011-11-28 1.0
Title: Pairwise Constraints Clustering
Description: There are 4 main functions in this package: ckmeans(), lcvqe(), mpckm() and ccls(). They take an unlabeled dataset and two lists of must-link and cannot-link constraints as input and produce a clustering as output.
Author: Tran Khanh Hiep, Nguyen Minh Duc
Maintainer: Tran Khanh Hiep <hieptkse03059@fpt.edu.vn>
Diff between conclust versions 1.0 dated 2016-06-24 and 1.1 dated 2016-08-15
DESCRIPTION | 10 +++++----- MD5 | 8 +++++--- R/ccls.R |only build/partial.rdb |binary man/ccls.Rd |only man/conclust-package.Rd | 7 ++++++- 6 files changed, 16 insertions(+), 9 deletions(-)
Title: Rmetrics - Autoregressive Conditional Heteroskedastic Modelling
Description: Environment for teaching "Financial Engineering and
Computational Finance".
Author: Diethelm Wuertz and Yohan Chalabi with contribution from Michal
Miklovic, Chris Boudt, Pierre Chausse and others
Maintainer: Yohan Chalabi <yohan.chalabi@rmetrics.org>
Diff between fGarch versions 3010.82 dated 2013-05-01 and 3010.82.1 dated 2016-08-15
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- NAMESPACE | 2 ++ R/garch-Hessian.R | 2 +- R/mgarch-FitFromFormula.R | 2 +- man/methods-predict.Rd | 3 ++- src/Makevars | 2 -- src/math.f | 24 ++++++++++++------------ 8 files changed, 29 insertions(+), 28 deletions(-)