Title: Tools for Simulation Studies in Parallel
Description: Tools for setting up ("design"), conducting, and evaluating
large-scale simulation studies with graphics and tables, including
parallel computations.
Author: Marius Hofert and Martin Maechler <maechler@stat.math.ethz.ch>
Maintainer: Marius Hofert <marius.hofert@uwaterloo.ca>
Diff between simsalapar versions 1.0-7 dated 2015-12-22 and 1.0-8 dated 2016-01-02
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/graphics.R | 25 ++++++++++++++++--------- man/mayplot.Rd | 23 ++++++++++++----------- 4 files changed, 35 insertions(+), 27 deletions(-)
Title: Straightforward 'BibTeX' and 'BibLaTeX' Bibliography Management
Description: Provides tools for importing and working with
bibliographic references. It greatly enhances the 'bibentry' class by
providing a class 'BibEntry' which stores 'BibTeX' and 'BibLaTeX' references,
supports 'UTF-8' encoding, and can be easily searched by any field, by date
ranges, and by various formats for name lists (author by last names,
translator by full names, etc.). Entries can be updated, combined, sorted,
printed in a number of styles, and exported. 'BibTeX' and 'BibLaTeX' '.bib' files
can be read into 'R' and converted to 'BibEntry' objects. Interfaces to 'NCBI Entrez',
'CrossRef', and 'Zotero' are provided for importing references and
references can be created from locally stored 'PDF' files using 'Poppler'. Includes
functions for citing and generating a bibliography with hyperlinks for
documents prepared with 'RMarkdown' or 'RHTML'.
Author: Mathew W. McLean [aut, cre]
Maintainer: Mathew W. McLean <mathew.w.mclean@gmail.com>
Diff between RefManageR versions 0.8.63 dated 2015-06-09 and 0.10.5 dated 2016-01-02
RefManageR-0.10.5/RefManageR/DESCRIPTION | 14 RefManageR-0.10.5/RefManageR/LICENSE | 4 RefManageR-0.10.5/RefManageR/MD5 | 148 +++---- RefManageR-0.10.5/RefManageR/NAMESPACE | 202 +++++----- RefManageR-0.10.5/RefManageR/R/04InternalFunctions.R | 161 ++++---- RefManageR-0.10.5/RefManageR/R/05makeBibLatex.R | 69 +-- RefManageR-0.10.5/RefManageR/R/07makeBibLatexAuthoryear.R | 54 +- RefManageR-0.10.5/RefManageR/R/08asBibEntry.R | 1 RefManageR-0.10.5/RefManageR/R/09sort.R | 2 RefManageR-0.10.5/RefManageR/R/BibEntryAddOp.R | 2 RefManageR-0.10.5/RefManageR/R/BibEntryCombineOp.R | 3 RefManageR-0.10.5/RefManageR/R/BibEntryDollarExtract.R | 3 RefManageR-0.10.5/RefManageR/R/BibEntryExtractOp.R | 13 RefManageR-0.10.5/RefManageR/R/BibEntryReplaceBibEntry.R | 4 RefManageR-0.10.5/RefManageR/R/BibEntryReplaceOp.R | 1 RefManageR-0.10.5/RefManageR/R/GetDOIs.R | 4 RefManageR-0.10.5/RefManageR/R/NamesAssign.R | 1 RefManageR-0.10.5/RefManageR/R/ReadBib.R | 16 RefManageR-0.10.5/RefManageR/R/ReadCrossRef.R | 8 RefManageR-0.10.5/RefManageR/R/ReadGS.R | 4 RefManageR-0.10.5/RefManageR/R/ReadPDFs.R | 7 RefManageR-0.10.5/RefManageR/R/ReadPDFsSupport.R | 171 ++++---- RefManageR-0.10.5/RefManageR/R/ReadPubMed.R | 25 - RefManageR-0.10.5/RefManageR/R/RefManageR-package.R | 4 RefManageR-0.10.5/RefManageR/R/WriteBib.R | 2 RefManageR-0.10.5/RefManageR/R/asdataframe.R | 12 RefManageR-0.10.5/RefManageR/R/format.R | 10 RefManageR-0.10.5/RefManageR/R/open.BibEntry.R | 5 RefManageR-0.10.5/RefManageR/R/print.R | 2 RefManageR-0.10.5/RefManageR/R/rmdCite.R | 11 RefManageR-0.10.5/RefManageR/README.md | 37 + RefManageR-0.10.5/RefManageR/build/vignette.rds |binary RefManageR-0.10.5/RefManageR/inst/NEWS | 18 RefManageR-0.10.5/RefManageR/inst/doc/TestAlphabetic.html | 18 RefManageR-0.10.5/RefManageR/inst/doc/TestHtml.html | 106 ++--- RefManageR-0.10.5/RefManageR/inst/doc/TestRmd.html | 4 RefManageR-0.10.5/RefManageR/inst/doc/manual.pdf |binary RefManageR-0.10.5/RefManageR/man/BibEntry.Rd | 260 ++++++------- RefManageR-0.10.5/RefManageR/man/BibOptions.Rd | 256 ++++++------ RefManageR-0.10.5/RefManageR/man/Cite.Rd | 228 +++++------ RefManageR-0.10.5/RefManageR/man/FindBibEntry.Rd | 26 - RefManageR-0.10.5/RefManageR/man/GetBibEntryWithDOI.Rd | 74 +-- RefManageR-0.10.5/RefManageR/man/GetDOIs.Rd | 86 ++-- RefManageR-0.10.5/RefManageR/man/GetPubMedByID.Rd | 88 ++-- RefManageR-0.10.5/RefManageR/man/GetPubMedRelated.Rd | 118 ++--- RefManageR-0.10.5/RefManageR/man/LookupPubMedID.Rd | 86 ++-- RefManageR-0.10.5/RefManageR/man/ReadBib.Rd | 89 ++-- RefManageR-0.10.5/RefManageR/man/ReadCrossRef.Rd | 124 +++--- RefManageR-0.10.5/RefManageR/man/ReadGS.Rd | 144 +++---- RefManageR-0.10.5/RefManageR/man/ReadPDFs.Rd | 114 ++--- RefManageR-0.10.5/RefManageR/man/ReadPubMed.Rd | 114 ++--- RefManageR-0.10.5/RefManageR/man/ReadZotero.Rd | 148 +++---- RefManageR-0.10.5/RefManageR/man/RefManageR-package.Rd | 158 +++---- RefManageR-0.10.5/RefManageR/man/SearchBib.Rd | 246 ++++++------ RefManageR-0.10.5/RefManageR/man/UpdateFieldName.Rd | 66 +-- RefManageR-0.10.5/RefManageR/man/WriteBib.Rd | 104 ++--- RefManageR-0.10.5/RefManageR/man/as.BibEntry.Rd | 116 ++--- RefManageR-0.10.5/RefManageR/man/as.data.frame.BibEntry.Rd | 72 +-- RefManageR-0.10.5/RefManageR/man/c.BibEntry.Rd | 82 ++-- RefManageR-0.10.5/RefManageR/man/cash-.BibEntry.Rd | 76 +-- RefManageR-0.10.5/RefManageR/man/cash-set-.BibEntry.Rd | 94 ++-- RefManageR-0.10.5/RefManageR/man/head.BibEntry.Rd | 70 +-- RefManageR-0.10.5/RefManageR/man/levels.BibEntry.Rd | 70 +-- RefManageR-0.10.5/RefManageR/man/merge.BibEntry.Rd | 162 ++++---- RefManageR-0.10.5/RefManageR/man/names.BibEntry.Rd | 68 +-- RefManageR-0.10.5/RefManageR/man/open.BibEntry.Rd | 94 ++-- RefManageR-0.10.5/RefManageR/man/print.BibEntry.Rd | 140 +++---- RefManageR-0.10.5/RefManageR/man/sort.BibEntry.Rd | 152 +++---- RefManageR-0.10.5/RefManageR/man/sub-sub-.BibEntry.Rd | 104 ++--- RefManageR-0.10.5/RefManageR/man/sub-subset-.BibEntry.Rd | 72 +-- RefManageR-0.10.5/RefManageR/man/subset-.BibEntry.Rd | 130 +++--- RefManageR-0.10.5/RefManageR/man/toBiblatex.Rd | 174 ++++---- RefManageR-0.10.5/RefManageR/man/unlist.BibEntry.Rd | 110 ++--- RefManageR-0.10.5/RefManageR/tests/testthat/test-sort.R | 2 RefManageR-0.8.63/RefManageR/inst/Rmd/TestPandoc.Rmd |only RefManageR-0.8.63/RefManageR/inst/pdf |only 76 files changed, 2784 insertions(+), 2679 deletions(-)
Title: Procedures to Generate Patterns under Computerized Adaptive
Testing
Description: Generation of response patterns under dichotomous and polytomous computerized adaptive testing (CAT) framework.
Author: David Magis (U Liege, Belgium), Gilles Raiche (UQAM, Canada), Juan Ramon Barrada (U Zaragoza, Spain)
Maintainer: David Magis <david.magis@ulg.ac.be>
Diff between catR versions 3.5 dated 2015-09-27 and 3.6 dated 2016-01-02
DESCRIPTION | 8 +- MD5 | 20 ++--- NEWS | 22 +++++ R/Pi.R | 199 +++++++++++++++++++++++++++++--------------------- R/genDichoMatrix.R | 5 - man/eapSem.Rd | 2 man/genDichoMatrix.Rd | 8 -- man/genPolyMatrix.Rd | 2 man/nextItem.Rd | 4 - man/randomCAT.Rd | 2 man/thetaEst.Rd | 2 11 files changed, 164 insertions(+), 110 deletions(-)
Title: Approximate String Matching and String Distance Functions
Description: Implements an approximate string matching version of R's native
'match' function. Can calculate various string distances based on edits
(damerau-levenshtein, hamming, levenshtein, optimal sting alignment), qgrams (q-
gram, cosine, jaccard distance) or heuristic metrics (jaro, jaro-winkler). An
implementation of soundex is provided as well. Distances can be computed between
character vectors while taking proper care of encoding or between integer
vectors representing generic sequences.
Author: Mark van der Loo [aut, cre],
Jan van der Laan [ctb],
R Core Team [ctb],
Nick Logan [ctb]
Maintainer: Mark van der Loo <mark.vanderloo@gmail.com>
Diff between stringdist versions 0.9.4 dated 2015-10-26 and 0.9.4.1 dated 2016-01-02
DESCRIPTION | 21 ++++++------ MD5 | 50 ++++++++++++++--------------- NAMESPACE | 2 - NEWS | 6 +++ R/doc_parallel.R | 4 +- R/stringsim.R | 14 +++++--- man/amatch.Rd | 18 +++++----- man/phonetic.Rd | 26 +++++++-------- man/printable_ascii.Rd | 4 +- man/qgrams.Rd | 8 ++-- man/seq_amatch.Rd | 16 ++++----- man/seq_dist.Rd | 18 +++++----- man/seq_qgrams.Rd | 2 - man/seq_sim.Rd | 4 +- man/stringdist-encoding.Rd | 18 +++++----- man/stringdist-metrics.Rd | 64 +++++++++++++++++++------------------- man/stringdist-package.Rd | 10 ++--- man/stringdist-parallelization.Rd | 15 +++----- man/stringdist.Rd | 14 ++++---- man/stringsim.Rd | 20 +++++++---- src/Rstringdist.c | 33 ++++++++++++++----- src/dl.c | 8 ++-- src/lv.c | 9 +++-- src/osa.c | 4 +- src/utils.h | 6 ++- tests/testthat/testStringdist.R | 18 ++++++++++ 26 files changed, 233 insertions(+), 179 deletions(-)
Title: Fast and Accurate Trisomy Prediction in Non-Invasive Prenatal
Testing
Description: Fast and accurate trisomy prediction in non-invasive prenatal
testing.
Author: Dirk de Weerd, Lennart Johansson
Maintainer: Lennart Johansson <l.johansson@umcg.nl>
Diff between NIPTeR versions 1.0.0 dated 2015-11-06 and 1.0.1 dated 2016-01-02
DESCRIPTION | 12 +++---- MD5 | 56 +++++++++++++++++----------------- R/best_fit_beta.R | 12 +++++++ R/bin_sample.R | 16 +++++++++ R/chi_correction.R | 11 ++++++ R/control_group.R | 32 +++++++++++++++++++ R/diagnose_control_group.R | 6 +++ R/gc_correct.R | 10 ++++++ R/ncv_calculation.R | 7 ++++ R/prepare_ncv_template.R | 9 +++++ R/regression.R | 7 ++++ R/z_score.R | 7 ++++ build/vignette.rds |binary inst/doc/NIPTeR.Rmd | 5 +++ inst/doc/NIPTeR.html | 8 +++- man/add_samples_controlgroup.Rd | 12 +++++++ man/as_control_group.Rd | 11 ++++++ man/bin_bam_sample.Rd | 16 +++++++++ man/calculate_ncv_score.Rd | 8 ++++ man/calculate_z_score.Rd | 8 ++++ man/chi_correct.Rd | 11 ++++++ man/diagnose_control_group.Rd | 6 +++ man/gc_correct.Rd | 11 ++++++ man/match_control_group.Rd | 15 +++++++++ man/perform_regression.Rd | 7 ++++ man/prepare_ncv.Rd | 10 ++++++ man/remove_duplicates_controlgroup.Rd | 6 +++ man/remove_sample_controlgroup.Rd | 7 ++++ vignettes/NIPTeR.Rmd | 5 +++ 29 files changed, 295 insertions(+), 36 deletions(-)
Title: R for Amplicon-Sequencing-Based Microbial-Ecology
Description: Characterizing environmental microbiota diversity using amplicon-based next generation sequencing (NGS) data. Functions are developed to manipulate operational taxonomic unit (OTU) table, perform descriptive and inferential statistics, and generate publication-quality plots.
Author: Wen Chen, Joshua Simpson, C. Andre Levesque
Maintainer: Wen Chen <Wen.Chen@agr.gc.ca>
Diff between RAM versions 1.2.1.2 dated 2015-12-01 and 1.2.1.3 dated 2016-01-02
ChangeLog | 7 DESCRIPTION | 16 LICENSE | 2 MD5 | 198 ++++++------ NAMESPACE | 12 NEWS | 23 + R/assist.ado.R | 28 - R/core.R | 716 +++++++++++++++++++++---------------------- R/group.Taxa.R | 99 ++---- R/group_CLUST.R | 234 +++++++------- R/metadata.R | 721 +++++++++++++++++++++----------------------- R/ordination_functions.R | 8 R/phylo_taxonomy.R | 214 ++++++------- R/plot_misc.R | 107 ++---- R/process_data.R | 2 R/summary.R | 5 R/validation_functions.R | 36 +- build/RAM.pdf |binary man/ITS1_and_ITS2.Rd | 12 man/LCA.OTU.Rd | 42 +- man/META.clust.Rd | 54 +-- man/OTU.diversity.Rd | 52 +-- man/OTU.ord.Rd | 106 +++--- man/OTU.rarefy.Rd | 15 man/OTU.recap.Rd | 38 +- man/OTU.subsets.Rd | 35 -- man/RAM-package.Rd | 50 +-- man/RAM.dates.Rd | 15 man/RAM.factors.Rd | 65 +-- man/RAM.input.formatting.Rd | 17 - man/RAM.pal.Rd | 6 man/RAM.plotting.Rd | 98 ++--- man/RAM.rank.formatting.Rd | 20 - man/Taxa.ord.Rd | 118 +++---- man/alignment.Rd | 8 man/assist.NB.Rd | 49 +- man/assist.ado.Rd | 86 ++--- man/assist.ordination.Rd | 47 +- man/col.splitup.Rd | 52 +-- man/combine.OTU.Rd | 14 man/core.OTU.Rd | 35 +- man/core.OTU.rank.Rd | 36 +- man/core.Taxa.Rd | 51 +-- man/correlation.Rd | 89 ++--- man/data.clust.Rd | 75 ++-- man/data.revamp.Rd | 82 ++--- man/dissim.Rd | 92 ++--- man/dissim.heatmap.Rd | 101 +++--- man/dissim.plot.Rd | 122 +++---- man/diversity.indices.Rd | 61 +-- man/envis.NB.Rd | 53 +-- man/factor.abundance.Rd | 50 +-- man/filter.META.Rd | 39 +- man/filter.OTU.Rd | 22 - man/filter.Taxa.Rd | 26 - man/fread.OTU.Rd | 42 +- man/fread.meta.Rd | 16 man/get.rank.Rd | 56 +-- man/group.OTU.Rd | 56 +-- man/group.Taxa.bar.Rd | 82 ++--- man/group.Taxa.box.Rd | 34 +- man/group.abund.Taxa.Rd | 39 +- man/group.abundance.Rd | 52 +-- man/group.abundance.meta.Rd | 51 +-- man/group.diversity.Rd | 84 ++--- man/group.heatmap.Rd | 76 ++-- man/group.heatmap.simple.Rd | 100 +++--- man/group.indicators.Rd | 118 +++---- man/group.rich.Rd | 28 - man/group.spatial.Rd | 68 +--- man/group.spec.Rd | 29 - man/group.temporal.Rd | 51 +-- man/group.venn.Rd | 55 +-- man/location.formatting.Rd | 10 man/match.data.Rd | 27 - man/meta.Rd | 25 - man/network_data.Rd | 32 - man/pcoa.plot.Rd | 176 +++++----- man/percent.classified.Rd | 18 - man/phylo_taxonomy.Rd | 71 ++-- man/phylog_taxonomy.Rd | 72 ++-- man/read.OTU.Rd | 51 +-- man/read.meta.Rd | 14 man/reset.META.Rd | 23 - man/sample.locations.Rd | 83 ++--- man/sample.map.Rd | 49 +- man/sample.sites.Rd | 38 +- man/seq_var.Rd | 126 +++---- man/shared.OTU.Rd | 25 - man/shared.Taxa.Rd | 25 - man/tax.abund.Rd | 79 ++-- man/tax.fill.Rd | 69 +--- man/tax.split.Rd | 72 +--- man/theme_ggplot.Rd | 9 man/top.groups.plot.Rd | 54 +-- man/transpose.LCA.Rd | 9 man/transpose.OTU.Rd | 11 man/valid.OTU.Rd | 11 man/valid.taxonomy.Rd | 42 +- man/write.data.Rd | 21 - 100 files changed, 3250 insertions(+), 3390 deletions(-)
Title: Isotonic Proportional Hazards Model
Description: Nonparametric estimation of an isotonic covariate effect for proprotional hazards model.
Author: Yunro Chung [cre], Anastasia Ivanova, Michael G. Hudgens and Jason P. Fine
Maintainer: Yunro Chung <yunro@live.unc.edu>
Diff between isoph versions 0.4 dated 2015-11-22 and 0.5 dated 2016-01-02
DESCRIPTION | 12 +++-- MD5 | 24 ++++++----- NAMESPACE | 2 R/RcppExports.R |only R/isoph.R | 38 +++++++++++++----- R/isoph.td.R | 63 +++++++++++++++++++++++++----- R/isoph.ti.R | 104 +++++++++++++++++++++++++++++++++++++++++---------- R/newton.raphson.R |only R/picm.R | 9 ---- R/plot.isoph.R | 17 ++++---- R/print.isoph.R | 8 ++- man/isoph-package.Rd | 6 +- man/isoph.Rd | 46 ++++++++++------------ src/BTFft.cpp |only src/RcppExports.cpp |only 15 files changed, 227 insertions(+), 102 deletions(-)