Title: Event-Related Potential (ERP) Data Exploration Made Easy
Description: A set of user-friendly functions to aid in organizing, plotting
and analyzing event-related potential (ERP) data. Provides an easy-to-learn
method to explore ERP data. Should be useful to those without a background
in computer programming, and to those who are new to ERPs (or new to the
more advanced ERP software available). Emphasis has been placed on highly
automated processes using functions with as few arguments as possible.
Expects processed (cleaned) data.
Author: Travis Moore [aut, cre]
Maintainer: Travis Moore <travis.m.moore@vanderbilt.edu>
Diff between erp.easy versions 0.6.2 dated 2015-09-24 and 0.6.3 dated 2015-09-25
DESCRIPTION | 16 ++++++++-------- MD5 | 2 +- 2 files changed, 9 insertions(+), 9 deletions(-)
Title: Bootstrapped Differences of Time Series
Description: Analyze differences among time series curves with Oleson et al's modified p-value technique.
Author: Michael Seedorff, Jacob Oleson, Grant Brown, Joseph Cavanaugh, and Bob McMurray
Maintainer: Michael Seedorff <michael-seedorff@uiowa.edu>
Diff between bdots versions 0.1.1 dated 2015-09-21 and 0.1.2 dated 2015-09-25
DESCRIPTION | 12 ++++++------ MD5 | 12 ++++++------ NAMESPACE | 4 +++- inst/doc/bdots.R | 40 +++++++++++++++++++++++----------------- inst/doc/bdots.Rnw | 13 ++++++++++--- inst/doc/bdots.pdf |binary vignettes/bdots.Rnw | 13 ++++++++++--- 7 files changed, 58 insertions(+), 36 deletions(-)
Title: Bias-Corrected Bayesian Classification with Selected Features
Description: Fully Bayesian Classification with a subset of high-dimensional features, such as expression levels of genes. The data are modeled with a hierarchical Bayesian models using heavy-tailed t distributions as priors. When a large number of features are available, one may like to select only a subset of features to use, typically those features strongly correlated with the response in training cases. Such a feature selection procedure is however invalid since the relationship between the response and the features has be exaggerated by feature selection. This package provides a way to avoid this bias and yield better-calibrated predictions for future cases when one uses F-statistic to select features.
Author: Longhai Li <longhai@math.usask.ca>
Maintainer: Longhai Li <longhai@math.usask.ca>
Diff between BCBCSF versions 1.0-0 dated 2013-01-18 and 1.0-1 dated 2015-09-25
DESCRIPTION | 23 ++++++----------------- MD5 | 8 ++++---- NAMESPACE | 6 +++++- R/comp_pred.r | 47 ++++++++++++++++++++++++++--------------------- R/tr-pr.r | 13 +++++++------ 5 files changed, 48 insertions(+), 49 deletions(-)
Title: Detecting Differentially Expressed Genes in Time Course RNA-Seq
Data
Description: Uses a negative binomial mixed-effects (NBME) model to detect nonparallel differential expression(NPDE) genes and parallel differential expression(PDE) genes in the time course RNA-seq data.
Author: Fan Gao, Xiaoxiao Sun
Maintainer: Fan Gao <fangaohz@gmail.com>
Diff between timeSeq versions 1.0.0 dated 2015-04-19 and 1.0.1 dated 2015-09-25
timeSeq-1.0.0/timeSeq/man/timeSeq_1.0-package.Rd |only timeSeq-1.0.1/timeSeq/DESCRIPTION | 17 ++-- timeSeq-1.0.1/timeSeq/MD5 | 36 ++++++--- timeSeq-1.0.1/timeSeq/NAMESPACE | 2 timeSeq-1.0.1/timeSeq/build |only timeSeq-1.0.1/timeSeq/data/Idgf2.RData |only timeSeq-1.0.1/timeSeq/inst |only timeSeq-1.0.1/timeSeq/man/Idgf2.Rd |only timeSeq-1.0.1/timeSeq/man/object_by_timeSeq.Rd | 6 - timeSeq-1.0.1/timeSeq/man/object_by_timeSeq.geneset.Rd | 6 - timeSeq-1.0.1/timeSeq/man/timeSeq.Rd | 62 ++++++++--------- timeSeq-1.0.1/timeSeq/man/timeSeq.geneset.Rd | 42 +++++------ timeSeq-1.0.1/timeSeq/man/timeSeq.genesetscreeplot.Rd | 6 - timeSeq-1.0.1/timeSeq/man/timeSeq.heatmap.Rd | 10 +- timeSeq-1.0.1/timeSeq/man/timeSeq.permutate.Rd | 38 +++++----- timeSeq-1.0.1/timeSeq/man/timeSeq.plot.Rd | 6 - timeSeq-1.0.1/timeSeq/man/timeSeq.screeplot.Rd | 4 - timeSeq-1.0.1/timeSeq/man/timeSeq.sort.Rd | 20 ++--- timeSeq-1.0.1/timeSeq/man/timeSeq_1.0.1-package.Rd |only timeSeq-1.0.1/timeSeq/vignettes |only 20 files changed, 135 insertions(+), 120 deletions(-)
Title: Betting Odds Conversion
Description: Conversion between the most common odds types for sports betting. Hong Kong odds, US odds, Decimal odds, Indonesian odds, Malaysian odds, and raw Probability are covered in this package.
Author: Marco Blume
Maintainer: Marco Blume <marco.blume@pinnaclesports.com>
Diff between odds.converter versions 1.1 dated 2015-06-04 and 1.2 dated 2015-09-25
odds.converter-1.1/odds.converter/R/odds.converter-internal.R |only odds.converter-1.2/odds.converter/DESCRIPTION | 8 +++--- odds.converter-1.2/odds.converter/MD5 | 12 ++++++++-- odds.converter-1.2/odds.converter/NEWS |only odds.converter-1.2/odds.converter/R/odds.2all.R |only odds.converter-1.2/odds.converter/README.md |only odds.converter-1.2/odds.converter/man/odds.dec2all.Rd |only odds.converter-1.2/odds.converter/man/odds.hk2all.Rd |only odds.converter-1.2/odds.converter/man/odds.indo2all.Rd |only odds.converter-1.2/odds.converter/man/odds.malay2all.Rd |only odds.converter-1.2/odds.converter/man/odds.prob2all.Rd |only odds.converter-1.2/odds.converter/man/odds.us2all.Rd |only 12 files changed, 14 insertions(+), 6 deletions(-)
More information about odds.converter at CRAN
Permanent link
Title: Analise multivariada (brazilian portuguese)
Description: Pacote para analise multivariada, que possui funcoes que executam analise de correspondencia simples (CA) e multipla (MCA), analise de componentes principais (PCA), analise de multiplos fatores (MFA) para dados quantitativos, qualitativos, de frequencia (MFACT) e dados mistos. Tambem possui outras funcoes uteis para a analise multivariada.
Author: Paulo Cesar Ossani <ossanipc@hotmail.com>
Marcelo Angelo Cirillo <macufla@dex.ufla.br>
Maintainer: Paulo Cesar Ossani <ossanipc@hotmail.com>
Diff between MVar.pt versions 1.4 dated 2015-09-09 and 1.5 dated 2015-09-25
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/Plot.CA.R | 36 ++++++++++++++++++++---------------- R/Plot.PCA.R | 36 +++++++++++++++++++++--------------- man/MVar.pt-package.Rd | 4 ++-- man/Plot.CA.Rd | 6 +++--- man/Plot.PCA.Rd | 4 +++- 7 files changed, 59 insertions(+), 47 deletions(-)
Title: Kernel Smoothing for Bivariate Copula Densities
Description: Provides fast implementations of kernel smoothing techniques for
bivariate copula densities, in particular density estimation and resampling.
Author: Thomas Nagler [aut, cre]
Maintainer: Thomas Nagler <thomas.nagler@tum.de>
Diff between kdecopula versions 0.1.0 dated 2015-09-10 and 0.2.0 dated 2015-09-25
kdecopula-0.1.0/kdecopula/man/kdecopula-package.Rd |only kdecopula-0.2.0/kdecopula/DESCRIPTION | 20 kdecopula-0.2.0/kdecopula/MD5 | 26 kdecopula-0.2.0/kdecopula/NAMESPACE | 7 kdecopula-0.2.0/kdecopula/NEWS.md |only kdecopula-0.2.0/kdecopula/R/dprhkdecop.R |only kdecopula-0.2.0/kdecopula/R/generics.R |only kdecopula-0.2.0/kdecopula/R/kdecop.R | 448 ++---------- kdecopula-0.2.0/kdecopula/R/kdecopula-package.R |only kdecopula-0.2.0/kdecopula/R/plot.kdecopula.R |only kdecopula-0.2.0/kdecopula/README.md |only kdecopula-0.2.0/kdecopula/inst/README-unnamed-chunk-3-1.png |only kdecopula-0.2.0/kdecopula/inst/README-unnamed-chunk-6-1.png |only kdecopula-0.2.0/kdecopula/inst/README-unnamed-chunk-7-1.png |only kdecopula-0.2.0/kdecopula/inst/README-unnamed-chunk-8-1.png |only kdecopula-0.2.0/kdecopula/inst/README-unnamed-chunk-9-1.png |only kdecopula-0.2.0/kdecopula/man/dkdecop.Rd |only kdecopula-0.2.0/kdecopula/man/kdecop.Rd | 163 ++-- kdecopula-0.2.0/kdecopula/man/kdecopula.Rd |only kdecopula-0.2.0/kdecopula/man/plot.kdecopula.Rd | 76 -- kdecopula-0.2.0/kdecopula/man/wdbc.Rd | 96 +- 21 files changed, 316 insertions(+), 520 deletions(-)
Title: Chemical Information from the Web
Description: Chemical information from around the web. This package interacts with a suite of web APIs for chemical information.
Author: Eduard Szoecs [aut, cre],
Daniel Muench [ctb],
Johannes Ranke [ctb]
Maintainer: Eduard Szoecs <eduardszoecs@gmail.com>
Diff between webchem versions 0.0.2 dated 2015-08-14 and 0.0.3 dated 2015-09-25
webchem-0.0.2/webchem/R/allanwood.R |only webchem-0.0.2/webchem/man/allanwood.Rd |only webchem-0.0.2/webchem/tests/testthat/test-allanwood.R |only webchem-0.0.3/webchem/DESCRIPTION | 21 ++++--- webchem-0.0.3/webchem/MD5 | 51 +++++++++++------ webchem-0.0.3/webchem/NAMESPACE | 10 +++ webchem-0.0.3/webchem/NEWS | 25 +++++++- webchem-0.0.3/webchem/R/alanwood.R |only webchem-0.0.3/webchem/R/cir.R | 9 ++- webchem-0.0.3/webchem/R/cts.R | 6 +- webchem-0.0.3/webchem/R/etox.R |only webchem-0.0.3/webchem/R/physprop.R |only webchem-0.0.3/webchem/R/ppdb.R |only webchem-0.0.3/webchem/R/webchem-deprecated.R |only webchem-0.0.3/webchem/data |only webchem-0.0.3/webchem/man/alanwood.Rd |only webchem-0.0.3/webchem/man/cir_query.Rd | 3 + webchem-0.0.3/webchem/man/cts_compinfo.Rd | 2 webchem-0.0.3/webchem/man/cts_convert.Rd | 4 - webchem-0.0.3/webchem/man/etox_basic.Rd |only webchem-0.0.3/webchem/man/etox_targets.Rd |only webchem-0.0.3/webchem/man/etox_tests.Rd |only webchem-0.0.3/webchem/man/get_etoxid.Rd |only webchem-0.0.3/webchem/man/pan.Rd | 2 webchem-0.0.3/webchem/man/physprop.Rd |only webchem-0.0.3/webchem/man/ppdb_buildidx.Rd |only webchem-0.0.3/webchem/man/ppdb_idx.Rd |only webchem-0.0.3/webchem/man/ppdb_query.Rd |only webchem-0.0.3/webchem/man/webchem-deprecated.Rd |only webchem-0.0.3/webchem/tests/testthat/test-alanwood.R |only webchem-0.0.3/webchem/tests/testthat/test-chemspider.R | 20 ++++++ webchem-0.0.3/webchem/tests/testthat/test-cir.R | 14 ++++ webchem-0.0.3/webchem/tests/testthat/test-cts.R | 31 +++++++++- webchem-0.0.3/webchem/tests/testthat/test-etox.R |only webchem-0.0.3/webchem/tests/testthat/test-pan.R | 18 ++++-- webchem-0.0.3/webchem/tests/testthat/test-physprop.R |only webchem-0.0.3/webchem/tests/testthat/test-ppdb.R |only webchem-0.0.3/webchem/tests/testthat/test-pubchem.R | 18 +++++- 38 files changed, 186 insertions(+), 48 deletions(-)
Title: Cardiovascular Safety Exposure-Response Modeling in Early-Phase
Clinical Studies
Description: Includes 100 mixed-effects model structures describing the relationship between drug concentration and QT interval, heart rate/pulse rate or blood pressure. Given an exposure-response dataset, the tool fits each model structure to the observed data.
Author: Daniela J Conrado [aut, cre], William S Denney [aut], Gregory J Hather [aut], Danny Chen [ctb]
Maintainer: Daniela J Conrado <danielac@metrumrg.com>
Diff between cardioModel versions 1.0 dated 2015-09-24 and 1.1 dated 2015-09-25
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/21_cardioModel.R | 45 ++++++++++++++++++++++++++------------------- R/data.R | 2 +- data/sim_QTcf.RData |binary man/sim_QTcf.Rd | 2 +- 6 files changed, 37 insertions(+), 30 deletions(-)
Title: Community Ecology Package
Description: Ordination methods, diversity analysis and other
functions for community and vegetation ecologists.
Author: Jari Oksanen, F. Guillaume Blanchet, Roeland Kindt, Pierre Legendre,
Peter R. Minchin, R. B. O'Hara, Gavin L. Simpson, Peter Solymos,
M. Henry H. Stevens, Helene Wagner
Maintainer: Jari Oksanen <jari.oksanen@oulu.fi>
Diff between vegan versions 2.3-0 dated 2015-05-26 and 2.3-1 dated 2015-09-25
DESCRIPTION | 10 +-- MD5 | 135 +++++++++++++++++++++--------------------- NAMESPACE | 4 - R/adonis.R | 6 - R/alias.cca.R | 4 - R/anosim.R | 3 R/anova.cca.R | 16 +++- R/anova.ccabyterm.R | 70 ++++++++++++++------- R/anova.ccalist.R | 30 +++++---- R/anova.ccanull.R | 21 ++++-- R/biplot.rda.R | 7 +- R/centroids.cca.R | 2 R/factorfit.R | 3 R/mantel.R | 3 R/mantel.partial.R | 3 R/metaMDS.R | 21 ++++-- R/metaMDSdist.R | 1 R/monoMDS.R | 2 R/mrpp.R | 3 R/mso.R | 4 - R/oecosimu.R | 11 ++- R/ordiR2step.R | 5 + R/ordiareatest.R | 3 R/permustats.R | 37 ++++++++--- R/permutest.betadisper.R | 10 +-- R/permutest.cca.R | 4 - R/plot.cca.R | 10 +-- R/plot.prc.R | 9 +- R/points.cca.R | 9 +- R/predict.cca.R | 11 ++- R/predict.rda.R | 11 ++- R/print.cca.R | 2 R/print.permutest.cca.R | 3 R/protest.R | 3 R/rarecurve.R | 10 +++ R/scalingUtils.R |only R/scores.cca.R | 22 +++--- R/scores.rda.R | 6 + R/simper.R | 3 R/summary.cca.R | 14 ++-- R/summary.prc.R | 7 -- R/text.cca.R | 9 +- R/tolerance.cca.R | 9 +- R/vectorfit.R | 3 data/BCI.env.rda |only inst/NEWS.Rd | 79 ++++++++++++++++++++++++ inst/doc/FAQ-vegan.pdf |binary inst/doc/NEWS.html | 92 ++++++++++++++++++++++++++++ inst/doc/decision-vegan.pdf |binary inst/doc/diversity-vegan.pdf |binary inst/doc/intro-vegan.pdf |binary man/BCI.Rd | 42 +++++++++---- man/adipart.Rd | 6 + man/anova.cca.Rd | 5 + man/biplot.rda.Rd | 22 +++++- man/cca.Rd | 4 - man/diversity.Rd | 107 ++++----------------------------- man/monoMDS.Rd | 2 man/permustats.Rd | 12 +-- man/plot.cca.Rd | 75 +++++++++++++++-------- man/prc.Rd | 23 +++++-- man/predict.cca.Rd | 16 +++- man/rarefy.Rd |only man/specaccum.Rd | 77 ++++++++++------------- man/tolerance.Rd | 8 +- vignettes/FAQ-vegan.pdf |binary vignettes/NEWS.html | 92 ++++++++++++++++++++++++++++ vignettes/decision-vegan.tex | 20 +++--- vignettes/diversity-vegan.tex | 78 ++++++++++++------------ vignettes/intro-vegan.tex | 50 +++++++-------- 70 files changed, 876 insertions(+), 493 deletions(-)
Title: Tools for Storing, Restoring and Searching for R Objects
Description: Data exploration and modelling is a process in which a lot of data
artifacts are produced. Artifacts like: subsets, data aggregates, plots,
statistical models, different versions of data sets and different versions
of results. The more projects we work with the more artifacts are produced
and the harder it is to manage these artifacts. Archivist helps to store
and manage artifacts created in R. Archivist allows you to store selected
artifacts as a binary files together with their metadata and relations.
Archivist allows to share artifacts with others, either through shared
folder or github. Archivist allows to look for already created artifacts by
using it's class, name, date of the creation or other properties. Makes it
easy to restore such artifacts. Archivist allows to check if new artifact
is the exact copy that was produced some time ago. That might be useful
either for testing or caching.
Author: Przemyslaw Biecek [aut, cre],
Marcin Kosinski [aut]
Maintainer: Przemyslaw Biecek <przemyslaw.biecek@gmail.com>
Diff between archivist versions 1.6 dated 2015-08-15 and 1.7 dated 2015-09-25
archivist-1.6/archivist/R/saveSetToRepo.R |only archivist-1.6/archivist/man/saveSetToRepo.Rd |only archivist-1.7/archivist/DESCRIPTION | 11 +- archivist-1.7/archivist/MD5 | 104 ++++++++++----------- archivist-1.7/archivist/NAMESPACE | 19 ++- archivist-1.7/archivist/NEWS.md |only archivist-1.7/archivist/R/Tags.R | 20 ++-- archivist-1.7/archivist/R/ahistory.R | 32 +++--- archivist-1.7/archivist/R/archivist-package.R | 26 ++--- archivist-1.7/archivist/R/archivistOptions.R | 2 archivist-1.7/archivist/R/aread.R | 30 ++++-- archivist-1.7/archivist/R/asearch.R | 39 +++++-- archivist-1.7/archivist/R/cache.R | 2 archivist-1.7/archivist/R/copyToRepo.R | 6 - archivist-1.7/archivist/R/createEmptyRepo.R | 14 +- archivist-1.7/archivist/R/deleteRepo.R | 11 +- archivist-1.7/archivist/R/getTags.R | 2 archivist-1.7/archivist/R/loadFromRepo.R | 10 +- archivist-1.7/archivist/R/magrittr.R | 4 archivist-1.7/archivist/R/rmFromRepo.R | 2 archivist-1.7/archivist/R/saveToRepo.R | 2 archivist-1.7/archivist/R/searchInRepo.R | 2 archivist-1.7/archivist/R/setRepo.R | 36 ++++--- archivist-1.7/archivist/R/shinySearchInLocalRepo.R | 38 ++++--- archivist-1.7/archivist/R/showRepo.R | 10 -- archivist-1.7/archivist/R/summaryRepo.R | 6 - archivist-1.7/archivist/R/zipRepo.R | 2 archivist-1.7/archivist/R/zzz.R | 2 archivist-1.7/archivist/inst |only archivist-1.7/archivist/man/Repository.Rd | 5 - archivist-1.7/archivist/man/Tags.Rd | 25 ++--- archivist-1.7/archivist/man/addTagsRepo.Rd | 5 - archivist-1.7/archivist/man/ahistory.Rd | 24 ++-- archivist-1.7/archivist/man/archivist-package.Rd | 5 - archivist-1.7/archivist/man/archivistOptions.Rd | 7 - archivist-1.7/archivist/man/aread.Rd | 18 ++- archivist-1.7/archivist/man/asearch.Rd | 15 +-- archivist-1.7/archivist/man/cache.Rd | 7 - archivist-1.7/archivist/man/copyToRepo.Rd | 9 - archivist-1.7/archivist/man/createEmptyRepo.Rd | 9 - archivist-1.7/archivist/man/deleteRepo.Rd | 13 +- archivist-1.7/archivist/man/getTags.Rd | 12 +- archivist-1.7/archivist/man/loadFromRepo.Rd | 7 - archivist-1.7/archivist/man/magrittr.Rd | 7 - archivist-1.7/archivist/man/md5hash.Rd | 5 - archivist-1.7/archivist/man/rmFromRepo.Rd | 6 - archivist-1.7/archivist/man/saveToRepo.Rd | 6 - archivist-1.7/archivist/man/searchInRepo.Rd | 7 - archivist-1.7/archivist/man/setRepo.Rd | 8 - archivist-1.7/archivist/man/shinySearchInRepo.Rd | 14 ++ archivist-1.7/archivist/man/showRepo.Rd | 15 --- archivist-1.7/archivist/man/summaryRepo.Rd | 11 +- archivist-1.7/archivist/man/zipRepo.Rd | 12 +- archivist-1.7/archivist/tests |only 54 files changed, 366 insertions(+), 318 deletions(-)
Title: The Skillings-Mack Test Statistic for Block Designs with Missing
Observations
Description: A generalization of the statistic used in Friedman's ANOVA method and in Durbin's rank test. This nonparametric statistical test is useful for the data obtained from block designs with missing observations occurring randomly. A resulting p-value is based on the chi-squared distribution and Monte Carlo method.
Author: Patchanok Srisuradetchai
Maintainer: Patchanok Srisuradetchai <s.patchanok@gmail.com>
Diff between Skillings.Mack versions 1.0-2 dated 2013-09-17 and 1.10 dated 2015-09-25
Skillings.Mack-1.0-2/Skillings.Mack/R/SkiMack.R |only Skillings.Mack-1.0-2/Skillings.Mack/man/SkiMack.Rd |only Skillings.Mack-1.10/Skillings.Mack/DESCRIPTION | 23 ++++++++++----------- Skillings.Mack-1.10/Skillings.Mack/MD5 | 8 +++---- Skillings.Mack-1.10/Skillings.Mack/NAMESPACE | 5 +++- Skillings.Mack-1.10/Skillings.Mack/R/Ski.Mack.R |only Skillings.Mack-1.10/Skillings.Mack/man/Ski.Mack.Rd |only 7 files changed, 20 insertions(+), 16 deletions(-)
More information about Skillings.Mack at CRAN
Permanent link
Title: Tools for the 'qdap' Package
Description: A collection of tools associated with the 'qdap' package
that may be useful outside of the context of text analysis.
Author: Bryan Goodrich [ctb],
Dason Kurkiewicz [ctb],
Kirill Muller [ctb],
Tyler Rinker [aut, cre]
Maintainer: Tyler Rinker <tyler.rinker@gmail.com>
Diff between qdapTools versions 1.1.0 dated 2014-12-21 and 1.3.1 dated 2015-09-25
DESCRIPTION | 24 ++++++------- MD5 | 69 ++++++++++++++++++++++------------------ NAMESPACE | 7 +++- NEWS | 25 +++++++++++++- R/list2df.R | 24 ++++++++----- R/loc_split.R | 43 +++++++++++++++++------- R/mtabulate.R | 50 +++++++++++++++++++++++----- R/read_docx.R | 14 ++++++-- R/repo2github.R | 4 +- R/run_split.R |only R/shift.R |only R/split_vector.R | 3 + R/start_end.R |only R/url_dl.R | 2 - README.md | 24 ++++++++----- inst/CITATION | 10 ++--- man/Deprecated.Rd | 3 + man/hash.Rd | 3 + man/id.Rd | 3 + man/list2df.Rd | 3 + man/loc_split.Rd | 8 ++-- man/lookup.Rd | 3 + man/lookup_e.Rd | 3 + man/mtabulate.Rd | 15 +++++--- man/pad.Rd | 3 + man/print.v_outer.Rd | 3 + man/read_docx.Rd | 15 ++++++-- man/repo2github.Rd | 3 + man/run_split.Rd |only man/shift.Rd |only man/split_vector.Rd | 6 ++- man/start_end.Rd |only man/text2color.Rd | 3 + man/timeconv.Rd | 3 + man/url_dl.Rd | 3 + man/v_outer.Rd | 3 + tests/testthat/test-mtabulate.R | 5 +- tests/testthat/test-run_split.R |only tests/testthat/test-shift.R |only tests/testthat/test-start_end.R |only 40 files changed, 262 insertions(+), 125 deletions(-)
Title: Population and Evolutionary Genetics Analysis System
Description: Functions for reading, writing, plotting, analysing, and manipulating allelic and haplotypic data, and for the analysis of population nucleotide sequences and micro-satellites including coalescence analyses.
Author: Emmanuel Paradis [aut, cre, cph],
Thibaut Jombart [aut, cph],
Klaus Schliep [aut, cph],
Alastair Potts [aut, cph],
David Winter [aut, cph]
Maintainer: Emmanuel Paradis <Emmanuel.Paradis@ird.fr>
Diff between pegas versions 0.8-1 dated 2015-06-24 and 0.8-2 dated 2015-09-25
DESCRIPTION | 8 +++--- MD5 | 26 ++++++++++----------- NAMESPACE | 12 ++++++--- NEWS | 35 ++++++++++++++++++++++++++++ R/amova.R | 16 ++++--------- R/conversion.R | 8 +++--- R/haplotype.R | 56 ++++++++++++++++++++++++++++++++++------------ build/vignette.rds |binary inst/doc/ReadingFiles.pdf |binary man/haploNet.Rd | 11 ++++++--- man/haplotype.loci.Rd | 4 ++- man/mst.Rd | 7 +++++ man/tajima.test.Rd | 4 +++ src/pegas.c | 16 ++++++++----- 14 files changed, 143 insertions(+), 60 deletions(-)
Title: A System for Embedded Scientific Computing and Reproducible
Research with R
Description: The OpenCPU system exposes an HTTP API for embedded scientific
computing with R. This provides scalable foundations for integrating R
based analysis and visualization modules into pipelines, web applications
or big data infrastructures. The OpenCPU server can run either as a
single-user development server within the interactive R session, or as a
high performance multi-user cloud server that builds on Linux, Nginx and
rApache. The current R package forms the core of the system. When loaded
in R, it automatically initiates the single-user server and displays the
web address in the console. Visit the OpenCPU website for detailed
information and documentation on the API.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between opencpu versions 1.4.6 dated 2015-01-31 and 1.5.1 dated 2015-09-25
DESCRIPTION | 9 +++---- MD5 | 50 ++++++++++++++++++++++---------------------- NEWS | 6 +++++ R/cmd_exists.R | 2 - R/emptyplot.R | 2 - R/eval_fork.R | 2 - R/eval_psock.R | 2 - R/extract.R | 14 ++++++------ R/fixplot.R | 4 +-- R/gettmpdir.R | 2 - R/github_install.R | 3 +- R/httpget_github.R | 2 - R/httpget_object.R | 6 ++--- R/httpget_webhook.R | 2 - R/httpuv_fork.R | 2 - R/listallusers.R | 2 - R/main.R | 2 - R/parse_arg.R | 2 - R/rapachehandler.R | 5 ++++ R/request.R | 5 ++-- R/res.R | 2 - R/rookhandler.R | 7 +++++- R/userlibpath.R | 24 ++++++++++++++++++--- build/vignette.rds |binary inst/doc/opencpu-paper.pdf |binary inst/doc/opencpu-server.pdf |binary 26 files changed, 96 insertions(+), 61 deletions(-)
Title: Access to the Neotoma Paleoecological Database Through R
Description: Access paleoecological datasets from the Neotoma Paleoecological
Database using the published API (http://api.neotomadb.org/). The functions
in this package access various pre-built API functions and attempt to return
the results from Neotoma in a usable format for researchers and the public.
Author: Simon J. Goring [aut, cre], Gavin L. Simpson [aut], Jeremiah P. Marsicek [ctb],
Karthik Ram [aut], Luke Sosalla [ctb]
Maintainer: Simon J. Goring <goring@wisc.edu>
Diff between neotoma versions 1.3.3 dated 2015-08-22 and 1.4.0 dated 2015-09-25
DESCRIPTION | 8 ++++---- MD5 | 12 +++++++----- NAMESPACE | 5 +++++ NEWS | 5 +++++ R/get_download.R | 10 +++++++--- R/plot-methods.R |only README.md | 7 ++++--- inst/img/Thumbs.db |only 8 files changed, 32 insertions(+), 15 deletions(-)
Title: Tools for Nanoparticle Simulation and Calculation of PDF and
Total Scattering Structure Function
Description: This software package implements functions to simulate spherical, ellipsoid and cubic polyatomic nanoparticles with arbitrary crystal structures and to calculate the associated pair-distribution function and X-ray/neutron total-scattering signals. It also provides a target function that can be used for simultaneous fitting of small- and wide-angle total scattering data in real and reciprocal spaces. The target function can be generated either as a sum of weighted residuals for individual datasets or as a vector of residuals suitable for optimization using multi-criteria algorithms (e.g. Pareto methods).
Author: Anton Gagin, Katharine Mullen, Igor Levin
Maintainer: Anton Gagin <av.gagin@gmail.com>
Diff between nanop versions 2.0-5 dated 2015-04-07 and 2.0-6 dated 2015-09-25
DESCRIPTION | 8 +-- MD5 | 8 +-- NAMESPACE | 3 + inst/CITATION | 54 ++++++++++----------- man/plotPart.Rd | 144 ++++++++++++++++++++++++++++---------------------------- 5 files changed, 110 insertions(+), 107 deletions(-)
Title: Multi-way Standard Error Clustering
Description: Exports two functions implementing
multi-way clustering using the method suggested by Cameron, Gelbach, &
Miller (2011) and cluster (or block)
bootstrapping for estimating variance-covariance matrices. Normal one and
two-way clustering matches the results of other common statistical
packages. Missing values are handled transparently and rudimentary
parallelization support is provided.
Author: Nathaniel Graham and Mahmood Arai and Björn Hagströmer
Maintainer: Nathaniel Graham <npgraham1@gmail.com>
Diff between multiwayvcov versions 1.2.1 dated 2014-10-20 and 1.2.2 dated 2015-09-25
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- NAMESPACE | 13 ++++++++++++- R/cluster_boot.r | 23 ++++++++++++++++++++++- R/cluster_vcov.r | 31 ++++++++++++++++++++++++++++--- man/cluster.boot.Rd | 11 ++++++++++- man/cluster.vcov.Rd | 17 +++++++++++++++-- man/petersen.Rd | 3 ++- 8 files changed, 101 insertions(+), 21 deletions(-)
Title: Estimation of Multinormal Mixture Distribution
Description: Fit multivariate mixture of normal distribution using
covariance structure.
Author: Charles-Edouard Giguere
Maintainer: Charles-Edouard Giguere <ce.giguere@gmail.ca>
Diff between mmeln versions 1.1 dated 2013-02-11 and 1.2 dated 2015-09-25
ChangeLog | 3 + DESCRIPTION | 16 +++-- MD5 | 22 +++---- NAMESPACE | 4 + R/cs.R | 147 ++++++++++++++++++++++++++++++--------------------- R/ind.R | 20 +++--- R/mmeln.R | 10 +-- R/mutil.R | 10 +-- man/estim.mmeln.Rd | 6 +- man/mmeln-package.Rd | 7 +- man/mmeln.Rd | 9 ++- man/post.Rd | 7 +- 12 files changed, 152 insertions(+), 109 deletions(-)
Title: Multi-Analysis Distance Sampling
Description: Performs distance sampling analyses on a number of species
accounting for unidentified sightings, model uncertainty and covariate
uncertainty.
Author: Laura Marshall
Maintainer: Laura Marshall <lhm@st-and.ac.uk>
Diff between mads versions 0.1.2 dated 2015-02-27 and 0.1.3 dated 2015-09-25
mads-0.1.2/mads/inst/testData/input_checks/ddf_dat_CD.csv |only mads-0.1.3/mads/DESCRIPTION | 10 mads-0.1.3/mads/MD5 | 91 ++-- mads-0.1.3/mads/NAMESPACE | 1 mads-0.1.3/mads/NEWS | 12 mads-0.1.3/mads/R/calculate.dht.R | 11 mads-0.1.3/mads/R/check.bootstrap.options.r | 2 mads-0.1.3/mads/R/check.covar.uncertainty.R | 4 mads-0.1.3/mads/R/execute.multi.analysis.R | 274 +++++++------- mads-0.1.3/mads/R/fit.ddf.models.R | 1 mads-0.1.3/mads/R/process.bootstrap.results.R | 2 mads-0.1.3/mads/R/resample.covariates.R | 4 mads-0.1.3/mads/R/rtpois.R | 3 mads-0.1.3/mads/R/summary.ma.species.R | 2 mads-0.1.3/mads/R/summary.ma.unid.R | 1 mads-0.1.3/mads/inst/tests/test_DataInputChecks.R | 133 +++++- mads-0.1.3/mads/inst/tests/test_singleObserver.R | 187 ++++----- mads-0.1.3/mads/man/accumulate.results.Rd | 3 mads-0.1.3/mads/man/calculate.dht.Rd | 14 mads-0.1.3/mads/man/check.convergence.Rd | 3 mads-0.1.3/mads/man/check.covar.uncertainty.Rd | 3 mads-0.1.3/mads/man/check.ddf.models.Rd | 3 mads-0.1.3/mads/man/check.species.code.definitions.Rd | 3 mads-0.1.3/mads/man/check.species.presence.Rd | 3 mads-0.1.3/mads/man/create.obs.table.Rd | 3 mads-0.1.3/mads/man/create.param.arrays.Rd | 3 mads-0.1.3/mads/man/create.result.arrays.Rd | 3 mads-0.1.3/mads/man/execute.multi.analysis.Rd | 15 mads-0.1.3/mads/man/fit.ddf.models.Rd | 3 mads-0.1.3/mads/man/format.dht.results.Rd | 3 mads-0.1.3/mads/man/get.datasets.Rd | 3 mads-0.1.3/mads/man/mae.warning.Rd | 3 mads-0.1.3/mads/man/model.description.Rd | 3 mads-0.1.3/mads/man/process.bootstrap.results.Rd | 3 mads-0.1.3/mads/man/process.warnings.Rd | 3 mads-0.1.3/mads/man/prorate.unidentified.Rd | 3 mads-0.1.3/mads/man/renumber.duplicates.Rd | 3 mads-0.1.3/mads/man/resample.covariates.Rd | 3 mads-0.1.3/mads/man/resample.data.Rd | 3 mads-0.1.3/mads/man/rtpois.Rd | 3 mads-0.1.3/mads/man/store.param.ests.Rd | 3 mads-0.1.3/mads/man/summary.ma.Rd | 3 mads-0.1.3/mads/man/summary.ma.allspecies.Rd | 3 mads-0.1.3/mads/man/summary.ma.allunid.Rd | 3 mads-0.1.3/mads/man/summary.ma.analysis.Rd | 3 mads-0.1.3/mads/man/summary.ma.species.Rd | 3 mads-0.1.3/mads/man/summary.ma.unid.Rd | 3 47 files changed, 497 insertions(+), 354 deletions(-)
Title: Penalized Likelihood Estimation and Prediction under the Joint
Cox Models Between Tumour Progression and Death for
Meta-Analysis
Description: Perform regression analyses under the joint Cox proportional hazards model between tumour progression and death for meta-analysis.
The method is applicable for meta-analysis combining several studies or for cluster survival data.
Author: Takeshi Emura
Maintainer: Takeshi Emura <takeshiemura@gmail.com>
Diff between joint.Cox versions 2.0 dated 2015-06-18 and 2.1 dated 2015-09-25
DESCRIPTION | 13 +++++++------ MD5 | 14 ++++++++------ NAMESPACE | 2 ++ R/F.window.R |only man/F.window.Rd |only man/dataOvarian.Rd | 10 +++++----- man/joint.Cox-package.Rd | 9 +++++---- man/jointCox.indep.reg.Rd | 4 ++-- man/jointCox.reg.Rd | 4 ++-- 9 files changed, 31 insertions(+), 25 deletions(-)
Title: Hidden State Speciation and Extinction
Description: Sets up and executes a HiSSE model (Hidden State Speciation and Extinction) on a phylogeny and character sets to test for hidden shifts in trait dependent rates of diversification.
Author: Jeremy M. Beaulieu <jbeaulieu@nimbios.org>, Brian O'Meara <bomeara@utk.edu>
Maintainer: Jeremy Beaulieu <jbeaulieu@nimbios.org>
Diff between hisse versions 1.1 dated 2015-06-16 and 1.2 dated 2015-09-25
DESCRIPTION | 15 ++++++++------- MD5 | 28 +++++++++++++++++++++------- NAMESPACE | 8 ++++++-- R/marginRecon.R | 7 ++----- R/plotHisse.R | 4 ++++ R/simulateHisse.R |only R/singleModels.R |only README.md |only build |only inst |only man/plotHisse.Rd | 21 +++++++++++---------- man/simToPhylo.Rd |only man/simulateHisse.Rd |only man/transMat.Rd | 2 +- tests/testthat/test_likelihood.R | 4 ++-- tests/testthat/test_simulator.R |only vignettes |only 17 files changed, 55 insertions(+), 34 deletions(-)
Title: Distance Sampling Simulations
Description: Performs distance sampling simulations. It repeatedly
generates instances of a user defined population within a given survey
region, generates realisations of a survey design (currently these must
be pre-generated using Distance software) and simulates the detection
process. The data are then analysed so that the results can be compared for
accuracy and precision across all replications. This will allow users to
select survey designs which will give them the best accuracy and precision
given their expectations about population distribution. Any uncertainty in
population distribution or population parameters can be included by running
the different survey designs for a number of different population
descriptions. An example simulation can be found in the help file
for make.simulation.
Author: Laura Marshall <lhm@st-and.ac.uk>
Maintainer: Laura Marshall <lhm@st-and.ac.uk>
Diff between DSsim versions 1.0.3 dated 2015-02-27 and 1.0.4 dated 2015-09-25
DESCRIPTION | 60 ++-- MD5 | 194 +++++++------- NAMESPACE | 69 +++-- NEWS | 18 + R/Class.Constructors.R | 73 +++-- R/DDF.Analysis.R | 66 ++--- R/DDF.Data.R | 29 +- R/Density.R | 105 +++----- R/Detectability.R | 42 +-- R/LT.Design.R | 52 +-- R/LT.EqAngle.ZZ.Design.R | 4 R/LT.EqSpace.ZZ.Design.R | 4 R/LT.Random.Design.R | 4 R/LT.Survey.R | 41 --- R/LT.Survey.Results.R | 169 +++++++++--- R/LT.Systematic.Design.R | 3 R/LT.User.Specified.Design.R | 3 R/Line.Transect.R | 38 +- R/Obs.Table.R | 3 R/PT.Design.R | 19 - R/Population.Description.R | 87 ++---- R/Population.R | 53 ++-- R/Region.R | 70 ++--- R/Region.Table.R | 3 R/Sample.Table.R | 3 R/Simulation.R | 431 +++++++++++++++++---------------- R/Simulation.Summary.R | 10 R/Single.Obs.DDF.Data.R | 23 - R/Single.Obs.LT.Survey.R | 34 -- R/Survey.Design.R | 38 -- R/Survey.R | 51 +-- R/add.dist.error.R | 1 R/add.summary.results.R | 1 R/calc.area.R | 13 R/calc.poss.detect.dists.R | 9 R/check.intersection.R | 1 R/check.shapefile.R | 4 R/coords.from.shapefile.R | 3 R/generate.pop.D.R | 20 - R/generate.pop.N.R | 2 R/generic.functions.R | 22 - R/get.ave.density.R | 8 R/get.bound.box.R | 17 - R/get.sampler.info.R | 2 R/get.surface.constant.R | 3 R/get.surface.gam.R | 2 R/hn.detect.R | 2 R/hr.detect.R | 1 R/is.gap.R | 12 R/modify.strata.for.analysis.R |only R/simulate.detections.R | 4 R/single.simulation.loop.R | 8 R/uf.detect.R |only man/DDF.Analysis-class.Rd | 41 +-- man/DDF.Data-class.Rd | 10 man/Density-class.Rd | 99 +------ man/Detectability-class.Rd | 37 +- man/LT.Design-class.Rd | 14 - man/LT.Survey-class.Rd | 14 - man/LT.Survey.Results-class.Rd | 83 +----- man/Line.Transect-class.Rd | 63 ---- man/Obs.Table-class.Rd | 8 man/PT.Design-class.Rd |only man/Population-class.Rd | 45 +-- man/Population.Description-class.Rd | 43 +-- man/Region-class.Rd | 113 ++------ man/Region.Table-class.Rd | 8 man/Sample.Table-class.Rd | 8 man/Simulation-class.Rd | 83 ++---- man/Simulation.Summary-class.Rd | 10 man/Single.Obs.DDF.Data-class.Rd | 47 --- man/Single.Obs.LT.Survey-class.Rd | 3 man/Survey-class.Rd | 15 - man/Survey.Design-class.Rd | 37 +- man/add.hotspot-methods.Rd | 8 man/create.bins.Rd | 3 man/create.region.table-methods.Rd | 9 man/create.sample.table-methods.Rd | 11 man/create.survey.results-methods.Rd | 13 man/description.summary.Rd | 9 man/generate.population-methods.Rd | 19 - man/generate.transects-methods.Rd | 19 - man/get.N-methods.Rd | 3 man/get.area-methods.Rd | 5 man/get.distance.data-methods.Rd | 9 man/make.ddf.analysis.list.Rd | 14 - man/make.density.Rd | 8 man/make.design.Rd | 6 man/make.detectability.Rd | 3 man/make.population.description.Rd | 3 man/make.region.Rd | 3 man/make.simulation.Rd | 3 man/plot.DDF.Data-methods.Rd |only man/plot.Density-methods.Rd |only man/plot.LT.Survey.Results-methods.Rd |only man/plot.Line.Transect-methods.Rd |only man/plot.Population-methods.Rd |only man/plot.Region-methods.Rd |only man/rename.duplicates.Rd | 3 man/run-methods.Rd | 12 man/run.analysis-methods.Rd | 13 man/show.Simulation-methods.Rd |only man/show.Simulation.Summary-methods.Rd |only man/summary.Simulation-methods.Rd |only 104 files changed, 1351 insertions(+), 1540 deletions(-)
Title: Bayesian Ordination and Regression AnaLysis
Description: Bayesian approaches for analyzing multivariate data in ecology. Estimation is performed using Markov Chain Monte Carlo (MCMC) methods via JAGS. Three types of models may be fitted: 1) With explanatory variables only, boral fits independent column GLMs to each column of the response matrix; 2) With latent variables only, boral fits a purely latent variable model for model-based unconstrained ordination; 3) With explanatory and latent variables, boral fits correlated column GLMs with latent variables to account for any residual correlation between the columns of the response matrix.
Author: Francis K.C. Hui
Maintainer: Francis Hui <fhui28@gmail.com>
Diff between boral versions 0.9 dated 2015-08-22 and 0.9.1 dated 2015-09-25
DESCRIPTION | 10 +++--- MD5 | 15 +++++---- R/auxilaryfunctions.R | 79 +++++++++++++++++++++++++++++++---------------- R/boral.jags.R | 83 ++++++++++++++++++++++++++++++-------------------- inst/NEWS.Rd | 82 ++++++++++++++++++++++++------------------------- man/boral-package.Rd | 2 - man/boral.Rd | 6 +-- tests |only 8 files changed, 161 insertions(+), 116 deletions(-)
Title: Extensions of Exponential Random Graph Models
Description: Extensions of Exponential Random Graph Models (ERGM): Temporal Exponential Random Graph Models (TERGM), Generalized Exponential Random Graph Models (GERGM), Temporal Network Autocorrelation Models (TNAM), and Relational Event Models (REM).
Author: Philip Leifeld [aut, cre],
Skyler J. Cranmer [aut],
Bruce A. Desmarais [aut]
Maintainer: Philip Leifeld <philip.leifeld@eawag.ch>
Diff between xergm versions 1.5 dated 2015-06-14 and 1.5.3 dated 2015-09-25
xergm-1.5.3/xergm/DESCRIPTION | 32 +++++++------ xergm-1.5.3/xergm/MD5 | 41 +---------------- xergm-1.5.3/xergm/NAMESPACE | 78 +-------------------------------- xergm-1.5.3/xergm/R/xergm.R |only xergm-1.5.3/xergm/man/xergm-package.Rd | 17 ++----- xergm-1.5/xergm/R/RcppExports.R |only xergm-1.5/xergm/R/btergm.R |only xergm-1.5/xergm/R/gof.R |only xergm-1.5/xergm/R/interpretation.R |only xergm-1.5/xergm/R/preprocess.R |only xergm-1.5/xergm/R/tnam.R |only xergm-1.5/xergm/data |only xergm-1.5/xergm/inst/extdata |only xergm-1.5/xergm/man/adjust.Rd |only xergm-1.5/xergm/man/btergm-class.Rd |only xergm-1.5/xergm/man/btergm.Rd |only xergm-1.5/xergm/man/chemnet.Rd |only xergm-1.5/xergm/man/getformula.Rd |only xergm-1.5/xergm/man/gof.Rd |only xergm-1.5/xergm/man/handleMissings.Rd |only xergm-1.5/xergm/man/interpret.Rd |only xergm-1.5/xergm/man/knecht.Rd |only xergm-1.5/xergm/man/plot.btergmgof.Rd |only xergm-1.5/xergm/man/preprocess.Rd |only xergm-1.5/xergm/man/simulate.btergm.Rd |only xergm-1.5/xergm/man/timecov.Rd |only xergm-1.5/xergm/man/tnam-terms.Rd |only xergm-1.5/xergm/man/tnam.Rd |only xergm-1.5/xergm/src |only 29 files changed, 31 insertions(+), 137 deletions(-)
Title: Phylogenetic Tools for Comparative Biology (and Other Things)
Description: Package contains various functions for phylogenetic analysis.
This functionality is concentrated in the phylogenetic analysis of
comparative data from species. For example, the package includes
functions for Bayesian and ML ancestral state estimation; visual
simulation of trait evolution; fitting models of trait evolution
with multiple Brownian rates and correlations; visualizing
discrete and continuous character evolution using colors or
projections into trait space; identifying the location of a change
in the rate of character evolution on the tree; fast Brownian motion
simulation and simulation under several other models of
continuous trait evolution; fitting a model of correlated binary
trait evolution; locating the position of a fossil or an recently
extinct lineage on a tree using continuous character data with ML;
plotting lineage accumulation through time, including across
multiple trees (such as a Bayesian posterior sample); conducting
an analysis called stochastic character mapping, in which character
histories for a discrete trait are sampled from their posterior
probability distribution under a model; conducting a multiple
(i.e., partial) Mantel test; fitting a phylogenetic regression model
with error in predictor and response variables; conducting a
phylogenetic principal components analysis, a phylogenetic
regression, a reduced major axis regression, a phylogenetic
canonical correlation analysis, and a phylogenetic ANOVA; projecting
a tree onto a geographic map; simulating discrete character
histories on the tree; and fitting a model in which a discrete
character evolves under the threshold model. In addition to this
phylogenetic comparative method functionality, the package also
contains functions for a wide range of other purposes in
phylogenetic biology. For instance, functionality in this package
includes (but is not restricted to): adding taxa to a tree
(including randomly, everywhere, or automatically to genera);
generating all bi- and multi-furcating trees for a set of taxa;
reducing a phylogeny to its backbone tree; dropping tips or adding
tips to special types of phylogenetic trees; exporting a tree as an
XML file; converting a tree with a mapped character to a tree with
singleton nodes and one character state per edge; estimating a
phylogeny using the least squares method; simulating birth-death
trees under a range of conditions; rerooting trees; a wide range
of visualizations of trees; and a variety of other manipulations
and analyses that phylogenetic biologists may find useful for
their research.
Author: Liam J. Revell
Maintainer: Liam J. Revell <liam.revell@umb.edu>
Diff between phytools versions 0.4-60 dated 2015-07-10 and 0.5-00 dated 2015-09-25
phytools-0.4-60/phytools/R/findMRCA.R |only phytools-0.4-60/phytools/R/getExtant.R |only phytools-0.5-00/phytools/DESCRIPTION | 8 phytools-0.5-00/phytools/MD5 | 179 +++++------ phytools-0.5-00/phytools/NAMESPACE | 37 +- phytools-0.5-00/phytools/R/add.everywhere.R | 7 phytools-0.5-00/phytools/R/add.random.R | 3 phytools-0.5-00/phytools/R/add.species.to.genus.R | 1 phytools-0.5-00/phytools/R/anc.Bayes.R | 4 phytools-0.5-00/phytools/R/anc.ML.R | 49 ++- phytools-0.5-00/phytools/R/anc.trend.R | 3 phytools-0.5-00/phytools/R/ancThresh.R | 2 phytools-0.5-00/phytools/R/backbonePhylo.R | 6 phytools-0.5-00/phytools/R/bmPlot.R | 4 phytools-0.5-00/phytools/R/brownie.lite.R | 2 phytools-0.5-00/phytools/R/brownieREML.R | 43 ++ phytools-0.5-00/phytools/R/collapseTree.R | 15 phytools-0.5-00/phytools/R/contMap.R | 6 phytools-0.5-00/phytools/R/cophylo.R |only phytools-0.5-00/phytools/R/densityMap.R | 14 phytools-0.5-00/phytools/R/drop.tip.simmap.R | 4 phytools-0.5-00/phytools/R/estDiversity.R | 1 phytools-0.5-00/phytools/R/evol.rate.mcmc.R | 8 phytools-0.5-00/phytools/R/evol.vcv.R | 5 phytools-0.5-00/phytools/R/evolvcv.lite.R | 1 phytools-0.5-00/phytools/R/export.as.xml.R | 4 phytools-0.5-00/phytools/R/fancyTree.R | 6 phytools-0.5-00/phytools/R/fastAnc.R | 55 +++ phytools-0.5-00/phytools/R/fastBM.R | 4 phytools-0.5-00/phytools/R/fitBayes.R | 4 phytools-0.5-00/phytools/R/fitDiversityModel.R | 2 phytools-0.5-00/phytools/R/fitMk.R |only phytools-0.5-00/phytools/R/fitPagel.R | 23 - phytools-0.5-00/phytools/R/locate.fossil.R | 3 phytools-0.5-00/phytools/R/locate.yeti.R | 1 phytools-0.5-00/phytools/R/ltt.R | 16 phytools-0.5-00/phytools/R/ltt95.R | 3 phytools-0.5-00/phytools/R/make.era.map.R | 15 phytools-0.5-00/phytools/R/make.simmap.R | 179 +++-------- phytools-0.5-00/phytools/R/map.overlap.R | 19 - phytools-0.5-00/phytools/R/map.to.singleton.R | 3 phytools-0.5-00/phytools/R/mrp.supertree.R | 4 phytools-0.5-00/phytools/R/multiRF.R | 4 phytools-0.5-00/phytools/R/paintSubTree.R | 8 phytools-0.5-00/phytools/R/pgls.Ives.R | 4 phytools-0.5-00/phytools/R/phenogram.R | 8 phytools-0.5-00/phytools/R/phyl.RMA.R | 3 phytools-0.5-00/phytools/R/phyl.cca.R | 3 phytools-0.5-00/phytools/R/phyl.pairedttest.R | 4 phytools-0.5-00/phytools/R/phyl.pca.R | 4 phytools-0.5-00/phytools/R/phyl.resid.R | 4 phytools-0.5-00/phytools/R/phylANOVA.R | 4 phytools-0.5-00/phytools/R/phylo.to.map.R | 12 phytools-0.5-00/phytools/R/phylomorphospace.R | 25 + phytools-0.5-00/phytools/R/phylomorphospace3d.R | 2 phytools-0.5-00/phytools/R/phylosig.R | 2 phytools-0.5-00/phytools/R/plotBranchbyTrait.R | 1 phytools-0.5-00/phytools/R/plotSimmap.R | 63 +++ phytools-0.5-00/phytools/R/plotTree.wBars.R | 1 phytools-0.5-00/phytools/R/ratebystate.R | 1 phytools-0.5-00/phytools/R/rateshift.R | 185 +++++++---- phytools-0.5-00/phytools/R/read.simmap.R | 8 phytools-0.5-00/phytools/R/rerootingMethod.R | 31 - phytools-0.5-00/phytools/R/roundPhylogram.R | 6 phytools-0.5-00/phytools/R/sim.corrs.R | 4 phytools-0.5-00/phytools/R/sim.history.R | 18 - phytools-0.5-00/phytools/R/sim.rates.R | 26 - phytools-0.5-00/phytools/R/splitplotTree.R | 24 + phytools-0.5-00/phytools/R/strahlerNumber.R | 6 phytools-0.5-00/phytools/R/threshBayes.R | 2 phytools-0.5-00/phytools/R/treeSlice.R | 73 +++- phytools-0.5-00/phytools/R/utilities.R | 358 +++++++++++++--------- phytools-0.5-00/phytools/R/write.simmap.R | 127 +++---- phytools-0.5-00/phytools/R/writeAncestors.R | 6 phytools-0.5-00/phytools/R/writeNexus.R | 4 phytools-0.5-00/phytools/README.md |only phytools-0.5-00/phytools/data/anoletree.rda |binary phytools-0.5-00/phytools/man/anoletree.Rd | 2 phytools-0.5-00/phytools/man/brownieREML.Rd | 3 phytools-0.5-00/phytools/man/cladelabels.Rd | 4 phytools-0.5-00/phytools/man/collapseTree.Rd | 2 phytools-0.5-00/phytools/man/cophylo.Rd |only phytools-0.5-00/phytools/man/densityMap.Rd | 2 phytools-0.5-00/phytools/man/fitMk.Rd |only phytools-0.5-00/phytools/man/markChanges.Rd |only phytools-0.5-00/phytools/man/minRotate.Rd | 9 phytools-0.5-00/phytools/man/plotSimmap.Rd | 3 phytools-0.5-00/phytools/man/rateshift.Rd | 7 phytools-0.5-00/phytools/man/reorderSimmap.Rd | 4 phytools-0.5-00/phytools/man/rerootingMethod.Rd | 4 phytools-0.5-00/phytools/man/sim.rates.Rd | 4 phytools-0.5-00/phytools/man/splitEdgeColor.Rd |only phytools-0.5-00/phytools/man/splitplotTree.Rd | 6 phytools-0.5-00/phytools/man/treeSlice.Rd | 4 phytools-0.5-00/phytools/man/write.simmap.Rd | 3 95 files changed, 1124 insertions(+), 707 deletions(-)
Title: Maximum Likelihood Models for Species Abundance Distributions
Description: Maximum likelihood tools to fit and compare models of species
abundance distributions and of species rank-abundance distributions.
Author: Paulo I. Prado, Murilo Dantas Miranda and Andre Chalom
Maintainer: Paulo I. Prado <prado@ib.usp.br>
Diff between sads versions 0.2.2 dated 2015-07-11 and 0.2.3 dated 2015-09-25
DESCRIPTION | 13 +++++++------ MD5 | 34 +++++++++++++++++----------------- NEWS | 8 +++++++- R/dmzsm.R | 4 ++-- R/dvolkov.R | 2 +- R/fitgeom.R | 11 ++++++----- R/fitnbinom.R | 8 ++++---- R/fitpoilog.R | 32 ++++++++++++++++---------------- R/fitsad.R | 12 +++++------- R/sads-methods.R | 6 +++--- README.md | 6 +++--- build/vignette.rds |binary inst/doc/sads_intro.R | 2 +- inst/doc/sads_intro.Rnw | 6 +++--- inst/doc/sads_intro.pdf |binary man/fitsad.Rd | 11 +++++++---- man/sads-package.Rd | 4 ++-- vignettes/sads_intro.Rnw | 6 +++--- 18 files changed, 87 insertions(+), 78 deletions(-)
Title: Statistical Inference for Partially Observed Markov Processes
Description: Tools for working with partially observed Markov processes (POMPs, AKA stochastic dynamical systems, state-space models). 'pomp' provides facilities for implementing POMP models, simulating them, and fitting them to time series data by a variety of frequentist and Bayesian methods. It is also a platform for the implementation of new inference methods.
Author: Aaron A. King [aut, cre],
Edward L. Ionides [aut],
Carles Breto [aut],
Stephen P. Ellner [ctb],
Matthew J. Ferrari [ctb],
Bruce E. Kendall [ctb],
Michael Lavine [ctb],
Dao Nguyen [ctb],
Daniel C. Reuman [ctb],
Helen Wearing [ctb],
Simon N. Wood [ctb],
Sebastian Funk [ctb]
Maintainer: Aaron A. King <kingaa@umich.edu>
Diff between pomp versions 1.1.1.1 dated 2015-08-20 and 1.2.1.1 dated 2015-09-25
pomp-1.1.1.1/pomp/inst/examples/dacca2.R |only pomp-1.1.1.1/pomp/inst/examples/ebola.R |only pomp-1.2.1.1/pomp/DESCRIPTION | 10 +++++----- pomp-1.2.1.1/pomp/MD5 | 22 ++++++++++------------ pomp-1.2.1.1/pomp/R/mif.R | 23 ++++++++++++++--------- pomp-1.2.1.1/pomp/R/pfilter-methods.R | 8 ++++---- pomp-1.2.1.1/pomp/R/pmcmc-methods.R | 20 ++++++++++++++++++++ pomp-1.2.1.1/pomp/build/partial.rdb |binary pomp-1.2.1.1/pomp/inst/NEWS | 17 +++++++++++++++++ pomp-1.2.1.1/pomp/inst/NEWS.Rd | 17 +++++++++++++++++ pomp-1.2.1.1/pomp/man/plugins.Rd | 19 ++++++++++++++++--- pomp-1.2.1.1/pomp/man/pmcmc.Rd | 18 +++++++++++------- pomp-1.2.1.1/pomp/man/sannbox.Rd | 10 ++++++++-- 13 files changed, 122 insertions(+), 42 deletions(-)