Title: Various R programming tools
Diff between gtools versions 3.3.1 dated 2014-03-01 and 3.4.0 dated 2014-04-17
Description: Various R programming tools
Author: Gregory R. Warnes, Ben Bolker, and Thomas Lumley
Maintainer: Gregory R. Warnes
ChangeLog | 5 +++++
DESCRIPTION | 8 ++++----
MD5 | 14 ++++++++------
NAMESPACE | 1 +
NEWS | 10 ++++++++++
R/ASCIIfy.R |only
inst/ChangeLog | 5 +++++
inst/NEWS | 10 ++++++++++
man/ASCIIfy.Rd |only
9 files changed, 43 insertions(+), 10 deletions(-)
More information about userfriendlyscience at CRAN
Permanent link
Title: SEER Setup and Use with A-Bomb Data
Diff between SEERaBomb versions 2013.4.3 dated 2013-12-12 and 2014.4.1 dated 2014-04-17
Description: This package contains codes that setup SEER
(Surveillance, Epidemiology and End Results) data use with R.
It includes SEER and Japanese A-Bomb survivor data analysis examples.
By using it, the portability of SEER R scripts should improve.
This package works only with the latest SEER release of April 15, 2014.
Author: Tomas Radivoyevitch
Maintainer: Tomas Radivoyevitch
DESCRIPTION | 12
MD5 | 48
NAMESPACE | 3
NEWS | 129 -
R/getFields.R | 76
R/mkAbomb.R | 124 -
R/mkHema87.R | 27
R/mkSEER.R | 105 -
inst/doc/gettingData.pdf |binary
inst/doc/overview.pdf |binary
inst/doc/papers/JCO2013/MDSAMLsurvMF.R | 130 -
inst/doc/papers/blood2012/blood2012fig4.R | 74
inst/doc/papers/blood2012/blood2012fig5a.R | 82
inst/doc/papers/blood2012/blood2012fig6.R | 66
inst/doc/papers/blood2012/dingliCMLFINAL3.R | 534 ++---
inst/doc/papers/blood2012/vIncidAPLCML.r | 96 -
inst/doc/papers/radiatEnvironBiophys2013/SupplementSEER.R | 1245 ++++++-------
inst/doc/papers/radiatEnvironBiophys2013/supplementAbomb.R | 1038 +++++-----
man/SEERaBomb-package.Rd | 74
man/figures/SEERaBombFig.png |binary
man/getFields.Rd | 58
man/mkAbomb.Rd | 44
man/mkHema87.Rd | 42
man/mkSEER.Rd | 79
man/pickFields.Rd | 80
25 files changed, 2101 insertions(+), 2065 deletions(-)
Title: Fit high dimensional mixtures of Poisson GLMs
Diff between poisson.glm.mix versions 1.1 dated 2013-06-20 and 1.2 dated 2014-04-17
More information about poisson.glm.mix at CRAN
Description: High dimensional mixtures of Poisson Generalized Linear models with three different parameterizations of Poisson means are considered. Moreover, partitioning the response variables into a set of blocks is possible. The package estimates parameters via EM algorithm. For an efficient initialization, a random splitting small-EM is introduced.
Author: Panagiotis Papastamoulis, Marie-Laure Martin-Magniette, Cathy Maugis-Rabusseau
Maintainer: Panagiotis Papastamoulis
DESCRIPTION | 18 ++++++------------
MD5 | 4 ++--
R/pois.glm.mix.R | 35 +++++++++++++++++++++++++++++++----
3 files changed, 39 insertions(+), 18 deletions(-)
Permanent link
Title: Multivariate Normal and t Distributions
Diff between mvtnorm versions 0.9-9998 dated 2014-04-09 and 0.9-9999 dated 2014-04-17
Description: Computes multivariate normal and t probabilities, quantiles,
random deviates and densities.
Author: Alan Genz, Frank Bretz, Tetsuhisa Miwa, Xuefei Mi, Friedrich Leisch,
Fabian Scheipl, Bjoern Bornkamp, Torsten Hothorn
Maintainer: Torsten Hothorn
DESCRIPTION | 8 ++++----
MD5 | 12 ++++++------
R/mvnorm.R | 40 ++++++++++++++++++++++++----------------
inst/doc/MVT_Rnews.pdf |binary
man/Mvnorm.Rd | 3 ++-
tests/bugfix-tests.R | 2 ++
tests/bugfix-tests.Rout.save | 9 ++++-----
7 files changed, 42 insertions(+), 32 deletions(-)
Title: Bayesian quantile regression
Diff between bayesQR versions 2.1 dated 2013-02-18 and 2.2 dated 2014-04-17
Description: Bayesian quantile regression using the asymmetric Laplace distribution, both continuous as well as binary dependent variables are supported. The package consists of implementations of the methods of Yu & Moyeed (2001), Benoit & Van den Poel (2012) and Al-Hamzawi, Yu & Benoit (2012). To speed up the calculations, the Markov Chain Monte Carlo core of all algorithms is programmed in Fortran and called from R.
Author: Dries F. Benoit, Rahim Al-Hamzawi, Keming Yu, Dirk Van den Poel
Maintainer: Dries F. Benoit
DESCRIPTION | 18 ++++++------------
MD5 | 18 +++++++++---------
R/plot.bayesQR.r | 44 +++++++++++++++++++++++++++++++++++++++++---
man/bayesQR.Rd | 4 ++--
man/plot.bayesQR.Rd | 13 +++++++++----
man/predict.bayesQR.Rd | 4 ++--
src/QRb_AL_mcmc.f95 | 1 -
src/QRb_mcmc.f95 | 3 +--
src/QRc_AL_mcmc.f95 | 1 -
src/QRc_mcmc.f95 | 3 +--
10 files changed, 71 insertions(+), 38 deletions(-)
Title: sjPlot - data visualization for statistics in social science
Diff between sjPlot versions 1.3 dated 2014-03-27 and 1.4.1 dated 2014-04-17
Description: Collection of several plotting / table output functions for
visualizing data and utility functions.
Author: Daniel Lüdecke
Maintainer: Daniel Luedecke
DESCRIPTION | 9
MD5 | 127 +-
NAMESPACE | 165 +-
NEWS | 546 ++++----
R/sjImportSPSS.R | 680 +++++-----
R/sjPlotAnova.R | 1397 +++++++++++-----------
R/sjPlotClusterAnalysis.R | 26
R/sjPlotCorr.R | 960 +++++++--------
R/sjPlotFrequencies.R | 80 -
R/sjPlotGroupFrequencies.R | 2699 +++++++++++++++++++++----------------------
R/sjPlotLikert.R | 1540 ++++++++++++------------
R/sjPlotLinreg.R | 2377 ++++++++++++++++++-------------------
R/sjPlotLinregMultiple.R | 1156 +++++++++---------
R/sjPlotOdds.R | 1592 ++++++++++++-------------
R/sjPlotOddsMultiple.R | 1192 +++++++++---------
R/sjPlotPropTable.R | 1744 +++++++++++++--------------
R/sjPlotScatter.R | 906 +++++++-------
R/sjPlotStackFrequencies.R | 46
R/sjRecode.R | 2084 +++++++++++++++++----------------
R/sjTabCorr.R | 186 ++
R/sjTabDataFrame.R | 765 ++++++------
R/sjTabFrequencies.R | 40
R/sjTabItemAnalysis.R | 759 ++++++------
R/sjTabLinReg.R | 1348 ++++++++++-----------
R/sjTabOdds.R | 1384 +++++++++++-----------
R/sjTabPCA.R | 1210 +++++++++----------
R/sjTabPropTable.R | 1556 ++++++++++++------------
R/sjTabSPSS.R | 650 +++++-----
R/sjTabStackFrq.R | 1088 ++++++++---------
man/sjPlot-package.Rd | 7
man/sjc.cluster.Rd | 8
man/sjc.qclus.Rd | 36
man/sji.getValueLabels.Rd | 3
man/sji.getVariableLabels.Rd | 3
man/sji.setValueLabels.Rd | 27
man/sji.setVariableLabels.Rd | 5
man/sji.viewSPSS.Rd | 43
man/sjp.aov1.Rd | 14
man/sjp.corr.Rd | 3
man/sjp.frq.Rd | 30
man/sjp.glm.Rd | 23
man/sjp.glm.ma.Rd | 2
man/sjp.glmm.Rd | 12
man/sjp.grpfrq.Rd | 980 +++++++--------
man/sjp.likert.Rd | 12
man/sjp.lm.Rd | 515 ++++----
man/sjp.lm.ma.Rd | 75 -
man/sjp.lm1.Rd | 2
man/sjp.lmm.Rd | 12
man/sjp.reglin.Rd | 197 +--
man/sjp.scatter.Rd | 8
man/sjp.stackfrq.Rd | 38
man/sjp.xtab.Rd | 57
man/sjt.corr.Rd | 367 +++--
man/sjt.df.Rd | 21
man/sjt.frq.Rd | 24
man/sjt.glm.Rd | 17
man/sjt.itemanalysis.Rd | 107 +
man/sjt.lm.Rd | 15
man/sjt.pca.Rd | 16
man/sjt.stackfrq.Rd | 20
man/sjt.xtab.Rd | 24
man/sju.chi2.gof.Rd | 3
man/sju.mic.Rd |only
man/sju.reliability.Rd | 5
65 files changed, 15889 insertions(+), 15154 deletions(-)
Title: Simulation and group sequential monitoring of randomized
multi-arm two-stage Phase IIb/III treatment efficacy trials
with time-to-event endpoints
Diff between seqDesign versions 1.0.0 dated 2014-02-25 and 1.0.1 dated 2014-04-17
Description: This package implements the preventive vaccine efficacy trial design of Gilbert, Grove et al. (2011, Statistical Communications in Infectious Diseases), and applies generally to individual-randomized clinical trials with multiple active treatment groups and a shared placebo group, with a study endpoint that is a time-to-event endpoint subject to right-censoring. The design accounts for the issues that the efficacy of the treatment/vaccine groups may take time to accrue while the multiple treatment administrations/vaccinations are given; there is interest in assessing the durability of treatment efficacy over time; and group sequential monitoring of each treatment arm for potential harm, non-efficacy/efficacy futility, and high efficacy is warranted. The design divides the trial into two stages of time periods, where each treatment is first evaluated for efficacy in the first stage of follow-up, and, if and only if it shows significant treatment efficacy in stage one, it is evaluated for longer-term durability of efficacy in stage two. The package produces plots and tables describing operating characteristics of a specified design including an unconditional power for intention-to-treat and per-protocol/as-treated analyses; trial duration; probabilities of the different possible trial outcomes (e.g., stopping early for efficacy futility); unconditional power for comparing treatment efficacy; and distributions of numbers of endpoint events occurring after the treatments/vaccinations are given, useful as input parameters for the design of studies of the association of biomarkers with outcome (surrogate endpoint problem). The code can be used for a single active treatment versus control design and for a single-stage design.
Author: Michal Juraska and Doug Grove, with contributions from Xuesong Yu and Peter B. Gilbert
Maintainer: Michal Juraska
seqDesign-1.0.0/seqDesign/inst/doc/seqDesignSampleReport.pdf |only
seqDesign-1.0.1/seqDesign/DESCRIPTION | 8
seqDesign-1.0.1/seqDesign/MD5 | 22
seqDesign-1.0.1/seqDesign/R/seqDesign.R | 822 ++--------
seqDesign-1.0.1/seqDesign/build/vignette.rds |binary
seqDesign-1.0.1/seqDesign/inst/doc/seqDesignInstructions.R | 4
seqDesign-1.0.1/seqDesign/inst/doc/seqDesignInstructions.Rnw | 6
seqDesign-1.0.1/seqDesign/inst/doc/seqDesignInstructions.pdf |binary
seqDesign-1.0.1/seqDesign/inst/extdata/seqDesignReport.Rnw | 584 ++++++-
seqDesign-1.0.1/seqDesign/inst/extdata/seqDesignReportSample.pdf |only
seqDesign-1.0.1/seqDesign/man/VEpowerPP.Rd | 36
seqDesign-1.0.1/seqDesign/man/censTrial.Rd | 4
seqDesign-1.0.1/seqDesign/vignettes/seqDesignInstructions.Rnw | 6
13 files changed, 798 insertions(+), 694 deletions(-)
Title: Interface to the Global Biodiversity Information Facility API
Diff between rgbif versions 0.5.0 dated 2014-02-16 and 0.6.0 dated 2014-04-17
Description: A programmatic interface to the
Web Service methods provided by the Global
Biodiversity Information Facility.
Author: Scott Chamberlain [aut, cre],
Carl Boettiger [aut],
Karthik Ram [aut],
Vijay Barve [aut],
Dan Mcglinn [aut]
Maintainer: Scott Chamberlain
DESCRIPTION | 12 -
MD5 | 322 +++++++++++++++++++-----------
NAMESPACE | 9
NEWS | 27 ++
R/check_wkt.r |only
R/dataset_metrics.r | 7
R/dataset_search.r | 6
R/dataset_suggest.r | 9
R/datasets.r | 5
R/elevation.r | 21 +
R/gist.r | 5
R/installations.r | 4
R/name_backbone.r | 62 +++--
R/name_lookup.r | 34 +--
R/name_suggest.r | 20 +
R/name_usage.r | 32 ++-
R/networks.r | 5
R/nodes.r | 5
R/occ_count.r | 51 ++--
R/occ_get.r | 20 +
R/occ_metadata.r | 14 -
R/occ_search.r | 131 ++++++++----
R/organizations.r | 5
R/parsenames.R | 6
R/rgbif-package.r | 12 +
R/stylegeojson.r | 6
R/togeojson.r | 2
R/zzz.r | 45 ++--
README.md | 32 +--
data/typestatus.rda |only
inst |only
man/blanktheme.Rd | 1
man/check_wkt.Rd |only
man/commas_to_periods.Rd | 3
man/count_facet.Rd | 13 -
man/create_gist.Rd | 10
man/dataset_metrics.Rd | 11 -
man/dataset_search.Rd | 123 +++++------
man/dataset_suggest.Rd | 73 ++----
man/datasetparser.Rd | 5
man/datasets.Rd | 23 +-
man/density_spplist-deprecated.Rd | 82 +++----
man/densitylist-deprecated.Rd | 49 ++--
man/elevation.Rd | 27 +-
man/gbif_capwords.Rd | 10
man/gbifdata-deprecated.Rd | 27 +-
man/gbifmap.Rd | 61 ++---
man/gbifmap_dens-deprecated.Rd | 61 ++---
man/gbifmap_list-deprecated.Rd | 61 ++---
man/gbifparser.Rd | 11 -
man/gbifparser_verbatim.Rd | 11 -
man/gbifxmlToDataFrame.Rd | 8
man/get_credentials.Rd | 1
man/gist.Rd | 30 +-
man/installations.Rd | 51 ++--
man/is.gbifdens-deprecated.Rd | 3
man/is.gbiflist-deprecated.Rd | 3
man/is.gbiflist_na-deprecated.Rd | 3
man/isocodes.Rd | 11 -
man/ldfast.Rd | 6
man/name_backbone.Rd | 69 +++---
man/name_lookup.Rd | 211 +++++++++----------
man/name_suggest.Rd | 29 +-
man/name_usage.Rd | 88 ++++----
man/namelkupparser.Rd | 6
man/networks.Rd | 35 +--
man/nodes.Rd | 15 -
man/occ_count.Rd | 61 ++---
man/occ_get.Rd | 39 +--
man/occ_metadata.Rd | 20 -
man/occ_search.Rd | 362 +++++++++++++++++++---------------
man/occurrencecount-deprecated.Rd | 232 +++++++++------------
man/occurrencedensity-deprecated.Rd | 1
man/occurrenceget-deprecated.Rd | 21 -
man/occurrencelist-deprecated.Rd | 267 ++++++++++---------------
man/occurrencelist_all-deprecated.Rd | 11 -
man/occurrencelist_many-deprecated.Rd | 274 ++++++++++---------------
man/organizations.Rd | 18 -
man/parsenames.Rd | 8
man/parseresults.Rd | 7
man/print.gbifdens-deprecated.Rd | 6
man/print.gbiflist-deprecated.Rd | 6
man/print.gbiflist_na-deprecated.Rd | 6
man/providers-deprecated.Rd | 24 +-
man/resources-deprecated.Rd | 32 +--
man/rgb_country_codes.Rd | 8
man/rgbif-deprecated.Rd | 29 +-
man/rgbif.Rd | 112 +++++-----
man/stylegeojson.Rd | 21 -
man/suggestfields.Rd | 1
man/taxoncount-deprecated.Rd | 11 -
man/taxonget-deprecated.Rd | 9
man/taxonsearch-deprecated.Rd | 53 ++--
man/taxrank.Rd | 5
man/togeojson.Rd | 46 +---
man/typestatus.Rd |only
tests/testthat/test-dataset_search.r | 8
tests/testthat/test-dataset_suggest.r | 8
tests/testthat/test-datasets.r | 3
tests/testthat/test-name_backbone.r | 12 -
tests/testthat/test-name_lookup.r | 2
tests/testthat/test-name_suggest.r | 4
tests/testthat/test-nodes.r | 4
tests/testthat/test-occ_count.r | 2
tests/testthat/test-occ_get.r | 17 -
tests/testthat/test-occ_metadata.r | 6
tests/testthat/test-occ_search.r | 73 ++++--
tests/testthat/test-organizations.r | 7
tests/testthat/test-stylegeojson.r | 6
vignettes/figure |only
vignettes/rgbif_vignette.Rmd | 12 -
vignettes/rgbif_vignette.html | 9
vignettes/rgbif_vignette.md | 12 -
vignettes/rgbif_vignette.pdf |binary
vignettes/rgbif_vignette_oldapi.Rmd | 38 +--
vignettes/rgbif_vignette_oldapi.html | 38 +--
vignettes/rgbif_vignette_oldapi.md | 38 +--
vignettes/rgbif_vignette_oldapi.pdf |binary
118 files changed, 2158 insertions(+), 1971 deletions(-)
Title: Protracted birth-death model of diversification
Diff between PBD versions 0.8 dated 2014-04-01 and 0.9 dated 2014-04-17
Description: Maximum likelihood analysis of the protracted speciation model
Author: Rampal S. Etienne
Maintainer: Rampal S. Etienne
DESCRIPTION | 8 ++++----
MD5 | 6 +++---
R/pbd_loglik.R | 10 +++++++---
man/PBD-package.Rd | 11 ++++++++---
4 files changed, 22 insertions(+), 13 deletions(-)