Title: Radiocarbon Dating, Age-Depth Modelling, Relative Sea Level Rate
Estimation, and Non-Parametric Phase Modelling
Description: Enables quick calibration of radiocarbon dates under various
calibration curves (including user generated ones); age-depth modelling
as per the algorithm of Haslett and Parnell (2008) <DOI:10.1111/j.1467-9876.2008.00623.x>; Relative sea level
rate estimation incorporating time uncertainty in polynomial regression
models (Parnell and Gehrels 2015) <DOI:10.1002/9781118452547.ch32>; non-parametric phase modelling via
Gaussian mixtures as a means to determine the activity of a site
(and as an alternative to the Oxcal function SUM; currently
unpublished), and reverse calibration of dates from calibrated into
un-calibrated years (also unpublished).
Author: Andrew Parnell
Maintainer: Andrew Parnell <Andrew.Parnell@mu.ie>
Diff between Bchron versions 4.2.7 dated 2018-02-27 and 4.3.0 dated 2018-06-15
DESCRIPTION | 12 +++--- MD5 | 70 ++++++++++++++++++++----------------- NAMESPACE | 4 ++ NEWS.md |only R/BchronCalibrate.R | 20 ++++------ R/BchronDensity.R | 6 +-- R/BchronDensityFast.R | 10 ++--- R/BchronRSL.R | 17 +++++--- R/Bchronology.R | 14 +++---- R/CreateCalCurve.R | 12 +++--- R/choosePositions.BchronologyRun.R |only R/coreInfluence.BchronologyRun.R |only R/data.R | 2 - R/dateInfluence.BchronologyRun.R | 18 ++++----- R/plot.BchronCalibratedDates.R | 8 ++-- R/plot.BchronDensityRun.R | 2 - R/plot.BchronDensityRunFast.R | 2 - R/plot.BchronRSLRun.R | 2 - R/summary.BchronRSLRun.R | 4 +- R/unCalibrate.R | 6 +-- inst/CITATION |only inst/doc/Bchron.html | 68 +++++++++++++++++------------------ man/BchronCalibrate.Rd | 20 ++++------ man/BchronDensity.Rd | 6 +-- man/BchronDensityFast.Rd | 8 +--- man/BchronRSL.Rd | 17 +++++--- man/Bchronology.Rd | 14 +++---- man/CreateCalCurve.Rd | 12 +++--- man/choosePositions.Rd |only man/coreInfluence.Rd |only man/dateInfluence.Rd | 18 ++++----- man/intcal13.Rd | 2 - man/plot.BchronCalibratedDates.Rd | 9 ++-- man/plot.BchronDensityRun.Rd | 4 +- man/plot.BchronDensityRunFast.Rd | 2 - man/plot.BchronRSLRun.Rd | 2 - man/summary.BchronRSLRun.Rd | 4 +- man/unCalibrate.Rd | 6 +-- src/Bchron.c | 1 39 files changed, 207 insertions(+), 195 deletions(-)
Title: Regularization Paths for Regression Models with Grouped
Covariates
Description: Efficient algorithms for fitting the regularization path of
linear or logistic regression models with grouped penalties. This
includes group selection methods such as group lasso, group MCP, and
group SCAD as well as bi-level selection methods such as the group
exponential lasso, the composite MCP, and the group bridge.
Author: Patrick Breheny [aut, cre], Yaohui Zeng [ctb]
Maintainer: Patrick Breheny <patrick-breheny@uiowa.edu>
Diff between grpreg versions 3.1-3 dated 2018-04-08 and 3.1-4 dated 2018-06-15
grpreg-3.1-3/grpreg/R/reorderGroups.R |only grpreg-3.1-3/grpreg/man/grpreg-internal.Rd |only grpreg-3.1-4/grpreg/DESCRIPTION | 8 - grpreg-3.1-4/grpreg/MD5 | 32 ++-- grpreg-3.1-4/grpreg/NEWS | 6 grpreg-3.1-4/grpreg/R/G.R |only grpreg-3.1-4/grpreg/R/gBridge.R | 23 +-- grpreg-3.1-4/grpreg/R/grpreg.R | 35 ++--- grpreg-3.1-4/grpreg/R/multi.R | 5 grpreg-3.1-4/grpreg/R/newXG.R | 46 +++--- grpreg-3.1-4/grpreg/R/plot.cv.R | 2 grpreg-3.1-4/grpreg/R/standardize.R | 8 - grpreg-3.1-4/grpreg/build/vignette.rds |binary grpreg-3.1-4/grpreg/inst/doc/penalties.pdf |binary grpreg-3.1-4/grpreg/inst/doc/quick-start.pdf |binary grpreg-3.1-4/grpreg/inst/tests/extra-features.R | 68 ---------- grpreg-3.1-4/grpreg/inst/tests/standardization-orthogonalization.R | 30 ++-- grpreg-3.1-4/grpreg/inst/tests/torture.R |only grpreg-3.1-4/grpreg/src/gdfit_gaussian.c | 11 - 19 files changed, 107 insertions(+), 167 deletions(-)
Title: Use Known Groups in High-Dimensional Data to Derive Scores for
Plots
Description: Cross-validated linear discriminant calculations determine
the optimum number of features. Test and training scores from
successive cross-validation steps determine, via a principal
components calculation, a low-dimensional global space onto which test
scores are projected, in order to plot them. Further functions are
included that are intended for didactic use. The package implements,
and extends, methods described in J.H. Maindonald and C.J. Burden (2005)
<https://journal.austms.org.au/V46/CTAC2004/Main/home.html>.
Author: John Maindonald
Maintainer: John Maindonald <jhmaindonald@gmail.com>
Diff between hddplot versions 0.57-5 dated 2017-09-03 and 0.59 dated 2018-06-15
DESCRIPTION | 8 +++--- MD5 | 37 +++++++++++++++--------------- R/scoreplot.R | 4 +-- build/partial.rdb |only build/vignette.rds |binary inst/doc/QUICKhddplot.pdf |binary man/hddplot.package.Rd | 21 +++++++++++------ man/scoreplot.Rd | 11 ++++---- vignettes/figs/key-Boxplots-1.pdf |binary vignettes/figs/key-Boxplots-2.pdf |binary vignettes/figs/key-cv-Bcell-gphAB-1.pdf |binary vignettes/figs/key-cv-Bcell-gphAB-2.pdf |binary vignettes/figs/key-cv-bad-1.pdf |binary vignettes/figs/key-cv-bad-2.pdf |binary vignettes/figs/key-misleading-plots-1.pdf |binary vignettes/figs/key-misleading-plots-2.pdf |binary vignettes/figs/key-plot-Fstats-1.pdf |binary vignettes/figs/key-plot-Fstats-2.pdf |binary vignettes/figs/key-plot-Fstats-3.pdf |binary vignettes/figs/key-plot-train-test-1.pdf |binary 20 files changed, 44 insertions(+), 37 deletions(-)
Title: Boosting Methods for 'GAMLSS'
Description: Boosting models for fitting generalized additive models for
location, shape and scale ('GAMLSS') to potentially high dimensional
data.
Author: Benjamin Hofner [aut, cre] (<https://orcid.org/0000-0003-2810-3186>),
Andreas Mayr [aut],
Nora Fenske [aut],
Janek Thomas [aut],
Matthias Schmid [aut]
Maintainer: Benjamin Hofner <benjamin.hofner@pei.de>
Diff between gamboostLSS versions 2.0-0 dated 2017-05-05 and 2.0-1 dated 2018-06-15
ChangeLog | 73 ++ DESCRIPTION | 23 MD5 | 42 - NAMESPACE | 5 R/cvrisk.R | 16 R/cvrisk.nc_mboostLSS.R | 6 R/gamboostLSS_intern.R | 10 README.md | 6 build/vignette.rds |binary data/india.RData |binary data/india.bnd.RData |binary inst/CITATION | 11 inst/NEWS.Rd | 17 inst/doc/gamboostLSS_Tutorial.Rnw | 8 inst/doc/gamboostLSS_Tutorial.pdf |binary man/cvrisk.Rd | 37 - man/gamboostLSS-package.Rd | 9 man/mboostLSS.Rd | 27 - man/methods.Rd | 1 man/stabsel.mboostLSS.Rd | 9 vignettes/bib.bib | 996 ++++++++++++++++++------------------- vignettes/gamboostLSS_Tutorial.Rnw | 8 22 files changed, 716 insertions(+), 588 deletions(-)
Title: Additional Functions for 'geoPAT' 2
Description: Supports analysis of spatial data processed with the 'geoPAT' 2
software <http://sil.uc.edu/cms/index.php?id=geopat2>.
Available features include creation of a grid based on the 'geoPAT' 2
grid header file.
Author: Jakub Nowosad [aut, cre] (<https://orcid.org/0000-0002-1057-3721>),
Space Informatics Lab [cph]
Maintainer: Jakub Nowosad <nowosad.jakub@gmail.com>
Diff between rgeopat2 versions 0.2.4 dated 2018-03-24 and 0.2.5 dated 2018-06-15
DESCRIPTION | 16 ++++++++-------- MD5 | 4 ++-- README.md | 28 +++++++++++++++++----------- 3 files changed, 27 insertions(+), 21 deletions(-)
Title: Stochastic Hybrid Models in Dynamic Networks
Description: Simulates stochastic hybrid models for transmission of infectious
diseases in dynamic networks. It is a metapopulation model in which each
node in the network is a sub-population and disease spreads within nodes
and among them, combining two approaches: stochastic simulation algorithm
or its approximations (Gillespie DT (2007)
<doi:10.1146/annurev.physchem.58.032806.104637>) and individual-based
approach, respectively. Movement among nodes are data based and can be
irregular. Equations that models spread within nodes are customizable and
there are two link types among nodes: migration and influence (commuting).
Author: Fernando S. Marques [aut, cre],
Jose H. H. Grisi-Filho [aut],
Marcos Amaku [aut]
Maintainer: Fernando S. Marques <fernandosix@gmail.com>
Diff between hybridModels versions 0.2.15 dated 2017-09-27 and 0.3.5 dated 2018-06-15
DESCRIPTION | 8 ++--- MD5 | 35 +++++++++++++----------- NEWS | 45 +++++++++++++++++++++++++++++++ R/build_model_class.R | 6 ++-- R/custom_infl.R | 14 +++++++++ R/custom_migr.R | 60 ++++++++++++++++++++++++++++++++++++------ R/data.R | 2 - R/hybrid_Model.R | 30 ++++++++++++++------- R/plot_HM.R | 3 +- R/sim_custom_infl.R | 4 ++ R/sim_custom_migr.R | 12 ++++---- R/sim_custom_migr_prob.R |only R/sim_custom_migr_rule.R |only R/sim_custom_migr_rule_prob.R |only README.md | 6 ++-- man/buildModelClass.Rd | 16 +++++++++-- man/hybridModel.Rd | 25 +++++++++++++---- man/networkSample.Rd | 2 - man/plot.Rd | 3 +- man/simHM.Rd | 3 +- 20 files changed, 211 insertions(+), 63 deletions(-)
Title: Business Analytics using R and Shiny
Description: A platform-independent browser-based interface for business
analytics in R, based on the shiny package. The application combines the
functionality of radiant.data, radiant.design, radiant.basics,
radiant.model, and radiant.multivariate.
Author: Vincent Nijs [aut, cre]
Maintainer: Vincent Nijs <radiant@rady.ucsd.edu>
Diff between radiant versions 0.8.0 dated 2017-04-29 and 0.9.5 dated 2018-06-15
radiant-0.8.0/radiant/man/update_radiant.Rd |only radiant-0.9.5/radiant/DESCRIPTION | 21 radiant-0.9.5/radiant/MD5 | 46 radiant-0.9.5/radiant/NAMESPACE | 4 radiant-0.9.5/radiant/NEWS.md | 51 radiant-0.9.5/radiant/R/radiant.R | 144 radiant-0.9.5/radiant/README.md | 70 radiant-0.9.5/radiant/build/build_mac.R | 49 radiant-0.9.5/radiant/build/build_radiant.R | 73 radiant-0.9.5/radiant/build/build_win.R | 26 radiant-0.9.5/radiant/build/clean_out_addins_menu.R |only radiant-0.9.5/radiant/build/vignette.rds |binary radiant-0.9.5/radiant/inst/app/for.shinyapps.io.R | 49 radiant-0.9.5/radiant/inst/app/global.R | 18 radiant-0.9.5/radiant/inst/app/rsconnect/shinyapps.io/vnijs/radiant.dcf | 8 radiant-0.9.5/radiant/inst/app/server.R | 34 radiant-0.9.5/radiant/inst/app/ui.R | 21 radiant-0.9.5/radiant/inst/doc/programming.R | 92 radiant-0.9.5/radiant/inst/doc/programming.Rmd | 105 radiant-0.9.5/radiant/inst/doc/programming.html | 1754 ++++++++-- radiant-0.9.5/radiant/inst/rstudio/addins.dcf | 17 radiant-0.9.5/radiant/man/radiant.Rd | 4 radiant-0.9.5/radiant/man/radiant_viewer.Rd |only radiant-0.9.5/radiant/man/radiant_window.Rd |only radiant-0.9.5/radiant/vignettes/_footer.md |only radiant-0.9.5/radiant/vignettes/images |only radiant-0.9.5/radiant/vignettes/programming.Rmd | 105 27 files changed, 2143 insertions(+), 548 deletions(-)
Title: Entropy-Based Segregation Indices
Description: Computes entropy-based segregation indices, as developed by
Theil (1971) <isbn:978-0471858454>, with a focus on
the Mutual Information Index (M) and Theil's Information Index (H).
The M, further described by Mora and Ruiz-Castillo (2011) <doi:10.1111/j.1467-9531.2011.01237.x>
and Frankel and Volij (2011) <doi:10.1016/j.jet.2010.10.008>,
is a measure of segregation that is highly decomposable. The package provides
tools to decompose the index by units and groups (local segregation),
and by within and between terms.
Includes standard error estimation by bootstrapping.
Author: Benjamin Elbers [aut, cre] (<https://orcid.org/0000-0001-5392-3448>)
Maintainer: Benjamin Elbers <be2239@columbia.edu>
Diff between segregation versions 0.0.1 dated 2018-04-17 and 0.1.0 dated 2018-06-15
segregation-0.0.1/segregation/tests/testthat/test_mutual_diff_mrc.R |only segregation-0.1.0/segregation/DESCRIPTION | 12 segregation-0.1.0/segregation/MD5 | 44 - segregation-0.1.0/segregation/NAMESPACE | 3 segregation-0.1.0/segregation/NEWS.md |only segregation-0.1.0/segregation/R/data.R | 4 segregation-0.1.0/segregation/R/ipf.R |only segregation-0.1.0/segregation/R/mutual.R | 325 +++++++--- segregation-0.1.0/segregation/R/mutual_difference.R | 310 +++++++-- segregation-0.1.0/segregation/R/segregation.R | 111 ++- segregation-0.1.0/segregation/README.md | 223 +++--- segregation-0.1.0/segregation/data/schools00.rda |binary segregation-0.1.0/segregation/data/schools05.rda |binary segregation-0.1.0/segregation/man/entropy.Rd |only segregation-0.1.0/segregation/man/ipf.Rd |only segregation-0.1.0/segregation/man/mutual_difference.Rd | 95 ++ segregation-0.1.0/segregation/man/mutual_local.Rd | 39 - segregation-0.1.0/segregation/man/mutual_total.Rd | 44 - segregation-0.1.0/segregation/man/mutual_within.Rd |only segregation-0.1.0/segregation/man/schools00.Rd | 2 segregation-0.1.0/segregation/man/schools05.Rd | 2 segregation-0.1.0/segregation/man/segregation.Rd | 26 segregation-0.1.0/segregation/tests/testthat/test_entropy.R |only segregation-0.1.0/segregation/tests/testthat/test_ipf.R |only segregation-0.1.0/segregation/tests/testthat/test_mutual_difference.R |only segregation-0.1.0/segregation/tests/testthat/test_mutual_local.R | 40 + segregation-0.1.0/segregation/tests/testthat/test_mutual_total.R | 69 +- segregation-0.1.0/segregation/tests/testthat/test_mutual_within.R |only 28 files changed, 942 insertions(+), 407 deletions(-)
Title: Randomization for Clinical Trials
Description: This tool enables the user to choose a randomization procedure
based on sound scientific criteria. It comprises the generation of
randomization sequences as well the assessment of randomization procedures
based on carefully selected criteria. Furthermore, 'randomizeR' provides a
function for the comparison of randomization procedures.
Author: David Schindler [aut],
Diane Uschner [aut, cre],
Martin Manolov [ctb],
Thi Mui Pham [ctb],
Ralf-Dieter Hilgers [aut, ths],
Nicole Heussen [aut, ths]
Maintainer: Diane Uschner <duschner@ukaachen.de>
Diff between randomizeR versions 1.4.1 dated 2018-06-05 and 1.4.2 dated 2018-06-15
DESCRIPTION | 8 MD5 | 227 ++-- NAMESPACE | 194 +-- NEWS.md | 7 R/randomizeRPackage.R | 98 - build/vignette.rds |binary inst/CITATION |only inst/doc/article.R | 190 +-- inst/doc/article.Rnw | 2056 +++++++++++++++++++------------------ inst/doc/article.pdf |binary inst/doc/comparison-example.R | 100 - inst/doc/comparison-example.pdf |binary inst/doc/desirability-example.R | 128 +- inst/doc/desirability-example.pdf |binary inst/doc/randomizeR-refCard.pdf |binary man/K.Rd | 28 man/N.Rd | 28 man/TV.Rd | 28 man/a.Rd | 28 man/abcdPar.Rd | 88 - man/abcdRand.Rd | 64 - man/assess.Rd | 180 +-- man/bbcdPar.Rd | 84 - man/bbcdRand.Rd | 64 - man/blocks.Rd | 28 man/bsdPar.Rd | 80 - man/bsdRand.Rd | 56 - man/cash-assessment-method.Rd | 34 man/cash-comparison-method.Rd | 34 man/cash-derFunc-method.Rd | 34 man/cash-desFunc-method.Rd | 34 man/cash-desScores-method.Rd | 34 man/cash-endpoint-method.Rd | 34 man/cash-evaluation-method.Rd | 34 man/cash-issue-method.Rd | 34 man/cash-probUnDesirable-method.Rd | 34 man/cash-randPar-method.Rd | 34 man/cash-randSeq-method.Rd | 34 man/chenPar.Rd | 90 - man/chenRand.Rd | 62 - man/chronBias.Rd | 186 +-- man/coin.Rd | 28 man/combineBias.Rd | 62 - man/compare.Rd | 138 +- man/corGuess.Rd | 86 - man/crPar.Rd | 84 - man/createParam.Rd | 106 - man/createSeq.Rd | 40 man/derFunc-class.Rd | 18 man/derFunc.Rd | 106 - man/desirability.Rd | 136 +- man/doublyF_opt.Rd | 58 - man/doublyF_value.Rd | 48 man/doublyF_values.Rd | 46 man/doublyT.Rd | 54 man/doublyTValues.Rd | 60 - man/ebcPar.Rd | 82 - man/evaluate.Rd | 158 +- man/gbcdPar.Rd | 86 - man/gbcdRand.Rd | 66 - man/genNcps.Rd | 58 - man/generateAllSequences.Rd | 256 ++-- man/generateRandomSequences.Rd | 594 +++++----- man/getCorGuesses.Rd | 56 - man/getDesFunc.Rd | 54 man/getDesScores.Rd | 142 +- man/getDesign.Rd | 222 +-- man/getExpectation.Rd | 134 +- man/getProbabilities.Rd | 150 +- man/getRandomizationList.Rd | 44 man/getbiasCS1.Rd | 42 man/getbiasCS2.Rd | 42 man/hadaPar.Rd | 86 - man/hasAllGroups.Rd | 38 man/hatMatrix.Rd | 34 man/imbal.Rd | 86 - man/issue.Rd | 114 +- man/lambda1.Rd | 38 man/lambda2.Rd | 38 man/makeBiasedExpectation.Rd | 42 man/makeDesignMatrix.Rd | 42 man/method.Rd | 28 man/mpPar.Rd | 88 - man/mti.Rd | 28 man/mu.Rd | 28 man/normEndp.Rd | 58 - man/overview.Rd | 284 ++--- man/pbrPar.Rd | 94 - man/plot.Rd | 90 - man/plotDes.Rd | 82 - man/plotEv.Rd | 84 - man/plotSeq.Rd | 42 man/probUnDes.Rd | 116 +- man/randBlocks.Rd | 28 man/randPar-class.Rd | 18 man/randPar.Rd | 78 - man/randSeq-class.Rd | 48 man/randomizeR-package.Rd | 90 - man/rarPar.Rd | 90 - man/ratio.Rd | 28 man/rho.Rd | 28 man/rpbrPar.Rd | 104 - man/rtbdPar.Rd | 92 - man/saveAssess.Rd | 46 man/saveRand.Rd | 46 man/seed.Rd | 32 man/selBias.Rd | 134 +- man/setPower.Rd | 94 - man/sigma.Rd | 28 man/summary.Rd | 128 +- man/tbdPar.Rd | 78 - man/type.Rd | 36 man/udPar.Rd | 88 - vignettes/article.Rnw | 2056 +++++++++++++++++++------------------ vignettes/references.bib | 1530 +++++++++++++-------------- 115 files changed, 7203 insertions(+), 6969 deletions(-)
Title: Multivariate Menu for Radiant: Business Analytics using R and
Shiny
Description: The Radiant Multivariate menu includes interfaces for perceptual
mapping, factor analysis, cluster analysis, and conjoint analysis. The
application extends the functionality in radiant.data.
Author: Vincent Nijs [aut, cre]
Maintainer: Vincent Nijs <radiant@rady.ucsd.edu>
Diff between radiant.multivariate versions 0.8.0 dated 2017-04-29 and 0.9.5 dated 2018-06-15
radiant.multivariate-0.8.0/radiant.multivariate/R/pmap.R |only radiant.multivariate-0.8.0/radiant.multivariate/inst/app/tools/analysis/pmap_ui.R |only radiant.multivariate-0.8.0/radiant.multivariate/inst/app/tools/help/figures/place_holder.txt |only radiant.multivariate-0.8.0/radiant.multivariate/inst/app/tools/help/pmap.md |only radiant.multivariate-0.8.0/radiant.multivariate/inst/app/www/js/run_return.js |only radiant.multivariate-0.8.0/radiant.multivariate/man/plot.pmap.Rd |only radiant.multivariate-0.8.0/radiant.multivariate/man/pmap.Rd |only radiant.multivariate-0.8.0/radiant.multivariate/man/store.conjoint.predict.by.Rd |only radiant.multivariate-0.8.0/radiant.multivariate/man/summary.pmap.Rd |only radiant.multivariate-0.9.5/radiant.multivariate/DESCRIPTION | 25 radiant.multivariate-0.9.5/radiant.multivariate/MD5 | 187 +- radiant.multivariate-0.9.5/radiant.multivariate/NAMESPACE | 24 radiant.multivariate-0.9.5/radiant.multivariate/NEWS.md | 85 - radiant.multivariate-0.9.5/radiant.multivariate/R/aaa.R | 28 radiant.multivariate-0.9.5/radiant.multivariate/R/conjoint.R | 776 ++++------ radiant.multivariate-0.9.5/radiant.multivariate/R/deprecated.R | 34 radiant.multivariate-0.9.5/radiant.multivariate/R/full_factor.R | 324 ++-- radiant.multivariate-0.9.5/radiant.multivariate/R/hclus.R | 228 +- radiant.multivariate-0.9.5/radiant.multivariate/R/kclus.R | 408 ++--- radiant.multivariate-0.9.5/radiant.multivariate/R/mds.R | 267 +-- radiant.multivariate-0.9.5/radiant.multivariate/R/pre_factor.R | 244 +-- radiant.multivariate-0.9.5/radiant.multivariate/R/prmap.R |only radiant.multivariate-0.9.5/radiant.multivariate/R/radiant.R | 41 radiant.multivariate-0.9.5/radiant.multivariate/README.md | 70 radiant.multivariate-0.9.5/radiant.multivariate/inst/app/global.R | 4 radiant.multivariate-0.9.5/radiant.multivariate/inst/app/help.R | 26 radiant.multivariate-0.9.5/radiant.multivariate/inst/app/init.R | 51 radiant.multivariate-0.9.5/radiant.multivariate/inst/app/server.R | 25 radiant.multivariate-0.9.5/radiant.multivariate/inst/app/tools/analysis/conjoint_ui.R | 665 +++++--- radiant.multivariate-0.9.5/radiant.multivariate/inst/app/tools/analysis/full_factor_ui.R | 306 ++- radiant.multivariate-0.9.5/radiant.multivariate/inst/app/tools/analysis/hclus_ui.R | 230 +- radiant.multivariate-0.9.5/radiant.multivariate/inst/app/tools/analysis/kclus_ui.R | 321 ++-- radiant.multivariate-0.9.5/radiant.multivariate/inst/app/tools/analysis/mds_ui.R | 251 ++- radiant.multivariate-0.9.5/radiant.multivariate/inst/app/tools/analysis/pre_factor_ui.R | 167 +- radiant.multivariate-0.9.5/radiant.multivariate/inst/app/tools/analysis/prmap_ui.R |only radiant.multivariate-0.9.5/radiant.multivariate/inst/app/tools/help/conjoint.md | 22 radiant.multivariate-0.9.5/radiant.multivariate/inst/app/tools/help/figures/conjoint_carpet_design.png |only radiant.multivariate-0.9.5/radiant.multivariate/inst/app/tools/help/figures/conjoint_corr_mat.png |only radiant.multivariate-0.9.5/radiant.multivariate/inst/app/tools/help/figures/conjoint_expand.png |only radiant.multivariate-0.9.5/radiant.multivariate/inst/app/tools/help/figures/conjoint_plot.png |only radiant.multivariate-0.9.5/radiant.multivariate/inst/app/tools/help/figures/conjoint_predict.png |only radiant.multivariate-0.9.5/radiant.multivariate/inst/app/tools/help/figures/conjoint_summary.png |only radiant.multivariate-0.9.5/radiant.multivariate/inst/app/tools/help/figures/conjoint_view.png |only radiant.multivariate-0.9.5/radiant.multivariate/inst/app/tools/help/figures/full_factor_plot.png |only radiant.multivariate-0.9.5/radiant.multivariate/inst/app/tools/help/figures/full_factor_plot_rotation.png |only radiant.multivariate-0.9.5/radiant.multivariate/inst/app/tools/help/figures/full_factor_summary.png |only radiant.multivariate-0.9.5/radiant.multivariate/inst/app/tools/help/figures/full_factor_summary_shopping.png |only radiant.multivariate-0.9.5/radiant.multivariate/inst/app/tools/help/figures/hclus_dendro.png |only radiant.multivariate-0.9.5/radiant.multivariate/inst/app/tools/help/figures/hclus_scree.png |only radiant.multivariate-0.9.5/radiant.multivariate/inst/app/tools/help/figures/kclus_cross_tabs_plot.png |only radiant.multivariate-0.9.5/radiant.multivariate/inst/app/tools/help/figures/kclus_cross_tabs_summary.png |only radiant.multivariate-0.9.5/radiant.multivariate/inst/app/tools/help/figures/kclus_plot.png |only radiant.multivariate-0.9.5/radiant.multivariate/inst/app/tools/help/figures/kclus_summary.png |only radiant.multivariate-0.9.5/radiant.multivariate/inst/app/tools/help/figures/kclus_transform_recode.png |only radiant.multivariate-0.9.5/radiant.multivariate/inst/app/tools/help/figures/mds_plot.png |only radiant.multivariate-0.9.5/radiant.multivariate/inst/app/tools/help/figures/mds_plot_flip.png |only radiant.multivariate-0.9.5/radiant.multivariate/inst/app/tools/help/figures/mds_plot_tpbrands.png |only radiant.multivariate-0.9.5/radiant.multivariate/inst/app/tools/help/figures/mds_summary.png |only radiant.multivariate-0.9.5/radiant.multivariate/inst/app/tools/help/figures/mds_summary_tpbrands.png |only radiant.multivariate-0.9.5/radiant.multivariate/inst/app/tools/help/figures/pre_factor_plot.png |only radiant.multivariate-0.9.5/radiant.multivariate/inst/app/tools/help/figures/pre_factor_summary.png |only radiant.multivariate-0.9.5/radiant.multivariate/inst/app/tools/help/figures/prmap_plot_all.png |only radiant.multivariate-0.9.5/radiant.multivariate/inst/app/tools/help/figures/prmap_plot_brands.png |only radiant.multivariate-0.9.5/radiant.multivariate/inst/app/tools/help/figures/prmap_plot_brands_attr.png |only radiant.multivariate-0.9.5/radiant.multivariate/inst/app/tools/help/figures/prmap_summary.png |only radiant.multivariate-0.9.5/radiant.multivariate/inst/app/tools/help/full_factor.md | 24 radiant.multivariate-0.9.5/radiant.multivariate/inst/app/tools/help/hclus.md | 14 radiant.multivariate-0.9.5/radiant.multivariate/inst/app/tools/help/kclus.md | 20 radiant.multivariate-0.9.5/radiant.multivariate/inst/app/tools/help/mds.md | 33 radiant.multivariate-0.9.5/radiant.multivariate/inst/app/tools/help/pre_factor.md | 22 radiant.multivariate-0.9.5/radiant.multivariate/inst/app/tools/help/prmap.md |only radiant.multivariate-0.9.5/radiant.multivariate/inst/app/ui.R | 16 radiant.multivariate-0.9.5/radiant.multivariate/inst/app/www/js/store.js |only radiant.multivariate-0.9.5/radiant.multivariate/man/carpet.Rd | 2 radiant.multivariate-0.9.5/radiant.multivariate/man/city.Rd | 2 radiant.multivariate-0.9.5/radiant.multivariate/man/city2.Rd | 2 radiant.multivariate-0.9.5/radiant.multivariate/man/clean_loadings.Rd | 8 radiant.multivariate-0.9.5/radiant.multivariate/man/computer.Rd | 2 radiant.multivariate-0.9.5/radiant.multivariate/man/conjoint.Rd | 5 radiant.multivariate-0.9.5/radiant.multivariate/man/full_factor.Rd | 6 radiant.multivariate-0.9.5/radiant.multivariate/man/hclus.Rd | 6 radiant.multivariate-0.9.5/radiant.multivariate/man/kclus.Rd | 4 radiant.multivariate-0.9.5/radiant.multivariate/man/mds.Rd | 8 radiant.multivariate-0.9.5/radiant.multivariate/man/movie.Rd | 2 radiant.multivariate-0.9.5/radiant.multivariate/man/mp3.Rd | 2 radiant.multivariate-0.9.5/radiant.multivariate/man/plot.conjoint.Rd | 6 radiant.multivariate-0.9.5/radiant.multivariate/man/plot.full_factor.Rd | 6 radiant.multivariate-0.9.5/radiant.multivariate/man/plot.hclus.Rd | 7 radiant.multivariate-0.9.5/radiant.multivariate/man/plot.kclus.Rd | 5 radiant.multivariate-0.9.5/radiant.multivariate/man/plot.mds.Rd | 12 radiant.multivariate-0.9.5/radiant.multivariate/man/plot.pre_factor.Rd | 5 radiant.multivariate-0.9.5/radiant.multivariate/man/plot.prmap.Rd |only radiant.multivariate-0.9.5/radiant.multivariate/man/pre_factor.Rd | 4 radiant.multivariate-0.9.5/radiant.multivariate/man/predict.conjoint.Rd | 12 radiant.multivariate-0.9.5/radiant.multivariate/man/predict_conjoint_by.Rd | 2 radiant.multivariate-0.9.5/radiant.multivariate/man/print.conjoint.predict.Rd | 2 radiant.multivariate-0.9.5/radiant.multivariate/man/prmap.Rd |only radiant.multivariate-0.9.5/radiant.multivariate/man/radiant.multivariate-deprecated.Rd | 14 radiant.multivariate-0.9.5/radiant.multivariate/man/radiant.multivariate.Rd | 7 radiant.multivariate-0.9.5/radiant.multivariate/man/radiant.multivariate_viewer.Rd |only radiant.multivariate-0.9.5/radiant.multivariate/man/radiant.multivariate_window.Rd |only radiant.multivariate-0.9.5/radiant.multivariate/man/retailers.Rd | 2 radiant.multivariate-0.9.5/radiant.multivariate/man/shopping.Rd | 2 radiant.multivariate-0.9.5/radiant.multivariate/man/store.conjoint.Rd | 11 radiant.multivariate-0.9.5/radiant.multivariate/man/store.conjoint.predict.Rd | 17 radiant.multivariate-0.9.5/radiant.multivariate/man/store.full_factor.Rd | 14 radiant.multivariate-0.9.5/radiant.multivariate/man/store.kclus.Rd | 12 radiant.multivariate-0.9.5/radiant.multivariate/man/summary.conjoint.Rd | 5 radiant.multivariate-0.9.5/radiant.multivariate/man/summary.full_factor.Rd | 6 radiant.multivariate-0.9.5/radiant.multivariate/man/summary.hclus.Rd | 2 radiant.multivariate-0.9.5/radiant.multivariate/man/summary.kclus.Rd | 3 radiant.multivariate-0.9.5/radiant.multivariate/man/summary.mds.Rd | 6 radiant.multivariate-0.9.5/radiant.multivariate/man/summary.pre_factor.Rd | 6 radiant.multivariate-0.9.5/radiant.multivariate/man/summary.prmap.Rd |only radiant.multivariate-0.9.5/radiant.multivariate/man/the_table.Rd | 8 radiant.multivariate-0.9.5/radiant.multivariate/man/toothpaste.Rd | 2 radiant.multivariate-0.9.5/radiant.multivariate/man/tpbrands.Rd | 2 radiant.multivariate-0.9.5/radiant.multivariate/tests/testthat/test_stats.R | 168 +- 118 files changed, 3098 insertions(+), 2237 deletions(-)
More information about radiant.multivariate at CRAN
Permanent link
Title: General Semiparametric Shared Frailty Model
Description: Simulates and fits semiparametric shared frailty models under a
wide range of frailty distributions using a consistent and
asymptotically-normal estimator. Currently supports: gamma, power variance
function, log-normal, and inverse Gaussian frailty models.
Author: Vinnie Monaco [aut, cre],
Malka Gorfine [aut],
Li Hsu [aut]
Maintainer: Vinnie Monaco <contact@vmonaco.com>
Diff between frailtySurv versions 1.3.3 dated 2018-06-05 and 1.3.4 dated 2018-06-15
DESCRIPTION | 8 +++---- MD5 | 16 +++++++------- NEWS.md | 6 +++++ R/frailtySurv.R | 2 - R/genfrail.control.R | 4 +-- R/print.summary.simfrail.R | 3 -- R/simfrail.R | 50 ++++++++++++++++++++++++++++++++------------- man/fitfrail.control.Rd | 2 - man/genfrail.control.Rd | 8 +++---- 9 files changed, 63 insertions(+), 36 deletions(-)
Title: Develop and Run Spatially Explicit Discrete Event Simulation
Models
Description: Metapackage for implementing a variety of event-based models, with
a focus on spatially explicit models. These include raster-based,
event-based, and agent-based models. The core simulation components
(provided by 'SpaDES.core') are built upon a discrete event simulation (DES;
see Matloff (2011) ch 7.8.3 <https://nostarch.com/artofr.htm>)
framework that facilitates modularity, and easily enables the user to
include additional functionality by running user-built simulation modules
(see also 'SpaDES.tools'). Included are numerous tools to visualize rasters
and other maps (via 'quickPlot'), and caching methods for reproducible
simulations (via 'reproducible'). Additional functionality is provided by
the 'SpaDES.addins' and 'SpaDES.shiny' packages.
Author: Alex M Chubaty [aut, cre],
Eliot J B McIntire [aut],
Yong Luo [ctb],
Steve Cumming [ctb],
Her Majesty the Queen in Right of Canada, as represented by the
Minister of Natural Resources Canada [cph]
Maintainer: Alex M Chubaty <alex.chubaty@gmail.com>
Diff between SpaDES versions 2.0.1 dated 2018-02-01 and 2.0.2 dated 2018-06-15
DESCRIPTION | 16 - MD5 | 18 - NEWS.md | 10 README.md | 20 - build/vignette.rds |binary inst/doc/iii-cache.R | 14 + inst/doc/iii-cache.Rmd | 78 +++++ inst/doc/iii-cache.html | 629 +++++++++++++++++++----------------------------- man/SpaDES-package.Rd | 2 vignettes/iii-cache.Rmd | 78 +++++ 10 files changed, 468 insertions(+), 397 deletions(-)
More information about QTL.gCIMapping.GUI at CRAN
Permanent link
Title: Dependency-Free Access to PNG Image Files
Description: Read and write access to PNG image files using the LodePNG
library. The package has no external dependencies.
Author: Jon Clayden [aut, cre],
Lode Vandevenne [aut]
Maintainer: Jon Clayden <code@clayden.org>
Diff between loder versions 0.1.2 dated 2017-05-30 and 0.2.0 dated 2018-06-15
DESCRIPTION | 10 - LICENCE | 2 MD5 | 48 +++++-- NAMESPACE | 3 NEWS.md | 8 + R/png.R | 119 ++++++++++++++++-- README.md | 14 ++ inst/extdata/pngsuite/ct1n0g04.png |only inst/extdata/pngsuite/cten0g04.png |only inst/extdata/pngsuite/ctgn0g04.png |only inst/extdata/pngsuite/ctzn0g04.png |only inst/extdata/pngsuite/xc1n0g08.png |only inst/extdata/pngsuite/xc9n2c08.png |only inst/extdata/pngsuite/xcrn0g04.png |only inst/extdata/pngsuite/xcsn0g01.png |only inst/extdata/pngsuite/xd0n2c08.png |only inst/extdata/pngsuite/xd3n2c08.png |only inst/extdata/pngsuite/xd9n2c08.png |only inst/extdata/pngsuite/xdtn0g01.png |only inst/extdata/pngsuite/xhdn0g08.png |only inst/extdata/pngsuite/xlfn0g04.png |only inst/extdata/pngsuite/xs1n0g01.png |only inst/extdata/pngsuite/xs2n0g01.png |only inst/extdata/pngsuite/xs4n0g01.png |only inst/extdata/pngsuite/xs7n0g01.png |only inst/extdata/pngsuite/z00n2c08.png |only man/inspectPng.Rd |only man/readPng.Rd | 19 ++ man/writePng.Rd | 40 ++++-- src/lodepng.c | 129 +++++++++++--------- src/lodepng.h | 14 +- src/main.c | 236 ++++++++++++++++++++++++++----------- tests/testthat/test-05-read.R | 23 +++ tests/testthat/test-10-metadata.R | 17 ++ tests/testthat/test-15-write.R | 28 ++++ 35 files changed, 537 insertions(+), 173 deletions(-)
Title: Cyclic Coordinate Descent for Logistic, Poisson and Survival
Analysis
Description: This model fitting tool incorporates cyclic coordinate descent and
majorization-minimization approaches to fit a variety of regression models
found in large-scale observational healthcare data. Implementations focus
on computational optimization and fine-scale parallelization to yield
efficient inference in massive datasets. Please see:
Suchard, Simpson, Zorych, Ryan and Madigan (2013) <doi:10.1145/2414416.2414791>.
Author: Marc A. Suchard [aut, cre],
Martijn J. Schuemie [aut],
Trevor R. Shaddox [aut],
Yuxi Tian [aut],
Sushil Mittal [ctb],
Observational Health Data Sciences and Informatics [cph],
Marcus Geelnard [cph, ctb] (provided the TinyThread library),
Rutgers University [cph, ctb] (provided the HParSearch routine),
R Development Core Team [cph, ctb] (provided the ZeroIn routine)
Maintainer: Marc A. Suchard <msuchard@ucla.edu>
Diff between Cyclops versions 1.3.2 dated 2018-05-06 and 1.3.4 dated 2018-06-15
Cyclops-1.3.2/Cyclops/tests/testthat/test-KKTSwindle.R |only Cyclops-1.3.4/Cyclops/DESCRIPTION | 41 ++- Cyclops-1.3.4/Cyclops/MD5 | 84 +++---- Cyclops-1.3.4/Cyclops/NAMESPACE | 3 Cyclops-1.3.4/Cyclops/NEWS | 14 + Cyclops-1.3.4/Cyclops/R/DataManagement.R | 34 ++ Cyclops-1.3.4/Cyclops/R/ModelFit.R | 15 - Cyclops-1.3.4/Cyclops/R/RcppExports.R | 4 Cyclops-1.3.4/Cyclops/R/SpecialPriors.R |only Cyclops-1.3.4/Cyclops/R/cyclops.R | 2 Cyclops-1.3.4/Cyclops/man/aconfint.Rd | 2 Cyclops-1.3.4/Cyclops/man/coef.cyclopsFit.Rd | 5 Cyclops-1.3.4/Cyclops/man/createNonSeparablePrior.Rd |only Cyclops-1.3.4/Cyclops/man/fitCyclopsModel.Rd | 2 Cyclops-1.3.4/Cyclops/man/getUnivariableSeparability.Rd |only Cyclops-1.3.4/Cyclops/man/vcov.cyclopsFit.Rd | 2 Cyclops-1.3.4/Cyclops/src/RcppExports.cpp | 13 + Cyclops-1.3.4/Cyclops/src/RcppModelData.cpp | 53 ++++ Cyclops-1.3.4/Cyclops/src/RcppProgressLogger.h | 56 ++-- Cyclops-1.3.4/Cyclops/src/cyclops/CcdInterface.cpp | 1 Cyclops-1.3.4/Cyclops/src/cyclops/Timer.cpp | 68 ----- Cyclops-1.3.4/Cyclops/src/cyclops/engine/AbstractModelSpecifics.cpp | 14 - Cyclops-1.3.4/Cyclops/src/cyclops/engine/AbstractModelSpecifics.h | 51 ++-- Cyclops-1.3.4/Cyclops/tests/testthat/test-believedBroken.R | 32 +- Cyclops-1.3.4/Cyclops/tests/testthat/test-conditionalPoisson.R | 2 Cyclops-1.3.4/Cyclops/tests/testthat/test-correlation.R | 2 Cyclops-1.3.4/Cyclops/tests/testthat/test-covariateRegularization.R | 8 Cyclops-1.3.4/Cyclops/tests/testthat/test-cprViaSql.R | 20 - Cyclops-1.3.4/Cyclops/tests/testthat/test-cv.R | 2 Cyclops-1.3.4/Cyclops/tests/testthat/test-dataConversionStratified.R | 84 +++---- Cyclops-1.3.4/Cyclops/tests/testthat/test-dataConversionUnstratified.R | 64 ++--- Cyclops-1.3.4/Cyclops/tests/testthat/test-dataManagement.R | 16 - Cyclops-1.3.4/Cyclops/tests/testthat/test-isSorted.R | 2 Cyclops-1.3.4/Cyclops/tests/testthat/test-largeBernoulli.R | 78 ++++++ Cyclops-1.3.4/Cyclops/tests/testthat/test-multitypePoisson.R | 114 +++++----- Cyclops-1.3.4/Cyclops/tests/testthat/test-normalization.R | 2 Cyclops-1.3.4/Cyclops/tests/testthat/test-offsetPoisson.R | 42 +-- Cyclops-1.3.4/Cyclops/tests/testthat/test-parameterizedPriors.R | 2 Cyclops-1.3.4/Cyclops/tests/testthat/test-predict.R | 2 Cyclops-1.3.4/Cyclops/tests/testthat/test-reductions.R | 22 + Cyclops-1.3.4/Cyclops/tests/testthat/test-smallBernoulli.R | 32 +- Cyclops-1.3.4/Cyclops/tests/testthat/test-smallCLR.R | 24 +- Cyclops-1.3.4/Cyclops/tests/testthat/test-sqlConstructor.R | 66 ++--- Cyclops-1.3.4/Cyclops/tests/testthat/test-survfit.R | 2 Cyclops-1.3.4/Cyclops/tests/testthat/test-xyConstructor.R | 4 45 files changed, 646 insertions(+), 440 deletions(-)
Title: 'Rcpp' Bindings for the 'Corpus Workbench' ('CWB')
Description: 'Rcpp' Bindings for the C code of the 'Corpus Workbench' ('CWB'), an indexing and query
engine to efficiently analyze large corpora (<http://cwb.sourceforge.net>). 'RcppCWB' is licensed
under the GNU GPL-3, in line with the GPL-3 license of the 'CWB' (<https://www.r-project.org/
Licenses/GPL-3>). The 'CWB' relies on 'pcre' (BSD license, see <https://www.pcre.org/
licence.txt>) and 'GLib' (LGPL license, see <https://www.gnu.org/licenses/lgpl-3.0.en.
html>). See the file LICENSE.note for further information. The package includes modified code of the
'rcqp' package (GPL-2, see <https://cran.r-project.org/package=rcqp>). The original work of the authors
of the 'rcqp' package is acknowledged with great respect, and they are listed as authors of this
package. To achieve cross-platform portability (including Windows), using 'Rcpp' for wrapper code
is the approach used by 'RcppCWB'.
Author: Andreas Blaette [aut, cre],
Bernard Desgraupes [aut],
Sylvain Loiseau [aut],
Oliver Christ [ctb],
Bruno Maximilian Schulze [ctb],
Stefan Evert [ctb],
Arne Fitschen [ctb]
Maintainer: Andreas Blaette <andreas.blaette@uni-due.de>
Diff between RcppCWB versions 0.2.3 dated 2018-05-13 and 0.2.4 dated 2018-06-15
RcppCWB-0.2.3/RcppCWB/src/cwb/config/platform/darwin-core2 |only RcppCWB-0.2.3/RcppCWB/src/cwb/config/platform/darwin-g4 |only RcppCWB-0.2.3/RcppCWB/src/cwb/config/platform/darwin-g5 |only RcppCWB-0.2.3/RcppCWB/src/cwb/config/platform/darwin-i386 |only RcppCWB-0.2.3/RcppCWB/src/cwb/cqp/paths.c |only RcppCWB-0.2.3/RcppCWB/src/cwb/cqp/paths.h |only RcppCWB-0.2.4/RcppCWB/DESCRIPTION | 13 RcppCWB-0.2.4/RcppCWB/MD5 | 365 - RcppCWB-0.2.4/RcppCWB/NAMESPACE | 6 RcppCWB-0.2.4/RcppCWB/NEWS.md | 18 RcppCWB-0.2.4/RcppCWB/R/RcppCWB_package.R | 8 RcppCWB-0.2.4/RcppCWB/R/RcppExports.R | 12 RcppCWB-0.2.4/RcppCWB/R/cbow.R | 3 RcppCWB-0.2.4/RcppCWB/R/checks.R | 79 RcppCWB-0.2.4/RcppCWB/R/cl.R | 10 RcppCWB-0.2.4/RcppCWB/R/count.R | 2 RcppCWB-0.2.4/RcppCWB/R/cqp.R | 7 RcppCWB-0.2.4/RcppCWB/R/cwb.R |only RcppCWB-0.2.4/RcppCWB/R/decode.R | 2 RcppCWB-0.2.4/RcppCWB/R/misc.R |only RcppCWB-0.2.4/RcppCWB/R/region_matrix.R | 4 RcppCWB-0.2.4/RcppCWB/R/zzz.R | 41 RcppCWB-0.2.4/RcppCWB/README.md | 121 RcppCWB-0.2.4/RcppCWB/cleanup | 5 RcppCWB-0.2.4/RcppCWB/configure | 8 RcppCWB-0.2.4/RcppCWB/inst/extdata/cwb/indexed_corpora/unga |only RcppCWB-0.2.4/RcppCWB/inst/extdata/cwb/registry/reuters | 4 RcppCWB-0.2.4/RcppCWB/inst/extdata/cwb/registry/unga |only RcppCWB-0.2.4/RcppCWB/man/RcppCWB-packge.Rd | 8 RcppCWB-0.2.4/RcppCWB/man/check_pkg_registry_files.Rd |only RcppCWB-0.2.4/RcppCWB/man/cl_attribute_size.Rd | 3 RcppCWB-0.2.4/RcppCWB/man/cl_lexicon_size.Rd | 2 RcppCWB-0.2.4/RcppCWB/man/cqp_initialize.Rd | 5 RcppCWB-0.2.4/RcppCWB/man/cqp_query.Rd | 2 RcppCWB-0.2.4/RcppCWB/man/cwb_utils.Rd |only RcppCWB-0.2.4/RcppCWB/man/get_cbow_matrix.Rd | 3 RcppCWB-0.2.4/RcppCWB/man/get_count_vector.Rd | 2 RcppCWB-0.2.4/RcppCWB/man/get_pkg_registry.Rd |only RcppCWB-0.2.4/RcppCWB/man/get_region_matrix.Rd | 2 RcppCWB-0.2.4/RcppCWB/man/p_attributes.Rd | 2 RcppCWB-0.2.4/RcppCWB/man/region_matrix_ops.Rd | 2 RcppCWB-0.2.4/RcppCWB/man/s_attribute_decode.Rd | 2 RcppCWB-0.2.4/RcppCWB/man/s_attributes.Rd | 3 RcppCWB-0.2.4/RcppCWB/man/use_tmp_registry.Rd |only RcppCWB-0.2.4/RcppCWB/src/Makevars.win | 2 RcppCWB-0.2.4/RcppCWB/src/RcppExports.cpp | 42 RcppCWB-0.2.4/RcppCWB/src/cl.cpp | 2 RcppCWB-0.2.4/RcppCWB/src/cl_min.h |only RcppCWB-0.2.4/RcppCWB/src/cqp.cpp | 4 RcppCWB-0.2.4/RcppCWB/src/cwb/AUTHORS | 12 RcppCWB-0.2.4/RcppCWB/src/cwb/CHANGES | 251 RcppCWB-0.2.4/RcppCWB/src/cwb/COPYING | 1366 ++++ RcppCWB-0.2.4/RcppCWB/src/cwb/CQi/auth.c | 74 RcppCWB-0.2.4/RcppCWB/src/cwb/CQi/auth.h | 16 RcppCWB-0.2.4/RcppCWB/src/cwb/CQi/cqi.h | 84 RcppCWB-0.2.4/RcppCWB/src/cwb/CQi/cqpserver.c | 471 + RcppCWB-0.2.4/RcppCWB/src/cwb/CQi/server.c | 607 +- RcppCWB-0.2.4/RcppCWB/src/cwb/CQi/server.h | 6 RcppCWB-0.2.4/RcppCWB/src/cwb/INSTALL | 210 RcppCWB-0.2.4/RcppCWB/src/cwb/Makefile | 83 RcppCWB-0.2.4/RcppCWB/src/cwb/README | 14 RcppCWB-0.2.4/RcppCWB/src/cwb/cl/Makefile | 100 RcppCWB-0.2.4/RcppCWB/src/cwb/cl/attributes.c | 348 - RcppCWB-0.2.4/RcppCWB/src/cwb/cl/attributes.h | 46 RcppCWB-0.2.4/RcppCWB/src/cwb/cl/binsert.c | 5 RcppCWB-0.2.4/RcppCWB/src/cwb/cl/bitfields.c | 9 RcppCWB-0.2.4/RcppCWB/src/cwb/cl/bitio.c | 69 RcppCWB-0.2.4/RcppCWB/src/cwb/cl/cdaccess.c | 679 +- RcppCWB-0.2.4/RcppCWB/src/cwb/cl/cdaccess.h | 3 RcppCWB-0.2.4/RcppCWB/src/cwb/cl/cl.h | 1413 +++- RcppCWB-0.2.4/RcppCWB/src/cwb/cl/class-mapping.c | 21 RcppCWB-0.2.4/RcppCWB/src/cwb/cl/compression.c | 9 RcppCWB-0.2.4/RcppCWB/src/cwb/cl/corpus.c | 226 RcppCWB-0.2.4/RcppCWB/src/cwb/cl/corpus.h | 9 RcppCWB-0.2.4/RcppCWB/src/cwb/cl/endian.c | 11 RcppCWB-0.2.4/RcppCWB/src/cwb/cl/endian2.h | 32 RcppCWB-0.2.4/RcppCWB/src/cwb/cl/fileutils.c | 278 RcppCWB-0.2.4/RcppCWB/src/cwb/cl/fileutils.h | 11 RcppCWB-0.2.4/RcppCWB/src/cwb/cl/globals.c | 13 RcppCWB-0.2.4/RcppCWB/src/cwb/cl/globals.h | 102 RcppCWB-0.2.4/RcppCWB/src/cwb/cl/lex.creg.c | 147 RcppCWB-0.2.4/RcppCWB/src/cwb/cl/lexhash.c | 305 - RcppCWB-0.2.4/RcppCWB/src/cwb/cl/list.c | 4 RcppCWB-0.2.4/RcppCWB/src/cwb/cl/macros.c | 166 RcppCWB-0.2.4/RcppCWB/src/cwb/cl/macros.h | 37 RcppCWB-0.2.4/RcppCWB/src/cwb/cl/makecomps.c | 145 RcppCWB-0.2.4/RcppCWB/src/cwb/cl/ngram-hash.c | 31 RcppCWB-0.2.4/RcppCWB/src/cwb/cl/registry.l | 6 RcppCWB-0.2.4/RcppCWB/src/cwb/cl/registry.tab.c | 43 RcppCWB-0.2.4/RcppCWB/src/cwb/cl/registry.y | 5 RcppCWB-0.2.4/RcppCWB/src/cwb/cl/regopt.c | 1355 +++- RcppCWB-0.2.4/RcppCWB/src/cwb/cl/regopt.h | 26 RcppCWB-0.2.4/RcppCWB/src/cwb/cl/special-chars.c | 2896 +++++++++- RcppCWB-0.2.4/RcppCWB/src/cwb/cl/special-chars.h | 7 RcppCWB-0.2.4/RcppCWB/src/cwb/cl/storage.c | 184 RcppCWB-0.2.4/RcppCWB/src/cwb/cl/storage.h | 35 RcppCWB-0.2.4/RcppCWB/src/cwb/cl/windows-mmap.c | 7 RcppCWB-0.2.4/RcppCWB/src/cwb/config.mk | 83 RcppCWB-0.2.4/RcppCWB/src/cwb/config/platform/darwin | 7 RcppCWB-0.2.4/RcppCWB/src/cwb/config/platform/darwin-64 | 14 RcppCWB-0.2.4/RcppCWB/src/cwb/config/platform/darwin-universal | 10 RcppCWB-0.2.4/RcppCWB/src/cwb/config/platform/linux | 5 RcppCWB-0.2.4/RcppCWB/src/cwb/config/platform/template | 14 RcppCWB-0.2.4/RcppCWB/src/cwb/config/platform/unix | 14 RcppCWB-0.2.4/RcppCWB/src/cwb/cqp/Makefile | 30 RcppCWB-0.2.4/RcppCWB/src/cwb/cqp/_options.h | 115 RcppCWB-0.2.4/RcppCWB/src/cwb/cqp/ascii-print.c | 83 RcppCWB-0.2.4/RcppCWB/src/cwb/cqp/attlist.c | 6 RcppCWB-0.2.4/RcppCWB/src/cwb/cqp/builtins.c | 150 RcppCWB-0.2.4/RcppCWB/src/cwb/cqp/builtins.h | 1 RcppCWB-0.2.4/RcppCWB/src/cwb/cqp/concordance.c | 1065 +-- RcppCWB-0.2.4/RcppCWB/src/cwb/cqp/concordance.h | 112 RcppCWB-0.2.4/RcppCWB/src/cwb/cqp/context_descriptor.c | 328 - RcppCWB-0.2.4/RcppCWB/src/cwb/cqp/context_descriptor.h | 88 RcppCWB-0.2.4/RcppCWB/src/cwb/cqp/corpmanag.c | 499 - RcppCWB-0.2.4/RcppCWB/src/cwb/cqp/corpmanag.h | 80 RcppCWB-0.2.4/RcppCWB/src/cwb/cqp/cqp.c | 130 RcppCWB-0.2.4/RcppCWB/src/cwb/cqp/cqp.h | 43 RcppCWB-0.2.4/RcppCWB/src/cwb/cqp/cqpcl.c | 10 RcppCWB-0.2.4/RcppCWB/src/cwb/cqp/eval.c | 743 +- RcppCWB-0.2.4/RcppCWB/src/cwb/cqp/eval.h | 148 RcppCWB-0.2.4/RcppCWB/src/cwb/cqp/groups.c | 202 RcppCWB-0.2.4/RcppCWB/src/cwb/cqp/groups.h | 6 RcppCWB-0.2.4/RcppCWB/src/cwb/cqp/hash.c | 8 RcppCWB-0.2.4/RcppCWB/src/cwb/cqp/html-print.c | 75 RcppCWB-0.2.4/RcppCWB/src/cwb/cqp/html-print.h | 1 RcppCWB-0.2.4/RcppCWB/src/cwb/cqp/latex-print.c | 243 RcppCWB-0.2.4/RcppCWB/src/cwb/cqp/lex.yy.c | 1833 +++--- RcppCWB-0.2.4/RcppCWB/src/cwb/cqp/llquery.c | 143 RcppCWB-0.2.4/RcppCWB/src/cwb/cqp/macro.c | 731 +- RcppCWB-0.2.4/RcppCWB/src/cwb/cqp/macro.h | 9 RcppCWB-0.2.4/RcppCWB/src/cwb/cqp/matchlist.c | 629 +- RcppCWB-0.2.4/RcppCWB/src/cwb/cqp/matchlist.h | 43 RcppCWB-0.2.4/RcppCWB/src/cwb/cqp/options.c | 391 - RcppCWB-0.2.4/RcppCWB/src/cwb/cqp/options.h | 115 RcppCWB-0.2.4/RcppCWB/src/cwb/cqp/output.c | 534 + RcppCWB-0.2.4/RcppCWB/src/cwb/cqp/output.h | 161 RcppCWB-0.2.4/RcppCWB/src/cwb/cqp/parse_actions.c | 578 + RcppCWB-0.2.4/RcppCWB/src/cwb/cqp/parse_actions.h | 36 RcppCWB-0.2.4/RcppCWB/src/cwb/cqp/parser.l | 35 RcppCWB-0.2.4/RcppCWB/src/cwb/cqp/parser.tab.c | 2777 +++++---- RcppCWB-0.2.4/RcppCWB/src/cwb/cqp/parser.tab.h | 384 - RcppCWB-0.2.4/RcppCWB/src/cwb/cqp/parser.y | 245 RcppCWB-0.2.4/RcppCWB/src/cwb/cqp/print-modes.c | 7 RcppCWB-0.2.4/RcppCWB/src/cwb/cqp/print-modes.h | 22 RcppCWB-0.2.4/RcppCWB/src/cwb/cqp/print_align.c | 325 - RcppCWB-0.2.4/RcppCWB/src/cwb/cqp/print_align.h | 10 RcppCWB-0.2.4/RcppCWB/src/cwb/cqp/ranges.c | 731 +- RcppCWB-0.2.4/RcppCWB/src/cwb/cqp/ranges.h | 119 RcppCWB-0.2.4/RcppCWB/src/cwb/cqp/regex2dfa.c | 691 +- RcppCWB-0.2.4/RcppCWB/src/cwb/cqp/regex2dfa.h | 12 RcppCWB-0.2.4/RcppCWB/src/cwb/cqp/sgml-print.c | 78 RcppCWB-0.2.4/RcppCWB/src/cwb/cqp/symtab.c | 60 RcppCWB-0.2.4/RcppCWB/src/cwb/cqp/symtab.h | 25 RcppCWB-0.2.4/RcppCWB/src/cwb/cqp/targets.c | 12 RcppCWB-0.2.4/RcppCWB/src/cwb/cqp/tree.c | 26 RcppCWB-0.2.4/RcppCWB/src/cwb/cqp/treemacros.h | 32 RcppCWB-0.2.4/RcppCWB/src/cwb/cqp/variables.c | 342 - RcppCWB-0.2.4/RcppCWB/src/cwb/cqp/variables.h | 80 RcppCWB-0.2.4/RcppCWB/src/cwb/definitions.mk | 93 RcppCWB-0.2.4/RcppCWB/src/cwb/editline/README | 2 RcppCWB-0.2.4/RcppCWB/src/cwb/install-scripts/cwb-config-basic | 62 RcppCWB-0.2.4/RcppCWB/src/cwb/install-scripts/cwb-install-fedora | 26 RcppCWB-0.2.4/RcppCWB/src/cwb/install-scripts/cwb-install-fedora-dnf |only RcppCWB-0.2.4/RcppCWB/src/cwb/install-scripts/cwb-install-mac-osx | 73 RcppCWB-0.2.4/RcppCWB/src/cwb/install-scripts/cwb-install-ubuntu | 28 RcppCWB-0.2.4/RcppCWB/src/cwb/utils/Makefile | 88 RcppCWB-0.2.4/RcppCWB/src/cwb/utils/_cwb_compress_rdx.c |only RcppCWB-0.2.4/RcppCWB/src/cwb/utils/_cwb_huffcode.c |only RcppCWB-0.2.4/RcppCWB/src/cwb/utils/_cwb_makeall.c |only RcppCWB-0.2.4/RcppCWB/src/cwb/utils/barlib.c | 66 RcppCWB-0.2.4/RcppCWB/src/cwb/utils/barlib.h | 35 RcppCWB-0.2.4/RcppCWB/src/cwb/utils/cwb-align-encode.c | 86 RcppCWB-0.2.4/RcppCWB/src/cwb/utils/cwb-align-show.c | 179 RcppCWB-0.2.4/RcppCWB/src/cwb/utils/cwb-align.c | 176 RcppCWB-0.2.4/RcppCWB/src/cwb/utils/cwb-atoi.c | 47 RcppCWB-0.2.4/RcppCWB/src/cwb/utils/cwb-compress-rdx.c | 165 RcppCWB-0.2.4/RcppCWB/src/cwb/utils/cwb-decode-nqrfile.c | 44 RcppCWB-0.2.4/RcppCWB/src/cwb/utils/cwb-decode.c | 500 + RcppCWB-0.2.4/RcppCWB/src/cwb/utils/cwb-describe-corpus.c | 34 RcppCWB-0.2.4/RcppCWB/src/cwb/utils/cwb-encode.c | 1060 +-- RcppCWB-0.2.4/RcppCWB/src/cwb/utils/cwb-huffcode.c | 141 RcppCWB-0.2.4/RcppCWB/src/cwb/utils/cwb-itoa.c | 11 RcppCWB-0.2.4/RcppCWB/src/cwb/utils/cwb-lexdecode.c | 75 RcppCWB-0.2.4/RcppCWB/src/cwb/utils/cwb-makeall.c | 92 RcppCWB-0.2.4/RcppCWB/src/cwb/utils/cwb-s-decode.c | 8 RcppCWB-0.2.4/RcppCWB/src/cwb/utils/cwb-s-encode.c | 547 + RcppCWB-0.2.4/RcppCWB/src/cwb/utils/cwb-scan-corpus.c | 607 +- RcppCWB-0.2.4/RcppCWB/src/cwb/utils/feature_maps.c | 618 +- RcppCWB-0.2.4/RcppCWB/src/cwb/utils/feature_maps.h | 63 RcppCWB-0.2.4/RcppCWB/src/higher_level_functions.cpp | 2 RcppCWB-0.2.4/RcppCWB/src/utils.cpp |only RcppCWB-0.2.4/RcppCWB/src/utils.h |only 193 files changed, 21340 insertions(+), 11888 deletions(-)
More information about populationPDXdesign at CRAN
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Title: Distribution-Free Confidence Region
Description: Constructs confidence regions without the need to know the sampling distribution of bivariate data. The method was proposed by Zhiqiu Hu & Rong-cai Yang (2013) <doi:10.1371/journal.pone.0081179.g001>.
Author: Zhiqiu Hu, Rong-cai Yang
Maintainer: Zhiqiu Hu <zhiqiu.hu@gmail.com>
Diff between distfree.cr versions 1.0 dated 2012-11-26 and 1.5.1 dated 2018-06-15
DESCRIPTION | 16 +++--- MD5 | 8 +-- NAMESPACE | 4 + R/distfree.cr.R | 140 +++++++++++++++++++++++++++++++++++------------------ man/distfree.cr.Rd | 17 +++--- 5 files changed, 119 insertions(+), 66 deletions(-)
Title: Dirichlet Process Bayesian Clustering, Profile Regression
Description: Bayesian clustering using a Dirichlet process mixture model. This model is an alternative to regression models, non-parametrically linking a response vector to covariate data through cluster membership. The package allows Bernoulli, Binomial, Poisson, Normal, survival and categorical response, as well as Normal and discrete covariates. It also allows for fixed effects in the response model, where a spatial CAR (conditional autoregressive) term can be also included. Additionally, predictions may be made for the response, and missing values for the covariates are handled. Several samplers and label switching moves are implemented along with diagnostic tools to assess convergence. A number of R functions for post-processing of the output are also provided. In addition to fitting mixtures, it may additionally be of interest to determine which covariates actively drive the mixture components. This is implemented in the package as variable selection. The main reference for the package is Liverani, Hastie, Azizi, Papathomas and Richardson (2015) <doi:10.18637/jss.v064.i07>.
Author: David I. Hastie, Silvia Liverani <liveranis@gmail.com> and Sylvia Richardson with contributions from Aurore J. Lavigne, Lucy Leigh, Lamiae Azizi, Xi Liu, Ruizhu Huang, Austin Gratton, Wei Jing
Maintainer: Silvia Liverani <liveranis@gmail.com>
Diff between PReMiuM versions 3.1.8 dated 2018-06-14 and 3.2.0 dated 2018-06-15
DESCRIPTION | 6 +++--- MD5 | 6 +++--- src/include/PReMiuMIO.h | 6 +++--- src/include/PReMiuMModel.h | 9 +++++++-- 4 files changed, 16 insertions(+), 11 deletions(-)
Title: Read/Write Files in Key-Value-Hierarchy Format
Description: The format KVH is a lightweight format that can be read/written both by humans and machines.
It can be useful in situations where XML or alike formats seem to be an overkill.
We provide an ability to parse KVH files in R pretty fast due to 'Rcpp' use.
Author: Serguei Sokol
Maintainer: Serguei Sokol <sokol@insa-toulouse.fr>
Diff between kvh versions 1.2 dated 2018-05-14 and 1.3 dated 2018-06-15
DESCRIPTION | 8 +-- MD5 | 16 +++--- NEWS | 6 ++ R/RcppExports.R | 8 +-- inst/include/kvh.h | 8 +-- man/kvh_read.Rd | 9 ++- src/RcppExports.cpp | 12 ++-- src/rcpp_kvh.cpp | 121 ++++++++++++++++++++++++++++++++++++++-------- tests/testthat/test_kvh.R | 50 ++++++++++++++++++- 9 files changed, 190 insertions(+), 48 deletions(-)
Title: Drug Interaction Modeling Based on Loewe Additivity Following
Harbron's Approach
Description: Perform assessment of synergy/antagonism for drug combinations based
on the Loewe additivity model, following Harbron's approach (Statistics in
Medicine, 2010, <doi:10.1002/sim.3916>). The package allows flexible modeling
of the drug interaction index and supports "2-stage" estimation in addition
to "1-stage" estimation, including bootstrap-based confidence intervals.
The method requires data on the monotherapy responses and the package
accommodates both checkerboard and ray designs. Functions are available for
graphical exploration of model goodness-of-fit and diagnostics, as well as
for synergy/antagonism assessment in 2D and 3D.
Author: Maxim Nazarov, Nele Goeyvaerts, Chris Harbron (original article and code)
Maintainer: Maxim Nazarov <maxim.nazarov@openanalytics.eu>
Diff between drugCombo versions 1.0.0 dated 2018-05-11 and 1.0.2 dated 2018-06-15
DESCRIPTION | 8 ++-- MD5 | 18 ++++----- R/plot.tauSurface.R | 16 +++++++- inst/NEWS | 9 +++- inst/doc/userGuide.R | 12 +++--- inst/doc/userGuide.Rmd | 10 ++--- inst/doc/userGuide.html | 72 ++++++++++++++++++++------------------- tests/testthat/test-fitModel.R | 24 ++++--------- tests/testthat/test-tauSurface.R | 58 +++++++++---------------------- vignettes/userGuide.Rmd | 10 ++--- 10 files changed, 112 insertions(+), 125 deletions(-)
Title: Bayesian Spectral Analysis Models using Gaussian Process Priors
Description: Contains functions to perform Bayesian inference
using a spectral analysis of Gaussian process priors.
Gaussian processes are represented with a Fourier series
based on cosine basis functions. Currently the package
includes parametric linear models, partial linear additive
models with/without shape restrictions, generalized linear
additive models with/without shape restrictions, and
density estimation model. To maximize computational
efficiency, the actual Markov chain Monte Carlo sampling
for each model is done using codes written in FORTRAN 90.
This software has been developed using funding supported by
Basic Science Research Program through the National Research
Foundation of Korea (NRF) funded by the Ministry of Education
(no. NRF-2016R1D1A1B03932178 and no. NRF-2017R1D1A3B03035235).
Author: Seongil Jo [aut, cre],
Taeryon Choi [aut],
Beomjo Park [aut, cre],
Peter J. Lenk [ctb]
Maintainer: Beomjo Park <beomjo@korea.ac.kr>
Diff between bsamGP versions 1.2.0 dated 2018-06-10 and 1.2.1 dated 2018-06-15
DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++-------------- README.md | 3 ++- src/bsaqam.f90 | 1 + src/bsaqamdpscale.f90 | 1 + src/bsaram.f90 | 1 + src/bsaramdplocationscale.f90 | 1 + src/bsaramdpscale.f90 | 1 + src/gblogitKS.f90 | 5 ++++- src/gbpoisMH.f90 | 8 +++++--- src/gbprobitAC.f90 | 6 +++++- src/gbsarlogitKS.f90 | 1 + src/gbsarlogitMH.f90 | 1 + src/gbsarnegbinMH.f90 | 1 + src/gbsarprobitAC.f90 | 1 + 15 files changed, 43 insertions(+), 24 deletions(-)
Title: Estimate Quantitative Genetics Parameters from Generalised
Linear Mixed Models
Description: Compute various quantitative genetics parameters from a Generalised Linear Mixed Model (GLMM) estimates. Especially, it yields the observed phenotypic mean, phenotypic variance and additive genetic variance.
Author: Pierre de Villemereuil <bonamy@horus.ens.fr>
Maintainer: Pierre de Villemereuil <bonamy@horus.ens.fr>
Diff between QGglmm versions 0.6.0 dated 2017-10-08 and 0.7.1 dated 2018-06-15
DESCRIPTION | 10 MD5 | 55 +- NAMESPACE | 6 NEWS.md | 33 + R/source.R | 973 +++++++++++++++++++++++++++++++++++----------- R/source.icc.R | 781 ++++++++++++++++++++++++++---------- R/source.mv.R | 665 +++++++++++++++++++++---------- R/source.ordinal.R | 96 ++-- README.md | 4 build/partial.rdb |only build/vignette.rds |binary inst/doc/QGglmmHowTo.Rnw | 488 ++++++++++++----------- inst/doc/QGglmmHowTo.pdf |binary man/QGglmm-package.Rd | 28 - man/QGicc.Rd | 89 ++-- man/QGlink.funcs.Rd | 34 - man/QGmean.Rd | 36 - man/QGmvicc.Rd | 84 +-- man/QGmvmean.Rd | 39 + man/QGmvparams.Rd | 77 +-- man/QGmvpred.Rd | 66 +-- man/QGmvpsi.Rd | 40 - man/QGparams.Rd | 87 ++-- man/QGpred.Rd | 52 +- man/QGpsi.Rd | 36 - man/QGvar.dist.Rd | 48 +- man/QGvar.exp.Rd | 52 +- man/QGvcov.Rd | 65 +-- vignettes/QGglmmHowTo.Rnw | 488 ++++++++++++----------- 29 files changed, 2847 insertions(+), 1585 deletions(-)
More information about IntervalSurgeon at CRAN
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Title: Flexible Gaussian Cluster Simulator
Description: Clustering is a central task in big data analyses and clusters are often Gaussian or near Gaussian. However, a flexible Gaussian cluster simulation tool with precise control over the size, variance, and spacing of the clusters in NXN dimensional space does not exist. This is why we created 'clusterlab'. The algorithm first creates X points equally spaced on the circumference of a circle in 2D space. These form the centers of each cluster to be simulated. Additional samples are added by adding Gaussian noise to each cluster center and concatenating the new sample co-ordinates. Then if the feature space is greater than 2D, the generated points are considered principal component scores and projected into N dimensional space using linear combinations using fixed eigenvectors. The algorithm is highly customizable and well suited to testing class discovery tools across a range of fields.
Author: Christopher R John
Maintainer: Christopher R John <chris.r.john86@gmail.com>
Diff between clusterlab versions 0.0.1.9 dated 2018-06-15 and 0.0.2.0 dated 2018-06-15
DESCRIPTION | 6 ++--- MD5 | 10 ++++----- inst/doc/introduction.R | 11 --------- inst/doc/introduction.Rmd | 36 +++++++++++++++----------------- inst/doc/introduction.html | 50 +++++++++++++++++++++++---------------------- vignettes/introduction.Rmd | 36 +++++++++++++++----------------- 6 files changed, 68 insertions(+), 81 deletions(-)
Title: Stratified and Personalised Models Based on Model-Based Trees
and Forests
Description: Model-based trees for subgroup analyses in clinical trials and
model-based forests for the estimation and prediction of personalised
treatment effects (personalised models). Currently partitioning of linear
models, lm(), generalised linear models, glm(), and Weibull models,
survreg(), is supported. Advanced plotting functionality is supported for
the trees and a test for parameter heterogeneity is provided for the
personalised models. For details on model-based trees for subgroup analyses
see Seibold, Zeileis and Hothorn (2016) <doi:10.1515/ijb-2015-0032>; for
details on model-based forests for estimation of individual treatment effects
see Seibold, Zeileis and Hothorn (2017) <doi:10.1177/0962280217693034>.
Author: Heidi Seibold [aut, cre],
Achim Zeileis [aut],
Torsten Hothorn [aut]
Maintainer: Heidi Seibold <heidi@seibold.co>
Diff between model4you versions 0.9-1 dated 2018-02-08 and 0.9-2 dated 2018-06-15
DESCRIPTION | 8 - MD5 | 35 +++-- R/helpers.R | 97 ++++++++++------ R/plot-pmtree.R | 259 +++++++++++++++++++++++--------------------- R/pmodel.R | 2 R/pmtree.R | 54 ++++----- inst/JORS/man_model4you.Rnw | 52 ++++---- inst/NEWS.Rd | 4 man/binomial_glm_plot.Rd | 22 +-- man/coxph_plot.Rd | 4 man/lm_plot.Rd | 7 - man/node_pmterminal.Rd | 10 - man/one_factor.Rd |only man/pmtree.Rd | 2 man/survreg_plot.Rd | 4 tests/test-pmodel.R | 30 ++--- tests/test-pmodel.Rout.save | 81 ++++++------- tests/test-pmtree.R | 94 +++++++++++++++ tests/test-pmtree.Rout.save | 182 +++++++++++++++++++++++++++--- 19 files changed, 608 insertions(+), 339 deletions(-)
Title: Adherence to Medications
Description: Computation of adherence to medications from Electronic Health care
Data and visualization of individual medication histories and adherence
patterns. The package implements a set of S3 classes and
functions consistent with current adherence guidelines and definitions.
It allows the computation of different measures of
adherence (as defined in the literature, but also several original ones),
their publication-quality plotting,
the interactive exploration of patient medication history and
the real-time estimation of adherence given various parameter settings.
Author: Dan Dediu [aut, cre],
Alexandra Dima [aut]
Maintainer: Dan Dediu <ddediu@gmail.com>
Diff between AdhereR versions 0.1.0 dated 2017-04-27 and 0.2.0 dated 2018-06-15
DESCRIPTION | 12 MD5 | 44 - NAMESPACE | 3 R/adherer.R | 1156 +++++++++++++++++++++++------ R/call-adherer-external.R |only build/vignette.rds |binary inst/doc/AdhereR-overview.R | 32 inst/doc/AdhereR-overview.Rmd | 57 + inst/doc/AdhereR-overview.html | 103 +- inst/doc/calling-AdhereR-from-python3.Rmd |only inst/doc/calling-AdhereR-from-python3.html |only inst/interactivePlotShiny |only inst/wrappers |only man/CMA0.Rd | 4 man/CMA_per_episode.Rd | 4 man/callAdhereR.Rd |only man/compute.event.int.gaps.Rd | 10 man/compute.treatment.episodes.Rd | 8 man/getCallerWrapperLocation.Rd |only man/plot.CMA0.Rd | 2 man/plot.CMA1.Rd | 2 man/plot.CMA_per_episode.Rd | 2 man/plot_interactive_cma.Rd | 18 vignettes/AdhereR-overview.Rmd | 57 + vignettes/calling-AdhereR-from-python3.Rmd |only vignettes/classes_adherer.png |only vignettes/plotting-interactive.jpg |only vignettes/plotting-python.jpg |only vignettes/plotting-r.jpg |only 29 files changed, 1200 insertions(+), 314 deletions(-)
Title: Spatial Point Pattern Analysis, Model-Fitting, Simulation, Tests
Description: Comprehensive open-source toolbox for analysing Spatial Point Patterns. Focused mainly on two-dimensional point patterns, including multitype/marked points, in any spatial region. Also supports three-dimensional point patterns, space-time point patterns in any number of dimensions, point patterns on a linear network, and patterns of other geometrical objects. Supports spatial covariate data such as pixel images.
Contains over 2000 functions for plotting spatial data, exploratory data analysis, model-fitting, simulation, spatial sampling, model diagnostics, and formal inference.
Data types include point patterns, line segment patterns, spatial windows, pixel images, tessellations, and linear networks.
Exploratory methods include quadrat counts, K-functions and their simulation envelopes, nearest neighbour distance and empty space statistics, Fry plots, pair correlation function, kernel smoothed intensity, relative risk estimation with cross-validated bandwidth selection, mark correlation functions, segregation indices, mark dependence diagnostics, and kernel estimates of covariate effects. Formal hypothesis tests of random pattern (chi-squared, Kolmogorov-Smirnov, Monte Carlo, Diggle-Cressie-Loosmore-Ford, Dao-Genton, two-stage Monte Carlo) and tests for covariate effects (Cox-Berman-Waller-Lawson, Kolmogorov-Smirnov, ANOVA) are also supported.
Parametric models can be fitted to point pattern data using the functions ppm(), kppm(), slrm(), dppm() similar to glm(). Types of models include Poisson, Gibbs and Cox point processes, Neyman-Scott cluster processes, and determinantal point processes. Models may involve dependence on covariates, inter-point interaction, cluster formation and dependence on marks. Models are fitted by maximum likelihood, logistic regression, minimum contrast, and composite likelihood methods.
A model can be fitted to a list of point patterns (replicated point pattern data) using the function mppm(). The model can include random effects and fixed effects depending on the experimental design, in addition to all the features listed above.
Fitted point process models can be simulated, automatically. Formal hypothesis tests of a fitted model are supported (likelihood ratio test, analysis of deviance, Monte Carlo tests) along with basic tools for model selection (stepwise(), AIC()) and variable selection (sdr). Tools for validating the fitted model include simulation envelopes, residuals, residual plots and Q-Q plots, leverage and influence diagnostics, partial residuals, and added variable plots.
Author: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>,
Rolf Turner <r.turner@auckland.ac.nz>
and Ege Rubak <rubak@math.aau.dk>,
with substantial contributions of code by
Kasper Klitgaard Berthelsen;
Ottmar Cronie;
Yongtao Guan;
Ute Hahn;
Abdollah Jalilian;
Marie-Colette van Lieshout;
Greg McSwiggan;
Tuomas Rajala;
Suman Rakshit;
Dominic Schuhmacher;
Rasmus Waagepetersen;
and Hangsheng Wang.
Additional contributions
by M. Adepeju;
C. Anderson;
Q.W. Ang;
J. Astrom;
M. Austenfeld;
S. Azaele;
M. Baddeley;
C. Beale;
M. Bell;
R. Bernhardt;
T. Bendtsen;
A. Bevan;
B. Biggerstaff;
A. Bilgrau;
L. Bischof;
C. Biscio;
R. Bivand;
J.M. Blanco Moreno;
F. Bonneu;
J. Burgos;
S. Byers;
Y.M. Chang;
J.B. Chen;
I. Chernayavsky;
Y.C. Chin;
B. Christensen;
J.-F. Coeurjolly;
K. Colyvas;
R. Constantine;
R. Corria Ainslie;
R. Cotton;
M. de la Cruz;
P. Dalgaard;
M. D'Antuono;
S. Das;
T. Davies;
P.J. Diggle;
P. Donnelly;
I. Dryden;
S. Eglen;
A. El-Gabbas;
B. Fandohan;
O. Flores;
E.D. Ford;
P. Forbes;
S. Frank;
J. Franklin;
N. Funwi-Gabga;
O. Garcia;
A. Gault;
J. Geldmann;
M. Genton;
S. Ghalandarayeshi;
J. Gilbey;
J. Goldstick;
P. Grabarnik;
C. Graf;
U. Hahn;
A. Hardegen;
M.B. Hansen;
M. Hazelton;
J. Heikkinen;
M. Hering;
M. Herrmann;
P. Hewson;
K. Hingee;
K. Hornik;
P. Hunziker;
J. Hywood;
R. Ihaka;
C. Icos;
A. Jammalamadaka;
R. John-Chandran;
D. Johnson;
M. Khanmohammadi;
R. Klaver;
P. Kovesi;
L. Kozmian-Ledward;
M. Kuhn;
J. Laake;
F. Lavancier;
T. Lawrence;
R.A. Lamb;
J. Lee;
G.P. Leser;
A. Li;
H.T. Li;
G. Limitsios;
A. Lister;
B. Madin;
M. Maechler;
J. Marcus;
K. Marchikanti;
R. Mark;
J. Mateu;
P. McCullagh;
U. Mehlig;
F. Mestre;
S. Meyer;
X.C. Mi;
L. De Middeleer;
R.K. Milne;
E. Miranda;
J. Moller;
I. Moncada;
M. Moradi;
V. Morera Pujol;
E. Mudrak;
G.M. Nair;
N. Najari;
N. Nava;
L.S. Nielsen;
F. Nunes;
J.R. Nyengaard;
J. Oehlschlaegel;
T. Onkelinx;
S. O'Riordan;
E. Parilov;
J. Picka;
N. Picard;
M. Porter;
S. Protsiv;
A. Raftery;
S. Rakshit;
B. Ramage;
P. Ramon;
X. Raynaud;
N. Read;
M. Reiter;
I. Renner;
T.O. Richardson;
B.D. Ripley;
E. Rosenbaum;
B. Rowlingson;
J. Rudokas;
J. Rudge;
C. Ryan;
F. Safavimanesh;
A. Sarkka;
C. Schank;
K. Schladitz;
S. Schutte;
B.T. Scott;
O. Semboli;
F. Semecurbe;
V. Shcherbakov;
G.C. Shen;
P. Shi;
H.-J. Ship;
T.L. Silva;
I.-M. Sintorn;
Y. Song;
M. Spiess;
M. Stevenson;
K. Stucki;
M. Sumner;
P. Surovy;
B. Taylor;
T. Thorarinsdottir;
L. Torres;
B. Turlach;
T. Tvedebrink;
K. Ummer;
M. Uppala;
A. van Burgel;
T. Verbeke;
M. Vihtakari;
A. Villers;
F. Vinatier;
S. Voss;
S. Wagner;
H. Wang;
H. Wendrock;
J. Wild;
C. Witthoft;
S. Wong;
M. Woringer;
M.E. Zamboni
and
A. Zeileis.
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat versions 1.55-1 dated 2018-04-05 and 1.56-0 dated 2018-06-15
DESCRIPTION | 12 - MD5 | 310 +++++++++++++++++++------------------ NAMESPACE | 49 +++++ NEWS | 200 +++++++++++++++++++++++ R/Kest.R | 17 +- R/as.im.R | 61 ++++--- R/cdftest.R | 14 + R/closepairs.R | 51 +++++- R/colourtables.R | 40 +++- R/deldir.R | 36 ++-- R/densityfun.R |only R/dffit.R |only R/digestCovariates.R | 4 R/distbdry.R | 18 -- R/distfun.R | 50 +++++ R/distfunlpp.R | 3 R/edges2triangles.R | 17 +- R/evalcovar.R | 28 ++- R/fv.R | 28 ++- R/images.R | 4 R/indicator.R | 11 + R/indices.R | 8 R/kernels.R | 17 +- R/kppm.R | 27 +-- R/leverage.R | 43 ++++- R/linim.R | 5 R/linnet.R | 15 + R/linnetsurgery.R | 25 ++ R/lppm.R | 41 +++- R/measures.R | 71 +++++++- R/metricPdt.R |only R/mincontrast.R | 10 - R/morphology.R | 7 R/nncross.R | 6 R/nnfun.R | 13 - R/options.R | 14 + R/pairwise.family.R | 13 + R/parres.R | 32 +-- R/pcfinhom.R | 6 R/plot.im.R | 24 ++ R/plot3d.R | 13 - R/ppp.R | 15 + R/pppmatch.R | 60 +++---- R/predict.ppm.R | 17 +- R/psp.R | 27 ++- R/random.R | 136 ++++++---------- R/randomNS.R | 7 R/randomlpp.R | 19 -- R/randommk.R | 25 +- R/randomonlines.R | 23 +- R/relrisk.ppm.R | 6 R/rescale.R | 1 R/resid4plot.R | 5 R/rmh.default.R | 4 R/rmh.ppm.R | 10 - R/simulatelppm.R | 10 - R/slrm.R | 12 - R/smooth.ppp.R | 8 R/smoothfun.R | 34 +++- R/solist.R | 4 R/sparse3Darray.R | 29 ++- R/strausshard.R | 9 - R/sysdata.rda |binary R/tess.R | 140 ++++++++++++---- R/util.R | 14 - build/vignette.rds |binary inst/doc/Nickname.txt | 2 inst/doc/datasets.pdf |binary inst/doc/getstart.R | 38 ++-- inst/doc/getstart.Rnw | 34 +--- inst/doc/getstart.pdf |binary inst/doc/packagesizes.txt | 1 inst/doc/replicated.R | 126 +++++++-------- inst/doc/replicated.Rnw | 14 + inst/doc/replicated.pdf |binary inst/doc/shapefiles.R | 40 ++-- inst/doc/shapefiles.Rnw | 20 +- inst/doc/shapefiles.pdf |binary inst/doc/updates.R | 8 inst/doc/updates.Rnw | 129 ++++++++++++++- inst/doc/updates.pdf |binary man/Kcross.inhom.Rd | 2 man/Kmeasure.Rd | 8 man/Smoothfun.ppp.Rd | 8 man/affine.lpp.Rd | 7 man/as.data.frame.owin.Rd | 9 - man/as.function.owin.Rd | 6 man/as.im.Rd | 65 +++++-- man/bugfixes.Rd | 3 man/closing.Rd | 10 - man/clusterfit.Rd | 11 - man/connected.Rd | 9 - man/connected.lpp.Rd | 9 - man/connected.tess.Rd |only man/dclf.test.Rd | 4 man/densityfun.Rd |only man/dfbetas.ppm.Rd | 12 - man/dffit.ppm.Rd |only man/dilation.Rd | 4 man/distfun.Rd | 4 man/emend.ppm.Rd | 2 man/fvnames.Rd | 9 - man/influence.ppm.Rd | 11 - man/insertVertices.Rd | 6 man/joinVertices.Rd |only man/kernel.moment.Rd | 3 man/kppm.Rd | 1 man/leverage.ppm.Rd | 22 +- man/linnet.Rd | 4 man/lurking.Rd | 8 man/matchingdist.Rd | 11 - man/measureContinuous.Rd |only man/measureVariation.Rd | 3 man/methods.distfun.Rd |only man/methods.linim.Rd | 5 man/methods.linnet.Rd | 4 man/methods.lpp.Rd | 6 man/msr.Rd | 51 +++++- man/parres.Rd | 12 - man/pcfinhom.Rd | 4 man/plot.ppm.Rd | 1 man/plot.psp.Rd | 19 +- man/plot.studpermutest.Rd |only man/plot.tess.Rd | 55 +++++- man/ppmInfluence.Rd | 13 + man/pppmatching.Rd | 12 - man/predict.ppm.Rd | 7 man/progressreport.Rd | 8 man/rectcontact.Rd |only man/rectdistmap.Rd |only man/rgbim.Rd | 10 - man/roc.Rd | 8 man/rpoisppOnLines.Rd | 7 man/runifpointOnLines.Rd | 10 - man/scanpp.Rd | 23 ++ man/sdr.Rd | 6 man/sessionLibs.Rd | 8 man/simplepanel.Rd | 4 man/simulate.kppm.Rd | 5 man/slrm.Rd | 12 - man/solist.Rd | 18 +- man/spatstat-internal.Rd | 33 ++- man/spatstat-package.Rd | 5 man/split.im.Rd | 5 man/studpermu.test.Rd | 11 - man/subfits.Rd | 2 man/tess.Rd | 13 - man/text.ppp.Rd | 4 man/with.msr.Rd | 3 src/init.c | 5 src/metricPdist.c |only src/metricPdist.h |only src/proto.h | 9 - tests/testsAtoF.R | 384 ++++++++++++++++++++++++++++++++++++++++++---- tests/testsGtoK.R | 198 ++++++++++++++++++++++- tests/testsLtoM.R | 310 +++++++++++++++++++++++++++++++++++-- tests/testsNtoP.R | 127 ++++++++++++++- tests/testsQtoR.R | 142 +++++++++++++++-- tests/testsStoZ.R | 328 ++++++++++++++++++++++++++++++++++++--- vignettes/getstart.Rnw | 34 +--- vignettes/replicated.Rnw | 14 + vignettes/shapefiles.Rnw | 20 +- vignettes/updates.Rnw | 129 ++++++++++++++- 163 files changed, 3563 insertions(+), 1142 deletions(-)
Title: Model Menu for Radiant: Business Analytics using R and Shiny
Description: The Radiant Model menu includes interfaces for linear and logistic
regression, naive Bayes, neural networks, classification and regression trees,
model evaluation, collaborative filtering, decision analysis, and simulation.
The application extends the functionality in radiant.data.
Author: Vincent Nijs [aut, cre]
Maintainer: Vincent Nijs <radiant@rady.ucsd.edu>
Diff between radiant.model versions 0.8.0 dated 2017-04-28 and 0.9.5 dated 2018-06-15
radiant.model-0.8.0/radiant.model/R/ann.R |only radiant.model-0.8.0/radiant.model/R/naivebayes.R |only radiant.model-0.8.0/radiant.model/data/cf.rda |only radiant.model-0.8.0/radiant.model/inst/app/tools/analysis/ann_ui.R |only radiant.model-0.8.0/radiant.model/inst/app/tools/help/ann.md |only radiant.model-0.8.0/radiant.model/inst/app/tools/help/figure |only radiant.model-0.8.0/radiant.model/inst/app/www/js/run_return.js |only radiant.model-0.8.0/radiant.model/man/ann.Rd |only radiant.model-0.8.0/radiant.model/man/cf.Rd |only radiant.model-0.8.0/radiant.model/man/plot.ann.Rd |only radiant.model-0.8.0/radiant.model/man/predict.ann.Rd |only radiant.model-0.8.0/radiant.model/man/print.ann.predict.Rd |only radiant.model-0.8.0/radiant.model/man/store_ann.Rd |only radiant.model-0.8.0/radiant.model/man/store_glm.Rd |only radiant.model-0.8.0/radiant.model/man/store_reg.Rd |only radiant.model-0.8.0/radiant.model/man/summary.ann.Rd |only radiant.model-0.9.5/radiant.model/COPYING | 6 radiant.model-0.9.5/radiant.model/DESCRIPTION | 37 radiant.model-0.9.5/radiant.model/MD5 | 253 +- radiant.model-0.9.5/radiant.model/NAMESPACE | 43 radiant.model-0.9.5/radiant.model/NEWS.md | 219 ++ radiant.model-0.9.5/radiant.model/R/aaa.R | 43 radiant.model-0.9.5/radiant.model/R/crs.R | 250 +- radiant.model-0.9.5/radiant.model/R/crtree.R | 573 +++--- radiant.model-0.9.5/radiant.model/R/deprecated.R | 22 radiant.model-0.9.5/radiant.model/R/dtree.R | 484 +++-- radiant.model-0.9.5/radiant.model/R/evalbin.R | 843 ++++---- radiant.model-0.9.5/radiant.model/R/evalreg.R | 170 + radiant.model-0.9.5/radiant.model/R/logistic.R | 710 ++++--- radiant.model-0.9.5/radiant.model/R/nb.R |only radiant.model-0.9.5/radiant.model/R/nn.R |only radiant.model-0.9.5/radiant.model/R/radiant.R | 50 radiant.model-0.9.5/radiant.model/R/regress.R | 892 +++++---- radiant.model-0.9.5/radiant.model/R/rfm.R | 264 -- radiant.model-0.9.5/radiant.model/R/simulater.R | 949 +++++----- radiant.model-0.9.5/radiant.model/README.md | 70 radiant.model-0.9.5/radiant.model/data/movie_contract.rda |only radiant.model-0.9.5/radiant.model/data/ratings.rda |only radiant.model-0.9.5/radiant.model/inst/app/global.R | 7 radiant.model-0.9.5/radiant.model/inst/app/help.R | 37 radiant.model-0.9.5/radiant.model/inst/app/init.R | 99 - radiant.model-0.9.5/radiant.model/inst/app/radiant.R | 30 radiant.model-0.9.5/radiant.model/inst/app/server.R | 23 radiant.model-0.9.5/radiant.model/inst/app/tools/analysis/crs_ui.R | 308 ++- radiant.model-0.9.5/radiant.model/inst/app/tools/analysis/crtree_ui.R | 672 ++++--- radiant.model-0.9.5/radiant.model/inst/app/tools/analysis/dtree_ui.R | 512 +++-- radiant.model-0.9.5/radiant.model/inst/app/tools/analysis/evalbin_ui.R | 406 ++-- radiant.model-0.9.5/radiant.model/inst/app/tools/analysis/evalreg_ui.R | 169 + radiant.model-0.9.5/radiant.model/inst/app/tools/analysis/logistic_ui.R | 708 ++++--- radiant.model-0.9.5/radiant.model/inst/app/tools/analysis/naivebayes_ui.R | 517 +++-- radiant.model-0.9.5/radiant.model/inst/app/tools/analysis/nn_ui.R |only radiant.model-0.9.5/radiant.model/inst/app/tools/analysis/regress_ui.R | 661 ++++-- radiant.model-0.9.5/radiant.model/inst/app/tools/analysis/rfm_ui.R | 1 radiant.model-0.9.5/radiant.model/inst/app/tools/analysis/simulater_ui.R | 828 +++++--- radiant.model-0.9.5/radiant.model/inst/app/tools/help/crs.md | 8 radiant.model-0.9.5/radiant.model/inst/app/tools/help/crtree.md | 8 radiant.model-0.9.5/radiant.model/inst/app/tools/help/dtree.Rmd | 23 radiant.model-0.9.5/radiant.model/inst/app/tools/help/dtree.md | 23 radiant.model-0.9.5/radiant.model/inst/app/tools/help/evalbin.md | 25 radiant.model-0.9.5/radiant.model/inst/app/tools/help/evalreg.md | 20 radiant.model-0.9.5/radiant.model/inst/app/tools/help/logistic.Rmd | 17 radiant.model-0.9.5/radiant.model/inst/app/tools/help/logistic.md | 17 radiant.model-0.9.5/radiant.model/inst/app/tools/help/nb.md | 8 radiant.model-0.9.5/radiant.model/inst/app/tools/help/nn.md |only radiant.model-0.9.5/radiant.model/inst/app/tools/help/regress.Rmd | 29 radiant.model-0.9.5/radiant.model/inst/app/tools/help/regress.md | 29 radiant.model-0.9.5/radiant.model/inst/app/tools/help/simulater.Rmd | 16 radiant.model-0.9.5/radiant.model/inst/app/tools/help/simulater.md | 14 radiant.model-0.9.5/radiant.model/inst/app/ui.R | 15 radiant.model-0.9.5/radiant.model/inst/app/www/js/store.js |only radiant.model-0.9.5/radiant.model/inst/app/www/style.css | 44 radiant.model-0.9.5/radiant.model/man/auc.Rd | 5 radiant.model-0.9.5/radiant.model/man/catalog.Rd | 2 radiant.model-0.9.5/radiant.model/man/confint_robust.Rd | 8 radiant.model-0.9.5/radiant.model/man/confusion.Rd | 14 radiant.model-0.9.5/radiant.model/man/crs.Rd | 12 radiant.model-0.9.5/radiant.model/man/crtree.Rd | 31 radiant.model-0.9.5/radiant.model/man/direct_marketing.Rd | 2 radiant.model-0.9.5/radiant.model/man/dtree.Rd | 5 radiant.model-0.9.5/radiant.model/man/evalbin.Rd | 18 radiant.model-0.9.5/radiant.model/man/evalreg.Rd | 18 radiant.model-0.9.5/radiant.model/man/find_max.Rd | 17 radiant.model-0.9.5/radiant.model/man/find_min.Rd | 13 radiant.model-0.9.5/radiant.model/man/houseprices.Rd | 2 radiant.model-0.9.5/radiant.model/man/ideal.Rd | 2 radiant.model-0.9.5/radiant.model/man/logistic.Rd | 12 radiant.model-0.9.5/radiant.model/man/minmax.Rd | 4 radiant.model-0.9.5/radiant.model/man/movie_contract.Rd |only radiant.model-0.9.5/radiant.model/man/nb.Rd | 7 radiant.model-0.9.5/radiant.model/man/nn.Rd |only radiant.model-0.9.5/radiant.model/man/plot.confusion.Rd | 10 radiant.model-0.9.5/radiant.model/man/plot.crs.Rd | 2 radiant.model-0.9.5/radiant.model/man/plot.crtree.Rd | 16 radiant.model-0.9.5/radiant.model/man/plot.dtree.Rd | 9 radiant.model-0.9.5/radiant.model/man/plot.evalbin.Rd | 15 radiant.model-0.9.5/radiant.model/man/plot.evalreg.Rd | 10 radiant.model-0.9.5/radiant.model/man/plot.logistic.Rd | 10 radiant.model-0.9.5/radiant.model/man/plot.model.predict.Rd | 8 radiant.model-0.9.5/radiant.model/man/plot.nb.Rd | 15 radiant.model-0.9.5/radiant.model/man/plot.nb.predict.Rd | 13 radiant.model-0.9.5/radiant.model/man/plot.nn.Rd |only radiant.model-0.9.5/radiant.model/man/plot.regress.Rd | 16 radiant.model-0.9.5/radiant.model/man/plot.repeater.Rd | 11 radiant.model-0.9.5/radiant.model/man/plot.simulater.Rd | 18 radiant.model-0.9.5/radiant.model/man/predict.crtree.Rd | 12 radiant.model-0.9.5/radiant.model/man/predict.logistic.Rd | 20 radiant.model-0.9.5/radiant.model/man/predict.nb.Rd | 23 radiant.model-0.9.5/radiant.model/man/predict.nn.Rd |only radiant.model-0.9.5/radiant.model/man/predict.regress.Rd | 16 radiant.model-0.9.5/radiant.model/man/predict_model.Rd | 6 radiant.model-0.9.5/radiant.model/man/print.nb.predict.Rd | 2 radiant.model-0.9.5/radiant.model/man/print.nn.predict.Rd |only radiant.model-0.9.5/radiant.model/man/radiant.model-deprecated.Rd | 10 radiant.model-0.9.5/radiant.model/man/radiant.model.Rd | 7 radiant.model-0.9.5/radiant.model/man/radiant.model_viewer.Rd |only radiant.model-0.9.5/radiant.model/man/radiant.model_window.Rd |only radiant.model-0.9.5/radiant.model/man/ratings.Rd |only radiant.model-0.9.5/radiant.model/man/regress.Rd | 8 radiant.model-0.9.5/radiant.model/man/repeater.Rd | 59 radiant.model-0.9.5/radiant.model/man/scaledf.Rd | 8 radiant.model-0.9.5/radiant.model/man/sensitivity.Rd | 3 radiant.model-0.9.5/radiant.model/man/sensitivity.dtree.Rd | 11 radiant.model-0.9.5/radiant.model/man/sim_cor.Rd |only radiant.model-0.9.5/radiant.model/man/sim_summary.Rd | 19 radiant.model-0.9.5/radiant.model/man/simulater.Rd | 49 radiant.model-0.9.5/radiant.model/man/store.crs.Rd | 15 radiant.model-0.9.5/radiant.model/man/store.model.Rd | 15 radiant.model-0.9.5/radiant.model/man/store.model.predict.Rd | 18 radiant.model-0.9.5/radiant.model/man/store.nb.predict.Rd | 20 radiant.model-0.9.5/radiant.model/man/summary.confusion.Rd | 10 radiant.model-0.9.5/radiant.model/man/summary.crs.Rd | 11 radiant.model-0.9.5/radiant.model/man/summary.crtree.Rd | 11 radiant.model-0.9.5/radiant.model/man/summary.dtree.Rd | 14 radiant.model-0.9.5/radiant.model/man/summary.evalbin.Rd | 9 radiant.model-0.9.5/radiant.model/man/summary.evalreg.Rd | 10 radiant.model-0.9.5/radiant.model/man/summary.logistic.Rd | 8 radiant.model-0.9.5/radiant.model/man/summary.nb.Rd | 4 radiant.model-0.9.5/radiant.model/man/summary.nn.Rd |only radiant.model-0.9.5/radiant.model/man/summary.regress.Rd | 8 radiant.model-0.9.5/radiant.model/man/summary.repeater.Rd | 5 radiant.model-0.9.5/radiant.model/man/summary.simulater.Rd | 4 radiant.model-0.9.5/radiant.model/man/var_check.Rd | 12 radiant.model-0.9.5/radiant.model/man/write.coeff.Rd | 10 radiant.model-0.9.5/radiant.model/tests/testthat/test_stats.R | 127 - 144 files changed, 7300 insertions(+), 4741 deletions(-)
Title: Automatic Forecasting Procedure
Description: Implements a procedure for forecasting time series data based on
an additive model where non-linear trends are fit with yearly, weekly, and
daily seasonality, plus holiday effects. It works best with time series
that have strong seasonal effects and several seasons of historical data.
Prophet is robust to missing data and shifts in the trend, and typically
handles outliers well.
Author: Sean Taylor [cre, aut],
Ben Letham [aut]
Maintainer: Sean Taylor <sjt@fb.com>
Diff between prophet versions 0.3 dated 2018-06-02 and 0.3.0.1 dated 2018-06-15
DESCRIPTION | 14 ++-- MD5 | 122 +++++++++++++++++------------------ R/diagnostics.R | 2 R/prophet.R | 47 +++++++------ build/vignette.rds |binary inst/doc/quick_start.html | 28 ++++---- man/add_changepoints_to_plot.Rd | 1 man/add_group_component.Rd | 1 man/add_regressor.Rd | 1 man/add_seasonality.Rd | 1 man/compile_stan_model.Rd | 1 man/coverage.Rd | 1 man/cross_validation.Rd | 1 man/df_for_plotting.Rd | 1 man/dyplot.prophet.Rd | 1 man/fit.prophet.Rd | 1 man/fourier_series.Rd | 1 man/generate_cutoffs.Rd | 1 man/get_prophet_stan_model.Rd | 1 man/initialize_scales_fn.Rd | 1 man/linear_growth_init.Rd | 1 man/logistic_growth_init.Rd | 1 man/mae.Rd | 1 man/make_all_seasonality_features.Rd | 1 man/make_future_dataframe.Rd | 1 man/make_holiday_features.Rd | 1 man/make_seasonality_features.Rd | 1 man/mape.Rd | 1 man/mse.Rd | 1 man/parse_seasonality_args.Rd | 1 man/performance_metrics.Rd | 1 man/piecewise_linear.Rd | 1 man/piecewise_logistic.Rd | 1 man/plot.prophet.Rd | 1 man/plot_cross_validation_metric.Rd | 1 man/plot_forecast_component.Rd | 1 man/plot_seasonality.Rd | 1 man/plot_weekly.Rd | 1 man/plot_yearly.Rd | 1 man/predict.prophet.Rd | 1 man/predict_seasonal_components.Rd | 1 man/predict_trend.Rd | 1 man/predict_uncertainty.Rd | 1 man/predictive_samples.Rd | 1 man/prophet.Rd | 1 man/prophet_copy.Rd | 1 man/prophet_plot_components.Rd | 1 man/regressor_column_matrix.Rd | 1 man/rmse.Rd | 1 man/rolling_mean.Rd | 1 man/sample_model.Rd | 1 man/sample_posterior_predictive.Rd | 1 man/sample_predictive_trend.Rd | 1 man/seasonality_plot_df.Rd | 1 man/set_auto_seasonalities.Rd | 1 man/set_changepoints.Rd | 1 man/set_date.Rd | 1 man/setup_dataframe.Rd | 1 man/time_diff.Rd | 1 man/validate_column_name.Rd | 1 man/validate_inputs.Rd | 1 tests/testthat/test_prophet.R | 27 ++++++- 62 files changed, 129 insertions(+), 166 deletions(-)
Title: Causal Mediation Analysis in Multisite Trials
Description: We implement multisite causal mediation analysis using the methods proposed by Qin and Hong (2017) <doi:10.3102/1076998617694879> and Qin, Hong, Deutsch, and Bein (under review). It enables causal mediation analysis in multisite trials, in which individuals are assigned to a treatment or a control group at each site. It allows for estimation and hypothesis testing for not only the population average but also the between-site variance of direct and indirect effects. This strategy conveniently relaxes the assumption of no treatment-by-mediator interaction while greatly simplifying the outcome model specification without invoking strong distributional assumptions. This package also provides a function that can further incorporate a sample weight and a nonresponse weight for multisite causal mediation analysis in the presence of complex sample and survey designs and non-random nonresponse, to enhance both the internal validity and external validity. Because the identification assumptions are not always warranted, the package also provides a weighting-based balance checking function for assessing the remaining overt bias, as well as a weighting-based sensitivity analysis function for further evaluating the potential bias related to omitted confounding or to propensity score model misspecification.
Author: Xu Qin, Guanglei Hong, Jonah Deutsch, and Edward Bein
Maintainer: Xu Qin <xuqin@uchicago.edu>
Diff between MultisiteMediation versions 0.0.1 dated 2017-02-26 and 0.0.2 dated 2018-06-15
DESCRIPTION | 14 MD5 | 21 NAMESPACE | 24 R/msmediate.R | 1438 +++++++++++++++++++++++++++++++++++++-- build |only data/sim.txt.gz |binary data/sim.weights.txt.gz |only man/balance.Rd |only man/msmediate.Rd | 10 man/msmediate.weights.Rd |only man/sensitivity.Rd |only man/sim.Rd | 17 man/sim.weights.Rd |only man/vartest.msmediate.Rd | 10 man/vartest.msmediate.weights.Rd |only 15 files changed, 1446 insertions(+), 88 deletions(-)
More information about MultisiteMediation at CRAN
Permanent link
Title: Model-Based Clustering and Classification with Mixtures of
Modified t Factor Analyzers
Description: Fits a family of mixtures of multivariate t-distributions under a continuous t-distributed latent variable structure for the purpose of clustering or classification. The alternating expectation-conditional maximization algorithm is used for parameter estimation.
Author: Jeffrey L. Andrews, Paul D. McNicholas, and Mathieu Chalifour
Maintainer: Jeffrey L. Andrews <jeff.andrews@ubc.ca>
Diff between mmtfa versions 0.1 dated 2015-06-13 and 0.3 dated 2018-06-15
ChangeLog | 12 +++++++++++- DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- NAMESPACE | 6 +++++- R/mmtfa.R | 9 +++++---- R/mmtfa.parallel.R | 4 ++-- R/mmtfaEM.R | 3 ++- man/mmtfa-package.Rd | 6 +++--- man/mmtfa.Rd | 14 +++++++------- 9 files changed, 48 insertions(+), 32 deletions(-)
Title: Distributions and Gradients
Description: Provides density, distribution function, quantile function and random
generation for the split normal and split-t distributions, and computes their
mean, variance, skewness and kurtosis for the two distributions (Li, F,
Villani, M. and Kohn, R. (2010) <doi:10.1016/j.jspi.2010.04.031>).
Author: Jiayue Zeng [aut, cre],
Feng Li [aut]
Maintainer: Jiayue Zeng <zengjiayue@126.com>
Diff between dng versions 0.1.1 dated 2017-11-22 and 0.2.0 dated 2018-06-15
dng-0.1.1/dng/man/dsplitt.Rd |only dng-0.1.1/dng/man/psplitt.Rd |only dng-0.1.1/dng/man/qsplitt.Rd |only dng-0.1.1/dng/man/rsplitt.Rd |only dng-0.1.1/dng/man/split-t.Rd |only dng-0.1.1/dng/src/rcpp_kurtosis.cpp |only dng-0.1.1/dng/src/rcpp_mean.cpp |only dng-0.1.1/dng/src/rcpp_skewness.cpp |only dng-0.1.1/dng/src/rcpp_var.cpp |only dng-0.2.0/dng/DESCRIPTION | 26 +- dng-0.2.0/dng/MD5 | 46 ++-- dng-0.2.0/dng/NAMESPACE | 4 dng-0.2.0/dng/R/RcppExports.R | 273 +++++++++++++++++++++++++++-- dng-0.2.0/dng/inst/CITATION |only dng-0.2.0/dng/inst/NEWS | 4 dng-0.2.0/dng/man/splitn.Rd |only dng-0.2.0/dng/man/splitn_moments.Rd |only dng-0.2.0/dng/man/splitt.Rd |only dng-0.2.0/dng/man/splitt_moments.Rd |only dng-0.2.0/dng/src/RcppExports.cpp | 171 +++++++++++++++--- dng-0.2.0/dng/src/rcpp_dsplitn.cpp |only dng-0.2.0/dng/src/rcpp_dsplitt.cpp | 89 +++++++-- dng-0.2.0/dng/src/rcpp_psplitn.cpp |only dng-0.2.0/dng/src/rcpp_psplitt.cpp | 36 --- dng-0.2.0/dng/src/rcpp_qsplitn.cpp |only dng-0.2.0/dng/src/rcpp_qsplitt.cpp | 24 -- dng-0.2.0/dng/src/rcpp_rsplitn.cpp |only dng-0.2.0/dng/src/rcpp_rsplitt.cpp | 25 -- dng-0.2.0/dng/src/rcpp_splitn_kurtosis.cpp |only dng-0.2.0/dng/src/rcpp_splitn_mean.cpp |only dng-0.2.0/dng/src/rcpp_splitn_skewness.cpp |only dng-0.2.0/dng/src/rcpp_splitn_var.cpp |only dng-0.2.0/dng/src/rcpp_splitt_kurtosis.cpp |only dng-0.2.0/dng/src/rcpp_splitt_mean.cpp |only dng-0.2.0/dng/src/rcpp_splitt_skewness.cpp |only dng-0.2.0/dng/src/rcpp_splitt_var.cpp |only dng-0.2.0/dng/tests |only 37 files changed, 546 insertions(+), 152 deletions(-)
Title: A Collection of Robust Statistical Methods
Description: A collection of robust statistical methods based on Wilcox' WRS functions. It implements robust t-tests (independent and dependent samples), robust ANOVA (including between-within subject designs), quantile ANOVA, robust correlation, robust mediation, and nonparametric ANCOVA models based on robust location measures.
Author: Patrick Mair [cre, aut],
Rand Wilcox [aut]
Maintainer: Patrick Mair <mair@fas.harvard.edu>
Diff between WRS2 versions 0.9-2 dated 2017-05-01 and 0.10-0 dated 2018-06-15
WRS2-0.10-0/WRS2/DESCRIPTION | 13 WRS2-0.10-0/WRS2/MD5 | 114 +- WRS2-0.10-0/WRS2/NAMESPACE | 7 WRS2-0.10-0/WRS2/R/bwtrim.R | 6 WRS2-0.10-0/WRS2/R/johansp.R | 82 +- WRS2-0.10-0/WRS2/R/lincon.R | 10 WRS2-0.10-0/WRS2/R/mcppb20.R | 3 WRS2-0.10-0/WRS2/R/med1way.R | 2 WRS2-0.10-0/WRS2/R/med1way.crit.R | 51 - WRS2-0.10-0/WRS2/R/med2way.R | 3 WRS2-0.10-0/WRS2/R/mom.R | 24 WRS2-0.10-0/WRS2/R/onesampb.R |only WRS2-0.10-0/WRS2/R/onestep.R | 32 WRS2-0.10-0/WRS2/R/pbad2way.R | 3 WRS2-0.10-0/WRS2/R/print.bwtrim.R |only WRS2-0.10-0/WRS2/R/print.mcp1.R | 2 WRS2-0.10-0/WRS2/R/print.med1way.R | 4 WRS2-0.10-0/WRS2/R/print.onesampb.R |only WRS2-0.10-0/WRS2/R/print.t1way.R | 6 WRS2-0.10-0/WRS2/R/print.t2way.R | 23 WRS2-0.10-0/WRS2/R/t1way.R | 4 WRS2-0.10-0/WRS2/R/t2way.R | 3 WRS2-0.10-0/WRS2/R/winvar.R | 33 WRS2-0.10-0/WRS2/build/vignette.rds |binary WRS2-0.10-0/WRS2/data/Leerkes.rda |binary WRS2-0.10-0/WRS2/data/Pygmalion.rda |binary WRS2-0.10-0/WRS2/data/WineTasting.rda |binary WRS2-0.10-0/WRS2/data/bush.rda |binary WRS2-0.10-0/WRS2/data/chile.rda |binary WRS2-0.10-0/WRS2/data/diet.rda |only WRS2-0.10-0/WRS2/data/electric.rda |binary WRS2-0.10-0/WRS2/data/essays.rda |binary WRS2-0.10-0/WRS2/data/eurosoccer.rda |binary WRS2-0.10-0/WRS2/data/goggles.rda |binary WRS2-0.10-0/WRS2/data/hangover.rda |binary WRS2-0.10-0/WRS2/data/invisibility.rda |binary WRS2-0.10-0/WRS2/data/movie.rda |binary WRS2-0.10-0/WRS2/data/picture.rda |binary WRS2-0.10-0/WRS2/data/spider.rda |binary WRS2-0.10-0/WRS2/data/swimming.rda |binary WRS2-0.10-0/WRS2/data/viagra.rda |binary WRS2-0.10-0/WRS2/inst/CITATION | 4 WRS2-0.10-0/WRS2/inst/NEWS.Rd | 35 WRS2-0.10-0/WRS2/inst/doc/WRS2.Rnw | 1339 ++++++++++++++++++++------------- WRS2-0.10-0/WRS2/inst/doc/WRS2.pdf |binary WRS2-0.10-0/WRS2/man/bwtrim.Rd | 16 WRS2-0.10-0/WRS2/man/diet.Rd |only WRS2-0.10-0/WRS2/man/hangover.Rd | 2 WRS2-0.10-0/WRS2/man/med1way.Rd | 18 WRS2-0.10-0/WRS2/man/med2way.Rd | 8 WRS2-0.10-0/WRS2/man/onesampb.Rd |only WRS2-0.10-0/WRS2/man/qanova.Rd | 2 WRS2-0.10-0/WRS2/man/rmanova.Rd | 2 WRS2-0.10-0/WRS2/man/rmanovab.Rd | 5 WRS2-0.10-0/WRS2/man/t1way.Rd | 7 WRS2-0.10-0/WRS2/man/t1waybt.Rd | 6 WRS2-0.10-0/WRS2/man/t2way.Rd | 7 WRS2-0.10-0/WRS2/man/trimse.Rd | 20 WRS2-0.10-0/WRS2/vignettes/WRS2.Rnw | 1339 ++++++++++++++++++++------------- WRS2-0.10-0/WRS2/vignettes/WRS2.bib | 218 ++++- WRS2-0.9-2/WRS2/inst/doc/WRS2.R |only WRS2-0.9-2/WRS2/man/WRS2-package.Rd |only 62 files changed, 2151 insertions(+), 1302 deletions(-)
Title: (Randomized) Quasi-Random Number Generators
Description: Functionality for generating (randomized) quasi-random numbers in
high dimensions.
Author: Marius Hofert [aut, cre],
Christiane Lemieux [aut]
Maintainer: Marius Hofert <marius.hofert@uwaterloo.ca>
Diff between qrng versions 0.0-3 dated 2016-06-13 and 0.0-4 dated 2018-06-15
DESCRIPTION | 9 MD5 | 20 NAMESPACE | 6 R/qrng.R | 16 demo/basket_options.R | 94 demo/test_functions.R | 16 man/qrng.Rd | 58 src/ghalton.c | 2 src/init.c | 2 src/sobol.c | 100 src/sobol.h |18754 ++++++++++++++++++++++++++++++++++++++++++++++++-- 11 files changed, 18571 insertions(+), 506 deletions(-)
Title: Learning Interactions via Hierarchical Group-Lasso
Regularization
Description: Group-Lasso INTERaction-NET. Fits linear pairwise-interaction models that satisfy strong hierarchy: if an interaction coefficient is estimated to be nonzero, then its two associated main effects also have nonzero estimated coefficients. Accommodates categorical variables (factors) with arbitrary numbers of levels, continuous variables, and combinations thereof. Implements the machinery described in the paper "Learning interactions via hierarchical group-lasso regularization" (JCGS 2015, Volume 24, Issue 3). Michael Lim & Trevor Hastie (2015) <DOI:10.1080/10618600.2014.938812>.
Author: Michael Lim, Trevor Hastie
Maintainer: Michael Lim <michael626@gmail.com>
Diff between glinternet versions 1.0.7 dated 2018-02-15 and 1.0.8 dated 2018-06-15
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/glinternet.r | 2 +- R/group_lasso.r | 4 ++-- src/fista.c | 20 ++++++++++++++------ src/glinternet_init.c | 4 ++-- 6 files changed, 28 insertions(+), 20 deletions(-)
Title: Flexible Gaussian Cluster Simulator
Description: Clustering is a central task in big data analyses and clusters are often Gaussian or near Gaussian. However, a flexible Gaussian cluster simulation tool with precise control over the size, variance, and spacing of the clusters in NXN dimensional space does not exist. This is why we created 'clusterlab'. The algorithm first creates X points equally spaced on the circumference of a circle in 2D space. These form the centers of each cluster to be simulated. Additional samples are added by adding Gaussian noise to each cluster center and concatenating the new sample co-ordinates. Then if the feature space is greater than 2D, the generated points are considered principal component scores and projected into N dimensional space using linear combinations using fixed eigenvectors. The algorithm is highly customizable and well suited to testing class discovery tools across a range of fields.
Author: Christopher R John
Maintainer: Christopher R John <chris.r.john86@gmail.com>
Diff between clusterlab versions 0.0.0.9 dated 2018-05-31 and 0.0.1.9 dated 2018-06-15
DESCRIPTION | 6 - MD5 | 14 +-- R/clusterlab.R | 183 ++++++++++++++++++++++++++++++++++----------- inst/doc/introduction.R | 18 ++++ inst/doc/introduction.Rmd | 44 +++++++++- inst/doc/introduction.html | 62 +++++++++++---- man/clusterlab.Rd | 11 ++ vignettes/introduction.Rmd | 44 +++++++++- 8 files changed, 301 insertions(+), 81 deletions(-)