Title: Evaluation of Failure Time Surrogate Endpoints in Individual
Patient Data Meta-Analyses
Description: Provides functions for the evaluation of
surrogate endpoints when both the surrogate and the true endpoint are failure
time variables. The approaches implemented are: (1) the two-step approach
(Burzykowski et al, 2001) <DOI:10.1111/1467-9876.00244> with a copula model (Clayton, Plackett, Hougaard) at
the first step and either a linear regression of log-hazard ratios at the second
step (either adjusted or not for measurement error); (2) mixed proportional
hazard models estimated via mixed Poisson GLM.
Author: Federico Rotolo [aut, cre],
Xavier Paoletti [ctr], Marc Buyse [ctr], Tomasz Burzykowski [ctr], Stefan Michiels [ctr]
Maintainer: Federico Rotolo <federico.rotolo@gustaveroussy.fr>
Diff between surrosurv versions 1.0.0 dated 2016-11-10 and 1.1.5 dated 2016-12-08
surrosurv-1.0.0/surrosurv/vignettes/copulas.bib |only surrosurv-1.0.0/surrosurv/vignettes/copulas.tex |only surrosurv-1.1.5/surrosurv/DESCRIPTION | 15 + surrosurv-1.1.5/surrosurv/MD5 | 47 ++--- surrosurv-1.1.5/surrosurv/NAMESPACE | 2 surrosurv-1.1.5/surrosurv/NEWS | 8 surrosurv-1.1.5/surrosurv/R/loocv.R | 31 ++- surrosurv-1.1.5/surrosurv/R/poisson_functions.R | 158 ++++++++++-------- surrosurv-1.1.5/surrosurv/R/poissonize.R | 69 +++++-- surrosurv-1.1.5/surrosurv/R/predict.R | 58 +++++- surrosurv-1.1.5/surrosurv/R/simData.R | 104 +++++------ surrosurv-1.1.5/surrosurv/R/surrosurv.R | 70 ++++--- surrosurv-1.1.5/surrosurv/build/partial.rdb |binary surrosurv-1.1.5/surrosurv/build/vignette.rds |binary surrosurv-1.1.5/surrosurv/inst/doc/copulas.Rnw | 98 +++++++++-- surrosurv-1.1.5/surrosurv/inst/doc/copulas.pdf |binary surrosurv-1.1.5/surrosurv/man/convergence.Rd | 2 surrosurv-1.1.5/surrosurv/man/loocv.Rd | 3 surrosurv-1.1.5/surrosurv/man/poissonize.Rd | 10 - surrosurv-1.1.5/surrosurv/man/simData.Rd | 30 +-- surrosurv-1.1.5/surrosurv/man/surrosurv.Rd | 34 ++- surrosurv-1.1.5/surrosurv/vignettes/copulas.Rnw | 98 +++++++++-- surrosurv-1.1.5/surrosurv/vignettes/loocv-1.pdf |only surrosurv-1.1.5/surrosurv/vignettes/poissonize-1.pdf |only surrosurv-1.1.5/surrosurv/vignettes/predictions-1.pdf |only surrosurv-1.1.5/surrosurv/vignettes/refs.bib |only surrosurv-1.1.5/surrosurv/vignettes/surrosurv.pdf |only surrosurv-1.1.5/surrosurv/vignettes/surrosurv.tex |only surrosurv-1.1.5/surrosurv/vignettes/survCurves-1.pdf |only 29 files changed, 566 insertions(+), 271 deletions(-)
Title: Bootstrap Methods for Network Inference
Description: Functions for analysis of network objects, which are imported or
simulated by the package. The non-parametric methods of analysis center
around snowball and bootstrap sampling.
Author: Leticia Ramirez-Ramirez, Kusha Nezafati, Yuzhou Chen,
Vyacheslav Lyubchich, Yulia Gel
Maintainer: Kusha Nezafati <kusha.nezafati@gmail.com>
Diff between snowboot versions 0.5.1 dated 2016-04-04 and 0.5.2 dated 2016-12-08
snowboot-0.5.1/snowboot/R/cross_validation.R |only snowboot-0.5.1/snowboot/man/cross_validation.Rd |only snowboot-0.5.2/snowboot/DESCRIPTION | 13 - snowboot-0.5.2/snowboot/MD5 | 32 +- snowboot-0.5.2/snowboot/NAMESPACE | 3 snowboot-0.5.2/snowboot/R/BparametersEst.R | 1 snowboot-0.5.2/snowboot/R/LSMI.R | 22 + snowboot-0.5.2/snowboot/R/Oempdegreedistrib0.R | 63 ++--- snowboot-0.5.2/snowboot/R/OempdegreedistribK.R | 183 +++++++------- snowboot-0.5.2/snowboot/R/RcppExports.R | 2 snowboot-0.5.2/snowboot/R/UNION_LSMI.R |only snowboot-0.5.2/snowboot/R/bootdeg.R | 23 + snowboot-0.5.2/snowboot/R/bootdeg0.R | 58 ++-- snowboot-0.5.2/snowboot/R/bootdegK.R | 235 ++++++++++--------- snowboot-0.5.2/snowboot/R/cross_validation_mean.R |only snowboot-0.5.2/snowboot/man/LSMI.Rd | 4 snowboot-0.5.2/snowboot/man/Union_LSMI.Rd |only snowboot-0.5.2/snowboot/man/bootdeg.Rd | 22 + snowboot-0.5.2/snowboot/man/cross_validation_mean.Rd |only snowboot-0.5.2/snowboot/src/RcppExports.cpp | 10 20 files changed, 364 insertions(+), 307 deletions(-)
Title: Collection of Convenient Functions for Common Statistical
Computations
Description: Collection of convenient functions for common statistical computations,
which are not directly provided by R's base or stats packages.
This package aims at providing, first, shortcuts for statistical
measures, which otherwise could only be calculated with additional
effort (like standard errors or root mean squared errors). Second,
these shortcut functions are generic (if appropriate), and can be
applied not only to vectors, but also to other objects as well
(e.g., the Coefficient of Variation can be computed for vectors,
linear models, or linear mixed models; the r2()-function returns
the r-squared value for 'lm', 'glm', 'merMod' or 'lme' objects).
The focus of most functions lies on summary statistics or fit
measures for regression models, including generalized linear
models and mixed effects models. However, some of the functions
also deal with other statistical measures, like Cronbach's Alpha,
Cramer's V, Phi etc.
Author: Daniel Lüdecke <d.luedecke@uke.de>
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjstats versions 0.6.0 dated 2016-10-31 and 0.7.0 dated 2016-12-08
sjstats-0.6.0/sjstats/R/cramer.R |only sjstats-0.6.0/sjstats/man/cramer.Rd |only sjstats-0.6.0/sjstats/man/get_re_var.Rd |only sjstats-0.6.0/sjstats/man/merMod_p.Rd |only sjstats-0.6.0/sjstats/man/rse.Rd |only sjstats-0.6.0/sjstats/man/weight2.Rd |only sjstats-0.6.0/sjstats/man/wtd_se.Rd |only sjstats-0.7.0/sjstats/DESCRIPTION | 13 sjstats-0.7.0/sjstats/MD5 | 129 ++---- sjstats-0.7.0/sjstats/NAMESPACE | 8 sjstats-0.7.0/sjstats/NEWS | 10 sjstats-0.7.0/sjstats/NEWS.md | 24 - sjstats-0.7.0/sjstats/R/S3-methods.R | 532 ++++++++++++------------- sjstats-0.7.0/sjstats/R/boot_ci.R | 14 sjstats-0.7.0/sjstats/R/bootstrap.R | 18 sjstats-0.7.0/sjstats/R/converge_ok.R | 122 ++--- sjstats-0.7.0/sjstats/R/cv.R | 8 sjstats-0.7.0/sjstats/R/efc.R | 63 +- sjstats-0.7.0/sjstats/R/eta_sq.R | 109 ++--- sjstats-0.7.0/sjstats/R/gof.R | 8 sjstats-0.7.0/sjstats/R/helpfunctions.R | 2 sjstats-0.7.0/sjstats/R/icc.R | 76 +-- sjstats-0.7.0/sjstats/R/internal_consistency.R | 25 - sjstats-0.7.0/sjstats/R/mean_n.R | 154 +++---- sjstats-0.7.0/sjstats/R/merMod_p.R | 233 +++++----- sjstats-0.7.0/sjstats/R/mwu.R | 30 - sjstats-0.7.0/sjstats/R/overdisp.R | 190 ++++---- sjstats-0.7.0/sjstats/R/phi.R | 71 ++- sjstats-0.7.0/sjstats/R/pred_vars.R | 90 ++-- sjstats-0.7.0/sjstats/R/prop.R |only sjstats-0.7.0/sjstats/R/pseudo_r2.R | 18 sjstats-0.7.0/sjstats/R/rmse.R | 72 +-- sjstats-0.7.0/sjstats/R/robust.R |only sjstats-0.7.0/sjstats/R/samplesize_lme.R | 27 - sjstats-0.7.0/sjstats/R/se.R | 26 - sjstats-0.7.0/sjstats/R/sjStatistics.R | 212 ++++----- sjstats-0.7.0/sjstats/R/std.R | 207 +++++---- sjstats-0.7.0/sjstats/R/std_b.R | 278 ++++++------- sjstats-0.7.0/sjstats/R/var_pop.R | 2 sjstats-0.7.0/sjstats/R/weight.R | 360 +++++++--------- sjstats-0.7.0/sjstats/build/partial.rdb |binary sjstats-0.7.0/sjstats/man/boot_ci.Rd | 15 sjstats-0.7.0/sjstats/man/bootstrap.Rd | 154 +++---- sjstats-0.7.0/sjstats/man/chisq_gof.Rd | 2 sjstats-0.7.0/sjstats/man/converge_ok.Rd | 2 sjstats-0.7.0/sjstats/man/cv.Rd | 5 sjstats-0.7.0/sjstats/man/deff.Rd | 82 ++- sjstats-0.7.0/sjstats/man/efc.Rd | 3 sjstats-0.7.0/sjstats/man/eta_sq.Rd | 7 sjstats-0.7.0/sjstats/man/get_model_pval.Rd | 18 sjstats-0.7.0/sjstats/man/icc.Rd | 247 +++++------ sjstats-0.7.0/sjstats/man/inequ_trend.Rd | 142 +++--- sjstats-0.7.0/sjstats/man/levene_test.Rd | 2 sjstats-0.7.0/sjstats/man/mean_n.Rd | 140 +++--- sjstats-0.7.0/sjstats/man/mwu.Rd | 13 sjstats-0.7.0/sjstats/man/phi.Rd | 21 sjstats-0.7.0/sjstats/man/pred_vars.Rd | 4 sjstats-0.7.0/sjstats/man/prop.Rd |only sjstats-0.7.0/sjstats/man/r2.Rd | 225 +++++----- sjstats-0.7.0/sjstats/man/re_var.Rd | 101 ++-- sjstats-0.7.0/sjstats/man/reliab_test.Rd | 321 +++++++-------- sjstats-0.7.0/sjstats/man/rmse.Rd | 43 +- sjstats-0.7.0/sjstats/man/robust.Rd |only sjstats-0.7.0/sjstats/man/se.Rd | 10 sjstats-0.7.0/sjstats/man/sjstats-package.Rd | 4 sjstats-0.7.0/sjstats/man/smpsize_lmm.Rd | 130 +++--- sjstats-0.7.0/sjstats/man/std.Rd | 14 sjstats-0.7.0/sjstats/man/std_beta.Rd | 140 +++--- sjstats-0.7.0/sjstats/man/var_pop.Rd | 2 sjstats-0.7.0/sjstats/man/weight.Rd | 15 sjstats-0.7.0/sjstats/man/wtd_sd.Rd | 14 71 files changed, 2543 insertions(+), 2464 deletions(-)
Title: R Client for Adobe Analytics API V1.4
Description: Functions for interacting with the Adobe Analytics API V1.4
(https://api.omniture.com/admin/1.4/rest/).
Author: Willem Paling, Randy Zwitch & Jowanza Joseph
Maintainer: Randy Zwitch <rzwitch+rsitecatalyst@gmail.com>
Diff between RSiteCatalyst versions 1.4.9 dated 2016-06-22 and 1.4.10 dated 2016-12-08
DESCRIPTION | 8 +- LICENSE | 4 - MD5 | 79 ++++++++++++-------- NAMESPACE | 6 + NEWS | 13 +++ R/GetClickMapReporting.R |only R/GetElements.R | 15 ++- R/GetMetrics.R | 10 ++ R/GetRealTimeSettings.R | 44 +++++++---- R/GetReport.R | 9 ++ R/GetReportSuiteGroups.R |only R/GetTimeStampEnabled.R |only R/GetVirtualReportSuiteSettings.R |only R/ParseDW.R |only R/QueueDataWarehouse.R |only R/QueueSummary.R | 2 R/RSiteCatalyst.R | 4 - R/ViewProcessingRules.R |only man/GetClickMapReporting.Rd |only man/GetElements.Rd | 12 ++- man/GetEndpoint.Rd | 7 + man/GetMetrics.Rd | 8 +- man/GetReportSuiteGroups.Rd |only man/GetTimeStampEnabled.Rd |only man/GetUsageLog.Rd | 7 + man/GetVirtualReportSuiteSettings.Rd |only man/ParseDW.Rd |only man/ParseFallout.Rd | 7 + man/ParseOvertime.Rd | 7 + man/ParsePathing.Rd | 7 + man/ParseRanked.Rd | 7 + man/ParseSummary.Rd | 7 + man/ParseTrended.Rd | 7 + man/QueueDataWarehouse.Rd |only man/QueueSummary.Rd | 2 man/RSiteCatalyst.Rd | 4 - man/ViewProcessingRules.Rd |only tests/testthat-queuedatawarehouse.R |only tests/testthat-view.R |only tests/testthat/test-getelements_dw.R |only tests/testthat/test-getmetrics_dw.R |only tests/testthat/test-getrealtimesettings.R | 4 + tests/testthat/test-getreportsuitegroups.R |only tests/testthat/test-gettimestampenabled.R |only tests/testthat/test-getvirtualreportsuitesettings.R |only tests/testthat/test-queuedatawarehouse.R |only tests/testthat/test-queuefallout.R | 8 +- tests/testthat/test-queueovertime.R | 48 ++++++------ tests/testthat/test-queuepathing.R | 8 +- tests/testthat/test-queueranked.R | 24 +++--- tests/testthat/test-queuetrended.R | 24 +++--- tests/testthat/test-viewprocessingrules.R |only 52 files changed, 243 insertions(+), 149 deletions(-)
Title: Finite Mixture Modeling, Clustering & Classification
Description: R functions for random univariate and multivariate finite mixture model generation, estimation, clustering and classification. Variables can be continuous, discrete, independent or dependent and may follow normal, lognormal, Weibull, gamma, binomial, Poisson or Dirac parametric families.
Author: Marko Nagode [aut, cre]
Maintainer: Marko Nagode <marko.nagode@fs.uni-lj.si>
Diff between rebmix versions 2.8.3 dated 2016-10-05 and 2.8.4 dated 2016-12-08
DESCRIPTION | 6 MD5 | 74 +++--- NAMESPACE | 3 R/AllClasses.R | 31 +- R/AllGenerics.R | 8 R/RCLRMIX.R | 43 +++ R/RCLSMIX.R | 10 R/REBMIX.R | 62 ++++- R/RNGMIX.R | 2 R/Zp.R |only R/is.error.R | 59 +++-- R/plot.RCLRMIX.R | 70 +++--- R/plot.RCLSMIX.R | 79 +++---- R/plot.REBMIX.R | 8 R/plot.RNGMIX.R | 20 - R/split.R | 8 R/summary.R | 64 ++++- build/vignette.rds |binary data/adult.rda |binary data/galaxy.rda |binary data/iris.rda |binary data/truck.rda |binary data/weibull.rda |binary data/weibullnormal.rda |binary data/wine.rda |binary inst/NEWS.Rd | 11 + inst/doc/rebmix.R | 105 +++------ inst/doc/rebmix.Rnw | 107 +++------ inst/doc/rebmix.pdf |binary man/RCLRMIX-class.Rd | 14 - man/REBMIX.Rd | 6 man/Zp.Rd |only man/iris.Rd | 2 man/wine.Rd | 2 src/rebmixf.cpp | 532 ++++++++++++++++++++----------------------------- src/rebmixf.h | 9 src/rebmvnormf.cpp | 4 src/rngmixf.cpp | 2 vignettes/rebmix.Rnw | 107 +++------ 39 files changed, 736 insertions(+), 712 deletions(-)
Title: A Collection of Functions to Implement a Class for Univariate
Polynomial Manipulations
Description: A collection of functions to implement a class for univariate
polynomial manipulations.
Author: Bill Venables [aut] (S original),
Kurt Hornik [aut, cre] (R port),
Martin Maechler [aut] (R port)
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between polynom versions 1.3-8 dated 2014-03-17 and 1.3-9 dated 2016-12-08
ChangeLog | 10 ++++++++++ DESCRIPTION | 12 ++++++------ MD5 | 6 +++--- inst/CITATION | 4 ++-- 4 files changed, 21 insertions(+), 11 deletions(-)
Title: Piecewise Structural Equation Modeling
Description: Implements piecewise structural equation models.
Author: Jon Lefcheck
Maintainer: Jon Lefcheck <jslefche@vims.edu>
Diff between piecewiseSEM versions 1.2.0 dated 2016-10-11 and 1.2.1 dated 2016-12-08
DESCRIPTION | 10 ++-- MD5 | 54 ++++++++++++------------ NEWS.md | 8 +++ R/get.formula.list.R | 6 ++ R/get.random.formula.R | 97 ++++++++++++++++++++++++++++---------------- R/get.scaled.data.R | 48 ++++++++++++++------- R/get.scaled.model.R | 6 ++ R/partial.resid.R | 30 +++++++++---- R/sem.aic.R | 28 ++++++++---- R/sem.basis.set.R | 4 - R/sem.coefs.R | 11 ++++ R/sem.fisher.c.R | 10 ++-- R/sem.fit.R | 28 +++++++++--- R/sem.lavaan.R | 2 R/sem.missing.paths.R | 69 ++++++++++++++++++------------- R/sem.model.fits.R | 35 ++++++++++++++- R/sem.predict.R | 4 - README.md | 4 - build/vignette.rds |binary inst/doc/piecewiseSEM.Rmd | 2 inst/doc/piecewiseSEM.html | 12 ++--- man/piecewiseSEM-package.Rd | 6 +- man/sem.aic.Rd | 9 +++- man/sem.basis.set.Rd | 4 - man/sem.fisher.c.Rd | 8 ++- man/sem.fit.Rd | 12 +++-- man/sem.missing.paths.Rd | 10 +++- vignettes/piecewiseSEM.Rmd | 2 28 files changed, 339 insertions(+), 180 deletions(-)
Title: Plot the Australian Coastline and States
Description: Functions for plotting Australia's coastline and state
boundaries.
Author: Bill Venables [aut] (S original),
Kurt Hornik [aut, cre] (R port)
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between oz versions 1.0-20 dated 2014-01-14 and 1.0-21 dated 2016-12-08
ChangeLog | 10 ++++++++++ DESCRIPTION | 10 +++++----- MD5 | 6 +++--- inst/CITATION | 4 ++-- 4 files changed, 20 insertions(+), 10 deletions(-)
Title: Natural Language Processing Utilities
Description: Utilities for Natural Language Processing.
Author: Kurt Hornik [aut, cre]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between NLPutils versions 0.0-3 dated 2015-06-24 and 0.0-4 dated 2016-12-08
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- man/diversity.Rd | 2 +- man/formality.Rd | 2 +- man/polarity.Rd | 2 +- man/stem.Rd | 2 +- 6 files changed, 12 insertions(+), 12 deletions(-)
Title: An API Client for the Internet Archive
Description: Search the Internet Archive, retrieve metadata, and download
files.
Author: Lincoln Mullen [aut, cre]
Maintainer: Lincoln Mullen <lincoln@lincolnmullen.com>
Diff between internetarchive versions 0.1.5 dated 2016-03-19 and 0.1.6 dated 2016-12-08
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- NAMESPACE | 2 +- NEWS.md | 4 ++++ R/ia_files.R | 2 +- R/ia_metadata.R | 2 +- R/internetarchive-package.R | 2 +- build/vignette.rds |binary inst/doc/internet-archive.html | 21 ++++++++++----------- tests/testthat/hecker_meta.rds |binary tests/testthat/hecker_txt.rds |binary tests/testthat/test-files-download.R | 2 ++ 12 files changed, 35 insertions(+), 30 deletions(-)
More information about internetarchive at CRAN
Permanent link
Title: Reproducible Data Retrieval from the ICPSR Archive
Description: Reproducible, programmatic retrieval of datasets from the
Inter-university Consortium for Political and Social Research archive.
Author: Frederick Solt [aut, cre],
Kellen Gracey [aut],
Eric Persson [ctb]
Maintainer: Frederick Solt <frederick-solt@uiowa.edu>
Diff between icpsrdata versions 0.2.0 dated 2016-10-20 and 0.3.0 dated 2016-12-08
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS.md | 3 +++ R/icpsrdownload.R | 4 ++-- build/vignette.rds |binary inst/doc/icpsrdata-vignette.html | 4 ++-- man/icpsr_download.Rd | 4 ++-- 7 files changed, 19 insertions(+), 16 deletions(-)
Title: Network Visualization in the 'ggplot2' Framework
Description: Network visualization in the 'ggplot2' framework. Network
functionality is provided in a single 'ggplot2' layer by calling the geom 'net'.
Layouts are calculated using the 'sna' package, example networks are included.
Author: Samantha Tyner, Heike Hofmann
Maintainer: Samantha Tyner <sctyner@iastate.edu>
Diff between geomnet versions 0.1.2.1 dated 2016-07-01 and 0.2.0 dated 2016-12-08
geomnet-0.1.2.1/geomnet/build |only geomnet-0.1.2.1/geomnet/inst/doc |only geomnet-0.1.2.1/geomnet/vignettes |only geomnet-0.2.0/geomnet/DESCRIPTION | 15 - geomnet-0.2.0/geomnet/MD5 | 47 ++-- geomnet-0.2.0/geomnet/NAMESPACE | 17 + geomnet-0.2.0/geomnet/NEWS.md |only geomnet-0.2.0/geomnet/R/data.r | 30 +- geomnet-0.2.0/geomnet/R/fortify-net.R |only geomnet-0.2.0/geomnet/R/geom-net.r | 287 ++++++++++++++++----------- geomnet-0.2.0/geomnet/R/geom2plotly.R |only geomnet-0.2.0/geomnet/R/network-tools.r | 2 geomnet-0.2.0/geomnet/R/stat-net.r | 99 +++++---- geomnet-0.2.0/geomnet/R/utils.R |only geomnet-0.2.0/geomnet/README.md | 132 +++++++++++- geomnet-0.2.0/geomnet/data/datalist | 1 geomnet-0.2.0/geomnet/data/protein.rda |binary geomnet-0.2.0/geomnet/man/as.adjmat.Rd |only geomnet-0.2.0/geomnet/man/as.edgedf.Rd |only geomnet-0.2.0/geomnet/man/football.Rd | 9 geomnet-0.2.0/geomnet/man/fortify.adjmat.Rd |only geomnet-0.2.0/geomnet/man/fortify.edgedf.Rd |only geomnet-0.2.0/geomnet/man/fortify.igraph.Rd |only geomnet-0.2.0/geomnet/man/fortify.network.Rd |only geomnet-0.2.0/geomnet/man/geom_circle.Rd | 4 geomnet-0.2.0/geomnet/man/geom_net.Rd | 172 ++++++++-------- geomnet-0.2.0/geomnet/man/lesmis.Rd | 5 geomnet-0.2.0/geomnet/man/metro_map.Rd | 2 geomnet-0.2.0/geomnet/man/mm.directed.Rd | 2 geomnet-0.2.0/geomnet/man/soccer.Rd | 6 30 files changed, 544 insertions(+), 286 deletions(-)
Title: Functions for Handling Dates
Description: Functions for handling dates.
Author: Terry Therneau [aut],
Thomas Lumley [trl] (R port),
Kjetil Halvorsen [trl] (R port),
Kurt Hornik [trl, ctb, cre] (R port)
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between date versions 1.2-34 dated 2014-03-17 and 1.2-35 dated 2016-12-08
ChangeLog | 10 ++++++++++ DESCRIPTION | 10 +++++----- MD5 | 6 +++--- inst/CITATION | 4 ++-- 4 files changed, 20 insertions(+), 10 deletions(-)
Title: Chronological Objects which can Handle Dates and Times
Description: Chronological objects which can handle dates and times.
Author: David James [aut] (S original),
Kurt Hornik [aut, trl, cre],
Gabor Grothendieck [ctb]
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between chron versions 2.3-47 dated 2015-06-24 and 2.3-48 dated 2016-12-08
ChangeLog | 10 ++++++++++ DESCRIPTION | 6 +++--- MD5 | 6 +++--- inst/CITATION | 4 ++-- 4 files changed, 18 insertions(+), 8 deletions(-)
Title: 'Rcpp' Integration for Numerical Computing Libraries
Description: A collection of open source libraries for numerical computing
(numerical integration, optimization, etc.) and their integration with
'Rcpp'.
Author: Yixuan Qiu [aut, cre],
Sreekumar Balan [aut] (Numerical integration library),
Matt Beall [aut] (Numerical integration library),
Mark Sauder [aut] (Numerical integration library),
Naoaki Okazaki [aut] (The libLBFGS library),
Thomas Hahn [aut] (The Cuba library)
Maintainer: Yixuan Qiu <yixuan.qiu@cos.name>
Diff between RcppNumerical versions 0.2-0 dated 2016-04-23 and 0.3-0 dated 2016-12-08
RcppNumerical-0.2-0/RcppNumerical/inst/include/optimization/lbfgs.h |only RcppNumerical-0.2-0/RcppNumerical/src/lbfgs.c |only RcppNumerical-0.3-0/RcppNumerical/DESCRIPTION | 20 +- RcppNumerical-0.3-0/RcppNumerical/MD5 | 42 +++-- RcppNumerical-0.3-0/RcppNumerical/R/RcppExports.R | 2 RcppNumerical-0.3-0/RcppNumerical/R/fastLR.R | 3 RcppNumerical-0.3-0/RcppNumerical/README.md | 32 ++-- RcppNumerical-0.3-0/RcppNumerical/build |only RcppNumerical-0.3-0/RcppNumerical/inst/AUTHORS | 2 RcppNumerical-0.3-0/RcppNumerical/inst/COPYRIGHTS | 6 RcppNumerical-0.3-0/RcppNumerical/inst/NEWS.Rd | 17 ++ RcppNumerical-0.3-0/RcppNumerical/inst/doc |only RcppNumerical-0.3-0/RcppNumerical/inst/include/Func.h | 6 RcppNumerical-0.3-0/RcppNumerical/inst/include/RcppNumerical.h | 2 RcppNumerical-0.3-0/RcppNumerical/inst/include/integration/Integrator.h | 2 RcppNumerical-0.3-0/RcppNumerical/inst/include/optimization/LBFGS |only RcppNumerical-0.3-0/RcppNumerical/inst/include/optimization/LBFGS.h |only RcppNumerical-0.3-0/RcppNumerical/inst/include/optimization/wrapper.h | 72 ++++------ RcppNumerical-0.3-0/RcppNumerical/man/fastLR.Rd | 3 RcppNumerical-0.3-0/RcppNumerical/src/RcppExports.cpp | 10 - RcppNumerical-0.3-0/RcppNumerical/src/cuhre/stddecl.h | 4 RcppNumerical-0.3-0/RcppNumerical/src/fastLR.cpp | 2 RcppNumerical-0.3-0/RcppNumerical/src/register_routines.c | 8 - RcppNumerical-0.3-0/RcppNumerical/vignettes |only 24 files changed, 125 insertions(+), 108 deletions(-)
Title: Programmatic Access to Data and Statistics from the World Bank
API
Description: Tools for searching and downloading data and statistics from
the World Bank Data API (<http://data.worldbank.org/developers/api-overview>)
and the World Bank Data Catalog API (<http://data.worldbank.org/developers/data-catalog-api>).
Author: Jesse Piburn [aut, cre],
UT-Battelle, LLC [cph]
Maintainer: Jesse Piburn <piburnjo@ornl.gov>
Diff between wbstats versions 0.1 dated 2016-04-22 and 0.1.1 dated 2016-12-08
DESCRIPTION | 8 MD5 | 21 + NEWS |only R/data.R | 2 R/wb.R | 31 ++ README.md | 196 ++++++++++-------- data/wb_cachelist.RData |binary inst/doc/Using_the_wbstats_package.Rmd | 2 inst/doc/Using_the_wbstats_package.html | 339 +++++++++++++++++--------------- man/wb.Rd | 10 man/wb_cachelist.Rd | 2 vignettes/Using_the_wbstats_package.Rmd | 2 12 files changed, 347 insertions(+), 266 deletions(-)
Title: Manipulate and Visualize VCF Data
Description: Facilitates easy manipulation of variant call format (VCF) data.
Functions are provided to rapidly read from and write to VCF files.
Once VCF data is read into R a parser function extracts matrices of data.
This information can then be used for quality control or other purposes.
Additional functions provide visualization of genomic data.
Once processing is complete data may be written to a VCF file (*.vcf.gz).
It also may be converted into other popular R objects (e.g., genlight, DNAbin).
VcfR provides a link between VCF data and familiar R software.
Author: Brian J. Knaus [cre, aut],
Niklaus J. Grunwald [aut],
Eric C. Anderson [ctb],
David J. Winter [ctb],
Zhian N. Kamvar [ctb]
Maintainer: Brian J. Knaus <briank.lists@gmail.com>
Diff between vcfR versions 1.2.0 dated 2016-07-25 and 1.3.0 dated 2016-12-08
DESCRIPTION | 16 - MD5 | 166 ++++++++------- NAMESPACE | 12 + R/AllClass.R | 3 R/INFO2df.R |only R/RcppExports.R | 165 ++++++++++++++- R/chromR-method.R | 31 ++ R/chromo_plot.R | 15 + R/create_chromR.R | 85 ++----- R/extract_gt.R | 103 +++++++-- R/fasta_output.R | 8 R/genotype_matrix_functions.R | 28 +- R/get_methods.R |only R/heatmap_bp.R | 124 ++++++++--- R/io_vcfR.R | 22 +- R/is_het.R | 5 R/ordisample.R |only R/proc_chromR.R | 70 ++++-- R/queryMETA.R |only R/summary_tables.R | 6 R/vcfR-method.R | 5 R/vcfR.R | 23 +- R/vcfR2DNAbin.R | 218 ++++++-------------- R/vcfR_conversion.R | 16 - R/vcfR_to_tidy_functions.R | 62 +++-- R/zzz.R |only README.md | 28 +- build/vignette.rds |binary inst/doc/converting_data.R | 6 inst/doc/converting_data.Rmd | 8 inst/doc/converting_data.html | 260 +++++++++++++++--------- inst/doc/filtering_data.html | 22 +- inst/doc/intro_to_vcfR.html | 28 +- inst/doc/ranking_data.html | 28 +- inst/doc/sequence_coverage.R | 9 inst/doc/sequence_coverage.Rmd | 9 inst/doc/sequence_coverage.html | 34 ++- inst/doc/vcf_data.html | 6 inst/doc/visualization_1.html | 20 - inst/doc/visualization_2.html | 10 man/AD_frequency.Rd | 5 man/INFO2df.Rd |only man/chromR-class.Rd | 2 man/create_chromR.Rd | 16 - man/extract_gt.Rd | 43 +++ man/fasta_output.Rd | 6 man/freq_peak.Rd |only man/getFIX.Rd |only man/heatmap_bp.Rd | 14 + man/io_vcfR.Rd | 18 + man/is_het.Rd | 5 man/masplit.Rd |only man/ordisample.Rd |only man/proc_chromR.Rd | 9 man/queryMETA.Rd |only man/vcfR-method.Rd | 8 man/vcfR.Rd | 18 + man/vcfR2DNAbin.Rd | 56 ++++- man/vcfR_conversion.Rd | 12 - man/vcfR_to_tidy_conversion.Rd | 41 +-- src/RcppExports.cpp | 211 +++++++++++-------- src/ad_frequency.cpp | 26 +- src/extractGT2NM.cpp | 114 ++++++++-- src/freq_peak.cpp |only src/is_het.cpp | 2 src/masplit.cpp |only src/vcfRCommon.cpp | 59 ++++- src/vcfRCommon.h | 1 src/vcf_io.cpp | 163 +++++++++++---- tests/testthat.R | 30 ++ tests/testthat/test_10_write_vcf.R |only tests/testthat/test_1_vcf.R | 165 +++++++++------ tests/testthat/test_2_chromR.R | 23 +- tests/testthat/test_3_extract_gt.R | 111 ++++++++-- tests/testthat/test_4_vcfR2DNAbin.R | 43 +++ tests/testthat/test_ad_frequency.R | 3 tests/testthat/test_addID.R | 1 tests/testthat/test_chromR_method.R | 10 tests/testthat/test_chromo_plot.R | 36 +++ tests/testthat/test_chromoqc.R | 8 tests/testthat/test_conversion.R | 25 +- tests/testthat/test_freq_peak.R |only tests/testthat/test_genotype_matrix_functions.R | 3 tests/testthat/test_get.R |only tests/testthat/test_heatmapbp.R | 3 tests/testthat/test_io.R | 4 tests/testthat/test_maf.R | 1 tests/testthat/test_rank_variants.R | 1 tests/testthat/test_vcfR_methods.R | 8 tests/testthat/test_vcfRtidy.R | 10 vignettes/converting_data.Rmd | 8 vignettes/sequence_coverage.Rmd | 9 92 files changed, 1991 insertions(+), 991 deletions(-)
Title: Variance Estimation for Sample Surveys by the Ultimate Cluster
Method
Description: Generation of domain variables, linearisation of several nonlinear population statistics (the ratio of two totals, weighted income percentile, relative median income ratio, at-risk-of-poverty rate, at-risk-of-poverty threshold, Gini coefficient, gender pay gap, the aggregate replacement ratio, the relative median income ratio, median income below at-risk-of-poverty gap, income quintile share ratio, relative median at-risk-of-poverty gap), computation of regression residuals in case of weight calibration, variance estimation of sample surveys by the ultimate cluster method (Hansen, Hurwitz and Madow,Theory, vol. I: Methods and Applications; vol. II: Theory. 1953, New York: John Wiley and Sons), variance estimation for longitudinal, cross-sectional measures and measures of change for single and multistage stage cluster sampling designs (Berger, Y. G., 2015, <doi:10.1111/rssa.12116>). Several other precision measures are derived - standard error, the coefficient of variation, the margin of error, confidence interval, design effect.
Author: Juris Breidaks [aut, cre],
Martins Liberts [aut],
Santa Ivanova [aut]
Maintainer: Juris Breidaks <Juris.Breidaks@csb.gov.lv>
Diff between vardpoor versions 0.7.8 dated 2016-11-01 and 0.8.0 dated 2016-12-08
DESCRIPTION | 10 +++++----- MD5 | 34 +++++++++++++++++----------------- R/linqsr.R | 16 ++++++++-------- R/vardchanges.R | 1 + R/vardchangespoor.R | 1 + R/vardcros.R | 1 + R/vardcrosannual.R | 1 + R/vardcrospoor.R | 1 + R/vardom.R | 32 ++++++++++++++++---------------- R/vardomh.R | 45 ++++++++++++++++++++++++++------------------- R/variance_est.R | 6 +++--- R/varpoord.R | 2 +- inst/CITATION | 4 ++-- inst/NEWS | 5 +++++ man/linrmir.Rd | 2 +- man/vardcrosannual.Rd | 4 ++-- man/vardomh.Rd | 2 +- man/vardpoor-package.Rd | 14 +++++++------- 18 files changed, 99 insertions(+), 82 deletions(-)
Title: Detection of Outliers in Time Series
Description: Detection of outliers in time series following the
Chen and Liu (1993) <DOI:10.2307/2290724> procedure.
Innovational outliers, additive outliers, level shifts,
temporary changes and seasonal level shifts are considered.
Author: Javier López-de-Lacalle <javlacalle@yahoo.es>
Maintainer: Javier López-de-Lacalle <javlacalle@yahoo.es>
Diff between tsoutliers versions 0.6-3 dated 2016-07-07 and 0.6-5 dated 2016-12-08
DESCRIPTION | 15 +- MD5 | 44 ++++--- NAMESPACE | 10 - NEWS | 49 ++++++++ R/coefs2poly.R | 139 ++++++------------------ R/find-consecutive-outliers.R |only R/locate-outliers.R | 224 +++++++++++++++++++++++++++------------ R/outliers-regressors-arima.R | 6 - R/print-tsoutliers.R | 12 +- R/remove-outliers.R | 69 ++++++++++-- R/tso.R | 80 +++++++++---- build/partial.rdb |only build/vignette.rds |binary inst/doc/tsoutliers-intro.R | 4 inst/doc/tsoutliers-intro.Rnw | 3 man/coefs2poly.Rd | 54 ++------- man/find-consecutive-outliers.Rd |only man/locate-outliers-loops.Rd | 2 man/locate-outliers.Rd | 2 man/outliers-effects.Rd | 14 +- man/print-tsoutliers.Rd |only man/remove-outliers.Rd | 2 man/tsoutliers-package.Rd | 3 man/tsoutliers.Rd | 12 -- vignettes/tsoutliers-intro.Rnw | 3 25 files changed, 439 insertions(+), 308 deletions(-)
Title: Statistical Exploration of Landscapes of Phylogenetic Trees
Description: Tools for the exploration of distributions of phylogenetic trees.
This package includes a shiny interface which can be started from R using
'treescapeServer()'.
Author: Thibaut Jombart [aut],
Michelle Kendall [aut, cre],
Jacob Almagro-Garcia [aut],
Caroline Colijn [aut]
Maintainer: Michelle Kendall <m.kendall@imperial.ac.uk>
Diff between treescape versions 1.10.17 dated 2016-09-29 and 1.10.18 dated 2016-12-08
DESCRIPTION | 8 MD5 | 155 NAMESPACE | 124 R/RcppExports.R | 14 R/data.R | 184 R/findGroves.R | 200 R/medTree.R | 434 - R/metrics.R | 1010 +-- R/plotGroves.R | 500 - R/plotTreeDiff.R | 362 - R/servers.R | 150 R/transmissionTrees.R | 436 - R/treescape.R | 300 README.md | 986 +-- build/vignette.rds |binary inst/doc/DengueVignette.R | 451 - inst/doc/DengueVignette.Rmd | 673 +- inst/doc/DengueVignette.html | 5120 ++++++++-------- inst/doc/TransmissionTreesVignette.R | 264 inst/doc/TransmissionTreesVignette.Rmd | 426 - inst/doc/TransmissionTreesVignette.html | 626 +- inst/doc/treescape.R | 306 - inst/doc/treescape.Rmd | 794 +- inst/doc/treescape.html | 6692 +++++++++++----------- inst/shiny/server.R | 2572 ++++---- inst/shiny/ui.R | 1352 ++-- inst/shiny/www/bootstrap.simplex.css | 20 inst/shiny/www/html/help.html | 414 - inst/shiny/www/styles.css | 20 man/DengueBEASTMCC.Rd | 54 man/DengueSeqs.Rd | 46 man/DengueTrees.Rd | 58 man/findGroves.Rd | 120 man/findMRCIs.Rd | 68 man/fluTrees.Rd | 52 man/linearMrca.Rd | 62 man/medTree.Rd | 174 man/multiDist.Rd | 108 man/plotGroves.Rd | 196 man/plotGrovesD3.Rd | 140 man/plotTreeDiff.Rd | 146 man/refTreeDist.Rd | 90 man/tipDiff.Rd | 86 man/treeDist.Rd | 106 man/treeVec.Rd | 98 man/treescape.Rd | 148 man/treescapeServer.Rd | 42 man/wiwMedTree.Rd | 90 man/wiwTreeDist.Rd | 74 man/woodmiceTrees.Rd | 56 tests/testthat.R | 8 tests/testthat/testbasics.R | 272 vignettes/DengueVignette.Rmd | 673 +- vignettes/DengueVignette.md |only vignettes/TransmissionTreesVignette.Rmd | 426 - vignettes/figs/BEASTtree_diffs-1.png |binary vignettes/figs/BEASTtree_diffs-2.png |binary vignettes/figs/compare_BEAST_to_other_trees-1.png |binary vignettes/figs/compare_BEAST_to_other_trees-2.png |binary vignettes/figs/compare_BEAST_to_other_trees-3.png |binary vignettes/figs/compare_trees_NJ_v_ML-1.png |binary vignettes/figs/distances-1.png |binary vignettes/figs/distances-2.png |binary vignettes/figs/igraph_tree1-1.png |binary vignettes/figs/make_NJ-1.png |binary vignettes/figs/plotgroves-1.png |binary vignettes/figs/scree_plot-1.png |binary vignettes/figs/see_ML_boots-1.png |binary vignettes/figs/see_NJ_boots-1.png |binary vignettes/figs/trees2_and_3-1.png |binary vignettes/figs/trees2_and_3-2.png |binary vignettes/figs/view_ML-1.png |binary vignettes/figs/wiwMedTreePlot-1.png |binary vignettes/figs/wiw_MDS1000-1.png |binary vignettes/figs/woodmiceCluster1-1.png |binary vignettes/figs/woodmiceMedian-1.png |binary vignettes/figs/woodmice_plotTreeDiff-1.png |binary vignettes/figs/woodmice_plotTreeDiff-2.png |binary vignettes/treescape.Rmd | 794 +- 79 files changed, 14395 insertions(+), 14385 deletions(-)
Title: Survey Planning Tools
Description: Tools for sample survey planning, including sample size calculation, estimation of expected precision for the estimates of totals, and calculation of optimal sample size allocation.
Author: Juris Breidaks [aut, cre],
Martins Liberts [aut],
Janis Jukams [aut]
Maintainer: Juris Breidaks <rcsb@csb.gov.lv>
Diff between surveyplanning versions 2.4 dated 2016-10-24 and 2.6 dated 2016-12-08
surveyplanning-2.4/surveyplanning/R/ratio_dom_optimal_allocation.R |only surveyplanning-2.4/surveyplanning/man/ratio_dom_optimal_allocation.Rd |only surveyplanning-2.6/surveyplanning/DESCRIPTION | 10 +- surveyplanning-2.6/surveyplanning/MD5 | 22 +++--- surveyplanning-2.6/surveyplanning/NAMESPACE | 3 surveyplanning-2.6/surveyplanning/R/expsize.R | 4 - surveyplanning-2.6/surveyplanning/R/optsize.R | 34 ++++++++-- surveyplanning-2.6/surveyplanning/R/prop_dom_optimal_allocation.R |only surveyplanning-2.6/surveyplanning/inst/CITATION | 4 - surveyplanning-2.6/surveyplanning/man/dom_optimal_allocation.Rd | 30 ++++++-- surveyplanning-2.6/surveyplanning/man/expvar.Rd | 5 + surveyplanning-2.6/surveyplanning/man/optsize.Rd | 30 ++++++-- surveyplanning-2.6/surveyplanning/man/prop_dom_optimal_allocation.Rd |only surveyplanning-2.6/surveyplanning/man/surveyplanning-package.Rd | 4 - 14 files changed, 100 insertions(+), 46 deletions(-)
More information about surveyplanning at CRAN
Permanent link
Title: Image Registration Using the NiftyReg Library
Description: Provides an R interface to the NiftyReg image registration tools
<http://sourceforge.net/projects/niftyreg/>. Linear and nonlinear registration
are supported, in two and three dimensions.
Author: Jon Clayden, based on original code by Marc Modat, Pankaj Daga and
others
Maintainer: Jon Clayden <code@clayden.org>
Diff between RNiftyReg versions 2.4.0 dated 2016-09-21 and 2.4.1 dated 2016-12-08
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- NEWS | 6 ++++++ src/DeformationField.cpp | 22 +++++++++++----------- src/DeformationField.h | 18 +++++++++--------- src/aladin.cpp | 4 ++-- src/aladin.h | 4 ++-- src/f3d.cpp | 8 ++++---- src/f3d.h | 8 ++++---- src/main.cpp | 1 + 10 files changed, 53 insertions(+), 46 deletions(-)
Title: Fast R and C++ Access to NIfTI Images
Description: Provides very fast access to images stored in the NIfTI-1 file
format <http://nifti.nimh.nih.gov/nifti-1>, with seamless synchronisation
between compiled C and interpreted R code. Not to be confused with
'RNiftyReg', which provides tools for image registration.
Author: Jon Clayden [cre, aut],
Bob Cox [aut],
Mark Jenkinson [aut],
Rick Reynolds [ctb],
Kate Fissell [ctb],
Jean-loup Gailly [cph],
Mark Adler [cph]
Maintainer: Jon Clayden <code@clayden.org>
Diff between RNifti versions 0.2.2 dated 2016-10-02 and 0.3.0 dated 2016-12-08
DESCRIPTION | 8 MD5 | 102 +++++----- NEWS | 14 + inst/doxygen/html/_nifti_image_8h_source.html | 81 ++++--- inst/doxygen/html/annotated.html | 7 inst/doxygen/html/class_r_nifti_1_1_nifti_image-members.html |only inst/doxygen/html/class_r_nifti_1_1_nifti_image.html |only inst/doxygen/html/classes.html | 2 inst/doxygen/html/functions.html | 70 +++--- inst/doxygen/html/functions_func.html | 60 ++--- inst/doxygen/html/functions_vars.html | 10 inst/doxygen/html/index.html | 2 inst/doxygen/html/search/all_0.js | 4 inst/doxygen/html/search/all_1.js | 2 inst/doxygen/html/search/all_2.js | 4 inst/doxygen/html/search/all_3.js | 2 inst/doxygen/html/search/all_4.js | 16 - inst/doxygen/html/search/all_5.js | 5 inst/doxygen/html/search/all_6.js | 6 inst/doxygen/html/search/all_7.js | 2 inst/doxygen/html/search/all_8.js | 2 inst/doxygen/html/search/all_9.js | 8 inst/doxygen/html/search/all_a.js | 8 inst/doxygen/html/search/all_b.js | 4 inst/doxygen/html/search/all_c.js | 2 inst/doxygen/html/search/all_d.js | 2 inst/doxygen/html/search/all_e.js | 2 inst/doxygen/html/search/classes_0.js | 2 inst/doxygen/html/search/classes_1.js | 2 inst/doxygen/html/search/functions_0.js | 2 inst/doxygen/html/search/functions_1.js | 2 inst/doxygen/html/search/functions_2.js | 2 inst/doxygen/html/search/functions_3.js | 2 inst/doxygen/html/search/functions_4.js | 12 - inst/doxygen/html/search/functions_5.js | 4 inst/doxygen/html/search/functions_6.js | 6 inst/doxygen/html/search/functions_7.js | 2 inst/doxygen/html/search/functions_8.js | 8 inst/doxygen/html/search/functions_9.js | 8 inst/doxygen/html/search/functions_a.js | 4 inst/doxygen/html/search/functions_b.js | 2 inst/doxygen/html/search/functions_c.js | 2 inst/doxygen/html/search/functions_d.js | 2 inst/doxygen/html/search/variables_0.js | 2 inst/doxygen/html/search/variables_1.js | 4 inst/doxygen/html/search/variables_2.js | 2 inst/doxygen/html/struct_r_nifti_1_1_nifti_image_1_1_block-members.html |only inst/doxygen/html/struct_r_nifti_1_1_nifti_image_1_1_block.html |only inst/include/RNifti.h | 4 inst/include/RNiftiAPI.h | 57 +++++ inst/include/lib/NiftiImage.h | 6 src/init.cpp | 7 src/main.cpp | 1 src/zlib/inflate.c | 5 54 files changed, 334 insertions(+), 241 deletions(-)
Title: Enhanced Quantitative Trading Modelling
Description: Download and organize historical market data from multiple sources like Yahoo (<https://finance.yahoo.com>), Google (<https://www.google.com/finance>), Finam (<https://www.finam.ru/profile/moex-akcii/sberbank/export/>), MOEX (<https://www.moex.com/en/derivatives/contracts.aspx>) and IQFeed (<https://www.iqfeed.net/symbolguide/index.cfm?symbolguide=lookup>). Code your trading algorithms in modern C++11 with powerful event driven tick processing API including trading costs and exchange communication latency and transform detailed data seamlessly into R. In just few lines of code you will be able to visualize every step of your trading model from tick data to multi dimensional heat maps.
Author: Stanislav Kovalevsky
Maintainer: Stanislav Kovalevsky <so.kovalevsky@gmail.com>
Diff between QuantTools versions 0.5.1 dated 2016-11-13 and 0.5.2 dated 2016-12-08
DESCRIPTION | 18 MD5 | 58 +- NAMESPACE | 7 NEWS.md |only R/RcppExports.R | 432 ++++++++++----------- R/doc.R | 2 R/doc_Processor.R | 299 +++++++------- R/doc_RollLinReg.R | 8 R/gen_futures_codes.R | 35 + R/get_market_data.R | 123 +++++ R/iqfeed.R | 67 ++- R/round_POSIXct.R | 8 R/settings.R | 235 +++++------ R/store_market_data.R | 719 +++++++++++++++++++++++------------ data/datalist | 2 inst/include/BackTest.h | 59 +- inst/include/BackTest/Order.h | 518 ++++++++++++------------- inst/include/BackTest/Processor.h | 717 +++++++++++++--------------------- inst/include/BackTest/Statistics.h |only inst/include/BackTest/Trade.h | 116 +++-- inst/include/CppToR.h |only inst/include/Indicators/RollLinReg.h | 8 inst/include/NPeriods.h |only man/cpp_Processor.Rd | 43 +- man/cpp_RollLinReg.Rd | 104 ++--- man/gen_futures_codes.Rd | 16 man/get_market_data.Rd | 25 + man/round_POSIXct.Rd | 6 man/settings.Rd | 6 man/store_market_data.Rd | 33 + src/RcppExports.cpp | 24 - src/roll_lm.cpp | 2 32 files changed, 2023 insertions(+), 1667 deletions(-)
Title: Kinetic Evaluation of Chemical Degradation Data
Description: Calculation routines based on the FOCUS Kinetics Report (2006,
2014). Includes a function for conveniently defining differential equation
models, model solution based on eigenvalues if possible or using numerical
solvers and a choice of the optimisation methods made available by the 'FME'
package. If a C compiler (on windows: 'Rtools') is installed, differential
equation models are solved using compiled C functions. Please note that no
warranty is implied for correctness of results or fitness for a particular
purpose.
Author: Johannes Ranke [aut, cre, cph],
Katrin Lindenberger [ctb],
René Lehmann [ctb],
Eurofins Regulatory AG [cph]
Maintainer: Johannes Ranke <jranke@uni-bremen.de>
Diff between mkin versions 0.9.44 dated 2016-06-28 and 0.9.45 dated 2016-12-08
DESCRIPTION | 13 +-- MD5 | 126 ++++++++++++++--------------- NAMESPACE | 1 NEWS.md | 112 ++++++++++++++------------ R/SFORB.solution.R | 4 R/add_err.R | 6 - R/endpoints.R | 12 +- R/ilr.R | 4 R/mkin_long_to_wide.R | 4 R/mkinds.R | 2 R/mkinerrmin.R | 14 +-- R/mkinfit.R | 93 +++++++++++---------- R/mkinmod.R | 23 +++-- R/mkinparplot.R | 22 ++--- R/mkinpredict.R | 26 +++--- R/mkinresplot.R | 10 +- R/mmkin.R | 10 +- R/plot.mkinfit.R | 50 +++++++---- R/plot.mmkin.R | 22 +++-- R/transform_odeparms.R | 10 +- README.md | 40 ++++----- TODO | 5 - build/vignette.rds |binary inst/doc/FOCUS_D.R | 12 +- inst/doc/FOCUS_D.Rmd | 21 ++-- inst/doc/FOCUS_D.html | 41 +++++---- inst/doc/FOCUS_L.R | 8 - inst/doc/FOCUS_L.Rmd | 48 +++++------ inst/doc/FOCUS_L.html | 175 ++++++++++++++++++++++------------------- inst/doc/FOCUS_Z.R | 20 ++-- inst/doc/FOCUS_Z.Rnw | 66 +++++++-------- inst/doc/FOCUS_Z.pdf |binary inst/doc/compiled_models.R | 10 +- inst/doc/compiled_models.Rmd | 28 +++--- inst/doc/compiled_models.html | 89 +++++++++++--------- inst/doc/mkin.R | 20 +++- inst/doc/mkin.Rmd | 58 +++++++------ inst/doc/mkin.html | 103 ++++++++++++++++-------- man/Extract.mmkin.Rd | 19 +++- man/add_err.Rd | 8 - man/endpoints.Rd | 8 + man/ilr.Rd | 2 man/mccall81_245T.Rd | 5 - man/mkin_long_to_wide.Rd | 8 - man/mkin_wide_to_long.Rd | 4 man/mkinerrmin.Rd | 9 -- man/mkinfit.Rd | 86 ++++++++++---------- man/mkinparplot.Rd | 9 -- man/mkinpredict.Rd | 26 +++--- man/mkinsub.Rd | 8 - man/mmkin.Rd | 15 +-- man/plot.mkinfit.Rd | 18 ++-- man/plot.mmkin.Rd | 14 ++- man/print.mkinmod.Rd | 9 +- man/schaefer07_complex_case.Rd | 8 + man/summary.mkinfit.Rd | 2 man/synthetic_data_for_UBA.Rd | 4 man/transform_odeparms.Rd | 26 +++--- vignettes/FOCUS_D.Rmd | 21 ++-- vignettes/FOCUS_L.Rmd | 48 +++++------ vignettes/FOCUS_Z.Rnw | 66 +++++++-------- vignettes/compiled_models.Rmd | 28 +++--- vignettes/mkin.Rmd | 58 +++++++------ vignettes/references.bib | 6 - 64 files changed, 994 insertions(+), 829 deletions(-)
More information about GreedyExperimentalDesign at CRAN
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Title: Bayesian Multilevel Mediation
Description: Easy estimation of Bayesian multilevel mediation models with Stan.
Author: Matti Vuorre [aut, cre]
Maintainer: Matti Vuorre <mv2521@columbia.edu>
Diff between bmlm versions 1.2.1 dated 2016-10-11 and 1.2.9 dated 2016-12-08
DESCRIPTION | 8 +-- MD5 | 13 +++-- NEWS.md | 4 + README.md | 61 ++++++++++++++++++++------- exec/bmlm.stan | 1 inst/CITATION |only inst/chunks/parameters.stan | 1 src/include/models.hpp | 96 ++++++++++++++------------------------------ 8 files changed, 93 insertions(+), 91 deletions(-)
Title: Regression Modeling Strategies
Description: Regression modeling, testing, estimation, validation,
graphics, prediction, and typesetting by storing enhanced model design
attributes in the fit. 'rms' is a collection of functions that
assist with and streamline modeling. It also contains functions for
binary and ordinal logistic regression models, ordinal models for
continuous Y with a variety of distribution families, and the Buckley-James
multiple regression model for right-censored responses, and implements
penalized maximum likelihood estimation for logistic and ordinary
linear models. 'rms' works with almost any regression model, but it
was especially written to work with binary or ordinal regression
models, Cox regression, accelerated failure time models,
ordinary linear models, the Buckley-James model, generalized least
squares for serially or spatially correlated observations, generalized
linear models, and quantile regression.
Author: Frank E Harrell Jr <f.harrell@vanderbilt.edu>
Maintainer: Frank E Harrell Jr <f.harrell@vanderbilt.edu>
Diff between rms versions 5.0-0 dated 2016-11-03 and 5.0-1 dated 2016-12-08
DESCRIPTION | 14 +- MD5 | 90 ++++++++-------- NEWS | 15 ++ R/Glm.s | 6 - R/Gls.s | 11 - R/Rq.s | 22 +-- R/anova.rms.s | 17 +-- R/bj.s | 7 - R/cph.s | 7 - R/ggplot.Predict.s | 21 +-- R/latex.cph.s | 8 - R/latex.lrm.s | 4 R/latex.ols.s | 2 R/latex.pphsm.s | 2 R/latex.psm.s | 2 R/latex.rms.s | 14 +- R/ols.s | 12 +- R/orm.s | 7 - R/print.psm.s | 6 - R/rmsMisc.s | 25 ++-- R/summary.rms.s | 278 +++++++++++++++++++++++++------------------------- R/survplotp.npsurv.s | 14 +- inst/tests/ggplot2.r | 6 - man/Glm.Rd | 10 + man/Gls.Rd | 32 ++--- man/Rq.Rd | 15 +- man/anova.rms.Rd | 15 +- man/bj.Rd | 10 + man/cph.Rd | 4 man/ggplot.Predict.Rd | 3 man/latex.cph.Rd | 2 man/latexrms.Rd | 20 +-- man/lrm.Rd | 5 man/orm.Rd | 11 + man/print.cph.Rd | 17 +-- man/print.ols.Rd | 25 ++-- man/psm.Rd | 14 +- man/rms-internal.Rd | 1 man/summary.rms.Rd | 12 +- man/survplot.Rd | 2 src/lrmfit.f | 42 +++++-- src/mlmats.f | 105 +++++++++++++----- src/ormuv.f | 10 - src/ratfor/ormuv.r | 6 - src/ratfor/robcovf.r | 4 src/robcovf.f | 6 - 46 files changed, 524 insertions(+), 437 deletions(-)
Title: Harrell Miscellaneous
Description: Contains many functions useful for data
analysis, high-level graphics, utility operations, functions for
computing sample size and power, importing and annotating datasets,
imputing missing values, advanced table making, variable clustering,
character string manipulation, conversion of R objects to LaTeX and html code,
and recoding variables.
Author: Frank E Harrell Jr <f.harrell@vanderbilt.edu>, with
contributions from Charles Dupont and many others.
Maintainer: Frank E Harrell Jr <f.harrell@vanderbilt.edu>
Diff between Hmisc versions 4.0-0 dated 2016-11-01 and 4.0-1 dated 2016-12-08
Hmisc-4.0-0/Hmisc/inst/tests/dataload.r |only Hmisc-4.0-1/Hmisc/DESCRIPTION | 14 Hmisc-4.0-1/Hmisc/INDEX | 2 Hmisc-4.0-1/Hmisc/MD5 | 67 +-- Hmisc-4.0-1/Hmisc/NAMESPACE | 1 Hmisc-4.0-1/Hmisc/NEWS | 27 + Hmisc-4.0-1/Hmisc/R/describe.s | 425 ++++++++------------- Hmisc-4.0-1/Hmisc/R/dotchart3.s | 18 Hmisc-4.0-1/Hmisc/R/dotchartpl.s | 6 Hmisc-4.0-1/Hmisc/R/gbayes.s | 8 Hmisc-4.0-1/Hmisc/R/ggfreqScatter.r | 19 Hmisc-4.0-1/Hmisc/R/html.s | 30 + Hmisc-4.0-1/Hmisc/R/latex.s | 39 + Hmisc-4.0-1/Hmisc/R/latexTherm.s | 30 - Hmisc-4.0-1/Hmisc/R/panel.bpplot.s | 12 Hmisc-4.0-1/Hmisc/R/plot.describe.s | 30 - Hmisc-4.0-1/Hmisc/R/scat1d.s | 153 +++++++ Hmisc-4.0-1/Hmisc/R/sedit.s | 58 +- Hmisc-4.0-1/Hmisc/R/summary.formula.s | 368 ++++++++---------- Hmisc-4.0-1/Hmisc/R/summaryM.s | 27 - Hmisc-4.0-1/Hmisc/R/summaryP.s | 2 Hmisc-4.0-1/Hmisc/R/upData.s | 33 - Hmisc-4.0-1/Hmisc/inst/tests/examples.Rmd | 17 Hmisc-4.0-1/Hmisc/inst/tests/gbayes.r |only Hmisc-4.0-1/Hmisc/inst/tests/latex.s | 53 ++ Hmisc-4.0-1/Hmisc/inst/tests/summaryM-customtest.r |only Hmisc-4.0-1/Hmisc/inst/tests/upData.r |only Hmisc-4.0-1/Hmisc/man/describe.Rd | 50 +- Hmisc-4.0-1/Hmisc/man/format.df.Rd | 7 Hmisc-4.0-1/Hmisc/man/ggfreqScatter.Rd | 12 Hmisc-4.0-1/Hmisc/man/histboxp.Rd |only Hmisc-4.0-1/Hmisc/man/html.Rd | 7 Hmisc-4.0-1/Hmisc/man/latex.Rd | 7 Hmisc-4.0-1/Hmisc/man/latexTherm.Rd | 12 Hmisc-4.0-1/Hmisc/man/scat1d.Rd | 2 Hmisc-4.0-1/Hmisc/man/summary.formula.Rd | 5 Hmisc-4.0-1/Hmisc/man/summaryM.Rd | 8 37 files changed, 908 insertions(+), 641 deletions(-)
Title: Output Analysis and Diagnostics for MCMC
Description: Provides functions for summarizing and plotting the
output from Markov Chain Monte Carlo (MCMC) simulations, as
well as diagnostic tests of convergence to the equilibrium
distribution of the Markov chain.
Author: Martyn Plummer [aut, cre, trl],
Nicky Best [aut],
Kate Cowles [aut],
Karen Vines [aut],
Deepayan Sarkar [aut],
Douglas Bates [aut],
Russell Almond [aut],
Arni Magnusson [aut]
Maintainer: Martyn Plummer <plummerm@iarc.fr>
Diff between coda versions 0.18-1 dated 2015-10-16 and 0.19-1 dated 2016-12-08
coda-0.18-1/coda/INDEX |only coda-0.19-1/coda/CHANGELOG | 12 ++++++ coda-0.19-1/coda/DESCRIPTION | 8 ++-- coda-0.19-1/coda/MD5 | 21 +++++----- coda-0.19-1/coda/NAMESPACE | 5 +- coda-0.19-1/coda/R/gelman.R | 3 + coda-0.19-1/coda/R/geweke.R | 2 - coda-0.19-1/coda/R/output.R | 77 +++++++++++++++++++++++++++++++++++---- coda-0.19-1/coda/data/line.rda |binary coda-0.19-1/coda/inst/CITATION | 4 +- coda-0.19-1/coda/man/densplot.Rd | 31 ++++++++++----- coda-0.19-1/coda/man/mcmc.Rd | 14 +++++-- 12 files changed, 136 insertions(+), 41 deletions(-)