Title: Regression Discontinuity Design Application
Description: Estimation of both single- and multiple-assignment Regression Discontinuity Designs
(RDDs). Provides both parametric (global) and non-parametric (local) estimation choices for
both sharp and fuzzy designs, along with power analysis and assumption checks.
Introductions to the underlying logic and analysis of RDDs are in
Thistlethwaite, D. L., Campbell, D. T. (1960) <doi:10.1037/h0044319> and
Lee, D. S., Lemieux, T. (2010) <doi:10.1257/jel.48.2.281>.
Author: Ze Jin [aut],
Wang Liao [aut],
Irena Papst [aut],
Wenyu Zhang [aut],
Felix Thoemmes [aut, cre],
Drew Dimmery [ctb] (Implementation of functions in R package rdd),
Bastiaan Quast [ctb] (Implementation of functions in R package
rddtools),
Matthieu Stigler [ctb] (Implementation of functions in R package
rddtools)
Maintainer: Felix Thoemmes <fjt36@cornell.edu>
Diff between rddapp versions 1.0.0 dated 2018-01-25 and 1.1.0 dated 2018-04-25
DESCRIPTION | 18 MD5 | 213 +-- NAMESPACE | 155 +- NEWS.md | 44 R/attr_check.R | 110 - R/bw_ik09.R | 234 +-- R/bw_ik12.R | 316 ++-- R/data.R | 40 R/dc_test.R | 588 ++++---- R/mfrd_est.R | 873 ++++++------ R/mrd_est.R | 639 ++++----- R/mrd_impute.R | 743 +++++----- R/mrd_power.R | 552 ++++--- R/mrd_sens_bw.R | 180 +- R/mrd_sens_cutoff.R | 238 +-- R/plot.mfrd.R | 298 ++-- R/plot.rd.R | 776 +++++------ R/predict.rd.R | 474 +++--- R/print.mfrd.R | 50 R/print.rd.R | 50 R/rd_est.R | 1021 +++++++------- R/rd_impute.R | 343 ++-- R/rd_power.R | 432 +++--- R/rd_sens_bw.R | 100 - R/rd_sens_cutoff.R | 114 - R/rd_type.R | 495 +++---- R/rddapp-package.R | 82 - R/sens_plot.R | 234 +-- R/shiny_run.R | 49 R/summary.mfrd.R |only R/summary.mrd.R |only R/summary.rd.R | 305 ++-- R/treat_assign.R | 62 R/var_center.R | 144 +- R/wt_kern.R | 86 - README.md | 99 - build/vignette.rds |binary inst/CITATION | 32 inst/doc/rddapp.Rmd | 24 inst/doc/rddapp.html | 290 ---- inst/shinyrdd/global.R | 66 inst/shinyrdd/help |only inst/shinyrdd/model_report.md | 74 - inst/shinyrdd/modules/assumption_check.R | 794 +++++------ inst/shinyrdd/modules/data_summary.R | 666 ++++----- inst/shinyrdd/modules/input_file.R | 530 +++---- inst/shinyrdd/modules/input_parameter.R | 1008 +++++++------- inst/shinyrdd/modules/input_power.R | 1736 ++++++++++++------------- inst/shinyrdd/modules/model_code.R | 130 - inst/shinyrdd/modules/model_estimate.R | 1445 ++++++++++---------- inst/shinyrdd/modules/power_code.R | 134 - inst/shinyrdd/modules/sensitivity_analysis.R | 900 ++++++------ inst/shinyrdd/modules/simulate_power.R | 700 +++++----- inst/shinyrdd/server.R | 134 - inst/shinyrdd/ui.R | 105 - inst/shinyrdd/ui_elements/page_about.R | 32 inst/shinyrdd/ui_elements/page_help.R | 31 inst/shinyrdd/ui_elements/page_model.R | 120 - inst/shinyrdd/ui_elements/page_power.R | 36 inst/shinyrdd/ui_elements/page_report.R | 26 inst/shinyrdd/utilities/format_summary_table.R | 170 +- inst/shinyrdd/utilities/summarize_model_data.R | 172 +- inst/shinyrdd/www/help_page.html |only inst/shinyrdd/www/test.html |only man/CARE.Rd | 58 man/attr_check.Rd | 56 man/bw_ik09.Rd | 74 - man/bw_ik12.Rd | 74 - man/dc_test.Rd | 149 +- man/mfrd_est.Rd | 127 - man/mrd_est.Rd | 224 +-- man/mrd_impute.Rd | 212 +-- man/mrd_power.Rd | 214 +-- man/mrd_sens_bw.Rd | 64 man/mrd_sens_cutoff.Rd | 62 man/plot.mfrd.Rd | 70 - man/plot.rd.Rd | 114 - man/predict.rd.Rd | 52 man/print.mfrd.Rd | 38 man/print.rd.Rd | 38 man/rd_est.Rd | 260 +-- man/rd_impute.Rd | 172 +- man/rd_power.Rd | 142 +- man/rd_sens_bw.Rd | 56 man/rd_sens_cutoff.Rd | 60 man/rd_type.Rd | 70 - man/rddapp-package.Rd | 96 - man/sens_plot.Rd | 76 - man/shiny_run.Rd | 40 man/summary.mfrd.Rd |only man/summary.mrd.Rd |only man/summary.rd.Rd | 51 man/treat_assign.Rd | 58 man/var_center.Rd | 64 man/wt_kern.Rd | 60 tests/testthat.R | 22 tests/testthat/test-bw-ik-09.R | 242 +-- tests/testthat/test-bw-ik-12.R | 72 - tests/testthat/test-dc-test.R | 154 +- tests/testthat/test-mfrd-est-sharp.R | 399 ++--- tests/testthat/test-mrd-est-fuzzy.R | 376 ++--- tests/testthat/test-mrd-est-sharp.R | 490 +++---- tests/testthat/test-predict-rd.R | 220 +-- tests/testthat/test-rd-est-fuzzy.R | 318 ++-- tests/testthat/test-rd-est-sharp.R | 316 ++-- vignettes/rddapp.Rmd | 24 106 files changed, 12590 insertions(+), 12386 deletions(-)
Title: R Actuarial Workshops
Description: In order to facilitate R instruction for actuaries, we have organized several
sets of publicly available data of interest to non-life actuaries. In addition, we suggest
a set of packages, which most practicing actuaries will use routinely. Finally, there is
an R markdown skeleton for basic reserve analysis.
Author: Brian A. Fannin [aut, cre]
Maintainer: Brian A. Fannin <captain@PirateGrunt.com>
Diff between raw versions 0.1.5 dated 2017-08-08 and 0.1.6 dated 2018-04-25
DESCRIPTION | 14 +++--- MD5 | 16 +++---- NEWS | 9 +++ build/vignette.rds |binary inst/doc/raw.R | 6 ++ inst/doc/raw.Rmd | 20 +++++--- inst/doc/raw.html | 43 +++++++++++++------ inst/rmarkdown/templates/reserveReview/template.yaml | 2 vignettes/raw.Rmd | 20 +++++--- 9 files changed, 84 insertions(+), 46 deletions(-)
Title: Numeric Routines for Optically Stimulated Luminescence Dating
Description: Package for optimizing regular numeric problems in optically stimulated luminescence
dating, such as: equivalent dose calculation, dose rate determination, growth curve fitting,
decay curve decomposition, statistical age model optimization, and statistical plot visualization.
Author: Jun Peng [aut, cre],
Bo Li [aut],
Jorge More [ctb],
Burton Garbow [ctb],
Kenneth Hillstrom [ctb],
John Burkardt [ctb],
Paul Gilbert [ctb],
Ravi Varadhan [ctb]
Maintainer: Jun Peng <pengjun10@mails.ucas.ac.cn>
Diff between numOSL versions 2.3 dated 2017-05-18 and 2.4 dated 2018-04-25
DESCRIPTION | 17 - MD5 | 52 ++-- R/analyseBINdata.R | 32 +- R/calED.R | 65 +++-- R/calSARED.R | 632 +++++++++++++++++++++++++++++++++----------------- R/calSGCED.R | 196 +++++++++++---- R/fastED.R | 26 +- R/fitGrowth.R | 64 +++-- R/lsNORM.R | 12 R/pickSARdata.R | 331 ++++++++++++++++++-------- R/psRadialPlot.R | 6 inst/CITATION | 13 - man/analyseBINdata.Rd | 2 man/as_analyseBIN.Rd | 4 man/calDA.Rd | 8 man/calED.Rd | 16 - man/calSARED.Rd | 23 + man/calSGCED.Rd | 14 - man/decomp.Rd | 12 man/fastED.Rd | 12 man/fitGrowth.Rd | 19 - man/lsNORM.Rd | 5 man/numOSL-package.Rd | 14 - man/pickBINdata.Rd | 14 - man/pickSARdata.Rd | 19 + man/psRadialPlot.Rd | 7 man/scaleSGCN.Rd | 11 27 files changed, 1096 insertions(+), 530 deletions(-)
Title: Monte Carlo Option Pricing Algorithms for Jump Diffusion Models
with Correlational Companies
Description: Black-Scholes model [Black (1973) <doi:10.1086/260062>] is important to calculate option prices in the stock market and a variety of improved models are studied. In this package, I propose methods in order to calculate both Black-Scholes model and Jump diffusion model [Kou (2002) <doi:10.1287/mnsc.48.8.1086.166>] by Monte Carlo methods. This package can be used for computational finance.
Author: Masashi Okada [aut, cre]
Maintainer: Masashi Okada <okadaalgorithm@gmail.com>
Diff between Jdmbs versions 1.1 dated 2018-01-16 and 1.2 dated 2018-04-25
DESCRIPTION | 12 +-- MD5 | 25 +++---- R/Jdmbs.R | 84 +++++++++++++++--------- R/JdmbsJump.R | 86 ++++++++++++++++--------- R/JdmbsNewJump.R | 93 ++++++++++++++++++--------- inst/doc/Jdmbs-vignette.R | 12 +-- inst/doc/Jdmbs-vignette.Rmd | 145 +++++++++++++++++++++---------------------- inst/doc/Jdmbs-vignette.pdf |binary man/jdm_bs.Rd | 34 +++++----- man/jdm_new_bs.Rd | 35 +++++----- man/normal_bs.Rd | 27 ++++---- vignettes/Jdmbs-vignette.Rmd | 145 +++++++++++++++++++++---------------------- vignettes/companies.png |binary vignettes/image.png |only 14 files changed, 391 insertions(+), 307 deletions(-)
Title: GC/LC-MS Data Analysis for Environmental Science
Description: Gas/Liquid Chromatography-Mass Spectrometer(GC/LC-MS) Data Analysis for Environmental Science. This package covered topics such as raw data process, molecular isotope ratio, matrix effects and Short-Chain Chlorinated Paraffins analysis etc. in environmental analysis.
Author: Miao YU [aut, cre] (<https://orcid.org/0000-0002-2804-6014>)
Maintainer: Miao YU <yufreecas@gmail.com>
Diff between enviGCMS versions 0.3.4 dated 2017-07-10 and 0.5.0 dated 2018-04-25
enviGCMS-0.3.4/enviGCMS/R/sva.R |only enviGCMS-0.3.4/enviGCMS/R/xcmsplus.R |only enviGCMS-0.3.4/enviGCMS/man/getmassdiff.Rd |only enviGCMS-0.5.0/enviGCMS/DESCRIPTION | 26 enviGCMS-0.5.0/enviGCMS/MD5 | 111 ++- enviGCMS-0.5.0/enviGCMS/NAMESPACE | 15 enviGCMS-0.5.0/enviGCMS/NEWS.md |only enviGCMS-0.5.0/enviGCMS/R/enviGCMS-deprecated.R |only enviGCMS-0.5.0/enviGCMS/R/general.R | 597 +++++++++++++++++---- enviGCMS-0.5.0/enviGCMS/R/io.R | 426 ++++++++++++++ enviGCMS-0.5.0/enviGCMS/R/mzrt.R |only enviGCMS-0.5.0/enviGCMS/R/peaks.R | 166 ++--- enviGCMS-0.5.0/enviGCMS/R/sccp.R |only enviGCMS-0.5.0/enviGCMS/R/shiny.R |only enviGCMS-0.5.0/enviGCMS/R/sysdata.rda |only enviGCMS-0.5.0/enviGCMS/build/vignette.rds |binary enviGCMS-0.5.0/enviGCMS/data |only enviGCMS-0.5.0/enviGCMS/inst/CITATION | 11 enviGCMS-0.5.0/enviGCMS/inst/doc/GCMSDA.Rmd | 62 +- enviGCMS-0.5.0/enviGCMS/inst/doc/GCMSDA.html | 84 +- enviGCMS-0.5.0/enviGCMS/inst/shinyapps |only enviGCMS-0.5.0/enviGCMS/man/Getisotopologues.Rd | 2 enviGCMS-0.5.0/enviGCMS/man/Mode.Rd |only enviGCMS-0.5.0/enviGCMS/man/enviGCMS-deprecated.Rd |only enviGCMS-0.5.0/enviGCMS/man/getQCraw.Rd | 2 enviGCMS-0.5.0/enviGCMS/man/getarea.Rd |only enviGCMS-0.5.0/enviGCMS/man/getareastd.Rd |only enviGCMS-0.5.0/enviGCMS/man/getbgremove.Rd | 2 enviGCMS-0.5.0/enviGCMS/man/getbiotechrep.Rd | 2 enviGCMS-0.5.0/enviGCMS/man/getdata.Rd | 13 enviGCMS-0.5.0/enviGCMS/man/getdata2.Rd |only enviGCMS-0.5.0/enviGCMS/man/getdoe.Rd |only enviGCMS-0.5.0/enviGCMS/man/getfeaturesanova.Rd | 16 enviGCMS-0.5.0/enviGCMS/man/getfeaturest.Rd | 21 enviGCMS-0.5.0/enviGCMS/man/getgrouprep.Rd | 2 enviGCMS-0.5.0/enviGCMS/man/getimputation.Rd |only enviGCMS-0.5.0/enviGCMS/man/getmassdefect.Rd | 5 enviGCMS-0.5.0/enviGCMS/man/getmd.Rd | 2 enviGCMS-0.5.0/enviGCMS/man/getmr.Rd |only enviGCMS-0.5.0/enviGCMS/man/getmzrt.Rd |only enviGCMS-0.5.0/enviGCMS/man/getmzrt2.Rd |only enviGCMS-0.5.0/enviGCMS/man/getmzrtcsv.Rd |only enviGCMS-0.5.0/enviGCMS/man/getsccp.Rd |only enviGCMS-0.5.0/enviGCMS/man/getsim.Rd | 2 enviGCMS-0.5.0/enviGCMS/man/gettechrep.Rd | 2 enviGCMS-0.5.0/enviGCMS/man/gettimegrouprep.Rd | 2 enviGCMS-0.5.0/enviGCMS/man/getupload.Rd | 11 enviGCMS-0.5.0/enviGCMS/man/getupload2.Rd |only enviGCMS-0.5.0/enviGCMS/man/gifmr.Rd |only enviGCMS-0.5.0/enviGCMS/man/plote.Rd | 4 enviGCMS-0.5.0/enviGCMS/man/plothm.Rd |only enviGCMS-0.5.0/enviGCMS/man/plotkms.Rd | 5 enviGCMS-0.5.0/enviGCMS/man/plotmr.Rd | 32 - enviGCMS-0.5.0/enviGCMS/man/plotmrc.Rd | 27 enviGCMS-0.5.0/enviGCMS/man/plotms.Rd | 2 enviGCMS-0.5.0/enviGCMS/man/plotmz.Rd | 6 enviGCMS-0.5.0/enviGCMS/man/plotpca.Rd | 20 enviGCMS-0.5.0/enviGCMS/man/plotrsd.Rd | 27 enviGCMS-0.5.0/enviGCMS/man/plottic.Rd | 6 enviGCMS-0.5.0/enviGCMS/man/runsccp.Rd |only enviGCMS-0.5.0/enviGCMS/man/sccp.Rd |only enviGCMS-0.5.0/enviGCMS/man/submd.Rd | 2 enviGCMS-0.5.0/enviGCMS/man/svabatch.Rd | 2 enviGCMS-0.5.0/enviGCMS/man/svacor.Rd | 2 enviGCMS-0.5.0/enviGCMS/man/svadata.Rd | 2 enviGCMS-0.5.0/enviGCMS/man/svapca.Rd | 2 enviGCMS-0.5.0/enviGCMS/man/svaplot.Rd | 2 enviGCMS-0.5.0/enviGCMS/man/svaupload.Rd | 2 enviGCMS-0.5.0/enviGCMS/tests |only enviGCMS-0.5.0/enviGCMS/vignettes/GCMSDA.Rmd | 62 +- 70 files changed, 1360 insertions(+), 427 deletions(-)
Title: The Official SolveBio API Client
Description: R language bindings for SolveBio's API.
SolveBio is a biomedical knowledge hub that enables life science
organizations to collect and harmonize the complex, disparate
"multi-omic" data essential for today's R&D and BI needs.
For more information, visit <https://www.solvebio.com>.
Author: David Caplan
Maintainer: David Caplan <dcaplan@solvebio.com>
Diff between solvebio versions 2.4.0 dated 2018-04-04 and 2.5.0 dated 2018-04-25
DESCRIPTION | 12 ++++---- MD5 | 29 ++++++++++++++------ NAMESPACE | 11 +++++++ NEWS.md | 10 +++++++ R/dataset.R | 48 ++++++++++++++++++++++++++++++++-- R/dataset_export.R | 27 +++++++++++++++++++ R/dataset_template.R |only R/object.R | 47 ++++++++++++++++++++++++++++++++- R/solvebio.R | 19 ++++++++----- R/task.R |only README.md | 2 - man/Dataset.activity.Rd |only man/DatasetExport.get_download_url.Rd |only man/DatasetTemplate.all.Rd |only man/DatasetTemplate.create.Rd |only man/DatasetTemplate.delete.Rd |only man/DatasetTemplate.retrieve.Rd |only man/DatasetTemplate.update.Rd |only man/Object.get_or_upload_file.Rd |only man/Task.all.Rd |only man/Task.follow.Rd |only man/Task.retrieve.Rd |only 22 files changed, 180 insertions(+), 25 deletions(-)
Title: Bootstrap Landing Home Pages for Shiny Applications
Description: Provides functions that wrap HTML Bootstrap
components code to enable the design and layout of informative landing home
pages for Shiny applications. This can lead to a better user experience for
the users and writing less HTML for the developer.
Author: Jasmine Dumas [aut, cre]
Maintainer: Jasmine Dumas <jasmine.dumas@gmail.com>
Diff between shinyLP versions 1.1.1 dated 2018-03-28 and 1.1.2 dated 2018-04-25
DESCRIPTION | 6 +++--- MD5 | 9 +++++---- NEWS.md | 5 +++++ R/thumbnail_label.R | 4 ++-- inst/shiny-examples/LPExample/rsconnect |only inst/shiny-examples/LPExample/ui.R | 7 ++----- 6 files changed, 17 insertions(+), 14 deletions(-)
Title: Using Dempster-Shafer Theory
Description: Using Dempster-Shafer Theory of Evidence, also called "Theory of Belief Functions". Basic probability assignments, or mass functions, can be defined on the subsets of a set of possible values. Two mass functions can be combined using Dempster's rule of combination. A mass function can be extended to a larger frame. Marginalization, i.e. reduction to a smaller frame can also be done. These features can be combined to analyze small belief networks and take into account situations where information cannot be satisfactorily described by probability distributions.
Author: Claude Boivin, Stat.ASSQ <webapp.cb@gmail.com>
Maintainer: Claude Boivin <webapp.cb@gmail.com>
Diff between dst versions 0.3 dated 2015-01-13 and 1.0.0 dated 2018-04-25
dst-0.3/dst/R/combmasses.R |only dst-0.3/dst/R/dempster.R |only dst-0.3/dst/R/dstCombListfacts.R |only dst-0.3/dst/R/dstCombListfacts2.R |only dst-0.3/dst/R/identRow.R |only dst-0.3/dst/R/initsing.R |only dst-0.3/dst/R/probCombListfacts.R |only dst-0.3/dst/R/rplau.R |only dst-0.3/dst/R/smppmexample.R |only dst-0.3/dst/R/tabresulSingl.R |only dst-0.3/dst/data |only dst-0.3/dst/man/combListfacts2.Rd |only dst-0.3/dst/man/combmasses.Rd |only dst-0.3/dst/man/dempster.Rd |only dst-0.3/dst/man/dst-package.Rd |only dst-0.3/dst/man/examples.Rd |only dst-0.3/dst/man/identRow.Rd |only dst-0.3/dst/man/initsing.Rd |only dst-0.3/dst/man/rplau.Rd |only dst-0.3/dst/man/smppmexample.Rd |only dst-0.3/dst/man/tabresults.Rd |only dst-1.0.0/dst/DESCRIPTION | 26 ++++---- dst-1.0.0/dst/MD5 | 114 +++++++++++++++++++++++--------------- dst-1.0.0/dst/NAMESPACE | 22 ++++--- dst-1.0.0/dst/NEWS |only dst-1.0.0/dst/R/addTobca.R |only dst-1.0.0/dst/R/bca.R | 96 +++++++++++++++++++++++++++++--- dst-1.0.0/dst/R/bcaRel.R |only dst-1.0.0/dst/R/belplau.R | 66 +++++++++++++++++++--- dst-1.0.0/dst/R/decode.R |only dst-1.0.0/dst/R/dotprod.R | 56 ++++++++++++++---- dst-1.0.0/dst/R/doubles.R | 35 +++++++++-- dst-1.0.0/dst/R/dsrwon.R | 109 +++++++++++++++++++++++++----------- dst-1.0.0/dst/R/dst.R |only dst-1.0.0/dst/R/elim.R |only dst-1.0.0/dst/R/encode.R |only dst-1.0.0/dst/R/extmin.R |only dst-1.0.0/dst/R/inters.R | 43 +++++++++++--- dst-1.0.0/dst/R/nameRows.R |only dst-1.0.0/dst/R/nzdsr.R | 89 +++++++++++++++++++++-------- dst-1.0.0/dst/R/plautrans.R | 53 +++++++++++++---- dst-1.0.0/dst/R/productSpace.R |only dst-1.0.0/dst/R/reduction.R |only dst-1.0.0/dst/R/shape.R |only dst-1.0.0/dst/R/tabresul.R | 89 ++++++++++++++++++++++------- dst-1.0.0/dst/README.md |only dst-1.0.0/dst/build |only dst-1.0.0/dst/inst |only dst-1.0.0/dst/man/addTobca.Rd |only dst-1.0.0/dst/man/bca.Rd | 75 ++++++++++++++++++------- dst-1.0.0/dst/man/bcaRel.Rd |only dst-1.0.0/dst/man/belplau.Rd | 63 +++++++++++++-------- dst-1.0.0/dst/man/decode.Rd |only dst-1.0.0/dst/man/dotprod.Rd | 77 +++++++++++-------------- dst-1.0.0/dst/man/doubles.Rd | 37 +++++------- dst-1.0.0/dst/man/dsrwon.Rd | 47 +++++++++------ dst-1.0.0/dst/man/dst.Rd |only dst-1.0.0/dst/man/elim.Rd |only dst-1.0.0/dst/man/encode.Rd |only dst-1.0.0/dst/man/extmin.Rd |only dst-1.0.0/dst/man/inters.Rd | 42 +++++++++----- dst-1.0.0/dst/man/nameRows.Rd |only dst-1.0.0/dst/man/nzdsr.Rd | 56 +++++++++--------- dst-1.0.0/dst/man/plautrans.Rd | 36 ++++++------ dst-1.0.0/dst/man/productSpace.Rd |only dst-1.0.0/dst/man/reduction.Rd |only dst-1.0.0/dst/man/shape.Rd |only dst-1.0.0/dst/man/tabresul.Rd |only dst-1.0.0/dst/tests |only dst-1.0.0/dst/vignettes |only 70 files changed, 841 insertions(+), 390 deletions(-)
Title: Manly Mixture Modeling and Model-Based Clustering
Description: The utility of this package includes finite mixture modeling and model-based clustering through Manly mixture models by Zhu and Melnykov (2016) <DOI:10.1016/j.csda.2016.01.015>. It also provides capabilities for forward and backward model selection procedures.
Author: Xuwen Zhu [aut, cre],
Volodymyr Melnykov [aut],
Michael Hutt [ctb, cph] (NM optimization in c),
Stephen Moshier [ctb, cph] (eigen calculations in c),
Rouben Rostamian [ctb, cph] (memory allocation in c)
Maintainer: Xuwen Zhu <xuwen.zhu@louisville.edu>
Diff between ManlyMix versions 0.1.13 dated 2018-04-25 and 0.1.14 dated 2018-04-25
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 4 ++++ demo/acidity.R | 24 ------------------------ 4 files changed, 11 insertions(+), 31 deletions(-)
Title: A Generalized Multiclass Support Vector Machine
Description: The GenSVM classifier is a generalized multiclass support vector
machine (SVM). This classifier aims to find decision boundaries that
separate the classes with as wide a margin as possible. In GenSVM, the
loss function is very flexible in the way that misclassifications are
penalized. This allows the user to tune the classifier to the dataset
at hand and potentially obtain higher classification accuracy than
alternative multiclass SVMs. Moreover, this flexibility means that
GenSVM has a number of other multiclass SVMs as special cases. One of
the other advantages of GenSVM is that it is trained in the primal
space, allowing the use of warm starts during optimization. This
means that for common tasks such as cross validation or repeated model
fitting, GenSVM can be trained very quickly. Based on: G.J.J. van den
Burg and P.J.F. Groenen (2018) <http://www.jmlr.org/papers/v17/14-526.html>.
Author: Gertjan van den Burg [aut, cre],
Patrick Groenen [ctb]
Maintainer: Gertjan van den Burg <gertjanvandenburg@gmail.com>
Diff between gensvm versions 0.1.0 dated 2018-04-19 and 0.1.1 dated 2018-04-25
gensvm-0.1.0/gensvm/src/gensvm/lib |only gensvm-0.1.1/gensvm/DESCRIPTION | 8 ++-- gensvm-0.1.1/gensvm/MD5 | 37 +++++++++++------------ gensvm-0.1.1/gensvm/R/coef.gensvm.grid.R | 2 - gensvm-0.1.1/gensvm/R/gensvm.grid.R | 4 +- gensvm-0.1.1/gensvm/R/gensvm.refit.R | 2 - gensvm-0.1.1/gensvm/R/plot.gensvm.grid.R | 2 - gensvm-0.1.1/gensvm/R/predict.gensvm.grid.R | 2 - gensvm-0.1.1/gensvm/R/print.gensvm.grid.R | 2 - gensvm-0.1.1/gensvm/README.md | 2 - gensvm-0.1.1/gensvm/man/coef.gensvm.grid.Rd | 2 - gensvm-0.1.1/gensvm/man/gensvm.grid.Rd | 4 +- gensvm-0.1.1/gensvm/man/gensvm.refit.Rd | 2 - gensvm-0.1.1/gensvm/man/plot.gensvm.grid.Rd | 2 - gensvm-0.1.1/gensvm/man/predict.gensvm.grid.Rd | 2 - gensvm-0.1.1/gensvm/man/print.gensvm.grid.Rd | 2 - gensvm-0.1.1/gensvm/src/Makevars | 15 +-------- gensvm-0.1.1/gensvm/src/gensvm/src/gensvm_init.c | 5 ++- gensvm-0.1.1/gensvm/src/gensvm/src/gensvm_rand.c | 33 +++++++++++++++++++- gensvm-0.1.1/gensvm/src/gensvm_wrapper.c | 3 + 20 files changed, 79 insertions(+), 52 deletions(-)
Title: Core Functions to Read and Fit 13c Time Series from Breath Tests
Description: Reads several formats of 13C data (IRIS/Wagner, BreathID) and CSV.
Creates artificial sample data for testing.
Fits Maes/Ghoos, Bluck-Coward self-correcting formula using 'nls', 'nlme'.
See Bluck L J C and Coward W A 2006 <doi:10.1088/0967-3334/27/3/006>.
Methods to
fit breath test curves with Bayesian Stan methods are refactored to
package 'breathteststan'. For a Shiny GUI, see
package 'dmenne/breathtestshiny' on github.
Author: Dieter Menne [aut, cre],
Menne Biomed Consulting Tuebingen [cph],
Benjamin Misselwitz [fnd],
Mark Fox [fnd],
Andreas Steingoetter [dtc],
University Hospital of Zurich, Dep. Gastroenterology [fnd, dtc]
Maintainer: Dieter Menne <dieter.menne@menne-biomed.de>
Diff between breathtestcore versions 0.4.0 dated 2017-10-13 and 0.4.1 dated 2018-04-25
DESCRIPTION | 8 MD5 | 56 +-- R/breathtest_parameters.R | 5 R/breathtestcore.R | 7 R/cleanup_data.R | 4 R/nlme_fit.R | 2 README.md | 21 - build/vignette.rds |binary data/usz_13c.rda |binary inst/doc/data_formats.Rmd | 11 inst/doc/data_formats.html | 506 +++++++++++++++++++++---------- inst/doc/methods_and_concepts.R | 4 inst/doc/methods_and_concepts.Rmd | 36 +- inst/doc/methods_and_concepts.html | 371 ++++++++++++++++++---- man/cleanup_data.Rd | 2 man/nlme_fit.Rd | 2 man/t50_bluck_coward.Rd | 2 man/t50_maes_ghoos_scintigraphy.Rd | 3 man/usz_13c.Rd | 5 man/usz_13c_d.Rd | 2 tests/testthat/test_cleanup_data.R | 1 tests/testthat/test_coef_by_group.R | 8 tests/testthat/test_coef_diff_by_group.R | 23 - tests/testthat/test_nlme_fit.R | 14 tests/testthat/test_read_iris_csv.R | 5 tests/testthat/test_usz_13c.R | 4 vignettes/breathtestcore.bib | 119 +++++-- vignettes/data_formats.Rmd | 11 vignettes/methods_and_concepts.Rmd | 36 +- 29 files changed, 887 insertions(+), 381 deletions(-)
More information about breathtestcore at CRAN
Permanent link
Title: Estimation using Sequential Offsetted Regression
Description: Estimation for longitudinal data following outcome dependent sampling using the sequential offsetted regression technique. Includes support for binary, count, and continuous data. The first regression is a logistic regression, which uses a known ratio (the probability of being sampled given that the subject/observation was referred divided by the probability of being sampled given that the subject/observation was no referred) as an offset to estimate the probability of being referred given outcome and covariates. The second regression uses this estimated probability to calculate the mean population response given covariates.
Author: Lee McDaniel [aut, cre],
Jonathan Schildcrout [aut]
Maintainer: Lee McDaniel <lmcda4@lsuhsc.edu>
Diff between SOR versions 0.23.0 dated 2016-12-09 and 0.23.1 dated 2018-04-25
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/common.R | 2 +- 3 files changed, 7 insertions(+), 7 deletions(-)
Title: Microbiome Regression-Based Kernel Association Test
Description: Test for overall association between microbiome composition data with a continuous or dichotomous outcome via phylogenetic kernels. The phenotype can be univariate continuous or binary phenotypes (Zhao et al. (2015) <doi:10.1016/j.ajhg.2015.04.003>), survival outcomes (Plantinga et al. (2017) <doi:10.1186/s40168-017-0239-9>), multivariate (Zhan et al. (2017) <doi:10.1002/gepi.22030>) and structured phenotypes (Zhan et al. (2017) <doi:10.1111/biom.12684>). For all these effect, the microbiome community effect was modeled nonparametrically through a kernel function, which can incorporate the phylogenetic tree information.
Author: Haotian Zheng [aut],
Xiang Zhan [aut],
Anna Plantinga [aut],
Michael Wu [aut],
Ni Zhao [aut, cre],
Jun Chen [aut]
Maintainer: Ni Zhao <nzhao10@jhu.edu>
Diff between MiRKAT versions 1.0 dated 2017-07-25 and 1.0.1 dated 2018-04-25
DESCRIPTION | 20 +++++++++++++------- MD5 | 6 +++--- R/helperFunction.R | 6 +++--- inst/doc/MiRKAT.pdf |binary 4 files changed, 19 insertions(+), 13 deletions(-)
Title: Semiparametric Competing Risks Regression under Interval
Censoring
Description: Semiparametric regression models for the cumulative incidence function with interval-censored competing risks data as described in Bakoyannis, Yu, & Yiannoutsos (2017) <doi:10.1002/sim.7350>. The main function fits the proportional subdistribution hazards model (Fine-Gray model), the proportional odds model, and other models that belong to the class of semiparametric generalized odds rate transformation models.
Author: Giorgos Bakoyannis <gbakogia@iu.edu>, Jun Park <jp84@iu.edu>
Maintainer: Jun Park <jp84@iu.edu>
Diff between intccr versions 1.0.0 dated 2018-03-30 and 1.0.1 dated 2018-04-25
intccr-1.0.0/intccr/data/longdat.rda |only intccr-1.0.0/intccr/data/simdat.rda |only intccr-1.0.0/intccr/man/longdat.Rd |only intccr-1.0.0/intccr/man/simdat.Rd |only intccr-1.0.1/intccr/DESCRIPTION | 10 ++-- intccr-1.0.1/intccr/MD5 | 46 +++++++++++----------- intccr-1.0.1/intccr/R/bssmle.R | 11 +++-- intccr-1.0.1/intccr/R/bssmle_se.R | 12 ++--- intccr-1.0.1/intccr/R/ciregic.R | 50 +++++++++++++++--------- intccr-1.0.1/intccr/R/dataprep.R | 12 ++--- intccr-1.0.1/intccr/R/longdat.R | 10 ++-- intccr-1.0.1/intccr/R/naive_b.R | 9 +--- intccr-1.0.1/intccr/R/simdat.R | 8 +-- intccr-1.0.1/intccr/R/surv2.R | 4 - intccr-1.0.1/intccr/data/longdata.rda |only intccr-1.0.1/intccr/data/simdata.rda |only intccr-1.0.1/intccr/man/Surv2.Rd | 4 - intccr-1.0.1/intccr/man/bssmle.Rd | 11 +++-- intccr-1.0.1/intccr/man/bssmle_se.Rd | 12 ++--- intccr-1.0.1/intccr/man/ciregic.Rd | 26 ++++++++---- intccr-1.0.1/intccr/man/dataprep.Rd | 12 ++--- intccr-1.0.1/intccr/man/longdata.Rd |only intccr-1.0.1/intccr/man/naive_b.Rd | 9 +--- intccr-1.0.1/intccr/man/predict.ciregic.Rd | 6 +- intccr-1.0.1/intccr/man/simdata.Rd |only intccr-1.0.1/intccr/man/summary.ciregic.Rd | 6 +- intccr-1.0.1/intccr/man/vcov.ciregic.Rd | 6 +- intccr-1.0.1/intccr/man/vcov.summary.ciregic.Rd | 6 +- 28 files changed, 153 insertions(+), 117 deletions(-)
Title: Predicts Oomycete Effectors
Description: Predicts cytoplasmic effector proteins using genomic data by searching for motifs of interest using regular expression searches and hidden Markov models (HMM) based in Haas et al. (2009) <doi:10.1038/nature08358>.
Author: Javier Tabima [aut, cre],
Niklaus J. Grunwald [ths]
Maintainer: Javier Tabima <tabimaj@oregonstate.edu>
Diff between effectR versions 1.0.0 dated 2018-01-17 and 1.0.1 dated 2018-04-25
DESCRIPTION | 6 - MD5 | 24 ++-- NEWS.md |only R/effector.summary.R | 8 + R/hmm.search.R | 105 ++++++++++++----- R/regex.search.R | 12 +- README.md | 222 +++++++++++++++++++++++++++++++++++++- build/vignette.rds |binary inst/doc/effectR.html | 4 inst/extdata/Alin_infestans.fasta |only inst/shiny/server.R | 8 + inst/shiny/ui.R | 8 - man/hmm.search.Rd | 33 ++++- man/regex.search.Rd | 12 +- 14 files changed, 375 insertions(+), 67 deletions(-)
Title: Bayesian Analysis of Heterogeneous Treatment Effect
Description: It is vital to assess the heterogeneity of treatment effects
(HTE) when making health care decisions for an individual patient or a group
of patients. Nevertheless, it remains challenging to evaluate HTE based
on information collected from clinical studies that are often designed and
conducted to evaluate the efficacy of a treatment for the overall population.
The Bayesian framework offers a principled and flexible approach to estimate
and compare treatment effects across subgroups of patients defined by their
characteristics. This package allows users to explore a wide range of Bayesian
HTE analysis models, and produce posterior inferences about HTE.
Author: Chenguang Wang [aut, cre],
Ravi Varadhan [aut],
Trustees of Columbia University [cph] (tools/make_cpp.R, R/stanmodels.R)
Maintainer: Chenguang Wang <cwang68@jhmi.edu>
Diff between beanz versions 2.1 dated 2017-05-07 and 2.2 dated 2018-04-25
beanz-2.1/beanz/cleanup |only beanz-2.1/beanz/cleanup.win |only beanz-2.1/beanz/exec |only beanz-2.1/beanz/src/Modules.cpp |only beanz-2.1/beanz/src/beanz_init.c |only beanz-2.1/beanz/src/include |only beanz-2.1/beanz/tools/make_cpp.R |only beanz-2.2/beanz/DESCRIPTION | 22 +- beanz-2.2/beanz/MD5 | 67 +++--- beanz-2.2/beanz/NEWS.md | 5 beanz-2.2/beanz/R/beanz_present.R | 34 ++- beanz-2.2/beanz/R/beanz_stan.R | 14 - beanz-2.2/beanz/R/stanmodels.R | 44 ++-- beanz-2.2/beanz/R/zzz.R | 11 - beanz-2.2/beanz/build/vignette.rds |binary beanz-2.2/beanz/inst/doc/beanz_vignettes.html | 271 ++++++++++++-------------- beanz-2.2/beanz/inst/include |only beanz-2.2/beanz/man/beanz-package.Rd | 4 beanz-2.2/beanz/man/bzCallStan.Rd | 1 beanz-2.2/beanz/man/bzComp.Rd | 15 - beanz-2.2/beanz/man/bzGailSimon.Rd | 1 beanz-2.2/beanz/man/bzGetSubgrp.Rd | 1 beanz-2.2/beanz/man/bzGetSubgrpRaw.Rd | 1 beanz-2.2/beanz/man/bzPredSubgrp.Rd | 1 beanz-2.2/beanz/man/bzRptTbl.Rd | 1 beanz-2.2/beanz/man/bzShiny.Rd | 1 beanz-2.2/beanz/man/bzSummary.Rd | 6 beanz-2.2/beanz/man/solvd.sub.Rd | 1 beanz-2.2/beanz/src/Makevars | 19 + beanz-2.2/beanz/src/Makevars.win |only beanz-2.2/beanz/src/init.cpp |only beanz-2.2/beanz/src/stan_files |only beanz-2.2/beanz/tests/testthat/test_present.R | 9 beanz-2.2/beanz/tools/make_cc.R |only 34 files changed, 271 insertions(+), 258 deletions(-)
Title: Straightforward 'BibTeX' and 'BibLaTeX' Bibliography Management
Description: Provides tools for importing and working with bibliographic
references. It greatly enhances the 'bibentry' class by providing a class
'BibEntry' which stores 'BibTeX' and 'BibLaTeX' references, supports 'UTF-8'
encoding, and can be easily searched by any field, by date ranges, and by
various formats for name lists (author by last names, translator by full names,
etc.). Entries can be updated, combined, sorted, printed in a number of styles,
and exported. 'BibTeX' and 'BibLaTeX' '.bib' files can be read into 'R' and
converted to 'BibEntry' objects. Interfaces to 'NCBI Entrez', 'CrossRef', and
'Zotero' are provided for importing references and references can be created
from locally stored 'PDF' files using 'Poppler'. Includes functions for citing
and generating a bibliography with hyperlinks for documents prepared with
'RMarkdown' or 'RHTML'.
Author: Mathew W. McLean [aut, cre]
Maintainer: Mathew W. McLean <mathew.w.mclean@gmail.com>
Diff between RefManageR versions 0.14.20 dated 2017-08-17 and 1.2.0 dated 2018-04-25
RefManageR-0.14.20/RefManageR/.Rinstignore |only RefManageR-0.14.20/RefManageR/inst/doc/120_status.svg |only RefManageR-0.14.20/RefManageR/inst/doc/ropensci_footer.png |only RefManageR-0.14.20/RefManageR/tests/testthat/file37cdf8d7193.bib |only RefManageR-1.2.0/RefManageR/DESCRIPTION | 8 RefManageR-1.2.0/RefManageR/MD5 | 100 ++++------ RefManageR-1.2.0/RefManageR/R/04InternalFunctions.R | 55 +++-- RefManageR-1.2.0/RefManageR/R/BibEntryAddOp.R | 26 ++ RefManageR-1.2.0/RefManageR/R/BibEntryAssignOp.R | 2 RefManageR-1.2.0/RefManageR/R/BibEntryReplaceOp.R | 2 RefManageR-1.2.0/RefManageR/R/CommonFormatFuns.R | 14 - RefManageR-1.2.0/RefManageR/R/GetBibEntryWithDOI.R | 8 RefManageR-1.2.0/RefManageR/R/GetDOIs.R | 10 - RefManageR-1.2.0/RefManageR/R/ReadBib.R | 16 - RefManageR-1.2.0/RefManageR/R/ReadCrossRef.R | 36 +-- RefManageR-1.2.0/RefManageR/R/ReadGS.R | 4 RefManageR-1.2.0/RefManageR/R/ReadPDFs.R | 10 - RefManageR-1.2.0/RefManageR/R/ReadPDFsSupport.R | 16 - RefManageR-1.2.0/RefManageR/R/ReadPubMed.R | 10 - RefManageR-1.2.0/RefManageR/R/ReadZotero.R | 8 RefManageR-1.2.0/RefManageR/R/WriteBib.R | 21 +- RefManageR-1.2.0/RefManageR/R/format.R | 20 +- RefManageR-1.2.0/RefManageR/R/open.BibEntry.R | 6 RefManageR-1.2.0/RefManageR/R/rmdCite.R | 26 +- RefManageR-1.2.0/RefManageR/README.md | 7 RefManageR-1.2.0/RefManageR/build/vignette.rds |binary RefManageR-1.2.0/RefManageR/inst/Bib/biblatexExamples.bib | 4 RefManageR-1.2.0/RefManageR/inst/Bib/test.bib | 48 ++-- RefManageR-1.2.0/RefManageR/inst/CITATION | 2 RefManageR-1.2.0/RefManageR/inst/NEWS.md | 61 ++++++ RefManageR-1.2.0/RefManageR/inst/doc/TestAlphabetic.html | 18 - RefManageR-1.2.0/RefManageR/inst/doc/TestHtml.html | 14 - RefManageR-1.2.0/RefManageR/inst/doc/TestRmd.html | 18 - RefManageR-1.2.0/RefManageR/inst/doc/manual.pdf |binary RefManageR-1.2.0/RefManageR/man/Cite.Rd | 23 +- RefManageR-1.2.0/RefManageR/man/GetBibEntryWithDOI.Rd | 6 RefManageR-1.2.0/RefManageR/man/GetDOIs.Rd | 4 RefManageR-1.2.0/RefManageR/man/ReadCrossRef.Rd | 4 RefManageR-1.2.0/RefManageR/man/ReadGS.Rd | 2 RefManageR-1.2.0/RefManageR/man/ReadPDFs.Rd | 6 RefManageR-1.2.0/RefManageR/man/ReadZotero.Rd | 2 RefManageR-1.2.0/RefManageR/man/WriteBib.Rd | 4 RefManageR-1.2.0/RefManageR/man/cash-set-.BibEntry.Rd | 2 RefManageR-1.2.0/RefManageR/man/macros/macros.Rd | 1 RefManageR-1.2.0/RefManageR/man/merge.BibEntry.Rd | 8 RefManageR-1.2.0/RefManageR/man/subset-.BibEntry.Rd | 2 RefManageR-1.2.0/RefManageR/tests/testthat/file2669698588fe.bib |only RefManageR-1.2.0/RefManageR/tests/testthat/test-GS.R | 8 RefManageR-1.2.0/RefManageR/tests/testthat/test-cites.R | 32 ++- RefManageR-1.2.0/RefManageR/tests/testthat/test-crossref.R | 18 - RefManageR-1.2.0/RefManageR/tests/testthat/test-methods.R | 21 ++ RefManageR-1.2.0/RefManageR/tests/testthat/test-pubmed.R | 8 RefManageR-1.2.0/RefManageR/tests/testthat/test-readPDF.R | 8 RefManageR-1.2.0/RefManageR/tests/testthat/test-zotero.R | 6 54 files changed, 450 insertions(+), 285 deletions(-)
Title: R Interface to 'ONNX'
Description: R Interface to 'ONNX' - Open Neural Network Exchange <https://onnx.ai/>.
'ONNX' provides an open source format for machine learning models.
It defines an extensible computation graph model, as well as definitions
of built-in operators and standard data types.
Author: Yuan Tang [aut, cre] (<https://orcid.org/0000-0001-5243-233X>),
ONNX Authors [aut, cph],
Facebook, Inc. [cph],
Microsoft Corporation [cph]
Maintainer: Yuan Tang <terrytangyuan@gmail.com>
Diff between onnx versions 0.0.1 dated 2018-03-06 and 0.0.2 dated 2018-04-25
onnx-0.0.1/onnx/NEWS |only onnx-0.0.2/onnx/DESCRIPTION | 17 ++--- onnx-0.0.2/onnx/MD5 | 17 ++++- onnx-0.0.2/onnx/NEWS.md |only onnx-0.0.2/onnx/README.md | 141 -------------------------------------------- onnx-0.0.2/onnx/build |only onnx-0.0.2/onnx/inst |only onnx-0.0.2/onnx/vignettes |only 8 files changed, 25 insertions(+), 150 deletions(-)
Title: Meta-Analysis of Significance Values
Description: The canonical way to perform meta-analysis involves using effect sizes.
When they are not available this package provides a number of methods for
meta-analysis of significance values including the methods of Edgington, Fisher,
Stouffer, Tippett, and Wilkinson; a number of data-sets to replicate published results;
and a routine for graphical display.
Author: Michael Dewey
Maintainer: Michael Dewey <lists@dewey.myzen.co.uk>
Diff between metap versions 0.8 dated 2017-01-22 and 0.9 dated 2018-04-25
DESCRIPTION | 8 +-- MD5 | 22 +++++---- NAMESPACE | 3 + NEWS | 5 ++ R/allmetap.R |only R/sumz.R | 6 +- build/vignette.rds |binary inst/doc/metap.R | 45 +++++++------------ inst/doc/metap.Rnw | 119 ++++++++++++++++++++++++++++++---------------------- inst/doc/metap.pdf |binary man/allmetap.Rd |only vignettes/metap.Rnw | 119 ++++++++++++++++++++++++++++++---------------------- vignettes/metap.bib | 10 ++++ 13 files changed, 196 insertions(+), 141 deletions(-)
Title: Bayesian Structure Learning in Graphical Models using
Birth-Death MCMC
Description: Provides statistical tools for Bayesian structure learning in undirected graphical models for continuous, discrete, and mixed data. The package is implemented the recent improvements in the Bayesian graphical models literature, including Mohammadi and Wit (2015) <https://doi:10.1214/14-BA889> and Mohammadi et al. (2017) <https://doi:10.1111/rssc.12171>. To speed up the computations, the BDMCMC sampling algorithms are implemented in parallel using OpenMP in C++.
Author: Reza Mohammadi <https://orcid.org/0000-0001-9538-0648> and Ernst Wit <https://orcid.org/0000-0002-3671-9610>
Maintainer: Reza Mohammadi <a.mohammadi@uva.nl>
Diff between BDgraph versions 2.46 dated 2018-04-17 and 2.47 dated 2018-04-25
DESCRIPTION | 14 +- MD5 | 99 ++++++++------- NAMESPACE | 5 NEWS | 3 R/bdgraph.R | 71 ++++++----- R/bdgraph.mpl.R | 23 ++- R/bdgraph.npn.R | 26 +++- R/bdgraph.sim.R | 211 +++++++-------------------------- R/bdgraph.ts.R | 63 +++++----- R/compare.R | 45 +++++-- R/gnorm.R | 25 +++- R/graph.sim.R |only R/hill_climb_algorithm.R | 45 ++++--- R/hill_climb_binary.R | 45 ++++--- R/pgraph.R | 26 +++- R/plinks.R | 101 +++++++++------- R/plotcoda.R | 21 ++- R/plotroc.R | 50 ++++++-- R/rgcwish.R | 53 +++++--- R/rgwish.R | 40 ++++-- R/rmvnorm.R | 17 ++ R/rwish.R | 26 +++- R/select.R | 48 +++++-- R/traceplot.R | 17 ++ R/transfer.R | 29 ++-- configure | 16 +- man/BDgraph-package.Rd | 9 - man/bdgraph.Rd | 286 +++++++++++++++++++++++----------------------- man/bdgraph.sim.Rd | 188 +++++++++++++++--------------- man/bdgraph.ts.Rd | 48 ++----- man/graph.sim.Rd |only man/plot.bdgraph.Rd | 108 ++++++++--------- man/plot.graph.Rd |only man/plot.sim.Rd | 90 +++++++------- man/rgcwish.Rd | 5 man/rgwish.Rd | 126 ++++++++++---------- man/rwish.Rd | 8 - src/bd_for_ts.cpp | 21 +-- src/copula.cpp | 19 +-- src/copula.h | 19 +-- src/gcgm_DMH.cpp | 20 +-- src/gcgm_bd.cpp | 20 +-- src/ggm_DMH.cpp | 20 +-- src/ggm_bd.cpp | 20 +-- src/ggm_mpl_bd.cpp | 20 +-- src/gm_mpl_Hill_Climb.cpp | 20 +-- src/gm_mpl_bd_dis.cpp | 24 +-- src/gm_rj.cpp | 20 +-- src/matrix.cpp | 19 +-- src/matrix.h | 20 +-- src/rgwish.cpp | 19 +-- src/rgwish.h | 19 +-- 52 files changed, 1213 insertions(+), 1074 deletions(-)
Title: Mittag-Leffler Family of Distributions
Description: Implements the Mittag-Leffler function, distribution,
random variate generation, and estimation. Based on the Laplace-Inversion
algorithm by Garrappa, R. (2015) <doi:10.1137/140971191>.
Author: Gurtek Gill [aut],
Peter Straka [aut, cre]
Maintainer: Peter Straka <p.straka@unsw.edu.au>
Diff between MittagLeffleR versions 0.2.0 dated 2017-11-07 and 0.3.0 dated 2018-04-25
MittagLeffleR-0.2.0/MittagLeffleR/inst/extdata |only MittagLeffleR-0.3.0/MittagLeffleR/DESCRIPTION | 22 MittagLeffleR-0.3.0/MittagLeffleR/MD5 | 36 MittagLeffleR-0.3.0/MittagLeffleR/NAMESPACE | 1 MittagLeffleR-0.3.0/MittagLeffleR/NEWS.md |only MittagLeffleR-0.3.0/MittagLeffleR/R/MLMLE.R |only MittagLeffleR-0.3.0/MittagLeffleR/R/MittagLeffleR.R | 40 MittagLeffleR-0.3.0/MittagLeffleR/R/MittagLefflerDist.R | 22 MittagLeffleR-0.3.0/MittagLeffleR/R/logMoments.R | 15 MittagLeffleR-0.3.0/MittagLeffleR/README.md | 86 +- MittagLeffleR-0.3.0/MittagLeffleR/build/vignette.rds |binary MittagLeffleR-0.3.0/MittagLeffleR/inst/CITATION | 2 MittagLeffleR-0.3.0/MittagLeffleR/inst/doc/MLdist.html | 408 +++++++--- MittagLeffleR-0.3.0/MittagLeffleR/inst/doc/parametrisation.Rmd | 2 MittagLeffleR-0.3.0/MittagLeffleR/inst/doc/parametrisation.pdf |binary MittagLeffleR-0.3.0/MittagLeffleR/inst/doc/probsNquantiles.pdf |binary MittagLeffleR-0.3.0/MittagLeffleR/man/MittagLeffleR-package.Rd | 53 - MittagLeffleR-0.3.0/MittagLeffleR/man/MittagLeffleR.Rd | 21 MittagLeffleR-0.3.0/MittagLeffleR/man/logMomentEstimator.Rd | 11 MittagLeffleR-0.3.0/MittagLeffleR/man/mlmle.Rd |only MittagLeffleR-0.3.0/MittagLeffleR/vignettes/parametrisation.Rmd | 2 21 files changed, 488 insertions(+), 233 deletions(-)
Title: R Tool for Factoring Big Integers
Description: Features the multiple polynomial quadratic sieve algorithm
for factoring large integers and a vectorized factoring function that
returns the complete factorization of an integer. Utilizes the C
library GMP (GNU Multiple Precision Arithmetic) and classes created
by Antoine Lucas et al. found in the 'gmp' package.
Author: Joseph Wood
Maintainer: Joseph Wood <jwood000@gmail.com>
Diff between bigIntegerAlgos versions 0.1.0 dated 2018-04-11 and 0.1.1 dated 2018-04-25
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS | 6 ++++++ README.md | 3 +++ man/divisorsBig.Rd | 2 +- src/Makevars.win | 1 + src/factorization.cc | 7 ++++--- src/quadraticsieve.cc | 5 +++-- tests/testthat/testQuadraticSieve.R | 6 +++--- 9 files changed, 32 insertions(+), 20 deletions(-)
More information about bigIntegerAlgos at CRAN
Permanent link
Title: Nowcast Analysis and Create Real-Time Data Basis
Description: Methods and tools to estimate 'forecasts' of Brazilian macroeconomic variables in the near future or the recent past, i.e. 'nowcast'. It allows: extract information in real time, creating a real time data base; estimate relationship between macroeconomic variables via dynamic factors; forecast time series in previous periods of reference; forecast time series in the current period of reference (nowcasting); recreate a data base simulating the information available in the past for evaluating forecasting models accuracy (pseudo real-time data base); access information available in a specific date in the past (real-time data base), for some variables.
Author: Daiane Marcolino de Mattos [aut, cre],
Guilherme Branco Gomes [aut],
Pedro Costa Ferreira [aut]
Maintainer: Daiane Marcolino de Mattos <daiane.mattos@fgv.br>
Diff between nowcasting versions 0.1.2 dated 2018-03-02 and 0.1.3 dated 2018-04-25
DESCRIPTION | 10 - MD5 | 52 +++--- R/BRGDP.R | 2 R/Bpanel.R | 55 +++---- R/PRTDB.R | 12 - R/RTDB.R | 404 ++++++++++++++++++++++++++-------------------------- R/USGDP.R | 4 R/USGDPshort.R |only R/add_legend.R |only R/method_2s.R | 10 - R/method_EM.r | 11 + R/month2qtr.R | 7 R/nowcast.R | 156 ++++++++++++-------- R/nowcast.plot.R | 93 +++++++---- R/nowcasting.R | 10 - R/qtr2month.r | 14 - data/USGDP.rda |binary data/USGDPshort.rda |only man/BRGDP.Rd | 2 man/Bpanel.Rd | 47 ++---- man/PRTDB.Rd | 10 - man/RTDB.Rd | 16 +- man/USGDP.Rd | 4 man/USGDPshort.Rd |only man/month2qtr.Rd | 9 - man/nowcast.Rd | 79 +++++----- man/nowcast.plot.Rd | 39 ++--- man/nowcasting.Rd | 10 - man/qtr2month.Rd | 14 - 29 files changed, 585 insertions(+), 485 deletions(-)
Title: Functions and Datasets for the Book by Keon-Woong Moon
Description: Several analysis-related functions for the book entitled "R
statistics and graph for medical articles" (written in Korean), version 1,
by Keon-Woong Moon with Korean demographic data with several plot
functions.
Author: Keon-Woong Moon [aut, cre]
Maintainer: Keon-Woong Moon <cardiomoon@gmail.com>
Diff between moonBook versions 0.1.3 dated 2015-02-14 and 0.1.8 dated 2018-04-25
moonBook-0.1.3/moonBook/vignettes/figure |only moonBook-0.1.8/moonBook/DESCRIPTION | 11 moonBook-0.1.8/moonBook/MD5 | 129 ++++---- moonBook-0.1.8/moonBook/NAMESPACE | 61 +++ moonBook-0.1.8/moonBook/NEWS | 32 ++ moonBook-0.1.8/moonBook/R/ORplot.R | 16 - moonBook-0.1.8/moonBook/R/densityplot.R | 27 + moonBook-0.1.8/moonBook/R/mycph.R | 61 ++- moonBook-0.1.8/moonBook/R/mycsv.R | 6 moonBook-0.1.8/moonBook/R/myhtml.R | 8 moonBook-0.1.8/moonBook/R/mylatex.R | 14 moonBook-0.1.8/moonBook/R/mytable.R | 293 +++++++++++++------ moonBook-0.1.8/moonBook/README.md | 186 ++++++------ moonBook-0.1.8/moonBook/build/vignette.rds |binary moonBook-0.1.8/moonBook/inst/CITATION |only moonBook-0.1.8/moonBook/inst/doc/moonBook.R | 30 - moonBook-0.1.8/moonBook/inst/doc/moonBook.Rmd | 8 moonBook-0.1.8/moonBook/inst/doc/moonBook.html | 210 +++++++------ moonBook-0.1.8/moonBook/inst/extdata |only moonBook-0.1.8/moonBook/man/HRplot.Rd | 4 moonBook-0.1.8/moonBook/man/ORplot.Rd | 3 moonBook-0.1.8/moonBook/man/ORplot.sub.Rd | 5 moonBook-0.1.8/moonBook/man/acs.Rd | 5 moonBook-0.1.8/moonBook/man/cbind.mytable.Rd | 7 moonBook-0.1.8/moonBook/man/centerprint.Rd | 5 moonBook-0.1.8/moonBook/man/densityplot.Rd | 5 moonBook-0.1.8/moonBook/man/extractHR.Rd | 5 moonBook-0.1.8/moonBook/man/extractOR.Rd | 9 moonBook-0.1.8/moonBook/man/figures |only moonBook-0.1.8/moonBook/man/my.chisq.test.Rd | 3 moonBook-0.1.8/moonBook/man/my.t.test.Rd | 3 moonBook-0.1.8/moonBook/man/mycph.Rd | 5 moonBook-0.1.8/moonBook/man/mycsv.Rd | 3 moonBook-0.1.8/moonBook/man/mycsv.cbind.mytable.Rd | 3 moonBook-0.1.8/moonBook/man/mycsv.mytable.Rd | 3 moonBook-0.1.8/moonBook/man/myhtml.Rd | 8 moonBook-0.1.8/moonBook/man/myhtmlHead.Rd | 3 moonBook-0.1.8/moonBook/man/mylatex.Rd | 12 moonBook-0.1.8/moonBook/man/mytable.Rd | 16 - moonBook-0.1.8/moonBook/man/mytable.sub.Rd | 7 moonBook-0.1.8/moonBook/man/mytable2.Rd | 17 - moonBook-0.1.8/moonBook/man/mytable2df.Rd | 3 moonBook-0.1.8/moonBook/man/mytable2html.Rd | 3 moonBook-0.1.8/moonBook/man/num_summary.Rd | 3 moonBook-0.1.8/moonBook/man/obj2linecount.Rd | 3 moonBook-0.1.8/moonBook/man/p2sig.Rd | 3 moonBook-0.1.8/moonBook/man/print.cbind.mytable.Rd | 3 moonBook-0.1.8/moonBook/man/print.mytable.Rd | 3 moonBook-0.1.8/moonBook/man/printmytable2.Rd | 3 moonBook-0.1.8/moonBook/man/r.Rd | 3 moonBook-0.1.8/moonBook/man/radial.Rd | 5 moonBook-0.1.8/moonBook/man/rank2group.Rd | 8 moonBook-0.1.8/moonBook/man/reprint.Rd | 5 moonBook-0.1.8/moonBook/man/space.Rd | 3 moonBook-0.1.8/moonBook/man/summary.cbind.mytable.Rd | 3 moonBook-0.1.8/moonBook/man/summary.mytable.Rd | 4 moonBook-0.1.8/moonBook/man/validColname.Rd | 12 moonBook-0.1.8/moonBook/vignettes/moonBook.Rmd | 8 58 files changed, 785 insertions(+), 513 deletions(-)
Title: Breast Cancer Risk Assessment
Description: Functions provide risk projections of invasive breast cancer based on Gail model according to National Cancer Institute's Breast Cancer Risk Assessment Tool algorithm for specified race/ethnic groups and age intervals.
Author: Fanni Zhang
Maintainer: Fanni Zhang <zhangf@imsweb.com>
Diff between BCRA versions 1.0 dated 2015-04-29 and 2.0 dated 2018-04-25
DESCRIPTION | 8 - MD5 | 58 +++---- NAMESPACE | 3 R/absolute.risk.R | 373 ++++++++++++++++++++++++------------------------- R/check.summary.R | 12 - R/error.table.R | 12 - R/error.table.all.R | 12 - R/list.constants.R | 46 +++--- R/recode.check.R | 260 ++++++++++++++++++---------------- R/relative.risk.R | 17 +- R/risk.summary.R | 23 +-- data/BrCa_1_AR.rda |binary data/BrCa_beta.rda |binary data/BrCa_lambda1.rda |binary data/BrCa_lambda2.rda |binary data/exampledata.rda |binary man/BCRA-package.Rd | 36 ++-- man/BrCa_1_AR.Rd | 43 ++--- man/BrCa_beta.Rd | 43 ++--- man/BrCa_lambda1.Rd | 56 +++---- man/BrCa_lambda2.Rd | 54 +++---- man/absolute.risk.Rd | 22 +- man/check.summary.Rd | 14 - man/error.table.Rd | 4 man/error.table.all.Rd | 5 man/exampledata.Rd | 10 - man/list.constants.Rd | 2 man/recode.check.Rd | 30 ++- man/relative.risk.Rd | 4 man/risk.summary.Rd | 9 - 30 files changed, 596 insertions(+), 560 deletions(-)
Title: Implementation of Support Vector Machines Plus (SVM+)
Description: Implementation of Support Vector Machines Plus (SVM+) for classification problems. See (Vladimir et. al, 2009, <doi:10.1016/j.neunet.2009.06.042>) for theoretical details and see (Li et. al, 2016, <https://github.com/okbalefthanded/svmplus_matlab>) for implementation details in 'MATLAB'.
Author: Niharika Gauraha and Ola Spjuth
Maintainer: Niharika Gauraha <niharika.gauraha@farmbio.uu.se>
Diff between svmplus versions 1.0.0 dated 2018-04-23 and 1.0.1 dated 2018-04-25
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- R/svmPlus.R | 8 ++++---- R/utils.R | 2 +- man/SVMP.Rd | 34 +++++++++++++++++++++++++++++++--- 5 files changed, 44 insertions(+), 16 deletions(-)
Title: Simple Features for R
Description: Support for simple features, a standardized way to encode spatial vector data. Binds
to 'GDAL' for reading and writing data, to 'GEOS' for geometrical operations, and to 'PROJ' for projection
conversions and datum transformations.
Author: Edzer Pebesma [aut, cre] (<https://orcid.org/0000-0001-8049-7069>),
Roger Bivand [ctb] (<https://orcid.org/0000-0003-2392-6140>),
Etienne Racine [ctb],
Michael Sumner [ctb],
Ian Cook [ctb],
Tim Keitt [ctb],
Robin Lovelace [ctb],
Hadley Wickham [ctb],
Jeroen Ooms [ctb] (<https://orcid.org/0000-0002-4035-0289>),
Kirill Müller [ctb]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between sf versions 0.6-1 dated 2018-03-22 and 0.6-2 dated 2018-04-25
sf-0.6-1/sf/man/dplyr.Rd |only sf-0.6-1/sf/man/ops.Rd |only sf-0.6-1/sf/tests/testthat/test_postgis.R |only sf-0.6-2/sf/DESCRIPTION | 33 - sf-0.6-2/sf/MD5 | 162 ++++--- sf-0.6-2/sf/NAMESPACE | 39 - sf-0.6-2/sf/NEWS.md | 22 + sf-0.6-2/sf/R/RcppExports.R | 6 sf-0.6-2/sf/R/aggregate.R | 4 sf-0.6-2/sf/R/arith.R | 79 ++- sf-0.6-2/sf/R/bbox.R | 10 sf-0.6-2/sf/R/crop.R |only sf-0.6-2/sf/R/crs.R | 17 sf-0.6-2/sf/R/db.R | 369 +++++++++++------- sf-0.6-2/sf/R/deprecated.R |only sf-0.6-2/sf/R/geom.R | 13 sf-0.6-2/sf/R/init.R | 1 sf-0.6-2/sf/R/jitter.R | 7 sf-0.6-2/sf/R/join.R | 25 - sf-0.6-2/sf/R/plot.R | 16 sf-0.6-2/sf/R/read.R | 138 ++++-- sf-0.6-2/sf/R/sample.R | 6 sf-0.6-2/sf/R/sf.R | 40 + sf-0.6-2/sf/R/sfc.R | 17 sf-0.6-2/sf/R/sfg.R | 39 + sf-0.6-2/sf/R/sgbp.R | 11 sf-0.6-2/sf/R/sp.R | 57 ++ sf-0.6-2/sf/R/tidyverse.R | 126 ++++-- sf-0.6-2/sf/R/transform.R | 4 sf-0.6-2/sf/configure | 8 sf-0.6-2/sf/configure.ac | 6 sf-0.6-2/sf/inst/doc/sf1.Rmd | 15 sf-0.6-2/sf/inst/doc/sf1.html | 47 +- sf-0.6-2/sf/inst/doc/sf2.R | 6 sf-0.6-2/sf/inst/doc/sf2.Rmd | 8 sf-0.6-2/sf/inst/doc/sf2.html | 14 sf-0.6-2/sf/inst/doc/sf3.html | 6 sf-0.6-2/sf/inst/doc/sf4.html | 2 sf-0.6-2/sf/inst/doc/sf5.html | 15 sf-0.6-2/sf/inst/doc/sf6.html | 2 sf-0.6-2/sf/inst/gpkg/nospatial.gpkg |only sf-0.6-2/sf/man/Ops.Rd |only sf-0.6-2/sf/man/aggregate.sf.Rd | 5 sf-0.6-2/sf/man/coerce-methods.Rd | 30 + sf-0.6-2/sf/man/dbDataType.Rd |only sf-0.6-2/sf/man/geos_binary_pred.Rd | 4 sf-0.6-2/sf/man/geos_combine.Rd | 4 sf-0.6-2/sf/man/sf-deprecated.Rd |only sf-0.6-2/sf/man/sf.Rd | 4 sf-0.6-2/sf/man/sfc.Rd | 4 sf-0.6-2/sf/man/st_bbox.Rd | 4 sf-0.6-2/sf/man/st_crop.Rd |only sf-0.6-2/sf/man/st_crs.Rd | 8 sf-0.6-2/sf/man/st_make_grid.Rd | 2 sf-0.6-2/sf/man/st_precision.Rd | 2 sf-0.6-2/sf/man/st_read.Rd | 108 +++-- sf-0.6-2/sf/man/st_transform.Rd | 4 sf-0.6-2/sf/man/st_write.Rd | 65 +-- sf-0.6-2/sf/man/tidyverse.Rd |only sf-0.6-2/sf/src/RcppExports.cpp | 20 sf-0.6-2/sf/src/gdal.cpp | 16 sf-0.6-2/sf/src/gdal.h |only sf-0.6-2/sf/src/gdal_read.cpp | 32 + sf-0.6-2/sf/src/gdal_utils.cpp | 56 ++ sf-0.6-2/sf/src/gdal_write.cpp | 37 + sf-0.6-2/sf/src/geos.cpp | 6 sf-0.6-2/sf/src/sfg.cpp |only sf-0.6-2/sf/tests/crs.R | 6 sf-0.6-2/sf/tests/crs.Rout.save | 9 sf-0.6-2/sf/tests/geos.R | 2 sf-0.6-2/sf/tests/geos.Rout.save | 19 sf-0.6-2/sf/tests/plot.Rout.save | 5 sf-0.6-2/sf/tests/sfc.R | 29 + sf-0.6-2/sf/tests/sfc.Rout.save | 119 +++++ sf-0.6-2/sf/tests/sfg.R | 9 sf-0.6-2/sf/tests/sfg.Rout.save | 26 + sf-0.6-2/sf/tests/testthat.Rout.save | 33 - sf-0.6-2/sf/tests/testthat/deprecated-db.R |only sf-0.6-2/sf/tests/testthat/test_crs.R | 10 sf-0.6-2/sf/tests/testthat/test_deprecated-db.R |only sf-0.6-2/sf/tests/testthat/test_gdal.R | 6 sf-0.6-2/sf/tests/testthat/test_postgis_ODBC.R |only sf-0.6-2/sf/tests/testthat/test_postgis_RPostgreSQL.R |only sf-0.6-2/sf/tests/testthat/test_postgis_RPostgres.R |only sf-0.6-2/sf/tests/testthat/test_read.R | 9 sf-0.6-2/sf/tests/testthat/test_sf.R | 11 sf-0.6-2/sf/tests/testthat/test_sp.R | 34 + sf-0.6-2/sf/tests/testthat/test_write.R | 12 sf-0.6-2/sf/tests/zzz.Rout.save | 4 sf-0.6-2/sf/vignettes/sf1.Rmd | 15 sf-0.6-2/sf/vignettes/sf2.Rmd | 8 91 files changed, 1424 insertions(+), 723 deletions(-)
Title: Dynamic Model Averaging with Grid Search
Description: Perform dynamic model averaging with grid search as in Dangl and Halling (2012) <doi:10.1016/j.jfineco.2012.04.003> using parallel computing.
Author: Leopoldo Catania [aut,cre], Nima Nonejad [aut]
Maintainer: Leopoldo Catania <leopoldo.catania@econ.au.dk>
Diff between eDMA versions 1.5-0 dated 2018-02-21 and 1.5-1 dated 2018-04-25
ChangeLog |only DESCRIPTION | 10 +++++----- MD5 | 22 ++++++++++++---------- build/partial.rdb |binary inst |only man/BacktestDMA.Rd | 2 +- man/DMA-class.Rd | 2 +- man/DMA.Rd | 4 ++-- man/Lag.Rd | 2 +- man/PowerSet.Rd | 2 +- man/SimData.Rd | 3 ++- man/SimulateDLM.Rd | 4 ++-- man/eDMA-package.Rd | 12 +++++++----- 13 files changed, 34 insertions(+), 29 deletions(-)
Title: Retriving Aphia Information from World Register of Marine
Species
Description: Retrieves taxonomic information from <http://www.marinespecies.org> using WoRMS' RESTful Webservice. Utility functions aim at taxonomic consistency.
Author: Jan Holstein [aut, cre, cph]
Maintainer: Jan Holstein <janmholstein@gmail.com>
Diff between worms versions 0.2.1 dated 2017-06-18 and 0.2.2 dated 2018-04-25
worms-0.2.1/worms/README.md |only worms-0.2.2/worms/DESCRIPTION | 8 ++--- worms-0.2.2/worms/MD5 | 7 ++--- worms-0.2.2/worms/R/worms_func.R | 41 +++++++++++++++++++++++------- worms-0.2.2/worms/man/wormsconsolidate.Rd | 5 ++- 5 files changed, 43 insertions(+), 18 deletions(-)
Title: Functions for Set-Theoretic Multi-Method Research and Advanced
QCA
Description: Functions for performing set-theoretic multi-method research, QCA for clustered data, theory evaluation, Enhanced Standard Analysis, indirect calibration, radar visualisations. Additionally it includes data to replicate the examples in the book by C. Q. Schneider and C. Wagemann "Set Theoretic Methods for the Social Sciences", Cambridge University Press and in the online appendix.
Author: Juraj Medzihorsky [aut],
Ioana-Elena Oana [aut, cre],
Mario Quaranta [aut],
Carsten Q. Schneider [aut]
Maintainer: Ioana-Elena Oana <oana_ioana-elena@phd.ceu.edu>
Diff between SetMethods versions 2.3 dated 2017-12-01 and 2.3.1 dated 2018-04-25
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- NEWS | 4 ++++ R/cases.suf.dcv.R | 4 ++-- R/cases.theory.evaluation.R | 26 +++++++++++++++++++++++++- R/esa.R | 16 ++++++++-------- R/print.casestheoryeval.R | 3 ++- R/theory.evaluation.R | 2 +- R/zzz.R | 4 ++-- man/SetMethods-package.Rd | 4 ++-- man/esa.Rd | 10 +++++----- 11 files changed, 65 insertions(+), 36 deletions(-)
Title: Graph Plotting Methods, Psychometric Data Visualization and
Graphical Model Estimation
Description: Weighted network visualization and analysis, as well as Gaussian graphical model computation. See Epskamp et al. (2012) <doi:10.18637/jss.v048.i04>.
Author: Sacha Epskamp, Giulio Costantini, Jonas Haslbeck, Angelique O. J. Cramer, Lourens J. Waldorp, Verena D. Schmittmann and Denny Borsboom
Maintainer: Sacha Epskamp <mail@sachaepskamp.com>
Diff between qgraph versions 1.4.4 dated 2017-09-02 and 1.5 dated 2018-04-25
DESCRIPTION | 11 +- MD5 | 56 ++++++----- NAMESPACE | 14 ++ NEWS | 14 ++ R/00PolyShapes.R | 70 +++++++++++++ R/PLOT.R | 3 R/addTitle.R | 4 R/centrality.R | 7 + R/centralityFunctions.R | 12 +- R/centralityPlot.R | 39 +++++-- R/centralityTable.R | 2 R/clusteringPlot.R | 16 ++- R/findGraph.R | 4 R/flow.R |only R/ggmFit.R | 13 +- R/ggmModSelect.R |only R/glasso_methods.R | 157 +++++++++++++++++++++++++++---- R/glasso_tests.R |only R/layout.R | 7 + R/logGaus.R | 3 R/mutualInformation.R |only R/pathways.R | 7 + R/qgraph.R | 130 +++++++++++++++++++++---- R/vein.R |only man/CentAndClusfuns.Rd | 14 +- man/EBICglasso.Rd | 21 ++-- man/centrality.Rd | 2 man/flow.Rd |only man/ggmFit.Rd | 5 man/ggmModSelect.Rd |only man/mutualInformation.Rd |only man/qgraph.Rd | 18 --- man/qgraph.layout.fruchtermanreingold.Rd | 7 - 33 files changed, 512 insertions(+), 124 deletions(-)
Title: Manly Mixture Modeling and Model-Based Clustering
Description: The utility of this package includes finite mixture modeling and model-based clustering through Manly mixture models by Zhu and Melnykov (2016) <DOI:10.1016/j.csda.2016.01.015>. It also provides capabilities for forward and backward model selection procedures.
Author: Xuwen Zhu [aut, cre],
Volodymyr Melnykov [aut],
Michael Hutt [ctb, cph] (NM optimization in c),
Stephen Moshier [ctb, cph] (eigen calculations in c),
Rouben Rostamian [ctb, cph] (memory allocation in c)
Maintainer: Xuwen Zhu <xuwen.zhu@louisville.edu>
Diff between ManlyMix versions 0.1.12 dated 2018-04-21 and 0.1.13 dated 2018-04-25
DESCRIPTION | 8 ++++---- MD5 | 7 ++++--- NEWS | 4 ++++ demo/00Index | 1 + demo/ManlyKmeans3.R |only 5 files changed, 13 insertions(+), 7 deletions(-)
Title: Functions for Extreme Value Distributions
Description: Extends simulation, distribution, quantile and density
functions to univariate and multivariate parametric extreme
value distributions, and provides fitting functions which
calculate maximum likelihood estimates for univariate and
bivariate maxima models, and for univariate and bivariate
threshold models.
Author: Alec Stephenson. Function fbvpot by Chris Ferro.
Maintainer: Alec Stephenson <alec_stephenson@hotmail.com>
Diff between evd versions 2.3-2 dated 2015-12-25 and 2.3-3 dated 2018-04-25
DESCRIPTION | 8 +- MD5 | 31 +++++----- NAMESPACE | 2 R/bvdist.R | 43 ++++++-------- R/bvfit.R | 109 ++++++++++++++++++------------------- R/bvpot.R | 71 ++++++++++-------------- R/mdiag.R | 100 ++++++++++++++++++--------------- R/mvdist.R | 8 +- R/stocproc.R | 29 +++------ R/uvfit.R | 24 +++----- build/vignette.rds |binary inst/CHANGES | 8 ++ inst/CITATION | 4 - inst/doc/Multivariate_Extremes.pdf |binary man/plot.bvevd.Rd | 4 + man/plot.uvevd.Rd | 4 + src/evd_init.c |only 17 files changed, 219 insertions(+), 226 deletions(-)
Title: A Package for Statistical Analysis in Epidemiology
Description: Functions for demographic and epidemiological analysis in
the Lexis diagram, i.e. register and cohort follow-up data, in
particular representation, manipulation and simulation of multistate
data - the Lexis suite of functions, which includes interfaces to
'mstate', 'etm' and 'cmprsk' packages.
Also contains functions for Age-Period-Cohort and Lee-Carter
modeling and a function for interval censored data and some useful
functions for tabulation and plotting, as well as a number of
epidemiological data sets.
Author: Bendix Carstensen [aut, cre],
Martyn Plummer [aut],
Esa Laara [ctb],
Michael Hills [ctb]
Maintainer: Bendix Carstensen <b@bxc.dk>
Diff between Epi versions 2.26 dated 2018-03-11 and 2.28 dated 2018-04-25
CHANGES | 19 ++++++++- DESCRIPTION | 8 +-- MD5 | 22 +++++----- NAMESPACE | 3 - R/Ns.r | 114 +++++++++++++++++++++++++++++--------------------------- R/ci.lin.R | 55 ++++++++++++++------------- R/matshade.R |only man/LCa.fit.Rd | 26 ++++++------ man/Ns.Rd | 11 +++-- man/apc.LCa.Rd | 9 ++-- man/ci.lin.Rd | 41 ++++++++++++++++---- man/erl.Rd | 11 +++-- man/matshade.Rd |only 13 files changed, 193 insertions(+), 126 deletions(-)
Title: Continuous Biomarker Assessment by Exhaustive Survival Analysis
Description: In routine practice, biomarker performance is calculated by
splitting a patient cohort at some arbitrary level, often by median gene
expression. The logic behind this is to divide patients into “high” or “low”
expression groups that in turn correlate with either good or poor prognosis.
However, this median-split approach assumes that the data set composition
adheres to a strict 1:1 proportion of high vs. low expression, that for
every one “low” there is an equivalent “high”. In reality, data sets are
often heterogeneous in their composition (Perou, CM et al., 2000
<doi:10.1038/35021093>)- i.e. this 1:1 relationship is unlikely to exist and
the true relationship unknown. Given this limitation, it remains difficult
to determine where the most significant separation should be made. For
example, estrogen receptor (ER) status determined by immunohistochemistry is
standard practice in predicting hormone therapy response, where ER is found
in an ~1:3 ratio (-:+) in the population (Selli, C et al., 2016
<doi:10.1186/s13058-016-0779-0>). We would expect therefore, upon dividing
patients by ER expression, 25% to be classified “low” and 75% “high”, and
an otherwise 50-50 split to incorrectly classify 25% of our patient cohort,
rendering our survival estimate under powered. 'survivALL' is a data-driven
approach to calculate the relative survival estimates for all possible
points of separation - i.e. at all possible ratios of “high” vs. “low” -
allowing a measure’s relationship with survival to be more reliably
determined and quantified. We see this as a solution to a flaw in common
research practice, namely the failure of a true biomarker as part of a
meta-analysis.
Author: Dominic Pearce [aut, cre]
Maintainer: Dominic Pearce <dominic.pearce@ed.ac.uk>
Diff between survivALL versions 0.9.2 dated 2018-03-01 and 0.9.3 dated 2018-04-25
DESCRIPTION | 6 MD5 | 25 +-- NEWS.md |only R/allHR.R | 12 + R/allPvals.R | 33 +++- R/survivALL.R | 8 - inst/doc/basic-usage.html | 2 inst/doc/bootstrapping-and-hr-thresholds.html | 188 +++++++++++++------------- inst/doc/rationale.html | 2 man/allHR.Rd | 7 man/allPvals.Rd | 24 ++- man/plotALL.Rd |binary man/survivALL.Rd | 12 + tests/testthat/test-allPvals.R | 4 14 files changed, 190 insertions(+), 133 deletions(-)
Title: Latent Variable Network Modeling
Description: Estimate, fit and compare Structural Equation Models (SEM) and network models (Gaussian Graphical Models; GGM) using OpenMx. Allows for two possible generalizations to include GGMs in SEM: GGMs can be used between latent variables (latent network modeling; LNM) or between residuals (residual network modeling; RNM). For details, see Epskamp, Rhemtulla and Borsboom (2017) <doi:10.1007/s11336-017-9557-x>.
Author: Sacha Epskamp
Maintainer: Sacha Epskamp <mail@sachaepskamp.com>
Diff between lvnet versions 0.3.2 dated 2017-09-02 and 0.3.3 dated 2018-04-25
lvnet-0.3.2/lvnet/man/ggmFit.Rd |only lvnet-0.3.3/lvnet/DESCRIPTION | 6 +++--- lvnet-0.3.3/lvnet/MD5 | 7 +++---- lvnet-0.3.3/lvnet/NAMESPACE | 4 +--- lvnet-0.3.3/lvnet/NEWS | 3 +++ 5 files changed, 10 insertions(+), 10 deletions(-)
Title: Labelled Data Utility Functions
Description: Collection of functions dealing with labelled data, like reading and
writing data between R and other statistical software packages like 'SPSS',
'SAS' or 'Stata', and working with labelled data. This includes easy ways
to get, set or change value and variable label attributes, to convert
labelled vectors into factors or numeric (and vice versa), or to deal with
multiple declared missing values.
Author: Daniel Lüdecke <d.luedecke@uke.de>
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjlabelled versions 1.0.9 dated 2018-04-24 and 1.0.10 dated 2018-04-25
DESCRIPTION | 8 ++--- MD5 | 10 +++---- NAMESPACE | 1 R/deprecated.R | 3 ++ inst/doc/intro_sjlabelled.html | 56 ++++++++++++++++++++--------------------- inst/doc/labelleddata.html | 4 +- 6 files changed, 43 insertions(+), 39 deletions(-)
Title: Generative Mechanism Estimation in Temporal Complex Networks
Description: Statistical methods for estimating preferential attachment and node fitness generative mechanisms in temporal complex networks are provided. Thong Pham et al. (2015) <10.1371/journal.pone.0137796>. Thong Pham et al.(2016) <doi:10.1038/srep32558>.
Author: Thong Pham, Paul Sheridan, Hidetoshi Shimodaira
Maintainer: Thong Pham <thongpham@thongpham.net>
Diff between PAFit versions 1.0.0.3 dated 2018-02-05 and 1.0.0.4 dated 2018-04-25
PAFit-1.0.0.3/PAFit/R/prep_simulate_true_net.R |only PAFit-1.0.0.4/PAFit/DESCRIPTION | 12 - PAFit-1.0.0.4/PAFit/MD5 | 120 ++++++------- PAFit-1.0.0.4/PAFit/NAMESPACE | 11 - PAFit-1.0.0.4/PAFit/R/CreateDataCV.R | 5 PAFit-1.0.0.4/PAFit/R/Jeong.R | 4 PAFit-1.0.0.4/PAFit/R/Newman.R | 6 PAFit-1.0.0.4/PAFit/R/PAFit.R | 28 +-- PAFit-1.0.0.4/PAFit/R/generate_BA.R | 8 PAFit-1.0.0.4/PAFit/R/generate_BB.R | 15 - PAFit-1.0.0.4/PAFit/R/generate_ER.R | 8 PAFit-1.0.0.4/PAFit/R/generate_fit_only.R | 14 - PAFit-1.0.0.4/PAFit/R/generate_net.R | 43 ++-- PAFit-1.0.0.4/PAFit/R/joint_estimate.R | 10 - PAFit-1.0.0.4/PAFit/R/one_cycle.R | 4 PAFit-1.0.0.4/PAFit/R/only_A_estimate.R | 13 - PAFit-1.0.0.4/PAFit/R/only_F_estimate.R | 5 PAFit-1.0.0.4/PAFit/R/plot.Full_PAFit_result.R | 42 +--- PAFit-1.0.0.4/PAFit/R/plot.PAFit_net.R | 29 ++- PAFit-1.0.0.4/PAFit/R/plot.pa_result.R | 2 PAFit-1.0.0.4/PAFit/R/plot.pafit_result.r | 19 +- PAFit-1.0.0.4/PAFit/R/print.Linear_PA_test_result.R |only PAFit-1.0.0.4/PAFit/R/print.full_pafit_result.R | 2 PAFit-1.0.0.4/PAFit/R/print.pa_result.R | 2 PAFit-1.0.0.4/PAFit/R/print.pafit_data.r | 2 PAFit-1.0.0.4/PAFit/R/print.pafit_result.r | 2 PAFit-1.0.0.4/PAFit/R/summary.Linear_PA_test_result.R |only PAFit-1.0.0.4/PAFit/R/summary.full_pafit_result.R | 2 PAFit-1.0.0.4/PAFit/R/summary.pa_result.R | 2 PAFit-1.0.0.4/PAFit/R/summary.pafit_result.r | 2 PAFit-1.0.0.4/PAFit/R/test_linear_PA.R |only PAFit-1.0.0.4/PAFit/inst/CITATION | 2 PAFit-1.0.0.4/PAFit/inst/NEWS.Rd | 14 + PAFit-1.0.0.4/PAFit/inst/doc/Tutorial.pdf |binary PAFit-1.0.0.4/PAFit/man/ComplexNetCoauthor.rd | 8 PAFit-1.0.0.4/PAFit/man/Jeong.rd | 26 +- PAFit-1.0.0.4/PAFit/man/Newman.rd | 19 +- PAFit-1.0.0.4/PAFit/man/PAFit-package.Rd | 6 PAFit-1.0.0.4/PAFit/man/generate_BA.rd | 8 PAFit-1.0.0.4/PAFit/man/generate_BB.rd | 24 -- PAFit-1.0.0.4/PAFit/man/generate_ER.rd | 6 PAFit-1.0.0.4/PAFit/man/generate_fit_only.rd | 24 -- PAFit-1.0.0.4/PAFit/man/generate_net.Rd | 34 --- PAFit-1.0.0.4/PAFit/man/joint_estimate.rd | 47 +++-- PAFit-1.0.0.4/PAFit/man/only_A_estimate.rd | 44 +++- PAFit-1.0.0.4/PAFit/man/only_F_estimate.rd | 26 ++ PAFit-1.0.0.4/PAFit/man/plot.PAFit_net.Rd | 4 PAFit-1.0.0.4/PAFit/man/plot.PA_result.rd | 2 PAFit-1.0.0.4/PAFit/man/print.PA_result.rd | 2 PAFit-1.0.0.4/PAFit/man/summary.PA_result.rd | 2 PAFit-1.0.0.4/PAFit/man/test_linear_PA.rd |only PAFit-1.0.0.4/PAFit/src/init.c | 5 PAFit-1.0.0.4/PAFit/tests/loop_joint_estimate.R | 12 - PAFit-1.0.0.4/PAFit/tests/test_GenerateNet_final_padding.R | 2 PAFit-1.0.0.4/PAFit/tests/test_GetStatistics_compress_2.R | 2 PAFit-1.0.0.4/PAFit/tests/test_GetStatistics_undirected.R | 4 PAFit-1.0.0.4/PAFit/tests/test_Newman_Kong.R | 2 PAFit-1.0.0.4/PAFit/tests/test_joint_estimate.R | 2 PAFit-1.0.0.4/PAFit/tests/test_only_A.R | 2 PAFit-1.0.0.4/PAFit/tests/test_only_F.R | 2 PAFit-1.0.0.4/PAFit/tests/test_overall.R | 2 PAFit-1.0.0.4/PAFit/tests/test_test_linear_PA.R |only PAFit-1.0.0.4/PAFit/tests/test_true_f.R | 2 PAFit-1.0.0.4/PAFit/tests/test_variance_s.R | 2 64 files changed, 397 insertions(+), 352 deletions(-)
Title: Path Diagrams for Lavaan Models via DiagrammeR
Description: Plots path diagrams from models in lavaan using the plotting
functionality from the DiagrammeR package. DiagrammeR provides nice path diagrams
via Graphviz, and these functions make it easy to generate these diagrams from a
lavaan path model without having to write the DOT language graph specification.
Author: Alex Lishinski
Maintainer: Alex Lishinski <alexlishinski@gmail.com>
Diff between lavaanPlot versions 0.3.0 dated 2018-01-26 and 0.5.1 dated 2018-04-25
DESCRIPTION | 8 +- MD5 | 23 +++---- NAMESPACE | 3 NEWS.md | 23 +++++++ R/lavaanPlot.R | 124 +++++++++++++++++++++++++++++++------- inst/doc/Intro_to_lavaanPlot.R | 38 +++++++++++ inst/doc/Intro_to_lavaanPlot.Rmd | 53 ++++++++++++++-- inst/doc/Intro_to_lavaanPlot.html | 82 ++++++++++++++++++------- man/buildCall.Rd | 14 +--- man/buildPaths.Rd | 7 +- man/lavaanPlot.Rd | 19 ----- man/sig_stars.Rd |only vignettes/Intro_to_lavaanPlot.Rmd | 53 ++++++++++++++-- 13 files changed, 352 insertions(+), 95 deletions(-)
Title: Forest Plots from Regression Models
Description: Produces forest plots using 'ggplot2' from models produced by functions
such as stats::lm(), stats::glm() and survival::coxph().
Author: Nick Kennedy <r@nick-kennedy.com>
Maintainer: Nick Kennedy <r@nick-kennedy.com>
Diff between forestmodel versions 0.4.3 dated 2017-04-16 and 0.5.0 dated 2018-04-25
DESCRIPTION | 13 ++++--- MD5 | 12 +++---- NEWS | 12 ++++++- R/forest_model.R | 91 ++++++++++++++++++++++++++++++++----------------------- R/forest_rma.R | 2 - R/glob_vars.R | 3 + README.md | 2 - 7 files changed, 82 insertions(+), 53 deletions(-)
Title: Convert Base Plot to 'grob' Object
Description: Convert base plot function call (using expression or formula) to 'grob' object that compatible to the 'grid' ecosystem. With this package, we are able to e.g. using 'cowplot' to align base plots with 'ggplot' objects and using 'ggsave' to export base plot to file.
Author: Guangchuang Yu [aut, cre] (<https://orcid.org/0000-0002-6485-8781>)
Maintainer: Guangchuang Yu <guangchuangyu@gmail.com>
Diff between base2grob versions 0.0.2 dated 2018-03-15 and 0.0.3 dated 2018-04-25
base2grob-0.0.2/base2grob/R/base_plot_fun.R |only base2grob-0.0.2/base2grob/R/grid-draw.R |only base2grob-0.0.3/base2grob/DESCRIPTION | 16 +++----- base2grob-0.0.3/base2grob/MD5 | 15 +++---- base2grob-0.0.3/base2grob/NAMESPACE | 7 --- base2grob-0.0.3/base2grob/R/base2grob.R | 43 +++++++++++++--------- base2grob-0.0.3/base2grob/README.md |only base2grob-0.0.3/base2grob/build/vignette.rds |binary base2grob-0.0.3/base2grob/inst/doc/base2grob.html | 10 ++--- base2grob-0.0.3/base2grob/man/base2grob.Rd | 21 ++-------- 10 files changed, 51 insertions(+), 61 deletions(-)
Title: Zebra-Striped Tables in LaTeX and HTML Formats
Description: Makes zebra-striped tables (tables with alternating row colors)
in LaTeX and HTML formats easily from a data.frame, matrix, lm, aov, anova,
glm, coxph, nls, fitdistr, mytable and cbind.mytable objects.
Author: Keon-Woong Moon [aut, cre]
Maintainer: Keon-Woong Moon <cardiomoon@gmail.com>
Diff between ztable versions 0.1.5 dated 2015-02-15 and 0.1.8 dated 2018-04-25
DESCRIPTION | 12 MD5 | 157 +- NAMESPACE | 45 NEWS | 27 R/parallelTables.R | 1 R/print.ztable.html.R | 128 + R/zcolors.R | 4 R/ztable.R | 184 ++ R/ztable.cbind.mytable.R | 2 R/ztable.mytable.R | 2 R/ztable1.R | 44 R/ztable2.R | 214 ++- R/zzz.R | 2 build/vignette.rds |binary inst/doc/ztable.R | 115 + inst/doc/ztable.Rmd | 42 inst/doc/ztable.html | 2894 +++++++++++++++++++++++++++++++++++++++----- inst/ztableDemo |only man/addCellColor.Rd | 3 man/addColColor.Rd | 3 man/addFrontColor.Rd |only man/addRowColor.Rd | 3 man/addSigColor.Rd |only man/addSubColNames.Rd | 7 man/addcgroup.Rd | 13 man/addrgroup.Rd | 12 man/align2html.Rd | 3 man/align2lines.Rd | 3 man/align2nd.Rd | 3 man/alignCheck.Rd | 3 man/alignCount.Rd | 3 man/cGroupSpan.Rd | 3 man/caption2minipage.Rd | 3 man/colGroupCount.Rd | 3 man/data2table.Rd | 3 man/define_colors.Rd | 9 man/extractAlign.Rd | 3 man/getNewAlign.Rd | 7 man/getNewSpanCol.Rd | 3 man/getNewSpanRow.Rd | 3 man/getspanRowData.Rd | 9 man/getspanRowLength.Rd | 3 man/hlines.Rd | 5 man/isGroupCol.Rd | 3 man/isspanCol.Rd | 7 man/isspanRow.Rd | 3 man/make.cell.color.Rd | 9 man/make.frontcolor.Rd |only man/myhtmlStyle.Rd | 8 man/name2rgb.Rd | 3 man/parallelTables.Rd | 3 man/parallelTablesHTML.Rd | 3 man/parallelTablesLatex.Rd | 3 man/print.ztable.Rd | 3 man/printHTMLHead.Rd | 3 man/printLatexHead.Rd | 3 man/printRowGroup.Rd | 3 man/print_ztable.Rd | 3 man/repColor.Rd | 3 man/spanCol.Rd | 3 man/spanColWidth.Rd | 3 man/spanRow.Rd | 3 man/tableLength.Rd | 3 man/totalCol.Rd | 3 man/tr.Rd | 3 man/tr2.Rd | 3 man/update_ztable.Rd | 34 man/validColor.Rd | 3 man/validColor2.Rd | 3 man/vline2align.Rd | 3 man/vlines.Rd | 3 man/zcolors.Rd | 7 man/ztable.Rd | 40 man/ztable.cbind.mytable.Rd | 3 man/ztable.mytable.Rd | 3 man/ztable2html.Rd | 3 man/ztable2latex.Rd | 3 man/ztable2viewer.Rd | 3 man/ztable_sub.Rd | 23 vignettes/ztable.Rmd | 42 80 files changed, 3510 insertions(+), 727 deletions(-)