Title: Load Data from 'MyTarget API'
Description: Allows work with 'MyTarget API' <https://target.my.com/adv/api-marketing/> and
load data by ads, campaigns and statistic from
your ads account.
Author: Alexey Seleznev
Maintainer: Alexey Seleznev <selesnow@gmail.com>
Diff between rmytarget versions 1.1 dated 2018-09-28 and 1.1.1 dated 2018-11-09
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/myTarAuth.R | 36 +++++++++++++++++++++--------------- build/partial.rdb |binary 4 files changed, 28 insertions(+), 22 deletions(-)
Title: Regression Estimation and Presentation
Description: A collection of functions for interpretation and presentation
of regression analysis. These functions are used
to produce the statistics lectures in
<http://pj.freefaculty.org/guides>. Includes regression
diagnostics, regression tables, and plots of interactions and
"moderator" variables. The emphasis is on "mean-centered" and
"residual-centered" predictors. The vignette 'rockchalk' offers a
fairly comprehensive overview. The vignette 'Rstyle' has advice
about coding in R. The package title 'rockchalk' refers to our
school motto, 'Rock Chalk Jayhawk, Go K.U.'.
Author: Paul E. Johnson [aut, cre],
Gabor Grothendieck [ctb]
Maintainer: Paul E. Johnson <pauljohn@ku.edu>
Diff between rockchalk versions 1.8.117 dated 2018-09-12 and 1.8.129 dated 2018-11-09
rockchalk-1.8.117/rockchalk/vignettes/plots |only rockchalk-1.8.129/rockchalk/DESCRIPTION | 12 rockchalk-1.8.129/rockchalk/MD5 | 47 rockchalk-1.8.129/rockchalk/NAMESPACE | 1 rockchalk-1.8.129/rockchalk/R/descriptiveTable.R | 23 rockchalk-1.8.129/rockchalk/R/outreg.R | 331 ++++-- rockchalk-1.8.129/rockchalk/R/predictOMatic.R | 3 rockchalk-1.8.129/rockchalk/R/summarize.R | 3 rockchalk-1.8.129/rockchalk/inst/ChangeLog | 15 rockchalk-1.8.129/rockchalk/inst/doc/Rchaeology.R | 74 - rockchalk-1.8.129/rockchalk/inst/doc/Rchaeology.Rnw | 21 rockchalk-1.8.129/rockchalk/inst/doc/Rchaeology.pdf |binary rockchalk-1.8.129/rockchalk/inst/doc/Rstyle.R | 8 rockchalk-1.8.129/rockchalk/inst/doc/Rstyle.Rnw | 34 rockchalk-1.8.129/rockchalk/inst/doc/Rstyle.pdf |binary rockchalk-1.8.129/rockchalk/inst/doc/rockchalk.R | 103 +- rockchalk-1.8.129/rockchalk/inst/doc/rockchalk.Rnw | 359 +++---- rockchalk-1.8.129/rockchalk/inst/doc/rockchalk.pdf |binary rockchalk-1.8.129/rockchalk/man/descriptiveTable.Rd | 17 rockchalk-1.8.129/rockchalk/man/outreg.Rd | 174 ++- rockchalk-1.8.129/rockchalk/vignettes/Rchaeology.Rnw | 21 rockchalk-1.8.129/rockchalk/vignettes/Rstyle.Rnw | 34 rockchalk-1.8.129/rockchalk/vignettes/rockchalk.Rnw | 359 +++---- rockchalk-1.8.129/rockchalk/vignettes/rockchalk.bib | 2 rockchalk-1.8.129/rockchalk/vignettes/rockchalk.lyx | 901 ++++++++++++++++--- 25 files changed, 1701 insertions(+), 841 deletions(-)
Title: Working with Dynamic Models for Agriculture and Environment
Description: R package accompanying the book Working with dynamic models for agriculture and environment, by Daniel Wallach (INRA), David Makowski (INRA), James W. Jones (U.of Florida), Francois Brun (ACTA). 3rd edition 2018-09-27.
Author: Francois Brun (ACTA), David Makowski (INRA), Daniel Wallach (INRA), James W. Jones (U.of Florida).
Maintainer: Francois Brun <francois.brun@acta.asso.fr>
Diff between ZeBook versions 1.0 dated 2018-03-13 and 1.1 dated 2018-11-09
DESCRIPTION | 12 +++++------ MD5 | 38 ++++++++++++++++++++----------------- R/ZeBook.r | 6 ++--- R/maize.data_MetaModelling.r |only data/datalist | 1 data/maize.data_MetaModelling.rda |only demo/00Index | 1 demo/ch11MetaModelling.r |only man/ZeBook-package.Rd | 6 ++--- man/carcass.EMI.model.Rd | 6 ++--- man/carcass.model.Rd | 3 +- man/cotton.model.Rd | 4 +-- man/lactation.calf.model.Rd | 4 +-- man/lactation.machine.model.Rd | 4 +-- man/maize.data_MetaModelling.Rd |only man/maize_cir.model.Rd | 3 +- man/maize_cir_rue.model.Rd | 4 +-- man/maize_cir_rue_ear.model.Rd | 4 +-- man/population.age.matrix.model.Rd | 8 +++---- man/population.age.model.ode.Rd | 8 +++---- man/predator.prey.model.Rd | 5 ++-- man/zakoks.original.model.Rd | 5 ++-- 22 files changed, 66 insertions(+), 56 deletions(-)
Title: R Interface to 'FishBase'
Description: A programmatic interface to <http://www.fishbase.org>, re-written
based on an accompanying 'RESTful' API. Access tables describing over 30,000
species of fish, their biology, ecology, morphology, and more. This package also
supports experimental access to <http://www.sealifebase.org> data, which contains
nearly 200,000 species records for all types of aquatic life not covered by
'FishBase.'
Author: Carl Boettiger [cre, aut] (<https://orcid.org/0000-0002-1642-628X>),
Scott Chamberlain [aut] (<https://orcid.org/0000-0003-1444-9135>),
Duncan Temple Lang [aut],
Peter Wainwright [aut]
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between rfishbase versions 2.1.2 dated 2017-04-19 and 3.0.0 dated 2018-11-09
rfishbase-2.1.2/rfishbase/NEWS |only rfishbase-2.1.2/rfishbase/R/check_and_parse.R |only rfishbase-2.1.2/rfishbase/R/heartbeat.R |only rfishbase-2.1.2/rfishbase/man/heartbeat.Rd |only rfishbase-2.1.2/rfishbase/man/ping.Rd |only rfishbase-2.1.2/rfishbase/man/sci_to_common.Rd |only rfishbase-2.1.2/rfishbase/tests/testthat/test_check_and_parse.R |only rfishbase-2.1.2/rfishbase/tests/testthat/test_docs.R |only rfishbase-2.1.2/rfishbase/tests/testthat/test_heartbeat.R |only rfishbase-2.1.2/rfishbase/tests/testthat/test_parse_name.R |only rfishbase-2.1.2/rfishbase/tests/testthat/test_sealifebase.R |only rfishbase-3.0.0/rfishbase/DESCRIPTION | 28 rfishbase-3.0.0/rfishbase/MD5 | 355 ++++-- rfishbase-3.0.0/rfishbase/NAMESPACE | 36 rfishbase-3.0.0/rfishbase/NEWS.md |only rfishbase-3.0.0/rfishbase/R/00-endpoint.R | 131 -- rfishbase-3.0.0/rfishbase/R/brains.R |only rfishbase-3.0.0/rfishbase/R/common_names.R | 148 -- rfishbase-3.0.0/rfishbase/R/distribution.R | 89 - rfishbase-3.0.0/rfishbase/R/docs.R | 30 rfishbase-3.0.0/rfishbase/R/fb_tbl.R |only rfishbase-3.0.0/rfishbase/R/list_fields.R | 34 rfishbase-3.0.0/rfishbase/R/load_taxa.R | 208 ++- rfishbase-3.0.0/rfishbase/R/morpho_physio.R | 13 rfishbase-3.0.0/rfishbase/R/population_dynamics.R | 2 rfishbase-3.0.0/rfishbase/R/refs.R | 29 rfishbase-3.0.0/rfishbase/R/species.R | 32 rfishbase-3.0.0/rfishbase/R/species_list.R | 92 - rfishbase-3.0.0/rfishbase/R/species_names.R | 23 rfishbase-3.0.0/rfishbase/R/synonyms.R | 104 - rfishbase-3.0.0/rfishbase/R/sysdata.rda |only rfishbase-3.0.0/rfishbase/R/taxonomy.R |only rfishbase-3.0.0/rfishbase/R/trophic_ecology.R | 21 rfishbase-3.0.0/rfishbase/R/zzz.R |only rfishbase-3.0.0/rfishbase/README.md | 579 ++++++---- rfishbase-3.0.0/rfishbase/build/vignette.rds |binary rfishbase-3.0.0/rfishbase/inst/doc/tutorial.R | 29 rfishbase-3.0.0/rfishbase/inst/doc/tutorial.Rmd | 77 - rfishbase-3.0.0/rfishbase/inst/doc/tutorial.html | 326 +++-- rfishbase-3.0.0/rfishbase/inst/extdata |only rfishbase-3.0.0/rfishbase/man/brains.Rd |only rfishbase-3.0.0/rfishbase/man/c_code.Rd | 14 rfishbase-3.0.0/rfishbase/man/common_names.Rd | 29 rfishbase-3.0.0/rfishbase/man/common_to_sci.Rd | 23 rfishbase-3.0.0/rfishbase/man/country.Rd | 19 rfishbase-3.0.0/rfishbase/man/countrysub.Rd | 19 rfishbase-3.0.0/rfishbase/man/countrysubref.Rd | 24 rfishbase-3.0.0/rfishbase/man/diet.Rd | 19 rfishbase-3.0.0/rfishbase/man/distribution.Rd | 15 rfishbase-3.0.0/rfishbase/man/docs.Rd | 17 rfishbase-3.0.0/rfishbase/man/ecology.Rd | 17 rfishbase-3.0.0/rfishbase/man/ecosystem.Rd | 19 rfishbase-3.0.0/rfishbase/man/estimate.Rd |only rfishbase-3.0.0/rfishbase/man/faoareas.Rd | 20 rfishbase-3.0.0/rfishbase/man/fecundity.Rd | 19 rfishbase-3.0.0/rfishbase/man/fooditems.Rd | 19 rfishbase-3.0.0/rfishbase/man/genetics.Rd |only rfishbase-3.0.0/rfishbase/man/introductions.Rd | 19 rfishbase-3.0.0/rfishbase/man/larvae.Rd | 19 rfishbase-3.0.0/rfishbase/man/length_freq.Rd | 19 rfishbase-3.0.0/rfishbase/man/length_length.Rd | 19 rfishbase-3.0.0/rfishbase/man/length_weight.Rd | 19 rfishbase-3.0.0/rfishbase/man/list_fields.Rd | 15 rfishbase-3.0.0/rfishbase/man/load_taxa.Rd | 15 rfishbase-3.0.0/rfishbase/man/maturity.Rd | 19 rfishbase-3.0.0/rfishbase/man/morphology.Rd | 19 rfishbase-3.0.0/rfishbase/man/morphometrics.Rd | 19 rfishbase-3.0.0/rfishbase/man/oxygen.Rd | 19 rfishbase-3.0.0/rfishbase/man/popchar.Rd | 19 rfishbase-3.0.0/rfishbase/man/popgrowth.Rd | 19 rfishbase-3.0.0/rfishbase/man/popqb.Rd | 19 rfishbase-3.0.0/rfishbase/man/predators.Rd | 19 rfishbase-3.0.0/rfishbase/man/ration.Rd | 19 rfishbase-3.0.0/rfishbase/man/reexports.Rd |only rfishbase-3.0.0/rfishbase/man/references.Rd | 17 rfishbase-3.0.0/rfishbase/man/reproduction.Rd | 19 rfishbase-3.0.0/rfishbase/man/spawning.Rd | 19 rfishbase-3.0.0/rfishbase/man/species.Rd | 19 rfishbase-3.0.0/rfishbase/man/species_list.Rd | 17 rfishbase-3.0.0/rfishbase/man/species_names.Rd | 12 rfishbase-3.0.0/rfishbase/man/speed.Rd | 19 rfishbase-3.0.0/rfishbase/man/stocks.Rd | 19 rfishbase-3.0.0/rfishbase/man/swimming.Rd | 19 rfishbase-3.0.0/rfishbase/man/synonyms.Rd | 28 rfishbase-3.0.0/rfishbase/man/taxonomy.Rd |only rfishbase-3.0.0/rfishbase/man/validate_names.Rd | 20 rfishbase-3.0.0/rfishbase/tests/testthat.R | 1 rfishbase-3.0.0/rfishbase/tests/testthat/test_commonnames.R | 26 rfishbase-3.0.0/rfishbase/tests/testthat/test_distribution.R | 9 rfishbase-3.0.0/rfishbase/tests/testthat/test_ecology.R | 4 rfishbase-3.0.0/rfishbase/tests/testthat/test_endpoint.R | 11 rfishbase-3.0.0/rfishbase/tests/testthat/test_list_fields.R | 14 rfishbase-3.0.0/rfishbase/tests/testthat/test_load_taxa.R | 13 rfishbase-3.0.0/rfishbase/tests/testthat/test_maturity.R | 6 rfishbase-3.0.0/rfishbase/tests/testthat/test_morpho_physio.R | 3 rfishbase-3.0.0/rfishbase/tests/testthat/test_population_dynamics.R | 2 rfishbase-3.0.0/rfishbase/tests/testthat/test_species.R | 63 - rfishbase-3.0.0/rfishbase/tests/testthat/test_species_list.R | 2 rfishbase-3.0.0/rfishbase/tests/testthat/test_synonyms.R | 30 rfishbase-3.0.0/rfishbase/vignettes/tutorial.Rmd | 77 - 100 files changed, 1786 insertions(+), 1638 deletions(-)
Title: Continuous Time Structural Equation Modelling
Description: A hierarchical, multivariate, continuous (and discrete) time dynamic modelling
package for panel and time series data, using stochastic differential
equations. Contains a faster frequentist set of functions using OpenMx for
single subject and mixed-effects (random intercepts only) structural
equation models, or a hierarchical Bayesian implementation using Stan that
allows for random effects and non-linearity over all model parameters.
Allows for modelling of multiple noisy measurements of multiple stochastic
processes, time varying input / event covariates, and time invariant
covariates used to predict the parameters.
Author: Charles Driver [aut, cre, cph],
Manuel Voelkle [aut, cph],
Han Oud [aut, cph]
Maintainer: Charles Driver <driver@mpib-berlin.mpg.de>
Diff between ctsem versions 2.6.5 dated 2018-06-25 and 2.7.4 dated 2018-11-09
ctsem-2.6.5/ctsem/data/datalist |only ctsem-2.6.5/ctsem/man/ctFitR.Rd |only ctsem-2.6.5/ctsem/vignettes/hierarchical.tex |only ctsem-2.7.4/ctsem/DESCRIPTION | 19 ctsem-2.7.4/ctsem/MD5 | 175 - ctsem-2.7.4/ctsem/NAMESPACE | 6 ctsem-2.7.4/ctsem/NEWS | 9 ctsem-2.7.4/ctsem/R/ctCI.R | 2 ctsem-2.7.4/ctsem/R/ctCheckFit.R | 48 ctsem-2.7.4/ctsem/R/ctDataHelp.R | 6 ctsem-2.7.4/ctsem/R/ctDiscretePars.R | 117 ctsem-2.7.4/ctsem/R/ctFit.R | 11 ctsem-2.7.4/ctsem/R/ctFitR.R | 32 ctsem-2.7.4/ctsem/R/ctGenerate.R | 7 ctsem-2.7.4/ctsem/R/ctKalman.R | 2 ctsem-2.7.4/ctsem/R/ctMultigroupFit.R | 2 ctsem-2.7.4/ctsem/R/ctPlotArray.R | 21 ctsem-2.7.4/ctsem/R/ctStanContinuousPars.R |only ctsem-2.7.4/ctsem/R/ctStanFit.R | 2111 +++++++--------- ctsem-2.7.4/ctsem/R/ctStanModel.R | 10 ctsem-2.7.4/ctsem/R/ctStanParMatrices.R | 25 ctsem-2.7.4/ctsem/R/ctStanPlotPost.R | 27 ctsem-2.7.4/ctsem/R/ctStanPostPredict.R | 140 - ctsem-2.7.4/ctsem/R/ctStanSummary.R | 80 ctsem-2.7.4/ctsem/R/ctStanTIpredMarginal.R | 2 ctsem-2.7.4/ctsem/R/ctStanTIpredeffects.R | 6 ctsem-2.7.4/ctsem/R/ctStanUpdModel.R |only ctsem-2.7.4/ctsem/R/ctdataupdate.R |only ctsem-2.7.4/ctsem/R/ctsem.R | 6 ctsem-2.7.4/ctsem/R/ctsemUtils.R | 12 ctsem-2.7.4/ctsem/R/ctsmupdate.R | 8 ctsem-2.7.4/ctsem/R/extract.ctStanFit.R | 17 ctsem-2.7.4/ctsem/R/isdiag.R | 4 ctsem-2.7.4/ctsem/R/optimstan.R |only ctsem-2.7.4/ctsem/R/plot.ctStanFit.R | 7 ctsem-2.7.4/ctsem/R/plot.ctStanModel.R | 42 ctsem-2.7.4/ctsem/R/plot.ctsemFit.R | 4 ctsem-2.7.4/ctsem/R/priorcheck.R |only ctsem-2.7.4/ctsem/R/stanWplot.R | 90 ctsem-2.7.4/ctsem/R/stan_confidenceRegion.R | 2 ctsem-2.7.4/ctsem/R/stan_reinitsf.R |only ctsem-2.7.4/ctsem/R/stanmodels.R | 17 ctsem-2.7.4/ctsem/data/ctExample2.rda |binary ctsem-2.7.4/ctsem/data/ctExample4.rda |binary ctsem-2.7.4/ctsem/data/ctstantestdat.rda |binary ctsem-2.7.4/ctsem/data/ctstantestfit.rda |binary ctsem-2.7.4/ctsem/inst/doc/ctsem.pdf | 855 +++--- ctsem-2.7.4/ctsem/inst/doc/hierarchical.pdf |binary ctsem-2.7.4/ctsem/inst/doc/hierarchical.rnw | 14 ctsem-2.7.4/ctsem/man/Kalman.Rd | 8 ctsem-2.7.4/ctsem/man/ctCI.Rd | 2 ctsem-2.7.4/ctsem/man/ctCheckFit.Rd | 7 ctsem-2.7.4/ctsem/man/ctFit.Rd | 22 ctsem-2.7.4/ctsem/man/ctGenerate.Rd | 2 ctsem-2.7.4/ctsem/man/ctIndplot.Rd | 7 ctsem-2.7.4/ctsem/man/ctIntervalise.Rd | 9 ctsem-2.7.4/ctsem/man/ctKalman.Rd | 4 ctsem-2.7.4/ctsem/man/ctKalmanPlot.Rd | 16 ctsem-2.7.4/ctsem/man/ctModel.Rd | 6 ctsem-2.7.4/ctsem/man/ctMultigroupFit.Rd | 2 ctsem-2.7.4/ctsem/man/ctPlot.Rd | 4 ctsem-2.7.4/ctsem/man/ctPlotArray.Rd | 11 ctsem-2.7.4/ctsem/man/ctPostPredict.Rd | 8 ctsem-2.7.4/ctsem/man/ctStanContinuousPars.Rd | 2 ctsem-2.7.4/ctsem/man/ctStanDiscretePars.Rd | 6 ctsem-2.7.4/ctsem/man/ctStanDiscreteParsPlot.Rd | 16 ctsem-2.7.4/ctsem/man/ctStanFit.Rd | 363 ++ ctsem-2.7.4/ctsem/man/ctStanPlotPost.Rd | 7 ctsem-2.7.4/ctsem/man/ctStanPostPredict.Rd | 20 ctsem-2.7.4/ctsem/man/ctStanTIpredeffects.Rd | 4 ctsem-2.7.4/ctsem/man/ctStanUpdModel.Rd |only ctsem-2.7.4/ctsem/man/ctstantestfit.Rd | 6 ctsem-2.7.4/ctsem/man/extract.ctStanFit.Rd |only ctsem-2.7.4/ctsem/man/isdiag.Rd | 4 ctsem-2.7.4/ctsem/man/optimstan.Rd |only ctsem-2.7.4/ctsem/man/plot.ctStanFit.Rd | 7 ctsem-2.7.4/ctsem/man/plot.ctStanModel.Rd | 5 ctsem-2.7.4/ctsem/man/plot.ctsemFitMeasure.Rd | 8 ctsem-2.7.4/ctsem/man/stanWplot.Rd | 7 ctsem-2.7.4/ctsem/man/stan_confidenceRegion.Rd | 2 ctsem-2.7.4/ctsem/man/summary.ctStanFit.Rd | 8 ctsem-2.7.4/ctsem/src/Makevars | 7 ctsem-2.7.4/ctsem/src/Makevars.win | 17 ctsem-2.7.4/ctsem/src/stan_files/ctsm.stan | 2199 ++++++++--------- ctsem-2.7.4/ctsem/src/stan_files32 |only ctsem-2.7.4/ctsem/tests/fixedvalsunspot.R |only ctsem-2.7.4/ctsem/tests/testthat/ctStanFitTests.R | 5 ctsem-2.7.4/ctsem/tests/testthat/differenttraits.R | 15 ctsem-2.7.4/ctsem/tests/testthat/kalmanVram.R | 4 ctsem-2.7.4/ctsem/tests/testthat/nonlinearVlinear.R |only ctsem-2.7.4/ctsem/tests/testthat/singleprocess.R | 25 ctsem-2.7.4/ctsem/tests/testthat/test-objectiveEquiv.R | 88 ctsem-2.7.4/ctsem/tests/testthat/test-stantipred.R | 9 ctsem-2.7.4/ctsem/tests/testthat/ukfpoptest.R |only ctsem-2.7.4/ctsem/tools/make_cc.R | 7 ctsem-2.7.4/ctsem/vignettes/hierarchical.rnw | 14 96 files changed, 3583 insertions(+), 3316 deletions(-)
Title: An Arsenal of 'R' Functions for Large-Scale Statistical
Summaries
Description: An Arsenal of 'R' functions for large-scale statistical summaries,
which are streamlined to work within the latest reporting tools in 'R' and
'RStudio' and which use formulas and versatile summary statistics for summary
tables and models. The primary functions include tableby(), a Table-1-like
summary of multiple variable types 'by' the levels of a categorical
variable; paired(), a Table-1-like summary of multiple variable types paired across
two time points; modelsum(), which performs simple model fits on the same endpoint
for many variables (univariate or adjusted for standard covariates);
freqlist(), a powerful frequency table across many categorical variables;
compare.data.frame(), the S3 method for comparing data.frames; and
write2(), a function to output tables to a document.
Author: Ethan Heinzen [aut, cre],
Jason Sinnwell [aut],
Elizabeth Atkinson [aut],
Tina Gunderson [aut],
Gregory Dougherty [aut],
Patrick Votruba [ctb],
Ryan Lennon [ctb],
Andrew Hanson [ctb],
Krista Goergen [ctb],
Emily Lundt [ctb],
Brendan Broderick [ctb]
Maintainer: Ethan Heinzen <heinzen.ethan@mayo.edu>
Diff between arsenal versions 1.4.0 dated 2018-09-18 and 1.5.0 dated 2018-11-09
DESCRIPTION | 11 +- MD5 | 115 ++++++++++++------------ NAMESPACE | 5 - NEWS.md | 28 +++++ R/arsenal.R | 3 R/formulize.R | 17 ++- R/internal.functions.R | 70 ++++++++++++++ R/paired.R | 40 ++++++-- R/summary.modelsum.R | 11 +- R/summary.tableby.R | 20 ++-- R/tableby.R | 23 ++-- R/tableby.control.R | 5 - R/tableby.stat.tests.R | 5 + R/tableby.stats.R | 22 +--- inst/doc/compare.html | 2 inst/doc/freqlist.R | 3 inst/doc/freqlist.Rmd | 10 ++ inst/doc/freqlist.html | 8 + inst/doc/labels.html | 2 inst/doc/modelsum.R | 3 inst/doc/modelsum.Rmd | 10 ++ inst/doc/modelsum.html | 90 ++++++++++--------- inst/doc/paired.Rmd | 2 inst/doc/paired.html | 3 inst/doc/tableby.R | 12 ++ inst/doc/tableby.Rmd | 33 +++++- inst/doc/tableby.html | 112 +++++++++++++++++------ inst/doc/write2.html | 2 man/compare.data.frame.Rd | 1 man/comparison.control.Rd | 11 +- man/diffs.Rd | 4 man/formulize.Rd | 11 ++ man/freqlist.Rd | 11 +- man/keep.labels.Rd | 1 man/mdy.Date.Rd | 1 man/mockstudy.Rd | 1 man/modelsum.Rd | 4 man/modelsum.control.Rd | 13 +- man/padjust.Rd |only man/paired.Rd | 25 ++++- man/paired.control.Rd | 4 man/summary.freqlist.Rd | 6 - man/summary.modelsum.Rd | 12 +- man/summary.tableby.Rd | 12 +- man/tableby.Rd | 4 man/tableby.control.Rd | 26 ++--- man/tableby.stats.Rd | 15 +-- man/tableby.stats.internal.Rd | 4 man/write2.Rd | 19 ++-- man/yaml.Rd | 1 tests/testthat/test_formulize.R | 9 + tests/testthat/test_tableby.R | 180 +++++++++++++++++++++++--------------- tests/testthat/test_write2.R | 2 tests/testthat/write2.lm.pdf.md | 2 tests/testthat/write2.yaml.pdf.md | 2 vignettes/freqlist.Rmd | 10 ++ vignettes/modelsum.Rmd | 10 ++ vignettes/paired.Rmd | 2 vignettes/tableby.Rmd | 33 +++++- 59 files changed, 746 insertions(+), 357 deletions(-)
Title: Template Model Builder: A General Random Effect Tool Inspired by
'ADMB'
Description: With this tool, a user should be able to quickly implement
complex random effect models through simple C++ templates. The package combines
'CppAD' (C++ automatic differentiation), 'Eigen' (templated matrix-vector
library) and 'CHOLMOD' (sparse matrix routines available from R) to obtain
an efficient implementation of the applied Laplace approximation with exact
derivatives. Key features are: Automatic sparseness detection, parallelism
through 'BLAS' and parallel user templates.
Author: Kasper Kristensen [aut, cre, cph],
Brad Bell [cph],
Hans Skaug [ctb],
Arni Magnusson [ctb],
Casper Berg [ctb],
Anders Nielsen [ctb],
Martin Maechler [ctb],
Theo Michelot [ctb],
Mollie Brooks [ctb],
Alex Forrence [ctb],
Christoffer Moesgaard Albertsen [ctb],
Cole Monnahan [ctb]
Maintainer: Kasper Kristensen <kaskr@dtu.dk>
Diff between TMB versions 1.7.14 dated 2018-06-23 and 1.7.15 dated 2018-11-09
DESCRIPTION | 16 ++++++++-------- MD5 | 16 ++++++++-------- NEWS | 10 ++++++++++ R/TMB.R | 4 +++- inst/include/convert.hpp | 5 +---- inst/include/tmb_core.hpp | 28 ++++++++++++++-------------- inst/include/tmbutils/array.hpp | 1 + inst/include/tmbutils/density.hpp | 6 +++--- man/MakeADFun.Rd | 3 +++ 9 files changed, 51 insertions(+), 38 deletions(-)
Title: A System of Plotting Optimized for Speed and Modularity
Description: A high-level plotting system, built using 'grid' graphics, that is
optimized for speed and modularity. This has great utility for quick
visualizations when testing code, with the key benefit that visualizations
are updated independently of one another.
Author: Eliot J B McIntire [aut, cre] (<https://orcid.org/0000-0002-6914-8316>),
Alex M Chubaty [aut] (<https://orcid.org/0000-0001-7146-8135>),
Her Majesty the Queen in Right of Canada, as represented by the
Minister of Natural Resources Canada [cph]
Maintainer: Eliot J B McIntire <eliot.mcintire@canada.ca>
Diff between quickPlot versions 0.1.5 dated 2018-10-01 and 0.1.6 dated 2018-11-09
.aspell/defaults.R | 12 DESCRIPTION | 16 MD5 | 152 NAMESPACE | 296 - NEWS.md | 86 R/environment.R | 186 - R/plotting-classes.R | 654 ++-- R/plotting-colours.R | 1216 +++---- R/plotting-helpers.R | 5565 +++++++++++++++++------------------ R/plotting-other.R | 1116 +++---- R/plotting.R | 1594 +++++----- R/quickPlot-classes.R | 54 R/quickPlot-package.R | 108 R/zzz.R | 30 README.md | 92 build/vignette.rds |binary inst/doc/iii-plotting.R | 382 +- inst/doc/iii-plotting.Rmd | 942 ++--- inst/doc/iii-plotting.html | 879 ++--- inst/examples/example_Plot.R | 202 - inst/examples/example_makeLines.R | 52 inst/examples/example_setColors.R | 112 man/Plot-internal.Rd | 236 - man/Plot.Rd | 734 ++-- man/arrangeViewports.Rd | 58 man/arrangement-class.Rd | 146 man/assignQuickPlot.Rd | 72 man/clearPlot.Rd | 298 - man/dev.Rd | 78 man/divergentColors.Rd | 106 man/equalExtent.Rd | 70 man/existsQuickPlot.Rd | 52 man/fortify.Rd | 28 man/getQuickPlot.Rd | 48 man/getSetColors.Rd | 274 - man/grid-functions.Rd | 44 man/griddedClasses-class.Rd | 52 man/hasBbox.Rd | 40 man/identifyGrobToPlot.Rd | 72 man/isRstudioServer.Rd | 28 man/layerNames.Rd | 150 man/makeColorMatrix.Rd | 108 man/makeLayout.Rd | 66 man/makeLines.Rd | 114 man/makeList.Rd | 56 man/makeQuickPlot.Rd | 88 man/makeViewports.Rd | 54 man/newPlot.Rd | 96 man/numLayers.Rd | 110 man/objectNames.Rd | 62 man/parOrig.Rd | 18 man/parseArgs.Rd | 56 man/parseElems.Rd | 58 man/plotGrob.Rd | 220 - man/prepareRaster.Rd | 68 man/quickPlot-class.Rd | 98 man/quickPlot-classes.Rd | 68 man/quickPlot-package.Rd | 80 man/quickPlotEnv.Rd | 28 man/quickPlotGrob-class.Rd | 100 man/quickPlotMouseClicks.Rd | 186 - man/quickPlotObjects-class.Rd | 38 man/quickPlottables-class.Rd | 40 man/sample-maps.Rd | 54 man/sp2sl.Rd | 64 man/spatialObjects-class.Rd | 60 man/thin.Rd | 302 - man/unittrim.Rd | 42 man/updateQuickPlot.Rd | 62 man/whereInStack.Rd | 166 - tests/test-all.R | 4 tests/testthat/test-Plot-do-call.R | 80 tests/testthat/test-Plot-nonVisual.R | 158 tests/testthat/test-Plot.R | 2118 ++++++------- tests/testthat/test-clickExtent.R | 58 tests/testthat/test-examples.R | 32 tests/testthat/test-spelling.R | 58 vignettes/iii-plotting.Rmd | 942 ++--- 78 files changed, 11172 insertions(+), 11172 deletions(-)
Title: Statistical Toolbox for Radiometric Geochronology
Description: Plots U-Pb data on Wetherill and Tera-Wasserburg concordia diagrams. Calculates concordia and discordia ages. Performs linear regression of measurements with correlated errors using 'York', 'Titterington' and 'Ludwig' approaches. Generates Kernel Density Estimates (KDEs) and Cumulative Age Distributions (CADs). Produces Multidimensional Scaling (MDS) configurations and Shepard plots of multi-sample detrital datasets using the Kolmogorov-Smirnov distance as a dissimilarity measure. Calculates 40Ar/39Ar ages, isochrons, and age spectra. Computes weighted means accounting for overdispersion. Calculates U-Th-He (single grain and central) ages, logratio plots and ternary diagrams. Processes fission track data using the external detector method and LA-ICP-MS, calculates central ages and plots fission track and other data on radial (a.k.a. 'Galbraith') plots. Constructs total Pb-U, Pb-Pb, K-Ca, Re-Os, Sm-Nd, Lu-Hf, Rb-Sr and 230Th-U isochrons as well as 230Th-U evolution plots.
Author: Pieter Vermeesch [aut, cre]
Maintainer: Pieter Vermeesch <p.vermeesch@ucl.ac.uk>
Diff between IsoplotR versions 2.1 dated 2018-10-20 and 2.2 dated 2018-11-09
DESCRIPTION | 8 - MD5 | 66 +++++++------- R/UPb.R | 22 +++- R/agespectrum.R | 21 +++- R/cad.R | 101 ++++++++++++--------- R/central.R | 5 - R/ci.R | 34 +++---- R/concordia.R | 58 ++++++------ R/errorellipse.R | 90 +++++++++++++------ R/evolution.R | 161 +++++++++++++++++----------------- R/helioplot.R | 74 ++++++++++----- R/io.R | 2 R/isochron.R | 224 +++++++++++++++++++++++++++--------------------- R/kde.R | 127 +++++++++++++++++---------- R/mds.R | 13 +- R/peakfit.R | 12 +- R/radialplot.R | 242 +++++++++++++++++++++++++++++++++------------------- R/regression.R | 2 R/toolbox.R | 148 +++++++++++++++++++++++++++++-- R/weightedmean.R | 155 ++++++++++++++++++++++----------- README.md | 3 data/examples.rda |binary inst/CITATION | 2 man/agespectrum.Rd | 7 + man/cad.Rd | 30 +++--- man/concordia.Rd | 15 ++- man/evolution.Rd | 12 ++ man/helioplot.Rd | 12 ++ man/isochron.Rd | 34 +++++-- man/kde.Rd | 92 ++++++++++--------- man/ludwig.Rd | 4 man/mds.Rd | 5 - man/radialplot.Rd | 75 ++++++++++------ man/weightedmean.Rd | 37 +++++-- 34 files changed, 1192 insertions(+), 701 deletions(-)
Title: A Framework for Dimensionality Reduction
Description: A collection of dimensionality reduction
techniques from R packages and a common
interface for calling the methods.
Author: Guido Kraemer [aut, cre]
Maintainer: Guido Kraemer <gkraemer@bgc-jena.mpg.de>
Diff between dimRed versions 0.2.0 dated 2018-11-08 and 0.2.1 dated 2018-11-09
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- NAMESPACE | 2 ++ 3 files changed, 8 insertions(+), 6 deletions(-)
Title: Detrend Images
Description: Detrend fluorescence microscopy image series for fluorescence
fluctuation and correlation spectroscopy ('FCS' and 'FFS') analysis. This
package contains functionality published in a 2016 paper
<doi:10.1093/bioinformatics/btx434> but it has been extended since then with
the Robin Hood algorithm and thus contains unpublished work.
Author: Rory Nolan [aut, cre] (<https://orcid.org/0000-0002-5239-4043>),
Luis Alvarez [ctb, cph] (<https://orcid.org/0000-0003-1316-1906>),
Sergi Padilla-Parra [ctb, ths, cph]
(<https://orcid.org/0000-0002-8010-9481>)
Maintainer: Rory Nolan <rorynoolan@gmail.com>
Diff between detrendr versions 0.5.1 dated 2018-04-24 and 0.6.0 dated 2018-11-09
detrendr-0.5.1/detrendr/inst/doc/detrendr.R |only detrendr-0.5.1/detrendr/inst/doc/detrendr.Rmd |only detrendr-0.5.1/detrendr/inst/doc/detrendr.html |only detrendr-0.5.1/detrendr/vignettes/detrendr.Rmd |only detrendr-0.6.0/detrendr/DESCRIPTION | 48 - detrendr-0.6.0/detrendr/MD5 | 100 +- detrendr-0.6.0/detrendr/NEWS.md | 28 detrendr-0.6.0/detrendr/R/RcppExports.R | 8 detrendr-0.6.0/detrendr/R/best_degree.R | 83 +- detrendr-0.6.0/detrendr/R/best_l.R | 103 +- detrendr-0.6.0/detrendr/R/best_swaps.R | 367 +++++---- detrendr-0.6.0/detrendr/R/best_tau.R | 81 +- detrendr-0.6.0/detrendr/R/brightness.R | 1 detrendr-0.6.0/detrendr/R/class_constructors.R | 51 - detrendr-0.6.0/detrendr/R/detrend.R | 405 ++++++---- detrendr-0.6.0/detrendr/R/detrendr.R | 2 detrendr-0.6.0/detrendr/R/dir_detrend.R | 117 +- detrendr-0.6.0/detrendr/R/frame_stats.R | 1 detrendr-0.6.0/detrendr/R/iterators.R | 4 detrendr-0.6.0/detrendr/R/myrs.R | 56 - detrendr-0.6.0/detrendr/R/pillar_stats.R | 16 detrendr-0.6.0/detrendr/R/polynom.R | 28 detrendr-0.6.0/detrendr/R/utils.R | 166 +++- detrendr-0.6.0/detrendr/R/vec_stats.R | 1 detrendr-0.6.0/detrendr/build/vignette.rds |binary detrendr-0.6.0/detrendr/inst/WORDLIST |only detrendr-0.6.0/detrendr/inst/doc/batch-mode.R |only detrendr-0.6.0/detrendr/inst/doc/batch-mode.Rmd |only detrendr-0.6.0/detrendr/inst/doc/batch-mode.html |only detrendr-0.6.0/detrendr/inst/doc/single-images.R |only detrendr-0.6.0/detrendr/inst/doc/single-images.Rmd |only detrendr-0.6.0/detrendr/inst/doc/single-images.html |only detrendr-0.6.0/detrendr/inst/extdata/2ch100frame.tif |only detrendr-0.6.0/detrendr/inst/extdata/bleached.tif |binary detrendr-0.6.0/detrendr/man/best_swaps.Rd | 6 detrendr-0.6.0/detrendr/man/best_tau.Rd | 3 detrendr-0.6.0/detrendr/man/detrend-directory.Rd | 14 detrendr-0.6.0/detrendr/man/detrended_img.Rd | 11 detrendr-0.6.0/detrendr/man/detrending.Rd | 14 detrendr-0.6.0/detrendr/man/detrendr.Rd | 1 detrendr-0.6.0/detrendr/man/figures |only detrendr-0.6.0/detrendr/man/rfromboxes.Rd | 3 detrendr-0.6.0/detrendr/man/rtoboxes.Rd | 3 detrendr-0.6.0/detrendr/src/RcppExports.cpp | 24 detrendr-0.6.0/detrendr/src/anyNA.cpp | 2 detrendr-0.6.0/detrendr/tests/spelling.R |only detrendr-0.6.0/detrendr/tests/testthat/test-anyNA.R |only detrendr-0.6.0/detrendr/tests/testthat/test-best_params.R | 118 ++ detrendr-0.6.0/detrendr/tests/testthat/test-class_constructors.R | 33 detrendr-0.6.0/detrendr/tests/testthat/test-detrend.R | 220 +++-- detrendr-0.6.0/detrendr/tests/testthat/test-dir_detrend.R | 190 +++- detrendr-0.6.0/detrendr/tests/testthat/test-frame_stats.R |only detrendr-0.6.0/detrendr/tests/testthat/test-iterators.R | 1 detrendr-0.6.0/detrendr/tests/testthat/test-myrs.R | 93 +- detrendr-0.6.0/detrendr/tests/testthat/test-pillar_stats.R | 68 + detrendr-0.6.0/detrendr/tests/testthat/test-polynom.R | 16 detrendr-0.6.0/detrendr/tests/testthat/test-smooth.R | 8 detrendr-0.6.0/detrendr/tests/testthat/test-utils.R | 111 ++ detrendr-0.6.0/detrendr/vignettes/batch-mode.Rmd |only detrendr-0.6.0/detrendr/vignettes/single-images.Rmd |only 60 files changed, 1797 insertions(+), 808 deletions(-)
Title: Declare and Diagnose Research Designs
Description: Researchers can characterize and learn about the properties of
research designs before implementation using `DeclareDesign`. Ex ante
declaration and diagnosis of designs can help researchers clarify the
strengths and limitations of their designs and to improve their
properties, and can help readers evaluate a research strategy prior
to implementation and without access to results. It can also make it
easier for designs to be shared, replicated, and critiqued.
Author: Graeme Blair [aut, cre],
Jasper Cooper [aut],
Alexander Coppock [aut],
Macartan Humphreys [aut],
Neal Fultz [aut]
Maintainer: Graeme Blair <graeme.blair@ucla.edu>
Diff between DeclareDesign versions 0.10.0 dated 2018-07-29 and 0.12.0 dated 2018-11-09
DeclareDesign-0.10.0/DeclareDesign/build |only DeclareDesign-0.10.0/DeclareDesign/inst/doc |only DeclareDesign-0.10.0/DeclareDesign/man/DeclareDesign-deprecated.Rd |only DeclareDesign-0.10.0/DeclareDesign/vignettes |only DeclareDesign-0.12.0/DeclareDesign/DESCRIPTION | 15 - DeclareDesign-0.12.0/DeclareDesign/MD5 | 102 +++---- DeclareDesign-0.12.0/DeclareDesign/NAMESPACE | 9 DeclareDesign-0.12.0/DeclareDesign/NEWS.md | 6 DeclareDesign-0.12.0/DeclareDesign/R/construct_design.R | 6 DeclareDesign-0.12.0/DeclareDesign/R/declare_assignment.R | 20 - DeclareDesign-0.12.0/DeclareDesign/R/declare_estimand.R | 8 DeclareDesign-0.12.0/DeclareDesign/R/declare_estimator.R | 121 ++++++-- DeclareDesign-0.12.0/DeclareDesign/R/declare_potential_outcomes.R | 2 DeclareDesign-0.12.0/DeclareDesign/R/declare_sampling.R | 6 DeclareDesign-0.12.0/DeclareDesign/R/deprecated.R | 23 - DeclareDesign-0.12.0/DeclareDesign/R/design_helper_functions.R | 89 +++++- DeclareDesign-0.12.0/DeclareDesign/R/diagnose_design.R | 30 +- DeclareDesign-0.12.0/DeclareDesign/R/diagnosis_helper_functions.R | 7 DeclareDesign-0.12.0/DeclareDesign/R/expand_design.R | 127 +++------ DeclareDesign-0.12.0/DeclareDesign/R/simulate_design.R | 136 ++++++---- DeclareDesign-0.12.0/DeclareDesign/R/utilities.R | 9 DeclareDesign-0.12.0/DeclareDesign/man/declare_estimand.Rd | 8 DeclareDesign-0.12.0/DeclareDesign/man/declare_estimator.Rd | 25 + DeclareDesign-0.12.0/DeclareDesign/man/declare_potential_outcomes.Rd | 2 DeclareDesign-0.12.0/DeclareDesign/man/deprecated.Rd |only DeclareDesign-0.12.0/DeclareDesign/man/diagnose_design.Rd | 10 DeclareDesign-0.12.0/DeclareDesign/man/expand_conditions.Rd | 4 DeclareDesign-0.12.0/DeclareDesign/man/expand_design.Rd | 13 DeclareDesign-0.12.0/DeclareDesign/man/plus-.dd.Rd | 6 DeclareDesign-0.12.0/DeclareDesign/man/post_design.Rd | 21 + DeclareDesign-0.12.0/DeclareDesign/man/reexports.Rd |only DeclareDesign-0.12.0/DeclareDesign/man/reshape_diagnosis.Rd | 2 DeclareDesign-0.12.0/DeclareDesign/man/set_citation.Rd | 3 DeclareDesign-0.12.0/DeclareDesign/man/simulate_design.Rd | 7 DeclareDesign-0.12.0/DeclareDesign/tests/testthat/test-assignment.R | 39 ++ DeclareDesign-0.12.0/DeclareDesign/tests/testthat/test-bootstrap-diagnosands.R | 16 + DeclareDesign-0.12.0/DeclareDesign/tests/testthat/test-demo.R | 4 DeclareDesign-0.12.0/DeclareDesign/tests/testthat/test-deprecated.R | 10 DeclareDesign-0.12.0/DeclareDesign/tests/testthat/test-describe_variable.R | 12 DeclareDesign-0.12.0/DeclareDesign/tests/testthat/test-design-library.R |only DeclareDesign-0.12.0/DeclareDesign/tests/testthat/test-diagnosands.R | 1 DeclareDesign-0.12.0/DeclareDesign/tests/testthat/test-diagnose-design.R | 50 +++ DeclareDesign-0.12.0/DeclareDesign/tests/testthat/test-estimands.R | 4 DeclareDesign-0.12.0/DeclareDesign/tests/testthat/test-estimators.R | 8 DeclareDesign-0.12.0/DeclareDesign/tests/testthat/test-expand-design.R | 26 + DeclareDesign-0.12.0/DeclareDesign/tests/testthat/test-fanout.R | 59 +++- DeclareDesign-0.12.0/DeclareDesign/tests/testthat/test-get-estimates.R |only DeclareDesign-0.12.0/DeclareDesign/tests/testthat/test-model.R | 61 +++- DeclareDesign-0.12.0/DeclareDesign/tests/testthat/test-multiple-estimands-one-estimator.R | 2 DeclareDesign-0.12.0/DeclareDesign/tests/testthat/test-noncompliance.R | 5 DeclareDesign-0.12.0/DeclareDesign/tests/testthat/test-post-estimation.R | 18 - DeclareDesign-0.12.0/DeclareDesign/tests/testthat/test-potential-outcomes.R | 21 + DeclareDesign-0.12.0/DeclareDesign/tests/testthat/test-simulate-design.R | 36 ++ DeclareDesign-0.12.0/DeclareDesign/tests/testthat/test-subset.R | 4 54 files changed, 805 insertions(+), 388 deletions(-)
Title: Extract Text from Microsoft Word Documents
Description: Wraps the 'AntiWord' utility to extract text from Microsoft
Word documents. The utility only supports the old 'doc' format, not the
new xml based 'docx' format. Use the 'xml2' package to read the latter.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>),
Adri van Os [cph] (Author 'antiword' utility)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between antiword versions 1.2 dated 2018-10-07 and 1.3 dated 2018-11-09
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS | 3 +++ R/antiword.R | 5 +---- 4 files changed, 11 insertions(+), 11 deletions(-)
Title: Discrete-Event Simulation for R
Description: A process-oriented and trajectory-based Discrete-Event Simulation
(DES) package for R. It is designed as a generic yet powerful framework. The
architecture encloses a robust and fast simulation core written in 'C++' with
automatic monitoring capabilities. It provides a rich and flexible R API that
revolves around the concept of trajectory, a common path in the simulation
model for entities of the same type. Documentation about 'simmer' is provided
by several vignettes included in this package, via the paper by Ucar, Smeets
& Azcorra (2018, <arXiv:1705.09746>), and the paper by Ucar, Hernández,
Serrano & Azcorra (2018, <doi:10.1109/MCOM.2018.1700960>);
see 'citation("simmer")' for details.
Author: Iñaki Ucar [aut, cph, cre] (<https://orcid.org/0000-0001-6403-5550>),
Bart Smeets [aut, cph]
Maintainer: Iñaki Ucar <iucar@fedoraproject.org>
Diff between simmer versions 4.0.1 dated 2018-09-10 and 4.1.0 dated 2018-11-09
DESCRIPTION | 14 ++- MD5 | 94 ++++++++++---------- NAMESPACE | 6 - NEWS.md | 17 +++ R/RcppExports.R | 36 ++++---- R/schedule-class.R | 15 +-- R/simmer-class.R | 102 ++++++++++++++-------- R/simmer-methods.R | 93 +++++++++++++------- R/trajectory-activities.R | 32 +------ R/trajectory-methods.R | 2 R/utils.R | 5 + R/wrap-class.R | 112 +++++++++++++------------ build/vignette.rds |binary inst/CITATION | 6 - inst/doc/simmer-01-introduction.html | 46 ++++------ inst/doc/simmer-02-jss.pdf |binary inst/doc/simmer-03-trajectories.html | 18 +--- inst/doc/simmer-04-bank-1.html | 14 +-- inst/doc/simmer-04-bank-2.html | 18 +--- inst/doc/simmer-05-simpy.html | 14 +-- inst/doc/simmer-06-queueing.html | 16 +-- inst/doc/simmer-07-ctmc.html | 20 ++-- inst/doc/simmer-08-philosophers.html | 18 +--- inst/doc/simmer-aa-5G.html | 14 +-- inst/include/simmer/activity/rollback.h | 14 +-- inst/include/simmer/process/manager.h | 39 +++++--- inst/include/simmer/simulator.h | 58 ------------ inst/include/simmer/simulator_impl.h | 101 ++++++---------------- man/add_global.Rd |only man/add_resource.Rd | 6 - man/get_capacity.Rd | 19 ++-- man/get_n_generated.Rd | 16 +-- man/set_attribute.Rd | 5 - man/set_trajectory.Rd | 3 man/simmer.Rd | 5 - man/timeout.Rd | 4 man/trajectory.Rd | 2 src/RcppExports.cpp | 95 ++++++++++++++------- src/process.cpp | 28 ++++-- src/resource.cpp | 71 ++++++++++----- src/simulator.cpp | 85 ++++++++++++++++-- tests/testthat/test-simmer-dataframe.R | 2 tests/testthat/test-simmer-generator.R | 2 tests/testthat/test-simmer-global.R |only tests/testthat/test-simmer-resource-schedule.R | 47 +++++++--- tests/testthat/test-simmer.R | 41 ++++----- tests/testthat/test-trajectory-rollback.R | 11 ++ tests/testthat/test-trajectory-select.R | 19 ++++ tests/testthat/test-trajectory-setattribute.R | 4 49 files changed, 773 insertions(+), 616 deletions(-)
Title: Quickly Create Elegant Regression Results Tables and Plots when
Modelling
Description: Generate regression results tables and plots in final
format for publication. Explore models and export directly to PDF
and 'Word' using 'RMarkdown'.
Author: Ewen Harrison [aut, cre],
Tom Drake [aut],
Riinu Ots [aut]
Maintainer: Ewen Harrison <ewen.harrison@ed.ac.uk>
Diff between finalfit versions 0.8.7 dated 2018-09-21 and 0.8.8 dated 2018-11-09
finalfit-0.8.7/finalfit/man/ff_describe.Rd |only finalfit-0.8.7/finalfit/man/interp.median.Rd |only finalfit-0.8.7/finalfit/man/interp.quantiles.Rd |only finalfit-0.8.7/finalfit/man/kurtosi.Rd |only finalfit-0.8.7/finalfit/man/skew.Rd |only finalfit-0.8.8/finalfit/DESCRIPTION | 10 finalfit-0.8.8/finalfit/MD5 | 86 finalfit-0.8.8/finalfit/NAMESPACE | 19 finalfit-0.8.8/finalfit/NEWS.md | 14 finalfit-0.8.8/finalfit/R/ff_glimpse.R | 181 - finalfit-0.8.8/finalfit/R/ff_interaction.R |only finalfit-0.8.8/finalfit/R/ff_metrics.R |only finalfit-0.8.8/finalfit/R/ff_newdata.R | 36 finalfit-0.8.8/finalfit/R/finalfit.R | 746 +++-- finalfit-0.8.8/finalfit/R/finalfit_internal_functions.R | 767 +---- finalfit-0.8.8/finalfit/R/finalfit_package.R | 14 finalfit-0.8.8/finalfit/R/fit2df.R | 794 ++--- finalfit-0.8.8/finalfit/R/missing_glimpse.R |only finalfit-0.8.8/finalfit/R/missing_plot.R | 1 finalfit-0.8.8/finalfit/R/summaryfactorlist.R | 1379 +++++----- finalfit-0.8.8/finalfit/R/surv_plot.R | 4 finalfit-0.8.8/finalfit/README.md | 3 finalfit-0.8.8/finalfit/inst/doc/bootstrap.html | 28 finalfit-0.8.8/finalfit/inst/doc/export.html | 45 finalfit-0.8.8/finalfit/inst/doc/finalfit.html | 2 finalfit-0.8.8/finalfit/inst/doc/missing.html | 53 finalfit-0.8.8/finalfit/man/condense_fit.Rd | 6 finalfit-0.8.8/finalfit/man/extract_fit.Rd | 42 finalfit-0.8.8/finalfit/man/ff_glimpse.Rd | 14 finalfit-0.8.8/finalfit/man/ff_interaction.Rd |only finalfit-0.8.8/finalfit/man/ff_label.Rd |only finalfit-0.8.8/finalfit/man/ff_metrics.Rd |only finalfit-0.8.8/finalfit/man/finalfit-package.Rd | 11 finalfit-0.8.8/finalfit/man/finalfit.Rd | 43 finalfit-0.8.8/finalfit/man/fit2df.Rd | 58 finalfit-0.8.8/finalfit/man/missing_df.Rd | 1 finalfit-0.8.8/finalfit/man/missing_glimpse.Rd |only finalfit-0.8.8/finalfit/man/summary_factorlist.Rd | 10 finalfit-0.8.8/finalfit/man/summary_factorlist0.Rd | 8 finalfit-0.8.8/finalfit/man/summary_factorlist1.Rd | 8 finalfit-0.8.8/finalfit/man/summary_factorlist2.Rd | 8 finalfit-0.8.8/finalfit/man/summary_factorlist3.Rd | 8 finalfit-0.8.8/finalfit/man/summary_factorlist4.Rd | 8 finalfit-0.8.8/finalfit/man/summary_factorlist5.Rd | 8 finalfit-0.8.8/finalfit/tests |only finalfit-0.8.8/finalfit/vignettes/export_cache/html/unnamed-chunk-8_7b1d29257e73baaeb9bec379b79b6c81.RData |binary 46 files changed, 2167 insertions(+), 2248 deletions(-)
Title: Cell Type Deconvolution from Gene Expressions
Description: Deconvolving cell types from high-throughput gene profiling data.
Author: Gregory Hunt
Maintainer: Gregory Hunt <gjhunt@umich.edu>
Diff between dtangle versions 0.3.0 dated 2018-07-05 and 0.3.1 dated 2018-11-09
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- R/combine_Y_refs.R | 14 +++++++++++++- R/find_markers_fn.R | 15 ++++++++++++--- R/phats_fn.R | 2 ++ R/process_markers.R | 1 + build/vignette.rds |binary inst/doc/basic-deconvolution.html | 11 ++++++----- man/find_markers.Rd | 4 ++-- 9 files changed, 49 insertions(+), 24 deletions(-)
Title: Bayesian Dose-Finding Designs using Pharmacokinetics (PK) for
Phase I Clinical Trials
Description: Statistical methods involving PK measures are provided, in the dose allocation process during a Phase I clinical trials. These methods, proposed by Ursino et al, (2017) <doi:10.1002/bimj.201600084>, enter pharmacokinetics (PK) in the dose finding designs in different ways, including covariates models, dependent variable or hierarchical models. This package provides functions to generate data from several scenarios and functions to run simulations which their objective is to determine the maximum tolerated dose (MTD).
Author: Artemis Toumazi [cre, aut],
Sarah Zohar [aut],
Moreno Ursino [aut],
Trustees of Columbia University [cph] (R/stanmodels.R),
French National Institute of Health and Medical Research [cph]
Maintainer: Artemis Toumazi <artemis.toumazi@gmail.com>
Diff between dfpk versions 3.5.0 dated 2018-07-29 and 3.5.1 dated 2018-11-09
DESCRIPTION | 14 MD5 | 6 src/Makevars | 3 src/include/models.hpp | 1531 ++++++++++++++++++++++++------------------------- 4 files changed, 783 insertions(+), 771 deletions(-)
Title: Bayesian Multilevel Mediation
Description: Easy estimation of Bayesian multilevel mediation models with Stan.
Author: Matti Vuorre [aut, cre] (<https://orcid.org/0000-0001-5052-066X>)
Maintainer: Matti Vuorre <mv2521@columbia.edu>
Diff between bmlm versions 1.3.8 dated 2018-10-17 and 1.3.9 dated 2018-11-09
DESCRIPTION | 12 +++++++----- MD5 | 20 ++++++++++---------- NAMESPACE | 1 + NEWS.md | 4 ++++ man/mlm.Rd | 4 ++-- man/mlm_pars_plot.Rd | 6 +++--- man/mlm_path_plot.Rd | 4 ++-- man/mlm_spaghetti_plot.Rd | 8 ++++---- man/mlm_summary.Rd | 4 ++-- src/Makevars | 4 ++-- src/Makevars.win | 5 ++--- 11 files changed, 39 insertions(+), 33 deletions(-)
Title: Bayesian Dynamic Factor Analysis (DFA) with 'Stan'
Description: Implements Bayesian dynamic factor analysis with 'Stan'. Dynamic
factor analysis is a dimension reduction tool for multivariate time series.
'bayesdfa' extends conventional dynamic factor models in several ways.
First, extreme events may be estimated in the latent trend by modeling
process error with a student-t distribution. Second, autoregressive and
moving average components can be optionally included. Third, the estimated
dynamic factors can be analyzed with hidden Markov models to evaluate
support for latent regimes.
Author: Eric J. Ward [aut, cre],
Sean C. Anderson [aut],
Luis A. Damiano [aut],
Mary E. Hunsicker, [ctb],
Mike A. Litzow [ctb],
Trustees of Columbia University [cph]
Maintainer: Eric J. Ward <eric.ward@noaa.gov>
Diff between bayesdfa versions 0.1.0 dated 2018-09-19 and 0.1.1 dated 2018-11-09
DESCRIPTION | 9 MD5 | 22 - NEWS.md | 4 build/vignette.rds |binary inst/doc/bayesdfa.html | 422 +++++++++++++++++------ man/fit_dfa.Rd | 10 man/is_converged.Rd | 4 man/plot_loadings.Rd | 4 man/sim_dfa.Rd | 4 man/trend_cor.Rd | 5 src/Makevars | 2 src/include/models.hpp | 866 +++++++++++++++++++++++++++++++------------------ 12 files changed, 908 insertions(+), 444 deletions(-)
Title: Bayesian Regression with Time-Varying Coefficients
Description: Bayesian dynamic regression models where the regression
coefficients can vary over time as random walks.
Gaussian, Poisson, and binomial observations are supported.
The Markov chain Monte Carlo computations are done using
Hamiltonian Monte Carlo provided by Stan, using a state space representation
of the model in order to marginalise over the coefficients for efficient sampling.
For non-Gaussian models, walker uses the importance sampling type estimators based on
approximate marginal MCMC as in Vihola, Helske, Franks (2017, <arXiv:1609.02541>).
Author: Jouni Helske [aut, cre] (<https://orcid.org/0000-0001-7130-793X>)
Maintainer: Jouni Helske <jouni.helske@iki.fi>
Diff between walker versions 0.2.3 dated 2018-10-23 and 0.2.3-1 dated 2018-11-09
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- README.md | 4 ++++ inst/doc/walker.html | 10 +++++----- src/Makevars | 8 ++++++-- src/Makevars.win | 8 ++++++-- 6 files changed, 31 insertions(+), 19 deletions(-)
Title: Survival Analysis in Health Economic Evaluation
Description: Contains a suite of functions for survival analysis in health economics. These can be used to run survival models under a frequentist (based on maximum likelihood) or a Bayesian approach (both based on Integrated Nested Laplace Approximation or Hamiltonian Monte Carlo). The user can specify a set of parametric models using a common notation and select the preferred mode of inference. The results can also be post-processed to produce probabilistic sensitivity analysis and can be used to export the output to an Excel file (e.g. for a Markov model, as often done by modellers and practitioners).
Author: Gianluca Baio [aut, cre]
Maintainer: Gianluca Baio <gianluca@stats.ucl.ac.uk>
Diff between survHE versions 1.0.64 dated 2018-10-19 and 1.0.65 dated 2018-11-09
DESCRIPTION | 12 ++++++------ MD5 | 12 ++++++++---- README.md |only man/survHE-package.Rd | 2 +- src/Makevars | 2 +- src/Makevars.win | 2 +- src/include |only src/stan_files/chunks/common_functions.stan |only tools/make_cpp.R |only 9 files changed, 17 insertions(+), 13 deletions(-)
Title: Group Sequential Design Class for Clinical Trials
Description: S4 class object for creating and managing group sequential designs. It calculates the efficacy and futility boundaries at each look. It allows modifying the design and tracking the design update history.
Author: David A Schoenfeld, PhD and Hui Zheng, PhD
Maintainer: Hui Zheng <hzheng1@mgh.harvard.edu>
Diff between seqmon versions 2.1 dated 2016-10-12 and 2.2 dated 2018-11-09
seqmon-2.1/seqmon/R/sequential_design_class.R |only seqmon-2.1/seqmon/man/calcBoundaries-methods.Rd |only seqmon-2.1/seqmon/man/curtailDesign-methods.Rd |only seqmon-2.1/seqmon/man/getProbabilities-methods.Rd |only seqmon-2.1/seqmon/man/plotBoundaries-methods.Rd |only seqmon-2.1/seqmon/man/printSummary-methods.Rd |only seqmon-2.1/seqmon/man/printSummary.Rd |only seqmon-2.1/seqmon/man/setAlphaspendfString-methods.Rd |only seqmon-2.1/seqmon/man/setBaseAlphaspendf-methods.Rd |only seqmon-2.1/seqmon/man/setBaseBetaspendf-methods.Rd |only seqmon-2.1/seqmon/man/setBetaspendfString-methods.Rd |only seqmon-2.1/seqmon/man/setCurrentLook-methods.Rd |only seqmon-2.1/seqmon/man/setDatestamp-methods.Rd |only seqmon-2.1/seqmon/man/setNoncentrality-methods.Rd |only seqmon-2.1/seqmon/man/setTimes-methods.Rd |only seqmon-2.1/seqmon/man/updateDesign-methods.Rd |only seqmon-2.2/seqmon/DESCRIPTION | 10 ++-- seqmon-2.2/seqmon/LICENSE | 2 seqmon-2.2/seqmon/MD5 | 33 ++++---------- seqmon-2.2/seqmon/NAMESPACE | 8 ++- seqmon-2.2/seqmon/R/sequential_design_classV2.2.R |only seqmon-2.2/seqmon/man/print.Rd |only seqmon-2.2/seqmon/man/seqmon-package.Rd | 3 + seqmon-2.2/seqmon/man/sequential.design-class.Rd | 42 +++++++++--------- seqmon-2.2/seqmon/man/setDatestamp.Rd | 2 seqmon-2.2/seqmon/man/summary.Rd |only seqmon-2.2/seqmon/man/updateDesign.Rd | 3 + 27 files changed, 50 insertions(+), 53 deletions(-)
Title: A Collection of Efficient and Extremely Fast R Functions
Description: A collection of fast (utility) functions for data analysis. Column- and row- wise means, medians, variances, minimums, maximums, many t, F and G-square tests, many regressions (normal, logistic, Poisson), are some of the many fast functions. Reference: Tsagris M, Papadakis M. (2018). Taking R to its limits: 70+ tips. PeerJ Preprints 6:e26605v1 <doi:10.7287/peerj.preprints.26605v1>.
Author: Manos Papadakis, Michail Tsagris, Marios Dimitriadis, Stefanos Fafalios, Ioannis Tsamardinos, Matteo Fasiolo, Giorgos Borboudakis, John Burkardt, Changliang Zou, Kleanthi Lakiotaki and Christina Chatzipantsiou.
Maintainer: Manos Papadakis <rfastofficial@gmail.com>
Diff between Rfast versions 1.9.1 dated 2018-07-20 and 1.9.2 dated 2018-11-09
Rfast-1.9.1/Rfast/R/eigs.sym.R |only Rfast-1.9.1/Rfast/R/which_isFactor.R |only Rfast-1.9.1/Rfast/man/eigs.sym.Rd |only Rfast-1.9.1/Rfast/man/which_isFactor.Rd |only Rfast-1.9.1/Rfast/src/reg_lib2.cpp |only Rfast-1.9.1/Rfast/src/reg_lib2.h |only Rfast-1.9.1/Rfast/src/remove_from_namespace.cpp |only Rfast-1.9.1/Rfast/src/which_isFactor.cpp |only Rfast-1.9.2/Rfast/DESCRIPTION | 14 Rfast-1.9.2/Rfast/MD5 | 132 +++---- Rfast-1.9.2/Rfast/NAMESPACE | 2 Rfast-1.9.2/Rfast/NEWS.md | 79 +++- Rfast-1.9.2/Rfast/R/Stack.R | 56 --- Rfast-1.9.2/Rfast/R/colvm.mle.R | 4 Rfast-1.9.2/Rfast/R/cor.fbed.R | 53 +- Rfast-1.9.2/Rfast/R/dirknn.cv.R |only Rfast-1.9.2/Rfast/R/eigen.sym.R |only Rfast-1.9.2/Rfast/R/el.test1.R | 46 +- Rfast-1.9.2/Rfast/R/gammacon.R | 42 +- Rfast-1.9.2/Rfast/R/gammareg.R | 41 +- Rfast-1.9.2/Rfast/R/gammaregs.R | 76 ++-- Rfast-1.9.2/Rfast/R/invgauss.reg.R | 58 +-- Rfast-1.9.2/Rfast/R/invgauss.regs.R | 2 Rfast-1.9.2/Rfast/R/multinom.mle.R | 4 Rfast-1.9.2/Rfast/R/multinom.regs.R | 4 Rfast-1.9.2/Rfast/R/omp.R | 170 ++++++--- Rfast-1.9.2/Rfast/R/score.glms.R | 7 Rfast-1.9.2/Rfast/R/spml.mle.R | 2 Rfast-1.9.2/Rfast/R/spml.reg.R | 49 -- Rfast-1.9.2/Rfast/R/spml.regs.R | 2 Rfast-1.9.2/Rfast/R/ufactor.R | 1 Rfast-1.9.2/Rfast/R/univglms.R | 1 Rfast-1.9.2/Rfast/R/univglms2.R | 9 Rfast-1.9.2/Rfast/man/Rfast-package.Rd | 4 Rfast-1.9.2/Rfast/man/checkNamespace.Rd | 2 Rfast-1.9.2/Rfast/man/dirknn.Rd | 2 Rfast-1.9.2/Rfast/man/dirknn.cv.Rd |only Rfast-1.9.2/Rfast/man/dmvnorm.Rd | 6 Rfast-1.9.2/Rfast/man/eigen.sym.Rd |only Rfast-1.9.2/Rfast/man/g2Test.Rd | 2 Rfast-1.9.2/Rfast/man/g2Test_univariate.Rd | 2 Rfast-1.9.2/Rfast/man/g2tests.Rd | 2 Rfast-1.9.2/Rfast/man/gammareg.Rd | 4 Rfast-1.9.2/Rfast/man/gammaregs.Rd | 2 Rfast-1.9.2/Rfast/man/gchi2Test.Rd | 4 Rfast-1.9.2/Rfast/man/invgauss.reg.Rd | 2 Rfast-1.9.2/Rfast/man/knn.Rd | 2 Rfast-1.9.2/Rfast/man/knn.cv.Rd | 2 Rfast-1.9.2/Rfast/man/multinom.regs.Rd | 6 Rfast-1.9.2/Rfast/man/ompr.Rd | 2 Rfast-1.9.2/Rfast/man/permcor.Rd | 14 Rfast-1.9.2/Rfast/man/spatmed.reg.Rd | 2 Rfast-1.9.2/Rfast/man/spml.reg.Rd | 5 Rfast-1.9.2/Rfast/man/which.is.Rd |only Rfast-1.9.2/Rfast/src/Norm.cpp | 2 Rfast-1.9.2/Rfast/src/Sort.cpp | 6 Rfast-1.9.2/Rfast/src/add_to_namespace.cpp | 47 ++ Rfast-1.9.2/Rfast/src/check.cpp | 19 - Rfast-1.9.2/Rfast/src/col_row_utilities.cpp | 49 +- Rfast-1.9.2/Rfast/src/colweibull_mle.cpp | 58 --- Rfast-1.9.2/Rfast/src/dir_knn.cpp | 21 - Rfast-1.9.2/Rfast/src/group.cpp | 14 Rfast-1.9.2/Rfast/src/init.c | 10 Rfast-1.9.2/Rfast/src/multinom_regs.cpp | 140 +++++++ Rfast-1.9.2/Rfast/src/my_k_sorted_array.cpp | 9 Rfast-1.9.2/Rfast/src/reg_lib.cpp | 427 ++++++++---------------- Rfast-1.9.2/Rfast/src/reg_lib.h | 35 - Rfast-1.9.2/Rfast/src/sort_unique.cpp | 198 +++++------ Rfast-1.9.2/Rfast/src/spml.cpp | 351 +++++++++++-------- Rfast-1.9.2/Rfast/src/system_files.cpp | 33 + Rfast-1.9.2/Rfast/src/templates.h | 7 Rfast-1.9.2/Rfast/src/topological_sort.cpp | 6 Rfast-1.9.2/Rfast/src/weib_reg.cpp | 78 ++-- Rfast-1.9.2/Rfast/src/weibull_mle.cpp |only 74 files changed, 1307 insertions(+), 1122 deletions(-)
Title: Genotype Quality Control with 'PLINK'
Description: Genotyping arrays enable the direct measurement of an individuals
genotype at thousands of markers. 'plinkQC' facilitates genotype quality
control for genetic association studies as described by Anderson and
colleagues (2010) <doi:10.1038/nprot.2010.116>. It makes 'PLINK' basic
statistics (e.g. missing genotyping rates per individual, allele frequencies
per genetic marker) and relationship functions accessible from 'R' and
generates a per-individual and per-marker quality control report.
Individuals and markers that fail the quality control can subsequently be
removed to generate a new, clean dataset. Removal of individuals based on
relationship status is optimised to retain as many individuals as possible
in the study.
Author: Hannah Meyer [aut, cre] (<https://orcid.org/0000-0003-4564-0899>)
Maintainer: Hannah Meyer <hannah@ebi.ac.uk>
Diff between plinkQC versions 0.1.1 dated 2018-11-06 and 0.2.0 dated 2018-11-09
DESCRIPTION | 8 MD5 | 90 ++++--- NAMESPACE | 3 NEWS.md | 20 + R/applyQC.R | 161 +++++++------ R/individualQC.R | 434 +++++++++++-------------------------- R/markerQC.R | 194 ++++++---------- R/utils.R | 71 ++++-- README.md | 4 inst/doc/AncestryCheck.R | 2 inst/doc/AncestryCheck.Rmd | 2 inst/doc/AncestryCheck.pdf |binary inst/doc/Genomes1000.pdf |binary inst/doc/HapMap.pdf |binary inst/doc/plinkQC.R | 29 +- inst/doc/plinkQC.Rmd | 31 +- inst/doc/plinkQC.pdf |binary man/checkPlink.Rd | 15 - man/check_ancestry.Rd | 11 man/check_het_and_miss.Rd | 11 man/check_hwe.Rd | 11 man/check_maf.Rd | 17 - man/check_relatedness.Rd | 11 man/check_sex.Rd | 15 - man/check_snp_missingness.Rd | 11 man/cleanData.Rd | 13 - man/evaluate_check_het_and_miss.Rd | 2 man/evaluate_check_sex.Rd | 15 - man/overviewPerIndividualQC.Rd | 4 man/perIndividualQC.Rd | 44 +-- man/perMarkerQC.Rd | 17 - man/run_check_ancestry.Rd | 11 man/run_check_heterozygosity.Rd | 11 man/run_check_missingness.Rd | 11 man/run_check_relatedness.Rd | 11 man/run_check_sex.Rd | 11 tests/testthat/data.fail-IBD.IDs | 1 tests/testthat/data.remove.IDs | 21 + vignettes/AncestryCheck.Rmd | 2 vignettes/checkAncestry.png |only vignettes/checkHetImiss.png |only vignettes/checkRelatedness.png |only vignettes/checkSex.png |only vignettes/hwe.png |only vignettes/individualQC.png |only vignettes/maf.png |only vignettes/markerQC.png |only vignettes/overviewAncestryQC.png |only vignettes/overviewMarkerQC.png |only vignettes/overviewQC.png |only vignettes/plinkQC.Rmd | 31 +- vignettes/snpmissingness.png |only 52 files changed, 646 insertions(+), 710 deletions(-)
Title: Simulating and Conducting Phase 123 Trials
Description: Contains three simulation functions for implementing the entire Phase 123 trial and the separate Eff-Tox and Phase 3 portions of the trial, which may be beneficial for use on clusters. The functions AssignEffTox() and RandomizeEffTox() assign doses to patient cohorts during phase 12 and Reoptimize() determines the optimal dose to continue with during Phase 3. The functions ReturnMeansAgent() and ReturnMeanControl() gives the true mean survival for the agent doses and control and ReturnOCS() gives the operating characteristics of the design.
Author: Andrew G Chapple
Maintainer: Andrew G Chapple <achapp@lsuhsc.edu>
Diff between Phase123 versions 1.9 dated 2018-11-06 and 2.0 dated 2018-11-09
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/ReturnOCS.R | 10 +++++++--- R/SimPhase123.R | 2 +- 4 files changed, 14 insertions(+), 10 deletions(-)
Title: Modeling and Analysis of Stochastic Systems
Description: Compute important quantities when we consider stochastic systems that are observed continuously. Such as, Cost model, Limiting distribution, Transition matrix, Transition distribution and Occupancy matrix. The methods are described, for example, Ross S. (2014), Introduction to Probability Models. Eleven Edition. Academic Press.
Author: Carlos Alberto Cardozo Delgado
Maintainer: Carlos Alberto Cardozo Delgado <cardozorpackages@gmail.com>
Diff between modesto versions 0.1.0 dated 2018-11-03 and 0.1.1 dated 2018-11-09
DESCRIPTION | 9 +++++---- MD5 | 12 ++++++++---- NAMESPACE | 5 +++++ R/ETCt.R |only R/LimDist.R |only R/Mt.R | 5 +++-- man/ETCt.Rd |only man/LimDist.Rd |only man/Mt.Rd | 3 ++- 9 files changed, 23 insertions(+), 11 deletions(-)
Title: MALDI Mass Spectrometry Data Robust Pre-Processing and Analysis
Description: Provides methods for quality control and robust pre-processing and analysis of MALDI mass spectrometry data.
Author: Javier Palarea-Albaladejo
Maintainer: Javier Palarea-Albaladejo <javier.palarea@bioss.ac.uk>
Diff between MALDIrppa versions 1.0.1 dated 2017-09-19 and 1.0.1-2 dated 2018-11-09
DESCRIPTION | 8 ++++---- MD5 | 17 +++++++++-------- NEWS | 7 +++++++ build/vignette.rds |binary inst/CITATION |only inst/doc/MALDIrppa_vignette.Rmd | 4 ++++ inst/doc/MALDIrppa_vignette.html | 20 +++++++++++--------- man/MALDIrppa-package.Rd | 4 ++-- tests/testthat/test_all.R | 4 ++-- vignettes/MALDIrppa_vignette.Rmd | 4 ++++ 10 files changed, 43 insertions(+), 25 deletions(-)
Title: Multilevel Joint Modelling Multiple Imputation
Description: Similarly to Schafer's package 'pan', 'jomo' is a package for multilevel joint modelling multiple imputation (Carpenter and Kenward, 2013) <doi: 10.1002/9781119942283>.
Novel aspects of 'jomo' are the possibility of handling binary and categorical data through latent normal variables, the option to use cluster-specific covariance matrices and to impute compatibly with the substantive model.
Author: Matteo Quartagno, James Carpenter
Maintainer: Matteo Quartagno <m.quartagno@ucl.ac.uk>
Diff between jomo versions 2.6-4 dated 2018-08-30 and 2.6-5 dated 2018-11-09
DESCRIPTION | 12 +-- MD5 | 130 ++++++++++++++++++++--------------------- R/jomo.clmm.MCMCchain.R | 20 ++++-- R/jomo.clmm.R | 2 R/jomo.coxph.MCMCchain.R | 9 ++ R/jomo.glm.MCMCchain.R | 9 ++ R/jomo.glmer.MCMCchain.R | 18 ++++- R/jomo.lm.MCMCchain.R | 9 ++ R/jomo.lmer.MCMCchain.R | 18 ++++- R/jomo.polr.MCMCchain.R | 9 ++ R/jomo1cat.MCMCchain.R | 9 ++ R/jomo1con.MCMCchain.R | 9 ++ R/jomo1mix.MCMCchain.R | 9 ++ R/jomo1rancat.MCMCchain.R | 9 ++ R/jomo1rancathr.MCMCchain.R | 9 ++ R/jomo1rancon.MCMCchain.R | 9 ++ R/jomo1ranconhr.MCMCchain.R | 9 ++ R/jomo1ranmix.MCMCchain.R | 9 ++ R/jomo1ranmixhr.MCMCchain.R | 9 ++ R/jomo2com.MCMCchain.R | 18 ++++- R/jomo2hr.MCMCchain.R | 18 ++++- man/jomo.MCMCchain.Rd | 8 -- man/jomo.Rd | 19 ++++- man/jomo.clmm.MCMCchain.Rd | 11 --- man/jomo.clmm.Rd | 9 +- man/jomo.coxph.Rd | 3 man/jomo.glm.MCMCchain.Rd | 8 -- man/jomo.glm.Rd | 15 ++-- man/jomo.glmer.MCMCchain.Rd | 11 --- man/jomo.glmer.Rd | 12 +-- man/jomo.lm.MCMCchain.Rd | 9 +- man/jomo.lm.Rd | 11 +-- man/jomo.lmer.MCMCchain.Rd | 14 +--- man/jomo.lmer.Rd | 8 -- man/jomo.polr.MCMCchain.Rd | 16 ++--- man/jomo.polr.Rd | 19 ++--- man/jomo.smc.MCMCchain.Rd | 16 ++--- man/jomo.smc.Rd | 15 ++-- man/jomo1.MCMCchain.Rd | 8 -- man/jomo1.Rd | 12 ++- man/jomo1cat.MCMCchain.Rd | 11 ++- man/jomo1cat.Rd | 14 +++- man/jomo1con.MCMCchain.Rd | 8 +- man/jomo1con.Rd | 29 +-------- man/jomo1mix.MCMCchain.Rd | 13 +--- man/jomo1mix.Rd | 31 ++------- man/jomo1ran.MCMCchain.Rd | 12 +-- man/jomo1ran.Rd | 11 ++- man/jomo1rancat.MCMCchain.Rd | 10 +-- man/jomo1rancat.Rd | 11 ++- man/jomo1rancathr.MCMCchain.Rd | 11 +-- man/jomo1rancathr.Rd | 13 ++-- man/jomo1rancon.MCMCchain.Rd | 14 ++-- man/jomo1rancon.Rd | 30 +-------- man/jomo1ranconhr.MCMCchain.Rd | 18 +++-- man/jomo1ranconhr.Rd | 29 ++------- man/jomo1ranmix.MCMCchain.Rd | 12 +-- man/jomo1ranmix.Rd | 35 ++--------- man/jomo1ranmixhr.MCMCchain.Rd | 14 ++-- man/jomo1ranmixhr.Rd | 33 ++-------- man/jomo2.MCMCchain.Rd | 6 + man/jomo2.Rd | 16 +++-- man/jomo2com.MCMCchain.Rd | 14 +++- man/jomo2com.Rd | 13 ++-- man/jomo2hr.MCMCchain.Rd | 13 ++-- man/jomo2hr.Rd | 13 ++-- 66 files changed, 528 insertions(+), 483 deletions(-)
Title: Inference in Randomized Controlled Trials with Death and
Missingness
Description: In randomized studies involving severely ill patients, functional
outcomes are often unobserved due to missed clinic visits, premature
withdrawal or death. It is well known that if these unobserved functional
outcomes are not handled properly, biased treatment comparisons can be
produced. In this package, we implement a procedure for comparing treatments
that is based on the composite endpoint of both the functional outcome and
survival. The procedure was proposed in Wang et al. (2016) <DOI:10.1111/biom.12594>.
It considers missing data imputation with a sensitivity
analysis strategy to handle the unobserved functional outcomes not due to
death.
Author: Chenguang Wang [aut, cre],
Andrew Leroux [aut, cre],
Elizabeth Colantuoni [aut],
Daniel O Scharfstein [aut],
Trustees of Columbia University [cph] (tools/make_cpp.R, R/stanmodels.R)
Maintainer: Chenguang Wang <cwang68@jhmi.edu>
Diff between idem versions 3.5 dated 2018-04-12 and 4.0 dated 2018-11-09
idem-3.5/idem/cleanup |only idem-3.5/idem/cleanup.win |only idem-3.5/idem/exec |only idem-3.5/idem/src/Modules.cpp |only idem-3.5/idem/src/include |only idem-3.5/idem/tools/make_cpp.R |only idem-4.0/idem/DESCRIPTION | 20 idem-4.0/idem/MD5 | 44 idem-4.0/idem/R/idem_data.R | 3 idem-4.0/idem/R/stanmodels.R | 44 idem-4.0/idem/R/zzz.R | 11 idem-4.0/idem/build/vignette.rds |binary idem-4.0/idem/inst/doc/vignette.html |18955 ++++++++++++-------------------- idem-4.0/idem/inst/include |only idem-4.0/idem/inst/shiny/composite_ui.R | 16 idem-4.0/idem/inst/shiny/server.R | 11 idem-4.0/idem/man/imData.Rd | 7 idem-4.0/idem/man/imImpAll.Rd | 6 idem-4.0/idem/man/imImpSingle.Rd | 3 idem-4.0/idem/man/imInfer.Rd | 3 idem-4.0/idem/man/plot.IDEMIMP.Rd | 4 idem-4.0/idem/man/plot.IDEMINFER.Rd | 4 idem-4.0/idem/man/print.IDEMERROR.Rd | 3 idem-4.0/idem/src/Makevars | 22 idem-4.0/idem/src/Makevars.win |only idem-4.0/idem/src/init.cpp |only idem-4.0/idem/src/stan_files |only idem-4.0/idem/tools/make_cc.R |only 28 files changed, 7671 insertions(+), 11485 deletions(-)
Title: Efficient Designs for Discrete Choice Experiments
Description: Generates efficient designs for discrete choice experiments based on the multinomial logit model, and individually adapted designs for the mixed multinomial logit model. The generated designs can be presented on screen and choice data can be gathered using a shiny application. Crabbe M, Akinc D and Vandebroek M (2014) <doi:10.1016/j.trb.2013.11.008>.
Author: Frits Traets [aut, cre]
Maintainer: Frits Traets <frits.traets@kuleuven.be>
Diff between idefix versions 0.3.1 dated 2018-10-15 and 0.3.3 dated 2018-11-09
DESCRIPTION | 6 - MD5 | 25 ++++--- NAMESPACE | 1 R/Fullsets_ucpp.R | 4 + R/efficiency_algorithms.R | 63 ++++++++++++++----- R/efficiency_criterions.R | 148 ++++++++++++++++++++++++++++++++++------------ R/estimation_support.R | 9 +- R/generation.R | 12 +-- R/importance_sampling.R | 2 R/shiny_support.R | 59 +++++++++++++----- build/partial.rdb |binary man/DBerr.Rd |only man/Decode.Rd | 9 ++ man/SeqDB.Rd | 6 - 14 files changed, 247 insertions(+), 97 deletions(-)
Title: Generalized Linear Mixed Models with Robust Random Fields for
Spatiotemporal Modeling
Description: Implements Bayesian spatial and spatiotemporal models that
optionally allow for extreme spatial deviations through time. 'glmmfields'
uses a predictive process approach with random fields implemented through
a multivariate-t distribution instead of the usual multivariate normal.
Sampling is conducted with 'Stan'. References: Anderson and Ward (2018)
<doi:10.1002/ecy.2403>.
Author: Sean C. Anderson [aut, cre],
Eric J. Ward [aut],
Trustees of Columbia University [cph]
Maintainer: Sean C. Anderson <sean@seananderson.ca>
Diff between glmmfields versions 0.1.0 dated 2018-06-24 and 0.1.1 dated 2018-11-09
glmmfields-0.1.0/glmmfields/inst/test.R |only glmmfields-0.1.1/glmmfields/DESCRIPTION | 17 glmmfields-0.1.1/glmmfields/MD5 | 41 glmmfields-0.1.1/glmmfields/NAMESPACE | 6 glmmfields-0.1.1/glmmfields/NEWS.md | 19 glmmfields-0.1.1/glmmfields/R/format_data.R | 29 glmmfields-0.1.1/glmmfields/R/predict.R | 6 glmmfields-0.1.1/glmmfields/R/stan_pars.R | 1 glmmfields-0.1.1/glmmfields/build/vignette.rds |binary glmmfields-0.1.1/glmmfields/exec/glmmfields.stan | 19 glmmfields-0.1.1/glmmfields/inst/doc/spatial-glms.html | 486 ++------- glmmfields-0.1.1/glmmfields/man/format_data.Rd | 7 glmmfields-0.1.1/glmmfields/man/glmmfields.Rd | 10 glmmfields-0.1.1/glmmfields/man/predict.Rd | 4 glmmfields-0.1.1/glmmfields/man/sim_glmmfields.Rd | 11 glmmfields-0.1.1/glmmfields/src/Makevars | 5 glmmfields-0.1.1/glmmfields/src/include/models.hpp | 524 ++++++---- glmmfields-0.1.1/glmmfields/tests/testthat/test-fit-ar-processes.R | 155 ++ glmmfields-0.1.1/glmmfields/tests/testthat/test-fit-basic.R | 56 - glmmfields-0.1.1/glmmfields/tests/testthat/test-fit-observation-models.R | 26 glmmfields-0.1.1/glmmfields/tests/testthat/test-fit-with-predictors.R | 8 glmmfields-0.1.1/glmmfields/tests/testthat/test-stations.R | 2 22 files changed, 775 insertions(+), 657 deletions(-)
Title: Hierarchical Modelling of Faecal Egg Counts
Description: An implementation of Bayesian hierarchical models
for faecal egg count data to assess anthelmintic
efficacy. Bayesian inference is done via MCMC sampling using Stan.
Author: Craig Wang [aut, cre] (<https://orcid.org/0000-0003-1804-2463>),
Michaela Paul [aut],
Tea Isler [ctb],
Reinhard Furrer [ctb] (<https://orcid.org/0000-0002-6319-2332>),
Trustees of Columbia University [cph] (src/init.cpp, tools/make_cc.R,
R/stanmodels.R)
Maintainer: Craig Wang <craig.wang@uzh.ch>
Diff between eggCounts versions 2.1-1 dated 2018-10-16 and 2.1-2 dated 2018-11-09
eggCounts-2.1-1/eggCounts/cleanup |only eggCounts-2.1-1/eggCounts/cleanup.win |only eggCounts-2.1-1/eggCounts/exec |only eggCounts-2.1-1/eggCounts/inst/chunks/license.stan |only eggCounts-2.1-1/eggCounts/tools/make_cpp.R |only eggCounts-2.1-2/eggCounts/DESCRIPTION | 16 - eggCounts-2.1-2/eggCounts/MD5 | 39 +- eggCounts-2.1-2/eggCounts/R/stanmodels.R | 25 - eggCounts-2.1-2/eggCounts/R/zzz.R | 7 eggCounts-2.1-2/eggCounts/inst/include |only eggCounts-2.1-2/eggCounts/man/eggCounts-package.Rd | 4 eggCounts-2.1-2/eggCounts/src/Makevars | 21 + eggCounts-2.1-2/eggCounts/src/Makevars.win | 21 + eggCounts-2.1-2/eggCounts/src/include/models.hpp | 279 +++++++++++++++++++++ eggCounts-2.1-2/eggCounts/src/init.cpp | 7 eggCounts-2.1-2/eggCounts/src/stan_files |only eggCounts-2.1-2/eggCounts/tools/make_cc.R |only 17 files changed, 365 insertions(+), 54 deletions(-)
Title: Multi-Data-Driven Sparse PLS Robust to Missing Samples
Description: Allows to build Multi-Data-Driven Sparse PLS models. Multi-blocks with
high-dimensional settings are particularly sensible to this.
Author: Hadrien Lorenzo [aut, cre]
Maintainer: Hadrien Lorenzo <hadrien.lorenzo.2015@gmail.com>
Diff between ddsPLS versions 1.0.2 dated 2018-11-06 and 1.0.3 dated 2018-11-09
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/perf_mddsPLS.R | 19 +++++-------------- build/partial.rdb |binary inst/doc/ddsPLS.html | 4 ++-- 5 files changed, 14 insertions(+), 23 deletions(-)
Title: Easy Linguistics Document Writing with R Markdown
Description: Provides 'Shiny gadgets' to search, type, and insert IPA symbols
into documents or scripts, requiring only knowledge about phonetics or
'X-SAMPA'. Also provides functions to facilitate the rendering of IPA
symbols in 'LaTeX' and PDF format, making IPA symbols properly rendered
in all output formats. A minimal R Markdown template for authoring
Linguistics related documents is also bundled with the package.
Author: Yongfu Liao [aut, cre, cph] (<https://orcid.org/0000-0002-1814-2993>)
Maintainer: Yongfu Liao <liao961120@gmail.com>
Diff between linguisticsdown versions 1.0.1 dated 2018-09-30 and 1.1.0 dated 2018-11-09
DESCRIPTION | 21 +++++++++++++-------- MD5 | 7 ++++--- NEWS.md |only R/sysdata.rda |binary README.md | 15 ++++++++++----- 5 files changed, 27 insertions(+), 16 deletions(-)
More information about linguisticsdown at CRAN
Permanent link
Title: Discovery of Motifs in Spatial-Time Series
Description: Allows to identify motifs in spatial-time series. A motif is a previously unknown subsequence of a (spatial) time series with relevant number of occurrences. For this purpose, the Combined Series Approach (CSA) is used.
Author: Amin Bazaz [aut] (Polytech'Montpellier),
Heraldo Borges [aut, cre] (CEFET/RJ),
Eduardo Ogasawara [aut] (CEFET/RJ)
Maintainer: Heraldo Borges <stmotif@eic.cefet-rj.br>
Diff between STMotif versions 1.0.0 dated 2018-10-22 and 1.0.1 dated 2018-11-09
DESCRIPTION | 9 MD5 | 32 - NAMESPACE | 1 NEWS.md | 4 R/mainFunction.R | 367 ++++++++++---------- R/subFunction.R | 46 +- R/visualization.R | 56 +-- inst/doc/discovery-motifs.Rmd | 2 inst/doc/discovery-motifs.html | 6 inst/doc/examples.R | 5 inst/doc/examples.Rmd | 7 inst/doc/examples.html | 647 ++++++++++++++++++++---------------- inst/doc/normalization-and-sax.html | 4 inst/doc/search-stmotifs.html | 400 +++++++++------------- man/intensityDataset.Rd | 6 vignettes/discovery-motifs.Rmd | 2 vignettes/examples.Rmd | 7 17 files changed, 830 insertions(+), 771 deletions(-)
Title: Descriptive Statistics, Transition Plots, and More
Description: Tools for making the descriptive "Table 1" used in medical
articles, a transition plot for showing changes between categories,
flow charts by extending the grid package, a method for
variable selection based on the SVD, Bézier lines with arrows complementing the
ones in the 'grid' package, and more.
Author: Max Gordon <max@gforge.se>
Maintainer: Max Gordon <max@gforge.se>
Diff between Gmisc versions 1.6.4 dated 2018-09-19 and 1.7 dated 2018-11-09
Gmisc-1.6.4/Gmisc/tests/testthat/Rplots.pdf |only Gmisc-1.7/Gmisc/DESCRIPTION | 14 ++--- Gmisc-1.7/Gmisc/MD5 | 31 +++++++------ Gmisc-1.7/Gmisc/NAMESPACE | 4 + Gmisc-1.7/Gmisc/NEWS | 5 ++ Gmisc-1.7/Gmisc/R/boxGrobs.R | 5 +- Gmisc-1.7/Gmisc/R/retrieve_and_has.R |only Gmisc-1.7/Gmisc/inst/doc/Descriptives.html | 40 ++++++++--------- Gmisc-1.7/Gmisc/inst/doc/Grid-based_flowcharts.R | 9 +++ Gmisc-1.7/Gmisc/inst/doc/Grid-based_flowcharts.Rmd | 23 +++++++++ Gmisc-1.7/Gmisc/inst/doc/Grid-based_flowcharts.html | 40 ++++++++++++----- Gmisc-1.7/Gmisc/inst/doc/Transition-class.html | 36 +++++++-------- Gmisc-1.7/Gmisc/inst/doc/transitionPlot.html | 38 ++++++++-------- Gmisc-1.7/Gmisc/man/box.Rd | 2 Gmisc-1.7/Gmisc/man/boxPropGrob.Rd | 2 Gmisc-1.7/Gmisc/man/has.Rd |only Gmisc-1.7/Gmisc/man/retrieve.Rd |only Gmisc-1.7/Gmisc/tests/testthat/test-retrieve_and_has.R |only Gmisc-1.7/Gmisc/vignettes/Grid-based_flowcharts.Rmd | 23 +++++++++ 19 files changed, 180 insertions(+), 92 deletions(-)
Title: MCMC Sampling from 'TMB' Model Object using 'Stan'
Description: Enables all 'rstan' functionality for a 'TMB' model object, in particular MCMC sampling and chain visualization. Sampling can be performed with or without Laplace approximation for the random effects.
Author: Kasper Kristensen
Maintainer: Kasper Kristensen <kaskr@dtu.dk>
Diff between tmbstan versions 1.0.0 dated 2017-12-19 and 1.0.1 dated 2018-11-09
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/tmbstan.R | 7 ++++++- src/Makevars | 2 +- 4 files changed, 14 insertions(+), 9 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-08-03 0.2.1
2017-02-08 0.1.6
2015-02-20 0.1-5
2013-08-31 0.1-4
2013-01-28 0.1-2
2012-05-27 0.1-0
Title: A Test Environment for HTTP Requests
Description: Testing and documenting code that communicates with remote servers
can be painful. Dealing with authentication, server state,
and other complications can make testing seem too costly to
bother with. But it doesn't need to be that hard. This package enables one
to test all of the logic on the R sides of the API in your package without
requiring access to the remote service. Importantly, it provides three
contexts that mock the network connection in different ways, as well as
testing functions to assert that HTTP requests were---or were
not---made. It also allows one to safely record real API responses to use as
test fixtures. The ability to save responses and load them offline also
enables one to write vignettes and other dynamic documents that can be
distributed without access to a live server.
Author: Neal Richardson [aut, cre]
Maintainer: Neal Richardson <neal.p.richardson@gmail.com>
Diff between httptest versions 3.1.0 dated 2018-06-19 and 3.2.0 dated 2018-11-09
DESCRIPTION | 10 ++++---- MD5 | 39 +++++++++++++++++--------------- NAMESPACE | 2 + NEWS.md | 37 ++++++++++++++++++------------ R/capture-requests.R | 22 +++++++++++++++--- R/expect-request.R | 40 +++++++++++++++++++++++++++------ R/trace.R | 24 ++++++++++++++++--- R/use-httptest.R |only README.md | 26 +++++++++------------ build/vignette.rds |binary inst/WORDLIST | 1 inst/doc/httptest.Rmd | 11 ++------- inst/doc/httptest.html | 10 ++------ man/expect_verb.Rd | 24 ++++++++++++++----- man/fake_response.Rd | 4 +-- man/redact.Rd | 3 -- man/use_httptest.Rd |only tests/testthat/helper.R | 7 +++++ tests/testthat/test-capture-requests.R | 10 ++++++++ tests/testthat/test-mock-api.R | 20 ++++++++++++++++ tests/testthat/test-use-httptest.R |only vignettes/httptest.Rmd | 11 ++------- 22 files changed, 200 insertions(+), 101 deletions(-)