Title: C++ Implementations of Phylogenetic Cladogenesis Calculations
Description: Various cladogenesis-related calculations that are slow in pure R are implemented in C++ with Rcpp. These include the calculation of the probability of various scenarios for the inheritance of geographic range at the divergence events on a phylogenetic tree, and other calculations necessary for models which are not continuous-time markov chains (CTMC), but where change instead occurs instantaneously at speciation events. Typically these models must assess the probability of every possible combination of (ancestor state, left descendent state, right descendent state). This means that there are up to (# of states)^3 combinations to investigate, and in biogeographical models, there can easily be hundreds of states, so calculation time becomes an issue. C++ implementation plus clever tricks (many combinations can be eliminated a priori) can greatly speed the computation time over naive R implementations. CITATION INFO: This package is the result of my Ph.D. research, please cite the package if you use it! Type: citation(package="cladoRcpp") to get the citation information.
Author: Nicholas J. Matzke [aut, cre, cph]
Maintainer: Nicholas J. Matzke <nickmatzke.ncse@gmail.com>
Diff between cladoRcpp versions 0.14.4 dated 2014-05-18 and 0.15 dated 2018-10-08
cladoRcpp-0.14.4/cladoRcpp/inst/REFERENCES.bib |only cladoRcpp-0.14.4/cladoRcpp/man/cladoRcpp-package.Rd |only cladoRcpp-0.15/cladoRcpp/DESCRIPTION | 21 cladoRcpp-0.15/cladoRcpp/MD5 | 52 - cladoRcpp-0.15/cladoRcpp/NAMESPACE | 34 cladoRcpp-0.15/cladoRcpp/NEWS | 23 cladoRcpp-0.15/cladoRcpp/R/cladoRcpp-package.R | 8 cladoRcpp-0.15/cladoRcpp/R/cladoRcpp.R | 392 ++++++++-- cladoRcpp-0.15/cladoRcpp/inst/CITATION |only cladoRcpp-0.15/cladoRcpp/man/Rcpp_combn_zerostart.Rd | 52 - cladoRcpp-0.15/cladoRcpp/man/areas_list_to_states_list_old.Rd | 101 -- cladoRcpp-0.15/cladoRcpp/man/numstates_from_numareas.Rd | 122 +-- cladoRcpp-0.15/cladoRcpp/man/rcpp_areas_list_to_states_list.Rd | 86 -- cladoRcpp-0.15/cladoRcpp/man/rcpp_calc_anclikes_sp.Rd | 317 +++----- cladoRcpp-0.15/cladoRcpp/man/rcpp_calc_anclikes_sp_COOprobs.Rd | 237 ++---- cladoRcpp-0.15/cladoRcpp/man/rcpp_calc_anclikes_sp_COOweights_faster.Rd | 251 ++---- cladoRcpp-0.15/cladoRcpp/man/rcpp_calc_anclikes_sp_prebyte.Rd | 198 +---- cladoRcpp-0.15/cladoRcpp/man/rcpp_calc_anclikes_sp_rowsums.Rd | 205 +---- cladoRcpp-0.15/cladoRcpp/man/rcpp_calc_anclikes_sp_using_COOprobs.Rd | 101 +- cladoRcpp-0.15/cladoRcpp/man/rcpp_calc_rowsums_for_COOweights_columnar.Rd | 94 -- cladoRcpp-0.15/cladoRcpp/man/rcpp_calc_splitlikes_using_COOweights_columnar.Rd | 94 -- cladoRcpp-0.15/cladoRcpp/man/rcpp_convolve.Rd | 55 - cladoRcpp-0.15/cladoRcpp/man/rcpp_mult2probvect.Rd | 39 cladoRcpp-0.15/cladoRcpp/man/rcpp_states_list_to_DEmat.Rd | 112 +- cladoRcpp-0.15/cladoRcpp/man/strsplit3.Rd | 27 cladoRcpp-0.15/cladoRcpp/src/basics.cpp | 1 cladoRcpp-0.15/cladoRcpp/src/basics.h | 1 cladoRcpp-0.15/cladoRcpp/src/calc_anclikes_sp.cpp | 130 ++- cladoRcpp-0.15/cladoRcpp/src/init.c |only 29 files changed, 1393 insertions(+), 1360 deletions(-)
Title: Generate PMML for Various Models
Description: The Predictive Model Markup Language (PMML) is an XML-based language which provides a way for applications to define machine learning, statistical and data mining models and to share models between PMML compliant applications. More information about the PMML industry standard and the Data Mining Group can be found at <http://www.dmg.org>. The generated PMML can be imported into any PMML consuming application, such as Zementis Predictive Analytics products, which integrate with web services, relational database systems and deploy natively on Hadoop in conjunction with Hive, Spark or Storm, as well as allow predictive analytics to be executed for IBM z Systems mainframe applications and real-time, streaming analytics platforms.
Author: Graham Williams, Tridivesh Jena, Wen Ching Lin, Michael Hahsler
(arules), Software AG, Hemant Ishwaran, Udaya B. Kogalur, Rajarshi Guha,
Dmitriy Bolotov
Maintainer: Tridivesh Jena <rpmmlsupport@softwareag.com>
Diff between pmml versions 1.5.5 dated 2018-07-06 and 1.5.6 dated 2018-10-08
DESCRIPTION | 22 +-- MD5 | 18 +- R/pmml.R | 5 R/pmml.xgboost.R | 28 ++-- build/vignette.rds |binary inst/ChangeLog | 5 inst/doc/packages_and_functions.html | 217 +++++++---------------------------- man/addOutputField.Rd | 4 man/pmml.Rd | 12 - man/pmml.xgb.Booster.Rd | 5 10 files changed, 93 insertions(+), 223 deletions(-)
Title: Univariate and Multivariate Model-Based Clustering in
Group-Specific Functional Subspaces
Description: The funHDDC algorithm (Schmutz et al., 2018) allows to cluster functional univariate or multivariate data by modeling each group within a specific functional subspace.
Author: A Schmutz, J. Jacques & C. Bouveyron
Maintainer: Charles Bouveyron <charles.bouveyron@gmail.com>
Diff between funHDDC versions 2.1.0 dated 2018-08-13 and 2.2.0 dated 2018-10-08
funHDDC-2.1.0/funHDDC/inst/doc/funHDDC.pdf |only funHDDC-2.1.0/funHDDC/inst/extdata |only funHDDC-2.2.0/funHDDC/DESCRIPTION | 12 +-- funHDDC-2.2.0/funHDDC/MD5 | 30 ++++--- funHDDC-2.2.0/funHDDC/R/plot.mfpca.R | 4 - funHDDC-2.2.0/funHDDC/R/predict.funHDDC.R | 2 funHDDC-2.2.0/funHDDC/R/slopeHeuristic.R | 9 ++ funHDDC-2.2.0/funHDDC/build |only funHDDC-2.2.0/funHDDC/inst/doc/funHDDC.R |only funHDDC-2.2.0/funHDDC/inst/doc/funHDDC.Rmd |only funHDDC-2.2.0/funHDDC/inst/doc/funHDDC.html |only funHDDC-2.2.0/funHDDC/man/funHDDC.Rd | 104 ++++++++++++++------------- funHDDC-2.2.0/funHDDC/man/mfpca.Rd | 17 ++-- funHDDC-2.2.0/funHDDC/man/plot.mfpca.Rd | 13 +-- funHDDC-2.2.0/funHDDC/man/predict.funHDDC.Rd | 53 +++++++------ funHDDC-2.2.0/funHDDC/man/slopeHeuristic.Rd | 69 ++++++++++------- funHDDC-2.2.0/funHDDC/man/triangle.Rd | 2 funHDDC-2.2.0/funHDDC/man/trigo.Rd | 37 ++++----- funHDDC-2.2.0/funHDDC/vignettes |only 19 files changed, 192 insertions(+), 160 deletions(-)
Title: Download Weather Data from the Environment and Climate Change
Canada Website
Description: Provides means for downloading historical weather data from
the Environment and Climate Change Canada website
(<http://climate.weather.gc.ca/historical_data/search_historic_data_e.html>).
Data can be downloaded from multiple stations and over large date ranges
and automatically processed into a single dataset. Tools are also provided
to identify stations either by name or proximity to a location.
Author: Steffi LaZerte [aut, cre] (<https://orcid.org/0000-0002-7690-8360>),
Sam Albers [ctb] (<https://orcid.org/0000-0002-9270-7884>)
Maintainer: Steffi LaZerte <steffi@steffi.ca>
Diff between weathercan versions 0.2.7 dated 2018-07-05 and 0.2.8 dated 2018-10-08
DESCRIPTION | 21 ++- MD5 | 150 ++++++++++++++++++++++----- NAMESPACE | 1 NEWS.md | 11 ++ R/data.R | 1 R/stations.R | 23 +++- R/sysdata.rda |binary R/utils.R | 87 ++++------------ R/weather.R | 15 +- R/weathercan-pkg.R | 4 build/vignette.rds |binary data/finches.rda |binary data/flags.rda |binary data/glossary.rda |binary data/kamloops.rda |binary data/kamloops_day.rda |binary data/pg.rda |binary data/stations.rda |binary inst/doc/flags.html | 16 +- inst/doc/glossary.html | 4 inst/doc/interpolate_data.html | 10 - inst/doc/weathercan.html | 194 ++++++++++++++++++------------------ man/get_tz.Rd |only man/stations.Rd | 1 man/stations_dl.Rd | 3 man/tz_calc.Rd | 30 ----- man/weather_interp.Rd | 4 tests/testthat/test_02_utils.R | 22 ---- tests/testthat/test_03_station_dl.R | 7 - tools/readme/kam_plt-1.png |binary vignettes/articles/mapping.Rmd |only vignettes/articles/mapping_shp |only vignettes/articles/mapping_svg |only 33 files changed, 330 insertions(+), 274 deletions(-)
Title: Create Interactive Chart with the JavaScript 'Billboard' Library
Description: Provides an 'htmlwidgets' interface to 'billboard.js',
a re-usable easy interface JavaScript chart library, based on D3 v4+.
Chart types include line charts, scatterplots, bar/lollipop charts, histogram/density plots, pie/donut charts and gauge charts.
All charts are interactive, and a proxy method is implemented to smoothly update a chart without rendering it again in 'shiny' apps.
Author: Victor Perrier [aut, cre],
Fanny Meyer [aut],
NAVER Corp [cph] (billboard library)
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>
Diff between billboarder versions 0.2.3 dated 2018-08-07 and 0.2.4 dated 2018-10-08
billboarder-0.2.3/billboarder/inst/htmlwidgets/lib/billboard-1.4.1 |only billboarder-0.2.3/billboarder/inst/htmlwidgets/lib/billboard-1.5.1 |only billboarder-0.2.3/billboarder/inst/img |only billboarder-0.2.4/billboarder/DESCRIPTION | 8 billboarder-0.2.4/billboarder/MD5 | 70 +++---- billboarder-0.2.4/billboarder/NAMESPACE | 7 billboarder-0.2.4/billboarder/NEWS.md | 8 billboarder-0.2.4/billboarder/R/billboarder-shiny.R | 1 billboarder-0.2.4/billboarder/R/billboarder.R | 54 ++++- billboarder-0.2.4/billboarder/README.md | 68 +++++- billboarder-0.2.4/billboarder/inst/doc/billboarder-intro.html | 100 +++++----- billboarder-0.2.4/billboarder/inst/doc/billboarder-mapping.html | 46 ++-- billboarder-0.2.4/billboarder/inst/doc/billboarder-options.html | 86 ++++---- billboarder-0.2.4/billboarder/inst/htmlwidgets/billboarder.yaml | 5 billboarder-0.2.4/billboarder/inst/htmlwidgets/lib/billboard-1.6 |only billboarder-0.2.4/billboarder/man/figures |only billboarder-0.2.4/billboarder/man/set_theme.Rd |only 17 files changed, 272 insertions(+), 181 deletions(-)
Title: Solving Mixed Model Equations in R
Description: Structural multivariate-univariate linear mixed model solver for multiple random effects allowing the specification of variance-covariance structures for random effects and allowing the fit of heterogeneous variance models (Covarrubias-Pazaran, 2016 <doi:10.1371/journal.pone.0156744>; Maier et al., 2015 <doi:10.1016/j.ajhg.2014.12.006>). ML/REML estimates can be obtained using the Direct-Inversion Newton-Raphson, and Efficient Mixed Model Association algorithms. Designed for genomic prediction and genome wide association studies (GWAS), particularly focused in the p > n problem (more coefficients than observations) to include multiple relationship matrices or other covariance structures. Spatial models can be fitted using the two-dimensional spline functionality in sommer.
Author: Giovanny Covarrubias-Pazaran
Maintainer: Giovanny Covarrubias-Pazaran <cova_ruber@live.com.mx>
Diff between sommer versions 3.5 dated 2018-07-02 and 3.6 dated 2018-10-08
CHANGELOG | 9 ++++- DESCRIPTION | 8 ++-- MD5 | 71 ++++++++++++++++++++++---------------------- R/GWAS.R | 14 ++++---- R/NR.R | 8 ++++ R/mmer.R | 16 ++++----- R/mmer2.R | 44 ++++++++++++++++----------- R/score.calcMV.R | 2 - R/spl2D.R |only build/vignette.rds |binary data/BTdata.RData |binary data/CPdata.RData |binary data/ExpDesigns.RData |binary data/F1geno.RData |binary data/FDdata.RData |binary data/HDdata.RData |binary data/PolyData.RData |binary data/RICE.RData |binary data/Technow_data.RData |binary data/augment.RData |binary data/cornHybrid.RData |binary data/example.RData |binary data/gryphondata.RData |binary data/h2example.RData |binary data/my.colors.RData |binary data/wheatLines.RData |binary data/yates.oats.RData |binary inst/doc/sommer.R | 14 ++++++++ inst/doc/sommer.Rmd | 19 +++++++++++ inst/doc/sommer.pdf |binary inst/doc/sommer.start.Rmd | 22 ++++++++++++- inst/doc/sommer.start.pdf |binary man/mmer2.Rd | 6 +-- vignettes/sommer.Rmd | 19 +++++++++++ vignettes/sommer.html | 46 +++++++++++++++++++++------- vignettes/sommer.start.Rmd | 22 ++++++++++++- vignettes/sommer.start.html | 49 ++++++++++++++++++++++-------- 37 files changed, 264 insertions(+), 105 deletions(-)
Title: Network Dynamic Temporal Visualizations
Description: Renders dynamic network data from 'networkDynamic' objects as movies, interactive animations, or other representations of changing relational structures and attributes.
Author: Skye Bender-deMoll [cre, aut],
Martina Morris [ctb]
Maintainer: Skye Bender-deMoll <skyebend@uw.edu>
Diff between ndtv versions 0.12.2 dated 2018-05-13 and 0.12.3 dated 2018-10-08
ChangeLog | 1 DESCRIPTION | 8 MD5 | 12 inst/doc/ndtv.R | 84 inst/doc/ndtv.Rnw | 11 inst/doc/ndtv.pdf | 5433 ++++++++++++++++++++++++++--------------------------- vignettes/ndtv.Rnw | 11 7 files changed, 2773 insertions(+), 2787 deletions(-)
More information about IntrinioStockAPI at CRAN
Permanent link
Title: Computing Response Similarity Indices for Multiple-Choice Tests
Description: Contains several IRT and non-IRT based response similarity indices proposed in the literature for multiple-choice examinations such as the Omega index, Wollack (1997) <doi:10.1177/01466216970214002>; Generalized Binomial Test, van der Linden & Sotaridona (2006) <doi:10.3102/10769986031003283>; K index, K1 and K2 indices, Sotaridona & Meijer (2002) <doi:10.1111/j.1745-3984.2002.tb01138.x>; and S1 and S2 indices, Sotaridona & Meijer (2003) <doi:10.1111/j.1745-3984.2003.tb01096.x>.
Author: Cengiz Zopluoglu
Maintainer: Cengiz Zopluoglu <c.zopluoglu@miami.edu>
Diff between CopyDetect versions 1.2 dated 2016-04-27 and 1.3 dated 2018-10-08
CopyDetect-1.2/CopyDetect/R/CopyDetect1.r |only CopyDetect-1.2/CopyDetect/R/CopyDetect2.r |only CopyDetect-1.2/CopyDetect/data/ipar.RData |only CopyDetect-1.2/CopyDetect/data/simulated.data.RData |only CopyDetect-1.2/CopyDetect/man/CopyDetect1.Rd |only CopyDetect-1.2/CopyDetect/man/CopyDetect2.Rd |only CopyDetect-1.2/CopyDetect/man/ipar.Rd |only CopyDetect-1.2/CopyDetect/man/simulated.data.Rd |only CopyDetect-1.3/CopyDetect/DESCRIPTION | 15 - CopyDetect-1.3/CopyDetect/LICENSE | 2 CopyDetect-1.3/CopyDetect/MD5 | 30 +-- CopyDetect-1.3/CopyDetect/NAMESPACE | 22 +- CopyDetect-1.3/CopyDetect/NEWS | 17 + CopyDetect-1.3/CopyDetect/R/print.CopyDetect.r | 160 ++++++++-------- CopyDetect-1.3/CopyDetect/R/print.CopyDetect2.r | 190 +++++++++---------- CopyDetect-1.3/CopyDetect/R/print.CopyDetectCenter.r |only CopyDetect-1.3/CopyDetect/R/print.CopyDetectMany.r |only CopyDetect-1.3/CopyDetect/R/similarity1.r |only CopyDetect-1.3/CopyDetect/R/similarity2.r |only CopyDetect-1.3/CopyDetect/data/form1.RData |only CopyDetect-1.3/CopyDetect/data/form2.RData |only CopyDetect-1.3/CopyDetect/man/form1.Rd |only CopyDetect-1.3/CopyDetect/man/form2.Rd |only CopyDetect-1.3/CopyDetect/man/similarity1.Rd |only CopyDetect-1.3/CopyDetect/man/similarity2.Rd |only 25 files changed, 244 insertions(+), 192 deletions(-)
Title: Stylometric Analyses
Description: Supervised and unsupervised multivariate methods, supplemented by GUI and some visualizations, to perform various analyses in the field of computational stylistics, authorship attribution, etc. For further reference, see Eder et al. (2016), <https://journal.r-project.org/archive/2016/RJ-2016-007/index.html>.
Author: Maciej Eder, Jan Rybicki, Mike Kestemont
Maintainer: Maciej Eder <maciejeder@gmail.com>
Diff between stylo versions 0.6.7 dated 2018-05-26 and 0.6.8 dated 2018-10-08
DESCRIPTION | 8 MD5 | 24 +- NEWS.md | 10 + R/classify.R | 294 +++++++++++++++++------------------- R/load.corpus.R | 18 +- R/load.corpus.and.parse.R | 10 - R/make.samples.R | 34 ++-- R/oppose.R | 127 +++++++-------- R/parse.pos.tags.R | 7 R/print.stylo.results.R | 49 ++---- R/stylo.R | 375 ++++++++++++++++++++++------------------------ R/txt.to.words.R | 14 + R/txt.to.words.ext.R | 19 ++ 13 files changed, 501 insertions(+), 488 deletions(-)
Title: Invariant Causal Prediction
Description: Confidence intervals for causal effects, using data collected in different experimental or environmental conditions. Hidden variables can be included in the model with a more experimental version.
Author: Nicolai Meinshausen
Maintainer: Nicolai Meinshausen <meinshausen@stat.math.ethz.ch>
Diff between InvariantCausalPrediction versions 0.7-1 dated 2017-10-03 and 0.7-2 dated 2018-10-08
InvariantCausalPrediction-0.7-1/InvariantCausalPrediction/R/causalDantzig.R |only InvariantCausalPrediction-0.7-1/InvariantCausalPrediction/man/causalDantzig.Rd |only InvariantCausalPrediction-0.7-1/InvariantCausalPrediction/man/plot.causalDantzig.Rd |only InvariantCausalPrediction-0.7-1/InvariantCausalPrediction/man/summary.causalDantzig.Rd |only InvariantCausalPrediction-0.7-2/InvariantCausalPrediction/DESCRIPTION | 12 +++---- InvariantCausalPrediction-0.7-2/InvariantCausalPrediction/MD5 | 16 +++------- InvariantCausalPrediction-0.7-2/InvariantCausalPrediction/NAMESPACE | 15 --------- InvariantCausalPrediction-0.7-2/InvariantCausalPrediction/R/getpval.R | 2 - InvariantCausalPrediction-0.7-2/InvariantCausalPrediction/man/ICP.Rd | 2 - InvariantCausalPrediction-0.7-2/InvariantCausalPrediction/man/InvariantCausalPrediction-package.Rd | 8 ++--- InvariantCausalPrediction-0.7-2/InvariantCausalPrediction/man/hiddenICP.Rd | 13 ++------ 11 files changed, 22 insertions(+), 46 deletions(-)
More information about InvariantCausalPrediction at CRAN
Permanent link
Title: Fluid Data Transformations
Description: Supplies higher-order fluid data transform operators that include pivot and anti-pivot as special cases.
The methodology is describe in 'Zumel', 2018, "Fluid data reshaping with 'cdata'", <http://winvector.github.io/FluidData/FluidDataReshapingWithCdata.html> , doi:10.5281/zenodo.1173299 .
Based on the 'DBI' database interface.
Author: John Mount [aut, cre],
Nina Zumel [aut],
Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>
Diff between cdata versions 1.0.1 dated 2018-09-22 and 1.0.2 dated 2018-10-08
DESCRIPTION | 10 ++++---- MD5 | 23 +++++++++--------- NEWS.md | 5 ++++ R/LocalOps.R | 19 ++++++++++----- R/RowsColumns.R | 50 +++++++++++++++++++++++++---------------- README.md | 2 - inst/doc/cdata.html | 6 ++-- man/blocks_to_rowrecs.Rd | 2 - man/pivot_to_rowrecs.Rd | 11 ++++++++- man/rowrecs_to_blocks.Rd | 6 ++-- man/unpivot_to_blocks.Rd | 15 ++++++++++-- tests/testthat/testRowColOps.R | 31 ++++++++++++++----------- tests/testthat/test_check.R |only 13 files changed, 115 insertions(+), 65 deletions(-)
Title: A Collection of Handy, Useful Functions
Description: A set of little functions that have been found useful to do little
odds and ends such as plotting the results of K-means clustering, substituting
special text characters, viewing parts of a data.frame, constructing formulas
from text and building design and response matrices.
Author: Jared P. Lander [cre, aut],
Nicholas Galasinao [ctb],
Joshua Kraut [ctb],
Daniel Chen [ctb]
Maintainer: Jared P. Lander <packages@jaredlander.com>
Diff between useful versions 1.2.5 dated 2018-06-09 and 1.2.6 dated 2018-10-08
DESCRIPTION | 10 +++++----- MD5 | 29 ++++++++++++++++------------- NAMESPACE | 1 + NEWS.md | 27 +++++++++++++++------------ R/formatters.r | 36 +++++++++++++++++++++++++++++++----- R/loadPackages.r |only R/tsPlot.r | 2 +- man/WhichCorner.Rd | 4 ++-- man/compare.list.Rd | 2 +- man/corner.Rd | 3 ++- man/fortify.ts.Rd | 5 +++-- man/load_packages.Rd |only man/multiple.Rd | 13 ++++++++++--- man/plotTimesSeries.Rd | 4 ++-- man/useful.Rd | 1 - tests/testthat/test-formatters.r | 30 ++++++++++++++++-------------- tests/testthat/test-load-packages.R |only 17 files changed, 105 insertions(+), 62 deletions(-)
Title: Generate Assorted Books and Documents with R 'bookdown' Package
Description: A collection and selector of R 'bookdown' templates. 'bookdownplus' helps you write academic journal articles, guitar books, chemical equations, mails, calendars, and diaries. R 'bookdownplus' extends the features of 'bookdown', and simplifies the procedure. Users only have to choose a template, clarify the book title and author name, and then focus on writing the text. No need to struggle in 'YAML' and 'LaTeX'.
Author: Peng Zhao
Maintainer: Peng Zhao <pzhao@pzhao.net>
Diff between bookdownplus versions 1.4.6 dated 2018-09-10 and 1.5.1 dated 2018-10-08
bookdownplus-1.4.6/bookdownplus/inst/images/mail.pdf |only bookdownplus-1.4.6/bookdownplus/inst/zip |only bookdownplus-1.4.6/bookdownplus/man/mail_bodysize.Rd |only bookdownplus-1.4.6/bookdownplus/man/mail_font.Rd |only bookdownplus-1.4.6/bookdownplus/man/mail_fontsize.Rd |only bookdownplus-1.4.6/bookdownplus/man/mail_style.Rd |only bookdownplus-1.4.6/bookdownplus/man/mail_theme.Rd |only bookdownplus-1.4.6/bookdownplus/man/more_output.Rd |only bookdownplus-1.4.6/bookdownplus/man/poster_theme.Rd |only bookdownplus-1.4.6/bookdownplus/man/template.Rd |only bookdownplus-1.5.1/bookdownplus/DESCRIPTION | 10 bookdownplus-1.5.1/bookdownplus/MD5 | 108 +-- bookdownplus-1.5.1/bookdownplus/NAMESPACE | 12 bookdownplus-1.5.1/bookdownplus/R/fun.R | 583 +++++-------------- bookdownplus-1.5.1/bookdownplus/R/internal.R |only bookdownplus-1.5.1/bookdownplus/inst/templates |only bookdownplus-1.5.1/bookdownplus/man/backup.Rd |only bookdownplus-1.5.1/bookdownplus/man/bd.Rd | 8 bookdownplus-1.5.1/bookdownplus/man/bookdownplus.Rd | 148 ---- bookdownplus-1.5.1/bookdownplus/man/copyfolder.Rd |only bookdownplus-1.5.1/bookdownplus/man/create.Rd |only bookdownplus-1.5.1/bookdownplus/man/get_output.Rd |only bookdownplus-1.5.1/bookdownplus/man/get_template.Rd |only bookdownplus-1.5.1/bookdownplus/man/share.Rd | 17 24 files changed, 218 insertions(+), 668 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 2.5.1 dated 2018-07-10 and 2.6.0 dated 2018-10-08
DESCRIPTION | 10 - MD5 | 13 +- NAMESPACE | 1 NEWS.md | 5 R/shiny.R | 294 +++++++++++++++++++++++++++++++++++++---------- README.md | 9 + man/protectedServer.Rd | 2 man/protectedServerJS.Rd |only 8 files changed, 261 insertions(+), 73 deletions(-)
Title: SPatially aUTomatic deNoising for Ims toolKit
Description: A set of tools for the peak filtering of mass spectrometry
imaging data (MSI or IMS) based on spatial distribution of signal. Given a
region-of-interest (ROI), representing the spatial region where the informative signal is expected to be
localized, a series of filters determine which peak signals are characterized by
an implausible spatial distribution. The filters reduce the dataset dimensionality
and increase its information vs noise ratio, improving the quality of the
unsupervised analysis results, reducing data dimensionality and simplifying
the chemical interpretation.
Author: Paolo Inglese [aut, cre],
Goncalo Correia [aut, ctb]
Maintainer: Paolo Inglese <p.inglese14@imperial.ac.uk>
Diff between SPUTNIK versions 1.0.3.4 dated 2018-09-18 and 1.0.4.1 dated 2018-10-08
DESCRIPTION | 12 - MD5 | 32 +- NAMESPACE | 3 R/examples/sparseness.R | 5 R/filter_global.R | 212 +++++++++--------- R/graph_funcs.R | 558 ++++++++++++++++++++++++------------------------ R/ms.image_methods.R | 9 R/msi.dataset_funcs.R | 218 +++++++++--------- R/msi.dataset_methods.R | 2 R/mz_funcs.R | 416 ++++++++++++++++++----------------- R/sparseness_funcs.R | 33 ++ man/NMI.Rd | 2 man/gini.index.Rd | 3 man/refAndROIimages.Rd | 5 man/scatter.ratio.Rd | 3 man/spatial.chaos.Rd | 3 man/splitPeaksFilter.Rd | 4 17 files changed, 773 insertions(+), 747 deletions(-)
Title: Easy Regression
Description: Performs analysis of regression in simple designs with quantitative treatments,
including mixed models and non linear models.
Author: Emmanuel Arnhold
Maintainer: Emmanuel Arnhold <emmanuelarnhold@yahoo.com.br>
Diff between easyreg versions 1.0 dated 2016-10-13 and 2.0 dated 2018-10-08
DESCRIPTION | 14 MD5 | 17 NAMESPACE | 4 R/bl.R | 1397 ++++++++++++++++++++++++++++++++++++++++++++++--- R/er1.R | 92 ++- R/regplot.R | 130 +++- inst |only man/bl.Rd | 67 ++ man/easyreg-package.Rd | 4 man/regplot.Rd | 46 + 10 files changed, 1610 insertions(+), 161 deletions(-)
Title: Extensions to 'ggplot2' for Radiation Spectra
Description: Additional annotations, and stats for plotting "light"
spectra with 'ggplot2', together with specializations of ggplot()
and plot() methods for spectral data stored in objects of the classes
defined in package 'photobiology' and a plot() method for objects of
class "waveband", also defined in package 'photobiology'. Part of the
'r4photobiology' suite, Aphalo P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.
Author: Pedro J. Aphalo [aut, cre] (<https://orcid.org/0000-0003-3385-972X>),
Titta K. Kotilainen [ctb] (<https://orcid.org/0000-0002-2822-9734>)
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between ggspectra versions 0.2.4-1 dated 2018-05-07 and 0.3.0 dated 2018-10-08
ggspectra-0.2.4-1/ggspectra/R/axis-utils_wlength.R |only ggspectra-0.2.4-1/ggspectra/R/plot-cps-spct.R |only ggspectra-0.2.4-1/ggspectra/R/plot-filter-spct.R |only ggspectra-0.2.4-1/ggspectra/R/plot-raw-spct.R |only ggspectra-0.2.4-1/ggspectra/R/plot-response-spct.R |only ggspectra-0.3.0/ggspectra/DESCRIPTION | 21 ggspectra-0.3.0/ggspectra/MD5 | 198 - ggspectra-0.3.0/ggspectra/NAMESPACE | 10 ggspectra-0.3.0/ggspectra/NEWS | 25 ggspectra-0.3.0/ggspectra/R/autoplot.R |only ggspectra-0.3.0/ggspectra/R/axis-utils-wlength.R |only ggspectra-0.3.0/ggspectra/R/common-plot-utils.R |only ggspectra-0.3.0/ggspectra/R/ggplot-methods.R | 12 ggspectra-0.3.0/ggspectra/R/ggspectra.R | 10 ggspectra-0.3.0/ggspectra/R/plot-calibration-spct.R | 59 ggspectra-0.3.0/ggspectra/R/plot-cps-spct.r |only ggspectra-0.3.0/ggspectra/R/plot-filter-spct.r |only ggspectra-0.3.0/ggspectra/R/plot-raw-spct.r |only ggspectra-0.3.0/ggspectra/R/plot-response-spct.r |only ggspectra-0.3.0/ggspectra/R/plot-source-spct.r | 121 ggspectra-0.3.0/ggspectra/R/plot-waveband.R | 15 ggspectra-0.3.0/ggspectra/R/stat-color.R | 12 ggspectra-0.3.0/ggspectra/R/stat-find-wls.R |only ggspectra-0.3.0/ggspectra/R/stat-label-peaks.R | 243 - ggspectra-0.3.0/ggspectra/R/stat-peaks.R | 34 ggspectra-0.3.0/ggspectra/R/stat-wb-box.R | 38 ggspectra-0.3.0/ggspectra/R/stat-wb-column.R | 49 ggspectra-0.3.0/ggspectra/R/stat-wb-contribution.R | 44 ggspectra-0.3.0/ggspectra/R/stat-wb-hbar.R | 36 ggspectra-0.3.0/ggspectra/R/stat-wb-irrad.R | 64 ggspectra-0.3.0/ggspectra/R/stat-wb-label.R | 26 ggspectra-0.3.0/ggspectra/R/stat-wb-mean.R | 61 ggspectra-0.3.0/ggspectra/R/stat-wb-relative.R | 22 ggspectra-0.3.0/ggspectra/R/stat-wb-sirrad.R | 64 ggspectra-0.3.0/ggspectra/R/stat-wb-total.R | 64 ggspectra-0.3.0/ggspectra/R/stat-wl-strip.R | 4 ggspectra-0.3.0/ggspectra/R/stat-wl-summary.R | 30 ggspectra-0.3.0/ggspectra/README.md | 103 ggspectra-0.3.0/ggspectra/build/vignette.rds |binary ggspectra-0.3.0/ggspectra/inst/doc/userguide1-grammar.R | 52 ggspectra-0.3.0/ggspectra/inst/doc/userguide1-grammar.Rmd | 55 ggspectra-0.3.0/ggspectra/inst/doc/userguide1-grammar.html | 1371 +++++----- ggspectra-0.3.0/ggspectra/inst/doc/userguide2-plot-methods.R | 47 ggspectra-0.3.0/ggspectra/inst/doc/userguide2-plot-methods.Rmd | 97 ggspectra-0.3.0/ggspectra/inst/doc/userguide2-plot-methods.html | 499 ++- ggspectra-0.3.0/ggspectra/man/A_internal_label.Rd | 8 ggspectra-0.3.0/ggspectra/man/A_plot.Rd | 19 ggspectra-0.3.0/ggspectra/man/Afr_plot.Rd | 30 ggspectra-0.3.0/ggspectra/man/O_plot.Rd | 22 ggspectra-0.3.0/ggspectra/man/R_plot.Rd | 20 ggspectra-0.3.0/ggspectra/man/Rfr_specular_label.Rd | 4 ggspectra-0.3.0/ggspectra/man/T_plot.Rd | 20 ggspectra-0.3.0/ggspectra/man/Tfr_internal_label.Rd | 4 ggspectra-0.3.0/ggspectra/man/autoplot.Rd |only ggspectra-0.3.0/ggspectra/man/cal_plot.Rd | 18 ggspectra-0.3.0/ggspectra/man/color_chart.Rd | 5 ggspectra-0.3.0/ggspectra/man/cps_label.Rd | 4 ggspectra-0.3.0/ggspectra/man/cps_plot.Rd | 14 ggspectra-0.3.0/ggspectra/man/decoration.Rd | 4 ggspectra-0.3.0/ggspectra/man/e_plot.Rd | 25 ggspectra-0.3.0/ggspectra/man/e_rsp_plot.Rd | 24 ggspectra-0.3.0/ggspectra/man/exponent2prefix.Rd | 4 ggspectra-0.3.0/ggspectra/man/figures/README-example-1.png |binary ggspectra-0.3.0/ggspectra/man/figures/README-example2-1.png |binary ggspectra-0.3.0/ggspectra/man/find_idfactor.Rd |only ggspectra-0.3.0/ggspectra/man/gg2spectra-ggproto.Rd | 29 ggspectra-0.3.0/ggspectra/man/ggplot.Rd | 32 ggspectra-0.3.0/ggspectra/man/ggspectra-package.Rd | 18 ggspectra-0.3.0/ggspectra/man/plot.calibration_spct.Rd | 26 ggspectra-0.3.0/ggspectra/man/plot.cps_spct.Rd | 36 ggspectra-0.3.0/ggspectra/man/plot.filter_spct.Rd | 30 ggspectra-0.3.0/ggspectra/man/plot.generic_spct.Rd |only ggspectra-0.3.0/ggspectra/man/plot.object_spct.Rd | 31 ggspectra-0.3.0/ggspectra/man/plot.raw_spct.Rd | 38 ggspectra-0.3.0/ggspectra/man/plot.reflector_spct.Rd | 40 ggspectra-0.3.0/ggspectra/man/plot.response_spct.Rd | 37 ggspectra-0.3.0/ggspectra/man/plot.source_spct.Rd | 33 ggspectra-0.3.0/ggspectra/man/plot.waveband.Rd | 20 ggspectra-0.3.0/ggspectra/man/q_plot.Rd | 24 ggspectra-0.3.0/ggspectra/man/q_rsp_plot.Rd | 24 ggspectra-0.3.0/ggspectra/man/raw_plot.Rd | 24 ggspectra-0.3.0/ggspectra/man/s.e.irrad_label.Rd | 8 ggspectra-0.3.0/ggspectra/man/scale_x_wl_continuous.Rd | 6 ggspectra-0.3.0/ggspectra/man/scale_y_counts_continuous.Rd | 4 ggspectra-0.3.0/ggspectra/man/scale_y_cps_continuous.Rd | 5 ggspectra-0.3.0/ggspectra/man/scale_y_s.e.irrad_continuous.Rd | 4 ggspectra-0.3.0/ggspectra/man/scale_y_s.e.response_continuous.Rd | 4 ggspectra-0.3.0/ggspectra/man/sec_axis_w_number.Rd | 2 ggspectra-0.3.0/ggspectra/man/stat_color.Rd | 20 ggspectra-0.3.0/ggspectra/man/stat_find_qtys.Rd |only ggspectra-0.3.0/ggspectra/man/stat_find_wls.Rd |only ggspectra-0.3.0/ggspectra/man/stat_label_peaks.Rd | 138 - ggspectra-0.3.0/ggspectra/man/stat_peaks.Rd | 21 ggspectra-0.3.0/ggspectra/man/stat_wb_box.Rd | 26 ggspectra-0.3.0/ggspectra/man/stat_wb_column.Rd | 21 ggspectra-0.3.0/ggspectra/man/stat_wb_contribution.Rd | 3 ggspectra-0.3.0/ggspectra/man/stat_wb_hbar.Rd | 3 ggspectra-0.3.0/ggspectra/man/stat_wb_irrad.Rd | 37 ggspectra-0.3.0/ggspectra/man/stat_wb_label.Rd | 18 ggspectra-0.3.0/ggspectra/man/stat_wb_mean.Rd | 33 ggspectra-0.3.0/ggspectra/man/stat_wb_relative.Rd | 25 ggspectra-0.3.0/ggspectra/man/stat_wb_sirrad.Rd | 33 ggspectra-0.3.0/ggspectra/man/stat_wb_total.Rd | 34 ggspectra-0.3.0/ggspectra/man/stat_wl_strip.Rd | 10 ggspectra-0.3.0/ggspectra/man/stat_wl_summary.Rd | 13 ggspectra-0.3.0/ggspectra/man/w_length_label.Rd | 14 ggspectra-0.3.0/ggspectra/man/w_number.Rd | 2 ggspectra-0.3.0/ggspectra/vignettes/userguide1-grammar.Rmd | 55 ggspectra-0.3.0/ggspectra/vignettes/userguide2-plot-methods.Rmd | 97 109 files changed, 2845 insertions(+), 1944 deletions(-)
Title: Deming, Thiel-Sen and Passing-Bablock Regression
Description: Generalized Deming regression, Theil-Sen regression and Passing-Bablock regression functions.
Author: Terry Therneau
Maintainer: Terry Therneau <therneau.terry@mayo.edu>
Diff between deming versions 1.2 dated 2018-06-19 and 1.3 dated 2018-10-08
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- R/deming.R | 1 - inst/NEWS.Rd | 6 ++++++ inst/doc/deming.pdf |binary noweb/demingsource.Rnw | 1 - tests/dtest.R | 11 +++++++++++ tests/dtest.Rout.save | 21 ++++++++++++++++----- 8 files changed, 43 insertions(+), 17 deletions(-)
Title: Simulation-Based Quasi-Likelihood Estimation
Description: A simulation-based quasi-likelihood method (Baaske, M., Ballani, F., v.d. Boogaart, K.G. (2014) <doi:10.5566/ias.v33.p107-119>) for parameter estimation of parametric statistical models for which closed-form representations of distributional characteristics are unavailable and can only be obtained by computationally intensive simulations of the model.
Author: Markus Baaske [aut, cre, cph],
K. Gerald van den Boogaart [ths]
Maintainer: Markus Baaske <markus.baaske@uni-jena.de>
Diff between qle versions 0.17 dated 2018-03-16 and 0.18 dated 2018-10-08
DESCRIPTION | 12 - MD5 | 92 ++++++----- NAMESPACE | 1 NEWS | 14 + R/covariance.R | 4 R/krige.R | 133 +++++++++++++++- R/qle-package.R | 36 ++++ R/qleTest.R | 57 +++--- R/qsOpt.R | 170 ++++++++++++-------- R/simQLData.R | 70 +++++--- build/vignette.rds |binary data/datalist | 2 data/matclust.rda |binary data/mm1q.rda |only data/normal.rda |binary data/qleresult.rda |only inst/doc/qle_with_R.R | 372 +++++++++++++++++++++++++++------------------ inst/doc/qle_with_R.Rnw | 365 +++++++++++++++++++++++++------------------- inst/doc/qle_with_R.pdf |binary inst/examples |only man/OPT.Rd |only man/QLmodel.Rd | 3 man/checkMultRoot.Rd | 7 man/crossValTx.Rd | 6 man/estim.Rd | 2 man/fitCov.Rd | 3 man/fitSIRFk.Rd | 2 man/getQLmodel.Rd | 4 man/krige.Rd | 2 man/mahalDist.Rd | 8 man/mm1q.Rd |only man/multiDimLHS.Rd | 4 man/multiSearch.Rd | 13 - man/optStat.Rd |only man/qle.Rd | 51 ++++-- man/qleTest.Rd | 14 + man/qscoring.Rd | 3 man/qsd.Rd | 2 man/setCovModel.Rd | 6 man/setQLdata.Rd | 4 man/updateCovModels.Rd | 4 src/Makevars | 11 + src/error.h | 11 - tests/test_normal_mahal.R |only vignettes/introduction.tex | 3 vignettes/qle_with_R.Rnw | 365 +++++++++++++++++++++++++------------------- vignettes/qlebib.bib | 13 + 47 files changed, 1183 insertions(+), 686 deletions(-)
Title: Computing Comorbidity Scores
Description: Computing comorbidity scores such as the weighted Charlson score
(Charlson, 1987 <doi:10.1016/0021-9681(87)90171-8>) and the Elixhauser
comorbidity score (Elixhauser, 1998 <doi:10.1097/00005650-199801000-00004>)
using ICD-9-CM or ICD-10 codes (Quan, 2005 <doi:10.1097/01.mlr.0000182534.19832.83>).
Author: Alessandro Gasparini [aut, cre]
(<https://orcid.org/0000-0002-8319-7624>),
Hojjat Salmasian [ctb] (ICD-9-CM scores)
Maintainer: Alessandro Gasparini <ag475@leicester.ac.uk>
Diff between comorbidity versions 0.1.1 dated 2018-03-30 and 0.2.0 dated 2018-10-08
DESCRIPTION | 26 MD5 | 72 NAMESPACE | 10 NEWS.md | 88 R/comorbidity-package.R |only R/comorbidity.R | 372 +-- R/data.R | 164 + R/detect.R |only R/factorise.R |only R/labelled.R |only R/sample_diag.R | 130 - R/scores.R | 338 +-- R/sysdata.rda |only R/tidy.R |only README.md | 630 +++-- build/partial.rdb |only build/vignette.rds |binary data/australia10.rda |only data/datalist |only data/icd10cm_2017.rda |only data/icd10cm_2018.rda |only data/nhds2010.rda |only inst/CITATION | 26 inst/doc/comorbidityscores.R | 84 inst/doc/comorbidityscores.Rmd | 658 +++--- inst/doc/comorbidityscores.html | 1224 +++++------ man/australia10.Rd |only man/comorbidity-package.Rd |only man/comorbidity.Rd | 272 +- man/figures |only man/icd10_2009.Rd | 52 man/icd10_2011.Rd | 52 man/icd10cm_2017.Rd |only man/icd10cm_2018.Rd |only man/icd9_2015.Rd | 50 man/nhds2010.Rd |only man/sample_diag.Rd | 64 tests/testthat.R | 6 tests/testthat/test-charlson-icd10.R | 2542 +++++++++++------------ tests/testthat/test-charlson-icd9.R | 1784 ++++++++-------- tests/testthat/test-comorbidity.R | 1018 ++++----- tests/testthat/test-data.R | 26 tests/testthat/test-elixhauser-icd10.R | 3592 ++++++++++++++++----------------- tests/testthat/test-elixhauser-icd9.R | 2754 ++++++++++++------------- tests/testthat/test-sample_diag.R | 162 - vignettes/comorbidityscores.Rmd | 658 +++--- 46 files changed, 8442 insertions(+), 8412 deletions(-)
Title: Output Analysis and Diagnostics for MCMC
Description: Provides functions for summarizing and plotting the
output from Markov Chain Monte Carlo (MCMC) simulations, as
well as diagnostic tests of convergence to the equilibrium
distribution of the Markov chain.
Author: Martyn Plummer [aut, cre, trl],
Nicky Best [aut],
Kate Cowles [aut],
Karen Vines [aut],
Deepayan Sarkar [aut],
Douglas Bates [aut],
Russell Almond [aut],
Arni Magnusson [aut]
Maintainer: Martyn Plummer <martyn.plummer@gmail.com>
Diff between coda versions 0.19-1 dated 2016-12-08 and 0.19-2 dated 2018-10-08
CHANGELOG | 3 +++ DESCRIPTION | 12 ++++++------ MD5 | 10 +++++----- R/gelman.R | 5 +++-- data/line.rda |binary man/gelman.plot.Rd | 6 ++++-- 6 files changed, 21 insertions(+), 15 deletions(-)
Title: Fits a Principal Curve in Arbitrary Dimension
Description: Fitting a principal curve to a data matrix in arbitrary dimensions.
Author: Trevor Hastie [aut],
Andreas Weingessel [aut],
Kurt Hornik [aut] (<https://orcid.org/0000-0003-4198-9911>),
Henrik Bengtsson [ctb] (HenrikBengtsson),
Robrecht Cannoodt [aut, cre] (<https://orcid.org/0000-0003-3641-729X>,
rcannood)
Maintainer: Robrecht Cannoodt <rcannood@gmail.com>
Diff between princurve versions 2.1.2.1 dated 2018-08-02 and 2.1.3 dated 2018-10-08
princurve-2.1.2.1/princurve/R/data.R |only princurve-2.1.2.1/princurve/build |only princurve-2.1.2.1/princurve/data |only princurve-2.1.2.1/princurve/inst/doc |only princurve-2.1.2.1/princurve/man/benchmarks.Rd |only princurve-2.1.2.1/princurve/man/figures/README_example-1.gif |only princurve-2.1.2.1/princurve/tests/testthat/test-timings.R |only princurve-2.1.2.1/princurve/vignettes |only princurve-2.1.3/princurve/DESCRIPTION | 62 +++---- princurve-2.1.3/princurve/MD5 | 32 +-- princurve-2.1.3/princurve/R/get.lam.R | 8 princurve-2.1.3/princurve/R/principal.curve.R | 9 - princurve-2.1.3/princurve/README.md | 82 ++++++---- princurve-2.1.3/princurve/inst/NEWS | 8 princurve-2.1.3/princurve/man/figures/README_example-1.png |only princurve-2.1.3/princurve/man/figures/README_princurve-1.png |only princurve-2.1.3/princurve/man/principal.curve.Rd | 2 princurve-2.1.3/princurve/man/principal_curve.Rd | 5 princurve-2.1.3/princurve/tests/testthat/test-legacy_princurve.R | 24 -- princurve-2.1.3/princurve/tests/testthat/test-principal_curve.R | 8 princurve-2.1.3/princurve/tests/testthat/test-project_to_curve.R | 8 21 files changed, 126 insertions(+), 122 deletions(-)
Title: Prais-Winsten Estimator for AR(1) Serial Correlation
Description: The Prais-Winsten estimator takes into account AR(1) serial correlation of the errors in a linear regression model. The procedure recursively estimates the coefficients and the error autocorrelation of the specified model until sufficient convergence of the AR(1) coefficient is attained.
Author: Franz X. Mohr [aut, cre]
Maintainer: Franz X. Mohr <prais.r@outlook.com>
Diff between prais versions 0.1.1 dated 2015-03-19 and 1.0.0 dated 2018-10-08
prais-0.1.1/prais/R/prais.winsten.R |only prais-0.1.1/prais/man/prais-package.Rd |only prais-0.1.1/prais/man/prais.winsten.Rd |only prais-1.0.0/prais/DESCRIPTION | 26 +++++++++++++++++--------- prais-1.0.0/prais/MD5 | 15 ++++++++++----- prais-1.0.0/prais/NAMESPACE | 8 +++++++- prais-1.0.0/prais/R/prais_winsten.R |only prais-1.0.0/prais/R/print.prais.R |only prais-1.0.0/prais/R/print.summary.prais.R |only prais-1.0.0/prais/R/pw_transform.R |only prais-1.0.0/prais/R/summary.prais.R |only prais-1.0.0/prais/man/prais_winsten.Rd |only prais-1.0.0/prais/man/pw_transform.Rd |only prais-1.0.0/prais/man/summary.prais.Rd |only 14 files changed, 34 insertions(+), 15 deletions(-)
Title: Projection Pursuit for Cluster Identification
Description: Implements recently developed projection
pursuit algorithms for finding optimal linear cluster
separators. The clustering algorithms use optimal
hyperplane separators based on minimum density, Pavlidis et. al (2016) <https://jmlr.csail.mit.edu/papers/volume17/15-307/15-307.pdf>;
minimum normalised cut, Hofmeyr (2017) <doi:10.1109/TPAMI.2016.2609929>;
and maximum variance ratio clusterability, Hofmeyr and Pavlidis (2015) <doi:10.1109/SSCI.2015.116>.
Author: David Hofmeyr <dhofmeyr@sun.ac.za> [aut, cre]
Nicos Pavlidis <n.pavlidis@lancaster.ac.uk> [aut]
Maintainer: David Hofmeyr <dhofmeyr@sun.ac.za>
Diff between PPCI versions 0.1.2 dated 2018-03-15 and 0.1.3 dated 2018-10-08
DESCRIPTION | 11 MD5 | 53 - NAMESPACE | 12 R/MCDC.R | 824 +++++++++++------------ R/density.R | 1234 +++++++++++++++++------------------ R/image_plots.R |only R/min_cut.R | 897 ++++++++++++------------- R/multi_var_projections.R |only R/newplots.R | 104 ++ R/nodeplot.R | 77 +- R/prune.R | 722 +++++++++----------- build/partial.rdb |binary man/PPCI-package.Rd | 94 +- man/hp_plot.Rd | 17 man/mcdc.Rd | 96 +- man/mcdr.Rd |only man/mch.Rd | 95 +- man/mddc.Rd | 2 man/mddr.Rd |only man/mdh.Rd | 101 +- man/ncutdc.Rd | 90 +- man/ncutdr.Rd |only man/ncuth.Rd | 93 +- man/node_plot.Rd | 42 - man/optidigits_mean_images.Rd |only man/plot.ppci_cluster_solution.Rd |only man/plot.ppci_hyperplane_solution.Rd |only man/plot.ppci_projection_solution.Rd |only man/success_ratio.Rd | 60 - man/tree_plot.Rd | 42 - man/tree_prune.Rd | 2 man/tree_split.Rd | 4 32 files changed, 2395 insertions(+), 2277 deletions(-)
Title: Tools for Epidemiologists
Description: Provides set of functions aimed at epidemiologists.
They include commands for measures of association and impact for case control studies and cohort studies.
They may be particularly useful for outbreak investigations and include univariate and stratified analyses.
The functions for cohort studies include the CS(), CSTable() and CSInter() commands.
The functions for case control studies include the CC(), CCTable() and CCInter() commands.
Author: Jean Pierre Decorps [aut, cre],
Esther Kissling [ctb]
Maintainer: Jean Pierre Decorps <jp.decorps@epiconcept.fr>
Diff between EpiStats versions 1.1 dated 2018-06-05 and 1.2 dated 2018-10-08
DESCRIPTION | 8 ++--- MD5 | 26 ++++++++++------- NAMESPACE | 6 ++-- R/01_EpiFuns.R | 33 ++++++++++++++++++++++ R/CC_.R | 38 +++++++++++++------------ R/crosstable.R |only R/orderFactors.R |only README.md | 4 ++ build/vignette.rds |binary inst/doc/EpiStats.R | 35 +++++++++++++++++++++++ inst/doc/EpiStats.Rmd | 73 +++++++++++++++++++++++++++++++++++++++++++++---- inst/doc/EpiStats.pdf |binary man/CC.Rd | 5 ++- man/crossTable.Rd |only man/orderFactors.Rd |only vignettes/EpiStats.Rmd | 73 +++++++++++++++++++++++++++++++++++++++++++++---- 16 files changed, 254 insertions(+), 47 deletions(-)
Title: Kriging Methods for Computer Experiments
Description: Estimation, validation and prediction of kriging models. Important functions : km, print.km, plot.km, predict.km.
Author: Olivier Roustant, David Ginsbourger, Yves Deville. Contributors: Clement Chevalier, Yann Richet.
Maintainer: Olivier Roustant <roustant@emse.fr>
Diff between DiceKriging versions 1.5.5 dated 2015-04-24 and 1.5.6 dated 2018-10-08
DiceKriging-1.5.5/DiceKriging/R/covStruct_Scaling_Affine.R |only DiceKriging-1.5.5/DiceKriging/inst/tests |only DiceKriging-1.5.5/DiceKriging/man/affineScalingFun.Rd |only DiceKriging-1.5.5/DiceKriging/man/affineScalingGrad.Rd |only DiceKriging-1.5.5/DiceKriging/man/covAffineScaling-class.Rd |only DiceKriging-1.5.5/DiceKriging/tests/run-all.R |only DiceKriging-1.5.6/DiceKriging/CHANGELOG | 19 DiceKriging-1.5.6/DiceKriging/DESCRIPTION | 15 DiceKriging-1.5.6/DiceKriging/MD5 | 75 +- DiceKriging-1.5.6/DiceKriging/NAMESPACE | 22 DiceKriging-1.5.6/DiceKriging/R/checkNames.R | 54 +- DiceKriging-1.5.6/DiceKriging/R/covStruct.create.R | 19 DiceKriging-1.5.6/DiceKriging/R/covStruct_Base_TensorProduct.R | 10 DiceKriging-1.5.6/DiceKriging/R/covStruct_Scaling.R | 106 +++- DiceKriging-1.5.6/DiceKriging/R/covStruct_User.R | 2 DiceKriging-1.5.6/DiceKriging/R/covStruct_XtraClass_Union.R | 2 DiceKriging-1.5.6/DiceKriging/R/covStruct_XtraMethods.R | 19 DiceKriging-1.5.6/DiceKriging/R/km.R | 13 DiceKriging-1.5.6/DiceKriging/R/kmEstimate.R | 30 - DiceKriging-1.5.6/DiceKriging/R/kmNoNugget.init.R | 2 DiceKriging-1.5.6/DiceKriging/R/kmStruct.R | 10 DiceKriging-1.5.6/DiceKriging/R/scalingFun.R | 226 +++++++- DiceKriging-1.5.6/DiceKriging/R/scalingGrad.R | 23 DiceKriging-1.5.6/DiceKriging/README.md |only DiceKriging-1.5.6/DiceKriging/man/DiceKriging-package.Rd | 8 DiceKriging-1.5.6/DiceKriging/man/checkNames.Rd | 10 DiceKriging-1.5.6/DiceKriging/man/covKernel-class.Rd | 2 DiceKriging-1.5.6/DiceKriging/man/covMatrixDerivative.Rd | 4 DiceKriging-1.5.6/DiceKriging/man/covScaling-class.Rd | 9 DiceKriging-1.5.6/DiceKriging/man/covStruct.create.Rd | 2 DiceKriging-1.5.6/DiceKriging/man/covUser-class.Rd | 4 DiceKriging-1.5.6/DiceKriging/man/km.Rd | 26 - DiceKriging-1.5.6/DiceKriging/man/predict.km.Rd | 2 DiceKriging-1.5.6/DiceKriging/man/scalingFun1d.Rd |only DiceKriging-1.5.6/DiceKriging/src/DiceKriging.h |only DiceKriging-1.5.6/DiceKriging/src/Scaling.c | 259 ++++++---- DiceKriging-1.5.6/DiceKriging/src/init.c |only DiceKriging-1.5.6/DiceKriging/tests/testthat |only DiceKriging-1.5.6/DiceKriging/tests/testthat.R |only 39 files changed, 630 insertions(+), 343 deletions(-)
Title: Quantify the Relationship Between Development Rate and
Temperature in Ectotherms
Description: A set of functions to quantify the relationship between development
rate and temperature and to build phenological models. The package comprises
a set of models and estimated parameters borrowed from a literature review
in ectotherms. The methods and literature review are described in Rebaudo
et al. (2018) <doi:10.1111/2041-210X.12935> and Rebaudo and Rabhi (2018)
<doi:10.1111/eea.12693>. An example can be found in Rebaudo et al. (2017)
<doi:10.1007/s13355-017-0480-5>.
Author: Francois Rebaudo [aut, cre] (2016-2018),
Camila Benavides [ctb] (M2 student; 2018),
Tanusson Selvarajah [ctb] (L2 student; 2018),
Nicolas Bonnal [ctb] (M1 student; 2018),
Badre Rabhi [ctb] (L2 student; 2017),
Quentin Struelens [ctb] (VIA; 2016)
Maintainer: Francois Rebaudo <francois.rebaudo@ird.fr>
Diff between devRate versions 0.1.8 dated 2018-07-06 and 0.1.9 dated 2018-10-08
DESCRIPTION | 6 - MD5 | 92 ++++++++++++------------- NEWS.md | 3 R/devRate_pheno.R | 14 ++- build/vignette.rds |binary data/analytis_77.RData |binary data/bayoh_03.RData |binary data/beta_16.RData |binary data/beta_95.RData |binary data/bieri1_83.RData |binary data/briere1_99.RData |binary data/briere2_99.RData |binary data/campbell_74.RData |binary data/damos_08.RData |binary data/damos_11.RData |binary data/davidson_44.RData |binary data/devRateEqList.RData |binary data/harcourtYee_82.RData |binary data/hilbertLogan_83.RData |binary data/janisch_32.RData |binary data/kontodimas_04.RData |binary data/lactin1_95.RData |binary data/lactin2_95.RData |binary data/lamb_92.RData |binary data/logan10_76.RData |binary data/logan6_76.RData |binary data/perf2_11.RData |binary data/poly2.RData |binary data/poly4.RData |binary data/ratkowsky_82.RData |binary data/ratkowsky_83.RData |binary data/regniere_12.RData |binary data/rootsq_82.RData |binary data/schoolfieldHigh_81.RData |binary data/schoolfieldLow_81.RData |binary data/schoolfield_81.RData |binary data/sharpeDeMichele_77.RData |binary data/shi_11.RData |binary data/stinner_74.RData |binary data/taylor_81.RData |binary data/wagner_88.RData |binary data/wang_82.RData |binary data/wangengel_98.RData |binary inst/doc/guiaDelUsuario.html | 150 +++++++++++++++++++++--------------------- inst/doc/modelEvaluation.html | 10 +- inst/doc/quickUserGuide.html | 146 ++++++++++++++++++++-------------------- man/devRateIBM.Rd | 9 +- 47 files changed, 220 insertions(+), 210 deletions(-)
Title: Constrained Spatiotemporal Mixed Models for Exposure Estimation
Description: The approach of constrained spatiotemporal mixed models is to make reliable estimation of air pollutant concentrations at high spatiotemporal
resolution (Li, L., Zhang, J., Meng, X., Fang, Y., Ge, Y., Wang, J., Wang, C., Wu, J., Kan, H. (2018) <doi.org/10.1016/j.rse.2018.09.001>;
Li, L., Lurmann, F., Habre, R., Urman, R., Rappaport, E., Ritz, B., Chen, J., Gilliland, F., Wu, J., (2017) <doi:10.1021/acs.est.7b01864>).
This package is an extensive tool for this modeling approach with support of block Kriging (Goovaerts, P. (1997) <http://www.gbv.de/dms/goettingen/229148123.pdf>)
and uses the PM2.5 modeling as examples. It provides the following functionality:
(1) Extraction of covariates from the satellite images such as GeoTiff and NC4 raster;
(2) Generation of temporal basis functions to simulate the seasonal trends in the study regions;
(3) Generation of the regional monthly or yearly means of air pollutant concentration;
(4) Generation of Thiessen polygons and spatial effect modeling;
(5) Ensemble modeling for spatiotemporal mixed models, supporting multi-core parallel computing;
(6) Integrated predictions with or without weights of the model's performance, supporting multi-core parallel computing;
(7) Constrained optimization to interpolate the missing values;
(8) Generation of the grid surfaces of air pollutant concentration estimates at high resolution;
(9) Block Kriging for regional mean estimation at multiple scales.
Author: Lianfa Li,
Maintainer: Lianfa Li <lspatial@gmail.com>
Diff between sptemExp versions 0.1.1 dated 2017-09-01 and 0.1.3 dated 2018-10-08
DESCRIPTION | 9 +++++---- MD5 | 17 +++++++++++------ R/RcppExports.R | 8 ++++++++ R/tpolygonsByBorder.R | 4 ++-- README | 2 ++ man/exeCluster.Rd |only man/extractVNC4.Rd | 5 ++--- man/getClusterCt.Rd |only src/RcppExports.cpp | 26 ++++++++++++++++++++++++++ src/ufcls.cpp |only src/ufcls_lib.cpp |only src/ufcls_lib.h |only 12 files changed, 56 insertions(+), 15 deletions(-)
Title: Methods for Detecting Safety Signals in Clinical Trials Using
Body-Systems (System Organ Classes)
Description: Methods for detecting safety signals in clinical trials using groupings of adverse events by body-system or system organ class.The package title c212 is in reference to the original Engineering and Physical Sciences Research Council (UK) funded project which was named CASE 2/12.
Author: Raymond Carragher <raymond.carragher@strath.ac.uk>
Maintainer: Raymond Carragher <raymond.carragher@strath.ac.uk>
Diff between c212 versions 0.93 dated 2017-04-06 and 0.94 dated 2018-10-08
DESCRIPTION | 8 MD5 | 138 +- R/c212.interim.1a.hier2.lev0.R | 12 R/c212.interim.1a.hier2.lev1.R | 12 R/c212.interim.1a.hier3.lev0.R | 12 R/c212.interim.1a.hier3.lev1.R | 23 R/c212.interim.1a.hier3.lev2.R | 12 R/c212.interim.BB.hier2.lev0.R | 12 R/c212.interim.BB.hier2.lev1.R | 12 R/c212.interim.BB.hier3.lev0.R | 12 R/c212.interim.BB.hier3.lev1.R | 26 R/c212.interim.BB.hier3.lev1.summary.stats.R | 4 R/c212.interim.BB.hier3.lev2.R | 12 man/RCS/c212.1a.rd,v | 1 man/RCS/c212.BB.rd,v | 1 man/RCS/c212.FDR.data.rd,v | 1 man/RCS/c212.Package.rd,v | 1 man/RCS/c212.bin.test.rd,v | 1 man/RCS/c212.convergence.diag.rd,v | 1 man/RCS/c212.fisher.test.rd,v | 1 man/RCS/c212.gen.initial.values.rd,v | 1 man/RCS/c212.interim.1a.hier2.rd,v | 1 man/RCS/c212.interim.1a.hier3.rd,v | 1 man/RCS/c212.interim.BB.hier2.rd,v | 1 man/RCS/c212.interim.BB.hier3.rd,v | 1 man/RCS/c212.interim.MLE.rd,v | 1 man/RCS/c212.monitor.samples.rd,v | 1 man/RCS/c212.plot.eot.data.rd,v | 1 man/RCS/c212.plot.interim.data.rd,v | 1 man/RCS/c212.plot.samples.rd,v | 1 man/RCS/c212.pointmass.weights.rd,v | 1 man/RCS/c212.print.convergence.summary.rd,v | 1 man/RCS/c212.print.summary.stats.rd,v | 1 man/RCS/c212.ptheta.rd,v | 1 man/RCS/c212.sim.control.params.rd,v | 1 man/RCS/c212.summary.stats.rd,v | 1 man/RCS/c212.trial.data.rd,v | 1 man/RCS/c212.trial.interval.data1.rd,v | 1 man/RCS/c212.trial.interval.data2.rd,v | 1 man/RCS/c2122FDR.rd,v | 1 man/RCS/c212BH.adjust.pvals.rd,v | 1 man/RCS/c212BH.rd,v | 1 man/RCS/c212BONF.rd,v | 1 man/RCS/c212DFDR.rd,v | 1 man/RCS/c212GBH.rd,v | 1 man/RCS/c212LSL.rd,v | 1 man/RCS/c212NOADJ.rd,v | 1 man/RCS/c212TST.rd,v | 1 man/RCS/c212ssBH.rd,v | 1 src/c2121a_poisson_mc_hier2_lev0.cpp | 1305 ++++++++++++++------------- src/c2121a_poisson_mc_hier2_lev0.h | 38 src/c2121a_poisson_mc_hier2_lev1.cpp | 520 +--------- src/c2121a_poisson_mc_hier2_lev1.h | 22 src/c2121a_poisson_mc_hier3_lev0.cpp | 659 ++++--------- src/c2121a_poisson_mc_hier3_lev0.h | 20 src/c2121a_poisson_mc_hier3_lev1.cpp | 442 --------- src/c2121a_poisson_mc_hier3_lev1.h | 23 src/c2121a_poisson_mc_hier3_lev2.cpp | 524 ---------- src/c2121a_poisson_mc_hier3_lev2.h | 24 src/c212BB_poisson_mc_hier2_lev0.cpp | 476 ++------- src/c212BB_poisson_mc_hier2_lev0.h | 17 src/c212BB_poisson_mc_hier2_lev1.cpp | 546 ++--------- src/c212BB_poisson_mc_hier2_lev1.h | 26 src/c212BB_poisson_mc_hier3_lev0.cpp | 800 +++++----------- src/c212BB_poisson_mc_hier3_lev0.h | 26 src/c212BB_poisson_mc_hier3_lev1.cpp | 682 ++------------ src/c212BB_poisson_mc_hier3_lev1.h | 28 src/c212BB_poisson_mc_hier3_lev2.cpp | 660 ++----------- src/c212BB_poisson_mc_hier3_lev2.h | 29 src/c212_exec.cpp | 16 70 files changed, 2194 insertions(+), 5020 deletions(-)
Title: Polygonal Symbolic Data Analysis
Description: An implementation of symbolic polygonal data analysis. The package presents the estimation of main descriptive statistical measures, e.g, mean, covariance, variance, correlation and coefficient of variation.
In addition, transformation of the data in polygons. Empirical probability distribution function based on
polygonal histogram and regression models are presented.
Author: Wagner Silva [aut, cre, ths],
Renata Souza [aut],
Francisco Cysneiros [aut]
Maintainer: Wagner Silva <wjfs@cin.ufpe.br>
Diff between psda versions 1.0.0 dated 2017-09-05 and 1.0.1 dated 2018-10-08
DESCRIPTION | 10 ++++----- MD5 | 56 +++++++++++++++++++++++++++--------------------------- R/pconvex.R | 2 - R/pcorr.R | 4 +-- R/pcov.R | 2 - R/pfreq.R | 1 R/plr.R | 2 - R/pmean.R | 5 +--- R/pmean_id.R | 2 - R/pplot.R | 2 - R/psim.R | 2 - R/psmi.R | 4 +-- R/ptransform.R | 4 +-- R/pvar.R | 4 +-- R/pvari.R | 2 - inst/CITATION | 12 +++++------ man/pconvex.Rd | 2 - man/pcorr.Rd | 4 +-- man/pcov.Rd | 2 - man/pfreq.Rd | 3 -- man/plr.Rd | 2 - man/pmean.Rd | 5 +--- man/pmean_id.Rd | 2 - man/pplot.Rd | 2 - man/psim.Rd | 2 - man/psmi.Rd | 4 +-- man/ptransform.Rd | 4 +-- man/pvar.Rd | 4 +-- man/pvari.Rd | 2 - 29 files changed, 74 insertions(+), 78 deletions(-)