Title: Simultaneous Truth and Performance Level Estimation
Description: An implementation of Simultaneous Truth and
Performance Level Estimation (STAPLE) <doi:10.1109/TMI.2004.828354>. This
method is used when there are multiple raters for an object, typically an
image, and this method fuses these ratings into one rating. It uses an
expectation-maximization method to estimate this rating and the individual
specificity/sensitivity for each rater.
Author: John Muschelli [aut, cre]
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between stapler versions 0.6.5 dated 2018-02-02 and 0.6.6 dated 2019-03-06
DESCRIPTION | 11 +-- MD5 | 19 +++--- NEWS.md | 8 ++ R/staple_binmat.R | 1 README.md |only build/vignette.rds |binary inst/WORDLIST |only inst/doc/staple_example.html | 134 ++++++++++++++++++++++++------------------- man/staple_bin_mat.Rd | 1 man/staple_multi_mat.Rd | 3 tests/spelling.R |only tests/testthat/test-binmat.R | 2 12 files changed, 108 insertions(+), 71 deletions(-)
Title: Compute the Rectangular Statistical Cartogram
Description: Provides an interface and a C++ implementation of the RecMap MP2
construction heuristic (see 'citation("recmap")' for details). This algorithm
draws maps according to a given statistical value (e.g., election results,
population or epidemiological data). The basic idea of the RecMap algorithm is
that each map region (e.g., different countries) is represented by a
rectangle. The area of each rectangle represents the statistical value given
as input (maintain zero cartographic error). Documentation about RecMap is
provided by a vignette included in this package.
Author: Christian Panse [aut, cre] (<https://orcid.org/0000-0003-1975-3064>)
Maintainer: Christian Panse <Christian.Panse@gmail.com>
Diff between recmap versions 1.0.0 dated 2018-09-16 and 1.0.1 dated 2019-03-06
recmap-1.0.0/recmap/inst/include/dg |only recmap-1.0.0/recmap/inst/include/html |only recmap-1.0.0/recmap/inst/include/latex |only recmap-1.0.0/recmap/src/html |only recmap-1.0.0/recmap/src/latex |only recmap-1.0.1/recmap/DESCRIPTION | 6 recmap-1.0.1/recmap/MD5 | 176 +----------------- recmap-1.0.1/recmap/README.md | 14 + recmap-1.0.1/recmap/build/partial.rdb |binary recmap-1.0.1/recmap/build/vignette.rds |binary recmap-1.0.1/recmap/data/datalist |only recmap-1.0.1/recmap/inst/doc/recmap.html | 16 - recmap-1.0.1/recmap/inst/recmap.pdf |only recmap-1.0.1/recmap/inst/shiny-examples/server.R | 4 recmap-1.0.1/recmap/inst/shiny-examples/ui.R | 21 +- recmap-1.0.1/recmap/tests/testthat/test-recmapGRASP.R | 5 16 files changed, 50 insertions(+), 192 deletions(-)
Title: Furniture for Quantitative Scientists
Description: Contains four main functions (i.e., four pieces of furniture):
table1() which produces a well-formatted table of descriptive statistics common as Table 1
in research articles, tableC() which produces a well-formatted table of correlations,
tableF() which provides frequency counts, and washer() which
is helpful in cleaning up the data. These furniture-themed functions are designed
to simplify common tasks in quantitative analysis. Other data summary and cleaning tools
are also available.
Author: Tyson S. Barrett [aut, cre] (<https://orcid.org/0000-0002-2137-1391>),
Emily Brignone [aut],
Daniel J. Laxman [aut]
Maintainer: Tyson S. Barrett <t.barrett@aggiemail.usu.edu>
Diff between furniture versions 1.8.7 dated 2018-11-10 and 1.9.0 dated 2019-03-06
DESCRIPTION | 12 - MD5 | 34 +-- NEWS.md | 10 R/Table1.R | 92 ++++++-- R/table1_utils.R | 113 +++++++--- R/utils.R | 42 ++-- build/vignette.rds |binary inst/CITATION | 9 inst/doc/Furniture.R | 8 inst/doc/Furniture.Rmd | 8 inst/doc/Furniture.html | 444 ++++++++++++++++++++++--------------------- inst/doc/Table1.R | 23 -- inst/doc/Table1.Rmd | 24 -- inst/doc/Table1.html | 241 +++++++++++------------ man/table1.Rd | 4 tests/testthat/test_table1.R | 36 +++ vignettes/Furniture.Rmd | 8 vignettes/Table1.Rmd | 24 -- 18 files changed, 636 insertions(+), 496 deletions(-)
Title: Spatial Objects of the Czech Republic
Description: Administrative regions, rivers and water bodies of the Czech Republic.
Author: Jindra Lacko
Maintainer: Jindra Lacko <jindra.lacko@gmail.com>
Diff between RCzechia versions 1.3.2 dated 2019-01-04 and 1.3.3 dated 2019-03-06
DESCRIPTION | 8 ++++---- LICENSE | 2 +- MD5 | 40 ++++++++++++++++++++-------------------- NEWS.md | 3 +++ R/RCzechia.R | 13 +++++++++++-- R/casti.R | 6 +++--- R/chr_uzemi.R | 6 +++--- R/kraje.R | 6 +++--- R/lesy.R | 6 +++--- R/obce_body.R | 6 +++--- R/obce_polygony.R | 6 +++--- R/okresy.R | 6 +++--- R/orp_polygony.R | 6 +++--- R/plochy.R | 6 +++--- R/reky.R | 6 +++--- R/republika.R | 6 +++--- R/silnice.R | 6 +++--- R/zeleznice.R | 6 +++--- README.md | 2 +- inst/doc/vignette.html | 8 ++++---- man/RCzechia-package.Rd | 15 +++++++++++++-- 21 files changed, 96 insertions(+), 73 deletions(-)
Title: Generalized Linear Mixed Model Association Tests
Description: Perform association tests using generalized linear mixed models (GLMMs) in genome-wide association studies (GWAS) and sequencing association studies. First, GMMAT fits a GLMM with covariate adjustment and random effects to account for population structure and familial or cryptic relatedness. For GWAS, GMMAT performs score tests for each genetic variant as proposed in Chen et al. (2016) <DOI:10.1016/j.ajhg.2016.02.012>. For candidate gene studies, GMMAT can also perform Wald tests to get the effect size estimate for each genetic variant. For rare variant analysis from sequencing association studies, GMMAT performs the variant Set Mixed Model Association Tests (SMMAT) as proposed in Chen et al. (2019) <DOI:10.1016/j.ajhg.2018.12.012>, including the burden test, the sequence kernel association test (SKAT), SKAT-O and an efficient hybrid test of the burden test and SKAT, based on user-defined variant sets.
Author: Han Chen, Matthew P. Conomos
Maintainer: Han Chen <Han.Chen.2@uth.tmc.edu>
Diff between GMMAT versions 1.0.3 dated 2019-01-30 and 1.0.4 dated 2019-03-06
DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++-------------- build/vignette.rds |binary data/example.rda |binary inst/doc/GMMAT.Rnw | 4 ++-- inst/doc/GMMAT.pdf |binary man/GMMAT-package.Rd | 6 +++--- man/SMMAT.Rd | 2 +- man/SMMAT.meta.Rd | 2 +- tests/testthat/test_SMMAT.R | 6 ++++++ tests/testthat/test_SMMAT.meta.R | 6 ++++++ tests/testthat/test_glmm.score.R | 6 ++++++ tests/testthat/test_glmm.wald.R | 4 ++++ tests/testthat/test_glmmkin.R | 6 ++++++ vignettes/GMMAT.Rnw | 4 ++-- 15 files changed, 55 insertions(+), 27 deletions(-)
Title: Utilities for 'Glmnet'
Description: Provides a formula interface for the 'glmnet' package for
elasticnet regression, a method for cross-validating the alpha parameter,
and other quality-of-life tools.
Author: Microsoft [cph], Hong Ooi [aut, cre]
Maintainer: Hong Ooi <hongooi@microsoft.com>
Diff between glmnetUtils versions 1.1.1 dated 2019-01-17 and 1.1.2 dated 2019-03-06
DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++-------------- NEWS.md | 4 ++++ R/cvaGlmnetFormula.r | 4 ++-- README.md | 6 ++++++ build/vignette.rds |binary inst/doc/intro.html | 4 ++-- inst/doc/intro.rmd | 14 +++++++------- man/cv.glmnet.Rd | 9 +++++---- man/cva.glmnet.Rd | 16 ++++++++-------- man/glmnet.Rd | 10 +++++----- man/glmnet.model.matrix.Rd | 4 ++-- man/glmnetUtils.Rd | 1 - tests/testthat/test3_cva_glmnet.R | 2 +- vignettes/intro.rmd | 14 +++++++------- 15 files changed, 67 insertions(+), 57 deletions(-)
Title: Google Citation Parser
Description: Scrapes Google Citation pages and creates data frames of
citations over time.
Author: John Muschelli [aut, cre] (<https://orcid.org/0000-0001-6469-1750>)
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between gcite versions 0.9.3 dated 2018-11-19 and 0.10.1 dated 2019-03-06
DESCRIPTION | 13 +++++---- MD5 | 54 ++++++++++++++++++++-------------------- NAMESPACE | 1 NEWS.md | 6 +++- R/gcite.R | 7 +++++ R/gcite_author_info.R | 5 ++- R/gcite_citation_index.R | 2 - R/gcite_citation_page.R | 2 - R/gcite_cite_over_time.R | 4 +- R/gcite_paper_df.R | 2 - R/gcite_papers.R | 2 - R/gcite_url.R | 3 +- R/gcite_user_info.R | 2 - R/gcite_username.R | 20 +++++++++++--- R/is_travis.R | 7 +++++ inst |only man/gcite.Rd | 8 +++++ man/gcite_author_info.Rd | 2 - man/gcite_citation_index.Rd | 2 - man/gcite_citation_page.Rd | 2 - man/gcite_cite_over_time.Rd | 4 +- man/gcite_paper_df.Rd | 2 - man/gcite_papers.Rd | 2 - man/gcite_url.Rd | 3 +- man/gcite_user_info.Rd | 2 - man/gcite_username.Rd | 4 +- man/is_travis.Rd | 4 ++ tests/spelling.R |only tests/testthat/test-zero_hist.R | 13 +++++---- 29 files changed, 114 insertions(+), 64 deletions(-)
Title: Repeatability Estimation for Gaussian and Non-Gaussian Data
Description: Estimating repeatability (intra-class
correlation) from Gaussian, binary, proportion and Poisson data.
Author: Martin Stoffel <martin.adam.stoffel@gmail.com>,
Shinichi Nakagawa <s.nakagawa@unsw.edu.au>,
Holger Schielzeth <holger.schielzeth@uni-jena.de>
Maintainer: Martin Stoffel <martin.adam.stoffel@gmail.com>
Diff between rptR versions 0.9.21 dated 2018-01-04 and 0.9.22 dated 2019-03-06
DESCRIPTION | 12 ++++---- MD5 | 34 ++++++++++++------------ NEWS.md | 7 ++++- R/rpt.R | 2 - R/rptBinary.R | 16 ++++++++++- build/vignette.rds |binary inst/doc/rptR.html | 50 +++++++++++++++++++++++++----------- man/plot.rpt.Rd | 4 +- man/rpt.Rd | 10 +++---- man/rptBinary.Rd | 8 ++--- man/rptGaussian.Rd | 6 ++-- man/rptProportion.Rd | 8 ++--- tests/testthat/test-rpt.R | 1 tests/testthat/test-rptBinary.R | 1 tests/testthat/test-rptGaussian.R | 1 tests/testthat/test-rptPoisson.R | 1 tests/testthat/test-rptProportion.R | 1 tests/testthat/test-summary.rpt.R | 1 18 files changed, 104 insertions(+), 59 deletions(-)
Title: Tools for Polyploid Microsatellite Analysis
Description: A collection of tools to handle microsatellite data of
any ploidy (and samples of mixed ploidy) where allele copy number is not
known in partially heterozygous genotypes. It can import and export data in
ABI 'GeneMapper', 'Structure', 'ATetra', 'Tetrasat'/'Tetra', 'GenoDive', 'SPAGeDi',
'POPDIST', 'STRand', and binary presence/absence formats. It can calculate
pairwise distances between individuals using a stepwise mutation model or
infinite alleles model, with or without taking ploidies and allele frequencies
into account. These distances can be used for the calculation of clonal
diversity statistics or used for further analysis in R. Allelic diversity
statistics and Polymorphic Information Content are also available. polysat can
assist the user in estimating the ploidy of samples, and it can estimate allele
frequencies in populations, calculate pairwise or global differentiation statistics
based on those frequencies, and export allele frequencies to 'SPAGeDi' and 'adegenet'.
Functions are also included for assigning alleles to isoloci in cases where one pair
of microsatellite primers amplifies alleles from two or more independently
segregating isoloci. polysat is described by Clark and Jasieniuk (2011)
<doi:10.1111/j.1755-0998.2011.02985.x> and Clark and Schreier (2017)
<doi:10.1111/1755-0998.12639>.
Author: Lindsay V. Clark [aut, cre] (<https://orcid.org/0000-0002-3881-9252>),
Alistair J. Hall [ctb] (<https://orcid.org/0000-0001-9293-8909>),
Handunnethi Nihal de Silva [ctb],
Tyler William Smith [ctb] (<https://orcid.org/0000-0001-7683-2653>)
Maintainer: Lindsay V. Clark <lvclark@illinois.edu>
Diff between polysat versions 1.7-3 dated 2018-06-07 and 1.7-4 dated 2019-03-06
DESCRIPTION | 25 MD5 | 24 NAMESPACE | 4 NEWS | 17 R/classes_generics_methods.R | 45 + R/dataexport.R | 1079 +++++++++++++++++++++--------------------- R/individual_distance.R | 2 build/vignette.rds |binary inst/doc/allopolyVignette.pdf |binary inst/doc/polysattutorial.pdf |binary man/genambig-class.Rd | 9 man/read.Structure.Rd | 2 man/write.Structure.Rd | 11 13 files changed, 656 insertions(+), 562 deletions(-)
Title: Paginate the HTML Output of R Markdown with CSS for Print
Description: Use the paged media properties in CSS and the JavaScript
library 'paged.js' to split the content of an HTML document into discrete
pages. Each page can have its page size, page numbers, margin boxes, and
running headers, etc. Applications of this package include books, letters,
reports, papers, business cards, resumes, and posters.
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>),
Romain Lesur [aut, cph] (<https://orcid.org/0000-0002-0721-5595>),
Christophe Dervieux [ctb] (<https://orcid.org/0000-0003-4474-2498>),
RStudio, Inc. [cph],
Adam Hyde [ctb] (paged.js in resources/js/),
Min-Zhong Lu [ctb] (resume.css in resources/css/),
Zulko [ctb] (poster-relaxed.css in resources/css/)
Maintainer: Yihui Xie <xie@yihui.name>
Diff between pagedown versions 0.1 dated 2019-01-02 and 0.2 dated 2019-03-06
DESCRIPTION | 11 MD5 | 42 - NAMESPACE | 1 NEWS.md |only R/card.R | 18 R/chrome.R | 354 ++++++++++- R/paged.R | 43 + R/utils.R | 9 README.md | 13 inst/resources/csl |only inst/resources/css/jss-fonts.css |only inst/resources/css/jss-page.css |only inst/resources/css/jss.css |only inst/resources/css/resume.css | 6 inst/resources/html/card.html | 135 +++- inst/resources/html/jss_paged.html |only inst/resources/html/resume.html | 23 inst/resources/html/ws-server.html |only inst/resources/js/chrome_print.js |only inst/resources/js/config.js | 13 inst/resources/lua/jss.lua |only inst/rmarkdown/templates/business-card/skeleton/skeleton.Rmd | 41 - inst/rmarkdown/templates/jss-paged |only man/business_card.Rd | 14 man/chrome_print.Rd | 66 +- man/html_paged.Rd | 5 man/jss_paged.Rd |only 27 files changed, 649 insertions(+), 145 deletions(-)
Title: Data-Limited Methods Toolkit
Description: Development, simulation testing, and implementation of management
procedures for data-limited fisheries
(see Carruthers & Hordyk (2018) <doi:10.1111/2041-210X.13081>).
Author: Tom Carruthers [aut, cre],
Adrian Hordyk [aut],
M. Bryan [ctb],
HF. Geremont [ctb],
C. Grandin [ctb],
W. Harford [ctb],
Q. Huynh [ctb],
C. Walters [ctb]
Maintainer: Tom Carruthers <t.carruthers@fisheries.ubc.ca>
Diff between DLMtool versions 5.2.3 dated 2018-09-11 and 5.3 dated 2019-03-06
DLMtool-5.2.3/DLMtool/man/simYears.Rd |only DLMtool-5.3/DLMtool/DESCRIPTION | 20 DLMtool-5.3/DLMtool/MD5 | 314 - DLMtool-5.3/DLMtool/NAMESPACE | 15 DLMtool-5.3/DLMtool/NEWS.md | 40 DLMtool-5.3/DLMtool/R/Blow_funcs.R | 13 DLMtool-5.3/DLMtool/R/Data2csv.R |only DLMtool-5.3/DLMtool/R/Data_Functions.R | 306 - DLMtool-5.3/DLMtool/R/Data_Plotting.R | 8 DLMtool-5.3/DLMtool/R/Data_make_update.R |only DLMtool-5.3/DLMtool/R/DefineClasses.r | 717 +--- DLMtool-5.3/DLMtool/R/Fease_Functions.R | 38 DLMtool-5.3/DLMtool/R/MPs_Input.R | 334 + DLMtool-5.3/DLMtool/R/MPs_Output.R | 115 DLMtool-5.3/DLMtool/R/MPs_SupportingFunctions.R | 37 DLMtool-5.3/DLMtool/R/MSE_Plotting.R | 70 DLMtool-5.3/DLMtool/R/MSE_Plotting_PMs.R | 56 DLMtool-5.3/DLMtool/R/MSE_functions.R | 74 DLMtool-5.3/DLMtool/R/Misc_Exported.R | 111 DLMtool-5.3/DLMtool/R/Misc_Internal.R | 459 ++ DLMtool-5.3/DLMtool/R/OM_Plotting.R | 61 DLMtool-5.3/DLMtool/R/OM_functions.R | 2 DLMtool-5.3/DLMtool/R/OM_init_doc.R | 122 DLMtool-5.3/DLMtool/R/PMtable.R |only DLMtool-5.3/DLMtool/R/RcppExports.R | 75 DLMtool-5.3/DLMtool/R/Roxy_DataObjects.r | 14 DLMtool-5.3/DLMtool/R/SampleOM.R | 139 DLMtool-5.3/DLMtool/R/Turing.R | 150 DLMtool-5.3/DLMtool/R/aaImportFrom.R | 6 DLMtool-5.3/DLMtool/R/data2OMfunctions.r | 45 DLMtool-5.3/DLMtool/R/popdyn.R | 1032 ++++- DLMtool-5.3/DLMtool/R/runMSE.r | 1755 ++++------ DLMtool-5.3/DLMtool/R/sysdata.rda |binary DLMtool-5.3/DLMtool/data/Albacore.RData |binary DLMtool-5.3/DLMtool/data/Atlantic_mackerel.RData |binary DLMtool-5.3/DLMtool/data/Blue_shark.RData |binary DLMtool-5.3/DLMtool/data/Bluefin_tuna.RData |binary DLMtool-5.3/DLMtool/data/Bluefin_tuna_WAtl.RData |binary DLMtool-5.3/DLMtool/data/Butterfish.RData |binary DLMtool-5.3/DLMtool/data/China_rockfish.RData |binary DLMtool-5.3/DLMtool/data/Cobia.RData |binary DLMtool-5.3/DLMtool/data/DataDescription.RData |binary DLMtool-5.3/DLMtool/data/DecE_Dom.RData |binary DLMtool-5.3/DLMtool/data/DecE_HDom.RData |binary DLMtool-5.3/DLMtool/data/DecE_NDom.RData |binary DLMtool-5.3/DLMtool/data/Example_datafile.RData |binary DLMtool-5.3/DLMtool/data/FlatE_Dom.RData |binary DLMtool-5.3/DLMtool/data/FlatE_HDom.RData |binary DLMtool-5.3/DLMtool/data/FlatE_NDom.RData |binary DLMtool-5.3/DLMtool/data/FleetDescription.RData |binary DLMtool-5.3/DLMtool/data/Generic_DecE.RData |binary DLMtool-5.3/DLMtool/data/Generic_FlatE.RData |binary DLMtool-5.3/DLMtool/data/Generic_Fleet.RData |binary DLMtool-5.3/DLMtool/data/Generic_IncE.RData |binary DLMtool-5.3/DLMtool/data/Generic_Obs.RData |binary DLMtool-5.3/DLMtool/data/Gulf_blue_tilefish.RData |binary DLMtool-5.3/DLMtool/data/Herring.RData |binary DLMtool-5.3/DLMtool/data/ImpDescription.RData |binary DLMtool-5.3/DLMtool/data/Imprecise_Biased.RData |binary DLMtool-5.3/DLMtool/data/Imprecise_Unbiased.RData |binary DLMtool-5.3/DLMtool/data/IncE_HDom.RData |binary DLMtool-5.3/DLMtool/data/IncE_NDom.RData |binary DLMtool-5.3/DLMtool/data/LHdatabase.RData |binary DLMtool-5.3/DLMtool/data/Low_Effort_Non_Target.RData |binary DLMtool-5.3/DLMtool/data/MSEDescription.RData |only DLMtool-5.3/DLMtool/data/Mackerel.RData |binary DLMtool-5.3/DLMtool/data/OMDescription.RData |binary DLMtool-5.3/DLMtool/data/ObsDescription.RData |binary DLMtool-5.3/DLMtool/data/Overages.RData |binary DLMtool-5.3/DLMtool/data/Perfect_Imp.RData |binary DLMtool-5.3/DLMtool/data/Perfect_Info.RData |binary DLMtool-5.3/DLMtool/data/Porgy.RData |binary DLMtool-5.3/DLMtool/data/Precise_Biased.RData |binary DLMtool-5.3/DLMtool/data/Precise_Unbiased.RData |binary DLMtool-5.3/DLMtool/data/Red_snapper.RData |binary DLMtool-5.3/DLMtool/data/ReqData.RData |binary DLMtool-5.3/DLMtool/data/Rockfish.RData |binary DLMtool-5.3/DLMtool/data/SimulatedData.RData |binary DLMtool-5.3/DLMtool/data/Simulation_1.RData |binary DLMtool-5.3/DLMtool/data/Snapper.RData |binary DLMtool-5.3/DLMtool/data/Sole.RData |binary DLMtool-5.3/DLMtool/data/StockDescription.RData |binary DLMtool-5.3/DLMtool/data/Target_All_Fish.RData |binary DLMtool-5.3/DLMtool/data/Targeting_Small_Fish.RData |binary DLMtool-5.3/DLMtool/data/Toothfish.RData |binary DLMtool-5.3/DLMtool/data/datalist | 1 DLMtool-5.3/DLMtool/data/ourReefFish.RData |binary DLMtool-5.3/DLMtool/data/testOM.RData |binary DLMtool-5.3/DLMtool/data/tiny.RData |binary DLMtool-5.3/DLMtool/inst/Data.csv | 140 DLMtool-5.3/DLMtool/inst/Data.xlsx |binary DLMtool-5.3/DLMtool/inst/OM.rmd | 9 DLMtool-5.3/DLMtool/inst/OM.xlsx |binary DLMtool-5.3/DLMtool/inst/PLimitTable.Rmd |only DLMtool-5.3/DLMtool/inst/PLimitTable2.Rmd |only DLMtool-5.3/DLMtool/inst/PObjTable.Rmd |only DLMtool-5.3/DLMtool/inst/PObjTable2.Rmd |only DLMtool-5.3/DLMtool/man/BK.Rd | 2 DLMtool-5.3/DLMtool/man/CALsimp.Rd |only DLMtool-5.3/DLMtool/man/DCAC.Rd | 14 DLMtool-5.3/DLMtool/man/DDe.Rd | 2 DLMtool-5.3/DLMtool/man/DLMextra.Rd | 4 DLMtool-5.3/DLMtool/man/Data-class.Rd | 13 DLMtool-5.3/DLMtool/man/Data2csv.Rd |only DLMtool-5.3/DLMtool/man/DataDescription.Rd | 2 DLMtool-5.3/DLMtool/man/EtargetLopt.Rd | 2 DLMtool-5.3/DLMtool/man/Fdem.Rd | 2 DLMtool-5.3/DLMtool/man/FilterSmooth.Rd | 2 DLMtool-5.3/DLMtool/man/Fleet-class.Rd | 10 DLMtool-5.3/DLMtool/man/Fratio.Rd | 2 DLMtool-5.3/DLMtool/man/Growth2OM.Rd | 8 DLMtool-5.3/DLMtool/man/Hist-class.Rd |only DLMtool-5.3/DLMtool/man/ITM.Rd | 2 DLMtool-5.3/DLMtool/man/Imp-class.Rd | 2 DLMtool-5.3/DLMtool/man/Islope1.Rd | 2 DLMtool-5.3/DLMtool/man/Islope_.Rd | 2 DLMtool-5.3/DLMtool/man/Itarget1.Rd | 3 DLMtool-5.3/DLMtool/man/ItargetE1.Rd | 3 DLMtool-5.3/DLMtool/man/Itarget_.Rd | 3 DLMtool-5.3/DLMtool/man/Itargeteff_.Rd | 3 DLMtool-5.3/DLMtool/man/L2A.Rd | 4 DLMtool-5.3/DLMtool/man/LBSPR.Rd | 47 DLMtool-5.3/DLMtool/man/LBSPR_.Rd | 4 DLMtool-5.3/DLMtool/man/LBSPRgen.Rd | 12 DLMtool-5.3/DLMtool/man/Lratio_BHI.Rd | 13 DLMtool-5.3/DLMtool/man/LstepCC1.Rd | 3 DLMtool-5.3/DLMtool/man/LstepCE1.Rd | 3 DLMtool-5.3/DLMtool/man/Ltarget1.Rd | 3 DLMtool-5.3/DLMtool/man/LtargetE1.Rd | 3 DLMtool-5.3/DLMtool/man/MSE-class.Rd | 36 DLMtool-5.3/DLMtool/man/MSEDescription.Rd |only DLMtool-5.3/DLMtool/man/OM-class.Rd | 33 DLMtool-5.3/DLMtool/man/PMLimit.Rd |only DLMtool-5.3/DLMtool/man/Pplot2.Rd | 19 DLMtool-5.3/DLMtool/man/Rcontrol.Rd | 2 DLMtool-5.3/DLMtool/man/RealFease.Rd |only DLMtool-5.3/DLMtool/man/ReqData.Rd | 2 DLMtool-5.3/DLMtool/man/SPSRA.Rd | 2 DLMtool-5.3/DLMtool/man/SimulatedData.Rd | 4 DLMtool-5.3/DLMtool/man/Stock-class.Rd | 10 DLMtool-5.3/DLMtool/man/TradePlot.Rd | 15 DLMtool-5.3/DLMtool/man/Uses.Rd |only DLMtool-5.3/DLMtool/man/YPR.Rd | 2 DLMtool-5.3/DLMtool/man/avail.Rd | 4 DLMtool-5.3/DLMtool/man/boxplot.Data.Rd | 5 DLMtool-5.3/DLMtool/man/checkMSE.Rd | 3 DLMtool-5.3/DLMtool/man/curE.Rd | 4 DLMtool-5.3/DLMtool/man/getq3.Rd | 2 DLMtool-5.3/DLMtool/man/gettempvar.Rd | 8 DLMtool-5.3/DLMtool/man/plot-OM.Rd | 2 DLMtool-5.3/DLMtool/man/popdynCPP.Rd | 4 DLMtool-5.3/DLMtool/man/runMSE.Rd | 40 DLMtool-5.3/DLMtool/man/simCAA.Rd |only DLMtool-5.3/DLMtool/man/simCAL.Rd |only DLMtool-5.3/DLMtool/src/LBSPR.cpp | 47 DLMtool-5.3/DLMtool/src/RcppExports.cpp | 234 - DLMtool-5.3/DLMtool/src/genLenComp.cpp | 131 DLMtool-5.3/DLMtool/src/popddynCPP.cpp | 22 DLMtool-5.3/DLMtool/tests/manual/run-tests-code.R | 59 DLMtool-5.3/DLMtool/tests/manual/test-code/test-Data2csv.R |only DLMtool-5.3/DLMtool/tests/manual/test-code/test-Data_Plotting.R | 11 DLMtool-5.3/DLMtool/tests/manual/test-code/test-MSE_Plotting.R | 7 DLMtool-5.3/DLMtool/tests/manual/test-code/test-OM_Plotting.R | 4 DLMtool-5.3/DLMtool/tests/manual/test-code/test-PMobjects.R | 2 DLMtool-5.3/DLMtool/tests/manual/test-code/test-RealIndices.R |only DLMtool-5.3/DLMtool/tests/manual/test-code/test-checkPopdyn.R |only DLMtool-5.3/DLMtool/tests/manual/test-code/test-runMSE.R | 12 DLMtool-5.3/DLMtool/tests/manual/test-code/test-slotDescription.R | 4 DLMtool-5.3/DLMtool/tests/manual/test_dev |only 169 files changed, 4177 insertions(+), 3006 deletions(-)
Title: Nonparametrics with Clustered Binary and Multinomial Data
Description: Implements non-parametric analyses for clustered
binary and multinomial data. The elements of the cluster are assumed
exchangeable, and identical joint distribution (also known as marginal
compatibility, or reproducibility) is assumed for clusters of different
sizes. A trend test based on stochastic ordering is implemented.
Author: Aniko Szabo [aut, cre]
Maintainer: Aniko Szabo <aszabo@mcw.edu>
Diff between CorrBin versions 1.5 dated 2015-01-05 and 1.6 dated 2019-03-06
DESCRIPTION | 16 ++++---- MD5 | 79 +++++++++++++++++++++---------------------- NAMESPACE | 13 +++++-- R/CBData.R | 4 ++ R/CMData.R | 4 ++ R/ExchMultinomial.R | 5 ++ R/Reprod.R | 6 ++- R/aaa-generics1.R | 2 - build/vignette.rds |binary data/dehp.rda |binary data/egde.rda |binary data/shelltox.rda |binary inst/doc/CorrBinVignette.R | 1 inst/doc/CorrBinVignette.pdf |binary man/CBData.Rd | 12 +++--- man/CMData.Rd | 12 +++--- man/CorrBin-internal.Rd | 18 ++++----- man/CorrBin-package.Rd | 36 +++++++++---------- man/Extract.Rd | 16 ++++---- man/GEE.trend.test.Rd | 12 +++--- man/NOSTASOT.Rd | 12 +++--- man/RS.trend.test.Rd | 12 +++--- man/SO.LRT.Rd | 12 +++--- man/SO.mc.est.Rd | 16 ++++---- man/SO.trend.test.Rd | 16 ++++---- man/jointprobs.Rd | 15 ++++---- man/mc.est.Rd | 39 +++++++++++---------- man/mc.test.chisq.Rd | 29 +++++++++------ man/multi.corr.Rd | 7 ++- man/multinom.gen.Rd | 16 ++++---- man/pdf.Rd | 16 ++++---- man/ran.CBData.Rd | 12 +++--- man/ran.CMData.Rd | 23 ++++++------ man/read.CBData.Rd | 10 ++--- man/read.CMData.Rd | 12 +++--- man/soControl.Rd | 16 ++++---- man/trend.test.Rd | 12 +++--- man/uniprobs.Rd | 6 +-- man/unwrap.Rd | 30 +++++++++------- src/ReprodCalcs.c | 23 +++++------- src/init.c |only 41 files changed, 318 insertions(+), 252 deletions(-)
Title: Tools for Parsing and Generating XML Within R and S-Plus
Description: Many approaches for both reading and
creating XML (and HTML) documents (including DTDs), both local
and accessible via HTTP or FTP. Also offers access to an
'XPath' "interpreter".
Author: Duncan Temple Lang and the CRAN Team (including Tomas Kalibera)
Maintainer: ORPHANED
Diff between XML versions 3.98-1.18 dated 2019-03-04 and 3.98-1.19 dated 2019-03-06
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- src/DocParse.c | 23 +++++++++++++++-------- src/EventParse.c | 13 +++++++------ src/Utils.c | 4 ++-- src/XMLEventParse.c | 10 +++++----- src/schema.c | 4 ++-- src/xmlsecurity.c | 1 + src/xpath.c | 14 +++++++------- 9 files changed, 51 insertions(+), 42 deletions(-)
Title: Tools: moving window statistics, GIF, Base64, ROC AUC, etc.
Description: Contains several basic utility functions including: moving
(rolling, running) window statistic functions, read/write for
GIF and ENVI binary files, fast calculation of AUC, LogitBoost
classifier, base64 encoder/decoder, round-off-error-free sum
and cumsum, etc.
Author: Jarek Tuszynski <jaroslaw.w.tuszynski@saic.com>
Maintainer: ORPHANED
Diff between caTools versions 1.17.1.1 dated 2018-07-20 and 1.17.1.2 dated 2019-03-06
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/Gif2R.cpp | 7 +++++-- 3 files changed, 10 insertions(+), 7 deletions(-)
Title: Perceptual Analysis, Visualization and Organization of Spectral
Color Data in R
Description: A cohesive framework for parsing, analyzing and organizing color
from spectral data.
Author: Rafael Maia [aut, cre] (<https://orcid.org/0000-0002-7563-9795>),
Thomas White [aut] (<https://orcid.org/0000-0001-8493-9450>),
Hugo Gruson [aut] (<https://orcid.org/0000-0002-4094-1476>),
John Endler [aut],
Chad Eliason [aut],
Pierre-Paul Bitton [aut] (<https://orcid.org/0000-0001-5984-2331>)
Maintainer: Rafael Maia <rm72@zips.uakron.edu>
Diff between pavo versions 2.0.0 dated 2018-09-22 and 2.1.0 dated 2019-03-06
pavo-2.0.0/pavo/R/as.rimg.r |only pavo-2.0.0/pavo/R/as.rspec.r |only pavo-2.0.0/pavo/R/pavo-deprecated.R |only pavo-2.0.0/pavo/R/plot.colspace.r |only pavo-2.0.0/pavo/R/plot.rspec.r |only pavo-2.0.0/pavo/R/points.colspace.r |only pavo-2.0.0/pavo/inst/doc/pavo.R |only pavo-2.0.0/pavo/inst/doc/pavo.Rmd |only pavo-2.0.0/pavo/inst/doc/pavo.html |only pavo-2.0.0/pavo/inst/extdata/specsdata.rda |only pavo-2.0.0/pavo/man/pavo-deprecated.Rd |only pavo-2.0.0/pavo/vignettes/pavo.Rmd |only pavo-2.1.0/pavo/DESCRIPTION | 47 - pavo-2.1.0/pavo/MD5 | 332 ++++---- pavo-2.1.0/pavo/NAMESPACE | 27 pavo-2.1.0/pavo/NEWS.md | 178 ++-- pavo-2.1.0/pavo/R/adjacent.R | 378 ++++----- pavo-2.1.0/pavo/R/aggplot.R | 59 - pavo-2.1.0/pavo/R/aggspec.R | 27 pavo-2.1.0/pavo/R/as.rimg.R |only pavo-2.1.0/pavo/R/as.rspec.R |only pavo-2.1.0/pavo/R/axistetra.R | 13 pavo-2.1.0/pavo/R/bootcoldist.R | 30 pavo-2.1.0/pavo/R/categorical.R | 41 pavo-2.1.0/pavo/R/catplot.R | 26 pavo-2.1.0/pavo/R/cie.R | 15 pavo-2.1.0/pavo/R/cieplot.R | 42 - pavo-2.1.0/pavo/R/classify.R | 443 ++++------ pavo-2.1.0/pavo/R/coc.R | 41 pavo-2.1.0/pavo/R/cocplot.R | 23 pavo-2.1.0/pavo/R/coldist.R | 865 ++++++++------------- pavo-2.1.0/pavo/R/coldist2mat.R | 14 pavo-2.1.0/pavo/R/colspace.r | 38 pavo-2.1.0/pavo/R/data-bgandilum.R | 1 pavo-2.1.0/pavo/R/data-flowers.R | 6 pavo-2.1.0/pavo/R/data-sicalis.R | 2 pavo-2.1.0/pavo/R/data-teal.R | 2 pavo-2.1.0/pavo/R/data-transmissiondata.R | 1 pavo-2.1.0/pavo/R/data-ttvertex.R | 1 pavo-2.1.0/pavo/R/data-vissyst.R | 1 pavo-2.1.0/pavo/R/diplot.R | 34 pavo-2.1.0/pavo/R/dispace.R | 34 pavo-2.1.0/pavo/R/explorespec.R | 94 -- pavo-2.1.0/pavo/R/getimg.R | 76 + pavo-2.1.0/pavo/R/getspec.R | 20 pavo-2.1.0/pavo/R/hexagon.R | 36 pavo-2.1.0/pavo/R/hexplot.R | 38 pavo-2.1.0/pavo/R/internal.R | 3 pavo-2.1.0/pavo/R/is.colspace.R |only pavo-2.1.0/pavo/R/is.vismodel.R |only pavo-2.1.0/pavo/R/jnd2xyz.R | 9 pavo-2.1.0/pavo/R/jndplot.R | 32 pavo-2.1.0/pavo/R/jndrot.R | 32 pavo-2.1.0/pavo/R/legendtetra.R | 6 pavo-2.1.0/pavo/R/merge.rspec.R | 9 pavo-2.1.0/pavo/R/pavo-package.R | 5 pavo-2.1.0/pavo/R/peakshape.R | 136 +-- pavo-2.1.0/pavo/R/plot.colspace.R |only pavo-2.1.0/pavo/R/plot.rimg.R | 35 pavo-2.1.0/pavo/R/plot.rspec.R |only pavo-2.1.0/pavo/R/plotsmooth.R | 42 - pavo-2.1.0/pavo/R/points.colspace.R |only pavo-2.1.0/pavo/R/procimg.R | 237 ++--- pavo-2.1.0/pavo/R/procspec.R | 67 - pavo-2.1.0/pavo/R/projplot.R | 64 - pavo-2.1.0/pavo/R/projpoints.R | 32 pavo-2.1.0/pavo/R/segplot.R | 38 pavo-2.1.0/pavo/R/segspace.R | 56 - pavo-2.1.0/pavo/R/sensdata.R | 29 pavo-2.1.0/pavo/R/sensmodel.R | 22 pavo-2.1.0/pavo/R/spec2rgb.R | 89 -- pavo-2.1.0/pavo/R/subset.rspec.R | 14 pavo-2.1.0/pavo/R/summary.colspace.R | 37 pavo-2.1.0/pavo/R/summary.rimg.R | 20 pavo-2.1.0/pavo/R/summary.rspec.R | 51 - pavo-2.1.0/pavo/R/summary.vismodel.R | 5 pavo-2.1.0/pavo/R/sysdata.rda |binary pavo-2.1.0/pavo/R/tcspace.R | 29 pavo-2.1.0/pavo/R/tcsplot.R | 57 - pavo-2.1.0/pavo/R/tcspoints.R | 8 pavo-2.1.0/pavo/R/tcsvol.R | 11 pavo-2.1.0/pavo/R/tetraplot.R | 43 - pavo-2.1.0/pavo/R/triplot.R | 25 pavo-2.1.0/pavo/R/trispace.R | 32 pavo-2.1.0/pavo/R/vismodel.R | 451 +++------- pavo-2.1.0/pavo/R/vol.R | 35 pavo-2.1.0/pavo/R/voloverlap.R | 39 pavo-2.1.0/pavo/README.md | 62 - pavo-2.1.0/pavo/build/partial.rdb |only pavo-2.1.0/pavo/build/vignette.rds |binary pavo-2.1.0/pavo/data/flowers.rda |binary pavo-2.1.0/pavo/data/sicalis.rda |binary pavo-2.1.0/pavo/data/teal.rda |binary pavo-2.1.0/pavo/inst/CITATION | 10 pavo-2.1.0/pavo/inst/WORDLIST |only pavo-2.1.0/pavo/inst/doc/analysing.R |only pavo-2.1.0/pavo/inst/doc/analysing.Rmd |only pavo-2.1.0/pavo/inst/doc/analysing.html |only pavo-2.1.0/pavo/inst/doc/importing_processing.R |only pavo-2.1.0/pavo/inst/doc/importing_processing.Rmd |only pavo-2.1.0/pavo/inst/doc/importing_processing.html |only pavo-2.1.0/pavo/inst/doc/overview.R |only pavo-2.1.0/pavo/inst/doc/overview.Rmd |only pavo-2.1.0/pavo/inst/doc/overview.html |only pavo-2.1.0/pavo/inst/doc/spectraldesc.Rmd | 6 pavo-2.1.0/pavo/inst/extdata/specsdata.rds |only pavo-2.1.0/pavo/inst/testdata/images/formats |only pavo-2.1.0/pavo/inst/testdata/images/vig |only pavo-2.1.0/pavo/man/adjacent.Rd | 83 +- pavo-2.1.0/pavo/man/aggplot.Rd | 11 pavo-2.1.0/pavo/man/aggspec.Rd | 5 pavo-2.1.0/pavo/man/as.rimg.Rd | 18 pavo-2.1.0/pavo/man/as.rspec.Rd | 21 pavo-2.1.0/pavo/man/axistetra.Rd | 6 pavo-2.1.0/pavo/man/bootcoldist.Rd | 14 pavo-2.1.0/pavo/man/categorical.Rd | 7 pavo-2.1.0/pavo/man/catplot.Rd | 7 pavo-2.1.0/pavo/man/cie.Rd | 15 pavo-2.1.0/pavo/man/cieplot.Rd | 23 pavo-2.1.0/pavo/man/classify.Rd | 10 pavo-2.1.0/pavo/man/coc.Rd | 7 pavo-2.1.0/pavo/man/cocplot.Rd | 9 pavo-2.1.0/pavo/man/coldist.Rd | 48 - pavo-2.1.0/pavo/man/coldist2mat.Rd | 11 pavo-2.1.0/pavo/man/colspace.Rd | 27 pavo-2.1.0/pavo/man/diplot.Rd | 21 pavo-2.1.0/pavo/man/dispace.Rd | 7 pavo-2.1.0/pavo/man/explorespec.Rd | 4 pavo-2.1.0/pavo/man/flowers.Rd | 6 pavo-2.1.0/pavo/man/getimg.Rd | 7 pavo-2.1.0/pavo/man/getspec.Rd | 11 pavo-2.1.0/pavo/man/hexagon.Rd | 11 pavo-2.1.0/pavo/man/hexplot.Rd | 23 pavo-2.1.0/pavo/man/img_conversion.Rd | 4 pavo-2.1.0/pavo/man/is.colspace.Rd |only pavo-2.1.0/pavo/man/is.vismodel.Rd |only pavo-2.1.0/pavo/man/jnd2xyz.Rd | 5 pavo-2.1.0/pavo/man/jndplot.Rd | 3 pavo-2.1.0/pavo/man/jndrot.Rd | 3 pavo-2.1.0/pavo/man/legendtetra.Rd | 6 pavo-2.1.0/pavo/man/merge.rspec.Rd | 6 pavo-2.1.0/pavo/man/pavo-package.Rd | 14 pavo-2.1.0/pavo/man/peakshape.Rd | 11 pavo-2.1.0/pavo/man/plot.colspace.Rd | 40 pavo-2.1.0/pavo/man/plot.rimg.Rd | 8 pavo-2.1.0/pavo/man/plot.rspec.Rd | 17 pavo-2.1.0/pavo/man/plotsmooth.Rd | 6 pavo-2.1.0/pavo/man/points.colspace.Rd | 6 pavo-2.1.0/pavo/man/procimg.Rd | 17 pavo-2.1.0/pavo/man/procspec.Rd | 7 pavo-2.1.0/pavo/man/projplot.Rd | 25 pavo-2.1.0/pavo/man/segplot.Rd | 20 pavo-2.1.0/pavo/man/segspace.Rd | 7 pavo-2.1.0/pavo/man/sensdata.Rd | 21 pavo-2.1.0/pavo/man/sensmodel.Rd | 12 pavo-2.1.0/pavo/man/sicalis.Rd | 2 pavo-2.1.0/pavo/man/spec2rgb.Rd | 25 pavo-2.1.0/pavo/man/subset.rspec.Rd | 11 pavo-2.1.0/pavo/man/summary.colspace.Rd | 28 pavo-2.1.0/pavo/man/summary.rimg.Rd | 4 pavo-2.1.0/pavo/man/summary.rspec.Rd | 16 pavo-2.1.0/pavo/man/summary.vismodel.Rd | 4 pavo-2.1.0/pavo/man/tcspace.Rd | 7 pavo-2.1.0/pavo/man/tcsplot.Rd | 46 - pavo-2.1.0/pavo/man/teal.Rd | 2 pavo-2.1.0/pavo/man/tetraplot.Rd | 13 pavo-2.1.0/pavo/man/triplot.Rd | 29 pavo-2.1.0/pavo/man/trispace.Rd | 7 pavo-2.1.0/pavo/man/vismodel.Rd | 38 pavo-2.1.0/pavo/man/vol.Rd | 17 pavo-2.1.0/pavo/man/voloverlap.Rd | 11 pavo-2.1.0/pavo/tests/spelling.R |only pavo-2.1.0/pavo/tests/testthat/known_output |only pavo-2.1.0/pavo/tests/testthat/test-S3rspec.R | 16 pavo-2.1.0/pavo/tests/testthat/test-coldist.R | 57 + pavo-2.1.0/pavo/tests/testthat/test-colspace.R | 105 ++ pavo-2.1.0/pavo/tests/testthat/test-general.R | 15 pavo-2.1.0/pavo/tests/testthat/test-images.R | 49 + pavo-2.1.0/pavo/tests/testthat/test-import.R | 15 pavo-2.1.0/pavo/tests/testthat/test-processing.R | 90 ++ pavo-2.1.0/pavo/tests/testthat/test-vismodel.R | 68 + pavo-2.1.0/pavo/vignettes/analysing.Rmd |only pavo-2.1.0/pavo/vignettes/fig/workflow.png |binary pavo-2.1.0/pavo/vignettes/importing_processing.Rmd |only pavo-2.1.0/pavo/vignettes/main.bib |only pavo-2.1.0/pavo/vignettes/overview.Rmd |only pavo-2.1.0/pavo/vignettes/spectraldesc.Rmd | 6 187 files changed, 2973 insertions(+), 3221 deletions(-)
Title: 'SCS' Plug-in for the 'R' Optimization Infrastructure
Description: Enhances the 'R' Optimization Infrastructure ('ROI') package
with the 'SCS' solver for solving convex cone problems.
Author: Florian Schwendinger [aut, cre]
Maintainer: Florian Schwendinger <FlorianSchwendinger@gmx.at>
Diff between ROI.plugin.scs versions 0.3-0 dated 2017-10-22 and 0.3-1 dated 2019-03-06
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NAMESPACE | 1 - R/plugin.R | 5 +---- 4 files changed, 8 insertions(+), 12 deletions(-)
More information about ROI.plugin.scs at CRAN
Permanent link
Title: Search and Retrieve Scientific Publication Records from PubMed
Description: Query NCBI Entrez and retrieve PubMed records in XML or text format. Process PubMed records by extracting and aggregating data from selected fields. A large number of records can be easily downloaded via this simple-to-use interface to the NCBI PubMed API.
Author: Damiano Fantini
Maintainer: Damiano Fantini <damiano.fantini@gmail.com>
Diff between easyPubMed versions 2.11 dated 2019-01-23 and 2.12 dated 2019-03-06
easyPubMed-2.11/easyPubMed/inst/doc/easyPubMed_01_getting_started.R |only easyPubMed-2.11/easyPubMed/inst/doc/easyPubMed_01_getting_started.Rmd |only easyPubMed-2.11/easyPubMed/inst/doc/easyPubMed_01_getting_started.html |only easyPubMed-2.11/easyPubMed/vignettes/easyPubMed_01_getting_started.Rmd |only easyPubMed-2.12/easyPubMed/DESCRIPTION | 8 - easyPubMed-2.12/easyPubMed/MD5 | 16 +- easyPubMed-2.12/easyPubMed/R/articles_to_list.R | 79 ++++++++-- easyPubMed-2.12/easyPubMed/build/vignette.rds |binary easyPubMed-2.12/easyPubMed/inst/doc/getting_started_with_easyPubMed.R |only easyPubMed-2.12/easyPubMed/inst/doc/getting_started_with_easyPubMed.Rmd |only easyPubMed-2.12/easyPubMed/inst/doc/getting_started_with_easyPubMed.html |only easyPubMed-2.12/easyPubMed/man/articles_to_list.Rd | 5 easyPubMed-2.12/easyPubMed/vignettes/getting_started_with_easyPubMed.Rmd |only 13 files changed, 86 insertions(+), 22 deletions(-)
Title: Lining Up Two Sets of Measurements
Description: Tools for detecting and correcting sample mix-ups between two sets
of measurements, such as between gene expression data on two tissues.
Author: Karl W Broman <broman@wisc.edu>
Maintainer: Karl W Broman <broman@wisc.edu>
Diff between lineup versions 0.37-10 dated 2018-03-23 and 0.37-11 dated 2019-03-06
lineup-0.37-10/lineup/inst/LICENSE.md |only lineup-0.37-11/lineup/ChangeLog | 10 + lineup-0.37-11/lineup/DESCRIPTION | 15 +- lineup-0.37-11/lineup/MD5 | 88 ++++++++-------- lineup-0.37-11/lineup/R/calc.locallod.R | 2 lineup-0.37-11/lineup/R/combinedist.R | 2 lineup-0.37-11/lineup/R/corbetw2mat.R | 2 lineup-0.37-11/lineup/R/distee.R | 4 lineup-0.37-11/lineup/R/disteg.R | 2 lineup-0.37-11/lineup/R/find.gene.pseudomarker.R | 2 lineup-0.37-11/lineup/R/findCommonID.R | 2 lineup-0.37-11/lineup/R/fscale.R | 2 lineup-0.37-11/lineup/R/omitdiag.R | 2 lineup-0.37-11/lineup/R/plot.lineupdist.R | 2 lineup-0.37-11/lineup/R/plot2dist.R | 2 lineup-0.37-11/lineup/R/plotEGclass.R | 2 lineup-0.37-11/lineup/R/pulldiag.R | 2 lineup-0.37-11/lineup/R/subset.lineupdist.R | 2 lineup-0.37-11/lineup/R/summary.lineupdist.R | 2 lineup-0.37-11/lineup/R/util.R | 2 lineup-0.37-11/lineup/README.md | 2 lineup-0.37-11/lineup/build/vignette.rds |binary lineup-0.37-11/lineup/data/expr1.rda |binary lineup-0.37-11/lineup/data/expr2.rda |binary lineup-0.37-11/lineup/data/f2cross.rda |binary lineup-0.37-11/lineup/data/genepos.rda |binary lineup-0.37-11/lineup/data/pmap.rda |binary lineup-0.37-11/lineup/inst/CITATION |only lineup-0.37-11/lineup/inst/doc/lineup.html | 24 ++++ lineup-0.37-11/lineup/man/calc.locallod.Rd | 2 lineup-0.37-11/lineup/man/combinedist.Rd | 2 lineup-0.37-11/lineup/man/corbetw2mat.Rd | 2 lineup-0.37-11/lineup/man/distee.Rd | 6 - lineup-0.37-11/lineup/man/disteg.Rd | 5 lineup-0.37-11/lineup/man/find.gene.pseudomarker.Rd | 2 lineup-0.37-11/lineup/man/findCommonID.Rd | 2 lineup-0.37-11/lineup/man/fscale.Rd | 2 lineup-0.37-11/lineup/man/lineupversion.Rd | 2 lineup-0.37-11/lineup/man/omitdiag.Rd | 2 lineup-0.37-11/lineup/man/plot.lineupdist.Rd | 2 lineup-0.37-11/lineup/man/plot2dist.Rd | 8 - lineup-0.37-11/lineup/man/plotEGclass.Rd | 7 - lineup-0.37-11/lineup/man/pulldiag.Rd | 2 lineup-0.37-11/lineup/man/subset.lineupdist.Rd | 3 lineup-0.37-11/lineup/man/summary.lineupdist.Rd | 2 lineup-0.37-11/lineup/tests/testthat/test-corbetw2mat.R | 2 46 files changed, 129 insertions(+), 97 deletions(-)
Title: Analyzing Gastric Emptying from MRI or Scintigraphy
Description: Fits gastric emptying time series from MRI or scintigraphic measurements
using nonlinear mixed-model population fits with 'nlme' and Bayesian methods with
Stan; computes derived parameters such as t50 and AUC.
Author: Dieter Menne [aut, cre]
Maintainer: Dieter Menne <dieter.menne@menne-biomed.de>
Diff between gastempt versions 0.4.3 dated 2018-11-10 and 0.4.4 dated 2019-03-06
DESCRIPTION | 6 MD5 | 93 +++--- NAMESPACE | 82 ++--- R/fitfuncs.r | 330 ++++++++++----------- R/fitnlme.R | 471 +++++++++++++++--------------- R/fitparams.R | 140 ++++----- R/gastempt-internal.R | 254 ++++++++-------- R/runshiny.R | 22 - R/simulate_gastempt.R | 369 ++++++++++++------------ R/stan_gastempt.R | 344 +++++++++++----------- R/stan_model_names.R | 42 +- R/zzz.R | 8 README.md | 140 ++++----- build/vignette.rds |binary inst/doc/gastempt.Rmd | 34 +- inst/doc/gastempt.html | 488 ++++++++++++++++---------------- inst/shiny/global.R | 102 +++--- inst/shiny/rsconnect |only inst/shiny/server.R | 404 +++++++++++++------------- inst/shiny/ui.R | 238 +++++++-------- inst/shiny/www/gastempt.css | 202 ++++++------- man/coef.nlme_gastempt.Rd | 38 +- man/coef.stan_gastempt.Rd | 38 +- man/gastemptfunc.Rd | 184 ++++++------ man/nlme_gastempt.Rd | 151 ++++----- man/plot.nlme_gastempt.Rd | 38 +- man/plot.stan_gastempt.Rd | 40 +- man/run_shiny.Rd | 28 - man/simulate_gastempt.Rd | 137 ++++---- man/stan_gastempt.Rd | 136 ++++---- man/stan_model_names.Rd | 46 +-- man/t50.Rd | 38 +- src/stan_files/chunks/license.stan | 16 - src/stan_files/linexp_gastro_1b.stan | 98 +++--- src/stan_files/linexp_gastro_1c.stan | 78 ++--- src/stan_files/linexp_gastro_1d.stan | 84 ++--- src/stan_files/linexp_gastro_2b.stan | 196 ++++++------ src/stan_files/linexp_gastro_2c.stan | 192 ++++++------ src/stan_files/powexp_gastro_1b.stan | 98 +++--- src/stan_files/powexp_gastro_2c.stan | 198 ++++++------ tests/test-all.R | 10 tests/testthat/test-fitfuncs.R | 318 ++++++++++---------- tests/testthat/test-fitnlme.R | 215 +++++++------- tests/testthat/test-fitparams.R | 239 +++++++-------- tests/testthat/test-simulate_gastempt.R | 213 +++++++------ tests/testthat/test-stan.R | 346 +++++++++++----------- tools/make_cc.R | 96 +++--- vignettes/gastempt.Rmd | 34 +- 48 files changed, 3542 insertions(+), 3532 deletions(-)
Title: Psychometric Functions from the Waller Lab
Description: Computes fungible coefficients and Monte Carlo data. Underlying theory for these functions is described in the following publications:
Waller, N. (2008). Fungible Weights in Multiple Regression. Psychometrika, 73(4), 691-703, <DOI:10.1007/s11336-008-9066-z>.
Waller, N. & Jones, J. (2009). Locating the Extrema of Fungible Regression Weights.
Psychometrika, 74(4), 589-602, <DOI:10.1007/s11336-008-9087-7>.
Waller, N. G. (2016). Fungible Correlation Matrices:
A Method for Generating Nonsingular, Singular, and Improper Correlation Matrices for
Monte Carlo Research. Multivariate Behavioral Research, 51(4), 554-568, <DOI:10.1080/00273171.2016.1178566>.
Jones, J. A. & Waller, N. G. (2015). The normal-theory and asymptotic distribution-free (ADF)
covariance matrix of standardized regression coefficients: theoretical extensions
and finite sample behavior. Psychometrika, 80, 365-378, <DOI:10.1007/s11336-013-9380-y>.
Waller, N. G. (2018). Direct Schmid-Leiman transformations and rank-deficient loadings matrices. Psychometrika, 83, 858-870. <DOI:10.1007/s11336-017-9599-0>.
Author: Niels Waller [aut, cre],
Jeff Jones [ctb],
Casey Giordano [ctb]
Maintainer: Niels Waller <nwaller@umn.edu>
Diff between fungible versions 1.79 dated 2019-03-01 and 1.80 dated 2019-03-06
fungible-1.79/fungible/R/Standardize.R |only fungible-1.79/fungible/man/Standardize.Rd |only fungible-1.80/fungible/DESCRIPTION | 10 - fungible-1.80/fungible/MD5 | 50 ++++----- fungible-1.80/fungible/NAMESPACE | 3 fungible-1.80/fungible/R/Omega.R | 4 fungible-1.80/fungible/R/SLi.R | 4 fungible-1.80/fungible/R/SchmidLeiman.R | 81 ++++++++++++-- fungible-1.80/fungible/R/faMain.R | 146 ++++++++++++--------------- fungible-1.80/fungible/R/faSort.R | 63 +++++++++-- fungible-1.80/fungible/R/faStandardize.R |only fungible-1.80/fungible/R/fapa.R | 7 - fungible-1.80/fungible/R/orderFactors.R |only fungible-1.80/fungible/R/promaxQ.R | 126 ++++++++++++++++++----- fungible-1.80/fungible/inst/CITATION | 4 fungible-1.80/fungible/inst/doc/fungible.pdf |binary fungible-1.80/fungible/man/BiFAD.Rd | 5 fungible-1.80/fungible/man/Omega.Rd | 4 fungible-1.80/fungible/man/SLi.Rd | 5 fungible-1.80/fungible/man/SchmidLeiman.Rd | 110 ++++++++++++-------- fungible-1.80/fungible/man/faAlign.Rd | 5 fungible-1.80/fungible/man/faMain.Rd | 5 fungible-1.80/fungible/man/faSort.Rd | 14 +- fungible-1.80/fungible/man/faStandardize.Rd |only fungible-1.80/fungible/man/faX.Rd | 5 fungible-1.80/fungible/man/fals.Rd | 5 fungible-1.80/fungible/man/fapa.Rd | 5 fungible-1.80/fungible/man/orderFactors.Rd |only fungible-1.80/fungible/man/promaxQ.Rd | 116 ++++++++++++++++----- 29 files changed, 519 insertions(+), 258 deletions(-)
Title: Archetypoid Algorithms and Anomaly Detection
Description: Collection of several algorithms to obtain archetypoids with small and large databases and with both classical
multivariate data and functional data (univariate and multivariate). Some of these algorithms also allow to detect
anomalies (outliers).
Author: Guillermo Vinue, Irene Epifanio
Maintainer: Guillermo Vinue <Guillermo.Vinue@uv.es>
Diff between adamethods versions 1.1 dated 2018-11-26 and 1.2 dated 2019-03-06
DESCRIPTION | 16 +- MD5 | 136 ++++++++--------- NEWS | 9 + R/adalara.R | 22 +- R/adalara_no_paral.R | 22 +- R/archetypoids_funct_multiv_robust.R | 5 R/archetypoids_funct_multiv_robust_internal.R | 5 R/archetypoids_funct_robust.R | 5 R/archetypoids_funct_robust_internal.R | 5 R/archetypoids_norm_frob.R | 5 R/archetypoids_norm_frob_internal.R | 5 R/archetypoids_robust.R | 5 R/archetypoids_robust_internal.R | 5 R/bisquare_function.R | 5 R/do_ada.R | 3 R/do_ada_robust.R | 6 R/do_alphas_rss.R | 1 R/do_alphas_rss_multiv.R | 1 R/do_fada.R | 2 R/do_fada_multiv.R | 1 R/do_fada_multiv_robust.R | 6 R/do_fada_robust.R | 7 R/do_kNNo.R | 7 R/fadalara.R | 14 + R/fadalara_no_paral.R | 15 + R/frobenius_norm_funct_multiv_robust.R | 5 R/frobenius_norm_funct_robust.R | 5 R/frobenius_norm_robust.R | 5 R/int_prod_mat.R | 5 R/int_prod_mat_funct.R | 5 R/int_prod_mat_sq.R | 5 R/int_prod_mat_sq_funct.R | 5 R/stepArchetypesRawData_funct_multiv_robust.R | 5 R/stepArchetypesRawData_funct_multiv_robust_internal.R | 5 R/stepArchetypesRawData_funct_robust.R | 5 R/stepArchetypesRawData_funct_robust_internal.R | 5 R/stepArchetypesRawData_norm_frob.R | 5 R/stepArchetypesRawData_norm_frob_internal.R | 5 R/stepArchetypesRawData_robust.R | 5 R/stepArchetypesRawData_robust_internal.R | 5 man/adalara.Rd | 12 + man/adalara_no_paral.Rd | 12 + man/archetypoids_funct_multiv_robust.Rd | 5 man/archetypoids_funct_robust.Rd | 5 man/archetypoids_norm_frob.Rd | 5 man/archetypoids_robust.Rd | 5 man/bisquare_function.Rd | 5 man/do_ada.Rd | 3 man/do_ada_robust.Rd | 6 man/do_alphas_rss.Rd | 1 man/do_alphas_rss_multiv.Rd | 1 man/do_fada.Rd | 2 man/do_fada_multiv.Rd | 1 man/do_fada_multiv_robust.Rd | 6 man/do_fada_robust.Rd | 7 man/do_knno.Rd | 7 man/fadalara.Rd | 12 + man/fadalara_no_paral.Rd | 12 + man/frobenius_norm_funct_multiv_robust.Rd | 5 man/frobenius_norm_funct_robust.Rd | 5 man/frobenius_norm_robust.Rd | 5 man/int_prod_mat.Rd | 5 man/int_prod_mat_funct.Rd | 5 man/int_prod_mat_sq.Rd | 5 man/int_prod_mat_sq_funct.Rd | 5 man/stepArchetypesRawData_funct_multiv_robust.Rd | 5 man/stepArchetypesRawData_funct_robust.Rd | 5 man/stepArchetypesRawData_norm_frob.Rd | 5 man/stepArchetypesRawData_robust.Rd | 5 69 files changed, 350 insertions(+), 200 deletions(-)
Title: Splitting Conic Solver
Description: Solves convex cone programs via operator splitting. Can solve:
linear programs (LPs), second-order cone programs (SOCPs), semidefinite programs
(SDPs), exponential cone programs (ECPs), and power cone programs (PCPs), or
problems with any combination of those cones. SCS uses AMD (a set of routines for permuting sparse matrices prior to factorization) and LDL (a sparse LDL' factorization and solve package) from 'SuiteSparse' (<http://www.suitesparse.com>).
Author: Florian Schwendinger [ctb, cre],
Brendan O'Donoghue [aut, cph],
Timothy A. Davis [cph],
Patrick R. Amestory [cph],
Iain S. Duff [cph]
Maintainer: Florian Schwendinger <FlorianSchwendinger@gmx.at>
Diff between scs versions 1.1-1 dated 2016-02-23 and 1.2-3 dated 2019-03-06
scs-1.1-1/scs/demo |only scs-1.1-1/scs/src/scs/include/constants.h |only scs-1.1-1/scs/src/scs/include/linAlg.h |only scs-1.1-1/scs/src/scs/include/linSys.h |only scs-1.1-1/scs/src/scs/src/linAlg.c |only scs-1.2-3/scs/DESCRIPTION | 13 scs-1.2-3/scs/MD5 | 99 scs-1.2-3/scs/NAMESPACE | 5 scs-1.2-3/scs/R/scs.R | 71 scs-1.2-3/scs/R/sparse.R |only scs-1.2-3/scs/README.md | 153 scs-1.2-3/scs/cleanup | 4 scs-1.2-3/scs/inst/CITATION | 19 scs-1.2-3/scs/man/scs.Rd | 26 scs-1.2-3/scs/man/scs_control.Rd |only scs-1.2-3/scs/src/Makevars | 4 scs-1.2-3/scs/src/scs/include/accel.h |only scs-1.2-3/scs/src/scs/include/cones.h | 52 scs-1.2-3/scs/src/scs/include/cs.h | 39 scs-1.2-3/scs/src/scs/include/ctrlc.h | 28 scs-1.2-3/scs/src/scs/include/glbopts.h | 157 scs-1.2-3/scs/src/scs/include/linalg.h |only scs-1.2-3/scs/src/scs/include/linsys.h |only scs-1.2-3/scs/src/scs/include/normalize.h | 111 scs-1.2-3/scs/src/scs/include/scs.h | 182 - scs-1.2-3/scs/src/scs/include/scs_blas.h | 41 scs-1.2-3/scs/src/scs/include/util.h | 63 scs-1.2-3/scs/src/scs/linsys/amatrix.h | 14 scs-1.2-3/scs/src/scs/linsys/common.c | 510 +- scs-1.2-3/scs/src/scs/linsys/common.h | 11 scs-1.2-3/scs/src/scs/linsys/direct/external/SuiteSparse_config.h | 5 scs-1.2-3/scs/src/scs/linsys/direct/external/amd.h | 66 scs-1.2-3/scs/src/scs/linsys/direct/external/amd_1.c | 4 scs-1.2-3/scs/src/scs/linsys/direct/external/amd_2.c | 26 scs-1.2-3/scs/src/scs/linsys/direct/external/amd_aat.c | 24 scs-1.2-3/scs/src/scs/linsys/direct/external/amd_info.c | 40 scs-1.2-3/scs/src/scs/linsys/direct/external/amd_internal.h | 4 scs-1.2-3/scs/src/scs/linsys/direct/external/amd_order.c | 36 scs-1.2-3/scs/src/scs/linsys/direct/external/ldl.c | 2 scs-1.2-3/scs/src/scs/linsys/direct/private.c | 418 +- scs-1.2-3/scs/src/scs/linsys/direct/private.h | 27 scs-1.2-3/scs/src/scs/src/accel.c |only scs-1.2-3/scs/src/scs/src/cones.c | 1409 ++++--- scs-1.2-3/scs/src/scs/src/cs.c | 276 - scs-1.2-3/scs/src/scs/src/ctrlc.c | 67 scs-1.2-3/scs/src/scs/src/linalg.c |only scs-1.2-3/scs/src/scs/src/normalize.c |only scs-1.2-3/scs/src/scs/src/scs.c | 1780 +++++----- scs-1.2-3/scs/src/scs/src/scs_version.c | 7 scs-1.2-3/scs/src/scs/src/util.c | 344 + scs-1.2-3/scs/src/scs/test |only scs-1.2-3/scs/src/scs_init.c |only scs-1.2-3/scs/src/scsr.c | 432 +- scs-1.2-3/scs/tests |only 54 files changed, 3439 insertions(+), 3130 deletions(-)
Title: C++ Classes to Embed R in C++ Applications
Description: C++ classes to embed R in C++ applications
A C++ class providing the R interpreter is offered by this package
making it easier to have "R inside" your C++ application. As R itself
is embedded into your application, a shared library build of R is
required. This works on Linux, OS X and even on Windows provided you
use the same tools used to build R itself. d Numerous examples are
provided in the eight subdirectories of the examples/ directory of
the installed package: standard, 'mpi' (for parallel computing), 'qt'
(showing how to embed 'RInside' inside a Qt GUI application), 'wt'
(showing how to build a "web-application" using the Wt toolkit),
'armadillo' (for 'RInside' use with 'RcppArmadillo') and 'eigen' (for
'RInside' use with 'RcppEigen'). The examples use 'GNUmakefile(s)'
with GNU extensions, so a GNU make is required (and will use the
'GNUmakefile' automatically). 'Doxygen'-generated documentation of
the C++ classes is available at the 'RInside' website as well.
Author: Dirk Eddelbuettel and Romain Francois
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RInside versions 0.2.14 dated 2017-05-04 and 0.2.15 dated 2019-03-06
ChangeLog | 33 +++++++++++++++++++++++++++++++++ DESCRIPTION | 39 ++++++++++++++++++--------------------- MD5 | 14 +++++++------- README.md | 4 ++-- inst/NEWS.Rd | 16 +++++++++++++++- src/Makevars.win | 2 +- src/RInside.cpp | 41 ++++++++++++++++++++++++++--------------- src/setenv/setenv.c | 12 ++++++++++-- 8 files changed, 112 insertions(+), 49 deletions(-)
Title: Design Menu for Radiant: Business Analytics using R and Shiny
Description: The Radiant Design menu includes interfaces for design of
experiments, sampling, and sample size calculation. The application extends
the functionality in radiant.data.
Author: Vincent Nijs [aut, cre]
Maintainer: Vincent Nijs <radiant@rady.ucsd.edu>
Diff between radiant.design versions 0.9.7 dated 2018-10-06 and 0.9.9 dated 2019-03-06
DESCRIPTION | 14 +- MD5 | 53 +++---- NAMESPACE | 73 +++++----- NEWS.md | 7 + R/radiant.R | 15 +- R/sample_size.R | 17 +- R/sample_size_comp.R | 159 +++++++++++++++++------ R/sampling.R | 2 inst/app/tools/analysis/doe_ui.R | 2 inst/app/tools/analysis/sample_size_comp_ui.R | 79 +++++++++-- inst/app/tools/analysis/sample_size_ui.R | 84 +++++++----- inst/app/tools/help/doe.md | 6 inst/app/tools/help/figures/sample_size_ex1a.png |binary inst/app/tools/help/figures/sample_size_ex1b.png |binary inst/app/tools/help/figures/sample_size_ex2a.png |binary inst/app/tools/help/figures/sample_size_ex2b.png |binary inst/app/tools/help/sample_size.Rmd | 4 inst/app/tools/help/sample_size.md | 4 inst/app/tools/help/sample_size_comp.Rmd | 5 inst/app/tools/help/sample_size_comp.md | 5 inst/app/tools/help/sampling.md | 2 man/plot.sample_size_comp.Rd |only man/radiant.design.Rd | 7 - man/radiant.design_viewer.Rd | 7 - man/radiant.design_window.Rd | 7 - man/sample_size.Rd | 2 man/sample_size_comp.Rd | 6 tests/testthat/test_stats.R | 59 ++++++++ 28 files changed, 430 insertions(+), 189 deletions(-)
More information about radiant.design at CRAN
Permanent link
Title: Basics Menu for Radiant: Business Analytics using R and Shiny
Description: The Radiant Basics menu includes interfaces for probability
calculation, central limit theorem simulation, comparing means and proportions,
goodness-of-fit testing, cross-tabs, and correlation. The application extends
the functionality in radiant.data.
Author: Vincent Nijs [aut, cre]
Maintainer: Vincent Nijs <radiant@rady.ucsd.edu>
Diff between radiant.basics versions 0.9.7 dated 2018-10-06 and 0.9.9 dated 2019-03-06
DESCRIPTION | 14 ++-- MD5 | 62 +++++++++--------- NEWS.md | 20 +++++ R/aaa.R | 2 R/compare_means.R | 30 ++++---- R/compare_props.R | 27 ++++--- R/correlation.R | 4 - R/cross_tabs.R | 4 - R/goodness.R | 4 - R/radiant.R | 15 +++- R/single_mean.R | 6 - R/single_prop.R | 46 +++++++++---- inst/app/tools/analysis/compare_props_ui.R | 12 ++- inst/app/tools/analysis/single_prop_ui.R | 8 +- inst/app/tools/help/clt.md | 2 inst/app/tools/help/compare_means.md | 25 ++++++- inst/app/tools/help/compare_props.md | 25 ++++++- inst/app/tools/help/correlation.md | 4 - inst/app/tools/help/cross_tabs.md | 4 - inst/app/tools/help/figures/compare_means_summary.png |binary inst/app/tools/help/figures/compare_props_summary.png |binary inst/app/tools/help/figures/single_prop_summary.png |binary inst/app/tools/help/goodness.md | 4 - inst/app/tools/help/prob_calc.Rmd | 2 inst/app/tools/help/prob_calc.md | 2 inst/app/tools/help/single_mean.md | 4 - inst/app/tools/help/single_prop.md | 4 - man/radiant.basics.Rd | 7 +- man/radiant.basics_viewer.Rd | 7 +- man/radiant.basics_window.Rd | 7 +- man/single_prop.Rd | 5 + tests/testthat/test_stats.R | 4 - 32 files changed, 236 insertions(+), 124 deletions(-)
More information about radiant.basics at CRAN
Permanent link
Title: Co-Expression Differential Network Analysis
Description: Categorize links and nodes from multiple networks in 3 categories: Common links (alpha) specific links (gamma), and different links (beta). Also categorizes the links into sub-categories and groups. The package includes a visualization tool for the networks. More information about the methodology can be found at: Gysi et. al., 2018 <arXiv:1802.00828>.
Author: Deisy Morselli Gysi, Tiago de Miranda Fragoso, Eivind Almaas and Katja Nowick.
Maintainer: Deisy Morselli Gysi <deisy@bioinf.uni-leipzig.de>
Diff between CoDiNA versions 1.1 dated 2018-07-06 and 1.1.1 dated 2019-03-06
DESCRIPTION | 10 MD5 | 50 +-- NAMESPACE | 80 ++--- R/as.igraph.R | 69 ++-- R/makeDiffNet.R | 271 ++++++++--------- R/plot2.R | 676 +++++++++++++++++++++---------------------- R/summary.R | 88 ++--- build/vignette.rds |binary data/AST.RData |binary data/CTR.RData |binary data/GLI.RData |binary data/OLI.RData |binary inst/doc/Running-CoDiNA.R | 102 +++--- inst/doc/Running-CoDiNA.html | 478 +++++++++++++++--------------- man/Categorize.Rd | 40 +- man/ClusterNodes.Rd | 48 +-- man/CreateFullBase.Rd | 46 +- man/MakeDiffNet.Rd | 69 ++-- man/OrderNames.Rd | 52 +-- man/PhiCategory.Rd | 40 +- man/Recode.Rd | 34 +- man/as.igraph.Rd | 71 ++-- man/normalize.Rd | 42 +- man/plot.CoDiNA.Rd | 120 +++---- man/print.CoDiNA.Rd | 60 +-- man/summary.CoDiNA.Rd | 60 +-- 26 files changed, 1269 insertions(+), 1237 deletions(-)
Title: Modelling Heterogeneity in Paired Comparison Data
Description: Performs 'BTLLasso' as described by Schauberger and Tutz (2019): BTLLasso - A Common Framework and Software Package for the Inclusion and Selection of Covariates in Bradley-Terry Models, Journal of Statistical Software, to appear) and Schauberger and Tutz (2017) <doi:10.1177/1471082X17693086>. BTLLasso is a method to include different types of variables in paired comparison models and, therefore, to allow for heterogeneity between subjects. Variables can be subject-specific, object-specific and subject-object-specific and can have an influence on the attractiveness/strength of the objects. Suitable L1 penalty terms are used to cluster certain effects and to reduce the complexity of the models.
Author: Gunther Schauberger
Maintainer: Gunther Schauberger <gunther.schauberger@tum.de>
Diff between BTLLasso versions 0.1-8 dated 2019-02-21 and 0.1-9 dated 2019-03-06
DESCRIPTION | 15 ++++++--------- MD5 | 16 ++++++++-------- NAMESPACE | 2 +- R/boot.BTLLasso.R | 2 +- man/boot.BTLLasso.Rd | 4 ++-- man/ctrl.BTLLasso.Rd | 15 ++++++++------- man/cv.BTLLasso.Rd | 4 ++-- man/paths.Rd | 3 ++- man/plot.boot.BTLLasso.Rd | 6 +++--- 9 files changed, 33 insertions(+), 34 deletions(-)
Title: Interface to 'Python'
Description: Interface to 'Python' modules, classes, and functions. When calling
into 'Python', R data types are automatically converted to their equivalent 'Python'
types. When values are returned from 'Python' to R they are converted back to R
types. Compatible with all versions of 'Python' >= 2.7.
Author: JJ Allaire [aut, cre],
Kevin Ushey [aut],
RStudio [cph, fnd],
Yuan Tang [aut, cph] (<https://orcid.org/0000-0001-5243-233X>),
Dirk Eddelbuettel [ctb, cph],
Bryan Lewis [ctb, cph],
Marcus Geelnard [ctb, cph] (TinyThread library,
http://tinythreadpp.bitsnbites.eu/)
Maintainer: JJ Allaire <jj@rstudio.com>
Diff between reticulate versions 1.11 dated 2019-02-27 and 1.11.1 dated 2019-03-06
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 4 ++++ tests/testthat/test-python-virtual-environments.R | 1 + 4 files changed, 11 insertions(+), 6 deletions(-)
Title: Comparison of Phylogenetic Trees Using Quartet and Bipartition
Measures
Description: Calculates the number of four-taxon subtrees consistent with a pair
of cladograms, calculating the symmetric quartet distance of Bandelt & Dress (1986),
Reconstructing the shape of a tree from observed dissimilarity data,
Advances in Applied Mathematics, 7, 309-343 <doi:10.1016/0196-8858(86)90038-2>,
and using the tqDist algorithm of Sand et al. (2014), tqDist: a library for
computing the quartet and triplet distances between binary or general trees,
Bioinformatics, 30, 2079–2080 <doi:10.1093/bioinformatics/btu157>
for pairs of bifurcating trees.
Author: Martin R. Smith [aut, cre, cph]
(<https://orcid.org/0000-0001-5660-1727>),
Andreas Sand [ant],
Gerth Stølting Brodal [ant],
Rolf Fagerberg [ant],
Thomas Mailund [ant],
Christian N. S. Pedersen [ant],
Jens Johansen [ant],
Morten K. Holt [ant]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between Quartet versions 1.0.1 dated 2019-01-22 and 1.0.2 dated 2019-03-06
DESCRIPTION | 8 +++---- MD5 | 34 ++++++++++++++++---------------- NEWS.md | 7 ++++++ R/ReleaseQuestions.R | 1 R/data.R | 9 ++++++-- README.md | 4 +-- build/partial.rdb |binary data/sq_trees.rda |binary inst/REFERENCES.bib | 9 +++++--- inst/doc/Critical-distances.pdf |binary inst/doc/Tree-distance-metrics.R | 1 inst/doc/Tree-distance-metrics.Rmd | 1 inst/doc/Tree-distance-metrics.pdf |binary man/sq_trees.Rd | 11 +++++++--- tests/testthat/test-PartitionDistance.R | 5 ++-- tests/testthat/test-TernaryPoints.R | 21 ++++++++++--------- tests/testthat/test-ZZZ-Metrics.R | 6 +++-- vignettes/Tree-distance-metrics.Rmd | 1 18 files changed, 72 insertions(+), 46 deletions(-)
Title: A Graphical User Interface for Dexter
Description: Classical Test and Item analysis,
Item Response analysis and data management for educational and psychological tests.
Author: jesse koops [aut, cre],
Eva de Schipper [aut],
Ivailo Partchev [aut, ctb],
Gunter Maris [aut, ctb],
Timo Bechger [aut, ctb],
Gareth Watts [aut, cph] (author of jquery.sparkline),
Hakim El Hattab [aut, cph] (author of zoom.js)
Maintainer: jesse koops <jesse.koops@cito.nl>
Diff between dextergui versions 0.1.5 dated 2018-11-05 and 0.1.6 dated 2019-03-06
DESCRIPTION | 25 ++- MD5 | 31 ++- NEWS.md | 7 R/gui.R | 69 +++++--- R/misc.R | 3 R/serve.R | 115 +++++++++++--- build/vignette.rds |binary inst/doc/dextergui.html | 364 +++++++++++++++++++++++++++++++++++----------- inst/www/dt_extensions.js | 8 - inst/www/shinydexter.css | 30 +++ inst/www/zoom.js |only man/dextergui.Rd | 5 vignettes/img |only 13 files changed, 497 insertions(+), 160 deletions(-)
Title: Presentation Ninja
Description: Create HTML5 slides with R Markdown and the JavaScript library
'remark.js' (<https://remarkjs.com>).
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>),
Benjie Gillam [ctb],
Claus Thorn Ekstrøm [ctb],
Daniel Anderson [ctb],
Dawei Lang [ctb],
Garrick Aden-Buie [ctb],
John Little [ctb],
Joseph Casillas [ctb],
Michael Wayne Kearney [ctb],
Nan-Hung Hsieh [ctb],
Ole Petter Bang [ctb] (CSS in
rmarkdown/templates/xaringan/resources/default.css),
Patrick Schratz [ctb],
Sean Lopp [ctb],
Lucy D'Agostino McGowan [ctb] (<https://orcid.org/0000-0001-7297-9359>),
Emi Tanaka [ctb],
Yongfu Liao [ctb],
Malcolm Barrett [ctb] (<https://orcid.org/0000-0003-0299-5825>),
Alessandro Gasparini [ctb] (<https://orcid.org/0000-0002-8319-7624>),
Yue Jiang [ctb] (<https://orcid.org/0000-0002-9798-5517>)
Maintainer: Yihui Xie <xie@yihui.name>
Diff between xaringan versions 0.8 dated 2018-10-23 and 0.9 dated 2019-03-06
DESCRIPTION | 20 + MD5 | 31 +- NAMESPACE | 1 R/render.R | 123 ++++++++-- R/utils.R | 65 +++++ README.md | 7 build/vignette.rds |binary inst/examples/fc-demo.Rmd |only inst/examples/uol-demo.Rmd |only inst/rmarkdown/templates/xaringan/resources/default.html | 22 + inst/rmarkdown/templates/xaringan/resources/fc-fonts.css |only inst/rmarkdown/templates/xaringan/resources/fc.css |only inst/rmarkdown/templates/xaringan/resources/js/after.js |only inst/rmarkdown/templates/xaringan/resources/js/print-css.js | 21 + inst/rmarkdown/templates/xaringan/resources/js/ws-handler.js |only inst/rmarkdown/templates/xaringan/resources/rutgers.css | 1 inst/rmarkdown/templates/xaringan/resources/uol-fonts.css |only inst/rmarkdown/templates/xaringan/resources/uol.css |only inst/rmarkdown/templates/xaringan/skeleton/skeleton.Rmd | 18 - inst/rmarkdown/templates/xaringan_zh-CN/skeleton/skeleton.Rmd | 17 - man/decktape.Rd |only 21 files changed, 256 insertions(+), 70 deletions(-)
Title: Regression Analysis and Forecasting Using Textual Data from a
Time-Varying Dictionary
Description: Provides functionalities based on the paper "Time Varying Dictionary and the Predictive Power of FED Minutes" (Lima, 2018) <doi:10.2139/ssrn.3312483>. It selects the most predictive terms, that we call time-varying dictionary using supervised machine learning techniques as lasso and elastic net.
Author: Luiz Renato Lima [aut],
Lucas Godeiro [aut, cre]
Maintainer: Lucas Godeiro <lucas.godeiro@hotmail.com>
Diff between TextForecast versions 0.1.0 dated 2019-02-08 and 0.1.1 dated 2019-03-06
DESCRIPTION | 10 MD5 | 26 - NAMESPACE | 2 R/get_collocations.R | 2 R/tv_sentiment_index.R | 5 R/tv_sentiment_index_all_coefs.R |only README.md | 30 + build/vignette.rds |binary inst/doc/textforecast.R | 17 inst/doc/textforecast.Rmd | 58 ++ inst/doc/textforecast.html | 742 +++++++++++++++++++++++------------- man/get_collocations.Rd | 2 man/tv_sentiment_index.Rd | 5 man/tv_sentiment_index_all_coefs.Rd |only vignettes/textforecast.Rmd | 58 ++ 15 files changed, 676 insertions(+), 281 deletions(-)
Title: Simulation and Analysis of Random Fields
Description: Methods for the inference on and the simulation of Gaussian fields are provided, as well as methods for the simulation of extreme value random fields.
Author: Martin Schlather [aut, cre], Alexander Malinowski [aut], Marco Oesting [aut], Daphne Boecker [aut], Kirstin Strokorb [aut], Sebastian Engelke [aut], Johannes Martini [aut], Felix Ballani [aut], Olga Moreva [aut], Jonas Auel[ctr], Peter Menck [ctr], Sebastian Gross [ctr], Ulrike Ober [ctb], Paulo Ribeiro [ctb], Brian D. Ripley [ctb], Richard Singleton [ctb], Ben Pfaff [ctb], R Core Team [ctb]
Maintainer: Martin Schlather <schlather@math.uni-mannheim.de>
Diff between RandomFields versions 3.3.4 dated 2019-02-28 and 3.3.6 dated 2019-03-06
DESCRIPTION | 6 +++--- MD5 | 5 +++-- R/zzz.R | 2 +- configure.ac |only 4 files changed, 7 insertions(+), 6 deletions(-)
Title: Geostatistical Modelling with Likelihood and Bayes
Description: Geostatistical modelling facilities using Raster and SpatialPoints
objects are provided. Non-Gaussian models are fit using INLA, and Gaussian
geostatistical models use Maximum Likelihood Estimation. For details see Brown (2015) <doi:10.18637/jss.v063.i12>.
Author: Patrick Brown <patrick.brown@utoronto.ca>[aut, cre], Robert Hijmans [ctb]
Maintainer: Patrick Brown <patrick.brown@utoronto.ca>
Diff between geostatsp versions 1.7.2 dated 2018-07-13 and 1.7.7 dated 2019-03-06
DESCRIPTION | 16 +++++++-------- MD5 | 50 +++++++++++++++++++++++++------------------------ NAMESPACE | 2 - R/0gm.R | 27 +++++++++++++++++--------- R/RFsimulate.R | 4 +-- R/glgm.R | 33 ++++++++++++++++++++++++++++++-- R/matern.R | 2 + R/param.R | 5 ++++ R/postExp.R |only R/priorLegacy.R | 2 - build/geostatsp.pdf |binary build/vignette.rds |binary data/gambiaUTM.RData |binary data/loaloa.RData |binary data/murder.RData |binary data/rongelapUTM.RData |binary data/swissRain.RData |binary data/swissRainR.RData |binary data/torontoPop.RData |binary data/wheat.RData |binary inst/doc/glgm.Rnw | 2 - inst/doc/glgm.pdf |binary inst/doc/lgcp.pdf |binary man/RFsimulate.Rd | 3 +- man/postExp.Rd |only src/matern.c | 12 +++++------ vignettes/glgm.Rnw | 2 - 27 files changed, 104 insertions(+), 56 deletions(-)
Title: Preference Ranking Organization METHod for Enrichment of
Evaluations
Description: Functions which can be used to support the Multicriteria Decision Analysis (MCDA) process
involving multiple criteria, by PROMETHEE (Preference Ranking Organization METHod for Enrichment of Evaluations).
Author: Giuliano Resce, Menelaos Tasiou, Francesco Vidoli
Maintainer: Francesco Vidoli <fvidoli@gmail.com>
Diff between PROMETHEE versions 1.0 dated 2018-11-03 and 1.1 dated 2019-03-06
DESCRIPTION | 9 +++++---- MD5 | 12 ++++++++---- NAMESPACE | 2 +- NEWS | 4 +++- R/PROMETHEE_OW.R |only data |only man/Austria.Rd |only man/PROMETHEE.Rd | 2 +- man/PROMETHEE_OW.Rd |only 9 files changed, 18 insertions(+), 11 deletions(-)
Title: A Laboratory for Recursive Partytioning
Description: A computational toolbox for recursive partitioning.
The core of the package is ctree(), an implementation of
conditional inference trees which embed tree-structured
regression models into a well defined theory of conditional
inference procedures. This non-parametric class of regression
trees is applicable to all kinds of regression problems, including
nominal, ordinal, numeric, censored as well as multivariate response
variables and arbitrary measurement scales of the covariates.
Based on conditional inference trees, cforest() provides an
implementation of Breiman's random forests. The function mob()
implements an algorithm for recursive partitioning based on
parametric models (e.g. linear models, GLMs or survival
regression) employing parameter instability tests for split
selection. Extensible functionality for visualizing tree-structured
regression models is available. The methods are described in
Hothorn et al. (2006) <doi:10.1198/106186006X133933>,
Zeileis et al. (2008) <doi:10.1198/106186008X319331> and
Strobl et al. (2007) <doi:10.1186/1471-2105-8-25>.
Author: Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>),
Kurt Hornik [aut],
Carolin Strobl [aut],
Achim Zeileis [aut] (<https://orcid.org/0000-0003-0918-3766>)
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between party versions 1.3-2 dated 2019-03-01 and 1.3-3 dated 2019-03-06
DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++-------------- R/zInitMethods.R | 6 +----- inst/NEWS | 5 +++++ inst/doc/MOB.pdf |binary inst/doc/party.pdf |binary src/Convenience.c | 7 ++++--- src/IndependenceTest.c | 11 +++++++---- src/LinearStatistic.c | 8 ++++---- src/Memory.c | 10 +++++----- src/RandomForest.c | 6 +++--- src/Splits.c | 8 +++++--- src/SurrogateSplits.c | 7 ++++--- src/Utils.c | 22 ++++++++++++++++------ src/Utils.h | 1 + 15 files changed, 73 insertions(+), 54 deletions(-)
Title: Classes for Relational Data
Description: Tools to create and modify network objects. The network class can represent a range of relational data types, and supports arbitrary vertex/edge/graph attributes.
Author: Carter T. Butts [aut, cre],
David Hunter [ctb],
Mark Handcock [ctb],
Skye Bender-deMoll [ctb],
Jeffrey Horner [ctb],
Li Wang [ctb]
Maintainer: Carter T. Butts <buttsc@uci.edu>
Diff between network versions 1.13.0.1 dated 2018-04-02 and 1.14-377 dated 2019-03-06
ChangeLog | 11 +++++ DESCRIPTION | 17 +++++---- MD5 | 72 +++++++++++++++++++------------------- NAMESPACE | 19 ++++++++-- R/access.R | 38 ++++++-------------- R/as.edgelist.R | 50 ++++++++++++++++++-------- R/coercion.R | 62 +++++++++++++++++++++++++++++++-- R/misc.R | 8 ++-- R/operators.R | 16 +++++++- R/plot.R | 3 + R/printsum.R | 25 +++++++++---- README.md |only build/vignette.rds |binary data/emon.RData |binary data/flo.RData |binary inst/CITATION | 72 ++++++++++++++------------------------ inst/doc/networkVignette.pdf |binary inst/include/netregistration.h | 48 ++++++++++++------------- inst/network.api/networkapi.c | 50 +++++++++++++------------- inst/network.api/networkapi.h | 6 +-- man/as.edgelist.Rd | 24 +++++++----- man/as.matrix.network.Rd | 76 ++++++++++++++++++++++++++++++----------- man/get.edges.Rd | 2 - man/network-internal.Rd | 8 +++- man/network-package.Rd | 4 +- man/network.dyadcount.Rd | 3 + man/network.edgecount.Rd | 3 + man/network.extraction.Rd | 7 ++- man/network.naedgecount.Rd | 3 + man/network.size.Rd | 3 + src/Rinit.c | 32 ++++++++++++++++- src/access.c | 14 ++++--- src/access.h | 4 +- src/constructors.c | 6 +-- src/utils.c | 4 +- tests/as.edgelist_tests.R | 12 +++++- tests/general.tests2.R | 9 +++- tests/speedTests.R |only 38 files changed, 451 insertions(+), 260 deletions(-)
Title: Multivariate Ordinal Regression Models
Description: A flexible framework for fitting multivariate
ordinal regression models with composite likelihood methods.
Author: Rainer Hirk [aut, cre],
Kurt Hornik [aut],
Laura Vana [aut],
Alan Genz [ctb] (Fortran Code)
Maintainer: Rainer Hirk <rhirk@wu.ac.at>
Diff between mvord versions 0.3.4 dated 2019-02-20 and 0.3.5 dated 2019-03-06
DESCRIPTION | 8 MD5 | 12 NEWS | 3 inst/doc/vignette_mvord.pdf |binary inst/doc/vignette_mvord2.html | 4 tests/check_mvord_errors.R | 755 +++++++++++++++++++++--------------------- tests/check_toy_example.R | 3 7 files changed, 396 insertions(+), 389 deletions(-)
Title: Residual Diagnostics for Hierarchical (Multi-Level / Mixed)
Regression Models
Description: The 'DHARMa' package uses a simulation-based approach to create
readily interpretable scaled (quantile) residuals for fitted (generalized) linear mixed
models. Currently supported are linear and generalized linear (mixed) models from 'lme4'
(classes 'lmerMod', 'glmerMod'), 'glmmTMB' and 'spaMM', generalized additive models ('gam' from
'mgcv'), 'glm' (including 'negbin' from 'MASS', but excluding quasi-distributions) and 'lm' model
classes. Moreover, externally created simulations, e.g. posterior predictive simulations
from Bayesian software such as 'JAGS', 'STAN', or 'BUGS' can be processed as well.
The resulting residuals are standardized to values between 0 and 1 and can be interpreted
as intuitively as residuals from a linear regression. The package also provides a number of
plot and test functions for typical model misspecification problems, such as
over/underdispersion, zero-inflation, and residual spatial and temporal autocorrelation.
Author: Florian Hartig [aut, cre] (Theoretical Ecology, University of
Regensburg, Regensburg, Germany)
Maintainer: Florian Hartig <florian.hartig@biologie.uni-regensburg.de>
Diff between DHARMa versions 0.2.3 dated 2019-02-12 and 0.2.4 dated 2019-03-06
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NEWS | 9 +++++++++ R/tests.R | 8 +++++--- inst/doc/DHARMa.Rmd | 5 ++--- inst/doc/DHARMa.html | 25 ++++++++++++++++++++++--- man/testDispersion.Rd | 8 +++++--- tests/testthat/Rplots.pdf |binary tests/testthat/testCreateDharma.R | 10 ++++++++-- vignettes/DHARMa.Rmd | 5 ++--- 10 files changed, 66 insertions(+), 30 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-02-20 0.2-0
2017-04-07 0.1-0
Title: Time Value of Money Functions
Description: Functions for managing cashflows and interest rate curves.
Author: Juan Manuel Truppia
Maintainer: Juan Manuel Truppia <jmtruppia@gmail.com>
Diff between tvm versions 0.3.0 dated 2015-08-21 and 0.4.0 dated 2019-03-06
DESCRIPTION | 9 LICENSE | 2 MD5 | 67 +- NAMESPACE | 55 +- NEWS.md | 20 R/CfFuncs.R | 482 ++++++++++---------- R/CurveFuncs.R | 406 +++++++++-------- R/tvm-package.R | 16 README.md | 92 +-- build/vignette.rds |binary inst/doc/intro.R | 38 - inst/doc/intro.Rmd | 150 +++--- inst/doc/intro.html | 946 +++++++++++++++++++++++----------------- man/adjust_disc.Rd | 39 - man/cashflow.Rd | 37 - man/cft.Rd | 61 +- man/disc_cf.Rd | 39 - man/disc_value.Rd |only man/find_rate.Rd | 55 +- man/irr.Rd | 49 +- man/loan.Rd | 55 +- man/npv.Rd | 49 +- man/plot.rate_curve.Rd | 53 +- man/pmt.Rd | 49 +- man/rate.Rd | 57 +- man/rate_curve.Rd | 89 +-- man/rem.Rd | 43 - man/sub-.rate_curve.Rd | 55 +- man/tvm.Rd | 21 man/xirr.Rd | 51 +- man/xnpv.Rd | 47 + tests/test-all.R | 2 tests/testthat/test_cashflows.R | 32 - tests/testthat/test_curves.R | 90 +-- vignettes/intro.Rmd | 150 +++--- 35 files changed, 1829 insertions(+), 1577 deletions(-)