Title: Sequential Quadratic Programming for Fast Maximum-Likelihood
Estimation of Mixture Proportions
Description: Provides optimization algorithms based on sequential
quadratic programming (SQP) for maximum likelihood estimation of the
mixture proportions in a finite mixture model where the component
densities are known. The algorithms are expected to obtain solutions
that are at least as accurate as the state-of-the-art MOSEK
interior-point solver (called by function "KWDual" in the 'REBayes'
package), and they are expected to arrive at solutions more quickly
in large data sets. The algorithms are described in Y. Kim,
P. Carbonetto, M. Stephens & M. Anitescu (2018) <arXiv:1806.01412>.
Author: Youngseok Kim [aut],
Peter Carbonetto [aut, cre],
Mihai Anitescu [aut],
Matthew Stephens [aut],
Jason Willwerscheid [ctb],
Jean Morrison [ctb]
Maintainer: Peter Carbonetto <peter.carbonetto@gmail.com>
Diff between mixsqp versions 0.1-97 dated 2019-02-18 and 0.2-2 dated 2019-10-16
mixsqp-0.1-97/mixsqp/man/mixSQP.Rd |only mixsqp-0.2-2/mixsqp/DESCRIPTION | 11 mixsqp-0.2-2/mixsqp/MD5 | 32 mixsqp-0.2-2/mixsqp/R/RcppExports.R | 4 mixsqp-0.2-2/mixsqp/R/datasim.R | 25 mixsqp-0.2-2/mixsqp/R/misc.R | 24 mixsqp-0.2-2/mixsqp/R/mixsqp.R | 243 ++++-- mixsqp-0.2-2/mixsqp/R/rebayes.R | 2 mixsqp-0.2-2/mixsqp/README.md | 18 mixsqp-0.2-2/mixsqp/build/vignette.rds |binary mixsqp-0.2-2/mixsqp/inst/doc/mixsqp-intro.R | 18 mixsqp-0.2-2/mixsqp/inst/doc/mixsqp-intro.html | 632 ++++++---------- mixsqp-0.2-2/mixsqp/man/mixsqp.Rd |only mixsqp-0.2-2/mixsqp/man/simulatemixdata.Rd | 9 mixsqp-0.2-2/mixsqp/src/RcppExports.cpp | 8 mixsqp-0.2-2/mixsqp/src/mixsqp.cpp | 353 ++++---- mixsqp-0.2-2/mixsqp/tests/testthat/ashr.example.RData |only mixsqp-0.2-2/mixsqp/tests/testthat/smashr.example.RData |only mixsqp-0.2-2/mixsqp/tests/testthat/test_mixsqp.R | 130 ++- 19 files changed, 772 insertions(+), 737 deletions(-)
Title: Find, Map, and Gather Environmental Data and Metadata
Description: A tool for locating, mapping, and gathering environmental data and metadata, worldwide. Users can search for and filter metadata from > 157,000 environmental monitoring stations among 219 countries/territories and >20 networks/organizations via elevation, location, active dates, elements measured (e.g., temperature, precipitation), country, network, and/or known identifier. Future updates to the package will allow the user to obtain datasets from stations within the database.
Author: Josh Roberti [aut, cre],
Cody Flagg [aut],
Lee Stanish [aut],
Robert Lee [aut]
Maintainer: Josh Roberti <jaroberti87@gmail.com>
Diff between metScanR versions 1.2.2 dated 2019-02-02 and 1.2.3 dated 2019-10-16
DESCRIPTION | 8 ++-- MD5 | 66 +++++++++++++++++---------------- NAMESPACE | 1 NEWS.md | 4 ++ R/data.R | 98 ++++++++++++++++++++++++++++++++++++++++++++++---- R/getCountry.R | 33 +++++++++++++++- R/getDates.R | 33 +++++++++++++++- R/getElevation.R | 33 +++++++++++++++- R/getID.R | 33 +++++++++++++++- R/getNearby.R | 36 +++++++++++++++++- R/getNetwork.R | 33 +++++++++++++++- R/getStation.R | 33 +++++++++++++++- R/getTerritory.R | 33 +++++++++++++++- R/getVars.R | 33 +++++++++++++++- R/mapResults.R |only R/mapSiteFinder.R | 21 ++++++++-- R/siteFinder.R | 52 +++++++++++++++++++++----- R/updateDatabase.R | 34 +++++++++++++++-- data/dbLog.rda |binary man/dbLog.Rd | 8 ---- man/getCountry.Rd | 38 ------------------- man/getDates.Rd | 40 -------------------- man/getElevation.Rd | 38 ------------------- man/getId.Rd | 48 ------------------------ man/getNearby.Rd | 39 ------------------- man/getNetwork.Rd | 53 --------------------------- man/getStation.Rd | 36 ------------------ man/getTerritory.Rd | 53 --------------------------- man/getVars.Rd | 36 ------------------ man/mapResults.Rd |only man/mapSiteFinder.Rd | 12 ------ man/metScanR_DB.Rd | 7 --- man/metScanR_terms.Rd | 8 ---- man/siteFinder.Rd | 12 ------ man/updateDatabase.Rd | 36 ------------------ 35 files changed, 516 insertions(+), 532 deletions(-)
Title: Distributed-Lag Linear Structural Equation Models
Description: Inference functionalities for distributed-lag linear structural equation models (DLSEMs). DLSEMs are Markovian structural causal models where each factor of the joint probability distribution is a distributed-lag linear regression (Magrini, 2018 <doi:10.2478/bile-2018-0012>; Magrini et al., 2019 <doi:10.1007/s11135-019-00855-z>). DLSEMs account for temporal delays in the dependence relationships among the variables and allow to perform dynamic causal inference by assessing causal effects at different time lags. Endpoint-constrained quadratic, quadratic decreasing and gamma lag shapes are available.
Author: Alessandro Magrini
Maintainer: Alessandro Magrini <alessandro.magrini@unifi.it>
Diff between dlsem versions 2.4.3 dated 2019-08-20 and 2.4.4 dated 2019-10-16
Changelog | 6 + DESCRIPTION | 8 - MD5 | 23 ++- NAMESPACE | 9 - R/dlsem.r | 254 +++++++++++++++++++++---------------------- build/vignette.rds |binary inst/doc/dlsem_vignette.R | 4 inst/doc/dlsem_vignette.Rnw | 23 +-- inst/doc/dlsem_vignette.pdf |binary man/compareModels.Rd |only man/dlsem-package.Rd | 4 man/dlsem.Rd | 16 +- vignettes/dlsem_vignette.Rnw | 23 +-- 13 files changed, 184 insertions(+), 186 deletions(-)
Title: Chaotic Time Series Analysis
Description: Provides several algorithms for the purpose of detecting chaotic signals inside univariate time series. We focus on methods derived from chaos theory which estimate the complexity of a dataset through exploring the structure of the attractor. We have taken into account the Lyapunov exponents as an ergodic measure. We have implemented the Jacobian method by a fit through neural networks in order to estimate both the largest and the spectrum of Lyapunov exponents. We have considered the full sample and three different methods of subsampling by blocks (non-overlapping, equally spaced and bootstrap) to estimate them. In addition, it is possible to make inference about them and know if the estimated Lyapunov exponents values are or not statistically significant. This library can be used with time series whose time-lapse is fixed or variable. That is, it considers time series whose observations are sampled at fixed or variable time intervals. For a review see David Ruelle and Floris Takens (1971) <doi:10.1007/BF01646553>, Ramazan Gencay and W. Davis Dechert (1992) <doi:10.1016/0167-2789(92)90210-E>, Jean-Pierre Eckmann and David Ruelle (1995) <doi:10.1103/RevModPhys.57.617>, Mototsugu Shintani and Oliver Linton (2004) <doi:10.1016/S0304-4076(03)00205-7>, Jeremy P. Huke and David S. Broomhead (2007) <doi:10.1088/0951-7715/20/9/011>.
Author: Julio E. Sandubete [aut, cre],
Lorenzo Escot [aut]
Maintainer: Julio E. Sandubete <jsandube@ucm.es>
Diff between DChaos versions 0.1-2 dated 2019-05-29 and 0.1-3 dated 2019-10-16
DESCRIPTION | 11 ++++++----- MD5 | 12 +++++++----- NAMESPACE | 5 +++++ R/embedding.R | 30 ++++++++++++++++++------------ R/infmutua.R |only R/jacobi.R | 35 ++++++++++++++++------------------- R/lyapunov.max.R | 33 +++++++++++++-------------------- man/infmutua.Rd |only 8 files changed, 65 insertions(+), 61 deletions(-)
Title: Retrieve and Analyze Clinical Trials in Public Registers
Description: Provides functions for querying, retrieving and analysing
protocol- and results-related information on clinical trials from
two public registers, the European Union Clinical Trials Register
(EUCTR, <https://www.clinicaltrialsregister.eu/>) and
ClinicalTrials.gov (CTGOV, <https://clinicaltrials.gov/>). The
information is transformed and then stored in a database (mongo).
Functions are provided for accessing and analysing the locally
stored information on the clinical trials, as well as for
identifying duplicate records. The package is motivated by the need
for aggregating and trend-analysing the design, conduct and outcomes
across clinical trials.
Author: Ralf Herold [aut, cre] (<https://orcid.org/0000-0002-8148-6748>)
Maintainer: Ralf Herold <ralf.herold@mailbox.org>
Diff between ctrdata versions 0.18.2 dated 2019-05-01 and 1.0 dated 2019-10-16
ctrdata-0.18.2/ctrdata/exec/variety.js |only ctrdata-0.18.2/ctrdata/inst/doc/ctrdata_get_started.R |only ctrdata-0.18.2/ctrdata/inst/doc/ctrdata_get_started.Rmd |only ctrdata-0.18.2/ctrdata/inst/doc/ctrdata_get_started.html |only ctrdata-0.18.2/ctrdata/inst/doc/ctrdata_usage_examples.R |only ctrdata-0.18.2/ctrdata/inst/doc/ctrdata_usage_examples.Rmd |only ctrdata-0.18.2/ctrdata/inst/doc/ctrdata_usage_examples.html |only ctrdata-0.18.2/ctrdata/inst/image/README-ctrdata_json.jpg |only ctrdata-0.18.2/ctrdata/inst/image/README-ctrdata_results_json_euctr.png |only ctrdata-0.18.2/ctrdata/man/ctrMongo.Rd |only ctrdata-0.18.2/ctrdata/tests/testthat |only ctrdata-0.18.2/ctrdata/tests/testthat.R |only ctrdata-0.18.2/ctrdata/vignettes/pvaluetotalparticipants.png |only ctrdata-1.0/ctrdata/DESCRIPTION | 39 ctrdata-1.0/ctrdata/MD5 | 121 ctrdata-1.0/ctrdata/NAMESPACE | 12 ctrdata-1.0/ctrdata/NEWS.md | 13 ctrdata-1.0/ctrdata/R/ctrdata.R | 5 ctrdata-1.0/ctrdata/R/main.R | 1704 ++++++---- ctrdata-1.0/ctrdata/R/onload.R | 68 ctrdata-1.0/ctrdata/R/utils.R | 1662 ++++++--- ctrdata-1.0/ctrdata/README.md | 417 +- ctrdata-1.0/ctrdata/build/vignette.rds |binary ctrdata-1.0/ctrdata/exec/euctr2json.sh | 95 ctrdata-1.0/ctrdata/exec/xml2json.php | 2 ctrdata-1.0/ctrdata/exec/xml2json_euctrresults.php | 2 ctrdata-1.0/ctrdata/inst/doc/ctrdata_get_started.pdf |only ctrdata-1.0/ctrdata/inst/doc/ctrdata_get_started.pdf.asis |only ctrdata-1.0/ctrdata/inst/doc/ctrdata_usage_examples.pdf |only ctrdata-1.0/ctrdata/inst/doc/ctrdata_usage_examples.pdf.asis |only ctrdata-1.0/ctrdata/inst/image/README-ctrdata_json_mongodb.jpg |only ctrdata-1.0/ctrdata/inst/image/README-ctrdata_json_sqlite.jpg |only ctrdata-1.0/ctrdata/inst/image/README-ctrdata_results_json_euctr.jpg |only ctrdata-1.0/ctrdata/inst/image/README-ctrdata_results_neuroblastoma.png |only ctrdata-1.0/ctrdata/inst/image/README-ctrdata_sequence_diagram.jpeg |binary ctrdata-1.0/ctrdata/inst/tinytest |only ctrdata-1.0/ctrdata/man/addMetaData.Rd | 16 ctrdata-1.0/ctrdata/man/checkDoc.Rd |only ctrdata-1.0/ctrdata/man/ctrDb.Rd |only ctrdata-1.0/ctrdata/man/ctrFindActiveSubstanceSynonyms.Rd | 2 ctrdata-1.0/ctrdata/man/ctrGetQueryUrlFromBrowser.Rd | 12 ctrdata-1.0/ctrdata/man/ctrLoadQueryIntoDb.Rd | 149 ctrdata-1.0/ctrdata/man/ctrLoadQueryIntoDbCtgov.Rd | 88 ctrdata-1.0/ctrdata/man/ctrLoadQueryIntoDbEuctr.Rd | 88 ctrdata-1.0/ctrdata/man/ctrOpenSearchPagesInBrowser.Rd | 12 ctrdata-1.0/ctrdata/man/ctrRerunQuery.Rd | 41 ctrdata-1.0/ctrdata/man/ctrdata.Rd | 5 ctrdata-1.0/ctrdata/man/dbCTRAnnotateQueryRecords.Rd | 31 ctrdata-1.0/ctrdata/man/dbCTRLoadJSONFiles.Rd | 12 ctrdata-1.0/ctrdata/man/dbCTRUpdateQueryHistory.Rd | 33 ctrdata-1.0/ctrdata/man/dbFindFields.Rd | 57 ctrdata-1.0/ctrdata/man/dbFindIdsUniqueTrials.Rd | 32 ctrdata-1.0/ctrdata/man/dbGetFieldsIntoDf.Rd | 38 ctrdata-1.0/ctrdata/man/dbQueryHistory.Rd | 33 ctrdata-1.0/ctrdata/man/dfFindUniqueEuctrRecord.Rd | 13 ctrdata-1.0/ctrdata/man/dfListExtractKey.Rd |only ctrdata-1.0/ctrdata/man/dfMergeTwoVariablesRelevel.Rd | 25 ctrdata-1.0/ctrdata/man/installCygwinWindowsDoInstall.Rd | 4 ctrdata-1.0/ctrdata/man/installCygwinWindowsTest.Rd | 7 ctrdata-1.0/ctrdata/man/installFindBinary.Rd | 15 ctrdata-1.0/ctrdata/tests/tinytest.R |only ctrdata-1.0/ctrdata/vignettes/Rplot02.png |binary ctrdata-1.0/ctrdata/vignettes/Rplot03.png |binary ctrdata-1.0/ctrdata/vignettes/ctrdata_get_started.Rmd | 205 - ctrdata-1.0/ctrdata/vignettes/ctrdata_get_started.pdf.asis |only ctrdata-1.0/ctrdata/vignettes/ctrdata_usage_examples.Rmd | 940 +++-- ctrdata-1.0/ctrdata/vignettes/ctrdata_usage_examples.pdf.asis |only ctrdata-1.0/ctrdata/vignettes/ctrdatapvaluesphase23.png |binary ctrdata-1.0/ctrdata/vignettes/ph1paedoncopen.png |binary ctrdata-1.0/ctrdata/vignettes/phase1_paed_oncol.png |binary 70 files changed, 3674 insertions(+), 2324 deletions(-)
Title: Test Coverage for Packages
Description: Track and report code coverage for your package and (optionally)
upload the results to a coverage service like 'Codecov' <http://codecov.io> or
'Coveralls' <http://coveralls.io>. Code coverage is a measure of the amount of
code being exercised by a set of tests. It is an indirect measure of test
quality and completeness. This package is compatible with any testing
methodology or framework and tracks coverage of both R code and compiled
C/C++/FORTRAN code.
Author: Jim Hester [aut, cre],
Willem Ligtenberg [ctb],
Kirill Müller [ctb],
Henrik Bengtsson [ctb],
Steve Peak [ctb],
Kirill Sevastyanenko [ctb],
Jon Clayden [ctb],
Robert Flight [ctb],
Eric Brown [ctb],
Brodie Gaslam [ctb],
Will Beasley [ctb],
Robert Krzyzanowski [ctb],
Markus Wamser [ctb],
Karl Forner [ctb],
Gergely Daróczi [ctb],
Jouni Helske [ctb],
Kun Ren [ctb],
Jeroen Ooms [ctb],
Ken Williams [ctb],
Chris Campbell [ctb],
David Hugh-Jones [ctb],
Qin Wang [ctb],
Ivan Sagalaev [ctb, cph] (highlight.js library),
Mark Otto [ctb] (Bootstrap library),
Jacob Thornton [ctb] (Bootstrap library),
Bootstrap contributors [ctb] (Bootstrap library),
Twitter, Inc [cph] (Bootstrap library)
Maintainer: Jim Hester <james.f.hester@gmail.com>
Diff between covr versions 3.3.1 dated 2019-08-23 and 3.3.2 dated 2019-10-16
DESCRIPTION | 8 MD5 | 20 NAMESPACE | 86 ++-- NEWS.md | 4 R/covr.R | 2 README.md | 3 build/vignette.rds |binary inst/doc/how_it_works.R | 70 +-- inst/doc/how_it_works.html | 938 ++++++++++++++++++++++---------------------- tests/testthat.R | 6 tests/testthat/test-utils.R | 9 11 files changed, 576 insertions(+), 570 deletions(-)
Title: Quantitative Support of Decision Making under Uncertainty
Description: Supporting the quantitative analysis of binary welfare based
decision making processes using Monte Carlo simulations. Decision support
is given on two levels: (i) The actual decision level is to choose between
two alternatives under probabilistic uncertainty. This package calculates
the optimal decision based on maximizing expected welfare. (ii) The meta
decision level is to allocate resources to reduce the uncertainty in the
underlying decision problem, i.e to increase the current information to
improve the actual decision making process. This problem is dealt with
using the Value of Information Analysis. The Expected Value of
Information for arbitrary prospective estimates can be calculated as
well as Individual Expected Value of Perfect Information.
The probabilistic calculations are done via Monte Carlo
simulations. This Monte Carlo functionality can be used on its own.
Author: Eike Luedeling [cre, aut] (University of Bonn),
Lutz Goehring [aut] (ICRAF and Lutz Goehring Consulting),
Katja Schiffers [aut] (University of Bonn)
Maintainer: Eike Luedeling <eike@eikeluedeling.com>
Diff between decisionSupport versions 1.103.8 dated 2018-10-15 and 1.105.2 dated 2019-10-16
DESCRIPTION | 24 - MD5 | 70 +-- NAMESPACE | 13 R/chance_event.R | 2 R/decisionSupport-package.R | 9 R/discount.R | 2 R/empirical_EVPI.R |only R/estimate.R | 14 R/estimate_read_csv_old.R | 2 R/gompertz_yield.R | 2 R/make_CPT.R | 2 R/multi_EVPI.R |only R/plsr.mcSimulation.R | 4 R/random_state.R | 2 R/rdistq_fit.R | 2 R/rmvnorm90ci_exact.R | 2 R/sample_CPT.R | 2 R/sample_simple_CPT.R | 2 R/temp_situations.R | 2 R/vv.R | 2 build/vignette.rds |binary inst/doc/wildfire_example.html | 872 ++++++++++++++++++++++++++--------------- man/chance_event.Rd | 3 man/decisionSupport-package.Rd | 9 man/discount.Rd | 5 man/empirical_EVPI.Rd |only man/estimate_read_csv.Rd | 6 man/estimate_write_csv.Rd | 6 man/gompertz_yield.Rd | 5 man/make_CPT.Rd | 6 man/multi_EVPI.Rd |only man/plsr.mcSimulation.Rd | 4 man/random_state.Rd | 8 man/rmvnorm90ci_exact.Rd | 2 man/sample_CPT.Rd | 4 man/sample_simple_CPT.Rd | 4 man/temp_situations.Rd | 5 man/vv.Rd | 5 38 files changed, 683 insertions(+), 419 deletions(-)
More information about decisionSupport at CRAN
Permanent link
Title: Contextualization and Evaluation of COI-5P Barcode Data
Description: Designed for the cleaning, contextualization and assessment of cytochrome c oxidase I DNA barcode data (COI-5P, or the five prime portion of COI).
It contains functions for placing COI-5P barcode sequences into a common reading frame, translating DNA sequences to amino acids and for assessing
the likelihood that a given barcode sequence includes an insertion or deletion error. The error assessment relies on the comparison of input sequences
against nucleotide and amino acid profile hidden Markov models (for details see Durbin et al. 1998, ISBN: 9780521629713) trained on a taxonomically
diverse set of reference sequences. The functions are provided as a complete pipeline and are also available individually for efficient and targeted
analysis of barcode data.
Author: Cameron M. Nugent
Maintainer: Cameron M. Nugent <nugentc@uoguelph.ca>
Diff between coil versions 1.0.0 dated 2019-10-09 and 1.0.1 dated 2019-10-16
DESCRIPTION | 9 ++--- MD5 | 46 +++++++++++++------------- R/coi5p.r | 77 +++++++++++++++++++++++++++++++++----------- R/coil.r |only R/datasets.r | 8 +++- R/pipeline.r | 18 +++++----- R/print.r | 4 +- R/translation.r | 21 +++++------- README.md | 8 ++++ inst/doc/coil-vignette.R | 2 - inst/doc/coil-vignette.Rmd | 2 - inst/doc/coil-vignette.html | 3 - man/censored_translation.Rd | 17 ++++----- man/coi5p.Rd | 13 ++++--- man/coi5p_pipe.Rd | 12 +++--- man/coil.Rd |only man/example_barcode_data.Rd | 6 +++ man/example_nt_string.Rd | 2 - man/flatten_coi5p.Rd | 6 +-- man/frame.Rd | 14 ++++++-- man/indel_check.Rd | 41 +++++++++++++++++++---- man/print.coi5p.Rd | 4 +- man/translate.Rd | 13 +++++-- man/which_trans_table.Rd | 4 +- vignettes/coil-vignette.Rmd | 2 - 25 files changed, 211 insertions(+), 121 deletions(-)
Title: Simulation of Study Data
Description: Simulates data sets in order to explore modeling techniques or
better understand data generating processes. The user specifies a set of
relationships between covariates, and generates data based on these
specifications. The final data sets can represent data from randomized
control trials, repeated measure (longitudinal) designs, and cluster
randomized trials. Missingness can be generated using various
mechanisms (MCAR, MAR, NMAR).
Author: Keith Goldfeld [aut, cre]
Maintainer: Keith Goldfeld <Keith.Goldfeld@nyumc.org>
Diff between simstudy versions 0.1.14 dated 2019-08-09 and 0.1.15 dated 2019-10-16
DESCRIPTION | 10 +++++----- MD5 | 30 +++++++++++++++++------------- NAMESPACE | 1 + NEWS.md | 5 +++++ R/RcppExports.R | 4 ++++ R/addMarkov.R | 21 +++++++++++++++++---- R/genCorOrdCat.R | 4 ++-- R/genMarkov.R | 10 ++++++++-- R/int_binEPmethod.R | 17 ++++++++++++----- R/trimData.R |only inst/doc/simstudy.html | 4 ++-- man/addMarkov.Rd | 7 +++++-- man/genMarkov.Rd | 9 ++++++++- man/trimData.Rd |only src/RcppExports.cpp | 14 ++++++++++++++ src/srcRcpp.cpp | 28 ++++++++++++++++++++++++++++ tests |only 17 files changed, 128 insertions(+), 36 deletions(-)
Title: NHDPlus Tools
Description: Tools for traversing and working with National Hydrography Dataset Plus (NHDPlus) data. All methods implemented in 'nhdplusTools' are available in the NHDPlus documentation available from the US Environmental Protection Agency <https://www.epa.gov/waterdata/basic-information>.
Author: David Blodgett [aut, cre],
Michael Johnson [ctb]
Maintainer: David Blodgett <dblodgett@usgs.gov>
Diff between nhdplusTools versions 0.3.8 dated 2019-08-27 and 0.3.9 dated 2019-10-16
DESCRIPTION | 20 MD5 | 30 - NAMESPACE | 5 NEWS.md | 5 R/calc_network.R | 4 R/downloading_tools.R |only README.md | 4 inst/doc/nhdplusTools.R | 304 +++++------ inst/doc/nhdplusTools.html | 1031 +++++++++++++++----------------------- inst/doc/plot_nhdplus.R | 202 +++---- inst/doc/plot_nhdplus.html | 760 ++++++++++------------------ inst/doc/point_indexing.R | 128 ++-- inst/doc/point_indexing.html | 583 ++++++++------------- man/check7z.Rd |only man/download_nhdplusv2.Rd |only man/download_rf1.Rd |only man/download_wbd.Rd |only man/downloader.Rd |only tests/testthat/test_get_nhdplus.R | 20 19 files changed, 1320 insertions(+), 1776 deletions(-)
Title: Exact Tests and Confidence Intervals for 2x2 Tables
Description: Calculates conditional exact tests (Fisher's exact test, Blaker's exact test, or exact McNemar's test) and unconditional exact tests (including score-based tests on differences in proportions, ratios of proportions, and odds ratios, and Boshcloo's test) with appropriate matching confidence intervals, and provides power and sample size calculations. Gives melded confidence intervals for the binomial case. Gives boundary-optimized rejection region test (Gabriel, et al, 2018, <DOI:10.1002/sim.7579>), an unconditional exact test for the situation where the controls are all expected to fail.
Author: Michael P. Fay, Sally A. Hunsberger, Martha Nason, Erin Gabriel
Maintainer: Michael P. Fay <mfay@niaid.nih.gov>
Diff between exact2x2 versions 1.6.3 dated 2018-07-27 and 1.6.3.1 dated 2019-10-16
ChangeLog | 3 +++ DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- build/vignette.rds |binary inst/doc/exact2x2.pdf |binary inst/doc/exact2x2Validation.pdf |binary inst/doc/exactMcNemar.pdf |binary inst/doc/midpAdjustment.pdf |binary inst/doc/unconditionalExact2x2Tests.pdf |binary tests/testthat/test_Exact.R | 14 +++++++------- 10 files changed, 24 insertions(+), 21 deletions(-)
Title: Read Large Text Files
Description: Read large text files by splitting them in smaller files.
Package 'bigreadr' also provides some convenient wrappers around fread()
and fwrite() from package 'data.table'.
Author: Florian Privé [aut, cre]
Maintainer: Florian Privé <florian.prive.21@gmail.com>
Diff between bigreadr versions 0.1.10 dated 2019-09-17 and 0.1.11 dated 2019-10-16
bigreadr-0.1.10/bigreadr/R/utils.R |only bigreadr-0.1.11/bigreadr/DESCRIPTION | 19 ++++--- bigreadr-0.1.11/bigreadr/MD5 | 18 +++---- bigreadr-0.1.11/bigreadr/NAMESPACE | 6 ++ bigreadr-0.1.11/bigreadr/R/bigreadr-package.R | 1 bigreadr-0.1.11/bigreadr/R/bind.R |only bigreadr-0.1.11/bigreadr/R/read.R | 44 ------------------ bigreadr-0.1.11/bigreadr/man/bigreadr-package.Rd | 2 bigreadr-0.1.11/bigreadr/man/cbind_df.Rd | 2 bigreadr-0.1.11/bigreadr/man/rbind_df.Rd | 2 bigreadr-0.1.11/bigreadr/tests/testthat/test-nlines.R | 4 - 11 files changed, 33 insertions(+), 65 deletions(-)
Title: log Normal Linear Regression
Description: Functions to fits simple linear regression models with log normal errors
and identity link (taking the responses on the original scale). See
Muggeo (2018) <doi:10.13140/RG.2.2.18118.16965>.
Author: Vito M. R. Muggeo [aut, cre] (<https://orcid.org/0000-0002-3386-4054>)
Maintainer: Vito M. R. Muggeo <vito.muggeo@unipa.it>
Diff between logNormReg versions 0.2-0 dated 2018-10-16 and 0.3-0 dated 2019-10-16
DESCRIPTION | 8 +- MD5 | 19 +++-- NAMESPACE | 3 NEWS | 11 ++- R/extractAIC.lognlm.R |only R/logLik.lognlm.R | 25 ++++--- R/lognlm.R | 144 ++++++++++++++++++++++----------------------- build/partial.rdb |binary man/logLik.lognlm.Rd | 146 ++++++++++++++++++++++++---------------------- man/logNormReg-package.Rd | 4 - man/lognlm.Rd | 7 +- 11 files changed, 193 insertions(+), 174 deletions(-)
Title: Create Details HTML Tag for Markdown and Package Documentation
Description: Create a details HTML tag around R objects to place in a
Markdown, 'Rmarkdown' and 'roxygen2' documentation.
Author: Jonathan Sidi [aut, cre]
Maintainer: Jonathan Sidi <yonicd@gmail.com>
Diff between details versions 0.1.0 dated 2019-10-09 and 0.1.1 dated 2019-10-16
DESCRIPTION | 10 +-- MD5 | 48 ++++++++-------- NAMESPACE | 3 + NEWS.md | 6 ++ R/details.R | 22 +++++-- R/parts.R | 5 + R/print.R | 16 +++++ README.md | 11 ++- build/vignette.rds |binary inst/doc/custom.R | 22 +++++-- inst/doc/custom.Rmd | 28 +++++++-- inst/doc/custom.html | 116 ++++++++++++++++++++++++--------------- inst/doc/objects.R | 8 +- inst/doc/objects.Rmd | 8 +- inst/doc/sessioninfo.R | 2 inst/doc/sessioninfo.Rmd | 4 + inst/doc/sessioninfo.html | 115 ++++++++++++++------------------------ inst/doc/tests_and_coverage.html | 2 man/details.Rd | 22 +++++-- tests/README.md | 31 +++++----- tests/testthat/helpers.R | 10 ++- tests/testthat/test-basic.R | 7 ++ vignettes/custom.Rmd | 28 +++++++-- vignettes/objects.Rmd | 8 +- vignettes/sessioninfo.Rmd | 4 + 25 files changed, 321 insertions(+), 215 deletions(-)
Title: Miscellaneous Functions in C++
Description: Provides utility functions that are simply, frequently used,
but may require higher performance that what can be obtained from base R.
Incidentally provides support for 'reverse geocoding', such as matching a point
with its nearest neighbour in another array. Used as a complement to package
'hutils' by sacrificing compilation or installation time for higher running
speeds. The name is a portmanteau of the author and 'Rcpp'.
Author: Hugh Parsonage [aut, cre]
Maintainer: Hugh Parsonage <hugh.parsonage@gmail.com>
Diff between hutilscpp versions 0.2.0 dated 2019-08-20 and 0.3.0 dated 2019-10-16
DESCRIPTION | 6 MD5 | 51 +- NAMESPACE | 1 NEWS.md | 65 ++ R/RcppExports.R | 20 R/are_even.R | 108 ++-- R/as_integer_if_safe.R | 58 +- R/pmax_pure_C.R | 14 R/range_rcpp.R | 165 +++--- R/utils.R | 10 R/which_first.R | 758 +++++++++++++++++-------------- R/xor2.R |only man/as_integer_if_safe.Rd | 23 man/range_rcpp.Rd | 6 man/xor2.Rd |only src/RcppExports.cpp | 67 ++ src/cpphutils.h | 2 src/do_even.cpp | 17 src/do_range.cpp | 88 +++ src/do_sum_dbl_par.cpp |only src/do_which_first.cpp | 150 ++++++ src/do_xor2.cpp |only src/is_safe2int.cpp | 41 + src/logical3.cpp | 1 tests/testthat/test-are_even.R | 81 ++- tests/testthat/test-as_integer_if_safe.R | 18 tests/testthat/test-range-cpp.R | 164 +++--- tests/testthat/test-which_first.R | 743 +++++++++++++++++------------- tests/testthat/test-xor2.R |only 29 files changed, 1703 insertions(+), 954 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),
Jonathan Williman [ctb] (<https://orcid.org/0000-0001-5080-4435>)
Maintainer: Alessandro Gasparini <alessandro.gasparini@ki.se>
Diff between comorbidity versions 0.5.0 dated 2019-08-20 and 0.5.1 dated 2019-10-16
DESCRIPTION | 12 +- MD5 | 18 ++- NEWS.md | 6 + R/comorbidity-package.R | 5 - R/comorbidity.R | 18 +-- README.md | 6 - build/partial.rdb |binary inst/doc/comorbidityscores.html | 182 ++++++++++++++++++++-------------------- man/comorbidity-package.Rd | 2 tests/testthat/test-#20.R |only tests/testthat/test-nrow.R |only 11 files changed, 130 insertions(+), 119 deletions(-)
Title: Nonparametric Tests for Equality of Location Against Ordered
Alternatives
Description: Performs nonparametric tests for equality of location against ordered alternatives.
Author: Bulent Altunkaynak [aut, cre], Hamza Gamgam [aut]
Maintainer: Bulent Altunkaynak <bulenta@gazi.edu.tr>
Diff between npordtests versions 1.1 dated 2018-11-26 and 1.2 dated 2019-10-16
DESCRIPTION | 16 ++++++++++------ MD5 | 48 +++++++++++++++++++++++++++++++----------------- NAMESPACE | 3 ++- R/AtTest.R | 1 - R/TmTest.R | 4 ++-- data |only man/AtTest.rd | 15 ++++++++------- man/FtmTest.rd | 15 ++++++--------- man/GcTest.rd | 17 +++++++++-------- man/Jdata.Rd |only man/JtTest.rd | 17 +++++++++-------- man/KtpTest.rd | 15 ++++++--------- man/Lehmann.Rd |only man/LsTest.rd | 15 ++++++++------- man/LtTest.rd | 15 ++++++++------- man/MjtTest.rd | 27 ++++++++++++++++----------- man/Neuhauser.Rd |only man/RsTest.rd | 17 +++++++++-------- man/SsTest.rd | 15 ++++++++------- man/StTest.rd | 17 +++++++++-------- man/TmTest.rd | 17 +++++++++-------- man/WsTest.rd | 15 ++++++++------- man/chicks.Rd |only man/hvwi.Rd |only man/hypertension.Rd |only tests |only 26 files changed, 158 insertions(+), 131 deletions(-)
Title: Multiscalar Territorial Analysis
Description: Build multiscalar territorial analysis based on various contexts.
Author: Ronan Ysebaert [aut],
Nicolas Lambert [aut],
Timothée Giraud [aut, cre]
Maintainer: Timothée Giraud <timothee.giraud@cnrs.fr>
Diff between MTA versions 0.1.2 dated 2018-05-14 and 0.2.0 dated 2019-10-16
MTA-0.1.2/MTA/man/com.spdf.Rd |only MTA-0.1.2/MTA/man/ept.spdf.Rd |only MTA-0.1.2/MTA/vignettes/MTA_Scenario_cache |only MTA-0.1.2/MTA/vignettes/MTA_Scenario_files |only MTA-0.2.0/MTA/DESCRIPTION | 14 MTA-0.2.0/MTA/MD5 | 131 - MTA-0.2.0/MTA/NAMESPACE | 4 MTA-0.2.0/MTA/R/gdev.R | 92 - MTA-0.2.0/MTA/R/internals.R | 44 MTA-0.2.0/MTA/R/mapmst.R |only MTA-0.2.0/MTA/R/mas.R | 84 MTA-0.2.0/MTA/R/mst.R | 160 - MTA-0.2.0/MTA/R/package.R | 46 MTA-0.2.0/MTA/R/sdev.R | 165 - MTA-0.2.0/MTA/R/tdev.R | 90 - MTA-0.2.0/MTA/README.md | 5 MTA-0.2.0/MTA/build/vignette.rds |binary MTA-0.2.0/MTA/data/GrandParisMetropole.RData |binary MTA-0.2.0/MTA/inst/doc/MTA.Rmd | 34 MTA-0.2.0/MTA/inst/doc/MTA.html | 436 ++-- MTA-0.2.0/MTA/inst/doc/MTA_Scenario.R | 640 +++++++ MTA-0.2.0/MTA/inst/doc/MTA_Scenario.Rmd | 962 +++++----- MTA-0.2.0/MTA/inst/doc/MTA_Scenario.html | 2406 +++++++++++++-------------- MTA-0.2.0/MTA/man/MTA.Rd | 15 MTA-0.2.0/MTA/man/com.Rd | 3 MTA-0.2.0/MTA/man/ept.Rd |only MTA-0.2.0/MTA/man/gdev.Rd | 75 MTA-0.2.0/MTA/man/mapmst.Rd |only MTA-0.2.0/MTA/man/mas.Rd | 33 MTA-0.2.0/MTA/man/mst.Rd | 87 MTA-0.2.0/MTA/man/sdev.Rd | 117 - MTA-0.2.0/MTA/man/tdev.Rd | 76 MTA-0.2.0/MTA/vignettes/MTA.Rmd | 34 MTA-0.2.0/MTA/vignettes/MTA_Scenario.Rmd | 962 +++++----- 34 files changed, 3501 insertions(+), 3214 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-03-23 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-05-01 0.1.1
2017-03-23 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-10-01 0.3.1
2015-08-21 0.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-11-15 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-06-25 1.7.9-5
2019-05-15 1.7.8-4
2019-04-27 1.7.7-1
2019-04-22 1.7.6-3
2019-01-25 1.7.5-3
2017-12-21 1.7.4-7
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-04-29 2.0
2014-07-04 1.0
Title: Weighting for Covariate Balance in Observational Studies
Description: Generates weights to form equivalent groups in observational studies with point or longitudinal treatments by easing and extending the functionality of the R packages 'twang' for generalized boosted modeling (McCaffrey, Ridgeway & Morral, 2004) <doi:10.1037/1082-989X.9.4.403>, 'CBPS' for covariate balancing propensity score weighting (Imai & Ratkovic, 2014) <doi:10.1111/rssb.12027>, 'ebal' for entropy balancing (Hainmueller, 2012) <doi:10.1093/pan/mpr025>, 'optweight' for optimization-based weights (Zubizarreta, 2015) <doi:10.1080/01621459.2015.1023805>, 'ATE' for empirical balancing calibration weighting (Chan, Yam, & Zhang, 2016) <doi:10.1111/rssb.12129>, and 'SuperLearner' for stacked machine learning-based propensity scores (Pirracchio, Petersen, & van der Laan, 2015) <doi:10.1093/aje/kwu253>. Also allows for assessment of weights and checking of covariate balance by interfacing directly with 'cobalt'.
Author: Noah Greifer [aut, cre] (<https://orcid.org/0000-0003-3067-7154>)
Maintainer: Noah Greifer <noah.greifer@gmail.com>
Diff between WeightIt versions 0.6.0 dated 2019-09-05 and 0.7.0 dated 2019-10-16
DESCRIPTION | 18 MD5 | 73 +-- NAMESPACE | 6 NEWS.md | 19 R/SHARED.R | 333 +++++++++++---- R/as.weightit.R | 9 R/functions_for_processing.R | 214 +++++++-- R/get.w.R | 3 R/ps.cont.R | 35 + R/sbps.R |only R/trim.R | 8 R/weightit.R | 17 R/weightit.fit.R | 21 R/weightit2method.R | 623 ++++++++++++++++++++++++---- R/weightitMSM.R | 13 README.md | 83 ++- build/partial.rdb |binary inst/doc/WeightIt_A0_basic_use.R | 117 ++--- inst/doc/WeightIt_A0_basic_use.Rmd | 23 - inst/doc/WeightIt_A0_basic_use.html | 790 +++++++++++++++++++++++++++++++++--- man/as.weightit.Rd | 6 man/get_w_from_ps.Rd | 10 man/make_full_rank.Rd | 2 man/method-cbps.Rd | 4 man/method-ebal.Rd | 10 man/method-ebcw.Rd | 6 man/method-gbm.Rd | 52 +- man/method-npcbps.Rd | 8 man/method-optweight.Rd | 4 man/method-ps.Rd | 13 man/method-super.Rd | 6 man/method-twang.Rd |only man/method-user.Rd | 5 man/ps.cont.Rd | 6 man/sbps.Rd |only man/trim.Rd | 4 man/weightit.Rd | 7 man/weightitMSM.Rd | 5 vignettes/WeightIt_A0_basic_use.Rmd | 23 - 39 files changed, 2040 insertions(+), 536 deletions(-)
Title: Stepwise Regression Analysis
Description: Stepwise regression analysis for variable selection can be used to get the best candidate final regression model in univariate or multivariate regression analysis with the 'forward', 'backward' and 'bidirection' steps. Besides, best subset selection is included in this package. Procedure can use Akaike information criterion, corrected Akaike information criterion, Bayesian information criterion, Hannan and Quinn information criterion, corrected Hannan and Quinn information criterion, Schwarz criterion and significance levels as selection criteria. Multicollinearity detection in regression model are performed by checking tolerance value. Continuous variables nested within class effect and weighted stepwise regression are also considered.
Author: Junhui Li,Xiaohuan Lu,Kun Cheng,Wenxin Liu
Maintainer: Junhui Li <junhuili@cau.edu.cn>
Diff between StepReg versions 1.2.1 dated 2019-09-20 and 1.3.0 dated 2019-10-16
DESCRIPTION | 10 MD5 | 14 NAMESPACE | 1 R/bestsubset.R |only R/stepwise.R | 884 +++++++++++++++++++++++++++---------------------- man/ModelFitStat.Rd | 2 man/StepReg-package.Rd | 8 man/bestsubset.Rd |only man/stepwise.Rd | 44 -- 9 files changed, 524 insertions(+), 439 deletions(-)
Title: Interactive Statistical Data Visualization
Description: An extendable toolkit for interactive data visualization and exploration.
Author: Adrian Waddell [aut],
R. Wayne Oldford [aut, cre, ths],
Zehao Xu [ctb],
Martin Gauch [ctb]
Maintainer: R. Wayne Oldford <rwoldford@uwaterloo.ca>
Diff between loon versions 1.2.2 dated 2019-03-23 and 1.2.3 dated 2019-10-16
DESCRIPTION | 28 MD5 | 300 +- NAMESPACE | 10 NEWS.md | 8 R/L2_Distance.R |only R/datasets.R | 117 - R/inspectors.R | 108 R/l_ColorList.R | 330 +- R/l_compound.R | 19 R/l_copyStates.R |only R/l_export.R | 76 R/l_glyph_image.R | 21 R/l_glyphs.R | 256 +- R/l_help.R | 32 R/l_hist.R | 179 + R/l_info.R | 2 R/l_layer_map.R | 11 R/l_pairs.R | 115 R/l_plot.R | 289 +- R/l_plot3D.R | 90 R/l_plot_decomposed_ts.R | 80 R/l_plot_density.R | 29 R/l_plot_stl.R | 63 R/l_plot_ts.R | 274 +- R/l_saveStatesRDS.R |only R/l_serialaxes.R | 200 + R/l_state_names.R | 2 R/l_web.R |only R/loon-package.R | 46 R/loonGrob.R | 1737 +++++++-------- R/loonGrob_l_compound.R | 2 R/loonGrob_l_layer_graph.R | 26 R/loonGrob_l_layer_scatterplot.R | 78 R/loonGrob_l_navigator.R | 2 R/loonGrob_l_pairs.R | 167 - R/loonGrob_l_serialaxes.R | 729 +++--- R/loonGrob_l_ts.R | 22 R/onLoad.R | 2 README.md |only build/vignette.rds |binary demo/l_glyph_sizes.R | 84 demo/l_glyphs.R | 130 - demo/l_map.R | 67 demo/l_ng_images_faces.R | 26 demo/l_ng_images_frey_LLE.R | 28 demo/l_ng_images_frey_isomap.R | 30 inst/doc/Rmarkdown.R | 39 inst/doc/Rmarkdown.Rmd | 61 inst/doc/Rmarkdown.html | 557 +--- inst/doc/introduction.R | 28 inst/doc/introduction.Rmd | 40 inst/doc/introduction.html | 1437 ++++-------- inst/doc/minorities.R | 36 inst/doc/minorities.Rmd | 74 inst/doc/minorities.html | 1524 +++++-------- inst/doc/teaching-example-smoothing.R | 24 inst/doc/teaching-example-smoothing.Rmd | 34 inst/doc/teaching-example-smoothing.html | 764 ++---- inst/tcl/loon/library/oo_Axes3DVisual.tcl | 18 inst/tcl/loon/library/oo_Decorated_View.tcl | 2 inst/tcl/loon/library/oo_GraphWorldviewVisual.tcl | 2 inst/tcl/loon/library/oo_Graphswitch.tcl | 2 inst/tcl/loon/library/oo_HistogramInspectorAnalysis.tcl | 2 inst/tcl/loon/library/oo_HistogramVisual.tcl | 10 inst/tcl/loon/library/oo_Histogram_Controller.tcl | 4 inst/tcl/loon/library/oo_Histogram_Model.tcl | 2 inst/tcl/loon/library/oo_ItemLabel_Controller.tcl | 2 inst/tcl/loon/library/oo_LayerVisual.tcl | 2 inst/tcl/loon/library/oo_LayerVisual1.tcl | 2 inst/tcl/loon/library/oo_LayerVisualN.tcl | 6 inst/tcl/loon/library/oo_Layered_View.tcl | 4 inst/tcl/loon/library/oo_LineVisual.tcl | 2 inst/tcl/loon/library/oo_LinesVisual.tcl | 2 inst/tcl/loon/library/oo_NavigatorVisual.tcl | 4 inst/tcl/loon/library/oo_Plot_View.tcl | 6 inst/tcl/loon/library/oo_PointrangeGlyphVisual.tcl | 8 inst/tcl/loon/library/oo_PointsVisual.tcl | 2 inst/tcl/loon/library/oo_PolygonGlyphVisual.tcl | 4 inst/tcl/loon/library/oo_PolygonVisual.tcl | 2 inst/tcl/loon/library/oo_PolygonsVisual.tcl | 2 inst/tcl/loon/library/oo_Rotate3D_Controller.tcl | 2 inst/tcl/loon/library/oo_Scatterplot3D_Controller.tcl | 1 inst/tcl/loon/library/oo_Scatterplot3D_Model.tcl | 8 inst/tcl/loon/library/oo_Scatterplot3D_View.tcl | 7 inst/tcl/loon/library/oo_ScatterplotVisual.tcl | 6 inst/tcl/loon/library/oo_SerialaxesInspectorAnalysis.tcl | 2 inst/tcl/loon/library/oo_SpiroGlyphVisual.tcl | 4 inst/tcl/loon/library/oo_SweepBrush_Controller.tcl | 4 inst/tcl/loon/library/oo_TempMove_Controller.tcl | 4 inst/tcl/loon/library/oo_TextVisual.tcl | 2 inst/tcl/loon/library/oo_TextsVisual.tcl | 2 inst/tcl/loon/library/oo_WorldviewMap.tcl | 2 inst/tcl/loon/library/oo_ZoomPan_Controller.tcl | 2 inst/tcl/loon/library/optionDatabase.tcl | 112 inst/tcl/loon/library/x_synchronize.tcl | 6 inst/tcl/loon/pkgIndex.tcl | 4 man/L2_distance.Rd |only man/UsAndThem.Rd | 13 man/color_loon.Rd | 40 man/figures/logo.png |only man/hex12tohex6.Rd | 4 man/l_copyStates.Rd |only man/l_createCompoundGrob.Rd | 4 man/l_export.Rd | 23 man/l_export_valid_formats.Rd | 14 man/l_getLocations.Rd | 25 man/l_getPlots.Rd | 5 man/l_glyph_add.Rd | 21 man/l_glyph_add.default.Rd | 17 man/l_glyph_add_image.Rd | 14 man/l_glyph_add_pointrange.Rd | 18 man/l_glyph_add_polygon.Rd | 37 man/l_glyph_add_serialaxes.Rd | 15 man/l_glyph_add_text.Rd | 12 man/l_glyph_delete.Rd | 13 man/l_glyph_getLabel.Rd | 12 man/l_glyph_getType.Rd | 12 man/l_glyph_ids.Rd | 13 man/l_glyph_relabel.Rd | 13 man/l_help.Rd | 11 man/l_hist.Rd | 30 man/l_info_states.Rd | 6 man/l_layer.map.Rd | 9 man/l_loon_inspector.Rd | 2 man/l_pairs.Rd | 2 man/l_plot.Rd | 83 man/l_plot.decomposed.ts.Rd | 46 man/l_plot.default.Rd | 123 - man/l_plot.density.Rd | 27 man/l_plot.map.Rd | 2 man/l_plot.stl.Rd | 47 man/l_plot3D.Rd | 27 man/l_plot3D.default.Rd | 83 man/l_plot_arguments.Rd |only man/l_plot_ts.Rd | 33 man/l_primitiveGlyphs.Rd | 21 man/l_saveStatesRDS.Rd |only man/l_scale3D.Rd | 4 man/l_serialaxes.Rd | 167 + man/l_setColorList.Rd | 117 - man/l_setColorList_ColorBrewer.Rd | 4 man/l_setColorList_hcl.Rd | 8 man/l_state_names.Rd | 5 man/l_web.Rd |only man/loon.Rd | 36 man/loon_palette.Rd | 4 man/minority.Rd | 41 man/names.loon.Rd | 6 man/olive.Rd | 33 man/oliveLocations.Rd | 19 man/plot.loon.Rd | 2 tests/test_loonGrob.R | 150 - vignettes/Archive.zip |only vignettes/Rmarkdown.Rmd | 61 vignettes/introduction.Rmd | 40 vignettes/minorities.Rmd | 74 vignettes/teaching-example-smoothing.Rmd | 34 157 files changed, 6667 insertions(+), 5706 deletions(-)
Title: Access the Bioconductor Project Package Repository
Description: A convenient tool to install and update Bioconductor packages.
Author: Martin Morgan [aut] (<https://orcid.org/0000-0002-5874-8148>),
Marcel Ramos [ctb, cre] (<https://orcid.org/0000-0002-3242-0582>)
Maintainer: Marcel Ramos <marcel.ramos@roswellpark.org>
Diff between BiocManager versions 1.30.7 dated 2019-10-07 and 1.30.8 dated 2019-10-16
DESCRIPTION | 8 +- MD5 | 25 +++---- NEWS | 8 ++ R/install.R | 26 ++++--- R/utilities.R | 16 ++-- inst/doc/BiocManager.R | 34 +++++++--- inst/doc/BiocManager.Rmd | 73 +++++++++++++++++++-- inst/doc/BiocManager.html | 125 +++++++++++++++++-------------------- tests/testthat.R | 11 ++- tests/testthat/test_inet.R |only tests/testthat/test_install.R | 10 +- tests/testthat/test_repositories.R | 22 ++---- tests/testthat/test_version.R | 20 ++--- vignettes/BiocManager.Rmd | 73 +++++++++++++++++++-- 14 files changed, 297 insertions(+), 154 deletions(-)