Title: Simulate Genetic Sequence Data for Pedigrees
Description: Methods to simulate genetic sequence data for pedigrees, with
functionality to simulate genetic heterogeneity among pedigrees.
Christina Nieuwoudt, Angela Brooks-Wilson,
and Jinko Graham (2019) <doi:10.1101/534552>.
Author: Christina Nieuwoudt [aut, cre],
Jinko Graham [aut]
Maintainer: Christina Nieuwoudt <cnieuwou@sfu.ca>
Diff between SimRVSequences versions 0.1.2 dated 2019-03-12 and 0.1.3 dated 2019-04-23
DESCRIPTION | 6 - MD5 | 14 +-- R/sim_StudySeqFunctions.R | 15 ++++ inst/doc/SimRVSequences.Rmd | 2 inst/doc/SimRVSequences.html | 136 +++++++++++++++++++------------------- man/sim_RVstudy.Rd | 2 tests/testthat/test_sim_RVstudy.R | 13 +++ vignettes/SimRVSequences.Rmd | 2 8 files changed, 111 insertions(+), 79 deletions(-)
More information about SimRVSequences at CRAN
Permanent link
Title: Unit Testing for R
Description: Software testing is important, but, in part because it is
frustrating and boring, many of us avoid it. 'testthat' is a testing framework
for R that is easy learn and use, and integrates with your existing 'workflow'.
Author: Hadley Wickham [aut, cre],
RStudio [cph, fnd],
R Core team [ctb] (Implementation of utils::recover())
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between testthat versions 2.1.0 dated 2019-04-22 and 2.1.1 dated 2019-04-23
DESCRIPTION | 6 +++--- MD5 | 16 ++++++++-------- NEWS.md | 4 ++++ tests/testthat/test-expect-error.R | 2 ++ tests/testthat/test-expect-error.txt | 10 +++++----- tests/testthat/test-expect-output.R | 4 +++- tests/testthat/test-expect-setequal.R | 12 +++++++----- tests/testthat/test-expect-warning.R | 2 ++ tests/testthat/test-expect-warning.txt | 8 ++++---- 9 files changed, 38 insertions(+), 26 deletions(-)
Title: Powerful and Reliable Tools for Running System Commands in R
Description: Drop-in replacements for the base system2() function with fine control
and consistent behavior across platforms. Supports clean interruption, timeout,
background tasks, and streaming STDIN / STDOUT / STDERR over binary or text
connections. Arguments on Windows automatically get encoded and quoted to work
on different locales.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>),
Gábor Csárdi [ctb]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between sys versions 3.1 dated 2019-03-10 and 3.2 dated 2019-04-23
DESCRIPTION | 6 ++--- LICENSE | 2 - MD5 | 11 +++++---- NEWS | 6 +++++ src/exec.c | 5 ++++ src/win32/exec.c | 50 +++++++++++++++++++++++++++++++++--------- tests/testthat/test-nesting.R |only 7 files changed, 61 insertions(+), 19 deletions(-)
More information about robustSingleCell at CRAN
Permanent link
Title: Detects Fraud in Online Surveys by Tracing, Scoring, and
Visualizing IP Addresses
Description: Takes an array of IPs and the keys for the services the user wishes to use (IP Hub, IP Intel, and Proxycheck),
and passes these to all respective APIs. Returns a dataframe with the IP addresses (used for merging),
country, ISP, labels for non-US IP Addresses, VPS use, and recommendations for blocking. The package
also provides optional visualization tools for checking the distributions.
Author: Ryan Kennedy [aut, cre],
Philip Waggoner [aut],
Scott Clifford [ctb]
Maintainer: Ryan Kennedy <rkennedy@uh.edu>
Diff between rIP versions 0.1.1 dated 2018-10-16 and 1.1.1 dated 2019-04-23
DESCRIPTION | 21 +++--- MD5 | 8 +- R/rIP.R | 181 ++++++++++++++++++++++++++++++++++++++++++++++--------- README.md | 44 +++++++++++-- man/getIPinfo.Rd | 30 ++++++--- 5 files changed, 227 insertions(+), 57 deletions(-)
Title: Mass Spectrometry Metabolomics Feature Clustering and
Interpretation
Description: A feature clustering algorithm for non-targeted mass spectrometric metabolomics data. This method is compatible with gas and liquid chromatography coupled mass spectrometry, including indiscriminant tandem mass spectromery <DOI: 10.1021/ac501530d> data.
Author: Corey D. Broeckling, Fayyaz Afsar, Steffan Neumann, Asa Ben-Hur, Jessica Prenni.
Maintainer: "Broeckling,Corey" <Corey.Broeckling@ColoState.EDU>
Diff between RAMClustR versions 1.0.4 dated 2019-02-13 and 1.0.6 dated 2019-04-23
ChangeLog | 9 ++- DESCRIPTION | 11 ++-- MD5 | 24 ++++---- NAMESPACE | 2 R/annotate.R | 6 +- R/do.findmain.R | 1 R/get.synonyms.R | 1 R/getClassyFire.R | 37 +++++++++++-- R/import.msfinder.formulas.R | 11 +++- R/ramclustR.R | 118 ++++++++++++++++++++++++++++++------------- inst/doc/RAMClustR.html | 4 - man/annotate.Rd | 4 - man/getClassyFire.Rd | 7 +- 13 files changed, 167 insertions(+), 68 deletions(-)
Title: Common Public Health Statistics and their Confidence Intervals
Description: Functions to calculate commonly used public health statistics and
their confidence intervals using methods approved for use in the production
of Public Health England indicators such as those presented via Fingertips
(<http://fingertips.phe.org.uk/>). It provides functions for the generation
of proportions, crude rates, means, directly standardised rates, indirectly
standardised rates, standardised mortality ratios, slope and relative index
of inequality and life expectancy.
Statistical methods are referenced in the following publications.
Breslow NE, Day NE (1987) <doi:10.1002/sim.4780080614>.
Dobson et al (1991) <doi:10.1002/sim.4780100317>.
Armitage P, Berry G (2002) <doi:10.1002/9780470773666>.
Wilson EB. (1927) <doi:10.1080/01621459.1927.10502953>.
Altman DG et al (2000, ISBN: 978-0-727-91375-3).
Chiang CL. (1968, ISBN: 978-0-882-75200-6).
Newell C. (1994, ISBN: 978-0-898-62451-9).
Eayres DP, Williams ES (2004) <doi:10.1136/jech.2003.009654>.
Silcocks PBS et al (2001) <doi:10.1136/jech.55.1.38>.
Low and Low (2004) <doi:10.1093/pubmed/fdh175>.
Author: Anderson Georgina [aut, cre],
Fox Sebastian [ctb],
Francis Matthew [ctb],
Fryers Paul [ctb],
Clegg Emma [ctb]
Maintainer: Anderson Georgina <georgina.anderson@phe.gov.uk>
Diff between PHEindicatormethods versions 1.1.1 dated 2019-04-18 and 1.1.2 dated 2019-04-23
DESCRIPTION | 6 MD5 | 14 NEWS.md | 5 inst/doc/DSR-vignette.html | 108 ++--- inst/doc/Introduction_to_PHEindicatormethods.html | 466 +++++++++++----------- inst/doc/WorkedExamples_phe_sii.html | 156 +++---- tests/testthat/testLifeExpectancy.R | 22 - tests/testthat/testProportions.R | 4 8 files changed, 393 insertions(+), 388 deletions(-)
More information about PHEindicatormethods at CRAN
Permanent link
Title: Semi-Supervised Model for Geographical Document Classification
Description: Semi-supervised model for geographical document classification (Watanabe 2018) <doi:10.1080/21670811.2017.1293487>.
This package currently contains seed dictionaries in English, German, French, Spanish, Japanese, Russian and Chinese (Simplified and Traditional).
Author: Kohei Watanabe [aut, cre, cph],
Stefan Müller [aut],
Dani Madrid-Morales [aut],
Katerina Tertytchnaya [aut],
Ke Cheng [aut],
Chung-hong Chan [aut],
Claude Grasland [aut]
Maintainer: Kohei Watanabe <watanabe.kohei@gmail.com>
Diff between newsmap versions 0.6.4 dated 2019-02-24 and 0.6.7 dated 2019-04-23
DESCRIPTION | 8 ++-- MD5 | 13 ++++--- NAMESPACE | 1 NEWS.md | 24 ++++++++----- R/textmodel_newsmap.R | 46 ++++++++++++++++++++++---- data/data_dictionary_newsmap_ja.RData |binary man/afe.Rd |only tests/testthat/test-textmodel_newsmap.R | 55 ++++++++++++++++++++++---------- 8 files changed, 105 insertions(+), 42 deletions(-)
Title: Model and Analyse Interval Data
Description: Implements methodologies for modelling interval data by Normal
and Skew-Normal distributions, considering appropriate parameterizations of
the variance-covariance matrix that takes into account the intrinsic nature of
interval data, and lead to four different possible configuration structures.
The Skew-Normal parameters can be estimated by maximum likelihood, while Normal
parameters may be estimated by maximum likelihood or robust trimmed maximum
likelihood methods.
Author: Pedro Duarte Silva <psilva@porto.ucp.pt>, Paula Brito
<mpbrito.fep.up.pt>
Maintainer: Pedro Duarte Silva <psilva@porto.ucp.pt>
Diff between MAINT.Data versions 2.0.0 dated 2018-10-17 and 2.1.1 dated 2019-04-23
MAINT.Data-2.0.0/MAINT.Data/src/Makevars |only MAINT.Data-2.1.1/MAINT.Data/CHANGELOG | 23 ++ MAINT.Data-2.1.1/MAINT.Data/DESCRIPTION | 8 MAINT.Data-2.1.1/MAINT.Data/MD5 | 23 +- MAINT.Data-2.1.1/MAINT.Data/NAMESPACE | 2 MAINT.Data-2.1.1/MAINT.Data/R/DACrossVal.R | 179 ++++++++++-------- MAINT.Data-2.1.1/MAINT.Data/R/IData.R | 149 ++++++++------ MAINT.Data-2.1.1/MAINT.Data/R/mle.R | 2 MAINT.Data-2.1.1/MAINT.Data/man/DACrossVal.Rd | 8 MAINT.Data-2.1.1/MAINT.Data/man/MAINT.Data-package.Rd | 4 MAINT.Data-2.1.1/MAINT.Data/man/Robda-methods.Rd | 12 - MAINT.Data-2.1.1/MAINT.Data/man/lda-methods.Rd | 3 MAINT.Data-2.1.1/MAINT.Data/man/qda-methods.Rd | 3 13 files changed, 231 insertions(+), 185 deletions(-)
Title: Tools for Working with Multidimensional Data
Description: Provides various tools for working with multidimensional
data in R and C++, including extremely fast nearest-neighbor- and range-
queries without the overhead of linked tree nodes.
Author: Timothy Keitt [aut, cre]
Maintainer: Timothy Keitt <tkeitt@gmail.com>
Diff between kdtools versions 0.3.1 dated 2018-04-26 and 0.4.1 dated 2019-04-23
DESCRIPTION | 8 MD5 | 52 ++--- NAMESPACE | 9 + NEWS.md | 9 + R/RcppExports.R | 12 + R/arrayvec.R | 2 R/kdtools.R | 58 ++++++ build/vignette.rds |binary inst/doc/kdtools.R | 1 inst/doc/kdtools.Rmd | 3 inst/doc/kdtools.html | 86 ++++----- inst/doc/methods.R | 47 ++++- inst/doc/methods.Rmd | 131 +++++++++++--- inst/doc/methods.html | 195 +++++++++++++-------- inst/include/kdtools.h | 279 ++++++++++++++++++++++++------- man/figures/README-unnamed-chunk-1-1.png |binary man/kdsort.Rd | 14 + man/nneighb.Rd | 4 man/search.Rd | 4 src/RcppExports.cpp | 41 ++++ src/arrayvec.h | 16 + src/kdtools.cpp | 142 ++++++++++++--- tests/testthat/test_nn.R | 36 +++- tests/testthat/test_search.R | 37 +++- tests/testthat/test_sort.R | 16 + vignettes/kdtools.Rmd | 3 vignettes/methods.Rmd | 131 +++++++++++--- 27 files changed, 1023 insertions(+), 313 deletions(-)
Title: Dynamic Modeling and Parameter Estimation in ODE Models
Description: The framework provides functions to generate ODEs of reaction
networks, parameter transformations, observation functions, residual functions,
etc. The framework follows the paradigm that derivative information should be
used for optimization whenever possible. Therefore, all major functions produce
and can handle expressions for symbolic derivatives.
Author: Daniel Kaschek
Maintainer: Daniel Kaschek <daniel.kaschek@gmail.com>
Diff between dMod versions 0.4.2 dated 2018-08-09 and 1.0.0 dated 2019-04-23
DESCRIPTION | 16 - MD5 | 123 +++++++------ NAMESPACE | 11 + R/classes.R | 45 ++++ R/dMod.R | 3 R/data.R | 29 +-- R/dataClass.R | 66 ++++--- R/eqnClass.R | 7 R/eventClass.R | 2 R/objClass.R | 63 +++--- R/parClass.R | 12 - R/parameters.R | 9 R/plots.R | 2 R/prdClass.R | 27 +- R/prediction.R | 34 ++- R/statistics.R | 388 ++++++++++++++++++++++++++++++------------ R/steadyStates.R |only R/symmetryDetection.R | 8 R/tools.R | 51 +++-- R/trust.R | 65 +++++-- R/trustL1.R |only build/vignette.rds |binary inst/CITATION |only inst/code/sbmlAmiciDmod.py |only inst/doc/dMod.html | 33 ++- inst/examples/datalist.R | 3 inst/examples/errmodel.R | 14 + inst/examples/events.R | 141 +++++++++++++-- inst/examples/odemodel.R | 20 ++ inst/examples/plotting.R | 106 ++++++----- inst/examples/steadystates.R |only inst/examples/sumdatalist.R | 4 inst/examples/test_LOQ.R | 35 ++- man/P.Rd | 3 man/Pexpl.Rd | 5 man/Pimpl.Rd | 3 man/Y.Rd | 9 man/as.eqnvec.Rd | 4 man/compile.Rd | 5 man/covariates.Rd | 2 man/datalist.Rd | 25 +- man/eventlist.Rd | 2 man/forcingsSymb.Rd | 4 man/funC0.Rd | 6 man/getParameters.Rd | 3 man/match.fnargs.Rd |only man/msParframe.Rd |only man/mstrust.Rd | 11 - man/normL2.Rd | 5 man/odemodel.Rd | 26 ++ man/parlist.Rd | 2 man/parvec.Rd | 4 man/plotCombined.Rd | 111 ++++++------ man/plotData.Rd | 106 ++++++----- man/plotPrediction.Rd | 106 ++++++----- man/plotProfile.Rd | 3 man/plotResiduals.Rd | 3 man/plus-.datalist.Rd | 4 man/profile.Rd | 8 man/python_version_request.Rd |only man/python_version_rpython.Rd |only man/python_version_sys.Rd |only man/res.Rd | 4 man/steadyStates.Rd |only man/strpad.Rd | 3 man/symmetryDetection.Rd | 16 + man/trust.Rd | 23 ++ man/write.eqnlist.Rd | 2 68 files changed, 1201 insertions(+), 624 deletions(-)
Title: A 'dplyr' Back End for Databases
Description: A 'dplyr' back end for databases that allows you to
work with remote database tables as if they are in-memory data frames.
Basic features works with any database that has a 'DBI' back end; more
advanced features require 'SQL' translation to be provided by the
package author.
Author: Hadley Wickham [aut, cre],
Edgar Ruiz [aut],
RStudio [cph, fnd]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between dbplyr versions 1.3.0 dated 2019-01-09 and 1.4.0 dated 2019-04-23
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Title: Normalisation Tools for Inter-Condition Variability of ChIP-Seq
Data
Description: Inter-sample condition variability is a key challenge of normalising ChIP-seq data. This implementation uses either spike-in or a second factor as a control for normalisation. Input can either be from 'DiffBind' or a matrix formatted for 'DESeq2'. The output is either a 'DiffBind' object or the default 'DESeq2' output. Either can then be processed as normal. Supporting manuscript Guertin, Markowetz and Holding (2017) <doi:10.1101/182261>.
Author: Andrew N Holding
Maintainer: Andrew N Holding <andrew.holding@cruk.cam.ac.uk>
Diff between Brundle versions 1.0.8 dated 2018-02-15 and 1.0.9 dated 2019-04-23
DESCRIPTION | 8 ++++---- MD5 | 32 ++++++++++++++++---------------- R/brundle.R | 1 + README.md | 1 + data/dbaControl.rda |binary data/dbaExperiment.rda |binary data/jg.conditions.rda |binary data/jg.controlCountsTreated.rda |binary data/jg.controlCountsUntreated.rda |binary data/jg.controlPeakset.rda |binary data/jg.controlPeaksetDeSeq.rda |binary data/jg.controlResultsDeseq.rda |binary data/jg.experimentPeakset.rda |binary data/jg.experimentResultsDeseq.rda |binary man/Brundle.Rd | 4 ++-- man/jg.applyNormalisation.Rd | 4 ++-- man/jg.plotDeSeq.Rd | 1 + 17 files changed, 27 insertions(+), 24 deletions(-)
Title: Easy-to-Use Tools for Common Forms of Random Assignment and
Sampling
Description: Generates random assignments for common experimental designs and
random samples for common sampling designs.
Author: Alexander Coppock [aut, cre],
Jasper Cooper [ctb],
Neal Fultz [ctb] (C version of restricted partitions)
Maintainer: Alexander Coppock <acoppock@gmail.com>
Diff between randomizr versions 0.16.1 dated 2018-07-11 and 0.18.0 dated 2019-04-23
DESCRIPTION | 9 MD5 | 112 +-- R/block_and_cluster_ra.R | 22 R/block_ra.R | 39 + R/cluster_ra.R | 20 R/cluster_rs.R | 63 +- R/complete_ra.R | 45 + R/complete_rs.R | 46 + R/declare_ra.R | 5 R/declare_rs.R | 6 R/generated_methods.R | 48 + R/helper_functions.R | 582 ++++++++++++++------ R/simple_ra.R | 19 R/simple_rs.R | 17 R/strata_and_cluster_rs.R | 22 R/strata_rs.R | 32 + R/zzz.R | 32 - build/vignette.rds |binary inst/doc/randomizr_vignette.Rmd | 12 inst/doc/randomizr_vignette.html | 734 +++++++++++++++++--------- man/block_and_cluster_ra.Rd | 11 man/block_and_cluster_ra_probabilities.Rd | 11 man/block_ra.Rd | 22 man/block_ra_probabilities.Rd | 12 man/cluster_ra.Rd | 10 man/cluster_ra_probabilities.Rd | 11 man/cluster_rs.Rd | 8 man/cluster_rs_probabilities.Rd | 9 man/complete_ra.Rd | 15 man/complete_ra_probabilities.Rd | 10 man/complete_rs.Rd | 13 man/complete_rs_probabilities.Rd | 7 man/conduct_ra.Rd | 15 man/declare_ra.Rd | 13 man/declare_rs.Rd | 8 man/draw_rs.Rd | 9 man/obtain_condition_probabilities.Rd | 11 man/obtain_inclusion_probabilities.Rd | 10 man/simple_ra.Rd | 11 man/simple_ra_probabilities.Rd | 11 man/simple_rs.Rd | 9 man/simple_rs_probabilities.Rd | 9 man/strata_and_cluster_rs.Rd | 7 man/strata_and_cluster_rs_probabilities.Rd | 8 man/strata_rs.Rd | 17 man/strata_rs_probabilities.Rd | 9 tests/testthat/test-block_ra.R | 23 tests/testthat/test-cluster_ra.R | 13 tests/testthat/test-cluster_rs.R | 18 tests/testthat/test-complete_ra.R | 17 tests/testthat/test-complete_rs.R | 14 tests/testthat/test-simple_ra.R | 10 tests/testthat/test-simple_rs.R | 13 tests/testthat/test-strata_rs.R | 34 + tests/testthat/test_assignment_declarations.R | 16 tests/testthat/test_sampling_declarations.R | 15 vignettes/randomizr_vignette.Rmd | 12 57 files changed, 1705 insertions(+), 631 deletions(-)
Title: Simulating Realistic Gene Expression Data
Description: The Ultimate Microrray Prediction, Reality and Inference
Engine (UMPIRE) is a package to facilitate the simulation of realistic
microarray data sets with link to associate outcomes. See Zhang and
Coombes (2012) <doi:10.1186/1471-2105-13-S13-S1>.
Author: Kevin R. Coombes, Jiexin Zhang
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between Umpire versions 1.3.5 dated 2018-05-18 and 1.3.6 dated 2019-04-23
DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++++++---------- build/vignette.rds |binary inst/doc/Umpire.pdf |binary tests/t01-indNormal.R | 1 + tests/t01-indNormal.Rout.save |only tests/t02-1-engine.R | 1 + tests/t02-1-engine.Rout.save |only tests/t02-indLogNorm.R | 1 + tests/t02-indLogNorm.Rout.save |only tests/t03-mvn.R | 1 + tests/t03-mvn.Rout.save |only tests/t05-noise.R | 1 + tests/t05-noise.Rout.save |only tests/t06-engineAct.R | 1 + tests/t06-engineAct.Rout.save |only tests/t07-cancerModel.R | 1 + tests/t07-cancerModel.Rout.save |only tests/t08-cancerEngine.Rout.save |only 19 files changed, 29 insertions(+), 14 deletions(-)
Title: Threshing and Reaping for Principal Components
Description: Defines the classes used to identify
outliers (threshing) and compute the number of significant principal
components and number of clusters (reaping) in a joint application
of PCA and hierarchical clustering. See Wang et al., 2018,
<doi:10.1186/s12859-017-1998-9>.
Author: Kevin R. Coombes
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between Thresher versions 1.1.0 dated 2019-03-07 and 1.1.1 dated 2019-04-23
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- data/savedSims.rda |binary inst/doc/Thresher.pdf |binary tests/01-label.Rout.save | 6 +++--- tests/01-remap.R | 1 + tests/01-remap.Rout.save | 3 ++- tests/02-thresh.R | 3 ++- tests/02-thresh.Rout.save | 9 +++++---- tests/04-reap.R | 1 + tests/04-reap.Rout.save | 3 ++- 11 files changed, 30 insertions(+), 24 deletions(-)
Title: Finding the Number of Significant Principal Components
Description: Implements methods to automate the Auer-Gervini graphical
Bayesian approach for determining the number of significant
principal components. Automation uses clustering, change points, or
simple statistical models to distinguish "long" from "short" steps
in a graph showing the posterior number of components as a function
of a prior parameter. See <doi:10.1101/237883>.
Author: Kevin R. Coombes, Min Wang
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between PCDimension versions 1.1.9 dated 2018-05-18 and 1.1.10 dated 2019-04-23
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ build/vignette.rds |binary data/spca.rda |binary inst/doc/PCDimension.pdf |binary tests/00-auer.R | 1 + tests/00-auer.Rout.save | 7 ++++--- 7 files changed, 15 insertions(+), 13 deletions(-)
Title: Classes and Methods for Training and Using Binary Prediction
Models
Description: Defines classes and methods to learn models and use them
to predict binary outcomes. These are generic tools, but we also
include specific examples for many common classifiers.
Author: Kevin R. Coombes
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between Modeler versions 3.4.3 dated 2018-05-18 and 3.4.4 dated 2019-04-23
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- build/vignette.rds |binary inst/doc/Modeler.pdf |binary tests/t00-filter.R | 1 + tests/t00-filter.Rout.save | 7 ++++--- tests/t00-pruner.R | 1 + tests/t00-pruner.Rout.save | 7 ++++--- 8 files changed, 21 insertions(+), 17 deletions(-)
Title: Bayesian Estimation for Finite Mixture of Distributions
Description: Provides statistical tools for Bayesian estimation for finite mixture of distributions, mainly mixture of Gamma, Normal and t-distributions. The package is implemented the recent improvements in Bayesian literature for the finite mixture of distributions, including Mohammadi and et al. (2013) <doi:10.1007/s00180-012-0323-3> and Mohammadi and Salehi-Rad (2012) <doi:10.1080/03610918.2011.588358>.
Author: Reza Mohammadi <https://orcid.org/0000-0001-9538-0648>
Maintainer: Reza Mohammadi <a.mohammadi@uva.nl>
Diff between bmixture versions 1.2 dated 2018-07-05 and 1.3 dated 2019-04-23
DESCRIPTION | 9 +- MD5 | 73 +++++++++++---------- NAMESPACE | 9 -- NEWS | 6 - R/bmixgamma.R | 88 ++++++++++++-------------- R/bmixnorm.R | 128 +++++++++++++++++++------------------- R/bmixnorm_bdmcmc.R | 127 +++++++++++++++++++------------------ R/bmixt.R | 89 ++++++++++++-------------- R/mixgamma.R | 24 ++++--- R/mixnorm.R | 28 ++++---- R/mixt.R | 24 ++++--- R/rdirichlet.R | 14 ++-- inst/CITATION | 6 - man/bmixgamma.Rd | 72 +++++++++------------ man/bmixnorm.Rd | 60 ++++++++--------- man/bmixt.Rd | 62 ++++++++---------- man/bmixture-package.Rd | 18 ++--- man/mixgamma.Rd | 21 ++---- man/mixnorm.Rd | 19 ++--- man/mixt.Rd | 21 ++---- man/plot.bmixgamma.Rd | 8 +- man/plot.bmixnorm.Rd | 8 +- man/plot.bmixt.Rd | 8 +- man/print.bmixgamma.Rd | 4 - man/print.bmixnorm.Rd | 4 - man/print.bmixt.Rd | 4 - man/rdirichlet.Rd | 11 +-- man/summary.bmixgamma.Rd | 4 - man/summary.bmixnorm.Rd | 4 - man/summary.bmixt.Rd | 4 - src/bmix_gamma.cpp | 121 +++++++++++++++++++---------------- src/bmix_norm.cpp | 136 +++++++++++++++++++++------------------- src/bmix_t.cpp | 158 ++++++++++++++++++++++++----------------------- src/dmix_hat_x_seq.cpp | 63 +++++++++--------- src/funs_in_mcmc.cpp | 21 +++--- src/funs_in_mcmc.h | 17 ++--- src/init.c | 10 -- src/util_bmixture.h |only 38 files changed, 743 insertions(+), 740 deletions(-)
Title: Basic Functions for Pre-Processing Microarrays
Description: Provides classes to pre-process microarray gene
expression data as part of the OOMPA collection of packages
described at <http://oompa.r-forge.r-project.org/>.
Author: Kevin R. Coombes
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between PreProcess versions 3.1.5 dated 2018-05-16 and 3.1.6 dated 2019-04-23
PreProcess-3.1.5/PreProcess/tests/test07-complete-channel.Rout.save |only PreProcess-3.1.6/PreProcess/DESCRIPTION | 8 +- PreProcess-3.1.6/PreProcess/MD5 | 28 +++++----- PreProcess-3.1.6/PreProcess/build/vignette.rds |binary PreProcess-3.1.6/PreProcess/inst/doc/oompa-prep.pdf |binary PreProcess-3.1.6/PreProcess/tests/test01-utility.R | 1 PreProcess-3.1.6/PreProcess/tests/test01-utility.Rout.save | 10 +-- PreProcess-3.1.6/PreProcess/tests/test03-channel-type.Rout.save | 6 +- PreProcess-3.1.6/PreProcess/tests/test04-channel.R | 1 PreProcess-3.1.6/PreProcess/tests/test04-channel.Rout.save | 7 +- PreProcess-3.1.6/PreProcess/tests/test05-processor.R | 1 PreProcess-3.1.6/PreProcess/tests/test05-processor.Rout.save | 7 +- PreProcess-3.1.6/PreProcess/tests/test06-pipeline.R | 1 PreProcess-3.1.6/PreProcess/tests/test06-pipeline.Rout.save | 7 +- PreProcess-3.1.6/PreProcess/tests/test07-complete-channel.R | 1 PreProcess-3.1.6/PreProcess/tests/test07-complete-channel.Rout |only 16 files changed, 43 insertions(+), 35 deletions(-)
Title: Class Unions, Matrix Operations, and Color Schemes for OOMPA
Description: Provides the class unions that must be
preloaded in order for the basic tools in the OOMPA (Object-Oriented
Microarray and Proteomics Analysis) project to be defined and loaded.
It also includes vectorized operations for row-by-row means,
variances, and t-tests. Finally, it provides new color schemes.
Details on the packages in the OOMPA project can be found at
<http://oompa.r-forge.r-project.org/>.
Author: Kevin R. Coombes
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between oompaBase versions 3.2.6 dated 2018-05-17 and 3.2.7 dated 2019-04-23
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- build/vignette.rds |binary inst/doc/oompa.pdf |binary tests/testMatrixOps.R | 1 + tests/testMatrixOps.Rout.save | 10 +++++----- 6 files changed, 15 insertions(+), 14 deletions(-)
Title: Interface to the 'g:Profiler' Toolset
Description: A toolset for functional enrichment analysis and visualization, gene/protein/SNP identifier conversion and mapping orthologous genes across species via 'g:Profiler' (<https://biit.cs.ut.ee/gprofiler>).
The main tools are:
(1) 'g:GOSt' - functional enrichment analysis and visualization of gene lists;
(2) 'g:Convert' - gene/protein/transcript identifier conversion across various namespaces;
(3) 'g:Orth' - orthology search across species;
(4) 'g:SNPense' - mapping SNP rs identifiers to chromosome positions, genes and variant effects
This package is an R interface corresponding to the 2019 update of 'g:Profiler' and provides access to 'g:Profiler' for versions 'e94_eg41_p11' and higher. See the package 'gProfileR' for accessing older versions from the 'g:Profiler' toolset.
Author: Liis Kolberg <liis.kolberg@ut.ee>, Uku Raudvere <uku.raudvere@ut.ee>
Maintainer: Liis Kolberg <liis.kolberg@ut.ee>
Diff between gprofiler2 versions 0.1.2 dated 2019-04-08 and 0.1.3 dated 2019-04-23
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/gprofiler2.R | 9 ++++++--- 3 files changed, 11 insertions(+), 8 deletions(-)
Title: Classes and Methods for Cross Validation of "Class Prediction"
Algorithms
Description: Defines classes and methods to cross-validate various
binary classification algorithms used for "class prediction"
problems.
Author: Kevin R. Coombes
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between CrossValidate versions 2.3.2 dated 2018-05-17 and 2.3.3 dated 2019-04-23
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- build/vignette.rds |binary inst/doc/CrossVal.pdf |binary tests/testCV.R | 1 + tests/testCV.Rout.save | 7 ++++--- 6 files changed, 14 insertions(+), 12 deletions(-)
Title: Classes and Methods for "Class Discovery" with Microarrays or
Proteomics
Description: Defines the classes used for "class discovery" problems
in the OOMPA project (<http://oompa.r-forge.r-project.org/>). Class
discovery primarily consists of unsupervised clustering methods with
attempts to assess their statistical significance.
Author: Kevin R. Coombes
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between ClassDiscovery versions 3.3.9 dated 2018-10-03 and 3.3.11 dated 2019-04-23
ClassDiscovery-3.3.11/ClassDiscovery/DESCRIPTION | 8 ClassDiscovery-3.3.11/ClassDiscovery/MD5 | 53 +- ClassDiscovery-3.3.11/ClassDiscovery/NEWS | 11 ClassDiscovery-3.3.11/ClassDiscovery/TODO |only ClassDiscovery-3.3.11/ClassDiscovery/inst/doc/maha-test.pdf |binary ClassDiscovery-3.3.11/ClassDiscovery/inst/doc/oompa-cd.pdf |binary ClassDiscovery-3.3.11/ClassDiscovery/man/cd08-0-PCanova-class.Rd | 2 ClassDiscovery-3.3.11/ClassDiscovery/tests/exprSet-example.R | 1 ClassDiscovery-3.3.11/ClassDiscovery/tests/exprSet-example.Rout.save | 5 ClassDiscovery-3.3.11/ClassDiscovery/tests/test00-color.Rout.save | 34 - ClassDiscovery-3.3.11/ClassDiscovery/tests/test01-distance.R | 1 ClassDiscovery-3.3.11/ClassDiscovery/tests/test01-distance.Rout.save | 101 ++-- ClassDiscovery-3.3.11/ClassDiscovery/tests/test02-cluster.R | 1 ClassDiscovery-3.3.11/ClassDiscovery/tests/test02-cluster.Rout.save | 7 ClassDiscovery-3.3.11/ClassDiscovery/tests/test02.1-just.R | 4 ClassDiscovery-3.3.11/ClassDiscovery/tests/test02.1-just.Rout.save | 68 +- ClassDiscovery-3.3.11/ClassDiscovery/tests/test03-boot.R | 1 ClassDiscovery-3.3.11/ClassDiscovery/tests/test03-boot.Rout.save | 249 +++++----- ClassDiscovery-3.3.11/ClassDiscovery/tests/test04-perturb.R | 1 ClassDiscovery-3.3.11/ClassDiscovery/tests/test04-perturb.Rout.save | 249 +++++----- ClassDiscovery-3.3.11/ClassDiscovery/tests/test04.1-gpca.R | 1 ClassDiscovery-3.3.11/ClassDiscovery/tests/test04.1-gpca.Rout.save | 43 - ClassDiscovery-3.3.11/ClassDiscovery/tests/test05-spca.R | 1 ClassDiscovery-3.3.11/ClassDiscovery/tests/test05-spca.Rout |only ClassDiscovery-3.3.11/ClassDiscovery/tests/test06-mosaic.R | 1 ClassDiscovery-3.3.11/ClassDiscovery/tests/test06-mosaic.Rout.save | 103 ++-- ClassDiscovery-3.3.11/ClassDiscovery/tests/test07-pcanova.R | 1 ClassDiscovery-3.3.11/ClassDiscovery/tests/test07-pcanova.Rout.save | 77 +-- ClassDiscovery-3.3.9/ClassDiscovery/tests/test05-spca.Rout.save |only 29 files changed, 528 insertions(+), 495 deletions(-)
More information about ClassDiscovery at CRAN
Permanent link
Title: The Bimodality Index
Description: Defines the functions used to compute the
bimodal index as defined by Wang et al. (2009)
<https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2730180/>,
<doi:10.4137/CIN.S2846>.
Author: Kevin R. Coombes
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between BimodalIndex versions 1.1.7 dated 2018-10-17 and 1.1.8 dated 2019-04-23
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- inst/doc/bim.pdf |binary tests/test09-bimodal.R | 1 + tests/test09-bimodal.Rout.save | 7 ++++--- 5 files changed, 13 insertions(+), 11 deletions(-)
Title: Create and (Interactively) Modify Nested Hierarchies
Description: Provides functionality to generate, (interactively) modify (by adding, removing and renaming nodes) and convert nested hierarchies between different formats.
These tree like structures can be used to define for example complex hierarchical tables used for statistical disclosure control.
Author: Bernhard Meindl [aut, cre]
Maintainer: Bernhard Meindl <Bernhard.Meindl@statistik.gv.at>
Diff between sdcHierarchies versions 0.17 dated 2019-03-07 and 0.18 dated 2019-04-23
DESCRIPTION | 8 MD5 | 19 - NAMESPACE | 1 NEWS.md | 9 R/hier_grid.R |only build/vignette.rds |binary inst/doc/usage.R | 17 + inst/doc/usage.Rmd | 30 ++ inst/doc/usage.html | 546 +++++++++++++++++++++++++++++++--------- man/hier_grid.Rd |only tests/testthat/test_hier_grid.R |only vignettes/usage.Rmd | 30 ++ 12 files changed, 520 insertions(+), 140 deletions(-)
More information about sdcHierarchies at CRAN
Permanent link
Title: Qualitative Palettes with Many Colors
Description: Tools for creating, viewing, and assessing qualitative
palettes with many (20-30 or more) colors.
Author: Kevin R. Coombes, Guy Brock
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between Polychrome versions 1.2.0 dated 2019-03-17 and 1.2.1 dated 2019-04-23
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- inst/doc/color-deficits.html | 6 +++--- inst/doc/creatingPalettes.html | 4 ++-- tests/testXform.R | 1 + tests/testXform.Rout.save | 7 ++++--- 6 files changed, 19 insertions(+), 17 deletions(-)
Title: Classes and Methods for "Class Comparison" Problems on
Microarrays
Description: Defines the classes used for "class comparison" problems
in the OOMPA project (<http://oompa.r-forge.r-project.org/>). Class
comparison includes tests for differential expression; see Simon's
book for details on typical problem types.
Author: Kevin R. Coombes
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between ClassComparison versions 3.1.6 dated 2018-05-17 and 3.1.7 dated 2019-04-23
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- TODO | 3 +++ build/vignette.rds |binary inst/doc/oompa-cc.pdf |binary tests/testBum.R | 1 + tests/testBum.Rout.save | 7 ++++--- tests/testDiff.R | 1 + tests/testDiff.Rout.save | 5 +++-- 9 files changed, 24 insertions(+), 17 deletions(-)
More information about ClassComparison at CRAN
Permanent link
Title: Machine Learning Models and Tools
Description: Meta-package for statistical and machine learning with a common interface for model fitting, prediction, performance assessment, and presentation of results. Supports predictive modeling of numerical, categorical, and censored time-to-event outcomes and resample (bootstrap and cross-validation) estimation of model performance.
Author: Brian J Smith [aut, cre]
Maintainer: Brian J Smith <brian-j-smith@uiowa.edu>
Diff between MachineShop versions 1.2.0 dated 2019-02-15 and 1.3.0 dated 2019-04-23
MachineShop-1.2.0/MachineShop/R/setAs.R |only MachineShop-1.3.0/MachineShop/DESCRIPTION | 21 MachineShop-1.3.0/MachineShop/MD5 | 229 + MachineShop-1.3.0/MachineShop/NAMESPACE | 46 MachineShop-1.3.0/MachineShop/NEWS.md | 40 MachineShop-1.3.0/MachineShop/R/AllClasses.R | 651 ----- MachineShop-1.3.0/MachineShop/R/MLControl.R |only MachineShop-1.3.0/MachineShop/R/MLMetric.R |only MachineShop-1.3.0/MachineShop/R/MLModel.R |only MachineShop-1.3.0/MachineShop/R/ML_AdaBagModel.R | 5 MachineShop-1.3.0/MachineShop/R/ML_AdaBoostModel.R | 5 MachineShop-1.3.0/MachineShop/R/ML_BARTMachineModel.R | 13 MachineShop-1.3.0/MachineShop/R/ML_BARTModel.R | 20 MachineShop-1.3.0/MachineShop/R/ML_BlackBoostModel.R | 19 MachineShop-1.3.0/MachineShop/R/ML_C50Model.R | 6 MachineShop-1.3.0/MachineShop/R/ML_CForestModel.R | 17 MachineShop-1.3.0/MachineShop/R/ML_CoxModel.R | 23 MachineShop-1.3.0/MachineShop/R/ML_EarthModel.R | 13 MachineShop-1.3.0/MachineShop/R/ML_FDAModel.R | 3 MachineShop-1.3.0/MachineShop/R/ML_GAMBoostModel.R | 16 MachineShop-1.3.0/MachineShop/R/ML_GBMModel.R | 29 MachineShop-1.3.0/MachineShop/R/ML_GLMBoostModel.R | 23 MachineShop-1.3.0/MachineShop/R/ML_GLMModel.R | 13 MachineShop-1.3.0/MachineShop/R/ML_GLMNetModel.R | 22 MachineShop-1.3.0/MachineShop/R/ML_KNNModel.R | 4 MachineShop-1.3.0/MachineShop/R/ML_LARSModel.R | 13 MachineShop-1.3.0/MachineShop/R/ML_LDAModel.R | 3 MachineShop-1.3.0/MachineShop/R/ML_LMModel.R | 10 MachineShop-1.3.0/MachineShop/R/ML_MDAModel.R | 3 MachineShop-1.3.0/MachineShop/R/ML_NNetModel.R | 10 MachineShop-1.3.0/MachineShop/R/ML_NaiveBayesModel.R | 6 MachineShop-1.3.0/MachineShop/R/ML_PLSModel.R | 15 MachineShop-1.3.0/MachineShop/R/ML_POLRModel.R | 10 MachineShop-1.3.0/MachineShop/R/ML_QDAModel.R | 6 MachineShop-1.3.0/MachineShop/R/ML_RPartModel.R | 17 MachineShop-1.3.0/MachineShop/R/ML_RandomForestModel.R | 11 MachineShop-1.3.0/MachineShop/R/ML_RangerModel.R | 13 MachineShop-1.3.0/MachineShop/R/ML_SVMModel.R | 14 MachineShop-1.3.0/MachineShop/R/ML_StackedModel.R | 8 MachineShop-1.3.0/MachineShop/R/ML_SuperModel.R | 23 MachineShop-1.3.0/MachineShop/R/ML_SurvRegModel.R | 4 MachineShop-1.3.0/MachineShop/R/ML_TreeModel.R | 4 MachineShop-1.3.0/MachineShop/R/ML_XGBModel.R | 11 MachineShop-1.3.0/MachineShop/R/MachineShop-package.R | 17 MachineShop-1.3.0/MachineShop/R/ModelFrame.R | 295 ++ MachineShop-1.3.0/MachineShop/R/ModelRecipe.R |only MachineShop-1.3.0/MachineShop/R/append.R | 28 MachineShop-1.3.0/MachineShop/R/calibration.R | 159 + MachineShop-1.3.0/MachineShop/R/confusion.R | 49 MachineShop-1.3.0/MachineShop/R/convert.R | 20 MachineShop-1.3.0/MachineShop/R/data.R |only MachineShop-1.3.0/MachineShop/R/dependence.R | 43 MachineShop-1.3.0/MachineShop/R/diff.R | 22 MachineShop-1.3.0/MachineShop/R/extract.R |only MachineShop-1.3.0/MachineShop/R/fit.R | 44 MachineShop-1.3.0/MachineShop/R/grid.R | 15 MachineShop-1.3.0/MachineShop/R/lift.R | 21 MachineShop-1.3.0/MachineShop/R/metricinfo.R | 2 MachineShop-1.3.0/MachineShop/R/metrics-factor.R | 56 MachineShop-1.3.0/MachineShop/R/metrics-numeric.R | 48 MachineShop-1.3.0/MachineShop/R/modelinfo.R | 2 MachineShop-1.3.0/MachineShop/R/performance.R | 56 MachineShop-1.3.0/MachineShop/R/performance_curve.R | 69 MachineShop-1.3.0/MachineShop/R/plots.R | 6 MachineShop-1.3.0/MachineShop/R/predict.R | 27 MachineShop-1.3.0/MachineShop/R/predictors.R |only MachineShop-1.3.0/MachineShop/R/resample.R | 123 - MachineShop-1.3.0/MachineShop/R/response.R | 59 MachineShop-1.3.0/MachineShop/R/show.R | 85 MachineShop-1.3.0/MachineShop/R/summary.R | 6 MachineShop-1.3.0/MachineShop/R/survival.R | 351 ++ MachineShop-1.3.0/MachineShop/R/tune.R | 47 MachineShop-1.3.0/MachineShop/R/utils.R | 118 - MachineShop-1.3.0/MachineShop/R/varimp.R | 38 MachineShop-1.3.0/MachineShop/README.md | 21 MachineShop-1.3.0/MachineShop/data |only MachineShop-1.3.0/MachineShop/inst/doc/Introduction.R | 79 MachineShop-1.3.0/MachineShop/inst/doc/Introduction.Rmd | 238 +- MachineShop-1.3.0/MachineShop/inst/doc/Introduction.html | 1757 +++++++-------- MachineShop-1.3.0/MachineShop/inst/doc/MLModels.html | 4 MachineShop-1.3.0/MachineShop/man/BARTMachineModel.Rd | 4 MachineShop-1.3.0/MachineShop/man/BARTModel.Rd | 4 MachineShop-1.3.0/MachineShop/man/CForestModel.Rd | 4 MachineShop-1.3.0/MachineShop/man/CoxModel.Rd | 2 MachineShop-1.3.0/MachineShop/man/GLMModel.Rd | 4 MachineShop-1.3.0/MachineShop/man/GLMNetModel.Rd | 4 MachineShop-1.3.0/MachineShop/man/ICHomes.Rd |only MachineShop-1.3.0/MachineShop/man/LARSModel.Rd | 4 MachineShop-1.3.0/MachineShop/man/LMModel.Rd | 4 MachineShop-1.3.0/MachineShop/man/MLControl.Rd | 10 MachineShop-1.3.0/MachineShop/man/MLMetric.Rd | 2 MachineShop-1.3.0/MachineShop/man/MLModel.Rd | 11 MachineShop-1.3.0/MachineShop/man/MachineShop-package.Rd | 17 MachineShop-1.3.0/MachineShop/man/ModelFrame-methods.Rd | 26 MachineShop-1.3.0/MachineShop/man/NNetModel.Rd | 4 MachineShop-1.3.0/MachineShop/man/PLSModel.Rd | 4 MachineShop-1.3.0/MachineShop/man/POLRModel.Rd | 6 MachineShop-1.3.0/MachineShop/man/RandomForestModel.Rd | 4 MachineShop-1.3.0/MachineShop/man/SVMModel.Rd | 6 MachineShop-1.3.0/MachineShop/man/StackedModel.Rd | 6 MachineShop-1.3.0/MachineShop/man/SuperModel.Rd | 6 MachineShop-1.3.0/MachineShop/man/SurvMatrix.Rd | 15 MachineShop-1.3.0/MachineShop/man/XGBModel.Rd | 2 MachineShop-1.3.0/MachineShop/man/calibration.Rd | 20 MachineShop-1.3.0/MachineShop/man/confusion.Rd | 7 MachineShop-1.3.0/MachineShop/man/diff-methods.Rd | 2 MachineShop-1.3.0/MachineShop/man/dot-.Rd | 7 MachineShop-1.3.0/MachineShop/man/extract-methods.Rd |only MachineShop-1.3.0/MachineShop/man/fit-methods.Rd | 11 MachineShop-1.3.0/MachineShop/man/lift.Rd | 7 MachineShop-1.3.0/MachineShop/man/metrics.Rd | 10 MachineShop-1.3.0/MachineShop/man/performance.Rd | 19 MachineShop-1.3.0/MachineShop/man/performance_curve.Rd | 4 MachineShop-1.3.0/MachineShop/man/predict.Rd | 18 MachineShop-1.3.0/MachineShop/man/resample-methods.Rd | 13 MachineShop-1.3.0/MachineShop/man/response-methods.Rd | 20 MachineShop-1.3.0/MachineShop/man/t.test.Rd | 10 MachineShop-1.3.0/MachineShop/man/tune-methods.Rd | 27 MachineShop-1.3.0/MachineShop/tests/testthat/Rplots.pdf |binary MachineShop-1.3.0/MachineShop/vignettes/Introduction.Rmd | 238 +- MachineShop-1.3.0/MachineShop/vignettes/bibliography.bib | 71 121 files changed, 3399 insertions(+), 2538 deletions(-)
Title: Accelerating 'ggplot2'
Description: The aim of 'ggplot2' is to aid in visual data investigations. This
focus has led to a lack of facilities for composing specialised plots.
'ggforce' aims to be a collection of mainly new stats and geoms that fills
this gap. All additional functionality is aimed to come through the official
extension system so using 'ggforce' should be a stable experience.
Author: Thomas Lin Pedersen [cre, aut]
(<https://orcid.org/0000-0002-5147-4711>),
RStudio [cph]
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>
Diff between ggforce versions 0.2.1 dated 2019-03-12 and 0.2.2 dated 2019-04-23
DESCRIPTION | 8 MD5 | 8 NEWS.md | 7 R/sina.R | 2 inst/doc/Visual_Guide.html | 379 ++++++++++++++++++++++----------------------- 5 files changed, 205 insertions(+), 199 deletions(-)
Title: Spatiotemporal Arrays, Raster and Vector Data Cubes
Description: Reading, manipulating, writing and plotting
spatiotemporal arrays (raster and vector data cubes) in 'R', using 'GDAL'
bindings provided by 'sf', and 'NetCDF' bindings by 'ncmeta' and 'RNetCDF'.
Author: Edzer Pebesma [aut, cre] (<https://orcid.org/0000-0001-8049-7069>),
Michael Sumner [ctb] (<https://orcid.org/0000-0002-2471-7511>),
Etienne Racine [ctb],
Adriano Fantini [ctb],
David Blodgett [ctb]
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between stars versions 0.3-0 dated 2019-02-24 and 0.3-1 dated 2019-04-23
DESCRIPTION | 23 +++--- MD5 | 138 ++++++++++++++++++++------------------ NAMESPACE | 10 ++ NEWS.md | 6 + R/aggregate.R | 36 +++++++--- R/dimensions.R | 107 +++++++++++++++++------------ R/geom.R |only R/init.R | 2 R/intervals.R | 21 +++++ R/ncdf.R | 157 ++++++++++++++++++++++++++++++++++++++------ R/ops.R | 34 +++++++-- R/plot.R | 13 ++- R/proxy.R | 67 +++++++++++++----- R/read.R | 4 - R/sf.R | 13 --- R/spacetime.R | 16 ++-- R/stars.R | 87 +++++++++++++++++++----- R/subset.R | 29 +++++--- R/tidyverse.R | 28 +++++-- R/warp.R | 3 R/write.R | 57 ++++++++++++--- build/vignette.rds |binary inst/doc/stars1.html | 115 +++++++++++++++++++++++++------- inst/doc/stars2.html | 142 ++++++++++++++++++++++++++++----------- inst/doc/stars3.html | 86 +++++++++++++++++++++--- inst/doc/stars4.html | 67 ++++++++++++++++++ inst/doc/stars5.R | 4 - inst/doc/stars5.Rmd | 4 - inst/doc/stars5.html | 70 ++++++++++++++++++- inst/docker/trusty |only inst/nc/bcsd_obs_1999.nc |binary inst/nc/reduced.R |only inst/nc/reduced.nc |binary inst/nc/test_stageiv_xyt.nc |binary man/aggregate.stars.Rd | 3 man/plot.stars.Rd | 5 + man/read_ncdf.Rd | 15 ++-- man/st_apply.Rd | 10 ++ man/st_as_sf.Rd | 2 man/st_coordinates.Rd | 13 ++- man/st_crop.Rd | 5 + man/write_stars.Rd | 4 - tests/aggregate.R | 2 tests/aggregate.Rout.save | 30 ++++---- tests/area.R | 2 tests/area.Rout.save | 11 +-- tests/curvilinear.R | 2 tests/curvilinear.Rout.save | 11 +-- tests/gridtypes.R | 4 - tests/gridtypes.Rout.save | 39 ++++------ tests/nc.Rout.save | 4 - tests/netcdf.R | 1 tests/netcdf.Rout.save | 41 +++++------ tests/plot.R | 2 tests/plot.Rout.save | 11 +-- tests/predict.R |only tests/predict.Rout.save |only tests/proxy.R | 1 tests/proxy.Rout.save | 71 ++++++++++--------- tests/rasterize.R | 2 tests/rasterize.Rout.save | 13 +-- tests/redimension.R | 2 tests/redimension.Rout.save | 53 +++++++------- tests/sp.R | 2 tests/sp.Rout.save | 11 +-- tests/stars.R | 2 tests/stars.Rout.save | 47 ++++++++----- tests/testthat.R | 2 tests/testthat.Rout.save | 13 +-- tests/warp.R | 5 - tests/warp.Rout.save | 13 +-- vignettes/contour.png |only vignettes/stars5.Rmd | 4 - 73 files changed, 1241 insertions(+), 556 deletions(-)
Title: Tools for Spatial Data
Description: For curve, surface and function fitting with an emphasis
on splines, spatial data and spatial statistics. The major methods
include cubic, and thin plate splines, Kriging, and compactly supported
covariance functions for large data sets. The splines and Kriging methods are
supported by functions that can determine the smoothing parameter
(nugget and sill variance) and other covariance function parameters by cross
validation and also by restricted maximum likelihood. For Kriging
there is an easy to use function that also estimates the correlation
scale (range parameter). A major feature is that any covariance function
implemented in R and following a simple format can be used for
spatial prediction. There are also many useful functions for plotting
and working with spatial data as images. This package also contains
an implementation of sparse matrix methods for large spatial data
sets and currently requires the sparse matrix (spam) package. Use
help(fields) to get started and for an overview. The fields source
code is deliberately commented and provides useful explanations of
numerical details as a companion to the manual pages. The commented
source code can be viewed by expanding source code version
and looking in the R subdirectory. The reference for fields can be generated
by the citation function in R and has DOI <doi:10.5065/D6W957CT>. Development
of this package was supported in part by the National Science Foundation Grant
1417857 and the National Center for Atmospheric Research. See the Fields URL
for a vignette on using this package and some background on spatial statistics.
Author: Douglas Nychka [aut, cre],
Reinhard Furrer [aut],
John Paige [aut],
Stephan Sain [aut]
Maintainer: Douglas Nychka <douglasnychka@gmail.com>
Diff between fields versions 9.6.1 dated 2019-04-22 and 9.7 dated 2019-04-23
DESCRIPTION | 15 + MD5 | 265 +++++++++++++++++----------------- R/Krig.family.R | 4 R/QSreg.R |only R/color.scale.R | 8 - R/fastTps.family.R | 6 R/fields.style.R | 3 R/image.family.R | 5 R/mKrig.R | 9 - R/print.spatialProcess.R | 13 + R/print.summary.spatialProcess.R | 4 R/printGCVWarnings.R | 8 - R/profile.R | 4 inst/CITATION | 2 man/BD.Rd | 2 man/CO.Rd | 2 man/CO2.Rd | 2 man/CovarianceUpper.Rd | 2 man/Exponential.Rd | 2 man/FORTRAN.internal.Rd | 2 man/Krig.Amatrix.Rd | 2 man/Krig.Rd | 2 man/Krig.engine.default.Rd | 2 man/Krig.null.function.Rd | 2 man/Krig.replicates.Rd | 5 man/MLESpatialProcess.Rd | 2 man/NorthAmericanRainfall.Rd | 2 man/QTps.Rd | 34 +++- man/RCMexample.Rd | 2 man/REML.test.Rd | 2 man/RMprecip.Rd | 2 man/Tps.Rd | 20 +- man/US.Rd | 2 man/US.dat.Rd | 2 man/Wendland.Rd | 2 man/WorldBank.Rd | 2 man/add.image.Rd | 2 man/arrow.plot.Rd | 2 man/as.image.Rd | 2 man/as.surface.Rd | 2 man/bplot.Rd | 2 man/bplot.xy.Rd | 2 man/colorbar.plot.Rd | 2 man/compactToMat.Rd | 2 man/cover.design.Rd | 2 man/drape.plot.Rd | 2 man/exp.cov.Rd | 2 man/fields-internal.Rd | 2 man/fields-stuff.Rd | 2 man/fields.Rd | 27 +-- man/fields.grid.Rd | 2 man/fields.hints.Rd | 2 man/fields.tests.Rd | 2 man/flame.Rd | 2 man/gcv.Krig.Rd | 2 man/grid.list.Rd | 2 man/image.cov.Rd | 2 man/image.plot.Rd | 2 man/image.smooth.Rd | 2 man/image2lz.Rd | 2 man/interp.surface.Rd | 2 man/lennon.Rd | 2 man/mKrig.MLE.Rd | 6 man/mKrig.Rd | 6 man/mKrigMLE.Rd | 6 man/minitri.Rd | 2 man/ozone.Rd | 2 man/ozone2.Rd | 2 man/plot.Krig.Rd | 2 man/plot.surface.Rd | 2 man/poly.image.Rd | 2 man/predict.Krig.Rd | 2 man/predictSE.Krig.Rd | 2 man/predictSurface.Rd | 2 man/print.Krig.Rd | 2 man/pushpin.Rd | 2 man/qsreg.Rd | 2 man/quilt.plot.Rd | 2 man/rat.diet.Rd | 2 man/rdist.Rd | 2 man/rdist.earth.Rd | 2 man/registeredC.Rd | 2 man/ribbon.plot.Rd | 2 man/set.panel.Rd | 2 man/sim.Krig.Rd | 2 man/sim.rf.Rd | 2 man/smooth.2d.Rd | 2 man/spam2lz.Rd | 2 man/spatialProcess.Rd | 2 man/splint.Rd | 2 man/sreg.Rd | 2 man/stats.Rd | 2 man/stats.bin.Rd | 2 man/summary.Krig.Rd | 2 man/summary.ncdf.Rd | 2 man/supportsArg.Rd | 2 man/surface.Krig.Rd | 2 man/tim.colors.Rd | 4 man/transformx.Rd | 2 man/vgram.Rd | 2 man/vgram.matrix.Rd | 2 man/world.Rd | 2 man/xline.Rd | 2 man/yline.Rd | 2 tests/Krig.Z.test.Rout.save | 8 - tests/Krig.se.W.Rout.save | 8 - tests/Krig.se.grid.test.Rout.save | 8 - tests/Krig.se.test.Rout.save | 8 - tests/Krig.test.Rout.save | 8 - tests/Krig.test.W.Rout.save | 8 - tests/KrigGCVREML.test.Rout.save | 8 - tests/Likelihood.test.Rout.save | 8 - tests/REMLest.test.Rout.save | 8 - tests/Tps.test.Rout.save | 8 - tests/Wend.test.Rout.save | 8 - tests/cov.test.Rout.save | 8 - tests/cov.test2.Rout.save | 8 - tests/derivative.test.Rout.save | 8 - tests/diag.multiply.test.Rout.save | 8 - tests/diagonal2.test.Rout.save | 8 - tests/evlpoly.test.Rout.save | 8 - tests/fastTpsPredict.test.Rout.save | 8 - tests/mKrig.MLE.test.Rout.save | 10 - tests/mKrig.Z.Rout.save | 8 - tests/mKrig.parameters.test.Rout.save | 8 - tests/mKrig.se.test.Rout.save | 8 - tests/mKrig.test.R | 2 tests/mKrig.test.Rout.save | 6 tests/mKrigMLETest.Rout.save | 8 - tests/mKrigREMLTest.Rout.save | 8 - tests/misc.test.Rout.save | 8 - tests/spam.test.Rout.save | 8 - tests/sreg.test.Rout.save | 8 - tests/vgram.test.Rout.save | 8 - 134 files changed, 453 insertions(+), 399 deletions(-)
Title: Interface to 'ECMWF' and 'CDS' Data Web Services
Description: Programmatic interface to the European Centre for Medium-Range
Weather Forecasts dataset web services (ECMWF; <https://www.ecmwf.int/>)
and Copernicus's Climate Data Store (CDS;
<https://cds.climate.copernicus.eu>). Allows for easy downloads of weather
forecasts and climate reanalysis data in R.
Author: Koen Hufkens [aut, cre] (<https://orcid.org/0000-0002-5070-8109>),
Reto Stauffer [ctb] (<https://orcid.org/0000-0002-3798-5507>),
Elio Campitelli [ctb] (<https://orcid.org/0000-0002-7742-9230>)
Maintainer: Koen Hufkens <koen.hufkens@gmail.com>
Diff between ecmwfr versions 1.2.0 dated 2019-04-19 and 1.2.1 dated 2019-04-23
DESCRIPTION | 6 +- MD5 | 30 +++++------ R/addin.R | 9 +++ R/zzz.R | 14 ++++- inst/doc/advanced_vignette.R | 66 +++++++------------------ inst/doc/advanced_vignette.Rmd | 28 ---------- inst/doc/advanced_vignette.html | 44 +--------------- inst/doc/cds_vignette.html | 4 - inst/doc/webapi_vignette.R | 47 ++++------------- inst/doc/webapi_vignette.Rmd | 37 ++------------ inst/doc/webapi_vignette.html | 19 ++++--- tests/testthat/test_cds.R | 48 +++++++++--------- tests/testthat/test_ecmwf.r | 87 +++++++++++++++++++++++++-------- tests/testthat/test_helper_functions.R | 66 +++++++++++++++++++------ vignettes/advanced_vignette.Rmd | 28 ---------- vignettes/webapi_vignette.Rmd | 37 ++------------ 16 files changed, 244 insertions(+), 326 deletions(-)
Title: Authentication Services for Azure Active Directory
Description: Provides Azure Active Directory (AAD) authentication functionality for R users of Microsoft's 'Azure' cloud <https://azure.microsoft.com/>. Use this package to obtain 'OAuth' 2.0 tokens for services including Azure Resource Manager, Azure Storage and others. It supports both AAD v1.0 and v2.0, as well as multiple authentication methods, including device code and resource owner grant. Tokens are cached in a user-specific directory obtained using the 'rappdirs' package. The interface is based on the 'OAuth' framework in the 'httr' package, but customised and streamlined for Azure.
Author: Hong Ooi [aut, cre],
httr development team [ctb] (Original OAuth listener code),
Scott Holden [ctb] (Advice on AAD authentication),
Chris Stone [ctb] (Advice on AAD authentication),
Microsoft [cph]
Maintainer: Hong Ooi <hongooi@microsoft.com>
Diff between AzureAuth versions 1.0.1 dated 2019-03-22 and 1.0.2 dated 2019-04-23
DESCRIPTION | 6 MD5 | 20 - NEWS.md | 5 R/AzureAuth.R | 8 R/token.R | 2 README.md | 4 inst/doc/token.Rmd | 6 inst/doc/token.html | 584 ++++++++++++++++++++++++++++--------------------- man/AzureR_dir.Rd | 2 man/get_azure_token.Rd | 2 vignettes/token.Rmd | 6 11 files changed, 372 insertions(+), 273 deletions(-)
Title: Multiple Locus Association Mapping on a Genome-Wide Scale
Description: An implementation of multiple-locus association mapping on a genome-wide scale. 'Eagle' can handle inbred and outbred study populations, populations of arbitrary unknown complexity, and data larger than the memory capacity of the computer. Since 'Eagle' is based on linear mixed models, it is best suited to the analysis of data on continuous traits. However, it can tolerate non-normal data. 'Eagle' reports, as its findings, the best set of snp in strongest association with a trait. For users unfamiliar with R, to perform an analysis, run 'OpenGUI()'. This opens a web browser to the menu-driven user interface for the input of data, and for performing genome-wide analysis.
Author: Andrew George [aut, cre],
Joshua Bowden [ctb],
Ryan Stephenson [ctb],
Hyun Kang [ctb],
Noah Zaitlen [ctb],
Claire Wade [ctb],
Andrew Kirby [ctb],
David Heckerman [ctb],
Mark Daly [ctb],
Eleazar Eskin [ctb]
Maintainer: Andrew George <andrew.george@csiro.au>
Diff between Eagle versions 1.3.0 dated 2019-01-31 and 1.4.0 dated 2019-04-23
DESCRIPTION | 6 - MD5 | 16 ++-- R/AM.R | 22 +++--- R/ReadPheno.R | 22 ++++-- R/build_design_matrix.R | 2 R/form_results.R | 22 ++++-- R/summary_am.R | 165 ++++++++++++++++++++++++++---------------------- inst/shiny_app/app.R | 2 man/SummaryAM.Rd | 13 --- 9 files changed, 153 insertions(+), 117 deletions(-)
Title: Poisson-Tweedie Generalized Linear Mixed Model
Description: Fits Poisson-Tweedie generalized linear mixed model.
Likelihood approximation based on adaptive Gauss Hermite quadrature rule.
Author: Mirko Signorelli [aut, cre],
Pietro Spitali [aut],
Roula Tsonaka [aut]
Maintainer: Mirko Signorelli <m.signorelli@lumc.nl>
Diff between ptmixed versions 0.0.1 dated 2019-02-12 and 0.0.2 dated 2019-04-23
DESCRIPTION | 6 +- MD5 | 14 ++--- R/GHpoints.R | 11 ++-- R/loglik.R | 7 +- R/ptmixed.R | 51 +++++++++--------- R/starting-values.R | 139 +++++++++++++++++++++------------------------------ man/loglik.pt.1re.Rd | 6 -- man/ptmixed.Rd | 21 +++---- 8 files changed, 116 insertions(+), 139 deletions(-)
Title: Unicode Data and Utilities
Description: Data from Unicode 12.0.0 and related utilities.
Author: Kurt Hornik [aut, cre] (<https://orcid.org/0000-0003-4198-9911>)
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between Unicode versions 11.0.0-1 dated 2018-06-30 and 12.0.0-1 dated 2019-04-23
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/basics.R | 2 +- R/sysdata.rda |binary 4 files changed, 8 insertions(+), 8 deletions(-)
Title: Species-Habitat Associations
Description: Analyse species-habitat associations in R. Therefore, information about the
location of the species is needed and about the environmental conditions. To test
for significance habitat associations, one of the two components is randomized.
Methods are mainly based on Plotkin et al. (2000) <doi:10.1006/jtbi.2000.2158> and
Harms et al. (2001) <doi:10.1111/j.1365-2745.2001.00615.x>.
Author: Maximillian H.K. Hesselbarth [aut, cre]
(<https://orcid.org/0000-0003-1125-9918>),
Marco Sciaini [aut] (<https://orcid.org/0000-0002-3042-5435>)
Maintainer: Maximillian H.K. Hesselbarth <maximilian.hesselbarth@uni-goettingen.de>
Diff between shar versions 0.3 dated 2019-03-25 and 0.3.1 dated 2019-04-23
shar-0.3.1/shar/DESCRIPTION | 6 shar-0.3.1/shar/MD5 | 77 +++----- shar-0.3.1/shar/NEWS.md | 6 shar-0.3.1/shar/R/calculate_energy.R | 2 shar-0.3.1/shar/R/classify_habitats.R | 102 +++++------ shar-0.3.1/shar/R/estimate_pcf_fast.R | 2 shar-0.3.1/shar/R/fit_point_process.R | 2 shar-0.3.1/shar/R/randomize_raster.R | 2 shar-0.3.1/shar/R/reconstruct_marks.R | 2 shar-0.3.1/shar/R/reconstruct_pattern.R | 2 shar-0.3.1/shar/R/results_habitat_association.R | 4 shar-0.3.1/shar/R/translate_raster.R | 2 shar-0.3.1/shar/build/vignette.rds |binary shar-0.3.1/shar/inst/doc/get_started.R |only shar-0.3.1/shar/inst/doc/get_started.Rmd |only shar-0.3.1/shar/inst/doc/get_started.html |only shar-0.3.1/shar/man/calculate_energy.Rd | 2 shar-0.3.1/shar/man/classify_habitats.Rd | 10 - shar-0.3.1/shar/man/estimate_pcf_fast.Rd | 2 shar-0.3.1/shar/man/figures/README-plot-random_pattern-1.png |binary shar-0.3.1/shar/man/figures/README-plot-random_pattern-2.png |binary shar-0.3.1/shar/man/figures/README-plot_habitat-random-1.png |binary shar-0.3.1/shar/man/fit_point_process.Rd | 2 shar-0.3.1/shar/man/randomize_raster.Rd | 2 shar-0.3.1/shar/man/reconstruct_marks.Rd | 2 shar-0.3.1/shar/man/reconstruct_pattern.Rd | 2 shar-0.3.1/shar/man/results_habitat_association.Rd | 4 shar-0.3.1/shar/man/translate_raster.Rd | 2 shar-0.3.1/shar/src/Makevars | 2 shar-0.3.1/shar/src/Makevars.win | 2 shar-0.3.1/shar/tests/testthat/test-estimate_pcf_fast.R | 7 shar-0.3.1/shar/tests/testthat/test-randomize_raster.R | 10 - shar-0.3.1/shar/tests/testthat/test-translate_raster.R | 8 shar-0.3.1/shar/vignettes/get_started.Rmd |only shar-0.3/shar/inst/doc/background.R |only shar-0.3/shar/inst/doc/background.Rmd |only shar-0.3/shar/inst/doc/background.html |only shar-0.3/shar/inst/doc/publication_record.Rmd |only shar-0.3/shar/inst/doc/publication_record.html |only shar-0.3/shar/inst/doc/reconstruct_multiple_patterns.R |only shar-0.3/shar/inst/doc/reconstruct_multiple_patterns.Rmd |only shar-0.3/shar/inst/doc/reconstruct_multiple_patterns.html |only shar-0.3/shar/vignettes/background.Rmd |only shar-0.3/shar/vignettes/gamma_vs_reconstruction.png |only shar-0.3/shar/vignettes/methods_overview.png |only shar-0.3/shar/vignettes/pattern_reconstruction.gif |only shar-0.3/shar/vignettes/publication_record.Rmd |only shar-0.3/shar/vignettes/random_walk.gif |only shar-0.3/shar/vignettes/reconstruct_multiple_patterns.Rmd |only 49 files changed, 139 insertions(+), 127 deletions(-)
Title: Use 'Python' from Within 'R'
Description: Interact with 'Python' <https://www.python.org/> from within 'R'.
Author: Florian Schwendinger [aut, cre],
Kimyen Truong [ctb]
Maintainer: Florian Schwendinger <FlorianSchwendinger@gmx.at>
Diff between PythonInR versions 0.1-6 dated 2018-09-17 and 0.1-7 dated 2019-04-23
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- R/PyExec.R | 3 +-- R/PythonInR.R | 2 +- README.md | 4 +--- configure | 11 +++-------- man/pyConnect.Rd | 2 +- man/pyExecfile.Rd | 3 +-- src/CastRObjects.c | 2 +- src/Python_Explicit_Linking.h | 3 ++- 10 files changed, 24 insertions(+), 32 deletions(-)
Title: Selected ISO Codes
Description: ISO language, territory, currency, script and character codes.
Provides ISO 639 language codes, ISO 3166 territory codes, ISO 4217
currency codes, ISO 15924 script codes, and the ISO 8859 character codes
as well as the UN M.49 area codes.
Author: Christian Buchta [aut],
Kurt Hornik [aut, cre] (<https://orcid.org/0000-0003-4198-9911>)
Maintainer: Kurt Hornik <Kurt.Hornik@R-project.org>
Diff between ISOcodes versions 2019.02.13 dated 2019-02-13 and 2019.04.22 dated 2019-04-23
DESCRIPTION | 6 +++--- MD5 | 28 ++++++++++++++-------------- data/ISO_15924.rda |binary data/ISO_3166_1.rda |binary data/ISO_3166_2.rda |binary data/ISO_3166_3.rda |binary data/ISO_4217.rda |binary data/ISO_4217_Historic.rda |binary data/ISO_639_2.rda |binary data/ISO_639_3.rda |binary data/ISO_639_3_Retirements.rda |binary data/ISO_639_5.rda |binary data/ISO_8859.rda |binary data/UN_M.49_Countries.rda |binary data/UN_M.49_Regions.rda |binary 15 files changed, 17 insertions(+), 17 deletions(-)
Title: Read and Write Ecological Metadata Language Files
Description: Work with Ecological Metadata Language ('EML') files.
'EML' is a widely used metadata standard in the ecological and
environmental sciences, described in Jones et al. (2006),
<doi:10.1146/annurev.ecolsys.37.091305.110031>.
Author: Carl Boettiger [aut, cre, cph]
(<https://orcid.org/0000-0002-1642-628X>),
Matthew B. Jones [aut] (<https://orcid.org/0000-0003-0077-4738>),
Mitchell Maier [ctb] (<https://orcid.org/0000-0001-6955-0535>),
Bryce Mecum [ctb] (<https://orcid.org/0000-0002-0381-3766>),
Maëlle Salmon [ctb] (<https://orcid.org/0000-0002-2815-0399>),
Jeanette Clark [ctb] (<https://orcid.org/0000-0003-4703-1974>)
Maintainer: Carl Boettiger <cboettig@gmail.com>
Diff between EML versions 1.0.3 dated 2017-05-02 and 2.0.0 dated 2019-04-23
EML-1.0.3/EML/R/classes-stmml.R |only EML-1.0.3/EML/R/classes.R |only EML-1.0.3/EML/R/coercions.R |only EML-1.0.3/EML/R/eml_find.R |only EML-1.0.3/EML/R/eml_view.R |only EML-1.0.3/EML/R/get_TextType.R |only EML-1.0.3/EML/R/get_coverage.R |only EML-1.0.3/EML/R/is_standardUnit.R |only EML-1.0.3/EML/R/literature_coercions.R |only EML-1.0.3/EML/R/methods.R |only EML-1.0.3/EML/R/s4_to_xml.R |only EML-1.0.3/EML/R/show_methods.R |only EML-1.0.3/EML/R/xml_to_s4.R |only EML-1.0.3/EML/R/zzz.R |only EML-1.0.3/EML/inst/doc/metadata-repositories.R |only EML-1.0.3/EML/inst/doc/metadata-repositories.Rmd |only EML-1.0.3/EML/inst/doc/metadata-repositories.html |only EML-1.0.3/EML/inst/doc/parsing-EML.R |only EML-1.0.3/EML/inst/doc/parsing-EML.Rmd |only EML-1.0.3/EML/inst/doc/parsing-EML.html |only EML-1.0.3/EML/inst/notebook |only EML-1.0.3/EML/inst/templates |only EML-1.0.3/EML/inst/units |only EML-1.0.3/EML/inst/xsd |only EML-1.0.3/EML/man/c-methods.Rd |only EML-1.0.3/EML/man/eml_find.Rd |only EML-1.0.3/EML/man/eml_locate_schema.Rd |only EML-1.0.3/EML/man/eml_view.Rd |only EML-1.0.3/EML/man/get_TextType.Rd |only EML-1.0.3/EML/man/get_taxonomicCoverage.Rd |only EML-1.0.3/EML/tests/testthat/eml-utf8.xml |only EML-1.0.3/EML/tests/testthat/example-eml-invalid.xml |only EML-1.0.3/EML/tests/testthat/example-eml-valid.xml |only EML-1.0.3/EML/tests/testthat/test-TextType.R |only EML-1.0.3/EML/tests/testthat/test-attributes.R |only EML-1.0.3/EML/tests/testthat/test-coercions.R |only EML-1.0.3/EML/tests/testthat/test-coverage.R |only EML-1.0.3/EML/tests/testthat/test-eml.R |only EML-1.0.3/EML/tests/testthat/test-physical.R |only EML-1.0.3/EML/tests/testthat/test-testfiles.R |only EML-1.0.3/EML/tests/testthat/test-validation.R |only EML-1.0.3/EML/tests/testthat/test-view.R |only EML-1.0.3/EML/vignettes/metadata-repositories.Rmd |only EML-1.0.3/EML/vignettes/parsing-EML.Rmd |only EML-2.0.0/EML/DESCRIPTION | 75 EML-2.0.0/EML/LICENSE |only EML-2.0.0/EML/MD5 | 306 -- EML-2.0.0/EML/NAMESPACE | 41 EML-2.0.0/EML/NEWS.md | 26 EML-2.0.0/EML/R/as_person.R |only EML-2.0.0/EML/R/eml2.R |only EML-2.0.0/EML/R/eml_get.R | 92 EML-2.0.0/EML/R/eml_validate.R | 113 - EML-2.0.0/EML/R/get_attributes.R | 365 --- EML-2.0.0/EML/R/get_unitList.R | 69 EML-2.0.0/EML/R/get_unit_id.R |only EML-2.0.0/EML/R/read_eml.R | 33 EML-2.0.0/EML/R/set_TextType.R | 70 EML-2.0.0/EML/R/set_attributes.R | 591 +++-- EML-2.0.0/EML/R/set_coverage.R | 349 +-- EML-2.0.0/EML/R/set_methods.R | 46 EML-2.0.0/EML/R/set_physical.R | 116 - EML-2.0.0/EML/R/set_responsibleParty.R |only EML-2.0.0/EML/R/set_software.R |only EML-2.0.0/EML/R/set_unitList.R | 160 - EML-2.0.0/EML/R/shiny_attributes.R |only EML-2.0.0/EML/R/shiny_attributes_app.R |only EML-2.0.0/EML/R/sysdata.rda |only EML-2.0.0/EML/R/template_constructor.R |only EML-2.0.0/EML/R/write_eml.R | 73 EML-2.0.0/EML/README.md | 380 ++- EML-2.0.0/EML/build/vignette.rds |binary EML-2.0.0/EML/data |only EML-2.0.0/EML/inst/WORDLIST |only EML-2.0.0/EML/inst/doc/creating-EML.R | 141 - EML-2.0.0/EML/inst/doc/creating-EML.Rmd | 184 - EML-2.0.0/EML/inst/doc/creating-EML.html | 798 ++++--- EML-2.0.0/EML/inst/doc/working-with-units.R | 75 EML-2.0.0/EML/inst/doc/working-with-units.Rmd | 149 - EML-2.0.0/EML/inst/doc/working-with-units.html | 1521 ++------------ EML-2.0.0/EML/inst/examples/create-full-eml.R | 193 + EML-2.0.0/EML/inst/examples/eml_summary.R | 2 EML-2.0.0/EML/inst/examples/hf-205.R | 16 EML-2.0.0/EML/inst/examples/hf205-01-TPexp1.csv |only EML-2.0.0/EML/inst/examples/resolve_references.R | 15 EML-2.0.0/EML/inst/extdata |only EML-2.0.0/EML/inst/htmlwidgets |only EML-2.0.0/EML/inst/udunits |only EML-2.0.0/EML/man/build_factors.Rd |only EML-2.0.0/EML/man/build_units_table.Rd |only EML-2.0.0/EML/man/detect_delim.Rd |only EML-2.0.0/EML/man/eml.Rd |only EML-2.0.0/EML/man/eml_get.Rd | 36 EML-2.0.0/EML/man/eml_validate.Rd | 17 EML-2.0.0/EML/man/figures |only EML-2.0.0/EML/man/get_attributes.Rd | 14 EML-2.0.0/EML/man/get_numberType.Rd |only EML-2.0.0/EML/man/get_unitList.Rd | 12 EML-2.0.0/EML/man/get_unit_id.Rd |only EML-2.0.0/EML/man/htmlwidgets_attributes.Rd |only EML-2.0.0/EML/man/is_standardUnit.Rd | 5 EML-2.0.0/EML/man/read_eml.Rd | 13 EML-2.0.0/EML/man/reexports.Rd |only EML-2.0.0/EML/man/set_TextType.Rd | 2 EML-2.0.0/EML/man/set_attributes.Rd | 30 EML-2.0.0/EML/man/set_coverage.Rd | 21 EML-2.0.0/EML/man/set_methods.Rd | 5 EML-2.0.0/EML/man/set_physical.Rd | 24 EML-2.0.0/EML/man/set_responsibleParty.Rd |only EML-2.0.0/EML/man/set_software.Rd |only EML-2.0.0/EML/man/set_taxonomicCoverage.Rd | 68 EML-2.0.0/EML/man/set_unitList.Rd | 60 EML-2.0.0/EML/man/shiny_attributes.Rd |only EML-2.0.0/EML/man/table_to_r.Rd |only EML-2.0.0/EML/man/write_eml.Rd | 5 EML-2.0.0/EML/tests/spelling.R |only EML-2.0.0/EML/tests/testthat/test-additional-tests.R |only EML-2.0.0/EML/tests/testthat/test-eml2.R |only EML-2.0.0/EML/tests/testthat/test-eml_get.R | 54 EML-2.0.0/EML/tests/testthat/test-get_attributes.R |only EML-2.0.0/EML/tests/testthat/test-set_attributes.R |only EML-2.0.0/EML/tests/testthat/test-set_responsibleParty.R |only EML-2.0.0/EML/tests/testthat/test-set_taxonomicCoverage.R |only EML-2.0.0/EML/tests/testthat/test-units.R | 137 - EML-2.0.0/EML/tests/testthat/test_detect_delim.R |only EML-2.0.0/EML/tests/testthat/test_get_unit_id.R |only EML-2.0.0/EML/vignettes/creating-EML.Rmd | 184 - EML-2.0.0/EML/vignettes/working-with-units.Rmd | 149 - 128 files changed, 2871 insertions(+), 3964 deletions(-)
Title: Estimate ED50 and Its Confidence Interval
Description: Functions of five estimation method for ED50 (50 percent effective dose) are provided, and they are respectively
Dixon-Mood method (1948) <doi:10.2307/2280071>, Choi's original turning point method (1990) <doi:10.2307/2531453> and it's modified version given by
us, as well as logistic regression and isotonic regression. Besides, the package also supports
comparison between two estimation results.
Author: Yongbo Gan, Zhijian Yang, Wei Mei
Maintainer: Yongbo Gan <yongbogan@whu.edu.cn>
Diff between ed50 versions 0.1.0 dated 2018-11-28 and 0.1.1 dated 2019-04-23
DESCRIPTION | 10 +++---- MD5 | 12 ++++---- NAMESPACE | 13 +++++++-- R/estimate.R | 20 ++++++++------ R/generateData.R | 72 ++++++++++++++++++++++++++++++---------------------- man/estimate.Rd | 7 +++-- man/generateData.Rd | 9 ++++-- 7 files changed, 87 insertions(+), 56 deletions(-)
Title: Methods for Joint Dimension Reduction and Clustering
Description: A class of methods that combine dimension reduction and clustering of continuous, categorical or mixed-type data. For continuous data, the package contains implementations of factorial K-means (Vichi and Kiers 2001; <DOI:10.1016/S0167-9473(00)00064-5>) and reduced K-means (De Soete and Carroll 1994; <DOI:10.1007/978-3-642-51175-2_24>); both methods that combine principal component analysis with K-means clustering. For categorical data, the package provides MCA K-means (Hwang, Dillon and Takane 2006; <DOI:10.1007/s11336-004-1173-x>), i-FCB (Iodice D'Enza and Palumbo 2013, <DOI:10.1007/s00180-012-0329-x>) and Cluster Correspondence Analysis (van de Velden, Iodice D'Enza and Palumbo 2017; <DOI:10.1007/s11336-016-9514-0>), which combine multiple correspondence analysis with K-means. For mixed-type data, it provides mixed Reduced K-means and mixed Factorial K-means (van de Velden, Iodice D'Enza and Markos 2019; <DOI:10.1002/wics.1456>), which combine PCA for mixed-type data with K-means.
Author: Angelos Markos [aut, cre], Alfonso Iodice D'Enza [aut], Michel van de Velden [ctb]
Maintainer: Angelos Markos <amarkos@gmail.com>
Diff between clustrd versions 1.2.2 dated 2018-05-06 and 1.3 dated 2019-04-23
clustrd-1.2.2/clustrd/R/multiplot.R |only clustrd-1.3/clustrd/DESCRIPTION | 13 clustrd-1.3/clustrd/MD5 | 65 +- clustrd-1.3/clustrd/NAMESPACE | 17 clustrd-1.3/clustrd/R/EmptyKmeans.r | 6 clustrd-1.3/clustrd/R/MCAk.r | 189 ++++++- clustrd-1.3/clustrd/R/boot_clusmca.R |only clustrd-1.3/clustrd/R/boot_cluspca.R |only clustrd-1.3/clustrd/R/boot_cluspcamix.R |only clustrd-1.3/clustrd/R/clusCA.R | 148 +++++ clustrd-1.3/clustrd/R/clusmca.R | 15 clustrd-1.3/clustrd/R/cluspca.R | 735 ++++++++++++++++++++++------- clustrd-1.3/clustrd/R/cluspcamix.R |only clustrd-1.3/clustrd/R/clusval.R | 2 clustrd-1.3/clustrd/R/distEuclidean.R |only clustrd-1.3/clustrd/R/fitted.cluspcamix.R |only clustrd-1.3/clustrd/R/global_bootclus.R |only clustrd-1.3/clustrd/R/iFCB.r | 118 ++++ clustrd-1.3/clustrd/R/local_bootclus.R |only clustrd-1.3/clustrd/R/outOfIndependence.r | 3 clustrd-1.3/clustrd/R/plot.clusmca.R | 8 clustrd-1.3/clustrd/R/plot.cluspcamix.R |only clustrd-1.3/clustrd/R/plot.tuneclus.R | 4 clustrd-1.3/clustrd/R/print.cluspcamix.R |only clustrd-1.3/clustrd/R/summary.cluspcamix.R |only clustrd-1.3/clustrd/R/tune_clusmca.R | 2 clustrd-1.3/clustrd/R/tune_cluspca.R | 5 clustrd-1.3/clustrd/R/tune_cluspcamix.R |only clustrd-1.3/clustrd/R/tuneclus.R | 6 clustrd-1.3/clustrd/data/bribery.rda |only clustrd-1.3/clustrd/data/diamond.rda |only clustrd-1.3/clustrd/data/hsq.rda |binary clustrd-1.3/clustrd/man/bribery.Rd |only clustrd-1.3/clustrd/man/clusmca.Rd | 13 clustrd-1.3/clustrd/man/cluspca.Rd | 17 clustrd-1.3/clustrd/man/cluspcamix.Rd |only clustrd-1.3/clustrd/man/diamond.Rd |only clustrd-1.3/clustrd/man/global_bootclus.Rd |only clustrd-1.3/clustrd/man/hsq.Rd | 64 +- clustrd-1.3/clustrd/man/local_bootclus.Rd |only clustrd-1.3/clustrd/man/plot.clusmca.Rd | 2 clustrd-1.3/clustrd/man/plot.cluspca.Rd | 2 clustrd-1.3/clustrd/man/plot.cluspcamix.Rd |only clustrd-1.3/clustrd/man/tuneclus.Rd | 46 + 44 files changed, 1140 insertions(+), 340 deletions(-)
Title: Local Correlation, Spatial Inequalities, Geographically Weighted
Regression and Other Tools
Description: Provides researchers and educators with easy-to-learn user friendly tools for calculating
key spatial statistics and to apply simple as well as advanced methods of spatial analysis in real data.
These include: Local Pearson and Geographically Weighted Pearson Correlation Coefficients,
Spatial Inequality Measures (Gini, Spatial Gini, LQ, Focal LQ), Spatial Autocorrelation
(Global and Local Moran's I), several Geographically Weighted Regression techniques and other
Spatial Analysis tools (other geographically weighted statistics). This package also contains functions for
measuring the significance of each statistic calculated, mainly based on Monte Carlo simulations.
Author: Stamatis Kalogirou [aut, cre]
Maintainer: Stamatis Kalogirou <stamatis@lctools.science>
Diff between lctools versions 0.2-6 dated 2017-08-04 and 0.2-7 dated 2019-04-23
DESCRIPTION | 12 +++---- MD5 | 28 ++++++++--------- R/gwr.bw.R | 2 - R/l.moransI.R | 57 ++++++++++++++++++++++++++++------- R/moransI.v.R | 4 +- build/vignette.rds |binary data/GR.Municipalities.RData |binary data/VotesGR.RData |binary inst/doc/SpatialAutocorrelation.Rmd | 2 - inst/doc/SpatialAutocorrelation.pdf |binary inst/doc/SpatialInequalities.pdf |binary man/GR.Municipalities.Rd | 2 - man/l.moransI.Rd | 9 ++++- man/lctools-package.Rd | 4 +- vignettes/SpatialAutocorrelation.Rmd | 2 - 15 files changed, 82 insertions(+), 40 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-08-31 1.0.9
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-10-30 1.1.0
Title: Multivariate VAM Fitting
Description: Fits a multivariate value-added model (VAM), see Broatch, Green, and Karl (2018) <doi:10.32614/RJ-2018-033> and Broatch and Lohr (2012) <doi:10.3102/1076998610396900>, with normally distributed test scores and a binary outcome indicator. A pseudo-likelihood approach, Wolfinger (1993) <doi:10.1080/00949659308811554>, is used for the estimation of this joint generalized linear mixed model. The inner loop of the pseudo-likelihood routine (estimation of a linear mixed model) occurs in the framework of the EM algorithm presented by Karl, Yang, and Lohr (2013) <DOI:10.1016/j.csda.2012.10.004>. This material is based upon work supported by the National Science Foundation under grants DRL-1336027 and DRL-1336265.
Author: Andrew T. Karl, Jennifer Broatch, and Jennifer Green
Maintainer: Andrew Karl <akarl@asu.edu>
Diff between RealVAMS versions 0.4-1 dated 2018-04-20 and 0.4-3 dated 2019-04-23
RealVAMS-0.4-1/RealVAMS/NEWS |only RealVAMS-0.4-3/RealVAMS/DESCRIPTION | 12 RealVAMS-0.4-3/RealVAMS/MD5 | 22 RealVAMS-0.4-3/RealVAMS/NAMESPACE | 1 RealVAMS-0.4-3/RealVAMS/R/REML_Rm.R |only RealVAMS-0.4-3/RealVAMS/R/vp_cp.R | 3259 ++++++++++++------------ RealVAMS-0.4-3/RealVAMS/inst |only RealVAMS-0.4-3/RealVAMS/man/REML_Rm.Rd |only RealVAMS-0.4-3/RealVAMS/man/RealVAMS-package.Rd | 8 RealVAMS-0.4-3/RealVAMS/man/RealVAMS.Rd | 7 RealVAMS-0.4-3/RealVAMS/src/Makevars | 15 RealVAMS-0.4-3/RealVAMS/src/Makevars.win | 17 RealVAMS-0.4-3/RealVAMS/src/REML_Rm.cpp |only RealVAMS-0.4-3/RealVAMS/src/init.c | 4 14 files changed, 1733 insertions(+), 1612 deletions(-)
Title: R Client for the Microsoft Cognitive Services 'Text-to-Speech'
REST API
Description: R Client for the Microsoft Cognitive Services
'Text-to-Speech' REST API, including voice synthesis. A valid account
must be registered at the Microsoft Cognitive Services website
<https://www.microsoft.com/cognitive-services/> in order to
obtain a (free) API key. Without an API key, this package will not
work properly.
Author: John Muschelli [aut, cre] (<https://orcid.org/0000-0001-6469-1750>)
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between mscstts versions 0.4.0 dated 2018-11-19 and 0.5.1 dated 2019-04-23
mscstts-0.4.0/mscstts/man/create_ssml.Rd |only mscstts-0.4.0/mscstts/man/get_ms_tts_key.Rd |only mscstts-0.4.0/mscstts/man/get_ms_tts_token.Rd |only mscstts-0.4.0/mscstts/man/language_to_ms_name.Rd |only mscstts-0.5.1/mscstts/DESCRIPTION | 12 mscstts-0.5.1/mscstts/MD5 | 40 - mscstts-0.5.1/mscstts/NAMESPACE | 24 mscstts-0.5.1/mscstts/NEWS.md | 10 mscstts-0.5.1/mscstts/R/create_ssml.R | 44 + mscstts-0.5.1/mscstts/R/language_to_ms_name.R | 15 mscstts-0.5.1/mscstts/R/ms_list_voices.R |only mscstts-0.5.1/mscstts/R/ms_locales.R | 646 +++++++++++++++++-- mscstts-0.5.1/mscstts/R/ms_synthesize.R | 154 +++- mscstts-0.5.1/mscstts/R/ms_tts_auth.R | 101 ++ mscstts-0.5.1/mscstts/R/show.token.R | 8 mscstts-0.5.1/mscstts/README.md | 22 mscstts-0.5.1/mscstts/man/figures |only mscstts-0.5.1/mscstts/man/ms_create_ssml.Rd |only mscstts-0.5.1/mscstts/man/ms_get_tts_key.Rd |only mscstts-0.5.1/mscstts/man/ms_get_tts_token.Rd |only mscstts-0.5.1/mscstts/man/ms_language_to_ms_name.Rd |only mscstts-0.5.1/mscstts/man/ms_list_voices.Rd |only mscstts-0.5.1/mscstts/man/ms_read_synthesis.Rd |only mscstts-0.5.1/mscstts/man/ms_synthesize.Rd | 42 - mscstts-0.5.1/mscstts/man/print.token.Rd | 3 mscstts-0.5.1/mscstts/tests/testthat/test-api_keys.R | 8 mscstts-0.5.1/mscstts/tests/testthat/test-synth.R | 2 27 files changed, 947 insertions(+), 184 deletions(-)
Title: Constrained Generalized Additive Model
Description: A constrained generalized additive model is fitted by the cgam routine. Given a set of predictors, each of which may have a shape or order restrictions, the maximum likelihood estimator for the constrained generalized additive model is found using an iteratively re-weighted cone projection algorithm. The ShapeSelect routine chooses a subset of predictor variables and describes the component relationships with the response. For each predictor, the user needs only specify a set of possible shape or order restrictions. A model selection method chooses the shapes and orderings of the relationships as well as the variables. The cone information criterion (CIC) is used to select the best combination of variables and shapes. A genetic algorithm may be used when the set of possible models is large. In addition, the cgam routine implements a two-dimensional isotonic regression using warped-plane splines without additivity assumptions. It can also fit a convex or concave regression surface with triangle splines without additivity assumptions. See Mary C. Meyer (2013)<doi:10.1080/10485252.2013.797577> for more details.
Author: Mary C. Meyer and Xiyue Liao
Maintainer: Xiyue Liao <liaoxiyue2011@gmail.com>
Diff between cgam versions 1.12 dated 2018-11-08 and 1.13 dated 2019-04-23
ChangeLog | 4 + DESCRIPTION | 8 +-- MD5 | 10 ++-- R/cgam.R | 128 +++++++++++++++++++++++++++++++++++++++++------------------- R/cgamm.R | 97 +++++++++++++++++++++++++++++++++++++++------ man/cgam.Rd | 4 - 6 files changed, 188 insertions(+), 63 deletions(-)