Title: Methods and Measures for Brain, Cognitive, and Psychometric
Network Analysis
Description: Implements network analysis and graph theory measures used in neuroscience, cognitive science, and psychology. Methods include various filtering methods and approaches such as threshold, dependency (Kenett, Tumminello, Madi, Gur-Gershogoren, Mantegna, & Ben-Jacob, 2010 <doi:10.1371/journal.pone.0015032>), Information Filtering Networks (Barfuss, Massara, Di Matteo, & Aste, 2016 <doi:10.1103/PhysRevE.94.062306>), and Efficiency-Cost Optimization (Fallani, Latora, & Chavez, 2017 <doi:10.1371/journal.pcbi.1005305>). Brain methods include the recently developed Connectome Predictive Modeling (see references in package). Also implements several network measures including local network characteristics (e.g., centrality), community-level network characteristics (e.g., community centrality), global network characteristics (e.g., clustering coefficient), and various other measures associated with the reliability and reproducibility of network analysis.
Author: Alexander Christensen
Maintainer: Alexander Christensen <alexpaulchristensen@gmail.com>
Diff between NetworkToolbox versions 1.2.0 dated 2018-07-25 and 1.2.1 dated 2018-09-19
DESCRIPTION | 10 +++++----- MD5 | 48 +++++++++++++++++++++++++----------------------- NAMESPACE | 1 + NEWS | 10 ++++++++++ R/LoGo.R | 7 ++++++- R/comm.close.R | 27 +++++++++++++-------------- R/hybrid.R | 8 ++------ R/nams.R | 23 ++++++++++++----------- R/net.coverage.R | 14 ++++++++++++-- R/resp.rep.R |only R/threshold.R | 6 +----- man/LoGo.Rd | 4 +++- man/bootgen.Rd | 4 ++-- man/comcat.Rd | 4 ++-- man/comm.close.Rd | 12 +++++++++--- man/cpmEV.Rd | 4 ++-- man/cpmIV.Rd | 7 ++++--- man/depend.Rd | 4 ++-- man/hybrid.Rd | 5 ++--- man/nams.Rd | 12 +++++------- man/net.coverage.Rd | 12 +++++++++++- man/neuralnetfilter.Rd | 4 ++-- man/resp.rep.Rd |only man/smallworldness.Rd | 4 ++-- man/stable.Rd | 4 ++-- man/threshold.Rd | 8 ++------ 26 files changed, 137 insertions(+), 105 deletions(-)
More information about NetworkToolbox at CRAN
Permanent link
Title: Descriptive Statistics, Transition Plots, and More
Description: Tools for making the descriptive "Table 1" used in medical
articles, a transition plot for showing changes between categories,
flow charts by extending the grid package, a method for
variable selection based on the SVD, Bézier lines with arrows complementing the
ones in the 'grid' package, and more.
Author: Max Gordon <max@gforge.se>
Maintainer: Max Gordon <max@gforge.se>
Diff between Gmisc versions 1.6.2 dated 2018-06-20 and 1.6.4 dated 2018-09-19
DESCRIPTION | 10 - MD5 | 79 ++++++------- NEWS | 8 + R/Gmisc.R | 2 R/fastDoCall.R | 2 README.md | 4 inst/doc/Descriptives.html | 56 ++++----- inst/doc/Grid-based_flowcharts.html | 20 +-- inst/doc/Transition-class.html | 36 +++--- inst/doc/transitionPlot.Rmd | 2 inst/doc/transitionPlot.html | 40 +++--- inst/examples/data-SCB_example.R | 2 inst/include/Gmisc.h | 6 - man/Gmisc-package.Rd | 2 man/bezierArrowGradient.Rd | 4 man/bezierArrowSmpl.Rd | 6 - man/box.Rd | 11 - man/boxPropGrob.Rd | 16 +- man/connect.Rd | 10 - man/describeFactors.Rd | 1 man/describeMean.Rd | 1 man/describeMedian.Rd | 4 man/describeProp.Rd | 5 man/docx_document.Rd | 4 man/fastDoCall.Rd | 2 man/figCapNo.Rd | 1 man/figCapNoLast.Rd | 1 man/figCapNoNext.Rd | 1 man/getDescriptionStatsBy.Rd | 14 +- man/getPval.Rd | 1 man/mergeDesc.Rd | 1 man/prTcPlotArrows.Rd | 6 - man/prTpGetBoxPositions.Rd | 4 man/prTpPlotArrows.Rd | 7 - man/prTpPlotBoxes.Rd | 10 - man/transitionPlot.Rd | 15 +- src/Gmisc_lines.cpp | 48 ++++---- src/bezierArrowFn.cpp | 12 +- tests/testthat/Rplots.pdf |only tests/testthat/test-getDescriptionStats.R | 176 +++++++++++++++--------------- vignettes/transitionPlot.Rmd | 2 41 files changed, 328 insertions(+), 304 deletions(-)
Title: Extension of `data.frame`
Description: Fast aggregation of large data (e.g. 100GB in RAM), fast ordered joins, fast add/modify/delete of columns by group using no copies at all, list columns, friendly and fast character-separated-value read/write. Offers a natural and flexible syntax, for faster development.
Author: Matt Dowle [aut, cre],
Arun Srinivasan [aut],
Jan Gorecki [ctb],
Michael Chirico [ctb],
Pasha Stetsenko [ctb],
Tom Short [ctb],
Steve Lianoglou [ctb],
Eduard Antonyan [ctb],
Markus Bonsch [ctb],
Hugh Parsonage [ctb]
Maintainer: Matt Dowle <mattjdowle@gmail.com>
Diff between data.table versions 1.11.4 dated 2018-05-27 and 1.11.6 dated 2018-09-19
DESCRIPTION | 6 MD5 | 142 NAMESPACE | 3 NEWS.md | 97 R/IDateTime.R | 91 R/as.data.table.R | 6 R/between.R | 15 R/bmerge.R | 10 R/cedta.R | 19 R/data.table.R | 243 - R/fcast.R | 4 R/foverlaps.R | 2 R/fread.R | 80 R/fwrite.R | 19 R/onAttach.R | 2 R/onLoad.R | 4 R/setkey.R | 73 R/setops.R | 9 R/test.data.table.R | 76 R/utils.R | 29 build/vignette.rds |binary inst/doc/datatable-benchmarking.Rmd | 102 inst/doc/datatable-benchmarking.html | 400 +- inst/doc/datatable-faq.html | 1417 +++++---- inst/doc/datatable-importing.html | 428 +- inst/doc/datatable-intro.R | 33 inst/doc/datatable-intro.Rmd | 238 - inst/doc/datatable-intro.html | 1785 ++++++------ inst/doc/datatable-keys-fast-subset.R | 13 inst/doc/datatable-keys-fast-subset.Rmd | 19 inst/doc/datatable-keys-fast-subset.html | 1224 ++++---- inst/doc/datatable-reference-semantics.html | 928 +++--- inst/doc/datatable-reshape.html | 816 +++-- inst/doc/datatable-secondary-indices-and-auto-indexing.Rmd | 8 inst/doc/datatable-secondary-indices-and-auto-indexing.html | 845 +++-- inst/tests/other.Rraw | 15 inst/tests/tests.Rraw | 369 +- man/IDateTime.Rd | 5 man/J.Rd | 9 man/as.matrix.Rd | 53 man/assign.Rd | 2 man/chmatch.Rd | 8 man/data.table.Rd | 24 man/dcast.data.table.Rd | 2 man/foverlaps.Rd | 2 man/frank.Rd | 10 man/fread.Rd | 14 man/fsort.Rd | 10 man/fwrite.Rd | 2 man/setNumericRounding.Rd | 2 man/setcolorder.Rd | 4 man/setkey.Rd | 2 man/setops.Rd | 11 man/setorder.Rd | 12 man/special-symbols.Rd | 2 man/truelength.Rd | 4 man/tstrsplit.Rd | 2 src/assign.c | 42 src/data.table.h | 2 src/fmelt.c | 47 src/forder.c | 32 src/fread.c | 13 src/freadR.c | 4 src/fwrite.c | 8 src/gsumm.c | 149 - src/rbindlist.c | 27 src/reorder.c | 2 src/uniqlist.c | 140 vignettes/datatable-benchmarking.Rmd | 102 vignettes/datatable-intro.Rmd | 238 - vignettes/datatable-keys-fast-subset.Rmd | 19 vignettes/datatable-secondary-indices-and-auto-indexing.Rmd | 8 72 files changed, 6278 insertions(+), 4305 deletions(-)
Title: Flexible and Efficient Evaluation of Principal
Surrogates/Treatment Effect Modifiers
Description: Implements estimation and testing procedures for evaluating an intermediate biomarker response as a principal surrogate of a clinical response to treatment (i.e., principal stratification effect modification analysis), as described in Juraska M, Huang Y, and Gilbert PB, Inference on treatment effect modification by biomarker response in a three-phase sampling design (under review). The methods avoid the restrictive 'placebo structural risk' modeling assumption common to past methods and further improve robustness by the use of nonparametric kernel smoothing for biomarker density estimation. A randomized controlled two-group clinical efficacy trial is assumed with an ordered categorical or continuous univariate biomarker response measured at a fixed timepoint post-randomization and with a univariate baseline surrogate measure allowed to be observed in only a subset of trial participants with an observed biomarker response (see the flexible three-phase sampling design in the paper for details). Bootstrap-based procedures are available for pointwise and simultaneous confidence intervals and testing of four relevant hypotheses. Summary and plotting functions are provided for estimation results.
Author: Michal Juraska [aut, cre]
Maintainer: Michal Juraska <mjuraska@fredhutch.org>
Diff between pssmooth versions 1.0.0 dated 2018-07-29 and 1.0.1 dated 2018-09-19
DESCRIPTION | 11 +- MD5 | 18 ++-- NEWS |binary R/pssmooth.R | 180 +++++++++++++++++++++++++++++------------------ man/bootRiskCurve.Rd | 15 +-- man/plotMCEPcurve.Rd | 15 +++ man/riskCurve.Rd | 12 +-- man/summary.riskCurve.Rd | 4 - man/testConstancy.Rd | 4 - man/testEquality.Rd | 8 +- 10 files changed, 160 insertions(+), 107 deletions(-)
Title: Simulates LOX Drop Testing
Description: Generates simulated data representing the LOX drop testing
process (also known as impact testing). A simulated process allows for
accelerated study of test behavior. Functions are provided to simulate
trials, test series, and groups of test series. Functions for creating plots
specific to this process are also included. Test attributes and criteria can
be set arbitrarily. This work is not endorsed by or affiliated with NASA.
See "ASTM G86-17, Standard Test Method for Determining Ignition Sensitivity
of Materials to Mechanical Impact in Ambient Liquid Oxygen and Pressurized
Liquid and Gaseous Oxygen Environments" <doi:10.1520/G0086-17>.
Author: Chad Ross [aut, cre]
Maintainer: Chad Ross <chad.ross@gmail.com>
Diff between droptest versions 0.1.2 dated 2018-08-18 and 0.1.3 dated 2018-09-19
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 3 +++ R/dtrials.R | 2 +- 4 files changed, 10 insertions(+), 7 deletions(-)
Title: A XML-Based Testing Framework for Automated Component Tests of R
Packages
Description: This provides a framework for R packages developed for
a regulatory environment. It is based on the 'testthat' unit testing system and provides the adapter
functionalities for XML-based test case definition as well as for standardized
reporting of the test results.
Author: Sebastian Wolf [aut, cre],
Matthias Pfeifer [aut, ctb],
Sergej Potapov [ctb],
Roche [cph, fnd]
Maintainer: Sebastian Wolf <sebastian.wolf.sw1@roche.com>
Diff between RTest versions 1.1.8.0 dated 2018-08-24 and 1.1.9.0 dated 2018-09-19
DESCRIPTION | 14 MD5 | 172 +++++----- R/utils.test.R | 60 --- R/utils.xmlRead.R | 46 -- build/vignette.rds |binary inst/doc/RTest.R | 176 +++++----- inst/doc/RTest.pdf |binary man/RTest.Rd | 62 +-- man/RTest.cat.Rd | 40 +- man/RTest.print.Rd | 40 +- man/RTestCase-class.Rd | 124 +++---- man/RTestCase.Rd | 256 +++++++-------- man/RTestCollection-class.Rd | 52 +-- man/clearTest.Rd | 54 +-- man/exec.Rd | 126 +++---- man/execAdapter.Rd | 90 ++--- man/execCache.Rd | 101 ++--- man/getExecDetails.html.Rd | 59 +-- man/getExecStates.Rd | 56 +-- man/getExecSummary.Rd | 50 +- man/getExecSummary.html.Rd | 50 +- man/getID.Rd | 50 +- man/getRTM.Rd | 60 +-- man/getRTMInMatrixShape.Rd | 72 ++-- man/getRTMInfos.Rd | 68 +-- man/getSynopsis.Rd | 50 +- man/getTC.Rd | 48 +- man/getTestFor.Rd | 50 +- man/getTestResult.Rd | 50 +- man/getType.Rd | 50 +- man/getValidTCs.Rd | 56 +-- man/getXMLRoot.Rd | 50 +- man/getXMLSourceFileName.Rd | 50 +- man/getXMLSourcePath.Rd | 50 +- man/htmlify_string.Rd | 56 +-- man/importTC.Rd | 48 +- man/importTCsFromDir.Rd | 64 +-- man/initializeTests.Rd | 48 +- man/normalizeDate.Rd | 78 ++-- man/package_md5.Rd | 58 +-- man/png2base64.Rd | 66 +-- man/readXMLInputData.Rd | 84 ++-- man/setTestMethod.Rd | 102 ++--- man/show-RTestCase-method.Rd | 42 +- man/show-RTestCollection-method.Rd | 78 ++-- man/summary-RTestCollection-method.Rd | 48 +- man/systemInfo.RInst.Rd | 40 +- man/systemInfo.host.Rd | 40 +- man/systemInfo.packages.Rd | 52 +-- man/test.RTest.funct_01.Rd | 42 +- man/test.RTest.test_returnValue_data.frame_cellbycell.Rd | 42 +- man/test.Rd | 116 +++--- man/test_execution.Rd | 114 +++--- man/test_fun.Rd | 58 +-- man/test_manualCheck_confirmWindow.Rd | 66 +-- man/test_manualCheck_file.Rd | 66 +-- man/test_returnValue_data.frame_cellbycell.Rd | 58 +-- man/test_returnValue_data.frame_shape.Rd | 162 ++++----- man/test_returnValue_image.Rd | 122 +++---- man/test_returnValue_list_nodebynode.Rd | 58 +-- man/test_returnValue_variable.Rd | 119 +++--- man/test_returnValue_vector_elementbyelement.Rd | 118 +++--- man/writeExecSummary.html.Rd | 75 ++-- man/xmlFromList.Rd | 104 +++--- man/xmlRead.default.Rd | 112 +++--- man/xmlReadData_data.frame.Rd | 80 ++-- man/xmlReadData_image.Rd | 72 ++-- man/xmlReadData_list.Rd | 90 ++--- man/xmlReadData_text.Rd | 60 +-- man/xmlReadData_to_list.Rd | 92 ++--- man/xmlReadData_variable.Rd | 62 +-- man/xmlReadData_vector.Rd | 62 +-- man/xmlWriteContext.Rd | 60 +-- man/xmlWriteData_data.frame.Rd | 54 +-- man/xmlWriteData_variable.Rd | 54 +-- man/xmlWriteData_vector.Rd | 54 +-- man/xmlWriteInputData.Rd | 44 +- man/xmlWriteSynopsis.Rd | 76 ++-- man/xmlWriteTest.Rd | 52 +-- man/xmlWriteTestFunction.Rd | 76 ++-- man/xmlWriteTestSpec.Rd | 44 +- man/xmlWriteTest_data.frame_cellbycell.Rd | 70 ++-- man/xmlWriteTest_execution.Rd | 56 +-- man/xmlWriteTest_list_nodebynode.Rd | 66 +-- man/xmlWriteTest_variable.Rd | 58 +-- man/xmlWriteTest_vector_elementbyelement.Rd | 66 +-- man/xmlWriteTests.Rd | 44 +- 87 files changed, 3002 insertions(+), 3058 deletions(-)
Title: Knowledge Space Theory
Description: Knowledge space theory by Doignon and Falmagne (1999)
<doi:10.1007/978-3-642-58625-5> is a set- and order-theoretical
framework, which proposes mathematical formalisms to operationalize
knowledge structures in a particular domain. The 'kst' package provides
basic functionalities to generate, handle, and manipulate knowledge
structures and knowledge spaces.
Author: Christina Stahl [aut],
David Meyer [aut],
Cord Hockemeyer [aut, cre]
Maintainer: Cord Hockemeyer <cord.hockemeyer@uni-graz.at>
Diff between kst versions 0.4-0 dated 2018-04-13 and 0.5-0 dated 2018-09-19
Changelog | 13 ++++++- DESCRIPTION | 15 +++++--- MD5 | 57 ++++++++++++++++++-------------- NAMESPACE | 8 ++++ R/as.famset.R | 1 R/as.relation.kfamset.R |only R/closure.kbase.R | 76 ++++++++++++++++++++++--------------------- R/closure.kfamset.R |only R/kbase.R | 2 - R/kdomain.R | 9 +++-- R/kfamset.R |only R/kneighbourhood.R | 1 R/kspace.R | 2 - R/kstructure.R | 2 - R/plot.kbase.R |only R/plot.kfamset.R |only R/reduction.kfamset.R |only build/vignette.rds |binary inst/doc/kst.R | 40 +++++++++++++++++------ inst/doc/kst.Rnw | 80 ++++++++++++++++++++++++++++++++++++++++------ inst/doc/kst.pdf |binary man/as.binaryMatrix.Rd | 4 +- man/as.famset.Rd | 2 - man/as.relation.Rd | 9 +++-- man/closure.Rd | 17 ++++++--- man/kdomain.Rd | 7 ++-- man/kneighbourhood.Rd | 2 - man/kstructure.Rd | 7 +++- man/plot.Rd | 19 ++++++---- man/reduction.Rd | 4 +- man/space_property.Rd | 7 ++-- vignettes/kst-classes.png |only vignettes/kst.Rnw | 80 ++++++++++++++++++++++++++++++++++++++++------ 33 files changed, 332 insertions(+), 132 deletions(-)
Title: Prediction of Therapeutic Success
Description: In personalized medicine, one wants to know, for a given patient and his or her outcome for a predictor (pre-treatment variable), how likely it is that a treatment will be more beneficial than an alternative treatment. This package allows for the quantification of the predictive causal association (i.e., the association between the predictor variable and the individual causal effect of the treatment) and related metrics. Part of this software has been developed using funding provided from the European Union's 7th Framework Programme for research, technological development and demonstration under Grant Agreement no 602552.
Author: Wim Van der Elst, Ariel Alonso & Geert Molenberghs
Maintainer: Wim Van der Elst <Wim.vanderelst@gmail.com>
Diff between EffectTreat versions 0.3 dated 2017-01-27 and 0.4 dated 2018-09-19
DESCRIPTION | 8 ++++---- MD5 | 13 ++++++++----- NAMESPACE | 3 +++ NEWS | 2 ++ R/Min.Max.Multivar.PCA.R | 28 ++++++++++++++-------------- R/Min.R2.delta.R |only man/Min.R2.delta.Rd |only man/plot.Min.R2.delta.Rd |only man/summary.gen.Rd | 40 +++++++++++++++++++++------------------- 9 files changed, 52 insertions(+), 42 deletions(-)
Title: S3 Infrastructure for Regular and Irregular Time Series (Z's
Ordered Observations)
Description: An S3 class with methods for totally ordered indexed
observations. It is particularly aimed at irregular time series
of numeric vectors/matrices and factors. zoo's key design goals
are independence of a particular index/date/time class and
consistency with ts and base R by providing methods to extend
standard generics.
Author: Achim Zeileis [aut, cre] (<https://orcid.org/0000-0003-0918-3766>),
Gabor Grothendieck [aut],
Jeffrey A. Ryan [aut],
Joshua M. Ulrich [ctb],
Felix Andrews [ctb]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between zoo versions 1.8-3 dated 2018-07-16 and 1.8-4 dated 2018-09-19
DESCRIPTION | 8 ++++---- MD5 | 20 ++++++++++---------- NAMESPACE | 6 ++++++ NEWS | 7 +++++++ R/zzz.R | 6 ++++-- build/vignette.rds |binary inst/doc/zoo-design.pdf | 14 +++++++------- inst/doc/zoo-faq.pdf |binary inst/doc/zoo-quickref.pdf |binary inst/doc/zoo-read.pdf |binary inst/doc/zoo.pdf |binary 11 files changed, 38 insertions(+), 23 deletions(-)
Title: Run 'R CMD check' from 'R' and Capture Results
Description: Run 'R CMD check' from 'R' programmatically, and capture the
results of the individual checks.
Author: Gábor Csárdi
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between rcmdcheck versions 1.2.1 dated 2016-09-28 and 1.3.0 dated 2018-09-19
rcmdcheck-1.2.1/rcmdcheck/inst/screenshot.png |only rcmdcheck-1.2.1/rcmdcheck/tests/testthat/test.R |only rcmdcheck-1.3.0/rcmdcheck/DESCRIPTION | 22 rcmdcheck-1.3.0/rcmdcheck/LICENSE | 4 rcmdcheck-1.3.0/rcmdcheck/MD5 | 96 +++- rcmdcheck-1.3.0/rcmdcheck/NAMESPACE | 24 + rcmdcheck-1.3.0/rcmdcheck/R/api.R |only rcmdcheck-1.3.0/rcmdcheck/R/auto_clean.R |only rcmdcheck-1.3.0/rcmdcheck/R/background.R |only rcmdcheck-1.3.0/rcmdcheck/R/build.R | 46 +- rcmdcheck-1.3.0/rcmdcheck/R/callback.R | 225 ++++++---- rcmdcheck-1.3.0/rcmdcheck/R/compare.R | 110 ---- rcmdcheck-1.3.0/rcmdcheck/R/comparison-summary.R |only rcmdcheck-1.3.0/rcmdcheck/R/comparison.R |only rcmdcheck-1.3.0/rcmdcheck/R/cran.R | 12 rcmdcheck-1.3.0/rcmdcheck/R/package.R | 150 ++++++ rcmdcheck-1.3.0/rcmdcheck/R/parse.R | 162 +++++-- rcmdcheck-1.3.0/rcmdcheck/R/print.R | 66 ++ rcmdcheck-1.3.0/rcmdcheck/R/session-info.R |only rcmdcheck-1.3.0/rcmdcheck/R/styles.R |only rcmdcheck-1.3.0/rcmdcheck/R/utils.R | 90 +++- rcmdcheck-1.3.0/rcmdcheck/R/xopen.R |only rcmdcheck-1.3.0/rcmdcheck/inst/NEWS.md | 42 + rcmdcheck-1.3.0/rcmdcheck/inst/README.markdown | 12 rcmdcheck-1.3.0/rcmdcheck/inst/rcmdcheck.gif |only rcmdcheck-1.3.0/rcmdcheck/man/check_details.Rd |only rcmdcheck-1.3.0/rcmdcheck/man/compare_checks.Rd | 5 rcmdcheck-1.3.0/rcmdcheck/man/compare_to_cran.Rd | 7 rcmdcheck-1.3.0/rcmdcheck/man/cran_check_flavours.Rd | 1 rcmdcheck-1.3.0/rcmdcheck/man/cran_check_results.Rd | 1 rcmdcheck-1.3.0/rcmdcheck/man/data_frame.Rd | 17 rcmdcheck-1.3.0/rcmdcheck/man/myrep.Rd | 1 rcmdcheck-1.3.0/rcmdcheck/man/parse_check.Rd | 6 rcmdcheck-1.3.0/rcmdcheck/man/parse_check_url.Rd | 1 rcmdcheck-1.3.0/rcmdcheck/man/print.rcmdcheck.Rd |only rcmdcheck-1.3.0/rcmdcheck/man/print.rcmdcheck_comparison.Rd |only rcmdcheck-1.3.0/rcmdcheck/man/rcmdcheck.Rd | 35 + rcmdcheck-1.3.0/rcmdcheck/man/rcmdcheck_process.Rd |only rcmdcheck-1.3.0/rcmdcheck/man/xopen.rcmdcheck.Rd |only rcmdcheck-1.3.0/rcmdcheck/tests/testthat/REDCapR-fail.log |only rcmdcheck-1.3.0/rcmdcheck/tests/testthat/REDCapR-ok.log |only rcmdcheck-1.3.0/rcmdcheck/tests/testthat/RSQLServer-install |only rcmdcheck-1.3.0/rcmdcheck/tests/testthat/bad1/DESCRIPTION | 9 rcmdcheck-1.3.0/rcmdcheck/tests/testthat/bad1/NAMESPACE | 2 rcmdcheck-1.3.0/rcmdcheck/tests/testthat/bad1/R/package.R | 13 rcmdcheck-1.3.0/rcmdcheck/tests/testthat/bad1/man |only rcmdcheck-1.3.0/rcmdcheck/tests/testthat/bad1/tests |only rcmdcheck-1.3.0/rcmdcheck/tests/testthat/bad1/vignettes |only rcmdcheck-1.3.0/rcmdcheck/tests/testthat/bad2 |only rcmdcheck-1.3.0/rcmdcheck/tests/testthat/bikedata-ok.log |only rcmdcheck-1.3.0/rcmdcheck/tests/testthat/comparison-newly-failing.txt |only rcmdcheck-1.3.0/rcmdcheck/tests/testthat/dataonderivatives-test |only rcmdcheck-1.3.0/rcmdcheck/tests/testthat/fixtures |only rcmdcheck-1.3.0/rcmdcheck/tests/testthat/helpers.R |only rcmdcheck-1.3.0/rcmdcheck/tests/testthat/minimal-ee.log |only rcmdcheck-1.3.0/rcmdcheck/tests/testthat/minimal-ewn.log |only rcmdcheck-1.3.0/rcmdcheck/tests/testthat/minimal-ok.log |only rcmdcheck-1.3.0/rcmdcheck/tests/testthat/parse-install-fail.txt |only rcmdcheck-1.3.0/rcmdcheck/tests/testthat/parse-test-fail.txt |only rcmdcheck-1.3.0/rcmdcheck/tests/testthat/test-auto_clean.R |only rcmdcheck-1.3.0/rcmdcheck/tests/testthat/test-comparison.R |only rcmdcheck-1.3.0/rcmdcheck/tests/testthat/test-errors.R |only rcmdcheck-1.3.0/rcmdcheck/tests/testthat/test-parse.R |only rcmdcheck-1.3.0/rcmdcheck/tests/testthat/test-rcmdcheck.R |only 64 files changed, 814 insertions(+), 345 deletions(-)
Title: Feature Selection (Including Multiple Solutions) and Bayesian
Networks
Description: Many feature selection methods for a wide range of response variables, including minimal, statistically-equivalent and equally-predictive feature subsets. Bayesian network algorithms and related functions are also included. The package name 'MXM' stands for "Mens eX Machina", meaning "Mind from the Machine" in Latin. Reference: Feature Selection with the R Package MXM: Discovering Statistically Equivalent Feature Subsets, Lagani, V. and Athineou, G. and Farcomeni, A. and Tsagris, M. and Tsamardinos, I. (2017). Journal of Statistical Software, 80(7). <doi:10.18637/jss.v080.i07>.
Author: Michail Tsagris [aut, cre],
Ioannis Tsamardinos [aut, cph],
Vincenzo Lagani [aut, cph],
Giorgos Athineou [aut],
Giorgos Borboudakis [ctb],
Anna Roumpelaki [ctb]
Maintainer: Michail Tsagris <mtsagris@csd.uoc.gr>
Diff between MXM versions 1.3.9 dated 2018-08-27 and 1.4.0 dated 2018-09-19
MXM-1.3.9/MXM/R/waldmmpc.path.R |only MXM-1.3.9/MXM/inst/doc/mxm_mmpc_tutorial.R |only MXM-1.3.9/MXM/inst/doc/mxm_mmpc_tutorial.Rmd |only MXM-1.3.9/MXM/inst/doc/mxm_mmpc_tutorial.html |only MXM-1.3.9/MXM/vignettes/mxm_mmpc_tutorial.Rmd |only MXM-1.4.0/MXM/DESCRIPTION | 9 - MXM-1.4.0/MXM/MD5 | 156 +++++++++++++------------ MXM-1.4.0/MXM/NAMESPACE | 6 MXM-1.4.0/MXM/R/InternalMMPC.R | 15 -- MXM-1.4.0/MXM/R/InternalMMPC.gee.R | 6 MXM-1.4.0/MXM/R/InternalMMPC.glmm.R | 5 MXM-1.4.0/MXM/R/InternalMMPC.timeclass.R | 6 MXM-1.4.0/MXM/R/InternalSES.R | 6 MXM-1.4.0/MXM/R/InternalSES.gee.R | 6 MXM-1.4.0/MXM/R/InternalSES.glmm.R | 6 MXM-1.4.0/MXM/R/InternalSES.timeclass.R | 6 MXM-1.4.0/MXM/R/MMPC.R | 7 - MXM-1.4.0/MXM/R/MMPC.gee.R | 10 - MXM-1.4.0/MXM/R/MMPC.glmm.R | 6 MXM-1.4.0/MXM/R/MMPC.timeclass.R | 11 + MXM-1.4.0/MXM/R/SES.R | 10 - MXM-1.4.0/MXM/R/SES.gee.R | 11 + MXM-1.4.0/MXM/R/SES.glmm.R | 13 +- MXM-1.4.0/MXM/R/SES.timeclass.R | 9 - MXM-1.4.0/MXM/R/boot.gomp.R |only MXM-1.4.0/MXM/R/bs.reg.R | 16 +- MXM-1.4.0/MXM/R/cond.regs.R | 30 ++-- MXM-1.4.0/MXM/R/cv.gomp.R | 2 MXM-1.4.0/MXM/R/cv.mmpc.R | 14 +- MXM-1.4.0/MXM/R/cv.permmmpc.R | 2 MXM-1.4.0/MXM/R/cv.permses.R | 2 MXM-1.4.0/MXM/R/cv.ses.R | 2 MXM-1.4.0/MXM/R/cv.waldmmpc.R | 2 MXM-1.4.0/MXM/R/cv.waldses.R | 2 MXM-1.4.0/MXM/R/cvmmpc.par.R | 10 - MXM-1.4.0/MXM/R/cvpermmmpc.par.R | 4 MXM-1.4.0/MXM/R/cvpermses.par.R | 4 MXM-1.4.0/MXM/R/cvses.par.R | 4 MXM-1.4.0/MXM/R/cvwaldmmpc.par.R | 4 MXM-1.4.0/MXM/R/cvwaldses.par.R | 6 MXM-1.4.0/MXM/R/fbed.lr.R | 4 MXM-1.4.0/MXM/R/gomp.R | 36 ++--- MXM-1.4.0/MXM/R/gomp2.R | 3 MXM-1.4.0/MXM/R/mmpc.model.R | 10 - MXM-1.4.0/MXM/R/mmpc.path.R | 22 +-- MXM-1.4.0/MXM/R/mmpc2.R | 9 - MXM-1.4.0/MXM/R/perm.Internalmmpc.R | 16 -- MXM-1.4.0/MXM/R/perm.Internalses.R | 10 - MXM-1.4.0/MXM/R/perm.mmpc.R | 12 + MXM-1.4.0/MXM/R/perm.mmpc.path.R |only MXM-1.4.0/MXM/R/perm.ses.R | 10 - MXM-1.4.0/MXM/R/plotnetwork.R | 2 MXM-1.4.0/MXM/R/ses.timeclass.model.R | 2 MXM-1.4.0/MXM/R/spml.bsreg.R |only MXM-1.4.0/MXM/R/spml.reg2.R |only MXM-1.4.0/MXM/R/testIndOrdinal.R | 10 - MXM-1.4.0/MXM/R/testIndSPML.R | 29 +++- MXM-1.4.0/MXM/R/univregs.R | 55 ++++---- MXM-1.4.0/MXM/R/wald.Internalmmpc.R | 10 - MXM-1.4.0/MXM/R/wald.Internalses.R | 10 - MXM-1.4.0/MXM/R/wald.mmpc.R | 16 +- MXM-1.4.0/MXM/R/wald.mmpc.path.R |only MXM-1.4.0/MXM/R/wald.ses.R | 10 - MXM-1.4.0/MXM/build/vignette.rds |binary MXM-1.4.0/MXM/inst/doc/FBED_KVerrou_2_5.html | 10 - MXM-1.4.0/MXM/inst/doc/FS_guide.ltx | 3 MXM-1.4.0/MXM/inst/doc/FS_guide.pdf |binary MXM-1.4.0/MXM/inst/doc/MMPC_tutorial.R |only MXM-1.4.0/MXM/inst/doc/MMPC_tutorial.Rmd |only MXM-1.4.0/MXM/inst/doc/MMPC_tutorial.html |only MXM-1.4.0/MXM/inst/doc/Networks_KVerrou.R |only MXM-1.4.0/MXM/inst/doc/Networks_KVerrou.Rmd |only MXM-1.4.0/MXM/inst/doc/Networks_KVerrou.html |only MXM-1.4.0/MXM/inst/doc/SES_KMVerrou_11_12.html | 38 +++--- MXM-1.4.0/MXM/inst/doc/article.pdf |binary MXM-1.4.0/MXM/inst/doc/guide.pdf |binary MXM-1.4.0/MXM/man/MXM-internal.Rd | 5 MXM-1.4.0/MXM/man/MXM-package.Rd | 13 -- MXM-1.4.0/MXM/man/MXMCondIndTests.Rd | 2 MXM-1.4.0/MXM/man/gomp.Rd | 22 +++ MXM-1.4.0/MXM/man/mmpc.path.Rd | 11 + MXM-1.4.0/MXM/man/mmpc2.Rd | 2 MXM-1.4.0/MXM/man/pc.or.Rd | 29 ++-- MXM-1.4.0/MXM/man/pc.skel.Rd | 7 - MXM-1.4.0/MXM/man/testIndSPML.Rd | 6 MXM-1.4.0/MXM/vignettes/FS_guide.ltx | 3 MXM-1.4.0/MXM/vignettes/MMPC_tutorial.Rmd |only MXM-1.4.0/MXM/vignettes/Networks_KVerrou.Rmd |only 88 files changed, 423 insertions(+), 412 deletions(-)
Title: Tools for Handling Spatial Objects
Description: Set of tools for manipulating geographic data. It includes binary access to 'GSHHG' shoreline files. The package also provides interface wrappers for exchanging spatial objects with packages such as 'PBSmapping', 'spatstat', 'maps', 'RArcInfo', 'Stata tmap', 'WinBUGS', 'Mondrian', and others.
Author: Roger Bivand [cre, aut] (<https://orcid.org/0000-0003-2392-6140>),
Nicholas Lewin-Koh [aut],
Edzer Pebesma [ctb],
Eric Archer [ctb],
Adrian Baddeley [ctb],
Nick Bearman [ctb],
Hans-Jörg Bibiko [ctb],
Steven Brey [ctb],
Jonathan Callahan [ctb],
German Carrillo [ctb],
Stéphane Dray [ctb],
David Forrest [ctb],
Michael Friendly [ctb],
Patrick Giraudoux [ctb],
Duncan Golicher [ctb],
Virgilio Gómez Rubio [ctb],
Patrick Hausmann [ctb],
Karl Ove Hufthammer [ctb],
Thomas Jagger [ctb],
Kent Johnson [ctb],
Sebastian Luque [ctb],
Don MacQueen [ctb],
Andrew Niccolai [ctb],
Edzer Pebesma [ctb],
Oscar Perpiñán Lamigueiro [ctb],
Tom Short [ctb],
Greg Snow [ctb],
Ben Stabler [ctb],
Murray Stokely [ctb],
Rolf Turner [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between maptools versions 0.9-3 dated 2018-07-31 and 0.9-4 dated 2018-09-19
ChangeLog | 16 ++++++++++++++++ DESCRIPTION | 12 ++++++------ MD5 | 10 +++++----- NAMESPACE | 15 +++++++++++++++ R/AAA.R | 26 ++++++++++++++------------ inst/doc/combine_maptools.pdf |binary 6 files changed, 56 insertions(+), 23 deletions(-)
Title: Kalman Filter and Smoother for Exponential Family State Space
Models
Description: State space modelling is an efficient and flexible framework for
statistical inference of a broad class of time series and other data. KFAS
includes computationally efficient functions for Kalman filtering, smoothing,
forecasting, and simulation of multivariate exponential family state space models,
with observations from Gaussian, Poisson, binomial, negative binomial, and gamma
distributions. See the paper by Helske (2017) <doi:10.18637/jss.v078.i10> for details.
Author: Jouni Helske <jouni.helske@iki.fi>
Maintainer: Jouni Helske <jouni.helske@iki.fi>
Diff between KFAS versions 1.3.2 dated 2018-05-21 and 1.3.3 dated 2018-09-19
ChangeLog | 5 DESCRIPTION | 8 MD5 | 86 +-- NAMESPACE | 156 +++--- R/KFS.R | 1209 ++++++++++++++++++++++++------------------------- R/coef.KFS.R | 217 ++++---- R/hatvalues.KFS.R | 96 +-- R/mvInnovations.R | 89 +-- R/predict.SSModel.R | 730 ++++++++++++++--------------- R/print.objects.R | 186 +++---- R/residuals.KFS.R | 214 ++++---- R/rstandard.KFS.R | 159 +++--- inst/doc/KFAS.pdf |binary man/Extract.SSModel.Rd | 168 +++--- man/GlobalTemp.Rd | 42 - man/KFAS-defunct.Rd | 78 +-- man/KFAS.Rd | 1110 ++++++++++++++++++++++---------------------- man/KFS.Rd | 488 ++++++++++--------- man/SSModel.Rd | 518 ++++++++++---------- man/alcohol.Rd | 30 - man/approxSSM.Rd | 190 +++---- man/artransform.Rd | 68 +- man/boat.Rd | 148 ++--- man/checkModel.Rd | 94 +-- man/coef.SSModel.Rd | 146 ++--- man/fitSSM.Rd | 264 +++++----- man/fitted.SSModel.Rd | 128 ++--- man/hatvalues.KFS.Rd | 76 +-- man/importanceSSM.Rd | 178 +++---- man/ldl.Rd | 62 +- man/logLik.SSModel.Rd | 242 ++++----- man/mvInnovations.Rd | 78 +-- man/plot.SSModel.Rd | 72 +- man/predict.SSModel.Rd | 204 ++++---- man/print.KFS.Rd | 44 - man/print.SSModel.Rd | 32 - man/rename_states.Rd | 62 +- man/residuals.KFS.Rd | 82 +-- man/rstandard.KFS.Rd | 164 +++--- man/sexratio.Rd | 104 ++-- man/signal.Rd | 110 ++-- man/simulateSSM.Rd | 232 ++++----- man/transformSSM.Rd | 80 +-- src/filter1step.f95 | 522 ++++++++++----------- 44 files changed, 4503 insertions(+), 4468 deletions(-)
Title: Isotope Ratio Meta-Analysis
Description: Calculation of consensus values for atomic weights, isotope amount ratios, and isotopic abundances with the associated uncertainties using multivariate meta-regression approach for consensus building.
Author: Juris Meija and Antonio Possolo
Maintainer: Juris Meija <juris.meija@nrc-cnrc.gc.ca>
Diff between CIAAWconsensus versions 1.2 dated 2017-08-18 and 1.3 dated 2018-09-19
CIAAWconsensus-1.2/CIAAWconsensus/data/ciaaw.mass.rda |only CIAAWconsensus-1.2/CIAAWconsensus/man/ciaaw.mass.Rd |only CIAAWconsensus-1.3/CIAAWconsensus/DESCRIPTION | 6 - CIAAWconsensus-1.3/CIAAWconsensus/MD5 | 22 +++--- CIAAWconsensus-1.3/CIAAWconsensus/NEWS | 5 - CIAAWconsensus-1.3/CIAAWconsensus/R/ciaaw.R | 45 ++++++------- CIAAWconsensus-1.3/CIAAWconsensus/data/ciaaw.mass.2003.rda |only CIAAWconsensus-1.3/CIAAWconsensus/data/ciaaw.mass.2012.rda |only CIAAWconsensus-1.3/CIAAWconsensus/data/ciaaw.mass.2016.rda |only CIAAWconsensus-1.3/CIAAWconsensus/data/iridium.data.rda |binary CIAAWconsensus-1.3/CIAAWconsensus/man/at.weight.Rd | 3 CIAAWconsensus-1.3/CIAAWconsensus/man/ciaaw.mass.2003.Rd |only CIAAWconsensus-1.3/CIAAWconsensus/man/ciaaw.mass.2012.Rd |only CIAAWconsensus-1.3/CIAAWconsensus/man/ciaaw.mass.2016.Rd |only CIAAWconsensus-1.3/CIAAWconsensus/man/iridium.data.Rd | 2 CIAAWconsensus-1.3/CIAAWconsensus/man/normalize.ratios.Rd | 3 16 files changed, 48 insertions(+), 38 deletions(-)
More information about CIAAWconsensus at CRAN
Permanent link
Title: Web-Based Interactive Omics Visualization
Description: Tool-set of modules for creating web-based applications that use plot based strategies to visualize and analyze multi-omics data.
This package utilizes the 'shiny' and 'plotly' frameworks to provide a user friendly dashboard for interactive plotting.
Author: Hendrik Schultheis [aut, cre],
Jens Preussner [aut],
Looso Mario [aut]
Maintainer: Hendrik Schultheis <hendrik.schultheis@mpi-bn.mpg.de>
Diff between wilson versions 2.0.1 dated 2018-07-20 and 2.0.2 dated 2018-09-19
DESCRIPTION | 8 MD5 | 49 NAMESPACE | 1 NEWS.md | 2 R/clarion.R | 1 README.md | 4 build/vignette.rds |binary exec/sampleSelector_example.R |only inst/doc/intro.html | 4 man/colorPicker.Rd | 4 man/create_geneview.Rd | 9 man/create_heatmap.Rd | 8 man/create_pca.Rd | 11 man/create_scatterplot.Rd | 4 man/download.Rd | 4 man/global_cor_heatmap.Rd | 5 man/log_message.Rd | 4 man/orNumeric.Rd | 5 man/orTextual.Rd | 4 man/parse_MaxQuant.Rd | 4 man/pca.Rd | 4 man/scatterPlot.Rd | 4 man/searchData.Rd | 4 tests/figs/create-static-plots/static-scatterplot.svg |40143 ------------------ tests/testthat/test-download.R | 3 tests/testthat/test-static-plots.R | 2 26 files changed, 146 insertions(+), 40145 deletions(-)
More information about SplitSoftening at CRAN
Permanent link
Title: Chronological Bayesian Models Integrating Optically Stimulated
Luminescence and Radiocarbon Age Dating
Description: Bayesian analysis of luminescence data and C-14 age estimates. Bayesian models are based on the following publications: Combes, B. & Philippe, A. (2017) <doi:10.1016/j.quageo.2017.02.003> and Combes et al (2015) <doi:10.1016/j.quageo.2015.04.001>. This includes, amongst others, data import, export, application of age models and palaeodose model.
Author: Claire Christophe [aut],
Anne Philippe [aut, cre],
Sebastian Kreutzer [aut] (<https://orcid.org/0000-0002-0734-2199>),
Guillaume Guerin [aut] (<https://orcid.org/0000-0001-6298-5579>)
Maintainer: Anne Philippe <anne.philippe@univ-nantes.fr>
Diff between BayLum versions 0.1.2 dated 2018-06-22 and 0.1.3 dated 2018-09-19
BayLum-0.1.2/BayLum/R/ScatterSamples.R |only BayLum-0.1.2/BayLum/man/ScatterSamples.Rd |only BayLum-0.1.3/BayLum/DESCRIPTION | 16 BayLum-0.1.3/BayLum/MD5 | 46 +- BayLum-0.1.3/BayLum/NAMESPACE | 2 BayLum-0.1.3/BayLum/NEWS.md | 25 + BayLum-0.1.3/BayLum/R/AgeC14_Computation.R | 262 +++++++----- BayLum-0.1.3/BayLum/R/AgeS_Computation.R | 135 +++--- BayLum-0.1.3/BayLum/R/Age_Computation.R | 166 ++++--- BayLum-0.1.3/BayLum/R/Age_OSLC14.R | 155 ++++--- BayLum-0.1.3/BayLum/R/Palaeodose_Computation.R | 22 - BayLum-0.1.3/BayLum/R/combine_DataFiles.R | 10 BayLum-0.1.3/BayLum/R/plot_Ages.R |only BayLum-0.1.3/BayLum/R/plot_Scatterplots.R |only BayLum-0.1.3/BayLum/build/vignette.rds |binary BayLum-0.1.3/BayLum/inst/doc/BayLum.html | 226 +++++----- BayLum-0.1.3/BayLum/man/AgeC14_Computation.Rd | 139 ++---- BayLum-0.1.3/BayLum/man/AgeS_Computation.Rd | 132 ++---- BayLum-0.1.3/BayLum/man/Age_Computation.Rd | 162 +++---- BayLum-0.1.3/BayLum/man/Age_OSLC14.Rd | 140 +++--- BayLum-0.1.3/BayLum/man/LT_RegenDose.Rd | 6 BayLum-0.1.3/BayLum/man/Palaeodose_Computation.Rd | 14 BayLum-0.1.3/BayLum/man/combine_DataFiles.Rd | 2 BayLum-0.1.3/BayLum/man/plot_Ages.Rd |only BayLum-0.1.3/BayLum/man/plot_Scatterplots.Rd |only BayLum-0.1.3/BayLum/tests/testthat/test_plot_Ages.R |only BayLum-0.1.3/BayLum/tests/testthat/test_plot_MCMC.R | 2 BayLum-0.1.3/BayLum/tests/testthat/test_plot_Scatterplots.R |only 28 files changed, 901 insertions(+), 761 deletions(-)
Title: Model Audit - Verification, Validation, and Error Analysis
Description: Provides an easy to use unified interface for creating validation plots for any model.
The 'auditor' helps to avoid repetitive work consisting of writing code needed to create residual plots.
This visualizations allow to asses and compare the goodness of fit, performance, and similarity of models.
Author: Alicja Gosiewska [aut, cre],
Przemyslaw Biecek [aut, ths]
Maintainer: Alicja Gosiewska <alicjagosiewska@gmail.com>
Diff between auditor versions 0.3.0 dated 2018-08-27 and 0.3.1 dated 2018-09-19
DESCRIPTION | 14 ++++----- MD5 | 46 +++++++++++++++--------------- NEWS.md | 3 + R/plotPrediction.R | 2 - R/plotROC.R | 2 - inst/doc/model_evaluation_audit.Rmd | 8 ++--- inst/doc/model_evaluation_audit.html | 12 +++---- inst/doc/model_fit_audit.Rmd | 8 ++--- inst/doc/model_fit_audit.html | 22 +++++++------- inst/doc/model_performance_audit.Rmd | 8 ++--- inst/doc/model_performance_audit.html | 12 +++---- inst/doc/model_residuals_audit.Rmd | 8 ++--- inst/doc/model_residuals_audit.html | 40 +++++++++++++------------- inst/doc/observation_influence_audit.Rmd | 8 ++--- inst/doc/observation_influence_audit.html | 10 +++--- man/plotPrediction.Rd | 2 - man/plotROC.Rd | 2 - tests/testthat/objects_for_tests.R | 1 tests/testthat/test_errors.R | 4 +- vignettes/model_evaluation_audit.Rmd | 8 ++--- vignettes/model_fit_audit.Rmd | 8 ++--- vignettes/model_performance_audit.Rmd | 8 ++--- vignettes/model_residuals_audit.Rmd | 8 ++--- vignettes/observation_influence_audit.Rmd | 8 ++--- 24 files changed, 128 insertions(+), 124 deletions(-)
Title: Compare Two Data Frames and Summarise the Difference
Description: Easy comparison of two tabular data
objects in R. Specifically designed to show differences between two sets of
data in a useful way that should make it easier to understand the differences,
and if necessary, help you work out how to remedy them. Aims
to offer a more useful output than all.equal() when your two data sets do not
match, but isn't intended to replace all.equal() as a way to test for equality.
Author: Rob Noble-Eddy [aut, cre],
Sarah Johnston [aut],
Sarah Pollicott [aut],
Merlijn van Horssen [aut],
Lukas Drapal [ctb],
Nikolaos Perrakis [ctb],
Nikhil Thomas Joy [ctb],
Shahriar Asta [ctb],
Karandeep Lidher [ctb],
Dan Kellett [ctb],
Kevin Chisholm [ctb],
Laura Joy [ctb],
Fergus Wadsley [ctb],
Heather Hackett [ctb],
David Robinson [ctb],
Cheryl Renton [ctb],
Matt Triggs [ctb],
Krishan Bhasin [ctb],
Carola Deppe [ctb],
Ruijing Li [ctb],
John Swift [ctb]
Maintainer: Rob Noble-Eddy <opensource@capitalone.com>
Diff between dataCompareR versions 0.1.1 dated 2017-11-14 and 0.1.2 dated 2018-09-19
DESCRIPTION | 16 +- MD5 | 63 ++++++----- R/out_printrcompareobject.R | 14 ++ R/out_saveReport.R | 21 +++ R/out_summaryrcompareobject.R | 17 ++- R/out_unifiedOutputGenerator.R | 6 - R/pd_matchRows.R | 16 ++ R/rc_rCompare.R | 39 +++++-- R/rco_createRowMatching.R | 5 R/vd_checkEmpty.R | 37 ++++++ build/vignette.rds |binary inst/doc/dataCompareR.Rmd | 16 ++ inst/doc/dataCompareR.html | 55 +++++----- man/checkEmpty.Rd | 2 man/checkNA.Rd |only man/generateMismatchData.Rd | 1 man/isSingleNA.Rd |only man/print.dataCompareRobject.Rd | 1 man/rCompare.Rd | 1 man/saveReport.Rd | 10 + man/summary.dataCompareRobject.Rd | 1 man/warnLargeData.Rd |only tests/testthat/testCheckEmpty.R | 13 +- tests/testthat/testCheckNA.R |only tests/testthat/testCheckPrintObject.R | 118 +++++++++++++++++++++ tests/testthat/testLargeDataWarning.R |only tests/testthat/testMakeValidNames.R | 14 +- tests/testthat/testPrintSummaryRcompareObject.R | 131 ++++++++++++++++++++++++ tests/testthat/testRCompareStructure.R | 131 ++++++++++++++++++++++++ tests/testthat/testSaveReport.R | 74 +++++++++++++ tests/testthat/testcreateReportText.R | 8 - tests/testthat/testing.Rmd | 8 - tests/testthat/testing.html | 6 - tests/testthat/testing.md | 6 - vignettes/dataCompareR.Rmd | 16 ++ 35 files changed, 726 insertions(+), 120 deletions(-)
Title: Estimation and Validation Methods for Subgroup Identification
and Personalized Medicine
Description: Provides functions for fitting and validation of models for subgroup
identification and personalized medicine / precision medicine under the general subgroup
identification framework of Chen et al. (2017) <doi:10.1111/biom.12676>.
This package is intended for use for both randomized controlled trials and
observational studies.
Author: Jared Huling [aut, cre],
Aaron Potvien [ctb],
Alexandros Karatzoglou [cph],
Alex Smola [cph]
Maintainer: Jared Huling <jaredhuling@gmail.com>
Diff between personalized versions 0.2.0 dated 2018-09-18 and 0.2.1 dated 2018-09-19
DESCRIPTION | 10 MD5 | 46 - R/calculate_treatment_effects.R | 72 + R/est_subgroup_effects.R | 36 R/fit_losses.R | 154 ++- R/fit_subgroup.R | 26 R/plot_compare.R | 13 R/plot_subgroup_fitted.R | 2 R/predict_subgroup.R | 5 R/print_subgroup.R | 31 R/validate_subgroup.R | 15 README.md | 2 inst/doc/usage_of_the_personalized_package.Rmd | 10 inst/doc/usage_of_the_personalized_package.html | 116 +- man/fit.subgroup.Rd | 10 man/plot.Rd | 2 man/plotCompare.Rd | 13 man/treatment.effects.Rd | 10 man/validate.subgroup.Rd | 11 tests/testthat/test-fitsubgroup.R | 946 ++++++++++++------------ tests/testthat/test-validatesubgroup.R | 165 ++-- tests/testthat/test-wksvm.R | 153 ++- vignettes/usage_of_the_personalized_package.Rmd | 10 vignettes/vis_val-1.png |binary 24 files changed, 1039 insertions(+), 819 deletions(-)
Title: Generative Mechanism Estimation in Temporal Complex Networks
Description: Statistical methods for estimating preferential attachment and node fitness generative mechanisms in temporal complex networks are provided. Thong Pham et al. (2015) <doi:10.1371/journal.pone.0137796>. Thong Pham et al.(2016) <doi:10.1038/srep32558>.
Author: Thong Pham, Paul Sheridan, Hidetoshi Shimodaira
Maintainer: Thong Pham <thongpham@thongpham.net>
Diff between PAFit versions 1.0.0.6 dated 2018-08-28 and 1.0.0.7 dated 2018-09-19
DESCRIPTION | 8 ++++---- MD5 | 22 +++++++++++----------- R/PAFit.R | 30 +++++++----------------------- R/one_cycle.R | 12 ++++++++---- R/print.pafit_result.r | 4 ++-- R/summary.pafit_data.r | 4 ++-- R/summary.pafit_result.r | 4 ++-- build/vignette.rds |binary inst/NEWS.Rd | 8 ++++++++ inst/doc/Tutorial.pdf.asis | 2 +- man/PAFit-package.Rd | 4 ++-- vignettes/Tutorial.pdf.asis | 2 +- 12 files changed, 48 insertions(+), 52 deletions(-)
Title: Tables for Quantitative Scientists
Description: Contains three main functions (i.e., three pieces of furniture):
table1() which produces a well-formatted table of descriptives common as Table 1
in research articles, tableC() which produces a well-formatted table of correlations,
tableF() which provides frequency counts, and washer() which
is helpful in cleaning up the data. These furniture-themed functions are designed
to simplify common tasks in quantitative analysis. Other data summary and cleaning tools
are also available.
Author: Tyson S. Barrett [aut, cre] (<https://orcid.org/0000-0002-2137-1391>),
Emily Brignone [aut],
Daniel J. Laxman [aut]
Maintainer: Tyson S. Barrett <t.barrett@aggiemail.usu.edu>
Diff between furniture versions 1.7.9 dated 2018-06-01 and 1.8.0 dated 2018-09-19
furniture-1.7.9/furniture/man/figures/furniture_hex.jpg |only furniture-1.7.9/furniture/man/figures/furniture_hex.pdf |only furniture-1.7.9/furniture/man/figures/furniture_hex.png |only furniture-1.7.9/furniture/man/pipe.Rd |only furniture-1.8.0/furniture/DESCRIPTION | 14 furniture-1.8.0/furniture/MD5 | 51 - furniture-1.8.0/furniture/NAMESPACE | 8 furniture-1.8.0/furniture/NEWS.md | 9 furniture-1.8.0/furniture/R/Table1.R | 119 ++- furniture-1.8.0/furniture/R/rowmeans.R | 86 ++ furniture-1.8.0/furniture/R/table1_utils.R | 34 furniture-1.8.0/furniture/R/to_latex2.R | 3 furniture-1.8.0/furniture/R/utils.R | 58 + furniture-1.8.0/furniture/R/zzz.R | 45 + furniture-1.8.0/furniture/build/vignette.rds |binary furniture-1.8.0/furniture/inst/doc/Furniture.R | 4 furniture-1.8.0/furniture/inst/doc/Furniture.Rmd | 14 furniture-1.8.0/furniture/inst/doc/Furniture.html | 342 ++++------ furniture-1.8.0/furniture/inst/doc/Table1.R | 16 furniture-1.8.0/furniture/inst/doc/Table1.Rmd | 25 furniture-1.8.0/furniture/inst/doc/Table1.html | 212 +++--- furniture-1.8.0/furniture/man/figures/furniture_hex_v2.pdf |only furniture-1.8.0/furniture/man/figures/furniture_hex_v2_full.png |only furniture-1.8.0/furniture/man/figures/furniture_hex_v2_small.png |only furniture-1.8.0/furniture/man/long.Rd | 4 furniture-1.8.0/furniture/man/mutate_rowmeans.Rd |only furniture-1.8.0/furniture/man/mutate_rowsums.Rd |only furniture-1.8.0/furniture/man/table1.Rd | 9 furniture-1.8.0/furniture/tests/testthat/test_table1.R | 7 furniture-1.8.0/furniture/vignettes/Furniture.Rmd | 14 furniture-1.8.0/furniture/vignettes/Table1.Rmd | 25 31 files changed, 658 insertions(+), 441 deletions(-)
Title: L1-Penalized Censored Gaussian Graphical Models
Description: The l1-penalized censored Gaussian graphical model is an extension of the graphical lasso estimator developed to handle datasets with censored observations. An EM-like algorithm is implemented to estimate the parameters of the censored Gaussian graphical models.
Author: Luigi Augugliaro
Maintainer: Luigi Augugliaro <luigi.augugliaro@unipa.it>
Diff between cglasso versions 1.0.0 dated 2018-09-14 and 1.1.0 dated 2018-09-19
cglasso-1.0.0/cglasso/R/coef.cglasso.R |only cglasso-1.0.0/cglasso/R/plot.cglasso.R |only cglasso-1.0.0/cglasso/R/summary.cglasso.R |only cglasso-1.1.0/cglasso/ChangeLog |only cglasso-1.1.0/cglasso/DESCRIPTION | 12 +-- cglasso-1.1.0/cglasso/MD5 | 97 ++++++++++++++----------- cglasso-1.1.0/cglasso/NAMESPACE | 38 ++++++--- cglasso-1.1.0/cglasso/R/cglasso.R | 16 ++-- cglasso-1.1.0/cglasso/R/cglasso.fit.R | 8 +- cglasso-1.1.0/cglasso/R/coef.glasso.R | 2 cglasso-1.1.0/cglasso/R/coef.mglasso.R |only cglasso-1.1.0/cglasso/R/datacggm.R | 5 - cglasso-1.1.0/cglasso/R/ebic.cglasso.R | 8 +- cglasso-1.1.0/cglasso/R/ebic.glasso.R | 8 +- cglasso-1.1.0/cglasso/R/ebic.mglasso.R |only cglasso-1.1.0/cglasso/R/glasso.R | 3 cglasso-1.1.0/cglasso/R/loglik.R | 48 +++++------- cglasso-1.1.0/cglasso/R/make_summary_table.R | 2 cglasso-1.1.0/cglasso/R/mglasso.R |only cglasso-1.1.0/cglasso/R/mglasso.fit.R |only cglasso-1.1.0/cglasso/R/mle.cglasso.R | 4 - cglasso-1.1.0/cglasso/R/mle.glasso.R | 2 cglasso-1.1.0/cglasso/R/mle.mglasso.R |only cglasso-1.1.0/cglasso/R/parini.R | 15 ++- cglasso-1.1.0/cglasso/R/plot.glasso.R | 4 - cglasso-1.1.0/cglasso/R/plot.mglasso.R |only cglasso-1.1.0/cglasso/R/print.cglasso.R | 4 - cglasso-1.1.0/cglasso/R/print.glasso.R | 2 cglasso-1.1.0/cglasso/R/scale.datacggm.R |only cglasso-1.1.0/cglasso/R/summary.datacggm.R | 4 - cglasso-1.1.0/cglasso/R/summary.glasso.R | 2 cglasso-1.1.0/cglasso/R/to_graph.R | 8 +- cglasso-1.1.0/cglasso/data |only cglasso-1.1.0/cglasso/man/MKMEP.Rd |only cglasso-1.1.0/cglasso/man/aic.Rd | 38 ++++++++- cglasso-1.1.0/cglasso/man/cglasso-package.Rd | 11 +- cglasso-1.1.0/cglasso/man/cglasso.Rd | 16 ++-- cglasso-1.1.0/cglasso/man/coef.Rd | 46 +++++++++--- cglasso-1.1.0/cglasso/man/datacggm.Rd | 7 + cglasso-1.1.0/cglasso/man/ebic.Rd | 40 ++++++++-- cglasso-1.1.0/cglasso/man/glasso.Rd | 12 +-- cglasso-1.1.0/cglasso/man/loglik.Rd | 29 ++++++- cglasso-1.1.0/cglasso/man/mglasso.Rd |only cglasso-1.1.0/cglasso/man/mle.Rd | 99 +++++++++++++++++++++----- cglasso-1.1.0/cglasso/man/plot.Rd | 51 ++++++++++--- cglasso-1.1.0/cglasso/man/rdatacggm.Rd | 5 - cglasso-1.1.0/cglasso/man/scale.datacggm.Rd |only cglasso-1.1.0/cglasso/man/summary.Rd | 33 ++++++-- cglasso-1.1.0/cglasso/man/summary.datacggm.Rd | 2 cglasso-1.1.0/cglasso/man/to_graph.Rd | 36 ++++++++- cglasso-1.1.0/cglasso/src/cglasso.f90 | 43 +++++++---- cglasso-1.1.0/cglasso/src/cglasso.h | 28 +++++-- cglasso-1.1.0/cglasso/src/glassosub.f90 | 2 cglasso-1.1.0/cglasso/src/impute.f90 |only cglasso-1.1.0/cglasso/src/init.c | 4 - cglasso-1.1.0/cglasso/src/mglasso_algo1.f90 |only cglasso-1.1.0/cglasso/src/mlemglasso.f90 |only cglasso-1.1.0/cglasso/src/trace_mglasso.c |only cglasso-1.1.0/cglasso/src/trace_mlemglasso.c |only 59 files changed, 547 insertions(+), 247 deletions(-)
Title: Domain-Specific Language for Building PLS Structural Equation
Models
Description: A powerful, easy to write and easy to modify syntax for
specifying and estimating Partial Least Squares (PLS) path models allowing for the latest estimation methods
for Consistent PLS as per Dijkstra & Henseler (2015, MISQ 39(2): 297-316), adjusted interactions as per
Henseler & Chin (2010) <doi:10.1080/10705510903439003> and bootstrapping utilizing
parallel processing as per Hair et al. (2017, ISBN:978-1483377445).
Author: Soumya Ray [aut, ths],
Nicholas Danks [aut, cre],
Juan Manuel Velasquez Estrada [aut]
Maintainer: Nicholas Danks <nicholasdanks@hotmail.com>
Diff between seminr versions 0.5.1 dated 2018-09-10 and 0.5.2 dated 2018-09-19
DESCRIPTION | 8 MD5 | 44 ++--- R/bootstrap.R | 16 + inst/doc/SEMinR.html | 20 +- man/bootstrap_model.Rd | 6 tests/fixtures/boostrapmatrix1.csv | 8 tests/fixtures/boostrapmatrix2.csv | 10 - tests/fixtures/boot_HTMT.csv | 6 tests/fixtures/boot_loadings.csv | 26 +-- tests/fixtures/boot_weights.csv | 26 +-- tests/fixtures/composite_indicator_weights_p_values.csv | 10 - tests/fixtures/composite_indicator_weights_t_values.csv | 10 - tests/fixtures/factor_discriminant_validity_p_values.csv | 6 tests/fixtures/factor_discriminant_validity_t_values.csv | 6 tests/fixtures/pvalues.csv | 6 tests/fixtures/tvalues.csv | 6 tests/testthat/test-bootstrap.R | 129 ++------------- tests/testthat/test-consistent.R | 10 - tests/testthat/test-inner_weighting.R | 12 - tests/testthat/test-metric.R | 2 tests/testthat/test-output.r | 12 - tests/testthat/test-summary.R | 60 +----- tests/testthat/test_validity.R | 6 23 files changed, 166 insertions(+), 279 deletions(-)
Title: Patches to Use 'dplyr' on Remote Data Sources
Description: Patches to use 'dplyr' on remote data sources ('SQL' databases,
'Spark' 2.0.0 and above) in a reliable "generic" fashion (generic meaning
user code works similarly on all such sources, without needing per-source
adaption). Due to the fluctuating nature of 'dplyr'/'dbplyr'/'rlang' 'APIs' this package
is going into maintenance mode. Most of the 'replyr' functions are already
done better by one of the non-monolithic replacement packages: 'wrapr', 'seplyr', 'rquery',
or 'cdata'.
Author: John Mount [aut, cre],
Nina Zumel [aut],
Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>
Diff between replyr versions 0.9.7 dated 2018-07-20 and 0.9.8 dated 2018-09-19
DESCRIPTION | 14 +++++++------- MD5 | 36 ++++++++++++++++++------------------ NEWS.md | 4 ++++ R/addIds.R | 3 ++- README.md | 6 +++--- inst/doc/DependencySorting.html | 22 +++++++++++----------- inst/doc/ParametricExample.html | 4 ++-- inst/doc/coalesce.html | 8 ++++---- inst/doc/joinController.html | 18 +++++++++--------- inst/doc/letExample.html | 8 ++++---- inst/doc/replyr.html | 10 +++++----- inst/doc/summary.html | 8 ++++---- man/inspectDescrAndJoinPlan.Rd | 3 ++- man/replyr_add_ids.Rd | 5 +++-- man/replyr_check_ranks.Rd | 4 ++-- man/replyr_coalesce.Rd | 3 ++- man/replyr_copy_to.Rd | 4 ++-- man/replyr_inTest.Rd | 3 ++- man/replyr_summary.Rd | 4 ++-- 19 files changed, 88 insertions(+), 79 deletions(-)
Title: Classes and Methods for Seismic Data Analysis
Description: Provides classes and methods for seismic data analysis. The
base classes and methods are inspired by the python code found in
the 'ObsPy' python toolbox <https://github.com/obsypy/obspy>. Additional classes and
methods support data returned by web services provided by the 'IRIS DMC'
<http://service.iris.edu/>.
Author: Jonathan Callahan [aut],
Rob Casey [aut],
Gillian Sharer [aut, cre],
Mary Templeton [aut],
Chad Trabant [ctb]
Maintainer: Gillian Sharer <gillian@iris.washington.edu>
Diff between IRISSeismic versions 1.4.8 dated 2018-05-07 and 1.4.9 dated 2018-09-19
IRISSeismic-1.4.8/IRISSeismic/src/libmseed/libmseed.map |only IRISSeismic-1.4.9/IRISSeismic/DESCRIPTION | 6 IRISSeismic-1.4.9/IRISSeismic/MD5 | 269 ++++------ IRISSeismic-1.4.9/IRISSeismic/R/Class-IrisClient.R | 118 +++- IRISSeismic-1.4.9/IRISSeismic/R/Class-Stream.R | 4 IRISSeismic-1.4.9/IRISSeismic/R/Class-Trace.R | 17 IRISSeismic-1.4.9/IRISSeismic/inst/doc/IRISSeismic-intro.html | 14 IRISSeismic-1.4.9/IRISSeismic/man/IRISSeismic-package.Rd | 7 IRISSeismic-1.4.9/IRISSeismic/man/crossSpectrum.Rd | 6 IRISSeismic-1.4.9/IRISSeismic/man/envelope.Rd | 4 IRISSeismic-1.4.9/IRISSeismic/man/getAvailability.Rd | 2 IRISSeismic-1.4.9/IRISSeismic/man/getEvent.Rd | 4 IRISSeismic-1.4.9/IRISSeismic/man/getTraveltime.Rd | 4 IRISSeismic-1.4.9/IRISSeismic/man/hilbert.Rd | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/ChangeLog | 11 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/INSTALL.md | 19 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/README.md | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/ms_addselect.3 | 12 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/ms_addselect_comp.3 | 12 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/ms_bigendianhost.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/ms_blktdesc.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/ms_blktlen.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/ms_btime2isotimestr.3 | 8 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/ms_btime2mdtimestr.3 | 8 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/ms_btime2seedtimestr.3 | 8 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/ms_btime3hptime.3 | 8 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/ms_detect.3 | 6 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/ms_doy2md.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/ms_encodingstr.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/ms_errorstr.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/ms_find_reclen.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/ms_freeselections.3 | 12 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/ms_genfactmult.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/ms_gswap.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/ms_gswap2.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/ms_gswap2a.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/ms_gswap3.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/ms_gswap4.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/ms_gswap4a.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/ms_gswap8.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/ms_gswap8a.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/ms_hptime2btime.3 | 8 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/ms_hptime2isotimestr.3 | 8 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/ms_hptime2mdtimestr.3 | 8 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/ms_hptime2seedtimestr.3 | 8 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/ms_intro.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/ms_log.3 | 14 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/ms_log_l.3 | 14 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/ms_loginit.3 | 14 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/ms_loginit_l.3 | 14 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/ms_lookup.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/ms_matchselect.3 | 12 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/ms_md2doy.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/ms_parse_raw.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/ms_printselections.3 | 12 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/ms_ratapprox.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/ms_readleapsecondfile.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/ms_readleapseconds.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/ms_readmsr.3 | 10 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/ms_readmsr_r.3 | 10 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/ms_readselectionsfile.3 | 12 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/ms_readtracelist.3 | 10 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/ms_readtracelist_selection.3 | 10 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/ms_readtracelist_timewin.3 | 10 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/ms_readtraces.3 | 10 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/ms_readtraces_selection.3 | 10 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/ms_readtraces_timewin.3 | 10 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/ms_recsrcname.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/ms_samplesize.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/ms_seedtimestr2hptime.3 | 8 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/ms_selection.3 | 12 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/ms_splitsrcname.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/ms_srcname.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/ms_strncpclean.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/ms_strncpopen.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/ms_time.3 | 8 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/ms_time2hptime.3 | 8 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/ms_timestr2hptime.3 | 8 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/ms_writemseed.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/msr_addblockette.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/msr_duplicate.3 | 6 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/msr_endtime.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/msr_free.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/msr_free_blktchain.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/msr_host_latency.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/msr_init.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/msr_nomsamprate.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/msr_normalize_header.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/msr_pack.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/msr_pack_header.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/msr_parse.3 | 6 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/msr_parse_selection.3 | 6 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/msr_print.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/msr_samprate.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/msr_srcname.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/msr_starttime.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/msr_starttime_uc.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/msr_unpack.3 | 6 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/msr_writemseed.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/mst_addmsr.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/mst_addmsrtogroup.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/mst_addspan.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/mst_addtracetogroup.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/mst_convertsamples.3 | 6 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/mst_findadjacent.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/mst_findmatch.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/mst_free.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/mst_freegroup.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/mst_groupheal.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/mst_groupsort.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/mst_init.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/mst_initgroup.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/mst_pack.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/mst_packgroup.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/mst_printgaplist.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/mst_printsynclist.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/mst_printtracelist.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/mst_srcname.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/mst_writemseed.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/mst_writemseedgroup.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/mstl_addmsr.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/mstl_convertsamples.3 | 6 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/mstl_free.3 | 6 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/mstl_init.3 | 6 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/mstl_printgaplist.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/mstl_printsynclist.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/doc/mstl_printtracelist.3 | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/genutils.c | 9 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/libmseed.def | 1 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/libmseed.h | 10 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/logging.c | 4 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/msrutils.c | 22 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/temp.sh | 7 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/traceutils.c | 6 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/unpack.c | 11 IRISSeismic-1.4.9/IRISSeismic/src/libmseed/unpackdata.c | 2 136 files changed, 678 insertions(+), 537 deletions(-)
Title: Analysis of Data with Mixed Measurement Error and
Misclassification in Covariates
Description: Implementation of the augmented
Simulation-Extrapolation (SIMEX) algorithm proposed by Yi et al. (2015) <doi:10.1080/01621459.2014.922777>
for analyzing the data with mixed measurement error and misclassification. The main
function provides a similar summary output as that of glm() function. Both parametric and
empirical SIMEX are considered in the package.
Author: Qihuang Zhang <qihuang.zhang@uwaterloo.ca>, Grace Y. Yi <yyi@uwaterloo.ca>
Maintainer: Qihuang Zhang <qihuang.zhang@uwaterloo.ca>
Diff between augSIMEX versions 2.2 dated 2018-07-23 and 3.0 dated 2018-09-19
augSIMEX-2.2/augSIMEX/R/plotaugSIMEX.R |only augSIMEX-2.2/augSIMEX/R/plotaugSIMEXbottomright.R |only augSIMEX-2.2/augSIMEX/man/plotaugSIMEX.Rd |only augSIMEX-3.0/augSIMEX/DESCRIPTION | 10 - augSIMEX-3.0/augSIMEX/MD5 | 38 +++++-- augSIMEX-3.0/augSIMEX/NAMESPACE | 22 ++++ augSIMEX-3.0/augSIMEX/R/SIMEX_functions.R | 25 +++- augSIMEX-3.0/augSIMEX/R/augSIMEX.R | 111 ++++++++++++++-------- augSIMEX-3.0/augSIMEX/R/coef.augSIMEX.R |only augSIMEX-3.0/augSIMEX/R/logLik.augSIMEX.R |only augSIMEX-3.0/augSIMEX/R/model.frame.augSIMEX.R |only augSIMEX-3.0/augSIMEX/R/model.matrix.augSIMEX.R |only augSIMEX-3.0/augSIMEX/R/plot.augSIMEX.R |only augSIMEX-3.0/augSIMEX/R/predict.augSIMEX.R |only augSIMEX-3.0/augSIMEX/R/print.augSIMEX.R | 18 --- augSIMEX-3.0/augSIMEX/R/print.summary.augSIMEX.R |only augSIMEX-3.0/augSIMEX/R/residuals.augSIMEX.R |only augSIMEX-3.0/augSIMEX/R/summary.augSIMEX.R | 8 - augSIMEX-3.0/augSIMEX/R/vcov.augSIMEX.R |only augSIMEX-3.0/augSIMEX/data/GeneRepeat.rda |only augSIMEX-3.0/augSIMEX/data/GeneUni.rda |only augSIMEX-3.0/augSIMEX/man/GeneRepeat.Rd |only augSIMEX-3.0/augSIMEX/man/GeneUni.Rd |only augSIMEX-3.0/augSIMEX/man/augSIMEX.Rd | 89 ++++++++--------- augSIMEX-3.0/augSIMEX/man/coef.augSIMEX.Rd |only augSIMEX-3.0/augSIMEX/man/glmscore.Rd | 2 augSIMEX-3.0/augSIMEX/man/logLik.augSIMEX.Rd |only augSIMEX-3.0/augSIMEX/man/plot.augSIMEX.Rd |only augSIMEX-3.0/augSIMEX/man/predict.augSIMEX.Rd |only augSIMEX-3.0/augSIMEX/man/residuals.augSIMEX.Rd |only augSIMEX-3.0/augSIMEX/man/vcov.augSIMEX.Rd |only 31 files changed, 198 insertions(+), 125 deletions(-)