Title: Utilities for Sampling
Description: Interactive tools for generating random samples. Users select an
.xlsx or .csv file with population data and are walked through selecting the
sample type (Simple Random Sample or Stratified), the number of backups
desired, and a "stratify_on" value (if desired). The sample size is determined
using a normal approximation to the hypergeometric distribution based on
Nicholson (1956) <doi:10.1214/aoms/1177728270>. An .xlsx file is created
with the sample and key metadata for reference. It is menu-driven and lets
users pick an output directory. See vignettes for a detailed walk-through.
Author: Paul West [aut, cre]
Maintainer: Paul West <fp8049@gmail.com>
Diff between whSample versions 0.9.0 dated 2020-08-31 and 0.9.2 dated 2020-09-02
DESCRIPTION | 10 +++++---- MD5 | 14 ++++++------ NAMESPACE | 1 R/sampler.R | 14 +++++++----- README.md | 48 +++++++++++++++++++++++--------------------- inst/doc/Using_sampler.Rmd | 4 ++- inst/doc/Using_sampler.html | 3 +- vignettes/Using_sampler.Rmd | 4 ++- 8 files changed, 55 insertions(+), 43 deletions(-)
Title: Amos Tanay's Group High Performance Statistical Utilities
Description: A collection of high performance utilities to compute distance,
correlation, auto correlation, clustering and other tasks.
Contains graph clustering algorithm described in "MetaCell: analysis of
single-cell RNA-seq data using K-nn graph partitions" (Yael Baran,
Akhiad Bercovich, Arnau Sebe-Pedros, Yaniv Lubling, Amir Giladi,
Elad Chomsky, Zohar Meir, Michael Hoichman, Aviezer Lifshitz & Amos Tanay,
2019 <doi:10.1186/s13059-019-1812-2>).
Author: Michael Hoichman
Maintainer: Michael Hoichman <misha@hoichman.com>
Diff between tgstat versions 2.3.14 dated 2020-08-19 and 2.3.16 dated 2020-09-02
DESCRIPTION | 8 - MD5 | 30 ++-- NEWS.md | 9 + inst/doc/manual.pdf |binary src/HashFunc.h | 5 src/corgraph.cpp | 22 +-- src/correlation.cpp | 296 ++++++++++++++++++++++++------------------------ src/correlation_knn.cpp | 160 ++++++++++++------------- src/dist.cpp | 124 +++++++++----------- src/graph2cluster.cpp | 208 +++++++++++++++------------------ src/graph2cluster.h | 4 src/knn.cpp | 96 +++++++-------- src/matrix_tapply.cpp | 59 ++++----- src/tgstat.cpp | 32 +++-- src/tgstat.h | 28 +++- src/utils.cpp | 4 16 files changed, 546 insertions(+), 539 deletions(-)
Title: Summary Tables and Plots for Statistical Models and Data:
Beautiful, Customizable, and Publication-Ready
Description: Create beautiful and customizable tables to summarize several
statistical models side-by-side. Draw coefficient plots, multi-level
cross-tabs, dataset summaries, balance tables (a.k.a. "Table 1s"), and
correlation matrices. This package supports dozens of statistical models,
and it can produce tables in HTML, LaTeX, Word, Markdown, PDF, PowerPoint,
Excel, RTF, JPG, or PNG. Tables can easily be embedded in 'Rmarkdown' or
'knitr' dynamic documents.
Author: Vincent Arel-Bundock [aut, cre]
(<https://orcid.org/0000-0003-2042-7063>)
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Diff between modelsummary versions 0.5.1 dated 2020-08-02 and 0.6.0 dated 2020-09-02
modelsummary-0.5.1/modelsummary/R/All.R |only modelsummary-0.5.1/modelsummary/R/extract.R |only modelsummary-0.5.1/modelsummary/man/extract.Rd |only modelsummary-0.5.1/modelsummary/man/statistic_override_function.Rd |only modelsummary-0.5.1/modelsummary/man/statistic_override_lmtest.Rd |only modelsummary-0.5.1/modelsummary/man/statistic_override_matrix.Rd |only modelsummary-0.5.1/modelsummary/man/statistic_override_vector.Rd |only modelsummary-0.6.0/modelsummary/DESCRIPTION | 23 modelsummary-0.6.0/modelsummary/MD5 | 97 ++- modelsummary-0.6.0/modelsummary/NAMESPACE | 17 modelsummary-0.6.0/modelsummary/NEWS.md | 8 modelsummary-0.6.0/modelsummary/R/datasummary.R | 7 modelsummary-0.6.0/modelsummary/R/datasummary_balance.R | 11 modelsummary-0.6.0/modelsummary/R/datasummary_correlation.R | 4 modelsummary-0.6.0/modelsummary/R/extract_gof.R | 22 modelsummary-0.6.0/modelsummary/R/extract_models.R |only modelsummary-0.6.0/modelsummary/R/extract_statistic_override.R | 165 +++--- modelsummary-0.6.0/modelsummary/R/factory.R | 13 modelsummary-0.6.0/modelsummary/R/factory_dataframe.R | 2 modelsummary-0.6.0/modelsummary/R/factory_flextable.R | 7 modelsummary-0.6.0/modelsummary/R/factory_gt.R | 2 modelsummary-0.6.0/modelsummary/R/factory_huxtable.R | 7 modelsummary-0.6.0/modelsummary/R/factory_kableExtra.R | 37 - modelsummary-0.6.0/modelsummary/R/glance_custom.R | 3 modelsummary-0.6.0/modelsummary/R/gof_map.R | 5 modelsummary-0.6.0/modelsummary/R/modelplot.R | 31 - modelsummary-0.6.0/modelsummary/R/modelsummary.R | 78 +- modelsummary-0.6.0/modelsummary/R/parse_output_arg.R | 61 +- modelsummary-0.6.0/modelsummary/R/reexport.R |only modelsummary-0.6.0/modelsummary/R/sanity_checks.R | 270 +++++----- modelsummary-0.6.0/modelsummary/R/utils_rounding.R | 2 modelsummary-0.6.0/modelsummary/README.md | 21 modelsummary-0.6.0/modelsummary/build/modelsummary.pdf |binary modelsummary-0.6.0/modelsummary/man/All.Rd | 30 - modelsummary-0.6.0/modelsummary/man/AllObs.Rd |only modelsummary-0.6.0/modelsummary/man/Arguments.Rd |only modelsummary-0.6.0/modelsummary/man/DropEmpty.Rd |only modelsummary-0.6.0/modelsummary/man/Factor.Rd |only modelsummary-0.6.0/modelsummary/man/Format.Rd |only modelsummary-0.6.0/modelsummary/man/Heading.Rd |only modelsummary-0.6.0/modelsummary/man/Multicolumn.Rd |only modelsummary-0.6.0/modelsummary/man/Paste.Rd |only modelsummary-0.6.0/modelsummary/man/Percent.Rd |only modelsummary-0.6.0/modelsummary/man/PlusMinus.Rd |only modelsummary-0.6.0/modelsummary/man/RowFactor.Rd |only modelsummary-0.6.0/modelsummary/man/RowNum.Rd |only modelsummary-0.6.0/modelsummary/man/check_dependency.Rd |only modelsummary-0.6.0/modelsummary/man/colLabels.Rd |only modelsummary-0.6.0/modelsummary/man/datasummary.Rd | 2 modelsummary-0.6.0/modelsummary/man/datasummary_balance.Rd | 8 modelsummary-0.6.0/modelsummary/man/extract_gof.Rd | 5 modelsummary-0.6.0/modelsummary/man/extract_models.Rd |only modelsummary-0.6.0/modelsummary/man/factory_dataframe.Rd | 1 modelsummary-0.6.0/modelsummary/man/factory_kableExtra.Rd | 2 modelsummary-0.6.0/modelsummary/man/gof_map.Rd | 6 modelsummary-0.6.0/modelsummary/man/labelSubset.Rd |only modelsummary-0.6.0/modelsummary/man/modelplot.Rd | 15 modelsummary-0.6.0/modelsummary/man/modelsummary.Rd | 22 modelsummary-0.6.0/modelsummary/man/msummary.Rd | 22 modelsummary-0.6.0/modelsummary/man/override_statistic.Rd |only modelsummary-0.6.0/modelsummary/man/override_statistic.character.Rd |only modelsummary-0.6.0/modelsummary/man/override_statistic.function.Rd |only modelsummary-0.6.0/modelsummary/man/override_statistic.matrix.Rd |only modelsummary-0.6.0/modelsummary/man/override_statistic.numeric.Rd |only modelsummary-0.6.0/modelsummary/man/rowLabels.Rd |only 65 files changed, 583 insertions(+), 423 deletions(-)
Title: Linked Micromap Plots
Description: This group of functions simplifies the creation of linked micromap
plots.
Author: Quinn Payton [aut],
Tony Olsen [aut],
Marc Weber [ctb],
Michael McManus [ctb],
Tom Kincaid [ctb],
Marcus W. Beck [cre, ctb]
Maintainer: Marcus W. Beck <mbeck@tbep.org>
Diff between micromap versions 1.9.3 dated 2018-02-08 and 1.9.4 dated 2020-09-02
DESCRIPTION | 18 - MD5 | 19 - R/MapGraphs.r | 9 data/OrEcoLevel3.rda |binary data/USstates.rda |binary data/WSA3.rda |binary inst/CITATION | 2 inst/NEWS.Rd | 16 + inst/doc/Introduction_Guide.R | 393 +++++++++++++++++++-------------------- vignettes/Introduction_Guide.tex |only vignettes/txeco.RData |binary 11 files changed, 237 insertions(+), 220 deletions(-)
Title: Tools for Spatial Data
Description: For curve, surface and function fitting with an emphasis
on splines, spatial data, geostatistics, 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 the 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, the National Center for Atmospheric Research, and Colorado School of Mines.
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],
Florian Gerber [aut],
Matthew Iverson [aut],
University Corporation for Atmospheric Research [cph]
Maintainer: Douglas Nychka <douglasnychka@gmail.com>
Diff between fields versions 10.3 dated 2020-02-04 and 11.4 dated 2020-09-02
fields-10.3/fields/R/mKrigMLEJoint.R |only fields-11.4/fields/DESCRIPTION | 16 - fields-11.4/fields/MD5 | 120 ++++---- fields-11.4/fields/NAMESPACE | 6 fields-11.4/fields/R/Krig.family.R | 7 fields-11.4/fields/R/MLESpatialProcess.R | 95 ++++-- fields-11.4/fields/R/circulantEmbedding.R |only fields-11.4/fields/R/circulantEmbeddingSetup.R |only fields-11.4/fields/R/fields.mkpoly.R | 29 +- fields-11.4/fields/R/image.plot.R | 2 fields-11.4/fields/R/mKrigCheckXY.R | 3 fields-11.4/fields/R/mKrigMLEGrid.R | 109 +------ fields-11.4/fields/R/mKrigMLEJointNew.R |only fields-11.4/fields/R/makeMultiIndex.R |only fields-11.4/fields/R/plot.spatialProcess.R | 60 ++-- fields-11.4/fields/R/poly.image.R | 3 fields-11.4/fields/R/print.spatialProcessSummary.R | 17 + fields-11.4/fields/R/sim.spatialProcess.R | 9 fields-11.4/fields/R/simSpatialData.R |only fields-11.4/fields/R/spatialProcess.R | 155 ++++++---- fields-11.4/fields/R/summary.spatialProcess.R | 22 + fields-11.4/fields/man/MLESpatialProcess.Rd | 217 +++++++++------ fields-11.4/fields/man/RMprecip.Rd | 4 fields-11.4/fields/man/fields-stuff.Rd | 9 fields-11.4/fields/man/fields.Rd | 5 fields-11.4/fields/man/grid.list.Rd | 29 +- fields-11.4/fields/man/image.plot.Rd | 133 ++++++--- fields-11.4/fields/man/mKrigMLE.Rd | 155 ++++++---- fields-11.4/fields/man/plot.Krig.Rd | 7 fields-11.4/fields/man/registeredC.Rd | 2 fields-11.4/fields/man/sim.Krig.Rd | 61 +++- fields-11.4/fields/man/sim.rf.Rd | 175 +++++++++--- fields-11.4/fields/man/spatialProcess.Rd | 136 ++++++--- fields-11.4/fields/tests/Krig.Z.test.Rout.save | 8 fields-11.4/fields/tests/Krig.se.W.Rout.save | 8 fields-11.4/fields/tests/Krig.se.grid.test.Rout.save | 8 fields-11.4/fields/tests/Krig.se.test.Rout.save | 8 fields-11.4/fields/tests/Krig.test.Rout.save | 8 fields-11.4/fields/tests/Krig.test.W.Rout.save | 8 fields-11.4/fields/tests/KrigGCVREML.test.Rout.save | 8 fields-11.4/fields/tests/Likelihood.test.Rout.save | 8 fields-11.4/fields/tests/REMLest.test.Rout.save | 8 fields-11.4/fields/tests/SEFixedParameters.Rout.save | 8 fields-11.4/fields/tests/Tps.test.Rout.save | 8 fields-11.4/fields/tests/Wend.test.Rout.save | 8 fields-11.4/fields/tests/cov.test.Rout.save | 8 fields-11.4/fields/tests/cov.test2.Rout.save | 8 fields-11.4/fields/tests/derivative.test.Rout.save | 8 fields-11.4/fields/tests/diag.multiply.test.Rout.save | 8 fields-11.4/fields/tests/diagonal2.test.Rout.save | 8 fields-11.4/fields/tests/evlpoly.test.Rout.save | 8 fields-11.4/fields/tests/fastTpsPredict.test.Rout.save | 8 fields-11.4/fields/tests/mKrig.MLE.test.Rout.save | 8 fields-11.4/fields/tests/mKrig.Z.Rout.save | 8 fields-11.4/fields/tests/mKrig.parameters.test.Rout.save | 8 fields-11.4/fields/tests/mKrig.se.test.Rout.save | 8 fields-11.4/fields/tests/mKrig.test.Rout.save | 8 fields-11.4/fields/tests/mKrigMLETest.R | 127 +++++--- fields-11.4/fields/tests/mKrigMLETest.Rout.save | 51 ++- fields-11.4/fields/tests/mKrigREMLTest.Rout.save | 8 fields-11.4/fields/tests/misc.test.Rout.save | 8 fields-11.4/fields/tests/spam.test.Rout.save | 8 fields-11.4/fields/tests/sreg.test.Rout.save | 8 fields-11.4/fields/tests/vgram.test.Rout.save | 8 64 files changed, 1253 insertions(+), 743 deletions(-)
Title: Analysis of NCES Education Survey and Assessment Data
Description: Read in and analyze functions for education survey and assessment data from the National Center for Education Statistics (NCES) <https://nces.ed.gov/>, including National Assessment of Educational Progress (NAEP) data <https://nces.ed.gov/nationsreportcard/> and data from the International Assessment Database: Organisation for Economic Co-operation and Development (OECD) <https://www.oecd.org/>, including Programme for International Student Assessment (PISA), Teaching and Learning International Survey (TALIS), Programme for the International Assessment of Adult Competencies (PIAAC), and International Association for the Evaluation of Educational Achievement (IEA) <https://www.iea.nl/>, including Trends in International Mathematics and Science Study (TIMSS), TIMSS Advanced, Progress in International Reading Literacy Study (PIRLS), International Civic and Citizenship Study (ICCS), International Computer and Information Literacy Study (ICILS), and Civic Education Study (CivEd).
Author: Paul Bailey [aut, cre],
Ahmad Emad [aut],
Huade Huo [aut],
Michael Lee [aut],
Yuqi Liao [aut],
Alex Lishinski [aut],
Trang Nguyen [aut],
Qingshu Xie [aut],
Jiao Yu [aut],
Ting Zhang [aut],
Eric Buehler [ctb],
Jeppe Bundsgaard [ctb],
Ren C'deBaca [ctb],
Anders Astrup Christensen [ctb]
Maintainer: Paul Bailey <pbailey@air.org>
Diff between EdSurvey versions 2.5.0 dated 2020-04-13 and 2.6.1 dated 2020-09-02
EdSurvey-2.5.0/EdSurvey/tests/edsurvey_warnings_out.csv |only EdSurvey-2.6.1/EdSurvey/DESCRIPTION | 23 EdSurvey-2.6.1/EdSurvey/MD5 | 349 ++-- EdSurvey-2.6.1/EdSurvey/NAMESPACE | 6 EdSurvey-2.6.1/EdSurvey/R/achievementLevels.R | 30 EdSurvey-2.6.1/EdSurvey/R/contourPlot.R | 10 EdSurvey-2.6.1/EdSurvey/R/cor.sdf.R | 178 +- EdSurvey-2.6.1/EdSurvey/R/downloadECLS_K.R | 20 EdSurvey-2.6.1/EdSurvey/R/downloadICCS.R | 1 EdSurvey-2.6.1/EdSurvey/R/downloadICILS.R | 1 EdSurvey-2.6.1/EdSurvey/R/downloadPIAAC.R | 13 EdSurvey-2.6.1/EdSurvey/R/downloadPISA.R | 35 EdSurvey-2.6.1/EdSurvey/R/downloadTALIS.R | 124 + EdSurvey-2.6.1/EdSurvey/R/edsurvey.data.frame.R | 160 + EdSurvey-2.6.1/EdSurvey/R/edsurvey.data.frame.list.R | 20 EdSurvey-2.6.1/EdSurvey/R/edsurveyTable.R | 120 + EdSurvey-2.6.1/EdSurvey/R/gap.R | 153 + EdSurvey-2.6.1/EdSurvey/R/getData.R | 200 +- EdSurvey-2.6.1/EdSurvey/R/glm.sdf.R | 32 EdSurvey-2.6.1/EdSurvey/R/lm.sdf.R | 31 EdSurvey-2.6.1/EdSurvey/R/mvrlm.sdf.R | 12 EdSurvey-2.6.1/EdSurvey/R/percentile.R | 58 EdSurvey-2.6.1/EdSurvey/R/readBPS_2014.R | 2 EdSurvey-2.6.1/EdSurvey/R/readECLS_B.R |only EdSurvey-2.6.1/EdSurvey/R/readECLS_K2011.R | 211 ++ EdSurvey-2.6.1/EdSurvey/R/readHSLS.R | 7 EdSurvey-2.6.1/EdSurvey/R/readICCS.R | 67 EdSurvey-2.6.1/EdSurvey/R/readICILS.R | 10 EdSurvey-2.6.1/EdSurvey/R/readNAEP.r | 24 EdSurvey-2.6.1/EdSurvey/R/readPIAAC.R | 109 + EdSurvey-2.6.1/EdSurvey/R/readPIRLS.R | 8 EdSurvey-2.6.1/EdSurvey/R/readPISA.R | 259 ++- EdSurvey-2.6.1/EdSurvey/R/readTALIS.R | 150 + EdSurvey-2.6.1/EdSurvey/R/readTIMSS.R | 76 EdSurvey-2.6.1/EdSurvey/R/readTIMSSAdv.R | 8 EdSurvey-2.6.1/EdSurvey/R/readUTILS.R | 1 EdSurvey-2.6.1/EdSurvey/R/read_ePIRLS.R | 6 EdSurvey-2.6.1/EdSurvey/R/rebindAttributes.R | 2 EdSurvey-2.6.1/EdSurvey/R/summary2.R | 2 EdSurvey-2.6.1/EdSurvey/R/waldTest.R | 2 EdSurvey-2.6.1/EdSurvey/build/vignette.rds |binary EdSurvey-2.6.1/EdSurvey/inst/NEWS.Rd | 50 EdSurvey-2.6.1/EdSurvey/inst/doc/introduction.Rmd | 6 EdSurvey-2.6.1/EdSurvey/inst/doc/introduction.html | 572 ++++-- EdSurvey-2.6.1/EdSurvey/inst/extdata/PIAACDict.rds |binary EdSurvey-2.6.1/EdSurvey/inst/extdata/PISAal.rds |binary EdSurvey-2.6.1/EdSurvey/man/DoFCorrection.Rd | 188 +- EdSurvey-2.6.1/EdSurvey/man/SD.Rd | 244 +- EdSurvey-2.6.1/EdSurvey/man/achievementLevels.Rd | 401 ++-- EdSurvey-2.6.1/EdSurvey/man/contourPlot.Rd | 7 EdSurvey-2.6.1/EdSurvey/man/cor.sdf.Rd | 331 ++- EdSurvey-2.6.1/EdSurvey/man/downloadECLS_K.Rd | 97 - EdSurvey-2.6.1/EdSurvey/man/downloadHSLS.Rd | 86 - EdSurvey-2.6.1/EdSurvey/man/downloadPIAAC.Rd | 72 EdSurvey-2.6.1/EdSurvey/man/downloadPISA.Rd | 134 - EdSurvey-2.6.1/EdSurvey/man/downloadTALIS.Rd | 72 EdSurvey-2.6.1/EdSurvey/man/downloadTIMSS.Rd | 104 - EdSurvey-2.6.1/EdSurvey/man/downloadTIMSSAdv.Rd | 102 - EdSurvey-2.6.1/EdSurvey/man/download_ePIRLS.Rd | 92 - EdSurvey-2.6.1/EdSurvey/man/edsurvey-class.Rd | 495 +++-- EdSurvey-2.6.1/EdSurvey/man/edsurvey.data.frame.list.Rd | 294 +-- EdSurvey-2.6.1/EdSurvey/man/examples/DoFCorrection.R | 2 EdSurvey-2.6.1/EdSurvey/man/examples/SD.R | 2 EdSurvey-2.6.1/EdSurvey/man/examples/achievementLevels.R | 1 EdSurvey-2.6.1/EdSurvey/man/examples/downloadECLS_K.R | 6 EdSurvey-2.6.1/EdSurvey/man/examples/downloadHSLS.R | 4 EdSurvey-2.6.1/EdSurvey/man/examples/downloadPIAAC.R | 4 EdSurvey-2.6.1/EdSurvey/man/examples/downloadPISA.R | 4 EdSurvey-2.6.1/EdSurvey/man/examples/downloadTALIS.R | 11 EdSurvey-2.6.1/EdSurvey/man/examples/downloadTIMSS.R | 6 EdSurvey-2.6.1/EdSurvey/man/examples/downloadTIMSSAdv.R | 6 EdSurvey-2.6.1/EdSurvey/man/examples/download_ePIRLS.R | 6 EdSurvey-2.6.1/EdSurvey/man/examples/edsurvey-class.R | 2 EdSurvey-2.6.1/EdSurvey/man/examples/edsurvey.data.frame.list.R | 12 EdSurvey-2.6.1/EdSurvey/man/examples/gap.R | 10 EdSurvey-2.6.1/EdSurvey/man/examples/getData.R | 4 EdSurvey-2.6.1/EdSurvey/man/examples/getPlausibleValue.R | 2 EdSurvey-2.6.1/EdSurvey/man/examples/getWeightJkReplicates.R | 2 EdSurvey-2.6.1/EdSurvey/man/examples/hasPlausibleValue.R | 2 EdSurvey-2.6.1/EdSurvey/man/examples/isWeight.R | 2 EdSurvey-2.6.1/EdSurvey/man/examples/levelsSDF.R | 2 EdSurvey-2.6.1/EdSurvey/man/examples/lm.sdf.R | 1 EdSurvey-2.6.1/EdSurvey/man/examples/merge.light.edsurvey.data.frame.R | 3 EdSurvey-2.6.1/EdSurvey/man/examples/nrow.edsurvey.data.frame.R | 3 EdSurvey-2.6.1/EdSurvey/man/examples/percentile.R | 2 EdSurvey-2.6.1/EdSurvey/man/examples/readBB_2001.R | 2 EdSurvey-2.6.1/EdSurvey/man/examples/readBB_2003.R | 2 EdSurvey-2.6.1/EdSurvey/man/examples/readBB_2012.R | 2 EdSurvey-2.6.1/EdSurvey/man/examples/readBPS_1994.R | 2 EdSurvey-2.6.1/EdSurvey/man/examples/readBPS_2001.R | 2 EdSurvey-2.6.1/EdSurvey/man/examples/readBPS_2009.R | 2 EdSurvey-2.6.1/EdSurvey/man/examples/readBPS_2014.R | 2 EdSurvey-2.6.1/EdSurvey/man/examples/readBTLS.R | 18 EdSurvey-2.6.1/EdSurvey/man/examples/readECLS_K1998.R | 6 EdSurvey-2.6.1/EdSurvey/man/examples/readECLS_K2011.R | 10 EdSurvey-2.6.1/EdSurvey/man/examples/readELS.R | 22 EdSurvey-2.6.1/EdSurvey/man/examples/readHSB_SO.R | 2 EdSurvey-2.6.1/EdSurvey/man/examples/readHSB_SR.R | 2 EdSurvey-2.6.1/EdSurvey/man/examples/readHSLS.R | 13 EdSurvey-2.6.1/EdSurvey/man/examples/readICCS.R | 2 EdSurvey-2.6.1/EdSurvey/man/examples/readICILS.R | 2 EdSurvey-2.6.1/EdSurvey/man/examples/readPIAAC.R | 3 EdSurvey-2.6.1/EdSurvey/man/examples/readPIRLS.R | 2 EdSurvey-2.6.1/EdSurvey/man/examples/readPISA.R | 3 EdSurvey-2.6.1/EdSurvey/man/examples/readTALIS.R | 14 EdSurvey-2.6.1/EdSurvey/man/examples/readTIMSS.R | 4 EdSurvey-2.6.1/EdSurvey/man/examples/readTIMSSAdv.R | 2 EdSurvey-2.6.1/EdSurvey/man/examples/read_ePIRLS.R | 2 EdSurvey-2.6.1/EdSurvey/man/examples/recode.sdf.R | 2 EdSurvey-2.6.1/EdSurvey/man/examples/rename.sdf.R | 2 EdSurvey-2.6.1/EdSurvey/man/examples/searchSDF.R | 2 EdSurvey-2.6.1/EdSurvey/man/examples/showCodebook.R | 2 EdSurvey-2.6.1/EdSurvey/man/examples/showCutPoints.R | 2 EdSurvey-2.6.1/EdSurvey/man/examples/showPlausibleValues.R | 2 EdSurvey-2.6.1/EdSurvey/man/examples/showWeights.R | 2 EdSurvey-2.6.1/EdSurvey/man/examples/subset.edsurvey.data.frame.R | 7 EdSurvey-2.6.1/EdSurvey/man/examples/updatePlausibleValue.R | 2 EdSurvey-2.6.1/EdSurvey/man/examples/varEstToCov.R | 2 EdSurvey-2.6.1/EdSurvey/man/gap.Rd | 840 +++++----- EdSurvey-2.6.1/EdSurvey/man/getData.Rd | 358 ++-- EdSurvey-2.6.1/EdSurvey/man/getPlausibleValue.Rd | 76 EdSurvey-2.6.1/EdSurvey/man/getWeightJkReplicates.Rd | 62 EdSurvey-2.6.1/EdSurvey/man/hasPlausibleValue.Rd | 82 EdSurvey-2.6.1/EdSurvey/man/isWeight.Rd | 78 EdSurvey-2.6.1/EdSurvey/man/levelsSDF.Rd | 88 - 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EdSurvey-2.6.1/EdSurvey/man/readPIAAC.Rd | 145 - EdSurvey-2.6.1/EdSurvey/man/readPIRLS.Rd | 162 - EdSurvey-2.6.1/EdSurvey/man/readPISA.Rd | 191 +- EdSurvey-2.6.1/EdSurvey/man/readTALIS.Rd | 160 + EdSurvey-2.6.1/EdSurvey/man/readTIMSS.Rd | 222 +- EdSurvey-2.6.1/EdSurvey/man/readTIMSSAdv.Rd | 164 - EdSurvey-2.6.1/EdSurvey/man/read_ePIRLS.Rd | 146 - EdSurvey-2.6.1/EdSurvey/man/recode.sdf.Rd | 80 EdSurvey-2.6.1/EdSurvey/man/rename.sdf.Rd | 100 - EdSurvey-2.6.1/EdSurvey/man/searchSDF.Rd | 122 - EdSurvey-2.6.1/EdSurvey/man/showCodebook.Rd | 122 - EdSurvey-2.6.1/EdSurvey/man/showCutPoints.Rd | 58 EdSurvey-2.6.1/EdSurvey/man/showPlausibleValues.Rd | 62 EdSurvey-2.6.1/EdSurvey/man/showWeights.Rd | 60 EdSurvey-2.6.1/EdSurvey/man/subset.Rd | 243 +- EdSurvey-2.6.1/EdSurvey/man/updatePlausibleValue.Rd | 82 EdSurvey-2.6.1/EdSurvey/man/varEstToCov.Rd | 166 + EdSurvey-2.6.1/EdSurvey/tests/testthat/REF-0-main.R | 52 EdSurvey-2.6.1/EdSurvey/tests/testthat/REF-2-esdfl.R | 32 EdSurvey-2.6.1/EdSurvey/tests/testthat/REF-3-TIMSS.R | 10 EdSurvey-2.6.1/EdSurvey/tests/testthat/REF-5-piaac.R | 63 EdSurvey-2.6.1/EdSurvey/tests/testthat/REF-6-ECLS_K.R | 8 EdSurvey-2.6.1/EdSurvey/tests/testthat/gddat.rds |binary EdSurvey-2.6.1/EdSurvey/tests/testthat/test-0-main.R | 21 EdSurvey-2.6.1/EdSurvey/tests/testthat/test-2-esdfl.R | 14 EdSurvey-2.6.1/EdSurvey/tests/testthat/test-3-TIMSS.R | 20 EdSurvey-2.6.1/EdSurvey/tests/testthat/test-4-pisa.R | 3 EdSurvey-2.6.1/EdSurvey/tests/testthat/test-5-piaac.R | 8 EdSurvey-2.6.1/EdSurvey/tests/testthat/test-6-ECLS_K.R | 14 EdSurvey-2.6.1/EdSurvey/tests/testthat/test-8-HSLS.R | 4 EdSurvey-2.6.1/EdSurvey/vignettes/introduction.Rmd | 6 177 files changed, 7465 insertions(+), 5856 deletions(-)
Title: Manipulation Testing Based on Density Discontinuity
Description: Density discontinuity testing (a.k.a. manipulation testing) is commonly employed in regression discontinuity designs and other program evaluation settings to detect perfect self-selection (manipulation) around a cutoff where treatment/policy assignment changes. This package implements manipulation testing procedures using the local polynomial density estimators: rddensity() to construct test statistics and p-values given a prespecified cutoff, rdbwdensity() to perform data-driven bandwidth selection, and rdplotdensity() to construct density plots.
Author: Matias D. Cattaneo, Michael Jansson, Xinwei Ma
Maintainer: Xinwei Ma <x1ma@ucsd.edu>
Diff between rddensity versions 2.0 dated 2020-08-05 and 2.1 dated 2020-09-02
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++----------- R/rdbwdensity.R | 6 +++--- R/rddensity-package.R | 18 +++++++++--------- R/rddensity.R | 14 +++++++------- R/rddensity_senate.R | 2 +- R/rdplotdensity.R | 14 +++++++------- man/rdbwdensity.Rd | 6 +++--- man/rddensity-package.Rd | 18 +++++++++--------- man/rddensity.Rd | 14 +++++++------- man/rddensity_senate.Rd | 2 +- man/rdplotdensity.Rd | 14 +++++++------- 12 files changed, 68 insertions(+), 68 deletions(-)
Title: Tabular Data Backed by Partitioned 'fst' Files
Description: Intended for larger-than-memory tabular data, 'prt' objects provide an interface to read row and/or column subsets into memory as data.table objects. Data queries, constructed as 'R' expressions, are evaluated using the non-standard evaluation framework provided by 'rlang' and file-backing is powered by the fast and efficient 'fst' package.
Author: Nicolas Bennett [aut, cre],
Drago Plecko [ctb]
Maintainer: Nicolas Bennett <nicolas.bennett@stat.math.ethz.ch>
Diff between prt versions 0.1.0 dated 2020-08-18 and 0.1.1 dated 2020-09-02
DESCRIPTION | 6 +++--- MD5 | 9 +++++---- NEWS.md |only inst/doc/prt.html | 4 ++-- man/formatting.Rd | 2 +- tests/testthat/test-format.R | 2 ++ 6 files changed, 13 insertions(+), 10 deletions(-)
Title: Graph-Based Landscape De-Fragmentation
Description: Provides a set of tools to help the de-fragmentation process. It works by prioritizing the different sections of linear infrastructures (e.g. roads, power-lines) to increase the available amount of a given resource.
Author: Frederico Mestre, Fernando Ascensao, A. Marcia Barbosa
Maintainer: Frederico Mestre <mestre.frederico@gmail.com>
Diff between gDefrag versions 0.2 dated 2019-11-18 and 0.3 dated 2020-09-02
DESCRIPTION | 8 +- MD5 | 19 ++--- R/edge.creation.R | 127 ++++++++++++++++++++++++++-------- R/gDefrag.full.R | 7 + R/node.creation.R | 79 +++++++++++++++++---- R/plotgraph.R | 64 ++++++++++++++--- R/prioritize.R | 85 ++++++++++++++++++----- README.md |only build/partial.rdb |binary data/road_P.rda |binary man/gDefrag.full.Rd | 192 ++++++++++++++++++++++++++-------------------------- 11 files changed, 402 insertions(+), 179 deletions(-)
Title: The Tidymodels Extension for Time Series Modeling
Description: The time series forecasting framework for use with the 'tidymodels' ecosystem.
Models include ARIMA, Exponential Smoothing, and additional time series models
from the 'forecast' and 'prophet' packages. Refer to "Forecasting Principles & Practice, Second edition"
(<https://otexts.com/fpp2/>).
Refer to "Prophet: forecasting at scale"
(<https://research.fb.com/blog/2017/02/prophet-forecasting-at-scale/>.).
Author: Matt Dancho [aut, cre],
Business Science [cph]
Maintainer: Matt Dancho <mdancho@business-science.io>
Diff between modeltime versions 0.0.2 dated 2020-07-03 and 0.1.0 dated 2020-09-02
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modeltime-0.1.0/modeltime/R/modeltime-accuracy.R | 115 modeltime-0.1.0/modeltime/R/modeltime-calibrate.R | 178 modeltime-0.1.0/modeltime/R/modeltime-forecast-plot.R | 21 modeltime-0.1.0/modeltime/R/modeltime-forecast.R | 561 +- modeltime-0.1.0/modeltime/R/modeltime-refit.R | 27 modeltime-0.1.0/modeltime/R/modeltime-residuals-plot.R |only modeltime-0.1.0/modeltime/R/modeltime-residuals.R |only modeltime-0.1.0/modeltime/R/modeltime-table.R | 110 modeltime-0.1.0/modeltime/R/parsnip-arima_boost.R | 7 modeltime-0.1.0/modeltime/R/parsnip-arima_boost_data.R | 4 modeltime-0.1.0/modeltime/R/parsnip-arima_reg.R | 6 modeltime-0.1.0/modeltime/R/parsnip-arima_reg_data.R | 4 modeltime-0.1.0/modeltime/R/parsnip-exp_smoothing.R | 4 modeltime-0.1.0/modeltime/R/parsnip-exp_smoothing_data.R | 3 modeltime-0.1.0/modeltime/R/parsnip-nnetar_reg.R |only modeltime-0.1.0/modeltime/R/parsnip-nnetar_reg_data.R |only modeltime-0.1.0/modeltime/R/parsnip-prophet_boost.R | 133 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| 2 modeltime-0.1.0/modeltime/man/combine_modeltime_tables.Rd |only modeltime-0.1.0/modeltime/man/get_tbats_description.Rd |only modeltime-0.1.0/modeltime/man/is_calibrated.Rd |only modeltime-0.1.0/modeltime/man/is_modeltime_model.Rd |only modeltime-0.1.0/modeltime/man/is_modeltime_table.Rd |only modeltime-0.1.0/modeltime/man/mdl_time_forecast.Rd | 5 modeltime-0.1.0/modeltime/man/modeltime_accuracy.Rd | 10 modeltime-0.1.0/modeltime/man/modeltime_forecast.Rd | 64 modeltime-0.1.0/modeltime/man/modeltime_residuals.Rd |only modeltime-0.1.0/modeltime/man/nnetar_fit_impl.Rd |only modeltime-0.1.0/modeltime/man/nnetar_params.Rd |only modeltime-0.1.0/modeltime/man/nnetar_predict_impl.Rd |only modeltime-0.1.0/modeltime/man/nnetar_reg.Rd |only modeltime-0.1.0/modeltime/man/plot_modeltime_forecast.Rd | 4 modeltime-0.1.0/modeltime/man/plot_modeltime_residuals.Rd |only modeltime-0.1.0/modeltime/man/prophet_boost.Rd | 49 modeltime-0.1.0/modeltime/man/prophet_fit_impl.Rd | 23 modeltime-0.1.0/modeltime/man/prophet_params.Rd | 28 modeltime-0.1.0/modeltime/man/prophet_reg.Rd | 48 modeltime-0.1.0/modeltime/man/prophet_xgboost_fit_impl.Rd | 6 modeltime-0.1.0/modeltime/man/pull_modeltime_residuals.Rd |only modeltime-0.1.0/modeltime/man/seasonal_reg.Rd |only modeltime-0.1.0/modeltime/man/stlm_arima_fit_impl.Rd | 2 modeltime-0.1.0/modeltime/man/stlm_arima_predict_impl.Rd | 4 modeltime-0.1.0/modeltime/man/stlm_ets_fit_impl.Rd | 2 modeltime-0.1.0/modeltime/man/stlm_ets_predict_impl.Rd | 4 modeltime-0.1.0/modeltime/man/tbats_fit_impl.Rd |only modeltime-0.1.0/modeltime/man/tbats_predict_impl.Rd |only modeltime-0.1.0/modeltime/man/update_model_description.Rd |only modeltime-0.1.0/modeltime/tests/testthat.R | 2 modeltime-0.1.0/modeltime/tests/testthat/test-algo-arima_boost-Arima.R | 19 modeltime-0.1.0/modeltime/tests/testthat/test-algo-arima_boost-auto_arima.R | 141 modeltime-0.1.0/modeltime/tests/testthat/test-algo-nnetar_reg.R |only modeltime-0.1.0/modeltime/tests/testthat/test-algo-prophet_boost.R | 103 modeltime-0.1.0/modeltime/tests/testthat/test-algo-prophet_reg.R | 96 modeltime-0.1.0/modeltime/tests/testthat/test-algo-seasonal_decomp_arima.R | 81 modeltime-0.1.0/modeltime/tests/testthat/test-algo-seasonal_decomp_ets.R | 14 modeltime-0.1.0/modeltime/tests/testthat/test-algo-seasonal_reg_tbats.R |only modeltime-0.1.0/modeltime/tests/testthat/test-helpers-combine-modeltime-tables.R |only modeltime-0.1.0/modeltime/tests/testthat/test-helpers-update-modeltime-tables.R |only modeltime-0.1.0/modeltime/tests/testthat/test-modeltime_table-forecast-accuracy-refitting.R | 395 - modeltime-0.1.0/modeltime/tests/testthat/test-modeltime_table-no-calib-refit.R |only modeltime-0.1.0/modeltime/tests/testthat/test-results-accuracy-tables.R |only modeltime-0.1.0/modeltime/tests/testthat/test-results-forecast-plots.R |only modeltime-0.1.0/modeltime/tests/testthat/test-tune_workflows.R | 84 modeltime-0.1.0/modeltime/vignettes/extending-modeltime.Rmd | 2 modeltime-0.1.0/modeltime/vignettes/getting-started-with-modeltime.Rmd | 38 modeltime-0.1.0/modeltime/vignettes/temp |only 99 files changed, 2689 insertions(+), 2759 deletions(-)
Title: Comprehensive Automatized Evaluation of Distribution Models for
Count Data
Description: A large number of measurements generate count data. This is a statistical data type
that only assumes non-negative integer values and is generated by counting. Typically, counting
data can be found in biomedical applications, such as the analysis of DNA double-strand breaks.
The number of DNA double-strand breaks can be counted in individual cells using various
bioanalytical methods. For diagnostic applications, it is relevant to record the distribution of
the number data in order to determine their biomedical significance (Roediger, S. et al., 2018.
Journal of Laboratory and Precision Medicine. <doi:10.21037/jlpm.2018.04.10>). The software
offers functions for a comprehensive automated evaluation of distribution models of count
data. In addition to programmatic interaction, a graphical user interface (web server)
is included, which enables fast and interactive data-scientific analyses. The user is supported
in selecting the most suitable counting distribution for his own data set.
Author: Jaroslaw Chilimoniuk [cre, ctb]
(<https://orcid.org/0000-0001-5467-018X>),
Alicja Gosiewska [ctb] (<https://orcid.org/0000-0001-6563-5742>),
Jadwiga Słowik [ctb] (<https://orcid.org/0000-0003-3466-8933>),
Michal Burdukiewicz [aut] (<https://orcid.org/0000-0001-8926-582X>),
Stefan Roediger [ctb] (<https://orcid.org/0000-0002-1441-6512>)
Maintainer: Jaroslaw Chilimoniuk <jaroslaw.chilimoniuk@gmail.com>
Diff between countfitteR versions 1.2 dated 2020-08-10 and 1.3 dated 2020-09-02
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- README.md | 4 ++-- inst/CITATION | 2 +- inst/WORDLIST | 2 +- inst/doc/countfitteR.html | 4 ++-- 6 files changed, 14 insertions(+), 14 deletions(-)
Title: A Tool for Automating Download and Preprocessing of MODIS Land
Products Data
Description: Allows automating the creation of time series of rasters derived
from MODIS Satellite Land Products data. It performs several typical
preprocessing steps such as download, mosaicking, reprojection and resize
of data acquired on a specified time period. All processing parameters
can be set using a user-friendly GUI. Users can select which layers of
the original MODIS HDF files they want to process, which additional
Quality Indicators should be extracted from aggregated MODIS Quality
Assurance layers and, in the case of Surface Reflectance products
, which Spectral Indexes should be computed from the original reflectance
bands. For each output layer, outputs are saved as single-band raster
files corresponding to each available acquisition date. Virtual files
allowing access to the entire time series as a single file are also created.
Command-line execution exploiting a previously saved processing options
file is also possible, allowing to automatically update time series
related to a MODIS product whenever a new image is available.
Author: Lorenzo Busetto [aut, cre] (<https://orcid.org/0000-0001-9634-6038>),
Luigi Ranghetti [aut] (<https://orcid.org/0000-0001-6207-5188>),
Leah Wasser [rev] (Leah Wasser reviewed the package for rOpenSci, see
https://github.com/ropensci/software-review/issues/184),
Jeff Hanson [rev] (Jeff Hanson reviewed the package for rOpenSci, see
https://github.com/ropensci/software-review/issues/184)
Maintainer: Lorenzo Busetto <lbusett@gmail.com>
Diff between MODIStsp versions 1.4.0 dated 2020-05-10 and 2.0.2 dated 2020-09-02
MODIStsp-1.4.0/MODIStsp/R/MODIStsp_reset_options.R |only MODIStsp-1.4.0/MODIStsp/R/ask_permission.R |only MODIStsp-1.4.0/MODIStsp/R/create_help_messages.R |only MODIStsp-1.4.0/MODIStsp/R/gh_changeproj.R |only MODIStsp-1.4.0/MODIStsp/R/gh_help.R |only MODIStsp-1.4.0/MODIStsp/R/gh_load_extent.R |only MODIStsp-1.4.0/MODIStsp/R/gh_selcat.R |only MODIStsp-1.4.0/MODIStsp/R/gh_selectmap.R |only MODIStsp-1.4.0/MODIStsp/R/gh_sellayers.R |only MODIStsp-1.4.0/MODIStsp/R/gh_selprod.R |only MODIStsp-1.4.0/MODIStsp/R/gh_tiles_from_bbox.R |only MODIStsp-1.4.0/MODIStsp/R/gh_view_extent.R |only MODIStsp-1.4.0/MODIStsp/R/gui_helpers.R |only MODIStsp-1.4.0/MODIStsp/R/load_opts.R |only MODIStsp-1.4.0/MODIStsp/inst/ExtData/Launcher |only MODIStsp-1.4.0/MODIStsp/inst/ExtData/MODIS_Tiles.gif |only MODIStsp-1.4.0/MODIStsp/inst/doc/MODIStsp.pdf |only MODIStsp-1.4.0/MODIStsp/inst/testdata/VI_16Days_500m_v6 |only MODIStsp-1.4.0/MODIStsp/man/MODIStsp_reset_options.Rd |only MODIStsp-1.4.0/MODIStsp/man/ask_permission.Rd |only MODIStsp-1.4.0/MODIStsp/man/load_opts.Rd |only MODIStsp-1.4.0/MODIStsp/tests/testthat/test_create_help_messages.R |only MODIStsp-1.4.0/MODIStsp/tests/testthat/test_modistspGUI.R |only MODIStsp-1.4.0/MODIStsp/vignettes/Figure_1_Vignette.png |only MODIStsp-1.4.0/MODIStsp/vignettes/Figure_2_new.png |only MODIStsp-1.4.0/MODIStsp/vignettes/Figure_3.png |only MODIStsp-1.4.0/MODIStsp/vignettes/MAIN_GUI.png |only MODIStsp-1.4.0/MODIStsp/vignettes/NEWIND_GUI.png |only MODIStsp-1.4.0/MODIStsp/vignettes/SELECT_GUI.png |only MODIStsp-1.4.0/MODIStsp/vignettes/figure_4.png |only MODIStsp-2.0.2/MODIStsp/DESCRIPTION | 36 MODIStsp-2.0.2/MODIStsp/MD5 | 258 - MODIStsp-2.0.2/MODIStsp/NAMESPACE | 29 MODIStsp-2.0.2/MODIStsp/NEWS.md | 19 MODIStsp-2.0.2/MODIStsp/R/MODIStsp.R | 674 ++-- MODIStsp-2.0.2/MODIStsp/R/MODIStsp_GUI.R | 1373 ---------- MODIStsp-2.0.2/MODIStsp/R/MODIStsp_addindex.R | 437 --- MODIStsp-2.0.2/MODIStsp/R/MODIStsp_download.R | 55 MODIStsp-2.0.2/MODIStsp/R/MODIStsp_extract.R | 6 MODIStsp-2.0.2/MODIStsp/R/MODIStsp_get_prodlayers.R |only MODIStsp-2.0.2/MODIStsp/R/MODIStsp_process.R | 415 +-- MODIStsp-2.0.2/MODIStsp/R/MODIStsp_process_QA_bits.R | 7 MODIStsp-2.0.2/MODIStsp/R/MODIStsp_process_bands.R | 247 + MODIStsp-2.0.2/MODIStsp/R/MODIStsp_process_indexes.R | 12 MODIStsp-2.0.2/MODIStsp/R/MODIStsp_resetindexes.R | 43 MODIStsp-2.0.2/MODIStsp/R/MODIStsp_vrt_create.R | 27 MODIStsp-2.0.2/MODIStsp/R/bbox_from_file.R | 9 MODIStsp-2.0.2/MODIStsp/R/check_formula_errors.R | 18 MODIStsp-2.0.2/MODIStsp/R/check_proc_opts.R |only MODIStsp-2.0.2/MODIStsp/R/check_projection.R | 2 MODIStsp-2.0.2/MODIStsp/R/get_mod_dates.R | 4 MODIStsp-2.0.2/MODIStsp/R/get_mod_dirs.R | 18 MODIStsp-2.0.2/MODIStsp/R/get_mod_filenames.R | 29 MODIStsp-2.0.2/MODIStsp/R/get_reqbands.R | 16 MODIStsp-2.0.2/MODIStsp/R/get_yeardates.R | 5 MODIStsp-2.0.2/MODIStsp/R/load_prodopts.R | 35 MODIStsp-2.0.2/MODIStsp/R/process_message.R | 21 MODIStsp-2.0.2/MODIStsp/R/reproj_bbox.R | 21 MODIStsp-2.0.2/MODIStsp/R/set_bandind_matrix.R | 8 MODIStsp-2.0.2/MODIStsp/R/shinygui_saveopts.R |only MODIStsp-2.0.2/MODIStsp/R/split_nodata_values.R | 9 MODIStsp-2.0.2/MODIStsp/R/tiles_from_bbox.R |only MODIStsp-2.0.2/MODIStsp/README.md | 304 -- MODIStsp-2.0.2/MODIStsp/build/vignette.rds |binary MODIStsp-2.0.2/MODIStsp/inst/ExtData/MODIStsp_ProdOpts.xml | 14 MODIStsp-2.0.2/MODIStsp/inst/ExtData/Previous/MODIStsp_ProdOpts.RData |binary MODIStsp-2.0.2/MODIStsp/inst/ExtData/Previous/MODIStsp_indexes.json |only MODIStsp-2.0.2/MODIStsp/inst/ExtData/Previous/mstp_defaults.json |only MODIStsp-2.0.2/MODIStsp/inst/WORDLIST | 49 MODIStsp-2.0.2/MODIStsp/inst/app |only MODIStsp-2.0.2/MODIStsp/inst/doc/MODIStsp.R | 244 - MODIStsp-2.0.2/MODIStsp/inst/doc/MODIStsp.Rmd | 689 ----- MODIStsp-2.0.2/MODIStsp/inst/doc/MODIStsp.html |only MODIStsp-2.0.2/MODIStsp/inst/testdata/MODIStsp_2017-12-17.json | 4 MODIStsp-2.0.2/MODIStsp/inst/testdata/test01.json | 37 MODIStsp-2.0.2/MODIStsp/inst/testdata/test01a.json | 39 MODIStsp-2.0.2/MODIStsp/inst/testdata/test02.json | 35 MODIStsp-2.0.2/MODIStsp/inst/testdata/test03.json | 41 MODIStsp-2.0.2/MODIStsp/inst/testdata/test03a.json | 41 MODIStsp-2.0.2/MODIStsp/inst/testdata/test04.json | 33 MODIStsp-2.0.2/MODIStsp/inst/testdata/test04a.json | 33 MODIStsp-2.0.2/MODIStsp/inst/testdata/test04b.json | 6 MODIStsp-2.0.2/MODIStsp/inst/testdata/test04c.json | 35 MODIStsp-2.0.2/MODIStsp/inst/testdata/test05.json | 37 MODIStsp-2.0.2/MODIStsp/inst/testdata/test05a.json | 39 MODIStsp-2.0.2/MODIStsp/inst/testdata/test06.json | 34 MODIStsp-2.0.2/MODIStsp/inst/testdata/test06a.json |only MODIStsp-2.0.2/MODIStsp/inst/testdata/test06b.json |only MODIStsp-2.0.2/MODIStsp/inst/testdata/test07.json | 32 MODIStsp-2.0.2/MODIStsp/inst/testdata/test07b.json | 34 MODIStsp-2.0.2/MODIStsp/inst/testdata/test_MOD10A2.json | 31 MODIStsp-2.0.2/MODIStsp/inst/testdata/test_MOD13A2.json | 31 MODIStsp-2.0.2/MODIStsp/inst/testdata/test_addindex.json | 6 MODIStsp-2.0.2/MODIStsp/inst/testdata/test_extract.json | 31 MODIStsp-2.0.2/MODIStsp/inst/testdata/test_mask.json | 6 MODIStsp-2.0.2/MODIStsp/inst/testdata/testtemp_win.json | 6 MODIStsp-2.0.2/MODIStsp/man/MODIStsp.Rd | 220 + MODIStsp-2.0.2/MODIStsp/man/MODIStsp_GUI.Rd | 80 MODIStsp-2.0.2/MODIStsp/man/MODIStsp_addindex.Rd | 65 MODIStsp-2.0.2/MODIStsp/man/MODIStsp_download.Rd | 7 MODIStsp-2.0.2/MODIStsp/man/MODIStsp_extract.Rd | 6 MODIStsp-2.0.2/MODIStsp/man/MODIStsp_get_prodlayers.Rd |only MODIStsp-2.0.2/MODIStsp/man/MODIStsp_get_prodnames.Rd |only MODIStsp-2.0.2/MODIStsp/man/MODIStsp_process.Rd | 217 - MODIStsp-2.0.2/MODIStsp/man/MODIStsp_process_bands.Rd | 41 MODIStsp-2.0.2/MODIStsp/man/MODIStsp_resetindexes.Rd | 15 MODIStsp-2.0.2/MODIStsp/man/MODIStsp_vrt_create.Rd | 40 MODIStsp-2.0.2/MODIStsp/man/check_proc_opts.Rd |only MODIStsp-2.0.2/MODIStsp/man/get_reqbands.Rd | 29 MODIStsp-2.0.2/MODIStsp/man/get_yeardates.Rd | 4 MODIStsp-2.0.2/MODIStsp/man/install_MODIStsp_launcher.Rd | 174 - MODIStsp-2.0.2/MODIStsp/man/load_prodopts.Rd | 6 MODIStsp-2.0.2/MODIStsp/man/process_message.Rd | 7 MODIStsp-2.0.2/MODIStsp/man/set_bandind_matrix.Rd | 37 MODIStsp-2.0.2/MODIStsp/man/split_nodata_values.Rd | 2 MODIStsp-2.0.2/MODIStsp/tests/testthat/test_MODIStsp_00.R | 16 MODIStsp-2.0.2/MODIStsp/tests/testthat/test_MODIStsp_01.R | 10 MODIStsp-2.0.2/MODIStsp/tests/testthat/test_MODIStsp_02.R | 2 MODIStsp-2.0.2/MODIStsp/tests/testthat/test_MODIStsp_03.R | 20 MODIStsp-2.0.2/MODIStsp/tests/testthat/test_MODIStsp_04.R | 3 MODIStsp-2.0.2/MODIStsp/tests/testthat/test_MODIStsp_05.R | 4 MODIStsp-2.0.2/MODIStsp/tests/testthat/test_MODIStsp_06.R | 23 MODIStsp-2.0.2/MODIStsp/tests/testthat/test_MODIStsp_07.R | 5 MODIStsp-2.0.2/MODIStsp/tests/testthat/test_MODIStsp_addindex.R | 29 MODIStsp-2.0.2/MODIStsp/tests/testthat/test_MODIStsp_extract.R | 2 MODIStsp-2.0.2/MODIStsp/tests/testthat/test_MODIStsp_resetindexes.R | 12 MODIStsp-2.0.2/MODIStsp/tests/testthat/test_get_yeardates.R | 8 MODIStsp-2.0.2/MODIStsp/vignettes/GUI_1.PNG |only MODIStsp-2.0.2/MODIStsp/vignettes/GUI_2_bbox.PNG |only MODIStsp-2.0.2/MODIStsp/vignettes/GUI_2_file.PNG |only MODIStsp-2.0.2/MODIStsp/vignettes/GUI_2_tiles.PNG |only MODIStsp-2.0.2/MODIStsp/vignettes/GUI_3.PNG |only MODIStsp-2.0.2/MODIStsp/vignettes/GUI_bar.PNG |only MODIStsp-2.0.2/MODIStsp/vignettes/GUI_newind.PNG |only MODIStsp-2.0.2/MODIStsp/vignettes/MODIStsp.Rmd | 689 ----- 135 files changed, 2273 insertions(+), 5224 deletions(-)
Title: Bayesian Dynamic Factor Analysis (DFA) with 'Stan'
Description: Implements Bayesian dynamic factor analysis with 'Stan'. Dynamic
factor analysis is a dimension reduction tool for multivariate time series.
'bayesdfa' extends conventional dynamic factor models in several ways.
First, extreme events may be estimated in the latent trend by modeling
process error with a student-t distribution. Second, autoregressive and
moving average components can be optionally included. Third, the estimated
dynamic factors can be analyzed with hidden Markov models to evaluate
support for latent regimes.
Author: Eric J. Ward [aut, cre],
Sean C. Anderson [aut],
Luis A. Damiano [aut],
Mary E. Hunsicker, [ctb],
Mike A. Litzow [ctb],
Trustees of Columbia University [cph]
Maintainer: Eric J. Ward <eric.ward@noaa.gov>
Diff between bayesdfa versions 0.1.3 dated 2019-05-22 and 0.1.5 dated 2020-09-02
bayesdfa-0.1.3/bayesdfa/inst/doc/covariates.R |only bayesdfa-0.1.3/bayesdfa/inst/doc/covariates.Rmd |only bayesdfa-0.1.3/bayesdfa/inst/doc/covariates.html |only bayesdfa-0.1.3/bayesdfa/vignettes/covariates.Rmd |only bayesdfa-0.1.5/bayesdfa/DESCRIPTION | 8 bayesdfa-0.1.5/bayesdfa/MD5 | 90 +- bayesdfa-0.1.5/bayesdfa/NAMESPACE | 1 bayesdfa-0.1.5/bayesdfa/NEWS.md | 4 bayesdfa-0.1.5/bayesdfa/R/find_dfa_trends.R | 2 bayesdfa-0.1.5/bayesdfa/R/find_regimes.R | 2 bayesdfa-0.1.5/bayesdfa/R/find_swans.R | 2 bayesdfa-0.1.5/bayesdfa/R/fit_dfa.R | 206 ++++- bayesdfa-0.1.5/bayesdfa/R/fit_regimes.R | 2 bayesdfa-0.1.5/bayesdfa/R/invert_chains.R | 2 bayesdfa-0.1.5/bayesdfa/R/loo.R | 4 bayesdfa-0.1.5/bayesdfa/R/plot_fitted.R | 34 bayesdfa-0.1.5/bayesdfa/R/plot_loadings.R | 2 bayesdfa-0.1.5/bayesdfa/R/plot_regime_model.R | 2 bayesdfa-0.1.5/bayesdfa/R/plot_trends.R | 2 bayesdfa-0.1.5/bayesdfa/R/predicted.R | 11 bayesdfa-0.1.5/bayesdfa/R/rotate_trends.R | 2 bayesdfa-0.1.5/bayesdfa/R/trend_cor.R | 2 bayesdfa-0.1.5/bayesdfa/build/vignette.rds |binary bayesdfa-0.1.5/bayesdfa/inst/doc/bayesdfa.R | 42 - bayesdfa-0.1.5/bayesdfa/inst/doc/bayesdfa.Rmd | 16 bayesdfa-0.1.5/bayesdfa/inst/doc/bayesdfa.html | 221 ++--- bayesdfa-0.1.5/bayesdfa/man/find_dfa_trends.Rd | 16 bayesdfa-0.1.5/bayesdfa/man/find_inverted_chains.Rd | 2 bayesdfa-0.1.5/bayesdfa/man/find_regimes.Rd | 16 bayesdfa-0.1.5/bayesdfa/man/find_swans.Rd | 2 bayesdfa-0.1.5/bayesdfa/man/fit_dfa.Rd | 86 +- bayesdfa-0.1.5/bayesdfa/man/fit_regimes.Rd | 15 bayesdfa-0.1.5/bayesdfa/man/hmm_init.Rd | 4 bayesdfa-0.1.5/bayesdfa/man/is_converged.Rd | 3 bayesdfa-0.1.5/bayesdfa/man/loo.Rd | 6 bayesdfa-0.1.5/bayesdfa/man/plot_fitted.Rd | 2 bayesdfa-0.1.5/bayesdfa/man/plot_loadings.Rd | 14 bayesdfa-0.1.5/bayesdfa/man/plot_regime_model.Rd | 13 bayesdfa-0.1.5/bayesdfa/man/plot_trends.Rd | 10 bayesdfa-0.1.5/bayesdfa/man/predicted.Rd | 2 bayesdfa-0.1.5/bayesdfa/man/rotate_trends.Rd | 2 bayesdfa-0.1.5/bayesdfa/man/sim_dfa.Rd | 18 bayesdfa-0.1.5/bayesdfa/man/trend_cor.Rd | 15 bayesdfa-0.1.5/bayesdfa/src/stan_files/dfa.stan | 391 +++++++--- bayesdfa-0.1.5/bayesdfa/tests/testthat/test-fit.R | 63 + bayesdfa-0.1.5/bayesdfa/vignettes/bayesdfa.Rmd | 16 bayesdfa-0.1.5/bayesdfa/vignettes/combining_data.Rmd.orig |only bayesdfa-0.1.5/bayesdfa/vignettes/compositional.Rmd.orig |only bayesdfa-0.1.5/bayesdfa/vignettes/covariates.Rmd.orig |only bayesdfa-0.1.5/bayesdfa/vignettes/estimate_process_sigma.Rmd.orig |only 50 files changed, 945 insertions(+), 408 deletions(-)
Title: Single Cell Mapper
Description: Description of scMappR R package adapted from pre-print. The single cell mapper (scMappR) R package contains a suite of bioinformatic tools that provide experimentally relevant cell-type specific information to a list of differentially expressed genes (DEG). The function "scMappR_and_pathway_analysis" reranks DEGs to generate cell-type specificity scores called cell-weighted fold-changes. Users input a list of DEGs, normalized counts, and a signature matrix into this function. scMappR then re-weights bulk DEGs by cell-type specific expression from the signature matrix, cell-type proportions from RNA-seq deconvolution and the ratio of cell-type proportions between the two conditions to account for changes in cell-type proportion. With cwFold-changes calculated, scMappR uses two approaches to utilize cwFold-changes to complete cell-type specific pathway analysis. The "process_dgTMatrix_lists" function in the scMappR package contains an automated scRNA-seq processing pipeline where users input scRNA-seq count data, which is made compatible for scMappR and other R packages that analyze scRNA-seq data. We further used this to store hundreds up regularly updating signature matrices. The functions "tissue_by_celltype_enrichment", "tissue_scMappR_internal", and "tissue_scMappR_custom" combine these consistently processed scRNAseq count data with gene-set enrichment tools to allow for cell-type marker enrichment of a generic gene list (e.g. GWAS hits). Reference: Sokolowski,D.J., Faykoo-Martinez,M., Erdman,L., Hou,H., Chan,C., Zhu,H., Holmes,M.M., Goldenberg,A. and Wilson,M.D. (2020) Single-cell mapper (scMappR): using scRNA-seq to infer cell-type specificities of differentially expressed genes. BioRxiv, 10.1101/2020.08.24.265298.
Author: Dustin Sokolowski [aut, cre],
Mariela Faykoo-Martinez [aut],
Lauren Erdman [aut],
Houyun Hou [aut],
Cadia Chan [aut],
Helen Zhu [aut],
Melissa Holmes [aut],
Anna Goldenberg [aut],
Michael Wilson [aut]
Maintainer: Dustin Sokolowski <dustin.sokolowski@sickkids.ca>
Diff between scMappR versions 0.1.3 dated 2020-07-20 and 0.1.4 dated 2020-09-02
DESCRIPTION | 21 +++++++++++++-------- MD5 | 16 +++++++++------- NAMESPACE | 1 + R/get_signature_matrices.R |only R/make_TF_barplot.R | 5 +++-- R/plotBP.R | 5 +++-- R/process_dgTMatrix_lists.R | 33 +++++++++++++++++++++++++++++++-- R/tissue_scMappR_internal.R | 20 +++++++++++++++++++- README.md | 12 +++++++++++- man/get_signature_matrices.Rd |only 10 files changed, 90 insertions(+), 23 deletions(-)
Title: Toolbox for Model Building and Forecasting
Description: Implements functions and instruments for regression model building and its
application to forecasting. The main scope of the package is in variables selection
and models specification for cases of time series data. This includes promotional
modelling, selection between different dynamic regressions with non-standard
distributions of errors, selection based on cross validation, solutions to the fat
regression model problem and more. Models developed in the package are tailored
specifically for forecasting purposes. So as a results there are several methods
that allow producing forecasts from these models and visualising them.
Author: Ivan Svetunkov [aut, cre] (Lecturer at Centre for Marketing Analytics
and Forecasting, Lancaster University, UK),
Yves R. Sagaert [ctb] (Visiting Research at Centre for Marketing
Analytics and Forecasting, Lancaster University, UK)
Maintainer: Ivan Svetunkov <ivan@svetunkov.ru>
Diff between greybox versions 0.6.1 dated 2020-08-10 and 0.6.2 dated 2020-09-02
DESCRIPTION | 12 MD5 | 77 ++-- NAMESPACE | 17 NEWS | 26 + R/alm.R | 195 +++++++---- R/bcnorm.R | 2 R/coefbootstrap.R |only R/detector-dst-leap.R |only R/gnorm.R | 24 + R/lmCombine.R | 3 R/lmDynamic.R | 4 R/mcor.R | 3 R/methods.R | 748 ++++++++++++++++++++++++------------------- R/rmcb.R | 2 R/ro.R | 56 +-- R/stepwise.R | 15 R/temporaldummy.R | 7 README.md | 21 - build/partial.rdb |binary inst/doc/alm.R | 9 inst/doc/alm.Rmd | 56 ++- inst/doc/alm.html | 247 ++++++++------ inst/doc/greybox.Rmd | 23 - inst/doc/greybox.html | 8 inst/doc/maUsingGreybox.html | 4 inst/doc/ro.R | 8 inst/doc/ro.Rmd | 17 inst/doc/ro.html | 58 +-- man/actuals.Rd | 2 man/alm.Rd | 2 man/bcnorm-distribution.Rd | 2 man/coef.alm.Rd |only man/coefbootstrap.Rd |only man/detectdst.Rd |only man/outlierdummy.Rd | 2 man/predict.greybox.Rd | 3 man/rmcb.Rd | 2 man/ro.Rd | 52 +- man/temporaldummy.Rd | 2 vignettes/alm.Rmd | 56 ++- vignettes/greybox.Rmd | 23 - vignettes/ro.Rmd | 17 42 files changed, 1109 insertions(+), 696 deletions(-)
Title: Distributed Representations of Words
Description: Learn vector representations of words by continuous bag of words and skip-gram implementations of the 'word2vec' algorithm.
The techniques are detailed in the paper "Distributed Representations of Words and Phrases and their Compositionality" by Mikolov et al. (2013), available at <arXiv:1310.4546>.
Author: Jan Wijffels [aut, cre, cph] (R wrapper),
BNOSAC [cph] (R wrapper),
Max Fomichev [ctb, cph] (Code in src/word2vec)
Maintainer: Jan Wijffels <jwijffels@bnosac.be>
Diff between word2vec versions 0.2.1 dated 2020-06-12 and 0.3.0 dated 2020-09-02
DESCRIPTION | 10 +++--- MD5 | 22 ++++++++------ NAMESPACE | 2 + NEWS.md | 4 ++ R/RcppExports.R | 8 +++++ R/doc2vec.R |only R/pkg.R | 1 R/word2vec.R | 3 +- man/doc2vec.Rd |only src/RcppExports.cpp | 29 +++++++++++++++++++ src/rcpp_word2vec.cpp | 56 ++++++++++++++++++++++++++++++++++++++ src/word2vec/include/word2vec.hpp | 4 +- src/word2vec/lib/word2vec.cpp | 4 +- 13 files changed, 123 insertions(+), 20 deletions(-)
Title: An Extensible Approach to Flux Balance Analysis
Description: A toolkit for Flux Balance Analysis and related
metabolic modeling techniques. Functions are provided for: parsing
models in tabular format, converting parsed metabolic models to input
formats for common linear programming solvers, and
evaluating and applying gene-protein-reaction mappings. In addition, there
are wrappers to parse a model, select a solver, find the metabolic fluxes,
and return the results applied to the original model. Compared to other
packages in this field, this package puts a much heavier focus on
providing reusable components that can be used in the design of new
implementation of new techniques, in particular those that involve large
parameter sweeps. For a background on the theory, see What is Flux Balance
Analysis <doi:10.1038/nbt.1614>.
Author: Max Conway [aut, cre]
Maintainer: Max Conway <conway.max1@gmail.com>
Diff between fbar versions 0.5.2 dated 2018-12-03 and 0.6.0 dated 2020-09-02
DESCRIPTION | 15 MD5 | 68 +- NEWS.md | 8 R/convenience_wrappers.R | 4 R/data.R | 4 R/deprecated.R | 2 R/gene_associate.R | 2 R/parsing_and_conversion.R | 8 README.md | 124 ++- build/vignette.rds |binary inst/doc/Introduction.R | 8 inst/doc/Introduction.Rmd | 2 inst/doc/Introduction.html | 398 ++++++++++-- inst/doc/Multi-Objective_Optimization_case_study.R | 14 inst/doc/Multi-Objective_Optimization_case_study.html | 574 ++++++++++++------ inst/doc/Tutorial.R | 12 inst/doc/Tutorial.html | 380 +++++++++-- man/decompose_metabolites.Rd | 6 man/ecoli_core.Rd | 8 man/expanded_to_ROI.Rd | 9 man/expanded_to_glpk.Rd | 9 man/expanded_to_gurobi.Rd | 11 man/fbar.Rd | 1 man/find_flux_variability_df.Rd | 3 man/gene_associate.Rd | 11 man/iJO1366.Rd | 8 man/nutrient_types.Rd | 6 man/reactiontbl_to_expanded.Rd | 9 man/reactiontbl_to_gurobi.Rd | 9 man/recompose_metabolites.Rd | 7 tests/testthat/test-ROI.R | 4 tests/testthat/test-full-size.R | 2 tests/testthat/test-gene_expression_processing.R | 4 tests/testthat/test-metabolite-parsing.R | 6 vignettes/Introduction.Rmd | 2 35 files changed, 1282 insertions(+), 456 deletions(-)
Title: An Framework for Reducing Elemental LAICPMS Data from Solid
Structures
Description: Aims to facilitate the reduction of elemental microchemistry data from solid-phase LAICPMS analysis (laser ablation inductive coupled plasma mass spectrometry). The 'elementR' package provides a reactive and user friendly interface (based on a 'shiny' application) and a set of 'R6' classes for conducting all steps needed for an optimal data reduction while leaving maximum control for user. For more details about the methods used in 'elementR', see Sirot et al (2017) <DOI:10.1111/2041-210X.12822>.
Author: Charlotte Sirot, Francois Guilhaumon
Maintainer: Charlotte Sirot <charlott.sirot@gmail.com>
Diff between elementR versions 1.3.6 dated 2018-05-06 and 1.3.7 dated 2020-09-02
DESCRIPTION | 10 MD5 | 16 NAMESPACE | 4 R/App.R | 7552 +++++++++++++++++++--------------------- R/classElementR_R6.R | 408 +- R/zzz.R |only README.md |only inst/elementR_documentation.pdf |binary man/elementR_project.Rd | 6 man/elementR_repStandard.Rd | 4 10 files changed, 4035 insertions(+), 3965 deletions(-)
Title: Predict Environmental Conditions from Biological Observations
Description: Imports benthic count data, reformats this data, and
computes environmental inferences from this data.
Author: Lester L. Yuan
Maintainer: Lester L. Yuan <yuan.lester@epa.gov>
Diff between bio.infer versions 1.3-3 dated 2014-02-12 and 1.3-6 dated 2020-09-02
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ NAMESPACE | 9 ++++++++- R/get.otu.R | 18 +++++++++--------- R/infergui.R | 20 +++++++++++++------- R/view.te.R | 3 ++- man/get.otu.Rd | 16 ++++++++-------- 7 files changed, 51 insertions(+), 37 deletions(-)
Title: Likelihood Estimation of Stochastic Volatility Models
Description: Parameter estimation for stochastic volatility models using maximum likelihood. The latent log-volatility is
integrated out of the likelihood using the Laplace approximation. The models are fitted via 'TMB' (Template Model
Builder) (Kristensen, Nielsen, Berg, Skaug, and Bell (2016) <doi:10.18637/jss.v070.i05>).
Author: Jens Christian Wahl <jens.c.wahl@gmail.com>
Maintainer: Jens Christian Wahl <jens.c.wahl@gmail.com>
Diff between stochvolTMB versions 0.1.0 dated 2020-09-02 and 0.1.1 dated 2020-09-02
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- inst/doc/stochvolTMB_vignette.html | 8 ++++---- src/stochvolTMB.cpp | 2 +- tests/testthat/test_objects/estimate_parameters.rds |binary 5 files changed, 12 insertions(+), 12 deletions(-)
Title: Detection and Analysis of Insect Defoliation Signals in Tree
Rings
Description: Tools to identify, quantify, analyze, and visualize growth
suppression events in tree rings that are often produced by insect
defoliation. Described in Guiterman et al. (2020) <doi:10.1016/j.dendro.2020.125750>.
Author: Chris Guiterman [aut, cre] (<https://orcid.org/0000-0002-9706-9332>),
Ann Lynch [aut] (<https://orcid.org/0000-0002-8043-3855>),
Jodi Axelson [aut] (<https://orcid.org/0000-0002-1799-6364>)
Maintainer: Chris Guiterman <chguiterman@email.arizona.edu>
Diff between dfoliatR versions 0.1.0 dated 2020-03-04 and 0.2.0 dated 2020-09-02
dfoliatR-0.1.0/dfoliatR/inst/extdata/EFKDF2.TRE |only dfoliatR-0.1.0/dfoliatR/man/events_table.Rd |only dfoliatR-0.2.0/dfoliatR/DESCRIPTION | 16 - dfoliatR-0.2.0/dfoliatR/MD5 | 99 +++--- dfoliatR-0.2.0/dfoliatR/NAMESPACE | 22 + dfoliatR-0.2.0/dfoliatR/NEWS.md | 21 + dfoliatR-0.2.0/dfoliatR/R/data.R | 38 ++ dfoliatR-0.2.0/dfoliatR/R/main.R | 100 ++---- dfoliatR-0.2.0/dfoliatR/R/plotting.R | 113 ++++--- dfoliatR-0.2.0/dfoliatR/R/stats.R | 176 ++++++----- dfoliatR-0.2.0/dfoliatR/R/utils.R | 40 +- dfoliatR-0.2.0/dfoliatR/README.md | 125 ++++++- dfoliatR-0.2.0/dfoliatR/data/dmj_defol.rda |binary dfoliatR-0.2.0/dfoliatR/data/dmj_h.rda |binary dfoliatR-0.2.0/dfoliatR/data/dmj_nh.rda |binary dfoliatR-0.2.0/dfoliatR/data/dmj_obr.rda |binary dfoliatR-0.2.0/dfoliatR/data/efk_defol.rda |only dfoliatR-0.2.0/dfoliatR/data/efk_h.rda |only dfoliatR-0.2.0/dfoliatR/data/efk_nh.rda |only dfoliatR-0.2.0/dfoliatR/data/efk_obr.rda |only dfoliatR-0.2.0/dfoliatR/inst/CITATION |only dfoliatR-0.2.0/dfoliatR/inst/doc/intro-to-dfoliatR.html | 207 +++++++------ dfoliatR-0.2.0/dfoliatR/inst/extdata/BAC2.CRN | 129 ++------ dfoliatR-0.2.0/dfoliatR/inst/extdata/EFKARS.TRE |only dfoliatR-0.2.0/dfoliatR/inst/extdata/ef_read.R | 17 - dfoliatR-0.2.0/dfoliatR/man/as.defol.Rd | 52 +-- dfoliatR-0.2.0/dfoliatR/man/as.obr.Rd | 54 +-- dfoliatR-0.2.0/dfoliatR/man/as_defol.Rd | 52 +-- dfoliatR-0.2.0/dfoliatR/man/as_obr.Rd | 54 +-- dfoliatR-0.2.0/dfoliatR/man/defol.Rd | 58 +-- dfoliatR-0.2.0/dfoliatR/man/defol_stats.Rd | 49 +-- dfoliatR-0.2.0/dfoliatR/man/defoliate_trees.Rd | 159 +++++---- dfoliatR-0.2.0/dfoliatR/man/dmj_defol.Rd | 7 dfoliatR-0.2.0/dfoliatR/man/dmj_h.Rd | 6 dfoliatR-0.2.0/dfoliatR/man/dmj_nh.Rd | 4 dfoliatR-0.2.0/dfoliatR/man/dmj_obr.Rd | 4 dfoliatR-0.2.0/dfoliatR/man/ef_defol.Rd | 4 dfoliatR-0.2.0/dfoliatR/man/ef_h.Rd | 6 dfoliatR-0.2.0/dfoliatR/man/ef_nh.Rd | 6 dfoliatR-0.2.0/dfoliatR/man/ef_obr.Rd | 4 dfoliatR-0.2.0/dfoliatR/man/efk_defol.Rd |only dfoliatR-0.2.0/dfoliatR/man/efk_h.Rd |only dfoliatR-0.2.0/dfoliatR/man/efk_nh.Rd |only dfoliatR-0.2.0/dfoliatR/man/efk_obr.Rd |only dfoliatR-0.2.0/dfoliatR/man/figures |only dfoliatR-0.2.0/dfoliatR/man/get_defol_events.Rd | 2 dfoliatR-0.2.0/dfoliatR/man/gsi.Rd | 77 ++-- dfoliatR-0.2.0/dfoliatR/man/id_defoliation.Rd | 113 +++---- dfoliatR-0.2.0/dfoliatR/man/obr.Rd | 97 +++--- dfoliatR-0.2.0/dfoliatR/man/outbreak.Rd | 95 ++--- dfoliatR-0.2.0/dfoliatR/man/outbreak_stats.Rd | 60 ++- dfoliatR-0.2.0/dfoliatR/man/plot_defol.Rd | 48 +-- dfoliatR-0.2.0/dfoliatR/man/plot_outbreak.Rd | 50 +-- dfoliatR-0.2.0/dfoliatR/tests/testthat/test-defoliate.R | 11 dfoliatR-0.2.0/dfoliatR/tests/testthat/test-is.functions.R |only dfoliatR-0.2.0/dfoliatR/tests/testthat/test-outbreak.R | 10 dfoliatR-0.2.0/dfoliatR/tests/testthat/test-samp_depth.R |only 57 files changed, 1237 insertions(+), 948 deletions(-)
Title: Segmentation and Classification of Accelerometer Data
Description: Segmentation and classification procedures for data from the 'Activinsights GENEActiv' <https://www.activinsights.com/products/geneactiv/> accelerometer that provides the user with a model to guess behaviour from test data where behaviour is missing.
Includes a step counting algorithm, a function to create segmented data with custom features and a function to use recursive partitioning provided in the function rpart() of the 'rpart' package to create classification models.
Author: Chris Campbell [aut],
Aimee Gott [aut],
Joss Langford [aut],
Charles Sweetland [aut, cre],
Activinsights Ltd [cph]
Maintainer: Charles Sweetland <charles@springhead-data.com>
Diff between GENEAclassify versions 1.4.18 dated 2019-08-21 and 1.5.1 dated 2020-09-02
GENEAclassify-1.4.18/GENEAclassify/man/GENEAamplitude.Rd |only GENEAclassify-1.4.18/GENEAclassify/man/GENEAdistance.Rd |only GENEAclassify-1.4.18/GENEAclassify/man/GENEAwavelength.Rd |only GENEAclassify-1.4.18/GENEAclassify/man/debias.Rd |only GENEAclassify-1.4.18/GENEAclassify/man/getZeros.Rd |only GENEAclassify-1.4.18/GENEAclassify/man/runmean.Rd |only GENEAclassify-1.4.18/GENEAclassify/man/stepCounter2.Rd |only GENEAclassify-1.5.1/GENEAclassify/DESCRIPTION | 30 GENEAclassify-1.5.1/GENEAclassify/MD5 | 74 - GENEAclassify-1.5.1/GENEAclassify/NAMESPACE | 16 GENEAclassify-1.5.1/GENEAclassify/R/changeTimes.R | 89 - GENEAclassify-1.5.1/GENEAclassify/R/classifyGENEA.R | 106 - GENEAclassify-1.5.1/GENEAclassify/R/dataImport.R | 66 GENEAclassify-1.5.1/GENEAclassify/R/getGENEAsegments.R | 527 +++---- GENEAclassify-1.5.1/GENEAclassify/R/segmentation.R | 467 ++++-- GENEAclassify-1.5.1/GENEAclassify/R/statistics.R | 282 +++ GENEAclassify-1.5.1/GENEAclassify/R/stepCounter.R | 726 +--------- GENEAclassify-1.5.1/GENEAclassify/README.md | 2 GENEAclassify-1.5.1/GENEAclassify/build/vignette.rds |binary GENEAclassify-1.5.1/GENEAclassify/inst/doc/GENEAclassifyDemo.R | 46 GENEAclassify-1.5.1/GENEAclassify/inst/doc/GENEAclassifyDemo.Rmd | 8 GENEAclassify-1.5.1/GENEAclassify/inst/doc/GENEAclassifyDemo.html | 717 ++++++--- GENEAclassify-1.5.1/GENEAclassify/inst/vignettes |only GENEAclassify-1.5.1/GENEAclassify/man/CirDisp.Rd |only GENEAclassify-1.5.1/GENEAclassify/man/CirKurt.Rd |only GENEAclassify-1.5.1/GENEAclassify/man/CirSD.Rd |only GENEAclassify-1.5.1/GENEAclassify/man/CirSkew.Rd |only GENEAclassify-1.5.1/GENEAclassify/man/CirVar.Rd |only GENEAclassify-1.5.1/GENEAclassify/man/GENEAclassify-package.Rd | 32 GENEAclassify-1.5.1/GENEAclassify/man/GENEAcount.Rd | 52 GENEAclassify-1.5.1/GENEAclassify/man/MeanDir.Rd |only GENEAclassify-1.5.1/GENEAclassify/man/TrainingData.Rd | 4 GENEAclassify-1.5.1/GENEAclassify/man/abssumdiff.Rd | 2 GENEAclassify-1.5.1/GENEAclassify/man/changeTimes.Rd | 13 GENEAclassify-1.5.1/GENEAclassify/man/classifyGENEA.Rd | 122 - GENEAclassify-1.5.1/GENEAclassify/man/createGENEAmodel.Rd | 14 GENEAclassify-1.5.1/GENEAclassify/man/dataImport.Rd | 15 GENEAclassify-1.5.1/GENEAclassify/man/find_peaks.Rd | 2 GENEAclassify-1.5.1/GENEAclassify/man/getGENEAsegments.Rd | 94 - GENEAclassify-1.5.1/GENEAclassify/man/impact.Rd |only GENEAclassify-1.5.1/GENEAclassify/man/radians.Rd |only GENEAclassify-1.5.1/GENEAclassify/man/segmentation.Rd | 87 - GENEAclassify-1.5.1/GENEAclassify/man/stepCounter.Rd | 63 GENEAclassify-1.5.1/GENEAclassify/man/trainingFit.Rd | 6 GENEAclassify-1.5.1/GENEAclassify/vignettes/GENEAclassifyDemo.Rmd | 8 GENEAclassify-1.5.1/GENEAclassify/vignettes/GENEAclassifyDemo.md |only 46 files changed, 1831 insertions(+), 1839 deletions(-)
Title: Estimation of Parameter-Dependent Network Centrality Measures
Description: Provides methods for estimating parameter-dependent network centrality measures with linear-in-means models. Both non linear least squares and maximum likelihood estimators are implemented. The methods allow for both link and node heterogeneity in network effects, endogenous network formation and the presence of unconnected nodes. The routines also compare the explanatory power of parameter-dependent network centrality measures with those of standard measures of network centrality. Benefits and features of the 'econet' package are illustrated using data from Battaglini and Patacchini (2018) and Battaglini, Patacchini, and Leone Sciabolazza (2020). For additional details, see the vignette.
Author: Marco Battaglini [aut] (<https://orcid.org/0000-0001-9690-0721>),
Valerio Leone Sciabolazza [aut, cre]
(<https://orcid.org/0000-0003-2537-3084>),
Eleonora Patacchini [aut] (<https://orcid.org/0000-0002-3510-2969>),
Sida Peng [aut] (<https://orcid.org/0000-0002-2151-0523>)
Maintainer: Valerio Leone Sciabolazza <valerio.leonesciabolazza@uniparthenope.it>
Diff between econet versions 0.1.91 dated 2020-08-28 and 0.1.92 dated 2020-09-02
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- R/net_dep.R | 4 ++-- R/quantify.R | 2 +- inst/doc/econet.pdf |binary man/net_dep.Rd | 5 +++-- 6 files changed, 14 insertions(+), 13 deletions(-)
Title: Thematic Cartography
Description: Create and integrate maps in your R workflow. This package helps
to design cartographic representations such as proportional symbols,
choropleth, typology, flows or discontinuities maps. It also offers several
features that improve the graphic presentation of maps, for instance, map
palettes, layout elements (scale, north arrow, title...), labels or legends.
See Giraud and Lambert (2017) <doi:10.1007/978-3-319-57336-6_13>.
Author: Timothée Giraud [cre, aut] (<https://orcid.org/0000-0002-1932-3323>),
Nicolas Lambert [aut],
Diego Hernangómez [ctb] (<https://orcid.org/0000-0001-8457-4658>),
Ian Fellows [cph] (no overlap algorithm for labels, from wordcloud
package)
Maintainer: Timothée Giraud <timothee.giraud@cnrs.fr>
Diff between cartography versions 2.4.1 dated 2020-04-20 and 2.4.2 dated 2020-09-02
DESCRIPTION | 10 +++++----- MD5 | 26 +++++++++++++------------- NEWS.md | 9 +++++++++ R/getTiles.R | 2 +- R/palettes.R | 2 +- README.md | 9 ++++----- build/vignette.rds |binary data/nuts2006.RData |binary inst/doc/cartography.R | 2 +- inst/doc/cartography.Rmd | 2 +- inst/doc/cartography.html | 18 +++++++++--------- man/carto.pal.Rd | 2 +- man/getTiles.Rd | 2 +- vignettes/cartography.Rmd | 2 +- 14 files changed, 47 insertions(+), 39 deletions(-)
Title: Functions for Working with Two- And Four-Parameter Beta
Probability Distributions
Description: Package providing a number of functions for working with the Two- and Four-
parameter Beta distributions, including alternative parameterizations and calculation
of moments. Includes functions for estimating classification accuracy, diagnostic
performance and consistency, using what's known as the Livingston and Lewis approach
in the educational-measurement literature as the base method.
Livingston and Lewis (1995) <doi:10.1111/j.1745-3984.1995.tb00462.x>.
Hanson (1991) <https://files.eric.ed.gov/fulltext/ED344945.pdf>.
Glas, Lijmer, Prins, Bonsel and Bossuyt (2003) <doi:10.1016/S0895-4356(03)00177-X>.
Author: Haakon Haakstad
Maintainer: Haakon Haakstad <h.t.haakstad@cemo.uio.no>
Diff between betafunctions versions 1.2.0 dated 2020-06-10 and 1.2.1 dated 2020-09-02
DESCRIPTION | 6 +- MD5 | 21 +++---- NAMESPACE | 1 NEWS.md | 6 ++ R/betafunctions.R | 36 +++++++++++- R/classification.R | 56 ++++++++++--------- man/Beta.2p.fit.Rd |only man/Beta.4p.fit.Rd | 7 +- man/LL.CA.Rd | 152 ++++++++++++++++++++++++++--------------------------- man/LL.ROC.Rd | 6 +- man/cba.Rd | 2 man/ccStats.Rd | 2 12 files changed, 170 insertions(+), 125 deletions(-)
Title: Ratio-of-Uniforms Simulation with Transformation
Description: Uses the generalized ratio-of-uniforms (RU) method to simulate
from univariate and (low-dimensional) multivariate continuous distributions.
The user specifies the log-density, up to an additive constant. The RU
algorithm is applied after relocation of mode of the density to zero, and
the user can choose a tuning parameter r. For details see Wakefield, Gelfand
and Smith (1991) <DOI:10.1007/BF01889987>, Efficient generation of random
variates via the ratio-of-uniforms method, Statistics and Computing (1991)
1, 129-133. A Box-Cox variable transformation can be used to make the input
density suitable for the RU method and to improve efficiency. In the
multivariate case rotation of axes can also be used to improve efficiency.
From version 1.2.0 the 'Rcpp' package
<https://cran.r-project.org/package=Rcpp> can be used to improve efficiency.
Author: Paul J. Northrop [aut, cre, cph]
Maintainer: Paul J. Northrop <p.northrop@ucl.ac.uk>
Diff between rust versions 1.3.9 dated 2020-07-21 and 1.3.10 dated 2020-09-02
DESCRIPTION | 12 ++++---- MD5 | 42 +++++++++++++++--------------- NEWS.md | 6 ++++ R/box_cox_functions_rcpp.R | 4 +- R/gp_example.R | 12 ++++---- R/ru_sampling.R | 2 - R/ru_sampling_rcpp.R | 4 +- R/rust-internal.R | 7 ++--- R/rust.R | 4 +- inst/doc/rust-a-vignette.html | 8 ++--- inst/doc/rust-b-when-to-use-vignette.html | 4 +- inst/doc/rust-c-using-rcpp-vignette.Rmd | 4 +- inst/doc/rust-c-using-rcpp-vignette.html | 32 +++++++++++----------- man/find_lambda_one_d_rcpp.Rd | 2 - man/find_lambda_rcpp.Rd | 2 - man/gpd_init.Rd | 6 ++-- man/gpd_logpost.Rd | 2 - man/ru.Rd | 2 - man/ru_rcpp.Rd | 4 +- man/rust.Rd | 4 +- vignettes/rust-c-using-rcpp-vignette.Rmd | 4 +- vignettes/rust.bib | 12 ++++---- 22 files changed, 92 insertions(+), 87 deletions(-)
Title: Data Structures, Summaries, and Visualisations for Missing Data
Description: Missing values are ubiquitous in data and need to be explored and
handled in the initial stages of analysis. 'naniar' provides data structures
and functions that facilitate the plotting of missing values and examination
of imputations. This allows missing data dependencies to be explored with
minimal deviation from the common work patterns of 'ggplot2' and tidy data.
The work is fully discussed at Tierney & Cook (2018) <arXiv:1809.02264>.
Author: Nicholas Tierney [aut, cre] (<https://orcid.org/0000-0003-1460-8722>),
Di Cook [aut] (<https://orcid.org/0000-0002-3813-7155>),
Miles McBain [aut] (<https://orcid.org/0000-0003-2865-2548>),
Colin Fay [aut] (<https://orcid.org/0000-0001-7343-1846>),
Mitchell O'Hara-Wild [ctb],
Jim Hester [ctb],
Luke Smith [ctb]
Maintainer: Nicholas Tierney <nicholas.tierney@gmail.com>
Diff between naniar versions 0.5.2 dated 2020-06-29 and 0.6.0 dated 2020-09-02
naniar-0.5.2/naniar/R/shadow-verifiers.R |only naniar-0.5.2/naniar/man/as_shadow.data.frame.Rd |only naniar-0.5.2/naniar/man/is_shadow.Rd |only naniar-0.5.2/naniar/man/new_nabular.Rd |only naniar-0.5.2/naniar/man/new_shadow.Rd |only naniar-0.5.2/naniar/tests/testthat/test-bind-shadow.R |only naniar-0.6.0/naniar/DESCRIPTION | 12 naniar-0.6.0/naniar/MD5 | 324 +++---- naniar-0.6.0/naniar/NAMESPACE | 5 naniar-0.6.0/naniar/NEWS.md | 8 naniar-0.6.0/naniar/R/add-cols.R | 26 naniar-0.6.0/naniar/R/add-n-prop-miss.R | 15 naniar-0.6.0/naniar/R/cast-shadows.R | 8 naniar-0.6.0/naniar/R/data-common-na-numbers.R | 1 naniar-0.6.0/naniar/R/data-common-na-strings.R | 3 naniar-0.6.0/naniar/R/data-oceanbuoys.R | 26 naniar-0.6.0/naniar/R/data-pedestrian.R | 3 naniar-0.6.0/naniar/R/data-riskfactors.R | 6 naniar-0.6.0/naniar/R/geom-miss-point.R | 4 naniar-0.6.0/naniar/R/gg-miss-case-cumsum.R | 2 naniar-0.6.0/naniar/R/gg-miss-case.R | 6 naniar-0.6.0/naniar/R/gg-miss-fct.R | 3 naniar-0.6.0/naniar/R/gg-miss-span.R | 4 naniar-0.6.0/naniar/R/gg-miss-var.R | 3 naniar-0.6.0/naniar/R/gg-miss-which.R | 2 naniar-0.6.0/naniar/R/impute-median.R | 5 naniar-0.6.0/naniar/R/impute_below.R | 9 naniar-0.6.0/naniar/R/impute_mean.R | 4 naniar-0.6.0/naniar/R/miss-prop-pct-summary.R | 3 naniar-0.6.0/naniar/R/miss-x-cumsum.R | 7 naniar-0.6.0/naniar/R/miss-x-run.R | 5 naniar-0.6.0/naniar/R/miss-x-span.R | 3 naniar-0.6.0/naniar/R/miss-x-summary.R | 12 naniar-0.6.0/naniar/R/miss-x-table.R | 9 naniar-0.6.0/naniar/R/nabular.R | 15 naniar-0.6.0/naniar/R/prop-pct-var-case-miss-complete.R | 12 naniar-0.6.0/naniar/R/replace-with-na.R | 27 naniar-0.6.0/naniar/R/scoped-replace-with-na.R | 8 naniar-0.6.0/naniar/R/shade.R | 40 naniar-0.6.0/naniar/R/shadow-recode.R | 18 naniar-0.6.0/naniar/R/shadow-shifters.R | 3 naniar-0.6.0/naniar/R/shadows.R | 243 +---- naniar-0.6.0/naniar/R/utils.R | 9 naniar-0.6.0/naniar/R/where-na.R | 2 naniar-0.6.0/naniar/README.md | 432 ++++------ naniar-0.6.0/naniar/build/vignette.rds |binary naniar-0.6.0/naniar/inst/WORDLIST | 4 naniar-0.6.0/naniar/inst/doc/exploring-imputed-values.html | 404 ++++----- naniar-0.6.0/naniar/inst/doc/getting-started-w-naniar.R | 16 naniar-0.6.0/naniar/inst/doc/getting-started-w-naniar.Rmd | 29 naniar-0.6.0/naniar/inst/doc/getting-started-w-naniar.html | 247 ++--- naniar-0.6.0/naniar/inst/doc/naniar-visualisation.Rmd | 7 naniar-0.6.0/naniar/inst/doc/naniar-visualisation.html | 178 +--- naniar-0.6.0/naniar/inst/doc/replace-with-na.Rmd | 2 naniar-0.6.0/naniar/inst/doc/replace-with-na.html | 352 +++----- naniar-0.6.0/naniar/inst/doc/special-missing-values.html | 148 +-- naniar-0.6.0/naniar/man/add_any_miss.Rd | 1 naniar-0.6.0/naniar/man/add_label_missings.Rd | 1 naniar-0.6.0/naniar/man/add_miss_cluster.Rd | 3 naniar-0.6.0/naniar/man/add_prop_miss.Rd | 15 naniar-0.6.0/naniar/man/add_shadow_shift.Rd | 2 naniar-0.6.0/naniar/man/as_shadow.Rd | 8 naniar-0.6.0/naniar/man/bind_shadow.Rd | 2 naniar-0.6.0/naniar/man/cast_shadow.Rd | 3 naniar-0.6.0/naniar/man/cast_shadow_shift.Rd | 1 naniar-0.6.0/naniar/man/cast_shadow_shift_label.Rd | 4 naniar-0.6.0/naniar/man/common_na_numbers.Rd | 1 naniar-0.6.0/naniar/man/common_na_strings.Rd | 3 naniar-0.6.0/naniar/man/figures/README-facet-by-month-1.png |binary naniar-0.6.0/naniar/man/figures/README-geom-miss-point-1.png |binary naniar-0.6.0/naniar/man/figures/README-gg-miss-span-1.png |binary naniar-0.6.0/naniar/man/figures/README-shadow-impute-1.png |binary naniar-0.6.0/naniar/man/figures/README-shadow-w-ggplot-1.png |binary naniar-0.6.0/naniar/man/geom_miss_point.Rd | 4 naniar-0.6.0/naniar/man/gg_miss_case.Rd | 3 naniar-0.6.0/naniar/man/gg_miss_case_cumsum.Rd | 2 naniar-0.6.0/naniar/man/gg_miss_fct.Rd | 3 naniar-0.6.0/naniar/man/gg_miss_span.Rd | 4 naniar-0.6.0/naniar/man/gg_miss_var.Rd | 3 naniar-0.6.0/naniar/man/gg_miss_which.Rd | 2 naniar-0.6.0/naniar/man/impute_below_at.Rd | 9 naniar-0.6.0/naniar/man/label_missings.Rd | 3 naniar-0.6.0/naniar/man/miss_case_cumsum.Rd | 3 naniar-0.6.0/naniar/man/miss_case_summary.Rd | 6 naniar-0.6.0/naniar/man/miss_case_table.Rd | 3 naniar-0.6.0/naniar/man/miss_prop_summary.Rd | 3 naniar-0.6.0/naniar/man/miss_summary.Rd | 3 naniar-0.6.0/naniar/man/miss_var_cumsum.Rd | 4 naniar-0.6.0/naniar/man/miss_var_run.Rd | 5 naniar-0.6.0/naniar/man/miss_var_span.Rd | 3 naniar-0.6.0/naniar/man/miss_var_summary.Rd | 3 naniar-0.6.0/naniar/man/miss_var_table.Rd | 4 naniar-0.6.0/naniar/man/miss_var_which.Rd | 2 naniar-0.6.0/naniar/man/oceanbuoys.Rd | 26 naniar-0.6.0/naniar/man/pct-miss-complete-var.Rd | 6 naniar-0.6.0/naniar/man/pedestrian.Rd | 3 naniar-0.6.0/naniar/man/prop-miss-complete-var.Rd | 6 naniar-0.6.0/naniar/man/recode_shadow.Rd | 4 naniar-0.6.0/naniar/man/replace_with_na.Rd | 7 naniar-0.6.0/naniar/man/replace_with_na_all.Rd | 8 naniar-0.6.0/naniar/man/riskfactors.Rd | 6 naniar-0.6.0/naniar/man/scoped-impute_mean.Rd | 4 naniar-0.6.0/naniar/man/scoped-impute_median.Rd | 5 naniar-0.6.0/naniar/man/shade.Rd | 8 naniar-0.6.0/naniar/man/shadow_expand_relevel.Rd | 10 naniar-0.6.0/naniar/man/shadow_shift.Rd | 3 naniar-0.6.0/naniar/man/update_shadow.Rd | 4 naniar-0.6.0/naniar/man/which_are_shade.Rd | 2 naniar-0.6.0/naniar/tests/figs/deps.txt | 2 naniar-0.6.0/naniar/tests/figs/geom-miss-point/geom-miss-point-jitter.svg | 206 ---- naniar-0.6.0/naniar/tests/figs/geom-miss-point/geom-miss-point-prop-jitter.svg | 202 ---- naniar-0.6.0/naniar/tests/figs/geom-miss-point/geom-miss-point-prop.svg | 204 ---- naniar-0.6.0/naniar/tests/figs/geom-miss-point/geom-miss-point.svg | 208 ---- naniar-0.6.0/naniar/tests/figs/gg-miss-case-cumsum/gg-miss-case-cumsum.svg | 60 - naniar-0.6.0/naniar/tests/figs/gg-miss-case/gg-miss-case-group-and-sort-show-pct.svg | 407 +-------- naniar-0.6.0/naniar/tests/figs/gg-miss-case/gg-miss-case-group-and-sort.svg | 413 +-------- naniar-0.6.0/naniar/tests/figs/gg-miss-case/gg-miss-case-group-show-pct.svg | 407 +-------- naniar-0.6.0/naniar/tests/figs/gg-miss-case/gg-miss-case-group.svg | 413 +-------- naniar-0.6.0/naniar/tests/figs/gg-miss-case/gg-miss-case-plot-show-pct.svg | 221 ----- naniar-0.6.0/naniar/tests/figs/gg-miss-case/gg-miss-case-sort-show-pct.svg | 221 ----- naniar-0.6.0/naniar/tests/figs/gg-miss-case/gg-miss-case-sort.svg | 221 ----- naniar-0.6.0/naniar/tests/figs/gg-miss-case/gg-miss-case.svg | 221 ----- naniar-0.6.0/naniar/tests/figs/gg-miss-fct/gg-miss-fct.svg | 381 +------- naniar-0.6.0/naniar/tests/figs/gg-miss-span/gg-miss-span-group.svg | 211 +--- naniar-0.6.0/naniar/tests/figs/gg-miss-span/gg-miss-span.svg | 52 - naniar-0.6.0/naniar/tests/figs/gg-miss-var-cumsum/gg-miss-var-cumsum.svg | 74 - naniar-0.6.0/naniar/tests/figs/gg-miss-var-plot/gg-miss-var-group-pct.svg | 293 +----- naniar-0.6.0/naniar/tests/figs/gg-miss-var-plot/gg-miss-var-pct.svg | 76 - naniar-0.6.0/naniar/tests/figs/gg-miss-var-plot/gg-miss-var-plot-group.svg | 301 +----- naniar-0.6.0/naniar/tests/figs/gg-miss-var-plot/gg-miss-var.svg | 71 - naniar-0.6.0/naniar/tests/figs/gg-miss-which/gg-miss-which.svg | 38 naniar-0.6.0/naniar/tests/testthat/test-add-any-miss.R | 25 naniar-0.6.0/naniar/tests/testthat/test-add-label-missings.R | 44 - naniar-0.6.0/naniar/tests/testthat/test-add-label-shadow.R | 51 - naniar-0.6.0/naniar/tests/testthat/test-add-shadow.R | 13 naniar-0.6.0/naniar/tests/testthat/test-as-shadow.R | 26 naniar-0.6.0/naniar/tests/testthat/test-gather-shadow.R | 21 naniar-0.6.0/naniar/tests/testthat/test-geom-miss-point.R | 45 - naniar-0.6.0/naniar/tests/testthat/test-gg-miss-case-cumsum.R | 15 naniar-0.6.0/naniar/tests/testthat/test-gg-miss-case.R | 55 - naniar-0.6.0/naniar/tests/testthat/test-gg-miss-fct.R | 14 naniar-0.6.0/naniar/tests/testthat/test-gg-miss-span.R | 26 naniar-0.6.0/naniar/tests/testthat/test-gg-miss-var-cumsum.R | 14 naniar-0.6.0/naniar/tests/testthat/test-gg-miss-var-plot.R | 31 naniar-0.6.0/naniar/tests/testthat/test-gg-miss-which.R | 14 naniar-0.6.0/naniar/tests/testthat/test-impute-below.R | 17 naniar-0.6.0/naniar/tests/testthat/test-impute-median.R | 2 naniar-0.6.0/naniar/tests/testthat/test-impute_mean.R | 2 naniar-0.6.0/naniar/tests/testthat/test-miss-case-summary.R | 33 naniar-0.6.0/naniar/tests/testthat/test-miss-case-table.R | 15 naniar-0.6.0/naniar/tests/testthat/test-miss-var-summary.R | 40 naniar-0.6.0/naniar/tests/testthat/test-miss-var-table.R | 25 naniar-0.6.0/naniar/tests/testthat/test-miss-x-pct.R | 75 - naniar-0.6.0/naniar/tests/testthat/test-n-miss.R | 4 naniar-0.6.0/naniar/tests/testthat/test-nabular.R | 54 - naniar-0.6.0/naniar/tests/testthat/test-prop-complete.R | 9 naniar-0.6.0/naniar/tests/testthat/test-prop_row.R | 23 naniar-0.6.0/naniar/tests/testthat/test-replace-with-na.R | 24 naniar-0.6.0/naniar/tests/testthat/test-shade-verifiers.R | 3 naniar-0.6.0/naniar/tests/testthat/test-shadow-identifiers.R | 10 naniar-0.6.0/naniar/tests/testthat/test-shadow-long.R | 2 naniar-0.6.0/naniar/tests/testthat/test-special-missing-values.R | 76 - naniar-0.6.0/naniar/tests/testthat/test-unbind.R | 12 naniar-0.6.0/naniar/vignettes/getting-started-w-naniar.Rmd | 29 naniar-0.6.0/naniar/vignettes/naniar-visualisation.Rmd | 7 naniar-0.6.0/naniar/vignettes/replace-with-na.Rmd | 2 166 files changed, 2669 insertions(+), 6024 deletions(-)
Title: API for UK Energy Market Information
Description: Allows users to access live UK energy market information via various APIs.
Author: Timothy Wong [aut, cre]
Maintainer: Timothy Wong <timothy.wong@hotmail.co.uk>
Diff between ukgasapi versions 0.17 dated 2019-11-14 and 0.18 dated 2020-09-02
DESCRIPTION | 14 ++++---- MD5 | 16 +++++---- NAMESPACE | 1 R/bmrsIndoItsdo.R |only R/dataItemExplorer.R | 77 ++++++++++++++++++++++++------------------------ inst/doc/vignette.Rmd | 2 - inst/doc/vignette.html | 6 +-- man/bmrsIndoItsdo.Rd |only man/dataItemExplorer.Rd | 13 ++++---- vignettes/vignette.Rmd | 2 - 10 files changed, 69 insertions(+), 62 deletions(-)
Title: Interface to 'Zenodo' REST API
Description: Provides an Interface to 'Zenodo' (<https://zenodo.org>) REST API,
including management of depositions, attribution of DOIs by 'Zenodo' and
upload of files.
Author: Emmanuel Blondel [aut, cre] (<https://orcid.org/0000-0002-5870-5762>),
Julien Barde [ctb] (<https://orcid.org/0000-0002-3519-6141>),
Stephen Eglen [ctb] (<https://orcid.org/0000-0001-8607-8025>),
Hans Van Calster [ctb] (<https://orcid.org/0000-0001-8595-8426>),
Floris Vanderhaeghe [ctb] (<https://orcid.org/0000-0002-6378-6229>)
Maintainer: Emmanuel Blondel <emmanuel.blondel1@gmail.com>
Diff between zen4R versions 0.3 dated 2019-08-27 and 0.4 dated 2020-09-02
DESCRIPTION | 23 +++-- MD5 | 38 +++++--- NAMESPACE | 7 + NEWS.md | 22 +++++ R/ZenodoManager.R | 161 +++++++++++++++++++++++++++----------- R/ZenodoRecord.R | 148 +++++++++++++++++++++++++++++++--- R/zen4R.R | 9 +- R/zen4R_downloader.R |only R/zen4R_pat.R |only R/zen4R_versioning.R |only README.md | 4 man/ZenodoManager.Rd | 31 ++++--- man/ZenodoRecord.Rd | 36 +++++++- man/ZenodoRequest.Rd | 5 - man/download_zenodo.Rd |only man/get_versions.Rd |only man/human_filesize.Rd |only man/zen4R.Rd | 4 man/zen4RLogger.Rd | 5 - tests/test-all.R | 11 +- tests/testthat/test_communities.R | 6 - tests/testthat/test_grants.R | 13 +-- tests/testthat/test_records.R | 68 +++++++++++----- 23 files changed, 447 insertions(+), 144 deletions(-)
Title: False Discovery Exceedance Controlling Multiple Testing
Procedures
Description: Multiple testing procedures for heterogeneous and discrete tests as described in Döhler and Roquain (2019) <arXiv:1912.04607v1>. The main algorithms of the paper are available as continuous, discrete and weighted versions.
Author: Sebastian Döhler [aut],
Florian Junge [aut, cre],
Etienne Roquain [ctb]
Maintainer: Florian Junge <florian.junge@h-da.de>
Diff between FDX versions 1.0.1 dated 2020-03-20 and 1.0.2 dated 2020-09-02
DESCRIPTION | 12 ++++++------ MD5 | 8 ++++---- NEWS.md | 5 ++++- src/dist_fun.cpp | 27 +++++++++++++-------------- src/dist_fun.h | 2 +- 5 files changed, 28 insertions(+), 26 deletions(-)
Title: Enhancements for 'broom' and 'easystats' Package Families
Description: Provides helper functions that assist in data
analysis workflows involving regression analyses. The goal is to
combine the functionality offered by different set of packages
('broom', 'broom.mixed', 'parameters', and 'performance') through a
common syntax to return tidy dataframes containing model parameters
and performance measure summaries. The 'grouped_' variants of the
generics provides a convenient way to execute functions across a
combination of grouping variable(s) in a dataframe.
Author: Indrajeet Patil [aut, cre, cph]
(<https://orcid.org/0000-0003-1995-6531>)
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>
Diff between broomExtra versions 4.0.4 dated 2020-07-24 and 4.0.5 dated 2020-09-02
DESCRIPTION | 10 MD5 | 24 NEWS.md | 4 R/easystats_to_tidy_names.R | 1 R/generics_easystats.R | 9 R/grouped_generics.R | 50 - README.md | 1254 ++++++++++++++++----------------- build/broomExtra.pdf |binary man/grouped_augment.Rd | 17 man/grouped_glance.Rd | 16 man/grouped_tidy.Rd | 17 tests/testthat/test-grouped_generics.R | 106 +- tests/testthat/test-hybrid_generics.R | 15 13 files changed, 725 insertions(+), 798 deletions(-)
Title: Adrian Dusa's Miscellaneous
Description: Contains functions used across packages 'QCA', 'DDIwR', and 'venn'.
Interprets and translates, factorizes and negates SOP - Sum of Products
expressions, for both binary and multi-value crisp sets, and extracts information
(set names, set values) from those expressions. Other functions perform various
other checks if possibly numeric (even if all numbers reside in a character vector)
and coerce to numeric, or check if the numbers are whole. It also offers, among
many others, a highly flexible recoding routine.
Author: Adrian Dusa [aut, cre, cph] (<https://orcid.org/0000-0002-3525-9253>)
Maintainer: Adrian Dusa <dusa.adrian@unibuc.ro>
Diff between admisc versions 0.8 dated 2020-04-18 and 0.9 dated 2020-09-02
DESCRIPTION | 8 ++++---- MD5 | 14 ++++++++------ NAMESPACE | 1 + R/export.R |only R/factorize.R | 2 +- R/translate.R | 4 ++-- inst/ChangeLog | 13 +++++++++---- man/admisc.package.Rd | 4 ++-- man/export.Rd |only 9 files changed, 27 insertions(+), 19 deletions(-)
Title: Tidy Interface to 'data.table'
Description: A tidy interface to 'data.table' that is 'rlang' compatible,
giving users the speed of 'data.table' with the clean syntax of the tidyverse.
Author: Mark Fairbanks [aut, cre],
Tyson Barrett [ctb],
Ivan Leung [ctb],
Ross Kennedy [ctb],
Lionel Henry [ctb],
Matt Carlson [ctb],
Abdessabour Moutik [ctb]
Maintainer: Mark Fairbanks <mark.t.fairbanks@gmail.com>
Diff between tidytable versions 0.5.4 dated 2020-08-10 and 0.5.5 dated 2020-09-02
tidytable-0.5.4/tidytable/R/desc.R |only tidytable-0.5.4/tidytable/R/select_helpers.R |only tidytable-0.5.4/tidytable/man/desc..Rd |only tidytable-0.5.4/tidytable/man/starts_with..Rd |only tidytable-0.5.5/tidytable/DESCRIPTION | 21 - tidytable-0.5.5/tidytable/MD5 | 139 ++++------ tidytable-0.5.5/tidytable/NAMESPACE | 37 +- tidytable-0.5.5/tidytable/NEWS.md | 28 ++ tidytable-0.5.5/tidytable/R/arrange.R | 2 tidytable-0.5.5/tidytable/R/as_tidytable.R | 10 tidytable-0.5.5/tidytable/R/bind.R | 14 - tidytable-0.5.5/tidytable/R/case.R | 5 tidytable-0.5.5/tidytable/R/complete.R | 31 +- tidytable-0.5.5/tidytable/R/count.R | 2 tidytable-0.5.5/tidytable/R/crossing.R | 9 tidytable-0.5.5/tidytable/R/distinct.R | 4 tidytable-0.5.5/tidytable/R/drop_na.R | 4 tidytable-0.5.5/tidytable/R/expand.R | 16 + tidytable-0.5.5/tidytable/R/fill.R | 2 tidytable-0.5.5/tidytable/R/filter.R | 2 tidytable-0.5.5/tidytable/R/get_dummies.R | 2 tidytable-0.5.5/tidytable/R/group_split.R | 2 tidytable-0.5.5/tidytable/R/ifelse.R | 2 tidytable-0.5.5/tidytable/R/join.R | 50 +++ tidytable-0.5.5/tidytable/R/map.R | 16 - tidytable-0.5.5/tidytable/R/map2.R | 16 - tidytable-0.5.5/tidytable/R/mutate.R | 10 tidytable-0.5.5/tidytable/R/mutate_across.R | 6 tidytable-0.5.5/tidytable/R/n.R | 2 tidytable-0.5.5/tidytable/R/nest.R | 2 tidytable-0.5.5/tidytable/R/pivot_longer.R | 2 tidytable-0.5.5/tidytable/R/pivot_wider.R | 10 tidytable-0.5.5/tidytable/R/pull.R | 33 +- tidytable-0.5.5/tidytable/R/relocate.R | 8 tidytable-0.5.5/tidytable/R/rename.R | 4 tidytable-0.5.5/tidytable/R/rename_with.R | 2 tidytable-0.5.5/tidytable/R/replace_na.R | 25 - tidytable-0.5.5/tidytable/R/row_number.R | 2 tidytable-0.5.5/tidytable/R/select.R | 4 tidytable-0.5.5/tidytable/R/separate.R | 2 tidytable-0.5.5/tidytable/R/slice.R | 38 +- tidytable-0.5.5/tidytable/R/summarize_across.R | 20 - tidytable-0.5.5/tidytable/R/tidytable-package.R | 7 tidytable-0.5.5/tidytable/R/tidytable.R | 3 tidytable-0.5.5/tidytable/R/top_n.R | 2 tidytable-0.5.5/tidytable/R/transmute.R | 2 tidytable-0.5.5/tidytable/R/unite.R | 2 tidytable-0.5.5/tidytable/R/unnest.R | 8 tidytable-0.5.5/tidytable/R/utils-selectors.R | 19 - tidytable-0.5.5/tidytable/R/vctrs-tidytable.R |only tidytable-0.5.5/tidytable/README.md | 33 +- tidytable-0.5.5/tidytable/man/as_tidytable.Rd | 4 tidytable-0.5.5/tidytable/man/bind_cols..Rd | 6 tidytable-0.5.5/tidytable/man/case..Rd | 2 tidytable-0.5.5/tidytable/man/complete..Rd | 8 tidytable-0.5.5/tidytable/man/dt_verb.Rd | 19 - tidytable-0.5.5/tidytable/man/figures/logo.png |binary tidytable-0.5.5/tidytable/man/left_join..Rd | 3 tidytable-0.5.5/tidytable/man/mutate..Rd | 9 tidytable-0.5.5/tidytable/man/mutate_across..Rd | 3 tidytable-0.5.5/tidytable/man/pull..Rd | 15 - tidytable-0.5.5/tidytable/man/replace_na..Rd | 2 tidytable-0.5.5/tidytable/man/slice..Rd | 14 - tidytable-0.5.5/tidytable/man/summarize_across..Rd | 2 tidytable-0.5.5/tidytable/man/tidytable-vctrs.Rd |only tidytable-0.5.5/tidytable/tests/testthat/test-complete.R | 7 tidytable-0.5.5/tidytable/tests/testthat/test-expand.R | 2 tidytable-0.5.5/tidytable/tests/testthat/test-join.R | 20 + tidytable-0.5.5/tidytable/tests/testthat/test-pull.R | 16 + tidytable-0.5.5/tidytable/tests/testthat/test-rename.R | 14 - tidytable-0.5.5/tidytable/tests/testthat/test-replace_na.R | 6 tidytable-0.5.5/tidytable/tests/testthat/test-select.R | 2 tidytable-0.5.5/tidytable/tests/testthat/test-slice.R | 9 tidytable-0.5.5/tidytable/tests/testthat/test-vctrs-tidytable.R |only 74 files changed, 492 insertions(+), 331 deletions(-)
Title: Subgroup Specific Optimal Dose Assignment
Description: Chooses subgroup specific optimal doses in a phase I dose finding clinical trial allowing for subgroup combination and simulates clinical trials under the subgroup specific time to event continual reassessment method. Chapple, A.G., Thall, P.F. (2018) <doi:10.1002/pst.1891>.
Author: Andrew Chapple
Maintainer: Andrew Chapple <achapp@lsuhsc.edu>
Diff between SubTite versions 4.0.0 dated 2020-08-28 and 4.0.1 dated 2020-09-02
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/GetSubTite.R | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
Title: End-to-End Marine Food Web Model
Description: A dynamic model of
the big-picture, whole ecosystem effects of hydrodynamics,
temperature, nutrients, and fishing on continental shelf marine
food webs. The package has been developed from a prototype described
in: Heath, M.R. (2012) <doi:10.1016/j.pocean.2012.03.004>
Ecosystem limits to food web fluxes and fisheries yields in
the North Sea simulated with an end-to-end food web model.
Progress in Oceanography (Special issue: End-to-end modelling:
Towards Comparative Analysis of Marine Ecosystem Organisation)
102, 42-66.
Author: Michael Heath [aut],
Ian Thurlbeck [ctb]
Maintainer: Michael Heath <m.heath@strath.ac.uk>
Diff between StrathE2E2 versions 3.1.0 dated 2020-07-08 and 3.2.0 dated 2020-09-02
DESCRIPTION | 8 MD5 | 100 - NEWS.md | 11 R/CredInt_make_aamass_results.R | 6 R/CredInt_make_daily_flux_results.R | 32 R/CredInt_make_daily_migration_results.R | 32 R/CredInt_make_daily_results.R | 36 R/StrathE2E2.R | 16 R/aggregate_model_output.R | 14 R/assemble_flow_matrix_from_model_annual_output.R | 50 R/boxplot_annual_compare_observations.R | 8 R/boxplot_annual_compare_observations_with_ci.R | 8 R/boxplot_annual_compare_runs.R | 8 R/build_model_parameters.R | 46 R/calculate_uptakes.R | 74 - R/compare_two_runs_aam.R | 4 R/derive_annual_results_inshore.R | 72 - R/derive_annual_results_offshore.R | 72 - R/derive_annual_results_wholedomain.R | 110 +- R/derive_model_target_results.R | 50 R/e2e_plot_eco.R | 2 R/e2e_plot_sens_mc.R | 3 R/e2e_run_sens.R | 3 R/internal.R | 30 R/monthly_averages_of_final_year.R | 4 R/perturb_parameters.R | 128 +- R/perturb_parameters_all.R | 124 +- R/plot_final_year_time_series_data.R | 8 R/plot_full_length_timeseries.R | 4 R/plot_inshore_vs_offshore_anavmass.R | 6 R/read_fitted_parameters.R | 26 R/read_initial_state.R | 40 R/write_fitted_parameters.R | 30 README.md | 8 inst/doc/StrathE2E2_CheatSheet.pdf |binary inst/extdata/Internal.data/StrathE2E_parameter_list.csv | 42 inst/extdata/Models/North_Sea/1970-1999/Param/initial_values_NORTH_SEA_1970-1999.csv | 4 inst/extdata/Models/North_Sea/1970-1999/Target/annual_observed_NORTH_SEA_1970-1999.csv | 4 inst/extdata/Models/North_Sea/2003-2013/Param/initial_values_NORTH_SEA_2003-2013.csv | 4 inst/extdata/Models/North_Sea/2003-2013/Target/annual_observed_NORTH_SEA_2003-2013.csv | 4 man/StrathE2E2-package.Rd | 16 man/e2e_plot_eco.Rd | 2 man/e2e_plot_sens_mc.Rd | 4 man/e2e_run_sens.Rd | 4 src/StrathE2E2_ecology_model_function.c | 546 +++++----- tests/testdata/models/Testbed/Const/Param/initial_values_Testbed.csv | 4 tests/testdata/models/Testbed/Const/Target/annual_observed_Testbed.csv | 4 tests/testthat/test-fish-fluxes.R | 36 tests/testthat/test-top-predator-fluxes.R | 20 tests/testthat/test-zooplankton-and-larvae-fluxes.R | 138 +- vignettes/CheatSheet.pdf |binary 51 files changed, 1013 insertions(+), 992 deletions(-)
Title: Species Sensitivity Distributions
Description: Species sensitivity distributions are
cumulative probability distributions which are fitted to
toxicity concentrations for different species as described by
Posthuma et al.(2001) <isbn:9781566705783>.
The ssdtools package uses Maximum Likelihood to fit distributions
such as the log-normal, gamma, log-logistic,
log-Gumbel, Gompertz and Weibull.
The user can provide custom distributions.
Multiple distributions can be averaged using Information Criteria.
Confidence intervals on hazard concentrations and proportions are produced by
parametric bootstrapping.
Author: Joe Thorley [aut, cre, ctr] (<https://orcid.org/0000-0002-7683-4592>),
Carl Schwarz [aut, ctr],
Angeline Tillmanns [ctb],
Ali Azizishirazi [ctb],
Rebecca Fisher [ctb],
David Fox [ctb],
Kathleen McTavish [ctb],
Heather Thompson [ctb],
Andy Teucher [ctb],
Emilie Doussantousse [ctb],
Stephanie Hazlitt [ctb],
Nan-Hung Hsieh [ctb],
Sergio Ibarra Espinosa [ctb],
Province of British Columbia [cph]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>
Diff between ssdtools versions 0.3.1 dated 2020-09-01 and 0.3.2 dated 2020-09-02
DESCRIPTION | 6 +++--- MD5 | 24 ++++++++++++------------ NEWS.md | 5 +++++ README.md | 4 ++-- inst/WORDLIST | 1 + inst/doc/distributions.Rmd | 4 ++-- inst/doc/distributions.html | 8 ++++---- inst/doc/exposure-plots.html | 4 ++-- inst/doc/faqs.html | 4 ++-- inst/doc/small-sample-bias-ref.html | 4 ++-- inst/doc/ssdtools.html | 6 +++--- vignettes/distributions.Rmd | 4 ++-- vignettes/references.bib | 4 ++-- 13 files changed, 42 insertions(+), 36 deletions(-)
Title: Nonlinear Nonparametric Statistics
Description: Nonlinear nonparametric statistics using partial moments. Partial moments are the elements of variance and asymptotically approximate the area of f(x). These robust statistics provide the basis for nonlinear analysis while retaining linear equivalences. NNS offers: Numerical integration, Numerical differentiation, Clustering, Correlation, Dependence, Causal analysis, ANOVA, Regression, Classification, Seasonality, Autoregressive modeling, Normalization and Stochastic dominance. All routines based on: Viole, F. and Nawrocki, D. (2013), Nonlinear Nonparametric Statistics: Using Partial Moments (ISBN: 1490523995).
Author: Fred Viole
Maintainer: Fred Viole <ovvo.financial.systems@gmail.com>
Diff between NNS versions 0.5.4.3 dated 2020-07-31 and 0.5.5 dated 2020-09-02
DESCRIPTION | 10 MD5 | 168 ++++++++-------- R/ANOVA.R | 4 R/ARMA.R | 4 R/ARMA_optim.R | 2 R/Boost.R | 7 R/Causation.R | 2 R/Co_PM_dep.R | 2 R/Dependence.R | 2 R/FSD.R | 4 R/LPM_UPM_VaR.R | 2 R/Multivariate_Regression.R | 14 - R/NNS_Distance.R | 2 R/NNS_VAR.R | 8 R/NNS_meboot.R | 4 R/NNS_term_matrix.R | 2 R/Normalization.R | 2 R/Numerical_Differentiation.R | 2 R/Partial_Moments.R | 28 +- R/Partition_Map.R | 2 R/Regression.R | 22 +- R/SD_Efficient_Set.R | 4 R/SSD.R | 2 R/Seasonality_Test.R | 2 R/Stack.R | 22 +- R/TSD.R | 2 R/Uni_SD_Routines.R | 8 R/dy_d_wrt.R | 12 - R/dy_dx.R | 2 R/gvload.R | 2 README.md | 112 +++++----- build/vignette.rds |binary inst/doc/NNSvignette_Classification.Rmd | 10 inst/doc/NNSvignette_Classification.html | 114 ++++++----- inst/doc/NNSvignette_Clustering_and_Regression.Rmd | 10 inst/doc/NNSvignette_Clustering_and_Regression.html | 182 +++++++++-------- inst/doc/NNSvignette_Correlation_and_Dependence.Rmd | 8 inst/doc/NNSvignette_Correlation_and_Dependence.html | 188 +++++++++--------- inst/doc/NNSvignette_Forecasting.Rmd | 6 inst/doc/NNSvignette_Forecasting.html | 196 ++++++++++--------- inst/doc/NNSvignette_Partial_Moments.Rmd | 10 inst/doc/NNSvignette_Partial_Moments.html | 148 ++++++++------ man/Co.LPM.Rd | 2 man/Co.UPM.Rd | 2 man/D.LPM.Rd | 2 man/D.UPM.Rd | 2 man/LPM.Rd | 2 man/LPM.VaR.Rd | 2 man/LPM.ratio.Rd | 4 man/NNS.ANOVA.Rd | 4 man/NNS.ARMA.Rd | 4 man/NNS.ARMA.optim.Rd | 2 man/NNS.CDF.Rd | 4 man/NNS.FSD.Rd | 4 man/NNS.FSD.uni.Rd | 4 man/NNS.PDF.Rd | 2 man/NNS.SD.efficient.set.Rd | 4 man/NNS.SSD.Rd | 2 man/NNS.SSD.uni.Rd | 2 man/NNS.TSD.Rd | 2 man/NNS.TSD.uni.Rd | 2 man/NNS.VAR.Rd | 8 man/NNS.boost.Rd | 4 man/NNS.caus.Rd | 2 man/NNS.dep.Rd | 2 man/NNS.dep.hd.Rd | 2 man/NNS.diff.Rd | 2 man/NNS.distance.Rd | 2 man/NNS.meboot.Rd | 4 man/NNS.norm.Rd | 2 man/NNS.part.Rd | 2 man/NNS.reg.Rd | 2 man/NNS.seas.Rd | 2 man/NNS.stack.Rd | 2 man/NNS.term.matrix.Rd | 2 man/PM.matrix.Rd | 4 man/UPM.Rd | 2 man/UPM.ratio.Rd | 2 man/dy.d_.Rd | 7 man/dy.dx.Rd | 2 vignettes/NNSvignette_Classification.Rmd | 10 vignettes/NNSvignette_Clustering_and_Regression.Rmd | 10 vignettes/NNSvignette_Correlation_and_Dependence.Rmd | 8 vignettes/NNSvignette_Forecasting.Rmd | 6 vignettes/NNSvignette_Partial_Moments.Rmd | 10 85 files changed, 800 insertions(+), 684 deletions(-)
Title: Simulated Predicted Probabilities for Multinomial Logit Models
Description: Functions to easily return simulated predicted probabilities and
first differences for multinomial logit models. It takes a specified
scenario and a multinomial model to predict probabilities with a set of
coefficients, drawn from a simulated sampling distribution. The simulated
predictions allow for meaningful plots with means and confidence intervals.
The methodological approach is based on the principles laid out by King,
Tomz, and Wittenberg (2000) <doi:10.2307/2669316> and Hanmer and Ozan Kalkan
(2016) <doi:10.1111/j.1540-5907.2012.00602.x>.
Author: Manuel Neumann [aut, cre] (<https://orcid.org/0000-0002-7953-3939>)
Maintainer: Manuel Neumann <manuel.neumann@mzes.uni-mannheim.de>
Diff between MNLpred versions 0.0.3 dated 2020-07-02 and 0.0.4 dated 2020-09-02
DESCRIPTION | 11 ++++--- MD5 | 28 +++++++++--------- NEWS.md | 4 ++ R/mnl_fd2_ova.R | 8 ++++- R/mnl_pred_ova.R | 27 ++++++++++++++---- README.md | 26 ++++++++--------- inst/CITATION | 4 +- inst/doc/OVA_Predictions_For_MNL.Rmd | 2 - inst/doc/OVA_Predictions_For_MNL.html | 36 ++++++++++++------------ man/figures/README-first_differences_plot-1.png |binary man/figures/README-prediction_plot1-1.png |binary man/figures/README-prediction_plot2-1.png |binary man/figures/README-static_fd_plot-1.png |binary tests/testthat/test_inputvariants.R | 23 ++++++++++++++- vignettes/OVA_Predictions_For_MNL.Rmd | 2 - 15 files changed, 110 insertions(+), 61 deletions(-)
Title: Two-Stage Adaptive Dose-Finding Clinical Trial Design
Description: Simulate and implement early phase two-stage adaptive dose-finding design for binary and quasi-continuous toxicity endpoints. See Chiuzan et al. (2018) for further reading <DOI:10.1080/19466315.2018.1462727>.
Author: Alyssa Vanderbeek [aut, cre],
Laura Cosgrove [ctb],
Elizabeth Garrett-Mayer [ctb],
Cody Chiuzan [ctb]
Maintainer: Alyssa Vanderbeek <amv2187@columbia.edu>
Diff between iAdapt versions 0.1.0 dated 2019-08-29 and 2.0.0 dated 2020-09-02
iAdapt-0.1.0/iAdapt/inst/doc/Simulation_example.R |only iAdapt-0.1.0/iAdapt/inst/doc/Simulation_example.Rmd |only iAdapt-0.1.0/iAdapt/inst/doc/Simulation_example.html |only iAdapt-0.1.0/iAdapt/vignettes/Simulation_example.Rmd |only iAdapt-2.0.0/iAdapt/DESCRIPTION | 21 - iAdapt-2.0.0/iAdapt/MD5 | 80 ++++-- iAdapt-2.0.0/iAdapt/NAMESPACE | 10 iAdapt-2.0.0/iAdapt/R/LRtox.R | 20 - iAdapt-2.0.0/iAdapt/R/LRtox.nTTP.R |only iAdapt-2.0.0/iAdapt/R/beta.ab.R | 52 ++-- iAdapt-2.0.0/iAdapt/R/dlt.prob.R |only iAdapt-2.0.0/iAdapt/R/eff.stg1.R | 24 - iAdapt-2.0.0/iAdapt/R/eff.stg1.nTTP.R |only iAdapt-2.0.0/iAdapt/R/get.thresh.R |only iAdapt-2.0.0/iAdapt/R/nTTP.indiv.sim.R |only iAdapt-2.0.0/iAdapt/R/rand.prob.R | 8 iAdapt-2.0.0/iAdapt/R/rand.stg2.R | 91 ++++--- iAdapt-2.0.0/iAdapt/R/rand.stg2.nTTP.R |only iAdapt-2.0.0/iAdapt/R/safe.dose.R | 13 - iAdapt-2.0.0/iAdapt/R/safe.dose.nTTP.R |only iAdapt-2.0.0/iAdapt/R/sim.plot.R |only iAdapt-2.0.0/iAdapt/R/sim.summary.R | 65 ++--- iAdapt-2.0.0/iAdapt/R/sim.trials.R | 29 +- iAdapt-2.0.0/iAdapt/R/sim.trials.nTTP.R |only iAdapt-2.0.0/iAdapt/R/tox.profile.R | 30 -- iAdapt-2.0.0/iAdapt/R/tox.profile.nTTP.R |only iAdapt-2.0.0/iAdapt/build/vignette.rds |binary iAdapt-2.0.0/iAdapt/data |only iAdapt-2.0.0/iAdapt/inst/doc/DLT_simulation_example.R |only iAdapt-2.0.0/iAdapt/inst/doc/DLT_simulation_example.Rmd |only iAdapt-2.0.0/iAdapt/inst/doc/DLT_simulation_example.html |only iAdapt-2.0.0/iAdapt/inst/doc/Implementation_example.R | 23 + iAdapt-2.0.0/iAdapt/inst/doc/Implementation_example.Rmd | 173 ++++++++------ iAdapt-2.0.0/iAdapt/inst/doc/Implementation_example.html | 55 +++- iAdapt-2.0.0/iAdapt/inst/doc/nTTP_simulation_example.R |only iAdapt-2.0.0/iAdapt/inst/doc/nTTP_simulation_example.Rmd |only iAdapt-2.0.0/iAdapt/inst/doc/nTTP_simulation_example.html |only iAdapt-2.0.0/iAdapt/man/LRtox.Rd | 8 iAdapt-2.0.0/iAdapt/man/LRtox.nTTP.Rd |only iAdapt-2.0.0/iAdapt/man/TOX.Rd |only iAdapt-2.0.0/iAdapt/man/dlt.prob.Rd |only iAdapt-2.0.0/iAdapt/man/eff.stg1.Rd | 22 - iAdapt-2.0.0/iAdapt/man/eff.stg1.nTTP.Rd |only iAdapt-2.0.0/iAdapt/man/get.thresh.Rd |only iAdapt-2.0.0/iAdapt/man/nTTP.indiv.sim.Rd |only iAdapt-2.0.0/iAdapt/man/rand.stg2.Rd | 25 +- iAdapt-2.0.0/iAdapt/man/rand.stg2.nTTP.Rd |only iAdapt-2.0.0/iAdapt/man/safe.dose.Rd | 5 iAdapt-2.0.0/iAdapt/man/safe.dose.nTTP.Rd |only iAdapt-2.0.0/iAdapt/man/sim.plot.Rd |only iAdapt-2.0.0/iAdapt/man/sim.summary.Rd | 16 - iAdapt-2.0.0/iAdapt/man/sim.trials.Rd | 15 - iAdapt-2.0.0/iAdapt/man/sim.trials.nTTP.Rd |only iAdapt-2.0.0/iAdapt/man/tox.profile.Rd | 14 - iAdapt-2.0.0/iAdapt/man/tox.profile.nTTP.Rd |only iAdapt-2.0.0/iAdapt/vignettes/DLT_simulation_example.Rmd |only iAdapt-2.0.0/iAdapt/vignettes/Implementation_example.Rmd | 173 ++++++++------ iAdapt-2.0.0/iAdapt/vignettes/nTTP_simulation_example.Rmd |only 58 files changed, 590 insertions(+), 382 deletions(-)
Title: A Collection of Fluorescence Fluctuation Spectroscopy Analysis
Methods
Description: This is a package for fluorescence fluctuation spectroscopy data analysis methods such as spFCS, FCCS, scanning-FCS, pCF, N&B and pCOMB, among others.
In addition, several data detrending tools are provided. For an extensive user's guide for the use of FCSlib, please navigate to (<https://github.com/FCSlib/FCSlib/tree/master/Documentation>).
Sample data can be found at (<https://github.com/FCSlib/FCSlib/tree/master/Sample%20Data>).
Author: Raúl Pinto Cámara, Adan Guerrero, Alejandro Linares, José Damián Martínez Reyes, Haydee Hernández.
Maintainer: Raúl Pinto Cámara <support.fcslib@mail.ibt.unam.mx>
Diff between FCSlib versions 1.1.1 dated 2020-08-06 and 1.2.0 dated 2020-09-02
FCSlib-1.1.1/FCSlib/R/Cy5_100nM.R |only FCSlib-1.1.1/FCSlib/data/Cy5_100nM.RData |only FCSlib-1.1.1/FCSlib/man/Cy5_100nM.Rd |only FCSlib-1.2.0/FCSlib/DESCRIPTION | 27 +++++------ FCSlib-1.2.0/FCSlib/MD5 | 74 +++++++++++++++++++------------ FCSlib-1.2.0/FCSlib/NAMESPACE | 16 ++++++ FCSlib-1.2.0/FCSlib/R/Cy5.R |only FCSlib-1.2.0/FCSlib/R/V2.R | 6 +- FCSlib-1.2.0/FCSlib/R/asynACTCSPC.R |only FCSlib-1.2.0/FCSlib/R/binMatrix.R |only FCSlib-1.2.0/FCSlib/R/binTimeSeries.R |only FCSlib-1.2.0/FCSlib/R/boxcarDetrend.R |only FCSlib-1.2.0/FCSlib/R/expDetrend.R |only FCSlib-1.2.0/FCSlib/R/fcs.R | 11 ++-- FCSlib-1.2.0/FCSlib/R/fitFCS.R | 17 +++---- FCSlib-1.2.0/FCSlib/R/gcf.R | 6 +- FCSlib-1.2.0/FCSlib/R/nbline.R | 52 ++++----------------- FCSlib-1.2.0/FCSlib/R/norm.vector.R |only FCSlib-1.2.0/FCSlib/R/pcf.R | 63 ++++++-------------------- FCSlib-1.2.0/FCSlib/R/pcomb.R | 28 +++++------ FCSlib-1.2.0/FCSlib/R/polyDetrend.R |only FCSlib-1.2.0/FCSlib/R/readFileFcs.R | 2 FCSlib-1.2.0/FCSlib/R/readFileModel.R | 2 FCSlib-1.2.0/FCSlib/R/readFileSPC.R |only FCSlib-1.2.0/FCSlib/R/simplifyFCS.R | 42 ++++++++++------- FCSlib-1.2.0/FCSlib/R/smoothCarpet.R | 2 FCSlib-1.2.0/FCSlib/R/tiff_to_mtx.R |only FCSlib-1.2.0/FCSlib/data/Cy5.RData |only FCSlib-1.2.0/FCSlib/data/datalist | 2 FCSlib-1.2.0/FCSlib/man/Cy5.Rd |only FCSlib-1.2.0/FCSlib/man/V2.Rd | 6 +- FCSlib-1.2.0/FCSlib/man/asynACTCSPC.Rd |only FCSlib-1.2.0/FCSlib/man/binMatrix.Rd |only FCSlib-1.2.0/FCSlib/man/binTimeSeries.Rd |only FCSlib-1.2.0/FCSlib/man/boxcarDetrend.Rd |only FCSlib-1.2.0/FCSlib/man/expDetrend.Rd |only FCSlib-1.2.0/FCSlib/man/fcs.Rd | 6 +- FCSlib-1.2.0/FCSlib/man/fitFCS.Rd | 8 +-- FCSlib-1.2.0/FCSlib/man/gcf.Rd | 6 +- FCSlib-1.2.0/FCSlib/man/nbline.Rd | 41 ++--------------- FCSlib-1.2.0/FCSlib/man/norm.vector.Rd |only FCSlib-1.2.0/FCSlib/man/pcf.Rd | 32 +------------ FCSlib-1.2.0/FCSlib/man/pcomb.Rd | 8 +-- FCSlib-1.2.0/FCSlib/man/polyDetrend.Rd |only FCSlib-1.2.0/FCSlib/man/readFileFCS.Rd | 2 FCSlib-1.2.0/FCSlib/man/readFileModel.Rd | 2 FCSlib-1.2.0/FCSlib/man/readFileSPC.Rd |only FCSlib-1.2.0/FCSlib/man/simplifyFCS.Rd | 5 +- FCSlib-1.2.0/FCSlib/man/smoothCarpet.Rd | 2 FCSlib-1.2.0/FCSlib/man/tiff_to_mtx.Rd |only 50 files changed, 197 insertions(+), 271 deletions(-)
Title: Fast Estimators for Design-Based Inference
Description: Fast procedures for small set of commonly-used, design-appropriate estimators with robust standard errors and confidence intervals. Includes estimators for linear regression, instrumental variables regression, difference-in-means, Horvitz-Thompson estimation, and regression improving precision of experimental estimates by interacting treatment with centered pre-treatment covariates introduced by Lin (2013) <doi:10.1214/12-AOAS583>.
Author: Graeme Blair [aut, cre],
Jasper Cooper [aut],
Alexander Coppock [aut],
Macartan Humphreys [aut],
Luke Sonnet [aut],
Neal Fultz [ctb],
Lily Medina [ctb],
Russell Lenth [ctb]
Maintainer: Graeme Blair <graeme.blair@ucla.edu>
Diff between estimatr versions 0.22.0 dated 2020-03-19 and 0.24.0 dated 2020-09-02
DESCRIPTION | 14 +++--- MD5 | 57 ++++++++++++++------------- NAMESPACE | 4 + NEWS.md | 7 +++ R/S3_glance.R | 22 +++++----- R/S3_nobs.R | 8 ++- R/S3_summary.R | 2 R/S3_tidy.R | 39 ++++++++++++++---- R/S3_update.R |only R/S3_vcov.R | 13 +----- R/estimatr_difference_in_means.R | 52 ++++++++++++------------ R/estimatr_horvitz_thompson.R | 14 +++--- R/estimatr_iv_robust.R | 11 ++--- R/helper_clean_model_data.R | 9 ++-- R/helper_extract.R | 2 R/helper_lm_robust_fit.R | 4 - R/helper_return.R | 5 ++ R/helper_starprep.R | 4 - man/estimatr_glancers.Rd | 12 ++--- man/estimatr_tidiers.Rd | 18 ++++++-- man/horvitz_thompson.Rd | 4 - man/iv_robust.Rd | 2 src/lm_robust_helper.cpp | 36 +++++++++-------- tests/testthat/test-arg-checking.R |only tests/testthat/test-iv-robust.R | 9 +++- tests/testthat/test-lm-cluster.R | 6 ++ tests/testthat/test-lm-robust-fes.R | 20 +++++++++ tests/testthat/test-lm-robust.R | 10 ++-- tests/testthat/test-modelsummary.R |only tests/testthat/test-return.R | 2 tests/testthat/test-s3-methods.R | 75 ++++++++++++++++++++++++++++++------ 31 files changed, 302 insertions(+), 159 deletions(-)
Title: Relational Data Models
Description: Provides tools for working with multiple related
tables, stored as data frames or in a relational database. Multiple
tables (data and metadata) are stored in a compound object, which can
then be manipulated with a pipe-friendly syntax.
Author: Tobias Schieferdecker [aut],
Kirill Müller [aut, cre] (<https://orcid.org/0000-0002-1416-3412>),
Darko Bergant [aut],
Katharina Brunner [ctb],
James Wondrasek [ctb],
energie360° AG [fnd],
cynkra GmbH [fnd, cph]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>
Diff between dm versions 0.1.6 dated 2020-07-29 and 0.1.7 dated 2020-09-02
DESCRIPTION | 15 ++-- MD5 | 44 ++++++------- NEWS.md | 6 + R/db-helpers.R | 18 +---- R/db-interface.R | 10 +++ R/dm-from-src.R | 2 R/learn.R | 22 ++++-- R/zzz.R | 2 inst/doc/dm.html | 4 - inst/doc/howto-dm-db.html | 8 +- inst/doc/howto-dm-df.html | 4 - inst/doc/howto-dm-theory.html | 12 +-- inst/doc/tech-dm-cdm.html | 4 - inst/doc/tech-dm-class.html | 12 +-- inst/doc/tech-dm-draw.html | 4 - inst/doc/tech-dm-filter.html | 22 +++--- inst/doc/tech-dm-join.html | 4 - inst/doc/tech-dm-low-level.html | 4 - man/dm_from_src.Rd | 4 - tests/testthat/helper-src.R | 6 - tests/testthat/test-dm-from-src.R | 3 tests/testthat/test-learn.R | 120 ++++++++++++++++++++------------------ vignettes/setup/setup.R | 4 - 23 files changed, 185 insertions(+), 149 deletions(-)
Title: EMF Graphics Output Device
Description: Output graphics to EMF+/EMF.
Author: Philip Johnson
Maintainer: Philip Johnson <plfj@umd.edu>
Diff between devEMF versions 4.0 dated 2020-08-28 and 4.0-1 dated 2020-09-02
devEMF-4.0-1/devEMF/DESCRIPTION | 8 - devEMF-4.0-1/devEMF/MD5 | 17 +- devEMF-4.0-1/devEMF/NEWS | 4 devEMF-4.0-1/devEMF/configure | 252 +++++++++++++++++++++++++++++++--- devEMF-4.0-1/devEMF/configure.ac | 33 ++-- devEMF-4.0-1/devEMF/man/emf.Rd | 4 devEMF-4.0-1/devEMF/src/devEMF.cpp | 2 devEMF-4.0-1/devEMF/src/emf.h | 2 devEMF-4.0-1/devEMF/src/fontmetrics.h | 6 devEMF-4.0/devEMF/src/fontembed.h |only 10 files changed, 277 insertions(+), 51 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-03-02 0.6.0
2017-06-20 0.5.0
2016-11-01 0.4.0
Title: Extreme Gradient Boosting
Description: Extreme Gradient Boosting, which is an efficient implementation
of the gradient boosting framework from Chen & Guestrin (2016) <doi:10.1145/2939672.2939785>.
This package is its R interface. The package includes efficient linear
model solver and tree learning algorithms. The package can automatically
do parallel computation on a single machine which could be more than 10
times faster than existing gradient boosting packages. It supports
various objective functions, including regression, classification and ranking.
The package is made to be extensible, so that users are also allowed to define
their own objectives easily.
Author: Tianqi Chen [aut],
Tong He [aut, cre],
Michael Benesty [aut],
Vadim Khotilovich [aut],
Yuan Tang [aut] (<https://orcid.org/0000-0001-5243-233X>),
Hyunsu Cho [aut],
Kailong Chen [aut],
Rory Mitchell [aut],
Ignacio Cano [aut],
Tianyi Zhou [aut],
Mu Li [aut],
Junyuan Xie [aut],
Min Lin [aut],
Yifeng Geng [aut],
Yutian Li [aut],
XGBoost contributors [cph] (base XGBoost implementation)
Maintainer: Tong He <hetong007@gmail.com>
Diff between xgboost versions 1.1.1.1 dated 2020-06-14 and 1.2.0.1 dated 2020-09-02
xgboost-1.1.1.1/xgboost/src/src/common/probability_distribution.cc |only xgboost-1.1.1.1/xgboost/src/src/common/timer.cu |only xgboost-1.1.1.1/xgboost/src/src/data/device_dmatrix.cu |only xgboost-1.1.1.1/xgboost/src/src/data/device_dmatrix.h |only xgboost-1.1.1.1/xgboost/tests/testthat/test_lint.R |only xgboost-1.2.0.1/xgboost/DESCRIPTION | 20 xgboost-1.2.0.1/xgboost/MD5 | 350 ++--- xgboost-1.2.0.1/xgboost/R/callbacks.R | 40 xgboost-1.2.0.1/xgboost/R/utils.R | 95 + xgboost-1.2.0.1/xgboost/R/xgb.Booster.R | 29 xgboost-1.2.0.1/xgboost/R/xgb.DMatrix.R | 10 xgboost-1.2.0.1/xgboost/R/xgb.DMatrix.save.R | 8 xgboost-1.2.0.1/xgboost/R/xgb.create.features.R | 50 xgboost-1.2.0.1/xgboost/R/xgb.cv.R | 43 xgboost-1.2.0.1/xgboost/R/xgb.dump.R | 28 xgboost-1.2.0.1/xgboost/R/xgb.ggplot.R | 48 xgboost-1.2.0.1/xgboost/R/xgb.importance.R | 85 - xgboost-1.2.0.1/xgboost/R/xgb.model.dt.tree.R | 84 - xgboost-1.2.0.1/xgboost/R/xgb.plot.deepness.R | 54 xgboost-1.2.0.1/xgboost/R/xgb.plot.importance.R | 4 xgboost-1.2.0.1/xgboost/R/xgb.plot.multi.trees.R | 40 xgboost-1.2.0.1/xgboost/R/xgb.plot.shap.R | 10 xgboost-1.2.0.1/xgboost/R/xgb.plot.tree.R | 48 xgboost-1.2.0.1/xgboost/R/xgb.save.R | 34 xgboost-1.2.0.1/xgboost/R/xgb.train.R | 38 xgboost-1.2.0.1/xgboost/R/xgb.unserialize.R | 21 xgboost-1.2.0.1/xgboost/configure | 16 xgboost-1.2.0.1/xgboost/configure.ac | 4 xgboost-1.2.0.1/xgboost/demo/basic_walkthrough.R | 36 xgboost-1.2.0.1/xgboost/demo/boost_from_prediction.R | 10 xgboost-1.2.0.1/xgboost/demo/caret_wrapper.R | 10 xgboost-1.2.0.1/xgboost/demo/create_sparse_matrix.R | 22 xgboost-1.2.0.1/xgboost/demo/cross_validation.R | 18 xgboost-1.2.0.1/xgboost/demo/custom_objective.R | 22 xgboost-1.2.0.1/xgboost/demo/early_stopping.R | 10 xgboost-1.2.0.1/xgboost/demo/generalized_linear_model.R | 11 xgboost-1.2.0.1/xgboost/demo/gpu_accelerated.R | 10 xgboost-1.2.0.1/xgboost/demo/interaction_constraints.R | 90 - xgboost-1.2.0.1/xgboost/demo/poisson_regression.R | 9 xgboost-1.2.0.1/xgboost/demo/predict_first_ntree.R | 20 xgboost-1.2.0.1/xgboost/demo/predict_leaf_indices.R | 30 xgboost-1.2.0.1/xgboost/demo/tweedie_regression.R | 20 xgboost-1.2.0.1/xgboost/inst/doc/discoverYourData.R | 2 xgboost-1.2.0.1/xgboost/inst/doc/discoverYourData.Rmd | 14 xgboost-1.2.0.1/xgboost/inst/doc/discoverYourData.html | 14 xgboost-1.2.0.1/xgboost/inst/doc/xgboost.R | 4 xgboost-1.2.0.1/xgboost/inst/doc/xgboost.Rnw | 68 - xgboost-1.2.0.1/xgboost/inst/doc/xgboost.pdf |binary xgboost-1.2.0.1/xgboost/inst/doc/xgboostPresentation.R | 2 xgboost-1.2.0.1/xgboost/inst/doc/xgboostPresentation.Rmd | 4 xgboost-1.2.0.1/xgboost/inst/doc/xgboostPresentation.html | 14 xgboost-1.2.0.1/xgboost/inst/make-r-def.R |only xgboost-1.2.0.1/xgboost/man/a-compatibility-note-for-saveRDS-save.Rd |only xgboost-1.2.0.1/xgboost/man/xgb.Booster.complete.Rd | 2 xgboost-1.2.0.1/xgboost/man/xgb.create.features.Rd | 10 xgboost-1.2.0.1/xgboost/man/xgb.cv.Rd | 11 xgboost-1.2.0.1/xgboost/man/xgb.dump.Rd | 8 xgboost-1.2.0.1/xgboost/man/xgb.importance.Rd | 16 xgboost-1.2.0.1/xgboost/man/xgb.load.Rd | 6 xgboost-1.2.0.1/xgboost/man/xgb.model.dt.tree.Rd | 12 xgboost-1.2.0.1/xgboost/man/xgb.plot.deepness.Rd | 6 xgboost-1.2.0.1/xgboost/man/xgb.plot.tree.Rd | 4 xgboost-1.2.0.1/xgboost/man/xgb.save.Rd | 16 xgboost-1.2.0.1/xgboost/man/xgb.train.Rd | 28 xgboost-1.2.0.1/xgboost/src/Makevars.in | 2 xgboost-1.2.0.1/xgboost/src/Makevars.win | 2 xgboost-1.2.0.1/xgboost/src/amalgamation/xgboost-all0.cc | 2 xgboost-1.2.0.1/xgboost/src/include/xgboost/base.h | 14 xgboost-1.2.0.1/xgboost/src/include/xgboost/c_api.h | 354 ++++- xgboost-1.2.0.1/xgboost/src/include/xgboost/data.h | 106 + xgboost-1.2.0.1/xgboost/src/include/xgboost/generic_parameters.h | 2 xgboost-1.2.0.1/xgboost/src/include/xgboost/host_device_vector.h | 6 xgboost-1.2.0.1/xgboost/src/include/xgboost/json.h | 12 xgboost-1.2.0.1/xgboost/src/include/xgboost/json_io.h | 71 - xgboost-1.2.0.1/xgboost/src/include/xgboost/learner.h | 6 xgboost-1.2.0.1/xgboost/src/include/xgboost/predictor.h | 1 xgboost-1.2.0.1/xgboost/src/include/xgboost/span.h | 9 xgboost-1.2.0.1/xgboost/src/include/xgboost/version_config.h | 2 xgboost-1.2.0.1/xgboost/src/rabit/include/rabit/base.h |only xgboost-1.2.0.1/xgboost/src/rabit/include/rabit/internal/utils.h | 3 xgboost-1.2.0.1/xgboost/src/rabit/src/allreduce_base.cc | 3 xgboost-1.2.0.1/xgboost/src/rabit/src/allreduce_robust.cc | 3 xgboost-1.2.0.1/xgboost/src/rabit/src/c_api.cc | 65 - xgboost-1.2.0.1/xgboost/src/rabit/src/engine.cc | 5 xgboost-1.2.0.1/xgboost/src/rabit/src/engine_base.cc | 3 xgboost-1.2.0.1/xgboost/src/rabit/src/engine_empty.cc | 3 xgboost-1.2.0.1/xgboost/src/rabit/src/engine_mock.cc | 3 xgboost-1.2.0.1/xgboost/src/rabit/src/engine_mpi.cc | 3 xgboost-1.2.0.1/xgboost/src/src/CMakeLists.txt | 45 xgboost-1.2.0.1/xgboost/src/src/c_api/c_api.cc | 133 +- xgboost-1.2.0.1/xgboost/src/src/c_api/c_api.cu | 27 xgboost-1.2.0.1/xgboost/src/src/c_api/c_api_error.cc | 3 xgboost-1.2.0.1/xgboost/src/src/c_api/c_api_error.h | 6 xgboost-1.2.0.1/xgboost/src/src/cli_main.cc | 545 +++++--- xgboost-1.2.0.1/xgboost/src/src/common/charconv.cc |only xgboost-1.2.0.1/xgboost/src/src/common/charconv.h |only xgboost-1.2.0.1/xgboost/src/src/common/column_matrix.h | 11 xgboost-1.2.0.1/xgboost/src/src/common/config.h | 18 xgboost-1.2.0.1/xgboost/src/src/common/device_helpers.cu | 27 xgboost-1.2.0.1/xgboost/src/src/common/device_helpers.cuh | 217 ++- xgboost-1.2.0.1/xgboost/src/src/common/hist_util.cc | 137 +- xgboost-1.2.0.1/xgboost/src/src/common/hist_util.cu | 488 ++----- xgboost-1.2.0.1/xgboost/src/src/common/hist_util.cuh |only xgboost-1.2.0.1/xgboost/src/src/common/hist_util.h | 96 - xgboost-1.2.0.1/xgboost/src/src/common/host_device_vector.cc | 10 xgboost-1.2.0.1/xgboost/src/src/common/host_device_vector.cu | 37 xgboost-1.2.0.1/xgboost/src/src/common/io.cc | 94 - xgboost-1.2.0.1/xgboost/src/src/common/io.h | 12 xgboost-1.2.0.1/xgboost/src/src/common/json.cc | 296 ++-- xgboost-1.2.0.1/xgboost/src/src/common/observer.h | 2 xgboost-1.2.0.1/xgboost/src/src/common/probability_distribution.h | 158 +- xgboost-1.2.0.1/xgboost/src/src/common/quantile.cu |only xgboost-1.2.0.1/xgboost/src/src/common/quantile.cuh |only xgboost-1.2.0.1/xgboost/src/src/common/quantile.h | 194 --- xgboost-1.2.0.1/xgboost/src/src/common/random.h | 1 xgboost-1.2.0.1/xgboost/src/src/common/survival_util.cc | 248 --- xgboost-1.2.0.1/xgboost/src/src/common/survival_util.h | 331 ++++- xgboost-1.2.0.1/xgboost/src/src/common/timer.cc | 19 xgboost-1.2.0.1/xgboost/src/src/common/timer.h | 2 xgboost-1.2.0.1/xgboost/src/src/data/adapter.h | 3 xgboost-1.2.0.1/xgboost/src/src/data/array_interface.h | 71 - xgboost-1.2.0.1/xgboost/src/src/data/data.cc | 233 +++ xgboost-1.2.0.1/xgboost/src/src/data/data.cu | 42 xgboost-1.2.0.1/xgboost/src/src/data/device_adapter.cuh | 89 - xgboost-1.2.0.1/xgboost/src/src/data/ellpack_page.cu | 202 ++- xgboost-1.2.0.1/xgboost/src/src/data/ellpack_page.cuh | 21 xgboost-1.2.0.1/xgboost/src/src/data/ellpack_page_source.cu | 24 xgboost-1.2.0.1/xgboost/src/src/data/iterative_device_dmatrix.cu |only xgboost-1.2.0.1/xgboost/src/src/data/iterative_device_dmatrix.h |only xgboost-1.2.0.1/xgboost/src/src/data/proxy_dmatrix.cu |only xgboost-1.2.0.1/xgboost/src/src/data/proxy_dmatrix.h |only xgboost-1.2.0.1/xgboost/src/src/data/simple_dmatrix.cc | 38 xgboost-1.2.0.1/xgboost/src/src/data/simple_dmatrix.cu | 54 xgboost-1.2.0.1/xgboost/src/src/data/sparse_page_source.h | 15 xgboost-1.2.0.1/xgboost/src/src/gbm/gbtree.cc | 3 xgboost-1.2.0.1/xgboost/src/src/gbm/gbtree_model.cc | 24 xgboost-1.2.0.1/xgboost/src/src/learner.cc | 107 + xgboost-1.2.0.1/xgboost/src/src/metric/elementwise_metric.cu | 17 xgboost-1.2.0.1/xgboost/src/src/metric/metric.cc | 3 xgboost-1.2.0.1/xgboost/src/src/metric/multiclass_metric.cu | 28 xgboost-1.2.0.1/xgboost/src/src/metric/survival_metric.cc | 104 - xgboost-1.2.0.1/xgboost/src/src/metric/survival_metric.cu |only xgboost-1.2.0.1/xgboost/src/src/objective/aft_obj.cc | 115 - xgboost-1.2.0.1/xgboost/src/src/objective/aft_obj.cu |only xgboost-1.2.0.1/xgboost/src/src/objective/multiclass_obj.cu | 4 xgboost-1.2.0.1/xgboost/src/src/objective/rank_obj.cu | 2 xgboost-1.2.0.1/xgboost/src/src/objective/regression_loss.h | 31 xgboost-1.2.0.1/xgboost/src/src/objective/regression_obj.cu | 4 xgboost-1.2.0.1/xgboost/src/src/predictor/cpu_predictor.cc | 14 xgboost-1.2.0.1/xgboost/src/src/predictor/gpu_predictor.cu | 77 - xgboost-1.2.0.1/xgboost/src/src/predictor/predictor.cc | 1 xgboost-1.2.0.1/xgboost/src/src/tree/constraints.cuh | 10 xgboost-1.2.0.1/xgboost/src/src/tree/gpu_hist/driver.cuh |only xgboost-1.2.0.1/xgboost/src/src/tree/gpu_hist/evaluate_splits.cu |only xgboost-1.2.0.1/xgboost/src/src/tree/gpu_hist/evaluate_splits.cuh |only xgboost-1.2.0.1/xgboost/src/src/tree/gpu_hist/feature_groups.cu |only xgboost-1.2.0.1/xgboost/src/src/tree/gpu_hist/feature_groups.cuh |only xgboost-1.2.0.1/xgboost/src/src/tree/gpu_hist/gradient_based_sampler.cu | 4 xgboost-1.2.0.1/xgboost/src/src/tree/gpu_hist/histogram.cu | 64 - xgboost-1.2.0.1/xgboost/src/src/tree/gpu_hist/histogram.cuh | 4 xgboost-1.2.0.1/xgboost/src/src/tree/gpu_hist/row_partitioner.cu | 51 xgboost-1.2.0.1/xgboost/src/src/tree/gpu_hist/row_partitioner.cuh | 31 xgboost-1.2.0.1/xgboost/src/src/tree/param.h | 19 xgboost-1.2.0.1/xgboost/src/src/tree/updater_gpu_hist.cu | 624 +++------- xgboost-1.2.0.1/xgboost/src/src/tree/updater_histmaker.cc | 2 xgboost-1.2.0.1/xgboost/src/src/tree/updater_prune.cc | 6 xgboost-1.2.0.1/xgboost/src/src/tree/updater_quantile_hist.cc | 472 +++++-- xgboost-1.2.0.1/xgboost/src/src/tree/updater_quantile_hist.h | 189 ++- xgboost-1.2.0.1/xgboost/src/xgboost_R.cc | 6 xgboost-1.2.0.1/xgboost/tests/testthat.R | 2 xgboost-1.2.0.1/xgboost/tests/testthat/test_basic.R | 104 - xgboost-1.2.0.1/xgboost/tests/testthat/test_callbacks.R | 48 xgboost-1.2.0.1/xgboost/tests/testthat/test_custom_objective.R | 33 xgboost-1.2.0.1/xgboost/tests/testthat/test_dmatrix.R | 36 xgboost-1.2.0.1/xgboost/tests/testthat/test_gc_safety.R | 4 xgboost-1.2.0.1/xgboost/tests/testthat/test_glm.R | 8 xgboost-1.2.0.1/xgboost/tests/testthat/test_helpers.R | 56 xgboost-1.2.0.1/xgboost/tests/testthat/test_interaction_constraints.R | 24 xgboost-1.2.0.1/xgboost/tests/testthat/test_interactions.R | 60 xgboost-1.2.0.1/xgboost/tests/testthat/test_model_compatibility.R |only xgboost-1.2.0.1/xgboost/tests/testthat/test_monotone.R | 29 xgboost-1.2.0.1/xgboost/tests/testthat/test_parameter_exposure.R | 4 xgboost-1.2.0.1/xgboost/tests/testthat/test_poisson_regression.R | 6 xgboost-1.2.0.1/xgboost/tests/testthat/test_ranking.R |only xgboost-1.2.0.1/xgboost/tests/testthat/test_update.R | 18 xgboost-1.2.0.1/xgboost/vignettes/discoverYourData.Rmd | 14 xgboost-1.2.0.1/xgboost/vignettes/xgboost.Rnw | 68 - xgboost-1.2.0.1/xgboost/vignettes/xgboost.bib | 2 xgboost-1.2.0.1/xgboost/vignettes/xgboostPresentation.Rmd | 4 189 files changed, 4978 insertions(+), 3905 deletions(-)
Title: The Universal Character Encoding Detector
Description: R bindings of the 'uchardet', encoding detector library from Mozilla
(<https://www.freedesktop.org/wiki/Software/uchardet/>). It takes a sequence
of bytes in an unknown character encoding and without any additional
information, and attempts to get the encoding of the text. All return names of
the encodings are iconv-compatible.
Author: Artem Klevtsov [aut, cre] (<https://orcid.org/0000-0003-0492-6647>),
Philipp Upravitelev [ctb]
Maintainer: Artem Klevtsov <a.a.klevtsov@gmail.com>
Diff between uchardet versions 1.0.6 dated 2020-04-27 and 1.1.0 dated 2020-09-02
uchardet-1.0.6/uchardet/R/RcppExports.R |only uchardet-1.0.6/uchardet/inst/include |only uchardet-1.0.6/uchardet/src/RcppExports.cpp |only uchardet-1.0.6/uchardet/src/detect-file.cpp |only uchardet-1.0.6/uchardet/src/detect-raw.cpp |only uchardet-1.0.6/uchardet/src/detect-str.cpp |only uchardet-1.1.0/uchardet/DESCRIPTION | 14 uchardet-1.1.0/uchardet/MD5 | 59 +- uchardet-1.1.0/uchardet/NAMESPACE | 3 uchardet-1.1.0/uchardet/NEWS.md | 10 uchardet-1.1.0/uchardet/R/detect.R |only uchardet-1.1.0/uchardet/R/uchardet-package.R | 7 uchardet-1.1.0/uchardet/README.md | 13 uchardet-1.1.0/uchardet/build/vignette.rds |binary uchardet-1.1.0/uchardet/inst/doc/uchardet.R | 40 + uchardet-1.1.0/uchardet/inst/doc/uchardet.Rmd | 89 +--- uchardet-1.1.0/uchardet/inst/doc/uchardet.html | 207 ++++------ uchardet-1.1.0/uchardet/inst/tinytest/setup.R | 2 uchardet-1.1.0/uchardet/inst/tinytest/test-detect-file.R | 15 uchardet-1.1.0/uchardet/inst/tinytest/test-detect-raw.R | 19 uchardet-1.1.0/uchardet/inst/tinytest/test-detect-str.R | 14 uchardet-1.1.0/uchardet/man/detect_file_enc.Rd | 43 +- uchardet-1.1.0/uchardet/man/detect_raw_enc.Rd | 14 uchardet-1.1.0/uchardet/man/detect_str_enc.Rd | 2 uchardet-1.1.0/uchardet/man/uchardet.Rd | 84 +++- uchardet-1.1.0/uchardet/src/Makevars | 2 uchardet-1.1.0/uchardet/src/Makevars.win |only uchardet-1.1.0/uchardet/src/detect.cpp |only uchardet-1.1.0/uchardet/src/init.cpp |only uchardet-1.1.0/uchardet/src/uchardet/CMakeLists.txt | 6 uchardet-1.1.0/uchardet/src/uchardet/README.md | 41 + uchardet-1.1.0/uchardet/src/uchardet/doc/README.maintainer | 8 uchardet-1.1.0/uchardet/src/uchardet/src/tools/CMakeLists.txt | 17 uchardet-1.1.0/uchardet/src/uchardet/src/tools/uchardet.cpp | 5 uchardet-1.1.0/uchardet/vignettes/uchardet.Rmd | 89 +--- 35 files changed, 459 insertions(+), 344 deletions(-)
Title: Ridge Regression with Automatic Selection of the Penalty
Parameter
Description: Linear and logistic ridge regression functions. Additionally includes special functions for
genome-wide single-nucleotide polymorphism (SNP) data.
Author: Steffen Moritz [aut, cre] (<https://orcid.org/0000-0002-0085-1804>),
Erika Cule [aut],
Dan Frankowski [aut]
Maintainer: Steffen Moritz <steffen.moritz10@gmail.com>
Diff between ridge versions 2.5 dated 2020-03-20 and 2.6 dated 2020-09-02
DESCRIPTION | 10 +++++----- MD5 | 17 +++++++++-------- NEWS.md | 6 ++++++ README.md | 14 ++++++++------ cleanup | 2 -- configure.ac | 1 + man/figures |only src/computePvals.h | 1 - src/depends.h | 1 + src/ridgeRegressionFunctions.h | 1 - 10 files changed, 30 insertions(+), 23 deletions(-)
Title: Path Component Fit Indices for Latent Structural Equation Models
Description: Functions for computing fit indices for
evaluating the path component of latent variable structural equation models.
Available fit indices include RMSEA-P and NSCI-P originally presented and evaluated
by Williams and O'Boyle (2011) <doi:10.1177/1094428110391472> and demonstrated by
O'Boyle and Williams (2011) <doi:10.1037/a0020539> and Williams, O'Boyle, & Yu (2020)
<doi:10.1177/1094428117736137>. Also included are fit indices described by
Hancock and Mueller (2011) <doi:10.1177/0013164410384856>.
Author: Steven Andrew Culpepper [aut, cre]
(<https://orcid.org/0000-0003-4226-6176>),
Larry Williams [aut]
Maintainer: Steven Andrew Culpepper <sculpepp@illinois.edu>
Diff between pathmodelfit versions 1.0.4 dated 2020-08-18 and 1.0.5 dated 2020-09-02
DESCRIPTION | 6 ++--- MD5 | 6 ++--- R/pathmodelfit.R | 58 ++++++++++++++++++++++++++++++++++++++++------------ man/pathmodelfit.Rd | 2 - 4 files changed, 52 insertions(+), 20 deletions(-)
Title: Local Polynomial Density Estimation and Inference
Description: Without imposing stringent distributional assumptions or shape restrictions, nonparametric estimation has been popular in economics and other social sciences for counterfactual analysis, program evaluation, and policy recommendations. This package implements a novel density (and derivatives) estimator based on local polynomial regressions: lpdensity() to construct local polynomial based density (and derivatives) estimator, and lpbwdensity() to perform data-driven bandwidth selection.
Author: Matias D. Cattaneo, Michael Jansson, Xinwei Ma
Maintainer: Xinwei Ma <x1ma@ucsd.edu>
Diff between lpdensity versions 2.0 dated 2020-08-04 and 2.1 dated 2020-09-02
DESCRIPTION | 8 ++++---- MD5 | 28 ++++++++++++++-------------- R/lpbwdensity.R | 8 ++++---- R/lpdensity-package.R | 12 ++++++------ R/lpdensity.R | 12 ++++++------ man/bw_IMSE.Rd | 16 ++++++++++++++-- man/bw_IROT.Rd | 16 ++++++++++++++-- man/bw_MSE.Rd | 16 ++++++++++++++-- man/bw_ROT.Rd | 16 ++++++++++++++-- man/lpbwdensity.Rd | 25 +++++++++++++++++-------- man/lpdensity-package.Rd | 12 ++++++------ man/lpdensity.Rd | 36 ++++++++++++++++++++++++------------ man/lpdensity.plot.Rd | 35 ++++++++++++++++++++++++++++------- man/lpdensity_fn.Rd | 15 +++++++++++++-- man/plot.lpdensity.Rd | 35 ++++++++++++++++++++++++++++------- 15 files changed, 206 insertions(+), 84 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-08-19 0.0.1.4