Title: Spatial Survey Design and Analysis
Description: This group of functions implements algorithms for design and
analysis of probability surveys. The functions are tailored for Generalized
Random Tessellation Stratified survey designs.
Author: Tom Kincaid [aut, cre],
Tony Olsen [aut],
Don Stevens [ctb],
Christian Platt [ctb],
Denis White [ctb],
Richard Remington [ctb]
Maintainer: Tom Kincaid <Kincaid.Tom@epa.gov>
Diff between spsurvey versions 3.2 dated 2016-08-16 and 3.3 dated 2016-08-19
spsurvey-3.2/spsurvey/src/order.h |only spsurvey-3.3/spsurvey/DESCRIPTION | 10 + spsurvey-3.3/spsurvey/MD5 | 103 ++++++++---------- spsurvey-3.3/spsurvey/R/AAA.R | 2 spsurvey-3.3/spsurvey/R/grts.R | 7 + spsurvey-3.3/spsurvey/R/grtsarea.R | 7 + spsurvey-3.3/spsurvey/R/grtslin.R | 7 + spsurvey-3.3/spsurvey/R/grtspts.R | 7 + spsurvey-3.3/spsurvey/R/irs.R | 7 + spsurvey-3.3/spsurvey/R/irsarea.R | 7 + spsurvey-3.3/spsurvey/R/irslin.R | 7 + spsurvey-3.3/spsurvey/R/read.dbf.R | 7 + spsurvey-3.3/spsurvey/R/read.shape.R | 7 + spsurvey-3.3/spsurvey/R/sbcframe.R | 7 + spsurvey-3.3/spsurvey/inst/CITATION | 4 spsurvey-3.3/spsurvey/inst/NEWS.Rd | 20 +++ spsurvey-3.3/spsurvey/inst/doc/Area_Analysis.Rnw | 2 spsurvey-3.3/spsurvey/inst/doc/Area_Analysis.pdf |binary spsurvey-3.3/spsurvey/inst/doc/Area_Design.R | 58 +++++----- spsurvey-3.3/spsurvey/inst/doc/Area_Design.Rnw | 13 ++ spsurvey-3.3/spsurvey/inst/doc/Area_Design.pdf |binary spsurvey-3.3/spsurvey/inst/doc/CDF_Analysis.Rnw | 2 spsurvey-3.3/spsurvey/inst/doc/CDF_Analysis.pdf |binary spsurvey-3.3/spsurvey/inst/doc/CDF_Deconvolution.Rnw | 2 spsurvey-3.3/spsurvey/inst/doc/CDF_Deconvolution.pdf |binary spsurvey-3.3/spsurvey/inst/doc/CHANGES.pdf |binary spsurvey-3.3/spsurvey/inst/doc/Change_Analysis.Rnw | 2 spsurvey-3.3/spsurvey/inst/doc/Change_Analysis.pdf |binary spsurvey-3.3/spsurvey/inst/doc/Finite_Analysis.Rnw | 2 spsurvey-3.3/spsurvey/inst/doc/Finite_Analysis.pdf |binary spsurvey-3.3/spsurvey/inst/doc/Finite_Design.R | 58 +++++----- spsurvey-3.3/spsurvey/inst/doc/Finite_Design.Rnw | 13 ++ spsurvey-3.3/spsurvey/inst/doc/Finite_Design.pdf |binary spsurvey-3.3/spsurvey/inst/doc/Linear_Analysis.Rnw | 2 spsurvey-3.3/spsurvey/inst/doc/Linear_Analysis.pdf |binary spsurvey-3.3/spsurvey/inst/doc/Linear_Design.R | 58 +++++----- spsurvey-3.3/spsurvey/inst/doc/Linear_Design.Rnw | 13 ++ spsurvey-3.3/spsurvey/inst/doc/Linear_Design.pdf |binary spsurvey-3.3/spsurvey/inst/doc/README.pdf |binary spsurvey-3.3/spsurvey/inst/doc/Risk_Analysis.Rnw | 2 spsurvey-3.3/spsurvey/inst/doc/Risk_Analysis.pdf |binary spsurvey-3.3/spsurvey/inst/doc/UserGuide.pdf |binary spsurvey-3.3/spsurvey/src/shapeParser.c | 30 +---- spsurvey-3.3/spsurvey/vignettes/Area_Analysis.Rnw | 2 spsurvey-3.3/spsurvey/vignettes/Area_Design.Rnw | 13 ++ spsurvey-3.3/spsurvey/vignettes/CDF_Analysis.Rnw | 2 spsurvey-3.3/spsurvey/vignettes/CDF_Deconvolution.Rnw | 2 spsurvey-3.3/spsurvey/vignettes/Change_Analysis.Rnw | 2 spsurvey-3.3/spsurvey/vignettes/Finite_Analysis.Rnw | 2 spsurvey-3.3/spsurvey/vignettes/Finite_Design.Rnw | 13 ++ spsurvey-3.3/spsurvey/vignettes/Linear_Analysis.Rnw | 2 spsurvey-3.3/spsurvey/vignettes/Linear_Design.Rnw | 13 ++ spsurvey-3.3/spsurvey/vignettes/Risk_Analysis.Rnw | 2 53 files changed, 335 insertions(+), 184 deletions(-)
Title: USGS ScienceBase Tools
Description: Tools for interacting with U.S. Geological Survey ScienceBase
<https://www.sciencebase.gov> interfaces. ScienceBase is a data cataloging and
collaborative data management platform. Functions included for querying
ScienceBase, and creating and fetching datasets.
Author: Luke Winslow [aut, cre],
Scott Chamberlain [aut],
Alison Appling [aut],
Jordan Read [aut]
Maintainer: Luke Winslow <lwinslow@usgs.gov>
Diff between sbtools versions 1.0.2 dated 2016-06-23 and 1.1.3 dated 2016-08-19
DESCRIPTION | 10 +++++----- MD5 | 20 ++++++++++---------- NAMESPACE | 2 ++ NEWS.md | 17 +++++++++++++++++ R/REST_helpers.R | 23 ++++++++++++++++++----- R/item_list_children.R | 24 ++++-------------------- R/item_rm.R | 2 +- R/item_rm_recursive.R | 10 ++++------ R/items_create.R | 4 ++-- README.md | 1 - man/item_list_children.Rd | 10 +++------- 11 files changed, 66 insertions(+), 57 deletions(-)
Title: R Interface to the 'QuantLib' Library
Description: The 'RQuantLib' package makes parts of 'QuantLib' accessible from R
The 'QuantLib' project aims to provide a comprehensive software framework
for quantitative finance. The goal is to provide a standard open source library
for quantitative analysis, modeling, trading, and risk management of financial
assets.
Author: Dirk Eddelbuettel, Khanh Nguyen (during 2009-2010), Terry Leitch (2016)
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RQuantLib versions 0.4.2 dated 2015-12-03 and 0.4.3 dated 2016-08-19
ChangeLog | 119 +++++++++++ DESCRIPTION | 22 +- MD5 | 65 +++--- NAMESPACE | 13 + R/RcppExports.R | 20 + R/affine.R |only R/bermudan.R | 226 +++++++++++++-------- R/bond.R | 44 +++- R/datasets.R |only R/discount.R | 27 +- R/inline.R | 13 - R/sabr.R |only R/zzz.R | 6 README.md | 8 configure | 32 ++ configure.ac | 2 data |only inst/NEWS.Rd | 38 +++ inst/include/rquantlib_internal.h | 17 + inst/shiny/SabrSwaption |only inst/unitTests/runit.businessdayconvention.R |only inst/unitTests/runit.schedule.R |only man/AffineSwaption.Rd |only man/BermudanSwaption.Rd | 104 ++++----- man/BondUtilities.Rd | 5 man/DiscountCurve.Rd | 21 + man/Enum.Rd | 8 man/FixedRateBond.Rd | 2 man/SabrSwaption.Rd |only man/tsQuotes.Rd |only man/vcube.Rd |only src/RcppExports.cpp | 69 +++++- src/affine.cpp |only src/bermudan.cpp | 290 ++++++++++++++++++++++----- src/curves.cpp | 188 ++++++++++++----- src/discount.cpp | 48 ++-- src/sabr.cpp |only src/utils.cpp | 12 + 38 files changed, 1042 insertions(+), 357 deletions(-)
Title: Access to the Neotoma Paleoecological Database Through R
Description: Access paleoecological datasets from the Neotoma Paleoecological
Database using the published API (http://api.neotomadb.org/). The functions
in this package access various pre-built API functions and attempt to return
the results from Neotoma in a usable format for researchers and the public.
Author: Simon J. Goring [aut, cre], Gavin L. Simpson [aut], Jeremiah P. Marsicek
[ctb], Karthik Ram [aut], Luke Sosalla [ctb]
Maintainer: Simon J. Goring <goring@wisc.edu>
Diff between neotoma versions 1.6.0 dated 2016-07-27 and 1.6.1 dated 2016-08-19
DESCRIPTION | 10 ++-- MD5 | 26 +++++++---- NAMESPACE | 11 ++++ NEWS | 7 +++ R/Stratiplot.download.R |only R/ages.R |only R/get_chroncontrol.R | 81 ++++++++++++++++++++++++++++------- R/get_dataset.R | 11 ++-- R/print.chroncontrol.R |only R/read_bacon.R |only R/write_agefile.R | 3 - README.md | 7 ++- man/Stratiplot.download.Rd |only man/Stratiplot.download_list.Rd |only man/ages.Rd |only man/get_chroncontrol.dataset.Rd |only man/get_chroncontrol.dataset_list.Rd |only man/read_bacon.Rd |only tests/testthat/test_neotoma.R | 10 ++++ 19 files changed, 129 insertions(+), 37 deletions(-)
Title: Ensemble Learning Algorithms Based on Support Vector Machines
Description: Three ensemble learning algorithms based on support vector machines.
They all train support vector machines on subset of data and combine the result.
Author: Tong He <hetong007@gmail.com>, Aydin Demircioglu <aydin.demircioglu@ini.ruhr-uni-bochum.de>
Maintainer: Tong He <hetong007@gmail.com>
Diff between SwarmSVM versions 0.1 dated 2015-07-15 and 0.1-2 dated 2016-08-19
SwarmSVM-0.1-2/SwarmSVM/DESCRIPTION | 8 SwarmSVM-0.1-2/SwarmSVM/MD5 | 99 SwarmSVM-0.1-2/SwarmSVM/NAMESPACE | 58 SwarmSVM-0.1-2/SwarmSVM/R/SwarmSVM.R | 36 SwarmSVM-0.1-2/SwarmSVM/R/alphasvm.R | 1936 +++++----- SwarmSVM-0.1-2/SwarmSVM/R/clusterSVM.R | 656 +-- SwarmSVM-0.1-2/SwarmSVM/R/compute.r | 66 SwarmSVM-0.1-2/SwarmSVM/R/dcSVM.R | 813 ++-- SwarmSVM-0.1-2/SwarmSVM/R/gater.R | 134 SwarmSVM-0.1-2/SwarmSVM/R/gaterSVM.R | 514 +- SwarmSVM-0.1-2/SwarmSVM/R/neuralnet.r | 1876 ++++----- SwarmSVM-0.1-2/SwarmSVM/R/prediction.r | 196 - SwarmSVM-0.1-2/SwarmSVM/R/utils.R | 390 +- SwarmSVM-0.1-2/SwarmSVM/R/zzz.R | 22 SwarmSVM-0.1-2/SwarmSVM/build/vignette.rds |binary SwarmSVM-0.1-2/SwarmSVM/inst/benchmark/clustered_SVM.R | 314 - SwarmSVM-0.1-2/SwarmSVM/inst/benchmark/clustered_SVM_Repeat.R | 540 +- SwarmSVM-0.1-2/SwarmSVM/inst/benchmark/dc_SVM.R | 386 - SwarmSVM-0.1-2/SwarmSVM/inst/benchmark/gater_SVM.R | 270 - SwarmSVM-0.1-2/SwarmSVM/inst/benchmark/preprocess_data.R | 310 - SwarmSVM-0.1-2/SwarmSVM/inst/benchmark/utils.R | 90 SwarmSVM-0.1-2/SwarmSVM/inst/doc/SwarmSVM.R | 21 SwarmSVM-0.1-2/SwarmSVM/inst/doc/SwarmSVM.Rmd | 33 SwarmSVM-0.1-2/SwarmSVM/inst/doc/SwarmSVM.html | 218 - SwarmSVM-0.1-2/SwarmSVM/man/SwarmSVM.Rd | 48 SwarmSVM-0.1-2/SwarmSVM/man/alphasvm.Rd | 388 +- SwarmSVM-0.1-2/SwarmSVM/man/cluster.fun.kkmeans.Rd | 38 SwarmSVM-0.1-2/SwarmSVM/man/cluster.fun.mlpack.old.Rd | 38 SwarmSVM-0.1-2/SwarmSVM/man/cluster.predict.kkmeans.Rd | 34 SwarmSVM-0.1-2/SwarmSVM/man/clusterSVM.Rd | 214 - SwarmSVM-0.1-2/SwarmSVM/man/csvmTransform.Rd | 44 SwarmSVM-0.1-2/SwarmSVM/man/dcSVM.Rd | 183 SwarmSVM-0.1-2/SwarmSVM/man/eucliDist.Rd | 34 SwarmSVM-0.1-2/SwarmSVM/man/gater.Rd | 70 SwarmSVM-0.1-2/SwarmSVM/man/gaterSVM.Rd | 140 SwarmSVM-0.1-2/SwarmSVM/man/kmeans.predict.Rd | 34 SwarmSVM-0.1-2/SwarmSVM/man/plot.alphasvm.Rd | 74 SwarmSVM-0.1-2/SwarmSVM/man/predict.alphasvm.Rd | 56 SwarmSVM-0.1-2/SwarmSVM/man/predict.clusterSVM.Rd | 46 SwarmSVM-0.1-2/SwarmSVM/man/predict.dcSVM.Rd | 40 SwarmSVM-0.1-2/SwarmSVM/man/predict.gater.Rd | 40 SwarmSVM-0.1-2/SwarmSVM/man/predict.gaterSVM.Rd | 42 SwarmSVM-0.1-2/SwarmSVM/man/svmguide1.Rd | 32 SwarmSVM-0.1-2/SwarmSVM/man/write.alphasvm.Rd | 44 SwarmSVM-0.1-2/SwarmSVM/tests/testthat.R | 8 SwarmSVM-0.1-2/SwarmSVM/tests/testthat/test_alphasvm.R | 110 SwarmSVM-0.1-2/SwarmSVM/tests/testthat/test_clusterSVM.R | 262 - SwarmSVM-0.1-2/SwarmSVM/tests/testthat/test_dcSVM.R | 99 SwarmSVM-0.1-2/SwarmSVM/tests/testthat/test_gaterSVM.R | 134 SwarmSVM-0.1-2/SwarmSVM/vignettes/SwarmSVM.Rmd | 33 SwarmSVM-0.1/SwarmSVM/README.md |only 51 files changed, 5562 insertions(+), 5709 deletions(-)
Title: Simple, Consistent Wrappers for Common String Operations
Description: A consistent, simple and easy to use set of wrappers around the
fantastic 'stringi' package. All function and argument names (and positions)
are consistent, all functions deal with "NA"'s and zero length vectors
in the same way, and the output from one function is easy to feed into
the input of another.
Author: Hadley Wickham [aut, cre, cph],
RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>
Diff between stringr versions 1.0.0 dated 2015-04-30 and 1.1.0 dated 2016-08-19
stringr-1.0.0/stringr/R/stringr.R |only stringr-1.0.0/stringr/man/stringr.Rd |only stringr-1.1.0/stringr/DESCRIPTION | 12 + stringr-1.1.0/stringr/MD5 | 129 +++++++++++--------- stringr-1.1.0/stringr/NAMESPACE | 6 stringr-1.1.0/stringr/NEWS.md |only stringr-1.1.0/stringr/R/c.r | 12 + stringr-1.1.0/stringr/R/count.r | 15 -- stringr-1.1.0/stringr/R/data.R |only stringr-1.1.0/stringr/R/detect.r | 11 - stringr-1.1.0/stringr/R/extract.r | 33 ++--- stringr-1.1.0/stringr/R/interp.R |only stringr-1.1.0/stringr/R/locate.r | 32 +--- stringr-1.1.0/stringr/R/match.r | 21 +-- stringr-1.1.0/stringr/R/modifiers.r | 44 +++++- stringr-1.1.0/stringr/R/pad-trim.r | 39 +++++- stringr-1.1.0/stringr/R/replace.r | 64 +++++++-- stringr-1.1.0/stringr/R/split.r | 32 +--- stringr-1.1.0/stringr/R/subset.R | 10 - stringr-1.1.0/stringr/R/view.R |only stringr-1.1.0/stringr/R/word.r | 4 stringr-1.1.0/stringr/README.md | 5 stringr-1.1.0/stringr/build/vignette.rds |binary stringr-1.1.0/stringr/data |only stringr-1.1.0/stringr/inst/doc/stringr.Rmd | 4 stringr-1.1.0/stringr/inst/doc/stringr.html | 98 ++++++++------- stringr-1.1.0/stringr/inst/htmlwidgets |only stringr-1.1.0/stringr/man/case.Rd | 2 stringr-1.1.0/stringr/man/invert_match.Rd | 2 stringr-1.1.0/stringr/man/modifier-deprecated.Rd | 4 stringr-1.1.0/stringr/man/modifiers.Rd | 9 - stringr-1.1.0/stringr/man/pipe.Rd | 2 stringr-1.1.0/stringr/man/str_c.Rd | 14 +- stringr-1.1.0/stringr/man/str_conv.Rd | 2 stringr-1.1.0/stringr/man/str_count.Rd | 2 stringr-1.1.0/stringr/man/str_detect.Rd | 2 stringr-1.1.0/stringr/man/str_dup.Rd | 2 stringr-1.1.0/stringr/man/str_extract.Rd | 10 - stringr-1.1.0/stringr/man/str_interp.Rd |only stringr-1.1.0/stringr/man/str_length.Rd | 2 stringr-1.1.0/stringr/man/str_locate.Rd | 2 stringr-1.1.0/stringr/man/str_match.Rd | 9 + stringr-1.1.0/stringr/man/str_order.Rd | 2 stringr-1.1.0/stringr/man/str_pad.Rd | 5 stringr-1.1.0/stringr/man/str_replace.Rd | 4 stringr-1.1.0/stringr/man/str_replace_na.Rd | 4 stringr-1.1.0/stringr/man/str_split.Rd | 8 - stringr-1.1.0/stringr/man/str_sub.Rd | 4 stringr-1.1.0/stringr/man/str_subset.Rd | 2 stringr-1.1.0/stringr/man/str_trim.Rd | 2 stringr-1.1.0/stringr/man/str_trunc.Rd |only stringr-1.1.0/stringr/man/str_view.Rd |only stringr-1.1.0/stringr/man/str_wrap.Rd | 2 stringr-1.1.0/stringr/man/stringr-data.Rd |only stringr-1.1.0/stringr/man/word.Rd | 2 stringr-1.1.0/stringr/tests/testthat/test-detect.r | 20 +-- stringr-1.1.0/stringr/tests/testthat/test-dup.r | 12 - stringr-1.1.0/stringr/tests/testthat/test-extract.r | 10 - stringr-1.1.0/stringr/tests/testthat/test-interp.r |only stringr-1.1.0/stringr/tests/testthat/test-join.r | 6 stringr-1.1.0/stringr/tests/testthat/test-length.r | 18 +- stringr-1.1.0/stringr/tests/testthat/test-locate.r | 28 +--- stringr-1.1.0/stringr/tests/testthat/test-match.r | 26 ++-- stringr-1.1.0/stringr/tests/testthat/test-pad.r | 10 - stringr-1.1.0/stringr/tests/testthat/test-replace.r |only stringr-1.1.0/stringr/tests/testthat/test-split.r | 77 ++++++----- stringr-1.1.0/stringr/tests/testthat/test-sub.r | 48 +++---- stringr-1.1.0/stringr/tests/testthat/test-subset.r |only stringr-1.1.0/stringr/tests/testthat/test-trim.r | 18 +- stringr-1.1.0/stringr/tests/testthat/test-word.r |only stringr-1.1.0/stringr/tests/testthat/test-wrap.r |only stringr-1.1.0/stringr/vignettes/stringr.Rmd | 4 72 files changed, 552 insertions(+), 395 deletions(-)
Title: Classes with Reference Semantics
Description: The R6 package allows the creation of classes with reference
semantics, similar to R's built-in reference classes. Compared to reference
classes, R6 classes are simpler and lighter-weight, and they are not built
on S4 classes so they do not require the methods package. These classes
allow public and private members, and they support inheritance, even when
the classes are defined in different packages.
Author: Winston Chang [aut, cre]
Maintainer: Winston Chang <winston@stdout.org>
Diff between R6 versions 2.1.2 dated 2016-01-25 and 2.1.3 dated 2016-08-19
DESCRIPTION | 7 - MD5 | 51 +++++----- NAMESPACE | 4 NEWS | 12 ++ R/aslist.R |only R/clone.R | 20 ++-- R/print.R | 13 ++ README.md | 2 build/vignette.rds |binary inst/doc/Debugging.Rmd | 9 - inst/doc/Debugging.html | 21 +--- inst/doc/Introduction.R | 10 +- inst/doc/Introduction.Rmd | 21 ++-- inst/doc/Introduction.html | 41 +++----- inst/doc/Performance.Rmd | 9 - inst/doc/Performance.html | 182 ++++++++++++++++++-------------------- inst/doc/Portable.Rmd | 9 - inst/doc/Portable.html | 21 +--- man/R6Class.Rd | 2 man/as.list.R6.Rd |only tests/testthat/helper.R |only tests/testthat/test-clone.R | 12 ++ tests/testthat/test-nonportable.R | 14 +- tests/testthat/test-portable.R | 16 +-- vignettes/Debugging.Rmd | 9 - vignettes/Introduction.Rmd | 21 ++-- vignettes/Performance.Rmd | 9 - vignettes/Portable.Rmd | 9 - 28 files changed, 272 insertions(+), 252 deletions(-)
Title: Forecasting of Univariate Time Series Using the Pattern
Sequence-Based Forecasting (PSF) Algorithm
Description: Pattern Sequence Based Forecasting (PSF) takes univariate
time series data as input and assist to forecast its future values.
This algorithm forecasts the behavior of time series
based on similarity of pattern sequences. Initially, clustering is done with the
labeling of samples from database. The labels associated with samples are then
used for forecasting the future behaviour of time series data. The further
technical details and references regarding PSF are discussed in Vignette.
Author: Neeraj Bokde, Gualberto Asencio-Cortes and Francisco Martinez-Alvarez
Maintainer: Neeraj Bokde <neerajdhanraj@gmail.com>
Diff between PSF versions 0.2.1 dated 2016-06-18 and 0.3 dated 2016-08-19
PSF-0.2.1/PSF/R/AUTO_PSF.R |only PSF-0.2.1/PSF/R/Mean_Errors.R |only PSF-0.2.1/PSF/R/norm_denorm.R |only PSF-0.2.1/PSF/R/plot_PSF.R |only PSF-0.2.1/PSF/R/pred_for_w.R |only PSF-0.2.1/PSF/R/pred_for_w_plot.R |only PSF-0.2.1/PSF/man/AUTO_PSF.Rd |only PSF-0.2.1/PSF/man/data_denorm.Rd |only PSF-0.2.1/PSF/man/data_norm.Rd |only PSF-0.2.1/PSF/man/mae.Rd |only PSF-0.2.1/PSF/man/optimum_k.Rd |only PSF-0.2.1/PSF/man/optimum_w.Rd |only PSF-0.2.1/PSF/man/plot_PSF.Rd |only PSF-0.2.1/PSF/man/pred_for_w.Rd |only PSF-0.2.1/PSF/man/pred_for_w_plot.Rd |only PSF-0.2.1/PSF/man/rmse.Rd |only PSF-0.3/PSF/DESCRIPTION | 26 +-- PSF-0.3/PSF/MD5 | 40 +--- PSF-0.3/PSF/NAMESPACE | 26 --- PSF-0.3/PSF/R/convert_datatype.R |only PSF-0.3/PSF/R/optimum_k.R | 64 +++---- PSF-0.3/PSF/R/optimum_w.R | 124 +++------------ PSF-0.3/PSF/R/psf.R |only PSF-0.3/PSF/R/psf_plot.R |only PSF-0.3/PSF/R/psf_predict.R |only PSF-0.3/PSF/build/vignette.rds |binary PSF-0.3/PSF/inst/doc/PSF_vignette.R | 72 ++++++-- PSF-0.3/PSF/inst/doc/PSF_vignette.Rmd | 269 +++++++++++++++++---------------- PSF-0.3/PSF/inst/doc/PSF_vignette.html | 247 ++++++++++++++++-------------- PSF-0.3/PSF/man/psf.Rd |only PSF-0.3/PSF/man/psf_plot.Rd |only PSF-0.3/PSF/vignettes/PSF_vignette.Rmd | 269 +++++++++++++++++---------------- 32 files changed, 565 insertions(+), 572 deletions(-)
Title: Evaluate Differentially Private Algorithms for Publishing
Cumulative Distribution Functions
Description: Designed by and for the community of differential privacy algorithm developers. It can be used to empirically evaluate and visualize Cumulative Distribution Functions incorporating noise that satisfies differential privacy, with numerous options made to streamline collection of utility measurements across variations of key parameters, such as epsilon, domain size, sample size, data shape, etc. Developed by researchers at Harvard PSI.
Author: Daniel Muise [aut,cre],
Kobbi Nissim [aut],
Georgios Kellaris [aut]
Maintainer: Daniel Muise <dmuise@stanford.edu>
Diff between CDF.PSIdekick versions 1.1 dated 2016-08-18 and 1.2 dated 2016-08-19
DESCRIPTION | 6 +- MD5 | 6 +- R/RcppExports.R | 8 +-- src/smooth.cpp | 125 +++++++++++++++++++++++++++++--------------------------- 4 files changed, 76 insertions(+), 69 deletions(-)
Title: Bayesian Generalized Linear Regression
Description: Bayesian Generalized Linear Regression.
Author: Gustavo de los Campos, Paulino Perez Rodriguez,
Maintainer: Paulino Perez Rodriguez <perpdgo@colpos.mx>
Diff between BGLR versions 1.0.4 dated 2015-04-07 and 1.0.5 dated 2016-08-19
BGLR-1.0.4/BGLR/R/util_plink.R |only BGLR-1.0.4/BGLR/demo/BRR_windows.R |only BGLR-1.0.5/BGLR/CHANGELOG | 5 BGLR-1.0.5/BGLR/DESCRIPTION | 10 - BGLR-1.0.5/BGLR/MD5 | 41 +++-- BGLR-1.0.5/BGLR/NAMESPACE | 12 + BGLR-1.0.5/BGLR/R/BGLR.R | 292 ++++++++++++++++++++++-------------- BGLR-1.0.5/BGLR/R/utils.R |only BGLR-1.0.5/BGLR/build/vignette.rds |binary BGLR-1.0.5/BGLR/demo/00Index | 2 BGLR-1.0.5/BGLR/demo/BRR_sets.R |only BGLR-1.0.5/BGLR/inst/md |only BGLR-1.0.5/BGLR/man/BGLR.Rd | 4 BGLR-1.0.5/BGLR/man/getVariances.Rd |only BGLR-1.0.5/BGLR/man/readBinMat.Rd |only 15 files changed, 233 insertions(+), 133 deletions(-)
Title: Statistical Disclosure Control Methods for Anonymization of
Microdata and Risk Estimation
Description: Data from statistical agencies and other institutions are mostly
confidential. This package can be used for the generation of anonymized
(micro)data, i.e. for the creation of public- and scientific-use files. In
addition, various risk estimation methods are included. Note that the package
'sdcMicroGUI' includes a graphical user interface for various methods in this
package.
Author: Matthias Templ, Alexander Kowarik, Bernhard Meindl
Maintainer: Matthias Templ <matthias.templ@gmail.com>
Diff between sdcMicro versions 4.6.0 dated 2015-10-01 and 4.6.1 dated 2016-08-19
DESCRIPTION | 17 - MD5 | 167 +++++----- NAMESPACE | 2 R/GUIfunctions.R | 5 R/LocalRecProg.R | 2 R/addNoise.r | 2 R/freqCalc.r | 2 R/localSuppression.R | 14 R/plotMicro.R | 3 R/pram.R | 2 R/printFunctions.R | 2 R/report.R | 17 - R/suda2.R | 71 +++- build/vignette.rds |binary data/CASCrefmicrodata.rda |binary data/EIA.rda |binary data/Tarragona.rda |binary data/casc1.rda |binary data/francdat.rda |binary data/free1.rda |binary data/microData.rda |binary data/testdata.RData |binary data/testdata2.RData |binary inst/doc/sdc_guidelines.R | 28 - inst/doc/sdc_guidelines.pdf |binary inst/doc/sdc_guidelines.rnw | 676 ++++++++++++++++++++--------------------- man/CASCrefmicrodata.Rd | 4 man/EIA.Rd | 4 man/LLmodGlobalRisk.Rd | 2 man/LocalRecProg.Rd | 7 man/Tarragona.Rd | 3 man/addNoise.Rd | 8 man/calcRisks.Rd | 4 man/casc1.Rd | 4 man/dRisk.Rd | 4 man/dRiskRMD.Rd | 4 man/dUtility.Rd | 4 man/dataGen.Rd | 4 man/extractManipData.Rd | 4 man/francdat.Rd | 3 man/free1.Rd | 4 man/freqCalc.Rd | 4 man/generateStrata.Rd | 4 man/globalRecode.Rd | 4 man/groupVars.Rd | 4 man/indivRisk.Rd | 4 man/localSupp.Rd | 4 man/localSuppression.Rd | 4 man/mafast.Rd | 4 man/measure_risk.Rd | 4 man/microData.Rd | 4 man/microaggrGower.Rd | 4 man/microaggregation.Rd | 8 man/modRisk.Rd | 4 man/plot.localSuppression.Rd | 5 man/plot.sdcMicroObj.Rd | 4 man/plotMicro.Rd | 5 man/pram.Rd | 5 man/print.freqCalc.Rd | 4 man/print.indivRisk.Rd | 4 man/print.localSuppression.Rd | 5 man/print.micro.Rd | 4 man/print.modrisk.Rd | 2 man/print.pram.Rd | 2 man/print.sdcMicroObj.Rd | 4 man/print.suda2.Rd | 3 man/rankSwap.Rd | 2 man/removeDirectID.Rd | 4 man/renameVars.Rd | 4 man/report.Rd | 4 man/sdcMicro-package.Rd | 4 man/sdcMicroObj-class.Rd | 5 man/shuffle.Rd | 4 man/suda2.Rd | 37 +- man/summary.freqCalc.Rd | 4 man/summary.micro.Rd | 4 man/summary.pram.Rd | 4 man/testdata.Rd | 4 man/topBotCoding.Rd | 4 man/valTable.Rd | 3 man/varToFactor.Rd | 4 tests/reporting_test.R | 6 tests/testthat/test_addNoise.R |only tests/testthat/test_freqCalc.R | 224 ++++++------- vignettes/sdc_guidelines.rnw | 676 ++++++++++++++++++++--------------------- 85 files changed, 1182 insertions(+), 991 deletions(-)
Title: Fast and Simple Object Serialization to Protocol Buffers
Description: Optimized C++ implementations for reading and writing protocol-buffers.
Currently supports 'rexp.proto' for serializing R objects and 'geobuf.proto' for
geojson data. This lightweight package is complementary to the much larger
'RProtoBuf' package which provides a full featured toolkit for working with
protocol-buffers in R.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between protolite versions 1.3 dated 2016-07-06 and 1.4 dated 2016-08-19
DESCRIPTION | 17 +++++++++-------- MD5 | 32 ++++++++++++++++++++++---------- NAMESPACE | 5 +++++ NEWS | 3 +++ R/RcppExports.R | 8 ++++++++ R/geobuf.R |only README.md | 42 +++++++++++++++++++++++++++++++++--------- cleanup |only configure | 4 ++-- man/geobuf.Rd |only src/Makevars.win | 13 +++++++------ src/RcppExports.cpp | 23 +++++++++++++++++++++++ src/geobuf.cpp |only src/geobuf.pb.cc |only src/geobuf.proto |only src/init.cpp |only src/rexp.pb.cc |only src/rexp.proto | 1 + src/ungeobuf.cpp |only tests/testthat/test-geobuf.R |only tests/testthat/test.json |only tests/testthat/test.pb |only tools/winlibs.R | 8 ++++---- 23 files changed, 117 insertions(+), 39 deletions(-)
Title: Advanced Image-Processing in R
Description: Bindings to ImageMagick: the most comprehensive open-source image
processing library available. Supports many common formats (png, jpeg, tiff,
pdf, etc) and manipulations (rotate, scale, crop, trim, flip, blur, etc).
All operations are vectorized via the Magick++ STL meaning they operate either
on a single frame or a series of frames for working with layers, collages,
or animation. In RStudio images are automatically previewed when printed to
the console, resulting in an interactive editing environment.
Author: Jeroen Ooms
Maintainer: Jeroen Ooms <jeroen.ooms@stat.ucla.edu>
Diff between magick versions 0.2.1 dated 2016-08-10 and 0.2.2 dated 2016-08-19
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- NEWS | 4 ++++ R/edit.R | 3 ++- R/transformations.R | 2 +- configure | 23 +++++++++++++++++++---- man/transformations.Rd | 2 +- src/Makevars.win | 8 ++++---- src/config.cc | 7 +++++-- src/transformations.cpp | 13 +++++++++++++ tools/winlibs.R | 4 ++-- 11 files changed, 64 insertions(+), 28 deletions(-)
Title: Improved Laplace Approximation for Integrals of Unimodal
Functions
Description: Improved Laplace approximation for integrals of unimodal functions.
The method requires user-supplied R functions for: the integrand, its gradient
and its Hessian matrix. The computations are run in parallel.
Author: Erlis Ruli [aut, cre], Nicola Sartori [aut], Laura Ventura [aut]
Maintainer: Erlis Ruli <erlisr@yahoo.it>
Diff between iLaplace versions 1.0.0 dated 2015-09-28 and 1.1.0 dated 2016-08-19
DESCRIPTION | 15 +-- MD5 | 30 +++--- NAMESPACE | 8 + R/RcppExports.R | 16 --- R/auxiliaryFns.R | 234 +++++++++++++++++++++++++++++++++--------------- R/iLap.R | 82 +++++++--------- R/iLap2d.R | 126 +++++++++++-------------- R/iLapCW.R |only R/iLapCW_par.R |only R/iLap_par.R |only R/iLaplace.R | 12 -- man/iLap.Rd | 27 +++-- man/iLap2d.Rd | 28 +++-- man/iLapCW.Rd |only man/iLapCW_par.Rd |only man/iLap_par.Rd |only man/iLaplace-package.Rd | 15 +-- src/RcppExports.cpp | 53 +--------- src/funs.cpp | 165 ++++++++++++++++++++++++--------- 19 files changed, 456 insertions(+), 355 deletions(-)
Title: Penalization in Large Scale Generalized Linear Array Models
Description: Efficient design matrix free procedure for penalized estimation
in large scale 2 and 3-dimensional generalized linear array models. Currently
either Lasso or SCAD penalized estimation is possible for the followings models:
The Gaussian model with identity link, the Binomial model with logit link, the
Poisson model with log link and the Gamma model with log link.
Author: Adam Lund
Maintainer: Adam Lund <adam.lund@math.ku.dk>
Diff between glamlasso versions 2.0 dated 2016-08-03 and 2.0.1 dated 2016-08-19
DESCRIPTION | 13 ++++-- MD5 | 20 +++++----- man/RH.Rd | 6 +-- man/glamlasso.Rd | 86 +++++++++++++++++++++++----------------------- man/glamlasso_internal.Rd | 2 - man/objective.Rd | 20 +++++----- man/predict.glamlasso.Rd | 24 ++++++------ man/print.glamlasso.Rd | 10 +++-- src/Makevars | 3 + src/auxfunc.h | 2 - src/rcppfunc.cpp | 7 +-- 11 files changed, 100 insertions(+), 93 deletions(-)
Title: A Genetic-Based Assay for the Identification of Cell Lines
Description: The SNP Panel Identification Assay (SPIA) is a package that enables an accurate determination of cell line identity from the genotype of single nucleotide polymorphisms (SNPs). The SPIA test allows to discern when two cell lines are close enough to be called similar and when they are not. Details about the method are available at "Demichelis et al. (2008) SNP panel identification assay (SPIA): a genetic-based assay for the identification of cell lines. Nucleic Acids Res., 3, 2446-2456".
Author: Francesca Demichelis <francesca.demichelis@unitn.it>, Davide Prandi <davide.prandi@unitn.it>
Maintainer: Davide Prandi <davide.prandi@unitn.it>
Diff between SPIAssay versions 1.0.0 dated 2011-08-04 and 1.1.0 dated 2016-08-19
DESCRIPTION | 25 ++---- MD5 |only NAMESPACE | 3 R/ComputingSPIADistance.R | 26 +++---- R/SPIAPlot.R | 4 - R/SPIATest.R | 2 man/ComputingSPIADistance.Rd | 20 ++--- man/SPIAPlot.Rd | 14 ++- man/SPIATest.Rd | 158 +++++++++++++++++++++++-------------------- man/SPIAssay.Rd | 136 ++++++++++++++++++------------------- man/getSPIALimits.Rd | 2 man/toSPIAData.Rd | 2 12 files changed, 201 insertions(+), 191 deletions(-)
Title: Random Portfolio Generation
Description: A collection of tools used to generate
various types of random portfolios. The weights of these
portfolios are random variables derived from truncated
continuous random variables.
Author: Frederick Novomestky <fn334@nyu.edu>
Maintainer: Frederick Novomestky <fn334@nyu.edu>
Diff between rportfolios versions 1.0 dated 2012-01-06 and 1.0-1 dated 2016-08-19
rportfolios-1.0-1/rportfolios/DESCRIPTION | 23 - rportfolios-1.0-1/rportfolios/MD5 | 139 ++++++---- rportfolios-1.0-1/rportfolios/NAMESPACE | 22 + rportfolios-1.0-1/rportfolios/R/collapse.segments.R |only rportfolios-1.0-1/rportfolios/R/extract.segments.R |only rportfolios-1.0-1/rportfolios/R/overweight.segments.R |only rportfolios-1.0-1/rportfolios/R/portfolio.composite.R |only rportfolios-1.0-1/rportfolios/R/portfolio.difference.R |only rportfolios-1.0-1/rportfolios/R/portfolio.diversification.R |only rportfolios-1.0-1/rportfolios/R/ractive.R | 11 rportfolios-1.0-1/rportfolios/R/ractive.test.R | 14 - rportfolios-1.0-1/rportfolios/R/random.active.R | 59 +++- rportfolios-1.0-1/rportfolios/R/random.active.test.R | 78 ++++- rportfolios-1.0-1/rportfolios/R/random.benchmark.R |only rportfolios-1.0-1/rportfolios/R/random.benchmark.test.R |only rportfolios-1.0-1/rportfolios/R/random.bounded.R |only rportfolios-1.0-1/rportfolios/R/random.bounded.test.R |only rportfolios-1.0-1/rportfolios/R/random.equal.R | 20 + rportfolios-1.0-1/rportfolios/R/random.equal.test.R | 22 + rportfolios-1.0-1/rportfolios/R/random.general.R | 46 ++- rportfolios-1.0-1/rportfolios/R/random.general.test.R | 48 ++- rportfolios-1.0-1/rportfolios/R/random.longonly.R | 89 ++++-- rportfolios-1.0-1/rportfolios/R/random.longonly.test.R | 93 +++++- rportfolios-1.0-1/rportfolios/R/random.longshort.R | 92 +++++- rportfolios-1.0-1/rportfolios/R/random.longshort.test.R | 108 ++++++- rportfolios-1.0-1/rportfolios/R/random.shortonly.R | 29 +- rportfolios-1.0-1/rportfolios/R/random.shortonly.test.R | 30 +- rportfolios-1.0-1/rportfolios/R/rbenchmark.R |only rportfolios-1.0-1/rportfolios/R/rbenchmark.test.R |only rportfolios-1.0-1/rportfolios/R/rbounded.R |only rportfolios-1.0-1/rportfolios/R/rbounded.test.R |only rportfolios-1.0-1/rportfolios/R/requal.R | 6 rportfolios-1.0-1/rportfolios/R/requal.test.R | 26 - rportfolios-1.0-1/rportfolios/R/rgeneral.R | 25 - rportfolios-1.0-1/rportfolios/R/rgeneral.test.R | 24 - rportfolios-1.0-1/rportfolios/R/rlongonly.R | 33 +- rportfolios-1.0-1/rportfolios/R/rlongonly.test.R | 28 -- rportfolios-1.0-1/rportfolios/R/rlongshort.R | 23 - rportfolios-1.0-1/rportfolios/R/rlongshort.test.R | 19 - rportfolios-1.0-1/rportfolios/R/rshortonly.R | 39 +- rportfolios-1.0-1/rportfolios/R/rshortonly.test.R | 22 - rportfolios-1.0-1/rportfolios/R/segment.complement.R |only rportfolios-1.0-1/rportfolios/R/set.segments.R |only rportfolios-1.0-1/rportfolios/R/underweight.segments.R |only rportfolios-1.0-1/rportfolios/R/vector.rescale.weights.R |only rportfolios-1.0-1/rportfolios/man/collapse.segments.Rd |only rportfolios-1.0-1/rportfolios/man/extract.segments.Rd |only rportfolios-1.0-1/rportfolios/man/overweight.segments.Rd |only rportfolios-1.0-1/rportfolios/man/portfolio.composite.Rd |only rportfolios-1.0-1/rportfolios/man/portfolio.difference.Rd |only rportfolios-1.0-1/rportfolios/man/portfolio.diversification.Rd |only rportfolios-1.0-1/rportfolios/man/ractive.Rd | 6 rportfolios-1.0-1/rportfolios/man/ractive.test.Rd | 47 +-- rportfolios-1.0-1/rportfolios/man/random.active.Rd | 6 rportfolios-1.0-1/rportfolios/man/random.active.test.Rd | 8 rportfolios-1.0-1/rportfolios/man/random.benchmark.Rd |only rportfolios-1.0-1/rportfolios/man/random.benchmark.test.Rd |only rportfolios-1.0-1/rportfolios/man/random.bounded.Rd |only rportfolios-1.0-1/rportfolios/man/random.bounded.test.Rd |only rportfolios-1.0-1/rportfolios/man/random.equal.Rd | 9 rportfolios-1.0-1/rportfolios/man/random.equal.test.Rd | 5 rportfolios-1.0-1/rportfolios/man/random.general.Rd | 7 rportfolios-1.0-1/rportfolios/man/random.general.test.Rd | 7 rportfolios-1.0-1/rportfolios/man/random.longonly.Rd | 9 rportfolios-1.0-1/rportfolios/man/random.longonly.test.Rd | 47 ++- rportfolios-1.0-1/rportfolios/man/random.longshort.Rd | 7 rportfolios-1.0-1/rportfolios/man/random.longshort.test.Rd | 6 rportfolios-1.0-1/rportfolios/man/random.shortonly.Rd | 5 rportfolios-1.0-1/rportfolios/man/random.shortonly.test.Rd | 5 rportfolios-1.0-1/rportfolios/man/rbenchmark.Rd |only rportfolios-1.0-1/rportfolios/man/rbenchmark.test.Rd |only rportfolios-1.0-1/rportfolios/man/rbounded.Rd |only rportfolios-1.0-1/rportfolios/man/rbounded.test.Rd |only rportfolios-1.0-1/rportfolios/man/requal.Rd | 5 rportfolios-1.0-1/rportfolios/man/requal.test.Rd | 34 +- rportfolios-1.0-1/rportfolios/man/rgeneral.Rd | 7 rportfolios-1.0-1/rportfolios/man/rgeneral.test.Rd | 7 rportfolios-1.0-1/rportfolios/man/rlongonly.Rd | 5 rportfolios-1.0-1/rportfolios/man/rlongonly.test.Rd | 5 rportfolios-1.0-1/rportfolios/man/rlongshort.Rd | 10 rportfolios-1.0-1/rportfolios/man/rlongshort.test.Rd | 7 rportfolios-1.0-1/rportfolios/man/rshortonly.Rd | 5 rportfolios-1.0-1/rportfolios/man/rshortonly.test.Rd | 5 rportfolios-1.0-1/rportfolios/man/segment.complement.Rd |only rportfolios-1.0-1/rportfolios/man/set.segments.Rd |only rportfolios-1.0-1/rportfolios/man/underweight.segments.Rd |only rportfolios-1.0/rportfolios/R/qqunif.R |only rportfolios-1.0/rportfolios/random.longonly.test.R |only rportfolios-1.0/rportfolios/rlongonly.R |only rportfolios-1.0/rportfolios/rlongonly.test.R |only 90 files changed, 958 insertions(+), 474 deletions(-)
Title: GWAS for Multiple Observations on Related Individuals
Description: Performs genome-wide association studies on individuals that are both related and have repeated measurements.
Author: Lars Ronnegard
Maintainer: Lars Ronnegard <lrn@du.se>
Diff between RepeatABEL versions 1.0 dated 2015-11-24 and 1.1 dated 2016-08-19
ChangeLog |only DESCRIPTION | 8 MD5 | 19 build/vignette.rds |binary inst/CITATION | 68 +-- inst/doc/RepeatABEL_vignette.R | 392 ++++++++++---------- inst/doc/RepeatABEL_vignette.Rnw | 728 +++++++++++++++++++------------------- inst/doc/RepeatABEL_vignette.pdf |binary man/RepeatABEL-package.Rd | 83 ++-- man/preFitModel.Rd | 2 vignettes/RepeatABEL_vignette.Rnw | 728 +++++++++++++++++++------------------- 11 files changed, 1015 insertions(+), 1013 deletions(-)
Title: Downscaling Species Occupancy
Description: A set of functions that downscales species occupancy at
coarse grain sizes to predict species occupancy at fine grain sizes.
Author: Charles Marsh [aut, cre]
Maintainer: Charles Marsh <charliem2003@gmail.com>
Diff between downscale versions 1.2-1 dated 2016-03-10 and 1.2-2 dated 2016-08-19
DESCRIPTION | 12 ++++++------ MD5 | 30 +++++++++++++++--------------- NEWS | 6 ++++++ R/OptimiseParametersFNB.R | 11 +++++++---- R/PredictFunctions.R | 15 ++++++++------- R/StartingParams.R | 13 +++++++------ R/upgrain.R | 3 ++- build/vignette.rds |binary inst/doc/Downscaling.pdf |binary inst/doc/Upgraining.pdf |binary man/downscale.Rd | 18 +++++++++--------- man/ensemble.downscale.Rd | 6 +++--- man/figures/Equations.png |binary man/figures/Params.png |binary man/upgrain.Rd | 4 ++-- vignettes/figures/Saturation.png |binary 16 files changed, 65 insertions(+), 53 deletions(-)
Title: Wilcoxon Rank Sum Test for Clustered Data
Description: Non-parametric tests (Wilcoxon rank sum test and Wilcoxon signed rank test) for clustered data.
Author: Yujing Jiang [aut, cre],
Mei-Ling Ting Lee [ctb],
Jun Yan [ctb]
Maintainer: Yujing Jiang <yujing.jiang@uconn.edu>
Diff between clusrank versions 0.2-3 dated 2016-07-18 and 0.4-1 dated 2016-08-19
clusrank-0.2-3/clusrank/R/cluswilcox.R |only clusrank-0.2-3/clusrank/R/print.R |only clusrank-0.2-3/clusrank/man/cluswilcox.test.Rd |only clusrank-0.2-3/clusrank/man/group.Rd |only clusrank-0.2-3/clusrank/man/print.ctest.Rd |only clusrank-0.4-1/clusrank/DESCRIPTION | 8 clusrank-0.4-1/clusrank/MD5 | 31 +-- clusrank-0.4-1/clusrank/NAMESPACE | 8 clusrank-0.4-1/clusrank/R/RcppExports.R | 16 - clusrank-0.4-1/clusrank/R/clusWilcox.R |only clusrank-0.4-1/clusrank/R/clusranksum.R | 256 +++++++++++-------------- clusrank-0.4-1/clusrank/R/clussignrank.R | 158 +++++++-------- clusrank-0.4-1/clusrank/R/recodeFun.R | 33 +-- clusrank-0.4-1/clusrank/R/special.R | 126 ++++++++---- clusrank-0.4-1/clusrank/man/clusWilcox.test.Rd |only clusrank-0.4-1/clusrank/man/cluster.Rd | 6 clusrank-0.4-1/clusrank/man/stratum.Rd | 6 clusrank-0.4-1/clusrank/src/Fprop.cpp | 51 ++-- clusrank-0.4-1/clusrank/src/RcppExports.cpp | 47 ---- clusrank-0.4-1/clusrank/src/exact.cpp | 133 ++++++------ 20 files changed, 433 insertions(+), 446 deletions(-)