Title: Genetics Input/Output Functions
Description: Implements readers and writers for file formats associated with genetics data. Reading and writing plink BED/BIM/FAM formats is fully supported, including a lightning-fast BED reader and writer implementations. Other functions are 'readr' wrappers that are more constrained, user-friendly, and efficient for these particular applications; handles plink and eigenstrat tables (FAM, BIM, IND, and SNP files). There are also "make" functions for FAM and BIM tables with default values to go with simulated genotype data.
Author: Alejandro Ochoa [aut, cre] (<https://orcid.org/0000-0003-4928-3403>)
Maintainer: Alejandro Ochoa <alejandro.ochoa@duke.edu>
Diff between genio versions 1.0.9 dated 2019-05-24 and 1.0.10 dated 2019-05-28
DESCRIPTION | 6 - MD5 | 16 +- NEWS.md | 7 + inst/doc/genio.R | 6 - inst/doc/genio.Rmd | 6 - inst/doc/genio.html | 298 +++++++++++++++++++++++++------------------------- src/read_bed_cpp.cpp | 32 +++-- src/write_bed_cpp.cpp | 1 vignettes/genio.Rmd | 6 - 9 files changed, 205 insertions(+), 173 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 source code version
and looking in the R subdirectory. The reference for fields can be generated
by the citation function in R and has DOI <doi:10.5065/D6W957CT>. Development
of this package was supported in part by the National Science Foundation Grant
1417857 and the National Center for Atmospheric Research. See the Fields URL
for a vignette on using this package and some background on spatial statistics.
Author: Douglas Nychka [aut, cre],
Reinhard Furrer [aut],
John Paige [aut],
Stephan Sain [aut],
University Corporation for Atmospheric Research [cph]
Maintainer: Douglas Nychka <douglasnychka@gmail.com>
Diff between fields versions 9.8-1 dated 2019-05-14 and 9.8-3 dated 2019-05-28
DESCRIPTION | 18 +++++--- MD5 | 70 +++++++++++++++++----------------- inst/CITATION | 2 man/RCMexample.Rd | 8 +-- man/RMprecip.Rd | 4 - tests/Krig.Z.test.Rout.save | 6 +- tests/Krig.se.W.Rout.save | 6 +- tests/Krig.se.grid.test.Rout.save | 6 +- tests/Krig.se.test.Rout.save | 6 +- tests/Krig.test.Rout.save | 6 +- tests/Krig.test.W.Rout.save | 6 +- tests/KrigGCVREML.test.Rout.save | 6 +- tests/Likelihood.test.Rout.save | 6 +- tests/REMLest.test.Rout.save | 6 +- tests/SEFixedParameters.Rout.save | 4 - tests/Tps.test.Rout.save | 6 +- tests/Wend.test.Rout.save | 6 +- tests/cov.test.Rout.save | 4 - tests/cov.test2.R | 10 +++- tests/cov.test2.Rout.save | 10 ++-- tests/derivative.test.Rout.save | 6 +- tests/diag.multiply.test.Rout.save | 6 +- tests/diagonal2.test.Rout.save | 6 +- tests/evlpoly.test.Rout.save | 6 +- tests/fastTpsPredict.test.Rout.save | 6 +- tests/mKrig.MLE.test.Rout.save | 6 +- tests/mKrig.Z.Rout.save | 6 +- tests/mKrig.parameters.test.Rout.save | 6 +- tests/mKrig.se.test.Rout.save | 6 +- tests/mKrig.test.Rout.save | 6 +- tests/mKrigMLETest.Rout.save | 6 +- tests/mKrigREMLTest.Rout.save | 6 +- tests/misc.test.Rout.save | 6 +- tests/spam.test.Rout.save | 6 +- tests/sreg.test.Rout.save | 6 +- tests/vgram.test.Rout.save | 6 +- 36 files changed, 149 insertions(+), 143 deletions(-)
Title: Computing Expectations and Marginal Likelihoods for Permutations
Description: A set of functions for computing expected permutation matrices given a matrix of likelihoods for each individual assignment. It has been written to accompany the forthcoming paper 'Computing expectations and marginal likelihoods for permutations'. Publication details will be updated as soon as they are finalized.
Author: Ben Powell
Maintainer: Ben Powell <ben.powell@york.ac.uk>
Diff between expperm versions 1.2 dated 2019-05-23 and 1.6 dated 2019-05-28
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- build/partial.rdb |binary man/expperm-package.Rd | 6 +++++- src/ryser.cpp | 3 +-- 5 files changed, 14 insertions(+), 11 deletions(-)
Title: Authoring Books and Technical Documents with R Markdown
Description: Output formats and utilities for authoring books and technical documents with R Markdown.
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>),
JJ Allaire [ctb],
Albert Kim [ctb],
Alessandro Samuel-Rosa [ctb],
Andrzej Oles [ctb],
Aust Frederik [ctb] (<https://orcid.org/0000-0003-4900-788X>),
Bastiaan Quast [ctb],
Ben Marwick [ctb],
Chester Ismay [ctb],
Christophe Dervieux [ctb],
Clifton Franklund [ctb],
Daniel Emaasit [ctb],
David Shuman [ctb],
Dean Attali [ctb],
Drew Tyre [ctb],
Ellis Valentiner [ctb],
Frans van Dunne [ctb],
Hadley Wickham [ctb],
Jeff Allen [ctb],
Jennifer Bryan [ctb],
Jonathan McPhers [ctb],
Junwen Huang [ctb],
Kevin Cheung [ctb],
Kevin Ushey [ctb],
Kim Seonghyun [ctb],
Kirill Muller [ctb],
Luciano Selzer [ctb],
Matthew Lincoln [ctb],
Maximilian Held [ctb],
Michael Sachs [ctb],
Michal Bojanowski [ctb],
Noam Ross [ctb],
Peter Hickey [ctb],
Sahir Bhatnagar [ctb],
Steve Simpson [ctb],
Thierry Onkelinx [ctb] (<https://orcid.org/0000-0001-8804-4216>),
Vincent Fulco [ctb],
Yixuan Qiu [ctb],
Zhuoer Dong [ctb],
RStudio Inc [cph],
Bartek Szopka [ctb] (The jQuery Highlight plugin),
jQuery Foundation [cph] (jQuery library),
jQuery contributors [ctb, cph] (jQuery library; authors listed in
inst/resources/AUTHORS),
MathQuill contributors [ctb] (The MathQuill library; authors listed in
inst/resources/AUTHORS),
FriendCode Inc [cph, ctb] (The gitbook style, with modifications)
Maintainer: Yihui Xie <xie@yihui.name>
Diff between bookdown versions 0.10 dated 2019-05-10 and 0.11 dated 2019-05-28
DESCRIPTION | 12 ++++++------ MD5 | 8 ++++---- R/render.R | 2 +- R/utils.R | 8 +++++--- inst/resources/gitbook/js/app.min.js | 2 +- 5 files changed, 17 insertions(+), 15 deletions(-)
Title: Multilevel Modeling of Dendroclimatical Fluctuations
Description: Multilevel ecological data series (MEDS) are sequences of observations ordered according to temporal/spatial hierarchies that are defined by sample designs, with sample variability confined to ecological factors. Dendroclimatic MEDS of tree rings and climate are modeled into normalized fluctuations of tree growth and aridity. Modeled fluctuations (model frames) are compared with Mantel correlograms on multiple levels defined by sample design. Package implementation can be understood by running examples in modelFrame(), and muleMan() functions.
Author: Wilson Lara <wilarhen@gmail.com>, Felipe Bravo <fbravo@pvs.uva.es>
Maintainer: Wilson Lara <wilarhen@gmail.com>
Diff between BIOdry versions 0.5 dated 2017-04-20 and 0.6 dated 2019-05-28
DESCRIPTION | 8 ++++---- MD5 | 32 ++++++++++++++++---------------- NEWS | 6 ++++++ R/frametoLme.R | 31 ++++++++++++++++++------------- R/modelFrame.R | 34 ++++++++++++++++------------------ R/muleMan.R | 21 +++++++++++++++------ R/plot.modelFrame.R | 22 +++++++++++++++------- R/plot.muleMan.R | 23 ++++++++++++++++------- R/summary.modelFrame.R | 22 ++++++++++++++++------ build/partial.rdb |binary man/BIOdry-package.Rd | 3 +++ man/frametoLme.Rd | 29 +++++++++++++++++------------ man/modelFrame.Rd | 34 ++++++++++++++++------------------ man/muleMan.Rd | 21 +++++++++++++++------ man/plot.modelFrame.Rd | 22 +++++++++++++++------- man/plot.muleMan.Rd | 23 ++++++++++++++++------- man/summary.modelFrame.Rd | 22 ++++++++++++++++------ 17 files changed, 220 insertions(+), 133 deletions(-)
Title: Read, Write and Edit XLSX Files
Description: Simplifies the creation of Excel .xlsx files by providing a high
level interface to writing, styling and editing worksheets. Through the use of
'Rcpp', read/write times are comparable to the 'xlsx' and 'XLConnect' packages
with the added benefit of removing the dependency on Java.
Author: Alexander Walker [aut, cre],
Luca Braglia [ctb]
Maintainer: ORPHANED
gcc 9 warnings
Diff between openxlsx versions 4.1.0 dated 2018-05-26 and 4.1.0.1 dated 2019-05-28
DESCRIPTION | 14 ++++++++++---- MD5 | 10 +++++----- build/vignette.rds |binary inst/doc/Introduction.pdf |binary inst/doc/formatting.pdf |binary src/read_workbook.cpp | 4 ++-- 6 files changed, 17 insertions(+), 11 deletions(-)
Title: Effect Displays for Linear, Generalized Linear, and Other Models
Description: Graphical and tabular effect displays, e.g., of interactions, for
various statistical models with linear predictors.
Author: John Fox [aut, cre],
Sanford Weisberg [aut],
Brad Price [aut],
Michael Friendly [aut],
Jangman Hong [aut],
Robert Andersen [ctb],
David Firth [ctb],
Steve Taylor [ctb],
R Core Team [ctb]
Maintainer: John Fox <jfox@mcmaster.ca>
Diff between effects versions 4.1-0 dated 2018-11-30 and 4.1-1 dated 2019-05-28
DESCRIPTION | 15 MD5 | 32 NEWS | 10 R/Effect.R | 12 R/plot-methods.R | 7 R/predictorEffects.R | 383 +++++----- R/utilities.R | 1183 ++++++++++++++++--------------- build/vignette.rds |binary inst/CITATION | 9 inst/doc/adding-Effect-methods.pdf |binary inst/doc/partial-residuals.pdf |binary inst/doc/predictor-effects-gallery.Rnw | 4 inst/doc/predictor-effects-gallery.pdf |binary man/effect.Rd | 1185 +++++++++++++++----------------- man/effects-package.Rd | 9 man/predictorEffects.Rd | 2 vignettes/predictor-effects-gallery.Rnw | 4 17 files changed, 1463 insertions(+), 1392 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-01-10 1.1.2
Title: 'ViennaCL' C++ Header Files
Description: 'ViennaCL' is a free open-source linear algebra library
for computations on many-core architectures (GPUs, MIC) and
multi-core CPUs. The library is written in C++ and supports 'CUDA',
'OpenCL', and 'OpenMP' (including switches at runtime).
I have placed these libraries in this package as a more efficient
distribution system for CRAN. The idea is that you can write a package
that depends on the 'ViennaCL' library and yet you do not need to
distribute a copy of this code with your package.
Author: Charles Determan Jr.
Maintainer: Charles Determan Jr <cdetermanjr@gmail.com>
Diff between RViennaCL versions 1.7.1.7 dated 2017-10-15 and 1.7.1.8 dated 2019-05-28
DESCRIPTION | 10 MD5 | 508 NAMESPACE | 3 build/partial.rdb |binary inst/include/viennacl/backend/cpu_ram.hpp | 342 inst/include/viennacl/backend/cuda.hpp | 412 inst/include/viennacl/backend/mem_handle.hpp | 500 inst/include/viennacl/backend/memory.hpp | 1256 - inst/include/viennacl/backend/opencl.hpp | 302 inst/include/viennacl/backend/util.hpp | 536 inst/include/viennacl/circulant_matrix.hpp | 718 inst/include/viennacl/compressed_compressed_matrix.hpp | 1238 - inst/include/viennacl/compressed_matrix.hpp | 2629 +-- inst/include/viennacl/context.hpp | 176 inst/include/viennacl/coordinate_matrix.hpp | 1012 - inst/include/viennacl/detail/matrix_def.hpp | 540 inst/include/viennacl/detail/vector_def.hpp | 700 inst/include/viennacl/device_specific/builtin_database/common.hpp | 438 inst/include/viennacl/device_specific/builtin_database/devices/accelerator/fallback.hpp | 170 inst/include/viennacl/device_specific/builtin_database/devices/cpu/fallback.hpp | 168 inst/include/viennacl/device_specific/builtin_database/devices/gpu/amd/ev/cedar.hpp | 128 inst/include/viennacl/device_specific/builtin_database/devices/gpu/amd/ev/cypress.hpp | 130 inst/include/viennacl/device_specific/builtin_database/devices/gpu/amd/ni/barts.hpp | 128 inst/include/viennacl/device_specific/builtin_database/devices/gpu/amd/ni/devastator.hpp | 128 inst/include/viennacl/device_specific/builtin_database/devices/gpu/amd/ni/scrapper.hpp | 128 inst/include/viennacl/device_specific/builtin_database/devices/gpu/amd/si/tahiti.hpp | 168 inst/include/viennacl/device_specific/builtin_database/devices/gpu/amd/vi/hawaii.hpp | 168 inst/include/viennacl/device_specific/builtin_database/devices/gpu/fallback.hpp | 168 inst/include/viennacl/device_specific/builtin_database/devices/gpu/nv/f/ge_gt_540m.hpp | 118 inst/include/viennacl/device_specific/builtin_database/devices/gpu/nv/f/ge_gtx_470.hpp | 166 inst/include/viennacl/device_specific/builtin_database/devices/gpu/nv/f/ge_gtx_580.hpp | 168 inst/include/viennacl/device_specific/builtin_database/devices/gpu/nv/f/tesla_c2050.hpp | 168 inst/include/viennacl/device_specific/builtin_database/devices/gpu/nv/k/tesla_k20m.hpp | 168 inst/include/viennacl/device_specific/builtin_database/devices/gpu/nv/m/ge_gtx_750_ti.hpp | 170 inst/include/viennacl/device_specific/builtin_database/devices/gpu/nv/tesla/ge_gtx_260.hpp | 168 inst/include/viennacl/device_specific/builtin_database/matrix_product.hpp | 488 inst/include/viennacl/device_specific/execute.hpp | 110 inst/include/viennacl/device_specific/execution_handler.hpp | 204 inst/include/viennacl/device_specific/forwards.h | 588 inst/include/viennacl/device_specific/lazy_program_compiler.hpp | 148 inst/include/viennacl/device_specific/mapped_objects.hpp | 1024 - inst/include/viennacl/device_specific/templates/matrix_product_template.hpp | 1718 +- inst/include/viennacl/device_specific/templates/template_base.hpp | 1192 - inst/include/viennacl/device_specific/templates/utils.hpp | 210 inst/include/viennacl/device_specific/tree_parsing.hpp | 1048 - inst/include/viennacl/device_specific/utils.hpp | 1158 - inst/include/viennacl/ell_matrix.hpp | 724 inst/include/viennacl/fft.hpp | 564 inst/include/viennacl/forwards.h | 2112 +- inst/include/viennacl/hankel_matrix.hpp | 686 inst/include/viennacl/hyb_matrix.hpp | 884 - inst/include/viennacl/io/matrix_market.hpp | 880 - inst/include/viennacl/linalg/amg.hpp | 796 inst/include/viennacl/linalg/amg_operations.hpp | 476 inst/include/viennacl/linalg/bicgstab.hpp | 1196 - inst/include/viennacl/linalg/bisect.hpp | 358 inst/include/viennacl/linalg/bisect_gpu.hpp | 346 inst/include/viennacl/linalg/cg.hpp | 880 - inst/include/viennacl/linalg/circulant_matrix_operations.hpp | 150 inst/include/viennacl/linalg/cuda/amg_operations.hpp | 1646 +- inst/include/viennacl/linalg/cuda/bisect_kernel_calls.hpp | 332 inst/include/viennacl/linalg/cuda/bisect_kernel_large.hpp | 1856 +- inst/include/viennacl/linalg/cuda/bisect_kernel_large_multi.hpp | 554 inst/include/viennacl/linalg/cuda/bisect_kernel_large_onei.hpp | 360 inst/include/viennacl/linalg/cuda/bisect_kernel_small.hpp | 522 inst/include/viennacl/linalg/cuda/bisect_util.hpp | 1226 - inst/include/viennacl/linalg/cuda/common.hpp | 602 inst/include/viennacl/linalg/cuda/direct_solve.hpp | 824 - inst/include/viennacl/linalg/cuda/fft_operations.hpp | 1716 +- inst/include/viennacl/linalg/cuda/ilu_operations.hpp | 1332 - inst/include/viennacl/linalg/cuda/iterative_operations.hpp | 4098 ++--- inst/include/viennacl/linalg/cuda/matrix_operations.hpp | 4544 ++--- inst/include/viennacl/linalg/cuda/matrix_operations_col.hpp | 3144 +-- inst/include/viennacl/linalg/cuda/matrix_operations_prod.hpp | 5774 +++---- inst/include/viennacl/linalg/cuda/matrix_operations_row.hpp | 2384 +- inst/include/viennacl/linalg/cuda/misc_operations.hpp | 182 inst/include/viennacl/linalg/cuda/nmf_operations.hpp | 304 inst/include/viennacl/linalg/cuda/scalar_operations.hpp | 750 inst/include/viennacl/linalg/cuda/sparse_matrix_operations.hpp | 5618 +++--- inst/include/viennacl/linalg/cuda/sparse_matrix_operations_solve.hpp | 1522 - inst/include/viennacl/linalg/cuda/spgemm.hpp | 1586 - inst/include/viennacl/linalg/cuda/spgemm_rmerge.hpp | 1330 - inst/include/viennacl/linalg/cuda/vector_operations.hpp | 6064 +++---- inst/include/viennacl/linalg/detail/amg/amg_base.hpp | 416 inst/include/viennacl/linalg/detail/bisect/bisect_kernel_calls.hpp | 382 inst/include/viennacl/linalg/detail/bisect/bisect_large.hpp | 284 inst/include/viennacl/linalg/detail/bisect/bisect_small.hpp | 192 inst/include/viennacl/linalg/detail/bisect/config.hpp | 88 inst/include/viennacl/linalg/detail/bisect/gerschgorin.hpp | 188 inst/include/viennacl/linalg/detail/bisect/structs.hpp | 364 inst/include/viennacl/linalg/detail/bisect/util.hpp | 212 inst/include/viennacl/linalg/detail/ilu/block_ilu.hpp | 1234 - inst/include/viennacl/linalg/detail/ilu/chow_patel_ilu.hpp | 632 inst/include/viennacl/linalg/detail/ilu/common.hpp | 526 inst/include/viennacl/linalg/detail/ilu/ilu0.hpp | 758 inst/include/viennacl/linalg/detail/ilu/ilut.hpp | 1384 - inst/include/viennacl/linalg/detail/op_applier.hpp | 268 inst/include/viennacl/linalg/detail/op_executor.hpp | 172 inst/include/viennacl/linalg/detail/spai/block_matrix.hpp | 172 inst/include/viennacl/linalg/detail/spai/block_vector.hpp | 154 inst/include/viennacl/linalg/detail/spai/fspai.hpp | 804 inst/include/viennacl/linalg/detail/spai/qr.hpp | 994 - inst/include/viennacl/linalg/detail/spai/small_matrix.hpp | 226 inst/include/viennacl/linalg/detail/spai/spai-dynamic.hpp | 1374 - inst/include/viennacl/linalg/detail/spai/spai-static.hpp | 384 inst/include/viennacl/linalg/detail/spai/spai.hpp | 1664 +- inst/include/viennacl/linalg/detail/spai/spai_tag.hpp | 286 inst/include/viennacl/linalg/detail/spai/sparse_vector.hpp | 170 inst/include/viennacl/linalg/direct_solve.hpp | 1160 - inst/include/viennacl/linalg/eig.hpp | 58 inst/include/viennacl/linalg/fft_operations.hpp | 962 - inst/include/viennacl/linalg/gmres.hpp | 1476 - inst/include/viennacl/linalg/hankel_matrix_operations.hpp | 132 inst/include/viennacl/linalg/host_based/amg_operations.hpp | 3152 +-- inst/include/viennacl/linalg/host_based/common.hpp | 298 inst/include/viennacl/linalg/host_based/direct_solve.hpp | 614 inst/include/viennacl/linalg/host_based/fft_operations.hpp | 1712 +- inst/include/viennacl/linalg/host_based/ilu_operations.hpp | 1344 - inst/include/viennacl/linalg/host_based/iterative_operations.hpp | 1890 +- inst/include/viennacl/linalg/host_based/matrix_operations.hpp | 4338 ++--- inst/include/viennacl/linalg/host_based/misc_operations.hpp | 160 inst/include/viennacl/linalg/host_based/nmf_operations.hpp | 494 inst/include/viennacl/linalg/host_based/scalar_operations.hpp | 324 inst/include/viennacl/linalg/host_based/sparse_matrix_operations.hpp | 4250 ++--- inst/include/viennacl/linalg/host_based/spgemm_vector.hpp | 1410 - inst/include/viennacl/linalg/host_based/vector_operations.hpp | 2496 +-- inst/include/viennacl/linalg/ichol.hpp | 456 inst/include/viennacl/linalg/ilu.hpp | 66 inst/include/viennacl/linalg/ilu_operations.hpp | 668 inst/include/viennacl/linalg/inner_prod.hpp | 372 inst/include/viennacl/linalg/iterative_operations.hpp | 850 - inst/include/viennacl/linalg/jacobi_precond.hpp | 282 inst/include/viennacl/linalg/lanczos.hpp | 1030 - inst/include/viennacl/linalg/lu.hpp | 454 inst/include/viennacl/linalg/matrix_operations.hpp | 2840 +-- inst/include/viennacl/linalg/maxmin.hpp | 304 inst/include/viennacl/linalg/misc_operations.hpp | 188 inst/include/viennacl/linalg/mixed_precision_cg.hpp | 398 inst/include/viennacl/linalg/nmf.hpp | 182 inst/include/viennacl/linalg/norm_1.hpp | 208 inst/include/viennacl/linalg/norm_2.hpp | 280 inst/include/viennacl/linalg/norm_frobenius.hpp | 146 inst/include/viennacl/linalg/norm_inf.hpp | 216 inst/include/viennacl/linalg/opencl/amg_operations.hpp | 916 - inst/include/viennacl/linalg/opencl/bisect_kernel_calls.hpp | 354 inst/include/viennacl/linalg/opencl/common.hpp | 228 inst/include/viennacl/linalg/opencl/direct_solve.hpp | 306 inst/include/viennacl/linalg/opencl/fft_operations.hpp | 700 inst/include/viennacl/linalg/opencl/ilu_operations.hpp | 520 inst/include/viennacl/linalg/opencl/iterative_operations.hpp | 1890 +- inst/include/viennacl/linalg/opencl/kernels/amg.hpp | 786 inst/include/viennacl/linalg/opencl/kernels/bisect.hpp | 5290 +++--- inst/include/viennacl/linalg/opencl/kernels/compressed_compressed_matrix.hpp | 220 inst/include/viennacl/linalg/opencl/kernels/compressed_matrix.hpp | 3406 ++-- inst/include/viennacl/linalg/opencl/kernels/coordinate_matrix.hpp | 810 inst/include/viennacl/linalg/opencl/kernels/ell_matrix.hpp | 442 inst/include/viennacl/linalg/opencl/kernels/fft.hpp | 622 inst/include/viennacl/linalg/opencl/kernels/hyb_matrix.hpp | 480 inst/include/viennacl/linalg/opencl/kernels/ilu.hpp | 1010 - inst/include/viennacl/linalg/opencl/kernels/iterative.hpp | 3238 +-- inst/include/viennacl/linalg/opencl/kernels/matrix.hpp | 2730 +-- inst/include/viennacl/linalg/opencl/kernels/matrix_element.hpp | 300 inst/include/viennacl/linalg/opencl/kernels/matrix_solve.hpp | 360 inst/include/viennacl/linalg/opencl/kernels/nmf.hpp | 198 inst/include/viennacl/linalg/opencl/kernels/scalar.hpp | 566 inst/include/viennacl/linalg/opencl/kernels/scan.hpp | 388 inst/include/viennacl/linalg/opencl/kernels/sliced_ell_matrix.hpp | 270 inst/include/viennacl/linalg/opencl/kernels/spai.hpp | 1262 - inst/include/viennacl/linalg/opencl/kernels/svd.hpp | 1406 - inst/include/viennacl/linalg/opencl/kernels/vector.hpp | 1734 +- inst/include/viennacl/linalg/opencl/kernels/vector_element.hpp | 446 inst/include/viennacl/linalg/opencl/matrix_operations.hpp | 2214 +- inst/include/viennacl/linalg/opencl/misc_operations.hpp | 138 inst/include/viennacl/linalg/opencl/nmf_operations.hpp | 278 inst/include/viennacl/linalg/opencl/scalar_operations.hpp | 410 inst/include/viennacl/linalg/opencl/sparse_matrix_operations.hpp | 2488 +-- inst/include/viennacl/linalg/opencl/vandermonde_matrix_operations.hpp | 136 inst/include/viennacl/linalg/opencl/vector_operations.hpp | 2700 +-- inst/include/viennacl/linalg/power_iter.hpp | 258 inst/include/viennacl/linalg/prod.hpp | 740 inst/include/viennacl/linalg/qr-method-common.hpp | 376 inst/include/viennacl/linalg/qr-method.hpp | 1666 +- inst/include/viennacl/linalg/qr.hpp | 1338 - inst/include/viennacl/linalg/row_scaling.hpp | 408 inst/include/viennacl/linalg/scalar_operations.hpp | 484 inst/include/viennacl/linalg/spai.hpp | 584 inst/include/viennacl/linalg/sparse_matrix_operations.hpp | 842 - inst/include/viennacl/linalg/sum.hpp | 272 inst/include/viennacl/linalg/svd.hpp | 1094 - inst/include/viennacl/linalg/toeplitz_matrix_operations.hpp | 156 inst/include/viennacl/linalg/tql2.hpp | 524 inst/include/viennacl/linalg/vandermonde_matrix_operations.hpp | 142 inst/include/viennacl/linalg/vector_operations.hpp | 2822 +-- inst/include/viennacl/matrix.hpp | 8126 +++++----- inst/include/viennacl/matrix_proxy.hpp | 1190 - inst/include/viennacl/meta/enable_if.hpp | 86 inst/include/viennacl/meta/predicate.hpp | 1068 - inst/include/viennacl/meta/result_of.hpp | 1262 - inst/include/viennacl/meta/tag_of.hpp | 780 inst/include/viennacl/misc/bandwidth_reduction.hpp | 76 inst/include/viennacl/misc/cuthill_mckee.hpp | 1222 - inst/include/viennacl/misc/gibbs_poole_stockmeyer.hpp | 854 - inst/include/viennacl/ocl/backend.hpp | 728 inst/include/viennacl/ocl/command_queue.hpp | 184 inst/include/viennacl/ocl/context.hpp | 1656 +- inst/include/viennacl/ocl/device.hpp | 2992 +-- inst/include/viennacl/ocl/device_utils.hpp | 382 inst/include/viennacl/ocl/enqueue.hpp | 296 inst/include/viennacl/ocl/error.hpp | 1374 - inst/include/viennacl/ocl/forwards.h | 126 inst/include/viennacl/ocl/handle.hpp | 460 inst/include/viennacl/ocl/kernel.hpp | 1610 - inst/include/viennacl/ocl/local_mem.hpp | 102 inst/include/viennacl/ocl/platform.hpp | 290 inst/include/viennacl/ocl/program.hpp | 172 inst/include/viennacl/ocl/utils.hpp | 170 inst/include/viennacl/range.hpp | 152 inst/include/viennacl/scalar.hpp | 1748 +- inst/include/viennacl/scheduler/execute.hpp | 580 inst/include/viennacl/scheduler/execute_axbx.hpp | 762 inst/include/viennacl/scheduler/execute_elementwise.hpp | 904 - inst/include/viennacl/scheduler/execute_generic_dispatcher.hpp | 268 inst/include/viennacl/scheduler/execute_matrix_dispatcher.hpp | 370 inst/include/viennacl/scheduler/execute_matrix_prod.hpp | 812 inst/include/viennacl/scheduler/execute_scalar_assign.hpp | 384 inst/include/viennacl/scheduler/execute_scalar_dispatcher.hpp | 262 inst/include/viennacl/scheduler/execute_util.hpp | 648 inst/include/viennacl/scheduler/execute_vector_dispatcher.hpp | 400 inst/include/viennacl/scheduler/forwards.h | 1708 +- inst/include/viennacl/scheduler/io.hpp | 560 inst/include/viennacl/scheduler/preset.hpp | 210 inst/include/viennacl/slice.hpp | 154 inst/include/viennacl/sliced_ell_matrix.hpp | 766 inst/include/viennacl/toeplitz_matrix.hpp | 768 inst/include/viennacl/tools/adapter.hpp | 842 - inst/include/viennacl/tools/entry_proxy.hpp | 468 inst/include/viennacl/tools/matrix_generation.hpp | 292 inst/include/viennacl/tools/matrix_size_deducer.hpp | 532 inst/include/viennacl/tools/random.hpp | 168 inst/include/viennacl/tools/sha1.hpp | 474 inst/include/viennacl/tools/shared_ptr.hpp | 358 inst/include/viennacl/tools/timer.hpp | 246 inst/include/viennacl/tools/tools.hpp | 630 inst/include/viennacl/traits/clear.hpp | 124 inst/include/viennacl/traits/context.hpp | 130 inst/include/viennacl/traits/fill.hpp | 136 inst/include/viennacl/traits/handle.hpp | 638 inst/include/viennacl/traits/row_major.hpp | 112 inst/include/viennacl/traits/size.hpp | 910 - inst/include/viennacl/traits/start.hpp | 204 inst/include/viennacl/traits/stride.hpp | 144 inst/include/viennacl/vandermonde_matrix.hpp | 684 inst/include/viennacl/vector.hpp | 6662 ++++---- inst/include/viennacl/vector_proxy.hpp | 680 inst/include/viennacl/version.hpp | 62 255 files changed, 115393 insertions(+), 115391 deletions(-)
Title: Visualization Tools for Genealogical Data
Description: Methods for searching through genealogical data and displaying the results. Plotting algorithms assist with data exploration and publication-quality image generation. Includes interactive genealogy visualization tools. Provides parsing and calculation methods for variables in descendant branches of interest. Uses the Grammar of Graphics.
Author: Lindsay Rutter, Susan Vanderplas, Di Cook
Maintainer: Lindsay Rutter <lindsayannerutter@gmail.com>
Diff between ggenealogy versions 0.4.0 dated 2019-05-23 and 1.0.0 dated 2019-05-28
DESCRIPTION | 6 +- MD5 | 62 ++++++++++++------------ NEWS.md | 6 ++ R/allFunctions.R | 115 ++++++++++++++++++++++++++++++++++++++++++++-- build/partial.rdb |only inst/CITATION |only inst/doc/ggenealogy.R | 74 ++++++++++++++--------------- inst/doc/ggenealogy.Rnw | 8 ++- inst/doc/ggenealogy.pdf |binary man/buildAncDesCoordDF.Rd | 3 + man/buildAncDesTotalDF.Rd | 7 ++ man/buildAncList.Rd | 7 ++ man/buildDesList.Rd | 7 ++ man/getAncestors.Rd | 7 ++ man/getBasicStatistics.Rd | 7 ++ man/getBranchQual.Rd | 7 ++ man/getBranchQuant.Rd | 8 ++- man/getChild.Rd | 7 ++ man/getDegree.Rd | 7 ++ man/getDescendants.Rd | 7 ++ man/getEdges.Rd | 7 ++ man/getNodes.Rd | 7 ++ man/getParent.Rd | 7 ++ man/getPath.Rd | 7 ++ man/getVariable.Rd | 7 ++ man/isChild.Rd | 7 ++ man/isParent.Rd | 7 ++ man/plotAncDes.Rd | 7 ++ man/plotDegMatrix.Rd | 8 ++- man/plotPath.Rd | 7 ++ man/plotPathOnAll.Rd | 7 ++ man/plotVariableMatrix.Rd | 8 ++- vignettes/ggenealogy.Rnw | 8 ++- 33 files changed, 360 insertions(+), 79 deletions(-)
Title: MR Spectroscopy Analysis Tools
Description: Tools for reading, visualising and processing Magnetic Resonance
Spectroscopy data.
Author: Martin Wilson [cre, aut],
John Muschelli [ctb]
Maintainer: Martin Wilson <martin@pipegrep.co.uk>
Diff between spant versions 0.13.0 dated 2019-04-25 and 0.14.0 dated 2019-05-28
DESCRIPTION | 8 +- MD5 | 48 +++++++++------- NAMESPACE | 6 ++ NEWS.md | 11 +++ R/amp_scaling.R | 5 + R/basis_set.R | 34 +++++++---- R/fit_display.R | 27 ++++++++- R/fitting.R | 73 +++++++++++++++++++++---- R/interactive_plotting.R | 18 +++--- R/mrs_data_proc.R | 125 +++++++++++++++++++++++++++++++++++++++----- R/qm_simulation.R | 37 +++++-------- R/utils.R | 3 + build/vignette.rds |binary inst/doc/spant-intro.html | 12 ++-- man/auto_phase.Rd |only man/basis2mrs_data.Rd | 8 ++ man/collapse_to_dyns.Rd |only man/decimate_mrs.Rd |only man/fit_amps.Rd |only man/get_subset.Rd |only man/int_spec.Rd | 2 man/mean.mrs_data.Rd |only man/plot_fit_slice_inter.Rd | 4 - man/plot_slice_map_inter.Rd | 7 +- man/scale_amp_molar.Rd | 5 + man/sim_basis.Rd | 13 +--- man/stackplot.fit_result.Rd | 14 ++++ man/write_basis.Rd | 2 28 files changed, 339 insertions(+), 123 deletions(-)
Title: Cancer Registry Data Analysis and Visualisation
Description: Tools for basic and advance cancer statistics and graphics.
Groups individual data, merges registry data and population data, calculates age-specific rate, age-standardized rate, estimated annual percentage rate with standards error. Creates graphics across variable and
time, such as age-specific trends, bar chart and period-cohort trends.
Author: Mathieu Laversanne [aut, cre],
Cancer Surveillance Unit [cph]
Maintainer: Mathieu Laversanne <laversannem@iarc.fr>
Diff between Rcan versions 1.3.64 dated 2018-12-17 and 1.3.70 dated 2019-05-28
Rcan-1.3.64/Rcan/R/Rcan-internal.R |only Rcan-1.3.64/Rcan/R/csu_ageSpecific.r |only Rcan-1.3.70/Rcan/DESCRIPTION | 15 Rcan-1.3.70/Rcan/MD5 | 51 +- Rcan-1.3.70/Rcan/NAMESPACE | 1 Rcan-1.3.70/Rcan/R/csu_ageSpecific.R |only Rcan-1.3.70/Rcan/R/csu_bar_top.R |only Rcan-1.3.70/Rcan/R/csu_group_cases.R |only Rcan-1.3.70/Rcan/R/csu_merge_cases_pop.R |only Rcan-1.3.70/Rcan/R/helper.r | 271 ++++++++++++++- Rcan-1.3.70/Rcan/R/zzz.R | 4 Rcan-1.3.70/Rcan/build/partial.rdb |binary Rcan-1.3.70/Rcan/data/ICD_group_CI5.rda |only Rcan-1.3.70/Rcan/data/ICD_group_GLOBOCAN.rda |only Rcan-1.3.70/Rcan/data/data_individual_file.rda |only Rcan-1.3.70/Rcan/data/data_population_file.rda |only Rcan-1.3.70/Rcan/data/datalist | 4 Rcan-1.3.70/Rcan/inst/testdata/csu_group_cases_test1.rds |only Rcan-1.3.70/Rcan/inst/testdata/csu_merge_cases_pop1.rds |only Rcan-1.3.70/Rcan/man/ICD_group_CI5.Rd |only Rcan-1.3.70/Rcan/man/ICD_group_GLOBOCAN.Rd |only Rcan-1.3.70/Rcan/man/Rcan-package.Rd | 43 ++ Rcan-1.3.70/Rcan/man/csu_ageSpecific.Rd | 4 Rcan-1.3.70/Rcan/man/csu_ageSpecific_top.Rd | 4 Rcan-1.3.70/Rcan/man/csu_asr.Rd | 6 Rcan-1.3.70/Rcan/man/csu_bar_top.Rd |only Rcan-1.3.70/Rcan/man/csu_eapc.Rd | 6 Rcan-1.3.70/Rcan/man/csu_group_cases.Rd |only Rcan-1.3.70/Rcan/man/csu_merge_cases_pop.Rd |only Rcan-1.3.70/Rcan/man/csu_registry_data_1.Rd | 8 Rcan-1.3.70/Rcan/man/csu_registry_data_2.Rd | 10 Rcan-1.3.70/Rcan/man/csu_time_trend.Rd | 8 Rcan-1.3.70/Rcan/man/csu_trendCohortPeriod.Rd | 5 Rcan-1.3.70/Rcan/man/data_individual_file.Rd |only Rcan-1.3.70/Rcan/man/data_population_file.Rd |only Rcan-1.3.70/Rcan/tests/testthat/test-Rcan.R | 51 ++ 36 files changed, 443 insertions(+), 48 deletions(-)
Title: Parsing and Evaluation Tools that Provide More Details than the
Default
Description: Parsing and evaluation tools that make it easy to recreate the
command line behaviour of R.
Author: Hadley Wickham [aut],
Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>),
Michael Lawrence [ctb],
Thomas Kluyver [ctb],
Jeroen Ooms [ctb],
Barret Schloerke [ctb],
Adam Ryczkowski [ctb],
Hiroaki Yutani [ctb],
Michel Lang [ctb],
Karolis Koncevičius [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between evaluate versions 0.13 dated 2019-02-12 and 0.14 dated 2019-05-28
evaluate-0.13/evaluate/NEWS |only evaluate-0.14/evaluate/DESCRIPTION | 12 ++++++---- evaluate-0.14/evaluate/LICENSE | 2 - evaluate-0.14/evaluate/MD5 | 14 +++++++----- evaluate-0.14/evaluate/NAMESPACE | 1 evaluate-0.14/evaluate/NEWS.md |only evaluate-0.14/evaluate/R/eval.r | 8 ++++--- evaluate-0.14/evaluate/R/hooks.r | 32 +++++++++++++++++++++++++---- evaluate-0.14/evaluate/README.md |only evaluate-0.14/evaluate/man/remove_hooks.Rd |only 10 files changed, 50 insertions(+), 19 deletions(-)
Title: Semiparametric Factor and Regression Models for Symmetric
Relational Data
Description: Estimation of the parameters in a model for
symmetric relational data (e.g., the above-diagonal part of a
square matrix), using a model-based eigenvalue decomposition
and regression. Missing data is accommodated, and a posterior
mean for missing data is calculated under the assumption that
the data are missing at random. The marginal distribution of
the relational data can be arbitrary, and is fit with an
ordered probit specification. See Hoff (2007) <arXiv:0711.1146>
for details on the model.
Author: Peter Hoff
Maintainer: Peter Hoff <peter.hoff@duke.edu>
Diff between eigenmodel versions 1.10 dated 2018-06-03 and 1.11 dated 2019-05-28
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS.md | 3 ++- R/eigenmodel-package.R | 2 +- R/eigenmodel_mcmc.R | 3 +-- man/eigenmodel-package.Rd | 2 +- 6 files changed, 14 insertions(+), 14 deletions(-)
Title: A Time Input Widget for Shiny
Description: Provides a time input widget for Shiny. This widget allows intuitive time input in the
'[hh]:[mm]:[ss]' or '[hh]:[mm]' (24H) format by using a separate numeric input for each time
component. The interface with R uses date-time objects. See the project page for more
information and examples.
Author: Gerhard Burger [aut, cre]
Maintainer: Gerhard Burger <burger.ga@gmail.com>
Diff between shinyTime versions 0.2.1 dated 2016-10-07 and 1.0.0 dated 2019-05-28
DESCRIPTION | 13 +++- MD5 | 30 ++++++----- NEWS.md | 9 ++- R/input-time.R | 23 ++++++-- R/utils.R | 26 ++++++++- R/zzz.R | 2 README.md | 107 +++++++++++++++++++++++++++-------------- inst/WORDLIST |only inst/example/app.R | 13 +++- inst/example/rsconnect |only inst/www/input_binding_time.js | 23 ++++++++ man/figures |only man/shinyTime.Rd | 1 man/shinyTimeExample.Rd | 4 - man/timeInput.Rd | 18 ++++-- man/updateTimeInput.Rd | 4 - tests |only 17 files changed, 192 insertions(+), 81 deletions(-)
Title: R Interface to 'lp_solve' Version 5.5.2.0
Description: The lpSolveAPI package provides an R interface to 'lp_solve',
a Mixed Integer Linear Programming (MILP) solver with support for pure
linear, (mixed) integer/binary, semi-continuous and special ordered sets
(SOS) models.
Author: lp_solve <http://lpsolve.sourceforge.net/>,
Kjell Konis <kjell.konis@me.com>.
Maintainer: ORPHANED
Diff between lpSolveAPI versions 5.5.2.0-17 dated 2016-01-13 and 5.5.2.0-17.1 dated 2019-05-28
DESCRIPTION | 11 +++++++---- MD5 | 8 ++++---- inst/include/lp_bit.h | 44 ++++++++++++++++++++++---------------------- src/RlpSolve.c | 1 + src/lp_solve/lp_MPS.c | 2 +- 5 files changed, 35 insertions(+), 31 deletions(-)
Title: Interface to 'Lp_solve' v. 5.5 to Solve Linear/Integer Programs
Description: Lp_solve is freely available (under LGPL 2) software for
solving linear, integer and mixed integer programs. In this
implementation we supply a "wrapper" function in C and some R
functions that solve general linear/integer problems,
assignment problems, and transportation problems. This version
calls lp_solve version 5.5.
Author: Michel Berkelaar and others
Maintainer: ORPHANED
Diff between lpSolve versions 5.6.13 dated 2015-09-19 and 5.6.13.1 dated 2019-05-28
DESCRIPTION | 11 +++++++---- MD5 | 7 ++++--- src/init.c |only src/lp_MPS.c | 2 +- src/sparselib.c | 2 +- 5 files changed, 13 insertions(+), 9 deletions(-)
Title: Extra String Manipulation Functions
Description: There are some things that I wish were easier with the 'stringr'
or 'stringi' packages. The foremost of these is the extraction of numbers
from strings. 'stringr' and 'stringi' make you figure out the regular
expression for yourself; 'strex' takes care of this for you. There are many
other handy functionalities in 'strex'. Contributions to this package are
encouraged: it is intended as a miscellany of string manipulation functions
that cannot be found in 'stringi' or 'stringr'.
Author: Rory Nolan [aut, cre] (<https://orcid.org/0000-0002-5239-4043>)
Maintainer: Rory Nolan <rorynoolan@gmail.com>
Diff between strex versions 1.0.1 dated 2019-05-12 and 1.0.2 dated 2019-05-28
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++----------- NEWS.md | 6 ++++++ build/partial.rdb |binary inst/doc/alphordering-numbers.html | 4 ++-- inst/doc/argument-matching.html | 4 ++-- inst/doc/before-and-after.html | 4 ++-- inst/doc/important-miscellany.html | 4 ++-- inst/doc/numbers-in-strings.html | 4 ++-- src/split-by-nums.cpp | 11 +++++------ src/substrs.cpp | 2 +- src/substrs.h | 2 +- 12 files changed, 37 insertions(+), 32 deletions(-)
Title: A Wrapper for Querying KISTERS 'WISKI' Databases via the 'KiWIS'
API
Description: A wrapper for querying 'WISKI' databases via the 'KiWIS' 'REST' API. 'WISKI' is an 'SQL' relational database
used for the collection and storage of water data developed by KISTERS and 'KiWIS' is a 'REST' service that provides
access to 'WISKI' databases via HTTP requests (<https://water.kisters.de/en/technology-trends/kisters-and-open-data/>).
Contains a list of default databases (called 'hubs') and also allows users to provide their own 'KiWIS' URL.
Supports the entire query process- from metadata to specific time series values. All data is returned as tidy tibbles.
Author: Ryan Whaley [aut, cre],
Sam Albers [ctb]
Maintainer: Ryan Whaley <rdgwhaley@gmail.com>
Diff between kiwisR versions 0.1.5 dated 2019-04-12 and 0.1.6 dated 2019-05-28
DESCRIPTION | 8 MD5 | 36 ++-- NEWS.md | 25 ++ R/ki_group_list.R | 24 +- R/ki_station_list.R | 46 +++-- R/ki_timeseries_list.R | 56 +++--- R/ki_timeseries_values.R | 82 +++------ R/utils.R | 23 ++ README.md | 245 +++++++++++++++++------------ man/ki_group_list.Rd | 2 man/ki_station_list.Rd | 8 man/ki_timeseries_list.Rd | 8 man/ki_timeseries_values.Rd | 9 - tests/testthat/helper-kiwisR.R | 28 +++ tests/testthat/test_ki_group_list.R | 10 - tests/testthat/test_ki_station_list.R | 40 ++-- tests/testthat/test_ki_timeseries_list.R | 58 ++++-- tests/testthat/test_ki_timeseries_values.R | 81 ++++++--- tests/testthat/test_utils.R | 2 19 files changed, 481 insertions(+), 310 deletions(-)
Title: Empirical Transition Matrix
Description: The etm (empirical transition matrix) package permits to estimate the matrix of transition probabilities for any time-inhomogeneous multistate model with finite state space using the Aalen-Johansen estimator. Functions for data preparation and for displaying are also included (Allignol et al., 2011 <doi:10.18637/jss.v038.i04>). Functionals of the Aalen-Johansen estimator, e.g., excess length-of-stay in an intermediate state, can also be computed (Allignol et al. 2011 <doi:10.1007/s00180-010-0200-x>).
Author: Arthur Allignol
Maintainer: Arthur Allignol <arthur.allignol@gmail.com>
Diff between etm versions 1.0.4 dated 2018-07-11 and 1.0.5 dated 2019-05-28
DESCRIPTION | 6 - MD5 | 16 +- build/vignette.rds |binary inst/doc/etmCIF_tutorial.pdf |binary man/closPseudo.Rd | 71 ++++++------ tests/test.etmCIF.R | 112 +++++++++---------- tests/test.etmCIF.Rout.save | 251 +++++++++++++------------------------------ tests/tests.etm.R | 65 +++++------ tests/tests.etm.Rout.save | 198 ++++++++------------------------- 9 files changed, 263 insertions(+), 456 deletions(-)
Title: Automatic Calibration by Evolutionary Multi Objective Algorithm
Description: Multi-objective optimizer initially developed for the calibration of hydrological models.
The algorithm is a hybrid of the MEAS algorithm (Efstratiadis and Koutsoyiannis (2005) <doi:10.13140/RG.2.2.32963.81446>) by using the directional search method based on the simplexes of the objective space
and the epsilon-NGSA-II algorithm with the method of classification of the parameter vectors archiving management by epsilon-dominance (Reed and Devireddy <doi:10.1142/9789812567796_0004>).
Author: Nicolas Le Moine [aut],
Celine Monteil [aut],
Frederic Hendrickx [ctb],
Fabrice Zaoui [aut, cre]
Maintainer: Fabrice Zaoui <fabrice.zaoui@edf.fr>
Diff between caRamel versions 1.0 dated 2018-03-05 and 1.1 dated 2019-05-28
DESCRIPTION | 8 MD5 | 94 ++-- NAMESPACE | 3 NEWS | 18 R/Cextrap.R | 2 R/Cinterp.R | 2 R/Crecombination.R | 2 R/Cusecovar.R | 2 R/Dimprove.R | 2 R/boxes.R | 2 R/caRamel.R | 784 ++++++++++++++++++++--------------------- R/decrease_pop.R | 4 R/dominate.R | 60 +-- R/dominated.R | 2 R/downsize.R | 2 R/matvcov.R | 2 R/newXval.R | 450 +++++++++++------------ R/pareto.R | 78 ++-- R/plot_caramel.R |only R/plot_pareto.R |only R/plot_population.R |only R/rselect.R | 2 R/val2rank.R | 2 R/vol_splx.R | 2 README.md |only build/vignette.rds |binary inst/doc/Test_Constraints.R |only inst/doc/Test_Constraints.Rmd |only inst/doc/Test_Constraints.html |only inst/doc/Test_Functions.R | 204 +++++----- inst/doc/Test_Functions.html | 689 +++++++++++++++++++++--------------- man/Cextrap.Rd | 82 ++-- man/Cinterp.Rd | 82 ++-- man/Crecombination.Rd | 66 +-- man/Cusecovar.Rd | 66 +-- man/Dimprove.Rd | 60 +-- man/boxes.Rd | 60 +-- man/caRamel-package.Rd |only man/caRamel.Rd | 213 +++++------ man/decrease_pop.Rd | 86 ++-- man/dominate.Rd | 54 +- man/dominated.Rd | 60 +-- man/downsize.Rd | 66 +-- man/matvcov.Rd | 60 +-- man/newXval.Rd | 104 ++--- man/pareto.Rd | 54 +- man/plot_caramel.Rd |only man/plot_pareto.Rd |only man/plot_population.Rd |only man/rselect.Rd | 60 +-- man/val2rank.Rd | 60 +-- man/vol_splx.Rd | 54 +- tests/testthat/Rplots.pdf |binary vignettes/Test_Constraints.Rmd |only 54 files changed, 1931 insertions(+), 1772 deletions(-)
Title: Fast Adaptive Spectral Clustering for Single and Multi-View Data
Description: A self-tuning spectral clustering method for single or multi-view data. 'Spectrum' uses a new type of adaptive density aware kernel that strengthens local connections in the graph. It uses a tensor product graph data integration and diffusion procedure to integrate different data sources and reduce noise. 'Spectrum' uses either the eigengap or multimodality gap heuristics to determine the number of clusters. 'Spectrum' was developed for clustering complex single and multi-omic data. However, the method is sufficiently flexible so that a wide range of Gaussian and non-Gaussian structures can be clustered with automatic selection of K.
Author: Christopher R John, David Watson
Maintainer: Christopher R John <chris.r.john86@gmail.com>
Diff between Spectrum versions 0.5 dated 2019-04-08 and 0.6 dated 2019-05-28
DESCRIPTION | 8 - MD5 | 16 +- R/spectrum.R | 239 ++++++++++++++++++++++++++-------------- build/vignette.rds |binary inst/doc/Spectrum_vignette.R | 30 ++++- inst/doc/Spectrum_vignette.Rmd | 81 +++++++++---- inst/doc/Spectrum_vignette.pdf |binary man/Spectrum.Rd | 12 +- vignettes/Spectrum_vignette.Rmd | 81 +++++++++---- 9 files changed, 317 insertions(+), 150 deletions(-)
Title: FROC Analysis by Bayesian Approaches
Description: Provides new methods for the so-called Free-response Receiver Operating Characteristic (FROC) analysis. The ultimate aim of FROC analysis is to compare observer performances, which means comparing characteristics, such as area under the curve (AUC) or figure of merit (FOM). In this package, we only use the notion of AUC for modality comparison, where by "modality", we mean imaging methods such as Magnetic Resonance Imaging (MRI), Computed Tomography (CT), Positron Emission Tomography (PET),...,etc. So there is a problem that which imaging method is better to detect lesions from shadows in radiographs. To solve modality comparison issues, this package provides new methods using hierarchical Bayesian models proposed by the author of this package. Using this package, one can obtain at least one conclusion that which imaging methods are better for finding lesions in radiographs with the case of your data. Fitting FROC statistical models is sometimes not so good, it can easily confirm by drawing FROC curves and comparing these curves and the points constructed by False Positive fractions (FPFs) and True Positive Fractions (TPFs), we can validate the goodness of fit intuitively. Such validation is also implemented by the Chi square goodness of fit statistics in the Bayesian context which means that the parameter is not deterministic, thus by integrating it with the posterior predictive measure, we get a desired value. To compare modalities (imaging methods: MRI,CT,PET,...,etc), we evaluate AUCs for each modality. FROC is developed by Dev Chakraborty, his FROC model in his 1989 paper relies on the maximal likelihood methodology. The author modified and provided the alternative Bayesian FROC model. Strictly speaking, his model does not coincide with models in this package. In FROC context, we means by multiple reader and multiple case (MRMC) the case of the number of reader or modality is two or more. The MRMC data is available for functions of this package. I hope that medical researchers use not only the frequentist method but also alternative Bayesian methods. In medical research, many problems are considered under only frequentist methods, such as the notion of p-values. But p-value is sometimes misunderstood. Bayesian methods provide very simple, direct, intuitive answer for research questions. Combining frequentist methods with Bayesian methods, we can obtain more reliable answer for research questions. Please execute the following R scripts from the R (R studio) console, demo(demo_MRMC, package = "BayesianFROC"); demo(demo_srsc, package = "BayesianFROC"); demo(demo_stan, package = "BayesianFROC"); demo(demo_drawcurves_srsc, package = "BayesianFROC"); demo_Bayesian_FROC(); demo_Bayesian_FROC_without_pause(). References: Dev Chakraborty (1989) <doi:10.1118/1.596358> Maximum likelihood analysis of free - response receiver operating characteristic (FROC) data. Pre-print: Issei Tsunoda; Bayesian Models for free-response receiver operating characteristic analysis. See the vignettes for more details.
Author: Issei Tsunoda [aut, cre]
Maintainer: Issei Tsunoda <tsunoda.issei1111@gmail.com>
Diff between BayesianFROC versions 0.1.1 dated 2019-05-09 and 0.1.2 dated 2019-05-28
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Title: Estimation of Overlapping in Empirical Distributions
Description: Functions for estimating the overlapping area of two or more kernel density estimations from empirical data.
Author: Massimiliano Pastore
Maintainer: Massimiliano Pastore <massimiliano.pastore@unipd.it>
Diff between overlapping versions 1.5.2 dated 2018-12-20 and 1.5.3 dated 2019-05-28
DESCRIPTION | 9 +++++---- MD5 | 14 ++++++++------ NAMESPACE | 2 +- NEWS | 43 +++++++++++++++++++++++-------------------- R/boot.overlap.R |only man/boot.overlap.Rd |only man/cutnumeric.Rd | 2 +- man/final.plot.Rd | 2 +- man/overlap.Rd | 4 +++- 9 files changed, 42 insertions(+), 34 deletions(-)
Title: Nested and Crossed Block Designs for Factorial, Fractional
Factorial and Unstructured Treatment Sets
Description: Constructs D-optimal or near D-optimal nested and crossed
block designs for unstructured or general factorial treatment designs.
The treatment design, if required, is found from a model
matrix design formula and can be added sequentially, if required.
The block design is found from a defined
set of block factors and is conditional on the defined treatment design.
The block factors are added in sequence and each added block factor
is optimized conditional on all previously added block factors.
The block design can have repeated nesting down to any required
depth of nesting with either simple nested blocks or a
crossed blocks design at each level of nesting. Outputs include a table
showing the allocation of treatments to blocks and tables showing
the achieved D-efficiency factors for each block and treatment design.
Author: R. N. Edmondson.
Maintainer: Rodney Edmondson <rodney.edmondson@gmail.com>
Diff between blocksdesign versions 3.4 dated 2019-02-20 and 3.5 dated 2019-05-28
DESCRIPTION | 8 MD5 | 8 R/blocks.r | 20 R/design.r | 1332 ++++++++++++++++++++++++++--------------------------- build/vignette.rds |binary 5 files changed, 692 insertions(+), 676 deletions(-)
Title: Encoding of Sequences Based on Frequency Matrix Chaos Game
Representation
Description: Sequences encoding by using the chaos game representation.
Löchel et al. (2019) <doi:10.1101/575324>.
Author: Dominik Eger and Hannah Franziska Löchel
Maintainer: Hannah Franziska Löchel <loechelh@mathematik.uni-marburg.de>
Diff between kaos versions 0.1.0 dated 2019-03-13 and 0.1.1 dated 2019-05-28
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/cgr.R | 4 ---- 3 files changed, 5 insertions(+), 9 deletions(-)
Title: Confirmatory Adaptive Clinical Trial Design and Analysis
Description: Design and analysis of confirmatory adaptive clinical trials with continuous, binary, and survival endpoints according to the methods described in the monograph by Wassmer and Brannath (2016) <doi:10.1007/978-3-319-32562-0>. This includes classical group sequential as well as multi-stage adaptive hypotheses tests that are based on the combination testing principle.
Author: Gernot Wassmer [aut],
Friedrich Pahlke [aut, cre]
Maintainer: Friedrich Pahlke <friedrich.pahlke@rpact.com>
Diff between rpact versions 1.0.0 dated 2018-10-30 and 2.0.0 dated 2019-05-28
rpact-1.0.0/rpact/man/AnalysisResults_plot.Rd |only rpact-1.0.0/rpact/man/Dataset_plot.Rd |only rpact-1.0.0/rpact/man/StageResults_plot.Rd |only rpact-1.0.0/rpact/man/StageResults_print.Rd |only rpact-1.0.0/rpact/man/StageResults_summary.Rd |only rpact-1.0.0/rpact/man/TrialDesignPlan_print.Rd |only rpact-1.0.0/rpact/man/TrialDesignSet_plot.Rd |only rpact-1.0.0/rpact/man/TrialDesignSet_print.Rd |only rpact-1.0.0/rpact/man/TrialDesign_plot.Rd |only rpact-1.0.0/rpact/man/TrialDesign_summary.Rd |only rpact-1.0.0/rpact/man/rpact-package.Rd |only rpact-1.0.0/rpact/src/rpact_init.c |only rpact-2.0.0/rpact/DESCRIPTION | 37 rpact-2.0.0/rpact/MD5 | 206 rpact-2.0.0/rpact/NAMESPACE | 41 rpact-2.0.0/rpact/NEWS.md | 31 rpact-2.0.0/rpact/R/RcppExports.R |only rpact-2.0.0/rpact/R/class_analysis_dataset.R | 97 rpact-2.0.0/rpact/R/class_analysis_results.R | 77 rpact-2.0.0/rpact/R/class_analysis_stage_results.R | 100 rpact-2.0.0/rpact/R/class_core_parameter_set.R | 448 rpact-2.0.0/rpact/R/class_core_plot_settings.R | 56 rpact-2.0.0/rpact/R/class_design.R | 269 rpact-2.0.0/rpact/R/class_design_plan.R | 1698 ++- rpact-2.0.0/rpact/R/class_design_power_and_asn.R | 72 rpact-2.0.0/rpact/R/class_design_set.R | 517 - rpact-2.0.0/rpact/R/class_event_probabilities.R |only rpact-2.0.0/rpact/R/class_simulation_results.R |only rpact-2.0.0/rpact/R/class_time.R |only rpact-2.0.0/rpact/R/f_analysis.R | 265 rpact-2.0.0/rpact/R/f_analysis_means.R | 72 rpact-2.0.0/rpact/R/f_analysis_rates.R | 92 rpact-2.0.0/rpact/R/f_analysis_survival.R | 113 rpact-2.0.0/rpact/R/f_core_assertions.R | 546 + rpact-2.0.0/rpact/R/f_core_constants.R | 535 - rpact-2.0.0/rpact/R/f_core_output_formats.R | 97 rpact-2.0.0/rpact/R/f_core_plot.R |only rpact-2.0.0/rpact/R/f_core_utilities.R | 473 - rpact-2.0.0/rpact/R/f_design_fisher_combination_test.R | 31 rpact-2.0.0/rpact/R/f_design_group_sequential.R | 311 rpact-2.0.0/rpact/R/f_design_sample_size_calculator.R | 4613 ++++++++-- rpact-2.0.0/rpact/R/f_design_utilities.R |only rpact-2.0.0/rpact/R/f_simulation_means.R |only rpact-2.0.0/rpact/R/f_simulation_rates.R |only rpact-2.0.0/rpact/R/f_simulation_survival.R |only rpact-2.0.0/rpact/R/pkgname.R | 40 rpact-2.0.0/rpact/inst |only rpact-2.0.0/rpact/man/AccrualTime.Rd |only rpact-2.0.0/rpact/man/EventProbabilities.Rd |only rpact-2.0.0/rpact/man/FrameSet_as.matrix.Rd |only rpact-2.0.0/rpact/man/NumberOfSubjects.Rd |only rpact-2.0.0/rpact/man/ParameterSet_as.data.frame.Rd | 5 rpact-2.0.0/rpact/man/ParameterSet_print.Rd | 8 rpact-2.0.0/rpact/man/PiecewiseSurvivalTime.Rd |only rpact-2.0.0/rpact/man/PowerAndAverageSampleNumberResult_as.data.frame.Rd | 4 rpact-2.0.0/rpact/man/SimulationResults.Rd |only rpact-2.0.0/rpact/man/SimulationResultsMeans.Rd |only rpact-2.0.0/rpact/man/SimulationResultsRates.Rd |only rpact-2.0.0/rpact/man/SimulationResultsSurvival.Rd |only rpact-2.0.0/rpact/man/StageResults_as.data.frame.Rd | 6 rpact-2.0.0/rpact/man/TrialDesignGroupSequential.Rd | 5 rpact-2.0.0/rpact/man/TrialDesignPlanMeans.Rd | 5 rpact-2.0.0/rpact/man/TrialDesignPlanRates.Rd | 5 rpact-2.0.0/rpact/man/TrialDesignPlanSurvival.Rd | 5 rpact-2.0.0/rpact/man/TrialDesignPlanSurvival_summary.Rd |only rpact-2.0.0/rpact/man/TrialDesign_as.data.frame.Rd | 5 rpact-2.0.0/rpact/man/getAccrualTime.Rd |only rpact-2.0.0/rpact/man/getAnalysisResults.Rd | 38 rpact-2.0.0/rpact/man/getAvailablePlotTypes.Rd |only rpact-2.0.0/rpact/man/getConditionalPower.Rd | 4 rpact-2.0.0/rpact/man/getData.Rd |only rpact-2.0.0/rpact/man/getDesignFisher.Rd | 6 rpact-2.0.0/rpact/man/getDesignGroupSequential.Rd | 104 rpact-2.0.0/rpact/man/getDesignInverseNormal.Rd | 100 rpact-2.0.0/rpact/man/getEventProbabilities.Rd |only rpact-2.0.0/rpact/man/getFinalConfidenceInterval.Rd | 2 rpact-2.0.0/rpact/man/getLogLevel.Rd |only rpact-2.0.0/rpact/man/getNumberOfSubjects.Rd |only rpact-2.0.0/rpact/man/getPiecewiseSurvivalTime.Rd |only rpact-2.0.0/rpact/man/getPowerAndAverageSampleNumber.Rd | 19 rpact-2.0.0/rpact/man/getPowerMeans.Rd |only rpact-2.0.0/rpact/man/getPowerRates.Rd |only rpact-2.0.0/rpact/man/getPowerSurvival.Rd |only rpact-2.0.0/rpact/man/getRawData.Rd |only rpact-2.0.0/rpact/man/getSampleSizeMeans.Rd | 53 rpact-2.0.0/rpact/man/getSampleSizeRates.Rd | 62 rpact-2.0.0/rpact/man/getSampleSizeSurvival.Rd | 265 rpact-2.0.0/rpact/man/getSimulationMeans.Rd |only rpact-2.0.0/rpact/man/getSimulationRates.Rd |only rpact-2.0.0/rpact/man/getSimulationSurvival.Rd |only rpact-2.0.0/rpact/man/getStageResults.Rd | 25 rpact-2.0.0/rpact/man/plot.AnalysisResults.Rd |only rpact-2.0.0/rpact/man/plot.Dataset.Rd |only rpact-2.0.0/rpact/man/plot.SimulationResults.Rd |only rpact-2.0.0/rpact/man/plot.StageResults.Rd |only rpact-2.0.0/rpact/man/plot.TrialDesign.Rd |only rpact-2.0.0/rpact/man/plot.TrialDesignPlan.Rd |only rpact-2.0.0/rpact/man/plot.TrialDesignSet.Rd |only rpact-2.0.0/rpact/man/readDataset.Rd | 5 rpact-2.0.0/rpact/man/readDatasets.Rd | 7 rpact-2.0.0/rpact/man/resetLogLevel.Rd |only rpact-2.0.0/rpact/man/rpact.Rd |only rpact-2.0.0/rpact/man/setLogLevel.Rd |only rpact-2.0.0/rpact/man/testPackage.Rd |only rpact-2.0.0/rpact/man/utilitiesForPiecewiseExponentialDistribution.Rd |only rpact-2.0.0/rpact/man/utilitiesForSurvivalTrials.Rd |only rpact-2.0.0/rpact/man/writeDataset.Rd | 12 rpact-2.0.0/rpact/man/writeDatasets.Rd | 4 rpact-2.0.0/rpact/src/RcppExports.cpp |only rpact-2.0.0/rpact/src/f_simulation_survival.cpp |only rpact-2.0.0/rpact/src/rpact.c | 1 rpact-2.0.0/rpact/tests |only 112 files changed, 8491 insertions(+), 3101 deletions(-)
Title: Record Linkage in R
Description: Provides functions for linking and de-duplicating data sets.
Methods based on a stochastic approach are implemented as well as
classification algorithms from the machine learning domain.
Author: Andreas Borg <andreas.borg.public@posteo.de>, Murat Sariyar <murat.sariyar@charite.de>
Maintainer: ORPHANED
Diff between RecordLinkage versions 0.4-11 dated 2019-03-14 and 0.4-11.1 dated 2019-05-28
DESCRIPTION | 12 ++++++++---- MD5 | 14 +++++++------- build/vignette.rds |binary inst/doc/BigData.pdf |binary inst/doc/EVT.pdf |binary inst/doc/Supervised.pdf |binary inst/doc/WeightBased.pdf |binary src/phonet.c | 4 ++-- 8 files changed, 17 insertions(+), 13 deletions(-)
Title: Functions for Clustering of Presence-Absence, Abundance and
Multilocus Genetic Data
Description: Distance-based parametric bootstrap tests for clustering with
spatial neighborhood information. Some distance measures,
Clustering of presence-absence, abundance and multilocus genetical data
for species delimitation, nearest neighbor
based noise detection. Try package?prabclus for on overview.
Author: Christian Hennig <christian.hennig@unibo.it>,
Bernhard Hausdorf <Hausdorf@zoologie.uni-hamburg.de>
Maintainer: ORPHANED
Diff between prabclus versions 2.2-7 dated 2019-01-17 and 2.2-7.1 dated 2019-05-28
DESCRIPTION | 14 +++++++++----- MD5 | 14 +++++++------- R/abundfunctions.R | 5 +---- man/abundtest.Rd | 12 ++++++------ man/prab.sarestimate.Rd | 20 ++++++++++---------- man/regpop.sar.Rd | 6 +++--- tests/Examples/prabclus-Ex.Rout.save | 18 +++++++++--------- tests/prabclustests.Rout.save | 14 ++++++++------ 8 files changed, 53 insertions(+), 50 deletions(-)
Title: Coloured Formatting for Columns
Description: Provides 'pillar' and 'colonnade' generics designed for formatting columns
of data using the full range of colours provided by modern terminals.
Author: Kirill Müller [aut, cre],
Hadley Wickham [aut],
RStudio [cph]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>
Diff between pillar versions 1.4.0 dated 2019-05-11 and 1.4.1 dated 2019-05-28
DESCRIPTION | 15 +++++++-------- MD5 | 13 +++++++------ NAMESPACE | 4 ++++ NEWS.md | 8 ++++++++ R/type-sum.R | 4 +++- R/vctrs.R |only R/zzz.R | 4 +--- build/pillar.pdf |binary 8 files changed, 30 insertions(+), 18 deletions(-)
Title: The Moving Epidemic Method
Description: The Moving Epidemic Method, created by T Vega and JE Lozano (2012, 2015) <doi:10.1111/j.1750-2659.2012.00422.x>, <doi:10.1111/irv.12330>, allows the weekly assessment of the epidemic and intensity status to help in routine respiratory infections surveillance in health systems. Allows the comparison of different epidemic indicators, timing and shape with past epidemics and across different regions or countries with different surveillance systems. Also, it gives a measure of the performance of the method in terms of sensitivity and specificity of the alert week.
Author: Jose E. Lozano [aut, cre]
Maintainer: Jose E. Lozano <lozalojo@gmail.com>
Diff between mem versions 2.14 dated 2018-11-08 and 2.15 dated 2019-05-28
DESCRIPTION | 10 MD5 | 124 ++--- NAMESPACE | 3 R/calcular.indicadores.2.timings.R | 454 ++++++++++-------- R/calcular.indicadores.R | 653 +++++++++++++------------- R/calcular.map.R | 30 - R/calcular.optimo.R | 23 R/calcular.optimo.criterio.R | 42 - R/calcular.optimo.derivada.R | 40 - R/calcular.optimo.original.R | 30 - R/calcular.optimo.pendiente.R | 26 - R/comparar.metodos.R | 31 - R/epimem.R | 20 R/extraer.datos.curva.map.R | 16 R/extraer.datos.epi.R | 16 R/extraer.datos.optimo.map.R | 16 R/extraer.datos.post.epi.R | 16 R/extraer.datos.pre.epi.R | 16 R/full.series.graph.R | 409 ++++++++-------- R/memevolution.R | 145 +++-- R/memgoodness.R | 110 +++- R/memintensity.R | 5 R/memmodel.R | 839 ++++++++++++++++------------------ R/memstability.R | 68 +- R/memsurveillance.R | 622 ++++++++++++------------- R/memsurveillance.animated.R | 125 ++--- R/memtiming.R | 245 ++++----- R/memtrend.R | 82 +-- R/min.fix.na.R | 12 R/optimal.tickmarks.R | 40 - R/optimum.by.inspection.R | 217 ++++---- R/output.ci.R | 2 R/processPlots.R | 525 +++++++++++---------- R/roc.analysis.R | 33 - R/transformdata.R | 93 +-- R/transformdata.back.R | 125 ++--- R/transformseries.R | 78 +-- R/transformseries.loess.R | 25 - R/transformseries.multiple.R | 141 +++-- R/transformseries.odd.R | 16 R/transformseries.spline.R |only R/transformseries.twowaves.R | 18 man/calcular.indicadores.2.timings.Rd | 5 man/calcular.indicadores.Rd | 2 man/full.series.graph.Rd | 5 man/memevolution.Rd | 3 man/memgoodness.Rd | 25 - man/memintensity.Rd | 5 man/memmodel.Rd | 9 man/memstability.Rd | 3 man/memsurveillance.Rd | 43 + man/memsurveillance.animated.Rd | 17 man/memtiming.Rd | 8 man/memtrend.Rd | 5 man/optimum.by.inspection.Rd | 4 man/processPlots.Rd | 3 man/roc.analysis.Rd | 12 man/transformdata.Rd | 5 man/transformdata.back.Rd | 5 man/transformseries.Rd | 6 man/transformseries.loess.Rd | 2 man/transformseries.multiple.Rd | 2 man/transformseries.spline.Rd |only man/transformseries.twowaves.Rd | 2 64 files changed, 3016 insertions(+), 2696 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-04-21 0.3
Title: S3 Infrastructure for Regular and Irregular Time Series (Z's
Ordered Observations)
Description: An S3 class with methods for totally ordered indexed
observations. It is particularly aimed at irregular time series
of numeric vectors/matrices and factors. zoo's key design goals
are independence of a particular index/date/time class and
consistency with ts and base R by providing methods to extend
standard generics.
Author: Achim Zeileis [aut, cre] (<https://orcid.org/0000-0003-0918-3766>),
Gabor Grothendieck [aut],
Jeffrey A. Ryan [aut],
Joshua M. Ulrich [ctb],
Felix Andrews [ctb]
Maintainer: Achim Zeileis <Achim.Zeileis@R-project.org>
Diff between zoo versions 1.8-5 dated 2019-03-21 and 1.8-6 dated 2019-05-28
DESCRIPTION | 8 ++-- MD5 | 44 ++++++++++++------------- NEWS | 11 ++++++ R/zoo.R | 6 +-- build/vignette.rds |binary inst/doc/zoo-design.pdf |binary inst/doc/zoo-faq.pdf |binary inst/doc/zoo-quickref.pdf |binary inst/doc/zoo-read.pdf |binary inst/doc/zoo.pdf |binary man/aggregate.zoo.Rd | 1 man/as.zoo.Rd | 3 + man/coredata.Rd | 3 + man/ggplot2.zoo.Rd | 3 + man/index.Rd | 3 + man/is.regular.Rd | 3 + man/rollapply.Rd | 3 + man/rollmean.Rd | 3 + man/window.zoo.Rd | 3 + man/yearmon.Rd | 5 ++ man/yearqtr.Rd | 5 ++ man/zoo.Rd | 3 + tests/Examples/zoo-Ex.Rout.save | 68 ++++++++++++++++++++++++++++------------ 23 files changed, 127 insertions(+), 48 deletions(-)
Title: Log Rotation and Conditional Backups
Description: Conditionally rotate or back-up files based on
their size or the date of the last backup; inspired by the 'Linux'
utility 'logrotate'.
Author: Stefan Fleck [aut, cre] (<https://orcid.org/0000-0003-3344-9851>)
Maintainer: Stefan Fleck <stefan.b.fleck@gmail.com>
Diff between rotor versions 0.2.1 dated 2019-05-16 and 0.2.2 dated 2019-05-28
rotor-0.2.1/rotor/R/BackupQueueDate.R |only rotor-0.2.1/rotor/R/BackupQueueDateTime.R |only rotor-0.2.1/rotor/R/BackupQueueIndex.R |only rotor-0.2.1/rotor/R/parse_datetime.R |only rotor-0.2.1/rotor/tests/testthat/test_BackupQueueDate.R |only rotor-0.2.1/rotor/tests/testthat/test_BackupQueueDateTime.R |only rotor-0.2.1/rotor/tests/testthat/test_BackupQueueIndex.R |only rotor-0.2.2/rotor/DESCRIPTION | 15 rotor-0.2.2/rotor/MD5 | 54 rotor-0.2.2/rotor/NEWS.md | 14 rotor-0.2.2/rotor/R/BackupQueue.R | 651 +++++++ rotor-0.2.2/rotor/R/DryRunMemory.R | 2 rotor-0.2.2/rotor/R/list_backups.R | 49 rotor-0.2.2/rotor/R/parsers.R |only rotor-0.2.2/rotor/R/rotate.R | 108 - rotor-0.2.2/rotor/R/rotate_date.R | 54 rotor-0.2.2/rotor/R/rotate_time.R | 58 rotor-0.2.2/rotor/R/utils-fs.R | 22 rotor-0.2.2/rotor/R/utils-predicates.R | 101 + rotor-0.2.2/rotor/R/utils-rd.R |only rotor-0.2.2/rotor/R/utils.R | 72 rotor-0.2.2/rotor/README.md | 73 rotor-0.2.2/rotor/inst/WORDLIST | 7 rotor-0.2.2/rotor/inst/benchmarks |only rotor-0.2.2/rotor/man/BackupQueue.Rd | 133 + rotor-0.2.2/rotor/man/rotate.Rd | 60 rotor-0.2.2/rotor/man/rotor-package.Rd | 5 rotor-0.2.2/rotor/tests/testthat/test_BackupQueue.R | 985 +++++++++++- rotor-0.2.2/rotor/tests/testthat/test_parsers.R |only rotor-0.2.2/rotor/tests/testthat/test_rotate.R | 16 rotor-0.2.2/rotor/tests/testthat/test_rotate_date.R | 171 -- rotor-0.2.2/rotor/tests/testthat/test_rotate_time.R | 16 rotor-0.2.2/rotor/tests/testthat/test_utils-predicates.R | 161 + 33 files changed, 2250 insertions(+), 577 deletions(-)
Title: A Universal Non-Uniform Random Number Generator
Description: A universal non-uniform random number generator
for quite arbitrary distributions with piecewise twice
differentiable densities.
Author: Josef Leydold, Carsten Botts and Wolfgang H\"ormann
Maintainer: Josef Leydold <josef.leydold@wu.ac.at>
Diff between Tinflex versions 1.4 dated 2019-05-09 and 1.5 dated 2019-05-28
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS | 6 ++++++ R/hat.R | 28 +++++++++++++++++++++++----- man/Tinflex-package.Rd | 4 ++-- 5 files changed, 39 insertions(+), 15 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-07-20 1.15.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-06-05 3.0.0
2018-03-03 2.0.0
Title: Encoding of Nucleotide Sequences into Numeric Feature Vectors
Description: We describe fifteen different splice site sequence encoding schemes that have been used in earlier studies for mapping of splice site sequences into numeric feature vectors. These encoding schemes will also be helpful for transforming other nucleotide sequences into numeric forms, provided they are of equal length. These encoding schemes will help the computational biologist working in the field of classification (binary or multiclass) or prediction involving nucleic acid sequences of equal length.
Author: Prabina Kumar Meher
Maintainer: Prabina Kumar Meher <meherprabin@yahoo.com>
Diff between EncDNA versions 1.0.1 dated 2018-10-01 and 1.0.2 dated 2019-05-28
DESCRIPTION | 9 +++++---- MD5 | 4 ++-- data/droso.rda |binary 3 files changed, 7 insertions(+), 6 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-08-20 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-05-13 1.0.0
Title: Tools for Units of Measurement
Description: Collection of tools to make working with physical measurements
easier. Convert between metric and imperial units, or calculate a dimension's
unknown value from other dimensions' measurements.
Author: Matthew A. Birk
Maintainer: Matthew A. Birk <matthewabirk@gmail.com>
Diff between measurements versions 1.3.0 dated 2018-12-09 and 1.4.0 dated 2019-05-28
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NEWS | 5 +++++ R/conv_unit.R | 37 +++++++++++++++++++++++++++++++++++-- man/conv_unit.Rd | 1 + 5 files changed, 50 insertions(+), 11 deletions(-)
Title: Dependencies for the 'jamovi' Framework
Description: A framework for creating rich interactive analyses for the jamovi
platform (see <https://www.jamovi.org> for more information).
Author: Jonathon Love
Maintainer: Jonathon Love <jon@thon.cc>
Diff between jmvcore versions 0.9.6.4 dated 2019-03-28 and 1.0.0 dated 2019-05-28
DESCRIPTION | 8 +-- MD5 | 24 +++++----- NAMESPACE | 1 R/analysis.R | 10 +++- R/column.R | 2 R/html.R | 12 ++++- R/options.R | 7 ++ R/preformatted.R | 2 R/utils.R | 104 ++++++++++++++++++++++++++++++++++++++------ inst/jamovi.proto | 2 man/Options.Rd | 3 + man/stringifyTerm.Rd | 5 +- tests/testthat/test-utils.R | 18 +++++++ 13 files changed, 163 insertions(+), 35 deletions(-)