Title: A Tool Set for Analyzing Political Behavior Data
Description: Provides functions for analyzing political behavior data, including measures of political fragmentation, seat apportionment, and graphical demonstrations.
Author: Daniel Marcelino [aut, cre]
Maintainer: Daniel Marcelino <dmarcelino@live.com>
Diff between SciencesPo versions 1.3.8 dated 2015-10-19 and 1.3.9 dated 2016-01-22
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Title: Regression Analysis of Sparse Asynchronous Longitudinal Data
Description: Estimation of regression models for sparse asynchronous longitudinal observations, where time-dependent response and covariates are mismatched and observed intermittently within subjects. Kernel weighted estimating equations are used for generalized linear models with either time-invariant or time-dependent coefficients.
Author: Hongyuan Cao, Donglin Zeng, Jialiang Li, Jason P. Fine, and Shannon T. Holloway
Maintainer: Shannon T. Holloway <sthollow@ncsu.edu>
Diff between AsynchLong versions 1.0 dated 2015-02-22 and 2.0 dated 2016-01-22
DESCRIPTION | 12 +-- MD5 | 51 ++++++++------- NAMESPACE | 11 ++- R/SD.R | 102 +++++++++++++++---------------- R/asynchHK.R |only R/asynchLV.R | 47 +++++++------- R/asynchTD.R | 75 +++++++++++++---------- R/asynchTI.R | 72 +++++++++++----------- R/asynchWLV.R |only R/betaHat.R | 132 ++++++++++++++++++++--------------------- R/distances.R | 141 +++++++++++++++++++++++++++++++++++++++---- R/duFunc.R | 80 ++++++++++++------------ R/kernelAuto.R | 148 +++++++++++++++++++++++++++------------------- R/kernelFixed.R | 66 +++++++++++++++++++- R/optFunc.R | 112 ++++++++++++++++++---------------- R/plotTD.R | 46 +++++++------- R/preprocessX.R | 56 +++++++++-------- R/preprocessY.R | 31 +++++---- R/uFunc.R | 61 +++++++++--------- R/uFuncIden.R | 54 ++++++++-------- R/zzz.R |only man/AsynchLong-package.Rd | 12 ++- man/asynchDataTD.Rd | 2 man/asynchDataTI.Rd | 2 man/asynchHK.Rd |only man/asynchLV.Rd | 2 man/asynchTD.Rd | 2 man/asynchTI.Rd | 5 - man/asynchWLV.Rd |only 29 files changed, 787 insertions(+), 535 deletions(-)
Title: Evaluation of Surrogate Endpoints in Clinical Trials
Description: In a clinical trial, it frequently occurs that the most credible outcome to evaluate the effectiveness of a new therapy (the true endpoint) is difficult to measure. In such a situation, it can be an effective strategy to replace the true endpoint by a biomarker that is easier to measure and that allows for a prediction of the treatment effect on the true endpoint (a surrogate endpoint). The package 'Surrogate' allows for an evaluation of the appropriateness of a candidate surrogate endpoint based on the meta-analytic, information-theoretic, and causal-inference frameworks. Part of this software has been developed using funding provided from the European Union's 7th Framework Programme for research, technological development and demonstration under Grant Agreement no 602552.
Author: Wim Van der Elst, Paul Meyvisch, Ariel Alonso & Geert Molenberghs
Maintainer: Wim Van der Elst <Wim.vanderelst@gmail.com>
Diff between Surrogate versions 0.1-64 dated 2015-11-21 and 0.1-66 dated 2016-01-22
DESCRIPTION | 10 MD5 | 30 + NAMESPACE | 10 NEWS | 13 R/ICA.BinBin.Grid.Sample.R | 781 +++++++++++++++++++++++++++++++++++++++++- R/MaxEntICABinBin.R |only R/MaxEntSPFBinBin.R |only R/SummaryMaxEntSPFBinBin.R |only R/plot.MaxEntSPF.BinBin.R |only R/plot_MaxEntICABinBin.R |only R/plot_SPPBinBin.R | 1 R/summary_MaxEntICABinBin.R |only man/ICA.BinBin.Grid.Full.Rd | 2 man/ICA.BinBin.Grid.Sample.Rd | 14 man/ICABinBin.Rd | 4 man/MaxEntICABinBin.Rd |only man/MaxEntSPFBinBin.Rd |only man/SPP.BinBin.Rd | 19 - man/plot.MaxEntICABinBin.Rd |only man/plot.MaxEntSPFBinBin.Rd |only man/summary.gen.Rd | 4 21 files changed, 849 insertions(+), 39 deletions(-)
Title: Interface to Species Occurrence Data Sources
Description: A programmatic interface to many species occurrence data sources,
including 'GBIF', 'USGS's' 'BISON', 'iNaturalist', Berkeley 'Ecoinformatics'
Engine 'eBird', 'AntWeb', and 'iDigBio'. Includes functionality for
retrieving species occurrence data, and combining that data.
Author: Scott Chamberlain [aut, cre],
Karthik Ram [aut],
Ted Hart [aut]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between spocc versions 0.4.0 dated 2015-10-02 and 0.4.4 dated 2016-01-22
DESCRIPTION | 31 ++++++-------- LICENSE | 2 MD5 | 85 ++++++++++++++++++++------------------ NAMESPACE | 9 ++-- R/antweb_helpers.R |only R/as.ecoengine.R | 2 R/ecoengine_helpers.R |only R/occ.r | 4 - R/occ2df.R | 17 +------ R/occ_names.R | 80 ++++++++++++++++++------------------ R/occ_names_options.R | 1 R/plugin_helpers.R |only R/plugins.r | 94 +++++-------------------------------------- R/spocc-package.R | 40 ++++++++++++++++-- R/zzz.r | 19 ++++++++ README.md | 79 +++++++++++++++++++----------------- build/vignette.rds |binary inst/doc/spocc_vignette.Rmd | 5 +- inst/doc/spocc_vignette.html | 4 + man/as.antweb.Rd | 6 +- man/as.bison.Rd | 10 ++-- man/as.ecoengine.Rd | 2 man/as.gbif.Rd | 10 ++-- man/as.idigbio.Rd | 4 - man/as.inat.Rd | 2 man/as.vertnet.Rd | 2 man/bbox2wkt.Rd | 2 man/fixnames.Rd | 6 +- man/inspect.Rd | 4 - man/occ.Rd | 20 +++++---- man/occ2df.Rd | 2 man/occ_coverage.Rd | 2 man/occ_names.Rd | 4 - man/occ_names_options.Rd | 2 man/occ_options.Rd | 2 man/spocc-package.Rd | 48 ++++++++++++++++++++- man/spocc_capwords.Rd | 4 - man/spocc_colClasses.Rd | 4 - man/spocc_duplicates.Rd | 20 ++++----- man/spocc_objects.Rd | 6 +- man/spocc_type_sum.Rd | 2 man/wkt.Rd | 2 man/wkt_vis.Rd | 6 +- tests/testthat/test-occ.R | 57 ++++++++++++++++---------- vignettes/spocc_vignette.Rmd | 5 +- 45 files changed, 377 insertions(+), 329 deletions(-)
Title: Statistical Inference for MOdular NEtworks (SIMoNe)
Description: Implements the inference of
co-expression networks based on partial correlation
coefficients from either steady-state or time-course
transcriptomic data. Note that with both type of data this
package can deal with samples collected in different
experimental conditions and therefore not identically
distributed. In this particular case, multiple but related
networks are inferred on one simone run.
Author: Julien Chiquet <julien.chiquet@genopole.cnrs.fr>, Gilles
Grasseau <gilles.grasseau@genopole.cnrs.fr>, Camille
Charbonnier <camille.charbonnier@genopole.cnrs.fr>, Christophe
Ambroise <christophe.ambroise@genopole.cnrs.fr>.
Maintainer: Julien Chiquet <julien.chiquet@genopole.cnrs.fr>
Diff between simone versions 1.0-2 dated 2013-12-16 and 1.0-3 dated 2016-01-22
DESCRIPTION | 33 +++++++++++++++++---------------- MD5 | 12 ++++++------ NAMESPACE | 3 +++ NEWS | 3 +++ R/init.R | 4 ++-- inst/CITATION | 18 +++++++++--------- man/simone.Rd | 2 ++ 7 files changed, 42 insertions(+), 33 deletions(-)
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 1.7.0-0 dated 2015-10-31 and 1.7.1-0 dated 2016-01-22
RViennaCL-1.7.0-0/RViennaCL/inst/NEW.Rd |only RViennaCL-1.7.0-0/RViennaCL/inst/include/viennacl/device_specific/builtin_database/matrix_axpy.hpp |only RViennaCL-1.7.0-0/RViennaCL/inst/include/viennacl/device_specific/builtin_database/reduction.hpp |only RViennaCL-1.7.0-0/RViennaCL/inst/include/viennacl/device_specific/builtin_database/row_wise_reduction.hpp |only RViennaCL-1.7.0-0/RViennaCL/inst/include/viennacl/device_specific/builtin_database/vector_axpy.hpp |only RViennaCL-1.7.0-0/RViennaCL/inst/include/viennacl/device_specific/templates/matrix_axpy_template.hpp |only RViennaCL-1.7.0-0/RViennaCL/inst/include/viennacl/device_specific/templates/reduction_template.hpp |only RViennaCL-1.7.0-0/RViennaCL/inst/include/viennacl/device_specific/templates/row_wise_reduction_template.hpp |only RViennaCL-1.7.0-0/RViennaCL/inst/include/viennacl/device_specific/templates/vector_axpy_template.hpp |only RViennaCL-1.7.1-0/RViennaCL/DESCRIPTION | 9 RViennaCL-1.7.1-0/RViennaCL/MD5 | 516 ++-- RViennaCL-1.7.1-0/RViennaCL/README.md | 2 RViennaCL-1.7.1-0/RViennaCL/build/partial.rdb |binary RViennaCL-1.7.1-0/RViennaCL/inst/NEWS.Rd |only RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/backend/cpu_ram.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/backend/cuda.hpp | 9 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/backend/mem_handle.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/backend/memory.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/backend/opencl.hpp | 9 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/backend/util.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/circulant_matrix.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/compressed_compressed_matrix.hpp | 39 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/compressed_matrix.hpp | 46 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/context.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/coordinate_matrix.hpp | 55 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/detail/matrix_def.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/detail/vector_def.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/device_specific/builtin_database/common.hpp | 56 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/device_specific/builtin_database/devices/accelerator/fallback.hpp | 56 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/device_specific/builtin_database/devices/cpu/fallback.hpp | 56 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/device_specific/builtin_database/devices/gpu/amd/ev/cedar.hpp | 35 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/device_specific/builtin_database/devices/gpu/amd/ev/cypress.hpp | 59 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/device_specific/builtin_database/devices/gpu/amd/ni/barts.hpp | 35 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/device_specific/builtin_database/devices/gpu/amd/ni/devastator.hpp | 35 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/device_specific/builtin_database/devices/gpu/amd/ni/scrapper.hpp | 35 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/device_specific/builtin_database/devices/gpu/amd/si/tahiti.hpp | 60 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/device_specific/builtin_database/devices/gpu/amd/vi/hawaii.hpp | 60 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/device_specific/builtin_database/devices/gpu/fallback.hpp | 56 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/device_specific/builtin_database/devices/gpu/nv/f/ge_gt_540m.hpp | 48 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/device_specific/builtin_database/devices/gpu/nv/f/ge_gtx_470.hpp | 61 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/device_specific/builtin_database/devices/gpu/nv/f/ge_gtx_580.hpp | 60 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/device_specific/builtin_database/devices/gpu/nv/f/tesla_c2050.hpp | 60 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/device_specific/builtin_database/devices/gpu/nv/k/tesla_k20m.hpp | 76 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/device_specific/builtin_database/devices/gpu/nv/m/ge_gtx_750_ti.hpp | 59 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/device_specific/builtin_database/devices/gpu/nv/tesla/ge_gtx_260.hpp | 60 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/device_specific/builtin_database/matrix_product.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/device_specific/execute.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/device_specific/execution_handler.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/device_specific/forwards.h | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/device_specific/lazy_program_compiler.hpp | 7 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/device_specific/mapped_objects.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/device_specific/templates/matrix_product_template.hpp | 46 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/device_specific/templates/template_base.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/device_specific/templates/utils.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/device_specific/tree_parsing.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/device_specific/utils.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/ell_matrix.hpp | 54 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/fft.hpp | 7 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/forwards.h | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/hankel_matrix.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/hyb_matrix.hpp | 52 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/io/matrix_market.hpp | 37 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/amg.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/amg_operations.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/bicgstab.hpp | 7 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/bisect.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/bisect_gpu.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/cg.hpp | 5 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/circulant_matrix_operations.hpp | 5 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/cuda/amg_operations.hpp | 5 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/cuda/bisect_kernel_calls.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/cuda/bisect_kernel_large.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/cuda/bisect_kernel_large_multi.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/cuda/bisect_kernel_large_onei.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/cuda/bisect_kernel_small.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/cuda/bisect_util.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/cuda/common.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/cuda/direct_solve.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/cuda/fft_operations.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/cuda/ilu_operations.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/cuda/iterative_operations.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/cuda/matrix_operations.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/cuda/matrix_operations_col.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/cuda/matrix_operations_prod.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/cuda/matrix_operations_row.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/cuda/misc_operations.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/cuda/nmf_operations.hpp | 5 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/cuda/scalar_operations.hpp | 5 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/cuda/sparse_matrix_operations.hpp | 436 ++- RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/cuda/sparse_matrix_operations_solve.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/cuda/spgemm.hpp | 23 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/cuda/spgemm_rmerge.hpp | 7 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/cuda/vector_operations.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/detail/amg/amg_base.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/detail/bisect/bisect_kernel_calls.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/detail/bisect/bisect_large.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/detail/bisect/bisect_small.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/detail/bisect/config.hpp | 2 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/detail/bisect/gerschgorin.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/detail/bisect/structs.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/detail/bisect/util.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/detail/ilu/block_ilu.hpp | 19 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/detail/ilu/chow_patel_ilu.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/detail/ilu/common.hpp | 19 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/detail/ilu/ilu0.hpp | 15 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/detail/ilu/ilut.hpp | 15 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/detail/op_applier.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/detail/op_executor.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/detail/spai/block_matrix.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/detail/spai/block_vector.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/detail/spai/fspai.hpp | 33 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/detail/spai/qr.hpp | 9 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/detail/spai/small_matrix.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/detail/spai/spai-dynamic.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/detail/spai/spai-static.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/detail/spai/spai.hpp | 25 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/detail/spai/spai_tag.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/detail/spai/sparse_vector.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/direct_solve.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/eig.hpp | 2 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/fft_operations.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/gmres.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/hankel_matrix_operations.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/host_based/amg_operations.hpp | 37 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/host_based/common.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/host_based/direct_solve.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/host_based/fft_operations.hpp | 5 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/host_based/ilu_operations.hpp | 21 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/host_based/iterative_operations.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/host_based/matrix_operations.hpp | 499 ++-- RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/host_based/misc_operations.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/host_based/nmf_operations.hpp | 5 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/host_based/scalar_operations.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/host_based/sparse_matrix_operations.hpp | 117 - RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/host_based/spgemm_vector.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/host_based/vector_operations.hpp | 162 + RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/ichol.hpp | 13 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/ilu.hpp | 2 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/ilu_operations.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/inner_prod.hpp | 19 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/iterative_operations.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/jacobi_precond.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/lanczos.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/lu.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/matrix_operations.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/maxmin.hpp | 13 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/misc_operations.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/mixed_precision_cg.hpp | 5 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/nmf.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/norm_1.hpp | 7 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/norm_2.hpp | 5 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/norm_frobenius.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/norm_inf.hpp | 7 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/amg_operations.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/bisect_kernel_calls.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/common.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/direct_solve.hpp | 5 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/fft_operations.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/ilu_operations.hpp | 7 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/iterative_operations.hpp | 4 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/kernels/amg.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/kernels/bisect.hpp | 5 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/kernels/compressed_compressed_matrix.hpp | 13 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/kernels/compressed_matrix.hpp | 159 + RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/kernels/coordinate_matrix.hpp | 24 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/kernels/ell_matrix.hpp | 24 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/kernels/fft.hpp | 5 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/kernels/hyb_matrix.hpp | 22 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/kernels/ilu.hpp | 5 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/kernels/iterative.hpp | 20 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/kernels/matrix.hpp | 703 ++++-- RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/kernels/matrix_element.hpp |only RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/kernels/matrix_solve.hpp | 5 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/kernels/nmf.hpp | 5 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/kernels/scalar.hpp | 5 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/kernels/scan.hpp | 5 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/kernels/sliced_ell_matrix.hpp | 24 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/kernels/spai.hpp | 5 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/kernels/svd.hpp | 5 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/kernels/vector.hpp | 882 ++++++-- RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/kernels/vector_element.hpp |only RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/matrix_operations.hpp | 579 ++++- RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/misc_operations.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/nmf_operations.hpp | 5 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/scalar_operations.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/sparse_matrix_operations.hpp | 279 +- RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/vandermonde_matrix_operations.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/opencl/vector_operations.hpp | 1101 +++++++--- RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/power_iter.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/prod.hpp | 7 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/qr-method-common.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/qr-method.hpp | 7 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/qr.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/row_scaling.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/scalar_operations.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/spai.hpp | 5 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/sparse_matrix_operations.hpp | 13 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/sum.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/svd.hpp | 7 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/toeplitz_matrix_operations.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/tql2.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/vandermonde_matrix_operations.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/linalg/vector_operations.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/matrix.hpp | 63 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/matrix_proxy.hpp | 108 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/meta/enable_if.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/meta/predicate.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/meta/result_of.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/meta/tag_of.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/misc/bandwidth_reduction.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/misc/cuthill_mckee.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/misc/gibbs_poole_stockmeyer.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/ocl/backend.hpp | 19 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/ocl/command_queue.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/ocl/context.hpp | 127 - RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/ocl/device.hpp | 7 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/ocl/device_utils.hpp | 12 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/ocl/enqueue.hpp | 23 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/ocl/error.hpp | 7 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/ocl/forwards.h | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/ocl/handle.hpp | 9 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/ocl/kernel.hpp | 43 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/ocl/local_mem.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/ocl/platform.hpp | 11 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/ocl/program.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/ocl/utils.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/range.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/scalar.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/scheduler/execute.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/scheduler/execute_axbx.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/scheduler/execute_elementwise.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/scheduler/execute_generic_dispatcher.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/scheduler/execute_matrix_dispatcher.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/scheduler/execute_matrix_prod.hpp | 23 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/scheduler/execute_scalar_assign.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/scheduler/execute_scalar_dispatcher.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/scheduler/execute_util.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/scheduler/execute_vector_dispatcher.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/scheduler/forwards.h | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/scheduler/io.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/scheduler/preset.hpp | 386 --- RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/slice.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/sliced_ell_matrix.hpp | 43 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/toeplitz_matrix.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/tools/adapter.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/tools/entry_proxy.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/tools/matrix_generation.hpp | 5 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/tools/matrix_size_deducer.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/tools/random.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/tools/sha1.hpp | 1 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/tools/shared_ptr.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/tools/timer.hpp | 4 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/tools/tools.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/traits/clear.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/traits/context.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/traits/fill.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/traits/handle.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/traits/row_major.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/traits/size.hpp | 7 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/traits/start.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/traits/stride.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/vandermonde_matrix.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/vector.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/vector_proxy.hpp | 3 RViennaCL-1.7.1-0/RViennaCL/inst/include/viennacl/version.hpp | 2 265 files changed, 5198 insertions(+), 3460 deletions(-)
Title: Base Package for Phylogenetic Structures and Comparative Data
Description: Provides a base S4 class for comparative methods, incorporating
one or more trees and trait data.
Author: R Hackathon et al. (alphabetically: Ben Bolker, Marguerite Butler,
Peter Cowan, Damien de Vienne, Dirk Eddelbuettel, Mark Holder, Thibaut
Jombart, Steve Kembel, Francois Michonneau, David Orme, Brian O'Meara,
Emmanuel Paradis, Jim Regetz, Derrick Zwickl)
Maintainer: Francois Michonneau <francois.michonneau@gmail.com>
Diff between phylobase versions 0.8.0 dated 2015-07-24 and 0.8.2 dated 2016-01-22
DESCRIPTION | 15 +++---- MD5 | 92 +++++++++++++++++++++---------------------- NAMESPACE | 2 NEWS.md | 3 + R/phylo4d-methods.R | 2 R/treePlot.R | 6 +- build/vignette.rds |binary man/MRCA.Rd | 4 - man/addData-methods.Rd | 4 - man/ancestors.Rd | 5 +- man/checkPhylo4.Rd | 2 man/edgeLength-methods.Rd | 4 - man/edges-accessors.Rd | 4 - man/extractTree.Rd | 3 - man/formatData.Rd | 2 man/geospiza.Rd | 4 + man/getNode-methods.Rd | 6 +- man/labels-methods.Rd | 3 - man/multiPhylo-class.Rd | 2 man/nTips-methods.Rd | 2 man/nodeId-methods.Rd | 4 - man/owls4.Rd | 4 + man/pdata-class.Rd | 2 man/pdata.Rd | 2 man/phylo4-class.Rd | 2 man/phylo4-methods.Rd | 13 +++--- man/phylo4d-accessors.Rd | 5 +- man/phylo4d-class.Rd | 4 - man/phylo4d-methods.Rd | 5 +- man/phyloXXYY.Rd | 6 ++ man/phylobase-package.Rd | 2 man/phylobase.options.Rd | 3 - man/phylobubbles.Rd | 4 + man/phylomat-class.Rd | 6 +- man/plotOneTree.Rd | 3 - man/print-methods.Rd | 6 ++ man/readNexus.Rd | 2 man/reorder-methods.Rd | 2 man/root-methods.Rd | 2 man/setAs-methods.Rd | 2 man/shortestPath-methods.Rd | 2 man/subset-methods.Rd | 2 man/summary-methods.Rd | 5 +- man/tdata-methods.Rd | 4 - man/tip.data.plot.Rd | 2 man/treePlot-methods.Rd | 3 - man/treeStructure-methods.Rd | 4 + 47 files changed, 150 insertions(+), 116 deletions(-)
Title: Phylogenetic Analysis in R
Description: Phylogenetic analysis in R: Estimation of phylogenetic
trees and networks using Maximum Likelihood, Maximum Parsimony,
distance methods and Hadamard conjugation.
Author: Klaus Schliep [aut, cre],
Emmanuel Paradis [aut],
Alastair Potts [aut]
Maintainer: Klaus Schliep <klaus.schliep@gmail.com>
Diff between phangorn versions 2.0.1 dated 2015-12-14 and 2.0.2 dated 2016-01-22
DESCRIPTION | 13 ++-- MD5 | 28 +++++----- NAMESPACE | 9 +-- NEWS | 10 +++ R/fitch.R | 133 +++++++++++++++++++++++++++++++++++++++++++++++---- R/parsimony.R | 28 +++++++--- R/phyDat.R | 24 ++++++--- R/phylo.R | 37 +++++++++----- README.md | 8 ++- man/bootstrap.pml.Rd | 13 +++- man/parsimony.Rd | 5 + man/phyDat.Rd | 1 src/Makevars | 4 - src/fitch.c | 32 +++++++----- src/ml.c | 44 +++++++++++----- 15 files changed, 296 insertions(+), 93 deletions(-)
Title: Tests of Non-Nested Models
Description: Testing non-nested models via theory supplied by Vuong (1989).
Includes tests of model distinguishability and of model fit that can be applied
to both nested and non-nested models. Also includes functionality to obtain
confidence intervals associated with AIC and BIC. This material is based on work
supported by the National Science Foundation under Grant Number SES-1061334.
Author: Edgar Merkle and Dongjun You
Maintainer: Edgar Merkle <merklee@missouri.edu>
Diff between nonnest2 versions 0.2 dated 2014-12-04 and 0.3 dated 2016-01-22
DESCRIPTION | 26 +++++++++++++++----------- MD5 | 26 +++++++++++++++++--------- NAMESPACE | 24 +++++++++++++++++++++++- NEWS | 11 +++++++++++ R/icci.R | 11 ++++++++--- R/llcont.R | 21 +++++++++++++++++++-- R/vuongtest.R | 55 +++++++++++++++++++++++++++++++++++++++++-------------- build |only inst |only man/icci.Rd | 4 +++- man/llcont.Rd | 6 ++++-- man/vuongtest.Rd | 4 +++- tests |only vignettes |only 14 files changed, 144 insertions(+), 44 deletions(-)
Title: Tools for the Analysis of Ecosystem Metabolism
Description: A collection of tools for the calculation of freewater metabolism.
Author: Luke Winslow, Jake Zwart, Ryan Batt, Jessica Corman, Hilary Dugan, Paul
Hanson, Aline Jaimes, Jordan Read, Richard Woolway
Maintainer: Luke Winslow <lawinslow@gmail.com>
Diff between LakeMetabolizer versions 1.3.3 dated 2015-05-28 and 1.4.1 dated 2016-01-22
LakeMetabolizer-1.3.3/LakeMetabolizer/README.md |only LakeMetabolizer-1.4.1/LakeMetabolizer/DESCRIPTION | 9 LakeMetabolizer-1.4.1/LakeMetabolizer/MD5 | 79 ++-- LakeMetabolizer-1.4.1/LakeMetabolizer/NAMESPACE | 13 LakeMetabolizer-1.4.1/LakeMetabolizer/R/addNAs.R | 7 LakeMetabolizer-1.4.1/LakeMetabolizer/R/calc.zeng.R | 1 LakeMetabolizer-1.4.1/LakeMetabolizer/R/helper.functions.R | 1 LakeMetabolizer-1.4.1/LakeMetabolizer/R/metab.R | 22 - LakeMetabolizer-1.4.1/LakeMetabolizer/R/metab.bayesian.R | 25 + LakeMetabolizer-1.4.1/LakeMetabolizer/R/metab.mle.R | 77 +++- LakeMetabolizer-1.4.1/LakeMetabolizer/R/metab.ols.R | 3 LakeMetabolizer-1.4.1/LakeMetabolizer/R/o2.at.sat.R | 197 +++++++----- LakeMetabolizer-1.4.1/LakeMetabolizer/demo/fig_timeseries.R | 7 LakeMetabolizer-1.4.1/LakeMetabolizer/man/calc.lw.net.Rd | 10 LakeMetabolizer-1.4.1/LakeMetabolizer/man/calc.zeng.Rd | 6 LakeMetabolizer-1.4.1/LakeMetabolizer/man/get.Ts.Rd | 2 LakeMetabolizer-1.4.1/LakeMetabolizer/man/get.vars.Rd | 2 LakeMetabolizer-1.4.1/LakeMetabolizer/man/getSchmidt.Rd | 8 LakeMetabolizer-1.4.1/LakeMetabolizer/man/has.vars.Rd | 2 LakeMetabolizer-1.4.1/LakeMetabolizer/man/is.day.Rd | 2 LakeMetabolizer-1.4.1/LakeMetabolizer/man/is.night.Rd | 2 LakeMetabolizer-1.4.1/LakeMetabolizer/man/k.read.Rd | 38 +- LakeMetabolizer-1.4.1/LakeMetabolizer/man/k.read.base.Rd | 39 +- LakeMetabolizer-1.4.1/LakeMetabolizer/man/k600.2.kGAS.Rd | 8 LakeMetabolizer-1.4.1/LakeMetabolizer/man/load.all.data.Rd | 6 LakeMetabolizer-1.4.1/LakeMetabolizer/man/load.meta.Rd | 4 LakeMetabolizer-1.4.1/LakeMetabolizer/man/metab.Rd | 57 +-- LakeMetabolizer-1.4.1/LakeMetabolizer/man/metab.bayesian.Rd | 40 +- LakeMetabolizer-1.4.1/LakeMetabolizer/man/metab.bookkeep.Rd | 20 - LakeMetabolizer-1.4.1/LakeMetabolizer/man/metab.kalman.Rd | 24 - LakeMetabolizer-1.4.1/LakeMetabolizer/man/metab.mle.Rd | 36 +- LakeMetabolizer-1.4.1/LakeMetabolizer/man/metab.ols.Rd | 16 LakeMetabolizer-1.4.1/LakeMetabolizer/man/o2.at.sat.Rd | 99 ++++-- LakeMetabolizer-1.4.1/LakeMetabolizer/man/par.to.sw.Rd | 6 LakeMetabolizer-1.4.1/LakeMetabolizer/man/rmv.vars.Rd | 2 LakeMetabolizer-1.4.1/LakeMetabolizer/man/sun.rise.set.Rd | 4 LakeMetabolizer-1.4.1/LakeMetabolizer/man/sw.to.par.Rd | 7 LakeMetabolizer-1.4.1/LakeMetabolizer/man/temp.kalman.Rd | 6 LakeMetabolizer-1.4.1/LakeMetabolizer/man/var.indx.Rd | 2 LakeMetabolizer-1.4.1/LakeMetabolizer/man/wind.scale.Rd | 12 LakeMetabolizer-1.4.1/LakeMetabolizer/src/mleLoop.c | 24 + 41 files changed, 574 insertions(+), 351 deletions(-)
More information about LakeMetabolizer at CRAN
Permanent link
Title: Item Response Models for Multiple Ratings
Description:
Implements some item response models for multiple
ratings, including the hierarchical rater model,
conditional maximum likelihood estimation of linear
logistic partial credit model and a wrapper function
to the commercial FACETS program.
Author:
Alexander Robitzsch [aut, cre], Jan Steinfeld [aut]
Maintainer:
Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between immer versions 0.2-0 dated 2015-11-04 and 0.3-0 dated 2016-01-22
DESCRIPTION | 28 +++++++++++++++------------- MD5 | 38 +++++++++++++++++++------------------- R/MHprop_hrm.R | 7 +++++-- R/anova_immer.R | 3 ++- R/immer_HRM.R | 6 +++--- R/immer_cml.R | 1 - R/rtrnorm.R | 2 +- data/data.immer01a.rda |binary data/data.immer01b.rda |binary data/data.immer02.rda |binary data/data.immer03.rda |binary data/data.immer04a.rda |binary data/data.immer04b.rda |binary data/data.immer05.rda |binary data/data.immer06.rda |binary data/data.immer07.rda |binary inst/NEWS | 13 +++++++++++-- man/immer-package.Rd | 4 ++-- man/immer_HRM.Rd | 2 +- man/immer_cml.Rd | 2 +- 20 files changed, 60 insertions(+), 46 deletions(-)
Title: Spatial Visualization with ggplot2
Description: A collection of functions to visualize spatial data and models
on top of static maps from various online sources (e.g Google Maps and Stamen
Maps). It includes tools common to those tasks, including functions for
geolocation and routing.
Author: David Kahle [aut, cre],
Hadley Wickham [aut]
Maintainer: David Kahle <david.kahle@gmail.com>
Diff between ggmap versions 2.6 dated 2015-12-19 and 2.6.1 dated 2016-01-22
DESCRIPTION | 6 +- MD5 | 116 ++++++++++++++++++++++---------------------- NEWS | 10 +++ R/LonLat2XY.R | 30 ++++++----- R/OSM_scale_lookup.R | 5 + R/XY2LonLat.R | 2 R/bb2bbox.R | 13 ++--- R/calc_zoom.r | 14 +++-- R/crime.R | 7 +- R/file_drawer.R | 11 ++-- R/geocode.R | 36 ++++++++----- R/get_cloudmademap.R | 31 ++++++----- R/get_googlemap.R | 122 +++++++++++++++++++++++------------------------ R/get_map.R | 42 ++++++++-------- R/get_navermap.R | 46 +++++++++++------ R/get_openstreetmap.R | 1 R/get_stamenmap.R | 33 ++++++++---- R/ggimage.R | 6 +- R/gglocator.R | 17 ++++-- R/ggplot2.R | 2 R/inset.R | 18 +++--- R/make_bbox.R | 27 +++++----- R/mapdist.R | 2 R/mutate_geocode.R | 8 +-- R/qmap.R | 6 +- R/qmplot.R | 44 +++++++++------- R/revgeocode.R | 25 ++++++--- R/route.R | 6 +- R/theme_inset.R | 36 ++++++------- R/theme_nothing.R | 8 +-- R/wind.R | 19 +++++-- R/zips.R | 9 ++- README.md | 49 +++++++++++++----- man/LonLat2XY.Rd | 9 ++- man/OSM_scale_lookup.Rd | 5 + man/bb2bbox.Rd | 13 ++--- man/calc_zoom.Rd | 14 +++-- man/crime.Rd | 3 - man/file_drawer.Rd | 11 ++-- man/geocode.Rd | 34 +++++++------ man/get_cloudmademap.Rd | 31 ++++++----- man/get_googlemap.Rd | 121 ++++++++++++++++++++++++---------------------- man/get_map.Rd | 42 ++++++++-------- man/get_navermap.Rd | 46 +++++++++++------ man/get_openstreetmap.Rd | 1 man/get_stamenmap.Rd | 33 ++++++++---- man/ggimage.Rd | 6 +- man/gglocator.Rd | 11 +++- man/inset.Rd | 18 +++--- man/make_bbox.Rd | 11 ++-- man/mutate_geocode.Rd | 8 +-- man/qmap.Rd | 6 +- man/qmplot.Rd | 44 +++++++++------- man/revgeocode.Rd | 20 +++++-- man/route.Rd | 4 - man/theme_inset.Rd | 22 ++++---- man/theme_nothing.Rd | 7 +- man/wind.Rd | 9 ++- man/zips.Rd | 12 +++- 59 files changed, 780 insertions(+), 568 deletions(-)
Title: Alternative Implementations of Base R Functions
Description: Alternative implementations of some base R functions, including sort, order, and match. Functions are simplified but can be faster or have other advantages.
Author: Craig Varrichio <canthony427@gmail.com>
Maintainer: Craig Varrichio <canthony427@gmail.com>
Diff between grr versions 0.9 dated 2016-01-19 and 0.9.1 dated 2016-01-22
DESCRIPTION | 11 +++++------ MD5 | 14 +++++++------- R/grr.R | 46 +++++++++++++++++++++++++++++++++++++--------- man/grr.Rd | 11 ++++++++--- man/matches.Rd | 2 ++ man/order2.Rd | 16 ++++++++++++++-- man/sort2.Rd | 17 ++++++++++++++--- src/grr.cpp | 21 +++++++++++---------- 8 files changed, 98 insertions(+), 40 deletions(-)
Title: ARTFIMA Model Estimation
Description: Fit and simulate ARTFIMA. Theoretical autocovariance function and spectral density function for stationary ARTFIMA.
Author: A. I. McLeod, Mark M. Meerschaert, Farzad Sabzikar
Maintainer: A.I. McLeod <aimcleod@uwo.ca>
Diff between artfima versions 1.1 dated 2015-11-08 and 1.2 dated 2016-01-22
artfima-1.1/artfima/data/Huron.rda |only artfima-1.1/artfima/data/NileMin.rda |only artfima-1.1/artfima/data/Ogden.rda |only artfima-1.1/artfima/data/SeriesA.rda |only artfima-1.1/artfima/man/Huron.Rd |only artfima-1.1/artfima/man/NileMin.Rd |only artfima-1.1/artfima/man/Ogden.Rd |only artfima-1.1/artfima/man/SeriesA.Rd |only artfima-1.2/artfima/DESCRIPTION | 12 - artfima-1.2/artfima/MD5 | 41 ++-- artfima-1.2/artfima/NAMESPACE | 7 artfima-1.2/artfima/NEWS | 16 + artfima-1.2/artfima/R/artSim.R | 3 artfima-1.2/artfima/R/artfima.R | 172 ++++++++++---------- artfima-1.2/artfima/R/informationMatrixARTFIMA.R |only artfima-1.2/artfima/R/print.artfima.R | 21 +- artfima-1.2/artfima/R/sdfartfima.R | 5 artfima-1.2/artfima/build/partial.rdb |binary artfima-1.2/artfima/data/SB32.rda |only artfima-1.2/artfima/inst |only artfima-1.2/artfima/man/SB32.Rd |only artfima-1.2/artfima/man/artfima-package.Rd | 2 artfima-1.2/artfima/man/artfima.Rd | 28 +-- artfima-1.2/artfima/man/informationMatrixARTFIMA.Rd |only artfima-1.2/artfima/man/print.artfima.Rd | 2 artfima-1.2/artfima/man/sdfartfima.Rd | 14 + artfima-1.2/artfima/man/seARTFIMA.Rd |only 27 files changed, 171 insertions(+), 152 deletions(-)
Title: Approximate Bayesian Computation via Random Forests
Description: Performs Approximate Bayesian Computation (ABC) model choice via random forests.
Author: Jean-Michel Marin [aut, cre],
Pierre Pudlo [aut],
Christian P. Robert [ctb],
Arnaud Estoup [ctb]
Maintainer: Jean-Michel Marin <jean-michel.marin@umontpellier.fr>
Diff between abcrf versions 0.9-4 dated 2015-08-18 and 1.1 dated 2016-01-22
DESCRIPTION | 28 +++++++++---------- MD5 | 20 +++++++------ NAMESPACE | 18 ++++++------ R/abcrf.R | 38 ++++++++++++++++++------- R/err.abcrf.R |only R/plot.abcrf.R | 57 +++++++++++++++++++++++++++++++------- R/predict.abcrf.R | 45 +++++++++++++++++++----------- man/abcrf.Rd | 75 +++++++++++++++++++++++++++------------------------ man/err.abcrf.Rd |only man/plot.abcrf.Rd | 33 ++++++++++++---------- man/predict.abcrf.Rd | 44 +++++++++++++++++------------ man/snp.Rd | 12 ++++---- 12 files changed, 228 insertions(+), 142 deletions(-)
Title: Utilities from "Seminar fuer Statistik" ETH Zurich
Description: Useful utilities ['goodies'] from Seminar fuer Statistik ETH
Zurich, quite a few related to graphics; many ported from S-plus times.
Author: Martin Maechler et al.
Maintainer: Martin Maechler <maechler@stat.math.ethz.ch>
Diff between sfsmisc versions 1.0-28 dated 2015-08-15 and 1.0-29 dated 2016-01-22
DESCRIPTION | 15 ++++--- MD5 | 83 ++++++++++++++++++++++--------------------- NAMESPACE | 17 +++++--- R/loessDemo.R |only R/misc-goodies.R | 66 ++++++++++++++++++++++++++++------ R/prime-numbers-fn.R | 46 ++++++++++++----------- R/sessionInfo-ext.R |only R/str_data.R | 29 +++++++++------ TODO | 37 ++++++++++--------- inst/NEWS.Rd | 22 +++++++++++ man/AsciiToInt.Rd | 2 - man/Deprecated.Rd | 2 - man/axTexpr.Rd | 4 +- man/capture-n-write.Rd | 16 +++++++- man/diagX.Rd | 2 - man/errbar.Rd | 2 - man/hatMat.Rd | 4 +- man/iterate.lin.recursion.Rd | 2 - man/loessDemo.Rd |only man/mult.fig.Rd | 2 - man/n.code.Rd | 2 - man/p.arrows.Rd | 2 - man/p.datum.Rd | 2 - man/p.profileTraces.Rd | 2 - man/p.tachoPlot.Rd | 4 +- man/polyn.eval.Rd | 2 - man/pretty10exp.Rd | 2 - man/printTable2.Rd | 2 - man/prt.DEBUG.Rd | 10 ++--- man/ps.latex.Rd | 2 - man/quadrant.Rd | 2 - man/read.org.table.Rd |only man/rrange.Rd | 17 ++++++-- man/sessionInfoX.Rd |only man/signi.Rd | 2 - man/str_data.Rd | 4 -- man/toLatex.numeric.Rd | 2 - man/u.Datumvonheute.Rd | 4 +- man/u.assign0.Rd | 4 +- man/u.boxplot.x.Rd | 2 - man/u.date.Rd | 6 +-- man/u.datumdecode.Rd | 4 +- man/wrapFormula.Rd | 5 ++ man/xy.grid.Rd | 2 - man/xy.unique.x.Rd | 4 +- 45 files changed, 277 insertions(+), 162 deletions(-)
Title: Global Optimization by Differential Evolution in C++
Description: An efficient C++ based implementation of the 'DEoptim'
function which performs global optimization by differential evolution.
Its creation was motivated by trying to see if the old approximation "easier,
shorter, faster: pick any two" could in fact be extended to achieving all
three goals while moving the code from plain old C to modern C++. The
initial version did in fact do so, but a good part of the gain was due to
an implicit code review which eliminated a few inefficiencies which have
since been eliminated in 'DEoptim'.
Author: Dirk Eddelbuettel extending DEoptim (by David Ardia, Katharine Mullen,
Brian Peterson, Joshua Ulrich) which itself is based on DE-Engine (by Rainer Storn)
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RcppDE versions 0.1.4 dated 2015-09-05 and 0.1.5 dated 2016-01-22
ChangeLog | 12 +++++++++++- DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- build/vignette.rds |binary inst/doc/RcppDE.pdf |binary src/devol.cpp | 6 +++--- 6 files changed, 23 insertions(+), 13 deletions(-)
Title: Big Data in-Database Analytics with Teradata Aster
Description: A consistent set of tools to perform in-database analytics
on Teradata Aster Big Data Discovery Platform. toaster (a.k.a 'to Aster')
embraces simple 2-step approach: compute in Aster - visualize and analyze
in R. Its `compute` functions use combination of SQL and
SQL/MR functions running in Aster database - highly scalable parallel
and distributed analytical platform. Then `create` functions visualize
results with boxplots, scatterplots, histograms, heatmaps, word clouds,
maps, or slope graphs. Advanced options such as faceting, coloring,
labeling, and others are supported with most functions.
Author: Gregory Kanevsky [aut, cre],
Nick Switanek [aut]
Maintainer: Gregory Kanevsky <gregory.kanevsky@teradata.com>
Diff between toaster versions 0.4.1 dated 2015-12-23 and 0.4.2 dated 2016-01-22
DESCRIPTION | 6 MD5 | 34 +-- NEWS | 36 ++++ R/computeKmeans.R | 18 +- R/maps.R | 118 ++++++++++--- R/plotting.R | 47 +++-- R/plottingKmeans.R | 2 R/showData.R | 11 - demo/baseball-heatmap.R | 4 man/createBoxplot.Rd | 9 - man/createBubblechart.Rd | 11 + man/createCentroidPlot.Rd | 7 man/createHeatmap.Rd | 8 man/createMap.Rd | 74 +++++--- man/createPopPyramid.Rd | 7 man/showData.Rd | 13 - tests/testthat/test-computeKmeans.R | 307 +++++++++++++++++++++++++++++++----- tests/testthat/test-createMap.R | 19 +- 18 files changed, 569 insertions(+), 162 deletions(-)
Title: Single and Multi-Objective Optimization Test Functions
Description: Provides generators for a high number of both single- and multi-
objective test functions which are frequently used for the benchmarking of
(numerical) optimization algorithms. Moreover, it offers a set of convenient
functions to generate, plot and work with objective functions.
Author: Jakob Bossek [aut, cre]
Maintainer: Jakob Bossek <j.bossek@gmail.com>
Diff between smoof versions 1.1 dated 2015-11-24 and 1.2 dated 2016-01-22
smoof-1.1/smoof/R/filterFunctionByTags.R |only smoof-1.1/smoof/R/makeFunctionByName.R |only smoof-1.1/smoof/man/makeFunctionByName.Rd |only smoof-1.2/smoof/DESCRIPTION | 12 smoof-1.2/smoof/MD5 | 243 +++++----- smoof-1.2/smoof/NAMESPACE | 15 smoof-1.2/smoof/NEWS | 26 + smoof-1.2/smoof/R/conversion.R |only smoof-1.2/smoof/R/filterFunctionsByTags.R |only smoof-1.2/smoof/R/getAvailableTags.R | 3 smoof-1.2/smoof/R/getBoxConstraints.R | 2 smoof-1.2/smoof/R/getID.R |only smoof-1.2/smoof/R/hasConstraints.R | 2 smoof-1.2/smoof/R/makeBBOBFunction.R | 6 smoof-1.2/smoof/R/makeFunctionsByName.R |only smoof-1.2/smoof/R/makeMultiObjectiveFunction.R | 6 smoof-1.2/smoof/R/makeObjectiveFunction.R | 11 smoof-1.2/smoof/R/makeSingleObjectiveFunction.R | 4 smoof-1.2/smoof/R/makeUFFunction.R | 3 smoof-1.2/smoof/R/mof.dtlz1.R | 9 smoof-1.2/smoof/R/mof.dtlz2.R | 9 smoof-1.2/smoof/R/mof.dtlz3.R | 9 smoof-1.2/smoof/R/mof.dtlz4.R | 9 smoof-1.2/smoof/R/mof.dtlz5.R | 9 smoof-1.2/smoof/R/mof.dtlz6.R | 9 smoof-1.2/smoof/R/mof.dtlz7.R | 7 smoof-1.2/smoof/R/mof.zdt1.R | 7 smoof-1.2/smoof/R/mof.zdt2.R | 7 smoof-1.2/smoof/R/mof.zdt3.R | 7 smoof-1.2/smoof/R/mof.zdt4.R | 7 smoof-1.2/smoof/R/mof.zdt6.R | 7 smoof-1.2/smoof/R/plot.autoplot.R | 41 + smoof-1.2/smoof/R/plot.plot.R | 28 - smoof-1.2/smoof/R/shouldBeMinimized.R | 2 smoof-1.2/smoof/R/sof.ackley.R | 7 smoof-1.2/smoof/R/sof.adjiman.R | 6 smoof-1.2/smoof/R/sof.alpine01.R | 7 smoof-1.2/smoof/R/sof.alpine02.R | 9 smoof-1.2/smoof/R/sof.aluffi-pentini.R | 6 smoof-1.2/smoof/R/sof.bartels.conn.R | 6 smoof-1.2/smoof/R/sof.beale.R | 6 smoof-1.2/smoof/R/sof.bent.cigar.R | 6 smoof-1.2/smoof/R/sof.bird.R | 6 smoof-1.2/smoof/R/sof.bohachevsky.n1.R | 7 smoof-1.2/smoof/R/sof.booth.R | 6 smoof-1.2/smoof/R/sof.branin.R | 6 smoof-1.2/smoof/R/sof.brent.R | 6 smoof-1.2/smoof/R/sof.brown.R | 7 smoof-1.2/smoof/R/sof.bukin.n2.R | 6 smoof-1.2/smoof/R/sof.bukin.n4.R | 6 smoof-1.2/smoof/R/sof.bukin.n6.R | 6 smoof-1.2/smoof/R/sof.carrom.table.R | 6 smoof-1.2/smoof/R/sof.chichinadze.R | 6 smoof-1.2/smoof/R/sof.chung.reynolds.R | 7 smoof-1.2/smoof/R/sof.complex.R | 6 smoof-1.2/smoof/R/sof.cosine.mixture.R | 7 smoof-1.2/smoof/R/sof.cross.in.tray.R | 6 smoof-1.2/smoof/R/sof.cube.R | 6 smoof-1.2/smoof/R/sof.deckkers.aarts.R | 6 smoof-1.2/smoof/R/sof.deflected.corrugated.spring.R | 8 smoof-1.2/smoof/R/sof.dixon.price.R | 7 smoof-1.2/smoof/R/sof.double.sum.R | 7 smoof-1.2/smoof/R/sof.drop.wave.R | 7 smoof-1.2/smoof/R/sof.easom.R | 6 smoof-1.2/smoof/R/sof.eggcrate.R | 6 smoof-1.2/smoof/R/sof.eggholder.R | 7 smoof-1.2/smoof/R/sof.el.attar.vidyasagar.dutta.R | 6 smoof-1.2/smoof/R/sof.engvall.R | 6 smoof-1.2/smoof/R/sof.exponential.R | 7 smoof-1.2/smoof/R/sof.freudenstein.roth.R | 6 smoof-1.2/smoof/R/sof.giunta.R | 6 smoof-1.2/smoof/R/sof.goldstein.price.R | 6 smoof-1.2/smoof/R/sof.griewank.R | 7 smoof-1.2/smoof/R/sof.hansen.R | 6 smoof-1.2/smoof/R/sof.himmelblau.R | 6 smoof-1.2/smoof/R/sof.holder.table.n1.R | 6 smoof-1.2/smoof/R/sof.holder.table.n2.R | 6 smoof-1.2/smoof/R/sof.hosaki.R | 6 smoof-1.2/smoof/R/sof.hyper.ellipsoid.R | 7 smoof-1.2/smoof/R/sof.jennrichsampson.R | 6 smoof-1.2/smoof/R/sof.judge.R | 6 smoof-1.2/smoof/R/sof.keane.R | 6 smoof-1.2/smoof/R/sof.kearfott.R | 6 smoof-1.2/smoof/R/sof.leon.R | 6 smoof-1.2/smoof/R/sof.matyas.R | 6 smoof-1.2/smoof/R/sof.mccormick.R | 6 smoof-1.2/smoof/R/sof.michalewicz.R | 8 smoof-1.2/smoof/R/sof.mpm2.R | 24 smoof-1.2/smoof/R/sof.periodic.R | 6 smoof-1.2/smoof/R/sof.powell.sum.R | 7 smoof-1.2/smoof/R/sof.price.n1.R | 6 smoof-1.2/smoof/R/sof.price.n2.R | 6 smoof-1.2/smoof/R/sof.price.n4.R | 4 smoof-1.2/smoof/R/sof.rastrigin.R | 7 smoof-1.2/smoof/R/sof.rosenbrock.R | 7 smoof-1.2/smoof/R/sof.schaffer.function.2.R | 6 smoof-1.2/smoof/R/sof.schaffer.function.4.R | 6 smoof-1.2/smoof/R/sof.schwefel.R | 7 smoof-1.2/smoof/R/sof.shubert.R | 6 smoof-1.2/smoof/R/sof.six.hump.camel.back.function.R | 6 smoof-1.2/smoof/R/sof.sphere.R | 7 smoof-1.2/smoof/R/sof.styblinski.tang.R | 6 smoof-1.2/smoof/R/sof.sum.of.different.powers.R | 7 smoof-1.2/smoof/R/sof.three.hump.camel.R | 6 smoof-1.2/smoof/R/sof.trecanni.R | 6 smoof-1.2/smoof/R/sof.zettl.R | 6 smoof-1.2/smoof/R/visualizeParetoOptimalFront.R | 78 +-- smoof-1.2/smoof/R/zzz.R | 2 smoof-1.2/smoof/man/autoplot.smoof_function.Rd | 7 smoof-1.2/smoof/man/conversion.Rd |only smoof-1.2/smoof/man/filterFunctionsByTags.Rd | 2 smoof-1.2/smoof/man/getID.Rd |only smoof-1.2/smoof/man/makeFunctionsByName.Rd |only smoof-1.2/smoof/man/makeMPM2Function.Rd | 10 smoof-1.2/smoof/man/makeMultiObjectiveFunction.Rd | 9 smoof-1.2/smoof/man/makeSingleObjectiveFunction.Rd | 7 smoof-1.2/smoof/man/plot1DNumeric.Rd | 7 smoof-1.2/smoof/man/plot2DNumeric.Rd | 8 smoof-1.2/smoof/man/visualizeParetoOptimalFront.Rd | 34 - smoof-1.2/smoof/tests/testthat/Rplots.pdf |binary smoof-1.2/smoof/tests/testthat/test_conversion.R |only smoof-1.2/smoof/tests/testthat/test_counting_evaluations.R | 4 smoof-1.2/smoof/tests/testthat/test_helpers.R | 6 smoof-1.2/smoof/tests/testthat/test_logging.R | 30 + smoof-1.2/smoof/tests/testthat/test_makeFunctionByName.R | 33 - smoof-1.2/smoof/tests/testthat/test_makeSingleObjectiveFunction.R | 2 smoof-1.2/smoof/tests/testthat/test_plotting.R | 29 - smoof-1.2/smoof/tests/testthat/test_soofuns.R | 1 128 files changed, 758 insertions(+), 485 deletions(-)
Title: Programming with Big Data -- Scalable Linear Algebra Packages
Description: Utilizing scalable linear algebra packages mainly
including BLACS, PBLAS, and ScaLAPACK in double precision via
pbdMPI based on ScaLAPACK version 2.0.2.
Author: Wei-Chen Chen [aut, cre],
Drew Schmidt [aut],
George Ostrouchov [aut],
Pragneshkumar Patel [aut],
Brian Ripley [ctb] (Solaris & Mac)
Maintainer: Wei-Chen Chen <wccsnow@gmail.com>
Diff between pbdSLAP versions 0.2-0 dated 2014-12-24 and 0.2-1 dated 2016-01-22
pbdSLAP-0.2-0/pbdSLAP/README |only pbdSLAP-0.2-0/pbdSLAP/data |only pbdSLAP-0.2-1/pbdSLAP/ChangeLog | 9 ++ pbdSLAP-0.2-1/pbdSLAP/DESCRIPTION | 14 ++-- pbdSLAP-0.2-1/pbdSLAP/MD5 | 35 +++++----- pbdSLAP-0.2-1/pbdSLAP/R/000_globalVariables.r | 4 - pbdSLAP-0.2-1/pbdSLAP/R/slap_blacs.r | 12 +-- pbdSLAP-0.2-1/pbdSLAP/README.md |only pbdSLAP-0.2-1/pbdSLAP/configure | 2 pbdSLAP-0.2-1/pbdSLAP/configure.ac | 3 pbdSLAP-0.2-1/pbdSLAP/demo/gridinfo.r | 8 +- pbdSLAP-0.2-1/pbdSLAP/inst/CITATION | 14 ++-- pbdSLAP-0.2-1/pbdSLAP/inst/doc/pbdSLAP-guide.Rnw | 19 +++-- pbdSLAP-0.2-1/pbdSLAP/inst/doc/pbdSLAP-guide.pdf |binary pbdSLAP-0.2-1/pbdSLAP/man/slap_gridinfo.Rd | 4 - pbdSLAP-0.2-1/pbdSLAP/src/REDIST/Makefile | 3 pbdSLAP-0.2-1/pbdSLAP/src/REDIST/pigemr.c |only pbdSLAP-0.2-1/pbdSLAP/src/REDIST/pigemr2.c |only pbdSLAP-0.2-1/pbdSLAP/src/REDIST/pitrmr.c |only pbdSLAP-0.2-1/pbdSLAP/src/REDIST/pitrmr2.c |only pbdSLAP-0.2-1/pbdSLAP/vignettes/pbdSLAP-guide.Rnw | 19 +++-- pbdSLAP-0.2-1/pbdSLAP/vignettes/pbdSLAP-include/01-copyright.tex | 2 22 files changed, 83 insertions(+), 65 deletions(-)
Title: Network Generator for Combinatorial Graph Problems
Description: Methods for the generation of a wide range of network geographies,
e.g., grid networks or clustered networks. Useful for the generation of
benchmarking instances for the investigation of, e.g., Vehicle-Routing-Problems
or Travelling Salesperson Problems.
Author: Jakob Bossek [aut, cre]
Maintainer: Jakob Bossek <j.bossek@gmail.com>
Diff between netgen versions 1.2 dated 2015-11-24 and 1.3 dated 2016-01-22
netgen-1.2/netgen/R/getInstanceOverview.R |only netgen-1.3/netgen/DESCRIPTION | 10 netgen-1.3/netgen/MD5 | 60 +++-- netgen-1.3/netgen/NAMESPACE | 6 netgen-1.3/netgen/NEWS | 15 + netgen-1.3/netgen/R/exportToTSPlibFormat.R | 53 +++- netgen-1.3/netgen/R/filterTSPInstances.R |only netgen-1.3/netgen/R/generateRandomNetwork.R | 2 netgen-1.3/netgen/R/getTSPInstancesOverview.R |only netgen-1.3/netgen/R/getValidEdgeWeightTypes.R |only netgen-1.3/netgen/R/helpers.R | 15 + netgen-1.3/netgen/R/importFromTSPlibFormat.R | 3 netgen-1.3/netgen/R/isEuclidean.R |only netgen-1.3/netgen/R/makeNetwork.R | 41 +++ netgen-1.3/netgen/R/pointMatching.R | 27 +- netgen-1.3/netgen/R/printNetwork.R | 5 netgen-1.3/netgen/R/rescaleNetwork.R | 48 +++- netgen-1.3/netgen/man/exportToTSPlibFormat.Rd | 9 netgen-1.3/netgen/man/filterTSPInstances.Rd |only netgen-1.3/netgen/man/getOptimalPointMatching.Rd | 10 netgen-1.3/netgen/man/getTSPInstancesOverview.Rd |only netgen-1.3/netgen/man/getValidEdgeWeightTypes.Rd |only netgen-1.3/netgen/man/isEuclidean.Rd |only netgen-1.3/netgen/man/isNetwork.Rd |only netgen-1.3/netgen/man/makeNetwork.Rd | 13 - netgen-1.3/netgen/man/quoted.Rd |only netgen-1.3/netgen/man/rescaleNetwork.Rd | 17 - netgen-1.3/netgen/tests/testthat/test_asType.R | 52 ++-- netgen-1.3/netgen/tests/testthat/test_dynamise.R | 46 ++-- netgen-1.3/netgen/tests/testthat/test_generateClusteredNetwork.R | 102 ++++----- netgen-1.3/netgen/tests/testthat/test_generateGridNetwork.R | 32 +- netgen-1.3/netgen/tests/testthat/test_generateRandomNetwork.R | 37 +-- netgen-1.3/netgen/tests/testthat/test_getTSPInstancesOverview.R |only netgen-1.3/netgen/tests/testthat/test_import.R | 1 netgen-1.3/netgen/tests/testthat/test_morphInstances.R | 108 +++++----- netgen-1.3/netgen/tests/testthat/test_plots.R | 90 ++++---- netgen-1.3/netgen/tests/testthat/test_rescaleNetwork.R | 73 +++--- 37 files changed, 514 insertions(+), 361 deletions(-)
Title: Calculations and Visualisations Related to Geometric
Morphometrics
Description: A toolset for Geometric Morphometrics and mesh processing. This
includes (among other stuff) mesh deformations based on reference points,
permutation tests, detection of outliers, processing of sliding
semi-landmarks and semi-automated surface landmark placement.
Author: Stefan Schlager [aut, cre, cph],
Gregory Jefferis [ctb]
Maintainer: Stefan Schlager <stefan.schlager@uniklinik-freiburg.de>
Diff between Morpho versions 2.3.1 dated 2015-12-15 and 2.3.1.1 dated 2016-01-22
DESCRIPTION | 8 ++++---- MD5 | 38 +++++++++++++++++++------------------- R/Morpho-package.R | 4 ++-- R/deform.grid.r | 5 +++-- R/permuvec.r | 2 +- R/vertex.r | 1 + inst/NEWS.Rd | 10 ++++++++++ man/Morpho-package.Rd | 4 ++-- man/deformGrid3d.Rd | 5 ++++- src/CVAdists.cpp | 14 ++++++-------- src/armaGinv.cpp | 3 +-- src/asymPerm.cpp | 21 +++++++++------------ src/covPCA.cpp | 12 ++++-------- src/createL.cpp | 6 ++---- src/edgePlane.cpp | 3 ++- src/meshres.cpp | 17 +++++++++-------- src/permudistArma.cpp | 11 +++++------ src/points2mesh.cpp | 28 +++++++++++----------------- src/tpsfx.cpp | 14 ++++++++------ src/updateNormals.cpp | 20 +++++++++----------- 20 files changed, 112 insertions(+), 114 deletions(-)
Title: A General-Purpose Package for Dynamic Report Generation in R
Description: Provides a general-purpose tool for dynamic report generation in R
using Literate Programming techniques.
Author: Yihui Xie [aut, cre],
Adam Vogt [ctb],
Alastair Andrew [ctb],
Alex Zvoleff [ctb],
Andre Simon [ctb] (the CSS files under inst/themes/ were derived from
the Highlight package http://www.andre-simon.de),
Aron Atkins [ctb],
Aaron Wolen [ctb],
Ashley Manton [ctb],
Ben Baumer [ctb],
Brian Diggs [ctb],
Cassio Pereira [ctb],
David Robinson [ctb],
Donald Arseneau [ctb, cph] (the framed package at inst/misc/framed.sty),
Doug Hemken [ctb],
Duncan Murdoch [ctb],
Fabian Hirschmann [ctb],
Fitch Simeon [ctb],
Frank E Harrell Jr [ctb] (the Sweavel package at inst/misc/Sweavel.sty),
Gregoire Detrez [ctb],
Hadley Wickham [ctb],
Heewon Jeon [ctb],
Henrik Bengtsson [ctb],
Hiroaki Yutani [ctb],
Jake Burkhead [ctb],
James Manton [ctb],
Jared Lander [ctb],
Jason Punyon [ctb],
Jeff Arnold [ctb],
Jeremy Ashkenas [ctb, cph] (the CSS file at
inst/misc/docco-classic.css),
Jeremy Stephens [ctb],
Jim Hester [ctb],
Joe Cheng [ctb],
Johannes Ranke [ctb],
John Honaker [ctb],
John Muschelli [ctb],
Jonathan Keane [ctb],
JJ Allaire [ctb],
Johan Toloe [ctb],
Joseph Larmarange [ctb],
Julien Barnier [ctb],
Kaiyin Zhong [ctb],
Kevin K. Smith [ctb],
Kirill Mueller [ctb],
Kohske Takahashi [ctb],
Michael Friendly [ctb],
Michal Bojanowski [ctb],
Michel Kuhlmann [ctb],
Nacho Caballero [ctb],
Nick Salkowski [ctb],
Noam Ross [ctb],
Qiang Li [ctb],
Ramnath Vaidyanathan [ctb],
Richard Cotton [ctb],
Robert Krzyzanowski [ctb],
Romain Francois [ctb],
Scott Kostyshak [ctb],
Sebastian Meyer [ctb],
Sietse Brouwer [ctb],
Simon de Bernard [ctb],
Taiyun Wei [ctb],
Thibaut Assus [ctb],
Thibaut Lamadon [ctb],
Thomas Leeper [ctb],
Tom Torsney-Weir [ctb],
Trevor Davis [ctb],
Viktoras Veitas [ctb],
Weicheng Zhu [ctb],
Wush Wu [ctb],
Zachary Foster [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between knitr versions 1.12 dated 2016-01-07 and 1.12.3 dated 2016-01-22
DESCRIPTION | 15 ++++++++++----- MD5 | 31 ++++++++++++++++--------------- R/block.R | 10 ++++++---- R/hooks-md.R | 5 ++++- R/plot.R | 4 +--- build/knitr.pdf |binary inst/doc/docco-classic.html | 2 +- inst/doc/docco-linear.html | 2 +- inst/doc/knit_expand.html | 4 ++-- inst/doc/knit_print.html | 23 +++++++++-------------- inst/doc/knitr-html.html | 2 +- inst/doc/knitr-intro.html | 19 +++++++------------ inst/doc/knitr-markdown.html | 4 ++-- inst/doc/knitr-refcard.pdf |binary tests/testit/knit-tikzDevice.Rnw |only tests/testit/test-hooks.R | 2 +- tests/testit/test-plot.R | 6 ++++++ 17 files changed, 67 insertions(+), 62 deletions(-)
Title: Full Text of 'Scholarly' Articles Across Many Data Sources
Description: Provides a single interface to many sources of full text
'scholarly' data, including 'Biomed Central', Public Library of
Science, 'Pubmed Central', 'eLife', 'F1000Research', 'PeerJ',
'Pensoft', 'Hindawi', 'arXiv' 'preprints', and more. Functionality
included for searching for articles, downloading full or partial
text, downloading supplementary materials, converting to various
data formats used in and outside of R.
Author: Scott Chamberlain [aut, cre]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between fulltext versions 0.1.4 dated 2015-10-02 and 0.1.6 dated 2016-01-22
fulltext-0.1.4/fulltext/tests/testthat/test-ft_get.R |only fulltext-0.1.6/fulltext/DESCRIPTION | 9 fulltext-0.1.6/fulltext/LICENSE | 2 fulltext-0.1.6/fulltext/MD5 | 90 +- fulltext-0.1.6/fulltext/NAMESPACE | 7 fulltext-0.1.6/fulltext/R/europe_pmc_utils.R | 2 fulltext-0.1.6/fulltext/R/ft_browse.R | 3 fulltext-0.1.6/fulltext/R/ft_get_si.R | 320 ++------- fulltext-0.1.6/fulltext/R/ft_get_si_plugins.R |only fulltext-0.1.6/fulltext/R/ft_get_si_utils.R |only fulltext-0.1.6/fulltext/R/ft_search.R | 20 fulltext-0.1.6/fulltext/R/fulltext-package.R | 6 fulltext-0.1.6/fulltext/R/plugins_search.R | 13 fulltext-0.1.6/fulltext/README.md | 123 +-- fulltext-0.1.6/fulltext/build/vignette.rds |binary fulltext-0.1.6/fulltext/inst/doc/fulltext_vignette.Rmd | 529 +++++++--------- fulltext-0.1.6/fulltext/inst/doc/fulltext_vignette.html | 516 +++++++-------- fulltext-0.1.6/fulltext/inst/doc/getting_fulltext.Rmd | 89 +- fulltext-0.1.6/fulltext/inst/doc/getting_fulltext.html | 87 +- fulltext-0.1.6/fulltext/inst/ignore/config.R |only fulltext-0.1.6/fulltext/inst/ignore/elsevier_code.R |only fulltext-0.1.6/fulltext/inst/vign/fulltext_vignette.Rmd | 9 fulltext-0.1.6/fulltext/inst/vign/fulltext_vignette.md | 529 +++++++--------- fulltext-0.1.6/fulltext/inst/vign/getting_fulltext.Rmd | 12 fulltext-0.1.6/fulltext/inst/vign/getting_fulltext.md | 89 +- fulltext-0.1.6/fulltext/man/bmc.Rd | 2 fulltext-0.1.6/fulltext/man/bmc_search.Rd | 2 fulltext-0.1.6/fulltext/man/cache.Rd | 2 fulltext-0.1.6/fulltext/man/chunks.Rd | 2 fulltext-0.1.6/fulltext/man/collect.Rd | 8 fulltext-0.1.6/fulltext/man/eupmc.Rd | 20 fulltext-0.1.6/fulltext/man/extract_tools.Rd | 22 fulltext-0.1.6/fulltext/man/ft_browse.Rd | 4 fulltext-0.1.6/fulltext/man/ft_extract.Rd | 12 fulltext-0.1.6/fulltext/man/ft_extract_corpus.Rd | 2 fulltext-0.1.6/fulltext/man/ft_get.Rd | 2 fulltext-0.1.6/fulltext/man/ft_get_si.Rd | 106 ++- fulltext-0.1.6/fulltext/man/ft_links.Rd | 14 fulltext-0.1.6/fulltext/man/ft_providers.Rd | 2 fulltext-0.1.6/fulltext/man/ft_search.Rd | 14 fulltext-0.1.6/fulltext/man/ft_serialize.Rd | 10 fulltext-0.1.6/fulltext/man/ft_type_sum.Rd | 2 fulltext-0.1.6/fulltext/man/fulltext-package.Rd | 21 fulltext-0.1.6/fulltext/man/pdfx.Rd | 14 fulltext-0.1.6/fulltext/man/pipe.Rd | 2 fulltext-0.1.6/fulltext/tests/testthat/test-ft_get.r |only fulltext-0.1.6/fulltext/tests/testthat/test-ft_get_si.r | 20 fulltext-0.1.6/fulltext/vignettes/fulltext_vignette.Rmd | 529 +++++++--------- fulltext-0.1.6/fulltext/vignettes/getting_fulltext.Rmd | 89 +- 49 files changed, 1580 insertions(+), 1776 deletions(-)
Title: Did You Mean?
Description: Add a "Did You Mean" feature to the R interactive. With this
package, error messages for misspelled input of variable names or package names
suggest what you really want to do in addition to notification of the mistake.
Author: Kosei Abe [aut, cre], Richard Cotton [ctb]
Maintainer: Kosei Abe <mail@recyclebin.jp>
Diff between DYM versions 0.1.1 dated 2015-06-15 and 0.2 dated 2016-01-22
DESCRIPTION | 19 +++---- MD5 | 28 +++++----- NAMESPACE | 6 +- R/DYM.R | 48 +++++++++++++----- R/findSimilarName.R | 49 ++++++++++++++++-- R/getNames.R | 1 R/hooks.R | 2 inst/po/en@quot/LC_MESSAGES/R-DYM.mo |binary inst/po/ja/LC_MESSAGES/R-DYM.mo |binary man/DYM.Rd | 21 +++++++- man/findSimilarName.Rd | 36 +++++++++++-- man/getMissingVariable.Rd | 2 man/getNames.Rd | 2 man/isVariableName.Rd | 2 tests/testthat/test-findSimilarName.R | 89 +++++++++++++++++++++++++++++----- 15 files changed, 237 insertions(+), 68 deletions(-)