Title: Access to the 'Vagalume' API
Description: Provides access to the 'Vagalume' API <https://api.vagalume.com.br>.
The data extracted is basically lyrics of songs and information about
artists/bands.
Author: Bruna Wundervald
Maintainer: Bruna Wundervald <brunadaviesw@gmail.com>
Diff between vagalumeR versions 0.1.3 dated 2018-07-20 and 0.1.4 dated 2018-11-22
DESCRIPTION | 14 +++++++------- MD5 | 14 ++++++++------ NAMESPACE | 2 ++ R/artistInfo.R | 7 ++++--- R/relatedInfo.R | 5 ++--- R/songNames.R | 6 ++---- R/topLyrics.R | 5 ++--- R/utils.R |only man/pipe.Rd |only 9 files changed, 27 insertions(+), 26 deletions(-)
Title: Companion Animal Population Management
Description: Quantitative analysis to support companion animal population
management. Some functions assist survey sampling tasks (calculate sample
size for simple and complex designs, select sampling units and estimate
population parameters) while others assist the modelling of population
dynamics. For demographic characterizations and population management
evaluations see: "Baquero, et al." (2018),
<doi:10.1016/j.prevetmed.2018.07.006>. For modelling of
population dynamics see: "Baquero et al." (2016),
<doi:10.1016/j.prevetmed.2015.11.009>. For sampling methods
see: "Levy PS & Lemeshow S" (2013), "ISBN-10: 0470040076";
"Lumley" (2010), "ISBN: 978-0-470-28430-8".
Author: Oswaldo Santos Baquero [aut, cre],
Marcos Amaku [ctb],
Fernando Ferreira [ctb]
Maintainer: Oswaldo Santos Baquero <baquero@usp.br>
Diff between capm versions 0.13.5 dated 2018-10-02 and 0.13.8 dated 2018-11-22
DESCRIPTION | 8 ++--- MD5 | 26 ++++++++--------- NEWS | 15 +++++++++ R/Calculate2StageSampleSize.R | 1 R/MapkmlPSU.R | 21 +++++++++---- R/PlotImmigrationFlow.R | 2 - R/PlotLocalSens.R | 8 ++--- R/SolveIASA.R | 59 +++++++++++++++++++-------------------- R/capm-package.R | 4 +- man/Calculate2StageSampleSize.Rd | 1 man/MapkmlPSU.Rd | 4 +- man/PlotLocalSens.Rd | 8 ++--- man/SolveIASA.Rd | 11 ++++--- man/capm-package.Rd | 4 +- 14 files changed, 101 insertions(+), 71 deletions(-)
Title: Bayesian Spectral Inference for Stationary Time Series
Description: Implementations of Bayesian parametric, nonparametric and semiparametric procedures for univariate and multivariate time series. The package is based on the methods presented in C. Kirch et al (2018) <doi:10.1214/18-BA1126> and A. Meier (2018) <https://opendata.uni-halle.de//handle/1981185920/13470>. It was supported by DFG grant KI 1443/3-1.
Author: Alexander Meier [aut, cre],
Claudia Kirch [aut],
Matthew C. Edwards [aut],
Renate Meyer [aut]
Maintainer: Alexander Meier <alexander.meier@ovgu.de>
Diff between beyondWhittle versions 1.0 dated 2018-07-16 and 1.1 dated 2018-11-22
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Title: Tools for Building OLS Regression Models
Description: Tools designed to make it easier for users, particularly beginner/intermediate R users
to build ordinary least squares regression models. Includes comprehensive regression output,
heteroskedasticity tests, collinearity diagnostics, residual diagnostics, measures of influence,
model fit assessment and variable selection procedures.
Author: Aravind Hebbali [aut, cre]
Maintainer: Aravind Hebbali <hebbali.aravind@gmail.com>
Diff between olsrr versions 0.5.1 dated 2018-05-06 and 0.5.2 dated 2018-11-22
olsrr-0.5.1/olsrr/inst/doc/reference-media.Rmd |only olsrr-0.5.1/olsrr/inst/doc/reference-media.html |only olsrr-0.5.1/olsrr/vignettes/reference-media.Rmd |only olsrr-0.5.2/olsrr/DESCRIPTION | 17 olsrr-0.5.2/olsrr/MD5 | 126 ++-- olsrr-0.5.2/olsrr/NAMESPACE | 15 olsrr-0.5.2/olsrr/NEWS.md | 14 olsrr-0.5.2/olsrr/R/ols-added-variable-plot.R | 77 -- olsrr-0.5.2/olsrr/R/ols-all-possible-regression.R | 6 olsrr-0.5.2/olsrr/R/ols-bartlett-test.R | 2 olsrr-0.5.2/olsrr/R/ols-best-subsets-regression.R | 4 olsrr-0.5.2/olsrr/R/ols-breusch-pagan-test.R | 4 olsrr-0.5.2/olsrr/R/ols-collinearity-diagnostics.R | 2 olsrr-0.5.2/olsrr/R/ols-cooks-d-barplot.R | 78 -- olsrr-0.5.2/olsrr/R/ols-cooks-d-chart.R | 8 olsrr-0.5.2/olsrr/R/ols-correlations.R | 4 olsrr-0.5.2/olsrr/R/ols-dfbetas-panel.R | 52 - olsrr-0.5.2/olsrr/R/ols-dffits-plot.R | 6 olsrr-0.5.2/olsrr/R/ols-diagnostics-panel.R | 14 olsrr-0.5.2/olsrr/R/ols-dsresid-vs-pred-plot.R | 48 - olsrr-0.5.2/olsrr/R/ols-f-test.R | 2 olsrr-0.5.2/olsrr/R/ols-hadi-plot.R | 2 olsrr-0.5.2/olsrr/R/ols-influence-measures.R | 2 olsrr-0.5.2/olsrr/R/ols-normality-tests.R | 2 olsrr-0.5.2/olsrr/R/ols-plots-data.R |only olsrr-0.5.2/olsrr/R/ols-regress_compute.R | 2 olsrr-0.5.2/olsrr/R/ols-resid-vs-regressor-plot-shiny.R | 2 olsrr-0.5.2/olsrr/R/ols-residual-fit-spread-plot.R | 29 - olsrr-0.5.2/olsrr/R/ols-residual-plus-component-plot.R | 4 olsrr-0.5.2/olsrr/R/ols-residual-vs-regressor-plot.R | 24 olsrr-0.5.2/olsrr/R/ols-response-profile.R | 2 olsrr-0.5.2/olsrr/R/ols-rstud-vs-lev-plot.R | 80 -- olsrr-0.5.2/olsrr/R/ols-score-test.R | 8 olsrr-0.5.2/olsrr/R/ols-standardized-residual-chart.R | 35 - olsrr-0.5.2/olsrr/R/ols-stepaic-backward-regression.R | 11 olsrr-0.5.2/olsrr/R/ols-stepaic-both-regression.R | 9 olsrr-0.5.2/olsrr/R/ols-stepaic-forward-regression.R | 10 olsrr-0.5.2/olsrr/R/ols-stepwise-backward-regression.R | 9 olsrr-0.5.2/olsrr/R/ols-stepwise-forward-regression.R | 17 olsrr-0.5.2/olsrr/R/ols-stepwise-regression.R | 19 olsrr-0.5.2/olsrr/R/ols-studentized-residual-plot.R | 64 -- olsrr-0.5.2/olsrr/R/output.R | 322 ----------- olsrr-0.5.2/olsrr/R/zzz.R | 2 olsrr-0.5.2/olsrr/README.md | 41 - olsrr-0.5.2/olsrr/build/vignette.rds |binary olsrr-0.5.2/olsrr/inst/application/ui.R | 2 olsrr-0.5.2/olsrr/inst/doc/heteroskedasticity.html | 334 ++++++++++-- olsrr-0.5.2/olsrr/inst/doc/influence_measures.html | 342 ++++++++++-- olsrr-0.5.2/olsrr/inst/doc/intro.html | 340 ++++++++++-- olsrr-0.5.2/olsrr/inst/doc/regression_diagnostics.html | 338 ++++++++++-- olsrr-0.5.2/olsrr/inst/doc/residual_diagnostics.html | 308 +++++++++-- olsrr-0.5.2/olsrr/inst/doc/variable_selection.html | 432 +++++++++++----- olsrr-0.5.2/olsrr/man/ols_prep_avplot_data.Rd |only olsrr-0.5.2/olsrr/man/ols_prep_cdplot_data.Rd |only olsrr-0.5.2/olsrr/man/ols_prep_cdplot_outliers.Rd |only olsrr-0.5.2/olsrr/man/ols_prep_dfbeta_data.Rd |only olsrr-0.5.2/olsrr/man/ols_prep_dfbeta_outliers.Rd |only olsrr-0.5.2/olsrr/man/ols_prep_dsrvf_data.Rd |only olsrr-0.5.2/olsrr/man/ols_prep_outlier_obs.Rd |only olsrr-0.5.2/olsrr/man/ols_prep_regress_x.Rd |only olsrr-0.5.2/olsrr/man/ols_prep_regress_y.Rd |only olsrr-0.5.2/olsrr/man/ols_prep_rfsplot_fmdata.Rd |only olsrr-0.5.2/olsrr/man/ols_prep_rstudlev_data.Rd |only olsrr-0.5.2/olsrr/man/ols_prep_rvsrplot_data.Rd |only olsrr-0.5.2/olsrr/man/ols_prep_srchart_data.Rd |only olsrr-0.5.2/olsrr/man/ols_prep_srplot_data.Rd |only olsrr-0.5.2/olsrr/man/ols_step_backward_aic.Rd | 4 olsrr-0.5.2/olsrr/man/ols_step_backward_p.Rd | 4 olsrr-0.5.2/olsrr/man/ols_step_both_aic.Rd | 5 olsrr-0.5.2/olsrr/man/ols_step_both_p.Rd | 4 olsrr-0.5.2/olsrr/man/ols_step_forward_aic.Rd | 4 olsrr-0.5.2/olsrr/man/ols_step_forward_p.Rd | 4 olsrr-0.5.2/olsrr/tests/testthat/test-utility.R | 19 73 files changed, 1946 insertions(+), 1369 deletions(-)
Title: Item Based Collaborative Filtering for Multi-Trait and
Multi-Environment Data
Description: Implements the item based collaborative filtering (IBCF) method for continues phenotypes in the context of plant breeding where data are collected for various traits that were studied in various environments proposed by Montesinos-López et al. (2017) <doi:10.1534/g3.117.300309>.
Author: Francisco Javier Luna-Vazquez [aut, cre]
(<https://orcid.org/0000-0002-5370-7152>),
Osval Antonio Montesinos-Lopez [aut]
(<https://orcid.org/0000-0002-3973-6547>),
Abelardo Montesinos-Lopez [aut],
Jose Crossa [aut] (<https://orcid.org/0000-0001-9429-5855>)
Maintainer: Francisco Javier Luna-Vazquez <frahik@gmail.com>
Diff between IBCF.MTME versions 1.4-2 dated 2018-10-22 and 1.5-1 dated 2018-11-22
DESCRIPTION | 11 +- MD5 | 46 ++++---- NAMESPACE | 56 +++++----- NEWS.md | 77 ++++++++------ R/CrossValidation.R | 262 +++++++++++++++++++++++++-------------------------- R/IBCF.R | 260 ++++++++++++++++++++++++++------------------------ R/IBCFYear.R | 20 +-- R/Td2M.R | 2 R/Title.R | 6 - R/methods.R | 6 - man/CV.RandomPart.Rd | 94 +++++++++--------- man/IBCF.MTME.Rd | 20 +-- man/IBCF.Rd | 64 ++++++------ man/IBCF.Years.Rd | 84 ++++++++-------- man/Wheat_IBCF.Rd | 36 +++---- man/Year_IBCF.Rd | 68 ++++++------- man/barplot.IBCFY.Rd | 36 +++---- man/getMatrixForm.Rd | 68 ++++++------- man/getTidyForm.Rd | 66 ++++++------ man/plot.IBCF.Rd | 36 +++---- man/print.IBCF.Rd | 38 +++---- man/print.IBCFY.Rd | 38 +++---- man/summary.IBCF.Rd | 42 ++++---- man/summary.IBCFY.Rd | 36 +++---- 24 files changed, 744 insertions(+), 728 deletions(-)
Title: GeoJSON to Simple Feature Converter
Description: Converts Between GeoJSON and simple feature objects.
Author: David Cooley [aut, cre]
Maintainer: David Cooley <dcooley@symbolix.com.au>
Diff between geojsonsf versions 1.2 dated 2018-10-19 and 1.2.1 dated 2018-11-22
geojsonsf-1.2.1/geojsonsf/DESCRIPTION | 14 geojsonsf-1.2.1/geojsonsf/MD5 | 71 +-- geojsonsf-1.2.1/geojsonsf/NAMESPACE | 3 geojsonsf-1.2.1/geojsonsf/NEWS.md | 5 geojsonsf-1.2.1/geojsonsf/R/RcppExports.R | 8 geojsonsf-1.2.1/geojsonsf/R/geojson_sf.R | 65 -- geojsonsf-1.2.1/geojsonsf/R/geojsonsf-package.R | 1 geojsonsf-1.2.1/geojsonsf/R/scratch.R |only geojsonsf-1.2.1/geojsonsf/R/sf_geojson.R |only geojsonsf-1.2.1/geojsonsf/README.md | 21 geojsonsf-1.2.1/geojsonsf/inst/doc/geojson-sf-conversions.html | 4 geojsonsf-1.2.1/geojsonsf/inst/include/geojsonsf |only geojsonsf-1.2.1/geojsonsf/man/df_geojson.Rd |only geojsonsf-1.2.1/geojsonsf/man/sf_geojson.Rd | 6 geojsonsf-1.2.1/geojsonsf/man/sfc_geojson.Rd | 2 geojsonsf-1.2.1/geojsonsf/src/RcppExports.cpp | 27 + geojsonsf-1.2.1/geojsonsf/src/df_geojson.cpp |only geojsonsf-1.2.1/geojsonsf/src/geojson_properties.cpp | 2 geojsonsf-1.2.1/geojsonsf/src/geojson_sfc.cpp | 6 geojsonsf-1.2.1/geojsonsf/src/geojson_sfg.cpp | 81 ++- geojsonsf-1.2.1/geojsonsf/src/geojson_to_sf.cpp | 31 - geojsonsf-1.2.1/geojsonsf/src/geojson_to_wkt.cpp | 14 geojsonsf-1.2.1/geojsonsf/src/geojson_validate.cpp | 6 geojsonsf-1.2.1/geojsonsf/src/geojson_wkt.cpp | 6 geojsonsf-1.2.1/geojsonsf/src/read_geojson.cpp | 10 geojsonsf-1.2.1/geojsonsf/src/sf_geojson.cpp | 224 ++++------ geojsonsf-1.2.1/geojsonsf/tests/testthat/test-df_geojson.R |only geojsonsf-1.2.1/geojsonsf/tests/testthat/test-downcast.R |only geojsonsf-1.2.1/geojsonsf/tests/testthat/test-geojson_sf.R | 12 geojsonsf-1.2/geojsonsf/inst/include/geojson_properties.h |only geojsonsf-1.2/geojsonsf/inst/include/geojson_sfc.h |only geojsonsf-1.2/geojsonsf/inst/include/geojson_sfg.h |only geojsonsf-1.2/geojsonsf/inst/include/geojson_to_sf.h |only geojsonsf-1.2/geojsonsf/inst/include/geojson_validate.h |only geojsonsf-1.2/geojsonsf/inst/include/geojson_wkt.h |only geojsonsf-1.2/geojsonsf/inst/include/geojsonsf.h |only geojsonsf-1.2/geojsonsf/inst/include/geometrycollection |only geojsonsf-1.2/geojsonsf/inst/include/utils |only geojsonsf-1.2/geojsonsf/inst/include/writers |only 39 files changed, 303 insertions(+), 316 deletions(-)
Title: Mining Rigs for Specialized Subset Sum, Multi-Subset Sum,
Multidimensional Subset Sum, Multidimensional Knapsack,
Generalized Assignment Problems
Description: Specialized solvers for combinatorial optimization problems in the Subset Sum family. These solvers differ from the mainstream in the options of (i) restricting subset size, (ii) bounding subset elements, (iii) mining real-value sets with predefined subset sum errors, and (iv) finding one or more subsets in limited time. A novel algorithm for mining the one-dimensional Subset Sum induced algorithms for the multi-Subset Sum and the multidimensional Subset Sum. The latter decomposes the problem in a novel approach, and the multi-threaded framework offers exact algorithms to the multidimensional Knapsack and the Generalized Assignment problems. Package updates include (a) renewed implementation of the multi-Subset Sum, multidimensional Knapsack and Generalized Assignment solvers; (b) availability of bounding solution space in the multidimensional Subset Sum; (c) fundamental data structure and architectural changes for enhanced cache locality and better chance of SIMD vectorization; (d) an option of mapping real-domain problems to the integer domain with user-controlled precision loss, and those integers are further zipped non-uniformly in 64-bit buffers. Arithmetic on compressed integers is done by bit-manipulation and the design has virtually zero speed lag relative to normal integers arithmetic. The consequent reduction in dimensionality could yield substantial acceleration. Aggressive compiling, e.g. g++ '-Ofast', may speed up mining on some platforms. See package vignette (<arXiv:1612.04484v3>) for more details.
Author: Charlie Wusuo Liu
Maintainer: Charlie Wusuo Liu <liuwusuo@gmail.com>
Diff between FLSSS versions 7.6 dated 2018-08-28 and 7.7 dated 2018-11-22
FLSSS-7.6/FLSSS/man/GAPintegerized.Rd |only FLSSS-7.7/FLSSS/DESCRIPTION | 9 FLSSS-7.7/FLSSS/MD5 | 71 FLSSS-7.7/FLSSS/NAMESPACE | 14 FLSSS-7.7/FLSSS/R/RcppExports.R | 110 FLSSS-7.7/FLSSS/R/gap.r | 269 +- FLSSS-7.7/FLSSS/R/knapsack.r | 531 ++-- FLSSS-7.7/FLSSS/R/rfunsLegacy.r |only FLSSS-7.7/FLSSS/R/rinterface.r | 160 + FLSSS-7.7/FLSSS/inst |only FLSSS-7.7/FLSSS/man/FLSSS.Rd | 2 FLSSS-7.7/FLSSS/man/GAP.Rd | 32 FLSSS-7.7/FLSSS/man/mFLSSSparImposeBounds.Rd | 4 FLSSS-7.7/FLSSS/man/mmKnapsack.Rd | 350 +- FLSSS-7.7/FLSSS/man/mmKnapsackIntegerized.Rd | 20 FLSSS-7.7/FLSSS/src/GAP.cpp | 1742 +++++++++----- FLSSS-7.7/FLSSS/src/Gknapsack.cpp | 12 FLSSS-7.7/FLSSS/src/RcppExports.cpp | 101 FLSSS-7.7/FLSSS/src/findBoundInterface.cpp | 10 FLSSS-7.7/FLSSS/src/flsssVariableTree.cpp |only FLSSS-7.7/FLSSS/src/header/dnyTasking.hpp | 13 FLSSS-7.7/FLSSS/src/header/mPATclass.hpp | 39 FLSSS-7.7/FLSSS/src/header/macros.hpp | 3 FLSSS-7.7/FLSSS/src/header/mflsssOBJ.hpp | 2705 ++++++++++------------- FLSSS-7.7/FLSSS/src/header/mvalFindBound.hpp | 114 FLSSS-7.7/FLSSS/src/legacy/GAP.cpp |only FLSSS-7.7/FLSSS/src/legacy/GAPintegerized.Rd |only FLSSS-7.7/FLSSS/src/legacy/PATclass.hpp |only FLSSS-7.7/FLSSS/src/legacy/gap.r |only FLSSS-7.7/FLSSS/src/legacy/mPATclass.hpp |only FLSSS-7.7/FLSSS/src/legacy/macros.hpp |only FLSSS-7.7/FLSSS/src/legacy/multiDstack.hpp | 133 - FLSSS-7.7/FLSSS/src/legacy/multiDstack02.hpp |only FLSSS-7.7/FLSSS/src/legacy/mvalFindBound.hpp |only FLSSS-7.7/FLSSS/src/legacy/mvalOperation.hpp |only FLSSS-7.7/FLSSS/src/legacy/oneDfindBound.hpp |only FLSSS-7.7/FLSSS/src/legacy/oneDoperation.hpp |only FLSSS-7.7/FLSSS/src/legacy/raiseSupressBound.hpp |only FLSSS-7.7/FLSSS/src/legacy/singleDstack.hpp |only FLSSS-7.7/FLSSS/src/legacy/triMat.hpp |only FLSSS-7.7/FLSSS/src/legacy/triMatOneD.hpp |only FLSSS-7.7/FLSSS/src/mflsss.cpp | 8 FLSSS-7.7/FLSSS/src/mflsssVariableTree.cpp |only FLSSS-7.7/FLSSS/src/testIntegerize.cpp | 1 FLSSS-7.7/FLSSS/tests/debugTests |only FLSSS-7.7/FLSSS/tests/examples/GAP.r | 120 - FLSSS-7.7/FLSSS/tests/examples/mmKnapsack.r | 117 47 files changed, 3536 insertions(+), 3154 deletions(-)
Title: Next-Generation Sequencing (NGS) Data Analysis Toolkit
Description: Can be used to facilitate the analysis of NGS data, such as visualization, conversion of data format for WEB service input and other purpose.
Author: Jianfeng Li [aut, cre] (<https://orcid.org/0000-0003-2349-208X>)
Maintainer: Jianfeng Li <lee_jianfeng@sjtu.edu.cn>
Diff between ngstk versions 0.2.1 dated 2018-01-04 and 0.2.3 dated 2018-11-22
ChangeLog | 89 - DESCRIPTION | 17 MD5 | 123 + NAMESPACE | 17 NEWS.md |only R/bin.R |only R/cbioportal_trasefer.R | 12 R/cli.R |only R/format.R | 16 R/future.R |only R/log.R | 10 R/ngstk.R | 5 R/proteinpaint_transefer.R | 6 R/time_stamp.R |only README.md | 129 +- build/vignette.rds |binary inst/doc/ngstk.R | 36 inst/doc/ngstk.Rmd | 52 inst/doc/ngstk.html | 1555 +++++++++++++------------ inst/extdata/bin |only inst/extdata/config/theme.toml | 71 + inst/extdata/tools/annovar |only inst/extdata/tools/deseq2 |only inst/extdata/tools/rbash |only man/batch_file.Rd | 5 man/figures |only man/format_filenames.Rd | 13 man/format_pp_meta_fusions.Rd | 3 man/format_pp_meta_gender.Rd | 4 man/fusions2oncoprinter.Rd | 21 man/fusions2pp.Rd | 17 man/fusions2pp_meta.Rd | 17 man/fusions_filter.Rd | 11 man/get_files_ctime.Rd | 4 man/get_files_mtime.Rd | 4 man/make_option.Rd |only man/merge_table_files.Rd | 8 man/muts2mutation_mapper.Rd | 21 man/muts2oncoprinter.Rd | 21 man/muts2pp.Rd | 17 man/opt_parser.Rd |only man/par_download.Rd |only man/parse_args.Rd |only man/parse_args2.Rd |only man/print_help.Rd |only man/rbin.Rd |only man/show_handlers.Rd | 4 man/show_mhandlers.Rd | 8 man/split_row_file.Rd | 10 man/supress_any_message.Rd |only man/time_stamp.Rd |only tests/testthat.R | 1 tests/testthat/test_a_utils.R | 4 tests/testthat/test_b_proteinpaint_transefer.R | 7 tests/testthat/test_c_proteinpaint_utils.R | 13 tests/testthat/test_d_filter.R | 9 tests/testthat/test_e_handler.R | 4 tests/testthat/test_f_cbioportal_transefer.R | 3 tests/testthat/test_g_file.R | 4 tests/testthat/test_h_log.R | 15 tests/testthat/test_k_split.R | 26 tests/testthat/test_l_format.R | 8 tests/testthat/test_m_time_stamp.R |only tests/testthat/test_n_future.R |only tests/testthat/test_o_cli.R |only tests/testthat/test_p_bin.R |only vignettes/ngstk.Rmd | 52 67 files changed, 1519 insertions(+), 953 deletions(-)
Title: Simple Fisheries Stock Assessment Methods
Description: A variety of simple fish stock assessment methods.
Detailed vignettes are available on the fishR website <http://derekogle.com/fishR/>.
Author: Derek Ogle [aut, cre] (<https://orcid.org/0000-0002-0370-9299>),
Powell Wheeler [aut] (Added method='Burnham' to removal()),
Alexis Dinno [aut] (Provided base functionality of dunnTest())
Maintainer: Derek Ogle <derek@derekogle.com>
Diff between FSA versions 0.8.21 dated 2018-11-03 and 0.8.22 dated 2018-11-22
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ NEWS.md | 4 ++++ inst/CITATION | 6 ++++-- tests/testthat/Rplots.pdf |binary tests/testthat/test_VonBertalanffy_VALIDATE.R | 4 ++-- tests/testthat/test_metaM_VALIDATE.R | 2 +- 7 files changed, 22 insertions(+), 16 deletions(-)
Title: Animal Social Network Inference and Permutations for Ecologists
Description: Implements several tools that are used in animal social network analysis. In particular, this package provides the tools to infer groups and generate networks from observation data, perform permutation tests on the data, calculate lagged association rates, and performed multiple regression analysis on social network data.
Author: Damien R. Farine <dfarine@orn.mpg.de>
Maintainer: Damien R. Farine <dfarine@orn.mpg.de>
Diff between asnipe versions 1.1.10 dated 2018-07-06 and 1.1.11 dated 2018-11-22
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/gmmevents.R | 3 ++- R/network_permutation.R | 30 +++++++++++++++++++++++++++--- R/network_swap.R | 30 +++++++++++++++++++++++++++--- man/asnipe-package.Rd | 4 ++-- man/network_permutation.Rd | 11 +++++++---- man/network_swap.Rd | 8 ++++++-- 8 files changed, 82 insertions(+), 26 deletions(-)
Title: Read Rectangular Text Data
Description: The goal of 'readr' is to provide a fast and friendly way to read
rectangular data (like 'csv', 'tsv', and 'fwf'). It is designed to flexibly
parse many types of data found in the wild, while still cleanly failing when
data unexpectedly changes.
Author: Hadley Wickham [aut],
Jim Hester [aut, cre],
Romain Francois [aut],
R Core Team [ctb] (Date time code adapted from R),
RStudio [cph, fnd],
Jukka Jylänki [ctb, cph] (grisu3 implementation),
Mikkel Jørgensen [ctb, cph] (grisu3 implementation)
Maintainer: Jim Hester <james.hester@rstudio.com>
Diff between readr versions 1.2.0 dated 2018-11-22 and 1.2.1 dated 2018-11-22
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 4 ++++ inst/doc/readr.html | 14 +++++++------- tests/testthat/test-melt-csv.R | 1 + tests/testthat/test-read-csv.R | 1 + 6 files changed, 21 insertions(+), 15 deletions(-)
Title: Modelling Multivariate Data with Additive Bayesian Networks
Description: Bayesian network analysis is a form of probabilistic graphical models which derives from empirical data a directed acyclic graph, DAG, describing the dependency structure between random variables. An additive Bayesian network model consists of a form of a DAG where each node comprises a generalized linear model, GLM. Additive Bayesian network models are equivalent to Bayesian multivariate regression using graphical modelling, they generalises the usual multivariable regression, GLM, to multiple dependent variables. 'abn' provides routines to help determine optimal Bayesian network models for a given data set, where these models are used to identify statistical dependencies in messy, complex data. The additive formulation of these models is equivalent to multivariate generalised linear modelling (including mixed models with iid random effects). The usual term to describe this model selection process is structure discovery. The core functionality is concerned with model selection - determining the most robust empirical model of data from interdependent variables. Laplace approximations are used to estimate goodness of fit metrics and model parameters, and wrappers are also included to the INLA package which can be obtained from <http://www.r-inla.org>. A comprehensive set of documented case studies, numerical accuracy/quality assurance exercises, and additional documentation are available from the 'abn' website.
Author: Gilles Kratzer [aut, cre] (<https://orcid.org/0000-0002-5929-8935>),
Fraser Ian Lewis [aut],
Reinhard Furrer [ctb] (<https://orcid.org/0000-0002-6319-2332>),
Marta Pittavino [ctb] (<https://orcid.org/0000-0002-1232-1034>)
Maintainer: Gilles Kratzer <gilles.kratzer@math.uzh.ch>
Diff between abn versions 1.2 dated 2018-08-10 and 1.3 dated 2018-11-22
abn-1.2/abn/inst/doc/abn_v1.0.2.R |only abn-1.2/abn/inst/doc/abn_v1.0.2.Rnw |only abn-1.2/abn/inst/doc/abn_v1.0.2.pdf |only abn-1.2/abn/vignettes/Bootstrapping.png |only abn-1.2/abn/vignettes/ComparisonOfNetworkScore.pdf |only abn-1.2/abn/vignettes/DAG_cycle.pdf |only abn-1.2/abn/vignettes/MargPlots_PigsData.pdf |only abn-1.2/abn/vignettes/PigsArea.png |only abn-1.2/abn/vignettes/Pigs_PostBootPlots.pdf |only abn-1.2/abn/vignettes/Summary.png |only abn-1.2/abn/vignettes/abn.bib |only abn-1.2/abn/vignettes/abn_v1.0.2-concordance.tex |only abn-1.2/abn/vignettes/abn_v1.0.2.Rnw |only abn-1.2/abn/vignettes/dagcon.pdf |only abn-1.2/abn/vignettes/dagcon.png |only abn-1.2/abn/vignettes/map1_10var.dot |only abn-1.2/abn/vignettes/map1_10var.pdf |only abn-1.2/abn/vignettes/map1_10var.png |only abn-1.2/abn/vignettes/map_1par.dot |only abn-1.2/abn/vignettes/map_1par.pdf |only abn-1.2/abn/vignettes/mydag.dot |only abn-1.2/abn/vignettes/mydag.pdf |only abn-1.2/abn/vignettes/mydag_all.pdf |only abn-1.2/abn/vignettes/mydagcts.pdf |only abn-1.2/abn/vignettes/plbinaryNode.png |only abn-1.2/abn/vignettes/postbootpigs.pdf |only abn-1.2/abn/vignettes/var33_MASTER.pdf |only abn-1.3/abn/DESCRIPTION | 11 ++-- abn-1.3/abn/MD5 | 52 +++++---------------- abn-1.3/abn/R/abn-toolbox.R | 7 ++ abn-1.3/abn/R/fitabn_mle.R | 15 ------ abn-1.3/abn/R/heuristic_search.R | 29 +++++++++-- abn-1.3/abn/R/link-strength.R | 2 abn-1.3/abn/build/vignette.rds |binary abn-1.3/abn/inst/CITATION | 2 abn-1.3/abn/inst/doc/abn_v1.3.pdf |only abn-1.3/abn/inst/doc/abn_v1.3.pdf.asis |only abn-1.3/abn/man/link_strength.Rd | 2 abn-1.3/abn/src/abn_toolbox.cpp | 4 - abn-1.3/abn/src/irls_poisson.cpp | 2 abn-1.3/abn/src/irls_poisson_fast.cpp | 2 abn-1.3/abn/vignettes/abn_v1.3.pdf.asis |only 42 files changed, 58 insertions(+), 70 deletions(-)
Title: String Distance Calculation with Tidy Data Principles
Description: Calculation of string distance following the tidy data principles. Built on top
of the 'stringdist' package.
Author: Colin Fay [aut, cre] (<https://orcid.org/0000-0001-7343-1846>),
Dmytro Perepolkin [ctb] (<https://orcid.org/0000-0001-8558-6183>)
Maintainer: Colin Fay <contact@colinfay.me>
Diff between tidystringdist versions 0.1.2 dated 2018-01-04 and 0.1.3 dated 2018-11-22
DESCRIPTION | 20 +- MD5 | 31 ++-- NAMESPACE | 5 NEWS.md | 8 - R/tidycomb.R | 4 R/tidystringdist.R | 15 +- R/utils.R | 15 +- build/vignette.rds |binary inst/doc/Getting_started.R | 29 +--- inst/doc/Getting_started.Rmd | 65 +++------ inst/doc/Getting_started.html | 226 ++++++++++++++------------------- inst/doc/tests_and_coverage.R |only inst/doc/tests_and_coverage.Rmd |only inst/doc/tests_and_coverage.html |only man/tidy_stringdist.Rd | 4 tests/README.md |only tests/testthat/test-tidy_string_dist.R | 26 +++ vignettes/Getting_started.Rmd | 65 +++------ vignettes/tests_and_coverage.Rmd |only 19 files changed, 234 insertions(+), 279 deletions(-)
More information about tidystringdist at CRAN
Permanent link
Title: Labelled Data Utility Functions
Description: Collection of functions dealing with labelled data, like reading and
writing data between R and other statistical software packages like 'SPSS',
'SAS' or 'Stata', and working with labelled data. This includes easy ways
to get, set or change value and variable label attributes, to convert
labelled vectors into factors or numeric (and vice versa), or to deal with
multiple declared missing values.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>)
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>
Diff between sjlabelled versions 1.0.14 dated 2018-09-12 and 1.0.15 dated 2018-11-22
DESCRIPTION | 13 ++--- MD5 | 28 ++++++------ NEWS.md | 10 ++++ R/as_labelled.R | 4 - R/drop_labels.R | 2 R/get_labels.R | 54 ++--------------------- R/get_model_labels.R | 12 ++++- R/is_labelled.R | 20 ++++---- README.md | 4 - inst/doc/intro_sjlabelled.R | 8 ++- inst/doc/intro_sjlabelled.Rmd | 16 ++++-- inst/doc/intro_sjlabelled.html | 95 +++++++++++++++++++++-------------------- inst/doc/labelleddata.html | 4 - man/get_labels.Rd | 7 +-- vignettes/intro_sjlabelled.Rmd | 16 ++++-- 15 files changed, 141 insertions(+), 152 deletions(-)
Title: Gene Set Enrichment Analysis via Integration of Metabolic
Networks and RNA-Seq Data
Description: Integrates metabolic networks and RNA-seq data to construct condition-specific series of metabolic sub-networks and applies to gene set enrichment analysis (Tran et al. (2018) <doi:10.1093/bioinformatics/bty929>).
Author: Van Du T. Tran [aut, cre], Marco Pagni [aut]
Maintainer: Van Du T. Tran <thuong.tran@sib.swiss>
Diff between metaboGSE versions 1.1.0 dated 2018-08-07 and 1.2.0 dated 2018-11-22
DESCRIPTION | 13 MD5 | 57 +-- NAMESPACE | 1 R/data.R | 8 R/rescue.R | 100 +++-- R/submnet.R | 842 ++++++++++++++++++--------------------------- build/vignette.rds |binary data/exprMaguire.RData |binary data/iMK735.RData |binary data/yarli2GO.RData |binary data/yarliGOdata.RData |binary data/yarliGSE.RData |binary data/yarliSubmnets.RData |binary inst/CITATION | 8 inst/NEWS.Rd |only inst/doc/metaboGSE.R | 15 inst/doc/metaboGSE.Rmd | 39 +- inst/doc/metaboGSE.pdf |binary man/diagnosticTolerance.Rd | 4 man/fitness.Rd | 7 man/rescue.Rd | 6 man/rmGenes.Rd | 4 man/scoreGeneDel.Rd | 8 man/submnet.Rd | 12 man/yarli2GO.Rd | 2 man/yarliGOdata.Rd | 2 man/yarliGSE.Rd | 2 man/yarliSubmnets.Rd | 2 vignettes/bibliography.bib | 10 vignettes/metaboGSE.Rmd | 39 +- 30 files changed, 537 insertions(+), 644 deletions(-)
Title: R Interface to 'Keras'
Description: Interface to 'Keras' <https://keras.io>, a high-level neural
networks 'API'. 'Keras' was developed with a focus on enabling fast experimentation,
supports both convolution based networks and recurrent networks (as well as
combinations of the two), and runs seamlessly on both 'CPU' and 'GPU' devices.
Author: JJ Allaire [aut, cre],
François Chollet [aut, cph],
RStudio [ctb, cph, fnd],
Google [ctb, cph, fnd],
Yuan Tang [ctb, cph] (<https://orcid.org/0000-0001-5243-233X>),
Daniel Falbel [ctb, cph],
Wouter Van Der Bijl [ctb, cph],
Martin Studer [ctb, cph],
Sigrid Keydana [ctb]
Maintainer: JJ Allaire <jj@rstudio.com>
Diff between keras versions 2.2.0 dated 2018-08-24 and 2.2.4 dated 2018-11-22
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Title: Estimation Methods for Gravity Models
Description: A wrapper of different standard estimation methods for gravity models.
This package provides estimation methods for log-log models and multiplicative models.
Author: Anna-Lena Woelwer [aut],
Jan Pablo Burgard [aut],
Joshua Kunst [aut],
Mauricio Vargas [aut, cre]
Maintainer: Mauricio Vargas <mvargas@dcc.uchile.cl>
Diff between gravity versions 0.8.5 dated 2018-09-20 and 0.9.0 dated 2018-11-22
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Title: Functions for Community Data and Ordinations
Description: A collection of functions useful in (vegetation) community analyses and ordinations. Includes automatic species selection for ordination diagrams, species response curves and rank-abundance curves as well as calculation and sorting of synoptic tables.
Author: Friedemann Goral [aut, cre],
Jenny Schellenberg [aut]
Maintainer: Friedemann Goral <fgoral@gwdg.de>
Diff between goeveg versions 0.3.3 dated 2017-01-25 and 0.4.2 dated 2018-11-22
DESCRIPTION | 15 ++++++++------- MD5 | 44 ++++++++++++++++++++++++-------------------- NAMESPACE | 30 ++++++++++++++++-------------- NEWS.md | 7 +++++++ R/cv.r | 1 + R/dimcheckMDS.R | 15 +++++++++------ R/ordiselect.r | 8 +++++--- R/racurve.r | 8 +++++--- R/racurves.r | 10 ++++++---- R/sem.r | 1 + R/specresponse.R | 25 +++++++++++++++---------- R/synsort.R |only R/syntable.R |only README.md | 3 ++- man/cv.Rd | 2 +- man/dimcheckMDS.Rd | 16 ++++++++-------- man/ordiselect.Rd | 6 +++--- man/racurve.Rd | 18 +++++++++--------- man/racurves.Rd | 16 ++++++++-------- man/schedenenv.Rd | 1 - man/schedenveg.Rd | 1 - man/sem.Rd | 2 +- man/specresponse.Rd | 16 ++++++++-------- man/synsort.Rd |only man/syntable.Rd |only 25 files changed, 137 insertions(+), 108 deletions(-)
Title: Bayesian Inference of Non-Linear and Non-Gaussian State Space
Models
Description: Efficient methods for Bayesian inference of state space models
via particle Markov chain Monte Carlo and parallel importance sampling type weighted
Markov chain Monte Carlo (Vihola, Helske, and Franks, 2017, <arXiv:1609.02541>).
Gaussian, Poisson, binomial, or negative binomial
observation densities and basic stochastic volatility models with Gaussian state
dynamics, as well as general non-linear Gaussian models and discretised diffusion models
are supported.
Author: Jouni Helske, Matti Vihola
Maintainer: Jouni Helske <jouni.helske@iki.fi>
Diff between bssm versions 0.1.5 dated 2018-05-23 and 0.1.6-1 dated 2018-11-22
DESCRIPTION | 11 MD5 | 124 - NEWS | 6 R/approx.R | 174 - R/as_gssm.R | 254 +- R/bootstrap_filter.R | 296 +- R/bssm-package.R | 112 - R/check_arguments.R | 220 +- R/ekpf_filter.R | 70 R/importance_sample.R | 140 - R/initial_signal.R | 52 R/kfilter.R | 308 +-- R/loglik.R | 240 +- R/models.R | 3289 ++++++++++++++++----------------- R/particle_smoother.R | 436 ++-- R/plot.predict_bssm.R | 138 - R/predict.R | 560 ++--- R/print_mcmc.R | 480 ++-- R/priors.R | 222 +- R/run_mcmc.R | 14 R/sim_smoother.R | 166 - R/smoother.R | 406 ++-- R/zzz.R | 6 build/vignette.rds |binary inst/CITATION | 40 inst/doc/bssm.R | 50 inst/doc/bssm.Rmd | 723 +++---- inst/doc/bssm.pdf |binary inst/doc/growth_model.Rmd | 326 +-- inst/doc/growth_model.pdf |binary man/autoplot.predict_bssm.Rd | 4 man/gaussian_approx.Rd | 4 man/gssm.Rd | 4 man/importance_sample.Rd | 19 man/lgg_ssm.Rd | 4 man/ng_bsm.Rd | 5 man/nlg_ssm.Rd | 3 man/run_mcmc_g.Rd | 16 man/run_mcmc_ng.Rd | 43 man/summary.mcmc_output.Rd | 4 man/svm.Rd | 1 src/R_sde.cpp | 7 src/RcppExports.cpp | 1 src/mcmc.cpp | 40 src/sde_amcmc.cpp | 2 src/stratified_sample.cpp | 2 src/ugg_bsm.cpp | 12 src/ung_amcmc.cpp | 5 src/ung_bsm.cpp | 12 tests/test_all.R | 4 tests/testthat/test_approx.R | 162 - tests/testthat/test_as_gssm.R | 56 tests/testthat/test_basics.R | 216 +- tests/testthat/test_bootstrap_filter.R | 176 - tests/testthat/test_is.R | 56 tests/testthat/test_mcmc.R | 160 - tests/testthat/test_models.R | 134 - vignettes/bssm.Rmd | 723 +++---- vignettes/bssm.bib | 714 +++---- vignettes/growth_model.Rmd | 326 +-- vignettes/lgg_ssm_template.cpp | 254 +- vignettes/nlg_ssm_template.cpp | 296 +- vignettes/sde_ssm_template.cpp | 160 - 63 files changed, 6355 insertions(+), 6133 deletions(-)
Title: Time Series Representations
Description: Methods for representations (i.e. dimensionality reduction, preprocessing, feature extraction) of time series to help more accurate and effective time series data mining.
Non-data adaptive, data adaptive, model-based and data dictated (clipped) representation methods are implemented. Also min-max and z-score normalisations, and forecasting accuracy measures are implemented.
Author: Peter Laurinec [aut, cre] (<https://orcid.org/0000-0002-3501-8783>)
Maintainer: Peter Laurinec <tsreprpackage@gmail.com>
Diff between TSrepr versions 1.0.1 dated 2018-06-01 and 1.0.2 dated 2018-11-22
DESCRIPTION | 10 +- MD5 | 71 ++++++++-------- NAMESPACE | 1 NEWS.md | 7 + R/RcppExports.R | 84 ++++++++++++++++---- R/model_based_repr.R | 8 + R/windowing.R | 4 build/vignette.rds |binary inst/doc/TSrepr_extentions.html | 12 +- inst/doc/TSrepr_representations_of_time_series.Rmd | 18 ++-- inst/doc/TSrepr_representations_of_time_series.html | 41 +++++---- inst/doc/TSrepr_representations_use_case.Rmd | 4 inst/doc/TSrepr_representations_use_case.html | 19 ++-- man/clipping.Rd | 10 +- man/coef_comp.Rd | 2 man/denorm_min_max.Rd | 5 + man/denorm_z.Rd | 5 + man/fast_stat.Rd | 4 man/maape.Rd |only man/mape.Rd | 2 man/repr_feaclip.Rd | 25 +++-- man/repr_feacliptrend.Rd | 5 + man/repr_gam.Rd | 4 man/repr_lm.Rd | 4 man/repr_seas_profile.Rd | 4 man/repr_windowing.Rd | 5 + man/smape.Rd | 2 man/trending.Rd | 3 src/FeatureClippingTrending.cpp | 43 ++++++---- src/RcppExports.cpp | 13 +++ src/measures.cpp | 39 ++++++++- src/normalizations.cpp | 8 + src/reprsClassical.cpp | 4 tests/testthat/test_acc_measures.R | 2 vignettes/TSrepr_representations_of_time_series.Rmd | 18 ++-- vignettes/TSrepr_representations_use_case.Rmd | 4 vignettes/papers.bib | 10 ++ 37 files changed, 350 insertions(+), 150 deletions(-)
Title: Supplementary Item Response Theory Models
Description: Supplementary functions for item response models aiming
to complement existing R packages. The functionality includes among others
multidimensional compensatory and noncompensatory IRT models
(Reckase, 2009, <doi:10.1007/978-0-387-89976-3>),
MCMC for hierarchical IRT models and testlet models
(Fox, 2010, <doi:10.1007/978-1-4419-0742-4>),
NOHARM (Fraser & McDonald, 1982, <doi:10.1207/s15327906mbr2302_9>),
Rasch copula model (Braeken, 2011, <doi:10.1007/s11336-010-9190-4>;
Schroeders, Robitzsch & Schipolowski, 2014, <doi:10.1111/jedm.12054>),
faceted and hierarchical rater models (DeCarlo, Kim & Johnson, 2011,
<doi:10.1111/j.1745-3984.2011.00143.x>),
ordinal IRT model (ISOP; Scheiblechner, 1995, <doi:10.1007/BF02301417>),
DETECT statistic (Stout, Habing, Douglas & Kim, 1996,
<doi:10.1177/014662169602000403>), local structural equation modeling
(LSEM; Hildebrandt, Luedtke, Robitzsch, Sommer & Wilhelm, 2016,
<doi:10.1080/00273171.2016.1142856>).
Author: Alexander Robitzsch [aut,cre] (<https://orcid.org/0000-0002-8226-3132>)
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>
Diff between sirt versions 2.7-50 dated 2018-07-10 and 3.0-32 dated 2018-11-22
sirt-2.7-50/sirt/src/noharm_sirt_rcpp.cpp |only sirt-3.0-32/sirt/DESCRIPTION | 13 sirt-3.0-32/sirt/MD5 | 341 +++--- sirt-3.0-32/sirt/R/IRT.expectedCounts_sirt.R | 7 sirt-3.0-32/sirt/R/IRT.factor.scores.sirt.R | 12 sirt-3.0-32/sirt/R/IRT.factor.scores.xxirt.R | 11 sirt-3.0-32/sirt/R/IRT.mle.R | 42 sirt-3.0-32/sirt/R/IRT.modelfit.sirt.R | 32 sirt-3.0-32/sirt/R/R2conquest.R | 4 sirt-3.0-32/sirt/R/RcppExports.R | 66 - sirt-3.0-32/sirt/R/automatic.recode.R | 2 sirt-3.0-32/sirt/R/fit.adisop.R | 41 sirt-3.0-32/sirt/R/fit.gradedresponse.R | 24 sirt-3.0-32/sirt/R/gom.jml.R | 6 sirt-3.0-32/sirt/R/latent.regression.em.normal.R | 4 sirt-3.0-32/sirt/R/latent.regression.em.raschtype.R | 4 sirt-3.0-32/sirt/R/linking_haberman_als.R | 23 sirt-3.0-32/sirt/R/logLik_sirt.R | 5 sirt-3.0-32/sirt/R/lsem.estimate.R | 45 sirt-3.0-32/sirt/R/lsem.permutationTest.R | 47 sirt-3.0-32/sirt/R/mcmc.2pno.R | 5 sirt-3.0-32/sirt/R/mcmc.2pno.ml.R | 39 sirt-3.0-32/sirt/R/mcmc.2pnoh.R | 5 sirt-3.0-32/sirt/R/mcmc.3pno.testlet.R | 12 sirt-3.0-32/sirt/R/mcmc.3pno.testlet_output.R | 132 +- sirt-3.0-32/sirt/R/mcmc_3pno_testlet_draw_itempars.R | 2 sirt-3.0-32/sirt/R/mirt.wrapper.calc.counts.R | 10 sirt-3.0-32/sirt/R/rasch.copula2_aux.R | 7 sirt-3.0-32/sirt/R/rasch.jml.R | 544 ++++------- sirt-3.0-32/sirt/R/rasch_jml_centeritems.R |only sirt-3.0-32/sirt/R/rasch_jml_centerpersons.R |only sirt-3.0-32/sirt/R/rasch_jml_emp_discrim.R |only sirt-3.0-32/sirt/R/rasch_jml_itemfit.R |only sirt-3.0-32/sirt/R/rasch_jml_person_parameters_summary.R |only sirt-3.0-32/sirt/R/rasch_jml_update_b.R |only sirt-3.0-32/sirt/R/rm.sdt.R | 8 sirt-3.0-32/sirt/R/sirt_sign_space.R |only sirt-3.0-32/sirt/R/sirt_summary_cat_label_equal_value.R |only sirt-3.0-32/sirt/R/sirt_summary_label_equal_value.R |only sirt-3.0-32/sirt/R/summary.latent.regression.R | 4 sirt-3.0-32/sirt/R/summary.lsem.R | 6 sirt-3.0-32/sirt/R/summary.lsem.permutationTest.R | 3 sirt-3.0-32/sirt/R/summary.rasch.jml.R |only sirt-3.0-32/sirt/README.md | 2 sirt-3.0-32/sirt/build |only sirt-3.0-32/sirt/data/data.activity.itempars.rda |binary sirt-3.0-32/sirt/data/data.befki.rda |binary sirt-3.0-32/sirt/data/data.befki_resp.rda |binary sirt-3.0-32/sirt/data/data.big5.qgraph.rda |binary sirt-3.0-32/sirt/data/data.big5.rda |binary sirt-3.0-32/sirt/data/data.bs07a.rda |binary sirt-3.0-32/sirt/data/data.eid.kap4.rda |binary sirt-3.0-32/sirt/data/data.eid.kap5.rda |binary sirt-3.0-32/sirt/data/data.eid.kap6.rda |binary sirt-3.0-32/sirt/data/data.eid.kap7.rda |binary sirt-3.0-32/sirt/data/data.eid.rda |binary sirt-3.0-32/sirt/data/data.ess2005.rda |binary sirt-3.0-32/sirt/data/data.g308.rda |binary sirt-3.0-32/sirt/data/data.inv4gr.rda |binary sirt-3.0-32/sirt/data/data.liking.science.rda |binary sirt-3.0-32/sirt/data/data.long.rda |binary sirt-3.0-32/sirt/data/data.lsem01.rda |binary sirt-3.0-32/sirt/data/data.math.rda |binary sirt-3.0-32/sirt/data/data.mcdonald.LSAT6.rda |binary sirt-3.0-32/sirt/data/data.mcdonald.act15.rda |binary sirt-3.0-32/sirt/data/data.mcdonald.rape.rda |binary sirt-3.0-32/sirt/data/data.mixed1.rda |binary sirt-3.0-32/sirt/data/data.ml1.rda |binary sirt-3.0-32/sirt/data/data.ml2.rda |binary sirt-3.0-32/sirt/data/data.noharm18.rda |binary sirt-3.0-32/sirt/data/data.noharmExC.rda |binary sirt-3.0-32/sirt/data/data.pars1.2pl.rda |binary sirt-3.0-32/sirt/data/data.pars1.rasch.rda |binary sirt-3.0-32/sirt/data/data.pirlsmissing.rda |binary sirt-3.0-32/sirt/data/data.pisaMath.rda |binary sirt-3.0-32/sirt/data/data.pisaPars.rda |binary sirt-3.0-32/sirt/data/data.pisaRead.rda |binary sirt-3.0-32/sirt/data/data.pw01.rda |binary sirt-3.0-32/sirt/data/data.ratings1.rda |binary sirt-3.0-32/sirt/data/data.ratings2.rda |binary sirt-3.0-32/sirt/data/data.ratings3.rda |binary sirt-3.0-32/sirt/data/data.raw1.rda |binary sirt-3.0-32/sirt/data/data.read.rda |binary sirt-3.0-32/sirt/data/data.reck21.rda |binary sirt-3.0-32/sirt/data/data.reck61DAT1.rda |binary sirt-3.0-32/sirt/data/data.reck61DAT2.rda |binary sirt-3.0-32/sirt/data/data.reck73C1a.rda |binary sirt-3.0-32/sirt/data/data.reck73C1b.rda |binary sirt-3.0-32/sirt/data/data.reck75C2.rda |binary sirt-3.0-32/sirt/data/data.reck78ExA.rda |binary sirt-3.0-32/sirt/data/data.reck79ExB.rda |binary sirt-3.0-32/sirt/data/data.si01.rda |binary sirt-3.0-32/sirt/data/data.si02.rda |binary sirt-3.0-32/sirt/data/data.si03.rda |binary sirt-3.0-32/sirt/data/data.si04.rda |binary sirt-3.0-32/sirt/data/data.si05.rda |binary sirt-3.0-32/sirt/data/data.si06.rda |binary sirt-3.0-32/sirt/data/data.timss.rda |binary sirt-3.0-32/sirt/data/data.timss07.G8.RUS.rda |binary sirt-3.0-32/sirt/inst/NEWS | 24 sirt-3.0-32/sirt/man/IRT.mle.Rd | 8 sirt-3.0-32/sirt/man/Q3.Rd | 11 sirt-3.0-32/sirt/man/Q3.testlet.Rd | 6 sirt-3.0-32/sirt/man/R2noharm.Rd | 6 sirt-3.0-32/sirt/man/R2noharm.jackknife.Rd | 5 sirt-3.0-32/sirt/man/brm.sim.Rd | 10 sirt-3.0-32/sirt/man/btm.Rd | 39 sirt-3.0-32/sirt/man/class.accuracy.rasch.Rd | 4 sirt-3.0-32/sirt/man/conf.detect.Rd | 22 sirt-3.0-32/sirt/man/data.befki.Rd | 5 sirt-3.0-32/sirt/man/data.big5.Rd | 4 sirt-3.0-32/sirt/man/data.ess2005.Rd | 4 sirt-3.0-32/sirt/man/data.g308.Rd | 4 sirt-3.0-32/sirt/man/data.si.Rd | 6 sirt-3.0-32/sirt/man/detect.index.Rd | 10 sirt-3.0-32/sirt/man/dif.logistic.regression.Rd | 9 sirt-3.0-32/sirt/man/equating.rasch.jackknife.Rd | 4 sirt-3.0-32/sirt/man/expl.detect.Rd | 14 sirt-3.0-32/sirt/man/f1d.irt.Rd | 13 sirt-3.0-32/sirt/man/fit.isop.Rd | 10 sirt-3.0-32/sirt/man/fuzcluster.Rd | 4 sirt-3.0-32/sirt/man/fuzdiscr.Rd | 6 sirt-3.0-32/sirt/man/gom.em.Rd | 21 sirt-3.0-32/sirt/man/greenyang.reliability.Rd | 14 sirt-3.0-32/sirt/man/invariance.alignment.Rd | 12 sirt-3.0-32/sirt/man/isop.Rd | 18 sirt-3.0-32/sirt/man/isop.scoring.Rd | 8 sirt-3.0-32/sirt/man/isop.test.Rd | 4 sirt-3.0-32/sirt/man/latent.regression.em.raschtype.Rd | 14 sirt-3.0-32/sirt/man/lc.2raters.Rd | 12 sirt-3.0-32/sirt/man/linking.haberman.Rd | 10 sirt-3.0-32/sirt/man/lsdm.Rd | 17 sirt-3.0-32/sirt/man/lsem.estimate.Rd | 11 sirt-3.0-32/sirt/man/lsem.permutationTest.Rd | 6 sirt-3.0-32/sirt/man/marginal.truescore.reliability.Rd | 8 sirt-3.0-32/sirt/man/mcmc.2pno.ml.Rd | 14 sirt-3.0-32/sirt/man/mcmc.2pnoh.Rd | 6 sirt-3.0-32/sirt/man/mcmc.3pno.testlet.Rd | 13 sirt-3.0-32/sirt/man/modelfit.sirt.Rd | 17 sirt-3.0-32/sirt/man/noharm.sirt.Rd | 8 sirt-3.0-32/sirt/man/np.dich.Rd | 4 sirt-3.0-32/sirt/man/pbivnorm2.Rd | 15 sirt-3.0-32/sirt/man/pcm.fit.Rd | 4 sirt-3.0-32/sirt/man/personfit.stat.Rd | 9 sirt-3.0-32/sirt/man/pgenlogis.Rd | 8 sirt-3.0-32/sirt/man/plausible.value.imputation.raschtype.Rd | 6 sirt-3.0-32/sirt/man/polychoric2.Rd | 4 sirt-3.0-32/sirt/man/prmse.subscores.scales.Rd | 11 sirt-3.0-32/sirt/man/prob.guttman.Rd | 10 sirt-3.0-32/sirt/man/qmc.nodes.Rd | 7 sirt-3.0-32/sirt/man/rasch.copula.Rd | 14 sirt-3.0-32/sirt/man/rasch.evm.pcm.Rd | 8 sirt-3.0-32/sirt/man/rasch.jml.Rd | 24 sirt-3.0-32/sirt/man/rasch.jml.jackknife1.Rd | 4 sirt-3.0-32/sirt/man/rasch.mirtlc.Rd | 15 sirt-3.0-32/sirt/man/rasch.mml.Rd | 22 sirt-3.0-32/sirt/man/rasch.pairwise.Rd | 25 sirt-3.0-32/sirt/man/rasch.pairwise.itemcluster.Rd | 7 sirt-3.0-32/sirt/man/rasch.pml3.Rd | 25 sirt-3.0-32/sirt/man/rasch.va.Rd | 14 sirt-3.0-32/sirt/man/reliability.nonlinearSEM.Rd | 4 sirt-3.0-32/sirt/man/rm.facets.Rd | 4 sirt-3.0-32/sirt/man/rm.sdt.Rd | 7 sirt-3.0-32/sirt/man/sim.qm.ramsay.Rd | 16 sirt-3.0-32/sirt/man/sim.raschtype.Rd | 23 sirt-3.0-32/sirt/man/sirt-package.Rd | 108 +- sirt-3.0-32/sirt/man/smirt.Rd | 9 sirt-3.0-32/sirt/man/stratified.cronbach.alpha.Rd | 7 sirt-3.0-32/sirt/man/testlet.marginalized.Rd | 6 sirt-3.0-32/sirt/man/tetrachoric2.Rd | 14 sirt-3.0-32/sirt/man/unidim.test.csn.Rd | 7 sirt-3.0-32/sirt/man/wle.rasch.Rd | 6 sirt-3.0-32/sirt/man/wle.rasch.jackknife.Rd | 9 sirt-3.0-32/sirt/src/Makevars | 2 sirt-3.0-32/sirt/src/Makevars.win | 2 sirt-3.0-32/sirt/src/RcppExports.cpp | 318 +++--- sirt-3.0-32/sirt/src/sirt_rcpp_noharm.cpp |only sirt-3.0-32/sirt/src/sirt_rcpp_rm_sdt.cpp | 5 178 files changed, 1398 insertions(+), 1334 deletions(-)
Title: A Button-Based GUI for Financial and Economic Data Analysis
Description: A GUI designed to support the analysis of financial-economic time
series data.
Author: Ho Tsung-wu
Maintainer: Ho Tsung-wu <tsungwu@ntnu.edu.tw>
Diff between iClick versions 1.4 dated 2018-02-24 and 1.5 dated 2018-11-22
DESCRIPTION | 10 +++++----- MD5 | 34 +++++++++++++++++----------------- R/iClick_VisAssetPrice.R | 13 ++++++++----- man/VIF_no.Rd | 2 +- man/boxPlotX.Rd | 4 ++-- man/calendarHeat.Rd | 4 ++-- man/cumulatedPlotX.Rd | 6 +++--- man/cutAndStack.Rd | 4 ++-- man/drawdownPlotX.Rd | 2 +- man/drawupPlotX.Rd | 2 +- man/iClick-package.Rd | 4 ++-- man/iClick.ARIMA.Rd | 2 +- man/iClick.GARCH.Rd | 2 +- man/iClick.VisAssetPrice.Rd | 4 ++-- man/iClick.VisOneReturns.Rd | 2 +- man/iClick.lm.Rd | 2 +- man/qqnormPlotX.Rd | 4 ++-- man/seriesPlotX.Rd | 2 +- 18 files changed, 53 insertions(+), 50 deletions(-)
Title: Weighting for Covariate Balance in Observational Studies
Description: Generates weights to form equivalent groups in observational studies by easing and extending the functionality of the R packages 'twang' (Ridgeway et al., 2017) <https://CRAN.R-project.org/package=twang> for generalized boosted modeling, 'CBPS' (Fong, Ratkovic, & Imai, 2018) <https://CRAN.R-project.org/package=CBPS> for covariate balancing propensity score weighting, 'ebal' (Hainmueller, 2014) <https://CRAN.R-project.org/package=ebal> for entropy balancing, 'sbw' (Zubizarreta, 2015) <doi:10.1080/01621459.2015.1023805>, and 'ATE' (Haris & Chan, 2015) <https://CRAN.R-project.org/package=ATE> for empirical balancing calibration weighting. Also allows for assessment of weights and checking of covariate balance by interfacing directly with 'cobalt' (Greifer, 2018) <https://CRAN.R-project.org/package=cobalt>.
Author: Noah Greifer [aut, cre]
Maintainer: Noah Greifer <noah.greifer@gmail.com>
Diff between WeightIt versions 0.4.0 dated 2018-06-25 and 0.5.0 dated 2018-11-22
DESCRIPTION | 12 MD5 | 53 +- NAMESPACE | 2 NEWS.md | 16 R/functions_for_processing.R | 273 ++++++++---- R/ps.cont.R | 6 R/trim.R | 28 - R/weightit.R | 88 ++-- R/weightit.fit.R | 130 +++++- R/weightit2method.R | 766 +++++++++++++++++++++++++++++------- R/weightitMSM.R | 236 +++++++---- README.md | 51 +- build/partial.rdb |binary build/vignette.rds |binary inst/doc/WeightIt_A0_basic_use.R | 6 inst/doc/WeightIt_A0_basic_use.Rmd | 18 inst/doc/WeightIt_A0_basic_use.html | 377 ++++++++++++++--- man/method-cbps.Rd |only man/method-ebal.Rd |only man/method-ebcw.Rd |only man/method-gbm.Rd |only man/method-npcbps.Rd |only man/method-optweight.Rd |only man/method-ps.Rd |only man/method-super.Rd |only man/method-user.Rd |only man/ps.cont.Rd | 18 man/summary.weightit.Rd | 6 man/trim.Rd | 2 man/weightit.Rd | 136 +----- man/weightitMSM.Rd | 38 + vignettes/WeightIt_A0_basic_use.Rmd | 18 32 files changed, 1610 insertions(+), 670 deletions(-)
Title: Read Rectangular Text Data
Description: The goal of 'readr' is to provide a fast and friendly way to read
rectangular data (like 'csv', 'tsv', and 'fwf'). It is designed to flexibly
parse many types of data found in the wild, while still cleanly failing when
data unexpectedly changes.
Author: Hadley Wickham [aut],
Jim Hester [aut, cre],
Romain Francois [aut],
R Core Team [ctb] (Date time code adapted from R),
RStudio [cph, fnd],
Jukka Jylänki [ctb, cph] (grisu3 implementation),
Mikkel Jørgensen [ctb, cph] (grisu3 implementation)
Maintainer: Jim Hester <james.hester@rstudio.com>
Diff between readr versions 1.1.1 dated 2017-05-16 and 1.2.0 dated 2018-11-22
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Title: Maximum Likelihood Analysis of Animal Movement Behavior Using
Multivariate Hidden Markov Models
Description: Extended tools for analyzing telemetry data using generalized hidden Markov models. Features of momentuHMM (pronounced ``momentum'') include data pre-processing and visualization, fitting HMMs to location and auxiliary biotelemetry or environmental data, biased and correlated random walk movement models, multiple imputation for incorporating location measurement error and missing data, user-specified design matrices and constraints for covariate modelling of parameters, decoding of the state process, visualization of fitted models, model checking and selection, and simulation. See McClintock and Michelot (2018) <doi:10.1111/2041-210X.12995>.
Author: Brett McClintock, Theo Michelot
Maintainer: Brett McClintock <brett.mcclintock@noaa.gov>
Diff between momentuHMM versions 1.4.2 dated 2018-06-20 and 1.4.3 dated 2018-11-22
DESCRIPTION | 20 +- MD5 | 212 ++++++++++++++--------------- NAMESPACE | 2 NEWS | 31 ++++ R/AIC_momentuHMM.R | 3 R/CIbeta.R | 6 R/CIreal.R | 23 +-- R/MIfitHMM.R | 58 ++++--- R/MIpool.R | 52 ++++--- R/RcppExports.R | 10 - R/checkPar0.R | 50 ++++++ R/crawlMerge.R | 6 R/crawlWrap.R | 164 ++++++++++++---------- R/exGen.R | 12 - R/expandPar.R |only R/fitHMM.R | 173 +++++++++++++++++------ R/getPar.R | 10 + R/getPar0.R | 37 ++--- R/getWorkBounds.R | 4 R/logAlpha.R | 4 R/logBeta.R | 4 R/momentuHMM.R | 2 R/momentuHMM_utils.R | 44 +++--- R/nLogLike.R | 16 +- R/plotSpatialCov.R | 3 R/plotStationary.R | 19 +- R/plot_crwData.R | 6 R/plot_miHMM.R | 11 - R/plot_miSum.R | 18 -- R/plot_momentuHMM.R | 15 +- R/print_miHMM.R | 11 - R/print_miSum.R | 16 +- R/print_momentuHMM.R | 5 R/pseudoRes.R | 7 R/simData.R | 172 ++++++++++++++--------- R/stationary.R | 4 R/timeInStates.R | 8 - R/viterbi.R | 2 README.md | 10 - data/example.RData |binary inst/doc/momentuHMM.R | 68 +++++---- inst/doc/momentuHMM.Rnw | 88 +++++++----- inst/doc/momentuHMM.pdf |binary man/MIfitHMM.Rd | 29 ++- man/MIpool.Rd | 9 - man/checkPar0.Rd | 8 - man/crawlMerge.Rd | 6 man/crawlWrap.Rd | 24 +-- man/example.Rd | 3 man/expandPar.Rd |only man/fitHMM.Rd | 40 ++++- man/getPar0.Rd | 23 +-- man/momentuHMM.Rd | 2 man/nLogLike.Rd | 16 +- man/nLogLike_rcpp.Rd | 4 man/plot.crwData.Rd | 6 man/plot.miHMM.Rd | 11 - man/plot.miSum.Rd | 11 - man/print.miHMM.Rd | 11 - man/print.miSum.Rd | 11 - man/simData.Rd | 23 ++- man/trMatrix_rcpp.Rd | 4 src/RcppExports.cpp | 14 + src/momentuHMM_init.c | 10 - src/nLogLike.cpp | 7 src/trMatrix.cpp | 5 vignettes/elephantExample.R | 4 vignettes/greySealExample_TPM.R | 50 +++--- vignettes/harbourSealExample.R | 81 ++++++----- vignettes/master.bib | 11 + vignettes/momentuHMM-concordance.tex | 12 - vignettes/momentuHMM.Rnw | 88 +++++++----- vignettes/nfsExample.R | 45 ++++-- vignettes/northernFulmarExample.R | 37 +++-- vignettes/plot_elephantResults001.pdf |binary vignettes/plot_elephantResults002.pdf |binary vignettes/plot_elephantResults009.pdf |binary vignettes/plot_elephantResults010.pdf |binary vignettes/plot_elephantResults012.pdf |binary vignettes/plot_elephantResults013.pdf |binary vignettes/plot_elephantResults015.pdf |binary vignettes/plot_elephantResults016.pdf |binary vignettes/plot_elephantResults017.pdf |binary vignettes/plot_greySealResults002.pdf |binary vignettes/plot_greySealResults006.pdf |binary vignettes/plot_greySealResults009.pdf |binary vignettes/plot_greySealResults013.pdf |binary vignettes/plot_greySealResults1.png |binary vignettes/plot_greySealResults2.png |binary vignettes/plot_groupExample001.pdf |binary vignettes/plot_groupExampleCentroid001.pdf |binary vignettes/plot_groupExampleResults007.pdf |binary vignettes/plot_groupExampleResults008.pdf |binary vignettes/plot_harbourSeal.png |binary vignettes/plot_harbourSealResults020.pdf |binary vignettes/plot_nfsResults.pdf |binary vignettes/plot_northernFulmarExample.png |binary vignettes/plot_sesResults001.pdf |binary vignettes/plot_sesResults003.pdf |binary vignettes/plot_sesResults007.pdf |binary vignettes/plot_sesResults009.pdf |binary vignettes/plot_turtleResults001.pdf | 57 ++++--- vignettes/plot_turtleResults002.pdf |binary vignettes/plot_turtleResults004.pdf |binary vignettes/plot_turtleResults2.pdf |binary vignettes/turtleExample.R | 8 - vignettes/vignette_examples.R | 31 ---- vignettes/vignette_inputs.RData |binary 108 files changed, 1264 insertions(+), 843 deletions(-)
Title: Multi-States Semi-Markov Models
Description: Functions for fitting multi-state semi-Markov models to longitudinal data. A parametric maximum likelihood estimation method adapted to deal with Exponential, Weibull and Exponentiated Weibull distributions is considered. Right-censoring can be taken into account and both constant and time-varying covariates can be included using a Cox proportional model. Reference: A. Krol and P. Saint-Pierre (2015) <doi:10.18637/jss.v066.i06>.
Author: Agnieszka Listwon-Krol, Philippe Saint-Pierre
Maintainer: Agnieszka Listwon-Krol <krol@lunenfeld.ca>
Diff between SemiMarkov versions 1.4.4 dated 2018-05-29 and 1.4.5 dated 2018-11-22
DESCRIPTION | 8 - MD5 | 4 R/SemiMarkov.r | 447 +++++++++++++++++++++++++++++++++------------------------ 3 files changed, 271 insertions(+), 188 deletions(-)
Title: Generating Various Numerical Representation Schemes for Protein
Sequences
Description: Comprehensive toolkit for generating various numerical
features of protein sequences described in Xiao et al. (2015)
<DOI:10.1093/bioinformatics/btv042>. For full functionality,
the software 'ncbi-blast+' is needed, see
<https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download>
for more information.
Author: Nan Xiao [aut, cre] (<https://orcid.org/0000-0002-0250-5673>),
Qing-Song Xu [aut],
Dong-Sheng Cao [aut]
Maintainer: Nan Xiao <me@nanx.me>
Diff between protr versions 1.5-1 dated 2018-07-13 and 1.5-2 dated 2018-11-22
DESCRIPTION | 8 LICENSE | 2 MD5 | 36 NEWS.md | 11 R/misc-05-getUniProt.R | 4 R/par-01-parSeqSim.R | 109 +- inst/doc/protr.Rmd | 8 inst/doc/protr.html | 2233 ++++++++++++++++++++++++++++++++++++------------ man/extractAPAAC.Rd | 4 man/extractPAAC.Rd | 4 man/extractPSSM.Rd | 17 man/extractProtFPGap.Rd | 3 man/parGOSim.Rd | 4 man/parSeqSim.Rd | 9 man/protseg.Rd | 4 man/twoGOSim.Rd | 4 man/twoSeqSim.Rd | 13 vignettes/protr.Rmd | 8 vignettes/protr.css | 313 ------ 19 files changed, 1834 insertions(+), 960 deletions(-)
Title: Hydrologic Indices for Daily Time Series Data
Description: Calculates a suite of hydrologic indices for daily time series data that are widely used in hydrology and stream ecology.
Author: Nick Bond
Maintainer: Nick Bond <n.bond@latrobe.edu.au>
Diff between hydrostats versions 0.2.5 dated 2016-11-17 and 0.2.6 dated 2018-11-22
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ NEWS | 8 ++++++++ R/baseflows.R | 7 ++++++- R/high.spells.R | 4 ++-- R/low.spells.R | 4 ++-- README.md | 2 +- 7 files changed, 29 insertions(+), 16 deletions(-)