Title: The 'jamovi' Analyses
Description: A suite of common statistical methods such as descriptives,
t-tests, ANOVAs, regression, correlation matrices, proportion tests,
contingency tables, and factor analysis. This package is also useable from
the 'jamovi' statistical spreadsheet (see <https://www.jamovi.org> for more
information).
Author: Ravi Selker, Jonathon Love, Damian Dropmann
Maintainer: Jonathon Love <jon@thon.cc>
Diff between jmv versions 0.9.6.1 dated 2019-04-22 and 1.0.8 dated 2019-10-23
jmv-0.9.6.1/jmv/R/deprecated.R |only jmv-1.0.8/jmv/DESCRIPTION | 14 jmv-1.0.8/jmv/MD5 | 108 ++--- jmv-1.0.8/jmv/NAMESPACE | 2 jmv-1.0.8/jmv/R/00jmv.R |only jmv-1.0.8/jmv/R/ancova.b.R | 180 ++++++--- jmv-1.0.8/jmv/R/ancova.h.R | 71 ++- jmv-1.0.8/jmv/R/anova.h.R | 46 +- jmv-1.0.8/jmv/R/anovanp.b.R | 17 jmv-1.0.8/jmv/R/anovanp.h.R | 36 + jmv-1.0.8/jmv/R/anovaonew.h.R | 14 jmv-1.0.8/jmv/R/anovarm.b.R | 77 +++ jmv-1.0.8/jmv/R/anovarm.h.R | 97 +++- jmv-1.0.8/jmv/R/anovarmnp.h.R | 8 jmv-1.0.8/jmv/R/cfa.h.R | 7 jmv-1.0.8/jmv/R/conttables.b.R | 16 jmv-1.0.8/jmv/R/conttables.h.R | 46 +- jmv-1.0.8/jmv/R/conttablespaired.h.R | 20 - jmv-1.0.8/jmv/R/corrmatrix.b.R | 27 + jmv-1.0.8/jmv/R/corrmatrix.h.R | 18 jmv-1.0.8/jmv/R/descriptives.b.R | 172 +++++--- jmv-1.0.8/jmv/R/descriptives.h.R | 13 jmv-1.0.8/jmv/R/efa.h.R | 15 jmv-1.0.8/jmv/R/html.b.R |only jmv-1.0.8/jmv/R/html.h.R |only jmv-1.0.8/jmv/R/linreg.b.R | 67 ++- jmv-1.0.8/jmv/R/linreg.h.R | 61 ++- jmv-1.0.8/jmv/R/loglinear.h.R | 13 jmv-1.0.8/jmv/R/logregbin.h.R | 19 jmv-1.0.8/jmv/R/logregmulti.h.R | 18 jmv-1.0.8/jmv/R/logregord.h.R | 15 jmv-1.0.8/jmv/R/mancova.h.R | 17 jmv-1.0.8/jmv/R/pca.b.R | 5 jmv-1.0.8/jmv/R/pca.h.R | 8 jmv-1.0.8/jmv/R/proptest2.h.R | 7 jmv-1.0.8/jmv/R/proptestn.h.R | 17 jmv-1.0.8/jmv/R/reliability.h.R | 10 jmv-1.0.8/jmv/R/ttestis.b.R | 11 jmv-1.0.8/jmv/R/ttestis.h.R | 22 - jmv-1.0.8/jmv/R/ttestones.h.R | 14 jmv-1.0.8/jmv/R/ttestps.h.R | 16 jmv-1.0.8/jmv/inst/doc/new-syntax.html | 509 ++++++++++---------------- jmv-1.0.8/jmv/man/ANOVA.Rd | 21 - jmv-1.0.8/jmv/man/ancova.Rd | 14 jmv-1.0.8/jmv/man/anovaNP.Rd | 4 jmv-1.0.8/jmv/man/anovaRM.Rd | 6 jmv-1.0.8/jmv/man/contTables.Rd | 12 jmv-1.0.8/jmv/man/corrMatrix.Rd | 6 jmv-1.0.8/jmv/man/efa.Rd | 4 jmv-1.0.8/jmv/man/linReg.Rd | 16 jmv-1.0.8/jmv/man/mancova.Rd | 4 jmv-1.0.8/jmv/man/ttestPS.Rd | 6 jmv-1.0.8/jmv/tests/testthat.R | 2 jmv-1.0.8/jmv/tests/testthat/testanovarm.R | 1 jmv-1.0.8/jmv/tests/testthat/testconttables.R | 1 jmv-1.0.8/jmv/tests/testthat/testcorrmatrix.R | 4 jmv-1.0.8/jmv/tests/testthat/testlinreg.R | 10 57 files changed, 1153 insertions(+), 791 deletions(-)
Title: Securely Wrangle Dataset According to Data Usage Agreement
Description: Create shareable data sets from raw data files that
contain protected elements. Relying on master crosswalk
files that list restricted variables, package functions
warn users about possible violations of data usage
agreement and prevent writing protected elements.
Author: Benjamin Skinner [aut, cre] (<https://orcid.org/0000-0002-0337-7415>)
Maintainer: Benjamin Skinner <btskinner@coe.ufl.edu>
Diff between duawranglr versions 0.6.3 dated 2018-09-16 and 0.6.4 dated 2019-10-23
DESCRIPTION | 14 - MD5 | 14 - NEWS.md | 8 build/vignette.rds |binary inst/doc/duawranglr.html | 7 inst/doc/securing_data.Rmd | 1 inst/doc/securing_data.html | 437 +++++++++++++++++++++++--------------------- vignettes/securing_data.Rmd | 1 8 files changed, 265 insertions(+), 217 deletions(-)
Title: Rename and Encode Data Frames Using External Crosswalk Files
Description: A pair of functions for renaming and encoding data frames
using external crosswalk files. It is especially useful when
constructing master data sets from multiple smaller data
sets that do not name or encode variables consistently
across files. Based on similar commands in 'Stata'.
Author: Benjamin Skinner [aut, cre] (<https://orcid.org/0000-0002-0337-7415>)
Maintainer: Benjamin Skinner <btskinner@coe.ufl.edu>
Diff between crosswalkr versions 0.2.4 dated 2019-03-04 and 0.2.5 dated 2019-10-23
DESCRIPTION | 14 MD5 | 12 NEWS.md | 18 + build/vignette.rds |binary inst/doc/crosswalkr.Rmd | 3 inst/doc/crosswalkr.html | 827 +++++++++++++++++++++++++---------------------- vignettes/crosswalkr.Rmd | 3 7 files changed, 475 insertions(+), 402 deletions(-)
Title: Toolkit for Credit Modeling
Description: Provides a highly efficient R tool suite for Credit Modeling, Analysis and Visualization. Contains infrastructure functionalities such as data exploration and preparation, missing values treatment, outliers treatment, variable derivation, variable selection, dimensionality reduction, grid search for hyper parameters, data mining and visualization, model evaluation, strategy analysis etc. This package is designed to make the development of binary classification models (machine learning based models as well as credit scorecard) simpler and faster.
Author: Dongping Fan [aut, cre]
Maintainer: Dongping Fan <fdp@pku.edu.cn>
Diff between creditmodel versions 1.1.4 dated 2019-09-29 and 1.1.5 dated 2019-10-23
creditmodel-1.1.4/creditmodel/inst/doc/demo.R |only creditmodel-1.1.4/creditmodel/inst/doc/demo.html |only creditmodel-1.1.4/creditmodel/inst/doc/demo.rmd |only creditmodel-1.1.4/creditmodel/man/feature_select_wrapper.Rd |only creditmodel-1.1.4/creditmodel/man/multi_left_jion.Rd |only creditmodel-1.1.4/creditmodel/man/read_dt.Rd |only creditmodel-1.1.4/creditmodel/man/reduce_high_cor.Rd |only creditmodel-1.1.4/creditmodel/man/save_dt.Rd |only creditmodel-1.1.4/creditmodel/tests |only creditmodel-1.1.4/creditmodel/vignettes/demo.rmd |only creditmodel-1.1.5/creditmodel/DESCRIPTION | 10 creditmodel-1.1.5/creditmodel/MD5 | 83 creditmodel-1.1.5/creditmodel/NAMESPACE | 26 creditmodel-1.1.5/creditmodel/NEWS.md | 94 creditmodel-1.1.5/creditmodel/R/data_anaylsis.R | 23 creditmodel-1.1.5/creditmodel/R/data_cleansing.R | 76 creditmodel-1.1.5/creditmodel/R/data_exploration.R | 4 creditmodel-1.1.5/creditmodel/R/data_process_tools.R | 316 +- creditmodel-1.1.5/creditmodel/R/data_transformation.R | 384 ++ creditmodel-1.1.5/creditmodel/R/data_visualization.R | 124 creditmodel-1.1.5/creditmodel/R/essential_algorithms.R | 23 creditmodel-1.1.5/creditmodel/R/example_data.r | 256 - creditmodel-1.1.5/creditmodel/R/model_training.R | 1474 +++++------ creditmodel-1.1.5/creditmodel/R/outliers_missing_treatment.R | 13 creditmodel-1.1.5/creditmodel/R/variable_binning.R | 8 creditmodel-1.1.5/creditmodel/R/variable_selection.R | 1145 +++++--- creditmodel-1.1.5/creditmodel/R/zzz.R | 12 creditmodel-1.1.5/creditmodel/build/vignette.rds |binary creditmodel-1.1.5/creditmodel/inst/doc/introduction.R |only creditmodel-1.1.5/creditmodel/inst/doc/introduction.Rmd |only creditmodel-1.1.5/creditmodel/inst/doc/introduction.html |only creditmodel-1.1.5/creditmodel/man/data_cleansing.Rd | 2 creditmodel-1.1.5/creditmodel/man/derived_ts_vars.Rd | 16 creditmodel-1.1.5/creditmodel/man/fast_high_cor_filter.Rd | 16 creditmodel-1.1.5/creditmodel/man/feature_selector.Rd |only creditmodel-1.1.5/creditmodel/man/gbm_filter.Rd | 4 creditmodel-1.1.5/creditmodel/man/high_cor_selector.Rd |only creditmodel-1.1.5/creditmodel/man/lasso_filter.Rd | 2 creditmodel-1.1.5/creditmodel/man/lendingclub.Rd | 256 - creditmodel-1.1.5/creditmodel/man/log_trans.Rd | 4 creditmodel-1.1.5/creditmodel/man/multi_left_join.Rd |only creditmodel-1.1.5/creditmodel/man/plot_table.Rd | 25 creditmodel-1.1.5/creditmodel/man/psi_iv_filter.Rd | 24 creditmodel-1.1.5/creditmodel/man/ranking_percent_proc.Rd |only creditmodel-1.1.5/creditmodel/man/read_data.Rd |only creditmodel-1.1.5/creditmodel/man/reduce_high_cor_filter.Rd |only creditmodel-1.1.5/creditmodel/man/rowAny.Rd | 15 creditmodel-1.1.5/creditmodel/man/save_data.Rd |only creditmodel-1.1.5/creditmodel/man/time_series_proc.Rd |only creditmodel-1.1.5/creditmodel/man/training_model.Rd | 25 creditmodel-1.1.5/creditmodel/man/xgb_filter.Rd | 8 creditmodel-1.1.5/creditmodel/man/xgb_params.Rd | 8 creditmodel-1.1.5/creditmodel/vignettes/introduction.Rmd |only 53 files changed, 2327 insertions(+), 2149 deletions(-)
Title: Tools for Choice Model Estimation and Application
Description: The Choice Modelling Centre (CMC) at the University of Leeds
has developed flexible code for the estimation and application
of choice models in R. Users are able to write their own
model functions or use a mix of already available ones. Random heterogeneity,
both continuous and discrete and at the level of individuals and
choices, can be incorporated for all models. There is support for both standalone
models and hybrid model structures. Both classical
and Bayesian estimation is available, and multiple discrete
continuous models are covered in addition to discrete choice.
Multi-threading processing is supported for estimation and a large
number of pre and post-estimation routines, including for computing posterior
(individual-level) distributions are available.
For examples, a manual, and a support forum, visit
www.ApolloChoiceModelling.com. For more information on choice
models see Train, K. (2009) <isbn:978-0-521-74738-7> and Hess,
S. & Daly, A.J. (2014) <isbn:978-1-781-00314-5> for an overview
of the field.
Author: Stephane Hess [aut],
David Palma [aut, cre]
Maintainer: David Palma <D.Palma@leeds.ac.uk>
Diff between apollo versions 0.0.8 dated 2019-09-09 and 0.0.9 dated 2019-10-23
apollo-0.0.8/apollo/R/apollo_lcUnconditionals.R |only apollo-0.0.9/apollo/DESCRIPTION | 8 - apollo-0.0.9/apollo/MD5 | 44 +++--- apollo-0.0.9/apollo/NAMESPACE | 1 apollo-0.0.9/apollo/R/apollo_addLog.R | 5 apollo-0.0.9/apollo/R/apollo_combineResults.R | 2 apollo-0.0.9/apollo/R/apollo_estimate.R | 132 +++++++++++++++---- apollo-0.0.9/apollo/R/apollo_lcUnconditionals.r |only apollo-0.0.9/apollo/R/apollo_mdcevInside.R | 2 apollo-0.0.9/apollo/R/apollo_mdcevOutside.R | 2 apollo-0.0.9/apollo/R/apollo_modelOutput.R | 23 ++- apollo-0.0.9/apollo/R/apollo_ol.R | 8 - apollo-0.0.9/apollo/R/apollo_prepareProb.R | 9 + apollo-0.0.9/apollo/R/apollo_printLog.R | 15 +- apollo-0.0.9/apollo/R/apollo_saveOutput.R | 10 + apollo-0.0.9/apollo/R/apollo_searchStart.R | 23 +-- apollo-0.0.9/apollo/R/apollo_validateControl.R | 30 ++-- apollo-0.0.9/apollo/R/apollo_validateInputs.R | 13 + apollo-0.0.9/apollo/inst/doc/apollofirstexample.html | 12 - apollo-0.0.9/apollo/man/apollo_lcUnconditionals.Rd | 2 apollo-0.0.9/apollo/man/apollo_ol.Rd | 2 apollo-0.0.9/apollo/man/apollo_searchStart.Rd | 23 +-- apollo-0.0.9/apollo/man/apollo_validateControl.Rd | 24 +-- apollo-0.0.9/apollo/man/apollo_validateInputs.Rd | 2 24 files changed, 270 insertions(+), 122 deletions(-)
Title: 'NOAA' Weather Data from R
Description: Client for many 'NOAA' data sources including the 'NCDC' climate
'API' at <https://www.ncdc.noaa.gov/cdo-web/webservices/v2>, with functions for
each of the 'API' 'endpoints': data, data categories, data sets, data types,
locations, location categories, and stations. In addition, we have an interface
for 'NOAA' sea ice data, the 'NOAA' severe weather inventory, 'NOAA' Historical
Observing 'Metadata' Repository ('HOMR') data, 'NOAA' storm data via 'IBTrACS',
tornado data via the 'NOAA' storm prediction center, and more.
Author: Scott Chamberlain [aut, cre],
Brooke Anderson [ctb],
Maëlle Salmon [ctb],
Adam Erickson [ctb],
Nicholas Potter [ctb],
Joseph Stachelek [ctb],
Alex Simmons [ctb],
Karthik Ram [ctb],
Hart Edmund [ctb]
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rnoaa versions 0.9.0 dated 2019-09-26 and 0.9.2 dated 2019-10-23
DESCRIPTION | 8 +- MD5 | 110 +++++++++++++++++----------------- NEWS.md | 14 ++++ R/gefs.R | 82 ++++++++++++++++++------- R/isd.R | 8 +- R/meteo_utils.r | 6 + R/tornadoes.R | 6 - README.md | 6 - inst/doc/buoy_vignette.R | 7 -- inst/doc/buoy_vignette.Rmd | 7 -- inst/doc/buoy_vignette.html | 4 - inst/doc/homr_vignette.R | 7 -- inst/doc/homr_vignette.Rmd | 15 ++-- inst/doc/homr_vignette.html | 12 +-- inst/doc/ncdc_attributes.R | 7 -- inst/doc/ncdc_attributes.Rmd | 7 -- inst/doc/ncdc_attributes.html | 4 - inst/doc/ncdc_vignette.R | 7 -- inst/doc/ncdc_vignette.Rmd | 8 -- inst/doc/ncdc_vignette.html | 7 -- inst/doc/ncdc_workflow.R | 7 -- inst/doc/ncdc_workflow.Rmd | 7 -- inst/doc/ncdc_workflow.html | 4 - inst/doc/rnoaa_ropenaq.R | 7 -- inst/doc/rnoaa_ropenaq.Rmd | 7 -- inst/doc/rnoaa_ropenaq.html | 4 - inst/doc/seaice_vignette.R | 7 -- inst/doc/seaice_vignette.Rmd | 7 -- inst/doc/seaice_vignette.html | 4 - inst/doc/storms_vignette.R | 7 -- inst/doc/storms_vignette.Rmd | 66 ++++++++------------ inst/doc/storms_vignette.html | 71 ++++++++------------- inst/doc/swdi_vignette.R | 7 -- inst/doc/swdi_vignette.Rmd | 16 +++- inst/doc/swdi_vignette.html | 8 +- man/gefs.Rd | 25 ++++--- man/isd.Rd | 4 - man/meteo_coverage.Rd | 6 + man/tornadoes.Rd | 2 tests/testthat/test-arc2.R | 2 tests/testthat/test-check_response.r | 4 + tests/testthat/test-gefs.R | 72 +++++++++++++++++----- tests/testthat/test-ghcnd.R | 4 + tests/testthat/test-ghcnd_splitvars.R | 2 tests/testthat/test-isd.R | 2 tests/testthat/test-tornadoes.R | 2 tests/testthat/test-vis_miss.R | 6 + vignettes/buoy_vignette.Rmd | 7 -- vignettes/homr_vignette.Rmd | 15 ++-- vignettes/ncdc_attributes.Rmd | 7 -- vignettes/ncdc_vignette.Rmd | 8 -- vignettes/ncdc_workflow.Rmd | 7 -- vignettes/rnoaa_ropenaq.Rmd | 7 -- vignettes/seaice_vignette.Rmd | 7 -- vignettes/storms_vignette.Rmd | 66 ++++++++------------ vignettes/swdi_vignette.Rmd | 16 +++- 56 files changed, 454 insertions(+), 378 deletions(-)
Title: Finite Mixture of Multivariate Censored/Missing Data
Description: It fits finite mixture models for censored or/and missing data using several multivariate distributions. Point estimation and asymptotic inference (via empirical information matrix) are offered as well as censored data generation. Pairwise scatter and contour plots can be generated. Possible multivariate distributions are the well-known normal, Student-t and skew-normal distributions. This package is an complement of Lachos, V. H., Moreno, E. J. L., Chen, K. & Cabral, C. R. B. (2017) <doi:10.1016/j.jmva.2017.05.005> for the multivariate skew-normal case.
Author: Francisco H. C. de Alencar [aut, cre],
Christian E. Galarza [aut],
Larissa A. Matos [ctb],
Victor H. Lachos [ctb]
Maintainer: Francisco H. C. de Alencar <hildemardealencar@gmail.com>
Diff between CensMFM versions 1.4 dated 2019-10-16 and 1.5 dated 2019-10-23
DESCRIPTION | 6 MD5 | 10 R/EM.MSNC.R | 1520 ++++++++++++++++++++++++------------------------- R/USER_rMMSN.contour.R | 14 build/partial.rdb |binary man/rMMSN.contour.Rd | 286 ++++----- 6 files changed, 924 insertions(+), 912 deletions(-)
Title: Interface to Unidata netCDF (Version 4 or Earlier) Format Data
Files
Description: Provides a high-level R interface to data files written using Unidata's netCDF library (version 4 or earlier), which are binary data files that are portable across platforms and include metadata information in addition to the data sets. Using this package, netCDF files (either version 4 or "classic" version 3) can be opened and data sets read in easily. It is also easy to create new netCDF dimensions, variables, and files, in either version 3 or 4 format, and manipulate existing netCDF files. This package replaces the former ncdf package, which only worked with netcdf version 3 files. For various reasons the names of the functions have had to be changed from the names in the ncdf package. The old ncdf package is still available at the URL given below, if you need to have backward compatibility. It should be possible to have both the ncdf and ncdf4 packages installed simultaneously without a problem. However, the ncdf package does not provide an interface for netcdf version 4 files.
Author: David Pierce <dpierce@ucsd.edu>
Maintainer: David Pierce <dpierce@ucsd.edu>
Diff between ncdf4 versions 1.16.1 dated 2019-03-11 and 1.17 dated 2019-10-23
ChangeLog | 6 ++++++ DESCRIPTION | 8 ++++---- MD5 | 44 ++++++++++++++++++++++++-------------------- R/ncdf4.R | 8 ++++++-- R/ncdf4_priv_var.R | 14 ++++++++++---- configure.ac | 3 ++- man/ancvar_put.Rd | 6 ++++++ man/nc_create.Rd | 3 +++ man/nc_open.Rd | 3 +++ man/nc_sync.Rd | 3 +++ man/ncatt_get.Rd | 5 +++++ man/ncatt_put.Rd | 3 +++ man/ncdim_def.Rd | 4 ++++ man/ncvar_add.Rd | 3 +++ man/ncvar_change_missval.Rd | 3 +++ man/ncvar_def.Rd | 4 ++++ man/ncvar_get.Rd | 2 ++ man/ncvar_rename.Rd | 3 +++ man/print.ncdf4.Rd | 2 ++ src/Makevars.win | 16 +++++++++++++++- src/ncdf.c | 11 +++++------ tools/aclocal.m4 |only tools/configure.ac |only tools/regenerate |only tools/winlibs.R |only 25 files changed, 116 insertions(+), 38 deletions(-)
Title: Compile and Preview Snippets of 'LaTeX' in 'RStudio'
Description: Compile and preview snippets of 'LaTeX'. Can be
used directly from the R console, from 'RStudio', in Shiny apps and R
Markdown documents. Must have 'pdflatex' or 'xelatex' or 'lualatex' in
'PATH'.
Author: Jonathan Sidi [aut, cre],
Daniel Polhamus [aut]
Maintainer: Jonathan Sidi <yonis@metrumrg.com>
Diff between texPreview versions 1.3.2 dated 2019-05-05 and 1.4.0 dated 2019-10-23
texPreview-1.3.2/texPreview/R/sysdata.rda |only texPreview-1.3.2/texPreview/inst/examples/pkpdTikz |only texPreview-1.3.2/texPreview/inst/examples/rmarkdown |only texPreview-1.3.2/texPreview/inst/examples/shiny |only texPreview-1.3.2/texPreview/inst/examples/tikz/credit-rationing.tex |only texPreview-1.4.0/texPreview/DESCRIPTION | 43 texPreview-1.4.0/texPreview/MD5 | 134 texPreview-1.4.0/texPreview/NAMESPACE | 20 texPreview-1.4.0/texPreview/NEWS.md | 7 texPreview-1.4.0/texPreview/R/build_lines.R | 37 texPreview-1.4.0/texPreview/R/build_usepackage.R | 1 texPreview-1.4.0/texPreview/R/get_texpackages.R | 1 texPreview-1.4.0/texPreview/R/kable.R |only texPreview-1.4.0/texPreview/R/opts.R | 7 texPreview-1.4.0/texPreview/R/print.R |only texPreview-1.4.0/texPreview/R/texPreview-deprecated.R | 104 texPreview-1.4.0/texPreview/R/tex_build.R | 19 texPreview-1.4.0/texPreview/R/tex_cleanup.R | 14 texPreview-1.4.0/texPreview/R/tex_image.R | 22 texPreview-1.4.0/texPreview/R/tex_preview.R | 386 + texPreview-1.4.0/texPreview/R/tex_return.R | 69 texPreview-1.4.0/texPreview/R/tex_viewer.R | 2 texPreview-1.4.0/texPreview/R/utils.R |only texPreview-1.4.0/texPreview/R/zzz.R | 3 texPreview-1.4.0/texPreview/README.md | 28 texPreview-1.4.0/texPreview/build/texPreview.pdf |only texPreview-1.4.0/texPreview/build/vignette.rds |binary texPreview-1.4.0/texPreview/inst/doc/classes.R |only texPreview-1.4.0/texPreview/inst/doc/classes.Rmd |only texPreview-1.4.0/texPreview/inst/doc/classes.html |only texPreview-1.4.0/texPreview/inst/doc/kable.R |only texPreview-1.4.0/texPreview/inst/doc/kable.Rmd |only texPreview-1.4.0/texPreview/inst/doc/kable.html |only texPreview-1.4.0/texPreview/inst/doc/rmarkdown.R | 7 texPreview-1.4.0/texPreview/inst/doc/rmarkdown.Rmd | 7 texPreview-1.4.0/texPreview/inst/doc/rmarkdown.html | 30 texPreview-1.4.0/texPreview/inst/doc/slickr.R | 7 texPreview-1.4.0/texPreview/inst/doc/slickr.Rmd | 9 texPreview-1.4.0/texPreview/inst/doc/slickr.html | 1544 +++++- texPreview-1.4.0/texPreview/inst/doc/tests_and_coverage.html | 9 texPreview-1.4.0/texPreview/inst/doc/tex_packages.html | 15 texPreview-1.4.0/texPreview/inst/doc/tikz.R |only texPreview-1.4.0/texPreview/inst/doc/tikz.Rmd |only texPreview-1.4.0/texPreview/inst/doc/tikz.html |only texPreview-1.4.0/texPreview/inst/examples/tikz/credit_rationing.tex |only texPreview-1.4.0/texPreview/inst/examples/tikz/pd_model.tex |only texPreview-1.4.0/texPreview/inst/examples/tikz/pk_model.tex |only texPreview-1.4.0/texPreview/inst/examples/tikz/two_compartment.tex |only texPreview-1.4.0/texPreview/inst/examples/toy |only texPreview-1.4.0/texPreview/inst/tmpl.tex | 2 texPreview-1.4.0/texPreview/man/BuildUsepackage.Rd |only texPreview-1.4.0/texPreview/man/as_kable.Rd |only texPreview-1.4.0/texPreview/man/build_usepackage.Rd | 3 texPreview-1.4.0/texPreview/man/figures |only texPreview-1.4.0/texPreview/man/getTexPackages.Rd |only texPreview-1.4.0/texPreview/man/get_texpackages.Rd | 1 texPreview-1.4.0/texPreview/man/pipe.Rd |only texPreview-1.4.0/texPreview/man/texPreview.Rd |only texPreview-1.4.0/texPreview/man/tex_opts.Rd | 8 texPreview-1.4.0/texPreview/man/tex_preview.Rd | 188 texPreview-1.4.0/texPreview/tests/README.md | 2227 +++++++++- texPreview-1.4.0/texPreview/tests/testthat/helper-functions.R | 12 texPreview-1.4.0/texPreview/tests/testthat/test-error.R |only texPreview-1.4.0/texPreview/tests/testthat/test-kable.R |only texPreview-1.4.0/texPreview/tests/testthat/test-packages.R |only texPreview-1.4.0/texPreview/tests/testthat/test-print.R |only texPreview-1.4.0/texPreview/tests/testthat/test-tex.R | 33 texPreview-1.4.0/texPreview/vignettes/classes.Rmd |only texPreview-1.4.0/texPreview/vignettes/kable.Rmd |only texPreview-1.4.0/texPreview/vignettes/rmarkdown.Rmd | 7 texPreview-1.4.0/texPreview/vignettes/slickr.Rmd | 9 texPreview-1.4.0/texPreview/vignettes/tikz.Rmd |only 72 files changed, 4173 insertions(+), 842 deletions(-)
Title: R Bayesian Evidence Synthesis Tools
Description: Tool-set to support Bayesian evidence synthesis. This
includes meta-analysis, (robust) prior derivation from historical
data, operating characteristics and analysis (1 and 2 sample
cases). Please refer to Neuenschwander et al. (2010)
<doi:10.1177/1740774509356002> and Schmidli et al. (2014)
<doi:10.1111/biom.12242> for details on the methodology.
Author: Novartis Pharma AG [cph],
Sebastian Weber [aut, cre],
Beat Neuenschwander [ctb],
Heinz Schmidli [ctb],
Baldur Magnusson [ctb],
Yue Li [ctb],
Satrajit Roychoudhury [ctb],
Trustees of Columbia University [cph] (R/stanmodels.R, configure,
configure.win)
Maintainer: Sebastian Weber <sebastian.weber@novartis.com>
Diff between RBesT versions 1.5-3 dated 2019-08-28 and 1.5-4 dated 2019-10-23
RBesT-1.5-3/RBesT/inst/include/meta_header.hpp |only RBesT-1.5-3/RBesT/inst/include/stan |only RBesT-1.5-3/RBesT/src/init.cpp |only RBesT-1.5-3/RBesT/src/stan_files |only RBesT-1.5-3/RBesT/tools/make_cc.R |only RBesT-1.5-4/RBesT/DESCRIPTION | 22 RBesT-1.5-4/RBesT/MD5 | 78 +-- RBesT-1.5-4/RBesT/NAMESPACE | 9 RBesT-1.5-4/RBesT/R/RBesT-package.R | 15 RBesT-1.5-4/RBesT/R/decision2S_boundary.R | 48 +- RBesT-1.5-4/RBesT/R/mixess.R | 20 RBesT-1.5-4/RBesT/R/stanmodels.R | 56 -- RBesT-1.5-4/RBesT/R/sysdata.rda |binary RBesT-1.5-4/RBesT/build/vignette.rds |binary RBesT-1.5-4/RBesT/configure |only RBesT-1.5-4/RBesT/configure.win |only RBesT-1.5-4/RBesT/data/AS.rda |binary RBesT-1.5-4/RBesT/data/colitis.rda |binary RBesT-1.5-4/RBesT/data/crohn.rda |binary RBesT-1.5-4/RBesT/data/transplant.rda |binary RBesT-1.5-4/RBesT/inst/NEWS | 6 RBesT-1.5-4/RBesT/inst/doc/PoS_codata.html | 470 ++++++++++---------- RBesT-1.5-4/RBesT/inst/doc/PoS_interim.html | 184 ++++--- RBesT-1.5-4/RBesT/inst/doc/RBesT.pdf |binary RBesT-1.5-4/RBesT/inst/doc/customizing_plots.html | 302 ++++++------ RBesT-1.5-4/RBesT/inst/doc/introduction.html | 320 ++++++------- RBesT-1.5-4/RBesT/inst/doc/introduction_normal.html | 378 ++++++++-------- RBesT-1.5-4/RBesT/inst/doc/robustMAP.html | 190 ++++---- RBesT-1.5-4/RBesT/inst/doc/variances_MAP.html | 184 ++++--- RBesT-1.5-4/RBesT/inst/include/stan_meta_header.hpp |only RBesT-1.5-4/RBesT/inst/sbc/calibration.md5 | 6 RBesT-1.5-4/RBesT/inst/sbc/launch_sbc.sh | 8 RBesT-1.5-4/RBesT/inst/sbc/sbc_report.html | 94 ++-- RBesT-1.5-4/RBesT/inst/stan |only RBesT-1.5-4/RBesT/man/RBesT-package.Rd | 4 RBesT-1.5-4/RBesT/man/ess.Rd | 31 + RBesT-1.5-4/RBesT/src/Makevars | 13 RBesT-1.5-4/RBesT/src/Makevars.win | 17 RBesT-1.5-4/RBesT/src/RcppExports.cpp |only RBesT-1.5-4/RBesT/src/stanExports_gMAP.cc |only RBesT-1.5-4/RBesT/src/stanExports_gMAP.h |only RBesT-1.5-4/RBesT/tests/testthat/test-oc2S.R | 41 + RBesT-1.5-4/RBesT/tools/build.sh | 9 43 files changed, 1334 insertions(+), 1171 deletions(-)
Title: Tools to Visualize, Manipulate, and Summarize MCMC Output
Description: Performs key functions for MCMC analysis using minimal code - visualizes, manipulates, and summarizes MCMC output. Functions support simple and straightforward subsetting of model parameters within the calls, and produce presentable and 'publication-ready' output. MCMC output may be derived from Bayesian model output fit with JAGS, Stan, or other MCMC samplers.
Author: Casey Youngflesh [aut, cre] (<https://orcid.org/0000-0001-6343-3311>),
Christian Che-Castaldo [aut] (<https://orcid.org/0000-0002-7670-2178>),
Tyler Hardy [ctb]
Maintainer: Casey Youngflesh <caseyyoungflesh@gmail.com>
Diff between MCMCvis versions 0.13.1 dated 2019-09-25 and 0.13.3 dated 2019-10-23
DESCRIPTION | 6 ++-- MD5 | 20 ++++++------- NEWS.md | 13 ++++++++ R/MCMCchains.R | 23 ++++++++++++++- R/MCMCpstr.R | 2 - R/MCMCsummary.R | 51 ++++++++++++++++++++-------------- inst/doc/MCMCvis.R | 6 ++-- inst/doc/MCMCvis.Rmd | 8 ++--- inst/doc/MCMCvis.html | 64 +++++++++++++++++++++---------------------- tests/testthat/test_master.R | 5 ++- vignettes/MCMCvis.Rmd | 8 ++--- 11 files changed, 125 insertions(+), 81 deletions(-)
Title: Poisson-Tweedie Generalized Linear Mixed Model
Description: Fits Poisson-Tweedie generalized linear mixed
model. Likelihood approximation based on adaptive Gauss Hermite
quadrature rule.
Author: Mirko Signorelli [aut, cre],
Pietro Spitali [aut],
Roula Tsonaka [aut]
Maintainer: Mirko Signorelli <m.signorelli@lumc.nl>
Diff between ptmixed versions 0.3.1 dated 2019-09-17 and 0.4.1 dated 2019-10-23
ptmixed-0.3.1/ptmixed/inst/NEWS.Rmd |only ptmixed-0.4.1/ptmixed/DESCRIPTION | 17 +++--- ptmixed-0.4.1/ptmixed/MD5 | 38 +++++++------- ptmixed-0.4.1/ptmixed/NAMESPACE | 1 ptmixed-0.4.1/ptmixed/R/nbglm.R | 14 +++-- ptmixed-0.4.1/ptmixed/R/nbmixed.R | 4 - ptmixed-0.4.1/ptmixed/R/ptglm.R | 18 ++++--- ptmixed-0.4.1/ptmixed/R/ptmixed.R | 4 - ptmixed-0.4.1/ptmixed/R/ranef.R | 17 +++--- ptmixed-0.4.1/ptmixed/R/starting-values.R | 71 ++++++++++++++++------------ ptmixed-0.4.1/ptmixed/R/summary-ptglm.R | 22 +++++--- ptmixed-0.4.1/ptmixed/R/summary-ptglmm.R | 23 +++++---- ptmixed-0.4.1/ptmixed/R/wald-test.R |only ptmixed-0.4.1/ptmixed/inst/NEWS.md |only ptmixed-0.4.1/ptmixed/man/nbglm.Rd | 2 ptmixed-0.4.1/ptmixed/man/nbmixed.Rd | 2 ptmixed-0.4.1/ptmixed/man/ptglm.Rd | 2 ptmixed-0.4.1/ptmixed/man/ptmixed.Rd | 2 ptmixed-0.4.1/ptmixed/man/ranef.Rd | 19 ++++--- ptmixed-0.4.1/ptmixed/man/summary.ptglm.Rd | 10 ++- ptmixed-0.4.1/ptmixed/man/summary.ptglmm.Rd | 11 ++-- ptmixed-0.4.1/ptmixed/man/wald.test.Rd |only 22 files changed, 161 insertions(+), 116 deletions(-)
Title: Methods for Graphical Models and Causal Inference
Description: Functions for causal structure
learning and causal inference using graphical models. The main algorithms
for causal structure learning are PC (for observational data without hidden
variables), FCI and RFCI (for observational data with hidden variables),
and GIES (for a mix of data from observational studies
(i.e. observational data) and data from experiments
involving interventions (i.e. interventional data) without hidden
variables). For causal inference the IDA algorithm, the Generalized
Backdoor Criterion (GBC), the Generalized Adjustment Criterion (GAC)
and some related functions are implemented. Functions for incorporating
background knowledge are provided.
Author: Markus Kalisch [aut, cre],
Alain Hauser [aut],
Martin Maechler [aut],
Diego Colombo [ctb],
Doris Entner [ctb],
Patrik Hoyer [ctb],
Antti Hyttinen [ctb],
Jonas Peters [ctb],
Nicoletta Andri [ctb],
Emilija Perkovic [ctb],
Preetam Nandy [ctb],
Philipp Ruetimann [ctb],
Daniel Stekhoven [ctb],
Manuel Schuerch [ctb],
Marco Eigenmann [ctb]
Maintainer: Markus Kalisch <kalisch@stat.math.ethz.ch>
Diff between pcalg versions 2.6-6 dated 2019-09-16 and 2.6-7 dated 2019-10-23
pcalg-2.6-6/pcalg/tests/nohup.out |only pcalg-2.6-6/pcalg/vignettes/auto |only pcalg-2.6-6/pcalg/vignettes/pcalgDoc-concordance.tex |only pcalg-2.6-6/pcalg/vignettes/vignette2018-concordance.tex |only pcalg-2.6-7/pcalg/DESCRIPTION | 8 pcalg-2.6-7/pcalg/MD5 | 22 -- pcalg-2.6-7/pcalg/NAMESPACE | 1 pcalg-2.6-7/pcalg/R/AllClasses.R | 14 + pcalg-2.6-7/pcalg/R/gies.R | 153 +++++++++------ pcalg-2.6-7/pcalg/inst/doc/pcalgDoc.pdf |binary pcalg-2.6-7/pcalg/inst/doc/vignette2018.pdf |binary pcalg-2.6-7/pcalg/man/opt.target.Rd |only pcalg-2.6-7/pcalg/src/gies.cpp | 12 - pcalg-2.6-7/pcalg/tests/test_coercion.R |only pcalg-2.6-7/pcalg/tests/test_opttarget.R |only 15 files changed, 129 insertions(+), 81 deletions(-)
Title: Connect to 'AWS Athena' using R 'AWS SDK' 'paws' ('DBI'
Interface)
Description: Designed to be compatible with the 'R' package 'DBI' (Database Interface)
when connecting to Amazon Web Service ('AWS') Athena <https://aws.amazon.com/athena/>.
To do this the 'R' 'AWS' Software Development Kit ('SDK') 'paws'
<https://github.com/paws-r/paws> is used as a driver.
Author: Dyfan Jones [aut, cre]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>
Diff between noctua versions 1.0.0 dated 2019-10-20 and 1.1.0 dated 2019-10-23
DESCRIPTION | 11 +++--- MD5 | 29 +++++++++-------- NAMESPACE | 3 - NEWS.md | 23 +++++++++++++ R/Connection.R | 20 +++++++----- R/DataTypes.R | 2 - R/Driver.R | 7 ---- R/Result.R | 13 ++++--- R/Table.R | 13 ++----- R/athena_low_api.R | 58 ++++++++++++++++------------------- R/noctua.R | 3 + R/utils.R | 58 +++++++++++++---------------------- README.md | 17 ++++------ tests/testthat/helper.R | 26 +++------------ tests/testthat/test-athena-request.R |only tests/testthat/test-datatransfer.R | 15 +++++++-- 16 files changed, 148 insertions(+), 150 deletions(-)
Title: Principal Component Analysis in High-Dimensional Data
Description: In high-dimensional settings:
Estimate the number of distant spikes based on the Generalized Spiked Population (GSP) model.
Estimate the population eigenvalues, angles between the sample and population eigenvectors, correlations between the sample and population PC scores, and the asymptotic shrinkage factors.
Adjust the shrinkage bias in the predicted PC scores.
Dey, R. and Lee, S. (2019) <doi.org/10.1016/j.jmva.2019.02.007>.
Author: Rounak Dey, Seunggeun Lee
Maintainer: Rounak Dey <deyrnk@umich.edu>
Diff between hdpca versions 1.0.0 dated 2016-08-02 and 1.1.3 dated 2019-10-23
hdpca-1.0.0/hdpca/data/Example.RData |only hdpca-1.0.0/hdpca/data/datalist |only hdpca-1.0.0/hdpca/man/Example.rd |only hdpca-1.1.3/hdpca/DESCRIPTION | 9 + hdpca-1.1.3/hdpca/MD5 | 17 +-- hdpca-1.1.3/hdpca/NAMESPACE | 2 hdpca-1.1.3/hdpca/R/pca_functions.R | 157 ++++++++++++++++++++++----------- hdpca-1.1.3/hdpca/data/hapmap.RData |only hdpca-1.1.3/hdpca/man/hapmap.rd |only hdpca-1.1.3/hdpca/man/hdpc_est.Rd | 21 +++- hdpca-1.1.3/hdpca/man/pc_adjust.Rd | 21 +++- hdpca-1.1.3/hdpca/man/select.nspike.Rd | 20 +++- 12 files changed, 168 insertions(+), 79 deletions(-)
Title: Time Series Regression Models with Distributed Lag Models
Description: Provides time series regression models with one predictor using finite distributed lag models, polynomial (Almon) distributed lag models, geometric distributed lag models with Koyck transformation, and autoregressive distributed lag models. It also consists of functions for computation of h-step ahead forecasts from these models. See Baltagi (2011) <doi:10.1007/978-3-642-20059-5> for more information.
Author: Haydar Demirhan [aut, cre, cph] (<https://orcid.org/0000-0002-8565-4710>)
Maintainer: Haydar Demirhan <haydar.demirhan@rmit.edu.au>
Diff between dLagM versions 1.0.18 dated 2019-10-18 and 1.0.19 dated 2019-10-23
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS.md | 5 +++++ R/ardlBound.R | 1 + R/ardlBoundOrders.R | 6 +++--- build/partial.rdb |binary man/ardlBound.Rd | 2 +- man/ardlBoundOrders.Rd | 2 +- man/dLagM-package.Rd | 4 ++-- 9 files changed, 25 insertions(+), 19 deletions(-)
Title: Functions to Analyze Single System Data
Description: Functions to visually and statistically analyze single system data.
Author: Charles Auerbach [aut, cre],
Wendy Zeitlin [aut]
Maintainer: Charles Auerbach <auerbach@yu.edu>
Diff between SSDforR versions 1.5.9 dated 2019-09-28 and 1.5.10 dated 2019-10-23
DESCRIPTION | 8 ++++---- MD5 | 10 ++++++++-- NAMESPACE | 1 + R/RMarrow.R |only R/RMlines.R |only R/RMtext.R |only man/RMarrow.Rd |only man/RMlines.Rd |only man/RMtext.Rd |only 9 files changed, 13 insertions(+), 6 deletions(-)
Title: Data Analysis and Parameter Estimation Using Item Response
Theory
Description: Parameter estimation, computation of probability, information, and
(log-)likelihood, and visualization of item/test characteristic curves and
item/test information functions for three uni-dimensional item response theory
models: the 3-parameter-logistic model, generalized partial credit model,
and graded response model. The full documentation and tutorials are at
<https://github.com/xluo11/Rirt>.
Author: Xiao Luo [aut, cre]
Maintainer: Xiao Luo <xluo1986@gmail.com>
Diff between Rirt versions 0.0.1 dated 2019-08-22 and 0.0.2 dated 2019-10-23
DESCRIPTION | 11 - MD5 | 22 +- NAMESPACE | 6 R/estimate_mixed.R |only R/helpers.R | 372 +++++++++++++++++++++++++------------------------- R/model_3pl.R | 3 R/model_gpcm.R | 3 R/model_grm.R | 17 -- R/model_mixed.R |only man/estimate_mixed.Rd |only man/model_3pl.Rd | 5 man/model_gpcm.Rd | 4 man/model_grm.Rd | 4 man/model_mixed.Rd |only 14 files changed, 230 insertions(+), 217 deletions(-)
Title: Species Abundance Distributions with Independent-Species
Assumption
Description: Computes the probability of a set of species abundances of a single or multiple samples of individuals with one or more guilds under a mainland-island model. One must specify the mainland (metacommunity) model and the island (local) community model. It assumes that species fluctuate independently. The package also contains functions to simulate under this model. See Haegeman, B. & R.S. Etienne (2017). A general sampling formula for community structure data. Methods in Ecology & Evolution 8: 1506-1519 <doi:10.1111/2041-210X.12807>.
Author: Rampal S. Etienne & Bart Haegeman
Maintainer: Rampal S. Etienne <r.s.etienne@rug.nl>
Diff between SADISA versions 1.1 dated 2019-04-04 and 1.2 dated 2019-10-23
SADISA-1.1/SADISA/R/pmdl_sim.R |only SADISA-1.1/SADISA/man/pmdl_sim.Rd |only SADISA-1.2/SADISA/DESCRIPTION | 10 +++++----- SADISA-1.2/SADISA/MD5 | 16 +++++++--------- SADISA-1.2/SADISA/NAMESPACE | 1 - SADISA-1.2/SADISA/R/SADISA_loglik.R | 1 - SADISA-1.2/SADISA/R/SADISA_sim.R | 4 ---- SADISA-1.2/SADISA/build/vignette.rds |binary SADISA-1.2/SADISA/data/datasets.RData |binary SADISA-1.2/SADISA/data/fitresults.RData |binary 10 files changed, 12 insertions(+), 20 deletions(-)
Title: Connect to 'AWS Athena' using 'Boto3' ('DBI' Interface)
Description: Designed to be compatible with the R package 'DBI' (Database Interface)
when connecting to Amazon Web Service ('AWS') Athena <https://aws.amazon.com/athena/>.
To do this 'Python' 'Boto3' Software Development Kit ('SDK')
<https://boto3.amazonaws.com/v1/documentation/api/latest/index.html> is used as a driver.
Author: Dyfan Jones [aut, cre]
Maintainer: Dyfan Jones <dyfan.r.jones@gmail.com>
Diff between RAthena versions 1.2.0 dated 2019-10-14 and 1.3.0 dated 2019-10-23
DESCRIPTION | 11 ++++++----- MD5 | 20 ++++++++++---------- NAMESPACE | 3 +-- NEWS.md | 21 +++++++++++++++++++++ R/DataTypes.R | 2 +- R/RAthena.R | 3 ++- R/Result.R | 7 +++---- R/table.R | 13 ++++--------- R/util.R | 18 ------------------ README.md | 26 ++++++++++++++------------ tests/testthat/test-datatransfer.R | 14 +++++++++++--- 11 files changed, 73 insertions(+), 65 deletions(-)
Title: 'linl' is not 'Letter'
Description: A 'LaTeX' Letter class for 'rmarkdown', using the
'pandoc-letter' template adapted for use with 'markdown'.
Author: Dirk Eddelbuettel and Aaron Wolen
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between linl versions 0.0.3 dated 2018-12-15 and 0.0.4 dated 2019-10-23
ChangeLog | 37 ++++++++++++++++++++ DESCRIPTION | 12 +++--- MD5 | 30 ++++++++++------ R/linl.R | 4 +- README.md | 8 +++- build/vignette.rds |binary inst/NEWS.Rd | 11 +++++ inst/doc/linl.Rmd | 1 inst/doc/linl.pdf |binary inst/rmarkdown/templates/pdf/resources/template.tex | 7 +++ man/linl.Rd | 5 ++ tests |only vignettes/examples/letterfoot.R |only vignettes/examples/letterfoot.pdf |only vignettes/linl.Rmd | 1 15 files changed, 96 insertions(+), 20 deletions(-)
Title: Basic Functions for Supporting an Implementation of Best-Worst
Scaling
Description: Provides three basic functions that support an implementation of object case (Case 1) best-worst scaling: one for converting a two-level orthogonal main-effect design/balanced incomplete block design into questions; one for creating a data set suitable for analysis; and one for calculating count-based scores. For details on best-worst scaling, see Louviere et al. (2015) <doi:10.1017/CBO9781107337855>.
Author: Hideo Aizaki
Maintainer: Hideo Aizaki <azk-r@spa.nifty.com>
Diff between support.BWS versions 0.2-0 dated 2018-02-09 and 0.2-1 dated 2019-10-23
DESCRIPTION | 10 ++-- MD5 | 11 ++--- NEWS | 3 + R/bws.dataset.R | 92 +++++++++++++++++++++++++++++++++++++++++++++ inst |only man/bws.dataset.Rd | 10 ++++ man/support.BWS-package.Rd | 10 ++-- 7 files changed, 121 insertions(+), 15 deletions(-)
Title: Spatio-Temporal Under-Five Mortality Methods for Estimation
Description: Provides methods for estimating, projecting, and plotting spatio-temporal
under-five mortality rates, described in Mercer et al. (2015) <doi:10.1214/15-AOAS872>
and Li et al. (2019) <doi:10.1371/journal.pone.0210645>.
Author: Bryan D Martin [aut],
Zehang R Li [cre, aut],
Yuan Hsiao [aut],
Jessica Godwin [aut],
Jon Wakefield [aut],
Samuel J Clark [aut],
Geir-Arne Fuglstad [aut],
Andrea Riebler [aut]
Maintainer: Zehang R Li <lizehang@gmail.com>
Diff between SUMMER versions 0.2.3 dated 2019-04-02 and 0.3.0 dated 2019-10-23
SUMMER-0.2.3/SUMMER/inst/doc/summer-vignette.pdf |only SUMMER-0.2.3/SUMMER/inst/doc/summer-vignette.pdf.asis |only SUMMER-0.2.3/SUMMER/man/countrySummary.Rd |only SUMMER-0.2.3/SUMMER/man/countrySummary_mult.Rd |only SUMMER-0.2.3/SUMMER/man/fitSpace.Rd |only SUMMER-0.2.3/SUMMER/man/plot.projINLA.Rd |only SUMMER-0.2.3/SUMMER/man/projINLA.Rd |only SUMMER-0.2.3/SUMMER/vignettes/summer-vignette.pdf.asis |only SUMMER-0.3.0/SUMMER/DESCRIPTION | 31 SUMMER-0.3.0/SUMMER/MD5 | 106 +- SUMMER-0.3.0/SUMMER/NAMESPACE | 20 SUMMER-0.3.0/SUMMER/NEWS.md |only SUMMER-0.3.0/SUMMER/R/BRFSS.R | 3 SUMMER-0.3.0/SUMMER/R/DemoData.R | 3 SUMMER-0.3.0/SUMMER/R/DemoData2.R | 3 SUMMER-0.3.0/SUMMER/R/DemoMap.R | 4 SUMMER-0.3.0/SUMMER/R/DemoMap2.R | 3 SUMMER-0.3.0/SUMMER/R/INLA-internal-pc.R |only SUMMER-0.3.0/SUMMER/R/INLA-internals.R |only SUMMER-0.3.0/SUMMER/R/Kendata.R |only SUMMER-0.3.0/SUMMER/R/SUMMER.R | 1 SUMMER-0.3.0/SUMMER/R/aggregateSurvey.R | 8 SUMMER-0.3.0/SUMMER/R/countrySummary.R | 38 SUMMER-0.3.0/SUMMER/R/countrySummary_mult.R | 19 SUMMER-0.3.0/SUMMER/R/fitINLA.R | 752 ++++++---------- SUMMER-0.3.0/SUMMER/R/fitINLA2.R |only SUMMER-0.3.0/SUMMER/R/fitspace.R | 113 +- SUMMER-0.3.0/SUMMER/R/getAdjusted.R |only SUMMER-0.3.0/SUMMER/R/getAmat.R |only SUMMER-0.3.0/SUMMER/R/getBirths.R | 74 + SUMMER-0.3.0/SUMMER/R/getCounts.R |only SUMMER-0.3.0/SUMMER/R/getDiag.R |only SUMMER-0.3.0/SUMMER/R/hatchPlot.R |only SUMMER-0.3.0/SUMMER/R/mapPlot.R | 23 SUMMER-0.3.0/SUMMER/R/mapPoints.R |only SUMMER-0.3.0/SUMMER/R/plot_projINLA.R | 171 +-- SUMMER-0.3.0/SUMMER/R/projINLA.R | 442 +++++++-- SUMMER-0.3.0/SUMMER/README.md | 40 SUMMER-0.3.0/SUMMER/build/vignette.rds |binary SUMMER-0.3.0/SUMMER/data/KenData.rda |only SUMMER-0.3.0/SUMMER/data/datalist | 1 SUMMER-0.3.0/SUMMER/inst/doc/summer-vignette.html |only SUMMER-0.3.0/SUMMER/inst/doc/summer-vignette.html.asis |only SUMMER-0.3.0/SUMMER/inst/doc/u5mr-vignette.html |only SUMMER-0.3.0/SUMMER/inst/doc/u5mr-vignette.html.asis |only SUMMER-0.3.0/SUMMER/inst/doc/u5mr-vignette2.html |only SUMMER-0.3.0/SUMMER/inst/doc/u5mr-vignette2.html.asis |only SUMMER-0.3.0/SUMMER/man/BRFSS.Rd | 2 SUMMER-0.3.0/SUMMER/man/DemoData.Rd | 2 SUMMER-0.3.0/SUMMER/man/DemoData2.Rd | 2 SUMMER-0.3.0/SUMMER/man/DemoMap.Rd | 2 SUMMER-0.3.0/SUMMER/man/DemoMap2.Rd | 2 SUMMER-0.3.0/SUMMER/man/KenData.Rd |only SUMMER-0.3.0/SUMMER/man/aggregateSurvey.Rd | 4 SUMMER-0.3.0/SUMMER/man/fitGeneric.Rd |only SUMMER-0.3.0/SUMMER/man/fitINLA.Rd | 93 - SUMMER-0.3.0/SUMMER/man/fitINLA2.Rd |only SUMMER-0.3.0/SUMMER/man/getAdjusted.Rd |only SUMMER-0.3.0/SUMMER/man/getAmat.Rd |only SUMMER-0.3.0/SUMMER/man/getBirths.Rd | 15 SUMMER-0.3.0/SUMMER/man/getCounts.Rd |only SUMMER-0.3.0/SUMMER/man/getDiag.Rd |only SUMMER-0.3.0/SUMMER/man/getDirect.Rd |only SUMMER-0.3.0/SUMMER/man/getDirectList.Rd |only SUMMER-0.3.0/SUMMER/man/getSmoothed.Rd |only SUMMER-0.3.0/SUMMER/man/hatchPlot.Rd |only SUMMER-0.3.0/SUMMER/man/iid.new.Rd |only SUMMER-0.3.0/SUMMER/man/iid.new.pc.Rd |only SUMMER-0.3.0/SUMMER/man/mapPlot.Rd | 10 SUMMER-0.3.0/SUMMER/man/mapPoints.Rd |only SUMMER-0.3.0/SUMMER/man/plot.SUMMERproj.Rd |only SUMMER-0.3.0/SUMMER/man/rw.new.Rd |only SUMMER-0.3.0/SUMMER/man/rw.new.pc.Rd |only SUMMER-0.3.0/SUMMER/man/st.new.Rd |only SUMMER-0.3.0/SUMMER/man/st.new.pc.Rd |only SUMMER-0.3.0/SUMMER/vignettes/summer-vignette.html.asis |only SUMMER-0.3.0/SUMMER/vignettes/u5mr-vignette.html.asis |only SUMMER-0.3.0/SUMMER/vignettes/u5mr-vignette2.html.asis |only 78 files changed, 1178 insertions(+), 809 deletions(-)
Title: Density Based Clustering of Applications with Noise (DBSCAN) and
Related Algorithms
Description: A fast reimplementation of several density-based algorithms of
the DBSCAN family for spatial data. Includes the DBSCAN (density-based spatial
clustering of applications with noise) and OPTICS (ordering points to identify
the clustering structure) clustering algorithms HDBSCAN (hierarchical DBSCAN) and the LOF (local outlier
factor) algorithm. The implementations use the kd-tree data structure (from
library ANN) for faster k-nearest neighbor search. An R interface to fast kNN
and fixed-radius NN search is also provided.
See Hahsler M, Piekenbrock M and Doran D (2019) <doi:10.18637/jss.v091.i01>.
Author: Michael Hahsler [aut, cre, cph],
Matthew Piekenbrock [aut, cph],
Sunil Arya [ctb, cph],
David Mount [ctb, cph]
Maintainer: Michael Hahsler <mhahsler@lyle.smu.edu>
Diff between dbscan versions 1.1-4 dated 2019-08-05 and 1.1-5 dated 2019-10-23
dbscan-1.1-4/dbscan/src/R_kNN.h |only dbscan-1.1-4/dbscan/src/init.c |only dbscan-1.1-5/dbscan/DESCRIPTION | 13 dbscan-1.1-5/dbscan/MD5 | 69 dbscan-1.1-5/dbscan/NAMESPACE | 5 dbscan-1.1-5/dbscan/NEWS.md | 14 dbscan-1.1-5/dbscan/R/NN.R | 16 dbscan-1.1-5/dbscan/R/RcppExports.R | 70 dbscan-1.1-5/dbscan/R/frNN.R | 55 dbscan-1.1-5/dbscan/R/kNN.R | 49 dbscan-1.1-5/dbscan/R/sNN.R | 53 dbscan-1.1-5/dbscan/R/sNNclust.R | 2 dbscan-1.1-5/dbscan/README.md | 7 dbscan-1.1-5/dbscan/build/partial.rdb |only dbscan-1.1-5/dbscan/inst/CITATION |only dbscan-1.1-5/dbscan/inst/doc/dbscan.R | 47 dbscan-1.1-5/dbscan/inst/doc/dbscan.Rnw | 7 dbscan-1.1-5/dbscan/inst/doc/dbscan.pdf |binary dbscan-1.1-5/dbscan/inst/doc/hdbscan.Rmd | 3 dbscan-1.1-5/dbscan/inst/doc/hdbscan.html | 3 dbscan-1.1-5/dbscan/man/dbscan.Rd | 18 dbscan-1.1-5/dbscan/man/frNN.Rd | 22 dbscan-1.1-5/dbscan/man/hdbscan.Rd | 11 dbscan-1.1-5/dbscan/man/kNN.Rd | 26 dbscan-1.1-5/dbscan/man/optics.Rd | 9 dbscan-1.1-5/dbscan/man/sNN.Rd | 14 dbscan-1.1-5/dbscan/src/R_JP.cpp | 21 dbscan-1.1-5/dbscan/src/R_frNN.cpp | 86 + dbscan-1.1-5/dbscan/src/R_kNN.cpp | 80 + dbscan-1.1-5/dbscan/src/R_regionQuery.cpp | 30 dbscan-1.1-5/dbscan/src/R_regionQuery.h | 7 dbscan-1.1-5/dbscan/src/RcppExports.cpp | 82 + dbscan-1.1-5/dbscan/tests/testthat/test-frNN.R | 24 dbscan-1.1-5/dbscan/tests/testthat/test-kNN.R | 46 dbscan-1.1-5/dbscan/tests/testthat/test-sNN.R |only dbscan-1.1-5/dbscan/vignettes/dbscan.Rnw | 7 dbscan-1.1-5/dbscan/vignettes/dbscan.bib | 1820 ++++++++++++------------- dbscan-1.1-5/dbscan/vignettes/hdbscan.Rmd | 3 38 files changed, 1580 insertions(+), 1139 deletions(-)
Title: Retrieve and Analyze Clinical Trials in Public Registers
Description: Provides functions for querying, retrieving and analysing
protocol- and results-related information on clinical trials from
two public registers, the European Union Clinical Trials Register
(EUCTR, <https://www.clinicaltrialsregister.eu/>) and
ClinicalTrials.gov (CTGOV, <https://clinicaltrials.gov/>). The
information is transformed and then stored in a database (nodbi).
Functions are provided for accessing and analysing the locally
stored information on the clinical trials, as well as for
identifying duplicate records. The package is motivated by the need
for aggregating and trend-analysing the design, conduct and outcomes
across clinical trials.
Author: Ralf Herold [aut, cre] (<https://orcid.org/0000-0002-8148-6748>)
Maintainer: Ralf Herold <ralf.herold@mailbox.org>
Diff between ctrdata versions 1.0 dated 2019-10-16 and 1.0.1 dated 2019-10-23
DESCRIPTION | 10 +++++----- MD5 | 10 +++++----- NEWS.md | 4 ++++ R/main.R | 6 +++--- inst/tinytest/ctrdata_euctr.R | 8 +++++--- tests/tinytest.R | 8 +++++--- 6 files changed, 27 insertions(+), 19 deletions(-)
Title: Basket Trial Analysis
Description: Implementation of multisource exchangeability models for Bayesian analyses of prespecified subgroups arising in the context of basket trial design and monitoring. The R 'basket' package facilitates implementation of the binary, symmetric multi-source exchangeability model (MEM) with posterior inference arising from both exact computation and Markov chain Monte Carlo sampling. Analysis output includes full posterior samples as well as posterior probabilities, highest posterior density (HPD) interval boundaries, effective sample sizes (ESS), mean and median estimations, posterior exchangeability probability matrices, and maximum a posteriori MEMs. In addition to providing "basketwise" analyses, the package includes similar calculations for "clusterwise" analyses for which subgroups are combined into meta-baskets, or clusters, using graphical clustering algorithms that treat the posterior exchangeability probabilities as edge weights. In addition plotting tools are provided to visualize basket and cluster densities as well as their exchangeability. References include Hyman, D.M., Puzanov, I., Subbiah, V., Faris, J.E., Chau, I., Blay, J.Y., Wolf, J., Raje, N.S., Diamond, E.L., Hollebecque, A. and Gervais, R (2015) <doi:10.1056/NEJMoa1502309>; Hobbs, B.P. and Landin, R. (2018) <doi:10.1002/sim.7893>; Hobbs, B.P., Kane, M.J., Hong, D.S. and Landin, R. (2018) <doi:10.1093/annonc/mdy457>; and Kaizer, A.M., Koopmeiners, J.S. and Hobbs, B.P. (2017) <doi:10.1093/biostatistics/kxx031>.
Author: Nan Chen [aut],
Brian Hobbs [aut],
Alex Kaizer [aut],
Michael J. Kane [aut, cre] (<https://orcid.org/0000-0003-1899-6662>)
Maintainer: Michael J. Kane <michael.kane@yale.edu>
Diff between basket versions 0.9.2 dated 2019-05-14 and 0.9.10 dated 2019-10-23
DESCRIPTION | 22 MD5 | 59 - NAMESPACE | 4 NEWS.md | 10 R/accessors.r | 432 +++++------ R/basket.r | 103 ++ R/mem-exact.r | 232 ++++-- R/mem-mcmc.r | 140 +++ R/package-doc.r | 2 R/plot.r | 17 R/summary.r | 8 R/update.r | 224 ++--- R/util.r | 1052 +++++++++++++++------------- build/vignette.rds |binary inst/doc/using-the-basket-package.R | 27 inst/doc/using-the-basket-package.Rmd | 25 inst/doc/using-the-basket-package.html | 100 +- man/basket-package.Rd | 1 man/basket.Rd |only man/cluster_membership.Rd |only man/mem_exact.Rd | 10 man/mem_mcmc.Rd | 9 tests/testthat/reference_data/mem-exact.rds |binary tests/testthat/reference_data/mem-mcmc1.rds |binary tests/testthat/reference_data/mem-mcmc2.rds |binary tests/testthat/test-errors.r | 2 tests/testthat/test-exact.r | 19 tests/testthat/test-mcmc.r | 22 tests/testthat/test-plot.r | 5 tests/testthat/test-update.r | 5 vignettes/using-the-basket-package.Rmd | 25 vignettes/vemu_basket.rds |only 32 files changed, 1552 insertions(+), 1003 deletions(-)
Title: Groupwise Statistics, LSmeans, Linear Contrasts, Utilities
Description: Contains:
1) Facilities for working with grouped data: 'do' something to data
stratified 'by' some variables.
2) LSmeans (least-squares means), general linear contrasts.
3) Miscellaneous other utilities.
Author: Søren Højsgaard <sorenh@math.aau.dk> and Ulrich Halekoh
<uhalekoh@health.sdu.dk>
Maintainer: Søren Højsgaard <sorenh@math.aau.dk>
Diff between doBy versions 4.6-2 dated 2018-08-30 and 4.6-3 dated 2019-10-23
doBy-4.6-2/doBy/R/data-NIRmilk.R |only doBy-4.6-2/doBy/R/data-breastcancer.R |only doBy-4.6-2/doBy/R/data-budworm.R |only doBy-4.6-2/doBy/R/data-codstom.R |only doBy-4.6-2/doBy/R/data-crimerate.R |only doBy-4.6-2/doBy/R/data-haldCement.R |only doBy-4.6-2/doBy/R/data-milkman.R |only doBy-4.6-2/doBy/R/data-potatoes.R |only doBy-4.6-2/doBy/inst/doc/doBy.R |only doBy-4.6-2/doBy/inst/doc/doBy.Rnw |only doBy-4.6-2/doBy/inst/doc/doBy.pdf |only doBy-4.6-2/doBy/vignettes/doBy.Rnw |only doBy-4.6-2/doBy/vignettes/doBy.bib |only doBy-4.6-3/doBy/ChangeLog | 13 doBy-4.6-3/doBy/DESCRIPTION | 15 doBy-4.6-3/doBy/MD5 | 79 ++--- doBy-4.6-3/doBy/NAMESPACE | 75 +++- doBy-4.6-3/doBy/R/BY-lmBy.R |only doBy-4.6-3/doBy/R/data-doBy.R | 419 +++++++++++++++++++++++++++ doBy-4.6-3/doBy/R/esticon.R | 112 +++++-- doBy-4.6-3/doBy/R/linest_compute.R | 309 +++++++++---------- doBy-4.6-3/doBy/R/linest_matrix.R | 165 ++++++---- doBy-4.6-3/doBy/R/linest_utilities.R | 45 -- doBy-4.6-3/doBy/R/subSeq.R | 52 --- doBy-4.6-3/doBy/R/taylor.R |only doBy-4.6-3/doBy/README.md | 1 doBy-4.6-3/doBy/build/vignette.rds |binary doBy-4.6-3/doBy/data/datalist | 1 doBy-4.6-3/doBy/data/fev.rda |only doBy-4.6-3/doBy/inst/doc/doby.R |only doBy-4.6-3/doBy/inst/doc/doby.Rnw |only doBy-4.6-3/doBy/inst/doc/doby.pdf |only doBy-4.6-3/doBy/inst/doc/linest-lsmeans.Rnw | 2 doBy-4.6-3/doBy/inst/doc/linest-lsmeans.pdf |binary doBy-4.6-3/doBy/man/by-lmby.Rd |only doBy-4.6-3/doBy/man/data-NIRmilk.Rd | 2 doBy-4.6-3/doBy/man/data-breastcancer.Rd | 2 doBy-4.6-3/doBy/man/data-budworm.Rd | 2 doBy-4.6-3/doBy/man/data-codstom.Rd | 2 doBy-4.6-3/doBy/man/data-crimeRate.Rd | 2 doBy-4.6-3/doBy/man/data-haldCement.Rd | 2 doBy-4.6-3/doBy/man/data-milkman.Rd | 2 doBy-4.6-3/doBy/man/data-potatoes.Rd | 2 doBy-4.6-3/doBy/man/doBy-internal.Rd | 6 doBy-4.6-3/doBy/man/dot-rhsf2list.Rd |only doBy-4.6-3/doBy/man/esticon.Rd | 26 + doBy-4.6-3/doBy/man/fev.Rd |only doBy-4.6-3/doBy/man/linest-matrix.Rd | 11 doBy-4.6-3/doBy/man/linest.Rd | 31 + doBy-4.6-3/doBy/man/taylor.Rd |only doBy-4.6-3/doBy/vignettes/doby.Rnw |only doBy-4.6-3/doBy/vignettes/doby.bib |only doBy-4.6-3/doBy/vignettes/linest-lsmeans.Rnw | 2 53 files changed, 934 insertions(+), 446 deletions(-)
Title: Access the Bioconductor Project Package Repository
Description: A convenient tool to install and update Bioconductor packages.
Author: Martin Morgan [aut] (<https://orcid.org/0000-0002-5874-8148>),
Marcel Ramos [ctb, cre] (<https://orcid.org/0000-0002-3242-0582>)
Maintainer: Marcel Ramos <marcel.ramos@roswellpark.org>
Diff between BiocManager versions 1.30.8 dated 2019-10-16 and 1.30.9 dated 2019-10-23
DESCRIPTION | 6 ++--- MD5 | 22 ++++++++++---------- NAMESPACE | 3 +- NEWS | 9 ++++++++ R/install.R | 2 - R/utilities.R | 11 ++++++++-- R/version.R | 46 +++++++++++++++++++++++++++++------------- R/zzz.R | 31 +++++++--------------------- README.md | 8 ++----- man/version.Rd | 4 +-- tests/testthat.R | 10 +++++++++ tests/testthat/test_version.R | 3 ++ 12 files changed, 93 insertions(+), 62 deletions(-)
Title: Analysis and Mining of Multilayer Social Networks
Description: Functions for the creation/generation and analysis of multilayer social networks.
Author: Matteo Magnani, Davide Vega, Mikael Dubik (glouvain). The package uses functions from eclat (www.borgelt.net/eclat.html), for association rule mining, Eigen (eigen.tuxfamily.org) and spectra (https://spectralib.org), for matrix manipulation, Infomap (www.mapequation.org), for the Infomap community detection method, and Howard Hinnant's date and time library (https://github.com/HowardHinnant/date). The code from this libraries has been included in our source package.
Maintainer: Matteo Magnani <matteo.magnani@it.uu.se>
Diff between multinet versions 3.0.3 dated 2019-07-13 and 3.1.0 dated 2019-10-23
multinet-3.0.3/multinet/src/include |only multinet-3.0.3/multinet/src/multinet/mnet/community/infomap_utils.cpp |only multinet-3.0.3/multinet/src/multinet/mnet/datastructures/graphs/AttributedHomogeneousMultilayerNetwork.cpp |only multinet-3.0.3/multinet/src/multinet/mnet/datastructures/graphs/AttributedMultiplexNetwork.cpp |only multinet-3.0.3/multinet/src/multinet/mnet/datastructures/graphs/AttributedTwoModeNetwork.cpp |only multinet-3.0.3/multinet/src/multinet/mnet/datastructures/graphs/HomogeneousMultilayerNetwork.cpp |only multinet-3.0.3/multinet/src/multinet/mnet/datastructures/graphs/MultiplexNetwork.cpp |only multinet-3.0.3/multinet/src/multinet/mnet/datastructures/graphs/OrderedMultiplexNetwork.cpp |only multinet-3.0.3/multinet/src/multinet/mnet/datastructures/stores/DynamicSimpleInterlayerEdgeStore.cpp_tbd |only multinet-3.0.3/multinet/src/multinet/mnet/datastructures/stores/SimpleInterlayerEdgeStore.cpp_tbd |only multinet-3.0.3/multinet/src/multinet/mnet/io/read_attributed_homogeneous_multilayer_network.cpp |only multinet-3.0.3/multinet/src/multinet/mnet/io/read_attributed_multiplex_network.cpp |only multinet-3.0.3/multinet/src/multinet/mnet/io/read_multiplex_network.cpp |only multinet-3.0.3/multinet/src/multinet/mnet/io/read_ordered_multiplex_network.cpp |only multinet-3.0.3/multinet/src/multinet/mnet/layout |only multinet-3.0.3/multinet/src/multinet/net/community/abacus.cpp |only multinet-3.0.3/multinet/src/multinet/net/datastructures/connectivity |only multinet-3.0.3/multinet/src/multinet/net/datastructures/graphs/AttributedEmptyGraph.cpp |only multinet-3.0.3/multinet/src/multinet/net/datastructures/graphs/AttributedSimpleGraph.cpp |only multinet-3.0.3/multinet/src/multinet/net/datastructures/graphs/MultiGraph.cpp |only multinet-3.0.3/multinet/src/multinet/net/datastructures/graphs/SimpleGraph.cpp |only multinet-3.0.3/multinet/src/multinet/net/datastructures/objects |only multinet-3.0.3/multinet/src/multinet/net/datastructures/stores/EmptyEdgeStore.cpp |only multinet-3.0.3/multinet/src/multinet/net/datastructures/stores/VertexStore.cpp_tbd |only multinet-3.0.3/multinet/src/multinet/net/io/read_attibuted_empty_graph.cpp |only multinet-3.0.3/multinet/src/multinet/net/io/read_attibuted_simple_graph.cpp |only multinet-3.0.3/multinet/src/multinet/net/io/read_multi_graph.cpp |only multinet-3.0.3/multinet/src/multinet/net/io/read_simple_graph.cpp |only multinet-3.0.3/multinet/src/multinet/tnet/datastructures/graphs |only multinet-3.0.3/multinet/src/multinet/tnet/io |only multinet-3.0.3/multinet/src/multinet/tnet/transformation |only multinet-3.0.3/multinet/src/multinet/wnet/datastructures/graphs |only multinet-3.0.3/multinet/src/multinet/wnet/io |only multinet-3.0.3/multinet/src/multinet/xnet/datastructures/graphs |only multinet-3.0.3/multinet/src/multinet/xnet/io |only multinet-3.1.0/multinet/DESCRIPTION | 8 multinet-3.1.0/multinet/MD5 | 647 ++++------ multinet-3.1.0/multinet/NAMESPACE | 1 multinet-3.1.0/multinet/NEWS | 10 multinet-3.1.0/multinet/R/deprecated.R | 9 multinet-3.1.0/multinet/R/functions.R | 49 multinet-3.1.0/multinet/R/igraph.R | 22 multinet-3.1.0/multinet/man/ActorMeasures.Rd | 31 multinet-3.1.0/multinet/man/Attributes.Rd | 21 multinet-3.1.0/multinet/man/Classes.Rd | 7 multinet-3.1.0/multinet/man/Communities.Rd | 38 multinet-3.1.0/multinet/man/Conversion.Rd | 10 multinet-3.1.0/multinet/man/Deprecated.Rd | 6 multinet-3.1.0/multinet/man/Directionality.Rd | 15 multinet-3.1.0/multinet/man/DistanceMeasures.Rd | 9 multinet-3.1.0/multinet/man/Generation.Rd | 8 multinet-3.1.0/multinet/man/IO.Rd | 20 multinet-3.1.0/multinet/man/LayerMeasures.Rd | 12 multinet-3.1.0/multinet/man/Layout.Rd | 18 multinet-3.1.0/multinet/man/Manipulation.Rd | 47 multinet-3.1.0/multinet/man/Navigation.Rd | 14 multinet-3.1.0/multinet/man/Plot.Rd | 30 multinet-3.1.0/multinet/man/Predefined.Rd | 16 multinet-3.1.0/multinet/man/Properties.Rd | 35 multinet-3.1.0/multinet/man/Transformation.Rd | 18 multinet-3.1.0/multinet/man/multinet-package.Rd | 12 multinet-3.1.0/multinet/src/Makevars | 6 multinet-3.1.0/multinet/src/Makevars.win | 6 multinet-3.1.0/multinet/src/eclat/tract/src/tract.c | 4 multinet-3.1.0/multinet/src/infomap/infomap/InfomapBase.cpp | 34 multinet-3.1.0/multinet/src/infomap/infomap/InfomapBase.h | 4 multinet-3.1.0/multinet/src/infomap/infomap/InfomapContext.cpp | 8 multinet-3.1.0/multinet/src/infomap/infomap/InfomapContext.h | 4 multinet-3.1.0/multinet/src/infomap/infomap/InfomapGreedyCommon.h | 6 multinet-3.1.0/multinet/src/infomap/infomap/InfomapGreedyTypeSpecialized.h | 14 multinet-3.1.0/multinet/src/infomap/infomap/MemoryNetworkAdapter.cpp | 2 multinet-3.1.0/multinet/src/infomap/infomap/NetworkAdapter.cpp | 2 multinet-3.1.0/multinet/src/infomap/infomap/Node.cpp | 3 multinet-3.1.0/multinet/src/infomap/infomap/Node.h | 2 multinet-3.1.0/multinet/src/infomap/infomap/TreeData.h | 2 multinet-3.1.0/multinet/src/infomap/io/HierarchicalNetwork.cpp | 8 multinet-3.1.0/multinet/src/lib/eigen3/Eigen/SPQRSupport | 2 multinet-3.1.0/multinet/src/lib/eigen3/Eigen/src/Core/StableNorm.h | 2 multinet-3.1.0/multinet/src/lib/eigen3/Eigen/src/OrderingMethods/Eigen_Colamd.h | 12 multinet-3.1.0/multinet/src/lib/eigen3/Eigen/src/plugins/ArrayCwiseUnaryOps.h | 6 multinet-3.1.0/multinet/src/lib/infomap/infomap/InfomapBase.cpp | 34 multinet-3.1.0/multinet/src/lib/infomap/infomap/InfomapBase.h | 4 multinet-3.1.0/multinet/src/lib/infomap/infomap/InfomapContext.cpp | 8 multinet-3.1.0/multinet/src/lib/infomap/infomap/InfomapContext.h | 4 multinet-3.1.0/multinet/src/lib/infomap/infomap/InfomapGreedyCommon.h | 6 multinet-3.1.0/multinet/src/lib/infomap/infomap/InfomapGreedyTypeSpecialized.h | 14 multinet-3.1.0/multinet/src/lib/infomap/infomap/MemoryNetworkAdapter.cpp | 2 multinet-3.1.0/multinet/src/lib/infomap/infomap/NetworkAdapter.cpp | 2 multinet-3.1.0/multinet/src/lib/infomap/infomap/Node.cpp | 3 multinet-3.1.0/multinet/src/lib/infomap/infomap/Node.h | 2 multinet-3.1.0/multinet/src/lib/infomap/infomap/TreeData.h | 2 multinet-3.1.0/multinet/src/lib/infomap/io/HierarchicalNetwork.cpp | 8 multinet-3.1.0/multinet/src/multinet/algorithms |only multinet-3.1.0/multinet/src/multinet/community |only multinet-3.1.0/multinet/src/multinet/core/attributes/Attribute.cpp | 2 multinet-3.1.0/multinet/src/multinet/core/attributes/Attribute.hpp |only multinet-3.1.0/multinet/src/multinet/core/attributes/AttributeType.cpp | 2 multinet-3.1.0/multinet/src/multinet/core/attributes/AttributeType.hpp |only multinet-3.1.0/multinet/src/multinet/core/attributes/AttributeValueMap.hpp |only multinet-3.1.0/multinet/src/multinet/core/attributes/MainMemoryAttributeValueMap.hpp |only multinet-3.1.0/multinet/src/multinet/core/attributes/Text.cpp | 2 multinet-3.1.0/multinet/src/multinet/core/attributes/Text.hpp |only multinet-3.1.0/multinet/src/multinet/core/attributes/Time.cpp | 4 multinet-3.1.0/multinet/src/multinet/core/attributes/Time.hpp |only multinet-3.1.0/multinet/src/multinet/core/attributes/Value.hpp |only multinet-3.1.0/multinet/src/multinet/core/attributes/conversion.cpp | 10 multinet-3.1.0/multinet/src/multinet/core/attributes/conversion.hpp |only multinet-3.1.0/multinet/src/multinet/core/attributes/date.hpp |only multinet-3.1.0/multinet/src/multinet/core/datastructures/containers |only multinet-3.1.0/multinet/src/multinet/core/datastructures/objects/NamedObject.cpp | 10 multinet-3.1.0/multinet/src/multinet/core/datastructures/objects/NamedObject.hpp |only multinet-3.1.0/multinet/src/multinet/core/datastructures/objects/Object.cpp | 61 multinet-3.1.0/multinet/src/multinet/core/datastructures/objects/Object.hpp |only multinet-3.1.0/multinet/src/multinet/core/datastructures/observers/GenericObserver.hpp |only multinet-3.1.0/multinet/src/multinet/core/datastructures/observers/Observer.hpp |only multinet-3.1.0/multinet/src/multinet/core/datastructures/observers/ObserverStore.cpp | 11 multinet-3.1.0/multinet/src/multinet/core/datastructures/observers/ObserverStore.hpp |only multinet-3.1.0/multinet/src/multinet/core/datastructures/observers/Subject.hpp |only multinet-3.1.0/multinet/src/multinet/core/datastructures/propertymatrix |only multinet-3.1.0/multinet/src/multinet/core/exceptions/DuplicateElementException.cpp | 2 multinet-3.1.0/multinet/src/multinet/core/exceptions/DuplicateElementException.hpp |only multinet-3.1.0/multinet/src/multinet/core/exceptions/ElementNotFoundException.cpp | 2 multinet-3.1.0/multinet/src/multinet/core/exceptions/ElementNotFoundException.hpp |only multinet-3.1.0/multinet/src/multinet/core/exceptions/ExternalLibException.cpp | 2 multinet-3.1.0/multinet/src/multinet/core/exceptions/ExternalLibException.hpp |only multinet-3.1.0/multinet/src/multinet/core/exceptions/FileNotFoundException.cpp | 2 multinet-3.1.0/multinet/src/multinet/core/exceptions/FileNotFoundException.hpp |only multinet-3.1.0/multinet/src/multinet/core/exceptions/NullPtrException.cpp | 2 multinet-3.1.0/multinet/src/multinet/core/exceptions/NullPtrException.hpp |only multinet-3.1.0/multinet/src/multinet/core/exceptions/OperationNotSupportedException.cpp | 2 multinet-3.1.0/multinet/src/multinet/core/exceptions/OperationNotSupportedException.hpp |only multinet-3.1.0/multinet/src/multinet/core/exceptions/OutOfBoundsException.cpp |only multinet-3.1.0/multinet/src/multinet/core/exceptions/OutOfBoundsException.hpp |only multinet-3.1.0/multinet/src/multinet/core/exceptions/WrongFormatException.cpp | 2 multinet-3.1.0/multinet/src/multinet/core/exceptions/WrongFormatException.hpp |only multinet-3.1.0/multinet/src/multinet/core/exceptions/WrongParameterException.cpp | 2 multinet-3.1.0/multinet/src/multinet/core/exceptions/WrongParameterException.hpp |only multinet-3.1.0/multinet/src/multinet/core/exceptions/assert_not_null.cpp | 2 multinet-3.1.0/multinet/src/multinet/core/exceptions/assert_not_null.hpp |only multinet-3.1.0/multinet/src/multinet/core/stores |only multinet-3.1.0/multinet/src/multinet/core/utils/CSVReader.cpp | 6 multinet-3.1.0/multinet/src/multinet/core/utils/CSVReader.hpp |only multinet-3.1.0/multinet/src/multinet/core/utils/Counter.hpp |only multinet-3.1.0/multinet/src/multinet/core/utils/hashing.hpp |only multinet-3.1.0/multinet/src/multinet/core/utils/math.hpp |only multinet-3.1.0/multinet/src/multinet/core/utils/pretty_printing.hpp |only multinet-3.1.0/multinet/src/multinet/core/utils/random.cpp | 4 multinet-3.1.0/multinet/src/multinet/core/utils/random.hpp |only multinet-3.1.0/multinet/src/multinet/core/utils/string.cpp | 2 multinet-3.1.0/multinet/src/multinet/core/utils/string.hpp |only multinet-3.1.0/multinet/src/multinet/core/utils/tuple.hpp |only multinet-3.1.0/multinet/src/multinet/creation |only multinet-3.1.0/multinet/src/multinet/generation |only multinet-3.1.0/multinet/src/multinet/io |only multinet-3.1.0/multinet/src/multinet/layout |only multinet-3.1.0/multinet/src/multinet/measures |only multinet-3.1.0/multinet/src/multinet/mnet/community/MLCPMCommunity.hpp |only multinet-3.1.0/multinet/src/multinet/mnet/community/PillarCommunity.hpp |only multinet-3.1.0/multinet/src/multinet/mnet/community/VertexLayerCommunity.hpp |only multinet-3.1.0/multinet/src/multinet/mnet/community/abacus.hpp |only multinet-3.1.0/multinet/src/multinet/mnet/community/common.hpp |only multinet-3.1.0/multinet/src/multinet/mnet/community/cutils.cpp | 2 multinet-3.1.0/multinet/src/multinet/mnet/community/cutils.hpp |only multinet-3.1.0/multinet/src/multinet/mnet/community/glouvain.cpp | 4 multinet-3.1.0/multinet/src/multinet/mnet/community/glouvain.hpp |only multinet-3.1.0/multinet/src/multinet/mnet/community/infomap.hpp |only multinet-3.1.0/multinet/src/multinet/mnet/community/infomap_utils.hpp |only multinet-3.1.0/multinet/src/multinet/mnet/community/lart.hpp |only multinet-3.1.0/multinet/src/multinet/mnet/community/ml-cpm.hpp |only multinet-3.1.0/multinet/src/multinet/mnet/community/modularity.hpp |only multinet-3.1.0/multinet/src/multinet/mnet/community/normalized_mutual_information.hpp |only multinet-3.1.0/multinet/src/multinet/mnet/datastructures/graphs/MultilayerNetwork.hpp |only multinet-3.1.0/multinet/src/multinet/mnet/datastructures/graphs/MultilayerNetworkType.hpp |only multinet-3.1.0/multinet/src/multinet/mnet/datastructures/objects |only multinet-3.1.0/multinet/src/multinet/mnet/datastructures/observers |only multinet-3.1.0/multinet/src/multinet/mnet/datastructures/stores/AttributeStoreWrapper.hpp |only multinet-3.1.0/multinet/src/multinet/mnet/datastructures/stores/Attributed.hpp |only multinet-3.1.0/multinet/src/multinet/mnet/datastructures/stores/AttributedDynamicInterlayerSimpleEdgeStore.hpp |only multinet-3.1.0/multinet/src/multinet/mnet/datastructures/stores/Attributes.hpp |only multinet-3.1.0/multinet/src/multinet/mnet/datastructures/stores/DynamicInterlayerEdgeStore.hpp |only multinet-3.1.0/multinet/src/multinet/mnet/datastructures/stores/DynamicInterlayerSimpleEdgeStore.hpp |only multinet-3.1.0/multinet/src/multinet/mnet/datastructures/stores/UserDefinedAttrs.hpp |only multinet-3.1.0/multinet/src/multinet/mnet/datastructures/stores/VertexOverlappingLayerStore.hpp |only multinet-3.1.0/multinet/src/multinet/mnet/io/MultilayerIOFileSection.hpp |only multinet-3.1.0/multinet/src/multinet/mnet/io/MultilayerMetadata.hpp |only multinet-3.1.0/multinet/src/multinet/mnet/io/read_common.cpp | 24 multinet-3.1.0/multinet/src/multinet/mnet/io/read_common.hpp |only multinet-3.1.0/multinet/src/multinet/net/community/cutils.cpp | 2 multinet-3.1.0/multinet/src/multinet/net/community/cutils.hpp |only multinet-3.1.0/multinet/src/multinet/net/datastructures/containers |only multinet-3.1.0/multinet/src/multinet/net/datastructures/graphs/Graph.hpp |only multinet-3.1.0/multinet/src/multinet/net/datastructures/graphs/GraphType.hpp |only multinet-3.1.0/multinet/src/multinet/net/datastructures/observers/AdjVertexCheckObserver.hpp |only multinet-3.1.0/multinet/src/multinet/net/datastructures/observers/NoLoopCheckObserver.cpp | 2 multinet-3.1.0/multinet/src/multinet/net/datastructures/observers/NoLoopCheckObserver.hpp |only multinet-3.1.0/multinet/src/multinet/net/datastructures/observers/PropagateAddEraseObserver.hpp |only multinet-3.1.0/multinet/src/multinet/net/datastructures/observers/PropagateObserver.hpp |only multinet-3.1.0/multinet/src/multinet/net/datastructures/olap |only multinet-3.1.0/multinet/src/multinet/net/datastructures/stores/AttrMultiEdgeStore.cpp |only multinet-3.1.0/multinet/src/multinet/net/datastructures/stores/AttrMultiEdgeStore.hpp |only multinet-3.1.0/multinet/src/multinet/net/datastructures/stores/AttrSimpleEdgeStore.cpp |only multinet-3.1.0/multinet/src/multinet/net/datastructures/stores/AttrSimpleEdgeStore.hpp |only multinet-3.1.0/multinet/src/multinet/net/datastructures/stores/AttrVertexStore.cpp |only multinet-3.1.0/multinet/src/multinet/net/datastructures/stores/AttrVertexStore.hpp |only multinet-3.1.0/multinet/src/multinet/net/datastructures/stores/EdgeStore.cpp |only multinet-3.1.0/multinet/src/multinet/net/datastructures/stores/EdgeStore.hpp |only multinet-3.1.0/multinet/src/multinet/net/datastructures/stores/MDEdgeStore.hpp |only multinet-3.1.0/multinet/src/multinet/net/datastructures/stores/MDSimpleEdgeStore.hpp |only multinet-3.1.0/multinet/src/multinet/net/datastructures/stores/MultiEdgeStore.cpp | 2 multinet-3.1.0/multinet/src/multinet/net/datastructures/stores/MultiEdgeStore.hpp |only multinet-3.1.0/multinet/src/multinet/net/datastructures/stores/SimpleEdgeStore.cpp | 192 ++ multinet-3.1.0/multinet/src/multinet/net/datastructures/stores/SimpleEdgeStore.hpp |only multinet-3.1.0/multinet/src/multinet/net/datastructures/stores/VertexStore.cpp |only multinet-3.1.0/multinet/src/multinet/net/datastructures/stores/VertexStore.hpp |only multinet-3.1.0/multinet/src/multinet/net/datastructures/stores2 |only multinet-3.1.0/multinet/src/multinet/net/io/GraphIOFileSection.cpp | 6 multinet-3.1.0/multinet/src/multinet/net/io/GraphIOFileSection.hpp |only multinet-3.1.0/multinet/src/multinet/net/io/GraphMetadata.hpp |only multinet-3.1.0/multinet/src/multinet/net/io/read_common.cpp | 7 multinet-3.1.0/multinet/src/multinet/net/io/read_common.hpp |only multinet-3.1.0/multinet/src/multinet/net/io/write_common.hpp |only multinet-3.1.0/multinet/src/multinet/networks |only multinet-3.1.0/multinet/src/multinet/objects |only multinet-3.1.0/multinet/src/multinet/olap |only multinet-3.1.0/multinet/src/multinet/operations |only multinet-3.1.0/multinet/src/multinet/tnet/datastructures/stores |only multinet-3.1.0/multinet/src/multinet/transformation |only multinet-3.1.0/multinet/src/multinet/wnet/datastructures/stores |only multinet-3.1.0/multinet/src/multinet/xnet/datastructures/stores/MessageStore.cpp | 5 multinet-3.1.0/multinet/src/multinet/xnet/datastructures/stores/MessageStore.hpp |only multinet-3.1.0/multinet/src/multinet/xnet/datastructures/stores/Texts.hpp |only multinet-3.1.0/multinet/src/r_functions.cpp | 212 +-- multinet-3.1.0/multinet/src/r_functions.h | 4 multinet-3.1.0/multinet/src/rcpp_module_definition.cpp | 98 - multinet-3.1.0/multinet/src/rcpp_utils.cpp | 32 multinet-3.1.0/multinet/src/rcpp_utils.h | 26 236 files changed, 1162 insertions(+), 917 deletions(-)