Title: Robust Mixture Regression
Description: Finite mixture models are a popular technique for modelling unobserved heterogeneity or to approximate general distribution functions in a semi-parametric way. They are used in a lot of different areas such as astronomy, biology, economics, marketing or medicine.
This package is the implementation of popular robust mixture regression methods based on different algorithms including: fleximix, finite mixture models and latent class regression; CTLERob, component-wise adaptive trimming likelihood estimation; mixbi, bi-square estimation; mixL, Laplacian distribution; mixt, t-distribution; TLE, trimmed likelihood estimation.
The implemented algorithms includes: CTLERob stands for Component-wise adaptive Trimming Likelihood Estimation based mixture regression; mixbi stands for mixture regression based on bi-square estimation; mixLstands for mixture regression based on Laplacian distribution; TLE stands for Trimmed Likelihood Estimation based mixture regression. For more detail of the algorithms, please refer to below references.
Reference: Chun Yu, Weixin Yao, Kun Chen (2017) <doi:10.1002/cjs.11310>.
NeyKov N, Filzmoser P, Dimova R et al. (2007) <doi:10.1016/j.csda.2006.12.024>.
Bai X, Yao W. Boyer JE (2012) <doi:10.1016/j.csda.2012.01.016>.
Wennan Chang, Xinyu Zhou, Yong Zang, Chi Zhang, Sha Cao (2020) <arXiv:2005.11599>.
Author: Sha Cao [aut, cph, ths],
Wennan Chang [aut, cre],
Chi Zhang [aut, ctb, ths]
Maintainer: Wennan Chang <wnchang@iu.edu>
Diff between RobMixReg versions 0.2.0 dated 2020-05-11 and 0.2.1 dated 2020-05-26
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NEWS.md | 5 +++++ README.md | 48 ++++++++++++++++++++++++++++++++++++++++++------ 4 files changed, 54 insertions(+), 13 deletions(-)
Title: Eigenvalues and Singular Values and Vectors from Large Matrices
Description: R interface to 'PRIMME' <http://www.cs.wm.edu/~andreas/software>, a C library for computing a few
eigenvalues and their corresponding eigenvectors of a real symmetric or complex
Hermitian matrix, or generalized Hermitian eigenproblem. It can also compute
singular values and vectors of a square or rectangular matrix. 'PRIMME' finds
largest, smallest, or interior singular/eigenvalues and can use preconditioning
to accelerate convergence. General description of the methods are provided in the papers
Stathopoulos (2010, <doi:10.1145/1731022.1731031>) and Wu (2017, <doi:10.1137/16M1082214>).
See 'citation("PRIMME")' for details.
Author: Eloy Romero [aut, cre],
Andreas Stathopoulos [aut],
College of William & Mary [cph]
Maintainer: Eloy Romero <eloy@cs.wm.edu>
Diff between PRIMME versions 3.0-0 dated 2019-07-25 and 3.1-1 dated 2020-05-26
DESCRIPTION | 24 - MD5 | 65 +- R/eigs.R | 82 +-- R/svds.R | 14 inst/include/primme.h | 2 inst/include/primme_eigs.h | 2 inst/include/primme_ls.h |only man/eigs_sym.Rd | 16 man/svds.Rd | 15 src/primme/eigs/auxiliary_eigs.c | 78 +++ src/primme/eigs/auxiliary_eigs.h | 228 +++++++++- src/primme/eigs/auxiliary_eigs_normal.c | 2 src/primme/eigs/convergence.c | 10 src/primme/eigs/correction.c | 4 src/primme/eigs/inner_solve.c | 7 src/primme/eigs/main_iter.c | 136 +++--- src/primme/eigs/main_iter.h | 72 +-- src/primme/eigs/ortho.c | 16 src/primme/eigs/primme_c.c | 18 src/primme/eigs/primme_c.h | 127 ++++- src/primme/eigs/primme_interface.c | 417 +++++++++--------- src/primme/eigs/restart.c | 20 src/primme/eigs/solve_projection.c | 4 src/primme/include/auxiliary.h | 132 +++++ src/primme/include/blaslapack.h | 102 ---- src/primme/include/common.h | 17 src/primme/include/primme_interface.h | 12 src/primme/linalg/auxiliary.c | 58 ++ src/primme/linalg/blaslapack.c | 38 - src/primme/linalg/magma_wrapper.c | 6 src/primme/svds/primme_svds_c.c | 567 +++++++++++++++++++------ src/primme/svds/primme_svds_c.h | 708 ++++++++++++++++++++++++++++---- src/primme/svds/primme_svds_interface.c | 294 ++++++------- src/primme/zhegv.c | 10 34 files changed, 2303 insertions(+), 1000 deletions(-)
Title: Factorization of Sparse Counts Matrices Through Poisson
Likelihood
Description: Creates a low-rank factorization of a sparse counts matrix by maximizing Poisson likelihood with l1/l2 regularization
with all non-negative latent factors (e.g. for recommender systems or topic modeling) (Cortes, (2018) <arXiv:1811.01908>).
Similar to hierarchical Poisson factorization, but follows an optimization-based approach with regularization instead of a
hierarchical structure, and is fit through either proximal gradient or conjugate gradient instead of
variational inference.
Author: David Cortes
Maintainer: David Cortes <david.cortes.rivera@gmail.com>
Diff between poismf versions 0.1.3 dated 2019-09-04 and 0.2.0 dated 2020-05-26
poismf-0.1.3/poismf/R/RcppExports.R |only poismf-0.1.3/poismf/man/predict_all.Rd |only poismf-0.1.3/poismf/src/RcppExports.cpp |only poismf-0.1.3/poismf/src/pgd.cpp |only poismf-0.1.3/poismf/src/rwrapper.cpp |only poismf-0.2.0/poismf/DESCRIPTION | 23 poismf-0.2.0/poismf/LICENSE | 2 poismf-0.2.0/poismf/MD5 | 34 poismf-0.2.0/poismf/NAMESPACE | 16 poismf-0.2.0/poismf/R/poismf.R | 1382 ++++++++++++++++++------ poismf-0.2.0/poismf/man/calc.all.counts.Rd |only poismf-0.2.0/poismf/man/evaluate.poisson.llk.Rd |only poismf-0.2.0/poismf/man/factors.Rd |only poismf-0.2.0/poismf/man/factors.single.Rd |only poismf-0.2.0/poismf/man/get.factor.matrices.Rd |only poismf-0.2.0/poismf/man/get.model.mappings.Rd |only poismf-0.2.0/poismf/man/poismf.Rd | 215 ++- poismf-0.2.0/poismf/man/poismf_unsafe.Rd |only poismf-0.2.0/poismf/man/predict.poismf.Rd | 88 - poismf-0.2.0/poismf/man/topN.Rd |only poismf-0.2.0/poismf/man/topN.new.Rd |only poismf-0.2.0/poismf/src/Makevars | 5 poismf-0.2.0/poismf/src/nonnegcg.c |only poismf-0.2.0/poismf/src/poismf.c |only poismf-0.2.0/poismf/src/poismf.h |only poismf-0.2.0/poismf/src/pred.c |only poismf-0.2.0/poismf/src/rwrapper.c |only poismf-0.2.0/poismf/src/topN.c |only 28 files changed, 1308 insertions(+), 457 deletions(-)
Title: Base Package for 'Outsider'
Description: Base package for 'outsider' <https://github.com/ropensci/outsider>.
The 'outsider' package and its sister packages enable the installation and
running of external, command-line software within R. This base package is a
key dependency of the user-facing 'outsider' package as it provides the
utilities for interfacing between 'Docker' <https://www.docker.com> and R.
It is intended that end-users of 'outsider' do not directly work with this
base package.
Author: Dom Bennett [aut, cre] (<https://orcid.org/0000-0003-2722-1359>),
Hannes Hettling [ctb] (<https://orcid.org/0000-0003-4144-2238>),
Daniele Silvestro [ctb] (<https://orcid.org/0000-0003-0100-0961>),
Rutger Vos [ctb] (<https://orcid.org/0000-0001-9254-7318>),
Alexandre Antonelli [ctb] (<https://orcid.org/0000-0003-1842-9297>),
Anna Krystalli [rev]
Maintainer: Dom Bennett <dominic.john.bennett@gmail.com>
Diff between outsider.base versions 0.1.1 dated 2020-05-22 and 0.1.2 dated 2020-05-26
DESCRIPTION | 6 +++--- MD5 | 4 ++-- tests/testthat/test-ssh.R | 3 +++ 3 files changed, 8 insertions(+), 5 deletions(-)
Title: Interactive Analytic Networks
Description: Create interactive analytic networks. It joins the data analysis power of R to obtain coincidences, co-occurrences and correlations, and the visualization libraries of 'JavaScript' in one package. The methods are described in Escobar and Martinez-Uribe (2020) <doi:10.18637/jss.v093.i11>.
Author: Modesto Escobar <modesto@usal.es>,
David Barrios <metal@usal.es>,
Carlos Prieto <cprietos@usal.es>,
Luis Martinez-Uribe <lmartinez@usal.es>.
Maintainer: Modesto Escobar <modesto@usal.es>
Diff between netCoin versions 1.1.24 dated 2020-02-03 and 1.1.25 dated 2020-05-26
DESCRIPTION | 12 - MD5 | 51 ++--- R/netcoin.R | 156 +++++++++++------ R/network.R | 2 R/timeline.R | 25 ++ R/utils.R | 74 ++++---- build/partial.rdb |only inst/CITATION |only inst/doc/netCoin.html | 4 inst/doc/surCoin.html | 6 inst/www/barplot.js | 4 inst/www/ca.js | 2 inst/www/en.js | 2 inst/www/es.js | 2 inst/www/functions.js | 8 inst/www/network.js | 409 +++++++++++++++++++++++++++++---------------- inst/www/styles.css | 41 ++++ inst/www/timeline.js | 181 ++++++++++++++----- man/allNet.Rd | 7 man/asNodes.Rd | 6 man/coin.Rd | 6 man/dichotomize.Rd | 6 man/edgeList.Rd | 6 man/fromIgraph.Rd | 7 man/netCoin.Rd | 11 - man/surCoin.Rd | 7 man/timeCoin.Rd | 17 + vignettes/notebook.nb.html |only 28 files changed, 717 insertions(+), 335 deletions(-)
Title: NanoString Quality Control Dashboard
Description: NanoString nCounter data are gene expression assays
where there is no need for the use of enzymes or amplification
protocols and work with fluorescent barcodes (Geiss et al. (2018)
<doi:10.1038/nbt1385>). Each barcode is assigned a
messenger-RNA/micro-RNA (mRNA/miRNA) which after bonding with its
target can be counted. As a result each count of a specific barcode
represents the presence of its target mRNA/miRNA. 'NACHO' (NAnoString
quality Control dasHbOard) is able to analyse the exported NanoString
nCounter data and facilitates the user in performing a quality
control. 'NACHO' does this by visualising quality control metrics,
expression of control genes, principal components and sample specific
size factors in an interactive web application.
Author: Mickaël Canouil [aut, cre] (<https://orcid.org/0000-0002-3396-4549>),
Roderick Slieker [aut] (<https://orcid.org/0000-0003-0961-9152>),
Gerard Bouland [aut]
Maintainer: Mickaël Canouil <mickael.canouil@cnrs.fr>
Diff between NACHO versions 1.0.0 dated 2020-01-09 and 1.0.1 dated 2020-05-26
NACHO-1.0.0/NACHO/LICENSE |only NACHO-1.0.1/NACHO/DESCRIPTION | 18 +- NACHO-1.0.1/NACHO/MD5 | 63 ++++----- NACHO-1.0.1/NACHO/NEWS.md | 12 + NACHO-1.0.1/NACHO/R/GSE74821.R | 2 NACHO-1.0.1/NACHO/R/autoplot.R | 6 NACHO-1.0.1/NACHO/R/check_outliers.R | 2 NACHO-1.0.1/NACHO/R/load_rcc.R | 26 +-- NACHO-1.0.1/NACHO/R/norm_glm.R | 2 NACHO-1.0.1/NACHO/R/normalise.R | 14 +- NACHO-1.0.1/NACHO/R/print.R | 2 NACHO-1.0.1/NACHO/R/render.R | 2 NACHO-1.0.1/NACHO/R/visualise.R | 14 +- NACHO-1.0.1/NACHO/README.md | 7 - NACHO-1.0.1/NACHO/build/vignette.rds |binary NACHO-1.0.1/NACHO/inst/app/app.R | 8 - NACHO-1.0.1/NACHO/inst/app/utils.R | 8 - NACHO-1.0.1/NACHO/inst/app/www/nacho_hex.png |binary NACHO-1.0.1/NACHO/inst/doc/NACHO-analysis.html | 44 +++--- NACHO-1.0.1/NACHO/inst/doc/NACHO.R | 28 ++-- NACHO-1.0.1/NACHO/inst/doc/NACHO.Rmd | 30 ++-- NACHO-1.0.1/NACHO/inst/doc/NACHO.html | 174 +++++++++++++------------ NACHO-1.0.1/NACHO/man/GSE74821.Rd | 6 NACHO-1.0.1/NACHO/man/NACHO-package.Rd | 8 - NACHO-1.0.1/NACHO/man/autoplot.nacho.Rd | 2 NACHO-1.0.1/NACHO/man/check_outliers.Rd | 2 NACHO-1.0.1/NACHO/man/figures/nacho_hex.png |binary NACHO-1.0.1/NACHO/man/load_rcc.Rd | 20 +- NACHO-1.0.1/NACHO/man/normalise.Rd | 14 +- NACHO-1.0.1/NACHO/man/print.nacho.Rd | 2 NACHO-1.0.1/NACHO/man/render.Rd | 2 NACHO-1.0.1/NACHO/man/visualise.Rd | 14 +- NACHO-1.0.1/NACHO/vignettes/NACHO.Rmd | 30 ++-- 33 files changed, 285 insertions(+), 277 deletions(-)
Title: Protein Quantification in Mass Spectrometry-Based Proteomics
Description: An implementation of the maximal
peptide ratio extraction module of the MaxLFQ algorithm by
Cox et al. (2014) <doi:10.1074/mcp.M113.031591> in a complete
pipeline for processing proteomics data in data-independent acquisition mode
(Pham et al. 2020 <doi:10.1093/bioinformatics/btz961>).
It offers additional options for protein quantification using the N most intense
fragment ions, using all
fragment ions, and a wrapper for the median polish algorithm by Tukey (1977, ISBN:0201076160).
Author: Thang Pham [aut, cre, cph, ctb]
(<https://orcid.org/0000-0003-0333-2492>),
Alex Henneman [ctb] (<https://orcid.org/0000-0002-3746-4410>)
Maintainer: Thang Pham <t.pham@amsterdamumc.nl>
Diff between iq versions 1.5 dated 2020-05-18 and 1.7 dated 2020-05-26
DESCRIPTION | 6 MD5 | 8 inst/doc/iq-fast.html | 142 +++++++-------- inst/doc/iq.html | 4 src/iq.cpp | 445 ++++++++++++++++++++++++-------------------------- 5 files changed, 302 insertions(+), 303 deletions(-)
Title: Advanced and Fast Data Transformation
Description: A C/C++ based package for advanced data transformation in R that is
extremely fast, flexible and parsimonious to code with and programmer
friendly. It is well integrated with 'dplyr', 'plm' and 'data.table'.
--- Key Features: ---
(1) Advanced data programming: A full set of fast statistical functions
supporting grouped and weighted computations on vectors, matrices and
data frames. Fast (ordered) and programmable grouping, factor
generation, manipulation of data frames and data object conversions.
(2) Advanced aggregation: Fast and easy multi-data-type, multi-function,
weighted, parallelized and fully customized data aggregation.
(3) Advanced transformations: Fast (grouped, weighted) replacing and
sweeping out of statistics, scaling / standardizing, centering (i.e.
between and within transformations), higher-dimensional centering
(i.e. multiple fixed effects transformations), linear
prediction and partialling-out.
(4) Advanced time-computations: Fast (sequences of) lags / leads, and
(lagged / leaded, iterated, quasi-, log-) differences and growth
rates on (unordered) time-series and panel data. Multivariate auto,
partial and cross-correlation functions for panel data.
Panel data to (ts-)array conversions.
(5) List processing: (Recursive) list search / identification, extraction /
subsetting, data-apply, and generalized row-binding / unlisting in 2D.
(6) Advanced data exploration: Fast (grouped, weighted, panel-decomposed)
summary statistics for complex multilevel / panel data.
Author: Sebastian Krantz [aut, cre],
Matt Dowle [ctb],
Arun Srinivasan [ctb],
Simen Gaure [ctb],
Dirk Eddelbuettel [ctb],
R Core Team and contributors worldwide [ctb],
Martyn Plummer [cph],
1999-2016 The R Core Team [cph]
Maintainer: Sebastian Krantz <sebastian.krantz@graduateinstitute.ch>
Diff between collapse versions 1.2.0 dated 2020-05-19 and 1.2.1 dated 2020-05-26
DESCRIPTION | 8 MD5 | 80 - NAMESPACE | 2 NEWS.md | 7 R/GRP.R | 2 R/fFtest.R | 43 R/fmode.R | 16 R/small_helper.R | 25 inst/NEWS.Rd | 12 inst/doc/collapse_and_dplyr.R | 124 +- inst/doc/collapse_and_dplyr.Rmd | 176 ++-- inst/doc/collapse_and_dplyr.html | 564 ++++++------ inst/doc/collapse_and_plm.R | 154 ++- inst/doc/collapse_and_plm.Rmd | 291 ++++-- inst/doc/collapse_and_plm.html | 1655 ++++++++++++++++++++------------------ inst/doc/collapse_intro.R | 83 - inst/doc/collapse_intro.Rmd | 169 ++- inst/doc/collapse_intro.html | 1147 +++++++++++++------------- man/GGDC10S.Rd | 24 man/GRP.Rd | 2 man/collapse-documentation.Rd | 1 man/collapse-global-options.Rd | 1 man/descr.Rd | 4 man/fFtest.Rd | 2 man/fmode.Rd | 2 man/fscale.Rd | 4 man/qsu.Rd | 1 man/quick-conversion.Rd | 27 man/small-helper.Rd | 9 man/summary-statistics.Rd | 2 man/varying.Rd | 2 src/ExportSymbols.cpp | 5 src/base_radixsort.c | 2 src/data.table.h | 4 src/fdiff_fgrowth.cpp | 36 src/flag.cpp | 24 src/seqid_groupid.cpp | 41 tests/testthat/test-psmat-psacf.R | 2 vignettes/collapse_and_dplyr.Rmd | 176 ++-- vignettes/collapse_and_plm.Rmd | 291 ++++-- vignettes/collapse_intro.Rmd | 169 ++- 41 files changed, 2904 insertions(+), 2485 deletions(-)
Title: Time Aware Tibbles
Description: Built on top of the 'tibble' package, 'tibbletime' is an extension
that allows for the creation of time aware tibbles. Some immediate
advantages of this include: the ability to perform time-based subsetting
on tibbles, quickly summarising and aggregating results by time periods,
and creating columns that can be used as 'dplyr' time-based groups.
Author: Davis Vaughan [aut, cre],
Matt Dancho [aut]
Maintainer: Davis Vaughan <davis@rstudio.com>
Diff between tibbletime versions 0.1.3 dated 2019-09-20 and 0.1.4 dated 2020-05-26
DESCRIPTION | 10 MD5 | 58 ++--- NEWS.md | 5 R/aaa.R | 6 R/coercion.R | 2 R/collapse_index.R | 4 R/compat-dplyr.R | 2 R/new.R | 2 R/reconstruct.R | 8 README.md | 15 - inst/doc/TT-01-time-based-filtering.R | 24 +- inst/doc/TT-01-time-based-filtering.html | 162 +++++++------- inst/doc/TT-02-changing-time-periods.R | 16 - inst/doc/TT-02-changing-time-periods.html | 124 ++++++---- inst/doc/TT-03-rollify-for-rolling-analysis.R | 28 +- inst/doc/TT-03-rollify-for-rolling-analysis.html | 260 ++++++++++++----------- inst/doc/TT-04-use-with-dplyr.R | 10 inst/doc/TT-04-use-with-dplyr.Rmd | 2 inst/doc/TT-04-use-with-dplyr.html | 248 +++++++++++---------- man/FANG.Rd | 6 man/FB.Rd | 6 man/as_period.Rd | 10 man/ceiling_index.Rd | 4 man/collapse_by.Rd | 12 - man/collapse_index.Rd | 12 - man/create_series.Rd | 10 man/floor_index.Rd | 4 man/reexports.Rd | 2 tests/testthat/test_as_period.R | 3 vignettes/TT-04-use-with-dplyr.Rmd | 2 30 files changed, 582 insertions(+), 475 deletions(-)
Title: Perform Spatial Error Estimation and Variable Importance in
Parallel
Description: Implements spatial error estimation and
permutation-based variable importance measures for predictive models
using spatial cross-validation and spatial block bootstrap.
Author: Alexander Brenning [aut, cre] (<https://orcid.org/0000-0001-6640-679X>),
Patrick Schratz [aut] (<https://orcid.org/0000-0003-0748-6624>),
Tobias Herrmann [aut] (<https://orcid.org/0000-0001-9768-0708>)
Maintainer: Alexander Brenning <alexander.brenning@uni-jena.de>
Diff between sperrorest versions 3.0.0 dated 2020-04-13 and 3.0.1 dated 2020-05-26
DESCRIPTION | 6 - MD5 | 14 +-- NAMESPACE | 1 NEWS.md | 10 ++ R/sperrorest-package.R | 2 README.md | 126 ++++++++++++++++---------------- build/vignette.rds |binary inst/doc/spatial-modeling-use-case.html | 28 +++---- 8 files changed, 99 insertions(+), 88 deletions(-)
Title: A Simple HTTP Server to Serve Static Files or Dynamic Documents
Description: Start an HTTP server in R to serve static files, or dynamic
documents that can be converted to HTML files (e.g., R Markdown) under a
given directory.
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>),
Carson Sievert [ctb],
Jesse Anderson [ctb],
Ramnath Vaidyanathan [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between servr versions 0.16 dated 2020-03-02 and 0.17 dated 2020-05-26
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- NEWS | 6 ++++++ R/utils.R | 8 ++++++-- README.md | 11 +++++------ man/browse_last.Rd | 6 +++++- man/dynamic_site.Rd | 18 +++++++++++------- man/httd.Rd | 9 ++++++++- man/server_config.Rd | 14 +++++++++++--- 9 files changed, 64 insertions(+), 32 deletions(-)
Title: R Interface for Bokeh
Description: A native R plotting library that provides a flexible declarative interface for creating interactive web-based graphics, backed by the Bokeh visualization library <https://bokeh.pydata.org/>.
Author: Ryan Hafen [aut, cre],
Kenton Russell [ctb],
Jonathan Owen [ctb],
Barret Schloerke [ctb],
Saptasrhi Guha [ctb],
Continuum Analytics, Inc. [aut, cph] (Bokeh library in htmlwidgets/lib,
https://bokeh.pydata.org)
Maintainer: Ryan Hafen <rhafen@gmail.com>
Diff between rbokeh versions 0.5.0 dated 2016-10-11 and 0.5.1 dated 2020-05-26
rbokeh-0.5.0/rbokeh/inst/doc/docs.Rmd |only rbokeh-0.5.0/rbokeh/inst/doc/docs.html |only rbokeh-0.5.0/rbokeh/inst/doc/tutorial.Rmd |only rbokeh-0.5.0/rbokeh/inst/doc/tutorial.html |only rbokeh-0.5.0/rbokeh/inst/htmlwidgets/lib/bokehjs/bokeh-compiler.min.js |only rbokeh-0.5.0/rbokeh/vignettes/docs.Rmd |only rbokeh-0.5.0/rbokeh/vignettes/tutorial.Rmd |only rbokeh-0.5.1/rbokeh/DESCRIPTION | 17 rbokeh-0.5.1/rbokeh/LICENSE.note | 2 rbokeh-0.5.1/rbokeh/MD5 | 247 +++----- rbokeh-0.5.1/rbokeh/NEWS.md | 5 rbokeh-0.5.1/rbokeh/R/attr_mapping.R | 2 rbokeh-0.5.1/rbokeh/R/constants.R | 2 rbokeh-0.5.1/rbokeh/R/fig_axis.R | 2 rbokeh-0.5.1/rbokeh/R/fig_gmap.R | 27 rbokeh-0.5.1/rbokeh/R/fig_layer.R | 5 rbokeh-0.5.1/rbokeh/R/fig_legend.R | 22 rbokeh-0.5.1/rbokeh/R/fig_tool.R | 19 rbokeh-0.5.1/rbokeh/R/json_helpers.R | 6 rbokeh-0.5.1/rbokeh/R/layer_bar.R | 3 rbokeh-0.5.1/rbokeh/R/layer_glyphs.R | 12 rbokeh-0.5.1/rbokeh/R/layer_hexbin.R | 8 rbokeh-0.5.1/rbokeh/R/layer_image.R | 16 rbokeh-0.5.1/rbokeh/R/layer_lines.R | 27 rbokeh-0.5.1/rbokeh/R/layer_map.R | 3 rbokeh-0.5.1/rbokeh/R/layer_points.R | 3 rbokeh-0.5.1/rbokeh/R/layer_shapes.R | 15 rbokeh-0.5.1/rbokeh/R/layer_stats.R | 15 rbokeh-0.5.1/rbokeh/R/layer_text.R | 3 rbokeh-0.5.1/rbokeh/R/make_glyph.R | 2 rbokeh-0.5.1/rbokeh/R/output_gist.R | 6 rbokeh-0.5.1/rbokeh/R/output_save.R | 4 rbokeh-0.5.1/rbokeh/R/rbokeh-package.R | 6 rbokeh-0.5.1/rbokeh/R/theme_palettes.R | 2 rbokeh-0.5.1/rbokeh/R/theme_title.R | 6 rbokeh-0.5.1/rbokeh/README.md | 16 rbokeh-0.5.1/rbokeh/build/vignette.rds |binary rbokeh-0.5.1/rbokeh/inst/doc/rbokeh-pkg.Rmd |only rbokeh-0.5.1/rbokeh/inst/doc/rbokeh-pkg.html |only rbokeh-0.5.1/rbokeh/inst/htmlwidgets/lib/bokehjs/bokeh-widgets.min.css | 3 rbokeh-0.5.1/rbokeh/inst/htmlwidgets/lib/bokehjs/bokeh-widgets.min.js | 92 ++- rbokeh-0.5.1/rbokeh/inst/htmlwidgets/lib/bokehjs/bokeh.min.css | 3 rbokeh-0.5.1/rbokeh/inst/htmlwidgets/lib/bokehjs/bokeh.min.js | 306 ++++------ rbokeh-0.5.1/rbokeh/inst/htmlwidgets/rbokeh.yaml | 2 rbokeh-0.5.1/rbokeh/man/b_eval.Rd | 1 rbokeh-0.5.1/rbokeh/man/bokeh_render_json.Rd | 1 rbokeh-0.5.1/rbokeh/man/catjitter.Rd | 1 rbokeh-0.5.1/rbokeh/man/console_callback.Rd | 1 rbokeh-0.5.1/rbokeh/man/custom_callback.Rd | 1 rbokeh-0.5.1/rbokeh/man/data_name_list.Rd | 1 rbokeh-0.5.1/rbokeh/man/debug_callback.Rd | 1 rbokeh-0.5.1/rbokeh/man/elements.Rd | 1 rbokeh-0.5.1/rbokeh/man/figure.Rd | 39 - 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Title: Sassy 'UML' Diagrams
Description: A tool for drawing sassy 'UML' diagrams based on a simple syntax,
see <http://www.nomnoml.com>. Supports styling, R Markdown and exporting diagrams
in the PNG format.
Author: Javier Luraschi [aut, cre],
Andrie de Vries [aut],
Daniel Kallin [aut] (nomnoml.js library, http://nomnoml.com),
RStudio [cph]
Maintainer: Javier Luraschi <javier@rstudio.com>
Diff between nomnoml versions 0.1.0 dated 2019-06-13 and 0.2.0 dated 2020-05-26
DESCRIPTION | 18 MD5 | 46 NEWS.md |only R/nomnoml.R | 24 R/zzz.R | 2 README.md | 54 inst/examples |only inst/htmlwidgets/lib/dagre/dagre.min.js | 3 inst/htmlwidgets/lib/lodash/lodash.js |15982 ++++++++++++++++++++------------ inst/htmlwidgets/lib/nomnoml/nomnoml.js | 2461 ++-- inst/htmlwidgets/nomnoml.js | 38 inst/htmlwidgets/nomnoml.yaml | 27 man/figures |only man/nomnoml.Rd | 5 tests |only tools/readme/nomnoml-decorator-2.png |binary tools/readme/nomnoml-decorator-3.png |binary tools/readme/nomnoml-decorator-4.png |only tools/readme/nomnoml-multiline-2.png |binary tools/readme/nomnoml-multiline-3.png |only tools/readme/nomnoml-svg-1.png |only tools/readme/nomnoml-svg-3.png |only tools/readme/nomnoml-vertical-2.png |only tools/readme/unnamed-chunk-2-3.png |only 24 files changed, 11947 insertions(+), 6713 deletions(-)
Title: HTTP and WebSocket Server Library
Description: Provides low-level socket and protocol support for handling
HTTP and WebSocket requests directly from within R. It is primarily
intended as a building block for other packages, rather than making it
particularly easy to create complete web applications using httpuv alone.
httpuv is built on top of the libuv and http-parser C libraries, both of
which were developed by Joyent, Inc. (See LICENSE file for libuv and
http-parser license information.)
Author: Joe Cheng, Hector Corrada Bravo [ctb], Jeroen Ooms [ctb],
Winston Chang [ctb]
Maintainer: Joe Cheng <joe@rstudio.com>
Diff between httpuv versions 1.5.2 dated 2019-09-11 and 1.5.3.1 dated 2020-05-26
httpuv-1.5.2/httpuv/src/libuv/android-configure-arm |only httpuv-1.5.2/httpuv/src/libuv/android-configure-arm64 |only httpuv-1.5.2/httpuv/src/libuv/android-configure-x86 |only httpuv-1.5.2/httpuv/src/libuv/android-configure-x86_64 |only httpuv-1.5.2/httpuv/src/libuv/appveyor.yml |only httpuv-1.5.2/httpuv/src/libuv/common.gypi |only httpuv-1.5.2/httpuv/src/libuv/gyp_uv.py |only httpuv-1.5.2/httpuv/src/libuv/samples |only httpuv-1.5.2/httpuv/src/libuv/test/test.gyp |only httpuv-1.5.2/httpuv/src/libuv/uv.gyp |only httpuv-1.5.2/httpuv/src/libuv/vcbuild.bat |only httpuv-1.5.3.1/httpuv/DESCRIPTION | 8 httpuv-1.5.3.1/httpuv/MD5 | 362 +-- httpuv-1.5.3.1/httpuv/NEWS.md | 115 - httpuv-1.5.3.1/httpuv/R/httpuv.R | 28 httpuv-1.5.3.1/httpuv/README.md | 147 + httpuv-1.5.3.1/httpuv/man/PipeServer.Rd | 53 httpuv-1.5.3.1/httpuv/man/Server.Rd | 77 httpuv-1.5.3.1/httpuv/man/WebServer.Rd | 53 httpuv-1.5.3.1/httpuv/man/WebSocket.Rd | 102 + httpuv-1.5.3.1/httpuv/man/staticPath.Rd | 10 httpuv-1.5.3.1/httpuv/man/staticPathOptions.Rd | 11 httpuv-1.5.3.1/httpuv/src/Makevars | 5 httpuv-1.5.3.1/httpuv/src/libuv/AUTHORS | 54 httpuv-1.5.3.1/httpuv/src/libuv/CMakeLists.txt | 544 +++-- httpuv-1.5.3.1/httpuv/src/libuv/CONTRIBUTING.md | 5 httpuv-1.5.3.1/httpuv/src/libuv/ChangeLog | 659 +++++++ httpuv-1.5.3.1/httpuv/src/libuv/MAINTAINERS.md | 4 httpuv-1.5.3.1/httpuv/src/libuv/Makefile.am | 97 - httpuv-1.5.3.1/httpuv/src/libuv/Makefile.in | 808 ++++++-- httpuv-1.5.3.1/httpuv/src/libuv/README.md | 214 -- httpuv-1.5.3.1/httpuv/src/libuv/SUPPORTED_PLATFORMS.md | 12 httpuv-1.5.3.1/httpuv/src/libuv/configure | 99 - httpuv-1.5.3.1/httpuv/src/libuv/configure.ac | 25 httpuv-1.5.3.1/httpuv/src/libuv/docs/src/async.rst | 4 httpuv-1.5.3.1/httpuv/src/libuv/docs/src/design.rst | 6 httpuv-1.5.3.1/httpuv/src/libuv/docs/src/fs.rst | 165 + httpuv-1.5.3.1/httpuv/src/libuv/docs/src/fs_event.rst | 2 httpuv-1.5.3.1/httpuv/src/libuv/docs/src/guide/about.rst | 6 httpuv-1.5.3.1/httpuv/src/libuv/docs/src/guide/basics.rst | 37 httpuv-1.5.3.1/httpuv/src/libuv/docs/src/guide/filesystem.rst | 51 httpuv-1.5.3.1/httpuv/src/libuv/docs/src/guide/introduction.rst | 6 httpuv-1.5.3.1/httpuv/src/libuv/docs/src/guide/networking.rst | 19 httpuv-1.5.3.1/httpuv/src/libuv/docs/src/guide/processes.rst | 59 httpuv-1.5.3.1/httpuv/src/libuv/docs/src/guide/threads.rst | 24 httpuv-1.5.3.1/httpuv/src/libuv/docs/src/guide/utilities.rst | 14 httpuv-1.5.3.1/httpuv/src/libuv/docs/src/handle.rst | 19 httpuv-1.5.3.1/httpuv/src/libuv/docs/src/index.rst | 8 httpuv-1.5.3.1/httpuv/src/libuv/docs/src/misc.rst | 145 + httpuv-1.5.3.1/httpuv/src/libuv/docs/src/pipe.rst | 11 httpuv-1.5.3.1/httpuv/src/libuv/docs/src/signal.rst | 11 httpuv-1.5.3.1/httpuv/src/libuv/docs/src/sphinx-plugins/manpage.py | 3 httpuv-1.5.3.1/httpuv/src/libuv/docs/src/static/diagrams.key/Data/st0-311.jpg |binary httpuv-1.5.3.1/httpuv/src/libuv/docs/src/static/diagrams.key/Data/st1-475.jpg |binary httpuv-1.5.3.1/httpuv/src/libuv/docs/src/stream.rst | 4 httpuv-1.5.3.1/httpuv/src/libuv/docs/src/tcp.rst | 15 httpuv-1.5.3.1/httpuv/src/libuv/docs/src/threadpool.rst | 4 httpuv-1.5.3.1/httpuv/src/libuv/docs/src/tty.rst | 39 httpuv-1.5.3.1/httpuv/src/libuv/docs/src/udp.rst | 70 httpuv-1.5.3.1/httpuv/src/libuv/docs/src/version.rst | 2 httpuv-1.5.3.1/httpuv/src/libuv/include/uv.h | 157 + httpuv-1.5.3.1/httpuv/src/libuv/include/uv/errno.h | 5 httpuv-1.5.3.1/httpuv/src/libuv/include/uv/unix.h | 30 httpuv-1.5.3.1/httpuv/src/libuv/include/uv/version.h | 4 httpuv-1.5.3.1/httpuv/src/libuv/include/uv/win.h | 8 httpuv-1.5.3.1/httpuv/src/libuv/src/fs-poll.c | 2 httpuv-1.5.3.1/httpuv/src/libuv/src/random.c |only httpuv-1.5.3.1/httpuv/src/libuv/src/threadpool.c | 6 httpuv-1.5.3.1/httpuv/src/libuv/src/timer.c | 11 httpuv-1.5.3.1/httpuv/src/libuv/src/unix/aix-common.c | 142 - httpuv-1.5.3.1/httpuv/src/libuv/src/unix/aix.c | 185 + httpuv-1.5.3.1/httpuv/src/libuv/src/unix/android-ifaddrs.c | 3 httpuv-1.5.3.1/httpuv/src/libuv/src/unix/async.c | 121 - httpuv-1.5.3.1/httpuv/src/libuv/src/unix/atomic-ops.h | 43 httpuv-1.5.3.1/httpuv/src/libuv/src/unix/bsd-ifaddrs.c | 20 httpuv-1.5.3.1/httpuv/src/libuv/src/unix/core.c | 340 ++- httpuv-1.5.3.1/httpuv/src/libuv/src/unix/cygwin.c | 5 httpuv-1.5.3.1/httpuv/src/libuv/src/unix/darwin-proctitle.c | 153 - httpuv-1.5.3.1/httpuv/src/libuv/src/unix/darwin.c | 22 httpuv-1.5.3.1/httpuv/src/libuv/src/unix/freebsd.c | 39 httpuv-1.5.3.1/httpuv/src/libuv/src/unix/fs.c | 613 +++++- httpuv-1.5.3.1/httpuv/src/libuv/src/unix/fsevents.c | 14 httpuv-1.5.3.1/httpuv/src/libuv/src/unix/haiku.c |only httpuv-1.5.3.1/httpuv/src/libuv/src/unix/ibmi.c | 352 +++ httpuv-1.5.3.1/httpuv/src/libuv/src/unix/internal.h | 47 httpuv-1.5.3.1/httpuv/src/libuv/src/unix/kqueue.c | 56 httpuv-1.5.3.1/httpuv/src/libuv/src/unix/linux-core.c | 240 ++ httpuv-1.5.3.1/httpuv/src/libuv/src/unix/linux-inotify.c | 67 httpuv-1.5.3.1/httpuv/src/libuv/src/unix/linux-syscalls.c | 219 -- httpuv-1.5.3.1/httpuv/src/libuv/src/unix/linux-syscalls.h | 80 httpuv-1.5.3.1/httpuv/src/libuv/src/unix/netbsd.c | 35 httpuv-1.5.3.1/httpuv/src/libuv/src/unix/openbsd.c | 70 httpuv-1.5.3.1/httpuv/src/libuv/src/unix/os390-syscalls.c | 117 + httpuv-1.5.3.1/httpuv/src/libuv/src/unix/os390-syscalls.h | 6 httpuv-1.5.3.1/httpuv/src/libuv/src/unix/os390.c | 14 httpuv-1.5.3.1/httpuv/src/libuv/src/unix/pipe.c | 8 httpuv-1.5.3.1/httpuv/src/libuv/src/unix/posix-poll.c | 2 httpuv-1.5.3.1/httpuv/src/libuv/src/unix/process.c | 89 httpuv-1.5.3.1/httpuv/src/libuv/src/unix/proctitle.c | 69 httpuv-1.5.3.1/httpuv/src/libuv/src/unix/random-devurandom.c |only httpuv-1.5.3.1/httpuv/src/libuv/src/unix/random-getentropy.c |only httpuv-1.5.3.1/httpuv/src/libuv/src/unix/random-getrandom.c |only httpuv-1.5.3.1/httpuv/src/libuv/src/unix/random-sysctl-linux.c |only httpuv-1.5.3.1/httpuv/src/libuv/src/unix/signal.c | 21 httpuv-1.5.3.1/httpuv/src/libuv/src/unix/stream.c | 15 httpuv-1.5.3.1/httpuv/src/libuv/src/unix/sunos.c | 15 httpuv-1.5.3.1/httpuv/src/libuv/src/unix/tcp.c | 29 httpuv-1.5.3.1/httpuv/src/libuv/src/unix/thread.c | 37 httpuv-1.5.3.1/httpuv/src/libuv/src/unix/tty.c | 37 httpuv-1.5.3.1/httpuv/src/libuv/src/unix/udp.c | 407 ++++ httpuv-1.5.3.1/httpuv/src/libuv/src/uv-common.c | 89 httpuv-1.5.3.1/httpuv/src/libuv/src/uv-common.h | 4 httpuv-1.5.3.1/httpuv/src/libuv/src/win/core.c | 9 httpuv-1.5.3.1/httpuv/src/libuv/src/win/error.c | 1 httpuv-1.5.3.1/httpuv/src/libuv/src/win/fs-fd-hash-inl.h |only httpuv-1.5.3.1/httpuv/src/libuv/src/win/fs.c | 940 +++++++++- httpuv-1.5.3.1/httpuv/src/libuv/src/win/internal.h | 2 httpuv-1.5.3.1/httpuv/src/libuv/src/win/pipe.c | 151 - httpuv-1.5.3.1/httpuv/src/libuv/src/win/process.c | 13 httpuv-1.5.3.1/httpuv/src/libuv/src/win/stream.c | 7 httpuv-1.5.3.1/httpuv/src/libuv/src/win/tcp.c | 38 httpuv-1.5.3.1/httpuv/src/libuv/src/win/tty.c | 502 +++-- httpuv-1.5.3.1/httpuv/src/libuv/src/win/udp.c | 150 + httpuv-1.5.3.1/httpuv/src/libuv/src/win/util.c | 145 + httpuv-1.5.3.1/httpuv/src/libuv/src/win/winapi.c | 9 httpuv-1.5.3.1/httpuv/src/libuv/src/win/winapi.h | 14 httpuv-1.5.3.1/httpuv/src/libuv/src/win/winsock.c | 47 httpuv-1.5.3.1/httpuv/src/libuv/src/win/winsock.h | 8 httpuv-1.5.3.1/httpuv/src/libuv/test/benchmark-list.h | 1 httpuv-1.5.3.1/httpuv/src/libuv/test/benchmark-multi-accept.c | 8 httpuv-1.5.3.1/httpuv/src/libuv/test/benchmark-ping-udp.c |only httpuv-1.5.3.1/httpuv/src/libuv/test/echo-server.c | 55 httpuv-1.5.3.1/httpuv/src/libuv/test/fixtures/lorem_ipsum.txt |only httpuv-1.5.3.1/httpuv/src/libuv/test/run-benchmarks.c | 3 httpuv-1.5.3.1/httpuv/src/libuv/test/run-tests.c | 18 httpuv-1.5.3.1/httpuv/src/libuv/test/runner-unix.c | 33 httpuv-1.5.3.1/httpuv/src/libuv/test/runner-win.c | 33 httpuv-1.5.3.1/httpuv/src/libuv/test/runner.c | 30 httpuv-1.5.3.1/httpuv/src/libuv/test/runner.h | 6 httpuv-1.5.3.1/httpuv/src/libuv/test/task.h | 123 + httpuv-1.5.3.1/httpuv/src/libuv/test/test-cwd-and-chdir.c | 10 httpuv-1.5.3.1/httpuv/src/libuv/test/test-dlerror.c | 4 httpuv-1.5.3.1/httpuv/src/libuv/test/test-env-vars.c | 58 httpuv-1.5.3.1/httpuv/src/libuv/test/test-fs-copyfile.c | 26 httpuv-1.5.3.1/httpuv/src/libuv/test/test-fs-event.c | 82 httpuv-1.5.3.1/httpuv/src/libuv/test/test-fs-fd-hash.c |only httpuv-1.5.3.1/httpuv/src/libuv/test/test-fs-open-flags.c |only httpuv-1.5.3.1/httpuv/src/libuv/test/test-fs-poll.c | 39 httpuv-1.5.3.1/httpuv/src/libuv/test/test-fs-readdir.c |only httpuv-1.5.3.1/httpuv/src/libuv/test/test-fs.c | 697 ++++++- httpuv-1.5.3.1/httpuv/src/libuv/test/test-get-currentexe.c | 21 httpuv-1.5.3.1/httpuv/src/libuv/test/test-get-memory.c | 12 httpuv-1.5.3.1/httpuv/src/libuv/test/test-get-passwd.c | 2 httpuv-1.5.3.1/httpuv/src/libuv/test/test-gethostname.c | 2 httpuv-1.5.3.1/httpuv/src/libuv/test/test-gettimeofday.c |only httpuv-1.5.3.1/httpuv/src/libuv/test/test-homedir.c | 2 httpuv-1.5.3.1/httpuv/src/libuv/test/test-ip4-addr.c | 4 httpuv-1.5.3.1/httpuv/src/libuv/test/test-ip6-addr.c | 9 httpuv-1.5.3.1/httpuv/src/libuv/test/test-ipc.c | 325 +-- httpuv-1.5.3.1/httpuv/src/libuv/test/test-list.h | 111 + httpuv-1.5.3.1/httpuv/src/libuv/test/test-pipe-getsockname.c | 2 httpuv-1.5.3.1/httpuv/src/libuv/test/test-platform-output.c | 4 httpuv-1.5.3.1/httpuv/src/libuv/test/test-poll-close-doesnt-corrupt-stack.c | 6 httpuv-1.5.3.1/httpuv/src/libuv/test/test-poll-closesocket.c | 5 httpuv-1.5.3.1/httpuv/src/libuv/test/test-poll.c | 37 httpuv-1.5.3.1/httpuv/src/libuv/test/test-process-title-threadsafe.c | 25 httpuv-1.5.3.1/httpuv/src/libuv/test/test-process-title.c | 62 httpuv-1.5.3.1/httpuv/src/libuv/test/test-queue-foreach-delete.c | 26 httpuv-1.5.3.1/httpuv/src/libuv/test/test-random.c |only httpuv-1.5.3.1/httpuv/src/libuv/test/test-signal-pending-on-close.c |only httpuv-1.5.3.1/httpuv/src/libuv/test/test-spawn.c | 57 httpuv-1.5.3.1/httpuv/src/libuv/test/test-stdio-over-pipes.c | 135 - 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Title: Calculate Crosstab and Topline Tables of Weighted Survey Data
Description: Calculate common types of tables for weighted survey data.
Options include topline and (2-way and 3-way) crosstab tables of
categorical or ordinal data as well as summary tables of weighted
numeric variables. Optionally, include the margin of error at
selected confidence intervals including the design effect. The
design effect is calculated as described by
Kish (1965) <doi:10.1002/bimj.19680100122> beginning
on page 257. Output takes the form of tibbles (simple data frames).
This package conveniently handles labelled data, such as that
commonly used by 'Stata' and 'SPSS.' Complex survey design is
not supported at this time.
Author: John D. Johnson [aut, cre]
Maintainer: John D. Johnson <john.d.johnson@marquette.edu>
Diff between pollster versions 0.1.1 dated 2020-04-08 and 0.1.2 dated 2020-05-26
DESCRIPTION | 10 +++++----- MD5 | 14 +++++++------- NEWS.md | 4 ++++ R/Crosstab.R | 15 ++++++++++----- R/Crosstab3way.R | 4 ++-- R/moeCrosstab.R | 3 ++- build/vignette.rds |binary man/illinois.Rd | 6 ++++-- 8 files changed, 34 insertions(+), 22 deletions(-)
Title: Bayesian Estimation for Finite Mixture of Distributions
Description: Provides statistical tools for Bayesian estimation of finite mixture of distributions, mainly mixture of Gamma, Normal and t-distributions. The package is implemented the Bayesian literature for the finite mixture of distributions, including Mohammadi and et al. (2013) <doi:10.1007/s00180-012-0323-3> and Mohammadi and Salehi-Rad (2012) <doi:10.1080/03610918.2011.588358>.
Author: Reza Mohammadi [aut, cre] (<https://orcid.org/0000-0001-9538-0648>)
Maintainer: Reza Mohammadi <a.mohammadi@uva.nl>
Diff between bmixture versions 1.5 dated 2020-05-13 and 1.6 dated 2020-05-26
bmixture-1.5/bmixture/NEWS |only bmixture-1.6/bmixture/DESCRIPTION | 12 +++++------- bmixture-1.6/bmixture/MD5 | 7 ++++--- bmixture-1.6/bmixture/NEWS.md |only bmixture-1.6/bmixture/README.md |only bmixture-1.6/bmixture/man/bmixture-package.Rd | 2 +- 6 files changed, 10 insertions(+), 11 deletions(-)
Title: Statistical Methods for Regional Counts
Description: Implements statistical methods for analyzing the counts of areal data,
with a focus on the detection of spatial clusters and clustering. The package has a heavy emphasis on spatial scan methods, which were first introduced by Kulldorff and Nagarwalla (1995) <doi:10.1002/sim.4780140809> and Kulldorff (1997) <doi:10.1080/03610929708831995>.
Author: Joshua French
Maintainer: Joshua French <joshua.french@ucdenver.edu>
Diff between smerc versions 1.1 dated 2019-09-19 and 1.2 dated 2020-05-26
smerc-1.1/smerc/R/arg_check_dmst_zones.R |only smerc-1.1/smerc/R/arg_check_scan_test.R |only smerc-1.1/smerc/R/arg_check_scan_zones.R |only smerc-1.1/smerc/R/arg_check_sim.R |only smerc-1.1/smerc/R/csg.R |only smerc-1.1/smerc/R/dc.test.R |only smerc-1.1/smerc/R/dmst.test.R |only smerc-1.1/smerc/R/dweights.R |only smerc-1.1/smerc/R/edmst.test.R |only smerc-1.1/smerc/R/elliptic.test.R |only smerc-1.1/smerc/R/fast.test.R |only smerc-1.1/smerc/R/flex.test.R |only smerc-1.1/smerc/R/mlf.test.R |only smerc-1.1/smerc/R/mlink.test.R |only smerc-1.1/smerc/R/plot.scan.R |only smerc-1.1/smerc/R/plot.tango.R |only smerc-1.1/smerc/R/prep.results.R |only smerc-1.1/smerc/R/rflex.test.R |only smerc-1.1/smerc/R/scan-class.R |only smerc-1.1/smerc/R/scan.stat2.R |only smerc-1.1/smerc/R/uls.test.R |only smerc-1.1/smerc/man/arg_check_bn_test.Rd |only smerc-1.1/smerc/man/arg_check_cepp_test.Rd |only smerc-1.1/smerc/man/arg_check_dmst_zones.Rd |only smerc-1.1/smerc/man/arg_check_scan_test.Rd |only smerc-1.1/smerc/man/arg_check_scan_zones.Rd |only smerc-1.1/smerc/man/arg_check_sim.Rd |only smerc-1.1/smerc/man/arg_check_tango_test.Rd |only smerc-1.1/smerc/man/dweights.Rd |only smerc-1.1/smerc/man/plot.scan.Rd |only smerc-1.1/smerc/man/prep.scan.Rd |only smerc-1.1/smerc/man/prep.scan2.Rd |only smerc-1.2/smerc/DESCRIPTION | 15 smerc-1.2/smerc/MD5 | 291 ++++++----- smerc-1.2/smerc/NAMESPACE | 170 +++--- smerc-1.2/smerc/NEWS | 4 smerc-1.2/smerc/R/arg_check_functions.R |only smerc-1.2/smerc/R/bn.test.R | 291 +++++------ smerc-1.2/smerc/R/casewin.R | 95 +-- smerc-1.2/smerc/R/cepp.sim.R | 4 smerc-1.2/smerc/R/cepp.test.R | 138 +---- smerc-1.2/smerc/R/color.clusters.R | 80 +-- smerc-1.2/smerc/R/csg2.R |only smerc-1.2/smerc/R/dc.sim.R | 90 +-- smerc-1.2/smerc/R/dc.test2.R |only smerc-1.2/smerc/R/dc.zones.R | 129 ++--- smerc-1.2/smerc/R/distinct.R | 74 +- smerc-1.2/smerc/R/dmst.sim.R | 90 +-- smerc-1.2/smerc/R/dmst.test2.R |only smerc-1.2/smerc/R/dmst.zones.R | 184 ++++--- smerc-1.2/smerc/R/edmst.test2.R |only smerc-1.2/smerc/R/edmst.zones.R | 118 ++-- smerc-1.2/smerc/R/elliptic.nn.R | 15 smerc-1.2/smerc/R/elliptic.sim.R | 131 ++--- smerc-1.2/smerc/R/elliptic.test2.R |only smerc-1.2/smerc/R/fast.sim.R | 93 +-- smerc-1.2/smerc/R/fast.test2.R |only smerc-1.2/smerc/R/flex.sim.R | 183 +++---- smerc-1.2/smerc/R/flex.test2.R |only smerc-1.2/smerc/R/flex.zones.R | 19 smerc-1.2/smerc/R/lget.R |only smerc-1.2/smerc/R/mc.pvalue.R | 41 - smerc-1.2/smerc/R/mlf.test2.R |only smerc-1.2/smerc/R/mlink.test2.R |only smerc-1.2/smerc/R/mst.all.R | 254 +++++----- smerc-1.2/smerc/R/mst.seq.R | 402 ++++++++-------- smerc-1.2/smerc/R/nn.cumsum.R | 81 +-- smerc-1.2/smerc/R/nnpop.R | 2 smerc-1.2/smerc/R/noz.R |only smerc-1.2/smerc/R/nydf.R | 58 +- smerc-1.2/smerc/R/nypoly.R | 26 - smerc-1.2/smerc/R/nyw.R | 29 - smerc-1.2/smerc/R/rflex.test2.R |only smerc-1.2/smerc/R/rflex.zones.R | 26 - smerc-1.2/smerc/R/scan.sim.R | 174 ++++-- smerc-1.2/smerc/R/scan.stat.R |only smerc-1.2/smerc/R/scan.test.R | 402 +++++++++------- smerc-1.2/smerc/R/scan.zones.R | 95 ++- smerc-1.2/smerc/R/sig_noc.R |only smerc-1.2/smerc/R/smerc_cluster-plot.R |only smerc-1.2/smerc/R/smerc_cluster-print.R |only smerc-1.2/smerc/R/smerc_cluster-summary.R |only smerc-1.2/smerc/R/smerc_cluster.R |only smerc-1.2/smerc/R/tango-plot.R |only smerc-1.2/smerc/R/tango-print.R |only smerc-1.2/smerc/R/tango.stat.R | 22 smerc-1.2/smerc/R/tango.test.R | 246 ++++----- smerc-1.2/smerc/R/tango.weights.R |only smerc-1.2/smerc/R/uls.sim.R | 101 ++-- smerc-1.2/smerc/R/uls.test2.R |only smerc-1.2/smerc/R/uls.zones.R | 216 ++++---- smerc-1.2/smerc/R/zones.sum.R | 59 +- smerc-1.2/smerc/inst |only smerc-1.2/smerc/man/arg_check_rflex_zones.Rd | 14 smerc-1.2/smerc/man/bn.test.Rd | 34 - smerc-1.2/smerc/man/casewin.Rd | 102 ++-- smerc-1.2/smerc/man/cepp.sim.Rd | 4 smerc-1.2/smerc/man/cepp.test.Rd | 32 - smerc-1.2/smerc/man/cepp.weights.Rd | 78 +-- smerc-1.2/smerc/man/color.clusters.Rd | 80 +-- smerc-1.2/smerc/man/combine.zones.Rd | 52 +- smerc-1.2/smerc/man/csg.Rd | 119 ++-- smerc-1.2/smerc/man/dc.sim.Rd | 3 smerc-1.2/smerc/man/dc.test.Rd | 41 + smerc-1.2/smerc/man/dc.zones.Rd | 45 + smerc-1.2/smerc/man/dist.ellipse.Rd | 66 +- smerc-1.2/smerc/man/distinct.Rd | 18 smerc-1.2/smerc/man/dmst.sim.Rd | 3 smerc-1.2/smerc/man/dmst.test.Rd | 73 +- smerc-1.2/smerc/man/dmst.zones.Rd | 41 + smerc-1.2/smerc/man/edmst.sim.Rd | 3 smerc-1.2/smerc/man/edmst.test.Rd | 35 - smerc-1.2/smerc/man/edmst.zones.Rd | 59 +- smerc-1.2/smerc/man/elliptic.nn.Rd | 24 smerc-1.2/smerc/man/elliptic.sim.Rd | 19 smerc-1.2/smerc/man/elliptic.test.Rd | 35 + smerc-1.2/smerc/man/elliptic.zones.Rd | 9 smerc-1.2/smerc/man/fast.sim.Rd | 6 smerc-1.2/smerc/man/fast.test.Rd | 33 - smerc-1.2/smerc/man/fast.zones.Rd | 118 ++-- smerc-1.2/smerc/man/flex.sim.Rd | 22 smerc-1.2/smerc/man/flex.test.Rd | 63 +- smerc-1.2/smerc/man/flex.zones.Rd | 21 smerc-1.2/smerc/man/knn.Rd | 6 smerc-1.2/smerc/man/lget.Rd |only smerc-1.2/smerc/man/mc.pvalue.Rd | 13 smerc-1.2/smerc/man/mlf.test.Rd | 75 ++ smerc-1.2/smerc/man/mlf.zones.Rd | 34 - smerc-1.2/smerc/man/mlink.sim.Rd | 3 smerc-1.2/smerc/man/mlink.test.Rd | 83 +-- smerc-1.2/smerc/man/mlink.zones.Rd | 41 + smerc-1.2/smerc/man/mst.all.Rd | 20 smerc-1.2/smerc/man/mst.seq.Rd | 24 smerc-1.2/smerc/man/nn.cumsum.Rd | 19 smerc-1.2/smerc/man/nn2zones.Rd | 52 +- smerc-1.2/smerc/man/nndist.Rd | 2 smerc-1.2/smerc/man/nndup.Rd | 54 +- smerc-1.2/smerc/man/noz.Rd |only smerc-1.2/smerc/man/nydf.Rd | 40 + smerc-1.2/smerc/man/nypoly.Rd | 14 smerc-1.2/smerc/man/nyw.Rd | 17 smerc-1.2/smerc/man/plot.smerc_cluster.Rd |only smerc-1.2/smerc/man/plot.tango.Rd | 5 smerc-1.2/smerc/man/print.smerc_cluster.Rd |only smerc-1.2/smerc/man/print.tango.Rd |only smerc-1.2/smerc/man/rflex.midp.Rd | 6 smerc-1.2/smerc/man/rflex.sim.Rd | 21 smerc-1.2/smerc/man/rflex.test.Rd | 79 ++- smerc-1.2/smerc/man/rflex.zones.Rd | 25 smerc-1.2/smerc/man/scan.nn.Rd | 102 ++-- smerc-1.2/smerc/man/scan.sim.Rd | 34 + smerc-1.2/smerc/man/scan.stat.Rd | 18 smerc-1.2/smerc/man/scan.test.Rd | 46 + smerc-1.2/smerc/man/scan.zones.Rd | 2 smerc-1.2/smerc/man/sig_noc.Rd |only smerc-1.2/smerc/man/smerc_cluster.Rd |only smerc-1.2/smerc/man/summary.smerc_cluster.Rd |only smerc-1.2/smerc/man/tango.stat.Rd | 21 smerc-1.2/smerc/man/tango.test.Rd | 59 +- smerc-1.2/smerc/man/tango.weights.Rd |only smerc-1.2/smerc/man/uls.sim.Rd | 19 smerc-1.2/smerc/man/uls.test.Rd | 35 - smerc-1.2/smerc/man/uls.zones.Rd | 108 ++-- smerc-1.2/smerc/man/w2segments.Rd | 2 smerc-1.2/smerc/man/zones.sum.Rd | 6 smerc-1.2/smerc/tests/testthat/test-cepp.test-ref.R |only smerc-1.2/smerc/tests/testthat/test-cepp.test.R | 2 smerc-1.2/smerc/tests/testthat/test-dc.test-ref.R |only smerc-1.2/smerc/tests/testthat/test-dmst.test-ref.R |only smerc-1.2/smerc/tests/testthat/test-edmst.test-ref.R |only smerc-1.2/smerc/tests/testthat/test-elliptic.test-ref.R |only smerc-1.2/smerc/tests/testthat/test-fast.test-ref.R |only smerc-1.2/smerc/tests/testthat/test-flex.test-ref.R |only smerc-1.2/smerc/tests/testthat/test-lints.R | 19 smerc-1.2/smerc/tests/testthat/test-mlf.test-ref.R |only smerc-1.2/smerc/tests/testthat/test-mlink.test-ref.R |only smerc-1.2/smerc/tests/testthat/test-rflex.test-ref.R |only smerc-1.2/smerc/tests/testthat/test-scan_sim.R |only smerc-1.2/smerc/tests/testthat/test-uls.test-ref.R |only 179 files changed, 3733 insertions(+), 3073 deletions(-)
Title: Summary Tables for Statistical Models: Beautiful, Customizable,
and Publication-Ready
Description: Create beautiful and customizable summary tables for statistical
models. 'modelsummary' leverages the power of the 'gt', 'kableExtra' and
'broom' packages. It supports dozens of model types, and can produce tables
in HTML, LaTeX, RTF, Text/Markdown, JPG, PNG, and LaTeX formats. The tables
can also be integrated in 'Rmarkdown', 'knitr', or 'Sweave' dynamic
documents.
Author: Vincent Arel-Bundock [aut, cre]
(<https://orcid.org/0000-0003-2042-7063>)
Maintainer: Vincent Arel-Bundock <vincent.arel-bundock@umontreal.ca>
Diff between modelsummary versions 0.2.1 dated 2020-04-30 and 0.3.0 dated 2020-05-26
DESCRIPTION | 29 + MD5 | 50 +-- NAMESPACE | 2 NEWS.md | 17 - R/build_gt.R |only R/build_kableExtra.R |only R/clean_latex.R | 148 +-------- R/extract.R | 13 R/extract_estimates.R | 22 - R/extract_gof.R | 7 R/modelsummary.R | 154 +++++---- R/sanity_checks.R | 32 +- R/stars.R | 5 R/tidiers.R | 33 ++ README.md | 604 ++++++-------------------------------- man/build_gt.Rd |only man/build_kableExtra.Rd |only man/clean_latex.Rd | 32 -- man/extract.Rd | 24 + man/extract_estimates.Rd | 24 + man/extract_statistic_override.Rd | 8 man/glance.MIresult.Rd |only man/glance.mira.Rd | 6 man/knit_latex.Rd | 28 - man/modelsummary.Rd | 76 ++-- man/msummary.Rd | 76 ++-- man/sanity_checks.Rd | 34 +- man/statistic_override_vector.Rd | 8 man/tidy.MIresult.Rd |only 29 files changed, 533 insertions(+), 899 deletions(-)
Title: Formula-Driven Table Generation
Description: Computes and displays complex tables of summary statistics.
Output may be in LaTeX, HTML, plain text, or an R
matrix for further processing.
Author: Duncan Murdoch
Maintainer: Duncan Murdoch <murdoch.duncan@gmail.com>
Diff between tables versions 0.8.8 dated 2019-05-13 and 0.9.3 dated 2020-05-26
DESCRIPTION | 15 - MD5 | 64 ++++--- NAMESPACE | 15 + R/All.R | 2 R/RowFactor.R | 8 R/html.tabular.R | 238 ++++++++++++++-------------- R/knit_print.R | 7 R/latex.tabular.R | 246 +++++++++++++++-------------- R/table.R |only R/toKable.R | 7 build/vignette.rds |binary inst/NEWS | 10 + inst/doc/HTML.R | 28 +-- inst/doc/HTML.Rmd | 8 inst/doc/HTML.html | 379 +++++++++++++++++++-------------------------- inst/doc/knitrTables.R |only inst/doc/knitrTables.Rmd |only inst/doc/knitrTables.pdf |only inst/doc/tables.R | 231 ++++++++++++++------------- inst/doc/tables.Rnw | 174 ++++++++++++-------- inst/doc/tables.pdf |binary inst/todo.txt | 7 man/All.Rd | 2 man/Hline.Rd | 2 man/Paste.Rd | 2 man/PlusMinus.Rd | 2 man/RowFactor.Rd | 11 - man/as.tabular.Rd | 1 man/html.tabular.Rd | 31 ++- man/latex.tabular.Rd | 25 ++ man/latexTable.Rd |only man/table_options.Rd | 8 vignettes/HTML.Rmd | 8 vignettes/knitrTables.Rmd |only vignettes/tables.Rnw | 174 ++++++++++++-------- vignettes/tables.Rout.save | 212 +++++++++++++------------ 36 files changed, 1009 insertions(+), 908 deletions(-)
Title: Interface to 'Matba Rofex' Trading API
Description: Execute API calls to the 'Matba Rofex' <https://apihub.primary.com.ar> trading platform. Functionality includes accessing account data and current holdings, retrieving investment quotes, placing and canceling orders, and getting reference data for instruments.
Author: Augusto Hassel [aut, cre],
Juan Francisco Gomez [ctb],
Matba Rofex [cph]
Maintainer: Augusto Hassel <ahassel@primary.com.ar>
Diff between rRofex versions 1.6.9 dated 2020-05-20 and 1.6.11 dated 2020-05-26
rRofex-1.6.11/rRofex/DESCRIPTION | 6 rRofex-1.6.11/rRofex/MD5 | 22 +- rRofex-1.6.11/rRofex/NAMESPACE | 1 rRofex-1.6.11/rRofex/NEWS.md | 14 + rRofex-1.6.11/rRofex/R/functions.R | 53 ++++-- rRofex-1.6.11/rRofex/R/rRofex.R | 2 rRofex-1.6.11/rRofex/README.md | 167 +++++++++++++++++---- rRofex-1.6.11/rRofex/man/figures/logo.png |only rRofex-1.6.11/rRofex/man/rRofex-package.Rd | 2 rRofex-1.6.11/rRofex/man/trading_account.Rd | 52 +++--- rRofex-1.6.11/rRofex/man/trading_account_report.Rd | 64 ++++---- rRofex-1.6.11/rRofex/man/trading_md.Rd | 18 +- rRofex-1.6.9/rRofex/man/figures/r-rofex.png |only 13 files changed, 274 insertions(+), 127 deletions(-)
Title: Functions to Study Etiologic Heterogeneity
Description: A collection of functions related to the study of etiologic heterogeneity both across disease subtypes and across individual disease markers. The included functions allow one to quantify the extent of etiologic heterogeneity in the context of a case-control study, and provide p-values to test for etiologic heterogeneity across individual risk factors. Begg CB, Zabor EC, Bernstein JL, Bernstein L, Press MF, Seshan VE (2013) <doi: 10.1002/sim.5902>.
Author: Emily C. Zabor [aut, cre]
Maintainer: Emily C. Zabor <zabore2@ccf.org>
Diff between riskclustr versions 0.2 dated 2019-09-07 and 0.3 dated 2020-05-26
DESCRIPTION | 12 ++++++------ MD5 | 40 ++++++++++++++++++++-------------------- NEWS.md | 4 ++++ R/eh_test_marker.R | 6 +++--- R/eh_test_subtype.R | 6 +++--- README.md | 1 + build/vignette.rds |binary inst/doc/calculate_d.R | 8 ++++---- inst/doc/calculate_d.html | 13 +++++-------- inst/doc/contribute.R | 2 +- inst/doc/contribute.html | 13 +++++-------- inst/doc/eh_test.R | 42 +++++++++++++++++++++--------------------- inst/doc/eh_test.html | 13 +++++-------- inst/doc/factor_pvalue.R | 14 +++++++------- inst/doc/factor_pvalue.html | 13 +++++-------- inst/doc/optimal_d.R | 8 ++++---- inst/doc/optimal_d.html | 19 ++++++++++--------- man/eh_test_marker.Rd | 2 +- man/eh_test_subtype.Rd | 2 +- man/optimal_kmeans_d.Rd | 3 +-- man/subtype_data.Rd | 6 ++++-- 21 files changed, 111 insertions(+), 116 deletions(-)
Title: Support for Orientation Data
Description: Representations, conversions and display of orientation SO(3) data.
See the orientlib help topic for details.
Author: Duncan Murdoch
Maintainer: Duncan Murdoch <murdoch.duncan@gmail.com>
Diff between orientlib versions 0.10.3 dated 2013-03-22 and 0.10.4 dated 2020-05-26
DESCRIPTION | 16 MD5 | 58 +- NAMESPACE | 90 +-- NEWS | 150 ++--- R/boats.r | 214 ++++---- R/orientlib.r | 1110 +++++++++++++++++++++---------------------- R/orientlm.r | 128 ++-- R/utils.r | 80 +-- inst/doc/orientlib_paper.pdf |binary man/boat3d.Rd | 146 ++--- man/coerce-methods.Rd | 50 - man/eulerzxz.Rd | 72 +- man/eulerzyx.Rd | 76 +- man/index-methods.Rd | 78 +-- man/length-methods.Rd | 30 - man/matrix-classes.Rd | 82 +-- man/matrix-methods.Rd | 22 man/mean-methods.Rd | 30 - man/nearest.Rd | 78 +-- man/orientation-class.Rd | 72 +- man/orientlib.Rd | 162 +++--- man/orientlm.Rd | 156 +++--- man/quaternion.Rd | 68 +- man/rotation.distance.Rd | 78 +-- man/rotmatrix.Rd | 56 +- man/rotvector.Rd | 62 +- man/skewmatrix.Rd | 70 +- man/skewvector.Rd | 70 +- man/vector-classes.Rd | 140 ++--- man/weighted.mean-methods.Rd | 42 - 30 files changed, 1745 insertions(+), 1741 deletions(-)
Title: Extended Mixed Models Using Latent Classes and Latent Processes
Description: Estimation of various extensions of the mixed models including latent class mixed models, joint latent latent class mixed models and mixed models for curvilinear univariate or multivariate longitudinal outcomes using a maximum likelihood estimation method.
Author: Cecile Proust-Lima, Viviane Philipps, Amadou Diakite and Benoit Liquet
Maintainer: Cecile Proust-Lima <cecile.proust-lima@inserm.fr>
Diff between lcmm versions 1.8.1 dated 2019-06-26 and 1.8.1.1 dated 2020-05-26
DESCRIPTION | 6 MD5 | 34 - build/vignette.rds |binary inst/doc/introduction.R | 20 inst/doc/introduction.html | 401 +++++++++++--- inst/doc/latent_class_model_with_hlme.R | 44 - inst/doc/latent_class_model_with_hlme.html | 586 ++++++++++++++------ inst/doc/latent_process_model_with_lcmm.R | 34 - inst/doc/latent_process_model_with_lcmm.Rmd | 6 inst/doc/latent_process_model_with_lcmm.html | 563 ++++++++++++++------ inst/doc/latent_process_model_with_multlcmm.R | 40 - inst/doc/latent_process_model_with_multlcmm.html | 642 +++++++++++++++-------- inst/doc/pre_normalizing.R | 34 - inst/doc/pre_normalizing.html | 417 +++++++++++--- inst/doc/usual_problems.R | 2 inst/doc/usual_problems.html | 206 +++++++ src/lcmm.h | 2 vignettes/latent_process_model_with_lcmm.Rmd | 6 18 files changed, 2182 insertions(+), 861 deletions(-)
Title: Catalogue of Life Toolkit
Description: A programmatic interface to <http://sp2000.org.cn>, re-written based on an accompanying 'Species 2000' API. Access tables describing catalogue of the Chinese known species of animals, plants, fungi, micro-organisms, and more. This package also supports access to catalogue of life global <http://catalogueoflife.org> and catalogue of life Taiwan <http://taibnet.sinica.edu.tw/home_eng.php?>. The development of 'SP2000' package were supported by Biodiversity Survey and Assessment Project of the Ministry of Ecology and Environment, China <No.2019HJ2096001006> and Yunnan University's Research Innovation Fund for Graduate Students <No.2019227>.
Author: Liuyong Ding [aut, cre],
Minrui Huang [ctb],
Ke Yang [ctb],
Jun Wang [ctb],
Juan Tao [ctb],
Chengzhi Ding [ctb],
Daming He [ctb]
Maintainer: Liuyong Ding <ly_ding@126.com>
Diff between SP2000 versions 0.0.7 dated 2020-05-22 and 0.0.8 dated 2020-05-26
SP2000-0.0.7/SP2000/R/download_CoLChina.R |only SP2000-0.0.7/SP2000/R/find_Synonyms.R |only SP2000-0.0.7/SP2000/R/get_CoLGlobal.R |only SP2000-0.0.7/SP2000/R/get_CoLTaiwan.R |only SP2000-0.0.7/SP2000/R/get_RedlistChina.R |only SP2000-0.0.7/SP2000/R/open_URL.R |only SP2000-0.0.7/SP2000/R/search_familyID.R |only SP2000-0.0.7/SP2000/R/search_taxonID.R |only SP2000-0.0.7/SP2000/man/download_CoLChina.Rd |only SP2000-0.0.7/SP2000/man/find_Synonyms.Rd |only SP2000-0.0.7/SP2000/man/get_CoLGlobal.Rd |only SP2000-0.0.7/SP2000/man/get_CoLTaiwan.Rd |only SP2000-0.0.7/SP2000/man/get_RedlistChina.Rd |only SP2000-0.0.7/SP2000/man/open_URL.Rd |only SP2000-0.0.7/SP2000/man/search_familyID.Rd |only SP2000-0.0.7/SP2000/man/search_taxonID.Rd |only SP2000-0.0.8/SP2000/DESCRIPTION | 10 ++--- SP2000-0.0.8/SP2000/MD5 | 44 +++++++++++----------- SP2000-0.0.8/SP2000/NAMESPACE | 16 ++++---- SP2000-0.0.8/SP2000/NEWS | 4 ++ SP2000-0.0.8/SP2000/R/download_colchina.R |only SP2000-0.0.8/SP2000/R/find_synonyms.R |only SP2000-0.0.8/SP2000/R/get_colglobal.R |only SP2000-0.0.8/SP2000/R/get_coltaiwan.R |only SP2000-0.0.8/SP2000/R/get_redlistchina.R |only SP2000-0.0.8/SP2000/R/open_url.R |only SP2000-0.0.8/SP2000/R/search_checklist.R | 4 +- SP2000-0.0.8/SP2000/R/search_familyid.R |only SP2000-0.0.8/SP2000/R/search_taxonid.R |only SP2000-0.0.8/SP2000/man/download_colchina.Rd |only SP2000-0.0.8/SP2000/man/find_synonyms.Rd |only SP2000-0.0.8/SP2000/man/get_colglobal.Rd |only SP2000-0.0.8/SP2000/man/get_coltaiwan.Rd |only SP2000-0.0.8/SP2000/man/get_redlistchina.Rd |only SP2000-0.0.8/SP2000/man/open_url.Rd |only SP2000-0.0.8/SP2000/man/search_checklist.Rd | 4 +- SP2000-0.0.8/SP2000/man/search_familyid.Rd |only SP2000-0.0.8/SP2000/man/search_taxonid.Rd |only SP2000-0.0.8/SP2000/tests/testthat/test_api_key.R | 8 ++-- 39 files changed, 47 insertions(+), 43 deletions(-)
Title: Web-Based Interactive Omics Visualization
Description: Tool-set of modules for creating web-based applications that use plot based strategies to visualize and analyze multi-omics data.
This package utilizes the 'shiny' and 'plotly' frameworks to provide a user friendly dashboard for interactive plotting.
Author: Hendrik Schultheis [aut, cre],
Jens Preussner [aut],
Looso Mario [aut]
Maintainer: Hendrik Schultheis <hendrik.schultheis@mpi-bn.mpg.de>
Diff between wilson versions 2.3.1 dated 2019-11-18 and 2.4.0 dated 2020-05-26
wilson-2.3.1/wilson/tests/figs |only wilson-2.4.0/wilson/DESCRIPTION | 12 wilson-2.4.0/wilson/MD5 | 105 +++--- wilson-2.4.0/wilson/NAMESPACE | 1 wilson-2.4.0/wilson/NEWS.md | 4 wilson-2.4.0/wilson/R/and.R | 42 +- wilson-2.4.0/wilson/R/clarion.R | 173 ++++++++-- wilson-2.4.0/wilson/R/function.R | 14 wilson-2.4.0/wilson/R/installer.R |only wilson-2.4.0/wilson/R/orTextual.R | 35 ++ wilson-2.4.0/wilson/README.md | 2 wilson-2.4.0/wilson/build/vignette.rds |binary wilson-2.4.0/wilson/inst/doc/intro.R | 2 wilson-2.4.0/wilson/inst/doc/intro.Rmd | 2 wilson-2.4.0/wilson/inst/doc/intro.html | 17 - wilson-2.4.0/wilson/man/Clarion.Rd | 274 ++++++++++++++--- wilson-2.4.0/wilson/man/and.Rd | 19 - wilson-2.4.0/wilson/man/andUI.Rd | 34 +- wilson-2.4.0/wilson/man/colorPicker.Rd | 11 wilson-2.4.0/wilson/man/colorPickerUI.Rd | 12 wilson-2.4.0/wilson/man/columnSelector.Rd | 16 wilson-2.4.0/wilson/man/columnSelectorUI.Rd | 42 +- wilson-2.4.0/wilson/man/create_geneview.Rd | 21 - wilson-2.4.0/wilson/man/create_heatmap.Rd | 24 + wilson-2.4.0/wilson/man/create_pca.Rd | 27 + wilson-2.4.0/wilson/man/create_scatterplot.Rd | 35 +- wilson-2.4.0/wilson/man/download.Rd | 12 wilson-2.4.0/wilson/man/featureSelector.Rd | 15 wilson-2.4.0/wilson/man/forceArgs.Rd | 38 +- wilson-2.4.0/wilson/man/geneView.Rd | 15 wilson-2.4.0/wilson/man/global_cor_heatmap.Rd | 14 wilson-2.4.0/wilson/man/heatmap.Rd | 15 wilson-2.4.0/wilson/man/install_app.Rd |only wilson-2.4.0/wilson/man/label.Rd | 15 wilson-2.4.0/wilson/man/limit.Rd | 50 +-- wilson-2.4.0/wilson/man/log_message.Rd | 7 wilson-2.4.0/wilson/man/marker.Rd | 46 +- wilson-2.4.0/wilson/man/orNumeric.Rd | 16 wilson-2.4.0/wilson/man/orNumericUI.Rd | 36 +- wilson-2.4.0/wilson/man/orTextual.Rd | 18 - wilson-2.4.0/wilson/man/orTextualUI.Rd | 36 +- wilson-2.4.0/wilson/man/parse_MaxQuant.Rd | 15 wilson-2.4.0/wilson/man/pca.Rd | 12 wilson-2.4.0/wilson/man/scatterPlot.Rd | 15 wilson-2.4.0/wilson/man/searchData.Rd | 9 wilson-2.4.0/wilson/man/sequentialPalettes.Rd | 34 +- wilson-2.4.0/wilson/man/set_logger.Rd | 42 +- wilson-2.4.0/wilson/man/tobias_parser.Rd | 18 - wilson-2.4.0/wilson/man/transformation.Rd | 12 wilson-2.4.0/wilson/man/transformationUI.Rd | 12 wilson-2.4.0/wilson/tests/testthat/test-download.R | 3 wilson-2.4.0/wilson/tests/testthat/test-static-plots.R | 28 + wilson-2.4.0/wilson/vignettes/intro.Rmd | 2 53 files changed, 1015 insertions(+), 444 deletions(-)
Title: 'dplyr'-Like Syntax for Summary Statistics of Survey Data
Description: Use piping, verbs like 'group_by' and 'summarize', and other
'dplyr' inspired syntactic style when calculating summary statistics on survey
data using functions from the 'survey' package.
Author: Greg Freedman Ellis [aut, cre],
Thomas Lumley [ctb],
Tomasz Żółtak [ctb],
Ben Schneider [ctb]
Maintainer: Greg Freedman Ellis <greg.freedman@gmail.com>
Diff between srvyr versions 0.3.9 dated 2020-05-04 and 0.3.10 dated 2020-05-26
DESCRIPTION | 12 +- MD5 | 22 ++-- NEWS.md | 4 R/summarise.r | 12 +- README.md | 8 + inst/doc/extending-srvyr.R | 12 +- inst/doc/extending-srvyr.Rmd | 12 +- inst/doc/extending-srvyr.html | 199 ++++++++++++++++++++---------------------- inst/doc/srvyr-database.html | 190 ++++++++++++++++++++-------------------- inst/doc/srvyr-vs-survey.html | 4 man/summarise.Rd | 8 - vignettes/extending-srvyr.Rmd | 12 +- 12 files changed, 263 insertions(+), 232 deletions(-)
Title: Robust Re-Scaling to Better Recover Latent Effects in Data
Description: Non-linear transformations of data to better discover latent effects. Applies a sequence of three transformations (1) a Gaussianizing transformation, (2) a Z-score transformation, and (3) an outlier removal transformation. A publication describing the method has the following citation: Gregory J. Hunt, Mark A. Dane, James E. Korkola, Laura M. Heiser & Johann A. Gagnon-Bartsch (2020) "Automatic Transformation and Integration to Improve Visualization and Discovery of Latent Effects in Imaging Data", Journal of Computational and Graphical Statistics, <doi:10.1080/10618600.2020.1741379>.
Author: Gregory Hunt [aut, cre],
Johann Gagnon-Bartsch [aut]
Maintainer: Gregory Hunt <ghunt@wm.edu>
Diff between rrscale versions 0.1.3 dated 2019-03-13 and 1.0 dated 2020-05-26
DESCRIPTION | 21 +- MD5 | 31 +-- NAMESPACE | 8 R/rrscale.R | 169 ++++++++++------ build/vignette.rds |binary inst/CITATION |only inst/doc/ragged.R |only inst/doc/ragged.Rmd |only inst/doc/ragged.html |only inst/doc/rescaling_data.R | 42 ++-- inst/doc/rescaling_data.Rmd | 30 ++- inst/doc/rescaling_data.html | 408 ++++++++++++++++++++++++++++++++--------- man/rrscale.Rd | 31 ++- tests/testthat/always_test.R | 27 ++ tests/testthat/basic_ref.rds |binary tests/testthat/basic_ref10.rds |only tests/testthat/test-basic.R | 52 ++--- tests/testthat/test-nloptr.R |only vignettes/ragged.Rmd |only vignettes/rescaling_data.Rmd | 30 ++- 20 files changed, 593 insertions(+), 256 deletions(-)
Title: Functions to Make Surveys Processing Easier
Description: Set of functions to make the processing and analysis of
surveys easier : interactive shiny apps and addins for data recoding,
contingency tables, dataset metadata handling, and several convenience
functions.
Author: Julien Barnier [aut, cre],
François Briatte [aut],
Joseph Larmarange [aut]
Maintainer: Julien Barnier <julien.barnier@ens-lyon.fr>
Diff between questionr versions 0.7.0 dated 2018-11-26 and 0.7.1 dated 2020-05-26
questionr-0.7.0/questionr/R/questionr-package.R |only questionr-0.7.0/questionr/man/questionr.Rd |only questionr-0.7.1/questionr/DESCRIPTION | 20 +-- questionr-0.7.1/questionr/MD5 | 102 +++++++--------- questionr-0.7.1/questionr/NAMESPACE | 3 questionr-0.7.1/questionr/NEWS.md | 11 + questionr-0.7.1/questionr/R/datasets.R | 18 +- questionr-0.7.1/questionr/R/icut.R | 14 +- questionr-0.7.1/questionr/R/iorder.R | 14 +- questionr-0.7.1/questionr/R/irec.R | 28 ++-- questionr-0.7.1/questionr/R/lookfor.R | 97 ++------------- questionr-0.7.1/questionr/R/tables.R | 24 +++ questionr-0.7.1/questionr/R/weighting.R | 40 ++---- questionr-0.7.1/questionr/build/vignette.rds |binary questionr-0.7.1/questionr/data/fecondite.RData |binary questionr-0.7.1/questionr/data/fertility.RData |binary questionr-0.7.1/questionr/data/happy.RData |binary questionr-0.7.1/questionr/data/hdv2003.RData |binary questionr-0.7.1/questionr/data/rp2012.RData |binary questionr-0.7.1/questionr/data/rp99.RData |binary questionr-0.7.1/questionr/inst/doc/recoding_addins.html | 20 ++- questionr-0.7.1/questionr/inst/shiny/css/ifuncs.css | 4 questionr-0.7.1/questionr/man/children.Rd | 5 questionr-0.7.1/questionr/man/clipcopy.Rd | 13 +- questionr-0.7.1/questionr/man/cprop.Rd | 36 ++++- questionr-0.7.1/questionr/man/cross.multi.table.Rd | 13 +- questionr-0.7.1/questionr/man/describe.Rd | 15 -- questionr-0.7.1/questionr/man/enfants.Rd | 5 questionr-0.7.1/questionr/man/fecondite.Rd | 6 questionr-0.7.1/questionr/man/femmes.Rd | 7 - questionr-0.7.1/questionr/man/fertility.Rd | 6 questionr-0.7.1/questionr/man/format.proptab.Rd | 3 questionr-0.7.1/questionr/man/freq.Rd | 14 +- questionr-0.7.1/questionr/man/hdv2003.Rd | 7 - questionr-0.7.1/questionr/man/households.Rd | 5 questionr-0.7.1/questionr/man/icut.Rd | 9 - questionr-0.7.1/questionr/man/iorder.Rd | 7 - questionr-0.7.1/questionr/man/irec.Rd | 7 - questionr-0.7.1/questionr/man/lookfor.Rd | 26 +--- questionr-0.7.1/questionr/man/ltabs.Rd | 9 + questionr-0.7.1/questionr/man/menages.Rd | 5 questionr-0.7.1/questionr/man/multi.table.Rd | 3 questionr-0.7.1/questionr/man/print.proptab.Rd | 3 questionr-0.7.1/questionr/man/prop.Rd | 36 ++++- questionr-0.7.1/questionr/man/quant.cut.Rd | 3 questionr-0.7.1/questionr/man/rp2012.Rd | 7 - questionr-0.7.1/questionr/man/rp99.Rd | 7 - questionr-0.7.1/questionr/man/rprop.Rd | 36 ++++- questionr-0.7.1/questionr/man/tabs.Rd | 16 ++ questionr-0.7.1/questionr/man/women.Rd | 7 - questionr-0.7.1/questionr/man/wtd.mean.Rd | 13 +- questionr-0.7.1/questionr/man/wtd.table.Rd | 12 + questionr-0.7.1/questionr/tests/testthat/test_tables.R | 7 + 53 files changed, 399 insertions(+), 344 deletions(-)
Title: Tools for Working with Geohashes
Description: Tools for working with Gustavo Niemeyer's geohash coordinate system, including API for interacting with other common R GIS libraries.
Author: Michael Chirico [aut, cre],
Dmitry Shkolnik [ctb]
Maintainer: Michael Chirico <MichaelChirico4@gmail.com>
Diff between geohashTools versions 0.3.0 dated 2019-10-03 and 0.3.1 dated 2020-05-26
geohashTools-0.3.0/geohashTools/src/geohash.c |only geohashTools-0.3.1/geohashTools/DESCRIPTION | 8 +- geohashTools-0.3.1/geohashTools/MD5 | 27 ++++---- geohashTools-0.3.1/geohashTools/NEWS.md | 18 +++++ geohashTools-0.3.1/geohashTools/R/gh_decode.R | 4 + geohashTools-0.3.1/geohashTools/R/gis_tools.R | 2 geohashTools-0.3.1/geohashTools/man/gh_decode.Rd | 4 - geohashTools-0.3.1/geohashTools/src/decode.c |only geohashTools-0.3.1/geohashTools/src/encode.c |only geohashTools-0.3.1/geohashTools/src/geohash.h | 3 geohashTools-0.3.1/geohashTools/src/neighbors.c |only geohashTools-0.3.1/geohashTools/src/utils.c |only geohashTools-0.3.1/geohashTools/tests/testthat.R | 1 geohashTools-0.3.1/geohashTools/tests/testthat/test-decode.R | 12 +++ geohashTools-0.3.1/geohashTools/tests/testthat/test-encode.R | 3 geohashTools-0.3.1/geohashTools/tests/testthat/test-gis-tools.R | 31 +++++----- geohashTools-0.3.1/geohashTools/tests/testthat/test-neighbors.R | 2 17 files changed, 82 insertions(+), 33 deletions(-)
Title: A Framework for Investment Strategy Simulation
Description: Provides a framework for performing discrete (share-level) simulations of
investment strategies. Simulated portfolios optimize exposure to an input signal subject
to constraints such as position size and factor exposure.
Author: Jeff Enos [cre, aut],
David Kane [aut],
Strand Technologies, Inc. [cph]
Maintainer: Jeff Enos <jeff@strand.tech>
Diff between strand versions 0.1.2 dated 2020-05-23 and 0.1.3 dated 2020-05-26
DESCRIPTION | 8 - MD5 | 26 ++--- NEWS.md | 7 + R/Simulation.R | 39 ------- R/strand.R | 39 +++++++ R/utilities.R | 18 +++ README.md | 11 +- inst/doc/strand.R | 43 +++++--- inst/doc/strand.Rmd | 167 ++++++++++++++++++++++----------- inst/doc/strand.html | 251 +++++++++++++++++++++++++++++++------------------- man/Simulation.Rd | 38 ------- man/strand-package.Rd | 39 +++++++ vignettes/sample.yaml | 13 -- vignettes/strand.Rmd | 167 ++++++++++++++++++++++----------- 14 files changed, 544 insertions(+), 322 deletions(-)
Title: The Skew-Normal and Related Distributions Such as the Skew-t
Description: Build and manipulate probability distributions of the skew-normal
family and some related ones, notably the skew-t family, and provide related
statistical methods for data fitting and model diagnostics, in the univariate
and the multivariate case.
Author: Adelchi Azzalini [aut, cre] (<https://orcid.org/0000-0002-7583-1269>)
Maintainer: Adelchi Azzalini <adelchi.azzalini@unipd.it>
Diff between sn versions 1.6-1 dated 2020-04-01 and 1.6-2 dated 2020-05-26
DESCRIPTION | 10 - MD5 | 33 ++- NEWS | 38 ++-- R/sn-funct.R | 335 ++++++++++++++++++++++------------------ R/sn_S4.R | 5 build |only data/ais.rda |binary data/barolo.rda |binary data/frontier.rda |binary data/wines.rda |binary inst/CITATION | 19 +- inst/doc/how_to_sample.pdf.asis |only inst/doc/pkg-overview.html | 2 inst/doc/pkg-overview.html.asis |only inst/doc/pkg_sn-intro.pdf.asis |only man/dmsn.Rd | 10 - man/dsn.Rd | 9 + man/makeSECdistr.Rd | 8 vignettes |only 19 files changed, 271 insertions(+), 198 deletions(-)
Title: A Tidy Interface for Simulating Multivariate Data
Description: Provides pipe-friendly (%>%) wrapper functions for MASS::mvrnorm() to create simulated multivariate data sets
with groups of variables with different degrees of variance, covariance, and effect size.
Author: Eric Scott [aut, cre] (<https://orcid.org/0000-0002-7430-7879>)
Maintainer: Eric Scott <scottericr@gmail.com>
Diff between holodeck versions 0.2.0 dated 2019-04-16 and 0.2.1 dated 2020-05-26
DESCRIPTION | 18 MD5 | 32 NEWS.md | 6 README.md | 155 +-- build/vignette.rds |binary inst/doc/simulating-data.R | 58 - inst/doc/simulating-data.Rmd | 36 inst/doc/simulating-data.html | 1318 +++---------------------------- man/figures/README-unnamed-chunk-2-1.png |binary man/figures/README-unnamed-chunk-4-1.png |binary man/figures/README-unnamed-chunk-5-1.png |binary man/holodeck.Rd | 1 man/sim_cat.Rd | 5 man/sim_covar.Rd | 8 man/sim_discr.Rd | 5 tests/testthat/test-sim_multvar.R | 148 ++- vignettes/simulating-data.Rmd | 36 17 files changed, 366 insertions(+), 1460 deletions(-)
Title: Model Selection and Multimodel Inference Made Easy
Description: Automated model selection and model-averaging. Provides a
wrapper for glm and other functions, automatically generating
all possible models (under constraints set by the user) with
the specified response and explanatory variables, and finding
the best models in terms of some Information Criterion (AIC,
AICc or BIC). Can handle very large numbers of candidate
models. Features a Genetic Algorithm to find the best models
when an exhaustive screening of the candidates is not feasible.
Author: Vincent Calcagno [aut, cre]
Maintainer: Vincent Calcagno <vincent.calcagno@inrae.fr>
Diff between glmulti versions 1.0.7.1 dated 2019-04-14 and 1.0.8 dated 2020-05-26
ChangeLog | 3 +++ DESCRIPTION | 17 +++++++++-------- MD5 | 17 +++++++++-------- NAMESPACE | 3 +++ R/glmulti.r | 4 ++-- java |only man/coef.glmulti.Rd | 3 ++- man/glmulti-methods.Rd | 6 +++--- man/glmulti.Rd | 21 ++++++++++++++------- man/write.Rd | 7 ++++--- 10 files changed, 49 insertions(+), 32 deletions(-)
Title: Spatial Data Framework for ggplot2
Description: Spatial data plus the power of the ggplot2 framework means easier mapping when input
data are already in the form of spatial objects.
Author: Dewey Dunnington [aut, cre] (<https://orcid.org/0000-0002-9415-4582>),
Brent Thorne [ctb] (<https://orcid.org/0000-0002-1099-3857>)
Maintainer: Dewey Dunnington <dewey@fishandwhistle.net>
Diff between ggspatial versions 1.1.1 dated 2020-04-27 and 1.1.2 dated 2020-05-26
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- R/df-spatial-sf.R | 2 +- tests/testthat/test-annotation-north-arrow.R | 5 +++-- tests/testthat/test-df-spatial-sp.R | 18 ++++++++++++++++++ 5 files changed, 29 insertions(+), 10 deletions(-)
Title: 'ggplot2' Faceting Utilities for Geographical Data
Description: Provides geofaceting functionality for 'ggplot2'. Geofaceting arranges a sequence of plots of data for different geographical entities into a grid that preserves some of the geographical orientation.
Author: Ryan Hafen [aut, cre],
Barret Schloerke [ctb]
Maintainer: Ryan Hafen <rhafen@gmail.com>
Diff between geofacet versions 0.1.10 dated 2019-03-13 and 0.2.0 dated 2020-05-26
geofacet-0.1.10/geofacet/data/london_boroughs_grid.rda |only geofacet-0.1.10/geofacet/data/us_state_grid4.rda |only geofacet-0.1.10/geofacet/inst/doc/docs.Rmd |only geofacet-0.1.10/geofacet/inst/doc/docs.html |only geofacet-0.1.10/geofacet/inst/doc/rd.Rmd |only geofacet-0.1.10/geofacet/inst/doc/rd.html |only geofacet-0.1.10/geofacet/man/plus-.gg.Rd |only geofacet-0.1.10/geofacet/vignettes/docs.Rmd |only geofacet-0.1.10/geofacet/vignettes/rd.Rmd |only geofacet-0.1.10/geofacet/vignettes/rd_index.yaml |only geofacet-0.2.0/geofacet/DESCRIPTION | 18 geofacet-0.2.0/geofacet/MD5 | 255 ++- geofacet-0.2.0/geofacet/NAMESPACE | 7 geofacet-0.2.0/geofacet/NEWS.md | 8 geofacet-0.2.0/geofacet/R/facet_geo.R | 133 +- geofacet-0.2.0/geofacet/R/grid_auto.R | 17 geofacet-0.2.0/geofacet/R/grid_docs.R | 642 +++++++++- geofacet-0.2.0/geofacet/R/valid_grids.R | 58 geofacet-0.2.0/geofacet/README.md | 4 geofacet-0.2.0/geofacet/build/vignette.rds |binary geofacet-0.2.0/geofacet/data/af_prov_grid1.rda |only 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geofacet-0.2.0/geofacet/tests/testthat/test-auto.R | 2 geofacet-0.2.0/geofacet/tests/testthat/test-break.R | 2 geofacet-0.2.0/geofacet/tests/testthat/test-examples.R | 4 geofacet-0.2.0/geofacet/tests/testthat/test-zzz-lintr.R | 14 geofacet-0.2.0/geofacet/vignettes/geofacet.Rmd |only 176 files changed, 1512 insertions(+), 232 deletions(-)
Title: Implementation of the Empirical Bayes Method
Description: Implements a Bayesian-like approach to the high-dimensional sparse linear regression problem based on an empirical or data-dependent prior distribution, which can be used for estimation/inference on the model parameters, variable selection, and prediction of a future response. The method was first presented in Martin, Ryan and Mess, Raymond and Walker, Stephen G (2017) <doi:10.3150/15-BEJ797>. More details focused on the prediction problem are given in Martin, Ryan and Tang, Yiqi (2019) <arXiv:1903.00961>.
Author: Yiqi Tang, Ryan Martin
Maintainer: Yiqi Tang <ytang22@ncsu.edu>
Diff between ebreg versions 0.1.1 dated 2020-05-21 and 0.1.2 dated 2020-05-26
DESCRIPTION | 6 ++--- MD5 | 8 +++--- R/ebproject.R | 23 ++++++++++++------- build/partial.rdb |binary tests/testthat/test_ebproject.R | 48 ++++++++++++++++++---------------------- 5 files changed, 44 insertions(+), 41 deletions(-)
Title: CRISPR Pooled Screen Analysis using Beta-Binomial Test
Description: Provides functions for hit gene identification and quantification of sgRNA (single-guided RNA) abundances for CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) pooled screen data analysis.
Details are in Jeong et al. (2019) <doi:10.1101/gr.245571.118> and Baggerly et al. (2003) <doi:10.1093/bioinformatics/btg173>.
Author: Hyun-Hwan Jeong [aut, cre]
Maintainer: Hyun-Hwan Jeong <hyun-hwan.jeong@bcm.edu>
Diff between CB2 versions 1.3.2 dated 2020-05-12 and 1.3.3 dated 2020-05-26
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/helpers.R | 23 ++++++++++++++++++----- README.md | 8 ++++++++ inst/doc/cb2-input-handling.html | 4 ++-- inst/doc/cb2-tutorial.html | 6 +++--- man/measure_gene_stats.Rd | 6 ++++-- tests/testthat/test.toydata.R | 26 ++++++++++++++++++++++++++ 8 files changed, 72 insertions(+), 23 deletions(-)
Title: Association Measurement Through Cross Rank Increments
Description: Computes robust association measures that do not
presuppose linearity. The xi correlation (xicor) is based
on cross correlation between ranked increments.
The reference for the methods implemented here is
Chatterjee, Sourav (2020) <arXiv:1909.10140>
This package includes the Galton peas example.
Author: Susan Holmes [aut,cre], Sourav Chatterjee [aut]
Maintainer: Susan Holmes <sp.holmes@gmail.com>
Diff between XICOR versions 0.3.2 dated 2020-04-28 and 0.3.3 dated 2020-05-26
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/calculateXI.R | 6 +++--- 3 files changed, 9 insertions(+), 9 deletions(-)
Title: Tools to Conduct Meteorological Normalisation on Air Quality
Data
Description: An integrated set of tools to allow data users to conduct
meteorological normalisation on air quality data. This meteorological
normalisation technique uses predictive random forest models to remove
variation of pollutant concentrations so trends and interventions can be
explored in a robust way. For examples, see Grange et al. (2018)
<doi:10.5194/acp-18-6223-2018> and Grange and Carslaw (2019)
<doi:10.1016/j.scitotenv.2018.10.344>.
Author: Stuart K. Grange [cre, aut] (<https://orcid.org/0000-0003-4093-3596>)
Maintainer: Stuart K. Grange <stuart.grange@york.ac.uk>
Diff between rmweather versions 0.1.3 dated 2018-11-12 and 0.1.4 dated 2020-05-26
DESCRIPTION | 10 +++---- MD5 | 53 +++++++++++++++++++-------------------- NAMESPACE | 3 +- NEWS.md | 12 ++++++++ R/dplyr_re_exports.R | 4 +- R/rmw_clip.R | 3 +- R/rmw_do_all.R | 4 -- R/rmw_find_breakpoints.R | 4 +- R/rmw_model_statistics.R | 2 - R/rmw_normalise.R | 12 +++++--- R/rmw_partial_dependencies.R | 13 +++++---- R/rmw_predict.R | 2 - R/rmw_prepare_data.R | 52 ++++++++++++++++++++++---------------- R/rmw_train_model.R | 15 ++++++----- R/rmweather_helpers.R | 13 +++------ R/rmweather_plotting_functions.R | 39 ++++++++++++++++++---------- README.md | 7 ++--- man/data_london.Rd | 6 ++-- man/data_london_normalised.Rd | 6 ++-- man/figures/logo.png |only man/model_london.Rd | 4 ++ man/rmw_do_all.Rd | 19 +++++++++++-- man/rmw_normalise.Rd | 14 ++++++++-- man/rmw_partial_dependencies.Rd | 3 -- man/rmw_plot_test_prediction.Rd | 4 ++ man/rmw_predict.Rd | 3 -- man/rmw_prepare_data.Rd | 11 +++++--- man/rmw_train_model.Rd | 13 +++++++-- 28 files changed, 202 insertions(+), 129 deletions(-)
Title: Multinomial Logit Models
Description: Maximum Likelihood estimation of random utility discrete
choice models, as described in Kenneth Train (2009) Discrete Choice
Methods with Simulations <doi:10.1017/CBO9780511805271>.
Author: Yves Croissant [aut, cre]
Maintainer: Yves Croissant <yves.croissant@univ-reunion.fr>
Diff between mlogit versions 1.0-3.1 dated 2020-03-12 and 1.1-0 dated 2020-05-26
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Title: Antares Visualizations
Description: Visualize results generated by Antares, a powerful open source software
developed by RTE to simulate and study electric power systems
(more information about Antares here: <https://github.com/AntaresSimulatorTeam/Antares_Simulator>).
This package provides functions that create interactive charts to help
Antares users visually explore the results of their simulations.
Author: Veronique Bachelier [aut, cre],
Jalal-Edine Zawam [aut],
Francois Guillem [aut],
Benoit Thieurmel [aut],
Titouan Robert [aut],
Baptiste Seguinot [ctb],
RTE [cph]
Maintainer: Veronique Bachelier <veronique.bachelier@rte-france.com>
Diff between antaresViz versions 0.15.1 dated 2020-02-24 and 0.15.2 dated 2020-05-26
antaresViz-0.15.1/antaresViz/NEWS |only antaresViz-0.15.2/antaresViz/DESCRIPTION | 12 ++--- antaresViz-0.15.2/antaresViz/MD5 | 20 ++++----- antaresViz-0.15.2/antaresViz/NAMESPACE | 2 antaresViz-0.15.2/antaresViz/NEWS.md |only antaresViz-0.15.2/antaresViz/R/plot_XY.R | 38 +++++++++--------- antaresViz-0.15.2/antaresViz/R/stack_prod.R | 34 +++++++++------- antaresViz-0.15.2/antaresViz/build/vignette.rds |binary antaresViz-0.15.2/antaresViz/inst/doc/antaresViz.html | 4 - antaresViz-0.15.2/antaresViz/man/limitSizeGraph.Rd | 38 +++++++++--------- antaresViz-0.15.2/antaresViz/man/plotXY.Rd | 12 ++--- antaresViz-0.15.2/antaresViz/man/runAppAntaresViz.Rd | 26 ++++++------ 12 files changed, 97 insertions(+), 89 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-02-04 1.1.0
2016-12-21 1.0.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2015-01-21 1.3
Title: Insightful Research Tools
Description: Insightful Research Tools.
Author: William Constantine [cre, aut]
Maintainer: ORPHANED
Diff between ifultools versions 2.0-5 dated 2019-03-04 and 2.0-5.1 dated 2020-05-26
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- src/RSInterface.h | 6 +++--- src/init.c | 6 +++--- src/wav_modw.c | 2 +- 5 files changed, 15 insertions(+), 15 deletions(-)
Title: Bounded Memory Linear and Generalized Linear Models
Description: Regression for data too large to fit in memory. This package functions exactly like the 'biglm' package, but works with later versions of R.
Author: Thomas Lumley [aut],
Christophe Dutang [ctb],
Alan Miller [ctb] (Algorithm AS 274),
Morven Gentleman [ctb] (Algorithm AS 75),
Mark Purver [cre]
Maintainer: Mark Purver <mark_purver@hotmail.com>
Diff between biglmm versions 0.9-1 dated 2018-07-31 and 0.9-2 dated 2020-05-26
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/boundedQRf.f | 6 +++--- 3 files changed, 8 insertions(+), 8 deletions(-)
Title: bounded memory linear and generalized linear models
Description: Regression for data too large to fit in memory
Author: Thomas Lumley
Maintainer: Thomas Lumley <tlumley@u.washington.edu>
Diff between biglm versions 0.9-1 dated 2013-05-15 and 0.9-2 dated 2020-05-26
DESCRIPTION | 6 +++--- MD5 | 6 +++--- src/boundedQR.c | 8 +++++--- src/boundedQRf.f | 6 +++--- 4 files changed, 14 insertions(+), 12 deletions(-)
Title: Functions to Perform Isotonic Regression
Description: Linear order and unimodal order (univariate)
isotonic regression; bivariate isotonic regression
with linear order on both variables.
Author: Rolf Turner <r.turner@auckland.ac.nz>
Maintainer: Rolf Turner <r.turner@auckland.ac.nz>
Diff between Iso versions 0.0-18 dated 2019-06-05 and 0.0-18.1 dated 2020-05-26
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/init.c | 7 ++++--- 3 files changed, 9 insertions(+), 8 deletions(-)
Title: Independent Multiple-Sample Greedy Equivalence Search
Implementation
Description: Functions for the implementation of Independent Multiple-sample
Greedy Equivalence Search (IMaGES), a causal inference algorithm for creating
aggregate graphs and structural equation modeling data for one or more
datasets. This package is useful for time series data with specific regions of
interest. This implementation is inspired by the paper "Six problems
for causal inference from fMRI" by Ramsey, Hanson, Hanson, Halchenko, Poldrack,
and Glymour (2010) <DOI:10.1016/j.neuroimage.2009.08.065>. The IMaGES algorithm uses a modified BIC score to compute goodness
of fit of edge additions, subtractions, and turns across all datasets and
returns a representative graph, along with structural equation modeling data for
the global graph and individual datasets, means, and standard errors. Functions
for plotting the resulting graph(s) are provided. This package is built upon the
'pcalg' package.
Author: Noah Frazier-Logue [aut, cre],
Stephen Jose Hanson [aut],
Markus Kalisch [ctb],
Alain Hauser [ctb],
Martin Maechler [ctb],
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]
Maintainer: Noah Frazier-Logue <n.frazier.logue@nyu.edu>
Diff between IMaGES versions 0.1 dated 2019-01-25 and 0.1.1 dated 2020-05-26
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/init.c | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
Title: General Smoothing Splines
Description: A comprehensive package for structural multivariate
function estimation using smoothing splines.
Author: Chong Gu <chong@purdue.edu>
Maintainer: Chong Gu <chong@purdue.edu>
Diff between gss versions 2.2-1 dated 2020-05-17 and 2.2-2 dated 2020-05-26
ChangeLog | 8 ++++++++ DESCRIPTION | 8 ++++---- INDEX | 2 ++ MD5 | 10 ++++++---- NAMESPACE | 2 +- R/sscomp.R |only man/sscomp.Rd |only 7 files changed, 21 insertions(+), 9 deletions(-)
Title: Clustering and Classification with the Contaminated Normal
Description: Fits mixtures of multivariate contaminated normal distributions
(with eigen-decomposed scale matrices) via the expectation conditional-
maximization algorithm under a clustering or classification paradigm
Methods are described in Antonio Punzo, Angelo Mazza, and Paul D McNicholas (2018) <doi:10.18637/jss.v085.i10>.
Author: Antonio Punzo, Angelo Mazza, Paul D. McNicholas
Maintainer: Angelo Mazza <a.mazza@unict.it>
Diff between ContaminatedMixt versions 1.3.4 dated 2019-08-27 and 1.3.4.1 dated 2020-05-26
DESCRIPTION | 6 +++--- MD5 | 6 +++--- src/ContaminatedMixt_init.c | 5 ++++- src/Uncontam.c | 2 +- 4 files changed, 11 insertions(+), 8 deletions(-)
More information about ContaminatedMixt at CRAN
Permanent link
Title: C5.0 Decision Trees and Rule-Based Models
Description: C5.0 decision trees and rule-based models for pattern recognition that extend the work of Quinlan (1993, ISBN:1-55860-238-0).
Author: Max Kuhn [aut, cre],
Steve Weston [ctb],
Mark Culp [ctb],
Nathan Coulter [ctb],
Ross Quinlan [aut] (Author of imported C code),
RuleQuest Research [cph] (Copyright holder of imported C code),
Rulequest Research Pty Ltd. [cph] (Copyright holder of imported C code)
Maintainer: Max Kuhn <mxkuhn@gmail.com>
Diff between C50 versions 0.1.3 dated 2020-01-13 and 0.1.3.1 dated 2020-05-26
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/extern.h | 3 ++- 3 files changed, 7 insertions(+), 6 deletions(-)
Title: Beyond the Border - Kernel Density Estimation for Urban
Geography
Description: The kernelSmoothing() function allows you to square and smooth geolocated data. It calculates a classical kernel smoothing (conservative) or a geographically weighted median. There are four major call modes of the function.
The first call mode is kernelSmoothing(obs, epsg, cellsize, bandwith) for a classical kernel smoothing and automatic grid.
The second call mode is kernelSmoothing(obs, epsg, cellsize, bandwith, quantiles) for a geographically weighted median and automatic grid.
The third call mode is kernelSmoothing(obs, epsg, cellsize, bandwith, centroids) for a classical kernel smoothing and user grid.
The fourth call mode is kernelSmoothing(obs, epsg, cellsize, bandwith, quantiles, centroids) for a geographically weighted median and user grid.
Geographically weighted summary statistics : a framework for localised exploratory data analysis, C.Brunsdon & al., in Computers, Environment and Urban Systems C.Brunsdon & al. (2002) <doi:10.1016/S0198-9715(01)00009-6>,
Statistical Analysis of Spatial and Spatio-Temporal Point Patterns, Third Edition, Diggle, pp. 83-86, (2003) <doi:10.1080/13658816.2014.937718>.
Author: Arlindo Dos Santos [cre],
Francois Semecurbe [drt, aut],
Auriane Renaud [ctb],
Cynthia Faivre [ctb],
Thierry Cornely [ctb],
Farida Marouchi [ctb],
Farida Marouchi [ctb]
Maintainer: Arlindo Dos Santos <Arlindo.Dos-Santos@insee.fr>
Diff between btb versions 0.1.30 dated 2018-05-23 and 0.1.30.1 dated 2020-05-26
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/init.c | 2 +- 3 files changed, 6 insertions(+), 6 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-09-04 2019.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-04-28 0.5.2
2020-04-14 0.5.1