Title: A Wrapper Around 'WebTRIS' Traffic Flow API from Highways
England
Description: Provides functions to query data from the 'WebTRIS' Traffic Flow API (from Highways England) into tidy data frames.
The API documentation is available here: <http://webtris.highwaysengland.co.uk/api/swagger/ui/index>.
Author: Ivo Wengraf [cre],
Will Bowditch [aut]
Maintainer: Ivo Wengraf <Ivo.Wengraf@RACFoundation.org>
Diff between webTRISr versions 0.1.1 dated 2018-10-19 and 0.2.0 dated 2019-08-07
DESCRIPTION | 23 +++++++++++++---------- MD5 | 12 ++++++------ NEWS.md | 7 ++++--- R/api_wrappers.R | 10 +++++++++- README.md | 4 ++-- man/webtris_sites.Rd | 7 ++++++- tests/testthat/test_WTsites.R | 15 ++++++++++----- 7 files changed, 50 insertions(+), 28 deletions(-)
Title: Simulate Joint Distribution
Description: Simulate multivariate correlated data given nonparametric marginals and their covariance structure characterized by a Pearson or Spearman correlation matrix. The simulator engages the problem from a purely computational perspective. It assumes no statistical models such as copulas or parametric distributions, and can approximate the target correlations regardless of theoretical feasibility. The algorithm integrates and advances the Iman-Conover (1982) approach <doi:10.1080/03610918208812265> and the Ruscio-Kaczetow iteration (2008) <doi:10.1080/00273170802285693>. Package functions are carefully implemented in C++ for squeezing computing speed, suitable for large input in a manycore environment. Precision of the approximation and computing speed both outperform various CRAN packages to date by substantial margins. Benchmarks are detailed in function examples. A simple heuristic algorithm is additionally designed to optimize the joint distribution in the post-simulation stage. This heuristic demonstrated not only strong capability of cost reduction, but also good potential of achieving the same level of precision of approximation without the enhanced Iman-Conover-Ruscio-Kaczetow.
Author: Charlie Wusuo Liu
Maintainer: Charlie Wusuo Liu <liuwusuo@gmail.com>
Diff between SimJoint versions 0.2.1 dated 2019-06-18 and 0.2.2 dated 2019-08-07
DESCRIPTION | 8 ++++---- MD5 | 7 ++++--- inst/NEWS.Rd |only inst/doc/SimulatedJointDistribution.pdf |binary tests/funtionExamples/SJpearson_eg.r | 30 +++++++++++++++--------------- 5 files changed, 23 insertions(+), 22 deletions(-)
Title: Producing and Reproducing Results
Description: A system for embedded scientific computing and reproducible research with R.
The OpenCPU server exposes a simple but powerful HTTP api for RPC and data interchange
with R. This provides a reliable and scalable foundation for statistical services or
building R web applications. The OpenCPU server runs either as a single-user development
server within the interactive R session, or as a multi-user Linux stack based on Apache2.
The entire system is fully open source and permissively licensed. The OpenCPU website
has detailed documentation and example apps.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>
Diff between opencpu versions 2.1.2 dated 2019-05-12 and 2.1.3 dated 2019-08-07
DESCRIPTION | 9 ++++----- MD5 | 12 ++++++------ NEWS | 4 ++++ R/httpget_webhook.R | 4 ++-- R/utils.R | 20 +++++++++++++++----- build/vignette.rds |binary inst/doc/opencpu-paper.pdf |binary 7 files changed, 31 insertions(+), 18 deletions(-)
Title: Mainardi-Wright Family of Distributions
Description: Implements random number generation, plotting, and estimation algorithms for the two-parameter one-sided and two-sided M-Wright (Mainardi-Wright) family.
The M-Wright distributions naturally generalize the widely used one-sided (Airy and half-normal or half-Gaussian) and symmetric (Airy and Gaussian or normal) models.
These are widely studied in time-fractional differential equations. References: Cahoy and Minkabo (2017) <doi:10.3233/MAS-170388>; Cahoy (2012) <doi:10.1007/s00180-011-0269-x>; Cahoy (2012) <doi:10.1080/03610926.2010.543299>; Cahoy (2011); Mainardi, Mura, and Pagnini (2010) <doi:10.1155/2010/104505>.
Author: Dexter Cahoy
Maintainer: Dexter Cahoy <cahoyd@uhd.edu>
Diff between MWright versions 0.3.0 dated 2019-08-05 and 0.3.2 dated 2019-08-07
DESCRIPTION | 10 +++++----- MD5 | 42 +++++++++++++++++++++--------------------- R/MWright.R | 4 ++-- R/distn1side.R | 2 +- R/distn2side.R | 15 +++++++-------- R/int1side.R | 2 +- R/int2side.R | 2 +- R/plot2side.R | 2 +- R/point1side.R | 2 +- R/point2side.R | 2 +- R/randnumber1sided.R | 2 +- R/randnumber2sided.R | 2 +- man/MWright.Rd | 4 ++-- man/dmwright2.Rd | 2 +- man/int_est1.Rd | 2 +- man/int_est2.Rd | 2 +- man/pmwright1.Rd | 2 +- man/pmwright2.Rd | 4 ++-- man/point_est1.Rd | 2 +- man/point_est2.Rd | 2 +- man/rmwright1.Rd | 2 +- man/rmwright2.Rd | 2 +- 22 files changed, 55 insertions(+), 56 deletions(-)
Title: Composable Preprocessing Operators and Pipelines for Machine
Learning
Description: Toolset that enriches 'mlr' with a diverse set of preprocessing
operators. Composable Preprocessing Operators ("CPO"s) are first-class
R objects that can be applied to data.frames and 'mlr' "Task"s to modify
data, can be attached to 'mlr' "Learner"s to add preprocessing to machine
learning algorithms, and can be composed to form preprocessing pipelines.
Author: Martin Binder [aut, cre],
Bernd Bischl [ctb],
Michel Lang [ctb],
Lars Kotthoff [ctb]
Maintainer: Martin Binder <developer.mb706@doublecaret.com>
Diff between mlrCPO versions 0.3.4-3 dated 2019-05-11 and 0.3.4-4 dated 2019-08-07
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++----------- README.md | 2 +- inst/doc/a_1_getting_started.html | 10 +++++++--- inst/doc/a_2_mlrCPO_core.html | 10 +++++++--- inst/doc/a_3_all_CPOs.html | 10 +++++++--- inst/doc/a_4_custom_CPOs.html | 12 ++++++++---- inst/doc/z_1_getting_started_terse.html | 10 +++++++--- inst/doc/z_2_mlrCPO_core_terse.html | 10 +++++++--- inst/doc/z_3_all_CPOs_terse.html | 10 +++++++--- inst/doc/z_4_custom_CPOs_terse.html | 10 +++++++--- tests/testthat/test_cpo_makeCols.R | 4 ++-- 12 files changed, 74 insertions(+), 42 deletions(-)
Title: Interface to the California Data Exchange Center
Description: Connect to the California Data Exchange Center (CDEC)
Web Service <http://cdec.water.ca.gov/>. 'CDEC' provides a centralized
database to store, process, and exchange real-time hydrologic information
gathered by various cooperators throughout California. The 'CDEC' Web Service
<http://cdec.water.ca.gov/dynamicapp/wsSensorData> provides a data download
service for accessing historical records.
Author: Michael Koohafkan [aut, cre]
Maintainer: Michael Koohafkan <michael.koohafkan@gmail.com>
Diff between cder versions 0.1-0 dated 2019-08-03 and 0.2-0 dated 2019-08-07
cder-0.1-0/cder/man/cder_query.Rd |only cder-0.2-0/cder/DESCRIPTION | 14 ++-- cder-0.2-0/cder/MD5 | 27 +++++-- cder-0.2-0/cder/NAMESPACE | 7 ++ cder-0.2-0/cder/R/deprecated.r |only cder-0.2-0/cder/R/list.r |only cder-0.2-0/cder/R/query.r | 104 +++++++++++++++++++++++++++--- cder-0.2-0/cder/inst/doc/quickstart.html | 105 ++++++++++++++++--------------- cder-0.2-0/cder/inst/doc/quickstart.rmd | 81 +++++++++++++---------- cder-0.2-0/cder/man/Deprecated.Rd |only cder-0.2-0/cder/man/basic_query.Rd | 2 cder-0.2-0/cder/man/cdec-search.Rd |only cder-0.2-0/cder/man/cdec_meta.Rd |only cder-0.2-0/cder/man/cdec_query.Rd |only cder-0.2-0/cder/man/cdec_query_group.Rd |only cder-0.2-0/cder/man/group.spec.Rd |only cder-0.2-0/cder/man/station.spec.Rd |only cder-0.2-0/cder/tests |only cder-0.2-0/cder/vignettes/quickstart.rmd | 81 +++++++++++++---------- 19 files changed, 278 insertions(+), 143 deletions(-)
Title: Sparse Identification of Nonlinear Dynamics
Description: This implements the Brunton et al (2016; PNAS <doi:10.1073/pnas.1517384113>) sparse
identification algorithm for finding ordinary differential equations for a measured
system from raw data (SINDy). The package includes a set of additional tools for
working with raw data, with an emphasis on cognitive science applications (Dale
and Bhat, in press <doi:10.1016/j.cogsys.2018.06.020>).
Author: Rick Dale and Harish S. Bhat
Maintainer: Rick Dale <racdale@gmail.com>
Diff between sindyr versions 0.2.1 dated 2018-09-10 and 0.2.2 dated 2019-08-07
DESCRIPTION | 8 ++++---- MD5 | 4 ++-- R/sindy.R | 7 ++++--- 3 files changed, 10 insertions(+), 9 deletions(-)
Title: Helper Functions for 'mlr3'
Description: Frequently used helper functions and assertions
used in 'mlr3' and its companion packages. Comes with helper functions
for functional programming, for printing, to work with 'data.table',
as well as some generally useful 'R6' classes. This package also
supersedes the package 'BBmisc'.
Author: Michel Lang [cre, aut] (<https://orcid.org/0000-0001-9754-0393>)
Maintainer: Michel Lang <michellang@gmail.com>
Diff between mlr3misc versions 0.1.1 dated 2019-07-23 and 0.1.2 dated 2019-08-07
DESCRIPTION | 8 ++--- MD5 | 46 +++++++++++++++++++++------------- NAMESPACE | 8 +++++ NEWS.md | 16 ++++++++++- R/Dictionary.R | 20 ++++++++------ R/distinct_values.R |only R/encapsulate.R | 11 ++++---- R/keep_in_bounds.R |only R/named_list.R | 2 - R/named_vector.R |only R/rowwise_table.R | 11 ++++++-- R/set_names.R | 18 +++++++++++-- README.md | 4 ++ man/Dictionary.Rd | 12 ++++---- man/distinct_values.Rd |only man/encapsulate.Rd | 11 ++++---- man/keep_in_bounds.Rd |only man/named_list.Rd | 2 - man/named_vector.Rd |only man/rowwise_table.Rd | 6 +++- man/set_names.Rd | 10 +++++-- src |only tests/testthat/setup.R | 3 ++ tests/testthat/test_Dictionary.R | 9 ++++++ tests/testthat/test_distinct_values.R |only tests/testthat/test_keep_in_bounds.R |only tests/testthat/test_named_vector.R |only tests/testthat/test_rowwise_table.R | 3 ++ tests/testthat/test_set_names.R |only 29 files changed, 140 insertions(+), 60 deletions(-)
Title: Tools for St. Louis Crime Data
Description: Provides a set of tools for creating yearly data sets of St. Louis
Metropolitan Police Department (SLMPD) crime data, which are available from
January 2008 onward as monthly CSV releases on their website
(<http:www.slmpd.org/Crimereports.shtml>). Once data are validated and created
(monthly data releases have varying numbers of columns
as well as different column names and formats), 'compstatr' also provides
functions for categorizing and mapping crimes in St. Louis. The categorization
tools that are provided will also work with any police department that uses 5
and 6 digit numeric codes to identify specific crimes. These data provide researchers
and policy makers detailed data for St. Louis, which in the last several years
has had some of the highest or the highest violent crime rates in the United States.
Author: Christopher Prener [aut, cre],
Cree Foeller [aut],
Taylor Braswell [com]
Maintainer: Christopher Prener <chris.prener@slu.edu>
Diff between compstatr versions 0.1.1 dated 2019-04-24 and 0.2.0 dated 2019-08-07
DESCRIPTION | 10 - MD5 | 100 ++++++++------- NAMESPACE | 19 ++ NEWS.md | 9 + R/address.R | 2 R/categorize.R | 8 - R/collapse.R | 27 +--- R/create.R | 14 +- R/dates.R | 4 R/filter.R | 4 R/get.R |only R/index.R |only R/january2018.R | 40 +++--- R/last_update.R |only R/spatial.R | 12 - R/standardize.R | 87 ++++--------- R/validate.R | 24 +-- README.md | 102 ++++++++++++--- build/vignette.rds |binary data/january2018.rda |binary inst/doc/compstatr.Rmd | 85 ++++++++++-- inst/doc/compstatr.html | 238 +++++++++++++++++++++--------------- inst/testdata/year17.rda |binary inst/testdata/yearList10.rda |binary inst/testdata/yearList13.rda |binary inst/testdata/yearList17.rda |binary inst/testdata/yearList18.rda |binary man/cs_address.Rd | 2 man/cs_create_index.Rd |only man/cs_crime.Rd | 2 man/cs_crime_cat.Rd | 6 man/cs_filter_count.Rd | 2 man/cs_filter_crime.Rd | 2 man/cs_get_data.Rd |only man/cs_last_update.Rd |only man/cs_missingXY.Rd | 2 man/cs_parse_date.Rd | 2 man/cs_parse_month.Rd | 2 man/cs_projectXY.Rd | 6 man/cs_replace0.Rd | 4 man/january2018.Rd | 40 +++--- tests/testthat/test_address.R | 16 +- tests/testthat/test_crime.R | 74 +++++------ tests/testthat/test_crime_cat.R | 20 +-- tests/testthat/test_extract_month.R | 4 tests/testthat/test_filter_count.R | 8 - tests/testthat/test_filter_crime.R | 70 +++++----- tests/testthat/test_get_data.R |only tests/testthat/test_last_update.R |only tests/testthat/test_missingXY.R | 14 +- tests/testthat/test_parse_date.R | 12 - tests/testthat/test_parse_month.R | 10 - tests/testthat/test_projectXY.R | 16 +- tests/testthat/test_replace0.R | 14 +- vignettes/compstatr.Rmd | 85 ++++++++++-- 55 files changed, 707 insertions(+), 491 deletions(-)
Title: A GeoJson Processing Toolkit
Description: Includes functions for processing GeoJson objects <https://en.wikipedia.org/wiki/GeoJSON> relying on 'RFC 7946' <https://tools.ietf.org/pdf/rfc7946.pdf>. The geojson encoding is based on 'json11', a tiny JSON library for 'C++11' <https://github.com/dropbox/json11>. Furthermore, the source code is exported in R through the 'Rcpp' and 'RcppArmadillo' packages.
Author: Lampros Mouselimis <mouselimislampros@gmail.com>
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>
Diff between geojsonR versions 1.0.6 dated 2018-09-23 and 1.0.7 dated 2019-08-07
DESCRIPTION | 10 ++++---- MD5 | 28 +++++++++++------------ NAMESPACE | 2 - NEWS.md | 9 ++++++- R/RcppExports.R | 4 +-- R/utils.R | 45 +++++++++++++++++++++++-------------- README.md | 2 - inst/doc/the_geojsonR_package.html | 37 +++++++++++++++++++++++++++--- man/Dump_From_GeoJson.Rd | 7 +++-- man/FROM_GeoJson.Rd | 11 ++++----- man/Features_2Collection.Rd | 23 +++++++++++++----- src/FROM_geojson.cpp | 38 +++++++++++++++++++++++++------ src/RcppExports.cpp | 7 +++-- src/init.c | 4 +-- tests/testthat/test-geojson.R | 13 ++++++++++ 15 files changed, 167 insertions(+), 73 deletions(-)
Title: Automatic Short Form Creation
Description: Performs automatic creation of short forms of scales with an
ant colony optimization algorithm and a Tabu search. As implemented in the
package, the ant colony algorithm randomly selects items to build a model of
a specified length, then updates the probability of item selection according
to the fit of the best model within each set of searches. The algorithm
continues until the same items are selected by multiple ants a given number
of times in a row. On the other hand, the Tabu search changes one parameter at
a time to be either free, constrained, or fixed while keeping track of the
changes made and putting changes that result in worse fit in a "tabu" list
so that the algorithm does not revisit them for some number of searches.
See Leite, Huang, & Marcoulides (2008) <doi:10.1080/00273170802285743> for
an applied example of the ant colony algorithm, and Marcoulides & Falk (2018)
<doi:10.1080/10705511.2017.1409074> for an applied example of the Tabu search.
Author: Anthony Raborn [aut, cre],
Walter Leite [aut]
Maintainer: Anthony Raborn <anthony.w.raborn@gmail.com>
Diff between ShortForm versions 0.4.2 dated 2018-10-17 and 0.4.3 dated 2019-08-07
DESCRIPTION | 10 +- MD5 | 20 ++--- R/ACO_lavaan.R | 56 ++++++++++------ R/Tabu_sem.R | 67 ++++++++++--------- R/Tabu_shortform.R | 133 ++++++++++++++++++++------------------ R/shortform_plots.R | 35 ++++++++-- R/simulated_annealing_internals.R | 120 ++++++++++++++++++++-------------- man/antcolony.lavaan.Rd | 16 ++-- man/plot.Rd | 8 +- man/tabu.sem.Rd | 8 +- man/tabuShortForm.Rd | 2 11 files changed, 277 insertions(+), 198 deletions(-)
Title: Quantile Regression
Description: Estimation and inference methods for models of conditional quantiles:
Linear and nonlinear parametric and non-parametric (total variation penalized) models
for conditional quantiles of a univariate response and several methods for handling
censored survival data. Portfolio selection methods based on expected shortfall
risk are also included.
Author: Roger Koenker [cre, aut],
Stephen Portnoy [ctb] (Contributions to Censored QR code),
Pin Tian Ng [ctb] (Contributions to Sparse QR code),
Achim Zeileis [ctb] (Contributions to dynrq code essentially identical
to his dynlm code),
Philip Grosjean [ctb] (Contributions to nlrq code),
Brian D Ripley [trl, ctb] (Initial (2001) R port from S (to my
everlasting shame -- how could I have been so slow to adopt R!) and
for numerous other suggestions and useful advice)
Maintainer: Roger Koenker <rkoenker@illinois.edu>
Diff between quantreg versions 5.42.1 dated 2019-07-27 and 5.51 dated 2019-08-07
DESCRIPTION | 6 +++--- MD5 | 14 +++++++------- build/vignette.rds |binary inst/ChangeLog | 1 + man/plot.summary.rqs.Rd | 6 +++--- man/rq.Rd | 2 +- src/ratfor/rqbr.r | 3 ++- src/rqbr.f | 14 +++++++------- 8 files changed, 24 insertions(+), 22 deletions(-)
Title: Render Markdown with the C Library 'Sundown'
Description: Provides R bindings to the 'Sundown' Markdown rendering library
(<https://github.com/vmg/sundown>). Markdown is a plain-text formatting
syntax that can be converted to 'XHTML' or other formats. See
<http://en.wikipedia.org/wiki/Markdown> for more information about Markdown.
Author: JJ Allaire [aut],
Jeffrey Horner [aut],
Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>),
Henrik Bengtsson [ctb],
Jim Hester [ctb],
Yixuan Qiu [ctb],
Kohske Takahashi [ctb],
Adam November [ctb],
Nacho Caballero [ctb],
Jeroen Ooms [ctb],
Thomas Leeper [ctb],
Joe Cheng [ctb],
Andrzej Oles [ctb],
Vicent Marti [aut, cph] (The Sundown library),
Natacha Porte [aut, cph] (The Sundown library),
RStudio [cph]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between markdown versions 1.0 dated 2019-06-07 and 1.1 dated 2019-08-07
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS | 7 +++++++ R/renderMarkdown.R | 3 +-- build/vignette.rds |binary 5 files changed, 16 insertions(+), 10 deletions(-)
More information about DistributionTest at CRAN
Permanent link
Title: Efficient Bayesian Inference for Time-Varying Parameter Models
with Shrinkage
Description: Efficient Markov chain Monte Carlo (MCMC) algorithms for fully Bayesian estimation of time-varying parameter models with shrinkage priors. Details on the algorithms used are provided in Bitto and Frühwirth-Schnatter (2019) <doi:10.1016/j.jeconom.2018.11.006>.
Author: Peter Knaus [aut, cre] (<https://orcid.org/0000-0001-6498-7084>),
Angela Bitto-Nemling [aut],
Annalisa Cadonna [aut] (<https://orcid.org/0000-0003-0360-7628>),
Sylvia Frühwirth-Schnatter [aut]
(<https://orcid.org/0000-0003-0516-5552>),
Daniel Winkler [ctb],
Kemal Dingic [ctb]
Maintainer: Peter Knaus <peter.knaus@wu.ac.at>
Diff between shrinkTVP versions 1.0.1 dated 2019-07-15 and 1.0.2 dated 2019-08-07
DESCRIPTION | 9 +++++---- MD5 | 20 ++++++++++++++++---- NEWS.md | 5 +++++ R/simTVP.R | 5 +---- build |only inst |only src/log_ratio_value.cpp | 2 +- vignettes |only 8 files changed, 28 insertions(+), 13 deletions(-)
Title: Sensitivity Analysis and Optimum Experiment Design for Microbial
Inactivation
Description: Extends the bioinactivation package with functions for Sensitivity
Analysis and Optimum Experiment Design.
Author: Alberto Garre [aut, cre],
Jose Lucas Penalver-Soto [aut],
Pablo S. Fernandez [aut],
Jose A. Egea [aut]
Maintainer: Alberto Garre <garre.alberto@gmail.com>
Diff between bioOED versions 0.1.4 dated 2018-04-17 and 0.2.1 dated 2019-08-07
DESCRIPTION | 20 MD5 | 70 ++- NAMESPACE | 29 + NEWS.md | 19 R/FIM_calculation.R | 174 ++++---- R/OED_isothermal.R |only R/OED_isothermal_limit.R |only R/OED_noPenalty.R | 3 R/OED_penalty.R | 5 R/calculate_sensitivity.R | 202 ++++----- R/detection_limits.R |only R/isothermal_S3.R |only R/isothermal_criterions.R |only R/isothermal_sensitivities.R |only R/methods_S3.R | 122 ++--- R/optimize_ref_temp.R | 322 +++++++-------- R/zzz.R |only build/vignette.rds |binary inst/doc/vignette_bioOED.R | 32 - inst/doc/vignette_bioOED.Rmd | 39 - inst/doc/vignette_bioOED.html | 648 ++++++++++++++++--------------- inst/doc/vignette_bioOED_isothermal.R |only inst/doc/vignette_bioOED_isothermal.Rmd |only inst/doc/vignette_bioOED_isothermal.html |only man/calculate_isothermal_FIM.Rd |only man/calculate_limit.Rd |only man/calculate_pars_correlation.Rd | 4 man/criterium_A_iso.Rd |only man/criterium_Amod_iso.Rd |only man/criterium_D_iso.Rd |only man/criterium_E_iso.Rd |only man/criterium_Emod_iso.Rd |only man/detFIM.Rd |only man/detection_bigelow.Rd |only man/detection_mafart.Rd |only man/detection_peleg.Rd |only man/get_detection.Rd |only man/get_isothermal_correlation.Rd |only man/inactivation_OED.Rd | 7 man/inactivation_OED_penalty.Rd | 12 man/inactivation_sens_handler.Rd | 4 man/isothermal_OED.Rd |only man/isothermal_OED_limit.Rd |only man/isothermal_sensitivities.Rd |only man/plot.IsoSensitivities.Rd |only man/plot.OEDisothermal.Rd |only man/sensitivities_Bigelow.Rd |only man/sensitivities_Mafart.Rd |only man/sensitivities_Peleg.Rd |only man/sensitivity_inactivation.Rd | 5 vignettes/vignette_bioOED.Rmd | 39 - vignettes/vignette_bioOED_isothermal.Rmd |only 52 files changed, 938 insertions(+), 818 deletions(-)
Title: Open Machine Learning and Open Data Platform
Description: We provide an R interface to 'OpenML.org' which is an online machine learning platform where researchers can access open data, download and upload data sets, share their machine learning tasks and experiments and organize them online to work and collaborate with other researchers.
The R interface allows to query for data sets with specific properties, and allows the downloading and uploading of data sets, tasks, flows and runs.
See <https://www.openml.org/guide/api> for more information.
Author: Giuseppe Casalicchio <giuseppe.casalicchio@stat.uni-muenchen.de>,
Bernd Bischl <bernd_bischl@gmx.net>,
Dominik Kirchhoff <dom.kirchhoff@gmail.com>,
Michel Lang <michellang@gmail.com>,
Benjamin Hofner <benjamin.hofner@fau.de>,
Jakob Bossek <j.bossek@gmail.com>,
Pascal Kerschke <kerschke@uni-muenster.de>,
Joaquin Vanschoren <joaquin.vanschoren@gmail.com>
Maintainer: Giuseppe Casalicchio <giuseppe.casalicchio@stat.uni-muenchen.de>
Diff between OpenML versions 1.8 dated 2018-03-02 and 1.9 dated 2019-08-07
DESCRIPTION | 15 MD5 | 158 +-- NAMESPACE | 5 NEWS | 10 R/OMLDataSetDescription_Class.R | 6 R/OMLDataSet_Class.R | 28 R/OMLFlow_Class.R | 2 R/OMLRunParList_Class.R | 13 R/OMLRun_Class.R | 2 R/OMLSeedParList_Class.R | 11 R/OMLStudy_Class.R |only R/OMLTask_Class.R | 2 R/chunkOMLlist.R | 1 R/convertMlrLearnerToOMLFlow.R | 25 R/convertOMLDataSetToMlr.R | 6 R/convertOMLRunToBMR.R | 2 R/convertOMLSplitsToMlr.R | 8 R/deleteOMLObject.R | 4 R/download.R | 2 R/extractOMLStudyIds.R | 11 R/getOMLDataSet.R | 11 R/getOMLStudy.R | 18 R/helpers.R | 6 R/listOMLEstimationProcedures.R | 12 R/listOMLRuns.R | 5 R/listOMLStudies.R | 60 - R/runTaskMlr.R | 3 R/uploadOMLDataSet.R | 8 R/uploadOMLStudy.R |only R/uploadOMLTask.R |only R/writeOMLDataSetXML.R | 4 R/writeOMLStudyXML.R |only R/writeOMLTaskXML.R |only R/zzz.R | 3 build/vignette.rds |binary inst/doc/OpenML.html | 1863 ++++++++++++++++++++++++++++++++++--- man/OMLDataSet.Rd | 8 man/OMLDataSetDescription.Rd | 12 man/chunkOMLlist.Rd | 1 man/configuration.Rd | 1 man/convertMlrTaskToOMLDataSet.Rd | 1 man/convertOMLDataSetToMlr.Rd | 1 man/convertOMLFlowToMlr.Rd | 1 man/convertOMLMlrRunToBMR.Rd | 1 man/convertOMLRunToBMR.Rd | 1 man/convertOMLTaskToMlr.Rd | 6 man/deleteOMLObject.Rd | 6 man/extractOMLStudyIds.Rd | 7 man/getOMLConfig.Rd | 1 man/getOMLDataSet.Rd | 2 man/getOMLDataSetQualities.Rd | 1 man/getOMLFlow.Rd | 2 man/getOMLRun.Rd | 5 man/getOMLStudy.Rd | 1 man/getOMLTask.Rd | 2 man/listOMLDataSetQualities.Rd | 1 man/listOMLDataSets.Rd | 10 man/listOMLEstimationProcedures.Rd | 1 man/listOMLEvaluationMeasures.Rd | 1 man/listOMLFlows.Rd | 5 man/listOMLRunEvaluations.Rd | 1 man/listOMLRuns.Rd | 7 man/listOMLSetup.Rd | 1 man/listOMLStudies.Rd | 29 man/listOMLTaskTypes.Rd | 2 man/listOMLTasks.Rd | 4 man/loadOMLConfig.Rd | 1 man/makeOMLFlow.Rd | 7 man/makeOMLFlowParameter.Rd | 1 man/makeOMLRun.Rd | 8 man/makeOMLRunParameter.Rd | 1 man/makeOMLStudy.Rd |only man/makeOMLTask.Rd | 3 man/runTaskFlow.Rd | 1 man/runTaskMlr.Rd | 5 man/saveOMLConfig.Rd | 1 man/setOMLConfig.Rd | 1 man/tagging.Rd | 4 man/uploadOMLDataSet.Rd | 7 man/uploadOMLFlow.Rd | 10 man/uploadOMLRun.Rd | 11 man/uploadOMLStudy.Rd |only man/uploadOMLTask.Rd |only vignettes/OpenML.Rmd | 24 84 files changed, 2134 insertions(+), 377 deletions(-)
Title: Interact with the 'OneLogin' API
Description: The identity provider ['OneLogin']<http://onelogin.com> is used for
authentication via Single Sign On (SSO). This package provides an R interface to their API.
Author: Alex Gold [aut, cre],
Cole Arendt [ctb]
Maintainer: Alex Gold <alexkgold@gmail.com>
Diff between onelogin versions 0.1.0 dated 2019-07-30 and 0.2.0 dated 2019-08-07
DESCRIPTION | 8 +- MD5 | 39 +++++++++-- NAMESPACE | 26 +++++++ R/invites.R |only R/onelogin.R | 138 ++++++++++++++++++++++++++++++++++++--- R/roles.R |only R/tokens.R |only R/users.R |only R/utils-pipe.R |only README.md |only man/ol_invite_gen_link.Rd |only man/ol_invite_send_link.Rd |only man/ol_role_get_by_id.Rd |only man/ol_roles_get.Rd |only man/ol_token_get.Rd |only man/ol_token_get_rate_limit.Rd |only man/ol_token_refresh.Rd |only man/ol_token_revoke.Rd |only man/ol_user_assign_role.Rd |only man/ol_user_create.Rd |only man/ol_user_delete.Rd |only man/ol_user_get_apps.Rd |only man/ol_user_get_by_id.Rd |only man/ol_user_get_custom_fields.Rd |only man/ol_user_get_roles.Rd |only man/ol_user_lock_account.Rd |only man/ol_user_log_out.Rd |only man/ol_user_pwd_cleartext.Rd |only man/ol_user_pwd_sha256_salt.Rd |only man/ol_user_remove_role.Rd |only man/ol_user_set_custom_attr.Rd |only man/ol_user_set_state.Rd |only man/ol_user_update.Rd |only man/ol_users_get.Rd |only man/onelogin.Rd | 4 - man/pipe.Rd |only 36 files changed, 197 insertions(+), 18 deletions(-)
Title: Statistical Reporting for Scientific Publications,
Epidemiological Studies and Clinical Trials
Description: Export to 'Microsoft Word' or R markdown documents nicely formatted tables of descriptive or inferential statistics. Can be used within the scope of clinical trials, or for any scientific publications. Descriptive tables for quantitative statistics (mean, median, max etc..) and/or qualitative statistics (frequencies and percentages) are available along with formatted tables of Least Square Means of Linear Models, Linear Mixed Models, Cox Models and Generalized Linear Mixed Models. It works mainly with 'emmeans' 'officer' and 'flextable' packages.
Author: Jean-Francois Collin
Maintainer: Jean-Francois Collin <jfcollin@live.fr>
Diff between ClinReport versions 0.9.1.12 dated 2019-04-02 and 0.9.1.13.1 dated 2019-08-07
ClinReport-0.9.1.12/ClinReport/R/data-data.R |only ClinReport-0.9.1.12/ClinReport/data/data.RData |only ClinReport-0.9.1.12/ClinReport/man/data.Rd |only ClinReport-0.9.1.13.1/ClinReport/DESCRIPTION | 16 ClinReport-0.9.1.13.1/ClinReport/MD5 | 126 - ClinReport-0.9.1.13.1/ClinReport/NAMESPACE | 5 ClinReport-0.9.1.13.1/ClinReport/NEWS.md | 31 ClinReport-0.9.1.13.1/ClinReport/R/add.stat.desc.R | 18 ClinReport-0.9.1.13.1/ClinReport/R/data.R |only ClinReport-0.9.1.13.1/ClinReport/R/desc.R | 7 ClinReport-0.9.1.13.1/ClinReport/R/gg_desc_lsmeans.R | 9 ClinReport-0.9.1.13.1/ClinReport/R/gg_desc_quali.R | 25 ClinReport-0.9.1.13.1/ClinReport/R/gg_desc_quanti.R | 8 ClinReport-0.9.1.13.1/ClinReport/R/make.label.R |only ClinReport-0.9.1.13.1/ClinReport/R/pkgname.R | 15 ClinReport-0.9.1.13.1/ClinReport/R/plot.desc.R | 13 ClinReport-0.9.1.13.1/ClinReport/R/prettyp.R | 2 ClinReport-0.9.1.13.1/ClinReport/R/print.desc.R | 12 ClinReport-0.9.1.13.1/ClinReport/R/regroup.desc.R | 17 ClinReport-0.9.1.13.1/ClinReport/R/report.doc.R | 130 - ClinReport-0.9.1.13.1/ClinReport/R/report.lsmeans.R | 250 +- ClinReport-0.9.1.13.1/ClinReport/R/report.modelinfo.R |only ClinReport-0.9.1.13.1/ClinReport/R/report.quali.R | 158 + ClinReport-0.9.1.13.1/ClinReport/R/report.quanti.R | 102 - ClinReport-0.9.1.13.1/ClinReport/R/spacetable.R | 4 ClinReport-0.9.1.13.1/ClinReport/R/split.desc.R | 4 ClinReport-0.9.1.13.1/ClinReport/README.md | 23 ClinReport-0.9.1.13.1/ClinReport/build/vignette.rds |binary ClinReport-0.9.1.13.1/ClinReport/data/datafake.rda |only ClinReport-0.9.1.13.1/ClinReport/data/time_to_cure.rda |only ClinReport-0.9.1.13.1/ClinReport/inst/TODO | 27 ClinReport-0.9.1.13.1/ClinReport/inst/data.creation.R | 27 ClinReport-0.9.1.13.1/ClinReport/inst/dev_check_build.R | 31 ClinReport-0.9.1.13.1/ClinReport/inst/doc/clinreport_graphics.R | 30 ClinReport-0.9.1.13.1/ClinReport/inst/doc/clinreport_graphics.Rmd | 38 ClinReport-0.9.1.13.1/ClinReport/inst/doc/clinreport_graphics.html | 680 +++---- ClinReport-0.9.1.13.1/ClinReport/inst/doc/clinreport_modify_outputs.R | 23 ClinReport-0.9.1.13.1/ClinReport/inst/doc/clinreport_modify_outputs.Rmd | 29 ClinReport-0.9.1.13.1/ClinReport/inst/doc/clinreport_modify_outputs.html | 720 +++---- ClinReport-0.9.1.13.1/ClinReport/inst/doc/clinreport_vignette_get_started.R | 45 ClinReport-0.9.1.13.1/ClinReport/inst/doc/clinreport_vignette_get_started.Rmd | 75 ClinReport-0.9.1.13.1/ClinReport/inst/doc/clinreport_vignette_get_started.html | 947 ++++------ ClinReport-0.9.1.13.1/ClinReport/inst/doc/clinreport_vignette_standard.R |only ClinReport-0.9.1.13.1/ClinReport/inst/doc/clinreport_vignette_standard.Rmd |only ClinReport-0.9.1.13.1/ClinReport/inst/doc/clinreport_vignette_standard.html |only ClinReport-0.9.1.13.1/ClinReport/inst/report.ae.R |only ClinReport-0.9.1.13.1/ClinReport/inst/test.R | 2 ClinReport-0.9.1.13.1/ClinReport/inst/transpose.desc.R |only ClinReport-0.9.1.13.1/ClinReport/man/ClinReport.Rd | 15 ClinReport-0.9.1.13.1/ClinReport/man/add.stat.Rd | 16 ClinReport-0.9.1.13.1/ClinReport/man/datafake.Rd |only ClinReport-0.9.1.13.1/ClinReport/man/desc.Rd | 7 ClinReport-0.9.1.13.1/ClinReport/man/figures/README-unnamed-chunk-1-1.png |binary ClinReport-0.9.1.13.1/ClinReport/man/gg_desc_lsmeans.Rd | 9 ClinReport-0.9.1.13.1/ClinReport/man/gg_desc_quali.Rd | 8 ClinReport-0.9.1.13.1/ClinReport/man/gg_desc_quanti.Rd | 8 ClinReport-0.9.1.13.1/ClinReport/man/make.label.Rd |only ClinReport-0.9.1.13.1/ClinReport/man/plot.desc.Rd | 13 ClinReport-0.9.1.13.1/ClinReport/man/prettyp.Rd | 2 ClinReport-0.9.1.13.1/ClinReport/man/regroup.Rd | 12 ClinReport-0.9.1.13.1/ClinReport/man/report.doc.Rd | 109 - ClinReport-0.9.1.13.1/ClinReport/man/report.lsmeans.Rd | 95 - ClinReport-0.9.1.13.1/ClinReport/man/report.modelinfo.Rd |only ClinReport-0.9.1.13.1/ClinReport/man/report.quali.Rd | 38 ClinReport-0.9.1.13.1/ClinReport/man/report.quanti.Rd | 42 ClinReport-0.9.1.13.1/ClinReport/man/spacetable.Rd | 4 ClinReport-0.9.1.13.1/ClinReport/man/split.desc.Rd | 4 ClinReport-0.9.1.13.1/ClinReport/man/time_to_cure.Rd |only ClinReport-0.9.1.13.1/ClinReport/vignettes/clinreport-vignette.R | 8 ClinReport-0.9.1.13.1/ClinReport/vignettes/clinreport_graphics.Rmd | 38 ClinReport-0.9.1.13.1/ClinReport/vignettes/clinreport_modify_outputs.Rmd | 29 ClinReport-0.9.1.13.1/ClinReport/vignettes/clinreport_vignette_get_started.Rmd | 75 ClinReport-0.9.1.13.1/ClinReport/vignettes/clinreport_vignette_standard.Rmd |only 73 files changed, 2212 insertions(+), 1969 deletions(-)
Title: R Interface to the 'QuantLib' Library
Description: The 'RQuantLib' package makes parts of 'QuantLib' accessible from R
The 'QuantLib' project aims to provide a comprehensive software framework
for quantitative finance. The goal is to provide a standard open source library
for quantitative analysis, modeling, trading, and risk management of financial
assets.
Author: Dirk Eddelbuettel, Khanh Nguyen (2009-2010), Terry Leitch (since 2016)
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between RQuantLib versions 0.4.9 dated 2019-05-19 and 0.4.10 dated 2019-08-07
ChangeLog | 17 +++++++++++++++++ DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- configure | 18 +++++++++--------- configure.ac | 2 +- inst/NEWS.Rd | 12 ++++++++++++ src/Makevars.win | 11 ++++++++--- tools/winlibs.R | 17 ++++++++++++----- 8 files changed, 70 insertions(+), 29 deletions(-)
Title: Hidden Markov Models with Discrete Non-Parametric Observation
Distributions
Description: Fits hidden Markov models with discrete non-parametric
observation distributions to data sets. The observations may
be univariate or bivariate. Simulates data from such models.
Finds most probable underlying hidden states, the most
probable sequences of such states, and the log likelihood
of a collection of observations given the parameters of
the model. Auxiliary predictors are accommodated in the
univariate setting.
Author: Rolf Turner
Maintainer: Rolf Turner <r.turner@auckland.ac.nz>
Diff between hmm.discnp versions 2.1-5 dated 2018-11-26 and 2.1-11 dated 2019-08-07
ChangeLog | 78 +++++++++++++++++++++++++ DESCRIPTION | 8 +- MD5 | 120 +++++++++++++++++++-------------------- NAMESPACE | 1 R/check.yval.R | 8 -- R/derivf.R | 37 +++++++----- R/derivp.R | 30 ++++++--- R/extract.multipleHmmDataSets.R |only R/ffun.R | 13 ++-- R/fitted.hmm.discnp.R | 30 +++------ R/hmm.R | 10 ++- R/hmmUV.R | 49 +++++++++++---- R/logLikHmm.R | 2 R/misstify.R | 34 ++++++++--- R/mps.R | 20 ++++-- R/nafracCalc.R | 15 ++++ R/pr.R | 22 ++++--- R/predict.hmm.discnp.R | 35 ++++++++--- R/predictEngineHmmDiscnp.R |only R/revise.ispd.R | 4 - R/rhmm.default.R | 6 + R/sp.R | 99 +++++++------------------------- R/update.hmm.discnp.R | 10 +-- R/viterbi.R | 18 ++++- data/Bovine.rda |binary data/Cryptosporidiosis.rda |binary data/Downloads.rda |binary data/EricssonB_Jul2.rda |binary data/FattyLiver.rda |binary data/FattyLiver2.rda |binary data/Hanta.rda |binary data/IPs.rda |binary data/InfantEEGsleepstates.rda |binary data/LegionnairesDisease.rda |binary data/OffshoreRigcountsAlaska.rda |binary data/PriceStability.rda |binary data/Strikes.rda |binary data/SydColDisc.rda |binary data/WoodPeweeSong.rda |binary data/ccprSim.rda |binary data/ftLiardFlows.rda |binary data/goldparticle380.rda |binary data/lesionCount.rda |binary data/linLandFlows.rda |binary data/portMannFlows.rda |binary data/portMannSedCon.rda |binary data/portMannSedLoads.rda |binary inst/Ratfor/bfun.r | 4 - inst/Ratfor/recurse.r | 2 man/fitted.hmm.discnp.Rd | 95 +++++++++++++++++++++++------- man/hmm.Rd | 16 +++-- man/hmm.discnp-internal.Rd | 9 ++ man/logLikHmm.Rd | 7 +- man/misstify.Rd | 70 ++++++++++++++++------ man/nafracCalc.Rd | 34 ++++++++--- man/predict.hmm.discnp.Rd | 89 ++++++++++++++++------------ man/sp.Rd | 110 ++++++++++++++--------------------- man/update.hmm.discnp.Rd | 7 +- man/viterbi.Rd | 24 ++++--- src/bfun.f | 4 - src/init.c | 2 src/recurse.f | 3 62 files changed, 688 insertions(+), 437 deletions(-)
Title: R Graphics Output in LaTeX Format
Description: Provides a graphics output device for R that records plots
in a LaTeX-friendly format. The device transforms plotting
commands issued by R functions into LaTeX code blocks. When
included in a LaTeX document, these blocks are interpreted with
the help of 'TikZ'---a graphics package for TeX and friends
written by Till Tantau. Using the 'tikzDevice', the text of R
plots can contain LaTeX commands such as mathematical formula.
The device also allows arbitrary LaTeX code to be inserted into
the output stream.
Author: Charlie Sharpsteen [aut],
Cameron Bracken [aut],
Kirill Müller [ctb],
Yihui Xie [ctb],
Ralf Stubner [cre],
Nico Bellack [ctb]
Maintainer: Ralf Stubner <ralf.stubner@gmail.com>
Diff between tikzDevice versions 0.12 dated 2018-07-02 and 0.12.3 dated 2019-08-07
DESCRIPTION | 19 ++++++++++--------- MD5 | 23 ++++++++++++----------- NEWS.md | 26 ++++++++++++++++++++++++++ R/latexStrWidth.R | 12 ++++++++---- R/tikz.R | 8 +++++--- R/tikzDevice-package.R | 6 +++--- build/vignette.rds |binary inst/doc/tikzDevice.pdf |binary man/tikz.Rd | 16 +++++++++------- man/tikzAnnotate.Rd | 4 ++-- man/tikzDevice-package.Rd | 6 +++--- src/tikzDevice.c | 30 ++++++++++++++++++++++++++---- tests/testthat/test_misc.R |only 13 files changed, 104 insertions(+), 46 deletions(-)
Title: Inferring Developmental Chronologies from Single-Cell RNA
Sequencing Data
Description: An accurate and easy tool for performing linear trajectory inference on
single cells using single-cell RNA sequencing data. In addition, SCORPIUS
provides functions for discovering the most important genes with respect to
the reconstructed trajectory, as well as nice visualisation tools.
Cannoodt et al. (2016) <doi:10.1101/079509>.
Author: Robrecht Cannoodt [aut, cre] (<https://orcid.org/0000-0003-3641-729X>,
rcannood),
Wouter Saelens [ctb] (<https://orcid.org/0000-0002-7114-6248>, zouter)
Maintainer: Robrecht Cannoodt <rcannood@gmail.com>
Diff between SCORPIUS versions 1.0.4 dated 2019-08-05 and 1.0.4.1 dated 2019-08-07
DESCRIPTION | 6 +++--- MD5 | 6 +++--- README.md | 2 -- tests/testthat/test-sparse.R | 11 +++++++---- 4 files changed, 13 insertions(+), 12 deletions(-)
Title: A Package for Statistical Analysis in Epidemiology
Description: Functions for demographic and epidemiological analysis in
the Lexis diagram, i.e. register and cohort follow-up data, in
particular representation, manipulation and simulation of multistate
data - the Lexis suite of functions, which includes interfaces to
'mstate', 'etm' and 'cmprsk' packages.
Also contains functions for Age-Period-Cohort and Lee-Carter
modeling and a function for interval censored data and some useful
functions for tabulation and plotting, as well as a number of
epidemiological data sets.
Author: Bendix Carstensen [aut, cre],
Martyn Plummer [aut],
Esa Laara [ctb],
Michael Hills [ctb]
Maintainer: Bendix Carstensen <b@bxc.dk>
Diff between Epi versions 2.37 dated 2019-05-23 and 2.38 dated 2019-08-07
Epi-2.37/Epi/R/qspr.R |only Epi-2.37/Epi/man/bdendo11.Rd |only Epi-2.37/Epi/vignettes/auto |only Epi-2.37/Epi/vignettes/simLexis.rwl |only Epi-2.37/Epi/vignettes/yll.rwl |only Epi-2.38/Epi/CHANGES | 16 Epi-2.38/Epi/DESCRIPTION | 10 Epi-2.38/Epi/MD5 | 129 +++---- Epi-2.38/Epi/R/poisreg.R | 50 +- Epi-2.38/Epi/R/twoby2.R | 11 Epi-2.38/Epi/data/bdendo.rda |binary Epi-2.38/Epi/data/bdendo11.rda |binary Epi-2.38/Epi/inst/doc/flup.R | 109 ++--- Epi-2.38/Epi/inst/doc/flup.pdf |binary Epi-2.38/Epi/inst/doc/simLexis.R | 16 Epi-2.38/Epi/inst/doc/simLexis.pdf |binary Epi-2.38/Epi/inst/doc/yll.R | 16 Epi-2.38/Epi/inst/doc/yll.pdf |binary Epi-2.38/Epi/man/N2Y.Rd | 2 Epi-2.38/Epi/man/Relevel.Rd | 2 Epi-2.38/Epi/man/bdendo.Rd | 21 - Epi-2.38/Epi/man/bootLexis.Rd | 2 Epi-2.38/Epi/man/ci.lin.Rd | 2 Epi-2.38/Epi/man/crr.Lexis.rd | 2 Epi-2.38/Epi/man/in.span.Rd | 2 Epi-2.38/Epi/man/lgrep.Rd | 2 Epi-2.38/Epi/man/matshade.Rd | 2 Epi-2.38/Epi/man/rbind.Lexis.Rd | 3 Epi-2.38/Epi/man/rm.tr.Rd | 2 Epi-2.38/Epi/man/simLexis.Rd | 2 Epi-2.38/Epi/vignettes/flup-Ieff.pdf |binary Epi-2.38/Epi/vignettes/flup-IeffR.pdf |binary Epi-2.38/Epi/vignettes/flup-RR-int.pdf |binary Epi-2.38/Epi/vignettes/flup-box1.pdf |binary Epi-2.38/Epi/vignettes/flup-box4.pdf |binary Epi-2.38/Epi/vignettes/flup-dmL1.pdf |binary Epi-2.38/Epi/vignettes/flup-dmL2.pdf |binary Epi-2.38/Epi/vignettes/flup-dur-int-RR.pdf |binary Epi-2.38/Epi/vignettes/flup-dur-int.pdf |binary Epi-2.38/Epi/vignettes/flup-ins-time.pdf |binary Epi-2.38/Epi/vignettes/flup-mbox.pdf |binary Epi-2.38/Epi/vignettes/flup-mboxr.pdf |binary Epi-2.38/Epi/vignettes/flup-pr-a.pdf |binary Epi-2.38/Epi/vignettes/flup-sep-HR.pdf |binary Epi-2.38/Epi/vignettes/flup-sep-mort.pdf | 6 Epi-2.38/Epi/vignettes/flup-splint.pdf |binary Epi-2.38/Epi/vignettes/flup.R | 109 ++--- Epi-2.38/Epi/vignettes/flup.pdf |binary Epi-2.38/Epi/vignettes/flup.rnw | 105 +++-- Epi-2.38/Epi/vignettes/flup.rwl | 113 +++--- Epi-2.38/Epi/vignettes/flup.tex | 190 +++++----- Epi-2.38/Epi/vignettes/simLexis-boxes.pdf |binary Epi-2.38/Epi/vignettes/simLexis-comp-0.pdf |binary Epi-2.38/Epi/vignettes/simLexis-mort-int.pdf |binary Epi-2.38/Epi/vignettes/simLexis-pstate0.pdf |binary Epi-2.38/Epi/vignettes/simLexis-pstatex.pdf |binary Epi-2.38/Epi/vignettes/simLexis-pstatey.pdf |binary Epi-2.38/Epi/vignettes/simLexis.R | 16 Epi-2.38/Epi/vignettes/simLexis.rnw | 2 Epi-2.38/Epi/vignettes/simLexis.tex | 492 ++++++++++++++++----------- Epi-2.38/Epi/vignettes/yll-imm.pdf |binary Epi-2.38/Epi/vignettes/yll-states.pdf |binary Epi-2.38/Epi/vignettes/yll-sus.pdf |binary Epi-2.38/Epi/vignettes/yll-tot.pdf |binary Epi-2.38/Epi/vignettes/yll.R | 16 Epi-2.38/Epi/vignettes/yll.pdf |binary Epi-2.38/Epi/vignettes/yll.rnw | 2 Epi-2.38/Epi/vignettes/yll.tex | 320 ++++++++++------- 68 files changed, 998 insertions(+), 774 deletions(-)
Title: Dimensionality Reduction Methods in a Common Format
Description: Provides a common interface for applying dimensionality reduction methods,
such as Principal Component Analysis ('PCA'), Independent Component Analysis ('ICA'), diffusion maps,
Locally-Linear Embedding ('LLE'), t-distributed Stochastic Neighbor Embedding ('t-SNE'),
and Uniform Manifold Approximation and Projection ('UMAP').
Has built-in support for sparse matrices.
Author: Robrecht Cannoodt [aut] (<https://orcid.org/0000-0003-3641-729X>,
rcannood),
Wouter Saelens [aut, cre] (<https://orcid.org/0000-0002-7114-6248>,
zouter)
Maintainer: Wouter Saelens <wouter.saelens@gmail.com>
Diff between dyndimred versions 1.0.1 dated 2019-05-24 and 1.0.2 dated 2019-08-07
DESCRIPTION | 14 ++++++++------ MD5 | 23 ++++++++++++----------- R/dimred.R | 1 + R/dimred_landmark_mds.R | 1 + R/dimred_tsne.R | 1 + R/dimred_umap.R | 1 + README.md |only inst/NEWS | 8 ++++++-- inst/NEWS.md | 8 ++++++-- man/dimred.Rd | 1 + man/dimred_landmark_mds.Rd | 1 + man/dimred_tsne.Rd | 1 + man/dimred_umap.Rd | 1 + 13 files changed, 40 insertions(+), 21 deletions(-)
Title: (Randomized) Quasi-Random Number Generators
Description: Functionality for generating (randomized) quasi-random numbers in
high dimensions.
Author: Marius Hofert [aut, cre],
Christiane Lemieux [aut]
Maintainer: Marius Hofert <marius.hofert@uwaterloo.ca>
Diff between qrng versions 0.0-5 dated 2018-06-21 and 0.0-6 dated 2019-08-07
DESCRIPTION | 8 MD5 | 30 NAMESPACE | 17 R/qrng.R | 58 R/test_functions.R |only TODO |only demo/00Index | 2 demo/basket_options.R | 6 demo/sobol_examples.R |only demo/test_functions.R | 4 man/qrng.Rd | 103 man/test_functions.Rd |only src/ghalton.c | 46 src/ghalton.h | 48 src/init.c | 2 src/korobov.c | 2 src/sobol.c |18367 +++++++++++++++++++++++++++++++++++++++++++++++++- src/sobol.h |18350 ------------------------------------------------- 18 files changed, 18531 insertions(+), 18512 deletions(-)
Title: k-Nearest Neighbor Join for Spatial Data
Description: K-nearest neighbor search for projected and non-projected 'sf' spatial layers. Nearest neighbor search uses (1) C code from 'GeographicLib' for lon-lat point layers, (2) function nn2() from package 'RANN' for projected point layers, or (3) function st_distance() from package 'sf' for line or polygon layers.
Author: Michael Dorman [aut, cre],
Johnathan Rush [ctb],
Ian Hough [ctb],
Charles F.F Karney [ctb, cph] (Author of included C code from
'GeographicLib' for geodesic distance)
Maintainer: Michael Dorman <dorman@post.bgu.ac.il>
Diff between nngeo versions 0.2.8 dated 2019-05-12 and 0.2.9 dated 2019-08-07
DESCRIPTION | 12 ++++++------ LICENSE | 2 +- MD5 | 34 ++++++++++++++++++++++++---------- NAMESPACE | 6 ++++++ NEWS.md | 13 ++++++++++--- R/data.R | 11 +++++++++++ R/raster_aspect.R |only R/raster_clump.R |only R/raster_extract.R |only R/raster_focal.R |only R/raster_slope.R |only R/raster_trim.R |only R/st_segments.R | 1 - build/vignette.rds |binary data/dem.RData |only inst/doc/intro.pdf |binary man/dem.Rd |only man/nngeo-package.Rd | 2 +- man/raster_aspect.Rd |only man/raster_clump.Rd |only man/raster_extract.Rd |only man/raster_focal.Rd |only man/raster_slope.Rd |only man/raster_trim.Rd |only man/st_segments.Rd | 1 - 25 files changed, 59 insertions(+), 23 deletions(-)
Title: Network Meta-Analysis using Frequentist Methods
Description: A comprehensive set of functions providing frequentist methods for network meta-analysis and supporting Schwarzer et al. (2015) <DOI:10.1007/978-3-319-21416-0>, Chapter 8 "Network Meta-Analysis":
- frequentist network meta-analysis following Rücker (2012) <DOI:10.1002/jrsm.1058>;
- net heat plot and design-based decomposition of Cochran's Q according to Krahn et al. (2013) <DOI:10.1186/1471-2288-13-35>;
- measures characterizing the flow of evidence between two treatments by König et al. (2013) <DOI:10.1002/sim.6001>;
- ranking of treatments (frequentist analogue of SUCRA) according to Rücker & Schwarzer (2015) <DOI:10.1186/s12874-015-0060-8>;
- partial order of treatment rankings ('poset') and Hasse diagram for 'poset' (Carlsen & Bruggemann, 2014) <DOI:10.1002/cem.2569>; (Rücker & Schwarzer, 2017) <DOI:10.1002/jrsm.1270>;
- split direct and indirect evidence to check consistency (Dias et al., 2010) <DOI:10.1002/sim.3767>, (Efthimiou et al., 2019) <DOI:10.1002/sim.8158>;
- league table with network meta-analysis results;
- additive network meta-analysis for combinations of treatments (Rücker et al., 2019) <DOI:10.1002/bimj.201800167>;
- network meta-analysis of binary data using the Mantel-Haenszel or non-central hypergeometric distribution method (Efthimiou et al., 2019) <DOI:10.1002/sim.8158>;
- 'comparison-adjusted' funnel plot (Chaimani & Salanti, 2012) <DOI:10.1002/jrsm.57>;
- automated drawing of network graphs described in Rücker & Schwarzer (2016) <DOI:10.1002/jrsm.1143>.
Author: Gerta Rücker [aut] (<https://orcid.org/0000-0002-2192-2560>),
Ulrike Krahn [aut],
Jochem König [aut] (<https://orcid.org/0000-0003-4683-0360>),
Orestis Efthimiou [aut] (<https://orcid.org/0000-0002-0955-7572>),
Guido Schwarzer [aut, cre] (<https://orcid.org/0000-0001-6214-9087>)
Maintainer: Guido Schwarzer <sc@imbi.uni-freiburg.de>
Diff between netmeta versions 1.0-1 dated 2019-01-02 and 1.1-0 dated 2019-08-07
netmeta-1.0-1/netmeta/R/print.netconnection.R |only netmeta-1.0-1/netmeta/R/print.netleague.R |only netmeta-1.0-1/netmeta/R/print.netposet.R |only netmeta-1.0-1/netmeta/R/print.netrank.R |only netmeta-1.0-1/netmeta/R/print.netsplit.R |only netmeta-1.0-1/netmeta/R/print.summary.netcomb.R |only netmeta-1.0-1/netmeta/R/print.summary.netmeta.R |only netmeta-1.0-1/netmeta/data/Dong2013.txt.gz |only netmeta-1.0-1/netmeta/data/Gurusamy2011.txt.gz |only netmeta-1.0-1/netmeta/data/Linde2015.csv.gz |only netmeta-1.0-1/netmeta/data/Linde2016.csv.gz |only netmeta-1.0-1/netmeta/data/Senn2013.txt.gz |only netmeta-1.0-1/netmeta/data/Woods2010.csv.gz |only netmeta-1.0-1/netmeta/data/dietaryfat.csv.gz |only netmeta-1.0-1/netmeta/data/parkinson.csv.gz |only netmeta-1.0-1/netmeta/data/smokingcessation.csv.gz |only netmeta-1.1-0/netmeta/DESCRIPTION | 46 netmeta-1.1-0/netmeta/MD5 | 207 - netmeta-1.1-0/netmeta/NAMESPACE | 195 - netmeta-1.1-0/netmeta/NEWS | 82 netmeta-1.1-0/netmeta/R/Dong2013.R |only netmeta-1.1-0/netmeta/R/Gurusamy2011.R |only netmeta-1.1-0/netmeta/R/Linde2015.R |only netmeta-1.1-0/netmeta/R/Linde2016.R |only netmeta-1.1-0/netmeta/R/Senn2013.R |only netmeta-1.1-0/netmeta/R/Woods2010.R |only netmeta-1.1-0/netmeta/R/as.data.frame.netmeta.R | 35 netmeta-1.1-0/netmeta/R/chkmultiarm.R | 2 netmeta-1.1-0/netmeta/R/decomp.design.R | 134 netmeta-1.1-0/netmeta/R/dietaryfat.R |only netmeta-1.1-0/netmeta/R/discomb.R | 1474 +++++--- netmeta-1.1-0/netmeta/R/forest-internal.R |only netmeta-1.1-0/netmeta/R/forest.netbind.R | 92 netmeta-1.1-0/netmeta/R/forest.netcomb.R | 137 netmeta-1.1-0/netmeta/R/forest.netmeta.R | 335 +- netmeta-1.1-0/netmeta/R/forest.netsplit.R | 142 netmeta-1.1-0/netmeta/R/funnel.netmeta.R | 170 + netmeta-1.1-0/netmeta/R/hasse.R | 99 netmeta-1.1-0/netmeta/R/multiarm.R | 36 netmeta-1.1-0/netmeta/R/netbind.R | 91 netmeta-1.1-0/netmeta/R/netcomb.R | 320 + netmeta-1.1-0/netmeta/R/netconnection.R | 178 + netmeta-1.1-0/netmeta/R/netdistance.R | 30 netmeta-1.1-0/netmeta/R/netgraph-internal.R |only netmeta-1.1-0/netmeta/R/netgraph.R | 906 ----- netmeta-1.1-0/netmeta/R/netgraph.netimpact.R |only netmeta-1.1-0/netmeta/R/netgraph.netmeta.R |only netmeta-1.1-0/netmeta/R/netheat.R | 105 netmeta-1.1-0/netmeta/R/netimpact.R |only netmeta-1.1-0/netmeta/R/netleague.R | 277 + netmeta-1.1-0/netmeta/R/netmatrix.R | 71 netmeta-1.1-0/netmeta/R/netmeasures.R | 113 netmeta-1.1-0/netmeta/R/netmeta-package.R |only netmeta-1.1-0/netmeta/R/netmeta.R | 512 ++- netmeta-1.1-0/netmeta/R/netmetabin.R | 3481 +++++++++++---------- netmeta-1.1-0/netmeta/R/netposet.R | 337 ++ netmeta-1.1-0/netmeta/R/netrank.R | 196 + netmeta-1.1-0/netmeta/R/netsplit.R | 590 +++ netmeta-1.1-0/netmeta/R/nma.additive.R | 3 netmeta-1.1-0/netmeta/R/pairwise.R | 389 ++ netmeta-1.1-0/netmeta/R/parkinson.R |only netmeta-1.1-0/netmeta/R/plot.netposet.R | 197 + netmeta-1.1-0/netmeta/R/plot.netrank.R |only netmeta-1.1-0/netmeta/R/print.decomp.design.R | 40 netmeta-1.1-0/netmeta/R/print.netbind.R | 54 netmeta-1.1-0/netmeta/R/print.netcomb.R | 63 netmeta-1.1-0/netmeta/R/print.netimpact.R |only netmeta-1.1-0/netmeta/R/print.netmeta.R | 81 netmeta-1.1-0/netmeta/R/smokingcessation.R |only netmeta-1.1-0/netmeta/R/stress.R | 8 netmeta-1.1-0/netmeta/R/summary.netcomb.R | 271 + netmeta-1.1-0/netmeta/R/summary.netmeta.R | 721 ++++ netmeta-1.1-0/netmeta/R/treats.R | 50 netmeta-1.1-0/netmeta/data/Dong2013.rda |only netmeta-1.1-0/netmeta/data/Gurusamy2011.rda |only netmeta-1.1-0/netmeta/data/Linde2015.rda |only netmeta-1.1-0/netmeta/data/Linde2016.rda |only netmeta-1.1-0/netmeta/data/Senn2013.rda |only netmeta-1.1-0/netmeta/data/Woods2010.rda |only netmeta-1.1-0/netmeta/data/dietaryfat.rda |only netmeta-1.1-0/netmeta/data/parkinson.rda |only netmeta-1.1-0/netmeta/data/smokingcessation.rda |only netmeta-1.1-0/netmeta/man/Dong2013.Rd | 63 netmeta-1.1-0/netmeta/man/Gurusamy2011.Rd | 63 netmeta-1.1-0/netmeta/man/Linde2015.Rd | 110 netmeta-1.1-0/netmeta/man/Linde2016.Rd | 51 netmeta-1.1-0/netmeta/man/Senn2013.Rd | 106 netmeta-1.1-0/netmeta/man/Woods2010.Rd | 63 netmeta-1.1-0/netmeta/man/as.data.frame.netmeta.Rd | 54 netmeta-1.1-0/netmeta/man/decomp.design.Rd | 257 - netmeta-1.1-0/netmeta/man/dietaryfat.Rd | 97 netmeta-1.1-0/netmeta/man/discomb.Rd | 519 +-- netmeta-1.1-0/netmeta/man/forest.netbind.Rd | 145 netmeta-1.1-0/netmeta/man/forest.netcomb.Rd | 192 - netmeta-1.1-0/netmeta/man/forest.netmeta.Rd | 308 + netmeta-1.1-0/netmeta/man/forest.netsplit.Rd | 298 - netmeta-1.1-0/netmeta/man/funnel.netmeta.Rd | 311 - netmeta-1.1-0/netmeta/man/hasse.Rd | 108 netmeta-1.1-0/netmeta/man/netbind.Rd | 125 netmeta-1.1-0/netmeta/man/netcomb.Rd | 416 +- netmeta-1.1-0/netmeta/man/netconnection.Rd | 138 netmeta-1.1-0/netmeta/man/netdistance.Rd | 40 netmeta-1.1-0/netmeta/man/netgraph.Rd | 359 -- netmeta-1.1-0/netmeta/man/netgraph.netimpact.Rd |only netmeta-1.1-0/netmeta/man/netgraph.netmeta.Rd |only netmeta-1.1-0/netmeta/man/netheat.Rd | 194 - netmeta-1.1-0/netmeta/man/netimpact.Rd |only netmeta-1.1-0/netmeta/man/netleague.Rd | 206 - netmeta-1.1-0/netmeta/man/netmatrix.Rd | 91 netmeta-1.1-0/netmeta/man/netmeasures.Rd | 191 - netmeta-1.1-0/netmeta/man/netmeta-package.Rd | 268 - netmeta-1.1-0/netmeta/man/netmeta.Rd | 831 ++--- netmeta-1.1-0/netmeta/man/netmetabin.Rd | 680 ++-- netmeta-1.1-0/netmeta/man/netposet.Rd | 310 - netmeta-1.1-0/netmeta/man/netrank.Rd | 185 - netmeta-1.1-0/netmeta/man/netsplit.Rd | 395 +- netmeta-1.1-0/netmeta/man/pairwise.Rd | 497 +- netmeta-1.1-0/netmeta/man/parkinson.Rd | 106 netmeta-1.1-0/netmeta/man/plot.netposet.Rd | 282 - netmeta-1.1-0/netmeta/man/plot.netrank.Rd |only netmeta-1.1-0/netmeta/man/print.decomp.design.Rd | 73 netmeta-1.1-0/netmeta/man/print.netbind.Rd | 54 netmeta-1.1-0/netmeta/man/print.netcomb.Rd | 158 netmeta-1.1-0/netmeta/man/print.netimpact.Rd |only netmeta-1.1-0/netmeta/man/print.netmeta.Rd | 267 - netmeta-1.1-0/netmeta/man/smokingcessation.Rd | 81 netmeta-1.1-0/netmeta/man/summary.netcomb.Rd |only netmeta-1.1-0/netmeta/man/summary.netmeta.Rd |only netmeta-1.1-0/netmeta/man/treats.Rd | 69 129 files changed, 13309 insertions(+), 7722 deletions(-)
Title: Landscape Metrics for Categorical Map Patterns
Description: Calculates landscape metrics for categorical landscape patterns in
a tidy workflow. 'landscapemetrics' reimplements the most common metrics from
'FRAGSTATS' (<https://www.umass.edu/landeco/research/fragstats/fragstats.html>)
and new ones from the current literature on landscape metrics.
This package supports 'raster' spatial objects and takes
RasterLayer, RasterStacks, RasterBricks or lists of RasterLayer from the
'raster' package as input arguments. It further provides utility functions
to visualize patches, select metrics and building blocks to develop new
metrics.
Author: Maximillian H.K. Hesselbarth [aut, cre]
(<https://orcid.org/0000-0003-1125-9918>),
Marco Sciaini [aut] (<https://orcid.org/0000-0002-3042-5435>),
Jakub Nowosad [aut] (<https://orcid.org/0000-0002-1057-3721>),
Sebastian Hanss [aut] (<https://orcid.org/0000-0002-3990-4897>),
Laura J. Graham [ctb] (Input on package structure),
Jeffrey Hollister [ctb] (Input on package structure),
Kimberly A. With [ctb] (Input on package structure),
Florian Privé [ctb] (Original author of underlying C++ code for
get_nearestneighbour() function),
Jeremy VanDerWal [ctb] (Original author of underlying C code for
get_patches() function),
Matt Strimas-Mackey [ctb] (Bugfix in sample_metrics())
Maintainer: Maximillian H.K. Hesselbarth <maximilian.hesselbarth@uni-goettingen.de>
Diff between landscapemetrics versions 1.2 dated 2019-07-02 and 1.2.1 dated 2019-08-07
DESCRIPTION | 6 MD5 | 744 ++-- NAMESPACE | 1874 +++++----- NEWS.md | 229 - R/RcppExports.R | 202 - R/calculate_correlation.R | 364 +- R/calculate_lsm.R | 936 ++--- R/construct_buffer.R | 360 +- R/data.R | 250 - R/data_info.R | 86 R/extract_lsm.R | 870 ++-- R/get_patches.R | 668 +-- R/landscapemetrics-package.R | 106 R/list_lsm.R | 410 +- R/lsm_l_condent.R | 354 +- R/lsm_l_ent.R | 308 - R/lsm_l_joinent.R | 336 - R/lsm_l_mutinf.R | 352 - R/matrix_to_raster.R | 164 R/onUnload.R | 16 R/options_landscapemetrics.R | 64 R/pad_raster.R | 546 +-- R/proj_info.R | 104 R/sample_lsm.R | 994 ++--- R/scale_sample.R | 802 ++-- R/scale_window.R | 780 ++-- R/show_correlation.R | 588 +-- R/spatialize_lsm.R | 592 +-- R/window_lsm.R | 982 ++--- build/vignette.rds |binary inst/CITATION | 28 inst/doc/getstarted.R | 190 - inst/doc/getstarted.Rmd | 364 +- inst/doc/getstarted.html | 1192 +++--- man/augusta_nlcd.Rd | 42 man/calculate_correlation.Rd | 68 man/calculate_lsm.Rd | 248 - man/check_landscape.Rd | 96 man/construct_buffer.Rd | 120 man/data_info.Rd | 54 man/extract_lsm.Rd | 196 - man/figures/README-unnamed-chunk-1-1.png |binary man/fragstats_class_augusta_nlcd.Rd | 32 man/fragstats_class_landscape.Rd | 32 man/fragstats_class_podlasie.Rd | 32 man/fragstats_landscape_augusta_nlcd.Rd | 32 man/fragstats_landscape_landscape.Rd | 32 man/fragstats_landscape_podlasie.Rd | 32 man/fragstats_patch_augusta_nlcd.Rd | 32 man/fragstats_patch_landscape.Rd | 32 man/fragstats_patch_podlasie.Rd | 32 man/get_adjacencies.Rd | 156 man/get_boundaries.Rd | 126 man/get_circumscribingcircle.Rd | 122 man/get_nearestneighbour.Rd | 104 man/get_patches.Rd | 194 - man/get_unique_values.Rd | 126 man/landscape.Rd | 36 man/landscapemetrics.Rd | 92 man/list_lsm.Rd | 112 man/lsm_abbreviations_names.Rd | 50 man/lsm_c_ai.Rd | 126 man/lsm_c_area_cv.Rd | 134 man/lsm_c_area_mn.Rd | 136 man/lsm_c_area_sd.Rd | 142 man/lsm_c_ca.Rd | 134 man/lsm_c_cai_cv.Rd | 166 man/lsm_c_cai_mn.Rd | 160 man/lsm_c_cai_sd.Rd | 164 man/lsm_c_circle_cv.Rd | 150 man/lsm_c_circle_mn.Rd | 146 man/lsm_c_circle_sd.Rd | 146 man/lsm_c_clumpy.Rd | 122 man/lsm_c_cohesion.Rd | 136 man/lsm_c_contig_cv.Rd | 156 man/lsm_c_contig_mn.Rd | 154 man/lsm_c_contig_sd.Rd | 156 man/lsm_c_core_cv.Rd | 158 man/lsm_c_core_mn.Rd | 154 man/lsm_c_core_sd.Rd | 156 man/lsm_c_cpland.Rd | 150 man/lsm_c_dcad.Rd | 156 man/lsm_c_dcore_cv.Rd | 164 man/lsm_c_dcore_mn.Rd | 158 man/lsm_c_dcore_sd.Rd | 164 man/lsm_c_division.Rd | 128 man/lsm_c_ed.Rd | 148 man/lsm_c_enn_cv.Rd | 158 man/lsm_c_enn_mn.Rd | 158 man/lsm_c_enn_sd.Rd | 158 man/lsm_c_frac_cv.Rd | 146 man/lsm_c_frac_mn.Rd | 138 man/lsm_c_frac_sd.Rd | 144 man/lsm_c_gyrate_cv.Rd | 148 man/lsm_c_gyrate_mn.Rd | 146 man/lsm_c_gyrate_sd.Rd | 146 man/lsm_c_iji.Rd | 132 man/lsm_c_lpi.Rd | 128 man/lsm_c_lsi.Rd | 134 man/lsm_c_mesh.Rd | 138 man/lsm_c_ndca.Rd | 158 man/lsm_c_nlsi.Rd | 132 man/lsm_c_np.Rd | 120 man/lsm_c_pafrac.Rd | 152 man/lsm_c_para_cv.Rd | 140 man/lsm_c_para_mn.Rd | 140 man/lsm_c_para_sd.Rd | 140 man/lsm_c_pd.Rd | 130 man/lsm_c_pladj.Rd | 114 man/lsm_c_pland.Rd | 126 man/lsm_c_shape_cv.Rd | 142 man/lsm_c_shape_mn.Rd | 142 man/lsm_c_shape_sd.Rd | 142 man/lsm_c_split.Rd | 134 man/lsm_c_tca.Rd | 156 man/lsm_c_te.Rd | 140 man/lsm_l_ai.Rd | 130 man/lsm_l_area_cv.Rd | 134 man/lsm_l_area_mn.Rd | 136 man/lsm_l_area_sd.Rd | 132 man/lsm_l_cai_cv.Rd | 166 man/lsm_l_cai_mn.Rd | 160 man/lsm_l_cai_sd.Rd | 164 man/lsm_l_circle_cv.Rd | 146 man/lsm_l_circle_mn.Rd | 144 man/lsm_l_circle_sd.Rd | 148 man/lsm_l_cohesion.Rd | 126 man/lsm_l_condent.Rd | 134 man/lsm_l_contag.Rd | 136 man/lsm_l_contig_cv.Rd | 156 man/lsm_l_contig_mn.Rd | 154 man/lsm_l_contig_sd.Rd | 156 man/lsm_l_core_cv.Rd | 160 man/lsm_l_core_mn.Rd | 156 man/lsm_l_core_sd.Rd | 158 man/lsm_l_dcad.Rd | 156 man/lsm_l_dcore_cv.Rd | 164 man/lsm_l_dcore_mn.Rd | 158 man/lsm_l_dcore_sd.Rd | 162 man/lsm_l_division.Rd | 134 man/lsm_l_ed.Rd | 148 man/lsm_l_enn_cv.Rd | 158 man/lsm_l_enn_mn.Rd | 158 man/lsm_l_enn_sd.Rd | 158 man/lsm_l_ent.Rd | 116 man/lsm_l_frac_cv.Rd | 146 man/lsm_l_frac_mn.Rd | 144 man/lsm_l_frac_sd.Rd | 144 man/lsm_l_gyrate_cv.Rd | 148 man/lsm_l_gyrate_mn.Rd | 146 man/lsm_l_gyrate_sd.Rd | 146 man/lsm_l_iji.Rd | 134 man/lsm_l_joinent.Rd | 128 man/lsm_l_lpi.Rd | 128 man/lsm_l_lsi.Rd | 134 man/lsm_l_mesh.Rd | 138 man/lsm_l_msidi.Rd | 132 man/lsm_l_msiei.Rd | 122 man/lsm_l_mutinf.Rd | 130 man/lsm_l_ndca.Rd | 158 man/lsm_l_np.Rd | 122 man/lsm_l_pafrac.Rd | 152 man/lsm_l_para_cv.Rd | 140 man/lsm_l_para_mn.Rd | 140 man/lsm_l_para_sd.Rd | 140 man/lsm_l_pd.Rd | 130 man/lsm_l_pladj.Rd | 114 man/lsm_l_pr.Rd | 110 man/lsm_l_prd.Rd | 120 man/lsm_l_rpr.Rd | 136 man/lsm_l_shape_cv.Rd | 142 man/lsm_l_shape_mn.Rd | 142 man/lsm_l_shape_sd.Rd | 142 man/lsm_l_shdi.Rd | 122 man/lsm_l_shei.Rd | 126 man/lsm_l_sidi.Rd | 132 man/lsm_l_siei.Rd | 132 man/lsm_l_split.Rd | 134 man/lsm_l_ta.Rd | 124 man/lsm_l_tca.Rd | 154 man/lsm_l_te.Rd | 124 man/lsm_p_area.Rd | 138 man/lsm_p_cai.Rd | 166 man/lsm_p_circle.Rd | 148 man/lsm_p_contig.Rd | 158 man/lsm_p_core.Rd | 164 man/lsm_p_enn.Rd | 158 man/lsm_p_frac.Rd | 146 man/lsm_p_gyrate.Rd | 142 man/lsm_p_ncore.Rd | 166 man/lsm_p_para.Rd | 140 man/lsm_p_perim.Rd | 118 man/lsm_p_shape.Rd | 144 man/matrix_to_raster.Rd | 82 man/options_landscapemetrics.Rd | 56 man/pad_raster.Rd | 136 man/podlasie_ccilc.Rd | 36 man/proj_info.Rd | 54 man/raster_to_points.Rd | 86 man/rcpp_cell_from_xy.Rd | 38 man/rcpp_create_neighborhood.Rd | 38 man/rcpp_get_nearest_neighbor.Rd | 44 man/rcpp_xy_from_matrix.Rd | 36 man/sample_lsm.Rd | 234 - man/scale_sample.Rd | 170 man/scale_window.Rd | 178 - man/show_cores.Rd | 148 man/show_correlation.Rd | 90 man/show_lsm.Rd | 140 man/show_patches.Rd | 112 man/spatialize_lsm.Rd | 144 man/window_lsm.Rd | 172 tests/testthat.R | 10 tests/testthat/helper-brick.R | 8 tests/testthat/helper-landscapes.R | 34 tests/testthat/helper-points.R | 36 tests/testthat/test-calculate-lsm.R | 238 - tests/testthat/test-calculate_correlation.R | 140 tests/testthat/test-check-landscape.R | 138 tests/testthat/test-construct-buffer.R | 62 tests/testthat/test-extract-lsm.R | 272 - tests/testthat/test-get-circumscribungcircle.R | 146 tests/testthat/test-get-patches.R | 46 tests/testthat/test-get-unique-values.R | 182 - tests/testthat/test-list-lsm.R | 182 - tests/testthat/test-lsm-c-area-cv.R | 48 tests/testthat/test-lsm-c-area-mn.R | 50 tests/testthat/test-lsm-c-area-sd.R | 48 tests/testthat/test-lsm-c-ca.R | 52 tests/testthat/test-lsm-c-cai-cv.R | 50 tests/testthat/test-lsm-c-cai-mn.R | 50 tests/testthat/test-lsm-c-cai-sd.R | 46 tests/testthat/test-lsm-c-circle-cv.R | 52 tests/testthat/test-lsm-c-circle-mn.R | 48 tests/testthat/test-lsm-c-circle-sd.R | 48 tests/testthat/test-lsm-c-clumpy.R | 48 tests/testthat/test-lsm-c-cohesion.R | 50 tests/testthat/test-lsm-c-contig-cv.R | 50 tests/testthat/test-lsm-c-contig-mn.R | 50 tests/testthat/test-lsm-c-contig-sd.R | 50 tests/testthat/test-lsm-c-core-cv.R | 46 tests/testthat/test-lsm-c-core-mn.R | 46 tests/testthat/test-lsm-c-core-sd.R | 46 tests/testthat/test-lsm-c-cpland.R | 48 tests/testthat/test-lsm-c-dcad.R | 48 tests/testthat/test-lsm-c-dcore_cv.R | 46 tests/testthat/test-lsm-c-dcore_mn.R | 46 tests/testthat/test-lsm-c-dcore_sd.R | 46 tests/testthat/test-lsm-c-division.R | 48 tests/testthat/test-lsm-c-ed.R | 48 tests/testthat/test-lsm-c-enn-cv.R | 46 tests/testthat/test-lsm-c-enn-mn.R | 46 tests/testthat/test-lsm-c-enn-sd.R | 46 tests/testthat/test-lsm-c-frac-cv.R | 46 tests/testthat/test-lsm-c-frac-mn.R | 46 tests/testthat/test-lsm-c-frac-sd.R | 46 tests/testthat/test-lsm-c-gyrate-cv.R | 46 tests/testthat/test-lsm-c-gyrate-mn.R | 46 tests/testthat/test-lsm-c-gyrate-sd.R | 46 tests/testthat/test-lsm-c-iji.R | 68 tests/testthat/test-lsm-c-lpi.R | 48 tests/testthat/test-lsm-c-lsi.R | 48 tests/testthat/test-lsm-c-mesh.R | 48 tests/testthat/test-lsm-c-ndca.R | 48 tests/testthat/test-lsm-c-nlsi.R | 48 tests/testthat/test-lsm-c-np.R | 48 tests/testthat/test-lsm-c-pafrac.R | 76 tests/testthat/test-lsm-c-para-cv.R | 46 tests/testthat/test-lsm-c-para-mn.R | 46 tests/testthat/test-lsm-c-para-sd.R | 46 tests/testthat/test-lsm-c-pd.R | 48 tests/testthat/test-lsm-c-pladj.R | 48 tests/testthat/test-lsm-c-pland.R | 48 tests/testthat/test-lsm-c-shape-cv.R | 46 tests/testthat/test-lsm-c-shape-mn.R | 46 tests/testthat/test-lsm-c-shape-sd.R | 46 tests/testthat/test-lsm-c-split.R | 48 tests/testthat/test-lsm-c-tca.R | 48 tests/testthat/test-lsm-c-te.R | 64 tests/testthat/test-lsm-l-ai.R | 48 tests/testthat/test-lsm-l-area-cv.R | 46 tests/testthat/test-lsm-l-area-mn.R | 50 tests/testthat/test-lsm-l-area-sd.R | 50 tests/testthat/test-lsm-l-cai-cv.R | 50 tests/testthat/test-lsm-l-cai-mn.R | 50 tests/testthat/test-lsm-l-cai-sd.R | 50 tests/testthat/test-lsm-l-circle-cv.R | 50 tests/testthat/test-lsm-l-circle-mn.R | 50 tests/testthat/test-lsm-l-circle-sd.R | 50 tests/testthat/test-lsm-l-cohesion.R | 48 tests/testthat/test-lsm-l-condent.R 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tests/testthat/test-lsm-l-joinent.R | 48 tests/testthat/test-lsm-l-lpi.R | 48 tests/testthat/test-lsm-l-lsi.R | 48 tests/testthat/test-lsm-l-mesh.R | 48 tests/testthat/test-lsm-l-msidi.R | 48 tests/testthat/test-lsm-l-msiei.R | 48 tests/testthat/test-lsm-l-mutinf.R | 48 tests/testthat/test-lsm-l-ndca.R | 48 tests/testthat/test-lsm-l-np.R | 48 tests/testthat/test-lsm-l-pafrac.R | 66 tests/testthat/test-lsm-l-para-cv.R | 46 tests/testthat/test-lsm-l-para-mn.R | 46 tests/testthat/test-lsm-l-para-sd.R | 46 tests/testthat/test-lsm-l-pd.R | 48 tests/testthat/test-lsm-l-pladj.R | 48 tests/testthat/test-lsm-l-pr.R | 48 tests/testthat/test-lsm-l-prd.R | 48 tests/testthat/test-lsm-l-rpr.R | 48 tests/testthat/test-lsm-l-shape-cv.R | 46 tests/testthat/test-lsm-l-shape-mn.R | 46 tests/testthat/test-lsm-l-shape-sd.R | 46 tests/testthat/test-lsm-l-shdi.R | 48 tests/testthat/test-lsm-l-shei.R | 48 tests/testthat/test-lsm-l-sidi.R | 48 tests/testthat/test-lsm-l-siei.R | 48 tests/testthat/test-lsm-l-split.R | 48 tests/testthat/test-lsm-l-ta.R | 48 tests/testthat/test-lsm-l-tca.R | 48 tests/testthat/test-lsm-l-te.R | 66 tests/testthat/test-lsm-p-area.R | 50 tests/testthat/test-lsm-p-cai.R | 46 tests/testthat/test-lsm-p-circle.R | 54 tests/testthat/test-lsm-p-contig.R | 50 tests/testthat/test-lsm-p-core.R | 68 tests/testthat/test-lsm-p-enn.R | 50 tests/testthat/test-lsm-p-frac.R | 50 tests/testthat/test-lsm-p-gyrate.R | 50 tests/testthat/test-lsm-p-nca.R | 50 tests/testthat/test-lsm-p-para.R | 50 tests/testthat/test-lsm-p-perim.R | 54 tests/testthat/test-lsm-p-shape.R | 48 tests/testthat/test-matrix-to-raster.R | 96 tests/testthat/test-options-landscapemetrics.R | 24 tests/testthat/test-pad-raster.R | 84 tests/testthat/test-rcpp-get-coocurrence-matrix.R | 204 - tests/testthat/test-rcpp-get-entropy.R | 46 tests/testthat/test-sample-lsm.R | 428 +- tests/testthat/test-scale-sample.R | 200 - tests/testthat/test-scale-window.R | 164 tests/testthat/test-show-cores.R | 106 tests/testthat/test-show-correlation.R | 116 tests/testthat/test-show-lsm.R | 96 tests/testthat/test-show-patches.R | 74 tests/testthat/test-spatialize-lsm.R | 152 tests/testthat/test-unique-values.R | 26 tests/testthat/test-window-lsm.R | 84 tests/testthat/test_fragstats.R | 3884 +++++++++++----------- vignettes/getstarted.Rmd | 364 +- 373 files changed, 26580 insertions(+), 26497 deletions(-)
More information about landscapemetrics at CRAN
Permanent link
Title: Fast Extraction from Raster Datasets using Polygons
Description: Provides a replacement for the 'extract' function from the 'raster' package
that is suitable for extracting raster values using 'sf' polygons.
Author: Daniel Baston [aut, cre],
ISciences, LLC [cph]
Maintainer: Daniel Baston <dbaston@isciences.com>
Diff between exactextractr versions 0.1.0 dated 2019-08-01 and 0.1.1 dated 2019-08-07
DESCRIPTION | 7 +++-- MD5 | 11 ++++---- NEWS.md |only configure | 59 +++++++++++++++++++++++++++++++++++------------ configure.ac | 36 ++++++++++++++++++++-------- man/coverage_fraction.Rd | 6 ++++ src/exact_extract.cpp | 4 +-- 7 files changed, 89 insertions(+), 34 deletions(-)
Title: Derive Polygenic Risk Score Based on Emprical Bayes Theory
Description: EB-PRS is a novel method that leverages information for effect sizes across all the markers to improve the prediction accuracy. No parameter tuning is needed in the method, and no external information is needed. This R-package provides the calculation of polygenic risk scores from the given training summary statistics and testing data. We can use EB-PRS to extract main information, estimate Empirical Bayes parameters, derive polygenic risk scores for each individual in testing data, and evaluate the PRS according to AUC and predictive r2.
Author: Shuang Song [aut, cre], Wei Jiang [aut], Lin Hou [aut] and Hongyu Zhao [aut]
Maintainer: Shuang Song <song-s19@mails.tsinghua.edu.cn>
Diff between EBPRS versions 1.1.2 dated 2019-02-14 and 1.1.5 dated 2019-08-07
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ R/extractInfo.R | 2 +- R/findPara.R | 17 +++++++++++------ R/getEffectSize.R | 16 ++++++++++------ man/extractInfo.Rd | 2 +- man/getEffectSize.Rd | 2 +- 7 files changed, 35 insertions(+), 26 deletions(-)
Title: Helper Functions to Install and Maintain 'TeX Live', and Compile
'LaTeX' Documents
Description: Helper functions to install and maintain the 'LaTeX' distribution
named 'TinyTeX' (<https://yihui.name/tinytex/>), a lightweight, cross-platform,
portable, and easy-to-maintain version of 'TeX Live'. This package also
contains helper functions to compile 'LaTeX' documents, and install missing
'LaTeX' packages automatically.
Author: Yihui Xie [aut, cre, cph] (<https://orcid.org/0000-0003-0645-5666>),
RStudio, Inc. [cph],
Fernando Cagua [ctb],
Ethan Heinzen [ctb]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between tinytex versions 0.14 dated 2019-06-25 and 0.15 dated 2019-08-07
DESCRIPTION | 6 +++--- MD5 | 4 ++-- R/latex.R | 24 ++++++++++++++---------- 3 files changed, 19 insertions(+), 15 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 0.14 dated 2019-06-11 and 0.15 dated 2019-08-07
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS | 6 ++++++ R/static.R | 3 ++- 4 files changed, 14 insertions(+), 7 deletions(-)
Title: 'ggplot2' Based Publication Ready Plots
Description: The 'ggplot2' package is excellent and flexible for elegant data
visualization in R. However the default generated plots requires some formatting
before we can send them for publication. Furthermore, to customize a 'ggplot',
the syntax is opaque and this raises the level of difficulty for researchers
with no advanced R programming skills. 'ggpubr' provides some easy-to-use
functions for creating and customizing 'ggplot2'- based publication ready plots.
Author: Alboukadel Kassambara [aut, cre]
Maintainer: Alboukadel Kassambara <alboukadel.kassambara@gmail.com>
Diff between ggpubr versions 0.2.1 dated 2019-06-23 and 0.2.2 dated 2019-08-07
DESCRIPTION | 17 ++-- MD5 | 28 +++---- NAMESPACE | 6 + NEWS.md | 20 +++++ R/add_summary.R | 25 ++++-- R/compare_means.R | 10 +- R/geom_bracket.R |only R/geom_exec.R | 14 +++ R/ggadd.R | 13 ++- R/ggline.R | 1 R/stat_pvalue_manual.R | 176 +++++++++++++++++++++++++++++++++------------- R/utilities.R | 11 ++ man/add_summary.Rd | 22 +++-- man/geom_bracket.Rd |only man/ggadd.Rd | 18 +++- man/stat_pvalue_manual.Rd | 41 +++++++--- 16 files changed, 290 insertions(+), 112 deletions(-)
Title: A Wrapper of the JavaScript Library 'DataTables'
Description: Data objects in R can be rendered as HTML tables using the
JavaScript library 'DataTables' (typically via R Markdown or Shiny). The
'DataTables' library has been included in this R package. The package name
'DT' is an abbreviation of 'DataTables'.
Author: Yihui Xie [aut, cre],
Joe Cheng [aut],
Xianying Tan [aut],
JJ Allaire [ctb],
Maximilian Girlich [ctb],
Greg Freedman Ellis [ctb],
Johannes Rauh [ctb],
jQuery contributors [ctb, cph] (jQuery in htmlwidgets/lib),
SpryMedia Limited [ctb, cph] (DataTables in htmlwidgets/lib),
Brian Reavis [ctb, cph] (selectize.js in htmlwidgets/lib),
Leon Gersen [ctb, cph] (noUiSlider in htmlwidgets/lib),
Bartek Szopka [ctb, cph] (jquery.highlight.js in htmlwidgets/lib),
RStudio Inc [cph]
Maintainer: Yihui Xie <xie@yihui.name>
Diff between DT versions 0.7 dated 2019-06-11 and 0.8 dated 2019-08-07
DESCRIPTION | 13 ++++++------- MD5 | 16 ++++++++-------- R/datatables.R | 17 +++++++++++++---- R/format.R | 48 ++++++++++++++++++++++++------------------------ R/shiny.R | 2 +- build/vignette.rds |binary inst/doc/DT.html | 14 +++++++++----- man/dataTableOutput.Rd | 2 +- man/datatable.Rd | 4 +++- 9 files changed, 65 insertions(+), 51 deletions(-)
Title: Grouped Statistical Analyses in a Tidy Way
Description: Collection of functions to run statistical tests
across all combinations of multiple grouping variables.
Author: Indrajeet Patil [aut, cre] (<https://orcid.org/0000-0003-1995-6531>)
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>
Diff between groupedstats versions 0.0.7 dated 2019-06-05 and 0.0.8 dated 2019-08-07
groupedstats-0.0.7/groupedstats/man/compound.Rd |only groupedstats-0.0.7/groupedstats/man/pipe.Rd |only groupedstats-0.0.7/groupedstats/tests/testthat/test_lm_effsize_ci.R |only groupedstats-0.0.7/groupedstats/tests/testthat/test_signif_column.R |only groupedstats-0.0.7/groupedstats/tests/testthat/test_specify_decimal_p.R |only groupedstats-0.0.8/groupedstats/DESCRIPTION | 22 groupedstats-0.0.8/groupedstats/MD5 | 83 +- groupedstats-0.0.8/groupedstats/NAMESPACE | 10 groupedstats-0.0.8/groupedstats/NEWS.md | 14 groupedstats-0.0.8/groupedstats/R/global_vars.R | 8 groupedstats-0.0.8/groupedstats/R/grouped_aov.R | 126 +-- groupedstats-0.0.8/groupedstats/R/grouped_lm.R | 15 groupedstats-0.0.8/groupedstats/R/grouped_lmer.R | 6 groupedstats-0.0.8/groupedstats/R/grouped_proptest.R | 6 groupedstats-0.0.8/groupedstats/R/grouped_robustslr.R | 21 groupedstats-0.0.8/groupedstats/R/grouped_slr.R | 7 groupedstats-0.0.8/groupedstats/R/grouped_summary.R | 337 ++------ groupedstats-0.0.8/groupedstats/R/grouped_ttest.R | 24 groupedstats-0.0.8/groupedstats/R/grouped_wilcox.R | 124 +-- groupedstats-0.0.8/groupedstats/R/lm_effsize_ci.R | 66 - groupedstats-0.0.8/groupedstats/R/reexports.R | 14 groupedstats-0.0.8/groupedstats/R/signif_column.R | 94 -- groupedstats-0.0.8/groupedstats/R/specify_decimal_p.R | 47 - groupedstats-0.0.8/groupedstats/R/utils-tidy.R | 24 groupedstats-0.0.8/groupedstats/README.md | 388 +++++----- groupedstats-0.0.8/groupedstats/inst/WORDLIST | 5 groupedstats-0.0.8/groupedstats/man/figures/README-grouped_summary3-1.png |binary groupedstats-0.0.8/groupedstats/man/grouped_aov.Rd | 12 groupedstats-0.0.8/groupedstats/man/grouped_lm.Rd | 6 groupedstats-0.0.8/groupedstats/man/grouped_lmer.Rd | 4 groupedstats-0.0.8/groupedstats/man/grouped_proptest.Rd | 2 groupedstats-0.0.8/groupedstats/man/grouped_robustslr.Rd | 2 groupedstats-0.0.8/groupedstats/man/grouped_slr.Rd | 9 groupedstats-0.0.8/groupedstats/man/grouped_summary.Rd | 21 groupedstats-0.0.8/groupedstats/man/grouped_ttest.Rd | 22 groupedstats-0.0.8/groupedstats/man/grouped_wilcox.Rd | 10 groupedstats-0.0.8/groupedstats/man/lm_effsize_ci.Rd | 4 groupedstats-0.0.8/groupedstats/man/lm_effsize_standardizer.Rd | 6 groupedstats-0.0.8/groupedstats/man/reexports.Rd | 5 groupedstats-0.0.8/groupedstats/man/signif_column.Rd | 24 groupedstats-0.0.8/groupedstats/man/specify_decimal_p.Rd | 20 groupedstats-0.0.8/groupedstats/tests/README.md | 75 + groupedstats-0.0.8/groupedstats/tests/testthat/test-grouped_lm.R |only groupedstats-0.0.8/groupedstats/tests/testthat/test-grouped_summary.R |only groupedstats-0.0.8/groupedstats/tests/testthat/test-lm_effsize_ci.R |only groupedstats-0.0.8/groupedstats/tests/testthat/test-lm_effsize_standardizer.R |only groupedstats-0.0.8/groupedstats/tests/testthat/test-signif_column.R |only groupedstats-0.0.8/groupedstats/tests/testthat/test-specify_decimal_p.R |only 48 files changed, 747 insertions(+), 916 deletions(-)
Title: Automated Deconvolution Augmentation of Profiles for Tissue
Specific Cells
Description: Augments existing or de-novo cell-type signature matrices to deconvolve bulk gene expression data.
Useful for building signature matrices from single cell RNAseq data, determine cell type deconvolution
spillover, and hierarchical deconvolution to use spillover to increase deconvolution accuracy. Please cite:
Danziger SA et al. (2019) ADAPTS: Automated Deconvolution Augmentation of Profiles for
Tissue Specific cells <doi:10.1101/633958>. This package expands on the techniques outlined in Newman AM,
Liu CL, Green MR, Gentles AJ, Feng W, Xu Y,
Hoang CD, Diehn M, Alizadeh, AA (2015) <doi:10.1038/nmeth.3337>'s Nature Methods paper:
'Robust enumeration of cell subsets from tissue expression profiles' to allow a user to easily add
their own cell types (e.g. a tumor specific cell type) to Newman's LM22 or other signature matrix.
Author: Samuel A Danziger
Maintainer: Samuel A Danziger <sam.danziger@gmail.com>
Diff between ADAPTS versions 0.9.20 dated 2019-06-17 and 0.9.21 dated 2019-08-07
DESCRIPTION | 6 ++--- MD5 | 6 ++--- R/MakeSigMatrix.R | 61 ++++++++++++++++++++++++++++++++++-------------------- man/rankByT.Rd | 8 ++++--- 4 files changed, 50 insertions(+), 31 deletions(-)