Title: Query Search Interfaces
Description: Provides a search interface to look up terms
on 'Google', 'Bing', 'DuckDuckGo', 'Startpage', 'Ecosia', 'rseek',
'Twitter', 'StackOverflow', 'RStudio Community', 'GitHub', and 'BitBucket'.
Upon searching, a browser window will open with the aforementioned search
results.
Author: James Balamuta [aut, cre] (<https://orcid.org/0000-0003-2826-8458>),
Alex Rossell Hayes [ctb] (<https://orcid.org/0000-0001-9412-0457>)
Maintainer: James Balamuta <balamut2@illinois.edu>
Diff between searcher versions 0.0.5 dated 2020-02-06 and 0.0.6 dated 2021-07-24
DESCRIPTION | 24 +-- MD5 | 28 +-- NAMESPACE | 2 NEWS.md | 28 +++ R/index-sites.R | 6 R/search-functions.R | 44 ++++- R/utilities.R | 8 - README.md | 45 +++-- build/vignette.rds |binary inst/doc/search-patterns.Rmd | 5 inst/doc/search-patterns.html | 255 ++++----------------------------- man/search_site.Rd | 48 ++++-- man/searcher-package.Rd | 12 + tests/testthat/test-search-functions.R | 28 +++ vignettes/search-patterns.Rmd | 5 15 files changed, 238 insertions(+), 300 deletions(-)
Title: Easily Access Song Lyrics from Genius.com
Description: Easily access song lyrics in a tidy way.
Author: Josiah Parry [aut, cre],
Nathan Barr [aut, ctb],
Chris Billingham [ctb],
Evan Oppenheimer [ctb]
Maintainer: Josiah Parry <josiah.parry@gmail.com>
Diff between genius versions 2.2.2 dated 2020-05-28 and 2.2.3 dated 2021-07-24
genius-2.2.2/genius/build |only genius-2.2.2/genius/inst/doc |only genius-2.2.2/genius/vignettes |only genius-2.2.3/genius/DESCRIPTION | 14 ++-- genius-2.2.3/genius/MD5 | 38 ++++++------- genius-2.2.3/genius/NAMESPACE | 13 +++- genius-2.2.3/genius/NEWS.md | 17 ++++- genius-2.2.3/genius/R/add_genius.R | 56 +++++++++---------- genius-2.2.3/genius/R/calc_self_sim.R | 6 +- genius-2.2.3/genius/R/genius_album.R | 8 +- genius-2.2.3/genius/R/genius_lyrics.R | 14 ++-- genius-2.2.3/genius/R/genius_tracklist.R | 16 ++--- genius-2.2.3/genius/R/genius_url.R | 81 +++++++++++++++++----------- genius-2.2.3/genius/R/globals.R |only genius-2.2.3/genius/R/utils-pipe.R |only genius-2.2.3/genius/man/add_genius.Rd | 56 +++++++++---------- genius-2.2.3/genius/man/calc_self_sim.Rd | 6 +- genius-2.2.3/genius/man/genius_album.Rd | 6 +- genius-2.2.3/genius/man/genius_lyrics.Rd | 7 +- genius-2.2.3/genius/man/genius_tracklist.Rd | 2 genius-2.2.3/genius/man/genius_url.Rd | 9 ++- genius-2.2.3/genius/man/pipe.Rd |only 22 files changed, 192 insertions(+), 157 deletions(-)
Title: Access NASA's Exoplanet Archive Data
Description: The goal of exoplanets is to provide access to
NASA's Exoplanet Archive TAP Service. For more information regarding
the API please read the documentation
<https://exoplanetarchive.ipac.caltech.edu/index.html>.
Author: Tyler Littlefield [aut, cre] (<https://orcid.org/0000-0002-6020-1125>),
Maëlle Salmon [ctb, rev],
Mathida Chuk [ctb]
Maintainer: Tyler Littlefield <tylerlittlefield@hey.com>
Diff between exoplanets versions 0.2.1 dated 2021-05-17 and 0.2.2 dated 2021-07-24
DESCRIPTION | 6 +- MD5 | 20 ++++---- NEWS.md | 4 + README.md | 52 ++++++++-------------- build/vignette.rds |binary data/tableinfo.rda |binary inst/doc/exoplanets.Rmd | 38 ++++++++-------- inst/doc/exoplanets.html | 42 ++++++++--------- man/tableinfo.Rd | 2 vignettes/exoplanets.Rmd | 38 ++++++++-------- vignettes/exoplanets_vignette_img-discovery-1.png |binary 11 files changed, 97 insertions(+), 105 deletions(-)
Title: Unicode Text Processing
Description: Process and print 'UTF-8' encoded international
text (Unicode). Input, validate, normalize, encode, format, and
display.
Author: Patrick O. Perry [aut, cph],
Kirill Müller [cre],
Unicode, Inc. [cph, dtc] (Unicode Character Database)
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>
Diff between utf8 versions 1.2.1 dated 2021-03-12 and 1.2.2 dated 2021-07-24
DESCRIPTION | 10 MD5 | 28 build/vignette.rds |binary inst/doc/utf8.html | 10 src/utf8lite/src/private/charwidth.h | 1564 +++++++++++++++++------------------ src/utf8lite/tests/check_charwidth.c | 44 src/utf8lite/tests/check_graphscan.c | 22 src/utf8lite/util/gen-charwidth.py | 2 tests/testthat.R | 10 tests/testthat/_snaps |only tests/testthat/helper-locale.R | 9 tests/testthat/helper-output.R |only tests/testthat/test-utf8_encode.R | 26 tests/testthat/test-utf8_format.R | 232 ++--- tests/testthat/test-utf8_print.R | 27 tests/testthat/test-utf8_width.R | 28 16 files changed, 1027 insertions(+), 985 deletions(-)
Title: Computation of Variance-Based Sensitivity Indices
Description: It allows to rapidly compute, bootstrap and plot up to third-order Sobol'-based sensitivity indices using several state-of-the-art first and total-order estimators. Sobol' indices can be computed either for models that yield a scalar as a model output or for systems of differential equations. The package also provides a suit of benchmark tests functions and several options to obtain publication-ready figures of the model output uncertainty and sensitivity-related analysis. An overview of Sobol'-based sensitivity indices can be found in Saltelli et al. (2008, ISBN:9780470059975) and in Puy, Lo Piano, Saltelli, and Levin (2021) <arXiv:2101.10103>.
Author: Arnald Puy [aut, cre] (<https://orcid.org/0000-0001-9469-2156>),
Bertrand Ioos [ctb] (Author of included 'sensitivity' fragments),
Gilles Pujol [ctb] (Author of included 'sensitivity' fragments),
RStudio [cph] (Copyright holder of included 'sensitivity' fragments)
Maintainer: Arnald Puy <arnald.puy@pm.me>
Diff between sensobol versions 1.0.2 dated 2021-05-30 and 1.0.3 dated 2021-07-24
DESCRIPTION | 6 +++--- MD5 | 17 +++++++++-------- NEWS.md | 7 +++++++ R/sensobol-package.R | 31 +++++++++++++++++++++++++------ R/sobol_ode.R | 37 +++++++++++++++++++++++++------------ build/partial.rdb |binary inst/REFERENCES.bib | 11 ++++++++++- inst/doc/sensobol.pdf |binary man/sensobol-package.Rd |only man/sobol_ode.Rd | 27 ++++++++++++++++----------- 10 files changed, 95 insertions(+), 41 deletions(-)
Title: Parse and Manipulate Research Patient Data Registry ('RPDR')
Text Queries
Description: Functions to load Research Patient Data Registry ('RPDR') text queries from Partners Healthcare institutions into R.
The package also provides helper functions to manipulate data and execute common procedures
such as finding the closest radiological exams considering a given timepoint, or creating a DICOM header database
from the downloaded images. 'parseRPDR' currently supports txt sources: "mrn", "con", "dem", "enc", "rdt", "lab",
"med", "dia", "rfv", "prc", "phy", "lno", "car", "dis", "end", "hnp", "opn", "pat", "prg", "pul", "rad" and "vis".
All functionalities are parallelized for fast and efficient analyses.
Author: Marton Kolossvary [aut, cre]
Maintainer: Marton Kolossvary <mkolossvary@mgh.harvard.edu>
Diff between parseRPDR versions 0.1.2 dated 2021-06-06 and 0.2.0 dated 2021-07-24
DESCRIPTION | 16 ++++---- MD5 | 78 ++++++++++++++++++++------------------- NAMESPACE | 1 NEWS.md | 15 +++++++ R/convert_lab.R | 35 +++++++++++------ R/create_img_db.R |only R/dcm_db.R |only R/find_exam_bm.R | 10 +++-- R/find_exam_ram.R | 10 +++-- R/load_base.R | 2 - R/load_con.R | 2 - R/load_dem.R | 2 - R/load_dia.R | 2 - R/load_enc.R | 2 - R/load_lab.R | 2 - R/load_lno.R | 2 - R/load_med.R | 2 - R/load_mrn.R | 2 - R/load_notes.R | 2 - R/load_phy.R | 2 - R/load_prc.R | 2 - R/load_rdt.R | 2 - R/load_rfv.R | 2 - README.md | 100 +++++++++++++++++++++++++++++++++++++++------------ man/convert_lab.Rd | 16 +++++--- man/create_img_db.Rd |only man/dcm_db.Rd |only man/figures/logo.png |binary man/load_base.Rd | 2 - man/load_con.Rd | 2 - man/load_dem.Rd | 2 - man/load_dia.Rd | 2 - man/load_enc.Rd | 2 - man/load_lab.Rd | 2 - man/load_lno.Rd | 2 - man/load_med.Rd | 2 - man/load_mrn.Rd | 2 - man/load_notes.Rd | 2 - man/load_phy.Rd | 2 - man/load_prc.Rd | 2 - man/load_rdt.Rd | 2 - man/load_rfv.Rd | 2 - 42 files changed, 218 insertions(+), 119 deletions(-)
Title: R at the Command-Line via 'r'
Description: A scripting and command-line front-end
is provided by 'r' (aka 'littler') as a lightweight binary wrapper around
the GNU R language and environment for statistical computing and graphics.
While R can be used in batch mode, the r binary adds full support for
both 'shebang'-style scripting (i.e. using a hash-mark-exclamation-path
expression as the first line in scripts) as well as command-line use in
standard Unix pipelines. In other words, r provides the R language without
the environment.
Author: Dirk Eddelbuettel and Jeff Horner
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between littler versions 0.3.12 dated 2020-10-07 and 0.3.13 dated 2021-07-24
ChangeLog | 115 +++++ DESCRIPTION | 11 MD5 | 50 +- R/test.R | 2 README.md | 1 build/vignette.rds |binary configure | 41 +- configure.ac | 5 inst/NEWS.Rd | 30 + inst/doc/littler-examples.Rmd | 3 inst/doc/littler-examples.html | 688 ++++++++++------------------------ inst/doc/littler-faq.Rmd | 5 inst/doc/littler-faq.html | 285 -------------- inst/examples/compiledDeps.r |only inst/examples/cranIncoming.r | 2 inst/examples/getRStudioDesktop.r | 4 inst/examples/getRStudioServer.r | 3 inst/examples/installRSPM.r | 4 inst/examples/kitten.r | 17 inst/examples/rcc.r | 16 inst/examples/roxy.r | 3 inst/examples/silenceTwitterAccount.r |only inst/examples/tt.r | 4 src/littler.c | 7 tests/simpleTests.R | 9 vignettes/littler-examples.Rmd | 3 vignettes/littler-faq.Rmd | 5 27 files changed, 463 insertions(+), 850 deletions(-)
Title: Continuous Norming
Description: Conventional methods for producing standard scores in psychometrics or biometrics
are often plagued with "jumps" or "gaps" (i.e., discontinuities) in norm tables and low
confidence for assessing extreme scores. The continuous norming method introduced by A.
Lenhard et al. (2016, <doi:10.1177/1073191116656437>; 2019, <doi:10.1371/journal.pone.0222279>) and generates continuous test norm
scores on the basis of the raw data from standardization samples, without requiring
assumptions about the distribution of the raw data: Norm scores are directly established
from raw data by modeling the latter ones as a function of both percentile scores and an
explanatory variable (e.g., age). The method minimizes bias arising from sampling and
measurement error, while handling marked deviations from normality, addressing bottom
or ceiling effects and capturing almost all of the variance in the original norm data
sample. An online demonstration is available via <https://cnorm.shinyapps.io/cNORM/>.
Author: Wolfgang Lenhard [cre, aut] (<https://orcid.org/0000-0002-8184-6889>),
Alexandra Lenhard [aut],
Sebastian Gary [aut]
Maintainer: Wolfgang Lenhard <wolfgang.lenhard@uni-wuerzburg.de>
Diff between cNORM versions 2.0.3 dated 2021-04-10 and 2.0.4 dated 2021-07-24
DESCRIPTION | 8 +++---- MD5 | 32 +++++++++++++++--------------- NEWS.md | 19 +++++++++++++++-- R/cNORM.R | 2 - R/data.R | 4 +-- R/modelling.R | 23 +++++++++++++++------ R/plot.R | 18 +++++++--------- R/predict.R | 50 ++++++++++++++++++++++++++++++++--------------- README.md | 6 +++++ build/vignette.rds |binary inst/doc/cNORM-Demo.Rmd | 2 - inst/doc/cNORM-Demo.html | 8 +++---- man/CDC.Rd | 4 +-- man/getNormScoreSE.Rd | 13 ++++++++---- man/plotNorm.Rd | 6 ----- man/predictNorm.Rd | 15 +++++++------- vignettes/cNORM-Demo.Rmd | 2 - 17 files changed, 131 insertions(+), 81 deletions(-)
Title: Interface allowing R to use OpenCL
Description: This package provides an interface to OpenCL, allowing R to leverage computing power of GPUs and other HPC accelerator devices.
Author: Simon Urbanek <Simon.Urbanek@r-project.org>, Aaron Puchert <aaronpuchert@alice-dsl.net>
Maintainer: Simon Urbanek <Simon.Urbanek@r-project.org>
Diff between OpenCL versions 0.2-1 dated 2020-03-09 and 0.2-2 dated 2021-07-24
DESCRIPTION | 6 +++--- MD5 | 22 ++++++++++++---------- NAMESPACE | 7 +++++-- NEWS | 6 ++++++ R/clBuffer.R | 14 +++++++------- R/ocl.R | 18 +++++++++--------- src/buffer.c | 4 ++-- src/c.h |only src/ocl.c | 2 +- src/reg.c |only src/wrap.c | 7 ++++++- tests/buffer.Rout.save | 40 +++++++++++++++++++++++++++++----------- tests/kernel.Rout.save | 14 ++++++++++---- 13 files changed, 90 insertions(+), 50 deletions(-)
Title: Read and write JPEG images
Description: This package provides an easy and simple way to read, write and display bitmap images stored in the JPEG format. It can read and write both files and in-memory raw vectors.
Author: Simon Urbanek <Simon.Urbanek@r-project.org>
Maintainer: Simon Urbanek <Simon.Urbanek@r-project.org>
Diff between jpeg versions 0.1-8.1 dated 2019-10-24 and 0.1-9 dated 2021-07-24
DESCRIPTION | 6 +++--- MD5 | 13 +++++++------ NAMESPACE | 2 +- NEWS | 9 +++++++++ R/read.R | 2 +- R/write.R | 4 ++-- src/reg.c |only src/write.c | 19 ++++++++++++++----- 8 files changed, 37 insertions(+), 18 deletions(-)
Title: Alt String Implementation
Description: Provides an extendable, performant and multithreaded 'alt-string' implementation backed by 'C++' vectors and strings.
Author: Travers Ching [aut, cre, cph],
Phillip Hazel [ctb] (Bundled PCRE2 code),
Zoltan Herczeg [ctb, cph] (Bundled PCRE2 code),
University of Cambridge [cph] (Bundled PCRE2 code),
Tilera Corporation [cph] (Stack-less Just-In-Time compiler bundled with
PCRE2),
Yann Collet [ctb, cph] (Yann Collet is the author of the bundled xxHash
code)
Maintainer: Travers Ching <traversc@gmail.com>
Diff between stringfish versions 0.15.1 dated 2021-03-16 and 0.15.2 dated 2021-07-24
ChangeLog | 3 +++ DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- build/vignette.rds |binary inst/doc/vignette.html | 11 +++++++++-- inst/include/sf_internal.h | 2 +- src/RcppExports.cpp | 5 +++++ src/sf_functions.cpp | 2 +- 8 files changed, 30 insertions(+), 15 deletions(-)
Title: Advanced and Fast Data Transformation
Description: A C/C++ based package for advanced data transformation and
statistical computing in R that is extremely fast, flexible and
parsimonious to code with, class-agnostic and programmer friendly.
It is well integrated with base R, 'dplyr' / (grouped) 'tibble',
'data.table', 'plm' (panel-series and data frames), 'sf' data frames, and
non-destructively handles other matrix or data frame based classes (such as
'ts', 'xts' / 'zoo', 'timeSeries', 'tsibble', 'tibbletime' etc.)
--- Key Features: ---
(1) Advanced statistical programming: A full set of fast statistical functions
supporting grouped and weighted computations on vectors, matrices and
data frames. Fast and programmable grouping, ordering, unique values / rows,
factor generation and interactions. Fast and flexible functions for data
manipulation 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 row / column arithmetic, (grouped) replacing
and sweeping out of statistics, (grouped, weighted) scaling / standardizing,
between (averaging) and (quasi-)within (centering / demeaning) transformations,
higher-dimensional centering (i.e. multiple fixed effects transformations),
linear prediction / partialling-out, linear model fitting and testing.
(4) Advanced time-computations: Fast (sequences of) lags / leads, and
(lagged / leaded, iterated, quasi-, log-) differences, (compounded)
growth rates, and cumulative sums on (unordered, irregular) 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, splitting,
extraction / subsetting, data-apply, and generalized recursive
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],
Laurent Berge [ctb],
Dirk Eddelbuettel [ctb],
Josh Pasek [ctb],
Kevin Tappe [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 1.6.4 dated 2021-07-13 and 1.6.5 dated 2021-07-24
DESCRIPTION | 12 ++++---- MD5 | 50 +++++++++++++++++------------------ NEWS.md | 7 +++- R/GRP.R | 28 ++++++++----------- R/fhdbetween_fhdwithin.R | 34 +++++++++++------------ R/fsubset_ftransform.R | 22 +++++++++------ R/pwcor_pwcov_pwnobs.R | 4 +- R/qsu.R | 2 - R/quick_conversion.R | 34 ++++++++++++++--------- R/recode_replace.R | 2 - R/roworder_colorder_rename.R | 8 ++--- R/rsplit.R | 6 ++-- R/small_helper.R | 10 +++---- inst/doc/collapse_documentation.html | 4 +- man/collapse-documentation.Rd | 2 - man/fnth.Rd | 2 - man/fsubset.Rd | 3 ++ man/qsu.Rd | 2 - man/quick-conversion.Rd | 8 ++--- src/ExportSymbols.cpp | 12 ++++---- src/RcppExports.cpp | 5 +++ src/data.table.h | 8 ++++- src/data.table_init.c | 2 + src/data.table_rbindlist.c | 2 - src/data.table_subset.c | 46 +++++++++----------------------- src/data.table_utils.c | 4 +- 26 files changed, 163 insertions(+), 156 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-07-19 0.1.1
Title: Make Data Based on Different Geographies Comparable
Description: Several functions to allow comparisons of data across different geographies, in particular for Canadian census data from different censuses.
Author: Jens von Bergmann [aut, cre] (creator and maintainer)
Maintainer: Jens von Bergmann <jens@mountainmath.ca>
Diff between tongfen versions 0.3 dated 2020-11-04 and 0.3.3 dated 2021-07-24
DESCRIPTION | 16 - MD5 | 56 ++- NAMESPACE | 1 NEWS.md | 12 R/helpers.R | 2 R/tongfen.R | 109 ++++++- R/tongfen_ca.R | 17 - R/tongfen_ca_estimate.R |only R/tongfen_us.R | 4 README.md | 34 +- build/tongfen.pdf |binary build/vignette.rds |binary inst/doc/polling_districts.R | 4 inst/doc/polling_districts.Rmd | 4 inst/doc/polling_districts.html | 580 ++++++++++++-------------------------- inst/doc/tongfen-ca-estimate.R |only inst/doc/tongfen-ca-estimate.Rmd |only inst/doc/tongfen-ca-estimate.html |only inst/doc/tongfen.R | 4 inst/doc/tongfen.Rmd | 4 inst/doc/tongfen.html | 466 +++++++++--------------------- inst/doc/tongfen_ca.R | 2 inst/doc/tongfen_ca.Rmd | 2 inst/doc/tongfen_ca.html | 353 +++++------------------ inst/doc/tongfen_us.html | 300 +++---------------- man/get_tongfen_ca_census.Rd | 4 man/tongfen_estimate.Rd | 4 man/tongfen_estimate_ca_census.Rd |only vignettes/polling_districts.Rmd | 4 vignettes/tongfen-ca-estimate.Rmd |only vignettes/tongfen.Rmd | 4 vignettes/tongfen_ca.Rmd | 2 32 files changed, 675 insertions(+), 1313 deletions(-)
Title: Sparse Group Variable Selection for Gene-Environment
Interactions in the Longitudinal Study
Description: Recently, regularized variable selection has emerged as a powerful tool to identify and dissect gene-environment interactions. Nevertheless, in longitudinal studies with high dimensional genetic factors, regularization methods for G×E interactions have not been systematically developed. In this package, we provide the implementation of sparse group variable selection, based on both the quadratic inference function (QIF) and generalized estimating equation (GEE), to accommodate the bi-level selection for longitudinal G×E studies with high dimensional genomic features. Alternative methods conducting only the group or individual level selection have also been included. The core modules of the package have been developed in C++.
Author: Fei Zhou, Xi Lu, Jie Ren, Kun Fan, Cen Wu
Maintainer: Fei Zhou <feiz@ksu.edu>
Diff between springer versions 0.1.2 dated 2020-07-05 and 0.1.3 dated 2021-07-24
DESCRIPTION | 12 +++++++----- MD5 | 13 +++++++------ R/dmcp.R | 6 +++--- R/springer-package.R | 25 +++++++++++++------------ build |only man/dmcp.Rd | 6 +++--- man/springer-package.Rd | 25 +++++++++++++------------ src/RcppExports.cpp | 5 +++++ 8 files changed, 51 insertions(+), 41 deletions(-)
Title: Plot 'rpart' Models: An Enhanced Version of 'plot.rpart'
Description: Plot 'rpart' models. Extends plot.rpart() and text.rpart()
in the 'rpart' package.
Author: Stephen Milborrow
Maintainer: Stephen Milborrow <milbo@sonic.net>
Diff between rpart.plot versions 3.0.9 dated 2020-09-17 and 3.1.0 dated 2021-07-24
DESCRIPTION | 7 -- MD5 | 43 ++++++------- NEWS | 7 +- R/layout.R | 38 ++++++------ R/lib.R | 2 R/prp.R | 11 +-- inst/doc/prp.pdf |binary inst/slowtests/makeclean.bat |only inst/slowtests/rpart.report.bat | 2 inst/slowtests/test.describe.col.bat | 2 inst/slowtests/test.imports.Rout.save | 98 +++++++++++++++---------------- inst/slowtests/test.imports.bat | 2 inst/slowtests/test.na.bat | 2 inst/slowtests/test.palette.bat | 2 inst/slowtests/test.rpart.plot.R | 6 + inst/slowtests/test.rpart.plot.Rout.save | 26 +++++--- inst/slowtests/test.rpart.plot.bat | 2 inst/slowtests/test.rpart.rules.bat | 2 inst/slowtests/test.type5.bat | 2 inst/slowtests/usersplits.bat | 2 inst/slowtests/vignette.bat | 2 inst/slowtests/webpage.figs.bat | 2 man/ptitanic.Rd | 4 - 23 files changed, 144 insertions(+), 120 deletions(-)
Title: Simulation of Chromosomal Regions Shared by Family Members
Description: Simulation of segments shared identical-by-descent (IBD) by
pedigree members. Using sex specific recombination rates along the
human genome (Halldorsson et al. (2019)
<doi:10.1126/science.aau1043>), phased chromosomes are simulated for
all pedigree members. Applications include calculation of realised
relatedness coefficients and IBD segment distributions. 'ibdsim2' is
part of the 'ped suite' collection of packages for pedigree analysis.
A detailed presentation of the 'ped suite', including a separate
chapter on 'ibdsim2', is available in the book 'Pedigree analysis in
R' (Vigeland, 2021, ISBN:9780128244302). A 'shiny' app for visualising
and comparing IBD distributions is available at
<https://magnusdv.shinyapps.io/ibdsim2-shiny/>.
Author: Magnus Dehli Vigeland [aut, cre]
(<https://orcid.org/0000-0002-9134-4962>)
Maintainer: Magnus Dehli Vigeland <m.d.vigeland@medisin.uio.no>
Diff between ibdsim2 versions 1.3.0 dated 2020-11-13 and 1.4.0 dated 2021-07-24
DESCRIPTION | 46 +++-- MD5 | 43 ++--- NAMESPACE | 3 NEWS.md | 26 ++- R/findPattern.R | 179 +++++++++++++++------- R/haploDraw.R | 6 R/map_constructors.R | 10 - R/plotSegmentDistribution.R | 13 - R/profileSimIBD.R | 4 R/realisedCoeffs.R | 46 +++-- R/segment_utils.R | 134 ++++++++++++++-- R/utils.R | 4 R/zeroIBD.R | 6 README.md | 47 ++--- build/partial.rdb |binary man/extractIds.Rd |only man/figures/README-ibdsim2-example-distplot-1.png |binary man/findPattern.Rd | 28 ++- man/loadMap.Rd | 2 man/segmentStats.Rd |only src/RcppExports.cpp | 5 tests/testthat/test-maps.R | 2 tests/testthat/test-patterns.R |only tests/testthat/test-segments.R | 18 +- 24 files changed, 439 insertions(+), 183 deletions(-)
Title: Miscellaneous Functions in C++
Description: Provides utility functions that are simply, frequently used,
but may require higher performance that what can be obtained from base R.
Incidentally provides support for 'reverse geocoding', such as matching a point
with its nearest neighbour in another array. Used as a complement to package
'hutils' by sacrificing compilation or installation time for higher running
speeds. The name is a portmanteau of the author and 'Rcpp'.
Author: Hugh Parsonage [aut, cre],
Simon Urbanek [ctb] (fastmatch components)
Maintainer: Hugh Parsonage <hugh.parsonage@gmail.com>
Diff between hutilscpp versions 0.7.2 dated 2021-06-14 and 0.8.0 dated 2021-07-24
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 8 ++++++++ src/Crange.c | 39 +++++++++++++++++++++++++++++++++++++-- src/Cwhich_first.c | 4 ++-- 5 files changed, 54 insertions(+), 11 deletions(-)