Title: Simple Data Frames
Description: Provides a 'tbl_df' class (the 'tibble') that
provides stricter checking and better formatting than the traditional
data frame.
Author: Kirill Müller [aut, cre],
Hadley Wickham [aut],
Romain Francois [ctb],
Jennifer Bryan [ctb],
RStudio [cph]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>
Diff between tibble versions 3.0.2 dated 2020-07-07 and 3.0.3 dated 2020-07-10
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++----------- NEWS.md | 11 +++++++++++ R/compat-lifecycle.R | 1 - R/print.R | 3 +-- build/vignette.rds |binary inst/doc/extending.html | 16 ++++++++++++++++ inst/doc/invariants.html | 16 ++++++++++++++++ inst/doc/tibble.html | 16 ++++++++++++++++ inst/doc/types.html | 25 ++++++++++++++++++++----- tests/testthat/test-as_tibble.R | 2 ++ tests/testthat/test-matrix.R | 2 ++ 12 files changed, 98 insertions(+), 22 deletions(-)
Title: 'Drat' R Archive Template
Description: Creation and use of R Repositories via helper functions
to insert packages into a repository, and to add repository information
to the current R session. Two primary types of repositories are support:
gh-pages at GitHub, as well as local repositories on either the same machine
or a local network. Drat is a recursive acronym: Drat R Archive Template.
Author: Dirk Eddelbuettel with contributions by Carl Boettiger, Neal Fultz,
Sebastian Gibb, Colin Gillespie, Jan Górecki, Matt Jones, Thomas Leeper,
Steven Pav, Jan Schulz, Christoph Stepper, Felix G.M. Ernst and Patrick
Schratz.
Maintainer: Dirk Eddelbuettel <edd@debian.org>
Diff between drat versions 0.1.6 dated 2020-05-30 and 0.1.7 dated 2020-07-10
ChangeLog | 77 +++++++++++++++ DESCRIPTION | 13 +- MD5 | 46 +++++---- NAMESPACE | 9 + R/archivePackages.R | 142 +++++++++++++++++++++------- R/insertPackage.R | 80 ++++++++++++--- R/pruneRepo.R | 169 ++++++++++++++++++++++++++------- build/vignette.rds |binary inst/NEWS.Rd | 15 ++ inst/doc/CombiningDratAndTravis.html | 16 +++ inst/doc/DratFAQ.html | 16 +++ inst/doc/DratForPackageAuthors.html | 16 +++ inst/doc/DratForPackageUsers.html | 16 +++ inst/doc/WhyDrat.html | 16 +++ inst/extdata |only man/archivePackages.Rd | 20 +++ man/insertPackage.Rd | 9 + man/pruneRepo.Rd | 53 +++++++++- tests/skeleton_git2r.R | 177 ++++++++++++++++++++++++++++++++++- 19 files changed, 761 insertions(+), 129 deletions(-)
Title: Yield Per Recruit
Description: An implementation of equilibrium-based yield per recruit methods.
Yield per recruit methods can used to estimate the optimal yield for a fish population
as described by Walters and Martell (2004) <isbn:0-691-11544-3>.
The yield can be based on the number of fish caught (or harvested) or
biomass caught for all fish or just large (trophy) individuals.
Author: Joe Thorley [aut, cre] (<https://orcid.org/0000-0002-7683-4592>),
Poisson Consulting [cph, fnd]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>
Diff between ypr versions 0.5.0 dated 2020-03-18 and 0.5.1 dated 2020-07-10
DESCRIPTION | 8 +++---- LICENSE | 2 - MD5 | 17 ++++++++------- NEWS.md | 4 +++ R/base.R | 7 +++--- README.md | 28 +++++++++---------------- build/vignette.rds |binary inst/WORDLIST |only inst/doc/ypr.html | 49 ++++++++++++++++++++++++++------------------- man/plot.ypr_population.Rd | 15 +++---------- 10 files changed, 65 insertions(+), 65 deletions(-)
Title: Ask Yes-No Questions
Description: Asks Yes-No questions with variable or custom responses.
Author: Joe Thorley [aut, cre] (<https://orcid.org/0000-0002-7683-4592>),
Hadley Wickham [aut] (<https://orcid.org/0000-0003-4757-117X>)
Maintainer: Joe Thorley <joe@poissonconsulting.ca>
Diff between yesno versions 0.1.1 dated 2020-03-04 and 0.1.2 dated 2020-07-10
DESCRIPTION | 10 +++++----- MD5 | 16 ++++++++-------- NEWS.md | 4 ++++ R/yesno.R | 9 ++++++--- R/yesno2.R | 9 ++++++--- README.md | 23 +++-------------------- man/yesno.Rd | 9 ++++++--- man/yesno2.Rd | 3 ++- tests/testthat/test-yesno2.R | 8 ++++++++ 9 files changed, 48 insertions(+), 43 deletions(-)
Title: Data Import, Cleaning, and Conversions for Swimming Results
Description: There are two goals for 'SwimmeR' as presently constructed. The first is reading in swimming results from html or pdf sources and returning tidy dataframes. The second is working with the resulting data. To this end 'SwimmeR' converts swimming times (performances) between the computationally useful
format of seconds, reported to the 100ths place (eg 95.37), and the conventional reporting format (1:35.37) used in the swimming community, as well as providing tools for assigning team names etc.
Additionally 'SwimmeR' has functions for drawing single-elimination brackets and also converts times between the various pool sizes used in competitive swimming, namely 50m length (LCM), 25m length (SCM)
and 25y length (SCY).
Author: Greg Pilgrim [aut, cre] (<https://orcid.org/0000-0001-7831-442X>),
Caitlin Baldwin [ctb]
Maintainer: Greg Pilgrim <gpilgrim2670@gmail.com>
Diff between SwimmeR versions 0.2.0 dated 2020-04-10 and 0.3.0 dated 2020-07-10
DESCRIPTION | 29 LICENSE | 4 MD5 | 81 NAMESPACE | 85 NEWS.md | 19 R/Course_Convert.R | 182 R/Course_Convert_DF.R | 208 R/King200Breast.R | 28 R/Read_Results.R | 102 R/SwimR.R | 12 R/Swim_Parse.R | 2223 ++++---- R/draw_bracket.R |only R/fold.R |only R/get_mode.R |only R/globals.R | 46 R/mmss_format.R | 53 R/relay_aggregate.R | 18 R/sec_format.R | 61 R/sec_format_helper.R | 57 R/test_sets.R | 4 R/utils-pipe.R | 22 README.md | 184 build/vignette.rds |binary inst/doc/SwimmeR.R | 152 inst/doc/SwimmeR.Rmd | 281 - inst/doc/SwimmeR.html | 962 ++- inst/extdata/Swim_Parse_Testing.R | 2264 ++++----- inst/extdata/df_test.csv | 7688 +++++++++++++++---------------- inst/extdata/larger_Swim_Parse_test.R | 104 man/King200Breast.Rd | 38 man/Read_Results.Rd | 61 man/Swim_Parse.Rd | 96 man/SwimmeR.Rd | 32 man/draw_bracket.Rd |only man/fold.Rd |only man/get_mode.Rd |only man/mmss_format.Rd | 60 man/sec_format_helper.Rd | 34 tests/testthat.R | 8 tests/testthat/test-Course_Convert.R | 6 tests/testthat/test-Course_Convert_DF.R | 22 tests/testthat/test-Read_Results_works.R | 39 tests/testthat/test-Swim_Parse_works.R | 248 - tests/testthat/test-get_mode.R |only vignettes/SwimmeR.Rmd | 281 - 45 files changed, 8045 insertions(+), 7749 deletions(-)
Title: Pin, Discover and Share Resources
Description: Pin remote resources into a local cache to work offline,
improve speed and avoid recomputing; discover and share resources
in local folders, 'GitHub', 'Kaggle' or 'RStudio Connect'. Resources can
be anything from 'CSV', 'JSON', or image files to arbitrary R objects.
Author: Javier Luraschi [aut, cre],
RStudio [cph]
Maintainer: Javier Luraschi <javier@rstudio.com>
Diff between pins versions 0.4.2 dated 2020-07-05 and 0.4.3 dated 2020-07-10
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NAMESPACE | 1 + NEWS.md | 10 ++++++++++ R/board_datatxt.R | 4 +++- R/board_extensions.R | 2 ++ man/custom-boards.Rd | 3 +++ 7 files changed, 28 insertions(+), 10 deletions(-)
Title: Coloured Formatting for Columns
Description: Provides 'pillar' and 'colonnade' generics designed
for formatting columns of data using the full range of colours
provided by modern terminals.
Author: Kirill Müller [aut, cre],
Hadley Wickham [aut],
RStudio [cph]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>
Diff between pillar versions 1.4.5 dated 2020-07-09 and 1.4.6 dated 2020-07-10
DESCRIPTION | 6 +++--- MD5 | 9 +++++---- NEWS.md | 5 +++++ R/strrep.R |only R/zzz.R | 6 ++++++ tests/testthat/test-format_time.R | 1 + 6 files changed, 20 insertions(+), 7 deletions(-)
Title: Linguistic Phonetic Fieldwork Tools
Description: There are a lot of different typical tasks that have to be solved during phonetic research and experiments. This includes creating a presentation that will contain all stimuli, renaming and concatenating multiple sound files recorded during a session, automatic annotation in 'Praat' TextGrids (this is one of the sound annotation standards provided by 'Praat' software, see Boersma & Weenink 2018 <http://www.fon.hum.uva.nl/praat/>), creating an html table with annotations and spectrograms, and converting multiple formats ('Praat' TextGrid, 'ELAN', 'EXMARaLDA', 'Audacity', subtitles '.srt', and 'FLEx' flextext). All of these tasks can be solved by a mixture of different tools (any programming language has programs for automatic renaming, and Praat contains scripts for concatenating and renaming files, etc.). 'phonfieldwork' provides a functionality that will make it easier to solve those tasks independently of any additional tools. You can also compare the functionality with other packages: 'rPraat' <https://CRAN.R-project.org/package=rPraat>, 'textgRid' <https://CRAN.R-project.org/package=textgRid>.
Author: George Moroz [aut, cre] (<https://orcid.org/0000-0003-1990-6083>)
Maintainer: George Moroz <agricolamz@gmail.com>
Diff between phonfieldwork versions 0.0.6 dated 2020-06-20 and 0.0.7 dated 2020-07-10
phonfieldwork-0.0.6/phonfieldwork/R/example_textgrid.R |only phonfieldwork-0.0.6/phonfieldwork/data |only phonfieldwork-0.0.6/phonfieldwork/man/example_textgrid.Rd |only phonfieldwork-0.0.7/phonfieldwork/DESCRIPTION | 18 - phonfieldwork-0.0.7/phonfieldwork/MD5 | 94 +++-- phonfieldwork-0.0.7/phonfieldwork/NAMESPACE | 7 phonfieldwork-0.0.7/phonfieldwork/NEWS | 25 + phonfieldwork-0.0.7/phonfieldwork/R/annotate_textgrid.R | 3 phonfieldwork-0.0.7/phonfieldwork/R/audacity_to_df.R |only phonfieldwork-0.0.7/phonfieldwork/R/concatenate_soundfiles.R | 56 ++- phonfieldwork-0.0.7/phonfieldwork/R/create_image_look_up.R | 4 phonfieldwork-0.0.7/phonfieldwork/R/create_subannotation.R | 16 phonfieldwork-0.0.7/phonfieldwork/R/create_viewer.R | 67 +++ phonfieldwork-0.0.7/phonfieldwork/R/df_to_tier.R | 34 + phonfieldwork-0.0.7/phonfieldwork/R/draw_sound.R | 157 ++++++-- phonfieldwork-0.0.7/phonfieldwork/R/draw_spectrogram.R | 175 +++++++--- phonfieldwork-0.0.7/phonfieldwork/R/eaf_to_df.R | 158 ++++----- phonfieldwork-0.0.7/phonfieldwork/R/exb_to_df.R | 122 +++--- phonfieldwork-0.0.7/phonfieldwork/R/extract_intervals.R | 8 phonfieldwork-0.0.7/phonfieldwork/R/flextext_to_df.R | 10 phonfieldwork-0.0.7/phonfieldwork/R/get_sound_durations.R | 8 phonfieldwork-0.0.7/phonfieldwork/R/get_textgrid_names.R | 2 phonfieldwork-0.0.7/phonfieldwork/R/set_textgrid_names.R | 3 phonfieldwork-0.0.7/phonfieldwork/R/srt_to_df.R |only phonfieldwork-0.0.7/phonfieldwork/R/textgrid_to_df.R | 55 +-- phonfieldwork-0.0.7/phonfieldwork/R/tier_to_df.R | 38 +- phonfieldwork-0.0.7/phonfieldwork/build |only phonfieldwork-0.0.7/phonfieldwork/inst/doc |only phonfieldwork-0.0.7/phonfieldwork/inst/extdata/test.TextGrid |only phonfieldwork-0.0.7/phonfieldwork/inst/extdata/test.eaf | 8 phonfieldwork-0.0.7/phonfieldwork/inst/extdata/test.srt |only phonfieldwork-0.0.7/phonfieldwork/inst/extdata/test_audacity.txt |only phonfieldwork-0.0.7/phonfieldwork/inst/rmarkdown/templates/annotation_viewer/skeleton/skeleton.Rmd | 26 + phonfieldwork-0.0.7/phonfieldwork/man/annotate_textgrid.Rd | 3 phonfieldwork-0.0.7/phonfieldwork/man/audacity_to_df.Rd |only phonfieldwork-0.0.7/phonfieldwork/man/concatenate_soundfiles.Rd | 15 phonfieldwork-0.0.7/phonfieldwork/man/create_subannotation.Rd | 3 phonfieldwork-0.0.7/phonfieldwork/man/create_viewer.Rd | 5 phonfieldwork-0.0.7/phonfieldwork/man/df_to_tier.Rd | 10 phonfieldwork-0.0.7/phonfieldwork/man/draw_sound.Rd | 31 + phonfieldwork-0.0.7/phonfieldwork/man/draw_spectrogram.Rd | 52 +- phonfieldwork-0.0.7/phonfieldwork/man/eaf_to_df.Rd | 8 phonfieldwork-0.0.7/phonfieldwork/man/exb_to_df.Rd | 8 phonfieldwork-0.0.7/phonfieldwork/man/extract_intervals.Rd | 2 phonfieldwork-0.0.7/phonfieldwork/man/flextext_to_df.Rd | 4 phonfieldwork-0.0.7/phonfieldwork/man/get_textgrid_names.Rd | 2 phonfieldwork-0.0.7/phonfieldwork/man/set_textgrid_names.Rd | 3 phonfieldwork-0.0.7/phonfieldwork/man/srt_to_df.Rd |only phonfieldwork-0.0.7/phonfieldwork/man/textgrid_to_df.Rd | 10 phonfieldwork-0.0.7/phonfieldwork/man/tier_to_df.Rd | 8 phonfieldwork-0.0.7/phonfieldwork/vignettes |only 51 files changed, 825 insertions(+), 433 deletions(-)
Title: Beautiful Bubbles for 'shiny' and 'rmarkdown' Backgrounds
Description: Creates bubbles within 'shiny' and 'rmarkdown' backgrounds using the 'bubbly-bg' 'JavaScript' library.
Author: Mohamed El Fodil Ihaddaden [aut, cre],
David Åse [cph] (bubbly-bg library)
Maintainer: Mohamed El Fodil Ihaddaden <ihaddaden.fodeil@gmail.com>
Diff between bubblyr versions 0.1.0 dated 2020-06-29 and 0.1.1 dated 2020-07-10
DESCRIPTION | 6 - MD5 | 15 ++-- NEWS.md |only R/bubbly.R | 164 ++++++++++++++++++++++++++++++++++++++++++++- README.md | 19 +++++ inst/doc/Introduction.R | 11 ++- inst/doc/Introduction.Rmd | 17 ++++ inst/doc/Introduction.html | 55 +++++++++------ vignettes/Introduction.Rmd | 17 ++++ 9 files changed, 271 insertions(+), 33 deletions(-)
Title: Distances Between Phylogenetic Trees
Description: Implements measures of tree similarity, including
information-based generalized Robinson-Foulds distances
(Phylogenetic Information Distance, Clustering Information Distance,
Matching Split Information Distance; Smith, 2020)
<doi:10.1093/bioinformatics/btaa614>;
Jaccard-Robinson-Foulds distances (Bocker et al. 2013)
<doi:10.1007/978-3-642-40453-5_13>,
including the Nye et al. (2006) metric <doi:10.1093/bioinformatics/bti720>;
the Matching Split Distance (Bogdanowicz & Giaro 2012)
<doi:10.1109/TCBB.2011.48>;
Maximum Agreement Subtree distances;
the Kendall-Colijn (2016) distance <doi:10.1093/molbev/msw124>, and the
Nearest Neighbour Interchange (NNI) distance, approximated per Li et al.
(1996) <doi:10.1007/3-540-61332-3_168>.
Calculates the median of a set of trees under any distance metric.
Author: Martin R. Smith [aut, cre, cph, prg]
(<https://orcid.org/0000-0001-5660-1727>),
Roy Jonker [prg, cph],
Yong Yang [ctb, cph],
Yi Cao [ctb, cph]
Maintainer: Martin R. Smith <martin.smith@durham.ac.uk>
Diff between TreeDist versions 1.0.0 dated 2020-06-30 and 1.1.1 dated 2020-07-10
TreeDist-1.0.0/TreeDist/R/data.R |only TreeDist-1.0.0/TreeDist/R/sysdata.rda |only TreeDist-1.0.0/TreeDist/R/utilities.R |only TreeDist-1.0.0/TreeDist/inst/doc/Tree-distance-interpretation.R |only TreeDist-1.0.0/TreeDist/inst/doc/Tree-distance-interpretation.Rmd |only TreeDist-1.0.0/TreeDist/inst/doc/Tree-distance-interpretation.html |only TreeDist-1.0.0/TreeDist/man/SplitsInBinaryTree.Rd |only TreeDist-1.0.0/TreeDist/tests/testthat/test-utilities.R |only TreeDist-1.0.0/TreeDist/vignettes/Tree-distance-interpretation.Rmd |only TreeDist-1.1.1/TreeDist/DESCRIPTION | 13 TreeDist-1.1.1/TreeDist/MD5 | 95 +- TreeDist-1.1.1/TreeDist/NAMESPACE | 12 TreeDist-1.1.1/TreeDist/NEWS.md | 24 TreeDist-1.1.1/TreeDist/R/Information.R | 11 TreeDist-1.1.1/TreeDist/R/tree_distance_info.R | 6 TreeDist-1.1.1/TreeDist/R/tree_distance_nni.R | 94 ++ TreeDist-1.1.1/TreeDist/R/tree_distance_nye.R | 3 TreeDist-1.1.1/TreeDist/R/tree_distance_spr.R | 4 TreeDist-1.1.1/TreeDist/R/tree_distance_utilities.R | 4 TreeDist-1.1.1/TreeDist/R/tree_information.R | 2 TreeDist-1.1.1/TreeDist/R/zzz.R | 6 TreeDist-1.1.1/TreeDist/build/partial.rdb |binary TreeDist-1.1.1/TreeDist/build/vignette.rds |binary TreeDist-1.1.1/TreeDist/inst/REFERENCES.bib | 20 TreeDist-1.1.1/TreeDist/inst/WORDLIST | 3 TreeDist-1.1.1/TreeDist/inst/doc/Generalized-RF.html | 80 -- TreeDist-1.1.1/TreeDist/inst/doc/Robinson-Foulds.html | 76 -- TreeDist-1.1.1/TreeDist/inst/doc/Using-TreeDist.Rmd | 2 TreeDist-1.1.1/TreeDist/inst/doc/Using-TreeDist.html | 72 -- TreeDist-1.1.1/TreeDist/inst/doc/information.html | 62 - TreeDist-1.1.1/TreeDist/inst/doc/using-distances.R | 2 TreeDist-1.1.1/TreeDist/inst/doc/using-distances.Rmd | 4 TreeDist-1.1.1/TreeDist/inst/doc/using-distances.html | 344 ++++------ TreeDist-1.1.1/TreeDist/man/AllSplitPairings.Rd | 7 TreeDist-1.1.1/TreeDist/man/ClusteringEntropy.Rd | 2 TreeDist-1.1.1/TreeDist/man/CompareAll.Rd | 4 TreeDist-1.1.1/TreeDist/man/MeilaVariationOfInformation.Rd | 2 TreeDist-1.1.1/TreeDist/man/NNIDist.Rd | 39 + TreeDist-1.1.1/TreeDist/man/NyeSimilarity.Rd | 1 TreeDist-1.1.1/TreeDist/man/SPRDist.Rd | 4 TreeDist-1.1.1/TreeDist/man/SplitEntropy.Rd | 2 TreeDist-1.1.1/TreeDist/man/TreeDist-package.Rd | 6 TreeDist-1.1.1/TreeDist/man/TreeDistance.Rd | 6 TreeDist-1.1.1/TreeDist/src/lap.cpp | 2 TreeDist-1.1.1/TreeDist/src/mast.cpp | 5 TreeDist-1.1.1/TreeDist/src/nni_distance.cpp | 109 ++- TreeDist-1.1.1/TreeDist/src/tree_distances.cpp | 2 TreeDist-1.1.1/TreeDist/src/tree_distances.h | 22 TreeDist-1.1.1/TreeDist/tests/testthat/test-plot.R | 6 TreeDist-1.1.1/TreeDist/tests/testthat/test-tree_distance.R | 3 TreeDist-1.1.1/TreeDist/tests/testthat/test-tree_distance_nni.R | 84 +- TreeDist-1.1.1/TreeDist/vignettes/Using-TreeDist.Rmd | 2 TreeDist-1.1.1/TreeDist/vignettes/using-distances.Rmd | 4 53 files changed, 723 insertions(+), 528 deletions(-)
Title: Metabolomics and Spectral Data Analysis and Mining
Description: Provides a set of methods for metabolomics
data analysis, including data loading in different formats,
pre-processing, metabolite identification, univariate and multivariate
data analysis, machine learning, feature selection and pathway analysis. Case studies
can be found on the website: <http://bio.di.uminho.pt/metabolomicspackage/index.html>.
This package suggests 'rcytoscapejs', a package not in mainstream repositories. If you need to install it,
use: devtools::install_github('cytoscape/r-cytoscape.js@v0.0.7').
Author: Christopher Costa <chrisbcl@hotmail.com> [aut],
Marcelo Maraschin <mtocsy@gmail.com> [aut],
Miguel Rocha <mrocha@di.uminho.pt> [aut, cre],
Sara Cardoso <saracardoso501@gmail.com> [aut],
Telma Afonso <telma.afonso94@gmail.com> [aut],
C. Beleites [cph],
Jie Hao [cph]
Maintainer: Miguel Rocha <mrocha@di.uminho.pt>
Diff between specmine versions 3.0.0 dated 2020-07-10 and 3.0.1 dated 2020-07-10
DESCRIPTION | 10 +++++----- MD5 | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-)
Title: Sorted L1 Penalized Estimation
Description: Efficient implementations for Sorted L-One Penalized Estimation
(SLOPE): generalized linear models regularized with the sorted L1-norm
(Bogdan et al. (2015) <doi:10/gfgwzt>). Supported models include ordinary
least-squares regression, binomial regression, multinomial regression, and
Poisson regression. Both dense and sparse predictor matrices are supported.
In addition, the package features predictor screening rules that enable fast
and efficient solutions to high-dimensional problems.
Author: Johan Larsson [aut, cre] (<https://orcid.org/0000-0002-4029-5945>),
Jonas Wallin [aut] (<https://orcid.org/0000-0003-0381-6593>),
Malgorzata Bogdan [aut],
Ewout van den Berg [aut],
Chiara Sabatti [aut],
Emmanuel Candes [aut],
Evan Patterson [aut],
Weijie Su [aut],
Jerome Friedman [ctb] (code adapted from 'glmnet'),
Trevor Hastie [ctb] (code adapted from 'glmnet'),
Rob Tibshirani [ctb] (code adapted from 'glmnet'),
Balasubramanian Narasimhan [ctb] (code adapted from 'glmnet'),
Noah Simon [ctb] (code adapted from 'glmnet'),
Junyang Qian [ctb] (code adapted from 'glmnet'),
Akarsh Goyal [ctb]
Maintainer: Johan Larsson <johan.larsson@stat.lu.se>
Diff between SLOPE versions 0.3.0 dated 2020-07-02 and 0.3.2 dated 2020-07-10
DESCRIPTION | 14 +++++----- MD5 | 30 ++++++++++----------- NEWS.md | 25 +++++++++++++++++ R/SLOPE.R | 12 +++++++- inst/WORDLIST | 10 +------ inst/doc/introduction.html | 12 ++++---- man/SLOPE-package.Rd | 1 man/SLOPE.Rd | 6 ++++ src/SLOPE.cpp | 16 ++++++----- src/families/family.h | 53 +++++++++++++++++++++++++++++++------- src/families/gaussian.h | 5 ++- src/infeasibility.h | 2 - tests/testthat/test-lasso.R | 18 ++++++------ tests/testthat/test-multinomial.R | 6 ++-- tests/testthat/test-poisson.R | 13 +++++---- tests/testthat/test-solvers.R | 6 ++-- 16 files changed, 154 insertions(+), 75 deletions(-)
Title: Quantitative Trait Locus Mapping in Experimental Crosses
Description: Provides a set of tools to perform quantitative
trait locus (QTL) analysis in experimental crosses. It is a
reimplementation of the 'R/qtl' package to better handle
high-dimensional data and complex cross designs.
Broman et al. (2018) <doi:10.1534/genetics.118.301595>.
Author: Karl W Broman [aut, cre] (<https://orcid.org/0000-0002-4914-6671>),
R Core Team [ctb]
Maintainer: Karl W Broman <broman@wisc.edu>
Diff between qtl2 versions 0.22-8 dated 2020-06-26 and 0.22-11 dated 2020-07-10
DESCRIPTION | 16 +++++----- MD5 | 64 +++++++++++++++++++++--------------------- NEWS.md | 19 +++++++++++- README.md | 33 +-------------------- src/bayes_int.cpp | 4 +- src/binreg_eigen.cpp | 8 ++--- src/cross_ail.cpp | 4 +- src/cross_ail3.cpp | 4 +- src/cross_ail3pk.cpp | 4 +- src/cross_ailpk.cpp | 6 +-- src/cross_bc.cpp | 2 - src/cross_dh6.cpp | 2 - src/cross_do.cpp | 2 - src/cross_do_util.cpp | 8 ++--- src/cross_dof1.cpp | 2 - src/cross_dopk.cpp | 2 - src/cross_f2.cpp | 4 +- src/cross_f2pk.cpp | 6 +-- src/cross_genail.cpp | 2 - src/cross_genril.cpp | 2 - src/cross_hs.cpp | 2 - src/cross_hspk.cpp | 2 - src/cross_magic19.cpp | 4 +- src/cross_riself.cpp | 2 - src/cross_riself16.cpp | 2 - src/cross_riself4.cpp | 2 - src/cross_riself8.cpp | 2 - src/cross_risib.cpp | 4 +- src/cross_risib4.cpp | 2 - src/cross_risib8.cpp | 4 +- src/lmm.cpp | 2 - src/snpprobs.cpp | 4 +- tests/testthat/test-viterbi.R | 6 ++- 33 files changed, 111 insertions(+), 121 deletions(-)
Title: A Toolkit for Recursive Partytioning
Description: A toolkit with infrastructure for representing, summarizing, and
visualizing tree-structured regression and classification models. This
unified infrastructure can be used for reading/coercing tree models from
different sources ('rpart', 'RWeka', 'PMML') yielding objects that share
functionality for print()/plot()/predict() methods. Furthermore, new and improved
reimplementations of conditional inference trees (ctree()) and model-based
recursive partitioning (mob()) from the 'party' package are provided based
on the new infrastructure. A description of this package was published
by Hothorn and Zeileis (2015) <http://jmlr.org/papers/v16/hothorn15a.html>.
Author: Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>),
Heidi Seibold [ctb] (<https://orcid.org/0000-0002-8960-9642>),
Achim Zeileis [aut] (<https://orcid.org/0000-0003-0918-3766>)
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between partykit versions 1.2-8 dated 2020-06-10 and 1.2-9 dated 2020-07-10
DESCRIPTION | 10 ++--- MD5 | 57 ++++++++++++++++++++++------ R/extree.R | 19 +++++++-- build/vignette.rds |binary inst/NEWS.Rd | 12 +++++- inst/ULGcourse-2020 |only inst/doc/constparty.pdf |binary inst/doc/ctree.R | 1 inst/doc/ctree.pdf |binary inst/doc/mob.pdf |binary inst/doc/partykit.pdf |binary tests/bugfixes.R | 15 +++++++ tests/bugfixes.Rout.save | 19 ++++++++- vignettes/ctree.Rout.save | 92 +++++++++++++++++++++++----------------------- 14 files changed, 152 insertions(+), 73 deletions(-)
Title: Simulated Maximum Likelihood Estimation of Mixed Logit Models
for Large Datasets
Description: Specification and estimation of multinomial logit
models. Large datasets and complex models are supported, with an
intuitive syntax. Multinomial Logit Models, Mixed models, random
coefficients and Hybrid Choice are all supported. For more
information, see Molloy et al. (2019) <doi:10.3929/ethz-b-000334289>.
Author: Joseph Molloy [aut, cre]
Maintainer: Joseph Molloy <joseph.molloy@ivt.baug.ethz.ch>
Diff between mixl versions 1.1.2 dated 2020-03-21 and 1.2.0 dated 2020-07-10
DESCRIPTION | 12 MD5 | 98 - R/compile_posterior.R | 184 +-- R/compiler.R | 196 +-- R/examples/av_matrix.R | 10 R/examples/extract_av_cols.R | 10 R/examples/extract_indiv_data.R | 10 R/examples/generate_default_availabilities.R | 6 R/examples/model_stats.R | 40 R/examples/posteriors.R | 54 R/examples/probabilities.R | 50 R/examples/specify_model.R | 38 R/helper_functions.R | 138 +- R/mle.R | 344 ++--- R/model_stats.R | 27 R/preprocessor.R | 334 ++--- R/probabilities.R | 207 +-- R/tex.R | 188 +-- build/vignette.rds |binary inst/doc/user-guide.R | 12 inst/doc/user-guide.Rmd | 280 ++-- inst/doc/user-guide.html | 736 ++++++------ inst/include/MIXL_OPENMP_FLAG |only inst/include/MIXL_OPENMP_FLAG.in |only man/av_matrix.Rd | 54 man/check_inputs.Rd | 62 - man/compileUtilityFunction.Rd | 32 man/create_halton_draws.Rd | 52 man/estimate.Rd | 156 +- man/extract_av_cols.Rd | 54 man/extract_indiv_data.Rd | 54 man/generate_default_availabilities.Rd | 50 man/mixl-package.Rd | 108 - man/posteriors.Rd | 102 - man/print.mixl.Rd | 80 - man/print.summary.mixl.Rd | 78 - man/probabilities.Rd | 126 +- man/specify_model.Rd | 124 +- man/summary.mixl.Rd | 84 - man/summary_tex.Rd | 34 src |only tests/testthat.R | 10 tests/testthat/23_wtp_pooled_hybrid_ol_dalynorm_utilities.R |only tests/testthat/test_hybrid_choice.R |only tests/testthat/test_maxlikelihood.R | 274 ++-- tests/testthat/test_posteriors.R | 374 +++--- tests/testthat/test_prediction.R | 212 +-- tests/testthat/test_variable_identification.R | 248 ++-- tests/testthat/test_variable_replacement.R | 158 +- tests/testthat/test_variable_validation.R | 114 - vignettes/user-guide.Rmd | 280 ++-- vignettes/user-guide.md | 20 52 files changed, 2991 insertions(+), 2923 deletions(-)
Title: Fast Imputations Using 'Rcpp' and 'Armadillo'
Description: Fast imputations under the object-oriented programming paradigm.
Moreover there are offered a few functions built to work with popular R packages such as 'data.table' or 'dplyr'.
The biggest improvement in time performance could be achieve for a calculation where a grouping variable have to be used.
A single evaluation of a quantitative model for the multiple imputations is another major enhancement.
A new major improvement is one of the fastest predictive mean matching in the R world because of presorting and binary search.
Author: Maciej Nasinski [aut, cre]
Maintainer: Maciej Nasinski <nasinski.maciej@gmail.com>
Diff between miceFast versions 0.6.1 dated 2020-07-06 and 0.6.2 dated 2020-07-10
miceFast-0.6.1/miceFast/R/miceFast.R |only miceFast-0.6.1/miceFast/R/pmm.R |only miceFast-0.6.2/miceFast/DESCRIPTION | 6 miceFast-0.6.2/miceFast/MD5 | 18 miceFast-0.6.2/miceFast/NEWS.md | 17 miceFast-0.6.2/miceFast/inst/doc/miceFast-intro.R | 546 ++++++++++-------- miceFast-0.6.2/miceFast/inst/doc/miceFast-intro.Rmd | 536 ++++++++++-------- miceFast-0.6.2/miceFast/inst/doc/miceFast-intro.html | 549 ++++++++++--------- miceFast-0.6.2/miceFast/src/R_funs.cpp | 2 miceFast-0.6.2/miceFast/tests/testthat/test-vif.R | 7 miceFast-0.6.2/miceFast/vignettes/miceFast-intro.Rmd | 536 ++++++++++-------- 11 files changed, 1220 insertions(+), 997 deletions(-)
Title: Ensemble of Phalanxes
Description: An ensemble method for the statistical detection of
a rare class in two-class classification problems. The method uses an
ensemble of classifiers where the constituent
models of the ensemble use disjoint subsets (phalanxes) of explanatory
variables. We provide an implementation of the phalanx-formation algorithm.
Please see Tomal et al. (2015) <doi:10.1214/14-AOAS778>,
Tomal et al. (2016) <doi:10.1021/acs.jcim.5b00663>, and
Tomal et al. (2019) <arXiv:1706.06971> for more details.
Author: Jabed Tomal [aut, cre],
Grace Hsu [aut],
William Welch [aut],
Marcia Wang [ctb]
Maintainer: Jabed Tomal <jtomal@tru.ca>
Diff between EPX versions 1.0.0 dated 2020-07-03 and 1.0.1 dated 2020-07-10
DESCRIPTION | 12 +- MD5 | 34 +++--- R/BNhold.R | 9 - R/BNsample.R | 6 - R/cvEPX.R | 35 +++--- R/epx.R | 156 ++++++++++++++-------------- R/epx_algorithm.R | 14 +- R/harvest.R | 46 ++++---- R/plotEPX.R | 2 R/predictEPX.R | 10 - R/summaryEPX.R | 15 +- man/BNhold.Rd | 63 +++++------ man/BNsample.Rd | 64 +++++------ man/cv.epx.Rd | 181 ++++++++++++++++----------------- man/epx.Rd | 286 +++++++++++++++++++++++++++-------------------------- man/harvest.Rd | 66 ++++++------ man/plot.epx.Rd | 128 +++++++++++------------ man/summary.epx.Rd | 71 ++++++------- 18 files changed, 601 insertions(+), 597 deletions(-)
Title: Estimating and Mapping Disaggregated Indicators
Description: Functions that support estimating, assessing and mapping regional
disaggregated indicators. So far, estimation methods comprise direct estimation,
the model-based unit-level approach Empirical Best Prediction (see "Small area
estimation of poverty indicators" by Molina and Rao (2010) <doi:10.1002/cjs.10051>),
the area-level model (see "Estimates of income for small places: An
application of James-Stein procedures to Census Data" by (Fay and Herriot 1979)
<doi:10.1080/01621459.1979.10482505>) and various extensions of it (adjusted variance estimation methods,
log and arcsin transformation, spatial, robust and measurement error models),
as well as their precision estimates. The assessment of the used model
is supported by a summary and diagnostic plots. For a suitable presentation of
estimates, map plots can be easily created. Furthermore, results can easily be
exported to excel. For a detailed description of the package and the methods used
see "The {R} Package {emdi} for Estimating and Mapping Regionally Disaggregated Indicators"
by Kreutzmann et al. (2019) <doi:10.18637/jss.v091.i07>.
Author: Sylvia Harmening [aut],
Ann-Kristin Kreutzmann [aut],
Soeren Pannier [aut, cre],
Natalia Rojas-Perilla [aut],
Nicola Salvati [aut],
Timo Schmid [aut],
Matthias Templ [aut],
Nikos Tzavidis [aut],
Nora Würz [aut]
Maintainer: Soeren Pannier <soeren.pannier@fu-berlin.de>
Diff between emdi versions 2.0.0 dated 2020-07-07 and 2.0.1 dated 2020-07-10
DESCRIPTION | 10 +++--- MD5 | 16 +++++----- NEWS.md | 5 +++ R/compare_plot.R | 6 +-- inst/COPYRIGHTS | 4 +- inst/doc/vignette_fh.pdf |binary man/compare_plot.Rd | 2 - man/compare_plot.emdi.Rd | 2 - tests/testthat/test_fh_variance.R | 58 ++++++++++++++++++++++++-------------- 9 files changed, 63 insertions(+), 40 deletions(-)
Title: Tools for Descriptive Statistics
Description: A collection of miscellaneous basic statistic functions and convenience wrappers for efficiently describing data. The author's intention was to create a toolbox, which facilitates the (notoriously time consuming) first descriptive tasks in data analysis, consisting of calculating descriptive statistics, drawing graphical summaries and reporting the results. The package contains furthermore functions to produce documents using MS Word (or PowerPoint) and functions to import data from Excel. Many of the included functions can be found scattered in other packages and other sources written partly by Titans of R. The reason for collecting them here, was primarily to have them consolidated in ONE instead of dozens of packages (which themselves might depend on other packages which are not needed at all), and to provide a common and consistent interface as far as function and arguments naming, NA handling, recycling rules etc. are concerned. Google style guides were used as naming rules (in absence of convincing alternatives). The 'BigCamelCase' style was consequently applied to functions borrowed from contributed R packages as well.
Author: Andri Signorell [aut, cre],
Ken Aho [ctb],
Andreas Alfons [ctb],
Nanina Anderegg [ctb],
Tomas Aragon [ctb],
Antti Arppe [ctb],
Adrian Baddeley [ctb],
Kamil Barton [ctb],
Ben Bolker [ctb],
Hans W. Borchers [ctb],
Frederico Caeiro [ctb],
Stephane Champely [ctb],
Daniel Chessel [ctb],
Leanne Chhay [ctb],
Clint Cummins [ctb],
Michael Dewey [ctb],
Harold C. Doran [ctb],
Stephane Dray [ctb],
Charles Dupont [ctb],
Dirk Eddelbuettel [ctb],
Jeff Enos [ctb],
Claus Ekstrom [ctb],
Martin Elff [ctb],
Richard W. Farebrother [ctb],
John Fox [ctb],
Romain Francois [ctb],
Michael Friendly [ctb],
Tal Galili [ctb],
Matthias Gamer [ctb],
Joseph L. Gastwirth [ctb],
Yulia R. Gel [ctb],
Vilmantas Gegzna [ctb],
Juergen Gross [ctb],
Gabor Grothendieck [ctb],
Frank E. Harrell Jr [ctb],
Richard Heiberger [ctb],
Michael Hoehle [ctb],
Christian W. Hoffmann [ctb],
Soeren Hojsgaard [ctb],
Torsten Hothorn [ctb],
Markus Huerzeler [ctb],
Wallace W. Hui [ctb],
Pete Hurd [ctb],
Rob J. Hyndman [ctb],
Pablo J. Villacorta Iglesias [ctb],
Christopher Jackson [ctb],
Matthias Kohl [ctb],
Mikko Korpela [ctb],
Max Kuhn [ctb],
Detlew Labes [ctb],
Duncan Temple Lang [ctb],
Friederich Leisch [ctb],
Jim Lemon [ctb],
Dong Li [ctb],
Martin Maechler [ctb],
Arni Magnusson [ctb],
Ben Mainwaring [ctb],
Daniel Malter [ctb],
George Marsaglia [ctb],
John Marsaglia [ctb],
Alina Matei [ctb],
David Meyer [ctb],
Weiwen Miao [ctb],
Giovanni Millo [ctb],
Yongyi Min [ctb],
David Mitchell [ctb],
Franziska Mueller [ctb],
Markus Naepflin [ctb],
Daniel Navarro [ctb],
Henric Nilsson [ctb],
Klaus Nordhausen [ctb],
Derek Ogle [ctb],
Hong Ooi [ctb],
Nick Parsons [ctb],
Sandrine Pavoine [ctb],
Tony Plate [ctb],
Roland Rapold [ctb],
William Revelle [ctb],
Tyler Rinker [ctb],
Brian D. Ripley [ctb],
Caroline Rodriguez [ctb],
Nathan Russell [ctb],
Nick Sabbe [ctb],
Venkatraman E. Seshan [ctb],
Greg Snow [ctb],
Michael Smithson [ctb],
Karline Soetaert [ctb],
Werner A. Stahel [ctb],
Alec Stephenson [ctb],
Mark Stevenson [ctb],
Ralf Stubner [ctb],
Matthias Templ [ctb],
Terry Therneau [ctb],
Yves Tille [ctb],
Luis Torgo [ctb],
Adrian Trapletti [ctb],
Joshua Ulrich [ctb],
Kevin Ushey [ctb],
Jeremy VanDerWal [ctb],
Bill Venables [ctb],
John Verzani [ctb],
Gregory R. Warnes [ctb],
Stefan Wellek [ctb],
Hadley Wickham [ctb],
Rand R. Wilcox [ctb],
Peter Wolf [ctb],
Daniel Wollschlaeger [ctb],
Joseph Wood [ctb],
Ying Wu [ctb],
Thomas Yee [ctb],
Achim Zeileis [ctb]
Maintainer: Andri Signorell <andri@signorell.net>
Diff between DescTools versions 0.99.36 dated 2020-05-23 and 0.99.37 dated 2020-07-10
DescTools-0.99.36/DescTools/man/CentralValue.Rd |only DescTools-0.99.36/DescTools/man/WrdInsertBookmark.Rd |only DescTools-0.99.36/DescTools/src/Barnard.c |only DescTools-0.99.37/DescTools/DESCRIPTION | 14 DescTools-0.99.37/DescTools/MD5 | 60 - DescTools-0.99.37/DescTools/NAMESPACE | 14 DescTools-0.99.37/DescTools/NEWS | 47 DescTools-0.99.37/DescTools/R/DescTools.r | 671 +++++++++-- DescTools-0.99.37/DescTools/R/Imputation.R | 6 DescTools-0.99.37/DescTools/R/LinMod.R | 1079 ++++++++++++------- DescTools-0.99.37/DescTools/R/StatsAndCIs.r | 40 DescTools-0.99.37/DescTools/R/Tests.r | 237 ++-- DescTools-0.99.37/DescTools/README.md | 4 DescTools-0.99.37/DescTools/build/vignette.rds |binary DescTools-0.99.37/DescTools/man/Append.Rd | 2 DescTools-0.99.37/DescTools/man/BarnardTest.Rd | 46 DescTools-0.99.37/DescTools/man/CochranQTest.Rd | 9 DescTools-0.99.37/DescTools/man/DescTools-package.Rd | 8 DescTools-0.99.37/DescTools/man/FisherZ.Rd | 4 DescTools-0.99.37/DescTools/man/Format.Rd | 64 - DescTools-0.99.37/DescTools/man/KnnImputation.Rd | 5 DescTools-0.99.37/DescTools/man/PlotCashFlow.Rd | 9 DescTools-0.99.37/DescTools/man/PlotConDens.Rd |only DescTools-0.99.37/DescTools/man/PlotLinesA.Rd | 12 DescTools-0.99.37/DescTools/man/PseudoR2.Rd | 3 DescTools-0.99.37/DescTools/man/RgbToCmy.Rd |only DescTools-0.99.37/DescTools/man/SplitToCol.Rd |only DescTools-0.99.37/DescTools/man/StrExtract.Rd | 5 DescTools-0.99.37/DescTools/man/StrSplit.Rd |only DescTools-0.99.37/DescTools/man/StrTrunc.Rd | 29 DescTools-0.99.37/DescTools/man/TOne.Rd | 9 DescTools-0.99.37/DescTools/man/ToWrd.Rd | 38 DescTools-0.99.37/DescTools/man/WrdBookmark.Rd | 67 - DescTools-0.99.37/DescTools/src/init.c | 6 DescTools-0.99.37/DescTools/tests/TestsPseudoR2.R |only 35 files changed, 1767 insertions(+), 721 deletions(-)
Title: Breast Cancer Risk Assessment
Description: Functions provide risk projections of invasive breast cancer based on Gail model according to National Cancer Institute's Breast Cancer Risk Assessment Tool algorithm for specified race/ethnic groups and age intervals.
Gail MH, Brinton LA, et al (1989) <doi:10.1093/jnci/81.24.1879>.
Marthew PB, Gail MH, et al (2016) <doi:10.1093/jnci/djw215>.
Author: Fanni Zhang
Maintainer: Fanni Zhang <rstatpackages@gmail.com>
Diff between BCRA versions 2.1.1 dated 2020-06-18 and 2.1.2 dated 2020-07-10
DESCRIPTION | 14 ++++++++------ MD5 | 6 +++--- R/recode.check.R | 2 +- man/BCRA-package.Rd | 4 ++-- 4 files changed, 14 insertions(+), 12 deletions(-)
Title: Clopper-Pearson Confidence Interval and Generalized Binomial
Distribution
Description: Density, distribution function, quantile function and random generation for the Generalized Binomial Distribution. Functions to compute the Clopper-Pearson Confidence Interval and the required sample size. Enhanced model for burn-in studies, where failures are tackled by countermeasures.
Author: Horst Lewitschnig, David Lenzi
Maintainer: Horst Lewitschnig <Horst.Lewitschnig@infineon.com>
Diff between GenBinomApps versions 1.0-2 dated 2014-06-30 and 1.1 dated 2020-07-10
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- NAMESPACE | 1 + R/dgbinom.R | 2 +- 4 files changed, 9 insertions(+), 8 deletions(-)
Title: Keyboard and Mouse Input Simulation for Windows OS
Description: Control your keyboard and mouse with R code by simulating key presses and mouse clicks. The input simulation is implemented with the Windows API.
Author: Jim Chen [aut, cre],
Jeff Keller [aut, ctb],
Garry Hopwood [ctb],
Chieh Hsu [ctb]
Maintainer: Jim Chen <jim71183@gmail.com>
Diff between KeyboardSimulator versions 2.5.0 dated 2020-04-14 and 2.5.1 dated 2020-07-10
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- NEWS | 5 +++++ R/main.R | 22 ++++++++++++++++++---- README.md | 2 +- 5 files changed, 33 insertions(+), 14 deletions(-)
More information about KeyboardSimulator at CRAN
Permanent link
Title: Tidy Tools for Forecasting
Description: Tidies up the forecasting modeling and prediction work flow,
extends the 'broom' package
with 'sw_tidy', 'sw_glance', 'sw_augment', and 'sw_tidy_decomp' functions
for various forecasting models,
and enables converting 'forecast' objects to
"tidy" data frames with 'sw_sweep'.
Author: Matt Dancho [aut, cre],
Davis Vaughan [aut]
Maintainer: Matt Dancho <mdancho@business-science.io>
Diff between sweep versions 0.2.2 dated 2019-10-08 and 0.2.3 dated 2020-07-10
DESCRIPTION | 15 MD5 | 74 +-- NAMESPACE | 3 NEWS.md | 10 R/global_vars.R | 2 R/sw_augment.R | 2 R/sw_sweep.R | 6 R/sweep-package.R | 4 R/tidiers_arima.R | 2 R/tidiers_ets.R | 2 R/tidiers_robets.R | 2 R/tidiers_stl.R | 83 +++ R/utils-broom.R | 21 README.md | 6 build/vignette.rds |binary inst/doc/SW00_Introduction_to_sweep.R | 40 - inst/doc/SW00_Introduction_to_sweep.html | 385 +++++++++-------- inst/doc/SW01_Forecasting_Time_Series_Groups.R | 34 - inst/doc/SW01_Forecasting_Time_Series_Groups.html | 485 +++++++++++----------- inst/doc/SW02_Forecasting_Multiple_Models.R | 46 +- inst/doc/SW02_Forecasting_Multiple_Models.html | 411 +++++++++--------- man/arima_string.Rd | 2 man/bats_string.Rd | 2 man/bike_sales.Rd | 6 man/sw_augment.Rd | 2 man/sw_sweep.Rd | 3 man/sweep_package.Rd | 6 man/tbats_string.Rd | 2 man/tidiers_HoltWinters.Rd | 6 man/tidiers_StructTS.Rd | 3 man/tidiers_arima.Rd | 16 man/tidiers_bats.Rd | 6 man/tidiers_decomposed_ts.Rd | 3 man/tidiers_ets.Rd | 6 man/tidiers_nnetar.Rd | 3 man/tidiers_robets.Rd | 6 man/tidiers_stl.Rd | 43 + tests/testthat/test_tidiers_lm.R | 4 38 files changed, 992 insertions(+), 760 deletions(-)
Title: Process Control and Internal Validation of Forensic STR Kits
Description: An open source platform for validation and process control.
Tools to analyze data from internal validation of forensic short tandem
repeat (STR) kits are provided. The tools are developed to provide
the necessary data to conform with guidelines for internal validation
issued by the European Network of Forensic Science Institutes (ENFSI)
DNA Working Group, and the Scientific Working Group on DNA Analysis Methods
(SWGDAM). A front-end graphical user interface is provided.
More information about each function can be found in the
respective help documentation.
Author: Oskar Hansson
Maintainer: Oskar Hansson <oskhan@ous-hf.no>
Diff between strvalidator versions 2.2.0 dated 2019-03-22 and 2.3.0 dated 2020-07-10
strvalidator-2.2.0/strvalidator/tests/testthat/test-tableBalance.r |only strvalidator-2.3.0/strvalidator/DESCRIPTION | 15 strvalidator-2.3.0/strvalidator/MD5 | 457 +- strvalidator-2.3.0/strvalidator/NAMESPACE | 7 strvalidator-2.3.0/strvalidator/NEWS | 53 strvalidator-2.3.0/strvalidator/R/addData_gui.r | 203 strvalidator-2.3.0/strvalidator/R/addDye_gui.r | 148 strvalidator-2.3.0/strvalidator/R/addMarker_gui.r | 122 strvalidator-2.3.0/strvalidator/R/addSize_gui.r | 128 strvalidator-2.3.0/strvalidator/R/auditTrail.R | 17 strvalidator-2.3.0/strvalidator/R/calculateAT6_gui.r | 214 strvalidator-2.3.0/strvalidator/R/calculateAT_gui.r | 370 + strvalidator-2.3.0/strvalidator/R/calculateAllT.r | 2 strvalidator-2.3.0/strvalidator/R/calculateAllT_gui.r | 142 strvalidator-2.3.0/strvalidator/R/calculateAllele_gui.r | 131 strvalidator-2.3.0/strvalidator/R/calculateCapillary_gui.r | 153 strvalidator-2.3.0/strvalidator/R/calculateConcordance_gui.r | 222 - strvalidator-2.3.0/strvalidator/R/calculateCopies_gui.r | 146 strvalidator-2.3.0/strvalidator/R/calculateDropout.r | 16 strvalidator-2.3.0/strvalidator/R/calculateDropout_gui.r | 246 - strvalidator-2.3.0/strvalidator/R/calculateHb_gui.r | 246 - strvalidator-2.3.0/strvalidator/R/calculateHeight_gui.r | 241 - strvalidator-2.3.0/strvalidator/R/calculateLb.r | 41 strvalidator-2.3.0/strvalidator/R/calculateLb_gui.r | 339 + strvalidator-2.3.0/strvalidator/R/calculateMixture_gui.r | 232 - strvalidator-2.3.0/strvalidator/R/calculateOL_gui.r | 144 strvalidator-2.3.0/strvalidator/R/calculateOverlap_gui.r | 178 strvalidator-2.3.0/strvalidator/R/calculatePeaks_gui.r | 189 strvalidator-2.3.0/strvalidator/R/calculatePullup_gui.r | 320 + strvalidator-2.3.0/strvalidator/R/calculateRatio_gui.r | 317 + strvalidator-2.3.0/strvalidator/R/calculateResultType_gui.r | 230 - strvalidator-2.3.0/strvalidator/R/calculateSlope_gui.r | 240 - strvalidator-2.3.0/strvalidator/R/calculateSpike_gui.R | 156 strvalidator-2.3.0/strvalidator/R/calculateStatistics.r |only strvalidator-2.3.0/strvalidator/R/calculateStatistics_gui.r |only strvalidator-2.3.0/strvalidator/R/calculateStutter_gui.r | 336 + strvalidator-2.3.0/strvalidator/R/calculateT.r | 4 strvalidator-2.3.0/strvalidator/R/checkDataset.r | 60 strvalidator-2.3.0/strvalidator/R/checkSubset_gui.r | 160 strvalidator-2.3.0/strvalidator/R/colNames.r | 2 strvalidator-2.3.0/strvalidator/R/columns_gui.r | 178 strvalidator-2.3.0/strvalidator/R/combineBinsAndPanels.r | 2 strvalidator-2.3.0/strvalidator/R/combine_gui.r | 140 strvalidator-2.3.0/strvalidator/R/cropData_gui.r | 368 + strvalidator-2.3.0/strvalidator/R/editData_gui.r | 257 - strvalidator-2.3.0/strvalidator/R/export.r | 10 strvalidator-2.3.0/strvalidator/R/export_gui.r | 432 + strvalidator-2.3.0/strvalidator/R/filterProfile_gui.r | 334 + strvalidator-2.3.0/strvalidator/R/generateEPG_gui.r | 256 - strvalidator-2.3.0/strvalidator/R/getKit.r | 9 strvalidator-2.3.0/strvalidator/R/getSetting.r |only strvalidator-2.3.0/strvalidator/R/getStrings.r |only strvalidator-2.3.0/strvalidator/R/ggsave_gui.r | 222 - strvalidator-2.3.0/strvalidator/R/guessProfile_gui.r | 140 strvalidator-2.3.0/strvalidator/R/import_gui.r | 255 - strvalidator-2.3.0/strvalidator/R/listObjects.r | 83 strvalidator-2.3.0/strvalidator/R/makeKit_gui.r | 274 - strvalidator-2.3.0/strvalidator/R/modelDropout_gui.r | 494 +- strvalidator-2.3.0/strvalidator/R/plotAT_gui.r | 268 + strvalidator-2.3.0/strvalidator/R/plotBalance_gui.r | 608 +- strvalidator-2.3.0/strvalidator/R/plotCapillary_gui.r | 335 + strvalidator-2.3.0/strvalidator/R/plotContamination_gui.r | 183 strvalidator-2.3.0/strvalidator/R/plotDistribution_gui.r | 442 +- strvalidator-2.3.0/strvalidator/R/plotDropout_gui.r | 494 +- strvalidator-2.3.0/strvalidator/R/plotGroups_gui.r | 289 + strvalidator-2.3.0/strvalidator/R/plotKit_gui.r | 190 strvalidator-2.3.0/strvalidator/R/plotPeaks_gui.r | 224 - strvalidator-2.3.0/strvalidator/R/plotPrecision_gui.r | 1106 +++-- strvalidator-2.3.0/strvalidator/R/plotPullup_gui.r | 347 + strvalidator-2.3.0/strvalidator/R/plotRatio_gui.r | 245 - strvalidator-2.3.0/strvalidator/R/plotResultType_gui.r | 221 - strvalidator-2.3.0/strvalidator/R/plotSlope_gui.r | 252 - strvalidator-2.3.0/strvalidator/R/plotStutter_gui.r | 875 +++- strvalidator-2.3.0/strvalidator/R/readBinsFile.r | 8 strvalidator-2.3.0/strvalidator/R/removeArtefact_gui.r | 138 strvalidator-2.3.0/strvalidator/R/removeSpike_gui.r | 136 strvalidator-2.3.0/strvalidator/R/saveObject.r | 92 strvalidator-2.3.0/strvalidator/R/slim_gui.r | 269 - strvalidator-2.3.0/strvalidator/R/strvalidator.r | 2180 +++++++--- strvalidator-2.3.0/strvalidator/R/tableBalance.r | 7 strvalidator-2.3.0/strvalidator/R/tableBalance_gui.r | 164 strvalidator-2.3.0/strvalidator/R/tableCapillary.r | 7 strvalidator-2.3.0/strvalidator/R/tableCapillary_gui.r | 185 strvalidator-2.3.0/strvalidator/R/tablePrecision.r | 7 strvalidator-2.3.0/strvalidator/R/tablePrecision_gui.r | 557 +- strvalidator-2.3.0/strvalidator/R/tableStutter.r | 6 strvalidator-2.3.0/strvalidator/R/tableStutter_gui.r | 170 strvalidator-2.3.0/strvalidator/R/trim_gui.r | 247 - strvalidator-2.3.0/strvalidator/inst/extdata/languages |only strvalidator-2.3.0/strvalidator/inst/extdata/settings.txt |only strvalidator-2.3.0/strvalidator/man/addColor.Rd | 117 strvalidator-2.3.0/strvalidator/man/addData.Rd | 104 strvalidator-2.3.0/strvalidator/man/addData_gui.Rd | 61 strvalidator-2.3.0/strvalidator/man/addDye_gui.Rd | 75 strvalidator-2.3.0/strvalidator/man/addMarker.Rd | 62 strvalidator-2.3.0/strvalidator/man/addMarker_gui.Rd | 66 strvalidator-2.3.0/strvalidator/man/addOrder.Rd | 85 strvalidator-2.3.0/strvalidator/man/addSize.Rd | 69 strvalidator-2.3.0/strvalidator/man/addSize_gui.Rd | 61 strvalidator-2.3.0/strvalidator/man/auditTrail.Rd | 136 strvalidator-2.3.0/strvalidator/man/calculateAT.Rd | 195 strvalidator-2.3.0/strvalidator/man/calculateAT6.Rd | 141 strvalidator-2.3.0/strvalidator/man/calculateAT6_gui.Rd | 66 strvalidator-2.3.0/strvalidator/man/calculateAT_gui.Rd | 70 strvalidator-2.3.0/strvalidator/man/calculateAllT.Rd | 124 strvalidator-2.3.0/strvalidator/man/calculateAllT_gui.Rd | 66 strvalidator-2.3.0/strvalidator/man/calculateAllele.Rd | 89 strvalidator-2.3.0/strvalidator/man/calculateAllele_gui.Rd | 60 strvalidator-2.3.0/strvalidator/man/calculateCapillary.Rd | 67 strvalidator-2.3.0/strvalidator/man/calculateCapillary_gui.Rd | 66 strvalidator-2.3.0/strvalidator/man/calculateConcordance.Rd | 100 strvalidator-2.3.0/strvalidator/man/calculateConcordance_gui.Rd | 66 strvalidator-2.3.0/strvalidator/man/calculateCopies.Rd | 91 strvalidator-2.3.0/strvalidator/man/calculateCopies_gui.Rd | 66 strvalidator-2.3.0/strvalidator/man/calculateDropout.Rd | 206 strvalidator-2.3.0/strvalidator/man/calculateDropout_gui.Rd | 64 strvalidator-2.3.0/strvalidator/man/calculateHb.Rd | 115 strvalidator-2.3.0/strvalidator/man/calculateHb_gui.Rd | 66 strvalidator-2.3.0/strvalidator/man/calculateHeight.Rd | 147 strvalidator-2.3.0/strvalidator/man/calculateHeight_gui.Rd | 82 strvalidator-2.3.0/strvalidator/man/calculateLb.Rd | 197 strvalidator-2.3.0/strvalidator/man/calculateLb_gui.Rd | 66 strvalidator-2.3.0/strvalidator/man/calculateMixture.Rd | 142 strvalidator-2.3.0/strvalidator/man/calculateMixture_gui.Rd | 66 strvalidator-2.3.0/strvalidator/man/calculateOL.Rd | 64 strvalidator-2.3.0/strvalidator/man/calculateOL_gui.Rd | 72 strvalidator-2.3.0/strvalidator/man/calculateOverlap.Rd | 81 strvalidator-2.3.0/strvalidator/man/calculateOverlap_gui.Rd | 80 strvalidator-2.3.0/strvalidator/man/calculatePeaks.Rd | 116 strvalidator-2.3.0/strvalidator/man/calculatePeaks_gui.Rd | 68 strvalidator-2.3.0/strvalidator/man/calculatePullup.Rd | 125 strvalidator-2.3.0/strvalidator/man/calculatePullup_gui.Rd | 66 strvalidator-2.3.0/strvalidator/man/calculateRatio.Rd | 135 strvalidator-2.3.0/strvalidator/man/calculateRatio_gui.Rd | 66 strvalidator-2.3.0/strvalidator/man/calculateResultType.Rd | 98 strvalidator-2.3.0/strvalidator/man/calculateResultType_gui.Rd | 66 strvalidator-2.3.0/strvalidator/man/calculateSlope.Rd | 97 strvalidator-2.3.0/strvalidator/man/calculateSlope_gui.Rd | 66 strvalidator-2.3.0/strvalidator/man/calculateSpike.Rd | 106 strvalidator-2.3.0/strvalidator/man/calculateSpike_gui.Rd | 66 strvalidator-2.3.0/strvalidator/man/calculateStatistics.Rd |only strvalidator-2.3.0/strvalidator/man/calculateStatistics_gui.Rd |only strvalidator-2.3.0/strvalidator/man/calculateStutter.Rd | 116 strvalidator-2.3.0/strvalidator/man/calculateStutter_gui.Rd | 66 strvalidator-2.3.0/strvalidator/man/calculateT.Rd | 85 strvalidator-2.3.0/strvalidator/man/checkDataset.Rd | 80 strvalidator-2.3.0/strvalidator/man/checkSubset.Rd | 79 strvalidator-2.3.0/strvalidator/man/checkSubset_gui.Rd | 66 strvalidator-2.3.0/strvalidator/man/colConvert.Rd | 69 strvalidator-2.3.0/strvalidator/man/colNames.Rd | 71 strvalidator-2.3.0/strvalidator/man/columns.Rd | 131 strvalidator-2.3.0/strvalidator/man/columns_gui.Rd | 55 strvalidator-2.3.0/strvalidator/man/combineBinsAndPanels.Rd | 72 strvalidator-2.3.0/strvalidator/man/combine_gui.Rd | 54 strvalidator-2.3.0/strvalidator/man/cropData_gui.Rd | 78 strvalidator-2.3.0/strvalidator/man/detectKit.Rd | 56 strvalidator-2.3.0/strvalidator/man/editData_gui.Rd | 91 strvalidator-2.3.0/strvalidator/man/export.Rd | 118 strvalidator-2.3.0/strvalidator/man/export_gui.Rd | 76 strvalidator-2.3.0/strvalidator/man/filterProfile.Rd | 129 strvalidator-2.3.0/strvalidator/man/filterProfile_gui.Rd | 72 strvalidator-2.3.0/strvalidator/man/generateEPG.Rd | 145 strvalidator-2.3.0/strvalidator/man/generateEPG_gui.Rd | 66 strvalidator-2.3.0/strvalidator/man/getDb.Rd | 64 strvalidator-2.3.0/strvalidator/man/getKit.Rd | 91 strvalidator-2.3.0/strvalidator/man/getSetting.Rd |only strvalidator-2.3.0/strvalidator/man/getStrings.Rd |only strvalidator-2.3.0/strvalidator/man/ggsave_gui.Rd | 78 strvalidator-2.3.0/strvalidator/man/guessProfile.Rd | 86 strvalidator-2.3.0/strvalidator/man/guessProfile_gui.Rd | 66 strvalidator-2.3.0/strvalidator/man/heightToPeak.Rd | 56 strvalidator-2.3.0/strvalidator/man/import.Rd | 161 strvalidator-2.3.0/strvalidator/man/import_gui.Rd | 63 strvalidator-2.3.0/strvalidator/man/listObjects.Rd | 80 strvalidator-2.3.0/strvalidator/man/makeKit_gui.Rd | 69 strvalidator-2.3.0/strvalidator/man/maskAT.Rd | 128 strvalidator-2.3.0/strvalidator/man/modelDropout_gui.Rd | 240 - strvalidator-2.3.0/strvalidator/man/plotAT_gui.Rd | 65 strvalidator-2.3.0/strvalidator/man/plotBalance_gui.Rd | 78 strvalidator-2.3.0/strvalidator/man/plotCapillary_gui.Rd | 72 strvalidator-2.3.0/strvalidator/man/plotContamination_gui.Rd | 78 strvalidator-2.3.0/strvalidator/man/plotDistribution_gui.Rd | 80 strvalidator-2.3.0/strvalidator/man/plotDropout_gui.Rd | 78 strvalidator-2.3.0/strvalidator/man/plotGroups_gui.Rd | 78 strvalidator-2.3.0/strvalidator/man/plotKit_gui.Rd | 57 strvalidator-2.3.0/strvalidator/man/plotPeaks_gui.Rd | 68 strvalidator-2.3.0/strvalidator/man/plotPrecision_gui.Rd | 74 strvalidator-2.3.0/strvalidator/man/plotPullup_gui.Rd | 72 strvalidator-2.3.0/strvalidator/man/plotRatio_gui.Rd | 70 strvalidator-2.3.0/strvalidator/man/plotResultType_gui.Rd | 70 strvalidator-2.3.0/strvalidator/man/plotSlope_gui.Rd | 70 strvalidator-2.3.0/strvalidator/man/plotStutter_gui.Rd | 72 strvalidator-2.3.0/strvalidator/man/readBinsFile.Rd | 48 strvalidator-2.3.0/strvalidator/man/readPanelsFile.Rd | 48 strvalidator-2.3.0/strvalidator/man/ref1.Rd | 4 strvalidator-2.3.0/strvalidator/man/ref11.Rd | 4 strvalidator-2.3.0/strvalidator/man/ref2.Rd | 4 strvalidator-2.3.0/strvalidator/man/ref3.Rd | 4 strvalidator-2.3.0/strvalidator/man/ref4.Rd | 36 strvalidator-2.3.0/strvalidator/man/ref51.Rd | 4 strvalidator-2.3.0/strvalidator/man/ref52.Rd | 4 strvalidator-2.3.0/strvalidator/man/ref61.Rd | 4 strvalidator-2.3.0/strvalidator/man/ref62.Rd | 4 strvalidator-2.3.0/strvalidator/man/ref7.Rd | 4 strvalidator-2.3.0/strvalidator/man/removeArtefact.Rd | 85 strvalidator-2.3.0/strvalidator/man/removeArtefact_gui.Rd | 60 strvalidator-2.3.0/strvalidator/man/removeSpike.Rd | 70 strvalidator-2.3.0/strvalidator/man/removeSpike_gui.Rd | 60 strvalidator-2.3.0/strvalidator/man/saveObject.Rd | 85 strvalidator-2.3.0/strvalidator/man/scrambleAlleles.Rd | 56 strvalidator-2.3.0/strvalidator/man/set1.Rd | 4 strvalidator-2.3.0/strvalidator/man/set2.Rd | 4 strvalidator-2.3.0/strvalidator/man/set3.Rd | 4 strvalidator-2.3.0/strvalidator/man/set4.Rd | 4 strvalidator-2.3.0/strvalidator/man/set5.Rd | 4 strvalidator-2.3.0/strvalidator/man/set6.Rd | 4 strvalidator-2.3.0/strvalidator/man/set7.Rd | 4 strvalidator-2.3.0/strvalidator/man/slim.Rd | 68 strvalidator-2.3.0/strvalidator/man/slim_gui.Rd | 61 strvalidator-2.3.0/strvalidator/man/sortMarker.Rd | 56 strvalidator-2.3.0/strvalidator/man/strvalidator-package.Rd | 122 strvalidator-2.3.0/strvalidator/man/strvalidator.Rd | 66 strvalidator-2.3.0/strvalidator/man/tableBalance.Rd | 60 strvalidator-2.3.0/strvalidator/man/tableBalance_gui.Rd | 66 strvalidator-2.3.0/strvalidator/man/tableCapillary.Rd | 58 strvalidator-2.3.0/strvalidator/man/tableCapillary_gui.Rd | 66 strvalidator-2.3.0/strvalidator/man/tablePrecision.Rd | 66 strvalidator-2.3.0/strvalidator/man/tablePrecision_gui.Rd | 66 strvalidator-2.3.0/strvalidator/man/tableStutter.Rd | 58 strvalidator-2.3.0/strvalidator/man/tableStutter_gui.Rd | 66 strvalidator-2.3.0/strvalidator/man/trim.Rd | 113 strvalidator-2.3.0/strvalidator/man/trim_gui.Rd | 61 strvalidator-2.3.0/strvalidator/tests/testthat/test-calculateStatistics.r |only 233 files changed, 20478 insertions(+), 9785 deletions(-)
Title: Convert Tibbles or Data Frames to Xts Easily
Description: Facilitate the movement between data frames to 'xts'. Particularly
useful when moving from 'tidyverse' to the widely used 'xts' package, which is
the input format of choice to various other packages. It also allows the user
to use a 'spread_by' argument for a character column 'xts' conversion.
Author: Nico Katzke [aut, cre]
Maintainer: Nico Katzke <nfkatzke@gmail.com>
Diff between tbl2xts versions 0.1.3 dated 2019-08-01 and 1.0.0 dated 2020-07-10
DESCRIPTION | 16 +++--- MD5 | 46 ++++++++++++----- NAMESPACE | 4 + R/data.R | 3 - R/tbl_xts.R | 47 +++++++---------- R/xts_tbl.R | 5 + README.md | 108 +++++++++++++++++++++++++---------------- build/vignette.rds |binary data/TRI.rda |binary inst/doc/tbl2xts_vignette.Rmd | 76 +++++++++++++++------------- inst/doc/tbl2xts_vignette.html | 95 +++++++++++++++++++++--------------- inst/docs |only man/TRI.Rd | 9 ++- man/tbl_xts.Rd | 6 -- man/xts_tbl.Rd | 2 vignettes/tbl2xts_vignette.Rmd | 76 +++++++++++++++------------- 16 files changed, 283 insertions(+), 210 deletions(-)
Title: Meta-CART: A Flexible Approach to Identify Moderators in
Meta-Analysis
Description: Meta-CART integrates classification and regression trees (CART) into meta-analysis. Meta-CART is a flexible approach to identify interaction effects between moderators in meta-analysis. The method is described in Dusseldorp et al. (2014) <doi:10.1037/hea0000018> and Li et al. (2017) <doi:10.1111/bmsp.12088>.
Author: Xinru Li [aut, cre], Elise Dusseldorp [aut, cph], Kaihua Liu [ctb] (supported with the plot function), Juan Claramunt [ctb], Jacqueline Meulman [ctb]
Maintainer: Juan Claramunt <j.claramunt.gonzalez@fsw.leidenuniv.nl>
Diff between metacart versions 2.0-2 dated 2019-12-06 and 2.0-3 dated 2020-07-10
DESCRIPTION | 10 +- MD5 | 78 ++++++++-------- NAMESPACE | 2 NEWS | 5 + R/RcppExports.R | 150 ++++++++++++++++---------------- man/CI_draw.Rd | 52 +++++------ man/FEmrt.Rd | 209 +++++++++++++++++++++++--------------------- man/REmrt.Rd | 219 ++++++++++++++++++++++++----------------------- man/REmrt_GS_.Rd | 56 ++++++------ man/SimData.Rd | 46 ++++----- man/Xvalid_all.Rd | 58 ++++++------ man/compute_rebetQ.Rd | 42 ++++----- man/dat.BCT2009.Rd | 92 +++++++++---------- man/dat.balanced.Rd | 46 ++++----- man/dot-ComputeY.Rd | 40 ++++---- man/dot-PredY.Rd | 32 +++--- man/dot-ReplaceNA.Rd | 46 ++++----- man/dot-compute_re_Q_.Rd | 54 +++++------ man/dot-compute_tau_.Rd | 50 +++++----- man/dot-partition.Rd | 50 +++++----- man/encodeHtml.Rd | 34 +++---- man/find_second_split.Rd | 60 ++++++------ man/find_triplet.Rd | 64 ++++++------- man/make_first_split.Rd | 48 +++++----- man/metacart-package.Rd | 112 ++++++++++++------------ man/oval_draw.Rd | 54 +++++------ man/plot.FEmrt.Rd | 42 ++++----- man/plot.REmrt.Rd | 40 ++++---- man/predict.FEmrt.Rd | 42 ++++----- man/predict.REmrt.Rd | 42 ++++----- man/prednode_cpp.Rd | 32 +++--- man/print.FEmrt.Rd | 36 +++---- man/print.REmrt.Rd | 36 +++---- man/re.cutoff_cpp.Rd | 56 ++++++------ man/summary.FEmrt.Rd | 50 +++++----- man/summary.REmrt.Rd | 50 +++++----- man/treepruner.Rd | 44 ++++----- man/updateNodes.Rd | 42 ++++----- src/RcppExports.cpp | 2 src/testxvalid.cpp | 4 40 files changed, 1125 insertions(+), 1102 deletions(-)
Title: Bootstrap Inference for Multiple Imputation
Description: Bootstraps and imputes incomplete datasets. Then performs inference on estimates obtained from analysing the imputed datasets as proposed by von Hippel and Bartlett (2019) <arXiv:1210.0870v10>.
Author: Jonathan Bartlett
Maintainer: Jonathan Bartlett <j.w.bartlett@bath.ac.uk>
Diff between bootImpute versions 1.0.0 dated 2019-07-18 and 1.1.0 dated 2020-07-10
DESCRIPTION | 10 +- MD5 | 22 +++-- NEWS.md |only R/bootImpute.R | 161 +++++++++++++++++++++++++++++++++++------ R/bootMice.R | 10 +- R/bootSmcfcs.R | 10 +- man/bootImpute.Rd | 29 +++++-- man/bootImputeAnalyse.Rd | 23 ++++- man/bootMice.Rd | 14 ++- man/bootSmcfcs.Rd | 14 ++- man/ex_linquad.Rd | 6 + tests/testthat.R | 1 tests/testthat/test_parallel.R |only 13 files changed, 231 insertions(+), 69 deletions(-)
Title: Visualising Splicing at Single-Cell Resolution
Description: Alternative splicing produces a variety of different protein products from a given gene. 'VALERIE' enables visualisation of alternative splicing events from high-throughput single-cell RNA-sequencing experiments. 'VALERIE' computes percent spliced-in (PSI) values for user-specified genomic coordinates corresponding to alternative splicing events. PSI is the proportion of sequencing reads supporting the included exon/intron as defined by Shiozawa (2018) <doi:10.1038/s41467-018-06063-x>. PSI are inferred from sequencing reads data based on specialised infrastructures for representing and computing annotated genomic ranges by Lawrence (2013) <doi:10.1371/journal.pcbi.1003118>. Computed PSI for each single cell are subsequently presented in the form of a heatmap implemented using the 'pheatmap' package by Kolde (2010) <https://CRAN.R-project.org/package=pheatmap>. Board overview of the mean PSI difference and associated p-values across different user-defined groups of single cells are presented in the form of a line graph using the 'ggplot2' package by Wickham (2007) <https://CRAN.R-project.org/package=ggplot2>.
Author: Sean Wen
Maintainer: Sean Wen <sean.wenwx@gmail.com>
Diff between VALERIE versions 1.0.0 dated 2020-02-11 and 1.1.0 dated 2020-07-10
VALERIE-1.0.0/VALERIE/README.md |only VALERIE-1.0.0/VALERIE/inst/extdata/Plots/2_MXE_Plots_PKM.png |only VALERIE-1.1.0/VALERIE/DESCRIPTION | 8 - VALERIE-1.1.0/VALERIE/MD5 | 52 ++++------ VALERIE-1.1.0/VALERIE/R/Script_VALERIE_PlotPSI_A3SS_MultiGroups.R | 2 VALERIE-1.1.0/VALERIE/R/Script_VALERIE_PlotPSI_A3SS_TwoGroups.R | 2 VALERIE-1.1.0/VALERIE/R/Script_VALERIE_PlotPSI_A5SS_MultiGroups.R | 2 VALERIE-1.1.0/VALERIE/R/Script_VALERIE_PlotPSI_A5SS_TwoGroups.R | 2 VALERIE-1.1.0/VALERIE/R/Script_VALERIE_PlotPSI_MXE_MultiGroups.R | 2 VALERIE-1.1.0/VALERIE/R/Script_VALERIE_PlotPSI_MXE_TwoGroup.R | 2 VALERIE-1.1.0/VALERIE/R/Script_VALERIE_PlotPSI_RI_MultiGroups.R | 2 VALERIE-1.1.0/VALERIE/R/Script_VALERIE_PlotPSI_RI_TwoGroups.R | 2 VALERIE-1.1.0/VALERIE/R/Script_VALERIE_PlotPSI_SE_MultiGroups.R | 2 VALERIE-1.1.0/VALERIE/R/Script_VALERIE_PlotPSI_SE_TwoGroups.R | 2 VALERIE-1.1.0/VALERIE/build/vignette.rds |binary VALERIE-1.1.0/VALERIE/inst/doc/VALERIE.pdf |binary VALERIE-1.1.0/VALERIE/inst/extdata/Plots/1_SE_Plots_Mbp.pdf |binary VALERIE-1.1.0/VALERIE/man/PlotPSI.A3SS.MultiGroups.Rd | 15 -- VALERIE-1.1.0/VALERIE/man/PlotPSI.A3SS.TwoGroups.Rd | 13 -- VALERIE-1.1.0/VALERIE/man/PlotPSI.A5SS.MultiGroups.Rd | 15 -- VALERIE-1.1.0/VALERIE/man/PlotPSI.A5SS.TwoGroups.Rd | 13 -- VALERIE-1.1.0/VALERIE/man/PlotPSI.MXE.MultiGroups.Rd | 15 -- VALERIE-1.1.0/VALERIE/man/PlotPSI.MXE.TwoGroups.Rd | 13 -- VALERIE-1.1.0/VALERIE/man/PlotPSI.RI.MultiGroups.Rd | 15 -- VALERIE-1.1.0/VALERIE/man/PlotPSI.RI.TwoGroups.Rd | 13 -- VALERIE-1.1.0/VALERIE/man/PlotPSI.Rd | 17 --- VALERIE-1.1.0/VALERIE/man/PlotPSI.SE.MultiGroups.Rd | 15 -- VALERIE-1.1.0/VALERIE/man/PlotPSI.SE.TwoGroups.Rd | 13 -- 28 files changed, 78 insertions(+), 159 deletions(-)
Title: Summarize and Explore the Data
Description: Exploratory analysis on any input data describing the structure and the relationships present in the data. The package automatically select the variable and does related descriptive statistics. Analyzing information value, weight of evidence, custom tables, summary statistics, graphical techniques will be performed for both numeric and categorical predictors.
Author: Dayanand Ubrangala [aut, cre],
Kiran R [aut, ctb],
Ravi Prasad Kondapalli [aut, ctb],
Sayan Putatunda [aut, ctb]
Maintainer: Dayanand Ubrangala <daya6489@gmail.com>
Diff between SmartEDA versions 0.3.5 dated 2020-04-25 and 0.3.6 dated 2020-07-10
DESCRIPTION | 13 +++--- MD5 | 44 +++++++++++------------ NEWS.md | 12 ++++++ R/fn_Overview_data.R | 71 ++++++++++++++++++++++--------------- R/fn_exp_numeric.R | 1 R/fn_exp_numeric_viz.R | 6 ++- R/fn_exp_outliers.R | 4 +- README.md | 11 +++-- inst/doc/CustomTable.html | 87 ++++++++++++++++++++++------------------------ inst/doc/SmartEDA.R | 4 +- inst/doc/SmartEDA.Rmd | 10 ++--- inst/doc/SmartEDA.html | 77 ++++++++++++++++++++-------------------- man/ExpCTable.Rd | 12 +++++- man/ExpCatStat.Rd | 15 ++++++- man/ExpCatViz.Rd | 18 +++++++-- man/ExpCustomStat.Rd | 12 +++++- man/ExpData.Rd | 16 ++++---- man/ExpNumStat.Rd | 18 ++++++--- man/ExpNumViz.Rd | 22 +++++++++-- man/ExpOutliers.Rd | 10 ++++- man/ExpParcoord.Rd | 10 ++++- man/ExpReport.Rd | 15 ++++++- vignettes/SmartEDA.Rmd | 10 ++--- 23 files changed, 303 insertions(+), 195 deletions(-)
Title: Tide Heights
Description: Calculates tide heights based on tide station harmonics.
It includes the harmonics data for 637 US stations.
The harmonics data was converted from <https://github.com/poissonconsulting/rtide/blob/master/data-raw/harmonics-dwf-20151227-free.tar.bz2>,
NOAA web site data processed by David Flater for 'XTide'.
The code to calculate tide heights from the harmonics is based on 'XTide'.
Author: Joe Thorley [aut, cre] (<https://orcid.org/0000-0002-7683-4592>),
Luke Miller [aut],
Abram Fleishman [aut],
Poisson Consulting [cph]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>
Diff between rtide versions 0.0.7 dated 2020-03-18 and 0.0.8 dated 2020-07-10
DESCRIPTION | 14 +++++++------- MD5 | 13 +++++++------ NEWS.md | 5 +++++ README.md | 22 ++++++---------------- inst |only man/brandywine.Rd | 6 ++++-- man/harmonics.Rd | 4 +++- man/monterey.Rd | 6 ++++-- 8 files changed, 36 insertions(+), 34 deletions(-)
Title: Read and Write ODS Files
Description: Import ODS (OpenDocument Spreadsheet) into R as a data frame. Also support writing data frame into ODS file.
Author: Gerrit-Jan Schutten, Chung-hong Chan, Thomas J. Leeper, John Foster, and other contributors
Maintainer: Chung-hong Chan <chainsawtiney@gmail.com>
Diff between readODS versions 1.6.7 dated 2018-11-26 and 1.7.0 dated 2020-07-10
readODS-1.6.7/readODS/man/get_num_sheet_in_ods.Rd |only readODS-1.6.7/readODS/man/ods_sheets.Rd |only readODS-1.6.7/readODS/tests/testdata/megairis.ods |only readODS-1.6.7/readODS/tests/testthat/test.ods |only readODS-1.7.0/readODS/DESCRIPTION | 17 readODS-1.7.0/readODS/MD5 | 35 - readODS-1.7.0/readODS/NAMESPACE | 14 readODS-1.7.0/readODS/R/readODS.R | 241 +++++----- readODS-1.7.0/readODS/R/writeODS.R | 170 +++++-- readODS-1.7.0/readODS/README.md | 195 ++++++-- readODS-1.7.0/readODS/build |only readODS-1.7.0/readODS/inst/doc |only readODS-1.7.0/readODS/man/figures |only readODS-1.7.0/readODS/man/get_num_sheets_in_ods.Rd |only readODS-1.7.0/readODS/man/list_ods_sheets.Rd |only readODS-1.7.0/readODS/man/read_ods.Rd | 24 readODS-1.7.0/readODS/man/write_ods.Rd | 32 + readODS-1.7.0/readODS/tests/testdata/cellranger_issue57.ods |only readODS-1.7.0/readODS/tests/testdata/starwars10.rds |only readODS-1.7.0/readODS/tests/testthat/test_cellranger.R |only readODS-1.7.0/readODS/tests/testthat/test_legacy.R | 50 +- readODS-1.7.0/readODS/tests/testthat/test_verbose.R |only readODS-1.7.0/readODS/tests/testthat/test_write_ods.R | 12 readODS-1.7.0/readODS/tests/testthat/test_write_ods_append_update.R |only readODS-1.7.0/readODS/vignettes |only 25 files changed, 542 insertions(+), 248 deletions(-)
Title: Accurate Floating Point Sums and Products
Description: Most of the time floating point arithmetic does
approximately the right thing. When adding sums or having products
of numbers that greatly differ in magnitude, the floating point
arithmetic may be incorrect. This package implements the Kahan
(1965) sum <doi:10.1145/363707.363723>, Neumaier (1974) sum
<doi:10.1002/zamm.19740540106>, pairwise-sum (adapted from 'NumPy',
See Castaldo (2008) <doi:10.1137/070679946> for a discussion of
accuracy), and arbitrary precision sum (adapted from the fsum in
'Python' ; Shewchuk (1997)
<http://www.cs.berkeley.edu/~jrs/papers/robustr.pdf>). In addition,
products are changed to long double precision for accuracy, or
changed into a log-sum for accuracy.
Author: Matthew Fidler [aut, cre, cph],
Raymond Hettinger [cph, aut],
Jonathan Shewchuk [cph, aut],
Julian Taylor [cph, aut],
Nathaniel Smith [cph, aut],
NumPy Team [cph],
Python Team [cph]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between PreciseSums versions 0.3 dated 2018-04-12 and 0.4 dated 2020-07-10
DESCRIPTION | 8 - MD5 | 30 ++-- NAMESPACE | 22 +-- R/sums.R | 310 +++++++++++++++++++++++----------------------- man/fsum.Rd | 88 ++++++------- man/kahanSum.Rd | 48 +++---- man/neumaierSum.Rd | 48 +++---- man/pairwiseSum.Rd | 66 ++++----- man/psProd.Rd | 34 ++--- man/psSetProd.Rd | 54 ++++---- man/psSetSum.Rd | 66 +++++---- man/psSum.Rd | 34 ++--- src/install.libs.R | 34 ++--- src/sum.c | 52 ++++++- tests/testthat.R | 8 - tests/testthat/test-sum.R | 50 +++---- 16 files changed, 494 insertions(+), 458 deletions(-)
Title: Parallel Simulation Studies
Description: Perform flexible simulation studies using one or multiple computer cores.
The package is set up to be usable on high-performance clusters in addition
to being run locally, see examples on <https://github.com/SachaEpskamp/parSim>.
Author: Sacha Epskamp
Maintainer: Sacha Epskamp <mail@sachaepskamp.com>
Diff between parSim versions 0.1.1 dated 2019-06-21 and 0.1.4 dated 2020-07-10
DESCRIPTION | 8 - MD5 | 9 + NAMESPACE | 17 +-- R/parSim.R | 283 ++++++++++++++++++++++++++++++---------------------------- README.md |only man/parSim.Rd | 250 +++++++++++++++++++++++++-------------------------- 6 files changed, 294 insertions(+), 273 deletions(-)
Title: Influential Case Detection Methods for Factor Analysis and
Structural Equation Models
Description: Tools for detecting and summarize influential cases that
can affect exploratory and confirmatory factor analysis models as well as
structural equation models more generally (Chalmers, 2015, <doi:10.1177/0146621615597894>;
Flora, D. B., LaBrish, C. & Chalmers, R. P., 2012, <10.3389/fpsyg.2012.00055>).
Author: Phil Chalmers [aut, cre]
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between faoutlier versions 0.7.2 dated 2017-07-22 and 0.7.4 dated 2020-07-10
DESCRIPTION | 13 ++++---- MD5 | 36 +++++++++++----------- NEWS.md | 3 + R/GOF.R | 10 +++--- R/LD.R | 10 +++--- R/forward.search.R | 25 ++++++++------- R/gCD.R | 56 ++++++++++++++++------------------- R/obs.resid.R | 6 +-- build/partial.rdb |binary man/GOF.Rd | 19 ++++++++--- man/LD.Rd | 19 ++++++++--- man/faoutlier.Rd | 1 man/forward.search.Rd | 28 +++++++++++++---- man/gCD.Rd | 21 +++++++------ man/obs.resid.Rd | 16 ++++++---- tests/testthat/test-GOF.R | 16 +++++----- tests/testthat/test-LD.R | 14 ++++---- tests/testthat/test-forward.search.R | 8 ++--- tests/testthat/test-gCD.R | 22 ++++++------- 19 files changed, 182 insertions(+), 141 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. See Song et al. (2020) <doi:10.1371/journal.pcbi.1007565> for a detailed presentation of the method.
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 2.0.3 dated 2020-02-12 and 2.0.4 dated 2020-07-10
DESCRIPTION | 6 +++--- MD5 | 6 +++--- R/findPara.R | 14 ++++++++++++-- man/EBPRS.Rd | 8 ++++++++ 4 files changed, 26 insertions(+), 8 deletions(-)
Title: Manipulate Date, POSIXct and hms Vectors
Description: Manipulates date ('Date'), date time ('POSIXct') and
time ('hms') vectors. Date/times are considered discrete and are
floored whenever encountered. Times are wrapped and time zones are
maintained unless explicitly altered by the user.
Author: Joe Thorley [aut, cre] (<https://orcid.org/0000-0002-7683-4592>),
Poisson Consulting [cph, fnd]
Maintainer: Joe Thorley <joe@poissonconsulting.ca>
Diff between dttr2 versions 0.2.0 dated 2020-05-01 and 0.3.0 dated 2020-07-10
dttr2-0.2.0/dttr2/man/is.datetime.Rd |only dttr2-0.3.0/dttr2/DESCRIPTION | 28 +++++++----- dttr2-0.3.0/dttr2/LICENSE | 2 dttr2-0.3.0/dttr2/MD5 | 39 +++++++++++------- dttr2-0.3.0/dttr2/NAMESPACE | 7 +++ dttr2-0.3.0/dttr2/NEWS.md | 13 ++++++ dttr2-0.3.0/dttr2/R/complete.R | 4 - dttr2-0.3.0/dttr2/R/dayte-time.R | 11 ++++- dttr2-0.3.0/dttr2/R/internal.R | 2 dttr2-0.3.0/dttr2/R/is.R | 20 +++++++-- dttr2-0.3.0/dttr2/R/seq.R | 4 - dttr2-0.3.0/dttr2/R/sys-date-time.R |only dttr2-0.3.0/dttr2/R/sys-date.R |only dttr2-0.3.0/dttr2/R/sys-time.R |only dttr2-0.3.0/dttr2/README.md | 11 +++-- dttr2-0.3.0/dttr2/inst |only dttr2-0.3.0/dttr2/man/dtt_dayte_time.Rd | 9 +++- dttr2-0.3.0/dttr2/man/dtt_sys_date.Rd |only dttr2-0.3.0/dttr2/man/dtt_sys_date_time.Rd |only dttr2-0.3.0/dttr2/man/dtt_sys_time.Rd |only dttr2-0.3.0/dttr2/man/dttr2-package.Rd | 6 +- dttr2-0.3.0/dttr2/man/is_date_time.Rd |only dttr2-0.3.0/dttr2/tests/testthat/test-dayte-time.R |only dttr2-0.3.0/dttr2/tests/testthat/test-is.R | 6 ++ dttr2-0.3.0/dttr2/tests/testthat/test-sys-date-time.R |only dttr2-0.3.0/dttr2/tests/testthat/test-sys-date.R |only dttr2-0.3.0/dttr2/tests/testthat/test-sys-time.R |only 27 files changed, 117 insertions(+), 45 deletions(-)
Title: Miscellaneous Functions from Alexey Shipunov
Description: A collection of functions for data manipulation, plotting and statistical computing,
to use separately or with the book "Visual Statistics. Use R!":
Shipunov (2020) <http://ashipunov.info/shipunov/software/r/r-en.htm>.
Most useful functions:
Bclust(), Jclust() and BootA() which bootstrap hierarchical clustering;
Recode() which does multiple recoding in a fast, simple and flexible way;
Misclass() which outputs confusion matrix even if classes are not concerted;
Overlap() which measures group separation on any projection;
Biarrows() which converts any scatterplot into biplot;
and Pleiad() which is fast and flexible correlogram.
Author: Alexey Shipunov [aut, cre], Paul Murrell [ctb], Marcello D'Orazio [ctb], Stephen Turner [ctb], Eugeny Altshuler [ctb], Roland Rau [ctb], Marcus W Beck [ctb], Sebastian Gibb [ctb], Weiliang Qiu [ctb], Emmanuel Paradis [ctb], Roger Koenker [ctb], R Core Team [ctb]
Maintainer: Alexey Shipunov <dactylorhiza@gmail.com>
Diff between shipunov versions 1.9 dated 2020-07-01 and 1.10 dated 2020-07-10
DESCRIPTION | 14 +++---- MD5 | 64 ++++++++++++++++++++---------------- NAMESPACE | 2 - NEWS | 17 +++++++-- R/aaa.r | 93 ----------------------------------------------------- R/bclust.r | 41 +++++++++++++++-------- R/dotcharts.r | 92 +++++++++++++++++++++++++++++----------------------- R/ellipses.r | 5 +- R/ex_col.r |only R/gower_dist.r | 5 +- R/hulls.r | 22 +++--------- R/jclust.r | 83 ++++++++++++++++++++++------------------------- R/linechart.r |only R/overlap.r | 26 -------------- R/pinhull.r | 6 --- R/polys.r |only R/squares.r |only R/str.r |only TODO | 14 +------ man/Bclabels.Rd | 36 +++++++++++++++++--- man/Bclust.Rd | 8 +++- man/BestOverlap.Rd | 46 ++++++++++++++++++-------- man/Dotcharts.Rd | 55 ++++++++++++++++++------------- man/Ellipses.Rd | 17 ++++----- man/Ex.col.Rd | 22 ++++++++---- man/Fence.Rd |only man/Gower.dist.Rd | 68 +++++++++++++++++++++++++++++--------- man/Hulls.Rd | 35 +++++++++---------- man/Jclust.Rd | 43 +++++++++++++++++++----- man/Linechart.Rd | 13 +++++-- man/Overlap.Rd | 15 +++++--- man/Pinhull.Rd | 13 +++---- man/Polyarea.Rd |only man/Polycenter.Rd |only man/Squares.Rd | 20 ++++++----- man/Str.Rd | 26 +++++++++++++- man/Tcoords.Rd | 13 ++++++- 37 files changed, 492 insertions(+), 422 deletions(-)
Title: Star Layer for 'ggplot2'
Description: To create the regular polygon layer for easily discernible shapes,
we developed the package, it can be easily used if you know the 'ggplot2'.
Author: Shuangbin Xu [aut, cre] (<https://orcid.org/0000-0003-3513-5362>)
Maintainer: Shuangbin Xu <xshuangbin@163.com>
Diff between ggstar versions 0.0.6 dated 2020-05-15 and 0.0.9 dated 2020-07-10
DESCRIPTION | 8 ++-- MD5 | 28 ++++++++------- NAMESPACE | 5 ++ NEWS.md | 27 +++++++++++++++ R/draw-key.R | 17 ++++++--- R/geom-star.R | 56 ++++++++++++++++++++++--------- R/primitive.R | 72 ++++++++++++++++++++++++++++++++++------ R/scale-identity.R |only R/utilities.R | 47 ++++++++++++++++++-------- build/vignette.rds |binary inst/doc/ggstar.R | 10 ++--- inst/doc/ggstar.Rmd | 20 ++++++----- inst/doc/ggstar.html | 56 ++++++++++++++++--------------- man/geom_star.Rd | 13 +++++++ man/scale_starshape_identity.Rd |only vignettes/ggstar.Rmd | 20 ++++++----- 16 files changed, 266 insertions(+), 113 deletions(-)
Title: Parse, Format, and Validate International Phone Numbers
Description: Parse, format, and validate international phone
numbers using Google's 'libphonenumber' java library,
<https://github.com/google/libphonenumber>.
Author: Danny Smith [aut, cre],
The Social Research Centre [cph]
Maintainer: Danny Smith <danny@gorcha.org>
Diff between dialr versions 0.3.1 dated 2020-04-04 and 0.3.2 dated 2020-07-10
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NEWS.md | 6 ++++++ inst/doc/dialr.html | 16 ++++++++++++++++ inst/doc/oneshot.html | 16 ++++++++++++++++ tests/testthat/setup-all.R | 15 +++++---------- tests/testthat/test-carrier.R | 8 +++++--- tests/testthat/test-geocoder.R | 24 +++++++++++++----------- tests/testthat/test-phone.R | 5 ----- tests/testthat/test-timezone.R | 6 ++++-- 10 files changed, 78 insertions(+), 44 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2017-07-03 1.1.1
2017-01-26 1.1.0
2016-08-08 1.0.6
2016-06-28 1.0.4
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-06-06 2.4.6
2020-02-07 2.4.5
2019-09-02 2.4.4
2019-05-09 2.4.3
2019-04-25 2.4.2
2019-04-04 2.4.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-06-26 0.6.2
2020-06-26 0.6.3
Title: Leland Wilkinson's Algorithm for Detecting Multidimensional
Outliers
Description: An implementation of an algorithm for outlier detection that can handle a) data with a mixed categorical and continuous variables, b) many columns of data, c) many rows of data, d) outliers that mask other outliers, and e) both unidimensional and multidimensional datasets. Unlike ad hoc methods found in many machine learning papers, HDoutliers is based on a distributional model that uses probabilities to determine outliers.
Author: Chris Fraley [aut, cre],
Leland Wilkinson [ctb]
Maintainer: Chris Fraley <cfraley@tableau.com>
Diff between HDoutliers versions 1.0.1 dated 2020-04-01 and 1.0.2 dated 2020-07-10
CHANGELOG | 3 + DESCRIPTION | 12 +++---- MD5 | 7 ++-- R/dataTrans.R | 63 +++++++++++++++++++++----------------- inst/doc/hdoutliersTechReport.pdf |only 5 files changed, 46 insertions(+), 39 deletions(-)
Title: Dysregulated Pathway Identification Analysis
Description: It is used to identify dysregulated pathways based on a pre-ranked gene pair list. A fast algorithm is used to make the computation really fast. The data in package 'DysPIAData' is needed.
Author: Limei Wang [aut, cre],
Jin Li [aut, ctb]
Maintainer: Limei Wang <lemon619@gmail.com>
Diff between DysPIA versions 1.2 dated 2020-06-24 and 1.3 dated 2020-07-10
DESCRIPTION | 14 +++++++------- MD5 | 32 ++++++++++++++++---------------- NAMESPACE | 19 ++++++++++++++----- R/DysGPS.R | 13 +++++++------ R/DysPIA.R | 28 +++++++++++++++------------- R/DyspiaSig.R | 3 ++- R/calEdgeCorScore_ESEA.R | 16 +++++++++------- data/DysGPS_p53.rda |binary data/DyspiaRes_p53.rda |binary data/gene_expression_p53.rda |binary man/DysGPS.Rd | 8 ++++---- man/DysPIA.Rd | 6 ++---- man/DyspiaSig.Rd | 2 +- man/DyspiaSimpleImpl.Rd | 2 +- man/calEdgeCorScore_ESEA.Rd | 6 +++--- man/calcDyspiaStat.Rd | 2 +- man/setUpBPPARAM.Rd | 2 +- 17 files changed, 83 insertions(+), 70 deletions(-)
Title: Generate Tile Maps
Description: Implements an algorithm for generating maps, known as tile maps,
in which each region is represented by a single tile of the same shape and
size. The algorithm was first proposed in "Generating Tile Maps" by Graham
McNeill and Scott Hale (2017) <doi:10.1111/cgf.13200>. Functions allow
users to generate, plot, and compare square or hexagon tile maps.
Author: Kaelyn Rosenberg [aut, cre]
Maintainer: Kaelyn Rosenberg <kaerosenberg@gmail.com>
Diff between tilemaps versions 0.1.0 dated 2020-06-19 and 0.2.0 dated 2020-07-10
DESCRIPTION | 6 +-- MD5 | 27 ++++++++------ NAMESPACE | 1 NEWS.md |only R/create_island.R |only README.md | 43 ++++++++++++++++++---- build/vignette.rds |binary inst/doc/tilemaps.R | 22 ++++++++++- inst/doc/tilemaps.Rmd | 31 +++++++++++++++- inst/doc/tilemaps.html | 65 ++++++++++++++++++++-------------- man/create_island.Rd |only man/figures/README-add-islands-1.png |only man/figures/README-governor-map-1.png |binary man/figures/README-many-maps-1.png |binary man/figures/README-single-map-1.png |binary man/figures/logo.png |only vignettes/tilemaps.Rmd | 31 +++++++++++++++- 17 files changed, 174 insertions(+), 52 deletions(-)
Title: Access the Weekly 'TidyTuesday' Project Dataset
Description: 'TidyTuesday' is a project by the 'R4DS Online Learning Community' in which they
post a weekly dataset onto post a weekly dataset in a public data repository
(<https://github.com/rfordatascience/tidytuesday>) for people to
analyze and visualize. This package provides the tools to easily download this data and the
description of the source.
Author: Ellis Hughes [aut, cre],
Jon Harmon [ctb],
Thomas Mock [ctb],
R4DS Online Learning Community [dtc]
Maintainer: Ellis Hughes <ellishughes@live.com>
Diff between tidytuesdayR versions 1.0.0 dated 2020-06-26 and 1.0.1 dated 2020-07-10
DESCRIPTION | 11 ++++--- MD5 | 44 ++++++++++++++++++------------- NAMESPACE | 5 +++ NEWS.md | 6 ++++ R/github_api.R | 3 +- R/last_tuesday.R |only R/tt_available.R | 8 ++--- R/tt_check_date.R | 16 +++++++++++ R/tt_compile.R | 4 +- R/tt_load.R | 2 - R/tt_load_gh.R | 4 +- R/tt_master_file.R | 2 - R/use_tidytemplate.R |only R/utils.R | 6 ++-- inst |only man/available.Rd | 2 - man/last_tuesday.Rd |only man/pipe.Rd | 24 ++++++++-------- man/printing.Rd | 4 +- man/readme.Rd | 2 - man/tt_date.Rd |only man/tt_load.Rd | 2 - man/tt_load_gh.Rd | 4 +- man/use_tidytemplate.Rd |only tests/testthat/helper-tt_ref_test_that.R | 20 ++++++++++++++ tests/testthat/test-11-last_tuesday.R |only tests/testthat/test-12-encoding.R |only 27 files changed, 113 insertions(+), 56 deletions(-)
Title: Computerized Adaptive Testing with Multidimensional Item
Response Theory
Description: Provides tools to generate an HTML interface for creating adaptive
and non-adaptive educational and psychological tests using the shiny
package (Chalmers (2016) <doi:10.18637/jss.v071.i05>).
Suitable for applying unidimensional and multidimensional
computerized adaptive tests (CAT) using item response theory methodology and for
creating simple questionnaires forms to collect response data directly in R.
Additionally, optimal test designs (e.g., "shadow testing") are supported
for tests which contain a large number of item selection constraints.
Finally, package contains tools useful for performing Monte Carlo simulations
for studying the behavior of computerized adaptive test banks.
Author: Phil Chalmers [aut, cre] (<https://orcid.org/0000-0001-5332-2810>)
Maintainer: Phil Chalmers <rphilip.chalmers@gmail.com>
Diff between mirtCAT versions 1.9.3 dated 2019-06-28 and 1.10 dated 2020-07-10
DESCRIPTION | 8 MD5 | 78 - NAMESPACE | 64 - NEWS.md | 665 +++++++------ R/DesignClass.R | 23 R/PersonClass.R | 152 +-- R/ShinyGUIClass.R | 296 +++--- R/TestClass.R | 188 +-- R/createShinyGUI.R | 108 +- R/extract.mirtCAT.R | 390 ++++---- R/findNextCATItem.R | 826 ++++++++--------- R/getPerson.R | 78 - R/mirtCAT.R | 1666 +++++++++++++++++----------------- R/mirtCAT_preamble.R | 526 +++++----- R/run_pattern.R | 4 R/server.R | 528 +++++----- R/ui.R | 75 - R/updateDesign.R | 73 + R/util.R | 688 +++++++------- build/partial.rdb |binary build/vignette.rds |binary inst/doc/mirtCAT-vignettes.html | 356 +++---- man/computeCriteria.Rd | 151 +-- man/createSessionName.Rd | 42 man/createShinyGUI.Rd | 97 +- man/extract.mirtCAT.Rd | 352 +++---- man/findNextItem.Rd | 358 +++---- man/generate.mirt_object.Rd | 199 ++-- man/generate_pattern.Rd | 114 +- man/getPerson.Rd | 78 - man/get_mirtCAT_env.Rd | 38 man/mirtCAT-package.Rd | 72 - man/mirtCAT.Rd | 1745 ++++++++++++++++++------------------ man/mirtCAT_preamble.Rd | 94 - man/updateDesign.Rd | 143 +- tests/GUI-tests/GUI-tests.R | 705 +++++++------- tests/tests/test-mirtCAT_classify.R | 108 +- tests/tests/test-mirtCAT_extra.R | 229 ++-- tests/tests/test-mirtCAT_multi.R | 214 ++-- tests/tests/test-mirtCAT_uni.R | 501 +++++----- 40 files changed, 6133 insertions(+), 5899 deletions(-)