Title: Subset and Flag Data Frames with Times by the Use of Periods
Description: Data frames with time information are subset and flagged with period information. Data frames with times are dealt as timeDF objects and periods are represented as periodDF objects.
Author: Toshihiro Umehara [aut, cre]
Maintainer: Toshihiro Umehara <toshi@niceume.com>
Diff between timeDF versions 0.9.0 dated 2024-01-09 and 0.9.1 dated 2024-04-28
DESCRIPTION | 8 +-- MD5 | 42 ++++++++++++++--- NAMESPACE | 13 +++++ R/adjust_periodDF.R | 9 +++ R/as.data.frame.timeDF.R | 8 ++- R/as.timeDF.R | 4 + R/listTimeDF.R |only R/select_timeDF.R |only R/sort_timeDF.R |only R/utils_periodDF.R |only R/utils_timeDF.R |only R/validate_sorted_timeDF.R |only R/validate_timeDF.R |only README.md | 54 +++++++++++++++++++++++ build/partial.rdb |binary configure.ac | 2 inst/unit_tests/test_listTimeDF_to_timeDF.R |only inst/unit_tests/test_period_type.R |only inst/unit_tests/test_select_timeDF.R |only inst/unit_tests/test_sort_timeDF.R |only inst/unit_tests/test_split_timeDF_by_intervals.R |only inst/unit_tests/test_validate_listTimeDF.R |only inst/unit_tests/test_validate_sorted_timeDF.R |only inst/unit_tests/test_validate_timeDF.R |only man/as.data.frame.timeDF.Rd | 3 - man/listTimeDF_to_timeDF.Rd |only man/period_type.Rd |only man/select_timeDF.Rd |only man/sort_timeDF.Rd |only man/split_timeDF_by_intervals.Rd |only man/time_vec.Rd |only man/validate_listTimeDF.Rd |only man/validate_sorted_timeDF.Rd |only man/validate_timeDF.Rd |only 34 files changed, 125 insertions(+), 18 deletions(-)
Title: Infer Ploidy of Single Cells
Description: Compute ploidy of single cells (or nuclei)
based on single-cell (or single-nucleus)
ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing)
data <https://github.com/fumi-github/scPloidy>.
Author: Fumihiko Takeuchi [aut, cre]
Maintainer: Fumihiko Takeuchi <fumihiko@takeuchi.name>
Diff between scPloidy versions 0.3.0 dated 2022-09-12 and 0.6.2 dated 2024-04-28
DESCRIPTION | 14 MD5 | 40 NAMESPACE | 16 R/ATAC-seq.R | 388 - R/GSE129785_SU008_Tumor_Pre.R |only R/cnv.R |only R/inferploidy.R |only README.md | 8 build/partial.rdb |binary build/vignette.rds |binary data/GSE129785_SU008_Tumor_Pre.RData |only data/SHR_m154211.RData |binary inst/doc/CNV.R |only inst/doc/CNV.Rmd |only inst/doc/CNV.html |only inst/doc/intro.R | 12 inst/doc/intro.Rmd | 8 inst/doc/intro.html | 365 - man/GSE129785_SU008_Tumor_Pre.Rd |only man/cnv.Rd |only man/fragmentoverlapcount.Rd | 10 man/ploidy.Rd | 40 tests/testthat/testdata/SHR_m154211.result.txt | 7776 ++++++++++++------------- tests/testthat/testscPloidy.R | 22 vignettes/CNV.Rmd |only vignettes/intro.Rmd | 8 26 files changed, 4507 insertions(+), 4200 deletions(-)
Title: Preprocessing and Analyzing Web Tracking Data
Description: Data structures and methods to work with web tracking data. The functions cover data preprocessing steps, enriching web tracking data with external information and methods for the analysis of digital behavior as used in several academic papers (e.g., Clemm von Hohenberg et al., 2023 <doi:10.17605/OSF.IO/M3U9P>; Stier et al., 2022 <doi:10.1017/S0003055421001222>).
Author: David Schoch [aut, cre] ,
Bernhard Clemm von Hohenberg [aut]
,
Frank Mangold [aut] ,
Sebastian Stier [aut]
Maintainer: David Schoch <david@schochastics.net>
Diff between webtrackR versions 0.1.0 dated 2023-08-31 and 0.3.0 dated 2024-04-28
webtrackR-0.1.0/webtrackR/R/audience_networks.R |only webtrackR-0.1.0/webtrackR/man/audience_incidence.Rd |only webtrackR-0.1.0/webtrackR/man/audience_network.Rd |only webtrackR-0.1.0/webtrackR/tests/testthat/test-audience_networks.R |only webtrackR-0.3.0/webtrackR/DESCRIPTION | 13 webtrackR-0.3.0/webtrackR/MD5 | 95 - webtrackR-0.3.0/webtrackR/NAMESPACE | 34 webtrackR-0.3.0/webtrackR/NEWS.md | 9 webtrackR-0.3.0/webtrackR/R/classify.R | 87 - webtrackR-0.3.0/webtrackR/R/data.R | 5 webtrackR-0.3.0/webtrackR/R/indices.R | 116 + webtrackR-0.3.0/webtrackR/R/preprocess.R | 650 ++++------ webtrackR-0.3.0/webtrackR/R/summarize.R | 230 +-- webtrackR-0.3.0/webtrackR/R/sysdata.rda |only webtrackR-0.3.0/webtrackR/R/utils.R | 42 webtrackR-0.3.0/webtrackR/R/webtrackR-package.R | 11 webtrackR-0.3.0/webtrackR/R/wt_dt.R | 127 - webtrackR-0.3.0/webtrackR/README.md | 119 - webtrackR-0.3.0/webtrackR/build/partial.rdb |binary webtrackR-0.3.0/webtrackR/build/vignette.rds |only webtrackR-0.3.0/webtrackR/data/domain_list.rda |binary webtrackR-0.3.0/webtrackR/data/fake_tracking.rda |only webtrackR-0.3.0/webtrackR/data/testdt_tracking.rda |binary webtrackR-0.3.0/webtrackR/inst/doc |only webtrackR-0.3.0/webtrackR/man/add_duration.Rd | 8 webtrackR-0.3.0/webtrackR/man/add_next_visit.Rd | 2 webtrackR-0.3.0/webtrackR/man/add_panelist_data.Rd | 4 webtrackR-0.3.0/webtrackR/man/add_previous_visit.Rd | 2 webtrackR-0.3.0/webtrackR/man/add_referral.Rd | 6 webtrackR-0.3.0/webtrackR/man/add_session.Rd | 3 webtrackR-0.3.0/webtrackR/man/add_title.Rd | 4 webtrackR-0.3.0/webtrackR/man/atkinson_index.Rd |only webtrackR-0.3.0/webtrackR/man/classify_visits.Rd | 18 webtrackR-0.3.0/webtrackR/man/create_urldummy.Rd | 4 webtrackR-0.3.0/webtrackR/man/deduplicate.Rd | 12 webtrackR-0.3.0/webtrackR/man/dissimilarity_index.Rd |only webtrackR-0.3.0/webtrackR/man/drop_query.Rd | 2 webtrackR-0.3.0/webtrackR/man/extract_domain.Rd | 9 webtrackR-0.3.0/webtrackR/man/extract_host.Rd | 9 webtrackR-0.3.0/webtrackR/man/extract_path.Rd | 9 webtrackR-0.3.0/webtrackR/man/fake_tracking.Rd |only webtrackR-0.3.0/webtrackR/man/isolation_index.Rd | 24 webtrackR-0.3.0/webtrackR/man/parse_path.Rd |only webtrackR-0.3.0/webtrackR/man/sum_activity.Rd | 2 webtrackR-0.3.0/webtrackR/man/sum_durations.Rd | 6 webtrackR-0.3.0/webtrackR/man/sum_visits.Rd | 6 webtrackR-0.3.0/webtrackR/man/testdt_tracking.Rd | 2 webtrackR-0.3.0/webtrackR/man/wt_dt.Rd | 17 webtrackR-0.3.0/webtrackR/tests/testthat/test-classify.R | 162 +- webtrackR-0.3.0/webtrackR/tests/testthat/test-indices.R | 49 webtrackR-0.3.0/webtrackR/tests/testthat/test-preprocess.R | 550 ++++---- webtrackR-0.3.0/webtrackR/tests/testthat/test-summarize.R | 262 +--- webtrackR-0.3.0/webtrackR/tests/testthat/test-wt_dt.R | 71 - webtrackR-0.3.0/webtrackR/vignettes |only 54 files changed, 1400 insertions(+), 1381 deletions(-)
Title: Testing for Shiny Applications
Description: Automated unit testing of Shiny applications through a headless 'Chromium' browser.
Author: Barret Schloerke [cre, aut] ,
Posit Software, PBC [cph, fnd],
Winston Chang [ctb] ,
Gabor Csardi [ctb] ,
Hadley Wickham [ctb] ,
Mango Solutions [cph, ccp]
Maintainer: Barret Schloerke <barret@posit.co>
Diff between shinytest2 versions 0.3.1 dated 2023-08-26 and 0.3.2 dated 2024-04-28
DESCRIPTION | 12 +-- MD5 | 78 +++++++++++----------- NEWS.md | 12 +++ R/app-driver-expect-download.R | 4 - R/app-driver-expect-js.R | 14 ++-- R/app-driver-expect-screenshot.R | 4 - R/app-driver-expect-values.R | 6 - R/app-driver-initialize.R | 2 R/app-driver-node.R | 4 - R/app-driver-timeout.R | 4 - R/app-driver-wait.R | 2 R/chromote-methods.R | 4 - R/compare-screenshot-threshold.R | 2 R/httr.R | 2 R/migrate.R | 2 R/platform.R | 2 R/record-test.R | 6 - R/save-app.R | 25 ++++++- R/shinytest2-package.R | 6 + R/use.R | 2 build/vignette.rds |binary inst/WORDLIST | 13 +-- inst/doc/in-depth.html | 8 +- inst/doc/robust.html | 6 - inst/doc/shinytest2.R | 2 inst/doc/shinytest2.html | 12 +-- inst/doc/use-application-audit.R | 2 inst/doc/use-application-audit.html | 8 +- inst/doc/use-ci.Rmd | 18 ++++- inst/doc/use-ci.html | 112 ++++++++++++++++---------------- inst/doc/use-package.html | 4 - inst/doc/using-monkey-testing.R | 2 inst/doc/using-monkey-testing.html | 16 ++-- inst/doc/z-migration.R | 2 inst/doc/z-migration.html | 4 - inst/doc/zzz-faq.html | 4 - man/AppDriver.Rd | 2 man/record_test.Rd | 4 - tests/testthat/test-app-duplicate-ids.R | 15 ++-- vignettes/use-ci.Rmd | 18 ++++- 40 files changed, 258 insertions(+), 187 deletions(-)
Title: Mixed Model Association Test for GEne-Environment Interaction
Description: Use a 'glmmkin' class object (GMMAT package) from the null model to perform generalized linear mixed model-based single-variant and variant set main effect tests, gene-environment interaction tests, and joint tests for association, as proposed in Wang et al. (2020) <DOI:10.1002/gepi.22351>.
Author: Xinyu Wang [aut],
Han Chen [aut, cre],
Duy Pham [aut],
Kenneth Westerman [ctb],
Cong Pan [aut],
Eric Biggers [ctb, cph] ,
Tino Reichardt [ctb, cph] library),
Meta Platforms, Inc. and affiliates [cph] library)
Maintainer: Han Chen <han.chen.2@uth.tmc.edu>
Diff between MAGEE versions 1.4.0 dated 2024-04-23 and 1.4.1 dated 2024-04-28
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- inst/doc/MAGEE.Rnw | 9 +++++++-- inst/doc/MAGEE.pdf |binary man/MAGEE-package.Rd | 4 ++-- src/fitglmm.cpp | 5 +---- src/fitmagee.cpp | 2 +- src/registerDynamicSymbol.c | 4 ++-- vignettes/MAGEE.Rnw | 9 +++++++-- 9 files changed, 32 insertions(+), 25 deletions(-)
Title: Complex Matrix Algebra with 'Eigen'
Description: Matrix algebra using the 'Eigen' C++ library: determinant,
rank, inverse, pseudo-inverse, kernel and image, QR decomposition,
Cholesky decomposition, Schur decomposition, Hessenberg decomposition,
linear least-squares problems. Also provides matrix functions such as
exponential, logarithm, power, sine and cosine. Complex matrices are
supported.
Author: Stephane Laurent
Maintainer: Stephane Laurent <laurent_step@outlook.fr>
Diff between EigenR versions 1.2.3 dated 2022-05-18 and 1.3.0 dated 2024-04-28
DESCRIPTION | 25 ++++++--- MD5 | 73 +++++++++++++++-------------- NAMESPACE | 3 + NEWS.md | 6 ++ R/EigenR.R | 77 ++++++++++++++++++++++++++++++ R/RcppExports.R | 16 ++++++ R/SparseMatrix.R | 108 +++++++++++++++++++++---------------------- README.md | 99 +++++++++++++++++++++++---------------- man/Eigen_Hessenberg.Rd |only man/Eigen_QR.Rd | 44 ++++++++--------- man/Eigen_UtDU.Rd | 68 +++++++++++++-------------- man/Eigen_absdet.Rd | 50 +++++++++---------- man/Eigen_chol.Rd | 74 ++++++++++++++--------------- man/Eigen_complexSchur.Rd |only man/Eigen_cos.Rd | 48 +++++++++---------- man/Eigen_cosh.Rd | 46 +++++++++--------- man/Eigen_det.Rd | 54 ++++++++++----------- man/Eigen_exp.Rd | 34 ++++++------- man/Eigen_inverse.Rd | 34 ++++++------- man/Eigen_isInjective.Rd | 48 +++++++++---------- man/Eigen_isInvertible.Rd | 44 ++++++++--------- man/Eigen_isSurjective.Rd | 46 +++++++++--------- man/Eigen_kernel.Rd | 63 +++++++++++++------------ man/Eigen_kernelDimension.Rd | 50 +++++++++---------- man/Eigen_log.Rd | 42 ++++++++-------- man/Eigen_logabsdet.Rd | 52 ++++++++++---------- man/Eigen_pinverse.Rd | 70 +++++++++++++-------------- man/Eigen_pow.Rd | 46 +++++++++--------- man/Eigen_range.Rd | 44 ++++++++--------- man/Eigen_rank.Rd | 34 ++++++------- man/Eigen_realSchur.Rd |only man/Eigen_sin.Rd | 34 ++++++------- man/Eigen_sinh.Rd | 46 +++++++++--------- man/Eigen_sqrt.Rd | 52 ++++++++++---------- man/SparseMatrix.Rd | 78 +++++++++++++++---------------- src/Hessenberg.cpp |only src/Makevars | 2 src/Makevars.win | 2 src/RcppExports.cpp | 50 +++++++++++++++++++ src/Schur.cpp |only 40 files changed, 924 insertions(+), 738 deletions(-)
Title: Bayesian Deep Gaussian Processes using MCMC
Description: Performs Bayesian posterior inference for deep Gaussian processes
following Sauer, Gramacy, and Higdon (2023, <doi:10.48550/arXiv.2012.08015>). See Sauer
(2023, <http://hdl.handle.net/10919/114845>) for comprehensive methodological
details and <https://bitbucket.org/gramacylab/deepgp-ex/> for a variety of
coding examples. Models are trained through MCMC including elliptical
slice sampling of latent Gaussian layers and Metropolis-Hastings
sampling of kernel hyperparameters. Vecchia-approximation for faster
computation is implemented following Sauer, Cooper, and Gramacy
(2023, <doi:10.48550/arXiv.2204.02904>). Downstream tasks include sequential design
through active learning Cohn/integrated mean squared error
(ALC/IMSE; Sauer, Gramacy, and Higdon, 2023), optimization through
expected improvement (EI; Gramacy, Sauer, and Wycoff, 2022 <doi:10.48550/arXiv.2112.07457>),
and contour location through entropy
(Booth, Renganathan, and Gramacy, 2024 <doi:10.48 [...truncated...]
Author: Annie S. Booth <annie_booth@ncsu.edu>
Maintainer: Annie S. Booth <annie_booth@ncsu.edu>
Diff between deepgp versions 1.1.1 dated 2023-08-07 and 1.1.2 dated 2024-04-28
DESCRIPTION | 41 - MD5 | 62 +- NAMESPACE | 1 R/ALC.R | 44 - R/IMSE.R | 44 - R/checks.R | 23 R/continue.R | 45 + R/deepgp-package.R | 42 - R/fit.R | 87 ++- R/general.R | 47 - R/gibbs.R | 22 R/gibbs_vecchia.R | 48 - R/mcmc.R | 2 R/plot.R | 2 R/predict.R | 724 +++++++++------------------- R/predict_vecchia.R | 689 ++++++++++----------------- R/trim.R | 6 R/vecchia.R | 42 + README.md | 27 - build/vignette.rds |binary inst/doc/deepgp.Rmd | 7 inst/doc/deepgp.html | 1192 +++++++++++++++++++++++++++++++++++------------ man/ALC.Rd | 2 man/IMSE.Rd | 2 man/deepgp-package.Rd | 41 - man/fit_one_layer.Rd | 10 man/fit_three_layer.Rd | 11 man/fit_two_layer.Rd | 11 man/predict.Rd | 24 src/vecchia.cpp | 10 vignettes/deepgp.Rmd | 7 vignettes/references.bib | 7 32 files changed, 1827 insertions(+), 1495 deletions(-)
Title: Interface to the Computer Algebra System 'Giac'
Description: 'Giac'
<https://www-fourier.ujf-grenoble.fr/~parisse/giac/doc/en/cascmd_en/cascmd_en.html>
is a general purpose symbolic algebra software. It powers the
graphical interface 'Xcas'. This package allows to execute 'Giac'
commands in 'R'.
Author: Stephane Laurent [aut, cre],
Renee De Graeve [cph] ,
Bernard Parisse [cph]
Maintainer: Stephane Laurent <laurent_step@outlook.fr>
Diff between giacR versions 1.0.0 dated 2023-08-17 and 1.0.1 dated 2024-04-28
DESCRIPTION | 6 +++--- MD5 | 8 ++++---- NEWS.md | 5 +++++ R/zzz.R | 2 ++ man/Giac.Rd | 8 ++++---- 5 files changed, 18 insertions(+), 11 deletions(-)
Title: Find Pattern in Files
Description: Creates a HTML widget which displays the results of searching
for a pattern in files in a given folder. The results can be viewed in
the 'RStudio' viewer pane, included in a 'R Markdown' document or in a
'Shiny' application. Also provides a 'Shiny' application allowing to run
this widget and to navigate in the files found by the search. Instead of
creating a HTML widget, it is also possible to get the results of the
search in a 'tibble'. The search is performed by the 'grep' command-line
utility.
Author: Stephane Laurent [aut, cre],
Rob Burns [ctb, cph]
Maintainer: Stephane Laurent <laurent_step@outlook.fr>
Diff between findInFiles versions 0.4.0 dated 2022-04-11 and 0.5.0 dated 2024-04-28
findInFiles-0.4.0/findInFiles/inst/ztemp |only findInFiles-0.5.0/findInFiles/DESCRIPTION | 41 findInFiles-0.5.0/findInFiles/LICENSE.note | 62 findInFiles-0.5.0/findInFiles/MD5 | 49 findInFiles-0.5.0/findInFiles/NAMESPACE | 41 findInFiles-0.5.0/findInFiles/NEWS.md | 41 findInFiles-0.5.0/findInFiles/R/findInFiles.R | 153 findInFiles-0.5.0/findInFiles/R/grepInFiles.R | 122 findInFiles-0.5.0/findInFiles/R/shiny.R | 10 findInFiles-0.5.0/findInFiles/README.md | 14 findInFiles-0.5.0/findInFiles/inst/example/folder/f.R | 6 findInFiles-0.5.0/findInFiles/inst/example/folder/subfolder/g.R | 6 findInFiles-0.5.0/findInFiles/inst/example/folder/subfolder/subsubfolder/h.R | 6 findInFiles-0.5.0/findInFiles/inst/htmlwidgets/findInFiles.yaml | 12 findInFiles-0.5.0/findInFiles/inst/htmlwidgets/lib/ansi-to-html.css | 22 findInFiles-0.5.0/findInFiles/inst/htmlwidgets/lib/ansi-to-html_bundle.js | 1712 +++++----- findInFiles-0.5.0/findInFiles/inst/shinyApp/global.R | 14 findInFiles-0.5.0/findInFiles/inst/shinyApp/server.R | 69 findInFiles-0.5.0/findInFiles/inst/shinyApp/ui.R | 64 findInFiles-0.5.0/findInFiles/inst/shinyApp/www/shinyFIF.css | 15 findInFiles-0.5.0/findInFiles/man/FIF2dataframe.Rd | 52 findInFiles-0.5.0/findInFiles/man/FIF2tibble.Rd | 50 findInFiles-0.5.0/findInFiles/man/findInFiles-shiny.Rd | 220 - findInFiles-0.5.0/findInFiles/man/findInFiles.Rd | 222 - findInFiles-0.5.0/findInFiles/man/shinyFIF.Rd | 38 25 files changed, 1693 insertions(+), 1348 deletions(-)
Title: Bindings for Bayesian TidyModels
Description: Fit Bayesian models using 'brms'/'Stan' with 'parsnip'/'tidymodels'
via 'bayesian' <doi:10.5281/zenodo.4426836>. 'tidymodels' is a collection of
packages for machine learning; see Kuhn and Wickham (2020) <https://www.tidymodels.org>).
The technical details of 'brms' and 'Stan' are described in Bürkner (2017)
<doi:10.18637/jss.v080.i01>, Bürkner (2018) <doi:10.32614/RJ-2018-017>,
and Carpenter et al. (2017) <doi:10.18637/jss.v076.i01>.
Author: Hamada S. Badr [aut, cre] ,
Paul-Christian Buerkner [aut]
Maintainer: Hamada S. Badr <badr@jhu.edu>
Diff between bayesian versions 0.0.9 dated 2022-06-16 and 1.0.1 dated 2024-04-28
DESCRIPTION | 12 - LICENSE | 2 MD5 | 28 +- NAMESPACE | 1 NEWS.md | 17 + R/bayesian.R | 23 -- R/bayesian_init.R | 2 R/bayesian_load.R | 1 R/bayesian_make.R | 176 +++++++++++---- README.md | 6 build/vignette.rds |binary inst/CITATION | 9 inst/doc/BugReports.html | 232 +++++++++++++++++++- inst/doc/GetStarted.html | 522 ++++++++++++++++++++++++++++++++++------------- man/bayesian.Rd | 4 15 files changed, 787 insertions(+), 248 deletions(-)
Title: Bindings for Additive TidyModels
Description: Fit Generalized Additive Models (GAM) using 'mgcv' with 'parsnip'/'tidymodels'
via 'additive' <doi:10.5281/zenodo.4784245>. 'tidymodels' is a collection of
packages for machine learning; see Kuhn and Wickham (2020) <https://www.tidymodels.org>).
The technical details of 'mgcv' are described in Wood (2017)
<doi:10.1201/9781315370279>.
Author: Hamada S. Badr [aut, cre]
Maintainer: Hamada S. Badr <badr@jhu.edu>
Diff between additive versions 0.0.5 dated 2022-06-16 and 1.0.1 dated 2024-04-28
DESCRIPTION | 12 - LICENSE | 2 MD5 | 28 +- NAMESPACE | 2 NEWS.md | 13 + R/additive.R | 23 -- R/additive_init.R | 4 R/additive_load.R | 1 R/additive_make.R | 111 ++++++++-- README.md | 6 build/vignette.rds |binary inst/CITATION | 9 inst/doc/BugReports.html | 229 ++++++++++++++++++++-- inst/doc/GetStarted.html | 482 +++++++++++++++++++++++++++++++++++------------ man/additive.Rd | 18 - 15 files changed, 713 insertions(+), 227 deletions(-)
Title: Threshing and Reaping for Principal Components
Description: Defines the classes used to identify
outliers (threshing) and compute the number of significant principal
components and number of clusters (reaping) in a joint application
of PCA and hierarchical clustering. See Wang et al., 2018,
<doi:10.1186/s12859-017-1998-9>.
Author: Kevin R. Coombes
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between Thresher versions 1.1.3 dated 2019-12-17 and 1.1.4 dated 2024-04-28
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- build/vignette.rds |binary data/savedSims.rda |binary inst/doc/Thresher.pdf |binary man/01-dataObjects.Rd | 8 ++++---- 6 files changed, 13 insertions(+), 13 deletions(-)
Title: Partial LeAst Squares for Multiomic Analysis
Description: Contains tools for supervised analyses of incomplete, overlapping
multiomics datasets. Applies partial least squares in multiple steps to find
models that predict survival outcomes. See Yamaguchi et al. (2023)
<doi:10.1101/2023.03.10.532096>.
Author: Kevin R. Coombes [cre, aut],
Kyoko Yamaguchi [aut],
Salma Abdelbaky [aut]
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between plasma versions 1.0.0 dated 2023-03-13 and 1.1.3 dated 2024-04-28
plasma-1.0.0/plasma/inst/bib/plasma.log |only plasma-1.1.3/plasma/DESCRIPTION | 8 ++++---- plasma-1.1.3/plasma/MD5 | 25 +++++++++++++------------ plasma-1.1.3/plasma/R/02-fitCoxModel.R | 2 ++ plasma-1.1.3/plasma/R/03-manyCoxModels.R | 3 +++ plasma-1.1.3/plasma/R/06-weights.R | 22 +++++++++++++--------- plasma-1.1.3/plasma/build/vignette.rds |binary plasma-1.1.3/plasma/data/mirESCA.rda |binary plasma-1.1.3/plasma/data/tfESCA.rda |binary plasma-1.1.3/plasma/inst/bib/theory.Rmd |only plasma-1.1.3/plasma/inst/bib/theory.pdf |only plasma-1.1.3/plasma/inst/doc/plasma.pdf |binary plasma-1.1.3/plasma/man/01-TCGA-ESCA-data.Rd | 2 +- plasma-1.1.3/plasma/man/02-fitCoxModel.Rd | 2 +- plasma-1.1.3/plasma/man/04-plasma-class.Rd | 6 ++++-- 15 files changed, 41 insertions(+), 29 deletions(-)
Title: Data to Illustrate OOMPA Algorithms
Description: This is a data-only package to provide example data for
other packages that are part of the "Object-Oriented Microrray and
Proteomics Analysis" suite of packages. These are described in more
detail at the package URL.
Author: Kevin R. Coombes
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between oompaData versions 3.1.3 dated 2022-12-02 and 3.1.4 dated 2024-04-28
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ data/clinical.info.rda |binary data/expression.data.rda |binary data/gene.info.rda |binary data/lungData.rda |binary man/cd09-1-lungData.Rd | 5 ++--- 7 files changed, 12 insertions(+), 13 deletions(-)
Title: Automated Estimation of Sigmoidal and Piecewise Linear Mixed
Models
Description: Estimation of relatively complex nonlinear mixed-effects models, including the Sigmoidal Mixed Model and the Piecewise Linear Mixed Model with abrupt or smooth transition, through a single intuitive line of code and with automated generation of starting values.
Author: Maude Wagner [aut, cre] ,
Emmanuelle Comets [ctb],
Ana W. Capuano [aut]
Maintainer: Maude Wagner <maude_wagner@rush.edu>
Diff between nlive versions 0.3.0 dated 2024-04-17 and 0.4.0 dated 2024-04-28
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/nlive.R | 15 ++++++++------- R/nlive.pmma.R | 14 ++++++++------ R/nlive.pmms.R | 15 ++++++++------- R/nlive.smm.R | 17 ++++++++--------- 6 files changed, 41 insertions(+), 38 deletions(-)
Title: Extending the Newman Studentized Range Statistic to
Transcriptomics
Description: Extends the classical Newman studentized range statistic
in various ways that can be applied to genome-scale transcriptomic
or other expression data.
Author: Zachary Abrams, Greg Gershkowitz, Anoushka Joglekar,
Chao Liu, Kevin R. Coombes
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between NewmanOmics versions 1.0.10 dated 2022-05-18 and 1.0.11 dated 2024-04-28
DESCRIPTION | 8 +++--- MD5 | 12 ++++----- build/vignette.rds |binary data/GSE6631.rda |binary data/LungPair.rda |binary inst/doc/newmanomics.html | 55 +++++++++++++++++++++++++-------------------- man/03-MixOf3Beta-class.Rd | 4 +-- 7 files changed, 43 insertions(+), 36 deletions(-)
Title: Clustering and Visualizing Distance Matrices
Description: Defines the classes used to explore, cluster and
visualize distance matrices, especially those arising from binary
data. See Abrams and colleagues, 2021, <doi:10.1093/bioinformatics/btab037>.
Author: Kevin R. Coombes, Caitlin E. Coombes
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between Mercator versions 1.1.2 dated 2022-06-30 and 1.1.4 dated 2024-04-28
DESCRIPTION | 8 +-- MD5 | 26 ++++----- R/05-graph.R | 2 R/06-som-umap.R | 2 build/vignette.rds |binary data/CML1000.rda |binary data/CML500.rda |binary data/fakedata.rda |binary data/lgfFeatures.rda |binary inst/doc/mercVis.html | 129 ++++++++++++++++++++++++++----------------------- inst/doc/mercator.html | 19 ++++--- inst/doc/umap-som.html | 100 ++++++++++++++++++++----------------- man/Mercator-class.Rd | 12 ++-- man/threshLGF.Rd | 3 - 14 files changed, 163 insertions(+), 138 deletions(-)
Title: Classes and Methods for "Class Discovery" with Microarrays or
Proteomics
Description: Defines the classes used for "class discovery" problems
in the OOMPA project (<http://oompa.r-forge.r-project.org/>). Class
discovery primarily consists of unsupervised clustering methods with
attempts to assess their statistical significance.
Author: Kevin R. Coombes
Maintainer: Kevin R. Coombes <krc@silicovore.com>
Diff between ClassDiscovery versions 3.4.0 dated 2021-07-16 and 3.4.5 dated 2024-04-28
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- build/vignette.rds |binary inst/doc/maha-test.pdf |binary inst/doc/oompa-cd.pdf |binary man/cd01-0-distanceMatrix.Rd | 2 +- man/cd02-1-cluster3.Rd | 2 +- man/cd03-0-ClusterTest-class.Rd | 2 +- man/cd08-0-PCanova-class.Rd | 2 +- 9 files changed, 16 insertions(+), 16 deletions(-)
More information about ClassDiscovery at CRAN
Permanent link
Title: A Tool for Creating Custom Neural Networks in C++ and using Them
in R
Description: Contains a module to define neural networks from custom components and versions of Autoencoder, BP, LVQ, MAM NN.
Author: Vasilis Nikolaidis [aut, cph, cre]
Maintainer: Vasilis Nikolaidis <v.nikolaidis@uop.gr>
Diff between nnlib2Rcpp versions 0.2.6 dated 2024-04-25 and 0.2.7 dated 2024-04-28
DESCRIPTION | 6 +++--- MD5 | 6 +++--- inst/doc/intro.pdf |binary src/nn_lvq.cpp | 12 +++++------- 4 files changed, 11 insertions(+), 13 deletions(-)
Title: Miscellaneous Functions for Metabarcoding Analysis
Description: Facilitate the description, transformation, exploration, and reproducibility of metabarcoding analyses. 'MiscMetabar' is mainly built on top of the 'phyloseq', 'dada2' and 'targets' R packages. It helps to build reproducible and robust bioinformatics pipelines in R. 'MiscMetabar' makes ecological analysis of alpha and beta-diversity easier, more reproducible and more powerful by integrating a large number of tools. Important features are described in Taudière A. (2023) <doi:10.21105/joss.06038>.
Author: Adrien Taudiere [aut, cre, cph]
Maintainer: Adrien Taudiere <adrien.taudiere@zaclys.net>
Diff between MiscMetabar versions 0.7.10 dated 2024-03-08 and 0.9.1 dated 2024-04-28
MiscMetabar-0.7.10/MiscMetabar/R/tuckeyTest.R |only MiscMetabar-0.9.1/MiscMetabar/DESCRIPTION | 18 MiscMetabar-0.9.1/MiscMetabar/MD5 | 194 - MiscMetabar-0.9.1/MiscMetabar/NAMESPACE | 28 MiscMetabar-0.9.1/MiscMetabar/NEWS.md | 33 MiscMetabar-0.9.1/MiscMetabar/R/Deseq2_edgeR.R | 47 MiscMetabar-0.9.1/MiscMetabar/R/MiscMetabar-package.R | 6 MiscMetabar-0.9.1/MiscMetabar/R/alpha_div_test.R |only MiscMetabar-0.9.1/MiscMetabar/R/beta_div_test.R | 958 +++++ MiscMetabar-0.9.1/MiscMetabar/R/blast.R | 4 MiscMetabar-0.9.1/MiscMetabar/R/controls.R | 2 MiscMetabar-0.9.1/MiscMetabar/R/dada_phyloseq.R | 493 ++ MiscMetabar-0.9.1/MiscMetabar/R/data.R | 4 MiscMetabar-0.9.1/MiscMetabar/R/miscellanous.R | 65 MiscMetabar-0.9.1/MiscMetabar/R/plot_functions.R | 1649 ++++++---- MiscMetabar-0.9.1/MiscMetabar/R/speedyseq_functions.R | 6 MiscMetabar-0.9.1/MiscMetabar/R/table_functions.R | 345 +- MiscMetabar-0.9.1/MiscMetabar/R/targets_misc.R | 7 MiscMetabar-0.9.1/MiscMetabar/R/vsearch.R | 22 MiscMetabar-0.9.1/MiscMetabar/README.md | 109 MiscMetabar-0.9.1/MiscMetabar/inst/doc/MiscMetabar.html | 134 MiscMetabar-0.9.1/MiscMetabar/man/LCBD_pq.Rd | 14 MiscMetabar-0.9.1/MiscMetabar/man/SRS_curve_pq.Rd | 12 MiscMetabar-0.9.1/MiscMetabar/man/Tengeler2020_pq.Rd | 4 MiscMetabar-0.9.1/MiscMetabar/man/accu_plot_balanced_modality.Rd |only MiscMetabar-0.9.1/MiscMetabar/man/accu_samp_threshold.Rd | 2 MiscMetabar-0.9.1/MiscMetabar/man/add_blast_info.Rd | 2 MiscMetabar-0.9.1/MiscMetabar/man/add_funguild_info.Rd | 24 MiscMetabar-0.9.1/MiscMetabar/man/add_new_taxonomy_pq.Rd | 2 MiscMetabar-0.9.1/MiscMetabar/man/adonis_rarperm_pq.Rd |only MiscMetabar-0.9.1/MiscMetabar/man/ancombc_pq.Rd | 60 MiscMetabar-0.9.1/MiscMetabar/man/as_binary_otu_table.Rd | 2 MiscMetabar-0.9.1/MiscMetabar/man/asv2otu.Rd | 18 MiscMetabar-0.9.1/MiscMetabar/man/biplot_pq.Rd | 2 MiscMetabar-0.9.1/MiscMetabar/man/build_phytree_pq.Rd | 4 MiscMetabar-0.9.1/MiscMetabar/man/chimera_removal_vs.Rd | 2 MiscMetabar-0.9.1/MiscMetabar/man/circle_pq.Rd | 12 MiscMetabar-0.9.1/MiscMetabar/man/compare_pairs_pq.Rd | 1 MiscMetabar-0.9.1/MiscMetabar/man/diff_fct_diff_class.Rd | 4 MiscMetabar-0.9.1/MiscMetabar/man/dist_bycol.Rd | 4 MiscMetabar-0.9.1/MiscMetabar/man/distri_1_taxa.Rd |only MiscMetabar-0.9.1/MiscMetabar/man/fac2col.Rd |only MiscMetabar-0.9.1/MiscMetabar/man/figures/README-example-1.png |binary MiscMetabar-0.9.1/MiscMetabar/man/figures/README-unnamed-chunk-5-1.png |binary MiscMetabar-0.9.1/MiscMetabar/man/figures/README-unnamed-chunk-6-1.png |binary MiscMetabar-0.9.1/MiscMetabar/man/figures/README-unnamed-chunk-7-1.png |only MiscMetabar-0.9.1/MiscMetabar/man/filter_asv_blast.Rd | 2 MiscMetabar-0.9.1/MiscMetabar/man/formattable_pq.Rd |only MiscMetabar-0.9.1/MiscMetabar/man/funky_color.Rd | 5 MiscMetabar-0.9.1/MiscMetabar/man/ggaluv_pq.Rd |only MiscMetabar-0.9.1/MiscMetabar/man/ggbetween_pq.Rd | 20 MiscMetabar-0.9.1/MiscMetabar/man/ggscatt_pq.Rd |only MiscMetabar-0.9.1/MiscMetabar/man/ggvenn_pq.Rd | 41 MiscMetabar-0.9.1/MiscMetabar/man/glmutli_pq.Rd |only MiscMetabar-0.9.1/MiscMetabar/man/graph_test_pq.Rd | 10 MiscMetabar-0.9.1/MiscMetabar/man/heat_tree_pq.Rd | 3 MiscMetabar-0.9.1/MiscMetabar/man/hill_pq.Rd | 74 MiscMetabar-0.9.1/MiscMetabar/man/hill_test_rarperm_pq.Rd |only MiscMetabar-0.9.1/MiscMetabar/man/hill_tuckey_pq.Rd | 10 MiscMetabar-0.9.1/MiscMetabar/man/iNEXT_pq.Rd | 4 MiscMetabar-0.9.1/MiscMetabar/man/merge_samples2.Rd | 2 MiscMetabar-0.9.1/MiscMetabar/man/multi_biplot_pq.Rd | 2 MiscMetabar-0.9.1/MiscMetabar/man/multipatt_pq.Rd | 20 MiscMetabar-0.9.1/MiscMetabar/man/multitax_bar_pq.Rd | 12 MiscMetabar-0.9.1/MiscMetabar/man/normalize_prop_pq.Rd |only MiscMetabar-0.9.1/MiscMetabar/man/plot_LCBD_pq.Rd | 42 MiscMetabar-0.9.1/MiscMetabar/man/plot_SCBD_pq.Rd | 19 MiscMetabar-0.9.1/MiscMetabar/man/plot_ancombc_pq.Rd |only MiscMetabar-0.9.1/MiscMetabar/man/plot_deseq2_pq.Rd | 31 MiscMetabar-0.9.1/MiscMetabar/man/plot_edgeR_pq.Rd | 14 MiscMetabar-0.9.1/MiscMetabar/man/plot_guild_pq.Rd | 40 MiscMetabar-0.9.1/MiscMetabar/man/plot_tsne_pq.Rd | 12 MiscMetabar-0.9.1/MiscMetabar/man/plot_var_part_pq.Rd |only MiscMetabar-0.9.1/MiscMetabar/man/psmelt_samples_pq.Rd |only MiscMetabar-0.9.1/MiscMetabar/man/rarefy_sample_count_by_modality.Rd |only MiscMetabar-0.9.1/MiscMetabar/man/read_pq.Rd | 2 MiscMetabar-0.9.1/MiscMetabar/man/rename_samples.Rd | 4 MiscMetabar-0.9.1/MiscMetabar/man/ridges_pq.Rd | 25 MiscMetabar-0.9.1/MiscMetabar/man/rotl_pq.Rd | 2 MiscMetabar-0.9.1/MiscMetabar/man/sankey_pq.Rd | 12 MiscMetabar-0.9.1/MiscMetabar/man/select_one_sample.Rd | 2 MiscMetabar-0.9.1/MiscMetabar/man/signif_ancombc.Rd |only MiscMetabar-0.9.1/MiscMetabar/man/summary_plot_pq.Rd | 2 MiscMetabar-0.9.1/MiscMetabar/man/tax_datatable.Rd | 18 MiscMetabar-0.9.1/MiscMetabar/man/taxa_as_columns.Rd |only MiscMetabar-0.9.1/MiscMetabar/man/taxa_as_rows.Rd |only MiscMetabar-0.9.1/MiscMetabar/man/taxa_only_in_one_level.Rd |only MiscMetabar-0.9.1/MiscMetabar/man/tbl_sum_samdata.Rd | 25 MiscMetabar-0.9.1/MiscMetabar/man/track_wkflow.Rd | 4 MiscMetabar-0.9.1/MiscMetabar/man/track_wkflow_samples.Rd | 8 MiscMetabar-0.9.1/MiscMetabar/man/transp.Rd |only MiscMetabar-0.9.1/MiscMetabar/man/treemap_pq.Rd | 52 MiscMetabar-0.9.1/MiscMetabar/man/tsne_pq.Rd | 6 MiscMetabar-0.9.1/MiscMetabar/man/upset_pq.Rd | 193 - MiscMetabar-0.9.1/MiscMetabar/man/upset_test_pq.Rd | 9 MiscMetabar-0.9.1/MiscMetabar/man/var_par_pq.Rd |only MiscMetabar-0.9.1/MiscMetabar/man/var_par_rarperm_pq.Rd |only MiscMetabar-0.9.1/MiscMetabar/man/venn_pq.Rd | 20 MiscMetabar-0.9.1/MiscMetabar/man/vs_search_global.Rd | 18 MiscMetabar-0.9.1/MiscMetabar/tests/testthat/Rplots.pdf |binary MiscMetabar-0.9.1/MiscMetabar/tests/testthat/test_adonis.R | 3 MiscMetabar-0.9.1/MiscMetabar/tests/testthat/test_deprecated.R | 5 MiscMetabar-0.9.1/MiscMetabar/tests/testthat/test_deseq2_edgeR.R | 26 MiscMetabar-0.9.1/MiscMetabar/tests/testthat/test_figures_alpha_div.R | 36 MiscMetabar-0.9.1/MiscMetabar/tests/testthat/test_figures_beta_div.R | 328 + MiscMetabar-0.9.1/MiscMetabar/tests/testthat/test_figures_taxo.R | 266 - MiscMetabar-0.9.1/MiscMetabar/tests/testthat/test_table_functions.R | 38 MiscMetabar-0.9.1/MiscMetabar/tests/testthat/test_targets.R | 20 MiscMetabar-0.9.1/MiscMetabar/tests/testthat/test_tuckey.R | 6 MiscMetabar-0.9.1/MiscMetabar/vignettes/bibliography.bib | 15 110 files changed, 4120 insertions(+), 1681 deletions(-)
Title: Soil Organic Carbon and CN Ratio Driven Nitrogen Modelling
Framework
Description: Can be used to model the fate of soil organic carbon and soil organic nitrogen and to calculate N mineralisation rates. Provides a framework that numerically solves differential equations of soil organic carbon models based on first-order kinetics and extends these models to include the nitrogen component. The name 'sorcering' is an acronym for 'Soil ORganic Carbon & CN Ratio drIven Nitrogen modellinG framework'.
Author: Marc Scherstjanoi [aut, cre],
Rene Dechow [aut]
Maintainer: Marc Scherstjanoi <marc.scherstjanoi@thuenen.de>
Diff between sorcering versions 1.0.0.1 dated 2023-12-18 and 1.0.1 dated 2024-04-28
DESCRIPTION | 8 ++++---- MD5 | 17 +++++++++-------- NEWS.md |only build/partial.rdb |binary build/sorcering.pdf |binary build/stage23.rdb |binary inst/doc/sorcering.pdf |binary man/sorcering.Rd | 2 +- src/sorcering.cpp | 29 +++++++++++++++++++++-------- vignettes/sorcering_vignette.pdf |binary 10 files changed, 35 insertions(+), 21 deletions(-)
Title: Enrichment Analysis Utilizing Active Subnetworks
Description: Enrichment analysis enables researchers to uncover mechanisms
underlying a phenotype. However, conventional methods for enrichment
analysis do not take into account protein-protein interaction information,
resulting in incomplete conclusions. pathfindR is a tool for enrichment
analysis utilizing active subnetworks. The main function identifies active
subnetworks in a protein-protein interaction network using a user-provided
list of genes and associated p values. It then performs enrichment analyses
on the identified subnetworks, identifying enriched terms (i.e. pathways or,
more broadly, gene sets) that possibly underlie the phenotype of interest.
pathfindR also offers functionalities to cluster the enriched terms and
identify representative terms in each cluster, to score the enriched terms
per sample and to visualize analysis results. The enrichment, clustering and
other methods implemented in pathfindR are described in detail in
Ulgen E, Ozisik O, Sezerman OU. 2019. pathfindR: An R [...truncated...]
Author: Ege Ulgen [cre, cph] ,
Ozan Ozisik [aut]
Maintainer: Ege Ulgen <egeulgen@gmail.com>
Diff between pathfindR versions 2.3.1 dated 2024-01-19 and 2.4.0 dated 2024-04-28
pathfindR-2.3.1/pathfindR/man/download_KGML_file.Rd |only pathfindR-2.3.1/pathfindR/man/download_kegg_png.Rd |only pathfindR-2.3.1/pathfindR/man/obtain_colored_url.Rd |only pathfindR-2.3.1/pathfindR/man/visualize_hsa_KEGG.Rd |only pathfindR-2.3.1/pathfindR/vignettes/hsaKEGG_diagram.png |only pathfindR-2.4.0/pathfindR/DESCRIPTION | 12 pathfindR-2.4.0/pathfindR/MD5 | 89 pathfindR-2.4.0/pathfindR/NAMESPACE | 2 pathfindR-2.4.0/pathfindR/NEWS.md | 14 pathfindR-2.4.0/pathfindR/R/comparison.R | 2 pathfindR-2.4.0/pathfindR/R/data_generation.R | 94 pathfindR-2.4.0/pathfindR/R/scoring.R | 4 pathfindR-2.4.0/pathfindR/R/visualization.R | 519 +---- pathfindR-2.4.0/pathfindR/build/vignette.rds |binary pathfindR-2.4.0/pathfindR/inst/doc/comparing_results.R | 2 pathfindR-2.4.0/pathfindR/inst/doc/comparing_results.html | 4 pathfindR-2.4.0/pathfindR/inst/doc/intro_vignette.R | 91 pathfindR-2.4.0/pathfindR/inst/doc/intro_vignette.Rmd | 85 pathfindR-2.4.0/pathfindR/inst/doc/intro_vignette.html | 244 +- pathfindR-2.4.0/pathfindR/inst/doc/manual_execution.html | 8 pathfindR-2.4.0/pathfindR/inst/doc/non_hs_analysis.R | 2 pathfindR-2.4.0/pathfindR/inst/doc/non_hs_analysis.html | 4 pathfindR-2.4.0/pathfindR/inst/doc/obtain_data.R | 4 pathfindR-2.4.0/pathfindR/inst/doc/obtain_data.html | 6 pathfindR-2.4.0/pathfindR/inst/doc/visualization_vignette.R | 26 pathfindR-2.4.0/pathfindR/inst/doc/visualization_vignette.Rmd | 34 pathfindR-2.4.0/pathfindR/inst/doc/visualization_vignette.html | 62 pathfindR-2.4.0/pathfindR/inst/extdata/resultActiveSubnetworkSearch.txt | 1020 +++++++++- pathfindR-2.4.0/pathfindR/man/color_kegg_pathway.Rd | 12 pathfindR-2.4.0/pathfindR/man/get_biogrid_pin.Rd | 4 pathfindR-2.4.0/pathfindR/man/pathfindR.Rd | 2 pathfindR-2.4.0/pathfindR/man/visualize_KEGG_diagram.Rd |only pathfindR-2.4.0/pathfindR/man/visualize_term_interactions.Rd | 10 pathfindR-2.4.0/pathfindR/man/visualize_terms.Rd | 35 pathfindR-2.4.0/pathfindR/tests/testthat/test-active_snw_search.R | 4 pathfindR-2.4.0/pathfindR/tests/testthat/test-data_generation.R | 108 - pathfindR-2.4.0/pathfindR/tests/testthat/test-enrichment.R | 2 pathfindR-2.4.0/pathfindR/tests/testthat/test-visualization.R | 159 - pathfindR-2.4.0/pathfindR/vignettes/combined_graph.png |binary pathfindR-2.4.0/pathfindR/vignettes/enrichment_chart.png |binary pathfindR-2.4.0/pathfindR/vignettes/example_interaction_vis.png |binary pathfindR-2.4.0/pathfindR/vignettes/example_kegg_pathway_diagram.png |only pathfindR-2.4.0/pathfindR/vignettes/hmap.png |binary pathfindR-2.4.0/pathfindR/vignettes/intro_vignette.Rmd | 85 pathfindR-2.4.0/pathfindR/vignettes/man_enrichment_chart.png |binary pathfindR-2.4.0/pathfindR/vignettes/score_hmap.png |binary pathfindR-2.4.0/pathfindR/vignettes/term_gene.png |binary pathfindR-2.4.0/pathfindR/vignettes/upset.png |binary pathfindR-2.4.0/pathfindR/vignettes/visualization_vignette.Rmd | 34 49 files changed, 1778 insertions(+), 1005 deletions(-)
Title: Datasets and Code Examples from P. J. Aphalo's "Learn R" Book
Description: Data, scripts and code from chunks used as examples in the book
"Learn R: As a Language" 1ed and 2ed by Pedro J. Aphalo.
ISBN 9780367182533 (pbk 1ed); ISBN 9780367182557 (hbk 1ed); ISBN 9780429060342 (ebk 1ed).
Author: Pedro J. Aphalo [aut, cre]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>
Diff between learnrbook versions 1.0.2-1 dated 2023-02-15 and 2.0.1 dated 2024-04-28
learnrbook-1.0.2-1/learnrbook/inst/example-chunks/purl-output.zip |only learnrbook-1.0.2-1/learnrbook/man/figures/cover-small.png |only learnrbook-1.0.2-1/learnrbook/man/pkgs_all.Rd |only learnrbook-1.0.2-1/learnrbook/man/pkgs_ch_data.Rd |only learnrbook-1.0.2-1/learnrbook/man/pkgs_ch_data_io.Rd |only learnrbook-1.0.2-1/learnrbook/man/pkgs_ch_graphics.Rd |only learnrbook-1.0.2-1/learnrbook/vignettes/images |only learnrbook-2.0.1/learnrbook/DESCRIPTION | 23 learnrbook-2.0.1/learnrbook/MD5 | 57 learnrbook-2.0.1/learnrbook/NEWS.md | 26 learnrbook-2.0.1/learnrbook/R/learnrbook.R | 5 learnrbook-2.0.1/learnrbook/R/used-packages-data.R | 76 learnrbook-2.0.1/learnrbook/README.md | 79 learnrbook-2.0.1/learnrbook/build/vignette.rds |binary learnrbook-2.0.1/learnrbook/data/pkgs-in-book.rda |binary learnrbook-2.0.1/learnrbook/data/volcano-example.rda |binary learnrbook-2.0.1/learnrbook/data/weather-wk-25-2019-tb.rda |binary learnrbook-2.0.1/learnrbook/data/wind-data.rda |binary learnrbook-2.0.1/learnrbook/inst/doc/user-guide.R | 29 learnrbook-2.0.1/learnrbook/inst/doc/user-guide.Rmd | 244 - learnrbook-2.0.1/learnrbook/inst/doc/user-guide.html | 288 - learnrbook-2.0.1/learnrbook/inst/example-chunks/R-code-from-examples-learnrbook-1ed.zip |only learnrbook-2.0.1/learnrbook/inst/example-chunks/R-code-from-examples-learnrbook-2ed.zip |only learnrbook-2.0.1/learnrbook/inst/extdata/cloudindex.idx | 1121 ------ learnrbook-2.0.1/learnrbook/inst/extdata/rcatsidx.idx | 1121 ------ learnrbook-2.0.1/learnrbook/inst/extdata/rindex.idx | 1121 ------ learnrbook-2.0.1/learnrbook/inst/extdata/using-r-main-crc.idx | 1752 +--------- learnrbook-2.0.1/learnrbook/man/figures/cover-small-1ed.png |only learnrbook-2.0.1/learnrbook/man/figures/cover-small-2ed.jpg |only learnrbook-2.0.1/learnrbook/man/learnrbook-package.Rd | 8 learnrbook-2.0.1/learnrbook/man/pkgs_all_1ed.Rd |only learnrbook-2.0.1/learnrbook/man/pkgs_all_2ed.Rd |only learnrbook-2.0.1/learnrbook/man/pkgs_ch10_2ed.Rd |only learnrbook-2.0.1/learnrbook/man/pkgs_ch6_1ed.Rd |only learnrbook-2.0.1/learnrbook/man/pkgs_ch7_1ed.Rd |only learnrbook-2.0.1/learnrbook/man/pkgs_ch8_1ed.Rd |only learnrbook-2.0.1/learnrbook/man/pkgs_ch8_2ed.Rd |only learnrbook-2.0.1/learnrbook/man/pkgs_ch9_2ed.Rd |only learnrbook-2.0.1/learnrbook/vignettes/user-guide.Rmd | 244 - 39 files changed, 926 insertions(+), 5268 deletions(-)
Title: Multi-Format Archive and Compression Support
Description: Bindings to 'libarchive' <http://www.libarchive.org> the
Multi-format archive and compression library. Offers R connections and
direct extraction for many archive formats including 'tar', 'ZIP',
'7-zip', 'RAR', 'CAB' and compression formats including 'gzip',
'bzip2', 'compress', 'lzma' and 'xz'.
Author: Jim Hester [aut] ,
Gabor Csardi [aut, cre],
Ondrej Holy [cph] ,
RStudio [cph, fnd]
Maintainer: Gabor Csardi <csardi.gabor@gmail.com>
Diff between archive versions 1.1.7 dated 2023-12-11 and 1.1.8 dated 2024-04-28
archive-1.1.7/archive/build |only archive-1.1.8/archive/DESCRIPTION | 10 +-- archive-1.1.8/archive/MD5 | 59 ++++++++++++++----- archive-1.1.8/archive/NEWS.md | 6 + archive-1.1.8/archive/R/cpp11.R | 40 ++++++------- archive-1.1.8/archive/cleanup | 5 - archive-1.1.8/archive/configure | 15 +++- archive-1.1.8/archive/man/archive_read.Rd | 6 + archive-1.1.8/archive/man/archive_write.Rd | 6 + archive-1.1.8/archive/man/archive_write_files.Rd | 6 + archive-1.1.8/archive/man/file_connections.Rd | 3 archive-1.1.8/archive/man/macros |only archive-1.1.8/archive/src/Makevars.in | 3 archive-1.1.8/archive/src/Makevars.ucrt | 2 archive-1.1.8/archive/src/Makevars.win | 2 archive-1.1.8/archive/src/archive_extract.cpp | 7 +- archive-1.1.8/archive/src/cpp11 |only archive-1.1.8/archive/src/cpp11.cpp | 70 +++++++++++------------ archive-1.1.8/archive/tools/dynamic-help.R |only 19 files changed, 145 insertions(+), 95 deletions(-)
Title: Diagnostic Index Expectation Maximisation in R
Description: Likelihood-based genome polarisation finds which alleles of genomic markers
belong to which side of the barrier.
Co-estimates which individuals belong to either side of the barrier and barrier strength.
Uses expectation maximisation in likelihood framework. The method is described in
Baird et al. (2023) <doi:10.1111/2041-210X.14010>.
Author: Natalia Martinkova [aut, cre] ,
Stuart Baird [aut]
Maintainer: Natalia Martinkova <martinkova@ivb.cz>
Diff between diemr versions 1.2.2 dated 2023-07-11 and 1.2.3 dated 2024-04-28
diemr-1.2.2/diemr/inst/extdata/testdata.vcf |only diemr-1.2.2/diemr/tests/testthat/multiallelic-01.txt |only diemr-1.2.2/diemr/tests/testthat/test-01.txt |only diemr-1.2.2/diemr/tests/testthat/test-02.txt |only diemr-1.2.2/diemr/tests/testthat/test-03.txt |only diemr-1.2.3/diemr/DESCRIPTION | 6 diemr-1.2.3/diemr/MD5 | 23 - diemr-1.2.3/diemr/NEWS.md | 8 diemr-1.2.3/diemr/R/vcf2diem.r | 216 +++++----- diemr-1.2.3/diemr/inst/CITATION | 2 diemr-1.2.3/diemr/inst/doc/Importing-data-for-genome-polarisation.html | 4 diemr-1.2.3/diemr/inst/doc/diemr-diagnostic-index-expecation-maximisation-in-r.Rmd | 2 diemr-1.2.3/diemr/inst/doc/diemr-diagnostic-index-expecation-maximisation-in-r.html | 10 diemr-1.2.3/diemr/man/vcf2diem.Rd | 44 +- diemr-1.2.3/diemr/vignettes/diemr-diagnostic-index-expecation-maximisation-in-r.Rmd | 2 15 files changed, 185 insertions(+), 132 deletions(-)
Title: Biological Entity Dictionary (BED)
Description: An interface for the 'Neo4j' database providing
mapping between different identifiers of biological entities.
This Biological Entity Dictionary (BED)
has been developed to address three main challenges.
The first one is related to the completeness of identifier mappings.
Indeed, direct mapping information provided by the different systems
are not always complete and can be enriched by mappings provided by other
resources.
More interestingly, direct mappings not identified by any of these
resources can be indirectly inferred by using mappings to a third reference.
For example, many human Ensembl gene ID are not directly mapped to any
Entrez gene ID but such mappings can be inferred using respective mappings
to HGNC ID. The second challenge is related to the mapping of deprecated
identifiers. Indeed, entity identifiers can change from one resource
release to another. The identifier history is provided by some resources,
such as Ensembl or the NCBI, but it is generally not used by mapping [...truncated...]
Author: Patrice Godard [aut, cre, cph]
Maintainer: Patrice Godard <patrice.godard@gmail.com>
Diff between BED versions 1.5.0 dated 2024-01-18 and 1.5.1 dated 2024-04-28
DESCRIPTION | 10 MD5 | 26 R/dumpEnsCore.R | 9 R/dumpUniprotDb.R | 27 R/getUniprot.R | 4 build/vignette.rds |binary inst/Documentation/BED-Model/BED.png |only inst/doc/BED.R | 19 inst/doc/BED.Rmd | 20 inst/doc/BED.html | 9909 +++++++++++++++++++---------------- inst/pkgdown.yml | 4 man/dumpUniprotDb.Rd | 10 man/getUniprot.Rd | 5 vignettes/BED.Rmd | 20 vignettes/img/BED-data-model.png |only 15 files changed, 5530 insertions(+), 4533 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-03-14 1.0-4
2014-08-14 1.0-3
2014-01-08 1.0-2
2013-02-15 1.0-1
2012-11-17 1.0.0
Title: Create, Read, Write, and Work with 'iCalander' Files, Calendars
and Scheduling Data
Description: Provides function to create, read, write, and work with
'iCalander' files (which typically have '.ics' or '.ical' extensions),
and the scheduling data, calendars and timelines of people,
organisations and other entities that they represent. 'iCalendar' is
an open standard for exchanging calendar and scheduling information
between users and computers, described at <https://icalendar.org/>.
Author: Robin Lovelace [aut, cre] ,
Layik Hama [aut] ,
Ollie Lloyd [ctb]
Maintainer: Robin Lovelace <rob00x@gmail.com>
Diff between calendar versions 0.0.1 dated 2019-02-11 and 0.1.0 dated 2024-04-28
DESCRIPTION | 57 ++++--- MD5 | 53 +++--- R/ic_date.R | 13 + R/ic_event.R | 2 R/ic_find.R | 1 R/ic_read.R | 8 - R/ical.R | 11 - README.md | 63 ++++--- build/vignette.rds |binary inst/doc/ical-creating-calendars.R | 8 - inst/doc/ical-creating-calendars.html | 271 ++++++++++++++++++++-------------- man/calendar.Rd | 1 man/formats.Rd | 4 man/holidays.Rd | 4 man/ic_attributes_vec.Rd | 8 - man/ic_char_event.Rd | 6 man/ic_character.Rd | 6 man/ic_event.Rd | 16 +- man/ic_list.Rd | 2 man/ic_spec.Rd | 3 man/ic_write.Rd | 6 man/ical_example.Rd | 6 man/ical_outlook.Rd | 4 man/properties.Rd | 6 man/properties_core.Rd | 4 man/properties_ical.Rd | 4 tests/testthat/test-ic-extract.R |only tests/testthat/test-ic-read.R |only tests/testthat/test-ic-spec.R |only 29 files changed, 346 insertions(+), 221 deletions(-)
Title: Tools for Analyzing Remote Sensing Forest Data
Description: Tools for analyzing remote sensing forest data, including functions for detecting treetops from canopy models, outlining tree crowns, and calculating textural metrics.
Author: Andrew Plowright [aut, cre],
Jean-Romain Roussel [ctb]
Maintainer: Andrew Plowright <andrew.plowright@alumni.ubc.ca>
Diff between ForestTools versions 1.0.1 dated 2023-10-02 and 1.0.2 dated 2024-04-28
ForestTools-1.0.1/ForestTools/R/ForestTools-package.R |only ForestTools-1.0.1/ForestTools/R/RcppExports.R |only ForestTools-1.0.1/ForestTools/R/glcm_stats.R |only ForestTools-1.0.1/ForestTools/build |only ForestTools-1.0.1/ForestTools/inst/doc |only ForestTools-1.0.1/ForestTools/man/ForestTools-package.Rd |only ForestTools-1.0.1/ForestTools/man/glcm0.Rd |only ForestTools-1.0.1/ForestTools/man/glcm135.Rd |only ForestTools-1.0.1/ForestTools/man/glcm45.Rd |only ForestTools-1.0.1/ForestTools/man/glcm90.Rd |only ForestTools-1.0.1/ForestTools/man/glcm_features.Rd |only ForestTools-1.0.1/ForestTools/src |only ForestTools-1.0.1/ForestTools/tests/testthat/validation_data/glcm_features |only ForestTools-1.0.1/ForestTools/vignettes |only ForestTools-1.0.2/ForestTools/DESCRIPTION | 16 - ForestTools-1.0.2/ForestTools/MD5 | 77 ++--- ForestTools-1.0.2/ForestTools/NAMESPACE | 2 ForestTools-1.0.2/ForestTools/NEWS.md | 55 +++- ForestTools-1.0.2/ForestTools/R/glcm.R | 136 +++------- ForestTools-1.0.2/ForestTools/README.md | 65 +++- ForestTools-1.0.2/ForestTools/inst/guides |only ForestTools-1.0.2/ForestTools/man/glcm.Rd | 11 ForestTools-1.0.2/ForestTools/tests/testthat/test_data/ttops_orphans.Rda |binary ForestTools-1.0.2/ForestTools/tests/testthat/test_data/ttops_test.Rda |binary ForestTools-1.0.2/ForestTools/tests/testthat/test_glcm.R | 12 ForestTools-1.0.2/ForestTools/tests/testthat/test_glcm_internal.R | 123 ++++----- ForestTools-1.0.2/ForestTools/tests/testthat/validation_data/glcm_metrics |only 27 files changed, 264 insertions(+), 233 deletions(-)