Title: Repel Visually Similar Colors for Colorblind Users in Various
Plots
Description: Iterate and repel visually similar colors away in various 'ggplot2' plots. When many groups are plotted at the same time on multiple axes, for instance stacked bars or scatter plots, effectively ordering colors becomes difficult. This tool iterates through color combinations to find the best solution to maximize visual distinctness of nearby groups, so plots are more friendly toward colorblind users. This is achieved by two distance measurements, distance between groups within the plot, and CIELAB color space distances between colors as described in Carter et al., (2018) <doi:10.25039/TR.015.2018>.
Author: Rui Fu [cre, aut, cph]
Maintainer: Rui Fu <raysinensis@gmail.com>
Diff between colorrepel versions 0.3.0 dated 2024-09-29 and 0.4.1 dated 2025-01-18
DESCRIPTION | 10 +- MD5 | 32 ++++----- NAMESPACE | 1 NEWS.md | 12 +++ R/color_repel.R | 39 +++++++++-- R/interactive.R | 66 ++++++++++++++++--- R/utils.R | 135 ++++++++++++++++++++++++++++++++++++---- R/wrappers.R | 23 +++++- README.md | 11 ++- inst/scRNAseqUMAP_extra.png |binary man/average_clusters.Rd | 9 ++ man/average_clusters_rowwise.Rd | 2 man/color_repel.Rd | 8 ++ man/get_labs.Rd | 4 - man/gg_color_repel.Rd | 9 ++ man/ggplotly_background.Rd | 12 +++ man/label_repel.Rd | 3 17 files changed, 314 insertions(+), 62 deletions(-)
Title: Spatially Aware Cell-Cell Interaction Analysis
Description: Provides tools for analyzing spatial cell-cell interactions based on ligand-receptor pairs, including functions for local, regional, and global analysis using spatial transcriptomics data. Integrates with databases like 'CellChat' <http://www.cellchat.org/>, 'CellPhoneDB' <https://www.cellphonedb.org/>, 'Cellinker' <https://www.rna-society.org/cellinker/>, 'ICELLNET' <https://github.com/soumelis-lab/ICELLNET>, and 'ConnectomeDB' <https://humanconnectome.org/software/connectomedb/> to identify ligand-receptor pairs, visualize interactions through heatmaps, chord diagrams, and infer interactions on different spatial scales.
Author: Li-Ting Ku [aut, cre]
Maintainer: Li-Ting Ku <lku@mdanderson.org>
Diff between SpaCCI versions 1.0.2 dated 2024-10-24 and 1.0.3 dated 2025-01-18
DESCRIPTION | 10 MD5 | 49 ++- NAMESPACE | 1 R/RcppExports.R | 4 R/modeling.R | 185 ++++++-------- R/permutation.R | 3 R/result_local.R | 11 R/result_local_spatial_coords_df.R |only R/result_regional.R |only R/run_SpaCCI.R | 4 R/utils.R | 2 R/visiualization.R | 419 +++++++++++++++++++++++++++++++- data/result_global.rda |binary data/result_local.rda |binary data/result_local_spatial_coords_df.rda |only data/result_regional.rda |only man/Global_Permutations.Rd | 3 man/SpaCCI_global.Rd | 3 man/SpaCCI_region.Rd | 3 man/plot_SpaCCI_local.Rd | 9 man/plot_SpaCCI_local_Strength.Rd |only man/plot_Strength_Seurat.Rd |only man/plot_Strength_localized.Rd |only man/plot_localized.Rd | 10 man/result_local.Rd | 12 man/result_local_spatial_coords_df.Rd |only man/result_regional.Rd |only man/run_SpaCCI.Rd | 2 src/RcppExports.cpp | 9 src/permutation_func.cpp | 132 ++++------ 30 files changed, 628 insertions(+), 243 deletions(-)
Title: Data for Package 'Qindex'
Description: Example data used in package 'Qindex'.
Author: Tingting Zhan [aut, cre, cph] ,
Misung Yi [aut, cph] ,
Inna Chervoneva [aut, cph]
Maintainer: Tingting Zhan <tingtingzhan@gmail.com>
Diff between Qindex.data versions 0.1.2 dated 2025-01-17 and 0.1.3 dated 2025-01-18
DESCRIPTION | 27 ++++++++++----------- MD5 | 10 ++++---- R/Ki67.R | 56 ++++++++++++--------------------------------- data/Ki67.rda |binary man/Qindex.data-package.Rd | 6 ---- man/celldata.Rd | 30 ++++++++++++------------ 6 files changed, 49 insertions(+), 80 deletions(-)
Title: Computation and Decomposition of the Mutual Information Index
Description: The Mutual Information Index (M) introduced to social science literature by
Theil and Finizza (1971) <doi:10.1080/0022250X.1971.9989795> is a multigroup
segregation measure that is highly decomposable and that according to Frankel
and Volij (2011) <doi:10.1016/j.jet.2010.10.008> and Mora and Ruiz-Castillo
(2011) <doi:10.1111/j.1467-9531.2011.01237.x> satisfies the Strong Unit
Decomposability and Strong Group Decomposability properties. This package allows
computing and decomposing the total index value into its "between" and
"within" terms. These last terms can also be decomposed into their
contributions, either by group or unit characteristics. The factors that produce
each "within" term can also be displayed at the user's request. The results can
be computed considering a variable or sets of variables that define separate
clusters.
Author: Cristian Angulo-Gonzalez [aut, cre],
Rafael Fuentealba-Chaura [aut],
Ricardo Mora [aut],
Julio Rojas-Mora [aut],
FONDECYT/ANID Project 11170583 [fnd],
MCIN/AEI/10.13039/501100011033 [fnd],
UCT VIP Project FEQUIP2019-INRN-03 [fnd]
Maintainer: Cristian Angulo-Gonzalez <cristian_world@hotmail.cl>
Diff between mutualinf versions 2.0.1 dated 2025-01-16 and 2.0.2 dated 2025-01-18
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- R/get_contribution.R | 9 +++------ src/VectorHash.h | 1 + 4 files changed, 11 insertions(+), 13 deletions(-)
Title: Evolutionary Algorithm
Description: Runs a genetic algorithm using the 'AlphaSimR' machinery <doi:10.1093/g3journal/jkaa017> and the coalescent simulator 'MaCS' <doi:10.1101/gr.083634.108>.
Author: Giovanny Covarrubias-Pazaran [aut, cre]
Maintainer: Giovanny Covarrubias-Pazaran <cova_ruber@live.com.mx>
Diff between evola versions 1.0.2 dated 2024-09-26 and 1.0.4 dated 2025-01-18
evola-1.0.2/evola/inst/doc/evola.intro.R |only evola-1.0.2/evola/inst/doc/evola.intro.Rmd |only evola-1.0.2/evola/inst/doc/evola.intro.pdf |only evola-1.0.2/evola/vignettes/evola.intro.Rmd |only evola-1.0.2/evola/vignettes/evola.intro.html |only evola-1.0.4/evola/ChangeLog | 10 +- evola-1.0.4/evola/DESCRIPTION | 8 +- evola-1.0.4/evola/MD5 | 26 +++--- evola-1.0.4/evola/NAMESPACE | 5 - evola-1.0.4/evola/R/evolafit.R | 106 ++++++++++++++++++--------- evola-1.0.4/evola/R/utlis.R | 9 ++ evola-1.0.4/evola/build/vignette.rds |binary evola-1.0.4/evola/inst/doc/evola_intro.R |only evola-1.0.4/evola/inst/doc/evola_intro.Rmd |only evola-1.0.4/evola/inst/doc/evola_intro.html |only evola-1.0.4/evola/man/evola-package.Rd | 2 evola-1.0.4/evola/man/evolafit.Rd | 53 +++++++++---- evola-1.0.4/evola/man/fitnessf.Rd |only evola-1.0.4/evola/vignettes/evola_intro.Rmd |only 19 files changed, 147 insertions(+), 72 deletions(-)
Title: Quantity Calculus for R Vectors
Description: Integration of the 'units' and 'errors' packages for a complete
quantity calculus system for R vectors, matrices and arrays, with automatic
propagation, conversion, derivation and simplification of magnitudes and
uncertainties. Documentation about 'units' and 'errors' is provided in the
papers by Pebesma, Mailund & Hiebert (2016, <doi:10.32614/RJ-2016-061>) and
by Ucar, Pebesma & Azcorra (2018, <doi:10.32614/RJ-2018-075>), included in
those packages as vignettes; see 'citation("quantities")' for details.
Author: Inaki Ucar [aut, cph, cre]
Maintainer: Inaki Ucar <iucar@fedoraproject.org>
Diff between quantities versions 0.2.2 dated 2024-07-29 and 0.2.3 dated 2025-01-18
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++----------- NAMESPACE | 2 ++ NEWS.md | 4 ++++ R/errors.R | 17 ++++++++++++++++- README.md | 4 ++-- build/partial.rdb |binary build/vignette.rds |binary inst/doc/introduction.R | 10 +++++----- inst/doc/introduction.html | 20 ++++++-------------- inst/doc/parsing.html | 4 ++-- man/correl.Rd | 6 ++++++ 12 files changed, 57 insertions(+), 38 deletions(-)
Title: S3 Resource Resolver
Description: A S3 resource is provided by Amazon Web Services S3 or a S3-compatible object store (such as Minio).
The resource can be a tidy file to be downloaded from the object store, or a data lake (such as Delta Lake)
Parquet file to be read by Apache Spark.
Author: Yannick Marcon [aut, cre] ,
OBiBa group [cph]
Maintainer: Yannick Marcon <yannick.marcon@obiba.org>
Diff between s3.resourcer versions 1.1.1 dated 2023-05-07 and 1.1.2 dated 2025-01-18
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- README.md | 4 ++-- inst/resources/resource.js | 16 ++++++++-------- 4 files changed, 17 insertions(+), 17 deletions(-)
Title: Uncertainty Propagation for R Vectors
Description: Support for measurement errors in R vectors, matrices and arrays:
automatic uncertainty propagation and reporting.
Documentation about 'errors' is provided in the paper by Ucar, Pebesma &
Azcorra (2018, <doi:10.32614/RJ-2018-075>), included in this package as a
vignette; see 'citation("errors")' for details.
Author: Inaki Ucar [aut, cph, cre] ,
Lionel Henry [ctb],
RStudio [cph]
Maintainer: Inaki Ucar <iucar@fedoraproject.org>
Diff between errors versions 0.4.2 dated 2024-07-29 and 0.4.3 dated 2025-01-18
DESCRIPTION | 6 +++--- MD5 | 20 ++++++++++---------- NEWS.md | 6 ++++++ R/print.R | 18 +++++++++++++----- R/utils.R | 2 +- build/partial.rdb |binary build/vignette.rds |binary inst/doc/rjournal.R | 24 ++++++++++++------------ inst/doc/rjournal.pdf |binary man/format.errors.Rd | 9 ++++++++- tests/testthat/test-print.R | 3 +++ 11 files changed, 56 insertions(+), 32 deletions(-)
Title: Nonlinear Mixed Effects Models in Population PK/PD, Estimation
Routines
Description: Fit and compare nonlinear mixed-effects models in
differential equations with flexible dosing information commonly seen
in pharmacokinetics and pharmacodynamics (Almquist, Leander, and
Jirstrand 2015 <doi:10.1007/s10928-015-9409-1>). Differential equation
solving is by compiled C code provided in the 'rxode2' package (Wang,
Hallow, and James 2015 <doi:10.1002/psp4.12052>).
Author: Matthew Fidler [aut, cre] ,
Yuan Xiong [aut],
Rik Schoemaker [aut] ,
Justin Wilkins [aut] ,
Wenping Wang [aut],
Robert Leary [ctb],
Mason McComb [ctb] ,
Vipul Mann [aut],
Mirjam Trame [ctb],
Mahmoud Abdelwahab [ctb],
Teun Post [ctb],
Richard Hooijmai [...truncated...]
Maintainer: Matthew Fidler <matthew.fidler@gmail.com>
Diff between nlmixr2est versions 3.0.2 dated 2024-11-23 and 3.0.3 dated 2025-01-18
DESCRIPTION | 6 ++-- MD5 | 46 ++++++++++++++++++----------------- NAMESPACE | 1 NEWS.md | 14 ++++++++++ R/bobyqa.R | 1 R/focei.R | 15 +++++++++-- R/lbfgsb3c.R | 1 R/n1qn1.R | 1 R/newuoa.R | 1 R/nlm.R | 1 R/nlme.R | 1 R/nlminb.R | 1 R/nls.R | 1 R/optim.R | 1 R/preProcessCovariatesPresent.R |only R/rxsolve.R | 6 ++++ R/saem.R | 2 + R/saemControl.R | 2 - R/saemRxUiGet.R | 20 +++++++++++++-- R/saemRxUiGetModel.R | 16 +++++++----- R/uobyqa.R | 2 - man/saemControl.Rd | 2 - tests/testthat.R | 9 ++++++ tests/testthat/test-data-assert.R |only tests/testthat/test-saem-translate.R | 46 +++++++++++++++++++++++++++++++++++ 25 files changed, 157 insertions(+), 39 deletions(-)
Title: Perform HTTP Requests and Process the Responses
Description: Tools for creating and modifying HTTP requests, then
performing them and processing the results. 'httr2' is a modern
re-imagining of 'httr' that uses a pipe-based interface and solves
more of the problems that API wrapping packages face.
Author: Hadley Wickham [aut, cre],
Posit Software, PBC [cph, fnd],
Maximilian Girlich [ctb]
Maintainer: Hadley Wickham <hadley@posit.co>
Diff between httr2 versions 1.0.7 dated 2024-11-26 and 1.1.0 dated 2025-01-18
DESCRIPTION | 10 MD5 | 159 ++++++++------- NAMESPACE | 10 NEWS.md | 60 +++++ R/curl.R | 50 ++++ R/headers.R | 14 - R/httr2-package.R | 1 R/is-online.R |only R/iterate-responses.R | 13 + R/oauth-flow-auth-code.R | 31 +-- R/oauth-flow.R | 4 R/progress-bars.R | 3 R/req-auth-aws.R | 4 R/req-auth.R | 4 R/req-body.R | 5 R/req-headers.R | 29 ++ R/req-mock.R | 4 R/req-options.R | 2 R/req-perform-connection.R | 53 ++++- R/req-perform-stream.R | 6 R/req-perform.R | 6 R/req-promise.R | 13 + R/req-retries.R | 118 ++++++++--- R/req-url.R | 62 +++--- R/resp-headers.R | 4 R/resp-request.R |only R/resp-stream-aws.R | 26 +- R/resp-stream.R | 112 ++++++++--- R/sequential.R | 11 - R/test.R | 2 R/url.R | 295 ++++++++++++++++++++++------- R/utils-multi.R | 18 + R/utils.R | 29 ++ README.md | 29 +- inst/doc/httr2.html | 106 +++++----- man/is_online.Rd |only man/multi_req_perform.Rd | 3 man/progress_bars.Rd | 3 man/req_auth_basic.Rd | 4 man/req_body.Rd | 13 - man/req_dry_run.Rd | 7 man/req_headers.Rd | 22 +- man/req_oauth_auth_code.Rd | 27 +- man/req_oauth_password.Rd | 4 man/req_perform_connection.Rd | 24 ++ man/req_perform_iterative.Rd | 8 man/req_perform_parallel.Rd | 11 - man/req_perform_promise.Rd | 14 + man/req_perform_sequential.Rd | 11 - man/req_perform_stream.Rd | 6 man/req_retry.Rd | 70 +++--- man/req_url.Rd | 58 ++++- man/resp_request.Rd |only man/resp_stream_raw.Rd | 25 ++ man/resps_successes.Rd | 14 + man/url_build.Rd |only man/url_modify.Rd |only man/url_parse.Rd | 41 +--- man/url_query_parse.Rd |only tests/testthat/_snaps/curl.md | 79 ++++++- tests/testthat/_snaps/req-mock.md | 6 tests/testthat/_snaps/req-promise.md | 41 ++++ tests/testthat/_snaps/req-retries.md | 15 + tests/testthat/_snaps/req-url.md | 18 + tests/testthat/_snaps/req.md | 18 + tests/testthat/_snaps/resp-stream.md | 48 ++++ tests/testthat/_snaps/url.md | 101 +++++++++ tests/testthat/helper-promise.R |only tests/testthat/helper.R | 2 tests/testthat/test-curl.R | 31 ++- tests/testthat/test-multi-req.R | 8 tests/testthat/test-oauth-flow-auth-code.R | 4 tests/testthat/test-oauth-flow.R | 18 + tests/testthat/test-req-auth-aws.R | 14 - tests/testthat/test-req-headers.R | 2 tests/testthat/test-req-mock.R | 2 tests/testthat/test-req-perform.R | 9 tests/testthat/test-req-promise.R | 50 +--- tests/testthat/test-req-retries.R | 43 +++- tests/testthat/test-req-url.R | 17 + tests/testthat/test-req.R | 6 tests/testthat/test-resp-headers.R | 9 tests/testthat/test-resp-request.R |only tests/testthat/test-resp-stream.R | 87 +++++++- tests/testthat/test-url.R | 187 +++++++++++++++--- 85 files changed, 1857 insertions(+), 616 deletions(-)
Title: Manage Cached Files
Description: Suite of tools for managing cached files, targeting
use in other R packages. Uses 'rappdirs' for cross-platform paths.
Provides utilities to manage cache directories, including targeting
files by path or by key; cached directories can be compressed and
uncompressed easily to save disk space.
Author: Scott Chamberlain [aut] ,
Tamas Stirling [ctb, cre]
Maintainer: Tamas Stirling <stirling.tamas@gmail.com>
Diff between hoardr versions 0.5.4 dated 2024-01-23 and 0.5.5 dated 2025-01-18
DESCRIPTION | 8 +-- MD5 | 18 +++--- NEWS.md | 10 +++ R/hoard-package.R | 2 R/hoard_client.R | 6 +- build/vignette.rds |binary inst/doc/hoardr_vignette.R | 4 - inst/doc/hoardr_vignette.html | 109 +++++++++++++++++++++++++++--------------- man/hoard.Rd | 2 man/hoardr-package.Rd | 9 +++ 10 files changed, 111 insertions(+), 57 deletions(-)
Title: Calibration Performance
Description: Plots calibration curves and computes statistics for assessing calibration performance. See De Cock Campo (2023) <doi:10.48550/arXiv.2309.08559> and Van Calster et al. (2016) <doi:10.1016/j.jclinepi.2015.12.005>.
Author: De Cock Bavo [aut, cre],
Nieboer Daan [aut],
Van Calster Ben [aut],
Steyerberg Ewout [aut],
Vergouwe Yvonne [aut]
Maintainer: De Cock Bavo <bavo.decock@kuleuven.be>
Diff between CalibrationCurves versions 2.0.3 dated 2024-07-02 and 2.0.4 dated 2025-01-18
DESCRIPTION | 6 ++-- MD5 | 12 ++++---- R/genCalCurve.R | 2 - inst/doc/CalibrationCurves.R | 12 +++++++- inst/doc/CalibrationCurves.Rmd | 12 +++++++- inst/doc/CalibrationCurves.html | 55 ++++++++++++++++++++++++++-------------- vignettes/CalibrationCurves.Rmd | 12 +++++++- 7 files changed, 77 insertions(+), 34 deletions(-)
More information about CalibrationCurves at CRAN
Permanent link
Title: Cox MultiBlock Survival
Description: This software package provides Cox survival analysis for high-dimensional and multiblock datasets.
It encompasses a suite of functions dedicated from the classical Cox regression to newest analysis,
including Cox proportional hazards model, Stepwise Cox regression, and Elastic-Net Cox regression,
Sparse Partial Least Squares Cox regression (sPLS-COX) incorporating three distinct strategies,
and two Multiblock-PLS Cox regression (MB-sPLS-COX) methods. This tool is designed to adeptly handle
high-dimensional data, and provides tools for cross-validation, plot generation, and additional resources
for interpreting results. While references are available within the corresponding functions,
key literature is mentioned below.
Terry M Therneau (2024) <https://CRAN.R-project.org/package=survival>,
Noah Simon et al. (2011) <doi:10.18637/jss.v039.i05>,
Philippe Bastien et al. (2005) <doi:10.1016/j.csda.2004.02.005>,
Philippe Bastien (2008) <doi:10.1016/j.chemolab.2007.09.009& [...truncated...]
Author: Pedro Salguero Garcia [aut, cre, rev]
,
Sonia Tarazona Campos [ths],
Ana Conesa Cegarra [ths],
Kassu Mehari Beyene [ctb],
Luis Meira Machado [ctb],
Marta Sestelo [ctb],
Artur Araujo [ctb]
Maintainer: Pedro Salguero Garcia <pedrosalguerog@gmail.com>
Diff between Coxmos versions 1.0.2 dated 2024-03-25 and 1.1.0 dated 2025-01-18
Coxmos-1.0.2/Coxmos/man/cv.splsdacox_dynamic.Rd |only Coxmos-1.0.2/Coxmos/man/cv.splsdrcox_dynamic.Rd |only Coxmos-1.0.2/Coxmos/man/save_ggplot.svg.Rd |only Coxmos-1.0.2/Coxmos/man/save_ggplot_lst.svg.Rd |only Coxmos-1.0.2/Coxmos/man/splsdacox_dynamic.Rd |only Coxmos-1.0.2/Coxmos/man/splsdrcox_dynamic.Rd |only Coxmos-1.1.0/Coxmos/DESCRIPTION | 10 Coxmos-1.1.0/Coxmos/MD5 | 153 Coxmos-1.1.0/Coxmos/NAMESPACE | 23 Coxmos-1.1.0/Coxmos/R/Coxmos_common_functions.R |11857 +++++----- Coxmos-1.1.0/Coxmos/R/Coxmos_cox.R | 10 Coxmos-1.1.0/Coxmos/R/Coxmos_coxEN.R | 1928 - Coxmos-1.1.0/Coxmos/R/Coxmos_coxSW.R | 158 Coxmos-1.1.0/Coxmos/R/Coxmos_evaluation_functions.R | 53 Coxmos-1.1.0/Coxmos/R/Coxmos_isb_splsdacox_dynamic.R |only Coxmos-1.1.0/Coxmos/R/Coxmos_isb_splsdrcox.R |only Coxmos-1.1.0/Coxmos/R/Coxmos_isb_splsdrcox_dynamic.R |only Coxmos-1.1.0/Coxmos/R/Coxmos_isb_splsicox.R |only Coxmos-1.1.0/Coxmos/R/Coxmos_mb_splsdacox_dynamic.R | 202 Coxmos-1.1.0/Coxmos/R/Coxmos_mb_splsdrcox_dynamic.R | 248 Coxmos-1.1.0/Coxmos/R/Coxmos_multiblock_functions.R | 107 Coxmos-1.1.0/Coxmos/R/Coxmos_plot_functions.R | 1701 - Coxmos-1.1.0/Coxmos/R/Coxmos_sb_splsdacox_dynamic.R |only Coxmos-1.1.0/Coxmos/R/Coxmos_sb_splsdrcox.R | 2023 - Coxmos-1.1.0/Coxmos/R/Coxmos_sb_splsdrcox_dynamic.R |only Coxmos-1.1.0/Coxmos/R/Coxmos_sb_splsicox.R | 462 Coxmos-1.1.0/Coxmos/R/Coxmos_splsdacox_dynamic.R | 1939 - Coxmos-1.1.0/Coxmos/R/Coxmos_splsdrcox.R | 244 Coxmos-1.1.0/Coxmos/R/Coxmos_splsdrcox_dynamic.R | 146 Coxmos-1.1.0/Coxmos/R/Coxmos_splsdrcox_median.R |only Coxmos-1.1.0/Coxmos/R/Coxmos_splsicox.R | 2208 - Coxmos-1.1.0/Coxmos/R/cenROC.R | 15 Coxmos-1.1.0/Coxmos/README.md | 12 Coxmos-1.1.0/Coxmos/build/partial.rdb |binary Coxmos-1.1.0/Coxmos/inst/REFERENCES.bib | 114 Coxmos-1.1.0/Coxmos/inst/doc/Coxmos-MO-pipeline.R | 101 Coxmos-1.1.0/Coxmos/inst/doc/Coxmos-MO-pipeline.Rmd | 151 Coxmos-1.1.0/Coxmos/inst/doc/Coxmos-MO-pipeline.html | 1225 - Coxmos-1.1.0/Coxmos/inst/doc/Coxmos-pipeline.R | 102 Coxmos-1.1.0/Coxmos/inst/doc/Coxmos-pipeline.Rmd | 143 Coxmos-1.1.0/Coxmos/inst/doc/Coxmos-pipeline.html | 1161 Coxmos-1.1.0/Coxmos/man/coxEN.Rd | 5 Coxmos-1.1.0/Coxmos/man/coxSW.Rd | 4 Coxmos-1.1.0/Coxmos/man/cv.coxEN.Rd | 11 Coxmos-1.1.0/Coxmos/man/cv.isb.splsdacox.Rd |only Coxmos-1.1.0/Coxmos/man/cv.isb.splsdrcox.Rd | 464 Coxmos-1.1.0/Coxmos/man/cv.isb.splsdrcox_penalty.Rd |only Coxmos-1.1.0/Coxmos/man/cv.isb.splsicox.Rd | 141 Coxmos-1.1.0/Coxmos/man/cv.mb.splsdacox.Rd | 16 Coxmos-1.1.0/Coxmos/man/cv.mb.splsdrcox.Rd | 16 Coxmos-1.1.0/Coxmos/man/cv.sb.splsdacox.Rd |only Coxmos-1.1.0/Coxmos/man/cv.sb.splsdrcox.Rd | 475 Coxmos-1.1.0/Coxmos/man/cv.sb.splsdrcox_penalty.Rd |only Coxmos-1.1.0/Coxmos/man/cv.sb.splsicox.Rd | 4 Coxmos-1.1.0/Coxmos/man/cv.splsdacox.Rd |only Coxmos-1.1.0/Coxmos/man/cv.splsdrcox.Rd | 449 Coxmos-1.1.0/Coxmos/man/cv.splsdrcox_penalty.Rd |only Coxmos-1.1.0/Coxmos/man/cv.splsicox.Rd | 2 Coxmos-1.1.0/Coxmos/man/deleteZeroOrNearZeroVariance.mb.Rd | 6 Coxmos-1.1.0/Coxmos/man/eval_Coxmos_model_per_variable.list.Rd |only Coxmos-1.1.0/Coxmos/man/eval_Coxmos_models.Rd | 9 Coxmos-1.1.0/Coxmos/man/getAutoKM.Rd | 4 Coxmos-1.1.0/Coxmos/man/getAutoKM.list.Rd | 14 Coxmos-1.1.0/Coxmos/man/getCutoffAutoKM.list.Rd | 2 Coxmos-1.1.0/Coxmos/man/getDesign.MB.Rd |only Coxmos-1.1.0/Coxmos/man/getEPV.mb.Rd | 2 Coxmos-1.1.0/Coxmos/man/getTestKM.list.Rd | 10 Coxmos-1.1.0/Coxmos/man/isb.splsdacox.Rd |only Coxmos-1.1.0/Coxmos/man/isb.splsdrcox.Rd |only Coxmos-1.1.0/Coxmos/man/isb.splsdrcox_penalty.Rd |only Coxmos-1.1.0/Coxmos/man/isb.splsicox.Rd |only Coxmos-1.1.0/Coxmos/man/mb.splsdacox.Rd | 19 Coxmos-1.1.0/Coxmos/man/mb.splsdrcox.Rd | 13 Coxmos-1.1.0/Coxmos/man/plot_LP.multipleObservations.list.Rd | 10 Coxmos-1.1.0/Coxmos/man/plot_PLS_Coxmos.Rd | 2 Coxmos-1.1.0/Coxmos/man/plot_cox.event.list.Rd | 3 Coxmos-1.1.0/Coxmos/man/plot_forest.list.Rd | 3 Coxmos-1.1.0/Coxmos/man/plot_proportionalHazard.list.Rd | 3 Coxmos-1.1.0/Coxmos/man/plot_pseudobeta.list.Rd | 3 Coxmos-1.1.0/Coxmos/man/plot_pseudobeta_newObservation.list.Rd | 2 Coxmos-1.1.0/Coxmos/man/plot_time.list.Rd | 37 Coxmos-1.1.0/Coxmos/man/save_ggplot.Rd | 9 Coxmos-1.1.0/Coxmos/man/save_ggplot_lst.Rd | 7 Coxmos-1.1.0/Coxmos/man/sb.splsdacox.Rd |only Coxmos-1.1.0/Coxmos/man/sb.splsdrcox.Rd | 378 Coxmos-1.1.0/Coxmos/man/sb.splsdrcox_penalty.Rd |only Coxmos-1.1.0/Coxmos/man/sb.splsicox.Rd | 4 Coxmos-1.1.0/Coxmos/man/splsdacox.Rd |only Coxmos-1.1.0/Coxmos/man/splsdrcox.Rd | 395 Coxmos-1.1.0/Coxmos/man/splsdrcox_penalty.Rd |only Coxmos-1.1.0/Coxmos/vignettes/Coxmos-MO-pipeline.Rmd | 151 Coxmos-1.1.0/Coxmos/vignettes/Coxmos-pipeline.Rmd | 143 92 files changed, 15024 insertions(+), 14288 deletions(-)
Title: Analysis of MHC Data in Non-Model Species
Description: Fifteen tools for bioinformatics processing and analysis of major
histocompatibility complex (MHC) data. The functions are tailored for amplicon data
sets that have been filtered using the dada2 method (for more information on
dada2, visit <https://benjjneb.github.io/dada2/> ), but even other types of data
sets can be analyzed.
The ReplMatch() function matches replicates in data sets in order to evaluate
genotyping success.
The GetReplTable() and GetReplStats() functions perform such an evaluation.
The CreateFas() function creates a fasta file with all the sequences in the data
set.
The CreateSamplesFas() function creates individual fasta files for each sample in
the data set.
The DistCalc() function calculates Grantham, Sandberg, or p-distances from pairwise
comparisons of all sequences in a data set, and mean distances of all pairwise
comparisons within each sample in a data set. The function additionally outputs five
tables with physico-chemical z-descriptor values (based on S [...truncated...]
Author: Jacob Roved [aut, cre]
Maintainer: Jacob Roved <jacob.roved@biol.lu.se>
Diff between MHCtools versions 1.5.4 dated 2025-01-15 and 1.5.5 dated 2025-01-18
DESCRIPTION | 6 +-- MD5 | 68 +++++++++++++++++------------------ NEWS.md | 10 ++++- R/BootKmeans_func_20250108.R | 2 - R/ClusterMatch_func_20250108.R | 2 - R/CreateFas_func_20230321.R | 2 - R/CreateHpltOccTable_func_20221010.R | 2 - R/CreateSamplesFas_func_20230321.R | 2 - R/DistCalc_func_20230707.R | 2 - R/GetHpltStats_func_20200915.R | 2 - R/GetHpltTable_func_20200915.R | 2 - R/GetReplStats_func_20200914.R | 2 - R/GetReplTable_func_20200914.R | 2 - R/HpltFind_func_20230321.R | 2 - R/HpltMatch_func_20230322.R | 2 - R/NestTablesXL_func_20221012.R | 2 - R/PapaDiv_func_20230630.R | 2 - R/ReplMatch_func_20230321.R | 2 - R/zzz.R | 2 - README.md | 4 +- man/BootKmeans.Rd | 2 - man/ClusterMatch.Rd | 2 - man/CreateFas.Rd | 2 - man/CreateHpltOccTable.Rd | 2 - man/CreateSamplesFas.Rd | 2 - man/DistCalc.Rd | 2 - man/GetHpltStats.Rd | 2 - man/GetHpltTable.Rd | 2 - man/GetReplStats.Rd | 2 - man/GetReplTable.Rd | 2 - man/HpltFind.Rd | 2 - man/HpltMatch.Rd | 2 - man/NestTablesXL.Rd | 2 - man/PapaDiv.Rd | 2 - man/ReplMatch.Rd | 2 - 35 files changed, 78 insertions(+), 72 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2024-07-15 2.0.1
2024-02-13 2.0.0
Title: Functional Time Series Analysis
Description: Functions for visualizing, modeling, forecasting and hypothesis testing of functional time series.
Author: Rob Hyndman [aut] ,
Han Lin Shang [aut, cre, cph]
Maintainer: Han Lin Shang <hanlin.shang@mq.edu.au>
Diff between ftsa versions 6.4 dated 2024-01-23 and 6.5 dated 2025-01-18
ftsa-6.4/ftsa/R/FANOVA.R |only ftsa-6.4/ftsa/R/FCE_means.R |only ftsa-6.4/ftsa/R/FRE_means.R |only ftsa-6.4/ftsa/R/One_way_Residuals.R |only ftsa-6.4/ftsa/R/One_way_median_polish.R |only ftsa-6.4/ftsa/R/Substraction.R |only ftsa-6.4/ftsa/R/Two_way_Residuals.R |only ftsa-6.4/ftsa/R/Two_way_Residuals_means.R |only ftsa-6.4/ftsa/R/Two_way_median_polish.R |only ftsa-6.4/ftsa/R/combinat.R |only ftsa-6.4/ftsa/R/f.R |only ftsa-6.4/ftsa/R/fMBD.R |only ftsa-6.4/ftsa/R/get_median.R |only ftsa-6.4/ftsa/R/list.cbind.R |only ftsa-6.4/ftsa/R/list.do.R |only ftsa-6.4/ftsa/R/list.rbind.R |only ftsa-6.4/ftsa/R/mu_hat.R |only ftsa-6.4/ftsa/R/partition_column_Y_f.R |only ftsa-6.4/ftsa/R/partition_row_Y_f.R |only ftsa-6.4/ftsa/man/FANOVA.Rd |only ftsa-6.4/ftsa/man/One_way_Residuals.Rd |only ftsa-6.4/ftsa/man/One_way_median_polish.Rd |only ftsa-6.4/ftsa/man/Two_way_Residuals.Rd |only ftsa-6.4/ftsa/man/Two_way_Residuals_means.Rd |only ftsa-6.4/ftsa/man/Two_way_median_polish.Rd |only ftsa-6.5/ftsa/ChangeLog | 4 ++ ftsa-6.5/ftsa/DESCRIPTION | 8 ++-- ftsa-6.5/ftsa/MD5 | 35 ++------------------ ftsa-6.5/ftsa/NAMESPACE | 8 ---- ftsa-6.5/ftsa/man/farforecast.Rd | 4 +- ftsa-6.5/ftsa/man/long_run_covariance_estimation.Rd | 2 - 31 files changed, 17 insertions(+), 44 deletions(-)
Title: Read and Write Standard 'C' Types from Files, Connections and
Raw Vectors
Description: Interacting with binary files can be difficult because R's types
are a subset of what is generally supported by 'C'. This package provides a
suite of functions for reading and writing binary data (with files, connections,
and raw vectors) using 'C' type descriptions. These functions convert data
between 'C' types and R types while checking for values outside the
type limits, 'NA' values, etc.
Author: Mike Cheng [aut, cre, cph],
Anne Fu [ctb]
Maintainer: Mike Cheng <mikefc@coolbutuseless.com>
Diff between ctypesio versions 0.1.1 dated 2024-10-16 and 0.1.2 dated 2025-01-18
DESCRIPTION | 10 +++---- MD5 | 25 +++++++++++-------- NEWS.md | 10 +++++++ R/read-hex.R | 5 +++ R/read-utf.R | 6 ++-- R/write-float.R | 15 +++++++++-- R/write-int.R | 13 +++++++--- R/write-utf8.R | 15 +++++++++-- inst/doc/parse-jpeg.html | 37 +++++++++++++++-------------- inst/doc/wave-format.R | 44 +++++++++++++++++------------------ inst/doc/wave-format.html | 33 +++++++++++++------------- man/ctypesio-package.Rd | 2 - tests/testthat/test-raw-set-endian.R |only tests/testthat/test-str-raw.R |only tests/testthat/test-utf8-read.R |only 15 files changed, 128 insertions(+), 87 deletions(-)
Title: Geometrical Functionality of the 'spatstat' Family
Description: Defines spatial data types and supports geometrical operations
on them. Data types include point patterns, windows (domains),
pixel images, line segment patterns, tessellations and hyperframes.
Capabilities include creation and manipulation of data
(using command line or graphical interaction),
plotting, geometrical operations (rotation, shift, rescale,
affine transformation), convex hull, discretisation and
pixellation, Dirichlet tessellation, Delaunay triangulation,
pairwise distances, nearest-neighbour distances,
distance transform, morphological operations
(erosion, dilation, closing, opening), quadrat counting,
geometrical measurement, geometrical covariance,
colour maps, calculus on spatial domains,
Gaussian blur, level sets of images, transects of images,
intersections between objects, minimum distance matching.
(Excludes spatial data on a network, which are supported by
the package 'spatstat.linnet'.)
Author: Adrian Baddeley [aut, cre, cph]
,
Rolf Turner [aut, cph] ,
Ege Rubak [aut, cph] ,
Tilman Davies [ctb],
Ute Hahn [ctb],
Abdollah Jalilian [ctb],
Greg McSwiggan [ctb, cph],
Sebastian Meyer [ctb, cph],
Jens Oehlschlaegel [ctb, cph],
Suman Rakshit [ctb], [...truncated...]
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.geom versions 3.3-4 dated 2024-11-18 and 3.3-5 dated 2025-01-18
DESCRIPTION | 10 +-- MD5 | 85 +++++++++++++------------- NAMESPACE | 2 NEWS | 88 ++++++++++++++++++++++++++- R/colourtables.R | 81 +++++++++++++++---------- R/hyperframe.R | 4 - R/persp.im.R | 4 + R/persp.ppp.R | 26 +++++--- R/plot.anylist.R | 136 ++++++++++++++++++++++++++++++++++--------- R/plot.im.R | 142 +++++++++++++++++++++++++-------------------- R/rotate.R | 3 R/split.ppp.R | 26 +++++--- R/symbolmap.R | 8 +- R/texture.R | 56 +++++++++++++---- R/unstack.R | 4 - inst/doc/packagesizes.txt | 1 inst/info/packagesizes.txt | 1 man/as.hyperframe.Rd | 7 -- man/colourmap.Rd | 3 man/distfun.Rd | 12 +++ man/distmap.Rd | 13 +++- man/distmap.owin.Rd | 11 +++ man/distmap.ppp.Rd | 16 ++++- man/distmap.psp.Rd | 11 +++ man/hyperframe.Rd | 8 +- man/nndist.Rd | 11 +++ man/nndist.pp3.Rd | 11 +++ man/nndist.ppx.Rd | 11 +++ man/nndist.psp.Rd | 11 +++ man/pairdist.Rd | 11 +++ man/pairdist.pp3.Rd | 15 ++++ man/pairdist.ppp.Rd | 11 +++ man/pairdist.ppx.Rd | 14 +++- man/pairdist.psp.Rd | 14 +++- man/plot.anylist.Rd | 14 +++- man/plot.colourmap.Rd | 19 ++++-- man/plot.im.Rd | 34 +++++++++- man/plot.imlist.Rd | 30 +++++++-- man/plot.listof.Rd | 8 ++ man/plot.ppp.Rd | 42 +++++++------ man/plot.solist.Rd | 12 +++ man/plot.symbolmap.Rd | 2 man/plot.texturemap.Rd | 12 +++ man/rev.colourmap.Rd |only 44 files changed, 778 insertions(+), 262 deletions(-)