Title: Linear Quantile Mixture Models
Description: Estimate linear quantile mixtures based on Time-Constant (TC) and/or Time-Varying (TV), discrete, random coefficients.
Author: Maria Francesca Marino [aut, cre],
Marco Alfo' [aut],
Nicola Salvati [aut],
Maria Giovanna Ranalli [aut]
Maintainer: Maria Francesca Marino <mariafrancesca.marino@unifi.it>
Diff between lqmix versions 1.1 dated 2025-03-21 and 1.2 dated 2025-10-17
DESCRIPTION | 14 - MD5 | 147 ++++++++------ NAMESPACE | 96 +++++---- NEWS | 8 R/cd4.R | 8 R/coef.lqmix.R | 12 - R/coef.lqr.R | 6 R/coef.seach_lqmix.R | 42 ++-- R/dal.R | 13 - R/logLik.lqmix.R | 8 R/logLik.lqr.R | 4 R/logLik.search_lqmix.R | 4 R/lqmix.R | 120 +++++------ R/lqmixTC.R | 177 ++++++----------- R/lqmixTCTV.fit_intermittent.R | 12 - R/lqmixTCTV_intermittent.R | 220 +++++++-------------- R/lqmixTV.fit_intermittent.R | 4 R/lqmixTV_intermittent.R | 196 ++++++------------- R/lqr.R | 104 +++++----- R/lqr.fit.R | 124 ++++++------ R/pain.R | 63 +++--- R/plot.lqmix.R | 133 ++++++------- R/plot.search_lqmix.R | 290 +++++++++++++++------------- R/postComputeTC.R | 18 - R/postComputeTV_intermittent.R | 6 R/predict.lqmix.R |only R/predict.lqr.R |only R/predict.search_lqmix.R |only R/print.lqmix.R | 4 R/print.lqr.R | 4 R/print.search_lqmix.R | 8 R/print.summary.lqmix.R | 4 R/print.summary.lqr.R | 56 ++--- R/print.summary.search_lqmix.R | 4 R/residuals.lqmix.R |only R/residuals.lqr.R |only R/residuals.search_lqmix.R |only R/search_lqmix.R | 171 +++++++--------- R/summary.lqmix.R | 388 +++++++++++++++++++------------------- R/summary.lqr.R | 4 R/summary.search_lqmix.R | 26 +- R/varAL.R | 14 + R/vcov.lqmix.R |only R/vcov.lqr.R |only R/vcov.search_lqmix.R |only R/xyBuildHOM.R |only R/xyBuildTC.R |only R/xyBuildTCTV.R |only R/xyBuildTV.R |only build/partial.rdb |binary inst/REFERENCES.bib | 51 +++- man/cd4.Rd | 7 man/coef.lqmix.Rd | 6 man/coef.lqr.Rd | 6 man/coef.search_lqmix.Rd | 6 man/dal.Rd | 12 - man/logLik.lqmix.Rd | 8 man/logLik.lqr.Rd | 4 man/logLik.search_lqmix.Rd | 4 man/lqmix-package.Rd | 6 man/lqmix.Rd | 68 +++--- man/lqr.Rd | 25 +- man/pain.Rd | 6 man/plot.lqmix.Rd | 6 man/plot.search_lqmix.Rd | 6 man/predict.lqmix.Rd |only man/predict.lqr.Rd |only man/predict.search_lqmix.Rd |only man/print.lqmix.Rd | 4 man/print.lqr.Rd | 4 man/print.search_lqmix.Rd | 4 man/print.summary.lqmix.Rd | 4 man/print.summary.lqr.Rd | 4 man/print.summary.search_lqmix.Rd | 4 man/residuals.lqmix.Rd |only man/residuals.lqr.Rd |only man/residuals.search_lqmix.Rd |only man/search_lqmix.Rd | 42 ++-- man/summary.lqmix.Rd | 10 man/summary.lqr.Rd | 4 man/summary.search_lqmix.Rd | 26 +- man/varAL.Rd | 17 + man/vcov.lqmix.Rd |only man/vcov.lqr.Rd |only man/vcov.search_lqmix.Rd |only tests |only 86 files changed, 1400 insertions(+), 1456 deletions(-)
Title: Reads Mass Spectrometry Data in mzXML Format
Description: Functions for reading mass spectrometry data in mzXML format.
Author: Sebastian Gibb [aut, cre]
Maintainer: Sebastian Gibb <mail@sebastiangibb.de>
Diff between readMzXmlData versions 2.8.3 dated 2023-08-19 and 2.8.4 dated 2025-10-17
DESCRIPTION | 15 ++++++++------- MD5 | 16 ++++++++-------- NEWS | 4 ++++ R/package.R | 3 +-- R/readMzXmlDir-functions.R | 2 -- R/readMzXmlFile-functions.R | 2 -- man/readMzXmlData-package.Rd | 1 + man/readMzXmlDir.Rd | 2 -- man/readMzXmlFile.Rd | 2 -- 9 files changed, 22 insertions(+), 25 deletions(-)
Title: Investigating New Projection Pursuit Index Functions
Description: Projection pursuit is used to find interesting low-dimensional
projections of high-dimensional data by optimizing an index over all
possible projections. The 'spinebil' package contains methods to evaluate
the performance of projection pursuit index functions using tour methods.
A paper describing the methods can be found at <doi:10.1007/s00180-020-00954-8>.
Author: Ursula Laa [aut] ,
Dianne Cook [aut] ,
Tina Rashid Jafari [aut, cre]
Maintainer: Tina Rashid Jafari <tina.rashidjafari@gmail.com>
Diff between spinebil versions 1.0.4 dated 2025-09-17 and 1.0.5 dated 2025-10-17
DESCRIPTION | 7 ++- MD5 | 16 ++++---- NEWS.md | 5 ++ R/index_mean.R | 5 -- R/index_scale.R | 3 + R/sample_size_effect.R | 2 - inst/doc/more_descriptives.html | 39 ++------------------- inst/doc/ppi_diagnostics.html | 73 ++++++++++++---------------------------- inst/doc/spinebil.html | 41 +++------------------- 9 files changed, 54 insertions(+), 137 deletions(-)
Title: 'Neuroconductor' Base Package with Helper Functions for 'nifti'
Objects
Description: Base package for 'Neuroconductor', which includes many helper
functions that interact with objects of class 'nifti', implemented by
package 'oro.nifti', for reading/writing and also other manipulation
functions.
Author: John Muschelli [aut, cre]
Maintainer: John Muschelli <muschellij2@gmail.com>
Diff between neurobase versions 1.33.0 dated 2025-07-23 and 1.34.0 dated 2025-10-17
DESCRIPTION | 6 +++--- MD5 | 22 +++++++++++----------- NEWS.md | 5 +++++ R/flip_img.R | 2 +- R/ortho2.R | 42 ++++++++++++++++++++++++++++++++++-------- R/overlay2.R | 12 ++++++++---- inst/doc/neurobase.html | 4 ++-- inst/doc/nifti_basics.html | 6 +++--- inst/doc/simple_io.html | 2 +- man/flip_img.Rd | 2 +- man/multi_overlay.Rd | 5 +++-- man/ortho2.Rd | 8 ++++++++ 12 files changed, 80 insertions(+), 36 deletions(-)
Title: Fast Statistical Hypothesis Tests on Rows and Columns of
Matrices
Description: Functions to perform fast statistical hypothesis tests on rows/columns of matrices.
The main goals are: 1) speed via vectorization, 2) output that is detailed and easy to use,
3) compatibility with tests implemented in R (like those available in the 'stats' package).
Author: Karolis Koncevicius [aut, cre]
Maintainer: Karolis Koncevicius <karolis.koncevicius@gmail.com>
Diff between matrixTests versions 0.2.3 dated 2023-10-05 and 0.2.3.1 dated 2025-10-17
matrixTests-0.2.3.1/matrixTests/DESCRIPTION | 6 +++--- matrixTests-0.2.3.1/matrixTests/MD5 | 7 ++----- matrixTests-0.2.3.1/matrixTests/inst/benchmarks/R/plot.R |only matrixTests-0.2.3/matrixTests/inst/benchmarks/R/plot.r |only matrixTests-0.2.3/matrixTests/tests/wilcoxon_onesample_correctness.r |only matrixTests-0.2.3/matrixTests/tests/wilcoxon_paired_correctness.r |only matrixTests-0.2.3/matrixTests/tests/wilcoxon_twosample_correctness.r |only 7 files changed, 5 insertions(+), 8 deletions(-)
Title: 'Imath' Computer Graphics Linear Algebra Static Library
Description: Provides a static library for 'Imath'
(see <https://github.com/AcademySoftwareFoundation/Imath>),
a library for functions and data types common in computer graphics
applications, including a 16-bit floating-point type.
Author: Tyler Morgan-Wall [aut, cre] ,
Andrew Kunz [ctb, cph],
Antonio Rojas [ctb, cph],
Brecht Van Lommel [ctb, cph],
Cary Phillips [ctb, cph],
Christina Tempelaar-Lietz [ctb, cph],
Christopher Kulla [ctb, cph],
Daniel Kaneider [ctb, cph],
Dirk Lemstra [ctb [...truncated...]
Maintainer: Tyler Morgan-Wall <tylermw@gmail.com>
Diff between libimath versions 3.1.9-4 dated 2025-07-02 and 3.1.9-5 dated 2025-10-17
DESCRIPTION | 6 +++--- MD5 | 4 ++-- src/Makevars.win.in | 10 +++++----- 3 files changed, 10 insertions(+), 10 deletions(-)
Title: Pretty Time of Day
Description: Implements an S3 class for storing and formatting time-of-day
values, based on the 'difftime' class.
Author: Kirill Mueller [aut, cre] ,
R Consortium [fnd],
Posit Software, PBC [fnd]
Maintainer: Kirill Mueller <kirill@cynkra.com>
Diff between hms versions 1.1.3 dated 2023-03-21 and 1.1.4 dated 2025-10-17
DESCRIPTION | 35 ++++--- MD5 | 53 ++++++----- NAMESPACE | 7 + NEWS.md | 21 ++++ R/args.R | 26 +++-- R/cast.R | 9 +- R/coerce.R | 4 R/compat-purrr.R | 15 ++- R/hms-package.R |only R/hms.R | 101 +++++++++++++++++----- R/parse.R | 20 +++- R/pillar.R | 32 +++++-- R/round.R | 24 ++++- README.md | 135 +++++++++++++++++------------- man/hms-package.Rd | 5 - man/hms.Rd | 13 ++ man/round_hms.Rd | 12 ++ tests/testthat/_snaps/sequence.md |only tests/testthat/test-arith.R | 10 +- tests/testthat/test-coercion-deprecated.R | 25 +++-- tests/testthat/test-coercion.R | 59 +++++++++---- tests/testthat/test-combine.R | 4 tests/testthat/test-construct.R | 21 +++- tests/testthat/test-lubridate.R | 18 ++-- tests/testthat/test-output.R | 109 ++++++++++++------------ tests/testthat/test-parse.R | 15 ++- tests/testthat/test-round.R | 73 +++++++++++++++- tests/testthat/test-sequence.R |only tests/testthat/test-unique.R | 5 - 29 files changed, 586 insertions(+), 265 deletions(-)
Title: 'ggplot2' Based Publication Ready Plots
Description: The 'ggplot2' package is excellent and flexible for elegant data
visualization in R. However the default generated plots requires some formatting
before we can send them for publication. Furthermore, to customize a 'ggplot',
the syntax is opaque and this raises the level of difficulty for researchers
with no advanced R programming skills. 'ggpubr' provides some easy-to-use
functions for creating and customizing 'ggplot2'- based publication ready plots.
Author: Alboukadel Kassambara [aut, cre]
Maintainer: Alboukadel Kassambara <alboukadel.kassambara@gmail.com>
Diff between ggpubr versions 0.6.1 dated 2025-06-27 and 0.6.2 dated 2025-10-17
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 8 ++++++++ R/compare_means.R | 4 +++- tests/testthat/test-compare_means.R | 4 ++-- 5 files changed, 21 insertions(+), 11 deletions(-)
Title: Tools and Statistical Procedures in Plant Science
Description: The 'inti' package is part of the 'inkaverse' project for developing
different procedures and tools used in plant science and experimental designs.
The mean aim of the package is to support researchers during the planning of
experiments and data collection (tarpuy()), data analysis and graphics (yupana())
, and scientific writing.
Learn more about the 'inkaverse' project at <https://inkaverse.com/>.
Author: Flavio Lozano-Isla [aut, cre] ,
Maria Belen Kistner [ctb] ,
QuipoLab [ctb],
Inkaverse [cph]
Maintainer: Flavio Lozano-Isla <flozanoisla@gmail.com>
Diff between inti versions 0.6.8 dated 2025-08-30 and 0.6.9 dated 2025-10-17
inti-0.6.8/inti/inst/doc/apps.R |only inti-0.6.8/inti/inst/doc/heritability.qmd |only inti-0.6.8/inti/inst/doc/yupana.qmd |only inti-0.6.8/inti/vignettes/heritability.qmd |only inti-0.6.8/inti/vignettes/yupana.qmd |only inti-0.6.9/inti/DESCRIPTION | 13 inti-0.6.9/inti/MD5 | 114 - inti-0.6.9/inti/NEWS.md | 7 inti-0.6.9/inti/R/H2cal.R | 56 inti-0.6.9/inti/R/design_noreps.R | 16 inti-0.6.9/inti/R/design_repblock.R | 20 inti-0.6.9/inti/R/figure2qmd.R | 8 inti-0.6.9/inti/R/gdoc2qmd.R | 15 inti-0.6.9/inti/R/plot_smr.R | 22 inti-0.6.9/inti/R/table2qmd.R | 2 inti-0.6.9/inti/R/tarpuy_design.R | 12 inti-0.6.9/inti/R/tarpuy_plex.R | 6 inti-0.6.9/inti/R/tarpuy_traits.R | 6 inti-0.6.9/inti/R/yupana_mvr.R | 4 inti-0.6.9/inti/build/vignette.rds |binary inti-0.6.9/inti/inst/doc/apps.html | 6 inti-0.6.9/inti/inst/doc/apps.qmd | 7 inti-0.6.9/inti/inst/doc/heritability.R | 42 inti-0.6.9/inti/inst/doc/heritability.Rmd |only inti-0.6.9/inti/inst/doc/heritability.html | 1103 +++++----- inti-0.6.9/inti/inst/doc/policy.html | 2 inti-0.6.9/inti/inst/doc/rticles.html | 4 inti-0.6.9/inti/inst/doc/tarpuy.html | 2 inti-0.6.9/inti/inst/doc/yupana.R | 24 inti-0.6.9/inti/inst/doc/yupana.Rmd |only inti-0.6.9/inti/inst/doc/yupana.html | 408 ++- inti-0.6.9/inti/inst/extdata/_extensions/scihub/ReadMe.qmd | 69 inti-0.6.9/inti/inst/extdata/_extensions/scihub/article.qmd | 39 inti-0.6.9/inti/inst/extdata/_extensions/scihub/design/labels.qmd | 13 inti-0.6.9/inti/inst/extdata/_extensions/scihub/files/images |only inti-0.6.9/inti/inst/extdata/_extensions/scihub/files/zotero |only inti-0.6.9/inti/inst/extdata/_extensions/scihub/manuscript |only inti-0.6.9/inti/inst/tarpuy/rsconnect/shinyapps.io/flavjack/tarpuy-test.dcf | 2 inti-0.6.9/inti/inst/tarpuy/rsconnect/shinyapps.io/flavjack/tarpuy.dcf | 2 inti-0.6.9/inti/inst/yupana/rsconnect/shinyapps.io/flavjack/yupana-test.dcf | 2 inti-0.6.9/inti/inst/yupana/rsconnect/shinyapps.io/flavjack/yupana.dcf | 2 inti-0.6.9/inti/inst/yupana/server.R | 10 inti-0.6.9/inti/inst/yupana/www/auth.R | 6 inti-0.6.9/inti/man/H2cal.Rd | 33 inti-0.6.9/inti/man/design_noreps.Rd | 16 inti-0.6.9/inti/man/design_repblock.Rd | 20 inti-0.6.9/inti/man/figure2qmd.Rd | 8 inti-0.6.9/inti/man/gdoc2qmd.Rd | 10 inti-0.6.9/inti/man/jc_tombola.Rd | 4 inti-0.6.9/inti/man/met.Rd | 22 inti-0.6.9/inti/man/metamorphosis.Rd | 11 inti-0.6.9/inti/man/outliers_remove.Rd | 2 inti-0.6.9/inti/man/plot_smr.Rd | 6 inti-0.6.9/inti/man/potato.Rd | 38 inti-0.6.9/inti/man/remove_outliers.Rd | 2 inti-0.6.9/inti/man/table2qmd.Rd | 2 inti-0.6.9/inti/man/tarpuy_design.Rd | 22 inti-0.6.9/inti/man/tarpuy_plex.Rd | 10 inti-0.6.9/inti/man/tarpuy_plotdesign.Rd | 2 inti-0.6.9/inti/man/tarpuy_traits.Rd | 6 inti-0.6.9/inti/man/yupana_mvr.Rd | 4 inti-0.6.9/inti/vignettes/apps.qmd | 7 inti-0.6.9/inti/vignettes/heritability.Rmd |only inti-0.6.9/inti/vignettes/yupana.Rmd |only 64 files changed, 1332 insertions(+), 937 deletions(-)