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Title: Visualize Data on Spirals
Description: It visualizes data along an Archimedean spiral <https://en.wikipedia.org/wiki/Archimedean_spiral>,
makes so-called spiral graph or spiral chart.
It has two major advantages for visualization: 1. It is able to visualize data with very long axis with high
resolution. 2. It is efficient for time series data to reveal periodic patterns.
Author: Zuguang Gu [aut, cre]
Maintainer: Zuguang Gu <z.gu@dkfz.de>
Diff between spiralize versions 1.0.6 dated 2022-08-09 and 1.1.0 dated 2024-06-18
spiralize-1.0.6/spiralize/man/Subset.TRACK_META.Rd |only spiralize-1.0.6/spiralize/man/TRACK_META.Rd |only spiralize-1.0.6/spiralize/man/cartesian_to_xy.Rd |only spiralize-1.0.6/spiralize/man/current_track_index.Rd |only spiralize-1.0.6/spiralize/man/is_in_track.Rd |only spiralize-1.0.6/spiralize/man/n_tracks.Rd |only spiralize-1.0.6/spiralize/man/names.TRACK_META.Rd |only spiralize-1.0.6/spiralize/man/phylo_to_dendrogram.Rd |only spiralize-1.0.6/spiralize/man/polar_to_cartesian.Rd |only spiralize-1.0.6/spiralize/man/print.TRACK_META.Rd |only spiralize-1.0.6/spiralize/man/set_current_track.Rd |only spiralize-1.0.6/spiralize/man/spiral_xaxis.Rd |only spiralize-1.0.6/spiralize/man/xy_to_cartesian.Rd |only spiralize-1.0.6/spiralize/man/xy_to_polar.Rd |only spiralize-1.1.0/spiralize/DESCRIPTION | 24 spiralize-1.1.0/spiralize/LICENSE | 3 spiralize-1.1.0/spiralize/MD5 | 114 - spiralize-1.1.0/spiralize/NAMESPACE | 119 - spiralize-1.1.0/spiralize/NEWS | 13 spiralize-1.1.0/spiralize/R/dendrogram.R | 149 - spiralize-1.1.0/spiralize/R/example.R |only spiralize-1.1.0/spiralize/R/global.R | 52 spiralize-1.1.0/spiralize/R/graphics.R | 871 ++++------ spiralize-1.1.0/spiralize/R/initialize.R | 210 +- spiralize-1.1.0/spiralize/R/layout.R | 115 - spiralize-1.1.0/spiralize/R/spiral.R | 56 spiralize-1.1.0/spiralize/R/track.R | 362 ++-- spiralize-1.1.0/spiralize/R/transform.R | 181 +- spiralize-1.1.0/spiralize/R/util.R | 2 spiralize-1.1.0/spiralize/R/zzz.R | 2 spiralize-1.1.0/spiralize/build/vignette.rds |binary spiralize-1.1.0/spiralize/inst/CITATION | 17 spiralize-1.1.0/spiralize/inst/doc/spiralize.Rmd | 12 spiralize-1.1.0/spiralize/inst/doc/spiralize.html | 17 spiralize-1.1.0/spiralize/man/coordinate.Rd |only spiralize-1.1.0/spiralize/man/current_spiral.Rd | 47 spiralize-1.1.0/spiralize/man/current_spiral_vp.Rd | 15 spiralize-1.1.0/spiralize/man/get_track_data.Rd | 41 spiralize-1.1.0/spiralize/man/horizon_legend.Rd | 39 spiralize-1.1.0/spiralize/man/solve_theta_from_spiral_length.Rd | 29 spiralize-1.1.0/spiralize/man/spiral_arrow.Rd | 66 spiralize-1.1.0/spiralize/man/spiral_axis.Rd | 71 spiralize-1.1.0/spiralize/man/spiral_bars.Rd | 37 spiralize-1.1.0/spiralize/man/spiral_clear.Rd | 25 spiralize-1.1.0/spiralize/man/spiral_dendrogram.Rd | 29 spiralize-1.1.0/spiralize/man/spiral_git_commits.Rd |only spiralize-1.1.0/spiralize/man/spiral_highlight.Rd | 49 spiralize-1.1.0/spiralize/man/spiral_highlight_by_sector.Rd | 45 spiralize-1.1.0/spiralize/man/spiral_horizon.Rd | 86 spiralize-1.1.0/spiralize/man/spiral_info.Rd | 23 spiralize-1.1.0/spiralize/man/spiral_initialize.Rd | 80 spiralize-1.1.0/spiralize/man/spiral_initialize_by_gcoor.Rd | 26 spiralize-1.1.0/spiralize/man/spiral_initialize_by_time.Rd | 65 spiralize-1.1.0/spiralize/man/spiral_lines.Rd | 41 spiralize-1.1.0/spiralize/man/spiral_opt.Rd | 42 spiralize-1.1.0/spiralize/man/spiral_phylo.Rd | 75 spiralize-1.1.0/spiralize/man/spiral_pkg_downloads.Rd |only spiralize-1.1.0/spiralize/man/spiral_points.Rd | 37 spiralize-1.1.0/spiralize/man/spiral_polygon.Rd | 51 spiralize-1.1.0/spiralize/man/spiral_raster.Rd | 60 spiralize-1.1.0/spiralize/man/spiral_rect.Rd | 37 spiralize-1.1.0/spiralize/man/spiral_segments.Rd | 61 spiralize-1.1.0/spiralize/man/spiral_text.Rd | 74 spiralize-1.1.0/spiralize/man/spiral_track.Rd | 53 spiralize-1.1.0/spiralize/man/spiral_yaxis.Rd | 44 spiralize-1.1.0/spiralize/man/track_helper.Rd |only spiralize-1.1.0/spiralize/man/track_meta.Rd |only spiralize-1.1.0/spiralize/vignettes/spiralize.Rmd | 12 68 files changed, 1985 insertions(+), 1694 deletions(-)
Title: Unsupervised Learning Based Definition of Microbial Rare
Biosphere
Description: A tool to define rare biosphere. 'ulrb' solves the problem of the
definition of rarity by replacing arbitrary thresholds with an unsupervised machine
learning algorithm (partitioning around medoids, or k-medoids). This algorithm
works for any type of microbiome data, provided there is a species abundance table.
For validation of this method to different species abundance tables see Pascoal et al, 2024 (in peer-review).
This method also works for non-microbiome data.
Author: Francisco Pascoal [aut, cre] ,
Paula Branco [aut] ,
Luis Torgo [aut] ,
Rodrigo Costa [aut] ,
Catarina Magalhaes [aut]
Maintainer: Francisco Pascoal <fpascoal1996@gmail.com>
Diff between ulrb versions 0.1.3 dated 2023-11-17 and 0.1.5 dated 2024-06-18
DESCRIPTION | 24 MD5 | 46 - R/check_CH.R | 22 R/check_DB.R | 5 R/suggest_k.R | 12 README.md | 16 build/vignette.rds |binary inst/CITATION | 6 inst/doc/Glossary.R | 4 inst/doc/eco-analysis.R | 10 inst/doc/eco-analysis.html | 550 +++++++++++----------- inst/doc/explore-classifications.R | 28 - inst/doc/explore-classifications.Rmd | 20 inst/doc/explore-classifications.html | 746 +++++++++++++++---------------- inst/doc/ulrb-vignet.R | 8 inst/doc/ulrb-vignet.html | 290 ++++++------ man/check_CH.Rd | 14 man/check_DB.Rd | 2 man/define_rb.Rd | 2 man/figures/README-unnamed-chunk-3-1.png |only man/figures/README-unnamed-chunk-3-2.png |only man/suggest_k.Rd | 6 tests/testthat/test-define_rb.R | 12 tests/testthat/test-suggest_k.R | 4 vignettes/explore-classifications.Rmd | 20 25 files changed, 935 insertions(+), 912 deletions(-)
Title: An R Package for Extended Behavior Genetics Analysis
Description: The BGmisc R package offers a comprehensive suite of
functions tailored for extended behavior genetics analysis, including
model identification, calculating relatedness, pedigree conversion,
pedigree simulation, and more.
Author: S. Mason Garrison [aut, cre] ,
Michael D. Hunter [aut] ,
Xuanyu Lyu [aut] ,
Rachel N. Good [ctb],
Jonathan D. Trattner [aut] ,
S. Alexandra Burt [aut]
Maintainer: S. Mason Garrison <garrissm@wfu.edu>
Diff between BGmisc versions 1.3.1 dated 2024-06-16 and 1.3.2 dated 2024-06-18
DESCRIPTION | 21 +++--- MD5 | 26 +++---- NEWS.md | 4 + build/vignette.rds |binary inst/doc/analyticrelatedness.Rmd | 2 inst/doc/analyticrelatedness.html | 3 inst/doc/modelingrelatedness.html | 8 +- inst/doc/validation.Rmd | 4 - inst/doc/validation.html | 10 +-- tests/testthat/Rplots.pdf |binary tests/testthat/test-identifyModel.R | 28 ++++++++ tests/testthat/test-networks.R | 120 ++++++++++++++++++++---------------- vignettes/analyticrelatedness.Rmd | 2 vignettes/validation.Rmd | 4 - 14 files changed, 143 insertions(+), 89 deletions(-)
Title: Four-Step Biodiversity Analysis Based on 'iNEXT'
Description: Expands 'iNEXT' to include the estimation of sample completeness and evenness. The package provides simple functions to perform the following four-step biodiversity analysis:
STEP 1: Assessment of sample completeness profiles.
STEP 2a: Analysis of size-based rarefaction and extrapolation sampling curves to
determine whether the asymptotic diversity can be accurately estimated.
STEP 2b: Comparison of the observed and the estimated asymptotic diversity profiles.
STEP 3: Analysis of non-asymptotic coverage-based rarefaction and extrapolation sampling curves.
STEP 4: Assessment of evenness profiles.
The analyses in STEPs 2a, 2b and STEP 3 are mainly based on the previous 'iNEXT' package. Refer to the 'iNEXT' package for details. This package is mainly focusing on the computation for STEPs 1 and 4. See Chao et al. (2020) <doi:10.1111/1440-1703.12102> for statistical background.
Author: Anne Chao [aut, cre],
KaiHsiang Hu [ctb]
Maintainer: Anne Chao <chao@stat.nthu.edu.tw>
Diff between iNEXT.4steps versions 1.0.0 dated 2024-04-10 and 1.0.1 dated 2024-06-18
DESCRIPTION | 6 MD5 | 8 - NEWS | 3 R/MainFun.R | 109 ++++++-------- inst/doc/Vignette-iNEXT.4steps-April10.html | 208 ++++++++++++++-------------- 5 files changed, 163 insertions(+), 171 deletions(-)
Title: Clinical Data Review Tool
Description: Creation of interactive tables, listings and figures ('TLFs')
and associated report for exploratory analysis of data in a clinical trial,
e.g. for clinical oversight activities.
Interactive figures include sunburst, treemap, scatterplot, line plot and
barplot of counts data.
Interactive tables include table of summary statistics
(as counts of adverse events, enrollment table) and listings.
Possibility to compare data (summary table or listing) across two data batches/sets.
A clinical data review report is created via study-specific configuration
files and template 'R Markdown' reports contained in the package.
Author: Laure Cougnaud [aut, cre],
Michela Pasetto [aut],
Lennart Tuijnder [aut],
Adriaan Blommaert [aut],
Arne De Roeck [ctb, rev] ,
Open Analytics [cph]
Maintainer: Laure Cougnaud <laure.cougnaud@openanalytics.eu>
Diff between clinDataReview versions 1.6.0 dated 2024-06-13 and 1.6.1 dated 2024-06-18
DESCRIPTION | 8 +- MD5 | 14 ++-- R/plots-utility-axes.R | 9 ++ inst/NEWS | 2 inst/doc/clinDataReview-dataPreprocessing.html | 6 - inst/doc/clinDataReview-dataVisualization.html | 66 ++++++++++---------- inst/doc/clinDataReview-reporting.html | 6 - tests/testthat/test_scatterplotClinData.R | 80 +++++++++++++++++++++++++ 8 files changed, 139 insertions(+), 52 deletions(-)
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Title: Visualization of Patient Profiles
Description: Creation of patient profile visualizations for
exploration, diagnostic or monitoring purposes during a clinical trial.
These static visualizations display a patient-specific overview
of the evolution during the trial time frame of
parameters of interest (as laboratory, ECG, vital signs),
presence of adverse events, exposure to a treatment;
associated with metadata patient information,
as demography, concomitant medication.
The visualizations can be tailored for specific domain(s) or endpoint(s) of interest.
Visualizations are exported into patient profile report(s)
or can be embedded in custom report(s).
Author: Laure Cougnaud [aut, cre],
Margaux Faes [rev] ,
Open Analytics [cph]
Maintainer: Laure Cougnaud <laure.cougnaud@openanalytics.eu>
Diff between patientProfilesVis versions 2.0.8 dated 2024-06-13 and 2.0.9 dated 2024-06-18
DESCRIPTION | 8 +++---- MD5 | 24 +++++++++++----------- NAMESPACE | 2 + R/miscellaneous.R | 9 +++++--- R/report_defineIndex.R | 8 +++---- R/subjectProfileEventPlot.R | 18 +++++++++++++--- R/subjectProfileIntervalPlot.R | 9 +++++++- R/subjectProfileLinePlot.R | 17 ++++++++++++--- inst/NEWS | 3 ++ inst/doc/patientProfiles-template-SDTM.html | 6 ++--- inst/doc/patientProfilesVis-introduction.html | 28 +++++++++++++------------- man/defineIndex.Rd | 8 +++---- man/subjectProfileTheme.Rd | 6 ++--- 13 files changed, 90 insertions(+), 56 deletions(-)
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Title: Conducts Mokken Scale Analysis
Description: Contains functions for performing Mokken
scale analysis on test and questionnaire data.
It includes an automated item selection algorithm, and various checks of model assumptions.
Author: L. Andries van der Ark [aut, cre],
Letty Koopman [aut],
J. Hendrik Straat [ctb],
Don van den Bergh [ctb]
Maintainer: L. Andries van der Ark <L.A.vanderArk@uva.nl>
Diff between mokken versions 3.1.1 dated 2024-05-29 and 3.1.2 dated 2024-06-18
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- build/partial.rdb |binary man/ICC.Rd | 2 +- man/mokken-package.Rd | 9 +++++++-- 5 files changed, 16 insertions(+), 11 deletions(-)
Title: Analysis of Data from a Crossover Design with GEE
Description: Analyze data from a crossover design using generalized estimation equations (GEE), including carryover effects and various correlation structures based on the Kronecker product. It contains functions for semiparametric estimates of carry-over effects in repeated measures and allows estimation of complex carry-over effects. Related work includes: a) Cruz N.A., Melo O.O., Martinez C.A. (2023). "CrossCarry: An R package for the analysis of data from a crossover design with GEE". <doi:10.48550/arXiv.2304.02440>. b) Cruz N.A., Melo O.O., Martinez C.A. (2023). "A correlation structure for the analysis of Gaussian and non-Gaussian responses in crossover experimental designs with repeated measures". <doi:10.1007/s00362-022-01391-z> and c) Cruz N.A., Melo O.O., Martinez C.A. (2023). "Semiparametric generalized estimating equations for repeated measurements in cross-over designs". <doi:10.1177/09622802231158736>.
Author: Nelson Alirio Cruz Gutierrez [aut, cre, cph],
Oscar Orlando Melo [aut],
Carlos Alberto Martinez [aut]
Maintainer: Nelson Alirio Cruz Gutierrez <neacruzgu@unal.edu.co>
Diff between CrossCarry versions 0.1.0 dated 2023-04-11 and 0.2.0 dated 2024-06-18
DESCRIPTION | 10 ++++---- MD5 | 16 ++++++------- R/CrossGEE.R | 7 ++++- R/CrossGEEKron.R | 5 +++- R/CrossGEESP.R | 63 ++++++++++++++++++---------------------------------- R/globals.R | 3 +- man/CrossGEE.Rd | 9 +++++++ man/CrossGEEKron.Rd | 2 - man/CrossGEESP.Rd | 2 - 9 files changed, 59 insertions(+), 58 deletions(-)
Title: Gaussian Mixture Models, K-Means, Mini-Batch-Kmeans, K-Medoids
and Affinity Propagation Clustering
Description: Gaussian mixture models, k-means, mini-batch-kmeans, k-medoids and affinity propagation clustering with the option to plot, validate, predict (new data) and estimate the optimal number of clusters. The package takes advantage of 'RcppArmadillo' to speed up the computationally intensive parts of the functions. For more information, see (i) "Clustering in an Object-Oriented Environment" by Anja Struyf, Mia Hubert, Peter Rousseeuw (1997), Journal of Statistical Software, <doi:10.18637/jss.v001.i04>; (ii) "Web-scale k-means clustering" by D. Sculley (2010), ACM Digital Library, <doi:10.1145/1772690.1772862>; (iii) "Armadillo: a template-based C++ library for linear algebra" by Sanderson et al (2016), The Journal of Open Source Software, <doi:10.21105/joss.00026>; (iv) "Clustering by Passing Messages Between Data Points" by Brendan J. Frey and Delbert Dueck, Science 16 Feb 2007: Vol. 315, Issue 5814, pp. 972-976, <doi:10.1126/science.1136800>.
Author: Lampros Mouselimis [aut, cre] ,
Conrad Sanderson [cph] ,
Ryan Curtin [cph] ,
Siddharth Agrawal [cph] ),
Brendan Frey [cph] ),
Delbert Dueck [cph] ,
Vitalie Spinu [ctb]
Maintainer: Lampros Mouselimis <mouselimislampros@gmail.com>
Diff between ClusterR versions 1.3.2 dated 2023-12-04 and 1.3.3 dated 2024-06-18
DESCRIPTION | 10 ++-- MD5 | 10 ++-- NEWS.md | 5 ++ README.md | 5 -- inst/doc/the_clusterR_package.html | 12 ++-- src/export_inst_folder_headers.cpp | 91 ++++++++++++++++++++++++++++--------- 6 files changed, 93 insertions(+), 40 deletions(-)