Collection of Visium spatial gene expression datasets by 10X Genomics, formatted into objects of class SpatialExperiment. Data cover various organisms and tissues, and include: single- and multi-section experiments, as well as single sections subjected to both whole transcriptome and targeted panel analysis. Datasets may be used for testing of and as examples in packages, for tutorials and workflow demonstrations, or similar purposes.
The Readline library provides a set of functions for use by applications that allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. The Readline library includes additional functions to maintain a list of previously-entered command lines, to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.
Ceteris Paribus Profiles (What-If Plots) are designed to present model responses around selected points in a feature space. For example around a single prediction for an interesting observation. Plots are designed to work in a model-agnostic fashion, they are working for any predictive Machine Learning model and allow for model comparisons. Ceteris Paribus Plots supplement the Break Down Plots from breakDown package.
This package provides functions of five estimation method for ED50 (50 percent effective dose) are provided, and they are respectively Dixon-Mood method (1948) <doi:10.2307/2280071>, Choi's original turning point method (1990) <doi:10.2307/2531453> and it's modified version given by us, as well as logistic regression and isotonic regression. Besides, the package also supports comparison between two estimation results.
Designed to facilitate the preprocessing and linking of GIS (Geographic Information System) databases <https://www.sciencedirect.com/topics/computer-science/gis-database>, the R package GISINTEGRATION offers a robust solution for efficiently preparing GIS data for advanced spatial analyses. This package excels in simplifying intrica procedures like data cleaning, normalization, and format conversion, ensuring that the data are optimally primed for precise and thorough analysis.
Implement Bayesian multilevel modelling for compositional data. Compute multilevel compositional data and perform log-ratio transforms at between and within-person levels, fit Bayesian multilevel models for compositional predictors and outcomes, and run post-hoc analyses such as isotemporal substitution models. References: Le, Stanford, Dumuid, and Wiley (2025) <doi:10.1037/met0000750>, Le, Dumuid, Stanford, and Wiley (2024) <doi:10.48550/arXiv.2411.12407>.
The Open Data Format (ODF) is a new, non-proprietary, multilingual, metadata enriched, and zip-compressed data format with metadata structured in the Data Documentation Initiative (DDI) Codebook standard. This package allows reading and writing of data files in the Open Data Format (ODF) in R, and displaying metadata in different languages. For further information on the Open Data Format, see <https://opendataformat.github.io/>.
Computes optimal changepoint models using the Poisson likelihood for non-negative count data, subject to the PeakSeg constraint: the first change must be up, second change down, third change up, etc. For more info about the models and algorithms, read "Constrained Dynamic Programming and Supervised Penalty Learning Algorithms for Peak Detection" <https://jmlr.org/papers/v21/18-843.html> by TD Hocking et al.
This package provides a collection of functions for estimating spatial regimes, aggregations of neighboring spatial units that are homogeneous in functional terms. The term spatial regime, therefore, should not be understood as a synonym for cluster. More precisely, the term cluster does not presuppose any functional relationship between the variables considered, while the term regime is linked to a regressive relationship underlying the spatial process.
Facilitates querying data from the รข Facebook Marketing API', particularly for social science research <https://developers.facebook.com/docs/marketing-apis/>. Data from the Facebook Marketing API has been used for a variety of social science applications, such as for poverty estimation (Marty and Duhaut (2024) <doi:10.1038/s41598-023-49564-6>), disease surveillance (Araujo et al. (2017) <doi:10.48550/arXiv.1705.04045>), and measuring migration (Alexander, Polimis, and Zagheni (2020) <doi:10.1007/s11113-020-09599-3>). The package facilitates querying the number of Facebook daily/monthly active users for multiple location types (e.g., from around a specific coordinate to an administrative region) and for a number of attribute types (e.g., interests, behaviors, education level, etc). The package supports making complex queries within one API call and making multiple API calls across different locations and/or parameters.
Interactive data visualization for data practitioners. flourishcharts allows users to visualize their data using Flourish graphs that are grounded in data storytelling principles. Users can create racing bar & line charts, as well as other interactive elements commonly found in D3 graphics, easily in R and Python'. The package relies on an enterprise API provided by Flourish', a data visualization platform <https://developers.flourish.studio/api/introduction/>.
Identification of putative causal variants in genome-wide association studies using hybrid analysis of both the trio and population designs. The package implements the method in the paper: Yang, Y., Wang, Q., Wang, C., Buxbaum, J., & Ionita-Laza, I. (2024). KnockoffHybrid: A knockoff framework for hybrid analysis of trio and population designs in genome-wide association studies. The American Journal of Human Genetics, in press.
Helpers for customizing selected outputs from lavaan by Rosseel (2012) <doi:10.18637/jss.v048.i02> and print them. The functions are intended to be used by package developers in their packages and so are not designed to be user-friendly. They are designed to be let developers customize the tables by other functions. Currently the parameter estimates tables of a fitted object are supported.
Monte Carlo simulations of a game-theoretic model for the legal exemption system of the European cartel law are implemented in order to estimate the (mean) deterrent effect of this system. The input and output parameters of the simulated cartel opportunities can be visualized by three-dimensional projections. A description of the model is given in Moritz et al. (2018) <doi:10.1515/bejeap-2017-0235>.
This package implements an Entropy measure of dependence based on the Bhattacharya-Hellinger-Matusita distance. Can be used as a (nonlinear) autocorrelation/crosscorrelation function for continuous and categorical time series. The package includes tests for serial and cross dependence and nonlinearity based on it. Some routines have a parallel version that can be used in a multicore/cluster environment. The package makes use of S4 classes.
This package provides datasets for the nullranges package vignette, in particular example datasets for DNase hypersensitivity sites (DHS), CTCF binding sites, and CTCF genomic interactions. These are used to demonstrate generation of null hypothesis feature sets, either through block bootstrapping or matching, in the nullranges vignette. For more details, see the data object man pages, and the R scripts for object construction provided within the package.
Supports import/export for a number of datetime string standards and R datetime classes often including lossless re-export of any original reduced precision including ISO 8601 <https://en.wikipedia.org/wiki/ISO_8601> and pdfmark <https://opensource.adobe.com/dc-acrobat-sdk-docs/library/pdfmark/> datetime strings. Supports local/global datetimes with optional UTC offsets and/or (possibly heterogeneous) time zones with up to nanosecond precision.
Calculation of informative simultaneous confidence intervals for graphical described multiple test procedures and given information weights. Bretz et al. (2009) <doi:10.1002/sim.3495> and Brannath et al. (2024) <doi:10.48550/arXiv.2402.13719>. Furthermore, exploration of the behavior of the informative bounds in dependence of the information weights. Comparisons with compatible bounds are possible. Strassburger and Bretz (2008) <doi:10.1002/sim.3338>.
Read in SAS Data ('.sas7bdat Files) into Apache Spark from R. Apache Spark is an open source cluster computing framework available at <http://spark.apache.org>. This R package uses the spark-sas7bdat Spark package (<https://spark-packages.org/package/saurfang/spark-sas7bdat>) to import and process SAS data in parallel using Spark'. Hereby allowing to execute dplyr statements in parallel on top of SAS data.
The stress addition approach is an alternative to the traditional concentration addition or effect addition models. It allows the modelling of tri-phasic concentration-response relationships either as single toxicant experiments, in combination with an environmental stressor or as mixtures of two toxicants. See Liess et al. (2019) <doi:10.1038/s41598-019-51645-4> and Liess et al. (2020) <doi:10.1186/s12302-020-00394-7>.
Data for the mosaics package, consisting of (1) chromosome 22 ChIP and control sample data from a ChIP-seq experiment of STAT1 binding and H3K4me3 modification in MCF7 cell line from ENCODE database (HG19) and (2) chromosome 21 ChIP and control sample data from a ChIP-seq experiment of STAT1 binding, with mappability, GC content, and sequence ambiguity scores of human genome HG18.
This package allows importing most common specific structure (motif) types into R for use by functions provided by other Bioconductor motif-related packages. Motifs can be exported into most major motif formats from various classes as defined by other Bioconductor packages. A suite of motif and sequence manipulation and analysis functions are included, including enrichment, comparison, P-value calculation, shuffling, trimming, higher-order motifs, and others.
Collection of ancillary functions and utilities to be used in conjunction with the TraMineR package for sequence data exploration. Includes, among others, specific functions such as state survival plots, position-wise group-typical states, dynamic sequence indicators, and dissimilarities between event sequences. Also includes contributions by non-members of the TraMineR team such as methods for polyadic data and for the comparison of groups of sequences.
The package provides a single macro \randomize{TEXT} that typesets the characters of TEXT in random order, such that the resulting output appears correct, but most automated attempts to read the file will misunderstand it. This function allows one to include an email address in a TeX document and publish it online without fear of email address harvesters or spammers easily picking up the address.