Defines the classes and functions used to simulate and to analyze data sets describing copy number variants and, optionally, sequencing mutations in order to detect clonal subsets. See Zucker et al. (2019) <doi:10.1093/bioinformatics/btz057>.

Offers functionality which provides methods for data analyses and cleaning that can be flexibly applied across multiple variables and in groups. These include cleaning accidental text, contingent calculations, counting missing data, and building summarizations of the data.

Fit, plot and compare several (extreme value) distribution functions. Compute (truncated) distribution quantile estimates and plot return periods on a linear scale. On the fitting method, see Asquith (2011): Distributional Analysis with L-moment Statistics [...] ISBN 1463508417.

Interact with the application programming interface for the web annotation service Hypothes.is (See <http://hypothes.is> for more information.) Allows users to download data about public annotations, and create, retrieve, update, and delete their own annotations.

This package provides functions to perform robust nonparametric survival analysis with right censored data using a prior near-ignorant Dirichlet Process. Mangili, F., Benavoli, A., de Campos, C.P., Zaffalon, M. (2015) <doi:10.1002/bimj.201500062>.

Deploy file changes across multiple GitHub repositories using the GitHub Web API <https://docs.github.com/en/rest>. Allows synchronizing common files, Continuous Integration ('CI') workflows, or configurations across many repositories with a single command.

Multi Calculator of different scores to measure adherence to Mediterranean Diet, to compute them in nutriepidemiological data. Additionally, a sample dataset of this kind of data is provided, and some other minor tools useful in epidemiological studies.

Use health data in the Observational Medical Outcomes Partnership Common Data Model format in Spark'. Functionality includes creating all required tables and fields and creation of a single reference to the data. Native Spark functionality is supported.

Simultaneously evaluate multiple ordinal outcome measures. Applied data analysts in particular are faced with uncertainty in choosing appropriate statistical tests for ordinal data. The included shiny application allows users to simulate outcomes given different ordinal data distributions.

This package provides functions for easily reading and processing binary data files created by Pamguard (<https://www.pamguard.org/>). All functions for directly reading the binary data files are based on MATLAB code written by Michael Oswald.

This package provides three Quarto website templates as an R project, which are commonly used by academics. Templates for personal websites and course/workshop websites are included, as well as a template with minimal content for customization.

This package provides a simple function that anonymises a list of variables in a consistent way: anonymised factors are not recycled and the same original levels receive the same anonymised factor even if located in different datasets.

Sleep cycles are largely detected according to the originally proposed criteria by Feinberg & Floyd (1979) <doi:10.1111/j.1469-8986.1979.tb02991.x> as described in Blume & Cajochen (2021) <doi:10.1016/j.mex.2021.101318>.

Estimate the regression coefficients and the baseline hazard of proportional hazard Cox models with left, right or interval censored survival data using maximum penalised likelihood. A non-parametric smooth estimate of the baseline hazard function is provided.

Information on all of the TriMet stops in the Portland Metro Area. It includes information such as the longitude, latitude, cross street, and direction of the stop. TriMet has catalogued these stops, 6880 in total.

This package contains a function to randomize subjects, patients in groups of sequences (treatment sequences). If a blocksize is given, the randomization will be done within blocks. The randomization may be controlled by a Wald-Wolfowitz runs test. Functions to obtain the p-value of that test are included. The package is mainly intended for randomization of bioequivalence studies but may be used also for other clinical crossover studies. Contains two helper functions sequences() and williams() to get the sequences of commonly used designs in BE studies.

Randomization tests for the statistical comparison of i = two or more individual-based, sample-based or coverage-based rarefaction curves. The ecological null hypothesis is that the i samples were all drawn randomly from a single assemblage, with (necessarily) a single underlying species abundance distribution. The biogeographic null hypothesis is that the i samples were all drawn from different assemblages that, nonetheless, share similar species richness and species abundance distributions. Functions are described in L. Cayuela, N.J. Gotelli & R.K. Colwell (2015) <doi:10.1890/14-1261.1>.

This package provides methods for microarray analysis that take basic data types such as matrices and lists of vectors. These methods can be used standalone, be utilized in other packages, or be wrapped up in higher-level classes.

This package provides classes and methods for handling pedigree data. It also includes functions to calculate genetic relationship measures as relationship and inbreeding coefficients and other utilities. Note that package is not yet stable. Use it with care!

Calculates a single number for a whole sequence that reflects the propensity of a DNA binding protein to interact with it. The DNA binding protein has to be described with a PFM matrix, for example gotten from Jaspar.

Model that assesses daily exposure to air pollution, which considers daily population mobility on a geographical scale and the spatial and temporal variability of pollutant concentrations, in addition to traditional parameters such as exposure time and pollutant concentration.

This package creates a new chars class which looks like a string but is actually a vector of individual characters, making strings iterable. This class enables vector operations on strings such as reverse, sort, head, and set operations.

Logic game in the style of the early 1980s home computers that can be played in the R console. This game is inspired by Mastermind, a game that became popular in the 1970s. Can you break the code?

This package provides functions for finding smooth interpolating curves connecting a series of points in the plane. Curves may be open or closed, that is, with the first and last point of the curve at the initial point.