Fast Symbolic Multivariate Polynomials

Fast manipulation of symbolic multivariate polynomials using the 'Map' class of the Standard Template Library. The package uses print and coercion methods from the 'mpoly' package (Kahle 2013, "Multivariate polynomials in R", The R Journal, 5(1):162), but offers speed improvements. It is comparable in speed to the 'spray' package for sparse arrays, but retains the symbolic benefits of 'mpoly'. To cite the package in publications, use Hankin 2022 . Uses 'disordR' discipline.

Bayesian Calibration of Complex Computer Codes

Performs Bayesian calibration of computer models as per Kennedy and O'Hagan 2001. The package includes routines to find the hyperparameters and parameters; see the help page for stage1() for a worked example using the toy dataset. A tutorial is provided in the calex.Rnw vignette; and a suite of especially simple one dimensional examples appears in inst/doc/one.dim/.

Optimal Exact Tests for Multiple Binary Endpoints

Calculates exact hypothesis tests to compare a treatment and a reference group with respect to multiple binary endpoints. The tested null hypothesis is an identical multidimensional distribution of successes and failures in both groups. The alternative hypothesis is a larger success proportion in the treatment group in at least one endpoint. The tests are based on the multivariate permutation distribution of subjects between the two groups. For this permutation distribution, rejection regions are calculated that satisfy one of different possible optimization criteria. In particular, regions with maximal exhaustion of the nominal significance level, maximal power under a specified alternative or maximal number of elements can be found. Optimization is achieved by a branch-and-bound algorithm. By application of the closed testing principle, the global hypothesis tests are extended to multiple testing procedures.

Open GenBank Files

Opens complete record(s) with .gb extension from the NCBI/GenBank Nucleotide database and returns a list containing shaped record(s). These kind of files contains detailed records of DNA samples (locus, organism, type of sequence, source of the sequence...). An example of record can be found at < https://www.ncbi.nlm.nih.gov/nuccore/HE799070>.

Datasets for "Statistics: UnLocking the Power of Data"

Datasets for the third edition of "Statistics: Unlocking the Power of Data" by Lock^5 Includes version of datasets from earlier editions.

Confounder-Adjusted Survival Curves and Cumulative Incidence Functions

Estimate and plot confounder-adjusted survival curves using either 'Direct Adjustment', 'Direct Adjustment with Pseudo-Values', various forms of 'Inverse Probability of Treatment Weighting', two forms of 'Augmented Inverse Probability of Treatment Weighting', 'Empirical Likelihood Estimation' or 'Targeted Maximum Likelihood Estimation'. Also includes a significance test for the difference between two adjusted survival curves and the calculation of adjusted restricted mean survival times. Additionally enables the user to estimate and plot cause-specific confounder-adjusted cumulative incidence functions in the competing risks setting using the same methods (with some exceptions). For details, see Denz et. al (2023) .

Calculate the Care Density or Fragmented Care Density Given a Patient-Sharing Network

Given a patient-sharing network, calculate either the classic care density as proposed by Pollack et al. (2013) or the fragmented care density as proposed by Engels et al. (2024) . By utilizing the 'igraph' and 'data.table' packages, the provided functions scale well for very large graphs.

Imputation of High-Dimensional Count Data using Side Information

Analysis, imputation, and multiple imputation of count data using covariates. LORI uses a log-linear Poisson model where main row and column effects, as well as effects of known covariates and interaction terms can be fitted. The estimation procedure is based on the convex optimization of the Poisson loss penalized by a Lasso type penalty and a nuclear norm. LORI returns estimates of main effects, covariate effects and interactions, as well as an imputed count table. The package also contains a multiple imputation procedure. The methods are described in Robin, Josse, Moulines and Sardy (2019) .

Simulate Data from a DAG and Associated Node Information

Simulate complex data from a given directed acyclic graph and information about each individual node. Root nodes are simply sampled from the specified distribution. Child Nodes are simulated according to one of many implemented regressions, such as logistic regression, linear regression, poisson regression and more. Also includes a comprehensive framework for discrete-time simulation, which can generate even more complex longitudinal data.

The Symmetric Group: Permutations of a Finite Set

Manipulates invertible functions from a finite set to itself. Can transform from word form to cycle form and back. To cite the package in publications please use Hankin (2020) "Introducing the permutations R package", SoftwareX, volume 11 .