This article illustrates intRinsic, an R package that implements novel state-of-the-art likelihood-based estimators of the intrinsic dimension of a dataset, an essential quantity for most dimensionality reduction techniques. In order to make these novel estimators easily accessible, the package contains a small number of high-level functions that rely on a broader set of efficient, low-level routines. Generally speaking, intRinsic encompasses models that fall into two categories: homogeneous and heterogeneous intrinsic dimension estimators. The first category contains the two nearest neighbors estimator, a method derived from the distributional properties of the ratios of the distances between each data point and its first two closest neighbors. The functions dedicated to this method carry out inference under both the frequentist and Bayesian frameworks. In the second category, we find the heterogeneous intrinsic dimension algorithm, a Bayesian mixture model for which an efficient Gibbs sampler is implemented. After presenting the theoretical background, we demonstrate the performance of the models on simulated datasets. This way, we can facilitate the exposition by immediately assessing the validity of the results. Then, we employ the package to study the intrinsic dimension of the Alon dataset, obtained from a famous microarray experiment. Finally, we show how the estimation of homogeneous and heterogeneous intrinsic dimensions allows us to gain valuable insights into the topological structure of a dataset.

Many longitudinal studies collect data that have irregular observation times, often requiring the application of linear mixed models with time-varying outcomes. This paper presents an alternative that splits the quantitative analysis into two steps. The first step converts irregularly observed data into a set of repeated measures through the broken stick model. The second step estimates the parameters of scientific interest from the repeated measurements at the subject level. The broken stick model approximates each subject's trajectory by a series of connected straight lines. The breakpoints, specified by the user, divide the time axis into consecutive intervals common to all subjects. Specification of the model requires just three variables: time, measurement and subject. The model is a special case of the linear mixed model, with time as a linear B-spline and subject as the grouping factor. The main assumptions are: Subjects are exchangeable, trajectories between consecutive breakpoints are straight, random effects follow a multivariate normal distribution, and unobserved data are missing at random. The R package brokenstick v2.5.0 offers tools to calculate, predict, impute and visualize broken stick estimates. The package supports two optimization methods, including options to constrain the variance-covariance matrix of the random effects. We demonstrate six applications of the model: Detection of critical periods, estimation of the time-to-time correlations, profile analysis, curve interpolation, multiple imputation and personalized prediction of future outcomes by curve matching.

Recurrent event analyses have found a wide range of applications in biomedicine, public health, and engineering, among others, where study subjects may experience a sequence of event of interest during follow-up. The R package reReg offers a comprehensive collection of practical and easy-to-use tools for regression analysis of recurrent events, possibly with the presence of an informative terminal event. The regression framework is a general scale-change model which encompasses the popular Cox-type model, the accelerated rate model, and the accelerated mean model as special cases. Informative censoring is accommodated through a subject-specific frailty without any need for parametric specification. Different regression models are allowed for the recurrent event process and the terminal event. Also included are visualization and simulation tools.

We introduce a Python library, called jumpdiff, which includes all necessary functions to assess jump-diffusion processes. This library includes functions which compute a set of non-parametric estimators of all contributions composing a jump-diffusion process, namely the drift, the diffusion, and the stochastic jump strengths. Having a set of measurements from a jump-diffusion process, jumpdiff is able to retrieve the evolution equation producing data series statistically equivalent to the series of measurements. The back-end calculations are based on second-order corrections of the conditional moments expressed from the series of Kramers-Moyal coefficients. Additionally, the library is also able to test if stochastic jump contributions are present in the dynamics underlying a set of measurements. Finally, we introduce a simple iterative method for deriving secondorder corrections of any Kramers-Moyal coefficient.

This paper introduces the logitr R package for fast maximum likelihood estimation of multinomial logit and mixed logit models with unobserved heterogeneity across individuals, which is modeled by allowing parameters to vary randomly over individuals according to a chosen distribution. The package is faster than other similar packages such as mlogit, gmnl, mixl, and apollo, and it supports utility models specified with

Despite the large body of research on missing value distributions and imputation, there is comparatively little literature with a focus on how to make it easy to handle, explore, and impute missing values in data. This paper addresses this gap. The new methodology builds upon tidy data principles, with the goal of integrating missing value handling as a key part of data analysis workflows. We define a new data structure, and a suite of new operations. Together, these provide a connected framework for handling, exploring, and imputing missing values. These methods are available in the R package naniar.