Chi-square tests are computed with corrections.

This package provides methods to perform and analyse I-prior regression models. Estimation is done either via direct optimisation of the log-likelihood or an EM algorithm.

Launches a shiny application generating code to view tables in several ways, import/export tables, modify tables, make some basic graphics. IGoR is a graphic user interface designed to help beginners using simple functions around table management and exploration. Inspired by Rcmdr', IGoR is a code generator that, with simple inputs under a Shiny application, provides R code mainly built around the tidyverse or some packages in the direct line of the Mosaic project: the rio and ggformula packages. The generated code doesn't depend on IGoR and can be manually modified by the user or copied elsewhere.

Regression models for interval censored data. Currently supports Cox-PH, proportional odds, and accelerated failure time models. Allows for semi and fully parametric models (parametric only for accelerated failure time models) and Bayesian parametric models. Includes functions for easy visual diagnostics of model fits and imputation of censored data.

This package provides a tiny parser to extract mass spectra data and metadata table of mass spectrometry acquisition properties from mzML, mzXML and netCDF files introduced in <doi:10.1021/acs.jproteome.2c00120>.

Method for the calculation of copy numbers and calling of copy number alterations. The algorithm uses coverage data from amplicon sequencing of a sample cohort as input. The method includes significance assessment, correction for multiple testing and does not depend on normal DNA controls. Budczies (2016 Mar 15) <doi:10.18632/oncotarget.7451>.

The digits of the old version (before 2000 year) of Chinese ID Card Number is 15, this package aims to update to the current version of 18 digits. Besides, this package can help check whether the given ID is right or not.

Using embedded sdmx queries, get the data of more than 150 000 insee series from bdm macroeconomic database.

This package provides classes and functions for metrics calculation as part of the EarthScope MUSTANG project. The functionality in this package builds upon the base classes of the IRISSeismic package. Metrics include basic statistics as well as higher level health metrics that can help identify problematic seismometers.

An open source library for face detection in images. Provides a pretrained convolutional neural network based on <https://github.com/ShiqiYu/libfacedetection> which can be used to detect faces which have size greater than 10x10 pixels.

Send emails using the mailgun api. To use this package you will need an account from <https://www.mailgun.com> .

Let us consider a sample of patients who can suffer from several diseases simultaneously, in a given set of diseases. The goal of the implemented algorithm is to estimate the individual average cost of each disease, starting from the global health costs available for each patient.

This package implements the integrative conditional autoregressive horseshoe model discussed in Jendoubi, T., Ebbels, T.M. Integrative analysis of time course metabolic data and biomarker discovery. BMC Bioinformatics 21, 11 (2020) <doi:10.1186/s12859-019-3333-0>. The model consists in three levels: Metabolic pathways level modeling interdependencies between variables via a conditional auto-regressive (CAR) component, integrative analysis level to identify potential associations between heterogeneous omic variables via a Horseshoe prior and experimental design level to capture experimental design conditions through a mixed-effects model. The package also provides functions to simulate data from the model, construct pathway matrices, post process and plot model parameters.

This package provides a set of tools for processing and analyzing in vitro toxicokinetic measurements in a standardized and reproducible pipeline. The package was developed to perform frequentist and Bayesian estimation on a variety of in vitro toxicokinetic measurements including -- but not limited to -- chemical fraction unbound in the presence of plasma (f_up), intrinsic hepatic clearance (Clint, uL/min/million hepatocytes), and membrane permeability for oral absorption (Caco2). The methods provided by the package were described in Wambaugh et al. (2019) <doi:10.1093/toxsci/kfz205>.

Generate interactive volcano plots for exploring gene expression data. Built with ggplot2', the plots are rendered interactive using ggiraph', enabling users to hover over points to display detailed information or click to trigger custom actions.

An implementation of the Harris Corner Detection as described in the paper "An Analysis and Implementation of the Harris Corner Detector" by Sánchez J. et al (2018) available at <doi:10.5201/ipol.2018.229>. The package allows to detect relevant points in images which are characteristic to the digital image.

This package provides a set of functions to analyse and compare texts, using classical text mining functions, as well as those from theoretical ecology.

An instrumental variable estimator under structural cumulative additive intensity model is fitted, that leverages initial randomization as the IV. The estimator can be used to fit an additive hazards model under time to event data which handles treatment switching (treatment crossover) correctly. We also provide a consistent variance estimate.

Several functions to calculate two important indexes (IBR (Integrated Biomarker Response) and IBRv2 (Integrated Biological Response version 2)), it also calculates the standardized values for enzyme activity for each index, and it has a graphing function to perform radarplots that make great data visualization for this type of data. Beliaeff, B., & Burgeot, T. (2002). <https://pubmed.ncbi.nlm.nih.gov/12069320/>. Sanchez, W., Burgeot, T., & Porcher, J.-M. (2013).<doi:10.1007/s11356-012-1359-1>. Devin, S., Burgeot, T., Giambérini, L., Minguez, L., & Pain-Devin, S. (2014). <doi:10.1007/s11356-013-2169-9>. Minato N. (2022). <https://minato.sip21c.org/msb/>.

Deconvolution of mixed tumour profiles into normal and cancer for each patient, using the ISOpure algorithm in Quon et al. Genome Medicine, 2013 5:29. Deconvolution requires mixed tumour profiles and a set of unmatched "basis" normal profiles.

Manipulate integer-bounded intervals including finding overlaps, piling and merging.

Generalised linear models via the iteratively reweighted least squares algorithm. The functions perform logistic, Poisson and Gamma regression (ISBN:9780412317606), either for a single model or many regression models in a column-wise fashion.

Fit mixed-effects location scale models with spike-and-slab priors on the location random effects to identify units with unusual residual variances. The method is described in detail in Carmo, Williams and Rast (2025) <https://osf.io/sh6ne>.

Different functions includes constructing composite indicators, imputing missing data, and evaluating imputation techniques. Additionally, different tools for data normalization. Detailed methodologies of Indicator package are: OECD/European Union/EC-JRC (2008), "Handbook on Constructing Composite Indicators: Methodology and User Guide", OECD Publishing, Paris, <DOI:10.1787/533411815016>, Matteo Mazziotta & Adriano Pareto, (2018) "Measuring Well-Being Over Time: The Adjusted Mazziottaâ Pareto Index Versus Other Non-compensatory Indices" <DOI:10.1007/s11205-017-1577-5> and De Muro P., Mazziotta M., Pareto A. (2011), "Composite Indices of Development and Poverty: An Application to MDGs" <DOI:10.1007/s11205-010-9727-z>.