Computationally efficient tools for comparing all pairs of profiles in a DNA database. The expectation and covariance of the summary statistic is implemented for fast computing. Routines for estimating proportions of close related individuals are available. The use of wildcards (also called F- designation) is implemented. Dedicated functions ease plotting the results. See Tvedebrink et al. (2012) <doi:10.1016/j.fsigen.2011.08.001>. Compute the distribution of the numbers of alleles in DNA mixtures. See Tvedebrink (2013) <doi:10.1016/j.fsigss.2013.10.142>.

This package performs parametric and non-parametric estimation and simulation of drifting semi-Markov processes. The definition of parametric and non-parametric model specifications is also possible. Furthermore, three different types of drifting semi-Markov models are considered. These models differ in the number of transition matrices and sojourn time distributions used for the computation of a number of semi-Markov kernels, which in turn characterize the drifting semi-Markov kernel. For the parametric model estimation and specification, several discrete distributions are considered for the sojourn times: Uniform, Poisson, Geometric, Discrete Weibull and Negative Binomial. The non-parametric model specification makes no assumptions about the shape of the sojourn time distributions. Semi-Markov models are described in: Barbu, V.S., Limnios, N. (2008) <doi:10.1007/978-0-387-73173-5>. Drifting Markov models are described in: Vergne, N. (2008) <doi:10.2202/1544-6115.1326>. Reliability indicators of Drifting Markov models are described in: Barbu, V. S., Vergne, N. (2019) <doi:10.1007/s11009-018-9682-8>. We acknowledge the DATALAB Project <https://lmrs-num.math.cnrs.fr/projet-datalab.html> (financed by the European Union with the European Regional Development fund (ERDF) and by the Normandy Region) and the HSMM-INCA Project (financed by the French Agence Nationale de la Recherche (ANR) under grant ANR-21-CE40-0005).

This package provides functions providing an easy and intuitive way for fitting and clusters data using the Mixture of Unigrams models by means the Expectation-Maximization algorithm (Nigam, K. et al. (2000). <doi:10.1023/A:1007692713085>), Mixture of Dirichlet-Multinomials estimated by Gradient Descent (Anderlucci, Viroli (2020) <doi:10.1007/s11634-020-00399-3>) and Deep Mixture of Multinomials whose estimates are obtained with Gibbs sampling scheme (Viroli, Anderlucci (2020) <doi:10.1007/s11222-020-09989-9>). There are also functions for graphical representation of clusters obtained.

Load configuration from a .env file, that is in the current working directory, into environment variables.

This package provides a general framework using mixture Weibull distributions to accurately predict biomarker-guided trial duration accounting for heterogeneous population. Extensive simulations are performed to evaluate the impact of heterogeneous population and the dynamics of biomarker characteristics and disease on the study duration. Several influential parameters including median survival time, enrollment rate, biomarker prevalence and effect size are identified. Efficiency gains of biomarker-guided trials can be quantitatively compared to the traditional all-comers design. For reference, see Zhang et al. (2024) <arXiv:2401.00540>.

Calculate multiple or pairwise dissimilarity for orders q = 0-N (CqN; Chao et al. 2008 <doi:10/fcvn63>) for a set of species assemblages or interaction networks.

Quality control and formatting tools developed for the Copernicus Data Rescue Service. The package includes functions to handle the Station Exchange Format (SEF), various statistical tests for climate data at daily and sub-daily resolution, as well as functions to plot the data. For more information and documentation see <https://datarescue.climate.copernicus.eu/st_data-quality-control>.

An interface to explore, analyze, and visualize droplet digital PCR (ddPCR) data in R. This is the first non-proprietary software for analyzing two-channel ddPCR data. An interactive tool was also created and is available online to facilitate this analysis for anyone who is not comfortable with using R.

Statistical methods for retrospectively detecting changes in location and/or dispersion of univariate and multivariate variables. Data values are assumed to be independent, can be individual (one observation at each instant of time) or subgrouped (more than one observation at each instant of time). Control limits are computed, often using a permutation approach, so that a prescribed false alarm probability is guaranteed without making any parametric assumptions on the stable (in-control) distribution. See G. Capizzi and G. Masarotto (2018) <doi:10.1007/978-3-319-75295-2_1> for an introduction to the package.

Develop and evaluate treatment rules based on: (1) the standard indirect approach of split-regression, which fits regressions separately in both treatment groups and assigns an individual to the treatment option under which predicted outcome is more desirable; (2) the direct approach of outcome-weighted-learning proposed by Yingqi Zhao, Donglin Zeng, A. John Rush, and Michael Kosorok (2012) <doi:10.1080/01621459.2012.695674>; (3) the direct approach, which we refer to as direct-interactions, proposed by Shuai Chen, Lu Tian, Tianxi Cai, and Menggang Yu (2017) <doi:10.1111/biom.12676>. Please see the vignette for a walk-through of how to start with an observational dataset whose design is understood scientifically and end up with a treatment rule that is trustworthy statistically, along with an estimation of rule benefit in an independent sample.

This package provides a suite of tools are provided here to support authors in making their research more discoverable. check_keywords() - this function checks the keywords to assess whether they are already represented in the title and abstract. check_fields() - this function compares terminology used across the title, abstract and keywords to assess where terminological diversity (i.e. the use of synonyms) could increase the likelihood of the record being identified in a search. The function looks for terms in the title and abstract that also exist in other fields and highlights these as needing attention. suggest_keywords() - this function takes a full text document and produces a list of unigrams, bigrams and trigrams (1-, 2- or 2-word phrases) present in the full text after removing stop words (words with a low utility in natural language processing) that do not occur in the title or abstract that may be suitable candidates for keywords. suggest_title() - this function takes a full text document and produces a list of the most frequently used unigrams, bigrams and trigrams after removing stop words that do not occur in the abstract or keywords that may be suitable candidates for title words. check_title() - this function carries out a number of sub tasks: 1) it compares the length (number of words) of the title with the mean length of titles in major bibliographic databases to assess whether the title is likely to be too short; 2) it assesses the proportion of stop words in the title to highlight titles with low utility in search engines that strip out stop words; 3) it compares the title with a given sample of record titles from an .ris import and calculates a similarity score based on phrase overlap. This highlights the level of uniqueness of the title. This version of the package also contains functions currently in a non-CRAN package called litsearchr <https://github.com/elizagrames/litsearchr>.

This package provides functionality to infer trajectories from single-cell data, represent them into a common format, and adapt them. Other biological information can also be added, such as cellular grouping, RNA velocity and annotation. Saelens et al. (2019) <doi:10.1038/s41587-019-0071-9>.

Access and manage the application programming interface (API) of the United Nations Office for the Coordination of Humanitarian Affairs (OCHA) ReliefWeb disaster events at <https://reliefweb.int/disasters>. The package requires a minimal number of dependencies. It offers functionality to retrieve a user-defined sample of disaster events from ReliefWeb, providing an easy alternative to scraping the ReliefWeb website. It enables a seamless integration of regular data updates into the research work flow.

The set of teacher/class lessons is completed with a column that allocates a day to each lesson, so that the distribution of lessons by day, by class, and by teacher is as uniform as possible. <https://vlad.bazon.net/>.

Collection of functions for fitting and interpreting distributed lag interaction models (DLIM). A DLIM regresses a scalar outcome on repeated measures of exposure and allows for modification by a continuous variable. Includes a dlim() function for fitting, predict() function for inference, and plotting functions for visualization. Details on methodology are described in Demateis et al. (2024) <doi:10.1002/env.2843>.

Dominance analysis is a method that allows to compare the relative importance of predictors in multiple regression models: ordinary least squares, generalized linear models, hierarchical linear models, beta regression and dynamic linear models. The main principles and methods of dominance analysis are described in Budescu, D. V. (1993) <doi:10.1037/0033-2909.114.3.542> and Azen, R., & Budescu, D. V. (2003) <doi:10.1037/1082-989X.8.2.129> for ordinary least squares regression. Subsequently, the extensions for multivariate regression, logistic regression and hierarchical linear models were described in Azen, R., & Budescu, D. V. (2006) <doi:10.3102/10769986031002157>, Azen, R., & Traxel, N. (2009) <doi:10.3102/1076998609332754> and Luo, W., & Azen, R. (2013) <doi:10.3102/1076998612458319>, respectively.

Mechanisms to parallelize dependent tasks in a manner that optimizes the compute resources available. It provides access to "delayed" computations, which may be parallelized using futures. It is, to an extent, a facsimile of the Dask library (<https://www.dask.org/>), for the Python language.

Builds interactive d3.js hierarchical visualisation easily. D3partitionR makes it easy to build and customize sunburst, circle treemap, treemap, partition chart, ...

Doubly robust average partial effect estimation. This implementation contains methods for adding additional smoothness to plug-in regression procedures and for estimating score functions using smoothing splines. Details of the method can be found in Harvey Klyne and Rajen D. Shah (2023) <doi:10.48550/arXiv.2308.09207>.

Use dynamic programming method to solve l1 convex clustering with identical weights.

This package provides functions for deep learning estimation of Conditional Average Treatment Effects (CATEs) from meta-learner models and Population Average Treatment Effects on the Treated (PATT) in settings with treatment noncompliance using reticulate, TensorFlow and Keras3. Functions in the package also implements the conformal prediction framework that enables computation and illustration of conformal prediction (CP) intervals for estimated individual treatment effects (ITEs) from meta-learner models. Additional functions in the package permit users to estimate the meta-learner CATEs and the PATT in settings with treatment noncompliance using weighted ensemble learning via the super learner approach and R neural networks.

DECORATE (Diverse Ensemble Creation by Oppositional Relabeling of Artificial Training Examples) builds an ensemble of J48 trees by recursively adding artificial samples of the training data ("Melville, P., & Mooney, R. J. (2005) <DOI:10.1016/j.inffus.2004.04.001>").

Distributed Online Goodness-of-Fit Test can process the distributed datasets. The philosophy of the package is described in Guo G.(2024) <doi:10.1016/j.apm.2024.115709>.

This package provides a wrapper on top of the Domino Data Python SDK library. It lets you query and access Domino Data Sources directly from your R environment. Under the hood, Domino Data R SDK leverages the API provided by the Domino Data Python SDK', which must be installed as a prerequisite. Domino is a platform that makes it easy to run your code on scalable hardware, with integrated version control and collaboration features designed for analytical workflows. See <https://docs.dominodatalab.com/en/latest/api_guide/140b48/domino-data-api> for more information.