Designed for analyzing the Medical Information Mart for Intensive Care(MIMIC) dataset, a repository of freely accessible electronic health records. MIMER(MIMIC-enabled Research) package, offers a suite of data wrangling functions tailored specifically for preparing the dataset for research purposes, particularly in antimicrobial resistance(AMR) studies. It simplifies complex data manipulation tasks, allowing researchers to focus on their primary inquiries without being bogged down by wrangling complexities.

Functions, data sets and examples for the book: Yves Croissant (2024) "Microeconometrics with R", Chapman and Hall/CRC The R Series. The package includes a set of estimators for models used in microeconometrics, especially for count data and limited dependent variables. Test functions include score test, Hausman test, Vuong test, Sargan test and conditional moment test. A small subset of the data set used in the book is also included.

The package aims to identify miRNA sponge or ceRNA modules in heterogeneous data. It provides several functions to study miRNA sponge modules at single-sample and multi-sample levels, including popular methods for inferring gene modules (candidate miRNA sponge or ceRNA modules), and two functions to identify miRNA sponge modules at single-sample and multi-sample levels, as well as several functions to conduct modular analysis of miRNA sponge modules.

There is an increasing interest in investigating how the compositions of microbial communities are associated with human health and disease. In this package, we present a novel global testing method called aMiSPU, that is highly adaptive and thus high powered across various scenarios, alleviating the issue with the choice of a phylogenetic distance. Our simulations and real data analysis demonstrated that aMiSPU test was often more powerful than several competing methods while correctly controlling type I error rates.

This package implements methods for estimating generalized estimating equations (GEE) with advanced options for flexible modeling and handling missing data. This package provides tools to fit and analyze GEE models for longitudinal data, allowing users to address missingness using a variety of imputation techniques. It supports both univariate and multivariate modeling, visualization of missing data patterns, and facilitates the transformation of data for efficient statistical analysis. Designed for researchers working with complex datasets, it ensures robust estimation and inference in longitudinal and clustered data settings.

Calculate dissolved gas concentrations from raw MIMS (Membrane Inlet Mass Spectrometer) signal data. Use mimsy() on a formatted CSV file to return dissolved gas concentrations (mg and microMole) of N2, O2, Ar based on gas solubility at temperature, pressure, and salinity. See references Benson and Krause (1984), Garcia and Gordon (1992), Stull (1947), and Hamme and Emerson (2004) for more information. Easily save the output to a nicely-formatted multi-tab Excel workbook with mimsy.save(). Supports dual-temperature standard calibration for dual-bath MIMS setups.

This package provides a guidance system for analysis with missing data. It incorporates expert, up-to-date methodology to help researchers choose the most appropriate analysis approach when some data are missing. You provide the available data and the assumed causal structure, including the likely causes of missing data. midoc will advise which analysis approaches can be used, and how best to perform them. midoc follows the framework for the treatment and reporting of missing data in observational studies (TARMOS). Lee et al (2021). <doi:10.1016/j.jclinepi.2021.01.008>.

MIRit is an R package that provides several methods for investigating the relationships between miRNAs and genes in different biological conditions. In particular, MIRit allows to explore the functions of dysregulated miRNAs, and makes it possible to identify miRNA-gene regulatory axes that control biological pathways, thus enabling the users to unveil the complexity of miRNA biology. MIRit is an all-in-one framework that aims to help researchers in all the central aspects of an integrative miRNA-mRNA analyses, from differential expression analysis to network characterization.

This package provides an intuitive framework for ad-hoc statistical analysis of 1H-NMR metabolomics by Nightingale Health. It allows to easily explore new metabolomics measurements assayed by Nightingale Health, comparing the distributions with a large Consortium (BBMRI-nl); project previously published metabolic scores [<doi:10.1016/j.ebiom.2021.103764>, <doi:10.1161/CIRCGEN.119.002610>, <doi:10.1038/s41467-019-11311-9>, <doi:10.7554/eLife.63033>, <doi:10.1161/CIRCULATIONAHA.114.013116>, <doi:10.1007/s00125-019-05001-w>]; and calibrate the metabolic surrogate values to a desired dataset.

Designed for simplicity, a mirai evaluates an R expression asynchronously in a parallel process, locally or distributed over the network. The result is automatically available upon completion. Modern networking and concurrency, built on nanonext and NNG (Nanomsg Next Gen), ensures reliable and efficient scheduling over fast inter-process communications or TCP/IP secured by TLS. Distributed computing can launch remote resources via SSH or cluster managers. An inherently queued architecture handles many more tasks than available processes, and requires no storage on the file system. Innovative features include support for otherwise non-exportable reference objects, event-driven promises, and asynchronous parallel map.

Estimates random effect latent measurement models, wherein the loadings, residual variances, intercepts, latent means, and latent variances all vary across groups. The random effect variances of the measurement parameters are then modeled using a hierarchical inclusion model, wherein the inclusion of the variances (i.e., whether it is effectively zero or non-zero) is informed by similar parameters (of the same type, or of the same item). This additional hierarchical structure allows the evidence in favor of partial invariance to accumulate more quickly, and yields more certain decisions about measurement invariance. Martin, Williams, and Rast (2020) <doi:10.31234/osf.io/qbdjt>.

Microbial growth is often measured by growth curves i.e. a table of population sizes and times of measurements. This package allows to use such growth curve data to determine the duration of "microbial lag phase" i.e. the time needed for microbes to restart divisions. It implements the most commonly used methods to calculate the lag duration, these methods are discussed and described in Opalek et.al. 2022. Citation: Smug, B. J., Opalek, M., Necki, M., & Wloch-Salamon, D. (2024). Microbial lag calculator: A shiny-based application and an R package for calculating the duration of microbial lag phase. Methods in Ecology and Evolution, 15, 301â 307 <doi:10.1111/2041-210X.14269>.

Map image classification efficacy (MICE) adjusts the accuracy rate relative to a random classification baseline (Shao et al. (2021)<doi:10.1109/ACCESS.2021.3116526> and Tang et al. (2024)<doi:10.1109/TGRS.2024.3446950>). Only the proportions from the reference labels are considered, as opposed to the proportions from the reference and predictions, as is the case for the Kappa statistic. This package offers means to calculate MICE and adjusted versions of class-level user's accuracy (i.e., precision) and producer's accuracy (i.e., recall) and F1-scores. Class-level metrics are aggregated using macro-averaging. Functions are also made available to estimate confidence intervals using bootstrapping and statistically compare two classification results.

This is a method (MinED) for mining probability distributions using deterministic sampling which is proposed by Joseph, Wang, Gu, Lv, and Tuo (2019) <DOI:10.1080/00401706.2018.1552203>. The MinED samples can be used for approximating the target distribution. They can be generated from a density function that is known only up to a proportionality constant and thus, it might find applications in Bayesian computation. Moreover, the MinED samples are generated with much fewer evaluations of the density function compared to random sampling-based methods such as MCMC and therefore, this method will be especially useful when the unnormalized posterior is expensive or time consuming to evaluate. This research is supported by a U.S. National Science Foundation grant DMS-1712642.

mitch is an R package for multi-contrast enrichment analysis. At it’s heart, it uses a rank-MANOVA based statistical approach to detect sets of genes that exhibit enrichment in the multidimensional space as compared to the background. The rank-MANOVA concept dates to work by Cox and Mann (https://doi.org/10.1186/1471-2105-13-S16-S12). mitch is useful for pathway analysis of profiling studies with one, two or more contrasts, or in studies with multiple omics profiling, for example proteomic, transcriptomic, epigenomic analysis of the same samples. mitch is perfectly suited for pathway level differential analysis of scRNA-seq data. We have an established routine for pathway enrichment of Infinium Methylation Array data (see vignette). The main strengths of mitch are that it can import datasets easily from many upstream tools and has advanced plotting features to visualise these enrichments.

This package contains a mixture of statistical methods including the MCMC methods to analyze normal mixtures. Additionally, model based clustering methods are implemented to perform classification based on (multivariate) longitudinal (or otherwise correlated) data. The basis for such clustering is a mixture of multivariate generalized linear mixed models. The package is primarily related to the publications Komárek (2009, Comp. Stat. and Data Anal.) <doi:10.1016/j.csda.2009.05.006> and Komárek and Komárková (2014, J. of Stat. Soft.) <doi:10.18637/jss.v059.i12>. It also implements methods published in Komárek and Komárková (2013, Ann. of Appl. Stat.) <doi:10.1214/12-AOAS580>, Hughes, Komárek, Bonnett, Czanner, Garcà a-Fiñana (2017, Stat. in Med.) <doi:10.1002/sim.7397>, Jaspers, Komárek, Aerts (2018, Biom. J.) <doi:10.1002/bimj.201600253> and Hughes, Komárek, Czanner, Garcà a-Fiñana (2018, Stat. Meth. in Med. Res) <doi:10.1177/0962280216674496>.

Miscellaneous functions for (1) data management (e.g., grand-mean and group-mean centering, coding variables and reverse coding items, scale and cluster scores, reading and writing Excel and SPSS files), (2) descriptive statistics (e.g., frequency table, cross tabulation, effect size measures), (3) missing data (e.g., descriptive statistics for missing data, missing data pattern, Little's test of Missing Completely at Random, and auxiliary variable analysis), (4) multilevel data (e.g., multilevel descriptive statistics, within-group and between-group correlation matrix, multilevel confirmatory factor analysis, level-specific fit indices, cross-level measurement equivalence evaluation, multilevel composite reliability, and multilevel R-squared measures), (5) item analysis (e.g., confirmatory factor analysis, coefficient alpha and omega, between-group and longitudinal measurement equivalence evaluation), (6) statistical analysis (e.g., bootstrap confidence intervals, collinearity and residual diagnostics, dominance analysis, between- and within-subject analysis of variance, latent class analysis, t-test, z-test, sample size determination), and (7) functions to interact with Blimp and Mplus'.

Companion package of Carrion-i-Silvestre & Sansó (2023): "Generalized Extreme Value Approximation to the CUMSUMQ Test for Constant Unconditional Variance in Heavy-Tailed Time Series". It implements the Modified Iterative Cumulative Sum of Squares Algorithm, which is an extension of the Iterative Cumulative Sum of Squares (ICSS) Algorithm of Inclan and Tiao (1994), and it checks for changes in the unconditional variance of a time series controlling for the tail index of the underlying distribution. The fourth order moment is estimated non-parametrically to avoid the size problems when the innovations are non-Gaussian (see, Sansó et al., 2004). Critical values and p-values are generated using a Generalized Extreme Value distribution approach. References Carrion-i-Silvestre J.J & Sansó A (2023) <https://www.ub.edu/irea/working_papers/2023/202309.pdf>. Inclan C & Tiao G.C (1994) <doi:10.1080/01621459.1994.10476824>, Sansó A & Aragó V & Carrion-i-Silvestre J.L (2004) <https://dspace.uib.es/xmlui/bitstream/handle/11201/152078/524035.pdf>.

This package provides a collection of miscellaneous 3d plots, including isosurfaces.

This package provides tools for estimating, measuring and working with migration data.

This package provides UI widget and layout functions for writing Shiny apps that work well on small screens.

This package provides functions for creating designs for mixture experiments, making ternary contour plots, and making mixture effect plots.

The package contains functions for inferece of target gene regulation by miRNA, based on only target gene expression profile.

Mixed variable optimization for non-linear functions. Can optimize function whose inputs are a combination of continuous, ordered, and unordered variables.