An implementation of a number of Global Trend models for time series forecasting that are Bayesian generalizations and extensions of some Exponential Smoothing models. The main differences/additions include 1) nonlinear global trend, 2) Student-t error distribution, and 3) a function for the error size, so heteroscedasticity. The methods are particularly useful for short time series. When tested on the well-known M3 dataset, they are able to outperform all classical time series algorithms. The models are fitted with MCMC using the rstan package.

An implementation of EDM algorithms based on research software developed for internal use at the Sugihara Lab ('UCSD/SIO'). The package is implemented with Rcpp wrappers around the cppEDM library. It implements the simplex projection method from Sugihara & May (1990) <doi:10.1038/344734a0>, the S-map algorithm from Sugihara (1994) <doi:10.1098/rsta.1994.0106>, convergent cross mapping described in Sugihara et al. (2012) <doi:10.1126/science.1227079>, and, multiview embedding described in Ye & Sugihara (2016) <doi:10.1126/science.aag0863>.

This package provides implementations of a classifier based on the "Classification Based on Associations" (CBA). It can be used for building classification models from association rules. Rules are pruned in the order of precedence given by the sort criteria and a default rule is added. The final classifier labels provided instances. CBA was originally proposed by Liu, B. Hsu, W. and Ma, Y. Integrating Classification and Association Rule Mining. Proceedings KDD-98, New York, 27-31 August. AAAI. pp80-86 (1998, ISBN:1-57735-070-7).

REAPER is a digital audio production application offering multitrack audio and MIDI recording, editing, processing, mixing and mastering toolset. It supports a vast range of hardware, digital formats and plugins, and can be comprehensively extended, scripted and modified.

Fast tool to calculate the Adjusted Market Inefficiency Measure following Tran & Leirvik (2019) <doi:10.1016/j.frl.2019.03.004>. This tool provides rolling window estimates of the Adjusted Market Inefficiency Measure for multiple instruments simultaneously.

Pair of simple convenience functions to convert a vector of birth dates to age and age distributions. These functions may be helpful when related age and custom age distributions are desired given a vector of birth dates.

An implementation of calls designed to collect and organize in an easy way the data from the Steam API specifically for the Counter-Strike Global Offensive Game (CS Go) <https://developer.valvesoftware.com/wiki/Steam_Web_API>.

Estimate the direct and indirect (mediation) effects of treatment on the outcome when intermediate variables (mediators) are compositional and high-dimensional. Sohn, M.B. and Li, H. (2017). Compositional Mediation Analysis for Microbiome Studies. (AOAS: In revision).

Connectome Predictive Modelling (CPM) (Shen et al. (2017) <doi:10.1038/nprot.2016.178>) is a method to predict individual differences in behaviour from brain functional connectivity. cpmr provides a simple yet efficient implementation of this method.

Given a collection of intervals with integer start and end positions, find recurrently targeted regions and estimate the significance of finding. Randomization is implemented by parallel methods, either using local host machines, or submitting grid engine jobs.

Tissue-specific enrichment analysis to assess lists of candidate genes or RNA-Seq expression profiles. Pei G., Dai Y., Zhao Z. Jia P. (2019) deTS: Tissue-Specific Enrichment Analysis to decode tissue specificity. Bioinformatics, In submission.

This package implements the de-biased estimator for low-rank matrix completion and provides confidence intervals for entries of interest. See: by Chen et al. (2019) <doi:10.1073/pnas.1910053116>, Mai (2021) <arXiv:2103.11749>.

This package provides a wrapper for the API of the Danish Parliament. It makes it possible to get data from the API easily into a data frame. Learn more at <http://www.ft.dk/dokumenter/aabne_data>.

Server implementation of GraphQL <http://graphql.github.io/graphql-spec/>, a query language originally created by Facebook for describing data requirements on complex application data models. Visit <http://graphql.org> to learn more about GraphQL'.

This package provides a framework for multiple imputation for proteomics is proposed by Marie Chion, Christine Carapito and Frederic Bertrand (2021) <doi:10.1371/journal.pcbi.1010420>. It is dedicated to dealing with multiple imputation for proteomics.

This package provides a PNAS'-alike style for rmarkdown', derived from the Proceedings of the National Academy of Sciences of the United States of America ('PNAS') LaTeX style, and adapted for use with markdown and pandoc'.

Perform meta-analysis of single-case experiments, including calculating various effect size measures (SMD, PND, PEM and NAP) and probability combining (additive and multiplicative method), as discussed in Bulte and Onghena (2013) <doi:10.22237/jmasm/1383280020>.

This package provides a simple wrapper to easily design vanilla deep neural networks using Tensorflow'/'Keras backend for regression, classification and multi-label tasks, with some tweaks and tricks (skip shortcuts, embedding, feature selection and anomaly detection).

Succinctly and correctly format statistical summaries of various models and tests (F-test, Chi-Sq-test, Fisher-test, T-test, and rank-significance). This package also includes empirical tests, such as Monte Carlo and bootstrap distribution estimates.

Counting election votes and determining election results by different methods, including the single transferable vote or ranked choice, approval, score, plurality, condorcet and two-round runoff methods (Raftery et al., 2021 <doi:10.32614/RJ-2021-086>).

Analyze given data frame with multiple endpoints and return Kaplan-Meier survival probabilities together with the specified confidence interval. See Nabipoor M, Westerhout CM, Rathwell S, and Bakal JA (2023) <doi:10.1186/s12874-023-01857-0>.

R clients to the Web of Science and InCites <https://clarivate.com/products/data-integration/> APIs, which allow you to programmatically download publication and citation data indexed in the Web of Science and InCites databases.

Assigning probability scores to protein interactions captured in affinity purification mass spectrometry (AP-MS) expriments to infer protein-protein interactions. The output would facilitate non-specific background removal as contaminants are commonly found in AP-MS data.

This package helps with the analysis of array CGH data by detecting of the breakpoints in the genomic profiles and assignment of a status (gain, normal or loss) to each chromosomal regions identified.