Starting from user-supplied institutional data, these scripts transform, aggregate, and reshape the information to produce key-value pair data files that are able to be uploaded to IPEDS (Integrated Postsecondary Education Data System) through their submission portal <https://surveys.nces.ed.gov/ipeds/>. Starting data specifications can be found in the vignettes. Final files are saved locally to a location of the user's choice. User-friendly readable files can also be produced for purposes of data review and validation.

This package provides tools for assessment and quantification of individual identity information in animal signals. This package accompanies a research article by Linhart et al. (2019) <doi:10.1101/546143>: "Measuring individual identity information in animal signals: Overview and performance of available identity metrics".

Compute distributional quantities for an Integrated Gamma (IG) or Integrated Gamma Limit (IGL) copula, such as a cdf and density. Compute corresponding conditional quantities such as the cdf and quantiles. Generate data from an IG or IGL copula. See the vignette for formulas, or for a derivation, see Coia, V (2017) "Forecasting of Nonlinear Extreme Quantiles Using Copula Models." PhD Dissertation, The University of British Columbia.

This package provides a novel machine learning method for plant viruses diagnostic using genome sequencing data. This package includes three different machine learning models, random forest, XGBoost, and elastic net, to train and predict mapped genome samples. Mappability profile and unreliable regions are introduced to the algorithm, and users can build a mappability profile from scratch with functions included in the package. Plotting mapped sample coverage information is provided.

This package contains several tools to treat imaging flow cytometry data from ImageStream® and FlowSight® cytometers ('Amnis® Cytek®'). Provides an easy and simple way to read and write .fcs, .rif, .cif and .daf files. Information such as masks, features, regions and populations set within these files can be retrieved for each single cell. In addition, raw data such as images stored can also be accessed. Users, may hopefully increase their productivity thanks to dedicated functions to extract, visualize, manipulate and export IFC data. Toy data example can be installed through the IFCdata package of approximately 32 MB, which is available in a drat repository <https://gitdemont.github.io/IFCdata/>. See file COPYRIGHTS and file AUTHORS for a list of copyright holders and authors.

This package provides a joint mixture model has been developed by Majumdar et al. (2025) <doi:10.48550/arXiv.2412.17511> that integrates information from gene expression data and methylation data at the modelling stage to capture their inherent dependency structure, enabling simultaneous identification of differentially methylated cytosine-guanine dinucleotide (CpG) sites and differentially expressed genes. The model leverages a joint likelihood function that accounts for the nested structure in the data, with parameter estimation performed using an expectation-maximisation algorithm.

Allows an interactive assessment of the timing of interim analyses. The algorithm simulates both the recruitment and treatment/event phase of a clinical trial based on the package interim'.

This package provides a pipeline to process nominal mass spectrometry data to create .msp files for untargeted analyses.

An implementation to reconstruct individual patient data from Kaplan-Meier (K-M) survival curves, visualize and assess the accuracy of the reconstruction, then perform secondary analysis on the reconstructed data. We involve a simple function to extract the coordinates form the published K-M curves. The function is developed based on Poisot T. â s digitize package (2011) <doi:10.32614/RJ-2011-004> . For more complex and tangled together graphs, digitizing software, such as DigitizeIt (for MAC or windows) or ScanIt'(for windows) can be used to get the coordinates. Additional information should also be involved to increase the accuracy, like numbers of patients at risk (often reported at 5-10 time points under the x-axis of the K-M graph), total number of patients, and total number of events. The package implements the modified iterative K-M estimation algorithm (modified-iKM) improved upon the approach proposed by Guyot (2012) <doi:10.1186/1471-2288-12-9> with some modifications.

This package provides composable invertible transforms for (sparse) matrices.

This package provides functions to access data from public RESTful APIs including Nager.Date', World Bank API', and REST Countries API', retrieving real-time or historical data related to Indonesia, such as holidays, economic indicators, and international demographic and geopolitical indicators. The package also includes a curated collection of open datasets focused on Indonesia, covering topics such as consumer prices, poverty probability, food prices by region, tourism destinations, and minimum wage statistics. The package supports reproducible research and teaching by integrating reliable international APIs and structured datasets from public, academic, and government sources. For more information on the APIs, see: Nager.Date <https://date.nager.at/Api>, World Bank API <https://datahelpdesk.worldbank.org/knowledgebase/articles/889392>, and REST Countries API <https://restcountries.com/>.

This package contains a number of infix binary operators that may be useful in day to day practices.

Convert between bookmaker odds and probabilities. Eight different algorithms are available, including basic normalization, Shin's method (Hyun Song Shin, (1992) <doi:10.2307/2234526>), and others.

This package provides a collection of Irucka Embry's miscellaneous USGS data sets (USGS Parameter codes with fixed values, USGS global time zone codes, and US Air Force Global Engineering Weather Data). Irucka created these data sets while a Cherokee Nation Technology Solutions (CNTS) United States Geological Survey (USGS) Contractor and/or USGS employee.

This package provides user-friendly tools for calibration in survey sampling. The package is production-oriented, and its interface is inspired by the famous popular macro Calmar for SAS, so that Calmar users can quickly get used to icarus'. In addition to calibration (with linear, raking and logit methods), icarus features functions for calibration on tight bounds and penalized calibration.

Simulation of segments shared identical-by-descent (IBD) by pedigree members. Using sex specific recombination rates along the human genome (Halldorsson et al. (2019) <doi:10.1126/science.aau1043>), phased chromosomes are simulated for all pedigree members. Applications include calculation of realised relatedness coefficients and IBD segment distributions. ibdsim2 is part of the pedsuite collection of packages for pedigree analysis. A detailed presentation of the pedsuite', including a separate chapter on ibdsim2', is available in the book Pedigree analysis in R (Vigeland, 2021, ISBN:9780128244302). A Shiny app for visualising and comparing IBD distributions is available at <https://magnusdv.shinyapps.io/ibdsim2-shiny/>.

Leveraging information-theoretic measures like mutual information and v-measure to quantify spatial associations between patterns (Nowosad and Stepinski (2018) <doi:10.1080/13658816.2018.1511794>; Bai, H. et al. (2023) <doi:10.1080/24694452.2023.2223700>).

This package provides a port of Python's excellent itertools module to R for efficient looping.

It provides a general framework to analyse dependence between point processes in time. It includes parametric and non-parametric tests to study independence, and functions for generating and analysing different types of dependence.

Estimation and diagnostic tools for instrumental variables designs, which implements the guidelines proposed in Lal et al. (2023) <arXiv:2303.11399>, including bootstrapped confidence intervals, effective F-statistic, Anderson-Rubin test, valid-t ratio test, and local-to-zero tests.

Carries out instrumental variable estimation of causal effects, including power analysis, sensitivity analysis, and diagnostics. See Kang, Jiang, Zhao, and Small (2020) <http://pages.cs.wisc.edu/~hyunseung/> for details.

This package provides tools to analyze point patterns in space occurring over planar network structures derived from graph-related intensity measures for undirected, directed, and mixed networks. This package is based on the following research: Eckardt and Mateu (2018) <doi:10.1080/10618600.2017.1391695>. Eckardt and Mateu (2021) <doi:10.1007/s11749-020-00720-4>.

Imputation (replacement) of missing values in univariate time series. Offers several imputation functions and missing data plots. Available imputation algorithms include: Mean', LOCF', Interpolation', Moving Average', Seasonal Decomposition', Kalman Smoothing on Structural Time Series models', Kalman Smoothing on ARIMA models'. Published in Moritz and Bartz-Beielstein (2017) <doi:10.32614/RJ-2017-009>.

Note that imageData has been superseded by growthPheno'. The package growthPheno incorporates all the functionality of imageData and has functionality not available in imageData', but some imageData functions have been renamed. The imageData package is no longer maintained, but is retained for legacy purposes.