Implementation of some Individual Based Models (IBMs, sensu Grimm and Railsback 2005) and methods to create new ones, particularly for population dynamics models (reproduction, mortality and movement). The basic operations for the simulations are implemented in Rcpp for speed.

Synthesize images into characteristic features for time-series analysis or machine learning applications. The package was originally intended for monitoring volcanic eruptions in video data by highlighting and extracting regions above the vent associated with plume activity. However, the functions within are general and have wide applications for image processing, analyzing, filtering, and plotting.

This package performs Invariant Coordinate Selection (ICS) (Tyler, Critchley, Duembgen and Oja (2009) <doi:10.1111/j.1467-9868.2009.00706.x>) and especially ICS for multivariate outlier detection with application to quality control (Archimbaud, Nordhausen, Ruiz-Gazen (2018) <doi:10.1016/j.csda.2018.06.011>) using a shiny app.

This package provides access to low-level operating system mechanisms for performing atomic operations on shared data structures. Mutexes provide shared and exclusive locks. Semaphores act as counters. Message queues move text strings from one process to another. All these interprocess communication (IPC) tools can optionally block with or without a timeout. Implemented using the cross-platform boost C++ library <https://www.boost.org/doc/libs/release/libs/interprocess/>.

This package provides coefficients of interrater reliability that are generalized to cope with randomly incomplete (i.e. unbalanced) datasets without any imputation of missing values or any (row-wise or column-wise) omissions of actually available data. Applied to complete (balanced) datasets, these generalizations yield the same results as the common procedures, namely the Intraclass Correlation according to McGraw & Wong (1996) \doi10.1037/1082-989X.1.1.30 and the Coefficient of Concordance according to Kendall & Babington Smith (1939) \doi10.1214/aoms/1177732186.

This network estimation procedure eLasso, which is based on the Ising model, combines l1-regularized logistic regression with model selection based on the Extended Bayesian Information Criterion (EBIC). EBIC is a fit measure that identifies relevant relationships between variables. The resulting network consists of variables as nodes and relevant relationships as edges. Can deal with binary data.

This package provides functions to build, evaluate, and visualize insurance rating models. It simplifies the process of modeling premiums, and allows to analyze insurance risk factors effectively. The package employs a data-driven strategy for constructing insurance tariff classes, drawing on the work of Antonio and Valdez (2012) <doi:10.1007/s10182-011-0152-7>.

Reads the output of the PerkinElmer InForm software <http://www.perkinelmer.com/product/inform-cell-analysis-one-seat-cls135781>. In addition to cell-density count, it can derive statistics of intercellular spatial distance for each cell-type.

Carries out integrative clustering analysis using multiple types of genomic dataset using integrative Non-negative Matrix factorization.

This package provides a graphical user interface to the IsoplotR package for radiometric geochronology. The GUI runs in an internet browser and can either be used offline, or hosted on a server to provide online access to the IsoplotR toolbox.

Check if an externalptr is a null pointer. R does currently not have a native function for that purpose. This package contains a C function that returns TRUE in case of a null pointer.

Interface to the OpenGWAS database API <https://api.opengwas.io/api/>. Includes a wrapper to make generic calls to the API, plus convenience functions for specific queries.

Generates efficient designs for discrete choice experiments based on the multinomial logit model, and individually adapted designs for the mixed multinomial logit model. The generated designs can be presented on screen and choice data can be gathered using a shiny application. Traets F, Sanchez G, and Vandebroek M (2020) <doi:10.18637/jss.v096.i03>.

Decomposition of income inequality by groups formed of individuals possessing similar characteristics (e.g., sex, education, age) and their income sources at the same time. Decomposition of the Theil index is based on Giammatteo, M. (2007) <https://www.lisdatacenter.org/wps/liswps/466.pdf>. Decomposition of the squared coefficient of variation is based on Garcia-Penalosa, C., & Orgiazzi, E. (2013) <doi:10.1111/roiw.12054>.

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 tools for passing messages between R processes. Shiny examples are provided showing how to perform useful tasks such as: updating reactive values from within a future, progress bars for long running async tasks, and interrupting async tasks based on user input.

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.

Geostatistical interpolation has traditionally been done by manually fitting a variogram and then interpolating. Here, we introduce classes and methods that can do this interpolation automatically. Pebesma et al (2010) gives an overview of the methods behind and possible usage <doi:10.1016/j.cageo.2010.03.019>.

ISA is a metadata framework to manage an increasingly diverse set of life science, environmental and biomedical experiments. In isatabr methods for reading, modifying and writing of files in the ISA-Tab format are implemented. It also contains methods for processing assay data.

Finds optimal designs for nonlinear models using a metaheuristic algorithm called Imperialist Competitive Algorithm (ICA). See, for details, Masoudi et al. (2022) <doi:10.32614/RJ-2022-043>, Masoudi et al. (2017) <doi:10.1016/j.csda.2016.06.014> and Masoudi et al. (2019) <doi:10.1080/10618600.2019.1601097>.

This package implements a nonparametric maximum likelihood method for assessing potentially time-varying vaccine efficacy (VE) against SARS-CoV-2 infection under staggered enrollment and time-varying community transmission, allowing crossover of placebo volunteers to the vaccine arm. Lin, D. Y., Gu, Y., Zeng, D., Janes, H. E., and Gilbert, P. B. (2021) <doi:10.1093/cid/ciab630>.

Estimate test-retest reliability for complex sampling strategies and extract variances using IntraClass Effect Decomposition. Developed by Brandmaier et al. (2018) "Assessing reliability in neuroimaging research through intra-class effect decomposition (ICED)" <doi:10.7554/eLife.35718> Also includes functions to simulate data based on sampling strategy. Unofficial version release name: "Good work squirrels".

This package provides functions to access data from public RESTful APIs including World Bank API', and REST Countries API', retrieving real-time or historical data related to India, such as economic indicators, and international demographic and geopolitical indicators. Additionally, the package includes one of the largest curated collections of open datasets focused on India, covering topics such as population, economy, weather, politics, health, biodiversity, sports, agriculture, cybercrime, infrastructure, and more. 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: World Bank API <https://datahelpdesk.worldbank.org/knowledgebase/articles/889392>, REST Countries API <https://restcountries.com/>.

This package provides a dataset of the top colours of photos from Instagram taken in 2014 in the city of Vancouver, British Columbia, Canada. It consists of: top colour and counts data. This data was obtained using the Instagram API. Instagram is a web photo sharing service. It can be found at: <https://instagram.com>. The Instagram API is documented at: <https://instagram.com/developer/>.