This package provides a toolbox to read all R files inside a package and automatically generate @importFrom roxygen2 tags in the right place. Includes a shiny application to review the changes before applying them.

Inference of protein complex states from quantitative proteomics data. The package takes information on known stable protein interactions (i.e. protein components of the same complex) and assesses how protein quantitative ratios change between different conditions. It reports protein pairs for which relative protein quantities to each other have been significantly altered in the tested condition.

Computationally efficient procedures for regularized estimation with the semiparametric additive hazards regression model.

The goal of amp.sim is to transform NONMEM models into R syntax so they can be used for simulations using the deSolve', nlmixr2 or mrgsolve package. Additionally, functionality is included to aid simulations performed directly in NONMEM and to automatically create shiny apps for simulation models.

This package provides functions for Accurate and Speedy linkage map construction, manipulation and diagnosis of Doubled Haploid, Backcross and Recombinant Inbred R/qtl objects. This includes extremely fast linkage map clustering and optimal marker ordering using MSTmap (see Wu et al.,2008).

This package provides an efficient suite of R tools for scorecard modeling, analysis, and visualization. Including equal frequency binning, equidistant binning, K-means binning, chi-square binning, decision tree binning, data screening, manual parameter modeling, fully automatic generation of scorecards, etc. This package is designed to make scorecard development easier and faster. References include: 1. <http://shichen.name/posts/>. 2. Dong-feng Li(Peking University),Class PPT. 3. <https://zhuanlan.zhihu.com/p/389710022>. 4. <https://www.zhangshengrong.com/p/281oqR9JNw/>.

Perform first- and second-order multi-scale analyses derived from Ripley K-function (Ripley B. D. (1977) <doi:10.1111/j.2517-6161.1977.tb01615.x>), for univariate, multivariate and marked mapped data in rectangular, circular or irregular shaped sampling windows, with tests of statistical significance based on Monte Carlo simulations.

This package provides a set of fast and convenient functions to help conducting accessibility analyses. Given a pre-computed travel cost matrix and a land use dataset (containing for example the location of jobs, healthcare and population), the package allows one to calculate accessibility levels, and accessibility poverty and inequality. The package covers the majority of the most commonly used accessibility measures (such as cumulative opportunities, gravity-based and floating catchment areas methods), some cutting edge measures proposed in the literature (e.g. balancing cost and constrained accessibility) as well as the most frequently used inequality and poverty metrics (such as the Palma ratio, the concentration and Theil indices and the FGT family of measures).

Accumulated Local Effects (ALE) were initially developed as a model-agnostic approach for global explanations of the results of black-box machine learning algorithms. ALE has a key advantage over other approaches like partial dependency plots (PDP) and SHapley Additive exPlanations (SHAP): its values represent a clean functional decomposition of the model. As such, ALE values are not affected by the presence or absence of interactions among variables in a mode. Moreover, its computation is relatively rapid. This package reimplements the algorithms for calculating ALE data and develops highly interpretable visualizations for plotting these ALE values. It also extends the original ALE concept to add bootstrap-based confidence intervals and ALE-based statistics that can be used for statistical inference. For more details, see Okoli, Chitu. 2023. â Statistical Inference Using Machine Learning and Classical Techniques Based on Accumulated Local Effects (ALE).â arXiv. <doi:10.48550/arXiv.2310.09877>.

Age-Period-Cohort (APC) analyses are used to differentiate relevant drivers for long-term developments. The APCtools package offers visualization techniques and general routines to simplify the workflow of an APC analysis. Sophisticated functions are available both for descriptive and regression model-based analyses. For the former, we use density (or ridgeline) matrices and (hexagonally binned) heatmaps as innovative visualization techniques building on the concept of Lexis diagrams. Model-based analyses build on the separation of the temporal dimensions based on generalized additive models, where a tensor product interaction surface (usually between age and period) is utilized to represent the third dimension (usually cohort) on its diagonal. Such tensor product surfaces can also be estimated while accounting for further covariates in the regression model. See Weigert et al. (2021) <doi:10.1177/1354816620987198> for methodological details.

Perform one-dimensional spline regression with automatic knot selection. This package uses a penalized approach to select the most relevant knots. B-splines of any degree can be fitted. More details in Goepp et al. (2018)', "Spline Regression with Automatic Knot Selection", <arXiv:1808.01770>.

This package implements Bayesian estimation and inference for alpha-mixture survival models, including Weibull and Exponential based components, with tools for simulation and posterior summaries. The methods target applications in reliability and biomedical survival analysis. The package implements Bayesian estimation for the alpha-mixture methodology introduced in Asadi et al. (2019) <doi:10.1017/jpr.2019.72>.

Facilitate the analysis of data related to aquatic ecology, specifically the establishment of carbon budget. Currently, the package allows the below analysis. (i) the calculation of greenhouse gas flux based on data obtained from trace gas analyzer using the method described in Lin et al. (2024). (ii) the calculation of Dissolved Oxygen (DO) metabolism based on data obtained from dissolved oxygen data logger using the method described in Staehr et al. (2010). Yong et al. (2024) <doi:10.5194/bg-21-5247-2024>. Staehr et al. (2010) <doi:10.4319/lom.2010.8.0628>.

Accurate point and interval estimation methods for multiple linear regression coefficients, under classical normal and independent error assumptions, taking into account variable selection.

This package provides a tool for generating acronyms and initialisms from arbitrary text input.

Automates regression testing of package allelematch'. Over 2500 tests cover all functions in allelematch', reproduce the examples from the documentation, and include negative tests. The implementation is based on testthat'.

The goal of automatedRecLin is to perform record linkage (also known as entity resolution) in unsupervised or supervised settings. It compares pairs of records from two datasets using selected comparison functions to estimate the probability or density ratio between matched and non-matched records. Based on these estimates, it predicts a set of matches that maximizes entropy. For details see: Lee et al. (2022) <https://www150.statcan.gc.ca/n1/pub/12-001-x/2022001/article/00007-eng.htm>, Vo et al. (2023) <https://ideas.repec.org/a/eee/csdana/v179y2023ics0167947322002365.html>, Sugiyama et al. (2008) <doi:10.1007/s10463-008-0197-x>.

Tool is created for regression, prediction and forecast analysis of macroeconomic and credit data. The package includes functions from existing R packages adapted for banking sector of Kazakhstan. The purpose of the package is to optimize statistical functions for easier interpretation for bank analysts and non-statisticians. The package also provides helper functions for loading an insurance scoring dataset, a past case competition dataset for insurance risk scoring and fair pricing.

Download air quality and meteorological information of Chile from the National Air Quality System (S.I.N.C.A.)<https://sinca.mma.gob.cl/> dependent on the Ministry of the Environment and the Meteorological Directorate of Chile (D.M.C.)<https://www.meteochile.gob.cl/> dependent on the Directorate General of Civil Aeronautics.

Enables to compute the statistical indices of affluence (richness) with bootstrap errors, and inequality and polarization indices. Moreover, gives the possibility of calculation of affluence line. Some simple errors are fixed and it works with new version of Spatial Statistics packaged.

This package provides a function to calculate the concentration of un-ionized ammonia in the total ammonia in aqueous solution using the pH and temperature values.

This is a simple and powerful package to create, render, preview, and deploy documentation websites for R packages. It is a lightweight and flexible alternative to pkgdown', with support for many documentation generators, including Quarto', Docute', Docsify', and MkDocs'.

For a binary classification the adjusted sensitivity and specificity are measured for a given fixed threshold. If the threshold for either sensitivity or specificity is not given, the crossing point between the sensitivity and specificity curves are returned. For bootstrap procedures, mean and CI bootstrap values of sensitivity, specificity, crossing point between specificity and specificity as well as AUC and AUCPR can be evaluated.

This package performs approximate unconditional and permutation testing for 2x2 contingency tables. Motivated by testing for disease association with rare genetic variants in case-control studies. When variants are extremely rare, these tests give better control of Type I error than standard tests.