This package provides tools for 3D point cloud voxelisation, projection, geometrical and morphological description of trees (DBH, height, volume, crown diameter), analyses of temporal changes between different measurement times, distance based clustering and visualisation of 3D voxel clouds and 2D projection. Most analyses and algorithms provided in the package are based on the concept of space exploration and are described in Lecigne et al. (2018, <doi:10.1093/aob/mcx095>).

This package provides functions to allow users to build and analyze design consistent tree and random forest models using survey data from a complex sample design. The tree model algorithm can fit a linear model to survey data in each node obtained by recursively partitioning the data. The splitting variables and selected splits are obtained using a randomized permutation test procedure which adjusted for complex sample design features used to obtain the data. Likewise the model fitting algorithm produces design-consistent coefficients to any specified least squares linear model between the dependent and independent variables used in the end nodes. The main functions return the resulting binary tree or random forest as an object of "rpms" or "rpms_forest" type. The package also provides methods modeling a "boosted" tree or forest model and a tree model for zero-inflated data as well as a number of functions and methods available for use with these object types.

Thisp package enables you to track and report code coverage for your package and (optionally) upload the results to a coverage service. Code coverage is a measure of the amount of code being exercised by a set of tests. It is an indirect measure of test quality and completeness. This package is compatible with any testing methodology or framework and tracks coverage of both R code and compiled C/C++/FORTRAN code.

This package provides a function to make gene presence/absence calls based on distance from negative strand matching probesets (NSMP) which are derived from Affymetrix annotation. PANP is applied after gene expression values are created, and therefore can be used after any preprocessing method such as MAS5 or GCRMA, or PM-only methods like RMA. NSMP sets have been established for the HGU133A and HGU133-Plus-2.0 chipsets to date.

Bayesian hierarchical methods for the detection of differences in rates of related outcomes for multiple treatments for clustered observations (Carragher et al. (2020) <doi:10.1002/sim.8563>). This software was developed for the Precision Drug Theraputics: Risk Prediction in Pharmacoepidemiology project as part of a Rutherford Fund Fellowship at Health Data Research (UK), Medical Research Council (UK) award reference MR/S003967/1 (<https://gtr.ukri.org/>). Principal Investigator: Raymond Carragher.

It provides access to and information about the most important Brazilian economic time series - from the Getulio Vargas Foundation <http://portal.fgv.br/en>, the Central Bank of Brazil <http://www.bcb.gov.br> and the Brazilian Institute of Geography and Statistics <http://www.ibge.gov.br>. It also presents tools for managing, analysing (e.g. generating dynamic reports with a complete analysis of a series) and exporting these time series.

Cuddy-Della valle index gives the degree of instability present in the data by accommodating the effect of a trend. The adjusted R squared value of the best fitted model is chosen. The index is obtained by multiplying the coefficient of variation with square root of one minus the adjusted R-squared value. This package has been developed using concept of Shankar et al. (2022)<doi:10.3389/fsufs.2023.1208898>.

This package provides object-oriented database management tools for working with large datasets across multiple database systems. Features include robust connection management for SQL Server and PostgreSQL databases, advanced table operations with bulk data loading and upsert functionality, comprehensive data validation through customizable field type and content validators, efficient index management, and cross-database compatibility. Designed for high-performance data operations in surveillance systems and large-scale data processing workflows.

This package provides a collection of functions and jamovi module for the estimation approach to inferential statistics, the approach which emphasizes effect sizes, interval estimates, and meta-analysis. Nearly all functions are based on statpsych and metafor'. This package is still under active development, and breaking changes are likely, especially with the plot and hypothesis test functions. Data sets are included for all examples from Cumming & Calin-Jageman (2024) <ISBN:9780367531508>.

Impute the covariance matrix of incomplete data so that factor analysis can be performed. Imputations are made using multiple imputation by Multivariate Imputation with Chained Equations (MICE) and combined with Rubin's rules. Parametric Fieller confidence intervals and nonparametric bootstrap confidence intervals can be obtained for the variance explained by different numbers of principal components. The method is described in Nassiri et al. (2018) <doi:10.3758/s13428-017-1013-4>.

Meteorological Tools following the FAO56 irrigation paper of Allen et al. (1998) [1]. Functions for calculating: reference evapotranspiration (ETref), extraterrestrial radiation (Ra), net radiation (Rn), saturation vapor pressure (satVP), global radiation (Rs), soil heat flux (G), daylight hours, and more. [1] Allen, R. G., Pereira, L. S., Raes, D., & Smith, M. (1998). Crop evapotranspiration-Guidelines for computing crop water requirements-FAO Irrigation and drainage paper 56. FAO, Rome, 300(9).

This package provides functions to calculate hazard and survival function of Multi-Stage Clonal Expansion Models used in cancer epidemiology. For the Two-Stage Clonal Expansion Model an exact solution is implemented assuming piecewise constant parameters, see Heidenreich, Luebeck, Moolgavkar (1997) <doi:10.1111/j.1539-6924.1997.tb00878.x>. Numerical solutions are provided for its extensions, see also Little, Vineis, Li (2008) <doi:10.1016/j.jtbi.2008.05.027>.

This package performs analysis of one-way multivariate data, for small samples using Nonparametric techniques. Using approximations for ANOVA Type, Wilks Lambda, Lawley Hotelling, and Bartlett Nanda Pillai Test statics, the package compares the multivariate distributions for a single explanatory variable. The comparison is also performed using a permutation test for each of the four test statistics. The package also performs an all-subsets algorithm regarding variables and regarding factor levels.

This package provides methods to estimate finite-population parameters under nonresponse that is not missing at random (NMAR, nonignorable). Incorporates auxiliary information and user-specified response models, and supports independent samples and complex survey designs via objects from the survey package. Provides diagnostics and optional variance estimates. For methodological background see Qin, Leung and Shao (2002) <doi:10.1198/016214502753479338> and Riddles, Kim and Im (2016) <doi:10.1093/jssam/smv047>.

This package provides functions for implementing different versions of the OSCV method in the kernel regression and density estimation frameworks. The package mainly supports the following articles: (1) Savchuk, O.Y., Hart, J.D. (2017). Fully robust one-sided cross-validation for regression functions. Computational Statistics, <doi:10.1007/s00180-017-0713-7> and (2) Savchuk, O.Y. (2017). One-sided cross-validation for nonsmooth density functions, <arXiv:1703.05157>.

This package provides a toolbox for making R functions and capabilities more accessible to students and professionals from Epidemiology and Public Health related disciplines. Includes a function to report coefficients and confidence intervals from models using robust standard errors (when available), functions that expand ggplot2 plots and functions relevant for introductory papers in Epidemiology or Public Health. Please note that use of the provided data sets is for educational purposes only.

This package provides functions to visualise sports data. Converts data into a format suitable for plotting charts. Helps to ease the process of working with messy sports data to a more user friendly format. Football data is accessed through worldfootballR <https://github.com/JaseZiv/worldfootballR> which gets data from FBref <https://fbref.com/en>, Transfermarkt <https://www.transfermarkt.com/>, Understat <https://understat.com/>, and fotmob <https://www.fotmob.com/>.

Implementation of commonly used penalized functional linear regression models, including the Smooth and Locally Sparse (SLoS) method by Lin et al. (2016) <doi:10.1080/10618600.2016.1195273>, Nested Group bridge Regression (NGR) method by Guan et al. (2020) <doi:10.1080/10618600.2020.1713797>, Functional Linear Regression That's interpretable (FLIRTI) by James et al. (2009) <doi:10.1214/08-AOS641>, and the Penalized B-spline regression method.

This package provides methods for regression with high-dimensional predictors and univariate or maltivariate response variables. It considers the decomposition of the coefficient matrix that leads to the best approximation to the signal part in the response given any rank, and estimates the decomposition by solving a penalized generalized eigenvalue problem followed by a least squares procedure. Ruiyan Luo and Xin Qi (2017) <doi:10.1016/j.jmva.2016.09.005>.

Comprehensive set of tools for analyzing and manipulating functional data with non-uniform lengths. This package addresses two common scenarios in functional data analysis: Variable Domain Data, where the observation domain differs across samples, and Partially Observed Data, where observations are incomplete over the domain of interest. VDPO enhances the flexibility and applicability of functional data analysis in R'. See Amaro et al. (2024) <doi:10.48550/arXiv.2401.05839>.

This package provides a memory-efficient, visualize-enhanced, parallel-accelerated Genome-Wide Association Study (GWAS) tool. It can (1) effectively process large data, (2) rapidly evaluate population structure, (3) efficiently estimate variance components several algorithms, (4) implement parallel-accelerated association tests of markers three methods, (5) globally efficient design on GWAS process computing, (6) enhance visualization of related information. rMVP contains three models GLM (Alkes Price (2006) <DOI:10.1038/ng1847>), MLM (Jianming Yu (2006) <DOI:10.1038/ng1702>) and FarmCPU (Xiaolei Liu (2016) <doi:10.1371/journal.pgen.1005767>); variance components estimation methods EMMAX (Hyunmin Kang (2008) <DOI:10.1534/genetics.107.080101>;), FaSTLMM (method: Christoph Lippert (2011) <DOI:10.1038/nmeth.1681>, R implementation from GAPIT2': You Tang and Xiaolei Liu (2016) <DOI:10.1371/journal.pone.0107684> and SUPER': Qishan Wang and Feng Tian (2014) <DOI:10.1371/journal.pone.0107684>), and HE regression (Xiang Zhou (2017) <DOI:10.1214/17-AOAS1052>).

An interface to the BaM (Bayesian Modeling) engine, a Fortran'-based executable aimed at estimating a model with a Bayesian approach and using it for prediction, with a particular focus on uncertainty quantification. Classes are defined for the various building blocks of BaM inference (model, data, error models, Markov Chain Monte Carlo (MCMC) samplers, predictions). The typical usage is as follows: (1) specify the model to be estimated; (2) specify the inference setting (dataset, parameters, error models...); (3) perform Bayesian-MCMC inference; (4) read, analyse and use MCMC samples; (5) perform prediction experiments. Technical details are available (in French) in Renard (2017) <https://hal.science/hal-02606929v1>. Examples of applications include Mansanarez et al. (2019) <doi:10.1029/2018WR023389>, Le Coz et al. (2021) <doi:10.1002/hyp.14169>, Perret et al. (2021) <doi:10.1029/2020WR027745>, Darienzo et al. (2021) <doi:10.1029/2020WR028607> and Perret et al. (2023) <doi:10.1061/JHEND8.HYENG-13101>.

The Reproducible Open Coding Kit ('ROCK', and this package, rock') was developed to facilitate reproducible and open coding, specifically geared towards qualitative research methods. It was developed to be both human- and machine-readable, in the spirit of MarkDown and YAML'. The idea is that this makes it relatively easy to write other functions and packages to process ROCK files. The rock package contains functions for basic coding and analysis, such as collecting and showing coded fragments and prettifying sources, as well as a number of advanced analyses such as the Qualitative Network Approach and Qualitative/Unified Exploration of State Transitions. The ROCK and this rock package are described in the ROCK book (ZörgÅ & Peters, 2022; <https://rockbook.org>), in ZörgÅ & Peters (2024) <doi:10.1080/21642850.2022.2119144> and Peters, ZörgÅ and van der Maas (2022) <doi:10.31234/osf.io/cvf52>, and more information and tutorials are available at <https://rock.science>.

Create an interactive Shiny-based graphical user interface for exploring data stored in SummarizedExperiment objects, including row- and column-level metadata. The interface supports transmission of selections between plots and tables, code tracking, interactive tours, interactive or programmatic initialization, preservation of app state, and extensibility to new panel types via S4 classes. Special attention is given to single-cell data in a SingleCellExperiment object with visualization of dimensionality reduction results.