Calibrates Bayesian two-stage designs for single-arm phase II trials with time-to-event endpoints using a window-cohort with controlled roll-on. Interim monitoring is anchored to a locked interim cohort and a pre-specified follow-up requirement, so analysis timing remains predictable while preserving follow-up maturity. The package searches feasible interim rules, optimizes final sample size and decision thresholds, evaluates operating characteristics by Monte Carlo simulation, and supports exponential, Weibull, log-normal, log-logistic, and user-defined baseline survival models. Related published foundations include Simon (1989) <doi:10.1016/0197-2456(89)90015-9> and Cotterill and Whitehead (2015) <doi:10.1002/sim.6426>.

Implementation of the weighted iterative proportional fitting (WIPF) procedure for updating/adjusting a N-dimensional array given a weight structure and some target marginals. Acknowledgements: The author wish to thank Conselleria de Educación, Cultura, Universidades y Empleo (grant CIAICO/2023/031), Ministerio de Ciencia, Innovación y Universidades (grant PID2021-128228NB-I00) and Fundación Mapfre (grant Modelización espacial e intra-anual de la mortalidad en España. Una herramienta automática para el cálculo de productos de vida') for supporting this research.

This package provides workflows to prepare weather and climate time series from gridded and station data for SWAT ('Soil and Water Assessment Tool'). Supports data extraction, aggregation, interpolation, quality control, unit conversion, and export of per-location model input files. For the underlying model, see Arnold et al. (1998) "Large Area Hydrologic Modeling and Assessment Part I: Model Development" <doi:10.1111/j.1752-1688.1998.tb05961.x>.

It shows the connections between selected clusters from the latest time point and the clusters from all the previous time points. The transition matrices between time point t and t+1 are obtained from Waddington-OT analysis <https://github.com/ScialdoneLab/WOTPLY>.

This package provides tools for constructing, simulating, and analyzing large-scale water resources systems. The package provides functions to represent system components such as reservoirs, aquifers, rivers, diversions, and demand sites, and to simulate system behavior under Standard Operating Policy. It also supports the development and evaluation of water allocation strategies and hydropower operations within integrated water resources systems.

Converts pathways from WikiPathways GPML format or KEGG KGML format into igraph objects. Includes tools to find all cycles in the resulting graphs and determine which ones involve negative feedback (inhibition).

Calculates Windowed Cross Correlation for pairs of time series. Provides support for surrogate analysis for nonparametric test of significance. Calculates aggregate statistics over a range of parameter values. Plots the results as Windowed Cross Correlation plots and heat maps. The software is described in Boker, S. M., Rotondo, J. L., Xu, M., & King, K. (2002). Windowed cross-correlation and peak picking for the analysis of variability in the association between behavioral time series. Psychological Methods, 7(3), 338.

Top-Down mass spectrometry aims to identify entire proteins as well as their (post-translational) modifications or ions bound (eg Chen et al (2018) <doi:10.1021/acs.analchem.7b04747>). The pattern of internal fragments (Haverland et al (2017) <doi:10.1007/s13361-017-1635-x>) may reveal important information about the original structure of the proteins studied (Skinner et al (2018) <doi:10.1038/nchembio.2515> and Li et al (2018) <doi:10.1038/nchem.2908>). However, the number of possible internal fragments gets huge with longer proteins and subsequent identification of internal fragments remains challenging, in particular since the the accuracy of measurements with current mass spectrometers represents a limiting factor. This package attempts to deal with the complexity of internal fragments and allows identification of terminal and internal fragments from deconvoluted mass-spectrometry data.

This package provides Water Year Hydrologic Classification Indices based on measured unimpaired runoff (in million acre-feet). Data is provided by California Department of Water Resources and subject to revision.

This package provides a hierarchy of classes and methods for manipulating matrices formed implicitly from the sums of the inverses of other matrices, a situation commonly encountered in spatial statistics and related fields. Enables easy use of the Woodbury matrix identity and the matrix determinant lemma to allow computation (e.g., solving linear systems) without having to form the actual matrix. More information on the underlying linear algebra can be found in Harville, D. A. (1997) <doi:10.1007/b98818>.

This package implements inferential and graphic procedures for the semiparametric proportional means regression of weighted composite endpoint of recurrent event and death (Mao and Lin, 2016, <doi:10.1093/biostatistics/kxv050>).

Read Quake assets including bitmap images and textures in wal file format. This package also provides support for extracting these assets from WAD and PAK file archives. It can also read models in MDL and MD2 formats.

Makes research involving EMDAT and related datasets easier. These Datasets are manually filled and have several formatting and compatibility issues. Weed aims to resolve these with its functions.

Color palettes taken from the landscapes and cities of Washington state. Colors were extracted from a set of photographs, and then combined to form a set of continuous and discrete palettes. Continuous palettes were designed to be perceptually uniform, while discrete palettes were chosen to maximize contrast at several different levels of overall brightness and saturation. Each palette has been evaluated to ensure colors are distinguishable by colorblind people.

This package provides access to various word embedding methods (GloVe, fasttext and word2vec) to extract word vectors using a unified framework to increase reproducibility and correctness.

This package provides scalogram based wavelet tools for time series analysis: wavelet power spectrum, scalogram, windowed scalogram, windowed scalogram difference (see Bolos et al. (2017) <doi:10.1016/j.amc.2017.05.046>), scale index and windowed scale index (Benitez et al. (2010) <doi:10.1016/j.camwa.2010.05.010>).

Logging of scripts suitable for clinical trials using Quarto to create nice human readable logs. whirl enables execution of scripts in batch, while simultaneously creating logs for the execution of each script, and providing an overview summary log of the entire batch execution.

Create reproducible and transparent research projects in R'. This package is based on the Workflow for Open Reproducible Code in Science (WORCS), a step-by-step procedure based on best practices for Open Science. It includes an RStudio project template, several convenience functions, and all dependencies required to make your project reproducible and transparent. WORCS is explained in the tutorial paper by Van Lissa, Brandmaier, Brinkman, Lamprecht, Struiksma, & Vreede (2021). <doi:10.3233/DS-210031>.

This package implements an automated binning of numeric variables and factors with respect to a dichotomous target variable. Two approaches are provided: An implementation of fine and coarse classing that merges granular classes and levels step by step. And a tree-like approach that iteratively segments the initial bins via binary splits. Both procedures merge, respectively split, bins based on similar weight of evidence (WOE) values and stop via an information value (IV) based criteria. The package can be used with single variables or an entire data frame. It provides flexible tools for exploring different binning solutions and for deploying them to (new) data.

The efficient treatment and convenient analysis of experimental high-throughput (omics) data gets facilitated through this collection of diverse functions. Several functions address advanced object-conversions, like manipulating lists of lists or lists of arrays, reorganizing lists to arrays or into separate vectors, merging of multiple entries, etc. Another set of functions provides speed-optimized calculation of standard deviation (sd), coefficient of variance (CV) or standard error of the mean (SEM) for data in matrixes or means per line with respect to additional grouping (eg n groups of replicates). A group of functions facilitate dealing with non-redundant information, by indexing unique, adding counters to redundant or eliminating lines with respect redundancy in a given reference-column, etc. Help is provided to identify very closely matching numeric values to generate (partial) distance matrixes for very big data in a memory efficient manner or to reduce the complexity of large data-sets by combining very close values. Other functions help aligning a matrix or data.frame to a reference using partial matching or to mine an experimental setup to extract patterns of replicate samples. Many times large experimental datasets need some additional filtering, adequate functions are provided. Convenient data normalization is supported in various different modes, parameter estimation via permutations or boot-strap as well as flexible testing of multiple pair-wise combinations using the framework of limma is provided, too. Batch reading (or writing) of sets of files and combining data to arrays is supported, too.

This package provides function, wget_set(), to change the method (default to wget -c') using in download.file(). Using wget -c allowing continued downloading, which is especially useful for slow internet connection and for downloading large files. User can run wget_unset() to restore previous setting.

This package provides a shiny application that helps learners connect regression tables to fitted generalised linear models. Users construct models via drag-and-drop controls, obtain fitted equations and plain-language explanations generated by a large language model, and can view plots of the fitted model in settings with a single continuous covariate.

Students learning both econometrics and R may find the introduction to both challenging. The wooldridge data package aims to lighten the task by efficiently loading any data set found in the text with a single command. Data sets have been compressed to a fraction of their original size. Documentation files contain page numbers, the original source, time of publication, and notes from the author suggesting avenues for further analysis and research. If one needs an introduction to R model syntax, a vignette contains solutions to examples from chapters of the text. Data sets are from the 7th edition (Wooldridge 2020, ISBN-13 978-1-337-55886-0), and are backwards compatible with all previous versions of the text.

This package provides API access to the Walmart Open API <https://developer.walmartlabs.com/>, that contains data about stores, Value of the day and products which includes names, sale prices, shipping rates and taxonomies.