Theme and colour palettes for The Globe and Mail's graphics. Includes colour and fill scale functions, colour palette helpers and a Globe-styled ggplot2 theme object.

Better looking call stacks after an error.

This package provides a common way of validating a biological assay for is through a procedure, where m levels of an analyte are measured with n replicates at each level, and if all m estimates of the coefficient of variation (CV) are less than some prespecified level, then the assay is declared validated for precision within the range of the m analyte levels. Two limitations of this procedure are: there is no clear statistical statement of precision upon passing, and it is unclear how to modify the procedure for assays with constant standard deviation. We provide tools to convert such a procedure into a set of m hypothesis tests. This reframing motivates the m:n:q procedure, which upon completion delivers a 100q% upper confidence limit on the CV. Additionally, for a post-validation assay output of y, the method gives an ``effective standard deviation interval of log(y) plus or minus r, which is a 68% confidence interval on log(mu), where mu is the expected value of the assay output for that sample. Further, the m:n:q procedure can be straightforwardly applied to constant standard deviation assays. We illustrate these tools by applying them to a growth inhibition assay. This is an implementation of the methods described in Fay, Sachs, and Miura (2018) <doi:10.1002/sim.7528>.

Tracks parameter value, gradient, and Hessian at each iteration of numerical optimizers. Useful for analyzing optimization progress, diagnosing issues, and studying convergence behavior.

This package provides tools for Topological Data Analysis. The package focuses on statistical analysis of persistent homology and density clustering. For that, this package provides an R interface for the efficient algorithms of the C++ libraries GUDHI <https://project.inria.fr/gudhi/software/>, Dionysus <https://www.mrzv.org/software/dionysus/>, and PHAT <https://bitbucket.org/phat-code/phat/>. This package also implements methods from Fasy et al. (2014) <doi:10.1214/14-AOS1252> and Chazal et al. (2015) <doi:10.20382/jocg.v6i2a8> for analyzing the statistical significance of persistent homology features.

Demonstration functions that can be used in a classroom to demonstrate statistical concepts, or on your own to better understand the concepts or the programming.

Computes the solution path of the Terminating-LARS (T-LARS) algorithm. The T-LARS algorithm is a major building block of the T-Rex selector (see R package TRexSelector'). The package is based on the papers Machkour, Muma, and Palomar (2022) <arXiv:2110.06048>, Efron, Hastie, Johnstone, and Tibshirani (2004) <doi:10.1214/009053604000000067>, and Tibshirani (1996) <doi:10.1111/j.2517-6161.1996.tb02080.x>.

Improves the predictive performance of ridge and lasso regression exploiting one or more sources of prior information on the importance and direction of effects (Rauschenberger and others 2023, <doi:10.1093/bioinformatics/btad680>). For running the vignette (optional), install fwelnet and ecpc from <https://github.com/kjytay/fwelnet> and <https://github.com/Mirrelijn/ecpc>, respectively.

Deciphering hierarchy of agents exhibiting observable dominance events is a crucial problem in several disciplines, in particular in behavioural analysis of social animals, but also in social sciences and game theory. This package implements an inference approach based on graph theory, namely to extract the optimal acyclic subset of a weighted graph of dominance; this allows for hierarchy estimation through topological sorting. The package also contains infrastructure to investigate partially defined hierarchies and hierarchy dynamics.

Write modelling results into a database for tigreBrowser', a web-based tool for browsing figures and summary data of independent model fits, such as Gaussian process models fitted for each gene or other genomic element. The browser is available at <https://github.com/PROBIC/tigreBrowser>.

This package provides a plug-in for the tm text mining framework providing mail handling functionality.

This package provides a clinically meaningful measures of treatment effects for right-censored data are provided, based on the concept of Kendall's tau, along with the corresponding inference procedures. Two plots of tau processes, with the option to account for the cure fraction or not, are available. The plots of tau processes serve as useful graphical tools for monitoring the relative performances over time.

This package provides utility functions for plotting. Includes functions for color manipulation, plot customization, panel size control, data optimization for plots, and layout adjustments.

This package provides tools to calculate trait probability density functions (TPD) at any scale (e.g. populations, species, communities). TPD functions are used to compute several indices of functional diversity, as well as its partition across scales. These indices constitute a unified framework that incorporates the underlying probabilistic nature of trait distributions into uni- or multidimensional functional trait-based studies. See Carmona et al. (2016) <doi:10.1016/j.tree.2016.02.003> for further information.

This package provides a suite of auxiliary functions that enhance time series estimation and forecasting, including a robust anomaly detection routine based on Chen and Liu (1993) <doi:10.2307/2290724> (imported and wrapped from the tsoutliers package), utilities for managing calendar and time conversions, performance metrics to assess both point forecasts and distributional predictions, advanced simulation by allowing the generation of time series componentsâ such as trend, seasonal, ARMA, irregular, and anomaliesâ in a modular fashion based on the innovations form of the state space model and a number of transformation methods including Box-Cox, Logit, Softplus-Logit and Sigmoid.

Higher Criticism (HC) test between two frequency tables. Test is based on an adaptation of the Tukey-Donoho-Jin HC statistic to testing frequency tables described in Kipnis (2019) <arXiv:1911.01208>.

This package provides a collection of functions to plot acid/base titration curves (pH vs. volume of titrant), complexation titration curves (pMetal vs. volume of EDTA), redox titration curves (potential vs.volume of titrant), and precipitation titration curves (either pAnalyte or pTitrant vs. volume of titrant). Options include the titration of mixtures, the ability to overlay two or more titration curves, and the ability to show equivalence points.

This package provides a latent, quasi-independent truncation time is assumed to be linked with the observed dependent truncation time, the event time, and an unknown transformation parameter via a structural transformation model. The transformation parameter is chosen to minimize the conditional Kendall's tau (Martin and Betensky, 2005) <doi:10.1198/016214504000001538> or the regression coefficient estimates (Jones and Crowley, 1992) <doi:10.2307/2336782>. The marginal distribution for the truncation time and the event time are completely left unspecified. The methodology is applied to survival curve estimation and regression analysis.

Streamline the processing of Telraam data, sourced from open data mobility sensors. These tools range from data retrieval (without the need for API knowledge) to data visualization, including data preprocessing.

Visualizing cuts for either axis-align or non axis-align tree methods (e.g. decision tree, random tessellation process).

This package provides a consistent API to pull United States Department of Agriculture census and survey data from the National Agricultural Statistics Service (NASS) QuickStats service.

Non-parametric trend comparison of two independent samples with sequential subsamples. For more details, please refer to Wang, Stapleton, and Chen (2018) <doi:10.1080/00949655.2018.1482492>.

This package creates geographic map tiles from geospatial map files or non-geographic map tiles from simple image files. This package provides a tile generator function for creating map tile sets for use with packages such as leaflet'. In addition to generating map tiles based on a common raster layer source, it also handles the non-geographic edge case, producing map tiles from arbitrary images. These map tiles, which have a non-geographic, simple coordinate reference system (CRS), can also be used with leaflet when applying the simple CRS option. Map tiles can be created from an input file with any of the following extensions: tif, grd and nc for spatial maps and png, jpg and bmp for basic images. This package requires Python and the gdal library for Python'. Windows users are recommended to install OSGeo4W (<https://trac.osgeo.org/osgeo4w/>) as an easy way to obtain the required gdal support for Python'.

Fit a trio model via penalized maximum likelihood. The model is fit for a path of values of the penalty parameter. This package is based on Noah Simon, et al. (2011) <doi:10.1080/10618600.2012.681250>.