Simple Bootstrap Routines

Simple bootstrap routines.

Empirical Bayes Estimation and Inference

Kiefer-Wolfowitz maximum likelihood estimation for mixture models and some other density estimation and regression methods based on convex optimization. See Koenker and Gu (2017) REBayes: An R Package for Empirical Bayes Mixture Methods, Journal of Statistical Software, 82, 1--26, .

Time Series Modeling for Air Pollution and Health

Tools for specifying time series regression models.

Analysis of Factorial Experiments

Convenience functions for analyzing factorial experiments using ANOVA or mixed models. aov_ez(), aov_car(), and aov_4() allow specification of between, within (i.e., repeated-measures), or mixed (i.e., split-plot) ANOVAs for data in long format (i.e., one observation per row), automatically aggregating multiple observations per individual and cell of the design. mixed() fits mixed models using lme4::lmer() and computes p-values for all fixed effects using either Kenward-Roger or Satterthwaite approximation for degrees of freedom (LMM only), parametric bootstrap (LMMs and GLMMs), or likelihood ratio tests (LMMs and GLMMs). afex_plot() provides a high-level interface for interaction or one-way plots using ggplot2, combining raw data and model estimates. afex uses type 3 sums of squares as default (imitating commercial statistical software).

Calculate Design Parameters for Biomarker Validation Studies

Helps a clinical trial team discuss the clinical goals of a well-defined biomarker with a diagnostic, staging, prognostic, or predictive purpose. From this discussion will come a statistical plan for a (non-randomized) validation trial. Both prospective and retrospective trials are supported. In a specific focused discussion, investigators should determine the range of "discomfort" for the NNT, number needed to treat. The meaning of the discomfort range, [NNTlower, NNTupper], is that within this range most physicians would feel discomfort either in treating or withholding treatment. A pair of NNT values bracketing that range, NNTpos and NNTneg, become the targets of the study's design. If the trial can demonstrate that a positive biomarker test yields an NNT less than NNTlower, and that a negative biomarker test yields an NNT less than NNTlower, then the biomarker may be useful for patients. A highlight of the package is visualization of a "contra-Bayes" theorem, which produces criteria for retrospective case-controls studies.

Generalized Linear Models Extended

Extended techniques for generalized linear models (GLMs), especially for binary responses, including parametric links and heteroscedastic latent variables.

Enhanced Regression Nomogram Plot

A function to plot a regression nomogram of regression objects. Covariate distributions are superimposed on nomogram scales and the plot can be animated to allow on-the-fly changes to distribution representation and to enable outcome calculation.

Modeling and Plotting for Ecologist

It provides multiple functions that are useful for ecological research and teaching statistics to ecologists. It is based on data analysis courses offered at the Instituto de Ecología AC (INECOL). For references and published evidence see, Manrique-Ascencio, et al (2024) , Manrique-Ascencio et al (2024) , Ruiz-Guerra et al(2017) , Juarez-Fragoso et al (2024) , Papaqui-Bello et al (2024) .

Functions to Convert Between Weather Metrics

Functions to convert between weather metrics, including conversions for metrics of temperature, air moisture, wind speed, and precipitation. This package also includes functions to calculate the heat index from air temperature and air moisture.

File System Cache

Manages a file system cache. Regular files can be moved or copied to the cache folder. Sub-folders can be created in order to organize the files. Files can be located inside the cache using a glob function. Text contents can be easily stored in and retrieved from the cache using dedicated functions. It can be used for an application or a package, as a global cache, or as a per-user cache, in which case the standard OS user cache folder will be used (e.g.: on Linux $HOME/.cache/R/my_app_or_pkg_cache_folder).