lme4 - Linear Mixed-Effects Models using 'Eigen' and S4

Fit linear and generalized linear mixed-effects models. The models and their components are represented using S4 classes and methods. The core computational algorithms are implemented using the 'Eigen' C++ library for numerical linear algebra and 'RcppEigen' "glue".

Last updated 3 days ago

cpp

20.68 score 645 stars 1.5k dependents 35k scripts 459k downloads

broom.mixed - Tidying Methods for Mixed Models

Convert fitted objects from various R mixed-model packages into tidy data frames along the lines of the 'broom' package. The package provides three S3 generics for each model: tidy(), which summarizes a model's statistical findings such as coefficients of a regression; augment(), which adds columns to the original data such as predictions, residuals and cluster assignments; and glance(), which provides a one-row summary of model-level statistics.

Last updated 2 months ago

15.22 score 231 stars 37 dependents 4.0k scripts 40k downloads

gtools - Various R Programming Tools

Functions to assist in R programming, including: - assist in developing, updating, and maintaining R and R packages ('ask', 'checkRVersion', 'getDependencies', 'keywords', 'scat'), - calculate the logit and inverse logit transformations ('logit', 'inv.logit'), - test if a value is missing, empty or contains only NA and NULL values ('invalid'), - manipulate R's .Last function ('addLast'), - define macros ('defmacro'), - detect odd and even integers ('odd', 'even'), - convert strings containing non-ASCII characters (like single quotes) to plain ASCII ('ASCIIfy'), - perform a binary search ('binsearch'), - sort strings containing both numeric and character components ('mixedsort'), - create a factor variable from the quantiles of a continuous variable ('quantcut'), - enumerate permutations and combinations ('combinations', 'permutation'), - calculate and convert between fold-change and log-ratio ('foldchange', 'logratio2foldchange', 'foldchange2logratio'), - calculate probabilities and generate random numbers from Dirichlet distributions ('rdirichlet', 'ddirichlet'), - apply a function over adjacent subsets of a vector ('running'), - modify the TCP_NODELAY ('de-Nagle') flag for socket objects, - efficient 'rbind' of data frames, even if the column names don't match ('smartbind'), - generate significance stars from p-values ('stars.pval'), - convert characters to/from ASCII codes ('asc', 'chr'), - convert character vector to ASCII representation ('ASCIIfy'), - apply title capitalization rules to a character vector ('capwords').

Last updated 8 months ago

14.40 score 25 stars 1.1k dependents 11k scripts 144k downloads

bbmle - Tools for General Maximum Likelihood Estimation

Methods and functions for fitting maximum likelihood models in R. This package modifies and extends the 'mle' classes in the 'stats4' package.

Last updated 22 days ago

13.26 score 25 stars 111 dependents 1.4k scripts 17k downloads

reformulas - Machinery for Processing Random Effect Formulas

Takes formulas including random-effects components (formatted as in 'lme4', 'glmmTMB', etc.) and processes them. Includes various helper functions.

Last updated 4 months ago

10.92 score 5 stars 1.5k dependents 24 scripts 375k downloads

margins - Marginal Effects for Model Objects

An R port of the margins command from 'Stata', which can be used to calculate marginal (or partial) effects from model objects.

Last updated 7 months ago

9.85 score 2 stars 1 dependents 956 scripts 11k downloads

emdbook - Support Functions and Data for "Ecological Models and Data"

Auxiliary functions and data sets for "Ecological Models and Data", a book presenting maximum likelihood estimation and related topics for ecologists (ISBN 978-0-691-12522-0).

Last updated 8 months ago

8.04 score 4 stars 21 dependents 656 scripts 6.6k downloads

prediction - Tidy, Type-Safe 'prediction()' Methods

A one-function package containing prediction(), a type-safe alternative to predict() that always returns a data frame. The summary() method provides a data frame with average predictions, possibly over counterfactual versions of the data (à la the margins command in 'Stata'). Marginal effect estimation is provided by the related package, 'margins' <https://cran.r-project.org/package=margins>. The package currently supports common model types (e.g., lm, glm) from the 'stats' package, as well as numerous other model classes from other add-on packages. See the README file or main package documentation page for a complete listing.

Last updated 3 months ago

7.29 score 2 dependents 127 scripts 8.5k downloads

R2admb - 'ADMB' to R Interface Functions

A series of functions to call 'AD Model Builder' (i.e., compile and run models) from within R, read the results back into R as 'admb' objects, and provide standard accessors (i.e. coef(), vcov(), etc.)

Last updated 2 years ago

4.79 score 3 dependents 83 scripts 1.2k downloads