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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".

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cpp

21.75 score 687 stars 1.7k dependents 49k scripts 682k 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').

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14.81 score 27 stars 1.1k dependents 12k scripts 293k 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.

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14.06 score 230 stars 40 dependents 6.7k scripts 57k 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.

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13.50 score 25 stars 151 dependents 1.8k scripts 51k 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.

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12.15 score 7 stars 1.8k dependents 56 scripts 493k 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.

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10.82 score 3 stars 7 dependents 1.4k scripts 21k downloads

macpan2 - Fast and Flexible Compartmental Modelling

Tools for building and calibrating compartmental models of infectious disease.

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compartmental-modelsepidemiologyforecastingmixed-effectsmodel-fittingoptimizationsimulationsimulation-modelingcpp

9.03 score 8 stars 1 dependents 270 scripts

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).

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8.34 score 4 stars 23 dependents 586 scripts 13k 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.

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7.77 score 1 stars 8 dependents 136 scripts 18k downloads

mbest - Moment-Based Estimation for Hierarchical Models

Fast moment-based hierarchical model fitting. Implements methods from the papers "Fast Moment-Based Estimation for Hierarchical Models," by Perry (2017) and "Fitting a Deeply Nested Hierarchical Model to a Large Book Review Dataset Using a Moment-Based Estimator," by Zhang, Schmaus, and Perry (2018).

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6.22 score 26 stars 2 dependents 13 scripts 4.1k 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.)

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4.75 score 3 dependents 90 scripts 781 downloads

MEMSS - Data Sets from Mixed-Effects Models in S

Data sets and sample analyses from Pinheiro and Bates, "Mixed-effects Models in S and S-PLUS" (Springer, 2000).

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4.40 score 2 stars 95 scripts 13k downloads