Package: rethinking 2.42

Richard McElreath

rethinking: Statistical Rethinking book package

Utilities for fitting and comparing models

Authors:Richard McElreath

rethinking_2.42.tar.gz
rethinking_2.42.zip(r-4.5)rethinking_2.42.zip(r-4.4)rethinking_2.42.zip(r-4.3)
rethinking_2.42.tgz(r-4.5-any)rethinking_2.42.tgz(r-4.4-any)rethinking_2.42.tgz(r-4.3-any)
rethinking_2.42.tar.gz(r-4.5-noble)rethinking_2.42.tar.gz(r-4.4-noble)
rethinking.pdf |rethinking.html✨
rethinking/json (API)
NEWS

# Install 'rethinking' in R:

install.packages('rethinking', repos = c('https://staffanbetner.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/staffanbetner/rethinking/issues

Datasets:

AMTL - Ante-mortem Tooth Loss Data
AMTL_short - Ante-mortem Tooth Loss Data
Achehunting - Human forager hunting returns data
Boxes - Social learning experimental data
Crofoot - Capuchin monkey contests
Dinosaurs - Dinosaur growth data
Dissertations - Dissertation page length data
Fish - Fishing data
Hoogland - Prairie dog dispersal data
Howell1 - Howell !Kung demography data
Howell2 - Howell !Kung demography data
Hurricanes - Hurricane fatalities and gender of names
Kline - Oceanic islands data
Kline2 - Oceanic islands data
Laffer - Corporate tax rates and tax revenue for 20 nations
Moralizing_gods - Religious ideology and population growth
Panda_nuts - Chimpanzees cracking Panda nuts
Primates301 - Primate life history and social learning data
PrussianHorses - Numbers of soldiers killed by horse kicks in the Prussian army 1875-1894
Rinder - Livestock mortality data
Trolley - Experimental data on ethical dilemmas
UFClefties - Ultimate Fighting Championship matches
WaffleDivorce - Waffle House and marriage statistics
Wines2012 - Wine tasting scores, Princeton NJ 2012
bangladesh - Bangladesh contraceptive use data
cherry_blossoms - Japan Cherry Blossom Historical Data
chimpanzees - Chimpanzee prosocialty experiment data
foxes - Urban foxes
islands - Oceanic islands data
islandsDistMatrix - Oceanic islands data
milk - Primate milk data
reedfrogs - Data on reed frog predation experiments

On CRAN:

5.42 score 4.4k scripts 221 exports 33 dependencies

Last updated 3 months agofrom:953f01a28b. Checks:1 OK, 7 ERROR. Indexed: yes.

Target	Result	Latest binary
Doc / Vignettes	OK	Feb 01 2025
R-4.5-win	ERROR	Feb 01 2025
R-4.5-mac	ERROR	Feb 01 2025
R-4.5-linux	ERROR	Feb 01 2025
R-4.4-win	ERROR	Feb 01 2025
R-4.4-mac	ERROR	Feb 01 2025
R-4.3-win	ERROR	Feb 01 2025
R-4.3-mac	ERROR	Feb 01 2025

Exports:.requireCachedGenerics adjmat_from_dag AIC ani.saveqz anim_prior_predictive arrowspline axis_unscale bins blank blank2 brain_loo_plot brain_plot chainmode check_index choose.csv circle cloglog cmdstanr_model_write coef coeftab coeftab_plot coeftab_show coerce_index col.alpha col.desat col.dist compare concat confint_quad contour_xyz cov_GPL2 cov_GPL2_scal covmat cstan cv_data_slice cv_quap dag_arc dag_copy_coords dagfx_anim_backward dagfx_anim_forward dagfx_dot dashboard dbern dbeta2 dbetabinom dcategorical dens denschart deviance dgamma2 dgampois dgnorm dgpareto DIC dims divergence_tracker divergent dlaplace dlkjcorr dmvnorm dmvnorm2 dordlogit dpareto drawdag drawopenpaths dstudent dzagamma2 dzibinom dzipois ensemble extract_post_cstan extract_post_ulam extract_prior_ulam extract_prior_ulam_proto extract.prior extract.samples fclip flist flist_untag format_show glimmer goCaslonPro graphdag grau histospark HMC_2D_sample HMC2 HPDI htmlhelp ICweights image_xyz inv_cloglog inv_logit inv_unif lines_w lines_xkcd link link_ulam log_sum_exp logistic logit logLik LOO lppd make_bar make_ukey make.grid map map2stan map2stan.templates mcmcpairs mcmcpairs_old mcreplicate multilogistic nobs normalize pairs PCI pdfblank PI PIprimes plot plot2y plotchains plotpost plp pordlogit postcheck postlistprecis postmeans precis precis_cmdstanfit precis_format precis_plot precis_show precis_show_old precis.whitelist precisx predict_ordlogit progbar PSIS PSIS_list PSIS_map2stan PSIS_quap PSIS_stanfit PSIS_ulam PSISk quap rangi2 rank_mat rbern rbeta2 rbetabinom rcategorical replicate2 resample resample_old rethink_cmyk rethink_palette rgamma2 rgampois rgampois2 rgpareto Rho rinvwishart rlaplace rlkjcorr rmvnorm rmvnorm2 rordlogit rpareto rrformat rstudent rzibinom rzipois sample.naive.posterior sample.qa.posterior sd_pop sd2 se segmentsby set_nice_margins set_ulam_cmdstan setcran shade show.naive.posterior sim sim_core sim_happiness sim_train_test sim_ulam sim_ulam_new sim.train.test simplehist simplehist_old sketchdag softmax sparks stan stan_sampling_duration stan_total_samples stancode standardize stanergy summary test_ulam traceplot traceplot_ulam tracerplot trankplot ulam ulam_dists ulam_macros ulam_options unstandardize var_pop var2 vcov WAIC WAICp yn2bin

Dependencies:abind backports checkmate cli cmdstanr coda data.table distributional fansi generics glue jsonlite lattice lifecycle loo magrittr MASS matrixStats mvtnorm numDeriv pillar pkgconfig posterior processx ps R6 rlang shape tensorA tibble utf8 vctrs withr

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Statistical Rethinking package	rethinking-package rethinking
Human forager hunting returns data	Achehunting
Ante-mortem Tooth Loss Data	AMTL AMTL_short
Draw an axis with units on original scale	axis_unscale
Bangladesh contraceptive use data	bangladesh
Social learning experimental data	Boxes
Find mode of a continuous density estimate	chainmode
Japan Cherry Blossom Historical Data	cherry_blossoms
Chimpanzee prosocialty experiment data	chimpanzees
Coefficient tables	coeftab
Plots of coefficient tables	coeftab_plot
Build and check integer index variables	check_index coerce_index
Color utility functions	col.alpha col.desat col.dist grau
Compare fit models using WAIC or DIC	compare ICweights
Contour plot from equal length x,y,z vectors	contour_xyz
Capuchin monkey contests	Crofoot
Diagnostic trace and rank histogram plots for MCMC output	cv_quap
Beta-binomial probability density	dbetabinom rbetabinom
Density plots	dens
Gamma-Poisson probability density	dgampois rgampois
Dinosaur growth data	Dinosaurs
Dissertation page length data	Dissertations
LKJ correlation matrix probability density	dlkjcorr rlkjcorr
Multivariate Gaussian probability density	dmvnorm2 rmvnorm2
Ordered categorical log-odds probability density	dordlogit pordlogit rordlogit
Plot Directed Acyclic Graphs (dagitty)	drawdag drawopenpaths
Non-standard Student's t distribution	dstudent rstudent
Zero-augmented gamma probability density	dzagamma2
Zero-inflated binomial probability density	dzibinom rzibinom
Zero-inflated Poisson probability density	dzipois rzipois
Simulate an ensemble of posterior predictions	ensemble
Collect posterior or prior samples from a map or map2stan model	extract.prior extract.samples
Fishing data	Fish
Urban foxes	foxes
glm/glmer formulas to map/map2stan formulas	glimmer
Functions for simple HMC simulations	HMC2 HMC_2D_sample
Prairie dog dispersal data	Hoogland
Howell !Kung demography data	Howell1 Howell2
Confidence/credible intervals from samples	HPDI PCI PI
Hurricane fatalities and gender of names	Hurricanes
Heat map from equal length x,y,z vectors	image_xyz
Oceanic islands data	islands islandsDistMatrix Kline Kline2
Gift exchange data	KosterLeckie
Corporate tax rates and tax revenue for 20 nations	Laffer
Predictions for map and map2stan models	link link,lm-method link,map-method link,map2stan-method link-methods
Rethinking utility functions	log_sum_exp
Build RStan models from formulas	map2stan
Class 'map2stan': fitted map2stan Stan model	deviance,map2stan-method DIC,map2stan-method extract.samples,map2stan-method logLik,map2stan-method map2stan-class nobs,map2stan-method pairs,map2stan-method plot,map2stan-method show,map2stan-method sim,map2stan-method stancode,map2stan-method summary,map2stan-method vcov,map2stan-method WAIC,map2stan-method
Multi-core version of replicate	mcreplicate
Primate milk data	milk
Religious ideology and population growth	Moralizing_gods
Trace plot of map2stan chains	pairs.map pairs.map2stan
Chimpanzees cracking Panda nuts	Panda_nuts
Trace plot of map2stan chains	plot.map2stan
Plot posterior predictive check	postcheck
Precis of model fit	precis
Primate life history and social learning data	Primates301
Progress display	progbar
Numbers of soldiers killed by horse kicks in the Prussian army 1875-1894	PrussianHorses
Compute quadratic approximate posterior distribution	map quap
Data on reed frog predation experiments	reedfrogs
Resample map2stan fit	resample
Livestock mortality data	Rinder
Samples from quadratic posterior densities of models	sample.naive.posterior sample.qa.posterior
Shade density intervals	shade
Simulate posterior observations	sim sim,lm-method sim,map-method sim,map2stan-method sim-methods
Simulate in-sample and out-of-sample model performance	sim.train.test sim_train_test
Simple histograms	simplehist
Diagnostic trace and rank histogram plots for MCMC output	traceplot trankplot
Experimental data on ethical dilemmas	Trolley
Ultimate Fighting Championship matches	UFClefties
Build RStan models from formulas	ulam
Waffle House and marriage statistics	WaffleDivorce
Information Criteria and Pareto-Smoothed Importance Sampling Cross-Validation	DIC LOO PSIS WAIC
Wine tasting scores, Princeton NJ 2012	Wines2012