R/doc-datasets.R

In stan-dev/rstanarm: Bayesian Applied Regression Modeling via Stan

# Part of the rstanarm package for estimating model parameters
# Copyright (C) 2015, 2016, 2017 Trustees of Columbia University
# 
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 3
# of the License, or (at your option) any later version.
# 
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU General Public License for more details.
# 
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
# Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA.
#
#' Datasets for rstanarm examples
#' 
#' Small datasets for use in \pkg{rstanarm} examples and vignettes.
#'
#' @name rstanarm-datasets
#' @aliases kidiq roaches wells bball1970 bball2006 mortality tumors radon pbcLong pbcSurv
#' @format 
#' \describe{
#' \item{\code{bball1970}}{
#' Data on hits and at-bats from the 1970 Major League Baseball season for 18
#' players.
#' 
#' Source: Efron and Morris (1975).
#' 
#' 18 obs. of 5 variables
#' \itemize{
#' \item \code{Player} Player's last name
#' \item \code{Hits} Number of hits in the first 45 at-bats of the season
#' \item \code{AB} Number of at-bats (45 for all players)
#' \item \code{RemainingAB} Number of remaining at-bats (different for most players)
#' \item \code{RemainingHits} Number of remaining hits
#' }
#' }
#' \item{\code{bball2006}}{
#' Hits and at-bats for the entire 2006 American League season of Major League
#' Baseball.
#' 
#' Source: Carpenter (2009)
#' 
#' 302 obs. of 2 variables
#' \itemize{
#' \item \code{y} Number of hits
#' \item \code{K} Number of at-bats
#' }
#' }
#' \item{\code{kidiq}}{
#' Data from a survey of adult American women and their children 
#' (a subsample from the National Longitudinal Survey of Youth).
#' 
#' Source: Gelman and Hill (2007)
#' 
#' 434 obs. of 4 variables
#' \itemize{
#' \item \code{kid_score} Child's IQ score
#' \item \code{mom_hs} Indicator for whether the mother has a high school degree
#' \item \code{mom_iq} Mother's IQ score
#' \item \code{mom_age} Mother's age
#' }
#' }
#' \item{\code{mortality}}{
#' Surgical mortality rates in 12 hospitals performing cardiac surgery
#' in babies.
#' 
#' Source: Spiegelhalter et al. (1996).
#'
#' 12 obs. of 2 variables
#' \itemize{
#' \item \code{y} Number of deaths
#' \item \code{K} Number of surgeries
#' }
#' }
#' \item{\code{pbcLong,pbcSurv}}{
#' Longitudinal biomarker and time-to-event survival data for 40 patients 
#' with primary biliary cirrhosis who participated in a randomised 
#' placebo controlled trial of D-penicillamine conducted at the Mayo
#' Clinic between 1974 and 1984.
#' 
#' Source: Therneau and Grambsch (2000)
#' 
#' 304 obs. of 8 variables (\code{pbcLong}) and 40 obs. of 7 variables (\code{pbcSurv})
#' \itemize{
#' \item \code{age} in years
#' \item \code{albumin} serum albumin (g/dl)
#' \item \code{logBili} logarithm of serum bilirubin
#' \item \code{death} indicator of death at endpoint
#' \item \code{futimeYears} time (in years) between baseline and  
#'     the earliest of death, transplantion or censoring
#' \item \code{id} numeric ID unique to each individual
#' \item \code{platelet} platelet count
#' \item \code{sex} gender (m = male, f = female)
#' \item \code{status} status at endpoint (0 = censored, 
#'     1 = transplant, 2 = dead)
#' \item \code{trt} binary treatment code (0 = placebo, 1 = 
#'     D-penicillamine)
#' \item \code{year} time (in years) of the longitudinal measurements,
#'     taken as time since baseline)
#' }
#' }
#' 
#' \item{\code{radon}}{
#' Data on radon levels in houses in the state of Minnesota. 
#' 
#' Source: Gelman and Hill (2007)
#' 
#' 919 obs. of 4 variables
#' \itemize{
#' \item \code{log_radon} Radon measurement from the house (log scale)
#' \item \code{log_uranium} Uranium level in the county (log scale)
#' \item \code{floor} Indicator for radon measurement made on the first floor of
#' the house (0 = basement, 1 = first floor)
#' \item \code{county} County name (\code{\link{factor}})
#' }
#' }
#' \item{\code{roaches}}{
#' Data on the efficacy of a pest management system at reducing the number of
#' roaches in urban apartments.
#' 
#' Source: Gelman and Hill (2007)
#' 
#' 262 obs. of 6 variables
#' \itemize{
#' \item \code{y} Number of roaches caught
#' \item \code{roach1} Pretreatment number of roaches
#' \item \code{treatment} Treatment indicator
#' \item \code{senior} Indicator for only elderly residents in building
#' \item \code{exposure2} Number of days for which the roach traps were used
#' }
#' }
#' \item{\code{tumors}}{
#' Tarone (1982) provides a data set of tumor incidence in historical
#' control groups of rats; specifically endometrial stromal polyps in
#' female lab rats of type F344.  
#' 
#' Source: Gelman and Hill (2007)
#' 
#' 71 obs. of 2 variables
#' \itemize{
#' \item \code{y} Number of rats with tumors
#' \item \code{K} Number of rats
#' }
#' }
#' \item{\code{wells}}{
#' A survey of 3200 residents in a small area of Bangladesh suffering from
#' arsenic contamination of groundwater. Respondents with elevated arsenic
#' levels in their wells had been encouraged to switch their water source to a
#' safe public or private well in the nearby area and the survey was conducted
#' several years later to learn which of the affected residents had switched
#' wells.
#' 
#' Souce: Gelman and Hill (2007)
#' 
#' 3020 obs. of 5 variables
#' \itemize{
#' \item \code{switch} Indicator for well-switching
#' \item \code{arsenic} Arsenic level in respondent's well
#' \item \code{dist} Distance (meters) from the respondent's house to the
#' nearest well with safe drinking water.
#' \item \code{assoc} Indicator for member(s) of household participate
#' in community organizations
#' \item \code{educ} Years of education (head of household)
#' }
#' }
#' }
#' 
#' @references 
#' Carpenter, B. (2009) Bayesian estimators for the beta-binomial model of
#' batting ability. \url{https://web.archive.org/web/20220618114439/https://lingpipe-blog.com/2009/09/23/}
#' 
#' Efron, B. and Morris, C. (1975) Data analysis using Stein's estimator and its
#' generalizations. \emph{Journal of the American Statistical Association}
#' \strong{70}(350), 311--319.
#' 
#' @templateVar armRef \url{https://stat.columbia.edu/~gelman/arm/}
#' @template reference-gelman-hill
#' 
#' @references
#' Spiegelhalter, D., Thomas, A., Best, N., & Gilks, W. (1996) BUGS 0.5 
#' Examples. MRC Biostatistics Unit, Institute of Public health, Cambridge, UK.
#' 
#' Tarone, R. E. (1982) The use of historical control information in testing for
#' a trend in proportions. \emph{Biometrics} \strong{38}(1):215--220.
#' 
#' Therneau, T. and Grambsch, P. (2000) \emph{Modeling Survival Data: Extending 
#' the Cox Model}. Springer-Verlag, New York, US.
#' 
#' @examples
#' if (.Platform$OS.type != "windows" || .Platform$r_arch != "i386") {
#' # Using 'kidiq' dataset 
#' fit <- stan_lm(kid_score ~ mom_hs * mom_iq, data = kidiq, 
#'                prior = R2(location = 0.30, what = "mean"),
#'                # the next line is only to make the example go fast enough
#'                chains = 1, iter = 500, seed = 12345)
#' pp_check(fit, nreps = 20)
#' \donttest{
#' bayesplot::color_scheme_set("brightblue")
#' pp_check(fit, plotfun = "stat_grouped", stat = "median", 
#'          group = factor(kidiq$mom_hs, labels = c("No HS", "HS")))
#' }
#' }
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