The GUD
package provides probability density functions and sampling algorithms
for three key distributions from the General Unimodal Distribution (GUD)
family: the Flexible Gumbel (FG) distribution, the Double Two-Piece
(DTP) Student-t distribution, and the Two-Piece Scale (TPSC) Student-t
distribution. Additionally, this package includes a function for
Bayesian linear modal regression, leveraging these three distributions
for model fitting.
You can install the GUD package:
if (! require(GUD)) {
install.packages(pkgs = "GUD",
repos = "https://cran.rstudio.com/" )
} else {
require(GUD)
}
#> Loading required package: GUDThe general unimodal distribution (GUD) family is essentially a family
of two-component mixture distributions. The probability density function
(pdf) of a member of GUD family is $$
f\left(y \mid w, \theta, \boldsymbol{\xi}_1, \boldsymbol{\xi}_2\right)=w f_1\left(y \mid \theta, \boldsymbol{\xi}_1\right)+(1-w) f_2\left(y \mid \theta, \boldsymbol{\xi}_2\right),
$$ where
- The pdfs
$f_1\left(\cdot \mid \theta, \boldsymbol{\xi}_1\right)$ and$f_2\left(\cdot \mid \theta, \boldsymbol{\xi}_2\right)$ are unimodal at$\theta$ . - The pdfs
$f_1\left(\cdot \mid \theta, \boldsymbol{\xi}_1\right)$ and$f_2\left(\cdot \mid \theta, \boldsymbol{\xi}_2\right)$ are left-skewed and right-skewed respectively. - The mixture pdf
$f\left(\cdot \mid w, \theta, \boldsymbol{\xi}_1, \boldsymbol{\xi}_2\right)$ in (1) is continuous in its domain.
More details of the GUD family can be found in Liu, Q., Huang, X., & Bai, R. (2024).
In this section, we demonstrate how to use the GUD package to analyze
2003 United States Crime Data as in Section 2 of Liu, Q., Huang, X., &
Bai, R. (2024).
In “The Art and Science of Learning from Data, 5th edition” by Alan
Agresti, Christine A. Franklin, and Bernhard Klingenberg, an interesting
example about the 2003 United States crime data is presented to
demonstrate the influence of outliers in the classic linear regression
model. This example is very compelling and partially motivates the
construction of the Bayesian modal regression based on the GUD family.
This data contains the murder rate, percentage of college education,
poverty percentage, and metropolitan rate for the 50 states in the
United States and the District of Columbia (D.C.) from 2003. The murder
rate is defined as the annual number of murders per
# load data crime from the GUD package
df1 <- crime
# the conditional scatter plot matrices of U.S. crime data
if (require(lattice)) {
lattice::splom(~df1[c(6,4,9,3)],
main = NULL,
panel = function(x,y,...) {
panel.splom(x,y,...)
})
}
#> Loading required package: lattice
In the conditional scatter plot matrices, we notice an outlier, Washington, D.C., which stands out and does not follow the common pattern of other states.
Next, we demonstrate how to fit the Bayesian modal regression model based on the TPSC distribution to the 2003 United States crime data.
TPSC_model <- modal_regression(`murder rate` ~ college + poverty + metropolitan,
data = df1,
model = "TPSC",
chains = 2,
iter = 2000)
#>
#> SAMPLING FOR MODEL 'TPSC' NOW (CHAIN 1).
#> Chain 1:
#> Chain 1: Gradient evaluation took 3.2e-05 seconds
#> Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 0.32 seconds.
#> Chain 1: Adjust your expectations accordingly!
#> Chain 1:
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#> Chain 1:
#> Chain 1: Elapsed Time: 1.095 seconds (Warm-up)
#> Chain 1: 0.674 seconds (Sampling)
#> Chain 1: 1.769 seconds (Total)
#> Chain 1:
#>
#> SAMPLING FOR MODEL 'TPSC' NOW (CHAIN 2).
#> Chain 2:
#> Chain 2: Gradient evaluation took 1.1e-05 seconds
#> Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 0.11 seconds.
#> Chain 2: Adjust your expectations accordingly!
#> Chain 2:
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#> Chain 2:
#> Chain 2: Elapsed Time: 1.028 seconds (Warm-up)
#> Chain 2: 0.591 seconds (Sampling)
#> Chain 2: 1.619 seconds (Total)
#> Chain 2:One can summarize the Bayesian analysis using the summary function.
print(summary(TPSC_model), n = 7)
#> # A tibble: 113 × 10
#> variable mean median sd mad q5 q95 rhat ess_bulk ess_tail
#> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 w 0.276 0.282 0.117 0.126 0.0756 0.464 1.01 368. 235.
#> 2 delta 1.90 1.78 0.677 0.566 1.09 3.15 1.01 447. 582.
#> 3 sigma 1.17 1.16 0.265 0.257 0.760 1.62 1.00 540. 343.
#> 4 (Interc… 1.13 1.31 2.73 2.69 -3.71 5.26 1.00 698. 971.
#> 5 college -0.197 -0.201 0.0825 0.0812 -0.325 -0.0554 1.00 648. 995.
#> 6 poverty 0.244 0.248 0.138 0.147 0.0150 0.462 1.00 568. 784.
#> 7 metropo… 0.0627 0.0616 0.0143 0.0138 0.0413 0.0889 1.00 521. 640.
#> # ℹ 106 more rowsOne can present the traceplot of the MCMC chain using the
bayesplot::mcmc_trace function.
if (require(bayesplot)) {
bayesplot::mcmc_trace(TPSC_model, pars = c("(Intercept)",
"college",
"poverty",
"metropolitan"))
}
#> Loading required package: bayesplot
#> Warning: package 'bayesplot' was built under R version 4.3.1
#> This is bayesplot version 1.11.1
#> - Online documentation and vignettes at mc-stan.org/bayesplot
#> - bayesplot theme set to bayesplot::theme_default()
#> * Does _not_ affect other ggplot2 plots
#> * See ?bayesplot_theme_set for details on theme setting
The summary of posterior predictive distribution can be assessed using
the following command. Here ystar[1] represents the posterior
prediction of the first observation in the dataset, and so on.
summary(posterior::subset_draws(TPSC_model, variable = "ystar"))
#> # A tibble: 51 × 10
#> variable mean median sd mad q5 q95 rhat ess_bulk ess_tail
#> <chr> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
#> 1 ystar[1] 7.25 6.20 15.3 2.03 3.28 13.4 1.00 1791. 1717.
#> 2 ystar[2] 2.67 1.35 12.6 2.02 -1.55 9.87 1.00 2016. 1885.
#> 3 ystar[3] 7.12 6.06 7.78 1.90 3.36 12.7 1.00 1691. 2043.
#> 4 ystar[4] 6.62 5.54 11.3 2.36 2.24 12.5 1.00 1688. 1793.
#> 5 ystar[5] 7.37 6.20 8.39 1.96 3.36 13.6 1.00 1811. 1809.
#> 6 ystar[6] 3.85 2.71 6.18 2.09 -0.315 11.1 1.00 1937. 1937.
#> 7 ystar[7] 5.22 3.86 14.0 2.04 0.856 12.4 1.00 1475. 1937.
#> 8 ystar[8] 5.79 4.91 5.04 1.80 2.16 11.7 1.00 1891. 1478.
#> 9 ystar[9] 6.72 5.28 17.6 2.61 1.18 14.4 1.00 1422. 1693.
#> 10 ystar[10] 7.75 6.41 10.4 1.94 3.58 14.7 1.00 2065. 1687.
#> # ℹ 41 more rowsFurther comparisons between mean, median, and modal regression can be found in Section 2 of Liu, Q., Huang, X., & Bai, R. (2024) and Section 6 of Liu, Q., Huang, X., & Zhou, H. (2024).