Title: Functions for Stochastic Search Variable Selection (SSVS)
Version: 2.1.0
Description: Functions for performing stochastic search variable selection (SSVS) for binary and continuous outcomes and visualizing the results. SSVS is a Bayesian variable selection method used to estimate the probability that individual predictors should be included in a regression model. Using MCMC estimation, the method samples thousands of regression models in order to characterize the model uncertainty regarding both the predictor set and the regression parameters. For details see Bainter, McCauley, Wager, and Losin (2020) Improving practices for selecting a subset of important predictors in psychology: An application to predicting pain, Advances in Methods and Practices in Psychological Science 3(1), 66-80 <doi:10.1177/2515245919885617>.
URL: https://github.com/sabainter/SSVS
BugReports: https://github.com/sabainter/SSVS/issues
Depends: R (≥ 3.5.0)
Imports: bayestestR, BoomSpikeSlab, checkmate, ggplot2, graphics, rlang, stats, dplyr, magrittr, gridExtra
Suggests: AER, bslib, foreign, glue, knitr, mice, psych, reactable, readxl, rmarkdown, scales, shiny, shinyjs, shinyWidgets, testthat (≥ 3.0.0), tools, utils
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.3.2
Config/testthat/edition: 3
NeedsCompilation: no
Packaged: 2025-03-19 16:28:46 UTC; sbainter
Author: Sierra Bainter ORCID iD [cre, aut], Thomas McCauley [aut], Mahmoud Fahmy [aut], Dean Attali ORCID iD [aut]
Maintainer: Sierra Bainter <sbainter@miami.edu>
Repository: CRAN
Date/Publication: 2025-03-19 16:40:02 UTC

Pipe operator

Description

See magrittr::%>% for details.

Usage

lhs %>% rhs

Arguments

lhs

A value or the magrittr placeholder.

rhs

A function call using the magrittr semantics.

Value

The result of calling rhs(lhs).

Example dataset for ssvs function @format A data frame with 74 records and 76 variables

Description

Example dataset for ssvs function @format A data frame with 74 records and 76 variables

Usage

dat

Format

An object of class data.frame with 74 rows and 76 columns.

Imputed mtcars Dataset

Description

This dataset is a version of the mtcars dataset where random missing values were introduced, and multiple imputation was performed using the mice package.

Usage

imputed_mtcars

Format

A data frame with 160 rows and 13 variables

Details

Random missingness was introduced into 10% of the values in the original mtcars dataset. Multiple imputation was then performed using the mice package with the following parameters:

The dataset included here is the first completed dataset resulting from the multiple imputation process.

Source

Original dataset from datasets::mtcars, with missing values introduced and imputed.

Examples


data(imputed_mtcars)
head(imputed_mtcars)

Run an interactive analysis tool (Shiny app) that lets you perform SSVS in a browser

Description

Run an interactive analysis tool (Shiny app) that lets you perform SSVS in a browser

Usage

launch()

Plot results of an SSVS model

Description

Plot results of an SSVS model

Usage

## S3 method for class 'ssvs'
plot(x, threshold = 0.5, legend = TRUE, title = NULL, color = TRUE, ...)

Arguments

x

An ssvs result object obtained from ssvs()

threshold

An MIP threshold to show on the plot, must be between 0-1. If NULL, no threshold is used.

legend

If TRUE, show a legend for the shapes based on the threshold. Ignored if threshold = NULL.

title

The title of the plot. Set to NULL to use a default title.

color

If TRUE, the data points will be colored based on the threshold.

...

Ignored

Value

Creates a plot of the inclusion probabilities by variable

Examples


outcome <- "qsec"
predictors <- c("cyl", "disp", "hp", "drat", "wt", "vs", "am", "gear", "carb", "mpg")
results <- ssvs(x = predictors, y = outcome, data = mtcars, progress = FALSE)
plot(results)

Plot SSVS-MI Estimates and Marginal Inclusion Probabilities (MIP)

Description

This function creates a plot of SSVS-MI estimates with minimum and maximum and a plot for marginal inclusion probabilities (MIP) optional thresholds for highlighting significant predictors..

Usage

## S3 method for class 'ssvs_mi'
plot(
  x,
  type = "both",
  threshold = 0.5,
  legend = TRUE,
  est_title = NULL,
  mip_title = NULL,
  color = TRUE,
  ...
)

Arguments

x

An ssvs result object obtained from ssvs_mi()

type

Defaults to "both", can change to "estimate" or "MIP".

threshold

A numeric value (between 0 and 1) specifying the MIP threshold to highlight significant predictors. Defaults to 0.5.

legend

Logical indicating whether to include a legend for the threshold. Defaults to TRUE.

est_title

A character string specifying the plot title. Defaults to "SSVS-MI estimates".

mip_title

A character string specifying the plot title. Defaults to "Multiple Inclusion Probability for SSVS-MI".

color

Logical indicating whether to use color to highlight thresholds. Defaults to TRUE.

...

Ignored

Value

Two ggplot2 objects representing the plot of SSVS estimates and the plot of MIP with thresholds.

Examples


data(imputed_mtcars)
outcome <- 'qsec'
predictors <- c('cyl', 'disp', 'hp', 'drat', 'wt', 'vs', 'am', 'gear', 'carb','mpg')
imputation <- '.imp'
results <- ssvs_mi(data = imputed_mtcars, y = outcome, x = predictors, imp = imputation)
plot(results)

Print the summary of ssvs_mi

Description

Print the summary of ssvs_mi

Usage

## S3 method for class 'ssvs_mi_summary'
print(x, ...)

Print the summary of an SSVS model

Description

Print the summary of an SSVS model

Usage

## S3 method for class 'ssvs_summary'
print(x, ...)

Perform SSVS for continuous and binary outcomes

Description

For continuous outcomes, a basic Gibbs sampler is used. For binary outcomes, BoomSpikeSlab::logit.spike() is used.

Usage

ssvs(
  data,
  y,
  x,
  continuous = TRUE,
  inprob = 0.5,
  runs = 20000,
  burn = 5000,
  a1 = 0.01,
  b1 = 0.01,
  prec.beta = 0.1,
  progress = TRUE
)

Arguments

data

The dataframe used to extract predictors and response values

y

The response variable

x

The set of predictor variables

continuous

If TRUE, treat the response variable as continuous. If FALSE, treat the response variable as binary.

inprob

Prior inclusion probability value, which applies to all predictors. The prior inclusion probability reflects the prior belief that each predictor should be included in the model. A prior inclusion probability of .5 reflects the belief that each predictor has an equal probability of being included or excluded. Note that a value of .5 also implies a prior belief that the true model contains half of the candidate predictors. The prior inclusion probability will influence the magnitude of the marginal inclusion probabilities (MIPs), but the relative pattern of MIPs is expected to remain fairly consistent, see Bainter et al. (2020) for more information.

runs

Total number of iterations (including burn-in). Results are based on the Total - Burn-in iterations.

burn

Number of burn-in iterations. Burn-in iterations are discarded warmup iterations used to achieve MCMC convergence. You may increase the number of burn-in iterations if you are having convergence issues.

a1

Prior parameter for Gamma(a,b) distribution on the precision (1/variance) residual variance. Only used when continuous = TRUE.

b1

Prior parameter for Gamma(a,b) distribution on the precision (1/variance) residual variance. Only used when continuous = TRUE.

prec.beta

Prior precision (1/variance) for beta coefficients. Only used when continuous = TRUE.

progress

If TRUE, show progress of the model creation. When continuous = TRUE, progress plots will be created for every 1000 iterations. When continuous = FALSE, 10 progress messages will be printed. Only used when continuous = TRUE.

Value

An ssvs object that can be used in summary() or plot().

Examples


# Example 1: continuous response variable
outcome <- "qsec"
predictors <- c("cyl", "disp", "hp", "drat", "wt", "vs", "am", "gear", "carb", "mpg")
results <- ssvs(data = mtcars, x = predictors, y = outcome, progress = FALSE)

# Example 2: binary response variable
library(AER)
data(Affairs)
Affairs$hadaffair[Affairs$affairs > 0] <- 1
Affairs$hadaffair[Affairs$affairs == 0] <- 0
outcome <- "hadaffair"
predictors <- c("gender", "age", "yearsmarried", "children", "religiousness",
"education", "occupation", "rating")
results <- ssvs(data = Affairs, x = predictors, y = outcome, continuous = FALSE, progress = FALSE)

Perform SSVS on Multiply Imputed Datasets

Description

This function performs Stochastic Search Variable Selection (SSVS) analysis on multiply imputed datasets for a given set of predictors and a response variable. It supports continuous response variables and calculates aggregated results across multiple imputations.

Usage

ssvs_mi(
  data,
  y,
  x,
  imp,
  imp_num = 5,
  interval = 0.9,
  continuous = TRUE,
  progress = FALSE
)

Arguments

data

A dataframe containing the variables of interest, including an .imp column for imputation identifiers.

y

The response variable (character string).

x

A vector of predictor variable names.

imp

The imputation variable.

imp_num

The number of imputations to process (default is 5).

interval

Confidence interval level for summary results (default is 0.9).

continuous

Logical indicating if the response variable is continuous (default is TRUE).

progress

Logical indicating whether to display progress (default is FALSE).

Value

An ssvs_mi object containing aggregated results across imputations that can be used in summary().

Examples


data(imputed_mtcars)
outcome <- 'qsec'
predictors <- c('cyl', 'disp', 'hp', 'drat', 'wt', 'vs', 'am', 'gear', 'carb','mpg')
imputation <- '.imp'
agg_results <- ssvs_mi(data = imputed_mtcars, y = outcome, x = predictors, imp = imputation)

Summarize results of an SSVS model

Description

Summarize results from SSVS including marginal inclusion probabilities, Bayesian model averaged parameter estimates, and 95% highest posterior density credible intervals. Estimates and credible intervals are based on standardized X variables.

Usage

## S3 method for class 'ssvs'
summary(object, interval = 0.89, threshold = 0, ordered = FALSE, ...)

Arguments

object

An SSVS result object obtained from ssvs()

interval

The desired probability for the credible interval, specified as a decimal

threshold

Minimum MIP threshold where a predictor will be shown in the output, specified as a decimal

ordered

If TRUE, order the results based on MIP (in descending order)

...

Ignored

Value

A dataframe with results

Examples


outcome <- "qsec"
predictors <- c("cyl", "disp", "hp", "drat", "wt", "vs", "am", "gear", "carb", "mpg")
results <- ssvs(data = mtcars, x = predictors, y = outcome, progress = FALSE)
summary(results, interval = 0.9, ordered = TRUE)

Calculate Summary Statistics for SSVS-MI Results

Description

Computes summary statistics (average, minimum, and maximum) for beta coefficients, MIP and average nonzero beta coefficients from an SSVS result object.

Usage

## S3 method for class 'ssvs_mi'
summary(object, ...)

Arguments

object

An ssvs_mi result object obtained from ssvs_mi()

...

Ignored

Value

A data frame with results

Examples


data(imputed_mtcars)
outcome <- 'qsec'
predictors <- c('cyl', 'disp', 'hp', 'drat', 'wt', 'vs', 'am', 'gear', 'carb','mpg')
imputation <- '.imp'
results <- ssvs_mi(data = imputed_mtcars, y = outcome, x = predictors, imp = imputation)
summary_MI<-summary(results)
print(summary_MI)

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