Type: Package
Title: Bayesian Parameter Estimation and Forecasting for Epidemiological Models
Version: 1.0.0
Description: Methods for Bayesian parameter estimation and forecasting in epidemiological models. Functions enable model fitting using Bayesian methods and generate forecasts with uncertainty quantification. Implements approaches described in <doi:10.48550/arXiv.2411.05371> and <doi:10.1002/sim.9164>.
License: CC0
Encoding: UTF-8
Imports: bayesplot, readxl, openxlsx, rstan, ggplot2, dplyr
Depends: R (≥ 3.5.0)
URL: https://github.com/gchowell/BayesianFitForecast
BugReports: https://github.com/gchowell/BayesianFitForecast/issues
RoxygenNote: 7.3.2
Suggests: knitr, rmarkdown, testthat (≥ 3.0.0)
VignetteBuilder: knitr
Config/testthat/edition: 3
NeedsCompilation: no
Packaged: 2024-12-03 05:55:12 UTC; hamedkp
Author: Hamed Karami [aut], Amanda Bleichrodt [aut], Ruiyan Luo [aut], Gerardo Chowell [aut, cre]
Maintainer: Gerardo Chowell <gchowell@gsu.edu>
Repository: CRAN
Date/Publication: 2024-12-05 18:20:07 UTC

Run MCMC Analysis with Specified Option File

Description

This function runs an MCMC analysis based on the specified option file, sourcing auxiliary scripts, and executing the analysis.

Usage

Run_MCMC(option_file, excel_file = NULL, output_path = NULL)

Arguments

option_file

The name of the option file (e.g., "option1.R") located in the current working directory.

excel_file

The path to the Excel file containing the data.

output_path

Directory where the output will be saved. If NULL, uses a temporary directory.

Value

None. The function executes and saves results directly.

Examples

# Get path to the example option file included with package
option_file <- system.file("extdata", "option.R", 
                          package = "BayesianFitForecast")
                          
# Specify the path to the Excel file you want to analyze
excel_file <- system.file("extdata", "SanFrancisco.xlsx", 
                          package = "BayesianFitForecast")  # Modify this path accordingly
                          
# Run the MCMC analysis

Run_MCMC(option_file = option_file, excel_file = excel_file, output_path = NULL)

Run Analyze Results with Specified Data and Options

Description

This function performs an analysis based on the specified data file, option_file, Excel file, and it saves the results in the output_path. It loads auxiliary data, executes analysis steps, and saves the results.

Usage

Run_analyzeResults(
  data_file_location,
  option_file,
  excel_file,
  output_path = NULL
)

Arguments

data_file_location

The location of the data file which is generated after Run_MCMC.

option_file

The name of the option file (e.g., "option1.R") located in the current working directory.

excel_file

The path to an Excel file containing additional data. This parameter is required and must be a valid path to an existing file.

output_path

Directory where the output will be saved. If NULL, a temporary directory will be created and used.

Value

None. The function executes the analysis and saves the results to the specified output_path.

Examples

# Define file paths
data_file <- system.file("extdata", 
                          package = "BayesianFitForecast")
option_file <- system.file("extdata", "option.R", 
                          package = "BayesianFitForecast")
                                                     
excel_file <- system.file("extdata", "SanFrancisco.xlsx", 
                          package = "BayesianFitForecast")  
# Run the analysis

Run_analyzeResults(
  data_file = data_file, 
  option_file = option_file, 
  excel_file = excel_file, 
  output_path = NULL)


# Results are saved in the specified directory or temporary directory if none is provided.