multigroup.vaccine
Analyze Outbreak Models of Multi-Group Populations with Vaccination
Model infectious disease dynamics in populations with multiple subgroups having different vaccination rates, transmission characteristics, and contact patterns. Calculate final and intermediate outbreak sizes, form age-structured contact models with automatic fetching of U.S. census data, and explore vaccination scenarios with an interactive 'shiny' dashboard for a model with two subgroups, as described in Nguyen et al. (2024) <doi:10.1016/j.jval.2024.03.039> and Duong et al. (2026) <doi:10.1093/ofid/ofaf695.217>.
README
# Example Census Data
This directory contains example U.S. Census Bureau population estimate data files and city-specific American Community Survey (ACS) data included with the package.
### County-Level Census Data
- `cc-est2024-syasex-49.csv` - Utah (FIPS code 49) county-level population estimates by single-year age and sex, 2020-2024
### City-Level ACS Data
- `hildale_ut_2023.csv` - Hildale city, Utah population by age from ACS 5-Year Estimates (2019-2023)
- `hildale_ut_2023_metadata.csv` - Metadata for Hildale ACS data (variable descriptions)
- `colorado_city_az_2023.csv` - Colorado City town, Arizona population by age from ACS 5-Year Estimates (2019-2023)
- `colorado_city_az_2023_metadata.csv` - Metadata for Colorado City ACS data (variable descriptions)
- `centennial_park_az_2023.csv` - Centennial Park, AZ population by age from ACS 5-Year Estimates (2019-2023)
## Source
### County-Level Data
Data downloaded from the U.S. Census Bureau Population Estimates Program:
https://www2.census.gov/programs-surveys/popest/datasets/2020-2024/counties/asrh/
### City-Level Data
Data downloaded from the U.S. Census Bureau American Community Survey (ACS) 5-Year Estimates via data.census.gov:
- **Hildale, UT**: Table S0101 (Age and Sex), 2019-2023 ACS 5-Year Estimates
- **Colorado City, AZ**: Table S0101 (Age and Sex), 2019-2023 ACS 5-Year Estimates
- **Centennial Park, AZ**: Table S0101 (Age and Sex), 2019-2023 ACS 5-Year Estimates
## Usage
### County-Level Census Data
Access county data in your code using:
```r
library(multigroup.vaccine)
# Get the path to the example data file
utah_csv <- getCensusDataPath()
# Use it with getCensusData
slc_data <- getCensusData(
state_fips = "49",
county_name = "Salt Lake County",
year = 2024,
csv_path = getCensusDataPath()
)
```
### City-Level ACS Data
Access city data using:
```r
library(multigroup.vaccine)
# Load Hildale data with default 5-year age groups
hildale_data <- getCityData(
city_name = "Hildale city, Utah",
csv_path = system.file("extdata", "hildale_ut_2023.csv",
package = "multigroup.vaccine")
)
# Load Colorado City data
colorado_city_data <- getCityData(
city_name = "Colorado City town, Arizona",
csv_path = system.file("extdata", "colorado_city_az_2023.csv",
package = "multigroup.vaccine")
)
# Load with custom age groups
hildale_custom <- getCityData(
city_name = "Hildale city, Utah",
csv_path = system.file("extdata", "hildale_ut_2023.csv",
package = "multigroup.vaccine"),
age_groups = c(0, 5, 18, 65)
)
```
## Purpose
This file is included to:
1. Enable package examples to run without internet access
2. Support `R CMD check` and `pkgdown` building processes
3. Allow offline testing and development
4. Provide a working example for users
## Data Format
The CSV file contains the following columns:
- `SUMLEV` - Summary level (50 = county)
- `STATE` - State FIPS code
- `COUNTY` - County FIPS code
- `STNAME` - State name
- `CTYNAME` - County name
- `YEAR` - Estimate year code (1 = April 1, 2020 base; 2 = 2020; 3 = 2021; etc.)
- `AGE` - Single year of age (0-85+)
- `TOT_POP` - Total population
- `TOT_MALE` - Male population
- `TOT_FEMALE` - Female population
## Updating
To update this file with newer data:
```r
# Download the latest file
url <- "https://www2.census.gov/programs-surveys/popest/datasets/2020-2024/counties/asrh/cc-est2024-syasex-49.csv"
download.file(url, "inst/extdata/cc-est2024-syasex-49.csv")
```
Then rebuild the package documentation with `devtools::document()`.
Versions across snapshots
| Version | Repository | File | Size |
|---|---|---|---|
0.1.1 |
rolling linux/jammy R-4.5 | multigroup.vaccine_0.1.1.tar.gz |
501.0 KiB |
0.1.1 |
rolling linux/noble R-4.5 | multigroup.vaccine_0.1.1.tar.gz |
501.0 KiB |
0.1.1 |
rolling source/ R- | multigroup.vaccine_0.1.1.tar.gz |
450.2 KiB |
0.1.1 |
latest linux/jammy R-4.5 | multigroup.vaccine_0.1.1.tar.gz |
501.0 KiB |
0.1.1 |
latest linux/noble R-4.5 | multigroup.vaccine_0.1.1.tar.gz |
501.0 KiB |
0.1.1 |
latest source/ R- | multigroup.vaccine_0.1.1.tar.gz |
450.2 KiB |
0.1.1 |
2026-04-26 source/ R- | multigroup.vaccine_0.1.1.tar.gz |
450.2 KiB |
0.1.1 |
2026-04-23 source/ R- | multigroup.vaccine_0.1.1.tar.gz |
450.2 KiB |
0.1.1 |
2026-04-09 windows/windows R-4.5 | multigroup.vaccine_0.1.1.zip |
509.7 KiB |