The goal of epitraxr is to simplify the process of manipulating Epitrax data and generating reports. The package is targeted toward public health officials.
Installation
You can install the development version of epitraxr from GitHub with:
# install.packages("devtools")
devtools::install_github("EpiForeSITE/epitraxr")Examples
# Read the sample EpiTrax dataset included with the package
sample_file <- system.file("sample_data", "sample_epitrax_data.csv", package = "epitraxr")
epitrax_data <- read_epitrax_data(sample_file)
# Get the list of diseases in the dataset
diseases <- unique(epitrax_data$disease)
# Set up configuration
config <- list(
current_population = 102000,
avg_5yr_population = 97000,
rounding_decimals = 1
)
# Generate monthly counts report for 2024
monthly_counts <- create_report_monthly_counts(
data = epitrax_data,
y = 2024,
disease_names = diseases
)
monthly_counts
#> disease Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec
#> 1 Chickenpox 26 19 22 40 16 23 37 16 21 27 14 31
#> 2 COVID-19 81 99 84 120 89 101 125 93 80 117 99 103
#> 3 Influenza 116 96 130 151 115 100 139 135 113 138 96 137
#> 4 Measles 22 21 26 27 16 19 35 25 18 32 25 38
#> 5 Syphilis 22 22 23 24 18 29 15 20 13 23 21 39
# Generate YTD counts with rates per 100k (through May)
ytd_report <- create_report_ytd_counts(
data = epitrax_data,
disease_names = diseases,
y = 2024,
m = 5,
config = config,
as.rates = TRUE
)
ytd_report
#> disease Current_YTD_Rate_per_100k Avg_5yr_YTD_Rate_per_100k
#> 1 Chickenpox 286.3 107.6
#> 2 COVID-19 1167.6 630.9
#> 3 Influenza 1437.3 693.8
#> 4 Measles 298.0 151.8
#> 5 Syphilis 263.7 166.8