Getting Started with EpiLossR

Introduction

EpiLossR provides standardized tools for estimating direct economic losses associated with mortality and morbidity in animal diseases.

Version 0.1.0 focuses on two core functions:

  • mortality_loss()
  • morbidity_loss()

These functions return a common S3 object (epi_loss) with methods for printing, summarizing, plotting, and exporting results.

Mortality Loss

library(EpiLossR)

mort <- mortality_loss(
  animals = 100,
  mortality = 5,
  value = 10000
)

mort
#> 
#> EpiLossR
#> -----------------------------
#> Measure : Mortality Loss 
#> Estimate: 50,000 
#> Unit    : Currency

Summary

summary(mort)
#> 
#> EpiLossR Summary
#> ==============================
#> 
#> Measure : Mortality Loss 
#> Estimate: 50,000 
#> Unit    : Currency 
#> 
#> Inputs
#> ------
#> $animals
#> [1] 100
#> 
#> $mortality
#> [1] 5
#> 
#> $value
#> [1] 10000
#> 
#> 
#> Details
#> -------
#> $mortality_rate
#> [1] 0.05
#> 
#> $deaths
#> [1] 5

Plot

plot(mort)

Convert to Data Frame

as.data.frame(mort)
#>          Measure Estimate     Unit
#> 1 Mortality Loss    50000 Currency

Morbidity Loss

morb <- morbidity_loss(
  affected = 20,
  duration = 10,
  daily_loss = 100,
  treatment_cost = 5000
)

morb
#> 
#> EpiLossR
#> -----------------------------
#> Measure : Morbidity Loss 
#> Estimate: 25,000 
#> Unit    : Currency

Summary

summary(morb)
#> 
#> EpiLossR Summary
#> ==============================
#> 
#> Measure : Morbidity Loss 
#> Estimate: 25,000 
#> Unit    : Currency 
#> 
#> Inputs
#> ------
#> $affected
#> [1] 20
#> 
#> $duration
#> [1] 10
#> 
#> $daily_loss
#> [1] 100
#> 
#> $treatment_cost
#> [1] 5000
#> 
#> 
#> Details
#> -------
#> $production_loss
#> [1] 20000
#> 
#> $treatment_cost
#> [1] 5000

Plot

plot(morb)

Convert to Data Frame

as.data.frame(morb)
#>          Measure Estimate     Unit
#> 1 Morbidity Loss    25000 Currency

Session Information

sessionInfo()
#> R version 4.6.1 (2026-06-24)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 26.04.1 LTS
#> 
#> Matrix products: default
#> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
#> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.32.so;  LAPACK version 3.12.0
#> 
#> locale:
#>  [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
#>  [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
#>  [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
#>  [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
#>  [9] LC_ADDRESS=C               LC_TELEPHONE=C            
#> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       
#> 
#> time zone: Etc/UTC
#> tzcode source: system (glibc)
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#> [1] EpiLossR_0.1.0 rmarkdown_2.32
#> 
#> loaded via a namespace (and not attached):
#>  [1] digest_0.6.39    R6_2.6.1         fastmap_1.2.0    xfun_0.61       
#>  [5] maketools_1.3.2  cachem_1.1.0     knitr_1.52       htmltools_0.5.9 
#>  [9] buildtools_1.0.0 lifecycle_1.0.5  cli_3.6.6        sass_0.4.10     
#> [13] jquerylib_0.1.4  compiler_4.6.1   sys_3.4.3        tools_4.6.1     
#> [17] evaluate_1.0.5   bslib_0.12.0     yaml_2.3.12      otel_0.2.0      
#> [21] jsonlite_2.0.0   rlang_1.3.0