This short vignette provides coding examples on how to use the functions provided by the aquacultuR package to calculate Apparent Digestibility Coefficients of feeds, feed nutrients, and feed ingredients.

library(aquacultuR)
library(magrittr)
library(dplyr)

oldopts <- options()
options(digits = 3)

Data

Note: We could not find any published dataset on digestibility trials in data journals or Open Access repositories (Zenodo, Mendeley Data). We would thus appreciate data contributions from the aquaculture community!

The digestdm dataset contains two fictious diets that differ in their dry matter content and the mass fraction of marker that was found in the feces of an imaginary fish species.

digestdm
#> # A tibble: 2 × 4
#>   diet     dm std_feed std_feces
#>   <chr> <dbl>    <dbl>     <dbl>
#> 1 diet1  0.9      0.01     0.045
#> 2 diet2  0.95     0.01     0.04

The digestnut dataset contains the same two fictious feeds but the dataset is enriched by fictious total nitrogen contents from which the crude protein content of the samples can be estimated.

digestnut
#> # A tibble: 2 × 6
#>   diet     dm N_feed std_feed N_feces std_feces
#>   <chr> <dbl>  <dbl>    <dbl>   <dbl>     <dbl>
#> 1 diet1  0.9   0.064     0.01   0.016     0.045
#> 2 diet2  0.95  0.06      0.01   0.016     0.04

While the example data for the dry matter and specific nutrient digestibility calculations provided are constructed, the data for the calculation of ingredient digestibility originates from Bureau et al. (1999) and Bureau and Hua (2006). It contains all required data for a blood meal that was tested for apparent digestibility in the scope of the cited studies.

digestingr
#> # A tibble: 1 × 8
#>   diet_reference   ingredient   adc_reference adc_test dm_reference dm_ingr
#>   <chr>            <chr>                <dbl>    <dbl>        <dbl>   <dbl>
#> 1 reference diet b blood meal 2         0.923    0.902        0.928   0.895
#> # ℹ 2 more variables: CP_reference <dbl>, CP_ingr <dbl>

Dry matter digestibility

Based on the digestdm dataset, the Apparent Digestibility Coefficient for the dry matter fraction of a feed (\(\text{ADC}_{\text{DM}}\)) can immediately be calculated using the adc_dm() function.

digestdm %>%
  group_by(diet) %>%
  summarise(`ADC DM` = adc_dm(std_diet = std_feed, std_feces = std_feces))
#> # A tibble: 2 × 2
#>   diet  `ADC DM`
#>   <chr>    <dbl>
#> 1 diet1    0.778
#> 2 diet2    0.75

Note that the function default for the dry matter content of the feed is set to 1. This can be changed with the dm argument of the adc_dm() function. The dry matter content of the feces cannot be adjusted.

digestdm %>%
  group_by(diet) %>%
  summarise(`ADC DM` = adc_dm(
    dm = dm,
    std_diet = std_feed,
    std_feces = std_feces
  ))
#> # A tibble: 2 × 2
#>   diet  `ADC DM`
#>   <chr>    <dbl>
#> 1 diet1    0.8  
#> 2 diet2    0.762

Applied on a data frame or tibble, the code outputs the \(\text{ADC}_{\text{DM}}\) for each diet.

Nutrient digestibility

The Apparent Digestibility Coefficient for specific nutrients in a feed (\(\text{ADC}_{\text{nut}}\)) can be calculated analogously with the adc_nut() function. Here, additional function arguments are the mass fractions of the nutrient of interest in the feed and the feces in gram per gram.

digestnut %>%
  group_by(diet) %>%
  summarise(
    `ADC CP` = adc_nut(
      std_diet = std_feed,
      std_feces = std_feces,
      nut_diet = N_feed,
      nut_feces = N_feces
    )
  )
#> # A tibble: 2 × 2
#>   diet  `ADC CP`
#>   <chr>    <dbl>
#> 1 diet1    0.944
#> 2 diet2    0.933

Ingredient digestibility

Lastly, the Apparent Digestibility Coefficient can also be calculated for the dry matter fraction of a specific ingredient in a feed (\(\text{ADC}_{\text{ingr}}\)). This is possible with the adc_ingr() function that

digestingr %>%
  summarise(
    `ADC Ingredient` = adc_ingr(
      adc_test = adc_test,
      adc_ref = adc_reference,
      nut_ref = CP_reference,
      nut_ingr = CP_ingr
    )
  )
#> # A tibble: 1 × 1
#>   `ADC Ingredient`
#>              <dbl>
#> 1            0.875

Same as adc_dm(), the function assumes that the dry matter of the reference feed and the feed ingredient is 1 gram per gram by default. To change this, the function arguments dm_ref and dm_ingr can be used. In addition, the mass fraction of the feed ingredient into the test diet can be set by using the function argument incl_ingr. The default is 0.3 gram per gram.

digestingr %>%
  summarise(
    `ADC Ingredient` = adc_ingr(
      adc_test = adc_test,
      adc_ref = adc_reference,
      nut_ref = CP_reference,
      nut_ingr = CP_ingr,
      dm_ref = dm_reference,
      dm_ingr = dm_ingr
    )
  )
#> # A tibble: 1 × 1
#>   `ADC Ingredient`
#>              <dbl>
#> 1            0.874

The difference from the result stated in Bureau and Hua (2006) (\(\text{ADC} = 87.5\%\)) originates from rounding of the result.

Session info

sessionInfo()
#> R version 4.5.2 (2025-10-31)
#> Platform: x86_64-apple-darwin20
#> Running under: macOS Sequoia 15.7.3
#> 
#> Matrix products: default
#> BLAS:   /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRblas.0.dylib 
#> LAPACK: /Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.1
#> 
#> locale:
#> [1] C/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
#> 
#> time zone: Europe/Prague
#> tzcode source: internal
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> other attached packages:
#> [1] dplyr_1.1.4      magrittr_2.0.4   aquacultuR_1.1.1
#> 
#> loaded via a namespace (and not attached):
#>  [1] vctrs_0.7.0       cli_3.6.5         knitr_1.51        rlang_1.1.7      
#>  [5] xfun_0.56         otel_0.2.0        generics_0.1.4    jsonlite_2.0.0   
#>  [9] glue_1.8.0        htmltools_0.5.9   sass_0.4.10       rmarkdown_2.30   
#> [13] evaluate_1.0.5    jquerylib_0.1.4   tibble_3.3.1      fastmap_1.2.0    
#> [17] yaml_2.3.12       lifecycle_1.0.5   compiler_4.5.2    pkgconfig_2.0.3  
#> [21] rstudioapi_0.18.0 digest_0.6.39     R6_2.6.1          utf8_1.2.6       
#> [25] tidyselect_1.2.1  pillar_1.11.1     bslib_0.9.0       tools_4.5.2      
#> [29] cachem_1.1.0

options(oldopts)

References

Bureau DP, Harris AM, Cho CY (1999) Apparent digestibility of rendered animal protein ingredients for rainbow trout (oncorhynchus mykiss). Aquaculture 180:345–358. https://doi.org/10.1016/S0044-8486(99)00210-0

Bureau DP, Hua K (2006) Letter to the editor of aquaculture. Aquaculture 252:103–105. https://doi.org/10.1016/j.aquaculture.2006.01.028

Calculating Apparent Digestibility