Fungal Growth Assay on Human Faeces • fungalgrowth

Data from a laboratory assay investigating the growth of fungal species on human faeces and their effect on faecal physicochemical properties and bacterial indicator concentrations over 14 days post inoculation. Five fungal species were tested alongside untreated controls: Pleurotus ostreatus (MG1015, MG1010), Ganoderma lucidum, Stropharia fimicola (F35), and Trichoderma harzianum (T22).

Installation

You can install the development version of fungalgrowth from GitHub with:

# install.packages("devtools")
devtools::install_github("global-health-engineering/fungalgrowth")

## Run the following code in console if you don't have the packages
## install.packages(c("dplyr", "knitr", "readr", "stringr", "gt", "kableExtra"))
library(dplyr)
library(knitr)
library(readr)
library(stringr)
library(gt)
library(kableExtra)

Alternatively, you can download the individual datasets as a CSV or XLSX file from the table below.

Click Download CSV. A window opens that displays the CSV in your browser.
Right-click anywhere inside the window and select “Save Page As…”.
Save the file in a folder of your choice.

dataset	CSV	XLSX
experiment_setup	Download CSV	Download XLSX
experiment_endpoint	Download CSV	Download XLSX
faecal_measurements	Download CSV	Download XLSX
inoculum_species	Download CSV	Download XLSX
fungal_growth	Download CSV	Download XLSX

Data

The datasets capture a 14-day laboratory assay designed to study how fungal mycelium grows on human faeces and how that growth alters the substrate’s physicochemical and microbial properties. Five datasets describe the assay end to end: the experimental setup, the characterization of the inputs (faeces samples and fungal inocula), the daily time series of mycelium growth, and the endpoint measurements recorded 14 days post inoculation. Each dataset is lazy-loaded and ready to use as soon as the package is attached.

library(fungalgrowth)

experiment_setup

The dataset experiment_setup contains data about the experimental setup recorded at 0 days post inoculation (0 dpi), linking each treatment unit to its faeces sample and fungal inoculum along with the initial faeces wet weight on the plate. It has 132 observations and 4 variables

experiment_setup |>
  head(3) |>
  gt::gt() |>
  gt::as_raw_html()

id_treatment	id_inoc	id_faeces	wet_weight
1	1	1	15.53
2	1	1	15.81
3	1	1	15.43

For an overview of the variable names, see the following table.

variable_name	variable_type	unit	description
id_treatment	numeric	NA	Unique identifier for each experimental treatment unit.
id_inoc	numeric	NA	Identifier for the fungal inoculum used in this treatment; joins to inoculum_species.
id_faeces	numeric	NA	Identifier for the faeces sample used in this treatment; joins to faecal_measurements.
wet_weight	numeric	g	Wet weight of the faeces sample at day 0 post inoculation (0 dpi).

experiment_endpoint

The dataset experiment_endpoint contains data about the experimental measurements taken at 14 days post inoculation (14 dpi), including faeces wet and dry weights, pH, and bacterial indicator concentrations (E. coli, Enterococcus, total plate count) for each treatment unit. It has 132 observations and 7 variables

experiment_endpoint |> 
  head(3) |> 
  gt::gt() |>
  gt::as_raw_html()

id_treatment	wet_weight	dry_weight	ecoli_concentration	enterococcus_concentration	total_plate_count_concentration	ph
1	15.15	7.001594	0	0.0	0.000000e+00	5.18
2	15.48	6.952096	0	0.0	3.960396e+01	5.27
3	14.61	6.729455	0	178899.1	1.559633e+08	8.53

For an overview of the variable names, see the following table.

variable_name	variable_type	unit	description
id_treatment	numeric	NA	Unique identifier for each experimental treatment unit.
wet_weight	numeric	g	Wet weight of the faeces sample at day 14 post inoculation (14 dpi).
dry_weight	numeric	g	Dry weight of the faeces sample at day 14 post inoculation (14 dpi); derived from wet weight and water content.
ecoli_concentration	numeric	CFU/g	E. coli concentration at day 14 post inoculation (14 dpi).
enterococcus_concentration	numeric	CFU/g	Enterococcus concentration at day 14 post inoculation (14 dpi).
total_plate_count_concentration	numeric	CFU/g	Total plate count concentration at day 14 post inoculation (14 dpi).
ph	numeric	NA	pH of the faeces sample at day 14 post inoculation (14 dpi).

faecal_measurements

The dataset faecal_measurements contains data about the characterization of each faeces sample at 0 days post inoculation (0 dpi), including total faeces weight, additive composition, pH, water content, and bacterial indicator concentrations (E. coli, Enterococcus, total plate count) averaged across three replicates. It has 6 observations and 10 variables

faecal_measurements |>
  head(3) |>
  gt::gt() |>
  gt::as_raw_html()

id_faeces	weight_total	weight_additive	additive	additive_ratio	ph	water_content_mean	ecoli_concentration_mean	enterococcus_concentration_mean	total_plate_count_concentration_mean
1	394	197	wood chips	0.5	6.38	0.5541251	445626.2	384329.0	16545355
2	274	137	wood chips	0.5	6.44	0.5546023	6569243.5	200373.4	246047273
3	394	197	wood chips	0.5	6.04	0.5529212	6085053.9	2103578.7	62342903

For an overview of the variable names, see the following table.

variable_name	variable_type	unit	description
id_faeces	numeric	NA	Identifier for the faeces sample.
weight_total	numeric	g	Total weight of faeces collected before additive at 0 dpi.
weight_additive	numeric	g	Weight of additive mixed into the faeces at 0 dpi.
additive	character	NA	Type of additive mixed into the faeces at 0 dpi.
additive_ratio	numeric	proportion	Proportion of additive relative to total mixture weight at 0 dpi.
ph	numeric	NA	pH of the faeces-additive mixture at collection (0 dpi).
water_content_mean	numeric	proportion	Mean water content of the faeces sample at day 0 post inoculation (0 dpi); mean of 3 replicates.
ecoli_concentration_mean	numeric	CFU/g	Mean E. coli concentration at day 0 post inoculation (0 dpi); mean of 3 replicates.
enterococcus_concentration_mean	numeric	CFU/g	Mean Enterococcus concentration at day 0 post inoculation (0 dpi); mean of 3 replicates.
total_plate_count_concentration_mean	numeric	CFU/g	Mean total plate count concentration at day 0 post inoculation (0 dpi); mean of 3 replicates.

inoculum_species

The dataset inoculum_species contains data about the fungal inocula used in the assay, providing the mapping from each inoculum identifier to the fungal species. It has 44 observations and 2 variables

inoculum_species |>
  head(3) |>
  gt::gt() |>
  gt::as_raw_html()

id_inoc	species
1	ctrl
2	P. ostreatus MG1015
3	P. ostreatus MG1010

For an overview of the variable names, see the following table.

variable_name	variable_type	unit	description
id_inoc	numeric	NA	Identifier for the fungal inoculum.
species	character	NA	Fungal species used as inoculum.

fungal_growth

The dataset fungal_growth contains time-series observations of fungal mycelium growth on each treatment unit, with one row per treatment-observation date. Variables include mycelium area, contamination metrics, and growth descriptors recorded at each timepoint. It has 990 observations and 8 variables

fungal_growth |>
  head(3) |>
  gt::gt() |>
  gt::as_raw_html()

id_treatment	date	dpi	area_size	nr_contaminations	total_contamination_area	reproductive_structures	growth_description
1	2025-11-20	2	0	0	0	0	0
1	2025-11-21	3	0	0	0	0	0
1	2025-11-24	6	0	0	0	0	0

For an overview of the variable names, see the following table.

variable_name	variable_type	unit	description
id_treatment	numeric	NA	Identifier for the experimental treatment unit; joins to experiment_setup and experiment_endpoint.
date	Date	NA	Date of the growth observation measurement.
dpi	integer	days	Days post inoculation; days elapsed between this measurement and the first measurement for this treatment.
area_size	numeric	cm2	Area of fungal mycelium at the observation date.
nr_contaminations	numeric	NA	Number of macroscopically distinct contaminating fungi observed at this timepoint.
total_contamination_area	numeric	cm2	Total area of contamination summed across all observed contamination spots at this timepoint.
reproductive_structures	numeric	NA	Coded indicator of reproductive structures observed at this timepoint.
growth_description	numeric	NA	Mycelium health score assessed on a 0-5 scale by a single unblinded operator: 0: no visible mycelium, 1: sparse/dying mycelium, 2: patchy growth with signs of decline, 3: healthy mycelium covering but with clear visible substrate , 4: dense, vigorous mycelium some substrate visible, 5: dense mycelium mat without any visible material below the mycelium.

Example

library(fungalgrowth)
library(ggplot2)

ggplot(fungal_growth, aes(x = dpi, y = area_size, group = id_treatment)) +
  geom_line(alpha = 0.3) +
  labs(
    title = "Fungal mycelium growth over time",
    x = "Days post inoculation",
    y = "Area size (cm²)"
  ) +
  theme_minimal()

License

Data are available as CC-BY.

Citation

Please cite this package using:

citation("fungalgrowth")
#> To cite package 'fungalgrowth' in publications use:
#> 
#>   Peter J, Clavijo Daza A (2026). _fungalgrowth: Fungal Growth Assay on
#>   Human Faeces_. R package version 0.1.0,
#>   <https://github.com/Global-Health-Engineering/fungalgrowth>.
#> 
#> A BibTeX entry for LaTeX users is
#> 
#>   @Manual{,
#>     title = {fungalgrowth: Fungal Growth Assay on Human Faeces},
#>     author = {Jules Peter and Adriana {Clavijo Daza}},
#>     year = {2026},
#>     note = {R package version 0.1.0},
#>     url = {https://github.com/Global-Health-Engineering/fungalgrowth},
#>   }