2026 Joint Nature Conservation Committee (JNCC) R scripts used to run analyses for the assessment of the indicator “Potential Physical Loss of Predicted Biogenic Habitats” used in the UK Marine Strategy Part One 2026 update nonGeographicDataset https://portal.medin.org.uk/portal/start.php?tpc=010_fa3c390b-699e-46d4-822c-21702df17837 This dataset includes R scripts used to apply the indicator “Potential Physical Loss of Predicted Biogenic Habitats”. This indicator measures the potential physical loss of horse mussel reefs (Modiolus modiolus) and of eelgrass beds (Zostera marina) due to selected anthropogenic activities using habitat suitability models. These models were used to overcome the limitations of data paucity in the location and extent of these important habitats. Physical loss is defined as a permanent change to the seabed, which has lasted or is expected to last at least 12 years. For each assessed habitat, anthropogenic activities likely to cause potential physical loss were identified to obtain relevant spatial footprint data. The extent of overlap between the predicted suitable habitat and activity footprints were weighted by an activity-specific factor to estimate the amount of predicted suitable habitat potentially lost across and within UKMS sub-regions.