Occupied Patches Proportion Function
An Overview
The Occupied Patches Proportion function in MetaCommunityMetrics
provides a simple yet powerful metric for understanding the distribution and prevalence of species across different sites within a metacommunity. By calculating the averaged, minmum and maximum proportion of sites occupied across species, this function helps ecologists assess the spatial extent of species distributions and identify potential patterns of rarity or commonness across the landscape.
This function draws on the concepts discussed by Ehrlén & Eriksson (2000) in their study on dispersal limitation and patchy occupancy in forest herbs. According to their findings, low occupancy may indicate dispersal limitation or strong competition, while high occupancy could suggest mass effects due to high dispersal rates or the ability to thrive in various conditions.
The Function
MetaCommunityMetrics.prop_patches
— Functionprop_patches(presence::AbstractVector, species::AbstractVector, site::AbstractVector) -> DataFrame
Calculate the proportion of sites occupied by each species and summarize the results.
This function takes three vectors: presence
, species
, and site
, and performs the following steps:
Arguments
presence::AbstractVector
: Vector representing the occurence of species.species::AbstractVector
: Vector representing species names or IDs.site::AbstractVector
: Vector representing site names or IDs.
Returns
DataFrame
: A DataFrame containing the mean, minimum, and maximum proportion of sites occupied across all species.
Example
julia> using MetaCommunityMetrics
julia> df = load_sample_data()
53352×12 DataFrame
Row │ Year Month Day Sampling_date_order plot Species Abundance Presence Latitude Longitude standardized_temperature standardized_precipitation
│ Int64 Int64 Int64 Int64 Int64 String3 Int64 Int64 Float64 Float64 Float64 Float64
───────┼──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
1 │ 2010 1 16 1 1 BA 0 0 35.0 -110.0 0.829467 -1.4024
2 │ 2010 1 16 1 2 BA 0 0 35.0 -109.5 -1.12294 -0.0519895
3 │ 2010 1 16 1 4 BA 0 0 35.0 -108.5 -0.409808 -0.803663
4 │ 2010 1 16 1 8 BA 0 0 35.5 -109.5 -1.35913 -0.646369
5 │ 2010 1 16 1 9 BA 0 0 35.5 -109.0 0.0822 1.09485
⋮ │ ⋮ ⋮ ⋮ ⋮ ⋮ ⋮ ⋮ ⋮ ⋮ ⋮ ⋮ ⋮
53348 │ 2023 3 21 117 9 SH 0 0 35.5 -109.0 -0.571565 -0.836345
53349 │ 2023 3 21 117 10 SH 0 0 35.5 -108.5 -2.33729 -0.398522
53350 │ 2023 3 21 117 12 SH 1 1 35.5 -107.5 0.547169 1.03257
53351 │ 2023 3 21 117 16 SH 0 0 36.0 -108.5 -0.815015 0.95971
53352 │ 2023 3 21 117 23 SH 0 0 36.5 -108.0 0.48949 -1.59416
53342 rows omitted
julia> prop_patches(df.Presence, df.Species, df.plot)
1×3 DataFrame
Row │ mean_prop_patches min_prop_patches max_prop_patches
│ Float64 Float64 Float64
─────┼───────────────────────────────────────────────────────
1 │ 0.734649 0.0833333 1.0
References
- Ehrlén, J., & Eriksson, O. (2000). Dispersal Limitation and Patchy Occupancy in Forest Herbs. Ecology, 81(6), 1667-1674. https://doi.org:https://doi.org/10.1890/0012-9658(2000)081[1667:DLAPOI]2.0.CO;2