SPOM review: Broadening applications of stochastic patch occupancy models over three decades
Data files
Jan 29, 2026 version files 223.14 KB
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README.md
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Review_SPOMs_analyses_2023.R
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SPOM_database_column_key.csv
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SPOMs_database_2023.csv
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Abstract
Aim: Stochastic patch occupancy models (SPOMs) are a type of spatial population simulation. They are arguably well suited to guide conservation in human-altered landscapes, but their appropriateness for a wide range of species and landscape types has often been questioned. Here, we provide an overview of how SPOM research has expanded over the last three decades and discuss the untapped potential for these models to inform current conservation strategies.
Location: Worldwide
Methods: We carried out a systematic review of studies that have fitted SPOMs to real species and landscapes. We assessed temporal trends in SPOMs’ use in conservation and management studies, their taxonomic and geographic coverage, and the attributes of studied landscapes. We quantitatively and qualitatively evaluated whether the authors’ modelling choices reflected the perceived advantages and disadvantages of SPOMs.
Results: The proportion of SPOMs used to answer conservation questions has increased over time. Questions of where, when and how to conserve have all been addressed, sometimes considering additional aspects such as cost-effectiveness and climate change. Taxonomic diversity coverage has increased over time, and SPOMs have been used in landscapes with a higher proportion of suitable habitat. They have, however, been predominantly applied in temperate biomes. Few studies have explored parameter extrapolation in taxonomically and ecologically related species with mixed results.
Main conclusions: Over the past three decades, authors have exploited the simplicity and flexibility of SPOMs to answer a broad range of questions with practical implications. The use of SPOMs in less fragmented landscapes, and for an increasing range of taxa, suggests that the strictest definitions of their applicability can be challenged. SPOMs have untapped potential for informing conservation under climate change. Given the urgent need to plan for large numbers of species with limited data for fitting, SPOMs could better fulfill their potential to guide conservation if parameters could be extrapolated to data-deficient landscapes and species.
Database and statistical analyses for the review article "Broadening applications of stochastic patch occupancy models over three decades".
In the database:
NA - information not available in the main text or supplementary materials of the publication
SB - Publications found through 'snowball' search are not through keyword search
Code: R version used to run analyses: R 4.0
The supplementary information includes the following files:
Review_SPOMs_analyses_2023.R — Descriptive and statistical analyses performed:
- Species Numeralia (line 29)
- Species IUCN status (line 58)
- H1. Conservation and management studies have increased with time (line 87)
- H2. a. Taxonomic diversity has increased with time (line 111)
- H2. b. There is a taxonomic bias towards insects (line 153)
- H3. a. Biome diversity has increased with time (line 162)
- H3. b. There is a bias towards temperate biomes (line 204)
- H4. Propotion of suitable habitat has varied with time (line 216)
- H4. a. Landscape statistics (line 258)
- H4. b. Temporal trends (line 309)
- H5. Study length varies with interests (line 321)
- H6. Model complexity varies depending on interest (line 338)
SPOM_database_column_key.csv
| ID | Observation Identifier |
|---|---|
| authors | Authors |
| title | Publication title |
| year | Year of publication |
| Group | Generic name of taxonomic group |
| class | Taxonomic class |
| species | Scientific name as reported by authors |
| biome | Terrestria biome as per Terrestrial Ecoregions dataset (Dinerstein et al., 2017) |
| study_site | Site name as reported by authors |
| country | Country as reported by Authors |
| main_interest | Main interest of the study: A - description/application/assessment of SPOM; B - SPOMs comparison; C - insight to metapopulation dynamics of species; D - modelling for conservation or management purposes |
| aim | Study aim as described by the author's |
| model | Model names as reported by the authors: author's, SPOM developed by author(s) without name; Incidence function model (IFM); based on incidence function model but modified by the authors (IFM+); Levins metapopulation model (Levins); MANAGE; Propagule rain model (PRM). Source: Web of Science (WoS) or Snowball method (SB) |
| patch_definition | Patch definiton as described by the authors |
| no_patches | Number of patches |
| tot_extent | Total extent of study area |
| tot_patch_area | Total area of patches |
| mean_patch_area | Mean patch area |
| median_patch_area | Meadian patch area |
| max_patch_area | Maximum patch area |
| area_unit | Area unit |
| total_time_study | Total time of the study |
| metapop_status | Metapopulation status: 1 - asserted; 2 - tested and/or discussed |
| predictive_adequacy | Approach for assessing predictive adequacy: 1 - not assessed or in agreement with other studies; 2 - compared observed vs expected patch occupancy; 3 - statistical analyses to evaluate landscape variables and/or parameters performance |
SPOMs_database_2023.csv
Database including the records (135 observations) of 62 publications
We performed a systematic search within the Web of Science (WoS; https://www.webofscience.com). We carried out a combined search of the terms ‘Stochastic patch occupancy model’ with other terms relevant to the SPOM literature (Table 1), retrieving 2,757 publications. After reviewing the title, abstract, and keywords, we discarded all publications that: a) were not related to landscape ecology literature, b) used other types of landscape models (e.g., individual-based, agent-based, connectivity models, etc.), or c) were not empirical (i.e., were entirely theoretical), reducing the sample to 607papers. Next, we screened the full text of these papers and added 6 publications referenced within that were not found through the WoS search. Of these 613 applied articles, we excluded papers in which: a) virtual species or landscapes were used, b) landscapes were subject to experimental design, c) spatial analyses were grid-based (as opposed to patch-based), e) species detectability data were required, d) local-population dynamics models were applied (i.e. models that required population-specific data, such as survival and reproductive rates), obtaining a final selection of 82 publications, the publication period considered covered more than 30 years (1991-2023).
- Gutiérrez‐Arellano, Claudia; Crone, Elizabeth E.; Pettorelli, Nathalie; Hodgson, Jenny A. (2024). Broadening applications of stochastic patch occupancy models over three decades. Diversity and Distributions. https://doi.org/10.1111/ddi.13822
