DOI: 10.5061/dryad.pzgmsbcst
title: SPOM review: Broadening applications of stochastic patch occupancy models over three decades

description: 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.
description: 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).
description: # SPOM review: Broadening applications of stochastic patch occupancy
 models over three decades 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