ref-b5a6c332a7beaf120245paperAdvances and applications of occupancy models
This abstract describes a discussion of ecological occupancy estimation: inferring species occurrence and occupancy dynamics while allowing for missed detections or species misidentification. Its central message is that flexible models increase the investigator’s responsibility to define sites, sampling occasions, a period of static occurrence and detection criteria. Those definitions affect biological interpretation. The authors use an amphibian–pathogen system to illustrate the issues. Only the abstract and bibliographic record were supplied; this report cannot assess the detailed models or the applications’ empirical findings.
This is a partial reading. Its claims are limited to the material listed in the coverage record.
The idea
The problem
Species observations may miss a species or identify it incorrectly. Occupancy models aim to estimate occurrence and its dynamics despite those observation problems. The abstract frames study design as part of this inferential problem: investigators must decide what counts as a site, a repeated sampling occasion and a detection before model parameters can receive a biological interpretation. e-probleme-designe-interpretation
What this work contributes
The authors discuss recent occupancy estimation methods alongside the biological systems that motivated their development. The supplied abstract establishes this review-oriented scope, but does not enumerate the methods. e-review
The authors argue that model flexibility adds investigator responsibilities: defining sites, replicate sampling occasions, the period over which species occurrence is assumed static, and the criteria for detection. They state that biological inference and parameter interpretation depend on those definitions and on meeting model assumptions. These are abstract-level design principles; no computational procedure is supplied. e-designe-interpretatione-scope
The authors say they demonstrate the relevance of those definitions through applications within one amphibian–pathogen system, discuss criticisms of occupancy-model use, and derive suggestions for further research and model development. The abstract announces these arguments without providing their detailed evidence. e-applications
Source description summarizes the inspected material. Author claim preserves the authors’ attribution. Reader analysis and Open question are interpretive.
Taxonomy assessment
Catalog at reading time
Catalog updated
This assessment applies to the snapshot below. Check the current catalog entry before reusing it.
- Major category
- Foundational work
- Subcategories
- Surveys & technical resources
- Architecture
- Not applicable
- Prediction paradigm
- Not applicable
- Quadrant
- Not applicable
- Classification status
- Verified from primary sources
Classification assessment not applicable
The inspected abstract concerns ecological species occurrence and an amphibian–pathogen system. World-action-model architecture, action-prediction paradigm and quadrant labels are not applicable to that stated subject. This agrees with the catalog’s Not applicable entries and is compatible with its review-oriented subcategory. The abstract does not establish the work’s broader foundational importance for world-action modeling. e-probleme-reviewe-applications
These labels preserve the catalog snapshot used for this reading. The assessment audits that snapshot without changing the source classification.
Limits & reproduction
Limitations and open boundaries
The authors make biological inference conditional on study definitions and the ability to meet model assumptions. Model flexibility therefore does not, by itself, establish that a chosen design permits the intended biological conclusion. e-designe-interpretation
The abstract identifies one amphibian–pathogen system as its application setting. It supplies neither measurements nor comparative evaluations, so the scope and strength of empirical support across other biological systems cannot be assessed from this material. e-applicationse-scope
The abstract mentions criticism of occupancy-model use but does not identify the criticized settings or the authors’ responses. Specific failure modes cannot be attributed to this article from the supplied text. e-applicationse-scope
What a reproduction would require
An application-level reproduction would require the actual site definitions, replicate schedule, static-occurrence interval, detection criteria, observations, model specification and assumption checks. The abstract motivates the design requirements but supplies no operational values or complete procedure. e-designe-interpretatione-scope
Reader-proposed prerequisite check: with a complete application available, trace each reported parameter interpretation to the corresponding site, time and detection definitions. A mismatch would challenge interpretability under the authors’ stated criterion; this is a proposed documentation check, not a reproduced result. e-designe-interpretation
Questions to take further
- How do the application’s definitions of site and detection determine the biological meaning of occupancy?
- What evidence in the full applications supports the assumption that occurrence is static over the chosen period?
- Which criticisms discussed in the complete article concern model assumptions, and which concern study design or parameter interpretation?
What was read
- Sections inspected
- Advances and applications of occupancy models — title, author byline, journal and DOI
- Links
- Abstract — complete supplied abstract
- Suggested Citation and publication details
- Appendix
- Not established
- Figures inspected
- No figures recorded as inspected
- Tables inspected
- No tables recorded as inspected
Outside this reading
- External figure assets are not downloaded; HTML alt text and mathematical text are retained where available.
- Full article body or complete references were not established.
- The publisher Free Access PDF at https://besjournals.onlinelibrary.wiley.com/doi/pdf/10.1111/2041-210X.12100 was identified but not locally retrieved (HTTP 403); no full-paper reading or visual inspection is established.
- The complete supplied text chunk was read. This is a review of the USGS abstract and bibliographic record, not the complete journal article.
- No full methods, equations, fitting or inference algorithms, datasets, numerical results, ablations, detailed criticisms, or future-work proposals are supplied. Appendix existence and content are unknown.
- No PDF page, original scientific figure, table or final crop was available for visual inspection. No code was inspected and no experiment was reproduced.
- Identity disclosure: the title and DOI 10.1111/2041-210X.12100 match the catalog. The inspected byline reads Larissa Bailey; Darry I. MacKenzie; James D. Nichols. The catalog reads Larissa L Bailey; Darryl I MacKenzie; James D Nichols. These are substantially matching author identities; the source spelling and abbreviated Bailey name are preserved in metadata.
- Date/version disclosure: the USGS record gives September 04, 2013 and Year Published 2013, while the catalog gives the 2014 journal issue. Both identify Methods in Ecology and Evolution, volume 5, issue 12, pages 1269–1279. No article revision identifier or primary revision history is supplied, so the date discrepancy cannot establish a content revision or equivalence between editions.
- The record names Patuxent Wildlife Research Center as a contributing office, without assigning author affiliations. No author affiliation is asserted. Metadata uses the inspected HTML heading as its location because there is no inspected PDF title page.
- The method fields and results remain empty because the supplied abstract does not provide a recoverable model, fitting or inference procedure, or reported experimental findings. Its stated design principles are summarized as abstract-level contributions.
Evidence & sources
Evidence links resolve to these source locations. Expand an entry to inspect its supporting detail.
e-identityHTML heading “Advances and applications of occupancy models”, By line and DOI; Suggested Citation; publication details: Publication Date, Year Published, Volume, Issue, First page and Last page
The observed title matches exactly. The byline credits Larissa Bailey, Darry I. MacKenzie, and James D. Nichols. DOI is 10.1111/2041-210X.12100. The record dates publication to September 04, 2013 and lists Methods in Ecology and Evolution 5(12), pages 1269–1279; it supplies no revision identifier.
Advances and applications of occupancy modelse-problemHTML Abstract, sentence 1
The abstract describes models estimating species occurrence and occupancy dynamics while accounting for possible non-detection or species misidentification.
Advances and applications of occupancy modelse-reviewHTML Abstract, sentence 2
The authors discuss recent occupancy estimation methods and the biological systems motivating their development.
Advances and applications of occupancy modelse-designHTML Abstract, sentences 3–4
The authors associate model flexibility with added investigator demands and identify responsibility for defining sites, replicate sampling occasions, the period of assumed static occurrence and detection criteria.
Advances and applications of occupancy modelse-interpretationHTML Abstract, sentence 5
Biological inference and interpretation of model parameters depend on those definitions and the ability to meet model assumptions.
Advances and applications of occupancy modelse-applicationsHTML Abstract, sentences 6–7
The authors announce applications from a single amphibian–pathogen system, discussion of criticized uses of occupancy models, and suggestions for research and model development.
Advances and applications of occupancy modelse-scopeSupplied HTML record: Links, complete Abstract, Suggested Citation and publication details
The supplied record contains bibliographic information and an abstract, with a link to the publisher. It provides no article-body methods, equations, numerical experiment results, scientific figures or tables. Its Description field reports an 11-page article; those article pages are not contained in this supplied text.
Advances and applications of occupancy modelsSource record
Advances and applications of occupancy models
HTML · 446 extracted words · Accessed 7 Sept 2026
Source URL & fingerprint
https://pubs.usgs.gov/publication/70059793
- SHA-256
40b01ea22432c50bec4b60cb3f3905524002dd6f0cad940f70476dfa497484eb