R2ucare: An <scp>r</scp> package to perform goodness‐of‐fit tests for capture–recapture models

Giménez, Olivier; Lebreton, Jean‐Dominique; Choquet, Rémi; Pradel, Roger

doi:10.1111/2041-210x.13014

Cited by 91 publications

(52 citation statements)

References 26 publications

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“…Additional research is needed to test these hypotheses. Our findings emphasize the importance of checking for violations of the assumption of equal detectability in multispecies mark‐recapture studies, even when examining species thought to have highly comparable ecologies (Gimenez et al ).…”

Section: Discussionmentioning

confidence: 67%

“…In such models, Φ represents the apparent survival probability because the complementary estimate is a combination of mortality and permanent emigration. To our knowledge, no tests yet exist to assess goodness‐of‐fit (GOF) of CJS models with individual and temporal covariates (Gimenez et al ). Therefore, we summarized capture histories by frequency for each species to assess GOF for a fully time‐dependent, species‐specific CJS model.…”

Section: Methodsmentioning

confidence: 99%

“…Therefore, we summarized capture histories by frequency for each species to assess GOF for a fully time‐dependent, species‐specific CJS model. We examined GOF for each species with the R2ucare package (Gimenez et al ) in R, and found the model to fit the data adequately (ringed salamander:

χ_{31}^{2}

= 40.31, P = 0.12, spotted salamander:

χ_{31}^{2}

= 38.32, P = 0.17, small‐mouthed salamander:

χ_{33}^{2}

= 32.92, P = 0.47). Because individuals of each species were released simultaneously, we did not perform transience GOF testing (i.e., tests of components 3.SR and 3.SM).…”

Section: Methodsmentioning

confidence: 99%

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Estimating Survival for Elusive Juvenile Pond‐Breeding Salamanders

2020

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Juvenile vital rates have important effects on population dynamics for many species, but this demographic is often difficult to locate and track. As such, we frequently lack reliable estimates of juvenile survival, which are necessary for accurately assessing population stability and potential management approaches to conserve biodiversity. We estimated survival rates for elusive juveniles of 3 species, the ringed salamander (Ambystoma annulatum), spotted salamander (A. maculatum), and small‐mouthed salamander (A. texanum), using 2 approaches. First, we conducted an 11‐month (2016–2017) mark‐recapture study within semi‐natural enclosures and used Bayesian Cormack‐Jolly‐Seber models to estimate survival and recapture probabilities. Second, we inferred the expected annual juvenile survival rate given published vital rates for pre‐metamorphic and adult ambystomatids assuming stable population growth. For all 3 species, juvenile survival probabilities were constant across recapture occasions, whereas recapture probability estimates were time‐dependent. Further, survival and recapture probabilities among study species were similar. Post‐study sampling revealed that the initial study period median estimate of annual survival probability (0.39) underestimated the number of salamanders known alive at 11 months. We therefore appended approximately 1 year of opportunistic data, which produced a median annual survival probability of 0.50, encompassing salamanders that we knew to have been alive. Calculation from literature values suggested a mean annual terrestrial juvenile ambystomatid survival probability of 0.49. Similar results among our approaches indicated that juvenile survival estimates for the study species were robust and likely comparable to rates in nature. These estimates can now be confidently applied to research, monitoring, and management efforts for the study species and ecologically similar taxa. Our findings indicated that similarly robust vital rate estimates for subsets of ecologically and phylogenetically similar species can provide reasonable surrogate demographic information that can be used to reveal key factors influencing population viability for data‐deficient species. © 2020 The Wildlife Society.

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Section: Discussionmentioning

confidence: 67%

Section: Methodsmentioning

confidence: 99%

χ_{31}^{2}

= 40.31, P = 0.12, spotted salamander:

χ_{31}^{2}

= 38.32, P = 0.17, small‐mouthed salamander:

χ_{33}^{2}

= 32.92, P = 0.47). Because individuals of each species were released simultaneously, we did not perform transience GOF testing (i.e., tests of components 3.SR and 3.SM).…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Estimating Survival for Elusive Juvenile Pond‐Breeding Salamanders

2020

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“…Model convergence was confirmed both visually and by using the “R hat” Gelman–Rubin statistic (Gelman & Rubin, ). We assessed the goodness of fit of all our submodels using postpredictive checks and the R package R2ucare (Gimenez, Lebreton, Choquet, & Pradel, ) and found no clear evidence for lack of fit (Supporting Information Appendix ).…”

Section: Methodsmentioning

confidence: 99%

Quantifying the links between land use and population growth rate in a declining farmland bird

Paquet

Arlt

Knape

et al. 2019

Ecology and Evolution

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Land use is likely to be a key driver of population dynamics of species inhabiting anthropogenic landscapes, such as farmlands. Understanding the relationships between land use and variation in population growth rates is therefore critical for the management of many farmland species. Using 24 years of data of a declining farmland bird in an integrated population model, we examined how spatiotemporal variation in land use (defined as habitats with “Short” and “Tall” ground vegetation during the breeding season) and habitat‐specific demographic parameters relates to variation in population growth taking into account individual movements between habitats. We also evaluated contributions to population growth using transient life table response experiments which gives information on contribution of past variation of parameters and real‐time elasticities which suggests future scenarios to change growth rates. LTRE analyses revealed a clear contribution of Short habitats to the annual variation in population growth rate that was mostly due to fledgling recruitment, whereas there was no evidence for a contribution of Tall habitats. Only 18% of the variation in population growth was explained by the modeled local demography, the remaining variation being explained by apparent immigration (i.e., the residual variation). We discuss potential biological and methodological reasons for high contributions of apparent immigration in open populations. In line with LTRE analysis, real‐time elasticity analysis revealed that demographic parameters linked to Short habitats had a stronger potential to influence population growth rate than those of Tall habitats. Most particularly, an increase of the proportion of Short sites occupied by Old breeders could have a distinct positive impact on population growth. High‐quality Short habitats such as grazed pastures have been declining in southern Sweden. Converting low‐quality to high‐quality habitats could therefore change the present negative population trend of this, and other species with similar habitat requirements.

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“…We fit Cormack-Jolly-Seber (CJS) models within program MARK to estimate the probabilities of apparent annual survival (Φ, probability of remaining alive and remaining within the study area) and recapture (ρ) from our live-encounter banding records; as is standard for CJS models, adult thrushes newly captured in 2015 (the last primary period) were not included in our modeling effort (Cormack 1964, Jolly 1965, Seber 1965, White and Burnham 1999. Goodness-of-fit tests, including for overdispersion, conducted with the R package R2ucare (Gimenez et al 2018, R Core Team 2019), suggested that our data were appropriate for CJS models (Pradel et al 2005). We considered total net hours (a measure of netting effort) across June and July (2002-2015) as our only covariate modeling recapture probability.…”

Section: Modeling Survival Hypotheses and Choice Of Covariatesmentioning

confidence: 99%

Apparent survival of a range-restricted montane forest bird species is influenced by weather throughout the annual cycle

Hill¹,

Lloyd²,

McFarland³

et al. 2019

ACE

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To conserve small and fragmented populations, we need an understanding of their population dynamics. With a global population estimate of < 120,000, Bicknell's Thrush (Catharus bicknelli) is considered one of the Nearctic-Neotropical migrants at greatest risk of extinction. This range-restricted songbird breeds in high-elevation fir (Abies balsamea) forests of the northeastern United States and eastern Canada, and primarily overwinters in forests of the Dominican Republic. The Conservation Action Plan for Bicknell's Thrush identifies numerous actions that may help stem population declines and promote recovery of the species, yet the empirical data needed to prioritize among these actions are lacking. We fit Cormack-Jolly-Seber models with mark-recapture data to test a series of hypotheses about the factors that limit apparent survival in 178 adult Bicknell''s Thrush (50 females and 128 males) captured on the breeding grounds in Vermont (June-July, 2001-2015). We focused on putatively important factors from throughout their annual cycle: cyclical population dynamics of nest predators, and weather effects on food abundance on the breeding and wintering grounds. Apparent survival of Bicknell's Thrush was relatively stable (mean Φ = 0.61, 95% CI: 0.54, 0.68) over our 15-year study, and most strongly associated with fir mast production. Apparent survival was higher following years during which fir trees produced large mast crops (mean Φ = 0.67, 95% CI: 0.55, 0.79), compared to following nonmast years (Φ = 0.56 ± 0.06, 95% CI: 0.43, 0.68). These results are likely driven by the reduced red squirrel density and increased nesting success and site fidelity of adult thrushes following nonmast years. Apparent survival of Bicknell's Thrush was also associated with relatively wet conditions on the wintering grounds in Hispaniola as assessed via the El Niño-Southern Oscillation (ENSO) precipitation index (ESPI). These relatively wet December-March periods are likely linked to greater primary productivity and the local availability of fruits and arthropods consumed by Bicknell's Thrush. Our research provides the most comprehensive examination of potentially limiting factors on Bicknell's Thrush populations to date and suggests future avenues of research exploring the relationship between food availability, survival, and climate change induced reductions in rainfall for the Greater Antilles.

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R2ucare: An r package to perform goodness‐of‐fit tests for capture–recapture models

Cited by 91 publications

References 26 publications

Estimating Survival for Elusive Juvenile Pond‐Breeding Salamanders

Estimating Survival for Elusive Juvenile Pond‐Breeding Salamanders

Quantifying the links between land use and population growth rate in a declining farmland bird

Apparent survival of a range-restricted montane forest bird species is influenced by weather throughout the annual cycle

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