Journal articles: 'Abundance models'

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Potts, Joanne M., and Jane Elith. "Comparing species abundance models." Ecological Modelling 199, no. 2 (November 2006): 153–63. http://dx.doi.org/10.1016/j.ecolmodel.2006.05.025.

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He, Fangliang, Kevin Gaston, and Jianguo Wu. "On species occupancy-abundance models." Écoscience 9, no. 1 (January 2002): 119–26. http://dx.doi.org/10.1080/11956860.2002.11682698.

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Chave, Jérôme, David Alonso, and Rampal S. Etienne. "Comparing models of species abundance." Nature 441, no. 7089 (May 2006): E1. http://dx.doi.org/10.1038/nature04826.

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Bi, S. L., T. D. Li, L. H. Li, and W. M. Yang. "SOLAR MODELS WITH REVISED ABUNDANCE." Astrophysical Journal 731, no. 2 (April 1, 2011): L42. http://dx.doi.org/10.1088/2041-8205/731/2/l42.

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Duff, Thomas J., Tina L. Bell, and Alan York. "Patterns of plant abundances in natural systems: is there value in modelling both species abundance and distribution?" Australian Journal of Botany 59, no. 8 (2011): 719. http://dx.doi.org/10.1071/bt11017.

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In plant ecology it is common to use biophysical models to predict species distribution; however, spatial quantitative models of plant species remain rare. In practice, occupancy models are often assumed to indicate habitant quality and are used as surrogate abundance models. This study assessed the potential value of quantitative models of plants for ecosystem management applications by assessing patterns of occupancy and abundance within two closely related understorey plant species, Xanthorrhoea australis and X. caespitosa. Vegetation quadrats were surveyed in Eucalyptus woodland and cover-abundances were assessed using a metric pin intersection technique. A zero inflated generalised additive modelling process was used to assess the relationship of species occupancies and cover-abundances to environmental properties. The models were applied to mapped environmental data to create spatial predictions of occupancy and cover-abundance. Both species shared several predictor variables, but differing responses to these variables resulted in mutually exclusive distributions. No significant correlation was observed between occupancy and cover-abundance for X. australis, but strong correlation was evident for X. caespitosa. The strength of the occupancy and abundance relationship was found to differ greatly between the two species and is therefore likely to be species specific. Occupancy models have been used successfully as proxies for habitat quality models of plant species; however where occupancy and abundance of plants are driven by different influences occupancy will be a poor surrogate for abundance. Outcomes may be improved if occupancy models are validated for abundance or quantitative models are developed and tested for individual species.

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Latham, M. Cecilia, A. David M. Latham, Nathan F. Webb, Nicole A. Mccutchen, and Stan Boutin. "Can Occupancy–Abundance Models Be Used to Monitor Wolf Abundance?" PLoS ONE 9, no. 7 (July 23, 2014): e102982. http://dx.doi.org/10.1371/journal.pone.0102982.

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Sequeira, Ana M. M., Camille Mellin, Hector M. Lozano-Montes, Jessica J. Meeuwig, Mathew A. Vanderklift, Michael D. E. Haywood, Russell C. Babcock, and M. Julian Caley. "Challenges of transferring models of fish abundance between coral reefs." PeerJ 6 (April 17, 2018): e4566. http://dx.doi.org/10.7717/peerj.4566.

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Reliable abundance estimates for species are fundamental in ecology, fisheries, and conservation. Consequently, predictive models able to provide reliable estimates for un- or poorly-surveyed locations would prove a valuable tool for management. Based on commonly used environmental and physical predictors, we developed predictive models of total fish abundance and of abundance by fish family for ten representative taxonomic families for the Great Barrier Reef (GBR) using multiple temporal scenarios. We then tested if models developed for the GBR (reference system) could predict fish abundances at Ningaloo Reef (NR; target system), i.e., if these GBR models could be successfully transferred to NR. Models of abundance by fish family resulted in improved performance (e.g., 44.1% <R2 < 50.6% for Acanthuridae) compared to total fish abundance (9% <R2 < 18.6%). However, in contrast with previous transferability obtained for similar models for fish species richness from the GBR to NR, transferability for these fish abundance models was poor. When compared with observations of fish abundance collected in NR, our transferability results had low validation scores (R2 < 6%,p > 0.05). High spatio-temporal variability of patterns in fish abundance at the family and population levels in both reef systems likely affected the transferability of these models. Inclusion of additional predictors with potential direct effects on abundance, such as local fishing effort or topographic complexity, may improve transferability of fish abundance models. However, observations of these local-scale predictors are often not available, and might thereby hinder studies on model transferability and its usefulness for conservation planning and management.

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Fabrizio, Mary C., Jonathan Raz, and Rajesh Ramanath Bandekar. "Using linear models with correlated errors to analyze changes in abundance of Lake Michigan fishes: 1973-1992." Canadian Journal of Fisheries and Aquatic Sciences 57, no. 4 (April 1, 2000): 775–88. http://dx.doi.org/10.1139/f00-020.

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We examined annual changes in relative abundance of Lake Michigan fishes using linear models with correlated errors in space and time. Abundance of bloater (Coregonus hoyi), deepwater sculpin (Myoxocephalus thompsoni), slimy sculpin (Cottus cognatus), alewife (Alosa pseudoharengus), and rainbow smelt (Osmerus mordax) was monitored with bottom trawls at 10 discrete depths (between 18 and 110 m) off eight fixed ports from 1973 to 1992. The model describing abundance included fixed effects of year, port, depth, and interaction terms as well as quadratic and cubic effects of year and depth because changes in abundance were not strictly linear. Observed temporal trends in abundance varied with species and depth. Additionally, trends in alewife and slimy sculpin abundances depended on port. Cubic trends in the abundance of bloater and quadratic trends in deepwater sculpin and rainbow smelt abundances were similar among ports, permitting lakewide inferences for these species. Mean bloater abundance was low throughout the 1970s, increased during the 1980s, and reached high levels by 1990. Mean abundances of deepwater sculpin and rainbow smelt increased from 1973 to the mid-1980s and declined thereafter. The linear model with correlated errors can be readily applied to repeated-measures data from other fixed-station fishery surveys and is appropriate for data exhibiting spatial and temporal autocorrelations.

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Richer, M. G., M. L. McCall, and N. Arimoto. "Oxygen Abundances in Diffuse Ellipticals and the Metallicity-Luminosity Relation for Dwarf Galaxies." Symposium - International Astronomical Union 171 (1996): 439. http://dx.doi.org/10.1017/s0074180900233573.

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Using theoretical models of the planetary nebula populations in galaxies, we investigate whether the current oxygen abundances in bright planetary nebulae can be used to predict the oxygen abundance that persisted in the interstellar medium when star formation stopped. In all galaxies, these models predict that a gap develops between the abundances observed in bright planetary nebulae and those that persisted in the interstellar medium when star formation stopped. This abundance gap depends primarily upon the oxygen abundance achieved in the interstellar medium when star formation stopped, though it also has some sensitivity to the history of star formation. The gap is always less than 0.5dex in these models. For the Milky Way, the predicted abundance gap, 0.14dex, is identical to that observed. The abundance gap magnifies the abundance-related differences between diffuse ellipticals and dwarf irregulars found by Richer & McCall (1995, ApJ, 445, 642). Diffuse ellipticals are confirmed to have larger oxygen abundances than similarly luminous dwarf irregulars, and to have larger [O/Fe] ratios than dwarf irregulars with the same oxygen abundance. The simplest explanation for both of these observations is that diffuse ellipticals formed on shorter time scales than dwarf irregulars. Given this difference in the history of star formation, diffuse ellipticals cannot be the faded remnants of dwarf irregulars.

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PAULUCCI, L., and J. E. HORVATH. "NU-PROCESS IN EXOTIC MODELS." International Journal of Modern Physics D 19, no. 08n10 (August 2010): 1731–35. http://dx.doi.org/10.1142/s0218271810017238.

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The exact physical conditions generating the abundances of r-elements in environments such as supernovae explosions are still under debate. We evaluated the characteristics expected for the neutrino wind in the proposed model of type-II supernova driven by conversion of nuclear matter to strange matter. Neutrinos will change the final abundance of elements after freeze out of r-process nucleosynthesis, specially those close to mass peaks.

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Macreadie, Peter I., Rod M. Connolly, Gregory P. Jenkins, Jeremy S. Hindell, and Michael J. Keough. "Edge patterns in aquatic invertebrates explained by predictive models." Marine and Freshwater Research 61, no. 2 (2010): 214. http://dx.doi.org/10.1071/mf09072.

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Predictive frameworks for understanding and describing how animals respond to habitat fragmentation, particularly across edges, have been largely restricted to terrestrial systems. Abundances of zooplankton and meiofauna were measured across seagrass–sand edges and the patterns compared with predictive models of edge effects. Artificial seagrass patches were placed on bare sand, and zooplankton and meiofauna were sampled with tube traps at five positions (from patch edges: 12, 60 and 130 cm into seagrass; and 12 and 60 cm onto sand). Position effects consisted of the following three general patterns: (1) increases in abundance around the seagrass–sand edge (total abundance and cumaceans); (2) declining abundance from seagrass onto sand (calanoid copepods, harpacticoid copepods and amphipods); and (3) increasing abundance from seagrass onto sand (crustacean nauplii and bivalve larvae). The first two patterns are consistent with resource-distribution models, either as higher resources at the confluence of adjacent habitats or supplementation of resources from high-quality to low-quality habitat. The third pattern is consistent with reductions in zooplankton abundance as a consequence of predation or attenuation of currents by seagrass. The results show that predictive models of edge effects can apply to aquatic animals and that edges are important in structuring zooplankton and meiofauna assemblages in seagrass.

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Volkov, Igor, Jayanth R. Banavar, Fangliang He, Stephen P. Hubbell, and Amos Maritan. "Comparing models of species abundance (Reply)." Nature 441, no. 7089 (May 2006): E1—E2. http://dx.doi.org/10.1038/nature04827.

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13

Hughes, R. G. "Theories and Models of Species Abundance." American Naturalist 128, no. 6 (December 1986): 879–99. http://dx.doi.org/10.1086/284611.

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Mathis, John S. "Dust Models with Tight Abundance Constraints." Astrophysical Journal 472, no. 2 (December 1996): 643–55. http://dx.doi.org/10.1086/178094.

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Bradley, Bethany A. "Predicting abundance with presence-only models." Landscape Ecology 31, no. 1 (November 7, 2015): 19–30. http://dx.doi.org/10.1007/s10980-015-0303-4.

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Zhou, Chao, Huimin Wang, Hongyu Zhao, and Tao Wang. "fastANCOM: a fast method for analysis of compositions of microbiomes." Bioinformatics 38, no. 7 (February 3, 2022): 2039–41. http://dx.doi.org/10.1093/bioinformatics/btac060.

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Abstract Summary Analysis of compositions of microbiomes (ANCOM) compares the absolute abundances of microbes between two or more ecosystems using relative abundances in specimens derived from these ecosystems. Despite its impressive performance, there are two drawbacks to ANCOM. First, with K microbes it requires fitting K(K−1)/2 models for log-ratios of counts, and so can be computationally intensive. Second, it does not output P-values for microbes detected as differentially abundant. We propose a fast implementation of ANCOM, fastANCOM, that fits only K models for log-transformed counts. fastANCOM provides P-values to declare statistical significance and outputs log fold changes of abundance between groups. We demonstrate that fastANCOM compares favorably with existing differential abundance testing methods in terms of running time, false discovery rate and power. Availability and implementation fastANCOM is available at https://github.com/ZRChao/fastANCOM. Supplementary information Supplementary data are available at Bioinformatics online.

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Zaffos, Andrew, and Steven M. Holland. "Abundance and extinction in Ordovician–Silurian brachiopods, Cincinnati Arch, Ohio and Kentucky." Paleobiology 38, no. 2 (2012): 278–91. http://dx.doi.org/10.1666/10026.1.

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A basic hypothesis in extinction theory predicts that more abundant taxa have an evolutionary advantage over less abundant taxa, which should manifest as increased survivorship during major extinction events and longer fossil-record durations. Despite this, various paleontologic studies have found conflicting patterns, indicating a more complex relationship between abundance and extinction in the geologic past. This study tests the relationship between abundance and extinction among brachiopod genera within seven third-order depositional sequences spanning the Late Ordovician to Early Silurian (Katian–Aeronian) of the Cincinnati Arch.Contrary to predictions, abundance is not positively correlated with duration in this study. Abundance and duration range from strongly negatively correlated to uncorrelated depending on the spatial scale of analysis and the geologic intervals included, but correlations never indicate that abundance is an evolutionary advantage. In contrast, abundance was an advantageous trait prior to the Ordovician/Silurian extinction, and brachiopods with higher abundances were more likely to survive the event than less abundant brachiopods. While this result is in keeping with common models of extinction, it has not been observed previously at a mass extinction boundary. This may be further evidence that the Ordovician/Silurian extinction was not accompanied by a shift in the macroevolutionary selectivity regime.

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Smith, John-David T. "New neon-abundance results in Galactic WN and WC stars." Symposium - International Astronomical Union 212 (2003): 234–35. http://dx.doi.org/10.1017/s0074180900212187.

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The fast, dense winds which characterize Wolf-Rayet stars obscure their underlying cores, and complicate the verification of evolving core and nucleosynthesis models. A powerful technique for probing WR core evolution involves measuring abundances of wind-borne nuclear processed elements. Neon, in particular, undergoes a remarkable change in abundance during the later stages of a WR star's lifetime. By the end of the WC phase, it becomes the fourth most abundant element, after He, C and O (Maeder 1983).

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Babel, J. "Diffusion Models for Magnetic Ap Stars." International Astronomical Union Colloquium 138 (1993): 458–72. http://dx.doi.org/10.1017/s025292110002090x.

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AbstractProgress made in spectroscopy and in the diffusion theory permits now to make severe comparisons, based on line profiles, between theory and observation.We first review transport processes which are present in the atmospheric layers of Ap stars and discuss their relative importance. We then show that mass loss could play a key role for the creation of abundance maps. A mass loss model is proposed for 53 Cam and is compared, by spectrum synthesis, with visible and IUE high resolutions observations. The model accounts well for the line profiles of several elements with an exception for Ti. Furthermore, the abundance stratification predicted by this model gives close agreement with the large variation of the abundances of Cr and Fe found between the visible and UV domains. The diffusion-mass loss model finally permits to give a simple interpretation of the peculiar Ca II K lines observed in many Ap SrCrEu stars and in particular in 53 Cam, β CrB and HD 191742.

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Reggiani, Henrique, Kevin C. Schlaufman, Brian F. Healy, Joshua D. Lothringer, and David K. Sing. "Evidence that the Hot Jupiter WASP-77 A b Formed Beyond Its Parent Protoplanetary Disk’s H2O Ice Line." Astronomical Journal 163, no. 4 (March 10, 2022): 159. http://dx.doi.org/10.3847/1538-3881/ac4d9f.

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Abstract Idealized protoplanetary disk and giant planet formation models have been interpreted to suggest that a giant planet’s atmospheric abundances can be used to infer its formation location in its parent protoplanetary disk. It has recently been reported that the hot Jupiter WASP-77 A b has subsolar atmospheric carbon and oxygen abundances with a solar C/O abundance ratio. Assuming solar carbon and oxygen abundances for its host star WASP-77 A, WASP-77 A b’s atmospheric carbon and oxygen abundances possibly indicate that it accreted its envelope interior to its parent protoplanetary disk’s H2O ice line from carbon-depleted gas with little subsequent planetesimal accretion or core erosion. We show that the photospheric abundances of carbon and oxygen in WASP-77 A are supersolar with a subsolar C/O abundance ratio, implying that WASP-77 A b’s atmosphere has significantly substellar carbon and oxygen abundances with a superstellar C/O ratio. Our result possibly indicates that WASP-77 A b’s envelope was accreted by the planet beyond its parent protoplanetary disk's H2O ice line. While numerous theoretical complications to these idealized models have now been identified, the possibility of nonsolar protoplanetary disk abundance ratios confound even the most sophisticated protoplanetary disk and giant planet formation models. We therefore argue that giant planet atmospheric abundance ratios can only be meaningfully interpreted relative to the possibly nonsolar mean compositions of their parent protoplanetary disks as recorded in the photospheric abundances of their dwarf host stars.

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Nomoto, K., T. Shigeyama, and T. Tsujimoto. "Supernova Abundance Generation." Symposium - International Astronomical Union 145 (1991): 21–38. http://dx.doi.org/10.1017/s007418090022723x.

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Theoretical models of supernova explosions of various types are reviewed to obtain heavy element yields from supernovae. We focus on new models for SN 1987A, and Type Ia, Ib, and Ic supernovae. Maximum brightness and decline rate of their light curves suggest that 12–18 M⊙ stars produce larger amount of 56Ni than more massive stars. We discuss relative roles of various types of supernovae in the chemical evolution of galaxies.

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De los Ríos-Escalante, Patricio, Stefan Woelfl, Patricio Acevedo, and Manuel Castro. "Crustacean zooplankton communities, mixotrophic cililates, and optical properties in North Patagonian lakes, investigated by remote sensing." Crustaceana 93, no. 9-10 (October 29, 2020): 1065–78. http://dx.doi.org/10.1163/15685403-bja10022.

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Abstract North Patagonian lakes are characterized by their oligotrophic or oligo-mesotrophic status. These conditions bring with them, respectively, the presence of abundant mixotrophic ciliates and a low species number of crustacean zooplankton under oligotrophic status, and low numbers of mixotrophic ciliates and a high species number of zooplankton under oligo-mesotrophic status. The aims of the present study are, (1) to use remote sensing techniques for determining abundances of mixotrophic ciliates and crustacean zooplankton, and (2) to characterize these mixotrophic and zooplankton communities by using null models. The sensing was accomplished from a satellite, i.e., by measuring the reflectance of the sunlight on a waterbody, which result will vary according to the contents of the water column. The results of Principal Component Analysis (PCA) revealed that sites with low reflectance of all bands have a high abundance of Stentor accompanied by low zooplankton absolute abundance, whereas a markedly opposite situation was observed under high reflectance, where Stentor has low abundance in conjunction with high zooplankton absolute abundances. The null models revealed that the communities in the studied sites do not have structured species associations, and that there is an overlap of niches. These results obtained agree with similar observations for Argentinean Patagonian lakes.

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Li, Xinhai, Ning Li, Baidu Li, Yuehua Sun, and Erhu Gao. "AbundanceR: A Novel Method for Estimating Wildlife Abundance Based on Distance Sampling and Species Distribution Models." Land 11, no. 5 (April 29, 2022): 660. http://dx.doi.org/10.3390/land11050660.

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Appropriate field survey methods and robust modeling approaches play an important role in wildlife protection and habitat management because reliable information on wildlife distribution and abundance is important for conservation planning and actions. However, accurately estimating animal abundance is challenging in most species, as usually only a small proportion of the population can be detected during surveys. Species distribution models can predict the habitat suitability index, which differs from species abundance. We designed a method to adjust the results from species distribution models to achieve better accuracy for abundance estimation. This method comprises four steps: (1) conducting distance sampling, recording species occurrences, and surveying routes; (2) performing species distribution modeling using occurrence records and predicting animal abundance in each quadrat in the study area; (3) comparing the difference between field survey results and predicted abundance in quadrats along survey routes, adjusting model prediction, and summing up to obtain total abundance in the study area; (4) calculating uncertainty from three sources, i.e., distance sampling (using detection rate), species distribution models (using R squared), and differences between the field survey and model prediction [using the standard deviation of the ratio (observation/prediction) at different zones]. We developed an R package called abundanceR to estimate wildlife abundance and provided data for the Tibetan wild ass (Equus kiang) based on field surveys at the Three-River-Source National Park, as well as 29 layers of environmental variables covering the terrestrial areas of the planet. Our method can provide accurate estimation of abundance for animals inhabiting open areas that can be easily observed during distance sampling, and whose spatial heterogeneity of animal density within the study area can be accurately predicted using species distribution models.

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Poulin, R., J. L. Luque, F. Guilhaumon, and D. Mouillot. "Species abundance distributions and numerical dominance in gastrointestinal helminth communities of fish hosts." Journal of Helminthology 82, no. 3 (September 2008): 193–202. http://dx.doi.org/10.1017/s0022149x08982626.

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AbstractThe abundances of different species in a parasite community are never similar: there is typically one or a few numerically dominant species and many species with low abundance. Here, we determine whether basic features of parasite communities are associated with strong dominance by one or a few species, among 39 component communities of gastrointestinal helminths in marine fishes from Brazil. First, we tested whether the shape of the species abundance distribution in these communities fits that predicted by several theoretical models, using a goodness-of-fit procedure. Only the canonical lognormal model could be rejected for 5 out of 39 communities; all other comparisons of observed and predicted abundance distributions showed no significant differences, although this may be due to limited statistical power. Second, we used the ratio between the abundance of the most abundant species and either the second or third most abundant species, as indices of dominance; these show, for instance, that the dominant species in a community is typically twice, but sometimes over ten times, as abundant as the next most abundant species. We found that these ratios were not influenced by either the community's species richness, the mean number of individual parasites per host, or the taxonomic identity of the dominant species. However, the abundance ratio between the first and third most abundant species in a community was significantly correlated with an independent index of species interactivity, based on the likelihood that the different parasite species in a component community co-occur in the same host individuals: the difference in abundance between the dominant and third most abundant species was greater in communities characterized by weak interactions. These findings suggest that strong interactions may lead to greater evenness in the abundance of species, and that numerical dominance is more likely to result from interspecific differences in recruitment rates.

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Royle, J. Andrew, and Robert M. Dorazio. "Hierarchical models of animal abundance and occurrence." Journal of Agricultural, Biological, and Environmental Statistics 11, no. 3 (September 2006): 249–63. http://dx.doi.org/10.1198/108571106x129153.

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Jerkstrand, A. "Supernova abundance analysis with NLTE spectral models." Proceedings of the International Astronomical Union 15, S350 (April 2019): 306–10. http://dx.doi.org/10.1017/s1743921319009062.

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AbstractSupernovae provide environments with strong links to laboratory astrophysics. Diverse physical processes spanning from hot gas and semi-relativistic particles down to cold dusty clumps require extensive atomic data and understanding of processes across different physical regimes. The current status of modelling and analyzing supernova spectra is reviewed, with focus on recent results for diagnosing the production of oxygen and nickel.

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Huillet, Thierry E. "Stochastic species abundance models involving special copulas." Physica A: Statistical Mechanics and its Applications 490 (January 2018): 77–91. http://dx.doi.org/10.1016/j.physa.2017.08.021.

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Cerrito, P. B. "Density estimation applied to stochastic abundance models." Ecological Modelling 45, no. 3 (May 1989): 221–36. http://dx.doi.org/10.1016/0304-3800(89)90083-5.

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Péquignot, D., X. W. Liu, M. J. Barlow, P. J. Storey, and C. Morisset. "Bi-abundance Photoionization Models for Planetary Nebulae." Symposium - International Astronomical Union 209 (2003): 347–48. http://dx.doi.org/10.1017/s007418090020898x.

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A new class of planetary nebulae, in which abundances derived from optical recombination lines (ORL) seem to be much larger than those derived from collisionally excited lines (CEL) by up to one or two orders of magnitude is now well identified (Liu, these proceedings and references therein).Photoionization models including two components, one highly enriched in C, N, O, Ne and deficient in H and the other one of more usual composition, can account for most of the numerous spectroscopic data available from UV to far-IR in two of the best observed, most extreme examples, namely NGC 6153 and M142 (Péquignot et aI., 2002, and in preparation). The few discrepancies left can generally be understood in terms of inaccuracy of the observations (calibration of infrared line fluxes relative to the optical) and some atomic data, particularly in the unusual conditions prevailing in the H-deficient component.

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Charbonnel, Corinne, and Ana Palacios. "Rotating Models for Evolved Low-Mass Stars." Symposium - International Astronomical Union 215 (2004): 440–49. http://dx.doi.org/10.1017/s0074180900196019.

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Low mass stars (< 2-2.5 M⊙) exhibit, at all the stages of their evolution, signatures of processes that require challenging modeling beyond the standard stellar theory. In this paper we focus on their peculiarities while they climb the red giant branch (RGB). We first compare the classical predictions for abundance variations due to the first dredge-up with observational data in various environments. We show how clear spectroscopic diagnostics probe the nucleosynthesis and the internal mixing mechanisms that drive RGB stars. Coherent data reveal in particular the existence of a non-standard mixing process that changes their surface abundances at the so-called RGB bump. By reviewing the models presented so far to explain the various abundance anomalies, we show that the occurrence of this extra-mixing process is certainly related to rotation. Finally we discuss the so-called Li-flash which is expected to occur at the very beginning of the extra-mixing episode.

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Dors, O. L., R. Maiolino, M. V. Cardaci, G. F. Hägele, A. C. Krabbe, E. Pérez-Montero, and M. Armah. "Chemical abundances of Seyfert 2 AGNs – III. Reducing the oxygen abundance discrepancy." Monthly Notices of the Royal Astronomical Society 496, no. 3 (June 22, 2020): 3209–21. http://dx.doi.org/10.1093/mnras/staa1781.

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ABSTRACT We investigate the discrepancy between oxygen abundance estimations for narrow-line regions of active galactic nuclei (AGNs) type Seyfert 2 derived using direct estimations of the electron temperature (Te-method) and those derived using photoionization models. In view of this, observational emission-line ratios in the optical range ($3000 \: \lt \: \lambda (\mathring{\rm A}) \: \lt 7000$) of Seyfert 2 nuclei compiled from the literature were reproduced by detailed photoionization models built with the cloudy code. We find that the derived discrepancies are mainly due to the inappropriate use of the relations between temperatures of the low (t2) and high (t3) ionization gas zones derived for H ii regions in AGN chemical abundance studies. Using a photoionization model grid, we derived a new expression for t2 as a function of t3 valid for Seyfert 2 nuclei. The use of this new expression in the AGN estimation of the O/H abundances based on Te-method produces O/H abundances slightly lower (about 0.2 dex) than those derived from detailed photoionization models. We also find that the new formalism for the Te-method reduces by about 0.4 dex the O/H discrepancies between the abundances obtained from strong emission-line calibrations and those derived from direct estimations.

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Bannister, R. J., R. Brinkman, C. Wolff, C. Battershill, and R. de Nys. "The distribution and abundance of dictyoceratid sponges in relation to hydrodynamic features: identifying candidates and environmental conditions for sponge aquaculture." Marine and Freshwater Research 58, no. 7 (2007): 624. http://dx.doi.org/10.1071/mf07011.

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The distribution and abundance of dictyoceratid sponges was surveyed to a depth of 20 m at eleven locations within the Palm Island Group, Great Barrier Reef (GBR), Australia. These surveys were related to prevailing hydrodynamic conditions to identify candidates and environmental conditions for sponge aquaculture. Locations were classified as sheltered, intermediate and exposed using quantitative wave exposure and current force models. The species richness of dictyoceratid sponges was high with ten taxa, but the abundance of most species was low with patchy distributions. Two species, Coscinoderma sp. and Rhopaloeides odorabile, were abundant, and detailed surveys of these species were conducted at seven locations representing common habitats within the Palm Island Group. Coscinoderma sp. was present at all locations and although abundances differed significantly across locations, this was not related to hydrodynamic conditions. In contrast, R. odorabile was only present at exposed locations with low abundance. The higher abundance and broad distribution of Coscinoderma sp. supports its selection as an aquaculture candidate. In contrast, R. odorabile was less abundant and was restricted to high-energy environments making aquaculture more problematic. The present study demonstrates the importance of ecological data in the decision-making process for new species aquaculture.

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Gopalan, Gouthaman, David A. Culver, Lin Wu, and Bruce K. Trauben. "Effects of recent ecosystem changes on the recruitment of young-of-the-year fish in western Lake Erie." Canadian Journal of Fisheries and Aquatic Sciences 55, no. 12 (December 1, 1998): 2572–79. http://dx.doi.org/10.1139/f98-130.

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We compared the variability in forage fish recruitment over the last 27 years against major ecological changes that occurred in Lake Erie over the same time period. During a period of high adult walleye abundance and declining phosphorus loading (1976-1982), we observed a decline in the abundance of later hatching forage fish species (e.g., July) and those species that did not shift their diets from zooplankton to benthos during the summer of their life. During years of high young-of-the-year (YOY) white perch abundance (1983-1990), forage fishes whose hatching dates and (or) diet overlapped with YOY white perch declined in abundance. When the zebra mussel (Dreissena polymorpha) became abundant (1991-1995), most forage fishes showed no change in abundances. Given a YOY's ability to switch to benthos during summer, the date on which this occurred was determined by a combination of zooplankton abundance and fish size. Hence, the dates individual taxa of fish hatch relative to seasonal cycles of zooplankton abundance and the size at which they can undergo an ontogenetic diet shift to benthos and (or) fish could be influencing fish growth and recruitment and need to be incorporated into YOY recruitment models.

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Remien, Christopher H., Mariah J. Eckwright, and Benjamin J. Ridenhour. "Structural identifiability of the generalized Lotka–Volterra model for microbiome studies." Royal Society Open Science 8, no. 7 (July 2021): 201378. http://dx.doi.org/10.1098/rsos.201378.

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Population dynamic models can be used in conjunction with time series of species abundances to infer interactions. Understanding microbial interactions is a prerequisite for numerous goals in microbiome research, including predicting how populations change over time, determining how manipulations of microbiomes affect dynamics and designing synthetic microbiomes to perform tasks. As such, there is great interest in adapting population dynamic theory for microbial systems. Despite the appeal, numerous hurdles exist. One hurdle is that the data commonly obtained from DNA sequencing yield estimates of relative abundances, while population dynamic models such as the generalized Lotka–Volterra model track absolute abundances or densities. It is not clear whether relative abundance data alone can be used to infer parameters of population dynamic models such as the Lotka–Volterra model. We used structural identifiability analyses to determine the extent to which a time series of relative abundances can be used to parametrize the generalized Lotka–Volterra model. We found that only with absolute abundance data to accompany relative abundance estimates from sequencing can all parameters be uniquely identified. However, relative abundance data alone do contain information on relative interaction strengths, which is sufficient for many studies where the goal is to estimate key interactions and their effects on dynamics. Using synthetic data of a simple community for which we know the underlying structure, local practical identifiability analysis showed that modest amounts of both process and measurement error do not fundamentally affect these identifiability properties.

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Bengsen, Andrew, John Butler, and Pip Masters. "Estimating and indexing feral cat population abundances using camera traps." Wildlife Research 38, no. 8 (2011): 732. http://dx.doi.org/10.1071/wr11134.

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Context The ability to monitor changes in population abundance is critical to the success of pest animal management and research programs. Feral cats (Felis catus) are an important pest animal, but current monitoring techniques have limited sensitivity or are limited in use to particular circumstances or habitats. Recent advances in camera-trapping methods provide the potential to identify individual feral cats, and to use this information to estimate population abundances using capture–mark–recapture (CMR) methods. Aims Here, we use a manipulative study to test whether camera-trapping and CMR methods can be used to estimate feral cat abundances. Methods We established a grid of infrared cameras and lure stations over three pastoral properties on Kangaroo Island, Australia, for 15 days. We then reduced the population abundance with an intensive trapping program and repeated the camera survey. We estimated population abundances using robust design CMR models, and converted abundance estimates to densities using home-range data from GPS tracking. We also calculated relative abundance indices from the same data. Key results The CMR methods produced credible estimates of the change in population abundance, with useful confidence intervals, showing a statistically identifiable population decline from at least 0.7 cats km–2 before trapping down to 0.4 cats km–2 after trapping. The indexing method also showed a statistically identifiable decrease in abundance. Conclusions Camera-trapping and CMR methods can provide a useful method for monitoring changes in the absolute abundance of feral cat populations. Camera-trap data may also be used to produce indices of relative abundance when the assumptions of CMR models cannot be met. Implications These methods are widely applicable. The ability to reliably estimate feral cat abundances allows for more effective management than is generally available.

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Hollowell, David. "AGB Star Models." Highlights of Astronomy 9 (1992): 621–22. http://dx.doi.org/10.1017/s1539299600009850.

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Kovtyukh, V., B. Lemasle, G. Bono, I. A. Usenko, R. da Silva, A. Kniazev, E. K. Grebel, I. L. Andronov, L. Shakun, and L. Chinarova. "The MAGIC project – III. Radial and azimuthal Galactic abundance gradients using classical Cepheids." Monthly Notices of the Royal Astronomical Society 510, no. 2 (December 4, 2021): 1894–901. http://dx.doi.org/10.1093/mnras/stab3530.

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ABSTRACT Radial abundance gradients provide sound constraints for chemo-dynamical models of galaxies. Azimuthal variations of abundance ratios are solid diagnostics to understand their chemical enrichment. In this paper, we investigate azimuthal variations of abundances in the Milky Way using Cepheids. We provide the detailed chemical composition (25 elements) of 105 Classical Cepheids from high-resolution SALT spectra observed by the MAGIC project. Negative abundance gradients, with abundances decreasing from the inner to the outer disc, have been reported both in the Milky Way and in external galaxies, and our results are in full agreement with literature results. We find azimuthal variations of the oxygen abundance [O/H]. While a large number of external spirals show negligible azimuthal variations, the Milky Way seems to be one of the few galaxies with noticeable [O/H] azimuthal asymmetries. They reach ≈0.2 dex in the inner Galaxy and in the outer disc, where they are the largest, thus supporting similar findings for nearby spiral galaxies, as well as recent 2D chemo-dynamical models.

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Sipilä, O., and P. Caselli. "Hydrodynamics with gas–grain chemistry and radiative transfer: comparing dynamical and static models." Astronomy & Astrophysics 615 (July 2018): A15. http://dx.doi.org/10.1051/0004-6361/201732326.

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Context. We study the evolution of chemical-abundance gradients using dynamical and static models of starless cores. Aims. We aim to quantify if the chemical abundance gradients given by a dynamical model of core collapse, which includes time-dependent changes in density and temperature, differ greatly from abundances derived from static models where the density and temperature structures of the core are kept fixed as the chemistry evolves. Methods. We developed a new one-dimensional spherically symmetric hydrodynamics code that couples the hydrodynamics equations with a comprehensive time-dependent gas–grain chemical model, including deuterium and spin-state chemistry, and radiative transfer calculations to derive self-consistent time-dependent chemical-abundance gradients. We apply the code to model the collapse of a starless core up to the point when the infall flow becomes supersonic. Results. The abundances predicted by the dynamical and static models are almost identical at early times during the quiescent phase of core evolution. After the onset of core collapse, the results from the two models begin to diverge: at late times the static model generally underestimates abundances in the high-density regions near the core center, and overestimates them in the outer parts of the core. Deuterated species are clearly overproduced by the static model near the center of the model core. On the other hand, simulated lines of NH3 and N2H+ are brighter in the dynamical model because they originate in the central part of the core where the dynamical model predicts higher abundances than the static model. The reason for these differences is that the static model ignores the history of the density and temperature profiles which has a large impact on the abundances, and therefore on the molecular lines. Our results also indicate that the use of a very limited chemical network in hydrodynamical simulations may lead to an overestimate of the collapse timescale, and in some cases may prevent the collapse altogether. Limiting the set of molecular coolants has a similar effect. In our model, most of the line cooling near the center of the core is due to HCN, CO, and NO. Conclusions. Our results show that the use of a static physical model is not a reliable method of simulating chemical abundances in starless cores after the onset of gravitational collapse. The abundance differences between the dynamical and static models translate to large differences in line emission profiles, showing that the difference between the models is at the observable level. The adoption of complex chemistry and a comprehensive set of cooling molecules is necessary to model the collapse adequately.

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Kurucz, Robert L. "LTE Models." Highlights of Astronomy 11, no. 2 (1998): 646–49. http://dx.doi.org/10.1017/s1539299600018347.

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AbstractI can compute arbitrary-abundance models and spectra at high resolution using millions of atomic and diatomic molecular lines. Examples are given for Sakurai’s object and for a λBoo star. I am continuing to improve the input line data.

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Forsyth, David M., Steve R. McLeod, Michael P. Scroggie, and Matthew D. White. "Modelling the abundance of wildlife using field surveys and GIS: non-native sambar deer (Cervus unicolor) in the Yarra Ranges, south-eastern Australia." Wildlife Research 36, no. 3 (2009): 231. http://dx.doi.org/10.1071/wr08075.

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Combining abundance data collected in designed field surveys with biophysical data derived from geographic information systems is a powerful way to investigate predictors of spatial variation in the abundance of wildlife. We used such an approach to evaluate hypotheses about factors influencing the abundance of sambar deer (Cervus unicolour Kerr, 1792), a large non-native herbivore, in south-eastern Australia. We developed a spatial model for the abundance of sambar deer faecal pellets in a 3650-ha area in the Upper Yarra Ranges, Victoria. We counted the number of sambar deer faecal pellets along 100 randomly located transects and used a geographic information system to estimate biophysical variables around each transect. We formulated our hypotheses about how those variables might affect the abundance of sambar deer pellets into 22 candidate models and used the deviance information criterion to identify the ‘best’ model(s). Because five models had strong support we used model averaging to generate a predictive model. The three variables included in the predictive model were aspect (abundance of pellets declined with increasing ‘northerliness’ and increased with increasing ‘easterliness’), distance to water and elevation; the latter two variables were positively correlated and had a negative effect on the abundance of pellets. In contrast to previous models of sambar deer abundance in south-eastern Australia, our spatial predictions of the abundance of faecal pellets can be easily tested and updated. Our approach would be useful for modelling the abundances of other wildlife species at a range of spatial scales.

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Pérez-Mesa, V., O. Zamora, D. A. García-Hernández, Y. Ossorio, T. Masseron, B. Plez, A. Manchado, A. I. Karakas, and M. Lugaro. "On the circumstellar effects on the Li and Ca abundances in massive Galactic O-rich AGB stars." Proceedings of the International Astronomical Union 14, S343 (August 2018): 489–90. http://dx.doi.org/10.1017/s174392131800501x.

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AbstractWe explore the circumstellar effects on the Li and Ca abundances determination in a complete sample of massive Galactic AGB stars. The Li abundance is an indicator of the hot bottom burning (HBB) activation, while the total Ca abundance could be affected by overproduction of the short-lived radionuclide 41Ca by the s-process. Li abundances were previously studied with hydrostatic models, while Ca abundances are determined here for the first time. The pseudo-dynamical abundances of Li and Ca are very similar to the hydrostatic ones, indicating that circumstellar effects are almost negligible. The new Li abundances confirm the (super-)Li-rich character of the sample Li-detected stars, supporting the HBB activation in massive Galactic AGB stars. Most sample stars display nearly solar Ca abundances that are consistent with predictions from the s-process nucleosynthesis models. A minority of the sample stars show a significant Ca depletion. Possible reasons for their (unexpected) low Ca content are given.

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Kimura, Daniel K. "Analyzing Relative Abundance Indices with Log-Linear Models." North American Journal of Fisheries Management 8, no. 2 (May 1988): 175–80. http://dx.doi.org/10.1577/1548-8675(1988)008<0175:araiwl>2.3.co;2.

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Kinney, Adrienne C., Sean Current, and Joceline Lega. "Aedes-AI: Neural network models of mosquito abundance." PLOS Computational Biology 17, no. 11 (November 19, 2021): e1009467. http://dx.doi.org/10.1371/journal.pcbi.1009467.

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We present artificial neural networks as a feasible replacement for a mechanistic model of mosquito abundance. We develop a feed-forward neural network, a long short-term memory recurrent neural network, and a gated recurrent unit network. We evaluate the networks in their ability to replicate the spatiotemporal features of mosquito populations predicted by the mechanistic model, and discuss how augmenting the training data with time series that emphasize specific dynamical behaviors affects model performance. We conclude with an outlook on how such equation-free models may facilitate vector control or the estimation of disease risk at arbitrary spatial scales.

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Baldridge, Elita, David J. Harris, Xiao Xiao, and Ethan P. White. "An extensive comparison of species-abundance distribution models." PeerJ 4 (December 22, 2016): e2823. http://dx.doi.org/10.7717/peerj.2823.

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A number of different models have been proposed as descriptions of the species-abundance distribution (SAD). Most evaluations of these models use only one or two models, focus on only a single ecosystem or taxonomic group, or fail to use appropriate statistical methods. We use likelihood and AIC to compare the fit of four of the most widely used models to data on over 16,000 communities from a diverse array of taxonomic groups and ecosystems. Across all datasets combined the log-series, Poisson lognormal, and negative binomial all yield similar overall fits to the data. Therefore, when correcting for differences in the number of parameters the log-series generally provides the best fit to data. Within individual datasets some other distributions performed nearly as well as the log-series even after correcting for the number of parameters. The Zipf distribution is generally a poor characterization of the SAD.

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Lindell, C. A., W. H. Chomentowski, J. R. Zook, and S. A. Kaiser. "Generalizability of neotropical bird abundance and richness models." Animal Conservation 9, no. 4 (November 2006): 445–55. http://dx.doi.org/10.1111/j.1469-1795.2006.00060.x.

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Thomas, Daniel, Claudia Maraston, and Ralf Bender. "Stellar Population Models with Variable Element Abundance Ratios." Highlights of Astronomy 13 (2005): 189–90. http://dx.doi.org/10.1017/s1539299600015586.

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AbstractWe present a comprehensive set of new generation stellar population models of Lick absorption line indices, which for the first time include element abundance ratios different from solar. We computed the 21 Lick indices CN1, CN2, Ca4227, G4300, Fe4383, Ca4455, Fe4531, C24668, Hβ, Fe5015, Mg1, Mg2, Mgb, Fe5270, Fe5335, Fe5406, Fe5709, Fe5782, Na D, TiO1, and TiO2, in the wavelength range 4000 ≲ λ ≲ 6500 Å. Models are provided with: [α/Fe] = 0.0, 0.3, 0.5, [α/Ca] = -0.1, 0.0, 0.2, 0.5, and [α/N] = −0.5, 0.0; ages from 1 to 15 Gyr; total metallicities from 1/200 to 3.5 solar (-2.25 ≤ [Z/H] ≤ 0.67).

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Maunder, M. N., and P. J. Starr. "Fitting fisheries models to standardised CPUE abundance indices." Fisheries Research 63, no. 1 (July 2003): 43–50. http://dx.doi.org/10.1016/s0165-7836(03)00002-x.

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Lyth, David H. "The gravitino abundance in supersymmetric `new' inflation models." Physics Letters B 488, no. 3-4 (September 2000): 417–22. http://dx.doi.org/10.1016/s0370-2693(00)00878-9.

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Le Delliou, M., C. Lacey, C. M. Baugh, B. Guiderdoni, R. Bacon, H. Courtois, T. Sousbie, and S. L. Morris. "The abundance of Ly emitters in hierarchical models." Monthly Notices of the Royal Astronomical Society: Letters 357, no. 1 (February 1, 2005): L11—L15. http://dx.doi.org/10.1111/j.1745-3933.2005.00007.x.

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Lasky, Jesse R., and Timothy H. Keitt. "Abundance of Panamanian dry-forest birds along gradients of forest cover at multiple scales." Journal of Tropical Ecology 26, no. 1 (December 8, 2009): 67–78. http://dx.doi.org/10.1017/s0266467409990368.

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Abstract:Community structure and species’ abundances may be strongly correlated to patterns of forest cover, although such patterns are poorly known for tropical dry-forest birds, especially for those in Panamanian dry forests. Birds were distance-sampled during point counts in five dry-forest fragments in Panama. Distance from point count to forest edge and forest coverage at three spatial scales (500, 1000 and 2000-m radius) were compared as covariate predictors of the abundance of avian species and guilds. Each covariate was selected in at least two models of species or guild abundance. Abundance patterns were consistent with previously reported habitat associations for only two of seven open-habitat or forest-preferring species that showed forest cover-abundance relationships. Null models best described the abundance of all forest species and the subset of uncommon forest species. Thus many of these species appear insensitive to the forest-cover gradients studied. Total abundance of open-habitat-preferring species increased in dry forests with increasing forest coverage within 500 m, suggesting that the relationship between their abundance and vegetation structure are spatial-scale and habitat dependent. Nectarivores had lower abundance as forest cover within 1000 m increased, supporting previous claims that this group is tolerant of forest edges.

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Journal articles on the topic 'Abundance models'

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