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| - ''This list describes a number of operations and models that may be potentially useful to represent as actors and workflows (analytical models) within Kepler. When possible each such "component" includes a brief description and potential impact (e.g., for semantic mediation) as well as one or more citations for the component (e.g., where we spotted the component and definitive papers on the component).'' |
| + ''This list describes a number of operations and models that may be potentially useful to represent as actors and workflows (analytical models) within Kepler. When possible each such "component" includes a brief description and potential impact (e.g., for semantic mediation) as well as one or more citations for the component (e.g., where we spotted the use of the method and definitive papers describing or introducing the method).'' |
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| + ;__Determing Plot Layout__: |
| + ** ''Citation:'' (Sheiner 2003) |
| + ** ''Description:'' In Sheiner's paper, he described various plot "topologies" and the associated sampling schemes from such layouts. It seems like this would be a useful component: given a collection of data sets, display the plot topology across those datasets on a map. |
| + ** ''Application:'' This could be expressed as a query against an ontology that describes the spatial characteristics of a data set, and answered by the semantic description of the dataset to the ontology. The result of the query could then be used to display the topology of the plots across the heterogeneous data sets. |
| + ** ''Status:'' Is this useful? |
| + |
| + |
| + ;__Species-Area Curve Predictions__: |
| + ** ''Citation:'' (Sheiner 2003) |
| + ** ''Description:'' The properties of species-area curves have been predicted from models of community processes (Preston 1962a, Preston 1962b, Coleman 1981, Caswell and Cohen 1993, He and Legendre 2002, Plotkin and Muller-Landau 2002), which begin with an analytical model of species dispersal and interaction and then predict the relationship between species and area. |
| + ** ''Issues:'' In testing these models, it is important that the sampling scheme mirror the model assumptions, e.g., assuming metapopulation patch structure with no spatial component (Caswell and Cohen 1993), or assuming a contiguous spatial structure (Plotkin and Muller-Landau 2002). |
| + ** ''Application:'' These may be interesting examples of scientific workflows that could be incorporated into Kepler. There may be interesting semantic mediation issues. |
| + ** ''Status:'' Need to see if this is actually useful or practical. |
| + |
| + |
| + ;__Site by species matrix__: |
| + ** ''Citation:'' From Beam Working Group meeting ([BeamKnowledgeRepSept04]) |
| + ** ''Description:'' In the matrix, every row is a site, like a different quadrat, every column is a different species in the matrix, the value could be abundance, but typically is just species/absence (1 or 0's). Then, if you sum across the row, you know the number of species, e.g.. There might be also be a separate set of columns for location of the plot. You can then compute/estimate, via re-sampling (different algorithms for this), the species-area curves. Also, the goal is to capture the abundance, not just the presence/absence ... you want to use the abundance when possible. Also, there are tons of uses of these matrices. Abundance measured in various ways: relative and absolute, you can compute relative to absolute but not the other way; total biomass is an absolute / percent cover is a relative. Relative: hits, cover, touches. Absolute: count stems, biomass. |
| + ** ''Application:'' Given any marked up dataset, we should be able to construct one of these matrixes automatically. |
| + ** ''Caveat:'' The species area curves are really used within a decision making context typically... You want ways to analyze the species/area relationship varies with productivity. |
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| + # ''(Caswell and Cohen 1993)'' H. Caswell and J. Cohen. Local and regional regulation of species-area relations: a patch-occupancy model. Species diversity in ecological communities, pp. 99-107, 1993. |
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| + # ''(Coleman 1981)'' B. Coleman. On random placement and species-area relations. Mathematical Biosciences, 54:191-215, 1981. |
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| + # ''(He and Legendre 2002)'' F. He and P. Legendre. Species diversity patterns derived from species-area models. Ecology |
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| + # ''(Plotkin and Muller-Landau 2002)'' J. Plotkin and H. Muller-Landau. Sampling the species composition of a landscape. Ecology, 83:3344-3356, 2002. |
| + # ''(Preston 1962a)'' F. Preston. The canonical distribution of commonness and rarity, part I. Ecology, 43:185-215, 1962. |
| + # ''(Preston 1962b)'' F. Preston. The canonical distribution of commonness and rarity, part II. Ecology, 43:410-432, 1962. |
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| + # ''(Sheiner 2003)'' S. Sheiner. Six types of species-area curves. Global Ecology and Biogeography, 12:441-447, 2003. |
