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SDM : Species Distribution Modeling (SDM) is also known by several other names, including environmental niche modeling, ecological niche modeling, and habitat modeling. SDM refers to the process of creating mathematical formulas (models) to predict the geographic distribution of species based on where they have been found and the environmental conditions in those locations.
Algorithm : An algorithm is a procedure or formula for solving a problem. There are multiple algorithms for computing Species Distribution Models (SDM) which define the relationship between a set of points and the environmental values at those points. BiotaPhy and Lifemapper provide 12 algorithms
Presence-Absence Matrix (PAM) : A binary matrix containing species distributions of 0/1 indicating presence or non-presence in each grid cell of a region. The matrix may be thought of as a three-dimensional cube, of binary maps, with one layer per species. The 3-dimensional matrix is flattened into 2 dimensions, with rows representing sites with an x,y coordinate for the center of a gridcell on a map, and columns representing species.
Phylogenetic Tree : A data structure containing species names or identifiers for analyzing evolutionary patterns. BiotaPhy uses phylogenetic trees matching species data in a gridset to correlate evolutionary patterns with species distributions and landscape features. API documentation is at Tree.
Biogeographic Hypotheses : Spatial layers for testing the influence of geographic elements, such as geology, drainage basins, etc, on the biodiversity of a landscape. These can be in the form of raster or vector files. API documentation is at BioGeo.
MCPA : Meta-Community Phylogenetic Analysis, briefly explained at MCPA. MCPA is defined by Pedro Peres-Neto in https://onlinelibrary.wiley.com/doi/abs/10.1111/j.1461-0248.2010.01523.x
Ultrametric Tree : A tree whose total branch length from the root to each tip in the tree is the same.
Helmert Contrast : An encoding of data such that sites with values of 1 indicate that they fall on one side of a hypothesis, values of -1 indicate that they belong to the opposite side of the same hypothesis, and values of zero indicate that the cell does not fall on either side of the hypothesis.
Gridset : The organizing data structure for a single, or group of analyses. A package may be downloaded for visualization within the BiotaPhy web client, or further analyses in other software.
LM Library : Existing public data in a BiotaPhy installation, including input data, such as species points, environmental data layers, and computed SDMs.
Occurrence Layer : Point data representing specimens collected for a single species or taxa. Data contains a location, x and y, in some known geographic spatial reference system. Public data in BiotaPhy installations are in the 'Geographic' spatial reference system, latitude and longitude in decimal degrees. API documentation is at Occurrence Layer
Environmental Layer : Raster data representing environmental values for cells in a map. Data may be numeric or categorical, with only one value per cell. Public data in BiotaPhy installations are in the 'Geographic' spatial reference system, latitude and longitude in decimal degrees. API documentation is at Environmental Layer
Scenario : Scenarios consist of a set of environmental layers (i.e. elevation, precipitation, temperature, soil, etc). For Species Distribution Modeling, researchers often choose a set of 'present day' layers ("modeling scenario") as an input along with 'present day' species points. The environmental data may be global, or regional. The resulting models can be projected onto the same environmental dataset and/or one predicted for a different time period, or one for another region ("projection scenarios"). An example of predicted environmental data available in the BiotaPhy archive is climate data computed for the International Panel on Climate Change (IPCC) for its Fifth Assessment Report (AR5, 2013). API documentation is at Scenario.
Scenario Package : A Scenario Package consists of a set of scenarios with the same type of layers in each. Scenarios within a package can be used together, so species data may be modeled with one scenario and projected onto another scenario. Generally, "current day" species data is modeled with current day environmental data, then may be projected onto environmental data predicted for the past or future, or onto a different region. API documentation is at Scenario Package.
SDM Projection
: Computed SDM models may be applied, or projected back onto the same, or
matching Scenarios. A map created from the projection of this model onto
a Scenario is called an SDM Projection, and is a file of geospatial data in
raster format. Different algorithms produce projections with different values.
The Maxent algorithm produces projections with values denoting the predicted
presence as a value between 0 and 1. Other algorithms produce raster files
with only the values 1 (predicted present) or 0 (not predicted present). API
documentation is at SDM Projection.
Shapegrid : A grid encompassing the area of interest in a Gridset for multi-species analyses. In a gridset, different data layers are intersected with a Shapegrid to produce Matrices for analyses. Species layers are intersected to create a PAM, environmental layers are intersected to create an Environmental Matrix (GRIM) and Biogeographic Hypotheses are intersected to create a BioGeo Matrix. Intersection parameters define how values are computed for gridcells from the values in data layers. API documentation is at Shapegrid
Global PAM : A Presence-Absence Matrix (PAM) as described above, containing intersected data for all species in a gridset. A Global PAM usually refers to a very large PAM meant to be subsetted for further analysis. API documentation is at Global PAM.
Environmental Matrix (GRIM) : A matrix of values indicating the mean value of each of multiple environmental variables in a regular grid. The structure is the same of the PAM, but values are not binary. GRIM is an acronym for Geographic Reference Information Matrix.
Biogeographic Hypotheses and BioGeo Matrix : Spatial layers for testing the influence of geographic elements, such as geology, drainage basins, etc, on the biodiversity of a landscape. These can be in the form of raster or vector files. Biogeographic Hypotheses may be intersected with the Shapegrid to produce a BioGeo Matrix, used in MCPA computations. API documentation is at BioGeo.