raster_to_demes

raster_to_demes(raster, transformation='linear', max_local_size=1000, normalize=False, threshold=None, thresh_norm=False, inflection_point=0.5, slope=0.05)

Converts a raster to a 2D np.ndarray of deme sizes using either linear, threshold, or sigmoid transformation functions. For more detail about transformation functions, see this brief overview. Raster data should be continuous and positive. This function was created with the idea of taking in habitat suitability rasters scaled from 0 to 1, where 0 is no suitability and 1 is the highest suitability. However, it is flexible enough to accommodate other continuous rasters that can be coaxed to a 0 to 1 scale with the operation (data - np.min(data)) / (np.max(data) - np.min(data)) by setting the normalize flag to True.

Parameters

Name	Type	Description	Default
raster	Union[np.ndarray, rasterio.DatasetReader]	The input raster data. It can be a numpy array or a rasterio DatasetReader with one or more layers.	required
transformation	str	The transformation function to be used. Options are “linear”, “threshold”, and “sigmoid”. Default is “linear”.	'linear'
max_local_size	int	The maximum local deme size. Default is 1000.	1000
normalize	bool	Whether to normalize the raster data. Use if your data is not scaled from 0-1. Default is False.	False
threshold	float	The threshold value for the “threshold” transformation method. Default is None.	None
thresh_norm	bool	Whether to normalize the local deme size based on the average suitability above the threshold. This is useful when comparing thresholded simulations with linear or sigmoid simulations, to maintain similar landscape-wide population sizes across max_local_size values. Default is False.	False
inflection_point	float	The inflection point for the “sigmoid” transformation method. Default is 0.5.	0.5
slope	float	The slope value for the “sigmoid” transformation method. Default is 0.05.	0.05

Returns

Type	Description
np.ndarray	An ndarray of deme sizes.