lmpy.sdm.model
Module containing tools for creating an SDM.
Module Contents
Functions
|
|
|
Return a filename to indicate a layer label for an SDM raster in the directory. |
|
Create an SDM, Maxent model if there are enough points, rare species if not. |
|
Match headers with template layer. |
|
Project a Maxent model onto env. layers for a potential distribution map. |
Attributes
- lmpy.sdm.model._create_mask(point_tuples, ecoregions_filename, env_dir, maxent_arguments, logger)[source]
- lmpy.sdm.model.create_maxent_layer_label(sdm_dir, label_name, touch_file=True)[source]
Return a filename to indicate a layer label for an SDM raster in the directory.
- Parameters
sdm_dir (str) – Path for output file, same as the dir for associated matrix input
label_name (str) – Name to use in matrix headers
touch_file (bool) – True to create the file
- Returns
File signaling the
- Return type
label_filename (str)
Note
- This function assumes that only one SDM to be encoded will be in the same
directory.
- lmpy.sdm.model.create_sdm(min_points, csv_filename, env_dir, ecoregions_filename, work_dir, species_name, maxent_arguments=DEFAULT_MAXENT_OPTIONS, sp_key=Point.SPECIES_ATTRIBUTE, x_key=Point.X_ATTRIBUTE, y_key=Point.Y_ATTRIBUTE, create_mask=True, logger=None)[source]
Create an SDM, Maxent model if there are enough points, rare species if not.
- Parameters
min_points (int) – Number of points to determine whether to use Maxent or rare-species modeling
csv_filename (str) – input filename with species points
env_dir (str) – directory containing environmental layers for model creation
ecoregions_filename (str) – Vector file containing ecoregions or other environmental regions for masking in Maxent or intersecting with a convex hull in rare-species model
work_dir (str) – directory for temporary modeling files
maxent_arguments (str) – space-separated values for Maxent parameters
species_name (str) – name to use for the output model filename
sp_key (str) – fieldname of the column containing the species name for grouping
x_key (str) – fieldname of the column containing the longitude coordinate
y_key (str) – fieldname of the column containing the latitude coordinate
create_mask (bool) – flag indicating whether to create a mask for Maxent
logger (logging.logger) – Logger for writing messages to console and/or file.
- Returns
- either model raster filename for rare species model
or lambdas filename for Maxent
- Return type
output_filename
report (dict): dictionary containing relevant metadata about the model
- lmpy.sdm.model.match_headers(mask_filename, tmp_mask_filename, template_layer_filename)[source]
Match headers with template layer.
- Parameters
mask_filename – Input filename to update with headers
tmp_mask_filename – Raster filename fromm which to copy the values above the 6th
template_layer_filename – Layer filename from which to copy the first 6 values
- lmpy.sdm.model.project_sdm(maxent_lambdas_file, env_dir, species_name, work_dir, logger=None)[source]
Project a Maxent model onto env. layers for a potential distribution map.
Note
create_sdm creates a raster projected distribution map using the same environmental layers as were used for modeling. This function is intended to project an pre-created model onto different environmental layres.
- Parameters
maxent_lambdas_file (str) – input filename with Maxent rules
env_dir (str) – directory containing environmental layers for model projection
work_dir (str) – directory for temporary modeling files
species_name (str) – name to use for the output model filename
logger (logging.logger) – Logger for writing messages to console and/or file.
- Returns
output filename report (dict): dictionary containing relevant metadata about the model
- Return type
projection_raster_filename