sobig 0.1.0__py3-none-any.whl

sobig/__init__.py

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+"""Simulation of observations of biodiversity across gradients."""
+
+__version__ = "0.1.0"
+
+from .sobig import fEnv, Species, Sim, run_demo
+
+# Public API exports will go here as the package stabilizes.

sobig/_r/run_gdm.R

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+library(gdm)
+library(terra)
+
+# get file paths
+args <- commandArgs(trailingOnly = TRUE)
+site_survey_filename = args[1]
+env_rast_filename = args[2]
+abundance = as.logical(args[3])
+fits_filename = args[4]
+pca_rast_filename = args[5]
+
+# read site-survey table
+site_survey = read.csv(site_survey_filename)
+
+# read environmental raster data
+env_rast = terra::rast(env_rast_filename)
+
+# format data for analysis
+site_pair = gdm::formatsitepair(bioData=site_survey,
+                                bioFormat=1,
+                                abundance=abundance,
+                                siteColumn='site',
+                                XColumn='x',
+                                YColumn='y',
+                                predData=env_rast)
+
+# fit GDM
+mod = gdm::gdm(site_pair, geo=F)
+print(summary(mod))
+
+# save fitted functions
+fits = as.data.frame(isplineExtract(mod))
+write.csv(fits, fits_filename)
+
+# save first <=3 PCs of GDM-transformed env space
+env_rast_trans <- gdm::gdm.transform(model=mod, data=env_rast)
+pca_samp <- terra::prcomp(env_rast_trans, maxcell = 5e5)
+n_pcs = min(3, dim(env_rast)[3])
+pca_rast <- terra::predict(env_rast_trans, pca_samp, index=1:n_pcs)
+pca_rast <- terra::stretch(pca_rast)
+terra::writeRaster(pca_rast, pca_rast_filename, overwrite=T)
+cat("\nGDM OUTPUTS SAVED TO DISK.\n")