Species Distribution and Abundance Modelling at High Spatio-Temporal Resolution


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Documentation for package ‘dynamicSDM’ version 1.3.4

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brt_fit Fit boosted regression tree models to species distribution or abundance data.
convert_gbif Reformats GBIF data into 'dynamicSDM' data frame
dynamic_proj Project species distribution and abundance models onto dynamic environmental covariates.
dynamic_proj_covariates Combine explanatory variable rasters into covariates for each projection date.
dynamic_proj_dates Generate vector of dates for dynamic projections
dynamic_proj_GIF Create GIF of dynamic species distribution and abundance projections
extract_buffered_coords Extract spatially buffered and temporally dynamic explanatory variable data for occurrence records.
extract_buffered_raster Extract spatially buffered and temporally dynamic rasters of explanatory variable data.
extract_coords_combine Combine extracted explanatory variable data for occurrence records into single data frame.
extract_dynamic_coords Extract temporally dynamic explanatory variable data for occurrence records.
extract_dynamic_raster Extract temporally dynamic rasters of explanatory variables.
extract_static_coords Extract explanatory variables from static rasters
get_moving_window Generate a “moving window” matrix of optimal size
sample_cov_data Sample projection covariates three variables across for southern Africa.
sample_events_data Sample e-Bird sampling event records
sample_explan_data Sample species occurrence records with associated dynamic explanatory variables
sample_extent_data MULTIPOLYGON object for the extent of southern Africa
sample_filt_data Sample of filtered species occurrence records
sample_occ_data Sample species occurrence records
spatiotemp_autocorr Test for spatial and temporal autocorrelation in species distribution model explanatory data.
spatiotemp_bias Test for spatial and temporal bias in species occurrence records
spatiotemp_block Split occurrence records into spatial and temporal blocks for model fitting.
spatiotemp_check Check species occurrence record formatting, completeness and validity.
spatiotemp_extent Filter species occurrence records by a given spatial and temporal extent.
spatiotemp_pseudoabs Generate pseudo-absence record coordinates and dates
spatiotemp_resolution Filter species occurrence records by given spatial and temporal resolution
spatiotemp_thin Thin species occurrence records by spatial and temporal proximity.
spatiotemp_weights Calculate sampling effort across spatial and temporal buffer from species occurrence records