Species Distribution and Abundance Modelling at High Spatio-Temporal Resolution

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Documentation for package ‘dynamicSDM’ version 1.3.3

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

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