prep_input: Preparing output for the STAN run of the STEPPS Model

In PalEON-Project/stepps-cal: Spatially explicit vegetation reconstruction using proxy pollen data

Description

Preparing output for the STAN run of the STEPPS Model

Usage

prep_input(veg, pollen, target_taxa, grid, hood = 7e+05, dist_scale = 1e+06)

Arguments

veg	A table of vegetation data, generally gridded.
pollen	A table of available pollen data.
target_taxa	The taxa to be reconstructed. Must appear in both the vegetation and pollen data.
grid	A data grid to be used for calibration of class raster.
hood	Distance (in units native to the grid) from which to estimate regional neighborhood for the pollen-vegetation calibration. Default is 1e5, assumed to be meters (100km).
dist_scale	Currently not implemented.

Value

A list with parameters:

K

Number of taxa in the data.

N_cores

Number of sedimentary cores used in the analysis.

N_cells

Number of cells in the parent grid.

N_hood

Number of vegetation cells contributing to each pollen sample site.

y

Pollen counts, a matrix with N_cores rows and K columns.

r

Vegetation proportions, a matrix with N_cells rows and K columns.

idx_cores

The index for each sedimentary core, with respect to the vegetation grid.

idx_hood

The index of each neighbourhood cell for each core, with respect to the vegetation grid.

d

Distance matrix from each sedimentary core to each vegetation cell.

N_pot

The number of potentially contributing cells for each vegetation cell.

d_pot

The actual number of vegetation cells contributing to each pollen sample site.

Examples

{
  ## Not run: 
   stepps_input <- prep_input(veg    = veg_table,
                              pollen = pol_table,
                              target_taxa = target_taxa,
                              grid   = reconst_grid)
  
## End(Not run)
}

PalEON-Project/stepps-cal documentation built on May 14, 2019, 8:20 a.m.