make_spatial_info: Build objects related to spatial information

In merrillrudd/StreamUtils: Additional utilities for FishStats spatio-temporal modeling toolbox focusing on stream networks

Description

make_spatial_info builds a tagged list with all the spatial information needed for Data_Fn

Usage

make_spatial_info(n_x, Network_sz, Lon_i, Lat_i, Lon_x, Lat_x,
  Extrapolation_List, Method = "Mesh", grid_size_km = 50,
  grid_size_LL = 1, randomseed = 1, nstart = 100, iter.max = 1000,
  ...)

Arguments

n_x,	the number of nodes in the stream network
Network_sz	data frame of network information including column names 'parent_s', 'child_s', 'dist_s'
Lon_i,	Longitude for each sample
Lat_i,	Latitude for each sample
Lon_x,	Longitude for each child node
Lat_x,	Latitude for each child node
Extrapolation_List,	the output from Prepare_Extrapolation_Data_Fn
Method,	a character of either "Grid" or "Mesh" where "Grid" is a 2D AR1 process, and "Mesh" is the SPDE method with geometric anisotropy
grid_size_km,	the distance between grid cells for the 2D AR1 grid (determines spatial resolution when Method="Grid") when not using Method="Spherical_mesh"
grid_size_LL,	the distance between grid cells for the 2D AR1 grid (determines spatial resolution when Method="Grid") when using Method="Spherical_mesh"
...,	additional arguments passed to Calc_Kmeans

Value

Tagged list containing objects for running a VAST model

MeshList

A tagged list with inputs related to the SPDE mesh

GridList

A tagged list with inputs related to the 2D AR1 grid

a_xl

A data frame with areas for each knot and each strattum

loc_UTM

A data frame with the converted UTM coordinates for each sample

Kmeans

Output from Calc_Kmeans with knots for a triangulated mesh

knot_i

The knot associated with each sample

Method

The Method input (for archival purposes)

loc_x

The UTM location for each knot

merrillrudd/StreamUtils documentation built on May 29, 2019, 9:31 a.m.