select.sites: Site selection function

In dsouthwell/TestPackagev2: Spatially explicit power analysis in dynamic landscapes

Description

This function positions sites in the landscape for monitoring. Sites can be: 1) pre-selected by loading a file of the XY coordinates; 2) randomly selected at the start of each simulation; 3) randomly stratified across environmental layers at the start of each simulation, or; 3) positioned on cells with the highest expected species richness. If sites are selected randomly, they can also be divided between remote and non-remote areas given the ratio R

Usage

select.sites(sites, n.sites, R, all.loaded.sites, load.sites,
  new.site.selection, plot.sites)

Arguments

sites	Contains the XY coordinates of sites to be surveyed. The header of the x-coordinate should be an x, the header for the y-coordinate should be a y. If sites are to be selected randomly, dummy XY coordinates must still be provided.
n.sites	The number of sites to be monitored. If sites are pre-determined, this must be equal to the number of rows in the site coordinate matrix
R	The ratio of remote to non-remote sites. If R is 1, all sites will be in remote areas. If R is 0, no sites will be in remote areas, Setting R=0.6 means that 60 percent of randomly selected sites will be in remote areas
all.loaded.sites	Set to TRUE to monitor all of the XY coordinates loaded into the program, FALSE to monitor more than, or a subset of sites, loaded into the program. If n.sites is less than the number of loaded sites, a subset is selected randomly during each simulation. If n.sites is greater than the number of loaded sites, the remaining sites are positioned randomly throughout the landscape at the start of each simulation
load.sites	Set to TRUE only monitor at fixed coordinates in the landscape, FALSE if sites are to be randomly selected, randomly stratified across environmental layers, or positioned on cells with the highest expected species richness
new.site.selection	Set to 'random' to select sites randomly throughout the landscape, 'stratified' to randomly select equal number of sites with environmental strata, or 'maxocc' to position sites on cells with the highest relative species richness
plot.sites	Set to TRUE to plot the location of sites for the first simulation, FALSE to not plot the location of sites

Examples

#Load in fixed site coordinates to simulate monitoring at each site
load.sites <- TRUE
all.loaded.sites <- TRUE
new.site.selection <- 'random'
R <- 1
n.sites <- 150
plot.sites <- TRUE
xy.sites <- select.sites(sites, n.sites, R, all.loaded.sites, load.sites, new.site.selection, plot.sites) 

#Load in coordinates of 150 sites, but simulate monitoring at 200 sites
#Select the remaining 50 sites randomly throughout the landscape 
load.sites <- TRUE
all.loaded.sites <- FALSE
new.site.selection <- 'random'
R <- 1
n.sites <- 100
plot.sites <- TRUE
xy.sites <- select.sites(sites, n.sites, R, all.loaded.sites, load.sites, new.site.selection, plot.sites)

#Select 150 sites randomly stratified across environmental layers at the start of each simulation 
load.sites <- FALSE
all.loaded.sites <- FALSE
new.site.selection <- 'stratified'
R <- 1
n.sites <- 150
plot.sites <- TRUE
xy.sites <- select.sites(sites, n.sites, R, all.loaded.sites, load.sites, new.site.selection, plot.sites)

#Position 150 sites for monitoring on cells with the highest relative species richness
load.sites <- FALSE
all.loaded.sites <- FALSE
new.site.selection <- 'maxocc'
R <- 1
n.sites <- 150
plot.sites <- TRUE
xy.sites <- select.sites(sites, n.sites, R, all.loaded.sites, load.sites, new.site.selection, plot.sites)

dsouthwell/TestPackagev2 documentation built on May 28, 2019, 9:38 a.m.