Subsample points to deal with spatiotemporal bias in observations by defining
a grid in space and time, then sampling the given number of points from each
cell. sample_case_control() additionally samples presence and absence
independently.
sample_grid(x, res, t_res, n = 1, replace = FALSE, jitter = TRUE)
sample_case_control(x, res, t_res, n = 1, replace = FALSE, jitter = TRUE)data frame or sf object; the points to subsample. If x is a data
frame the coordinates should be provided as columns latitude and
longitude. The day of year should be expressed as an integer from 1-366.
numeric; the size in meters of the grid to sample from. This can be a 2 element vector indicating the x and y dimensions of the cells.
numeric; the temporal resolution for sampling expressed as a
proportion of the year. For example, 7 / 365 would result in sampling
from each week.
integer; the number of points to sample from each grid cell.
logical; whether to sample with replacement.
logical; to avoid always using the same grid for sampling, the grid can be jittered so that the origin is different each time this function is called.
Logical vector indicating which rows are selected.
if (FALSE) {
# download example data
path <- ebirdst_download("example_data", tifs_only = FALSE)
# or get the path if you already have the data downloaded
path <- get_species_path("example_data")
# test data to sample
preds <- load_predictions(path, return_sf = TRUE)
# sample on a 100, 4 month grid
s <- sample_grid(preds, res = 100000, t_res = 1 / 4)
preds_grid <- preds[s, ]
# case control sampling independently samples presence and absence
s <- sample_case_control(preds, res = 1000000, t_res = 1 / 12)
preds_cc <- preds[s, ]
# grid sampling preserves the presence/absence ratio
table(preds$obs > 0) / nrow(preds)
table(preds_grid$obs > 0) / nrow(preds_grid)
# while case control sampling increases the prevelance of presences
table(preds_cc$obs > 0) / nrow(preds_cc)
# plot
library(sf)
p <- par(mar = c(0, 0, 0, 0))
plot(st_geometry(preds), col = "black", pch = 19, cex = 0.2)
plot(st_geometry(preds_cc), col = "red", pch = 19, cex = 0.5, add = TRUE)
}