pattern causality

Usage

# S4 method for class 'sf'
pc(
  data,
  column,
  target,
  E = 2:10,
  k = E + 2,
  tau = 1,
  style = 1,
  lib = NULL,
  pred = NULL,
  dist.metric = "L2",
  zero.tolerance = max(k),
  relative = TRUE,
  weighted = TRUE,
  na.rm = TRUE,
  threads = detectThreads(),
  detrend = FALSE,
  nb = NULL
)

# S4 method for class 'SpatRaster'
pc(
  data,
  column,
  target,
  E = 2:10,
  k = E + 2,
  tau = 1,
  style = 1,
  lib = NULL,
  pred = NULL,
  dist.metric = "L2",
  zero.tolerance = max(k),
  relative = TRUE,
  weighted = TRUE,
  na.rm = TRUE,
  threads = detectThreads(),
  detrend = FALSE,
  grid.coord = TRUE
)

Arguments

data: observation data.
column: name of library variable.
target: name of target variable.
E: (optional) embedding dimensions.
k: (optional) number of nearest neighbors used.
tau: (optional) step of spatial lags.
style: (optional) embedding style (0 includes current state, 1 excludes it).
lib: (optional) libraries indices (input needed: vector - spatial vector, matrix - spatial raster).
pred: (optional) predictions indices (input requirement same as lib).
dist.metric: (optional) distance metric (L1: Manhattan, L2: Euclidean).
zero.tolerance: (optional) maximum number of zeros tolerated in signature space.
relative: (optional) whether to calculate relative changes in embeddings.
weighted: (optional) whether to weight causal strength.
na.rm: (optional) whether to remove NA samples in symbolic pattern generation.
threads: (optional) number of threads to use.
detrend: (optional) whether to remove the linear trend.
nb: (optional) neighbours list.
grid.coord: (optional) whether to detrend using cell center coordinates (TRUE) or row/column numbers (FALSE).

Value

A list

xmap: cross mapping performance
varname: name of target variable
method: method of cross mapping

References

Stavroglou, S.K., Pantelous, A.A., Stanley, H.E., Zuev, K.M., 2020. Unveiling causal interactions in complex systems. Proceedings of the National Academy of Sciences 117, 7599–7605.

Examples

columbus = sf::read_sf(system.file("case/columbus.gpkg", package="spEDM"))
# \donttest{
pc(columbus,"hoval","crime", E = 5:10)
#> The suggested E,k,tau for variable crime is 5, 7 and 1 
# }