pcm: partial cross mapping

In tEDM: Temporal Empirical Dynamic Modeling

partial cross mapping

Description

partial cross mapping

Usage

## S4 method for signature 'data.frame'
pcm(
  data,
  cause,
  effect,
  conds,
  libsizes = NULL,
  E = 3,
  tau = 0,
  k = E + 1,
  theta = 1,
  algorithm = "simplex",
  lib = NULL,
  pred = NULL,
  dist.metric = "L1",
  dist.average = TRUE,
  threads = length(pred),
  parallel.level = "low",
  bidirectional = TRUE,
  cumulate = FALSE,
  progressbar = TRUE
)

Arguments

data	observation data.
cause	name of causal variable.
effect	name of effect variable.
conds	name of conditioning variables.
libsizes	(optional) number of time points used.
E	(optional) embedding dimensions.
tau	(optional) step of time lags.
k	(optional) number of nearest neighbors.
theta	(optional) weighting parameter for distances, useful when algorithm is smap.
algorithm	(optional) prediction algorithm.
lib	(optional) libraries indices.
pred	(optional) predictions indices.
dist.metric	(optional) distance metric (L1: Manhattan, L2: Euclidean).
dist.average	(optional) whether to average distance.
threads	(optional) number of threads to use.
parallel.level	(optional) level of parallelism, low or high.
bidirectional	(optional) whether to examine bidirectional causality.
cumulate	(optional) serial or cumulative computation of partial cross mapping.
progressbar	(optional) whether to show the progress bar.

Value

A list

pxmap

partial cross mapping results

xmap

cross mapping results

varname

names of causal and effect variable

bidirectional

whether to examine bidirectional causality

References

Leng, S., Ma, H., Kurths, J. et al. Partial cross mapping eliminates indirect causal influences. Nat Commun 11, 2632 (2020).

Examples

sim = logistic_map(x = 0.4,y = 0.4,z = 0.4,step = 45,
                   beta_xy = 0.5, beta_xz = 0,
                   beta_yx = 0, beta_yz = 0.5,
                   beta_zx = 0, beta_zy = 0)
pcm(sim,"x","z","y",libsizes = seq(5,45,5),E = 10,k = 7,threads = 1)

tEDM documentation built on Aug. 25, 2025, 5:12 p.m.