Author: Wenbo Lyu

# Spatially Convergent Partial Cross Mapping

#### Wenbo Lyu

####
Last update: 2026-02-15
Last run: 2026-04-05

## Model principles

The methodological details are pending peer review and will be made available thereafter.

## Usage examples

### Example of spatial vector data

Load the `spEDM` package and columbus OH spatial analysis dataset:

    if (!requireNamespace("spEDM")) install.packages("spEDM")
    ## Loading required namespace: spEDM

    columbus = sf::read_sf(system.file("case/columbus.gpkg", package="spEDM"))
    columbus
    ## Simple feature collection with 49 features and 6 fields
    ## Geometry type: POLYGON
    ## Dimension:     XY
    ## Bounding box:  xmin: 5.874907 ymin: 10.78863 xmax: 11.28742 ymax: 14.74245
    ## Projected CRS: Undefined Cartesian SRS with unknown unit
    ## # A tibble: 49 × 7
    ##    hoval   inc  crime  open plumb discbd                                                  geom
    ##    <dbl> <dbl>  <dbl> <dbl> <dbl>  <dbl>                                             <POLYGON>
    ##  1  80.5 19.5  15.7   2.85  0.217   5.03 ((8.624129 14.23698, 8.5597 14.74245, 8.809452 14.73…
    ##  2  44.6 21.2  18.8   5.30  0.321   4.27 ((8.25279 14.23694, 8.282758 14.22994, 8.330711 14.2…
    ##  3  26.4 16.0  30.6   4.53  0.374   3.89 ((8.653305 14.00809, 8.81814 14.00205, 9.008951 13.9…
    ##  4  33.2  4.48 32.4   0.394 1.19    3.7  ((8.459499 13.82035, 8.473408 13.83227, 8.502935 13.…
    ##  5  23.2 11.3  50.7   0.406 0.625   2.83 ((8.685274 13.63952, 8.677577 13.72221, 8.90994 13.7…
    ##  6  28.8 16.0  26.1   0.563 0.254   3.78 ((9.401384 13.5504, 9.434411 13.69427, 9.605247 13.6…
    ##  7  75    8.44  0.178 0     2.40    2.74 ((8.037741 13.60752, 8.062716 13.60452, 8.072695 13.…
    ##  8  37.1 11.3  38.4   3.48  2.74    2.89 ((8.247527 13.58651, 8.2795 13.5965, 8.294443 13.604…
    ##  9  52.6 17.6  30.5   0.527 0.891   3.17 ((9.333297 13.27242, 9.671007 13.27361, 9.67701 13.2…
    ## 10  96.4 13.6  34.0   1.55  0.558   4.33 ((10.08251 13.03377, 10.0925 13.05275, 10.12649 13.0…
    ## # ℹ 39 more rows

We demonstrate how spatial vector data can be used in SCPCM analysis through a causal example examining the influences of the level of burglary incidents in a neighbourhood on house values, with neighbourhood household income included as a conditioning variable.

Determine minimum embedding dimensions:

    spEDM::fnn(columbus,"crime",E = 1:10)
    ## [spEDM] Output 'E:i' corresponds to the i-th valid embedding dimension.
    ## [spEDM] Input E values exceeding max embeddable dimension were truncated.
    ## [spEDM] Please map output indices to original E inputs before interpretation.
    ##        E:1        E:2        E:3        E:4        E:5        E:6        E:7        E:8
    ## 0.79591837 0.53061224 0.63265306 0.51020408 0.12244898 0.04081633 0.00000000 0.00000000
    spEDM::fnn(columbus,"hoval",E = 1:10)
    ## [spEDM] Output 'E:i' corresponds to the i-th valid embedding dimension.
    ## [spEDM] Input E values exceeding max embeddable dimension were truncated.
    ## [spEDM] Please map output indices to original E inputs before interpretation.
    ##        E:1        E:2        E:3        E:4        E:5        E:6        E:7        E:8
    ## 0.85714286 0.77551020 0.51020408 0.61224490 0.22448980 0.08163265 0.00000000 0.00000000
    spEDM::fnn(columbus,"inc",E = 1:10)
    ## [spEDM] Output 'E:i' corresponds to the i-th valid embedding dimension.
    ## [spEDM] Input E values exceeding max embeddable dimension were truncated.
    ## [spEDM] Please map output indices to original E inputs before interpretation.
    ##        E:1        E:2        E:3        E:4        E:5        E:6        E:7        E:8
    ## 0.73469388 0.24489796 0.30612245 0.38775510 0.24489796 0.04081633 0.00000000 0.00000000

Self prediction for parameter turning:

    spEDM::simplex(columbus,"crime","crime",E = 7:10,k=12)
    ## The suggested E,k,tau for variable crime is 8, 12 and 1
    spEDM::simplex(columbus,"hoval","hoval",E = 7:10,k=12)
    ## The suggested E,k,tau for variable hoval is 7, 12 and 1
    spEDM::simplex(columbus,"inc","inc",E = 7:10,k=12)
    ## The suggested E,k,tau for variable inc is 8, 12 and 1

Conduct SCPCM:

    crime_hoval = spEDM::scpcm(data = columbus,
                               cause = "crime",
                               effect = "hoval",
                               conds = "inc",
                               libsizes = seq(5, 45, by = 5),
                               E = c(8,7,8),
                               k = 12,
                               progressbar = FALSE)
    crime_hoval
    ## --------------------------------------
    ## ***partial cross mapping prediction***
    ## --------------------------------------
    ##   libsizes crime->hoval hoval->crime
    ## 1        5   0.08948688  0.022401607
    ## 2       10   0.14511673  0.062986079
    ## 3       15   0.16849249  0.080653365
    ## 4       20   0.20940427  0.040974217
    ## 5       25   0.23160147  0.026613757
    ## 6       30   0.24709326  0.001942294
    ## 7       35   0.29707812 -0.014879976
    ## 8       40   0.33591810 -0.028758126
    ## 9       45   0.36337200 -0.040204136
    ##
    ## ------------------------------
    ## ***cross mapping prediction***
    ## ------------------------------
    ##   libsizes crime->hoval hoval->crime
    ## 1        5    0.2224861    0.1378071
    ## 2       10    0.3023880    0.1880328
    ## 3       15    0.4005255    0.2085278
    ## 4       20    0.4681692    0.2203727
    ## 5       25    0.5098130    0.2293076
    ## 6       30    0.5467173    0.2326005
    ## 7       35    0.5732757    0.2331852
    ## 8       40    0.5822545    0.2361204
    ## 9       45    0.5883504    0.2364234

Visualize the result:

    if (!requireNamespace("cowplot")) install.packages("cowplot")
    ## Loading required namespace: cowplot

    fig1a = plot(crime_hoval,partial = FALSE,ylimits = c(0.1,0.75))
    fig1b = plot(crime_hoval,partial = TRUE,ylimits = c(-0.05,0.55))
    fig1 = cowplot::plot_grid(fig1a,fig1b,ncol = 2,label_fontfamily = 'serif',
                              labels = paste0('(',letters[1:2],')'))
    fig1

Figure 1. The cross mapping between crime and house value. a Crime–hoval causality without accounting for covariates. b Crime–hoval causality controlling for household income.

### Example of spatial raster data

Load the `spEDM` package and simulate raster data with a cyclic interaction structure \(x \rightarrow y \rightarrow z \rightarrow x\):

    if (!requireNamespace("fields")) install.packages("fields")
    ## Loading required namespace: fields
    if (!requireNamespace("MASS")) install.packages("MASS")

    sim_trispecies = \(nx,ny,seed = 123){
      grid = expand.grid(seq(0, 10, length.out = nx),
                         seq(0, 10, length.out = ny))
      cov.fun = \(d, range = 1.5, sill=1) sill * exp(-d/range)
      dist.mat = fields::rdist(grid)
      cov.mat = cov.fun(dist.mat, range=1.5, sill=1)
      set.seed(seed)
      res = replicate(3, {
        MASS::mvrnorm(1, rep(0, nrow(grid)), cov.mat) |>
          pmax(0) |>
          sdsfun::normalize_vector(0,1) |>
          matrix(nrow = nx, ncol = ny) |>
          terra::rast()
      }, simplify = FALSE)
      terra::rast(res)
    }

    species = sim_trispecies(20,20, seed = 42)
    names(species) = c("x","y","z")

    sim = spEDM::slm(species, x = "x", y = "y", z = "z", k = 4,
                     step = 15, transient = 1, threshold = Inf,
                     aggregate_fn = \(.x) mean(.x, na.rm = TRUE),
                     alpha_x = 0.05, alpha_y = 0.05, alpha_z = 0.05,
                     beta_xy = 1, beta_xz = 0, beta_yx = 0, beta_yz = 1,
                     beta_zx = 1, beta_zy = 0)

    terra::values(species[["x"]]) = sim$x
    terra::values(species[["y"]]) = sim$y
    terra::values(species[["z"]]) = sim$z
    species
    ## class       : SpatRaster
    ## size        : 20, 20, 3  (nrow, ncol, nlyr)
    ## resolution  : 1, 1  (x, y)
    ## extent      : 0, 20, 0, 20  (xmin, xmax, ymin, ymax)
    ## coord. ref. :
    ## source(s)   : memory
    ## names       :         x,         y,        z
    ## min values  : 0.9984091, 0.9983558, 0.998285
    ## max values  : 1.0009110, 1.0011445, 1.001050

Determine minimum embedding dimensions:

    spEDM::fnn(species, "x")
    ## [spEDM] Output 'E:i' corresponds to the i-th valid embedding dimension.
    ## [spEDM] Input E values exceeding max embeddable dimension were truncated.
    ## [spEDM] Please map output indices to original E inputs before interpretation.
    ##       E:1       E:2       E:3       E:4       E:5       E:6       E:7       E:8       E:9
    ## 0.8937824 0.3125000 0.0100000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
    spEDM::fnn(species, "y")
    ## [spEDM] Output 'E:i' corresponds to the i-th valid embedding dimension.
    ## [spEDM] Input E values exceeding max embeddable dimension were truncated.
    ## [spEDM] Please map output indices to original E inputs before interpretation.
    ##       E:1       E:2       E:3       E:4       E:5       E:6       E:7       E:8       E:9
    ## 0.9333333 0.2525000 0.0425000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000
    spEDM::fnn(species, "z")
    ## [spEDM] Output 'E:i' corresponds to the i-th valid embedding dimension.
    ## [spEDM] Input E values exceeding max embeddable dimension were truncated.
    ## [spEDM] Please map output indices to original E inputs before interpretation.
    ##       E:1       E:2       E:3       E:4       E:5       E:6       E:7       E:8       E:9
    ## 0.9238845 0.3375000 0.0625000 0.0200000 0.0000000 0.0000000 0.0000000 0.0000000 0.0000000

Self prediction for parameter turning:

    s1 = spEDM::simplex(species, "x", "x", E = 5:10, k = 15, tau = 1)
    s2 = spEDM::simplex(species, "y", "y", E = 5:10, k = 15, tau = 1)
    s3 = spEDM::simplex(species, "z", "z", E = 5:10, k = 15, tau = 1)
    list(s1,s2,s3)
    ## [[1]]
    ## The suggested E,k,tau for variable x is 7, 15 and 1
    ##
    ## [[2]]
    ## The suggested E,k,tau for variable y is 9, 15 and 1
    ##
    ## [[3]]
    ## The suggested E,k,tau for variable z is 5, 15 and 1

Due to the statistical aggregation performed after simulating with the spatial logistic map, we adopt a uniform embedding dimension for x, y, and z to reduce inference bias:

    if (!requireNamespace("purrr")) install.packages("purrr")
    ## Loading required namespace: purrr
    simplex_res = purrr::map2_dfr(list(s1,s2,s3), c("x","y","z"),
                                  \(.list,.name) dplyr::mutate(.list$xmap,variable = .name))
    ggplot2::ggplot(data = simplex_res) +
      ggplot2::geom_line(ggplot2::aes(x = E, y = rho, color = variable)) +
      ggplot2::theme_classic()

Figure 2. Self cross prediction skills for three variables.

Since the self-prediction performance of the y variable is relatively weaker than that of x and z, we select the embedding dimension that yields the strongest predictive performance for y as the final dimension, that is \(E = 9\).

Investigate the causation between x and z, with y as control variables:

    xz = spEDM::scpcm(species, "x", "z", "y", E = 9, k = 15,
                      libsizes = matrix(seq(50,400,50), ncol = 1),
                      progressbar = FALSE)
    xz
    ## --------------------------------------
    ## ***partial cross mapping prediction***
    ## --------------------------------------
    ##   libsizes       x->z      z->x
    ## 1       50 0.07977338 0.1020714
    ## 2      100 0.10473775 0.1762694
    ## 3      150 0.14175015 0.1959109
    ## 4      200 0.20562278 0.2543825
    ## 5      250 0.25500417 0.3300376
    ## 6      300 0.27904324 0.3956866
    ## 7      350 0.31249554 0.4597477
    ## 8      400 0.28091955 0.4843444
    ##
    ## ------------------------------
    ## ***cross mapping prediction***
    ## ------------------------------
    ##   libsizes      x->z      z->x
    ## 1       50 0.1542880 0.1368370
    ## 2      100 0.1827606 0.2217753
    ## 3      150 0.2426258 0.2781118
    ## 4      200 0.3239733 0.3487456
    ## 5      250 0.4035323 0.4185710
    ## 6      300 0.4653763 0.4835619
    ## 7      350 0.5190529 0.5553776
    ## 8      400 0.5658039 0.5938894

Visualize the result:

    fig2a = plot(xz,partial = FALSE,ylimits = c(0.05,0.65))
    fig2b = plot(xz,partial = TRUE,ylimits = c(0.05,0.65))
    fig2 = cowplot::plot_grid(fig2a,fig2b,ncol = 2,label_fontfamily = 'serif',
                              labels = paste0('(',letters[1:2],')'))
    fig2

Figure 3. The cross mapping between x and z. a x–z causality without accounting for y. b x–z causality controlling for y.