sensors4plumes (version 0.9.3)

similaritySD: Determine (spatial) similarity between sampling designs

Description

Takes sampling designs and a reference sampling design and computes similarity between them by various algorithms: number of coinciding sensors, sensors within a k-neighbourhood (based on get.knnx), Earth Mover's Distance (based on emd2d).

Usage

similaritySD(simulations, SD, referenceSD, type = "equal", k = 9, ...)

Arguments

simulations

Simulations object, needed to define spatial properties; not needed if type = "equal"

SD

vector, matrix (sampling designs in rows) or list of sampling designs; indices of the locations of simulations

referenceSD

sampling design (indices of the locations of simulations); all SD are compared to this sampling design

type

character, indicating comparison method, one of "equal", "Kneighbours", "EarthMoversDistance"

k

neighbourhood size, to be used for type = "Kneighbours", forwarded to get.knnx

...

parameters to be used for type = "EarthMoversDistance", forwarded to emd2d

Value

A vector of length referring to the number of sampling designs in SD with the similarity between these sampling designs and referenceSD respectively.

Details

Originally Earth Mover's Distance compares matrices of two distributions. We can use it for cases where all locations lie on a regular grid. Then a sampling design is represented by a matrix of all grid cells: each sensor is represented by 1, all other cells are 0 (for locations on a SpatialPolygrid, a sensor may belong to several cells, then the weight 1 is distributed evenly to all these cells).

Examples

# NOT RUN {
## ---------------- prepare data --------------------------
# simulations with SpatialPolygridDataFrame
data(radioactivePlumes)

# simulations with SpatialPixelsDataFrame
data(meuse.grid)
coordinates(meuse.grid) = ~ x + y
gridded(meuse.grid) = TRUE
meuseGSim = subset(radioactivePlumes, 
                  locations = 1:length(meuse.grid), plumes = 1:10)
meuseGSim@locations = meuse.grid

# simulations with rectangular SpatialPixelsDataFrame
data(SPixelsDF)
rectSim = subset(radioactivePlumes, 
                 locations = 1:length(SPixelsDF), plumes = 1:10)
rectSim@locations = SPixelsDF # not nice, no checking if sizes fit

# simulations with SpatialPointsDataFrame 
data(meuse)
coordinates(meuse) = ~ x + y
meuseSim = subset(radioactivePlumes, 
                  locations = length(meuse), plumes = 1:10)
meuseSim@locations = meuse # not nice, no checking if sizes fit

# for meuseSim
sds0 = c(10,  25,  42,  84,  90,  92,  94,  97, 120, 153)#sample.int(155, 10)
sds1 = matrix(c(97,   79,   40,   68,  131,
                57,   18,   38,  118,   14,
                23,   71,   22,   94,   27,
                125,  108,    4,   80,  129,
                130,   96,  101,  137,   19,
                77,  138,   32,   95,   88,
                140,   73,   43,  153,   12,
                8,  141,   92,   35,  102), 
              byrow = TRUE, nrow = 8)#matrix(sample.int(155, 40), nrow = 8)
sds2 = list(
  c(28, 59, 64, 78, 81),
  c(5,  13,  21,  31,  45,  91,  92, 122, 130, 141),
  c(1,   2,  19,  36,  50,  51,  58,  59,  90, 103, 105, 107, 112, 123, 132),
  c(34,  48,  49,  50,  71,  76,  77,  86,  92,  97, 100, 103, 104, 106, 108, 
  110, 113, 127, 134, 142)
)

# ------------- "equal" -----------------------------
  sim_1_1 = similaritySD(# no simulations needed
    SD = sds1, referenceSD = sds0, type = "equal")  

#------------- "Kneighbours" -------------------
  sim_2_1_1 = similaritySD(simulations = meuseGSim,
                              SD = sds2, referenceSD = sds0, 
                              type = "Kneighbours", k = 4)  
  sim_2_1_2 = similaritySD(simulations = meuseGSim,
                         SD = sds2, referenceSD = sds0, 
                         type = "Kneighbours", k = 9) 

# plot points for visual comparison
plot(coordinates(meuseSim@locations), pch = ".")
   points(coordinates(meuseSim@locations)[sds0,], cex = 0.5)
   for (i in seq(along = sds2)){
     points(coordinates(meuseSim@locations)[sds2[[i]],], 
            col = i + 1)
   }
#---------- "EarthMoversDistance"----------
  # SpatialPixelsDataFrame
  sim_3_1_3 = similaritySD(simulations = rectSim,
                                SD = c(2,9), referenceSD = c(3,8), 
                                type = "EarthMoversDistance")

  sim_3_1_4 = similaritySD(simulations = rectSim,
                                SD = c(3,8), referenceSD = c(4,5), 
                                type = "EarthMoversDistance")
  sim_3_1_5 = similaritySD(simulations = rectSim,
                                SD = c(3,8), referenceSD = c(4,5), 
                                type = "EarthMoversDistance", dist = "manhattan")  

  ## SpatialPolygridDataFrame
  sim_3_1_5 = similaritySD(simulations = radioactivePlumes,
                                SD = c(220, 503), referenceSD = c(224, 544), 
                                type = "EarthMoversDistance")  

# }