How to create a hyperframe containing groups of points with marks each associated with a unique window in R

Question

I'm having difficulty converting point patterns to a hyperframes despite on-line searches and consulting Baddeley and Rubak's Spatial Point Patterns: Methodology and Applications with R. I'm new to R and spatial stats. Any help would be much appreciated! My situation: I have a point shapefile and a polygon shapefile from GIS. The point shapefile contains x y coordinates along with many grouping variables, covariates, and response variables. The polygon shapefile contains plot coordinates where the points are located within, and includes a Plot ID column.

I need to characterize and analyze point patterns based on several factors, both within each plot and between plots. Note: the plot is the experimental unit. Based on readings, I've concluded a hyperframe is the most user-friendly method for analysis. As an example here's how I imagine the hyperframe:

PlotID  Point#  X Coord     Y Coord Color   Size    Sex     Weight  Growth
    A   1       514514.5    3372057 Red     Small   Female  10      0.5
    A   2       514484.2    3372062 Red     Medium  Male    14      0.6
    A   3       514517.8    3372017 Red     Large   Female  12      0.6
    B   1       524514.5    3372065 Blue    Small   Male    14      0.4
    B   2       524484.2    3372067 Blue    Small   Male    16      0.3
    B   3       524517.8    3372063 Blue    Large   Male    10      0.35
    C   1       504514.5    3372041 Red     Medium  Female  10      0.7
    C   2       504484.2    3372042 Red     Large   Female  12      0.4
    C   3       504517.8    3372038 Red     Small   Male    16      0.6
    D   1       504517.8    3372038 Blue    Small   Male    10      0.7
    D   2       504517.8    3372038 Blue    Medium  Female  12      0.3
    D   3       504517.8    3372038 Blue    Small   Male    16      0.6

The above hyperframe might be used to group point patterns by color to analyse differences in point patterns.

I successfully converted a simplified version of the shapefiles to a hyperframe by subsetting a single plot with its associated points. Here's the code:

    library(sp)
    library(spatstat)
    library(shapefiles)
    library(maptools)
    library(rgdal)

    x <- readShapeSpatial("Points_subset.shp") #creates a spatial points 
                                               #dataframe
    x.data <- slot(x,"data") #columns of the data frame used as marks 
    p <- readShapeSpatial("Plot_subset") #creates spatial polygons df.  
    w <- as(as(p,"SpatialPolygons"),"owin") #assign the plot boundary as the 
                                            #window of the point pattern
    y <- as(x, "SpatialPoints") #Assign point coordinates as spatial points
    z <- as(y, "ppp") #Convert to class "ppp"
    z <- z[w] #Assign the plot boundary as the window of the ppp
    marks(z) <- x.data #Attach the data.frame of variables to the ppp.
    plot(z) #Correctly produces 1 plot containing all points

However, when I apply the same process with multiple plots using a loop the hyperframe only includes information from a single plot. Here's code for multiple plots:

    xm <- readShapeSpatial("Points_All.shp")
    xm.data <- slot(xm,"data")
    xn <- levels(unique(xm$PlotID)) #identify all plots

    pm <- readShapeSpatial("Plots_All.shp") 

    for(i in 1:length(xn)) {
    pm2 <- subset(pm, pm$PlotID == xn[i])
    wm2 <- as(as(pm2,"SpatialPolygons"),"owin")#list of polygon windows
    xm2 <- subset(xm, xm$PlotID == xn[i])
    xm2.data <- subset(xm.data, xm.data$PlotID == xn[i])
    ym <- as(xm2, "SpatialPoints")
    zm2 <- as.ppp(coordinates(ym),wm2)
    marks(zm2) <- xm2.data
    unitname(zm) <- c("metre","metres")
    plot(zm2, main=paste(xn[i])) #plots each plot's points with correct 
                                 #window
    }

Investigate zm2

    str(zm2) # Although all plots print above, "str" shows only the first 
             #plot 
    View(zm2)#Contains only the points of the first plot

Convert to a hyperframe

    zm2.hyp <- as.hyperframe(zm2)
    str(zm2.hyp) #as above, contains a row for each point of the first plot.
                 #hyperframe should include points for all plots

How do I include all plots in the hyperframe?

Adrian Baddeley · Accepted Answer

Yes, you will need to arrange the data in a hyperframe for analysis. Each row of this hyperframe will contain all the data for one experimental unit -- that is, each row of the hyperframe will contain a point pattern including its boundary polygon.

However, in the first displayed box in your posting (headed "As an example here's how I imagine the hyperframe") each row contains the data for a single point. That's not what you want. The data in this box can be represented as a data.frame and your first task is to separate this into groups containing the data for each point pattern.

Suppose you have set up a data.frame containing all the data sketched in that first displayed box. Call it df. First we split this data frame into several data frames according to the PlotID variable:

dflist <- split(df, PlotID)

The result is a list, each element of which is a data frame, withdf[[i]] containing the coordinate data for the ith point pattern.

Next you want to match these data frames with the corresponding boundary polygons. Suppose you've collected the boundary polygons as a list blist where blist[[i]] is the ith polygon. To match up the coordinates and the boundaries,

plist <- mapply(as.ppp, X=dflist, W=blist, SIMPLIFY=FALSE)

The result should be a list of point patterns (all the other variables such as Sex, Colour will be "marks" attached to these patterns). From this list, you can build your hyperframe, e.g

H <- hyperframe(X=plist)

but you'll need more columns in the hyperframe to fit interesting models.

How to create a hyperframe containing groups of points with marks each associated with a unique window in R

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