How to create a list of Networks in R based on Time Series Data

I'm attempting to look at networks of individuals and site visits over a time series. Essentially, the end result I'd like to achieve is similar to the "beaches" dataset found in package "dnr". I have a larger dataset dput for a subset of which is shown at the bottom.

Basically I would like to split() this table by both Species and Week and then create an incidence matrix with rows of distinct values from TagID and columns based on distinct values in SiteVisits. Then i use package igraph and graph_from_incidence_matrix to create a unique network for each species for each week.

I started with an attempt to split the main table by species and then create new tables for each species for each week:

DFsplit <- split(DF, DF$Species)
DFsplit_cf <- split(DFsplit$Catfish, DFsplit$Catfish$Week)

this worked fine, but when I attempted to write a loop to build a network using this dataframe

network_builder <- function(data) {
  for(i in 1: length(data)) {
    adjacency <- xtabs(~ data[[i]][,3] + data[[i]][,4])
    network[i] <- graph_from_incidence_matrix(adjacency)
  }
}

network_builder(DFsplit_stb)

I received

 Error in model.frame.default(formula = ~data[[i]][, 3] + data[[i]][, 4]) : 
  invalid type (list) for variable 'data[[i]][, 3]'

I'm guessing there's a way to get around this error, but nothing I've tried is working. Also, if there is a cleaner way to do this, I'm all ears.

dput:

structure(list(Species = c("Striped Bass", "Striped Bass", "Striped Bass", 
"Striped Bass", "Striped Bass", "Striped Bass", "Striped Bass", 
"Striped Bass", "Striped Bass", "Striped Bass", "Striped Bass", 
"Striped Bass", "Striped Bass", "Striped Bass", "Striped Bass", 
"Striped Bass", "Striped Bass", "Striped Bass", "Striped Bass", 
"Striped Bass", "Striped Bass", "Striped Bass", "Striped Bass", 
"Striped Bass", "Striped Bass", "Striped Bass", "Striped Bass", 
"Striped Bass", "Striped Bass", "Striped Bass", "Striped Bass", 
"Striped Bass", "Striped Bass", "Striped Bass", "Striped Bass", 
"Striped Bass", "Striped Bass", "Striped Bass", "Striped Bass", 
"Striped Bass", "Striped Bass", "Striped Bass", "Striped Bass", 
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"Striped Bass", "Striped Bass", "Striped Bass", "Striped Bass", 
"Striped Bass", "Largemouth Bass", "Largemouth Bass", "Largemouth Bass", 
"Largemouth Bass", "Largemouth Bass", "Largemouth Bass", "Largemouth Bass", 
"Largemouth Bass", "Largemouth Bass", "Largemouth Bass", "Largemouth Bass", 
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"IC1", "RGD1", "RGD1", "IC3", "RGD1", "IC3", "IC2", "IC2", "IC1", 
"IC1", "IC1", "IC1", "IC3", "IC1", "IC3", "IC1", "IC3", "IC1", 
"IC3", "IC1", "IC1", "IC3", "IC1", "IC3", "IC2", "IC1", "IC3", 
"IC2", "IC1", "IC3", "IC2", "IC1", "IC3", "IC2", "IC1", "RGD1", 
"IC3", "IC2", "IC1", "RGD1", "IC3", "IC2", "IC1", "RGD1", "IC2", 
"IC1", "RGD1", "IC1", "IC1", "RGD1", "IC1", "IC1", "IC3", "IC2", 
"IC1", "IC3", "IC1", "IC3", "IC2", "IC1", "RGD1", "RGD1", "RGD1", 
"RGD1", "RGD1", "IC3", "IC2", "IC1", "RGD1", "RGD1", "IC1", "RGD1", 
"RGD1", "RGD1", "RGD1", "RGD1", "IC2", "RGD1", "IC1", "IC1", 
"RGD1", "IC3", "IC2", "IC1", "IC3", "IC2", "IC1", "IC3", "IC2", 
"IC1", "IC3", "IC2", "IC1", "IC3", "IC2", "IC1", "IC3", "IC2", 
"IC1", "IC3", "IC2", "IC1", "IC3", "IC2", "IC3", "IC2", "IC3", 
"IC2", "IC1", "IC3", "IC2", "IC1", "IC3", "IC2", "IC3", "IC2", 
"IC1", "IC3", "IC2", "IC1", "IC3", "IC2", "IC1", "IC3", "IC2", 
"IC1", "IC1", "IC1", "IC1", "IC3", "IC2", "IC1", "IC1", "IC1", 
"IC1", "IC1", "IC2", "IC1", "IC1", "IC2", "IC1", "IC2", "IC1", 
"IC1", "IC3", "IC2", "IC1", "IC2", "IC1", "IC3", "IC2", "RGD1", 
"RGD1", "RGD1", "RGD1", "RGD1", "RGD1", "RGD1", "RGD1", "IC1", 
"RGD1", "IC2", "IC1", "RGD1", "RGD1", "RGD1", "IC3", "IC1", "RGD1", 
"IC3", "IC2", "IC1", "IC3", "IC2", "IC1", "IC3", "IC2", "IC1", 
"RGD1", "IC3", "RGD1", "IC3", "RGD1", "IC3", "IC2", "RGD1", "IC3", 
"IC2", "RGD1", "RGD1", "IC2", "RGD1", "RGD1", "RGD1", "RGD1", 
"IC3", "IC2", "IC1", "RGD1", "RGD1", "IC2", "IC1", "RGD1", "RGD1", 
"IC1", "IC3", "IC2", "IC1", "RGD1", "RGD1", "IC3", "IC2", "IC1", 
"RGD1", "IC3", "IC2", "IC1", "RGD1", "IC3", "IC2", "IC1", "IC3", 
"IC2", "IC1", "RGD1", "IC3", "IC2", "IC1", "RGD1", "RGD1", "RGD1", 
"RGD1", "RGD1", "RGD1", "RGD1", "RGD1", "RGD1", "RGD1", "RGD1", 
"RGD1", "RGD1", "RGD1", "RGD1", "RGD1", "RGD1", "RGD1", "RGD1", 
"RGU1", "ORS1", "RGD1", "RGD1", "RGD1", "RGD1", "RGD1", "RGD1", 
"RGD1", "RGD1", "IC2", "IC1", "RGD1", "IC2", "IC1", "IC2", "IC1", 
"RGD1", "RGD1", "RGD1", "RGD1", "IC1", "IC2", "IC1", "RGD1", 
"IC2", "IC3", "IC1", "IC3", "IC1", "RGD1", "IC2", "IC1", "RGD1", 
"IC3", "IC2", "IC1", "RGD1", "IC3", "IC3", "IC3", "IC3", "IC2", 
"IC3", "IC2", "IC3", "IC2", "IC2", "IC1", "RGD1", "RGD1", "RGD1", 
"RGD1", "RGU1", "ORS1", "RGU1", "ORS1", "WC1", "WC2", "GL1", 
"WC3", "RGD1", "IC1", "IC1", "IC1", "IC3", "IC2", "IC3", "IC2", 
"IC1", "IC3", "IC2", "IC1", "IC3", "IC2", "IC1", "RGD1", "RGD1", 
"RGD1", "RGD1", "RGD1", "RGU1", "ORS1", "WC1", "WC2", "WC3", 
"RGU1", "ORS1", "WC1", "WC2", "WC3", "WC1", "WC2", "WC3", "WC1", 
"WC2", "WC3", "IC2", "IC1", "RGD1", "IC3", "IC2", "IC1", "IC3", 
"IC2")), class = c("tbl_df", "tbl", "data.frame"), row.names = c(NA, 
-500L))

Solution

I'm not sure if this is what you mean by an incidence table but we can do a lot of this at once with dplyr, tidyr and magrittr

x$count <- 1
x2 <- split(x, x$Species)
x2 <- lapply(x2, function(x){split(x,x$Week)})
x3 <- lapply(x2, function(x){lapply(X=x, function(y){
  y <- y %>% spread(key = "SiteVisits",
                    value = "count",
                    fill =0) %>%
    select(-Species, -Week) %>% as.data.frame()
  rownames(y) <- y$TagID
  y <- y[,-1]
  y <- graph_from_incidence_matrix(y)
  return(y)
})})

x3 will be a list structure where the final elements are the returned values of graph_from_incidence_matrix