Как создать список сетей в R на основе данных временных рядов

Question

Я пытаюсь посмотреть на сети отдельных людей и посещений сайтов за временной ряд. По сути, конечный результат, которого я хотел бы достичь, аналогичен набору данных "beaches", найденному в пакете "dnr". У меня есть большая база данных набора данных для подмножества, которое показано внизу.

В основном, я хотел бы split() эту таблицу как Species, так и Week, а затем создать матрицу инцидентности со строками различных значений из TagID и столбцов на основе различных значений в SiteVisits. Затем я использую пакеты igraph и graph_from_incidence_matrix, чтобы создать уникальную сеть для каждого вида для каждой недели.

Я начал с попытки разбить основную таблицу по видам, а затем создать новые таблицы для каждого вида для каждую неделю:

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

это работало нормально, но когда я попытался написать al oop для построения сети с использованием этого кадра данных

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)

я получил

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

Я предполагаю, что есть способ обойти эту ошибку, но ничего, что я пробовал, не работает. Кроме того, если есть более чистый способ сделать это, у меня все уши.

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", 
"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", "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", "Largemouth Bass", "Largemouth Bass", "Largemouth Bass", 
"Largemouth Bass", "Largemouth Bass", "Largemouth Bass", "Largemouth Bass", 
"Largemouth Bass", "Largemouth Bass", "Largemouth Bass", "Largemouth Bass", 
"Largemouth Bass", "Largemouth Bass", "Largemouth Bass", "Largemouth Bass", 
"Largemouth Bass", "Largemouth Bass", "Largemouth Bass", "Largemouth Bass", 
"Largemouth Bass", "Largemouth Bass", "Largemouth Bass", "Largemouth Bass", 
"Largemouth Bass", "Largemouth Bass", "Largemouth Bass", "Largemouth Bass", 
"Largemouth Bass", "Largemouth Bass", "Largemouth Bass", "Largemouth Bass", 
"Largemouth Bass", "Largemouth Bass", "Largemouth Bass", "Largemouth Bass", 
"Largemouth Bass", "Largemouth Bass", "Largemouth Bass", "Largemouth Bass", 
"Largemouth Bass", "Largemouth Bass", "Largemouth Bass", "Largemouth Bass", 
"Largemouth Bass", "Largemouth Bass", "Largemouth Bass", "Largemouth Bass", 
"Largemouth Bass", "Largemouth Bass", "Largemouth Bass", "Largemouth Bass", 
"Largemouth Bass", "Largemouth Bass", "Largemouth Bass", "Largemouth Bass", 
"Largemouth Bass", "Largemouth Bass", "Largemouth Bass", "Largemouth Bass", 
"Largemouth Bass", "Largemouth Bass", "Largemouth Bass", "Largemouth Bass", 
"Largemouth Bass", "Largemouth Bass", "Largemouth Bass", "Largemouth 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", "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", "Largemouth Bass", "Largemouth Bass", 
"Largemouth Bass", "Largemouth Bass", "Largemouth Bass", "Largemouth Bass", 
"Largemouth Bass", "Largemouth Bass", "Largemouth Bass", "Largemouth Bass", 
"Largemouth Bass", "Largemouth Bass", "Largemouth Bass", "Largemouth Bass", 
"Largemouth Bass", "Largemouth Bass", "Largemouth Bass", "Largemouth Bass", 
"Largemouth Bass", "Largemouth Bass", "Largemouth Bass", "Largemouth Bass", 
"Largemouth Bass", "Largemouth Bass", "Largemouth Bass", "Largemouth Bass", 
"Largemouth Bass", "Largemouth Bass", "Largemouth Bass", "Largemouth Bass", 
"Largemouth Bass", "Largemouth Bass", "Largemouth Bass", "Largemouth Bass", 
"Largemouth Bass", "Largemouth Bass", "Largemouth Bass", "Largemouth Bass", 
"Largemouth Bass", "Largemouth 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", 
"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", "Catfish", "Catfish", "Catfish", 
"Catfish", "Catfish", "Catfish", "Catfish", "Catfish", "Catfish", 
"Catfish", "Catfish", "Catfish", "Catfish", "Catfish", "Catfish", 
"Catfish", "Catfish", "Catfish", "Catfish", "Catfish", "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", "Largemouth Bass", "Largemouth 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", "Largemouth Bass", 
"Largemouth Bass", "Largemouth 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"), Week = c(74, 74, 75, 76, 77, 
77, 77, 77, 77, 77, 78, 78, 79, 79, 79, 79, 79, 79, 79, 80, 80, 
80, 80, 81, 83, 83, 83, 83, 83, 84, 84, 84, 84, 84, 85, 85, 85, 
85, 85, 86, 86, 86, 86, 87, 88, 89, 90, 91, 92, 92, 92, 93, 93, 
93, 93, 93, 94, 94, 94, 95, 95, 95, 95, 95, 96, 96, 96, 96, 96, 
96, 96, 96, 97, 97, 97, 97, 98, 99, 99, 99, 99, 99, 100, 101, 
101, 101, 101, 101, 101, 101, 101, 102, 103, 103, 103, 103, 103, 
104, 104, 104, 104, 105, 105, 105, 105, 106, 106, 106, 106, 107, 
107, 107, 107, 108, 109, 110, 54, 54, 55, 55, 55, 56, 56, 56, 
57, 57, 57, 58, 60, 60, 60, 61, 61, 68, 68, 68, 69, 70, 70, 71, 
72, 73, 74, 74, 75, 76, 76, 77, 78, 78, 79, 80, 80, 81, 84, 86, 
86, 87, 88, 89, 90, 90, 91, 91, 92, 92, 93, 93, 94, 97, 97, 98, 
98, 98, 100, 100, 100, 101, 101, 101, 103, 103, 103, 164, 165, 
165, 165, 165, 166, 166, 166, 167, 168, 168, 168, 57, 58, 58, 
59, 60, 61, 61, 61, 62, 62, 63, 63, 63, 66, 70, 71, 74, 75, 76, 
76, 76, 76, 77, 78, 79, 80, 81, 82, 83, 84, 84, 20, 6, 7, 8, 
8, 8, 9, 9, 9, 10, 10, 10, 11, 11, 11, 12, 12, 12, 13, 13, 13, 
14, 14, 14, 15, 15, 16, 16, 17, 17, 17, 204, 204, 204, 205, 205, 
206, 206, 206, 207, 207, 207, 208, 208, 208, 209, 209, 209, 210, 
216, 228, 233, 233, 233, 234, 235, 236, 237, 239, 239, 240, 241, 
241, 242, 242, 243, 244, 244, 244, 245, 245, 64, 64, 64, 65, 
66, 67, 68, 69, 70, 71, 72, 72, 73, 73, 73, 74, 75, 76, 76, 76, 
77, 77, 77, 78, 78, 78, 79, 79, 79, 79, 80, 80, 81, 81, 83, 83, 
83, 84, 84, 84, 85, 86, 86, 87, 94, 95, 97, 97, 97, 97, 98, 99, 
99, 99, 100, 102, 103, 103, 103, 105, 106, 107, 107, 107, 107, 
108, 108, 108, 108, 109, 109, 109, 110, 110, 110, 110, 111, 111, 
111, 111, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 
98, 99, 100, 101, 102, 102, 102, 153, 154, 155, 156, 157, 158, 
159, 160, 161, 161, 161, 162, 162, 163, 163, 163, 164, 165, 166, 
49, 14, 14, 185, 47, 74, 74, 75, 75, 75, 76, 76, 76, 78, 78, 
78, 79, 80, 81, 82, 83, 83, 84, 84, 85, 85, 3, 3, 146, 147, 148, 
149, 149, 149, 150, 150, 150, 150, 150, 150, 109, 77, 78, 79, 
20, 20, 21, 21, 21, 22, 22, 22, 23, 23, 23, 23, 24, 25, 26, 27, 
27, 40, 40, 40, 40, 41, 41, 45, 45, 45, 50, 50, 50, 52, 52, 52, 
45, 45, 45, 46, 46, 46, 48, 48), TagID = c(5004.24, 5004.24, 
5004.24, 5004.24, 5004.24, 5004.24, 5004.24, 5004.24, 5004.24, 
5004.24, 5004.24, 5004.24, 5004.24, 5004.24, 5004.24, 5004.24, 
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5004.24, 5004.24, 5004.24, 5004.24, 5004.24, 5004.24, 5004.24, 
5004.24, 5004.24, 5004.24, 5004.24, 5004.24, 5004.24, 5004.24, 
5004.24, 5004.24, 5004.24, 5004.24, 5004.24, 5004.24, 5004.24, 
5004.24, 5004.24, 5004.24, 5004.24, 5004.24, 5004.24, 5004.24, 
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5004.24, 5004.24, 5004.24, 5004.24, 5004.24, 5004.24, 5004.24, 
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5011.07, 5011.07, 5011.07, 5011.07, 5011.07, 5011.07, 5011.07, 
5017.06, 5025.22, 5025.22, 5025.22, 5025.22, 5025.22, 5025.22, 
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5025.22, 5025.22, 5025.22, 5025.22, 5025.22, 5025.22, 5025.22, 
5025.22, 5025.22, 5025.22, 5025.26, 5025.26, 5025.26, 5025.26, 
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5025.26, 5025.26, 5025.26, 5025.26, 5025.26, 5025.26, 5025.26, 
5025.26, 5025.26, 5025.26, 5025.26, 5025.26, 5025.26, 5025.26, 
5025.26, 5032.24, 5032.24, 5032.24, 5032.24, 5032.24, 5032.24, 
5032.24, 5032.24, 5032.24, 5032.24, 5032.24, 5032.24, 5032.24, 
5032.24, 5032.24, 5032.24, 5032.24, 5032.24, 5032.24, 5032.24, 
5032.24, 5032.24, 5032.24, 5032.24, 5032.24, 5032.24, 5032.24, 
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5032.24, 5032.24, 5032.24, 5032.24, 5032.24, 5032.24, 5032.24, 
5032.24, 5032.24, 5032.24, 5032.24, 5038.04, 5038.04, 5038.04, 
5038.04, 5038.04, 5038.04, 5038.04, 5038.04, 5038.04, 5038.04, 
5038.04, 5038.04, 5038.04, 5038.04, 5038.04, 5038.04, 5038.04, 
5038.04, 5038.04, 5038.04, 5039.03, 5039.03, 5039.03, 5039.03, 
5039.03, 5039.03, 5039.03, 5039.03, 5039.03, 5039.03, 5039.03, 
5039.03, 5039.03, 5039.03, 5039.03, 5039.03, 5039.03, 5039.03, 
5039.03, 5039.07, 5045, 5045, 5053.26, 5066.04, 5067.07, 5067.07, 
5067.07, 5067.07, 5067.07, 5067.07, 5067.07, 5067.07, 5067.07, 
5067.07, 5067.07, 5067.07, 5067.07, 5067.07, 5067.07, 5067.07, 
5067.07, 5067.07, 5067.07, 5067.07, 5067.07, 5073.06, 5073.06, 
5074.16, 5074.16, 5074.16, 5074.16, 5074.16, 5074.16, 5074.16, 
5074.16, 5074.16, 5074.16, 5074.16, 5074.16, 5088.11, 5094.04, 
5094.04, 5094.04, 5101.06, 5101.06, 5101.06, 5101.06, 5101.06, 
5101.06, 5101.06, 5101.06, 5101.06, 5101.06, 5101.06, 5101.06, 
5101.06, 5101.06, 5101.06, 5101.06, 5101.06, 5101.06, 5101.06, 
5101.06, 5101.06, 5101.06, 5101.06, 5101.06, 5101.06, 5101.06, 
5101.06, 5101.06, 5101.06, 5101.06, 5101.06, 5101.06, 5116.24, 
5116.24, 5116.24, 5116.24, 5116.24, 5116.24, 5116.24, 5116.24
), SiteVisits = c("IC1", "RGD1", "RGD1", "RGD1", "RGD1", "RGU1", 
"ORS1", "WC1", "WC2", "WC3", "WC2", "WC3", "IC3", "RGD1", "RGU1", 
"ORS1", "WC1", "WC2", "WC3", "RGD1", "RGU1", "WC2", "WC3", "WC3", 
"RGU1", "ORS1", "WC1", "WC2", "WC3", "RGU1", "ORS1", "WC1", "WC2", 
"WC3", "RGU1", "ORS1", "WC1", "WC2", "WC3", "RGD1", "RGU1", "ORS1", 
"WC1", "RGD1", "RGD1", "RGD1", "RGD1", "RGD1", "IC3", "IC1", 
"RGD1", "RGD1", "RGU1", "ORS1", "WC1", "WC2", "RGU1", "ORS1", 
"WC1", "RGU1", "ORS1", "WC1", "WC2", "WC3", "IC3", "IC1", "RGD1", 
"RGU1", "ORS1", "WC1", "WC2", "WC3", "RGD1", "WC1", "WC2", "WC3", 
"WC3", "RGD1", "RGU1", "WC1", "WC2", "WC3", "RGD1", "IC3", "IC2", 
"IC1", "RGD1", "RGU1", "WC1", "WC2", "WC3", "WC3", "RGD1", "RGU1", 
"WC1", "WC2", "WC3", "IC3", "IC2", "IC1", "RGD1", "IC3", "IC2", 
"IC1", "RGD1", "IC3", "IC2", "IC1", "RGD1", "IC3", "IC2", "IC1", 
"RGD1", "RGD1", "RGD1", "RGD1", "IC2", "IC1", "IC3", "IC2", "IC1", 
"IC3", "IC2", "IC1", "IC3", "IC2", "IC1", "IC1", "IC3", "IC2", 
"IC1", "IC2", "IC1", "IC3", "IC2", "IC1", "IC2", "IC3", "IC2", 
"IC1", "IC1", "IC1", "IC3", "IC1", "IC1", "IC3", "IC1", "IC1", 
"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))

Answer 1

Я не уверен, что это то, что вы подразумеваете под таблицей инцидентности, но мы можем сделать многое из этого сразу с dplyr, tidyr и 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 будет структура списка, где конечными элементами являются возвращаемые значения graph_from_incidence_matrix