如何根据时间序列数据在 R 中创建网络列表答案

【问题标题】：How to create a list of Networks in R based on Time Series Data如何根据时间序列数据在 R 中创建网络列表
【发布时间】：2020-01-22 19:30:43
【问题描述】：

我正在尝试查看时间序列中的个人网络和网站访问。本质上，我想要实现的最终结果类似于包"dnr" 中的"beaches" 数据集。我有一个更大的数据集 dput，其中的一个子集显示在底部。

基本上我想通过Species 和Week 来split() 这个表，然后创建一个关联矩阵，其中包含来自TagID 的不同值的行和基于SiteVisits 中不同值的列。然后我使用包igraph 和graph_from_incidence_matrix 每周为每个物种创建一个独特的网络。

我开始尝试按物种拆分主表，然后每周为每个物种创建新表：

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

这很好，但是当我尝试编写循环以使用此数据帧构建网络时

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)

我收到了

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

我猜有办法解决这个错误，但我尝试过的任何方法都不起作用。另外，如果有更清洁的方法可以做到这一点，我会全力以赴。

输入：

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", 
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"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", 
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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, 
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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, 
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"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))

【问题讨论】：

标签： r time-series network-analysis

【解决方案1】：

我不确定这是否是您所说的发病率表，但我们可以使用 dplyr、tidyr 和 magrittr 一次性完成很多工作

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 将是一个列表结构，其中最终元素是graph_from_incidence_matrix 的返回值

【讨论】：

部分，您确实创建了正确形式的关联表，但第二部分是困难的部分（网络构建）让我看看我是否能找到一种方法来解决这个问题。不幸的是，我认为物种和周的分裂对于每周为每个物种创建一个单一的网络是必要的。
pivot_wider 函数有点矫枉过正。使用两个lapply 函数，我们可以为每个组合制作关联表和图表。
完美，快速的x4 <- unlist(x3) 创建与海滩相同的结构！谢谢，我需要花一些时间查看这些 lapply 声明，但这似乎很棒。
y 的起始值本质上等同于调用x2[[Species]][[Week]]。这应该有助于理解最内部的函数调用。我永远找不到海滩数据集，但希望这足以满足您的问题。干杯！