为动态网络可视化格式化起点终点数据

Question

我正在研究政府机构如何随时间发生变化。计划是使用 ndtv 包来可视化更改。但是，我遇到了运行问题并且不知道我做错了什么！我怀疑我的数据格式不正确。

我有一个节点列表，其中列出了顶点 ID、机构名称、节点起点和节点终点：

nodelist <- read.csv("https://github.com/aterhorst/data/raw/master/edgelist.csv", header=T, stringsAsFactors = F)

和一个边列表显示开始，边的终点：

edgelist <- read.csv("https://github.com/aterhorst/data/raw/master/edgelist.csv", header=T, stringsAsFactors = F)

我可以很容易地创建网络对象：

library(tidyverse)
library(sna)
nw <- network(edgelist %>% select(head, tail),
              vertex_attr = nodelist %>% select(vertex.id, agency),
              vertex.attrnames = c("vertex.id", "agency"),
              directed = F)
print(nw)
plot(nw)

现在我想制作一个动态网络对象：

library(tsna)
library(ndtv)
dn <- networkDynamic(nw, 
                     edge.spells = edgelist,
                     vertex.spells = nodelist)

然后车轮脱落：

Error in networkDynamic(nw, edge.spells = edgelist, vertex.spells = nodelist) : 
  vertex.spells requires the vertex.id column to be numeric

我尝试将起点、终点从整数更改为数字 - 没有区别。我尝试了不同的方法来创建动态网络对象，例如

dn <- networkDynamic(edge.spells = edgelist)

这会产生此错误：

Initializing base.net of size 2020 imputed from maximum vertex id in edge records
Error in activate.edges(base.net, onset = edge.data[, 1], terminus = edge.data[,  : 
  Onset times must precede terminus times in activate.edges.

和：

dn <- networkDynamic(edge.spells = edgelist, vertex.spells = nodelist)

给我这个错误：

Error in networkDynamic(edge.spells = edgelist, vertex.spells = nodelist) : 
  vertex.spells requires the vertex.id column to be numeric

我尝试了 edge.spell 的顺序，结果是肯定的：

 dn <- networkDynamic(net, 
                      edge.spells = edgelist %>% select(onset, terminus, tail, head))

Edge activity in base.net was ignored
Created net.obs.period to describe network
 Network observation period info:
  Number of observation spells: 1 
  Maximal time range observed: 2014 until 2020 
  Temporal mode: continuous 
  Time unit: unknown 
  Suggested time increment: NA

一切顺利。现在，当我添加 vertex.spell 时，出现此错误：

dynamicNet <- networkDynamic(net, 
                         edge.spells = edgelist %>% select(onset, terminus, tail, head), 
                         vertex.spells = nodelist %>% select(onset, terminus, vertex.id) %>% 
                         mutate(vertex.id = as.numeric(vertex.id)))

Error in networkDynamic(net, edge.spells = edgelist %>% select(onset,  : 
  vertex.spells requires the vertex.id column to be numeric

这很奇怪，因为我已经明确指出 vertex.id 是数字！显然，我正在某处格式化，但在哪里并不明显。任何帮助将不胜感激。

Answer 1

在这种情况下，我认为您不需要先创建静态网络（虽然应该可以）。主要问题似乎只是列表中的列排序。帮助文件 ?networkDynamic 表明它需要 edge.spells 和 vertex.spells:

的特定顺序

edge.spells "... Assumed to be [onset,terminus,tail vertex.id, head vertex.id]. ..."

vertex.spells "...Assumed to be [onset,terminus,vertex.id]"

您的数据如下：

> head(nodelist)
  vertex.id                                  agency onset terminus
1         1                             AAF Company  2014     2020
2         2              Aboriginal Hostels Limited  2014     2020
3         3         Administrative Appeals Tribunal  2014     2020
4         4 Aged Care Quality and Safety Commission  2014     2020
5         5                   Airservices Australia  2014     2020
6         6  Albury-Wodonga Development Corporation  2014     2020
> head(edgelist)
  head tail onset terminus
1   10    3  2014     2020
2   10   11  2014     2020
3   10   12  2014     2020
4   10   18  2014     2020
5   10   22  2014     2020
6   10   23  2014     2020

所以如果你的数据列是 re-orderd..

nd <-networkDynamic(edge.spells = edgelist[,c(3,4,2,1)],
  vertex.spells=nodelist[,c(3,4,1)])

Initializing base.net of size 217 imputed from maximum vertex id in edge records
Created net.obs.period to describe network
 Network observation period info:
  Number of observation spells: 1 
  Maximal time range observed: 2014 until 2020 
  Temporal mode: continuous 
  Time unit: unknown 
  Suggested time increment: NA

这将创建网络对象和动态。由于您的 nodelist 每个顶点只有一行，因此可以使用

引入标签

network.vertex.names(nd)<-nodelist$agency

为动态网络可视化格式化起点终点数据

Formatting onset terminus data for dynamic network visualisation

r

animation

sna

statnet