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[英]How to calculate the transition probability matrix of a second order Markov Chain
[英]How to read a transition matrix into Cytoscape for Markov Chain modelling?
我想阅读用于Markov Chain建模的Cytoscape转换矩阵。 例如,我从这篇文章中借用下面的过渡矩阵(包括R代码): 创建三态马尔可夫链图
Cytoscape如何读取此类transitionMatrix
?
谢谢。
转换矩阵的格式
这是transitionMatrix的样子:
tired angry calm
tired 0.5 0.5 0.0
angry 0.0 0.2 0.8
calm 0.8 0.0 0.2
R代码
pre<-cbind(c(rep("tired",100),rep("angry",100),rep("calm",100)))
post<-cbind(c(rep("tired",50),rep("angry",70),rep("calm",100),rep("tired",80)))
df<-cbind(pre,post)
df<-as.data.frame(df)
colnames(df)<-c("pre","post")
states<-c("tired","angry","calm")
probsCase<-function(i,j){
sum(as.character(df$pre)==states[i] &
as.character(df$post)==states[j])/sum(as.character(df$pre)==states[i])
}
transitionMatrix<-outer(1:3,1:3,Vectorize(probsCase))
colnames(transitionMatrix)<-states
rownames(transitionMatrix)<-states
有一个名为aMatReader的应用程序,可让您读取邻接矩阵。
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