wenchuanData = read.csv("~/Desktop/Wenchuan no subject mcnally r october 9 2013 for ms may 14 2014.csv", header = TRUE) attach(wenchuanData) library("igraph", lib.loc="/Library/Frameworks/R.framework/Versions/3.0/Resources/library") library("qgraph", lib.loc="/Library/Frameworks/R.framework/Versions/3.0/Resources/library") library("car", lib.loc="/Library/Frameworks/R.framework/Versions/3.0/Resources/library") library("relaimpo", lib.loc="/Library/Frameworks/R.framework/Versions/3.0/Resources/library") library("ppcor", lib.loc="/Library/Frameworks/R.framework/Versions/3.0/Resources/library") wenchuan_qgraph_association=qgraph(cor(wenchuanData, use='pairwise.complete.obs'), layout = "spring", label.cex=.45, label.scale="FALSE", labels=colnames(wenchuanData)) #wenchuan_qgraph=qgraph(cor(wenchuanData, use='pairwise.complete.obs'), layout = "circle", labels=colnames(wenchuanData)) wenchuan_qgraph_association_threshold=qgraph(cor(wenchuanData, use='pairwise.complete.obs'), minimum=.3, layout = "spring", label.cex=.45, label.scale="FALSE", labels=colnames(wenchuanData)) #wenchuan_qgraph=qgraph(cor(wenchuanData, use='pairwise.complete.obs'), minimum=.3, layout = "circle", labels=colnames(wenchuanData)) wenchuan_qgraph_partialcorr=qgraph(cor(wenchuanData, use='pairwise.complete.obs'), graph="concentration", minimum=.1, layout = "spring", label.cex=.45, label.scale="FALSE", labels=colnames(wenchuanData)) cor(wenchuanData, use='pairwise.complete.obs') wenchuan_centrality <- centrality(wenchuan_qgraph_association) wenchuan_degree <- matrix(wenchuan_centrality$OutDegree, nrow=17, byrow=FALSE) wenchuan_closeness <- matrix(wenchuan_centrality$Closeness, nrow=17, byrow=FALSE) wenchuan_betweenness <- matrix(wenchuan_centrality$Betweenness, nrow=17, byrow=FALSE) wenchuan_centrality <- cbind(wenchuan_degree, wenchuan_closeness,wenchuan_betweenness) row.names(wenchuan_centrality) <- colnames(wenchuanData) colnames(wenchuan_centrality) <- c("Degree", "Closeness", "Betweenness") write.csv(wenchuan_centrality, "~/Desktop/wenchuan_centrality.csv") fit <- lm(intrusion ~ dreams + flash + upset + physior + avoidth + avoidact + amnesia + lossint + distant + numb + future + sleep + anger + concen + hyper + startle, data=wenchuanData) intrusion<- calc.relimp(fit,type=c("lmg"),rela=TRUE) intrusion_lmg<- as.data.frame(intrusion$lmg) fit <- lm(dreams ~ intrusion + flash + upset + physior + avoidth + avoidact + amnesia + lossint + distant + numb + future + sleep + anger + concen + hyper + startle, data=wenchuanData) dreams<- calc.relimp(fit,type=c("lmg"),rela=TRUE) dreams_lmg<- as.data.frame(dreams$lmg) fit <- lm(flash ~ intrusion + dreams + upset + physior + avoidth + avoidact + amnesia + lossint + distant + numb + future + sleep + anger + concen + hyper + startle, data=wenchuanData) flash<- calc.relimp(fit,type=c("lmg"),rela=TRUE) flash_lmg<- as.data.frame(flash$lmg) fit <- lm(upset ~ intrusion + dreams + flash + physior + avoidth + avoidact + amnesia + lossint + distant + numb + future + sleep + anger + concen + hyper + startle, data=wenchuanData) upset<- calc.relimp(fit,type=c("lmg"),rela=TRUE) upset_lmg<- as.data.frame(upset$lmg) fit <- lm(physior ~ intrusion + dreams + flash + upset + avoidth + avoidact + amnesia + lossint + distant + numb + future + sleep + anger + concen + hyper + startle, data=wenchuanData) physior<- calc.relimp(fit,type=c("lmg"),rela=TRUE) physior_lmg<- as.data.frame(physior$lmg) fit <- lm(avoidth ~ intrusion + dreams + flash + upset + physior + avoidact + amnesia + lossint + distant + numb + future + sleep + anger + concen + hyper + startle, data=wenchuanData) avoidth<- calc.relimp(fit,type=c("lmg"),rela=TRUE) avoidth_lmg<- as.data.frame(avoidth$lmg) fit <- lm(avoidact ~ intrusion + dreams + flash + upset + physior + avoidth + amnesia + lossint + distant + numb + future + sleep + anger + concen + hyper + startle, data=wenchuanData) avoidact<- calc.relimp(fit,type=c("lmg"),rela=TRUE) avoidact_lmg<- as.data.frame(avoidact$lmg) fit <- lm(amnesia ~ intrusion + dreams + flash + upset + physior + avoidth + avoidact + lossint + distant + numb + future + sleep + anger + concen + hyper + startle, data=wenchuanData) amnesia<- calc.relimp(fit,type=c("lmg"),rela=TRUE) amnesia_lmg<- as.data.frame(amnesia$lmg) fit <- lm(lossint ~ intrusion + dreams + flash + upset + physior + avoidth + avoidact + amnesia + distant + numb + future + sleep + anger + concen + hyper + startle, data=wenchuanData) lossint<- calc.relimp(fit,type=c("lmg"),rela=TRUE) lossint_lmg<- as.data.frame(lossint$lmg) fit <- lm(distant ~ intrusion + dreams + flash + upset + physior + avoidth + avoidact + amnesia + lossint + numb + future + sleep + anger + concen + hyper + startle, data=wenchuanData) distant<- calc.relimp(fit,type=c("lmg"),rela=TRUE) distant_lmg<- as.data.frame(distant$lmg) fit <- lm(numb ~ intrusion + dreams + flash + upset + physior + avoidth + avoidact + amnesia + lossint + distant + future + sleep + anger + concen + hyper + startle, data=wenchuanData) numb<- calc.relimp(fit,type=c("lmg"),rela=TRUE) numb_lmg<- as.data.frame(numb$lmg) fit <- lm(future ~ intrusion + dreams + flash + upset + physior + avoidth + avoidact + amnesia + lossint + distant + numb + sleep + anger + concen + hyper + startle, data=wenchuanData) future<- calc.relimp(fit,type=c("lmg"),rela=TRUE) future_lmg<- as.data.frame(future$lmg) fit <- lm(sleep ~ intrusion + dreams + flash + upset + physior + avoidth + avoidact + amnesia + lossint + distant + numb + future + anger + concen + hyper + startle, data=wenchuanData) sleep<- calc.relimp(fit,type=c("lmg"),rela=TRUE) sleep_lmg<- as.data.frame(sleep$lmg) fit <- lm(anger ~ intrusion + dreams + flash + upset + physior + avoidth + avoidact + amnesia + lossint + distant + numb + future + sleep + concen + hyper + startle, data=wenchuanData) anger<- calc.relimp(fit,type=c("lmg"),rela=TRUE) anger_lmg<- as.data.frame(anger$lmg) fit <- lm(concen ~ intrusion + dreams + flash + upset + physior + avoidth + avoidact + amnesia + lossint + distant + numb + future + sleep + anger + hyper + startle, data=wenchuanData) intrusion<- calc.relimp(fit,type=c("lmg"),rela=TRUE) concen_lmg<- as.data.frame(intrusion$lmg) fit <- lm(hyper ~ intrusion + dreams + flash + upset + physior + avoidth + avoidact + amnesia + lossint + distant + numb + future + sleep + anger + concen + startle, data=wenchuanData) hyper<- calc.relimp(fit,type=c("lmg"),rela=TRUE) hyper_lmg<- as.data.frame(hyper$lmg) fit <- lm(startle ~ intrusion + dreams + flash + upset + physior + avoidth + avoidact + amnesia + lossint + distant + numb + future + sleep + anger + concen + hyper, data=wenchuanData) startle<- calc.relimp(fit,type=c("lmg"),rela=TRUE) startle_lmg<- as.data.frame(startle$lmg) sort(intrusion_lmg$Row.Names, decreasing = FALSE) row.names(wenchuan_lmg)<-c("amnesia", "anger" , "avoidact", "avoidth", "concen", "distant", "dreams", "flash", "future", "hyper", "intrusion", "lossint", "numb", "physior", "sleep", "startle", "Upset") wenchuan_lmg <- merge(amnesia_lmg, anger_lmg, by=0, all=TRUE) rownames(wenchuan_lmg) <- wenchuan_lmg$Row.names wenchuan_lmg <- (merge(wenchuan_lmg, avoidact_lmg, by=0, all=TRUE))[,-1] rownames(wenchuan_lmg) <- wenchuan_lmg$Row.names wenchuan_lmg <- (merge(wenchuan_lmg, avoidth_lmg, by=0, all=TRUE))[,-1] rownames(wenchuan_lmg) <- wenchuan_lmg$Row.names wenchuan_lmg <- (merge(wenchuan_lmg, concen_lmg, by=0, all=TRUE))[,-1] rownames(wenchuan_lmg) <- wenchuan_lmg$Row.names wenchuan_lmg <- (merge(wenchuan_lmg, distant_lmg, by=0, all=TRUE))[,-1] rownames(wenchuan_lmg) <- wenchuan_lmg$Row.names wenchuan_lmg <- (merge(wenchuan_lmg, dreams_lmg, by=0, all=TRUE))[,-1] rownames(wenchuan_lmg) <- wenchuan_lmg$Row.names wenchuan_lmg <- (merge(wenchuan_lmg, flash_lmg, by=0, all=TRUE))[,-1] rownames(wenchuan_lmg) <- wenchuan_lmg$Row.names wenchuan_lmg <- (merge(wenchuan_lmg, future_lmg, by=0, all=TRUE))[,-1] rownames(wenchuan_lmg) <- wenchuan_lmg$Row.names wenchuan_lmg <- (merge(wenchuan_lmg, hyper_lmg, by=0, all=TRUE))[,-1] rownames(wenchuan_lmg) <- wenchuan_lmg$Row.names wenchuan_lmg <- (merge(wenchuan_lmg, intrusion_lmg, by=0, all=TRUE))[,-1] rownames(wenchuan_lmg) <- wenchuan_lmg$Row.names wenchuan_lmg <- (merge(wenchuan_lmg, lossint_lmg, by=0, all=TRUE))[,-1] rownames(wenchuan_lmg) <- wenchuan_lmg$Row.names wenchuan_lmg <- (merge(wenchuan_lmg, numb_lmg, by=0, all=TRUE))[,-1] rownames(wenchuan_lmg) <- wenchuan_lmg$Row.names wenchuan_lmg <- (merge(wenchuan_lmg, physior_lmg, by=0, all=TRUE))[,-1] rownames(wenchuan_lmg) <- wenchuan_lmg$Row.names wenchuan_lmg <- (merge(wenchuan_lmg, sleep_lmg, by=0, all=TRUE))[,-1] rownames(wenchuan_lmg) <- wenchuan_lmg$Row.names wenchuan_lmg <- (merge(wenchuan_lmg, startle_lmg, by=0, all=TRUE))[,-1] rownames(wenchuan_lmg) <- wenchuan_lmg$Row.names wenchuan_lmg <- (merge(wenchuan_lmg, upset_lmg, by=0, all=TRUE))[,-1] wenchuan_lmg <- wenchuan_lmg[,-1] wenchuan_lmg[is.na(wenchuan_lmg)] <- 0 names(wenchuan_lmg)<-c("amnesia", "anger" , "avoidact", "avoidth", "concen", "distant", "dreams", "flash", "future", "hyper", "intrusion", "lossint", "numb", "physior", "sleep", "startle", "upset") wenchuan_lmg_qgraph<-qgraph(wenchuan_lmg, diag=FALSE, directed=TRUE, layout="spring", label.cex=.45, label.scale="FALSE", labels=colnames(wenchuan_lmg)) wenchuan_lmg_centrality <- centrality(wenchuan_lmg_qgraph) wenchuan_lmg_degree <- matrix(wenchuan_lmg_centrality$OutDegree, nrow=17, byrow=FALSE) wenchuan_lmg_closeness <- matrix(wenchuan_lmg_centrality$Closeness, nrow=17, byrow=FALSE) wenchuan_lmg_betweenness <- matrix(wenchuan_lmg_centrality$Betweenness, nrow=17, byrow=FALSE) wenchuan_lmg_centrality <- cbind(wenchuan_lmg_degree, wenchuan_lmg_closeness,wenchuan_lmg_betweenness) row.names(wenchuan_lmg_centrality) <- names(wenchuan_lmg) colnames(wenchuan_lmg_centrality) <- c("Out_Degree", "Closeness", "Betweenness") write.csv(wenchuan_lmg_centrality, "~/Desktop/wenchuan_lmg_centrality.csv")