#Model for co-evolution advice and trust

advice.w1 <- as.matrix(read.table("g:/data/AR_157.txt"))
advice.w2 <- as.matrix(read.table("g:/data/AR_257.txt"))
advice.w3 <- as.matrix(read.table("g:/data/AR_357.txt"))
advice.w4 <- as.matrix(read.table("g:/data/AR_457.txt"))
trust.w1 <- as.matrix(read.table("g:/data/TR_157D.txt"))
trust.w2 <- as.matrix(read.table("g:/data/TR_257.txt"))
trust.w3 <- as.matrix(read.table("g:/data/TR_357.txt"))
trust.w4 <- as.matrix(read.table("g:/data/TR_457.txt"))
hier.mat <- as.matrix(read.table("g:/data/ACTHIE57.txt"))
age.mat <- as.matrix(read.table("g:/data/ACTAGE57.txt"))
gender.mat <- as.matrix(read.table("g:/data/ACTGEN57.txt"))
hierTo.mat <- as.matrix(read.table("g:/data/hier157.txt"))
hierFrom.mat <- as.matrix(read.table("g:/data/hier1t57.txt"))
sameDep.mat <- as.matrix(read.table("g:/data/samehi57.txt"))
advice.w1[advice.w1 %in% c(8,9)] <- NA
advice.w2[advice.w2 %in% c(8,9)] <- NA
advice.w3[advice.w3 %in% c(8,9)] <- NA
advice.w4[advice.w4 %in% c(8,9)] <- NA
trust.w1[trust.w1 %in% c(8,9)] <- NA
trust.w2[trust.w2 %in% c(8,9)] <- NA
trust.w3[trust.w3 %in% c(8,9)] <- NA
trust.w4[trust.w4 %in% c(8,9)] <- NA
age.mat[age.mat %in% c(99)] <- NA
trust.w1 <- as.numeric(trust.w1 >3)
trust.w2 <- as.numeric(trust.w2 >3)
trust.w3 <- as.numeric(trust.w3 >3)
trust.w4 <- as.numeric(trust.w4 >3)
advice <- sienaNet(array(c(advice.w1,advice.w2,advice.w3,advice.w4),dim=c(57,57,4)))
trust <- sienaNet(array(c(trust.w1,trust.w2,trust.w3,trust.w4),dim=c(57,57,4)))
hier <- coCovar(hier.mat[,1])
age <- coCovar(age.mat[,1])
gender <- coCovar(gender.mat[,1])
hierTo <- coDyadCovar(hierFrom.mat)
hierFrom <- coDyadCovar(hierTo.mat)
sameDep <- coDyadCovar(sameDep.mat)
mydata2 <- sienaDataCreate(advice, trust,hierFrom, hierTo, sameDep,hier, age, gender)
myeff2 <- getEffects(mydata2)
mymodel2 <- sienaModelCreate( projname="selectionAdviceTrustMod")
print01Report(mydata2, myeff2, modelname="selectionAdviceTrust")
myeff2

myeff2$effectName
fix(myeff2)

myeff2 <- includeEffects(myeff2, transTrip)
myeff2 <- includeEffects(myeff2, egoX, altX, simX,interaction1="gender")
myeff2 <- includeEffects(myeff2, inPopSqrt)
myeff2 <- includeEffects(myeff2, egoX, altX, simX,interaction1="hier")
myeff2 <- includeEffects(myeff2, egoX, altX, simX,interaction1="age")
myeff2 <- includeEffects(myeff2, X, interaction1="hierTo")
myeff2 <- includeEffects(myeff2, X, interaction1=c("hierFrom"))
myeff2 <- includeEffects(myeff2, X, interaction1=c("sameDep"))
myeff2 <- includeEffects(myeff2, cycle3)
myeff2 <- includeEffects(myeff2, outPopSqrt)
myeff2 <- includeEffects(myeff2, inOutAss)

#same uniplex for trust
myeff2 <- includeEffects(myeff2, transTrip, cycle3, name="trust")
myeff2 <- includeEffects(myeff2, egoX, altX, simX,interaction1="gender", name="trust")
myeff2 <- includeEffects(myeff2, egoX, altX, simX,interaction1="hier", name="trust")
myeff2 <- includeEffects(myeff2, egoX, altX, simX,interaction1="age", name="trust")
myeff2 <- includeEffects(myeff2, X, interaction1="hierTo", name="trust")
myeff2 <- includeEffects(myeff2, X, interaction1="hierFrom", name="trust")
myeff2 <- includeEffects(myeff2, X, interaction1="sameDep", name="trust")

#dyadic trust on advice
myeff2 <- includeEffects(myeff2, crprod, crprodRecip, crprodMutual, name="advice", interaction1="trust")
#triadic trust on advice
myeff2 <- includeEffects(myeff2, fromMutual, closure,to, name="advice", interaction1="trust")
#global degree trust on advice
myeff2 <- includeEffects(myeff2, inPopIntn, outActIntn, param=2, name="advice", interaction1="trust")

#dyadic advice on trust
myeff2 <- includeEffects(myeff2, crprod, crprodRecip, crprodMutual, name="trust", interaction1="advice")
#triadic advice on trust
myeff2 <- includeEffects(myeff2, fromMutual, closure,to, name="trust", interaction1="advice")
#global degree advice on trust
myeff2 <- includeEffects(myeff2, inPopIntn, outActIntn, param=2, name="trust", interaction1="advice")

answer6 <- siena07(mymodel2, data=mydata2, effects=myeff2, batch=TRUE, verbose=TRUE, nbrNodes=2, useCluster=TRUE)