## Not run:
#
# #########################################################
# #########################################################
#
# library("SemiParBIVProbit")
#
# data("war", package = "SemiParBIVProbit")
#
# ###################################################
# # Bivariate brobit model with partial observability
# ###################################################
#
# reb.eq <- onset ~ instab + oil + warl + lpopl + lmtnest + ethfrac +
# polity2l + s(gdpenl) + s(relfrac)
# gov.eq <- onset ~ instab + oil + warl + ncontig + nwstate + s(gdpenl)
#
# bpo <- SemiParBIVProbit(list(reb.eq, gov.eq), data = war, Model = "BPO")
# conv.check(bpo)
#
# # perhaps model is to complex
#
# set.seed(1)
# sbpo <- summary(bpo)
# sbpo$theta; sbpo$CItheta
#
# # let's exclude the correlation parameter in fitting
#
# bpo0 <- SemiParBIVProbit(list(reb.eq, gov.eq), data = war, Model = "BPO0")
# conv.check(bpo0)
#
# summary(bpo0)
#
#
# war.eq <- onset ~ instab + oil + warl + ncontig + nwstate + lpopl +
# lmtnest + ethfrac + polity2l + s(gdpenl) + s(relfrac)
# Probit <- gam(war.eq, family = binomial(link = "probit"), data = war)
# summary(Probit)
#
#
# coef(Probit)[(which(names(coef(Probit)) == "s(gdpenl).9"))]
#
# coef(bpo0)[(which(names(coef(bpo)) == "s(gdpenl).9"))]
#
#
# probitW <- bpoW <- bpoReb <- bpoGov <- NA
# gdp.grid <- seq(0, 8)
#
# median.values <- data.frame(t(apply(war, 2, FUN = median)))
#
# for (i in 1:length(gdp.grid)){
#
# newd <- median.values; newd$gdpenl <- gdp.grid[i]
# eta1 <- predict(bpo0, eq = 1, newd)
# eta2 <- predict(bpo0, eq = 2, newd)
# probitW[i] <- predict(Probit, newd, type = "response")
# bpoW[i] <- pnorm(eta1)*pnorm(eta2)
# bpoReb[i] <- pnorm(eta1)
# bpoGov[i] <- pnorm(eta2)
#
# }
#
#
# plot(gdp.grid, probitW, type = "l", ylim = c(0, 0.55), lwd = 2,
# col = "grey", xlab = "GDP per Capita (in thousands)",
# ylab = "Pr(Outcome)", main = "Probabilities for All Outcomes",
# cex.main = 1.5, cex.lab = 1.3, cex.axis = 1.3)
# lines(gdp.grid, bpoW, lwd = 2)
# lines(gdp.grid, bpoReb, lwd = 2, lty = 2)
# lines(gdp.grid, bpoGov, lwd = 2, lty = 3)
#
# #dev.copy(postscript, "probWAR.eps", width = 8)
# #dev.off()
#
# ## End(Not run)
#
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