Nothing
R/SemiParBIV.r
In GJRM: Generalised Joint Regression Modelling
Defines functions
SemiParBIV
Documented in
SemiParBIV
SemiParBIV <- function(formula, data = list(), weights = NULL, subset = NULL,
Model = "B", BivD = "N", margins = c("probit","probit"),
dof = 3, gamlssfit = FALSE,
fp = FALSE, hess = TRUE, infl.fac = 1, theta.fx = NULL,
rinit = 1, rmax = 100, iterlimsp = 50, tolsp = 1e-07,
gc.l = FALSE, parscale, extra.regI = "t", intf = FALSE, knots = NULL,
drop.unused.levels = TRUE,
min.dn = 1e-40, min.pr = 1e-16, max.pr = 0.999999){
##########################################################################################################################
# model set up and starting values
##########################################################################################################################
i.rho <- sp <- qu.mag <- n.sel <- y1.y2 <- y1.cy2 <- cy1.y2 <- cy1.cy2 <- cy <- cy1 <- inde <- y2m <- NULL
y00 <- y10 <- y0p <- y1p <- gam2TW <- NULL # for binary - tweedie margins
end <- X3.d2 <- X4.d2 <- X5.d2 <- X6.d2 <- X7.d2 <- X8.d2 <- l.sp3 <- l.sp4 <- l.sp5 <- l.sp6 <- l.sp7 <- l.sp8 <- l.sp9 <- i.rho <- 0
gam1 <- gam2 <- gam3 <- gam4 <- gam5 <- gam6 <- gam7 <- gam8 <- gam9 <- gamlss2 <- dof.st <- NULL
gamlss2 <- NULL
sp1 <- sp2 <- c.gam2 <- X2s <- X3s <- NULL
sp3 <- gp3 <- gam3 <- X3 <- NULL
sp4 <- gp4 <- gam4 <- X4 <- NULL
sp5 <- gp5 <- gam5 <- X5 <- NULL
sp6 <- gp6 <- gam6 <- X6 <- NULL
sp7 <- gp7 <- gam7 <- X7 <- NULL
sp8 <- gp8 <- gam8 <- X8 <- NULL
log.sig2 <- log.nu <- NULL
Sl.sf <- NULL
sp.method <- "perf"
BivD2 <- c("C0C90","C0C270","C180C90","C180C270",
"J0J90","J0J270","J180J90","J180J270",
"G0G90","G0G270","G180G90","G180G270","GAL0GAL90", "GAL0GAL270", "GAL180GAL90", "GAL180GAL270")
opc <- c("N","C0","C90","C180","C270","J0","J90","J180","J270","G0","G90","G180","G270","F","AMH","FGM","T","PL","HO","GAL0", "GAL90", "GAL180", "GAL270")
scc <- c("C0", "C180", "GAL0" , "GAL180","J0", "J180", "G0", "G180", BivD2)
sccn <- c("C90", "C270", "GAL90", "GAL270","J90", "J270", "G90", "G270")
mb <- c("B", "BSS", "BPO", "BPO0")
m2 <- c("N","GU","rGU","LO","LN","WEI","iG","GA","BE","FISK","GP","GPII","GPo")
m3 <- c("DAGUM","SM","TW")
m1d <- c("PO", "ZTP","DGP0")
m2d <- c("NBI", "NBII", "PIG","DGP","DGPII")
bl <- c("probit", "logit", "cloglog") # , "cauchit")
M <- list(m1d = m1d, m2 = m2, m2d = m2d, m3 = m3, BivD = BivD,
opc = opc, extra.regI = extra.regI, margins = margins, bl = bl, intf = intf,
theta.fx = theta.fx, Model = Model, mb = mb, BivD2 = BivD2, dof = dof)
surv.flex <- FALSE
M$K1 <- NULL
ct <- data.frame( c(opc),
c(1:14,55,56,57,60,61,62:65)
)
cta <- data.frame( c(opc),
c(1,3,23,13,33,6,26,16,36,4,24,14,34,5,55,56,2,60,61,62:65)
)
if(BivD %in% BivD2){
if(BivD %in% BivD2[1:4]) BivDt <- "C0"
if(BivD %in% BivD2[5:12]) BivDt <- "J0"
if(BivD %in% BivD2[13:16]) BivDt <- "C0" # useful for ass dep function but we calculate it differently, so ok like this
nC <- ct[which( ct[,1]==BivDt),2]
nCa <- cta[which(cta[,1]==BivDt),2]
}
if(!(BivD %in% BivD2)){
nC <- ct[which( ct[,1]==BivD),2]
nCa <- cta[which(cta[,1]==BivD),2]
}
#######################################################################################
if(!is.list(formula)) stop("You must specify a list of equations.")
M$l.flist <- l.flist <- length(formula)
pream.wm(formula, margins, M, l.flist, type = "biv")
form.check(formula, l.flist)
#######################################################################################
cl <- match.call()
mf <- match.call(expand.dots = FALSE)
pred.varR <- pred.var(formula, l.flist)
v1 <- pred.varR$v1
v2 <- pred.varR$v2
pred.n <- pred.varR$pred.n
fake.formula <- paste(v1[1], "~", paste(pred.n, collapse = " + "))
environment(fake.formula) <- environment(formula[[1]])
mf$formula <- fake.formula
mf$min.dn <- mf$min.pr <- mf$max.pr <- mf$ordinal <- mf$knots <- mf$dof <- mf$intf <- mf$theta.fx <- mf$Model <- mf$BivD <- mf$margins <- mf$fp <- mf$hess <- mf$infl.fac <- mf$rinit <- mf$rmax <- mf$iterlimsp <- mf$tolsp <- mf$gc.l <- mf$parscale <- mf$extra.regI <- mf$gamlssfit <- NULL
mf$drop.unused.levels <- drop.unused.levels
if(Model=="BSS") mf$na.action <- na.pass
mf[[1]] <- as.name("model.frame")
data <- eval(mf, parent.frame())
if(gc.l == TRUE) gc()
if(Model=="BSS"){
data[is.na(data[, v1[1]]), v1[1]] <- 0
indS <- data[, v1[1]]
indS[is.na(indS)] <- 0
indS <- as.logical(indS)
data[indS == FALSE, v2[1]] <- 0
data <- na.omit(data)
}
if(!("(weights)" %in% names(data))) {weights <- rep(1,dim(data)[1])
data$weights <- weights
names(data)[length(names(data))] <- "(weights)"} else weights <- data[,"(weights)"]
formula.eq1 <- formula[[1]]
formula.eq2 <- formula[[2]]
if(Model=="B"){
if(v1[1] %in% v2[-1]) end <- 1
if(v2[1] %in% v1[-1]) end <- 2
}
##############################################################
# Equation 1
##############################################################
gam1 <- eval(substitute(gam(formula.eq1, binomial(link = margins[1]), gamma=infl.fac, weights=weights,
data=data, knots = knots, drop.unused.levels = drop.unused.levels),list(weights=weights)))
X1 <- model.matrix(gam1)
X1.d2 <- dim(X1)[2]
l.sp1 <- length(gam1$sp)
y1 <- gam1$y
n <- length(y1)
if(l.sp1 != 0) sp1 <- gam1$sp
gp1 <- gam1$nsdf
inde <- rep(TRUE, n)
##############################################################
# Equation 2 for BPO and binary B
##############################################################
if((Model=="B" || Model=="BPO" || Model=="BPO0") && margins[2] %in% bl){
gam2 <- eval(substitute(gam(formula.eq2, binomial(link=margins[2]), gamma=infl.fac, weights=weights,
data=data, knots = knots, drop.unused.levels = drop.unused.levels),list(weights=weights))) # check at later stage the need of eval and substitute
X2 <- model.matrix(gam2)
X2.d2 <- dim(X2)[2]
l.sp2 <- length(gam2$sp)
y2 <- gam2$y
if(l.sp2 != 0) sp2 <- gam2$sp
if(Model=="B"){
y1.y2 <- y1*y2
y1.cy2 <- y1*(1-y2)
cy1.y2 <- (1-y1)*y2
cy1.cy2 <- (1-y1)*(1-y2)
}
if(Model=="BPO" || Model=="BPO0" ) cy <- 1 - y1
}
##############################################################
# Equation 2 for B and continuous/discrete response
##############################################################
if(Model=="B" && !(margins[2] %in% bl) ){
form.eq12R <- form.eq12(formula.eq2, data, v2, margins[2], m1d, m2d)
formula.eq2 <- form.eq12R$formula.eq1
formula.eq2r <- form.eq12R$formula.eq1r
y2 <- form.eq12R$y1
y2.test <- form.eq12R$y1.test
y2m <- form.eq12R$y1m
gam2 <- eval(substitute(gam(formula.eq2, gamma=infl.fac, weights=weights, data=data, knots = knots, drop.unused.levels = drop.unused.levels),list(weights=weights)))
gam2$formula <- formula.eq2r
names(gam2$model)[1] <- as.character(formula.eq2r[2])
y2 <- y2.test
if( margins[2] %in% c("LN") ) y2 <- log(y2)
X2 <- model.matrix(gam2)
X2.d2 <- dim(X2)[2]
l.sp2 <- length(gam2$sp)
if(l.sp2 != 0) sp2 <- gam2$sp
if(margins[2] != "TW") cy <- 1 - y1
if(margins[2] == "TW"){
formulamgcv <- formula[-c(1,5)]
formulamgcv[[2]] <- formula[-c(1,5)][[3]]
formulamgcv[[3]] <- formula[-c(1,5)][[2]]
gam2TW <- eval(substitute(gam(formulamgcv, gamma = infl.fac, weights = weights, data = data, knots = knots, drop.unused.levels = drop.unused.levels, family = twlss()), list(weights = weights)))
y2b <- y2 > 0
y00 <- (1 - y1)*(1 - y2b)
y10 <- y1*(1 - y2b)
y0p <- (1 - y1)*y2b
y1p <- y1*y2b
}
}
##############################################################
# Equation 2 for BSS
##############################################################
if(Model=="BSS"){
inde <- as.logical(y1)
gam2 <- eval(substitute(gam(formula.eq2, binomial(link = margins[2]), gamma=infl.fac, weights=weights,
data=data, subset=inde, knots = knots, drop.unused.levels = drop.unused.levels),list(weights=weights,inde=inde)))
######
# TEST
######
X2s <- try(predict.gam(gam2, newdata = data[,-dim(data)[2]], type = "lpmatrix"), silent = TRUE)
if(any(class(X2s)=="try-error")) stop("Check that the factor variables' levels\nin the selected sample are the same as those in the complete dataset.\nRead the Details section in ?gjrm for more details.")
######
X2.d2 <- length(gam2$coefficients)
X2 <- model.matrix(gam2)
y2 <- gam2$y
n.sel <- sum(as.numeric(inde))
l.sp2 <- length(gam2$sp)
if(l.sp2 != 0) sp2 <- gam2$sp
cy1 <- (1-y1)
y1.y2 <- y1[inde]*y2
y1.cy2 <- y1[inde]*(1-y2)
######################
# better starting values in BSS case
form.eq2imr <- update.formula(formula.eq2, ~. + imrGUANN)
p.g1 <- predict.gam(gam1)
imrGUANN <- data$imrGUANN <- dnorm(p.g1)/pnorm(p.g1)
gam2.1 <- eval(substitute(gam(form.eq2imr, gamma=infl.fac, binomial(link = margins[2]), weights=weights, data=data, subset=inde, knots = knots, drop.unused.levels = drop.unused.levels),list(weights = weights, inde = inde)))
pimr <- which(names(gam2.1$coefficients)=="imrGUANN")
c.gam2 <- gam2.1$coefficients[-pimr]
sia <- sqrt(mean(residuals(gam2.1, type = "deviance")^2)+mean(imrGUANN[inde]*(imrGUANN[inde]+p.g1[inde]))*gam2.1$coefficients["imrGUANN"]^2)[[1]]
co <- (gam2.1$coefficients["imrGUANN"]/sia)[[1]]
ass.s <- co
ass.s <- sign(ass.s)*ifelse(abs(ass.s) > 0.2, 0.2, abs(ass.s))
if(l.sp2 != 0) sp2 <- gam2.1$sp
}
##############################################################
gp2 <- gam2$nsdf
##############################################################
# Starting values for dependence parameter
##############################################################
if(is.null(theta.fx)){
if( !(Model %in% c("BPO0")) ){
if(Model=="B"){
res1 <- residuals(gam1)
res2 <- residuals(gam2)
ass.s <- cor(res1, res2, method = "kendall")
ass.s <- sign(ass.s)*ifelse(abs(ass.s) > 0.9, 0.9, abs(ass.s))
}
if(Model=="BPO") ass.s <- 0.01
i.rho <- ass.dp(ass.s, BivD, scc, sccn, nCa)
}
if(Model=="BPO0") i.rho <- 0
}
names(i.rho) <- "theta.star"
##############################################################
# Starting values for whole parameter vector
##############################################################
if(margins[2] != "TW"){
if(margins[1] %in% bl && margins[2] %in% c(bl,m1d) && Model %in% c("B","BPO") && is.null(theta.fx)) start.v <- c(gam1$coefficients, gam2$coefficients, i.rho)
if(Model == "BSS") start.v <- c(gam1$coefficients, c.gam2, i.rho)
if(Model == "BPO0") start.v <- c(gam1$coefficients, gam2$coefficients)
if(!is.null(theta.fx) && Model == "B" && margins[2] %in% bl ) start.v <- c(gam1$coefficients, gam2$coefficients)
if(margins[1] %in% bl && margins[2] %in% c(m2,m3,m2d) ){
start.snR <- startsn(margins[2], y2)
log.sig2 <- start.snR$log.sig2.1; names(log.sig2) <- "sigma.star"
if( margins[2] %in% c(m3) ){ log.nu <- start.snR$log.nu.1; names(log.nu) <- "nu.star"}
if(margins[2] %in% c(m2,m2d)) start.v <- c(gam1$coefficients, gam2$coefficients, log.sig2, i.rho)
if(margins[2] %in% m3) start.v <- c(gam1$coefficients, gam2$coefficients, log.sig2, log.nu, i.rho)
}
}
##############################################################
if(l.flist > 2){
if(margins[2] == "TW") log.nu <- log.sig2 <- 0.1
vo <- list(gam1 = gam1, gam2 = gam2, i.rho = i.rho, log.sig2 = log.sig2, log.nu = log.nu, n = n, drop.unused.levels = drop.unused.levels) # for TW
overall.svGR <- overall.svG(formula, data, ngc = 2, margins, M, vo, gam1, gam2, type = "biv", inde = inde, c.gam2 = c.gam2, knots = knots)
start.v = overall.svGR$start.v
X3 = overall.svGR$X3; X4 = overall.svGR$X4; X5 = overall.svGR$X5
X6 = overall.svGR$X6; X7 = overall.svGR$X7; X8 = overall.svGR$X8
X3.d2 = overall.svGR$X3.d2; X4.d2 = overall.svGR$X4.d2; X5.d2 = overall.svGR$X5.d2
X6.d2 = overall.svGR$X6.d2; X7.d2 = overall.svGR$X7.d2; X8.d2 = overall.svGR$X8.d2
gp3 = overall.svGR$gp3; gp4 = overall.svGR$gp4; gp5 = overall.svGR$gp5
gp6 = overall.svGR$gp6; gp7 = overall.svGR$gp7; gp8 = overall.svGR$gp8
gam3 = overall.svGR$gam3; gam4 = overall.svGR$gam4; gam5 = overall.svGR$gam5
gam6 = overall.svGR$gam6; gam7 = overall.svGR$gam7; gam8 = overall.svGR$gam8
l.sp3 = overall.svGR$l.sp3; l.sp4 = overall.svGR$l.sp4; l.sp5 = overall.svGR$l.sp5
l.sp6 = overall.svGR$l.sp6; l.sp7 = overall.svGR$l.sp7; l.sp8 = overall.svGR$l.sp8
sp3 = overall.svGR$sp3; sp4 = overall.svGR$sp4; sp5 = overall.svGR$sp5
sp6 = overall.svGR$sp6; sp7 = overall.svGR$sp7; sp8 = overall.svGR$sp8
X3s = overall.svGR$X3s; X4s = overall.svGR$X4s
if(margins[2] == "TW"){
gamlssfit <- FALSE # no need since I already use start.v from gam2TW
nams <- names(start.v)
start.v1TW <- start.v1 <- gam2TW$coefficients
X2.d2mgcv <- X2.d2
X3.d2mgcv <- X4.d2
X4.d2mgcv <- X3.d2
start.v1TW[1:X2.d2] <- start.v1[1:X2.d2mgcv]
start.v1TW[(X2.d2 + 1):(X2.d2 + X3.d2)] <- start.v1[(X2.d2mgcv + X3.d2mgcv + 1):(X2.d2mgcv + X3.d2mgcv + X4.d2mgcv)]
start.v1TW[(X2.d2 + X3.d2 + 1):(X2.d2 + X3.d2 + X4.d2)] <- start.v1[(X2.d2mgcv + 1):(X2.d2mgcv + X3.d2mgcv)]
start.v1 <- start.v1TW
start.v <- c(gam1$coefficients, start.v1, gam5$coefficients)
names(start.v) <- nams; rm(start.v1TW)
spmgcv <- gam2TW$sp
l.sp2mgcv <- l.sp2
l.sp3mgcv <- l.sp4
l.sp4mgcv <- l.sp3
if(l.sp2 != 0){ sp2 <- spmgcv[1:l.sp2mgcv]; names(sp2) <- names(gam2$sp)}
if(l.sp3 != 0){ sp3 <- spmgcv[(l.sp2mgcv + l.sp3mgcv + 1):(l.sp2mgcv + l.sp3mgcv + l.sp4mgcv)]; names(sp3) <- names(gam3$sp)}
if(l.sp4 != 0){ sp4 <- spmgcv[(l.sp2mgcv + 1):(l.sp2mgcv + l.sp3mgcv)]; names(sp4) <- names(gam4$sp)}
}
}
##########################################################
GAM <- list(gam1 = gam1, gam2 = gam2, gam3 = gam3, gam4 = gam4,
gam5 = gam5, gam6 = gam6, gam7 = gam7, gam8 = gam8, gam9 = gam9)
if( (l.sp1!=0 || l.sp2!=0 || l.sp3!=0 || l.sp4!=0 || l.sp5!=0 || l.sp6!=0 || l.sp7!=0 || l.sp8!=0) && fp==FALSE ){
L.GAM <- list(l.gam1 = length(gam1$coefficients), l.gam2 = length(gam2$coefficients), l.gam3 = length(gam3$coefficients), l.gam4 = length(gam4$coefficients),
l.gam5 = length(gam5$coefficients), l.gam6 = length(gam6$coefficients), l.gam7 = length(gam7$coefficients), l.gam8 = length(gam8$coefficients),
l.gam9 = 0)
L.SP <- list(l.sp1 = l.sp1, l.sp2 = l.sp2, l.sp3 = l.sp3, l.sp4 = l.sp4,
l.sp5 = l.sp5, l.sp6 = l.sp6, l.sp7 = l.sp7, l.sp8 = l.sp8, l.sp9 = l.sp9)
sp <- c(sp1, sp2, sp3, sp4, sp5, sp6, sp7, sp8)
qu.mag <- S.m(GAM, L.SP, L.GAM)
}
##########################################################
if(missing(parscale)) parscale <- 1
respvec <- list(y1 = y1,
y2 = y2,
y1.y2 = y1.y2,
y1.cy2 = y1.cy2,
cy1.y2 = cy1.y2,
cy1.cy2 = cy1.cy2,
cy1 = cy1,
cy = cy, univ = 0,
y00 = y00, y10 = y10, y0p = y0p, y1p = y1p)
my.env <- new.env()
my.env$signind <- 1
lsgam1 <- length(gam1$smooth)
lsgam2 <- length(gam2$smooth)
lsgam3 <- length(gam3$smooth)
lsgam4 <- length(gam4$smooth)
lsgam5 <- length(gam5$smooth)
lsgam6 <- length(gam6$smooth)
lsgam7 <- length(gam7$smooth)
lsgam8 <- length(gam8$smooth)
lsgam9 <- length(gam9$smooth)
VC <- list(lsgam1 = lsgam1, robust = FALSE, sp.fixed = NULL,K1 = NULL,
lsgam2 = lsgam2, Sl.sf = Sl.sf, sp.method = sp.method,
lsgam3 = lsgam3,
lsgam4 = lsgam4,
lsgam5 = lsgam5,
lsgam6 = lsgam6,
lsgam7 = lsgam7,
lsgam8 = lsgam8, lsgam9 = lsgam9,
X1 = X1, inde = inde,my.env=my.env,
X2 = X2,
X3 = X3,
X4 = X4,
X5 = X5,
X6 = X6,
X7 = X7,
X8 = X8,
X1.d2 = X1.d2,
X2.d2 = X2.d2,
X3.d2 = X3.d2,
X4.d2 = X4.d2,
X5.d2 = X5.d2,
X6.d2 = X6.d2,
X7.d2 = X7.d2,
X8.d2 = X8.d2,
gp1 = gp1,
gp2 = gp2,
gp3 = gp3,
gp4 = gp4,
gp5 = gp5,
gp6 = gp6,
gp7 = gp7,
gp8 = gp8,
l.sp1 = l.sp1,
l.sp2 = l.sp2,
l.sp3 = l.sp3,
l.sp4 = l.sp4,
l.sp5 = l.sp5,
l.sp6 = l.sp6,
l.sp7 = l.sp7,
l.sp8 = l.sp8,
l.sp9 = 0,
infl.fac = infl.fac,
weights = weights,
fp = fp, univ.gamls = FALSE,
hess = hess, nCa = nCa,
Model = Model, gamlssfit = gamlssfit,
end = end,
BivD = BivD, dof.st = log(dof - 2), dof = dof,
nC = nC, gc.l = gc.l, n = n, extra.regI = extra.regI,
parscale = parscale, margins = margins,
Cont = "NO", ccss = "no", m2 = m2, m3 = m3, m2d = m2d, m1d = m1d, m3d = NULL, bl = bl,
X2s = X2s, X3s = X3s, triv = FALSE, y2m = y2m,
theta.fx = theta.fx, i.rho = i.rho,
BivD2 = BivD2, cta = cta, ct = ct, zerov = -10, surv.flex = surv.flex, gp2.inf = NULL,
informative = "no",
zero.tol = 1e-02,
min.dn = min.dn, min.pr = min.pr, max.pr = max.pr,
y00 = y00, y10 = y10, y0p = y0p, y1p = y1p) # original n only needed in SemiParBIV.fit
if(gc.l == TRUE) gc()
##########################################################################################################################
if(gamlssfit == TRUE && !(margins[2] %in% bl)){
form.gamlR <- form.gaml(formula, l.flist, M, type = "biv")
gamlss2 <- eval(substitute(gamlss(form.gamlR$formula.gamlss2, data = data, weights = weights, subset = subset,
margin = margins[2], infl.fac = infl.fac,
rinit = rinit, rmax = rmax, iterlimsp = iterlimsp, tolsp = tolsp,
gc.l = gc.l, parscale = 1, extra.regI = extra.regI, drop.unused.levels = drop.unused.levels), list(weights=weights)))
# updated starting values
SP <- list(sp1 = sp1, sp2 = sp2, sp3 = sp3, sp4 = sp4, sp5 = sp5, sp6 = sp6, sp7 = sp7, sp8 = sp8)
gamls.upsvR <- gamls.upsv(gamlss1 = NULL, gamlss2, margins, M, l.flist, nstv = NULL, VC, GAM, SP, type = "biv")
sp <- gamls.upsvR$sp
start.v <- gamls.upsvR$start.v
}
##########################################################################################################################
##########################################################################################################################
if(Model %in% c("BSS", "BPO", "BPO0") || (Model == "B" && margins[2] %in% bl) ) gamlssfit <- VC$gamlssfit <- TRUE # useful for error massage and joint probs
func.opt <- func.OPT(margins, M, type = "biv")
SemiParFit <- SemiParBIV.fit(func.opt = func.opt, start.v = start.v,
rinit = rinit, rmax = rmax, iterlim = 100, iterlimsp = iterlimsp, tolsp = tolsp,
respvec = respvec, VC = VC, sp = sp, qu.mag = qu.mag)
##########################################################################################################################
# post estimation
##########################################################################################################################
SemiParFit.p <- SemiParBIV.fit.post(SemiParFit = SemiParFit, Model = Model, VC = VC, GAM)
SemiParFit <- SemiParFit.p$SemiParFit # useful for SS models, eta2 calculatons etc.
y2.m <- y2
if(margins[2] == "LN") y2.m <- exp(y2)
##########################################################################################################################
if(gc.l == TRUE) gc()
##########################################################################################################################
cov.c(SemiParFit)
##########################################################################################################################
gam1$call$data <- gam2$call$data <- gam3$call$data <- gam4$call$data <- gam5$call$data <- gam6$call$data <- gam7$call$data <- gam8$call$data <- cl$data
# for all.terms
##########################################################################################################################
# bit below useful for AT calculations when end is continuous
if( !(Model=="B" && !(margins[2] %in% bl) && end == 2) ) {dataset <- NULL; rm(data) } else { attr(data, "terms") <- NULL; dataset <- data; rm(data) }
formula.aux <- NULL
if(Model == "BSS"){
# this is for mice #
formula.aux <- formula
formula.aux[[1]] <- reformulate( attr(terms(formula.aux[[1]]), "term.labels"), response = "ry" )
environment(formula.aux[[1]]) <- environment(formula[[1]])
formula.aux[[2]] <- reformulate( attr(terms(formula.aux[[2]]), "term.labels"), response = "y" )
environment(formula.aux[[2]]) <- environment(formula[[2]])
###
}
L <- list(fit = SemiParFit$fit, dataset = dataset, formula = formula, SemiParFit = SemiParFit, mice.formula = formula.aux,
gam1 = gam1, gam2 = gam2, gam3 = gam3, gam4 = gam4, gam5 = gam5, gam6 = gam6, robust = FALSE,
gam7 = gam7, gam8 = gam8, gam9 = gam9, gam2TW = gam2TW,
coefficients = SemiParFit$fit$argument, coef.t = NULL, iterlimsp = iterlimsp,
weights = weights,
sp = SemiParFit.p$sp, iter.sp = SemiParFit$iter.sp,
l.sp1 = l.sp1, l.sp2 = l.sp2, l.sp3 = l.sp3,
l.sp4 = l.sp4, l.sp5 = l.sp5, l.sp6 = l.sp6,
l.sp7 = l.sp7, l.sp8 = l.sp8, l.sp9 = l.sp9, bl = bl,
fp = fp,
iter.if = SemiParFit$iter.if, iter.inner = SemiParFit$iter.inner,
theta = SemiParFit.p$theta,
theta.a = SemiParFit.p$theta.a,
OR = SemiParFit.p$OR,
GM = SemiParFit.p$GM,
n = n, n.sel = n.sel,
X1 = X1, X2 = X2, X3 = X3, X1.d2 = X1.d2, X2.d2 = X2.d2, X3.d2 = X3.d2,
X4 = X4, X5 = X5, X6 = X6, X7 = X7, X8 = X8, X4.d2 = X4.d2, X5.d2 = X5.d2,
X6.d2 = X6.d2, X7.d2 = X7.d2, X8.d2 = X8.d2,
He = SemiParFit.p$He, HeSh = SemiParFit.p$HeSh, Vb = SemiParFit.p$Vb, Ve = SemiParFit.p$Ve,
F = SemiParFit.p$F, F1 = SemiParFit.p$F1,
t.edf = SemiParFit.p$t.edf, edf = SemiParFit.p$edf,
edf11 = SemiParFit.p$edf11,
edf1 = SemiParFit.p$edf1, edf2 = SemiParFit.p$edf2, edf3 = SemiParFit.p$edf3,
edf4 = SemiParFit.p$edf4, edf5 = SemiParFit.p$edf5, edf6 = SemiParFit.p$edf6,
edf7 = SemiParFit.p$edf7, edf8 = SemiParFit.p$edf8,
edf1.1 = SemiParFit.p$edf1.1, edf1.2 = SemiParFit.p$edf1.2, edf1.3 = SemiParFit.p$edf1.3,
edf1.4 = SemiParFit.p$edf1.4, edf1.5 = SemiParFit.p$edf1.5, edf1.6 = SemiParFit.p$edf1.6,
edf1.7 = SemiParFit.p$edf1.7, edf1.8 = SemiParFit.p$edf1.8,
R = SemiParFit.p$R,
bs.mgfit = SemiParFit$bs.mgfit, conv.sp = SemiParFit$conv.sp,
wor.c = SemiParFit$wor.c,
p11 = SemiParFit$fit$p11, p10 = SemiParFit$fit$p10, p01 = SemiParFit$fit$p01, p00 = SemiParFit$fit$p00,
p1 = SemiParFit$fit$p1, p2 = SemiParFit$fit$p2,
eta1 = SemiParFit$fit$eta1, eta2 = SemiParFit$fit$eta2, etad = SemiParFit$fit$etad,
etas = SemiParFit$fit$etas, etan = SemiParFit$fit$etan,
y1 = y1, y2 = y2.m,
BivD = BivD, margins = margins,
logLik = SemiParFit.p$logLik,
nC = nC, hess = hess,
respvec = respvec, inde = inde,
qu.mag = qu.mag,
sigma2 = SemiParFit.p$sigma2, sigma2.a = SemiParFit.p$sigma2.a,
sigma = SemiParFit.p$sigma2, sigma.a = SemiParFit.p$sigma2.a,
nu = SemiParFit.p$nu, nu.a = SemiParFit.p$nu.a, Vb.t = SemiParFit.p$Vb.t,
gp1 = gp1, gp2 = gp2, gp3 = gp3, gp4 = gp4, gp5 = gp5, gp6 = gp6, gp7 = gp7, gp8 = gp8,
X2s = X2s, X3s = X3s, p1n=SemiParFit.p$p1n , p2n = SemiParFit.p$p2n,
VC = VC, Model = Model, magpp = SemiParFit$magpp,
gamlssfit = gamlssfit, Cont = "NO", tau = SemiParFit.p$tau,
tau.a = SemiParFit.p$tau.a, l.flist = l.flist, v1 = v1, v2 = v2, triv = FALSE, univar.gamlss = FALSE,
gamlss = gamlss2, BivD2 = BivD2, dof = dof, dof.a = dof, call = cl,
surv = FALSE, surv.flex = surv.flex)
if(BivD %in% BivD2){
L$teta1 <- SemiParFit$fit$teta1
L$teta.ind1 <- SemiParFit$fit$teta.ind1
L$teta2 <- SemiParFit$fit$teta2
L$teta.ind2 <- SemiParFit$fit$teta.ind2
L$Cop1 <- SemiParFit$fit$Cop1
L$Cop2 <- SemiParFit$fit$Cop2
}
class(L) <- c("SemiParBIV","gjrm")
L
}
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Defines functions SemiParBIV
Documented in SemiParBIV
SemiParBIV <- function(formula, data = list(), weights = NULL, subset = NULL,
Model = "B", BivD = "N", margins = c("probit","probit"),
dof = 3, gamlssfit = FALSE,
fp = FALSE, hess = TRUE, infl.fac = 1, theta.fx = NULL,
rinit = 1, rmax = 100, iterlimsp = 50, tolsp = 1e-07,
gc.l = FALSE, parscale, extra.regI = "t", intf = FALSE, knots = NULL,
drop.unused.levels = TRUE,
min.dn = 1e-40, min.pr = 1e-16, max.pr = 0.999999){
##########################################################################################################################
# model set up and starting values
##########################################################################################################################
i.rho <- sp <- qu.mag <- n.sel <- y1.y2 <- y1.cy2 <- cy1.y2 <- cy1.cy2 <- cy <- cy1 <- inde <- y2m <- NULL
y00 <- y10 <- y0p <- y1p <- gam2TW <- NULL # for binary - tweedie margins
end <- X3.d2 <- X4.d2 <- X5.d2 <- X6.d2 <- X7.d2 <- X8.d2 <- l.sp3 <- l.sp4 <- l.sp5 <- l.sp6 <- l.sp7 <- l.sp8 <- l.sp9 <- i.rho <- 0
gam1 <- gam2 <- gam3 <- gam4 <- gam5 <- gam6 <- gam7 <- gam8 <- gam9 <- gamlss2 <- dof.st <- NULL
gamlss2 <- NULL
sp1 <- sp2 <- c.gam2 <- X2s <- X3s <- NULL
sp3 <- gp3 <- gam3 <- X3 <- NULL
sp4 <- gp4 <- gam4 <- X4 <- NULL
sp5 <- gp5 <- gam5 <- X5 <- NULL
sp6 <- gp6 <- gam6 <- X6 <- NULL
sp7 <- gp7 <- gam7 <- X7 <- NULL
sp8 <- gp8 <- gam8 <- X8 <- NULL
log.sig2 <- log.nu <- NULL
Sl.sf <- NULL
sp.method <- "perf"
BivD2 <- c("C0C90","C0C270","C180C90","C180C270",
"J0J90","J0J270","J180J90","J180J270",
"G0G90","G0G270","G180G90","G180G270","GAL0GAL90", "GAL0GAL270", "GAL180GAL90", "GAL180GAL270")
opc <- c("N","C0","C90","C180","C270","J0","J90","J180","J270","G0","G90","G180","G270","F","AMH","FGM","T","PL","HO","GAL0", "GAL90", "GAL180", "GAL270")
scc <- c("C0", "C180", "GAL0" , "GAL180","J0", "J180", "G0", "G180", BivD2)
sccn <- c("C90", "C270", "GAL90", "GAL270","J90", "J270", "G90", "G270")
mb <- c("B", "BSS", "BPO", "BPO0")
m2 <- c("N","GU","rGU","LO","LN","WEI","iG","GA","BE","FISK","GP","GPII","GPo")
m3 <- c("DAGUM","SM","TW")
m1d <- c("PO", "ZTP","DGP0")
m2d <- c("NBI", "NBII", "PIG","DGP","DGPII")
bl <- c("probit", "logit", "cloglog") # , "cauchit")
M <- list(m1d = m1d, m2 = m2, m2d = m2d, m3 = m3, BivD = BivD,
opc = opc, extra.regI = extra.regI, margins = margins, bl = bl, intf = intf,
theta.fx = theta.fx, Model = Model, mb = mb, BivD2 = BivD2, dof = dof)
surv.flex <- FALSE
M$K1 <- NULL
ct <- data.frame( c(opc),
c(1:14,55,56,57,60,61,62:65)
)
cta <- data.frame( c(opc),
c(1,3,23,13,33,6,26,16,36,4,24,14,34,5,55,56,2,60,61,62:65)
)
if(BivD %in% BivD2){
if(BivD %in% BivD2[1:4]) BivDt <- "C0"
if(BivD %in% BivD2[5:12]) BivDt <- "J0"
if(BivD %in% BivD2[13:16]) BivDt <- "C0" # useful for ass dep function but we calculate it differently, so ok like this
nC <- ct[which( ct[,1]==BivDt),2]
nCa <- cta[which(cta[,1]==BivDt),2]
}
if(!(BivD %in% BivD2)){
nC <- ct[which( ct[,1]==BivD),2]
nCa <- cta[which(cta[,1]==BivD),2]
}
#######################################################################################
if(!is.list(formula)) stop("You must specify a list of equations.")
M$l.flist <- l.flist <- length(formula)
pream.wm(formula, margins, M, l.flist, type = "biv")
form.check(formula, l.flist)
#######################################################################################
cl <- match.call()
mf <- match.call(expand.dots = FALSE)
pred.varR <- pred.var(formula, l.flist)
v1 <- pred.varR$v1
v2 <- pred.varR$v2
pred.n <- pred.varR$pred.n
fake.formula <- paste(v1[1], "~", paste(pred.n, collapse = " + "))
environment(fake.formula) <- environment(formula[[1]])
mf$formula <- fake.formula
mf$min.dn <- mf$min.pr <- mf$max.pr <- mf$ordinal <- mf$knots <- mf$dof <- mf$intf <- mf$theta.fx <- mf$Model <- mf$BivD <- mf$margins <- mf$fp <- mf$hess <- mf$infl.fac <- mf$rinit <- mf$rmax <- mf$iterlimsp <- mf$tolsp <- mf$gc.l <- mf$parscale <- mf$extra.regI <- mf$gamlssfit <- NULL
mf$drop.unused.levels <- drop.unused.levels
if(Model=="BSS") mf$na.action <- na.pass
mf[[1]] <- as.name("model.frame")
data <- eval(mf, parent.frame())
if(gc.l == TRUE) gc()
if(Model=="BSS"){
data[is.na(data[, v1[1]]), v1[1]] <- 0
indS <- data[, v1[1]]
indS[is.na(indS)] <- 0
indS <- as.logical(indS)
data[indS == FALSE, v2[1]] <- 0
data <- na.omit(data)
}
if(!("(weights)" %in% names(data))) {weights <- rep(1,dim(data)[1])
data$weights <- weights
names(data)[length(names(data))] <- "(weights)"} else weights <- data[,"(weights)"]
formula.eq1 <- formula[[1]]
formula.eq2 <- formula[[2]]
if(Model=="B"){
if(v1[1] %in% v2[-1]) end <- 1
if(v2[1] %in% v1[-1]) end <- 2
}
##############################################################
# Equation 1
##############################################################
gam1 <- eval(substitute(gam(formula.eq1, binomial(link = margins[1]), gamma=infl.fac, weights=weights,
data=data, knots = knots, drop.unused.levels = drop.unused.levels),list(weights=weights)))
X1 <- model.matrix(gam1)
X1.d2 <- dim(X1)[2]
l.sp1 <- length(gam1$sp)
y1 <- gam1$y
n <- length(y1)
if(l.sp1 != 0) sp1 <- gam1$sp
gp1 <- gam1$nsdf
inde <- rep(TRUE, n)
##############################################################
# Equation 2 for BPO and binary B
##############################################################
if((Model=="B" || Model=="BPO" || Model=="BPO0") && margins[2] %in% bl){
gam2 <- eval(substitute(gam(formula.eq2, binomial(link=margins[2]), gamma=infl.fac, weights=weights,
data=data, knots = knots, drop.unused.levels = drop.unused.levels),list(weights=weights))) # check at later stage the need of eval and substitute
X2 <- model.matrix(gam2)
X2.d2 <- dim(X2)[2]
l.sp2 <- length(gam2$sp)
y2 <- gam2$y
if(l.sp2 != 0) sp2 <- gam2$sp
if(Model=="B"){
y1.y2 <- y1*y2
y1.cy2 <- y1*(1-y2)
cy1.y2 <- (1-y1)*y2
cy1.cy2 <- (1-y1)*(1-y2)
}
if(Model=="BPO" || Model=="BPO0" ) cy <- 1 - y1
}
##############################################################
# Equation 2 for B and continuous/discrete response
##############################################################
if(Model=="B" && !(margins[2] %in% bl) ){
form.eq12R <- form.eq12(formula.eq2, data, v2, margins[2], m1d, m2d)
formula.eq2 <- form.eq12R$formula.eq1
formula.eq2r <- form.eq12R$formula.eq1r
y2 <- form.eq12R$y1
y2.test <- form.eq12R$y1.test
y2m <- form.eq12R$y1m
gam2 <- eval(substitute(gam(formula.eq2, gamma=infl.fac, weights=weights, data=data, knots = knots, drop.unused.levels = drop.unused.levels),list(weights=weights)))
gam2$formula <- formula.eq2r
names(gam2$model)[1] <- as.character(formula.eq2r[2])
y2 <- y2.test
if( margins[2] %in% c("LN") ) y2 <- log(y2)
X2 <- model.matrix(gam2)
X2.d2 <- dim(X2)[2]
l.sp2 <- length(gam2$sp)
if(l.sp2 != 0) sp2 <- gam2$sp
if(margins[2] != "TW") cy <- 1 - y1
if(margins[2] == "TW"){
formulamgcv <- formula[-c(1,5)]
formulamgcv[[2]] <- formula[-c(1,5)][[3]]
formulamgcv[[3]] <- formula[-c(1,5)][[2]]
gam2TW <- eval(substitute(gam(formulamgcv, gamma = infl.fac, weights = weights, data = data, knots = knots, drop.unused.levels = drop.unused.levels, family = twlss()), list(weights = weights)))
y2b <- y2 > 0
y00 <- (1 - y1)*(1 - y2b)
y10 <- y1*(1 - y2b)
y0p <- (1 - y1)*y2b
y1p <- y1*y2b
}
}
##############################################################
# Equation 2 for BSS
##############################################################
if(Model=="BSS"){
inde <- as.logical(y1)
gam2 <- eval(substitute(gam(formula.eq2, binomial(link = margins[2]), gamma=infl.fac, weights=weights,
data=data, subset=inde, knots = knots, drop.unused.levels = drop.unused.levels),list(weights=weights,inde=inde)))
######
# TEST
######
X2s <- try(predict.gam(gam2, newdata = data[,-dim(data)[2]], type = "lpmatrix"), silent = TRUE)
if(any(class(X2s)=="try-error")) stop("Check that the factor variables' levels\nin the selected sample are the same as those in the complete dataset.\nRead the Details section in ?gjrm for more details.")
######
X2.d2 <- length(gam2$coefficients)
X2 <- model.matrix(gam2)
y2 <- gam2$y
n.sel <- sum(as.numeric(inde))
l.sp2 <- length(gam2$sp)
if(l.sp2 != 0) sp2 <- gam2$sp
cy1 <- (1-y1)
y1.y2 <- y1[inde]*y2
y1.cy2 <- y1[inde]*(1-y2)
######################
# better starting values in BSS case
form.eq2imr <- update.formula(formula.eq2, ~. + imrGUANN)
p.g1 <- predict.gam(gam1)
imrGUANN <- data$imrGUANN <- dnorm(p.g1)/pnorm(p.g1)
gam2.1 <- eval(substitute(gam(form.eq2imr, gamma=infl.fac, binomial(link = margins[2]), weights=weights, data=data, subset=inde, knots = knots, drop.unused.levels = drop.unused.levels),list(weights = weights, inde = inde)))
pimr <- which(names(gam2.1$coefficients)=="imrGUANN")
c.gam2 <- gam2.1$coefficients[-pimr]
sia <- sqrt(mean(residuals(gam2.1, type = "deviance")^2)+mean(imrGUANN[inde]*(imrGUANN[inde]+p.g1[inde]))*gam2.1$coefficients["imrGUANN"]^2)[[1]]
co <- (gam2.1$coefficients["imrGUANN"]/sia)[[1]]
ass.s <- co
ass.s <- sign(ass.s)*ifelse(abs(ass.s) > 0.2, 0.2, abs(ass.s))
if(l.sp2 != 0) sp2 <- gam2.1$sp
}
##############################################################
gp2 <- gam2$nsdf
##############################################################
# Starting values for dependence parameter
##############################################################
if(is.null(theta.fx)){
if( !(Model %in% c("BPO0")) ){
if(Model=="B"){
res1 <- residuals(gam1)
res2 <- residuals(gam2)
ass.s <- cor(res1, res2, method = "kendall")
ass.s <- sign(ass.s)*ifelse(abs(ass.s) > 0.9, 0.9, abs(ass.s))
}
if(Model=="BPO") ass.s <- 0.01
i.rho <- ass.dp(ass.s, BivD, scc, sccn, nCa)
}
if(Model=="BPO0") i.rho <- 0
}
names(i.rho) <- "theta.star"
##############################################################
# Starting values for whole parameter vector
##############################################################
if(margins[2] != "TW"){
if(margins[1] %in% bl && margins[2] %in% c(bl,m1d) && Model %in% c("B","BPO") && is.null(theta.fx)) start.v <- c(gam1$coefficients, gam2$coefficients, i.rho)
if(Model == "BSS") start.v <- c(gam1$coefficients, c.gam2, i.rho)
if(Model == "BPO0") start.v <- c(gam1$coefficients, gam2$coefficients)
if(!is.null(theta.fx) && Model == "B" && margins[2] %in% bl ) start.v <- c(gam1$coefficients, gam2$coefficients)
if(margins[1] %in% bl && margins[2] %in% c(m2,m3,m2d) ){
start.snR <- startsn(margins[2], y2)
log.sig2 <- start.snR$log.sig2.1; names(log.sig2) <- "sigma.star"
if( margins[2] %in% c(m3) ){ log.nu <- start.snR$log.nu.1; names(log.nu) <- "nu.star"}
if(margins[2] %in% c(m2,m2d)) start.v <- c(gam1$coefficients, gam2$coefficients, log.sig2, i.rho)
if(margins[2] %in% m3) start.v <- c(gam1$coefficients, gam2$coefficients, log.sig2, log.nu, i.rho)
}
}
##############################################################
if(l.flist > 2){
if(margins[2] == "TW") log.nu <- log.sig2 <- 0.1
vo <- list(gam1 = gam1, gam2 = gam2, i.rho = i.rho, log.sig2 = log.sig2, log.nu = log.nu, n = n, drop.unused.levels = drop.unused.levels) # for TW
overall.svGR <- overall.svG(formula, data, ngc = 2, margins, M, vo, gam1, gam2, type = "biv", inde = inde, c.gam2 = c.gam2, knots = knots)
start.v = overall.svGR$start.v
X3 = overall.svGR$X3; X4 = overall.svGR$X4; X5 = overall.svGR$X5
X6 = overall.svGR$X6; X7 = overall.svGR$X7; X8 = overall.svGR$X8
X3.d2 = overall.svGR$X3.d2; X4.d2 = overall.svGR$X4.d2; X5.d2 = overall.svGR$X5.d2
X6.d2 = overall.svGR$X6.d2; X7.d2 = overall.svGR$X7.d2; X8.d2 = overall.svGR$X8.d2
gp3 = overall.svGR$gp3; gp4 = overall.svGR$gp4; gp5 = overall.svGR$gp5
gp6 = overall.svGR$gp6; gp7 = overall.svGR$gp7; gp8 = overall.svGR$gp8
gam3 = overall.svGR$gam3; gam4 = overall.svGR$gam4; gam5 = overall.svGR$gam5
gam6 = overall.svGR$gam6; gam7 = overall.svGR$gam7; gam8 = overall.svGR$gam8
l.sp3 = overall.svGR$l.sp3; l.sp4 = overall.svGR$l.sp4; l.sp5 = overall.svGR$l.sp5
l.sp6 = overall.svGR$l.sp6; l.sp7 = overall.svGR$l.sp7; l.sp8 = overall.svGR$l.sp8
sp3 = overall.svGR$sp3; sp4 = overall.svGR$sp4; sp5 = overall.svGR$sp5
sp6 = overall.svGR$sp6; sp7 = overall.svGR$sp7; sp8 = overall.svGR$sp8
X3s = overall.svGR$X3s; X4s = overall.svGR$X4s
if(margins[2] == "TW"){
gamlssfit <- FALSE # no need since I already use start.v from gam2TW
nams <- names(start.v)
start.v1TW <- start.v1 <- gam2TW$coefficients
X2.d2mgcv <- X2.d2
X3.d2mgcv <- X4.d2
X4.d2mgcv <- X3.d2
start.v1TW[1:X2.d2] <- start.v1[1:X2.d2mgcv]
start.v1TW[(X2.d2 + 1):(X2.d2 + X3.d2)] <- start.v1[(X2.d2mgcv + X3.d2mgcv + 1):(X2.d2mgcv + X3.d2mgcv + X4.d2mgcv)]
start.v1TW[(X2.d2 + X3.d2 + 1):(X2.d2 + X3.d2 + X4.d2)] <- start.v1[(X2.d2mgcv + 1):(X2.d2mgcv + X3.d2mgcv)]
start.v1 <- start.v1TW
start.v <- c(gam1$coefficients, start.v1, gam5$coefficients)
names(start.v) <- nams; rm(start.v1TW)
spmgcv <- gam2TW$sp
l.sp2mgcv <- l.sp2
l.sp3mgcv <- l.sp4
l.sp4mgcv <- l.sp3
if(l.sp2 != 0){ sp2 <- spmgcv[1:l.sp2mgcv]; names(sp2) <- names(gam2$sp)}
if(l.sp3 != 0){ sp3 <- spmgcv[(l.sp2mgcv + l.sp3mgcv + 1):(l.sp2mgcv + l.sp3mgcv + l.sp4mgcv)]; names(sp3) <- names(gam3$sp)}
if(l.sp4 != 0){ sp4 <- spmgcv[(l.sp2mgcv + 1):(l.sp2mgcv + l.sp3mgcv)]; names(sp4) <- names(gam4$sp)}
}
}
##########################################################
GAM <- list(gam1 = gam1, gam2 = gam2, gam3 = gam3, gam4 = gam4,
gam5 = gam5, gam6 = gam6, gam7 = gam7, gam8 = gam8, gam9 = gam9)
if( (l.sp1!=0 || l.sp2!=0 || l.sp3!=0 || l.sp4!=0 || l.sp5!=0 || l.sp6!=0 || l.sp7!=0 || l.sp8!=0) && fp==FALSE ){
L.GAM <- list(l.gam1 = length(gam1$coefficients), l.gam2 = length(gam2$coefficients), l.gam3 = length(gam3$coefficients), l.gam4 = length(gam4$coefficients),
l.gam5 = length(gam5$coefficients), l.gam6 = length(gam6$coefficients), l.gam7 = length(gam7$coefficients), l.gam8 = length(gam8$coefficients),
l.gam9 = 0)
L.SP <- list(l.sp1 = l.sp1, l.sp2 = l.sp2, l.sp3 = l.sp3, l.sp4 = l.sp4,
l.sp5 = l.sp5, l.sp6 = l.sp6, l.sp7 = l.sp7, l.sp8 = l.sp8, l.sp9 = l.sp9)
sp <- c(sp1, sp2, sp3, sp4, sp5, sp6, sp7, sp8)
qu.mag <- S.m(GAM, L.SP, L.GAM)
}
##########################################################
if(missing(parscale)) parscale <- 1
respvec <- list(y1 = y1,
y2 = y2,
y1.y2 = y1.y2,
y1.cy2 = y1.cy2,
cy1.y2 = cy1.y2,
cy1.cy2 = cy1.cy2,
cy1 = cy1,
cy = cy, univ = 0,
y00 = y00, y10 = y10, y0p = y0p, y1p = y1p)
my.env <- new.env()
my.env$signind <- 1
lsgam1 <- length(gam1$smooth)
lsgam2 <- length(gam2$smooth)
lsgam3 <- length(gam3$smooth)
lsgam4 <- length(gam4$smooth)
lsgam5 <- length(gam5$smooth)
lsgam6 <- length(gam6$smooth)
lsgam7 <- length(gam7$smooth)
lsgam8 <- length(gam8$smooth)
lsgam9 <- length(gam9$smooth)
VC <- list(lsgam1 = lsgam1, robust = FALSE, sp.fixed = NULL,K1 = NULL,
lsgam2 = lsgam2, Sl.sf = Sl.sf, sp.method = sp.method,
lsgam3 = lsgam3,
lsgam4 = lsgam4,
lsgam5 = lsgam5,
lsgam6 = lsgam6,
lsgam7 = lsgam7,
lsgam8 = lsgam8, lsgam9 = lsgam9,
X1 = X1, inde = inde,my.env=my.env,
X2 = X2,
X3 = X3,
X4 = X4,
X5 = X5,
X6 = X6,
X7 = X7,
X8 = X8,
X1.d2 = X1.d2,
X2.d2 = X2.d2,
X3.d2 = X3.d2,
X4.d2 = X4.d2,
X5.d2 = X5.d2,
X6.d2 = X6.d2,
X7.d2 = X7.d2,
X8.d2 = X8.d2,
gp1 = gp1,
gp2 = gp2,
gp3 = gp3,
gp4 = gp4,
gp5 = gp5,
gp6 = gp6,
gp7 = gp7,
gp8 = gp8,
l.sp1 = l.sp1,
l.sp2 = l.sp2,
l.sp3 = l.sp3,
l.sp4 = l.sp4,
l.sp5 = l.sp5,
l.sp6 = l.sp6,
l.sp7 = l.sp7,
l.sp8 = l.sp8,
l.sp9 = 0,
infl.fac = infl.fac,
weights = weights,
fp = fp, univ.gamls = FALSE,
hess = hess, nCa = nCa,
Model = Model, gamlssfit = gamlssfit,
end = end,
BivD = BivD, dof.st = log(dof - 2), dof = dof,
nC = nC, gc.l = gc.l, n = n, extra.regI = extra.regI,
parscale = parscale, margins = margins,
Cont = "NO", ccss = "no", m2 = m2, m3 = m3, m2d = m2d, m1d = m1d, m3d = NULL, bl = bl,
X2s = X2s, X3s = X3s, triv = FALSE, y2m = y2m,
theta.fx = theta.fx, i.rho = i.rho,
BivD2 = BivD2, cta = cta, ct = ct, zerov = -10, surv.flex = surv.flex, gp2.inf = NULL,
informative = "no",
zero.tol = 1e-02,
min.dn = min.dn, min.pr = min.pr, max.pr = max.pr,
y00 = y00, y10 = y10, y0p = y0p, y1p = y1p) # original n only needed in SemiParBIV.fit
if(gc.l == TRUE) gc()
##########################################################################################################################
if(gamlssfit == TRUE && !(margins[2] %in% bl)){
form.gamlR <- form.gaml(formula, l.flist, M, type = "biv")
gamlss2 <- eval(substitute(gamlss(form.gamlR$formula.gamlss2, data = data, weights = weights, subset = subset,
margin = margins[2], infl.fac = infl.fac,
rinit = rinit, rmax = rmax, iterlimsp = iterlimsp, tolsp = tolsp,
gc.l = gc.l, parscale = 1, extra.regI = extra.regI, drop.unused.levels = drop.unused.levels), list(weights=weights)))
# updated starting values
SP <- list(sp1 = sp1, sp2 = sp2, sp3 = sp3, sp4 = sp4, sp5 = sp5, sp6 = sp6, sp7 = sp7, sp8 = sp8)
gamls.upsvR <- gamls.upsv(gamlss1 = NULL, gamlss2, margins, M, l.flist, nstv = NULL, VC, GAM, SP, type = "biv")
sp <- gamls.upsvR$sp
start.v <- gamls.upsvR$start.v
}
##########################################################################################################################
##########################################################################################################################
if(Model %in% c("BSS", "BPO", "BPO0") || (Model == "B" && margins[2] %in% bl) ) gamlssfit <- VC$gamlssfit <- TRUE # useful for error massage and joint probs
func.opt <- func.OPT(margins, M, type = "biv")
SemiParFit <- SemiParBIV.fit(func.opt = func.opt, start.v = start.v,
rinit = rinit, rmax = rmax, iterlim = 100, iterlimsp = iterlimsp, tolsp = tolsp,
respvec = respvec, VC = VC, sp = sp, qu.mag = qu.mag)
##########################################################################################################################
# post estimation
##########################################################################################################################
SemiParFit.p <- SemiParBIV.fit.post(SemiParFit = SemiParFit, Model = Model, VC = VC, GAM)
SemiParFit <- SemiParFit.p$SemiParFit # useful for SS models, eta2 calculatons etc.
y2.m <- y2
if(margins[2] == "LN") y2.m <- exp(y2)
##########################################################################################################################
if(gc.l == TRUE) gc()
##########################################################################################################################
cov.c(SemiParFit)
##########################################################################################################################
gam1$call$data <- gam2$call$data <- gam3$call$data <- gam4$call$data <- gam5$call$data <- gam6$call$data <- gam7$call$data <- gam8$call$data <- cl$data
# for all.terms
##########################################################################################################################
# bit below useful for AT calculations when end is continuous
if( !(Model=="B" && !(margins[2] %in% bl) && end == 2) ) {dataset <- NULL; rm(data) } else { attr(data, "terms") <- NULL; dataset <- data; rm(data) }
formula.aux <- NULL
if(Model == "BSS"){
# this is for mice #
formula.aux <- formula
formula.aux[[1]] <- reformulate( attr(terms(formula.aux[[1]]), "term.labels"), response = "ry" )
environment(formula.aux[[1]]) <- environment(formula[[1]])
formula.aux[[2]] <- reformulate( attr(terms(formula.aux[[2]]), "term.labels"), response = "y" )
environment(formula.aux[[2]]) <- environment(formula[[2]])
###
}
L <- list(fit = SemiParFit$fit, dataset = dataset, formula = formula, SemiParFit = SemiParFit, mice.formula = formula.aux,
gam1 = gam1, gam2 = gam2, gam3 = gam3, gam4 = gam4, gam5 = gam5, gam6 = gam6, robust = FALSE,
gam7 = gam7, gam8 = gam8, gam9 = gam9, gam2TW = gam2TW,
coefficients = SemiParFit$fit$argument, coef.t = NULL, iterlimsp = iterlimsp,
weights = weights,
sp = SemiParFit.p$sp, iter.sp = SemiParFit$iter.sp,
l.sp1 = l.sp1, l.sp2 = l.sp2, l.sp3 = l.sp3,
l.sp4 = l.sp4, l.sp5 = l.sp5, l.sp6 = l.sp6,
l.sp7 = l.sp7, l.sp8 = l.sp8, l.sp9 = l.sp9, bl = bl,
fp = fp,
iter.if = SemiParFit$iter.if, iter.inner = SemiParFit$iter.inner,
theta = SemiParFit.p$theta,
theta.a = SemiParFit.p$theta.a,
OR = SemiParFit.p$OR,
GM = SemiParFit.p$GM,
n = n, n.sel = n.sel,
X1 = X1, X2 = X2, X3 = X3, X1.d2 = X1.d2, X2.d2 = X2.d2, X3.d2 = X3.d2,
X4 = X4, X5 = X5, X6 = X6, X7 = X7, X8 = X8, X4.d2 = X4.d2, X5.d2 = X5.d2,
X6.d2 = X6.d2, X7.d2 = X7.d2, X8.d2 = X8.d2,
He = SemiParFit.p$He, HeSh = SemiParFit.p$HeSh, Vb = SemiParFit.p$Vb, Ve = SemiParFit.p$Ve,
F = SemiParFit.p$F, F1 = SemiParFit.p$F1,
t.edf = SemiParFit.p$t.edf, edf = SemiParFit.p$edf,
edf11 = SemiParFit.p$edf11,
edf1 = SemiParFit.p$edf1, edf2 = SemiParFit.p$edf2, edf3 = SemiParFit.p$edf3,
edf4 = SemiParFit.p$edf4, edf5 = SemiParFit.p$edf5, edf6 = SemiParFit.p$edf6,
edf7 = SemiParFit.p$edf7, edf8 = SemiParFit.p$edf8,
edf1.1 = SemiParFit.p$edf1.1, edf1.2 = SemiParFit.p$edf1.2, edf1.3 = SemiParFit.p$edf1.3,
edf1.4 = SemiParFit.p$edf1.4, edf1.5 = SemiParFit.p$edf1.5, edf1.6 = SemiParFit.p$edf1.6,
edf1.7 = SemiParFit.p$edf1.7, edf1.8 = SemiParFit.p$edf1.8,
R = SemiParFit.p$R,
bs.mgfit = SemiParFit$bs.mgfit, conv.sp = SemiParFit$conv.sp,
wor.c = SemiParFit$wor.c,
p11 = SemiParFit$fit$p11, p10 = SemiParFit$fit$p10, p01 = SemiParFit$fit$p01, p00 = SemiParFit$fit$p00,
p1 = SemiParFit$fit$p1, p2 = SemiParFit$fit$p2,
eta1 = SemiParFit$fit$eta1, eta2 = SemiParFit$fit$eta2, etad = SemiParFit$fit$etad,
etas = SemiParFit$fit$etas, etan = SemiParFit$fit$etan,
y1 = y1, y2 = y2.m,
BivD = BivD, margins = margins,
logLik = SemiParFit.p$logLik,
nC = nC, hess = hess,
respvec = respvec, inde = inde,
qu.mag = qu.mag,
sigma2 = SemiParFit.p$sigma2, sigma2.a = SemiParFit.p$sigma2.a,
sigma = SemiParFit.p$sigma2, sigma.a = SemiParFit.p$sigma2.a,
nu = SemiParFit.p$nu, nu.a = SemiParFit.p$nu.a, Vb.t = SemiParFit.p$Vb.t,
gp1 = gp1, gp2 = gp2, gp3 = gp3, gp4 = gp4, gp5 = gp5, gp6 = gp6, gp7 = gp7, gp8 = gp8,
X2s = X2s, X3s = X3s, p1n=SemiParFit.p$p1n , p2n = SemiParFit.p$p2n,
VC = VC, Model = Model, magpp = SemiParFit$magpp,
gamlssfit = gamlssfit, Cont = "NO", tau = SemiParFit.p$tau,
tau.a = SemiParFit.p$tau.a, l.flist = l.flist, v1 = v1, v2 = v2, triv = FALSE, univar.gamlss = FALSE,
gamlss = gamlss2, BivD2 = BivD2, dof = dof, dof.a = dof, call = cl,
surv = FALSE, surv.flex = surv.flex)
if(BivD %in% BivD2){
L$teta1 <- SemiParFit$fit$teta1
L$teta.ind1 <- SemiParFit$fit$teta.ind1
L$teta2 <- SemiParFit$fit$teta2
L$teta.ind2 <- SemiParFit$fit$teta.ind2
L$Cop1 <- SemiParFit$fit$Cop1
L$Cop2 <- SemiParFit$fit$Cop2
}
class(L) <- c("SemiParBIV","gjrm")
L
}
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