R/overall.svG.R
In KironmoyDas/KD-STAT0035-GMupdate: Generalised Joint Regression Modelling
Defines functions
overall.svG
Documented in
overall.svG
overall.svG <- function(formula, data, ngc, margins, M, vo, gam1, gam2, type = "copR", inde = NULL, c.gam2 = NULL, gam3 = NULL, knots = NULL){
X3 = X4 = X5 = X6 = X7 = X8 = X3.d2 = X4.d2 = X5.d2 = X6.d2 = X7.d2 = X8.d2 = NULL
gp3 = gp4 = gp5 = gp6 = gp7 = gp8 = NULL
gam4 = gam5 = gam6 = gam7 = gam8 = NULL
l.sp3 = l.sp4 = l.sp5 = l.sp6 = l.sp7 = l.sp8 = 0
sp3 = sp4 = sp5 = sp6 = sp7 = sp8 = NULL
X3s = X4s = X5s = NULL
Sl.sf2 <- Sl.sf3 <- NULL
if(type != "triv") gam3 <- NULL
if(type == "triv"){
formula.eq4 <- formula[[4]]
nad <- "theta12"
formula.eq4 <- as.formula( paste(nad,"~",formula.eq4[2],sep="") )
set.seed(1)
theta12 <- rnorm(vo$n, vo$theta12, 0.001)
rm(list=".Random.seed", envir=globalenv())
gam4 <- gam(formula.eq4, data = data, gamma = ngc, subset=inde, knots = knots, drop.unused.levels = vo$drop.unused.levels)
formula.eq5 <- formula[[5]]
nad <- "theta13"
formula.eq5 <- as.formula( paste(nad,"~",formula.eq5[2],sep="") )
set.seed(1)
theta13 <- rnorm(vo$n, vo$theta13, 0.001)
rm(list=".Random.seed", envir=globalenv())
gam5 <- gam(formula.eq5, data = data, gamma = ngc, subset=inde, knots = knots, drop.unused.levels = vo$drop.unused.levels)
formula.eq6 <- formula[[6]]
nad <- "theta23"
formula.eq6 <- as.formula( paste(nad,"~",formula.eq6[2],sep="") )
set.seed(1)
theta23 <- rnorm(vo$n, vo$theta23, 0.001)
rm(list=".Random.seed", envir=globalenv())
gam6 <- gam(formula.eq6, data = data, gamma = ngc, subset=inde, knots = knots, drop.unused.levels = vo$drop.unused.levels)
l.sp5 <- length(gam5$sp)
l.sp4 <- length(gam4$sp)
l.sp6 <- length(gam6$sp)
if(l.sp4 != 0){
ngc <- 2
while( any(round(summary(gam4)$edf, 1) > 1) ) {gam4 <- gam(formula.eq4, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp5 != 0){
ngc <- 2
while( any(round(summary(gam5)$edf, 1) > 1) ) {gam5 <- gam(formula.eq5, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp6 != 0){
ngc <- 2
while( any(round(summary(gam6)$edf, 1) > 1) ) {gam6 <- gam(formula.eq6, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
X4 <- model.matrix(gam4)
X4.d2 <- dim(X4)[2]
X5 <- model.matrix(gam5)
X5.d2 <- dim(X5)[2]
X6 <- model.matrix(gam6)
X6.d2 <- dim(X6)[2]
if(l.sp4 != 0) sp4 <- gam4$sp
environment(gam4$formula) <- environment(gam2$formula)
gp4 <- gam4$nsdf
if(l.sp5 != 0) sp5 <- gam5$sp
environment(gam5$formula) <- environment(gam2$formula)
gp5 <- gam5$nsdf
if(l.sp6 != 0) sp6 <- gam6$sp
environment(gam6$formula) <- environment(gam2$formula)
gp6 <- gam6$nsdf
start.v <- c(gam1$coefficients, gam2$coefficients, gam3$coefficients, gam4$coefficients, gam5$coefficients, gam6$coefficients )
}
if(type == "biv"){
if(M$l.flist == 3){
formula.eq3 <- formula[[3]]
nad <- "theta"
formula.eq3 <- as.formula( paste(nad,"~",formula.eq3[2],sep="") )
set.seed(1)
theta <- rnorm(vo$n, vo$i.rho, 0.001)
rm(list=".Random.seed", envir=globalenv())
gam3 <- gam(formula.eq3, data = data, gamma = ngc, subset=inde, knots = knots, drop.unused.levels = vo$drop.unused.levels)
if(M$Model=="BSS"){
######
# TEST
######
X3s <- try(predict.gam(gam3, newdata = data[,-dim(data)[2]], type = "lpmatrix"), silent = TRUE)
if(any(class(X3s)=="try-error")) stop("Check that the numbers of factor variables' levels\nin the selected sample are the same as those in the complete dataset.\nRead the Details section in ?SemiParBIV for more information.")
######
}
l.sp3 <- length(gam3$sp)
if(l.sp3 != 0){
ngc <- 2
while( any(round(summary(gam3)$edf, 1) > 1) ) {gam3 <- gam(formula.eq3, data = data, gamma = ngc + 1, subset=inde, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp3 != 0) sp3 <- gam3$sp
X3 <- model.matrix(gam3)
X3.d2 <- dim(X3)[2]
environment(gam3$formula) <- environment(gam2$formula)
gp3 <- gam3$nsdf
if(M$Model == "BSS") start.v <- c( gam1$coefficients, c.gam2, gam3$coefficients )
if(M$Model != "BSS") start.v <- c( gam1$coefficients, gam2$coefficients, gam3$coefficients )
}
if(M$l.flist == 4){
formula.eq3 <- formula[[3]]
formula.eq4 <- formula[[4]]
nad1 <- "sigma2"
nad2 <- "theta"
formula.eq3 <- as.formula( paste(nad1,"~",formula.eq3[2],sep="") )
formula.eq4 <- as.formula( paste(nad2,"~",formula.eq4[2],sep="") )
set.seed(1)
sigma2 <- rnorm(vo$n, vo$log.sig2, 0.001)
theta <- rnorm(vo$n, vo$i.rho, 0.001)
rm(list=".Random.seed", envir=globalenv())
gam3 <- gam(formula.eq3, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam4 <- gam(formula.eq4, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
l.sp3 <- length(gam3$sp)
l.sp4 <- length(gam4$sp)
if(l.sp3 != 0){
ngc <- 2
while( any(round(summary(gam3)$edf, 1) > 1) ) {gam3 <- gam(formula.eq3, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp4 != 0){
ngc <- 2
while( any(round(summary(gam4)$edf, 1) > 1) ) {gam4 <- gam(formula.eq4, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
X3 <- model.matrix(gam3)
X3.d2 <- dim(X3)[2]
X4 <- model.matrix(gam4)
X4.d2 <- dim(X4)[2]
if(l.sp3 != 0) sp3 <- gam3$sp
environment(gam3$formula) <- environment(gam2$formula)
gp3 <- gam3$nsdf
if(l.sp4 != 0) sp4 <- gam4$sp
environment(gam4$formula) <- environment(gam2$formula)
gp4 <- gam4$nsdf
start.v <- c(gam1$coefficients, gam2$coefficients, gam3$coefficients, gam4$coefficients )
}
if(M$l.flist == 5){
formula.eq3 <- formula[[3]]
formula.eq4 <- formula[[4]]
formula.eq5 <- formula[[5]]
nad1 <- "sigma2"
nad2 <- "nu"
nad3 <- "theta"
formula.eq3 <- as.formula( paste(nad1,"~",formula.eq3[2],sep="") )
formula.eq4 <- as.formula( paste(nad2,"~",formula.eq4[2],sep="") )
formula.eq5 <- as.formula( paste(nad3,"~",formula.eq5[2],sep="") )
set.seed(1)
sigma2 <- rnorm(vo$n, vo$log.sig2, 0.001)
nu <- rnorm(vo$n, vo$log.nu, 0.001)
theta <- rnorm(vo$n, vo$i.rho, 0.001)
rm(list=".Random.seed", envir=globalenv())
gam3 <- gam(formula.eq3, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam4 <- gam(formula.eq4, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam5 <- gam(formula.eq5, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
l.sp3 <- length(gam3$sp)
l.sp4 <- length(gam4$sp)
l.sp5 <- length(gam5$sp)
if(l.sp3 != 0){
ngc <- 2
while( any(round(summary(gam3)$edf, 1) > 1) ) {gam3 <- gam(formula.eq3, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp4 != 0){
ngc <- 2
while( any(round(summary(gam4)$edf, 1) > 1) ) {gam4 <- gam(formula.eq4, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp5 != 0){
ngc <- 2
while( any(round(summary(gam5)$edf, 1) > 1) ) {gam5 <- gam(formula.eq5, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
X3 <- model.matrix(gam3)
X3.d2 <- dim(X3)[2]
X4 <- model.matrix(gam4)
X4.d2 <- dim(X4)[2]
X5 <- model.matrix(gam5)
X5.d2 <- dim(X5)[2]
if(l.sp3 != 0) sp3 <- gam3$sp
environment(gam3$formula) <- environment(gam2$formula)
gp3 <- gam3$nsdf
if(l.sp4 != 0) sp4 <- gam4$sp
environment(gam4$formula) <- environment(gam2$formula)
gp4 <- gam4$nsdf
if(l.sp5 != 0) sp5 <- gam5$sp
environment(gam5$formula) <- environment(gam2$formula)
gp5 <- gam5$nsdf
start.v <- c(gam1$coefficients, gam2$coefficients, gam3$coefficients, gam4$coefficients, gam5$coefficients )
}
}
############################
if(type == "copR"){
BivD <- M$BivD
if(M$surv == TRUE) BivD <- "N"
if(margins[1] %in% c(M$m2,M$m3) && margins[2] %in% c(M$m2,M$m3) && BivD == "T"){
if(margins[1] %in% c(M$m2) && margins[2] %in% c(M$m2) ){
formula.eq3 <- formula[[3]]
formula.eq4 <- formula[[4]]
formula.eq5 <- formula[[5]]
formula.eq6 <- formula[[6]]
nad2.1 <- "sigma2.1"
nad2.2 <- "sigma2.2"
nad.3 <- "dof"
nad3 <- "theta"
formula.eq3 <- as.formula( paste(nad2.1,"~",formula.eq3[2],sep="") )
formula.eq4 <- as.formula( paste(nad2.2,"~",formula.eq4[2],sep="") )
formula.eq5 <- as.formula( paste(nad.3,"~", formula.eq5[2],sep="") )
formula.eq6 <- as.formula( paste( nad3,"~",formula.eq6[2],sep="") )
set.seed(1)
sigma2.1 <- rnorm(vo$n, vo$log.sig2.1, 0.001)
sigma2.2 <- rnorm(vo$n, vo$log.sig2.2, 0.001)
dof <- rnorm(vo$n, vo$dof.st, 0.001)
theta <- rnorm(vo$n, vo$i.rho, 0.001)
rm(list=".Random.seed", envir=globalenv())
gam3 <- gam(formula.eq3, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam4 <- gam(formula.eq4, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam5 <- gam(formula.eq5, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam6 <- gam(formula.eq6, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
l.sp3 <- length(gam3$sp)
l.sp4 <- length(gam4$sp)
l.sp5 <- length(gam5$sp)
l.sp6 <- length(gam6$sp)
if(l.sp3 != 0){
ngc <- 2
while( any(round(summary(gam3)$edf, 1) > 1) ) {gam3 <- gam(formula.eq3, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp4 != 0){
ngc <- 2
while( any(round(summary(gam4)$edf, 1) > 1) ) {gam4 <- gam(formula.eq4, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp5 != 0){
ngc <- 2
while( any(round(summary(gam5)$edf, 1) > 1) ) {gam5 <- gam(formula.eq5, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp6 != 0){
ngc <- 2
while( any(round(summary(gam6)$edf, 1) > 1) ) {gam6 <- gam(formula.eq6, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
X3 <- model.matrix(gam3)
X3.d2 <- dim(X3)[2]
X4 <- model.matrix(gam4)
X4.d2 <- dim(X4)[2]
X5 <- model.matrix(gam5)
X5.d2 <- dim(X5)[2]
X6 <- model.matrix(gam6)
X6.d2 <- dim(X6)[2]
if(l.sp3 != 0) sp3 <- gam3$sp
environment(gam3$formula) <- environment(gam2$formula)
gp3 <- gam3$nsdf
if(l.sp4 != 0) sp4 <- gam4$sp
environment(gam4$formula) <- environment(gam2$formula)
gp4 <- gam4$nsdf
if(l.sp5 != 0) sp5 <- gam5$sp
environment(gam5$formula) <- environment(gam2$formula)
gp5 <- gam5$nsdf
if(l.sp6 != 0) sp6 <- gam6$sp
environment(gam6$formula) <- environment(gam2$formula)
gp6 <- gam6$nsdf
start.v <- c(gam1$coefficients, gam2$coefficients, gam3$coefficients, gam4$coefficients, gam5$coefficients, gam6$coefficients )
}
if(margins[1] %in% c(M$m3) && margins[2] %in% c(M$m3)){
formula.eq3 <- formula[[3]]
formula.eq4 <- formula[[4]]
formula.eq5 <- formula[[5]]
formula.eq6 <- formula[[6]]
formula.eq7 <- formula[[7]]
formula.eq8 <- formula[[8]]
nad2.1 <- "sigma2.1"
nad2.2 <- "sigma2.2"
nad.1 <- "nu.1"
nad.2 <- "nu.2"
nad.3 <- "dof"
nad3 <- "theta"
formula.eq3 <- as.formula( paste(nad2.1,"~",formula.eq3[2],sep="") )
formula.eq4 <- as.formula( paste(nad2.2,"~",formula.eq4[2],sep="") )
formula.eq5 <- as.formula( paste(nad.1,"~", formula.eq5[2],sep="") )
formula.eq6 <- as.formula( paste(nad.2,"~", formula.eq6[2],sep="") )
formula.eq7 <- as.formula( paste(nad.3,"~", formula.eq7[2],sep="") )
formula.eq8 <- as.formula( paste( nad3,"~",formula.eq8[2],sep="") )
set.seed(1)
sigma2.1 <- rnorm(vo$n, vo$log.sig2.1, 0.001)
sigma2.2 <- rnorm(vo$n, vo$log.sig2.2, 0.001)
nu.1 <- rnorm(vo$n, vo$log.nu.1, 0.001)
nu.2 <- rnorm(vo$n, vo$log.nu.2, 0.001)
dof <- rnorm(vo$n, vo$dof.st, 0.001)
theta <- rnorm(vo$n, vo$i.rho, 0.001)
rm(list=".Random.seed", envir=globalenv())
gam3 <- gam(formula.eq3, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam4 <- gam(formula.eq4, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam5 <- gam(formula.eq5, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam6 <- gam(formula.eq6, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam7 <- gam(formula.eq7, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam8 <- gam(formula.eq8, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
l.sp3 <- length(gam3$sp)
l.sp4 <- length(gam4$sp)
l.sp5 <- length(gam5$sp)
l.sp6 <- length(gam6$sp)
l.sp7 <- length(gam7$sp)
l.sp8 <- length(gam8$sp)
if(l.sp3 != 0){
ngc <- 2
while( any(round(summary(gam3)$edf, 1) > 1) ) {gam3 <- gam(formula.eq3, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp4 != 0){
ngc <- 2
while( any(round(summary(gam4)$edf, 1) > 1) ) {gam4 <- gam(formula.eq4, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp5 != 0){
ngc <- 2
while( any(round(summary(gam5)$edf, 1) > 1) ) {gam5 <- gam(formula.eq5, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp6 != 0){
ngc <- 2
while( any(round(summary(gam6)$edf, 1) > 1) ) {gam6 <- gam(formula.eq6, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp7 != 0){
ngc <- 2
while( any(round(summary(gam7)$edf, 1) > 1) ) {gam7 <- gam(formula.eq7, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp8 != 0){
ngc <- 2
while( any(round(summary(gam8)$edf, 1) > 1) ) {gam8 <- gam(formula.eq8, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
X3 <- model.matrix(gam3)
X3.d2 <- dim(X3)[2]
X4 <- model.matrix(gam4)
X4.d2 <- dim(X4)[2]
X5 <- model.matrix(gam5)
X5.d2 <- dim(X5)[2]
X6 <- model.matrix(gam6)
X6.d2 <- dim(X6)[2]
X7 <- model.matrix(gam7)
X7.d2 <- dim(X7)[2]
X8 <- model.matrix(gam8)
X8.d2 <- dim(X8)[2]
if(l.sp3 != 0) sp3 <- gam3$sp
environment(gam3$formula) <- environment(gam2$formula)
gp3 <- gam3$nsdf
if(l.sp4 != 0) sp4 <- gam4$sp
environment(gam4$formula) <- environment(gam2$formula)
gp4 <- gam4$nsdf
if(l.sp5 != 0) sp5 <- gam5$sp
environment(gam5$formula) <- environment(gam2$formula)
gp5 <- gam5$nsdf
if(l.sp6 != 0) sp6 <- gam6$sp
environment(gam6$formula) <- environment(gam2$formula)
gp6 <- gam6$nsdf
if(l.sp7 != 0) sp7 <- gam7$sp
environment(gam7$formula) <- environment(gam2$formula)
gp7 <- gam7$nsdf
if(l.sp8 != 0) sp8 <- gam8$sp
environment(gam8$formula) <- environment(gam2$formula)
gp8 <- gam8$nsdf
start.v <- c(gam1$coefficients, gam2$coefficients, gam3$coefficients, gam4$coefficients, gam5$coefficients, gam6$coefficients, gam7$coefficients, gam8$coefficients )
}
if(margins[1] %in% c(M$m2) && margins[2] %in% c(M$m3) ){
formula.eq3 <- formula[[3]]
formula.eq4 <- formula[[4]]
formula.eq5 <- formula[[5]]
formula.eq6 <- formula[[6]]
formula.eq7 <- formula[[7]]
nad2.1 <- "sigma2.1"
nad2.2 <- "sigma2.2"
nad.2 <- "nu.2"
nad.3 <- "dof"
nad3 <- "theta"
formula.eq3 <- as.formula( paste(nad2.1,"~",formula.eq3[2],sep="") )
formula.eq4 <- as.formula( paste(nad2.2,"~",formula.eq4[2],sep="") )
formula.eq5 <- as.formula( paste(nad.2,"~", formula.eq5[2],sep="") )
formula.eq6 <- as.formula( paste(nad.3,"~", formula.eq6[2],sep="") )
formula.eq7 <- as.formula( paste( nad3,"~", formula.eq7[2],sep="") )
set.seed(1)
sigma2.1 <- rnorm(vo$n, vo$log.sig2.1, 0.001)
sigma2.2 <- rnorm(vo$n, vo$log.sig2.2, 0.001)
nu.2 <- rnorm(vo$n, vo$log.nu.2, 0.001)
dof <- rnorm(vo$n, vo$dof.st, 0.001)
theta <- rnorm(vo$n, vo$i.rho, 0.001)
rm(list=".Random.seed", envir=globalenv())
gam3 <- gam(formula.eq3, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam4 <- gam(formula.eq4, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam5 <- gam(formula.eq5, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam6 <- gam(formula.eq6, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam7 <- gam(formula.eq7, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
l.sp3 <- length(gam3$sp)
l.sp4 <- length(gam4$sp)
l.sp5 <- length(gam5$sp)
l.sp6 <- length(gam6$sp)
l.sp7 <- length(gam7$sp)
if(l.sp3 != 0){
ngc <- 2
while( any(round(summary(gam3)$edf, 1) > 1) ) {gam3 <- gam(formula.eq3, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp4 != 0){
ngc <- 2
while( any(round(summary(gam4)$edf, 1) > 1) ) {gam4 <- gam(formula.eq4, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp5 != 0){
ngc <- 2
while( any(round(summary(gam5)$edf, 1) > 1) ) {gam5 <- gam(formula.eq5, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp6 != 0){
ngc <- 2
while( any(round(summary(gam6)$edf, 1) > 1) ) {gam6 <- gam(formula.eq6, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp7 != 0){
ngc <- 2
while( any(round(summary(gam7)$edf, 1) > 1) ) {gam7 <- gam(formula.eq7, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
X3 <- model.matrix(gam3)
X3.d2 <- dim(X3)[2]
X4 <- model.matrix(gam4)
X4.d2 <- dim(X4)[2]
X5 <- model.matrix(gam5)
X5.d2 <- dim(X5)[2]
X6 <- model.matrix(gam6)
X6.d2 <- dim(X6)[2]
X7 <- model.matrix(gam7)
X7.d2 <- dim(X7)[2]
if(l.sp3 != 0) sp3 <- gam3$sp
environment(gam3$formula) <- environment(gam2$formula)
gp3 <- gam3$nsdf
if(l.sp4 != 0) sp4 <- gam4$sp
environment(gam4$formula) <- environment(gam2$formula)
gp4 <- gam4$nsdf
if(l.sp5 != 0) sp5 <- gam5$sp
environment(gam5$formula) <- environment(gam2$formula)
gp5 <- gam5$nsdf
if(l.sp6 != 0) sp6 <- gam6$sp
environment(gam6$formula) <- environment(gam2$formula)
gp6 <- gam6$nsdf
if(l.sp7 != 0) sp7 <- gam7$sp
environment(gam7$formula) <- environment(gam2$formula)
gp7 <- gam7$nsdf
start.v <- c(gam1$coefficients, gam2$coefficients, gam3$coefficients, gam4$coefficients, gam5$coefficients, gam6$coefficients, gam7$coefficients)
}
if(margins[1] %in% c(M$m3) && margins[2] %in% c(M$m2) ){
formula.eq3 <- formula[[3]]
formula.eq4 <- formula[[4]]
formula.eq5 <- formula[[5]]
formula.eq6 <- formula[[6]]
formula.eq7 <- formula[[7]]
nad2.1 <- "sigma2.1"
nad2.2 <- "sigma2.2"
nad.1 <- "nu.1"
nad.3 <- "dof"
nad3 <- "theta"
formula.eq3 <- as.formula( paste(nad2.1,"~",formula.eq3[2],sep="") )
formula.eq4 <- as.formula( paste(nad2.2,"~",formula.eq4[2],sep="") )
formula.eq5 <- as.formula( paste(nad.1,"~", formula.eq5[2],sep="") )
formula.eq6 <- as.formula( paste(nad.3,"~", formula.eq6[2],sep="") )
formula.eq7 <- as.formula( paste( nad3,"~", formula.eq7[2],sep="") )
set.seed(1)
sigma2.1 <- rnorm(vo$n, vo$log.sig2.1, 0.001)
sigma2.2 <- rnorm(vo$n, vo$log.sig2.2, 0.001)
nu.1 <- rnorm(vo$n, vo$log.nu.1, 0.001)
dof <- rnorm(vo$n, vo$dof.st, 0.001)
theta <- rnorm(vo$n, vo$i.rho, 0.001)
rm(list=".Random.seed", envir=globalenv())
gam3 <- gam(formula.eq3, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam4 <- gam(formula.eq4, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam5 <- gam(formula.eq5, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam6 <- gam(formula.eq6, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam7 <- gam(formula.eq7, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
l.sp3 <- length(gam3$sp)
l.sp4 <- length(gam4$sp)
l.sp5 <- length(gam5$sp)
l.sp6 <- length(gam6$sp)
l.sp7 <- length(gam7$sp)
if(l.sp3 != 0){
ngc <- 2
while( any(round(summary(gam3)$edf, 1) > 1) ) {gam3 <- gam(formula.eq3, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp4 != 0){
ngc <- 2
while( any(round(summary(gam4)$edf, 1) > 1) ) {gam4 <- gam(formula.eq4, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp5 != 0){
ngc <- 2
while( any(round(summary(gam5)$edf, 1) > 1) ) {gam5 <- gam(formula.eq5, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp6 != 0){
ngc <- 2
while( any(round(summary(gam6)$edf, 1) > 1) ) {gam6 <- gam(formula.eq6, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp7 != 0){
ngc <- 2
while( any(round(summary(gam7)$edf, 1) > 1) ) {gam7 <- gam(formula.eq7, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
X3 <- model.matrix(gam3)
X3.d2 <- dim(X3)[2]
X4 <- model.matrix(gam4)
X4.d2 <- dim(X4)[2]
X5 <- model.matrix(gam5)
X5.d2 <- dim(X5)[2]
X6 <- model.matrix(gam6)
X6.d2 <- dim(X6)[2]
X7 <- model.matrix(gam7)
X7.d2 <- dim(X7)[2]
if(l.sp3 != 0) sp3 <- gam3$sp
environment(gam3$formula) <- environment(gam2$formula)
gp3 <- gam3$nsdf
if(l.sp4 != 0) sp4 <- gam4$sp
environment(gam4$formula) <- environment(gam2$formula)
gp4 <- gam4$nsdf
if(l.sp5 != 0) sp5 <- gam5$sp
environment(gam5$formula) <- environment(gam2$formula)
gp5 <- gam5$nsdf
if(l.sp6 != 0) sp6 <- gam6$sp
environment(gam6$formula) <- environment(gam2$formula)
gp6 <- gam6$nsdf
if(l.sp7 != 0) sp7 <- gam7$sp
environment(gam7$formula) <- environment(gam2$formula)
gp7 <- gam7$nsdf
start.v <- c(gam1$coefficients, gam2$coefficients, gam3$coefficients, gam4$coefficients, gam5$coefficients, gam6$coefficients, gam7$coefficients)
}
}else{
if(margins[1] %in% c(M$m1d,M$bl) && margins[2] %in% c(M$m1d,M$bl)){
formula.eq3 <- formula[[3]]
nad3 <- "theta"
formula.eq3 <- as.formula( paste( nad3,"~",formula.eq3[2],sep="") )
set.seed(1)
theta <- rnorm(vo$n, vo$i.rho, 0.001)
rm(list=".Random.seed", envir=globalenv())
gam3 <- gam(formula.eq3, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
l.sp3 <- length(gam3$sp)
if(l.sp3 != 0){
ngc <- 2
while( any(round(summary(gam3)$edf, 1) > 1) ) {gam3 <- gam(formula.eq3, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
X3 <- model.matrix(gam3)
X3.d2 <- dim(X3)[2]
if(l.sp3 != 0) sp3 <- gam3$sp
environment(gam3$formula) <- environment(gam2$formula)
gp3 <- gam3$nsdf
start.v <- c(gam1$coefficients, gam2$coefficients, gam3$coefficients )
}
if(margins[1] %in% c(M$m1d) && margins[2] %in% c(M$m2,M$m2d)){
formula.eq3 <- formula[[3]]
formula.eq4 <- formula[[4]]
nad2.2 <- "sigma2.2"
nad3 <- "theta"
formula.eq3 <- as.formula( paste(nad2.2,"~",formula.eq3[2],sep="") )
formula.eq4 <- as.formula( paste( nad3,"~",formula.eq4[2],sep="") )
set.seed(1)
sigma2.2 <- rnorm(vo$n, vo$log.sig2.2, 0.001)
theta <- rnorm(vo$n, vo$i.rho, 0.001)
rm(list=".Random.seed", envir=globalenv())
gam3 <- gam(formula.eq3, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam4 <- gam(formula.eq4, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
l.sp3 <- length(gam3$sp)
l.sp4 <- length(gam4$sp)
if(l.sp3 != 0){
ngc <- 2
while( any(round(summary(gam3)$edf, 1) > 1) ) {gam3 <- gam(formula.eq3, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp4 != 0){
ngc <- 2
while( any(round(summary(gam4)$edf, 1) > 1) ) {gam4 <- gam(formula.eq4, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
X3 <- model.matrix(gam3)
X3.d2 <- dim(X3)[2]
X4 <- model.matrix(gam4)
X4.d2 <- dim(X4)[2]
if(l.sp3 != 0) sp3 <- gam3$sp
environment(gam3$formula) <- environment(gam2$formula)
gp3 <- gam3$nsdf
if(l.sp4 != 0) sp4 <- gam4$sp
environment(gam4$formula) <- environment(gam2$formula)
gp4 <- gam4$nsdf
start.v <- c(gam1$coefficients, gam2$coefficients, gam3$coefficients, gam4$coefficients )
}
if(margins[1] %in% c(M$m1d) && margins[2] %in% c(M$m3)){
formula.eq3 <- formula[[3]]
formula.eq4 <- formula[[4]]
formula.eq5 <- formula[[5]]
nad2.2 <- "sigma2.2"
nad.2 <- "nu.2"
nad3 <- "theta"
formula.eq3 <- as.formula( paste(nad2.2,"~",formula.eq3[2],sep="") )
formula.eq4 <- as.formula( paste(nad.2,"~", formula.eq4[2],sep="") )
formula.eq5 <- as.formula( paste( nad3,"~",formula.eq5[2],sep="") )
set.seed(1)
sigma2.2 <- rnorm(vo$n, vo$log.sig2.2, 0.001)
nu.2 <- rnorm(vo$n, vo$log.nu.2, 0.001)
theta <- rnorm(vo$n, vo$i.rho, 0.001)
rm(list=".Random.seed", envir=globalenv())
gam3 <- gam(formula.eq3, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam4 <- gam(formula.eq4, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam5 <- gam(formula.eq5, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
l.sp3 <- length(gam3$sp)
l.sp4 <- length(gam4$sp)
l.sp5 <- length(gam5$sp)
if(l.sp3 != 0){
ngc <- 2
while( any(round(summary(gam3)$edf, 1) > 1) ) {gam3 <- gam(formula.eq3, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp4 != 0){
ngc <- 2
while( any(round(summary(gam4)$edf, 1) > 1) ) {gam4 <- gam(formula.eq4, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp5 != 0){
ngc <- 2
while( any(round(summary(gam5)$edf, 1) > 1) ) {gam5 <- gam(formula.eq5, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
X3 <- model.matrix(gam3)
X3.d2 <- dim(X3)[2]
X4 <- model.matrix(gam4)
X4.d2 <- dim(X4)[2]
X5 <- model.matrix(gam5)
X5.d2 <- dim(X5)[2]
if(l.sp3 != 0) sp3 <- gam3$sp
environment(gam3$formula) <- environment(gam2$formula)
gp3 <- gam3$nsdf
if(l.sp4 != 0) sp4 <- gam4$sp
environment(gam4$formula) <- environment(gam2$formula)
gp4 <- gam4$nsdf
if(l.sp5 != 0) sp5 <- gam5$sp
environment(gam5$formula) <- environment(gam2$formula)
gp5 <- gam5$nsdf
start.v <- c(gam1$coefficients, gam2$coefficients, gam3$coefficients, gam4$coefficients, gam5$coefficients )
}
if(margins[1] %in% c(M$m2,M$m2d) && margins[2] %in% c(M$m2,M$m2d)){
formula.eq3 <- formula[[3]]
formula.eq4 <- formula[[4]]
formula.eq5 <- formula[[5]]
nad2.1 <- "sigma2.1"
nad2.2 <- "sigma2.2"
nad3 <- "theta"
formula.eq3 <- as.formula( paste(nad2.1,"~",formula.eq3[2],sep="") )
formula.eq4 <- as.formula( paste(nad2.2,"~",formula.eq4[2],sep="") )
formula.eq5 <- as.formula( paste( nad3,"~",formula.eq5[2],sep="") )
set.seed(1)
sigma2.1 <- rnorm(vo$n, vo$log.sig2.1, 0.001)
sigma2.2 <- rnorm(vo$n, vo$log.sig2.2, 0.001)
theta <- rnorm(vo$n, vo$i.rho, 0.001)
rm(list=".Random.seed", envir=globalenv())
gam3 <- gam(formula.eq3, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam4 <- gam(formula.eq4, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam5 <- gam(formula.eq5, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
l.sp3 <- length(gam3$sp)
l.sp4 <- length(gam4$sp)
l.sp5 <- length(gam5$sp)
if(l.sp3 != 0){
ngc <- 2
while( any(round(summary(gam3)$edf, 1) > 1) ) {gam3 <- gam(formula.eq3, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp4 != 0){
ngc <- 2
while( any(round(summary(gam4)$edf, 1) > 1) ) {gam4 <- gam(formula.eq4, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp5 != 0){
ngc <- 2
while( any(round(summary(gam5)$edf, 1) > 1) ) {gam5 <- gam(formula.eq5, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
X3 <- model.matrix(gam3)
X3.d2 <- dim(X3)[2]
X4 <- model.matrix(gam4)
X4.d2 <- dim(X4)[2]
X5 <- model.matrix(gam5)
X5.d2 <- dim(X5)[2]
if(l.sp3 != 0) sp3 <- gam3$sp
environment(gam3$formula) <- environment(gam2$formula)
gp3 <- gam3$nsdf
if(l.sp4 != 0) sp4 <- gam4$sp
environment(gam4$formula) <- environment(gam2$formula)
gp4 <- gam4$nsdf
if(l.sp5 != 0) sp5 <- gam5$sp
environment(gam5$formula) <- environment(gam2$formula)
gp5 <- gam5$nsdf
start.v <- c(gam1$coefficients, gam2$coefficients, gam3$coefficients, gam4$coefficients, gam5$coefficients )
}
if(margins[1] %in% c(M$m2,M$m2d) && margins[2] %in% c(M$bl)){
formula.eq3 <- formula[[3]]
formula.eq4 <- formula[[4]]
nad2.1 <- "sigma2.1"
nad3 <- "theta"
formula.eq3 <- as.formula( paste(nad2.1,"~",formula.eq3[2],sep="") )
formula.eq4 <- as.formula( paste( nad3,"~",formula.eq4[2],sep="") )
set.seed(1)
sigma2.1 <- rnorm(vo$n, vo$log.sig2.1, 0.001)
theta <- rnorm(vo$n, vo$i.rho, 0.001)
rm(list=".Random.seed", envir=globalenv())
gam3 <- gam(formula.eq3, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam4 <- gam(formula.eq4, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
l.sp3 <- length(gam3$sp)
l.sp4 <- length(gam4$sp)
if(l.sp3 != 0){
ngc <- 2
while( any(round(summary(gam3)$edf, 1) > 1) ) {gam3 <- gam(formula.eq3, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp4 != 0){
ngc <- 2
while( any(round(summary(gam4)$edf, 1) > 1) ) {gam4 <- gam(formula.eq4, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
X3 <- model.matrix(gam3)
X3.d2 <- dim(X3)[2]
X4 <- model.matrix(gam4)
X4.d2 <- dim(X4)[2]
if(l.sp3 != 0) sp3 <- gam3$sp
environment(gam3$formula) <- environment(gam2$formula)
gp3 <- gam3$nsdf
if(l.sp4 != 0) sp4 <- gam4$sp
environment(gam4$formula) <- environment(gam2$formula)
gp4 <- gam4$nsdf
start.v <- c(gam1$coefficients, gam2$coefficients, gam3$coefficients, gam4$coefficients)
}
if(margins[1] %in% c(M$m3,M$m3d) && margins[2] %in% c(M$bl) ){
formula.eq3 <- formula[[3]]
formula.eq4 <- formula[[4]]
formula.eq5 <- formula[[5]]
nad2.1 <- "sigma2.1"
nad.1 <- "nu.1"
nad3 <- "theta"
formula.eq3 <- as.formula( paste(nad2.1,"~",formula.eq3[2],sep="") )
formula.eq4 <- as.formula( paste(nad.1,"~", formula.eq4[2],sep="") )
formula.eq5 <- as.formula( paste( nad3,"~",formula.eq5[2],sep="") )
set.seed(1)
sigma2.1 <- rnorm(vo$n, vo$log.sig2.1, 0.001)
nu.1 <- rnorm(vo$n, vo$log.nu.1, 0.001)
theta <- rnorm(vo$n, vo$i.rho, 0.001)
rm(list=".Random.seed", envir=globalenv())
gam3 <- gam(formula.eq3, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam4 <- gam(formula.eq4, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam5 <- gam(formula.eq5, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
l.sp3 <- length(gam3$sp)
l.sp4 <- length(gam4$sp)
l.sp5 <- length(gam5$sp)
if(l.sp3 != 0){
ngc <- 2
while( any(round(summary(gam3)$edf, 1) > 1) ) {gam3 <- gam(formula.eq3, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp4 != 0){
ngc <- 2
while( any(round(summary(gam4)$edf, 1) > 1) ) {gam4 <- gam(formula.eq4, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp5 != 0){
ngc <- 2
while( any(round(summary(gam5)$edf, 1) > 1) ) {gam5 <- gam(formula.eq5, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
X3 <- model.matrix(gam3)
X3.d2 <- dim(X3)[2]
X4 <- model.matrix(gam4)
X4.d2 <- dim(X4)[2]
X5 <- model.matrix(gam5)
X5.d2 <- dim(X5)[2]
if(l.sp3 != 0) sp3 <- gam3$sp
environment(gam3$formula) <- environment(gam2$formula)
gp3 <- gam3$nsdf
if(l.sp4 != 0) sp4 <- gam4$sp
environment(gam4$formula) <- environment(gam2$formula)
gp4 <- gam4$nsdf
if(l.sp5 != 0) sp5 <- gam5$sp
environment(gam5$formula) <- environment(gam2$formula)
gp5 <- gam5$nsdf
start.v <- c(gam1$coefficients, gam2$coefficients, gam3$coefficients, gam4$coefficients, gam5$coefficients)
}
if(margins[1] %in% c(M$m3,M$m3d) && margins[2] %in% c(M$m3,M$m3d) ){
formula.eq3 <- formula[[3]]
formula.eq4 <- formula[[4]]
formula.eq5 <- formula[[5]]
formula.eq6 <- formula[[6]]
formula.eq7 <- formula[[7]]
nad2.1 <- "sigma2.1"
nad2.2 <- "sigma2.2"
nad.1 <- "nu.1"
nad.2 <- "nu.2"
nad3 <- "theta"
formula.eq3 <- as.formula( paste(nad2.1,"~",formula.eq3[2],sep="") )
formula.eq4 <- as.formula( paste(nad2.2,"~",formula.eq4[2],sep="") )
formula.eq5 <- as.formula( paste(nad.1,"~", formula.eq5[2],sep="") )
formula.eq6 <- as.formula( paste(nad.2,"~", formula.eq6[2],sep="") )
formula.eq7 <- as.formula( paste( nad3,"~",formula.eq7[2],sep="") )
set.seed(1)
sigma2.1 <- rnorm(vo$n, vo$log.sig2.1, 0.001)
sigma2.2 <- rnorm(vo$n, vo$log.sig2.2, 0.001)
nu.1 <- rnorm(vo$n, vo$log.nu.1, 0.001)
nu.2 <- rnorm(vo$n, vo$log.nu.2, 0.001)
theta <- rnorm(vo$n, vo$i.rho, 0.001)
rm(list=".Random.seed", envir=globalenv())
gam3 <- gam(formula.eq3, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam4 <- gam(formula.eq4, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam5 <- gam(formula.eq5, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam6 <- gam(formula.eq6, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam7 <- gam(formula.eq7, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
l.sp3 <- length(gam3$sp)
l.sp4 <- length(gam4$sp)
l.sp5 <- length(gam5$sp)
l.sp6 <- length(gam6$sp)
l.sp7 <- length(gam7$sp)
if(l.sp3 != 0){
ngc <- 2
while( any(round(summary(gam3)$edf, 1) > 1) ) {gam3 <- gam(formula.eq3, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp4 != 0){
ngc <- 2
while( any(round(summary(gam4)$edf, 1) > 1) ) {gam4 <- gam(formula.eq4, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp5 != 0){
ngc <- 2
while( any(round(summary(gam5)$edf, 1) > 1) ) {gam5 <- gam(formula.eq5, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp6 != 0){
ngc <- 2
while( any(round(summary(gam6)$edf, 1) > 1) ) {gam6 <- gam(formula.eq6, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp7 != 0){
ngc <- 2
while( any(round(summary(gam7)$edf, 1) > 1) ) {gam7 <- gam(formula.eq7, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
X3 <- model.matrix(gam3)
X3.d2 <- dim(X3)[2]
X4 <- model.matrix(gam4)
X4.d2 <- dim(X4)[2]
X5 <- model.matrix(gam5)
X5.d2 <- dim(X5)[2]
X6 <- model.matrix(gam6)
X6.d2 <- dim(X6)[2]
X7 <- model.matrix(gam7)
X7.d2 <- dim(X7)[2]
if(l.sp3 != 0) sp3 <- gam3$sp
environment(gam3$formula) <- environment(gam2$formula)
gp3 <- gam3$nsdf
if(l.sp4 != 0) sp4 <- gam4$sp
environment(gam4$formula) <- environment(gam2$formula)
gp4 <- gam4$nsdf
if(l.sp5 != 0) sp5 <- gam5$sp
environment(gam5$formula) <- environment(gam2$formula)
gp5 <- gam5$nsdf
if(l.sp6 != 0) sp6 <- gam6$sp
environment(gam6$formula) <- environment(gam2$formula)
gp6 <- gam6$nsdf
if(l.sp7 != 0) sp7 <- gam7$sp
environment(gam7$formula) <- environment(gam2$formula)
gp7 <- gam7$nsdf
start.v <- c(gam1$coefficients, gam2$coefficients, gam3$coefficients, gam4$coefficients, gam5$coefficients, gam6$coefficients, gam7$coefficients )
}
if(margins[1] %in% c(M$m2,M$m2d) && margins[2] %in% c(M$m3,M$m3d) ){
formula.eq3 <- formula[[3]]
formula.eq4 <- formula[[4]]
formula.eq5 <- formula[[5]]
formula.eq6 <- formula[[6]]
nad2.1 <- "sigma2.1"
nad2.2 <- "sigma2.2"
nad.2 <- "nu.2"
nad3 <- "theta"
formula.eq3 <- as.formula( paste(nad2.1,"~",formula.eq3[2],sep="") )
formula.eq4 <- as.formula( paste(nad2.2,"~",formula.eq4[2],sep="") )
formula.eq5 <- as.formula( paste(nad.2,"~", formula.eq5[2],sep="") )
formula.eq6 <- as.formula( paste( nad3,"~",formula.eq6[2],sep="") )
set.seed(1)
sigma2.1 <- rnorm(vo$n, vo$log.sig2.1, 0.001)
sigma2.2 <- rnorm(vo$n, vo$log.sig2.2, 0.001)
nu.2 <- rnorm(vo$n, vo$log.nu.2, 0.001)
theta <- rnorm(vo$n, vo$i.rho, 0.001)
rm(list=".Random.seed", envir=globalenv())
gam3 <- gam(formula.eq3, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam4 <- gam(formula.eq4, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam5 <- gam(formula.eq5, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam6 <- gam(formula.eq6, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
l.sp3 <- length(gam3$sp)
l.sp4 <- length(gam4$sp)
l.sp5 <- length(gam5$sp)
l.sp6 <- length(gam6$sp)
if(l.sp3 != 0){
ngc <- 2
while( any(round(summary(gam3)$edf, 1) > 1) ) {gam3 <- gam(formula.eq3, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp4 != 0){
ngc <- 2
while( any(round(summary(gam4)$edf, 1) > 1) ) {gam4 <- gam(formula.eq4, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp5 != 0){
ngc <- 2
while( any(round(summary(gam5)$edf, 1) > 1) ) {gam5 <- gam(formula.eq5, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp6 != 0){
ngc <- 2
while( any(round(summary(gam6)$edf, 1) > 1) ) {gam6 <- gam(formula.eq6, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
X3 <- model.matrix(gam3)
X3.d2 <- dim(X3)[2]
X4 <- model.matrix(gam4)
X4.d2 <- dim(X4)[2]
X5 <- model.matrix(gam5)
X5.d2 <- dim(X5)[2]
X6 <- model.matrix(gam6)
X6.d2 <- dim(X6)[2]
if(l.sp3 != 0) sp3 <- gam3$sp
environment(gam3$formula) <- environment(gam2$formula)
gp3 <- gam3$nsdf
if(l.sp4 != 0) sp4 <- gam4$sp
environment(gam4$formula) <- environment(gam2$formula)
gp4 <- gam4$nsdf
if(l.sp5 != 0) sp5 <- gam5$sp
environment(gam5$formula) <- environment(gam2$formula)
gp5 <- gam5$nsdf
if(l.sp6 != 0) sp6 <- gam6$sp
environment(gam6$formula) <- environment(gam2$formula)
gp6 <- gam6$nsdf
start.v <- c(gam1$coefficients, gam2$coefficients, gam3$coefficients, gam4$coefficients, gam5$coefficients, gam6$coefficients )
}
if(margins[1] %in% c(M$m3,M$m3d) && margins[2] %in% c(M$m2,M$m2d) ){
formula.eq3 <- formula[[3]]
formula.eq4 <- formula[[4]]
formula.eq5 <- formula[[5]]
formula.eq6 <- formula[[6]]
nad2.1 <- "sigma2.1"
nad2.2 <- "sigma2.2"
nad.1 <- "nu.1"
nad3 <- "theta"
formula.eq3 <- as.formula( paste(nad2.1,"~",formula.eq3[2],sep="") )
formula.eq4 <- as.formula( paste(nad2.2,"~",formula.eq4[2],sep="") )
formula.eq5 <- as.formula( paste(nad.1,"~", formula.eq5[2],sep="") )
formula.eq6 <- as.formula( paste( nad3,"~",formula.eq6[2],sep="") )
set.seed(1)
sigma2.1 <- rnorm(vo$n, vo$log.sig2.1, 0.001)
sigma2.2 <- rnorm(vo$n, vo$log.sig2.2, 0.001)
nu.1 <- rnorm(vo$n, vo$log.nu.1, 0.001)
theta <- rnorm(vo$n, vo$i.rho, 0.001)
rm(list=".Random.seed", envir=globalenv())
gam3 <- gam(formula.eq3, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam4 <- gam(formula.eq4, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam5 <- gam(formula.eq5, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam6 <- gam(formula.eq6, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
l.sp3 <- length(gam3$sp)
l.sp4 <- length(gam4$sp)
l.sp5 <- length(gam5$sp)
l.sp6 <- length(gam6$sp)
if(l.sp3 != 0){
ngc <- 2
while( any(round(summary(gam3)$edf, 1) > 1) ) {gam3 <- gam(formula.eq3, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp4 != 0){
ngc <- 2
while( any(round(summary(gam4)$edf, 1) > 1) ) {gam4 <- gam(formula.eq4, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp5 != 0){
ngc <- 2
while( any(round(summary(gam5)$edf, 1) > 1) ) {gam5 <- gam(formula.eq5, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp6 != 0){
ngc <- 2
while( any(round(summary(gam6)$edf, 1) > 1) ) {gam6 <- gam(formula.eq6, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
X3 <- model.matrix(gam3)
X3.d2 <- dim(X3)[2]
X4 <- model.matrix(gam4)
X4.d2 <- dim(X4)[2]
X5 <- model.matrix(gam5)
X5.d2 <- dim(X5)[2]
X6 <- model.matrix(gam6)
X6.d2 <- dim(X6)[2]
if(l.sp3 != 0) sp3 <- gam3$sp
environment(gam3$formula) <- environment(gam2$formula)
gp3 <- gam3$nsdf
if(l.sp4 != 0) sp4 <- gam4$sp
environment(gam4$formula) <- environment(gam2$formula)
gp4 <- gam4$nsdf
if(l.sp5 != 0) sp5 <- gam5$sp
environment(gam5$formula) <- environment(gam2$formula)
gp5 <- gam5$nsdf
if(l.sp6 != 0) sp6 <- gam6$sp
environment(gam6$formula) <- environment(gam2$formula)
gp6 <- gam6$nsdf
start.v <- c(gam1$coefficients, gam2$coefficients, gam3$coefficients, gam4$coefficients, gam5$coefficients, gam6$coefficients )
}
}
}
if(type == "gaml"){
sp2 <- NULL
if(margins %in% c(M$m2,M$m2d)){
formula.eq2 <- formula[[2]]
nad2.1 <- "sigma2"
formula.eq2 <- as.formula( paste(nad2.1,"~",formula.eq2[2], sep="") )
set.seed(1)
sigma2 <- rnorm(vo$n, vo$log.sig2.1, 0.001)
rm(list=".Random.seed", envir=globalenv())
gam2 <- gam(formula.eq2, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
if(M$sp.method != "perf"){
gam2ff <- gam(formula.eq2, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels, fit = FALSE)
Sl.sf2 <- Sl.setup(gam2ff)
rm(gam2ff)
}
l.sp2 <- length(gam2$sp)
if(l.sp2 != 0){
ngc <- 2
while( any(round(summary(gam2)$edf, 1) > 1) ) {gam2 <- gam(formula.eq2, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
X2 <- model.matrix(gam2)
X2.d2 <- dim(X2)[2]
if(l.sp2 != 0) sp2 <- gam2$sp
environment(gam2$formula) <- environment(gam1$formula)
gp2 <- gam2$nsdf
start.v <- c(gam1$coefficients, gam2$coefficients )
}
if(margins %in% c(M$m3,M$m3d)){
formula.eq2 <- formula[[2]]
formula.eq3 <- formula[[3]]
nad2.1 <- "sigma2"
nad.1 <- "nu"
formula.eq2 <- as.formula( paste(nad2.1,"~",formula.eq2[2],sep="") )
formula.eq3 <- as.formula( paste(nad.1,"~", formula.eq3[2],sep="") )
set.seed(1)
sigma2 <- rnorm(vo$n, vo$log.sig2.1, 0.001)
nu <- rnorm(vo$n, vo$log.nu.1, 0.001)
rm(list=".Random.seed", envir=globalenv())
gam2 <- gam(formula.eq2, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam3 <- gam(formula.eq3, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
if(M$sp.method != "perf"){
gam2ff <- gam(formula.eq2, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels, fit = FALSE)
gam3ff <- gam(formula.eq3, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels, fit = FALSE)
Sl.sf2 <- Sl.setup(gam2ff); Sl.sf3 <- Sl.setup(gam3ff)
rm(gam2ff, gam3ff)
}
l.sp2 <- length(gam2$sp)
l.sp3 <- length(gam3$sp)
if(l.sp2 != 0){
ngc <- 2
while( any(round(summary(gam2)$edf, 1) > 1) ) {gam2 <- gam(formula.eq2, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp3 != 0){
ngc <- 2
while( any(round(summary(gam3)$edf, 1) > 1) ) {gam3 <- gam(formula.eq3, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
X2 <- model.matrix(gam2)
X2.d2 <- dim(X2)[2]
X3 <- model.matrix(gam3)
X3.d2 <- dim(X3)[2]
if(l.sp2 != 0) sp2 <- gam2$sp
environment(gam2$formula) <- environment(gam1$formula)
gp2 <- gam2$nsdf
if(l.sp3 != 0) sp3 <- gam3$sp
environment(gam3$formula) <- environment(gam1$formula)
gp3 <- gam3$nsdf
start.v <- c(gam1$coefficients, gam2$coefficients, gam3$coefficients )
}
}
if(type == "copSS"){
if(M$l.flist == 3){
formula.eq3 <- formula[[3]]
nad1 <- "theta"
formula.eq3 <- as.formula( paste(nad1,"~",formula.eq3[2],sep="") )
set.seed(1)
theta <- rnorm(vo$n, vo$i.rho, 0.001)
rm(list=".Random.seed", envir=globalenv())
gam3 <- gam(formula.eq3, data = data, gamma = ngc, subset=inde, knots = knots, drop.unused.levels = vo$drop.unused.levels)
######
# TEST
######
X3s <- try(predict.gam(gam3, newdata = data[,-dim(data)[2]], type = "lpmatrix"), silent = TRUE)
if(any(class(X3s)=="try-error")) stop("Check that the numbers of factor variables' levels\nin the selected sample are the same as those in the complete dataset.\nRead the Details section in ?copulaSampleSel for more information.")
######
l.sp3 <- length(gam3$sp)
if(l.sp3 != 0){
ngc <- 2
while( any(round(summary(gam3)$edf, 1) > 1) ) {gam3 <- gam(formula.eq3, data = data, gamma = ngc + 1, subset=inde, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
X3 <- model.matrix(gam3)
X3.d2 <- dim(X3)[2]
if(l.sp3 != 0) sp3 <- gam3$sp
environment(gam3$formula) <- environment(gam2$formula)
gp3 <- gam3$nsdf
start.v <- c(gam1$coefficients, c.gam2, gam3$coefficients )
}
if(M$l.flist == 4){
formula.eq3 <- formula[[3]]
formula.eq4 <- formula[[4]]
nad1 <- "sigma2"
nad2 <- "theta"
formula.eq3 <- as.formula( paste(nad1,"~",formula.eq3[2],sep="") )
formula.eq4 <- as.formula( paste(nad2,"~",formula.eq4[2],sep="") )
set.seed(1)
sigma2 <- rnorm(vo$n, vo$log.sig2.2, 0.001)
theta <- rnorm(vo$n, vo$i.rho, 0.001)
rm(list=".Random.seed", envir=globalenv())
gam3 <- gam(formula.eq3, data = data, gamma = ngc, subset=inde, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam4 <- gam(formula.eq4, data = data, gamma = ngc, subset=inde, knots = knots, drop.unused.levels = vo$drop.unused.levels)
######
# TEST
######
X3s <- try(predict.gam(gam3, newdata = data[,-dim(data)[2]], type = "lpmatrix"), silent = TRUE)
if(any(class(X3s)=="try-error")) stop("Check that the numbers of factor variables' levels\nin the selected sample are the same as those in the complete dataset.\nRead the Details section in ?copulaSampleSel for more information.")
X4s <- try(predict.gam(gam4, newdata = data[,-dim(data)[2]], type = "lpmatrix"), silent = TRUE)
if(any(class(X4s)=="try-error")) stop("Check that the numbers of factor variables' levels\nin the selected sample are the same as those in the complete dataset.\nRead the Details section in ?copulaSampleSel for more information.")
######
l.sp3 <- length(gam3$sp)
l.sp4 <- length(gam4$sp)
if(l.sp3 != 0){
ngc <- 2
while( any(round(summary(gam3)$edf, 1) > 1) ) {gam3 <- gam(formula.eq3, data = data, gamma = ngc + 1, subset=inde, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp4 != 0){
ngc <- 2
while( any(round(summary(gam4)$edf, 1) > 1) ) {gam4 <- gam(formula.eq4, data = data, gamma = ngc + 1, subset=inde, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
X3 <- model.matrix(gam3)
X3.d2 <- dim(X3)[2]
X4 <- model.matrix(gam4)
X4.d2 <- dim(X4)[2]
if(l.sp3 != 0) sp3 <- gam3$sp
environment(gam3$formula) <- environment(gam2$formula)
gp3 <- gam3$nsdf
if(l.sp4 != 0) sp4 <- gam4$sp
environment(gam4$formula) <- environment(gam2$formula)
gp4 <- gam4$nsdf
start.v <- c(gam1$coefficients, c.gam2, gam3$coefficients, gam4$coefficients )
}
if(M$l.flist == 5){
formula.eq3 <- formula[[3]]
formula.eq4 <- formula[[4]]
formula.eq5 <- formula[[5]]
nad1 <- "sigma2"
nad2 <- "nu"
nad3 <- "theta"
formula.eq3 <- as.formula( paste(nad1,"~",formula.eq3[2],sep="") )
formula.eq4 <- as.formula( paste(nad2,"~",formula.eq4[2],sep="") )
formula.eq5 <- as.formula( paste(nad3,"~",formula.eq5[2],sep="") )
set.seed(1)
sigma2 <- rnorm(vo$n, vo$log.sig2.2, 0.001)
nu <- rnorm(vo$n, vo$log.nu.2, 0.001)
theta <- rnorm(vo$n, vo$i.rho, 0.001)
rm(list=".Random.seed", envir=globalenv())
gam3 <- gam(formula.eq3, data = data, gamma = ngc, subset=inde, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam4 <- gam(formula.eq4, data = data, gamma = ngc, subset=inde, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam5 <- gam(formula.eq5, data = data, gamma = ngc, subset=inde, knots = knots, drop.unused.levels = vo$drop.unused.levels)
######
# TEST
######
X3s <- try(predict.gam(gam3, newdata = data[,-dim(data)[2]], type = "lpmatrix"), silent = TRUE)
if(any(class(X3s)=="try-error")) stop("Check that the numbers of factor variables' levels\nin the selected sample are the same as those in the complete dataset.\nRead the Details section in ?copulaSampleSel for more information.")
X4s <- try(predict.gam(gam4, newdata = data[,-dim(data)[2]], type = "lpmatrix"), silent = TRUE)
if(any(class(X4s)=="try-error")) stop("Check that the numbers of factor variables' levels\nin the selected sample are the same as those in the complete dataset.\nRead the Details section in ?copulaSampleSel for more information.")
X5s <- try(predict.gam(gam5, newdata = data[,-dim(data)[2]], type = "lpmatrix"), silent = TRUE)
if(any(class(X5s)=="try-error")) stop("Check that the numbers of factor variables' levels\nin the selected sample are the same as those in the complete dataset.\nRead the Details section in ?copulaSampleSel for more information.")
######
l.sp3 <- length(gam3$sp)
l.sp4 <- length(gam4$sp)
l.sp5 <- length(gam5$sp)
if(l.sp3 != 0){
ngc <- 2
while( any(round(summary(gam3)$edf, 1) > 1) ) {gam3 <- gam(formula.eq3, data = data, gamma = ngc + 1, subset=inde, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp4 != 0){
ngc <- 2
while( any(round(summary(gam4)$edf, 1) > 1) ) {gam4 <- gam(formula.eq4, data = data, gamma = ngc + 1, subset=inde, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp5 != 0){
ngc <- 2
while( any(round(summary(gam5)$edf, 1) > 1) ) {gam5 <- gam(formula.eq5, data = data, gamma = ngc + 1, subset=inde, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
X3 <- model.matrix(gam3)
X3.d2 <- dim(X3)[2]
X4 <- model.matrix(gam4)
X4.d2 <- dim(X4)[2]
X5 <- model.matrix(gam5)
X5.d2 <- dim(X5)[2]
if(l.sp3 != 0) sp3 <- gam3$sp
environment(gam3$formula) <- environment(gam2$formula)
gp3 <- gam3$nsdf
if(l.sp4 != 0) sp4 <- gam4$sp
environment(gam4$formula) <- environment(gam2$formula)
gp4 <- gam4$nsdf
if(l.sp5 != 0) sp5 <- gam5$sp
environment(gam5$formula) <- environment(gam2$formula)
gp5 <- gam5$nsdf
start.v <- c(gam1$coefficients, c.gam2, gam3$coefficients, gam4$coefficients, gam5$coefficients )
}
}
L <- list(start.v = start.v,
X3 = X3, X4 = X4, X5 = X5, X6 = X6, X7 = X7, X8 = X8, X3.d2 = X3.d2, X4.d2 = X4.d2, X5.d2 = X5.d2, X6.d2 = X6.d2,
X7.d2 = X7.d2, X8.d2 = X8.d2, gp3 = gp3, gp4 = gp4, gp5 = gp5, gp6 = gp6, gp7 = gp7, gp8 = gp8,
gam3 = gam3, gam4 = gam4, gam5 = gam5, gam6 = gam6, gam7 = gam7, gam8 = gam8,
l.sp3 = l.sp3, l.sp4 = l.sp4, l.sp5 = l.sp5, l.sp6 = l.sp6, l.sp7 = l.sp7, l.sp8 = l.sp8,
sp3 = sp3, sp4 = sp4, sp5 = sp5, sp6 = sp6, sp7 = sp7, sp8 = sp8, X3s = X3s, X4s = X4s, X5s = X5s, Sl.sf2 = Sl.sf2, Sl.sf3= Sl.sf3)
if(type == "gaml") {L$X2 <- X2; L$X2.d2 <- X2.d2; L$gp2 <- gp2; L$gam2 <- gam2; L$l.sp2 <- l.sp2; L$sp2 <- sp2}
L
}
KironmoyDas/KD-STAT0035-GMupdate documentation built on Feb. 15, 2021, 12:17 a.m.
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Defines functions overall.svG
Documented in overall.svG
overall.svG <- function(formula, data, ngc, margins, M, vo, gam1, gam2, type = "copR", inde = NULL, c.gam2 = NULL, gam3 = NULL, knots = NULL){
X3 = X4 = X5 = X6 = X7 = X8 = X3.d2 = X4.d2 = X5.d2 = X6.d2 = X7.d2 = X8.d2 = NULL
gp3 = gp4 = gp5 = gp6 = gp7 = gp8 = NULL
gam4 = gam5 = gam6 = gam7 = gam8 = NULL
l.sp3 = l.sp4 = l.sp5 = l.sp6 = l.sp7 = l.sp8 = 0
sp3 = sp4 = sp5 = sp6 = sp7 = sp8 = NULL
X3s = X4s = X5s = NULL
Sl.sf2 <- Sl.sf3 <- NULL
if(type != "triv") gam3 <- NULL
if(type == "triv"){
formula.eq4 <- formula[[4]]
nad <- "theta12"
formula.eq4 <- as.formula( paste(nad,"~",formula.eq4[2],sep="") )
set.seed(1)
theta12 <- rnorm(vo$n, vo$theta12, 0.001)
rm(list=".Random.seed", envir=globalenv())
gam4 <- gam(formula.eq4, data = data, gamma = ngc, subset=inde, knots = knots, drop.unused.levels = vo$drop.unused.levels)
formula.eq5 <- formula[[5]]
nad <- "theta13"
formula.eq5 <- as.formula( paste(nad,"~",formula.eq5[2],sep="") )
set.seed(1)
theta13 <- rnorm(vo$n, vo$theta13, 0.001)
rm(list=".Random.seed", envir=globalenv())
gam5 <- gam(formula.eq5, data = data, gamma = ngc, subset=inde, knots = knots, drop.unused.levels = vo$drop.unused.levels)
formula.eq6 <- formula[[6]]
nad <- "theta23"
formula.eq6 <- as.formula( paste(nad,"~",formula.eq6[2],sep="") )
set.seed(1)
theta23 <- rnorm(vo$n, vo$theta23, 0.001)
rm(list=".Random.seed", envir=globalenv())
gam6 <- gam(formula.eq6, data = data, gamma = ngc, subset=inde, knots = knots, drop.unused.levels = vo$drop.unused.levels)
l.sp5 <- length(gam5$sp)
l.sp4 <- length(gam4$sp)
l.sp6 <- length(gam6$sp)
if(l.sp4 != 0){
ngc <- 2
while( any(round(summary(gam4)$edf, 1) > 1) ) {gam4 <- gam(formula.eq4, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp5 != 0){
ngc <- 2
while( any(round(summary(gam5)$edf, 1) > 1) ) {gam5 <- gam(formula.eq5, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp6 != 0){
ngc <- 2
while( any(round(summary(gam6)$edf, 1) > 1) ) {gam6 <- gam(formula.eq6, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
X4 <- model.matrix(gam4)
X4.d2 <- dim(X4)[2]
X5 <- model.matrix(gam5)
X5.d2 <- dim(X5)[2]
X6 <- model.matrix(gam6)
X6.d2 <- dim(X6)[2]
if(l.sp4 != 0) sp4 <- gam4$sp
environment(gam4$formula) <- environment(gam2$formula)
gp4 <- gam4$nsdf
if(l.sp5 != 0) sp5 <- gam5$sp
environment(gam5$formula) <- environment(gam2$formula)
gp5 <- gam5$nsdf
if(l.sp6 != 0) sp6 <- gam6$sp
environment(gam6$formula) <- environment(gam2$formula)
gp6 <- gam6$nsdf
start.v <- c(gam1$coefficients, gam2$coefficients, gam3$coefficients, gam4$coefficients, gam5$coefficients, gam6$coefficients )
}
if(type == "biv"){
if(M$l.flist == 3){
formula.eq3 <- formula[[3]]
nad <- "theta"
formula.eq3 <- as.formula( paste(nad,"~",formula.eq3[2],sep="") )
set.seed(1)
theta <- rnorm(vo$n, vo$i.rho, 0.001)
rm(list=".Random.seed", envir=globalenv())
gam3 <- gam(formula.eq3, data = data, gamma = ngc, subset=inde, knots = knots, drop.unused.levels = vo$drop.unused.levels)
if(M$Model=="BSS"){
######
# TEST
######
X3s <- try(predict.gam(gam3, newdata = data[,-dim(data)[2]], type = "lpmatrix"), silent = TRUE)
if(any(class(X3s)=="try-error")) stop("Check that the numbers of factor variables' levels\nin the selected sample are the same as those in the complete dataset.\nRead the Details section in ?SemiParBIV for more information.")
######
}
l.sp3 <- length(gam3$sp)
if(l.sp3 != 0){
ngc <- 2
while( any(round(summary(gam3)$edf, 1) > 1) ) {gam3 <- gam(formula.eq3, data = data, gamma = ngc + 1, subset=inde, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp3 != 0) sp3 <- gam3$sp
X3 <- model.matrix(gam3)
X3.d2 <- dim(X3)[2]
environment(gam3$formula) <- environment(gam2$formula)
gp3 <- gam3$nsdf
if(M$Model == "BSS") start.v <- c( gam1$coefficients, c.gam2, gam3$coefficients )
if(M$Model != "BSS") start.v <- c( gam1$coefficients, gam2$coefficients, gam3$coefficients )
}
if(M$l.flist == 4){
formula.eq3 <- formula[[3]]
formula.eq4 <- formula[[4]]
nad1 <- "sigma2"
nad2 <- "theta"
formula.eq3 <- as.formula( paste(nad1,"~",formula.eq3[2],sep="") )
formula.eq4 <- as.formula( paste(nad2,"~",formula.eq4[2],sep="") )
set.seed(1)
sigma2 <- rnorm(vo$n, vo$log.sig2, 0.001)
theta <- rnorm(vo$n, vo$i.rho, 0.001)
rm(list=".Random.seed", envir=globalenv())
gam3 <- gam(formula.eq3, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam4 <- gam(formula.eq4, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
l.sp3 <- length(gam3$sp)
l.sp4 <- length(gam4$sp)
if(l.sp3 != 0){
ngc <- 2
while( any(round(summary(gam3)$edf, 1) > 1) ) {gam3 <- gam(formula.eq3, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp4 != 0){
ngc <- 2
while( any(round(summary(gam4)$edf, 1) > 1) ) {gam4 <- gam(formula.eq4, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
X3 <- model.matrix(gam3)
X3.d2 <- dim(X3)[2]
X4 <- model.matrix(gam4)
X4.d2 <- dim(X4)[2]
if(l.sp3 != 0) sp3 <- gam3$sp
environment(gam3$formula) <- environment(gam2$formula)
gp3 <- gam3$nsdf
if(l.sp4 != 0) sp4 <- gam4$sp
environment(gam4$formula) <- environment(gam2$formula)
gp4 <- gam4$nsdf
start.v <- c(gam1$coefficients, gam2$coefficients, gam3$coefficients, gam4$coefficients )
}
if(M$l.flist == 5){
formula.eq3 <- formula[[3]]
formula.eq4 <- formula[[4]]
formula.eq5 <- formula[[5]]
nad1 <- "sigma2"
nad2 <- "nu"
nad3 <- "theta"
formula.eq3 <- as.formula( paste(nad1,"~",formula.eq3[2],sep="") )
formula.eq4 <- as.formula( paste(nad2,"~",formula.eq4[2],sep="") )
formula.eq5 <- as.formula( paste(nad3,"~",formula.eq5[2],sep="") )
set.seed(1)
sigma2 <- rnorm(vo$n, vo$log.sig2, 0.001)
nu <- rnorm(vo$n, vo$log.nu, 0.001)
theta <- rnorm(vo$n, vo$i.rho, 0.001)
rm(list=".Random.seed", envir=globalenv())
gam3 <- gam(formula.eq3, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam4 <- gam(formula.eq4, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam5 <- gam(formula.eq5, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
l.sp3 <- length(gam3$sp)
l.sp4 <- length(gam4$sp)
l.sp5 <- length(gam5$sp)
if(l.sp3 != 0){
ngc <- 2
while( any(round(summary(gam3)$edf, 1) > 1) ) {gam3 <- gam(formula.eq3, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp4 != 0){
ngc <- 2
while( any(round(summary(gam4)$edf, 1) > 1) ) {gam4 <- gam(formula.eq4, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp5 != 0){
ngc <- 2
while( any(round(summary(gam5)$edf, 1) > 1) ) {gam5 <- gam(formula.eq5, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
X3 <- model.matrix(gam3)
X3.d2 <- dim(X3)[2]
X4 <- model.matrix(gam4)
X4.d2 <- dim(X4)[2]
X5 <- model.matrix(gam5)
X5.d2 <- dim(X5)[2]
if(l.sp3 != 0) sp3 <- gam3$sp
environment(gam3$formula) <- environment(gam2$formula)
gp3 <- gam3$nsdf
if(l.sp4 != 0) sp4 <- gam4$sp
environment(gam4$formula) <- environment(gam2$formula)
gp4 <- gam4$nsdf
if(l.sp5 != 0) sp5 <- gam5$sp
environment(gam5$formula) <- environment(gam2$formula)
gp5 <- gam5$nsdf
start.v <- c(gam1$coefficients, gam2$coefficients, gam3$coefficients, gam4$coefficients, gam5$coefficients )
}
}
############################
if(type == "copR"){
BivD <- M$BivD
if(M$surv == TRUE) BivD <- "N"
if(margins[1] %in% c(M$m2,M$m3) && margins[2] %in% c(M$m2,M$m3) && BivD == "T"){
if(margins[1] %in% c(M$m2) && margins[2] %in% c(M$m2) ){
formula.eq3 <- formula[[3]]
formula.eq4 <- formula[[4]]
formula.eq5 <- formula[[5]]
formula.eq6 <- formula[[6]]
nad2.1 <- "sigma2.1"
nad2.2 <- "sigma2.2"
nad.3 <- "dof"
nad3 <- "theta"
formula.eq3 <- as.formula( paste(nad2.1,"~",formula.eq3[2],sep="") )
formula.eq4 <- as.formula( paste(nad2.2,"~",formula.eq4[2],sep="") )
formula.eq5 <- as.formula( paste(nad.3,"~", formula.eq5[2],sep="") )
formula.eq6 <- as.formula( paste( nad3,"~",formula.eq6[2],sep="") )
set.seed(1)
sigma2.1 <- rnorm(vo$n, vo$log.sig2.1, 0.001)
sigma2.2 <- rnorm(vo$n, vo$log.sig2.2, 0.001)
dof <- rnorm(vo$n, vo$dof.st, 0.001)
theta <- rnorm(vo$n, vo$i.rho, 0.001)
rm(list=".Random.seed", envir=globalenv())
gam3 <- gam(formula.eq3, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam4 <- gam(formula.eq4, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam5 <- gam(formula.eq5, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam6 <- gam(formula.eq6, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
l.sp3 <- length(gam3$sp)
l.sp4 <- length(gam4$sp)
l.sp5 <- length(gam5$sp)
l.sp6 <- length(gam6$sp)
if(l.sp3 != 0){
ngc <- 2
while( any(round(summary(gam3)$edf, 1) > 1) ) {gam3 <- gam(formula.eq3, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp4 != 0){
ngc <- 2
while( any(round(summary(gam4)$edf, 1) > 1) ) {gam4 <- gam(formula.eq4, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp5 != 0){
ngc <- 2
while( any(round(summary(gam5)$edf, 1) > 1) ) {gam5 <- gam(formula.eq5, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp6 != 0){
ngc <- 2
while( any(round(summary(gam6)$edf, 1) > 1) ) {gam6 <- gam(formula.eq6, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
X3 <- model.matrix(gam3)
X3.d2 <- dim(X3)[2]
X4 <- model.matrix(gam4)
X4.d2 <- dim(X4)[2]
X5 <- model.matrix(gam5)
X5.d2 <- dim(X5)[2]
X6 <- model.matrix(gam6)
X6.d2 <- dim(X6)[2]
if(l.sp3 != 0) sp3 <- gam3$sp
environment(gam3$formula) <- environment(gam2$formula)
gp3 <- gam3$nsdf
if(l.sp4 != 0) sp4 <- gam4$sp
environment(gam4$formula) <- environment(gam2$formula)
gp4 <- gam4$nsdf
if(l.sp5 != 0) sp5 <- gam5$sp
environment(gam5$formula) <- environment(gam2$formula)
gp5 <- gam5$nsdf
if(l.sp6 != 0) sp6 <- gam6$sp
environment(gam6$formula) <- environment(gam2$formula)
gp6 <- gam6$nsdf
start.v <- c(gam1$coefficients, gam2$coefficients, gam3$coefficients, gam4$coefficients, gam5$coefficients, gam6$coefficients )
}
if(margins[1] %in% c(M$m3) && margins[2] %in% c(M$m3)){
formula.eq3 <- formula[[3]]
formula.eq4 <- formula[[4]]
formula.eq5 <- formula[[5]]
formula.eq6 <- formula[[6]]
formula.eq7 <- formula[[7]]
formula.eq8 <- formula[[8]]
nad2.1 <- "sigma2.1"
nad2.2 <- "sigma2.2"
nad.1 <- "nu.1"
nad.2 <- "nu.2"
nad.3 <- "dof"
nad3 <- "theta"
formula.eq3 <- as.formula( paste(nad2.1,"~",formula.eq3[2],sep="") )
formula.eq4 <- as.formula( paste(nad2.2,"~",formula.eq4[2],sep="") )
formula.eq5 <- as.formula( paste(nad.1,"~", formula.eq5[2],sep="") )
formula.eq6 <- as.formula( paste(nad.2,"~", formula.eq6[2],sep="") )
formula.eq7 <- as.formula( paste(nad.3,"~", formula.eq7[2],sep="") )
formula.eq8 <- as.formula( paste( nad3,"~",formula.eq8[2],sep="") )
set.seed(1)
sigma2.1 <- rnorm(vo$n, vo$log.sig2.1, 0.001)
sigma2.2 <- rnorm(vo$n, vo$log.sig2.2, 0.001)
nu.1 <- rnorm(vo$n, vo$log.nu.1, 0.001)
nu.2 <- rnorm(vo$n, vo$log.nu.2, 0.001)
dof <- rnorm(vo$n, vo$dof.st, 0.001)
theta <- rnorm(vo$n, vo$i.rho, 0.001)
rm(list=".Random.seed", envir=globalenv())
gam3 <- gam(formula.eq3, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam4 <- gam(formula.eq4, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam5 <- gam(formula.eq5, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam6 <- gam(formula.eq6, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam7 <- gam(formula.eq7, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam8 <- gam(formula.eq8, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
l.sp3 <- length(gam3$sp)
l.sp4 <- length(gam4$sp)
l.sp5 <- length(gam5$sp)
l.sp6 <- length(gam6$sp)
l.sp7 <- length(gam7$sp)
l.sp8 <- length(gam8$sp)
if(l.sp3 != 0){
ngc <- 2
while( any(round(summary(gam3)$edf, 1) > 1) ) {gam3 <- gam(formula.eq3, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp4 != 0){
ngc <- 2
while( any(round(summary(gam4)$edf, 1) > 1) ) {gam4 <- gam(formula.eq4, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp5 != 0){
ngc <- 2
while( any(round(summary(gam5)$edf, 1) > 1) ) {gam5 <- gam(formula.eq5, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp6 != 0){
ngc <- 2
while( any(round(summary(gam6)$edf, 1) > 1) ) {gam6 <- gam(formula.eq6, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp7 != 0){
ngc <- 2
while( any(round(summary(gam7)$edf, 1) > 1) ) {gam7 <- gam(formula.eq7, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp8 != 0){
ngc <- 2
while( any(round(summary(gam8)$edf, 1) > 1) ) {gam8 <- gam(formula.eq8, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
X3 <- model.matrix(gam3)
X3.d2 <- dim(X3)[2]
X4 <- model.matrix(gam4)
X4.d2 <- dim(X4)[2]
X5 <- model.matrix(gam5)
X5.d2 <- dim(X5)[2]
X6 <- model.matrix(gam6)
X6.d2 <- dim(X6)[2]
X7 <- model.matrix(gam7)
X7.d2 <- dim(X7)[2]
X8 <- model.matrix(gam8)
X8.d2 <- dim(X8)[2]
if(l.sp3 != 0) sp3 <- gam3$sp
environment(gam3$formula) <- environment(gam2$formula)
gp3 <- gam3$nsdf
if(l.sp4 != 0) sp4 <- gam4$sp
environment(gam4$formula) <- environment(gam2$formula)
gp4 <- gam4$nsdf
if(l.sp5 != 0) sp5 <- gam5$sp
environment(gam5$formula) <- environment(gam2$formula)
gp5 <- gam5$nsdf
if(l.sp6 != 0) sp6 <- gam6$sp
environment(gam6$formula) <- environment(gam2$formula)
gp6 <- gam6$nsdf
if(l.sp7 != 0) sp7 <- gam7$sp
environment(gam7$formula) <- environment(gam2$formula)
gp7 <- gam7$nsdf
if(l.sp8 != 0) sp8 <- gam8$sp
environment(gam8$formula) <- environment(gam2$formula)
gp8 <- gam8$nsdf
start.v <- c(gam1$coefficients, gam2$coefficients, gam3$coefficients, gam4$coefficients, gam5$coefficients, gam6$coefficients, gam7$coefficients, gam8$coefficients )
}
if(margins[1] %in% c(M$m2) && margins[2] %in% c(M$m3) ){
formula.eq3 <- formula[[3]]
formula.eq4 <- formula[[4]]
formula.eq5 <- formula[[5]]
formula.eq6 <- formula[[6]]
formula.eq7 <- formula[[7]]
nad2.1 <- "sigma2.1"
nad2.2 <- "sigma2.2"
nad.2 <- "nu.2"
nad.3 <- "dof"
nad3 <- "theta"
formula.eq3 <- as.formula( paste(nad2.1,"~",formula.eq3[2],sep="") )
formula.eq4 <- as.formula( paste(nad2.2,"~",formula.eq4[2],sep="") )
formula.eq5 <- as.formula( paste(nad.2,"~", formula.eq5[2],sep="") )
formula.eq6 <- as.formula( paste(nad.3,"~", formula.eq6[2],sep="") )
formula.eq7 <- as.formula( paste( nad3,"~", formula.eq7[2],sep="") )
set.seed(1)
sigma2.1 <- rnorm(vo$n, vo$log.sig2.1, 0.001)
sigma2.2 <- rnorm(vo$n, vo$log.sig2.2, 0.001)
nu.2 <- rnorm(vo$n, vo$log.nu.2, 0.001)
dof <- rnorm(vo$n, vo$dof.st, 0.001)
theta <- rnorm(vo$n, vo$i.rho, 0.001)
rm(list=".Random.seed", envir=globalenv())
gam3 <- gam(formula.eq3, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam4 <- gam(formula.eq4, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam5 <- gam(formula.eq5, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam6 <- gam(formula.eq6, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam7 <- gam(formula.eq7, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
l.sp3 <- length(gam3$sp)
l.sp4 <- length(gam4$sp)
l.sp5 <- length(gam5$sp)
l.sp6 <- length(gam6$sp)
l.sp7 <- length(gam7$sp)
if(l.sp3 != 0){
ngc <- 2
while( any(round(summary(gam3)$edf, 1) > 1) ) {gam3 <- gam(formula.eq3, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp4 != 0){
ngc <- 2
while( any(round(summary(gam4)$edf, 1) > 1) ) {gam4 <- gam(formula.eq4, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp5 != 0){
ngc <- 2
while( any(round(summary(gam5)$edf, 1) > 1) ) {gam5 <- gam(formula.eq5, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp6 != 0){
ngc <- 2
while( any(round(summary(gam6)$edf, 1) > 1) ) {gam6 <- gam(formula.eq6, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp7 != 0){
ngc <- 2
while( any(round(summary(gam7)$edf, 1) > 1) ) {gam7 <- gam(formula.eq7, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
X3 <- model.matrix(gam3)
X3.d2 <- dim(X3)[2]
X4 <- model.matrix(gam4)
X4.d2 <- dim(X4)[2]
X5 <- model.matrix(gam5)
X5.d2 <- dim(X5)[2]
X6 <- model.matrix(gam6)
X6.d2 <- dim(X6)[2]
X7 <- model.matrix(gam7)
X7.d2 <- dim(X7)[2]
if(l.sp3 != 0) sp3 <- gam3$sp
environment(gam3$formula) <- environment(gam2$formula)
gp3 <- gam3$nsdf
if(l.sp4 != 0) sp4 <- gam4$sp
environment(gam4$formula) <- environment(gam2$formula)
gp4 <- gam4$nsdf
if(l.sp5 != 0) sp5 <- gam5$sp
environment(gam5$formula) <- environment(gam2$formula)
gp5 <- gam5$nsdf
if(l.sp6 != 0) sp6 <- gam6$sp
environment(gam6$formula) <- environment(gam2$formula)
gp6 <- gam6$nsdf
if(l.sp7 != 0) sp7 <- gam7$sp
environment(gam7$formula) <- environment(gam2$formula)
gp7 <- gam7$nsdf
start.v <- c(gam1$coefficients, gam2$coefficients, gam3$coefficients, gam4$coefficients, gam5$coefficients, gam6$coefficients, gam7$coefficients)
}
if(margins[1] %in% c(M$m3) && margins[2] %in% c(M$m2) ){
formula.eq3 <- formula[[3]]
formula.eq4 <- formula[[4]]
formula.eq5 <- formula[[5]]
formula.eq6 <- formula[[6]]
formula.eq7 <- formula[[7]]
nad2.1 <- "sigma2.1"
nad2.2 <- "sigma2.2"
nad.1 <- "nu.1"
nad.3 <- "dof"
nad3 <- "theta"
formula.eq3 <- as.formula( paste(nad2.1,"~",formula.eq3[2],sep="") )
formula.eq4 <- as.formula( paste(nad2.2,"~",formula.eq4[2],sep="") )
formula.eq5 <- as.formula( paste(nad.1,"~", formula.eq5[2],sep="") )
formula.eq6 <- as.formula( paste(nad.3,"~", formula.eq6[2],sep="") )
formula.eq7 <- as.formula( paste( nad3,"~", formula.eq7[2],sep="") )
set.seed(1)
sigma2.1 <- rnorm(vo$n, vo$log.sig2.1, 0.001)
sigma2.2 <- rnorm(vo$n, vo$log.sig2.2, 0.001)
nu.1 <- rnorm(vo$n, vo$log.nu.1, 0.001)
dof <- rnorm(vo$n, vo$dof.st, 0.001)
theta <- rnorm(vo$n, vo$i.rho, 0.001)
rm(list=".Random.seed", envir=globalenv())
gam3 <- gam(formula.eq3, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam4 <- gam(formula.eq4, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam5 <- gam(formula.eq5, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam6 <- gam(formula.eq6, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam7 <- gam(formula.eq7, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
l.sp3 <- length(gam3$sp)
l.sp4 <- length(gam4$sp)
l.sp5 <- length(gam5$sp)
l.sp6 <- length(gam6$sp)
l.sp7 <- length(gam7$sp)
if(l.sp3 != 0){
ngc <- 2
while( any(round(summary(gam3)$edf, 1) > 1) ) {gam3 <- gam(formula.eq3, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp4 != 0){
ngc <- 2
while( any(round(summary(gam4)$edf, 1) > 1) ) {gam4 <- gam(formula.eq4, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp5 != 0){
ngc <- 2
while( any(round(summary(gam5)$edf, 1) > 1) ) {gam5 <- gam(formula.eq5, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp6 != 0){
ngc <- 2
while( any(round(summary(gam6)$edf, 1) > 1) ) {gam6 <- gam(formula.eq6, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp7 != 0){
ngc <- 2
while( any(round(summary(gam7)$edf, 1) > 1) ) {gam7 <- gam(formula.eq7, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
X3 <- model.matrix(gam3)
X3.d2 <- dim(X3)[2]
X4 <- model.matrix(gam4)
X4.d2 <- dim(X4)[2]
X5 <- model.matrix(gam5)
X5.d2 <- dim(X5)[2]
X6 <- model.matrix(gam6)
X6.d2 <- dim(X6)[2]
X7 <- model.matrix(gam7)
X7.d2 <- dim(X7)[2]
if(l.sp3 != 0) sp3 <- gam3$sp
environment(gam3$formula) <- environment(gam2$formula)
gp3 <- gam3$nsdf
if(l.sp4 != 0) sp4 <- gam4$sp
environment(gam4$formula) <- environment(gam2$formula)
gp4 <- gam4$nsdf
if(l.sp5 != 0) sp5 <- gam5$sp
environment(gam5$formula) <- environment(gam2$formula)
gp5 <- gam5$nsdf
if(l.sp6 != 0) sp6 <- gam6$sp
environment(gam6$formula) <- environment(gam2$formula)
gp6 <- gam6$nsdf
if(l.sp7 != 0) sp7 <- gam7$sp
environment(gam7$formula) <- environment(gam2$formula)
gp7 <- gam7$nsdf
start.v <- c(gam1$coefficients, gam2$coefficients, gam3$coefficients, gam4$coefficients, gam5$coefficients, gam6$coefficients, gam7$coefficients)
}
}else{
if(margins[1] %in% c(M$m1d,M$bl) && margins[2] %in% c(M$m1d,M$bl)){
formula.eq3 <- formula[[3]]
nad3 <- "theta"
formula.eq3 <- as.formula( paste( nad3,"~",formula.eq3[2],sep="") )
set.seed(1)
theta <- rnorm(vo$n, vo$i.rho, 0.001)
rm(list=".Random.seed", envir=globalenv())
gam3 <- gam(formula.eq3, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
l.sp3 <- length(gam3$sp)
if(l.sp3 != 0){
ngc <- 2
while( any(round(summary(gam3)$edf, 1) > 1) ) {gam3 <- gam(formula.eq3, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
X3 <- model.matrix(gam3)
X3.d2 <- dim(X3)[2]
if(l.sp3 != 0) sp3 <- gam3$sp
environment(gam3$formula) <- environment(gam2$formula)
gp3 <- gam3$nsdf
start.v <- c(gam1$coefficients, gam2$coefficients, gam3$coefficients )
}
if(margins[1] %in% c(M$m1d) && margins[2] %in% c(M$m2,M$m2d)){
formula.eq3 <- formula[[3]]
formula.eq4 <- formula[[4]]
nad2.2 <- "sigma2.2"
nad3 <- "theta"
formula.eq3 <- as.formula( paste(nad2.2,"~",formula.eq3[2],sep="") )
formula.eq4 <- as.formula( paste( nad3,"~",formula.eq4[2],sep="") )
set.seed(1)
sigma2.2 <- rnorm(vo$n, vo$log.sig2.2, 0.001)
theta <- rnorm(vo$n, vo$i.rho, 0.001)
rm(list=".Random.seed", envir=globalenv())
gam3 <- gam(formula.eq3, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam4 <- gam(formula.eq4, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
l.sp3 <- length(gam3$sp)
l.sp4 <- length(gam4$sp)
if(l.sp3 != 0){
ngc <- 2
while( any(round(summary(gam3)$edf, 1) > 1) ) {gam3 <- gam(formula.eq3, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp4 != 0){
ngc <- 2
while( any(round(summary(gam4)$edf, 1) > 1) ) {gam4 <- gam(formula.eq4, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
X3 <- model.matrix(gam3)
X3.d2 <- dim(X3)[2]
X4 <- model.matrix(gam4)
X4.d2 <- dim(X4)[2]
if(l.sp3 != 0) sp3 <- gam3$sp
environment(gam3$formula) <- environment(gam2$formula)
gp3 <- gam3$nsdf
if(l.sp4 != 0) sp4 <- gam4$sp
environment(gam4$formula) <- environment(gam2$formula)
gp4 <- gam4$nsdf
start.v <- c(gam1$coefficients, gam2$coefficients, gam3$coefficients, gam4$coefficients )
}
if(margins[1] %in% c(M$m1d) && margins[2] %in% c(M$m3)){
formula.eq3 <- formula[[3]]
formula.eq4 <- formula[[4]]
formula.eq5 <- formula[[5]]
nad2.2 <- "sigma2.2"
nad.2 <- "nu.2"
nad3 <- "theta"
formula.eq3 <- as.formula( paste(nad2.2,"~",formula.eq3[2],sep="") )
formula.eq4 <- as.formula( paste(nad.2,"~", formula.eq4[2],sep="") )
formula.eq5 <- as.formula( paste( nad3,"~",formula.eq5[2],sep="") )
set.seed(1)
sigma2.2 <- rnorm(vo$n, vo$log.sig2.2, 0.001)
nu.2 <- rnorm(vo$n, vo$log.nu.2, 0.001)
theta <- rnorm(vo$n, vo$i.rho, 0.001)
rm(list=".Random.seed", envir=globalenv())
gam3 <- gam(formula.eq3, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam4 <- gam(formula.eq4, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam5 <- gam(formula.eq5, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
l.sp3 <- length(gam3$sp)
l.sp4 <- length(gam4$sp)
l.sp5 <- length(gam5$sp)
if(l.sp3 != 0){
ngc <- 2
while( any(round(summary(gam3)$edf, 1) > 1) ) {gam3 <- gam(formula.eq3, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp4 != 0){
ngc <- 2
while( any(round(summary(gam4)$edf, 1) > 1) ) {gam4 <- gam(formula.eq4, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp5 != 0){
ngc <- 2
while( any(round(summary(gam5)$edf, 1) > 1) ) {gam5 <- gam(formula.eq5, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
X3 <- model.matrix(gam3)
X3.d2 <- dim(X3)[2]
X4 <- model.matrix(gam4)
X4.d2 <- dim(X4)[2]
X5 <- model.matrix(gam5)
X5.d2 <- dim(X5)[2]
if(l.sp3 != 0) sp3 <- gam3$sp
environment(gam3$formula) <- environment(gam2$formula)
gp3 <- gam3$nsdf
if(l.sp4 != 0) sp4 <- gam4$sp
environment(gam4$formula) <- environment(gam2$formula)
gp4 <- gam4$nsdf
if(l.sp5 != 0) sp5 <- gam5$sp
environment(gam5$formula) <- environment(gam2$formula)
gp5 <- gam5$nsdf
start.v <- c(gam1$coefficients, gam2$coefficients, gam3$coefficients, gam4$coefficients, gam5$coefficients )
}
if(margins[1] %in% c(M$m2,M$m2d) && margins[2] %in% c(M$m2,M$m2d)){
formula.eq3 <- formula[[3]]
formula.eq4 <- formula[[4]]
formula.eq5 <- formula[[5]]
nad2.1 <- "sigma2.1"
nad2.2 <- "sigma2.2"
nad3 <- "theta"
formula.eq3 <- as.formula( paste(nad2.1,"~",formula.eq3[2],sep="") )
formula.eq4 <- as.formula( paste(nad2.2,"~",formula.eq4[2],sep="") )
formula.eq5 <- as.formula( paste( nad3,"~",formula.eq5[2],sep="") )
set.seed(1)
sigma2.1 <- rnorm(vo$n, vo$log.sig2.1, 0.001)
sigma2.2 <- rnorm(vo$n, vo$log.sig2.2, 0.001)
theta <- rnorm(vo$n, vo$i.rho, 0.001)
rm(list=".Random.seed", envir=globalenv())
gam3 <- gam(formula.eq3, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam4 <- gam(formula.eq4, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam5 <- gam(formula.eq5, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
l.sp3 <- length(gam3$sp)
l.sp4 <- length(gam4$sp)
l.sp5 <- length(gam5$sp)
if(l.sp3 != 0){
ngc <- 2
while( any(round(summary(gam3)$edf, 1) > 1) ) {gam3 <- gam(formula.eq3, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp4 != 0){
ngc <- 2
while( any(round(summary(gam4)$edf, 1) > 1) ) {gam4 <- gam(formula.eq4, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp5 != 0){
ngc <- 2
while( any(round(summary(gam5)$edf, 1) > 1) ) {gam5 <- gam(formula.eq5, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
X3 <- model.matrix(gam3)
X3.d2 <- dim(X3)[2]
X4 <- model.matrix(gam4)
X4.d2 <- dim(X4)[2]
X5 <- model.matrix(gam5)
X5.d2 <- dim(X5)[2]
if(l.sp3 != 0) sp3 <- gam3$sp
environment(gam3$formula) <- environment(gam2$formula)
gp3 <- gam3$nsdf
if(l.sp4 != 0) sp4 <- gam4$sp
environment(gam4$formula) <- environment(gam2$formula)
gp4 <- gam4$nsdf
if(l.sp5 != 0) sp5 <- gam5$sp
environment(gam5$formula) <- environment(gam2$formula)
gp5 <- gam5$nsdf
start.v <- c(gam1$coefficients, gam2$coefficients, gam3$coefficients, gam4$coefficients, gam5$coefficients )
}
if(margins[1] %in% c(M$m2,M$m2d) && margins[2] %in% c(M$bl)){
formula.eq3 <- formula[[3]]
formula.eq4 <- formula[[4]]
nad2.1 <- "sigma2.1"
nad3 <- "theta"
formula.eq3 <- as.formula( paste(nad2.1,"~",formula.eq3[2],sep="") )
formula.eq4 <- as.formula( paste( nad3,"~",formula.eq4[2],sep="") )
set.seed(1)
sigma2.1 <- rnorm(vo$n, vo$log.sig2.1, 0.001)
theta <- rnorm(vo$n, vo$i.rho, 0.001)
rm(list=".Random.seed", envir=globalenv())
gam3 <- gam(formula.eq3, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam4 <- gam(formula.eq4, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
l.sp3 <- length(gam3$sp)
l.sp4 <- length(gam4$sp)
if(l.sp3 != 0){
ngc <- 2
while( any(round(summary(gam3)$edf, 1) > 1) ) {gam3 <- gam(formula.eq3, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp4 != 0){
ngc <- 2
while( any(round(summary(gam4)$edf, 1) > 1) ) {gam4 <- gam(formula.eq4, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
X3 <- model.matrix(gam3)
X3.d2 <- dim(X3)[2]
X4 <- model.matrix(gam4)
X4.d2 <- dim(X4)[2]
if(l.sp3 != 0) sp3 <- gam3$sp
environment(gam3$formula) <- environment(gam2$formula)
gp3 <- gam3$nsdf
if(l.sp4 != 0) sp4 <- gam4$sp
environment(gam4$formula) <- environment(gam2$formula)
gp4 <- gam4$nsdf
start.v <- c(gam1$coefficients, gam2$coefficients, gam3$coefficients, gam4$coefficients)
}
if(margins[1] %in% c(M$m3,M$m3d) && margins[2] %in% c(M$bl) ){
formula.eq3 <- formula[[3]]
formula.eq4 <- formula[[4]]
formula.eq5 <- formula[[5]]
nad2.1 <- "sigma2.1"
nad.1 <- "nu.1"
nad3 <- "theta"
formula.eq3 <- as.formula( paste(nad2.1,"~",formula.eq3[2],sep="") )
formula.eq4 <- as.formula( paste(nad.1,"~", formula.eq4[2],sep="") )
formula.eq5 <- as.formula( paste( nad3,"~",formula.eq5[2],sep="") )
set.seed(1)
sigma2.1 <- rnorm(vo$n, vo$log.sig2.1, 0.001)
nu.1 <- rnorm(vo$n, vo$log.nu.1, 0.001)
theta <- rnorm(vo$n, vo$i.rho, 0.001)
rm(list=".Random.seed", envir=globalenv())
gam3 <- gam(formula.eq3, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam4 <- gam(formula.eq4, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam5 <- gam(formula.eq5, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
l.sp3 <- length(gam3$sp)
l.sp4 <- length(gam4$sp)
l.sp5 <- length(gam5$sp)
if(l.sp3 != 0){
ngc <- 2
while( any(round(summary(gam3)$edf, 1) > 1) ) {gam3 <- gam(formula.eq3, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp4 != 0){
ngc <- 2
while( any(round(summary(gam4)$edf, 1) > 1) ) {gam4 <- gam(formula.eq4, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp5 != 0){
ngc <- 2
while( any(round(summary(gam5)$edf, 1) > 1) ) {gam5 <- gam(formula.eq5, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
X3 <- model.matrix(gam3)
X3.d2 <- dim(X3)[2]
X4 <- model.matrix(gam4)
X4.d2 <- dim(X4)[2]
X5 <- model.matrix(gam5)
X5.d2 <- dim(X5)[2]
if(l.sp3 != 0) sp3 <- gam3$sp
environment(gam3$formula) <- environment(gam2$formula)
gp3 <- gam3$nsdf
if(l.sp4 != 0) sp4 <- gam4$sp
environment(gam4$formula) <- environment(gam2$formula)
gp4 <- gam4$nsdf
if(l.sp5 != 0) sp5 <- gam5$sp
environment(gam5$formula) <- environment(gam2$formula)
gp5 <- gam5$nsdf
start.v <- c(gam1$coefficients, gam2$coefficients, gam3$coefficients, gam4$coefficients, gam5$coefficients)
}
if(margins[1] %in% c(M$m3,M$m3d) && margins[2] %in% c(M$m3,M$m3d) ){
formula.eq3 <- formula[[3]]
formula.eq4 <- formula[[4]]
formula.eq5 <- formula[[5]]
formula.eq6 <- formula[[6]]
formula.eq7 <- formula[[7]]
nad2.1 <- "sigma2.1"
nad2.2 <- "sigma2.2"
nad.1 <- "nu.1"
nad.2 <- "nu.2"
nad3 <- "theta"
formula.eq3 <- as.formula( paste(nad2.1,"~",formula.eq3[2],sep="") )
formula.eq4 <- as.formula( paste(nad2.2,"~",formula.eq4[2],sep="") )
formula.eq5 <- as.formula( paste(nad.1,"~", formula.eq5[2],sep="") )
formula.eq6 <- as.formula( paste(nad.2,"~", formula.eq6[2],sep="") )
formula.eq7 <- as.formula( paste( nad3,"~",formula.eq7[2],sep="") )
set.seed(1)
sigma2.1 <- rnorm(vo$n, vo$log.sig2.1, 0.001)
sigma2.2 <- rnorm(vo$n, vo$log.sig2.2, 0.001)
nu.1 <- rnorm(vo$n, vo$log.nu.1, 0.001)
nu.2 <- rnorm(vo$n, vo$log.nu.2, 0.001)
theta <- rnorm(vo$n, vo$i.rho, 0.001)
rm(list=".Random.seed", envir=globalenv())
gam3 <- gam(formula.eq3, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam4 <- gam(formula.eq4, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam5 <- gam(formula.eq5, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam6 <- gam(formula.eq6, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam7 <- gam(formula.eq7, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
l.sp3 <- length(gam3$sp)
l.sp4 <- length(gam4$sp)
l.sp5 <- length(gam5$sp)
l.sp6 <- length(gam6$sp)
l.sp7 <- length(gam7$sp)
if(l.sp3 != 0){
ngc <- 2
while( any(round(summary(gam3)$edf, 1) > 1) ) {gam3 <- gam(formula.eq3, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp4 != 0){
ngc <- 2
while( any(round(summary(gam4)$edf, 1) > 1) ) {gam4 <- gam(formula.eq4, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp5 != 0){
ngc <- 2
while( any(round(summary(gam5)$edf, 1) > 1) ) {gam5 <- gam(formula.eq5, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp6 != 0){
ngc <- 2
while( any(round(summary(gam6)$edf, 1) > 1) ) {gam6 <- gam(formula.eq6, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp7 != 0){
ngc <- 2
while( any(round(summary(gam7)$edf, 1) > 1) ) {gam7 <- gam(formula.eq7, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
X3 <- model.matrix(gam3)
X3.d2 <- dim(X3)[2]
X4 <- model.matrix(gam4)
X4.d2 <- dim(X4)[2]
X5 <- model.matrix(gam5)
X5.d2 <- dim(X5)[2]
X6 <- model.matrix(gam6)
X6.d2 <- dim(X6)[2]
X7 <- model.matrix(gam7)
X7.d2 <- dim(X7)[2]
if(l.sp3 != 0) sp3 <- gam3$sp
environment(gam3$formula) <- environment(gam2$formula)
gp3 <- gam3$nsdf
if(l.sp4 != 0) sp4 <- gam4$sp
environment(gam4$formula) <- environment(gam2$formula)
gp4 <- gam4$nsdf
if(l.sp5 != 0) sp5 <- gam5$sp
environment(gam5$formula) <- environment(gam2$formula)
gp5 <- gam5$nsdf
if(l.sp6 != 0) sp6 <- gam6$sp
environment(gam6$formula) <- environment(gam2$formula)
gp6 <- gam6$nsdf
if(l.sp7 != 0) sp7 <- gam7$sp
environment(gam7$formula) <- environment(gam2$formula)
gp7 <- gam7$nsdf
start.v <- c(gam1$coefficients, gam2$coefficients, gam3$coefficients, gam4$coefficients, gam5$coefficients, gam6$coefficients, gam7$coefficients )
}
if(margins[1] %in% c(M$m2,M$m2d) && margins[2] %in% c(M$m3,M$m3d) ){
formula.eq3 <- formula[[3]]
formula.eq4 <- formula[[4]]
formula.eq5 <- formula[[5]]
formula.eq6 <- formula[[6]]
nad2.1 <- "sigma2.1"
nad2.2 <- "sigma2.2"
nad.2 <- "nu.2"
nad3 <- "theta"
formula.eq3 <- as.formula( paste(nad2.1,"~",formula.eq3[2],sep="") )
formula.eq4 <- as.formula( paste(nad2.2,"~",formula.eq4[2],sep="") )
formula.eq5 <- as.formula( paste(nad.2,"~", formula.eq5[2],sep="") )
formula.eq6 <- as.formula( paste( nad3,"~",formula.eq6[2],sep="") )
set.seed(1)
sigma2.1 <- rnorm(vo$n, vo$log.sig2.1, 0.001)
sigma2.2 <- rnorm(vo$n, vo$log.sig2.2, 0.001)
nu.2 <- rnorm(vo$n, vo$log.nu.2, 0.001)
theta <- rnorm(vo$n, vo$i.rho, 0.001)
rm(list=".Random.seed", envir=globalenv())
gam3 <- gam(formula.eq3, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam4 <- gam(formula.eq4, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam5 <- gam(formula.eq5, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam6 <- gam(formula.eq6, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
l.sp3 <- length(gam3$sp)
l.sp4 <- length(gam4$sp)
l.sp5 <- length(gam5$sp)
l.sp6 <- length(gam6$sp)
if(l.sp3 != 0){
ngc <- 2
while( any(round(summary(gam3)$edf, 1) > 1) ) {gam3 <- gam(formula.eq3, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp4 != 0){
ngc <- 2
while( any(round(summary(gam4)$edf, 1) > 1) ) {gam4 <- gam(formula.eq4, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp5 != 0){
ngc <- 2
while( any(round(summary(gam5)$edf, 1) > 1) ) {gam5 <- gam(formula.eq5, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp6 != 0){
ngc <- 2
while( any(round(summary(gam6)$edf, 1) > 1) ) {gam6 <- gam(formula.eq6, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
X3 <- model.matrix(gam3)
X3.d2 <- dim(X3)[2]
X4 <- model.matrix(gam4)
X4.d2 <- dim(X4)[2]
X5 <- model.matrix(gam5)
X5.d2 <- dim(X5)[2]
X6 <- model.matrix(gam6)
X6.d2 <- dim(X6)[2]
if(l.sp3 != 0) sp3 <- gam3$sp
environment(gam3$formula) <- environment(gam2$formula)
gp3 <- gam3$nsdf
if(l.sp4 != 0) sp4 <- gam4$sp
environment(gam4$formula) <- environment(gam2$formula)
gp4 <- gam4$nsdf
if(l.sp5 != 0) sp5 <- gam5$sp
environment(gam5$formula) <- environment(gam2$formula)
gp5 <- gam5$nsdf
if(l.sp6 != 0) sp6 <- gam6$sp
environment(gam6$formula) <- environment(gam2$formula)
gp6 <- gam6$nsdf
start.v <- c(gam1$coefficients, gam2$coefficients, gam3$coefficients, gam4$coefficients, gam5$coefficients, gam6$coefficients )
}
if(margins[1] %in% c(M$m3,M$m3d) && margins[2] %in% c(M$m2,M$m2d) ){
formula.eq3 <- formula[[3]]
formula.eq4 <- formula[[4]]
formula.eq5 <- formula[[5]]
formula.eq6 <- formula[[6]]
nad2.1 <- "sigma2.1"
nad2.2 <- "sigma2.2"
nad.1 <- "nu.1"
nad3 <- "theta"
formula.eq3 <- as.formula( paste(nad2.1,"~",formula.eq3[2],sep="") )
formula.eq4 <- as.formula( paste(nad2.2,"~",formula.eq4[2],sep="") )
formula.eq5 <- as.formula( paste(nad.1,"~", formula.eq5[2],sep="") )
formula.eq6 <- as.formula( paste( nad3,"~",formula.eq6[2],sep="") )
set.seed(1)
sigma2.1 <- rnorm(vo$n, vo$log.sig2.1, 0.001)
sigma2.2 <- rnorm(vo$n, vo$log.sig2.2, 0.001)
nu.1 <- rnorm(vo$n, vo$log.nu.1, 0.001)
theta <- rnorm(vo$n, vo$i.rho, 0.001)
rm(list=".Random.seed", envir=globalenv())
gam3 <- gam(formula.eq3, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam4 <- gam(formula.eq4, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam5 <- gam(formula.eq5, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam6 <- gam(formula.eq6, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
l.sp3 <- length(gam3$sp)
l.sp4 <- length(gam4$sp)
l.sp5 <- length(gam5$sp)
l.sp6 <- length(gam6$sp)
if(l.sp3 != 0){
ngc <- 2
while( any(round(summary(gam3)$edf, 1) > 1) ) {gam3 <- gam(formula.eq3, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp4 != 0){
ngc <- 2
while( any(round(summary(gam4)$edf, 1) > 1) ) {gam4 <- gam(formula.eq4, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp5 != 0){
ngc <- 2
while( any(round(summary(gam5)$edf, 1) > 1) ) {gam5 <- gam(formula.eq5, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp6 != 0){
ngc <- 2
while( any(round(summary(gam6)$edf, 1) > 1) ) {gam6 <- gam(formula.eq6, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
X3 <- model.matrix(gam3)
X3.d2 <- dim(X3)[2]
X4 <- model.matrix(gam4)
X4.d2 <- dim(X4)[2]
X5 <- model.matrix(gam5)
X5.d2 <- dim(X5)[2]
X6 <- model.matrix(gam6)
X6.d2 <- dim(X6)[2]
if(l.sp3 != 0) sp3 <- gam3$sp
environment(gam3$formula) <- environment(gam2$formula)
gp3 <- gam3$nsdf
if(l.sp4 != 0) sp4 <- gam4$sp
environment(gam4$formula) <- environment(gam2$formula)
gp4 <- gam4$nsdf
if(l.sp5 != 0) sp5 <- gam5$sp
environment(gam5$formula) <- environment(gam2$formula)
gp5 <- gam5$nsdf
if(l.sp6 != 0) sp6 <- gam6$sp
environment(gam6$formula) <- environment(gam2$formula)
gp6 <- gam6$nsdf
start.v <- c(gam1$coefficients, gam2$coefficients, gam3$coefficients, gam4$coefficients, gam5$coefficients, gam6$coefficients )
}
}
}
if(type == "gaml"){
sp2 <- NULL
if(margins %in% c(M$m2,M$m2d)){
formula.eq2 <- formula[[2]]
nad2.1 <- "sigma2"
formula.eq2 <- as.formula( paste(nad2.1,"~",formula.eq2[2], sep="") )
set.seed(1)
sigma2 <- rnorm(vo$n, vo$log.sig2.1, 0.001)
rm(list=".Random.seed", envir=globalenv())
gam2 <- gam(formula.eq2, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
if(M$sp.method != "perf"){
gam2ff <- gam(formula.eq2, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels, fit = FALSE)
Sl.sf2 <- Sl.setup(gam2ff)
rm(gam2ff)
}
l.sp2 <- length(gam2$sp)
if(l.sp2 != 0){
ngc <- 2
while( any(round(summary(gam2)$edf, 1) > 1) ) {gam2 <- gam(formula.eq2, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
X2 <- model.matrix(gam2)
X2.d2 <- dim(X2)[2]
if(l.sp2 != 0) sp2 <- gam2$sp
environment(gam2$formula) <- environment(gam1$formula)
gp2 <- gam2$nsdf
start.v <- c(gam1$coefficients, gam2$coefficients )
}
if(margins %in% c(M$m3,M$m3d)){
formula.eq2 <- formula[[2]]
formula.eq3 <- formula[[3]]
nad2.1 <- "sigma2"
nad.1 <- "nu"
formula.eq2 <- as.formula( paste(nad2.1,"~",formula.eq2[2],sep="") )
formula.eq3 <- as.formula( paste(nad.1,"~", formula.eq3[2],sep="") )
set.seed(1)
sigma2 <- rnorm(vo$n, vo$log.sig2.1, 0.001)
nu <- rnorm(vo$n, vo$log.nu.1, 0.001)
rm(list=".Random.seed", envir=globalenv())
gam2 <- gam(formula.eq2, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam3 <- gam(formula.eq3, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels)
if(M$sp.method != "perf"){
gam2ff <- gam(formula.eq2, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels, fit = FALSE)
gam3ff <- gam(formula.eq3, data = data, gamma = ngc, knots = knots, drop.unused.levels = vo$drop.unused.levels, fit = FALSE)
Sl.sf2 <- Sl.setup(gam2ff); Sl.sf3 <- Sl.setup(gam3ff)
rm(gam2ff, gam3ff)
}
l.sp2 <- length(gam2$sp)
l.sp3 <- length(gam3$sp)
if(l.sp2 != 0){
ngc <- 2
while( any(round(summary(gam2)$edf, 1) > 1) ) {gam2 <- gam(formula.eq2, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp3 != 0){
ngc <- 2
while( any(round(summary(gam3)$edf, 1) > 1) ) {gam3 <- gam(formula.eq3, data = data, gamma = ngc + 1, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
X2 <- model.matrix(gam2)
X2.d2 <- dim(X2)[2]
X3 <- model.matrix(gam3)
X3.d2 <- dim(X3)[2]
if(l.sp2 != 0) sp2 <- gam2$sp
environment(gam2$formula) <- environment(gam1$formula)
gp2 <- gam2$nsdf
if(l.sp3 != 0) sp3 <- gam3$sp
environment(gam3$formula) <- environment(gam1$formula)
gp3 <- gam3$nsdf
start.v <- c(gam1$coefficients, gam2$coefficients, gam3$coefficients )
}
}
if(type == "copSS"){
if(M$l.flist == 3){
formula.eq3 <- formula[[3]]
nad1 <- "theta"
formula.eq3 <- as.formula( paste(nad1,"~",formula.eq3[2],sep="") )
set.seed(1)
theta <- rnorm(vo$n, vo$i.rho, 0.001)
rm(list=".Random.seed", envir=globalenv())
gam3 <- gam(formula.eq3, data = data, gamma = ngc, subset=inde, knots = knots, drop.unused.levels = vo$drop.unused.levels)
######
# TEST
######
X3s <- try(predict.gam(gam3, newdata = data[,-dim(data)[2]], type = "lpmatrix"), silent = TRUE)
if(any(class(X3s)=="try-error")) stop("Check that the numbers of factor variables' levels\nin the selected sample are the same as those in the complete dataset.\nRead the Details section in ?copulaSampleSel for more information.")
######
l.sp3 <- length(gam3$sp)
if(l.sp3 != 0){
ngc <- 2
while( any(round(summary(gam3)$edf, 1) > 1) ) {gam3 <- gam(formula.eq3, data = data, gamma = ngc + 1, subset=inde, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
X3 <- model.matrix(gam3)
X3.d2 <- dim(X3)[2]
if(l.sp3 != 0) sp3 <- gam3$sp
environment(gam3$formula) <- environment(gam2$formula)
gp3 <- gam3$nsdf
start.v <- c(gam1$coefficients, c.gam2, gam3$coefficients )
}
if(M$l.flist == 4){
formula.eq3 <- formula[[3]]
formula.eq4 <- formula[[4]]
nad1 <- "sigma2"
nad2 <- "theta"
formula.eq3 <- as.formula( paste(nad1,"~",formula.eq3[2],sep="") )
formula.eq4 <- as.formula( paste(nad2,"~",formula.eq4[2],sep="") )
set.seed(1)
sigma2 <- rnorm(vo$n, vo$log.sig2.2, 0.001)
theta <- rnorm(vo$n, vo$i.rho, 0.001)
rm(list=".Random.seed", envir=globalenv())
gam3 <- gam(formula.eq3, data = data, gamma = ngc, subset=inde, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam4 <- gam(formula.eq4, data = data, gamma = ngc, subset=inde, knots = knots, drop.unused.levels = vo$drop.unused.levels)
######
# TEST
######
X3s <- try(predict.gam(gam3, newdata = data[,-dim(data)[2]], type = "lpmatrix"), silent = TRUE)
if(any(class(X3s)=="try-error")) stop("Check that the numbers of factor variables' levels\nin the selected sample are the same as those in the complete dataset.\nRead the Details section in ?copulaSampleSel for more information.")
X4s <- try(predict.gam(gam4, newdata = data[,-dim(data)[2]], type = "lpmatrix"), silent = TRUE)
if(any(class(X4s)=="try-error")) stop("Check that the numbers of factor variables' levels\nin the selected sample are the same as those in the complete dataset.\nRead the Details section in ?copulaSampleSel for more information.")
######
l.sp3 <- length(gam3$sp)
l.sp4 <- length(gam4$sp)
if(l.sp3 != 0){
ngc <- 2
while( any(round(summary(gam3)$edf, 1) > 1) ) {gam3 <- gam(formula.eq3, data = data, gamma = ngc + 1, subset=inde, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp4 != 0){
ngc <- 2
while( any(round(summary(gam4)$edf, 1) > 1) ) {gam4 <- gam(formula.eq4, data = data, gamma = ngc + 1, subset=inde, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
X3 <- model.matrix(gam3)
X3.d2 <- dim(X3)[2]
X4 <- model.matrix(gam4)
X4.d2 <- dim(X4)[2]
if(l.sp3 != 0) sp3 <- gam3$sp
environment(gam3$formula) <- environment(gam2$formula)
gp3 <- gam3$nsdf
if(l.sp4 != 0) sp4 <- gam4$sp
environment(gam4$formula) <- environment(gam2$formula)
gp4 <- gam4$nsdf
start.v <- c(gam1$coefficients, c.gam2, gam3$coefficients, gam4$coefficients )
}
if(M$l.flist == 5){
formula.eq3 <- formula[[3]]
formula.eq4 <- formula[[4]]
formula.eq5 <- formula[[5]]
nad1 <- "sigma2"
nad2 <- "nu"
nad3 <- "theta"
formula.eq3 <- as.formula( paste(nad1,"~",formula.eq3[2],sep="") )
formula.eq4 <- as.formula( paste(nad2,"~",formula.eq4[2],sep="") )
formula.eq5 <- as.formula( paste(nad3,"~",formula.eq5[2],sep="") )
set.seed(1)
sigma2 <- rnorm(vo$n, vo$log.sig2.2, 0.001)
nu <- rnorm(vo$n, vo$log.nu.2, 0.001)
theta <- rnorm(vo$n, vo$i.rho, 0.001)
rm(list=".Random.seed", envir=globalenv())
gam3 <- gam(formula.eq3, data = data, gamma = ngc, subset=inde, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam4 <- gam(formula.eq4, data = data, gamma = ngc, subset=inde, knots = knots, drop.unused.levels = vo$drop.unused.levels)
gam5 <- gam(formula.eq5, data = data, gamma = ngc, subset=inde, knots = knots, drop.unused.levels = vo$drop.unused.levels)
######
# TEST
######
X3s <- try(predict.gam(gam3, newdata = data[,-dim(data)[2]], type = "lpmatrix"), silent = TRUE)
if(any(class(X3s)=="try-error")) stop("Check that the numbers of factor variables' levels\nin the selected sample are the same as those in the complete dataset.\nRead the Details section in ?copulaSampleSel for more information.")
X4s <- try(predict.gam(gam4, newdata = data[,-dim(data)[2]], type = "lpmatrix"), silent = TRUE)
if(any(class(X4s)=="try-error")) stop("Check that the numbers of factor variables' levels\nin the selected sample are the same as those in the complete dataset.\nRead the Details section in ?copulaSampleSel for more information.")
X5s <- try(predict.gam(gam5, newdata = data[,-dim(data)[2]], type = "lpmatrix"), silent = TRUE)
if(any(class(X5s)=="try-error")) stop("Check that the numbers of factor variables' levels\nin the selected sample are the same as those in the complete dataset.\nRead the Details section in ?copulaSampleSel for more information.")
######
l.sp3 <- length(gam3$sp)
l.sp4 <- length(gam4$sp)
l.sp5 <- length(gam5$sp)
if(l.sp3 != 0){
ngc <- 2
while( any(round(summary(gam3)$edf, 1) > 1) ) {gam3 <- gam(formula.eq3, data = data, gamma = ngc + 1, subset=inde, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp4 != 0){
ngc <- 2
while( any(round(summary(gam4)$edf, 1) > 1) ) {gam4 <- gam(formula.eq4, data = data, gamma = ngc + 1, subset=inde, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
if(l.sp5 != 0){
ngc <- 2
while( any(round(summary(gam5)$edf, 1) > 1) ) {gam5 <- gam(formula.eq5, data = data, gamma = ngc + 1, subset=inde, knots = knots, drop.unused.levels = vo$drop.unused.levels); ngc <- ngc + 1; if(ngc > 5) break}
}
X3 <- model.matrix(gam3)
X3.d2 <- dim(X3)[2]
X4 <- model.matrix(gam4)
X4.d2 <- dim(X4)[2]
X5 <- model.matrix(gam5)
X5.d2 <- dim(X5)[2]
if(l.sp3 != 0) sp3 <- gam3$sp
environment(gam3$formula) <- environment(gam2$formula)
gp3 <- gam3$nsdf
if(l.sp4 != 0) sp4 <- gam4$sp
environment(gam4$formula) <- environment(gam2$formula)
gp4 <- gam4$nsdf
if(l.sp5 != 0) sp5 <- gam5$sp
environment(gam5$formula) <- environment(gam2$formula)
gp5 <- gam5$nsdf
start.v <- c(gam1$coefficients, c.gam2, gam3$coefficients, gam4$coefficients, gam5$coefficients )
}
}
L <- list(start.v = start.v,
X3 = X3, X4 = X4, X5 = X5, X6 = X6, X7 = X7, X8 = X8, X3.d2 = X3.d2, X4.d2 = X4.d2, X5.d2 = X5.d2, X6.d2 = X6.d2,
X7.d2 = X7.d2, X8.d2 = X8.d2, gp3 = gp3, gp4 = gp4, gp5 = gp5, gp6 = gp6, gp7 = gp7, gp8 = gp8,
gam3 = gam3, gam4 = gam4, gam5 = gam5, gam6 = gam6, gam7 = gam7, gam8 = gam8,
l.sp3 = l.sp3, l.sp4 = l.sp4, l.sp5 = l.sp5, l.sp6 = l.sp6, l.sp7 = l.sp7, l.sp8 = l.sp8,
sp3 = sp3, sp4 = sp4, sp5 = sp5, sp6 = sp6, sp7 = sp7, sp8 = sp8, X3s = X3s, X4s = X4s, X5s = X5s, Sl.sf2 = Sl.sf2, Sl.sf3= Sl.sf3)
if(type == "gaml") {L$X2 <- X2; L$X2.d2 <- X2.d2; L$gp2 <- gp2; L$gam2 <- gam2; L$l.sp2 <- l.sp2; L$sp2 <- sp2}
L
}
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