Nothing
R/pream.wm.r
In GJRM: Generalised Joint Regression Modelling
Defines functions
pream.wm
Documented in
pream.wm
pream.wm <- function(formula, margins, M, l.flist, type = "copR"){
#if(margins[2] %in% c("GU", "rGU", "LO", "LN", "WEI","iG", "DAGUM", "SM", "BE", "FISK","TW") ) stop("Check the next release for the final tested version of this model\nor get in touch to check progress.")
#scs <- c("WEI", "FISK", "LN", "LO", "N") # for survival models
#if(M$robust == TRUE) stop("Check the next release for the final tested version of this model\nor get in touch to check progress.")
#if(M$dep.cens == TRUE) stop("The dependent censoring case is work in progress. \nGet in touch should you wish to get more info.")
scs <- c("WEI", "FISK") # for survival models
######################################################################################################################################################
if(type == "ROY"){ # binary - binary/cont/discr models
if(length(margins) != 3) stop("You have to choose three margins.")
if(M$BivD1 == "T" && (M$dof1 <=2 || M$dof1 > 249)) stop("dof1 must be a number greater than 2 and smaller than 249.")
if(M$BivD2 == "T" && (M$dof2 <=2 || M$dof2 > 249)) stop("dof2 must be a number greater than 2 and smaller than 249.")
if(!(M$BivD1 %in% c(M$opc))) stop("Error in parameter BivD1 value. It should be one of:\nN, C0, C90, C180, C270, GAL0, GAL90, GAL180, GAL270, J0, J90, J180, J270, G0, G90, G180, G270, F, AMH, FGM, T, PL, HO.")
if(!(M$BivD2 %in% c(M$opc))) stop("Error in parameter BivD2 value. It should be one of:\nN, C0, C90, C180, C270, GAL0, GAL90, GAL180, GAL270, J0, J90, J180, J270, G0, G90, G180, G270, F, AMH, FGM, T, PL, HO.")
if(!(M$extra.regI %in% c("t","pC","sED"))) stop("Error in parameter extra.regI value. It should be one of:\nt, pC or sED.")
if(!(margins[1] %in% M$bl) ) stop("Error in first margin value. It should be one of:\nprobit, logit, cloglog.")
if(!(margins[2] %in% c(M$bl,M$m2,M$m3,M$m1d,M$m2d)) ) stop("Error in second margin value. It should be one of:\nprobit, logit, cloglog, N, GU, rGU, LO, LN, WEI, iG, GA, DAGUM, TW, SM, BE, FISK, PO, GP (and its versions), DGP (and its versions), ZTP, NBI, NBII, PIG.")
if(!(margins[3] %in% c(M$bl,M$m2,M$m3,M$m1d,M$m2d)) ) stop("Error in third margin value. It should be one of:\nprobit, logit, cloglog, N, GU, rGU, LO, LN, WEI, iG, GA, DAGUM, TW, SM, BE, FISK, PO, GP (and its versions), DGP (and its versions), ZTP, NBI, NBII, PIG.")
if( margins[2] %in% c(M$bl) && !(margins[3] %in% c(M$bl)) ) stop("The second and third margins must be of the same type (e.g., both binary).")
if(!(margins[2] %in% c(M$bl)) && margins[3] %in% c(M$bl) ) stop("The second and third margins must be of the same type (e.g., both binary).")
if( margins[2] %in% c(M$m2,M$m3) && !(margins[3] %in% c(M$m2,M$m3)) ) stop("The second and third margins must be of the same type (e.g., both continuous).")
if(!(margins[2] %in% c(M$m2,M$m3)) && margins[3] %in% c(M$m2,M$m3) ) stop("The second and third margins must be of the same type (e.g., both continuous).")
if( margins[2] %in% c(M$m1d,M$m2d) && !(margins[3] %in% c(M$m1d,M$m2d)) ) stop("The second and third margins must be of the same type (e.g., both discrete).")
if(!(margins[2] %in% c(M$m1d,M$m2d)) && margins[3] %in% c(M$m1d,M$m2d) ) stop("The second and third margins must be of the same type (e.g., both discrete).")
# this is because it is very unlikely that different distributions are required for equations 2 and 3, although it could be easily relaxed.
if( margins[2] %in% c(M$m2) && margins[3] %in% c(M$m3) ) stop("The second and third margins must have the same number of distributional parameters.")
if( margins[2] %in% c(M$m3) && margins[3] %in% c(M$m2) ) stop("The second and third margins must have the same number of distributional parameters.")
if( margins[2] %in% c(M$m1d) && margins[3] %in% c(M$m2d) ) stop("The second and third margins must have the same number of distributional parameters.")
if( margins[2] %in% c(M$m2d) && margins[3] %in% c(M$m1d) ) stop("The second and third margins must have the same number of distributional parameters.")
if( margins[2] %in% c(M$m3) && margins[3] %in% c(M$m3) ){
if( (margins[2] == "DAGUM" && margins[3] == "SM") || (margins[2] == "SM" && margins[3] == "DAGUM") ) stop("The second and third margins must have the same distribution.")
}
if(l.flist > 3 && margins[2] %in% c(M$bl) && margins[3] %in% c(M$bl) ){ if(l.flist!=5) stop("You need to specify five equations.") }
if(l.flist > 3 && margins[2] %in% c(M$m1d) && margins[3] %in% c(M$m1d)){ if(l.flist!=5) stop("You need to specify five equations.") }
if(l.flist > 3 && margins[2] %in% c(M$m2d) && margins[3] %in% c(M$m1d)){ if(l.flist!=6) stop("You need to specify six equations.") }
if(l.flist > 3 && margins[2] %in% c(M$m1d) && margins[3] %in% c(M$m2d)){ if(l.flist!=6) stop("You need to specify six equations.") }
if(l.flist > 3 && margins[2] %in% c(M$m2d) && margins[3] %in% c(M$m2d)){ if(l.flist!=7) stop("You need to specify seven equations.") }
if(l.flist > 3 && margins[2] %in% c(M$m2) && margins[3] %in% c(M$m2)){ if(l.flist!=7) stop("You need to specify seven equations.") }
if(l.flist > 3 && margins[2] %in% c(M$m2) && margins[3] %in% c(M$m3)){ if(l.flist!=8) stop("You need to specify eight equations.") }
if(l.flist > 3 && margins[2] %in% c(M$m3) && margins[3] %in% c(M$m2)){ if(l.flist!=8) stop("You need to specify eight equations.") }
if(l.flist > 3 && margins[2] %in% c(M$m3) && margins[3] %in% c(M$m3)){ if(l.flist!=9) stop("You need to specify nine equations.") }
if(margins[2] %in% c("GP", "GPII","GPo","DGP","DGPII", "DGP0")) stop("GP, GPII, GPo, DGP, DGPII not done yet.\nGet in touch for details.")
if(margins[3] %in% c("GP", "GPII","GPo","DGP","DGPII", "DGP0")) stop("GP, GPII, GPo, DGP, DGPII not done yet.\nGet in touch for details.")
if(margins[2] %in% c("TW") || margins[3] %in% c("TW")) stop("TW case not implemented yet.\nGet in touch for more info.")
}
if(type == "ord"){
if(M$BivD == "T" && (M$dof <=2 || M$dof > 249)) stop("dof must be a number greater than 2 and smaller than 249.")
# if(margins[2] %in% M$bl) stop("The second margin must be a continuous distribution.") # Removed as the ordinal-ordinal model is now implemented
if(M$Model %in% c("T", "TSS", "TESS")) stop("A trivariate model for ordinal responses with non-random sample selection is not currently supported by GJRM.")
if(M$Model == "BSS") stop("A bivariate model for ordinal responses with non-random sample selection is not currently supported by GJRM.")
if(M$Model %in% c("BPO", "BPO0")) stop("A bivariate model for ordinal responses with partial observability is not currently supported by GJRM.")
if(!(M$BivD %in% c(M$opc,M$BivD2))) stop("Error in parameter BivD value. It should be one of:\nN, C0, C90, C180, C270, GAL0, GAL90, GAL180, GAL270, J0, J90, J180, J270, G0, G90, G180, G270, F, AMH, FGM, T, PL, HO,\nC0C90, C0C270, C180C90, C180C270, GAL0GAL90, GAL0GAL270, GAL180GAL90, GAL180GAL270, J0J90, J0J270, J180J90, J180J270,\nG0G90, G0G270, G180G90, G180G270.")
if(!(M$extra.regI %in% c("t","pC","sED"))) stop("Error in parameter extra.regI value. It should be one of:\nt, pC or sED.")
if( !( margins[1] %in% c("probit", "logit") ) ) stop("Error in first margin value. It should be one of:\nprobit, logit.")
if(!(margins[2] %in% c(M$m2, "probit", "logit")) && M$intf == TRUE ) stop("Error in second margin value. It should be one of:\nN, GU, rGU, LO, LN, WEI, iG, GA, BE, FISK, probit, logit")
if(margins[2] %in% c(M$m1d,M$m2d) ) stop("Discrete margins are not allowed.")
if(margins[2] %in% c("TW") ) stop("Tweedie not yet allowed for. Get in touch for details.")
if(margins[2] %in% c("cloglog") ) stop("Complementary log-log not yet allowed for. Get in touch for details.")
if(l.flist > 2 && margins[2] %in% c(M$m2,M$m2d)){ if(l.flist!=4) stop("You need to specify four equations.") }
if(l.flist > 2 && margins[2] %in% M$m3 ){ if(l.flist!=5) stop("You need to specify five equations.") }
}
if(type == "biv"){ # binary - cont/discr models #
if(M$BivD == "T" && (M$dof <=2 || M$dof > 249)) stop("dof must be a number greater than 2 and smaller than 249.")
if(!is.null(M$theta.fx) && M$BivD != "N") stop("This approach is not currently implemented for non-Gaussian bivariate distributions.")
if(!is.null(M$theta.fx)) { if(M$Model != "B" && !(margins[2] %in% M$bl)) stop("Only bivariate Gaussian binary models with fixed theta are currenlty allowed for.")}
if(!is.null(M$theta.fx) ) { if( abs(M$theta.fx) > 0.999 ) stop("The theta value must be in the interval [-0.999,0.999].") }
if(M$Model == "BPO" && M$BivD != "N") stop("This model is not defined for copulae.")
if(M$Model == "BPO" && margins[1] != "probit" && margins[2] != "probit") stop("This model is not defined for the chosen margins.")
if(!(M$Model %in% M$mb)) stop("Error in parameter Model value. It should be one of:\nB, BSS, BPO, BPO0.")
if( M$Model == "BSS" && M$BivD %in% M$BivD2 ) stop("Mixed copulae can not be implemented for selection models.")
if(!(M$BivD %in% c(M$opc,M$BivD2))) stop("Error in parameter BivD value. It should be one of:\nN, C0, C90, C180, C270, GAL0, GAL90, GAL180, GAL270, J0, J90, J180, J270, G0, G90, G180, G270, F, AMH, FGM, T, PL, HO,\nC0C90, C0C270, C180C90, C180C270, GAL0GAL90, GAL0GAL270, GAL180GAL90, GAL180GAL270, J0J90, J0J270, J180J90, J180J270,\nG0G90, G0G270, G180G90, G180G270.")
if(!(M$extra.regI %in% c("t","pC","sED"))) stop("Error in parameter extra.regI value. It should be one of:\nt, pC or sED.")
if(!(margins[1] %in% M$bl) ) stop("Error in first margin value. It should be one of:\nprobit, logit, cloglog.")
if(!(margins[2] %in% c(M$bl,M$m2,M$m3)) && M$intf == FALSE ) stop("Error in second margin value. It should be one of:\nprobit, logit, cloglog.")
if(!(margins[2] %in% c(M$bl,M$m2,M$m3,M$m1d,M$m2d)) && M$intf == TRUE ) stop("Error in second margin value. It should be one of:\nN, GU, rGU, LO, LN, WEI, iG, GA, DAGUM, TW, SM, BE, FISK, PO, GP (and its versions), DGP (and its versions), ZTP, NBI, NBII, PIG.")
if(margins[2] %in% c(M$m2,M$m3,M$m1d,M$m2d) && (M$Model == "BPO" || M$Model == "BPO0") ) stop("For continuous/discrete responses, partial observability models\nare not allowed for.")
if(l.flist > 2 && margins[2] %in% c(M$bl,M$m1d)){ if(l.flist!=3) stop("You need to specify three equations.") }
if(l.flist > 2 && margins[2] %in% c(M$m2,M$m2d)){ if(l.flist!=4) stop("You need to specify four equations.") }
if(l.flist > 2 && margins[2] %in% M$m3 ){ if(l.flist!=5) stop("You need to specify five equations.") }
if( l.flist > 2 && M$Model == "BPO0") stop("You only need to specify two equations.\nThe chosen model does not have a correlation parameter.")
if( l.flist > 2 && M$Model == "B" && !is.null(M$theta.fx)) stop("You only need to specify two equations.\nThe chosen model is not allowed to estimate the theta parameter.")
if(margins[2] %in% c("TW") && l.flist != 5) stop("You need to specify five equations.")
if(margins[2] %in% c("GP", "GPII","GPo","DGP","DGPII")) stop("GP, GPII, GPo, DGP, DGPII not done yet.\nGet in touch for details.")
}
if(type == "triv"){
mmar <- c("probit", "logit", "cloglog")
if(!(M$Model %in% M$mb)) stop("Error in parameter Model value. It should be one of: T, TSS, TESS.")
if(!(margins[1] %in% mmar) ) stop("Error in first margin value. It should be one of:\nprobit, logit, cloglog.")
if(!(margins[2] %in% mmar) ) stop("Error in second margin value. It should be one of:\nprobit, logit, cloglog.")
if(!(margins[3] %in% mmar) ) stop("Error in third margin value. It should be one of:\nprobit, logit, cloglog.")
if(!(M$penCor %in% c("unpen", "ridge", "lasso", "alasso"))) stop("Error in parameter penCor value. It should be one of:\nunpen, ridge, lasso, alasso.")
if(is.null(M$w.alasso) && M$penCor == "alasso") stop("You must provide a vector of three weights when using alasso.")
if(length(M$w.alasso)!=3 && M$penCor == "alasso") stop("You must supply a vector made up of three weights.")
if(!(M$extra.regI %in% c("t","pC","sED"))) stop("Error in parameter extra.regI value. It should be one of:\nt, pC or sED.")
if(l.flist > 3 && M$penCor %in% c("ridge", "lasso", "alasso")) stop("This option is not currently allowed.")
if(l.flist > 3 && M$Chol == FALSE) stop("You must set Chol = TRUE.")
if(l.flist > 3 && M$Model %in% c("TSS", "TESS")) stop("You can not currently use more than three equations with the model chosen.")
######################################################################################################################################################
#if( M$Model %in% c("TSS","TESS") ) stop("Check the next release for the final tested version of this model\nor get in touch to check progress.")
######################################################################################################################################################
}
if(type == "copR"){
if(M$surv == TRUE){
if( !(margins[1] %in% c(M$m2,M$m3,M$bl)) ) stop("The first marginal distribution must be either continuous or probit, PO or PH.")
if( !(margins[2] %in% c(M$bl,scs)) ) stop("The second marginal distribution must be probit, PO or PH.")
if(margins[1] %in% c("TW") || margins[2] %in% c("TW") ) stop("Tweedie not yet allowed for. Get in touch for details.")
if(!is.null(M$c1) && length(table( M$c1 %in% c(0,1) ) ) > 1 ) stop("Your first censoring indicator is not binary. Please fix.")
if(!is.null(M$c2) && length(table( M$c2 %in% c(0,1) ) ) > 1 ) stop("Your second censoring indicator is not binary. Please fix.")
if(length(M$c1) != length(M$c2)) stop("The two censoring indicators must have the same length.")
if(l.flist > 2 && margins[1] %in% c(M$bl) && margins[2] %in% c(M$bl)){ if(l.flist!=3) stop("You need to specify three equations.") }
if(l.flist > 2 && margins[1] %in% c(M$m2) && margins[2] %in% c(M$bl)){ if(l.flist!=4) stop("You need to specify four equations.") }
if(l.flist > 2 && margins[1] %in% c(M$m3) && margins[2] %in% c(M$bl)){ if(l.flist!=5) stop("You need to specify five equations.") }
}
if(M$BivD == "T" && (M$dof <=2 || M$dof > 249)) stop("dof must be a number greater than 2 and smaller than 249.")
if( margins[1] %in% c(M$m2d) && margins[2] %in% c(M$m1d) ) stop("Please swap the two equations (and hence margins' specification).\nThe second instead of the first margin has to be a two-parameter discrete distribution.")
if( margins[1] %in% c(M$m2,M$m3) && margins[2] %in% c(M$m1d,M$m2d) ) stop("Please swap the two equations (and hence margins' specification).\nThe first instead of the second margin has to be discrete.")
if(!(M$BivD %in% c(M$opc,M$BivD2))) stop("Error in parameter BivD value. It should be one of:\nN, C0, C90, C180, C270, GAL0, GAL90, GAL180, GAL270, J0, J90, J180, J270, G0, G90, G180, G270, F, AMH, FGM, T, PL, HO, \nC0C90, C0C270, C180C90, C180C270, GAL0GAL90, GAL0GAL270, GAL180GAL90, GAL180GAL270, J0J90, J0J270, J180J90, J180J270,\nG0G90, G0G270, G180G90, G180G270.")
if(!(M$extra.regI %in% c("t","pC","sED"))) stop("Error in parameter extra.regI value. It should be one of:\nt, pC or sED.")
if(!(margins[1] %in% c(M$m2,M$m3,M$m1d,M$m2d,M$bl)) ) stop("Error in first margin value. It should be one of:\nN, GU, rGU, LO, LN, WEI, iG, GA, DAGUM, TW, SM, BE, FISK, NBI, NBII, PIG, PO, GP (and its versions), DGP (and its versions), ZTP\nor probit, logit, cloglog for survival models.")
if(!(margins[2] %in% c(M$m2,M$m3,M$m1d,M$m2d,M$bl)) ) stop("Error in second margin value. It should be one of:\nN, GU, rGU, LO, LN, WEI, iG, GA, DAGUM, TW, SM, BE, FISK, NBI, NBII, PIG, PO, GP (and its versions), DGP (and its versions), ZTP\nor probit, logit, cloglog for survival models.")
if(M$BivD == "T" && margins[1] %in% c(M$m2,M$m3) && margins[2] %in% c(M$m2,M$m3)){
if(l.flist > 2 && margins[1] %in% c(M$m2) && margins[2] %in% c(M$m2)){ if(l.flist!=6) stop("You need to specify six equations.") }
if(l.flist > 2 && margins[1] %in% c(M$m2) && margins[2] %in% c(M$m3)){ if(l.flist!=7) stop("You need to specify seven equations.") }
if(l.flist > 2 && margins[1] %in% c(M$m3) && margins[2] %in% c(M$m2)){ if(l.flist!=7) stop("You need to specify seven equations.") }
if(l.flist > 2 && margins[1] %in% c(M$m3) && margins[2] %in% c(M$m3)){ if(l.flist!=8) stop("You need to specify eight equations.") }
}else{
if(l.flist > 2 && margins[1] %in% c(M$m1d,M$bl) && margins[2] %in% c(M$m1d,M$bl)) { if(l.flist!=3) stop("You need to specify three equations.") }
if(l.flist > 2 && margins[1] %in% c(M$m2d) && margins[2] %in% c(M$m1d)) { if(l.flist!=4) stop("You need to specify four equations.") }
if(l.flist > 2 && margins[1] %in% c(M$m1d) && margins[2] %in% c(M$m2,M$m2d)) { if(l.flist!=4) stop("You need to specify four equations.") }
if(l.flist > 2 && margins[1] %in% c(M$m1d) && margins[2] %in% c(M$m3,M$m3d)) { if(l.flist!=5) stop("You need to specify five equations.") }
if(l.flist > 2 && margins[1] %in% c(M$m2,M$m2d) && margins[2] %in% c(M$m2,M$m2d)){ if(l.flist!=5) stop("You need to specify five equations.") }
if(l.flist > 2 && margins[1] %in% c(M$m2,M$m2d) && margins[2] %in% c(M$m3,M$m3d)){ if(l.flist!=6) stop("You need to specify six equations.") }
if(l.flist > 2 && margins[1] %in% c(M$m3,M$m3d) && margins[2] %in% c(M$m2,M$m2d)){ if(l.flist!=6) stop("You need to specify six equations.") }
if(l.flist > 2 && margins[1] %in% c(M$m3,M$m3d) && margins[2] %in% c(M$m3,M$m3d)){ if(l.flist!=7) stop("You need to specify seven equations.") }
}
if(margins[1] %in% c("GP","GPII","GPo","DGP","DGPII") || margins[2] %in% c("GP","GPII","GPo","DGP", "DGPII")) stop("GP, GPII, GPo, DGP, DGPII not done yet.\nGet in touch for details.")
##################################################################################################################################################################################################
# if( M$surv == TRUE && margins[1] %in% c(M$m2,M$m3) && margins[2] %in% c(M$bl) ) stop("Survival models with continuous and survival margins not ready yet.\nGet in touch to check progress.")
#if( margins[2] %in% c(M$m2,M$m3) && margins[1] %in% c(M$m1d,M$m2d) ) stop("The continuous - discrete margin case is not ready yet.\nGet in touch to check progress.")
##################################################################################################################################################################################################
}
if(type == "copSS"){
if(M$BivD == "T" && (M$dof <=2 || M$dof > 249)) stop("dof must be a number greater than 2 and smaller than 249.")
if(!(M$BivD %in% M$opc)) stop("Error in parameter BivD value. It should be one of: N, C0, C90, C180, C270, GAL0, GAL90, GAL180, GAL270, J0, J90, J180, J270, G0, G90, G180, G270, F, AMH, FGM, T, PL, HO.")
if(!(M$extra.regI %in% c("t","pC","sED"))) stop("Error in parameter extra.regI value. It should be one of: t, pC or sED.")
if(!(M$margins[1] %in% M$bl) ) stop("Error in first margin value. It should be one of:\nprobit, logit, cloglog.")
if(!(M$margins[2] %in% c(M$m2,M$m3,M$m1d,M$m2d)) ) stop("Error in second margin value. It should be one of:\nN, GU, rGU, LO, LN, WEI, iG, GA, DAGUM, TW, SM, BE, FISK, PO, GP (and its versions), DGP (and its versions), ZTP, NBI, NBII, PIG.")
###########################################
#if(M$margins[2] %in% c("TW") ) stop("Tweedie not yet allowed for. Get in touch for details.")
###########################################
if(l.flist > 2 && M$margins[2] %in% c(M$m1d) ){ if(l.flist!=3) stop("You need to specify three equations.") }
if(l.flist > 2 && M$margins[2] %in% c(M$m2,M$m2d)){ if(l.flist!=4) stop("You need to specify four equations.") }
if(l.flist > 2 && M$margins[2] %in% M$m3 ){ if(l.flist!=5) stop("You need to specify five equations.") }
if(M$margins[2] %in% c("TW") ){ if(l.flist!=5) stop("You need to specify five equations.") }
if(M$margins[2] %in% c("GP", "GPII", "GPo", "DGP","DGPII") ) stop("GP, GPII, GPo, DGP, DGPII not done yet.\nGet in touch for details.")
}
if(type == "gamls"){
if(M$surv == TRUE){
if( !(M$type.cens %in% c("R","L","I","mixed")) ) stop("The type of censoring can be R, L, I or mixed.")
if( !is.null(M$v.rB) && !is.character(M$v.rB) ) stop("v.rB must be a character variable.")
if( !(M$margin %in% c(scs,M$bl)) ) stop("The marginal distribution can be probit, PO or PH.")
if(is.null(M$cens) ) stop("You must provide the binary censoring indicator.")
if( M$type.cens %in% c("R","L","I") ){
if( length(table( M$cens %in% c(0,1) ) ) > 1 ) stop("Your censoring indicator is not binary. Please fix.")
}
if( M$type.cens %in% c("mixed") ){
if( !is.factor(M$cens) ) stop("The cens variable must be a factor variable.")
# NEW: include truncated censoring indicators
c.set <- c("R","L","I","U","RT","LT","IT","UT")
ucens <- unique(M$cens); l.uc <- length(ucens)
for(i in 1:l.uc){ if(!(ucens[i] %in% c.set)) stop("The cens variable can only take values in (R, L, I, U, RT, LT, IT, UT).")}
}
}
if(M$surv == TRUE && M$robust == TRUE) stop("It is not currently possible to fit robust survival models.")
if(!(M$extra.regI %in% c("t","pC","sED"))) stop("Error in parameter extra.regI value. It should be one of:\nt, pC or sED.")
if(!(M$margin %in% c(M$m2,M$m3,M$m1d,M$m2d, M$bl)) ) stop("Error in margin value. It should be one of:\nN, GU, rGU, LO, LN, WEI, iG, GA, GP, GPII, GPo, DGP, DGPII, DAGUM, TW, SM, BE, FISK, NBI, NBII, PIG, PO, GP (and its versions), DGP (and its versions), ZTP, GEVlink.")
if(l.flist > 1 && M$margin %in% c(M$m1d) ) stop("You need to specify one equation.")
if(l.flist > 1 && M$margin %in% c(M$m2,M$m2d) ){ if(l.flist!=2) stop("You need to specify two equations.") }
if(l.flist > 1 && M$margin %in% c(M$m3,M$m3d) ){ if(l.flist!=3) stop("You need to specify three equations.") }
if(l.flist !=3 && M$margin %in% c("TW") ) stop("You need to specify three equations.")
if(M$surv == TRUE && M$margin %in% M$bl && M$informative == "yes" && l.flist != 2 ) stop("You need to specify two equations.")
if(M$surv == TRUE && M$margin %in% M$bl && M$informative == "yes" && is.null(M$list.inf.cov)) stop("You need to specify a set of informative covariates otherwise use the non-informative model.")
if(M$surv == TRUE && M$margin %in% M$bl && M$informative == "yes" && M$type.cens != "R" ) stop("The informative model only allows for right censoring.")
}
}
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GJRM documentation built on July 9, 2023, 7:15 p.m.
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Defines functions pream.wm
Documented in pream.wm
pream.wm <- function(formula, margins, M, l.flist, type = "copR"){
#if(margins[2] %in% c("GU", "rGU", "LO", "LN", "WEI","iG", "DAGUM", "SM", "BE", "FISK","TW") ) stop("Check the next release for the final tested version of this model\nor get in touch to check progress.")
#scs <- c("WEI", "FISK", "LN", "LO", "N") # for survival models
#if(M$robust == TRUE) stop("Check the next release for the final tested version of this model\nor get in touch to check progress.")
#if(M$dep.cens == TRUE) stop("The dependent censoring case is work in progress. \nGet in touch should you wish to get more info.")
scs <- c("WEI", "FISK") # for survival models
######################################################################################################################################################
if(type == "ROY"){ # binary - binary/cont/discr models
if(length(margins) != 3) stop("You have to choose three margins.")
if(M$BivD1 == "T" && (M$dof1 <=2 || M$dof1 > 249)) stop("dof1 must be a number greater than 2 and smaller than 249.")
if(M$BivD2 == "T" && (M$dof2 <=2 || M$dof2 > 249)) stop("dof2 must be a number greater than 2 and smaller than 249.")
if(!(M$BivD1 %in% c(M$opc))) stop("Error in parameter BivD1 value. It should be one of:\nN, C0, C90, C180, C270, GAL0, GAL90, GAL180, GAL270, J0, J90, J180, J270, G0, G90, G180, G270, F, AMH, FGM, T, PL, HO.")
if(!(M$BivD2 %in% c(M$opc))) stop("Error in parameter BivD2 value. It should be one of:\nN, C0, C90, C180, C270, GAL0, GAL90, GAL180, GAL270, J0, J90, J180, J270, G0, G90, G180, G270, F, AMH, FGM, T, PL, HO.")
if(!(M$extra.regI %in% c("t","pC","sED"))) stop("Error in parameter extra.regI value. It should be one of:\nt, pC or sED.")
if(!(margins[1] %in% M$bl) ) stop("Error in first margin value. It should be one of:\nprobit, logit, cloglog.")
if(!(margins[2] %in% c(M$bl,M$m2,M$m3,M$m1d,M$m2d)) ) stop("Error in second margin value. It should be one of:\nprobit, logit, cloglog, N, GU, rGU, LO, LN, WEI, iG, GA, DAGUM, TW, SM, BE, FISK, PO, GP (and its versions), DGP (and its versions), ZTP, NBI, NBII, PIG.")
if(!(margins[3] %in% c(M$bl,M$m2,M$m3,M$m1d,M$m2d)) ) stop("Error in third margin value. It should be one of:\nprobit, logit, cloglog, N, GU, rGU, LO, LN, WEI, iG, GA, DAGUM, TW, SM, BE, FISK, PO, GP (and its versions), DGP (and its versions), ZTP, NBI, NBII, PIG.")
if( margins[2] %in% c(M$bl) && !(margins[3] %in% c(M$bl)) ) stop("The second and third margins must be of the same type (e.g., both binary).")
if(!(margins[2] %in% c(M$bl)) && margins[3] %in% c(M$bl) ) stop("The second and third margins must be of the same type (e.g., both binary).")
if( margins[2] %in% c(M$m2,M$m3) && !(margins[3] %in% c(M$m2,M$m3)) ) stop("The second and third margins must be of the same type (e.g., both continuous).")
if(!(margins[2] %in% c(M$m2,M$m3)) && margins[3] %in% c(M$m2,M$m3) ) stop("The second and third margins must be of the same type (e.g., both continuous).")
if( margins[2] %in% c(M$m1d,M$m2d) && !(margins[3] %in% c(M$m1d,M$m2d)) ) stop("The second and third margins must be of the same type (e.g., both discrete).")
if(!(margins[2] %in% c(M$m1d,M$m2d)) && margins[3] %in% c(M$m1d,M$m2d) ) stop("The second and third margins must be of the same type (e.g., both discrete).")
# this is because it is very unlikely that different distributions are required for equations 2 and 3, although it could be easily relaxed.
if( margins[2] %in% c(M$m2) && margins[3] %in% c(M$m3) ) stop("The second and third margins must have the same number of distributional parameters.")
if( margins[2] %in% c(M$m3) && margins[3] %in% c(M$m2) ) stop("The second and third margins must have the same number of distributional parameters.")
if( margins[2] %in% c(M$m1d) && margins[3] %in% c(M$m2d) ) stop("The second and third margins must have the same number of distributional parameters.")
if( margins[2] %in% c(M$m2d) && margins[3] %in% c(M$m1d) ) stop("The second and third margins must have the same number of distributional parameters.")
if( margins[2] %in% c(M$m3) && margins[3] %in% c(M$m3) ){
if( (margins[2] == "DAGUM" && margins[3] == "SM") || (margins[2] == "SM" && margins[3] == "DAGUM") ) stop("The second and third margins must have the same distribution.")
}
if(l.flist > 3 && margins[2] %in% c(M$bl) && margins[3] %in% c(M$bl) ){ if(l.flist!=5) stop("You need to specify five equations.") }
if(l.flist > 3 && margins[2] %in% c(M$m1d) && margins[3] %in% c(M$m1d)){ if(l.flist!=5) stop("You need to specify five equations.") }
if(l.flist > 3 && margins[2] %in% c(M$m2d) && margins[3] %in% c(M$m1d)){ if(l.flist!=6) stop("You need to specify six equations.") }
if(l.flist > 3 && margins[2] %in% c(M$m1d) && margins[3] %in% c(M$m2d)){ if(l.flist!=6) stop("You need to specify six equations.") }
if(l.flist > 3 && margins[2] %in% c(M$m2d) && margins[3] %in% c(M$m2d)){ if(l.flist!=7) stop("You need to specify seven equations.") }
if(l.flist > 3 && margins[2] %in% c(M$m2) && margins[3] %in% c(M$m2)){ if(l.flist!=7) stop("You need to specify seven equations.") }
if(l.flist > 3 && margins[2] %in% c(M$m2) && margins[3] %in% c(M$m3)){ if(l.flist!=8) stop("You need to specify eight equations.") }
if(l.flist > 3 && margins[2] %in% c(M$m3) && margins[3] %in% c(M$m2)){ if(l.flist!=8) stop("You need to specify eight equations.") }
if(l.flist > 3 && margins[2] %in% c(M$m3) && margins[3] %in% c(M$m3)){ if(l.flist!=9) stop("You need to specify nine equations.") }
if(margins[2] %in% c("GP", "GPII","GPo","DGP","DGPII", "DGP0")) stop("GP, GPII, GPo, DGP, DGPII not done yet.\nGet in touch for details.")
if(margins[3] %in% c("GP", "GPII","GPo","DGP","DGPII", "DGP0")) stop("GP, GPII, GPo, DGP, DGPII not done yet.\nGet in touch for details.")
if(margins[2] %in% c("TW") || margins[3] %in% c("TW")) stop("TW case not implemented yet.\nGet in touch for more info.")
}
if(type == "ord"){
if(M$BivD == "T" && (M$dof <=2 || M$dof > 249)) stop("dof must be a number greater than 2 and smaller than 249.")
# if(margins[2] %in% M$bl) stop("The second margin must be a continuous distribution.") # Removed as the ordinal-ordinal model is now implemented
if(M$Model %in% c("T", "TSS", "TESS")) stop("A trivariate model for ordinal responses with non-random sample selection is not currently supported by GJRM.")
if(M$Model == "BSS") stop("A bivariate model for ordinal responses with non-random sample selection is not currently supported by GJRM.")
if(M$Model %in% c("BPO", "BPO0")) stop("A bivariate model for ordinal responses with partial observability is not currently supported by GJRM.")
if(!(M$BivD %in% c(M$opc,M$BivD2))) stop("Error in parameter BivD value. It should be one of:\nN, C0, C90, C180, C270, GAL0, GAL90, GAL180, GAL270, J0, J90, J180, J270, G0, G90, G180, G270, F, AMH, FGM, T, PL, HO,\nC0C90, C0C270, C180C90, C180C270, GAL0GAL90, GAL0GAL270, GAL180GAL90, GAL180GAL270, J0J90, J0J270, J180J90, J180J270,\nG0G90, G0G270, G180G90, G180G270.")
if(!(M$extra.regI %in% c("t","pC","sED"))) stop("Error in parameter extra.regI value. It should be one of:\nt, pC or sED.")
if( !( margins[1] %in% c("probit", "logit") ) ) stop("Error in first margin value. It should be one of:\nprobit, logit.")
if(!(margins[2] %in% c(M$m2, "probit", "logit")) && M$intf == TRUE ) stop("Error in second margin value. It should be one of:\nN, GU, rGU, LO, LN, WEI, iG, GA, BE, FISK, probit, logit")
if(margins[2] %in% c(M$m1d,M$m2d) ) stop("Discrete margins are not allowed.")
if(margins[2] %in% c("TW") ) stop("Tweedie not yet allowed for. Get in touch for details.")
if(margins[2] %in% c("cloglog") ) stop("Complementary log-log not yet allowed for. Get in touch for details.")
if(l.flist > 2 && margins[2] %in% c(M$m2,M$m2d)){ if(l.flist!=4) stop("You need to specify four equations.") }
if(l.flist > 2 && margins[2] %in% M$m3 ){ if(l.flist!=5) stop("You need to specify five equations.") }
}
if(type == "biv"){ # binary - cont/discr models #
if(M$BivD == "T" && (M$dof <=2 || M$dof > 249)) stop("dof must be a number greater than 2 and smaller than 249.")
if(!is.null(M$theta.fx) && M$BivD != "N") stop("This approach is not currently implemented for non-Gaussian bivariate distributions.")
if(!is.null(M$theta.fx)) { if(M$Model != "B" && !(margins[2] %in% M$bl)) stop("Only bivariate Gaussian binary models with fixed theta are currenlty allowed for.")}
if(!is.null(M$theta.fx) ) { if( abs(M$theta.fx) > 0.999 ) stop("The theta value must be in the interval [-0.999,0.999].") }
if(M$Model == "BPO" && M$BivD != "N") stop("This model is not defined for copulae.")
if(M$Model == "BPO" && margins[1] != "probit" && margins[2] != "probit") stop("This model is not defined for the chosen margins.")
if(!(M$Model %in% M$mb)) stop("Error in parameter Model value. It should be one of:\nB, BSS, BPO, BPO0.")
if( M$Model == "BSS" && M$BivD %in% M$BivD2 ) stop("Mixed copulae can not be implemented for selection models.")
if(!(M$BivD %in% c(M$opc,M$BivD2))) stop("Error in parameter BivD value. It should be one of:\nN, C0, C90, C180, C270, GAL0, GAL90, GAL180, GAL270, J0, J90, J180, J270, G0, G90, G180, G270, F, AMH, FGM, T, PL, HO,\nC0C90, C0C270, C180C90, C180C270, GAL0GAL90, GAL0GAL270, GAL180GAL90, GAL180GAL270, J0J90, J0J270, J180J90, J180J270,\nG0G90, G0G270, G180G90, G180G270.")
if(!(M$extra.regI %in% c("t","pC","sED"))) stop("Error in parameter extra.regI value. It should be one of:\nt, pC or sED.")
if(!(margins[1] %in% M$bl) ) stop("Error in first margin value. It should be one of:\nprobit, logit, cloglog.")
if(!(margins[2] %in% c(M$bl,M$m2,M$m3)) && M$intf == FALSE ) stop("Error in second margin value. It should be one of:\nprobit, logit, cloglog.")
if(!(margins[2] %in% c(M$bl,M$m2,M$m3,M$m1d,M$m2d)) && M$intf == TRUE ) stop("Error in second margin value. It should be one of:\nN, GU, rGU, LO, LN, WEI, iG, GA, DAGUM, TW, SM, BE, FISK, PO, GP (and its versions), DGP (and its versions), ZTP, NBI, NBII, PIG.")
if(margins[2] %in% c(M$m2,M$m3,M$m1d,M$m2d) && (M$Model == "BPO" || M$Model == "BPO0") ) stop("For continuous/discrete responses, partial observability models\nare not allowed for.")
if(l.flist > 2 && margins[2] %in% c(M$bl,M$m1d)){ if(l.flist!=3) stop("You need to specify three equations.") }
if(l.flist > 2 && margins[2] %in% c(M$m2,M$m2d)){ if(l.flist!=4) stop("You need to specify four equations.") }
if(l.flist > 2 && margins[2] %in% M$m3 ){ if(l.flist!=5) stop("You need to specify five equations.") }
if( l.flist > 2 && M$Model == "BPO0") stop("You only need to specify two equations.\nThe chosen model does not have a correlation parameter.")
if( l.flist > 2 && M$Model == "B" && !is.null(M$theta.fx)) stop("You only need to specify two equations.\nThe chosen model is not allowed to estimate the theta parameter.")
if(margins[2] %in% c("TW") && l.flist != 5) stop("You need to specify five equations.")
if(margins[2] %in% c("GP", "GPII","GPo","DGP","DGPII")) stop("GP, GPII, GPo, DGP, DGPII not done yet.\nGet in touch for details.")
}
if(type == "triv"){
mmar <- c("probit", "logit", "cloglog")
if(!(M$Model %in% M$mb)) stop("Error in parameter Model value. It should be one of: T, TSS, TESS.")
if(!(margins[1] %in% mmar) ) stop("Error in first margin value. It should be one of:\nprobit, logit, cloglog.")
if(!(margins[2] %in% mmar) ) stop("Error in second margin value. It should be one of:\nprobit, logit, cloglog.")
if(!(margins[3] %in% mmar) ) stop("Error in third margin value. It should be one of:\nprobit, logit, cloglog.")
if(!(M$penCor %in% c("unpen", "ridge", "lasso", "alasso"))) stop("Error in parameter penCor value. It should be one of:\nunpen, ridge, lasso, alasso.")
if(is.null(M$w.alasso) && M$penCor == "alasso") stop("You must provide a vector of three weights when using alasso.")
if(length(M$w.alasso)!=3 && M$penCor == "alasso") stop("You must supply a vector made up of three weights.")
if(!(M$extra.regI %in% c("t","pC","sED"))) stop("Error in parameter extra.regI value. It should be one of:\nt, pC or sED.")
if(l.flist > 3 && M$penCor %in% c("ridge", "lasso", "alasso")) stop("This option is not currently allowed.")
if(l.flist > 3 && M$Chol == FALSE) stop("You must set Chol = TRUE.")
if(l.flist > 3 && M$Model %in% c("TSS", "TESS")) stop("You can not currently use more than three equations with the model chosen.")
######################################################################################################################################################
#if( M$Model %in% c("TSS","TESS") ) stop("Check the next release for the final tested version of this model\nor get in touch to check progress.")
######################################################################################################################################################
}
if(type == "copR"){
if(M$surv == TRUE){
if( !(margins[1] %in% c(M$m2,M$m3,M$bl)) ) stop("The first marginal distribution must be either continuous or probit, PO or PH.")
if( !(margins[2] %in% c(M$bl,scs)) ) stop("The second marginal distribution must be probit, PO or PH.")
if(margins[1] %in% c("TW") || margins[2] %in% c("TW") ) stop("Tweedie not yet allowed for. Get in touch for details.")
if(!is.null(M$c1) && length(table( M$c1 %in% c(0,1) ) ) > 1 ) stop("Your first censoring indicator is not binary. Please fix.")
if(!is.null(M$c2) && length(table( M$c2 %in% c(0,1) ) ) > 1 ) stop("Your second censoring indicator is not binary. Please fix.")
if(length(M$c1) != length(M$c2)) stop("The two censoring indicators must have the same length.")
if(l.flist > 2 && margins[1] %in% c(M$bl) && margins[2] %in% c(M$bl)){ if(l.flist!=3) stop("You need to specify three equations.") }
if(l.flist > 2 && margins[1] %in% c(M$m2) && margins[2] %in% c(M$bl)){ if(l.flist!=4) stop("You need to specify four equations.") }
if(l.flist > 2 && margins[1] %in% c(M$m3) && margins[2] %in% c(M$bl)){ if(l.flist!=5) stop("You need to specify five equations.") }
}
if(M$BivD == "T" && (M$dof <=2 || M$dof > 249)) stop("dof must be a number greater than 2 and smaller than 249.")
if( margins[1] %in% c(M$m2d) && margins[2] %in% c(M$m1d) ) stop("Please swap the two equations (and hence margins' specification).\nThe second instead of the first margin has to be a two-parameter discrete distribution.")
if( margins[1] %in% c(M$m2,M$m3) && margins[2] %in% c(M$m1d,M$m2d) ) stop("Please swap the two equations (and hence margins' specification).\nThe first instead of the second margin has to be discrete.")
if(!(M$BivD %in% c(M$opc,M$BivD2))) stop("Error in parameter BivD value. It should be one of:\nN, C0, C90, C180, C270, GAL0, GAL90, GAL180, GAL270, J0, J90, J180, J270, G0, G90, G180, G270, F, AMH, FGM, T, PL, HO, \nC0C90, C0C270, C180C90, C180C270, GAL0GAL90, GAL0GAL270, GAL180GAL90, GAL180GAL270, J0J90, J0J270, J180J90, J180J270,\nG0G90, G0G270, G180G90, G180G270.")
if(!(M$extra.regI %in% c("t","pC","sED"))) stop("Error in parameter extra.regI value. It should be one of:\nt, pC or sED.")
if(!(margins[1] %in% c(M$m2,M$m3,M$m1d,M$m2d,M$bl)) ) stop("Error in first margin value. It should be one of:\nN, GU, rGU, LO, LN, WEI, iG, GA, DAGUM, TW, SM, BE, FISK, NBI, NBII, PIG, PO, GP (and its versions), DGP (and its versions), ZTP\nor probit, logit, cloglog for survival models.")
if(!(margins[2] %in% c(M$m2,M$m3,M$m1d,M$m2d,M$bl)) ) stop("Error in second margin value. It should be one of:\nN, GU, rGU, LO, LN, WEI, iG, GA, DAGUM, TW, SM, BE, FISK, NBI, NBII, PIG, PO, GP (and its versions), DGP (and its versions), ZTP\nor probit, logit, cloglog for survival models.")
if(M$BivD == "T" && margins[1] %in% c(M$m2,M$m3) && margins[2] %in% c(M$m2,M$m3)){
if(l.flist > 2 && margins[1] %in% c(M$m2) && margins[2] %in% c(M$m2)){ if(l.flist!=6) stop("You need to specify six equations.") }
if(l.flist > 2 && margins[1] %in% c(M$m2) && margins[2] %in% c(M$m3)){ if(l.flist!=7) stop("You need to specify seven equations.") }
if(l.flist > 2 && margins[1] %in% c(M$m3) && margins[2] %in% c(M$m2)){ if(l.flist!=7) stop("You need to specify seven equations.") }
if(l.flist > 2 && margins[1] %in% c(M$m3) && margins[2] %in% c(M$m3)){ if(l.flist!=8) stop("You need to specify eight equations.") }
}else{
if(l.flist > 2 && margins[1] %in% c(M$m1d,M$bl) && margins[2] %in% c(M$m1d,M$bl)) { if(l.flist!=3) stop("You need to specify three equations.") }
if(l.flist > 2 && margins[1] %in% c(M$m2d) && margins[2] %in% c(M$m1d)) { if(l.flist!=4) stop("You need to specify four equations.") }
if(l.flist > 2 && margins[1] %in% c(M$m1d) && margins[2] %in% c(M$m2,M$m2d)) { if(l.flist!=4) stop("You need to specify four equations.") }
if(l.flist > 2 && margins[1] %in% c(M$m1d) && margins[2] %in% c(M$m3,M$m3d)) { if(l.flist!=5) stop("You need to specify five equations.") }
if(l.flist > 2 && margins[1] %in% c(M$m2,M$m2d) && margins[2] %in% c(M$m2,M$m2d)){ if(l.flist!=5) stop("You need to specify five equations.") }
if(l.flist > 2 && margins[1] %in% c(M$m2,M$m2d) && margins[2] %in% c(M$m3,M$m3d)){ if(l.flist!=6) stop("You need to specify six equations.") }
if(l.flist > 2 && margins[1] %in% c(M$m3,M$m3d) && margins[2] %in% c(M$m2,M$m2d)){ if(l.flist!=6) stop("You need to specify six equations.") }
if(l.flist > 2 && margins[1] %in% c(M$m3,M$m3d) && margins[2] %in% c(M$m3,M$m3d)){ if(l.flist!=7) stop("You need to specify seven equations.") }
}
if(margins[1] %in% c("GP","GPII","GPo","DGP","DGPII") || margins[2] %in% c("GP","GPII","GPo","DGP", "DGPII")) stop("GP, GPII, GPo, DGP, DGPII not done yet.\nGet in touch for details.")
##################################################################################################################################################################################################
# if( M$surv == TRUE && margins[1] %in% c(M$m2,M$m3) && margins[2] %in% c(M$bl) ) stop("Survival models with continuous and survival margins not ready yet.\nGet in touch to check progress.")
#if( margins[2] %in% c(M$m2,M$m3) && margins[1] %in% c(M$m1d,M$m2d) ) stop("The continuous - discrete margin case is not ready yet.\nGet in touch to check progress.")
##################################################################################################################################################################################################
}
if(type == "copSS"){
if(M$BivD == "T" && (M$dof <=2 || M$dof > 249)) stop("dof must be a number greater than 2 and smaller than 249.")
if(!(M$BivD %in% M$opc)) stop("Error in parameter BivD value. It should be one of: N, C0, C90, C180, C270, GAL0, GAL90, GAL180, GAL270, J0, J90, J180, J270, G0, G90, G180, G270, F, AMH, FGM, T, PL, HO.")
if(!(M$extra.regI %in% c("t","pC","sED"))) stop("Error in parameter extra.regI value. It should be one of: t, pC or sED.")
if(!(M$margins[1] %in% M$bl) ) stop("Error in first margin value. It should be one of:\nprobit, logit, cloglog.")
if(!(M$margins[2] %in% c(M$m2,M$m3,M$m1d,M$m2d)) ) stop("Error in second margin value. It should be one of:\nN, GU, rGU, LO, LN, WEI, iG, GA, DAGUM, TW, SM, BE, FISK, PO, GP (and its versions), DGP (and its versions), ZTP, NBI, NBII, PIG.")
###########################################
#if(M$margins[2] %in% c("TW") ) stop("Tweedie not yet allowed for. Get in touch for details.")
###########################################
if(l.flist > 2 && M$margins[2] %in% c(M$m1d) ){ if(l.flist!=3) stop("You need to specify three equations.") }
if(l.flist > 2 && M$margins[2] %in% c(M$m2,M$m2d)){ if(l.flist!=4) stop("You need to specify four equations.") }
if(l.flist > 2 && M$margins[2] %in% M$m3 ){ if(l.flist!=5) stop("You need to specify five equations.") }
if(M$margins[2] %in% c("TW") ){ if(l.flist!=5) stop("You need to specify five equations.") }
if(M$margins[2] %in% c("GP", "GPII", "GPo", "DGP","DGPII") ) stop("GP, GPII, GPo, DGP, DGPII not done yet.\nGet in touch for details.")
}
if(type == "gamls"){
if(M$surv == TRUE){
if( !(M$type.cens %in% c("R","L","I","mixed")) ) stop("The type of censoring can be R, L, I or mixed.")
if( !is.null(M$v.rB) && !is.character(M$v.rB) ) stop("v.rB must be a character variable.")
if( !(M$margin %in% c(scs,M$bl)) ) stop("The marginal distribution can be probit, PO or PH.")
if(is.null(M$cens) ) stop("You must provide the binary censoring indicator.")
if( M$type.cens %in% c("R","L","I") ){
if( length(table( M$cens %in% c(0,1) ) ) > 1 ) stop("Your censoring indicator is not binary. Please fix.")
}
if( M$type.cens %in% c("mixed") ){
if( !is.factor(M$cens) ) stop("The cens variable must be a factor variable.")
# NEW: include truncated censoring indicators
c.set <- c("R","L","I","U","RT","LT","IT","UT")
ucens <- unique(M$cens); l.uc <- length(ucens)
for(i in 1:l.uc){ if(!(ucens[i] %in% c.set)) stop("The cens variable can only take values in (R, L, I, U, RT, LT, IT, UT).")}
}
}
if(M$surv == TRUE && M$robust == TRUE) stop("It is not currently possible to fit robust survival models.")
if(!(M$extra.regI %in% c("t","pC","sED"))) stop("Error in parameter extra.regI value. It should be one of:\nt, pC or sED.")
if(!(M$margin %in% c(M$m2,M$m3,M$m1d,M$m2d, M$bl)) ) stop("Error in margin value. It should be one of:\nN, GU, rGU, LO, LN, WEI, iG, GA, GP, GPII, GPo, DGP, DGPII, DAGUM, TW, SM, BE, FISK, NBI, NBII, PIG, PO, GP (and its versions), DGP (and its versions), ZTP, GEVlink.")
if(l.flist > 1 && M$margin %in% c(M$m1d) ) stop("You need to specify one equation.")
if(l.flist > 1 && M$margin %in% c(M$m2,M$m2d) ){ if(l.flist!=2) stop("You need to specify two equations.") }
if(l.flist > 1 && M$margin %in% c(M$m3,M$m3d) ){ if(l.flist!=3) stop("You need to specify three equations.") }
if(l.flist !=3 && M$margin %in% c("TW") ) stop("You need to specify three equations.")
if(M$surv == TRUE && M$margin %in% M$bl && M$informative == "yes" && l.flist != 2 ) stop("You need to specify two equations.")
if(M$surv == TRUE && M$margin %in% M$bl && M$informative == "yes" && is.null(M$list.inf.cov)) stop("You need to specify a set of informative covariates otherwise use the non-informative model.")
if(M$surv == TRUE && M$margin %in% M$bl && M$informative == "yes" && M$type.cens != "R" ) stop("The informative model only allows for right censoring.")
}
}
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