Nothing
# target: the target value
# sesObject: the outcome of the ses
# nisgnat: Number of signatures and generated models. It could be numeric from 1 to total number of signatures or "all" for all the
## signatures. Default is 1.
ses.gee.model = function(target, dataset, reps = NULL, group, correl = "exchangeable", se = "jack",
wei = NULL, sesgee.Object, nsignat = 1, test = NULL) {
if ( sum( is.na(sesgee.Object@selectedVars) ) > 0 ) {
mod <- paste("No associations were found, hence no model is produced.")
signature <- NULL
res <- list(mod = mod, signature = signature)
} else {
if ( any(is.na(dataset) ) ) {
warning("The dataset contains missing values (NA) and they were replaced automatically by the variable (column) median (for numeric) or by the most frequent level (mode) if the variable is factor")
dataset <- apply( dataset, 2, function(x){ x[which(is.na(x))] = median(x, na.rm = TRUE) ; return(x) } )
}
if ( is.null(test) ) {
ci_test <- sesgee.Object@test
} else ci_test <- test
if ( nsignat == 1 || ( nsignat > 1 & nrow(sesgee.Object@signatures) == 1 ) ) {
signature <- sesgee.Object@selectedVars
if (test == "testIndGEEReg") {
oiko <- gaussian
} else if (test == "testIndGEELogistic") {
oiko <- binomial(logit)
} else if (test == "testIndGEEPois") {
oiko <- poisson(log)
} else if (test == "testIndGEEGamma") {
oiko <- Gamma(log)
} else if (test == "testIndGEENormLog") {
oiko <- gaussian(log)
}
if ( is.null(reps) ) {
mod <- try( geepack::geeglm( target ~ dataset[, signature], family = oiko, id = group, weights = wei, corstr = correl, std.err = se ), silent = TRUE)
} else {
mod <- try( geepack::geeglm( target ~ reps + dataset[, signature], family = oiko, id = group, weights = wei, corstr = correl, std.err = se ), silent = TRUE)
}
}
if ( is.null( colnames(dataset) ) ) {
names(signature) = paste("Var", signature, sep = " ")
} else names(signature) = colnames(dataset)[signature]
signature <- c(signature, bic)
names(signature)[length(signature)] = "bic"
res <- list(mod = mod, signature = signature)
############# more than one signatures
if ( nsignat > 1 & nrow(sesgee.Object@signatures) > 1 ) {
if ( nsignat > nrow(sesgee.Object@signatures) ) nsignat = nrow(sesgee.Object@signatures)
bic <- numeric(nsignat)
signature <- sesgee.Object@signatures[1:nsignat, , drop = FALSE]
mod <- list()
for ( i in 1:nsignat ) {
if (test == "testIndGEEReg") {
oiko <- gaussian
} else if(test == "testIndGEELogistic") {
oiko <- binomial(logit)
} else if (test == "testIndGEEPois") {
oiko <- poisson(log)
} else if (test == "testIndGEEGamma") {
oiko <- Gamma(log)
} else if (test == "testIndGEENormLog") {
oiko <- gaussian(log)
}
if ( is.null(reps) ) {
mod[[ i ]] <- try( geepack::geeglm( target ~ dataset[, signature], family = oiko, id = group, weights = wei, corstr = correl, std.err = se ), silent = TRUE)
} else {
mod[[ i ]] <- try( geepack::geeglm( target ~ reps + dataset[, signature], family = oiko, id = group, weights = wei, corstr = correl, std.err = se ), silent = TRUE)
}
}
signature <- cbind(signature, bic)
}
if ( nsignat == "all" ) {
signature <- sesgee.Object@signatures
bic <- numeric( nrow(signature) )
mod <- list()
for ( i in 1:nrow(signature) ) {
if (test == "testIndGEEReg") {
oiko <- gaussian
} else if(test == "testIndGEELogistic") {
oiko <- binomial(logit)
} else if (test == "testIndGEEPois") {
oiko <- poisson(log)
} else if (test == "testIndGEEGamma") {
oiko <- Gamma(log)
} else if (test == "testIndGEENormLog") {
oiko <- gaussian(log)
}
if ( is.null(reps) ) {
mod[[ i ]] <- try( geepack::geeglm( target ~ dataset[, signature], family = oiko, id = group, weights = wei, corstr = correl, std.err = se ), silent = TRUE)
} else {
mod[[ i ]] <- try( geepack::geeglm( target ~ reps + dataset[, signature], family = oiko, id = group, weights = wei, corstr = correl, std.err = se ), silent = TRUE)
}
}
signature <- cbind(signature, bic)
}
} ## if ( sum( is.na(sesgee.Object@selectedVars) ) > 0 ) {
res
}
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