#' @export
simeval_all_outliers_table <- function(simeval_directory,ebe_npde_outl_crit=-3,quiet=F) {
if(file.exists(file.path(working.directory,"simeval_run/raw_all_iofv.csv")) &&
file.exists(file.path(working.directory,"simeval_run/ebe_npde.csv"))) {
#ofv outliers
iofv_res <- i_ofv_res(file.path(simeval_directory, "raw_all_iofv.csv"),show.warning=F)
ofv_outliers <- iofv_res$ofv_outliertable
ID_deleted_ofv <- iofv_res$ID_deleted_ofv
# ebe_npde outliers
input_data <- input.data(file.path(simeval_directory, "ebe_npde.csv"),show.warning=F)
ebenpde_tmp <- input_data$ebenpde_tmp
n.subjects <- input_data$n.subjects
ebenpde_obs <- input_data$ebenpde_obs
ID_deleted_ebe <- input_data$ID_deleted
eta.names <- input_data$eta.names
if(n.subjects>1) { # will not work if only one ID
list_emp_distance <- empirical.distance(ebenpde_obs,n.subjects)
emp_distance <- list_emp_distance$emp_distance
out_tables <- data.for.plots(emp_distance,n.subjects,eta.names)
index_emp_distance <- out_tables$index_emp_distance
emp_distance_sort <- out_tables$emp_distance_sort
theor_distance <- out_tables$theor_distance
out_distance <- out_tables$out_distance
list_plot_1 <- plot_1(ebenpde_tmp,theor_distance,emp_distance_sort,index_emp_distance,
out_distance,n.subjects,outlying_criteria=ebe_npde_outl_crit,do_outlier_plot=FALSE,
model.filename='')
flag <- list_plot_1$flag
noutlier <- list_plot_1$noutlier
outlier_id_row <-list_plot_1$outlier_id_row
list_plot_2 <- plot_2(ebenpde_tmp,emp_distance_sort,theor_distance,index_emp_distance,
noutlier,flag,n.subjects,eta.names,outlying_criteria=ebe_npde_outl_crit,outlier_id_row,
do_outlier_plot=FALSE,model.filename='')
vector_theor_dist <- list_plot_2$vector_theor_dist
noutlier <- list_plot_2$noutlier
outlier_id_row <- list_plot_2$outlier_id_row
ebe.npde_outliers <- outlier.table.ebe.npde(ebenpde_tmp,eta.names,outlier_id_row)
if (ncol(ebe.npde_outliers) > 1) {
ebe.npde_outliers <- ebe.npde_outliers[,1:2]
} else {
ebe.npde_outliers <- data.frame()
}
} else {
ebe.npde_outliers <- data.frame()
}
#residual outliers
list_residuals <- outlier.table(residual.outliers.file=file.path(simeval_directory, "residual_outliers.csv"))
cwres.iwres_outliers <- list_residuals$outliers_count
residual_names <- list_residuals$residual_names
#all outlier table
all_outlier_table <- all_outlier_report_table(ofv_outliers,ebe.npde_outliers,cwres.iwres_outliers,
residual_names,ID_deleted_ebe,ID_deleted_ofv)
add_header_above <- c(" "=1,"Individual level"=2)
if(length(residual_names)>0) {
add_header_above <- c(" "=1,"Individual level"=2,"Observation level"=length(residual_names))
}
if(ncol(all_outlier_table)==1) {
add_header_above <- NULL
}
out <- list(all_outlier_table=all_outlier_table,
add_header_above=add_header_above,
files_exist=TRUE)
} else {
if(!file.exists(file.path(working.directory,"simeval_run/raw_all_iofv.csv")) && !quiet) {
message("WARNING: File ",file.path(working.directory,"simeval_run/raw_all_iofv.csv")," not found!")
}
if(!file.exists(file.path(working.directory,"simeval_run/ebe_npde.csv")) && !quiet) {
message("WARNING: File ",file.path(working.directory,"simeval_run/ebe_npde.csv")," not found!")
}
out <- list(files_exist=FALSE)
}
return(out)
}
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