#' @export
pdf.cdd <- function(raw.results.file,skipped.id.file,pdf.filename,
min.failed,cov.failed,cov.warnings,boundary,legend,cutoff_delta.ofv,
cutoff_cook,outlier_ID) {
#default for legend is FALSE
if (missing(legend)) {
legend <- FALSE
}
#default for legend is FALSE
if (missing(cutoff_cook)) {
cutoff_cook <- 0.8
}
# 1. Create table cdd.data
list_input_data <- create.data.full(raw.results.file,skipped.id.file)
cdd.data.all <- list_input_data$cdd.data.all
no.cook.cov <- list_input_data$no.cook.cov
ID_failed_cov <- list_input_data$ID_failed_cov
if(!(no.cook.cov)) {
## skip first record (no cases deleted)
cdd.data <- cdd.data.all[-1,]
# 2. Create tables cdd.warn and p1
p1 <- warnings.data(cdd.data,min.failed,cov.failed,cov.warnings,boundary)
if (class(p1) == "list") {
cdd.warn <- p1$cdd.warn
p1 <- p1$p1
}
# 3. Count not successful values
fail <- failed.values(cdd.data)
# create pdf file
pdf(file=pdf.filename,width=11.69, height=8.27)
# 4. calculate cutoff cov ratios
list_out <- cutoff.cov.cook(raw.results.file,skipped.id.file,cutoff_cook)
cutoff_cov <- list_out$cutoff_cov
cov.cook.data <- list_out$cov.cook.data
# 5. Create a plot
if (exists("cdd.warn")) {
plot_cdd(cov.cook.data,cutoff_cook,cutoff_cov,ID_failed_cov,legend,fail,cdd.warn)
} else {
plot_cdd(cov.cook.data,cutoff_cook,cutoff_cov,ID_failed_cov,legend,fail)
}
# create cutoff tables
# rotate column names
rotate = gridExtra::ttheme_default(colhead=list(fg_params=list(rot=90)))
#unlist
cook_outliers_data <- list_out$cook_outliers_data
infl_cook_data <- list_out$infl_cook_data
# draw a table
plot_table(cook_outliers_data,rotate=rotate)
cov_outliers_data <- list_out$cov_outliers_data
infl_cov_data <- list_out$infl_cov_data
# draw a table
plot_table(cov_outliers_data,rotate=rotate)
# 8. influential indivifuals
if (missing(outlier_ID)) {
# create needed data form plotting
list.delta.ofv <- delta.ofv.data(cdd.data.all,cutoff_delta.ofv=cutoff_delta.ofv)
data_plot <- list.delta.ofv$data_plot
row_infl <- list.delta.ofv$row_infl
fail_ID <- list.delta.ofv$fail_ID
infl_ofv <- list.delta.ofv$infl_ofv
# create a plot
plot_delta_ofv(data_plot,row_infl,fail_ID,cutoff_delta.ofv=cutoff_delta.ofv)
} else {
# create needed data for plotting
list.delta.ofv <- delta.ofv.data(cdd.data.all,cutoff_delta.ofv=cutoff_delta.ofv,outlier_ID)
data_plot <- list.delta.ofv$data_plot
row_outl_infl <- list.delta.ofv$row_outl_infl
row_outl <- list.delta.ofv$row_outl
row_infl <- list.delta.ofv$row_infl
fail_ID <- list.delta.ofv$fail_ID
infl_ofv <- list.delta.ofv$infl_ofv
# create a plot
plot_delta_ofv(data_plot,row_infl,fail_ID,row_outl,row_outl_infl,cutoff_delta.ofv=cutoff_delta.ofv)
}
# influential summary table
all_table <- all_infl_indiv_table(infl_ofv,infl_cook_data,infl_cov_data,fail_ID,ID_failed_cov)
plot_table(all_table)
#close pdf
dev.off()
} else {
message("Can't create a pdf file, because no cook score or cov ratio values are found in the raw results csv file!")
}
}
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