R/check.table.R

In EcoTroph: An Implementation of the EcoTroph Ecosystem Modelling Approach

#'  convert.list2tab enables to convert the list object returned by the create.ETdiagnosis function into a list of data.frames. These data.frames contain calculated variables by TL class and combinations of effort multipliers.
#' @param ecopath is the input table used in ET (possibly based on Ecopath data). The different variables are the group name, its trophic level, biomass, production, catches, omnivory index and accessibility (fraction of the group that can be catch assuming an infinite fishing effort).
#' @examples
#' data(ecopath_guinee)
#' check.table(ecopath_guinee)
#' @export

check.table <- function (ecopath)
{
if (is.data.frame(ecopath) == FALSE)
ecopath <- as.data.frame(ecopath)
names <- names(ecopath)
wanted <- c("group_name", "TL", "biomass", "prod", "accessibility", "OI")
verif <- is.na(match(wanted, names))
pb <- paste(wanted[which(verif == TRUE)], collapse = " ")
if (pb != "")
cat(paste("The column(s) ", pb, " is(are) not present (if the column OI is not present, it's not an issue but the use of the OI smooth (smooth_type=3) won't be possible).\n"))
if (length(grep("catch", names)) == 0)
print("No fleet/catches are detected. Even if no catches are made (MPA or no data), a column with 0 value must be entered. The name of the column has to be written as 'catch.something'.")

cat("\nCHECK OF THE NA VALUES, IF A MESSAGE APPEARS, PLEASE READ IT CAREFULLY AND FOLLOW THE INSTRUCTIONS. NO NA IS ACCEPTED AS INPUT DATA.\n\n")
for (i in wanted[which(verif == FALSE)]) {
if (match(NA, ecopath[, i], FALSE) > 0) {
if (i == "prod") {
pb <- paste(ecopath[is.na(ecopath$prod), ]$group_name, collapse = " ")
cat(paste("The column prod contains a NA for the group", pb, ", that's an issue if the concerned groups are not detritus. If the concerned group is a detritus group, change the NA value by 0; otherwhise check your table and correct by the right value (use fix() for example or reload it after correction).\n"))
}
else {
toto <- paste(i)
cat(paste("The column", i, "contains a NA, that's a problem! Check and correct the table (you can use fix()).\n"))
}}
}

for (pecheries in colnames(ecopath)[grep("catch", colnames(ecopath))]) {
if (match(NA, ecopath[, pecheries], FALSE) > 0) {
cat(paste("The column", pecheries, "contains NA. That's a problem! Even if no catches are made (MPA or no data), 0 value must be entered. Use fix() to change the NA by the proper value or reload the dataset after correction.\n"))
}}

cat("\nCHECK OF THE ACCESSIBILITY VALUES, IF A MESSAGE APPEARS, PLEASE READ IT CAREFULLY AND FOLLOW THE INSTRUCTIONS.\n\n")
for (pecheries in colnames(ecopath)[grep("catch", colnames(ecopath))]) {
for (i in 1:length(ecopath$group_name)) {
if ((ecopath[i, pecheries] > 0) && (ecopath[i,"accessibility"] == 0)){
cat(paste("The group", ecopath[i,"group_name"], "has a null accessibility, that's a problem! He is fished by the fishery", pecheries, "and consequently needs a positive value.\n"))
}}}

for (i in 1:length(ecopath$group_name)) {
if ((ecopath[i,"accessibility"] > 1)){
cat(paste("The group", ecopath[i,"group_name"], "has an accessibility value higher to 1, that's a problem! Choose a value between 0 and 1.\n"))
}}
}