library(readxl)
##-- Map ISSCFC and ISSCAAP ----
commodity <- readxl::read_xlsx("C:/Users/Taglionic/Desktop/Fisheries/Documents_fisheries/ybklang_12032019.xlsx",
sheet = 1, col_names = TRUE)
commodity <- as.data.table(commodity)
commodity_select <- commodity[ , .(`Internal Code`, `ISSCAAP Code`, `Fao Commodity Code`, `English Name`, `ICS Code`, `Conversion Factor`)]
isscaapNames <- readxl::read_xlsx("C:/Users/Taglionic/Documents/Github/faoswsFisheryStandardization/Input_documents/classification.xlsx",
sheet = 5, col_names = TRUE, skip = 1)
isscaapNames <- as.data.table(isscaapNames)
isscaapNames <- isscaapNames[ , .( `ISSCAAP group: name`, `ISSCAAP group: code`)]
setkey(isscaapNames)
isscaapNames <- isscaapNames[ !duplicated(isscaapNames)]
isscaapNames$`ISSCAAP group: code` <- as.character(isscaapNames$`ISSCAAP group: code`)
commodity2isscaap <- merge(commodity_select, isscaapNames, by.x = "ISSCAAP Code", by.y = "ISSCAAP group: code",
all = TRUE)
# Add some names that are not in the file
commodity2isscaap$`ISSCAAP group: name` <- ifelse(commodity2isscaap$`ISSCAAP Code`=="61", "Blue-whales, fin-whales",
ifelse(commodity2isscaap$`ISSCAAP Code`=="62", "Sperm-whales, pilot-whales",
ifelse(commodity2isscaap$`ISSCAAP Code`=="63","Eared seals, hair seals, walruses",
ifelse(commodity2isscaap$`ISSCAAP Code`=="81", "Pearls, mother-of-pearl, shells",
ifelse(commodity2isscaap$`ISSCAAP Code`=="94", "Miscellaneous aquatic plants",
ifelse(commodity2isscaap$`ISSCAAP Code`=="92", "Red seaweeds",
ifelse(commodity2isscaap$`ISSCAAP Code`=="82", "Corals",
ifelse(commodity2isscaap$`ISSCAAP Code`=="91", "Brown seaweeds",
ifelse(commodity2isscaap$`ISSCAAP Code`=="93", "Green seaweeds",
ifelse(commodity2isscaap$`ISSCAAP Code`=="83", "Sponges",
ifelse(commodity2isscaap$`ISSCAAP Code`=="64", "Miscellaneous aquatic mammals",
commodity2isscaap$`ISSCAAP group: name`) )))) )) ))))
# Add ICS codes
ics <- readxl::read_xlsx("C:/Users/Taglionic/Documents/Github/faoswsFisheryStandardization/Input_documents/classification.xlsx",
sheet = 1, col_names = TRUE)
ics <- as.data.table(ics)
ics <- ics[ , .(`ICS_FAOSTAT Code`, `English Name`)]
setnames(ics, "English Name", "ICS Label")
# Combine data.tables
commodity2isscaap_complete <- merge(commodity2isscaap, ics, by.x = "ICS Code", by.y = "ICS_FAOSTAT Code",
all.x = TRUE)
commodity2isscaap_final <- commodity2isscaap_complete[, .( `ICS Code`,
`ICS Label`,
`ISSCAAP Code`,
`ISSCAAP group: name`,
`Internal Code`,
`Fao Commodity Code`,
`English Name`,
`Conversion Factor`)]
commodity2isscaap_final <- commodity2isscaap_final[order(`ICS Code`),]
setnames(commodity2isscaap_final, names(commodity2isscaap_final),
c("ics", "ics_label", "isscaap", "isscaap_label", "internal_code", "isscfc", "isscfc_label", "conversion_factor"))
write.csv(commodity2isscaap_final, file = "C:/Users/Taglionic/Documents/Github/faoswsFisheryStandardization/Input_documents/isscfc_isscaap_classification.csv",
row.names = FALSE, fileEncoding = "UTF-8")
##-- Map ASFIS and ISSCAAP ----
isscaap2asfis <- readxl::read_xlsx("C:/Users/Taglionic/Documents/Github/faoswsFisheryStandardization/Input_documents/classification.xlsx",
sheet = 6, col_names = TRUE)
isscaap2asfis <- as.data.table(isscaap2asfis)
isscaap2asfis <- isscaap2asfis[ , . (ISSCAAP, TAXOCODE, `3A_CODE`, Scientific_name, English_name)]
setnames(isscaap2asfis, names(isscaap2asfis),
c("isscaap", "asfis_taxocode", "asfis_alphacode", "asfis_label_scientific", "asfis_label_english"))
isscaapLabels <- unique(commodity2isscaap_final[, .(isscaap, isscaap_label)])
isscaap2asfis_final <- merge(isscaap2asfis, isscaapLabels, by = "isscaap", all = TRUE)
isscaap2asfis_final <- isscaap2asfis_final[order(isscaap2asfis_final$isscaap)]
isscaap2asfis_final <- isscaap2asfis_final[, .(isscaap,
isscaap_label,
asfis_taxocode,
asfis_alphacode,
asfis_label_scientific,
asfis_label_english)]
write.csv(isscaap2asfis_final, file = "C:/Users/Taglionic/Documents/Github/faoswsFisheryStandardization/Input_documents/asfis_isscaap_classification.csv",
row.names = FALSE, fileEncoding = "UTF-8")
##-- Map ISSCFC and ASFIS through ISSCAAP ----
complete_table <- merge(isscaap2asfis_final, commodity2isscaap_final,
by = c("isscaap", "isscaap_label"), all = TRUE,
allow.cartesian = TRUE)
complete_table <- complete_table[order(complete_table$ics),]
complete_table <- complete_table[ , .(ics, ics_label, isscaap, isscaap_label,
internal_code, isscfc, isscfc_label,
asfis_taxocode, asfis_alphacode,
asfis_label_scientific, asfis_label_english)]
write.csv(complete_table, file = "C:/Users/Taglionic/Documents/Github/faoswsFisheryStandardization/Input_documents/FisheryClassification.csv",
row.names = FALSE, fileEncoding = "UTF-8")
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