AFA_secondary_functions

#Source functions for the AFA. Saved as AFA_secondary_functions.R

#Function to create canonical name from variables provided on the ACT plant cesus
canonical_name_for_ACT <- function(x) {
  #if only genus, return NA
  if(is.na(x[2])) {
    return(NA)}
  #if infraspecies is NA, then paste and collapse genus and species
  if(is.na(x[3])) {
    return(paste0(x[1:2], collapse = " "))}
  #any other case, paste and collapse genus, species and infraspecies
  else {
    return(paste0(x[1:3], collapse = " "))}
}

#Function to create phrase species name
phrasespNSW <- function(x) {
  #if no phrase name, return NA
  if(is.na(x[2])& !is.na(x[1])) {
    return(NA)}
  #if phrase name, paste and collapse genus and phrase name
  if(!is.na(x[2])& !is.na(x[1])) {
    return(paste0(x[1:2], collapse = ""))}
}

#Function. Step 1 for creating canonical name
canonical_name_NSW1 <- function(x) {
  #if there is no infraspecies, return species name
  if(is.na(x[2])& !is.na(x[1])) {
    return(paste0(x[1]))}
  #if there is infraspecies, paste and collapse
  if(!is.na(x[2])& !is.na(x[1])) {
    return(paste0(x[1:2], collapse = " "))}
}

#Function. Step 1 for creating canonical name
canonical_name_TAS1 <- function(x) {
  #if there is no infraspecies, return species name
  if(is.na(x[2])& !is.na(x[1])) {
    return(paste0(x[1]))}
  #if there is infraspecies, paste and collapse
  if(!is.na(x[2])& !is.na(x[1])) {
    return(paste0(x[1:2], collapse = " "))}
}

#Function. Step 2 for creating canonical name
canonical_name_NSW2 <- function(x) {
  #if there is no hybrids, return the canonical name obtained in the previous step
  if(is.na(x[2])& !is.na(x[1])) {
    return(paste0(x[1]))}
  #if there are hybrids, paste and collapse
  if(!is.na(x[2])& !is.na(x[1])) {
    return(paste0(x[1:2], collapse = ""))}
}

#Function. Step 2 for creating canonical name
canonical_name_TAS2 <- function(x) {
  #if there is no hybrids, return the canonical name obtained in the previous step
  if(is.na(x[2])& !is.na(x[1])) {
    return(paste0(x[1]))}
  #if there are hybrids, paste and collapse
  if(!is.na(x[2])& !is.na(x[1])) {
    return(paste0(x[1:2], collapse = " "))}
}

#function to create canonical name from variables provided on the NT plant census
canonical_name_from_scratch <- function(x) {
  #if only genus, return NA
  if(is.na(x[2])) {
    return(NA)}
  #if infraspecies rank is NA, then paste and collapse genus and species
  if(is.na(x[3])) {
    return(paste0(x[1:2], collapse = " "))}
  #if there is intraspecies rank, then paste and collapse genus, species, infraspecies rank and infraspecies epithet
  else {
    return(paste0(x[1:4], collapse = " "))}
} #close function


#same function than before but including authorship to create state name for the NT
state_name_from_scratch <- function(x) {
  if(is.na(x[2])) {
    return(NA)}
  if(is.na(x[4])) {
    return(paste0(x[1:3], collapse = " "))}
  if(is.na(x[6])) {
    return(paste0(x[1:5], collapse = " "))}
  else {
    return(paste0(x[1:6], collapse = " "))}
} #close function

#Function for TAS state name
state_name <- function(x) {
  #if accepted name is NA, keep full name
  if(is.na(x[1])) {
    return(paste0(x[2]))}
  #if accepted name as a record, keep accepted name
  else {
    return(paste0(x[1]))}
}

TAS_extinct_status <- function(x) { 
  # When extinct but with native origin, assign presumed extinct 
  if(is.na(x[1])) {
    return(paste0(x[2]))
  }
  if(x[1] == "presumed extinct" && x[2]== "native") {
    return(paste0(x[1]))
  }
  # When extinct but with alien origin, assign formerly introduced
  if(x[1] == "presumed extinct" && x[2]== "introduced") {
    return(paste0("formerly introduced"))
  }
  # When extinct and uncertain origin, assign presumed extinct 
  if(x[1] == "presumed extinct" && x[2]== "uncertain origin") {
    return(paste0("presumed extinct"))
  }
  #for any other combination, paste status appearing in origin
  else{
    return(paste0(x[2]))}
} #close function

#function to assign correct status for extinct species, depending on their origin
VIC_extinct_status <- function(x) { 
  # When extinct but with native origin, assign presumed extinct 
  if(x[1] == "extinct" && x[2]== "native") {
    return(paste0("presumed extinct"))
  }
  # When extinct but with alien origin, assign formerly introduced
  if(x[1] == "extinct" && x[2]== "introduced") {
    return(paste0("formerly introduced"))
  }
  # When extinct and uncertain origin, assign presumed extinct 
  if(x[1] == "extinct" && x[2]== "uncertain origin") {
    return(paste0("presumed extinct"))
  }
  #for any other combination, paste status appearing in origin
  else{
    return(paste0(x[2]))}
} #close function

#Function. Step 1 for creating canonical name
canonical_name_GRIIS1 <- function(x) {
  if(is.na(x[2])& !is.na(x[1])) {
    return(paste0(x[1]))}
  if(!is.na(x[2])) {
    return(paste0(x[1:2], collapse = " "))}
}

#Function. Step 2 for creating canonical name
canonical_name_GRIIS2 <- function(x) {
  #if there is no hybrids, return the canonical name obtained in the previous step
  if(is.na(x[2])& !is.na(x[1])) {
    return(paste0(x[1]))}
  #if there are hybrids, paste and collapse
  if(!is.na(x[2])& !is.na(x[1])) {
    return(paste0(x[1:2], collapse = " "))}
}

compare_status <- function(x) { #where x will be a row of the input df
  #When taxa_status == "excluded"
  if(!is.na(x[4])) if(x[4] == "excluded") {
    return("Taxon excluded on the APC")
  }
  if(is.na(x[4]) | x[4] != "excluded") {
    # When NA in APC_Alien_Status --> write "Not listed on the APC with the name appearing on the state flora"
    if(is.na(x[3])) {
      return("Not listed on the APC with the name appearing on the state flora")
    }
    #When NA in APC_name --> write Not recorded on the APC as present in this state"
    if(!is.na(x[3]) && is.na(x[2])) {
      return("Not recorded on the APC as present in this state")
    } 
    #When State_Alien_Status is NA
    if(is.na(x[1])) {
      return("Status not assigned on the state flora")
    }
    # When similar status in both columns --> write "Similar in state flora and APC"
   if(x[1] == x[2]) {
      return("Similar for the state flora and the APC")
    }
    # When differing --> write "According to the state flora is (copy --> State_Alien_Status), while according to the APC is (copy --> APC_Alien_Status)"
    if(x[1] != x[2]) {
      return(paste0("According to the state flora is ", x[1], ", while according to the APC is ", x[2]))
    }
  }
}

#function to return most conservative status
state_conservative_status <- function(x) { #where x will be a row of the input df
  # When NA in APC_Alien_Status, copy status from state census
  if(x[3] == "Taxon excluded on the APC") {
    return(paste0(x[1]))
  }
  if(x[3] == "Not listed on the APC with the name appearing on the state flora") {
    return(paste0(x[1]))
  }
  if(x[3] == "Not recorded on the APC as present in this state") {
    return(paste0(x[1]))
  }
  # When similar status in both columns, copy status from state census
  if(x[3] == "Similar for the state flora and the APC") {
    return(paste0(x[1]))
  }
  # When status not assign on state flora, copy status from the APC
  if(x[3] == "Status not assigned on the state flora") {
    return(paste0(x[2]))
  }
  # When differing but the status on state flora is the most conservative, copy status from the state census
  if(x[3]  == "According to the state flora is native, while according to the APC is presumed extinct" || 
     x[3]  == "According to the state flora is native potentially colonising, while according to the APC is native" ||
     x[3]  == "According to the state flora is native potentially colonising, while according to the APC is presumed extinct" || 
     x[3]  == "According to the state flora is native colonising, while according to the APC is native potentially colonising" || 
     x[3]  == "According to the state flora is native colonising, while according to the APC is native" || 
     x[3]  == "According to the state flora is native colonising, while according to the APC is presumed extinct" || 
     x[3]  == "According to the state flora is uncertain origin, while according to the APC is native" || 
     x[3]  == "According to the state flora is uncertain origin, while according to the APC is native colonising" ||
     x[3]  == "According to the state flora is uncertain origin, while according to the APC is native potentially colonising" ||
     x[3]  == "According to the state flora is uncertain origin, while according to the APC is presumed extinct" ||
     x[3]  == "According to the state flora is formerly introduced, while according to the APC is uncertain origin" ||
     x[3]  == "According to the state flora is formerly introduced, while according to the APC is native colonising" ||
     x[3]  == "According to the state flora is formerly introduced, while according to the APC is native potentially colonising" ||
     x[3]  == "According to the state flora is formerly introduced, while according to the APC is native" || 
     x[3]  == "According to the state flora is formerly introduced, while according to the APC is presumed extinct" ||
     x[3]  == "According to the state flora is formerly naturalised, while according to the APC is formerly introduced" ||
     x[3]  == "According to the state flora is formerly naturalised, while according to the APC is uncertain origin" ||
     x[3]  == "According to the state flora is formerly naturalised, while according to the APC is native colonising" ||
     x[3]  == "According to the state flora is formerly naturalised, while according to the APC is native potentially colonising" ||
     x[3]  == "According to the state flora is formerly naturalised, while according to the APC is native" || 
     x[3]  == "According to the state flora is formerly naturalised, while according to the APC is presumed extinct" ||
     x[3]  == "According to the state flora is doubtfully introduced, while according to the APC is formerly naturalised" || 
     x[3]  == "According to the state flora is doubtfully introduced, while according to the APC is formerly introduced" || 
     x[3]  == "According to the state flora is doubtfully introduced, while according to the APC is uncertain origin" ||
     x[3]  == "According to the state flora is doubtfully introduced, while according to the APC is native colonising" ||
     x[3]  == "According to the state flora is doubtfully introduced, while according to the APC is native potentially colonising" ||
     x[3]  == "According to the state flora is doubtfully introduced, while according to the APC is native" || 
     x[3]  == "According to the state flora is doubtfully introduced, while according to the APC is presumed extinct" || 
     x[3]  == "According to the state flora is doubtfully naturalised, while according to the APC is introduced" ||
     x[3]  == "According to the state flora is doubtfully naturalised, while according to the APC is doubtfully introduced" || 
     x[3]  == "According to the state flora is doubtfully naturalised, while according to the APC is formerly naturalised" || 
     x[3]  == "According to the state flora is doubtfully naturalised, while according to the APC is formerly introduced" || 
     x[3]  == "According to the state flora is doubtfully naturalised, while according to the APC is uncertain origin" ||
     x[3]  == "According to the state flora is doubtfully naturalised, while according to the APC is native colonising" ||
     x[3]  == "According to the state flora is doubtfully naturalised, while according to the APC is native potentially colonising" ||
     x[3]  == "According to the state flora is doubtfully naturalised, while according to the APC is native" || 
     x[3]  == "According to the state flora is doubtfully naturalised, while according to the APC is presumed extinct" || 
     x[3]  == "According to the state flora is introduced, while according to the APC is doubtfully introduced" ||     
     x[3]  == "According to the state flora is introduced, while according to the APC is formerly naturalised" ||
     x[3]  == "According to the state flora is introduced, while according to the APC is formerly introduced" ||
     x[3]  == "According to the state flora is introduced, while according to the APC is uncertain origin" || 
     x[3]  == "According to the state flora is introduced, while according to the APC is native colonising" ||
     x[3]  == "According to the state flora is introduced, while according to the APC is native potentially colonising"||
     x[3]  == "According to the state flora is introduced, while according to the APC is native" || 
     x[3]  == "According to the state flora is introduced, while according to the APC is presumed extinct" ||
     x[3]  == "According to the state flora is naturalised, while according to the APC is introduced" ||
     x[3]  == "According to the state flora is naturalised, while according to the APC is doubtfully naturalised" ||
     x[3]  == "According to the state flora is naturalised, while according to the APC is doubtfully introduced" || 
     x[3]  == "According to the state flora is naturalised, while according to the APC is formerly naturalised" ||
     x[3]  == "According to the state flora is naturalised, while according to the APC is formerly introduced" ||
     x[3]  == "According to the state flora is naturalised, while according to the APC is native colonising" ||
     x[3]  == "According to the state flora is naturalised, while according to the APC is native potentially colonising" ||
     x[3]  == "According to the state flora is naturalised, while according to the APC is native" || 
     x[3]  == "According to the state flora is naturalised, while according to the APC is presumed extinct") {
    return(paste0(x[1]))
  }
  # When differing but the status on the APC is the most conservative, copy status from the APC
  if(x[3] == "Status not assigned in the state flora"   ||
     x[3] == "According to the state flora is doubtfully naturalised, while according to the APC is naturalised"  ||
     x[3] == "According to the state flora is introduced, while according to the APC is naturalised" || 
     x[3] == "According to the state flora is introduced, while according to the APC is doubtfully naturalised"  || 
     x[3] == "According to the state flora is doubtfully introduced, while according to the APC is naturalised"  || 
     x[3] == "According to the state flora is doubtfully introduced, while according to the APC is introduced"  || 
     x[3] == "According to the state flora is doubtfully introduced, while according to the APC is doubtfully naturalised"  || 
     x[3] == "According to the state flora is formerly naturalised, while according to the APC is naturalised" || 
     x[3] == "According to the state flora is formerly naturalised, while according to the APC is introduced" || 
     x[3] == "According to the state flora is formerly naturalised, while according to the APC is doubtfully naturalised" ||      
     x[3] == "According to the state flora is formerly naturalised, while according to the APC is doubtfully introduced" || 
     x[3] == "According to the state flora is formerly introduced, while according to the APC is naturalised" || 
     x[3] == "According to the state flora is formerly introduced, while according to the APC is introduced" || 
     x[3] == "According to the state flora is formerly introduced, while according to the APC is doubtfully naturalised" || 
     x[3] == "According to the state flora is formerly introduced, while according to the APC is doubtfully introduced" || 
     x[3] == "According to the state flora is formerly introduced, while according to the APC is formerly naturalised" ||     
     x[3] == "According to the state flora is uncertain origin, while according to the APC is naturalised" ||
     x[3] == "According to the state flora is uncertain origin, while according to the APC is introduced" ||
     x[3] == "According to the state flora is uncertain origin, while according to the APC is doubtfully naturalised" || 
     x[3] == "According to the state flora is uncertain origin, while according to the APC is doubtfully introduced" || 
     x[3] == "According to the state flora is uncertain origin, while according to the APC is formerly naturalised" || 
     x[3] == "According to the state flora is uncertain origin, while according to the APC is formerly introduced" || 
     x[3] == "According to the state flora is native colonising, while according to the APC is naturalised"   || 
     x[3] == "According to the state flora is native colonising, while according to the APC is introduced"   || 
     x[3] == "According to the state flora is native colonising, while according to the APC is doubtfully naturalised"   || 
     x[3] == "According to the state flora is native colonising, while according to the APC is doubtfully introduced"   || 
     x[3] == "According to the state flora is native colonising, while according to the APC is formerly naturalised"   || 
     x[3] == "According to the state flora is native colonising, while according to the APC is formerly introduced"   || 
     x[3] == "According to the state flora is native colonising, while according to the APC is uncertain origin" || 
     x[3] == "According to the state flora is native potentially colonising, while according to the APC is naturalised"   || 
     x[3] == "According to the state flora is native potentially colonising, while according to the APC is introduced"   || 
     x[3] == "According to the state flora is native potentially colonising, while according to the APC is doubtfully naturalised"   || 
     x[3] == "According to the state flora is native potentially colonising, while according to the APC is doubtfully introduced"   || 
     x[3] == "According to the state flora is native potentially colonising, while according to the APC is formerly naturalised"   || 
     x[3] == "According to the state flora is native potentially colonising, while according to the APC is formerly introduced"   || 
     x[3] == "According to the state flora is native potentially colonising, while according to the APC is uncertain origin" || 
     x[3] == "According to the state flora is native potentially colonising, while according to the APC is native colonising"  || 
     x[3] == "According to the state flora is native, while according to the APC is naturalised"   || 
     x[3] == "According to the state flora is native, while according to the APC is introduced"   || 
     x[3] == "According to the state flora is native, while according to the APC is doubtfully naturalised"   || 
     x[3] == "According to the state flora is native, while according to the APC is doubtfully introduced"   || 
     x[3] == "According to the state flora is native, while according to the APC is formerly naturalised"   || 
     x[3] == "According to the state flora is native, while according to the APC is formerly introduced"   || 
     x[3] == "According to the state flora is native, while according to the APC is uncertain origin" || 
     x[3] == "According to the state flora is native, while according to the APC is native colonising" || 
     x[3] == "According to the state flora is native, while according to the APC is native potentially colonising"  || 
     x[3] == "According to the state flora is presumed extinct, while according to the APC is naturalised" ||
     x[3] == "According to the state flora is presumed extinct, while according to the APC is introduced" ||
     x[3] == "According to the state flora is presumed extinct, while according to the APC is doubtfully naturalised" ||
     x[3] == "According to the state flora is presumed extinct, while according to the APC is doubtfully introduced" ||
     x[3] == "According to the state flora is presumed extinct, while according to the APC is formerly naturalised" ||
     x[3] == "According to the state flora is presumed extinct, while according to the APC is formerly introduced" ||
     x[3] == "According to the state flora is presumed extinct, while according to the APC is uncertain origin" ||
     x[3] == "According to the state flora is presumed extinct, while according to the APC is native colonising" ||
     x[3] == "According to the state flora is presumed extinct, while according to the APC is native potentially colonising" ||
     x[3] == "According to the state flora is presumed extinct, while according to the APC is native") {
    return(paste0(x[2]))
  }
}

#function to assign equivalences of Darwin Core degree of establishment
state_establishment_means <- function(x) { #where x will be a row of the input df
  # When NA in APC_Alien_Status --> write "Not listed in APC with the name appearing in the state flora or listed but not recorded as present in this state"
  if(is.na(x[1])){
    return(NA)
  }
  if(x[1] == "native"|| 
     x[1] == "native colonising"|| 
     x[1] == "native potentially colonising") {
    return(paste0("native"))
  }
  if(x[1] == "uncertain origin") {
    return(paste0("uncertain"))
  }
  if(x[1] == "naturalised"|| 
     x[1] == "doubtfully naturalised"|| 
     x[1] == "formerly naturalised"|| 
     x[1] == "introduced"|| 
     x[1] == "doubtfully introduced") {
    return(paste0("introduced"))
  }
  # When differing but state flora is most conservative
  if(x[1]  == "presumed extinct"|| 
     x[1]  == "formerly introduced"){
    return(paste0("not enough information to assign establishment means"))
  }
  if(x[1]  == "listed on the APC but not recorded anywhere"|| 
     x[1]  == "recorded only in external territories"){
    return(NA)
  }
}

#function to assign equivalences of Darwin Core degree of establishment at the state level
state_degree_of_establishment <- function(x) { 
  if(is.na(x[1])){
    return(NA)
  }
  if(x[1] == "native"|| 
     x[1] == "native colonising"|| 
     x[1] == "native potentially colonising") {
    return(paste0("native"))
  }
  if(x[1] == "uncertain origin") {
    return(paste0("uncertain"))
  }
  if(x[1] == "naturalised"|| 
     x[1] == "doubtfully naturalised"){
    return(paste0("established"))
  }
  if(x[1] == "formerly naturalised"|| 
     x[1] == "introduced"|| 
     x[1] == "doubtfully introduced") {
    return(paste0("not enough information to assign degree of establishment"))
  }
  # When differing but state flora is most conservative
  if(x[1]  == "presumed extinct"|| 
     x[1]  == "formerly introduced"){
    return(paste0("not enough information to assign neither establishment means nor degree of establishment"))
  }
}

#function to compare the status we elucidated at national scale with the one recorded on the GRIIS
compare_status_GRIIS <- function(x) { #where x will be a row of the input df
  # When NA in APC_Alien_Status --> write "Not listed on the APC with the name appearing in the state flora or listed but not recorded as present in this state"
  if(is.na(x[2])) {
    return("Not listed on the GRIIS with the name appearing on the APC or not recorded as introduced at the national scale")
  }
  if(is.na(x[1])) {
    return("Not recorded in Australian states or main territories, only in external territories")
  }
  # When similar status in both columns --> write "Similar in state flora and APC"
  if(x[1] == x[2]) {
    return("Similar for our national status and the GRIIS")
  }
  # When differing --> write "According to the state flora is (copy --> State_Alien_Status), while according to the APC is (copy --> APC_Alien_Status)"
  if(x[1] != x[2]) {
    return(paste0("According to our national status is ", x[1], ", while according to the GRIIS is ", x[2]))
  }
}

return_conservative_status_GRIIS <- function(x) { #where x will be a row of the input df
  # When NA in APC_Alien_Status --> write "Not listed in APC with the name appearing in the state flora or listed but not recorded as present in this state"
  if(x[3] == "Not listed on the GRIIS with the name appearing on the APC or not recorded as introduced at national scale") {
    return(paste0(x[1]))
  }
  # When similar status in both columns --> write "Similar in state flora and APC"
  if(x[3] == "Not recorded in Australian states or main territories, only in external territories") {
    return(NA)
  }
  
  # When similar status in both columns --> write "Similar in state flora and APC"
  if(x[3] == "Similar for our national status and the GRIIS") {
    return(paste0(x[1]))
  }
  
  # When differing and our national status is native, it states as native
  if(x[3]  == "According to our national status is native, while according to the GRIIS is introduced" || 
     x[3]  == "According to our national status is native colonising, while according to the GRIIS is introduced" ||
     x[3]  == "According to our national status is native colonising potential, while according to the GRIIS is introduced"|| 
     x[3]  == "According to our national status is uncertain origin, while according to the GRIIS is introduced" ||
     x[3]  == "According to our national status is presumed extinct, while according to the GRIIS is introduced" || 
     x[3]  == "According to our national status is native, while according to the GRIIS is harmful invasive" || 
     x[3]  == "According to our national status is native colonising, while according to the GRIIS is harmful invasive" ||
     x[3]  == "According to our national status is native colonising potential, while according to GRIIS is harmful invasive"||
     x[3]  == "According to our national status is presumed extinct, while according to the GRIIS is harmful invasive" || 
     x[3]  == "According to our national status is uncertain origin, while according to the GRIIS is harmful invasive") {
    return(paste0(x[1]))
  }
  
  if(x[3]  == "According to our national status is naturalised, while according to the GRIIS is harmful invasive"|| 
     x[3]  == "According to our national status is formerly naturalised, while according to the GRIIS is harmful invasive" || 
     x[3]  == "According to our national status is introduced, while according to the GRIIS is harmful invasive" ||
     x[3]  == "According to our national status is doubtfully naturalised, while according to the GRIIS is harmful invasive"|| 
     x[3]  == "According to our national status is doubtfully introduced, while according to the GRIIS is harmful invasive"|| 
     x[3]  == "According to our national status is formerly introduced, while according to the GRIIS is harmful invasive"|| 
     x[3]  == "According to our national status is doubtfully introduced, while according to the GRIIS is introduced"|| 
     x[3]  == "According to our national status is formerly introduced, while according to the GRIIS is introduced") {
    return(paste0(x[2]))
  }
  # When differing but APC is most conservative
  else {
    return(paste0(x[1]))
  }
}

national_establishment_means <- function(x) { #where x will be a row of the input df
  # When NA in APC_Alien_Status --> write "Not listed on the APC with the name appearing on the state flora"
  if(is.na(x[1])){
    return(NA)
  }
  if(x[1] == "native"|| 
     x[1] == "native colonising"|| 
     x[1] == "native potentially colonising" ||
     x[1] == "Mismatch with GRIIS. native") {
    return(paste0("native"))
  }
  if(x[1] == "uncertain origin") {
    return(paste0("uncertain"))
  }
  if(x[1] == "naturalised"|| 
     x[1] == "harmful invasive"|| 
     x[1] == "doubtfully naturalised"|| 
     x[1] == "formerly naturalised"|| 
     x[1] == "introduced"|| 
     x[1] == "doubtfully introduced") {
    return(paste0("introduced"))
  }
  # When differing but state flora is most conservative
  if(x[1]  == "presumed extinct"|| 
     x[1]  == "formerly introduced"){
    return(paste0("not enough information to assign establishment means"))
  }
  if(x[1]  == "listed in APC but not recorded anywhere"|| 
     x[1]  == "recorded only in external territories"){
    return(NA)
  }
}

#function for equivalences with DC terminology degree of establishment for status at the national scale
national_degree_of_establishment <- function(x) { 
  if(is.na(x[1])){
    return(NA)
  }
  if(x[1] == "native") {
    return(paste0("native"))
  }
  if(x[1] == "uncertain") {
    return(NA)
  }
  if(x[1] == introduced && x[2] == "naturalised"|| 
     x[1] == introduced && x[2] == "doubtfully naturalised") {
    return(paste0("established"))
  }
  if(x[1] == introduced && x[2] == "harmful invasive") {
    return(paste0("invasive"))
  }
  if(x[1] == introduced && x[2] == "introduced"||    
     x[1] == introduced && x[2] == "formerly naturalised"||  
     x[1] == introduced && x[2] == "formerly introduced"){
    return(paste0("not enough information to assign degree of establishment"))
  }
  if(x[1]  == "not enough information to assign establishment means"){
    return(paste0("not enough information to assign neither establishment means nor degree of establishment"))
  }
}

###########CROSS APC TAXONOMY WITH GBIF AND WFO############
#get canonical name
cross_GBIF <- function(dataset) {
  cat('Starting cross reference process with GBIF. This can take some time')
  column_name <- colnames(dataset) [grep("canonical", colnames(dataset))]
  data_name <- subset(dataset, select=column_name)
   
  #cross names with GBIF backbone without fuzzy matchign
  GBIF <- name_backbone_checklist(data_name,verbose=FALSE)
  
  #match ACT's canonical name with GBIF's verbatim name (i.e. the original name that GBIF's matching function used)
  match_taxonomy <- match(data_name[,1], GBIF$verbatim_name)
  
  #include on the main matrix both GBIF's canonical and scientific name based on matching
  dataset$GBIF_canon_name <- GBIF$canonicalName[match_taxonomy]
  dataset$GBIF_name <- GBIF$scientificName[match_taxonomy]
  cat('Cross reference process with GBIF has now finished.')
  return(dataset)
}

cross_WFO <- function(dataset) {
  #download WFO
  #WFO.download (WFO.url ="http://104.198.143.165/files/WFO_Backbone/_WFOCompleteBackbone/WFO_Backbone.zip", save.dir = getwd(), WFO.remember = TRUE)
  
  #remember WFO
  WFO.remember(WFO.file = NULL, WFO.data = "WFO.data", WFO.pos = 1)
  
  column_name <- colnames(dataset) [grep("canonical", colnames(dataset))]
  #match with WFO without fuzzy matching- and prioritising accepted species names
  dataset1 <- WFO.match(spec.data= dataset, spec.name=column_name, WFO.data=WFO.data, Fuzzy=0, counter=1, verbose=FALSE)
  dataset2 <- WFO.one(dataset1, priority = "Accepted")
  
  #select the columns from WFO matching that we are interested in
  WFO <- subset(dataset2, select= c('scientificName', 'scientificNameAuthorship'))
  
  WFO$WFO_name <- paste(WFO$scientificName, WFO$scientificNameAuthorship)
  WFO <- select(WFO, -scientificNameAuthorship)
  dataset3 <- cbind(dataset, WFO)
  
  dataset3 <- rename(dataset3, WFO_canon_name=scientificName)
  dataset3$WFO_name <- str_replace_all(dataset3$WFO_name, "NA NA", "")
  dataset3$WFO_name[dataset3$WFO_name==""] <- NA
  return(dataset3)
}
###################

escape_curation_tasmania <- function(x) { 
  if(x[1] == "Medicago sativa L. nothosubsp * varia (Martyn) Arcang."){
    return(paste0("Medicago sativa nothosubsp * varia"))
  }
  if(x[1] == "Medicago sativa L. nothosubsp x varia (Martyn) Arcang.") {
    return(paste0("Medicago sativa nothosubsp x varia"))
  }
  else{
    return(paste0(x[2]))
  }
 }

#########################################
#end of secondary functions
#########################################