Nothing
R/FlagManager.R
In BeeBDC: Occurrence Data Cleaning
Defines functions
FlagManager
# This function was made by James Dorey to manage flags in the synonym lists
# For queries, please contact James Dorey at jbdorey[at]me.com
# This function was started on 15th May 2022 and last updated 17th May 2022
#' @importFrom dplyr %>%
FlagManager <- function(InSynList = DLdf,
flagCol = flags){
# locally bind variables to the function
. <- DLdf <- flags <- genus <- validName <- canonical <- NULL
#### Flags option ####
if(flagCol == "flags"){
base::writeLines(" - Using the flags column.")
# If there is no canonical_withFlags, make one with the canonical column, assuming it has flags
suppressWarnings( CWFtest <- InSynList$canonical_withFlags,
classes = "warning")
if(is.null(CWFtest) == TRUE){
canonical_withFlags <- InSynList$canonical
InSynList <- dplyr::mutate(InSynList, canonical_withFlags, .after = "canonical")
}
# IF all of the canonical_withFlags column is empty, replace it with the canonical valuse
if(all(CWFtest == "NA") == TRUE){
InSynList$canonical_withFlags <- InSynList$canonical
}
base::writeLines(" - 1. Remove flag from validName column...")
##### START ProgBar 1 ####
# Initializes the progress bar
pb1 <- utils::txtProgressBar(min = 0, # Minimum value of the progress bar
max = nrow(InSynList), # Maximum value of the progress bar
style = 3, # Progress bar style (also available style = 1 and style = 2)
width = NA, # Progress bar width. Defaults to getOption("width")
char = "=") # Character used to create the bar
# Remove flag from validName
for(i in 2:nrow(InSynList)){
if(is.na(InSynList$flags[i]) == FALSE){ # Enter statement only IF there is a flag present
InSynList$validName[i] <- sub(InSynList$flags[i], "", InSynList$validName[i] , fixed = TRUE) %>%
trimws( which = "right" , whitespace = "[\\, ]") # Trim some special characters from the END of the string
} # END IF statement
# Sets the progress bar to the current state
utils::setTxtProgressBar(pb1, i)
} # END loop COLUMNS
#### END progBar 1 ####
close(pb1) # Close the connection
# Clean up double spaces in data frame
InSynList <- as.data.frame(apply(InSynList, 2, FUN = stringr::str_squish ), stringsAsFactors = FALSE)
# Remove empty rows that contain the following strings
InSynList <- subset(InSynList, genus!="NA" & genus!="F" & genus!="V" & genus!="Discover" &
genus!="Updated:" & genus!="Other" & validName!="Kinds of" &
validName!="Scientific name" & canonical != "Kim, NA")
# Find annotations and add the instead to the flags column
# Which columns to search through
FlagAnnot_cols <- c("genus", "subgenus", "species", "infraspecies", "authorship")
# Which flags to find
FlagsAnnot <- c(
# Name flags
"_homonym[1-4]?","_homonytm","_homony","_sic","_sensu_lato",
"_unavailable","_invalid","_nomen_nudum","_emend",
" var "," subvar "," forma "," form "," race "," auct ","^var ","^subvar ","^forma ",
"^form ","^race ",
# unsure flags
" f ","^f "," m ","^m "," r ","^r "," ab ","^ab ",
# Specific cases
"_Urban_not_Pasteels","_Friese_not_Megerle","_Friese_not_H\\u00fcbner","_Friese_not_Stimpson",
# Author flags
"Auctorum, sensu","sensu auct not","Auct non","Auct, not","auct, not","_auct not_",
"_auct","^auct ") %>%
paste(collapse="|")
base::writeLines(" - 2. Find and add flags to the 'flags' column...")
#### START ProgBar 2 ####
# Initializes the progress bar
pb2 <- utils::txtProgressBar(min = 0, # Minimum value of the progress bar
max = length(FlagAnnot_cols), # Maximum value of the progress bar
style = 3, # Progress bar style (also available style = 1 and style = 2)
width = NA, # Progress bar width. Defaults to getOption("width")
char = "=") # Character used to create the bar
# Find and add flags to flag column
for(j in 1:length(FlagAnnot_cols)){ # COLUMNS
for(i in 1:nrow(InSynList)){ # ROWS
if(grepl(FlagsAnnot, InSynList[i,FlagAnnot_cols[j]], fixed = FALSE) == TRUE){
# Extract the flag from the string and add the column name
ExtractedFlag <- stringr::str_extract_all(InSynList[i,FlagAnnot_cols[j]],
FlagsAnnot, simplify = TRUE) %>%
paste(FlagAnnot_cols[j],.,sep=" ", collapse = "|") %>%
gsub(" ", " ",. ) # Remove double spaces
if( is.na(InSynList[i,"flags"]) == TRUE){ # If there is NO flag, insert this flag as is
InSynList[i,"flags"] <- ExtractedFlag
}else{ # If there IS a flag, ADD this to the existing flag
InSynList[i,"flags"] <- paste(InSynList[i,"flags"], ExtractedFlag, sep = " | ")
} # END if else statement
} # END find flag IF statement
} # END for loop of flag annotations - ROWS
# Sets the progress bar to the current state
utils::setTxtProgressBar(pb2, j)
} # END loop COLUMNS
#### END progBar 2 ####
close(pb2) # Close the connection
# Trim internal white spaces in flag column
InSynList$flags <- gsub(" \\| | \\||\\| ", "|", InSynList$flags)
# Remove these strings from the relevant columns now that they are saved as flags
TempCols <- as.data.frame(apply(InSynList[c("canonical",FlagAnnot_cols) ], 2,
function(y) gsub(FlagsAnnot, " ", y)))
# Replace existing columns with these new, trimmed, columns
InSynList[c(FlagAnnot_cols)] <- TempCols[, FlagAnnot_cols]
# Add the canonical column after the canonical column with flags - later convert to
# canonical and canonical_withFlags
CanTest <- InSynList$canonical
# IF there IS already a canonical column repalce that column with the new one...
if(is.null(CanTest) == FALSE){
InSynList$canonical <- TempCols$canonical
}else{
InSynList <- dplyr::mutate(InSynList, TempCols$canonical, .after = "canonical")
}
# Clean up double spaces in data frame
InSynList <- as.data.frame(apply(InSynList, 2, FUN = stringr::str_squish ), stringsAsFactors = FALSE)
} # END IF flags col
#### Notes option ####
if(flagCol == "notes"){
base::writeLines(" - Using the notes column.")
# If there is no canonical_withFlags, make one with the canonical column, assuming it has flags
suppressWarnings( CWFtest <- InSynList$canonical_withFlags,
classes = "warning")
if(is.null(CWFtest) == TRUE){
canonical_withFlags <- InSynList$canonical
InSynList <- dplyr::mutate(InSynList, canonical_withFlags, .after = "canonical")
}
# IF all of the canonical_withFlags column is empty, replace it with the canonical valuse
if(all(CWFtest == "NA") == TRUE){
InSynList$canonical_withFlags <- InSynList$canonical
}
base::writeLines(" - 1. Remove flag from validName column...")
##### START ProgBar 1 ####
# Initializes the progress bar
pb1 <- utils::txtProgressBar(min = 0, # Minimum value of the progress bar
max = nrow(InSynList), # Maximum value of the progress bar
style = 3, # Progress bar style (also available style = 1 and style = 2)
width = NA, # Progress bar width. Defaults to getOption("width")
char = "=") # Character used to create the bar
# Remove flag from validName
for(i in 2:nrow(InSynList)){
if(is.na(InSynList$notes[i]) == FALSE){ # Enter statement only IF there is a flag present
InSynList$validName[i] <- sub(InSynList$notes[i], "", InSynList$validName[i] , fixed = TRUE) %>%
trimws( which = "right" , whitespace = "[\\, ]") # Trim some special characters from the END of the string
} # END IF statement
# Sets the progress bar to the current state
utils::setTxtProgressBar(pb1, i)
} # END loop COLUMNS
#### END progBar 1 ####
close(pb1) # Close the connection
# Clean up double spaces in data frame
InSynList <- as.data.frame(apply(InSynList, 2, FUN = stringr::str_squish ), stringsAsFactors = FALSE)
# Remove empty rows that contain the following strings
InSynList <- subset(InSynList, genus!="NA" & genus!="F" & genus!="V" & genus!="Discover" &
genus!="Updated:" & genus!="Other" )
# Find annotations and add the instead to the flags column
# Which columns to search through
FlagAnnot_cols <- c("genus", "subgenus", "species", "infraspecies", "authorship")
# Which flags to find
FlagsAnnot <- c(
# Name flags
"_homonym[1-4]?","_homonytm","_homony","_sic","_sensu_lato",
"_unavailable","_invalid","_nomen_nudum","_emend",
" var "," subvar "," forma "," form "," race "," auct ","^var ","^subvar ","^forma ",
"^form ","^race ",
# unsure flags
" f ","^f "," m ","^m "," r ","^r "," ab ","^ab ",
# Specific cases
"_Urban_not_Pasteels","_Friese_not_Megerle","_Friese_not_H\\u00fcbner","_Friese_not_Stimpson",
# Author flags
"Auctorum, sensu","sensu auct not","Auct non","Auct, not","auct, not","_auct not_",
"_auct","^auct ") %>%
paste(collapse="|")
base::writeLines(" - 2. Find and add flags to the 'flags' column...")
#### START ProgBar 2 ####
# Initializes the progress bar
pb2 <- utils::txtProgressBar(min = 0, # Minimum value of the progress bar
max = length(FlagAnnot_cols), # Maximum value of the progress bar
style = 3, # Progress bar style (also available style = 1 and style = 2)
width = NA, # Progress bar width. Defaults to getOption("width")
char = "=") # Character used to create the bar
# Find and add flags to notes column
for(j in 1:length(FlagAnnot_cols)){ # COLUMNS
for(i in 1:nrow(InSynList)){ # ROWS
if(grepl(FlagsAnnot, InSynList[i,FlagAnnot_cols[j]], fixed = FALSE) == TRUE){
# Extract the flag from the string and add the column name
ExtractedFlag <- stringr::str_extract_all(InSynList[i,FlagAnnot_cols[j]],
FlagsAnnot, simplify = TRUE) %>%
paste(FlagAnnot_cols[j],.,sep=" ", collapse = "|") %>%
gsub(" ", " ",. ) # Remove double spaces
if( is.na(InSynList[i,"notes"]) == TRUE){ # If there is NO flag, insert this flag as is
InSynList[i,"notes"] <- ExtractedFlag
}else{ # If there IS a flag, ADD this to the existing flag
InSynList[i,"notes"] <- paste(InSynList[i,"notes"], ExtractedFlag, sep = " | ")
} # END if else statement
} # END find flag IF statement
} # END for loop of flag annotations - ROWS
# Sets the progress bar to the current state
utils::setTxtProgressBar(pb2, j)
} # END loop COLUMNS
#### END progBar 2 ####
close(pb2) # Close the connection
# Trim internal white spaces in flag column
InSynList$notes <- gsub(" \\| | \\||\\| ", "|", InSynList$notes)
# Remove these strings from the relevant columns now that they are saved as flags
TempCols <- as.data.frame(apply(InSynList[c("canonical",FlagAnnot_cols) ], 2,
function(y) gsub(FlagsAnnot, " ", y)))
# Replace existing columns with these new, trimmed, columns
InSynList[c(FlagAnnot_cols)] <- TempCols[, FlagAnnot_cols]
# Add the canonical column after the canonical column with flags - later convert to
# canonical and canonical_withFlags
CanTest <- InSynList$canonical
# IF there IS already a canonical column repalce that column with the new one...
if(is.null(CanTest) == FALSE){
InSynList$canonical <- TempCols$canonical
}else{
InSynList <- dplyr::mutate(InSynList, TempCols$canonical, .after = "canonical")
}
# Clean up double spaces in data frame
InSynList <- as.data.frame(apply(InSynList, 2, FUN = stringr::str_squish ), stringsAsFactors = FALSE)
} # END IF notes col
#### neither ####
if(flagCol != "flags" & flagCol != "notes"){
base::writeLines("!! The flagCol option must equal 'flags' or 'notes' !!")
}
#backupdf <- InSynList
#InSynList <- backupdf
# change column names
#colnames(InSynList) <- c("flags","taxonomic_status","source","accid","id","kingdom","phylum","class","order","family","subfamily","tribe","subtribe","validName","canonical_withFlags","canonical","genus","subgenus","species","infraspecies","authorship")
return(InSynList)
} # END FlagManager
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BeeBDC documentation built on Nov. 4, 2024, 9:06 a.m.
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Defines functions FlagManager
# This function was made by James Dorey to manage flags in the synonym lists
# For queries, please contact James Dorey at jbdorey[at]me.com
# This function was started on 15th May 2022 and last updated 17th May 2022
#' @importFrom dplyr %>%
FlagManager <- function(InSynList = DLdf,
flagCol = flags){
# locally bind variables to the function
. <- DLdf <- flags <- genus <- validName <- canonical <- NULL
#### Flags option ####
if(flagCol == "flags"){
base::writeLines(" - Using the flags column.")
# If there is no canonical_withFlags, make one with the canonical column, assuming it has flags
suppressWarnings( CWFtest <- InSynList$canonical_withFlags,
classes = "warning")
if(is.null(CWFtest) == TRUE){
canonical_withFlags <- InSynList$canonical
InSynList <- dplyr::mutate(InSynList, canonical_withFlags, .after = "canonical")
}
# IF all of the canonical_withFlags column is empty, replace it with the canonical valuse
if(all(CWFtest == "NA") == TRUE){
InSynList$canonical_withFlags <- InSynList$canonical
}
base::writeLines(" - 1. Remove flag from validName column...")
##### START ProgBar 1 ####
# Initializes the progress bar
pb1 <- utils::txtProgressBar(min = 0, # Minimum value of the progress bar
max = nrow(InSynList), # Maximum value of the progress bar
style = 3, # Progress bar style (also available style = 1 and style = 2)
width = NA, # Progress bar width. Defaults to getOption("width")
char = "=") # Character used to create the bar
# Remove flag from validName
for(i in 2:nrow(InSynList)){
if(is.na(InSynList$flags[i]) == FALSE){ # Enter statement only IF there is a flag present
InSynList$validName[i] <- sub(InSynList$flags[i], "", InSynList$validName[i] , fixed = TRUE) %>%
trimws( which = "right" , whitespace = "[\\, ]") # Trim some special characters from the END of the string
} # END IF statement
# Sets the progress bar to the current state
utils::setTxtProgressBar(pb1, i)
} # END loop COLUMNS
#### END progBar 1 ####
close(pb1) # Close the connection
# Clean up double spaces in data frame
InSynList <- as.data.frame(apply(InSynList, 2, FUN = stringr::str_squish ), stringsAsFactors = FALSE)
# Remove empty rows that contain the following strings
InSynList <- subset(InSynList, genus!="NA" & genus!="F" & genus!="V" & genus!="Discover" &
genus!="Updated:" & genus!="Other" & validName!="Kinds of" &
validName!="Scientific name" & canonical != "Kim, NA")
# Find annotations and add the instead to the flags column
# Which columns to search through
FlagAnnot_cols <- c("genus", "subgenus", "species", "infraspecies", "authorship")
# Which flags to find
FlagsAnnot <- c(
# Name flags
"_homonym[1-4]?","_homonytm","_homony","_sic","_sensu_lato",
"_unavailable","_invalid","_nomen_nudum","_emend",
" var "," subvar "," forma "," form "," race "," auct ","^var ","^subvar ","^forma ",
"^form ","^race ",
# unsure flags
" f ","^f "," m ","^m "," r ","^r "," ab ","^ab ",
# Specific cases
"_Urban_not_Pasteels","_Friese_not_Megerle","_Friese_not_H\\u00fcbner","_Friese_not_Stimpson",
# Author flags
"Auctorum, sensu","sensu auct not","Auct non","Auct, not","auct, not","_auct not_",
"_auct","^auct ") %>%
paste(collapse="|")
base::writeLines(" - 2. Find and add flags to the 'flags' column...")
#### START ProgBar 2 ####
# Initializes the progress bar
pb2 <- utils::txtProgressBar(min = 0, # Minimum value of the progress bar
max = length(FlagAnnot_cols), # Maximum value of the progress bar
style = 3, # Progress bar style (also available style = 1 and style = 2)
width = NA, # Progress bar width. Defaults to getOption("width")
char = "=") # Character used to create the bar
# Find and add flags to flag column
for(j in 1:length(FlagAnnot_cols)){ # COLUMNS
for(i in 1:nrow(InSynList)){ # ROWS
if(grepl(FlagsAnnot, InSynList[i,FlagAnnot_cols[j]], fixed = FALSE) == TRUE){
# Extract the flag from the string and add the column name
ExtractedFlag <- stringr::str_extract_all(InSynList[i,FlagAnnot_cols[j]],
FlagsAnnot, simplify = TRUE) %>%
paste(FlagAnnot_cols[j],.,sep=" ", collapse = "|") %>%
gsub(" ", " ",. ) # Remove double spaces
if( is.na(InSynList[i,"flags"]) == TRUE){ # If there is NO flag, insert this flag as is
InSynList[i,"flags"] <- ExtractedFlag
}else{ # If there IS a flag, ADD this to the existing flag
InSynList[i,"flags"] <- paste(InSynList[i,"flags"], ExtractedFlag, sep = " | ")
} # END if else statement
} # END find flag IF statement
} # END for loop of flag annotations - ROWS
# Sets the progress bar to the current state
utils::setTxtProgressBar(pb2, j)
} # END loop COLUMNS
#### END progBar 2 ####
close(pb2) # Close the connection
# Trim internal white spaces in flag column
InSynList$flags <- gsub(" \\| | \\||\\| ", "|", InSynList$flags)
# Remove these strings from the relevant columns now that they are saved as flags
TempCols <- as.data.frame(apply(InSynList[c("canonical",FlagAnnot_cols) ], 2,
function(y) gsub(FlagsAnnot, " ", y)))
# Replace existing columns with these new, trimmed, columns
InSynList[c(FlagAnnot_cols)] <- TempCols[, FlagAnnot_cols]
# Add the canonical column after the canonical column with flags - later convert to
# canonical and canonical_withFlags
CanTest <- InSynList$canonical
# IF there IS already a canonical column repalce that column with the new one...
if(is.null(CanTest) == FALSE){
InSynList$canonical <- TempCols$canonical
}else{
InSynList <- dplyr::mutate(InSynList, TempCols$canonical, .after = "canonical")
}
# Clean up double spaces in data frame
InSynList <- as.data.frame(apply(InSynList, 2, FUN = stringr::str_squish ), stringsAsFactors = FALSE)
} # END IF flags col
#### Notes option ####
if(flagCol == "notes"){
base::writeLines(" - Using the notes column.")
# If there is no canonical_withFlags, make one with the canonical column, assuming it has flags
suppressWarnings( CWFtest <- InSynList$canonical_withFlags,
classes = "warning")
if(is.null(CWFtest) == TRUE){
canonical_withFlags <- InSynList$canonical
InSynList <- dplyr::mutate(InSynList, canonical_withFlags, .after = "canonical")
}
# IF all of the canonical_withFlags column is empty, replace it with the canonical valuse
if(all(CWFtest == "NA") == TRUE){
InSynList$canonical_withFlags <- InSynList$canonical
}
base::writeLines(" - 1. Remove flag from validName column...")
##### START ProgBar 1 ####
# Initializes the progress bar
pb1 <- utils::txtProgressBar(min = 0, # Minimum value of the progress bar
max = nrow(InSynList), # Maximum value of the progress bar
style = 3, # Progress bar style (also available style = 1 and style = 2)
width = NA, # Progress bar width. Defaults to getOption("width")
char = "=") # Character used to create the bar
# Remove flag from validName
for(i in 2:nrow(InSynList)){
if(is.na(InSynList$notes[i]) == FALSE){ # Enter statement only IF there is a flag present
InSynList$validName[i] <- sub(InSynList$notes[i], "", InSynList$validName[i] , fixed = TRUE) %>%
trimws( which = "right" , whitespace = "[\\, ]") # Trim some special characters from the END of the string
} # END IF statement
# Sets the progress bar to the current state
utils::setTxtProgressBar(pb1, i)
} # END loop COLUMNS
#### END progBar 1 ####
close(pb1) # Close the connection
# Clean up double spaces in data frame
InSynList <- as.data.frame(apply(InSynList, 2, FUN = stringr::str_squish ), stringsAsFactors = FALSE)
# Remove empty rows that contain the following strings
InSynList <- subset(InSynList, genus!="NA" & genus!="F" & genus!="V" & genus!="Discover" &
genus!="Updated:" & genus!="Other" )
# Find annotations and add the instead to the flags column
# Which columns to search through
FlagAnnot_cols <- c("genus", "subgenus", "species", "infraspecies", "authorship")
# Which flags to find
FlagsAnnot <- c(
# Name flags
"_homonym[1-4]?","_homonytm","_homony","_sic","_sensu_lato",
"_unavailable","_invalid","_nomen_nudum","_emend",
" var "," subvar "," forma "," form "," race "," auct ","^var ","^subvar ","^forma ",
"^form ","^race ",
# unsure flags
" f ","^f "," m ","^m "," r ","^r "," ab ","^ab ",
# Specific cases
"_Urban_not_Pasteels","_Friese_not_Megerle","_Friese_not_H\\u00fcbner","_Friese_not_Stimpson",
# Author flags
"Auctorum, sensu","sensu auct not","Auct non","Auct, not","auct, not","_auct not_",
"_auct","^auct ") %>%
paste(collapse="|")
base::writeLines(" - 2. Find and add flags to the 'flags' column...")
#### START ProgBar 2 ####
# Initializes the progress bar
pb2 <- utils::txtProgressBar(min = 0, # Minimum value of the progress bar
max = length(FlagAnnot_cols), # Maximum value of the progress bar
style = 3, # Progress bar style (also available style = 1 and style = 2)
width = NA, # Progress bar width. Defaults to getOption("width")
char = "=") # Character used to create the bar
# Find and add flags to notes column
for(j in 1:length(FlagAnnot_cols)){ # COLUMNS
for(i in 1:nrow(InSynList)){ # ROWS
if(grepl(FlagsAnnot, InSynList[i,FlagAnnot_cols[j]], fixed = FALSE) == TRUE){
# Extract the flag from the string and add the column name
ExtractedFlag <- stringr::str_extract_all(InSynList[i,FlagAnnot_cols[j]],
FlagsAnnot, simplify = TRUE) %>%
paste(FlagAnnot_cols[j],.,sep=" ", collapse = "|") %>%
gsub(" ", " ",. ) # Remove double spaces
if( is.na(InSynList[i,"notes"]) == TRUE){ # If there is NO flag, insert this flag as is
InSynList[i,"notes"] <- ExtractedFlag
}else{ # If there IS a flag, ADD this to the existing flag
InSynList[i,"notes"] <- paste(InSynList[i,"notes"], ExtractedFlag, sep = " | ")
} # END if else statement
} # END find flag IF statement
} # END for loop of flag annotations - ROWS
# Sets the progress bar to the current state
utils::setTxtProgressBar(pb2, j)
} # END loop COLUMNS
#### END progBar 2 ####
close(pb2) # Close the connection
# Trim internal white spaces in flag column
InSynList$notes <- gsub(" \\| | \\||\\| ", "|", InSynList$notes)
# Remove these strings from the relevant columns now that they are saved as flags
TempCols <- as.data.frame(apply(InSynList[c("canonical",FlagAnnot_cols) ], 2,
function(y) gsub(FlagsAnnot, " ", y)))
# Replace existing columns with these new, trimmed, columns
InSynList[c(FlagAnnot_cols)] <- TempCols[, FlagAnnot_cols]
# Add the canonical column after the canonical column with flags - later convert to
# canonical and canonical_withFlags
CanTest <- InSynList$canonical
# IF there IS already a canonical column repalce that column with the new one...
if(is.null(CanTest) == FALSE){
InSynList$canonical <- TempCols$canonical
}else{
InSynList <- dplyr::mutate(InSynList, TempCols$canonical, .after = "canonical")
}
# Clean up double spaces in data frame
InSynList <- as.data.frame(apply(InSynList, 2, FUN = stringr::str_squish ), stringsAsFactors = FALSE)
} # END IF notes col
#### neither ####
if(flagCol != "flags" & flagCol != "notes"){
base::writeLines("!! The flagCol option must equal 'flags' or 'notes' !!")
}
#backupdf <- InSynList
#InSynList <- backupdf
# change column names
#colnames(InSynList) <- c("flags","taxonomic_status","source","accid","id","kingdom","phylum","class","order","family","subfamily","tribe","subtribe","validName","canonical_withFlags","canonical","genus","subgenus","species","infraspecies","authorship")
return(InSynList)
} # END FlagManager
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