R/species_names_correction.R
In AlbanSagouis/iClean: Cleaning and homogenising species names, coordinates and site names.
Defines functions
species_names_correction
Documented in
species_names_correction
#' Species names cleaning
#'
#' Use UTF-8 encoding to read and modify the code of the function
#' @param species_vector description
#' @param grouping_vector description
#' @param genus_name_extension description
#' @param numberHomogenisation if \code{TRUE} (the default), the length of numbers will be homogenised
#' among species names of a single study given in grouping_vector. If in a given study, the largest
#' number has 3 digits, all numbers will get zeroes concatened before. 1 -> 001.
#' @param delimiter Character wanted between words. Default to ' '.
#' @param replace_dots description
#' @param replace_question_marks description
#' @param erase_descriptor description
#' @param convert_to_ascii description
#' @return A vector of the same length as species_vector.
#' @author Alban Sagouis
#' @examples Write an example.
#'
#'
#' @export
# function that takes a vector of species names (species_vector) and makes corrections to it.
# http://tnrs.iplantcollaborative.org/TNRSapp.html
species_names_correction <- function(species_vector = NA,
grouping_vector = NA,
delimiter = " ",
convert_to_ascii = FALSE,
genus_name_extension = FALSE,
numberHomogenisation = FALSE,
replace_dots = FALSE,
replace_question_marks = FALSE,
erase_descriptor = TRUE
) {
if((genus_name_extension || numberHomogenisation) && all(is.na(grouping_vector))) stop("grouping_vector is missing")
if(class(grouping_vector) != "factor") grouping_vector <- factor(grouping_vector, levels = unique(grouping_vector))
# Accentuated characters such as Áêãçoàúü are converted to their basic equivalent Aeacoauu
if(convert_to_ascii) species_vector <- iconv(x=species_vector, from="latin1", to="ASCII//TRANSLIT")
# species names containing "-"
# "Ovidia pillo-pillo" should be Ovidia pillopillo? Both seem to be used, authors' choice should be respected.
# all "-grp." should be turned into nothing. In some of these cases, spaces are missing and sp will be collated to the genus name. So first, "-grp.sp" has to be turned into "-grp. sp"
species_vector <- gsub(pattern="-grp.sp", replacement=paste0(delimiter, "sp"), x=species_vector)
species_vector <- gsub(pattern="-grp.", replacement = delimiter, x=species_vector)
# all "-aggregate" should be deleted
species_vector <- gsub(pattern="-aggregate", replacement=delimiter, x=species_vector)
# there are also cases where aggregate has no hyphen before and they are also deleted
species_vector <- gsub(pattern="\\ aggregate", replacement=delimiter, x=species_vector)
# "m-number" species names are used for morphospecies and are treated in the morphospecies part.
######
# Unknown, Unidentified, indeterminate
# "u-number" should be transformed to "Unidentified number".
species_vector <- gsub(pattern="(u-)([[:digit:]]+)", replacement=paste0("Unidentified", delimiter,"\\2"), x=species_vector)
# "u4" should be transformed to "Unidentified 4"
species_vector <- gsub(pattern="\\_(u)([[:digit:]]+)", replacement=paste0(delimiter,"unidentified", delimiter,"\\2"), x=species_vector)
# "u_u22" should be transformed to "u unidentified 22"
species_vector <- gsub(pattern="^(u)([[:digit:]]+)", replacement=paste0("Unidentified", delimiter, "\\2"), x=species_vector)
# Unidentified species 3
species_vector <- gsub(pattern="^(Unidentified) (species) ([[:digit:]]+)", replacement=paste0("Unidentified", delimiter, "sp\\.", delimiter,"\\3"), x=species_vector)
# Indet. should be Indeterminate
species_vector <- gsub(pattern="Indet\\.\\ ", replacement=paste0("Indeterminate", delimiter), x=species_vector)
# names such as "Homalium_u1" are turned into "Homalium sp. 1"
# grep(pattern="^([A-Za-z]{2,})(\\_u)([[:digit:]])", x=species_vector, value=T)
species_vector <- gsub(pattern="^([A-Za-z]{2,})(\\_u)([[:digit:]]+)", replacement=paste0("\\1", delimiter, "sp.", delimiter, "\\3"), x=species_vector)
# replacing "-" ?
#species_vector[grep(x=species_vector, pattern="-"), ]
# replacing "." by the chosen delimiter
if(replace_dots) species_vector <- gsub(x=species_vector, pattern="\\.", replacement=delimiter) # aim? as is, messes with describer names.
# replacing "text0text" by "text text"
species_vector <- gsub(x=species_vector, pattern="([a-zA-Z])(0)([a-zA-Z])", replacement=paste0("\\1", delimiter, "\\3")) # because "sp07" should not be affected
# species names containing expressions between brackets
# all expressions between brackets should be deleted but there are exceptions where the brackets should be deleted but the text inside should remain: if there is "sp." between the brackets or any taxonomic name
# the space before should be deleted too but it can also be deleted later one when searching for all useless spaces at the end of species names.
#brackets <- unique(species_vector[grep(x=species_vector, pattern="\\([^}]*\\)")])
#species_vector <- gsub(x=species_vector, pattern="\\([^}]*\\)", replacement=delimiter)
# species names containing "?"
# should be looked at once all expressions between brackets have been deleted.
if(replace_question_marks) species_vector <- gsub(x=species_vector, pattern="\\?", replacement=delimiter)
# species names containing ","
# should be looked at once all expressions between brackets have been deleted.
species_vector <- gsub(x=species_vector, pattern=",", replacement=delimiter)
# species names containing "="
# should be all transformed into a single space
species_vector <- gsub(x=species_vector, pattern="=", replacement=delimiter)
# species names containing "#"
species_vector <- gsub(x=species_vector, pattern="\\#", replacement=delimiter)
# species names containing "<" or ">"
species_vector <- gsub(x=species_vector, pattern="<|>", replacement=delimiter)
# species names containing "_"
species_vector <- gsub(x=species_vector, pattern="_", replacement=delimiter)
# Species names with more than 2 words
# look for all forms of "sp." "s p." "s p" to check for typos.
if(length(grep(x=species_vector, pattern="(s\\ p)([[:digit:]])", value=F, fixed=F, perl=T))>0) warning(paste("Probable typo detected: space between genus name and sp misplaced in ", species_vector[grep(x=species_vector, pattern="(s\\ p)([[:digit:]])", value=F, fixed=F, perl=T)], sep=""))
# "Pyraustinisp.3" OR "Pyraustinisp3" -> "Pyraustini sp. 3"
#gsub(x=grep(x=species_vector, pattern="([[:alpha:]])(sp)([[:digit:]]*)[[:>:]]", value=T, perl=T), pattern="([[:alpha:]])(sp.)([[:digit:]]*)[[:>:]]", replacement="\\1 sp. \\3", perl=T)
species_vector <- gsub(x=species_vector, pattern="([[:alpha:]])(sp\\.)([[:digit:]]*)[[:>:]]|([[:alpha:]])(sp)([[:digit:]]*)[[:>:]]", replacement=paste0("\\1", delimiter,"sp.", delimiter, "\\3"), perl=T)
# spEOL -> sp.
species_vector <- gsub(x=species_vector, pattern="sp$|sp\\ $", replacement=paste0(delimiter, "sp\\."))
# sp .4 -> sp. 4
#gsub(x=grep(x=species_vector, pattern="(\\ sp)\\ \\.+([[:alnum:]])", "taxonomic.name", value=T, perl=T), pattern="(\\ sp)\\ \\.+([[:alnum:]])", "taxonomic.name", replacement="\\1\\.\\ \\2", fixed=F, perl=T)
species_vector <- gsub(x=species_vector, pattern="(\\ sp)\\ \\.+([[:alnum:]])", "taxonomic.name", replacement=paste0("\\1\\.", delimiter, "\\2"), fixed=F, perl=T)
# sp.4 -> sp. 4
#gsub(x=grep(x=species_vector, pattern="(\\ sp\\.)+([[:alnum:]])", value=T, perl=T), pattern="(\\ sp\\.)+([[:alnum:]])", replacement="\\1\\ \\2", fixed=F, perl=T)
species_vector <- gsub(x=species_vector, pattern="(\\ sp\\.)+([[:alnum:]])", replacement=paste0("\\1", delimiter, "\\2"), fixed=F, perl=T)
# sp4 -> sp. 4 ( sp04)
#gsub(x=grep(x=species_vector, pattern="(\\ sp)+([1-9A-Z])", value=T, perl=T), pattern="(\\ sp)+([1-9A-Z])", "taxonomic.name", replacement="\\1\\.\\ \\2", fixed=F, perl=T)
species_vector <- gsub(x=species_vector, pattern="(\\ sp)+([0-9A-Z])", replacement=paste0("\\1\\.", delimiter, "\\2"), fixed=F, perl=T) # not using alnum to avoid cutting words like splendens
# spbEOL -> sp.b
species_vector <- gsub(x=species_vector, pattern="(\\ sp)+([[:alnum:]])$", replacement=paste0("\\1\\.", delimiter, "\\2"), fixed=F, perl=T)
# sp 4 -> sp. 4
#gsub(x=grep(x=species_vector, pattern="(\\ sp)+(\\ [[:alnum:]])", value=T, perl=T), pattern="(\\ sp)+(\\ [[:alnum:]])", replacement="\\1\\.\\2", fixed=F, perl=T)
species_vector <- gsub(x=species_vector, pattern="(\\ sp)+(\\ )+([[:alnum:]])", replacement="\\1\\.\\3", fixed=F, perl=T)
# sp 4 -> sp. 4 (2 spaces)
#gsub(x=grep(x=species_vector, pattern="(\\ sp)+(\\ [[:alnum:]])", value=T, perl=T), pattern="(\\ sp)+(\\ [[:alnum:]])", replacement="\\1\\.\\2", fixed=F, perl=T)
species_vector <- gsub(x=species_vector, pattern="(\\ sp)+(\\ )+(\\ )+([[:alnum:]])", replacement="\\1\\.\\4", fixed=F, perl=T)
# spec. 4 -> sp. 4
#gsub(x=grep(x=species_vector, pattern="\\ spec\\.", value=T), pattern="\\ spec\\.", replacement="\\ sp\\.")
species_vector <- gsub(x=species_vector, pattern="\\ spec\\.", replacement=paste0(delimiter, "sp\\."))
# species 4 -> sp. 4
# gsub(x=grep(x=species_vector, pattern="(\\ species)+(\\ [[:digit:]])", value=T), pattern="(\\ species)+(\\ [[:digit:]])", replacement="\\ sp\\.\\2")
species_vector <- gsub(x=species_vector, pattern="(\\ species)+(\\ )+([[:digit:]])", replacement=paste0(delimiter, "sp\\.\\3"))
# " spp" should be " spp."
#gsub(x=grep(x=species_vector, pattern="\\ spp[^\\.]|\\ spp$", value=T), pattern="\\ spp[^\\.]|\\ spp$", replacement="\\ spp\\.\\ ")
species_vector <- gsub(x=species_vector, pattern="\\ spp[^\\.]|\\ spp$", replacement=paste0(delimiter, "spp\\.", delimiter))
# " aff " should be " aff. "
#gsub(x=grep(x=species_vector, pattern="\\ aff\\ |\\ aff$", value=T), pattern="\\ aff\\ |\\ aff$", replacement="\\ aff\\.\\ ")
species_vector <- gsub(x=species_vector, pattern="\\ aff\\ |\\ aff$", replacement=paste0(delimiter, "aff\\.", delimiter))
# " var " should be " var. "
species_vector <- gsub(x=species_vector, pattern="\\ var\\ |\\ var$", replacement=paste0(delimiter, "var\\.", delimiter))
# " nr " should be " nt. "
species_vector <- gsub(x=species_vector, pattern="\\ nr\\ |\\ nr$", replacement=paste0(delimiter, "nr\\.", delimiter))
# " cf " should be " cf. "
species_vector <- gsub(x=species_vector, pattern="\\ cf\\ |\\ cf$", replacement=paste0(delimiter, "cf\\.", delimiter))
species_vector <- gsub(x=species_vector, pattern="\\ CF\\ |\\ CF$", replacement=paste0(delimiter, "cf\\.", delimiter))
# " c.f. " should be " cf. "
species_vector <- gsub(x=species_vector, pattern="\\ c\\.f\\.\\ |\\ c\\.f\\.$", replacement=paste0(delimiter, "cf\\.", delimiter))
# " et al" should be " et al."
species_vector <- gsub(x=species_vector, pattern=" et al$| et al\\ ", replacement=paste0(delimiter,"et", delimiter, "al\\.", delimiter))
# morphospecies
# "morphospec 0562" -> "msp. 0562"
#gsub(x=grep(x=species_vector, pattern="(morphospec)(\\ [[:digit:]])", value=T, perl=T), pattern="(morphospec)(\\ [[:digit:]])", replacement="msp\\.\\ \\2", fixed=F, perl=T)
species_vector <- gsub(x=species_vector, pattern="(morphospec)(\\ )([[:digit:]])", replacement=paste0("msp\\.", delimiter, "\\3"), fixed=F, perl=T)
#gsub(x=grep(x=species_vector, pattern="(m-)([[:digit:]])", value=T, perl=T), pattern="(m-)([[:digit:]])", replacement="msp\\.\\ \\2", fixed=F, perl=T)
species_vector <- gsub(x=species_vector, pattern="(m-)([[:digit:]])", replacement=paste0("msp\\.", delimiter, "\\2"), fixed=F, perl=T)
# M3 -> msp. 3
# gsub(x=grep(x=species_vector, pattern="(.+)(M)([[:digit:]])", value=T, perl=T), pattern="(.+)(M)([[:digit:]])", replacement="\\1\\ msp\\.\\ \\3", fixed=F, perl=T)
species_vector <- gsub(x=species_vector, pattern="(.+)(M)([[:digit:]])", replacement=paste0("\\1", delimiter, "msp\\.", delimiter, "\\3"), fixed=F, perl=T)
# Genus1 -> Genus 1
species_vector <- gsub(x=species_vector, pattern="([[:alpha:]])([[:digit:]])", perl=T, replacement=paste0("\\1", delimiter, "\\2"))
# species codes such as Micrathena sp. A 1 should be sp. A1. Same for some fragment names.
# some species names have describer names outside of any brackets
# when the third word has a capital in the first letter "Onthophagus bidentatus Drapiez" OR "Uroxys pygmaeus Har." but not "Micrathena sp. D" Examples in Andr_2003. Paw paw Tortricid was modified inside the original file (Stireman)
#grep(species_vector, pattern="^([[:alpha:]])+(\\s)+([[:alpha:]])+(\\s+[[:upper:]]+[[:lower:]]{2,})", value=T)
#menu(c("yes","no"), title="Did you check that all cases covered by this regular expression are author name?")
if(erase_descriptor) species_vector <- gsub(species_vector, pattern="^([[:alpha:]]+)+(\\s)+([[:alpha:]]+)+(\\s+[[:upper:]]+[[:lower:]]{2,})", replacement=paste0("\\1", delimiter, "\\3"))
if(genus_name_extension) {
# when consecutive species are written like that: Quercus robur, Q. coccifera, function replaces Q. by Quercus.
species_vector <- unlist(tapply(species_vector, grouping_vector, iClean::extend_genus_names))
}
if(numberHomogenisation) species_vector <- unlist(tapply(species_vector, grouping_vector, iClean::homogeniseNumberLength))
# Deleting final spaces and look for double spaces
species_vector <- gsub(pattern="\\s{2,}", replacement=delimiter, x=species_vector) # 2 or more spaces
species_vector <- trimws(x=species_vector, which="both") # deleting leading an trailing spaces
species_vector <- gsub(x=species_vector, pattern="\\s", replacement = delimiter) # replace remaining spaces with delimiter
species_vector <- gsub(pattern=paste0(delimiter,"{2,}"), replacement=delimiter, x=species_vector) # 2 or more spaces
# Every first letter should be capitalised
species_vector <- gsub("(^[[:alpha:]])", x=species_vector, replacement="\\U\\1", perl=T)
return(species_vector)
}
AlbanSagouis/iClean documentation built on May 14, 2020, 9:06 p.m.
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Defines functions species_names_correction
Documented in species_names_correction
#' Species names cleaning
#'
#' Use UTF-8 encoding to read and modify the code of the function
#' @param species_vector description
#' @param grouping_vector description
#' @param genus_name_extension description
#' @param numberHomogenisation if \code{TRUE} (the default), the length of numbers will be homogenised
#' among species names of a single study given in grouping_vector. If in a given study, the largest
#' number has 3 digits, all numbers will get zeroes concatened before. 1 -> 001.
#' @param delimiter Character wanted between words. Default to ' '.
#' @param replace_dots description
#' @param replace_question_marks description
#' @param erase_descriptor description
#' @param convert_to_ascii description
#' @return A vector of the same length as species_vector.
#' @author Alban Sagouis
#' @examples Write an example.
#'
#'
#' @export
# function that takes a vector of species names (species_vector) and makes corrections to it.
# http://tnrs.iplantcollaborative.org/TNRSapp.html
species_names_correction <- function(species_vector = NA,
grouping_vector = NA,
delimiter = " ",
convert_to_ascii = FALSE,
genus_name_extension = FALSE,
numberHomogenisation = FALSE,
replace_dots = FALSE,
replace_question_marks = FALSE,
erase_descriptor = TRUE
) {
if((genus_name_extension || numberHomogenisation) && all(is.na(grouping_vector))) stop("grouping_vector is missing")
if(class(grouping_vector) != "factor") grouping_vector <- factor(grouping_vector, levels = unique(grouping_vector))
# Accentuated characters such as Áêãçoàúü are converted to their basic equivalent Aeacoauu
if(convert_to_ascii) species_vector <- iconv(x=species_vector, from="latin1", to="ASCII//TRANSLIT")
# species names containing "-"
# "Ovidia pillo-pillo" should be Ovidia pillopillo? Both seem to be used, authors' choice should be respected.
# all "-grp." should be turned into nothing. In some of these cases, spaces are missing and sp will be collated to the genus name. So first, "-grp.sp" has to be turned into "-grp. sp"
species_vector <- gsub(pattern="-grp.sp", replacement=paste0(delimiter, "sp"), x=species_vector)
species_vector <- gsub(pattern="-grp.", replacement = delimiter, x=species_vector)
# all "-aggregate" should be deleted
species_vector <- gsub(pattern="-aggregate", replacement=delimiter, x=species_vector)
# there are also cases where aggregate has no hyphen before and they are also deleted
species_vector <- gsub(pattern="\\ aggregate", replacement=delimiter, x=species_vector)
# "m-number" species names are used for morphospecies and are treated in the morphospecies part.
######
# Unknown, Unidentified, indeterminate
# "u-number" should be transformed to "Unidentified number".
species_vector <- gsub(pattern="(u-)([[:digit:]]+)", replacement=paste0("Unidentified", delimiter,"\\2"), x=species_vector)
# "u4" should be transformed to "Unidentified 4"
species_vector <- gsub(pattern="\\_(u)([[:digit:]]+)", replacement=paste0(delimiter,"unidentified", delimiter,"\\2"), x=species_vector)
# "u_u22" should be transformed to "u unidentified 22"
species_vector <- gsub(pattern="^(u)([[:digit:]]+)", replacement=paste0("Unidentified", delimiter, "\\2"), x=species_vector)
# Unidentified species 3
species_vector <- gsub(pattern="^(Unidentified) (species) ([[:digit:]]+)", replacement=paste0("Unidentified", delimiter, "sp\\.", delimiter,"\\3"), x=species_vector)
# Indet. should be Indeterminate
species_vector <- gsub(pattern="Indet\\.\\ ", replacement=paste0("Indeterminate", delimiter), x=species_vector)
# names such as "Homalium_u1" are turned into "Homalium sp. 1"
# grep(pattern="^([A-Za-z]{2,})(\\_u)([[:digit:]])", x=species_vector, value=T)
species_vector <- gsub(pattern="^([A-Za-z]{2,})(\\_u)([[:digit:]]+)", replacement=paste0("\\1", delimiter, "sp.", delimiter, "\\3"), x=species_vector)
# replacing "-" ?
#species_vector[grep(x=species_vector, pattern="-"), ]
# replacing "." by the chosen delimiter
if(replace_dots) species_vector <- gsub(x=species_vector, pattern="\\.", replacement=delimiter) # aim? as is, messes with describer names.
# replacing "text0text" by "text text"
species_vector <- gsub(x=species_vector, pattern="([a-zA-Z])(0)([a-zA-Z])", replacement=paste0("\\1", delimiter, "\\3")) # because "sp07" should not be affected
# species names containing expressions between brackets
# all expressions between brackets should be deleted but there are exceptions where the brackets should be deleted but the text inside should remain: if there is "sp." between the brackets or any taxonomic name
# the space before should be deleted too but it can also be deleted later one when searching for all useless spaces at the end of species names.
#brackets <- unique(species_vector[grep(x=species_vector, pattern="\\([^}]*\\)")])
#species_vector <- gsub(x=species_vector, pattern="\\([^}]*\\)", replacement=delimiter)
# species names containing "?"
# should be looked at once all expressions between brackets have been deleted.
if(replace_question_marks) species_vector <- gsub(x=species_vector, pattern="\\?", replacement=delimiter)
# species names containing ","
# should be looked at once all expressions between brackets have been deleted.
species_vector <- gsub(x=species_vector, pattern=",", replacement=delimiter)
# species names containing "="
# should be all transformed into a single space
species_vector <- gsub(x=species_vector, pattern="=", replacement=delimiter)
# species names containing "#"
species_vector <- gsub(x=species_vector, pattern="\\#", replacement=delimiter)
# species names containing "<" or ">"
species_vector <- gsub(x=species_vector, pattern="<|>", replacement=delimiter)
# species names containing "_"
species_vector <- gsub(x=species_vector, pattern="_", replacement=delimiter)
# Species names with more than 2 words
# look for all forms of "sp." "s p." "s p" to check for typos.
if(length(grep(x=species_vector, pattern="(s\\ p)([[:digit:]])", value=F, fixed=F, perl=T))>0) warning(paste("Probable typo detected: space between genus name and sp misplaced in ", species_vector[grep(x=species_vector, pattern="(s\\ p)([[:digit:]])", value=F, fixed=F, perl=T)], sep=""))
# "Pyraustinisp.3" OR "Pyraustinisp3" -> "Pyraustini sp. 3"
#gsub(x=grep(x=species_vector, pattern="([[:alpha:]])(sp)([[:digit:]]*)[[:>:]]", value=T, perl=T), pattern="([[:alpha:]])(sp.)([[:digit:]]*)[[:>:]]", replacement="\\1 sp. \\3", perl=T)
species_vector <- gsub(x=species_vector, pattern="([[:alpha:]])(sp\\.)([[:digit:]]*)[[:>:]]|([[:alpha:]])(sp)([[:digit:]]*)[[:>:]]", replacement=paste0("\\1", delimiter,"sp.", delimiter, "\\3"), perl=T)
# spEOL -> sp.
species_vector <- gsub(x=species_vector, pattern="sp$|sp\\ $", replacement=paste0(delimiter, "sp\\."))
# sp .4 -> sp. 4
#gsub(x=grep(x=species_vector, pattern="(\\ sp)\\ \\.+([[:alnum:]])", "taxonomic.name", value=T, perl=T), pattern="(\\ sp)\\ \\.+([[:alnum:]])", "taxonomic.name", replacement="\\1\\.\\ \\2", fixed=F, perl=T)
species_vector <- gsub(x=species_vector, pattern="(\\ sp)\\ \\.+([[:alnum:]])", "taxonomic.name", replacement=paste0("\\1\\.", delimiter, "\\2"), fixed=F, perl=T)
# sp.4 -> sp. 4
#gsub(x=grep(x=species_vector, pattern="(\\ sp\\.)+([[:alnum:]])", value=T, perl=T), pattern="(\\ sp\\.)+([[:alnum:]])", replacement="\\1\\ \\2", fixed=F, perl=T)
species_vector <- gsub(x=species_vector, pattern="(\\ sp\\.)+([[:alnum:]])", replacement=paste0("\\1", delimiter, "\\2"), fixed=F, perl=T)
# sp4 -> sp. 4 ( sp04)
#gsub(x=grep(x=species_vector, pattern="(\\ sp)+([1-9A-Z])", value=T, perl=T), pattern="(\\ sp)+([1-9A-Z])", "taxonomic.name", replacement="\\1\\.\\ \\2", fixed=F, perl=T)
species_vector <- gsub(x=species_vector, pattern="(\\ sp)+([0-9A-Z])", replacement=paste0("\\1\\.", delimiter, "\\2"), fixed=F, perl=T) # not using alnum to avoid cutting words like splendens
# spbEOL -> sp.b
species_vector <- gsub(x=species_vector, pattern="(\\ sp)+([[:alnum:]])$", replacement=paste0("\\1\\.", delimiter, "\\2"), fixed=F, perl=T)
# sp 4 -> sp. 4
#gsub(x=grep(x=species_vector, pattern="(\\ sp)+(\\ [[:alnum:]])", value=T, perl=T), pattern="(\\ sp)+(\\ [[:alnum:]])", replacement="\\1\\.\\2", fixed=F, perl=T)
species_vector <- gsub(x=species_vector, pattern="(\\ sp)+(\\ )+([[:alnum:]])", replacement="\\1\\.\\3", fixed=F, perl=T)
# sp 4 -> sp. 4 (2 spaces)
#gsub(x=grep(x=species_vector, pattern="(\\ sp)+(\\ [[:alnum:]])", value=T, perl=T), pattern="(\\ sp)+(\\ [[:alnum:]])", replacement="\\1\\.\\2", fixed=F, perl=T)
species_vector <- gsub(x=species_vector, pattern="(\\ sp)+(\\ )+(\\ )+([[:alnum:]])", replacement="\\1\\.\\4", fixed=F, perl=T)
# spec. 4 -> sp. 4
#gsub(x=grep(x=species_vector, pattern="\\ spec\\.", value=T), pattern="\\ spec\\.", replacement="\\ sp\\.")
species_vector <- gsub(x=species_vector, pattern="\\ spec\\.", replacement=paste0(delimiter, "sp\\."))
# species 4 -> sp. 4
# gsub(x=grep(x=species_vector, pattern="(\\ species)+(\\ [[:digit:]])", value=T), pattern="(\\ species)+(\\ [[:digit:]])", replacement="\\ sp\\.\\2")
species_vector <- gsub(x=species_vector, pattern="(\\ species)+(\\ )+([[:digit:]])", replacement=paste0(delimiter, "sp\\.\\3"))
# " spp" should be " spp."
#gsub(x=grep(x=species_vector, pattern="\\ spp[^\\.]|\\ spp$", value=T), pattern="\\ spp[^\\.]|\\ spp$", replacement="\\ spp\\.\\ ")
species_vector <- gsub(x=species_vector, pattern="\\ spp[^\\.]|\\ spp$", replacement=paste0(delimiter, "spp\\.", delimiter))
# " aff " should be " aff. "
#gsub(x=grep(x=species_vector, pattern="\\ aff\\ |\\ aff$", value=T), pattern="\\ aff\\ |\\ aff$", replacement="\\ aff\\.\\ ")
species_vector <- gsub(x=species_vector, pattern="\\ aff\\ |\\ aff$", replacement=paste0(delimiter, "aff\\.", delimiter))
# " var " should be " var. "
species_vector <- gsub(x=species_vector, pattern="\\ var\\ |\\ var$", replacement=paste0(delimiter, "var\\.", delimiter))
# " nr " should be " nt. "
species_vector <- gsub(x=species_vector, pattern="\\ nr\\ |\\ nr$", replacement=paste0(delimiter, "nr\\.", delimiter))
# " cf " should be " cf. "
species_vector <- gsub(x=species_vector, pattern="\\ cf\\ |\\ cf$", replacement=paste0(delimiter, "cf\\.", delimiter))
species_vector <- gsub(x=species_vector, pattern="\\ CF\\ |\\ CF$", replacement=paste0(delimiter, "cf\\.", delimiter))
# " c.f. " should be " cf. "
species_vector <- gsub(x=species_vector, pattern="\\ c\\.f\\.\\ |\\ c\\.f\\.$", replacement=paste0(delimiter, "cf\\.", delimiter))
# " et al" should be " et al."
species_vector <- gsub(x=species_vector, pattern=" et al$| et al\\ ", replacement=paste0(delimiter,"et", delimiter, "al\\.", delimiter))
# morphospecies
# "morphospec 0562" -> "msp. 0562"
#gsub(x=grep(x=species_vector, pattern="(morphospec)(\\ [[:digit:]])", value=T, perl=T), pattern="(morphospec)(\\ [[:digit:]])", replacement="msp\\.\\ \\2", fixed=F, perl=T)
species_vector <- gsub(x=species_vector, pattern="(morphospec)(\\ )([[:digit:]])", replacement=paste0("msp\\.", delimiter, "\\3"), fixed=F, perl=T)
#gsub(x=grep(x=species_vector, pattern="(m-)([[:digit:]])", value=T, perl=T), pattern="(m-)([[:digit:]])", replacement="msp\\.\\ \\2", fixed=F, perl=T)
species_vector <- gsub(x=species_vector, pattern="(m-)([[:digit:]])", replacement=paste0("msp\\.", delimiter, "\\2"), fixed=F, perl=T)
# M3 -> msp. 3
# gsub(x=grep(x=species_vector, pattern="(.+)(M)([[:digit:]])", value=T, perl=T), pattern="(.+)(M)([[:digit:]])", replacement="\\1\\ msp\\.\\ \\3", fixed=F, perl=T)
species_vector <- gsub(x=species_vector, pattern="(.+)(M)([[:digit:]])", replacement=paste0("\\1", delimiter, "msp\\.", delimiter, "\\3"), fixed=F, perl=T)
# Genus1 -> Genus 1
species_vector <- gsub(x=species_vector, pattern="([[:alpha:]])([[:digit:]])", perl=T, replacement=paste0("\\1", delimiter, "\\2"))
# species codes such as Micrathena sp. A 1 should be sp. A1. Same for some fragment names.
# some species names have describer names outside of any brackets
# when the third word has a capital in the first letter "Onthophagus bidentatus Drapiez" OR "Uroxys pygmaeus Har." but not "Micrathena sp. D" Examples in Andr_2003. Paw paw Tortricid was modified inside the original file (Stireman)
#grep(species_vector, pattern="^([[:alpha:]])+(\\s)+([[:alpha:]])+(\\s+[[:upper:]]+[[:lower:]]{2,})", value=T)
#menu(c("yes","no"), title="Did you check that all cases covered by this regular expression are author name?")
if(erase_descriptor) species_vector <- gsub(species_vector, pattern="^([[:alpha:]]+)+(\\s)+([[:alpha:]]+)+(\\s+[[:upper:]]+[[:lower:]]{2,})", replacement=paste0("\\1", delimiter, "\\3"))
if(genus_name_extension) {
# when consecutive species are written like that: Quercus robur, Q. coccifera, function replaces Q. by Quercus.
species_vector <- unlist(tapply(species_vector, grouping_vector, iClean::extend_genus_names))
}
if(numberHomogenisation) species_vector <- unlist(tapply(species_vector, grouping_vector, iClean::homogeniseNumberLength))
# Deleting final spaces and look for double spaces
species_vector <- gsub(pattern="\\s{2,}", replacement=delimiter, x=species_vector) # 2 or more spaces
species_vector <- trimws(x=species_vector, which="both") # deleting leading an trailing spaces
species_vector <- gsub(x=species_vector, pattern="\\s", replacement = delimiter) # replace remaining spaces with delimiter
species_vector <- gsub(pattern=paste0(delimiter,"{2,}"), replacement=delimiter, x=species_vector) # 2 or more spaces
# Every first letter should be capitalised
species_vector <- gsub("(^[[:alpha:]])", x=species_vector, replacement="\\U\\1", perl=T)
return(species_vector)
}
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