Nothing
R/annotation_label.R
In herblabel: Making Labels for Herbarium Specimens in RTF and More
#### Create RTF annotation labels
annotation_label <- function(dat = NULL, spellcheck = TRUE, outfile = "Annotation_Labels.rtf") {
if(is.null(dat)){
stop("dat should be specified")
}
herbdat000 <- dat
herbdat000[herbdat000 == ""] <- NA
if (any(is.na(herbdat000$GENUS))) {
warning(paste("\"GENUS\" not provided for row: ",
paste(which(is.na(herbdat000$GENUS)) +
1, collapse = ", ")))
}
if (any(is.na(herbdat000$IDENTIFIED_BY))) {
warning(paste("\"IDENTIFIED_BY\" not provided for row: ",
paste(which(is.na(herbdat000$IDENTIFIED_BY)) +
1, collapse = ", ")))
}
if (any(is.na(herbdat000$DATE_IDENTIFIED))) {
warning(paste("\"DATE_IDENTIFIED\" not provided for row: ",
paste(which(is.na(herbdat000$DATE_IDENTIFIED)) +
1, collapse = ", ")))
}
#### Formating Date
formatdate <- function(x){
if(!is.na(suppressWarnings(as.integer(x))) ){
if(!grepl("^darwin", R.version$os)){
x <- as.Date(as.integer(x), origin="1899-12-30") ### Default in MacOS
} else {
x <- as.Date(as.integer(x), origin = "1904-01-01") ### Default in Windows
}
}
res <- format(as.Date(x),"%d %B %Y")
return(res)
}
pgenus <- herblabel::pgenus
#### replace multiple commas and white space, and delete comma if it is the last one.
REPLACE <- function(x){
if(length(x) > 1){
stop("only one string is allowed")
}
bbb <- gsub(" +", " ", gsub(",+", ", ", gsub(", +", ",", x)))
bbb <- gsub("^[[:space:]]+|[[:space:]]+$", "", bbb)
endchar <- substr(bbb, nchar(bbb), nchar(bbb))
if(endchar == ","){
yyy <- gregexpr(pattern = ",", bbb)
res <- substr(bbb, start = 1, stop = ifelse(unlist(lapply(yyy, function(x){max(x)-1})) > 1,
unlist(lapply(yyy, function(x){max(x)-1})) , nchar(bbb)))
} else {
res <- bbb
}
res <- gsub("^[[:space:]]+|[[:space:]]+$", "", res)
return(res)
}
if(spellcheck){
sptemp <- paste( ifelse(is.na(herbdat000$GENUS), "", herbdat000$GENUS ),
ifelse(is.na(herbdat000$SPECIES), "", herbdat000$SPECIES ),
ifelse(is.na(herbdat000$AUTHOR_OF_SPECIES), "", herbdat000$AUTHOR_OF_SPECIES ),
ifelse(is.na(herbdat000$INFRASPECIFIC_RANK), "", herbdat000$INFRASPECIFIC_RANK ),
ifelse(is.na(herbdat000$INFRASPECIFIC_EPITHET), "", herbdat000$INFRASPECIFIC_EPITHET ),
ifelse(is.na(herbdat000$AUTHOR_OF_INFRASPECIFIC_RANK), "", herbdat000$AUTHOR_OF_INFRASPECIFIC_RANK),
sep = " ")
sptemp2 <- c()
for(i in 1:length(sptemp)){
sptemp2[i] <- REPLACE(sptemp[i])
}
tplsplist <- herblabel::tplsplist
ind <- (!sptemp2 %in% tplsplist) & (!gsub(" ", "", sptemp2 ) == "") ### Make sure the empty entries were excluded.
herbdat000$GENUS[ind] <- paste("\\cf2\\i0 Name not found. Check Spelling at {\\field{\\*\\fldinst{HYPERLINK \"http://www.theplantlist.org/\"}}{\\fldrslt{\\ul\\cf2 http://www.theplantlist.org/}}} or {\\field{\\*\\fldinst{HYPERLINK \"http://frps.eflora.cn/\"}}{\\fldrslt{\\ul\\cf2 http://frps.eflora.cn/}}} for:\\i ", herbdat000$GENUS[ind], sep = "")
herbdat000$AUTHOR_OF_INFRASPECIFIC_RANK[ind] <- paste(ifelse(is.na(herbdat000$AUTHOR_OF_INFRASPECIFIC_RANK[ind]), "", herbdat000$AUTHOR_OF_INFRASPECIFIC_RANK[ind]), "\\cf1", sep = "")
}
### {\\stylesheet {\\qj \\li0 \\ri0 \\widctlpar \\aspalpha \\aspnum \\adjustright \\lin0 \\rin0 \\itap0 \\fs21 \\kerning2 \\dbch \\af2 \\hich \\af0 \\loch \\f0 \\snext0 \\spriority0 Normal;}
### match.gf(herbdat000$FAMIL, herbdat000$GENUS)
### {\\*\\cs10 \\snext10 \\sunhideused \\spriority99 Default Paragraph Font;}
temp1 <- "{\\rtf1\\ansi\\ansicpg936\\deflangfe2052\\fcharset134\\deff1{\\fonttbl{\\f0\\froman\\fcharset134 SimSun;}{\\f1\\froman\\fcharset134 Times New Roman;}}{\\stylesheet{\\*\\cs3 Default Paragraph Font;}}{\\colortbl\\red255\\green0\\blue0;\\red0\\green255\\blue0;\\red0\\green0\\blue255;}\\paperw12240\\paperh15840\\margl1800\\margr1800\\margt1440\\margb1440\\gutter0\\ftnbj\\aenddoc\\jcompress1\\viewkind4\\viewscale100\\asianbrkrule\\allowfieldendsel\\snaptogridincell\\viewkind4\\sectd\\sbkpage\\pgwsxn11906\\pghsxn16838\\marglsxn600\\margrsxn600\\margtsxn720\\margbsxn10\\guttersxn0\\headery720\\footery720\\pgbrdropt0\\sectdefaultcl\\cols2\\colsx1080\\linebetcol1\\endnhere"
### fcharset134 to specify Chinese Font Herbarium Label Default Font Size if 18
### Default font is Time New Roman
temp2 <- c()
for (i in 1:nrow(herbdat000)) {
herbdat <- herbdat000[i, ]
### Set the size for each label
res <- c(
ifelse((is.na(herbdat$COLLECTOR))|(is.na(herbdat$COLLECTOR_NUMBER)),
"",
paste("{\\pard\\keep\\keepn\\fi0\\li0\\brsp20\\fs18\\sb100\\sa50 Coll.: ", herbdat$COLLECTOR, " #",herbdat$COLLECTOR_NUMBER, "\\par }", sep = "")),
ifelse(is.na(herbdat$TYPE_STATUS),
"",
paste("{\\pard\\keep\\keepn\\fi0\\li0\\brsp20\\sb100\\sa50\\fs20\\b ", toupper(as.character(herbdat$TYPE_STATUS)), "\\b0 of:\\par }", sep = "")),
ifelse((is.na(herbdat$FAMILY)),
"",
paste("{\\pard\\keep\\keepn\\fi0\\li0\\brsp20\\", ifelse((is.na(herbdat$TYPE_STATUS)), "sb20", "sb180"), "\\sa50\\fs20\\b ", as.character(herbdat$FAMILY), "\\b0\\par }", sep = "")
),
ifelse(((is.na(herbdat$GENUS) )&
(is.na(herbdat$SPECIES) )&
(is.na(herbdat$AUTHOR_OF_SPECIES) )&
(is.na(herbdat$INFRASPECIFIC_RANK) )&
(is.na(herbdat$INFRASPECIFIC_EPITHET) )&
(is.na(herbdat$AUTHOR_OF_INFRASPECIFIC_RANK))),
"",
paste("{\\pard\\keep\\keepn\\fi-288\\li288",
ifelse((is.na(herbdat$TYPE_STATUS)),
"\\sb180", "\\sb20"),
"\\sa20\\fs20\\b\\i ",
ifelse(is.na(herbdat$GENUS), "", as.character(herbdat$GENUS)),
"\\i0 \\i ",
ifelse((is.na(herbdat$SPECIES)), "\\i0 ", as.character(herbdat$SPECIES)),
"\\i0 ",
ifelse(is.na(herbdat$AUTHOR_OF_SPECIES), "", as.character(herbdat$AUTHOR_OF_SPECIES)),
" ",
ifelse(is.na(herbdat$INFRASPECIFIC_RANK), "", as.character(herbdat$INFRASPECIFIC_RANK)),
" \\i ",
ifelse(is.na(herbdat$INFRASPECIFIC_EPITHET), "", as.character(herbdat$INFRASPECIFIC_EPITHET)),
"\\i0 ",
ifelse(is.na(herbdat$AUTHOR_OF_INFRASPECIFIC_RANK), "", as.character(herbdat$AUTHOR_OF_INFRASPECIFIC_RANK)
),
"\\b0\\par }", sep = "")
),
ifelse(is.na(herbdat$TYPE_REF),
"",
paste("{\\pard\\keep\\keepn\\fi288\\li288\\brsp20\\sb10\\sa20\\fs16 " , ifelse(is.na(herbdat$TYPE_REF ), "", herbdat$TYPE_REF), " \\par}")
),
ifelse(is.na(herbdat$DET_NOTE),
"",
paste("{\\pard\\keep",
ifelse(((is.na(herbdat$TYPE_STATUS ))&
(is.na(herbdat$TYPE_REF ))&
(is.na(herbdat$FAMILY ))&
(is.na(herbdat$GENUS ))&
(is.na(herbdat$SPECIES ))&
(is.na(herbdat$AUTHOR_OF_SPECIES ))&
(is.na(herbdat$INFRASPECIFIC_RANK ))&
(is.na(herbdat$INFRASPECIFIC_EPITHET ))&
(is.na(herbdat$AUTHOR_OF_INFRASPECIFIC_RANK))), "\\sb150", "\\sb10")
,"\\sa20\\keepn\\fi0\\li0\\fs16 ", as.character(herbdat$DET_NOTE), " \\par}", sep = "")
),
paste("{\\pard\\keep", ifelse(((is.na(herbdat$TYPE_STATUS ))&
(is.na(herbdat$TYPE_REF ))&
(is.na(herbdat$FAMILY ))&
(is.na(herbdat$GENUS ))&
(is.na(herbdat$SPECIES ))&
(is.na(herbdat$AUTHOR_OF_SPECIES ))&
(is.na(herbdat$INFRASPECIFIC_RANK ))&
(is.na(herbdat$INFRASPECIFIC_EPITHET ))&
(is.na(herbdat$AUTHOR_OF_INFRASPECIFIC_RANK))&
(is.na(herbdat$DET_NOTE ))),
"\\sb800", # if all are missing, extent the space
"\\sb200"),
ifelse((is.na(herbdat$PROJECT)),
"\\sa150",
"\\sa10"),
"\\keepn\\fi0\\li0\\fs18\\tqr\\tx4850 ",
ifelse(is.na(herbdat$ABBREVIATION),
"",
paste(herbdat$ABBREVIATION,": ", sep = "")),
ifelse(is.na(herbdat$IDENTIFIED_BY),
"",
as.character(herbdat$IDENTIFIED_BY)),
"",
ifelse(is.na(herbdat$INSTITUTION),
"",
ifelse(is.na(herbdat$IDENTIFIED_BY),
paste(" ", as.character(herbdat$INSTITUTION), sep = ""),
paste(", ", as.character(herbdat$INSTITUTION), sep = ""))),
" \\tab ",
ifelse(is.na(herbdat$DATE_IDENTIFIED),
"",
tryCatch(formatdate(herbdat$DATE_IDENTIFIED),
error= function(e) {print("Warning: Date format incorrect, using original string");
herbdat$DATE_IDENTIFIED})
),
" \\par }", sep = ""
),
ifelse(is.na(herbdat$PROJECT),
"",
paste("{\\pard\\keep\\keepn\\fi0\\li0\\brsp20\\qc\\sb10\\sa150\\fs16 ",
as.character(herbdat$PROJECT), "\\par }", sep = "")
),
"{\\pard\\keep\\qc\\fs18 . . .\\sa100\\par}"
)
### End of one label
temp2 <- c(temp2, res) ### Add label to the RTF file.
}
template <- c(temp1, temp2, "}") ## End of the RTF file
res <- template[!template %in% ""]
res <- iconv(x = res, from = "UTF-8", to = "GB18030")
writeLines(res, outfile)
### Notice
cat("Annotation labels have been saved to:\n",
file.path(getwd(), outfile), "\n", sep = "")
}
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herblabel documentation built on May 2, 2019, 4:47 p.m.
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#### Create RTF annotation labels
annotation_label <- function(dat = NULL, spellcheck = TRUE, outfile = "Annotation_Labels.rtf") {
if(is.null(dat)){
stop("dat should be specified")
}
herbdat000 <- dat
herbdat000[herbdat000 == ""] <- NA
if (any(is.na(herbdat000$GENUS))) {
warning(paste("\"GENUS\" not provided for row: ",
paste(which(is.na(herbdat000$GENUS)) +
1, collapse = ", ")))
}
if (any(is.na(herbdat000$IDENTIFIED_BY))) {
warning(paste("\"IDENTIFIED_BY\" not provided for row: ",
paste(which(is.na(herbdat000$IDENTIFIED_BY)) +
1, collapse = ", ")))
}
if (any(is.na(herbdat000$DATE_IDENTIFIED))) {
warning(paste("\"DATE_IDENTIFIED\" not provided for row: ",
paste(which(is.na(herbdat000$DATE_IDENTIFIED)) +
1, collapse = ", ")))
}
#### Formating Date
formatdate <- function(x){
if(!is.na(suppressWarnings(as.integer(x))) ){
if(!grepl("^darwin", R.version$os)){
x <- as.Date(as.integer(x), origin="1899-12-30") ### Default in MacOS
} else {
x <- as.Date(as.integer(x), origin = "1904-01-01") ### Default in Windows
}
}
res <- format(as.Date(x),"%d %B %Y")
return(res)
}
pgenus <- herblabel::pgenus
#### replace multiple commas and white space, and delete comma if it is the last one.
REPLACE <- function(x){
if(length(x) > 1){
stop("only one string is allowed")
}
bbb <- gsub(" +", " ", gsub(",+", ", ", gsub(", +", ",", x)))
bbb <- gsub("^[[:space:]]+|[[:space:]]+$", "", bbb)
endchar <- substr(bbb, nchar(bbb), nchar(bbb))
if(endchar == ","){
yyy <- gregexpr(pattern = ",", bbb)
res <- substr(bbb, start = 1, stop = ifelse(unlist(lapply(yyy, function(x){max(x)-1})) > 1,
unlist(lapply(yyy, function(x){max(x)-1})) , nchar(bbb)))
} else {
res <- bbb
}
res <- gsub("^[[:space:]]+|[[:space:]]+$", "", res)
return(res)
}
if(spellcheck){
sptemp <- paste( ifelse(is.na(herbdat000$GENUS), "", herbdat000$GENUS ),
ifelse(is.na(herbdat000$SPECIES), "", herbdat000$SPECIES ),
ifelse(is.na(herbdat000$AUTHOR_OF_SPECIES), "", herbdat000$AUTHOR_OF_SPECIES ),
ifelse(is.na(herbdat000$INFRASPECIFIC_RANK), "", herbdat000$INFRASPECIFIC_RANK ),
ifelse(is.na(herbdat000$INFRASPECIFIC_EPITHET), "", herbdat000$INFRASPECIFIC_EPITHET ),
ifelse(is.na(herbdat000$AUTHOR_OF_INFRASPECIFIC_RANK), "", herbdat000$AUTHOR_OF_INFRASPECIFIC_RANK),
sep = " ")
sptemp2 <- c()
for(i in 1:length(sptemp)){
sptemp2[i] <- REPLACE(sptemp[i])
}
tplsplist <- herblabel::tplsplist
ind <- (!sptemp2 %in% tplsplist) & (!gsub(" ", "", sptemp2 ) == "") ### Make sure the empty entries were excluded.
herbdat000$GENUS[ind] <- paste("\\cf2\\i0 Name not found. Check Spelling at {\\field{\\*\\fldinst{HYPERLINK \"http://www.theplantlist.org/\"}}{\\fldrslt{\\ul\\cf2 http://www.theplantlist.org/}}} or {\\field{\\*\\fldinst{HYPERLINK \"http://frps.eflora.cn/\"}}{\\fldrslt{\\ul\\cf2 http://frps.eflora.cn/}}} for:\\i ", herbdat000$GENUS[ind], sep = "")
herbdat000$AUTHOR_OF_INFRASPECIFIC_RANK[ind] <- paste(ifelse(is.na(herbdat000$AUTHOR_OF_INFRASPECIFIC_RANK[ind]), "", herbdat000$AUTHOR_OF_INFRASPECIFIC_RANK[ind]), "\\cf1", sep = "")
}
### {\\stylesheet {\\qj \\li0 \\ri0 \\widctlpar \\aspalpha \\aspnum \\adjustright \\lin0 \\rin0 \\itap0 \\fs21 \\kerning2 \\dbch \\af2 \\hich \\af0 \\loch \\f0 \\snext0 \\spriority0 Normal;}
### match.gf(herbdat000$FAMIL, herbdat000$GENUS)
### {\\*\\cs10 \\snext10 \\sunhideused \\spriority99 Default Paragraph Font;}
temp1 <- "{\\rtf1\\ansi\\ansicpg936\\deflangfe2052\\fcharset134\\deff1{\\fonttbl{\\f0\\froman\\fcharset134 SimSun;}{\\f1\\froman\\fcharset134 Times New Roman;}}{\\stylesheet{\\*\\cs3 Default Paragraph Font;}}{\\colortbl\\red255\\green0\\blue0;\\red0\\green255\\blue0;\\red0\\green0\\blue255;}\\paperw12240\\paperh15840\\margl1800\\margr1800\\margt1440\\margb1440\\gutter0\\ftnbj\\aenddoc\\jcompress1\\viewkind4\\viewscale100\\asianbrkrule\\allowfieldendsel\\snaptogridincell\\viewkind4\\sectd\\sbkpage\\pgwsxn11906\\pghsxn16838\\marglsxn600\\margrsxn600\\margtsxn720\\margbsxn10\\guttersxn0\\headery720\\footery720\\pgbrdropt0\\sectdefaultcl\\cols2\\colsx1080\\linebetcol1\\endnhere"
### fcharset134 to specify Chinese Font Herbarium Label Default Font Size if 18
### Default font is Time New Roman
temp2 <- c()
for (i in 1:nrow(herbdat000)) {
herbdat <- herbdat000[i, ]
### Set the size for each label
res <- c(
ifelse((is.na(herbdat$COLLECTOR))|(is.na(herbdat$COLLECTOR_NUMBER)),
"",
paste("{\\pard\\keep\\keepn\\fi0\\li0\\brsp20\\fs18\\sb100\\sa50 Coll.: ", herbdat$COLLECTOR, " #",herbdat$COLLECTOR_NUMBER, "\\par }", sep = "")),
ifelse(is.na(herbdat$TYPE_STATUS),
"",
paste("{\\pard\\keep\\keepn\\fi0\\li0\\brsp20\\sb100\\sa50\\fs20\\b ", toupper(as.character(herbdat$TYPE_STATUS)), "\\b0 of:\\par }", sep = "")),
ifelse((is.na(herbdat$FAMILY)),
"",
paste("{\\pard\\keep\\keepn\\fi0\\li0\\brsp20\\", ifelse((is.na(herbdat$TYPE_STATUS)), "sb20", "sb180"), "\\sa50\\fs20\\b ", as.character(herbdat$FAMILY), "\\b0\\par }", sep = "")
),
ifelse(((is.na(herbdat$GENUS) )&
(is.na(herbdat$SPECIES) )&
(is.na(herbdat$AUTHOR_OF_SPECIES) )&
(is.na(herbdat$INFRASPECIFIC_RANK) )&
(is.na(herbdat$INFRASPECIFIC_EPITHET) )&
(is.na(herbdat$AUTHOR_OF_INFRASPECIFIC_RANK))),
"",
paste("{\\pard\\keep\\keepn\\fi-288\\li288",
ifelse((is.na(herbdat$TYPE_STATUS)),
"\\sb180", "\\sb20"),
"\\sa20\\fs20\\b\\i ",
ifelse(is.na(herbdat$GENUS), "", as.character(herbdat$GENUS)),
"\\i0 \\i ",
ifelse((is.na(herbdat$SPECIES)), "\\i0 ", as.character(herbdat$SPECIES)),
"\\i0 ",
ifelse(is.na(herbdat$AUTHOR_OF_SPECIES), "", as.character(herbdat$AUTHOR_OF_SPECIES)),
" ",
ifelse(is.na(herbdat$INFRASPECIFIC_RANK), "", as.character(herbdat$INFRASPECIFIC_RANK)),
" \\i ",
ifelse(is.na(herbdat$INFRASPECIFIC_EPITHET), "", as.character(herbdat$INFRASPECIFIC_EPITHET)),
"\\i0 ",
ifelse(is.na(herbdat$AUTHOR_OF_INFRASPECIFIC_RANK), "", as.character(herbdat$AUTHOR_OF_INFRASPECIFIC_RANK)
),
"\\b0\\par }", sep = "")
),
ifelse(is.na(herbdat$TYPE_REF),
"",
paste("{\\pard\\keep\\keepn\\fi288\\li288\\brsp20\\sb10\\sa20\\fs16 " , ifelse(is.na(herbdat$TYPE_REF ), "", herbdat$TYPE_REF), " \\par}")
),
ifelse(is.na(herbdat$DET_NOTE),
"",
paste("{\\pard\\keep",
ifelse(((is.na(herbdat$TYPE_STATUS ))&
(is.na(herbdat$TYPE_REF ))&
(is.na(herbdat$FAMILY ))&
(is.na(herbdat$GENUS ))&
(is.na(herbdat$SPECIES ))&
(is.na(herbdat$AUTHOR_OF_SPECIES ))&
(is.na(herbdat$INFRASPECIFIC_RANK ))&
(is.na(herbdat$INFRASPECIFIC_EPITHET ))&
(is.na(herbdat$AUTHOR_OF_INFRASPECIFIC_RANK))), "\\sb150", "\\sb10")
,"\\sa20\\keepn\\fi0\\li0\\fs16 ", as.character(herbdat$DET_NOTE), " \\par}", sep = "")
),
paste("{\\pard\\keep", ifelse(((is.na(herbdat$TYPE_STATUS ))&
(is.na(herbdat$TYPE_REF ))&
(is.na(herbdat$FAMILY ))&
(is.na(herbdat$GENUS ))&
(is.na(herbdat$SPECIES ))&
(is.na(herbdat$AUTHOR_OF_SPECIES ))&
(is.na(herbdat$INFRASPECIFIC_RANK ))&
(is.na(herbdat$INFRASPECIFIC_EPITHET ))&
(is.na(herbdat$AUTHOR_OF_INFRASPECIFIC_RANK))&
(is.na(herbdat$DET_NOTE ))),
"\\sb800", # if all are missing, extent the space
"\\sb200"),
ifelse((is.na(herbdat$PROJECT)),
"\\sa150",
"\\sa10"),
"\\keepn\\fi0\\li0\\fs18\\tqr\\tx4850 ",
ifelse(is.na(herbdat$ABBREVIATION),
"",
paste(herbdat$ABBREVIATION,": ", sep = "")),
ifelse(is.na(herbdat$IDENTIFIED_BY),
"",
as.character(herbdat$IDENTIFIED_BY)),
"",
ifelse(is.na(herbdat$INSTITUTION),
"",
ifelse(is.na(herbdat$IDENTIFIED_BY),
paste(" ", as.character(herbdat$INSTITUTION), sep = ""),
paste(", ", as.character(herbdat$INSTITUTION), sep = ""))),
" \\tab ",
ifelse(is.na(herbdat$DATE_IDENTIFIED),
"",
tryCatch(formatdate(herbdat$DATE_IDENTIFIED),
error= function(e) {print("Warning: Date format incorrect, using original string");
herbdat$DATE_IDENTIFIED})
),
" \\par }", sep = ""
),
ifelse(is.na(herbdat$PROJECT),
"",
paste("{\\pard\\keep\\keepn\\fi0\\li0\\brsp20\\qc\\sb10\\sa150\\fs16 ",
as.character(herbdat$PROJECT), "\\par }", sep = "")
),
"{\\pard\\keep\\qc\\fs18 . . .\\sa100\\par}"
)
### End of one label
temp2 <- c(temp2, res) ### Add label to the RTF file.
}
template <- c(temp1, temp2, "}") ## End of the RTF file
res <- template[!template %in% ""]
res <- iconv(x = res, from = "UTF-8", to = "GB18030")
writeLines(res, outfile)
### Notice
cat("Annotation labels have been saved to:\n",
file.path(getwd(), outfile), "\n", sep = "")
}
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