Nothing
utils::globalVariables(c("Paper", "Tag", "content", "cont"))
pubmed2df <- function(D) {
D <- D[nchar(D) > 0] # remove empty rows
for (i in 1:length(D)) {
if (substr(D[i], 1, 4) == " ") substr(D[i], 1, 4) <- substr(D[i - 1], 1, 4)
}
Papers <- which(regexpr("PMID-", D) == 1) # first row of each document
nP <- length(Papers) # number of docuemnts
rowPapers <- diff(c(Papers, length(D) + 1))
numPapers <- rep(1:nP, rowPapers)
DATA <- data.frame(Tag = substr(D, 1, 4), content = substr(D, 7, nchar(D)), Paper = numPapers)
DATA$Tag <- gsub(" ", "", DATA$Tag)
df <- DATA %>%
group_by(Paper, Tag) %>%
summarise(cont = paste(content, collapse = "---", sep = "")) %>%
arrange(Tag, Paper) %>%
pivot_wider(names_from = Tag, values_from = cont) %>%
ungroup()
df <- as.data.frame(df)
# rename field tags
error <- 0
old_labs <- c("AD", "AUID", "FAU", "IS", "IP", "SO", "JT", "TA", "MH", "PG", "PT", "VI", "DP")
new_labs <- c("C1", "OI", "AF", "SN", "IS", "SO2", "SO", "J9", "DE", "PP", "DT", "VL", "PY")
lab <- names(df)
for (j in 1:length(old_labs)) {
i <- which(lab %in% old_labs[j])
if (length(i) > 0) {
lab[i] <- new_labs[j]
} else {
error <- 1
}
}
names(df) <- lab
if (error == 1) {
cat("\nWarning:\nIn your file, some mandatory metadata are missing. Bibliometrix functions may not work properly!\n
Please, take a look at the vignettes:
- 'Data Importing and Converting' (https://www.bibliometrix.org/vignettes/Data-Importing-and-Converting.html)
- 'A brief introduction to bibliometrix' (https://www.bibliometrix.org/vignettes/Introduction_to_bibliometrix.html)\n\n")
}
# extract DOIs
df$DI <- trimws(unlist(lapply(strsplit(df$LID, "\\["), "[", 1)))
df$PY <- as.numeric(substr(df$PY, 1, 4))
### replace "---" with ";"
tagsComma <- c("AU", "AF", "DE", "AID", "OT", "PHST", "DT")
nolab <- setdiff(tagsComma, names(df))
tagsComma <- tagsComma[(!(tagsComma %in% nolab))]
df1 <- data.frame(lapply(df[tagsComma], function(x) {
gsub("---", ";", x)
}))
### replace "---" with " "
otherTags <- setdiff(names(df), tagsComma)
df2 <- data.frame(lapply(df[otherTags], function(x) {
trimES(gsub("---", " ", x))
}))
df <- cbind(df1, df2)
rm(df1, df2)
df$DB <- "PUBMED"
# remove * char from keywords
df$DE <- df$ID <- gsub("\\*", "", df$DE)
AB <- df$AB
TI <- df$TI
DE <- df$DE
df <- data.frame(lapply(df, toupper))
df$AB_raw <- AB
df$TI_raw <- TI
df$DE_raw <- DE
# add sep ; to affiliations
df$C1 <- gsub("\\.", ".;", df$C1)
df$RP <- NA
df <- df[names(df) != "Paper"]
return(df)
}
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