detect_: Detect file formatting information

In rmetaverse/synthesisr: Import, Assemble, and Deduplicate Bibliographic Datasets

Description

Bibliographic data can be stored in a number of different file types, meaning that detecting consistent attributes of those files is necessary if they are to be parsed accurately. These functions attempt to identify some of those key file attributes. Specifically, detect_parser determines which parse_ function to use; detect_delimiter and detect_lookup identify different attributes of RIS files; and detect_year attempts to fill gaps in publication years from other information stored in a data.frame.

Usage

detect_parser(x)

detect_delimiter(x)

detect_lookup(tags)

detect_year(df)

Arguments

x	A character vector containing bibliographic data
tags	A character vector containing RIS tags.
df	a data.frame containing bibliographic data

Value

detect_parser and detect_delimiter return a length-1 character; detect_year returns a character vector listing estimated publication years; and detect_lookup returns a data.frame.

Examples

revtools <- c(
  "",
  "PMID- 31355546",
  "VI  - 10",
  "IP  - 4",
  "DP  - 2019 Dec",
  "TI  - revtools: An R package to support article
         screening for evidence synthesis.",
  "PG  - 606-614",
  "LID - 10.1002/jrsm.1374 [doi]",
  "AU  - Westgate MJ",
  "LA  - eng",
  "PT  - Journal Article",
  "JT  - Research Synthesis Methods",
  ""
)

# detect basic attributes of ris files
detect_parser(revtools)
detect_delimiter(revtools)

# determine which tag format to use
tags <- trimws(unlist(lapply(
  strsplit(revtools, "- "),
  function(a){a[1]}
)))
pubmed_tag_list <- detect_lookup(tags[!is.na(tags)])

# find year data in other columns
df <- as.data.frame(parse_pubmed(revtools))
df$year <- detect_year(df)

rmetaverse/synthesisr documentation built on May 28, 2021, 7:57 p.m.