Syntax to Use Character Variable in Search

General
3

@andresrcs didn't admonish about reprex (FAQ: What's a reproducible example (`reprex`) and how do I create one?) Using a reprex, complete with representative data will attract quicker and more answers.

I'll throw in a few suggestions to deal with the malformed issns. I have to assume, though, that

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term='2369-2960'

is a well formed query. I can't check that with the API, which I don't have.

  1. Although df$issn represents a pattern of numerals separated by -, they are represented as character objects, rather than numeric objects. It's a fine point, but keeping that agnostic orientation makes using character mapping functions easier.

  2. With more than a handful of separate character patterns, it helps to isolate them in an object, then choose a function to extract them into an object that can be sent to a receiver function.

suppressPackageStartupMessages(library(dplyr))
suppressPackageStartupMessages(library(purrr))
suppressPackageStartupMessages(library(stringr))

# same as df$issn: replicated because df not in namespace here
search_for <- c("2369-2960", "1532-2777", "1876-2026", "1872-7727", "1872-7123", "1532-2777", "1542-7714", "1879-1190", "1090-2139", "1090-2139", "2369-2960")

# string patterns
# lazy programmer kludge on next line
chopoff <- " OR $"
good_form <- "\\d{4}-\\d{4}"
insert <-  " OR "

unique(search_for) %>%
  str_extract_all(.,good_form) %>% 
  flatten_chr %>%       # _chr because  want an error if any numeric objects
  str_c(., insert, collapse = "") %>%
  str_remove(.,chopoff) ->  issns


issns
#> [1] "2369-2960 OR 1532-2777 OR 1876-2026 OR 1872-7727 OR 1872-7123 OR 1542-7714 OR 1879-1190 OR 1090-2139"

Created on 2020-04-05 by the reprex package (v0.3.0)

Now issns is ready to be passed to EUtilsSummary as a simple argument. This would be easy to wrap into a function. The virtue is being able to see more clearly into issns and make further adjustments.