In jchrom/qbuildr: Build queries for PubMed using R operators

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "README-"
)

Use R operators to build queries for PubMed

This is an extension to R operators +, -, |, and @ to gain the ability to paste character vectors. This is useful when building queries for the PubMed database (see for example the rentrez package).

Get it from GitHub:

devtools::install_github("jchrom/qbuildr")

Why

Avoiding the explicit call to paste makes the code much cleaner:

library(qbuildr)

query = "eeg" + "epilepsy" - "temporal"
cat(query)

The @ operator can be used to add field specification:

query = "eeg" @ "TIAB" + "epilepsy" @ "MeSH"
cat(query)

You can build nested queries using the g function (for "group"). You can add field specification to multiple terms at once by providing a character vector:

query = "pain" @ "TIAB" +
  g("eeg" | "seeg", "MeSH") -
  g("mri" | "fmri" | "meg", "TIAB")
cat(query)

Operators still work the usual way with numeric or logical inputs, but they may be slower, so beware:

# With redefined operators
system.time(runif(10^7) + runif(10^7))

# With original operators
detach("package:qbuildr", unload = TRUE)
system.time(runif(10^7) + runif(10^7))

The advantages and pitfalls of this approach are discussed here and here.

jchrom/qbuildr documentation built on May 18, 2019, 10:23 p.m.