Building complex search strategies
Luke A McGuinness
2024-10-04
Source:vignettes/building-complex-search-strategies.Rmd
building-complex-search-strategies.Rmd
Building your search with Boolean operators
First load the medrxivr
package:
To find records that contain any of many terms, pass the terms as a
vector to the mx_search()
function, as in the code chunk
below. Query terms can include regular expression syntax - see the section at the end of this document on common regular
expression that may be useful when searching.
myquery <- c("dementia","vascular","alzheimer's") # Combined with Boolean OR
mx_results <- mx_search(data = mx_snapshot(), # Use daily snapshot for data
query = myquery)
#> Using medRxiv snapshot - 2022-07-06 01:09
#> Found 2272 record(s) matching your search.
To find records relevant to more than one topic domain, create a
vector for each topic (note: there is no upper limit on the number of
topics your can have) and combine these vectors into a list which is
then passed to the mx_search()
function:
topic1 <- c("dementia","vascular","alzheimer's") # Combined with Boolean OR
topic2 <- c("lipids","statins","cholesterol") # Combined with Boolean OR
myquery <- list(topic1, topic2) # Combined with Boolean AND
mx_results <- mx_search(data = mx_snapshot(),
query = myquery)
#> Using medRxiv snapshot - 2022-07-06 01:09
#> Found 143 record(s) matching your search.
Additional filters and options
Limit search by field
By default, a range of fields (title, abstract, first author,
subject, link (which contains DOI)) are searched, but you can limit the
search to a subset of these using the fields
argument:
# Limit search to title/abstract
mx_results <- mx_search(data = mx_snapshot(),
query = "dementia",
fields = c("title","abstract"))
#> Using medRxiv snapshot - 2022-07-06 01:09
#> Found 427 record(s) matching your search.
# Search by DOI
mx_results <- mx_search(data = mx_snapshot(),
query = "10.1101/2020.01.30.20019836",
fields = "link")
#> Using medRxiv snapshot - 2022-07-06 01:09
#> Found 1 record(s) matching your search.
Exclude records containing certain terms
Often it is useful to be able to exclude records that contain a certain term that is not relevant to your search. For example, in the search below, we are looking for records related to “dementia” alone by excluding those that mention “mild cognitive impairment”:
mx_results <- mx_search(data = mx_snapshot(),
query = "dementia",
NOT = "[Mm]ild cognitive impairment")
#> Using medRxiv snapshot - 2022-07-06 01:09
#> Found 366 record(s) matching your search.
Limit by date posted
You can define either/both of the earliest and latest date you wish to include records from. Note: the search is inclusive of both dates specified:
mx_results <- mx_search(data = mx_snapshot(),
query = "dementia",
from_date = "2020-01-01", # 1st Jan 2020
to_date = "2020-01-08") # 8th Jan 2020
#> Using medRxiv snapshot - 2022-07-06 01:09
#> Found 2 record(s) matching your search.
Return multiple versions of a record
medRxiv allows authors to upload a new version of their
preprint as often as they like. By default, medrxivr
only
returns the most recent version of the preprint, but if you are
interested in exploring how a record changed over time, you can retrieve
all versions of the preprint by setting
deduplicate = FALSE
mx_results <- mx_search(data = mx_snapshot(),
query = "10.1101/2020.01.30.20019836",
fields = "link",
deduplicate = FALSE)
#> Using medRxiv snapshot - 2022-07-06 01:09
#> Found 4 record(s) matching your search.
#> Note, there may be >1 version of the same record.
Useful syntax for the systematic reviewer
Capitalisation
Example regex: [Dd]ementia
Description: The search is case sensitive, so this
syntax allows you to find both Dementia and dementia using
a single term, rather than having to enter them separately. However,
setting the autocaps
argument of mx_search()
to TRUE
will automatically search for both capitalised and
uncapitalised versions of your search terms (e.g. with
auto_caps = TRUE
you just need to search for “dementia” to
find both Dementia and dementia - behind the scenes,
“dementia” is converted to “[Dd]ementia”.
Wildcard
Example regex: randomi*ation
Description: The wildcard operator “*” defines any
single alphanumeric character - in this case, the term will find both
randomisation and randomization.
NEAR
Example regex:
systematic NEAR4 review
Description: The “NEAR4” operator defines that up to 4
words can be between systematic and review and the search
will still find it. To change how far apart the terms are allowed to be,
simply change the number following NEAR (e.g. to find terms that are
only one word apart, the syntax would be
systematic NEAR1 review
). Please note that the
search is directional, in that the example term here will find
“systematic methods for the review”, but will not find “the review was
systematic”.
Word limits
Example regex: \\bNCOV\\b
Description: Sometimes it is useful to be able to
define the start and end of terms. For example, if you were searching
for NCOV-19, simply using ncov
as your search term would
also return records containing uncovered. Using \\b
allows you to define where the term beings and ends, thus excluding
false positive matches.
Example using these regexes
To find records that contain “Mendelian” within 4 words of “randomisation” (with varying capitalisation of “Mendelian” and UK/US spellings of “randomisation”), the following syntax is correct:
mx_results <- mx_search(data = mx_snapshot(),
query = "mendelian NEAR4 randomi*ation",
auto_caps = TRUE)
#> Using medRxiv snapshot - 2022-07-06 01:09
#> Found 431 record(s) matching your search.
Regex tester
To check whether your search term will find what you expect it to, there is a useful regex tester, designed by Adam Spannbauer.