You can install the development version of harmonydata from GitHub with:
#install.packages("devtools") # If you don't have devtools installed already.
library(devtools)
#> Warning: package 'devtools' was built under R version 4.3.1
#> Loading required package: usethis
#> Warning: package 'usethis' was built under R version 4.3.1
devtools::install_github("harmonydata/harmony_r")
#> Downloading GitHub repo harmonydata/harmony_r@HEAD
#> curl (5.0.1 -> 5.1.0) [CRAN]
#> uuid (1.1-0 -> 1.1-1) [CRAN]
#> Installing 2 packages: curl, uuid
#> Installing packages into 'C:/Users/User/AppData/Local/Temp/RtmpSayLpV/temp_libpath46f41b34616d'
#> (as 'lib' is unspecified)
#> package 'curl' successfully unpacked and MD5 sums checked
#> package 'uuid' successfully unpacked and MD5 sums checked
#>
#> The downloaded binary packages are in
#> C:\Users\User\AppData\Local\Temp\Rtmp2B8YOS\downloaded_packages
#> ── R CMD build ─────────────────────────────────────────────────────────────────
#> checking for file 'C:\Users\User\AppData\Local\Temp\Rtmp2B8YOS\remotes10e0572c1eef\harmonydata-harmony_r-9d0467a/DESCRIPTION' ... checking for file 'C:\Users\User\AppData\Local\Temp\Rtmp2B8YOS\remotes10e0572c1eef\harmonydata-harmony_r-9d0467a/DESCRIPTION' ... ✔ checking for file 'C:\Users\User\AppData\Local\Temp\Rtmp2B8YOS\remotes10e0572c1eef\harmonydata-harmony_r-9d0467a/DESCRIPTION'
#> ─ preparing 'harmonydata':
#> checking DESCRIPTION meta-information ... checking DESCRIPTION meta-information ... ✔ checking DESCRIPTION meta-information
#> ─ checking for LF line-endings in source and make files and shell scripts
#> ─ checking for empty or unneeded directories
#> Omitted 'LazyData' from DESCRIPTION
#> ─ building 'harmonydata_0.1.1.tar.gz'
#>
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#> Installing package into 'C:/Users/User/AppData/Local/Temp/RtmpSayLpV/temp_libpath46f41b34616d'
#> (as 'lib' is unspecified)Before starting, you can set up the domain for harmony. Using this function. By default it uses https://api.harmonydata.ac.uk
harmonydata::set_url()If you want to read in a raw (unstructured) PDF or Excel file, you can do this via a POST request to the REST API. This will convert the file into an Instrument object in JSON.It returns the instrument as a list.
library(harmonydata)
instrument = load_instruments_from_file(path = "examples/GAD-7.pdf")
names(instrument[[1]])
#> [1] "file_id" "instrument_id" "instrument_name" "file_name"
#> [5] "file_type" "file_section" "study" "sweep"
#> [9] "metadata" "language" "questions"You can also input a url containing the questionnaire.
instrument_2 = load_instruments_from_file("https://medfam.umontreal.ca/wp-content/uploads/sites/16/GAD-7-fran%C3%A7ais.pdf")
names(instrument_2[[1]])
#> [1] "file_id" "instrument_id" "instrument_name" "file_name"
#> [5] "file_type" "file_section" "study" "sweep"
#> [9] "metadata" "language" "questions"You can get a list containing the results of the match.Here we can see a list of similarity score for each question comapred to all the other questions in th other questionaire.
instruments = append(instrument, instrument_2)
match = match_instruments(instruments)
names(match)
#> [1] "questions" "matches" "query_similarity"Here is how the matches look like.
match$matches
#> [[1]]
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#> [1] 1
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#> [1] 0.6179736
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#> [1] 1
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#> [1] 1To run harmonydata locally, first you need to pull the docker image using the terminal.
docker pull harmonydata/harmonyapidocker run -p 8000:80 harmonyapiSet url to use localhost. Don’t forget to expose port 8000:
set_url(harmony_url = "http://localhost:8000")