Harmony R released!

Harmony R released!

We have developed the R package for Harmony. To get started, you need R installed on your system.

Click here to try an example in Google Colab.

Here’s a Jupyter Notebook with an example using Harmony in R

Installing R library

We are currently submitting the R library to CRAN.

In the meantime, you can install the development version of harmonydata from GitHub (documentation in the README file):

You also need devtools which will already be there if you are using R Studio. If not, you can install devtools with the following command in the R console:

install.packages("devtools") # If you don't have devtools installed already.

Next, to install Harmony, run:


Parsing a raw file into an Instrument

Let’s import Harmony and harmonise an instrument.

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.

instrument = load_instruments_from_file(path = "examples/GAD-7.pdf")
#>  [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") 
#>  [1] "file_id"         "instrument_id"   "instrument_name" "file_name"      
#>  [5] "file_type"       "file_section"    "study"           "sweep"          
#>  [9] "metadata"        "language"        "questions"

Matching instruments

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)
#> [1] "questions"        "matches"          "query_similarity"

Related Posts

Making Harmony sustainable long-term

Making Harmony sustainable long-term

Longevity is a tricky topic in software development. We’ve been thinking about how we can make sure that Harmony continues to operate for a long time in the future, since Harmony is intended as a public good for researchers to use with no strings attached. Sustainability assessment In April 2023, we completed the software sustainability assessment with the Software Sustainability Institute, which gave us 29 recommended improvements to make Harmony more sustainable.

Harmony update: new features and bug fixes

Harmony update: new features and bug fixes

Harmony update: new features and bug fixes We are pleased to announce the release of a new update to Harmony, our online platform for harmonising questions. This update includes a number of new features and bug fixes, designed to improve the user experience and make Harmony even more useful for researchers. New features: Complete reworking of the search functionality: The search functionality in Harmony has been completely rewritten to support Lucene-like queries.