Welcome
Pre-talk: Posit Cloud signup
Peri-talk: Follow along
Post-talk: Working with the ROCK, {rock}, or anything rocky
Appendix
- Terms used in the talk
- Citation and licensing

Welcome

This R Markdown file accompanies the talk The Potential of Interoperability in Qualitative Research by Szilvia Zörgő. The script below contains the main content of the talk, as well as points to tools with which you can interact and additional resources.

Resource	URL
ROCK Website	https://rock.science
Talk repository	https://gitlab.com/szilvia/interoperability_in_qual
Rendered version of script	https://szilvia.gitlab.io/interoperability_in_qual
Posit Cloud project	https://posit.cloud/content/10502356

Peri-talk: Follow along

The slides are available in the talk repository here.

Open datasets

We may find open datasets in online repositories, but they are usually isolated with poor metadata (e.g., files, creators, DOI, licensing, date/version). Just because a dataset is findable and accessible, doesn’t mean it is interoperable or reusable.

What is interoperability?

In general, it is a system’s/component’s ability to work with or use (part of) another system. For Open Science, it is a meaningfully interlinked network of (meta)data to enrich contextual knowledge about the data. Means to achieve this goal primarily include increasing machine-readability and reliance on FLOSS for data processing.

Challenges for qualitative data

There is an ongoing, fundamental debate on whether qualitative data can be shared, aggregated, or reused in a meaningful way. Other than these important questions, there is an overreliance on proprietary software (especially for analysis), and congruently, a lack of open-source infrastructure & tools.

Increasing interoperability

Possible via:
- File naming conventions (for more, see here)
- Qualified references (for more, see here)
- Controlled vocabularies (for more, see here)
- And standards (for more, see here)
For more on making qualitative data FAIR, see here.

The Reproducible Open Coding Kit (ROCK)

Human- and machine-readable, open standard for qualitative data
We are currently finishing up the manuscript containing a full description of the standard; a sneak peek pre-publication here.
For a more user-friendly version with instructions on using the R package {rock} for beginners, see The ROCK Book.
Or check out this blog post.

Basics of ROCK standard

This figure does not contain all conventions within the ROCK standard, but shows what a source may look like (both the plain text and the rendered HTML version).
Screenshot of a plain text and “prettified” source adhering to the ROCK standard

The {rock} R package

For more information on the package, see http://rock.science.
During the talk, I give you a walk-through of the major functionality from a conceptual perspective, then run the script below in Posit Cloud. Follow along the conceptual bit, then let’s run the script together!

Applications built on the ROCK standard

iROCK Interface for the ROCK to code and segment data

Shiny Apps:

Diamond for coding and segmenting data (instructions here)

Feldspar for creating a qualitative data table

Crystal for using the Qualitative Network Approach

For more Shiny apps, see http://rock.science.

Running this script in Posit Cloud

Part of the script below is uploaded to the Posit Cloud project for this talk. I will be running these commands and then generating an HTML version as an analysis script.

Getting there

Go to the Posit Cloud project
In the main directory, click on the .Rmd file to view it
Run these chunks in succession (follow my lead)

Set up rendering and file paths

### Optionally install the cutting-edge version of the {rock} package
install.packages(
  pkgs = 'https://codeberg.org/R-packages/rock/archive/dev.tar.gz',
  type = 'source',
  repos = NULL
);

## Installing package into 'C:/Users/szilv/AppData/Local/R/win-library/4.4'
## (as 'lib' is unspecified)

knitr::opts_chunk$set(
  echo = TRUE,
  eval = TRUE,
  comment = ""
);

basePath <- here::here();
dataPath <- file.path(basePath, "data");
dataPath_coded <- file.path(dataPath, "040---coded-sources");
scriptsPath <- file.path(basePath, "scripts");
resultsPath <- file.path(basePath, "results");

Examine raw data

Three plain text files containing data (i.e., “sources”) have been placed into the “010—raw-sources” subdirectory located within the data directory. Also, there are also some attributes of the mock data providers listed in the file called “case-attributes”.

Clean data

The cleaning command places each of the sentences in your data on a new line. The {rock} package enables you to code data line-by-line, and recognizes newline characters as indicators of this, lowest level of segmentation. The chunk below will write the cleaned sources found in “010—raw-sources” into the subdirectory “020—cleaned-sources”.

rock::clean_sources(
  input = file.path(dataPath, "010---raw-sources"),
  output = file.path(dataPath, "020---cleaned-sources"),
  preventOverwriting = FALSE
);

Add unique utterance identifiers

You may choose to add a unique identifier to each line of data (i.e., “utterances”). This is helpful, for example, if you want to merge different versions of the coded sources into a source that contains all codes applied by multiple researchers. The chunk below will write the sources with uids into the subdirectory “030—sources-with-uids”.

rock::prepend_ids_to_sources(
  input = file.path(dataPath, "020---cleaned-sources"),
  output = file.path(dataPath, "030---sources-with-uids"),
  preventOverwriting = FALSE
);

Parse sources

This command will assemble all your coded sources and attributes into an R object that can be employed to run analyses and other commands below. (Note, coded sources and attributes have been pre-added for your convenience.)

dat <-
  rock::parse_sources(
    dataPath,
    regex = "_coded|attributes"
  );

Inspect coded fragments for specific code(s)

This command allows you to collect and inspect coded fragments for certain codes, you can use the command below by changing the code labels “CodeA” and “CodeB” to the codes you’d like to inspect. You can modify the amount of context you wish to have around the coded utterance by changing “2” to any other number.

rock::inspect_coded_sources(
  path = here::here("data", "040---coded-sources"),
  fragments_args = list(
    codes = "CodeA|CodeB",
    context = 2
  )
);

Collected coded fragments for codes ‘CodeA’ & ‘CodeB’ with a total of 4 lines of context (2+2)

CodeA (path: codes>CodeA)

Source:
001_Source_cleaned_withUIDs_coded.rock

[[uid=7q0xb2bb]] Pellentesque ut blandit diam.

[[uid=7q0xb2bc]] Sed placerat velit arcu, nec rutrum elit varius et.

[[uid=7q0xb2bd]] Pellentesque vehicula purus sit amet velit laoreet ultricies. [[CodeA]] [[CodeD]]

[[uid=7q0xb2bf]] Donec a mollis ipsum.

[[uid=7q0xb2bg]] Aliquam eget metus vel ante porttitor fringilla in quis purus. [[CodeB]]

Source:
002_Source_cleaned_withUIDs_coded.rock

[[uid=7q0xb2df]] Aliquam eget metus vel ante porttitor fringilla in quis purus.

[[uid=7q0xb2dg]] Nunc placerat semper ultrices.

[[uid=7q0xb2dh]] Aliquam ac congue nunc. [[CodeA]]

[[uid=7q0xb2dj]] Morbi sit amet tempus turpis, quis tempus massa.

[[uid=7q0xb2dk]] Duis interdum diam enim.

Source:
003_Source_cleaned_withUIDs_coded.rock

[[uid=7q0xb2g7]] Ut sed mi purus.

[[uid=7q0xb2g8]] Pellentesque ut blandit diam.

[[uid=7q0xb2g9]] Sed placerat velit arcu, nec rutrum elit varius et. [[CodeA]] [[CodeB]] [[CodeC]]

[[uid=7q0xb2gb]] Pellentesque vehicula purus sit amet velit laoreet ultricies.

[[uid=7q0xb2gc]] Donec a mollis ipsum.

Source:
003_Source_cleaned_withUIDs_coded.rock

[[uid=7q0xb2gq]] Cras consequat lacus in augue pretium, et egestas lectus pellentesque.

[[uid=7q0xb2gr]] Mauris faucibus nec metus vel convallis.

[[uid=7q0xb2gs]] Fusce vulputate, orci nec sodales fringilla, turpis diam varius tellus, rhoncus pulvinar tellus odio egestas turpis. [[CodeA]]

[[uid=7q0xb2gt]] Praesent luctus sapien luctus odio bibendum, eu suscipit sem convallis. [[CodeD]]

[[uid=7q0xb2gw]] Vivamus tincidunt ante quis finibus feugiat.

Source:
003_Source_cleaned_withUIDs_coded.rock

[[uid=7q0xb2gx]] In tincidunt lorem vel dolor eleifend dictum.

[[uid=7q0xb2gy]]

[[uid=7q0xb2gz]] Fusce sit amet elit et justo facilisis finibus ut id dui. [[CodeC]] [[CodeA]]

[[uid=7q0xb2h0]] Vestibulum dolor diam, commodo non eros non, posuere gravida orci.

[[uid=7q0xb2h1]] Nam id efficitur metus, ut eleifend nulla. [[CodeA]]

Source:
003_Source_cleaned_withUIDs_coded.rock

[[uid=7q0xb2gz]] Fusce sit amet elit et justo facilisis finibus ut id dui. [[CodeC]] [[CodeA]]

[[uid=7q0xb2h0]] Vestibulum dolor diam, commodo non eros non, posuere gravida orci.

[[uid=7q0xb2h1]] Nam id efficitur metus, ut eleifend nulla. [[CodeA]]

[[uid=7q0xb2h2]] Vestibulum id porta erat. [[CodeD]]

[[uid=7q0xb2h3]] Curabitur bibendum varius auctor.

CodeB (path: codes>CodeB)

Source:
001_Source_cleaned_withUIDs_coded.rock

[[uid=7q0xb29g]] Nam facilisis id magna non facilisis.

[[uid=7q0xb29h]] Nulla facilisi.

[[uid=7q0xb29j]] Vivamus ullamcorper ligula magna, non blandit augue imperdiet in. [[CodeD]] [[CodeB]]

[[uid=7q0xb29k]] Sed felis sem, euismod et tincidunt quis, venenatis vel tellus.

[[uid=7q0xb29l]] Fusce non nisl tristique, ultricies augue eget, aliquet nisi.

Source:
001_Source_cleaned_withUIDs_coded.rock

[[uid=7q0xb29k]] Sed felis sem, euismod et tincidunt quis, venenatis vel tellus.

[[uid=7q0xb29l]] Fusce non nisl tristique, ultricies augue eget, aliquet nisi.

[[uid=7q0xb29m]] Sed elementum turpis eu tempus tincidunt. [[CodeB]] [[CodeD]]

[[uid=7q0xb29n]] Donec vel quam vel eros elementum ullamcorper non sed velit.

[[uid=7q0xb29p]] Suspendisse in finibus tortor, vehicula volutpat nulla. [[CodeC]]

Source:
001_Source_cleaned_withUIDs_coded.rock

[[uid=7q0xb2bd]] Pellentesque vehicula purus sit amet velit laoreet ultricies. [[CodeA]] [[CodeD]]

[[uid=7q0xb2bf]] Donec a mollis ipsum.

[[uid=7q0xb2bg]] Aliquam eget metus vel ante porttitor fringilla in quis purus. [[CodeB]]

[[uid=7q0xb2bh]] Nunc placerat semper ultrices.

[[uid=7q0xb2bj]] Aliquam ac congue nunc.

Source:
001_Source_cleaned_withUIDs_coded.rock

[[uid=7q0xb2bp]] Morbi et viverra libero, vitae convallis est.

[[uid=7q0xb2bq]] Orci varius natoque penatibus et magnis dis parturient montes, nascetur ridiculus mus.

[[uid=7q0xb2br]] In quis leo vel risus convallis fringilla id vitae odio. [[CodeB]]

[[uid=7q0xb2bs]] Cras consequat lacus in augue pretium, et egestas lectus pellentesque.

[[uid=7q0xb2bt]] Mauris faucibus nec metus vel convallis.

Source:
002_Source_cleaned_withUIDs_coded.rock

[[uid=7q0xb2d8]] Ut sed mi purus.

[[uid=7q0xb2d9]] Pellentesque ut blandit diam.

[[uid=7q0xb2db]] Sed placerat velit arcu, nec rutrum elit varius et. [[CodeB]] [[CodeD]]

[[uid=7q0xb2dc]] Pellentesque vehicula purus sit amet velit laoreet ultricies. [[CodeD]]

[[uid=7q0xb2dd]] Donec a mollis ipsum.

Source:
002_Source_cleaned_withUIDs_coded.rock

[[uid=7q0xb2ds]] Mauris faucibus nec metus vel convallis.

[[uid=7q0xb2dt]] Fusce vulputate, orci nec sodales fringilla, turpis diam varius tellus, rhoncus pulvinar tellus odio egestas turpis.

[[uid=7q0xb2dw]] Praesent luctus sapien luctus odio bibendum, eu suscipit sem convallis. [[CodeB]]

[[uid=7q0xb2dx]] Vivamus tincidunt ante quis finibus feugiat.

[[uid=7q0xb2dy]] In tincidunt lorem vel dolor eleifend dictum.

Source:
003_Source_cleaned_withUIDs_coded.rock

[[uid=7q0xb2g7]] Ut sed mi purus.

[[uid=7q0xb2g8]] Pellentesque ut blandit diam.

[[uid=7q0xb2g9]] Sed placerat velit arcu, nec rutrum elit varius et. [[CodeA]] [[CodeB]] [[CodeC]]

[[uid=7q0xb2gb]] Pellentesque vehicula purus sit amet velit laoreet ultricies.

[[uid=7q0xb2gc]] Donec a mollis ipsum.

Source:
003_Source_cleaned_withUIDs_coded.rock

[[uid=7q0xb2gm]] Morbi et viverra libero, vitae convallis est.

[[uid=7q0xb2gn]] Orci varius natoque penatibus et magnis dis parturient montes, nascetur ridiculus mus.

[[uid=7q0xb2gp]] In quis leo vel risus convallis fringilla id vitae odio. [[CodeB]]

[[uid=7q0xb2gq]] Cras consequat lacus in augue pretium, et egestas lectus pellentesque.

[[uid=7q0xb2gr]] Mauris faucibus nec metus vel convallis.

View code structure

With this command, {rock} creates a code tree, which can be flat or hierarchical depending on the employed codes. In this talk, we use a flat code structure.

rock::show_fullyMergedCodeTrees(dat)

View attributes table

Inspect attributes of data providers (cases) or other specified aspects of data provision.

rock::show_attribute_table(dat)

cid	sex	age	edu	Group
1	f	40s	MA	Expert
2	f	30s	BA	Novice
3	m	20s	MA	Novice

Inspect code frequencies

This command will allow you to see a bar chart of the code frequencies within the various sources they were applied. The command also produces a legend at the bottom of the visual to help identify the sources based on color.

rock::code_freq_hist(
  dat
);

Inspect code co-occurrences (heatmap)

Code co-occurrences can be visualized with a heatmap. This representation will use colors to indicate the code co-occurrence frequencies. Co-occurrences are defined as two or more codes occurring on the same line of data (utterance).

rock::create_cooccurrence_matrix(
    dat,
    plotHeatmap = TRUE);

      CodeA CodeB CodeC CodeD
CodeA     6     1     2     1
CodeB     1     8     1     3
CodeC     2     1     4     0
CodeD     1     3     0    11

Export qualitative data table (excel)

This command will enable a tabularized version of your dataset, which for example, can be employed to further process your data with software such as Epistemic Network Analysis (https://www.epistemicnetwork.org), or “merely” represent your coded data in a single file. In this dataset, rows are constituted by utterances, columns by variables and data. The file will be an Excel called “mergedSourceDf” located in the results subdirectory.

rock::export_mergedSourceDf_to_xlsx(
  dat,
  file.path(resultsPath,
            "mergedSourceDf.xlsx")
)

Warning in export_mergedSourceDf_to_file(x = x, file = file, exportArgs =
exportArgs, : The file you specified to export to
(D:/Sync/ROCK/workshops+talks/FAIR_Coffees_UM/interoperability_in_qual/results/mergedSourceDf.xlsx)
already exists, and `preventOverwriting` is set to `TRUE`, so I'm not writing
to disk. To override this, pass `preventOverwriting=FALSE`.

Merge coded sources

If multiple coders are applying different codes or coding schemes to the same dataset, or if a single coder is applying different codes in different rounds of coding, then merging coded sources may be useful. Merging means that you combine different coded versions of the same source into a “master” source that contains all applied codes. Merging is made possible via unique utterance identifiers (uids).

Some pre-coded versions of the data have been added to the subdirectory “041—coded-sources-for-merging”. A good practice is to create a “slug” for each coded version of the sources, for example, “_coder1” and “_coder2”, which you will see for the mock data. You need to choose a version of the coded source to be the foundation upon which the other versions are merged (indicated by “primarySourcesRegex” in the code below). For example, the command below says that all versions of each source should be “collapsed” onto the version with the slug: “_coder1”. The command below will write the merged sources into the same directory as where it found them, resulting in a merged version for each source that you placed into that directory.

rock::merge_sources(input = here::here("data",
                                             "041---coded-sources-for-merging"),
                          output = "same",
                          primarySourcesPath = here::here("data",
                                                          "041---coded-sources-for-merging"),
                          primarySourcesRegex = "_coder1\\.rock");

Knit to HTML

With the knitting function, we generate a rendered version of the analysis script and all outputs we viewed. Go to the top of the interface where it says “knit” and click.

Future directions

Currently, there are three ongoing projects in which we work towards making qualitative data more interoperable and qualitative research more transparent.

The Upcycled Clinic

(PI: Anna Harris, Maastricht University)
The ERC-funded grant examines creative repurposing in hospitals on an international scale. Part of the grant involves promoting Open | Science principles by developing novel methods/infrastructure (e.g., a rich metadata template for qualitative data) and setting an | | example in open ethnographic data.
More information on this project here.

Connected Open Machine-readable Meaningful Science (COMMS)

(PI: Szilvia Zörgő, Maastricht University)
Based on existing infrastructure (Psychological Construct Repository, Psycore), we aim to | | develop a set of interlinked repositories designed to support specific methodological approaches.
More information on this project here.

Enabling Open Science in Qualitative Research: The ROCK

(PI: GJ Peters, Open University)
The NWO grant enables us to develop a comprehensive interface for the ROCK encompassing most of the functionality of the R package.
More information on this project here.

Post-talk: Working with the ROCK, {rock}, or anything rocky

If you want to know more, or start a project adhering to the ROCK standard, and you cannot find the answers you’re looking for in the disclosed resources, feel free to get in touch!
ROCK official: info@rock.science
Szilvia Zörgő: s.zorgo@maastrichtuniversity.nl
GJ Peters: gjalt-jorn.peters@ou.nl

Appendix

Terms used in the talk

Code: Representation of a construct of interest in a qualitative study
Code ID: Machine-readable version of code label
Coding structure: Type of coding scheme, e.g., flat or hierarchical
Code label: Human-readable name of code
Coding scheme: Group of codes to be applied to qualitative data
Section break: Indicator of the end of a meaningful chunk of data (higher-level segmentation)
Segmentation: Dividing the data into meaningful chunks (for further analysis)
Unique utterance identifier: Identifies a single line in the dataset
Utterance: Smallest meaningful fragment of data (segmentation level where coding is performed)

For more on ROCK terminology, see here.

Citation and licensing

The Reproducible Open Coding Kit (ROCK) standard is licensed under CC0 1.0 Universal.
The {rock} R package is licensed under a GNU General Public License; for more see: https://rock.science.

ROCK citation:
Gjalt-Jorn Ygram Peters and Szilvia Zörgő (2025). rock: Reproducible Open Coding Kit. R package version 0.9.7. https://rock.opens.science

For more on ROCK materials licensing and citation, please see: https://rock.opens.science/authors.html#citation.

The Potential of Interoperability in Qualitative Research

Szilvia Zörgő

08:30:03 on 2025-06-17 CEST (UTC+0200)

Welcome

Pre-talk: Posit Cloud signup

Peri-talk: Follow along

Open datasets

What is interoperability?

Challenges for qualitative data

Increasing interoperability

The Reproducible Open Coding Kit (ROCK)

Basics of ROCK standard

The {rock} R package

Applications built on the ROCK standard

Running this script in Posit Cloud

Getting there

Set up rendering and file paths

Examine raw data

Clean data

Add unique utterance identifiers

Parse sources

Inspect coded fragments for specific code(s)

Collected coded fragments for codes ‘CodeA’ & ‘CodeB’ with a total of 4 lines of context (2+2)

CodeA (path: codes>CodeA)

CodeB (path: codes>CodeB)

View code structure

View attributes table

Inspect code frequencies

Inspect code co-occurrences (heatmap)

Export qualitative data table (excel)

Merge coded sources

Knit to HTML

Future directions

The Upcycled Clinic

Connected Open Machine-readable Meaningful Science (COMMS)

Enabling Open Science in Qualitative Research: The ROCK

Post-talk: Working with the ROCK, {rock}, or anything rocky

Appendix

Terms used in the talk

Citation and licensing