6. Using the web site

6.1. First

Log into CamCOPS via a web browser.

6.2. General navigation

Any time you see the CamCOPS logo (it’s at the top of most pages), you can click it to get back to the main menu.

6.3. Task, trackers, and clinical text views

Client devices upload tasks. You can view these individually in a variety of formats. You can also view numeric information over time for a patient in a tracker, and clinically relevant textual information for a patient in a clinical text view.

6.4. Set task filters

You can configure your CamCOPS session to filter tasks according to who, what, when, and administrative criteria. By default, no task filters are set.

Under who, you can specify an optional patient forename, surname, date of birth, sex, or any form of ID number in use on your server.

Under what, you can restrict to any subset of task types, and if you wish you can restrict to completed tasks. You can also specify text contents. For example, type in “paracetamol” to find clerkings that mention paracetamol anywhere.

Under when, you can specify start and/or end dates, to find tasks in that date range.

Under administrative criteria, you can restrict to specific uploading devices or users, or the group to which a task belongs.

As well as a “set filters” button, there is a “clear” button to clear all current filters.

6.5. View tasks

This page shows all tasks meeting your current filter criteria. Each task has hyperlinks to an HTML and a PDF version. Sometimes tasks are colour-coded (there’s a key at the bottom of the page).

The HTML view is fastest and has additional viewing options. However, you should not print the HTML view in a clinical environment, because it won’t have patient identifiers on each page. Use the PDF for that instead, or if you want to save the task as a single human-readable file.

When you view a task in HTML mode, there are some additional hyperlinks at the bottom:

  • View raw data as XML. This shows you the raw structure as XML, including stored data and calculated fields such as summary scores. One useful feature is that all fields have an associated comment, and these comments are displayed in the XML.

  • View anonymised version (HTML, PDF). This shows you a version with patient identification details hidden. It is not guaranteed to be free of identifying material, though; it makes no effort to remove patient details from free text, for example 5.

  • View PDF. A link to the PDF version.

(Administrators have additional options; see administrative options.)

PDF versions include patient identifiers on each page, to meet normal UK clinical standards, and if the task involved recording a clinician’s views or assessments, the PDF will include a template signature box for on-paper authentication by the clinician.

Specimen tasks in PDF format:

6.6. Trackers for numerical information

Many tasks produce numerical information, like total scores. Trackers allow you to view numerical information from these tasks, or a subset of them, over time. The resulting graphs are time-aligned within the tracker, across all tasks (i.e. all graphs have the same time axis).

Not all tasks offer trackers.

Some tasks offer more than one numerical value, and therefore provide more than one graph.

To configure a tracker, choose a patient by an ID number. You can, optionally, specify a start and/or end date, and you can restrict to specific tasks.

You can view trackers in HTML or PDF mode, or view the data used to generate them in XML format.

Specimen tracker:

Warning

Both trackers and CTVs collate information from multiple tasks. They therefore perform a consistency check to ensure that patient ID information is the same across all tasks. (Did someone mis-spell a name, for example – or worse, mis-file information by entering the wrong ID number?) Beware if the consistency check fails; you will need to ensure yourself that all the data relates to the same patient.

6.7. Clinical text views

Like a tracker, a clinical text view (CTV) collects information across many tasks for one patient. Like a tracker, a CTV is configured for a patient, and can be configured for a date range and/or a subset of tasks. Like a tracker (and like a book), a CTV flows from older to newer information. Unlike a tracker, a CTV produces text for each task, not numbers. The text is intended to be clinically useful. For example, simple questionnaires produce their summary information. The ACE-III produces its total but also its subscale scores. Clinical clerkings produce their full text. All tasks appear in the CTV, but some tasks simply indicate that they have been performed.

In the HTML view of a CTV, all tasks provide hyperlinks to the full representation of each task, so you can delve into more detail for any task of interest.

Specimen CTV:

Warning

Both trackers and CTVs collate information from multiple tasks. They therefore perform a consistency check to ensure that patient ID information is the same across all tasks. (Did someone mis-spell a name, for example – or worse, mis-file information by entering the wrong ID number?) Beware if the consistency check fails; you will need to ensure yourself that all the data relates to the same patient.

6.8. Research views

6.8.1. Basic research dump (fields and summaries)

This option allows you to download a spreadsheet or similar file that contains one worksheet for every current task 1, and includes raw data and summary measures (e.g. total scores).

Note

For example, the PHQ-9 stores the answers for 9 symptom questions in fields q1 to q9, and one overall impact answer in the q10 field; it also stores information to link the record to the patient in question, and some administrative information (relating to record history, editing time, etc.)

However, it doesn’t store summary information on the server 6; rather, summary measures are calculated on demand. For this task, summary measures include:

  • is_complete (Boolean): is the task complete (no missing values)?

  • total (integer): total score

  • n_core (integer): number of core depressive symptoms reaching threshold

  • n_other (integer): number of other depressive symptoms reaching threshold

  • n_total (integer): total number of symptoms reaching threshold

  • is_mds (Boolean): does this patient meet the PHQ9 criteria for major depressive syndrome?

  • is_ods (Boolean): does this patient meet the PHQ9 criteria for other depressive syndrome?

  • severity (text): textual description of depressive severity by the standard PHQ9 scoring method.

These summary measures are included in the research dumps.

You can choose to dump everything that you have permission for, or restrict to the criteria you’ve set in your current session filter, or specify tasks and/or groups manually.

Formats

The download formats include:

  • OpenOffice/LibreOffice spreadsheet (ODS) format.

  • Microsoft Excel (XLSX).

  • A ZIP file containing multiple TSV files, one per worksheet. This is the least human-friendly format, but is good for automatically importing into statistics packages.

  • An R script, which encapsulates the data and creates R objects for you. You can pull in the data from another script (or the command line) via th source command. It uses data.table.

There are also advanced data dumps in other formats (see below).

Delivery method

  • Serve immediately.

    Depending on your administrator’s preference, you may be permitted to download data with a single click. (“Immediate” downloads tie up part of the “front end” web server for a while as it builds the data file, which may be large, so it’s often preferable to permit just e-mail and queued download options, as below.)

  • E-mail.

    You can also choose to have the dump emailed to you, providing your user is set up with a valid email address. This is useful for large exports that may be time consuming.

  • Queued download.

    You can ask the server to build a file for you. It will e-mail you when it’s ready (assuming your e-mail address is configured) and you can then collect it from the Download area.

    Your administrator will set a time limit and a capacity limit for your download area. Files that get too old will be deleted, and you will not be allowed to create files that would exceed your capacity limit.

6.8.2. Advanced research dump (SQL or database)

This more sophisticated research dump generates a fully structured SQLite binary database of the data you select (or, if you prefer, the SQL text to create it). By default, BLOBs (binary large objects) are skipped, because they can be very large, but if you want, you can choose to include them.

You can choose the information you want exactly as for the basic research dump.

Some user information will be provided (e.g. user names), but security information (e.g. passwords) is removed prior to the download.

As for the basic research dump, summary information is added to tables as they are created. For example: the internal PHQ9 table contains scores for individual questions, but not the total (which is calculated dynamically). When you download the data, the total (amongst other things) is calculated and added to the data that you download (within the SQLite table or CSV file).

The delivery methods are as before.

6.8.3. Inspect table definitions

This option allows you to view the database structure of the CamCOPS server database, as data definition language (DDL), meaning the subset of SQL used to create tables. In SQL dialects that support it (e.g. MySQL), the DDL contains comments for every field, usually in considerable detail, so viewing the DDL this is a good way of understanding how CamCOPS tasks store their data.

6.8.4. Download area

This is where you can pick up data files that you have queued for downloading (see above).

6.9. Reports

CamCOPS has a set of build-in reports; for example, to count tasks, or list client devices, or find patients by diagnostic inclusion/exclusion criteria. You can explore and run these from the Reports menu.

Reports are used in two stages: (1) configure, (2) run.

The configuration stage provides an interface to select options for the report. This generally includes the output format (e.g. HTML, TSV), and sometimes much more (e.g. for the reports to find patient by diagnosis). Once you’ve chosen the options, click “View Report”. What the configuration stage actually does is to generate a URL for the final report.

The HTML view of the report shows the configuration parameters, the results (page by page), and the SQL used to generate the report.

The TSV option gives you the data in tab-separate values (TSV) format.

When you view the report in HTML format, you will see that the browser’s URL contains your report configuration information. This means that you can save this report for later.

For example, suppose you regularly want to find patients between the ages of 20 to 65 inclusive, with an ICD-9-CM inclusion diagnosis of depression (e.g. 311) 2, excluding bipolar affective disorder (e.g. anything starting 296) or eating disorders (e.g. 307.1). You could create a report with these age restrictions and inclusion and exclusion diagnoses, and view it. The URL would look like this:

https://my.camcops.site/report?diagnoses_inclusion=311%25&age_maximum=65&which_idnum=1&rows_per_page=&viewtype=html&diagnoses_exclusion=296%25&diagnoses_exclusion=307.1%25&age_minimum=20&report_id=diagnoses_finder_icd9cm&page=1

If you copy this URL, you can run the report again without having to configure it manually. Here’s an approximate ICD-10 equivalent (same age range; include F32% and F33%; exclude F30%, F31%, F50%):

https://my.camcops.site/report?diagnoses_inclusion=F32%25&diagnoses_inclusion=F33%25&age_maximum=65&which_idnum=1&rows_per_page=&viewtype=html&diagnoses_exclusion=F30%25&diagnoses_exclusion=F31%25&diagnoses_exclusion=F50%25&age_minimum=20&report_id=diagnoses_finder_icd10&page=1

To view a report’s SQL in a formatted state, paste it into an online SQL formatter 3.

6.10. Manage scheduled tasks for patients

You can schedule tasks for a patient to complete on their own tablet with the CamCOPS app running in Single User Mode.

The key pieces of information your patient needs to know are:

  • Where they can download CamCOPS for their tablet, phone, laptop etc (Google Play, Apple Store, GitHub)

  • The location of the CamCOPS server

  • Their unique access key

How you choose to communicate these to your patients is up to you. CamCOPS supports a simple email workflow.

Your task schedules and patients will be associated with a group that you administer. You must set the IP settings for this group to describe the contexts in which your group operates (clinical, commercial etc.). Any tasks you schedule for a patient need to be permitted for these contexts.

  • First of all create a task schedule for your study (Manage task schedules ‣ Add a task schedule). Here you can add an email template, which can be customised to include the location of the server and the patient’s unique access key.

  • Next add items to your schedule (Edit items from the table of schedules):

    • Select the task from the drop-down

    • Enter the time from the start of the schedule when the patient may begin the task and the time the patient has to complete the task. These times can be expressed as a combination of months, weeks and days (1 month = 30 days, 1 week = 7 days).

From the Patient Task Schedules page you can add a new patient. The patient must have enough identifiable information to match the uploading and finalizing ID policies of the group. Here you can also assign one or more task schedules to the patient. You can specify the start date of the schedule or leave it blank. If you leave it blank, the start date will be the date the patient first downloads the schedule from the server.

Advanced use: There is an optional form field to specify any patient-specific settings for the tasks. This is a JSON object keyed on the task table name e.g.:

{
  "task1": {
    "name1": "value1",
    "name2": "value2"
  },

  "task2": {
    "name1": "value1"
  }
}

Refer to the relevant task documentation for any settings that can be applied in this way.

If the patient has been successfully created, they should now appear in the table along with the unique access key that they need for registration. The address of the server is also displayed on this page for convenience. If you have provided an email address for the patient, the email link in this table will launch a mail client with the body of the email populated from the template associated with the schedule.

You can view a patient’s progress through the schedule by following the link to the named schedule from the table. From this table you can view the uploaded task responses as HTML or PDF. Anonymous tasks will be listed in this table but you will not see the responses.

Note

If you edit patient details after the patient has registered, the client will pick up the changes when it next picks up schedule updates.

If you change the patient’s ID numbers, though, the patient may have to redo tasks (complete tasks are sought by any current ID number).

6.11. Help

Click “CamCOPS documentation” for this manual.

6.12. Log out

Click “Log out” to end your CamCOPS session.


Footnotes

1

“Current” means that this download will skip historical versions of tasks that have been edited, and just provide the latest version.

2

ICD-9-CM diagnostic codes: https://en.wikipedia.org/wiki/List_of_ICD-9_codes_290%E2%80%93319:_mental_disorders

3

e.g. https://sqlformat.org/; https://www.freeformatter.com/sql-formatter.html

4

https://github.com/RudolfCardinal/camcops

5

For a software product that takes de-identification seriously, see e.g. CRATE, described in Cardinal RN (2017), https://doi.org/10.1186/s12911-017-0437-1, and available from https://crateanon.readthedocs.io/.

6

https://en.wikipedia.org/wiki/Database_normalization