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# HjerteTal

HjerteTal (HT) consists of four main components:

1.  DST project 706322

2.  github repository HF-Research/HTData

3.  github repository HF-Research/ht2

4.  hjertetal.dk

Here we describe the workflow from the raw register data to the public
shiny app which needs to be run at every update.

1.  DST project 706322: At the moment it is places in the folder
    V:\\Data\\Workdata\\706322\\MariannaMeaidi\\HJERTETAL_V2.\
    For now we have only updated the numbers for cardiovascular disease,
    and not congenital heart defects (the next step in the future). Both
    projects are constructed using the {targets} package. (see
    [https://books.ropensci.org/targets/](https://books.ropensci.org/drake/){.uri}).
    The definitions of all the outcomes (diseases, operations and
    medications) are kept in CSV files in the ‘input/’ directory, called
    ‘diag_ht2_table_ny, ‘behandling_table’, and ‘med_table’
    respectively. These tables contain the ICD/SKS/ATC definition, along
    with the patient type (ambulatory/admitted) and diagnosis type.
    Additionally, all outcomes are assigned a “HjerteTal code” or
    identifier that I use to refer to them in the R code (to avoid
    writing out the full name every time).

The export files that we use in the Shiny app are kept in TXT files in
the ‘output/’ directory. One file for each disease-group, one file for
the operations and one file for the medications. There is one file for
the output combos aswell.

When your programming is done and validated, you need to export the
export files out of DST and into GitHub.\

The final product - The Shiny App - is maintained on GitHub, which can
be found here: <https://github.com/HF-Research/ht2>. (Clone it to your
local machine to get started) . In the HTData folder you will find the
export data that will be used in the Shiny App. If you are unfamiliar
with Shiny, please start with this: <https://mastering-shiny.org/>.
There is lots and LOTS of tutorials online if you get stuck. This app is
developed and tested on a local machine before it is deployed to
shinyapps.io where it is hosted to be viable to the public. Both the
server code and the ui code are broken into separate files, one for each
“page” of the app (technically, one for each ‘NavbarPage’). There are 2
projects that are needed to run the Shiny app:

-   GitHub repository HF-Research/HTData: The R package that holds all
    HjeteTal’s data exported from DST.

    -   Dump the .txt files exported from DST into the ‘inst/extdata’
        directory

    -   Run the R scripts found in ‘data-raw’ directory (Note, these
        need to be modified/added to if there are changes to the format
        in which data from DST is exported)

    -   Re-build the package and push the changes (R-studio -\> Build
        -\> more -\> build source package). Remember to change the
        version number in the file DESCRIPTION.

    -   Install the package –\> Install –\> Install Package

-   Github repository HF-Research/ht2: The project that contains all the
    Shiny code. To update data in HjeteTal (for example, when a new year
    of data become available), the data is first put into a separate
    package called HTData. The process for updating the data for this
    package is:

-   In the ‘ht2’ projekct, re-run the data pre-processing.R script.
    Check if the newest version of HTData is loaded:
    packageVersion('HTData')

-   Check that everything works by running locally by running global.R and run runApp()

-   Check that everything works on the server by deploying to ‘ht-dev’
    (see the ‘deploy.R’ script)

-   Deploy to the production (see the same ‘deploy.R’ script)

PROJECT FOLDER STRUCTURE IN HT2:

Below is a description of each folder in the shiny project

• www/ contains various icon files and JS files for doing things like:
checking if the user is using Internet Explorer, Google analytics code –
note this is associated with the hf_forsking Google account

• ui/ contains the shiny code for the UI. Each navBar page has its own
script, and language specific objects are kept in their own language ui
script.

• server/ contains the code for the server logic. Like the UI code, each
navBar page has its own script.

• rsconnect/ This folder is automatically generate and updated when
deploying – do not manually edit

• R/ contains all the functions that are used in both the server and ui
scripts

• pre-processing/ contains the data-pre-processing script. All the other
scripts are not used

• language/ contains data files made during the pre-processing step.
These are made to reduce the time on start-up of the app for the
end-user.

• input_ui_text/ contains the CSV files that control the text show to
the user in both English and Danish. Not all the columns in each file
are used, some were added, but never ended up in the final version

o variable_ui_chd: contains the text for the description of the events
for congenital heart diseases (prevalence, incidence, etc)

o variable_ui: contain contains the text for the description of the
events for acquired heart diseases (prevalence, incidence, etc)

o update_descriptions_chd: describes any updated we make to the CHD
database. This is important as sometimes new data, or new methods mean
that the numbers might change, even for year back. This can cause worry
among users sometimes, so it is nice to explain why things change

o update_descriptions: Same as above, but for acquired CVDs

o ui_about_text_chd: contains the text for the ‘About’ or ‘Vejledning’
section o ui_about_text: same as above but for acquired CVDS o
outcome_descriptions_chd: contain the name, and description of the
outcomes (ie the diseases, procedures, or medications).

o outcome_descriptions: same as above but for acquired CVDs

o faq_chd: contains text for the FAQ table for CHDs

o faq: same as above but for acquired CVDs o ethnicity: contains
description for how ethnicity is defined in HjerteTal

o edu_description: contains description for how education groups are
defined in HjerteTal • inti/ contains the code for deploying the app to
shinyapps.io

• documentation/ I believe nothing in here is used anywhere

• data/ contains various data file that are use by the
data-preprocessing step (i.e. geographic data for the maps,
valid_output_combos (see 1.1.2 for a description of that file). Files
that are .rda or .fst file are datafiles created during the
data-preprocessing step. This folder is a bit of a mess, and there are
probably item that could be deleted

THINGS TO NOTE When you deploy to shinyapps.io, the shiny app will be
running on a Unix machine. Because this is different than the Windows
machine you will presumably be developing the app on, this can sometimes
cause bugs. One example, the way windows encodes non-latin characters is
different than Unix (I spent A LOT of time on this!), so when using
Danish-specific letters, it can be tricky. That’s why you often see
‘enc2utf8()’ surrounding Danish text. I do not entirely understand any
of this...