The following guide walks you through the basic steps to set up, build and deploy your own Cancer InFocus (CIF) dashboards using the v5-3 release. The end result is the “default” version of the Cancer InFocus dashboards. Additional tutorials will be available to help you customize CIF dashboards to meet your specific needs.
Note: If you have set up CIF under a previous version, you will find that some of the initial steps have changed. We recommend following these steps when you upgrade to v5-3. The changes instituted here are intended to facilitate greater consistency between users and reduce the need for troubleshooting.
First, you need to create a new folder in your working directory to
house all of the files for building the CIF dashboards. You can name
this whatever you want, though we suggest CIF_v5-3.
Download all of the files from the GitHub repo at
Cancer_InFocus/CIF Shiny/v5-3 into the folder you created
in Step 1.
Open CIFvars_v5-3.R, change the noted items inside the
Sys.setenv() function (marked with #!), and
run. CIFvars_v5-3.R will run the
system_setup_v5-3.R, data_download_v5-3.R,
cif_create_shapefiles_v5-3.R and
cif_geocode_facilities_v5-3.R files to set up and populate
the appropriate dashboard folders, download your catchment area data,
and add shapefiles and coordinates to your data. They will also place
the prepared data in the appropriate /www subfolders for
the dashboards you plan to build. Unlike previous versions, you do not
need to download your catchment area data from CancerInFocus.org
beforehand. Instead, by using the appropriate catchment area short name
for the \(\textit{ca}\) variable, the
data_download_v5-3.R script will automatically download and
begin processing the data for you.
This will likely take a few minutes to run, depending on the size of your catchment area. You should receive progress updates in your console in RStudio.
Note: The system_setup_v5-3.R file will
set up the appropriate folder structure for CIF and make sure you have
the correct packages and package versions installed. This only
needs to be run once. After the first successful run of this
script, you can highlight the corresponding lines in
CIFvars_v5-3.R and press Ctrl+Alt+C to comment them out for
future runs.
When you run CIFvars_v5-3.R, a placeholder logo will be
put in each dashboard folder. You will want to replace these with the
appropriate CIF logo files. These can be found on the GitHub repo at
Cancer_InFocus/CIF Shiny/Logo Files. The logo files and
associated dashboards are as follows:
...big_logo_light... for the CIF main
dashboard...profiles... AND
...big_logo... (no ‘light’) for CIF Profiles...2_big_logo_light... for CIF\(^2\) (Bivariate)...._hotspots... for CIF Hot Spots.If you do not have all of the logo files you need or are having difficulty locating them, please contact our team at CancerInFocus@uky.edu.
Open cif_create_app_v5-3.R, change the noted items under
### ITEMS TO ADJUST---- (marked with #!), and
run the R file. Make sure to use the same catchment area name for the
\(\textit{ca}\) variable as in all
previous steps.
If all of the steps above have been completed successfully, running this program will result in a browser window opening with your main Cancer InFocus dashboard.
If you want to include the version that allows users to upload custom
data to the dashboard, download and work with the
cif_create_app_v5-3_with_custom.R file instead of the
cif_create_app_v5-3.R file.
Note: Custom data uploaded by users is NOT written to permanent storage and is NOT available to other users. When a user closes the app (or goes inactive), any custom data they may have uploaded is erased. Nevertheless, your organization may want to perform their own risk assessment before building this option.
Similar to step 5, open the
cif_profiles_create_app_v5-3.R file, change the noted items
under ### ITEMS TO ADJUST ---- , and run. As before, make
sure to use the same catchment area name for the \(\textit{ca}\) variable as in all previous
steps.
Within the CIFReport_v5-3.Rmd file, locate the line
<!-- change to correct filename --> and adjust the logo file name in parentheses to the dark colored Cancer InFocus logo you received.
If all of the steps above have been completed successfully, running this program will result in a browser window opening with your CIF Profiles dashboard.
Open the file cif2_create_app_v5-3.R, change the noted
items under ### ITEMS TO ADJUST ----, and run. As before,
make sure to use the same catchment area name for the \(\textit{ca}\) variable.
If all of the steps above have been completed successfully, running this program will result in a browser window opening with your CIF\(^2\) (Bivariate) dashboard.
Open the file cif_hotspots_create_app_v5-3.R, change the
noted items under ### ITEMS TO ADJUST ----, and run. As
before, make sure to use the same catchment area name for the \(\textit{ca}\) variable.
If all of the steps above have been completed successfully, running this program will result in a browser window opening with your CIF Hot Spots dashboard.
These details refer to how to set up and deploy the main Cancer InFocus dashboard. For the CIF Profiles, CIF\(^2\) (Bivariate), and CIF Hot Spots dashboards, the instructions are the same, but the initial file names change.
Create an app.R file
Toward the top of the cif_create_app_v5-3.R file, remove
or comment out the two lines of code noted by #!#!#! , and
save the file as app.R. Each dashboard
must be renamed to app.R for Shiny servers
to recognize them.
Develop & Implement a Deployment Solution
A few options exist for deploying your Shiny dashboards. You can explore these in greater detail at https://shiny.rstudio.com/deploy/ , and decide which route is best for you in consultation with your informatics/IT teams.
By following these steps you will hopefully be able to get your initial CIF dashboards out into the world. If you run into any issues, or have any comments for improving this tutorial, please contact us at CancerInFocus@uky.edu.