The following guide walks you through the basic steps to set up, build and deploy your own Cancer InFocus (CIF) dashboards using the v5-2 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.

1. Folder Structure

First, you’ll want to set up a folder in your working directory to house all of your R files (name this whatever you want). You’ll need separate subfolders for each of the Cancer InFocus dashboards you choose to create. Our suggested naming convention for these subfolders are:

We will use these conventions throughout the document. Each dashboard folder should also be given one subfolder named www.

Your final folder setup, or directory, should look like this.

.
|-- ShinyCIF/
|   `-- www/
|-- ShinyCIFProfiles/
|   `-- www/
|-- ShinyCIFBivar/
|   `-- www/
`-- ShinyCIFHotspots/
    `-- www/

2. Download Files

Download the following files from GitHub,

and place them into the ShinyCIF folder you created.

If you plan to build CIF Profiles, download cif_profiles_create_app_v5-2.R into ShinyCIFProfiles and CIFReport_v5-2.Rmd into ShinyCIFProfiles/www.

If you plan to build CIF\(^2\) (Bivariate), download the file cif2_create_app_v5-2.R into ShinyCIFBivar and scatterplot_example.png into ShinyCIFBivar/www.

If you plan to build CIF Hot Spots, download the file cif_hotspots_create_app_v5-2.R into ShinyCIFHotspots.

At this point, you file directory should look like this.

.
|-- ShinyCIF/
|   |-- CIFvars_v5-2.R
|   |-- data_download_v5-2.R
|   |-- cif_create_shapefiles_v5-2.R
|   |-- cif_geocode_facilities_v5-2.R
|   |-- cif_create_app_v5-2.R
|   `-- www/
|-- ShinyCIFProfiles/
|   |-- cif_profiles_create_app_v5-2.R
|   `-- www/
|       `-- CIFReport_v5-2.Rmd
|-- ShinyCIFBivar/
|   |-- cif2_create_app_v5-2.R
|   `-- www/
|       |-- scatterplot_example.png
`-- ShinyCIFHotspots/
    |-- cif_hotspots_create_app_v5-2.R
    `-- www/

The first section, ShinyCIF, will be required, while the ShinyCIFProfiles, ShinyCIFBivar, and ShinyCIFHotspots sections will depend on your build choices.

Also, replace each case of uky with your organization’s corresponding catchment area short name (e.g. Maryland = ‘umd’ , Wake Forest = ‘wake’, etc.)

3. Add Logo Files

You will now place the logo files you’ve received into their appropriate /www subfolders.

You should receive the following logos files with the following phrases in the name.

After placing the logo files in their proper folders, your directory should resemble this, depending on how many dashboards you are working with.

.
|-- ShinyCIF/
|   |-- CIFvars_v5-2.R
|   |-- data_download_v5-2.R
|   |-- cif_create_shapefiles_v5-2.R
|   |-- cif_geocode_facilities_v5-2.R
|   |-- cif_create_app_v5-2.R
|   `-- www/
|       `-- cif_uky_big_logo_light_tm.png
|-- ShinyCIFProfiles/
|   |-- cif_profiles_create_app_v5-2.R
|   `-- www/
|       |-- CIFReport_v5-2.Rmd
|       |-- cif_profiles_uky_light.png
|       `-- cif_uky_big_logo_tm.png
|-- ShinyCIFBivar/
|   |-- cif2_create_app_v5-2.R
|   `-- www/
|       |-- cif_uky2_big_logo_light_tm.png
|       `-- scatterplot_example.png
`-- ShinyCIFHotspots/
    |-- cif_hotspots_create_app_v5-2.R
    `-- www/
        `-- cif_hotspots_uky_big_light.png

Again, the first section, ShinyCIF, will be required, while the ShinyCIFProfiles, ShinyCIFBivar, and ShinyCIFHotspots sections will depend on your build choices.

Also, replace each case of uky with your organization’s corresponding abbreviation (e.g. Maryland = umd , Wake Forest = wake, etc.)

4. Pre-process Data for Dashboards

Open CIFvars_v5-2.R, change the noted items inside the Sys.setenv() function (marked with #!), and run. CIFvars_v5-2.R will run the data_download_v5-2.R, cif_create_shapefiles_v5-2.R and cif_geocode_facilities_v5-2.R files to download your catchment area data and add shapefiles and coordinates to your data. They will also place your prepared 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_v5-2.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.

5. Build the Main CIF Dashboard

Open cif_create_app_v5-2.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_v5-2_with_custom.R file instead of the cif_create_app_v5-2.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.

Note: The main CIF dashboard, CIF\(^2\), and CIF Hot Spots require the package capture, which can be from installed GitHub using the following R code.

install.packages("remotes")
remotes::install_github("dreamRs/capture")

6. Build the CIF Profiles Dashboard

Similar to step 5, open the cif_profiles_create_app_v5-2.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_v5-2.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.

7. Build the CIF\(^2\) (Bivariate) Dashboard

Open the file cif2_create_app_v5-2.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.

8. Build the CIF Hot Spots Dashboard

Open the file cif_hotspots_create_app_v5-2.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.

9. Deploy Online

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.

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 .