README.md

In DurhamRegionHARP/ccmReportR: Wraps 'CCM' with Utility Functions

ccmReportR

ccmReportR is an R package that warps the CCM API with user friendly functions. The package implements actions from the Salesforce REST API.

Current features include: - OAuth2.0 authorization - Query records using the REST API

Installation

# install from CRAN
install.packages("ccmReportR")

# install the development version from GitHub
# install.packages("devtools")
devtools::install_github("DurhamRegionHARP/ccmReportR")

Usage

Authenticate

Authorization with CCM implements the OAuth2.0 Device Authorization Grant. After a successful authentication, an access token is stored in the operating system's keyring program (Keychain on macOS, Credential Store on Windows, etc.) for use in subsequent requests.

library(ccmReportR)

# Start the login process
login()
# You'll be prompted to visit a URL to complete the process
Open a browser and login at: https://mohcontacttracing.my.salesforce.com/setup/connect?user_code=25XPR

After completing the login process in a web browser, you should see Login successful! when you return to your R terminal.

Get Data

Use getCases, getExposures, and getOutbreaks to get a tibble of data from CCM. Typically, this is the starting point for most applications. Function parameters allow you to control how data are filtered and what fields are returned. Below, we fetch a list of cases from CCM. We specify the health unit, the data to return, the date range to include, and limit the results to confirmed cases. Notice the columns parameter contains a combination of CCM field names and labels.

# *N.B.* Health unit names in CCM follow a specific spelling.
# Id's have been truncated for safety.
myCases <- getCases(
    healthUnit = 'Durham Region Health Department',
    columns = c('Id', 'Reported Date', 'Classification'),
    from = "2020-10-12",
    to = "2020-10-15 23:59:59",
    confirmedOnly = TRUE
)
str(myCases)
# tibble [127 x 3] (S3: tbl_df/tbl/data.frame)
#  $ Id                   : chr [1:127] "5005X0000028f" "5005X0000028q" "5005X0000028v" "5005X0000028x" ...
#  $ CCM_Classification__c: chr [1:127] "CONFIRMED" "CONFIRMED" "CONFIRMED" "CONFIRMED" ...
#  $ CCM_ReportedDate__c  : chr [1:127] "2020-10-13T00:28:19.000+0000" "2020-10-13T08:23:53.000+0000" "2020-10-12T12:00:00.000+0000" 2020-10-12T12:00:00.000+0000" ...
 ```
### Attributes
Use `getCaseAttribute`, `getExposureAttribute`, or `getOutbreakAttribute` to get a `tibble` of related information. Currently supported attributes for cases include:
- Exposures
- Interventions
- Lab Results
- Outbreaks
- Risk Factors
- Symptoms

for exposures:
- Exposure investigations

and for outbreaks:
- Exposures
- Investigations
- Locations

Continuing with our previous example, let's get the interventions related to our list of cases. 
```r
# Id's have been redacted for safety.
interventions <- getCaseAttribute('interventions', myCases$Id)
str(interventions)
# tibble [314 x 8] (S3: tbl_df/tbl/data.frame)
#  $ Id                         : chr [1:314] "a1u5X0000005" "a1u5X0000005" "a1u5X0000005" "a1u5X0000005" ...
#  $ Case__c                    : chr [1:314] "5005X0000028f" "5005X0000028f" "5005X0000028f" "5005X0000028q" ...
#  $ RecordType.Name            : chr [1:314] "Non-Hospital Intervention" "Non-Hospital Intervention" "Non-Hospital Intervention" "Non-Hospital Intervention" ...
#  $ Intervention__c            : chr [1:314] "Self-Isolation at Private Residence" "Active Monitoring by PHU" "Education" "Active Monitoring by PHU" ...
#  $ Intervention_Information__c: chr [1:314] "YES" "YES" "YES" "YES" ...
#  $ Hospital_Name__r.Name      : chr [1:314] NA NA NA NA ...
#  $ Start_Date__c              : chr [1:314] "2020-10-10" "2020-10-12" "2020-10-12" "2020-10-16" ...
#  $ End_Date__c                : chr [1:314] "2020-10-18" "2020-10-18" "2020-10-18" NA ...

Road Map

This project is actively seeking input on how to best serve the community. We want to hear from you! Please file a issue or start a discussion.

Contributing

This project is an open-source initiative and we welcome all contributions. Thank you to all contributors for your time and support!

DurhamRegionHARP/ccmReportR documentation built on Feb. 19, 2021, 2:54 p.m.