In RollieParrish/ccdm: R functions for the Core Clinical Data Model (CCDM)

library(knitr)
library(ccdm)

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "man/figures/README-",
  out.width = "100%"
)

ccdm

The goal of ccdm is to facilitate the use of the Core Clinical Data Model (Core CDM) and other data sources in the Cloud Data Warehouse (CDW).

Installation

To install ccdm, the package remotes is required, and can be installed with install.packages("remotes").

If you are able to access GitHub.com, you can then install cddm on RStudio from GitHub with:

remotes::install_github("RollieParrish/ccdm")

Network security settings may prevent remotes::install_github() from accessing GitHub.com. If this is the case, ccdm can be installed by downloading the Package Archive and running the following code (replacing the section marked <>, including the arrows themselves):

remotes::install_local("<FILEPATH OF ccdm.*.tar.gz FILE>")

include_graphics("RStudio_install.png")

Assumptions/dependencies

This package assumes that:

you already have access to the Core CDM, EpicClarity, Synergy, & Callisto tables in the CDW
you have successfully configured your R environment to connect to Snowflake
you are somewhat familiar with the tidyverse style of working with remote database tables.

Examples

First, set up the connection to the CDW.

library(dplyr, warn.conflicts = FALSE)
library(ccdm)

conn <- connect_cdw()

The ccdm_tbl() function is use to create pointers to Core CDM tables. The conn connection defined above must be passed as the first parameter, followed by the name of a table. If a name is not specified, then a list of available tables will be displayed.

ccdm_tbl(conn)

Next we need to set up a pointer to a remote tables in Core CDM. HOSPITAL_ENCOUNTERS is the primary table and will probably used for most analytics projects.

Note: data has been de-identified and truncated to just a few columns in the examples below

hosp_enc <- ccdm_tbl(conn, "HOSPITAL_ENCOUNTERS")

hosp_enc

hosp_enc <- ccdm_tbl(conn, "HOSPITAL_ENCOUNTERS") %>%
    filter(ARRIVAL_DT == "2020-02-22") %>%
    filter(FACILITY_CD == "PSHMC") %>%
    filter(!is.na(AGE)) %>% 
    filter(!is.na(ARRIVAL_DTS)) %>%
    select(PAT_ENC_CSN_ID, AGE, SEX, FACILITY_CD, ACCOUNT_CLASS, ARRIVAL_DTS) %>%
    head() %>%
    collect() %>%
    mutate(
        PAT_ENC_CSN_ID = gsub("150[0-9]{6}", "150xxx", PAT_ENC_CSN_ID),
        ARRIVAL_DTS = gsub("2020.*22", "yyyy-mm-dd", ARRIVAL_DTS))  %>%
    arrange(PAT_ENC_CSN_ID)


hosp_enc %>% kable()