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ibdplexus

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Overview

ibdplexus is designed to work with data downloaded from the IBD Plexus Portal from the Crohn’s & Colitis Foundation. More information on Plexus and the cohorts can be found here. Functions include:

• load_data() loads unzipped data from Plexus
• load_zipped_data() loads zipped data from Plexus
• risk_summary() creates a summary table by visit for RISK
• sparc_summary() creates a summary table for SPARC
• calculate_disease_scores() calculates disease scores for SPARC
• sparc_scores() calculates disease scores at a specific time for SPARC
• sparc_medication() predicts the medication a SPARC participant is on at a specific time
• emr_extract_diagnosis() subsets the plexus extract based on specified ICD10 codes

Installation

You can install the released version of ibdplexus from github with:

# install.packages("devtools")
devtools::install_github("ccf-tfehlmann/ibdplexus")

User Guides

• <a href="https://github.com/ccf-tfehlmann/ibdplexus/blob/master/inst/userguides/sparc_summary-overview.md">sparc_summary()</a>

• <a href="https://github.com/ccf-tfehlmann/ibdplexus/blob/master/inst/userguides/medication-in-SPARC.md">sparc_medication()</a>

• <a href="https://github.com/ccf-tfehlmann/ibdplexus/blob/master/inst/userguides/risk-summary.md">risk_summary()</a>

• <a href="https://github.com/ccf-tfehlmann/ibdplexus/blob/master/inst/userguides/Diagnosis_EMR_Extract.md">Diagnosis_EMR_Extract</a>

Example

library(ibdplexus)

# Load in all data in IBD Plexus for the SPARC cohort ----
data <- load_data(datadir = "~/r_input/", cohort = "SPARC", domains = "ALL", data_type = "BOTH")


# Get Excel Tables and Data.Frames with Data Summarised within 60 days of the Enrollment Time Point ----

# SPARC Summary Table
e_sum <- sparc_summary(
  data = data,
  index_info = "ENROLLMENT",
  filename = "SPARC_SUMMARY_ENROLLMENT.xlsx",
  index_range = "60"
)


# SPARC Scores

e_scores <- sparc_scores(
  data = data,
  index_info = "ENROLLMENT",
  filename = "SPARC_SCORES_ENROLLMENT.xlsx",
  index_range = "60"
)


# SPARC Medication

e_med <- sparc_medication(
  data = data,
  index_info = "ENROLLMENT",
  filename = "SPARC_MEDICATION_ENROLLMENT.xlsx"
)