reconcileSubjectVisits: Function for doing something/something comparisons

In NateByers/Reconcile: Functions for reconciling study site data with biorepository database

Description

This function helps you see which subject/visit combinations are missing either in the site data or in the biorepository data.

Usage

reconcileSubjectVisits(report.type = c("data.no.samples", "samples.no.data"),
  repository.data, site.data, repo.subject.column, repo.visit.column,
  site.subject.column, site.visit.column)

Arguments

report.type	Which records to return
repository.data	data.frame of repository data with columns that will provide unique rows of interest
site.data	data.frame of site data with columns that will provide unique rows of interest
repo.subject.column	Column name of subject IDs in repository data.frame
repo.visit.column	Column name of visit in repository data.frame
site.subject.column	Column name of subject IDs in site data.frame
site.visit.column	Column name of visit in repository data.frame

Value

A data.frame with the appropriate column headings. If the report.type is "data.no.samples", then the column headings are from the site data.frame. If the report.type is "samples.no.data", then the column headings are from the repository data.frame

Examples

repository <- data.frame(subject = c(LETTERS[1:5], LETTERS[1:5]), visit = c(1:5, 1:5),
                         specimen = c(rep("blood", 5), rep("DNA", 5)),
                         stringsAsFactors = FALSE)

site <- data.frame(patno = c(LETTERS[2:6], LETTERS[2:6]), clinevent = c(2:6, 2:6),
                   specimen = c("RNA", rep("blood", 4), "Serum", rep("DNA",  4)),
                   stringsAsFactors = FALSE)

# Check to see if there is data from the site but no samples at the biorepository
reconcileSubjectVisits(report.type = "data.no.samples", repository.data = repository,
                       site.data = site, repo.subject.column = "subject",
                       repo.visit.column = "visit", site.subject.column = "patno",
                       site.visit.column = "clinevent")

# Check to see if there are samples at the biorepository but no data from the site
reconcileSubjectVisits(report.type = "data.no.samples", repository.data = repository,
                       site.data = site, repo.subject.column = "subject",
                       repo.visit.column = "visit", site.subject.column = "patno",
                       site.visit.column = "clinevent")

NateByers/Reconcile documentation built on Nov. 21, 2021, 4:12 p.m.