Get ADNI Baseline/Screening Diagnostics Summary

Usage

get_adni_blscreen_dxsum(.dxsum, visit_type = "baseline", phase = "Overall")

Arguments

.dxsum: Data.frame of DXSUM() eCRF
visit_type: Either baseline or screen diagnostic status, Default: 'baseline'
phase: Either Overall or ADNI study phase specific, Default: 'Overall'

Value

A data.frame with the following variables:

RID: Subject ID
ORIGPROT: Original study protocols
COLPROT: Study data collection protocols
EXAMDATE: Baseline/screening diagnostics assessment collection date
DIAGNOSIS: Diagnostics status.

Details

This function is used to extract either the baseline or screening diagnostics status subjects when they participate for the first time in ADNI study.

Screening Diagnostics Status: The diagnostics status collected at screening visit.

Baseline Diagnostics Status:

The diagnostics status collected at baseline visit.
The diagnostics status collected at screening status for subjects that did not have a baseline collected diagnostics status. The corresponding screening visit/exam date will be used as a baseline record.

NOTE: The result data will contains the screening diagnostics status of those who did not enrolled in the study (i.e. with screening failure) as their baseline diagnostics status. Required to adjust baseline diagnostics with corresponding subject enrollment date/enrollment flag. See examples for more information.

Examples

if (FALSE) { # \dontrun{
library(tidyverse)
library(ADNIMERGE2)

# Enrollment flag
enrollment_flag <- ADNIMERGE2::REGISTRY %>%
  get_adni_enrollment(.registry = .) %>%
  mutate(ENRLDT = as.Date(EXAMDATE)) %>%
  select(RID, ENRLDT)

# Baseline diagnostics status for newly enrolled subject in ADNI study
overall_baseline_dx <- get_adni_blscreen_dxsum(
  .dxsum = ADNIMERGE2::DXSUM,
  phase = "Overall",
  visit_type = "baseline"
) %>%
  left_join(
    enrollment_flag,
    by = "RID"
  ) %>%
  # Only enrolled subjects
  filter(ENRLFG %in% "Yes")

# Phase-specific baseline diagnostic status: -----
# When subject enrolled in ADNI3 study phase
adni3_baseline_dx <- get_adni_blscreen_dxsum(
  .dxsum = ADNIMERGE2::DXSUM,
  phase = "ADNI3",
  visit_type = "baseline"
) %>%
  left_join(
    enrollment_flag,
    by = "RID"
  ) %>%
  # Only enrolled subjects
  filter(ENRLFG %in% "Yes")

# Screening Diagnostics Status: -----
# When subject were screened for first time in ADNI study.
first_screen_dx <- get_adni_blscreen_dxsum(
  .dxsum = ADNIMERGE2::DXSUM,
  phase = "Overall",
  visit_type = "screen"
)
# Phase-specific screening diagnostic status: ------
# When subject were screened for ADNI4 study phase
adni3_screen_dx <- get_adni_blscreen_dxsum(
  .dxsum = ADNIMERGE2::DXSUM,
  phase = "ADNI4",
  visit_type = "screen"
)
} # }