synthdata_NACC: synthdata NACC

In UncertainInterval: Uncertain Interval Methods for Three-Way Cut-Point Determination in Test Results

Description

NACC MoCA synthetic example data (2433 observations of patients with no clinical assessment of cognitive impairment and 2644 observations with a clinical assessment of some form of cognitive impairment.

• ID patient id; sequential, randomly assigned

• center Alphanumeric id of the clinical center where the data has been collected (30 centers)

• ref.1 Gold standard (true status) at the first measurement. 0: no cognitive impairment 1: cognitive impairment

• MOCATOTS.1 Total MoCA score at the first measurement (0 .. 30)

• vdate.1 Date of the first measurement

• ref.2 Gold standard (true status) at the second measurement. 0: no cognitive impairment 1: cognitive impairment

• MOCATOTS.2 Total MoCA score at the second measurement (0 .. 30)

• vdate.2 Date of the second measurement

Details

For use as an example, a single data set of 6670 observations is generated based on the NACC dataset, from 30 different clinical centers. To generate the artificial data, the R package synthpop (Nowok B, Raab GM, Dibben C, 2016) is used to create the synthetic data, based on the original data from the Uniform Data Set (UDS), collected by the University of Washington’s National Alzheimer’s Coordinating Center (NACC). The syntetic data provide similar statistical results, but differ for each individual and each clinical center. These data are provided as data for the replication of the examples. Results of the real data are presented in Landsheer (In Press).

Researchers who want to use these data for other purposes than replication of the results presented here, are kindly requested to submit a new request for the original data to the NACC. The user of the data may either get a new file or request a file using the specifications of the original data file (https://www.alz.washington.edu/).

References

Nowok B, Raab GM, Dibben C (2016). “synthpop: Bespoke Creation of Synthetic Data in R.” Journal of Statistical Software, 74(11), 1–26. doi:10.18637/jss.v074.i11.

Landsheer, J. A. (In press). Impact of the Prevalence of Cognitive Impairment on the Accuracy of the Montreal Cognitive Assessment: The advantage of using two MoCA thresholds to identify error-prone test scores. Alzheimer Disease and Associated Disorders. https://doi.org/10.1097/WAD.0000000000000365

Examples

data(synthdata_NACC) # needs R version 3.5 or later
head(synthdata_NACC) # Show head of the dataset
nrow(synthdata_NACC) # total number of observations
# select part of data for the first measurement
# N.B. ref is not available when it is inconclusive
m1 = synthdata_NACC[!is.na(synthdata_NACC$MOCATOTS.1)
                   & !is.na(synthdata_NACC$ref.1), ]
# preliminary check data for possible missing values
addmargins(table(m1$ref.1, m1$MOCATOTS.1, useNA = 'always'))
# Show the data
barplotMD(m1$ref.1, m1$MOCATOTS.1)

# calculate the difference between the two measurements in days
ddiff = (m1$vdate.2 - m1$vdate.1)
# There is a wide variety !!!
summary(ddiff)
# Estimate the test-retest reliability
library(psych)
ICC(na.omit(cbind(m1$MOCATOTS.1, m1$MOCATOTS.2)))
# Reducing the variety of time between measurements:
timesel = (ddiff >= 335) & (ddiff <= 395)
ICC(na.omit(cbind(m1$MOCATOTS.1[timesel], m1$MOCATOTS.2[timesel])))

# error when using default calculated value for roll.length
# RPV(m1$ref.1, m1$MOCATOTS.1, reliability = .86)
RPV(m1$ref.1, m1$MOCATOTS.1, reliability = .86, roll.length = 5)

UncertainInterval documentation built on March 3, 2021, 1:10 a.m.