testCompareR (version 1.1.0)

summariseR: summariseR

Description

Summarises descriptive statistics associated with a single binary diagnostic test.

Usage

summariseR(df, dp = 1)

Value

A summary of the descriptive statistics of a binary diagnostic test, compared to a gold standard.

Arguments

df

A data frame or matrix with 2 columns (test1, gold). Flexible coding of positive and negative results permitted.

dp

Number of decimal places of output in summary tables. Defaults to 1. Kappa defaults to 3 decimal places unless user selects more.

Details

Confidence intervals for prevalence, diagnostic accuracies and predictive values are calculated using the interval for binomial proportions described by Yu et al. (2014). Confidence intervals for likelihood ratios are calculated using the methods recommended by Martín-Andrés and Álvarez-Hernández (2014). Cohen's kappa is a value between -1 and 1 which describes the agreement of the two tests, taking account of random agreement. A score of zero or less indicates the agreement could be entirely due to chance.

References

Yu, Guo & Xu (2014) JSCS. 2014; 84:5,1022-1038 tools:::Rd_expr_doi("10.1080/00949655.2012.738211")

Martín Andrés & Álvarez Hernández (2014) Stat Comput. 2014; 24,65–75 tools:::Rd_expr_doi("10.1007/s11222-012-9353-5")

Cohen (1960) Educ Psychol Meas. 1960; 20(1),37–46 tools:::Rd_expr_doi("10.1177/001316446002000104")

Examples

# simulate data
test1 <- c(rep(1, 300), rep(0, 100), rep(1, 55), rep(0, 145))
gold <- c(rep(1, 400), rep(0, 200))
dat <- data.frame(test1, gold)

# summarise descriptive statistics
result <- summariseR(dat, dp = 4)