Nonparametric Test for Limits of Agreement — agree

agree_np A non-parametric approach to limits of agreement. The hypothesis test is based on binomial proportions within the maximal allowable differences, and the limits are calculated with quantile regression.

agree_np(
  x,
  y,
  id = NULL,
  data,
  delta = NULL,
  prop_bias = FALSE,
  TOST = TRUE,
  agree.level = 0.95,
  conf.level = 0.95
)

Arguments

x: Name of column with first measurement.
y: Name of other column with the other measurement to compare to the first.
id: Column with subject identifier with samples are taken in replicates.
data: Data frame with all data.
delta: The threshold below which methods agree/can be considered equivalent and this argument is required. Equivalence Bound for Agreement or Maximal Allowable Difference.
prop_bias: Logical indicator (TRUE/FALSE) of whether proportional bias should be considered for the limits of agreement calculations.
TOST: Logical indicator (TRUE/FALSE) of whether to use two one-tailed tests for the limits of agreement. Default is TRUE.
agree.level: the agreement level required. Default is 95%. The proportion of data that should lie between the thresholds, for 95% limits of agreement this should be 0.95.
conf.level: the confidence level required. Default is 95%.

Value

Returns simple_agree object with the results of the agreement analysis.

loa: A data frame of the limits of agreement.
agree: A data frame of the binomial proportion of results in agreement.
h0_test: Decision from hypothesis test.
qr_mod: The quantile regression model.
call: The matched call

References

Bland, J. M., & Altman, D. G. (1999). Measuring agreement in method comparison studies. In Statistical Methods in Medical Research (Vol. 8, Issue 2, pp. 135–160). SAGE Publications. doi:10.1177/096228029900800204

Examples

data('reps')
agree_np(x = "x", y = "y", id = "id", data = reps, delta = 2)
#> Warning: Model has 4 prior weights, but we recovered 2 rows of data.
#> So prior weights were ignored.
#> Limit of Agreement = 95%
#> Binomial proportions test and quantile regression for LoA
#> 
#>            agreement lower.ci upper.ci
#> % within 2    0.8333   0.5914   0.9453
#> Hypothesis Test: don't reject h0
#> 
#> ###- Quantile Limits of Agreement (LoA) -###
#>           Estimate Lower CI Upper CI CI Level
#> Lower LoA    -1.12  -1.4605  -0.7795     0.90
#> Bias          0.04  -0.5234   0.6034     0.95
#> Upper LoA     2.97   2.3178   3.6222     0.90
#>