Limits of Agreement

Source: R/agreement_limit.R

[Maturing]

A function for calculating for Bland-Altman limits of agreement based on the difference between two measurements (difference = x-y). Please note that the package developer recommends reporting/using tolerance limits (see "tolerance_limit" function).

agreement_limit(
  x,
  y,
  id = NULL,
  data,
  data_type = c("simple", "nest", "reps"),
  loa_calc = c("mover", "blandaltman"),
  agree.level = 0.95,
  alpha = 0.05,
  prop_bias = FALSE,
  log_tf = FALSE,
  log_tf_display = c("ratio", "sympercent"),
  lmer_df = c("satterthwaite", "asymptotic"),
  lmer_limit = 3000
)

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. Default is "id" if no entry is provided.

data

Data frame with all data.

data_type

The type of data structure. Options include "simple" (all independent data points), "nest" (nested data) and "reps" (replicated data points).

loa_calc

The method by which the limits of agreement confidence intervals are calculated. Options are "mover" (Methods of Recovering Variances method) or "blandlatman" (Bland-Altman method).

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.

alpha

The alpha-level for confidence levels.

prop_bias

Logical indicator (TRUE/FALSE) of whether proportional bias should be considered for the limits of agreement calculations.

log_tf

Calculate limits of agreement using log-transformed data.

log_tf_display

The type of presentation for log-transformed results. The differences between methods can be displayed as a "ratio" or "sympercent".

lmer_df

Degrees of freedom method, only matters for if data_type is "nest". Default is "satterthwaite". The "asymptotic" method is faster but more liberal.

lmer_limit

Sample size limit for degrees of freedom method. If number of observations exceeds this limit, then the "asymptotic" method is utilized.

Value

Returns single loa class object with the results of the agreement analysis.

  • loa: A data frame containing the Limits of Agreement.

  • call:The matched call.

Details

The limits of agreement (LoA) are calculated in this function are based on the method originally detailed by Bland & Atlman (1986 & 1999). The loa_calc allow users to specify the calculative method for the LoA which can be based on Bland-Altman (1999) (loa_calc = "blandaltman"), or by the more accurate MOVER method of Zou (2013) and Donner & Zou (2012) (loa_calc = "mover").

References

MOVER methods:

Zou, G. Y. (2013). Confidence interval estimation for the Bland–Altman limits of agreement with multiple observations per individual. Statistical methods in medical research, 22(6), 630-642.

Donner, A., & Zou, G. Y. (2012). Closed-form confidence intervals for functions of the normal mean and standard deviation. Statistical Methods in Medical Research, 21(4), 347-359.

Bland & Altman methods:

Bland, J. M., & Altman, D. (1986). Statistical methods for assessing agreement between two methods of clinical measurement. The Lancet, 327(8476), 307-310.

Bland, J. M., & Altman, D. (1999). Measuring agreement in method comparison studies. Statistical methods in medical research, 8(2), 135-160.

Bland, J. M., & Altman, D. G. (1996). Statistics notes: measurement error proportional to the mean. BMJ, 313(7049), 106.

Examples

data('reps')

# Simple
agreement_limit(x = "x", y ="y", data = reps)
#> MOVER Limits of Agreement (LoA)
#> 95% LoA @ 5% Alpha-Level
#> Independent Data Points
#> 
#>    Bias           Bias CI Lower LoA Upper LoA            LoA CI
#>  0.4383 [-0.1669, 1.0436]    -1.947     2.824 [-3.0117, 3.8884]
#> 
#> SD of Differences = 1.217

# Replicates
agreement_limit(x = "x", y ="y", data = reps, id = "id", data_type = "rep")
#> MOVER Limits of Agreement (LoA)
#> 95% LoA @ 5% Alpha-Level
#> Data with Replicates
#> 
#>    Bias           Bias CI Lower LoA Upper LoA            LoA CI
#>  0.7152 [-1.5287, 2.9591]    -2.232     3.662 [-7.5482, 8.9786]
#> 
#> SD of Differences = 1.5036

# Nested
agreement_limit(x = "x", y ="y", data = reps, id = "id", data_type = "nest")
#> Cannot use mode = "satterthwaite" because *lmerTest* package is not installed
#> MOVER Limits of Agreement (LoA)
#> 95% LoA @ 5% Alpha-Level
#> Nested Data
#> 
#>    Bias           Bias CI Lower LoA Upper LoA            LoA CI
#>  0.7046 [-1.5512, 2.9604]    -2.153     3.562 [-7.4979, 8.9071]
#> 
#> SD of Differences = 1.4581