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Last data update: 2014.03.03

R: A Unified Approach for Assessment of Agreement

unified.agreement

R Documentation

A Unified Approach for Assessment of Agreement

Description

The unified approach calculates the agreement statistics for both continuous and categorical data to cover multiple readings from each of the n subjects.

Usage

unified.agreement(dataset, var = NA, k, m, CCC_a = 0.9775, CCC_a_intra = 0.995, CCC_a_inter = 0.9775, CCC_a_total = 0.9775, CP_a = 0.9, TDI_a = 150, TDI_a_intra = 75, TDI_a_inter = 150, TDI_a_total = 150, tran = 0, error = "prop", dec = 4, alpha = 0.025, iter = 35, toe = 1e-10)

Arguments

`dataset`	Name of your dataset.
`var`	Name of the dependent variables used in the dataset, if it is not specified, all the variables in the dataset will be used.
`k`	Number of methods/raters/instruments/assay, etc.
`m`	Number of replications for each methods/raters/instruments/assay, etc.
`CCC_a`	CCC allowance when there is no replications, the default is `CCC_a=0.9775`.
`CCC_a_intra`	Intra CCC allowance.
`CCC_a_inter`	Inter CCC allowance.
`CCC_a_total`	Total CCC allowance.
`CP_a`	CP allowance for continuous data.
`TDI_a`	TDI allowance when there is no replications for continuous data. The default is `TDI_a=150`.
`TDI_a_intra`	Intra TDI allowance for continuous data.
`TDI_a_inter`	Inter TDI allowance for continuous data.
`TDI_a_total`	Total TDI allowance for continuous data.
`tran`	If transformation is used for the dataset. `tran=0`: no transformation will be used for statistical inference. `tran=1` transformation such as Z, logit and log will be used for statistical inference. `tran=1` can be used for categorical data but the TDI and CP outputs would become irrelevant. Therefore, `tran=0` is recommended for all categorical data and `tran=1` is recommended for all continuous data.
`error`	`error="const"`: constant error structure for continuous data. When `error="const"`, TDI is an absolute difference with the same measurement unit as for the original data. `error="prop"`: proportional error structure for continuous data. When `error="prop"`, TDI is the percent change. Log transformation will be applied to original data. For categorical data, use `error="const"`.
`dec`	Significant digits after the decimal point printed for TDI when the `error="const"` is specified. The default is `dec=2`.
`alpha`	100(1-`alpha`)
`iter`	Number of iterations in the GEE step. The default is `iter=35`.
`toe`	The error tolerance of the GEE iteration. The default is `toe = 1e-10`.

Value

An object of class unified_agreement is returned, which contains all the estimated statistics and their confidence limits.

Author(s)

Yue Yu <yyu@imyy.net>

Examples

data(DCLHb);
ua <- unified.agreement(dataset=DCLHb, var=c("HEMOCUE1","HEMOCUE2","SIGMA1","SIGMA2"), k=2, m=2, CCC_a_intra=0.9943, CCC_a_inter=0.9775, CCC_a_total=0.9775, CP_a=0.9, tran=1, TDI_a_intra=75, TDI_a_inter=150, TDI_a_total=150, error="const", dec=1, alpha=0.05);
summary(ua);

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(Agreement)
Loading required package: R2HTML
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/Agreement/unified.agreement.Rd_%03d_medium.png", width=480, height=480)
> ### Name: unified.agreement
> ### Title: A Unified Approach for Assessment of Agreement
> ### Aliases: unified.agreement
> 
> ### ** Examples
> 
> data(DCLHb);
> ua <- unified.agreement(dataset=DCLHb, var=c("HEMOCUE1","HEMOCUE2","SIGMA1","SIGMA2"), k=2, m=2, CCC_a_intra=0.9943, CCC_a_inter=0.9775, CCC_a_total=0.9775, CP_a=0.9, tran=1, TDI_a_intra=75, TDI_a_inter=150, TDI_a_total=150, error="const", dec=1, alpha=0.05);
> summary(ua);
 Type  Statistics      CCC    Precision Accuracy TDI   CP     RBS   
 Intra Estimate        0.9986 0.9986    .        41.1  0.9973 .     
       95% Conf. Limit 0.9983 0.9983    .        46.2  0.9949 .     
       Allowance       0.9943 0.9943    .        75    0.9    .     
 Inter Estimate        0.9866 0.9866    1        127.3 0.9474 .     
       95% Conf. Limit 0.9825 0.9825    0.9987   145.9 0.9228 .     
       Allowance       0.9775 .         .        150   0.9    .     
 Total Estimate        0.9859 0.986     1        130.5 0.9412 0.0028
       95% Conf. Limit 0.9818 0.9818    0.9987   148.9 0.916  .     
       Allowance       0.9775 .         .        150   0.9    .     
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>