[R-sig-Epi] Gwet's AC1 Interrater reliability

[Griera]

On Thu, 3 May 2012 14:58:17 -0300
Pedro Emmanuel Alvarenga Americano do Brasil <emmanuel.brasil at gmail.com> wrote:

> R friends,
> 
> with some help of a friend and the original author I turn available this
> function which is helping me in some analysis. Perhaps it may be useful to
> others... :-)

Thanks a lot!!! Very useful!!

> 
>  1.
> Gwet KL. Computing inter-rater reliability and its variance in the presence
> of high agreement. Br J Math Stat Psychol. 2008 ;61(Pt 1):29–48.
> 
> # AC1 statistic for 2 raters special case
> # table = k x k table which represents table(rater1,rater2), must have
> equal number of rows and columns
> # N = population size which will be stick in standard error correction,
> N=Inf is no correction.
> # conflev = Confidence Level associated with the confidence interval (0.95
> is the default value)
> 
> AC1 <- function(table,conflev=0.95,N=Inf,print=TRUE){
>   if(dim(table)[1] != dim(table)[2]){
>   stop('The table should have the same number of rows and columns!')
>   }
>   n <- sum(table)
>   f <- n/N
>   pa <- sum(diag(table))/n # formula 18
>   q <- ncol(table) # number of categories
>   pkk <- diag(table)/n
>   pak <- sapply(1:q,function(i)sum(table[i,]))/n
>   pbk <- sapply(1:q,function(i)sum(table[,i]))/n
>   pik <- (pak + pbk)/2
>   pegama <- (sum(pik*(1-pik)))/(q-1)
>   gama <- (pa - pegama)/(1 - pegama) # AC1 statistics
>   # 2 raters special case variance
>   pkl <- table/n
>   soma <- 0;
>   for(k in 1:q){
> for(l in 1:q){
> soma <- soma + (pkl[k,l]*((1-(pik[k]+pik[l])/2)^2))
>  }
>   }
>   vgama <- ((1-f)/(n*(1-pegama)^2)) * (pa*(1-pa) -
> 4*(1-gama)*((1/(q-1))*sum(pkk*(1-pik)) - pa*pegama) + 4*((1-gama)^2) *
> ((1/((q-1)^2))*soma - pegama^2))
>   epgama <- sqrt(vgama)# AC1 standard error
>   lcb <- max(0,gama - epgama*qnorm(1-(1-conflev)/2,0,1)) # lower confidence
> bound
>   ucb <- min(1,gama + epgama*qnorm(1-(1-conflev)/2,0,1)) # upper confidence
> bound
>   if(print==TRUE){
>     cat('Raw agreement:',pa,'Chance-independent agreement:',pegama,'\n')
>     cat('Agreement coeficient (AC1):',gama,'AC1 standard
> error:',epgama,'\n')
>     cat(conflev*100,'% Confidence Interval (AC1): (',lcb,',',ucb,')\n')
>   }
>   invisible(c(pa,pegama,gama,epgama,lcb,ucb))
> }
> 
> # table3 <- matrix(c(118,2,5,0),nrow=2,ncol=2)
> # AC1(table3)
> # x <- AC1(table3,print=F)
> # print(x)
> 
> Regards,
> 
> Dr. Pedro Emmanuel A. A. do Brasil
> Curriculum Lattes:  http://lattes.cnpq.br/6597654894290806
> Instituto de Pesquisa Clínica Evandro Chagas
> Fundação Oswaldo Cruz
> Rio de Janeiro - Brasil
> Av. Brasil 4365,
> CEP 21040-360,
> Tel 55 21 3865-9648
> email: pedro.brasil at ipec.fiocruz.br
> email: emmanuel.brasil at gmail.com
> 
> ---Apoio aos softwares livres
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> www.broffice.org ou www.libreoffice.org - textos, planilhas ou
> apresentações.
> www.epidata.dk - entrada de dados.
> www.r-project.org - análise de dados.
> www.ubuntu.com - sistema operacional
> 
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