Package 'magree'

Title: Implements the O'Connell-Dobson-Schouten Estimators of Agreement for Multiple Observers
Description: Implements an interface to the legacy Fortran code from O'Connell and Dobson (1984) <DOI:10.2307/2531148>. Implements Fortran 77 code for the methods developed by Schouten (1982) <DOI:10.1111/j.1467-9574.1982.tb00774.x>. Includes estimates of average agreement for each observer and average agreement for each subject.
Authors: Mark Clements, Dianne O'Connell
Maintainer: Mark Clements <[email protected]>
License: GPL-3 | GPL-2
Version: 1.2
Built: 2024-10-31 16:32:17 UTC
Source: https://github.com/cran/magree

Help Index

Landis and Koch dataset.

Description

Canonical dataset for agreement for multiple observers described in Landis and Koch (Biometrics 1977; 33: 363-374).

Usage

data("landis")

Format

The format is: int [1:118, 1:7] 4 1 3 4 3 2 1 3 2 1 ... - attr(*, "dimnames")=List of 2 ..$ : chr [1:118] "1" "2" "3" "4" ... ..$ : chr [1:7] "A" "B" "C" "D" ...

Source

Landis and Koch (Biometrics 1977; 33: 363-374)

Examples

data(landis)
## maybe str(landis) ; plot(landis) ...

O'Connell-Dobson-Schouten estimators for multiobserver agreement.

Description

Use the O'Connell-Dobson-Schouten estimators of agreement for nominal or ordinal data.

Usage

magree(X, weights=c("unweighted","linear","quadratic"), score = NULL)

Arguments

X

A matrix or data-frame with observations/subjects as rows and raters as columns.

weights
"unweighted"

For nominal categories - only perfect agreement is counted.

"linear"

For ordinal categories where disagreement is proportional to the distance between the categories. This is analogous to the agreement weights wi,j=1−∣score[i]−score[j]∣/(max(score)−min(score))w_{i,j}=1-|score[i]-score[j]|/(max(score)-min(score)).

"quadratic"

For ordinal categories where disagreement is proportional to the square of the distance between the categories. This is analogous to the agreement weights wi,j=1−(score[i]−score[j])2/(max(score)−min(score))2w_{i,j}=1-(score[i]-score[j])^2/(max(score)-min(score))^2.
score

The scores that are to be assigned to the categories. Currently, this defaults to a sorted list of the unique values.

Details

The Fortran code from Professor Dianne O'Connell was adapted for R.

The output object is very similar to the Fortan code. Not all of the variance terms are currently used in the print and summary methods.

Value

oconnell

object from the oconnell function
schouten

object from the schouten function
call

As per sys.call(), to allow for using update

See Also

oconnell, schouten.

Examples

## Table 1 (O'Connell and Dobson, 1984)
summary(fit <- magree(landis, weights="unweighted"))
update(fit, weights="linear")
update(fit, weights="quadratic")

## Table 5, O'Connell and Dobson (1984)
magree(landis==1)
magree(landis==2)
magree(landis==3)
magree(landis==4)
magree(landis==5)

## Plot of the marginal distributions
plot(fit) 

## Plot of the average agreement by observer
plot(fit, type="kappa by observer")

O'Connell-Dobson estimators for multiobserver agreement.

Description

Use the O'Connell-Dobson estimator of agreement for nominal or ordinal data. This includes a range of statistics on agreement for assuming either distinct or homogeneous items.

Usage

oconnell(X, weights=c("unweighted","linear","quadratic"), i=NULL, score = NULL)

Arguments

X

A matrix or data-frame with observations/subjects as rows and observers as columns.

weights
"unweighted"

For nominal categories - only perfect agreement is counted.

"linear"

For ordinal categories where disagreement is proportional to the distance between the categories. This is analogous to the agreement weights wi,j=1−∣score[i]−score[j]∣/(max(score)−min(score))w_{i,j}=1-|score[i]-score[j]|/(max(score)-min(score)).

"quadratic"

For ordinal categories where disagreement is proportional to the square of the distance between the categories. This is analogous to the agreement weights wi,j=1−(score[i]−score[j])2/(max(score)−min(score))2w_{i,j}=1-(score[i]-score[j])^2/(max(score)-min(score))^2.
i

  1. For nominal categories - only perfect agreement is counted.

  2. For ordinal categories where disagreement is proportional to the distance between the categories. This is analogous to the agreement weights wi,j=1−∣score[i]−score[j]∣/(max(score)−min(score))w_{i,j}=1-|score[i]-score[j]|/(max(score)-min(score)).

  3. For ordinal categories where disagreement is proportional to the square of the distance between the categories. This is analogous to the agreement weights wi,j=1−(score[i]−score[j])2/(max(score)−min(score))2w_{i,j}=1-(score[i]-score[j])^2/(max(score)-min(score))^2.

This argument takes precedence over weights if it is specified.

score

The scores that are to be assigned to the categories. Currently, this defaults to 1:L, where L is the number of categories.

Details

The Fortran code from Professor Dianne O'Connell was adapted for R.

The output object is very similar to the Fortan code. Not all of the variance terms are currently used in the print, summary and plot methods.

Value

X

As input
i

As input
nrater

Number of observers
nscore

Number of categories
nsubj

Number of subjects
p1[j, k]

Probability of observer j giving score k when observers are distinct
p2[k]

Probability of score k when observers are homogeneous
w1[j, k]

Weighted average of d[] for observer j, score k
w2[k]

Weighted average of d[] for score k when observers are homogeneous
d[j]

Amount of disagreement for subject j
s1[j]

Chance-corrected agreement statistic for subject j when observers are distinct
s2[j]

Chance-corrected agreement statistic for subject j when observers are homogeneous; s[j]=1-d[j]/expdel.
delta[j, k]

j<k: amount of disagreement expected by change for observers j and k; j>k amount of disagreement expected by chance for observers j and k when observers are homogeneous
expd1

Amount of disagreement expected by chance in null case when observers are distinct
expd2

Amount of disagreement expected by chance when observers are homogeneous
dbar

Average value of d[] over all subjects
sav1

Chance-corrected agreement statistic over all subjects when observers are distinct
sav2

Chance-corrected agreement statistic over all subjects when observers are homogeneous
var0s1

Null variance of S when observers are distinct
var0s2

Null variance of S when observers are homogeneous
vars1

Unconstrained variance of S when observers are distinct
vars2

Unconstrained variance of S when observers are homogeneous
v0sav1

Null variance of Sav when observers are distinct
v0sav2

Null variance of Sav when observers are homogeneous
vsav1

Unconstrained variance of Sav when observers are distinct
vsav2

Unconstrained variance of Sav when observers are homogeneous
p0sav1

Probability of overall agreement due to chance when observers are distinct
p0sav2

Probability of overall agreement due to chance when observers are homogeneous
resp[i, j]

Response for observer i on subject j; transpose of X (BEWARE)
score(i)

Score associated with i'th category
call

As per sys.call(), to allow for using update

See Also

magree, schouten.

Examples

## Table 1 (O'Connell and Dobson, 1984)
summary(fit <- oconnell(landis, weights="unweighted"))
update(fit, weights="linear")
update(fit, weights="quadratic")

## Table 3 (O'Connell and Dobson, 1984)
slideTypeGroups <-
    list(c(2,3,5,26,31,34,42,58,59,67,70,81,103,120),
         c(7,10:13,17,23,30,41,51,55,56,60,65,71,73,76,86,87,105,111,116,119,124),
         c(4,6,24,25,27,29,39,48,68,77,79,94,101,102,117),
         c(9,32,36,44,52,62,84,95),
         c(35,53,69,72),
         c(8,15,18,19,47,64,82,93,98,99,107,110,112,115,121),
         c(1,16,22,49,63,66,78,90,100,113),
         c(28,37,40,61,108,114,118),
         106,
         43,
         83,
         c(54,57,88,91,126),
         c(74,104),
         38,
         46,
         c(89,122),
         c(80,92,96,123),
         85)
data.frame(SlideType=1:18,
           S1=sapply(slideTypeGroups,
                     function(ids) mean(fit$s1[as.character(ids)])),
           S2=sapply(slideTypeGroups,
                     function(ids) mean(fit$s2[as.character(ids)])))

## Table 5, O'Connell and Dobson (1984)
oconnell(landis==1)
oconnell(landis==2)
oconnell(landis==3)
oconnell(landis==4)
oconnell(landis==5)

## Plot of the marginal distributions
plot(fit)

plot methods for magree, oconnell and schouten objects

Description

plot methods for magree, oconnell and schouten objects

Usage

## S3 method for class 'magree'
plot(x, type = c("p1", "kappa by observer"),
xlab = NULL, ylab = NULL, main = NULL, ...)
## S3 method for class 'oconnell'
plot(x, type = c("p1"), xlab = NULL, ylab = NULL, main = NULL, ...)
## S3 method for class 'schouten'
plot(x, type = c("kappa by observer"), xlab = NULL,
ylab = NULL,
main = NULL, xdelta = 0.1, axes = TRUE, ...)

Arguments

x

magree, oconnell or schouten object.

type

Type of plot. For "p1", plot the probabilities by observer. For "kappa by observer", plot the kappas for each observer.

xlab

x-axis label

ylab

y-axis label

main

main label

xdelta

For plot.schouten and "kappa by observer", specifies the width of the brackets for the confidence intervals.

axes

Bool for whether to plot the axes.

...

other arguments passed to plot

Examples

fit <- schouten(landis)
plot(fit)
fit <- oconnell(landis)
plot(fit,type="p1")

print methods for magree objects

Description

print methods for magree objects

Usage

## S3 method for class 'magree'
print(x, ...)
## S3 method for class 'oconnell'
print(x, ...)
## S3 method for class 'schouten'
print(x, ...)

Arguments

x

the object to print

...

other arguments

Examples

print(magree(landis))

print method for summary.magree objects

Description

print method for summary.magree objects

Usage

## S3 method for class 'summary.magree'
print(x, ...)
## S3 method for class 'summary.oconnell'
print(x, ...)
## S3 method for class 'summary.schouten'
print(x, ...)

Arguments

x

summary object

...

other arguments passed to print.oconnell, which is passed to summary (if x is not already a summary object).

Examples

summary(magree(landis))

Schouten estimators for multiobserver agreement.

Description

Use the Schouten estimator of agreement for nominal or ordinal data. This includes a range of statistics on agreement.

Usage

schouten(X, weights=c("unweighted","linear","quadratic","user"), w=NULL,
score=NULL)

Arguments

X

A matrix or data-frame with subjects as rows and observers as columns.

weights
"unweighted"

For nominal categories - only perfect agreement is counted.

"linear"

For ordinal categories where disagreement is proportional to the distance between the categories. This is analogous to the agreement weights wi,j=1−∣i−j∣/(c−1)w_{i,j}=1-|i-j|/(c-1).

"quadratic"

For ordinal categories where disagreement is proportional to the square of the distance between the categories. This is analogous to the agreement weights wi,j=1−(i−j)2/(c−1)2w_{i,j}=1-(i-j)^2/(c-1)^2.

"user"

An indicator for a user-defined weight matrix. The weights argument will be defined as "user" if the w argument is specified.
w

A user-defined weights matrix. This argument takes precedence over weights and score if it is specified and the weight argument will be defined as "user".

score

A user-defined set of scores for each category. If this is not specified, it is assumed that score=1:L, where L is the number of categories. This is used with the weights argument to define the w matrix.

Details

Fortran code was written by Mark Clements based on the algorithms in Schouten (1982).

The output object is closely related to the Fortan code. Not all of the variance terms are currently used in the print, summary and plot methods.

Value

N

Number of subjects
M

Number of observers
L

Number of categories
data

Re-formatted X
w

Weight matrix
kab

Kappas between each pair of observers
ka

Average kappas for each observer
kappa

Average kappa
pab, pa, p, ma, qab, qa, q, oab, eab, oa, ea, o, e, wa, wab

Working fields
varkab

Variances for kab
varka

Variances for ka
vark

Variance for the kappa
covkka

Covariance term between the overall average kappa and the average kappas for each observer
chi

Chi-squared statistics comparing the overall average kappa and the average kappa for each observer (df=1 under the null hypothesis)
pchi

P-values that the overall average kappa equals the average kappa for each observer
var0kab

Variance for kab under the null hypothesis
var0ka

Variance for ka under the null hypothesis
var0k

Variance for the overall average kappa under the null hypothesis
p0

P-value for kappa=0
p0a

P-values that the average kappa for a observer equals zero (i.e. ka=0)
weights

As input
X

As input
call

As per sys.call(), to allow for using update

See Also

magree, oconnell.

Examples

## Weights matrix used by Schouten (1982)
w <- outer(1:5,1:5,function(x,y) ((x<=2 & y<=2) | (x>=3 & y>=3))+0)
fit <- schouten(landis,w=w) # user-defined weights

summary(fit) # Schouten (1982), Tables 2 and 5

## we can fit the same model with oconnell() or magree() using the score argument
magree(landis,score=c(1,1,2,2,2))

## plot of the average kappas by observer
plot(fit, type="kappa by observer")

summary method for magree objects

Description

summary method for magree objects

Usage

## S3 method for class 'magree'
summary(object, ...)
## S3 method for class 'oconnell'
summary(object, ci.transform = c("logit", "identity"), ci.p = 0.95, ...)
## S3 method for class 'schouten'
summary(object, ci.transform = c("logit", "identity"), ci.p = 0.95, ...)

Arguments

object

object to summarise

ci.transform

transformation used to calculate the confidence intervals. Either "logit" for a logit transform or "identity" for no transform.

ci.p

p value for the confidence interval.

...

unused additional arguments

Examples

summary(magree(landis))