Tcomb: Cuzick & Edwards Tcomb Test Statistic
In nnspat: Nearest Neighbor Methods for Spatial Patterns

Tcomb

R Documentation

Cuzick & Edwards Tcomb Test Statistic

Description

This function computes the value of Cuzick & Edwards T_{comb} test statistic in disease clustering, where T_{comb} is a linear combination of some T_k tests.

The argument cc.lab is case-control label, 1 for case, 0 for control, if the argument case.lab is NULL, then cc.lab should be provided in this fashion, if case.lab is provided, the labels are converted to 0's and 1's accordingly.

The argument klist is the vector of integers specifying the indices of the T_k values used in obtaining the T_{comb}.

The logical argument nonzero.mat (default=TRUE) is for using the A matrix if FALSE or just the matrix of nonzero locations in the A matrix (if TRUE) in the computations.

The logical argument asy.cov (default=FALSE) is for using the asymptotic covariance or the exact (i.e., finite sample) covariance for the vector of T_k values used in Tcomb in the standardization of T_{comb}. If asy.cov=TRUE, the asymptotic covariance is used, otherwise the exact covariance is used.

See page 87 of (\insertCitecuzick:1990;textualnnspat) for more details.

Usage

Tcomb(
  dat,
  cc.lab,
  klist,
  case.lab = NULL,
  nonzero.mat = TRUE,
  asy.cov = FALSE,
  ...
)

Arguments

`dat`	The data set in one or higher dimensions, each row corresponds to a data point.
`cc.lab`	Case-control labels, 1 for case, 0 for control
`klist`	`list` of integers specifying the indices of the `T_k` values used in obtaining the `T_{comb}`.
`case.lab`	The label used for cases in the `cc.lab` (if `cc.lab` is not provided then the labels are converted such that cases are 1 and controls are 0), default is `NULL`.
`nonzero.mat`	A logical argument (default is `TRUE`) to determine whether the `A` matrix or the matrix of nonzero locations of the `A` matrix will be used in the computation of `N_s` and `N_t`. If `TRUE` the nonzero location matrix is used, otherwise the `A` matrix itself is used.
`asy.cov`	A logical argument (default is `FALSE`) to determine whether asymptotic or exact (i.e., finite sample) covariances between `T_k` and `T_l` values are to be used to obtain the entries of the covariance matrix. If `TRUE` the asymptotic covariance values are used, otherwise exact covariance values are used.
`...`	are for further arguments, such as `method` and `p`, passed to the `dist` function.

Value

Returns the value of the T_{comb} test statistic

Author(s)

Elvan Ceyhan

References

\insertAllCited

Examples

n<-20  #or try sample(1:20,1) #try also n<-50, 100
Y<-matrix(runif(3*n),ncol=3)
cls<-sample(0:1,n,replace = TRUE)  #or try cls<-rep(0:1,c(10,10))
n1<-sum(cls==1)

kl<-sample(1:5,3) #try also sample(1:5,2)
kl
Tcomb(Y,cls,kl)
Tcomb(Y,cls,kl,method="max")
Tcomb(Y,cls+1,kl,case.lab=2)
Tcomb(Y,cls,kl,nonzero.mat = FALSE)
Tcomb(Y,cls,kl,asy.cov = TRUE)

#cls as a factor
na<-floor(n/2); nb<-n-na
fcls<-rep(c("a","b"),c(na,nb))
Tcomb(Y,fcls,kl,case.lab="a")

nnspat documentation built on May 29, 2024, 10:03 a.m.