funs.covNii | R Documentation |

Two functions: `covNii.ct`

and `covNii`

.

Both functions return the covariance matrix of the self entries (i.e. first column entries) in a
species correspondence contingency table (SCCT)
but have different arguments (see the parameter list below).
The covariance matrix is of dimension *k \times k* and its entries are *cov(S_i,S_j)* where *S_i* values are
the entries in the first column of SCCT (recall that *S_i* equals diagonal entry *N_{ii}* in the NNCT).
These covariances are valid under RL or conditional on *Q* and *R* under CSR.

The argument `ct`

which is used in `covNii.ct`

only, can be either the NNCT or SCCT.
And the argument `Vsq`

is the vector of variances of the diagonal entries *N_{ii}* in the NNCT or the self entries
(i.e. the first column) in the SCCT.

See also (\insertCiteceyhan:NNCorrespond2018;textualnnspat).

covNii.ct(ct, Vsq, Q, R) covNii(dat, lab, ...)

`ct` |
The NNCT or SCCT, used in |

`Vsq` |
The |

`Q` |
The number of shared NNs, used in |

`R` |
The number of reflexive NNs (i.e., twice the number of reflexive NN pairs), used in |

`dat` |
The data set in one or higher dimensions, each row corresponds to a data point,
used in |

`lab` |
The |

`...` |
are for further arguments, such as |

A `vector`

of length *k* whose entries are the variances of the self entries (i.e. first column) in a
species correspondence contingency table (SCCT).

The *k \times k* covariance matrix of cell counts *S_i* in the self (i.e., first) column of the SCCT
or of the diagonal cell counts *N_{ii}* for *i=1,…,k* in the NNCT.

Elvan Ceyhan

`scct`

, `cov.nnct`

, `cov.tct`

and `cov.nnsym`

n<-20 #or try sample(1:20,1) Y<-matrix(runif(3*n),ncol=3) ipd<-ipd.mat(Y) cls<-sample(1:2,n,replace = TRUE) #or try cls<-rep(1:2,c(10,10)) ct<-nnct(ipd,cls) W<-Wmat(ipd) Qv<-Qvec(W)$q Rv<-Rval(W) vsq<-varNii.ct(ct,Qv,Rv) covNii(Y,cls) covNii.ct(ct,vsq,Qv,Rv) covNii(Y,cls,method="max") #cls as a factor na<-floor(n/2); nb<-n-na fcls<-rep(c("a","b"),c(na,nb)) ct<-nnct(ipd,fcls) covNii(Y,fcls) covNii.ct(ct,vsq,Qv,Rv) ############# n<-40 Y<-matrix(runif(3*n),ncol=3) ipd<-ipd.mat(Y) cls<-sample(1:4,n,replace = TRUE) #or try cls<-rep(1:2,c(10,10)) ct<-nnct(ipd,cls) W<-Wmat(ipd) Qv<-Qvec(W)$q Rv<-Rval(W) vsq<-varNii.ct(ct,Qv,Rv) covNii(Y,cls) covNii.ct(ct,vsq,Qv,Rv)

nnspat documentation built on Aug. 30, 2022, 9:06 a.m.

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