Description Usage Arguments Value Author(s) References See Also Examples

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).

1 2 3 |

`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`

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 | ```
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)
``` |

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