mefa4 (version 0.3-11)

samp: Accessing and Replacing Parts of 'Mefa' Objects

Description

Methods to access and replace parts (elements, slots) of "Mefa" objects.

Usage

xtab(x)
"xtab<-"(x, value)
samp(x)
"samp<-"(x, value)
taxa(x)
"taxa<-"(x, value)

Value

An object of S4 class "Mefa".

Arguments

x

an object of S4 class "Mefa".

value

replacement value.

Author

Peter Solymos <[e-mail]>

Details

The [ method ensures that the xtab sparse matrix part and the corresponding attribute tables are subsetted correctly.

Validity check is performed when replacing slots of an object.

See Also

Mefa

Examples

x <- data.frame(
    sample = paste("Sample", c(1,1,2,2,3,4), sep="."),
    species = c(paste("Species", c(1,1,1,2,3), sep="."),  "zero.pseudo"),
    count = c(1,2,10,3,4,0),
    stringsAsFactors = TRUE)
samp <- data.frame(samples=levels(x$sample), var1=1:2,
    stringsAsFactors = TRUE)
taxa <- data.frame(specnames=levels(x$species), var2=c("b","a"),
    stringsAsFactors = TRUE)
rownames(samp) <- samp$samples
rownames(taxa) <- taxa$specnames
x1 <- Xtab(count ~ sample + species, x)
x3 <- Mefa(x1, samp, taxa)

## accessing the xtab slot
xtab(x3)
## replacing the slot value
x1[3,1] <- 999
xtab(x3) <- x1
xtab(x3)

## accessing and replacing the samp slot
samp(x3)
samp(x3) <- NULL
samp(x3)
samp(x3) <- samp[1:3,]
samp(x3)

## accessing and replacing the taxa slot
taxa(x3)
taxa(x3) <- NULL
taxa(x3)
taxa(x3) <- taxa[1:3,]
taxa(x3)

## subsetting
unclass(x3[3:2, 1:2])
unclass(x3[3:2,])
unclass(x3[,1:2])