TRAMPindexing: Index (Subset) TRAMPsamples and TRAMPknowns Objects
In TRAMPR: 'TRFLP' Analysis and Matching Package for R

Description Usage Arguments Details Warning Examples

This provides very basic support for subsetting TRAMPsamples and TRAMPknowns objects.

## S3 method for class 'TRAMPknowns'
x[i, na.interp=TRUE, ...]
## S3 method for class 'TRAMPsamples'
x[i, na.interp=TRUE, ...]

`x`	A `TRAMPsamples` or `TRAMPknowns` object.
`i`	A vector of `sample.fk` or `knowns.fk` values. For valid values, use `labels(x)`. If any index values are not present in `x`, then an error will be raised. Alternatively, this may be a logical vector, of the same length as the number of samples or knowns in `x`. See Examples for use of this.
`na.interp`	Logical: Controls how `NA` values should be interpreted when `i` is a logical vector.
`...`	Further arguments passed to or from other methods.

When indexing by logical vectors, NA values do not make valid indexes, but may be produced when testing columns that contain missing values, so these must be converted to either TRUE or FALSE. If i is a logical index that contains missing values (NAs), then na.interp controls how they will be interpreted:

If na.interp=TRUE, then TRUE, FALSE, NA becomes TRUE, FALSE, TRUE.
If na.interp=FALSE, then TRUE, FALSE, NA becomes TRUE, FALSE, FALSE.

For TRAMPknowns objects, if the file.pat element is specified as part of the object (see TRAMPknowns), then the subsetted TRAMPknowns object will be written to a file. This may not be what you want, so it is probably best to disable knowns writing by doing x$file.pat <- NULL before doing any subsetting (where x is the name of your TRAMPknowns object).

data(demo.samples)
data(demo.knowns)

## Subsetting by sample.fk values
labels(demo.samples)
demo.samples[c(101, 102, 110)]
labels(demo.samples[c(101, 102, 110)])

## Take just samples from the first 10 soilcores:
demo.samples[demo.samples$info$soilcore.fk <= 10]

## Indexing also works on TRAMPknowns:
demo.knowns[733]
labels(demo.knowns[733])