TRAMPR (version 1.0-10)

TRAMPindexing: Index (Subset) TRAMPsamples and TRAMPknowns Objects

Description

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

Usage

# S3 method for TRAMPknowns
[(x, i, na.interp=TRUE, ...)
# S3 method for TRAMPsamples
[(x, i, na.interp=TRUE, ...)

Arguments

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.

Warning

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).

Details

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.

Examples

# NOT RUN {
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])
# }