cover_trans: Convert cover scales to percent cover

Description

Convert values of a categorical cover scale to percentage values.

This function requires as input a coverconvert object which contains the conversion tables.

In the case of vegtable objects, the conversion is already embedded in the slot coverconvert.

Three rules are implemented for transformation, either top (values transformed to the top of the range), middle (transformation at the midpoint), and bottom (conversion at the lowest value of the range). In the later case, transformation ranges starting at 0% of cover can be set to a different value by the argument zeroto.

When replace=FALSE, existing values of cover in the vegtable object will be maintained. Since there is not a standard naming of cover values, in the transformation the name of cover variable should be indicated in the argument to.

Usage

# S4 method for character,coverconvert
cover_trans(x, conversion, from = NULL, rule = "top", zeroto = 0.1, ...)
# S4 method for factor,coverconvert
cover_trans(x, conversion, ...)
# S4 method for numeric,coverconvert
cover_trans(x, conversion, ...)
# S4 method for vegtable,missing
cover_trans(x, to, replace = FALSE, rule = "top", zeroto = 0.1, ...)

Value

Either a vector or a vegtable object.

Arguments

x: Either a factor or character vector, or a vegtable object.
conversion: An object of class vegtable.
from: Scale name of values in x as character value.
rule: Rule applied for the conversion (see details).
zeroto: Value used to replace levels with bottom at 0% cover.
...: Further arguments passed from or to other methods.
to: Name of the column in slot samples for writing converted values.
replace: Logical value indicating whether existing cover values should be replaced or not.

Author

Miguel Alvarez kamapu78@gmail.com

Examples

Run this code

## Check the available scales
summary(Kenya_veg@coverconvert)

## Conversion by default 'top' rule
Kenya_veg <- cover_trans(Kenya_veg, to="percent")
summary(as.factor(Kenya_veg@samples$percent))

## Conversion by 'middle' rule
Kenya_veg <- cover_trans(Kenya_veg, to="percent", rule="middle", replace=TRUE)
summary(as.factor(Kenya_veg@samples$percent))

## Conversion by 'bottom' rule
Kenya_veg <- cover_trans(Kenya_veg, to="percent", rule="bottom", replace=TRUE)
summary(as.factor(Kenya_veg@samples$percent))