Convert values of a categorical cover scale to percentage values.
This function requires as input a coverconvert object which contains the conversion tables.
Usage
# S4 method for class 'character,coverconvert'
cover_trans(x, conversion, from = NULL, rule = "top", zeroto = 0.1, ...)
# S4 method for class 'factor,coverconvert'
cover_trans(x, conversion, ...)
# S4 method for class 'numeric,coverconvert'
cover_trans(x, conversion, ...)
# S4 method for class 'vegtable,missing'
cover_trans(x, to, replace = FALSE, rule = "top", zeroto = 0.1, ...)Arguments
- x
Either a factor or character vector, or a vegtable object.
- conversion
An object of class vegtable.
- from
Scale name of values in
xas character value.- rule
A character value indicating the rule applied for cover transformation. Three rules are implemented for transformation, either
top(values transformed to the top of the range),middle(transformation at the midpoint), andbottom(conversion at the lowest value of the range). In the later case, if the bottom is zero cover, a fictive bottom value can be set by'zeroto'- zeroto
Value set for transformation of classes with bottom at 0% cover.
- ...
Further arguments passed from or to other methods.
- to
Name of the column in slot
samplesfor writing converted values.- replace
Logical value indicating whether existing cover values should be replaced by the new computed values or not.
Value
Either a vector or a vegtable object.
Author
Miguel Alvarez kamapu78@gmail.com
Examples
## Check the available scales
summary(Kenya_veg@coverconvert)
#> ## Number of cover scales: 3
#>
#> * scale 'br_bl':
#> Levels Range
#> 1 r 0 - 1
#> 2 + 0 - 1
#> 3 1 1 - 5
#> 4 2 5 - 25
#> 5 3 25 - 50
#> 6 4 50 - 75
#> 7 5 75 - 100
#>
#> * scale 'b_bbds':
#> Levels Range
#> 1 r 0 - 1
#> 2 + 0 - 1
#> 3 1 1 - 5
#> 4 2m 1 - 5
#> 5 2a 5 - 15
#> 6 2b 15 - 25
#> 7 3 25 - 50
#> 8 4 50 - 75
#> 9 5 75 - 100
#>
#> * scale 'ordin.':
#> Levels Range
#> 1 1 0 - 1
#> 2 2 0 - 1
#> 3 3 1 - 5
#> 4 4 1 - 5
#> 5 5 5 - 15
#> 6 6 15 - 25
#> 7 7 25 - 50
#> 8 8 50 - 75
#> 9 9 75 - 100
#>
## Conversion by default 'top' rule
Kenya_veg <- cover_trans(Kenya_veg, to = "percent")
summary(as.factor(Kenya_veg@samples$percent))
#> 1 5 15 25 50 75 100
#> 55943 9269 1158 4846 2004 841 480
## Conversion by 'middle' rule
Kenya_veg <- cover_trans(Kenya_veg, to = "percent", rule = "middle", replace = TRUE)
summary(as.factor(Kenya_veg@samples$percent))
#> 0.5 3 10 15 20 37.5 62.5 87.5
#> 55943 9269 1158 4364 482 2004 841 480
## Conversion by 'bottom' rule
Kenya_veg <- cover_trans(Kenya_veg, to = "percent", rule = "bottom", replace = TRUE)
summary(as.factor(Kenya_veg@samples$percent))
#> 0.1 1 5 15 25 50 75
#> 55943 9269 5522 482 2004 841 480