single_cover_value {ausplotsR}

Vegetation cover by height or growth form using TERN AusPlots data.

Description

Calculates a single vegetation cover value per site based on the plot-based point-intercept data from AusPlots (as generated by get_ausplots). Cover can be subsetted to vegetation that has a specified minimum or maximum height and/or by plant growth forms, allowing user defined definitions of e.g. grass or tree cover. For example, by default, forest cover is calculated per plot for tree growth forms of 5 metres or higher.

Usage

single_cover_value(veg.PI, in_canopy_sky=FALSE, 
by.growth_form=TRUE, min.height=5, max.height=NULL, 
my.growth_forms=c("Tree/Palm", "Tree Mallee"))

Arguments

veg.PI

The input raw point intercept data ($veg.PI) as generated in the get_ausplots function.

in_canopy_sky

Logical, whether to include in canopy sky hits to calculate 'opaque canopy cover' instead of 'projected foliage cover'. Set to TRUE to calculate opaque canopy cover (e.g., suitable for some applications such as comparison to remotely sensed cover products).

by.growth_form

Logical, whether to subset by plant growth form. If set to FALSE then only height subsetting occurs. Set to TRUE to calculate cover subsetted to specified growth forms.

min.height

Numeric, sets the height in m below which PI hits are ignored. This argument is used to calculate e.g. cover of trees 5 m high or higher. Can be set to zero to ignore height and include any plant hit. If you set min.height to a negative number you will get a nonsensical output!

max.height

Numeric, sets the height in m above which PI hits are ignored. This argument can be used to calculate ground cover of desired growth forms, for example.

my.growth_forms

A user-supplied character vector specifying growth forms to include in the cover calculation. Defaults to trees. Applies only when by.growth_form=TRUE, otherwise this argument is ignored and only the height rule is applied. For allowable growth forms, see unique(veg.PI$growth_form).

Details

All included point intercept hits are merged to give a single percent cover value with a maximum of 100. Cover partitioned by multiple plant growth forms can be calculated using growth_form_table, by species using species_table and fractional (green, brown or bare) cover using fractional_cover. Note, when min.height is set to zero and by.growth_form is set to FALSE, the output is nearly the same as the green cover fraction returned from fractional_cover. The values can differ, however, because fractional_cover applies a height rule in which the highest intercept at a given point is taken, whereas single_cover_value finds any green cover, leading to differences, most obviously, for example, when dead trees overhang green understorey. For such general cover purposes, we recommend fractional_cover. single_cover_value is best suited to cover subset by height and growth form.

Value

Returns a data.frame in which plots are rows identified by a unique site and visit identifier ('site_unique') and the returned cover value is given in the percentCover column.

Author(s)

Greg Guerin

See Also

get_ausplots

fractional_cover

Examples

## Not run: 
my.dat <- get_ausplots(bounding_box=c(140, 142, -20, -18), veg.PI=TRUE, 
site_info=FALSE)

#Default settings, where cover of trees 5 m or higher is calculated:
tree.cover <- single_cover_value(my.dat$veg.PI)
tree.cover

#Tussock grasses of any height (minimum height set to zero):
grass.cover <- single_cover_value(my.dat$veg.PI, 
my.growth_forms=c("Tussock grass"), min.height=0) 
grass.cover

#Any green veg at least 2 m in height:
veg.height.eg <- single_cover_value(my.dat$veg.PI, by.growth_form=FALSE, 
min.height=2)
veg.height.eg

#Any green veg up to 1 m high:
ground.cover <- single_cover_value(my.dat$veg.PI, by.growth_form=FALSE, 
min.height=0, max.height=1)
ground.cover

## End(Not run)