The variable naming system is a standard approach for naming allometric response variables and covariates. In the allometric modeling literature, a diverse set of names are available for many similar types of variables. For example, the frequently used acronym “DBH” is used to refer to the diameter at breast height, but DBH can refer to different measures of the stem, such as the diameter inside bark at breast height, or the diameter outside bark at breast height.
The variable naming system provides a standard set of names that clarify the use of the variable while remaining succinct and easy to write. In the variable naming system, the diameter outside bark at breast height is referred to as dsob. Let us inspect what this name means further as a motivating example.
The first two characters in any variable name are referred to as the “measure” and “component”, respectively. In the case of dsob the d refers to the diameter and the s refers to the stem. The remaining characters are modifiers that clarify the context of the measure-component pair. In this case o refers to outside bark and b refers to breast height.
The core structure of a variable name is:
[measure][component][...modifiers]The get_variable_def function allows the user to search
for existing variable definitions. For example, we can examine our
example variable "dsob"
get_variable_def("dsob")$description## [1] "diameter of the stem, outside bark at breast height"and find that it is the diameter of the stem, outside bark at breast height. We can view the full definition below, which includes a complete breakdown of the measure, component and modifiers of the variable name:
get_variable_def("dsob")## # A tibble: 1 × 10
## description component measure search_str modifier_1 modifier_2 measure_name component_name suffix scale_description
## <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
## 1 diameter of the stem, outside bark at breast height s d dsob o b diameter stem t treeIn the following sections we will discuss how variable names are structured.
All variable names begin with a “measure”. Measures describe the
dimensional aspects of what is being measured for the variable. In the
example above, we searched the naming system for d
(diameter) measures, but others are available. There are 10 established
measures:
## measure measure_name
## 1 a age
## 2 b biomass
## 3 d diameter
## 4 e density
## 5 g basal area
## 6 h height
## 7 r ratio
## 8 v volume
## 9 n angle
## 10 t temperatureWe recognize that the use of “measure” here is somewhat loose (e.g., diameter and height are both measures of length). However, the variable naming system is meant to preserve at least some connection to commonly used terms for variables in allometric modeling.
All variable names then have a second character that specifies the tree component. Components describe the part of the tree that is being measured. There are 13 established components:
## component component_name
## 1 b branch
## 2 c crown
## 3 f foliage
## 4 k bark
## 5 r root
## 6 s stem
## 7 t tree
## 8 u stump
## 9 w wood
## 10 h shrub
## 11 v cover
## 12 o topographic
## 13 l climaticMixing these first two character codes provides an expressive system
to refer to measures and components. For example, the biomass of
foliage, if one were interested in it, would begin bf, the
volume of the stem would be vs, and the diameter of the
stump would be du.
Within a given measure-component pair, a number of useful modifiers
are available. These are specific to the measure-component pair. We
highlight a few useful groups of modifiers below. For further
information users can call get_variable_def with the
measure-component pair of their choice.
ds) Modifiers
Some of the most common allometric variables are that of stem
diameter, which arise in taper modeling, merchantable heights and, of
course, diameter at breast height. ds modifiers enable a
user to specify these broad range of variables. The available
ds variables are:
get_variable_def("ds")## # A tibble: 5 × 10
## description component measure search_str modifier_1 modifier_2 measure_name component_name suffix scale_description
## <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
## 1 diameter of the stem, outside bark at breast height s d dsob o b diameter stem t tree
## 2 diameter of the stem, outside bark at a specified height s d dsoh o h diameter stem t tree
## 3 diameter of the stem, inside bark at a specified height s d dsih i h diameter stem t tree
## 4 diameter of the stem, inside bark at breast height s d dsib i b diameter stem t tree
## 5 diameter outside bark above the root collar s d dsoc o c diameter stem t treehs) Modifiers
Another common group of variables are those that describe stem height, such as the total height of the stem, site index, height of the stem to crown base, and many others.
get_variable_def("hs")## # A tibble: 13 × 10
## description component measure search_str height_modifier modifier measure_name component_name suffix scale_description
## <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
## 1 total height of the stem s h hst t "" height stem t tree
## 2 merchantable height of the stem s h hsm m "" height stem t tree
## 3 height of the stem above breast height s h hso o "" height stem t tree
## 4 height of the stem to crown base s h hsb b "" height stem t tree
## 5 height of the stem to crown base above breast height s h hsv v "" height stem t tree
## 6 height to a specified diameter (taper) s h hsd d "" height stem t tree
## 7 height to a diameter that is 0.75 times the diameter inside bark at breast height s h hsdip75 d "ip75" height stem t tree
## 8 height to a diameter that is 0.67 times the diameter outside bark at breast height s h hsdop67 d "op67" height stem t tree
## 9 site index (base age invariant function) s h hstixi t "ixi" height stem t tree
## 10 site index at 20 year base age s h hstix20 t "ix20" height stem t tree
## 11 site index at 50 year base age s h hstix50 t "ix50" height stem t tree
## 12 site index at 100 year base age s h hstix100 t "ix100" height stem t tree
## 13 distance from tip of stem to merchantibility limit s h hsl l "" height stem t treevs) Modifiers
Stem volume models are among the most common models available in
allometric, including volume of the stem inside or outside
bark, volume of the stem above breast height, and many others.
get_variable_def("vs")## # A tibble: 7 × 10
## description component measure search_str modifier_1 modifier_2 measure_name component_name suffix scale_description
## <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
## 1 volume of the entire stem inside bark, including top and stump s v vsia i a volume stem t tree
## 2 volume of the entire stem outside bark, including top and stump s v vsoa o a volume stem t tree
## 3 volume of the merchantable portion of the stem inside bark s v vsim i m volume stem t tree
## 4 volume of the merchantable portion of the stem outside bark s v vsom o m volume stem t tree
## 5 volume of the stem below breast height inside bark s v vsib i b volume stem t tree
## 6 volume of the stem above breast height inside bark s v vsio i o volume stem t tree
## 7 volume of the stem above breast height outside bark s v vsoo o o volume stem t treeb) Components and Modifiers
Biomass models compose a vast portion of the allometric modeling
literature. All biomass models are stored under the b
measure, and include component biomass models (e.g., branch, foliage,
etc.) as well as whole-tree biomass models.
get_variable_def("b")## # A tibble: 11 × 9
## description component measure search_str modifier measure_name component_name suffix scale_description
## <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
## 1 "branch biomass" b b bb "" biomass branch t tree
## 2 " dead branch biomass" b b bbd "d" biomass branch t tree
## 3 " live branch biomass" b b bbl "l" biomass branch t tree
## 4 "foliage biomass" f b bf "" biomass foliage t tree
## 5 "shrub biomass" h b bh "" biomass shrub t tree
## 6 "bark biomass" k b bk "" biomass bark t tree
## 7 "root biomass" r b br "" biomass root t tree
## 8 "stem biomass" s b bs "" biomass stem t tree
## 9 "stem + branch biomass" s b bsr "r" biomass stem t tree
## 10 "stem biomass without bark" s b bsi "i" biomass stem t tree
## 11 "tree biomass" t b bt "" biomass tree t treeTwo additional flags can be added to any variable name to indicate increment models (e.g., height increment) or change the spatial scale of the variable (e.g., plot-level biomass).
Increment flags exist as the prefix i_. For example, we
can modify the dsob variable to describe diameter outside
bark increment via i_dsob:
get_variable_def("i_dsob")## # A tibble: 1 × 12
## description component measure search_str modifier_1 modifier_2 measure_name component_name suffix scale_description prefix prefix_description
## <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
## 1 diameter of the stem, outside bark at breast height (increment) s d dsob o b diameter stem t tree i incrementScale flags exist as a suffix, with two suffixes available, one for
the plot scale, _p, and one for the stand scale,
_s. For example, we can refer to the stand-level basal area
as
get_variable_def("gs_s")## # A tibble: 1 × 8
## description component measure search_str measure_name component_name suffix scale_description
## <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
## 1 basal area (stand-level) s g gs basal area stem s standWe can even combine increment and scale flags to describe, for
example, stand-level growth variables, e.g., a stand-level basal area
increment would be expressed as i_gs_s
get_variable_def("i_gs_s")## # A tibble: 1 × 10
## description component measure search_str measure_name component_name suffix scale_description prefix prefix_description
## <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr> <chr>
## 1 basal area (stand-level increment) s g gs basal area stem s stand i increment