Comments (22)
ValentineHerr
commented on July 26, 2024
1
Hi @maurolepore ,
I will try to clarify the thinking process for the shrub allometric equation here:
A - If the DBH is needed (equations probably developed for shrubs that have a "tree" shape, with some branches along the stem), we need to apply the equation on the main stem of the shrub because we think that studies outside of ForestGEO do not measure every single stem at 1.3m but instead find the main obvious stem and measure that one only. From that one stem they get the whole AGB. If we were applying the equation on every single stem of the shrub we would overestimate the AGB because it would be assuming that each stem is actually its own shrub.
Once the equation is applied on the main stem, we get one AGB that needs to be redistributed to all stems, proportionally.
B. If the Basal Diameter is needed (equations probably developed for shrubs that have all their stems coming out of the stump), we need to estimate that basal diameter. Krista's idea was to assume "area preserving" which means that the sum of the area of all stems at 1.3m is equal to the area at the stump. From that basal area that we just calculated, we get the basal diameter (You found our that we can use the sqrt( dbh1^2 + dbh2^2 + ... ) instead of doing the whole area preserving calculation. Good).
Once the equation is applied on the one basal diameter, we get one AGB that needs to be redistributed to all stems, proportionally.
Is that clarification of any help ?
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maurolepore
commented on July 26, 2024
1
Adding to #41 (comment), this flowchart highlights diffences between stem and tree tables for tree and shrub life forms. I'll develop my thougths and code a bit more then may ask a few questions.
For tree tables there is information only for main stems, so each row gives the biomass of each main stem.
For stem tables:
- For trees, each row gives the biomass of one stem.
- For shrubs, biomass is given only for the row containing the main stem, and represents the biomass of the entire shrub; the biomass of all other (non-main) stems is
NA. This is simpler than redistributing biomass across multiple stems and gives the same total biomass per shrub and in total.
input
|
Is stem table?
|
|-no -> Is shrub?
| |-no: Warn biomass is of main stem. --------------------------------|
| |-yes: Warn biomass is of entire shrub. -----------------------------|
| |
|-yes -> Is Shrub? |
|-no ----------------------------------------------------------------|
|-yes |
| |
| |
--------------------------- ---------------
| main shrub-stem biomass | | row biomass |
--------------------------- ---------------
| |
| |
-----------------------------------------------------------
| result |
----------
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gonzalezeb
commented on July 26, 2024
1
I think your suggestion is good ("anything containing "shrub" is a shrub).
I can work more to refine when species life_form=Tree or Shrub. That's something I have to use when working with generic equations.
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maurolepore
commented on July 26, 2024
1
I assume that dbh_unit applies not only to dbh but also to dba. Right?
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maurolepore
commented on July 26, 2024
The steps described above concern the entire process for calculating biomass. For now, however, I would like to focus on the specific process to translate DBH (from users data) to DBA (required in some equations). With that translation we can then calculate the biomass of each individual stem (each row in a dataset with a DBH value), and then users can summarize the data however they want, e.g. totals by tag, species, quadrat. This issue is mentioned in your step a.4 as "calculate the diameter at the base of shrub, assuming area preserving", but How do we do this? (I'll now search for an answer in the code by Valentine that you sent me.)
Notice that once we translate DBH to DBA, the two pathways merge. That is, we no longer have a pathway (a) and a pathway (b), but a table with equations dependent on DBH or DBA that we can evaluate using DBH values from the user.
Some more general thoughts that I’ll clarify as I reveal the differences between the processes to calculate biomass of shrubs versus anything. Quotes are answers by Erika Gonzalez.
- How are shrubs identified in the equations table?
Column E specifies plant growth form (life_form). It could be tree or shrub.
- Is it appropriate to mix shrubs with other woods in the same table? Or is it more sensible to pull shrubs out into a separate table? (This we could do programatically so the master table remains the single interface to enter data.)
I don’t think it will be necessary. Although 38% in our list belong to shrub species; shrubs usually represent only 1% of the total biomass in a plot. It is important for us to present the best available equations, but many researchers would even care if we present a separate table.
-
Do we want users to have two functions, one for biomass of shrubs and another one for everything else? Or do we want to hide the different processes inside a single
-
Pro of separate functions: It's more transparent because the user has to explicitly calculate biomass for shrubs and other woods separately.
-
Con of separate functions: If it is very common that users will need to run the two functions every time, then the extra action, although small, becomes inconvenient.
-
I think we should present the two functions (or more), as it has given us so much headaches. Let give it to the world to enjoy!
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maurolepore
commented on July 26, 2024
@gonzalezeb , I may be very wrong, so please correct me.
If BD is equivalent to DBA, then Valentine's code shows that DBH and DBA are equivalent when the number of stems in a shrub is one. That means that to calculate the biomass of each individual stem in a shrub we can use directly DBH.
However, I'm confused when it comes to calculating the total biomass in a stem. It seems intuitive that the combined biomass of all stems of a shrub should be the sum of the biomass of the individual stems. Yet the equations I get show that the result is instead the square root of the sum of each DBH to the power of two (sqrt( dbh1^2 + dbh2^2 + ... )).
From Valentine's code
## calculate basal area contribution of each stem within a tree
BA <- (pi / 4) * x.shrub.BD$dbh^2 # basal area (at 1.3 m) in mm
tree.sum.BA.un <- tapply(BA, x.shrub.BD$tag, sum, na.rm = T) # sum of basal areas per tree
# ... more code here
## calulate diameter at base of shrub, assuming area preserving
tree.BD <- data.frame(tag = names(tree.sum.BA.un), BD = sqrt(tree.sum.BA.un / pi) * 2)tree.sum.BA.un is the sum of basal areas per tree. Next I explore the cases when a shrub has a single stem, then when it has multiple stems.
Case when a shrub has one stem
When a shrub has one stem, the sum of basal area equal basal area:
tree.sum.BA.un = BA = (pi / 4) * dbh^2Inserting BA into the formula of BD we can simplify terms until we end up with DBH. If follows:
BD = sqrt(tree.sum.BA.un / pi) * 2 =
sqrt(BA / pi) * 2 =
sqrt((pi / 4) * dbh^2 / pi) * 2 =
sqrt( pi / 4 * dbh^2 / pi) * 2 =
sqrt( 1 / 4 * dbh^2 ) * 2 =
sqrt( 1 / 2^(1/2) * dbh^2 ) * 2 =
sqrt(1) / sqrt(2^(1/2)) * sqrt(dbh^2) * 2 =
1 / 2 * dbh * 2 =
dbh/2 * 2 =
dbh = BDCase when a shrub has multiple stems
BD = sqrt(tree.sum.BA.un / pi) * 2 =
sqrt(BA1 + BA2 / pi) * 2 =
sqrt( pi / 4 * (dbh1^2 + dbh2^2) / pi) * 2 =
sqrt(4) * sqrt(dbh1^2 + dbh2^2) * 2 =
2 * sqrt(dbh1^2 + dbh2^2) * 2 =
sqrt(dbh1^2 + dbh2^2) =
sqrt(dbh1^2 + dbh2^2) = from allodb.
maurolepore
commented on July 26, 2024
@gonzalezeb, whenever you can, I'd love to have your thoughts (and maybe Valentine's) about my idea that DBH and DBA may be equivalent (comment just above this one).
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gonzalezeb
commented on July 26, 2024
Mauro, we think your approach is correct. DBH is equivalent to DBA when the shrub has only one stem. But when it has multiple stem, we just need to make sure to redistribute the biomass of main stem to other stems.
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gonzalezeb
commented on July 26, 2024
I think I will include @ValentineHerr if we have more questions..
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maurolepore
commented on July 26, 2024
@gonzalezeb and @ValentineHerr,
In preparation for my upcoming visit I'm reviewing this issue and I would like to capture this discussion by writing some code (building on top of @ValentineHerr's code and ideas). But before I do that, I would like to touch base and ask you if there is anything new I should be aware of.
My goal is to develop an easy way to calculate biomass given equations expressed in terms of DBH, DBA, or BA. However, right now I see no obvious way to link the equations table with the census data (and DBH values) that users provide. If you have anything to comment on this please do so at https://github.com/forestgeo/allodb/issues/36#issuecomment-422825299.
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maurolepore
commented on July 26, 2024
The division is less clear than I had expected. Below you can see equations which independent variable is dbh for "Shrub", for "Tree", and for "Tree or Shrub", and for "Shrub, small tree".
library(tidyverse)
allodb::master_tidy() %>%
select(life_form, equation_form, independent_variable) %>%
unique()
#> Joining `equations` and `sitespecies` by 'equation_id'; then `sites_info` by 'site'.
#> # A tibble: 31 x 3
#> life_form equation_form independent_variable
#> <chr> <chr> <chr>
#> 1 Tree 10^(a+b*(log10(dbh^c))) DBH
#> 2 Tree exp(a+b*log(dbh)) DBH
#> 3 Tree 10^(a+b*(log10(dbh))) DBH
#> 4 Shrub exp(a+b*log(dbh)) DBH
#> 5 Shrub, small tree exp(a+b*log(dbh)) DBH
#> 6 Tree or Shrub exp(a+b*log(dbh)) DBH
#> 7 Tree a+(b*dbh)+c*(dbh^d) DBH
#> 8 Shrub a*(dba^b) DBA
#> 9 Tree a*(dbh^b) DBH
#> 10 Shrub a*(dbh^b) DBH
#> # ... with 21 more rowsWhat criteria should I use to pick the equations that follow the path that @ValentineHerr described above for shrubs? Would this be okay? (i.e. anything containing "shrub" is a shrub).
is_shrub <- function(x) {
grepl("shrub", x, ignore.case = TRUE)
}
is_shrub(c("Tree", "Shrub", "Shrub, small tree", "Tree or Shrub"))
#> [1] FALSE TRUE TRUE TRUEfrom allodb.
maurolepore
commented on July 26, 2024
We now correclty handly shrub biomass for equaitons which independent variable is dbh. This example shows a small table with shrubs exclusively:
library(tidyverse)
library(fgeo.biomass)
shrubs <- fgeo.biomass::scbi_stem_shrub_tiny
equations <- shrubs %>%
add_species(scbi_species, "scbi") %>%
allo_find(dbh_unit = "mm")
#> Adding `site`.
#> Overwriting `sp`; it now stores Latin species names.
#> Adding `rowid`.
#> * Matching equations by site and species.
#> * Refining equations according to dbh.
#> * Using generic equations where expert equations can't be found.
#> Warning: Can't find equations for 26 rows (inserting `NA`).
biomass <- equations %>%
allo_evaluate(dbh_unit = "mm")
#> Shrub `biomass` given for main stems only but applies to the whole shrub.
#> Guessing `dbh` in [mm]
#> You may provide the `dbh` unit manually via the argument `dbh_unit`.
#> Converting `dbh` based on `dbh_unit`.
#> `biomass` values are given in [kg].
# Biomass given only for main stem but representes whole shrub biomass
with_biomass <- left_join(equations, biomass) %>%
select(1:6, dbh, biomass)
#> Joining, by = "rowid"
with_biomass
#> # A tibble: 34 x 8
#> rowid treeID stemID tag StemTag sp dbh biomass
#> <int> <dbl> <dbl> <dbl> <dbl> <chr> <dbl> <dbl>
#> 1 1 1111 1111 10133 1 lindera benzoin 50.9 5.56
#> 2 2 1111 32221 10133 2 lindera benzoin 18.5 NA
#> 3 3 1111 36962 10133 3 lindera benzoin 17.2 NA
#> 4 4 1111 38540 10133 4 lindera benzoin 17.2 NA
#> 5 5 1111 39225 10133 5 lindera benzoin 17.1 NA
#> 6 6 1111 39581 10133 6 lindera benzoin 15.9 NA
#> 7 7 2333 2333 20035 1 lindera benzoin 56.9 7.27
#> 8 8 2333 32434 20035 10 lindera benzoin 12.1 NA
#> 9 9 2333 37071 20035 11 lindera benzoin 15.9 NA
#> 10 10 2333 38598 20035 12 lindera benzoin 11.5 NA
#> # ... with 24 more rows
# More clearly showing whole-shrub biomass
left_join(equations, biomass) %>%
select(1:6, dbh, biomass) %>%
group_by(treeID, sp) %>%
summarise(whole_shrub_biomass = sum(biomass, na.rm = TRUE))
#> Joining, by = "rowid"
#> # A tibble: 5 x 3
#> # Groups: treeID [5]
#> treeID sp whole_shrub_biomass
#> <dbl> <chr> <dbl>
#> 1 1111 lindera benzoin 5.56
#> 2 2333 lindera benzoin 7.27
#> 3 5476 lindera benzoin 9.05
#> 4 22479 lindera benzoin 3.34
#> 5 28182 lindera benzoin 5.85Created on 2019-04-03 by the reprex package (v0.2.1)
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maurolepore
commented on July 26, 2024
This example includes both shrubs and trees:
library(tidyverse)
library(fgeo.biomass)
shrubs <- fgeo.biomass::scbi_stem_shrub_tiny
trees <- fgeo.biomass::scbi_stem_tree_tiny
data <- bind_rows(shrubs, trees)
equations <- data %>%
add_species(scbi_species, "scbi") %>%
allo_find(dbh_unit = "mm")
#> Adding `site`.
#> Overwriting `sp`; it now stores Latin species names.
#> Adding `rowid`.
#> * Matching equations by site and species.
#> * Refining equations according to dbh.
#> * Using generic equations where expert equations can't be found.
#> Warning: Can't find equations for 29 rows (inserting `NA`).
biomass <- equations %>%
allo_evaluate(dbh_unit = "mm")
#> Shrub `biomass` given for main stems only but applies to the whole shrub.
#> Guessing `dbh` in [mm]
#> You may provide the `dbh` unit manually via the argument `dbh_unit`.
#> Converting `dbh` based on `dbh_unit`.
#> `biomass` values are given in [kg].
#> Warning: Can't convert all units (inserting 29 missing values):
#> the 'from' argument is not an acceptable unit.
# Biomass given only for main stem but representes whole shrub biomass
with_biomass <- left_join(equations, biomass) %>%
select(1:6, dbh, biomass)
#> Joining, by = "rowid"
with_biomass
#> # A tibble: 46 x 8
#> rowid treeID stemID tag StemTag sp dbh biomass
#> <int> <dbl> <dbl> <dbl> <dbl> <chr> <dbl> <dbl>
#> 1 1 1111 1111 10133 1 lindera benzoin 50.9 5.56
#> 2 2 1111 32221 10133 2 lindera benzoin 18.5 NA
#> 3 3 1111 36962 10133 3 lindera benzoin 17.2 NA
#> 4 4 1111 38540 10133 4 lindera benzoin 17.2 NA
#> 5 5 1111 39225 10133 5 lindera benzoin 17.1 NA
#> 6 6 1111 39581 10133 6 lindera benzoin 15.9 NA
#> 7 7 2333 2333 20035 1 lindera benzoin 56.9 7.27
#> 8 8 2333 32434 20035 10 lindera benzoin 12.1 NA
#> 9 9 2333 37071 20035 11 lindera benzoin 15.9 NA
#> 10 10 2333 38598 20035 12 lindera benzoin 11.5 NA
#> # ... with 36 more rows
# More clearly showing whole-shrub biomass
left_join(equations, biomass) %>%
select(1:6, dbh, biomass) %>%
group_by(treeID, sp) %>%
summarise(whole_shrub_biomass = sum(biomass, na.rm = TRUE))
#> Joining, by = "rowid"
#> # A tibble: 10 x 3
#> # Groups: treeID [10]
#> treeID sp whole_shrub_biomass
#> <dbl> <chr> <dbl>
#> 1 509 fraxinus americana 497.
#> 2 1111 lindera benzoin 5.56
#> 3 2333 lindera benzoin 7.27
#> 4 5476 lindera benzoin 9.05
#> 5 12427 carpinus caroliniana 44.6
#> 6 13505 cercis canadensis 63.3
#> 7 22479 lindera benzoin 3.34
#> 8 25910 juglans nigra 564.
#> 9 28182 lindera benzoin 5.85
#> 10 28551 carya glabra 430.Created on 2019-04-03 by the reprex package (v0.2.1)
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maurolepore
commented on July 26, 2024
Here I confirm what I commented at #41 (comment)
diameter_at_base <- function(x) {
sqrt(sum(x^2, na.rm = TRUE))
}
# Same as
basal_diameter <- function(dbh) {
sqrt(sum(basal_area(dbh), na.rm = TRUE) / pi) * 2
}
basal_area <- function(dbh) {
pi / 4 * dbh^2
}
identical(basal_diameter(10), diameter_at_base(10))
#> [1] TRUE
random_dbh <- runif(10) * 100
random_dbh
#> [1] 7.409593 64.421704 25.298599 32.595740 78.228289 50.095644 29.966804
#> [8] 45.656978 15.480379 55.405035
identical(basal_diameter(random_dbh), diameter_at_base(random_dbh))
#> [1] TRUECreated on 2019-04-03 by the reprex package (v0.2.1)
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maurolepore
commented on July 26, 2024
For shrub equations which independent variable is dba ,
Which diameter does dbh_min_cm refer to (in allodb)?
a. The dbh of each individual stem.
b. The dba (diameter at base), calculated from the dbh of all stems together.
c. Other.
library(tidyverse)
allodb::master_tidy() %>%
filter(str_detect(equation_form, "dba")) %>%
select(equation_form, matches("min|max")) %>%
unique()
#> Joining `equations` and `sitespecies` by 'equation_id'; then `sites_info` by 'site'.
#> # A tibble: 18 x 3
#> equation_form dbh_min_cm dbh_max_cm
#> <chr> <dbl> <dbl>
#> 1 a*(dba^b) 0.18 4.31
#> 2 a*(dba^b) 0.12 0.69
#> 3 a*(dba^b) 0.2 1.2
#> 4 a*(dba^b) 0.3 0.9
#> 5 a*(dba^b) 0.28 1.59
#> 6 exp(a+b*log(dba)) 0.5 2.1
#> 7 exp(a+b*log(dba)) 0.6 2.5
#> 8 exp(a+b*log(dba)) 0.4 1.4
#> 9 exp(a+b*log(dba)) 0.6 3.6
#> 10 exp(a+b*log(dba)) 0.7 2.2
#> 11 exp(a+b*log(dba)) 0.1 1.1
#> 12 exp(a+b*log(dba)) 0.4 3.3
#> 13 exp(a+b*log(dba)) 0.4 11.5
#> 14 exp(a+b*log(dba)) 0.3 11.7
#> 15 exp(a+b*log(dba)) 0.3 6.5
#> 16 exp(a+b*log(dba)) 0.5 2.6
#> 17 a*(dba^b) 0.31 1.37
#> 18 a*(dba^b) 0.64 5.7Created on 2019-04-03 by the reprex package (v0.2.1)
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gonzalezeb
commented on July 26, 2024
Which diameter does dbh_min_cm refer to (in allodb)?
The dba range (for sampled stems) as given in original publication.
Maybe I need to specify that for each equation that uses dba. I can do it in the 'notes' column (currently called warning but I will replace the column name with notes)
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maurolepore
commented on July 26, 2024
The dba range (for sampled stems) as given in original publication.
Can you please extend a bit?
Say that a single shrub has three stems, s1, s2, and s3, with dbh values dbh1 = 1cm, dbh2 = 2cm, and dbh3 = 3cm. The resulting basal diameter (accounts for all three stems together) is this:
fgeo.biomass:::basal_diameter(c(1, 2, 3))
#> [1] 3.741657Now, say that for this species of shrub, dbh_min = 3.5cm.
Which statement is true:
a. No stem can use this equation because no stem is 3.5cm or greater.
b. All stems can use this equation because the basal diameter is greater than 3.5cm.
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maurolepore
commented on July 26, 2024
For consistency, we now also distribute the biomass of shrubs which independent variable is dbh. This is different from what I showed in #41 (comment) (where biomass was given only for main stems).
Now, all stems (of valid dbh range) of each shrub have a biomass value that results from calculating the total biomass from the main stem and redistributing it across stems based on the contribution of each stem to the total basal area.
library(tidyverse)
library(fgeo.biomass)
shrubs <- fgeo.biomass::scbi_stem_tiny_shrub
equations <- shrubs %>%
add_species(scbi_species, "scbi") %>%
allo_find(dbh_unit = "mm")
#> Adding `site`.
#> Overwriting `sp`; it now stores Latin species names.
#> Adding `rowid`.
#> * Matching equations by site and species.
#> * Refining equations according to dbh.
#> * Using generic equations where expert equations can't be found.
#> Warning: Can't find equations for 38 rows (inserting `NA`).
biomass <- equations %>%
allo_evaluate(dbh_unit = "mm")
#> Shrub `biomass` given for main stems only but applies to the whole shrub.
#> Guessing `dbh` in [mm]
#> You may provide the `dbh` unit manually via the argument `dbh_unit`.
#> Converting `dbh` based on `dbh_unit`.
#> `biomass` values are given in [kg].
left_join(equations, biomass) %>%
select(treeID, sp, eqn, dbh, matches("min|max"), biomass) %>%
group_by(treeID) %>%
mutate(n = sum(!is.na(biomass))) %>%
filter(n > 1) %>%
arrange(treeID, desc(biomass)) %>%
select(-n) %>%
print(n = Inf)
#> Joining, by = "rowid"
#> # A tibble: 32 x 7
#> # Groups: treeID [5]
#> treeID sp eqn dbh dbh_min_mm dbh_max_mm biomass
#> <dbl> <chr> <chr> <dbl> <dbl> <dbl> <dbl>
#> 1 2333 lindera ben~ exp(-2.2118 + ~ 56.9 30 640 3.75
#> 2 2333 lindera ben~ exp(-2.2118 + ~ 55.2 30 640 3.53
#> 3 2333 lindera ben~ <NA> 12.1 NA NA NA
#> 4 2333 lindera ben~ <NA> 15.9 NA NA NA
#> 5 2333 lindera ben~ <NA> 11.5 NA NA NA
#> 6 2333 lindera ben~ <NA> 11.1 NA NA NA
#> 7 2333 lindera ben~ <NA> 22.5 NA NA NA
#> 8 2333 lindera ben~ <NA> 23.7 NA NA NA
#> 9 2333 lindera ben~ <NA> 13.8 NA NA NA
#> 10 2333 lindera ben~ <NA> 26 NA NA NA
#> 11 2333 lindera ben~ <NA> 12 NA NA NA
#> 12 2333 lindera ben~ <NA> 19.2 NA NA NA
#> 13 2333 lindera ben~ <NA> 14.7 NA NA NA
#> 14 3805 hamamelis v~ 38.111 * (dba^~ 23.5 1.8 43.1 0.0891
#> 15 3805 hamamelis v~ 38.111 * (dba^~ 16.8 1.8 43.1 0.0127
#> 16 3805 hamamelis v~ 38.111 * (dba^~ 15.7 1.8 43.1 0.00858
#> 17 3805 hamamelis v~ 38.111 * (dba^~ 15.4 1.8 43.1 0.00768
#> 18 3805 hamamelis v~ 38.111 * (dba^~ 14.8 1.8 43.1 0.00610
#> 19 3805 hamamelis v~ 38.111 * (dba^~ 12.7 1.8 43.1 0.00251
#> 20 3805 hamamelis v~ <NA> 94.2 NA NA NA
#> 21 3805 hamamelis v~ <NA> 82.6 NA NA NA
#> 22 5476 lindera ben~ exp(-2.2118 + ~ 62.3 30 640 5.05
#> 23 5476 lindera ben~ exp(-2.2118 + ~ 43.7 30 640 2.49
#> 24 5476 lindera ben~ exp(-2.2118 + ~ 34.1 30 640 1.51
#> 25 6275 hamamelis v~ 38.111 * (dba^~ 42.6 1.8 43.1 1.73
#> 26 6275 hamamelis v~ 38.111 * (dba^~ 18.4 1.8 43.1 0.0133
#> 27 6275 hamamelis v~ 38.111 * (dba^~ 14.6 1.8 43.1 0.00348
#> 28 8302 hamamelis v~ 38.111 * (dba^~ 16.7 1.8 43.1 0.0554
#> 29 8302 hamamelis v~ 38.111 * (dba^~ 14.9 1.8 43.1 0.0286
#> 30 8302 hamamelis v~ 38.111 * (dba^~ 10 1.8 43.1 0.00283
#> 31 8302 hamamelis v~ <NA> 51.3 NA NA NA
#> 32 8302 hamamelis v~ <NA> 49 NA NA NACreated on 2019-04-04 by the reprex package (v0.2.1)
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maurolepore
commented on July 26, 2024
Here is a flowchart summary of the available code:
add_species() and add_equations()
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maurolepore
commented on July 26, 2024
Closing now. What remains unclear is now a separate issue
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gonzalezeb
commented on July 26, 2024
Hi Mauro, I cannot see the flowchart summary here
Here is a flowchart summary of the available code:
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maurolepore
commented on July 26, 2024
Sorry, I hadn't made the link public. Here you go:
https://drive.google.com/file/d/1HBHR4F3jkVDU9i_6s-rGdf7dWodbWYFh/view?usp=sharing
https://drive.google.com/file/d/1MJkD7hp2XNFOYA3eMaoXgKGbOP0J3WXa/view?usp=sharing
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- Remove needless calls to print() in examples
- Use simpler markdown syntax, e.g. replace \pkg{allodb} with *allodb*
- Review punctuation of helpfiles (title and other sections)
- Use simple comments to follow tidyverse styleguide "# blah" not "## blah"
- Reserve return() for early returns (tidyverse styleguide)
- Remove redundant reference to allodb
- Remove duplication in documentation
- Replace references to `f()` with [f()].
- Document default vaules in signature, not in `@param` or elsewhere
- If `coords` has wrong dimensions `get_biomass()` should throw an error HOT 2
- Support for the component ratio method HOT 1
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from allodb.