Allometry database harmonization
Miquel De Cáceres / Nicolas Martin-StPaul
2024-09-14
Source:vignettes/AllometryDatabaseHarmonization.Rmd
AllometryDatabaseHarmonization.RmdIntroduction
The availability of plant allometric equations continuously increases, as additional efforts are made in observational studies. This means that multiple data sources need to be harmonized before species parameter tables are build, in terms of:
a) Nomenclature of the response and predictor variables.
b) Allometric equation fitted.
c) Taxonomy of the measured biological entities. The result of this harmonization needs to be stored in a harmonized format for subsequent use when creating species parameter tables. This vignette illustrates the harmonization procedures for an example data set using package trait4models and the usual tidyverse packages. Harmonization of plant trait data is explained in a companion vignette.
Required packages
Assuming we have traits4models installed, we load it and other common packages that we will employ in this vignette:
Example dataset
As an example of allometric equations, we will use a small compilation of crown width models, from different sources, that depend on diameter at breast height:
DB_path <- "~/OneDrive/EMF_datasets/AllometryDatabases/"
db <- openxlsx::read.xlsx(paste0(DB_path, "Sources/TreeAllometries/TreeAllometries.xlsx"),
sheet= "Tree_CW_models")The data looks as follows:
db## Name a_cw b_cw Source
## 1 Abies alba 1.0963648 0.5380 Hasenauer (1997) - Abies alba
## 2 Acer 1.5189207 0.5285 Hasenauer (1997) - Acer spp.
## 3 Castanea sativa 1.3065630 0.5856 Condés & Sterba 2005
## 4 Fagus sylvatica 0.8386180 0.7347 Condés & Sterba 2005
## 5 Fraxinus 1.1951838 0.5665 Hasenauer (1997) - Fraxinus spp.
## 6 Pinus halepensis 0.6415296 0.7310 Condés & Sterba 2005
## 7 Pinus nigra 0.5076312 0.7699 Condés & Sterba 2005
## 8 Pinus pinaster 0.3889517 0.8307 Condés & Sterba 2005
## 9 Pinus radiata 0.8418950 0.6353 Condés & Sterba 2005
## 10 Pinus sylvestris 0.7474409 0.6716 Condés & Sterba 2005
## 11 Quercus ilex 0.5681897 0.7974 Condés & Sterba 2005
## 12 Quercus pyrenaica 0.7469926 0.7257 Condés & Sterba 2005
## 13 Quercus robur 0.0716000 0.6563 Condés & Sterba 2005
## 14 Quercus suber 0.4473000 0.7918 Sánchez-Gonzalez et al. 2007
## 15 Pinus 0.7474409 0.6716 Pinus sylvestris
## 16 Quercus 0.5681897 0.7974 Q.ilex
## 17 Abies 1.0963648 0.5380 Abies albaHarmonizing equations and notation
The allometric equation has two parameters that are used to estimate crown width from diameter at breast height (DBH). We start our harmonization by subsetting the necessary data:
db_var <- db |>
dplyr::rename(originalName = "Name",
a = "a_cw",
b = "b_cw",
Reference = "Source") Importantly, for the allometry to be used, we need to specify the equation:
db_var <- db_var |>
dplyr::mutate(Equation = "CrownWidth = a·DBH^b")We also add information on the response variable and predictor variable:
db_var <- db_var |>
dplyr::mutate(Response = "CrownWidth",
ResponseDescription = "Crown width (m)",
Predictor1 = "DBH",
PredictorDescription1 = "Diameter at breast height (cm)")If we want traits4models to correctly interpret the
allometric equation at the stage of model parameter filling, it is
important that columns Equation and Response
are appropriately filled. Note, in addition, that the allometric
equation starts with the name of the response on the left hand side of
the equation.
Finally, we may add the priority of processing:
db_var <- db_var |>
dplyr::mutate(Priority = 1) |>
dplyr::relocate(Reference, .after = PredictorDescription1)The database after harmonizing allometry information looks as follows:
db_var## originalName a b Equation Response
## 1 Abies alba 1.0963648 0.5380 CrownWidth = a·DBH^b CrownWidth
## 2 Acer 1.5189207 0.5285 CrownWidth = a·DBH^b CrownWidth
## 3 Castanea sativa 1.3065630 0.5856 CrownWidth = a·DBH^b CrownWidth
## 4 Fagus sylvatica 0.8386180 0.7347 CrownWidth = a·DBH^b CrownWidth
## 5 Fraxinus 1.1951838 0.5665 CrownWidth = a·DBH^b CrownWidth
## 6 Pinus halepensis 0.6415296 0.7310 CrownWidth = a·DBH^b CrownWidth
## 7 Pinus nigra 0.5076312 0.7699 CrownWidth = a·DBH^b CrownWidth
## 8 Pinus pinaster 0.3889517 0.8307 CrownWidth = a·DBH^b CrownWidth
## 9 Pinus radiata 0.8418950 0.6353 CrownWidth = a·DBH^b CrownWidth
## 10 Pinus sylvestris 0.7474409 0.6716 CrownWidth = a·DBH^b CrownWidth
## 11 Quercus ilex 0.5681897 0.7974 CrownWidth = a·DBH^b CrownWidth
## 12 Quercus pyrenaica 0.7469926 0.7257 CrownWidth = a·DBH^b CrownWidth
## 13 Quercus robur 0.0716000 0.6563 CrownWidth = a·DBH^b CrownWidth
## 14 Quercus suber 0.4473000 0.7918 CrownWidth = a·DBH^b CrownWidth
## 15 Pinus 0.7474409 0.6716 CrownWidth = a·DBH^b CrownWidth
## 16 Quercus 0.5681897 0.7974 CrownWidth = a·DBH^b CrownWidth
## 17 Abies 1.0963648 0.5380 CrownWidth = a·DBH^b CrownWidth
## ResponseDescription Predictor1 PredictorDescription1
## 1 Crown width (m) DBH Diameter at breast height (cm)
## 2 Crown width (m) DBH Diameter at breast height (cm)
## 3 Crown width (m) DBH Diameter at breast height (cm)
## 4 Crown width (m) DBH Diameter at breast height (cm)
## 5 Crown width (m) DBH Diameter at breast height (cm)
## 6 Crown width (m) DBH Diameter at breast height (cm)
## 7 Crown width (m) DBH Diameter at breast height (cm)
## 8 Crown width (m) DBH Diameter at breast height (cm)
## 9 Crown width (m) DBH Diameter at breast height (cm)
## 10 Crown width (m) DBH Diameter at breast height (cm)
## 11 Crown width (m) DBH Diameter at breast height (cm)
## 12 Crown width (m) DBH Diameter at breast height (cm)
## 13 Crown width (m) DBH Diameter at breast height (cm)
## 14 Crown width (m) DBH Diameter at breast height (cm)
## 15 Crown width (m) DBH Diameter at breast height (cm)
## 16 Crown width (m) DBH Diameter at breast height (cm)
## 17 Crown width (m) DBH Diameter at breast height (cm)
## Reference Priority
## 1 Hasenauer (1997) - Abies alba 1
## 2 Hasenauer (1997) - Acer spp. 1
## 3 Condés & Sterba 2005 1
## 4 Condés & Sterba 2005 1
## 5 Hasenauer (1997) - Fraxinus spp. 1
## 6 Condés & Sterba 2005 1
## 7 Condés & Sterba 2005 1
## 8 Condés & Sterba 2005 1
## 9 Condés & Sterba 2005 1
## 10 Condés & Sterba 2005 1
## 11 Condés & Sterba 2005 1
## 12 Condés & Sterba 2005 1
## 13 Condés & Sterba 2005 1
## 14 Sánchez-Gonzalez et al. 2007 1
## 15 Pinus sylvestris 1
## 16 Q.ilex 1
## 17 Abies alba 1Taxonomic harmonization
Package traits4models currently relies on World Flora Online for taxonomic harmonization, via package WorldFlora (Kindt 2020) available at CRAN. This latter package requires a static copy of the World Flora Online Taxonomic Backbone data that can be downloaded from the World Flora Online website. Note that you should use a different DOI reference when reporting your harmonization procedures. We are using here v.2024.06. We assume the user has already downloaded the backbone and stored it in a file called classification.csv.
WFO_file <- paste0(DB_path, "../PlantTraitDatabases/WFO_Backbone/classification.csv")Taxonomic harmonization is done by calling function
harmonize_taxonomy_WFO() with a data frame (where notation
and units are already harmonized) and the path to the WFO backbone (we
omit the console output):
db_post <- traits4models::harmonize_taxonomy_WFO(db_var, WFO_file)The function requires that the input data frame contains a column
called originalName, to identify the original taxa names
(additional columns are simply transferred to the output). It performs
both direct and fuzzy matching, which may lead to large processing time
for large datasets. If we inspect the resulting data frame, we will see
the additional columns, informing about accepted names and parent
taxonomic entities:
head(db_post)## originalName acceptedName acceptedNameAuthorship family genus
## 1 Abies alba Abies alba Mill. Pinaceae Abies
## 2 Acer Acer L. Sapindaceae Acer
## 3 Castanea sativa Castanea sativa Mill. Fagaceae Castanea
## 4 Fagus sylvatica Fagus sylvatica L. Fagaceae Fagus
## 5 Fraxinus Fraxinus Tourn. ex L. Oleaceae Fraxinus
## 6 Pinus halepensis Pinus halepensis Mill. Pinaceae Pinus
## specificEpithet taxonRank a b Equation Response
## 1 alba species 1.0963648 0.5380 CrownWidth = a·DBH^b CrownWidth
## 2 <NA> genus 1.5189207 0.5285 CrownWidth = a·DBH^b CrownWidth
## 3 sativa species 1.3065630 0.5856 CrownWidth = a·DBH^b CrownWidth
## 4 sylvatica species 0.8386180 0.7347 CrownWidth = a·DBH^b CrownWidth
## 5 <NA> genus 1.1951838 0.5665 CrownWidth = a·DBH^b CrownWidth
## 6 halepensis species 0.6415296 0.7310 CrownWidth = a·DBH^b CrownWidth
## ResponseDescription Predictor1 PredictorDescription1
## 1 Crown width (m) DBH Diameter at breast height (cm)
## 2 Crown width (m) DBH Diameter at breast height (cm)
## 3 Crown width (m) DBH Diameter at breast height (cm)
## 4 Crown width (m) DBH Diameter at breast height (cm)
## 5 Crown width (m) DBH Diameter at breast height (cm)
## 6 Crown width (m) DBH Diameter at breast height (cm)
## Reference Priority
## 1 Hasenauer (1997) - Abies alba 1
## 2 Hasenauer (1997) - Acer spp. 1
## 3 Condés & Sterba 2005 1
## 4 Condés & Sterba 2005 1
## 5 Hasenauer (1997) - Fraxinus spp. 1
## 6 Condés & Sterba 2005 1Checking harmonized allometry data
The packages includes function
check_harmonized_allometry() to check whether a given data
frame conforms in structure and content to what is later required for
parameter table filling:
check_harmonized_allometry(db_post)## ✔ The data frame is acceptable as harmonized allometry data source.In this case, the data set is ready to be used in parameter estimation. As an example, we can run the same checking function with the data base before taxonomic harmonization:
check_harmonized_allometry(db_var)## ! Required columns missing: acceptedName acceptedNameAuthorship family genus specificEpithet taxonRank## ! The data frame is not acceptable as harmonized allometry data source.Storing harmonized dataset
Harmonized data tables can be stored in .csv text format or compressed .rds format.
write.csv2(db_post, "Products/harmonized/tree_crown_width_europe.csv", row.names = FALSE)Note that all tables should be stored in the same directory, here in
the Products/harmonized/ path, for populate model
parameters.
Accessing harmonized allometry data
List of harmonized allometry databases
As mentioned in the introduction, here it is assumed that a set of plant allometry databases have been harmonized. In our case, harmonized data files have been stored in the following path:
harmonized_allometry_path = "~/OneDrive/EMF_datasets/AllometryDatabases/Products/harmonized"We can list the set of harmonized sources using:
allometry_files <- list.files(path = harmonized_allometry_path, full.names = FALSE)
allometry_files## [1] "shrub_crown_area_catalonia.csv"
## [2] "shrub_fine_fuel_biomass_catalonia.csv"
## [3] "shrub_total_biomass_catalonia.csv"
## [4] "tree_bark_thickness_catalonia.csv"
## [5] "tree_crown_ratio_europe.csv"
## [6] "tree_crown_width_europe.csv"
## [7] "tree_foliar_biomass_calvoalvarado_et_al_2024.csv"
## [8] "tree_foliar_biomass_catalonia.csv"
## [9] "tree_foliar_biomass_eslamdoust_et_al_2017.csv"
## [10] "tree_foliar_biomass_thom_et_al_2024.csv"Querying allometry data for particular response variable
Before filling any species parameter table, it may be useful to
inspect the amount of information available for particular response.
Package trait4models provides function
get_allometry_data():
fb_data <- get_allometry_data(harmonized_allometry_path, "FoliarBiomass",
progress = FALSE)
head(fb_data)## originalName acceptedName acceptedNameAuthorship
## 1 Tetragastris panamensis Protium stevensonii (Standl.) Daly
## 2 Virola koschnii Virola koschnyi Warb.
## 3 Carapa guianensis Carapa guianensis Aubl.
## 4 Vochysia ferruginea Vochysia ferruginea Mart.
## 5 Pentaclethra macroloba Pentaclethra macroloba (Willd.) Kuntze
## 6 Abies alba Abies alba Mill.
## family genus specificEpithet taxonRank
## 1 Burseraceae Protium stevensonii species
## 2 Myristicaceae Virola koschnyi species
## 3 Meliaceae Carapa guianensis species
## 4 Vochysiaceae Vochysia ferruginea species
## 5 Fabaceae Pentaclethra macroloba species
## 6 Pinaceae Abies alba species
## Equation a b
## 1 FoliarBiomass = a·DBH^b 0.0400000 1.737000
## 2 FoliarBiomass = a·DBH^b 0.0020000 2.468000
## 3 FoliarBiomass = a·DBH^b 0.0120000 2.089000
## 4 FoliarBiomass = a·DBH^b 0.6730000 1.058000
## 5 FoliarBiomass = a·DBH^b 0.9580000 0.757000
## 6 FoliarBiomass = a·DBH^b·exp(c·BAL)·DBH^(d·BAL) 0.1231138 1.452404
## Reference
## 1 Calvo-Alvarado et al. (2008) Allometric relationships predicting foliar biomass and leaf area:sapwood area ratio from tree height in five Costa Rican rain forest species. Tree Physiology 28: 1601-1608
## 2 Calvo-Alvarado et al. (2008) Allometric relationships predicting foliar biomass and leaf area:sapwood area ratio from tree height in five Costa Rican rain forest species. Tree Physiology 28: 1601-1608
## 3 Calvo-Alvarado et al. (2008) Allometric relationships predicting foliar biomass and leaf area:sapwood area ratio from tree height in five Costa Rican rain forest species. Tree Physiology 28: 1601-1608
## 4 Calvo-Alvarado et al. (2008) Allometric relationships predicting foliar biomass and leaf area:sapwood area ratio from tree height in five Costa Rican rain forest species. Tree Physiology 28: 1601-1608
## 5 Calvo-Alvarado et al. (2008) Allometric relationships predicting foliar biomass and leaf area:sapwood area ratio from tree height in five Costa Rican rain forest species. Tree Physiology 28: 1601-1608
## 6 Calculated IEFC
## Response ResponseDescription Predictor1 PredictorDescription1
## 1 FoliarBiomass Foliar biomass (kg) DBH Diameter at breast height (cm)
## 2 FoliarBiomass Foliar biomass (kg) DBH Diameter at breast height (cm)
## 3 FoliarBiomass Foliar biomass (kg) DBH Diameter at breast height (cm)
## 4 FoliarBiomass Foliar biomass (kg) DBH Diameter at breast height (cm)
## 5 FoliarBiomass Foliar biomass (kg) DBH Diameter at breast height (cm)
## 6 FoliarBiomass Foliar biomass (kg) DBH Diameter at breast height (cm)
## Priority c d Predictor2 PredictorDescription2
## 1 2 NA NA <NA> <NA>
## 2 2 NA NA <NA> <NA>
## 3 2 NA NA <NA> <NA>
## 4 2 NA NA <NA> <NA>
## 5 2 NA NA <NA> <NA>
## 6 1 0 0 BAL Basal area of larger trees (m2/ha)