DataHarmonization
Forest Inventories Harmonization & Correction
Source:vignettes/DataHarmonization.Rmd
DataHarmonization.RmdLoad DataHarmonization and datasets
Install DataHarmonization
devtools::install_github("Alliance-for-Tropical-Forest-Science/DataHarmonization", build_vignettes = TRUE)Load the packages
library(DataHarmonization)
library(knitr)
library(kableExtra)
library(shiny)
library(shinydashboard)
library(shinyjs)
library(shinyWidgets)
# library(ggplot2)Open the shiny app
# DataHarmonization::RunApp() # doest' work, why?
shiny::runGitHub( "Alliance-for-Tropical-Forest-Science/DataHarmonization", subdir = "inst/app") # data.tree, stringdistLoad the example dataset stored in the package
# data()Metadata of the output columns of the DataHarmonization package
- Comment (character): error type informations
Bota
- Family_DataHarmonizationCor (character): corrected
Family name
- FamilyCorSource (character): source of the Family
correction
- Genus_DataHarmonizationCor (character): corrected
Genus name
- Species_DataHarmonizationCor (character): corrected
Species name
- BotanicalCorrectionSource (character): source of the
Genus and Species correction
- ScientificName_DataHarmonizationCor (character): corrected
ScientificName
- VernName_DataHarmonizationCor (character): completed if
information available at IdTree level.
Life Status
- LifeStatus_DataHarmonizationCor (logical): corrected stem
life status.
Diameter
- Diameter_DataHarmonizationCor (numeric): corrected trees
diameter at default HOM
- DiameterCorrectionMeth (character): diameter correction
methode = “taper”/“local linear
regression”/“weighted mean” /phylogenetic
hierarchical(“species”/“genus”/“family”/“stand”)/“shift
realignment”/“Same value”.
- POM_DataHarmonizationCor (factor): POM value at
which the corrected diameters are proposed. Corresponds to the 1st
POM value at which the stem was measured
- HOM_DataHarmonizationCor (numeric): HOM value at
which the corrected diameters are proposed. Corresponds to the
DefaultHOM if Taper correction applied. If not,
corresponds to the 1st HOM value at which the stem was
measured
Recruitment
- CorrectedRecruit (logical): TRUE: the row was added to
represent the year when the stem was larger than the minimum diameter,
but absent from the dataset. FALSE: original dataset row.
Decomposed corrections
General errors detection
Detect errors - Remove duplicated rows - Check missing value in X-YTreeUTM/PlotArea/Plot/Subplot/Year/TreeFieldNum/ IdTree/IdStem/Diameter/POM/HOM/Family/Genus/Species/VernName - Check missing value (NA/0) in the measurement variables: “Diameter”, “HOM”, “TreeHeight”, “StemHeight” - Check of the unique association of the IdTree with plot, subplot and TreeFieldNum (at the site scale) - Check duplicated IdTree/IdStem in a census (at the site scale) - Check for trees outside the subplot (not implemented yet) - Check invariant coordinates per IdTree/IdStem - Check fix Plot and Subplot number (not implemented yet)
Botanical identification correction
- No special characters (typography)
- No family name in the Genus and Species columns (the suffix “aceae” is specific to the family name.
- Correct spelling of botanical names (Taxonstand or WorldFlora)
- Family & Scientific names match (BIOMASS::getTaxonomy or WorldFlora)
- Update the scientific botanical names with the current phylogenetic classification
- Check invariant botanical informations per IdTree (1 IdTree = 1 family, 1 scientific and 1 vernacular name)
Life status
if UseSize argument chosen : if Diameter != NA -> Alive If (the value in bold is modified by the value given after the arrow): (the “>” gives the chronological order of the sequence)
Dead > Alive -> NA
add rows for the forgotten censuses between 2 ‘Alive’ if chosen
Alive > Dead/NA > Alive -> Alive
Alive > NA > Dead -> NA
Alive > Dead > NA -> Dead
Alive > NA > NA: if DeathConfirmation > unseens -> NA if DeathConfirmation =< unseens -> Dead