BotanicalCorrection: Botanical Correction

In VincyaneBadouard/TreeData: Forest Inventories Harmonization & Correction

Botanical Correction

Description

Botanical Correction

Usage

BotanicalCorrection(Data, Source = NULL, WFOData = NULL, DetectOnly = FALSE)

Arguments

Data	Dataset (data.frame or data.table) The dataset must contain the columns: IdTree (character) Family (character) Genus (character) Species (character) VernName (character) ScientificName (character)
Source	(character) To correct and standardise, you can choose between: "TPL": The Plant List (http://www.theplantlist.org/) (faster but based on the 2013 taxonomy) "WFO": World Flora Online (http://www.worldfloraonline.org/) (long time but based on the 2022 taxonomy) NULL: if only error detection (DetectOnly = TRUE)
WFOData	To be filled in if the argument Source = "WFO". Data set with the static copy of the World Flora Online (WFO) Taxonomic Backbone data (from http://www.worldfloraonline.org/downloadData.) (data.frame or data.table)
DetectOnly	TRUE: Only detect errors, FALSE: detect and correct errors (Default: FALSE) (logical)

Details

• 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)

Value

Fill the Comment column with error type informations. If DetectOnly = FALSE, add columns:

• Family_TreeDataCor (character): corrected Family name

• FamilyCorSource (character): source of the Family correction

• Genus_TreeDataCor (character): corrected Genus name

• Species_TreeDataCor (character): corrected Species name

• BotanicalCorrectionSource (character): source of the Genus and Species correction

• ScientificName_TreeDataCor (character): corrected Scientific name

• VernName_TreeDataCor (character): completed if information available at IdTree level.

Examples

## Not run: 
library(data.table)
data(TestData)

# With The Plant List:
Rslt <- BotanicalCorrection(TestData, Source = "TPL")

ScfcCor <- unique(Rslt[ScientificNameCor != ScientificName,
                list(ScientificName, ScientificNameCor,
                Family, FamilyCor, FamilyCorSource,
                Genus, GenusCor,
                Species, SpeciesCor, Subspecies,
                BotanicalCorrectionSource, Comment)
                ])

FamCor <- unique(Rslt[FamilyCor != Family,
                list(ScientificName, ScientificNameCor,
                Family, FamilyCor, FamilyCorSource,
                Genus, GenusCor,
                Species, SpeciesCor, Subspecies,
                BotanicalCorrectionSource, Comment)
                ])

# With World Flora Online:
WFO_Backbone <- file.choose()
load(WFO_Backbone)

RsltWFO <- BotanicalCorrection(TestData, Source = "WFO", WFOData = WFO_Backbone)

ScfcCor <- unique(RsltWFO[ScientificNameCor != ScientificName,
                list(ScientificName, ScientificNameCor,
                Family, FamilyCor,
                Genus, GenusCor,
                Species, SpeciesCor, Subspecies,
                BotanicalCorrectionSource, Comment)
                ])

FamCor <- unique(RsltWFO[FamilyCor != Family,
                list(ScientificName, ScientificNameCor,
                Family, FamilyCor,
                Genus, GenusCor,
                Species, SpeciesCor, Subspecies,
                BotanicalCorrectionSource, Comment)
                ])

## End(Not run)

VincyaneBadouard/TreeData documentation built on Jan. 4, 2024, 2:56 a.m.