StatusCorrection: Status Correction

In VincyaneBadouard/TreeData: Forest Inventories Harmonization & Correction

Status Correction

Description

Detect errors, or detect errors and correct, the tree life status evolution over the censuses. Inspired by the code of Nino Page package (ForestData::correct_alive() and .correct_alive_tree())

Usage

StatusCorrection(
  Data,
  InvariantColumns = c("Site", "Genus_TreeDataCor", "Species_TreeDataCor",
    "Family_TreeDataCor", "ScientificName_TreeDataCor"),
  DeathConfirmation = 2,
  UseSize = FALSE,
  AddRowsForForgottenCensuses = TRUE,
  DetectOnly = FALSE,
  RemoveRBeforeAlive = FALSE,
  RemoveRAfterDeath = FALSE
)

Arguments

Data	Dataset (data.frame or data.table) The LifeStatus column must be coded as: - TRUE = alive, - FALSE = dead, - NA = unseen The Plot column is needed to add rows to the census where the plot was inventoried, where the tree was alive, but not recorded.
InvariantColumns	Vector with the names of the columns that are supposed to have always the same value for each measurement of the same tree (character). It is recommended to use the columns that have already been corrected, such as the columns containing the corrected botanical information.
DeathConfirmation	Number of times (censuses) needed for an unseen tree to be considered dead (numeric) (Default = 2 censuses)
UseSize	Use the size presence as a witness of the living status of the tree (logical) (Default = FALSE)
AddRowsForForgottenCensuses	TRUE: adds rows for forgotten censuses between 2 'Alive', FALSE: does not add any rows (logical)
DetectOnly	TRUE: Only detect errors, FALSE: detect and correct errors (logical)
RemoveRBeforeAlive	Do you want to delete the rows about the tree before it was seen alive for the 1st time? (logical)
RemoveRAfterDeath	After correction do you want to delete the rows concerning the tree after its death? (logical)

Details

• if UseSize : 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

Value

Fill the Comment column with error type informations. If DetectOnly = FALSE, add a LifeStatus_TreeDataCor column with the corrected trees life status.

Examples

library(data.table)
data(TestData)

selection <- c("101184", "101433","101435","101436")

# Write the sequence
TestData <- TestData[order(Year)] # arrange years in ascending order
TestData[IdTree == "101184", LifeStatus := c(TRUE, TRUE, TRUE, TRUE, FALSE)]
TestData[IdTree == "101433", LifeStatus := c(FALSE, TRUE, TRUE, TRUE, TRUE)]
TestData[IdTree == "101435", LifeStatus := c(TRUE, TRUE, NA, FALSE, TRUE)]
TestData[IdTree == "101436", LifeStatus := c(TRUE, NA, NA, FALSE, NA)]


Rslt <- StatusCorrection(TestData[IdTree %in% selection],
                         InvariantColumns = c("Site",
                                              "Genus",
                                              "Species",
                                              "Family",
                                              "ScientificName"))


LifeStatusCorrectionPlot(Rslt)

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