IndividualDiameterShiftCorrection: Individual Diameter Shift Correction

In VincyaneBadouard/TreeData: Forest Inventories Harmonization & Correction

Individual Diameter Shift Correction

Description

Correct for 'shift' diameter errors, based on the individual's non-abnormal growths. Greater weight is given to growths recorded at a diameter close to the one to correct. The weighted mean of the non-abnormal growths is computed and applied to correct the abnormal diameter.

Usage

IndividualDiameterShiftCorrection(
  DataTree = NULL,
  DBHCor,
  Time,
  cresc,
  cresc_abs,
  cresc_abn,
  coef = 0.9
)

Arguments

DataTree	A dataset corresponding to a single tree/stem's (1 IdTree/IdStem) measurements (data.frame or data.table) To be filled in if you want the column "DiameterCorrectionMeth" (correction method) to be filled in the corresponding row. Otherwise leave DataTree = NULL
DBHCor	Diameter vector (numeric)
Time	Time vector (numeric)
cresc	Annual diameter increment with NA instead of abnormal values (numeric)
cresc_abs	Absolute diameter increment (not divided by time between 2 values) with NA instead of abnormal values (numeric)
cresc_abn	Abnormal diameter increment positions (numeric)
coef	description... (numeric)

Details

Method:

1. Correct the 1st value of the shift ("weighted mean"):

• Compute the absolute difference between the DBH to correct and the others

• Give respective weights to the growth (cresc) values according to the distance to the DBH to correct

• Compute the weighted mean of the growths (cresc)

• Apply the weighted mean to correct the abnormal DBH

1. Correct the following values of the shift ("shift realignment"): Each value = the previous value + initial growth

Value

List of 2 objects:

• DBHCor (numeric vector): corrected by the method

• DataTree (data.table): with the DiameterCorrectionMeth column filled with correction method ("weighted mean", "shift realignment")

Examples

DBHCor = c(13:16, 16-4, (16-4)+2, (16-4)+3, 15-4, (15-4)+2)
Time = c(seq(2000,2008, by = 2), 2012, 2014,2016, 2020)
plot(Time, DBHCor)
cresc <- ComputeIncrementation(Var = DBHCor, Type = "annual", Time = Time)
cresc_abs <- ComputeIncrementation(Var = DBHCor, Type = "absolute", Time = Time)
cresc_abn <- which(cresc >= 5 | cresc_abs < -2) # abnormal values indices
cresc[cresc_abn] <- NA
cresc_abs[cresc_abn] <- NA

Rslt <- IndividualDiameterShiftCorrection(DBHCor = DBHCor, Time = Time,
                                  cresc = cresc, cresc_abs = cresc_abs,
                                  cresc_abn = cresc_abn)

library(ggplot2)
ggplot() +
  aes(x = Time) +
  geom_point(aes(y = Rslt$DBHCor),
             col = "forestgreen") +
  geom_line(aes(y = Rslt$DBHCor),
            col = "forestgreen") +
  geom_point(aes(y = DBHCor),
             col = "red") +
  geom_line(aes(y = DBHCor),
            col = "red") +
  theme_minimal() +
  labs(x = "Year", y = "Diameter (cm)")

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