Manage trees and plot coordinates with BIOMASS

In BIOMASS: Estimating Aboveground Biomass and Its Uncertainty in Tropical Forests

knitr::opts_chunk$set(
  collapse = TRUE, echo = TRUE,
  comment = "#>", fig.align = "center"
)
require(BIOMASS)
require(knitr)

Requirement

You need the following information to use the following function in your analysis :

• Dimension of the plots
• Coordinate GPS of minimum 3 points non-aligned and relatily far away with the corresponding relative coordinates
• The origin corner
• The X, Y directions

trees <- read.csv(system.file("external", "NouraguesPlot.csv",
  package = "BIOMASS", mustWork = TRUE
))

kable(head(trees), digits = 3, row.names = FALSE, caption = "Head of the table trees")

We can see in the table that we have for each trees the name of the plot we have, the xRel and yRel, the relative coordinate of the trees inside the plot. The rest of the column is for calculate the AGB at the end.

coord <- read.csv(system.file("external", "Coord.csv",
  package = "BIOMASS", mustWork = TRUE
))

plot(coord[, c("Long", "Lat")], asp = 1)

We can see on the plot that the corner coordinates are spread.

kable(head(coord), digits = 3, row.names = FALSE, caption = "Head of the table coord")

In the table, we have the name of the plot, the coordinate Lat, Long (or another projected coordinates), and xRel, yRel, the relative coordinate for the points observed.

To manage the plots

Import the dataset and visualisation

The plot is referenced in the longitude latitude coordinate so you must have the package proj4 if you are in this situation. If you have projected coordinate, you can continue with the projCoord argument instead of longlat argument.

Correct the GPS coordinate

correct_plot <- correctCoordGPS(
  longlat = coord[, c("Long", "Lat")],
  coordRel = coord[, c("xRel", "yRel")],
  rangeX = c(0, 100), rangeY = c(0, 100), drawPlot = TRUE,
  maxDist = 10, rmOutliers = TRUE
)

str(correct_plot, max.level = 1)

The output of the function is a list with a data.frame corner it's the corner of the plot, polygon the spatial polygon, outliers the vector with the line number of the outliers and codeUTM the UTM code for the polygon.

The outliers are calculated by a measure of distance between the predicted points and the GPS points. If this distance is higher than the value of maxDist, the point is considered like outliers.

Numbering the corner

We have to number the corner of the plot, it is working if we have exactly 4 points for each plot, so we have to do the correctCoordGPS before if we have not the correct number of points.

coord_num <- numberCorner(
  projCoord = correct_plot$cornerCoords,
  plot = rep("NB1", 4),
  origin = c(F, F, F, T),
  clockWise = TRUE
)


plot(coord_num[, c("X", "Y")], asp = 1)
text(coord_num[, c("X", "Y")], labels = coord_num[, "corner"], pos = 2, offset = 0.2)

On the graph, you can noted than the corner number 1 the origin of the plot.

Cut the plot in multiple subplot

subplot <- cutPlot(
  projCoord = coord_num[, c("X", "Y")],
  plot = coord_num[, c("plot")],
  corner = coord_num[, c("corner")],
  gridsize = 25, dimX = 100, dimY = 100
)

kable(head(subplot))

Trees managements

Attribute the trees to the subplot

trees$subplot <- attributeTree(trees[, c("xRel", "yRel")], rep("NB1", nrow(trees)), subplot)

Calculate the AGB and spatialisation

trees$AGB <- computeAGB(trees$D, trees$WD, H = trees$H)

AGB <- summaryByPlot(trees$AGB, trees$subplot, drawPlot = TRUE, subplot = subplot)

print(AGB)

Attribute the trees to GPS coordinates

There is two maners to attribute the trees to GPS coordinates

TreeCoord <- attributeTreeCoord(
  xy = trees[, c("xRel", "yRel")],
  plot = trees$plot,
  coordAbs = subplot,
  dim = c(100, 100)
)

kable(head(TreeCoord), digits = 3, row.names = FALSE, caption = "Head of the table TreeCoord")

If you want to have in GPS (longitude/latitude) coordinates (need to install proj4 first) :

#TreeCoord <- as.data.frame( proj4::project(TreeCoord, proj = correct_plot$codeUTM, inverse = TRUE) )

kable(head(TreeCoord), digits = 3, row.names = FALSE, caption = "Head of the table TreeCoord")

If you want to have the GPS (longitude/latitude) coordinates without passing through all this step however you must use the numberCorner function:

coordAbs = data.frame(X = c(4.066923, 4.067865, 4.067842, 4.066905), Y = c(52.68883, 52.68877, 52.68793, 52.68783))

ncoordAbs = numberCorner(projCoord = coordAbs, 
                                plot = rep("NB1", 4), 
                                origin = c(TRUE, FALSE, FALSE, FALSE), 
                                clockWise = TRUE)

TreeCoord <- attributeTreeCoord(
  xy = trees[, c("xRel", "yRel")],
  plot = trees$plot,
  coordAbs = ncoordAbs,
  dim = c(100, 100)
)

kable(head(TreeCoord), digits = 3, row.names = FALSE, caption = "Head of the table TreeCoord")

BIOMASS documentation built on Sept. 29, 2023, 5:09 p.m.