tree_metrics function

Tree Metrics

Calculates tree metrics from a QSM

tree_metrics(cylinder, verify = TRUE)

Arguments

• cylinder: QSM cylinder data frame
• verify: Verify QSM topology. Defaults to TRUE. If verify = TRUE, only topologically connected structures (e.g. a whole a tree or an individual branch) are eligible to run. This ensures all metrics are correct and verified. If verify = FALSE, the metrics are run, but not verified. This is strongly discouraged, but can enable the calculation of tree metrics on topologically disconnected structures.

Returns

Returns a list of tree metric data frames and a synthetic point cloud

Details

Calculates detailed tree, branch, and segment metrics from a QSM. Valid inputs require a connected QSM, which can be a whole tree or an individual branch. The outputs include all of the standard outputs from TreeQSM, and also additional variables, including, but not limited to, growth length, reverse branch order, branch segment or node relationships, and distances from twigs and the base of the tree, across various distribution metrics. Also included is a simulated point cloud of the tree, based on the QSM cylinder radii. When corrected with Real Twig, this allows for the testing and validation of point cloud diameter overestimation throughout the tree.

Examples

## TreeQSM Processing Chain
file <- system.file("extdata/QSM.mat", package = "rTwig")
cylinder <- import_treeqsm(file)$cylinder
cylinder <- update_cylinders(cylinder)
metrics <- tree_metrics(cylinder)
names(metrics)

## SimpleForest Processing Chain
file <- system.file("extdata/QSM.csv", package = "rTwig")
cylinder <- read.csv(file)
cylinder <- update_cylinders(cylinder)
metrics <- tree_metrics(cylinder)
names(metrics)

References

\insertRef TreeQSMrTwig

\insertRef growth_parameter1rTwig

\insertRef growth_parameter2rTwig

\insertRef treegraph2rTwig

\insertRef path_fractionrTwig