qsm2r is an R package to read in and analyze QSMs (quantitative structure models) created in Matlab using TreeQSM. QSMs stored in *.mat files can be read in using readQSM(). After changing the cylinder structure of QSMs, the updateQSM() function can be used to update the remaining data in the QSMs (e.g. branch data, crown statistics, ...) based on the edited data. Various summaries of the cylinder and branch data can be derived using a set of summary_cylinder_*() and summary_branch_*() functions. Different types of pruning treatments can be simulated using several pruning_*() functions.
To install the package from github, the package remotes is required.
# install package from github
remotes::install_github("zoeschindler/qsm2r")# load package
library(qsm2r)
# load qsm
file_path <- system.file("extdata", "QSM_Juglans_regia_M.mat", package="qsm2r")
qsm <- readQSM(file_path)
# get summary
print(qsm)
# show qsm
plot(qsm)
# pruning
qsm <- pruning_conventional(qsm, threshold_m = 3, method = "height", remove = TRUE)
# show pruned qsm
plot(qsm)
# check if branch & overview are up-to-date with cylinder
checkQSM(qsm)
# update branch & overview from cylinder
qsm <- updateQSM(qsm)
# check if branch & overview are up-to-date with cylinder
checkQSM(qsm)
# get qsm summary
print(qsm)Author: Zoe Schindler, Chair of Forest Growth and Dendroecology, University of Freiburg