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Modeling and Analysis","monthly_downloads":0,"total_dependent_repos":0,"total_dependent_packages":0,"readme":"---\noutput: github_document\n---\n\n\u003c!-- README.md is generated from README.Rmd. Please edit that file --\u003e\n\n```{r, include = FALSE}\nknitr::opts_chunk$set(\n  collapse = TRUE,\n  comment = \"#\u003e\",\n  fig.path = \"man/figures/README-\",\n  out.width = \"100%\"\n)\n```\n\n\u003cp align=\"center\"\u003e\n    \u003cimg src=\"man/figures/ITSMe_logo_RGB_nobg.jpg\" height=\"500\" \u003e\n\u003c/p\u003e\n\n\n## Goal\n\nThe goal of the **ITSMe** (Individual Tree Structural Metrics) R-package is to \nprovide easy to use functions to quickly obtain structural metrics from \nindividual tree point clouds and their respective quantitative structure models \n(QSMs). \n\n## Installation\n\nYou can install the development version of **ITSMe** from \n[GitHub](https://github.com/) with:\n\n``` r\n# install.packages(\"devtools\")\ndevtools::install_github(\"lmterryn/ITSMe\", build_vignettes = TRUE)\n```\nIf your installation is causing trouble try uninstalling and re-installing R and \nRStudio if possible.\n\n## Input\n\nThe functions are developed for tree point clouds obtained with TLS and QSMs \nobtained with [TreeQSM](https://github.com/InverseTampere/TreeQSM). The \nfunctions can, however, also be used on tree point clouds obtained \nfrom UAV-LS or MLS. You always need to keep in mind that the accuracy of \nthe metric measurements will depend on the quality of the data. \n\nThere is also an option to read QSMs generated by [RayCloudTools,\nRCT](https://github.com/csiro-robotics/raycloudtools). But at the moment the\nfunctions to calculate specific structural metrics only work for QSMs generated\nby treeQSM. However, several metrics such as the total tree volume can be\ndirectly extracted from the RCT QSM after reading it in using **ITSMe**.\n\n## Individual tree structural metrics \n\nStructural metrics that can be calculated with the **ITSMe** package are \nsummarised in the tables below.\n\n### Basic structural metrics\n\n| structural metric             | function name                     | input              |\n| ------------------------------|:---------------------------------:|-------------------:|\n| tree position                 | tree_position_pc, dbh_pc, dbh_qsm | point cloud        |\n| diameter at breast height (m) | dbh_pc, dbh_qsm                   | point cloud, QSM   |\n| diameter above buttresses (m) | dab_pc                            | point cloud        |\n| tree height (m)               | tree_height_pc, tree_height_qsm   | point cloud, QSM   |\n| projected area (m$^{2}$)      | projected_area_pc                 | point cloud        |\n| alpha volume (m$^{3}$)        | alpha_volume_pc                   | point cloud        |\n| tree volume (m$^{3}$)         | tree_volume_qsm                   | QSM                |\n| trunk volume (m$^{3}$)        | trunk_volume_qsm                  | QSM                |\n| total branch volume (m$^{3}$) | total_branch_volume_qsm           | QSM                |\n| total branch length (m)       | total_branch_length_qsm           | QSM                |\n| total cylinder length (m)     | total_cyl_length_qsm              | QSM                |\n\n\n### Structural metrics from Terryn et al. (2020)\n\nThese are the metrics defined in \n[Terryn et al. (2020)](https://doi.org/10.1016/j.isprsjprs.2020.08.009) \nwhich were adapted from \n[Akerblom et al. (2017)](https://doi.org/10.1016/j.rse.2016.12.002) \nexcept for the branch angle ratio and the relative volume ratio. Definitions of \nthe metrics can be found in the help files of the functions and the papers of \nTerryn et al. (2020) and Akerblom et al. (2017). Normalisation according to \nTerryn et al. (2020) as well as Akerblom et al. (2017) is possible through the \nnormalisation parameter included in the functions of the metrics that were \nadapted by Terryn et al. (2020). If the tree point cloud is provided along with \nthe TreeQSM in the functions, dbh and tree height values are based on the point \nclouds rather than the QSMs. When the buttress parameter is indicated \"TRUE\" the \ndiameter above buttresses instead of the diameter at breast height is used.\n\n\n| structural metric                         | function name                     | input              |\n| ------------------------------------------|:---------------------------------:|-------------------:|\n| stem branch angle (degrees)               | stem_branch_angle_qsm             | QSM                |\n| stem branch cluster size                  | stem_branch_cluster_size_qsm      | QSM                |\n| stem branch radius (-/m)                  | stem_branch_radius_qsm            | QSM (+point cloud) |\n| stem branch length (-/m)                  | stem_branch_length_qsm            | QSM (+point cloud) |\n| stem branch distance (-/m)                | stem_branch_distance_qsm          | QSM (+point cloud) |\n| dbh tree height ratio                     | dbh_height_ratio_qsm              | QSM (+point cloud) |\n| dbh tree volume ratio (m$^{-2}$)          | dbh_volume_ratio_qsm              | QSM (+point cloud) |\n| volume below 55                           | volume_below_55_qsm               | QSM                |\n| cylinder length volume ratio (m$^{-2}$)   | cylinder_length_volume_ratio_qsm  | QSM                |\n| shedding ratio                            | shedding_ratio_qsm                | QSM                |\n| branch angle ratio                        | branch_angle_ratio_qsm            | QSM                |\n| relative volume ratio                     | relative_volume_ratio_qsm         | QSM                |\n| crown start height                        | crown_start_height_qsm            | QSM (+point cloud) |\n| crown height                              | crown_height_qsm                  | QSM (+point cloud) |\n| crown evenness                            | crown_evenness_qsm                | QSM                |\n| crown diameter crown height ratio         | crown_diameterheight_ratio_qsm    | QSM (+point cloud) |\n| dbh minimum tree radius ratio             | dbh_minradius_ratio_qsm           | QSM (+point cloud) |\n\n## Examples\nFor complete workflows, have a look at the **ITSMe** vignette with: \n```{r eval = FALSE}\nvignette(\"ITSMe\")\n```\n\nCalculating the diameter at breast height versus the diameter above buttresses \nof a tree:\n```{r eval = FALSE}\nlibrary(ITSMe)\n# Read the point cloud file from the Specified path to the tree point cloud file\npc_tree \u003c- read_tree_pc(path = \"path/to/point/cloud.txt\")\n# Use dbh_pc function with default parameters and plot the fit\nout_dbh \u003c- dbh_pc(pc = pc_tree, plot = TRUE)\n# Access the dbh, residual and fdbh values from the output list\ndbh \u003c- out_dbh$dbh\nresidual_dbh \u003c- out_dbh$R2\nfdbh \u003c- out_dbh$fdbh\n# Use dab_pc function with default parameters and plot the fit\nout_dab \u003c- dab_pc(pc = pc_tree, plot = TRUE)\n# Access the dab, residual and fdab values from the output list\nddab \u003c- out_dab$dab\nresidual_dab \u003c- out_dab$R2\nfdab \u003c- out_dab$fdab\n```\n\n\u003cp align=\"center\"\u003e\n    \u003cimg src=\"man/figures/diameter_slice_example_butt.jpeg\" height=\"500\" \u003e\n\u003c/p\u003e\n\n\u003cp align=\"center\"\u003e\n    \u003cimg src=\"man/figures/dab_example.jpeg\" height=\"500\" \u003e\n\u003c/p\u003e\n\n\nCalculating the stem branch distance of a TreeQSM:\n```{r eval = FALSE}\nlibrary(ITSMe)\n# Read the TreeQSM file from the Specified path to the TreeQSM file\nqsm \u003c- read_tree_qsm(path = \"path/to/QSM.mat\")\n# Use stem_branch_distance_qsm function\nsbd \u003c- stem_branch_distance_qsm(\n  cylinder = qsm$cylinder,\n  treedata = qsm$treedata, normalisation = \"dbh\"\n)\n# Using the point cloud information for more accurate dbh normalisation\npc_tree \u003c- read_tree_pc(path = \"path/to/point/cloud.txt\")\nsbd \u003c- stem_branch_distance_qsm(\n  cylinder = qsm$cylinder,\n  treedata = qsm$treedata, normalisation = \"dbh\",\n  pc = pc_tree, buttress = TRUE\n)\n```\n\nCalculating a summary data.frame with the basic structural metrics \n(tree position, dbh, dab, tree height, projected area, 3D alpha volume) that \ncan be  obtained from individual tree point clouds for all point clouds in a \nspecific folder: \n```{r eval = FALSE}\nlibrary(ITSMe)\n# Run summary function with default parameter settings\nbasic_summary \u003c- summary_basic_pointcloud_metrics(\n  PCs_path = \"path/to/point/cloud/folder/\",\n  OUT_path = \"path/to/output/folder/\")\n```\nIf you set the plot parameter TRUE and provide an OUT_path, this function saves \na summary figure for each tree: \n\n\u003cp align=\"center\"\u003e\n    \u003cimg src=\"man/figures/summary.jpeg\" height=\"500\" \u003e\n\u003c/p\u003e\n\nCalculating a summary data.frame with the structural metrics defined by Terryn\net al. (2020) for all TreeQSMs in a specific folder: \n```{r eval = FALSE}\nlibrary(ITSMe)\n# Run summary function with default parameter settings\nqsm_summary \u003c- summary_qsm_metrics(\n  QSMs_path = \"path/to/QSM/folder/\",\n  version = \"2.3.0\",\n  PCs_path = \"path/to/point/cloud/folder/\",\n  extension = \".txt\"\n)\n```\n","funding_links":[],"readme_doi_urls":["https://doi.org/10.1016/j.isprsjprs.2020.08.009","https://doi.org/10.1016/j.rse.2016.12.002"],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":[],"project_url":"https://ost.ecosyste.ms/api/v1/projects/303791","html_url":"https://ost.ecosyste.ms/projects/303791"}