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Modeling and Analysis","monthly_downloads":669,"total_dependent_repos":0,"total_dependent_packages":0,"readme":"---\noutput: github_document\n---\n\n```{r include=FALSE}\nlibrary(dplyr)\nlibrary(tidyr)\nlibrary(lemon)\nlibrary(allometric)\n\nknitr::opts_chunk$set(\n  comment = \"#\u003e\"\n)\n\ninstall_models()\nallometric_models \u003c- load_models()\n\nn_models \u003c- nrow(allometric_models)\nn_pubs \u003c- length(unique(allometric_models$pub_id, na.rm = T))\n\ncontinents \u003c- read.csv(system.file(\"continents.csv\", package = \"allometric\"),\n  na.strings = \"\")\n\nsumm_categories \u003c- data.frame(\n  category = c(\n    rep(\"biomass component\", 8),\n    rep(\"other\", 6)\n  ),\n  model_type = c(\n    \"bark biomass\", \"branch biomass\", \"foliage biomass\", \"foliage ratio\",\n    \"branch ratio\", \"root biomass\", \"stem biomass\", \" biomass\", \"bark ratio\",\n    \"stem diameter\", \"stem ratio\", \"crown ratio\", \"stump diameter\",\n    \"VBAR\"\n  )\n)\n\nmodel_summ \u003c- allometric_models %\u003e%\n  unnest_models(\"country\") %\u003e%\n  left_join(continents, by = c(\"country\" = \"iso_3166_1_a2\")) %\u003e%\n  distinct(id, model_type, continent) %\u003e%\n  group_by(model_type, continent) %\u003e%\n  summarise(n=n()) %\u003e%\n  merge(summ_categories, all.x=T)\n\nmodel_summ[is.na(model_summ$category), 'category'] \u003c- model_summ$model_type[is.na(model_summ$category)]\n\nmodel_summ.fmt \u003c- model_summ %\u003e%\n  group_by(category, continent) %\u003e%\n  summarise(n = sum(n)) %\u003e%\n  tidyr::pivot_wider(names_from = \"continent\", values_from = \"n\") %\u003e%\n  replace_na(list(AS = 0, `NA` = 0, EU = 0, AF = 0, OC = 0, SA = 0))\n\nmodel_summ.fmt \u003c- bind_rows(\n  list(\n    model_summ.fmt %\u003e% filter(category != \"other\"),\n    model_summ.fmt %\u003e% filter(category == \"other\")\n  )\n)\n\n```\n\n# allometric \u003cpicture\u003e\u003csource media=\"(prefers-color-scheme: dark)\" srcset=\"https://raw.githubusercontent.com/allometric/allometric/master/man/figures/allo2-darkmode.svg\"\u003e\u003csource media=\"(prefers-color-scheme: light)\" srcset=\"https://raw.githubusercontent.com/allometric/allometric/master/man/figures/allo2.svg\"\u003e\u003cimg alt=\"Isometric logo of a tree\" height=\"210\" width=\"165\" align=\"right\"\u003e\u003c/picture\u003e\n\n\u003c!-- badges: start --\u003e\n[![R-CMD-check](https://github.com/allometric/allometric/actions/workflows/check-standard.yaml/badge.svg)](https://github.com/allometric/allometric/actions/workflows/check-standard.yaml)\n`r badger::badge_devel(\"allometric/allometric\", \"blue\")`\n[![codecov](https://codecov.io/gh/allometric/allometric/branch/master/graph/badge.svg?token=3V5KUFMO2X)](https://app.codecov.io/gh/allometric/allometric)\n[![Static Badge](https://img.shields.io/badge/YouTube-red)](https://www.youtube.com/playlist?list=PLP5y0kzuWunWiUHpgoppVlTC_c2KYlrRK)\n\u003c!-- badges: end --\u003e\n\n`allometric` is an R package for predicting tree attributes with allometric \nmodels. Thousands of allometric models exist in the scientific and technical\nforestry literature, and `allometric` is a platform for archiving and using this\nvast array of models in a robust and structured format. Get started by going to\nthe [Installation](#installation) section or the [documentation website](https://allometric.org).\n\n`allometric` also provides a structured language for adding models to the\npackage. If you are interested in helping the developer in this process please\nrefer to the [Contributing a Model](https://allometric.org/articles/installing_a_model.html) vignette.\n\nIn total **`allometric` contains `r n_models` models across `r n_pubs` publications**,\nrefer to the [Current Status](#current-status) for a more complete view of\navailable models.\n\n## Installation\n\nCurrently `allometric` can be installed via CRAN:\n\n```{r eval=FALSE}\ninstall.packages(\"allometric\")\n```\n\nFor the latest release version, please install directly from GitHub using\n`devtools`:\n\n```{r eval=FALSE}\ndevtools::install_github(\"allometric/allometric\")\n```\n\nBefore beginning, make sure to install the models locally by running\n\n```{r eval=F}\nlibrary(allometric)\ninstall_models()\n```\n\nThis installs all available models from the public [models](https://github.com/allometric/models) repository.\n\nFinally, load the models using the `load_models()` function into a variable:\n\n```{r}\nallometric_models \u003c- load_models()\nhead(allometric_models)\n```\n\n## Finding a Model\n\n`allometric_models` is a `tibble` dataframe. Each row represents one \nallometric model with various attributes. Users interact with this table the\nway they would with any other `tibble`.\n\nFor example, we can use `dplyr` to filter this table to find models for\nanalysis. Let's say I am interested in finding stem volume models for\n*Tsuga heterophylla*. First, let us filter the `model_type` to include only\nstem volume models\n\n```{r}\nstemvol_models \u003c- allometric_models %\u003e%\n  filter(model_type == \"stem volume\")\n\nstemvol_models\n```\n\nNext, we can filter to include only *Tsuga heterophylla* using a special\nspecifier called `Taxon` that enables rigorous searching of species:\n\n```{r}\ntsuga_het_taxon \u003c- Taxon(\n  family = \"Pinaceae\", genus = \"Tsuga\", species = \"heterophylla\"\n)\n\ntsuga_vol_models \u003c- stemvol_models %\u003e%\n  filter(purrr::map_lgl(taxa, ~ tsuga_het_taxon %in% .))\n\ntsuga_vol_models\n```\n\nWe can see that we have `r nrow(tsuga_vol_models)` models to choose from. Let's\nselect the model from the publication `poudel_2019`\n\n```{r}\ntsuga_poudel \u003c- tsuga_vol_models %\u003e% select_model(\"6142693f\")\n```\n\nThis example is very basic, and more complex search examples can be found in\nthe [`load_models()`](https://allometric.org/reference/load_models.html)\ndocumentation. Models can be searched not only by their taxonomic information,\nbut also the types of measurements the models require, their geographic region,\nand other attributes. We highly encourage users review the linked examples for\nproduction use of `allometric`.\n\n## Using the Model\n\n`tsuga_poudel` now represents an allometric model that can be used for \nprediction. We must next figure out how to use the model.\n\nUsing the standard output of `tsuga_poudel` we obtain a summary of the model form,\nthe response variable, the needed covariates and their units, a summary of\nthe model descriptors (i.e., what makes the model unique within the\npublication), and estimates of the parameters.\n\n```{r}\ntsuga_poudel\n```\n\nWe can see from the `Model Call` section that `tsuga_poudel` will require\ntwo covariates called `dsob`, which refers to diameter outside bark at\nbreast height, and `hst`, the height of the main stem. `allometric` uses a\nvariable naming system to determine the names of response variables and\ncovariates (refer to the [Variable Naming System vignette](https://allometric.org/articles/variable_naming_system.html)).\n\nUsing the `predict()` method we can easily use the function as defined\nby providing values of these two covariates.\n\n```{r eval=T}\npredict(tsuga_poudel, 12, 65)\n```\n\nor we can use the prediction function with a data frame of values\n\n```{r}\nmy_trees \u003c- data.frame(dias = c(12, 15, 20), heights = c(65, 75, 100))\npredict(tsuga_poudel, my_trees$dias, my_trees$heights)\n```\n\nor even using the convenience of `dplyr`\n\n```{r}\nmy_trees %\u003e%\n  mutate(vols = predict(tsuga_poudel, dias, heights))\n```\n\nThe above example is a very basic use case for `allometric`. Please refer to the\n[Common Inventory Use Cases vignette](https://allometric.org/articles/inventory_example.html)\nfor more complex examples.\n\n## Current Status\n\nIn total **`allometric` contains `r n_models` models across `r n_pubs` publications**.\n\n```{r echo=FALSE}\nknitr::kable(model_summ.fmt, format = \"markdown\")\n```\n\n## How Can I Help?\n\n`allometric` is a monumental undertaking, and already several people have come\nforward and added hundreds of models. There are several ways to help out. The\nfollowing list is ranked from the least to most difficult tasks.\n\n1. [Add missing publications as an Issue](https://github.com/allometric/models/issues/new?assignees=brycefrank\u0026labels=add+publication\u0026projects=\u0026template=add-models-from-a-publication.md\u0026title=%5BInsert+Author-Date+Citation%5D). \nWe always need help *finding publications* to add. If you know of a publication that is missing, feel free to add it as an Issue and we will eventually install the models contained inside.\n2.  [Find source material for a publication](https://github.com/allometric/models/labels/missing%20source).\nSome publications are missing their original source material. Usually these are very old legacy publications. If you know where a publication might be found, or who to contact, leave a note on any of these issues.\n3. [Help us digitize publications](https://github.com/allometric/models/labels/digitization%20needed). \nWe always need help *digitizing legacy reports*, at this link you will find a list of reports that need manual digitization. These can be handled by anyone with Excel and a cup of coffee.\n4. [Learn how to install and write models](https://allometric.org/articles/installing_a_model.html). \nMotivated users can learn how to install models directly using the package functions and git pull requests. Users comfortable with R and git can handle this task.\n\nOther ideas? Contact bfrank70@gmail.com to help out.\n\n## Next Steps\n\nThe following vignettes available on the [package website](https://allometric.org/index.html)\nprovide information to two primary audiences.\n\nUsers interested in finding models for analysis will find the following\ndocumentation most useful:\n\n- [Common Inventory Use Cases](https://allometric.org/articles/inventory_example.html)\n\nUsers interested in **contributing models** to the package will find these vignettes the most useful:\n\n- [Contributing a Model](https://allometric.org/articles/installing_a_model.html)\n- [Describing a Model with Descriptors](https://allometric.org/articles/descriptors.html)\n- [Variable Naming System](https://allometric.org/articles/variable_naming_system.html)\n","funding_links":[],"readme_doi_urls":[],"works":{},"citation_counts":{},"total_citations":0,"keywords_from_contributors":["reporting","selection"],"project_url":"https://ost.ecosyste.ms/api/v1/projects/46852","html_url":"https://ost.ecosyste.ms/projects/46852"}