forestNETN

This package contains functions that import database views from the NETN forest SQL database and or CSVs in the NETN forest data package and provides functions to query, summarize, and visualize NETN forest data. The R package can be installed using pak::pkg_install('doi-nps/forestNETN'). Previous archived versions of this R package can be found at www.github.com/katemmiller/forestNETN

This package includes the following functions:

• importData: Import views from SQL database, either through local installation (default), or by connecting to the server.
• importCSV: Import views as CSVs from NETN forest data package.
• exportCSV: Export views as CSVs.
• exportNPSForVeg: Export data in a format that works with the NCRN/NPSForVeg R package.
• joinLocEvent: Query plot location and event data.
• joinAdditionalSpecies: Query additional species data.
• joinCWDData: Query CWD volume data.
• joinMicroSaplings: Query sapling data collected in microplots.
• joinMicroSeedlings: Query seedling data collected in microplots.
• joinMicroShrubData: Query shrub data collected in microplots.
• joinMicroNotes: Query notes recorded in microplots.
• joinRegenData: Query summarized seedling and sapling data.
• joinQuadData: Query quadrat character data.
• joinQuadSpecies: Query quadrat specis data.
• joinQuadNotes: Query notes recorded in quadrats.
• joinSoilLabData: Query soil chemistry data from the lab.
• joinSoilSampleData: Query soil sample data collected in the field.
• joinStandData: Query stand data, including stand height.
• joinStandDisturbance: Query stand disturbance data.
• joinTreeData: Query tree data.
• joinTreeConditions: Query tree condition data.
• joinTreeFoliageCond: Query tree foliage condition data.
• joinTreeVineSpecies: Query vines recorded on trees.
• joinTreeNotes: Query notes recorded for trees.
• joinVisitNotes: Query all notes recorded for each specified visit.
• plotTreeGrowth: Plot tree growth and mortality over time.
• plotTreeMap: Plot tree maps showing tree status, diameter and location within a specified plot.
• prepTaxa: reshapes the plant taxa table for easier joining.
• sumQuadGuilds: summarize quadrat species cover by guilds and native vs exotic.
• sumSapDBHDist: summarize sapling diameter at breast height distributions by 1cm size class.
• sumSpeciesList: generate a list of all species observed on a plot during a given visit.
• sumStrStage: assign structural stage for each plot following the NETN Ecological Integrity Scorecard.
• sumTreeDBHDist: summarize tree diameter at breast height distributions by 10cm size class.
• theme_FHM: custom ggplot2 theme for plotting NETN forest data.

The docs/ folder includes the R Markdown files that generate the forestNETN tutorial website. The index.Rmd generates the index.html, which is the file used by the gitpage for this repo.