joinTreeConditions: joinTreeConditions: compiles live and dead tree conditions

In KateMMiller/forestNETN: Package for importing, joining and querying NETN forest database tables

joinTreeConditions: compiles live and dead tree conditions

Description

This function compiles tree condition data into a wide format with one row per tree visit and a column for each foliage condition type. Must run importData first. Abandoned plots and incomplete visits are excluded from function.

Usage

joinTreeConditions(
  park = "all",
  from = 2006,
  to = as.numeric(format(Sys.Date(), "%Y")),
  QAQC = FALSE,
  locType = c("VS", "all"),
  panels = 1:4,
  status = c("all", "active", "live", "dead"),
  speciesType = c("all", "native", "exotic", "invasive"),
  canopyPosition = c("all", "canopy"),
  dist_m = NA
)

Arguments

park	Combine data from all parks or one or more parks at a time. Valid inputs: "all" Includes all parks in the network "ACAD" Acadia NP only "MABI" Marsh-Billings-Rockefeller NHP only "MIMA" Minute Man NHP only "MORR" Morristown NHP only "ROVA" Roosevelt-Vanderbilt NHS only "SAGA" Saint-Gaudens NHS only "SARA" Saratoga NHP only "WEFA" Weir Farm NHS only
from	Year to start analysis, ranging from 2006 to current year
to	Year to stop analysis, ranging from 2006 to current year
QAQC	Allows you to remove or include QAQC events. FALSE Default. Only returns visits that are not QAQC visits TRUE Returns all visits, including QAQC visits
locType	Allows you to only include plots that are part of the GRTS sample design or include all plots, such as deer exclosures "VS" Only include plots that are part of the Vital Signs GRTS sample design "all" Include all plots, such as plots in deer exclosures or test plots.
panels	Allows you to select individual panels from 1 to 4. Default is all 4 panels (1:4). If more than one panel is selected, specify by c(1, 3), for example.
status	Filter by live, dead, or all. Acceptable options are: "all" Default. Includes all trees with any status, including excluded or missing. "active" Includes all trees with an active monitoring status, including "DF". "live" Live trees only "dead" Dead trees only. Note that prior to 2012, status was not assessed for dead trees and will be NA.
speciesType	Allows you to filter on native, exotic or include all species. "all" Default. Returns all species. "native" Returns native species only "exotic" Returns exotic species only
canopyPosition	Allows you to filter on tree crown class "all" Returns all canopy positions "canopy" Returns only dominant, codominant, and intermediate crown classes. Since only live trees are assigned crown classes, this also only returns live trees.
dist_m	Filter trees by a distance that is less than or equal to the specified distance in meters of the tree to the center of the plot. If no distance is specified, then all trees will be selected. For example, to select an area of trees that is 100 square meters in area, use a distance of 5.64m.

Value

returns a wide data frame with one row for each tree visit and tree conditions as columns. Note that vines in the crown and on the bole return the number of species in each condition. Remaining conditions are either 0 for absent or 1 for present. Only trees that are actively assessed for status are returned (e.g., trees with DF and DC status are not returned). If status = 'dead' is specified, only plots with dead trees are returned. Same goes for live trees, although fewer plots are affected. Status codes, such as VIN_B, CAVL, CAVS, which were added to the protocol later will return NA for years they were not assessed, otherwise codes are 0/1. The PM column indicates the tree status is missing for that visit.

Examples

## Not run: 
importData()
# compile tree condition data for live trees in all parks in cycle 3, excluding QAQC visits
trcond_c3 <- joinTreeConditions(from = 2014, to = 2017, status = 'live', QAQC = FALSE)

# compile tree condition for ROVA in 2019, including QAQC visits for active trees
ROVA_trees <- joinTreeConditions(park = "ROVA", from = 2019, to = 2019, status = 'active',
                                 QAQC = TRUE)

## End(Not run)

KateMMiller/forestNETN documentation built on Nov. 11, 2024, 6:07 a.m.