sumQuadGuilds: sumQuadGuilds: summarizes quadrat species data by guilds

In KateMMiller/forestMIDN: Package for importing, joining and querying MIDN forest database tables

sumQuadGuilds: summarizes quadrat species data by guilds

Description

This function summarizes output from joinQuadData and calculates average cover and quadrat frequency for each guild. Average cover is corrected for number of quadrats sampled. Guilds are tree, shrub, forb, fern, and graminoid. If herbaceous guild is split, then cover of ferns does not overlap with cover of herbaceous. If herbaceous guild is not split, then cover of herbaceous guild includes fern and other herbaceous (but not graminoid) species cover. Only works for complete events, but does include plots where a few quadrats were not sampled. Note that this function does not account for changes in the indicator list over time. Sampleing in 2019, all woody species were sampled in quadrats, and will show a large increase in tree and shrub cover as a result. Seedling cover recorded in the quadrat seedlings tab are not summarized here. For more information on how the indicator list has changed over time in MIDN, refer to Table S17.4 in the Summary of Major Protocol Changes and Deviations document located in the Long-Term Forest Monitoring Protocol IRMA Project: https://irma.nps.gov/Datastore/Reference/Profile/2189101.

Usage

sumQuadGuilds(
  park = "all",
  from = 2007,
  to = as.numeric(format(Sys.Date(), "%Y")),
  QAQC = FALSE,
  panels = 1:4,
  locType = c("VS", "all"),
  speciesType = c("all", "native", "exotic", "invasive"),
  splitHerb = TRUE,
  ...
)

Arguments

park	Combine data from all parks or one or more parks at a time. Valid inputs: "all" Includes all parks in the network "APCO" Appomattox Court House NHP only "ASIS" Assateague Island National Seashore "BOWA" Booker T. Washington NM only "COLO" Colonial NHP only "FRSP" Fredericksburg & Spotsylvania NMP only "GETT" Gettysburg NMP only "GEWA" George Washington Birthplace NM only "HOFU" Hopewell Furnace NHS only "PETE" Petersburg NBP only "RICH" Richmond NB only "SAHI" Sagamore Hill NHS only "THST" Thomas Stone NHS only "VAFO" Valley Forge NHP only
from	Year to start analysis, ranging from 2007 to current year
to	Year to stop analysis, ranging from 2007 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
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.
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.
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 "invasive" Returns species on the Indicator Invasive List
splitHerb	TRUE/FALSE. If TRUE (Default), splits the herbaceous group into forb and fern. If FALSE, then resulting data frame will be summarized for tree, shrub, herbaceous, and graminoid guilds.
...	Other arguments passed to function.

Value

Returns a data frame with average quadrat cover, percent quadrat frequency and quadrat frequency count for tree, shrub/vine, herbaceous, and graminoid for each plot visit. Data are either summarized for all species, native only, exotic only, or invasive only.

Examples

## Not run: 
importData()

# compile invasive quad data for all parks and most recent survey. Keep ferns in with herbs
inv_guilds <- sumQuadGuilds(speciesType = 'invasive', from = 2015, to = 2018, splitHerb = FALSE)

# compile native quad data for more recent survey in BOWA, with ferns and forbs split in separate guilds
BOWA_guilds <- sumQuadGuilds(speciesType = 'native', from = 2015, to = 2018, splitHerb = TRUE)

## End(Not run)

KateMMiller/forestMIDN documentation built on Nov. 10, 2024, 11:54 p.m.