joinQuadSpecies: joinQuadSpecies: compiles quadrat species data

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

joinQuadSpecies: compiles quadrat species data

Description

This function combines quadrat species data with species names and allows you to filter on species types, park, years, and visit type. Note that the Shrub guild also includes woody vine species. Species-level notes are returned. For quadrat-specific notes, use the joinQuadNotes() function.

Usage

joinQuadSpecies(
  park = "all",
  from = 2006,
  to = as.numeric(format(Sys.Date(), "%Y")),
  QAQC = FALSE,
  panels = 1:4,
  locType = c("VS", "all"),
  eventType = c("complete", "all"),
  speciesType = c("all", "native", "exotic", "invasive"),
  valueType = c("all", "midpoint", "classes", "averages"),
  returnNoCover = FALSE,
  ...
)

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
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.
eventType	Allows you to include only complete sampling events or all sampling events "complete" Default. Only include sampling events for a plot that are complete. "all Include all plot events with a record in tblCOMN.Event, including plots missing most of the data associated with that event (eg ACAD-029.2010). This feature is currently hard-coded in the function.
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
valueType	Allows you to return cover class midpoints (numeric) or cover class ranges (text) "all" Default. Returns columns for midpoint and cover classes for each quad "midpoint" Default. Returns numeric cover class midpoints, with Pct prefix. "classes" Returns the text cover class definitions, with Txt prefix. "averages" Returns only the plot-level average cover and percent frequency.
returnNoCover	Logical. If FALSE (default), drops species with 0 includes species percent cover across all quadrats. Argument is helpful for generating a plot species list (use TRUE) or calculating average cover (use FALSE).
...	Other arguments passed to function.

Value

Returns a dataframe with a row for each species/visit combination for quadrat data

Examples

## Not run: 
importData()
# compile quadrat data for invasive species in SARA for all years
SARA_quads <- joinQuadSpecies(park = 'SARA', speciesType = 'invasive')

# compile native species only for all parks in cycle 3
native_quads <- joinQuadSpecies(speciesType = 'native', from = 2014, to = 2017)

## End(Not run)

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