joinQuadSpecies: joinQuadSpecies: compiles quadrat species data

View source: R/joinQuadSpecies.R

joinQuadSpeciesR Documentation

joinQuadSpecies: compiles quadrat species data


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.


  park = "all",
  from = 2006,
  to = as.numeric(format(Sys.Date(), "%Y")),
  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,



Combine data from all parks or one or more parks at a time. Valid inputs:


Includes all parks in the network


Acadia NP only


Marsh-Billings-Rockefeller NHP only


Minute Man NHP only


Morristown NHP only


Roosevelt-Vanderbilt NHS only


Saint-Gaudens NHS only


Saratoga NHP only


Weir Farm NHS only


Year to start analysis, ranging from 2006 to current year


Year to stop analysis, ranging from 2006 to current year


Allows you to remove or include QAQC events.


Default. Only returns visits that are not QAQC visits


Returns all visits, including QAQC visits


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.


Allows you to only include plots that are part of the GRTS sample design or include all plots, such as deer exclosures.


Only include plots that are part of the Vital Signs GRTS sample design


Include all plots, such as plots in deer exclosures or test plots.


Allows you to include only complete sampling events or all sampling events


Default. Only include sampling events for a plot that are complete.


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.


Allows you to filter on native, exotic or include all species.


Default. Returns all species.


Returns native species only


Returns exotic species only


Returns species on the Indicator Invasive List


Allows you to return cover class midpoints (numeric) or cover class ranges (text)


Default. Returns columns for midpoint and cover classes for each quad


Default. Returns numeric cover class midpoints, with Pct prefix.


Returns the text cover class definitions, with Txt prefix.


Returns only the plot-level average cover and percent frequency.


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.


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


## Not run: 
# 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 April 1, 2024, 11:49 p.m.