joinMicroShrubData: joinMicroShrubData: compiles shrub data collected in...

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

joinMicroShrubData: compiles shrub data collected in microplots

Description

This function compiles shrub data collected in the microplots. For microplot or species-level notes run the joinMicroNotes function. Note that in 2006, only 1 microplot was sampled. Note that from 2006 to 2009, stem tallies were recorded instead of species, but average percent cover is NA. For more information on how methods evolved for shrubs in NETN, refer to 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

joinMicroShrubData(
  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"),
  ...
)

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, for each microplot/species combination. "classes" Returns the text cover class definitions, with Txt prefix, for each microplot/ species combination. "averages" Returns only the plot-level average cover and percent frequency per species.
...	Other arguments passed to function.

Value

returns a dataframe with shrub data collected in microplots

Examples

## Not run: 
importData()
# native shrubs in MORR all years
native_shrubs <- joinMicroShrubData(park ='MORR', speciesType = 'native')

# all parks with exotic shrubs in most recent survey
exotic_shrubs <- joinMicroShrubData(from = 2015, to = 2018, speciesType = 'exotic')

## End(Not run)

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