joinAdditionalSpecies: joinAdditionalSpecies: compiles additional species data

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

joinAdditionalSpecies: compiles additional species data

Description

This function compiles the additional species collected during a timed 15-minute plot search. This is primarily an internal function used for QAQC and to generate the species lists for makeSppList(). Note that the timed search wasn't implemented until 2009, and only included species on the MIDN indicator list, which has also had additions over time. Sampleing in 2019, all woody species were included in the timed search.For more information about how the indicator list and protocol had changed ovre time, refer to the Summary of Major Protocol Changes document for the MIDN forest protocol located in the Long-Term Forest Monitoring Protocol IRMA Project: https://irma.nps.gov/Datastore/Reference/Profile/2189101.

Usage

joinAdditionalSpecies(
  park = "all",
  from = 2007,
  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")
)

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.
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 COLO-380-2018). 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

Value

Returns a dataframe with a row for each species recorded during the timed search per visit.

Examples

## Not run: 
importData()
# compile invasive species found in plot search in VAFO for all years
SARA_quads <- joinAdditionalSpecies(park = 'VAFO', speciesType = 'invasive')

# compile all species, including QAQC visits for parks in cycle 3
native_quads <- joinQuadSpecies(from = 2015, to = 2018, QAQC = TRUE)

## End(Not run)

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