joinQuadSpecies: joinQuadSpecies: compiles quadrat species data

Description Usage Arguments Value Examples

View source: R/joinQuadSpecies.R

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

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joinQuadSpecies(
  park = "all",
  from = 2006,
  to = 2021,
  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.

"classes"

Returns the text cover class definitions, with Txt prefix.

"averages"

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

Value

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

Examples

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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)

KateMMiller/forestNETN documentation built on May 30, 2021, 6:39 a.m.