joinRegenData: joinRegenData: compiles seedling and sapling data

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

joinRegenData: compiles seedling and sapling data

Description

This function combines live seedling and sapling data collected in quadrats and microplots, and calculates the stocking index. Each row represents a species observed per visit. If no seedlings or saplings were observed, function returns "None present" for ScientificName and 0 for densities. If a record has a blank ScientificName and associated data, it means it's a missing value. These are rare, but mostly occur in data <2011. Note that the stocking index only includes saplings < 2.5cm DBH, but the sapling density returned is all saplings > 1cm and <10cm DBH. Must run importData first.

Usage

joinRegenData(
  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"),
  canopyForm = c("all", "canopy"),
  units = c("sq.m", "ha", "acres"),
  ...
)

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
canopyForm	Allows you to filter on species growth form "all" Default. Returns all species, including low canopy species. "canopy" Returns canopy-forming species only.
units	Calculates seedling and sapling densities based on different units. "sq.m" Default. Returns seedling and sapling densities and stocking index per square meter. "ha" Returns seedling and sapling densities per hectare and stocking index on McWilliams 100pt scale. "acres" Returns seedling and sapling densities per acre. Stocking index is same as sq.m.
...	Other arguments passed to function.

Value

returns a dataframe with seedling and sapling densities, stocking index.

Examples

## Not run: 
importCSV('./forest_csvs/')
# Compile seedling and sapling data for all parks and all species in most recent cycle,
# and only include seedlings >=15cm tall (default).
regen_data <- joinRegenData(canopyForm = 'all', from = 2015, to = 2018)

# compile regen data for canopy-forming (default), native species of all size classes in VAFO for all years
VAFO_regen <- joinRegenData(park = 'VAFO', speciesType = 'native')

# Compile seedling and sapling densities as stems/ha for all parks in most recent survey
regen_data <- joinRegenData(units = 'ha', from = 2015, to = 2018)

## End(Not run)

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