sumSpeciesList: sumSpeciesList: summarize a species list for each plot visit

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

sumSpeciesList: summarize a species list for each plot visit

Description

This function summarizes all species data collected in a plot visit, including live trees, microplots, quadrats, and additional species lists.

Usage

sumSpeciesList(
  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
...	Other arguments passed to function.

Value

Returns a dataframe with species list for each plot.

Examples

## Not run: 
importData()

# Compile number of invasive species found per plot in most recent survey for all parks
inv_spp <- sumSppList(speciesType = 'invasive', from = 2015, to = 2018)
inv_spp$present <- ifelse(is.na(inv_spp$ScientificName), 0, 1)
num_inv_per_plot <- inv_spp %>% group_by(Plot_Name) %>% summarize(numspp = sum(present, na.rm = T))

# Compile species list for FRSP in 2019
FRSP_spp <- sumSppList(park = 'FRSP', from = 2019, speciesType = 'all')


## End(Not run)

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