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

In KateMMiller/forestNETN: Package for importing, joining and querying NETN 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 = 2006,
  to = as.numeric(format(Sys.Date(), "%Y")),
  QAQC = FALSE,
  panels = 1:4,
  locType = c("VS", "all"),
  eventType = c("complete", "all"),
  numMicros = 3,
  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 "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.
numMicros	Allows you to select 1, 2, or 3 microplots of data to summarize
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 cycle 3 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 SARA in 2019
SARA_spp <- sumSppList(park = 'SARA', from = 2019)

## End(Not run)

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