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

View source: R/sumSpeciesList.R

sumSpeciesListR Documentation

sumSpeciesList: summarize a species list for each plot visit


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


  park = "all",
  from = 2006,
  to = as.numeric(format(Sys.Date(), "%Y")),
  panels = 1:4,
  locType = c("VS", "all"),
  eventType = c("complete", "all"),
  numMicros = 3,
  speciesType = c("all", "native", "exotic", "invasive"),



Combine data from all parks or one or more parks at a time. Valid inputs:


Includes all parks in the network


Acadia NP only


Marsh-Billings-Rockefeller NHP only


Minute Man NHP only


Morristown NHP only


Roosevelt-Vanderbilt NHS only


Saint-Gaudens NHS only


Saratoga NHP only


Weir Farm NHS only


Year to start analysis, ranging from 2006 to current year


Year to stop analysis, ranging from 2006 to current year


Allows you to remove or include QAQC events.


Default. Only returns visits that are not QAQC visits


Returns all visits, including QAQC visits


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.


Allows you to only include plots that are part of the GRTS sample design or include all plots, such as deer exclosures.


Only include plots that are part of the Vital Signs GRTS sample design


Include all plots, such as plots in deer exclosures or test plots.


Allows you to include only complete sampling events or all sampling events


Default. Only include sampling events for a plot that are complete.


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.


Allows you to select 1, 2, or 3 microplots of data to summarize


Allows you to filter on native, exotic or include all species.


Default. Returns all species.


Returns native species only


Returns exotic species only


Returns species on the Indicator Invasive List


Other arguments passed to function.


Returns a dataframe with species list for each plot.


## Not run: 

# 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$present <- ifelse($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 April 28, 2024, 8:48 a.m.