joinRegenData: joinRegenData: summarizes seedling and sapling data

View source: R/joinRegenData.R

joinRegenDataR Documentation

joinRegenData: summarizes seedling and sapling data


This function combines seedling and sapling data collected in 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. Permanently Missing species tallies for species or whole plots have NAs. These are rare, have always been low canopy species initially recorded as shrubs, and 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. For the few plots with > 10 saplings of a given species in a microplot, their counts are included in the stocking index only if the average DBH of saplings measured is <=2.5 cm. This may underestimate the stocking index for those plots, but their index values are still way higher than most plots. Must run importData() or importCSV() first.


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



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 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


Allows you to filter on species growth form


Default. Returns all species, including low canopy species.


Returns canopy-forming species only


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


Calculates seedling and sapling densities based on different units.


Default. Returns seedling and sapling densities per microplot.


Returns seedling and sapling densities per square meter


Returns seedling and sapling densities per hectare


Returns densities per acre


Other arguments passed to function.


returns a dataframe with seedling and sapling densities, and stocking index metrics for each species observed per visit.


## Not run: 
# compile seedling and sapling data for all parks and all species in cycle 3
regen_data <- joinRegenData(canopyForm = 'all', from = 2014, to = 2017)

# compile regen data for only canopy-forming (default) and native species in SAGA for all years
SAGA_regen <- joinRegenData(park = 'SAGA', speciesType = 'native')

# compile only 1 microplot of data for ACAD native canopy-forming species for all but first year
ACAD_regen_m1 <- joinRegenData(park = 'ACAD', speciesType = 'native', numMicros = 1, from = 2007)

## End(Not run)

KateMMiller/forestNETN documentation built on April 29, 2023, 10:36 p.m.