joinMicroSaplings: joinMicroSaplings: compiles sapling data collected in...

View source: R/joinMicroSaplings.R

joinMicroSaplingsR Documentation

joinMicroSaplings: compiles sapling data collected in microplots


This function compiles sapling data collected in microplots, with a record for each sapling measured, and its DBH. If no saplings were observed, returns "None present" for ScientificName and 0 for Count. 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. For the few plots with > 10 saplings of a given species within a microplot, the DBH is an average of measured sapling DBHs, and the count is the number of saplings that were counted and not measured for DBH. In every case, the Count column is >1, and can be filtered out, if needed by filtering Count == 1. Must run importData 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,



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


Other arguments passed to function.


returns a dataframe with sapling data


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

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

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

## End(Not run)

KateMMiller/forestNETN documentation built on April 28, 2024, 8:48 a.m.