View source: R/addStratumObservations.R
addStratumObservations | R Documentation |
Adds stratum observation records to a VegX object from a data table where rows are stratum observations.
addStratumObservations( target, x, mapping, methods, stratumDefinition, date.format = "%Y-%m-%d", missing.values = c(NA, ""), verbose = TRUE )
target |
The initial object of class |
x |
A data frame where each row corresponds to one stratum observation. Columns can be varied. |
mapping |
A named list whose elements are strings that correspond to column names in
|
methods |
A list measurement methods for |
stratumDefinition |
An object of class |
date.format |
A character string specifying the input format of dates (see |
missing.values |
A character vector of values that should be considered as missing observations/measurements. |
verbose |
A boolean flag to indicate console output of the data integration process. |
Missing value policy:
Missing plotName
, obsStartDate
or stratumName
values are interpreted as if the previous non-missing value has to be used to define plot observation.
Missing subPlotName
values are interpreted in that observation refers to the parent plotName.
Missing measurements are simply not added to the Veg-X document.
The modified object of class VegX
.
Wiser SK, Spencer N, De Caceres M, Kleikamp M, Boyle B & Peet RK (2011). Veg-X - an exchange standard for plot-based vegetation data
Other add functions:
addAggregateOrganismObservations()
,
addCommunityObservations()
,
addIndividualOrganismObservations()
,
addPlotGeometries()
,
addPlotLocations()
,
addPlotObservations()
,
addSiteCharacteristics()
,
addSiteObservations()
,
addSurfaceCoverObservations()
,
addTaxonBySiteData()
# Load source data data(mokihinui) # Define mapping mapping = list(plotName = "Plot", obsStartDate = "PlotObsStartDate", stratumName = "Tier", lowerLimitMeasurement = "TierLower", upperLimitMeasurement = "TierUpper", cover = "CoverClass") # Define cover scale coverscale = defineOrdinalScaleMethod(name = "Recce cover scale", description = "Recce recording method by Hurst/Allen", subject = "plant cover", citation = "Hurst, JM and Allen, RB. (2007) The Recce method for describing New Zealand vegetation – Field protocols. Landcare Research, Lincoln.", codes = c("P","1","2","3", "4", "5", "6"), quantifiableCodes = c("1","2","3", "4", "5", "6"), breaks = c(0, 1, 5, 25, 50, 75, 100), midPoints = c(0.05, 0.5, 15, 37.5, 62.5, 87.5), definitions = c("Presence", "<1%", "1-5%","6-25%", "26-50%", "51-75%", "76-100%")) # Define strata strataDef = defineMixedStrata(name = "Recce strata", description = "Standard Recce stratum definition", citation = "Hurst, JM and Allen, RB. (2007) The Recce method for describing New Zealand vegetation – Field protocols. Landcare Research, Lincoln.", heightStrataBreaks = c(0, 0.3,2.0,5, 12, 25, 50), heightStrataNames = paste0("Tier ",1:6), categoryStrataNames = "Tier 7", categoryStrataDefinition = "Epiphytes") # Create new Veg-X document with stratum observations x = addStratumObservations(newVegX(), moki_str, mapping = mapping, methods = list(lowerLimitMeasurement = "Stratum height/m", upperLimitMeasurement = "Stratum height/m", cover=coverscale), stratumDefinition = strataDef) # Examine results head(showElementTable(x, "stratumObservation"))
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.