addAggregateOrganismObservations: Add aggregate organism observation records
In miquelcaceres/VegX: Vegetation data in Veg-X

View source: R/addAggregateOrganismObservations.R

addAggregateOrganismObservations

R Documentation

Add aggregate organism observation records

Description

Adds aggregate organism observation records to a VegX object from a data frame where rows are observation records.

Usage

addAggregateOrganismObservations(
  target,
  x,
  mapping,
  methods = list(),
  stratumDefinition = NULL,
  date.format = "%Y-%m-%d",
  missing.values = c(NA, "0", ""),
  verbose = TRUE
)

Arguments

`target`	The initial object of class `VegX` to be modified
`x`	A data frame where each row corresponds to one aggregate organism observation. Columns can be varied.
`mapping`	A named list whose elements are strings that correspond to column names in `x`. Names of the list should be: `plotName` - A string identifying the vegetation plot within the data set (required). `subPlotName` - A string identifying a subplot of the plot given by `plotName` (optional). `obsStartDate` - Plot observation start date (required; see `date.format`). `organismName` - The string of a name, defined by the dataset author, and which does not follow nomenclatural codes. `taxonName` - The string of a taxon name (not necessarily including authority). `stratumName` - A string used to identify a stratum (see `stratumDefinition`; optional). `heightMeasurement` - Optional height at which the aggregated observation was made, e.g. in meters. It applies to all aggregate measurements (optional). `...` - User defined names used to map aggregate organism measurements, such as percent cover (optional).
`methods`	A list with measurement methods for `heightMeasurement` and all the user defined aggregate organism measurements (each method is an object of class `VegXMethodDefinition`). Alternatively, methods can be specified using strings if predefined methods exist (see `predefinedMeasurementMethod`).
`stratumDefinition`	An object of class `VegXStrataDefinition` indicating the definition of strata.
`date.format`	A character string specifying the input format of dates (see `as.Date`).
`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.

Details

The mapping should include either organismName or taxonName, but can include both of them if the source data set contains both taxon names and others that are not taxa. Missing value policy:

Missing plotName and obsStartDate values are interpreted as if the previous non-missing value has to be used to define aggregate organism observation.
Missing subPlotName values are interpreted in that observation refers to the parent plotName.
When stratumName values are missing the aggregate organism observation is not assigned to any stratum.
When both organismName and taxonName are missing (i.e. missing organism identity) the function generates an error.
Missing aggregate organism measurements are not added to the Veg-X document.

Value

The modified object of class VegX.

References

Wiser SK, Spencer N, De Caceres M, Kleikamp M, Boyle B & Peet RK (2011). Veg-X - an exchange standard for plot-based vegetation data

Examples

# Load source data
data(mokihinui)

# Define mapping
mapping = list(plotName = "Plot", obsStartDate = "PlotObsStartDate",
               taxonName = "NVSSpeciesName",
               stratumName = "Tier", cover = "Category")

# Define abundance 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 aggregate organism observations
x = addAggregateOrganismObservations(newVegX(), moki_tcv,
                 mapping = mapping,
                 methods = list(cover=coverscale),
                 stratumDefinition = strataDef)

# Inspect the result
head(showElementTable(x, "aggregateOrganismObservation"))


# Example with individual counts
data(mtfyffe)
mapping = list(plotName = "Plot", subPlotName = "Subplot", obsStartDate = "PlotObsStartDate",
               taxonName = "NVSSpeciesName", stratumName = "Tier", counts = "Value")
strataDef = defineHeightStrata(name = "Standard seedling/sapling strata",
               description = "Seedling/sapling stratum definition",
               heightBreaks = c(0, 15, 45, 75, 105, 135, 200),
               strataNames = as.character(1:6),
               strataDefinitions = c("0-15 cm", "16-45 cm", "46-75 cm", 
                                     "76-105 cm", "106-135 cm", "> 135 cm"))
x = addAggregateOrganismObservations(newVegX(), mtfyffe_counts, mapping,
               methods = list(counts="Individual plant counts"),
               stratumDefinition = strataDef)
head(showElementTable(x, "aggregateOrganismObservation"))

# Example with frequency in transects
data(takitimu)
mapping = list(plotName = "Plot", subPlotName = "Subplot", obsStartDate = "PlotObsStartDate",
               taxonName = "NVSSpeciesName", freq = "Value")
x = addAggregateOrganismObservations(newVegX(), taki_freq, mapping,
               methods = list(freq="Plant frequency/%"))
head(showElementTable(x, "aggregateOrganismObservation"))

miquelcaceres/VegX documentation built on Sept. 18, 2022, 7:04 p.m.