showElementTable.RdCoerces part of the information of a Veg-X object into a data frame
showElementTable(
x,
element = "plot",
IDs = FALSE,
subjects = FALSE,
max.nchar = 30
)An object of class VegX
The name of the main element to be coerced: 'project', 'plot', 'party', 'plotObservation', 'organismIdentity', 'stratum', 'stratumObservation', 'surfaceType', 'surfaceCoverObservation', 'aggregateOrganismObservation', 'individualOrganism', 'individualOrganismObservation', 'communityObservation', 'siteObservation', 'method', 'attribute', 'literatureCitation'.
A boolean flag to indicate whether internal identifiers should be included in the output.
A boolean flag to indicate whether method subjects should be included in the output.
Maximum number of characters in strings
a data frame
data(mokihinui)
# Create document 'x' with aggregate organism observations
mapping = list(plotName = "Plot", obsStartDate = "PlotObsStartDate",
taxonName = "NVSSpeciesName",
stratumName = "Tier", cover = "Category")
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%"))
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")
x = addAggregateOrganismObservations(newVegX(), moki_tcv,
mapping = mapping,
methods = c(cover=coverscale),
stratumDefinition = strataDef)
#> 1 additional aggregate organism measurements found: Category.
#> Measurement method 'Recce cover scale' added for 'cover'.
#> Stratum definition method 'Recce strata' added.
#> 7 new stratum definitions added.
#> 5 plot(s) parsed, 5 new added.
#> 5 plot observation(s) parsed, 5 new added.
#> 148 organism names(s) parsed, 148 new added.
#> 148 organism identitie(s) parsed, 148 new added.
#> 33 stratum observation(s) parsed, 33 new added.
#> 582 record(s) parsed, 582 new aggregate organism observation(s) added.
# Summary
summary(x)
#> ================================================================
#> Veg-X object (ver 2.0.0)
#> ----------------------------------------------------------------
#>
#> Projects: 0
#>
#> Plots: 5 [Parent plots: 5 Sub-plots: 0]
#>
#> Individual organisms: 0
#>
#> Organism names: 148
#>
#> Taxon concepts: 0
#>
#> Organism Identities: 148
#>
#> Vegetation strata: 7
#> 1. Tier 1 [1/Recce strata]
#> 2. Tier 2 [2/Recce strata]
#> 3. Tier 3 [3/Recce strata]
#> 4. Tier 4 [4/Recce strata]
#> 5. Tier 5 [5/Recce strata]
#> 6. Tier 6 [6/Recce strata]
#> 7. Tier 7 [7/Recce strata]
#>
#> Surface types: 0
#>
#> Parties: 0
#>
#> Literature citations: 2
#>
#> Methods: 2
#> 1. Recce cover scale [plant cover / 7 ordinal atts.]
#> 2. Recce strata [stratum mixed / 1 quantitative atts.]
#>
#> Plot observations: 5 [in parent plots: 5 in sub-plots: 0]
#>
#> Individual organism observations: 0
#>
#> Aggregated organism observations: 582
#>
#> Stratum observations: 33
#>
#> Community observations: 0
#>
#> Site observations: 0
#>
#> Surface cover observations: 0
#>
#> ================================================================
# show plot information
showElementTable(x, "plot")
#> plotName
#> 1 LGM38h
#> 2 LGM43h
#> 3 LGM45h
#> 4 LGM08r
#> 5 LGM16l
# show plot observation information
showElementTable(x, "plotObservation")
#> plotName obsStartDate
#> 1 LGM38h 2011-02-20
#> 2 LGM43h 2011-02-13
#> 3 LGM45h 2011-02-11
#> 4 LGM08r 2011-02-17
#> 5 LGM16l 2011-02-15
# show methods, attributes, citations
showElementTable(x, "method")
#> name description subject
#> 1 Recce cover scale Recce recording method by Hurst/Allen plant cover
#> 2 Recce strata Standard Recce stratum definition stratum mixed
#> attributeType attributeNumber
#> 1 ordinal 7
#> 2 quantitative 1
showElementTable(x, "attribute")
#> $quantitative
#> methodName methodSubject unit lowerLimit upperLimit
#> 8 Recce strata stratum mixed m 0 Inf
#>
#> $ordinal
#> methodName methodSubject code definition order lowerLimit upperLimit
#> 1 Recce cover scale plant cover P Presence 1 NA NA
#> 2 Recce cover scale plant cover 1 <1% 2 0 1
#> 3 Recce cover scale plant cover 2 1-5% 3 1 5
#> 4 Recce cover scale plant cover 3 6-25% 4 5 25
#> 5 Recce cover scale plant cover 4 26-50% 5 25 50
#> 6 Recce cover scale plant cover 5 51-75% 6 50 75
#> 7 Recce cover scale plant cover 6 76-100% 7 75 100
#> midPoint
#> 1 NA
#> 2 0.05
#> 3 0.50
#> 4 15.00
#> 5 37.50
#> 6 62.50
#> 7 87.50
#>
#> $qualitative
#> data frame with 0 columns and 0 rows
#>
showElementTable(x, "literatureCitation")
#> citationString DOI
#> 1 Hurst, JM and Allen, RB. (2... NA
#> 2 Hurst, JM and Allen, RB. (2... NA
# show aggregate organism observations (only some of them)
head(showElementTable(x, "aggregateOrganismObservation"))
#> plotName obsStartDate organismIdentityName stratumName agg_1_method
#> 1 LGM38h 2011-02-20 Dacrydium cupressinum Tier 1 Recce cover scale
#> 2 LGM38h 2011-02-20 Dacrydium cupressinum Tier 2 Recce cover scale
#> 3 LGM38h 2011-02-20 Dacrydium cupressinum Tier 6 Recce cover scale
#> 4 LGM38h 2011-02-20 Weinmannia racemosa Tier 2 Recce cover scale
#> 5 LGM38h 2011-02-20 Weinmannia racemosa Tier 3 Recce cover scale
#> 6 LGM38h 2011-02-20 Weinmannia racemosa Tier 4 Recce cover scale
#> agg_1_value
#> 1 3
#> 2 3
#> 3 1
#> 4 3
#> 5 4
#> 6 3