data-raw/ParacouProfile.R

In VincyaneBadouard/TreeData: Forest Inventories Harmonization & Correction

## code to prepare `ParacouProfile` dataset goes here

## 1st option to create (non-interactive) - may need to be updated if interactive_items.csv changes

if (!interactive()) {
  ParacouProfile <-
    list(
      TreeHeight = "none",
      XTreeUTM = "none",
      Date = "CensusDate",
      SubplotAreaMan = 0L,
      SpeciesVolume = "none",
      POM = "none",
      PlotAreaUnitMan = "ha",
      BHOMUnitMan = "none",
      PlotVolume = "none",
      BD = "none",
      PlotDensity = "none",
      IdStem = "none",
      YTreeSubplot = "none",
      PlotMan = "",
      YPlotUTM = "none",
      IdMeasure = "none",
      ScientificName = "none",
      SpeciesBasalAreaDensityUnitMan = "none",
      SubplotArea = "none",
      IdCensus = "none",
      XTreePlot = "none",
      PlotAreaMan = 0L,
      PlotElevation = "none",
      BPOM = "none",
      SpeciesDensityUnitMan = "none",
      CommercialSp = "CommercialSp",
      IsCommercialMan = "TRUE",
      SpeciesBasalAreaDensity = "none",
      YearMan = 0L,
      Subspecies = "none",
      Circ = "Circ",
      SpeciesTotalBasalAreaUnitMan = "none",
      PlotVolumeUnitMan = "none",
      PlotNDead = "none",
      XTreeSubplot = "none",
      Site = "Forest",
      MinDBH = "none",
      Day = "none",
      TreeUTMUnitMan = "none",
      PlotNLive = "none",
      SpeciesVolumeUnitMan = "none",
      BHOM = "none",
      IdTree = "idTree",
      LifeForm = "none",
      TreeSubplotUnitMan = "none",
      VernName = "VernName",
      PlotSpeciesRichness = "none",
      SiteMan = "",
      XSubplotUTM = "none",
      Authority = "none",
      BCirc = "none",
      PlotBasalAreaDensity = "none",
      TreePlotUnitMan = "none",
      Diameter = "none",
      Month = "none",
      HOMUnitMan = "none",
      SpeciesTotalBasalArea = "none",
      TreeHeightUnitMan = "none",
      Variety = "none",
      Family = "Family",
      HOM = "none",
      ScientificNameSepMan = "",
      BDUnitMan = "none",
      YSubplotUTM = "none",
      SpeciesCoverageIndex = "none",
      DiameterUnitMan = "none",
      PlotElevationMan = -999L,
      SubplotMan = "",
      DateFormatMan = "yyyy-mm-dd",
      Species = "Species",
      SpeciesRelativeDensity = "none",
      CircUnitMan = "cm",
      IdLevel = "none",
      XPlotUTM = "none",
      TreeFieldNum = "TreeFieldNum",
      YTreeUTM = "none",
      TreeLon = "none",
      BCircUnitMan = "none",
      SubplotLon = "none",
      Year = "CensusYear",
      LifeStatus = "CodeAlive",
      MinDBHMan = -999L,
      PlotArea = "PlotArea",
      PlotLon = "none",
      YTreePlot = "none",
      SpeciesRelativeDominance = "none",
      Subplot = "SubPlot",
      MinDBHUnitMan = "none",
      PlotDensityUnitMan = "none",
      PlotBasalAreaDensityUnitMan = "none",
      Plot = "Plot",
      SpeciesImportanceIndex = "none",
      SubplotAreaUnitMan = "none",
      Voucher = "none",
      TreeLat = "none",
      PlotLat = "none",
      StemFieldNum = "none",
      Genus = "Genus",
      SpeciesAbundance = "none",
      IsLiveMan = "TRUE",
      SubplotLat = "none",
      SpeciesDensity = "none",
      SpeciesRelativeFrequency = "none",
      MeasLevel = "Tree",
      Tidy = structure(0L, class = c("integer",
                                     "shinyActionButtonValue")),
      ClearValueName = structure(0L, class = c("integer",
                                               "shinyActionButtonValue")),
      TickedMelt3 = FALSE,
      Variablecolumns1 = c("Xfield",
                           "Yfield"),
      ValueName4 = "",
      TickedMelt1 = FALSE,
      ValueName5 = "",
      ValueName2 = "utm",
      TickedMelt4 = FALSE,
      TickedMelt5 = FALSE,
      Variablecolumns3 = c("Lat", "Lon"),
      ValueName3 = "L",
      TickedMelt2 = FALSE,
      Variablecolumns2 = c("Xutm", "Yutm"),
      ValueName1 = "field",
      AllCodes = structure(
        list(
          Column = "You have not selected columns for codes",
          Value = "You have not selected columns for codes",
          Definition = "You have not selected columns for codes",
          DefinitionSelector = "<select id=\"slct1\"><optgroup label=\"\">\n  <option value=\"[select or enter a definition]\" title=\"unselectable option\" selected=\"selected\">[select or enter a definition]</option>\n</optgroup><optgroup label=\"Dead tree codes\">\n  <option value=\"dead, stem standing\" title=\"ForestGEO code DS\">dead, stem standing</option>\n  <option value=\"dead, stem fallen\" title=\"ForestGEO code DC\">dead, stem fallen</option>\n  <option value=\"dead, only tag found\" title=\"ForestGEO code DT\">dead, only tag found</option>\n  <option value=\"presumed dead, no tag nor stem\" title=\"ForestGEO code DN\">presumed dead, no tag nor stem</option>\n  <option value=\"dead, harvested\" title=\"\">dead, harvested</option>\n  <option value=\"dead, poisoned\" title=\"\">dead, poisoned</option>\n</optgroup><optgroup label=\"Other info\">\n  <option value=\"any problem requiring further attention\" title=\"ForestGEO code P\">any problem requiring further attention</option>\n</optgroup><optgroup label=\"POM info\">\n  <option value=\"large buttress, requiring ladder to measure\" title=\"ForestGEO code B\">large buttress, requiring ladder to measure</option>\n  <option value=\"POM at alternative height, not breast height\" title=\"ForestGEO code A\">POM at alternative height, not breast height</option>\n  <option value=\"stem irregular where measured\" title=\"ForestGEO code I\">stem irregular where measured</option>\n  <option value=\"POM has changed since prior census\" title=\"ForestGEO code C\">POM has changed since prior census</option>\n</optgroup><optgroup label=\"Stem info\">\n  <option value=\"stem broken below breast height\" title=\"ForestGEO code X\">stem broken below breast height</option>\n  <option value=\"multiple stems\" title=\"ForestGEO code M\">multiple stems</option>\n  <option value=\"stem leaning\" title=\"ForestGEO code L\">stem leaning</option>\n  <option value=\"stem broken above breast height\" title=\"ForestGEO code Q\">stem broken above breast height</option>\n  <option value=\"prostrate stem\" title=\"ForestGEO code Y\">prostrate stem</option>\n  <option value=\"resprout (main stem broken but resprouted since last census)\" title=\"ForestGEO code R\">resprout (main stem broken but resprouted since last census)</option>\n  <option value=\"injured (tree fall, lightning, etc)\" title=\"These are grouped codes from the Paracou and Mbaiki sites; we could separate them into different types of damage but that might be a bit too long\">injured (tree fall, lightning, etc)</option>\n  <option value=\"dying\" title=\"\">dying</option>\n</optgroup></select>"
        ),
        row.names = c(NA,-1L),
        class = "data.frame"
      )
    )

}

# dput(ParacouProfile)

#### Save this data in the package ####
usethis::use_data(ParacouProfile, overwrite = TRUE)


## For ParacouProfile.Rmd  run next line of code and paste in the item section of R/ParacouProfile.R
x <- read.csv("inst/app/data/interactive_items.csv")

write.csv(
  paste0(
    "#'   \\item{",
    names(ParacouProfile),
    "}",
    ifelse(
      is.na(x$Label[match(names(ParacouProfile), x$ItemID)]),
      "{Some value created via interaction with the Shiny app",
      paste0(
        "{Value or column name in data set @ParacouSubset (",
        ParacouProfile,
        ") corresponding to ",
        x$Label[match(names(ParacouProfile), x$ItemID)]
      )
    ),
    "}"
  ),
  "clipboard",
  quote = F,
  row.names = F
)