R/standardizeSpeciesNames.R

In ianmseddy/PSPclean: Sources and standardizes permanent sample plot data

globalVariables(c(
  ":=", "Genus", "newSpeciesName", "Species"
))

#' standardize the species names in a given PSP measurement data.table
#'
#' @param speciesTable the tree measurement csv
#' @param forestInventorySource one of MBTSP, ABPSP, BCPSP, SKPSP, NWTTSP, NFIPSP.
#' @return the species table with standardized species names
#'
#' @export
standardizeSpeciesNames <- function(speciesTable, forestInventorySource) {
  #### Manitoba#####
  if (forestInventorySource == "MBPSP" | forestInventorySource == "MBTSP") {
    speciesTable[
      Species == "AE" | Species == "E" | Species == "WE",
      newSpeciesName := "white elm"
    ] # assume WE is white elm in MB PSP
    speciesTable[Species == "GA", newSpeciesName := "red ash"] # green ash = red ash
    speciesTable[Species == "WP", newSpeciesName := "white pine"]
    speciesTable[Species == "RP", newSpeciesName := "red pine"]
    speciesTable[Species == "JP" | Species == "jp", newSpeciesName := "jack pine"]
    speciesTable[Species == "SP", newSpeciesName := "scots pine"]
    speciesTable[
      Species == "BS" | Species == "bs" | Species == " BS",
      newSpeciesName := "black spruce"
    ]
    speciesTable[Species == "WS" | Species == "ws", newSpeciesName := "white spruce"]
    speciesTable[Species == "BF" | Species == "bf", newSpeciesName := "balsam fir"]
    speciesTable[Species == "TL" | Species == "tl", newSpeciesName := "tamarack larch"]
    speciesTable[Species == "EC", newSpeciesName := "eastern redcedar"]
    # assume cedar in original document is eastern redcedar
    speciesTable[Species == "TA" | Species == "ta", newSpeciesName := "trembling aspen"]
    speciesTable[Species == "LA", newSpeciesName := "largetooth aspen"]
    speciesTable[Species == "BA" | Species == "ba", newSpeciesName := "balsam poplar"]
    speciesTable[Species == "CO", newSpeciesName := "eastern cottonwood"]
    speciesTable[Species == "W", newSpeciesName := "willow"]
    speciesTable[Species == "WB" | Species == "wb", newSpeciesName := "white birch"]
    speciesTable[Species == "B" | Species == "BW", newSpeciesName := "basswood"]
    speciesTable[Species == "HB", newSpeciesName := "hackberry"]
    speciesTable[Species == "MM", newSpeciesName := "manitoba maple"]
    speciesTable[Species == "AS", newSpeciesName := "black ash"]
    # assume ash in original document is black ash
    speciesTable[Species == "HH", newSpeciesName := "hop-hornbeam"]
    speciesTable[Species == "BO", newSpeciesName := "white oak"]
    # assume bur oak in original document is white oak
  } else if (forestInventorySource == "BCPSP") {
    #### British Columbia ####
    speciesTable[Species == "TW", newSpeciesName := "western yew"]
    speciesTable[Species == "YC", newSpeciesName := "yellow cedar"]
    speciesTable[Species == "L", newSpeciesName := "alpine larch"]
    speciesTable[Species == "SB", newSpeciesName := "black spruce"]
    speciesTable[Species == "LT", newSpeciesName := "tamarack larch"]
    speciesTable[Species == "LW", newSpeciesName := "western larch"]
    speciesTable[Species == "SW", newSpeciesName := "white spruce"]
    speciesTable[Species == "EP", newSpeciesName := "white birch"]
    speciesTable[Species == "PLI", newSpeciesName := "lodgepole pine"]
    speciesTable[Species == "PW", newSpeciesName := "western white pine"]
    speciesTable[Species == "ACB", newSpeciesName := "balsam poplar"]
    speciesTable[Species == "S", newSpeciesName := "black spruce"]
    # S for spruce in original doc. assume S is black spruce
    speciesTable[Species == "PL", newSpeciesName := "lodgepole pine"]
    speciesTable[Species == "PY", newSpeciesName := "ponderosa pine"]
    speciesTable[Species == "ACT", newSpeciesName := "black cottonwood"]
    speciesTable[Species == "AT", newSpeciesName := "trembling aspen"]
    speciesTable[Species == "MB", newSpeciesName := "bigleaf maple"]
    speciesTable[Species == "E", newSpeciesName := "white birch"]
    # E for birch in original doc. assume S is white birch
    # speciesTable[Species == "XC", newSpeciesName := "unknow conifer"]
    speciesTable[Species == "BL", newSpeciesName := "subalpine fir"]
    speciesTable[Species == "EA", newSpeciesName := "white birch"]
    # EA is alaka paper birch, assume it is white birch here
    speciesTable[Species == "AC", newSpeciesName := "balsam poplar"]
    # speciesTable[Species == "X", newSpeciesName := "unknown"]
    speciesTable[Species == "B", newSpeciesName := "fir"]
    speciesTable[Species == "BG", newSpeciesName := "grand fir"]
    speciesTable[Species == "W", newSpeciesName := "willow"]
    speciesTable[Species == "DR", newSpeciesName := "red alder"]
    speciesTable[Species == "DM", newSpeciesName := "mountain alder"]
    speciesTable[Species == "PJ", newSpeciesName := "jack pine"]
    speciesTable[Species == "ZH", newSpeciesName := "hardwood"]
    speciesTable[Species == "SXW", newSpeciesName := "white spruce"]
    # SXW is hybrid between engelmann and white spruce
    speciesTable[Species == "XH", newSpeciesName := "hardwood"]
    speciesTable[Species == "SX", newSpeciesName := "white spruce"]
    speciesTable[Species == "SS", newSpeciesName := "sitka spruce"]
    # SX is hybrid
    speciesTable[Species == "A", newSpeciesName := "trembling aspen"]
    # A is aspen cottonwood and poplar, assume it is trembling aspen
    speciesTable[Species == "P", newSpeciesName := "lodgepole pine"]
    # P is pine Species, assume it is lodgepole pine
    speciesTable[Species == "MR", newSpeciesName := "douglas maple"]
    speciesTable[Species == "SE", newSpeciesName := "engelmann spruce"]
    speciesTable[Species == "FD", newSpeciesName := "douglas-fir"]
    speciesTable[Species == "BA", newSpeciesName := "pacific silver fir"] # this is amabilis fir
    speciesTable[Species == "CW", newSpeciesName := "western redcedar"]
    speciesTable[Species == "HW", newSpeciesName := "western hemlock"]
    speciesTable[Species == "FDI", newSpeciesName := "douglas-fir"]
    # speciesTable[Species == "SXE", newSpeciesName := "unknown"]
    speciesTable[Species == "D", newSpeciesName := "red alder"]
    # D is alder, assume red alder
    speciesTable[Species == "H", newSpeciesName := "western hemlock"]
    speciesTable[Species == "MV", newSpeciesName := "vine maple"]
    speciesTable[Species == "HM", newSpeciesName := "mountain hemlock"]
    speciesTable[Species == "EXP", newSpeciesName := "white birch"]
    speciesTable[Species == "WS", newSpeciesName := "scoulers willow"]
    speciesTable[Species == "AX", newSpeciesName := "trembling aspen"]
    # hybrid poplars for AX, assume trembling aspen
  } else if (forestInventorySource == "ABPSP") {
    #### Alberta ####
    # speciesTable[Species == "  ", newSpeciesName := "unknown"]
    speciesTable[Species == "AW", newSpeciesName := "trembling aspen"]
    speciesTable[Species == "BW", newSpeciesName := "white birch"]
    speciesTable[Species == "FA", newSpeciesName := "subalpine fir"]
    speciesTable[Species == "FB", newSpeciesName := "balsam fir"]
    speciesTable[Species == "FD", newSpeciesName := "douglas-fir"]
    speciesTable[Species == "LA", newSpeciesName := "alpine larch"]
    speciesTable[Species == "LT", newSpeciesName := "tamarack larch"]
    speciesTable[Species == "LW", newSpeciesName := "western larch"]
    # speciesTable[Species == "P ", newSpeciesName := "unknown"]
    speciesTable[Species == "PB", newSpeciesName := "balsam poplar"]
    speciesTable[Species == "PF", newSpeciesName := "limber pine"]
    speciesTable[Species == "PJ", newSpeciesName := "jack pine"]
    speciesTable[Species == "PL", newSpeciesName := "lodgepole pine"]
    speciesTable[Species == "PW", newSpeciesName := "whitebark pine"]
    speciesTable[Species == "SB", newSpeciesName := "black spruce"]
    speciesTable[Species == "SE", newSpeciesName := "engelmann spruce"]
    speciesTable[Species == "SW", newSpeciesName := "white spruce"]
  } else if (forestInventorySource == "SKPSP" | forestInventorySource == "SKTSP") {
    #### Sask ####
    # speciesTable[Species == "", newSpeciesName := "unknown"]
    speciesTable[Species == "BF", newSpeciesName := "balsam fir"]
    speciesTable[Species == "BP", newSpeciesName := "balsam poplar"]
    speciesTable[Species == "BS", newSpeciesName := "black spruce"]
    # speciesTable[Species == "DC", newSpeciesName := "unknown"] # what is this
    # speciesTable[Species == "DD", newSpeciesName := "unknown"] # what is this
    # speciesTable[Species == "DU", newSpeciesName := "unknown"] # what is this
    speciesTable[Species == "GA", newSpeciesName := "green ash"]
    speciesTable[Species == "JP", newSpeciesName := "jack pine"]
    speciesTable[Species == "MM", newSpeciesName := "manitoba maple"]
    # speciesTable[Species == "PC", newSpeciesName := "unknown"] # what is this
    speciesTable[Species == "TA", newSpeciesName := "trembling aspen"]
    speciesTable[Species == "TL", newSpeciesName := "tamarack larch"]
    # speciesTable[Species == "UI", newSpeciesName := "unknown"] # what is this
    speciesTable[Species == "WB", newSpeciesName := "white birch"]
    speciesTable[Species == "WE", newSpeciesName := "white elm"]
    speciesTable[Species == "WS", newSpeciesName := "white spruce"]
    # speciesTable[Species == "XX", newSpeciesName := "unknown"] # what is this
  } else if (forestInventorySource == "NWTTSP") {
    #### NWT####
    speciesTable[Species == "A", newSpeciesName := "trembling aspen"]
    speciesTable[Species == "BW", newSpeciesName := "white birch"]
    speciesTable[Species == "Bw", newSpeciesName := "white birch"]
    speciesTable[Species == "F", newSpeciesName := "balsam fir"]
    speciesTable[Species == "FB", newSpeciesName := "balsam fir"]
    speciesTable[Species == "L", newSpeciesName := "tamarack larch"]
    speciesTable[Species == "LT", newSpeciesName := "tamarack larch"]
    speciesTable[Species == "PB", newSpeciesName := "balsam poplar"]
    speciesTable[Species == "Pj", newSpeciesName := "jack pine"]
    speciesTable[Species == "PJ", newSpeciesName := "jack pine"]
    speciesTable[Species == "Pl", newSpeciesName := "lodgepole pine"]
    speciesTable[Species == "PL", newSpeciesName := "lodgepole pine"]
    speciesTable[Species == "Po", newSpeciesName := "balsam poplar"]
    speciesTable[Species == "PO", newSpeciesName := "balsam poplar"]
    speciesTable[Species == "Sb", newSpeciesName := "black spruce"]
    speciesTable[Species == "SB", newSpeciesName := "black spruce"]
    speciesTable[Species == "sw", newSpeciesName := "white spruce"]
    speciesTable[Species == "Sw", newSpeciesName := "white spruce"]
    speciesTable[Species == "SW", newSpeciesName := "white spruce"]
    speciesTable[Species == "W", newSpeciesName := "willow"]
  } else if (forestInventorySource == "NFIPSP") {
    #### NFI ####
    # the Species code system in NFI is different from provincial systems
    # the speciesTable for NFIPSP must have Genus and Species column
    speciesTable[
      Genus == "ABIE" & Species == "AMA",
      newSpeciesName := "pacific silver fir"
    ]
    speciesTable[
      Genus == "ABIE" & Species == "BAL",
      newSpeciesName := "balsam fir"
    ]
    speciesTable[
      Genus == "ABIE" & Species == "LAS",
      newSpeciesName := "subalpine fir"
    ]
    speciesTable[
      Genus == "ACER" & Species == "SAC",
      newSpeciesName := "silver maple"
    ]
    speciesTable[
      Genus == "ACER" & Species == "SAH",
      newSpeciesName := "sugar maple"
    ]
    speciesTable[
      Genus == "ACER" & Species == "SPI",
      newSpeciesName := "mountain maple"
    ]
    speciesTable[
      Genus == "ACER" & Species == "RUB",
      newSpeciesName := "red maple"
    ]
    speciesTable[
      Genus == "ALNU" & Species == "SPP",
      newSpeciesName := "alder"
    ]
    speciesTable[
      Genus == "ALNU" & Species == "INC",
      newSpeciesName := "gray alder"
    ]
    speciesTable[
      Genus == "ALNU" & Species == "RUB",
      newSpeciesName := "red alder"
    ]
    speciesTable[
      Genus == "ALNU" & Species == "CRI",
      newSpeciesName := "alder"
    ]
    speciesTable[
      Genus == "ALNU" & Species == "VIR",
      newSpeciesName := "sitka alder"
    ]
    speciesTable[
      Genus == "AMEL" & Species == "ALN",
      newSpeciesName := "saskatoon-berry"
    ]
    speciesTable[
      Genus == "BETU" & Species == "ALL",
      newSpeciesName := "yellow birch"
    ] # swamp birch
    speciesTable[
      Genus == "BETU" & Species == "GLA",
      newSpeciesName := "birch"
    ] #resin birch - is a shrub
    speciesTable[
      Genus == "BETU" & Species == "NAN",
      newSpeciesName := "birch"
    ] # nana birch - is a shrub
    speciesTable[
      Genus == "BETU" & Species == "NEO",
      newSpeciesName := "white birch"
    ] # alaska paper birch
    speciesTable[
      Genus == "BETU" & Species == "OCC",
      newSpeciesName := "white birch"
    ] # water birch
    speciesTable[
      Genus == "BETU" & Species == "POP",
      newSpeciesName := "grey birch"
    ]
    speciesTable[
      Genus == "BETU" & Species == "PAP",
      newSpeciesName := "white birch"
    ]
    speciesTable[
      Genus == "BETU" & Species == "PUM",
      newSpeciesName := "birch"
    ] # not found
    speciesTable[
      Genus == "BETU" & Species == "SPP",
      newSpeciesName := "birch"
    ] # water birch
    speciesTable[
      Genus == "CHAM" & Species == "NOO",
      newSpeciesName := "yellow cedar"
    ] # nootka cypress
    speciesTable[
      Genus == "CORN" & Species == "STO",
      newSpeciesName := "redosier dogwood"
    ]
    speciesTable[
      Genus == "CARY" & Species == "COR",
      newSpeciesName := "bitternut hickory"
    ]
    speciesTable[
      Genus == "FAGU" & Species == "GRA",
      newSpeciesName := "beech"
    ]
    speciesTable[
      Genus == "FRAX" & Species == "AME",
      newSpeciesName := "white ash"
    ]
    speciesTable[
      Genus == "FRAX" & Species == "NIG",
      newSpeciesName := "black ash"
    ]
    speciesTable[
      Genus == "FRAX" & Species == "PEN",
      newSpeciesName := "red ash"
    ]
    speciesTable[
      Genus == "GENC" & Species == "SPP",
      newSpeciesName := "softwood"
    ]
    speciesTable[
      Genus == "GENH" & Species == "SPP",
      newSpeciesName := "hardwood"
    ]
    speciesTable[
      Genus == "LARI" & Species == "LAR",
      newSpeciesName := "tamarack larch"
    ]
    speciesTable[
      Genus == "LARI" & Species == "OCC",
      newSpeciesName := "western larch"
    ]
    speciesTable[
      Genus == "OSTR" & Species == "VIR",
      newSpeciesName := "hop-hornbeam"
    ]
    speciesTable[
      Genus == "PICE" & Species == "ENG",
      newSpeciesName := "engelmann spruce"
    ]
    speciesTable[
      Genus == "PICE" & Species == "GLA",
      newSpeciesName := "white spruce"
    ]
    speciesTable[
      Genus == "PICE" & Species == "MAR",
      newSpeciesName := "black spruce"
    ]
    speciesTable[
      Genus == "PICE" & Species == "RUB",
      newSpeciesName := "red spruce"
    ]
    speciesTable[
      Genus == "PICE" & Species == "SIT",
      newSpeciesName := "sitka spruce"
    ]
    speciesTable[
      Genus == "PICE" & Species == "SPP",
      newSpeciesName := "spruce"
    ]
    speciesTable[
      Genus == "PINU" & Species == "BAN",
      newSpeciesName := "jack pine"
    ]
    speciesTable[
      Genus == "PINU" & Species == "CON",
      newSpeciesName := "lodgepole pine"
    ]
    speciesTable[
      Genus == "PINU" & Species == "PON",
      newSpeciesName := "ponderosa pine"
    ]
    speciesTable[
      Genus == "PINU" & Species == "RES",
      newSpeciesName := "red pine"
    ]
    speciesTable[
      Genus == "PINU" & Species == "STR",
      newSpeciesName := "white pine"
    ]
    speciesTable[
      Genus == "POPU" & Species == "BAL",
      newSpeciesName := "balsam poplar"
    ]
    speciesTable[
      Genus == "POPU" & Species == "GRA",
      newSpeciesName := "largetooth aspen"
    ]
    speciesTable[
      Genus == "POPU" & Species == "SPP",
      newSpeciesName := "poplar"
    ]
    speciesTable[
      Genus == "POPU" & Species == "TRE",
      newSpeciesName := "trembling aspen"
    ]
    speciesTable[
      Genus == "POPU" & Species == "TRI",
      newSpeciesName := "black cottonwood"
    ]
    speciesTable[
      Genus == "PRUN" & Species == "PEN",
      newSpeciesName := "pin cherry"
    ]
    speciesTable[
      Genus == "PRUN" & Species == "VIR",
      newSpeciesName := "choke cherry"
    ]
    speciesTable[
      Genus == "PSEU" & Species == "MEN",
      newSpeciesName := "douglas-fir"
    ]
    speciesTable[
      Genus == "QUER" & Species == "ALB",
      newSpeciesName := "white oak"
    ]
    speciesTable[
      Genus == "QUER" & Species == "MAC",
      newSpeciesName := "bur oak"
    ]
    speciesTable[
      Genus == "QUER" & Species == "RUB",
      newSpeciesName := "red oak"
    ]
    speciesTable[
      Genus == "SALI" & Species == "PED",
      newSpeciesName := "willow"
    ] # not found assume willow
    speciesTable[
      Genus == "SALI" & Species == "PLA",
      newSpeciesName := "willow"
    ] # not found assume willow
    speciesTable[
      Genus == "SALI" & Species == "SCO",
      newSpeciesName := "scouler willow"
    ]
    speciesTable[
      Genus == "SALI" & Species == "SPP",
      newSpeciesName := "willow"
    ]
    speciesTable[
      Genus == "SALI" & Species == "SPP",
      newSpeciesName := "willow"
    ]
    speciesTable[
      Genus == "SHEP" & Species == "CAN",
      newSpeciesName := "berry"
    ] # not found assume berry
    speciesTable[
      Genus == "TILI" & Species == "AME",
      newSpeciesName := "basswood"
    ]
    speciesTable[
      Genus == "TSUG" & Species == "CAN",
      newSpeciesName := "eastern hemlock"
    ] #
    speciesTable[
      Genus == "TSUG" & Species == "HET",
      newSpeciesName := "western hemlock"
    ] #
    speciesTable[
      Genus == "TSUG" & Species == "MER",
      newSpeciesName := "mountain hemlock"
    ] #
    speciesTable[
      Genus == "THUJ" & Species == "OCC",
      newSpeciesName := "eastern white-cedar"
    ] #
    speciesTable[
      Genus == "THUJ" & Species == "PLI",
      newSpeciesName := "western redcedar"
    ] #
    speciesTable[
      Genus == "ULMU" & Species == "AME",
      newSpeciesName := "white elm"
    ]
    speciesTable[
      Genus == "UNKN" & Species == "SPP",
      newSpeciesName := "unknown"
    ] #
  } else {
    stop("Please define the correct forestInventorySource among ")
  }
  speciesTable[is.na(newSpeciesName), newSpeciesName := "unknown"]
  return(speciesTable)
}
# the species with biomass equations
# c("alpine fir", "balsam fir", "balsam poplar", "basswood", "beech",
#   "black ash", "black cherry", "black cottonwood", "black spruce",
#   "douglas-fir", "eastern hemlock", "eastern redcedar", "eastern white-cedar",
#   "eastern white pine", "engelmann spruce", "grey birch", "hardwood",
#   "hickory", "hop-hornbeam", "jack pine", "largetooth aspen", "lodgepole pine",
#   "pacific silver fir", "red alder", "red ash", "red maple", "red oak",
#   "red pine", "red spruce", "silver maple", "sitka spruce", "softwood",
#   "subalpine fir", "sugar maple", "tamarack larch", "trembling aspen",
#   "western hemlock", "western redcedar", "white ash", "white birch",
#   "white elm", "white oak", "white spruce", "yellow birch")