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Merge the Data sets Extracted from Various datasources.

ec_db_merge.Rd

condition to run this function: all the data frames should have same fields follwing DwC standards: e.g. attribute_list <- c("source","catalogNumber", "basisOfRecord", "occurrenceStatus", "institutionCode", "verbatimEventDate", "scientificName", "individualCount", "organismQuantity", "abundance", "decimalLatitude", "decimalLongitude", "coordinateUncertaintyInMeters", "locality", "verbatimLocality", "municipality", "county", "stateProvince", "country", "countryCode") Assign manually the source name in "source" field. example - gbif, obis, invertEBase etc Assign values of individual count or organism count into abundance. Most online sources has one of them updated with specimen count. this function depends on successful download of data files, it also allow to input csv files from local system

Usage

ec_db_merge(
  db_list,
  datatype = "modern",
  occurrenceStatus = "occurrenceStatus",
  basisOfRecord = "basisOfRecord"
)

Arguments

db_list

list of data frames which we want to merge. e.g. GBIF, iDigbio, InvertEBase and any local file.

datatype

default "modern". datatype accept text input as "modern" or "fossil"

occurrenceStatus

default name for occurrenceStatus column is occurrenceStatus but a different name can be inserted if required.

basisOfRecord

default name for basis of record column is basis of record but a different name can be inserted if required.

Value

A data frame of occurrence records filtered to include only those classified as "modern" or "fossil".

Examples


db1 <- data.frame(
  species = "A",
  decimalLongitude = c(-120, -117, NA, NA),
  decimalLatitude = c(20, 34, NA, NA),
  catalogNumber = c("12345", "89888", "LACM8898", "SDNHM6767"),
  occurrenceStatus = c("present", "", "ABSENT", "Present"),
  basisOfRecord = c("preserved_specimen", "", "fossilspecimen", "material_sample"),
  source = "db1",
  abundance = c(1, NA, 8, 23)
)

db2 <- data.frame(
  species = "A",
  decimalLongitude = c(-120.2, -117.1, NA, NA),
  decimalLatitude = c(20.2, 34.1, NA, NA),
  catalogNumber = c("123452", "898828", "LACM82898", "SDNHM62767"),
  occurrenceStatus = c("present", "", "ABSENT", "Present"),
  basisOfRecord = c("preserved_specimen", "", "fossilspecimen", "material_sample"),
  source = "db2",
  abundance = c(1, 2, 3, 19)
)
db_list <- list(db1, db2)
merge_modern_data <- ec_db_merge(db_list = db_list, "modern")