Installation

This should automatically install the package from a CRAN mirror if you have one configured:

install.packages("ridigbio")

If R says the package is unavailable, you may not have set a CRAN mirror. You can do so with:

chooseCRANmirror()

If R says that a binary package is not available, your version of R may be too old. Please review the versions of R that CRAN has built packages for on the CRAN ridigbio package page. You can download the source package and install manually if there is no package built for your version of R. You may also need to install any dependencies.

install.packages("ridigbio", type="source")

On Linux, you may encounter an error during the installation process if you do not have libcurl installed. The method for installing libcurl will vary between distributions, but on Ubuntu you can install the latest version via:

sudo apt install libcurl4

Basic usage

library("ridigbio")
idig_search_records(rq=list(genus="galax"))
idig_search_records(rq=list(family="holothuriidae"), limit=1000)

Complete list of terms that can be used is available here. However, this only contains a subset of the fields. To see all raw fields available with the record API, you can run the following:

record_fields <- idig_meta_fields(type = "records", subset = "raw")
rfall <- data.frame(matrix(ncol = 3, nrow = 0))
for(i in 1:length(record_fields)){
  if(length(record_fields[[i]]) == 2){
    rf <- data.frame(matrix(ncol = 3, nrow = 0))
    rf[1, 1] <-  names(record_fields[i])
    rf[1, 2] <-  (record_fields[[i]])$type
    rf[1, 3] <-  (record_fields[[i]])$fieldName
    rfall <- rbind(rfall, rf)
  }else{
    sub <- record_fields[[i]]
    for(j in 1:length(sub)){
      rf <- data.frame(matrix(ncol = 3, nrow = 0))
      rf[1, 1] <-  names(sub[j])
      rf[1, 2] <-  (sub[[j]])$type
      rf[1, 3] <-  (sub[[j]])$fieldName
      rfall <- rbind(rfall, rf)
    }
  }
}
colnames(rfall) <- c("name", "type", "fieldName")

Recent updates

• Default fields returned to users have been updated to return research-grade fields. Previously, we returned the datecollected field by default, which we do not recommend to be used in scientific research.

  • What is datecollected? This is a field created during the data ingestion process. When a data provider does not provide a full date in the Darwin Core eventDate field, this complete value or the missing parts (i.e., month and/or day) are randomly generated and thus may lack any real meaning. The generated dates are difficult to detect, as they are randomly distributed. We are currently working to modify our ingestion pipeline to avoid randomly generating dates. However, dates remain an issue across biodiversity aggregators and the solution is not clear (see GBIF for example).
  • To prevent user misuse of this term, we will no longer be providing the datecollected field by default and will instead be returning the following fields: c("data.dwc:eventDate", "data.dwc:year", "data.dwc:month", "data.dwc:day").
    • Please be advised that these fields are not in date format. Instead, all dates will be text strings. There are many ways to convert these to dates, for example, see gatoRs remove_duplicate function or ridigbio proposed solution here.

• Additional documentation has been added to streamline data use.

License

MIT