barroso_dwc

Format Biodiversity Datasets into Darwin Core

barRoso::barroso_dwc()

Description

Formats a dataset of herbarium records into Darwin Core column names and value formats, so that records downloaded from different sources, such as GBIF, speciesLink, REFLORA and JABOT, can be combined and standardized together.

Details

The source of the dataset is recognized from its columns and values, or can be given in source. Then:

Columns named as Darwin Core terms in other cases, e.g. recordedby or decimallatitude, are renamed into the terms, e.g. recordedBy and decimalLatitude, for any source.
speciesLink: the columns of the older speciesLink format are renamed into Darwin Core terms, e.g. collector into recordedBy, collectornumber into recordNumber, latitude into decimalLatitude, and species (just the epithet) into specificEpithet; spp (the binomial) becomes species, as in GBIF. The year, month and day of identification become dateIdentified; the author is added to scientificName; dates like "23/11/2011" become "2011-11-23"; and a missing recordNumber is taken from fieldNumber.
REFLORA (as returned by refloraR): the determiner "Administrador" (the system user, given to most records) becomes NA; dates like "11/10/2006" become "2006-10-11"; type status in Latin like "ISOTYPUS" becomes "isotype"; and the institution of RB becomes "JBRJ", as in GBIF and JABOT.
JABOT (as returned by jabotR): dates like "2008-9-26" or "22/4/2020" become "2008-09-26" and "2020-04-22".
GBIF: downloads are already in Darwin Core, so only the column names are checked.

In all sources, a binomial species column is created from genus and specificEpithet when missing, as in GBIF downloads. Columns that are not Darwin Core terms are kept unchanged.

By default, all columns are returned as character. Downloads of the same source may otherwise have different column types, e.g. coordinatePrecision as integer in a species with values and as character in a species without them, as in the speciesLink API used by plantR::rspeciesLink(), and then they cannot be combined with dplyr::bind_rows().

barroso_cat() runs this function on each source before combining them.

Arguments

Argument	Description
df	A data frame of biodiversity records.
source	The source of the records: `"auto"` (default) to recognize it from the data, or one of `"speciesLink"`, `"REFLORA"`, `"JABOT"` or `"GBIF"`.
as_character	Logical; if `TRUE` (default), all columns are returned as character, so the outputs of different downloads can always be combined.
verbose	Logical; if `TRUE`, reports the source and what was changed.

Value

The data frame with Darwin Core column names and value formats.

Examples

splink <- data.frame(collector = "Queiroz, L. P.", collectornumber = "1350",
                     collectioncode = "HUEFS", genus = "Ormosia", species = "arborea",
                     scientificname = "Ormosia arborea",
                     scientificnameauthor = "(Vell.) Harms",
                     yearidentified = "2005", monthidentified = "3",
                     dayidentified = NA, latitude = "-12.97", longitude = "-38.5")
barroso_dwc(splink)

--- title: 'barroso_dwc' description: 'Format Biodiversity Datasets into Darwin Core' toc: true toc-depth: 3 --- ```{r} #| eval: false barRoso::barroso_dwc() ``` ### Description Formats a dataset of herbarium records into [Darwin Core](https://dwc.tdwg.org/terms/) column names and value formats, so that records downloaded from different sources, such as GBIF, speciesLink, REFLORA and JABOT, can be combined and standardized together. ### Details The source of the dataset is recognized from its columns and values, or can be given in `source`. Then: - Columns named as Darwin Core terms in other cases, e.g. `recordedby` or `decimallatitude`, are renamed into the terms, e.g. `recordedBy` and `decimalLatitude`, for any source. - speciesLink: the columns of the older speciesLink format are renamed into Darwin Core terms, e.g. `collector` into `recordedBy`, `collectornumber` into `recordNumber`, `latitude` into `decimalLatitude`, and `species` (just the epithet) into `specificEpithet`; `spp` (the binomial) becomes `species`, as in GBIF. The year, month and day of identification become `dateIdentified`; the author is added to `scientificName`; dates like `"23/11/2011"` become `"2011-11-23"`; and a missing `recordNumber` is taken from `fieldNumber`. - REFLORA (as returned by refloraR): the determiner `"Administrador"` (the system user, given to most records) becomes `NA`; dates like `"11/10/2006"` become `"2006-10-11"`; type status in Latin like `"ISOTYPUS"` becomes `"isotype"`; and the institution of RB becomes `"JBRJ"`, as in GBIF and JABOT. - JABOT (as returned by jabotR): dates like `"2008-9-26"` or `"22/4/2020"` become `"2008-09-26"` and `"2020-04-22"`. - GBIF: downloads are already in Darwin Core, so only the column names are checked. In all sources, a binomial `species` column is created from `genus` and `specificEpithet` when missing, as in GBIF downloads. Columns that are not Darwin Core terms are kept unchanged. By default, all columns are returned as character. Downloads of the same source may otherwise have different column types, e.g. `coordinatePrecision` as integer in a species with values and as character in a species without them, as in the speciesLink API used by `plantR::rspeciesLink()`, and then they cannot be combined with `dplyr::bind_rows()`. `barroso_cat()` runs this function on each source before combining them. ### Arguments | Argument | Description | |---|---| | df | A data frame of biodiversity records. | | source | The source of the records: `"auto"` (default) to recognize it from the data, or one of `"speciesLink"`, `"REFLORA"`, `"JABOT"` or `"GBIF"`. | | as_character | Logical; if `TRUE` (default), all columns are returned as character, so the outputs of different downloads can always be combined. | | verbose | Logical; if `TRUE`, reports the source and what was changed. | ### Value The data frame with Darwin Core column names and value formats. ### Examples ```r splink <- data.frame(collector = "Queiroz, L. P.", collectornumber = "1350", collectioncode = "HUEFS", genus = "Ormosia", species = "arborea", scientificname = "Ormosia arborea", scientificnameauthor = "(Vell.) Harms", yearidentified = "2005", monthidentified = "3", dayidentified = NA, latitude = "-12.97", longitude = "-38.5") barroso_dwc(splink) ```