classify_occ {naturaList} | R Documentation |
Classify occurrence records in levels of confidence in species identification
Description
Classifies occurrence records in levels of confidence in species identification
Usage
classify_occ(
occ,
spec = NULL,
na.rm.coords = TRUE,
crit.levels = c("det_by_spec", "not_spec_name", "image", "sci_collection", "field_obs",
"no_criteria_met"),
ignore.det.names = NULL,
spec.ambiguity = "not.spec",
institution.code = "institutionCode",
collection.code = "collectionCode",
catalog.number = "catalogNumber",
year = "year",
date.identified = "dateIdentified",
species = "species",
identified.by = "identifiedBy",
decimal.latitude = "decimalLatitude",
decimal.longitude = "decimalLongitude",
basis.of.record = "basisOfRecord",
media.type = "mediaType",
occurrence.id = "occurrenceID",
institution.source,
year.event,
scientific.name,
determined.by,
latitude,
longitude,
basis.of.rec,
occ.id
)
Arguments
occ |
data frame with occurrence records information. |
spec |
data frame with specialists' names. See details. |
na.rm.coords |
logical. If |
crit.levels |
character. Vector with levels of confidence in decreasing
order. The criteria allowed are |
ignore.det.names |
character vector indicating strings in
|
spec.ambiguity |
character. Indicates how to deal with ambiguity in
specialists names. |
institution.code |
column name of |
collection.code |
column name of |
catalog.number |
column name of |
year |
Column name of |
date.identified |
Column name of |
species |
column name of |
identified.by |
column name of |
decimal.latitude |
column name of |
decimal.longitude |
column name of |
basis.of.record |
column name with the specific nature of the data record. See details. |
media.type |
column name of |
occurrence.id |
column name of |
institution.source |
deprecated, use |
year.event |
deprecated, use |
scientific.name |
deprecated, use |
determined.by |
deprecated, use |
latitude |
deprecated, use |
longitude |
deprecated, use |
basis.of.rec |
deprecated, use |
occ.id |
deprecated, use |
Details
spec
data frame must have columns separating LastName
,
Name
and Abbrev
. See create_spec_df
function for a easy way to produce this data frame.
When ignore.det.name = NULL
(default), the function ignores
strings with "RRC ID Flag", "NA", "", "-" and "_".
When a character
vector is provided, the function adds the default strings to the provided
character vector and ignore all these strings as being a name of a taxonomist.
The function classifies the occurrence records in six levels of confidence in species identification. The six levels are:
-
det_by_spec
- when the identification was made by a specialists which is present in the list of specialists provided in thespec
argument; -
not_spec_name
- when the identification was made by a name who is not a specialist name provide inspec
; -
image
- the occurrence have not name of a identifier, but present an image associated; -
sci_collection
- the occurrence have not name of a identifier, but preserved in a scientific collection; -
field_obs
- the occurrence have not name of a identifier, but it was identified in field observation; no_criteria_met
- no other criteria was met.
The (decreasing) order of the levels in the character vector determines the classification level order.
basis.of.record
is a character vector with one of the following
types of record: PRESERVED_SPECIMEN
, PreservedSpecimen
,
HUMAN_OBSERVATION
or HumanObservation
, as in GBIF data
'basisOfRecord'.
media.type
uses the same pattern as GBIF mediaType column,
indicating the existence of an associated image with stillImage
.
Value
The occ
data frame plus the classification of each record
in a new column, named naturaList_levels
.
Author(s)
Arthur V. Rodrigues
See Also
Examples
data("A.setosa")
data("speciaLists")
occ.class <- classify_occ(A.setosa, speciaLists)