% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/occ_issues.r
\name{occ_issues}
\alias{occ_issues}
\title{Parse and examine further GBIF issues on a dataset.}
\usage{
occ_issues(.data, ..., mutate = NULL)
}
\arguments{
\item{.data}{Output from a call to \code{occ_search}, but only if \code{return="all"},
or \code{return="data"}, otherwise function stops with error}

\item{...}{Named parameters to only get back (e.g., cdround), or to remove (e.g. -cdround).}

\item{mutate}{(character) One of:
\itemize{
 \item split Split issues into new columns.
 \item split_expand Split into new columns, and expand issue names.
 \item expand Expand issue abbreviated codes into descriptive names.
}
For split and split_expand, values in cells become y ("yes") or n ("no").}
}
\description{
Parse and examine further GBIF issues on a dataset.
}
\details{
See also the vignette \code{Cleaning data using GBIF issues}.

Note that you can also query based on issues, e.g.,
\code{occ_search(taxonKey=1, issue='DEPTH_UNLIKELY')}. However, I imagine it's more likely
that you want to search for occurrences based on a taxonomic name, or geographic area,
not based on issues, so it makes sense to pull data down, then clean as needed
using this function.

This function only affects the \code{data} element in the \code{gbif} class that is
returned from a call to \code{\link[rgbif]{occ_search}}. Maybe in a future version
we will remove the associated records from the \code{hierarchy} and \code{media}
elements as they are remove from the \code{data} element.
}
\examples{
\dontrun{
## what do issues mean, can print whole table, or search for matches
head(gbif_issues())
gbif_issues()[ gbif_issues()$code \%in\% c('cdround','cudc','gass84','txmathi'), ]

# compare out data to after occ_issues use
(out <- occ_search(limit=100))
out \%>\% occ_issues(cudc)

# Parsing output by issue
(res <- occ_search(geometry='POLYGON((30.1 10.1, 10 20, 20 40, 40 40, 30.1 10.1))', limit = 50))

## or parse issues in various ways
### inlude only rows with gass84 issue
gg <- res \%>\% occ_issues(gass84)
NROW(res$data)
NROW(gg$data)
head(res$data)[,c(1:5)]
head(gg$data)[,c(1:5)]

### remove data rows with certain issue classes
res \%>\% occ_issues(-cdround, -cudc)

### split issues into separate columns
res \%>\% occ_issues(mutate = "split")
res \%>\% occ_issues(-cudc, -mdatunl, mutate = "split")
res \%>\% occ_issues(gass84, mutate = "split")

### expand issues to more descriptive names
res \%>\% occ_issues(mutate = "expand")

### split and expand
res \%>\% occ_issues(mutate = "split_expand")

### split, expand, and remove an issue class
res \%>\% occ_issues(-cudc, mutate = "split_expand")

## Or you can use occ_issues without \%>\%
occ_issues(res, -cudc, mutate = "split_expand")
}
}
\references{
\url{http://gbif.github.io/gbif-api/apidocs/org/gbif/api/vocabulary/OccurrenceIssue.html}
}