format_bdvis {bdvis} | R Documentation |
Prepare data frame for flagging functions
Description
format_bdvis
renames certain fields in the data frame to make sure the
other package functions knows how to use them. This step is highly
recommended for the proper working of the functions.
Usage
format_bdvis(
indf,
source = NULL,
config = NULL,
quiet = FALSE,
gettaxo = FALSE,
...
)
Arguments
indf |
Required. The data.frame on which to operate. |
source |
Optional. Indicates the package that was used to retrieve the
data. Currently accepted values are "rvertnet", "rgbif", "bdsns" or
"rinat". Either |
config |
Optional. Configuration object indicating mapping of field
names from the data.frame to the DarwinCore standard. Useful when importing
data multiple times from a source not available via the |
quiet |
Optional. Don't show any logging message at all. Defaults to FALSE. |
gettaxo |
optional. Call function gettaxo to build higher level taxanony. Defaults to FALSE. |
... |
Optional. If none of the previous is present, the four key
arguments ( |
Details
When invoked, there are three ways of indicating the function how to
transform the data.frame: using the source
parameter, providing a
config
object with field mapping, or passing individual values to the
mapping function. This is the order in which the function will parse
arguments; source
overrides config
, which overrides other
mapping arguments.
source
refers to the package that was used to retrieve the data.
Currently, three values are supported for this argument: "rgbif
",
"rvertnet
", "besns
" and "rinat
", but many more are on
their way. A caution with "besns
" data is he scientific name has to
be in the field "searchText
".
config
asks for a configuration object holding the mapping of the
field names. This option is basically a shortcut for those users with
custom-formatted data.frames who will use the same mapping many times, to
avoid having to type them each time. In practice, this object is a named list
with the following four fields: Latitude
, Longitude
,
Date_collected
and Scientific_name
. Each element must have a
string indicating the name of the column in the data.frame holding the values #' for that element. If the data.frame doesn't have one or more of these fields, #' put NA
in that element; otherwise, the function will throw an error.
See the examples section.
If none of the two is provided, the function expects the user to provide the mapping by passing the individual column names associated with the right term. See the examples section.
Value
The provided data frame, with field names changed to suite the functioning of further visualization functions.
See Also
Other Data preparation functions:
bdsummary()
,
getcellid()
,
gettaxo()
Examples
## Not run:
# Using the rgbif package and the source argument
if (requireNamespace("rinat", quietly=TRUE)) {
d <- get_inat_obs_project("reptileindia")
d <- format_bdvis(d, source="rinat")
# Using a configuration object, matches 'rinat' schema
conf <- list(Latitude <- "latitude",
Longitude <- "longitude",
Date_collected <- "Observed.on",
Scientific_name <- "Scientific.name")
d <- format_bdvis(d, config=conf)
# Passing individual parameters, all optional
d <- format_bdvis(d,
Latitude <- "lat",
Longitude <- "lng",
Date_collected <- "ObservedOn",
Scientific_name <- "sciname")
}
## End(Not run)