Description Usage Arguments Details References Examples
Set of S3 methods to summarize, filter and get unique occurrence data retrieved using occurrences
.
This uses information based on selections of assertions (quality assurance issues NBN has identified), spatial and temporal data.
1 2 3 4 5 6 7 8 9 10 11 12 | ## S3 method for class 'occurrences'
summary(object, ...)
## S3 method for class 'occurrences'
unique(x, incomparables = FALSE, spatial = 0,
temporal = NULL, na.rm = FALSE, ...)
## S3 method for class 'occurrences'
subset(x, remove.fatal = TRUE,
exclude.spatial = "error", exclude.temporal = "error",
exclude.taxonomic = "error", max.spatial.uncertainty,
keep.missing.spatial.uncertainty = TRUE, ...)
|
object |
list: an 'occurrence' object that has been downloaded using |
... |
not currently used |
x |
list: an 'occurrence' object that has been downloaded using |
incomparables |
logical/numeric: currently ignored, but needed for S3 method consistency |
spatial |
numeric: specifies a rounding value in decimal degrees used to to create a unique subset of the data. Value of 0 means no rounding and use values as is. Values <0 mean ignore spatial unique parameter |
temporal |
character: specifies the temporal unit for which to keep unique records; this can be by "year", "month", "yearmonth" or "full" date. NULL means ignore temporal unique parameter |
na.rm |
logical: keep (FALSE) or remove (TRUE) missing spatial or temporal data |
remove.fatal |
logical: remove flagged assertion issues that are considered "fatal"; see |
exclude.spatial |
character vector: defining flagged spatial assertion issues to be removed. Values can include 'warnings','error','missing','none'; see |
exclude.temporal |
character vector: defining flagged temporal assertion issues to be removed. Values can include 'warnings','error','missing','none'; see |
exclude.taxonomic |
character vector: defining flagged taxonomic assertion issues to be removed. Values can include 'warnings','error','missing','none'; see |
max.spatial.uncertainty |
numeric: number defining the maximum spatial uncertainty (in meters) one is willing to accept. |
keep.missing.spatial.uncertainty |
logical: keep (FALSE) or remove (TRUE) information missing spatial uncertainty data. |
unique
will give the min value for all columns that are not used in the aggregation.
http://stat.ethz.ch/R-manual/R-devel/library/methods/html/Methods.html
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 | ## Not run:
#download some observations
x <- occurrences(taxon="Leuctra geniculata",download_reason_id=10)
#summarize the occurrences
summary(x)
#keep spatially unique data at 0.01 degrees (latitude and longitude)
tt <- unique(x,spatial=0.01)
summary(tt)
#keep spatially unique data that is also unique year/month for the collection date
tt <- unique(x,spatial=0,temporal='yearmonth')
summary(tt)
#keep only information for which fatal or "error" assertions do not exist
tt <- subset(x)
summary(tt)
## End(Not run)
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