To avoid getting fungi, animals, etc, in my plant data, I added the parameter Scope = 'p', which according to the function docs should restrict my query to plants. However, my query still returned a handful of results that are not plants. Example code below (please add your own splinkkey):
splink_raw <- rspeciesLink(
Scope = "p",
stateProvince = "Sao Paulo", county = "AVARÉ AVARE",
key = splinkkey)
table(splink_raw$kingdom, useNA="always")
The result of this table is the following:
| Bacteria |
Chromista |
Fungi |
Plantae |
NA |
| 1 |
1 |
4 |
691 |
2 |
I assume this is some problem on the side of SpeciesLink (and we should probably send them note) but I'm opening this issue to let you know this option may not be reliable. We might prefer to filter by kingdom after the query, though there is a large number of entries with NA values for kingdom. For the same query as above but with default Scope, the table is:
| Animalia |
Arthropoda |
Bacteria |
Chromista |
Fungi |
Plantae |
NA |
| 220 |
3 |
1 |
1 |
4 |
691 |
133 |
To avoid getting fungi, animals, etc, in my plant data, I added the parameter
Scope = 'p', which according to the function docs should restrict my query to plants. However, my query still returned a handful of results that are not plants. Example code below (please add your own splinkkey):The result of this table is the following:
I assume this is some problem on the side of SpeciesLink (and we should probably send them note) but I'm opening this issue to let you know this option may not be reliable. We might prefer to filter by kingdom after the query, though there is a large number of entries with
NAvalues for kingdom. For the same query as above but with default Scope, the table is: