The package NSR is designed to interact with the Native Species Resolver of the Botanical Information and Ecology Network.
#Installing NSR
library(devtools)
install_github("EnquistLab/RNSR/NSR")#The easiest case: one species in one political division
library(NSR)
NSR_simple(species = "Acer rubrum",
country = "Canada",
state_province = "Ontario")## family genus species country state_province county_parish
## 1 Sapindaceae Acer Acer rubrum Canada Ontario
## poldiv_full poldiv_type native_status_country
## 1 Canada:Ontario state_province N
## native_status_state_province native_status_county_parish native_status
## 1 N N
## native_status_reason native_status_sources isIntroduced
## 1 Native to region, as per checklist powo, usda 0
## isCultivatedNSR is_cultivated_taxon user_id
## 1 0 0 1#Multiple species When submitting data into the NSR, the function expects a data.frame containing 5 columns as input, however only the columns âspeciesâ and âcountryâ (the first two) need to be populated. If you ever forget the input format, you can use the function NSR_template as a quick look-up, or to populate.
## species country state_province county_parish user_id
## 1 NA NA NA NA NA#Example data
#First, pull the example data that are included with the package
data("nsr_testfile")
head(nsr_testfile)## taxon country state_province county_parish user_id
## 1 Eucalyptus Australia Western Australia 1
## 2 Abrothallus bertianus Austria 2
## 3 Cocos nucifera Jamaica 3
## 4 Eucalyptus Mexico 4
## 5 Larrea tridentata Mexico 5
## 6 Pinus ayacahuite Mexico 6example_results <- NSR(nsr_testfile)
head(example_results)## family genus species country state_province
## 1 Myrtaceae Eucalyptus Australia Western Australia
## 2 Abrothallus Abrothallus bertianus Austria
## 3 Arecaceae Cocos Cocos nucifera Jamaica
## 4 Myrtaceae Eucalyptus Mexico
## 5 Zygophyllaceae Larrea Larrea tridentata Mexico
## 6 Pinaceae Pinus Pinus ayacahuite Mexico
## county_parish poldiv_full poldiv_type
## 1 Australia:Western Australia state_province
## 2 Austria country
## 3 Jamaica country
## 4 Mexico country
## 5 Mexico country
## 6 Mexico country
## native_status_country native_status_state_province
## 1 N N
## 2 A
## 3 I
## 4 I
## 5 N
## 6 N
## native_status_county_parish native_status
## 1 N
## 2 A
## 3 I
## 4 I
## 5 N
## 6 N
## native_status_reason native_status_sources isIntroduced
## 1 Native to region, as per checklist powo 0
## 2 Absent from all checklists for region powo 1
## 3 Introduced to region, as per checklist fwi, powo, weakley 1
## 4 Introduced to region, as per checklist powo 1
## 5 Native to region, as per checklist mexico, powo 0
## 6 Native to region, as per checklist mexico, powo 0
## isCultivatedNSR is_cultivated_taxon user_id
## 1 0 0 1
## 2 0 0 2
## 3 0 0 3
## 4 0 0 4
## 5 0 0 5
## 6 0 0 6#Source metadata To access metadata for the sources currently consulted by the NSR, use the function NSR_metadata(). To figure out which political divisions contain checklists that were consulted by the NSR, use the function NSR_political_divisions().
sources <- NSR_metadata()
checklist_per_political_divisions <- NSR_political_divisions()
# If you'd rather see which political divisions are available within each checklist, set "by_country" to FALSE
political_divisions_per_checklist <- NSR_political_divisions(by_country = FALSE)RetroSearch is an open source project built by @garambo | Open a GitHub Issue
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