NSR R package

Native Species Resolver

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 “species” and “country” (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.

head(NSR_template())

##   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                                       6

example_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)