tests/testthat/test-BIEN.r

In BIEN: Tools for Accessing the Botanical Information and Ecology Network Database

#Tests for BIEN package

#Normal testing
schema <- "public"

#List tests

test_that("List functions return a dataframe",{
  
  skip_if_offline()
  
  expect_that(BIEN_list_all(schema = schema),
              is_a("data.frame"))
  
  expect_that(BIEN_list_country("Bahamas",
                                schema = schema),
              is_a("data.frame"))
  
  expect_that(BIEN_list_county(country = "United States",
                               state = "Michigan",
                               county = "Kent",
                               cultivated = TRUE,
                               new.world = FALSE,
                               schema=schema),
              is_a("data.frame"))
  
  expect_that(BIEN_list_state(country = "United States",
                              state = "Rhode Island",
                              schema = schema),
              is_a("data.frame"))

})

#Metadata tests
test_that("Metadata functions return a dataframe",{
  
  skip_if_offline()
  
  expect_that(BIEN_metadata_database_version(schema = schema),
              is_a("data.frame"))
  
})

test_that("Metadata_citation function returns a list",{
  
  skip_if_offline()
  
  expect_that(BIEN_metadata_citation(),
              is_a("list"))
  
})


#Occurrence tests
# test_that("postGIS Occurrence functions return a dataframe",{
#   
#   skip_if_offline()
#   
#   skip_on_cran()
#   
#   expect_that(BIEN_occurrence_box(min.lat = 32.9,
#                                   max.lat = 33,
#                                   min.long = -114,
#                                   max.long = -113.9,
#                                   cultivated = TRUE,
#                                   new.world = FALSE,
#                                   all.taxonomy = T,
#                                   native.status = T,
#                                   natives.only = T,
#                                   observation.type = T,
#                                   political.boundaries = T,
#                                   schema=schema),
#               is_a("data.frame"))
# 
# 
# })



#Occurrence tests
test_that("Occurrence functions return a dataframe",{
  
 skip_if_offline()
  
 skip_on_cran()
  

 expect_that(BIEN_occurrence_country("Bahamas",
                                     schema = schema,
                                     collection.info = T,
                                     limit = 1),
             is_a("data.frame"))
 
 expect_that(BIEN_occurrence_county(country = "United States",
                                    state = "Arizona",
                                    county = "Pima",
                                    limit = 1,
                                    schema = schema),
             is_a("data.frame"))
 
 expect_that(BIEN_occurrence_family(family = "Cactaceae",
                                    limit = 1,
                                    schema = schema),
             is_a("data.frame"))
 
 expect_that(BIEN_occurrence_genus(genus = "Xanthium",
                                   schema = schema,
                                   limit = 10),
             is_a("data.frame"))
 
 expect_that(BIEN_occurrence_species(species = "Xanthium strumarium",
                                     cultivated = T,
                                     new.world = F,
                                     all.taxonomy = T,
                                     native.status = T,
                                     observation.type = T,
                                     political.boundaries = T,
                                     limit = 1,
                                     schema = schema),
             is_a("data.frame"))
 
 expect_that(BIEN_occurrence_state(country = "United States",
                                   state = "Rhode Island",
                                   schema = schema,
                                   limit = 10),
             is_a("data.frame"))
 
 expect_that(BIEN_occurrence_sf( BIEN_ranges_load_species(species = "Aa argyrolepis"),
                                              limit = 10),
             is_a("data.frame"))
 
 # expect_that(BIEN_occurrence_records_per_species(),
 #             is_a("data.frame"))
 
 })



#Phylogeny
test_that("Phylogeny functions return a phylogeny",{
  
  skip_if_offline()
  
  expect_that(BIEN_phylogeny_complete(n_phylogenies = 2,
                                      schema = schema),
              is_a("multiPhylo"))
  
  expect_that(BIEN_phylogeny_conservative(schema = schema),
              is_a("phylo"))
  
})

#Plot
test_that("Plot functions return a dataframe",{
  
  skip_if_offline()
  
  skip_on_cran()
  
 expect_that(BIEN_plot_country("Puerto Rico",
                               cultivated = T,
                               new.world = F,
                               all.taxonomy = T,
                               native.status = T,
                               political.boundaries = T,
                               all.metadata = T,
                               schema = schema,
                               limit = 1),
             is_a("data.frame"))
 
 expect_that(BIEN_plot_dataset(dataset = "SALVIAS",
                               schema = schema,
                               limit = 1),
             is_a("data.frame"))
 
 expect_that(BIEN_plot_datasource("test",
                                  schema = schema),
             is_a("data.frame"))
 
 expect_that(BIEN_plot_list_datasource(schema = schema),
             is_a("data.frame"))
 
 expect_that(BIEN_plot_list_sampling_protocols(schema = schema),
             is_a("data.frame"))
 
 expect_that(BIEN_plot_metadata(schema = schema),
             is_a("data.frame"))
 
 expect_that(BIEN_plot_name("test",
                            schema = schema,
                            collection.info = T),
             is_a("data.frame"))
 
 expect_that(BIEN_plot_sampling_protocol(sampling_protocol = "test",
                                         natives.only = T,
                                         schema = schema),
             is_a("data.frame"))
 
 expect_that(BIEN_plot_state(country = "United States",
                             state = "Michigan",
                             limit = 1,
                             schema = schema),
             is_a("data.frame"))
 
 })

#Ranges

test_that("Ranges functions return an sf",{
  
  skip_if_offline()
  
  expect_that(BIEN_ranges_load_species(species = "Abies amabilis",
                                       schema = schema),
              is_a("sf"))
  
})

#Stem

test_that("Stem functions return a dataframe",{
  
  skip_if_offline()
  
  skip_on_cran()
  
 expect_that(BIEN_stem_species(species = "Abies amabilis",
                               natives.only = T,
                               native.status = T,
                               collection.info = T,
                               schema = schema),
             is_a("data.frame"))
 
 expect_that(BIEN_stem_genus(genus = "Abies",
                             natives.only = T,
                             native.status = T,
                             schema = schema,
                             limit = 1),
             is_a("data.frame"))
 
 expect_that(BIEN_stem_family(family = "Selaginellaceae",
                              natives.only = T,
                              native.status = T,
                              schema = schema),
             is_a("data.frame"))

})

#Taxonomy
test_that("Taxonomy functions return a dataframe",{
  
  skip_if_offline()
  
  
  expect_that(BIEN_taxonomy_family("Cactaceae",
                                   schema = schema),
              is_a("data.frame"))
  
  expect_that(BIEN_taxonomy_genus("Xanthium",
                                  schema = schema),
              is_a("data.frame"))
  
  expect_that(BIEN_taxonomy_species("Xanthium strumarium",
                                    schema = schema),
              is_a("data.frame"))
  
})

#trait

test_that("Trait functions return a dataframe",{
  
  skip_if_offline()
  
  
  expect_that(BIEN_trait_family("Cactaceae",
                                schema = schema),
              is_a("data.frame"))
  
  expect_that(BIEN_trait_genus("Xanthium",
                               schema = schema),
              is_a("data.frame"))
  
  expect_that(BIEN_trait_list(schema = schema),
              is_a("data.frame"))
  
  expect_that(BIEN_trait_mean(species = "Xanthium strumarium",
                              trait = "leaf dry mass per leaf fresh mass",
                              schema = schema),
              is_a("data.frame"))
  
  expect_that(BIEN_trait_species("Xanthium strumrium",
                                 all.taxonomy = TRUE,
                                 political.boundaries = TRUE,
                                 schema = schema),
              is_a("data.frame"))
  
  expect_that(BIEN_trait_trait("leaf dry mass per leaf fresh mass",
                               schema = schema,
                               limit = 1),
              is_a("data.frame"))
  
  expect_that(BIEN_trait_traitbyfamily(trait = "leaf dry mass per leaf fresh mass",
                                       family = "Asteraceae",
                                       schema = schema,
                                       limit = 1),
              is_a("data.frame"))
  
  expect_that(BIEN_trait_traitbygenus(trait = "leaf dry mass per leaf fresh mass",
                                      genus = "Xanthium",
                                      schema = schema,
                                      limit = 1),
              is_a("data.frame"))
  
  expect_that(BIEN_trait_traitbyspecies(trait = "leaf dry mass per leaf fresh mass",
                                        species = "Xanthium strumarium",
                                        schema = schema,
                                        limit = 1),
              is_a("data.frame"))
  
  #expect_that(BIEN_trait_traits_per_species(schema=schema) ,is_a("data.frame"))
  
})