McLaren Park Observations and Interactions

McLarenFoodWeb.R

# retrieve trophic interactions related to species 
# that were recorded at or near McLaren Park
# using GloBI and GBIF

install.packages(c('rglobi', 'rgbif'))

mcLarenWKT <- 'POLYGON((-122.435 37.726,-122.406 37.726, -122.406 37.710, -122.435 37.710, -122.435 37.726))'
mcLarenObs <- rgbif::occ_search(geometry= mcLarenWKT)

gbifSpeciesKeys <- na.omit(unique(mcLarenObs$data$speciesKey))

globiTaxonIds <- paste('GBIF:', gbifSpeciesKeys, sep='')

trophicInteractions <- rglobi::get_interactions_by_taxa(sourcetaxon = globiTaxonIds, interactiontype='eats')

head(trophicInteractions)

trophicInteractions <- rglobi::get_interactions_by_taxa(sourcetaxon = globiTaxonIds, interactiontype='eats', showfield = c('source_taxon_external_id', 'source_taxon_path', 'interaction_type', 'target_taxon_external_id', 'target_taxon_path'))
#> head(trophicInteractions)
#  source_taxon_external_id
#1             GBIF:7342009
#2             GBIF:7341805
#3             GBIF:7341805
#4             GBIF:7341600
#5             GBIF:7341600
##             GBIF:7341600
#                                                                          source_taxon_path
#1 Animalia | Chordata | Aves | Passeriformes | Parulidae | Oreothlypis | Oreothlypis celata
#2   Animalia | Chordata | Aves | Passeriformes | Parulidae | Setophaga | Setophaga coronata
#3   Animalia | Chordata | Aves | Passeriformes | Parulidae | Setophaga | Setophaga coronata
#4  Animalia | Chordata | Aves | Passeriformes | Emberizidae | Melozone | Melozone crissalis
#5  Animalia | Chordata | Aves | Passeriformes | Emberizidae | Melozone | Melozone crissalis
#6  Animalia | Chordata | Aves | Passeriformes | Emberizidae | Melozone | Melozone crissalis
#  interaction_type target_taxon_external_id
#1             eats             GBIF:2013501
#2             eats             GBIF:2882803
#3             eats             GBIF:3190628
#4             eats             GBIF:3020559
#5             eats             GBIF:3190621
#6             eats                GBIF:1875
#                                                                                                  target_taxon_path
#1        Animalia | Arthropoda | Insecta | Hemiptera | Psylloidea | Psyllidae | Glycaspis | Glycaspis brimblecombei
#2                          Plantae | Magnoliophyta | Magnoliopsida | Ericales | Ericaceae | Arbutus | Arbutus unedo
#3     Plantae | Magnoliophyta | Magnoliopsida | Sapindales | Anacardiaceae | Toxicodendron | Toxicodendron radicans
#4                                             Plantae | Magnoliophyta | Magnoliopsida | Rosales | Rosaceae | Prunus
#5 Plantae | Magnoliophyta | Magnoliopsida | Sapindales | Anacardiaceae | Toxicodendron | Toxicodendron diversilobum
#6                                                     Animalia | Arthropoda | Insecta | Lepidoptera | Papilionoidea