here::i_am("r-tutorials/SDM-lab-spocc.qmd")here() starts at /Users/eli.holmes/Documents/GitHub/NOAAHackDaysdir_data <- here::here("r-tutorials", "data")SDM lab 1 - Downloading species data with spocc
First tell R where you are in the file structure. Before running this code, the folder specified by dir_data if it does not exist already.
Set the file paths.
# data as csv file
obs_csv <- file.path(dir_data, "obs.csv")
# data as geojson
obs_geo <- file.path(dir_data, "obs.geojson")Load libraries.
require(sf)
require(spocc)
require(knitr)
require(dplyr)
require(readr)
require(mapview)spocc R package
The spocc R package which allows us to query species occurrence data from a variety of sources:
spocc: A programmatic interface to many species occurrence data sources, including GBIF, iNaturalist, Berkeley Ecoinformatics Engine, eBird, iDigBio, VertNet, OBIS, and ALA. Includes functionality for retrieving species occurrence data, and combining that data.
Brown-throated sloth
This is a classic example for Species Distribution modeling. It is a sloth found in South America.
if (!file.exists(obs_csv)){
# get species occurrence data from GBIF with coordinates
res <- spocc::occ(
query = 'Bradypus variegatus',
from = 'gbif', has_coords = TRUE)
# extract data frame from result
df <- res$gbif$data[[1]]
# write data to a file
readr::write_csv(df, obs_csv)
}else{
df <- readr::read_csv(obs_csv)
}Rows: 500 Columns: 83
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr (55): name, issues, prov, scientificName, datasetKey, publishingOrgKey,...
dbl (21): longitude, latitude, key, crawlId, taxonKey, kingdomKey, phylumKe...
lgl (1): isInCluster
dttm (5): lastCrawled, lastParsed, dateIdentified, modified, lastInterpreted
date (1): eventDate
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
Look at the objects
Type names(res) and then names(res$gbif). Then type df to see what is in the dataframe.
Make a table of the first few lines of the dataframe.
knitr::kable(df %>% head)| name | longitude | latitude | issues | prov | key | scientificName | datasetKey | publishingOrgKey | installationKey | hostingOrganizationKey | publishingCountry | protocol | lastCrawled | lastParsed | crawlId | basisOfRecord | occurrenceStatus | taxonKey | kingdomKey | phylumKey | classKey | orderKey | familyKey | genusKey | speciesKey | acceptedTaxonKey | acceptedScientificName | kingdom | phylum | order | family | genus | species | genericName | specificEpithet | taxonRank | taxonomicStatus | iucnRedListCategory | dateIdentified | coordinateUncertaintyInMeters | continent | stateProvince | year | month | day | eventDate | modified | lastInterpreted | references | license | isInCluster | datasetName | recordedBy | identifiedBy | geodeticDatum | class | countryCode | country | rightsHolder | identifier | http://unknown.org/nick | verbatimEventDate | collectionCode | gbifID | verbatimLocality | occurrenceID | taxonID | catalogNumber | institutionCode | eventTime | http://unknown.org/captive | identificationID | occurrenceRemarks | sex | lifeStage | individualCount | vernacularName | locality | higherClassification | informationWithheld | infraspecificEpithet | identificationRemarks |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Bradypus variegatus Schinz, 1825 | -79.54650 | 8.987403 | cdc,cdround | gbif | 4011797263 | Bradypus variegatus Schinz, 1825 | 50c9509d-22c7-4a22-a47d-8c48425ef4a7 | 28eb1a3f-1c15-4a95-931a-4af90ecb574d | 997448a8-f762-11e1-a439-00145eb45e9a | 28eb1a3f-1c15-4a95-931a-4af90ecb574d | US | DWC_ARCHIVE | 2023-08-17 14:21:14 | 2023-08-18 13:22:12 | 390 | HUMAN_OBSERVATION | PRESENT | 2436353 | 1 | 44 | 359 | 1494 | 9418 | 2436350 | 2436353 | 2436353 | Bradypus variegatus Schinz, 1825 | Animalia | Chordata | Pilosa | Bradypodidae | Bradypus | Bradypus variegatus | Bradypus | variegatus | SPECIES | ACCEPTED | LC | 2023-01-02 21:10:21 | 61 | NORTH_AMERICA | Panamá | 2023 | 1 | 2 | 2023-01-02 | 2023-03-09 20:50:19 | 2023-08-18 13:22:12 | https://www.inaturalist.org/observations/145694886 | http://creativecommons.org/licenses/by/4.0/legalcode | FALSE | iNaturalist research-grade observations | Kai Squires | Kai Squires | WGS84 | Mammalia | PA | Panama | Kai Squires | 145694886 | squiresk | 2023/01/02 9:49 AM | Observations | 4011797263 | Panama City, Panama | https://www.inaturalist.org/observations/145694886 | 47067 | 145694886 | iNaturalist | 09:49:00-05:00 | wild | 324468453 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| Bradypus variegatus Schinz, 1825 | -84.68933 | 10.519427 | cdc,cdround | gbif | 4091593493 | Bradypus variegatus Schinz, 1825 | 50c9509d-22c7-4a22-a47d-8c48425ef4a7 | 28eb1a3f-1c15-4a95-931a-4af90ecb574d | 997448a8-f762-11e1-a439-00145eb45e9a | 28eb1a3f-1c15-4a95-931a-4af90ecb574d | US | DWC_ARCHIVE | 2023-08-17 14:21:14 | 2023-08-18 13:41:19 | 390 | HUMAN_OBSERVATION | PRESENT | 2436353 | 1 | 44 | 359 | 1494 | 9418 | 2436350 | 2436353 | 2436353 | Bradypus variegatus Schinz, 1825 | Animalia | Chordata | Pilosa | Bradypodidae | Bradypus | Bradypus variegatus | Bradypus | variegatus | SPECIES | ACCEPTED | LC | 2023-01-31 13:22:05 | 4 | NORTH_AMERICA | Alajuela | 2023 | 1 | 2 | 2023-01-02 | 2023-04-13 01:01:22 | 2023-08-18 13:41:19 | https://www.inaturalist.org/observations/145696593 | http://creativecommons.org/licenses/by-nc/4.0/legalcode | FALSE | iNaturalist research-grade observations | Jessica Rae | Wren | WGS84 | Mammalia | CR | Costa Rica | Jessica Rae | 145696593 | altoidsboi | 2023/01/02 3:54 PM | Observations | 4091593493 | Alajuela Province, San Carlos, Costa Rica | https://www.inaturalist.org/observations/145696593 | 47067 | 145696593 | iNaturalist | 15:54:00-06:00 | wild | 330896608 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| Bradypus variegatus Schinz, 1825 | -82.15604 | 9.316584 | cdc,cdround | gbif | 4028722131 | Bradypus variegatus Schinz, 1825 | 50c9509d-22c7-4a22-a47d-8c48425ef4a7 | 28eb1a3f-1c15-4a95-931a-4af90ecb574d | 997448a8-f762-11e1-a439-00145eb45e9a | 28eb1a3f-1c15-4a95-931a-4af90ecb574d | US | DWC_ARCHIVE | 2023-08-17 14:21:14 | 2023-08-18 13:41:57 | 390 | HUMAN_OBSERVATION | PRESENT | 2436353 | 1 | 44 | 359 | 1494 | 9418 | 2436350 | 2436353 | 2436353 | Bradypus variegatus Schinz, 1825 | Animalia | Chordata | Pilosa | Bradypodidae | Bradypus | Bradypus variegatus | Bradypus | variegatus | SPECIES | ACCEPTED | LC | 2023-01-03 18:24:03 | 75 | NORTH_AMERICA | Bocas del Toro | 2023 | 1 | 3 | 2023-01-03 | 2023-02-02 01:16:10 | 2023-08-18 13:41:57 | https://www.inaturalist.org/observations/145767431 | http://creativecommons.org/licenses/by-nc/4.0/legalcode | FALSE | iNaturalist research-grade observations | lucybrown19 | lucybrown19 | WGS84 | Mammalia | PA | Panama | lucybrown19 | 145767431 | lucybrown19 | Tue Jan 03 2023 11:36:24 GMT -0500 (EST) | Observations | 4028722131 | Bocas del Toro, PA-BC, PA | https://www.inaturalist.org/observations/145767431 | 47067 | 145767431 | iNaturalist | 11:36:24-05:00 | wild | 324686542 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| Bradypus variegatus Schinz, 1825 | -84.06505 | 10.449010 | cdc,cdround | gbif | 4011771409 | Bradypus variegatus Schinz, 1825 | 50c9509d-22c7-4a22-a47d-8c48425ef4a7 | 28eb1a3f-1c15-4a95-931a-4af90ecb574d | 997448a8-f762-11e1-a439-00145eb45e9a | 28eb1a3f-1c15-4a95-931a-4af90ecb574d | US | DWC_ARCHIVE | 2023-08-17 14:21:14 | 2023-08-18 13:41:03 | 390 | HUMAN_OBSERVATION | PRESENT | 2436353 | 1 | 44 | 359 | 1494 | 9418 | 2436350 | 2436353 | 2436353 | Bradypus variegatus Schinz, 1825 | Animalia | Chordata | Pilosa | Bradypodidae | Bradypus | Bradypus variegatus | Bradypus | variegatus | SPECIES | ACCEPTED | LC | 2023-01-03 19:44:25 | 5 | NORTH_AMERICA | Heredia | 2023 | 1 | 3 | 2023-01-03 | 2023-01-16 15:12:42 | 2023-08-18 13:41:03 | https://www.inaturalist.org/observations/145772860 | http://creativecommons.org/licenses/by/4.0/legalcode | FALSE | iNaturalist research-grade observations | Chris Harrison | Chris Harrison | WGS84 | Mammalia | CR | Costa Rica | Chris Harrison | 145772860 | sandboa | 2023-01-03 11:57:43 | Observations | 4011771409 | Sarapiquí, CR-HE, CR | https://www.inaturalist.org/observations/145772860 | 47067 | 145772860 | iNaturalist | 11:57:43-06:00 | wild | 324705982 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| Bradypus variegatus Schinz, 1825 | -79.64967 | 9.061424 | cdc,cdround | gbif | 4014910775 | Bradypus variegatus Schinz, 1825 | 50c9509d-22c7-4a22-a47d-8c48425ef4a7 | 28eb1a3f-1c15-4a95-931a-4af90ecb574d | 997448a8-f762-11e1-a439-00145eb45e9a | 28eb1a3f-1c15-4a95-931a-4af90ecb574d | US | DWC_ARCHIVE | 2023-08-17 14:21:14 | 2023-08-18 13:21:15 | 390 | HUMAN_OBSERVATION | PRESENT | 2436353 | 1 | 44 | 359 | 1494 | 9418 | 2436350 | 2436353 | 2436353 | Bradypus variegatus Schinz, 1825 | Animalia | Chordata | Pilosa | Bradypodidae | Bradypus | Bradypus variegatus | Bradypus | variegatus | SPECIES | ACCEPTED | LC | 2023-01-04 02:04:32 | 365 | NORTH_AMERICA | Panamá | 2023 | 1 | 3 | 2023-01-03 | 2023-03-09 20:50:14 | 2023-08-18 13:21:15 | https://www.inaturalist.org/observations/145797456 | http://creativecommons.org/licenses/by-nc/4.0/legalcode | FALSE | iNaturalist research-grade observations | Matt Cohen and Elizabeth Hargrave | Matt Cohen and Elizabeth Hargrave | WGS84 | Mammalia | PA | Panama | Matt Cohen and Elizabeth Hargrave | 145797456 | mattandeliz | 2023/01/03 9:02 AM | Observations | 4014910775 | Panama | https://www.inaturalist.org/observations/145797456 | 47067 | 145797456 | iNaturalist | 09:02:00-05:00 | wild | 324778216 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
| Bradypus variegatus Schinz, 1825 | -80.14370 | 8.602112 | cdc,cdround | gbif | 4015257923 | Bradypus variegatus Schinz, 1825 | 50c9509d-22c7-4a22-a47d-8c48425ef4a7 | 28eb1a3f-1c15-4a95-931a-4af90ecb574d | 997448a8-f762-11e1-a439-00145eb45e9a | 28eb1a3f-1c15-4a95-931a-4af90ecb574d | US | DWC_ARCHIVE | 2023-08-17 14:21:14 | 2023-08-18 13:40:25 | 390 | HUMAN_OBSERVATION | PRESENT | 2436353 | 1 | 44 | 359 | 1494 | 9418 | 2436350 | 2436353 | 2436353 | Bradypus variegatus Schinz, 1825 | Animalia | Chordata | Pilosa | Bradypodidae | Bradypus | Bradypus variegatus | Bradypus | variegatus | SPECIES | ACCEPTED | LC | 2023-01-05 00:14:33 | 171 | NORTH_AMERICA | Coclé | 2023 | 1 | 4 | 2023-01-04 | 2023-03-09 20:50:13 | 2023-08-18 13:40:25 | https://www.inaturalist.org/observations/145862390 | http://creativecommons.org/licenses/by-nc/4.0/legalcode | FALSE | iNaturalist research-grade observations | Matt Cohen and Elizabeth Hargrave | Matt Cohen and Elizabeth Hargrave | WGS84 | Mammalia | PA | Panama | Matt Cohen and Elizabeth Hargrave | 145862390 | mattandeliz | 2023/01/04 2:49 PM | Observations | 4015257923 | Anton Valley, Panama | https://www.inaturalist.org/observations/145862390 | 47067 | 145862390 | iNaturalist | 14:49:00-05:00 | wild | 324981107 | NA | NA | NA | NA | NA | NA | NA | NA | NA | NA |
Convert to points of observation from lon/lat columns in data frame. This part is using the sf R package to make our dataframe into a geospatial object. This way the mapping functions will be able to plot the points easily.
obs <- df %>%
sf::st_as_sf(
coords = c("longitude", "latitude"), # what columns have x and y
crs = sf::st_crs(4326)) %>% # what projection to use
dplyr::select(prov, key) # save space (optional)
# save the file
sf::write_sf(obs, obs_geo, delete_dsn=TRUE)
nrow(obs) # number of rows[1] 500The format of a bounding box is [min-longitude, min-latitude, max-longitude, max-latitude]
Plot using mapview.
mapview::mapview(obs, col.regions = "gray")